Please help us to improve our services and obtain funding for the
BCM Search Launcher
-- take a minute to complete our User Survey

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

  285   2.9  0.0  0.0  C01G08_CONSENSUS     59   92  (515) +  (TCTCCC)n Simple_repeat     5   38    (0)      



Alignments:
285  2.94  0.00  0.00  C01G08_CONSENSUS  59  92  (515)  C  (GGGAGA)n#Simple_repeat  (142)  38  5  0

  C01G08_CONSENSU     59 CCTCTCCCTCTCCCTCTCCCTCTCCCTCTCCTTC 92     
                                                        i  
C (GGGAGA)n#Simpl     38 CCTCTCCCTCTCCCTCTCCCTCTCCCTCTCCCTC 5      

Transitions / transversions = 1.00 (1 / 0)
Gap_init rate = 0.00 (0 / 34), avg. gap size = 0.00 (0 / 0)  



Masked Sequence:
>C01G08_CONSENSUS
CCTCCTTTGGTCCTTTCCACTATTATCAAAGACTTAAACAACCACACAAA
TATTATAANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNACTACAAC
CACCACCTCTCCTCCCACTTGAGCTTCTTTCCAATTTTACTCCTGCAAAT
GAAAGCTACAATAACACTACTGTTTTAAGTAGCACTATTATGAAATATCC
AAGTTTGGAGAAAATAGAAGAAGGTTTAGCACGAGCACGGGCCTCAATTC
AGGAATCTATCCGATCAAGGAACTATACTTCAGCCAACANANTAAATTTT
GTCCCCAAAGGATCCATTTACCTGAATCCACNCGCTTTTCATCAATTTAA
ACAGGANTCATTAAGANATGTTTGAANAAATTCAAGGTGTTGGGTTGTTA
TGAAGANGGAAAAGCNACCATTANTGCATGATGGGCCAGCAAATGATATA
TACTCCNTTGANGGTCAATTCCTTGATGAAATANACNACGAAGCTNAGTT
GGGAACCACTTCANGGCTGAACATCCTGATCAAGCACAATTTTCTTCCTT
CCCTTCAGCATACCAATGTTTGTTCACTATGTTTACNAGCCTATTCCAAA
AGCATTC



Summary:
==================================================
file name: /repeatmasker/tmp/RM2seq
sequences:            1
total length:       607 bp
GC level:         39.76 %
bases masked:        34 bp (  5.60 %)
==================================================
               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           34 bp     5.60 %
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=  C01G08_CONSENSUS
        (607 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:      = 2 Sequences     : less than 2 sequences

 EXPECTation Threshold
 (E parameter)
    |
    V   Observed Counts-->
  10000 456 116 |==========================================================
   6310 340  71 |===================================
   3980 269  75 |=====================================
   2510 194  47 |=======================
   1580 147  53 |==========================
   1000  94  34 |=================
    631  60  16 |========
    398  44   4 |==
    251  40  10 |=====
    158  30   5 |==
    100  25   3 |=
   63.1  22  11 |=====
   39.8  11   3 |=
   25.1   8   1 |:
   15.8   7   1 |:
 >>>>>>>>>>>>>>>>>>>>>  Expect = 10.0, Observed = 6  <<<<<<<<<<<<<<<<<
   10.0   6   1 |:
   6.31   5   0 |
   3.98   5   0 |
   2.51   5   0 |
   1.58   5   0 |
   1.00   5   0 |
   0.63   5   0 |
   0.40   5   0 |
   0.25   5   0 |
   0.16   5   0 |
   0.10   5   0 |
  0.063   5   1 |:


                                                                     Smallest
                                                                       Sum
                                                     Reading  High  Probability
Sequences producing High-scoring Segment Pairs:        Frame Score  P(N)      N
gi|9758008|dbj|BAB08605.1|(AB005235) contains similar... +1   127  3.3e-09   2
gi|6466945|gb|AAF13080.1|AC009176_7(AC009176) hypothe... +1   106  1.4e-05   2
gi|11358246|pir||T46112hypothetical protein T27B3.50 ... +1    95  1.6e-05   2
gi|8953374|emb|CAB96647.1|(AL360314) putative protein... +1   105  0.00097   1
gi|8953375|emb|CAB96648.1|(AL360314) putative protein... +1    86  0.058     2
gi|8096320|dbj|BAA95823.1|(AP002069) Similar to Arabi... +1    79  0.9999    3



Locally-aligned regions (HSPs) with respect to query sequence:

Locus_ID                Frame 2 Hits
gi|9758008             |                                            _____ 
gi|6466945             |                                            _____ 
gi|11358246            |                                            _____ 
gi|8953375             |                                           ______ 
gi|8096320             |                                            _____ 
                        __________________________________________________
Query sequence:        |            |           |           |            || 203
                       0           50         100         150          200


Locus_ID                Frame 1 Hits
gi|9758008             |          ________________________________        
gi|6466945             |                 ______________________           
gi|11358246            |                               _________          
gi|8953374             |          ___________________                     
gi|8953375             |                               _________          
gi|8096320             |          _____________  ____________________     
                        __________________________________________________
Query sequence:        |            |           |           |            || 203
                       0           50         100         150          200




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.



to_Entrezto_Relatedto_Related >gi|9758008|dbj|BAB08605.1|  (AB005235) contains similarity to limonene
            cyclase~gene_id:MED24.9 [Arabidopsis thaliana]
            Length = 408

Frame  2 hits (HSPs):                  ___                                
Frame  1 hits (HSPs):   _______________                                   
                        __________________________________________________
Database sequence:     |                  |                 |             | 408
                       0                150               300

  Plus Strand HSPs:

 Score = 127 (44.7 bits), Expect = 3.3e-09, Sum P(2) = 3.3e-09
 Identities = 40/127 (31%), Positives = 60/127 (47%), Frame = +1

Query:   133 NFTPANESYNNTTVLSSTIMKYPS-LEKIEEGLARARASIQESIRSRNYTSANXXNFVPK 309
             N T  + + ++T  L     +  S LEKIE  L +ARASI+ +         +  ++VP 
Sbjct:     3 NVTATSNNVSSTASLEPKKRRVLSNLEKIEFKLQKARASIKAASMD---DPVDDPDYVPL 59

Query:   310 GSIYLNPXAFHQFKQXSLRXV*XNSRCWVVMKXEKXPLXHDGPANDIYSXXGQFLDEIXX 489
             G +Y N   FH+    S   +    + +V  + E  PL HDGP   IYS  G F+ EI  
Sbjct:    60 GPMYWNAKVFHR----SYLEMEKQFKIYVYKEGEP-PLFHDGPCKSIYSMEGSFIYEIET 114

Query:   490 EAXLGTTS 513
             +    T +
Sbjct:   115 DTRFRTNN 122

 Score = 55 (19.4 bits), Expect = 3.3e-09, Sum P(2) = 3.3e-09
 Identities = 9/16 (56%), Positives = 12/16 (75%), Frame = +2

Query:   539 IFFLPFSIPMFVHYVY 586
             +F+LPFS+   V YVY
Sbjct:   128 VFYLPFSVVKMVRYVY 143


to_Entrezto_Relatedto_Related >gi|6466945|gb|AAF13080.1|AC009176_7  (AC009176) hypothetical protein
            [Arabidopsis thaliana]
            Length = 470

Frame  2 hits (HSPs):                       ___                           
Frame  1 hits (HSPs):            __________                               
                        __________________________________________________
Database sequence:     |               |               |               |  | 470
                       0             150             300             450

  Plus Strand HSPs:

 Score = 106 (37.3 bits), Expect = 1.4e-05, Sum P(2) = 1.4e-05
 Identities = 33/89 (37%), Positives = 47/89 (52%), Frame = +1

Query:   211 KIEEGLARARASIQESIRSRNYTSANXX-----NFVPKGSIYLNPXAFHQFKQXSLRXV* 375
             K+E  LA AR  I+E+    NY+S         ++VP G IY NP AFH+    S   + 
Sbjct:    87 KVEAELATARVLIREA--QLNYSSTTSSPLGDEDYVPHGDIYRNPYAFHR----SYLLME 140

