GapMind for catabolism of small carbon sources

 

Alignments for a candidate for tpi in Herbaspirillum seropedicae SmR1

Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate HSERO_RS08805 HSERO_RS08805 triosephosphate isomerase

Query= BRENDA::P0A858
         (255 letters)



>FitnessBrowser__HerbieS:HSERO_RS08805
          Length = 238

 Score =  210 bits (535), Expect = 2e-59
 Identities = 111/238 (46%), Positives = 147/238 (61%), Gaps = 1/238 (0%)

Query: 12  LNGSRHMVHELVSNLRKELAGVAGCAVAIAPPEMYIDMAKREAEGSHIMLGAQNVDLNLS 71
           +NGS      LV+ +++ LA  A C VA+  P  Y+   +    GS + LGAQ++  + S
Sbjct: 1   MNGSLAANAALVAGIKEGLAAQA-CDVAVCVPAPYLAQVQALVAGSPVGLGAQDMSAHAS 59

Query: 72  GAFTGETSAAMLKDIGAQYIIIGHSERRTYHKESDELIAKKFAVLKEQGLTPVLCIGETE 131
           GA+TGE SA+ML++ G QY+I+GHSERR YH ESD  +A K     + GL P++C+GET 
Sbjct: 60  GAYTGEVSASMLQEFGVQYVILGHSERRAYHGESDAAVAAKTVAALKAGLVPLVCVGETL 119

Query: 132 AENEAGKTEEVCARQIDAVLKTQGAAAFEGAVIAYEPVWAIGTGKSATPAQAQAVHKFIR 191
            + EAG+T  V   Q+D VL    A      V+AYEPVWAIGTGK+ATP  AQ VH  +R
Sbjct: 120 EQREAGQTNAVVGGQLDVVLAALSAEEAARIVVAYEPVWAIGTGKTATPEMAQEVHAMLR 179

Query: 192 DHIAKVDANIAEQVIIQYGGSVNASNAAELFAQPDIDGALVGGASLKADAFAVIVKAA 249
             +    A  A +V I YGGS+   NA +L A  DIDG L+GGA+LKA  F  I+ AA
Sbjct: 180 ARLGAKSAEAAAKVCILYGGSMKPDNAQQLLAMGDIDGGLIGGAALKAADFLAIINAA 237


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: 184
Number of extensions: 6
Number of successful extensions: 1
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: 238
Length adjustment: 24
Effective length of query: 231
Effective length of database: 214
Effective search space:    49434
Effective search space used:    49434
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 HSERO_RS08805 HSERO_RS08805 (triosephosphate isomerase)
to HMM TIGR00419 (tpiA: triose-phosphate isomerase (EC 5.3.1.1))

Software error:

../bin/blast/fastacmd -i /tmp/list.1138.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.1138.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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