GapMind for catabolism of small carbon sources

 

Alignments for a candidate for tpi in Dechlorosoma suillum PS

Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate Dsui_3052 Dsui_3052 triosephosphate isomerase

Query= BRENDA::P0A858
         (255 letters)



>FitnessBrowser__PS:Dsui_3052
          Length = 241

 Score =  240 bits (613), Expect = 2e-68
 Identities = 128/238 (53%), Positives = 163/238 (68%), Gaps = 3/238 (1%)

Query: 12  LNGSRHMVHELVSNLRKELAGVAGCAVAIAPPEMYIDMAKREAEGSHIMLGAQNVDLNLS 71
           L  +R ++  +V+ + K LA    CAV +  P  Y+  A++E   + +  GAQN+   +S
Sbjct: 5   LAANRSLLQGVVAGV-KGLAAAVECAVCVPYP--YLAQAQQELAKTEVSWGAQNLSEQVS 61

Query: 72  GAFTGETSAAMLKDIGAQYIIIGHSERRTYHKESDELIAKKFAVLKEQGLTPVLCIGETE 131
           GAFTGE SAAMLKD G +Y+I+GHSERR  + E D L+AKKF      GL P+LC+GET 
Sbjct: 62  GAFTGEVSAAMLKDFGCRYVIVGHSERRALYGEDDGLVAKKFKQALAGGLVPILCVGETL 121

Query: 132 AENEAGKTEEVCARQIDAVLKTQGAAAFEGAVIAYEPVWAIGTGKSATPAQAQAVHKFIR 191
           A+ E+G+  EV A Q+DAVL   G   F GAV+AYEPVWAIGTG +A+PAQAQAVH+ IR
Sbjct: 122 AQRESGQAAEVVAAQLDAVLDAAGVEVFAGAVVAYEPVWAIGTGLTASPAQAQAVHEGIR 181

Query: 192 DHIAKVDANIAEQVIIQYGGSVNASNAAELFAQPDIDGALVGGASLKADAFAVIVKAA 249
             +A  +A +A  V + YGGSV A NAAELFA PDIDGALVGGASL A+ F  I +AA
Sbjct: 182 ARLAARNAEVAAGVRVLYGGSVKAGNAAELFAMPDIDGALVGGASLVAEEFVAICRAA 239


Lambda     K      H
   0.316    0.130    0.366 

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: 195
Number of extensions: 9
Number of successful extensions: 2
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: 255
Length of database: 241
Length adjustment: 24
Effective length of query: 231
Effective length of database: 217
Effective search space:    50127
Effective search space used:    50127
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 Dsui_3052 Dsui_3052 (triosephosphate isomerase)
to HMM TIGR00419 (tpiA: triose-phosphate isomerase (EC 5.3.1.1))

Software error:

../bin/blast/fastacmd -i /tmp/list.12591.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.12591.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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