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 





Checking for E. coli insertion elements
Checking for E. coli insertion elements

Masked Sequence:
>'E14F04_L04_12.ab1'
CGGCCGGGGCAAGGGAAATGGTTACTCTGTTGGGTTTGGTACTTGCTCAG
GCAAGATTGTACCCGCAGCTCCATGAGGCTAGTATCATTCCATAGTCTTT
TCCAGTTGTGGTGGGAGGAGTTGTACAATCAAGAGCCTGCTTGTTTAATT
TACTCGGCGCATAATATGACTTTAATAAAGCTGGTTTTTTATGAGTATTA
TACTTTTTCTTTTTTTATGCTGTAGTGTGGATCCAACATTGGAATAAACC
AATACTTATAAAAAAAATATTATCAAATTCTCCGNNNNNNNNNNNNNNNN
NNNNNNNNNNNNCCNT




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  unpublished.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=  'E14F04_L04_12.ab1'
        (316 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:      = 11 Sequences     : less than 11 sequences

 EXPECTation Threshold
 (E parameter)
    |
    V   Observed Counts-->
  10000 2619 651 |===========================================================
   6310 1968 556 |==================================================
   3980 1412 533 |================================================
   2510  879 255 |=======================
   1580  624 231 |=====================
   1000  393 139 |============
    631  254  53 |====
    398  201  51 |====
    251  150  37 |===
    158  113  36 |===
    100   77  38 |===
   63.1   39  13 |=
   39.8   26   2 |:
   25.1   24   8 |:
   15.8   16   3 |:
 >>>>>>>>>>>>>>>>>>>>>  Expect = 10.0, Observed = 13  <<<<<<<<<<<<<<<<<
   10.0   13   1 |:
   6.31   12   0 |
   3.98   12   1 |:
   2.51   11   0 |
   1.58   11   0 |
   1.00   11   0 |
   0.63   11   2 |:
   0.40    9   2 |:
   0.25    7   6 |:
   0.16    1   0 |
   0.10    1   0 |
  0.063    1   0 |
  0.040    1   0 |
  0.025    1   0 |
  0.016    1   0 |
  0.010    1   0 |
 0.0063    1   1 |:


                                                                     Smallest
                                                                       Sum
                                                     Reading  High  Probability
Sequences producing High-scoring Segment Pairs:        Frame Score  P(N)      N
gi|3157928|gb|AAC17611.1|(AC002131) Similar to fumary... +2    96  0.0041    1
gi|8569274|pdb|1QCO|AChain A, Crystal Structure Of Fu... +2    81  0.17      1
gi|6753814ref|NP_034306.1| fumarylacetoacetate hydrol... +2    80  0.20      1
gi|8393349ref|NP_058877.1| fumarylacetoacetate hydrol... +2    80  0.20      1
gi|544273|sp|P35505|FAAA_MOUSEFUMARYLACETOACETASE (FU... +2    80  0.20      1
gi|253320|gb|AAB22822.1|fumarylacetoacetate hydrolase... +2    80  0.20      1
gi|8569272|pdb|1QCN|AChain A, Crystal Structure Of Fu... +2    80  0.21      1
gi|12313291|emb|CAC24418.1|(AL512978) Hypothetical [S... +1    80  0.26      1
gi|31291|emb|CAA36016.1|(X51728) fumarylacetoacetase ... +2    77  0.31      1
gi|4557587ref|NP_000128.1| fumarylacetoacetase [Homo ... +2    77  0.38      1
gi|12739036ref|XP_007704.2| fumarylacetoacetase [Homo... +2    77  0.40      1
gi|110562|pir||S25462Ig kappa chain V region - mouse ... +1    62  0.98      1
gi|197274|gb|AAA38993.1|(M31268) IgK chain [Mus muscu... +1    64  0.9995    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.



to_Entrezto_Relatedto_Related >gi|3157928|gb|AAC17611.1|  (AC002131) Similar to fumarylacetoacetate hydrolase,
            gb|L41670 from Emericella nidulans. [Arabidopsis thaliana]
            Length = 408

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

  Plus Strand HSPs:

 Score = 96 (33.8 bits), Expect = 0.0041, P = 0.0041
 Identities = 16/21 (76%), Positives = 20/21 (95%), Frame = +2

