GapMind for catabolism of small carbon sources

 

Alignments for a candidate for tpi in Burkholderia phytofirmans PsJN

Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate BPHYT_RS06610 BPHYT_RS06610 triosephosphate isomerase

Query= BRENDA::P0A858
         (255 letters)



>FitnessBrowser__BFirm:BPHYT_RS06610
          Length = 259

 Score =  216 bits (549), Expect = 5e-61
 Identities = 123/257 (47%), Positives = 156/257 (60%), Gaps = 6/257 (2%)

Query: 2   RHPLVMGNWKLNG---SRHMVHELVSNLRKELAGVAGCAVAIAPPEMYIDMAKREAEGSH 58
           R  LV+GNWK++G       + + V++   EL   A   V +  P  Y+  ++   EGS 
Sbjct: 5   RAKLVVGNWKMHGRLAENATLLQAVAHGAGELP--ADVRVGVCVPSPYLAQSQSLLEGSR 62

Query: 59  IMLGAQNVDLNLSGAFTGETSAAMLKDIGAQYIIIGHSERRTYHKESDELIAKKFAVLKE 118
           ++ G Q+V     GA+TGE +A M+ D GA   I+GHSERR YH+ES EL+A K     E
Sbjct: 63  VVWGVQDVSAFTHGAYTGEVAAPMVVDFGATLAIVGHSERRAYHRESAELVAVKTQRALE 122

Query: 119 QGLTPVLCIGETEAENEAGKTEEVCARQIDAVLKTQGAAAFEGAVIAYEPVWAIGTGKSA 178
            GLTP++C+GET  E EAG TE+V   Q+D VL           V+AYEPVWAIGTGKSA
Sbjct: 123 AGLTPIVCVGETLEEREAGLTEQVVGTQLDEVLAKLSVQEAARLVVAYEPVWAIGTGKSA 182

Query: 179 TPAQAQAVHKFIRDHIAKVDANIAEQVIIQYGGSVNASNAAELFAQPDIDGALVGGASLK 238
           +  QAQAVH F+R  +A   A +A+ V + YGGSV   NA ELF QPDIDG L+GGASLK
Sbjct: 183 SSEQAQAVHAFLRARLAAKGAAVAD-VPLLYGGSVKPENAEELFRQPDIDGGLIGGASLK 241

Query: 239 ADAFAVIVKAAEAAKQA 255
              F  I KAA A   A
Sbjct: 242 DQDFLAICKAAAATSVA 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: 191
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 BPHYT_RS06610 BPHYT_RS06610 (triosephosphate isomerase)
to HMM TIGR00419 (tpiA: triose-phosphate isomerase (EC 5.3.1.1))

Software error:

../bin/blast/fastacmd -i /tmp/list.5342.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.5342.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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