Align gluconate 2-dehydrogenase (EC 1.1.1.215) (characterized)
to candidate PP_3383 PP_3383 gluconate 2-dehydrogenase flavoprotein subunit
Query= BRENDA::C0LE03 (594 letters) >FitnessBrowser__Putida:PP_3383 Length = 594 Score = 1129 bits (2921), Expect = 0.0 Identities = 527/594 (88%), Positives = 568/594 (95%) Query: 1 MATVMKKVDAVIVGFGWTGAIMAKELTEAGLNVLALERGPMQDTYPDGNYPQVIDELTYS 60 MATV+ KVDAVIVGFGW GAIMAKELTEAGL+V+ALERGPMQDTYP+G+YPQVIDELTYS Sbjct: 1 MATVLNKVDAVIVGFGWAGAIMAKELTEAGLHVVALERGPMQDTYPEGSYPQVIDELTYS 60 Query: 61 VRKKLFQDISKETVTIRHSVNDVALPNRQLGAFLPGNGVGGAGLHWSGVHFRVDPIELRM 120 VRKKLF D+SKETVT+RHSVNDVALPNRQLGAFLPG GVGGAGLHWSGVHFRVDP+ELR+ Sbjct: 61 VRKKLFVDVSKETVTVRHSVNDVALPNRQLGAFLPGKGVGGAGLHWSGVHFRVDPVELRL 120 Query: 121 RSHYEERYGKNFIPKDMTIQDFGVSYEELEPFFDYAEKVFGTSGQAWTVKGQLVGDGKGG 180 RSHYEERYG+ FIP+ MTIQDFGVSYEELEP+FD+AEKVFGTSGQAWTVKGQ+VG+GKGG Sbjct: 121 RSHYEERYGRTFIPEGMTIQDFGVSYEELEPYFDFAEKVFGTSGQAWTVKGQVVGEGKGG 180 Query: 181 NPYAPDRSDHFPLESQKNTYSAQLFQKAANEVGYKPYNLPSANTSGPYTNPYGAQMGPCN 240 NPYAPDRS+ FPL +QKN SA+LF+KAA +GYKPYNLPSANTSGPYTNPYGAQMGPCN Sbjct: 181 NPYAPDRSNPFPLPAQKNVVSARLFEKAATSLGYKPYNLPSANTSGPYTNPYGAQMGPCN 240 Query: 241 FCGFCSGYVCYMYSKASPNVNILPALKPLPNFELRPNSHVLRVNLDSSKTRATGVTYVDG 300 FCGFCSGYVCYMYSKASPNVNILPAL+ +PNFELRPN+HVLRVNLD SK RATGVTY+D Sbjct: 241 FCGFCSGYVCYMYSKASPNVNILPALRQVPNFELRPNAHVLRVNLDDSKRRATGVTYIDA 300 Query: 301 QGREIEQPADLVILGAFQFHNVRLMLLSGIGKPYDPITGEGVVGKNFAYQNMATIKAYFD 360 QGRE+EQPA+LVIL AFQF+NVRLMLLSGIGKPYDP+ EGVVG+NFAYQNM T+KA+FD Sbjct: 301 QGREVEQPAELVILAAFQFNNVRLMLLSGIGKPYDPVKNEGVVGRNFAYQNMGTVKAFFD 360 Query: 361 KDVHTNNFIGAGGNGVAVDDFNADNFDHGPHGFVGGSPMWVNQAGSRPIAGTSNPPGTPA 420 KD +TNNFIGAGGNG+A+DDFNADNFDHGPHGFVGGSPMWVNQAGSRPIAGTSNPPGTPA Sbjct: 361 KDTYTNNFIGAGGNGIAIDDFNADNFDHGPHGFVGGSPMWVNQAGSRPIAGTSNPPGTPA 420 Query: 421 WGSAWKKATADYYTHQVSMDAHGAHQSYRGNYLDLDPVYRDAYGLPLLRMTFDWQENDIK 480 WGSAWKKATADYYTHQVSMDAHGAHQSYRGNYLDLDP YRDAYG PLLRMTFDWQENDIK Sbjct: 421 WGSAWKKATADYYTHQVSMDAHGAHQSYRGNYLDLDPTYRDAYGQPLLRMTFDWQENDIK 480 Query: 481 MNRFMVEKMGKIAEAMNPKAIALLGKKVGEHFNTASYQTTHLNGGAIMGTDPKTSALNRY 540 MN+FMV+K+ KIA+AMNPKAIA+LGK+V +HFNT SYQTTHLNGGAIMGTDPKTSALNRY Sbjct: 481 MNQFMVDKLSKIAQAMNPKAIAVLGKQVKDHFNTTSYQTTHLNGGAIMGTDPKTSALNRY 540 Query: 541 LQSWDVHNVFVPGASAFPQGLGYNPTGLVAALTYWSARAIREQYLKNPGPLVQA 594 LQSWDVHNVFVPGASAFPQGLGYNPTGLVAALTYWSARAIREQYLKNPGPLVQA Sbjct: 541 LQSWDVHNVFVPGASAFPQGLGYNPTGLVAALTYWSARAIREQYLKNPGPLVQA 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: 1564 Number of extensions: 53 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