Align 3-hydroxypropionate dehydrogenase (EC 1.1.1.59) (characterized)
to candidate PP_5064 PP_5064 choline dehydrogenase
Query= metacyc::MONOMER-15202 (579 letters) >FitnessBrowser__Putida:PP_5064 Length = 565 Score = 344 bits (883), Expect = 5e-99 Identities = 220/546 (40%), Positives = 305/546 (55%), Gaps = 33/546 (6%) Query: 36 FDYIVVGAGTAGCLLANRLSADPANRVLLIEAGGRDNYHW---IHIPVGYLYCINNPRTD 92 FDYI+VGAG+AG LA RL+ D VLL+EAGG D Y + +P + + R + Sbjct: 5 FDYIIVGAGSAGNTLATRLTEDAGVTVLLLEAGGPD-YRFDFRTQMPAALAFPLQGRRYN 63 Query: 93 WRFRTEPDPGLNGRSLIYPRGKTLGGCSSINGMLYLRGQARDYDGWAELTGDDAWRWDNC 152 W + T+P+P ++GR + RGK LGG S INGM Y+RG A D+DGWAEL G + W + +C Sbjct: 64 WAYETDPEPYMDGRRMECGRGKGLGGSSLINGMCYIRGNAMDFDGWAELPGLEDWTYLDC 123 Query: 153 LPDFMRHEDHYRLDEGGDADPDHYKFHGHGGEWRIEKQRLKW---QVLADFATAAVEAGV 209 LP ++R E D P+ Y HGGE + K + A V+AG Sbjct: 124 LP-------YFRKAETRDIGPNDY----HGGEGPVSVTTPKAGNNPLFHAMVEAGVQAGY 172 Query: 210 PRTRDFNRGDNEGVDAFEVN-QRSGWRWNASKAFLRGVEQRGNLTVWHSTQVLKLDFASG 268 PRT D N EG + ++G R + ++ +L ++R NLT+ ++ F Sbjct: 173 PRTEDLNGYQQEGFGPMDRTVTKNGRRSSTARGYLDQAKKRPNLTIVTHALTDRVLFDG- 231 Query: 269 EGSEPRCCGVT--VERAGKKVVTTARCEVVLSAGAIGSPQLLQLSGIGPTALLAEHAIPV 326 R GVT V + ++V AR EV++S+GAI SPQLLQ SG+GP ALL IPV Sbjct: 232 ----KRAIGVTYLVGDSEERVEARARKEVIVSSGAIASPQLLQRSGVGPRALLESLDIPV 287 Query: 327 VADLPGVGENLQDHLQIRSIYKVKGAKTLNTMANSLI--GKAKIGLEYILKRSGPMSMAP 384 V DLPGVGENLQDHL++ Y +L SL+ + IG E++ +G + Sbjct: 288 VHDLPGVGENLQDHLELYLQYACTQPVSLYP---SLLWWNQPAIGAEWMFNGTGIGASNQ 344 Query: 385 SQLCIFTRSSKEYEHPNLEYHVQPLSLEAFGQPLHDFPAITASVCNLNPTSRGTVRIKSG 444 + F R+ E++ PN++YH P+++ G A + ++ +RG +++KS Sbjct: 345 FEAGGFIRTRPEFKWPNIQYHFLPVAINYNGSNGVKEHGFQAHMGSMRSPARGRIQVKSK 404 Query: 445 NPRQAPAISPNYLSTEEDRQVAADSLRVTRHIASQPAFAKYDPEEFKPGVQYQSDEDLAR 504 +PRQ P+I NY+STE+D Q D +R+TR I +QPA Y E PG Q+DE L + Sbjct: 405 DPRQHPSILFNYMSTEQDWQEFRDGIRLTREIMAQPALDPYRGREISPGADVQTDEQLDK 464 Query: 505 LAGDIGTTIFHPVGTAKMGRDDDPMAVVDSHLRVRGVTGLRVVDASIMPTITSGNTNSPT 564 + T FHP + KMG DD MAVVD RV G+ GLRVVDASIMP I +GN N+ T Sbjct: 465 FIREHAETAFHPSCSCKMGTDD--MAVVDGEGRVHGMKGLRVVDASIMPLIITGNLNATT 522 Query: 565 LMIAEK 570 +MIAEK Sbjct: 523 IMIAEK 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: 988 Number of extensions: 52 Number of successful extensions: 7 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: 565 Length adjustment: 36 Effective length of query: 543 Effective length of database: 529 Effective search space: 287247 Effective search space used: 287247 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