Align 4-hydroxybutyrate-CoA ligase (EC 6.2.1.40) (characterized)
to candidate WP_008343095.1 BA79_RS07740 acyl--CoA ligase
Query= BRENDA::A4YDT1 (564 letters) >NCBI__GCF_000691145.1:WP_008343095.1 Length = 526 Score = 326 bits (835), Expect = 2e-93 Identities = 200/520 (38%), Positives = 289/520 (55%), Gaps = 18/520 (3%) Query: 37 RFNWVRDVFEDIHVKERGSKTALIWRDINTGEEAKLSYHELSLMSNRVLSTLRKHGLKKG 96 ++N V ++ H +E K AL W+D N G EA ++Y L +N++ L G KKG Sbjct: 11 QYNLVSEIEAFSHDQE---KIALHWQDGN-GHEAHVTYAALVEEANKIGHVLLNAGFKKG 66 Query: 97 DVVYLMTKVHPMHWAVFLAVIKGGFVMVPSATNLTVAEMKYRFSDLKPSAIISDSLRASV 156 D + +M ++++LA++K G V++P + L ++ YR + I + Sbjct: 67 DKIIVMVPRMLEAYSIYLAILKTGMVVIPCSEMLRAKDIDYRIEHAEAKGAIVYASFIQS 126 Query: 157 MEEALGSLKVEKFLIDGKRETWNSL----EDESSNAEPEDTRGEDVIINYFTSGTTGMPK 212 E + F I W ++ E++SS + DT D+ +TSGTTG PK Sbjct: 127 FEGTNQPKDFKTFSIGENDHGWTNIVAQKEEQSSELKLADTTRTDMAFLSYTSGTTGNPK 186 Query: 213 RVIHTAVSYPVGSITTASI--VGVRESDLHLNLSATGWAKFAWSSFFSPLLVGATVVGIN 270 V+HT + + TA+ + + E D + GW K+ WS S L GA G Sbjct: 187 GVVHTH-GWAYAHLRTAAKAWLSINEGDKVWATAGPGWQKWVWSPLLSVLGSGAE--GFV 243 Query: 271 YEGKLDTRRYLGEVENLGVTSFCAPPTAWRQFITLD-LDQFRFERLRSVVSAGEPLNPEV 329 Y GK + YL ++ + C PT +R +D L Q+ +L S VSAGEPLN EV Sbjct: 244 YGGKFNPDTYLELLQKNEINVLCCTPTEYRFMAKVDDLSQYELPKLHSAVSAGEPLNREV 303 Query: 330 IKIWKDKFNLTIRDFYGQTETTAMVGNFPFLKVKPGSMGKPHPLYDIRLLDDEGKEITKP 389 I +K F++ +RD YGQTE+T +VG + +KPGSMGKP P ++ ++D+ G +I P Sbjct: 304 IDTFKKHFDIEVRDGYGQTESTLLVGVLKGMDIKPGSMGKPTPGNEVEIIDENG-QICAP 362 Query: 390 YEVGHITVKLNPRPIGLFLGYSDEKKNMESFREG-YYYTGDKAYFDEEGYFYFVGRGDDV 448 E+G I V L LF Y + + ++ R G Y+ TGD+A DE+GYF+F R DD+ Sbjct: 363 GEIGDIAVHLETP--ALFKEYYKDAERTKAQRRGDYFITGDRAKKDEDGYFWFESRRDDI 420 Query: 449 IKTSDYRVGPFEVESALLEHPAVAEAAVVGVPDTVRWQLVKAYIVLKKGYMPSKELAEEI 508 I +S Y +GPFEVE AL++HPAV E AVV PD +R +VKAY+VL+ S EL +E+ Sbjct: 421 IVSSGYTIGPFEVEDALIKHPAVKECAVVASPDEIRGSIVKAYVVLRDASTQSDELIKEL 480 Query: 509 REKMKTLLSPYKVPRIIEFVDELPKTISGKIRRVELRKRE 548 + +K +PYK PR IEF+DELPKT S KIRRVELR+RE Sbjct: 481 QTHVKNTTAPYKYPREIEFIDELPKTPSAKIRRVELRERE 520 Lambda K H 0.318 0.137 0.402 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: 678 Number of extensions: 38 Number of successful extensions: 7 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: 564 Length of database: 526 Length adjustment: 35 Effective length of query: 529 Effective length of database: 491 Effective search space: 259739 Effective search space used: 259739 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