Align 3-hydroxypropionate dehydrogenase (EC 1.1.1.59) (characterized)
to candidate 14449 b0311 choline dehydrogenase (NCBI)
Query= metacyc::MONOMER-15202 (579 letters) >FitnessBrowser__Keio:14449 Length = 556 Score = 340 bits (873), Expect = 7e-98 Identities = 222/549 (40%), Positives = 296/549 (53%), Gaps = 29/549 (5%) Query: 36 FDYIVVGAGTAGCLLANRLSADPANRVLLIEAGGRDNYHW---IHIPVGYLYCINNPRTD 92 FDYI++GAG+AG +LA RL+ DP VLL+EAGG D Y + +P + + R + Sbjct: 3 FDYIIIGAGSAGNVLATRLTEDPNTSVLLLEAGGPD-YRFDFRTQMPAALAFPLQGKRYN 61 Query: 93 WRFRTEPDPGLNGRSLIYPRGKTLGGCSSINGMLYLRGQARDYDGWAELTGDDAWRWDNC 152 W + TEP+P +N R + RGK LGG S INGM Y+RG A D D WA+ G + W + +C Sbjct: 62 WAYETEPEPFMNNRRMECGRGKGLGGSSLINGMCYIRGNALDLDNWAQEPGLENWSYLDC 121 Query: 153 LPDFMRHEDHYRLDEGGDADPDHYKFHGHGGEWRIEKQRLKWQVLADFAT---AAVEAGV 209 LP +YR E D + Y HGG+ + K V F A V+AG Sbjct: 122 LP-------YYRKAETRDMGENDY----HGGDGPVSVTTSKPGVNPLFEAMIEAGVQAGY 170 Query: 210 PRTRDFNRGDNEGVDAFEVNQR-SGWRWNASKAFLRGVEQRGNLTVWHSTQVLKLDFASG 268 PRT D N EG + G R + ++ +L + R NLT+ + F Sbjct: 171 PRTDDLNGYQQEGFGPMDRTVTPQGRRASTARGYLDQAKSRPNLTIRTHAMTDHIIFDG- 229 Query: 269 EGSEPRCCGVTVERAGKKVVT--TARCEVVLSAGAIGSPQLLQLSGIGPTALLAEHAIPV 326 R GV + T TA EV+L AGAI SPQ+LQ SG+G LLAE IP+ Sbjct: 230 ----KRAVGVEWLEGDSTIPTRATANKEVLLCAGAIASPQILQRSGVGNAELLAEFDIPL 285 Query: 327 VADLPGVGENLQDHLQIRSIYKVKGAKTLNTMANSLIGKAKIGLEYILKRSGPMSMAPSQ 386 V +LPGVGENLQDHL++ Y+ K +L A + KIG E++ +G + + Sbjct: 286 VHELPGVGENLQDHLEMYLQYECKEPVSLYP-ALQWWNQPKIGAEWLFGGTGVGASNHFE 344 Query: 387 LCIFTRSSKEYEHPNLEYHVQPLSLEAFGQPLHDFPAITASVCNLNPTSRGTVRIKSGNP 446 F RS +E+ PN++YH P+++ G V ++ SRG VRIKS +P Sbjct: 345 AGGFIRSREEFAWPNIQYHFLPVAINYNGSNAVKEHGFQCHVGSMRSPSRGHVRIKSRDP 404 Query: 447 RQAPAISPNYLSTEEDRQVAADSLRVTRHIASQPAFAKYDPEEFKPGVQYQSDEDLARLA 506 Q PAI NY+S E+D Q D++R+TR I QPA +Y E PGV+ Q+DE L Sbjct: 405 HQHPAILFNYMSHEQDWQEFRDAIRITREIMHQPALDQYRGREISPGVECQTDEQLDEFV 464 Query: 507 GDIGTTIFHPVGTAKMGRDDDPMAVVDSHLRVRGVTGLRVVDASIMPTITSGNTNSPTLM 566 + T FHP GT KMG D+ M+VVD RV G+ GLRVVDASIMP I +GN N+ T+M Sbjct: 465 RNHAETAFHPCGTCKMGYDE--MSVVDGEGRVHGLEGLRVVDASIMPQIITGNLNATTIM 522 Query: 567 IAEKAAGWI 575 I EK A I Sbjct: 523 IGEKIADMI 531 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: 985 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: 556 Length adjustment: 36 Effective length of query: 543 Effective length of database: 520 Effective search space: 282360 Effective search space used: 282360 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