GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mmsB in Pseudomonas fluorescens FW300-N2C3

Align 3-hydroxyisobutyrate dehydrogenase (EC 1.1.1.31) (characterized)
to candidate AO356_07865 AO356_07865 3-hydroxyisobutyrate dehydrogenase

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



>FitnessBrowser__pseudo5_N2C3_1:AO356_07865
          Length = 295

 Score =  539 bits (1389), Expect = e-158
 Identities = 271/294 (92%), Positives = 282/294 (95%)

Query: 1   MKIAFIGLGNMGAPMARNLIKAGHSLNLVDLNKAVLAELAQLGGTISATAREAAQGAELV 60
           M IAFIGLGNMGAPMARNL+KAGHSLNL DLN+ VLAELA LGGT+SA+ R+AAQGA LV
Sbjct: 1   MNIAFIGLGNMGAPMARNLLKAGHSLNLFDLNQTVLAELAALGGTVSASPRDAAQGAALV 60

Query: 61  ITMLPAAVHVRSVWLGEDGVLAGIAKGVPAVDCSTIDPQTARDVAAAAAKQGVAMADAPV 120
           ITMLPAA HVRSVWLGEDGVLAGIA G PAVDCSTIDPQTARDVAAAAAKQGVAMADAPV
Sbjct: 61  ITMLPAAAHVRSVWLGEDGVLAGIAAGTPAVDCSTIDPQTARDVAAAAAKQGVAMADAPV 120

Query: 121 SGGTGGAAAGTLTFMVGATPELFATLQPVLAQMGRNIVHCGEVGTGQIAKICNNLLLAIS 180
           SGGTGGAAAGTLTFMVGAT ELFATLQPVLAQMGRNIVHCGEVGTGQIAKICNNLLL IS
Sbjct: 121 SGGTGGAAAGTLTFMVGATAELFATLQPVLAQMGRNIVHCGEVGTGQIAKICNNLLLGIS 180

Query: 181 MVGVSEAMALGDALGIDTQVLAGIINSSTGRCWSSEMYNPWPGIVETAPASRGYTGGFGA 240
           MVGVSEAMALGDALGIDTQVLAGIINSSTGRCWSS+ YNPWPG++ETAPASRGYTGGFGA
Sbjct: 181 MVGVSEAMALGDALGIDTQVLAGIINSSTGRCWSSDTYNPWPGVIETAPASRGYTGGFGA 240

Query: 241 ELMLKDLGLATEAARQAHQPVMLGAVAQQLYQAMSQRGEGGKDFSAIINSYRKP 294
           +LMLKDLGLATEAARQAHQPV+LGAVAQQLYQAMSQRGEGGKDFSAI+NSYRKP
Sbjct: 241 DLMLKDLGLATEAARQAHQPVVLGAVAQQLYQAMSQRGEGGKDFSAIVNSYRKP 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: 399
Number of extensions: 8
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: 295
Length adjustment: 26
Effective length of query: 268
Effective length of database: 269
Effective search space:    72092
Effective search space used:    72092
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 AO356_07865 AO356_07865 (3-hydroxyisobutyrate dehydrogenase)
to HMM TIGR01692 (mmsB: 3-hydroxyisobutyrate dehydrogenase (EC 1.1.1.31))

Software error:

../bin/blast/fastacmd -i /tmp/list.23873.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.23873.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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