Aligments for a candidate for MFS-glucose in Shewanella sp. ANA-3

GapMind for catabolism of small carbon sources

Aligments for a candidate for MFS-glucose in Shewanella sp. ANA-3

Align Glucose/galactose transporter (characterized, see rationale)
to candidate 7025147 Shewana3_2310 glucose/galactose transporter (RefSeq)

Query= uniprot:A0KXM0
         (423 letters)



>lcl|FitnessBrowser__ANA3:7025147 Shewana3_2310 glucose/galactose
           transporter (RefSeq)
          Length = 423

 Score =  813 bits (2100), Expect = 0.0
 Identities = 423/423 (100%), Positives = 423/423 (100%)

Query: 1   MASSINTSSHTSSVSEAGNGNYRFALVSLTSLFFMWGFITCLNDILIPHLKAVFSLNYTQ 60
           MASSINTSSHTSSVSEAGNGNYRFALVSLTSLFFMWGFITCLNDILIPHLKAVFSLNYTQ
Sbjct: 1   MASSINTSSHTSSVSEAGNGNYRFALVSLTSLFFMWGFITCLNDILIPHLKAVFSLNYTQ 60

Query: 61  AMLIQFCFFGAYFLVSIPAGQLVKRLGYQKGIVTGLVIASIGCGLFYPAASFATYGLFLG 120
           AMLIQFCFFGAYFLVSIPAGQLVKRLGYQKGIVTGLVIASIGCGLFYPAASFATYGLFLG
Sbjct: 61  AMLIQFCFFGAYFLVSIPAGQLVKRLGYQKGIVTGLVIASIGCGLFYPAASFATYGLFLG 120

Query: 121 ALFVLASGITILQVAANPYVNALGSSETASSRLNLTQAFNALGTTVAPFFGSILILSVAA 180
           ALFVLASGITILQVAANPYVNALGSSETASSRLNLTQAFNALGTTVAPFFGSILILSVAA
Sbjct: 121 ALFVLASGITILQVAANPYVNALGSSETASSRLNLTQAFNALGTTVAPFFGSILILSVAA 180

Query: 181 SVSSELAQANAEAEVVKLPYLLLAAALAVLAIIFAKLDLPVIREHSQAAAEEVQTHLGKT 240
           SVSSELAQANAEAEVVKLPYLLLAAALAVLAIIFAKLDLPVIREHSQAAAEEVQTHLGKT
Sbjct: 181 SVSSELAQANAEAEVVKLPYLLLAAALAVLAIIFAKLDLPVIREHSQAAAEEVQTHLGKT 240

Query: 241 SALQSMHLVLGAVGIFVYVGAEVSIGSFLVNFLGEAHIVGMPEEQAAHYIAYYWGGAMVG 300
           SALQSMHLVLGAVGIFVYVGAEVSIGSFLVNFLGEAHIVGMPEEQAAHYIAYYWGGAMVG
Sbjct: 241 SALQSMHLVLGAVGIFVYVGAEVSIGSFLVNFLGEAHIVGMPEEQAAHYIAYYWGGAMVG 300

Query: 301 RFIGSAVMQKIPAGTVLAFNAFMAALLVLVAMTTSGSVAMWAILGVGLFNSIMFPTIFSL 360
           RFIGSAVMQKIPAGTVLAFNAFMAALLVLVAMTTSGSVAMWAILGVGLFNSIMFPTIFSL
Sbjct: 301 RFIGSAVMQKIPAGTVLAFNAFMAALLVLVAMTTSGSVAMWAILGVGLFNSIMFPTIFSL 360

Query: 361 ALRDLGPHTSQGSGILCLAIVGGAIVPLLQGVLADNLGIQLAFILPVVCYGFILFYGAKG 420
           ALRDLGPHTSQGSGILCLAIVGGAIVPLLQGVLADNLGIQLAFILPVVCYGFILFYGAKG
Sbjct: 361 ALRDLGPHTSQGSGILCLAIVGGAIVPLLQGVLADNLGIQLAFILPVVCYGFILFYGAKG 420

Query: 421 SKM 423
           SKM
Sbjct: 421 SKM 423


Lambda     K      H
   0.326    0.138    0.402 

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: 710
Number of extensions: 15
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: 423
Length of database: 423
Length adjustment: 32
Effective length of query: 391
Effective length of database: 391
Effective search space:   152881
Effective search space used:   152881
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 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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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 preprint 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