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

   29   4.7  0.0  0.0  'E13A12_B12_02.ab1'    510  552   (54) +  AT_rich  Low_complexity     1   43    (0)      

Alignments:
29  4.65  0.00  0.00  'E13A12_B12_02.ab1'  510  552  (54)  C  AT_rich#Low_complexity  (257)  43  1  5

  'E13A12_B12_02.    510 TTTTTATTTAATATCTGTATTATATATAATTTTTTTTATTTAT 552    
                            v    vvv   i vvv  v     v    v        v 
C AT_rich#Low_com     43 TTTATATTATTTATTTTATTTTTATATTATTTATTTTATTTTT 1      

Transitions / transversions = 0.09 (1 / 11)
Gap_init rate = 0.00 (0 / 43), avg. gap size = 0.00 (0 / 0)  

Masked Sequence:
>'E13A12_B12_02.ab1'
TTACGGCCGGGGCCAGCAAGNATTTGCCTCTCTGAGGNATTACGGCAAAA
CTTACAGGNAAATGGGGTTTTGAAAAGCTTGTGTATAGAGACTCAATTAC
AGGAATTCGTAGAGATCGAAAATATGCAGTGCAACCACGGAGTTTGTATG
CAACAGGGGTGCACATGTCAATGGATCTATCAGGAAAGACAACACACAAA
ACTGAAGGTAGGATCAAATACTTCCACTATCATGGAACCATATCAGAAAG
GAGAGAAACATGTAAAATACTCGTCAACACAACACAAGTCACCCAGAACA
AAATCCCTTATGTGATGGACACCACAATGAGGGACACTGCTGGGGTAATC
AAGAAATTTGAGCTCAAGATGATTGGAACAAGGTTGCAGAAGACAAGGCA
ATAATGACATACCCCAAATCTCTCATTCCTTTTCTCTTGAACAGGAAATG
GGCTTTCCTATAAAGAAATATATAATTTAACTTGTGGCAGGATAAAAAAA
ATCTGAGAGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNCTGGTACAGATGGGGGTATATGATCTTGTTTCATATTTAATAAATTTT
TTTTGG

Summary:
==================================================
file name: /repeatmasker/tmp/RM2seq
sequences:            1
total length:       606 bp
GC level:         36.98 %
bases masked:        43 bp (  7.10 %)
==================================================
               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:       0            0 bp     0.00 %
Low complexity:       1           43 bp     7.10 %
==================================================

* 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=  'E13A12_B12_02.ab1'
        (606 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:      = 3 Sequences     : less than 3 sequences

 EXPECTation Threshold
 (E parameter)
    |
    V   Observed Counts-->
  10000 632 130 |===========================================
   6310 502  83 |===========================
   3980 419 152 |==================================================
   2510 267  88 |=============================
   1580 179  65 |=====================
   1000 114  33 |===========
    631  81  29 |=========
    398  52  21 |=======
    251  31   9 |===
    158  22   3 |=
    100  19   2 |:
   63.1  17   8 |==
   39.8   9   2 |:
   25.1   7   1 |:
   15.8   6   1 |:
 >>>>>>>>>>>>>>>>>>>>>  Expect = 10.0, Observed = 5  <<<<<<<<<<<<<<<<<
   10.0   5   1 |:


                                                                     Smallest
                                                                       Sum
                                                     Reading  High  Probability
Sequences producing High-scoring Segment Pairs:        Frame Score  P(N)      N
gi|8953765|dbj|BAA98120.1|(AB024024) gene_id:K15C23.1... +3   383  1.9e-34   1
gi|7452443|pir||T05325hypothetical protein F1C12.90 -... +3   356  1.4e-31   1
gi|6041838|gb|AAF02147.1|AC009853_7(AC009853) unknown... +3   152  5.8e-10   1
gi|11358255|pir||T50520hypothetical protein T27I15_80... +3   152  5.8e-10   1
gi|3901000|emb|CAA13637.1|(AJ235250) cytochrome b [Ce... -3    80  0.998     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.


 >gi|8953765|dbj|BAA98120.1|  (AB024024) gene_id:K15C23.12~pir||T05325~strong
            similarity to unknown protein [Arabidopsis thaliana]
            Length = 519

Frame  3 hits (HSPs):                                         ____________
                        __________________________________________________
Database sequence:     |              |             |              |      | 519
                       0            150           300            450

  Plus Strand HSPs:

 Score = 383 (134.8 bits), Expect = 1.9e-34, P = 1.9e-34
 Identities = 71/119 (59%), Positives = 88/119 (73%), Frame = +3

Query:    45 AKLTGKWGFEKLVYRDSITGIRRDRKYAVQPRSLYATGVHMSMDLSGKTTHKTEGRIKYF 224
             A+   KWGFEKL YRD     RRDRKYAVQPR+++ATGVHMS  L GKT H+ EG+I+YF
Sbjct:   401 ARTYRKWGFEKLAYRDVKKVPRRDRKYAVQPRNVFATGVHMSQHLQGKTYHRAEGKIRYF 460

Query:   225 HYHGTISERRETCKILVNTTQVTQNKIPYVMDTTMRDTAGVIKKFELKMIGTRLQKTRQ 401
             HYHG+IS+RRE C+ L N T++     PYV+DTTMRD    +K FE++ IG RL +TRQ
Sbjct:   461 HYHGSISQRREPCRHLYNGTRIVHENNPYVLDTTMRDIGLAVKTFEIRTIGDRLLRTRQ 519


 >gi|7452443|pir||T05325  hypothetical protein F1C12.90 - Arabidopsis thaliana
            >gi|2982434|emb|CAA18242.1| (AL022224) putative protein
            [Arabidopsis thaliana] >gi|7268812|emb|CAB79017.1| (AL161552)
            putative protein [Arabidopsis thaliana]
            Length = 504

