GapMind for Amino acid biosynthesis

 

Alignments for a candidate for gatB in Pseudomonas simiae WCS417

Align Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B; Asp/Glu-ADT subunit B; EC 6.3.5.- (characterized)
to candidate GFF834 PS417_04235 glutamyl-tRNA amidotransferase

Query= SwissProt::Q9RF06
         (475 letters)



>FitnessBrowser__WCS417:GFF834
          Length = 481

 Score =  457 bits (1175), Expect = e-133
 Identities = 225/481 (46%), Positives = 331/481 (68%), Gaps = 9/481 (1%)

Query: 1   MHFETVIGLEVHVELKTDSKMFSPSPAHFGAEPNSNTNVIDLAYPGVLPVVNKRAVDWAM 60
           M +E VIGLE+H +L T SK+FS S   FG+EPN+  +++DL  PGVLPV+N+ AV  A+
Sbjct: 1   MQWEVVIGLEIHTQLATQSKIFSGSATTFGSEPNTQASLVDLGMPGVLPVLNQEAVRMAV 60

Query: 61  RAAMALNMEIATESKFDRKNYFYPDNPKAYQISQFDQPIGENGYIDIEV-DGETKRIGIT 119
              +A++ EI   + F RKNYFYPD PK YQISQ + PI   G++DI + DG  KR+G+T
Sbjct: 61  MFGLAIDAEIGQHNVFARKNYFYPDLPKGYQISQMELPIVGKGHLDIPLEDGTIKRVGVT 120

Query: 120 RLHMEEDAGKSTHKGEY---SLVDLNRQGTPLIEIVSEPDIRSPKEAYAYLEKLRSIIQY 176
           R H+EEDAGKS H+ E+   + +DLNR GTPL+EIVSEPD+RS KEA AY++ + ++++Y
Sbjct: 121 RAHLEEDAGKSLHE-EFPGATGIDLNRAGTPLLEIVSEPDMRSAKEAVAYVKTIHALVRY 179

Query: 177 TGVSDVKMEEGSLRCDANISLRPYGQEKFGTKAELKNLNSFNYVRKGLEYEEKRQEEELL 236
            G+ D  M EGSLRCD N+S+RP GQ +FGT+ E+KN+NSF ++ K +  E +RQ E + 
Sbjct: 180 LGICDGNMAEGSLRCDCNVSIRPKGQVEFGTRCEIKNVNSFRFIEKAINSEVRRQIELIE 239

Query: 237 SGGEIGQETRRFDESTGKTILMRVKEGSDDYRYFPEPDIVPLYIDDAWKERVRQTIPELP 296
            GG++ Q+TR +D +  +T  MR KE ++DYRYFP+PD++P+ ++D++   +R T+PELP
Sbjct: 240 DGGKVIQQTRLYDPNKDETRAMRSKEEANDYRYFPDPDLLPVVLEDSFLNDIRATLPELP 299

Query: 297 DERKAKYVNELGLPAYDAHVLTLTKEMSDFFESTIEHGADVKLTSNWLMGGVNEYLNKNQ 356
            +++ ++  + GL  YDA VL  ++E +++FE  +    D KL +NW+M  +   LNK  
Sbjct: 300 QQKRERFQAQFGLSVYDASVLASSREQANYFEKVVSIAGDAKLAANWVMVELGSLLNKQG 359

Query: 357 VELLDTKLTPENLAGMIKLIEDGTMSSKIAKKVFPELAAKGGNAKQIMEDNGLVQISDEA 416
           +E+ +  ++ E L GM+  I+D T+S KIAK VF  +A+  G+A +I+E  GL Q++D  
Sbjct: 360 LEIDEAPVSAEQLGGMLLRIKDNTISGKIAKTVFEAMASGEGSADEIIEKRGLKQVTDSG 419

Query: 417 TLLKFVNEALDNNEQSVEDYKNG----KGKAMGFLVGQIMKASKGQANPQLVNQLLKQEL 472
            +   ++E L  N + VE Y+      +GK  GF VGQ MKASKG+ANPQ VN+LLK +L
Sbjct: 420 AISAVLDEMLAANAEQVEQYRAADEAKRGKMFGFFVGQAMKASKGKANPQQVNELLKSKL 479

Query: 473 D 473
           +
Sbjct: 480 E 480


Lambda     K      H
   0.313    0.133    0.373 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 636
Number of extensions: 24
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 475
Length of database: 481
Length adjustment: 34
Effective length of query: 441
Effective length of database: 447
Effective search space:   197127
Effective search space used:   197127
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 51 (24.3 bits)

Align candidate GFF834 PS417_04235 (glutamyl-tRNA amidotransferase)
to HMM TIGR00133 (gatB: aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, B subunit (EC 6.3.5.-))

Software error:

../bin/blast/fastacmd -i /tmp/list.5162.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.5162.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

For help, please send mail to the webmaster (help@microbesonline.org), giving this error message and the time and date of the error.