GapMind for catabolism of small carbon sources

 

Aligments for a candidate for etoh-dh-nad in Bacteroides thetaiotaomicron VPI-5482

Align Alcohol dehydrogenase 2; EC 1.1.1.1; Alcohol dehydrogenase II; ADH II (uncharacterized)
to candidate 353293 BT3767 lactaldehyde reductase (NCBI ptt file)

Query= curated2:F8DVL8
         (383 letters)



>lcl|FitnessBrowser__Btheta:353293 BT3767 lactaldehyde reductase
           (NCBI ptt file)
          Length = 384

 Score =  305 bits (780), Expect = 2e-87
 Identities = 166/357 (46%), Positives = 222/357 (62%), Gaps = 3/357 (0%)

Query: 30  GFKNALIVSDAFMNKSGVVKQVADLLKTQGINSAVYDGVMPNPTVTAVLEGLKILKDNNS 89
           GFK A  V+D  + K GV  ++  +     I   +Y  V  NPT+  V  G+   K + +
Sbjct: 28  GFKKAFFVTDKDLIKFGVAAEIIKVFDDNHIPYELYSDVKANPTIANVQNGVAAYKASGA 87

Query: 90  DFVISLGGGSPHDCAKAIALVATNG--GEVKDYEGIDKSKKPALPLMSINTTAGTASEMT 147
           DF+++LGGGS  D AK I +V  N    +VK  EG+  +K  A+P  ++ TTAGTA+E+T
Sbjct: 88  DFIVALGGGSSIDTAKGIGIVVNNPDFADVKSLEGVADTKHKAVPTFALPTTAGTAAEVT 147

Query: 148 RFCIITDEVRHVKMAIVDRHVTPMVSVNDPLLMVGMPKGLTAATGMDALTHAFEAYSSTA 207
              +I DE    KM  VD +  P V++ DP LM  MPKGLTAATGMDALTHA E+Y +  
Sbjct: 148 INYVIIDEDARKKMVCVDPNDIPAVAIVDPELMYSMPKGLTAATGMDALTHAIESYITPG 207

Query: 208 ATPITDACALKAASMIAKNLKTACDNGKDMPAREAMAYAQFLAGMAFNNASLGYVHAMAH 267
           A  ++D   LKA  MIA+NLK A DNGKD  AREAM+ AQ++AGM F+N  LG VH+MAH
Sbjct: 208 AWAMSDMFELKAIEMIAQNLKAAVDNGKDTVAREAMSQAQYIAGMGFSNVGLGIVHSMAH 267

Query: 268 QLGGYYNLPHGVCNAVLLPHVLAYNA-SVVAGRLKDVGVAMGLDIANLGDKEGAEATIQA 326
            LG +Y+ PHGV NA+LLP+V+ YNA S  A +   +  AMG++   + + EG +A I+A
Sbjct: 268 PLGAFYDTPHGVANALLLPYVMEYNAESPAAPKYIHIAKAMGVNTDGMTETEGVKAAIEA 327

Query: 327 VRDLAASIGIPANLTELGAKKEDVPLLADHALKDACALTNPRQGDQKEVEELFLSAF 383
           V+ L+ SIGIP  L E+  K+ED+P LA  A  D C   NPR     E+E L+  AF
Sbjct: 328 VKALSLSIGIPQKLHEINVKEEDIPALAVAAFNDVCTGGNPRPTSVAEIEVLYRKAF 384


Lambda     K      H
   0.316    0.132    0.373 

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: 375
Number of extensions: 16
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: 383
Length of database: 384
Length adjustment: 30
Effective length of query: 353
Effective length of database: 354
Effective search space:   124962
Effective search space used:   124962
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: 50 (23.9 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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