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
The files 
/repeatmasker/tmp/RM2sequpload_13869.stderr 
exist and will be overwritten.
Quit (^c) and rename files if you'd like to save them.


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

  384   2.2  0.0  0.0  SSH4A06.SEQ(1>459)      8   52  (377) +  (T)n     Simple_repeat     1   45    (0)      



Alignments:
384  2.22  0.00  0.00  SSH4A06.SEQ(1>459)  8  52  (377)  C  (A)n#Simple_repeat  (135)  45  1  5

  SSH4A06.SEQ(1>4      8 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTCTTTTTTTTTTTT 52     
                                                         i            
C (A)n#Simple_rep     45 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 1      

Transitions / transversions = 1.00 (1 / 0)
Gap_init rate = 0.00 (0 / 45), avg. gap size = 0.00 (0 / 0)  



Masked Sequence:
>SSH4A06.SEQ(1>459)
SACAAGCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNAGATACAGGAACAAATCTATTCCCACTAGCAATGAGAGGGAATAATTT
ATTTGACTGACTCAGCTTGATAAAGCGGACTTTGAAAATTACAATGCATG
CAGACAACTGCAAACACATGTAAAACACAGTGCCTTACAACTGTCTAATA
AAACAAAAGCACAATAACTATTTAATTTTAACTAAATAGAGCCCTCTAAA
TAATAATCAAACATTTATACTTCTTTGTGGATCTGCAAGCTGCAAATGCA
TCTTCCCACTCCATGACTTTCATTTTCACACTTTCTGTATGCATCCATGT
TGGGGGTTGTTGAAAAAAAAGTGCTACCTATTATTGGTAAGGTGGAGGGG
GTTGATTTGTAGTATTGTGAGTTGGGAAA



Summary:
==================================================
file name: /repeatmasker/tmp/RM2seq
sequences:            1
total length:       429 bp
GC level:         32.40 %
bases masked:        45 bp ( 10.49 %)
==================================================
               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           45 bp    10.49 %
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=  SSH4A06.SEQ(1>459)
        (429 letters)

  Translating both strands of query sequence in all 6 reading frames


Database:  nr
           505,245 sequences; 158,518,215 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 703 117 |=======================================
   6310 586  86 |============================
   3980 500 129 |===========================================
   2510 371 129 |===========================================
   1580 242  48 |================
   1000 194  67 |======================
    631 127  41 |=============
    398  86  39 |=============
    251  47   6 |==
    158  41   7 |==
    100  34   8 |==
   63.1  26   3 |=
   39.8  23   6 |==
   25.1  17   2 |:
   15.8  15   5 |=
 >>>>>>>>>>>>>>>>>>>>>  Expect = 10.0, Observed = 10  <<<<<<<<<<<<<<<<<
   10.0  10   0 |
   6.31  10   5 |=
   3.98   5   3 |=
   2.51   2   2 |:


                                                                     Smallest
                                                                       Sum
                                                     Reading  High  Probability
Sequences producing High-scoring Segment Pairs:        Frame Score  P(N)      N
gi|1703204|sp|P30231|AFP1_SINALCYSTEINE-RICH ANTIFUNG... +3    40  0.89      2
gi|2914400|pdb|1AYJ|   Determination Of The Three-Dim... +3    40  0.89      2
gi|124026|sp|P01061|IBB2_PHAANBOWMAN-BIRK TYPE PROTEI... -1    60  0.97      1
gi|68808|pir||TIZB1Bproteinase inhibitor (Bowman-Birk... -1    60  0.97      1
gi|1587460|prf||2206458Atrypsin inhibitor [Dipteryx a... -1    60  0.97      1
gi|68810|pir||TIMBtrypsin inhibitor (Bowman-Birk) - m... -1    59  0.992     1
gi|729798|sp|P01062|IBB_PHAAUBOWMAN-BIRK TYPE TRYPSIN... -1    59  0.992     1
gi|940028|gb|AAA74194.1|(U25669) trypsin inhibitor [s... -1    59  0.992     1
gi|1084384|pir||JC1066trypsin inhibitor - mung bean      -1    59  0.992     1
gi|102069|pir||B35349H+-transporting ATP synthase (EC... -3    58  0.998     1



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

Locus_ID                Frame 3 Hits
gi|1703204             |                                 ________         
gi|2914400             |                                 ________         
Prosite Hits:                                         ____                
                        __________________________________________________
Query sequence:        |                 |                |               | 143
                       0                50              100
__________________
Prosite hits:
   PROKAR_LIPOPROTEIN   Prokaryotic membrane lipoprotein lipid a 87..97
__________________


