GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mmsB in Sinorhizobium meliloti 1021

Align Probable 3-hydroxyisobutyrate dehydrogenase; HIBADH; EC 1.1.1.31 (uncharacterized)
to candidate SM_b20751 SM_b20751 3-hydroxyisobutyrate dehydrogenase

Query= curated2:P63936
         (294 letters)



>FitnessBrowser__Smeli:SM_b20751
          Length = 298

 Score =  320 bits (819), Expect = 3e-92
 Identities = 165/295 (55%), Positives = 202/295 (68%), Gaps = 1/295 (0%)

Query: 1   MTTIAFLGLGNMGAPMSANLVGAGHVVRGFDPAPTAASGAAAHGVAVFRSAPEAVAEADV 60
           MT IAF+GLGNMG PM+ANLV AGH V GFD +  + + AA  GV+V  S  +AV E + 
Sbjct: 1   MTKIAFIGLGNMGGPMAANLVKAGHAVTGFDLSEASRNAAAKTGVSVAGSIAQAVREMEC 60

Query: 61  VITMLPTGEVVRRCYTDVLAAARPATLFIDSSTISVTDAREVHALAESHGMLQLDAPVSG 120
           VITMLP    V   + ++L    P TL IDSSTI V  AR+VH  AE  G   LDAPVSG
Sbjct: 61  VITMLPASAHVLYVWDELLGFVDPGTLLIDSSTIDVESARKVHGFAEKAGCPSLDAPVSG 120

Query: 121 GVKGAAAATLAFMVGGDESTLRRARPVLEPMAGKIIHCGAAGAGQAAKVCNNMVLAVQQI 180
           G  GAAAATL FMVGG E    R + +LE M  KI+HCG AGAGQAAK+CNNM+L V   
Sbjct: 121 GTAGAAAATLTFMVGGSEGAFSRGKHLLEAMGKKIVHCGDAGAGQAAKICNNMILGVSMA 180

Query: 181 AIAEAFVLAEKLGLSAQSLFDVITGATGNCWAVHTNCPVPGPVPTSPANNDFKPGFSTAL 240
           A+ EAFVLAE+LGLS Q+LFDV + ++G CW++ T CPVPGPVPTSPAN  +KPGF+ +L
Sbjct: 181 AVCEAFVLAERLGLSHQALFDVASTSSGQCWSLTTYCPVPGPVPTSPANGGYKPGFAASL 240

Query: 241 MNKDLGLAMDAVAATGATAPLGSHAADIYAKF-AADHADLDFSAVIHTLRARADA 294
           M KDL L+  A +A+GA  P+G+ A  +Y+ F    H   DFSA+IH LR   +A
Sbjct: 241 MLKDLKLSQQAASASGAATPMGAQATQLYSLFEKLGHGAEDFSALIHLLRGNEEA 295


Lambda     K      H
   0.319    0.131    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: 285
Number of extensions: 13
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: 294
Length of database: 298
Length adjustment: 26
Effective length of query: 268
Effective length of database: 272
Effective search space:    72896
Effective search space used:    72896
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: 48 (23.1 bits)

Align candidate SM_b20751 SM_b20751 (3-hydroxyisobutyrate dehydrogenase)
to HMM TIGR01692 (mmsB: 3-hydroxyisobutyrate dehydrogenase (EC 1.1.1.31))

Software error:

../bin/blast/fastacmd -i /tmp/list.13580.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.13580.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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