GapMind for catabolism of small carbon sources

 

Alignments for a candidate for tpi in Paraburkholderia bryophila 376MFSha3.1

Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate H281DRAFT_04564 H281DRAFT_04564 triosephosphate isomerase

Query= BRENDA::P0A858
         (255 letters)



>FitnessBrowser__Burk376:H281DRAFT_04564
          Length = 259

 Score =  221 bits (562), Expect = 2e-62
 Identities = 123/255 (48%), Positives = 155/255 (60%), Gaps = 2/255 (0%)

Query: 2   RHPLVMGNWKLNGSRHMVHELVSNLRKELAGV-AGCAVAIAPPEMYIDMAKREAEGSHIM 60
           R  LV+GNWK++G       L+  + K  A + A   V +  P  Y+  A+   EGS ++
Sbjct: 5   RAKLVVGNWKMHGCLADNAGLLQAVAKGAAELPADVRVGVCVPSPYLAQAQSLLEGSRVV 64

Query: 61  LGAQNVDLNLSGAFTGETSAAMLKDIGAQYIIIGHSERRTYHKESDELIAKKFAVLKEQG 120
            G Q++     GA+TGE +A M+ D  A + I+GHSERR YH+ES EL+A K     E G
Sbjct: 65  WGVQDISAFTHGAYTGEVAAQMVADFSAAFAIVGHSERRAYHRESAELVAVKTQRALEAG 124

Query: 121 LTPVLCIGETEAENEAGKTEEVCARQIDAVLKTQGAAAFEGAVIAYEPVWAIGTGKSATP 180
           LTP++C+GET  E EAG TE+V   Q+D VL    A      V+AYEPVWAIGTGKSAT 
Sbjct: 125 LTPIVCVGETLEEREAGSTEQVVGAQLDEVLAKLSAEEAAHIVVAYEPVWAIGTGKSATS 184

Query: 181 AQAQAVHKFIRDHIAKVDANIAEQVIIQYGGSVNASNAAELFAQPDIDGALVGGASLKAD 240
            QAQAVH F+R  +A   A +A  V + YGGSV   NA ELF+Q DIDG L+GGASLK  
Sbjct: 185 EQAQAVHAFLRSRLAAKGAGVA-NVTLLYGGSVKPDNAEELFSQQDIDGGLIGGASLKDK 243

Query: 241 AFAVIVKAAEAAKQA 255
            F  I KAA A   A
Sbjct: 244 DFLAICKAAAATTAA 258


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: 203
Number of extensions: 10
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: 259
Length adjustment: 24
Effective length of query: 231
Effective length of database: 235
Effective search space:    54285
Effective search space used:    54285
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 H281DRAFT_04564 H281DRAFT_04564 (triosephosphate isomerase)
to HMM TIGR00419 (tpiA: triose-phosphate isomerase (EC 5.3.1.1))

Software error:

../bin/blast/fastacmd -i /tmp/list.21316.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.21316.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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