Alignments for a candidate for adh in Marinobacter adhaerens HP15

GapMind for catabolism of small carbon sources

Alignments for a candidate for adh in Marinobacter adhaerens HP15

Align Aldehyde dehydrogenase (EC 1.2.1.3) (characterized)
to candidate GFF3202 HP15_3144 NAD-dependent aldehyde dehydrogenase

Query= reanno::Marino:GFF3202
         (533 letters)



>FitnessBrowser__Marino:GFF3202
          Length = 533

 Score = 1086 bits (2808), Expect = 0.0
 Identities = 533/533 (100%), Positives = 533/533 (100%)

Query: 1   MGIGVYIEWVNAKGRVALRQTQQEVEIMIYAQPGKDGSVVSFKSRYENYIGGEWVAPVKG 60
           MGIGVYIEWVNAKGRVALRQTQQEVEIMIYAQPGKDGSVVSFKSRYENYIGGEWVAPVKG
Sbjct: 1   MGIGVYIEWVNAKGRVALRQTQQEVEIMIYAQPGKDGSVVSFKSRYENYIGGEWVAPVKG 60

Query: 61  QYFENITPVTGNVICEIPRSSAEDIDLALDAAHKAAPAWGKTSPTERSNILLKIADRIEA 120
           QYFENITPVTGNVICEIPRSSAEDIDLALDAAHKAAPAWGKTSPTERSNILLKIADRIEA
Sbjct: 61  QYFENITPVTGNVICEIPRSSAEDIDLALDAAHKAAPAWGKTSPTERSNILLKIADRIEA 120

Query: 121 NLEKLAVAETWDNGKAVRETLNADIPLAADHFRYFAGCLRAQEGHMGEIDHNTVAYHFHE 180
           NLEKLAVAETWDNGKAVRETLNADIPLAADHFRYFAGCLRAQEGHMGEIDHNTVAYHFHE
Sbjct: 121 NLEKLAVAETWDNGKAVRETLNADIPLAADHFRYFAGCLRAQEGHMGEIDHNTVAYHFHE 180

Query: 181 PLGVVGQIIPWNFPILMAAWKLGPCLAAGNCTVLKPAEQTPASILVLMEIIGDLLPPGVL 240
           PLGVVGQIIPWNFPILMAAWKLGPCLAAGNCTVLKPAEQTPASILVLMEIIGDLLPPGVL
Sbjct: 181 PLGVVGQIIPWNFPILMAAWKLGPCLAAGNCTVLKPAEQTPASILVLMEIIGDLLPPGVL 240

Query: 241 NIVNGYGIEAGQALATSKRIAKIAFTGSTPVGSHILKCAAENIIPSTVELGGKSPNIYFS 300
           NIVNGYGIEAGQALATSKRIAKIAFTGSTPVGSHILKCAAENIIPSTVELGGKSPNIYFS
Sbjct: 241 NIVNGYGIEAGQALATSKRIAKIAFTGSTPVGSHILKCAAENIIPSTVELGGKSPNIYFS 300

Query: 301 DVMKAEPEFIDKCVEGLVLAFFNQGEVCTCPSRALVQEDMFEEFMQKVVQRTKSIKRGNP 360
           DVMKAEPEFIDKCVEGLVLAFFNQGEVCTCPSRALVQEDMFEEFMQKVVQRTKSIKRGNP
Sbjct: 301 DVMKAEPEFIDKCVEGLVLAFFNQGEVCTCPSRALVQEDMFEEFMQKVVQRTKSIKRGNP 360

Query: 361 LDTDVQVGAQASKEQFDKIMSYLAIGKEEGAVVLTGGDREHLDEEFNNGFYIQPTLFKGD 420
           LDTDVQVGAQASKEQFDKIMSYLAIGKEEGAVVLTGGDREHLDEEFNNGFYIQPTLFKGD
Sbjct: 361 LDTDVQVGAQASKEQFDKIMSYLAIGKEEGAVVLTGGDREHLDEEFNNGFYIQPTLFKGD 420

Query: 421 NKMRVFQEEIFGPVVGVTTFKTEEEALAIANDTEFGLGAGVWTRDTNLAYRMGRNIQAGR 480
           NKMRVFQEEIFGPVVGVTTFKTEEEALAIANDTEFGLGAGVWTRDTNLAYRMGRNIQAGR
Sbjct: 421 NKMRVFQEEIFGPVVGVTTFKTEEEALAIANDTEFGLGAGVWTRDTNLAYRMGRNIQAGR 480

Query: 481 VWMNCYHAYPAHAAFGGYKKSGVGRETHKMALEHYQQTKCMLTSYDTNPLGFF 533
           VWMNCYHAYPAHAAFGGYKKSGVGRETHKMALEHYQQTKCMLTSYDTNPLGFF
Sbjct: 481 VWMNCYHAYPAHAAFGGYKKSGVGRETHKMALEHYQQTKCMLTSYDTNPLGFF 533


Lambda     K      H
   0.319    0.136    0.412 

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: 1057
Number of extensions: 28
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: 533
Length of database: 533
Length adjustment: 35
Effective length of query: 498
Effective length of database: 498
Effective search space:   248004
Effective search space used:   248004
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: 52 (24.6 bits)

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

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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