Align 4-hydroxybutyrate-CoA ligase (EC 6.2.1.40) (characterized)
to candidate RR42_RS25360 RR42_RS25360 acyl-CoA synthetase
Query= BRENDA::A4YDR9 (549 letters) >FitnessBrowser__Cup4G11:RR42_RS25360 Length = 554 Score = 376 bits (966), Expect = e-108 Identities = 212/530 (40%), Positives = 300/530 (56%), Gaps = 5/530 (0%) Query: 11 GVDPTGSWYSVLTPLLFLERAGKYFKDKTAVVYRDSRYTYSTFYDNVMVQASALMRRGFS 70 G+D + + LTPL FL+R + + D+TA+++ R ++ + ASAL++RG Sbjct: 9 GLDRRAANHMPLTPLHFLDRCAEQYPDRTAIIHGPVRQSWKVTRERCRQLASALVKRGVG 68 Query: 71 REDKLSFISRNRPEFLESFFGVPYAGGVLVPINFRLSPKEMAYIINHSDSKFVVVDEPYL 130 R D +S ++ N P +E+ G+P +G VL IN RL + +I+ H + K + VD + Sbjct: 69 RGDTVSILAPNTPAMVEAHHGIPLSGAVLNAINCRLDADGVRFIVAHGECKVLFVDREFS 128 Query: 131 NSLLEVKDQIKAEIILLEDPDNPSASETARKEVRMTYRELVKGGSRDPLPIPAKEEYSMI 190 E + ++++ D + + M Y + ++ G D + +E++ I Sbjct: 129 ALAAEALQGLPNAPLVIDIAD--ALAPAGEPIGAMEYEQFLREGDIDFPGVWPDDEWNAI 186 Query: 191 TLYYTSGTTGLPKGVMHHHRGAFLNAMAEVLEHQMDLNSVYLWTLPMFHAASWGFSWATV 250 L YTSGTT PKGV+ HRGA+L +M ++ + M YLWTLPMFHA W FSWA Sbjct: 187 ALNYTSGTTSDPKGVVPSHRGAYLMSMLQLTDWGMPRAPKYLWTLPMFHANGWCFSWAVT 246 Query: 251 AVGATNVCLDKVDYPLIYRLVEKERVTHMCAAPTVYVNLADYMKRNNLKFSNRVHMLVAG 310 A T+VCL KV I+ +E H CAAP V +LA + FS+ V + AG Sbjct: 247 AAAGTHVCLRKVTAANIFSAIEAYGADHFCAAPIVLSSLATATQEERRPFSHVVRIRTAG 306 Query: 311 AAPAPATLKAMQEIGGYMCHVYGLTETYGPHSICEWRREWDSLPLEEQAKLKARQGIPYV 370 + P + LKA+ E G + HVYG+TE G W+ +E+A+L ARQG Sbjct: 307 SPPPASVLKAVIEQGFDVEHVYGITEASGTPVSSYANPAWNEKSGDEKARLMARQGNRAA 366 Query: 371 SFE-MDVFDANG-KPVPWDGKTIGEVVMRGHNVALGYYKNPEKTAESFRDGWFHSGDAAV 428 E + V D + + VPWDG T GE+++RG+ V GY KNPE T +F GWFH+GD AV Sbjct: 367 GLEGLRVADPDTMESVPWDGTTQGELLLRGNIVMKGYLKNPEATEAAFAGGWFHTGDLAV 426 Query: 429 VHPDGYIEIVDRFKDLINTGGEKVSSILVEKTLMEIPGVKAVAVYGTPDEKWGEVVTARI 488 VHPDGY++I DR KD+I +GGE +SS+ VE L + P V AV P KWGE A I Sbjct: 427 VHPDGYVQITDRSKDVIISGGENISSVEVEDVLHQHPAVLIAAVVAQPHPKWGESPCAFI 486 Query: 489 ELQEGVKL-TEEEVIKFCKERLAHFECPKIVEFGPIPMTATGKMQKYVLR 537 EL+ GV TE E+I FC+ RLAH++CP V +G +P T TGK+QKY LR Sbjct: 487 ELKNGVAAPTEAEIIAFCRSRLAHYKCPTRVVYGALPKTGTGKIQKYRLR 536 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: 735 Number of extensions: 29 Number of successful extensions: 5 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: 554 Length adjustment: 36 Effective length of query: 513 Effective length of database: 518 Effective search space: 265734 Effective search space used: 265734 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: 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