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 GFF53 PS417_00270 alcohol dehydrogenase
Query= SwissProt::P0A388 (468 letters) >FitnessBrowser__WCS417:GFF53 Length = 420 Score = 469 bits (1208), Expect = e-137 Identities = 229/413 (55%), Positives = 293/413 (70%), Gaps = 6/413 (1%) Query: 12 AAFSLLAGTALAQTPDADSALVQKGAYVARLGDCVACHTALHGQSYAGGLEIKSPIGTIY 71 A F+L + +++ A++ L+++G Y+AR GDCVACHTA G+ +AGGL +++PIG IY Sbjct: 7 ATFALFSSCSVSA---AETDLIKQGEYLARAGDCVACHTAKGGKPFAGGLPMETPIGVIY 63 Query: 72 STNITPDPTYGIGRYTFAEFDEAVRHGIRKDGSTLYPAMPYPSFSRMTKEDMQALYAYFM 131 STNITPD T G+G Y+F +FD+AVRHG+ K GSTLYPAMPYPS++R++ DMQALYAYFM Sbjct: 64 STNITPDKT-GLGDYSFEDFDKAVRHGVAKSGSTLYPAMPYPSYARVSDSDMQALYAYFM 122 Query: 132 HGVKPVAQPDKQPDISWPLSMRWPLGIWRMMFSPSPKDFTPAPGTDPEIARGDYLVTGPG 191 GV+PVAQ +K DI WPLSMRWPL WR MF+P+ ++ DP I+RG YLV G G Sbjct: 123 KGVEPVAQENKDSDIPWPLSMRWPLAAWRWMFAPAVEEHQAQAVVDPVISRGAYLVEGLG 182 Query: 192 HCGACHTPRGFAMQEKALDAAGGPDFLSGGAPIDNWVAPSLRNDPVVGLGRWSEDDIYTF 251 HCGACHTPR MQEKAL A G FL+G AP++ W+A SLR D GLG WSE+ + F Sbjct: 183 HCGACHTPRALTMQEKALSATDGNAFLAGSAPLEGWIAKSLRGDHKDGLGSWSEEQLVQF 242 Query: 252 LKSGRIDHSAVFGGMGDVVAWSTQYFTDDDLHAIAKYLKSLPPVPPSQGNYTYDPSTANM 311 LK+GR D SAVFGGM DVV S QY +++DL AIA+YLKSLP V P +TYD A Sbjct: 243 LKTGRSDRSAVFGGMSDVVVHSMQYMSENDLTAIARYLKSLPAVDPKDSPHTYDKQVAEA 302 Query: 312 LASGNTASVPGADTYVKECAICHRNDGGGVARMFPPLAGNPVVVTENPTSLVNVIAHGGV 371 L G+ S GA Y+ CA CHR DG G R+FP LAGNPV+ T + TSL+N++ +GG Sbjct: 303 LWKGDD-SQRGASVYIDNCAACHRTDGHGYTRVFPALAGNPVLQTADATSLINIVLNGGT 361 Query: 372 LPPSNWAPSAVAMPGYSKSLSAQQIADVVNFIRTSWGNKAPGTVTAADVTKLR 424 LP ++ APS MP ++ LS Q++ADVV+F+R SWGN G ++AA V +R Sbjct: 362 LPATHTAPSTFTMPAFAWRLSDQEVADVVSFVRGSWGNTG-GAISAAQVADIR 413 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: 716 Number of extensions: 36 Number of successful extensions: 5 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: 420 Length adjustment: 32 Effective length of query: 436 Effective length of database: 388 Effective search space: 169168 Effective search space used: 169168 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