Query:   376 XNSRCWVVMKXEKXPLXHDGPANDIYSXXGQFLD 477
                + +V  + +  P+ H G   DIYS  G FL+
Sbjct:   141 KMFKIYVYEEGDP-PIFHYGLCKDIYSMEGLFLN 173

 Score = 63 (22.2 bits), Expect = 1.4e-05, Sum P(2) = 1.4e-05
 Identities = 8/19 (42%), Positives = 16/19 (84%), Frame = +2

Query:   539 IFFLPFSIPMFVHYVYXPI 595
             ++FLPFS+ M +H+++ P+
Sbjct:   192 VYFLPFSVVMILHHLFDPV 210


to_Entrezto_Relatedto_Related >gi|11358246|pir||T46112  hypothetical protein T27B3.50 - Arabidopsis thaliana
            >gi|6735291|emb|CAB68119.1| (AL137079) putative protein
            [Arabidopsis thaliana]
            Length = 340

Frame  2 hits (HSPs):           ___                                       
Frame  1 hits (HSPs):   ______                                            
                        __________________________________________________
Database sequence:     |                     |                     |      | 340
                       0                   150                   300

  Plus Strand HSPs:

 Score = 95 (33.4 bits), Expect = 1.6e-05, Sum P(2) = 1.6e-05
 Identities = 17/33 (51%), Positives = 22/33 (66%), Frame = +1

Query:   385 RCWVVMKXEKXPLXHDGPANDIYSXXGQFLDEI 483
             + W   + E+ PL HDGP NDIY   GQF+DE+
Sbjct:     5 KVWSYKEGEQ-PLVHDGPVNDIYGIEGQFIDEL 36

 Score = 73 (25.7 bits), Expect = 1.6e-05, Sum P(2) = 1.6e-05
 Identities = 13/18 (72%), Positives = 14/18 (77%), Frame = +2

Query:   542 FFLPFSIPMFVHYVYXPI 595
             FFLPFS+   VHYVY PI
Sbjct:    58 FFLPFSVANIVHYVYQPI 75


to_Entrezto_Relatedto_Related >gi|8953374|emb|CAB96647.1|  (AL360314) putative protein [Arabidopsis thaliana]
            Length = 162

Frame  1 hits (HSPs):                       ________________________      
                        __________________________________________________
Database sequence:     |               |              |              |    | 162
                       0              50            100            150

  Plus Strand HSPs:

 Score = 105 (37.0 bits), Expect = 0.00097, P = 0.00097
 Identities = 28/75 (37%), Positives = 42/75 (56%), Frame = +1

Query:   133 NFTPANESYNNTTVLSSTIMKYPSLEKIEEGLARARASIQES-----IRSRNYTSANXXN 297
             N T  N S +   V+        ++E+IEEGLA ARA+I+++      R R+ T+ +   
Sbjct:    68 NITSNNNSTSEVVVVEEVD---EAVERIEEGLAMARAAIRKAGEKNLRRDRDRTNNSDVG 124

Query:   298 FVPKGSIYLNPXAFHQFK 351
              V  GS+YLN   FHQ +
Sbjct:   125 VVSNGSVYLNAFTFHQLR 142


to_Entrezto_Relatedto_Related >gi|8953375|emb|CAB96648.1|  (AL360314) putative protein [Arabidopsis thaliana]
            Length = 336

Frame  2 hits (HSPs):          ____                                       
Frame  1 hits (HSPs):   ______                                            
                        __________________________________________________
Database sequence:     |                      |                     |     | 336
                       0                    150                   300

  Plus Strand HSPs:

 Score = 86 (30.3 bits), Expect = 0.059, Sum P(2) = 0.058
 Identities = 16/33 (48%), Positives = 21/33 (63%), Frame = +1

Query:   385 RCWVVMKXEKXPLXHDGPANDIYSXXGQFLDEI 483
             + W   + E  PL H GP N+IY+  GQF+DEI
Sbjct:     6 KIWTYREGE-APLFHKGPLNNIYAIEGQFMDEI 37

 Score = 49 (17.2 bits), Expect = 0.059, Sum P(2) = 0.058
 Identities = 7/20 (35%), Positives = 13/20 (65%), Frame = +2

