Align 3-hydroxypropionate dehydrogenase (EC 1.1.1.59) (characterized)
to candidate WP_018125681.1 B149_RS0113405 choline dehydrogenase
Query= metacyc::MONOMER-15202 (579 letters) >NCBI__GCF_000375485.1:WP_018125681.1 Length = 546 Score = 353 bits (905), Expect = e-101 Identities = 214/543 (39%), Positives = 302/543 (55%), Gaps = 20/543 (3%) Query: 36 FDYIVVGAGTAGCLLANRLSADPANRVLLIEAGGRDNY--HWIHIPVGYLYCINNPRTDW 93 +DYI++G G+AG +LANRLSADP +VL++EAG D+ IH+P Y + +W Sbjct: 4 YDYIIIGGGSAGSVLANRLSADPKTKVLVLEAGRPDHRLDFRIHMPAALTYPLAGKTYNW 63 Query: 94 RFRTEPDPGLNGRSLIYPRGKTLGGCSSINGMLYLRGQARDYDGWAELTGDDAWRWDNCL 153 + +EP+P +N R + PRGK LGG S INGM+Y+RG A DY+ W++ G + W + +CL Sbjct: 64 WYESEPEPWMNNRRIYQPRGKVLGGSSCINGMIYIRGNAMDYEKWSKDDGMENWSYAHCL 123 Query: 154 PDFMRHEDHYRLDEGGDADPDHYKFHGHGGEWRIEKQRLKWQVLADFATAAVEAGVPRTR 213 P F R E A D Y+ G G + + F A +AG P T+ Sbjct: 124 PYFRRFECR-------TAGADEYQ--GAVGPLYLTTPECDNPLFNAFFNAVQQAGYPLTK 174 Query: 214 DFNRGDNEGVDAFEVNQRSGWRWNASKAFLRGVEQRGNLTVWHSTQVLKLDFASGEGSEP 273 D N EG F+ N G R NA++A++ V+ R NLT+ ++ F Sbjct: 175 DVNGYQQEGFGKFDRNTYQGRRHNAARAYVHTVKNRRNLTIKCKAHTNRILFQG-----K 229 Query: 274 RCCGVTVERAGKKVVTTARCEVVLSAGAIGSPQLLQLSGIGPTALLAEHAIPVVADLPGV 333 R GV + G++ + E++ GAI SPQLLQLSGIG A L+ I VV +LPGV Sbjct: 230 RAVGVEYTK-GRRTMQAYGGEIISCGGAINSPQLLQLSGIGNGAELSSLGIDVVQNLPGV 288 Query: 334 GENLQDHLQIRSIYKVKGAKTLNTMANSLIGKAKIGLEYILKRSGPMSMAPSQLCIFTRS 393 GENLQDHL++ Y K ++ A + IGL+++ +G + + F RS Sbjct: 289 GENLQDHLELYVQYACKKPVSMFP-ALQWYNQPWIGLKWLFGHTGEAATNHFEAGGFIRS 347 Query: 394 SKEYEHPNLEYHVQPLSLEAFGQPLHDFPAITASVCNLNPTSRGTVRIKSGNPRQAPAIS 453 + + E+PNL+YH P+++ G ++ V +N RG V+IKS NP P+I Sbjct: 348 NDQVEYPNLQYHFLPIAIRYDGSAPNEGHGYQVHVGPMNTDVRGHVKIKSDNPADYPSIL 407 Query: 454 PNYLSTEEDRQVAADSLRVTRHIASQPAFAKYDPEEFKPGVQYQSDEDLARLAGDIGTTI 513 NYLSTE++R+ +++R TR I +QPAF + E PG Q Q+DE++ G + Sbjct: 408 FNYLSTEQERREWVEAIRKTREIMTQPAFDELRGRELAPGDQAQTDEEILDFVAREGESA 467 Query: 514 FHPVGTAKMGRDDDPMAVVDSHLRVRGVTGLRVVDASIMPTITSGNTNSPTLMIAEKAAG 573 +HP T MG D MAV D +RV GV GLRVVDAS+MP IT+GN +P +MIAEKAA Sbjct: 468 YHPSCTCAMGTHD--MAVTDPEMRVHGVDGLRVVDASVMPYITNGNIYAPVMMIAEKAAD 525 Query: 574 WIL 576 IL Sbjct: 526 MIL 528 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: 893 Number of extensions: 44 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: 546 Length adjustment: 36 Effective length of query: 543 Effective length of database: 510 Effective search space: 276930 Effective search space used: 276930 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 24 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