Query:    11 KGNGYSVGFGTCSGKIVPAAP 73
             KG+GY+VGFGTC+GKIVP+ P
Sbjct:   388 KGDGYNVGFGTCTGKIVPSPP 408


to_Entrezto_Related >gi|8569274|pdb|1QCO|A  Chain A, Crystal Structure Of Fumarylacetoacetate
            Hydrolase Complexed With Fumarate And Acetoacetate
            >gi|8569275|pdb|1QCO|B Chain B, Crystal Structure Of
            Fumarylacetoacetate Hydrolase Complexed With Fumarate And
            Acetoacetate
            Length = 423

Frame  2 hits (HSPs):                                                 ____
                        __________________________________________________
Database sequence:     |                 |                 |              | 423
                       0               150               300

  Plus Strand HSPs:

 Score = 81 (28.5 bits), Expect = 0.18, P = 0.17
 Identities = 15/27 (55%), Positives = 21/27 (77%), Frame = +2

Query:     2 GRGKGNGYSVGFGTCSGKIVPA-AP*G 79
             G  +G+GY VGFG C+GK++PA +P G
Sbjct:   396 GHCQGDGYRVGFGQCAGKVLPALSPAG 422


to_Entrezto_Related >gi|6753814  ref|NP_034306.1| fumarylacetoacetate hydrolase [Mus musculus]
            >gi|1083328|pir||A56825 fumarylacetoacetase (EC 3.7.1.2) - mouse
            >gi|50973|emb|CAA77819.1| (Z11774) fumarylacetoacetase [Mus
            musculus]
            Length = 419

Frame  2 hits (HSPs):                                                 ____
                        __________________________________________________
Database sequence:     |                 |                 |              | 419
                       0               150               300

  Plus Strand HSPs:

 Score = 80 (28.2 bits), Expect = 0.23, P = 0.20
 Identities = 13/22 (59%), Positives = 18/22 (81%), Frame = +2

Query:     2 GRGKGNGYSVGFGTCSGKIVPA 67
             G  +G+GY VGFG C+GK++PA
Sbjct:   394 GHCQGDGYRVGFGQCAGKVLPA 415


to_Entrezto_Related >gi|8393349  ref|NP_058877.1| fumarylacetoacetate hydrolase [Rattus norvegicus]
            >gi|119779|sp|P25093|FAAA_RAT FUMARYLACETOACETASE
            (FUMARYLACETOACETATE HYDROLASE) (BETA-DIKETONASE) (FAA)
            >gi|92242|pir||JH0467 fumarylacetoacetase (EC 3.7.1.2) - rat
            >gi|204090|gb|AAA41142.1| (M77694) fumarylacetoacetate hydrolase
            [Rattus norvegicus]
            Length = 419

Frame  2 hits (HSPs):                                                 ____
                        __________________________________________________
Database sequence:     |                 |                 |              | 419
                       0               150               300

  Plus Strand HSPs:

 Score = 80 (28.2 bits), Expect = 0.23, P = 0.20
 Identities = 13/22 (59%), Positives = 18/22 (81%), Frame = +2

Query:     2 GRGKGNGYSVGFGTCSGKIVPA 67
             G  +G+GY VGFG C+GK++PA
Sbjct:   394 GHCQGDGYRVGFGQCAGKVLPA 415


to_Entrezto_Relatedto_Relatedto_ec >gi|544273|sp|P35505|FAAA_MOUSE  FUMARYLACETOACETASE (FUMARYLACETOACETATE
            HYDROLASE) (BETA-DIKETONASE) (FAA) >gi|284750|pir||A40219
            fumarylacetoacetate hydrolase - mouse >gi|8569283|pdb|1QQJ|A Chain
            A, Crystal Structure Of Mouse Fumarylacetoacetate Hydrolase Refined
            At 1.55 Angstrom Resolution >gi|8569284|pdb|1QQJ|B Chain B, Crystal
            Structure Of Mouse Fumarylacetoacetate Hydrolase Refined At 1.55
            Angstrom Resolution >gi|193222|gb|AAA37591.1| (M84145)
            fumarylacetoacetate hydrolase [Mus musculus]
            Length = 419

Frame  2 hits (HSPs):                                                 ____
Annotated Domains:      __________________________________________________
                        __________________________________________________
Database sequence:     |                 |                 |              | 419
                       0               150               300
__________________

Annotated Domains:
   PFAM                 FAA_hydrolase: Fumarylacetoacetate (FAA) 145..359
   PRODOM               PD009659: FAAA(3) Q94272(1) O65374(1)    1..162
   PRODOM               PD002459: FAAA(3) HPCE(2) Q46978(2)      164..263
   PRODOM               PD009658: FAAA(3) Q94272(1) O65374(1)    266..414
   PROSITE              BZIP_BASIC: bZIP transcription factors b 82..97
__________________


