GapMind for catabolism of small carbon sources

 

Alignments for a candidate for tpi in Caulobacter crescentus NA1000

Align Triosephosphate isomerase; TIM; TPI; Triose-phosphate isomerase; EC 5.3.1.1 (characterized)
to candidate CCNA_01970 CCNA_01970 triosephosphate isomerase

Query= SwissProt::Q8L1Z5
         (254 letters)



>FitnessBrowser__Caulo:CCNA_01970
          Length = 253

 Score =  223 bits (569), Expect = 2e-63
 Identities = 117/242 (48%), Positives = 158/242 (65%), Gaps = 1/242 (0%)

Query: 6   RPFIAGNWKMNGTGESLGELRAIAAGISSDLGRLFEALICVPATLLSRAFDILGGENILL 65
           RP IAGNWKMNG   +L E RA+AA + +       A+   PATLL R    + G ++L 
Sbjct: 9   RPLIAGNWKMNGLSVALDEARAVAAALEAKPPAARVAIF-PPATLLHRLSQAVEGAHLLT 67

Query: 66  GGQNCHFDDYGPYTGDISAFMLKEAGASHVIIGHSERRTVYQESDAIVRAKVQAAWRAGL 125
           GGQ+CH    G +TGD+SA M+ +AG S VI GHSERRT + E+ A V  K +AA  AGL
Sbjct: 68  GGQDCHGKSSGAHTGDVSAEMVADAGGSLVICGHSERRTDHGETSAQVAGKAEAAAAAGL 127

Query: 126 VALICVGETLEERKSNKVLDVLTRQLEGSLPDGATAENIIIAYEPVWAVGTGNTATSADV 185
             ++CVGETLE R++ + +  +  Q+  SLP     +   +AYEP+WA+GTG TA+  ++
Sbjct: 128 EPIVCVGETLETREAGQAVSFVVSQVRDSLPTSLAGKAFSVAYEPLWAIGTGRTASVDNI 187

Query: 186 AEVHAFIHHKMHSRFGDEGAKIRLLYGGSVKPSNAFELLSTAHVNGALIGGASLKAIDFL 245
            E+HA I  ++ SRF ++G  + +LYGGSVKP NA E+L+   V GAL+GGASLKA DFL
Sbjct: 188 VEMHAAIRAELVSRFCEQGRTVLILYGGSVKPENAREILAAPEVGGALVGGASLKAKDFL 247

Query: 246 TI 247
            I
Sbjct: 248 AI 249


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: 218
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: 254
Length of database: 253
Length adjustment: 24
Effective length of query: 230
Effective length of database: 229
Effective search space:    52670
Effective search space used:    52670
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 CCNA_01970 CCNA_01970 (triosephosphate isomerase)
to HMM TIGR00419 (tpiA: triose-phosphate isomerase (EC 5.3.1.1))

Software error:

../bin/blast/fastacmd -i /tmp/list.29263.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.29263.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.