GapMind for catabolism of small carbon sources

 

Alignments for a candidate for tpi in Sinorhizobium meliloti 1021

Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate SMc01614 SMc01614 triosephosphate isomerase

Query= BRENDA::Q7X216
         (265 letters)



>FitnessBrowser__Smeli:SMc01614
          Length = 255

 Score =  203 bits (517), Expect = 3e-57
 Identities = 116/255 (45%), Positives = 158/255 (61%), Gaps = 8/255 (3%)

Query: 5   IWLGTSWKMNKPLSQAMAWCETLAARMPEGCHPAIQPFVIPSFTAIQPVSHFLQTHQLPL 64
           +W+GTSWKMNK L++AM + + LAA   +     IQ FVIP FTA + V   L+   + +
Sbjct: 6   LWVGTSWKMNKTLAEAMVFADGLAAA-DDARDQRIQRFVIPPFTAARQVKERLKATSVKV 64

Query: 65  LTGAQNMHEADQGAWTGEISAAMLAETGATLVELGHSERRAAFNESDAAINRKVHSALGH 124
             GAQNMH  D GAWTGEIS  ML++    +VELGHSERR  F E+D  +  K  +A+ H
Sbjct: 65  --GAQNMHWDDAGAWTGEISPVMLSDCDLDIVELGHSERREHFGETDRTVGLKTAAAVKH 122

Query: 125 GLRPLICIGDSAEEKRWQVSRESVVRQMKIALYGL-SHQQALRTLIAYEPVWAIGEHGTP 183
           GL PLICIG++  ++    +   + RQ++ A   L    +    L+AYEPVWAIG +G P
Sbjct: 123 GLVPLICIGETLAQREAGEADTVLKRQVEGAFAFLEGAARKAPVLLAYEPVWAIGVNGIP 182

Query: 184 ASPQEAGVIHQALRQALCERFGHETGTRIPLLYGGXVTLQNAVELLRQQEINGLFIGRAA 243
           A+   A   H+ + + + ER     G ++P+LYGG V  QN  EL+ Q  I+GLFIGR+A
Sbjct: 183 ATADYADARHRLIGE-VAER---ALGVKVPVLYGGSVNPQNCEELILQPHIDGLFIGRSA 238

Query: 244 WDAQGYCDIVQRVTQ 258
           WD  GY DI+QRV +
Sbjct: 239 WDVGGYLDILQRVAR 253


Lambda     K      H
   0.321    0.133    0.412 

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: 231
Number of extensions: 9
Number of successful extensions: 5
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: 265
Length of database: 255
Length adjustment: 24
Effective length of query: 241
Effective length of database: 231
Effective search space:    55671
Effective search space used:    55671
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 (21.9 bits)
S2: 47 (22.7 bits)

Align candidate SMc01614 SMc01614 (triosephosphate isomerase)
to HMM TIGR00419 (tpiA: triose-phosphate isomerase (EC 5.3.1.1))

Software error:

../bin/blast/fastacmd -i /tmp/list.28136.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.28136.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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