BLASTX+BEAUTY Search Results

WU-BLAST 2.0 search of the National Center for Biotechnology Information's NR Protein Database.

BEAUTY post-processing provided by the Human Genome Sequencing Center, Baylor College of Medicine.

BEAUTY Reference:
Worley KC, Culpepper P, Wiese BA, Smith RF. BEAUTY-X: enhanced BLAST searches for DNA queries. Bioinformatics 1998;14(10):890-1. Abstract

Worley KC, Wiese BA, Smith RF. BEAUTY: an enhanced BLAST-based search tool that integrates multiple biological information resources into sequence similarity search results. Genome Res 1995 Sep;5(2):173-84 Abstract

processing output:
cycle 1
cycle 2
cycle 3
cycle 4
Repeat sequence:
   SW  perc perc perc  query                position in query    matching repeat        position in  repeat
score  div. del. ins.  sequence             begin  end (left)    repeat   class/family  begin  end (left)  ID

  234   0.0  0.0  0.0  'E02B08_D07_07.ab1'    698  723    (0) +  (A)n     Simple_repeat     1   26    (0)      

Alignments:
234  0.00  0.00  0.00  'E02B08_D07_07.ab1'  698  723  (0)  (A)n#Simple_repeat  1  26  (154)  5

  'E02B08_D07_07.    698 AAAAAAAAAAAAAAAAAAAAAAAAAA 723    
                                                   
  (A)n#Simple_rep      1 AAAAAAAAAAAAAAAAAAAAAAAAAA 26

Transitions / transversions = 1.00 (0 / 0)
Gap_init rate = 0.00 (0 / 26), avg. gap size = 0.00 (0 / 0)  

Masked Sequence:
>'E02B08_D07_07.ab1'
ACCGATATTAGGGTTTCGGAGTCGTTGCAGAGCTGCGCGTTGATCTAGAA
AAATGGCGAGGATAAAGGTGTACGAGCTGAGGAATAAGGCGAAGGCGGAG
CTACTGAACCAGCTCAAGGATCTCAAGGCGGAGCTAGCCCTGCTCCGCGT
CGCCAAGGTTACCGGCGGCGCCCCAAACAAGCTCTCCAAAATTAAGGTGG
TGAGGCTATCGATAGCGCAGGTTTTGACGGTTATTTCCCAGAAGCAGAAA
GCGGCGCTGAGAGAGGCTTACAAGAAGAAGAAGTATTTGCCCCTTGACCT
CCGTCCCAAGAAGACTCGCGCCATTCGCAGACGCCTTACCAAACACCAGG
TGTCTTTGAAGACGGAACGTGAGAAGAAGAAGGAGCTGTACTTTCCACTA
AGAAAGTATGCGATCAAAGTTTAGGTTAGAATTGGTTTCAAGTTGCATTT
TTTAGGACAGTTACTTGTATTGAAATTTTAAGGTTTTGATGCCTGCCGCT
GGGGCAGCATTCCAATTATTAGTACCAGAGTTGTTTCAATGCTTGCATTA
AGTTTCCAAGGTCTATATGTTAAAACTAGAGTTGTTCGAGAAACTATTGT
TGCTTTCGGCCTTTAACTTTAAAGCGATTACCTGTTGAATGATCAATGGC
CGACCTTTATGAGTTGGGATTTATGCACATCTCACCGGTGGTTCCCCNNN
NNNNNNNNNNNNNNNNNNNNNNN

Summary:
==================================================
file name: /repeatmasker/tmp/RM2seq
sequences:            1
total length:       723 bp
GC level:         44.95 %
bases masked:        26 bp (  3.60 %)
==================================================
               number of      length   percentage
               elements*    occupied  of sequence
--------------------------------------------------
SINEs:                0            0 bp     0.00 %
      ALUs            0            0 bp     0.00 %
      MIRs            0            0 bp     0.00 %

LINEs:                0            0 bp     0.00 %
      LINE1           0            0 bp     0.00 %
      LINE2           0            0 bp     0.00 %
      L3/CR1          0            0 bp     0.00 %

LTR elements:         0            0 bp     0.00 %
      MaLRs           0            0 bp     0.00 %
      ERVL            0            0 bp     0.00 %
      ERV_classI      0            0 bp     0.00 %
      ERV_classII     0            0 bp     0.00 %

DNA elements:         0            0 bp     0.00 %
      MER1_type       0            0 bp     0.00 %
      MER2_type       0            0 bp     0.00 %

Unclassified:         0            0 bp     0.00 %

Total interspersed repeats:        0 bp     0.00 %


Small RNA:            0            0 bp     0.00 %

Satellites:           0            0 bp     0.00 %
Simple repeats:       1           26 bp     3.60 %
Low complexity:       0            0 bp     0.00 %
==================================================

* most repeats fragmented by insertions or deletions
  have been counted as one element

The sequence(s) were assumed to be of primate origin.
RepeatMasker version 07/16/2000               default
ProcessRepeats version 07/16/2000
Repbase version 03/31/2000


Reference:  Gish, Warren (1994-1997).  unpublished.
Gish, Warren and David J. States (1993).  Identification of protein coding
regions by database similarity search.  Nat. Genet. 3:266-72.

Notice:  statistical significance is estimated under the assumption that the
equivalent of one entire reading frame in the query sequence codes for protein
and that significant alignments will involve only coding reading frames.

Query=  'E02B08_D07_07.ab1'
        (723 letters)
  Translating both strands of query sequence in all 6 reading frames

Database:  nr
           625,274 sequences; 197,782,623 total letters.


     Observed Numbers of Database Sequences Satisfying
    Various EXPECTation Thresholds (E parameter values)

        Histogram units:      = 4 Sequences     : less than 4 sequences

 EXPECTation Threshold
 (E parameter)
    |
    V   Observed Counts-->
  10000 1154 230 |=========================================================
   6310  924 191 |===============================================
   3980  733 170 |==========================================
   2510  563 157 |=======================================
   1580  406  86 |=====================
   1000  320  73 |==================
    631  247  38 |=========
    398  209  44 |===========
    251  165  30 |=======
    158  135  35 |========
    100  100  15 |===
   63.1   85   7 |=
   39.8   78   4 |=
   25.1   74   8 |==
   15.8   66   6 |=
 >>>>>>>>>>>>>>>>>>>>>  Expect = 10.0, Observed = 60  <<<<<<<<<<<<<<<<<
   10.0   60   4 |=
   6.31   56   5 |=
   3.98   51   5 |=
   2.51   46   1 |:
   1.58   45   4 |=
   1.00   41   0 |
   0.63   41   2 |:
   0.40   39   1 |:
   0.25   38   0 |
   0.16   38   0 |
   0.10   38   2 |:
  0.063   36   0 |
  0.040   36   3 |:
  0.025   33   0 |
  0.016   33   4 |=
  0.010   29   2 |:
 0.0063   27   2 |:
 0.0040   25   1 |:
 0.0025   24   1 |:


                                                                     Smallest
                                                                       Sum
                                                     Reading  High  Probability
Sequences producing High-scoring Segment Pairs:        Frame Score  P(N)      N
gi|6984224|gb|AAF34800.1|AF227980_1(AF227980) 60S rib... +2   554  1.5e-52   1
gi|11276901|pir||T48282ribosomal protein L35-like - A... +2   528  8.4e-50   1
gi|6682230|gb|AAF23282.1|AC016661_7(AC016661) putativ... +2   527  1.1e-49   1
gi|7441176|pir||T00549ribosomal protein L35, cytosoli... +2   526  1.4e-49   1
gi|11276902|pir||T47656ribosomal protein L35-like - A... +2   513  3.3e-48   1
gi|132917|sp|P17078|RL35_RAT60S RIBOSOMAL PROTEIN L35... +2   409  3.4e-37   1
gi|6005860ref|NP_009140.1| ribosomal protein L35 [Hom... +2   405  9.1e-37   1
gi|12381877|dbj|BAB21248.1|(AB046395) ribosomal prote... +2   403  1.5e-36   1
gi|12735106ref|XP_005579.2| ribosomal protein L35 [Ho... +2   400  3.1e-36   1
gi|6094063|sp|O74904|RL35_SCHPO60S RIBOSOMAL PROTEIN ... +2   347  1.3e-30   1
gi|6320010ref|NP_010090.1| Ribosomal protein L35A; Rp... +2   324  3.5e-28   1
gi|7290609|gb|AAF46058.1|(AE003435) CG4111 gene produ... +2   323  4.4e-28   1
gi|464635|sp|P34662|RL35_CAEELPROBABLE 60S RIBOSOMAL ... +2   307  2.2e-26   1
gi|1710544|sp|P52817|RL35_BABBO60S RIBOSOMAL PROTEIN ... +2   305  3.6e-26   1
gi|2833359|sp|Q29361|RL35_PIG60S RIBOSOMAL PROTEIN L35   +2   301  9.5e-26   1
gi|477250|pir||A48451ribosomal protein L35.e, cytosol... +2   252  1.5e-20   1
gi|903860|gb|AAA70296.1|(M94732) 15 kDa vesicular-lik... +2   211  3.3e-16   1
gi|4165061|gb|AAD08656.1|(AF069312) ribosomal protein... +2   209  5.3e-16   1
gi|12381887|dbj|BAB21255.1|(AB046409) ribosomal prote... +2   122  1.8e-06   1
gi|1710528|sp|P54035|RL29_METJA50S RIBOSOMAL PROTEIN ... +2   114  1.4e-05   1
gi|132842|sp|P10971|RL29_HALMA50S RIBOSOMAL PROTEIN L... +2   104  0.00020   1
gi|226206|prf||1501256Cribosomal protein L33 [Haloarc... +2   102  0.00032   1
gi|10120938|pdb|1FFK|SChain S, Crystal Structure Of T... +2   102  0.00032   1
gi|132838|sp|P12873|RL29_BACSU50S RIBOSOMAL PROTEIN L... +2    95  0.0020    1
gi|132841|sp|P22665|RL29_HALHA50S RIBOSOMAL PROTEIN L... +2    93  0.0033    1
gi|132837|sp|P04457|RL29_BACST50S RIBOSOMAL PROTEIN L... +2    92  0.0043    1
gi|12643297|sp|Q9Z9K6|RL29_BACHD50S RIBOSOMAL PROTEIN... +2    92  0.0043    1
gi|7321300|emb|CAB82078.1|(AL161803) 50S ribosomal pr... +2    90  0.0072    1
gi|12721782|gb|AAK03491.1|(AE006177) RpL29 [Pasteurel... +2    89  0.0092    1
gi|2500321|sp|Q50310|RL29_MYCPN50S RIBOSOMAL PROTEIN ... +2    88  0.012     1
gi|2500319|sp|P55840|RL29_ACTAC50S RIBOSOMAL PROTEIN ... +2    88  0.012     1
gi|11499502ref|NP_070743.1| LSU ribosomal protein L29... +2    88  0.012     1
gi|11357029|pir||H82915ribosomal protein L29 UU239 [i... +2    88  0.012     1
gi|3122714|sp|O32989|RL29_MYCLE50S RIBOSOMAL PROTEIN ... +2    84  0.033     1
gi|3122708|sp|O26117|RL29_METTH50S RIBOSOMAL PROTEIN ... +2    84  0.033     1
gi|10178184|dbj|BAB11658.1|(AB013395) 50S ribosomal p... +2    98  0.036     1
gi|585878|sp|P38514|RL29_THEMA50S RIBOSOMAL PROTEIN L... +2    81  0.069     1
gi|6225990|sp|P95057|RL29_MYCTU50S RIBOSOMAL PROTEIN ... +2    81  0.069     1
gi|7674275|sp|Q9WVW8|RL29_STRPN50S RIBOSOMAL PROTEIN ... +2    76  0.22      1
gi|3122701|sp|O06050|RL29_MYCBO50S RIBOSOMAL PROTEIN ... +2    74  0.35      1
gi|11347345|pir||E8311550S ribosomal protein L29 PA42... +2    74  0.35      1
gi|132840|sp|P02429|RL29_ECOLI50S RIBOSOMAL PROTEIN L... +2    70  0.69      1
gi|3122706|sp|O24697|RL29_SYNP650S RIBOSOMAL PROTEIN ... +2    70  0.69      1
gi|1173014|sp|P46174|RL29_BUCAK50S RIBOSOMAL PROTEIN ... +2    69  0.78      1
gi|7439876|pir||JC5931high mobility group I HMGI chro... +1    69  0.78      1
gi|545157|gb|AAB29804.1|homeobox gene NvHBox-4 produc... +2    68  0.86      1
gi|3914739|sp|P56613|RL29_AQUAE50S RIBOSOMAL PROTEIN L29 +2    67  0.92      1
gi|7162180|emb|CAB76841.1|(AJ224860) ribosomal protei... +2    67  0.92      1
gi|7439879|pir||JC5933high mobility group I HMGI chro... +1    69  0.95      1
gi|3914735|sp|O52340|RL29_MYCGA50S RIBOSOMAL PROTEIN ... +2    81  0.95      1

Use the  and  icons to retrieve links to Entrez:
E = Retrieve Entrez links (e.g., Medline abstracts, FASTA-formatted sequence reports).
R = Retrieve links to Related sequences (neighbors).

