GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mmsB in Shewanella loihica PV-4

Align 3-hydroxyisobutyrate dehydrogenase; HIBADH; EC 1.1.1.31 (characterized)
to candidate 5209194 Shew_1672 3-hydroxyisobutyrate dehydrogenase (RefSeq)

Query= SwissProt::P28811
         (298 letters)



>FitnessBrowser__PV4:5209194
          Length = 299

 Score =  323 bits (828), Expect = 3e-93
 Identities = 174/300 (58%), Positives = 211/300 (70%), Gaps = 5/300 (1%)

Query: 1   MTDIAFLGLGNMGGPMAANLLKAGHRVNVFDLQPKAVLGLVEQGAQGADSALQCCEGAEV 60
           M  +AF+GLGNMGGPMA NL+KAG+ V  FDL   A+  +VE+GA  A SA      A+V
Sbjct: 1   MNTVAFIGLGNMGGPMAVNLVKAGYTVKAFDLSQTALSHVVEEGAMQAPSACAAAAAADV 60

Query: 61  VISMLPAGQHVESLYLGDD---GLLARVAGKPLLIDCSTIAPETARKVAEAAAAKGLTLL 117
           VI+MLPAG+HV SLYLGD+   G++  VA   LLIDCSTI  E+AR VAE A  KGL  +
Sbjct: 61  VITMLPAGKHVRSLYLGDEQNKGIIDVVADGTLLIDCSTIDAESARFVAEQAKTKGLEFI 120

Query: 118 DAPVSGGVGGARAGTLSFIVGGPAEGFARARPVLENMGRNIFHAGDHGAGQVAKICNNML 177
           DAPVSGG  GA AGTL+FI GG    F +A+ VL  MG NIFHAG  GAGQVAKICNNML
Sbjct: 121 DAPVSGGTAGAAAGTLTFICGGSDTAFEQAQGVLNVMGANIFHAGGPGAGQVAKICNNML 180

Query: 178 LGILMAGTAEALALGVKNGLDPAVLSEVMKQSSGGNWALNLYNPWPGVMPQAPASNGYAG 237
           L +LM GT+E++ +G+ +GLDP VLSE+MK SSGGNW L+ YNP P VM   P+SNGY G
Sbjct: 181 LSVLMVGTSESIQMGIDHGLDPKVLSEIMKVSSGGNWTLDKYNPCPDVMENVPSSNGYQG 240

Query: 238 GFQVRLMNKDLGLALANAQAVQASTPLGALARNLFSLHAQADAEHEGLDFSSIQKLYRGK 297
           GF V LM KDLGL+   A    +STP+GALAR+L+  HA+    +   DFSSI + +  K
Sbjct: 241 GFMVDLMVKDLGLSQEAALLSNSSTPMGALARSLYVNHARQG--NGKRDFSSIFEQFNKK 298


Lambda     K      H
   0.317    0.135    0.395 

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: 326
Number of extensions: 11
Number of successful extensions: 2
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: 298
Length of database: 299
Length adjustment: 27
Effective length of query: 271
Effective length of database: 272
Effective search space:    73712
Effective search space used:    73712
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 5209194 Shew_1672 (3-hydroxyisobutyrate dehydrogenase (RefSeq))
to HMM TIGR01692 (mmsB: 3-hydroxyisobutyrate dehydrogenase (EC 1.1.1.31))

Software error:

../bin/blast/fastacmd -i /tmp/list.24645.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.24645.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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