Align 3-hydroxypropionate dehydrogenase (EC 1.1.1.59) (characterized)
to candidate Ac3H11_1497 Choline dehydrogenase (EC 1.1.99.1)
Query= metacyc::MONOMER-15202 (579 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1497 Length = 526 Score = 311 bits (796), Expect = 5e-89 Identities = 201/551 (36%), Positives = 300/551 (54%), Gaps = 36/551 (6%) Query: 36 FDYIVVGAGTAGCLLANRLSADPANRVLLIEAGGRDNYHWIHIPVGYLYCINNPRTDWRF 95 FD+I++GAG+AGC+LA+RL RVLL+EAG + ++ +P ++ I R+ W + Sbjct: 3 FDHIIIGAGSAGCVLAHRL-VRAGRRVLLLEAGPTHEHPFVRMPAAFVRVIGTERS-WDY 60 Query: 96 RTEPDPGLNGRSLIYPRGKTLGGCSSINGMLYLRGQARDYDGWAELTGDDAWRWDNCLPD 155 +EP P NGR + P+G+ LGG SS+N M+Y+RGQA DYD W + G W W + LP Sbjct: 61 ASEPQPHANGRRMHVPQGRMLGGGSSLNAMVYIRGQAADYDSWRD-AGCTGWGWSDVLPA 119 Query: 156 FMRHEDHYRLDEGGDADPDHYKFHGHGGEWRIEKQRLKWQVLADFATAAVEAGVPRTRDF 215 F+R E + R A P HG G ++ + R + + A F AA +AG+P DF Sbjct: 120 FVRAESNERY-----AGP----LHGRDGPLQVSEPRFRHPLSAAFVAAAQQAGLPANPDF 170 Query: 216 NRGDNEGVDAFEVNQRSGWRWNASKAFLRGVEQRGNLTVWHSTQVLKLDFASGEGSEPRC 275 N + GV ++ G R + + +L V + L V V ++ +G R Sbjct: 171 NGTEQAGVGFYQSTTFRGERGSTAATYLAAVRRDERLAVRTGVHVRRILVEAG-----RA 225 Query: 276 CGVTVERAGKKVVTTARCEVVLSAGAIGSPQLLQLSGIGPTALLAEHAIPVVADLPGVGE 335 GV AG+ +V+LSAGA+ SPQLL LSGIGP L + IPV AD GVG+ Sbjct: 226 VGVEFMEAGQLQQVRCAQDVLLSAGALASPQLLMLSGIGPGEDLHKLGIPVHADSAGVGQ 285 Query: 336 NLQDHLQIRSIYKVKGAKTLNTMANSLIGK------AKIGLEYILKRSGPMSMAPSQLCI 389 N QDHL++ S+Y A+T + SL+G+ + GL++ L RSG ++ + Sbjct: 286 NYQDHLEV-SVY----ARTRRPI--SLLGQDQGLRALRHGLQWQLLRSGLLTSNVVESGG 338 Query: 390 FTRSSKEYEHPNLEYHVQPLSL-EAFGQPLHDFPAITASVCNLNPTSRGTVRIKSGNPRQ 448 F + P++++HV P+ + + +PL ++ + C L P SRGTV ++S +P Sbjct: 339 FV-DTLGTGRPDVQFHVLPVLVGDVEREPLPGH-GLSINPCFLRPQSRGTVSLRSPDPAH 396 Query: 449 APAISPNYLSTEEDRQVAADSLRVTRHIASQPAFAKYDPEEFKPGVQYQ-SDEDLARLAG 507 L + D +++ R I PA A+ E PG + SD + Sbjct: 397 PILFDAGALRVQADVDTLVRGVKLARRILRAPALAEVVEHELLPGAEATLSDAQVEAHVR 456 Query: 508 DIGTTIFHPVGTAKMGRDDDPMAVVDSHLRVRGVTGLRVVDASIMPTITSGNTNSPTLMI 567 T++HP GT +MG D +VVD+HLRVRGV GLRV DAS+MPT+ SGNTN+PT+M+ Sbjct: 457 SHAKTVYHPAGTCRMG--GDATSVVDTHLRVRGVAGLRVCDASVMPTLPSGNTNAPTIML 514 Query: 568 AEKAAGWILKS 578 AE+ A ++L++ Sbjct: 515 AERCAEFVLQA 525 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: 875 Number of extensions: 48 Number of successful extensions: 9 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: 526 Length adjustment: 36 Effective length of query: 543 Effective length of database: 490 Effective search space: 266070 Effective search space used: 266070 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