Align Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized)
to candidate WP_043744440.1 AMB_RS12570 acyl-CoA synthetase
Query= reanno::acidovorax_3H11:Ac3H11_3009 (578 letters) >NCBI__GCF_000009985.1:WP_043744440.1 Length = 544 Score = 192 bits (488), Expect = 3e-53 Identities = 160/529 (30%), Positives = 236/529 (44%), Gaps = 41/529 (7%) Query: 51 VHQGRRYTYAQLQTEAHRLASALLGMGLTPGDRVGIWSHNNAEWVLMQLATAQVGLVLVN 110 VH R+T+ Q RL SAL G+ GD V + + N G VL Sbjct: 41 VHGDLRFTWKQTYDRCRRLGSALAARGVGVGDTVAVMAANTPAAYEAAFGVPMTGGVLCA 100 Query: 111 INPAYRTAEVEYALNKVGCKLLVSMARFKTSDYLGMLRELAPEWQGQQPGHLQAAKLPQL 170 +N + + L K+L++ RE AP + +A L + Sbjct: 101 LNIRLDAEAIAFMLQHGEAKVLLTD------------REFAPTIK-------KALSLLEA 141 Query: 171 KTVVW-IDDEAGQGADEPGLLRFTELIARGNAADPRLAQVAAGLQATDPINIQFTSGTTG 229 K +V IDD A + G + + IA G DP A V D I + +TSGTTG Sbjct: 142 KPIVIDIDDAAVTTGEMLGEMEYEAFIAGG---DPEYAWVWPS-DEWDAIALNYTSGTTG 197 Query: 230 FPKGATLTHRNILNNGFFIGECMKLTPADRLCIPVPLYHCFGMVLGNLACFTHGATIVYP 289 PKG HR N +T +P++HC G G + Sbjct: 198 NPKGVVYHHRGAYINALGNVVNWGMTGHPVYLWTLPMFHCNGWCFPWTLAALAGTNVCLR 257 Query: 290 NDGFDPLTVLQTVQDERCTGLHGVPTMFIAELDHPRFAEFNLSTLRTGIMAGSPCPTEVM 349 D + ++ + T + G P + ++ P L + A +P P V+ Sbjct: 258 R--VDGGHMFAAIEKHKVTHMCGAPIVMGMLINAPEKDRRPLPHPVEFMTAAAPPPAAVI 315 Query: 350 KRVVEQMNLREITIAYGMTET-SPVSC----QSSTDTPLSKRVSTVGQ--VQPHLEVKIV 402 R+ Q +IT YG+TE P + + + PL +R + V+ E ++ Sbjct: 316 GRLESQGF--KITHVYGLTEVYGPATVCAWKEEWDELPLDERAKMKSRQGVRYVNEEAMM 373 Query: 403 DPDTGAVVPIGQ----RGEFCTKGYSVMHGYWGDEAKTREAIDEGGWMHTGDLATMDAEG 458 D ++VP+ + GE +G VM GY + + T EA GGW HTGDL A+G Sbjct: 374 VADPVSLVPVPKDGATMGEVFYRGNVVMKGYLKNPSATNEAFS-GGWFHTGDLGVWHADG 432 Query: 459 YVNIVGRIKDMVIRGGENIYPREIEEFLYRHPQVQDVQVVGVPDQKYGEELCAWIIAKPG 518 Y+ + R KD++I GGENI E+E LY+HP V + VV PD+K+GE CA+I K G Sbjct: 433 YIELKDRSKDIIISGGENISTIEVEGVLYQHPSVGEAAVVARPDEKWGETPCAFIGLKDG 492 Query: 519 TQPTEDDIRAFCKGQIAHYKVPRYIRFVTSFPMTVTGKIQKFKIRDEMK 567 T ++I AFC+ ++AHYK PR + F T+ P T TGK+QK+ +R+ K Sbjct: 493 ATATAEEIMAFCRERLAHYKCPRTVVF-TNLPKTSTGKVQKYVLREMAK 540 Lambda K H 0.320 0.136 0.412 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: 738 Number of extensions: 48 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: 578 Length of database: 544 Length adjustment: 36 Effective length of query: 542 Effective length of database: 508 Effective search space: 275336 Effective search space used: 275336 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