Use the  icon (if present) to retrieve links to the Sequence Retrieval System (SRS).

Use the  icon (if present) to retrieve links to the Ligand Enzyme and Chemical Compound Database .

Use the  icon (if present) to retrieve links to the Protein Data Bank database.

WARNING:  Descriptions of 10 database sequences were not reported due to the
          limiting value of parameter V = 50.



 >gi|6984224|gb|AAF34800.1|AF227980_1  (AF227980) 60S ribosomal protein L35
            [Euphorbia esula]
            Length = 123

Frame  2 hits (HSPs):   __________________________________________________
                        __________________________________________________
Database sequence:     |                   |                    |         | 123
                       0                  50                  100

  Plus Strand HSPs:

 Score = 554 (195.0 bits), Expect = 1.5e-52, P = 1.5e-52
 Identities = 114/123 (92%), Positives = 118/123 (95%), Frame = +2

Query:    53 MARIKVYELRNKAKAELLNQLKDLKAELALLRVAKVTGGAPNKLSKIKVVRLSIAQVLTV 232
             MARIKV+ELR K KAELLNQLKDLKAELALLRVAKVTGGAPNKLSKIKVVRLSIAQVLTV
Sbjct:     1 MARIKVHELRQKTKAELLNQLKDLKAELALLRVAKVTGGAPNKLSKIKVVRLSIAQVLTV 60

Query:   233 ISQKQKAALREAYKKKKYLPLDLRPKKTRAIRRRLTKHQVSLKTEREKKKELYFPLRKYA 412
             ISQKQK ALREAYK KK+LPLDLRPKKTRAIRRRLTKHQ SLKTEREKKKE+YFP+RKYA
Sbjct:    61 ISQKQKLALREAYKNKKFLPLDLRPKKTRAIRRRLTKHQQSLKTEREKKKEMYFPMRKYA 120

Query:   413 IKV 421
             IKV
Sbjct:   121 IKV 123


 >gi|11276901|pir||T48282  ribosomal protein L35-like - Arabidopsis thaliana
            >gi|7413650|emb|CAB85998.1| (AL162971) ribosomal protein L35-like
            [Arabidopsis thaliana]
            Length = 123

Frame  2 hits (HSPs):   __________________________________________________
                        __________________________________________________
Database sequence:     |                   |                    |         | 123
                       0                  50                  100

  Plus Strand HSPs:

 Score = 528 (185.9 bits), Expect = 8.4e-50, P = 8.4e-50
 Identities = 108/123 (87%), Positives = 116/123 (94%), Frame = +2

Query:    53 MARIKVYELRNKAKAELLNQLKDLKAELALLRVAKVTGGAPNKLSKIKVVRLSIAQVLTV 232
             MARIKV+ELR+K+K +L NQLK+ KAELALLRVAKVTGGAPNKLSKIKVVR SIAQVLTV
Sbjct:     1 MARIKVHELRDKSKTDLQNQLKEFKAELALLRVAKVTGGAPNKLSKIKVVRKSIAQVLTV 60

Query:   233 ISQKQKAALREAYKKKKYLPLDLRPKKTRAIRRRLTKHQVSLKTEREKKKELYFPLRKYA 412
             ISQKQK+ALREAYK KK LPLDLRPKKTRAIRRRLTKHQ SLKTEREKKKE+YFP+RKYA
Sbjct:    61 ISQKQKSALREAYKNKKLLPLDLRPKKTRAIRRRLTKHQASLKTEREKKKEMYFPVRKYA 120

Query:   413 IKV 421
             IKV
Sbjct:   121 IKV 123


 >gi|6682230|gb|AAF23282.1|AC016661_7  (AC016661) putative 60S ribosomal protein
            L35 [Arabidopsis thaliana]
            Length = 123

Frame  2 hits (HSPs):   __________________________________________________
                        __________________________________________________
Database sequence:     |                   |                    |         | 123
                       0                  50                  100

  Plus Strand HSPs:

 Score = 527 (185.5 bits), Expect = 1.1e-49, P = 1.1e-49
 Identities = 108/123 (87%), Positives = 116/123 (94%), Frame = +2

Query:    53 MARIKVYELRNKAKAELLNQLKDLKAELALLRVAKVTGGAPNKLSKIKVVRLSIAQVLTV 232
             MARIKV+ELR K+K++L NQLK+LKAELALLRVAKVTGGAPNKLSKIKVVR SIAQVLTV
Sbjct:     1 MARIKVHELREKSKSDLQNQLKELKAELALLRVAKVTGGAPNKLSKIKVVRKSIAQVLTV 60

Query:   233 ISQKQKAALREAYKKKKYLPLDLRPKKTRAIRRRLTKHQVSLKTEREKKKELYFPLRKYA 412
              SQKQK+ALREAYK KK LPLDLRPKKTRAIRRRLTKHQ SLKTEREKKKE+YFP+RKYA
Sbjct:    61 SSQKQKSALREAYKNKKLLPLDLRPKKTRAIRRRLTKHQASLKTEREKKKEMYFPIRKYA 120

Query:   413 IKV 421
             IKV
Sbjct:   121 IKV 123


 >gi|7441176|pir||T00549  ribosomal protein L35, cytosolic - Arabidopsis thaliana
            >gi|3355468|gb|AAC27830.1| (AC004218) 60S ribosomal protein L35
            [Arabidopsis thaliana]
            Length = 123

Frame  2 hits (HSPs):   __________________________________________________
                        __________________________________________________
Database sequence:     |                   |                    |         | 123
                       0                  50                  100

  Plus Strand HSPs:

 Score = 526 (185.2 bits), Expect = 1.4e-49, P = 1.4e-49
 Identities = 108/123 (87%), Positives = 115/123 (93%), Frame = +2

Query:    53 MARIKVYELRNKAKAELLNQLKDLKAELALLRVAKVTGGAPNKLSKIKVVRLSIAQVLTV 232
             MARIKV+ELR K+KA+L  QLK+ KAELALLRVAKVTGGAPNKLSKIKVVR SIAQVLTV
Sbjct:     1 MARIKVHELREKSKADLSGQLKEFKAELALLRVAKVTGGAPNKLSKIKVVRKSIAQVLTV 60

Query:   233 ISQKQKAALREAYKKKKYLPLDLRPKKTRAIRRRLTKHQVSLKTEREKKKELYFPLRKYA 412
             ISQKQK+ALREAYK KK LPLDLRPKKTRAIRRRLTKHQ SLKTEREKKKE+YFP+RKYA
Sbjct:    61 ISQKQKSALREAYKNKKLLPLDLRPKKTRAIRRRLTKHQASLKTEREKKKEMYFPIRKYA 120

Query:   413 IKV 421
             IKV
Sbjct:   121 IKV 123


 >gi|11276902|pir||T47656  ribosomal protein L35-like - Arabidopsis thaliana
            >gi|7019650|emb|CAB75751.1| (AL132954) ribosomal protein L35-like
            [Arabidopsis thaliana]
            Length = 123

Frame  2 hits (HSPs):   __________________________________________________
                        __________________________________________________
Database sequence:     |                   |                    |         | 123
                       0                  50                  100

  Plus Strand HSPs:

 Score = 513 (180.6 bits), Expect = 3.3e-48, P = 3.3e-48
 Identities = 105/123 (85%), Positives = 115/123 (93%), Frame = +2

Query:    53 MARIKVYELRNKAKAELLNQLKDLKAELALLRVAKVTGGAPNKLSKIKVVRLSIAQVLTV 232
             MARIKV+ELR+K+K++L  QLK+LKAELA LRVAKVTGGAPNKLSKIKVVR SIAQVLTV
Sbjct:     1 MARIKVHELRDKSKSDLSTQLKELKAELASLRVAKVTGGAPNKLSKIKVVRKSIAQVLTV 60

Query:   233 ISQKQKAALREAYKKKKYLPLDLRPKKTRAIRRRLTKHQVSLKTEREKKKELYFPLRKYA 412
              SQKQK+ALREAYK KK LPLDLRPKKTRAIRRRLTKHQ SLKTEREKKK++YFP+RKYA
Sbjct:    61 SSQKQKSALREAYKNKKLLPLDLRPKKTRAIRRRLTKHQASLKTEREKKKDMYFPIRKYA 120

Query:   413 IKV 421
             IKV
Sbjct:   121 IKV 123


 >gi|132917|sp|P17078|RL35_RAT  60S RIBOSOMAL PROTEIN L35 >gi|71362|pir||R5RT35
            ribosomal protein L35, cytosolic [validated] - rat
            >gi|57702|emb|CAA36001.1| (X51705) ribosomal protein L35 (AA 1-123)
            [Rattus rattus]
            Length = 123

Frame  2 hits (HSPs):   __________________________________________________
Annotated Domains:      _________________________________________________ 
                        __________________________________________________
Database sequence:     |                   |                    |         | 123
                       0                  50                  100
__________________

Annotated Domains:
   PFAM                 Ribosomal_L29: Ribosomal L29 protein     5..68
   PRODOM               PD186205: RL29(7) RL35(6)                1..61
   PRODOM               PD012183: RL35(6) O80626(1)              64..120
   PROSITE              RIBOSOMAL_L29: Ribosomal protein L29 sig 43..57
__________________


  Plus Strand HSPs:

 Score = 409 (144.0 bits), Expect = 3.4e-37, P = 3.4e-37
 Identities = 84/122 (68%), Positives = 101/122 (82%), Frame = +2

Query:    53 MARIKVYELRNKAKAELLNQLKDLKAELALLRVAKVTGGAPNKLSKIKVVRLSIAQVLTV 232
             MA+IK  +LR K K ELL QL DLK EL+ LRVAKVTGGA +KLSKI+VVR SIA+VLTV
Sbjct:     1 MAKIKARDLRGKKKEELLKQLDDLKVELSQLRVAKVTGGAASKLSKIRVVRKSIARVLTV 60

Query:   233 ISQKQKAALREAYKKKKYLPLDLRPKKTRAIRRRLTKHQVSLKTEREKKKELYFPLRKYA 412
             I+Q QK  LR+ YK KKY PLDLRPKKTRA+RRRLTKH+  LKT+++++KE  +PLRKYA
Sbjct:    61 INQTQKENLRKFYKGKKYKPLDLRPKKTRAMRRRLTKHEEKLKTKKQQRKERLYPLRKYA 120

