Align gluconate 2-dehydrogenase (EC 1.1.1.215) (characterized)
to candidate GFF52 PS417_00265 GMC family oxidoreductase
Query= BRENDA::C0LE03 (594 letters) >FitnessBrowser__WCS417:GFF52 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.
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:
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