Align Alcohol dehydrogenase (quinone), cytochrome c subunit; ADH; Alcohol dehydrogenase (quinone), subunit II; Cytochrome c-553; Cytochrome c553; Ethanol:Q2 reductase; G3-ADH subunit II; Quinohemoprotein-cytochrome c complex; Ubiquinol oxidase; EC 1.1.5.5 (characterized)
to candidate Dsui_2086 Dsui_2086 cytochrome c
Query= SwissProt::P0A388 (468 letters) >FitnessBrowser__PS:Dsui_2086 Length = 696 Score = 360 bits (925), Expect = e-104 Identities = 194/419 (46%), Positives = 256/419 (61%), Gaps = 15/419 (3%) Query: 10 SAAAF--SLLAGTALAQTPDADSALVQKGAYVARLGDCVACHTALHGQSYAGGLEIKSPI 67 +AA F S LA L + AD+ + +G Y+ARLGDCVACHTA G+S AGG E+ +P Sbjct: 23 AAATFLLSALAAAGLGRAEAADAGQIARGEYLARLGDCVACHTAEGGKSMAGGRELATPF 82 Query: 68 GTIYSTNITPDPTYGIGRYTFAEFDEAVRHGIRKDGSTLYPAMPYPSFSRMTKEDMQALY 127 G ++STNITPD GIG YTFA+FD A+R G+ DG LYPAMPYPS+++MT EDMQALY Sbjct: 83 GVLFSTNITPDKETGIGNYTFAQFDRAMRKGVAADGHNLYPAMPYPSYAKMTGEDMQALY 142 Query: 128 AYFMHGVKPVAQPDKQPDISWPLSMRWPLGIWRMMFSPSPKDFTPAPGTDPEIARGDYLV 187 AY M G+ PV Q +K + WP + RW L +W F + F P G D RG YLV Sbjct: 143 AYLMQGLAPVKQANKPTAMRWPFNQRWGLSLWNWAFLDA-TPFQPDAGKDATWNRGAYLV 201 Query: 188 TGPGHCGACHTPRGFAMQEKALDAAG--GPDFLSGGAPIDNWVAPSLRNDPVVGLGRWSE 245 G GHCGACHTPRG A QEKA+ AG G FL+ G +++W A SLR G W+ Sbjct: 202 QGLGHCGACHTPRGIAFQEKAMSDAGSKGKHFLA-GETVESWRALSLR-------GLWTV 253 Query: 246 DDIYTFLKSGRIDHSAVFGGMGDVVAWSTQYFTDDDLHAIAKYLKSLPPVPPSQGNYTYD 305 +D FLK+G+ + G M +V+ STQ+ D+DL AIA YLKSLPP + Sbjct: 254 EDTALFLKTGQNRFATASGNMAEVIHHSTQHVKDEDLVAIATYLKSLPPGEHELPAPSVP 313 Query: 306 PSTANMLASGNTASVPGADTYVKECAICHRNDGGGVARMFPPLAGNPVVVTENPTSLVNV 365 S GN S G YV+ C CHR DG GV+++FPPLAGNP V ++P +L+++ Sbjct: 314 RSEVAGKVPGNLFSSRGGLAYVQFCGDCHRQDGNGVSKIFPPLAGNPAVTAKDPATLLHI 373 Query: 366 IAHGGVLPPSNWAPSAVAMPGYSKSLSAQQIADVVNFIRTSWGNKAPGTVTAADVTKLR 424 G + P MPG+++ L+ Q++A+++ F+R+SWGN VTA+ V K+R Sbjct: 374 TLTGWKTASTAAHPRVFTMPGFAR-LNDQELAELITFVRSSWGNGGE-AVTASQVKKMR 430 Score = 29.3 bits (64), Expect = 4e-04 Identities = 12/35 (34%), Positives = 20/35 (57%), Gaps = 5/35 (14%) Query: 322 GADTYVKECAICHRNDGGGV-----ARMFPPLAGN 351 G Y ++CA+CH +G G+ ++PPL G+ Sbjct: 586 GKKIYAEQCAVCHGENGEGLKSADGKMVYPPLWGD 620 Lambda K H 0.317 0.134 0.425 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: 1041 Number of extensions: 66 Number of successful extensions: 8 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 468 Length of database: 696 Length adjustment: 36 Effective length of query: 432 Effective length of database: 660 Effective search space: 285120 Effective search space used: 285120 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: 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