Query:   413 IK 418
             +K
Sbjct:   121 VK 122


 >gi|6005860  ref|NP_009140.1| ribosomal protein L35 [Homo sapiens]
            >gi|1173039|sp|P42766|RL35_HUMAN 60S RIBOSOMAL PROTEIN L35
            >gi|7441177|pir||G01477 ribosomal protein L35 - human
            >gi|562074|gb|AAA51648.1| (U12465) ribosomal protein L35 [Homo
            sapiens] >gi|12653161|gb|AAH00348.1|AAH00348 (BC000348) ribosomal
            protein L35 [Homo sapiens]
            Length = 123

Frame  2 hits (HSPs):   __________________________________________________
                        __________________________________________________
Database sequence:     |                   |                    |         | 123
                       0                  50                  100

  Plus Strand HSPs:

 Score = 405 (142.6 bits), Expect = 9.1e-37, P = 9.1e-37
 Identities = 83/122 (68%), Positives = 101/122 (82%), Frame = +2

Query:    53 MARIKVYELRNKAKAELLNQLKDLKAELALLRVAKVTGGAPNKLSKIKVVRLSIAQVLTV 232
             MA+IK  +LR K K ELL QL DLK EL+ LRVAKVTGGA +KLSKI+VVR SIA+VLTV
Sbjct:     1 MAKIKARDLRGKKKEELLKQLDDLKVELSQLRVAKVTGGAASKLSKIRVVRKSIARVLTV 60

Query:   233 ISQKQKAALREAYKKKKYLPLDLRPKKTRAIRRRLTKHQVSLKTEREKKKELYFPLRKYA 412
             I+Q QK  LR+ YK KKY PLDLRPKKTRA+RRRL KH+ +LKT+++++KE  +PLRKYA
Sbjct:    61 INQTQKENLRKFYKGKKYKPLDLRPKKTRAMRRRLNKHEENLKTKKQQRKERLYPLRKYA 120

Query:   413 IK 418
             +K
Sbjct:   121 VK 122


 >gi|12381877|dbj|BAB21248.1|  (AB046395) ribosomal protein L35 [Gallus gallus]
            Length = 123

Frame  2 hits (HSPs):   __________________________________________________
                        __________________________________________________
Database sequence:     |                   |                    |         | 123
                       0                  50                  100

  Plus Strand HSPs:

 Score = 403 (141.9 bits), Expect = 1.5e-36, P = 1.5e-36
 Identities = 83/122 (68%), Positives = 101/122 (82%), Frame = +2

Query:    53 MARIKVYELRNKAKAELLNQLKDLKAELALLRVAKVTGGAPNKLSKIKVVRLSIAQVLTV 232
             MA+IK  +LR K K ELL QL DLK EL+ LRVAKVTGGA +KLSKI+VVR SIA+VLTV
Sbjct:     1 MAKIKARDLRGKKKEELLKQLDDLKVELSQLRVAKVTGGAASKLSKIRVVRKSIARVLTV 60

Query:   233 ISQKQKAALREAYKKKKYLPLDLRPKKTRAIRRRLTKHQVSLKTEREKKKELYFPLRKYA 412
             I+Q QK  LR+ YK KKY PLDLRPKKTRA+RRRL KH+ +LKT+++++KE  +P+RKYA
Sbjct:    61 INQTQKENLRKFYKGKKYKPLDLRPKKTRAMRRRLNKHEENLKTKKQQRKERLYPVRKYA 120

Query:   413 IK 418
             IK
Sbjct:   121 IK 122


 >gi|12735106  ref|XP_005579.2| ribosomal protein L35 [Homo sapiens]
            Length = 122

Frame  2 hits (HSPs):   __________________________________________________
                        __________________________________________________
Database sequence:     |                    |                   |         | 122
                       0                   50                 100

  Plus Strand HSPs:

 Score = 400 (140.8 bits), Expect = 3.1e-36, P = 3.1e-36
 Identities = 82/121 (67%), Positives = 100/121 (82%), Frame = +2

Query:    56 ARIKVYELRNKAKAELLNQLKDLKAELALLRVAKVTGGAPNKLSKIKVVRLSIAQVLTVI 235
             A+IK  +LR K K ELL QL DLK EL+ LRVAKVTGGA +KLSKI+VVR SIA+VLTVI
Sbjct:     1 AKIKARDLRGKKKEELLKQLDDLKVELSQLRVAKVTGGAASKLSKIRVVRKSIARVLTVI 60

Query:   236 SQKQKAALREAYKKKKYLPLDLRPKKTRAIRRRLTKHQVSLKTEREKKKELYFPLRKYAI 415
             +Q QK  LR+ YK KKY PLDLRPKKTRA+RRRL KH+ +LKT+++++KE  +PLRKYA+
Sbjct:    61 NQTQKENLRKFYKGKKYKPLDLRPKKTRAMRRRLNKHEENLKTKKQQRKERLYPLRKYAV 120

Query:   416 K 418
             K
Sbjct:   121 K 121


 >gi|6094063|sp|O74904|RL35_SCHPO  60S RIBOSOMAL PROTEIN L35
            >gi|7492911|pir||T41471 probable ribosomal protein L35 - fission
            yeast  (Schizosaccharomyces pombe) >gi|3647333|emb|CAA21057.1|
            (AL031644) putative ribosomal protein L35 [Schizosaccharomyces
            pombe]
            Length = 122

Frame  2 hits (HSPs):   __________________________________________________
                        __________________________________________________
Database sequence:     |                    |                   |         | 122
                       0                   50                 100

  Plus Strand HSPs:

 Score = 347 (122.2 bits), Expect = 1.3e-30, P = 1.3e-30
 Identities = 69/119 (57%), Positives = 91/119 (76%), Frame = +2

Query:    62 IKVYELRNKAKAELLNQLKDLKAELALLRVAKVTGGAPNKLSKIKVVRLSIAQVLTVISQ 241
             +K +ELR +++  L  QL++L+ ELA LRV K+ GG+ +KLSKIK  R  IA++LTVI++
Sbjct:     3 LKTFELRKQSQENLAEQLQELRQELASLRVQKIAGGSGSKLSKIKTTRKDIARILTVINE 62

Query:   242 KQKAALREAYKKKKYLPLDLRPKKTRAIRRRLTKHQVSLKTEREKKKELYFPLRKYAIK 418
               + A REAYK KKY+PLDLR KKTRAIRR LT ++ S KT ++ KKE YFPLRKYA+K
Sbjct:    63 SNRLAAREAYKNKKYIPLDLRQKKTRAIRRALTPYEQSRKTLKQIKKERYFPLRKYALK 121


 >gi|6320010  ref|NP_010090.1| Ribosomal protein L35A; Rpl35ap [Saccharomyces
            cerevisiae] >gi|6320065 ref|NP_010145.1| Ribosomal protein L35B;
            Rpl35bp [Saccharomyces cerevisiae] >gi|730559|sp|P39741|RL35_YEAST
            60S RIBOSOMAL PROTEIN L35 >gi|320697|pir||S30770 ribosomal protein
            L35.e, cytosolic - yeast (Saccharomyces cerevisiae)
            >gi|171218|gb|AAA34492.1| (M82913) ORF [Saccharomyces cerevisiae]
            >gi|172478|gb|AAA35000.1| (L02328) ribosomal protein [Saccharomyces
            cerevisiae] >gi|1004304|emb|CAA58256.1| (X83276) putative
            [Saccharomyces cerevisiae] >gi|1419225|emb|CAA65623.1| (X96876)
            ribosomal L35 protein [Saccharomyces cerevisiae]
            >gi|1431209|emb|CAA98709.1| (Z74184) ORF YDL136w [Saccharomyces
            cerevisiae] >gi|1431312|emb|CAA98768.1| (Z74239) ORF YDL191w
            [Saccharomyces cerevisiae]
            Length = 120

Frame  2 hits (HSPs):   __________________________________________________
                        __________________________________________________
Database sequence:     |                    |                    |        | 120
                       0                   50                  100

  Plus Strand HSPs:

 Score = 324 (114.1 bits), Expect = 3.5e-28, P = 3.5e-28
 Identities = 71/122 (58%), Positives = 92/122 (75%), Frame = +2

Query:    53 MARIKVYELRNKAKAELLNQLKDLKAELALLRVAKVTGGAPNKLSKIKVVRLSIAQVLTV 232
             MA +K YELR K+K +L +QL DLK ELA L+V K++   P+ L KIK VR SIA VLTV
Sbjct:     1 MAGVKAYELRTKSKEQLASQLVDLKKELAELKVQKLS--RPS-LPKIKTVRKSIACVLTV 57

Query:   233 ISQKQKAALREAYKKKKYLPLDLRPKKTRAIRRRLTKHQVSLKTEREKKKELYFPLRKYA 412
             I+++Q+ A+R+ YK KKY P DLR KKTRA+RR LTK + S  TE+++KK++ FP RKYA
Sbjct:    58 INEQQREAVRQLYKGKKYQPKDLRAKKTRALRRALTKFEASQVTEKQRKKQIAFPQRKYA 117

Query:   413 IK 418
             IK
Sbjct:   118 IK 119


 >gi|7290609|gb|AAF46058.1|  (AE003435) CG4111 gene product [Drosophila
            melanogaster]
            Length = 121

Frame  2 hits (HSPs):   __________________________________________________
                        __________________________________________________
Database sequence:     |                    |                   |         | 121
                       0                   50                 100

  Plus Strand HSPs:

 Score = 323 (113.7 bits), Expect = 4.4e-28, P = 4.4e-28
 Identities = 70/119 (58%), Positives = 86/119 (72%), Frame = +2

Query:    62 IKVYELRNKAKAELLNQLKDLKAELALLRVAKVTGGAPNKLSKIKVVRLSIAQVLTVISQ 241
             +K  ELR K K EL  QL +LK EL  LRVAKVTGGAP+KLSKI+VVR +IA+V  V+ Q
Sbjct:     2 VKCSELRIKDKKELTKQLDELKNELLSLRVAKVTGGAPSKLSKIRVVRKAIARVYIVMHQ 61

Query:   242 KQKAALREAYKKKKYLPLDLRPKKTRAIRRRLTKHQVSLKTEREKKKELYFPLRKYAIK 418
             KQK  LR+ +K KKY PLDLR KKTRAIR+ L+    + KT +E +K   FP RK+A+K
Sbjct:    62 KQKENLRKVFKNKKYKPLDLRKKKTRAIRKALSPRDANRKTLKEIRKRSVFPQRKFAVK 120


 >gi|464635|sp|P34662|RL35_CAEEL  PROBABLE 60S RIBOSOMAL PROTEIN L35
            >gi|630772|pir||S44905 ribosomal protein L35.e, cytosolic -
            Caenorhabditis elegans >gi|289771|gb|AAA28216.1| (L14429) homology
            with 60S ribosomal protein L35 in Rat; coded for by C. elegans
            expressed sequence tag CELXT00520 (GenBank: M79983); putative
            [Caenorhabditis elegans]
            Length = 123

Frame  2 hits (HSPs):   __________________________________________________
Annotated Domains:      __________________________________________________
                        __________________________________________________
Database sequence:     |                   |                    |         | 123
                       0                  50                  100
__________________

Annotated Domains:
   BLOCKS               BL00579A: Ribosomal protein L29 proteins 16..25
   BLOCKS               BL00579B: Ribosomal protein L29 proteins 35..64
   DOMO                 DM01863: RIBOSOMALPROTEINL29             1..122
   PFAM                 Ribosomal_L29: Ribosomal L29 protein     6..69
   PRODOM               PD186205: RL29(7) RL35(6)                1..62
   PRODOM               PD012183: RL35(6) O80626(1)              65..121
   PROSITE              RIBOSOMAL_L29: Ribosomal protein L29 sig 43..57
__________________