  Plus Strand HSPs:

 Score = 80 (28.2 bits), Expect = 0.23, P = 0.20
 Identities = 13/22 (59%), Positives = 18/22 (81%), Frame = +2

Query:     2 GRGKGNGYSVGFGTCSGKIVPA 67
             G  +G+GY VGFG C+GK++PA
Sbjct:   394 GHCQGDGYRVGFGQCAGKVLPA 415


to_Entrezto_Related >gi|253320|gb|AAB22822.1|  fumarylacetoacetate hydrolase, FAH [mice, Peptide,
            419 aa]
            Length = 419

Frame  2 hits (HSPs):                                                 ____
Annotated Domains:               ___                                      
                        __________________________________________________
Database sequence:     |                 |                 |              | 419
                       0               150               300
__________________

Annotated Domains:
   PROSITE              BZIP_BASIC: bZIP transcription factors b 82..97
__________________


  Plus Strand HSPs:

 Score = 80 (28.2 bits), Expect = 0.23, P = 0.20
 Identities = 13/22 (59%), Positives = 18/22 (81%), Frame = +2

Query:     2 GRGKGNGYSVGFGTCSGKIVPA 67
             G  +G+GY VGFG C+GK++PA
Sbjct:   394 GHCQGDGYRVGFGQCAGKVLPA 415


to_Entrezto_Related >gi|8569272|pdb|1QCN|A  Chain A, Crystal Structure Of Fumarylacetoacetate
            Hydrolase >gi|8569273|pdb|1QCN|B Chain B, Crystal Structure Of
            Fumarylacetoacetate Hydrolase
            Length = 421

Frame  2 hits (HSPs):                                                 ____
                        __________________________________________________
Database sequence:     |                 |                 |              | 421
                       0               150               300

  Plus Strand HSPs:

 Score = 80 (28.2 bits), Expect = 0.23, P = 0.21
 Identities = 13/22 (59%), Positives = 18/22 (81%), Frame = +2

Query:     2 GRGKGNGYSVGFGTCSGKIVPA 67
             G  +G+GY VGFG C+GK++PA
Sbjct:   396 GHCQGDGYRVGFGQCAGKVLPA 417


to_Entrezto_Relatedto_Related >gi|12313291|emb|CAC24418.1|  (AL512978) Hypothetical [Sulfolobus solfataricus]
            Length = 512

Frame  1 hits (HSPs):                                 ______              
                        __________________________________________________
Database sequence:     |              |              |             |      | 512
                       0            150            300           450

  Plus Strand HSPs:

 Score = 80 (28.2 bits), Expect = 0.30, P = 0.26
 Identities = 20/63 (31%), Positives = 31/63 (49%), Frame = +1

Query:    25 LCWVWYLLRQDCTRSSMRLVSFHSLFQLWWEELYNQEPACLIYSAHNMTLIKLVFYEYYT 204
             LC + Y    + T S+    +  S  QLW + L N  P  + YS ++ +     +YEYY 
Sbjct:   313 LCMIVYTY--NLTNSNSGFYTVGSYSQLWIKPLDNNSPVYITYSGYSYS-----YYEYYN 365

Query:   205 FSF 213
             F+F
Sbjct:   366 FTF 368


to_Entrezto_Relatedto_Related >gi|31291|emb|CAA36016.1|  (X51728) fumarylacetoacetase (AA 1-349) [Homo
            sapiens]
            Length = 349

Frame  2 hits (HSPs):                                                 ____
                        __________________________________________________
Database sequence:     |                     |                    |       | 349
                       0                   150                  300

  Plus Strand HSPs:

 Score = 77 (27.1 bits), Expect = 0.37, P = 0.31
 Identities = 12/22 (54%), Positives = 18/22 (81%), Frame = +2

Query:     2 GRGKGNGYSVGFGTCSGKIVPA 67
             G  +G+GY +GFG C+GK++PA
Sbjct:   324 GYCQGDGYRIGFGQCAGKVLPA 345


to_Entrezto_Related >gi|4557587  ref|NP_000128.1| fumarylacetoacetase [Homo sapiens]
            >gi|119778|sp|P16930|FAAA_HUMAN FUMARYLACETOACETASE
            (FUMARYLACETOACETATE HYDROLASE) (BETA-DIKETONASE) (FAA)
            >gi|106043|pir||A37926 fumarylacetoacetase (EC 3.7.1.2) - human
            >gi|182393|gb|AAA52422.1| (M55150) fumarylacetoacetate hydrolase
            [Homo sapiens]
            Length = 419

