Align 3-hydroxypropionate dehydrogenase (EC 1.1.1.59) (characterized)
to candidate WP_067911515.1 AQZ52_RS13155 choline dehydrogenase
Query= metacyc::MONOMER-15202 (579 letters) >NCBI__GCF_001519075.1:WP_067911515.1 Length = 555 Score = 384 bits (986), Expect = e-111 Identities = 228/541 (42%), Positives = 310/541 (57%), Gaps = 16/541 (2%) Query: 36 FDYIVVGAGTAGCLLANRLSADPANRVLLIEAGGRDNYHWIHIPVGYLYCINNPRTDWRF 95 FDYI+VGAG+AGC+LA+RLSAD ++VL++E GG D +I +P +N R +W + Sbjct: 8 FDYIIVGAGSAGCVLADRLSADGKHKVLVLEFGGSDQSIYIQMPSALAIPMNTTRWNWHY 67 Query: 96 RTEPDPGLNGRSLIYPRGKTLGGCSSINGMLYLRGQARDYDGWAELTGDDAWRWDNCLPD 155 +EP+PGL+GR L PRGK LGG SSING++Y+RG D++ W E G W + + LP Sbjct: 68 ESEPEPGLDGRVLHTPRGKGLGGSSSINGLVYIRGNPLDFERWEE-EGARGWNYASVLPY 126 Query: 156 FMRHEDHYRLDEGGDADPDHYKFHGHGGEWRIEKQRLKWQVLADFATAAVEAGVPRTRDF 215 F R E R DEGGD ++ G G L+ + + AA +AG T D Sbjct: 127 FKRAE---RRDEGGD------EYRGSDGPLDTRYGTLENPLNQAWLDAASQAGYALTDDV 177 Query: 216 NRGDNEGVDAFEVNQRSGWRWNASKAFLRGVEQRGNLTVWHSTQVLKLDFASGEGSEPRC 275 N EG ++ R+G R +A+KA+LR +R NLTV T ++ EG R Sbjct: 178 NGYRQEGFGRMDMTVRNGERCSAAKAYLRPAMRRSNLTVLQHTLATRVVM---EGK--RA 232 Query: 276 CGVTVERAGKKVVTTARCEVVLSAGAIGSPQLLQLSGIGPTALLAEHAIPVVADLPGVGE 335 GV +ER GK+ + A EV+L+ G I SPQLL+LSGIGP A LA+H I VVAD PGVG Sbjct: 233 VGVEIERYGKRSIVKAGREVILAGGPINSPQLLKLSGIGPAAELAQHGIAVVADRPGVGA 292 Query: 336 NLQDHLQIRSIYKVKGAKTLNTMANSLIGKAKIGLEYILKRSGPMSMAPSQLCIFTRSSK 395 NLQDHL+ TL AN L GK +G ++ +SG + + C F RS Sbjct: 293 NLQDHLEFYFQMACTQPVTLYKYAN-LFGKGLVGARWLFLKSGLGATNHFETCGFIRSKA 351 Query: 396 EYEHPNLEYHVQPLSLEAFGQPLHDFPAITASVCNLNPTSRGTVRIKSGNPRQAPAISPN 455 +P+++YH P+++ G L A V + SRGTV ++S +P P I N Sbjct: 352 GIRYPDIQYHFFPMAVSYDGNSLASEHGFQAHVGPMRSKSRGTVTLRSADPADKPVIRFN 411 Query: 456 YLSTEEDRQVAADSLRVTRHIASQPAFAKYDPEEFKPGVQYQSDEDLARLAGDIGTTIFH 515 Y++ +D + +R+TR I QPAFA + E +PG SDE + + +H Sbjct: 412 YMTHPDDIEEMRACVRLTREIFQQPAFAPWRGREIQPGADVTSDEAIDAFIRQKVESAYH 471 Query: 516 PVGTAKMGRDDDPMAVVDSHLRVRGVTGLRVVDASIMPTITSGNTNSPTLMIAEKAAGWI 575 P T KMG +DPMAVVD LRV GV GLRVVD+S+MP++T+GN N+PT+MI EK A I Sbjct: 472 PSCTCKMGAVNDPMAVVDPELRVIGVEGLRVVDSSVMPSVTTGNLNAPTIMIGEKGADHI 531 Query: 576 L 576 L Sbjct: 532 L 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: 944 Number of extensions: 39 Number of successful extensions: 4 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: 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