GapMind for catabolism of small carbon sources

 

Alignments for a candidate for tpi in Sphingomonas koreensis DSMZ 15582

Align Triosephosphate isomerase; TIM; TPI; Triose-phosphate isomerase; EC 5.3.1.1 (characterized)
to candidate Ga0059261_0254 Ga0059261_0254 triosephosphate isomerase (EC 5.3.1.1)

Query= SwissProt::Q8L1Z5
         (254 letters)



>FitnessBrowser__Korea:Ga0059261_0254
          Length = 248

 Score =  221 bits (564), Expect = 8e-63
 Identities = 123/245 (50%), Positives = 163/245 (66%), Gaps = 5/245 (2%)

Query: 6   RPFIAGNWKMNGTGESLGELRAIAAGISSDLGRLFEALICVPATLLSRAFDILGGENILL 65
           R  +AGNWKM+G   +L E+ AIA   +   G   +A +CVPATL++ A  +     + +
Sbjct: 3   RKLVAGNWKMHGLIAALPEIEAIAQAAAVTPG--VDAALCVPATLIAPAVTVAA--RMPI 58

Query: 66  GGQNCHFDDYGPYTGDISAFMLKEAGASHVIIGHSERRTVYQESDAIVRAKVQAAWRAGL 125
           GGQ+CH  D G +TG ISA ML+EAGA+  I+GHSERR    E+DA V+ K +AA R GL
Sbjct: 59  GGQDCHAADQGAHTGCISAAMLREAGAALTIVGHSERRANQGETDADVKGKAEAAHRHGL 118

Query: 126 VALICVGETLEERKSNKVLDVLTRQLEGSLPDGATAENIIIAYEPVWAVGTGNTATSADV 185
            A++CVGETLE+R + +   V+T QL GS+P+GA A+ + IAYEPVWA+GTG T T ADV
Sbjct: 119 NAILCVGETLEQRDAGQAEAVVTAQLAGSMPEGAAADWLSIAYEPVWAIGTGRTPTEADV 178

Query: 186 AEVHAFIHHKMHSRFGDE-GAKIRLLYGGSVKPSNAFELLSTAHVNGALIGGASLKAIDF 244
           A +H  I  K+    G E  A +R+LYGGSV  +NA  LL  A V+GAL+GGASL A  F
Sbjct: 179 AAMHGAIRAKLTELLGGETAAAMRVLYGGSVNGANAASLLGCADVDGALVGGASLTAEKF 238

Query: 245 LTICD 249
           + I +
Sbjct: 239 VPIIE 243


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: 233
Number of extensions: 8
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: 254
Length of database: 248
Length adjustment: 24
Effective length of query: 230
Effective length of database: 224
Effective search space:    51520
Effective search space used:    51520
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 Ga0059261_0254 Ga0059261_0254 (triosephosphate isomerase (EC 5.3.1.1))
to HMM TIGR00419 (tpiA: triose-phosphate isomerase (EC 5.3.1.1))

Software error:

../bin/blast/fastacmd -i /tmp/list.32437.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.32437.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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