Align 3-hydroxypropionate dehydrogenase (EC 1.1.1.59) (characterized)
to candidate BPHYT_RS19495 BPHYT_RS19495 choline dehydrogenase
Query= metacyc::MONOMER-15202 (579 letters) >FitnessBrowser__BFirm:BPHYT_RS19495 Length = 570 Score = 646 bits (1667), Expect = 0.0 Identities = 328/556 (58%), Positives = 403/556 (72%), Gaps = 24/556 (4%) Query: 30 TNNTHA-------FDYIVVGAGTAGCLLANRLSADPANRVLLIEAGGRDNYHWIHIPVGY 82 T+ THA FDYI+VGAGTAGC+LANRL+ DP +VLL+EAGG+D+YHWIH+PVGY Sbjct: 4 TDTTHATRRLEGEFDYIIVGAGTAGCVLANRLTQDPDVQVLLLEAGGKDDYHWIHVPVGY 63 Query: 83 LYCINNPRTDWRFRTEPDPGLNGRSLIYPRGKTLGGCSSINGMLYLRGQARDYDGWAELT 142 LYCI NPRTDW ++T+ + GLNGR+L YPRG+ LGG SSINGM+Y+RGQ DYD WA +T Sbjct: 64 LYCIGNPRTDWLYKTQAEAGLNGRALSYPRGRVLGGSSSINGMIYMRGQREDYDEWARVT 123 Query: 143 GDDAWRWDNCLPDFMRHEDHYRLDEGGDADPDHYKFHGHGGEWRIEKQRLKWQVLADFAT 202 D +W W++ LP F R EDH+ G ++ HG GG WR+EKQRLKW++L +F+ Sbjct: 124 NDASWSWNSVLPVFKRSEDHH----AGASES-----HGAGGPWRVEKQRLKWKILEEFSR 174 Query: 203 AAVEAGVPRTRDFNRGDNEGVDAFEVNQRSGWRWNASKAFLRGVEQRGNLTVWHSTQVLK 262 AA E G+P T DFNRGDN GV F+VNQ+ G RWNASKAFLR +R NLTV + Sbjct: 175 AAQETGIPATDDFNRGDNTGVGYFDVNQKRGIRWNASKAFLRPALKRPNLTVITGAYTQR 234 Query: 263 LDFASGEGSEPRCCGVTVERAGKKVVTTARCEVVLSAGAIGSPQLLQLSGIGPTALLAEH 322 + F EG RC GV + ARCEV+LS+GA+ SPQLL+LSGIG A L Sbjct: 235 VVF---EGR--RCTGVEYRGDNTDYLAKARCEVILSSGAVNSPQLLELSGIGNGARLQNL 289 Query: 323 AIPVVADLPGVGENLQDHLQIRSIYKVKGAKTLNTMANSLIGKAKIGLEYILKRSGPMSM 382 I VV DL GVGENLQDHLQ+R YKV G +TLNT + GK IG++Y +SGPMSM Sbjct: 290 GIEVVDDLRGVGENLQDHLQLRMAYKVDGVRTLNTASAHWWGKLLIGMQYAFFQSGPMSM 349 Query: 383 APSQLCIFTRSS---KEYEHPNLEYHVQPLSLEAFGQPLHDFPAITASVCNLNPTSRGTV 439 +PSQL F +S + P+LEYHVQPLSL+ FG+PLH F A TASVC L PTSRG++ Sbjct: 350 SPSQLGAFAKSDPGDRSLTRPDLEYHVQPLSLDRFGEPLHRFNAFTASVCQLRPTSRGSI 409 Query: 440 RIKSGNPRQAPAISPNYLSTEEDRQVAADSLRVTRHIASQPAFAKYDPEEFKPGVQYQSD 499 I+S + P I+PNYLST+ DR VAA++LR+TR IA+ PA A+Y P+E PG+QYQ++ Sbjct: 410 HIESADASAPPLIAPNYLSTDYDRHVAANALRLTRRIAAAPALARYRPQEILPGIQYQTE 469 Query: 500 EDLARLAGDIGTTIFHPVGTAKMGRDDDPMAVVDSHLRVRGVTGLRVVDASIMPTITSGN 559 E+L + AG +GTTIFHPVGT +MG DDP AVVD+ LRV GV GLRVVDAS+MPTITSGN Sbjct: 470 EELQQAAGAVGTTIFHPVGTCRMGTTDDPGAVVDNRLRVIGVDGLRVVDASVMPTITSGN 529 Query: 560 TNSPTLMIAEKAAGWI 575 TNSPTLMIAE+A+ I Sbjct: 530 TNSPTLMIAERASDMI 545 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: 991 Number of extensions: 36 Number of successful extensions: 4 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: 570 Length adjustment: 36 Effective length of query: 543 Effective length of database: 534 Effective search space: 289962 Effective search space used: 289962 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