GapMind for Amino acid biosynthesis

 

Alignments for a candidate for gatA in Paraburkholderia bryophila 376MFSha3.1

Align glutamyl-tRNAGln amidotransferase subunit A (EC 6.3.5.7) (characterized)
to candidate H281DRAFT_02221 H281DRAFT_02221 aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit A

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



>FitnessBrowser__Burk376:H281DRAFT_02221
          Length = 495

 Score =  468 bits (1205), Expect = e-136
 Identities = 247/494 (50%), Positives = 335/494 (67%), Gaps = 15/494 (3%)

Query: 3   LFDHKITELKQLIHKKEIKISDLVDESYKRIQAVDDKVQAFLALDEERARAYAKELDEAV 62
           + +  +TEL+  +  KE    +L     KRI A +  + AF+ +D +   A AK  D  +
Sbjct: 1   MHEKSLTELRAALAAKECSAVELAQLYLKRIDAANS-LNAFIQVDADLTLAQAKAADALL 59

Query: 63  DGRSEHGLLFGMPIGVKDNIVTKGLRTTCSSKILENFDPIYDATVVQRLQDAEAVTIGKL 122
                 G L G+PI  KD  VTKG R+T  SK+L N++  +DATVV+RLQ A  V +GK 
Sbjct: 60  HA-GHGGPLTGLPIAHKDVFVTKGWRSTAGSKMLSNYESPFDATVVERLQKAGMVCVGKT 118

Query: 123 NMDEFAMGSSTENSAYKLTKNPWNLDTVPGGSSGGSAAAVAAGEVPFSLGSDTGGSIRQP 182
           NMDEFAMGSS ENS +   +NPW+   VPGGSSGGSAAAVAA   P + G+DTGGSIRQP
Sbjct: 119 NMDEFAMGSSNENSYFGPVQNPWDRQAVPGGSSGGSAAAVAARLAPAATGTDTGGSIRQP 178

Query: 183 ASFCGVVGLKPTYGRVSRYGLVAFASSLDQIGPITRTVEDNAFLLQAISGVDKMDSTSAN 242
           ASF G+ G+KPTYGRVSRYG++AFASSLDQ GP+ ++  D A LL A++G D+ DSTS  
Sbjct: 179 ASFSGITGIKPTYGRVSRYGMIAFASSLDQGGPMAQSAADCATLLNAMAGFDERDSTSLV 238

Query: 243 VDVPDFLSSLTGDIK---------GLKIAVPKEYLGEGVGKEARESVLAALKVLEGLGAT 293
            D  D+   L    K         GL+I +PKEY G G+  + R S+ AALK  E LGAT
Sbjct: 239 RDDEDYTRYLGQPWKQDGAGKPLAGLRIGLPKEYFGAGLADDVRASIDAALKEYEALGAT 298

Query: 294 WEEVSLPHSKYALATYYLLSSSEASANLARFDGIRYGYRTDNADNLIDLYKQTRAEGFGN 353
             EVSLP ++ ++  YY+++ +EAS+NL+RFDG+R+G+R     +L+D+YK++RAEGFG 
Sbjct: 299 LVEVSLPKTELSIPVYYVIAPAEASSNLSRFDGVRFGHRAAEYRDLLDMYKKSRAEGFGP 358

Query: 354 EVKRRIMLGTFALSSGYYDAYYKKAQKVRTLIKKDFEDVFEKYDVIVGPTTPTPAFKIGE 413
           EVKRRIM+G + LS GYYDAYY +AQK+R +I +DF++ F++ DVI+GP  P+ A+ +G 
Sbjct: 359 EVKRRIMVGAYVLSHGYYDAYYLQAQKIRRIIAQDFQEAFKQCDVIMGPVAPSVAWDLGA 418

Query: 414 NTKDPLTMYANDILTIPVNLAGVPGISVPCGLADGL----PLGLQIIGKHFDESTVYRVA 469
              DP+ MY  D+ T+ V+LAG+PG+SVPCG   G     P+GLQIIG +F+E+ + +VA
Sbjct: 419 KGDDPVQMYLADVYTLSVSLAGLPGMSVPCGFGAGANAQRPVGLQIIGNYFNEARMLQVA 478

Query: 470 HAFEQATDHHKAKP 483
            AF++ATD H+  P
Sbjct: 479 DAFQRATDWHRKAP 492


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: 587
Number of extensions: 23
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: 495
Length adjustment: 34
Effective length of query: 451
Effective length of database: 461
Effective search space:   207911
Effective search space used:   207911
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 H281DRAFT_02221 H281DRAFT_02221 (aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit A)
to HMM TIGR00132 (gatA: aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, A subunit (EC 6.3.5.-))

Software error:

../bin/blast/fastacmd -i /tmp/list.3407.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.3407.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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