GapMind for Amino acid biosynthesis

 

Alignments for a candidate for leuC in Marinobacter adhaerens HP15

Align 3-isopropylmalate dehydratase large subunit; EC 4.2.1.33 (characterized)
to candidate GFF2655 HP15_2599 isopropylmalate isomerase large subunit

Query= CharProtDB::CH_024771
         (466 letters)



>FitnessBrowser__Marino:GFF2655
          Length = 469

 Score =  546 bits (1406), Expect = e-160
 Identities = 276/469 (58%), Positives = 347/469 (73%), Gaps = 7/469 (1%)

Query: 2   AKTLYEKLFDAHVVYEAENETPLLYIDRHLVHEVTSPQAFDGLRAHGR-PVRQPGKTFAT 60
           A+TLY+KL+  H+V E  + + LLYIDRHL+HEVT+PQAF GLR+ GR P R P    A 
Sbjct: 3   ARTLYDKLWQRHLVDELPDGSALLYIDRHLLHEVTTPQAFSGLRSAGRKPWRIPANV-AV 61

Query: 61  MDHNVSTQTKDINACG---EMARIQMQELIKNCKEFGVELYDLNHPYQGIVHVMGPEQGV 117
            DH V T+ +++   G    +AR Q++ L +NC+EFG+ L +L    QGIVHV+GPEQG+
Sbjct: 62  PDHAVPTRKRELGVAGIADRVARKQVETLSRNCEEFGIPLIELEDARQGIVHVVGPEQGL 121

Query: 118 TLPGMTIVCGDSHTATHGAFGALAFGIGTSEVEHVLATQTLKQGRAKTMKIEVQGKAAPG 177
           TLPGMTIVCGDSHT+THGAF  LA GIGTSEVEHVLATQTL+  + K M++  +G+   G
Sbjct: 122 TLPGMTIVCGDSHTSTHGAFATLAMGIGTSEVEHVLATQTLRTQKQKNMRVVFEGQPGFG 181

Query: 178 ITAKDIVLAIIGKTGSAGGTGHVVEFCGEAIRDLSMEGRMTLCNMAIEMGAKAGLVAPDE 237
           +T KD++LA+IG+ G+AGG G+ +E+ G AIR+LSMEGRMT+CNM+IE GA+AG+VA D 
Sbjct: 182 VTPKDLILALIGRIGTAGGNGYAIEYAGAAIRNLSMEGRMTICNMSIEAGARAGMVAYDR 241

Query: 238 TTFNYVKGRLHAPKGKDFDDAVAYWKTLQTDEGATFDTVVTLQAEEISPQVTWGTNPGQV 297
            T  YV+GR  AP G+  + A  YW+TL +D  A FD       E + PQVTWGT+P  V
Sbjct: 242 VTEQYVEGRPQAPVGERLEQAREYWRTLVSDAEADFDREEHFPLEALVPQVTWGTSPEMV 301

Query: 298 ISVNDNIPDPASFADPVERASAEKALAYMGLKPGIPLTEVAIDKVFIGSCTNSRIEDLRA 357
             ++   PD +  A P +R SA +AL YMGL+PG PL  ++IDKVFIGSCTN+R+EDLRA
Sbjct: 302 TGIDGKTPDLSQLA-PEKRESARRALDYMGLEPGRPLKGLSIDKVFIGSCTNARMEDLRA 360

Query: 358 AAEIAKGRKVAPGV-QALVVPGSGPVKAQAEAEGLDKIFIEAGFEWRLPGCSMCLAMNND 416
            A + +G+KV   V QAL+VPGSG V+ QAE EGLD IF  AGFEWR  GCSMCL MN+D
Sbjct: 361 VANLVQGQKVHRSVKQALIVPGSGQVRLQAEREGLDMIFRNAGFEWRAAGCSMCLGMNDD 420

Query: 417 RLNPGERCASTSNRNFEGRQGRGGRTHLVSPAMAAAAAVTGHFADIRNI 465
           RLNPGERCASTSNRNFEGRQG+GGRTHL+SP MAAAAA+ G   D+R +
Sbjct: 421 RLNPGERCASTSNRNFEGRQGKGGRTHLMSPLMAAAAALAGEITDVREV 469


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: 707
Number of extensions: 27
Number of successful extensions: 4
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: 469
Length adjustment: 33
Effective length of query: 433
Effective length of database: 436
Effective search space:   188788
Effective search space used:   188788
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 GFF2655 HP15_2599 (isopropylmalate isomerase large subunit)
to HMM TIGR00170 (leuC: 3-isopropylmalate dehydratase, large subunit (EC 4.2.1.33))

Software error:

../bin/blast/fastacmd -i /tmp/list.17254.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.17254.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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