Align alcohol dehydrogenase (EC 1.1.1.1) (characterized)
to candidate GFF4425 HP15_p187g133 glucose-methanol-choline oxidoreductase
Query= BRENDA::Q76HN6 (526 letters) >FitnessBrowser__Marino:GFF4425 Length = 536 Score = 571 bits (1472), Expect = e-167 Identities = 289/524 (55%), Positives = 370/524 (70%), Gaps = 3/524 (0%) Query: 4 DYLIVGAGSAGCVLANRLSADPSVTVCLLEAGPE-DRSPLIHTPLGLAAILPTRHVNWAF 62 DY+I+G GS+GC LA RLS +P V LLEAGP+ S LI TP + A++P + NWAF Sbjct: 5 DYIIIGGGSSGCTLAGRLSENPRSEVALLEAGPDRGSSALIRTPAAVVAMVPRKVNNWAF 64 Query: 63 KTTPQPGLGGRVGYQPRGKVLGGSSSINGMIYIRGHQDDFNDWQALGNEGWGFDDVLPYF 122 +TTPQPGL GR GYQPRG+VLGGSS+IN M YIRGH D++ W+A GNEGWGF+DVLPYF Sbjct: 65 ETTPQPGLNGRRGYQPRGRVLGGSSAINAMAYIRGHASDYDAWEAAGNEGWGFNDVLPYF 124 Query: 123 RKSEMHHGGSSEYHGGDGELYVSPANR-HAASEAFVESALRAGHSYNPDFNGATQEGAGY 181 +KSE + ++HG G L VS + + ++E+A + G+ DFNG QEG G Sbjct: 125 KKSEANQRFHDDWHGNSGPLKVSDLQSDNPFQKHYLEAARQVGYPITEDFNGPQQEGIGL 184 Query: 182 YDVTIRDGRRWSTATAFLKPVRH-RSNLTVLTHTHVESIVLLGKQATGVQALIKGSRVHL 240 Y VT +G RWS A+++P R R NL++ T + IV GK+A GV+ +G ++ Sbjct: 185 YQVTQLNGERWSAYRAYIEPHRSSRRNLSIHTEAIAQRIVFEGKRAIGVEFTRRGRLEYI 244 Query: 241 RARKEVILSAGAFGSPHLLMLSGIGSAAELEPQGIAPRHELPGVGQNLQDHADVVLCYKS 300 RARKEVILSAGAF SP LLMLSGIG AEL +GI H LPGVG+NLQDH D + Y+S Sbjct: 245 RARKEVILSAGAFQSPQLLMLSGIGDKAELSEKGIEVMHHLPGVGKNLQDHPDFIFGYRS 304 Query: 301 NDTSLLGFSLSGGVKMGKAMFDYARHRNGPVASNCAEAGAFLKTDPGLERPDIQLHSVIG 360 ND++LLG SL GG+ + Y + R G +ASN AE G FLKT P LE P+IQLH V+ Sbjct: 305 NDSNLLGLSLKGGMHGIRQFIKYRQTRRGLLASNFAEGGGFLKTSPELEAPNIQLHFVVA 364 Query: 361 TVDDHNRKLHWGHGFSCHVCVLRPKSIGSVGLASPDPRKAPRIDPNFLAHDDDVATLLKG 420 VDDH R+LH GHGFSCHVC+LRPKS G+V L + +P P IDP FL +DV L+ G Sbjct: 365 LVDDHARRLHRGHGFSCHVCLLRPKSRGTVVLKNNNPASPPVIDPGFLNDANDVEELVDG 424 Query: 421 YRITRDIIAQTPMASFGLRDMYSAGLHNDEQLIELLRKRTDTIYHPIGTCKMGQDEMAVV 480 Y++TR ++A +A F D ++A + D+Q+I++LR RTDT+YHP+GTCKMG + +VV Sbjct: 425 YKMTRRLMAAPALAKFCTEDPFTANVKTDKQIIDILRNRTDTVYHPVGTCKMGTSKDSVV 484 Query: 481 DSQLRVHGIEGLRVVDASIMPTLVGGNTNAAAIMIAERAAEWIA 524 D +LRV+G+EGLRVVDASIMPT++GGNTNA AIMIAE+AA+ IA Sbjct: 485 DPRLRVYGVEGLRVVDASIMPTIIGGNTNAPAIMIAEKAADLIA 528 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: 858 Number of extensions: 30 Number of successful extensions: 4 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: 536 Length adjustment: 35 Effective length of query: 491 Effective length of database: 501 Effective search space: 245991 Effective search space used: 245991 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