Align 4-hydroxybutyrate-CoA ligase (EC 6.2.1.40) (characterized)
to candidate WP_037568740.1 BS73_RS02005 AMP-binding protein
Query= BRENDA::A4YDR9 (549 letters) >NCBI__GCF_000744815.1:WP_037568740.1 Length = 532 Score = 417 bits (1072), Expect = e-121 Identities = 227/526 (43%), Positives = 322/526 (61%), Gaps = 27/526 (5%) Query: 19 YSVLTPLLFLERAGKYFKDKTAVVYRDSRYTYSTFYDNVMVQASALMRRGFSREDKLSFI 78 + LTP+ +L+RA D+TAVV R+TY+ +D A AL +R ++ + Sbjct: 13 FEPLTPVSYLDRAAAAHGDRTAVVDGGRRWTYAQLHDRCRRLAGALAP--LARNRPVAVL 70 Query: 79 SRNRPEFLESFFGVPYAGGVLVPINFRLSPKEMAYIINHSDSKFVVVDEPYLNSLLEVKD 138 + N LE+ FGVP+AG LVP+N RL+ E+A I+ HS++ ++ D + + + Sbjct: 71 APNTHVMLEAHFGVPWAGVPLVPVNTRLAAGEVARILEHSEAAVLIHDPAFDEVVADALA 130 Query: 139 QIKAEIILLEDPDNPSASETARKEVRMTYRELVKG---GSRDPLPIPAKEEYSMITLYYT 195 ++ A +L+ + Y L+ G G+R P +E ++++L YT Sbjct: 131 RLDAPPVLVRAGEG--------------YERLLAGAEPGARTPA-----DERALLSLNYT 171 Query: 196 SGTTGLPKGVMHHHRGAFLNAMAEVLEHQMDLNSVYLWTLPMFHAASWGFSWATVAVGAT 255 SGTTG PKGVM+HHRGA+L A+A V + ++V+LWTLPMFH W F WA A AT Sbjct: 172 SGTTGRPKGVMYHHRGAYLQALAMVGHTGLSPSAVHLWTLPMFHCNGWCFPWAVTAAAAT 231 Query: 256 NVCLDKVDYPLIYRLVEKERVTHMCAAPTVYVNLADYMKRNNLKFSNRVHMLVAGAAPAP 315 +VCL +V+ ++RL+ +E VTH+ APTV LA + L RV GA P+P Sbjct: 232 HVCLPRVEPAEVWRLIREEGVTHLNGAPTVLSMLAYAPEAGPLPHPVRV--ATGGAPPSP 289 Query: 316 ATLKAMQEIGGYMCHVYGLTETYGPHSICEWRREWDSLPLEEQAKLKARQGIP-YVSFEM 374 A L+ M E+G + H+YGLTET+GP +C+WR EWD L QA+LKARQG+ ++ + Sbjct: 290 AILRRMGELGFEVTHLYGLTETFGPAMLCDWRPEWDGLDAGAQARLKARQGVGNMIACQA 349 Query: 375 DVFDANGKPVPWDGKTIGEVVMRGHNVALGYYKNPEKTAESFRDGWFHSGDAAVVHPDGY 434 V +G VP DG +GE+ +RG+NV LGY+K+PE TA++ DGWF +GD V HPDGY Sbjct: 350 RVVAKDGGEVPADGTAVGEIALRGNNVMLGYFKDPEATAQAAPDGWFRTGDLGVRHPDGY 409 Query: 435 IEIVDRFKDLINTGGEKVSSILVEKTLMEIPGVKAVAVYGTPDEKWGEVVTARIELQEGV 494 IE+ DR KD+I +GGE ++S+ VE+ L E P V AV P EKWGEV A + L EG Sbjct: 410 IELRDRSKDIIVSGGENIASVEVEQALAEHPAVLEAAVVAAPHEKWGEVPVAYVALHEGA 469 Query: 495 KLTEEEVIKFCKERLAHFECPKIVEFGPIPMTATGKMQKYVLRNEA 540 T +E+I F +ERLAHF+ P+ V FGP+P T+TGK+QK+VLR+ A Sbjct: 470 AATADELIAFVRERLAHFKAPESVCFGPLPKTSTGKIQKFVLRDRA 515 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: 744 Number of extensions: 30 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: 532 Length adjustment: 35 Effective length of query: 514 Effective length of database: 497 Effective search space: 255458 Effective search space used: 255458 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 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