Align Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized)
to candidate WP_011765727.1 AZO_RS10080 2-aminobenzoate-CoA ligase
Query= reanno::acidovorax_3H11:Ac3H11_3009 (578 letters) >NCBI__GCF_000061505.1:WP_011765727.1 Length = 535 Score = 170 bits (431), Expect = 1e-46 Identities = 161/530 (30%), Positives = 241/530 (45%), Gaps = 61/530 (11%) Query: 44 EREALVSVHQGRRYTYAQLQTEAHRLASALL-GMGLTPGDRVGIWSHNNAEWVLMQLATA 102 ER A++ + +TY QL + +RLA L+ MGL PG+RV + N LA Sbjct: 54 ERPAIIG--KNIHWTYRQLHQQVNRLAHVLVEDMGLVPGNRVLLRGANTPWLAACWLAVW 111 Query: 103 QVGLVLVNINPAYRTAEVEYALNKVGCKLLVSMARFKTSDYLGMLRELAPEWQGQQPGHL 162 + G V V P R E++ L +S A S LA E + + Sbjct: 112 KAGGVAVGTMPLLRAKELKEILRLAE----ISHALCDAS--------LAEELEYAR---- 155 Query: 163 QAAKLPQLKTVVWIDDEAGQGADEPGLLRFTELIARGNAADPRLAQVAAGLQATDPINIQ 222 A+ P L+ V+ G+G EL AR + + VA ATDP I Sbjct: 156 --AESPTLRHVMLF----GEGG---------ELAARMDGKPDQFDTVATA--ATDPALIG 198 Query: 223 FTSGTTGFPKGATLTHRNILNN-GFFIGECMKLTPADRLCIPVPLYHCFGMVLGNLACF- 280 FTSGTTG PKG HR+++ F C+K T D PL FG LG L CF Sbjct: 199 FTSGTTGIPKGTIHFHRDVMAMCEVFPRHCLKPTQDDVFIGTPPLAFTFG--LGGLLCFP 256 Query: 281 --THGATIVYPNDGFDPLTVLQTVQDERCTGLHGVPTMF--IAELDHPRFAEFNLSTLRT 336 +T++ +PL +Q +QD + T PT + +A L ++++++L+ Sbjct: 257 LWARASTVLLEKLAPEPL--MQAIQDHQATVCFTSPTAYRQMAGL----VGKYDIASLKK 310 Query: 337 GIMAGSPCPTEVMKRVVEQMNLREITIAYGMTETSPVSCQSSTDTPLSKRVSTVGQVQPH 396 + AG PT+ + E + +I G TE + S D R +G++ P Sbjct: 311 CVSAGEALPTDTRDKWREASGI-QIHDGIGGTEMIHIYIASGPD---DYRPGALGKLLPG 366 Query: 397 LEVKIVDPDTGAVVPIGQRGEFCTKGYSVMHGYWGDEAKTREAIDEGGWMHTGDLATMDA 456 IVD D + P G+ G+ KG + Y DE + + GW GD MDA Sbjct: 367 YTGMIVDDDMNPLPP-GEVGKLAIKGPTGCR-YLADERQQNYV--KNGWNLPGDAFHMDA 422 Query: 457 EGYVNIVGRIKDMVIRGGENIYPREIEEFLYRHPQVQDVQVVGVPDQKYGEELCAWIIAK 516 +GY R+ D+++ G N+ E+E L HP V + V+GVPD G+ + A+++ K Sbjct: 423 DGYFYYHARVDDIIVTSGYNVSSPEVEWALLAHPAVAECGVIGVPDPDRGQIIKAFVVLK 482 Query: 517 PGTQPTE---DDIRAFCKGQIAHYKVPRYIRFVTSFPMTVTGKIQKFKIR 563 PG E ++ F K +A YK PR I +V + P T TGK+Q+F+++ Sbjct: 483 PGQVGDEAMTKTLQDFVKQTVAPYKYPRAIAYVDTLPRTETGKLQRFRLK 532 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: 772 Number of extensions: 37 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: 535 Length adjustment: 36 Effective length of query: 542 Effective length of database: 499 Effective search space: 270458 Effective search space used: 270458 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 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