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_RS22390 HSERO_RS22390 alcohol dehydrogenase
Query= SwissProt::P0A388 (468 letters) >FitnessBrowser__HerbieS:HSERO_RS22390 Length = 466 Score = 428 bits (1100), Expect = e-124 Identities = 213/420 (50%), Positives = 280/420 (66%), Gaps = 9/420 (2%) Query: 18 AGTALAQ------TPDADSALVQKGAYVARLGDCVACHTALHGQSYAGGLEIKSPIGTIY 71 A TALAQ + A+ + +GAY+AR GDCVACHT+ G +AGGL + SPIG IY Sbjct: 46 ADTALAQRIAAQGSASAEDQQILRGAYLARAGDCVACHTSKGGAPFAGGLALASPIGAIY 105 Query: 72 STNITPDPTYGIGRYTFAEFDEAVRHGIRKDGSTLYPAMPYPSFSRMTKEDMQALYAYFM 131 STNITPD +GIG +++ +F +R G+ K G T+YPAMPYPS+SR+T EDMQALYAYF Sbjct: 106 STNITPDKQHGIGDWSYEDFARLMRTGVTKAGYTVYPAMPYPSYSRLTDEDMQALYAYFS 165 Query: 132 HGVKPVAQPDKQPDISWPLSMRWPLGIWRMMFSPSPKDFTPAPGTDPEIARGDYLVTGPG 191 V P AQ ++ DI WPLSMRWPL +WR +F+P+P +TPA G+D E+ARG YLV G G Sbjct: 166 KAVPPSAQENRANDIPWPLSMRWPLALWRKVFAPTPAPYTPAAGSDQELARGAYLVEGLG 225 Query: 192 HCGACHTPRGFAMQEKALDAAGGPDFLSGGAPIDNWVAPSLRNDPVVGLGRWSEDDIYTF 251 HCG+CH+PR MQEKAL GG FLSGG +D W PSLRN+ G+ WS+ D+ F Sbjct: 226 HCGSCHSPRAVTMQEKALKEDGGRLFLSGGQVVDGWSVPSLRNEHGGGIAGWSQADLVEF 285 Query: 252 LKSGRIDHSAVFGGMGDVVAWSTQYFTDDDLHAIAKYLKSLPPVPPSQGNYTYDPSTANM 311 L++GR ++A FG M DV+ S QY +D DL+A+A+YL SLPP Y YD +TA Sbjct: 286 LRTGRNQYTASFGAMNDVIEDSMQYMSDADLNAMARYLLSLPP-RQQAAPYRYDSATAQA 344 Query: 312 LASGNTASVPGADTYVKECAICHRNDGGGVARMFPPLAGNPVVVTENPTSLVNVIAHGGV 371 G PGA Y+ CA CHR++G G + FP LAGNPV+ T + TS + +I GG Sbjct: 345 AYDGRPDG-PGARIYLDRCAACHRSNGTGYGKAFPALAGNPVLQTSDATSAIRIILQGGR 403 Query: 372 LPPSNWAPSAVAMPGYSKSLSAQQIADVVNFIRTSWGNKAPGTVTAADVTKLRDTGAPVS 431 P + A + + M Y++ L QQ+A+V ++I+T+WGN+ GT TAA+V K+R T PV+ Sbjct: 404 QPSTASATAGLVMAPYAQLLDDQQVAEVTSYIQTAWGNRG-GTTTAAEVAKVRKTAVPVA 462 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: 792 Number of extensions: 50 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: 466 Length adjustment: 33 Effective length of query: 435 Effective length of database: 433 Effective search space: 188355 Effective search space used: 188355 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