Align 3-hydroxypropionate dehydrogenase (EC 1.1.1.59) (characterized)
to candidate BPHYT_RS21745 BPHYT_RS21745 choline dehydrogenase
Query= metacyc::MONOMER-15202 (579 letters) >FitnessBrowser__BFirm:BPHYT_RS21745 Length = 551 Score = 466 bits (1200), Expect = e-136 Identities = 259/543 (47%), Positives = 338/543 (62%), Gaps = 18/543 (3%) Query: 36 FDYIVVGAGTAGCLLANRLSADPANRVLLIEAGGRDNYHWIHIPVGYLYCINNPRTDWRF 95 FD++VVGAG+AGC+LANRLS V L+EAG D + WIHIP+GY + +P +W F Sbjct: 5 FDFVVVGAGSAGCVLANRLSEGGRYSVCLLEAGPADRFMWIHIPIGYGKTMFHPVYNWGF 64 Query: 96 RTEPDPGLNGRSLIYPRGKTLGGCSSINGMLYLRGQARDYDGWAELTGDDAWRWDNCLPD 155 T+PDP ++ R L +PRG+TLGG SSING++Y+RGQ DYD WA L G+ W W +CLP Sbjct: 65 YTDPDPNMHNRRLYWPRGRTLGGSSSINGLIYVRGQRDDYDNWARL-GNRGWSWQDCLPY 123 Query: 156 FMRHEDHYRLDEGGDADPDHYKFHGHGGEWRIE-KQRLKWQVLADFATAAVEAGVPRTRD 214 F R E H L EG D G W KQR +++ F A+ GV D Sbjct: 124 FKRLE-HNELGEGPTRGVD-------GPLWASTIKQR--HELVDAFIEASNSLGVASIDD 173 Query: 215 FNRGDNEGVDAFEVNQRSGWRWNASKAFLRGVEQRGNLTVWHSTQVLKLDFASGEGSEPR 274 FN GD EGV +++ R G+R + + A+L+ QR NL V K+ F EG+ R Sbjct: 174 FNTGDQEGVGYYQLTTRRGFRCSTAVAYLKPARQRQNLHVETDAMASKILF---EGT--R 228 Query: 275 CCGVTVERAGKKVVTTARCEVVLSAGAIGSPQLLQLSGIGPTALLAEHAIPVVADLPGVG 334 CGV + G+ A EV+L+AGA+ SPQLLQLSG+GP ALL E IPVVA+ GVG Sbjct: 229 ACGVQYRQHGELREVRANREVILTAGALQSPQLLQLSGVGPAALLREFGIPVVANRAGVG 288 Query: 335 ENLQDHLQIRSIYKVKGAKTLNTMANSLIGKAKIGLEYILKRSGPMSMAPSQLCIFTRS- 393 ENLQDHLQIR IY+V T N S G+AK+GL++ L RSGP+++ +Q +F R+ Sbjct: 289 ENLQDHLQIRLIYEVTKPITTNDQLRSWTGRAKMGLQWALMRSGPLAVGINQGGMFCRAL 348 Query: 394 SKEYEHPNLEYHVQPLSLEAFGQPLHDFPAITASVCNLNPTSRGTVRIKSGNPRQAPAIS 453 +E P+ ++H LS ++ G +HDFP T S+C L P SRG VRI+S +PR+AP+I Sbjct: 349 PEESATPDTQFHFSTLSADSAGGNVHDFPGCTYSICQLRPESRGAVRIRSADPREAPSIQ 408 Query: 454 PNYLSTEEDRQVAADSLRVTRHIASQPAFAKYDPEEFKPGVQYQSDEDLARLAGDIGTTI 513 PNYL T+ DR+ +R R +A+ A E +PG Q+D++L + G TI Sbjct: 409 PNYLDTDLDRRTTIAGVRFARRVAAAQPMAGLMKREVRPGADAQTDDELLEFCREYGQTI 468 Query: 514 FHPVGTAKMGRDDDPMAVVDSHLRVRGVTGLRVVDASIMPTITSGNTNSPTLMIAEKAAG 573 FHP GTAKMG DP+AVVD LRV G GLRVVD SIMPT+ SGNTN P +M+AEKA+ Sbjct: 469 FHPSGTAKMGPAGDPLAVVDERLRVYGTQGLRVVDCSIMPTLVSGNTNVPIVMVAEKASD 528 Query: 574 WIL 576 IL Sbjct: 529 MIL 531 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: 874 Number of extensions: 41 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: 551 Length adjustment: 36 Effective length of query: 543 Effective length of database: 515 Effective search space: 279645 Effective search space used: 279645 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