  Plus Strand HSPs:

 Score = 307 (108.1 bits), Expect = 2.2e-26, P = 2.2e-26
 Identities = 65/122 (53%), Positives = 89/122 (72%), Frame = +2

Query:    53 MARIKVYELRNKAKAELLNQLKDLKAELALLRVAKVTGGAPNKLSKIKVVRLSIAQVLTV 232
             M ++K   LR + K  L  +L + K ELA LRV+KVTGGA +KLSKI+VVR +IA++LTV
Sbjct:     1 MTKLKCKSLRGEKKDALQKKLDEQKTELATLRVSKVTGGAASKLSKIRVVRKNIARLLTV 60

Query:   233 ISQKQKAALREAYKKKKYLPLDLRPKKTRAIRRRLTKHQVSLKTEREKKKELYFPLRKYA 412
             I+Q QK  LR+ Y   KY P+DLR KKTRAIRRRLT H++SL++ +++ K     +RK+A
Sbjct:    61 INQTQKQELRKFYADHKYKPIDLRLKKTRAIRRRLTAHELSLRSAKQQAKSRNQAVRKFA 120

Query:   413 IK 418
             +K
Sbjct:   121 VK 122


 >gi|1710544|sp|P52817|RL35_BABBO  60S RIBOSOMAL PROTEIN L35
            >gi|1223851|gb|AAC47013.1| (U33844) ribosomal protein L35 [Babesia
            bovis] >gi|1256577|gb|AAC48308.1| (U34076) ribosomal protein L35
            [Babesia bovis]
            Length = 123

Frame  2 hits (HSPs):   __________________________________________________
Annotated Domains:      __________________________________________________
                        __________________________________________________
Database sequence:     |                   |                    |         | 123
                       0                  50                  100
__________________

Annotated Domains:
   BLOCKS               BL00579A: Ribosomal protein L29 proteins 8..17
   BLOCKS               BL00579B: Ribosomal protein L29 proteins 35..64
   DOMO                 DM01863: RIBOSOMALPROTEINL29             1..122
   PFAM                 Ribosomal_L29: Ribosomal L29 protein     6..69
   PRODOM               PD186205: RL29(7) RL35(6)                1..62
   PRODOM               PD012183: RL35(6) O80626(1)              65..122
   PROSITE              RIBOSOMAL_L29: Ribosomal protein L29 sig 43..57
__________________


  Plus Strand HSPs:

 Score = 305 (107.4 bits), Expect = 3.6e-26, P = 3.6e-26
 Identities = 67/123 (54%), Positives = 89/123 (72%), Frame = +2

Query:    53 MARIKVYELRNKAKAELLNQLKDLKAELALLRVAKVTGGAPNKLSKIKVVRLSIAQVLTV 232
             M +IKVYELRNK  AELL QL+DLK E A +RV KVT  + +KLS+I V+R +IA+VLTV
Sbjct:     1 MEKIKVYELRNKTDAELLKQLEDLKQEYASMRVQKVTVTSTSKLSQIGVIRKAIAKVLTV 60

Query:   233 ISQKQKAALREAYKKKKYLPLDLRPKKTRAIRRRLTKHQVSLKTEREKKKELYFPLRKYA 412
              +Q+++   R+ Y K   +PL++RPK TRA RR LT  Q+ LKT +++KK   FP RKYA
Sbjct:    61 YNQRKREEARKQYTKISEMPLNMRPKLTRAKRRALTPKQLHLKTIKQRKKCENFPKRKYA 120

Query:   413 IKV 421
             + V
Sbjct:   121 LLV 123


 >gi|2833359|sp|Q29361|RL35_PIG  60S RIBOSOMAL PROTEIN L35
            Length = 94

Frame  2 hits (HSPs):   __________________________________________________
Annotated Domains:       ___________________________________              
                        __________________________________________________
Database sequence:     |          |         |          |          |       | 94
                       0         20        40         60         80
__________________

Annotated Domains:
   PFAM                 Ribosomal_L29: Ribosomal L29 protein     4..67
   PROSITE              RIBOSOMAL_L29: Ribosomal protein L29 sig 41..55
__________________


  Plus Strand HSPs:

 Score = 301 (106.0 bits), Expect = 9.5e-26, P = 9.5e-26
 Identities = 65/94 (69%), Positives = 75/94 (79%), Frame = +2

Query:    59 RIKVYELRNKAKAELLNQLKDLKAELALLRVAKVTGGAPNKLSKIKVVRLSIAQVLTVIS 238
             +I   +LR K K ELL QL+DLK EL+ LRV KVTGGA +KLSKI+VVR SIA+VLTVI+
Sbjct:     1 KIXARDLRGKKKEELLKQLEDLKVELSQLRVGKVTGGAASKLSKIRVVRKSIARVLTVIN 60

Query:   239 QKQKAALREAYKKKKYLPLDLRPKKTRAIRRRLT 340
             Q QK  LR+ YK KKY PLDLRPKKTRA+RRR T
Sbjct:    61 QTQKENLRKFYKGKKYKPLDLRPKKTRAMRRRST 94


 >gi|477250|pir||A48451  ribosomal protein L35.e, cytosolic - malaria parasite
            (Plasmodium falciparum) >gi|5262956|emb|CAA82284.2| (Z28975) Ag15
            [Plasmodium falciparum] >gi|738740|prf||2001401A 15kD antigen
            [Plasmodium falciparum]
            Length = 124

Frame  2 hits (HSPs):   ________________________________________________  
Annotated Domains:      __________________________________________________
                        __________________________________________________
Database sequence:     |                   |                   |          | 124
                       0                  50                 100
__________________

Annotated Domains:
   DOMO                 DM01863: RIBOSOMALPROTEINL29             1..124
__________________


  Plus Strand HSPs:

 Score = 252 (88.7 bits), Expect = 1.5e-20, P = 1.5e-20
 Identities = 57/121 (47%), Positives = 80/121 (66%), Frame = +2

Query:    53 MARIKVYELRNKAKAELLNQLKDLKAELALLRVAKVTGGAPNKLSKIKVVRLSIAQVLTV 232
             M+ +K YELR   K ELL++L +LK EL+ LR++K  G +  K SKI  VR ++A+VLTV
Sbjct:     1 MSNVKAYELRTLKKKELLDKLDELKKELSGLRISKALGNSA-KNSKIHGVRKNVARVLTV 59

Query:   233 ISQKQKAALREAYKKKKYLPLDLRPKKTRAIRRRLTKHQVSLKTEREKKKELYFPLRKYA 412
              +QK+K  LR+ YK KK+ P +LR K T+  R +L+  Q +  T R+KKK   FP RKY 
Sbjct:    60 YNQKRKMELRQLYKNKKFKPYNLRKKLTKNKRLQLSPKQKAAMTLRQKKKVQNFPQRKYL 119

Query:   413 I 415
             +
Sbjct:   120 V 120


 >gi|903860|gb|AAA70296.1|  (M94732) 15 kDa vesicular-like antigen [Plasmodium
            falciparum]
            Length = 105

Frame  2 hits (HSPs):   __________________________________________________
                        __________________________________________________
Database sequence:     |         |        |         |        |         |  | 105
                       0        20       40        60       80       100

  Plus Strand HSPs:

 Score = 211 (74.3 bits), Expect = 3.3e-16, P = 3.3e-16
 Identities = 49/106 (46%), Positives = 70/106 (66%), Frame = +2

Query:    53 MARIKVYELRNKAKAELLNQLKDLKAELALLRVAKVTGGAPNKLSKIKVVRLSIAQVLTV 232
             M+ +K YELR   K ELL++L +LK EL+ LR++K  G +  K SKI  VR ++A+VLTV
Sbjct:     1 MSNVKAYELRTLKKKELLDKLDELKKELSGLRISKALGNSA-KNSKIHGVRKNVARVLTV 59

Query:   233 ISQKQKAALREAYKKKKYLPLDLRPKKTRAIRRRLTKHQVSLKTER 370
              +QK+K  LR+ YK KK+ P +LR K T+  R +L+  Q +  T R
Sbjct:    60 YNQKRKMELRQLYKNKKFKPYNLRKKLTKNKRLQLSPKQKAAMTLR 105


 >gi|4165061|gb|AAD08656.1|  (AF069312) ribosomal protein L35 [Giardia
            intestinalis]
            Length = 124

Frame  2 hits (HSPs):   __________________________________________________
                        __________________________________________________
Database sequence:     |                   |                   |          | 124
                       0                  50                 100

  Plus Strand HSPs:

 Score = 209 (73.6 bits), Expect = 5.3e-16, P = 5.3e-16
 Identities = 46/124 (37%), Positives = 75/124 (60%), Frame = +2

Query:    53 MARIKVYELRNKAKAELLNQLKDLKAELALLRVAKVTGG-APNKLSKIKVVRLSIAQVLT 229
             M  +K  +L   ++ +L  +L DLK EL  LR  K T G  P ++++ +V +  +A+VLT
Sbjct:     1 MPGLKAKDLVGLSQEDLQRKLADLKRELLSLRTMKATAGPVPERIARFRVCKKDVARVLT 60

Query:   230 VISQKQKAALREAYKKKKYLPLDLRPKKTRAIRRRLTKHQVSLKTEREKKKELYFPLRKY 409
             VI+QK +   R A++  +++P   RP+ T A+R +LT+ Q  L   +  K++L FP  KY
Sbjct:    61 VINQKARDEARAAFEGAEHIPKTFRPRLTHAMRCQLTEKQKRLLPSKLMKRKLQFPKLKY 120

Query:   410 AIKV 421
             A+KV
Sbjct:   121 AVKV 124


 >gi|12381887|dbj|BAB21255.1|  (AB046409) ribosomal protein L35 [Homo sapiens]
            Length = 33

Frame  2 hits (HSPs):   __________________________________________________
                        __________________________________________________
Database sequence:     |                            |                     | 33
                       0                           20

  Plus Strand HSPs:

 Score = 122 (42.9 bits), Expect = 1.8e-06, P = 1.8e-06
 Identities = 27/33 (81%), Positives = 31/33 (93%), Frame = +2

Query:   143 LRVAKVTGGAPNKLSKIKVVRLSIAQVLTVISQ 241
             LRVAKVTGGA +KLSKI+VVR SIA+VLTVI+Q
Sbjct:     1 LRVAKVTGGAASKLSKIRVVRKSIARVLTVINQ 33


 >gi|1710528|sp|P54035|RL29_METJA  50S RIBOSOMAL PROTEIN L29P
            >gi|2129253|pir||F64357 ribosomal protein L29 - Methanococcus
            jannaschii >gi|1591164|gb|AAB98451.1| (U67497) LSU ribosomal
            protein L29P (rpmC) [Methanococcus jannaschii]
            Length = 70

Frame  2 hits (HSPs):   _______________________________________________   
Annotated Domains:      __________________________________________________
                        __________________________________________________
Database sequence:     |             |             |              |       | 70
                       0            20            40             60
__________________

Annotated Domains:
   BLOCKS               BL00579A: Ribosomal protein L29 proteins 8..17
   BLOCKS               BL00579B: Ribosomal protein L29 proteins 35..64
   DOMO                 DM01863: RIBOSOMALPROTEINL29             1..70
   PFAM                 Ribosomal_L29: Ribosomal L29 protein     6..69
   PRODOM               PD186205: RL29(7) RL35(6)                1..63
   PROSITE              RIBOSOMAL_L29: Ribosomal protein L29 sig 43..57
__________________


  Plus Strand HSPs:

 Score = 114 (40.1 bits), Expect = 1.4e-05, P = 1.4e-05
 Identities = 23/66 (34%), Positives = 43/66 (65%), Frame = +2