Locus_ID                Frame 1 Hits
gi|1703204             |                  ____                            
gi|2914400             |                  ____                            
                        __________________________________________________
Query sequence:        |                 |                |               | 143
                       0                50              100


Locus_ID                Frame -1 Hits
gi|124026              |                  _______                         
gi|68808               |                  _______                         
gi|1587460             |                  _______                         
gi|68810               |                  _______                         
gi|729798              |                  _______                         
gi|940028              |                  _______                         
gi|1084384             |                  _______                         
                        __________________________________________________
Query sequence:        |                 |                |               | 143
                       0                50              100


Locus_ID                Frame -3 Hits
gi|102069              |                ____________                      
                        __________________________________________________
Query sequence:        |                 |                |               | 143
                       0                50              100




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|1703204|sp|P30231|AFP1_SINAL  CYSTEINE-RICH ANTIFUNGAL PROTEIN 1 (AFP1) (M1)
            Length = 51

Frame  3 hits (HSPs):                                    _________________
Frame  1 hits (HSPs):                    ________                         
Annotated Domains:      __________________________________________________
                        __________________________________________________
Database sequence:     |                  |                   |           | 51
                       0                 20                  40
__________________

Annotated Domains:
   BLOCKS               BL00940A: Gamma-thionins family proteins 2..25
   BLOCKS               BL00940B: Gamma-thionins family proteins 40..51
   Entrez               pyrrolidone-carboxylic-acid site         1
   PFAM                 Gamma-thionin: Gamma-thionins family     2..51
   PRODOM               PD002594: THG1(3) AFP1(2) THG(2)         2..50
   PROSITE              GAMMA_THIONIN: Gamma-thionins family sig 2..25
__________________


  Plus Strand HSPs:

 Score = 40 (14.1 bits), Expect = 2.2, Sum P(2) = 0.89
 Identities = 8/21 (38%), Positives = 9/21 (42%), Frame = +3

Query:   288 SCKCIFPLHDFHFHTFCMHPC 350
             SC  +FP H       C  PC
Sbjct:    35 SCNYVFPAHK----CICYFPC 51

 Score = 36 (12.7 bits), Expect = 2.2, Sum P(2) = 0.89
 Identities = 5/8 (62%), Positives = 6/8 (75%), Frame = +1

Query:   163 NTCKTQCL 186
             N CK QC+
Sbjct:    19 NACKNQCI 26


to_Entrezto_Relatedto_pdb >gi|2914400|pdb|1AYJ|     Determination Of The Three-Dimensional Solution
            Structure Of Raphanus Sativus Antifungal Protein 1 (Rs-Afp1) By 1h
            Nmr, 20 Structures
            Length = 51

Frame  3 hits (HSPs):                                    _________________
Frame  1 hits (HSPs):                    ________                         
                        __________________________________________________
Database sequence:     |                  |                   |           | 51
                       0                 20                  40

  Plus Strand HSPs:

 Score = 40 (14.1 bits), Expect = 2.2, Sum P(2) = 0.89
 Identities = 8/21 (38%), Positives = 9/21 (42%), Frame = +3

Query:   288 SCKCIFPLHDFHFHTFCMHPC 350
             SC  +FP H       C  PC
Sbjct:    35 SCNYVFPAHK----CICYFPC 51

 Score = 36 (12.7 bits), Expect = 2.2, Sum P(2) = 0.89
 Identities = 5/8 (62%), Positives = 6/8 (75%), Frame = +1

Query:   163 NTCKTQCL 186
             N CK QC+
Sbjct:    19 NACKNQCI 26


to_Entrezto_Relatedto_Related >gi|124026|sp|P01061|IBB2_PHAAN  BOWMAN-BIRK TYPE PROTEINASE INHIBITORS I-A,
            I-B, AND I-A' >gi|68807|pir||TIZB1A proteinase inhibitor
            (Bowman-Birk) I-A - adzuki bean >gi|350609|prf||0709228A inhibitor
            IA,proteinase [Vigna angularis]
            Length = 78

Frame -1 hits (HSPs):                        ____________                 
Annotated Domains:            ________________________________________    
                        __________________________________________________
Database sequence:     |            |            |           |            | 78
                       0           20           40          60
__________________

Annotated Domains:
   BLOCKS               BL00281A: Bowman-Birk serine protease in 18..34
   BLOCKS               BL00281B: Bowman-Birk serine protease in 42..63
   DOMO                 DM00766: BOWMAN-BIRKINHIBITORREPEAT      11..48
   Entrez               active site: REACTIVE BOND (BY SIMILARIT 26..27
   Entrez               active site: REACTIVE BOND (BY SIMILARIT 53..54
   PFAM                 Bowman-Birk_leg: Bowman-Birk serine prot 18..72
   PRODOM               PD002168: IBB(8) IBB2(6) IBB1(4)         18..71
   PROSITE              BOWMAN_BIRK: Bowman-Birk serine protease 34..49
__________________


