Align Alcohol dehydrogenase (quinone), dehydrogenase subunit; ADH; Alcohol dehydrogenase (quinone), acceptor subunit; Alcohol dehydrogenase (quinone), subunit I; Ethanol:Q2 reductase; G3-ADH subunit I; Quinohemoprotein alcohol dehydrogenase; Quinohemoprotein-cytochrome c complex; Ubiquinol oxidase; EC 1.1.5.5 (characterized)
to candidate Pf6N2E2_1389 Quino(hemo)protein alcohol dehydrogenase, PQQ-dependent (EC 1.1.99.8)
Query= SwissProt::O05542 (757 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1389 Length = 618 Score = 322 bits (825), Expect = 4e-92 Identities = 207/575 (36%), Positives = 301/575 (52%), Gaps = 64/575 (11%) Query: 53 DWLSYGRSYSEQRYSPLDQINTENVGKLKLAWHYDL--DTNRGQEGTPLIVNGVMYATTN 110 D L YG + QR+SPL Q+N +NV KL AW Y + RGQE ++ +GV+Y T + Sbjct: 46 DVLQYGMGTNAQRWSPLAQVNDKNVFKLTPAWSYSFGDEKQRGQESQAIVSDGVVYVTGS 105 Query: 111 WSKMKALDAATGKLLWSYDPKVPGNIADRGCCDTVSRGAAYWNGKVYFGTFDGRLIALDA 170 +S++ ALDA TGK LW+Y+ ++P NI R CCD V+RGAA + K+YFGT D R++ALD Sbjct: 106 YSRVFALDAKTGKRLWTYNHRLPDNI--RPCCDVVNRGAAIYGDKIYFGTLDARVVALDK 163 Query: 171 KTGKLVWSVYTIPKEAQLG-HQRSYTVDGAPRIAK----GKVLI--GNGGAEFGARGFVS 223 TGK+VW+ + G H YT+ GAP + K GKVL+ G+ G EFG G + Sbjct: 164 NTGKVVWN-------KKFGDHAGGYTMTGAPVLIKDKTSGKVLLIHGSSGDEFGVVGQLF 216 Query: 224 AFDAETGKLDWRFFTVPNPENKPDGAASDDILMSKAYPTW--------GKNGAWKQQGGG 275 A D +TG+ W V + +G S KA P+W GK AW GG Sbjct: 217 ARDPDTGEEVWMRPFVEGHMGRLNGKDSTPTGDVKA-PSWPDDKTTETGKVEAWSH--GG 273 Query: 276 GTVWDSLVYDPVTDLVYLGVGNGSPWNYKFRSEGKG-----DNLFLGSIVAINPDTGKYV 330 G W S +D T+ + +G GN PWN R+ G D+L+ V ++P TG+ Sbjct: 274 GAPWQSASFDAETNTIIVGAGNPGPWNTWARTAKDGNPHDYDSLYTSGQVGVDPSTGEVK 333 Query: 331 WHFQETPMDEWDYTSVQQIMTLDMP-VNGEMRHVIVHAPKNGFFYIIDAKTGKFITGKPY 389 W +Q TP D WD++ +++ D +G++ HA +NGFFY++D GK P+ Sbjct: 334 WFYQHTPNDAWDFSGNNELVLFDYKDKDGKVVKATAHADRNGFFYVVDRNNGKLQNAFPF 393 Query: 390 TYE-NWANGLDPVTGRP------NYVPDALWTLTGKPWLGIPGELGGHNFAAMAYSPKTK 442 WA+ +D TGRP GKP P LGG N+ MAYS T Sbjct: 394 VDNITWASHIDLKTGRPVENAGQRPAKPLPGETKGKPVEVSPPFLGGKNWNPMAYSQDTG 453 Query: 443 LVYIPAQQIPLLYDGQKGGFKAYHDAWNLGLDMNKIGLFDDNDPEHVAAKKDFLKVLKGW 502 L Y+P Q Y ++ +K +G + + ++DD HV + L+ + Sbjct: 454 LFYVPGNQWKEEYWTEEVNYKKGSAYLGMGFRIKR--MYDD----HVGS----LRAMNPT 503 Query: 503 T--VAWDPEKMAPAFTINHKGPWNGGLLATAGNVIFQGLANGEFHAYDATNGNDLYSFPA 560 T V W+ ++ P + G+LAT GN++F G +G F A+DA G +L+ F Sbjct: 504 TGKVVWEHKEPLPLWA---------GVLATKGNLVFTGTGDGFFKAFDAKTGKELWKFQT 554 Query: 561 QSAIIAPPVTYTANGKQYVAVEVGWGGIYPFLYGG 595 S I++PP+T+ +G+Q++ V VG+GG P L+GG Sbjct: 555 GSGIVSPPITWEQDGEQFIGVTVGYGGAVP-LWGG 588 Lambda K H 0.317 0.136 0.435 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: 1954 Number of extensions: 179 Number of successful extensions: 24 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: 757 Length of database: 618 Length adjustment: 39 Effective length of query: 718 Effective length of database: 579 Effective search space: 415722 Effective search space used: 415722 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 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