Align alcohol dehydrogenase (EC 1.1.1.1) (characterized)
to candidate WP_057687529.1 ABB28_RS16885 choline dehydrogenase
Query= BRENDA::Q76HN6 (526 letters) >NCBI__GCF_001431535.1:WP_057687529.1 Length = 559 Score = 354 bits (909), Expect = e-102 Identities = 218/532 (40%), Positives = 303/532 (56%), Gaps = 16/532 (3%) Query: 2 EFDYLIVGAGSAGCVLANRLSADPSVTVCLLEAGPEDRSPLIHT--PLGLAAILPTRHVN 59 E+DY+I+GAGSAG VLA RL+ D V+V LLEAG D T P LA L + N Sbjct: 6 EYDYIIIGAGSAGNVLATRLTEDADVSVLLLEAGGPDYRLDFRTQMPAALAFPLQGKRYN 65 Query: 60 WAFKTTPQPGLGGRVGYQPRGKVLGGSSSINGMIYIRGHQDDFNDWQAL-GNEGWGFDDV 118 WA+KT P+P + R RGK LGGSS INGM YIRG+ D+++W ++ G E W + D Sbjct: 66 WAYKTDPEPHMNNRRMDCGRGKGLGGSSLINGMCYIRGNAMDYDNWASMPGLEDWTYADC 125 Query: 119 LPYFRKSEMHHGGSSEYHGGDGELYVS-PAN-RHAASEAFVESALRAGHSYNPDFNGATQ 176 LPYFRK+E G ++YHG DG L V+ P N + A +E+ ++AG+ D NG Q Sbjct: 126 LPYFRKAETRDIGGNDYHGSDGPLQVTTPKNGNNELFAAMIEAGVQAGYPRTDDLNGYQQ 185 Query: 177 EGAGYYDVTIRD-GRRWSTATAFLKPVRHRSNLTVLTHTHVESIVLLGKQATGVQALIKG 235 EG G D T+ GRR STA +L R R NLT++TH + I+ GK+A GV L Sbjct: 186 EGFGPMDRTVTPRGRRSSTARGYLDQARERPNLTIVTHALTDRILFAGKRAVGVAWLRND 245 Query: 236 SRVHLRARKEVILSAGAFGSPHLLMLSGIGSAAELEPQGIAPRHELPGVGQNLQDHADVV 295 RAR+EV+L GA SP +L SG+G A L GI H+LPGVG NLQDH ++ Sbjct: 246 EPQKARARREVLLCGGAIASPQVLQRSGVGPADLLRGLGIEVVHDLPGVGANLQDHLEMY 305 Query: 296 LCYKSNDTSLLGFSLSGGVKMGKAM---FDYARHRNGPVASNCAEAGAFLKTDPGLERPD 352 L Y+ SL+ +K+ ++ + G ASN E G F++++ + P+ Sbjct: 306 LQYECRKP----VSLAPALKLYNQPAIGAEWLFNGTGIGASNQFEGGGFIRSNEEFDWPN 361 Query: 353 IQLHSVIGTVDDHNRKLHWGHGFSCHVCVLRPKSIGSVGLASPDPRKAPRIDPNFLAHDD 412 +Q H + ++ + H F HV +R S G + + S DPR P I N+++H+ Sbjct: 362 LQYHFLPVAINYNGSNPIKEHSFQMHVGSMRSPSRGRIHVRSTDPRVHPSILFNYMSHEQ 421 Query: 413 DVATLLKGYRITRDIIAQTPMASFGLRDMY-SAGLHNDEQLIELLRKRTDTIYHPIGTCK 471 D G RITR+I Q ++ + R++ + L D ++ +R+ +T YHP + K Sbjct: 422 DWREFRDGIRITREIFGQPALSPYTGREISPGSQLRTDAEIDAFVREHAETAYHPSCSNK 481 Query: 472 MGQ--DEMAVVDSQLRVHGIEGLRVVDASIMPTLVGGNTNAAAIMIAERAAE 521 MG D MAVVD RVHG+EGLR++DASIMP +V GN NA IM+AE+ A+ Sbjct: 482 MGSAADPMAVVDGHGRVHGMEGLRIIDASIMPQVVTGNLNAPTIMMAEKLAD 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: 915 Number of extensions: 60 Number of successful extensions: 9 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: 559 Length adjustment: 35 Effective length of query: 491 Effective length of database: 524 Effective search space: 257284 Effective search space used: 257284 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