Align 3-hydroxypropionate dehydrogenase (EC 1.1.1.59) (characterized)
to candidate GFF2583 Psest_2633 choline dehydrogenase
Query= metacyc::MONOMER-15202 (579 letters) >FitnessBrowser__psRCH2:GFF2583 Length = 557 Score = 334 bits (857), Expect = 5e-96 Identities = 214/542 (39%), Positives = 297/542 (54%), Gaps = 22/542 (4%) Query: 36 FDYIVVGAGTAGCLLANRLSADPANRVLLIEAGGRDNY--HWIHIPVGYLYCINNPRTDW 93 +DYI++GAG+AG +LA RL+ D VLL+EAGG D +P Y + R +W Sbjct: 3 YDYIIIGAGSAGNVLAARLTEDADVSVLLLEAGGPDYRLDFRTQMPAALAYPLQGTRYNW 62 Query: 94 RFRTEPDPGLNGRSLIYPRGKTLGGCSSINGMLYLRGQARDYDGWAELTGDDAWRWDNCL 153 ++T+P+P +N R + RGK LGG S INGM Y+RG A DYD WA+ G + W + +CL Sbjct: 63 AYKTDPEPHMNNRRMDCGRGKGLGGSSLINGMCYIRGNALDYDNWAKAPGLEDWTYLDCL 122 Query: 154 PDFMRHEDHYRLDEGGDADPDHYKFHGHGGEWRIEKQRLKWQVLAD-FATAAVEAGVPRT 212 P ++R E D P+ Y HG G + R VL A V+AG PRT Sbjct: 123 P-------YFRKAESRDIGPNDY--HGGVGPVSVTTPRADNNVLFQAMVEAGVQAGYPRT 173 Query: 213 RDFNRGDNEGVDAFEVNQR-SGWRWNASKAFLRGVEQRGNLTVWHSTQVLKLDFASGEGS 271 D N EG + G R + ++ +L +R NLT+ ++ F EG Sbjct: 174 DDLNGYQQEGFGPMDRTVTPQGRRASTARGYLDQARERPNLTIETHAVTDRVLF---EGK 230 Query: 272 EPRCCGVTVERAGKK-VVTTARCEVVLSAGAIGSPQLLQLSGIGPTALLAEHAIPVVADL 330 R GV R K + AR EV+L GAI SPQ+LQ SG+GP ALL + V +L Sbjct: 231 --RAVGVRYLRDRKDPYIARARREVLLCGGAIASPQILQRSGVGPGALLRRVGVKPVHEL 288 Query: 331 PGVGENLQDHLQIRSIYKVKGAKTLNTMANSLIGKAKIGLEYILKRSGPMSMAPSQLCIF 390 PGVG+NLQDHL++ Y+ K +L A + IG E++ SG + + F Sbjct: 289 PGVGQNLQDHLEMYLQYECKQPVSLYP-ALKWWNQPAIGAEWLFLGSGIGASNQFEAGGF 347 Query: 391 TRSSKEYEHPNLEYHVQPLSLEAFGQPLHDFPAITASVCNLNPTSRGTVRIKSGNPRQAP 450 RSS E+E PN+++H P+++ G HD + A V ++ SRG + I+S +P + P Sbjct: 348 IRSSDEFEWPNIQFHFLPVAVSYNGSNAHDGHSFQAHVGSMRSPSRGRIEIRSTDPAEDP 407 Query: 451 AISPNYLSTEEDRQVAADSLRVTRHIASQPAFAKYDPEEFKPGVQYQSDEDLARLAGDIG 510 +I NY++ E+D + D +R+TR I +QPA Y E PG++ QSD +L + Sbjct: 408 SILFNYMAHEQDWREFRDGIRLTREIMNQPALDPYRGRELSPGIEAQSDAELDAFVREHA 467 Query: 511 TTIFHPVGTAKMGRDDDPMAVVDSHLRVRGVTGLRVVDASIMPTITSGNTNSPTLMIAEK 570 T +HP + KMG DD MAVVD RV G+ GLRVVDASIMP I +GN N+ T+MIAEK Sbjct: 468 ETAYHPSCSCKMGTDD--MAVVDGQGRVHGMEGLRVVDASIMPQIITGNLNATTIMIAEK 525 Query: 571 AA 572 A Sbjct: 526 IA 527 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: 981 Number of extensions: 60 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: 557 Length adjustment: 36 Effective length of query: 543 Effective length of database: 521 Effective search space: 282903 Effective search space used: 282903 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