GapMind for catabolism of small carbon sources

 

Alignments for a candidate for tpi in Sinorhizobium meliloti 1021

Align Triosephosphate isomerase; TIM; TPI; Triose-phosphate isomerase; EC 5.3.1.1 (characterized)
to candidate SMc01023 SMc01023 triosephosphate isomerase

Query= SwissProt::Q8L1Z5
         (254 letters)



>FitnessBrowser__Smeli:SMc01023
          Length = 256

 Score =  295 bits (754), Expect = 8e-85
 Identities = 147/254 (57%), Positives = 188/254 (74%)

Query: 1   MSPNIRPFIAGNWKMNGTGESLGELRAIAAGISSDLGRLFEALICVPATLLSRAFDILGG 60
           M+P+IRP +AGNWKMNGT  SL +++A+A G+  DL    +ALIC PATLL  A  +   
Sbjct: 1   MTPDIRPLVAGNWKMNGTRASLDQIKAMAEGVKGDLSARVDALICPPATLLYVATALCDD 60

Query: 61  ENILLGGQNCHFDDYGPYTGDISAFMLKEAGASHVIIGHSERRTVYQESDAIVRAKVQAA 120
             +++G Q+CH    G +TG++SA M+ +   +HVI+GHSERRT + E DA+VRAK +AA
Sbjct: 61  SPLMIGAQDCHQKQSGAHTGEVSAEMVADCFGTHVIVGHSERRTDHGEGDALVRAKTEAA 120

Query: 121 WRAGLVALICVGETLEERKSNKVLDVLTRQLEGSLPDGATAENIIIAYEPVWAVGTGNTA 180
             A LVA++CVGET EERK+ + LD+L RQL  SLPD ATAEN +IAYEPVWA+GTG T 
Sbjct: 121 HGADLVAIVCVGETEEERKAGRTLDILKRQLSESLPDQATAENTVIAYEPVWAIGTGLTP 180

Query: 181 TSADVAEVHAFIHHKMHSRFGDEGAKIRLLYGGSVKPSNAFELLSTAHVNGALIGGASLK 240
           T +DV E HAF+  ++ SRFG EG K+R+LYGGSVKPSNA EL+  A+V+GALIGGASLK
Sbjct: 181 TVSDVEEAHAFMRRELVSRFGAEGGKMRILYGGSVKPSNAKELMGVANVDGALIGGASLK 240

Query: 241 AIDFLTICDVYRKL 254
           A DFL I   Y +L
Sbjct: 241 ADDFLAIYRAYEEL 254


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: 252
Number of extensions: 12
Number of successful extensions: 1
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: 256
Length adjustment: 24
Effective length of query: 230
Effective length of database: 232
Effective search space:    53360
Effective search space used:    53360
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: 47 (22.7 bits)

Align candidate SMc01023 SMc01023 (triosephosphate isomerase)
to HMM TIGR00419 (tpiA: triose-phosphate isomerase (EC 5.3.1.1))

Software error:

../bin/blast/fastacmd -i /tmp/list.5744.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.5744.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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