Alignments for a candidate for etoh-dh-nad in Rhizobium leguminosarum 3841

GapMind for catabolism of small carbon sources

Alignments for a candidate for etoh-dh-nad in Rhizobium leguminosarum 3841

Align furfuryl alcohol dehydrogenase (EC 1.1.1.1) (characterized)
to candidate WP_041936742.1 RL_RS26020 alcohol dehydrogenase AdhP

Query= metacyc::MONOMER-17184
         (342 letters)



>NCBI__GCF_000009265.1:WP_041936742.1
          Length = 360

 Score =  456 bits (1172), Expect = e-133
 Identities = 221/339 (65%), Positives = 264/339 (77%), Gaps = 1/339 (0%)

Query: 4   MMKAAVVRAFGAPLTIDEVPVPQPGPGQVQVKIEASGVCHTDLHAADGDWPVKPTLPFIP 63
           +MKAAVVR FG PL I+ VPVP PGPG++ VK+ A GVCHTDLHAADGDWPVKPT PFIP
Sbjct: 8   LMKAAVVREFGKPLAIECVPVPVPGPGEILVKVVACGVCHTDLHAADGDWPVKPTPPFIP 67

Query: 64  GHEGVGYVSAVGSGVSRVKEGDRVGVPWLYSACGYCEHCLQGWETLCEKQQNTGYSVNGG 123
           GHE  G V+A+GSGV+  KEGD VGV WL+ AC  CE+C  GWETLCE Q NTGYS NGG
Sbjct: 68  GHEAAGIVAALGSGVTEFKEGDAVGVAWLHDACLRCEYCETGWETLCEHQHNTGYSCNGG 127

Query: 124 YGEYVVADPNYVGLLPDKVGFVEIAPILCAGVTVYKGLKVTDTRPGQWVVISGIGGLGHV 183
           + EYV+A   +   LP  V F EIAPILCAGVT YKGLK T+ RPG+WV ISG+GGLGHV
Sbjct: 128 FAEYVIASAAFAARLPQNVNFSEIAPILCAGVTTYKGLKETEARPGEWVAISGVGGLGHV 187

Query: 184 AVQYARAMGLRVAAVDIDDAKLNLARRLGAEVAVNARDTDPAAWLQK-EIGGAHGVLVTA 242
           A+QYA+AMGL+V A+D+  AKL+LAR++GA++A+N    D    + K   GGAHGVLVTA
Sbjct: 188 AIQYAKAMGLKVVALDVAAAKLDLARQVGADLALNVLSEDTIEKVLKVTSGGAHGVLVTA 247

Query: 243 VSPKAFSQAIGMVRRGGTIALNGLPPGDFGTPIFDVVLKGITIRGSIVGTRSDLQESLDF 302
           VSP AFSQA+ MVRR GT++L GLPPG+F  PIFDVVLK IT+RGSIVGTR DL E+L F
Sbjct: 248 VSPPAFSQALSMVRRKGTVSLVGLPPGNFPMPIFDVVLKRITVRGSIVGTRRDLDEALAF 307

Query: 303 AAHGDVKATVSTAKLDDVNDVFGRLREGKVEGRVVLDFS 341
           A  G V+A ++ A LDD+ND+F  L+ G +EGR+VLD +
Sbjct: 308 ATEGRVRAEIAKAPLDDINDIFAGLKAGTIEGRMVLDIA 346


Lambda     K      H
   0.319    0.139    0.427 

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: 405
Number of extensions: 16
Number of successful extensions: 2
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: 342
Length of database: 360
Length adjustment: 29
Effective length of query: 313
Effective length of database: 331
Effective search space:   103603
Effective search space used:   103603
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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources