Alignments for a candidate for PS417_04205 in Pseudomonas fluorescens FW300-N2E3

GapMind for catabolism of small carbon sources

Alignments for a candidate for PS417_04205 in Pseudomonas fluorescens FW300-N2E3

Align D-galacturonate transporter (MFS superfamily) (characterized)
to candidate AO353_05295 AO353_05295 glucarate transporter

Query= reanno::WCS417:GFF828
         (454 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_05295
          Length = 453

 Score =  846 bits (2186), Expect = 0.0
 Identities = 416/455 (91%), Positives = 442/455 (97%), Gaps = 3/455 (0%)

Query: 1   MQATKPTHVRYLILLMLFLVTTINYADRATIAIAGSSLQKDLGIDAVTLGYIFSAFGWAY 60
           MQATKPTHVRYLILLMLFLVTTINYADRATIAIAGSSLQKDLGIDAVTLGYIFSAFGWAY
Sbjct: 1   MQATKPTHVRYLILLMLFLVTTINYADRATIAIAGSSLQKDLGIDAVTLGYIFSAFGWAY 60

Query: 61  VAGQIPGGWLLDRFGSKKVYALSIFTWSLFTVLQGYVGEFGVSTAVVALFMLRFMVGLAE 120
           VAGQIPGGWLLDRFGSKKVYALSIFTWSLFTVLQGYVGEFGVSTA+VALF+LRF+VGLAE
Sbjct: 61  VAGQIPGGWLLDRFGSKKVYALSIFTWSLFTVLQGYVGEFGVSTAIVALFVLRFLVGLAE 120

Query: 121 APSFPGNARIVAAWFPTAERGTASAIFNSAQYFATVLFAPLMGWIVYSFGWQHVFIVMGV 180
           APSFPGNARIVAAWFPTAERGTASAIFNSAQYFATV+FAPLMGWIVYSFGWQHVF+VMG 
Sbjct: 121 APSFPGNARIVAAWFPTAERGTASAIFNSAQYFATVIFAPLMGWIVYSFGWQHVFMVMGG 180

Query: 181 IGIIFSLIWLKVIHSPRQHPMINEAEFNHIAANGAMVDMDQDKGKGKKTDGPKWDYIRQL 240
           IGI+FSLIWLK+IHSPRQHPMIN++EF HIA NG +VDMDQD  +GK++DGPKWDY+RQL
Sbjct: 181 IGIVFSLIWLKIIHSPRQHPMINDSEFKHIADNGGLVDMDQD--RGKRSDGPKWDYVRQL 238

Query: 241 LTNRMMLGVYLGQYCINGITYFFLTWFPVYLVQDRGMTILKAGFIASLPAICGFIGGVLG 300
           L+NRMMLGVYLGQYCINGITYFFLTWFPVYLVQ+RGMTILKAGFIASLPAICGFIGGVLG
Sbjct: 239 LSNRMMLGVYLGQYCINGITYFFLTWFPVYLVQERGMTILKAGFIASLPAICGFIGGVLG 298

Query: 301 GVISDYLLRKGHSLTFARKAPIIGGLLISSSIVACNYVDIEWMVVGFMALAFFGKGVGAL 360
           G+ISDYLLRKGHSLTFARKAPIIGGLL+S+SIVACNYV+IEW+VVGFMALAFFGKGVGAL
Sbjct: 299 GLISDYLLRKGHSLTFARKAPIIGGLLLSTSIVACNYVNIEWIVVGFMALAFFGKGVGAL 358

Query: 361 GWAVVSDTSPKQIAGLSGGLFNTFGNLASITTPIVIGYIISTTGSFKWALVFVGANALVA 420
           GWAVVSDTSPKQIAGLSGGLFN FGN+ASITTPIVIGYIISTTGSFKWALVFVG NALVA
Sbjct: 359 GWAVVSDTSPKQIAGLSGGLFNMFGNIASITTPIVIGYIISTTGSFKWALVFVGCNALVA 418

Query: 421 VFSYLVIVGPIKRVVLKEPPTQGPELT-RLTEAHS 454
           VFSYLVIVGPIKRVVLKEPP    +LT +L++AHS
Sbjct: 419 VFSYLVIVGPIKRVVLKEPPANDSQLTNKLSQAHS 453


Lambda     K      H
   0.327    0.142    0.444 

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: 926
Number of extensions: 33
Number of successful extensions: 5
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: 454
Length of database: 453
Length adjustment: 33
Effective length of query: 421
Effective length of database: 420
Effective search space:   176820
Effective search space used:   176820
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: 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