GapMind for Amino acid biosynthesis

 

Alignments for a candidate for asp-kinase in Shewanella loihica PV-4

Align fused aspartate kinase/homoserine dehydrogenase 1 (EC 2.7.2.4; EC 1.1.1.3) (characterized)
to candidate 5208568 Shew_1079 bifunctional aspartokinase I/homeserine dehydrogenase I (RefSeq)

Query= ecocyc::ASPKINIHOMOSERDEHYDROGI-MONOMER
         (820 letters)



>FitnessBrowser__PV4:5208568
          Length = 822

 Score =  913 bits (2359), Expect = 0.0
 Identities = 469/818 (57%), Positives = 596/818 (72%), Gaps = 4/818 (0%)

Query: 1   MRVLKFGGTSVANAERFLRVADILESNARQGQVATVLSAPAKITNHLVAMIEKTISGQDA 60
           M+V+KFGGTS+AN +RF   A I+ ++A +   A VLSAPA +TN L+ M++  ++G D 
Sbjct: 1   MKVMKFGGTSLANWQRFNSAAQIVLASAAEQPTAVVLSAPATVTNGLLEMVDLAVAGDDF 60

Query: 61  LPNISDAERIFAELLTGLAAAQ--PGFPLAQLKTFVDQEFAQIKHVLHGISLLGQCPDSI 118
            P +S    +F + L G AA++   G     L+  +  +    +  L G+ LLG+CPD++
Sbjct: 61  FPVLSQVHEVF-KTLYGQAASEVLSGEQSDSLEAVLAAQLKHWQDKLQGVVLLGECPDAV 119

Query: 119 NAALICRGEKMSIAIMAGVLEARGHNVTVIDPVEKLLAVGHYLESTVDIAESTRRIAASR 178
            A ++  GE++S A+M  ++ A G +   + P +  +A G  LES VDIA S +R A   
Sbjct: 120 RAEIVVGGERLSAALMEQLMLAAGVSANQLVPQQLFVAHGPALESVVDIAASKQRFAELS 179

Query: 179 IPADHMVLMAGFTAGNEKGELVVLGRNGSDYSAAVLAACLRADCCEIWTDVDGVYTCDPR 238
           + A  + +M GFTAG++ G +V LGRNGSDYSAAVL+AC+ A CCEIWTDVDGVY  DPR
Sbjct: 180 LDAHQVWVMPGFTAGDKDGRVVTLGRNGSDYSAAVLSACIDASCCEIWTDVDGVYNTDPR 239

Query: 239 QVPDARLLKSMSYQEAMELSYFGAKVLHPRTITPIAQFQIPCLIKNTGNPQAPGTLIGAS 298
            V DA+LL  +SYQEAMELSYFGAKVLHP+TI PIAQ+ IPC I+N+ NPQAPGTL+   
Sbjct: 240 VVADAKLLTQLSYQEAMELSYFGAKVLHPKTIAPIAQYHIPCYIRNSFNPQAPGTLVSNQ 299

Query: 299 RDEDELPVKGISNLNNMAMFSVSGPGMKGMVGMAARVFAAMSRARISVVLITQSSSEYSI 358
            DE  L VK ISNL+   MF ++GPGMKGMVGMA+R   A+SR+ +SV LITQSSSEYSI
Sbjct: 300 VDETGLNVKAISNLDEQTMFDIAGPGMKGMVGMASRTLGAISRSGVSVSLITQSSSEYSI 359

Query: 359 SFCVPQSDCVRAERAMQEEFYLELKEGLLEPLAVTERLAIISVVGDGMRTLRGISAKFFA 418
           SFCV   D  R   A+++EF LELK  +LE +A+   LAI+S++GDGMRT +G++ KFF 
Sbjct: 360 SFCVATQDAERVRVALEQEFELELKSEILEQIAMRHNLAIVSLIGDGMRTHKGVAGKFFQ 419

Query: 419 ALARANINIVAIAQGSSERSISVVVNNDDATTGVRVTHQMLFNTDQVIEVFVIGVGGVGG 478
           ALA+AN+NIVAIAQGSSERSIS V+        +   HQ LF+    ++VF++G G VG 
Sbjct: 420 ALAQANVNIVAIAQGSSERSISAVIELRKTKHAIAACHQSLFDVQHYLDVFLVGCGNVGA 479

Query: 479 ALLEQLKRQQSWLKNKHIDLRVCGVANSKALLTNVHGLNLENWQEELAQAKEPFNLGRLI 538
            LLEQ+K+Q   LK +HI +RVCGVANS+ +L +  G++L +WQ  LA +++  +L +++
Sbjct: 480 GLLEQIKQQTEMLKAQHITVRVCGVANSRHMLLDAKGIDLNHWQGLLADSQQACDLDKML 539

Query: 539 RLVKEYHLLNPVIVDCTSSQAVADQYADFLREGFHVVTPNKKANTSSMDYYHQLRYAAEK 598
              K+  LLNPV+VDCTS++AV+DQY   +  G HVVTPNKKANT   DYY  LR  A  
Sbjct: 540 AWAKDQQLLNPVLVDCTSNEAVSDQYVAVMNAGLHVVTPNKKANTRDYDYYRALRQTALH 599

Query: 599 SRRKFLYDTNVGAGLPVIENLQNLLNAGDELMKFSGILSGSLSYIFGKLDEGMSFSEATT 658
            RR+FLY+T VGAGLPVI+NL+ LL AGD+L KF+GILSGSLSYIFG LDEGMS SEAT 
Sbjct: 600 QRRQFLYETTVGAGLPVIDNLKKLLFAGDKLQKFNGILSGSLSYIFGMLDEGMSLSEATG 659

Query: 659 LAREMGYTEPDPRDDLSGMDVARKLLILARETGRELELADIEIEPVLPAEFNAEGDVAAF 718
           +ARE  +TEPDPRDDLSGMDVARK+LILARE G ++EL+DI++E VLP+ F+A GDV  F
Sbjct: 660 IAREKCFTEPDPRDDLSGMDVARKVLILAREVGMQIELSDIQVESVLPSHFDASGDVETF 719

Query: 719 MANLSQLDDLFAARVAKARDEGKVLRYVGNIDEDGVCRVKIAEVDGNDPLFKVKNGENAL 778
           MANLS LD   A RV  A+  GKVLRYVG IDE+G CRVKIAEVD  DPL+ VK GENAL
Sbjct: 720 MANLSALDGELAERVNSAKAAGKVLRYVGQIDEEG-CRVKIAEVDAKDPLYSVKGGENAL 778

Query: 779 AFYSHYYQPLPLVLRGYGAGNDVTAAGVFADLLRTLSW 816
           AFYS YYQP+P VLRGYGAG +VTAAGVFADLLRTL+W
Sbjct: 779 AFYSRYYQPIPFVLRGYGAGTEVTAAGVFADLLRTLNW 816


Lambda     K      H
   0.319    0.135    0.384 

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: 1515
Number of extensions: 40
Number of successful extensions: 5
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: 820
Length of database: 822
Length adjustment: 42
Effective length of query: 778
Effective length of database: 780
Effective search space:   606840
Effective search space used:   606840
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 56 (26.2 bits)

Align candidate 5208568 Shew_1079 (bifunctional aspartokinase I/homeserine dehydrogenase I (RefSeq))
to HMM TIGR00657 (aspartate kinase (EC 2.7.2.4))

Software error:

../bin/blast/fastacmd -i /tmp/list.14171.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.14171.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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