GapMind for catabolism of small carbon sources

 

Alignments for a candidate for tpi in Acidovorax sp. GW101-3H11

Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate Ac3H11_1454 Triosephosphate isomerase (EC 5.3.1.1)

Query= BRENDA::Q10657
         (247 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_1454
          Length = 249

 Score =  223 bits (568), Expect = 3e-63
 Identities = 128/247 (51%), Positives = 166/247 (67%), Gaps = 7/247 (2%)

Query: 3   RKFFVGGNWKMNGDYASVDGIVTFLNASADNSSVDVVVAPPAPYLAYAKSKLKAG--VLV 60
           +K  + GNWKMNG  A+ + ++  L A   + + DV VA PAPYLA  ++ L AG  V V
Sbjct: 4   KKKLIAGNWKMNGSLAANEVLLKALIAGLGDVTCDVAVAVPAPYLAQVQA-LTAGTAVAV 62

Query: 61  AAQNCYKVPKGAFTGEISPAMIKDLGLEWVILGHSERRHVFGESDALIAEKTVHALEAGI 120
           AAQ+  +   GA+TGE+S AM+KD G+ + ++GHSERR   GE+D  +AEK   AL AG+
Sbjct: 63  AAQDVSRYESGAYTGEVSVAMLKDFGVRYALVGHSERRQYHGETDVAVAEKAQRALAAGV 122

Query: 121 KVVFCIGEKLEEREAGHTKDVNFRQLQAIVD-KGVSWENIVIAYEPVWAIGTGKTASGEQ 179
             + C+GE LEEREAG T+ V  RQL A++   G     IV+AYEPVWAIGTG+TAS EQ
Sbjct: 123 TPIVCVGETLEEREAGQTEAVVKRQLAAVIHLNGHCISEIVVAYEPVWAIGTGRTASPEQ 182

Query: 180 AQEVHEWIRAFLKEKVSPAVADATRIIYGGSVTADNAAELGKKPDIDGFLVGGASLK-PD 238
           AQ VH  +RA L    +   AD  R++YGGS+ A NAA+L  +PDIDG LVGGASLK  D
Sbjct: 183 AQAVHAVLRAQL--AAASEHADRIRLLYGGSMNAGNAAQLLAQPDIDGGLVGGASLKAAD 240

Query: 239 FVKIINA 245
           F++II A
Sbjct: 241 FLQIIAA 247


Lambda     K      H
   0.317    0.134    0.396 

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: 187
Number of extensions: 11
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: 247
Length of database: 249
Length adjustment: 24
Effective length of query: 223
Effective length of database: 225
Effective search space:    50175
Effective search space used:    50175
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 (21.6 bits)
S2: 46 (22.3 bits)

Align candidate Ac3H11_1454 (Triosephosphate isomerase (EC 5.3.1.1))
to HMM TIGR00419 (tpiA: triose-phosphate isomerase (EC 5.3.1.1))

Software error:

../bin/blast/fastacmd -i /tmp/list.9807.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.9807.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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