Align 3-hydroxypropionate dehydrogenase (EC 1.1.1.59) (characterized)
to candidate H281DRAFT_02374 H281DRAFT_02374 choline dehydrogenase
Query= metacyc::MONOMER-15202 (579 letters) >FitnessBrowser__Burk376:H281DRAFT_02374 Length = 570 Score = 646 bits (1667), Expect = 0.0 Identities = 322/543 (59%), Positives = 398/543 (73%), Gaps = 17/543 (3%) Query: 36 FDYIVVGAGTAGCLLANRLSADPANRVLLIEAGGRDNYHWIHIPVGYLYCINNPRTDWRF 95 FDYI+VGAGTAGC+LANRL+ DP +VLL+EAGG+D+YHWIH+PVGYLYCI NPRTDW + Sbjct: 17 FDYIIVGAGTAGCVLANRLTEDPDVQVLLLEAGGKDDYHWIHVPVGYLYCIGNPRTDWLY 76 Query: 96 RTEPDPGLNGRSLIYPRGKTLGGCSSINGMLYLRGQARDYDGWAELTGDDAWRWDNCLPD 155 +T+ +PGLNGR+L YPRG+ LGG SSINGM+Y+RGQ DYD WA +T D +W W++ LP Sbjct: 77 KTQAEPGLNGRALSYPRGRVLGGSSSINGMIYMRGQREDYDEWARVTNDASWSWNSVLPV 136 Query: 156 FMRHEDHYRLDEGGDADPDHYKFHGHGGEWRIEKQRLKWQVLADFATAAVEAGVPRTRDF 215 F R EDH+ G+++ HG GG WR+EKQRLKW++L +F+ AA E G+P T DF Sbjct: 137 FKRSEDHH----SGESES-----HGAGGPWRVEKQRLKWKILEEFSKAAQETGIPATDDF 187 Query: 216 NRGDNEGVDAFEVNQRSGWRWNASKAFLRGVEQRGNLTVWHSTQVLKLDFASGEGSEPRC 275 NRGDN GV F+VNQ+ G RWNASKAFLR +R NLTV ++ F RC Sbjct: 188 NRGDNTGVGYFDVNQKRGIRWNASKAFLRPAMKRNNLTVITGAHTQRVVFDGR-----RC 242 Query: 276 CGVTVERAGKKVVTTARCEVVLSAGAIGSPQLLQLSGIGPTALLAEHAIPVVADLPGVGE 335 GV + ARCEV+LS+GA+ SPQLL+LSGIG A L I VV DL GVGE Sbjct: 243 TGVEYRGNETEYFAKARCEVILSSGAVNSPQLLELSGIGNGARLQNLGIDVVNDLRGVGE 302 Query: 336 NLQDHLQIRSIYKVKGAKTLNTMANSLIGKAKIGLEYILKRSGPMSMAPSQLCIFTRSS- 394 NLQDHLQ+R Y+V G +TLNT + GK IG++Y L +SGPMSM+PSQL F +S Sbjct: 303 NLQDHLQLRMAYQVDGVRTLNTASAHWWGKLMIGVQYALFQSGPMSMSPSQLGAFAKSDP 362 Query: 395 --KEYEHPNLEYHVQPLSLEAFGQPLHDFPAITASVCNLNPTSRGTVRIKSGNPRQAPAI 452 + P+LEYHVQPLSL+ FG+PLH F A TASVC L PTSRG++ I+S + P I Sbjct: 363 DDRSLTRPDLEYHVQPLSLDRFGEPLHRFNAFTASVCQLRPTSRGSIHIESTDAAAPPLI 422 Query: 453 SPNYLSTEEDRQVAADSLRVTRHIASQPAFAKYDPEEFKPGVQYQSDEDLARLAGDIGTT 512 +PNYLST+ DR VA+++LR+TR IA+ PA A+Y P E PG++YQ++E+L R AG +GTT Sbjct: 423 APNYLSTDYDRHVASNALRLTRRIAAAPALARYQPREILPGIEYQTEEELQRAAGLVGTT 482 Query: 513 IFHPVGTAKMGRDDDPMAVVDSHLRVRGVTGLRVVDASIMPTITSGNTNSPTLMIAEKAA 572 IFHPVGT +MG DDP AVVD+ LRV GV GLRVVDAS+MPTITSGNTNSPTLMIAE+A+ Sbjct: 483 IFHPVGTCRMGTTDDPGAVVDNRLRVIGVDGLRVVDASVMPTITSGNTNSPTLMIAERAS 542 Query: 573 GWI 575 I Sbjct: 543 DMI 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: 993 Number of extensions: 35 Number of successful extensions: 5 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