Align acetoacetate-CoA ligase (EC 6.2.1.16) (characterized)
to candidate 408300 DVU0748 acetyl-CoA synthetase
Query= BRENDA::D6EQU8 (658 letters) >MicrobesOnline__882:408300 Length = 648 Score = 231 bits (590), Expect = 6e-65 Identities = 181/612 (29%), Positives = 284/612 (46%), Gaps = 37/612 (6%) Query: 55 FWKAVTEWFDVRFSTPYARVLGDRTMPGAQWFPGATLNYAEHAL--RAAGTRPDEPALLY 112 FW+ E ++ + + VL D P +WFPGA N +AL + AL++ Sbjct: 49 FWEEAAE--ELEWFRRWDGVLDDSNAPFMRWFPGALCNIVHNALDRHIETSNRHRLALIW 106 Query: 113 VDETHEPAPVTWAELRRQVASLAAELRALGVRPGDRVSGYLPNIPQAVVALLATAAVGGV 172 E + T+ +L R+V LA +R+LGV GDRV Y+P +P+ V A+LA A +G V Sbjct: 107 EGEPGDSRRFTYFDLYREVNRLANAMRSLGVTKGDRVVIYMPPLPETVFAMLACAKIGAV 166 Query: 173 WTSCAPDFGARSVLDRFQQVEPVVLFTVDGYRYGGKEHDRRDTVAELRREL-PTLRA--- 228 ++ F ARS+ DR + P +L TVDG+ G+ + + L P RA Sbjct: 167 HSTVFGGFSARSLCDRVEDARPTLLLTVDGFYRNGRVVPLKPVADDAVDALSPEARAGLH 226 Query: 229 ---VIHIPLLGTEAPDGTLDW--ETLTAADAEPVYEQVPFDHPLWVLYSSGTTGLPKAIV 283 V+H L T DG W + + E + E + + PL+VLY+SGTTG PK +V Sbjct: 227 HVVVVHRAHLETPMRDGRDIWYHDLVRGQSTEALTEVLSANDPLFVLYTSGTTGKPKGLV 286 Query: 284 QSQGGILVEHLKQLGLHCDLGPGDRFFWYTSTGWMMWNF--LVSGLLTGTTIVLYDGSPG 341 S GG +V + + D+ P D F+ GW+ + + L+ GTT VLY+G P Sbjct: 287 HSHGGYMVGVHRTMRWVFDVRPTDIFWCTAEPGWITGHSYGVYGPLMAGTTTVLYEGHPL 346 Query: 342 FPATDAQWRIAERTGATLFGTSAAYV-MACRKAGVHPARDLDLSAIQCVATTGSPLPPDG 400 +P W + ER G T+ T + M R ++PAR D++ ++ +AT G P+ P+ Sbjct: 347 YPEAGRLWSMVERWGVTILYTVPTVIRMLMRFGPLYPARH-DITTLRLLATVGEPISPET 405 Query: 401 FRWLHDEFAAGGA---DLWIASVSGGTDVCSCFAGAVPTLPVHIGELQAPGLGTDLQSWD 457 + W + G D W + +G +P + G + P G D+ D Sbjct: 406 WVWFYRTIGRGRCPVLDTWWQTETG-----MIMVSPLPVSALKPGSVARPLPGVDVDIVD 460 Query: 458 PSGDPL-TDEVGELVVTNPMPSMPIRFWNDPDGSRYHDSYFDTYPGVWRHGDWITLTSRG 516 G P+ G LVV NP P+M + D + + Y++ +PG + GD G Sbjct: 461 GEGAPVPPGRGGLLVVKNPWPAMACGVFGDDEA--FRRLYWERFPGWYCTGDVARRDDDG 518 Query: 517 SVVIHGRSDSTLNRQGVRMGSADIYEAVERLPEIRESLVIGIEQPDGGYWMPLFVHL--- 573 + I GR+D + G R+G+A++ A+ P + E VIG+ G FV L Sbjct: 519 YIWIQGRADDVILIAGHRIGTAEMEAALASHPAVAECAVIGVPDRLKGEVGKAFVVLRDT 578 Query: 574 APGATLDDALLDRIKRTIRVNLSPRHVPDEVIEVPGIPHTLTGKRIEVPVKRLLQGTPLD 633 A + AL + +R L P V +V+ G+P +GK ++R+L+ + Sbjct: 579 EEAAAEEQALATSLVGHVRRELGPVAVIRDVVFREGLPRNRSGK----IMRRILRSE--E 632 Query: 634 KAVNPGSIDNLD 645 V G + L+ Sbjct: 633 MGVETGDLSTLE 644 Lambda K H 0.320 0.138 0.442 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: 1315 Number of extensions: 77 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: 658 Length of database: 648 Length adjustment: 38 Effective length of query: 620 Effective length of database: 610 Effective search space: 378200 Effective search space used: 378200 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: 54 (25.4 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