Align Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized)
to candidate WP_058929096.1 AU252_RS00800 long-chain fatty acid--CoA ligase
Query= reanno::acidovorax_3H11:Ac3H11_3009 (578 letters) >NCBI__GCF_001484605.1:WP_058929096.1 Length = 518 Score = 268 bits (686), Expect = 3e-76 Identities = 176/534 (32%), Positives = 276/534 (51%), Gaps = 33/534 (6%) Query: 31 IGAFFADMVARQPEREALVSVHQGRRYTYAQLQTEAHRLASALLGMGLTPGDRVGIWSHN 90 IG++ A R P+R ALV GRR +Y +L + LA AL +G+ GDR+ + + N Sbjct: 5 IGSWIAGRAFRDPDRIALVDGDTGRRRSYGELHERTNALADALTRLGVRRGDRIALLAMN 64 Query: 91 NAEWVLMQLATAQVGLVLVNINPAYRTAEVEYALNKVGCKLLVSMARFKTSDYLGMLREL 150 + E++ + LA A++G + V IN EV Y L G + V A+ L E+ Sbjct: 65 SPEFLEVMLAGAKMGAITVPINFRLSADEVRYVLEDSGATVFVHSAQ---------LAEV 115 Query: 151 APEWQGQQPGHLQAAKLPQLKTVVWIDDEAGQGADEPGLLRFTELIARGNAADPRLAQVA 210 A A++ L+ V+ I + A + E ++ G+ + Sbjct: 116 ASA----------ASRGLMLRFVLEIPSSVERAAQASSA--YEEFLSTGSTET-----LE 158 Query: 211 AGLQATDPINIQFTSGTTGFPKGATLTHRNILNNGFFIGECMK-LTPADRLCIPVPLYHC 269 + D I +TSGTTG PKGA +THRN+L + K L D PL+H Sbjct: 159 RDVAEEDVTLIMYTSGTTGVPKGAMITHRNLLWQTLHMITLAKGLNSYDVTVTAAPLFHI 218 Query: 270 FGMVLGNLACFTHGATIVYPNDGFDPLTVLQTVQDERCTGLHGVPTMFIAELDHPRFAEF 329 G+ L G T V + FDP ++ ++ E+ T + V +M+ A P Sbjct: 219 GGLATHTLPLLYLGGTTVIV-ESFDPAQTVELMEREKVTVMFLVASMWTAVSLLPDLDTK 277 Query: 330 NLSTLRTGIMAGSPCPTEVMKRVVEQMNLREITIAYGMTETSPVSCQSSTDTPLSKRVST 389 +LS ++ I G+P P ++ E+ + T YG+TE++ SC + + +SK + Sbjct: 278 DLSAVKYAISGGAPLPLPTLEFFDERGWV--FTEGYGLTESTCASCFLAPEYVVSK-AGS 334 Query: 390 VGQVQPHLEVKIVDPDTGAVVPIGQRGEFCTKGYSVMHGYWGDEAKTREAIDEGGWMHTG 449 VG H +++VD DT V +G+ GE +G ++ GYWG +T +A GGW HTG Sbjct: 335 VGHPVTHQRMRLVD-DTDRDVAVGEVGEILLQGPNIFAGYWGRPRETADAF-RGGWFHTG 392 Query: 450 DLATMDAEGYVNIVGRIKDMVIRGGENIYPREIEEFLYRHPQVQDVQVVGVPDQKYGEEL 509 DLA D++G++ +V R KDMVI GGEN+YP E+E+ L+RHP+V + V+G+PD K+GE + Sbjct: 393 DLARADSQGFLTLVDRKKDMVITGGENVYPIEVEQVLFRHPEVLEAAVIGLPDNKWGESV 452 Query: 510 CAWIIAKPGTQPTEDDIRAFCKGQIAHYKVPRYIRFVTSFPMTVTGKIQKFKIR 563 A ++ P + TE+++ A+ + ++AH+K PR I FV P TGK+ K +R Sbjct: 453 TAIVVRTPESTLTEEELIAWTRERLAHFKCPRRIEFVEELPRNATGKLLKRDLR 506 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: 649 Number of extensions: 39 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 578 Length of database: 518 Length adjustment: 36 Effective length of query: 542 Effective length of database: 482 Effective search space: 261244 Effective search space used: 261244 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 Apr 09 2024. 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