GapMind for Amino acid biosynthesis

 

Alignments for a candidate for gatA in Caulobacter crescentus NA1000

Align glutamyl-tRNAGln amidotransferase subunit A (EC 6.3.5.7) (characterized)
to candidate CCNA_02519 CCNA_02519 aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit A

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



>FitnessBrowser__Caulo:CCNA_02519
          Length = 489

 Score =  440 bits (1132), Expect = e-128
 Identities = 229/415 (55%), Positives = 295/415 (71%), Gaps = 7/415 (1%)

Query: 67  EHGLLFGMPIGVKDNIVTKGLRTTCSSKILENFDPIYDATVVQRLQDAEAVTIGKLNMDE 126
           E G L G P+GVKD   T G+RTT  SKILENF P Y++TV  +L    AV +GKLN+D+
Sbjct: 65  EAGPLEGAPLGVKDLFCTNGVRTTACSKILENFVPTYESTVTSQLWRDGAVMLGKLNLDQ 124

Query: 127 FAMGSSTENSAYKLTKNPWNLD-----TVPGGSSGGSAAAVAAGEVPFSLGSDTGGSIRQ 181
           FAMGSS E S +    NPW          PGGSSGGSAAAVAA     +  +DTGGSIRQ
Sbjct: 125 FAMGSSNETSYFGPVTNPWRAQGSTKALTPGGSSGGSAAAVAADLCLGATATDTGGSIRQ 184

Query: 182 PASFCGVVGLKPTYGRVSRYGLVAFASSLDQIGPITRTVEDNAFLLQAISGVDKMDSTSA 241
           PA+F G VG+KPTYGR SR+G+VAFASSLDQ GPI +TVED A LL ++SG D  DSTS 
Sbjct: 185 PAAFTGTVGIKPTYGRCSRWGVVAFASSLDQAGPIAKTVEDAALLLTSMSGHDPKDSTSL 244

Query: 242 NVDVPDFLSSLTGDIKGLKIAVPKEYLGEGVGKEARESVLAALKVLEGLGATWEEVSLPH 301
           ++ VPDF   +   +KGLKI +PKEY  + +  E  +     +  L+  G    ++SLPH
Sbjct: 245 DIPVPDFTQFVGKSVKGLKIGIPKEYRVDNMPAEIEKLWQDGIAWLKEAGCEIVDISLPH 304

Query: 302 SKYALATYYLLSSSEASANLARFDGIRYGYRTDNADNLIDLYKQTRAEGFGNEVKRRIML 361
           +KYAL  YY+++ +EAS+NLAR+DG+RYG R + A NL ++Y+ TRA GFG+EVKRRI++
Sbjct: 305 TKYALPAYYIVAPAEASSNLARYDGMRYGLREEGA-NLTEIYENTRASGFGDEVKRRILI 363

Query: 362 GTFALSSGYYDAYYKKAQKVRTLIKKDFEDVFEKYDVIVGPTTPTPAFKIGENTKDPLTM 421
           GT+ LS+GYYDAYY KA KVR  I +DF++ + + D I+ PT P+ AF +GEN+ DP+ M
Sbjct: 364 GTYVLSAGYYDAYYLKALKVRRRIAEDFDNAWTQCDAILTPTAPSAAFGLGENSNDPIAM 423

Query: 422 YANDILTIPVNLAGVPGISVPCGL-ADGLPLGLQIIGKHFDESTVYRVAHAFEQA 475
           Y ND+ T+  NLAG+PG+S+P GL A+GLPLGLQIIGK  DE+TV+ VA A E+A
Sbjct: 424 YLNDVFTVTTNLAGLPGLSLPAGLDANGLPLGLQIIGKPLDEATVFSVAGAVEKA 478


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: 610
Number of extensions: 25
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: 489
Length adjustment: 34
Effective length of query: 451
Effective length of database: 455
Effective search space:   205205
Effective search space used:   205205
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 CCNA_02519 CCNA_02519 (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.29453.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.29453.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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