GapMind for catabolism of small carbon sources

 

Alignments for a candidate for tpi in Marinobacter adhaerens HP15

Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate GFF3129 HP15_3071 triosephosphate isomerase

Query= BRENDA::P0A858
         (255 letters)



>FitnessBrowser__Marino:GFF3129
          Length = 252

 Score =  218 bits (556), Expect = 7e-62
 Identities = 119/252 (47%), Positives = 160/252 (63%), Gaps = 3/252 (1%)

Query: 1   MRHPLVMGNWKLNGSRHMVHELVSNLRKELAGVA-GCAVAIAPPEMYIDMAKREAEGSHI 59
           MR  +V GNWK+NGS+ +   LVS++R + A +  G  V I PP +Y+      A G  +
Sbjct: 1   MRRKIVAGNWKMNGSKDLAQTLVSDVRSQAASLDNGVEVVIIPPAIYVPDVVASA-GDVL 59

Query: 60  MLGAQNVDLNLSGAFTGETSAAMLKDIGAQYIIIGHSERRTYHKESDELIAKKFAVLKEQ 119
            +G QNV    SGA+TGE SA M  D G QY ++GHSERR    E+D  +A+K   +   
Sbjct: 60  SVGVQNVAQWASGAYTGEISADMALDQGCQYALVGHSERRQLFAETDAAVAEKVGRILAS 119

Query: 120 GLTPVLCIGETEAENEAGKTEEVCARQIDAVLKTQGAAAFEGAVIAYEPVWAIGTGKSAT 179
           GL  ++C+GET  E EAGK E V A Q+ A L T  +  ++  V+AYEPVWAIGTGK+AT
Sbjct: 120 GLQAMVCVGETLEEREAGKAETVVAAQVKAGLATVASEQWQRVVVAYEPVWAIGTGKTAT 179

Query: 180 PAQAQAVHKFIRDHIAKVDANIAEQVIIQYGGSVNASNAAELFAQPDIDGALVGGASLKA 239
              AQA+H  IR  ++++ A  A ++ + YGGSV A NAA LFA+PDIDG L+GGASLKA
Sbjct: 180 AQDAQAMHASIRQVLSEMGAP-ANEISLLYGGSVKADNAAALFAEPDIDGGLIGGASLKA 238

Query: 240 DAFAVIVKAAEA 251
           + F  I ++  A
Sbjct: 239 EDFVSICRSVPA 250


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: 158
Number of extensions: 7
Number of successful extensions: 3
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: 252
Length adjustment: 24
Effective length of query: 231
Effective length of database: 228
Effective search space:    52668
Effective search space used:    52668
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: 47 (22.7 bits)

Align candidate GFF3129 HP15_3071 (triosephosphate isomerase)
to HMM TIGR00419 (tpiA: triose-phosphate isomerase (EC 5.3.1.1))

Software error:

../bin/blast/fastacmd -i /tmp/list.25998.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.25998.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.