GapMind for catabolism of small carbon sources

 

Alignments for a candidate for deoC in Shewanella sp. ANA-3

Align deoxyribose-phosphate aldolase (EC 4.1.2.4) (characterized)
to candidate 7023821 Shewana3_1041 deoxyribose-phosphate aldolase (RefSeq)

Query= BRENDA::P0A6L0
         (259 letters)



>FitnessBrowser__ANA3:7023821
          Length = 256

 Score =  343 bits (880), Expect = 2e-99
 Identities = 179/252 (71%), Positives = 205/252 (81%), Gaps = 4/252 (1%)

Query: 1   MTDLKASSLRALKLMDLTTLNDDDTDEKVIALCHQAKTPVGNTAAICIYPRFIPIARKTL 60
           MTDLK ++ RA++LMDLTTLNDDDTD+KVI LCH+A TP GNTAAICIYPRFIPIARKTL
Sbjct: 1   MTDLKKAAQRAIELMDLTTLNDDDTDQKVIDLCHKAVTPAGNTAAICIYPRFIPIARKTL 60

Query: 61  KEQGTPEIRIATVTNFPHGNDDIDIALAETRAAIAYGADEVDVVFPYRALMAGNEQVGFD 120
            E G  +I+IATVTNFPHGNDDI IA+ ETRAA+AYGADEVDVVFPYRALM GNE VG++
Sbjct: 61  DELGAEDIQIATVTNFPHGNDDIAIAVLETRAAVAYGADEVDVVFPYRALMEGNESVGYE 120

Query: 121 LVKACKEACAAANVLLKVIIETGELKDEALIRKASEISIKAGADFIKTSTGKVAVNATPE 180
           LVKACKEAC   +VLLKVIIE+G L D ALIR+ASE+SI AGADFIKTSTGKV VNAT E
Sbjct: 121 LVKACKEAC--GDVLLKVIIESGVLADPALIRRASELSIDAGADFIKTSTGKVPVNATLE 178

Query: 181 SARIMMEVIRDMGVEKTVGFKPAGGVRTAEDAQKYLAIADELFGADWADARHYRFGASSL 240
           +A IM+ VI +   +  VGFKPAGGVR A  A ++L +A+ + GADW   R +RFGASSL
Sbjct: 179 AAEIMLTVISEKNTK--VGFKPAGGVRDAAQAAEFLGVAERILGADWVSPRTFRFGASSL 236

Query: 241 LASLLKALGHGD 252
           L SLL  L   D
Sbjct: 237 LNSLLHTLELAD 248


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: 223
Number of extensions: 7
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: 256
Length adjustment: 24
Effective length of query: 235
Effective length of database: 232
Effective search space:    54520
Effective search space used:    54520
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 7023821 Shewana3_1041 (deoxyribose-phosphate aldolase (RefSeq))
to HMM TIGR00126 (deoC: deoxyribose-phosphate aldolase (EC 4.1.2.4))

Software error:

../bin/blast/fastacmd -i /tmp/list.21214.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.21214.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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