GapMind for catabolism of small carbon sources

 

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

Align Inositol ABC transport system, permease protein IatP, component of The myoinositol (high affinity)/ D-ribose (low affinity) transporter IatP/IatA/IbpA. The structure of IbpA with myoinositol bound has been solved (characterized)
to candidate H281DRAFT_02703 H281DRAFT_02703 monosaccharide ABC transporter membrane protein, CUT2 family

Query= TCDB::B8H230
         (332 letters)



>FitnessBrowser__Burk376:H281DRAFT_02703
          Length = 333

 Score =  221 bits (563), Expect = 2e-62
 Identities = 122/300 (40%), Positives = 177/300 (59%)

Query: 32  LLLLVAVFGAANERFLTARNALNILSEVSIYGIIAVGMTFVILIGGIDVAVGSLLAFASI 91
           L+++      A+  FLT     NI+ +VS+ GI AVG TFVI+  GID++VGSL+A   +
Sbjct: 33  LVIICIALSIASPEFLTTSTLTNIMVQVSVVGIAAVGGTFVIITSGIDLSVGSLVALTGM 92

Query: 92  AAAYVVTAVVGDGPATWLIALLVSTLIGLAGGYVQGKAVTWLHVPAFIVTLGGMTVWRGA 151
            AA V+           +  L  +  +G A G + G AV WL +  FIVTL  M + RG 
Sbjct: 93  VAATVMAGSSPGAIGLGIAGLCAALAVGAAAGALNGLAVAWLRLVPFIVTLAMMAMARGL 152

Query: 152 TLLLNDGGPISGFNDAYRWWGSGEILFLPVPVVIFALVAAAGHVALRYTRYGRQVYAVGG 211
           TL ++DG     F +A+  +G+  +  LP+P+++  ++   GHV LR T +G QV+AVGG
Sbjct: 153 TLAISDGRTKFDFPNAFTAFGAKTVAGLPMPMIVMLVIFVIGHVLLRKTTFGHQVFAVGG 212

Query: 212 NAEAARLSGVNVDFITTSVYAIIGALAGLSGFLLSARLGSAEAVAGTGYELRVIASVVIG 271
           N EAARL+G+ V  +    Y + G  A ++G +L+ RL SA   A  G EL+VIA+VVIG
Sbjct: 213 NQEAARLAGIPVHRVVFLTYMLAGVTAAIAGIVLAGRLNSALPSAANGLELQVIAAVVIG 272

Query: 272 GASLTGGSGGVGGTVLGALLIGVLSNGLVMLHVTSYVQQVVIGLIIVAAVAFDHYARTHK 331
           G SL GG G + GT +G +LIGV++ GL +L V  +  Q + G +I AAV  D  ++  K
Sbjct: 273 GTSLAGGRGSIVGTFIGVVLIGVINVGLSLLGVNPFWTQFIQGGVIFAAVLLDALSQRRK 332


Lambda     K      H
   0.325    0.140    0.413 

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: 270
Number of extensions: 13
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: 332
Length of database: 333
Length adjustment: 28
Effective length of query: 304
Effective length of database: 305
Effective search space:    92720
Effective search space used:    92720
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 49 (23.5 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory