GapMind for catabolism of small carbon sources

 

Aligments for a candidate for gadh1 in Pseudomonas simiae WCS417

Align gluconate 2-dehydrogenase (EC 1.1.1.215) (characterized)
to candidate GFF52 PS417_00265 GMC family oxidoreductase

Query= BRENDA::C0LE03
         (594 letters)



>lcl|FitnessBrowser__WCS417:GFF52 PS417_00265 GMC family
           oxidoreductase
          Length = 594

 Score = 1189 bits (3076), Expect = 0.0
 Identities = 564/594 (94%), Positives = 584/594 (98%)

Query: 1   MATVMKKVDAVIVGFGWTGAIMAKELTEAGLNVLALERGPMQDTYPDGNYPQVIDELTYS 60
           MAT+MKKVDAVIVGFGWTGAIMAKELTEAGLNV+ALERGPMQDTYPDGNYPQVIDELTYS
Sbjct: 1   MATIMKKVDAVIVGFGWTGAIMAKELTEAGLNVVALERGPMQDTYPDGNYPQVIDELTYS 60

Query: 61  VRKKLFQDISKETVTIRHSVNDVALPNRQLGAFLPGNGVGGAGLHWSGVHFRVDPIELRM 120
           VRKKLFQDISKETVTIRHSVNDVALPNRQLGAFLPGNGVGGAGLHWSGVHFRVDPIELRM
Sbjct: 61  VRKKLFQDISKETVTIRHSVNDVALPNRQLGAFLPGNGVGGAGLHWSGVHFRVDPIELRM 120

Query: 121 RSHYEERYGKNFIPKDMTIQDFGVSYEELEPFFDYAEKVFGTSGQAWTVKGQLVGDGKGG 180
           RSHYEERYGK+FIPKDMTIQDFGVSYEELEPFFDYAEKVFGTSGQAWTVKGQLVG+G+GG
Sbjct: 121 RSHYEERYGKHFIPKDMTIQDFGVSYEELEPFFDYAEKVFGTSGQAWTVKGQLVGEGRGG 180

Query: 181 NPYAPDRSDHFPLESQKNTYSAQLFQKAANEVGYKPYNLPSANTSGPYTNPYGAQMGPCN 240
           NPYAPDRS+ FPLESQKNT SAQLFQKAA EVGYKPYNLPSANTSGPYTNPYGAQMGPCN
Sbjct: 181 NPYAPDRSNPFPLESQKNTVSAQLFQKAAAEVGYKPYNLPSANTSGPYTNPYGAQMGPCN 240

Query: 241 FCGFCSGYVCYMYSKASPNVNILPALKPLPNFELRPNSHVLRVNLDSSKTRATGVTYVDG 300
           FCGFCSGYVCYMYSKASPNVNILPAL+ +PNFELRPNSHVL+VNLDS+K++ATGVTY+D 
Sbjct: 241 FCGFCSGYVCYMYSKASPNVNILPALRQVPNFELRPNSHVLKVNLDSTKSKATGVTYIDA 300

Query: 301 QGREIEQPADLVILGAFQFHNVRLMLLSGIGKPYDPITGEGVVGKNFAYQNMATIKAYFD 360
           QGRE EQPA+LVILGAFQFHNVRLMLLSGIGKPYDPIT EGVVG+NFAYQNMATIKA+FD
Sbjct: 301 QGRECEQPAELVILGAFQFHNVRLMLLSGIGKPYDPITNEGVVGRNFAYQNMATIKAFFD 360

Query: 361 KDVHTNNFIGAGGNGVAVDDFNADNFDHGPHGFVGGSPMWVNQAGSRPIAGTSNPPGTPA 420
           KD HTNNFIGAGGNGVA+DDFNADNFDHGPHGFVGGSPMWVNQAGSRPIAGTSNPPGTPA
Sbjct: 361 KDTHTNNFIGAGGNGVAIDDFNADNFDHGPHGFVGGSPMWVNQAGSRPIAGTSNPPGTPA 420

Query: 421 WGSAWKKATADYYTHQVSMDAHGAHQSYRGNYLDLDPVYRDAYGLPLLRMTFDWQENDIK 480
           WGSAWK+ATADYYTHQVSMDAHGAHQSYRGNYLDLDPVYRDAYG PLLRMTFDWQENDIK
Sbjct: 421 WGSAWKRATADYYTHQVSMDAHGAHQSYRGNYLDLDPVYRDAYGQPLLRMTFDWQENDIK 480

Query: 481 MNRFMVEKMGKIAEAMNPKAIALLGKKVGEHFNTASYQTTHLNGGAIMGTDPKTSALNRY 540
           MNRFMVEKMGK+AEAMNPKAIA+LGKKVGEHFNTASYQTTHLNGGAIMGTDPKTSALNRY
Sbjct: 481 MNRFMVEKMGKVAEAMNPKAIAVLGKKVGEHFNTASYQTTHLNGGAIMGTDPKTSALNRY 540

Query: 541 LQSWDVHNVFVPGASAFPQGLGYNPTGLVAALTYWSARAIREQYLKNPGPLVQA 594
           LQ WDVHNVFVPGASAFPQGLGYNPTGLVAALTYWSARAIREQYLKNPGPLVQA
Sbjct: 541 LQCWDVHNVFVPGASAFPQGLGYNPTGLVAALTYWSARAIREQYLKNPGPLVQA 594


Lambda     K      H
   0.317    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: 1593
Number of extensions: 50
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: 594
Length of database: 594
Length adjustment: 37
Effective length of query: 557
Effective length of database: 557
Effective search space:   310249
Effective search space used:   310249
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 53 (25.0 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 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