Align gluconate 2-dehydrogenase (EC 1.1.1.215) (characterized)
to candidate BPHYT_RS30780 BPHYT_RS30780 GMC family oxidoreductase
Query= BRENDA::C0LE03 (594 letters) >FitnessBrowser__BFirm:BPHYT_RS30780 Length = 594 Score = 728 bits (1878), Expect = 0.0 Identities = 355/597 (59%), Positives = 431/597 (72%), Gaps = 6/597 (1%) Query: 1 MATVMK-KVDAVIVGFGWTGAIMAKELTEAGLNVLALERGPMQDTYPDGNYPQVIDELTY 59 MA + K KVDAV+VG GW+G+IMA EL +AGL V+ LERG +DTYPD YP+V DELT+ Sbjct: 1 MANISKPKVDAVVVGMGWSGSIMAIELADAGLTVVGLERGENRDTYPDFAYPKVADELTH 60 Query: 60 SVRKKLFQDISKETVTIRHSVNDVALPNRQLGAFLPGNGVGGAGLHWSGVHFRVDPIELR 119 R KL Q ++ ETVTIR +VALP RQ GAFL G+GVGG+G+HW+G +R EL+ Sbjct: 61 VQRFKLMQSLAHETVTIRRQAQEVALPLRQYGAFLFGDGVGGSGVHWNGFTYRATEAELK 120 Query: 120 MRSHYEERYGKNFIPKDMTIQDFGVSYEELEPFFDYAEKVFGTSGQAWTVKGQLVGDGKG 179 +RSHYE+RYGK FIP DMTIQD+ VS ELEPF+D E V GTSG+A + GQ VG G Sbjct: 121 LRSHYEQRYGKGFIPDDMTIQDWPVSAAELEPFYDRFEYVAGTSGKAGNLNGQSVG---G 177 Query: 180 GNPYAPDRSDHFPLESQKNTYSAQLFQKAANEVGYKPYNLPSANTSGPYTNPYGAQMGPC 239 GNP+ RS + L Y + LF +AA EVGY PY P++ S YTNPYG Q+GPC Sbjct: 178 GNPFEAPRSRDYALPPLPTAYPSMLFDQAAREVGYHPYPTPASIASKAYTNPYGMQLGPC 237 Query: 240 NFCGFCSGYVCYMYSKASPNVNILPALKPLPNFELRPNSHVLRVNLDSSKTRATGVTYVD 299 NFCG+C + CYM+SKASP ILPAL PNFELR S V++VNLDS+ RATGVTY+D Sbjct: 238 NFCGYCELFGCYMFSKASPQSCILPALARKPNFELRDRSAVVKVNLDSTGKRATGVTYID 297 Query: 300 GQGREIEQPADLVILGAFQFHNVRLMLLSGIGKPYDPITGEGVVGKNFAYQNMATIKAYF 359 QG +EQPAD+V L A+Q HNVRL+LLSGIGKPYDP TGEG VGKN+AYQ + I+ +F Sbjct: 298 AQGHTVEQPADIVALCAYQMHNVRLLLLSGIGKPYDPATGEGTVGKNYAYQKNSKIQVFF 357 Query: 360 DKDVHTNNFIGAGGNGVAVDDFNADNFDHGPHGFVGGSPMWVNQAGSRPIAGTSNPPGTP 419 DKDV N FIG+G GV DDFNADNFDHGP F+GG+ + G RPIA PPGTP Sbjct: 358 DKDVAINPFIGSGAGGVVYDDFNADNFDHGPLNFIGGAITFATVTGGRPIAQALVPPGTP 417 Query: 420 AWGSAWKKATADYYTHQVSMDAHGAHQSYRGNYLDLDPVYRDAYGLPLLRMTFDWQENDI 479 WGS WKKA D+Y H ++ G+ SYR NYLDLDP Y+DAYGLPLLRMTFDW++N+ Sbjct: 418 KWGSGWKKAVKDHYLHSFAISTQGSVMSYRDNYLDLDPTYKDAYGLPLLRMTFDWKDNEG 477 Query: 480 KMNRFMVEKMGKIAEAMNPK--AIALLGKKVGEHFNTASYQTTHLNGGAIMGTDPKTSAL 537 +M +F+ K +A AMNPK ++A+ K G+HF+ YQ+TH GGAI G P S + Sbjct: 478 RMTQFVSHKAADVARAMNPKPQSVAINAGKPGDHFDVGPYQSTHTTGGAIAGDRPDNSVV 537 Query: 538 NRYLQSWDVHNVFVPGASAFPQGLGYNPTGLVAALTYWSARAIREQYLKNPGPLVQA 594 N+YLQSWDV NVFV GA +FPQ LG NPTG + A+TY++A+ IRE YLKNPGPLVQA Sbjct: 538 NKYLQSWDVPNVFVTGACSFPQNLGINPTGTIGAMTYYAAKTIRETYLKNPGPLVQA 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: 1323 Number of extensions: 58 Number of successful extensions: 3 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