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 BPHYT_RS30785 BPHYT_RS30785 alcohol dehydrogenase
Query= SwissProt::P0A388 (468 letters) >FitnessBrowser__BFirm:BPHYT_RS30785 Length = 448 Score = 346 bits (887), Expect = 1e-99 Identities = 181/407 (44%), Positives = 245/407 (60%), Gaps = 10/407 (2%) Query: 25 TPDADSALVQKGAYVARLGDCVACHTALHGQSYAGGLEIKSPIGTIYSTNITPDPTYGIG 84 TP + A + KGAY+A++GDC ACHT Q +AGGL + +P GT+YSTNITPD + GIG Sbjct: 38 TPVSADAQLAKGAYLAKVGDCAACHTVNKAQPFAGGLPLATPFGTLYSTNITPDASTGIG 97 Query: 85 RYTFAEFDEAVRHGIRKDGSTLYPAMPYPSFSRMTKEDMQALYAYFMHGVKPVAQPDKQP 144 Y++A+F A+R GI KDG LYPAMPYPS++++ DM ALY YFM GVKP+ QPD+ Sbjct: 98 GYSYADFATALRQGIAKDGHRLYPAMPYPSYAKIDDADMHALYRYFMQGVKPIGQPDRAS 157 Query: 145 DISWPLSMRWPLGIWRMMFSPSPKDFTPAPGTDPEIARGDYLVTGPGHCGACHTPRGFAM 204 ++ +P ++R + +W +++ + P E RG YLV G HCGACHTP G Sbjct: 158 ELRFPFNVRALMTVWDRLYAHEQLPYQADPHQSVEWNRGAYLVQGLAHCGACHTPHGMLG 217 Query: 205 QEKALDAAGGPDFLSGGAPIDNWVAPSLRNDPVVGLGR---WSEDDIYTFLKSGRIDHSA 261 QE LD FLSG + W AP+LR WS+ D+ +L+SGR+ Sbjct: 218 QESVLDEKDNTAFLSGNT-LAGWYAPNLRGHKTQTSDSDNVWSKADLVAYLRSGRMHDGV 276 Query: 262 VFGGMGDVVAWSTQYFTDDDLHAIAKYLKSLP----PVPPSQGNYTYDPSTANMLASGNT 317 FG M +VV STQY DDDL+AIA YL S P PP+ TA L +G Sbjct: 277 AFGPMTEVVDDSTQYLHDDDLNAIATYLTSPPLQAGATPPAPQQTGRAEQTAIALRAGRV 336 Query: 318 ASVPGADTYVKECAICHRNDGGGVARMFPPLAGNPVVVTENPTSLVNVIAHGGVLPPSNW 377 S GA Y+ CA CHR DG G FP L GN V++ +P SL++++ G +P + Sbjct: 337 DS-SGARLYLDNCAACHRTDGTGAMPAFPSLRGNASVLSGDPASLIHIVLSGSHMPSTAA 395 Query: 378 APSAVAMPGYSKSLSAQQIADVVNFIRTSWGNKAPGTVTAADVTKLR 424 AP+ +AMP + L+ QQ+AD+++F+RTSWGN+A VTA +V K+R Sbjct: 396 APTPLAMPDFGWRLTDQQVADLLSFVRTSWGNRA-AAVTAGEVAKVR 441 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: 664 Number of extensions: 32 Number of successful extensions: 3 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: 448 Length adjustment: 33 Effective length of query: 435 Effective length of database: 415 Effective search space: 180525 Effective search space used: 180525 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