Align 4-hydroxybutyrate-CoA ligase (EC 6.2.1.40) (characterized)
to candidate WP_073038815.1 BUB04_RS09755 AMP-dependent synthetase
Query= BRENDA::A4YDR9 (549 letters) >NCBI__GCF_900129305.1:WP_073038815.1 Length = 557 Score = 261 bits (666), Expect = 6e-74 Identities = 181/537 (33%), Positives = 273/537 (50%), Gaps = 27/537 (5%) Query: 22 LTPLLFLERAGKYFKDKTAVVYRD-----SRYTYSTFYDNVMVQASALMRRGFSREDKLS 76 L + FL+ A + + + VV R+ R TY + V A AL G D++ Sbjct: 18 LNMITFLKHAARTYPE-AEVVSRNLDGSLHRTTYGETWIRVKRLAKALQGIGVRPGDRVG 76 Query: 77 FISRNRPEFLESFFGVPYAGGVLVPINFRLSPKEMAYIINHSDSKFVVVDEPYLNSLLEV 136 + N F+E +F V G VL+ +N R+S E AY++NHS+++FV V SLL + Sbjct: 77 ALDWNTHRFMELYFAVSGVGAVLLELNPRISGAERAYVVNHSEARFVAV----CASLLPL 132 Query: 137 KDQIKAE------IILLEDPDNPSASETARKEVRMTYRELVKGGSRDPLPIPAKEEYSMI 190 + + AE +I+L+D ETA Y L+ S D P +E S Sbjct: 133 MEPLAAECPTVQGVIVLDDLGR-GLPETAYPAAH-DYEALI-AESDDDFDFPWIDERSAC 189 Query: 191 TLYYTSGTTGLPKGVMHHHRGAFLNAMAEVLEHQMDLNSVYLWTLPMFHAASWGFSWATV 250 T YTSGTTG PKGV + HR +L+ +A M + V L +PMFHA WG + Sbjct: 190 TACYTSGTTGKPKGVYNSHRAMYLHTLAIAQALNMTQDDVILQIVPMFHAQGWGMFFCGP 249 Query: 251 AVGATNVCLDKV---DYPLIYRLVEKERVTHMCAAPTVYVNLADYMKRNNLKFSNRVHML 307 +GA V + D + L+ +++VT C AP +++ + ++K+ + K + Sbjct: 250 MLGAKLVFPGRYTMEDPSSLVDLLVEQKVTVTCGAPAIFLPMLHHIKKMSQKPDLTGLRM 309 Query: 308 VAGAAPAP-ATLKAMQEIGGY-MCHVYGLTETYGPHSICEWRREWDSLPLEEQAKLKARQ 365 ++GA P A +K E+GG + H YG TET ++ + L EE+ +L+ +Q Sbjct: 310 ISGATEPPLALMKGYHELGGARVIHAYGATETAPLVTVNHLKPTLKDLSEEERWELRKKQ 369 Query: 366 GIPYVSFEMDVFDANGKPVPWDGKTIGEVVMRGHNVALGYYKNPEKTAESFRDGWFHSGD 425 G+P ++ V +G +P DG +GEV++RG + YY +P RDG++ SGD Sbjct: 370 GLPVPGLDVKVVGPDGTELPRDGSKVGEVLIRGPWITRSYYNDPRSDESFARDGYWRSGD 429 Query: 426 AAVVHPDGYIEIVDRFKDLINTGGEKVSSILVEKTLMEIPGVKAVAVYGTPDEKWGEVVT 485 A + P+GY++I DRFKDLI +GGE +SSI +E +M P V AV G P KW E Sbjct: 430 AGTIDPNGYLKITDRFKDLIKSGGEWISSIDLENAIMAHPDVLEAAVIGIPHPKWEERPL 489 Query: 486 ARIELQEGVK--LTEEEVIKFCKERLAHFECPKIVEF-GPIPMTATGKMQKYVLRNE 539 A + QE + LT+E V+ F + A ++ P V F IP T+ GK K V R + Sbjct: 490 ALVVPQESARGTLTKEAVLDFIRPHFAKWQLPDDVLFVDAIPKTSVGKFAKRVAREQ 546 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: 739 Number of extensions: 37 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: 557 Length adjustment: 36 Effective length of query: 513 Effective length of database: 521 Effective search space: 267273 Effective search space used: 267273 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 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