Align Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized)
to candidate WP_043765768.1 U743_RS04305 long-chain-fatty-acid--CoA ligase
Query= reanno::acidovorax_3H11:Ac3H11_3009 (578 letters) >NCBI__GCF_000733765.1:WP_043765768.1 Length = 513 Score = 231 bits (589), Expect = 5e-65 Identities = 167/529 (31%), Positives = 253/529 (47%), Gaps = 35/529 (6%) Query: 40 ARQPEREALVSVHQGRRYTYAQLQTEAHRLASALLGMGLTPGDRVGIWSHNNAEWVLMQL 99 A Q +A +V RR ++ ++ RLA A+ +G+ GDRV I S N+ ++ Sbjct: 10 AVQTRGDATATVCGDRRRSWREVADRVARLAGAVQALGVQRGDRVAILSLNSDRYIEYLY 69 Query: 100 ATAQVGLVLVNINPAYRTAEVEYALNKVGCKLLVSMARFKTSDYLGMLRELAPEWQGQQP 159 A A G +N E+ Y L G ++L F + L LRE Sbjct: 70 AVAWAGAAANPVNIRMAPGEIAYTLEDSGSRVLFVDDTF--APMLPALRE---------- 117 Query: 160 GHLQAAKLPQLKTVVWIDDEAGQGADEPGLLRFTELIARGNAADPRLAQVAAGLQATDPI 219 ++ L+ V++ G G G F LIA A + AG + D Sbjct: 118 ------QVSALEQVIF----CGDGELPEGTQGFEALIA----AHGPVPDADAGEE--DLA 161 Query: 220 NIQFTSGTTGFPKGATLTHRNILNNGFFIGECMKLTPADRLCIPVPLYHCFGMVLGNLAC 279 + +T GTTG KG L+H N+++N + + P++H M Sbjct: 162 GLFYTGGTTGKAKGVMLSHDNVMHNMLNAIPILGYDASTVYLHAGPMFHLADMASTFAVT 221 Query: 280 FTHGATIVYPNDGFDPLTVLQTVQDERCTGLHGVPTMFIAELDHPRFAEFNLSTLRTGIM 339 G V P +PL L+ +Q E+ T VPTM L R EF+LS+LR + Sbjct: 222 AAGGVHCVIPRFDIEPL--LEIMQREKVTHTMLVPTMINMLLASGRIQEFDLSSLRRMLY 279 Query: 340 AGSPCPTEVMKRVVEQMNLREITIAYGMTETSPVSCQSSTDTPL--SKRVSTVGQVQPHL 397 SP P V+ R +E + T YG TE +P+ + S ++++ G + Sbjct: 280 GASPMPEAVLLRAMEALPTTGFTQGYGQTEAAPLITFMPPEAHYAGSDKLASAGVPGYSV 339 Query: 398 EVKIVDPDTGAVVPIGQRGEFCTKGYSVMHGYWGDEAKTREAIDEGGWMHTGDLATMDAE 457 +V I+D D G +P GQ GE C +G ++M GYW +T + +G W+ TGDL MD + Sbjct: 340 DVAIMDED-GTALPNGQVGEVCARGGNIMQGYWKRAEQTAATLRDG-WLRTGDLGYMDDD 397 Query: 458 GYVNIVGRIKDMVIRGGENIYPREIEEFLYRHPQVQDVQVVGVPDQKYGEELCAWIIAKP 517 G+V IV R KDM+I GGEN++ E+E +Y+HP VQ+ V+GVP +++GE + A ++ K Sbjct: 398 GFVFIVDRAKDMIISGGENVFSVEVEGAIYQHPDVQETAVIGVPSERWGEAVHAVVVPKA 457 Query: 518 GTQPTEDDIRAFCKGQIAHYKVPRYIRFVTS-FPMTVTGKIQKFKIRDE 565 G PTE I C+G IA YK+PR + + P++ GKI K +RD+ Sbjct: 458 GATPTEQAIIEHCRGVIADYKLPRSVEIRSEPLPVSGAGKILKTTLRDD 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: 697 Number of extensions: 41 Number of successful extensions: 6 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: 513 Length adjustment: 35 Effective length of query: 543 Effective length of database: 478 Effective search space: 259554 Effective search space used: 259554 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: 52 (24.6 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