GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xdhA in Skermanella stibiiresistens SB22

Align Sorbitol dehydrogenase; SDH; (R,R)-butanediol dehydrogenase; L-iditol 2-dehydrogenase; Polyol dehydrogenase; Ribitol dehydrogenase; RDH; Xylitol dehydrogenase; XDH; EC 1.1.1.-; EC 1.1.1.4; EC 1.1.1.14; EC 1.1.1.56; EC 1.1.1.9 (characterized)
to candidate WP_037449134.1 N825_RS07515 L-idonate 5-dehydrogenase

Query= SwissProt::Q00796
         (357 letters)



>NCBI__GCF_000576635.1:WP_037449134.1
          Length = 343

 Score =  222 bits (566), Expect = 1e-62
 Identities = 122/331 (36%), Positives = 195/331 (58%), Gaps = 8/331 (2%)

Query: 10  LSLVVHGPGDLRLENYPIPEPGPNEVLLRMHSVGICGSDVHYWEYGRIGNFIVKKPMVLG 69
           L +V+H P DLR+E  P    GP +V +R+ S GICGSD+HY+ +G  G   +++PM LG
Sbjct: 2   LGVVIHAPKDLRVEEIPATPLGPRDVQVRIASGGICGSDLHYYHHGGFGVVRIREPMALG 61

Query: 70  HEASGTVEKVGSSVKHLKPGDRVAIEPGAPRENDEFCKMGRYNLSPSIFFCAT----PPD 125
           HE +GTVEKVG+ V  +  G RVA+ P  P ++  +C+ G+ N    + F  +    P  
Sbjct: 62  HEIAGTVEKVGAEVSRVTVGQRVAVNPSRPCDDCRYCRAGQRNQCLDMRFIGSAMRFPHV 121

Query: 126 DGNLCRFYKHNAAFCYKLPDNVTFEEGALIEPLSVGIHACRRGGVTLGHKVLVCGAGPIG 185
            G   +    +      +   +T  E A+ EPL+V +HA  R G  +G +VLV G GPIG
Sbjct: 122 QGGFRQALAVDERQAIPIAPGMTMAEAAMAEPLAVCLHAASRAGSLMGARVLVTGCGPIG 181

Query: 186 MVTLLVAKAMGAAQVVVTDLSATRLSKAKEIGADLVLQISKESPQEIARKVEGQLGCKPE 245
            + ++ A+  GAA++VVTD+SA  LS A+ +GA   + I+ E P+ +A   + + G   +
Sbjct: 182 ALAVVAARFGGAAEIVVTDVSAYPLSLARSVGATHAINIA-EDPKALAPYGQDKGGF--D 238

Query: 246 VTIECTGAEASIQAGIYATRSGGNLVLVGLGSEMTTVPLLHAAIREVDIKGVFRYCNTWP 305
           V  E +G EA++   + A R GG +V +GLG +M  +P+     +E+ ++G FR+   + 
Sbjct: 239 VLFEASGNEAALLGALEAVRPGGIVVQLGLGGDM-KLPINLIVAKEIQLRGTFRFDGEFQ 297

Query: 306 VAISMLASKSVNVKPLVTHRFPLEKALEAFE 336
           +A+ ++ S  ++VKPLV+   P ++A+EAFE
Sbjct: 298 LAVDLMGSGLIDVKPLVSQTIPFQRAVEAFE 328


Lambda     K      H
   0.319    0.137    0.415 

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: 330
Number of extensions: 19
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: 357
Length of database: 343
Length adjustment: 29
Effective length of query: 328
Effective length of database: 314
Effective search space:   102992
Effective search space used:   102992
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 (21.7 bits)
S2: 49 (23.5 bits)

This GapMind analysis is from Sep 24 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