Align 3-hydroxypropionate dehydrogenase (EC 1.1.1.59) (characterized)
to candidate PfGW456L13_1082 Choline dehydrogenase (EC 1.1.99.1)
Query= metacyc::MONOMER-15202 (579 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1082 Length = 566 Score = 343 bits (880), Expect = 1e-98 Identities = 216/545 (39%), Positives = 302/545 (55%), Gaps = 27/545 (4%) Query: 36 FDYIVVGAGTAGCLLANRLSADPANRVLLIEAGGRD--NYHWIHIPVGYLYCINNPRTDW 93 FDYI++GAG+AG LA RL+ D VLL+EAGG D + +P + + R +W Sbjct: 5 FDYIIIGAGSAGNTLATRLTEDAGVTVLLLEAGGPDYRSDFRTQMPAALAFPLQGRRYNW 64 Query: 94 RFRTEPDPGLNGRSLIYPRGKTLGGCSSINGMLYLRGQARDYDGWAELTGDDAWRWDNCL 153 + T+P+P ++GR + RGK LGG S INGM Y+RG A DYDGWA+L G + W + +CL Sbjct: 65 AYETDPEPHMDGRRMECGRGKGLGGSSLINGMCYIRGNAMDYDGWAKLPGLEDWSYLDCL 124 Query: 154 PDFMRHEDHYRLDEGGDADPDHYKFHGHGGEWRIEKQRLKW---QVLADFATAAVEAGVP 210 P ++R E D P+ Y HGG+ + K + A V+AG P Sbjct: 125 P-------YFRKAETRDIGPNDY----HGGDGPVSVTTPKAGNNPLFHAMVEAGVQAGYP 173 Query: 211 RTRDFNRGDNEGVDAFE-VNQRSGWRWNASKAFLRGVEQRGNLTVWHSTQVLKLDFASGE 269 RT D N EG + G R + ++ +L ++R LT+ K+ F E Sbjct: 174 RTEDLNGYQQEGFGPMDRTVTPKGRRASTARGYLDVAKKRSTLTIVTHALTDKILF---E 230 Query: 270 GSEPRCCGVTVERAGKKVVTTARCEVVLSAGAIGSPQLLQLSGIGPTALLAEHAIPVVAD 329 G V A ++V AR EV+L +GAI SPQ+LQ SG+GP LL + IPVV D Sbjct: 231 GKRAVGVRYLVGAAEERVEVKARKEVLLCSGAIASPQILQRSGVGPAELLNKLDIPVVHD 290 Query: 330 LPGVGENLQDHLQIRSIYKVKGAKTLNTMANSLI--GKAKIGLEYILKRSGPMSMAPSQL 387 LPGVGENLQDHL++ Y +L SL+ + IG E++ +G + + Sbjct: 291 LPGVGENLQDHLELYLQYACTQPVSLYP---SLLWYNQPAIGAEWLFNGTGIGASNQFEA 347 Query: 388 CIFTRSSKEYEHPNLEYHVQPLSLEAFGQPLHDFPAITASVCNLNPTSRGTVRIKSGNPR 447 F R+ E+E PN++YH P+++ G A + ++ SRG ++ KS +PR Sbjct: 348 GGFIRTRPEFEWPNIQYHFLPVAINYNGSNGVKEHGFQAHMGSMRSPSRGRIQAKSKDPR 407 Query: 448 QAPAISPNYLSTEEDRQVAADSLRVTRHIASQPAFAKYDPEEFKPGVQYQSDEDLARLAG 507 Q P+I NY++TE+D Q D +R+TR I QPA + E PG++ Q+DE L + Sbjct: 408 QHPSILFNYMATEQDWQEFRDGIRLTREIMQQPALDAFRGREISPGIEVQTDEQLDKFIR 467 Query: 508 DIGTTIFHPVGTAKMGRDDDPMAVVDSHLRVRGVTGLRVVDASIMPTITSGNTNSPTLMI 567 + T FHP + KMG D+ MAVVDS RV G+ GLRVVDASIMP IT+GN N+PT+M+ Sbjct: 468 EHAETAFHPSCSCKMGTDE--MAVVDSEGRVHGMQGLRVVDASIMPIITTGNLNAPTIMM 525 Query: 568 AEKAA 572 AEK A Sbjct: 526 AEKIA 530 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: 961 Number of extensions: 48 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: 566 Length adjustment: 36 Effective length of query: 543 Effective length of database: 530 Effective search space: 287790 Effective search space used: 287790 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