Align 4-hydroxybutyrate-CoA ligase (EC 6.2.1.40) (characterized)
to candidate WP_008484014.1 B3C1_RS07740 AMP-binding protein
Query= BRENDA::A4YDR9 (549 letters) >NCBI__GCF_000299915.1:WP_008484014.1 Length = 558 Score = 167 bits (424), Expect = 7e-46 Identities = 153/555 (27%), Positives = 254/555 (45%), Gaps = 62/555 (11%) Query: 23 TPLL------FLERAGKYFKDKTAVVYRDS--RYTYSTFYDNVMVQASALMRRGFSREDK 74 TPLL L+ D A+V R R++YS + V A +L+R G + D+ Sbjct: 14 TPLLNMTIGDCLKEKATLHPDHPALVVRHQQIRWSYSQLLEQVDRLAISLLRLGIEKGDR 73 Query: 75 LSFISRNRPEFLESFFGVPYAGGVLVPINFRLSPKEMAYIINHSDSKFVVVDEPYLNS-L 133 + + N ++L F G ++V IN E+AY +N K ++ E + S Sbjct: 74 VGIWAPNCYQWLLVQFATARLGAIMVCINPNYQKSELAYALNKVQCKALICAEGFRQSNY 133 Query: 134 LEVKDQIKAEIILLEDPDNPSASETARKEVRMTYRELVKGGSR----------------- 176 L + + + E+ S +E + + + G +R Sbjct: 134 LAMLEALAPELA-----HTHSGAELDAQALPSLRHIITMGKARPGYLAFDWLMGDLTAED 188 Query: 177 ----DPLPIPAKEEYSMITLYYTSGTTGLPKGVMHHHRGAFLNAMAEVLEHQMDLNSVYL 232 D L + ++ I + +TSGTTG PKG H NA M Sbjct: 189 SALLDALDLSPQDP---INIQFTSGTTGNPKGATLSHHNILNNAKLVGDAMGMSPADKLC 245 Query: 233 WTLPMFHAASWGF-SWATVAVGATNVC-LDKVDYPLIYRLVEKERVTHMCAAPTVYVNLA 290 +P++H S VA GAT V + D + V +ER T + PT+++ Sbjct: 246 IPVPLYHCFGMVLGSLLCVAHGATAVFPAEAFDADSTLKAVSEERCTALHGVPTMFIAEL 305 Query: 291 DYMKRNNLKFSNRVHMLVAGAAPAPATLKAMQEIGGYMCHV------YGLTETYGPHSIC 344 ++ + + ++ ++AGA ++ M+++ G + H+ YG TE+ P + Sbjct: 306 EHPQFDQFDLTSLRTGVMAGAT---CPVELMKKVIGKL-HMEEVLIAYGQTES-SPINHI 360 Query: 345 EWRREWDSLPLEEQAKLKARQGIPYVSFEMDVFDANGKPVPWDGKTIGEVVMRGHNVALG 404 R + PLE++ + G E+ + DA G VP + GE+ R ++V LG Sbjct: 361 TLRDD----PLEKRIGTVGKAGAHQ---EVKIVDAFGDEVPLGER--GEICNRAYSVMLG 411 Query: 405 YYKNPEKTAESF-RDGWFHSGDAAVVHPDGYIEIVDRFKDLINTGGEKVSSILVEKTLME 463 Y+ +P+K+AE+ +DGW HSGD V+ DGY+++V R KD+I GGE + +E+ Sbjct: 412 YWDDPQKSAETVDQDGWLHSGDLGVMDQDGYVQVVGRIKDMIIRGGENIYPREIEEFYYR 471 Query: 464 IPGVKAVAVYGTPDEKWGEVVTARIELQEGVKLTEEEVIKFCKERLAHFECPKIVEF-GP 522 P V+ + V+G PD+K+GE V A + L+ G + EE+ F + L+HF+ P+ F Sbjct: 472 HPKVQDIQVFGIPDDKYGEQVCAWVMLRSGQQADAEEMRAFAEGELSHFKIPRHFHFVDN 531 Query: 523 IPMTATGKMQKYVLR 537 PMT TGK+QK+ +R Sbjct: 532 YPMTVTGKIQKFRMR 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: 671 Number of extensions: 35 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 549 Length of database: 558 Length adjustment: 36 Effective length of query: 513 Effective length of database: 522 Effective search space: 267786 Effective search space used: 267786 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