Align 3-hydroxypropionate dehydrogenase (EC 1.1.1.59) (characterized)
to candidate WP_086509898.1 BZY95_RS10635 choline dehydrogenase
Query= metacyc::MONOMER-15202 (579 letters) >NCBI__GCF_002151265.1:WP_086509898.1 Length = 563 Score = 354 bits (909), Expect = e-102 Identities = 225/545 (41%), Positives = 302/545 (55%), Gaps = 29/545 (5%) Query: 36 FDYIVVGAGTAGCLLANRLSADPANRVLLIEAGGRDNYHW---IHIPVGYLYCINNPRTD 92 FDY+++GAG+AG +LA RL+ D VLL+EAGG D Y + +P Y + R + Sbjct: 7 FDYVIIGAGSAGNVLAARLTEDADVSVLLLEAGGPD-YRFDFRTQMPAALAYPLQGKRYN 65 Query: 93 WRFRTEPDPGLNGRSLIYPRGKTLGGCSSINGMLYLRGQARDYDGWAELTGDDAWRWDNC 152 W F T+P+P +NGR + RGK LGG S INGM Y+RG A DYD WA L G WR+ +C Sbjct: 66 WAFETDPEPHMNGRRMECGRGKGLGGSSLINGMCYIRGNALDYDNWASLAGLSDWRYADC 125 Query: 153 LPDFMRHEDHYRLDEGGDADPDHYKFHGHGGEWRIEKQRL-KWQVLADFATAAVEAGVPR 211 LP F + E D G +A +HG G + + ++ F A V+AG P Sbjct: 126 LPYFRKAECR---DTGANA------YHGGDGPVHVTTPKAGNNELYRAFVDAGVQAGYPE 176 Query: 212 TRDFNRGDNEG---VDAFEVNQRSGWRWNASKAFLRGVEQRGNLTV-WHSTQVLKLDFAS 267 T D N EG +D F + G R + ++ +L + R NLT+ H+T D Sbjct: 177 TEDVNGYQQEGFGPMDRFVTPK--GRRSSTARGYLDQAKGRDNLTIETHATT----DVIE 230 Query: 268 GEGSEPRCCGVTVERAGKKVVTTARCEVVLSAGAIGSPQLLQLSGIGPTALLAEHAIPVV 327 EG R GV R G+ AR EV+L AGAI SPQ+L SGIG A L E IPVV Sbjct: 231 FEGK--RAVGVRYLRRGQTQQVRARREVLLCAGAIASPQILLRSGIGNPAHLREFDIPVV 288 Query: 328 ADLPGVGENLQDHLQIRSIYKVKGAKTLNTMANSLIGKAKIGLEYILKRSGPMSMAPSQL 387 +LPGVGENLQDHL++ Y+ K TL A + KIG E++L SG + + Sbjct: 289 HELPGVGENLQDHLEMYIQYECKQPITLYP-ALKWFNQPKIGAEWLLLGSGVGASNQFES 347 Query: 388 CIFTRSSKEYEHPNLEYHVQPLSLEAFGQPLHDFPAITASVCNLNPTSRGTVRIKSGNPR 447 C F R+ PNL+YH P+++ G+ A V ++ SRG +R+ S +P+ Sbjct: 348 CAFIRTHDAEPWPNLQYHFLPIAISYNGKSAVQAHGFQAHVGSMRSESRGRIRLTSRDPK 407 Query: 448 QAPAISPNYLSTEEDRQVAADSLRVTRHIASQPAFAKYDPEEFKPGVQYQSDEDLARLAG 507 AP+I NY+S E+D Q D++R+TR I +QPA Y E PG + +SDE L Sbjct: 408 AAPSILFNYMSREKDWQEFRDAIRLTREIIAQPAMDPYRGREISPGPEVESDEQLDAFVR 467 Query: 508 DIGTTIFHPVGTAKMGRDDDPMAVVDSHLRVRGVTGLRVVDASIMPTITSGNTNSPTLMI 567 + T +HP G+ +MG DD AVVD RV GV GLRVVDAS+ P I +GN N+PT+M+ Sbjct: 468 EHAETAYHPCGSCRMGEGDD--AVVDGQGRVHGVEGLRVVDASLFPVIPTGNLNAPTIML 525 Query: 568 AEKAA 572 AEK A Sbjct: 526 AEKIA 530 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: 972 Number of extensions: 51 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: 563 Length adjustment: 36 Effective length of query: 543 Effective length of database: 527 Effective search space: 286161 Effective search space used: 286161 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 Apr 09 2024. 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