Align 3-hydroxypropionate dehydrogenase (EC 1.1.1.59) (characterized)
to candidate BPHYT_RS09890 BPHYT_RS09890 choline dehydrogenase
Query= metacyc::MONOMER-15202 (579 letters) >FitnessBrowser__BFirm:BPHYT_RS09890 Length = 553 Score = 358 bits (919), Expect = e-103 Identities = 218/549 (39%), Positives = 303/549 (55%), Gaps = 24/549 (4%) Query: 36 FDYIVVGAGTAGCLLANRLSADPANRVLLIEAGGRDNYHWIHIPVGYLYCINNPRTDWRF 95 +DYI+VGAG+AGC+LANRLSA VLL+EAGG+D+ W IPVG+ N +W + Sbjct: 3 YDYIIVGAGSAGCILANRLSASGQYSVLLLEAGGKDSSFWFKIPVGFTKTYYNETYNWMY 62 Query: 96 RTEPDPGLNGRSLIYPRGKTLGGCSSINGMLYLRGQARDYDGWAELTGDDAWRWDNCLPD 155 +EP+ L+ R + PRGK GG SIN M+Y+RGQ D+D WA G+ W + + LP Sbjct: 63 YSEPEKELDNRPIYCPRGKVQGGSGSINAMIYVRGQPHDFDDWA-AAGNTGWAFRDVLPY 121 Query: 156 FMRHEDHYRLDEGGDADPDHYKFHGHGGEWRIEKQR-LKWQVLADFATAAVEAGVPRTRD 214 F + E H G+ D +HG G RI + + F +AG R+ D Sbjct: 122 FRKLESH----PLGNTD-----YHGADGPIRISPMKDAVHPICHVFLKGCDQAGYQRSDD 172 Query: 215 FNRGDNEGVDAFEVNQRSGWRWNASKAFLRGVEQRGNLTVWHSTQVLKLDFASGEGSEPR 274 FN EG ++VN R+G R ++S +L V R NLTV ++ F + Sbjct: 173 FNGAQFEGAGIYDVNTRNGQRSSSSFEYLHPVLSRKNLTVERDVLASRVLF----DGKQH 228 Query: 275 CCGVTVERAGKKVVTTARCEVVLSAGAIGSPQLLQLSGIGPTALLAEHAIPVVADLPGVG 334 GV+V + G A EV+LSAGA+ SP+LLQLSG+G +ALLA+H I +V +LP VG Sbjct: 229 AIGVSVMQNGTTRQFMATREVILSAGAVDSPKLLQLSGVGDSALLAKHRIAMVKELPAVG 288 Query: 335 ENLQDHLQIRSIYKVKGAKTLNTMANSLIGKAKIGLEYILKRSGPMSMAPSQLCIFTRSS 394 +NLQDHL + S Y KTLN L+GK K+GL+Y+L R GP++M+ +Q F + + Sbjct: 289 QNLQDHLCV-SFYYRANMKTLNDEMRPLLGKLKLGLQYLLTRKGPLAMSVNQSGGFFKGN 347 Query: 395 KEYEHPNLEYHVQPLSL------EAFGQPLHDFPAITASVCNLNPTSRGTVRIKSGNPRQ 448 PNL+ + PLS +A +P + + PTSRG++ I S Sbjct: 348 DLQTQPNLQLYFNPLSYRIPKSNKANLEP-EPYSGFLLAFNPCRPTSRGSIEIASNRAED 406 Query: 449 APAISPNYLSTEEDRQVAADSLRVTRHIASQPAFAKYDPEEFKPGVQYQSDEDLARLAGD 508 + I N L+TE+D + R + + PA EE PG Q + E + + Sbjct: 407 SAKIRINALTTEKDIDEVIQGCELVRKVMASPALKAITVEEISPGPQVNTREGFLQYFRE 466 Query: 509 IGTTIFHPVGTAKMGRDDDPMAVVDSHLRVRGVTGLRVVDASIMPTITSGNTNSPTLMIA 568 +I+H G+ MG DD +VVD+ LRV G+ GLRVVDASI P ITSGN N+PT+M+A Sbjct: 467 QSGSIYHLCGSCAMG-DDPRSSVVDARLRVHGIAGLRVVDASIFPNITSGNINAPTMMVA 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: 832 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: 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