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_02833 H281DRAFT_02833 Cytochrome c, mono- and diheme variants
Query= SwissProt::Q47945 (478 letters) >FitnessBrowser__Burk376:H281DRAFT_02833 Length = 438 Score = 317 bits (813), Expect = 4e-91 Identities = 182/440 (41%), Positives = 250/440 (56%), Gaps = 32/440 (7%) Query: 18 WKLAAAIGLMAVSFGAAHAQDA------DEALIKRGEYVARLSDCIACHTALHGQPYAGG 71 W L+ A + A AQDA D ALIKRGEY+A DC+ACHT G+P+AGG Sbjct: 8 WMLSGAFAWSSALPVCAFAQDAKAVDGNDAALIKRGEYLATAGDCMACHTTAKGKPFAGG 67 Query: 72 LEIKSP-IGTIYSTNITPDPEHGIGNYTLEDFTKALRKGIRKDGATVYPAMPYPEFARLS 130 L +K P +GTIYS+NITPDP+ GIG ++LEDF +ALRKG+ KDG +YPAMPY +A++S Sbjct: 68 LPLKVPMLGTIYSSNITPDPQTGIGTWSLEDFDRALRKGVSKDGHNLYPAMPYVSYAKVS 127 Query: 131 DDDIRAMYAFFMHGVKPVALQNKAPDISWPLSMRWPLGMWRAMFVPSMTPGVDKSISDPE 190 D D++A+YA+F +GV PV +A DI+WPL+MRWPL +W MF+ S P K E Sbjct: 128 DGDVKALYAYFRYGVVPVQQATRASDIAWPLNMRWPLTVWNWMFLKS-GPYQAKPQQSAE 186 Query: 191 VARGEYLVNGPGHCGECHTPRGFGMQVKAYGTAGGNAYLAGGAPIDNWIAPSLRSNSDTG 250 RG YLV G HC CHTPRGF MQ +A G GG+ + +W ++ S+ D+G Sbjct: 187 WNRGAYLVQGLAHCSTCHTPRGFAMQEQALDETGSG--FLGGSVLADWDGYNITSSPDSG 244 Query: 251 LGRWSEDDIVTFLKSGRIDHSA-VFGGMADVVAYSTQHWSDDDLRATAKYLKSMPAVPEG 309 +G WS +V +L++G + A G MA+ V +S SD D+ A A Y++++P V +G Sbjct: 245 IGGWSHTQLVQYLQTGSVPGLAQAAGPMAEAVEHSFSKMSDADIGAIATYVRTVPPVNDG 304 Query: 310 KNLGQDDG----------QTTALLNKGGQGNAG----AEVYLHNCAICHMNDGTGV-NRM 354 G G T +G N G A +YL NCA CH G G + Sbjct: 305 ---GAQSGSRSRSAWGKPSTDVARLRGVAMNDGTLDPARLYLGNCATCHQASGKGTPDGY 361 Query: 355 FPPLAGNPVVITDDPTSLANVVAFGGILPPTNSAPSAVAMPGFKNHLSDQEMADVVNFMR 414 +PPL N V +P +L V+ G +A + V MP F L+D ++A + N++ Sbjct: 362 YPPLLHNSTVGASNPGNLMQVILHG---VQRKAAGNDVGMPAFAAQLNDAQIAALTNYVT 418 Query: 415 KGWGNNAPGTVSASDIQKLR 434 +GN A VS D+ +LR Sbjct: 419 TQFGNPAAQRVSEKDVARLR 438 Lambda K H 0.317 0.134 0.421 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: 724 Number of extensions: 55 Number of successful extensions: 8 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: 478 Length of database: 438 Length adjustment: 33 Effective length of query: 445 Effective length of database: 405 Effective search space: 180225 Effective search space used: 180225 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