Align Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized)
to candidate WP_058857116.1 AS188_RS00055 long-chain fatty acid--CoA ligase
Query= reanno::acidovorax_3H11:Ac3H11_3009 (578 letters) >NCBI__GCF_001482365.1:WP_058857116.1 Length = 568 Score = 237 bits (604), Expect = 1e-66 Identities = 179/564 (31%), Positives = 274/564 (48%), Gaps = 35/564 (6%) Query: 23 DVPLIEQTIGAFFADMVARQPEREALVSVHQGRRYTYAQLQTEAHRLASALLGMGLTPGD 82 D+ L E ++ VAR R AL G R +YA+L + R A L +G+ GD Sbjct: 26 DLELPETSLVHMLERSVARHGHRPALEFF--GARTSYARLGEQVERAAEGLRRLGVAAGD 83 Query: 83 RVGIWSHNNAEWVLMQLATAQVGLVLVNINPAYRTAEVEYALNKVGCKLLVSMARFKTSD 142 RV I N + ++ A ++G V+V NP Y E+ + G ++ + R +D Sbjct: 84 RVAIVLPNCPQHIVAFYAVLRLGAVVVEHNPLYTAPELRHQFEDHGARVAIVWDR--AAD 141 Query: 143 YLGMLRE-------LAPEWQGQQPGHLQAA---KLPQLKTVVWIDDEAGQGADEPGLLRF 192 + L E +A + P +AA LP + A PG + + Sbjct: 142 RIRSLPEDLRLDAVVAVDVTQAMPRRTRAALRLPLPAARA-----SRAQLTGPAPGTIPW 196 Query: 193 TELIARGNAADPRLAQVAAGLQATDPINIQFTSGTTGFPKGATLTHRNILNNGFFIGECM 252 L+A A+P LA A D +Q+TSGTTG PKGA LTHRN+ +N +G+ Sbjct: 197 RRLVA----AEP-LAADHPRPTAHDLALLQYTSGTTGLPKGAMLTHRNLESNAL-MGQHW 250 Query: 253 KLTPADRLCIPV-PLYHCFGMVLGNLACFTHGATIV-YPNDGFDPLTVLQTVQDERCTGL 310 + D + V PL+H FG+ LG + GA +V +P D VL+ ++ R T L Sbjct: 251 LHSGEDEVVHGVLPLFHAFGLTLGVTFAMSLGARLVLFPTVRAD--LVLKALRRSRPTVL 308 Query: 311 HGVPTMFIAELDHPRFAEFNLSTLRTGIMAGSPCPTEVMKRVVEQMNLREITIAYGMTET 370 VP ++ LD +L + + P +++R E+ + YG+TE Sbjct: 309 PAVPPVYEKLLDAAEERGADLRGIAVAVSGAMTLPVPLVERW-ERATGGMLVEGYGLTEC 367 Query: 371 SP-VSCQSSTDTPLSKRVSTVGQVQPHLEVKIVDPDTGAVVPIGQRGEFCTKGYSVMHGY 429 SP V+C D S+R ++G P E+++VDP+T VP G GE +G V GY Sbjct: 368 SPLVACNPLND---SRRAGSIGVPFPSTEIRLVDPETLEDVPRGHEGELWVRGPQVFRGY 424 Query: 430 WGDEAKTREAIDEGGWMHTGDLATMDAEGYVNIVGRIKDMVIRGGENIYPREIEEFLYRH 489 W +T + E GW+ TGD+ T+D +G++ +V RIK+++I GG N+ P E+E L H Sbjct: 425 WKRPEETARVLVEDGWLRTGDVVTVDDDGFLRVVDRIKEVIITGGFNVAPTEVETALKLH 484 Query: 490 PQVQDVQVVGVPDQKYGEELCAWIIAKPGTQPTEDDIRAFCKGQIAHYKVPRYIRFVTSF 549 V D VVG+ D + GE + A ++ PG E +R C G++ YKVPR I V Sbjct: 485 DDVADAAVVGLDDGRGGEAVVAAVVLAPGAVLDEQALREHCYGKVTRYKVPRRIVAVEDL 544 Query: 550 PMTVTGKIQKFKIRDEMKDQLGLE 573 P T+ GK + ++R + + LG++ Sbjct: 545 PRTMLGKTLRREVRARL-EALGVQ 567 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: 730 Number of extensions: 34 Number of successful extensions: 4 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: 568 Length adjustment: 36 Effective length of query: 542 Effective length of database: 532 Effective search space: 288344 Effective search space used: 288344 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