GapMind for catabolism of small carbon sources

 

Alignments for a candidate for tpi in Marinobacter adhaerens HP15

Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate GFF2201 HP15_2155 triosephosphate isomerase

Query= BRENDA::P0A858
         (255 letters)



>FitnessBrowser__Marino:GFF2201
          Length = 268

 Score =  209 bits (531), Expect = 6e-59
 Identities = 112/258 (43%), Positives = 161/258 (62%), Gaps = 6/258 (2%)

Query: 1   MRHPLVMGNWKLNGSRHMVHELVSNLRKELAGVAGCA-VAIAPPEMYIDMAKREAEGSHI 59
           MR P+++GNWK+NGS      L+  +   L        + + PP  Y+   +     + I
Sbjct: 1   MRKPILIGNWKMNGSLQANQALMVRVLPRLRMFRKSVDLVVCPPHPYLFQVRDLLGYTGI 60

Query: 60  MLGAQNVDLNLSGAFTGETSAAMLKDIGAQYIIIGHSERRTYHKESDELIAKKFAVLKEQ 119
           MLGAQN    +SGA+TGE SA ML+++G +Y ++GHSERR    E ++ +A ++  + + 
Sbjct: 61  MLGAQNASGFVSGAYTGEVSATMLQEMGCRYALVGHSERRLLFGEGNQEVAARYRSVLQS 120

Query: 120 GLTPVLCIGETEAENEAGKTEEVCARQIDAVLKTQGAAAFEGAVIAYEPVWAIGTGKSAT 179
           GLTPVLC+GET  + E+G+T  +  +Q+ AV+   G AA    ++AYEPVWAIGTGK+AT
Sbjct: 121 GLTPVLCVGETLEDRESGRTGLIIEQQLQAVIDEVGLAAMANGIVAYEPVWAIGTGKTAT 180

Query: 180 PAQAQAVHKFIRDHIAKVDA----NIAEQVIIQYGGSVNASNAAELFAQPDIDGALVGGA 235
           P Q   VH+ IR  +AK       +I+E++ + YGGSV  +NA ELF+  D+DG L+GGA
Sbjct: 181 PEQVSEVHQQIRQFLAKSAPESADDISEELRVIYGGSVKVANAYELFSLADVDGGLIGGA 240

Query: 236 SLKADAFAVIVKA-AEAA 252
           SL AD F  I  A AEA+
Sbjct: 241 SLHADEFGTIAGALAEAS 258


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: 190
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: 255
Length of database: 268
Length adjustment: 25
Effective length of query: 230
Effective length of database: 243
Effective search space:    55890
Effective search space used:    55890
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: 47 (22.7 bits)

Align candidate GFF2201 HP15_2155 (triosephosphate isomerase)
to HMM TIGR00419 (tpiA: triose-phosphate isomerase (EC 5.3.1.1))

Software error:

../bin/blast/fastacmd -i /tmp/list.6769.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.6769.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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