Align alcohol dehydrogenase (EC 1.1.1.1) (characterized)
to candidate GFF4208 HP15_4148 glucose-methanol-choline oxidoreductase
Query= BRENDA::Q76HN6 (526 letters) >FitnessBrowser__Marino:GFF4208 Length = 542 Score = 485 bits (1248), Expect = e-141 Identities = 261/528 (49%), Positives = 336/528 (63%), Gaps = 7/528 (1%) Query: 3 FDYLIVGAGSAGCVLANRLSADPSVTVCLLEAGPEDRSPLIHTPLGLAAILPTRHVNWAF 62 FDY++VGAGSAGCVLA+RLSAD +VC+LEAGP S I TP AA + + NWAF Sbjct: 6 FDYIVVGAGSAGCVLADRLSADGRYSVCVLEAGPGKGSFTIRTPGAFAAHMFIKTYNWAF 65 Query: 63 KTTPQPGL-GGRVGYQPRGKVLGGSSSINGMIYIRGHQDDFNDWQALGNEGWGFDDVLPY 121 P L GG+ + PRGK LGGSS INGM+Y+RG ++D+++W+ALGNEGWG+ ++LPY Sbjct: 66 NARPDQQLRGGQPLFTPRGKGLGGSSLINGMLYVRGQKEDYDEWEALGNEGWGYAEMLPY 125 Query: 122 FRKSEMHHG-GSSEYHGGDGELYVSPAN--RHAASEAFVESALRAGHSYNPDFNGATQEG 178 F KSE H + YHG G LY+ + S AFV++A + G Y+ DFNGA QEG Sbjct: 126 FLKSEHHETLAGTPYHGKGGNLYIGAPETAEYPMSGAFVDAARQTGFPYSSDFNGAEQEG 185 Query: 179 AGYYDVTIRDGRRWSTATAFLKPVRHRSNLTVLTHTHVESIVLLGKQATGVQALIKGSRV 238 GY+ + I++GRR+ A A+LKP R NLTVLT V+ +VL G +A V+ K S + Sbjct: 186 VGYFHLNIKNGRRFGVADAYLKPAMSRQNLTVLTEARVKKLVLEGNRAVAVELRHKDSDL 245 Query: 239 HLRARKEVILSAGAFGSPHLLMLSGIGSAAELEPQGIAPRHELPGVGQNLQDHADVVLCY 298 L A +E+ILS GA SP LL LSGIG LE GI RHELPGVG+NLQ+H D + Sbjct: 246 VLNANREIILSGGAINSPQLLQLSGIGDHDALESLGIRCRHELPGVGKNLQEHVDACVLV 305 Query: 299 KSNDTSLLGFSLSGGVKMGKAMFDYARHRNGPVASNCAEAGAFLKTDPGLERPDIQLHSV 358 S + SL G +KM Y + G +A + EAG F+K+ + RPD+QLH + Sbjct: 306 SSRKNNGFTASLGGLLKMVPDTIRYFLSKRGKLAKSITEAGGFIKSSDSVNRPDVQLHML 365 Query: 359 IGTVDDHNR--KLHWGHGFSCHVCVLRPKSIGSVGLASPDPRKAPRIDPNFLAHDDDVAT 416 DD R KL G+S HVCVLRPKS G+V + S DP AP ID NF A DD Sbjct: 366 PLLFDDSGRDLKLMSNPGYSVHVCVLRPKSSGTVTITSADPFAAPEIDYNFFADPDDCKV 425 Query: 417 LLKGYRITRDIIAQTPMASFGLRDMY-SAGLHNDEQLIELLRKRTDTIYHPIGTCKMGQD 475 ++ G R R I+A + +++ A +DEQ+IE ++++ +YHP+GTCKMG D Sbjct: 426 MVDGIRQARRILAAKAFDDYRGEELHPGADRQSDEQIIEKVKEKVGLVYHPVGTCKMGTD 485 Query: 476 EMAVVDSQLRVHGIEGLRVVDASIMPTLVGGNTNAAAIMIAERAAEWI 523 MAVVD QLRVHG+ GLRVVDASIMP L+ GNTNA I IAE+AA+ I Sbjct: 486 RMAVVDPQLRVHGLGGLRVVDASIMPRLISGNTNAPTIAIAEKAADMI 533 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: 867 Number of extensions: 49 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: 542 Length adjustment: 35 Effective length of query: 491 Effective length of database: 507 Effective search space: 248937 Effective search space used: 248937 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