GapMind for catabolism of small carbon sources

 

Alignments for a candidate for galK in Shewanella amazonensis SB2B

Align galactose kinase (characterized)
to candidate 6936347 Sama_0536 galactokinase (RefSeq)

Query= CharProtDB::CH_024146
         (382 letters)



>FitnessBrowser__SB2B:6936347
          Length = 382

 Score =  314 bits (804), Expect = 3e-90
 Identities = 161/377 (42%), Positives = 229/377 (60%), Gaps = 3/377 (0%)

Query: 5   EKTQSLFANAFGYPATHTIQAPGRVNLIGEHTDYNDGFVLPCAIDYQTVISCAPRDDRKV 64
           ++   LF   FG  A    QAPGRVN+IGEHTDYNDGFVLP AI++ TVI+   R+D + 
Sbjct: 6   QRATKLFVQTFGTKADAYYQAPGRVNIIGEHTDYNDGFVLPAAINFHTVIAVKKREDDRF 65

Query: 65  RVMAADYENQLDEFSLDAPIVAHENYQWANYVRGVVKHLQLRNNSFGGVDMVISGNVPQG 124
           RV+   +  +L E+             W NY++G  + +        G+D+ +  ++P G
Sbjct: 66  RVVTEAFPGELREWRFGEEGEVTAGGDWVNYLKGFTQAVGQAGLKAKGLDLAVVSSIPMG 125

Query: 125 AGLSSSASLEVAVGTVLQQLYHLPLDGAQIALNGQEAENQFVGCNCGIMDQLISALGKKD 184
           AG SSS +LE+A GT L     L L    IA   Q  E++F G  CG+MD + SAL + D
Sbjct: 126 AGFSSSGALEIAFGTALNDTCQLHLSPMAIAQLAQRGESRFHGSTCGVMDHMTSALAEAD 185

Query: 185 HALLIDCRSLGTKAVSMPKGVAVVIINSNFKRTLVGSEYNTRREQCETGARFFQQPALRD 244
            ALLIDC  L  +AV +P  ++++I++S     L+   Y  R ++C   A FF   +LRD
Sbjct: 186 SALLIDCLDLDIEAVLIPDNLSLIIVHSPLDPKLLEEAYKARADECRDAAEFFGLDSLRD 245

Query: 245 VTIEEFNAVAHELDPIVAKRVRHILTENARTVEAASALEQGDLKRMGELMAESHASMRDD 304
           + ++E  A +  LD  + KR RH+++EN RT  A  AL++GD+ R+ ELMA SHAS+RDD
Sbjct: 246 LELDELKAASDVLDETLYKRARHVISENLRTQSAGRALKRGDVARLSELMALSHASLRDD 305

Query: 305 FEITVPQIDTLVEIVKAVIGDKGGVRMTGGGFGGCIVALIPEELVPAVQQAVAEQYEAKT 364
           FE+ VP+++TLV+I+   IGD+GGVRMT    G  +VAL+  +L  AV  AV  +Y AKT
Sbjct: 306 FELMVPEVETLVQIMAQAIGDRGGVRMTD---GCSVVALVEHDLTDAVVHAVESEYPAKT 362

Query: 365 GIKETFYVCKPSQGAGQ 381
           G++   Y+C PS GAG+
Sbjct: 363 GLEPVLYMCAPSAGAGR 379


Lambda     K      H
   0.318    0.134    0.389 

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: 314
Number of extensions: 13
Number of successful extensions: 3
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: 382
Length of database: 382
Length adjustment: 30
Effective length of query: 352
Effective length of database: 352
Effective search space:   123904
Effective search space used:   123904
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 (21.7 bits)
S2: 50 (23.9 bits)

Align candidate 6936347 Sama_0536 (galactokinase (RefSeq))
to HMM TIGR00131 (galK: galactokinase (EC 2.7.1.6))

Software error:

../bin/blast/fastacmd -i /tmp/list.2850.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.2850.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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