Align Acetate--CoA ligase CCL3; HlCCL3; 2-methylbutanoate--CoA ligase CCL4; 2-methylpropanoate--CoA ligase CCL4; Butanoate--CoA ligase CCL3; Hexanoate--CoA ligase CCL3; Isovalerate--CoA ligase CCL3; Pentanoate--CoA ligase CCL3; Propionate--CoA ligase CCL3; EC 6.2.1.1; EC 6.2.1.-; EC 6.2.1.17 (characterized)
to candidate Dsui_2808 Dsui_2808 acyl-CoA synthetase (AMP-forming)/AMP-acid ligase II
Query= SwissProt::M4IS88 (568 letters) >FitnessBrowser__PS:Dsui_2808 Length = 552 Score = 580 bits (1494), Expect = e-170 Identities = 290/556 (52%), Positives = 377/556 (67%), Gaps = 21/556 (3%) Query: 11 LPKNAANYTALTPLWFLERAATVHPTRTSVIHGSRHYTWLQTYHRCRQFASALNNHSIGL 70 L KNAANY L+PL F+ R+A ++P R SVIHG R YTWL+T++R R+ ASAL I Sbjct: 16 LEKNAANYVPLSPLTFIARSAYIYPERVSVIHGQRRYTWLETFNRARRLASALEARGIKE 75 Query: 71 GSTVAVIAPNVPALYEAHFAVPMAGAVVNCVNIRLNASTIAFLLGHSSAAAVMVDQEFFS 130 G TVAV+ N P +YE HF VP+ GAV+N +N RL+ +AF+L H A ++ D+E+ Sbjct: 76 GDTVAVMLNNTPEMYECHFGVPVTGAVLNTLNTRLDPEAVAFMLNHGEAKILITDKEYSH 135 Query: 131 LAEEALKILAQESKSHYKPPLLVVIGDESCDPKTLEYALKTGAIEYEKFLEGGDPEFDWK 190 + AL+ L + ++ V E P L G +YE L G P+++WK Sbjct: 136 IVGPALEKLGRSIV------VIDVNDSEYTGPGDL-----LGEKDYEALLAEGTPDYEWK 184 Query: 191 PPEDEWQSISLGYTSGTTASPKGVVLSHRGAYLMSLSASVVWGINEGAIYLWTLPMFHCN 250 P+DEW +ISL YTSGTT +PKGVV HRGAYL ++S V WG+ ++YLWTLPMFHCN Sbjct: 185 GPQDEWDAISLNYTSGTTGNPKGVVYHHRGAYLNAMSNIVSWGMPPHSVYLWTLPMFHCN 244 Query: 251 GWCYTWGMAAFCGTNICLRQVTAKGVYSAIAKYGVTHFCAAPVVLNTIVNAPPE--EAII 308 GWC+ W MAA GTN+CLR+V K + +I + VTH+C AP+V + + NAP E E I Sbjct: 245 GWCFPWTMAANAGTNVCLRRVDPKLILQSIRENKVTHYCGAPIVHSMLANAPAEWREGI- 303 Query: 309 PLPHLVHVMTAGAAPPPSVLFAMSEKGFKVAHTYGLSETYGPSTICAWKPEWDSLPPIKQ 368 H V + A A PP +V+ M++ GFK+ H YGL+ETYGP+++CA +PEW LP +Q Sbjct: 304 --NHGVSGLIAAAPPPAAVIEGMAKIGFKITHVYGLTETYGPASVCAQQPEWFDLPVGEQ 361 Query: 369 ARLNARQGVRYIALEGLDVVDTKTMKPVPADGTTMGEIVMRGNAVMKGYLKNPKANEESF 428 LN RQGVRY A E + V+D TM+ VP D TMGEI+ RGN VMKGYLKNPKA EESF Sbjct: 362 VNLNGRQGVRYHAQEAITVLDPATMEAVPWDNETMGEIMFRGNLVMKGYLKNPKATEESF 421 Query: 429 ADGWFHSGDLAVKHPDGYIEIKDRSKDIIISGGENISSLEVENTLYLHPAVLEVSVVARP 488 A G++H+GDLAV DGY++IKDRSKD+IISGGENISS+EVE+TLY HPAV+ +VVA P Sbjct: 422 AGGYYHTGDLAVMQADGYVKIKDRSKDVIISGGENISSIEVEDTLYRHPAVMAAAVVATP 481 Query: 489 DERWGESPCAFVTLKPNIDKSNEQVLAEDIIKFCKSKMPAYWVPKSVVFGPLPKTATGKI 548 D +WGE P AF+ LK + + +II+FC+ M + VPK V+FGPLPKT+TGKI Sbjct: 482 DPKWGEVPAAFIELKDGV-----SITEVEIIEFCREHMARFKVPKKVIFGPLPKTSTGKI 536 Query: 549 QKHVLRAKAKEMGALK 564 QK+VLR AK A++ Sbjct: 537 QKYVLREMAKSTAAIE 552 Lambda K H 0.318 0.134 0.415 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: 947 Number of extensions: 43 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: 568 Length of database: 552 Length adjustment: 36 Effective length of query: 532 Effective length of database: 516 Effective search space: 274512 Effective search space used: 274512 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 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 Apr 09 2024. The underlying query database was built on Apr 09 2024.
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