GapMind for catabolism of small carbon sources

 

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

Align deoxyribose-phosphate aldolase (EC 4.1.2.4) (characterized)
to candidate 5210372 Shew_2815 deoxyribose-phosphate aldolase (RefSeq)

Query= BRENDA::P0A6L0
         (259 letters)



>FitnessBrowser__PV4:5210372
          Length = 257

 Score =  343 bits (881), Expect = 2e-99
 Identities = 179/248 (72%), Positives = 206/248 (83%), Gaps = 3/248 (1%)

Query: 1   MTDLKASSLRALKLMDLTTLNDDDTDEKVIALCHQAKTPVGNTAAICIYPRFIPIARKTL 60
           M+DLK ++ +A++LMDLTTLNDDDTD+KVI LCH+AKTP GNTAAICIYPRFIPIARKTL
Sbjct: 1   MSDLKKAAQKAIELMDLTTLNDDDTDQKVIELCHKAKTPAGNTAAICIYPRFIPIARKTL 60

Query: 61  KEQGTPEIRIATVTNFPHGNDDIDIALAETRAAIAYGADEVDVVFPYRALMAGNEQVGFD 120
            E G  EI+IATVTNFPHGNDDI IA+ ETRAA+AYGADEVDVVFPYRALM GNE VG++
Sbjct: 61  NEMGCEEIKIATVTNFPHGNDDIAIAVLETRAAVAYGADEVDVVFPYRALMEGNETVGYE 120

Query: 121 LVKACKEACAAANVLLKVIIETGELKDEALIRKASEISIKAGADFIKTSTGKVAVNATPE 180
           LVKACKEAC   +VLLKVIIE+G L+D ALIRKASE+SI AGADFIKTSTGKV VNAT E
Sbjct: 121 LVKACKEAC-GDDVLLKVIIESGVLQDPALIRKASELSIDAGADFIKTSTGKVEVNATLE 179

Query: 181 SARIMMEVIRDMGVEKTVGFKPAGGVRTAEDAQKYLAIADELFGADWADARHYRFGASSL 240
           +A IMM VI +   +  VGFKPAGGVR A  A+++L +A+ L G  WA  R +RFGASSL
Sbjct: 180 AAEIMMTVIAEKNPK--VGFKPAGGVRDAAAAEEFLGVAERLLGKGWATPRTFRFGASSL 237

Query: 241 LASLLKAL 248
           L +LL  L
Sbjct: 238 LNNLLHTL 245


Lambda     K      H
   0.317    0.133    0.373 

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: 242
Number of extensions: 5
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: 259
Length of database: 257
Length adjustment: 24
Effective length of query: 235
Effective length of database: 233
Effective search space:    54755
Effective search space used:    54755
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: 47 (22.7 bits)

Align candidate 5210372 Shew_2815 (deoxyribose-phosphate aldolase (RefSeq))
to HMM TIGR00126 (deoC: deoxyribose-phosphate aldolase (EC 4.1.2.4))

Software error:

../bin/blast/fastacmd -i /tmp/list.16549.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.16549.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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