Align alcohol dehydrogenase (EC 1.1.1.1) (characterized)
to candidate WP_052368302.1 U743_RS16290 choline dehydrogenase
Query= BRENDA::Q76HN6 (526 letters) >NCBI__GCF_000733765.1:WP_052368302.1 Length = 556 Score = 585 bits (1508), Expect = e-171 Identities = 292/522 (55%), Positives = 364/522 (69%), Gaps = 1/522 (0%) Query: 3 FDYLIVGAGSAGCVLANRLSADPSVTVCLLEAGPEDRSPLIHTPLGLAAILPTRHVNWAF 62 +DY+I+G GSAGCVLANRLS DP TVCLLEAGP D+SP + PLG+AA+L + +NWAF Sbjct: 2 YDYIIIGGGSAGCVLANRLSEDPETTVCLLEAGPADKSPFVRIPLGMAALLRSPSLNWAF 61 Query: 63 KTTPQPGLGGRVGYQPRGKVLGGSSSINGMIYIRGHQDDFNDWQALGNEGWGFDDVLPYF 122 +T PQ GLGGR GYQPRGKVLGGSSSIN M+YIRGH+ D++ W GN GW FD+VLPYF Sbjct: 62 RTEPQAGLGGRRGYQPRGKVLGGSSSINAMVYIRGHRSDYDGWAEAGNSGWSFDEVLPYF 121 Query: 123 RKSEMHHGGSSEYHGGDGELYVSPANR-HAASEAFVESALRAGHSYNPDFNGATQEGAGY 181 +++E G+ +HG G L V+ HA + F+ +A GH DFNG EG GY Sbjct: 122 KRAENQERGADAFHGVGGPLNVADLRSPHAICDDFIAAAEEQGHKRVSDFNGPDMEGVGY 181 Query: 182 YDVTIRDGRRWSTATAFLKPVRHRSNLTVLTHTHVESIVLLGKQATGVQALIKGSRVHLR 241 + VT + G R STA A+L+PV R NLT++T + I + GK+A GV+ + H+ Sbjct: 182 FQVTQQAGDRCSTAKAYLEPVADRPNLTIITEAYATRIDMEGKRAVGVRYRKDDASHHVG 241 Query: 242 ARKEVILSAGAFGSPHLLMLSGIGSAAELEPQGIAPRHELPGVGQNLQDHADVVLCYKSN 301 ARKEV++SAGA SP LLMLSGIG EL+ GI HEL GVG NLQDH D V KS Sbjct: 242 ARKEVLVSAGALQSPQLLMLSGIGPREELDQHGIPICHELAGVGANLQDHLDYVTAVKSP 301 Query: 302 DTSLLGFSLSGGVKMGKAMFDYARHRNGPVASNCAEAGAFLKTDPGLERPDIQLHSVIGT 361 LG SLSGG +M +A+ Y R R G + SN AEAG FL++DP L PD+QLH + Sbjct: 302 SKEPLGISLSGGWQMLQALRTYRRFRTGKLTSNVAEAGGFLRSDPSLAAPDLQLHFAVAI 361 Query: 362 VDDHNRKLHWGHGFSCHVCVLRPKSIGSVGLASPDPRKAPRIDPNFLAHDDDVATLLKGY 421 +DDH RKLH GHG+SCHVC+L PKS G VGL S +P APRIDP FL+ D+D+ L+KG+ Sbjct: 362 LDDHGRKLHSGHGYSCHVCLLTPKSRGRVGLHSANPMAAPRIDPAFLSEDEDLERLVKGF 421 Query: 422 RITRDIIAQTPMASFGLRDMYSAGLHNDEQLIELLRKRTDTIYHPIGTCKMGQDEMAVVD 481 R ++I+ MA RD+Y+A + DEQ+ +R+R DT+YHP+GTC+MG+D AVVD Sbjct: 422 RRMQEILNAPAMARHRGRDIYTAHVRTDEQIRSAIRQRADTVYHPVGTCRMGRDSDAVVD 481 Query: 482 SQLRVHGIEGLRVVDASIMPTLVGGNTNAAAIMIAERAAEWI 523 QLRVHG+ GLRVVDASIMPT+V GNTNA IMI E+AAE I Sbjct: 482 EQLRVHGVAGLRVVDASIMPTVVRGNTNAPTIMIGEKAAEMI 523 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: 889 Number of extensions: 37 Number of successful extensions: 2 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: 556 Length adjustment: 35 Effective length of query: 491 Effective length of database: 521 Effective search space: 255811 Effective search space used: 255811 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