Align 3-hydroxypropionate dehydrogenase (EC 1.1.1.59) (characterized)
to candidate WP_045583809.1 AL072_RS25745 NAD(P)-binding protein
Query= metacyc::MONOMER-15202 (579 letters) >NCBI__GCF_001305595.1:WP_045583809.1 Length = 552 Score = 393 bits (1010), Expect = e-114 Identities = 230/550 (41%), Positives = 319/550 (58%), Gaps = 26/550 (4%) Query: 36 FDYIVVGAGTAGCLLANRLSADPANRVLLIEAGGRDNYHWIHIPVGYLYCINNPRTDWRF 95 +DYIVVGAG AGC LA RL+ D +RVLL+EAGGRD WIHIP+G + NP+ W+F Sbjct: 4 YDYIVVGAGAAGCALAARLTEDGRHRVLLLEAGGRDANIWIHIPLGVGKLLQNPKYVWQF 63 Query: 96 RTEPDPGLNGRSLIYPRGKTLGGCSSINGMLYLRGQARDYDGWAELTGDDAWRWDNCLPD 155 TEP+P L+G+ + +PRGK +GG SS+NGM+Y+RG +YD W L G+ W + + LP Sbjct: 64 MTEPEPALHGQRIYWPRGKVMGGSSSVNGMVYVRGDPEEYDHWRAL-GNPGWGYADLLPY 122 Query: 156 FMRHEDHYRLDEGGDADPDHYKFHGHGGEWRIEKQRLKW--QVLAD-FATAAVEAGVPRT 212 F R ED+ DP + G GG +I R W L+D + A +EAG+P Sbjct: 123 FKRMEDY------PQGDP---AYRGRGGPMKI-VNRGAWDPDPLSDAYLAACIEAGIPPN 172 Query: 213 RDFNRGDNEGVDAFEVNQRSGWRWNASKAFLRGVEQRGNLTVWHSTQVLKLDFASGEGSE 272 D+N EG + N R+G R +++ +L +R NL + + Q ++ F Sbjct: 173 EDYNATTLEGAAYLQQNGRNGRRCSSAAGYLATARKRPNLRIETNAQATRVLFQG----- 227 Query: 273 PRCCGVTVERAGKKVVTTARCEVVLSAGAIGSPQLLQLSGIGPTALLAEHAIPVVADLPG 332 R GV + G AR EV+LSAG++ SPQLL+LSGIG L IPVV LPG Sbjct: 228 TRAVGVEYRQDGILREARARGEVLLSAGSVQSPQLLELSGIGDERRLRALGIPVVTHLPG 287 Query: 333 VGENLQDHLQIRSIYKVKGAKTLNTMANSLIGKAKIGLEYILKRSGPMSMAPSQLCIFTR 392 VGE+L DHLQ+R ++ T+N M +S + + +GLEY+L R G +S S + R Sbjct: 288 VGESLLDHLQVRFTFECTRPITINDMIHSPVRRMMVGLEYVLFRRGLLSTTSSTVHAIAR 347 Query: 393 SSKEYEHPNLEYHVQPLS-LEAFGQP----LHDFPAITASVCNLNPTSRGTVRIKSGNPR 447 + E P+++ + +S + + + +P + V L P SRG++ I+S +P Sbjct: 348 TRPELPRPDVKIQLAQISGKDRYSRSKELGTDRYPGFSIGVFKLRPESRGSLHIRSADPL 407 Query: 448 QAPAISPNYLSTEEDRQVAADSLRVTRHIASQPAFAKYDPEEFKPGVQYQSDEDLARLAG 507 + P I PNYL +D Q D+ ++ R IA+QPAFA E +PG DEDL A Sbjct: 408 EPPEIRPNYLGHPKDEQTYVDAFKLIRRIAAQPAFAPLMAGERRPGPDTTRDEDLVDYAR 467 Query: 508 DIGTTIFHPVGTAKMGRDDDPMAVVDSHLRVRGVTGLRVVDASIMPTITSGNTNSPTLMI 567 G T +HP+ + +MG DD MAVVD+ LRVRGV GLRVVDASIMPT+ S NTN+P +MI Sbjct: 468 RTGQTSWHPISSCRMGTDD--MAVVDARLRVRGVQGLRVVDASIMPTMASPNTNAPAIMI 525 Query: 568 AEKAAGWILK 577 EK A +L+ Sbjct: 526 GEKGADLVLE 535 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: 935 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: 552 Length adjustment: 36 Effective length of query: 543 Effective length of database: 516 Effective search space: 280188 Effective search space used: 280188 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 24 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