Align alcohol dehydrogenase (EC 1.1.1.1) (characterized)
to candidate WP_011840648.1 RSPH17029_RS04355 choline dehydrogenase
Query= BRENDA::Q76HN6 (526 letters) >NCBI__GCF_000015985.1:WP_011840648.1 Length = 548 Score = 377 bits (967), Expect = e-109 Identities = 223/528 (42%), Positives = 306/528 (57%), Gaps = 12/528 (2%) Query: 3 FDYLIVGAGSAGCVLANRLSADPSVTVCLLEAGPEDRSPLIHTPLGLAAILPTRHVNWAF 62 FDY+IVGAGSAGC +A RL + +V ++E G D P I P L+ + +W Sbjct: 2 FDYIIVGAGSAGCAMAYRLG-EAGRSVLVVEHGGTDAGPFIQMPAALSYPMNMGIYDWGL 60 Query: 63 KTTPQPGLGGRVGYQPRGKVLGGSSSINGMIYIRGHQDDFNDWQALGNEGWGFDDVLPYF 122 KT P+P L GRV PRGKV+GGSSSINGM+Y+RGH DF+ W G GWGF DVLPYF Sbjct: 61 KTEPEPHLDGRVLATPRGKVIGGSSSINGMVYVRGHARDFDHWAESGATGWGFADVLPYF 120 Query: 123 RKSE-MHHGGSSEYHGGDGELYVSPANR-HAASEAFVESALRAGHSYNPDFNGATQEGAG 180 ++ E H G E+ G DG L+V+ R + AF+E+ +AG+ D+NGA QEG G Sbjct: 121 KRMENWHVPGDVEWRGHDGPLHVTRGPRSNPLFNAFIEAGRQAGYPVTDDYNGAAQEGFG 180 Query: 181 YYDVTIRDGRRWSTATAFLKPVRHRSNLTVLTHTHVESIVLLGKQATGVQALIKGSRVHL 240 + TI GRRWS A A+L+P R + LT +V+ +A GV+ +G R + Sbjct: 181 PMEATIWQGRRWSAANAYLRPAMKRFGVQ-LTRALALKVVIEEGRAVGVEVQRRGGREVI 239 Query: 241 RARKEVILSAGAFGSPHLLMLSGIGSAAELEPQGIAPRHELPGVGQNLQDHADVVLCYKS 300 RA +EVIL+A + +P LLMLSGIGSAA L GI + PGVG+NLQDH +V + + S Sbjct: 240 RAGREVILAASSLNTPKLLMLSGIGSAAHLAEHGIPVVADRPGVGRNLQDHLEVYMQFAS 299 Query: 301 ND--TSLLGFSLSGGVKMGKAMFDYARHRNGPVASNCAEAGAFLKTDPGLERPDIQLHSV 358 T ++L G V +G R G ASN EA AF+++ PG++ PDIQ H + Sbjct: 300 LQPVTLFKHWNLRGKVSIGAQWLFTGR---GLGASNQFEACAFIRSKPGVDYPDIQYHFL 356 Query: 359 IGTVDDHNRKLHWGHGFSCHVCVLRPKSIGSVGLASPDPRKAPRIDPNFLAHDDDVATLL 418 V + GHGF HV +R S GSV L S DP P I N+++ ++D Sbjct: 357 PIAVRYDGKAAAEGHGFQVHVGPMRSPSRGSVTLRSADPEAPPVIRFNYMSTEEDWQDFR 416 Query: 419 KGYRITRDIIAQTPMASFGLRDMY-SAGLHNDEQLIELLRKRTDTIYHPIGTCKMGQ--D 475 + R+TR+I Q F ++ A +D ++ +R ++ YHP GT ++G+ D Sbjct: 417 RCVRLTREIFGQEAFKPFVRHEIQPGAACASDAEIDAFIRAHVESAYHPCGTARIGRADD 476 Query: 476 EMAVVDSQLRVHGIEGLRVVDASIMPTLVGGNTNAAAIMIAERAAEWI 523 MAVVD + RV G+EGLRV D+SI P + GN NA +IM+ E+A++ I Sbjct: 477 PMAVVDPECRVIGVEGLRVADSSIFPRVTNGNLNAPSIMVGEKASDHI 524 Lambda K H 0.319 0.137 0.419 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: 890 Number of extensions: 47 Number of successful extensions: 7 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: 526 Length of database: 548 Length adjustment: 35 Effective length of query: 491 Effective length of database: 513 Effective search space: 251883 Effective search space used: 251883 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 52 (24.6 bits)
This GapMind analysis is from Apr 10 2024. 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