GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mmsB in Pseudomonas fluorescens FW300-N2E3

Align 3-hydroxyisobutyrate dehydrogenase (EC 1.1.1.31) (characterized)
to candidate AO353_05985 AO353_05985 3-hydroxyisobutyrate dehydrogenase

Query= reanno::pseudo3_N2E3:AO353_05985
         (294 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_05985
          Length = 294

 Score =  574 bits (1479), Expect = e-169
 Identities = 294/294 (100%), Positives = 294/294 (100%)

Query: 1   MKIAFIGLGNMGAPMARNLIKAGHSLNLVDLNKAVLAELAQLGGTISATAREAAQGAELV 60
           MKIAFIGLGNMGAPMARNLIKAGHSLNLVDLNKAVLAELAQLGGTISATAREAAQGAELV
Sbjct: 1   MKIAFIGLGNMGAPMARNLIKAGHSLNLVDLNKAVLAELAQLGGTISATAREAAQGAELV 60

Query: 61  ITMLPAAVHVRSVWLGEDGVLAGIAKGVPAVDCSTIDPQTARDVAAAAAKQGVAMADAPV 120
           ITMLPAAVHVRSVWLGEDGVLAGIAKGVPAVDCSTIDPQTARDVAAAAAKQGVAMADAPV
Sbjct: 61  ITMLPAAVHVRSVWLGEDGVLAGIAKGVPAVDCSTIDPQTARDVAAAAAKQGVAMADAPV 120

Query: 121 SGGTGGAAAGTLTFMVGATPELFATLQPVLAQMGRNIVHCGEVGTGQIAKICNNLLLAIS 180
           SGGTGGAAAGTLTFMVGATPELFATLQPVLAQMGRNIVHCGEVGTGQIAKICNNLLLAIS
Sbjct: 121 SGGTGGAAAGTLTFMVGATPELFATLQPVLAQMGRNIVHCGEVGTGQIAKICNNLLLAIS 180

Query: 181 MVGVSEAMALGDALGIDTQVLAGIINSSTGRCWSSEMYNPWPGIVETAPASRGYTGGFGA 240
           MVGVSEAMALGDALGIDTQVLAGIINSSTGRCWSSEMYNPWPGIVETAPASRGYTGGFGA
Sbjct: 181 MVGVSEAMALGDALGIDTQVLAGIINSSTGRCWSSEMYNPWPGIVETAPASRGYTGGFGA 240

Query: 241 ELMLKDLGLATEAARQAHQPVMLGAVAQQLYQAMSQRGEGGKDFSAIINSYRKP 294
           ELMLKDLGLATEAARQAHQPVMLGAVAQQLYQAMSQRGEGGKDFSAIINSYRKP
Sbjct: 241 ELMLKDLGLATEAARQAHQPVMLGAVAQQLYQAMSQRGEGGKDFSAIINSYRKP 294


Lambda     K      H
   0.317    0.132    0.382 

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: 429
Number of extensions: 4
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: 294
Length of database: 294
Length adjustment: 26
Effective length of query: 268
Effective length of database: 268
Effective search space:    71824
Effective search space used:    71824
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: 48 (23.1 bits)

Align candidate AO353_05985 AO353_05985 (3-hydroxyisobutyrate dehydrogenase)
to HMM TIGR01692 (mmsB: 3-hydroxyisobutyrate dehydrogenase (EC 1.1.1.31))

Software error:

../bin/blast/fastacmd -i /tmp/list.26762.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.26762.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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