Align gluconate 2-dehydrogenase (EC 1.1.1.215) (characterized)
to candidate BPHYT_RS23025 BPHYT_RS23025 GMC family oxidoreductase
Query= BRENDA::C0LE03 (594 letters) >FitnessBrowser__BFirm:BPHYT_RS23025 Length = 592 Score = 925 bits (2391), Expect = 0.0 Identities = 437/585 (74%), Positives = 496/585 (84%), Gaps = 3/585 (0%) Query: 8 VDAVIVGFGWTGAIMAKELTEAGLNVLALERGPMQDTYPDGNYPQVIDELTYSVRKKLFQ 67 VDAVIVGFGWTGAI+AKELTEAGL V+ALERG +DTYPDG YP IDELTY+VRKKLF Sbjct: 9 VDAVIVGFGWTGAILAKELTEAGLKVVALERGEYRDTYPDGAYPNTIDELTYNVRKKLFL 68 Query: 68 DISKETVTIRHSVNDVALPNRQLGAFLPGNGVGGAGLHWSGVHFRVDPIELRMRSHYEER 127 D+SK TV+IRH+ ND ALP RQL AFLPG GVGGAGLHWSGVHFR+ P ELR++SHYEER Sbjct: 69 DLSKTTVSIRHAPNDTALPYRQLAAFLPGEGVGGAGLHWSGVHFRITPEELRLKSHYEER 128 Query: 128 YGKNFIPKDMTIQDFGVSYEELEPFFDYAEKVFGTSGQAWTVKGQLVGDGKGGNPYAPDR 187 YGK FIP+ MTIQD+GVSY+ELEP FD+AEKVFGTSGQA+ V G++VGDG N Y R Sbjct: 129 YGKRFIPEGMTIQDYGVSYDELEPHFDFAEKVFGTSGQAYKVNGKVVGDG---NIYEAPR 185 Query: 188 SDHFPLESQKNTYSAQLFQKAANEVGYKPYNLPSANTSGPYTNPYGAQMGPCNFCGFCSG 247 SD+FPL +Q NTYSA+ F KAA E+G PY LPSANTSGPYTNPYG QMGPCNFCGFCSG Sbjct: 186 SDNFPLAAQLNTYSAERFGKAARELGLNPYRLPSANTSGPYTNPYGVQMGPCNFCGFCSG 245 Query: 248 YVCYMYSKASPNVNILPALKPLPNFELRPNSHVLRVNLDSSKTRATGVTYVDGQGREIEQ 307 Y CYMYSKASPN+NILPALK PNFELR HVLRV LD +K RA GVTYVD G E+ Q Sbjct: 246 YACYMYSKASPNLNILPALKQSPNFELRSRCHVLRVELDDTKKRAKGVTYVDPAGNEVFQ 305 Query: 308 PADLVILGAFQFHNVRLMLLSGIGKPYDPITGEGVVGKNFAYQNMATIKAYFDKDVHTNN 367 PADLVI+ AFQ+HNV L+LLSGIGKPYDPI+GEGVVG+NFAYQN++TI A+FDKD TN Sbjct: 306 PADLVIVAAFQYHNVHLLLLSGIGKPYDPISGEGVVGRNFAYQNLSTITAFFDKDTFTNP 365 Query: 368 FIGAGGNGVAVDDFNADNFDHGPHGFVGGSPMWVNQAGSRPIAGTSNPPGTPAWGSAWKK 427 FIGAGGNGVAVDDFNADNFDHGP GFVGGSP+WVNQAG++PI+G + P GTP WG+ WKK Sbjct: 366 FIGAGGNGVAVDDFNADNFDHGPLGFVGGSPLWVNQAGAKPISGIATPAGTPNWGADWKK 425 Query: 428 ATADYYTHQVSMDAHGAHQSYRGNYLDLDPVYRDAYGLPLLRMTFDWQENDIKMNRFMVE 487 + D+Y H +SMDAHG++ SYR +LDLDP YRD+YG PLLRMTFDW++NDIKM R++ Sbjct: 426 SVKDHYAHTISMDAHGSNMSYRDVFLDLDPTYRDSYGQPLLRMTFDWKDNDIKMARYVTG 485 Query: 488 KMGKIAEAMNPKAIALLGKKVGEHFNTASYQTTHLNGGAIMGTDPKTSALNRYLQSWDVH 547 +M KIA+ M PK+I + ++ G HF++ YQTTHL GGA+MGTDPKTS LNRYLQSWDVH Sbjct: 486 QMQKIAQQMGPKSINVYTREFGAHFDSRRYQTTHLVGGAVMGTDPKTSVLNRYLQSWDVH 545 Query: 548 NVFVPGASAFPQGLGYNPTGLVAALTYWSARAIREQYLKNPGPLV 592 NVFV GASAFPQG+GYNPTGLVAAL YWSARAIR QYLKNPGPLV Sbjct: 546 NVFVMGASAFPQGIGYNPTGLVAALAYWSARAIRTQYLKNPGPLV 590 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: 1475 Number of extensions: 70 Number of successful extensions: 2 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: 592 Length adjustment: 37 Effective length of query: 557 Effective length of database: 555 Effective search space: 309135 Effective search space used: 309135 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