GapMind for Amino acid biosynthesis

 

Alignments for a candidate for metB in Shewanella loihica PV-4

Align Cystathionine gamma-synthase; CGS; O-succinylhomoserine (thiol)-lyase; EC 2.5.1.48 (characterized)
to candidate 5208004 Shew_0520 O-succinylhomoserine (thiol)-lyase (RefSeq)

Query= SwissProt::P00935
         (386 letters)



>FitnessBrowser__PV4:5208004
          Length = 388

 Score =  461 bits (1186), Expect = e-134
 Identities = 235/381 (61%), Positives = 286/381 (75%), Gaps = 1/381 (0%)

Query: 3   RKQATIAVRSGLNDDEQYGCVVPPIHLSSTYNFTGFNEPRAHDYSRRGNPTRDVVQRALA 62
           RK AT AVR G+  D Q+G VVPPI+LS+ Y+F G  +PRA DYSR GNPTR ++  A+A
Sbjct: 4   RKLATAAVRRGIESDTQHGAVVPPIYLSTNYSFEGHQQPRAFDYSRSGNPTRSILGDAIA 63

Query: 63  ELEGGAGAVLTNTGMSAIHLVTTVFLKPGDLLVAPHDCYGGSYRLFDSLAKRGCYRVLFV 122
           ELE GA  V+T TGM+AI LVT++ L P DLLV PHDCYGGSYRLF +LAK+G +++L V
Sbjct: 64  ELEQGATGVVTCTGMAAITLVTSL-LGPEDLLVVPHDCYGGSYRLFTNLAKKGAFKLLVV 122

Query: 123 DQGDEQALRAALAEKPKLVLVESPSNPLLRVVDIAKICHLAREVGAVSVVDNTFLSPALQ 182
           DQ DE+AL  AL + PK+V +E+PSNPLLRVVDI  I   + +VGA  VVDNTFLSP LQ
Sbjct: 123 DQTDERALEQALTQSPKMVWLETPSNPLLRVVDIEAIAQASHKVGAQVVVDNTFLSPVLQ 182

Query: 183 NPLALGADLVLHSCTKYLNGHSDVVAGVVIAKDPDVVTELAWWANNIGVTGGAFDSYLLL 242
            PL LGAD+V+HS TKY+NGHSDVV G V+AKDP+V   L WW+N +G+TG AFDSYL L
Sbjct: 183 QPLQLGADIVVHSTTKYINGHSDVVGGAVVAKDPEVGELLHWWSNTLGLTGSAFDSYLTL 242

Query: 243 RGLRTLVPRMELAQRNAQAIVKYLQTQPLVKKLYHPSLPENQGHEIAARQQKGFGAMLSF 302
           RGLRTL  R+   Q NAQ ++  L     V+K+Y+P L E+ GHEIAARQQKGFGAMLSF
Sbjct: 243 RGLRTLAVRIREHQANAQKVLALLCDHKAVEKVYYPGLAEHPGHEIAARQQKGFGAMLSF 302

Query: 303 ELDGDEQTLRRFLGGLSLFTLAESLGGVESLISHAATMTHAGMAPEARAAAGISETLLRI 362
           EL G E  L  FL  L  F++AESLGGVESL++  ATMTH  M P+AR  AG+ +TL+R+
Sbjct: 303 ELKGGESALVAFLDALQYFSVAESLGGVESLVAVPATMTHRAMDPDARREAGVKDTLIRL 362

Query: 363 STGIEDGEDLIADLENGFRAA 383
           S GIEDGEDL+AD+  G  AA
Sbjct: 363 SVGIEDGEDLVADILAGLEAA 383


Lambda     K      H
   0.319    0.136    0.394 

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: 431
Number of extensions: 10
Number of successful extensions: 2
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: 386
Length of database: 388
Length adjustment: 30
Effective length of query: 356
Effective length of database: 358
Effective search space:   127448
Effective search space used:   127448
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 (21.7 bits)
S2: 50 (23.9 bits)

Align candidate 5208004 Shew_0520 (O-succinylhomoserine (thiol)-lyase (RefSeq))
to HMM TIGR02080 (metB: O-succinylhomoserine (thiol)-lyase (EC 2.5.1.48))

Software error:

../bin/blast/fastacmd -i /tmp/list.20305.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.20305.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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