GapMind for Amino acid biosynthesis

 

Alignments for a candidate for aroE in Caulobacter crescentus NA1000

Align Shikimate dehydrogenase (NADP(+)); SDH; EC 1.1.1.25 (uncharacterized)
to candidate CCNA_00003 CCNA_00003 shikimate 5-dehydrogenase

Query= curated2:Q9AC57
         (285 letters)



>FitnessBrowser__Caulo:CCNA_00003
          Length = 285

 Score =  550 bits (1417), Expect = e-161
 Identities = 285/285 (100%), Positives = 285/285 (100%)

Query: 1   MTNAITGAAIVGGVCGQPIKHSMSPVIHNAWIAAAGLDAAYVPFAPAADRFETFVDGLRG 60
           MTNAITGAAIVGGVCGQPIKHSMSPVIHNAWIAAAGLDAAYVPFAPAADRFETFVDGLRG
Sbjct: 1   MTNAITGAAIVGGVCGQPIKHSMSPVIHNAWIAAAGLDAAYVPFAPAADRFETFVDGLRG 60

Query: 61  GAVRGLNVTIPFKERALAVADTASDLARMAGAANLLVFNEDGSVHADNTDGPGLLGAIAI 120
           GAVRGLNVTIPFKERALAVADTASDLARMAGAANLLVFNEDGSVHADNTDGPGLLGAIAI
Sbjct: 61  GAVRGLNVTIPFKERALAVADTASDLARMAGAANLLVFNEDGSVHADNTDGPGLLGAIAI 120

Query: 121 QAPGFDVTAAPVVILGAGGAARGAVAALLLAGAPRIAVVNRTVARAQDLADTFGEKVVAK 180
           QAPGFDVTAAPVVILGAGGAARGAVAALLLAGAPRIAVVNRTVARAQDLADTFGEKVVAK
Sbjct: 121 QAPGFDVTAAPVVILGAGGAARGAVAALLLAGAPRIAVVNRTVARAQDLADTFGEKVVAK 180

Query: 181 GEDALPALLPEAGLIINATSLGLGGGAGPSADLTLTPKTAVVMDMVYKPLRTEFLRRAEA 240
           GEDALPALLPEAGLIINATSLGLGGGAGPSADLTLTPKTAVVMDMVYKPLRTEFLRRAEA
Sbjct: 181 GEDALPALLPEAGLIINATSLGLGGGAGPSADLTLTPKTAVVMDMVYKPLRTEFLRRAEA 240

Query: 241 AGRRTVDGLEMLLRQAIPTFETIYGQAPSPKIDVRVLALKLLGEV 285
           AGRRTVDGLEMLLRQAIPTFETIYGQAPSPKIDVRVLALKLLGEV
Sbjct: 241 AGRRTVDGLEMLLRQAIPTFETIYGQAPSPKIDVRVLALKLLGEV 285


Lambda     K      H
   0.319    0.136    0.390 

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: 412
Number of extensions: 9
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: 285
Length of database: 285
Length adjustment: 26
Effective length of query: 259
Effective length of database: 259
Effective search space:    67081
Effective search space used:    67081
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: 47 (22.7 bits)

Align candidate CCNA_00003 CCNA_00003 (shikimate 5-dehydrogenase)
to HMM TIGR00507 (aroE: shikimate dehydrogenase (EC 1.1.1.25))

Software error:

../bin/blast/fastacmd -i /tmp/list.16431.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.16431.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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