Align alcohol dehydrogenase (EC 1.1.1.1) (characterized)
to candidate H281DRAFT_00975 H281DRAFT_00975 choline dehydrogenase
Query= BRENDA::Q76HN6 (526 letters) >FitnessBrowser__Burk376:H281DRAFT_00975 Length = 553 Score = 364 bits (934), Expect = e-105 Identities = 218/536 (40%), Positives = 301/536 (56%), Gaps = 17/536 (3%) Query: 1 MEFDYLIVGAGSAGCVLANRLSADPSVTVCLLEAGPEDRSPLIHTPLGLAAILPTRHVNW 60 M +DY+IVGAGSAGC+LANRLSA +V LLEAG +D S P+G NW Sbjct: 1 MNYDYIIVGAGSAGCILANRLSASGEYSVLLLEAGGKDSSFWFKVPVGFTKTYYNETYNW 60 Query: 61 AFKTTPQPGLGGRVGYQPRGKVLGGSSSINGMIYIRGHQDDFNDWQALGNEGWGFDDVLP 120 + + P+ L R Y PRGKV GGS SIN MIY+RG DF+DW A GN GW F DVLP Sbjct: 61 MYYSEPEKELDNRPIYCPRGKVQGGSGSINAMIYVRGQPHDFDDWAAAGNPGWAFRDVLP 120 Query: 121 YFRKSEMHHGGSSEYHGGDGELYVSPANR--HAASEAFVESALRAGHSYNPDFNGATQEG 178 YFRK E H G +EYHG DG + +SP H F++ +AG+ + DFNGA EG Sbjct: 121 YFRKLESHPLGDTEYHGADGPIRISPMKDAVHPICHVFLKGCDQAGYRRSDDFNGAQFEG 180 Query: 179 AGYYDVTIRDGRRWSTATAFLKPVRHRSNLTVLTHTHVESIVLLGK-QATGVQALIKGSR 237 AG YDV R+G+R S++ +L P R NLTV + ++ GK +A GV G Sbjct: 181 AGIYDVNTRNGQRSSSSFEYLHPALARKNLTVEHNVLANRVLFEGKHRAIGVSVTQNGVA 240 Query: 238 VHLRARKEVILSAGAFGSPHLLMLSGIGSAAELEPQGIAPRHELPGVGQNLQDHADVVLC 297 A++EVIL+AGA SP LL LSG+G +A L GI ELP VGQNLQDH V Sbjct: 241 RRFMAKREVILAAGAVDSPKLLQLSGLGDSALLAKHGITTIKELPAVGQNLQDHLCVSFY 300 Query: 298 YKSNDTSLLG--FSLSGGVKMGKAMFDYARHRNGPVASNCAEAGAFLKTDPGLERPDIQL 355 Y++N +L L G +K+G Y R GP+A + ++G F + +P++QL Sbjct: 301 YRANVKTLNDELRPLIGKLKLG---LQYLLTRKGPLAMSVNQSGGFFRGSEREAQPNLQL 357 Query: 356 H-----SVIGTVDDHNRKLHWGHGFSCHVCVLRPKSIGSVGLASPDPRKAPRIDPNFLAH 410 + I + + + GF RP S GS+ +AS A +I N L Sbjct: 358 YFNPLSYRIPKSNKASLEPEPYSGFLLAFNPCRPTSRGSIEIASNRAEDAAKIRLNALTT 417 Query: 411 DDDVATLLKGYRITRDIIAQTPMASFGLRDMYSAG--LHNDEQLIELLRKRTDTIYHPIG 468 D+ +++G + R ++A + + ++ S G + + E ++ R+++ +IYH G Sbjct: 418 QKDIDEVIQGCELVRKVMASPALKEITVEEI-SPGPQVASRESFLQYFREQSGSIYHLCG 476 Query: 469 TCKMGQD-EMAVVDSQLRVHGIEGLRVVDASIMPTLVGGNTNAAAIMIAERAAEWI 523 +C MG D +VVD++LRVHG+ GLRVVDAS+ P + GN NA +M+AE+ A+ I Sbjct: 477 SCAMGNDPRTSVVDARLRVHGVAGLRVVDASVFPNITSGNINAPTMMVAEKGADMI 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: 763 Number of extensions: 42 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: 553 Length adjustment: 35 Effective length of query: 491 Effective length of database: 518 Effective search space: 254338 Effective search space used: 254338 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