GapMind for Amino acid biosynthesis

 

Alignments for a candidate for gatA in Synechococcus elongatus PCC 7942

Align glutamyl-tRNAGln amidotransferase subunit A (EC 6.3.5.7) (characterized)
to candidate Synpcc7942_2117 Synpcc7942_2117 aspartyl/glutamyl-tRNA amidotransferase subunit A

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



>FitnessBrowser__SynE:Synpcc7942_2117
          Length = 479

 Score =  550 bits (1417), Expect = e-161
 Identities = 278/479 (58%), Positives = 361/479 (75%), Gaps = 4/479 (0%)

Query: 8   ITELKQLIHKKEIKISDLVDESYKRIQAVDDKVQAFLALDEERARAYAKELDEAVDGRSE 67
           I EL   + +KE    ++ + + +RI+ ++ ++++FL +  ++A A AK +D+ +    E
Sbjct: 4   IRELHSQLVRKERSAVEIAEAALQRIETLEPQLKSFLHVTADQAIAQAKAVDQRIAAGEE 63

Query: 68  HGLLFGMPIGVKDNIVTKGLRTTCSSKILENFDPIYDATVVQRLQDAEAVTIGKLNMDEF 127
             LL G+PIG+KDN+ T+G+ TTC+SKIL+ F P Y++TV QRL +A AV +GK N+DEF
Sbjct: 64  ISLLAGIPIGIKDNLCTRGIPTTCASKILQGFVPPYESTVTQRLAEAGAVAVGKTNLDEF 123

Query: 128 AMGSSTENSAYKLTKNPWNLDTVPGGSSGGSAAAVAAGEVPFSLGSDTGGSIRQPASFCG 187
           AMGSSTENSAY+ T NPW+L  VPGGSSGGSAAAVAA E   +LGSDTGGSIRQPA+FCG
Sbjct: 124 AMGSSTENSAYQTTANPWDLTRVPGGSSGGSAAAVAADECVVALGSDTGGSIRQPAAFCG 183

Query: 188 VVGLKPTYGRVSRYGLVAFASSLDQIGPITRTVEDNAFLLQAISGVDKMDSTSANVDVPD 247
           VVGLKPTYG VSRYGLVA+ASSLDQIGP +R+VED A LL AI+G D  D+TS  V+VPD
Sbjct: 184 VVGLKPTYGLVSRYGLVAYASSLDQIGPFSRSVEDTAILLGAIAGHDPKDATSLKVEVPD 243

Query: 248 FLSSLTGDIKGLKIAVPKEYLGEGVGKEARESVLAALKVLEGLGATWEEVSLPHSKYALA 307
           +   L   + G+K+ V  E + +     A +++ AAL+VL+GLGA   E+S P   Y L 
Sbjct: 244 YTQFLKPSLAGIKVGVITETVTD---SPAGQAMQAALEVLQGLGAEIREISCPRFAYGLP 300

Query: 308 TYYLLSSSEASANLARFDGIRYGYRTDNADNLIDLYKQTRAEGFGNEVKRRIMLGTFALS 367
            YY+++ SEASANLAR+DG++YGYR + A+ LID+Y +TRAEGFG+EVKRRIM+GT+ALS
Sbjct: 301 AYYIIAPSEASANLARYDGVKYGYRVEEAETLIDMYCRTRAEGFGSEVKRRIMIGTYALS 360

Query: 368 SGYYDAYYKKAQKVRTLIKKDFEDVFEKYDVIVGPTTPTPAFKIGENTKDPLTMYANDIL 427
           +GYYDAYY KAQKVRTLIK+DFE  F + DV+V PTTPT AFK GE T DPL+MY +D++
Sbjct: 361 AGYYDAYYLKAQKVRTLIKQDFEAAFAEVDVLVSPTTPTTAFKAGEKTADPLSMYLSDLM 420

Query: 428 TIPVNLAGVPGISVPCGLAD-GLPLGLQIIGKHFDESTVYRVAHAFEQATDHHKAKPEL 485
           TIPVNLAG+PG+S+PCG  + GLP GLQIIG    E  V   A+A+EQAT+ H  +P L
Sbjct: 421 TIPVNLAGLPGLSLPCGFDEAGLPYGLQIIGNVLREDQVLHTAYAYEQATEWHLRQPAL 479


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: 616
Number of extensions: 17
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: 479
Length adjustment: 34
Effective length of query: 451
Effective length of database: 445
Effective search space:   200695
Effective search space used:   200695
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 Synpcc7942_2117 Synpcc7942_2117 (aspartyl/glutamyl-tRNA 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.1533.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.1533.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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