Align 3-hydroxypropionate dehydrogenase (EC 1.1.1.59) (characterized)
to candidate RR42_RS20290 RR42_RS20290 choline dehydrogenase
Query= metacyc::MONOMER-15202 (579 letters) >FitnessBrowser__Cup4G11:RR42_RS20290 Length = 566 Score = 679 bits (1752), Expect = 0.0 Identities = 342/540 (63%), Positives = 396/540 (73%), Gaps = 14/540 (2%) Query: 36 FDYIVVGAGTAGCLLANRLSADPANRVLLIEAGGRDNYHWIHIPVGYLYCINNPRTDWRF 95 +DYI+VGAG+AGC+LANRL+ DP VLL+EAGGRD+YHWIHIPVGYLYCI NPRTDW + Sbjct: 4 YDYIIVGAGSAGCVLANRLTQDPEVSVLLLEAGGRDDYHWIHIPVGYLYCIGNPRTDWMY 63 Query: 96 RTEPDPGLNGRSLIYPRGKTLGGCSSINGMLYLRGQARDYDGWAELTGDDAWRWDNCLPD 155 RT GL GRSL YPRG+ LGG SSINGM+Y+RGQ DYD WA LTGDD WRWDN LP Sbjct: 64 RTVAQAGLGGRSLGYPRGRVLGGSSSINGMIYMRGQREDYDDWARLTGDDGWRWDNVLPL 123 Query: 156 FMRHEDHYRLDEGGDADPDHYKFHGHGGEWRIEKQRLKWQVLADFATAAVEAGVPRTRDF 215 F R EDH+R GGD +FHG GGEWR+E QRL+W +L F AA +AG+PRT DF Sbjct: 124 FKRSEDHHR---GGD------EFHGAGGEWRVEGQRLRWDILERFIDAAEQAGIPRTDDF 174 Query: 216 NRGDNEGVDAFEVNQRSGWRWNASKAFLRGVEQRGNLTVWHSTQVLKLDFASGEGSEPRC 275 NRGDN GV FEVNQR G RWN +KAFLR +R NLT+ QV L FA RC Sbjct: 175 NRGDNFGVGYFEVNQRRGIRWNTAKAFLRRAAERPNLTIVTGAQVSALTFAGR-----RC 229 Query: 276 CGVTVERAGKKVVTTARCEVVLSAGAIGSPQLLQLSGIGPTALLAEHAIPVVADLPGVGE 335 GV GK AR EV+L+AGA+ +PQLL+LSGIG L I V LPGVGE Sbjct: 230 TGVDYLGGGKPFTAAAREEVILAAGAVNTPQLLELSGIGQPERLQAAGIAVRHALPGVGE 289 Query: 336 NLQDHLQIRSIYKVKGAKTLNTMANSLIGKAKIGLEYILKRSGPMSMAPSQLCIFTRSSK 395 NLQDHLQ+RS+ KV+G +TLNT A S GK IGL+Y + +SGPMSMAPSQL F RS Sbjct: 290 NLQDHLQLRSVVKVQGVRTLNTRAGSWWGKLGIGLQYAVNQSGPMSMAPSQLGAFARSDA 349 Query: 396 EYEHPNLEYHVQPLSLEAFGQPLHDFPAITASVCNLNPTSRGTVRIKSGNPRQAPAISPN 455 Y PNLEYHVQPLSL+ FG PLH F A TASVCNL PTSRG+V I + R AP I+PN Sbjct: 350 SYARPNLEYHVQPLSLDKFGDPLHRFNAFTASVCNLRPTSRGSVHIADPDFRHAPVIAPN 409 Query: 456 YLSTEEDRQVAADSLRVTRHIASQPAFAKYDPEEFKPGVQYQSDEDLARLAGDIGTTIFH 515 YL+T+ DR+VAADSLR+TR I + PA A Y P+E+ PG +++DE LA+ A +IGTTIFH Sbjct: 410 YLTTDADRKVAADSLRLTRRIVASPALAPYKPQEWLPGAAFETDEQLAQAASEIGTTIFH 469 Query: 516 PVGTAKMGRDDDPMAVVDSHLRVRGVTGLRVVDASIMPTITSGNTNSPTLMIAEKAAGWI 575 PVGT +MGR DDP AVVD LRV G+ GLRVVDASIMP ITSGNTNSPT+MIAE+A+ I Sbjct: 470 PVGTCRMGRPDDPQAVVDQRLRVIGIDGLRVVDASIMPLITSGNTNSPTIMIAERASDMI 529 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: 1042 Number of extensions: 37 Number of successful extensions: 3 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: 566 Length adjustment: 36 Effective length of query: 543 Effective length of database: 530 Effective search space: 287790 Effective search space used: 287790 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