Align Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized)
to candidate WP_011385011.1 AMB_RS13240 acyl-CoA synthetase
Query= reanno::acidovorax_3H11:Ac3H11_3009 (578 letters) >NCBI__GCF_000009985.1:WP_011385011.1 Length = 541 Score = 196 bits (498), Expect = 2e-54 Identities = 163/546 (29%), Positives = 242/546 (44%), Gaps = 41/546 (7%) Query: 34 FFADMVARQPEREALVSVHQGRRYTYAQLQTEAHRLASALLGMGLTPGDRVGIWSHNNAE 93 F A P+R A++ H R T+A+ +LA+AL G+ GD V + N E Sbjct: 25 FLERAAAVWPDRLAVI--HGPVRRTWAETFVRCRKLAAALTARGIGLGDTVALMGANTPE 82 Query: 94 WVLMQLATAQVGLVLVNINPAYRTAEVEYALNKVGCKLLVSMARFKTSDYLGMLRELAPE 153 G VL IN + + LN K+L++ RE +P Sbjct: 83 TFEAHFGVPLTGAVLNAINTRLDADAITFILNHAEAKILITD------------REFSPV 130 Query: 154 WQGQQPGHLQAAKLPQLKTVVWIDDEAGQGADEPGLLRFTELIARGNAADPRLAQVAAGL 213 + A L + V+ IDD +G + G + +L+ + P Sbjct: 131 VKKA------LAALGRTIPVIDIDDPQFKGGELLGEKNYEQLLDEAASEAPWTLPT---- 180 Query: 214 QATDPINIQFTSGTTGFPKGATLTHRNILNNGFFIGECMKLTPADRLCIPVPLYHCFGMV 273 I + +TSGTTG PKG HR N ++ +P++HC G Sbjct: 181 DEWQAIALNYTSGTTGNPKGVVYHHRGAHLNAVSNALSWQMGDNTVYLWTLPMFHCNGWC 240 Query: 274 LGNLACFTHGATIVYPNDGFDPLTVLQTVQDERCTGLHGVPTMFIAELDHPRFAEFNLST 333 G ++ + D ++ ++DE+ T G P + + P + +S Sbjct: 241 FPWTMAVVAGTSVCLRHVRVD--AIMGAIRDEKVTNFCGAPIVLNMINNAPAALKEGISH 298 Query: 334 LRTGIMAGSPCPTEVMKRVVEQMNLREITIAYGMTETSPVSCQSST-DTPLSKRVSTVGQ 392 + AG+ P V+ + E+M E+T YG+TE + Q D + Q Sbjct: 299 AVKVMTAGAAPPAPVIAGM-ERMGW-EVTHVYGLTECYGPTVQCVWHDKWNGLSIDEKAQ 356 Query: 393 VQ-------PHLE-VKIVDPDTGAVVPIGQR--GEFCTKGYSVMHGYWGDEAKTREAIDE 442 ++ P LE + I DP + P + GE +G +VM GY +E T EA Sbjct: 357 IKARQGVRGPMLEGLMIADPISLEPAPKDGKTVGEIFMRGNNVMKGYLKNEKATEEAF-A 415 Query: 443 GGWMHTGDLATMDAEGYVNIVGRIKDMVIRGGENIYPREIEEFLYRHPQVQDVQVVGVPD 502 GGW HTGDLA +GY+ I R KD++I GGENI E+E+ LY H V + VV PD Sbjct: 416 GGWFHTGDLAVCHPDGYIEIKDRSKDIIISGGENISSIEVEDILYAHLAVLEAAVVARPD 475 Query: 503 QKYGEELCAWIIAKPGTQPTEDDIRAFCKGQIAHYKVPRYIRFVTSFPMTVTGKIQKFKI 562 +K+GE CA+I K G + TE DI FC+ ++AH+KVPR I F P T TGK+QKF + Sbjct: 476 EKWGETPCAFIALKDGAEATEADIITFCRERMAHFKVPRTIVF-GGLPKTSTGKVQKFML 534 Query: 563 RDEMKD 568 R + K+ Sbjct: 535 RQKAKE 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: 650 Number of extensions: 27 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: 578 Length of database: 541 Length adjustment: 36 Effective length of query: 542 Effective length of database: 505 Effective search space: 273710 Effective search space used: 273710 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