GapMind for Amino acid biosynthesis

 

Alignments for a candidate for gatA in Acidovorax sp. GW101-3H11

Align glutamyl-tRNAGln amidotransferase subunit A (EC 6.3.5.7) (characterized)
to candidate Ac3H11_3338 Aspartyl-tRNA(Asn) amidotransferase subunit A (EC 6.3.5.6) @ Glutamyl-tRNA(Gln) amidotransferase subunit A (EC 6.3.5.7)

Query= metacyc::MONOMER-13955
         (485 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_3338
          Length = 497

 Score =  459 bits (1182), Expect = e-134
 Identities = 237/493 (48%), Positives = 329/493 (66%), Gaps = 12/493 (2%)

Query: 2   SLFDHKITELKQLIHKKEIKISDLVDESYKRIQAVDDKVQAFLALDEERARAYAKELDEA 61
           +L D  + +L   + ++ +   +       R QA    + A++A++ E   A A+  D A
Sbjct: 5   ALHDLGVAQLATELRERRVSAVEAAQHFLDRAQA-HQNLGAYVAVNPEITLAQARAQDAA 63

Query: 62  VDGRSEHGLLFGMPIGVKDNIVTKGLRTTCSSKILENFDPIYDATVVQRLQDAEAVTIGK 121
           +   +  G L G+PI  KD  VTKG  +T  SK+L  +   +DATVV +L DA AVT+GK
Sbjct: 64  IAAGTA-GPLAGVPIAHKDIFVTKGFPSTAGSKMLAGYQSPFDATVVTKLADAGAVTLGK 122

Query: 122 LNMDEFAMGSSTENSAYKLT--------KNPWNLDTVPGGSSGGSAAAVAAGEVPFSLGS 173
           LN DEFAMGS+ ENSA            +NPW  D +PGGSSGGSA AVAA   P   G+
Sbjct: 123 LNCDEFAMGSANENSAVAPVGTDAPAPVRNPWATDRIPGGSSGGSAVAVAARLAPAVTGT 182

Query: 174 DTGGSIRQPASFCGVVGLKPTYGRVSRYGLVAFASSLDQIGPITRTVEDNAFLLQAISGV 233
           DTGGSIRQPASFCG+ G+KPTYGR SRYG++AFASSLDQ GP+ R+ ED A LL A+ G 
Sbjct: 183 DTGGSIRQPASFCGITGIKPTYGRASRYGMIAFASSLDQAGPMARSAEDCALLLSAMCGP 242

Query: 234 DK-MDSTSANVDVPDFLSSLTGDIKGLKIAVPKEYLGEGVGKEARESVLAALKVLEGLGA 292
           D   DSTS +V   +F + L   I+GL+I +P E+ GEG+  + R +V  ALK  E LGA
Sbjct: 243 DPDRDSTSLDVPAENFSAKLNDSIEGLRIGIPAEFFGEGLAPDVRAAVDGALKEYEKLGA 302

Query: 293 TWEEVSLPHSKYALATYYLLSSSEASANLARFDGIRYGYRTDNADNLIDLYKQTRAEGFG 352
               +SLP ++ ++  YY+++ +EAS+NL+RFDG+++G+R  +  +L+D+YK+TRAEGFG
Sbjct: 303 KLVPISLPRTQLSIPVYYIIAPAEASSNLSRFDGVKFGHRAKDYSDLVDMYKKTRAEGFG 362

Query: 353 NEVKRRIMLGTFALSSGYYDAYYKKAQKVRTLIKKDFEDVFEKYDVIVGPTTPTPAFKIG 412
           +EVKRRIM+G + LS GYYDAYY +AQK+R +I  DF++ F+  D+I GP  PT A+K+G
Sbjct: 363 DEVKRRIMIGAYVLSHGYYDAYYLQAQKIRRMIADDFQNAFKSCDLIAGPVAPTVAWKLG 422

Query: 413 ENTKDPLTMYANDILTIPVNLAGVPGISVPCGLAD-GLPLGLQIIGKHFDESTVYRVAHA 471
           ++  DPL  Y  DI T+P +LAG+PG+SVP G  + G+P+GLQ++G +F E+ +   AH 
Sbjct: 423 DHGNDPLADYLADIFTLPGSLAGLPGMSVPAGFGEGGMPVGLQLLGNYFQEARLLNAAHR 482

Query: 472 FEQATDHHKAKPE 484
            +QATD H  +PE
Sbjct: 483 LQQATDFHLRRPE 495


Lambda     K      H
   0.315    0.134    0.381 

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: 632
Number of extensions: 26
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: 485
Length of database: 497
Length adjustment: 34
Effective length of query: 451
Effective length of database: 463
Effective search space:   208813
Effective search space used:   208813
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 52 (24.6 bits)

Align candidate Ac3H11_3338 (Aspartyl-tRNA(Asn) amidotransferase subunit A (EC 6.3.5.6) @ Glutamyl-tRNA(Gln) amidotransferase subunit A (EC 6.3.5.7))
to HMM TIGR00132 (gatA: aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, A subunit (EC 6.3.5.-))

Software error:

../bin/blast/fastacmd -i /tmp/list.27299.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.27299.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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