Align alcohol dehydrogenase (EC 1.1.1.1) (characterized)
to candidate WP_011911844.1 PST_RS03140 choline dehydrogenase
Query= BRENDA::Q76HN6 (526 letters) >NCBI__GCF_000013785.1:WP_011911844.1 Length = 537 Score = 524 bits (1349), Expect = e-153 Identities = 264/522 (50%), Positives = 350/522 (67%), Gaps = 1/522 (0%) Query: 3 FDYLIVGAGSAGCVLANRLSADPSVTVCLLEAGPEDRSPLIHTPLGLAAILPTRHVNWAF 62 FDY++VG G+AGCV+A+RLS DP+V+VCLLEAG D +PL+H P G+A ++PT NW + Sbjct: 7 FDYIVVGGGAAGCVVASRLSEDPAVSVCLLEAGGRDTNPLVHMPAGVAVMVPTAINNWQY 66 Query: 63 KTTPQPGLGGRVGYQPRGKVLGGSSSINGMIYIRGHQDDFNDWQALGNEGWGFDDVLPYF 122 +T Q GL GR+GYQPRGK LGGSSSIN M Y RGH ++F+DW+ALGN GW + +VLPYF Sbjct: 67 QTVAQKGLNGRIGYQPRGKTLGGSSSINAMAYHRGHPNNFDDWEALGNPGWSYQEVLPYF 126 Query: 123 RKSEMHHGGSSEYHGGDGELYVS-PANRHAASEAFVESALRAGHSYNPDFNGATQEGAGY 181 +++E + +E HG +G L V ++ + E F+E+ AG+ + D NGAT EG Sbjct: 127 KRAEHNEDFRNELHGQNGPLNVRFQSSPNPFIEKFIEAGAHAGYPHCVDPNGATMEGFSR 186 Query: 182 YDVTIRDGRRWSTATAFLKPVRHRSNLTVLTHTHVESIVLLGKQATGVQALIKGSRVHLR 241 V +DG+R S A A+L P R NL + TH H ++L G +A GV+ + G LR Sbjct: 187 VQVMQKDGQRCSAARAYLTPNLARPNLHIETHAHATRLLLEGTRAVGVEFIQHGVTRQLR 246 Query: 242 ARKEVILSAGAFGSPHLLMLSGIGSAAELEPQGIAPRHELPGVGQNLQDHADVVLCYKSN 301 A EVILS+GAF SP LL+LSGIG EL+ GI H+LPGVG+NL DH D V ++ Sbjct: 247 ANTEVILSSGAFNSPQLLLLSGIGPKDELQKLGIEVVHDLPGVGKNLVDHIDYVHPFRVE 306 Query: 302 DTSLLGFSLSGGVKMGKAMFDYARHRNGPVASNCAEAGAFLKTDPGLERPDIQLHSVIGT 361 +L G SL G + KA + Y R R G + SN AE AF+KT P L DI+L +I Sbjct: 307 SRALFGLSLRGAWDVLKATWQYFRQRKGMLTSNFAEGCAFVKTSPELREADIELAYIIAM 366 Query: 362 VDDHNRKLHWGHGFSCHVCVLRPKSIGSVGLASPDPRKAPRIDPNFLAHDDDVATLLKGY 421 DH R L+ GHG S H C+L PKS+G V LAS DP P IDP FL H DD+ATL+KGY Sbjct: 367 FADHGRTLYRGHGMSIHACLLYPKSVGQVTLASTDPLTPPLIDPAFLTHPDDIATLIKGY 426 Query: 422 RITRDIIAQTPMASFGLRDMYSAGLHNDEQLIELLRKRTDTIYHPIGTCKMGQDEMAVVD 481 +I R +I + + R++ + D ++ +++R R DT+YHPIGTCKMG D +AVVD Sbjct: 427 KIIRQVIEAPALQALKPREVLKVPMQTDAEIEQMIRNRADTLYHPIGTCKMGCDPLAVVD 486 Query: 482 SQLRVHGIEGLRVVDASIMPTLVGGNTNAAAIMIAERAAEWI 523 ++LRVHG++GLRVVDASIMPT+VG +T AA +MI E+AA++I Sbjct: 487 ARLRVHGLDGLRVVDASIMPTIVGCSTTAATVMIGEKAADFI 528 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: 831 Number of extensions: 30 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: 537 Length adjustment: 35 Effective length of query: 491 Effective length of database: 502 Effective search space: 246482 Effective search space used: 246482 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