GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mmsB in Cupriavidus basilensis 4G11

Align 3-hydroxyisobutyrate dehydrogenase subunit (EC 1.1.1.31) (characterized)
to candidate RR42_RS24030 RR42_RS24030 3-hydroxyisobutyrate dehydrogenase

Query= metacyc::MONOMER-11664
         (295 letters)



>FitnessBrowser__Cup4G11:RR42_RS24030
          Length = 298

 Score =  405 bits (1041), Expect = e-118
 Identities = 204/295 (69%), Positives = 237/295 (80%)

Query: 1   MRIAFIGLGNMGAPMARNLIKAGHQLNLFDLNKTVLAELAELGGQISPSPKDAAANSELV 60
           M IAFIGLGNMGAPMA NL+KAGH L +FDL+   +A     G   + SP++AAA ++LV
Sbjct: 1   MEIAFIGLGNMGAPMAANLLKAGHALTVFDLDANAVAAALLAGATSAGSPREAAARADLV 60

Query: 61  ITMLPAAAHVRSVYLNDDGVLAGIRPGTPTVDCSTIDPQTARDVSKAAAAKGVDMGDAPV 120
           ITMLPAAAHVR VYL +DGVLAG RPG P VDCSTIDP T R V++AAA++     DAPV
Sbjct: 61  ITMLPAAAHVRQVYLGEDGVLAGARPGVPMVDCSTIDPATVRTVAEAAASQDSPFADAPV 120

Query: 121 SGGTGGAAAGTLTFMVGASAELFASLKPVLEQMGRNIVHCGEVGTGQIAKICNNLLLGIS 180
           SGGTGGA AGTLTFMVGA   LF  ++PVL  MGRN+V CG  GTGQ+AKICNNLLLGIS
Sbjct: 121 SGGTGGAQAGTLTFMVGADQPLFERIRPVLLAMGRNVVPCGAPGTGQVAKICNNLLLGIS 180

Query: 181 MIGVSEAMALGNALGIDTKVLAGIINSSTGRCWSSDTYNPWPGIIETAPASRGYTGGFGA 240
           M+GVSEAMALG ALGID  VLAGIIN+STGRCWSSD+YNP+PG+   APA+RGY GGF A
Sbjct: 181 MMGVSEAMALGAALGIDPAVLAGIINTSTGRCWSSDSYNPYPGVQPAAPAARGYVGGFAA 240

Query: 241 ELMLKDLGLATEAARQAHQPVILGAVAQQLYQAMSLRGEGGKDFSAIVEGYRKKD 295
           +LMLKDLGLAT+AARQAHQP+ +GA+AQQLYQ+MS +G G  DFSA ++ Y K D
Sbjct: 241 DLMLKDLGLATDAARQAHQPLWMGALAQQLYQSMSQQGMGRLDFSACLKLYEKPD 295


Lambda     K      H
   0.317    0.134    0.386 

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: 362
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: 295
Length of database: 298
Length adjustment: 26
Effective length of query: 269
Effective length of database: 272
Effective search space:    73168
Effective search space used:    73168
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 (21.6 bits)
S2: 48 (23.1 bits)

Align candidate RR42_RS24030 RR42_RS24030 (3-hydroxyisobutyrate dehydrogenase)
to HMM TIGR01692 (mmsB: 3-hydroxyisobutyrate dehydrogenase (EC 1.1.1.31))

Software error:

../bin/blast/fastacmd -i /tmp/list.4788.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.4788.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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