Frame  3 hits (HSPs):                                         ____________
                        __________________________________________________
Database sequence:     |              |              |              |     | 504
                       0            150            300            450

  Plus Strand HSPs:

 Score = 356 (125.3 bits), Expect = 1.4e-31, P = 1.4e-31
 Identities = 67/119 (56%), Positives = 85/119 (71%), Frame = +3

Query:    45 AKLTGKWGFEKLVYRDSITGIRRDRKYAVQPRSLYATGVHMSMDLSGKTTHKTEGRIKYF 224
             A+   KWG EKL YRD     RRDRKYAVQP +++ATGVHMS +L GKT HK E +I+YF
Sbjct:   386 ARTYRKWGIEKLAYRDVKKVPRRDRKYAVQPENVFATGVHMSQNLQGKTYHKAESKIRYF 445

Query:   225 HYHGTISERRETCKILVNTTQVTQNKIPYVMDTTMRDTAGVIKKFELKMIGTRLQKTRQ 401
             HYHG+IS+RRE C+ L N ++V     PYV+DTT+ D    ++ FEL+ IG RL +TRQ
Sbjct:   446 HYHGSISQRREPCRQLFNDSRVVFENTPYVLDTTICDVGLAVRTFELRTIGDRLLRTRQ 504


 >gi|6041838|gb|AAF02147.1|AC009853_7  (AC009853) unknown protein [Arabidopsis
            thaliana]
            Length = 102

Frame  3 hits (HSPs):                            _________________________
                        __________________________________________________
Database sequence:     |         |         |        |         |         | | 102
                       0        20        40       60        80       100

  Plus Strand HSPs:

 Score = 152 (53.5 bits), Expect = 5.8e-10, P = 5.8e-10
 Identities = 30/49 (61%), Positives = 35/49 (71%), Frame = +3

Query:    45 AKLTGKWGFEKLVYRDSITGIRRDRKYAVQPRSLYATGVHMSMDLSGKT 191
             A+   KWG EKL YRD     RRDRKYAVQP +++A GVHMS +L GKT
Sbjct:    54 ARTYRKWGIEKLAYRDVKKVPRRDRKYAVQPENVFAIGVHMSQNLQGKT 102


 >gi|11358255|pir||T50520  hypothetical protein T27I15_80 - Arabidopsis thaliana
            >gi|8388615|emb|CAB94135.1| (AL358732) putative protein
            [Arabidopsis thaliana] >gi|8777409|dbj|BAA96999.1| (AB023039)
            gb|AAF02147.1~gene_id:MIF21.8~similar to unknown protein
            [Arabidopsis thaliana]
            Length = 102

Frame  3 hits (HSPs):                            _________________________
                        __________________________________________________
Database sequence:     |         |         |        |         |         | | 102
                       0        20        40       60        80       100

  Plus Strand HSPs:

 Score = 152 (53.5 bits), Expect = 5.8e-10, P = 5.8e-10
 Identities = 30/49 (61%), Positives = 35/49 (71%), Frame = +3

Query:    45 AKLTGKWGFEKLVYRDSITGIRRDRKYAVQPRSLYATGVHMSMDLSGKT 191
             A+   KWG EKL YRD     RRDRKYAVQP +++A GVHMS +L GKT
Sbjct:    54 ARTYRKWGIEKLAYRDVKKVPRRDRKYAVQPENVFAIGVHMSQNLQGKT 102


 >gi|3901000|emb|CAA13637.1|  (AJ235250) cytochrome b [Ceratosolen stupefactus]
            Length = 225

Frame -3 hits (HSPs):                                      ___________    
                        __________________________________________________
Database sequence:     |          |           |          |          |     | 225
                       0         50         100        150        200

  Minus Strand HSPs:

 Score = 80 (28.2 bits), Expect = 6.4, P = 1.0
 Identities = 17/45 (37%), Positives = 27/45 (60%), Frame = -3

Query:   376 PIILSSNFLITPAVSLIVVSIT*GILFWVTCVVLTSILHVSLLSD 242
             P+ L+SN+   P     VV    G+L W+ C++LT +L+  +LSD
Sbjct:   160 PMGLNSNYFKIPFNPYFVVKDLIGVLIWLMCLMLTCLLNPYILSD 204


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

  ctxfactor=5.96

  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    0.339   0.150   0.473  
               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    0.353   0.156   0.604  
               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    0.337   0.146   0.478  
               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    0.363   0.165   0.625  
               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    0.349   0.156   0.594  
               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    0.340   0.151   0.497  
               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       185       10.  76 3  12 22  0.12    34
                                                    31  0.12    37
   +2      0      201       183       10.  76 3  12 22  0.12    34
                                                    31  0.12    37
   +1      0      202       184       10.  76 3  12 22  0.12    34
                                                    31  0.12    37
   -1      0      202       184       10.  76 3  12 22  0.12    34
                                                    31  0.12    37
   -2      0      201       183       10.  76 3  12 22  0.12    34
                                                    31  0.12    37
   -3      0      201       183       10.  76 3  12 22  0.12    34
                                                    31  0.12    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:  5
  No. of states in DFA:  593 (58 KB)
  Total size of DFA:  223 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:  187.05u 1.31s 188.36t  Elapsed: 00:00:38
  Total cpu time:  187.09u 1.33s 188.42t  Elapsed: 00:00:38
  Start:  Wed Jan 23 17:51:22 2002   End:  Wed Jan 23 17:52:00 2002


Annotated Domains Database:   March 14, 2000 

Release Date:  March 14, 2000