Align Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized)
to candidate WP_086511719.1 BZY95_RS20375 cyclohexanecarboxylate-CoA ligase
Query= reanno::acidovorax_3H11:Ac3H11_3009 (578 letters) >NCBI__GCF_002151265.1:WP_086511719.1 Length = 548 Score = 222 bits (565), Expect = 3e-62 Identities = 167/539 (30%), Positives = 264/539 (48%), Gaps = 32/539 (5%) Query: 34 FFADMVARQPEREALVSVHQGR----RYTYAQLQTEAHRLASALLGMGLTPGDRVGIWSH 89 + + VA R A+V+ +YA+L + R+A+ L G+G+ GD V Sbjct: 29 YLDEAVASAAGRPAIVTYRMAEGSHDSLSYAELNEKVTRMAAGLAGLGVAKGDVVSCQLP 88 Query: 90 NNAEWVLMQLATAQVGLVLVNINPAYRTAEVEYALNKVGCKLLVSMARFKTSDYLGMLRE 149 N + + LA ++G VL + P +R E+ + L + K+ V F+ D+ M R Sbjct: 89 NWWQMTALHLACIRIGAVLNPLMPIFREHELRFMLAQAESKVFVVPGVFRGFDHAAMARG 148 Query: 150 LAPEWQGQQPGHLQAAKLPQLKTVVWIDDEAGQGADEPGLLRFTELIARGNAADPRLAQV 209 L A+L L+ V+ + G+G D + R + Sbjct: 149 LK-------------AELTALEQVLVV---GGEGVDSFETVLLERAWERETDTAALFRER 192 Query: 210 AAGLQATDPINIQFTSGTTGFPKGATLTHRNILNNGFFIGECMKLTPADRLCIPVPLYHC 269 G D + + +TSGTTG PKG T ++++ + L D + +P PL H Sbjct: 193 RPG--GDDVVQLLYTSGTTGKPKGVMHTSNTLMSHIRPFATRLGLGNDDTVFMPSPLAHQ 250 Query: 270 FGMVLGNLACFTHGATIVYPNDGFDPLTVLQTVQDERCTGLHGVPTMFIAELDHPRFAEF 329 G + G + AT V D + P + ++ ER + + G T F+A++ A Sbjct: 251 LGFLYGLMLPVYLQATAVL-QDTWKPAEAVDIIRAERPSLMLG-STPFLADIAEQAEAHG 308 Query: 330 -NLSTLRTGIMAGSPCPTEVMKRVVEQMNLREITIAYGMTETSPVSCQSSTDTPLSKRVS 388 +L +L+ + AG+P P+ ++++ + R I+ A+GMTE V+ D P S+ V Sbjct: 309 PDLQSLKLFMCAGAPIPSPLVEKAARNLPTRIIS-AWGMTENGAVTTTRPGDAP-SRAVH 366 Query: 389 TVGQVQPHLEVKIVDPDTGAVVPIGQRGEFCTKGYSVMHGYWGDEAKTREAIDEGGWMHT 448 T G P +E+K+ D + G +P GQ G +G S+ GY+ + +D GW T Sbjct: 367 TDGLPLPFMELKVTDLE-GNTLPPGQEGPLYVRGASLFVGYF--KQPELYGVDAEGWFPT 423 Query: 449 GDLATMDAEGYVNIVGRIKDMVIRGGENIYPREIEEFLYRHPQVQDVQVVGVPDQKYGEE 508 GDLA +D +GYV I GR KD+VIRGGENI +IE LY+HP +Q V +VG PD++ GE Sbjct: 424 GDLARLDEQGYVRITGRSKDVVIRGGENIPIVDIENALYQHPAIQAVALVGRPDERLGER 483 Query: 509 LCAWIIAKPGTQP-TEDDIRAF-CKGQIAHYKVPRYIRFVTSFPMTVTGKIQKFKIRDE 565 LCA++ K G + T DI AF + Q+ P ++ + P T +GKIQKFK+R++ Sbjct: 484 LCAYVTLKEGVESLTLTDITAFLSERQVTRQYQPEFLVVLDELPRTPSGKIQKFKLREQ 542 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: 662 Number of extensions: 34 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: 548 Length adjustment: 36 Effective length of query: 542 Effective length of database: 512 Effective search space: 277504 Effective search space used: 277504 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