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 H281DRAFT_01762 H281DRAFT_01762 Cytochrome c, mono- and diheme variants
Query= SwissProt::P0A388 (468 letters) >FitnessBrowser__Burk376:H281DRAFT_01762 Length = 450 Score = 343 bits (880), Expect = 7e-99 Identities = 187/406 (46%), Positives = 247/406 (60%), Gaps = 17/406 (4%) Query: 28 ADSALVQKGAYVARLGDCVACHTA-LHGQSYAGGLEIKSPIGTIYSTNITPDPTYGIGRY 86 +D AL+ +GAY+A+LGDC CHT G +AGGL + SP GTIYSTNITPDP GIGRY Sbjct: 48 SDPALISRGAYLAKLGDCAGCHTVPKQGAPFAGGLPMGSPFGTIYSTNITPDPQTGIGRY 107 Query: 87 TFAEFDEAVRHGIRKDGSTLYPAMPYPSFSRMTKEDMQALYAYFMHGVKPVAQPDKQPDI 146 ++A+F+ A+R G+ G LYPAMPY SF+++ DM ALYAYFMHGV+PVA + + Sbjct: 108 SYADFERALRDGVAPGGKRLYPAMPYASFTKINDSDMHALYAYFMHGVQPVAHRPPETKL 167 Query: 147 SWPLSMRWPLGIWRMMFSPSPKDFTPAPGTDPEIARGDYLVTGPGHCGACHTPRGFAMQE 206 +P S RW L W F + F P D RG Y+V GHCGACHTPRG +E Sbjct: 168 PFPFSQRWGLAFWDFAFVQHER-FIPDGKRDALWNRGAYIVQSLGHCGACHTPRGPGFEE 226 Query: 207 KALDAAGGPDFLSGGAPIDNWVAPSLRNDPVVGLGRWSEDDIYTFLKSGR-ID-HSAVFG 264 + D + +L+GG D+W AP+L DP GLGR S DI +FLKSG +D H FG Sbjct: 227 RGYDES-SKLYLTGGTN-DHWFAPNLTGDPGSGLGRLSPRDIASFLKSGHGVDVHVVTFG 284 Query: 265 GMGDVVAWSTQYFTDDDLHAIAKYLKSLPPVPPSQGNYTYDPSTANM------LASGNTA 318 M +VV S QYF+DDDL+A+A+YLKSL P Q + Y P+T + L +G Sbjct: 285 SMVEVVEDSGQYFSDDDLNAVARYLKSL---PARQSSGAYKPNTQKLQETAVSLKAGEVE 341 Query: 319 SVPGADTYVKECAICHRNDGGGVARMFPPLAGNPVVVTENPTSLVNVIAHGGVLPPSNWA 378 PGA Y+ CA CH+ DG G FP LAGNP V+ + +SL+ ++ GG P + Sbjct: 342 R-PGAGLYMSFCAKCHQADGRGEPHKFPALAGNPAVLAPDTSSLIRLVLEGGTSPQTENG 400 Query: 379 PSAVAMPGYSKSLSAQQIADVVNFIRTSWGNKAPGTVTAADVTKLR 424 P MP + + ++IA V++F+RT+WGN+A V DV+ +R Sbjct: 401 PIHREMPAFRNQFTDREIARVLSFVRTAWGNEA-RPVATRDVSTVR 445 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: 739 Number of extensions: 53 Number of successful extensions: 9 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: 450 Length adjustment: 33 Effective length of query: 435 Effective length of database: 417 Effective search space: 181395 Effective search space used: 181395 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