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

  768   6.9  0.0  0.0  'E05B07_C07_04.ab1'    197  298    (0) +  (A)n     Simple_repeat     1  102    (0)      

Alignments:
768  6.86  0.00  0.00  'E05B07_C07_04.ab1'  197  298  (0)  (A)n#Simple_repeat  1  102  (78)  5

  'E05B07_C07_04.    197 AAAAAAAAAAAAAGAAAAAAAAAAAAAAACAAAAAAAAAAAAAAAAAAAA 246    
                                      i               v                    
  (A)n#Simple_rep      1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 50

  'E05B07_C07_04.    247 AAACAAAAAAAAAAAAAAAAAAAAAAACNNAAAAAAAAAAAAAAAAAAAA 296    
                            v                       v??                    
  (A)n#Simple_rep     51 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 100

  'E05B07_C07_04.    297 NA 298    
                         ? 
  (A)n#Simple_rep    101 AA 102

Transitions / transversions = 0.33 (1 / 3)
Gap_init rate = 0.00 (0 / 102), avg. gap size = 0.00 (0 / 0)  

Masked Sequence:
>'E05B07_C07_04.ab1'
AGACTGTTCCATAAAAATGCTCCCATTATGACTTGAAAATAAAATGTNTT
TCCACTCAAAATTGTGCGGCTGAAAATAAAATGATCCATTATAGCTGGCC
GGCACTTCCCTCTTGTGCTCTTTAATTAATTAGTAAGAAGATTAACTGAG
ATAGCACAAGGGTAAAAATGGAAATGGAATTTATCCCGCTGTCTCCNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN

Summary:
==================================================
file name: /repeatmasker/tmp/RM2seq
sequences:            1
total length:       298 bp
GC level:         25.51 %
bases masked:       102 bp ( 34.23 %)
==================================================
               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          102 bp    34.23 %
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=  'E05B07_C07_04.ab1'
        (298 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:      = 5 Sequences     : less than 5 sequences

 EXPECTation Threshold
 (E parameter)
    |
    V   Observed Counts-->
  10000 1329 255 |===================================================
   6310 1074 242 |================================================
   3980  832 228 |=============================================
   2510  604 164 |================================
   1580  440 121 |========================
   1000  319  91 |==================
    631  228  80 |================
    398  148  72 |==============
    251   76  26 |=====
    158   50  24 |====
    100   26   4 |:
   63.1   22   8 |=
   39.8   14   3 |:
   25.1   11   2 |:
   15.8    9   3 |:
 >>>>>>>>>>>>>>>>>>>>>  Expect = 10.0, Observed = 6  <<<<<<<<<<<<<<<<<
   10.0    6   1 |:
   6.31    5   1 |:
   3.98    4   3 |:
   2.51    1   0 |
   1.58    1   0 |
   1.00    1   1 |:


                                                                     Smallest
                                                                       Sum
                                                     Reading  High  Probability
Sequences producing High-scoring Segment Pairs:        Frame Score  P(N)      N
gi|5442042|gb|AAD43221.1|AF111940_3(AF111940) LspH pr... -3    49  0.59      2
gi|7332060|gb|AAF60747.1|(AC024804) Hypothetical prot... -2    47  0.96      2
gi|12644356|sp|P80065|INVB_DAUCABETA-FRUCTOFURANOSIDA... -1    57  0.97      2
gi|480996|pir||S37590beta-fructofuranosidase (EC 3.2.... -1    57  0.97      2
gi|6014846|sp|P81376|CYB_PLAGACYTOCHROME B >gi|84249|... -3    49  0.993     2
gi|480998|pir||S37592beta-fructofuranosidase (EC 3.2.... -1    53  0.9999    2

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|5442042|gb|AAD43221.1|AF111940_3  (AF111940) LspH precursor [Legionella
            pneumophila]
            Length = 161

Frame -2 hits (HSPs):                                              _____  
Frame -3 hits (HSPs):                               _________             
                        __________________________________________________
Database sequence:     |               |              |               |   | 161
                       0              50            100             150

  Minus Strand HSPs:

 Score = 49 (17.2 bits), Expect = 0.89, Sum P(2) = 0.59
 Identities = 12/31 (38%), Positives = 20/31 (64%), Frame = -3

Query:   179 FHFHFYPCAISVNLLTN*LKSTRGKCRPAIM 87
             F  +++P  + ++L TN LK +RG   PAI+
Sbjct:    93 FKLYYFPKNVVISLKTN-LKHSRGN--PAII 120

 Score = 34 (12.0 bits), Expect = 0.89, Sum P(2) = 0.59
 Identities = 6/14 (42%), Positives = 8/14 (57%), Frame = -2

