Align alcohol dehydrogenase (EC 1.1.1.1) (characterized)
to candidate PfGW456L13_2692 Choline dehydrogenase (EC 1.1.99.1)
Query= BRENDA::Q76HN6 (526 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2692 Length = 567 Score = 419 bits (1078), Expect = e-121 Identities = 227/527 (43%), Positives = 322/527 (61%), Gaps = 8/527 (1%) Query: 2 EFDYLIVGAGSAGCVLANRLSADPSVTVCLLEAGPEDRSPLIHTPLGLAAILPTRHVNWA 61 ++DY+I+GAGSAGCVLANRLS DP+ +V +LE G D+S +I P + + T+ NW Sbjct: 10 KYDYIIIGAGSAGCVLANRLSEDPATSVLVLEFGGSDKSVVIQMPSAFSIPMNTKKYNWR 69 Query: 62 FKTTPQPGLGGRVGYQPRGKVLGGSSSINGMIYIRGHQDDFNDWQALGNEGWGFDDVLPY 121 ++T P+ L GR + PRGKVLGGSSSING++YIRGH DF++W++LG EGWG+ + LPY Sbjct: 70 YETEPETHLNGRRIHCPRGKVLGGSSSINGLVYIRGHALDFDEWESLGAEGWGYRNCLPY 129 Query: 122 FRKSEMHHGGSSEYHGGDGELYVSPAN--RHAASEAFVESALRAGHSYNPDFNGATQEGA 179 F+++E + G Y G G L+ + N ++ A+VE+ AG+ D NG QEG Sbjct: 130 FKRAESYESGGDSYRGQTGPLHTTNGNHMKNPLYGAWVEAGAEAGYIKTEDCNGYMQEGF 189 Query: 180 GYYDVTIRDGRRWSTATAFLKPVRHRSNLTVLTHTHVESIVLLGKQATGVQALIKGSRVH 239 G +T+++G R STA A+L+P R NLTV+TH ++L GK+A GV G Sbjct: 190 GAMHMTVKNGVRCSTANAYLRPAMGRPNLTVITHAMTRQVILEGKRAVGVMYDHGGQTHQ 249 Query: 240 LRARKEVILSAGAFGSPHLLMLSGIGSAAELEPQGIAPRHELPGVGQNLQDHADVVLCYK 299 + +EV++S+G GSPHLL SGIG A L GI RH+LPGVG+NLQDHA+V + + Sbjct: 250 VYCNREVLISSGPIGSPHLLQRSGIGPADVLRKAGIGVRHDLPGVGENLQDHAEVYIQFG 309 Query: 300 SNDTSLLGFSLSGGVKMGKAMFD--YARHRNGPVASNCAEAGAFLKTDPGLERPDIQLHS 357 + L + + K M + ++G A+N EAG F++++ GL PDIQ H Sbjct: 310 CKEPVTLNSKMD---PLSKLMIGLRWLLFKDGLGATNHFEAGGFIRSEKGLRWPDIQFHF 366 Query: 358 VIGTVDDHNRKLHWGHGFSCHVCVLRPKSIGSVGLASPDPRKAPRIDPNFLAHDDDVATL 417 + + K GHGF +PKS G V + S DP + P I N+L ++D Sbjct: 367 LPAAMRYDGNKPIKGHGFMVLTGPNKPKSRGYVRVRSADPYEHPEIRFNYLEREEDREGF 426 Query: 418 LKGYRITRDIIAQTPMASFGLRDMY-SAGLHNDEQLIELLRKRTDTIYHPIGTCKMGQDE 476 + R+TR+II Q M F ++ A + +DE L +R ++ YHP G+C+MG+DE Sbjct: 427 RRCIRLTREIIGQKAMDRFRDGEIAPGAQVTSDEDLDAFVRDNLESTYHPCGSCRMGEDE 486 Query: 477 MAVVDSQLRVHGIEGLRVVDASIMPTLVGGNTNAAAIMIAERAAEWI 523 MAVVDS+LRV GI GLRV+D+S+ PT GN NA IM+AERA++ + Sbjct: 487 MAVVDSELRVRGIAGLRVIDSSVFPTEPNGNLNAPTIMLAERASDLV 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: 828 Number of extensions: 38 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: 567 Length adjustment: 36 Effective length of query: 490 Effective length of database: 531 Effective search space: 260190 Effective search space used: 260190 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