Align alcohol dehydrogenase (EC 1.1.1.1) (characterized)
to candidate Ac3H11_1497 Choline dehydrogenase (EC 1.1.99.1)
Query= BRENDA::Q76HN6 (526 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1497 Length = 526 Score = 383 bits (984), Expect = e-111 Identities = 224/527 (42%), Positives = 299/527 (56%), Gaps = 9/527 (1%) Query: 1 MEFDYLIVGAGSAGCVLANRLSADPSVTVCLLEAGPEDRSPLIHTPLGLAAILPTRHVNW 60 M FD++I+GAGSAGCVLA+RL V LLEAGP P + P ++ T +W Sbjct: 1 MNFDHIIIGAGSAGCVLAHRL-VRAGRRVLLLEAGPTHEHPFVRMPAAFVRVIGTER-SW 58 Query: 61 AFKTTPQPGLGGRVGYQPRGKVLGGSSSINGMIYIRGHQDDFNDWQALGNEGWGFDDVLP 120 + + PQP GR + P+G++LGG SS+N M+YIRG D++ W+ G GWG+ DVLP Sbjct: 59 DYASEPQPHANGRRMHVPQGRMLGGGSSLNAMVYIRGQAADYDSWRDAGCTGWGWSDVLP 118 Query: 121 YFRKSEMHHGGSSEYHGGDGELYVS-PANRHAASEAFVESALRAGHSYNPDFNGATQEGA 179 F ++E + + HG DG L VS P RH S AFV +A +AG NPDFNG Q G Sbjct: 119 AFVRAESNERYAGPLHGRDGPLQVSEPRFRHPLSAAFVAAAQQAGLPANPDFNGTEQAGV 178 Query: 180 GYYDVTIRDGRRWSTATAFLKPVRHRSNLTVLTHTHVESIVLLGKQATGVQALIKGSRVH 239 G+Y T G R STA +L VR L V T HV I++ +A GV+ + G Sbjct: 179 GFYQSTTFRGERGSTAATYLAAVRRDERLAVRTGVHVRRILVEAGRAVGVEFMEAGQLQQ 238 Query: 240 LRARKEVILSAGAFGSPHLLMLSGIGSAAELEPQGIAPRHELPGVGQNLQDHADV-VLCY 298 +R ++V+LSAGA SP LLMLSGIG +L GI + GVGQN QDH +V V Sbjct: 239 VRCAQDVLLSAGALASPQLLMLSGIGPGEDLHKLGIPVHADSAGVGQNYQDHLEVSVYAR 298 Query: 299 KSNDTSLLGFSLSGGVKMGKAMFDYARHRNGPVASNCAEAGAFLKTDPGLERPDIQLHSV 358 SLLG G++ + + R+G + SN E+G F+ T G RPD+Q H + Sbjct: 299 TRRPISLLG--QDQGLRALRHGLQWQLLRSGLLTSNVVESGGFVDT-LGTGRPDVQFHVL 355 Query: 359 IGTVDDHNRKLHWGHGFSCHVCVLRPKSIGSVGLASPDPRKAPRIDPNFLAHDDDVATLL 418 V D R+ GHG S + C LRP+S G+V L SPDP D L DV TL+ Sbjct: 356 PVLVGDVEREPLPGHGLSINPCFLRPQSRGTVSLRSPDPAHPILFDAGALRVQADVDTLV 415 Query: 419 KGYRITRDIIAQTPMASFGLRDMY--SAGLHNDEQLIELLRKRTDTIYHPIGTCKMGQDE 476 +G ++ R I+ +A ++ + +D Q+ +R T+YHP GTC+MG D Sbjct: 416 RGVKLARRILRAPALAEVVEHELLPGAEATLSDAQVEAHVRSHAKTVYHPAGTCRMGGDA 475 Query: 477 MAVVDSQLRVHGIEGLRVVDASIMPTLVGGNTNAAAIMIAERAAEWI 523 +VVD+ LRV G+ GLRV DAS+MPTL GNTNA IM+AER AE++ Sbjct: 476 TSVVDTHLRVRGVAGLRVCDASVMPTLPSGNTNAPTIMLAERCAEFV 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: 805 Number of extensions: 57 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: 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 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