Align alcohol dehydrogenase (cytochrome c) (EC 1.1.2.8) (characterized)
to candidate WP_043530172.1 JH15_RS11025 cytochrome c
Query= BRENDA::D2SZY5 (472 letters) >NCBI__GCF_000759345.1:WP_043530172.1 Length = 435 Score = 348 bits (894), Expect = e-100 Identities = 190/438 (43%), Positives = 263/438 (60%), Gaps = 15/438 (3%) Query: 1 MMINRLKAALGAVAVGLLAGTSLAHAQNAD---EDLIKKGEYVARLGDCVACHTSLNGQK 57 ++I L AL ++ +G A + A AQ+ D + LI+KGEY+AR GDCVACHT+ + Sbjct: 3 IVIRLLSIALLSLFLGSQATHAQAPAQDRDPSRDALIEKGEYLARAGDCVACHTADENKM 62 Query: 58 YAGGLSIKTPIGTIYSTNITPDPTYGIGTYTFKEFDEAVRHGVRKDGATLYPAMPYPSFA 117 +AGGL+++TPIGTIYSTNITPDP GIG YT ++F A+R GV G LYPAMPYPS+A Sbjct: 63 FAGGLAMQTPIGTIYSTNITPDPETGIGRYTLEDFTRAMREGVTPAGHALYPAMPYPSYA 122 Query: 118 RMTQDDMKALYAYFMHGVQPIAQKNHPTDISWPMSMRWPLSIWRSVFAPAPKDFTPAPGT 177 R+T +DM+ALY YF+HGV+PI Q+N + I WP+SMRWPL IW +F P F P P Sbjct: 123 RITDEDMQALYVYFLHGVEPIQQQNRDSVIPWPLSMRWPLRIWSWMFTPDETGFDPDPER 182 Query: 178 DAEIARGEYLVTGPGHCGACHTPRGFGMQEKALDASGGPDFLGGGGVIDNWIAPSLRNDP 237 E RG YLV G GHCGACHTPRG QE+ A G FL GG +++ W + ++ +D Sbjct: 183 SDEWNRGAYLVEGLGHCGACHTPRGLAYQEQGFKA-GDNGFL-GGEMVEGWYSFNITSDS 240 Query: 238 VLGLGRWSDEDLFLFLKSGRTDHSA-AFGGMADVVGWSTQYYTDADLHAMVKYIKSLPPV 296 G+G W D+++ +L+ G A A G M +V+G S +Y DADL+A+ Y+KS+PP+ Sbjct: 241 EHGIGGWRDDEIVAYLRDGAVPGKAHAAGPMGEVIGHSLRYLDDADLYAIATYLKSVPPI 300 Query: 297 ---PPARGDYSYDASTAQMLDSNNFSGN---AGAKTYVEQCAICHRNDGGGVARMFPPLA 350 P+R A + +D F + AK Y+ CA CH + G G R P L Sbjct: 301 SDPEPSRFGQGEPADDVERMDDPGFVASPQGQAAKRYLTTCAYCHGDRGEGSRRGDPSLF 360 Query: 351 GNPVVVSDNPTSVAHIVVDGGVLPPTNWAPSAVAMPDYKNILSDQQIADVVNFIRSAWGN 410 + VV S + ++ ++++ GV TN V MP Y + L D+Q+A +VN++ +GN Sbjct: 361 NSSVVGSTHLNNLVRVILE-GVARETN--QGQVTMPGYADELDDEQMAQLVNYLVDRFGN 417 Query: 411 RAPANTTAADIQKLRLDH 428 DI +R H Sbjct: 418 PEAETLAPEDIAAMRSTH 435 Lambda K H 0.318 0.135 0.430 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: 701 Number of extensions: 46 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: 472 Length of database: 435 Length adjustment: 33 Effective length of query: 439 Effective length of database: 402 Effective search space: 176478 Effective search space used: 176478 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 (21.7 bits) S2: 51 (24.3 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