Align alcohol dehydrogenase (quinone) (EC 1.1.5.5) (characterized)
to candidate WP_086510114.1 BZY95_RS11790 PQQ-dependent dehydrogenase, methanol/ethanol family
Query= BRENDA::Q44002 (739 letters) >NCBI__GCF_002151265.1:WP_086510114.1 Length = 592 Score = 340 bits (871), Expect = 2e-97 Identities = 205/554 (37%), Positives = 282/554 (50%), Gaps = 46/554 (8%) Query: 57 MTYGRTYSEQRYSPLDQINRSNVGNLKLAWYLDL--DTNRGQEGTPLVIDGVMYATTNWS 114 +T G QRYSPL +N NV L+ W + RGQE PLV DGVMY T ++S Sbjct: 46 VTNGMGLHGQRYSPLTTLNTDNVHQLRPVWAFSFGGEKQRGQESQPLVKDGVMYVTGSYS 105 Query: 115 MMKAVDAATGKLLWSYDPRVPGNIADKGCCDTVNRGAAYWNGKVYFGTFDGRLIALDAKT 174 + AVDA TG+ +W Y+ R+P I CCD VNRGAA + KVYFGT D RL+ALD +T Sbjct: 106 RIWAVDAYTGEEIWQYEARLPDGIMP--CCDVVNRGAAIYGDKVYFGTLDARLVALDRET 163 Query: 175 GKLVWSVNTIPPEAELGKQRSYTVDGAPRIAKGRVIIGNGGSEFGARGFVTAFDAETGKV 234 G++ W +A + + AP + G++I G G EFG G + AFDAETG Sbjct: 164 GRVQWIKRVADYQA------GHAISAAPIVIDGKLITGVAGGEFGVVGTIFAFDAETGDE 217 Query: 235 DWRFFTAPNPKN------EPDHTASDSVLMNKAYQTWSPTGAWTRQGGGGTVWDSIVYDP 288 W T P + E + + +A TW P W Q GGG W YD Sbjct: 218 LW---TRPVIEGHMGYVYENGEAVENGITGGEAGLTW-PGDMW--QQGGGAPWLGGFYDA 271 Query: 289 VADLVYLGVGNGSPWNYKYRSEGKGDNLFLGSIVALKPETGEYVWHFQETPMDQWDFTSV 348 + +G GN +PWN R GDNL+ S +A+ P+ G WHFQ TP D WD+ V Sbjct: 272 DTHTLLIGTGNPAPWNSHLRP---GDNLYSSSRLAIDPDDGSIKWHFQATPNDGWDYDGV 328 Query: 349 QQIMTLDLPINGETRHVIVHAPKNGFFYIIDAKTGEFISGKNYV-YVNWASGLDPKTGRP 407 ++++ D NG A +NGFFY+++ + GEFI G + + WA GLD + GRP Sbjct: 329 NEVISFDYEENGSVIKAAATADRNGFFYVLNRENGEFIRGFPFADKITWAEGLD-ENGRP 387 Query: 408 IYNPDA-------LYTLTGKEWYGIPGDLGGHNFAAMAFSPKTGLVYIPAQQVPFLYTNQ 460 I+NP + G+ P LG N+ MA+S TGL YIP+ + N+ Sbjct: 388 IFNPAGRPGNPADVADERGESVQAYPAFLGAKNWNPMAYSQDTGLFYIPSNEWMMDIWNE 447 Query: 461 VGGFTPHPDSWNLGLDMNKVGIPDSPEAKQAFVKDLKGWIVAWDPQKQAEAWRVDHKGPW 520 P S+ G G P D G + A DP+ E WR +++ P Sbjct: 448 -------PVSYRKGAAYLGAGFTIRPAND-----DYIGVLRAVDPRTGEEVWRHENRAPL 495 Query: 521 NGGILATGGDLLFQGLANGEFHAYDATNGSDLFHFAADSGIIAPPVTYLANGKQYVAVEV 580 GG++ T G+L+F G G A+DA G +L+ F SG++ P+T+ +G+QYV+V Sbjct: 496 WGGVMTTAGNLVFTGTPEGYLKAFDAVTGEELWGFNTGSGVVGTPITWEMDGEQYVSVVS 555 Query: 581 GWGGIYPFFLGGLA 594 GWGG P + G +A Sbjct: 556 GWGGAVPLWGGEVA 569 Lambda K H 0.318 0.137 0.440 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: 1758 Number of extensions: 153 Number of successful extensions: 18 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: 739 Length of database: 592 Length adjustment: 38 Effective length of query: 701 Effective length of database: 554 Effective search space: 388354 Effective search space used: 388354 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: 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