Align 3-hydroxypropionate dehydrogenase (EC 1.1.1.59) (characterized)
to candidate H281DRAFT_00975 H281DRAFT_00975 choline dehydrogenase
Query= metacyc::MONOMER-15202 (579 letters) >FitnessBrowser__Burk376:H281DRAFT_00975 Length = 553 Score = 365 bits (938), Expect = e-105 Identities = 221/549 (40%), Positives = 308/549 (56%), Gaps = 24/549 (4%) Query: 36 FDYIVVGAGTAGCLLANRLSADPANRVLLIEAGGRDNYHWIHIPVGYLYCINNPRTDWRF 95 +DYI+VGAG+AGC+LANRLSA VLL+EAGG+D+ W +PVG+ N +W + Sbjct: 3 YDYIIVGAGSAGCILANRLSASGEYSVLLLEAGGKDSSFWFKVPVGFTKTYYNETYNWMY 62 Query: 96 RTEPDPGLNGRSLIYPRGKTLGGCSSINGMLYLRGQARDYDGWAELTGDDAWRWDNCLPD 155 +EP+ L+ R + PRGK GG SIN M+Y+RGQ D+D WA G+ W + + LP Sbjct: 63 YSEPEKELDNRPIYCPRGKVQGGSGSINAMIYVRGQPHDFDDWA-AAGNPGWAFRDVLPY 121 Query: 156 FMRHEDHYRLDEGGDADPDHYKFHGHGGEWRIEKQR-LKWQVLADFATAAVEAGVPRTRD 214 F + E H GD + +HG G RI + + F +AG R+ D Sbjct: 122 FRKLESH----PLGDTE-----YHGADGPIRISPMKDAVHPICHVFLKGCDQAGYRRSDD 172 Query: 215 FNRGDNEGVDAFEVNQRSGWRWNASKAFLRGVEQRGNLTVWHSTQVLKLDFASGEGSEPR 274 FN EG ++VN R+G R ++S +L R NLTV H+ ++ F EG R Sbjct: 173 FNGAQFEGAGIYDVNTRNGQRSSSSFEYLHPALARKNLTVEHNVLANRVLF---EGKH-R 228 Query: 275 CCGVTVERAGKKVVTTARCEVVLSAGAIGSPQLLQLSGIGPTALLAEHAIPVVADLPGVG 334 GV+V + G A+ EV+L+AGA+ SP+LLQLSG+G +ALLA+H I + +LP VG Sbjct: 229 AIGVSVTQNGVARRFMAKREVILAAGAVDSPKLLQLSGLGDSALLAKHGITTIKELPAVG 288 Query: 335 ENLQDHLQIRSIYKVKGAKTLNTMANSLIGKAKIGLEYILKRSGPMSMAPSQLCIFTRSS 394 +NLQDHL + S Y KTLN LIGK K+GL+Y+L R GP++M+ +Q F R S Sbjct: 289 QNLQDHLCV-SFYYRANVKTLNDELRPLIGKLKLGLQYLLTRKGPLAMSVNQSGGFFRGS 347 Query: 395 KEYEHPNLEYHVQPLSL------EAFGQPLHDFPAITASVCNLNPTSRGTVRIKSGNPRQ 448 + PNL+ + PLS +A +P + + PTSRG++ I S Sbjct: 348 EREAQPNLQLYFNPLSYRIPKSNKASLEP-EPYSGFLLAFNPCRPTSRGSIEIASNRAED 406 Query: 449 APAISPNYLSTEEDRQVAADSLRVTRHIASQPAFAKYDPEEFKPGVQYQSDEDLARLAGD 508 A I N L+T++D + R + + PA + EE PG Q S E + + Sbjct: 407 AAKIRLNALTTQKDIDEVIQGCELVRKVMASPALKEITVEEISPGPQVASRESFLQYFRE 466 Query: 509 IGTTIFHPVGTAKMGRDDDPMAVVDSHLRVRGVTGLRVVDASIMPTITSGNTNSPTLMIA 568 +I+H G+ MG +D +VVD+ LRV GV GLRVVDAS+ P ITSGN N+PT+M+A Sbjct: 467 QSGSIYHLCGSCAMG-NDPRTSVVDARLRVHGVAGLRVVDASVFPNITSGNINAPTMMVA 525 Query: 569 EKAAGWILK 577 EK A IL+ Sbjct: 526 EKGADMILE 534 Lambda K H 0.318 0.135 0.418 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: 847 Number of extensions: 37 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: 579 Length of database: 553 Length adjustment: 36 Effective length of query: 543 Effective length of database: 517 Effective search space: 280731 Effective search space used: 280731 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 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