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 Ac3H11_2872 Putative diheme cytochrome c-553
Query= SwissProt::P0A388 (468 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2872 Length = 426 Score = 286 bits (733), Expect = 7e-82 Identities = 158/394 (40%), Positives = 219/394 (55%), Gaps = 17/394 (4%) Query: 24 QTPDADSALVQKGAYVARLGDCVACHTALHGQSYAGGLEIKSPIGTIYSTNITPDPTYGI 83 +T + ALVQ+G Y+AR+G+C+ACHT G +AGG I++P G ++S+N+TPD GI Sbjct: 37 ETLQSTPALVQRGEYLARVGNCMACHTTQGGAPFAGGRGIETPFGVVHSSNLTPDKAQGI 96 Query: 84 GRYTFAEFDEAVRHGIRKDGSTLYPAMPYPSFSRMTKEDMQALYAYFMHGVKPVAQPDKQ 143 G +T AEF A+ HG KDG LYPA PYP+++++T+ED A++AY + VA+P++ Sbjct: 97 GSWTSAEFWRAMHHGRSKDGRLLYPAFPYPNYTQVTREDSDAIFAY-LQSQPAVAEPNRA 155 Query: 144 PDISWPLSMRWPLGIWRMMFSPSPKDFTPAPGTDPEIARGDYLVTGPGHCGACHTPRGFA 203 + +P + + LG+WR +F +P P E RG YLV G GHC ACHTPR Sbjct: 156 HALRFPYNTQAALGVWRALFF-TPGAPQPEATQSAEYNRGAYLVNGLGHCTACHTPR--- 211 Query: 204 MQEKALDAAGGPDFLSGG-APIDNWVAPSLRNDPVVGLGRWSEDDIYTFLKSGRIDHSAV 262 AL A +GG P+ NW AP+L G+ W DD+ LK+G +V Sbjct: 212 ---NALGATTDAKAFTGGLIPVQNWYAPALNAAHEAGVKEWKTDDVVALLKTGVAPQGSV 268 Query: 263 FGGMGDVVAWSTQYFTDDDLHAIAKYLKSLPPVPPSQGNYTYDPSTANMLASGNTASVPG 322 G M +VV S Q+ +D D A+A YL++LP + A A +A G Sbjct: 269 LGPMAEVVFRSAQHLSDADARAMAVYLQALP--------QQEHRALAAGAAPPASALARG 320 Query: 323 ADTYVKECAICHRNDGGGVARMFPPLAGNPVVVTENPTSLVNVIAHGGVLPPSNWAPSAV 382 A Y + CA CH + G G FP LAGN V +PT+LV V+ GG LP + P Sbjct: 321 AKVYEQHCAQCHGDQGQGEPGAFPALAGNRAVTLADPTNLVRVVLQGGYLPATAGNPRPH 380 Query: 383 AMPGYSKSLSAQQIADVVNFIRTSWGNKAPGTVT 416 MP + + LS + IA V +R SWGN+APG T Sbjct: 381 GMPPFQQLLSDEDIAAVTTLVRNSWGNRAPGVGT 414 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: 649 Number of extensions: 53 Number of successful extensions: 7 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: 426 Length adjustment: 33 Effective length of query: 435 Effective length of database: 393 Effective search space: 170955 Effective search space used: 170955 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