Query:    53 MARIKVYELRNKAKAELLNQLKDLKAELALLRVAKVTGGAPNKLSKIKVVRLSIAQVLTV 232
             MA ++  ELR  +  EL  +L +LK EL   R +K   GAP+   +++ +R +IA++LT+
Sbjct:     1 MAILRADELRGMSMEELKEKLVELKRELLKERASKAVAGAPSNPGRMREIRRTIARILTI 60

Query:   233 ISQKQK 250
             +++K++
Sbjct:    61 MNEKKR 66


 >gi|132842|sp|P10971|RL29_HALMA  50S RIBOSOMAL PROTEIN L29P (HMAL29) (HL33)
            >gi|2144779|pir||R5HS29 ribosomal protein L29 [validated] -
            Haloarcula marismortui >gi|148808|gb|AAA86866.1| (J05222) ribosomal
            protein L29 [Haloarcula marismortui]
            Length = 71

Frame  2 hits (HSPs):   ________________________________________________  
Annotated Domains:      ________________________________________________  
                        __________________________________________________
Database sequence:     |             |             |             |        | 71
                       0            20            40            60
__________________

Annotated Domains:
   BLOCKS               BL00579A: Ribosomal protein L29 proteins 19..28
   BLOCKS               BL00579B: Ribosomal protein L29 proteins 34..63
   PFAM                 Ribosomal_L29: Ribosomal L29 protein     5..68
   PRODOM               PD186205: RL29(7) RL35(6)                2..62
   PROSITE              RIBOSOMAL_L29: Ribosomal protein L29 sig 43..57
__________________


  Plus Strand HSPs:

 Score = 104 (36.6 bits), Expect = 0.00020, P = 0.00020
 Identities = 26/71 (36%), Positives = 40/71 (56%), Frame = +2

Query:    53 MARIKVYELRNKAKAELLNQLKDLKAELALLRVAKVTGGAPNKLSKIKVVRLSIAQVLTV 232
             M  + V E+R+   AE   +L DLK EL   R  +  GGAP    +IK +R +IA++ T+
Sbjct:     1 MTVLHVQEIRDMTPAEREAELDDLKTELLNARAVQAAGGAPENPGRIKELRKAIARIKTI 60

Query:   233 ISQKQKAALRE 265
               Q ++  L+E
Sbjct:    61 --QGEEGDLQE 69


 >gi|226206|prf||1501256C  ribosomal protein L33 [Haloarcula marismortui]
            Length = 69

Frame  2 hits (HSPs):    ________________________________________________ 
                        __________________________________________________
Database sequence:     |             |              |             |       | 69
                       0            20             40            60

  Plus Strand HSPs:

 Score = 102 (35.9 bits), Expect = 0.00032, P = 0.00032
 Identities = 25/68 (36%), Positives = 39/68 (57%), Frame = +2

Query:    62 IKVYELRNKAKAELLNQLKDLKAELALLRVAKVTGGAPNKLSKIKVVRLSIAQVLTVISQ 241
             + V E+R+   AE   +L DLK EL   R  +  GGAP    +IK +R +IA++ T+  Q
Sbjct:     3 LHVQEIRDMTPAEREAELDDLKTELLNARAVQAAGGAPENPGRIKELRKAIARIKTI--Q 60

Query:   242 KQKAALRE 265
              ++  L+E
Sbjct:    61 GEEGDLQE 68


 >gi|10120938|pdb|1FFK|S  Chain S, Crystal Structure Of The Large Ribosomal
            Subunit From Haloarcula Marismortui At 2.4 Angstrom Resolution
            Length = 70

Frame  2 hits (HSPs):    _______________________________________________  
                        __________________________________________________
Database sequence:     |             |             |              |       | 70
                       0            20            40             60

  Plus Strand HSPs:

 Score = 102 (35.9 bits), Expect = 0.00032, P = 0.00032
 Identities = 25/68 (36%), Positives = 39/68 (57%), Frame = +2

Query:    62 IKVYELRNKAKAELLNQLKDLKAELALLRVAKVTGGAPNKLSKIKVVRLSIAQVLTVISQ 241
             + V E+R+   AE   +L DLK EL   R  +  GGAP    +IK +R +IA++ T+  Q
Sbjct:     3 LHVQEIRDMTPAEREAELDDLKTELLNARAVQAAGGAPENPGRIKELRKAIARIKTI--Q 60

Query:   242 KQKAALRE 265
              ++  L+E
Sbjct:    61 GEEGDLQE 68


 >gi|132838|sp|P12873|RL29_BACSU  50S RIBOSOMAL PROTEIN L29 >gi|71322|pir||R5BS2L
            ribosomal protein L29 - Bacillus subtilis >gi|40148|emb|CAA33699.1|
            (X15664) L29 protein (AA 1-66) [Bacillus subtilis]
            >gi|1044972|gb|AAB06807.1| (L47971) ribosomal protein L29 [Bacillus
            subtilis] >gi|2632391|emb|CAB11900.1| (Z99104) ribosomal protein
            L29 [Bacillus subtilis]
            Length = 66

Frame  2 hits (HSPs):   ________________________________________________  
Annotated Domains:      _________________________________________________ 
                        __________________________________________________
Database sequence:     |              |              |              |     | 66
                       0             20             40             60
__________________

Annotated Domains:
   BLOCKS               BL00579A: Ribosomal protein L29 proteins 8..17
   BLOCKS               BL00579B: Ribosomal protein L29 proteins 31..60
   PFAM                 Ribosomal_L29: Ribosomal L29 protein     3..65
   PRODOM               PD193745: RL29_BACSU                     1..23
   PRODOM               PD001983: RL29(17) RK29(3) O31163(1)     25..64
   PROSITE              RIBOSOMAL_L29: Ribosomal protein L29 sig 39..53
__________________


  Plus Strand HSPs:

 Score = 95 (33.4 bits), Expect = 0.0020, P = 0.0020
 Identities = 25/65 (38%), Positives = 40/65 (61%), Frame = +2

Query:    62 IKVYELRNKAKAELLNQLKDLKAELALLRVAKVTGGAPNKLSKIKVVRLSIAQVLTVISQ 241
             +K  E+R+   AE+  ++K LK EL  LR    TG   N  ++I+ VR +IA++ TVI +
Sbjct:     1 MKANEIRDLTTAEIEQKVKSLKEELFNLRFQLATGQLENT-ARIREVRKAIARMKTVIRE 59

Query:   242 KQKAA 256
             ++ AA
Sbjct:    60 REIAA 64


 >gi|132841|sp|P22665|RL29_HALHA  50S RIBOSOMAL PROTEIN L29 (HHAL29)
            >gi|81065|pir||S11599 ribosomal protein L29 [similarity] -
            Halobacterium salinarum >gi|2425183|dbj|BAA22277.1| (AB006961)
            ribosomal protein L29 [Halobacterium halobium]
            >gi|10581166|gb|AAG19943.1| (AE005077) 50S ribosomal protein L29P;
            Rpl29p [Halobacterium sp. NRC-1]
            Length = 71

Frame  2 hits (HSPs):   ________________________________________________  
Annotated Domains:      __________________________________________________
                        __________________________________________________
Database sequence:     |             |             |             |        | 71
                       0            20            40            60
__________________

Annotated Domains:
   BLOCKS               BL00579A: Ribosomal protein L29 proteins 15..24
   BLOCKS               BL00579B: Ribosomal protein L29 proteins 35..64
   DOMO                 DM01863: RIBOSOMALPROTEINL29             1..71
   PFAM                 Ribosomal_L29: Ribosomal L29 protein     6..69
   PRODOM               PD186205: RL29(7) RL35(6)                1..63
   PROSITE              RIBOSOMAL_L29: Ribosomal protein L29 sig 43..57
__________________


  Plus Strand HSPs:

 Score = 93 (32.7 bits), Expect = 0.0033, P = 0.0033
 Identities = 23/71 (32%), Positives = 41/71 (57%), Frame = +2

Query:    53 MARIKVYELRNKAKAELLNQLKDLKAELALLRVAKVTGGAPNKLSKIKVVRLSIAQVLTV 232
             MA +   E+R+   AE   +L++L+ EL   +  K  GGAP+   +I  +R +IA++ TV
Sbjct:     1 MAILYTSEIRDMTPAEREAELEELRTELLNSKAVKAAGGAPDNPGRISELRKTIARIKTV 60

Query:   233 ISQKQKAALRE 265
               Q+++  L +
Sbjct:    61 --QREEGDLAD 69


 >gi|132837|sp|P04457|RL29_BACST  50S RIBOSOMAL PROTEIN L29 >gi|71321|pir||R5BS29
            ribosomal protein L29 - Bacillus stearothermophilus
            Length = 66

Frame  2 hits (HSPs):   ________________________________________________  
Annotated Domains:      _________________________________________________ 
                        __________________________________________________
Database sequence:     |              |              |              |     | 66
                       0             20             40             60
__________________

Annotated Domains:
   BLOCKS               BL00579A: Ribosomal protein L29 proteins 8..17
   BLOCKS               BL00579B: Ribosomal protein L29 proteins 31..60
   DOMO                 DM01647: RIBOSOMALPROTEINL29             1..62
   PFAM                 Ribosomal_L29: Ribosomal L29 protein     3..65
   PRODOM               PD193744: RL29_BACST                     1..23
   PRODOM               PD001983: RL29(17) RK29(3) O31163(1)     25..64
   PROSITE              RIBOSOMAL_L29: Ribosomal protein L29 sig 39..53
__________________


  Plus Strand HSPs:

 Score = 92 (32.4 bits), Expect = 0.0043, P = 0.0043
 Identities = 24/65 (36%), Positives = 38/65 (58%), Frame = +2

Query:    62 IKVYELRNKAKAELLNQLKDLKAELALLRVAKVTGGAPNKLSKIKVVRLSIAQVLTVISQ 241
             +K  E+R    AE+  ++K LK EL  LR    TG   N  ++I+ VR  IA++ T+I +
Sbjct:     1 MKAKEIRELTTAEIEQKIKALKEELFNLRFQLATGQLENT-ARIRQVRKDIARMKTIIRE 59

Query:   242 KQKAA 256
             ++ AA
Sbjct:    60 RELAA 64


 >gi|12643297|sp|Q9Z9K6|RL29_BACHD  50S RIBOSOMAL PROTEIN L29
            >gi|10172754|dbj|BAB03861.1| (AP001507) 50S ribosomal protein L29
            [Bacillus halodurans]
            Length = 67

Frame  2 hits (HSPs):   _____________________________________________     
                        __________________________________________________
Database sequence:     |              |              |              |     | 67
                       0             20             40             60

  Plus Strand HSPs:

 Score = 92 (32.4 bits), Expect = 0.0043, P = 0.0043
 Identities = 24/62 (38%), Positives = 36/62 (58%), Frame = +2

Query:    62 IKVYELRNKAKAELLNQLKDLKAELALLRVAKVTGGAPNKLSKIKVVRLSIAQVLTVISQ 241
             +K  ELRN   AE+  + K LK EL  LR    TG   N  ++I+ VR +IA+  TV+ +
Sbjct:     1 MKTNELRNLTTAEIEQKTKSLKEELFNLRFQLATGQLDNP-TRIREVRKNIARAKTVLRE 59

Query:   242 KQ 247
             ++
Sbjct:    60 RE 61


 >gi|7321300|emb|CAB82078.1|  (AL161803) 50S ribosomal protein L29 [Streptomyces
            coelicolor A3(2)]
            Length = 74

Frame  2 hits (HSPs):    ___________________________________________      
                        __________________________________________________
Database sequence:     |            |             |            |          | 74
                       0           20            40           60

  Plus Strand HSPs:

