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 AO356_30205 AO356_30205 alcohol dehydrogenase
Query= SwissProt::P0A388 (468 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_30205 Length = 444 Score = 382 bits (981), Expect = e-110 Identities = 197/411 (47%), Positives = 254/411 (61%), Gaps = 8/411 (1%) Query: 23 AQTPDADSALVQKGAYVARLGDCVACHTALHGQSYAGGLEIKSPIGTIYSTNITPDPTYG 82 A P AD+ LVQ+G YVARL DCVACH+ G +AGGLE+ +P+G+IY+TNITPD G Sbjct: 35 ASAPSADAQLVQRGEYVARLSDCVACHSTPKGAPFAGGLEMATPMGSIYATNITPDKQTG 94 Query: 83 IGRYTFAEFDEAVRHGIRKDGSTLYPAMPYPSFSRMTKEDMQALYAYFMHGVKPVAQPDK 142 IG Y+ A+FD AVR G+ DG LYPAMPYPS+++++ +D++ALYA+FM GVKP Q ++ Sbjct: 95 IGNYSLADFDRAVRSGVAADGHRLYPAMPYPSYAKLSDDDVRALYAFFMAGVKPAQQQNQ 154 Query: 143 QPDISWPLSMRWPLGIWRMMFSPSPKDFTPAPGTDPEIARGDYLVTGPGHCGACHTPRGF 202 Q I WPL+MRWPL +W F + P D RG Y+V G GHCG+CHTPR Sbjct: 155 QSHIPWPLNMRWPLALWNTAFVDDGA-YQAKPSEDALWNRGAYIVQGAGHCGSCHTPRSL 213 Query: 203 AMQEKALDAAGGPDFLSGGAPIDNWVAPSLRNDPVVGLGRWSEDDIYTFLKSGRIDHSAV 262 M EK+LD + FLSG +D W APSLR DP GLGRWSE +I +LK+GR HS V Sbjct: 214 TMNEKSLDESSA-TFLSGSL-LDGWYAPSLRQDPNTGLGRWSEQEIVDYLKTGRNAHSVV 271 Query: 263 FGGMGDVVAWSTQYFTDDDLHAIAKYLKSLPPVPPSQGNYTYDPSTANMLASGNTASVPG 322 G M +V STQY +D DL AIA YL SLP P G P + S PG Sbjct: 272 VGTMAEVFNNSTQYMSDPDLKAIAHYLVSLPGDPKRDG----PPWKPAAKLAEQPLSTPG 327 Query: 323 ADTYVKECAICHRNDGGGVARMFPPLAGNPVVVTENPTSLVNVIAHGGVLPPSNWAPSAV 382 A Y+ +C+ CH +DG G A PPLAG + + + +N +G +N P + Sbjct: 328 AANYMAKCSSCHGSDGSGQAPWIPPLAGASSSMVKEGATSINATLNGSERVVANGIPDSY 387 Query: 383 AMPGYSKSLSAQQIADVVNFIRTSWGNKAPGTVTAADVTKLRDTGAPVSSS 433 MP Y LS Q++ADV+ F+RTSWGN+ G V A +V +LR+ P SS+ Sbjct: 388 RMPPYRNQLSDQEVADVLTFVRTSWGNQG-GAVKADEVKELRERTNPASSN 437 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: 702 Number of extensions: 33 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: 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