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 N515DRAFT_2297 N515DRAFT_2297 Cytochrome c, mono- and diheme variants
Query= SwissProt::P0A388 (468 letters) >FitnessBrowser__Dyella79:N515DRAFT_2297 Length = 441 Score = 237 bits (604), Expect = 7e-67 Identities = 144/415 (34%), Positives = 207/415 (49%), Gaps = 27/415 (6%) Query: 21 ALAQTPDADSALVQKGAYVARLGDCVACHTALHGQSYAGGLEIKSPIGTIYSTNITPDPT 80 A A P + + V +G Y+ R DC ACHT GQ Y GG+ K P GTIYSTNIT D Sbjct: 41 AAAGAPASLTDPVARGEYLTRAADCAACHTVPGGQPYTGGVAFKMPFGTIYSTNITADKE 100 Query: 81 YGIGRYTFAEFDEAVRHGIRKDGSTLYPAMPYPSFSRMTKEDMQALYAYFMHGVKPVAQP 140 GIG ++ EF A+ G+RKDG LYPA PY S++ ++++D+ A+ AY + + P P Sbjct: 101 TGIGDWSDDEFVRALHAGVRKDGKPLYPAFPYTSYTALSRDDVLAIKAY-LFSLPPKHAP 159 Query: 141 DKQPDISWPLSMRWPLGIWRMMFSPSPKDFTPAPGTDPEIARGDYLVTGPGHCGACHTPR 200 + ++S+P RW L +W +F + + P G RG YL T GHC CHTPR Sbjct: 160 ARPNELSFPFDQRWGLSVWNALFLKKQR-YEPVQGKSQAWNRGAYLATALGHCDECHTPR 218 Query: 201 GFAMQEKALDAAGGPDFLSGGAPIDNWVAPSLRNDPVVGLGRWSEDDIYTFLKSGRID-H 259 A+ A D LSG + W A ++ +D G+G WSE + +L G Sbjct: 219 ------NAMYALKRGDALSGEV-LQGWKAYNITSDKTYGIGNWSEQQLADYLSKGHASGR 271 Query: 260 SAVFGGMGDVVAWSTQYFTDDDLHAIAKYLKSLPPVPPSQGNYTYDPSTANMLASGNTAS 319 G MG+VV +S QY T +D+ A+ YL+ V P QG+ + + LA ++AS Sbjct: 272 GTASGPMGEVVQYSLQYLTPEDIGALVTYLRE---VKPQQGSAGSEVNDRPALALASSAS 328 Query: 320 VPGADTYVK----------ECAICHRNDGGGVARMFPPLAGNPVVVTENPTSLVNVIAHG 369 PGA+ + C+ CH +G G L G +L VI G Sbjct: 329 APGAEELAQGGLGQHLFQGACSSCHLWNGQGRQSEAAALLGTQAANDPQAHNLTQVILQG 388 Query: 370 GVLPPSNWAPSAVAMPGYSKSLSAQQIADVVNFIRTSWGNKAPGTVTAADVTKLR 424 L A +MP + ++ + ++A + NF+ T +G K P T+TA +V K R Sbjct: 389 STL---RTAHGETSMPSFGQAYTDAEVAALGNFVLTHFGGK-PATLTADEVAKRR 439 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: 650 Number of extensions: 48 Number of successful extensions: 10 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: 441 Length adjustment: 33 Effective length of query: 435 Effective length of database: 408 Effective search space: 177480 Effective search space used: 177480 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