Align alcohol dehydrogenase (EC 1.1.1.1) (characterized)
to candidate H281DRAFT_02374 H281DRAFT_02374 choline dehydrogenase
Query= BRENDA::Q76HN6 (526 letters) >FitnessBrowser__Burk376:H281DRAFT_02374 Length = 570 Score = 406 bits (1043), Expect = e-117 Identities = 229/532 (43%), Positives = 318/532 (59%), Gaps = 12/532 (2%) Query: 2 EFDYLIVGAGSAGCVLANRLSADPSVTVCLLEAGPEDRSPLIHTPLGLAAILPTRHVNWA 61 EFDY+IVGAG+AGCVLANRL+ DP V V LLEAG +D IH P+G + +W Sbjct: 16 EFDYIIVGAGTAGCVLANRLTEDPDVQVLLLEAGGKDDYHWIHVPVGYLYCIGNPRTDWL 75 Query: 62 FKTTPQPGLGGRVGYQPRGKVLGGSSSINGMIYIRGHQDDFNDWQALGNE-GWGFDDVLP 120 +KT +PGL GR PRG+VLGGSSSINGMIY+RG ++D+++W + N+ W ++ VLP Sbjct: 76 YKTQAEPGLNGRALSYPRGRVLGGSSSINGMIYMRGQREDYDEWARVTNDASWSWNSVLP 135 Query: 121 YFRKSEMHHGGSSEYHGGDGELYVSPAN-RHAASEAFVESALRAGHSYNPDFNGATQEGA 179 F++SE HH G SE HG G V + E F ++A G DFN G Sbjct: 136 VFKRSEDHHSGESESHGAGGPWRVEKQRLKWKILEEFSKAAQETGIPATDDFNRGDNTGV 195 Query: 180 GYYDVTIRDGRRWSTATAFLKPVRHRSNLTVLTHTHVESIVLLGKQATGVQALIKGSRVH 239 GY+DV + G RW+ + AFL+P R+NLTV+T H + +V G++ TGV+ + Sbjct: 196 GYFDVNQKRGIRWNASKAFLRPAMKRNNLTVITGAHTQRVVFDGRRCTGVEYRGNETEYF 255 Query: 240 LRARKEVILSAGAFGSPHLLMLSGIGSAAELEPQGIAPRHELPGVGQNLQDHADVVLCYK 299 +AR EVILS+GA SP LL LSGIG+ A L+ GI ++L GVG+NLQDH + + Y+ Sbjct: 256 AKARCEVILSSGAVNSPQLLELSGIGNGARLQNLGIDVVNDLRGVGENLQDHLQLRMAYQ 315 Query: 300 SNDTSLLGFSLSGGVKMGKAMF--DYARHRNGPVASNCAEAGAFLKTDP---GLERPDIQ 354 + L + + GK M YA ++GP++ + ++ GAF K+DP L RPD++ Sbjct: 316 VDGVRTL--NTASAHWWGKLMIGVQYALFQSGPMSMSPSQLGAFAKSDPDDRSLTRPDLE 373 Query: 355 LHSVIGTVDDHNRKLHWGHGFSCHVCVLRPKSIGSVGLASPDPRKAPRIDPNFLAHDDDV 414 H ++D LH + F+ VC LRP S GS+ + S D P I PN+L+ D D Sbjct: 374 YHVQPLSLDRFGEPLHRFNAFTASVCQLRPTSRGSIHIESTDAAAPPLIAPNYLSTDYDR 433 Query: 415 ATLLKGYRITRDIIAQTPMASFGLRDMY-SAGLHNDEQLIELLRKRTDTIYHPIGTCKMG 473 R+TR I A +A + R++ +E+L TI+HP+GTC+MG Sbjct: 434 HVASNALRLTRRIAAAPALARYQPREILPGIEYQTEEELQRAAGLVGTTIFHPVGTCRMG 493 Query: 474 --QDEMAVVDSQLRVHGIEGLRVVDASIMPTLVGGNTNAAAIMIAERAAEWI 523 D AVVD++LRV G++GLRVVDAS+MPT+ GNTN+ +MIAERA++ I Sbjct: 494 TTDDPGAVVDNRLRVIGVDGLRVVDASVMPTITSGNTNSPTLMIAERASDMI 545 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: 807 Number of extensions: 45 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: 570 Length adjustment: 36 Effective length of query: 490 Effective length of database: 534 Effective search space: 261660 Effective search space used: 261660 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: 53 (25.0 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