GapMind for catabolism of small carbon sources

 

Alignments for a candidate for tpi in Dinoroseobacter shibae DFL-12

Align Triosephosphate isomerase; TIM; TPI; Triose-phosphate isomerase; EC 5.3.1.1 (characterized)
to candidate 3608685 Dshi_2078 Triose-phosphate isomerase (RefSeq)

Query= SwissProt::Q8L1Z5
         (254 letters)



>FitnessBrowser__Dino:3608685
          Length = 247

 Score =  231 bits (590), Expect = 8e-66
 Identities = 123/243 (50%), Positives = 160/243 (65%), Gaps = 4/243 (1%)

Query: 6   RPFIAGNWKMNGTGESLGELRAIAAGISSDLGRLFEALICVPATLLSRAFDILGGENILL 65
           R   AGNWKMNG   +L E  AI A  ++D     E L+C PATLL+       G  + +
Sbjct: 3   RKLAAGNWKMNGLRAALAEAEAITAAAAADGP---EVLLCPPATLLAPMAAQAEGTALQI 59

Query: 66  GGQNCHFDDYGPYTGDISAFMLKEAGASHVIIGHSERRTVYQESDAIVRAKVQAAWRAGL 125
           GGQ CH    G +TG +SA ML++AGAS+VI+GHSERR    E DA VRA+  AAW+AGL
Sbjct: 60  GGQYCHPAPSGAHTGHVSAPMLRDAGASYVIVGHSERRQDDGERDADVRAQTLAAWQAGL 119

Query: 126 VALICVGETLEERKSNKVLDVLTRQLEGSLPDGATAENIIIAYEPVWAVGTGNTATSADV 185
            A++CVGET  ER +   L ++  QL GS+PD AT  N+++AYEPVWA+GTG   +   +
Sbjct: 120 TAIVCVGETEAERDAANTLAIIGGQLAGSIPDTATGANLVVAYEPVWAIGTGRVPSVDQI 179

Query: 186 AEVHAFIHHKMHSRFGD-EGAKIRLLYGGSVKPSNAFELLSTAHVNGALIGGASLKAIDF 244
            EVH FI  ++  RFG+  G  +RLLYGGSVKP  A E+ + ++V+GAL+GGASLKA DF
Sbjct: 180 GEVHDFIRARLEQRFGEGVGRSVRLLYGGSVKPGIAAEIFAVSNVDGALVGGASLKAADF 239

Query: 245 LTI 247
             I
Sbjct: 240 TGI 242


Lambda     K      H
   0.320    0.137    0.403 

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: 247
Number of extensions: 10
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: 254
Length of database: 247
Length adjustment: 24
Effective length of query: 230
Effective length of database: 223
Effective search space:    51290
Effective search space used:    51290
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 (21.8 bits)
S2: 46 (22.3 bits)

Align candidate 3608685 Dshi_2078 (Triose-phosphate isomerase (RefSeq))
to HMM TIGR00419 (tpiA: triose-phosphate isomerase (EC 5.3.1.1))

Software error:

../bin/blast/fastacmd -i /tmp/list.28439.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.28439.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

For help, please send mail to the webmaster (help@microbesonline.org), giving this error message and the time and date of the error.