Query:   533 STIFFLPFSIPMFVHYVYXP 592
             +T+F++P  I   + +VY P
Sbjct:    52 ATVFYIPVGIVNIIRFVYRP 71


to_Entrezto_Relatedto_Related >gi|8096320|dbj|BAA95823.1|  (AP002069) Similar to Arabidopsis thaliana DNA
            chromosome 4, BAC clone F4D11 (AL022537) [Oryza sativa]
            >gi|8096330|dbj|BAA95833.1| (AP002069) Similar to Arabidopsis
            thaliana DNA chromosome 4, BAC clone F4D11 (AL022537) [Oryza
            sativa]
            Length = 919

Frame  2 hits (HSPs):                                  __                 
Frame  1 hits (HSPs):                          ___ _____                  
                        __________________________________________________
Database sequence:     |        |       |       |       |       |       | | 919
                       0      150     300     450     600     750     900

  Plus Strand HSPs:

 Score = 79 (27.8 bits), Expect = 8.8, Sum P(3) = 1.0
 Identities = 24/78 (30%), Positives = 40/78 (51%), Frame = +1

Query:   316 IYLNPXAFHQFKQXSLRXV*XNSRCWVVMKXEKXPLXHDGPANDIYSXXGQFLDEIXXEA 495
             +Y NP AF++    S   +    + +V  + E  P+ H+GP  +IY+  G+F++E+   A
Sbjct:   512 VYRNPAAFYR----SYVEMERRFKVYVYEEGEP-PIAHEGPCKNIYAVEGRFIEELELMA 566

Query:   496 X-LGTTSXLNILIKHN-FLP 549
               LG     +    H  FLP
Sbjct:   567 PPLGGVRTWDPARAHALFLP 586

 Score = 41 (14.4 bits), Expect = 8.8, Sum P(3) = 1.0
 Identities = 7/17 (41%), Positives = 9/17 (52%), Frame = +2

Query:   545 FLPFSIPMFVHYVYXPI 595
             FLP S+   V   Y P+
Sbjct:   584 FLPLSVSQMVQLAYRPL 600

 Score = 39 (13.7 bits), Expect = 8.8, Sum P(3) = 1.0
 Identities = 13/50 (26%), Positives = 23/50 (46%), Frame = +1

Query:   130 SNFTPANESYNNTTVLSSTI-MKYPSLEKIEEGLARARASIQESIRSRNY 276
             S+ +PA    N      + + M   +   +E  L  ARA+I+ + R R +
Sbjct:   429 SSSSPARRLSNGLAAERARMAMARAASPTVERELDAARAAIRRAARRRRH 478


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

  ctxfactor=5.89

  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    0.354   0.156   0.564  
               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    0.363   0.163   0.589  
               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    0.320   0.135   0.397  
               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    0.356   0.160   0.640  
               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    0.367   0.167   0.666  
               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    0.355   0.159   0.517  
               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      201       176       10.  75 3  12 22  0.11    34
                                                    31  0.11    37
   +2      0      202       178       10.  76 3  12 22  0.11    34
                                                    31  0.11    37
   +1      0      202       174       10.  75 3  12 22  0.11    34
                                                    31  0.11    37
   -1      0      202       180       10.  76 3  12 22  0.11    34
                                                    31  0.12    37
   -2      0      202       178       10.  76 3  12 22  0.11    34
                                                    31  0.11    37
   -3      0      201       174       10.  75 3  12 22  0.11    34
                                                    31  0.11    37


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:  6
  No. of states in DFA:  596 (59 KB)
  Total size of DFA:  202 KB (256 KB)
  Time to generate neighborhood:  0.01u 0.01s 0.02t  Elapsed: 00:00:00
  No. of threads or processors used:  6
  Search cpu time:  161.71u 1.03s 162.74t  Elapsed: 00:00:28
  Total cpu time:  161.72u 1.07s 162.79t  Elapsed: 00:00:28
  Start:  Wed Oct  3 11:45:50 2001   End:  Wed Oct  3 11:46:18 2001



Annotated Domains Database:   March 14, 2000 

Release Date:  March 14, 2000