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 WP_086510868.1 BZY95_RS15845 aldehyde oxidase
Query= SwissProt::P0A388 (468 letters) >NCBI__GCF_002151265.1:WP_086510868.1 Length = 999 Score = 207 bits (527), Expect = 1e-57 Identities = 145/438 (33%), Positives = 215/438 (49%), Gaps = 42/438 (9%) Query: 11 AAAFSLLAGTALAQTPDA--------------DSALVQKGAYVARLGDCVACHTALHGQS 56 AAA + +AGTA+ P + +++G VA GDC ACHTA GQ Sbjct: 570 AAALTAVAGTAVMAWPWKGAITPINRPAANLYSAETIERGRLVAAAGDCAACHTAEGGQE 629 Query: 57 YAGGLEIKSPIGTIYSTNITPDPTYGIGRYTFAEFDEAVRHGIRKDGSTLYPAMPYPSFS 116 AGG +P GT+YSTN+TPD GIGR+++A F+ A+RHGI +DG LYPA PY +F+ Sbjct: 630 NAGGRAFDTPFGTLYSTNLTPDEETGIGRWSYAAFERAMRHGISRDGKHLYPAFPYTAFA 689 Query: 117 RMTKEDMQALYAYFMHGVKPVAQPDKQPD-ISWPLSMRWPLGIWRMMFSPSPKDFTPAPG 175 +++ DMQALYAY M +P + + +S+P + R + W ++ P F P PG Sbjct: 690 KISDADMQALYAYLM--AQPAVSAETPANALSFPFNFRPLMAGWNALYH-DPNPFEPDPG 746 Query: 176 TDPEIARGDYLVTGPGHCGACHTPRGFAMQEKALDAAGGPDFLSGGAPIDNWVAPSLR-- 233 RG YL G GHC ACH+PR A+ A + GA +D W AP L Sbjct: 747 QSDLYNRGAYLAEGLGHCSACHSPR------NAMGAEQRGEHSLAGAMVDGWEAPPLNRL 800 Query: 234 -NDPVVGLGRWSEDDIYTFLKSGRID-HSAVFGGMGDVVAWSTQYFTDDDLHAIAKYLKS 291 P+ WSE +Y +L+ G H G M VVA + + D+ A+A Y+ + Sbjct: 801 SRSPI----PWSETSLYDYLRHGASSLHGVASGPMAPVVAGLGE-LPEYDVRALAHYV-A 854 Query: 292 LPPVPPSQGNYTYDPSTANMLA---SGNTASVPGADTYVKECAICHRNDG-GGVARMFPP 347 + P+ + T A +A SG G + CA CH +G Sbjct: 855 VQMDAPAGDSETVRADAAVRIATAQSGPAGMEEGERLFEGACASCHMENGTPSFTSAQTS 914 Query: 348 LAGNPVVVTENPTSLVNVIAHGGVLPPSNWAPSAVAMPGYSKSLSAQQIADVVNFIRTSW 407 LA N + +++P +++ I GGV ++ P MPG++ S S Q+ + ++R + Sbjct: 915 LALNTNLHSQHPDNVIQSIL-GGV--HADHVPGLGNMPGFADSFSDSQVVTLTAYLRARF 971 Query: 408 G-NKAPGTVTAADVTKLR 424 ++AP + VT +R Sbjct: 972 APDQAPWRNIESRVTTIR 989 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: 1410 Number of extensions: 86 Number of successful extensions: 5 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: 999 Length adjustment: 39 Effective length of query: 429 Effective length of database: 960 Effective search space: 411840 Effective search space used: 411840 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: 54 (25.4 bits)
This GapMind analysis is from Sep 24 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