GapMind for catabolism of small carbon sources

 

Alignments for a candidate for tpi in Pseudomonas fluorescens GW456-L13

Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate PfGW456L13_5091 Triosephosphate isomerase (EC 5.3.1.1)

Query= BRENDA::P0A858
         (255 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_5091
          Length = 247

 Score =  231 bits (589), Expect = 1e-65
 Identities = 123/246 (50%), Positives = 163/246 (66%), Gaps = 2/246 (0%)

Query: 5   LVMGNWKLNGSRHMVHELVSNLRKELAGVAGCAVAIAPPEMYIDMAKREAEGSHIMLGAQ 64
           +V GNWK++G+R  V EL++ LR +LA  +   VA+ PP ++I+      EG  I +GAQ
Sbjct: 1   MVAGNWKMHGTRASVAELINGLR-DLALPSSVDVAVFPPFLHINQVIEGLEGKSISVGAQ 59

Query: 65  NVDLNLS-GAFTGETSAAMLKDIGAQYIIIGHSERRTYHKESDELIAKKFAVLKEQGLTP 123
           N  +    GA TGE + + L D G   +++GHSERR    E D ++ +KFA  +  GLTP
Sbjct: 60  NSAVESGQGALTGEVAPSQLVDAGCSLVLVGHSERRQILGEQDAVLIRKFAAAQACGLTP 119

Query: 124 VLCIGETEAENEAGKTEEVCARQIDAVLKTQGAAAFEGAVIAYEPVWAIGTGKSATPAQA 183
           VLCIGET  + EAGKT EV +RQ+ ++++  G  AF  AVIAYEPVWAIGTG +ATP QA
Sbjct: 120 VLCIGETLEQREAGKTLEVVSRQLGSIIEELGVGAFAKAVIAYEPVWAIGTGLTATPQQA 179

Query: 184 QAVHKFIRDHIAKVDANIAEQVIIQYGGSVNASNAAELFAQPDIDGALVGGASLKADAFA 243
           Q VH  IR  +A  ++ +A+ V + YGGSV A+NA ELF  PDIDG L+GGASL AD F 
Sbjct: 180 QDVHAAIRAQLAAENSEVAQGVRLLYGGSVKAANAVELFGMPDIDGGLIGGASLNADEFG 239

Query: 244 VIVKAA 249
            I +AA
Sbjct: 240 AICRAA 245


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: 187
Number of extensions: 9
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: 247
Length adjustment: 24
Effective length of query: 231
Effective length of database: 223
Effective search space:    51513
Effective search space used:    51513
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 PfGW456L13_5091 (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.18181.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.18181.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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