Align alcohol dehydrogenase (EC 1.1.1.1) (characterized)
to candidate Ac3H11_4659 Choline dehydrogenase (EC 1.1.99.1)
Query= BRENDA::Q76HN6 (526 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_4659 Length = 529 Score = 527 bits (1357), Expect = e-154 Identities = 268/522 (51%), Positives = 353/522 (67%), Gaps = 3/522 (0%) Query: 3 FDYLIVGAGSAGCVLANRLSADPSVTVCLLEAGPEDRSPLIHTPLGLAAILPTRHVNWAF 62 FDY++VG GSAG VLA RL+ DPSV VCLLEAGP D S LIH P GLA + W F Sbjct: 2 FDYIVVGGGSAGSVLAGRLTEDPSVRVCLLEAGPADNSVLIHCPAGLAVMAKFELNGWGF 61 Query: 63 KTTPQPGLGGRVGYQPRGKVLGGSSSINGMIYIRGHQDDFNDWQALGNEGWGFDDVLPYF 122 TTPQ L R GYQPRGKVLGGSSSIN M+YIRG D++ W A GN GWG++DV PYF Sbjct: 62 NTTPQAALNNRRGYQPRGKVLGGSSSINAMVYIRGQHADYDHWAAQGNPGWGWEDVKPYF 121 Query: 123 RKSEMHHGGSSEYHGGDGELYVSP-ANRHAASEAFVESALRAGHSYNPDFNGATQEGAGY 181 ++E + G+ +HG G V+ + + S F E+ ++AG+ +N DFNGATQEG G Sbjct: 122 LRAEHNERGADAWHGQGGPFNVADLRSTNRFSHHFTEAGVQAGYPHNTDFNGATQEGVGL 181 Query: 182 YDVTIRDGRRWSTATAFLKPVRHRSNLTVLTHTHVESIVLLGKQATGVQALIKGSRVHLR 241 Y VT ++G R S A +L P RSNL V+T H I+ G +A GV+ G+ +R Sbjct: 182 YQVTHKNGERHSAAKGYLTPHLARSNLQVITDAHATRILFDGTRAVGVEYRQGGALKQVR 241 Query: 242 ARKEVILSAGAFGSPHLLMLSGIGSAAELEPQGIAPRHELPGVGQNLQDHADVVLCYKSN 301 A +EV+LSAGA SP LLMLSG+G AA L+ GI H+LPGVGQ+L DH DVV + Sbjct: 242 AGREVLLSAGALLSPQLLMLSGVGPAAHLQQHGIPVLHDLPGVGQHLHDHPDVVQVLDAP 301 Query: 302 D-TSLLGFSLSGGVKMGKAMFDYARHRNGPVASNCAEAGAFLKTDPGLERPDIQLHSVIG 360 + L G SLSG + + + ++ +HR G + +N AEAG F+K+DP PD+QLH VIG Sbjct: 302 ELKDLFGLSLSGMAQTLRGIVEWRKHRTGMLTTNFAEAGGFIKSDPSEAAPDLQLHFVIG 361 Query: 361 TVDDHNRKLHWGHGFSCHVCVLRPKSIGSVGLASPDPRKAPRIDPNFLAHDDDVATLLKG 420 + DH RK +GHG+S HVC+L+PKS GSV LAS DP P +DPNFLA DD+ +++G Sbjct: 362 KLVDHGRKTVFGHGYSAHVCLLQPKSRGSVTLASRDPMALPLVDPNFLADPDDMLRMVRG 421 Query: 421 YRITRDIIAQTPMASFGLRDM-YSAGLHNDEQLIELLRKRTDTIYHPIGTCKMGQDEMAV 479 ++ TR+I++Q +A FG +++ SA +D ++ + +R+ DTIYHP+GTC+MG + V Sbjct: 422 FQRTREILSQPALAKFGAKELAASASARSDAEIGQFIRQYADTIYHPVGTCRMGPGPLDV 481 Query: 480 VDSQLRVHGIEGLRVVDASIMPTLVGGNTNAAAIMIAERAAE 521 VD++LRVHG+ GLRVVDASIMP +V GNTNA +MIAE+A + Sbjct: 482 VDAELRVHGLAGLRVVDASIMPRIVSGNTNAPTVMIAEKAVD 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: 894 Number of extensions: 48 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: 529 Length adjustment: 35 Effective length of query: 491 Effective length of database: 494 Effective search space: 242554 Effective search space used: 242554 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