  Minus Strand HSPs:

 Score = 60 (21.1 bits), Expect = 3.6, P = 0.97
 Identities = 9/19 (47%), Positives = 14/19 (73%), Frame = -1

Query:   213 CAFVLLDSCKALCFTCVCS 157
             CA + LDSC + C +C+C+
Sbjct:    34 CADIRLDSCHSACKSCMCT 52


to_Entrezto_Related >gi|68808|pir||TIZB1B  proteinase inhibitor (Bowman-Birk) I-B - adzuki bean
            Length = 78

Frame -1 hits (HSPs):                        ____________                 
Annotated Domains:                 __________________________________     
                        __________________________________________________
Database sequence:     |            |            |           |            | 78
                       0           20           40          60
__________________

Annotated Domains:
   Entrez               domain: Bowman-Birk inhibitor repeat hom 19..45
   Entrez               domain: Bowman-Birk inhibitor repeat hom 46..71
   Entrez               inhibit site: Lys (trypsin)              26
   Entrez               inhibit site: Arg (trypsin)              53
   PROSITE              BOWMAN_BIRK: Bowman-Birk serine protease 34..49
__________________


  Minus Strand HSPs:

 Score = 60 (21.1 bits), Expect = 3.6, P = 0.97
 Identities = 9/19 (47%), Positives = 14/19 (73%), Frame = -1

Query:   213 CAFVLLDSCKALCFTCVCS 157
             CA + LDSC + C +C+C+
Sbjct:    34 CADIRLDSCHSACKSCMCT 52


to_Entrezto_Related >gi|1587460|prf||2206458A  trypsin inhibitor [Dipteryx alata]
            Length = 62

Frame -1 hits (HSPs):                   ________________                  
                        __________________________________________________
Database sequence:     |               |               |               |  | 62
                       0              20              40              60

  Minus Strand HSPs:

 Score = 60 (21.1 bits), Expect = 3.6, P = 0.97
 Identities = 10/20 (50%), Positives = 14/20 (70%), Frame = -1

Query:   216 YCAFVLLDSCKALCFTCVCS 157
             +C  V LDSC + C TC+C+
Sbjct:    21 HCHDVRLDSCHSDCETCICT 40


to_Entrezto_Related >gi|68810|pir||TIMB  trypsin inhibitor (Bowman-Birk) - mung bean
            Length = 72

Frame -1 hits (HSPs):                     ______________                  
Annotated Domains:              _____________________________________     
                        __________________________________________________
Database sequence:     |             |             |            |         | 72
                       0            20            40           60
__________________

Annotated Domains:
   Entrez               domain: Bowman-Birk inhibitor repeat hom 13..39
   Entrez               domain: Bowman-Birk inhibitor repeat hom 40..65
   Entrez               inhibit site: Lys (trypsin)              20
   Entrez               inhibit site: Arg (trypsin)              47
   PROSITE              BOWMAN_BIRK: Bowman-Birk serine protease 28..43
__________________


  Minus Strand HSPs:

 Score = 59 (20.8 bits), Expect = 4.8, P = 0.99
 Identities = 8/20 (40%), Positives = 15/20 (75%), Frame = -1

Query:   216 YCAFVLLDSCKALCFTCVCS 157
             +CA + L+SC + C +C+C+
Sbjct:    27 HCANIRLNSCHSACKSCICT 46


to_Entrezto_Relatedto_Related >gi|729798|sp|P01062|IBB_PHAAU  BOWMAN-BIRK TYPE TRYPSIN INHIBITOR
            Length = 72

Frame -1 hits (HSPs):                     ______________                  
Annotated Domains:             _______________________________________    
                        __________________________________________________
Database sequence:     |             |             |            |         | 72
                       0            20            40           60
__________________

Annotated Domains:
   Entrez               active site: INTERACTION WITH TRYPSIN.   20..21
   Entrez               active site: INTERACTION WITH TRYPSIN.   47..48
   PFAM                 Bowman-Birk_leg: Bowman-Birk serine prot 12..66
   PRODOM               PD002168: IBB(8) IBB2(6) IBB1(4)         12..65
   PROSITE              BOWMAN_BIRK: Bowman-Birk serine protease 28..43
__________________


  Minus Strand HSPs:

 Score = 59 (20.8 bits), Expect = 4.8, P = 0.99
 Identities = 8/20 (40%), Positives = 15/20 (75%), Frame = -1

