Align Acetate/butyrate--CoA ligase AAE7, peroxisomal; AMP-binding protein 7; AtAMPBP7; Acetyl-CoA synthetase; Acyl-activating enzyme 7; Butyryl-CoA synthetase; Protein ACETATE NON-UTILIZING 1; EC 6.2.1.1; EC 6.2.1.2 (characterized)
to candidate Dsui_2808 Dsui_2808 acyl-CoA synthetase (AMP-forming)/AMP-acid ligase II
Query= SwissProt::Q8VZF1 (569 letters) >FitnessBrowser__PS:Dsui_2808 Length = 552 Score = 575 bits (1483), Expect = e-168 Identities = 286/554 (51%), Positives = 379/554 (68%), Gaps = 19/554 (3%) Query: 12 LPKIPANYTALTPLWFLDRAAVVHPTRKSVIHGSREYTWRQTYDRCRRLASALADRSIGP 71 L K ANY L+PL F+ R+A ++P R SVIHG R YTW +T++R RRLASAL R I Sbjct: 16 LEKNAANYVPLSPLTFIARSAYIYPERVSVIHGQRRYTWLETFNRARRLASALEARGIKE 75 Query: 72 GSTVAIIAPNIPAMYEAHFGVPMCGAVLNCVNIRLNAPTVAFLLSHSQSSVIMVDQEFFT 131 G TVA++ N P MYE HFGVP+ GAVLN +N RL+ VAF+L+H ++ +++ D+E+ Sbjct: 76 GDTVAVMLNNTPEMYECHFGVPVTGAVLNTLNTRLDPEAVAFMLNHGEAKILITDKEYSH 135 Query: 132 LAEDSLRLMEEKAGSSFKRPLLIVIGDHT-CAPESLNRALSKGAIEYEDFLATGDPNYPW 190 + +L EK G S ++I + D P L G +YE LA G P+Y W Sbjct: 136 IVGPAL----EKLGRSI---VVIDVNDSEYTGPGDL-----LGEKDYEALLAEGTPDYEW 183 Query: 191 QPPADEWQSIALGYTSGTTASPKGVVLHHRGAYIMALSNPLIWGMQDGAVYLWTLPMFHC 250 + P DEW +I+L YTSGTT +PKGVV HHRGAY+ A+SN + WGM +VYLWTLPMFHC Sbjct: 184 KGPQDEWDAISLNYTSGTTGNPKGVVYHHRGAYLNAMSNIVSWGMPPHSVYLWTLPMFHC 243 Query: 251 NGWCFPWSLAVLSGTSICLRQVTAKEVYSMIAKYKVTHFCAAPVVLNAIVNAPKEDTILP 310 NGWCFPW++A +GT++CLR+V K + I + KVTH+C AP+V + + NAP E Sbjct: 244 NGWCFPWTMAANAGTNVCLRRVDPKLILQSIRENKVTHYCGAPIVHSMLANAPAEWRE-G 302 Query: 311 LPHTVHVMTAGAAPPPSVLFSMNQKGFRVAHTYGLSETYGPSTVCAWKPEWDSLPPETQA 370 + H V + A A PP +V+ M + GF++ H YGL+ETYGP++VCA +PEW LP Q Sbjct: 303 INHGVSGLIAAAPPPAAVIEGMAKIGFKITHVYGLTETYGPASVCAQQPEWFDLPVGEQV 362 Query: 371 KLNARQGVRYTGMEQLDVIDTQTGKPVPADGKTAGEIVFRGNMVMKGYLKNPEANKETFA 430 LN RQGVRY E + V+D T + VP D +T GEI+FRGN+VMKGYLKNP+A +E+FA Sbjct: 363 NLNGRQGVRYHAQEAITVLDPATMEAVPWDNETMGEIMFRGNLVMKGYLKNPKATEESFA 422 Query: 431 GGWFHSGDIAVKHPDNYIEIKDRSKDVIISGGENISSVEVENVVYHHPAVLEASVVARPD 490 GG++H+GD+AV D Y++IKDRSKDVIISGGENISS+EVE+ +Y HPAV+ A+VVA PD Sbjct: 423 GGYYHTGDLAVMQADGYVKIKDRSKDVIISGGENISSIEVEDTLYRHPAVMAAAVVATPD 482 Query: 491 ERWQESPCAFVTLKSDYEKHDQNKLAQDIMKFCREKLPAYWVPKSVVFGPLPKTATGKIQ 550 +W E P AF+ LK + +I++FCRE + + VPK V+FGPLPKT+TGKIQ Sbjct: 483 PKWGEVPAAFIELKDGVSITE-----VEIIEFCREHMARFKVPKKVIFGPLPKTSTGKIQ 537 Query: 551 KHILRTKAKEMGPV 564 K++LR AK + Sbjct: 538 KYVLREMAKSTAAI 551 Lambda K H 0.319 0.134 0.422 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: 921 Number of extensions: 47 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: 569 Length of database: 552 Length adjustment: 36 Effective length of query: 533 Effective length of database: 516 Effective search space: 275028 Effective search space used: 275028 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 (21.8 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