Aligments for a candidate for rhaB in Dinoroseobacter shibae DFL-12

GapMind for catabolism of small carbon sources

Aligments for a candidate for rhaB in Dinoroseobacter shibae DFL-12

Align Rhamnulokinase RhaK in alpha-proteobacteria (EC 2.7.1.5) (characterized)
to candidate 3609040 Dshi_2429 carbohydrate kinase FGGY (RefSeq)

Query= reanno::Dino:3609040
         (461 letters)



>FitnessBrowser__Dino:3609040
          Length = 461

 Score =  937 bits (2421), Expect = 0.0
 Identities = 461/461 (100%), Positives = 461/461 (100%)

Query: 1   MTRHVAVIDIGKTNAKLALVDRQSLTEISVITRPNTVLPGPPWPHFDVDGHWAFLLDGLR 60
           MTRHVAVIDIGKTNAKLALVDRQSLTEISVITRPNTVLPGPPWPHFDVDGHWAFLLDGLR
Sbjct: 1   MTRHVAVIDIGKTNAKLALVDRQSLTEISVITRPNTVLPGPPWPHFDVDGHWAFLLDGLR 60

Query: 61  DFQARHGIDAISITTHGACAALLQKDGALAAPILDYEHPGPDDTALAYDALRPPFSETGS 120
           DFQARHGIDAISITTHGACAALLQKDGALAAPILDYEHPGPDDTALAYDALRPPFSETGS
Sbjct: 61  DFQARHGIDAISITTHGACAALLQKDGALAAPILDYEHPGPDDTALAYDALRPPFSETGS 120

Query: 121 PRLAGGLNIGAQLFWQFHTDPALRDRTRQIVTYPQFWGAKLTGVTATDVTSLGCHTDLWN 180
           PRLAGGLNIGAQLFWQFHTDPALRDRTRQIVTYPQFWGAKLTGVTATDVTSLGCHTDLWN
Sbjct: 121 PRLAGGLNIGAQLFWQFHTDPALRDRTRQIVTYPQFWGAKLTGVTATDVTSLGCHTDLWN 180

Query: 181 PHAGAVSSLVDRLGLTGKLAPVRKPHDILGPVLPAVAAQTGLAPGTPVHCGIHDSNASLL 240
           PHAGAVSSLVDRLGLTGKLAPVRKPHDILGPVLPAVAAQTGLAPGTPVHCGIHDSNASLL
Sbjct: 181 PHAGAVSSLVDRLGLTGKLAPVRKPHDILGPVLPAVAAQTGLAPGTPVHCGIHDSNASLL 240

Query: 241 PYVLTQTSPFSVISTGTWVVAMSVGGRPVVLDPDLDTLINVTALGQPAPSARFMGGREHD 300
           PYVLTQTSPFSVISTGTWVVAMSVGGRPVVLDPDLDTLINVTALGQPAPSARFMGGREHD
Sbjct: 241 PYVLTQTSPFSVISTGTWVVAMSVGGRPVVLDPDLDTLINVTALGQPAPSARFMGGREHD 300

Query: 301 LATEGTGPPPSAQDLDHILSRQILLLPAVVPDTGPFKGQASRWEGDAPAPGTGARGAAVA 360
           LATEGTGPPPSAQDLDHILSRQILLLPAVVPDTGPFKGQASRWEGDAPAPGTGARGAAVA
Sbjct: 301 LATEGTGPPPSAQDLDHILSRQILLLPAVVPDTGPFKGQASRWEGDAPAPGTGARGAAVA 360

Query: 361 LYLALVTAECLSNIGHAGKIIVEGPFAGNRLYLEMLSVAMEADVVRASGTTGTSAGAALL 420
           LYLALVTAECLSNIGHAGKIIVEGPFAGNRLYLEMLSVAMEADVVRASGTTGTSAGAALL
Sbjct: 361 LYLALVTAECLSNIGHAGKIIVEGPFAGNRLYLEMLSVAMEADVVRASGTTGTSAGAALL 420

Query: 421 AGGDAGAPPRPDSLVALPAASKTRLRHYAAHWRQRARRRTP 461
           AGGDAGAPPRPDSLVALPAASKTRLRHYAAHWRQRARRRTP
Sbjct: 421 AGGDAGAPPRPDSLVALPAASKTRLRHYAAHWRQRARRRTP 461


Lambda     K      H
   0.319    0.136    0.422 

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: 1002
Number of extensions: 43
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: 461
Length of database: 461
Length adjustment: 33
Effective length of query: 428
Effective length of database: 428
Effective search space:   183184
Effective search space used:   183184
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: 51 (24.3 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, 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

GapMind for catabolism of small carbon sources