Align D-gluconate dehydrogenase cytochrome c subunit (EC 1.1.99.3) (characterized)
to candidate BPHYT_RS30785 BPHYT_RS30785 alcohol dehydrogenase
Query= metacyc::MONOMER-12746 (434 letters) >FitnessBrowser__BFirm:BPHYT_RS30785 Length = 448 Score = 380 bits (975), Expect = e-110 Identities = 205/424 (48%), Positives = 267/424 (62%), Gaps = 15/424 (3%) Query: 3 ALVIATLALLGSAAANAAEADQQALVQQGEYLARAGDCVACHTAKDGKPFAGGLPMETPI 62 AL A +A AD Q + +G YLA+ GDC ACHT +PFAGGLP+ TP Sbjct: 23 ALSSGANAQTSNATPTPVSADAQ--LAKGAYLAKVGDCAACHTVNKAQPFAGGLPLATPF 80 Query: 63 GVIYSTNITPD-KTGIGDYSFEDFDKAVRHGVAKGGSTLYPAMPFPSYARVSDADMQALY 121 G +YSTNITPD TGIG YS+ DF A+R G+AK G LYPAMP+PSYA++ DADM ALY Sbjct: 81 GTLYSTNITPDASTGIGGYSYADFATALRQGIAKDGHRLYPAMPYPSYAKIDDADMHALY 140 Query: 122 AYFMKGVAPVARDNQDSDIPWPLSMRWPLSIWRWMFAPSVETPAPAAGSDPVI-SRGAYL 180 YFM+GV P+ + ++ S++ +P ++R +++W ++A + P A V +RGAYL Sbjct: 141 RYFMQGVKPIGQPDRASELRFPFNVRALMTVWDRLYAHE-QLPYQADPHQSVEWNRGAYL 199 Query: 181 VEGLGHCGACHTPRALTMQEKALSASGGSDFLSGSAPLEGWIAKSLRGDHK----DGLGS 236 V+GL HCGACHTP + QE L + FLSG+ L GW A +LRG HK D Sbjct: 200 VQGLAHCGACHTPHGMLGQESVLDEKDNTAFLSGNT-LAGWYAPNLRG-HKTQTSDSDNV 257 Query: 237 WSEEQLVQFLKTGRSDRSAVFGGMSDVVVHSMQYMTDADLTAIARYLKSLP----ANDPK 292 WS+ LV +L++GR FG M++VV S QY+ D DL AIA YL S P A P Sbjct: 258 WSKADLVAYLRSGRMHDGVAFGPMTEVVDDSTQYLHDDDLNAIATYLTSPPLQAGATPPA 317 Query: 293 DQPHQYDKQVAQALWNGDDSKPGAAVYIDNCAACHRTDGHGYTRVFPALAGNPVLQSADA 352 Q +Q A AL G GA +Y+DNCAACHRTDG G FP+L GN + S D Sbjct: 318 PQQTGRAEQTAIALRAGRVDSSGARLYLDNCAACHRTDGTGAMPAFPSLRGNASVLSGDP 377 Query: 353 TSLIHIVLKGGTLPATHSAPSTFTMPAFAWRLSDQEVADVVNFIRSSWGNQASAVKPGDV 412 SLIHIVL G +P+T +AP+ MP F WRL+DQ+VAD+++F+R+SWGN+A+AV G+V Sbjct: 378 ASLIHIVLSGSHMPSTAAAPTPLAMPDFGWRLTDQQVADLLSFVRTSWGNRAAAVTAGEV 437 Query: 413 AALR 416 A +R Sbjct: 438 AKVR 441 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: 619 Number of extensions: 37 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: 448 Length adjustment: 32 Effective length of query: 402 Effective length of database: 416 Effective search space: 167232 Effective search space used: 167232 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