GapMind for catabolism of small carbon sources

 

Alignments for a candidate for tpi in Desulfovibrio vulgaris Miyazaki F

Align Triosephosphate isomerase; TIM; TPI; Triose-phosphate isomerase; EC 5.3.1.1 (characterized)
to candidate 8499579 DvMF_0348 Triose-phosphate isomerase (RefSeq)

Query= SwissProt::Q5SJR1
         (250 letters)



>FitnessBrowser__Miya:8499579
          Length = 251

 Score =  197 bits (502), Expect = 1e-55
 Identities = 113/247 (45%), Positives = 144/247 (58%), Gaps = 6/247 (2%)

Query: 5   LVAGNWKMHKTPSEARVWFAELKRLLP---PLQSEAAVLPAFPIL-PVAKEVLAETQVGY 60
           L+A NWKM+KT  EAR   A L  L     P   E  + P F  L PVA  +   T    
Sbjct: 4   LMAANWKMYKTAGEARTTAASLAALTADTLPDDREVVIFPQFTALSPVADALRHATGYSV 63

Query: 61  GAQDVSAHKEGAYTGEVSARMLSDLGCRYAIVGHSERRRYHGETDALVAEKAKRLLEEGI 120
           G QDV    EGAYTGE+S  ML D GC + + GHSERR   GE+D LV  K    +  G+
Sbjct: 64  GGQDVYPAAEGAYTGEISPGMLMDCGCAWVLTGHSERRHVIGESDELVGAKTAFSINAGL 123

Query: 121 TPILCVGEPLEVREKGEAVPYTLRQLRGSLEGVEPPG-PEALVIAYEPVWAIGTGKNATP 179
             +LC+GE +E RE G       RQL   L GV+    P A+ +AYEPVWAIGTGK A P
Sbjct: 124 KVVLCIGETIEEREAGRLGEVLERQLETGLAGVKGDAVPAAIAVAYEPVWAIGTGKVAGP 183

Query: 180 EDAEAMHQAIRKALSERYGEAFASRVRILYGGSVNPKNFADLLSMPNVDGGLVGGASLEL 239
            +    H  +R+ L  R+GE   + VRILYGGSV P+N  +++++ NVDG LVGGASL+ 
Sbjct: 184 PEIVEAHALVRQLLVARFGEGGVA-VRILYGGSVKPENAREIIALDNVDGVLVGGASLQA 242

Query: 240 ESFLALL 246
           +SF  ++
Sbjct: 243 DSFSRII 249


Lambda     K      H
   0.317    0.135    0.393 

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: 205
Number of extensions: 11
Number of successful extensions: 4
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: 250
Length of database: 251
Length adjustment: 24
Effective length of query: 226
Effective length of database: 227
Effective search space:    51302
Effective search space used:    51302
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 8499579 DvMF_0348 (Triose-phosphate isomerase (RefSeq))
to HMM TIGR00419 (tpiA: triose-phosphate isomerase (EC 5.3.1.1))

Software error:

../bin/blast/fastacmd -i /tmp/list.12593.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.12593.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.