Align gluconate 2-dehydrogenase (EC 1.1.1.215) (characterized)
to candidate BPHYT_RS01065 BPHYT_RS01065 GMC family oxidoreductase
Query= BRENDA::C0LE03 (594 letters) >FitnessBrowser__BFirm:BPHYT_RS01065 Length = 592 Score = 712 bits (1839), Expect = 0.0 Identities = 338/595 (56%), Positives = 433/595 (72%), Gaps = 4/595 (0%) Query: 1 MATVMKKVDAVIVGFGWTGAIMAKELTEAGLNVLALERGPMQDTYPDGNYPQVIDELTYS 60 M MK VD V++G GWTG+I++ EL GL V+ALERG +DT PD YP+ +DEL Y Sbjct: 1 MTKSMKPVDVVVIGLGWTGSILSMELASEGLEVVALERGHNRDTSPDYTYPKAVDELKYG 60 Query: 61 VRKKLFQDISKETVTIRHSVNDVALPNRQLGAFLPGNGVGGAGLHWSGVHFRVDPIELRM 120 +R +LF+ +S ETVT+RH V D A+P RQ AFL + VGGAG+HW+G +R P +++ Sbjct: 61 IRGELFRRLSLETVTVRHQVGDTAVPYRQYNAFLLPDNVGGAGVHWNGQLYRPSPEDMKF 120 Query: 121 RSHYEERYGKNFIPKDMTIQDFGVSYEELEPFFDYAEKVFGTSGQAWTVKGQLVGDGKGG 180 RSH ERYG F+P DMTIQD+ V++ ELEP+FD E + GTSGQA ++G+++ GG Sbjct: 121 RSHNVERYGAGFLPADMTIQDYDVTWNELEPYFDRFEYLNGTSGQAGNLRGKVLS---GG 177 Query: 181 NPYAPDRSDHFPLESQKNTYSAQLFQKAANEVGYKPYNLPSANTSGPYTNPYGAQMGPCN 240 NP+ RS +P + Y+A+LF AA E+GY P+ PSAN S PYTN YG ++GPCN Sbjct: 178 NPFEGPRSRAYPTPPVADQYAAKLFASAARELGYHPFPQPSANCSEPYTNFYGVRLGPCN 237 Query: 241 FCGFCSGYVCYMYSKASPNVNILPALKPLPNFELRPNSHVLRVNLDSSKTRATGVTYVDG 300 CGFC + C++YSK +P ILPAL PNFELR SHV+++N+DS+ RATGVTY+DG Sbjct: 238 LCGFCERFGCFLYSKGAPQTTILPALMRKPNFELRTQSHVVKINVDSTGKRATGVTYIDG 297 Query: 301 QGREIEQPADLVILGAFQFHNVRLMLLSGIGKPYDPITGEGVVGKNFAYQNMATIKAYFD 360 G E+ QPADLVIL +FQ +NVRLMLLSGIG+PYDP+TG+GV+GKNFAYQ M++ ++D Sbjct: 298 AGNEVFQPADLVILSSFQINNVRLMLLSGIGRPYDPVTGKGVIGKNFAYQMMSSTSVFYD 357 Query: 361 KDVHTNNFIGAGGNGVA-VDDFNADNFDHGPHGFVGGSPMWVNQAGSRPIAGTSNPPGTP 419 KDV N FI AG G VD+FN+D+FDHGPHGF+GG + Q G RPI + P GTP Sbjct: 358 KDVPINPFIAAGSGGSQIVDEFNSDHFDHGPHGFLGGGYIIGGQTGGRPIQQLAVPHGTP 417 Query: 420 AWGSAWKKATADYYTHQVSMDAHGAHQSYRGNYLDLDPVYRDAYGLPLLRMTFDWQENDI 479 AWG+ WK+A D+Y H ++ AHG+ +YR YLDLDP YRD+ GLP+LRMTFDW +N+ Sbjct: 418 AWGAQWKRAAKDHYLHTTNVVAHGSVMAYRDAYLDLDPTYRDSLGLPMLRMTFDWHDNEY 477 Query: 480 KMNRFMVEKMGKIAEAMNPKAIALLGKKVGEHFNTASYQTTHLNGGAIMGTDPKTSALNR 539 +M RF+ ++ +I MNPK+ + L +K G+HFN YQTTH GG I G DP++SALNR Sbjct: 478 RMTRFVTDRALEIVAKMNPKSHSTLMRKPGDHFNVREYQTTHTAGGVITGADPQSSALNR 537 Query: 540 YLQSWDVHNVFVPGASAFPQGLGYNPTGLVAALTYWSARAIREQYLKNPGPLVQA 594 YLQSWDV N+FV GASAFPQG+GYNPTGLV AL Y++A AIR QYLK PG LVQA Sbjct: 538 YLQSWDVPNLFVMGASAFPQGIGYNPTGLVGALAYFAADAIRTQYLKRPGALVQA 592 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: 1331 Number of extensions: 77 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: 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