Query:   216 YCAFVLLDSCKALCFTCVCS 157
             +CA + L+SC + C +C+C+
Sbjct:    27 HCANIRLNSCHSACKSCICT 46


to_Entrezto_Relatedto_Related >gi|940028|gb|AAA74194.1|  (U25669) trypsin inhibitor [synthetic construct]
            Length = 73

Frame -1 hits (HSPs):                     ______________                  
                        __________________________________________________
Database sequence:     |             |            |             |         | 73
                       0            20           40            60

  Minus Strand HSPs:

 Score = 59 (20.8 bits), Expect = 4.8, P = 0.99
 Identities = 8/20 (40%), Positives = 15/20 (75%), Frame = -1

Query:   216 YCAFVLLDSCKALCFTCVCS 157
             +CA + L+SC + C +C+C+
Sbjct:    28 HCANIRLNSCHSACKSCICT 47


to_Entrezto_Relatedto_Related >gi|1084384|pir||JC1066  trypsin inhibitor - mung bean
            Length = 73

Frame -1 hits (HSPs):                     ______________                  
Annotated Domains:              ______________________                    
                        __________________________________________________
Database sequence:     |             |            |             |         | 73
                       0            20           40            60
__________________

Annotated Domains:
   Entrez               domain: Bowman-Birk inhibitor repeat hom 14..40
   PROSITE              BOWMAN_BIRK: Bowman-Birk serine protease 29..44
__________________


  Minus Strand HSPs:

 Score = 59 (20.8 bits), Expect = 4.8, P = 0.99
 Identities = 8/20 (40%), Positives = 15/20 (75%), Frame = -1

Query:   216 YCAFVLLDSCKALCFTCVCS 157
             +CA + L+SC + C +C+C+
Sbjct:    28 HCANIRLNSCHSACKSCICT 47


to_Entrezto_Relatedto_Relatedto_ec >gi|102069|pir||B35349  H+-transporting ATP synthase (EC 3.6.1.34) protein 6 -
            Sauroleishmania tarentolae mitochondrion (SGC6) (fragment)
            Length = 67

Frame -3 hits (HSPs):        ____________________________                 
Annotated Domains:                                     ____________       
                        __________________________________________________
Database sequence:     |              |              |              |     | 67
                       0             20             40             60
__________________

Annotated Domains:
   PROSITE              CRYSTALLIN_BETAGAMMA: Crystallins beta a 43..58
__________________


  Minus Strand HSPs:

 Score = 58 (20.4 bits), Expect = 6.2, P = 1.0
 Identities = 16/37 (43%), Positives = 21/37 (56%), Frame = -3

Query:   235 LVKIK*LLCFCF------IRQL*GTVFYMCLQLSACI 143
             LV ++ LLCFC+      I  L   VFY+C +L  CI
Sbjct:     9 LVIMRILLCFCYSVWSRIIFVLPVNVFYICTELMFCI 45


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

  ctxfactor=5.95

  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    0.341   0.149   0.544  
               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    0.355   0.158   0.532  
               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    0.385   0.174   0.670  
               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    0.343   0.150   0.498  
               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    0.365   0.160   0.649  
               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    0.358   0.161   0.563  
               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      142       127       10.  71 3  12 22  0.10    33
                                                    29  0.12    35
   +2      0      142       127       10.  71 3  12 22  0.10    33
                                                    29  0.12    35
   +1      0      143       126       10.  71 3  12 22  0.10    33
                                                    29  0.12    35
   -1      0      143       128       10.  71 3  12 22  0.11    33
                                                    29  0.12    35
   -2      0      142       126       10.  71 3  12 22  0.10    33
                                                    29  0.12    35
   -3      0      142       127       10.  71 3  12 22  0.10    33
                                                    29  0.12    35


Statistics:

  Database:  /usr/local/dot5/sl_home/beauty/seqdb/blast/nr
    Title:  nr
    Release date:  unknown
    Posted date:  8:50 PM CDT May 27, 2000
    Format:  BLAST
  # of letters in database:  158,518,215
  # of sequences in database:  505,245
  # of database sequences satisfying E:  10
  No. of states in DFA:  591 (58 KB)
  Total size of DFA:  174 KB (192 KB)
  Time to generate neighborhood:  0.01u 0.00s 0.01t  Elapsed: 00:00:00
  No. of threads or processors used:  4
  Search cpu time:  164.58u 1.04s 165.62t  Elapsed: 00:01:11
  Total cpu time:  164.63u 1.06s 165.69t  Elapsed: 00:01:11
  Start:  Wed Feb 14 17:20:08 2001   End:  Wed Feb 14 17:21:19 2001



Annotated Domains Database:   March 14, 2000 

Release Date:  March 14, 2000