GapMind for catabolism of small carbon sources

 

Alignments for a candidate for tpi in Pseudomonas stutzeri RCH2

Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate GFF946 Psest_0975 triosephosphate isomerase

Query= BRENDA::P0A858
         (255 letters)



>FitnessBrowser__psRCH2:GFF946
          Length = 251

 Score =  235 bits (600), Expect = 6e-67
 Identities = 123/250 (49%), Positives = 165/250 (66%), Gaps = 2/250 (0%)

Query: 1   MRHPLVMGNWKLNGSRHMVHELVSNLRKELAGVAGCAVAIAPPEMYIDMAKREAEGSHIM 60
           MR P+V GNWK+NG+R  V ELV +LR +   V+   +A+ P  +++       +  H+ 
Sbjct: 1   MRRPMVAGNWKMNGTRASVAELVESLRMQALPVS-VEIAVFPSCLHVAQVLGGVDSKHVA 59

Query: 61  LGAQNVDL-NLSGAFTGETSAAMLKDIGAQYIIIGHSERRTYHKESDELIAKKFAVLKEQ 119
           +GAQ+    N  GA TGE SA    ++G +++++GHSERR    E+DE++++KF   +  
Sbjct: 60  VGAQDCAAQNGFGALTGEVSAEQFAEVGCEWVLVGHSERRLVLGETDEVVSRKFLAAQVG 119

Query: 120 GLTPVLCIGETEAENEAGKTEEVCARQIDAVLKTQGAAAFEGAVIAYEPVWAIGTGKSAT 179
           GL PVLC+GET  E EAG+T EV  RQ+  VL   G A FE AVIAYEPVWAIG+G +AT
Sbjct: 120 GLKPVLCLGETLEEREAGRTLEVVGRQLAQVLDDHGIAVFESAVIAYEPVWAIGSGLTAT 179

Query: 180 PAQAQAVHKFIRDHIAKVDANIAEQVIIQYGGSVNASNAAELFAQPDIDGALVGGASLKA 239
           P QAQ VH  IR+ +++ D  +A  V + YGGSV A NAAELF+  DIDG LVGGASLKA
Sbjct: 180 PEQAQEVHAAIREQLSRQDRQVAAGVRLLYGGSVKADNAAELFSMADIDGGLVGGASLKA 239

Query: 240 DAFAVIVKAA 249
           + F  I +AA
Sbjct: 240 NEFGAICRAA 249


Lambda     K      H
   0.316    0.130    0.366 

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: 180
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: 255
Length of database: 251
Length adjustment: 24
Effective length of query: 231
Effective length of database: 227
Effective search space:    52437
Effective search space used:    52437
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 GFF946 Psest_0975 (triosephosphate isomerase)
to HMM TIGR00419 (tpiA: triose-phosphate isomerase (EC 5.3.1.1))

Software error:

../bin/blast/fastacmd -i /tmp/list.23497.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.23497.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.