 Score = 90 (31.7 bits), Expect = 0.0072, P = 0.0072
 Identities = 23/64 (35%), Positives = 35/64 (54%), Frame = +2

Query:    56 ARIKVYELRNKAKAELLNQLKDLKAELALLRVAKVTGGAPNKLSKIKVVRLSIAQVLTVI 235
             A  K  ELR     ELL +L++ K EL  LR    TG   N   ++K VR  IA++ T++
Sbjct:     3 AGTKASELRELGNEELLAKLREAKEELFNLRFQAATGQLENH-GRLKAVRKDIARIYTLM 61

Query:   236 SQKQ 247
              +++
Sbjct:    62 RERE 65


 >gi|12721782|gb|AAK03491.1|  (AE006177) RpL29 [Pasteurella multocida]
            Length = 63

Frame  2 hits (HSPs):   _______________________________________________   
                        __________________________________________________
Database sequence:     |               |              |               |   | 63
                       0              20             40              60

  Plus Strand HSPs:

 Score = 89 (31.3 bits), Expect = 0.0093, P = 0.0092
 Identities = 25/61 (40%), Positives = 36/61 (59%), Frame = +2

Query:    62 IKVYELRNKAKAELLNQLKDLKAELALLRVAKVTGGAPNKLSKIKVVRLSIAQVLTVISQ 241
             +K  ELR K+  EL  +L +L  E   LR+   TG    +  ++K VR SIAQV TV+++
Sbjct:     1 MKAQELRTKSVEELNAELVNLLGEQFKLRMQAATGQL-QQTHQLKQVRRSIAQVKTVLTE 59

Query:   242 K 244
             K
Sbjct:    60 K 60


 >gi|2500321|sp|Q50310|RL29_MYCPN  50S RIBOSOMAL PROTEIN L29
            >gi|2127649|pir||S62803 ribosomal protein L29 - Mycoplasma
            pneumoniae (strain ATCC 29342) >gi|2146607|pir||S73984 ribosomal
            protein L29 - Mycoplasma pneumoniae (SGC3) (ATCC 29342)
            >gi|1215715|gb|AAC43708.1| (U34795) RplC [Mycoplasma pneumoniae]
            >gi|1674363|gb|AAB96306.1| (AE000061) ribosomal protein L29
            [Mycoplasma pneumoniae]
            Length = 111

Frame  2 hits (HSPs):     ______________________________________________  
Annotated Domains:      __________________________________________________
                        __________________________________________________
Database sequence:     |                      |                     |     | 111
                       0                     50                   100
__________________

Annotated Domains:
   BLOCKS               BL00579A: Ribosomal protein L29 proteins 6..15
   BLOCKS               BL00579B: Ribosomal protein L29 proteins 32..61
   PFAM                 Ribosomal_L29: Ribosomal L29 protein     4..66
   PRODOM               PD193749: RL29_MYCPN                     1..24
   PRODOM               PD001983: RL29(17) RK29(3) O31163(1)     26..62
   PRODOM               PD027290: RL29_MYCPN                     64..110
   PROSITE              RIBOSOMAL_L29: Ribosomal protein L29 sig 40..54
__________________


  Plus Strand HSPs:

 Score = 88 (31.0 bits), Expect = 0.012, P = 0.012
 Identities = 29/104 (27%), Positives = 49/104 (47%), Frame = +2

Query:    74 ELRNKAKAELLNQLKDLKAELALLRVAKVTGGAPNKLSKIKVVRLSIAQVLTVISQKQKA 253
             ELR K+  EL+  +  LK EL   R  K+  G  +K   I   R  +A +LT+++++ K 
Sbjct:     6 ELRQKSSEELVKLVIKLKGELLEYRF-KLAHGELDKPHLINQTRRLLATILTILTER-KL 63

Query:   254 ALREAYKKKKYLPLDLRPKKTRAIRRRLTKHQVSLKTEREKKKE 385
               +E   K K L          A ++ L  ++  L   R K+++
Sbjct:    64 NWQEEQAKYKLLTKKTNEAAVNAWKQHLEANKAKLLKSRAKRED 107


 >gi|2500319|sp|P55840|RL29_ACTAC  50S RIBOSOMAL PROTEIN L29
            >gi|1841330|dbj|BAA10955.1| (D64071) ribosomal protein L29
            [Actinobacillus actinomycetemcomitans]
            Length = 63

Frame  2 hits (HSPs):   _______________________________________________   
Annotated Domains:      __________________________________________________
                        __________________________________________________
Database sequence:     |               |              |               |   | 63
                       0              20             40              60
__________________

Annotated Domains:
   BLOCKS               BL00579A: Ribosomal protein L29 proteins 5..14
   BLOCKS               BL00579B: Ribosomal protein L29 proteins 31..60
   PFAM                 Ribosomal_L29: Ribosomal L29 protein     3..63
   PRODOM               PD188758: RL29(2)                        1..24
   PRODOM               PD001983: RL29(17) RK29(3) O31163(1)     26..59
   PROSITE              RIBOSOMAL_L29: Ribosomal protein L29 sig 39..53
__________________


  Plus Strand HSPs:

 Score = 88 (31.0 bits), Expect = 0.012, P = 0.012
 Identities = 24/61 (39%), Positives = 36/61 (59%), Frame = +2

Query:    62 IKVYELRNKAKAELLNQLKDLKAELALLRVAKVTGGAPNKLSKIKVVRLSIAQVLTVISQ 241
             +K  ELR K+  EL  +L +L  E   LR+   TG    +  ++K VR SIAQ+ TV+++
Sbjct:     1 MKAQELRTKSVEELNAELVNLLGEQFKLRMQAATGQL-QQTHQLKQVRRSIAQIKTVLTE 59

Query:   242 K 244
             K
Sbjct:    60 K 60


 >gi|11499502  ref|NP_070743.1| LSU ribosomal protein L29P (rpl29P)
            [Archaeoglobus fulgidus] >gi|3914730|sp|O28361|RL29_ARCFU 50S
            RIBOSOMAL PROTEIN L29P >gi|7441064|pir||E69489 LSU ribosomal
            protein L29P (rpl29P) homolog - Archaeoglobus fulgidus
            >gi|2648644|gb|AAB89356.1| (AE000971) LSU ribosomal protein L29P
            (rpl29P) [Archaeoglobus fulgidus]
            Length = 68

Frame  2 hits (HSPs):   _______________________________________________   
                        __________________________________________________
Database sequence:     |             |              |              |      | 68
                       0            20             40             60

  Plus Strand HSPs:

 Score = 88 (31.0 bits), Expect = 0.012, P = 0.012
 Identities = 19/64 (29%), Positives = 37/64 (57%), Frame = +2

Query:    53 MARIKVYELRNKAKAELLNQLKDLKAELALLRVAKVTGGAPNKLSKIKVVRLSIAQVLTV 232
             M  +K+ E+R  ++ E L +L++L+ EL  LR    +GGA     +I ++R  IA++   
Sbjct:     1 MKAVKMKEIREMSREEKLRKLRELELELLKLRTLVRSGGAVENPGRINLIRKDIARLKMA 60

Query:   233 ISQK 244
             + ++
Sbjct:    61 LCEE 64


 >gi|11357029|pir||H82915  ribosomal protein L29 UU239 [imported] - Ureaplasma
            urealyticum >gi|6899209|gb|AAF30648.1|AE002122_17 (AE002122)
            ribosomal protein L29 [Ureaplasma urealyticum]
            Length = 75

Frame  2 hits (HSPs):       _______________________________________       
                        __________________________________________________
Database sequence:     |            |             |            |          | 75
                       0           20            40           60

  Plus Strand HSPs:

 Score = 88 (31.0 bits), Expect = 0.012, P = 0.012
 Identities = 23/60 (38%), Positives = 36/60 (60%), Frame = +2

Query:    74 ELRNKAKAELLNQLKDLKAELALLRVAKVTGGAPNKLSKIKVVRLSIAQVLTVISQKQKA 253
             +LR K   EL   + +LKA+L  LR A   G A  KL   K +R +IA+ LT++++++ A
Sbjct:     7 DLRKKDSLELEKIVIELKAKLLELRFAAANGEA-EKLHTAKEIRKTIARALTILNERELA 65


 >gi|3122714|sp|O32989|RL29_MYCLE  50S RIBOSOMAL PROTEIN L29
            >gi|11276873|pir||T45372 ribosomal protein L29 [imported] -
            Mycobacterium leprae >gi|2344840|emb|CAB11442.1| (Z98756) ribosomal
            protein L29 [Mycobacterium leprae]
            Length = 80

Frame  2 hits (HSPs):        ____________________________________         
Annotated Domains:      ____________________________________________      
                        __________________________________________________
Database sequence:     |           |            |           |             | 80
                       0          20           40          60
__________________

Annotated Domains:
   BLOCKS               BL00579A: Ribosomal protein L29 proteins 9..18
   BLOCKS               BL00579B: Ribosomal protein L29 proteins 35..64
   PFAM                 Ribosomal_L29: Ribosomal L29 protein     7..69
   PRODOM               PD187666: RL29(3)                        1..27
   PRODOM               PD001983: RL29(17) RK29(3) O31163(1)     29..70
__________________


  Plus Strand HSPs:

 Score = 84 (29.6 bits), Expect = 0.033, P = 0.033
 Identities = 21/58 (36%), Positives = 33/58 (56%), Frame = +2

Query:    74 ELRNKAKAELLNQLKDLKAELALLRVAKVTGGAPNKLSKIKVVRLSIAQVLTVISQKQ 247
             ELR     EL+ +L++ K EL  LR    TG   N   +++ VR  IA+V TV+ +++
Sbjct:     9 ELRELTDEELIERLRESKEELFNLRFQMATGQLNNN-RRLRTVRHEIARVYTVLRERE 65


 >gi|3122708|sp|O26117|RL29_METTH  50S RIBOSOMAL PROTEIN L29P
            >gi|7441058|pir||C69220 ribosomal protein L29 - Methanobacterium
            thermoautotrophicum (strain Delta H) >gi|2621056|gb|AAB84529.1|
            (AE000795) ribosomal protein L35 (E.coli L29) [Methanothermobacter
            thermautotrophicus]
            Length = 64

Frame  2 hits (HSPs):   __________________________________________________
Annotated Domains:      __________________________________________________
                        __________________________________________________
Database sequence:     |              |               |               |   | 64
                       0             20              40              60
__________________

Annotated Domains:
   BLOCKS               BL00579A: Ribosomal protein L29 proteins 8..17
   BLOCKS               BL00579B: Ribosomal protein L29 proteins 35..64
   PFAM                 Ribosomal_L29: Ribosomal L29 protein     6..64
   PRODOM               PD186205: RL29(7) RL35(6)                1..63
   PROSITE              RIBOSOMAL_L29: Ribosomal protein L29 sig 43..57
__________________


  Plus Strand HSPs:

 Score = 84 (29.6 bits), Expect = 0.033, P = 0.033
 Identities = 21/64 (32%), Positives = 35/64 (54%), Frame = +2

Query:    53 MARIKVYELRNKAKAELLNQLKDLKAELALLRVAKVTGGAPNKLSKIKVVRLSIAQVLTV 232
             MA ++  E+R     EL  +L +LKAE A         G      K++ +R +IA+VLT+
Sbjct:     1 MAILRSEEIREMDGEELQKKLDELKAEYARYISKSAAAGIHENPGKMREIRRTIARVLTI 60

Query:   233 ISQK 244
             +++K
Sbjct:    61 MNEK 64


 >gi|10178184|dbj|BAB11658.1|  (AB013395) 50S ribosomal protein L29 [Arabidopsis
            thaliana]
            Length = 173

Frame  2 hits (HSPs):                    _________________________        
                        __________________________________________________
Database sequence:     |              |             |              |      | 173
                       0             50           100            150

