Align Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized)
to candidate WP_058929219.1 AU252_RS01520 AMP-binding protein
Query= reanno::acidovorax_3H11:Ac3H11_3009 (578 letters) >NCBI__GCF_001484605.1:WP_058929219.1 Length = 537 Score = 618 bits (1593), Expect = 0.0 Identities = 310/559 (55%), Positives = 389/559 (69%), Gaps = 26/559 (4%) Query: 16 SHARGATDVPLIEQTIGAFFADMVARQPEREALVSVHQGRRYTYAQLQTEAHRLASALLG 75 S+ +GA PL+ +TIG F VA+ EALV V GRR+T+A+L + + LA L+ Sbjct: 3 SYEKGAVVPPLLSETIGQSFERTVAQYSGNEALVEVASGRRWTWAELDRDVNDLAKGLVA 62 Query: 76 MGLTPGDRVGIWSHNNAEWVLMQLATAQVGLVLVNINPAYRTAEVEYALNKVGCKLLVSM 135 GL GDR+GIW+ N AEW L+Q ATA++G++LVN+NPAYRT E YA+N G ++L++ Sbjct: 63 AGLEKGDRLGIWAPNCAEWTLVQYATAKIGVILVNVNPAYRTHEFSYAVNHSGLRMLITA 122 Query: 136 ARFKTSDYLGMLRELAPEWQGQQPGHLQAAKLPQLKTVVWIDDEAGQGADEPGLLRFTEL 195 + FK+SDY M+ + A E P L+ V +ID + + L Sbjct: 123 SSFKSSDYRAMIEQAADE-------------TPSLERVAYIDTDD-----------WAHL 158 Query: 196 IARGNAADPRL-AQVAAGLQATDPINIQFTSGTTGFPKGATLTHRNILNNGFFIGECMKL 254 I G + + AQ A DPINIQ+TSGTTG+PKGATL+HRNILNNG+F E ++L Sbjct: 159 IDSGRTVENHVVAQRLADTMPDDPINIQYTSGTTGYPKGATLSHRNILNNGYFTTELIRL 218 Query: 255 TPADRLCIPVPLYHCFGMVLGNLACFTHGATIVYPNDGFDPLTVLQTVQDERCTGLHGVP 314 P DRLCIPVP YHCFGMV+G+L C +HG TIV P+ GFD L+ + DE+CT ++GVP Sbjct: 219 GPDDRLCIPVPFYHCFGMVMGSLGCVSHGTTIVIPSPGFDAEATLRAITDEKCTAVYGVP 278 Query: 315 TMFIAELDHPRFAEFNLSTLRTGIMAGSPCPTEVMKRVVEQMNLREITIAYGMTETSPVS 374 TMFIA +HP F +L++LRTGIMAGS CP +VM+R +E MNL EI+IAYGMTETSPVS Sbjct: 279 TMFIAMQNHPTFGSHDLTSLRTGIMAGSVCPVDVMQRCIEDMNLTEISIAYGMTETSPVS 338 Query: 375 CQSSTDTPLSKRVSTVGQVQPHLEVKIVDPDTGAVVPIGQRGEFCTKGYSVMHGYWGDEA 434 CQ+ + + +R +T+G+V PHLEVKIVDP TG V Q GEFCT+GYSVM GYW DE Sbjct: 339 CQTRANDDVERRTATIGRVHPHLEVKIVDPSTGDTVERDQTGEFCTRGYSVMLGYWNDEE 398 Query: 435 KTREAIDEGGWMHTGDLATMDAEGYVNIVGRIKDMVIRGGENIYPREIEEFLYRHPQVQD 494 KTREAID GWMHTGDL M +GY IVGRIKDMVIRGGENIYPREIEE+LY HP ++D Sbjct: 399 KTREAIDADGWMHTGDLGVMREDGYCTIVGRIKDMVIRGGENIYPREIEEYLYSHPDIED 458 Query: 495 VQVVGVPDQKYGEELCAWIIAKPGTQPTE-DDIRAFCKGQIAHYKVPRYIRFVTSFPMTV 553 VQV+GVPD KYGEELCA I K GT+P + IRAF G+IA YK+P Y+ V FP TV Sbjct: 459 VQVIGVPDAKYGEELCACIKMKAGTKPLDAPAIRAFINGKIARYKIPVYVIVVDEFPTTV 518 Query: 554 TGKIQKFKIRDEMKDQLGL 572 TGKI+K ++R+E LGL Sbjct: 519 TGKIRKNQLREEASTVLGL 537 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: 843 Number of extensions: 36 Number of successful extensions: 3 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: 537 Length adjustment: 36 Effective length of query: 542 Effective length of database: 501 Effective search space: 271542 Effective search space used: 271542 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 Apr 09 2024. 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