Align alcohol dehydrogenase (EC 1.1.1.1) (characterized)
to candidate BPHYT_RS21745 BPHYT_RS21745 choline dehydrogenase
Query= BRENDA::Q76HN6 (526 letters) >FitnessBrowser__BFirm:BPHYT_RS21745 Length = 551 Score = 419 bits (1077), Expect = e-121 Identities = 237/528 (44%), Positives = 304/528 (57%), Gaps = 5/528 (0%) Query: 3 FDYLIVGAGSAGCVLANRLSADPSVTVCLLEAGPEDRSPLIHTPLGLAAILPTRHVNWAF 62 FD+++VGAGSAGCVLANRLS +VCLLEAGP DR IH P+G + NW F Sbjct: 5 FDFVVVGAGSAGCVLANRLSEGGRYSVCLLEAGPADRFMWIHIPIGYGKTMFHPVYNWGF 64 Query: 63 KTTPQPGLGGRVGYQPRGKVLGGSSSINGMIYIRGHQDDFNDWQALGNEGWGFDDVLPYF 122 T P P + R Y PRG+ LGGSSSING+IY+RG +DD+++W LGN GW + D LPYF Sbjct: 65 YTDPDPNMHNRRLYWPRGRTLGGSSSINGLIYVRGQRDDYDNWARLGNRGWSWQDCLPYF 124 Query: 123 RKSEMHHGGSSEYHGGDGELYVSP-ANRHAASEAFVESALRAGHSYNPDFNGATQEGAGY 181 ++ E + G G DG L+ S RH +AF+E++ G + DFN QEG GY Sbjct: 125 KRLEHNELGEGPTRGVDGPLWASTIKQRHELVDAFIEASNSLGVASIDDFNTGDQEGVGY 184 Query: 182 YDVTIRDGRRWSTATAFLKPVRHRSNLTVLTHTHVESIVLLGKQATGVQALIKGSRVHLR 241 Y +T R G R STA A+LKP R R NL V T I+ G +A GVQ G +R Sbjct: 185 YQLTTRRGFRCSTAVAYLKPARQRQNLHVETDAMASKILFEGTRACGVQYRQHGELREVR 244 Query: 242 ARKEVILSAGAFGSPHLLMLSGIGSAAELEPQGIAPRHELPGVGQNLQDHADVVLCYKSN 301 A +EVIL+AGA SP LL LSG+G AA L GI GVG+NLQDH + L Y+ Sbjct: 245 ANREVILTAGALQSPQLLQLSGVGPAALLREFGIPVVANRAGVGENLQDHLQIRLIYEVT 304 Query: 302 DTSLLGFSLSGGVKMGKAMFDYARHRNGPVASNCAEAGAFLKTDP-GLERPDIQLHSVIG 360 L K +A R+GP+A + G F + P PD Q H Sbjct: 305 KPITTNDQLRSWTGRAKMGLQWALMRSGPLAVGINQGGMFCRALPEESATPDTQFHFSTL 364 Query: 361 TVDDHNRKLHWGHGFSCHVCVLRPKSIGSVGLASPDPRKAPRIDPNFLAHDDDVATLLKG 420 + D +H G + +C LRP+S G+V + S DPR+AP I PN+L D D T + G Sbjct: 365 SADSAGGNVHDFPGCTYSICQLRPESRGAVRIRSADPREAPSIQPNYLDTDLDRRTTIAG 424 Query: 421 YRITRDIIAQTPMASFGLRDMY-SAGLHNDEQLIELLRKRTDTIYHPIGTCKMGQ--DEM 477 R R + A PMA R++ A D++L+E R+ TI+HP GT KMG D + Sbjct: 425 VRFARRVAAAQPMAGLMKREVRPGADAQTDDELLEFCREYGQTIFHPSGTAKMGPAGDPL 484 Query: 478 AVVDSQLRVHGIEGLRVVDASIMPTLVGGNTNAAAIMIAERAAEWIAH 525 AVVD +LRV+G +GLRVVD SIMPTLV GNTN +M+AE+A++ I H Sbjct: 485 AVVDERLRVYGTQGLRVVDCSIMPTLVSGNTNVPIVMVAEKASDMILH 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: 787 Number of extensions: 34 Number of successful extensions: 6 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: 551 Length adjustment: 35 Effective length of query: 491 Effective length of database: 516 Effective search space: 253356 Effective search space used: 253356 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