Align 3-hydroxypropionate dehydrogenase (EC 1.1.1.59) (characterized)
to candidate WP_110754457.1 C7477_RS17345 choline dehydrogenase
Query= metacyc::MONOMER-15202 (579 letters) >NCBI__GCF_003217235.1:WP_110754457.1 Length = 555 Score = 364 bits (934), Expect = e-105 Identities = 213/540 (39%), Positives = 305/540 (56%), Gaps = 11/540 (2%) Query: 37 DYIVVGAGTAGCLLANRLSADPANRVLLIEAGGRDNYHWIHIPVGYLYCINNPRTDWRFR 96 D++++G+G+AG LA RLS + + V++IE GG D +I +P + +N DW F Sbjct: 4 DFVIIGSGSAGSALAYRLSENGKHSVIVIEFGGSDIGPFIQMPAALSFPMNMATYDWGFA 63 Query: 97 TEPDPGLNGRSLIYPRGKTLGGCSSINGMLYLRGQARDYDGWAELTGDDAWRWDNCLPDF 156 +EP+P L GRSL+ PRGK +GG SSINGM+Y+RG ARD+D WAE +G W + + LP F Sbjct: 64 SEPEPHLGGRSLVTPRGKVIGGSSSINGMVYVRGHARDFDHWAE-SGARGWAFADVLPYF 122 Query: 157 MRHEDHYRLDEGGDADPDHYKFHGHGGEWRIEKQRLKWQVLADFATAAVEAGVPRTRDFN 216 R E+ + + GG + + G G +++ K + F A +AG T D+N Sbjct: 123 KRMENAHFHENGGGGENG---WRGTDGPLHVQRGSRKNPLFHAFVEAGSQAGFQVTEDYN 179 Query: 217 RGDNEGVDAFEVNQRSGWRWNASKAFLRGVEQRGNLTVWHSTQVLKLDFASGEGSEPRCC 276 EG A E G RW+A+ A+L+ R N+ + K+ +G R Sbjct: 180 GEKQEGFGAMEQTIYRGRRWSAANAYLKPALNRQNVRLVRGL-ARKVVIENG-----RAT 233 Query: 277 GVTVERAGKKVVTTARCEVVLSAGAIGSPQLLQLSGIGPTALLAEHAIPVVADLPGVGEN 336 GV V G+ V AR EV++SA +I SP+LL LSGIGP A L E + V+AD PGVG+N Sbjct: 234 GVEVATGGRIRVARARREVIISASSINSPKLLMLSGIGPAAHLKERGVTVIADRPGVGQN 293 Query: 337 LQDHLQIRSIYKVKGAKTLNTMANSLIGKAKIGLEYILKRSGPMSMAPSQLCIFTRSSKE 396 LQDHL++ + TL + N L KA+IG +++ ++G + + F RS Sbjct: 294 LQDHLEVYIQQECIQPITLYSKLN-LFSKARIGAQWLFFKTGDGATNHFESAAFVRSKPG 352 Query: 397 YEHPNLEYHVQPLSLEAFGQPLHDFPAITASVCNLNPTSRGTVRIKSGNPRQAPAISPNY 456 E+P+++YH P+++ G+ + A V + SRG+V ++S +P++ P I NY Sbjct: 353 VEYPDIQYHFLPVAIRYDGKAAAESHGFQAHVGPMRSKSRGSVTLRSADPKEKPVIRFNY 412 Query: 457 LSTEEDRQVAADSLRVTRHIASQPAFAKYDPEEFKPGVQYQSDEDLARLAGDIGTTIFHP 516 +S +D +R+TR I Q AF Y E +PG QSDE++ + FHP Sbjct: 413 MSHPDDWADFRHCVRLTREIFGQAAFDPYRGREIQPGADVQSDEEIDDFIRAHVESAFHP 472 Query: 517 VGTAKMGRDDDPMAVVDSHLRVRGVTGLRVVDASIMPTITSGNTNSPTLMIAEKAAGWIL 576 GTAKMG DDPMAVVD RV GV GLRV D+SI P IT+GN N P++M+ EKAA IL Sbjct: 473 CGTAKMGSVDDPMAVVDPECRVIGVEGLRVADSSIFPRITNGNLNGPSMMVGEKAADHIL 532 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: 952 Number of extensions: 53 Number of successful extensions: 7 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 579 Length of database: 555 Length adjustment: 36 Effective length of query: 543 Effective length of database: 519 Effective search space: 281817 Effective search space used: 281817 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