  Plus Strand HSPs:

 Score = 98 (34.5 bits), Expect = 0.037, P = 0.036
 Identities = 29/91 (31%), Positives = 53/91 (58%), Frame = +2

Query:    44 SRKMARIKVYELRNKAKAELLNQLKDLKAELALLRVAKVTGGAPNKLSKIKVVRLSIAQV 223
             S++ A +K  E+R+K   +L  ++ DLK EL +LR+ K +     K S  + ++  +A++
Sbjct:    61 SKREAELK--EIRSKTTEQLQEEVVDLKGELFMLRLQK-SARNEFKSSDFRRMKKQVARM 117

Query:   224 LTVISQKQKAALREAYKKKKYLPLDLRPKKT 316
             LTV   K++  ++E  KK+    LD + KK+
Sbjct:   118 LTV---KREREIKEGIKKRLSRKLDRQWKKS 145


 >gi|585878|sp|P38514|RL29_THEMA  50S RIBOSOMAL PROTEIN L29
            >gi|481936|pir||S40196 ribosomal protein L29 - Thermotoga maritima
            (strain MSB8) >gi|437931|emb|CAA79785.1| (Z21677) ribosomal protein
            L29 [Thermotoga maritima] >gi|4982056|gb|AAD36558.1|AE001798_23
            (AE001798) ribosomal protein L29 [Thermotoga maritima]
            Length = 66

Frame  2 hits (HSPs):   ______________________________________________    
Annotated Domains:      _________________________________________________ 
                        __________________________________________________
Database sequence:     |              |              |              |     | 66
                       0             20             40             60
__________________

Annotated Domains:
   BLOCKS               BL00579A: Ribosomal protein L29 proteins 5..14
   BLOCKS               BL00579B: Ribosomal protein L29 proteins 31..60
   DOMO                 DM01647: RIBOSOMALPROTEINL29             1..62
   PFAM                 Ribosomal_L29: Ribosomal L29 protein     3..65
   PRODOM               PD193746: RL29_THEMA                     1..23
   PRODOM               PD001983: RL29(17) RK29(3) O31163(1)     25..63
   PROSITE              RIBOSOMAL_L29: Ribosomal protein L29 sig 39..53
__________________


  Plus Strand HSPs:

 Score = 81 (28.5 bits), Expect = 0.072, P = 0.069
 Identities = 21/62 (33%), Positives = 34/62 (54%), Frame = +2

Query:    62 IKVYELRNKAKAELLNQLKDLKAELALLRVAKVTGGAPNKLSKIKVVRLSIAQVLTVISQ 241
             +K  ELRN    EL N L++ K +L  LR     G   N  S IK+ +  IA++ T++ +
Sbjct:     1 MKASELRNYTDEELKNLLEEKKRQLMELRFQLAMGQLKNT-SLIKLTKRDIARIKTILRE 59

Query:   242 KQ 247
             ++
Sbjct:    60 RE 61


 >gi|6225990|sp|P95057|RL29_MYCTU  50S RIBOSOMAL PROTEIN L29
            >gi|7441056|pir||H70642 probable ribosomal protein L29 rpmC -
            Mycobacterium tuberculosis (strain H37RV)
            >gi|1806177|emb|CAB06433.1| (Z84395) rpmC [Mycobacterium
            tuberculosis]
            Length = 77

Frame  2 hits (HSPs):        _____________________________________        
                        __________________________________________________
Database sequence:     |            |            |            |           | 77
                       0           20           40           60

  Plus Strand HSPs:

 Score = 81 (28.5 bits), Expect = 0.072, P = 0.069
 Identities = 20/58 (34%), Positives = 32/58 (55%), Frame = +2

Query:    74 ELRNKAKAELLNQLKDLKAELALLRVAKVTGGAPNKLSKIKVVRLSIAQVLTVISQKQ 247
             ELR     EL  +L++ K EL  LR    TG   N   +++ VR  IA++ TV+ +++
Sbjct:     9 ELRELTDEELAERLRESKEELFNLRFQMATGQLNNN-RRLRTVRQEIARIYTVLRERE 65


 >gi|7674275|sp|Q9WVW8|RL29_STRPN  50S RIBOSOMAL PROTEIN L29
            >gi|4927748|gb|AAD33264.1|AF126059_5 (AF126059) RpL29
            [Streptococcus pneumoniae] >gi|4927757|gb|AAD33273.1| (AF126060)
            RpL29 [Streptococcus pneumoniae] >gi|4927766|gb|AAD33282.1|
            (AF126061) RpL29 [Streptococcus pneumoniae]
            Length = 68

Frame  2 hits (HSPs):   ________________________________________________  
                        __________________________________________________
Database sequence:     |             |              |              |      | 68
                       0            20             40             60

  Plus Strand HSPs:

 Score = 76 (26.8 bits), Expect = 0.25, P = 0.22
 Identities = 23/65 (35%), Positives = 37/65 (56%), Frame = +2

Query:    50 KMARIK--VYELRNKAKAELLNQLKDLKAELALLRVAKVTGGAPNKLSKIKVVRLSIAQV 223
             K+  +K  V ELR  ++ EL  +  +LK EL  LR    TG    + +++K V+  IA++
Sbjct:     2 KLNEVKEFVKELRGLSQEELAKRENELKKELFELRFQAATGQL-EQTARLKEVKKQIARI 60

Query:   224 LTVISQ 241
              TV S+
Sbjct:    61 KTVQSE 66


 >gi|3122701|sp|O06050|RL29_MYCBO  50S RIBOSOMAL PROTEIN L29
            >gi|2113874|emb|CAA73680.1| (Y13228) rpmC [Mycobacterium bovis BCG]
            Length = 75

Frame  2 hits (HSPs):        ___________________________________          
Annotated Domains:      ______________________________________________    
                        __________________________________________________
Database sequence:     |            |             |            |          | 75
                       0           20            40           60
__________________

Annotated Domains:
   BLOCKS               BL00579A: Ribosomal protein L29 proteins 9..18
   BLOCKS               BL00579B: Ribosomal protein L29 proteins 35..64
   PFAM                 Ribosomal_L29: Ribosomal L29 protein     7..69
   PRODOM               PD187666: RL29(3)                        1..27
   PRODOM               PD001983: RL29(17) RK29(3) O31163(1)     29..59
__________________


  Plus Strand HSPs:

 Score = 74 (26.0 bits), Expect = 0.42, P = 0.35
 Identities = 20/53 (37%), Positives = 28/53 (52%), Frame = +2

Query:    74 ELRNKAKAELLNQLKDLKAELALLRVAKVTGGAPNKLSKIKVVRLSIAQVLTV 232
             ELR     EL  +L++ K EL  LR    TG   N   +++ VR  IA++ TV
Sbjct:     9 ELRELTDEELAERLRESKEELFNLRFQMATGQLNNN-RRLRTVRQEIARIYTV 60


 >gi|11347345|pir||E83115  50S ribosomal protein L29 PA4255 [imported] -
            Pseudomonas aeruginosa (strain PAO1)
            >gi|9950472|gb|AAG07643.1|AE004841_21 (AE004841) 50S ribosomal
            protein L29 [Pseudomonas aeruginosa]
            Length = 63

Frame  2 hits (HSPs):   _______________________________________________   
                        __________________________________________________
Database sequence:     |               |              |               |   | 63
                       0              20             40              60

  Plus Strand HSPs:

 Score = 74 (26.0 bits), Expect = 0.42, P = 0.35
 Identities = 24/61 (39%), Positives = 36/61 (59%), Frame = +2

Query:    62 IKVYELRNKAKAELLNQLKDLKAELALLRVAKVTG--GAPNKLSKIKVVRLSIAQVLTVI 235
             +K  ELR K+  +L  QL  L  +   LR+ K TG  G  + LS++K     IA+V TV+
Sbjct:     1 MKANELREKSVEQLNEQLLGLLRDQFNLRMQKATGQLGQSHLLSQVK---RDIARVKTVL 57

Query:   236 SQK 244
             +Q+
Sbjct:    58 NQQ 60


 >gi|132840|sp|P02429|RL29_ECOLI  50S RIBOSOMAL PROTEIN L29 >gi|71320|pir||R5EC29
            ribosomal protein L29 [validated] - Escherichia coli
            >gi|42834|emb|CAA26468.1| (X02613) ribosomal protein L29 (rpmC) (aa
            1-63) [Escherichia coli] >gi|606246|gb|AAA58109.1| (U18997) 50S
            ribosomal subunit protein L29 [Escherichia coli]
            >gi|1789708|gb|AAC76337.1| (AE000408) 50S ribosomal subunit protein
            L29 [Escherichia coli K12] >gi|12517944|gb|AAG58433.1|AE005557_2
            (AE005557) 50S ribosomal subunit protein L29 [Escherichia coli
            O157:H7] >gi|223244|prf||0612186A ribosomal protein L29
            [Escherichia coli]
            Length = 63

Frame  2 hits (HSPs):   __________________________________________________
Annotated Domains:      __________________________________________________
                        __________________________________________________
Database sequence:     |               |              |               |   | 63
                       0              20             40              60
__________________

Annotated Domains:
   BLOCKS               BL00579A: Ribosomal protein L29 proteins 5..14
   BLOCKS               BL00579B: Ribosomal protein L29 proteins 31..60
   PFAM                 Ribosomal_L29: Ribosomal L29 protein     3..63
   PRODOM               PD193748: RL29_ECOLI                     1..24
   PRODOM               PD001983: RL29(17) RK29(3) O31163(1)     26..59
   PROSITE              RIBOSOMAL_L29: Ribosomal protein L29 sig 39..53
__________________


  Plus Strand HSPs:

 Score = 70 (24.6 bits), Expect = 1.2, P = 0.69
 Identities = 21/64 (32%), Positives = 35/64 (54%), Frame = +2

Query:    62 IKVYELRNKAKAELLNQLKDLKAELALLRVAKVTGGAPNKLSKIKVVRLSIAQVLTVISQ 241
             +K  ELR K+  EL  +L +L  E   LR+ +   G   +   +K VR  +A+V T++++
Sbjct:     1 MKAKELREKSVEELNTELLNLLREQFNLRM-QAASGQLQQSHLLKQVRRDVARVKTLLNE 59

Query:   242 KQKA 253
             K  A
Sbjct:    60 KAGA 63


 >gi|3122706|sp|O24697|RL29_SYNP6  50S RIBOSOMAL PROTEIN L29
            >gi|2446898|dbj|BAA22457.1| (AB000111) 50S ribosomal protein L29
            [Synechococcus sp.]
            Length = 64

Frame  2 hits (HSPs):   __________________________________________________
Annotated Domains:      __________________________________________________
                        __________________________________________________
Database sequence:     |              |               |               |   | 64
                       0             20              40              60
__________________

Annotated Domains:
   BLOCKS               BL00579A: Ribosomal protein L29 proteins 8..17
   BLOCKS               BL00579B: Ribosomal protein L29 proteins 34..63
   PFAM                 Ribosomal_L29: Ribosomal L29 protein     6..64
   PRODOM               PD193751: RL29_SYNP6                     1..26
   PRODOM               PD001983: RL29(17) RK29(3) O31163(1)     28..63
   PROSITE              RIBOSOMAL_L29: Ribosomal protein L29 sig 42..56
__________________


  Plus Strand HSPs:

 Score = 70 (24.6 bits), Expect = 1.2, P = 0.69
 Identities = 21/65 (32%), Positives = 35/65 (53%), Frame = +2

Query:    53 MARIKVYELRNKAKAELLNQLKDLKAELALLRVAKVTGGAPNKLSKIKVVRLSIAQVLTV 232
             MA  K+ ++RN + A+L  ++ + K EL  LR  + T     K    K  +  +AQ+LTV
Sbjct:     1 MALPKIEDVRNLSDADLAEKIAEAKRELFDLRFQRATRQL-EKPHLFKHTKHRLAQLLTV 59