Frame  2 hits (HSPs):                                                 ____
                        __________________________________________________
Database sequence:     |                 |                 |              | 419
                       0               150               300

  Plus Strand HSPs:

 Score = 77 (27.1 bits), Expect = 0.48, P = 0.38
 Identities = 12/22 (54%), Positives = 18/22 (81%), Frame = +2

Query:     2 GRGKGNGYSVGFGTCSGKIVPA 67
             G  +G+GY +GFG C+GK++PA
Sbjct:   394 GYCQGDGYRIGFGQCAGKVLPA 415


to_Entrezto_Related >gi|12739036  ref|XP_007704.2| fumarylacetoacetase [Homo sapiens]
            Length = 437

Frame  2 hits (HSPs):                                                  ___
                        __________________________________________________
Database sequence:     |                 |                |               | 437
                       0               150              300

  Plus Strand HSPs:

 Score = 77 (27.1 bits), Expect = 0.51, P = 0.40
 Identities = 12/22 (54%), Positives = 18/22 (81%), Frame = +2

Query:     2 GRGKGNGYSVGFGTCSGKIVPA 67
             G  +G+GY +GFG C+GK++PA
Sbjct:   412 GYCQGDGYRIGFGQCAGKVLPA 433


to_Entrezto_Relatedto_Related >gi|110562|pir||S25462  Ig kappa chain V region - mouse
            >gi|938263|emb|CAA47881.1| (X67623) IgG light chain V region [Mus
            musculus]
            Length = 91

Frame  1 hits (HSPs):          _________________________                  
                        __________________________________________________
Database sequence:     |          |          |          |          |      | 91
                       0         20         40         60         80

  Plus Strand HSPs:

 Score = 62 (21.8 bits), Expect = 3.9, P = 0.98
 Identities = 16/44 (36%), Positives = 24/44 (54%), Frame = +1

Query:    46 LRQDCT---RSSMRLVSFHSLFQLWWEELYNQEPACLIYSAHNM 168
             LRQ  T   R+S  + S+ + F  W+++   Q P  LIY A N+
Sbjct:    15 LRQRATISCRASESVDSYGNSFMHWYQQKPGQPPKLLIYHASNL 58


to_Entrezto_Relatedto_Related >gi|197274|gb|AAA38993.1|  (M31268) IgK chain [Mus musculus]
            Length = 110

Frame  1 hits (HSPs):         ____________________                        
                        __________________________________________________
Database sequence:     |        |        |        |        |         |    | 110
                       0       20       40       60       80       100

  Plus Strand HSPs:

 Score = 64 (22.5 bits), Expect = 7.6, P = 1.0
 Identities = 16/44 (36%), Positives = 24/44 (54%), Frame = +1

Query:    46 LRQDCT---RSSMRLVSFHSLFQLWWEELYNQEPACLIYSAHNM 168
             LRQ  T   R+S  + S+ + F  W+++   Q P  LIY A N+
Sbjct:    15 LRQRATISCRASESVDSYGNSFMYWYQQKPGQPPKLLIYRASNL 58


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    0.347   0.156   0.525  
               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   0.168   0.633  
               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    0.340   0.149   0.554  
               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    0.329   0.140   0.462  
               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    0.357   0.165   0.544  
               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   0.156   0.597  
               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      104        94       10.  65 3  12 22  0.098   32
                                                    28  0.12    33
   +2      0      105        94       10.  65 3  12 22  0.098   32
                                                    28  0.12    33
   +1      0      105        96       10.  66 3  12 22  0.10    32
                                                    28  0.095   34
   -1      0      105        94       10.  65 3  12 22  0.098   32
                                                    28  0.12    33
   -2      0      105        94       10.  65 3  12 22  0.098   32
                                                    28  0.12    33
   -3      0      104        95       10.  66 3  12 22  0.099   32
                                                    28  0.12    33


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:  13
  No. of states in DFA:  591 (58 KB)
  Total size of DFA:  150 KB (192 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:  105.53u 0.92s 106.45t  Elapsed: 00:00:48
  Total cpu time:  105.55u 0.95s 106.50t  Elapsed: 00:00:48
  Start:  Wed Jan 23 19:46:44 2002   End:  Wed Jan 23 19:47:32 2002



Annotated Domains Database:   March 14, 2000 

Release Date:  March 14, 2000