GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xdhA in Phaeobacter inhibens BS107

Align Sorbitol dehydrogenase; SDH; Polyol dehydrogenase; Ribitol dehydrogenase; RDH; Xylitol dehydrogenase; XDH; EC 1.1.1.-; EC 1.1.1.56; EC 1.1.1.9 (characterized)
to candidate GFF759 PGA1_c07730 putative zinc-binding alcohol dehydrogenase

Query= SwissProt::Q9FJ95
         (364 letters)



>FitnessBrowser__Phaeo:GFF759
          Length = 326

 Score =  122 bits (306), Expect = 1e-32
 Identities = 88/293 (30%), Positives = 133/293 (45%), Gaps = 34/293 (11%)

Query: 25  GINTLKIQPFLLPSVGPHDVRVRMKAVGICGSDVH-YLKTMRCADFVVKEPMVIGHECAG 83
           G+ TL  +   + +  P +  +R+ A GICGSD+H YL      D     P+++GHE AG
Sbjct: 8   GVETLVFRDVPMVAARPGEHLIRIHASGICGSDMHAYLGH----DNRRPAPLILGHEAAG 63

Query: 84  IIEEVGEEVKHLVVGDRVALEPGISCWRCNLCREGRYNLCPEMKFFATPPVHGSLANQVV 143
            IE+  +       G RV + P ++C  C  C  GR NLC   +  + PP  G+ A  V 
Sbjct: 64  TIEDGPQ------AGRRVTINPLVTCGSCAACAAGRENLCASRQIISMPPREGAFAQFVA 117

Query: 144 HPADLCFKLPENVSLEEGAMCEPLSVGVHACRRA----EVGPETNVLVMGAGPIGLVTML 199
            P      +PE+V L + A+ EPL+V  HA R A        E   LV+G G IGL   L
Sbjct: 118 MPERNLVTVPEDVPLSKAALAEPLAVSWHAARLALKALHPDMERRALVIGGGAIGLAAAL 177

Query: 200 AARAFSVPRIVIVDVDENRLA-VAKQLGADEIVQVTTNLEDVGSEVEQIQKAMGSNIDVT 258
           A RA  V  + + + +  R A +A   G   +           +E + I       + + 
Sbjct: 178 ALRAMGVEDVAVQEPNAARRAFLADHCGQQAV-----------AEFQGI-------VPLV 219

Query: 259 FDCAGFNKTMSTALAATRCGGKVCLVGMGHGIMTVPLTPAAAREVDVVGVFRY 311
            D  G+  T + A AA   GG +  VG+G     + +     +E+  +G + Y
Sbjct: 220 LDAVGYAATRAAASAAAAPGGVIAHVGLGEDAGGLDIRRMTLQEITFIGTYTY 272


Lambda     K      H
   0.321    0.137    0.417 

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: 312
Number of extensions: 24
Number of successful extensions: 4
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: 364
Length of database: 326
Length adjustment: 29
Effective length of query: 335
Effective length of database: 297
Effective search space:    99495
Effective search space used:    99495
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 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