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 HSERO_RS16735 HSERO_RS16735 alcohol dehydrogenase
Query= SwissProt::P0A388 (468 letters) >FitnessBrowser__HerbieS:HSERO_RS16735 Length = 444 Score = 439 bits (1128), Expect = e-127 Identities = 228/428 (53%), Positives = 288/428 (67%), Gaps = 10/428 (2%) Query: 1 MINRLKVTFSAAAFSLLAGTALAQT----PDADSALVQKGAYVARLGDCVACHTALHGQS 56 MI + AA SL A TA AQ+ P AD LVQ+G Y+A+ GDCVACHTA G+ Sbjct: 4 MIKHYFIAACAAVMSLSALTAAAQSNPAAPSADQQLVQRGEYLAKAGDCVACHTAKGGKP 63 Query: 57 YAGGLEIKSPIGTIYSTNITPDPTYGIGRYTFAEFDEAVRHGIRKDGSTLYPAMPYPSFS 116 +AGGL I +PIGT+YS+NITPD GIG Y+ +FD A+RHGIRKDG++LYPAMPYPS++ Sbjct: 64 FAGGLAIATPIGTVYSSNITPDKENGIGNYSEEDFDRALRHGIRKDGASLYPAMPYPSYA 123 Query: 117 RMTKEDMQALYAYFMHGVKPVAQPDKQPDISWPLSMRWPLGIWRMMFSPSPKDFTPAPGT 176 ++ D++ALYAYFMHGV+ P++ DI+WPLSMRWPL IWR +F+P+ P Sbjct: 124 KVKPADVKALYAYFMHGVQADPAPNRGVDITWPLSMRWPLSIWRKVFAPAVA--VDGPED 181 Query: 177 DPEIARGDYLVTGPGHCGACHTPRGFAMQEKALDAAGGPDFLSGGAPIDNWVAPSLRNDP 236 + + RG YLV G GHCGACHTPRG MQEKAL + FLSGG ID ++A +LR D Sbjct: 182 NSPLVRGQYLVEGLGHCGACHTPRGVGMQEKAL-SNDSSQFLSGGV-IDGYLANNLRGDG 239 Query: 237 VVGLGRWSEDDIYTFLKSGRIDHSAVFGGMGDVVAWSTQYFTDDDLHAIAKYLKSLPPVP 296 GLG WSE DI FLK+GR HSA FGGM DVVA STQY T++DL A+AKYLKSL PV Sbjct: 240 RDGLGNWSEADIVAFLKTGRNSHSAAFGGMADVVANSTQYMTEEDLSAMAKYLKSLKPVK 299 Query: 297 PSQGNYTYDPSTANMLASGNTASVPGADTYVKECAICHRNDGGGVARMFPPLAGNPVVVT 356 YD T L G+ S PGA ++ CA CHR+ G G FP LA +P V Sbjct: 300 DGTPALAYDDKTHQALRKGSDQS-PGAMAFLNNCAACHRSSGKGYDETFPSLALSPTVNA 358 Query: 357 ENPTSLVNVIAHGGVLPPSNWAPSAVAMPGYSKSLSAQQIADVVNFIRTSWGNKAPGTVT 416 ENP SL+ ++ G +P ++ AP+ AMP + LS Q++A+VV FIR+SWGN+A +V+ Sbjct: 359 ENPASLIRIVLEGAEMPWTHKAPTQFAMPAFGSRLSDQEVAEVVTFIRSSWGNQA-SSVS 417 Query: 417 AADVTKLR 424 A+DV K+R Sbjct: 418 ASDVAKVR 425 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: 705 Number of extensions: 41 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: 468 Length of database: 444 Length adjustment: 33 Effective length of query: 435 Effective length of database: 411 Effective search space: 178785 Effective search space used: 178785 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