Align 3-hydroxypropionate dehydrogenase (EC 1.1.1.59) (characterized)
to candidate PfGW456L13_3441 Choline dehydrogenase (EC 1.1.99.1)
Query= metacyc::MONOMER-15202 (579 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3441 Length = 539 Score = 306 bits (785), Expect = 1e-87 Identities = 204/546 (37%), Positives = 288/546 (52%), Gaps = 33/546 (6%) Query: 36 FDYIVVGAGTAGCLLANRLSADPANRVLLIEAGGRDNYHWIHIP--VGYLYCINNPRTDW 93 +DYI++GAG++GC+LANRLSAD VLLIE+G I +P +G L NP W Sbjct: 5 YDYIIIGAGSSGCVLANRLSADSTVSVLLIESGPDHTSALIAMPRGIGKLLNPGNPHV-W 63 Query: 94 RFRTEPDPGLNGRSLIYPRGKTLGGCSSINGMLYLRGQARDYDGWAELTGDDAWRWDNCL 153 ++ + G++ + +GKT+GG SS+NGM+Y+RG DYD W E G W W + Sbjct: 64 SYKAKRGEGMSDEQWL--KGKTIGGSSSVNGMVYVRGAPADYDNW-EAQGCTGWGWKDMG 120 Query: 154 PDFMRHEDHYRLDEGGDADPDHYKFHGHGGEWRIEKQRLKWQVLADFATAAVEAGVPRTR 213 F+ EDH +L + ++ G GG ++ + +AA + GV R Sbjct: 121 RQFVALEDH-QLGKS--------QWRGVGGPLKVTVHPSGDALCDAVISAAGKLGVARAE 171 Query: 214 DFNRGDNEGVDAFEVNQRSGW---RWNASKAFLRGVEQRGNLTVWHSTQVLKLDFASGEG 270 D N D+ F ++ W R++A+KAFL V R NLTV T V +++F Sbjct: 172 DTNHVDSVSQGGFGYQPQTTWKGQRFSAAKAFLDPVRTRPNLTVMTGTDVQRIEF----- 226 Query: 271 SEPRCCGVTVERAGKKVVTTARCEVVLSAGAIGSPQLLQLSGIGPTALLAEHAIPVVADL 330 S+ R C V V R EV+L AGAI SP+LLQLSGIGP LL I V+ D Sbjct: 227 SKRRACAVNVSGRAGLARFQVRREVLLCAGAIESPKLLQLSGIGPAGLLNALGIKVLQDA 286 Query: 331 PGVGENLQDHLQIRSIYKVKGAKTLNTMANSLIGKAKIG--LEYILKRSGPMSMAPSQLC 388 P VG NL++H+ + Y+V T + + G +G ++Y L++ GPM+ A + Sbjct: 287 PEVGRNLREHVYMAMQYRV----TRGSFNHCFHGVGLLGAVMQYFLRKKGPMTHAAHEAG 342 Query: 389 IFTRSSKEYEHPNLEYHVQPLSLEAFGQPLH--DFPAITASVCNLNPTSRGTVRIKSGNP 446 F ++ E + P+ + V S++ G + P +T L P S+G VRI+S + Sbjct: 343 GFIKTRPELDRPDAQIGVSLYSMDGDGNKVEIDKHPGLTIGGYFLRPQSQGEVRIQSTDA 402 Query: 447 RQAPAISPNYLSTEEDRQVAADSLRVTRHIASQPAFAKYDPEEFKPGVQYQSDEDLARLA 506 P I+ NYLS E DR A R R +A+QP + E PG Q +SDE + Sbjct: 403 SVPPRINANYLSAEIDRTSAIALFRWFRRLAAQPVLKPFIVGELTPGPQVESDEQILAAF 462 Query: 507 GDIGTTIFHPVGTAKMGRDDDPMAVVDSHLRVRGVTGLRVVDASIMPTITSGNTNSPTLM 566 G T FH GT +MG D +V+D LRVRGV GLRVVD S+MP + SGNTN+P + Sbjct: 463 RRYGQTAFHVSGTCRMG--GDSASVLDPQLRVRGVEGLRVVDTSVMPCLVSGNTNAPAMA 520 Query: 567 IAEKAA 572 IA +AA Sbjct: 521 IAMRAA 526 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: 835 Number of extensions: 53 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: 539 Length adjustment: 36 Effective length of query: 543 Effective length of database: 503 Effective search space: 273129 Effective search space used: 273129 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