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 AZOBR_RS04080 AZOBR_RS04080 cytochrome C
Query= SwissProt::P0A388 (468 letters) >FitnessBrowser__azobra:AZOBR_RS04080 Length = 288 Score = 112 bits (280), Expect = 2e-29 Identities = 97/301 (32%), Positives = 144/301 (47%), Gaps = 39/301 (12%) Query: 10 SAAAFSLLAG---TALAQTPDADSALVQKGAYVARLGDCVACHTA------LHGQSYAGG 60 S AA +L+G TA A+TP +S + + A V + C CHT + G+ AGG Sbjct: 9 SVAACLMLSGMIATAGAETPP-ESPVERGRALVNGIVACGNCHTPQGPNGPVAGRELAGG 67 Query: 61 LEIKSPIGTIYSTNITPDPTYGIGRYTFAEFDEAVRHGIRKDGSTLYPAMPYPSFSRMTK 120 T Y++NITPDP GIGR+T + A+R G R DGS + P MP+ + ++ Sbjct: 68 TPFVEEPFTAYASNITPDPETGIGRWTDEQLIAAIREGRRPDGSLIGPPMPFGFYRGLSD 127 Query: 121 EDMQALYAYFMHGVKPV--AQPDKQPDISWPLSMRWPLGIWRMMFSPSPKDFTPAPGTDP 178 D++A+ AY + V PV + P + ++ P + P+G P TDP Sbjct: 128 GDLRAIVAY-LRSVPPVRHSVPKSEYRMALPAAYGPPVG-----------SVAEIPRTDP 175 Query: 179 EIARGDYLVTGPGHCGACHTPRGFAMQEKALD----AAGGPDFLSGGAPIDNWVAPSLRN 234 + G Y+ GHC CHTP + + LD AGG +F P N V+ ++ Sbjct: 176 -VTYGAYMAGPLGHCMECHTP---MLPDGRLDMTRMGAGGRNFT---GPWGNAVSRNITQ 228 Query: 235 DPVVGLGRWSEDDIYTFLKSG-RIDHSAVFGGMGDVVAWSTQYFTDDDLHAIAKYLKSLP 293 D GLG W++ +I + G R D + MG S +D +L A+ YL++LP Sbjct: 229 DKEHGLGGWTDAEIRKAITEGVRPDGHRLSPPMGYHYYKS---MSDGELGALVAYLRTLP 285 Query: 294 P 294 P Sbjct: 286 P 286 Score = 66.2 bits (160), Expect = 1e-15 Identities = 54/177 (30%), Positives = 79/177 (44%), Gaps = 18/177 (10%) Query: 171 TPAPGTDPE--IARGDYLVTGPGHCGACHTPRGFAMQEKALDAAGGPDFLSGGAPIDNWV 228 T T PE + RG LV G CG CHTP+G + AGG F+ P + Sbjct: 22 TAGAETPPESPVERGRALVNGIVACGNCHTPQGPNGPVAGRELAGGTPFVE--EPFTAY- 78 Query: 229 APSLRNDPVVGLGRWSEDDIYTFLKSGRIDHSAVFGGMGDVVAWSTQYFTDDDLHAIAKY 288 A ++ DP G+GRW+++ + ++ GR ++ G + + +D DL AI Y Sbjct: 79 ASNITPDPETGIGRWTDEQLIAAIREGRRPDGSLIGPPMPFGFY--RGLSDGDLRAIVAY 136 Query: 289 LKSLPPVPPS--QGNYTYDPSTANMLASGNTASVPGAD--TY-------VKECAICH 334 L+S+PPV S + Y A G+ A +P D TY + C CH Sbjct: 137 LRSVPPVRHSVPKSEYRMALPAAYGPPVGSVAEIPRTDPVTYGAYMAGPLGHCMECH 193 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: 500 Number of extensions: 39 Number of successful extensions: 9 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 468 Length of database: 288 Length adjustment: 30 Effective length of query: 438 Effective length of database: 258 Effective search space: 113004 Effective search space used: 113004 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: 49 (23.5 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