GapMind for catabolism of small carbon sources

 

Alignments for a candidate for tpi in Echinicola vietnamensis KMM 6221, DSM 17526

Align Triosephosphate isomerase; TIM; TPI; Triose-phosphate isomerase; EC 5.3.1.1 (characterized)
to candidate Echvi_1196 Echvi_1196 triosephosphate isomerase

Query= SwissProt::Q8XKU1
         (248 letters)



>FitnessBrowser__Cola:Echvi_1196
          Length = 253

 Score =  238 bits (608), Expect = 7e-68
 Identities = 128/250 (51%), Positives = 164/250 (65%), Gaps = 4/250 (1%)

Query: 1   MRTPIIAGNWKMHYTIDEAVKLVEELKPLVKDAKCE---VVVCPTFVCLDAVKKAVEGT- 56
           MR  I+AGNWKM+ T +E  KL  E+  +VKD +     VV+ P FV    VKK + G  
Sbjct: 1   MRKKIVAGNWKMNGTQEEGQKLTSEIVNMVKDERISDVTVVLNPPFVHASNVKKLIGGVD 60

Query: 57  NIKVGAQNMHFEEKGAFTGEIAPRMLEAMNIDYVIIGHSERREYFNETDETCNKKVKAAF 116
           NI +G QN   +  GA+TGE +  +L +    YVIIGHSERREYF E++E   +KVK A 
Sbjct: 61  NIFLGGQNCSDKASGAYTGETSASILASFGATYVIIGHSERREYFAESNEQLTEKVKLAL 120

Query: 117 AHNLTPILCCGETLEQRENGTTNDVIKAQITADLEGLTKEQAEKVVIAYEPIWAIGTGKT 176
            + LTPI CCGE LE RE GT    +K Q+T  L GL++E   K+VIAYEPIWAIGTGKT
Sbjct: 121 ENGLTPIFCCGEPLEIREAGTHEAYVKDQLTESLFGLSEEDFAKIVIAYEPIWAIGTGKT 180

Query: 177 ATSDQANETIAAIRAMVAEMFGQEVADKVRIQYGGSVKPNTIAEQMAKSDIDGALVGGAS 236
           A+SDQA E  AAIRA +A  +G+++A+   I YGGS KP+   E  +K D+DG L+GGAS
Sbjct: 181 ASSDQAQEMHAAIRAHLASKYGEKIAEGTSILYGGSCKPDNAPEIFSKPDVDGGLIGGAS 240

Query: 237 LVAADFAQIV 246
           L + DF  I+
Sbjct: 241 LKSRDFVDII 250


Lambda     K      H
   0.316    0.131    0.376 

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: 8
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: 248
Length of database: 253
Length adjustment: 24
Effective length of query: 224
Effective length of database: 229
Effective search space:    51296
Effective search space used:    51296
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 Echvi_1196 Echvi_1196 (triosephosphate isomerase)
to HMM TIGR00419 (tpiA: triose-phosphate isomerase (EC 5.3.1.1))

Software error:

../bin/blast/fastacmd -i /tmp/list.1192.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.1192.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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