Align acetoacetate-CoA ligase (EC 6.2.1.16) (characterized)
to candidate WP_014026520.1 PYRFU_RS04855 acetate--CoA ligase
Query= BRENDA::D6EQU8 (658 letters) >NCBI__GCF_000223395.1:WP_014026520.1 Length = 656 Score = 235 bits (599), Expect = 5e-66 Identities = 184/623 (29%), Positives = 286/623 (45%), Gaps = 49/623 (7%) Query: 61 EWFDVRFSTPYARVLGDRTMPGAQWFPGATLNYAEHALRAAGTRP--DEPALLYVDETHE 118 EWF + +VL D P +WF G +N + +A+ R ++ A+++ E + Sbjct: 42 EWFKT-----WDKVLDDSNPPFYRWFVGGLINASYNAVDRHLKRGLRNKAAIIWEGEPGD 96 Query: 119 PAPVTWAELRRQVASLAAELRALGVRPGDRVSGYLPNIPQAVVALLATAAVGGVWTSCAP 178 +T+ +L R+V AA L LG+R GD ++ YLP IP+ + +LA A +G +T Sbjct: 97 TRVLTYYQLYREVNRFAAVLENLGLRKGDTIAFYLPMIPELPIFMLAAARLGITFTVVFS 156 Query: 179 DFGARSVLDRFQQVEPVVLFTVDGYRYGGKEHDRRDTVAELRRELPTLRAV--------- 229 F A+++ +R + VL T DG GK + + E P++ V Sbjct: 157 GFSAKALAERINDAKAKVLVTADGGFRRGKVIELKKIADEALEMAPSVETVIVVKNVTAR 216 Query: 230 ---IHIPLLGTEAPDGTLDWETLTAADAEPVYEQVPFDHPLWVLYSSGTTGLPKAIVQSQ 286 I +PL TE D L A +PV V HPL++LY+SGTTG PK +V S Sbjct: 217 GAKIDVPL--TEGRDYWLHNLLPAHAKVDPV--PVESTHPLFILYTSGTTGKPKGVVHST 272 Query: 287 GGILVEHLKQLGLHCDLGPGDRFFWYTSTGWMM-WNFLVSG-LLTGTTIVLYDGSPGFPA 344 GG LV + D+ P D F GW+ +++V G LL G T V+Y+G+P +PA Sbjct: 273 GGYLVWVYATMKWVFDVKPDDVMFCTADIGWITGHSYVVFGPLLHGITTVMYEGAPDYPA 332 Query: 345 TDAQWRIAERTGATLFGTSAAYVMACRKAGVHPARDLDLSAIQCVATTGSPLPPDGFRWL 404 D W+I E+ G T+F T+ + + G + DLS ++ + T G P+ P+ ++W Sbjct: 333 PDRWWQIVEKYGVTIFYTAPTAIRMLMRYGEEWVKKHDLSTLRILGTVGEPINPEAWKWY 392 Query: 405 HDEFAAGG-----ADLWIASVSGGTDVCSCFAGAVPTLPVHIGELQAPGLGTDLQSWDPS 459 + GG D W + +GG + A + +P+ G P G D Sbjct: 393 YT--VVGGERCPIVDTWWQTETGGIMISP--APGIQLVPLKPGSATYPLPGVDADVVCED 448 Query: 460 GDPL-TDEVGELVVTNPMPSMPIRFWNDPDGSRYHDSYFDTY----PGVWRH--GDWITL 512 G P + G LV+ P P M + W DP+ RY +Y+ + G W + D+ Sbjct: 449 GSPCPPGQRGYLVIKRPWPGMLMTLWGDPE--RYVRTYWQRFSKPEEGKWIYYPADYAMK 506 Query: 513 TSRGSVVIHGRSDSTLNRQGVRMGSADIYEAVERLPEIRESLVIGIEQPDGGYWMPLFVH 572 G I GR+D + G R+G+A+I A+ P + E+ V+G P G FV Sbjct: 507 DEDGYFWILGRADEVIKVAGHRLGTAEIESALVSHPAVAEAAVVGKPDPVKGEVPVAFVV 566 Query: 573 LAPGATLDDALLDRIKRTIRVNLSPRHVPDEVIEVPGIPHTLTGKRIEVPVKRLLQGTPL 632 L G T + L + +R L P VP + V +P T +GK + +K +L G Sbjct: 567 LRQGYTPSEELRHELVEHVRKTLGPIAVPAAIFFVEKLPKTRSGKIMRRVIKAVLLGK-- 624 Query: 633 DKAVNPGSIDNLDLLHFYEELAR 655 PG + L+ +E+ R Sbjct: 625 ----TPGDLTTLEDEASLDEIRR 643 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: 1430 Number of extensions: 93 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: 658 Length of database: 656 Length adjustment: 38 Effective length of query: 620 Effective length of database: 618 Effective search space: 383160 Effective search space used: 383160 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 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