GapMind for Amino acid biosynthesis

 

Alignments for a candidate for leuC in Shewanella oneidensis MR-1

Align 3-isopropylmalate dehydratase large subunit; EC 4.2.1.33 (characterized)
to candidate 203315 SO4234 3-isopropylmalate dehydratase, large subunit (NCBI ptt file)

Query= CharProtDB::CH_024771
         (466 letters)



>FitnessBrowser__MR1:203315
          Length = 474

 Score =  699 bits (1805), Expect = 0.0
 Identities = 340/461 (73%), Positives = 395/461 (85%)

Query: 3   KTLYEKLFDAHVVYEAENETPLLYIDRHLVHEVTSPQAFDGLRAHGRPVRQPGKTFATMD 62
           KTLY+K++DAH+V   E E P++Y+DRHLVHEVTSPQAF GL+  GR +R P KTFATMD
Sbjct: 11  KTLYQKVWDAHIVATPEGEAPIIYVDRHLVHEVTSPQAFSGLKVAGRQLRAPEKTFATMD 70

Query: 63  HNVSTQTKDINACGEMARIQMQELIKNCKEFGVELYDLNHPYQGIVHVMGPEQGVTLPGM 122
           HN ST++  ++A   MARIQ++ L +NCK+FGV LYD++HP QGIVHVMGPE G+TLPG 
Sbjct: 71  HNTSTRSASLDALSPMARIQVETLAQNCKDFGVLLYDIHHPNQGIVHVMGPELGITLPGT 130

Query: 123 TIVCGDSHTATHGAFGALAFGIGTSEVEHVLATQTLKQGRAKTMKIEVQGKAAPGITAKD 182
            IVCGDSHTATHGAFGALAFGIGTSEVEHVLATQTL+Q +AKTMKIEV+G+   G+TAKD
Sbjct: 131 VIVCGDSHTATHGAFGALAFGIGTSEVEHVLATQTLRQLKAKTMKIEVRGQVTDGVTAKD 190

Query: 183 IVLAIIGKTGSAGGTGHVVEFCGEAIRDLSMEGRMTLCNMAIEMGAKAGLVAPDETTFNY 242
           IVLAIIGK G  GGTG+VVEFCGEAI  LSMEGRMT+CNMAIEMGAKAG+VAPD+TTF+Y
Sbjct: 191 IVLAIIGKIGMDGGTGYVVEFCGEAIEALSMEGRMTVCNMAIEMGAKAGMVAPDQTTFDY 250

Query: 243 VKGRLHAPKGKDFDDAVAYWKTLQTDEGATFDTVVTLQAEEISPQVTWGTNPGQVISVND 302
           ++GR  APKG+D+  AVA WKTL+TD GA FD  V L A +I+PQ+TWGTNPGQV++++ 
Sbjct: 251 LEGREFAPKGEDWAQAVAEWKTLKTDVGAEFDATVVLDAADIAPQLTWGTNPGQVVAIDA 310

Query: 303 NIPDPASFADPVERASAEKALAYMGLKPGIPLTEVAIDKVFIGSCTNSRIEDLRAAAEIA 362
            +P+PA   +P  R+S EKAL Y+GL  G P+TEVAI+KVFIGSCTNSRIEDLR+AA+ A
Sbjct: 311 PVPNPADEVNPTIRSSMEKALDYIGLTAGTPMTEVAINKVFIGSCTNSRIEDLRSAAKHA 370

Query: 363 KGRKVAPGVQALVVPGSGPVKAQAEAEGLDKIFIEAGFEWRLPGCSMCLAMNNDRLNPGE 422
           KGRKVA GV A+VVPGSG VKAQAEAEGLDKIFIEAGFEWRLPGCSMCLAMN+DRL  G+
Sbjct: 371 KGRKVAAGVTAIVVPGSGQVKAQAEAEGLDKIFIEAGFEWRLPGCSMCLAMNDDRLEAGD 430

Query: 423 RCASTSNRNFEGRQGRGGRTHLVSPAMAAAAAVTGHFADIR 463
           RCASTSNRNFEGRQGRG RTHLVSPAMAAAAA+ GHF DIR
Sbjct: 431 RCASTSNRNFEGRQGRGSRTHLVSPAMAAAAAIAGHFVDIR 471


Lambda     K      H
   0.317    0.134    0.396 

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: 783
Number of extensions: 14
Number of successful extensions: 1
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: 466
Length of database: 474
Length adjustment: 33
Effective length of query: 433
Effective length of database: 441
Effective search space:   190953
Effective search space used:   190953
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 (21.7 bits)
S2: 51 (24.3 bits)

Align candidate 203315 SO4234 (3-isopropylmalate dehydratase, large subunit (NCBI ptt file))
to HMM TIGR00170 (leuC: 3-isopropylmalate dehydratase, large subunit (EC 4.2.1.33))

Software error:

../bin/blast/fastacmd -i /tmp/list.15346.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.15346.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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