GapMind for Amino acid biosynthesis

 

Alignments for a candidate for gatA in Desulfovibrio vulgaris Hildenborough

Align glutamyl-tRNAGln amidotransferase subunit A (EC 6.3.5.7) (characterized)
to candidate 206234 DVU0808 glutamyl-tRNA(Gln) amidotransferase, A subunit

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



>MicrobesOnline__882:206234
          Length = 489

 Score =  483 bits (1243), Expect = e-141
 Identities = 247/472 (52%), Positives = 335/472 (70%), Gaps = 6/472 (1%)

Query: 8   ITELKQLIHKKEIKISDLVDESYKRIQAVDDKVQAFLALDEERARAYAKELDEAVDGRSE 67
           +  ++  + ++E++  D V +   RI+  + ++ A L L  E A   A+ LD A  G   
Sbjct: 9   LAAIRDALARREVRAEDAVLDCLARIETTEPRIDALLHLRAEAAIEEARALDAA--GPDA 66

Query: 68  HGLLFGMPIGVKDNIVTKGLRTTCSSKILENFDPIYDATVVQRLQDAEAVTIGKLNMDEF 127
              L+G+P+ VKD + T G  TT  S+ILE+F P YDA  VQRL++A A+ +GK NMDEF
Sbjct: 67  SRPLWGVPVTVKDALTTAGTPTTAGSRILEDFVPFYDAFAVQRLREAGAIILGKNNMDEF 126

Query: 128 AMGSSTENSAYKLTKNPWNLDTVPGGSSGGSAAAVAAGEVPFSLGSDTGGSIRQPASFCG 187
           AMGSSTENSAYK T+NPW+   VPGGSSGGSAA+VAAG+   SLG+DTGGSIRQPAS CG
Sbjct: 127 AMGSSTENSAYKPTRNPWDTARVPGGSSGGSAASVAAGQCFASLGTDTGGSIRQPASLCG 186

Query: 188 VVGLKPTYGRVSRYGLVAFASSLDQIGPITRTVEDNAFLLQAISGVDKMDSTSANVDVPD 247
            VGLKPTYGRVSRYGL+A+ SSLDQIGP+TRTVED A ++  I+G DK DST A+  V D
Sbjct: 187 CVGLKPTYGRVSRYGLIAYGSSLDQIGPMTRTVEDAAIVMGVIAGHDKRDSTCADRPVED 246

Query: 248 FLSSLTG--DIKGLKIAVPKEYLGEGVGKEARESVLAALKVLEGLGATWEEVSLPHSKYA 305
           F ++L    D+ G++I VP E+ GEG+  E   S  AAL     LGAT  +V+LPH+  +
Sbjct: 247 FAAALASRHDLAGVRIGVPAEFWGEGLSPEVATSCRAALDAARDLGATIVDVALPHTPQS 306

Query: 306 LATYYLLSSSEASANLARFDGIRYGYRTDNADNLIDLYKQTRAEGFGNEVKRRIMLGTFA 365
           +A YY+++S+EAS+NLAR+DG+RYG R    ++L+DLY ++R+EG G+EV+RRIMLGT+ 
Sbjct: 307 IAAYYIVASAEASSNLARYDGVRYGKRAHAPEDLMDLYVRSRSEGLGDEVQRRIMLGTYV 366

Query: 366 LSSGYYDAYYKKAQKVRTLIKKDFEDVFEKYDVIVGPTTPTPAFKIGENTKDPLTMYAND 425
           LSSGYYDAYY+KA +VR  I +D+ + F   DVI GP +P  A+ +G  T DPL MY  D
Sbjct: 367 LSSGYYDAYYRKAAQVRRRILEDYRNAFATCDVICGPVSPVTAWPLGALTADPLQMYLMD 426

Query: 426 ILTIPVNLAGVPGISVPCGLA--DGLPLGLQIIGKHFDESTVYRVAHAFEQA 475
           + T+ +NLAG+PG+S+P GL    G+P+G+Q++G+ FDE+T+  V +   +A
Sbjct: 427 VFTLSLNLAGLPGLSLPVGLGTESGMPVGIQLLGRSFDEATLLSVGNVLSRA 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: 614
Number of extensions: 35
Number of successful extensions: 3
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 206234 DVU0808 (glutamyl-tRNA(Gln) amidotransferase, A subunit)
to HMM TIGR00132 (gatA: aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, A subunit (EC 6.3.5.-))

Software error:

../bin/blast/fastacmd -i /tmp/list.1867.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.1867.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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