Query:    57 EWKXILFSSHNGSI 16
             +W   L  SHNG +
Sbjct:   140 KWIAKLTGSHNGDL 153


 >gi|7332060|gb|AAF60747.1|  (AC024804) Hypothetical protein Y51H7BR.4
            [Caenorhabditis elegans]
            Length = 153

Frame -1 hits (HSPs):     ____                                            
Frame -2 hits (HSPs):               _________                             
                        __________________________________________________
Database sequence:     |                |               |               | | 153
                       0               50             100             150

  Minus Strand HSPs:

 Score = 47 (16.5 bits), Expect = 3.2, Sum P(2) = 0.96
 Identities = 9/25 (36%), Positives = 15/25 (60%), Frame = -2

Query:   126 IKEHKREVPASYNGSFYFQPHNFEW 52
             + E K+ + +S   +F  +P NFEW
Sbjct:    39 VYEDKQYISSSSMKNFLKKPTNFEW 63

 Score = 30 (10.6 bits), Expect = 3.2, Sum P(2) = 0.96
 Identities = 5/10 (50%), Positives = 8/10 (80%), Frame = -1

Query:   166 FTLVLSQLIF 137
             +T +L QL+F
Sbjct:     9 WTFILMQLVF 18


 >gi|12644356|sp|P80065|INVB_DAUCA  BETA-FRUCTOFURANOSIDASE, SOLUBLE ISOENZYME I
            PRECURSOR (SUCROSE-6-PHOSPHATE HYDROLASE) (INVERTASE) (SACCHARASE)
            >gi|480997|pir||S37591 beta-fructofuranosidase (EC 3.2.1.26)
            isozyme I class 1, soluble - carrot >gi|407055|emb|CAA53097.1|
            (X75351) beta-fructofuranosidase [Daucus carota]
            >gi|4454117|emb|CAA77267.1| (Y18707) beta-fructofuranosidase,
            isoform I [Daucus carota]
            Length = 661

Frame -1 hits (HSPs):      ___                                            
Frame -2 hits (HSPs):            ___                                      
                        __________________________________________________
Database sequence:     |           |          |          |           |    | 661
                       0         150        300        450         600

  Minus Strand HSPs:

 Score = 57 (20.1 bits), Expect = 3.5, Sum P(2) = 0.97
 Identities = 11/25 (44%), Positives = 19/25 (76%), Frame = -1

Query:   184 INSISIFTLVLSQLIFLLIN*RAQE 110
             ++S+ + TL+LS +IFLL+N   Q+
Sbjct:    46 VSSVLLSTLILSFVIFLLVNPNVQQ 70

 Score = 35 (12.3 bits), Expect = 3.5, Sum P(2) = 0.97
 Identities = 9/24 (37%), Positives = 12/24 (50%), Frame = -2

Query:    84 SFYFQPHNFEWKXILFSSHNGSIF 13
             SF+FQP    W     +  NG +F
Sbjct:   133 SFHFQPQE-NW----MNDPNGPLF 151


 >gi|480996|pir||S37590  beta-fructofuranosidase (EC 3.2.1.26) isozyme I class 2
            precursor, soluble - carrot >gi|407078|emb|CAA53098.1| (X75352)
            beta-fructofuranosidase [Daucus carota]
            Length = 661

Frame -1 hits (HSPs):      ___                                            
Frame -2 hits (HSPs):            ___                                      
Annotated Domains:             __________________________________________ 
                        __________________________________________________
Database sequence:     |           |          |          |           |    | 661
                       0         150        300        450         600
__________________

Annotated Domains:
   DOMO                 DM00269: GLYCOSYLHYDROLASESFAMILY32      105..641
   PROSITE              GLYCOSYL_HYDROL_F32: Glycosyl hydrolases 135..148
__________________


  Minus Strand HSPs:

 Score = 57 (20.1 bits), Expect = 3.5, Sum P(2) = 0.97
 Identities = 11/25 (44%), Positives = 19/25 (76%), Frame = -1

Query:   184 INSISIFTLVLSQLIFLLIN*RAQE 110
             ++S+ + TL+LS +IFLL+N   Q+
Sbjct:    46 VSSVLLSTLILSFVIFLLVNPNVQQ 70

 Score = 35 (12.3 bits), Expect = 3.5, Sum P(2) = 0.97
 Identities = 9/24 (37%), Positives = 12/24 (50%), Frame = -2

Query:    84 SFYFQPHNFEWKXILFSSHNGSIF 13
             SF+FQP    W     +  NG +F
Sbjct:   133 SFHFQPQE-NW----MNDPNGPLF 151


 >gi|6014846|sp|P81376|CYB_PLAGA  CYTOCHROME B >gi|84249|pir||A32566
            ubiquinol--cytochrome-c reductase (EC 1.10.2.2) cytochrome b -
            Plasmodium gallinaceum mitochondrion
            Length = 300

