Align D-gluconate dehydrogenase cytochrome c subunit (EC 1.1.99.3) (characterized)
to candidate N515DRAFT_0703 N515DRAFT_0703 Cytochrome c
Query= metacyc::MONOMER-12746 (434 letters) >FitnessBrowser__Dyella79:N515DRAFT_0703 Length = 429 Score = 286 bits (731), Expect = 1e-81 Identities = 164/410 (40%), Positives = 229/410 (55%), Gaps = 25/410 (6%) Query: 14 SAAANAAEADQQALVQQGEYLARAGDCVACHTAKDGKPFAGGLPMETPIGVIYSTNITPD 73 ++ +AA AL+ +GEYL GDC +CHT + G FAGG + TP G I + N+TPD Sbjct: 35 ASRVDAAALKDPALIAKGEYLTLVGDCASCHTGQGGARFAGGRVVGTPFGDIPAPNLTPD 94 Query: 74 K-TGIGDYSFEDFDKAVRHGVAKGGSTLYPAMPFPSYARVSDADMQALYAYFMKGVAPVA 132 + TG+G++SFE F +A+ GV + G LYPA P+ SY +VS D A++AY ++ + P+ Sbjct: 95 RETGLGEWSFEAFRQALHSGVDRHGQFLYPAFPYTSYTKVSRDDALAIFAY-LQSLPPLK 153 Query: 133 RDNQDSDIPWPLSMRWPLSIWRWMFAPSVETPAPAAGSDPVISRGAYLVEGLGHCGACHT 192 + + + +P ++R L WR ++ E A + S P +RGAYLV+GLGHC CH Sbjct: 154 QAAKQPGLGFPYNVRNTLKAWRALYFREGEYVADSTKS-PEWNRGAYLVQGLGHCNECHV 212 Query: 193 PR-ALTMQEKALSASGGSDFLSGSAPLEGWIAKSLRGDHKDGLGSWSEEQLVQFLKTGRS 251 R + S SGG P++ W A L GL WSE + LKTG+S Sbjct: 213 ERDSFGGMRSDQSLSGGQ------IPVQNWYAPDLSTQANGGLAGWSERDIADLLKTGQS 266 Query: 252 DRSAVFGGMSDVVVHSMQYMTDADLTAIARYLKSLPANDPKDQPHQYDKQVAQALWNGDD 311 + A FG M++VV S Q++ DADL AIA YL+SLPA Y+ + D Sbjct: 267 AKGAAFGPMAEVVARSTQHLNDADLHAIATYLQSLPARPRVS----YEPSLL-------D 315 Query: 312 SKP----GAAVYIDNCAACHRTDGHGYTRVFPALAGNPVLQSADATSLIHIVLKGGTLPA 367 +KP GA VY + CA CH DG G V+P L+GN + + I +VL GG P+ Sbjct: 316 TKPMLDQGAKVYAERCADCHGRDGQGVAGVYPPLSGNSSVNEPTGINAIRVVLLGGFAPS 375 Query: 368 THSAPSTFTMPAFAWRLSDQEVADVVNFIRSSWGNQASAVKPGDVAALRN 417 T P ++MP FA +L+D +VA VV +IR SWGNQA V+ DV R+ Sbjct: 376 TQGNPRPYSMPPFAQQLNDADVAAVVTYIRQSWGNQAPLVQERDVIKYRH 425 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: 584 Number of extensions: 26 Number of successful extensions: 7 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: 429 Length adjustment: 32 Effective length of query: 402 Effective length of database: 397 Effective search space: 159594 Effective search space used: 159594 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: 51 (24.3 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