Align alcohol dehydrogenase (EC 1.1.1.1) (characterized)
to candidate WP_099018731.1 CCS90_RS03360 choline dehydrogenase
Query= BRENDA::Q76HN6 (526 letters) >NCBI__GCF_002591915.1:WP_099018731.1 Length = 526 Score = 492 bits (1266), Expect = e-143 Identities = 262/528 (49%), Positives = 345/528 (65%), Gaps = 14/528 (2%) Query: 2 EFDYLIVGAGSAGCVLANRLSADPSVTVCLLEAGPEDRSPLIHTPLGLAAILPTRHVNWA 61 +FDY++VGAGSAGCVLANRLSAD TV L+EAG D +P+IH P GLA ++ + +NW Sbjct: 3 KFDYIVVGAGSAGCVLANRLSADGKHTVLLVEAGGTDWNPMIHMPAGLAKLVGFKSINWN 62 Query: 62 FKTTPQPGLGGRVGYQPRGKVLGGSSSINGMIYIRGHQDDFNDWQALGNEGWGFDDVLPY 121 + T P+P L R Y PRGKVLGGSSSIN M Y RGH+ D++ W+A GN GWG DVLPY Sbjct: 63 YDTEPEPQLNNRKLYWPRGKVLGGSSSINAMCYCRGHRKDYDHWEAQGNAGWGSKDVLPY 122 Query: 122 FRKSEMHHGGSSEYHGGDGELYVSP-ANRHAASEAFVESALRAGHSYNPDFNGATQEGAG 180 F KSE + +E+H DG L VS + S+ F+++A AG+ DFNG Q G G Sbjct: 123 FMKSENNQRLKNEFHSQDGLLSVSDHIYTNPLSDVFLDAAAEAGYQRTDDFNGLRQRGFG 182 Query: 181 YYDVTIRDGRRWSTATAFLKPVRHRSNLTVLTHTHVESIVLLGKQATGVQALIKGSRVHL 240 YY VT ++G+R STA AFLKP + RSNLTV T T + ++L K+ATG+ G L Sbjct: 183 YYQVTQKNGQRHSTAEAFLKPAKGRSNLTVWTKTLAQKVILKDKKATGLLVKKGGQLQQL 242 Query: 241 RARKEVILSAGAFGSPHLLMLSGIGSAAELEPQGIAPRHELPGVGQNLQDHADVVL---C 297 +A KEVILS+GA SP LLMLSGIG++ EL GI +HELPGVG+NLQDH DV L C Sbjct: 243 KANKEVILSSGAINSPQLLMLSGIGNSEELAHHGIQCQHELPGVGKNLQDHLDVCLVQHC 302 Query: 298 YKSNDTSLLGFSLSGGVKMGKAMFDYARHRNGPVASNCAEAGAFLKTDPGL-ERPDIQLH 356 + + LSG Y + GP SN AEAG F ++ + +RPD+Q H Sbjct: 303 SQDITYDTVNEVLSG--------LKYYLFKKGPGTSNVAEAGGFWQSPMAIDDRPDLQFH 354 Query: 357 SVIGTVDDHNRKLHWGHGFSCHVCVLRPKSIGSVGLASPDPRKAPRIDPNFLAHDDDVAT 416 V +DDH R G+G++ H+CVLRP+S G + L S +P P+I N+LA + D+ Sbjct: 355 FVPAMLDDHGRNRLKGNGYTLHMCVLRPESRGEIKLKSANPEDPPQIQANYLAVEHDLKI 414 Query: 417 LLKGYRITRDIIAQTPMASFGLRDMY-SAGLHNDEQLIELLRKRTDTIYHPIGTCKMGQD 475 +++G++I R I A F +++ + + DE++I+ +R + ++IYHPIGTCKMG D Sbjct: 415 MVEGFKIQRKIFAAKAFDEFRDDEIFPGSEVQTDEEIIDFIRNKAESIYHPIGTCKMGSD 474 Query: 476 EMAVVDSQLRVHGIEGLRVVDASIMPTLVGGNTNAAAIMIAERAAEWI 523 +MAVVD L+VHGIEGLRVVDAS MPTLV GNTNA IM+AE+ ++ I Sbjct: 475 DMAVVDQNLKVHGIEGLRVVDASAMPTLVSGNTNAPTIMMAEKISDVI 522 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: 793 Number of extensions: 36 Number of successful extensions: 5 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: 526 Length adjustment: 35 Effective length of query: 491 Effective length of database: 491 Effective search space: 241081 Effective search space used: 241081 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 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