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 RR42_RS10775 RR42_RS10775 alcohol dehydrogenase
Query= SwissProt::P0A388 (468 letters) >FitnessBrowser__Cup4G11:RR42_RS10775 Length = 434 Score = 360 bits (923), Expect = e-104 Identities = 188/404 (46%), Positives = 246/404 (60%), Gaps = 10/404 (2%) Query: 11 AAAFSLLAGTALAQTPDADSALVQKGAYVARLGDCVACHTALHGQSYAGGLEIKSPIGTI 70 A A LLA A +A V++G Y+A++ +C ACHT++ G +AGGL +K+ +GT+ Sbjct: 13 AFAVLLLAPCFAAAADAPGAAQVERGRYLAKVANCAACHTSVGGAPFAGGLPLKTGVGTV 72 Query: 71 YSTNITPDPTYGIGRYTFAEFDEAVRHGIRKDGSTLYPAMPYPSFSRMTKEDMQALYAYF 130 YSTNITPD GIG Y+F EFD A+R G+ + G LYPAMPYPS++R+ + D+QALYAY Sbjct: 73 YSTNITPDVDSGIGAYSFEEFDRALREGVARHGKRLYPAMPYPSYARLAEPDVQALYAYL 132 Query: 131 MHGVKPVAQPDKQPDISWPLSMRWPLGIWRMMFSPSPKDFTPAP---GTDPEIARGDYLV 187 VK V Q +P++ WP MRW L +W +F S P P G E RG YLV Sbjct: 133 RTEVKAVRQATAEPEMRWPFGMRWLLRVWNWLFLES----GPVPANAGQSVEWNRGAYLV 188 Query: 188 TGPGHCGACHTPRGFAMQEKALDAAGGPDFLSGGAPIDNWVAPSLRNDPVVGLGRWSEDD 247 HCGACHTPRG M EK LD FL+ GA ++ W + +LR DP GLG WS +D Sbjct: 189 QAVAHCGACHTPRGMLMAEKGLDER-SRHFLA-GASVEGWASTNLRGDPRTGLGTWSRED 246 Query: 248 IYTFLKSGRIDHSAVFGGMGDVVAWSTQYFTDDDLHAIAKYLKSLPPVPPSQGNYTYDPS 307 I +L +GR H+ FG M +V+A STQ+ T DL A+A YLKS+P + Y YD Sbjct: 247 IAEYLHTGRNAHATSFGPMSEVIASSTQFMTRPDLDAVAVYLKSVPGARSDETPYAYDAH 306 Query: 308 TANMLASGNTASVPGADTYVKECAICHRNDGGGVARMFPPLAGNPVVVTENPTSLVNVIA 367 TA+ LA G GA Y + C CH +G G AR+FPPLAGNP VV +P+SL N++ Sbjct: 307 TADALAQGR-FDATGARQYAEFCMPCHGANGKGFARVFPPLAGNPTVVDPDPSSLANLLL 365 Query: 368 HGGVLPPSNWAPSAVAMPGYSKSLSAQQIADVVNFIRTSWGNKA 411 G V A + MPGY +L Q++A+V+ FIRT WGN+A Sbjct: 366 DGAVTAHVGTAATDYHMPGYGWTLDNQELANVLTFIRTGWGNQA 409 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: 677 Number of extensions: 34 Number of successful extensions: 6 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: 468 Length of database: 434 Length adjustment: 33 Effective length of query: 435 Effective length of database: 401 Effective search space: 174435 Effective search space used: 174435 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