GapMind for Amino acid biosynthesis

 

Alignments for a candidate for fbp in Desulfovibrio vulgaris Miyazaki F

Align fructose-bisphosphate aldolase (EC 4.1.2.13) (characterized)
to candidate 8499233 DvMF_0013 fructose-1,6-bisphosphate aldolase, class II (RefSeq)

Query= BRENDA::O97447
         (323 letters)



>FitnessBrowser__Miya:8499233
          Length = 307

 Score =  291 bits (746), Expect = 1e-83
 Identities = 158/301 (52%), Positives = 204/301 (67%), Gaps = 5/301 (1%)

Query: 1   MPLCTLRQMLGEARKHKYGVGAFNVNNMEQIQGIMKAVVQLKSPVILQCSRGALKYSDMI 60
           MPL   +QM   A K  Y +GAFNVNNME IQGIM+A  + ++P+ILQ S GA KY+   
Sbjct: 1   MPLTGPKQMFERAYKEGYAIGAFNVNNMEIIQGIMQAAGEEQAPLILQVSAGARKYAGQN 60

Query: 61  YLKKLCEAALEKHPDIPICIHLDHGDTLESVKMAIDLGFSSVMIDASHHPFDENVRITKE 120
           Y+ KL EAAL    D+P+ +HLDHG      K  ID GF+SVM D SH P++EN+ +T++
Sbjct: 61  YIVKLIEAAL-MDTDLPVVLHLDHGQDFNICKDCIDGGFTSVMYDGSHLPYEENIAVTRQ 119

Query: 121 VVAYAHARSVSVEAELGTLGGIEEDVQNTVQL-TEPQDAKKFVELTGVDALAVAIGTSHG 179
           VV YAHAR V VEAELG L G+E++V     + T+P  A  FV+ TG D+LA+AIGTSHG
Sbjct: 120 VVEYAHARGVWVEAELGQLAGVEDEVSAEHSVYTDPDQAVDFVKRTGCDSLAIAIGTSHG 179

Query: 180 AYKFKSESDIRLAIDRVKTISD-LTGIPLVMHGSSSVPKDVKDMINKYGGKMPDAVGVPI 238
           AYKF  E+ +  A  R++ I+  L G PLV+HG+SSVP++  DM N YGGK+  A GVP 
Sbjct: 180 AYKFTGEAKLDFA--RLEKITSMLPGYPLVLHGASSVPQEFVDMANTYGGKVGSAKGVPE 237

Query: 239 ESIVHAIGEGVCKINVDSDSRMAMTGAIRKVFVEHPEKFDPRDYLGPGRDAITEMLIPKI 298
           + +  A   GVCKIN+D+D R+AMT  IRK F+E P  FDPR YL P RDA+  M+  KI
Sbjct: 238 DLLRKAATYGVCKINIDTDIRLAMTATIRKHFMEKPADFDPRAYLKPARDAVKNMVQHKI 297

Query: 299 K 299
           +
Sbjct: 298 R 298


Lambda     K      H
   0.318    0.135    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: 285
Number of extensions: 10
Number of successful extensions: 4
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: 323
Length of database: 307
Length adjustment: 27
Effective length of query: 296
Effective length of database: 280
Effective search space:    82880
Effective search space used:    82880
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 8499233 DvMF_0013 (fructose-1,6-bisphosphate aldolase, class II (RefSeq))
to HMM TIGR01859 (fba: fructose-1,6-bisphosphate aldolase, class II (EC 4.1.2.13))

Software error:

../bin/blast/fastacmd -i /tmp/list.27278.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.27278.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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