Align 4-hydroxybutyrate-CoA ligase (EC 6.2.1.40) (characterized)
to candidate Pf6N2E2_1726 3-methylmercaptopropionyl-CoA ligase (DmdB)
Query= BRENDA::A4YDR9 (549 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1726 Length = 540 Score = 416 bits (1070), Expect = e-121 Identities = 224/541 (41%), Positives = 315/541 (58%), Gaps = 17/541 (3%) Query: 10 EGVDPTGSWYSVLTPLLFLERAGKYFKDKTAVVYRDSRYTYSTFYDNVMVQASALMRRGF 69 +G PTG ++ LTPL F+ER + D AV++ R T++ Y ASAL RG Sbjct: 6 QGFAPTGVNHTALTPLSFIERTASVYPDYPAVIHGSIRRTWADTYRRCRRLASALAGRGI 65 Query: 70 SREDKLSFISRNRPEFLESFFGVPYAGGVLVPINFRLSPKEMAYIINHSDSKFVVVDEPY 129 + D ++ + N P LE+ FGVP G VL +N RL + +A+++ H ++K ++ D Sbjct: 66 GKNDTVAVMLPNIPAMLEAHFGVPMIGAVLNALNVRLDAEAIAFMLAHGEAKVLIADR-- 123 Query: 130 LNSLLEVKDQIKAEIILLEDP------DNPSASETARKEVRMTYRELVKGGSRDPLPIPA 183 E D ++A I +L+ P D+P E + + Y + G D Sbjct: 124 -----EFHDVVQAAIGMLDHPPLVIDLDDPEYGE-GQAVSELDYEAFLAEGDPDFAWQWP 177 Query: 184 KEEYSMITLYYTSGTTGLPKGVMHHHRGAFLNAMAEVLEHQMDLNSVYLWTLPMFHAASW 243 +E+ I+L YTSGTTG PKGV++HHRGA+LN++ + M + VYLWTLPMFH W Sbjct: 178 DDEWQAISLNYTSGTTGNPKGVVYHHRGAYLNSLGNQMTWAMGNHPVYLWTLPMFHCNGW 237 Query: 244 GFSWATVAVGATNVCLDKVDYPLIYRLVEKERVTHMCAAPTVYVNLADYMKRNNLKFSNR 303 + W A+ +V L +VD I L+ + ++TH+C AP V L + + Sbjct: 238 CYPWTVTALAGVHVFLRRVDPQKILNLIREHQITHLCGAPIVLNALVNMPDSAKAAIDHP 297 Query: 304 VHMLVAGAAPAPATLKAMQEIGGYMCHVYGLTETYGPHSICEWRREWDSLPLEEQAKLKA 363 V +VAGAAP + A++E+G + HVYGLTE YGP ++C W WD LPLE++A++KA Sbjct: 298 VSAMVAGAAPPAKVIGAVEEMGIKVTHVYGLTEVYGPVTLCAWHAAWDELPLEQRAQIKA 357 Query: 364 RQGIPYVSFE--MDVFDANGKPVPWDGKTIGEVVMRGHNVALGYYKNPEKTAESFRDGWF 421 RQG+ Y + E M +P P DG+TIGE+ MRG+ V GY KNP TAE+F GWF Sbjct: 358 RQGVRYPTLEGLMVADPRTLEPTPHDGQTIGEIFMRGNTVMKGYLKNPSATAEAFEGGWF 417 Query: 422 HSGDAAVVHPDGYIEIVDRFKDLINTGGEKVSSILVEKTLMEIPGVKAVAVYGTPDEKWG 481 H+GD AV H DGY+EI DR KD+I +GGE +S+I +E L P V AV PDEKWG Sbjct: 418 HTGDLAVTHADGYVEIRDRLKDIIISGGENISTIELEGVLYRHPAVLEAAVVARPDEKWG 477 Query: 482 EVVTARIELQ-EGVKLTEEEVIKFCKERLAHFECPKIVEFGPIPMTATGKMQKYVLRNEA 540 E A I L+ + + E E+I FC+E LA F+ P+ V F +P T+TGK+QK+VLR+ A Sbjct: 478 ETPCAFITLKSDHTDVREAEIISFCREHLAGFKVPRTVVFTQLPKTSTGKIQKFVLRDMA 537 Query: 541 K 541 K Sbjct: 538 K 538 Lambda K H 0.319 0.136 0.411 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: 783 Number of extensions: 42 Number of successful extensions: 4 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: 549 Length of database: 540 Length adjustment: 35 Effective length of query: 514 Effective length of database: 505 Effective search space: 259570 Effective search space used: 259570 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 52 (24.6 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