Align 3-hydroxypropionate dehydrogenase (EC 1.1.1.59) (characterized)
to candidate H281DRAFT_03365 H281DRAFT_03365 choline dehydrogenase
Query= metacyc::MONOMER-15202 (579 letters) >FitnessBrowser__Burk376:H281DRAFT_03365 Length = 546 Score = 355 bits (912), Expect = e-102 Identities = 216/547 (39%), Positives = 317/547 (57%), Gaps = 24/547 (4%) Query: 33 THAFDYIVVGAGTAGCLLANRLSADPANRVLLIEAGGRDNYHWIHIPVGYLYCINNPRTD 92 ++ DY++VGAGTAGC+LANRL+ DPA +V+L+EAG RD + +IH+P G++ +++P Sbjct: 3 SYTADYVIVGAGTAGCVLANRLTEDPAIKVILVEAGERDRHPFIHVPAGFVRLLDHPTVT 62 Query: 93 WRFRTEPDPGLNGRSLIYPRGKTLGGCSSINGMLYLRGQARDYDGWAELTGDDAWRWDNC 152 WR+RTE D G +GR++++PRG+ LGG S+ING+LY+R A D D W E +G + W + NC Sbjct: 63 WRYRTEADAGTSGRAILFPRGRGLGGSSAINGLLYVRPFAEDIDSW-EQSGANGWNFKNC 121 Query: 153 LPDFMRHEDHYRLDEGGDADPDHYKFHGHGGEWRIEKQRLKWQVLADFATAAVEAGVPRT 212 LP + R E EG G G ++ + + ++ AA G+ Sbjct: 122 LPFYSRSE---TWTEGSSPQ------RGTHGPIQVSRVKNPPEICGAVVEAAQRTGLDFV 172 Query: 213 RDFNRGDNEGVDAFEVNQ-RSG-WRWNASKAFLRGVEQRGNLTVWHSTQVLKLDFASGEG 270 D N D G + Q R G R +A++ +LR R NLTV QV L+ Sbjct: 173 DDPN-SDTRGPSIWYYQQTRDGRRRSSAARGYLRPAMARPNLTVVTGLQVSTLEMNGTHV 231 Query: 271 SEPRCCGVT-VERAGKKVVTTARCEVVLSAGAIGSPQLLQLSGIGPTALLAEHAIPVVAD 329 S G+ AG V A EV+LSAG +G+P+LL++SGIG A+L + Sbjct: 232 S-----GINGTTGAGIPVQIRATREVILSAGVVGTPRLLEMSGIGDKAVLDNAGVKTRIA 286 Query: 330 LPGVGENLQDHLQIRSIYKVKGAKTLNTMANSLIGKAKIGLEYILKRSGPMSMAPSQLCI 389 LPGVG NLQDH +R Y+V+GA T N A+ L A+ + Y++ +G ++ + + + Sbjct: 287 LPGVGNNLQDHYVVRLGYRVRGAGTANERAHGL-ALAREMMRYVVSGTGVLTYSAALVGG 345 Query: 390 FTRSSKEYEHPNLEYHVQPLSL-EAFGQPLHDFPAITASVCNLNPTSRGTVRIKSGNPRQ 448 F + ++ P++++ + P S E L P ++ V + P SRG V I S Sbjct: 346 FAQ-TRLATRPDVQFVIAPGSFAEGRIGVLESEPGVSCGVWQMRPESRGHVHITSSEITA 404 Query: 449 APAISPNYLSTEEDRQVAADSLRVTRHIASQPAFAKYDPEEFKPGVQYQSDEDLARLAGD 508 AP I+P+YLS+E DR + L++ R I +QP A+Y +E PG Q +DE L + D Sbjct: 405 APTIAPSYLSSELDRNTMVEGLKIGRRIFAQPEVARYIVDETVPGRQADTDEALLQYVRD 464 Query: 509 IGTTIFHPVGTAKMGRDDDPMAVVDSHLRVRGVTGLRVVDASIMPTITSGNTNSPTLMIA 568 G+T++H VGT +MG D+ M+VVDS +RVRG TGLRVVD S+MP+ITS NTN+ LM+A Sbjct: 465 NGSTVYHAVGTCRMGEDE--MSVVDSEMRVRGTTGLRVVDGSVMPSITSTNTNATVLMLA 522 Query: 569 EKAAGWI 575 E+AA I Sbjct: 523 ERAADMI 529 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: 859 Number of extensions: 36 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: 546 Length adjustment: 36 Effective length of query: 543 Effective length of database: 510 Effective search space: 276930 Effective search space used: 276930 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