Align alcohol dehydrogenase (EC 1.1.1.1) (characterized)
to candidate GFF2856 HP15_2800 glucose-methanol-choline oxidoreductase
Query= BRENDA::Q76HN6 (526 letters) >FitnessBrowser__Marino:GFF2856 Length = 537 Score = 548 bits (1413), Expect = e-160 Identities = 286/538 (53%), Positives = 363/538 (67%), Gaps = 14/538 (2%) Query: 1 MEFDYLIVGAGSAGCVLANRLSADPSVTVCLLEAGPEDRSPLIHTPLGLAAILPTRHV-- 58 M FDY+IVG GSAG V+A RLS DP V+VCLLEAG + L P G+ AI+P Sbjct: 1 MIFDYIIVGGGSAGAVMAARLSEDPDVSVCLLEAGGKGDHLLTRAPAGVVAIMPGHGKIN 60 Query: 59 NWAFKTTPQPGLGGRVGYQPRGKVLGGSSSINGMIYIRGHQDDFNDWQALGNEGWGFDDV 118 NWA T QP L GR G+QPRG+ LGGSS IN M+Y+RGH D++ W LG +GWG+DDV Sbjct: 61 NWALNTEQQPELAGRRGFQPRGRGLGGSSLINAMLYVRGHSADYDGWAELGCDGWGWDDV 120 Query: 119 LPYFRKSEMHHGGSSEYHGGDGELYV-SPANRHAASEAFVESALRAGHSYNPDFNGATQE 177 LPYFRK+E H GG+SEYHG DG L+V + SEAF+E+A G+ + DFN E Sbjct: 121 LPYFRKAECHEGGASEYHGADGPLHVCKQRSPRPISEAFIEAAKERGYPASEDFNTGDNE 180 Query: 178 GAGYYDVTI-----RDGRRWSTATAFLKPV-RHRSNLTVLTHTHVESIVLLGKQATGVQA 231 G G ++VT R+G R STA A+L P+ R+NL V+T I+ GK+A+GV+ Sbjct: 181 GVGLFEVTQFHDTERNGERCSTAAAYLYPIIEQRNNLKVVTGARATRILFNGKRASGVEY 240 Query: 232 LIKGSRVHLRARKEVILSAGAFGSPHLLMLSGIGSAAELEPQGIAPRHELPGVGQNLQDH 291 +KG + A +EVILSAGAFGSP LL LSG+G+ ++ P GI HELPGVG+NLQDH Sbjct: 241 RLKGQSLTASANREVILSAGAFGSPQLLQLSGVGNPDDILPHGIPMVHELPGVGRNLQDH 300 Query: 292 ADVVLCYKSNDTSLLGFSLSGGVKMGKAMFDYARHRNGPVASNCAEAGAFLKTDPGLERP 351 D +L YKS DT GFSL+G M + + G +AS AE AFLK+DP ++P Sbjct: 301 LDFILAYKSADTDNFGFSLTGMKNMLRHSLQWRTDGTGMIASPFAEGAAFLKSDPEQDKP 360 Query: 352 DIQLHSVIGTVDDHNRKLHWGHGFSCHVCVLRPKSIGSVGLASPDPRKAPRIDPNFLAHD 411 D+QLH V+ V+DH RKLHWGHGFSCHVC LRPKS G V L S DP P IDPN+L+ Sbjct: 361 DLQLHFVVSIVEDHARKLHWGHGFSCHVCNLRPKSRGRVFLLSADPMADPGIDPNYLSDP 420 Query: 412 DDVATLLKGYRITRDIIAQTPMASFGLRDMYSAGLH---NDEQLIELLRKRTDTIYHPIG 468 DD+ +KG +ITR+I+ ++ + +M+ G+H +DE+ +R R DTIYHP+G Sbjct: 421 DDLNLTIKGAKITREILEGPALSPYRQSEMF--GVHDGMSDEEWERHIRARADTIYHPVG 478 Query: 469 TCKMGQDEMAVVDSQLRVHGIEGLRVVDASIMPTLVGGNTNAAAIMIAERAAEWIAHG 526 TCKMG D++AVVDS L+VHG+EGLRVVDAS+MPTL+GGNTNA IMIAE+ A+ I G Sbjct: 479 TCKMGIDDLAVVDSSLKVHGLEGLRVVDASVMPTLIGGNTNAPTIMIAEKNADTIRTG 536 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: 950 Number of extensions: 34 Number of successful extensions: 6 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: 537 Length adjustment: 35 Effective length of query: 491 Effective length of database: 502 Effective search space: 246482 Effective search space used: 246482 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