GapMind for catabolism of small carbon sources

 

Aligments for a candidate for glcP in Sphingomonas koreensis DSMZ 15582

Align D-fructose transporter, sugar porter family (characterized)
to candidate Ga0059261_1777 Ga0059261_1777 MFS transporter, sugar porter (SP) family

Query= reanno::Korea:Ga0059261_1777
         (458 letters)



>lcl|FitnessBrowser__Korea:Ga0059261_1777 Ga0059261_1777 MFS
           transporter, sugar porter (SP) family
          Length = 458

 Score =  885 bits (2288), Expect = 0.0
 Identities = 458/458 (100%), Positives = 458/458 (100%)

Query: 1   MHSVSASFAGAPDEEARATVAIILSAAGAALGGLLFGFDTAVISGATQALQLQFGLTDAM 60
           MHSVSASFAGAPDEEARATVAIILSAAGAALGGLLFGFDTAVISGATQALQLQFGLTDAM
Sbjct: 1   MHSVSASFAGAPDEEARATVAIILSAAGAALGGLLFGFDTAVISGATQALQLQFGLTDAM 60

Query: 61  LGFTVASALIGTVLGSLIAGAPADRFGRKGVMLTVAIAYVVSSLGTGLAPDLNAFLVFRF 120
           LGFTVASALIGTVLGSLIAGAPADRFGRKGVMLTVAIAYVVSSLGTGLAPDLNAFLVFRF
Sbjct: 61  LGFTVASALIGTVLGSLIAGAPADRFGRKGVMLTVAIAYVVSSLGTGLAPDLNAFLVFRF 120

Query: 121 MGGLAIGAASVVTPIYIAEVSPARFRGRLVAMNQLNIVLGILIAFLSNYIIAGLVQYDVA 180
           MGGLAIGAASVVTPIYIAEVSPARFRGRLVAMNQLNIVLGILIAFLSNYIIAGLVQYDVA
Sbjct: 121 MGGLAIGAASVVTPIYIAEVSPARFRGRLVAMNQLNIVLGILIAFLSNYIIAGLVQYDVA 180

Query: 181 WRWMFGIVAVPSTIFLLVTLLLPESPRWLAIHGQADRARDVMQRLGFADPRAELARIELA 240
           WRWMFGIVAVPSTIFLLVTLLLPESPRWLAIHGQADRARDVMQRLGFADPRAELARIELA
Sbjct: 181 WRWMFGIVAVPSTIFLLVTLLLPESPRWLAIHGQADRARDVMQRLGFADPRAELARIELA 240

Query: 241 EAREEAAGKPRLFQRSHFTPVACAIAIAMFNQLSGINALLYYAPRIFELAGAGADSALLQ 300
           EAREEAAGKPRLFQRSHFTPVACAIAIAMFNQLSGINALLYYAPRIFELAGAGADSALLQ
Sbjct: 241 EAREEAAGKPRLFQRSHFTPVACAIAIAMFNQLSGINALLYYAPRIFELAGAGADSALLQ 300

Query: 301 SIAVGGTNLVFTVAALFLIDRFGRRPLLFVGSVICAATLLLVGWQLESAKPDGTLILFGL 360
           SIAVGGTNLVFTVAALFLIDRFGRRPLLFVGSVICAATLLLVGWQLESAKPDGTLILFGL
Sbjct: 301 SIAVGGTNLVFTVAALFLIDRFGRRPLLFVGSVICAATLLLVGWQLESAKPDGTLILFGL 360

Query: 361 LGFIAAFAMSQGAVIWVFISEVFPSAVRGKGQALGSTTHWVMAAAITWAFPVFAASVGGW 420
           LGFIAAFAMSQGAVIWVFISEVFPSAVRGKGQALGSTTHWVMAAAITWAFPVFAASVGGW
Sbjct: 361 LGFIAAFAMSQGAVIWVFISEVFPSAVRGKGQALGSTTHWVMAAAITWAFPVFAASVGGW 420

Query: 421 VFAFFGAMMLLQLLWTWKFMPETNGIALEDMNLGSARA 458
           VFAFFGAMMLLQLLWTWKFMPETNGIALEDMNLGSARA
Sbjct: 421 VFAFFGAMMLLQLLWTWKFMPETNGIALEDMNLGSARA 458


Lambda     K      H
   0.327    0.139    0.420 

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: 960
Number of extensions: 52
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: 458
Length of database: 458
Length adjustment: 33
Effective length of query: 425
Effective length of database: 425
Effective search space:   180625
Effective search space used:   180625
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 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