Align alcohol dehydrogenase [NAD(P)+] (EC 1.1.1.71); acetaldehyde dehydrogenase (acetylating) (EC 1.2.1.10) (characterized)
to candidate WP_003942060.1 C1M55_RS09025 iron-containing alcohol dehydrogenase
Query= BRENDA::A0A0H3W5U9 (873 letters) >NCBI__GCF_002893965.1:WP_003942060.1 Length = 401 Score = 179 bits (454), Expect = 3e-49 Identities = 128/437 (29%), Positives = 216/437 (49%), Gaps = 42/437 (9%) Query: 434 SVSDNVGVKHLLNIKTVAERRENMLWFRTPEKIYIKRGCLPVALDELKNVMGKKKAFIVT 493 SV+ V H ++ + A R ++ F PE ++ + A L+ G + F+VT Sbjct: 2 SVAYPDAVNHGVHRRGTAAR---LVKFHAPEIVFGIGSLVEAAHATLR--FGGFRPFLVT 56 Query: 494 DNFLYNNGYTKPITDKLDEMGIVHKTFFDVSPDPSLASAKAGAAEMLAFQPDTIIAVGGG 553 D L + G+ + D L E G+ + ++P+P AG + D IIA+GGG Sbjct: 57 DPGLIDAGWVSELEDHLTEQGLTATVWSGLTPNPKDFEIAAGFEVYQEGECDVIIALGGG 116 Query: 554 SAMDAAKIMWVMYEHPEVDFMDMAMRFMDIRKRVYTFPKMGQKAYFIAIPTSAGTGSEVT 613 S +DAAK + V+ + + +D + + + P + + +PT++GTG++V+ Sbjct: 117 SVIDAAKGVAVLAANGG-NILD----YEGVDQATKPIPPL------VMVPTTSGTGADVS 165 Query: 614 PFAVITDEKTGIKYPLADYELLPDMAIVDADMMMNAPKGLTAASGIDALTHALEAYVSML 673 F ++TD G K + L+PD+ ++D ++ P+ L AA+G+DALTH +EA+VS+ Sbjct: 166 QFCIVTDTTRGTKITIIGRALVPDVTVIDPRLLTTMPEWLNAATGLDALTHGIEAFVSLA 225 Query: 674 ATDYTDSLALRAIKMIFEYLPRAYENGASDPVAREKMANAATIAGMAFANAFLGVCHSMA 733 TD ALRA+ ++ E L ++ + AR MA A+ AG+AF NA LG H+M+ Sbjct: 226 HNPLTDHHALRAVGLVTENLVHTIQD-PMEMEARSVMAQASLEAGLAFTNAILGAAHAMS 284 Query: 734 HKLGAFYHLPHGVANALMINEVIRFNSS--EAPTKMGTFPQYDHPRTLERYAEIADYIGL 791 H++G LPHGV N +++ VIRFNS+ AP + IA + L Sbjct: 285 HQVGGMLDLPHGVINGILLPHVIRFNSTTDAAP-----------------FVAIAAALSL 327 Query: 792 KGKNN--EEKVENLIKAIDELKEKVGIRKTIKDYDIDEKEFLDRLDEMVEQAFDDQCTGT 849 + EE + ++ L +VG+ K + + + E++ L + A D C T Sbjct: 328 PEQRGTPEEAALAVADRVERLAREVGVPKGLGELGVREED----LSRLASFALLDACMST 383 Query: 850 NPRYPLMNEIRQMYLNA 866 NPR ++ ++ A Sbjct: 384 NPREATQEQMVALFRGA 400 Lambda K H 0.318 0.134 0.382 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: 768 Number of extensions: 38 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 1 Length of query: 873 Length of database: 401 Length adjustment: 37 Effective length of query: 836 Effective length of database: 364 Effective search space: 304304 Effective search space used: 304304 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: 53 (25.0 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