Align 4-hydroxybutyrate-CoA ligase (EC 6.2.1.40) (characterized)
to candidate 8499218 DvMF_0003 AMP-dependent synthetase and ligase (RefSeq)
Query= BRENDA::A4YDT1 (564 letters) >FitnessBrowser__Miya:8499218 Length = 557 Score = 341 bits (875), Expect = 4e-98 Identities = 205/534 (38%), Positives = 292/534 (54%), Gaps = 20/534 (3%) Query: 38 FNWVRDVFEDIHVKERGSKTALIWRDINTGEEAKLSYHELSLMSNRVLSTLRKHGLKKGD 97 FN+ DV + I + G I + G ++ ++ S ++ + LR G++KGD Sbjct: 27 FNFAFDVLDPIAAADPGR--LCIAHVDDAGVRRDYTFAWMAEASAKLANALRLRGIRKGD 84 Query: 98 VVYLMTKVHPMHWAVFLAVIKGGFVMVPSATNLTVAEMKYRFSDLKPSAIISDSLRASVM 157 V L+ W LA+ + G V +P+ LT ++ +R K +I D + Sbjct: 85 RVMLVLYRRIEFWVSMLALHRLGAVAIPAPAQLTPKDIVFRVERAKTRCVIVDHSITERV 144 Query: 158 EEALGSLKVEKFLI----DGKRETWNSLEDESSNAEPEDTR---------GEDVIINYFT 204 E A + D W + + AE R GED ++ +F+ Sbjct: 145 EAARPDCPGLAVCVQVGGDALPRGWVDYDTIFTPAEARFPRPESPLEFAGGEDPLLIFFS 204 Query: 205 SGTTGMPKRVIHTAVSYPVGSITTASIV-GVRESDLHLNLSATGWAKFAWSSFFSPLLVG 263 SGTTGMPK V H +YP+G + T + DLHL L+ TGW K W F+ + G Sbjct: 205 SGTTGMPKMVEHVH-TYPLGHLLTGMYWHDLVPGDLHLTLADTGWGKAVWGKFYGQWMAG 263 Query: 264 ATVVGINYEGKLDTRRYLGEVENLGVTSFCAPPTAWRQFITLDLDQFRFERLRSVVSAGE 323 A+V ++ GK + L + VT+FCAPPT +R + DL + +LR +AGE Sbjct: 264 ASVFVYDFRGKFEPAALLDVLAAHAVTTFCAPPTVYRFLVRQDLSAYDLSKLRHCTTAGE 323 Query: 324 PLNPEVIKIWKDKFNLTIRDFYGQTETTAMVGNFPFLKVKPGSMGKPHPLYDIRLLDDEG 383 LN V WK L I + YGQTETT + P + K GS+G+P P +D+ L D G Sbjct: 324 LLNDSVFHDWKAATGLEIHEGYGQTETTLQIATLPCMTPKAGSIGRPMPGWDVVLQDAAG 383 Query: 384 KEITKPYEVGHITVKL-NPRPIGLFLGYSDEKKNMESFR-EGYYYTGDKAYFDEEGYFYF 441 I P E G I V++ P+GLF GY +E + S GYY+TGDKA+ DE+GY++F Sbjct: 384 N-ICPPGEEGEICVRVAEGLPVGLFRGYLEEPEKTASVMFGGYYHTGDKAWMDEDGYYWF 442 Query: 442 VGRGDDVIKTSDYRVGPFEVESALLEHPAVAEAAVVGVPDTVRWQLVKAYIVLKKGYMPS 501 +GR DD+IK+S YR+GPFEVESAL+ HPAV EAAV GVPD +R Q VKA +VL GY S Sbjct: 443 LGRVDDLIKSSGYRIGPFEVESALVAHPAVVEAAVTGVPDPLRGQAVKATVVLAAGYTAS 502 Query: 502 KELAEEIREKMKTLLSPYKVPRIIEFVDELPKTISGKIRRVELRKREEEKRKKG 555 L +E+++ +K + +PYK PRII++V ELPKTISGKI+R E+R+R+++ G Sbjct: 503 DALTKELQDHVKKVTAPYKYPRIIDYVAELPKTISGKIKRAEIRERDQQASGPG 556 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: 733 Number of extensions: 38 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: 564 Length of database: 557 Length adjustment: 36 Effective length of query: 528 Effective length of database: 521 Effective search space: 275088 Effective search space used: 275088 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