Query:   233 ISQKQ 247
               ++Q
Sbjct:    60 ERERQ 64


 >gi|1173014|sp|P46174|RL29_BUCAK  50S RIBOSOMAL PROTEIN L29
            >gi|632223|pir||JC2274 ribosomal protein L29 - pea aphid symbiont
            bacterium >gi|710613|dbj|BAA06583.1| (D31786) ribosomal protein L29
            [Acyrthosiphon kondoi endosymbiont]
            Length = 63

Frame  2 hits (HSPs):   _______________________________________________   
Annotated Domains:      __________________________________________________
                        __________________________________________________
Database sequence:     |               |              |               |   | 63
                       0              20             40              60
__________________

Annotated Domains:
   BLOCKS               BL00579A: Ribosomal protein L29 proteins 5..14
   BLOCKS               BL00579B: Ribosomal protein L29 proteins 31..60
   DOMO                 DM01647: RIBOSOMALPROTEINL29             1..62
   PFAM                 Ribosomal_L29: Ribosomal L29 protein     3..63
   PRODOM               PD193747: RL29_ACYKS                     1..24
   PRODOM               PD001983: RL29(17) RK29(3) O31163(1)     26..59
   PROSITE              RIBOSOMAL_L29: Ribosomal protein L29 sig 39..53
__________________


  Plus Strand HSPs:

 Score = 69 (24.3 bits), Expect = 1.5, P = 0.78
 Identities = 20/61 (32%), Positives = 34/61 (55%), Frame = +2

Query:    62 IKVYELRNKAKAELLNQLKDLKAELALLRVAKVTGGAPNKLSKIKVVRLSIAQVLTVISQ 241
             +K  ELR K   EL  +L +L  E   LR+   +G    +   +K VR ++A+V T++++
Sbjct:     1 MKAQELREKGVEELNTELLNLLREQFNLRMQGASGQL-QQTHLLKQVRRNVARVKTLLTE 59

Query:   242 K 244
             K
Sbjct:    60 K 60


 >gi|7439876|pir||JC5931  high mobility group I HMGI chromosomal protein isoform
            C-alpha - human
            Length = 90

Frame  1 hits (HSPs):     _____________________                           
                        __________________________________________________
Database sequence:     |          |          |          |          |      | 90
                       0         20         40         60         80

  Plus Strand HSPs:

 Score = 69 (24.3 bits), Expect = 1.5, P = 0.78
 Identities = 18/39 (46%), Positives = 27/39 (69%), Frame = +1

Query:    88 GEGGATEPAQGSQGG-ASPAPRRQGYRRRPKQALQN*GGE 204
             GEG A +P+  +QG  A+PAP+++G R RP++  Q   GE
Sbjct:     5 GEG-AGQPSTSAQGQPAAPAPQKRG-RGRPRKQQQEPTGE 42


 >gi|545157|gb|AAB29804.1|  homeobox gene NvHBox-4 product {type 1 homeodomain}
            [Notophthalmus viridescens=newts, tail, Peptide Partial, 60 aa]
            Length = 60

Frame  2 hits (HSPs):       ______________________________________________
                        __________________________________________________
Database sequence:     |               |                |                 | 60
                       0              20               40

  Plus Strand HSPs:

 Score = 68 (23.9 bits), Expect = 1.9, P = 0.86
 Identities = 17/55 (30%), Positives = 29/55 (52%), Frame = +2

Query:   227 TVISQKQKAALREAYKKKKYLPLDLRPKKTRAIRRRLTKHQVSLKTEREKKKELY 391
             T+ S  Q AAL+  ++K +YL L  R +    +    T+ ++  +  R K K+LY
Sbjct:     6 TIYSSYQLAALQRRFQKAQYLALPERAELAAQLGLTQTQVKIWFQNRRSKFKKLY 60


 >gi|3914739|sp|P56613|RL29_AQUAE  50S RIBOSOMAL PROTEIN L29
            Length = 73

Frame  2 hits (HSPs):          _______________________________________    
Annotated Domains:            ___________________________________________ 
                        __________________________________________________
Database sequence:     |             |            |             |         | 73
                       0            20           40            60
__________________

Annotated Domains:
   PFAM                 Ribosomal_L29: Ribosomal L29 protein     10..72
   PRODOM               PD186205: RL29(7) RL35(6)                11..65
__________________


  Plus Strand HSPs:

 Score = 67 (23.6 bits), Expect = 2.5, P = 0.92
 Identities = 22/58 (37%), Positives = 30/58 (51%), Frame = +2

Query:    74 ELRNKAKAELLNQLKDLKAELALLRVAKVTGGAPNKLSKIKVVRLSIAQVLTVISQKQ 247
             ++R K   EL   L +L  EL  L       G  N +   KV + +IA+VLTVIS+ Q
Sbjct:    12 DIRYKRLQELEKLLDELYLELTRLSFYYQVQGLENPMEMSKV-KSNIARVLTVISEYQ 68


 >gi|7162180|emb|CAB76841.1|  (AJ224860) ribosomal protein L29 [Thermus
            thermophilus]
            Length = 67

Frame  2 hits (HSPs):   ________________________________________________  
                        __________________________________________________
Database sequence:     |              |              |              |     | 67
                       0             20             40             60

  Plus Strand HSPs:

 Score = 67 (23.6 bits), Expect = 2.5, P = 0.92
 Identities = 19/64 (29%), Positives = 39/64 (60%), Frame = +2

Query:    59 RIKVYELRNKAKAELLNQLKDLKAELALLRVAKVTGGAPNKLSKIKVVRLSIAQVLTVIS 238
             R ++ E R  +  EL   +++ K EL  LR  + + G  ++  KI+ ++  IA++LTV++
Sbjct:     2 RKQLEEARKLSPVELEKLVREKKRELMELRF-QASIGQLSQNHKIRDLKRQIARLLTVLN 60

Query:   239 QKQK 250
             +K++
Sbjct:    61 EKRR 64


 >gi|7439879|pir||JC5933  high mobility group I HMGI chromosomal protein isoform
            C-gamma - human
            Length = 96

Frame  1 hits (HSPs):     ____________________                            
                        __________________________________________________
Database sequence:     |         |          |         |          |        | 96
                       0        20         40        60         80

  Plus Strand HSPs:

 Score = 69 (24.3 bits), Expect = 3.0, P = 0.95
 Identities = 18/39 (46%), Positives = 27/39 (69%), Frame = +1

Query:    88 GEGGATEPAQGSQGG-ASPAPRRQGYRRRPKQALQN*GGE 204
             GEG A +P+  +QG  A+PAP+++G R RP++  Q   GE
Sbjct:     5 GEG-AGQPSTSAQGQPAAPAPQKRG-RGRPRKQQQEPTGE 42


 >gi|3914735|sp|O52340|RL29_MYCGA  50S RIBOSOMAL PROTEIN L29
            >gi|2766511|gb|AAB95395.1| (AF036708) ribosomal protein L29
            [Mycoplasma gallisepticum]
            Length = 153

Frame  2 hits (HSPs):   __________________________________                
Annotated Domains:      _______________________________________           
                        __________________________________________________
Database sequence:     |                |               |               | | 153
                       0               50             100             150
__________________

Annotated Domains:
   PFAM                 Ribosomal_L29: Ribosomal L29 protein     2..64
   PRODOM               PD001983: RL29(17) RK29(3) O31163(1)     24..63
   PRODOM               PD053493: RL29_MYCGA                     65..118
__________________


  Plus Strand HSPs:

 Score = 81 (28.5 bits), Expect = 3.1, P = 0.95
 Identities = 27/102 (26%), Positives = 52/102 (50%), Frame = +2

Query:    74 ELRNKAKAELLNQLKDLKAELALLRVAKVTGGAPNKLSKIKVVRLSIAQVLTVISQKQKA 253
             ELR K   EL+  +  LK  L   R  K+  G  +K   IK  R ++A+VLT+++++   
Sbjct:     4 ELRAKTNEELIQLVTQLKGRLLEYRF-KLAQGELDKTHIIKETRQTLARVLTILTERDVK 62

Query:   254 ALREAYKKKKYLPLDLRPKKTRAIRRRLTKHQVS-LKTEREKK 379
                 A     ++    + K+ +   +++ + +V+ LK  +EK+
Sbjct:    63 VNVNAMVSS-FVKEQTKQKEIQESVKKIKQLRVAKLKQNKEKR 104


WARNING:  HSPs involving 10 database sequences were not reported due to the
          limiting value of parameter B = 50.


Parameters:
  filter=none
  matrix=BLOSUM62
  V=50
  B=50
  E=10
  gi
  H=1
  sort_by_pvalue
  echofilter

  ctxfactor=6.00

  Query                        -----  As Used  -----    -----  Computed  ----
  Frame  MatID Matrix name     Lambda    K       H      Lambda    K       H
   Std.    0   BLOSUM62                                 0.318   0.135   0.401  
   +3      0   BLOSUM62        0.318   0.135   0.401    0.366   0.164   0.593  
               Q=9,R=2         0.244   0.0300  0.180     n/a     n/a     n/a
   +2      0   BLOSUM62        0.318   0.135   0.401    0.339   0.147   0.452  
               Q=9,R=2         0.244   0.0300  0.180     n/a     n/a     n/a
   +1      0   BLOSUM62        0.318   0.135   0.401    0.342   0.152   0.518  
               Q=9,R=2         0.244   0.0300  0.180     n/a     n/a     n/a
   -1      0   BLOSUM62        0.318   0.135   0.401    0.347   0.149   0.488  
               Q=9,R=2         0.244   0.0300  0.180     n/a     n/a     n/a
   -2      0   BLOSUM62        0.318   0.135   0.401    0.351   0.154   0.571  
               Q=9,R=2         0.244   0.0300  0.180     n/a     n/a     n/a
   -3      0   BLOSUM62        0.318   0.135   0.401    0.347   0.154   0.500  
               Q=9,R=2         0.244   0.0300  0.180     n/a     n/a     n/a

  Query
  Frame  MatID  Length  Eff.Length     E    S W   T  X   E2     S2
   +3      0      240       232       10.  78 3  12 22  0.11    35
                                                    32  0.098   39
   +2      0      240       232       10.  78 3  12 22  0.11    35
                                                    32  0.098   39
   +1      0      241       232       10.  78 3  12 22  0.11    35
                                                    32  0.098   39
   -1      0      241       232       10.  78 3  12 22  0.11    35
                                                    32  0.098   39
   -2      0      240       231       10.  78 3  12 22  0.11    35
                                                    32  0.097   39
   -3      0      240       232       10.  78 3  12 22  0.11    35
                                                    32  0.098   39


Statistics:

  Database:  /usr/local/dot5/sl_home/beauty/seqdb/blast/nr
    Title:  nr
    Release date:  unknown
    Posted date:  4:06 PM CST Feb 28, 2001
    Format:  BLAST
  # of letters in database:  197,782,623
  # of sequences in database:  625,274
  # of database sequences satisfying E:  60
  No. of states in DFA:  600 (59 KB)
  Total size of DFA:  216 KB (256 KB)
  Time to generate neighborhood:  0.02u 0.00s 0.02t  Elapsed: 00:00:00
  No. of threads or processors used:  6
  Search cpu time:  219.33u 1.07s 220.40t  Elapsed: 00:01:11
  Total cpu time:  219.39u 1.10s 220.49t  Elapsed: 00:01:11
  Start:  Wed Jan 16 18:25:03 2002   End:  Wed Jan 16 18:26:14 2002

WARNINGS ISSUED:  2


Annotated Domains Database:   March 14, 2000 

Release Date:  March 14, 2000