Align D-gluconate dehydrogenase cytochrome c subunit (EC 1.1.99.3) (characterized)
to candidate WP_007665341.1 BN137_RS16385 c-type cytochrome
Query= metacyc::MONOMER-12746 (434 letters) >NCBI__GCF_000319285.1:WP_007665341.1 Length = 398 Score = 353 bits (905), Expect = e-102 Identities = 203/418 (48%), Positives = 252/418 (60%), Gaps = 28/418 (6%) Query: 1 MKALVIATLALLGSAAANAAEADQQALVQQGEYLARAGDCVACHTAKDGKPFAGGLPMET 60 MK + + LAL A A QA+ +GEY+ARAGDC+ACHTA DG P AGG+ T Sbjct: 1 MKRITVLALALW------ATHAGAQAM-SRGEYVARAGDCMACHTAADGAPLAGGVKFAT 53 Query: 61 PIGVIYSTNITPDKT-GIGDYSFEDFDKAVRHGVAKGGSTLYPAMPFPSYARVSDADMQA 119 P+G IYSTNITPD T GIG YS+EDF +A+R GVAK G LYPAMP+PSYA++SD D++A Sbjct: 54 PLGDIYSTNITPDNTHGIGGYSYEDFARAMREGVAKDGHHLYPAMPYPSYAKMSDEDLRA 113 Query: 120 LYAYFMKGVAPVARDNQDSDIPWPLSMRWPLSIWRWMFAPSVETP-APAAGSDPVISRGA 178 LY Y M V P A N+DSDIPWPLSMRWPL IW +FA E P P A +RGA Sbjct: 114 LYEYLMNEVKPQATANRDSDIPWPLSMRWPLGIWNSLFAD--EKPFTPRADKSAQWNRGA 171 Query: 179 YLVEGLGHCGACHTPRALTMQEKALSASGGSDFLSGSAPLEGWIAKSLRGDHKDGLGSWS 238 YLV+G GHCGACHTPR + MQEKA FL+G L GW A SLRG S Sbjct: 172 YLVQGPGHCGACHTPRGIGMQEKAFD-ERDEQFLAGE-ELNGWYAPSLRG------LKMS 223 Query: 239 EEQLVQFLKTGRSDRSAVFGGMSDVVVHSMQYMTDADLTAIARYLKSLPANDPKDQPHQY 298 E L L+ GRS +A+ G M +VV +S QY++D D AIA YL SLP ++P + Sbjct: 224 EGDLTLLLRDGRSKHAALSGPMDEVVTNSTQYLSDDDNRAIASYLLSLPGSEPVKTQAPH 283 Query: 299 DKQVAQALWNGDDSKPGAAVYIDNCAACHRTDGHGYTRVFPALAGNPVLQSADATSLIHI 358 Q AL NG +Y CA CH ++G G PAL N + + + +L+ + Sbjct: 284 LSQA--ALENGHQ------LYARYCATCHASNGEGADYAVPALKDNLTVNADNPLTLLRV 335 Query: 359 VLKGGTLPATHSAPSTFTMPAFAWRLSDQEVADVVNFIRSSWGNQASAVKPGDVAALR 416 VL+GG T ++MP + W LSDQ+ ADV N+IR S+GN A+ V P V R Sbjct: 336 VLEGGKTAVT-ERHLPYSMPGYGWALSDQDAADVTNYIRGSFGNHAAPVTPDQVKDAR 392 Lambda K H 0.316 0.131 0.404 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: 627 Number of extensions: 45 Number of successful extensions: 8 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: 434 Length of database: 398 Length adjustment: 31 Effective length of query: 403 Effective length of database: 367 Effective search space: 147901 Effective search space used: 147901 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 (21.6 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Sep 24 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