Align alcohol dehydrogenase (EC 1.1.1.1) (characterized)
to candidate CCNA_02725 CCNA_02725 choline dehydrogenase
Query= BRENDA::Q76HN6 (526 letters) >FitnessBrowser__Caulo:CCNA_02725 Length = 555 Score = 462 bits (1188), Expect = e-134 Identities = 252/530 (47%), Positives = 335/530 (63%), Gaps = 12/530 (2%) Query: 3 FDYLIVGAGSAGCVLANRLSADPSVTVCLLEAGPEDRSPLIHTPLGLAAILPTR-HVNWA 61 FDY+++GAGSAGCVLA RL+ DP++ V LLEAG +++S L+ P G+ ++ + NW Sbjct: 6 FDYIVIGAGSAGCVLAARLTEDPNIKVLLLEAGGKNKSILVKMPAGVGQLIKDKGEQNWG 65 Query: 62 FKTTPQPGLGGRVGYQPRGKVLGGSSSINGMIYIRGHQDDFNDWQALGNEGWGFDDVLPY 121 F T +P L R + PRGK LGGSS+INGMIYIRGH D++ W+ +G GW + +VLPY Sbjct: 66 FWTEAEPHLDNRKLWWPRGKGLGGSSAINGMIYIRGHARDYDQWRQMGLTGWSYSEVLPY 125 Query: 122 FRKSEMHHGGSSEYHGGDGELYVSPANRHAA-SEAFVESALRAGHSYNPDFNGATQEGAG 180 F++SE HH G YHGG G L+VS + VE+ +AGH DFNG QEG G Sbjct: 126 FKRSETHHAGGDAYHGGSGPLHVSKGESDSPFYSTLVEAGRQAGHKTTKDFNGYQQEGFG 185 Query: 181 YYDVTIRDGRRWSTATAFLKPVRHRSNLTVLTHTHVESIVLLGKQATGVQALIKGSRVH- 239 YD+TIRDG+RWS A A+L R NLT +T I+L ++A GV+ ++ SR Sbjct: 186 PYDLTIRDGQRWSAAMAYLNQALSRPNLTCVTEACTTRIILDKRRAVGVEYVVGKSREKQ 245 Query: 240 -LRARKEVILSAGAFGSPHLLMLSGIGSAAELEPQGIAPRHELPGVGQNLQDHADVVLCY 298 A EV+LSAGA SP +L LSGIG+A +L P GIA HE GVG NLQDH DV + + Sbjct: 246 VAYADAEVLLSAGAVQSPQILQLSGIGAAEDLAPHGIAVAHESKGVGANLQDHLDVCVSW 305 Query: 299 KSNDTSLLGFSLSGGVKMGKAMFDYARHRNGPVASNCAEAGAFLKTDPGLERPDIQLHSV 358 + + + G K+G M +Y G E+GAFLK+ P L+RPD+Q+H V Sbjct: 306 TAKNLKTAYSANKGLNKLGVGM-NYMFFGKGLGRQQFLESGAFLKSRPDLDRPDLQIHGV 364 Query: 359 IGTVDDHNRKLHWGHGFSCHVCVLRPKSIGSVGLASPDPRKAPRIDPNFLAHDDDVATLL 418 + + DH + + GF+ HVC LRP+S G VGL S DP P I N+LA ++D + Sbjct: 365 LAIMQDHGKVVVEKDGFTLHVCQLRPESRGKVGLRSADPFDDPTILGNYLATEEDRRAIR 424 Query: 419 KGYRITRDIIAQTPMASFGLRDM-YSAG--LHNDEQLIELLRKRTDTIYHPIGTCKMG-- 473 +G RI R+ +AQ + RD Y+ G + +D L +R + +TIYHP+GTC+MG Sbjct: 425 EGVRIARETVAQAAFDPY--RDAEYAPGADVKSDADLDAWIRSKAETIYHPVGTCRMGVA 482 Query: 474 QDEMAVVDSQLRVHGIEGLRVVDASIMPTLVGGNTNAAAIMIAERAAEWI 523 D MAVVD QLRV G++GLRV+DAS+MPTL+GGNTNA IMIAERAA+ I Sbjct: 483 GDPMAVVDDQLRVQGVQGLRVIDASVMPTLIGGNTNAPTIMIAERAADLI 532 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: 868 Number of extensions: 40 Number of successful extensions: 7 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: 555 Length adjustment: 35 Effective length of query: 491 Effective length of database: 520 Effective search space: 255320 Effective search space used: 255320 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