Frame -3 hits (HSPs):    ____      ____                                   
Annotated Domains:      __________________________________________________
                        __________________________________________________
Database sequence:     |        |       |       |        |       |        | 300
                       0       50     100     150      200     250
__________________

Annotated Domains:
   Entrez               metal-binding site: IRON 1 (HEME B562 AX 78
   Entrez               metal-binding site: IRON 2 (HEME B566 AX 92
   PFAM                 cytochrome_b_N: Cytochrome b(N-terminal) 1..193
   PFAM                 cytochrome_b_C: Cytochrome b(C-terminal) 197..242
   PRODOM               PD015015: CYB(2)                         1..36
   PRODOM               PD000016: CYB(298) CYB6(21) QCRB(2)      38..103
   PRODOM               PD000017: CYB(297) CYB6(21) QCRB(2)      107..144
   PRODOM               PD067775: CYB_PLAGA                      146..199
   PRODOM               PD000019: CYB(301) PETD(23)              201..299
   PROSITE              CYTOCHROME_B_QO: Cytochrome b/b6 Qo site 209..214
__________________


  Minus Strand HSPs:

 Score = 49 (17.2 bits), Expect = 4.9, Sum P(2) = 0.99
 Identities = 8/18 (44%), Positives = 11/18 (61%), Frame = -3

Query:   182 KFHFHFYPCAISVNLLTN 129
             K H   YPC +++N L N
Sbjct:    10 KAHLLHYPCPLNINFLWN 27

 Score = 34 (12.0 bits), Expect = 4.9, Sum P(2) = 0.99
 Identities = 8/20 (40%), Positives = 11/20 (55%), Frame = -3

Query:    95 AIMDHFIFSRTILSGXTFYF 36
             AIMD + F     +G +F F
Sbjct:    67 AIMDGWCFRYMHATGASFVF 86


 >gi|480998|pir||S37592  beta-fructofuranosidase (EC 3.2.1.26) isozyme I class 3
            precursor, soluble - carrot >gi|407049|emb|CAA53099.1| (X75353)
            beta-fructofuranosidase [Daucus carota]
            Length = 661

Frame -1 hits (HSPs):      ___                                            
Frame -2 hits (HSPs):            ___                                      
Annotated Domains:             __________________________________________ 
                        __________________________________________________
Database sequence:     |           |          |          |           |    | 661
                       0         150        300        450         600
__________________

Annotated Domains:
   DOMO                 DM00269: GLYCOSYLHYDROLASESFAMILY32      105..641
   PROSITE              GLYCOSYL_HYDROL_F32: Glycosyl hydrolases 135..148
__________________


  Minus Strand HSPs:

 Score = 53 (18.7 bits), Expect = 9.0, Sum P(2) = 1.0
 Identities = 10/25 (40%), Positives = 18/25 (72%), Frame = -1

Query:   184 INSISIFTLVLSQLIFLLIN*RAQE 110
             ++S+ + TL+ S +IFLL+N   Q+
Sbjct:    46 VSSVLLATLIFSFVIFLLVNPNVQQ 70

 Score = 35 (12.3 bits), Expect = 9.0, Sum P(2) = 1.0
 Identities = 9/24 (37%), Positives = 12/24 (50%), Frame = -2

Query:    84 SFYFQPHNFEWKXILFSSHNGSIF 13
             SF+FQP    W     +  NG +F
Sbjct:   133 SFHFQPQE-NW----MNDPNGPLF 151


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

  ctxfactor=5.91

  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    0.345   0.147   0.517  
               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    0.382   0.181   0.709  
               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    0.371   0.169   0.642  
               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    0.362   0.164   0.575  
               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    0.346   0.154   0.545  
               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    0.343   0.149   0.514  
               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       98        64       10.  58 3  12 22  0.11    30
                                                    27  0.12    30
   +2      0       99        64       10.  58 3  12 22  0.11    30
                                                    27  0.12    30
   +1      0       99        65       10.  58 3  12 22  0.11    30
                                                    27  0.092   31
   -1      0       99        64       10.  58 3  12 22  0.11    30
                                                    27  0.12    30
   -2      0       99        64       10.  58 3  12 22  0.11    30
                                                    27  0.12    30
   -3      0       98        63       10.  58 3  12 22  0.11    30
                                                    26  0.12    30


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:  578 (57 KB)
  Total size of DFA:  114 KB (128 KB)
  Time to generate neighborhood:  0.01u 0.00s 0.01t  Elapsed: 00:00:00
  No. of threads or processors used:  6
  Search cpu time:  64.30u 1.01s 65.31t  Elapsed: 00:00:12
  Total cpu time:  64.34u 1.01s 65.35t  Elapsed: 00:00:12
  Start:  Fri Jan 18 13:17:44 2002   End:  Fri Jan 18 13:17:56 2002


Annotated Domains Database:   March 14, 2000 

Release Date:  March 14, 2000