GapMind for Amino acid biosynthesis

 

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

Align fused aspartate kinase/homoserine dehydrogenase 2 (EC 2.7.2.4; EC 1.1.1.3) (characterized)
to candidate 5208005 Shew_0521 bifunctional aspartate kinase II/homoserine dehydrogenase II (RefSeq)

Query= ecocyc::ASPKINIIHOMOSERDEHYDROGII-MONOMER
         (810 letters)



>FitnessBrowser__PV4:5208005
          Length = 797

 Score =  572 bits (1473), Expect = e-167
 Identities = 342/804 (42%), Positives = 479/804 (59%), Gaps = 26/804 (3%)

Query: 14  LHKFGGSSLADVKCYLRVAGIMAEYSQPDDMMVVSAAGSTTNQLINWLKLSQTDRLSAHQ 73
           LHKFGGSSLAD  CY RVA I+  +   DD++VVSAAG +TN L   L+L  TD+L   +
Sbjct: 6   LHKFGGSSLADADCYRRVAHILLTHGHSDDLIVVSAAGKSTNFLYRLLELCDTDQLWQEE 65

Query: 74  VQQTLRRYQCDLISGLLPAEEADSLISAFVSDLERLAALLD-SGINDAVYAEVVGHGEVW 132
           +Q  L  YQ +LI  LL  E+A SL     +D  +L +LL    +ND    +VV  GE W
Sbjct: 66  LQ-VLVSYQQNLIEQLLSNEQARSLRERLATDKSQLTSLLSLDELNDYQRNQVVSFGERW 124

Query: 133 SARLMSAVLNQQGLPAAWLDAREFLRAERAAQPQVDEGLSYPLLQQLLVQHPGKRLVVTG 192
           S+ L++A+L + G+ A  +DAR  L A+  A PQ+  G S   +Q LL  HP +RLV+TG
Sbjct: 125 SSCLLAALLRESGVAATDVDARTLLVADEGAVPQIRLGESRQKVQALLEAHPQERLVITG 184

Query: 193 FISRNNAGETVLLGRNGSDYSATQIGALAGVSRVTIWSDVAGVYSADPRKVKDACLLPLL 252
           FI  N  G+T+LLGRNGSD+SAT + +LA + RVTIW+DV GV++ADP ++ DA LL  +
Sbjct: 185 FICANEQGDTLLLGRNGSDFSATLLASLADIERVTIWTDVEGVFNADPNRINDAKLLKSM 244

Query: 253 RLDEASELARLAAPVLHARTLQPVSGSEIDLQLRCSYTPDQGSTRIERVLASGTGARIVT 312
            L EA+ LA L +PVLH RTLQP+  +E+ L +R SY P    T I    +S   A +VT
Sbjct: 245 SLTEANRLAHLGSPVLHNRTLQPLFDTEVSLAVRSSYAPHTDFTLIAPK-SSSASAPVVT 303

Query: 313 SHDDVCLIEFQVPASQDFKLAHKEIDQILK---RAQVRPLAV-GVHNDRQLLQFCYTSEV 368
           S   V L    +           E+ Q+L    +A + PLA   + + R  L F + ++ 
Sbjct: 304 SLSSVSLFSLTISV---------ELPQLLACFAQAGLTPLAYWSLAHGRAELAFTHENQK 354

Query: 369 ADSALKILDEAGLP-GELRLRQGLALVAMVGAGVTRNPLHCHRFWQQLKGQPVEFTWQSD 427
              A+     + L   EL+LR  L LVA+V A  +   L+   F + L  +        +
Sbjct: 355 QAQAIFEAKRSELGIDELQLRDDLGLVALVSADAS---LYRRGFSRLLSREAHPLC---N 408

Query: 428 DGISLVAVLRTGPTESLIQGLHQSVFRAEKRIGLVLFGKGNIGSRWLELFAREQSTLSAR 487
           DG+SLV ++       L Q +H+      KRIG++L G GNIG  W++LF R +  L+  
Sbjct: 409 DGLSLVTLVPKAQVNLLTQKVHRRCAGPRKRIGVLLLGIGNIGEAWIDLFKRARPVLNKE 468

Query: 488 TGFEFVLAGVVDSRRSLLSYDGLDASRALAFFNDEAVEQDEESLFLWMRAHPYDDLVVLD 547
                 L G++ S+++LLS   +D S     F +         LF  ++A   D+L+ LD
Sbjct: 469 LEVSVELVGLLSSKKALLSETDIDLSSWQQAFEERGTGWQYTHLFEQLQALNCDELIALD 528

Query: 548 VTASQQLADQYLDFASHGFHVISANKLAGASDSNKYRQIHDAFEKTGRHWLYNATVGAGL 607
           ++AS  L  QY +F + G H++SANKLAG+     Y+++          W YNA+ GAGL
Sbjct: 529 ISASADLTLQYPEFFARGIHIVSANKLAGSGPLAFYQELKQQLGNRRLFWRYNASCGAGL 588

Query: 608 PINHTVRDLIDSGDTILSISGIFSGTLSWLFLQFDGSVPFTELVDQAWQQGLTEPDPRDD 667
           P+ H + DL +SGD+I ++ GIFSGTL WLF  +D   PF+ELV +A   G+TEPDPRDD
Sbjct: 589 PVQHALNDLHNSGDSIEAVGGIFSGTLCWLFEHYDAKKPFSELVLEAKGLGITEPDPRDD 648

Query: 668 LSGKDVMRKLVILAREAGYNIEPDQVRVESLVPAHCEGGSIDHFFENGDELNEQMVQRLE 727
           LSG+D+ RKL+ILARE GY+IE D + +ESLVP       +D F +   EL+ +M+Q+ +
Sbjct: 649 LSGRDMQRKLLILAREIGYDIELDDIELESLVPTKLAEIPLDDFIKRMAELDGEMLQQYQ 708

Query: 728 AAREMGLVLRYVARFDANG---KARVGVEAVREDHPLASLLPCDNVFAIESRWYRDNPLV 784
           AA E   VLRYVA  D+     KA+VG++ V   HP A+L P DNVF I S +Y+DNPL+
Sbjct: 709 AAAEQNKVLRYVASLDSEQGQLKAKVGIQWVDRSHPYANLTPGDNVFVIRSDFYQDNPLI 768

Query: 785 IRGPGAGRDVTAGAIQSDINRLAQ 808
           IRGPGAGR+VTA A+QSD+ ++ +
Sbjct: 769 IRGPGAGREVTAAAVQSDLAQICR 792


Lambda     K      H
   0.320    0.135    0.397 

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: 1467
Number of extensions: 76
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: 810
Length of database: 797
Length adjustment: 41
Effective length of query: 769
Effective length of database: 756
Effective search space:   581364
Effective search space used:   581364
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: 55 (25.8 bits)

Align candidate 5208005 Shew_0521 (bifunctional aspartate kinase II/homoserine dehydrogenase II (RefSeq))
to HMM TIGR00657 (aspartate kinase (EC 2.7.2.4))

Software error:

../bin/blast/fastacmd -i /tmp/list.20725.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.20725.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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