Align D-gluconate dehydrogenase dehydrogenase subunit (EC 1.1.99.3) (characterized)
to candidate HSERO_RS16740 HSERO_RS16740 GMC family oxidoreductase
Query= metacyc::MONOMER-12745 (594 letters) >FitnessBrowser__HerbieS:HSERO_RS16740 Length = 593 Score = 732 bits (1890), Expect = 0.0 Identities = 356/596 (59%), Positives = 436/596 (73%), Gaps = 5/596 (0%) Query: 1 MATVMKKVDAVIVGFGWTGAIMAKELTEAGLNVLALERGPMQDTYPDGNYPQVIDELTYS 60 MA KVD V+VG GWTG+IM ELTEAGL+VLALERG M+DT D YP+ +DEL YS Sbjct: 1 MAIKKDKVDVVMVGLGWTGSIMGMELTEAGLSVLALERGDMRDTNTDTPYPKAVDELKYS 60 Query: 61 VRKKLFQDISKETVTIRHSVNDVALPNRQLGAFLPGNGVGGAGLHWSGVHFRVDPIELRM 120 VR LFQD+S+ETVTIRH+++DVA+P RQ G+FL G+GVGGAG HW+G+ +R P EL M Sbjct: 61 VRGALFQDLSRETVTIRHTLSDVAVPYRQHGSFLLGDGVGGAGFHWNGMMYRNLPEELEM 120 Query: 121 RSHYEERYGKNFIPKDMTIQDFGVSYEELEPFFDYAEKVFGTSGQAWTVRGQLVGDGKGG 180 R+H+E++YGK FIP+DMTIQD GV+Y+ELEPF+D++EKV SG+A ++GQ+V GG Sbjct: 121 RTHHEQKYGKKFIPEDMTIQDHGVTYKELEPFYDFSEKVMAVSGKAGNLKGQIV---PGG 177 Query: 181 NPYAPDRSDHFPLESQKNTYSAQLFQKAANDVGYKPYNLPSANTSGPYTNPYGAQMGPCN 240 NP +RSD FP + YSA L +KA DVGY PY P+AN S P+TNPYG ++GPCN Sbjct: 178 NPLEGERSDEFPTPPLQYQYSASLVEKAMRDVGYHPYPAPAANASQPFTNPYGVRIGPCN 237 Query: 241 FCGFCSGYVCYMYSKASPNVNILPALKPLPNFELRPNSHVLRVNLDSSKTRATGVTYVDG 300 +CGFC Y CYMYSKASP ILP L NFE+R + V++VNLD+S RATGVTY+D Sbjct: 238 YCGFCENYGCYMYSKASPQTTILPVLLKRKNFEVRTKAQVIKVNLDASGKRATGVTYIDA 297 Query: 301 QGREIEQPADLVILGAFQFHNVRLMLLSGIGKPYDPITGEGVVGKNFAYQNMATIKAYFD 360 QGRE+EQPADLV+L AFQ HNVRL+LLSGIGKPYDP+TGEGVVGKNFAYQ I Sbjct: 298 QGREVEQPADLVLLTAFQTHNVRLLLLSGIGKPYDPVTGEGVVGKNFAYQYNGGINVIMP 357 Query: 361 KDVHTNNFIGAGGNGVAVDDFNADNFDHGPHGFVGGSPMWVNQAGSRPIAGTSNPPG--T 418 K N FIG G GV +DD NAD FDHGP GF+GG+ + + G RPI PG Sbjct: 358 KGTQFNPFIGTGAGGVGMDDLNADQFDHGPLGFIGGASIRHVRYGGRPIKQAGTMPGEKV 417 Query: 419 PAWGSAWKKATADYYTHQVSMDAHGAHQSYRGNYLDLDPVYRDAYGLPLLRMTFDWQEND 478 P+WGS WK + D Y +++ G+ +YR YL LDP YRDA G PLLR+T +W+EN+ Sbjct: 418 PSWGSEWKASVQDAYQRTLTIGMSGSVMAYRDCYLSLDPTYRDANGQPLLRLTLNWKENE 477 Query: 479 IKMNRFMVEKMGKIAEAMNPKAIALLGKKVGEHFNTASYQTTHLNGGAIMGTDPKTSALN 538 KM ++ +M K+ +AMNP+ + +K G ++T YQ+THL GGAIMGT PK S +N Sbjct: 478 GKMLTYIASQMEKVGQAMNPEKVVKAVRKTGSSWDTRVYQSTHLTGGAIMGTTPKNSVVN 537 Query: 539 RYLQSWDVHNVFVPGASAFPQGLGYNPTGLVAALTYWSARAIREQYLKNPGPLVQA 594 +YLQSWDV NVFV GA AFPQ +GYNPTGLV AL Y SA+AIREQYLKNPGPLVQA Sbjct: 538 KYLQSWDVPNVFVYGACAFPQNMGYNPTGLVTALAYHSAKAIREQYLKNPGPLVQA 593 Lambda K H 0.318 0.136 0.423 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: 1271 Number of extensions: 57 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: 593 Length adjustment: 37 Effective length of query: 557 Effective length of database: 556 Effective search space: 309692 Effective search space used: 309692 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