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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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:

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:

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:

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:

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