Align Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized)
to candidate WP_048080214.1 EI99_RS01785 AMP-binding protein
Query= reanno::acidovorax_3H11:Ac3H11_3009 (578 letters) >NCBI__GCF_000746075.1:WP_048080214.1 Length = 553 Score = 539 bits (1388), Expect = e-157 Identities = 271/544 (49%), Positives = 362/544 (66%), Gaps = 7/544 (1%) Query: 28 EQTIGAFFADMVARQPEREALVSVHQGRRYTYAQLQTEAHRLASALLGMGLTPGDRVGIW 87 E TIG FF + P+RE +V + R+TY Q ++LA LL +G+T GD VGIW Sbjct: 5 EDTIGDFFEKQAEKDPDREFMVYPDRDLRFTYKQFDERVNKLAKGLLSIGVTKGDNVGIW 64 Query: 88 SHNNAEWVLMQLATAQVGLVLVNINPAYRTAEVEYALNKVGCKLLVSMARFKTSDYLGML 147 + N +W+ A ++G VLV +N AY++ E++Y L + K L F+ YL +L Sbjct: 65 ALNVPDWITFLFACGKIGAVLVTVNTAYKSHELDYVLKQSDMKALAITDGFRDVSYLKVL 124 Query: 148 RELAPEWQGQQPGHLQAAKLPQLKTVVWIDDEAGQGADEPGLLRFTELIARG-NAADPRL 206 EL PE + + G+L++ + P LK+V++I E +G L EL+ G + D +L Sbjct: 125 YELVPELKTSKRGNLESKEYPCLKSVIFIGQEKHRG-----LYNTRELLLLGKHTDDSKL 179 Query: 207 AQVAAGLQATDPINIQFTSGTTGFPKGATLTHRNILNNGFFIGECMKLTPADRLCIPVPL 266 + + D + +Q+TSGTTGFPKG LTH+NI+NNG++IGE +K T DRLC+ VP+ Sbjct: 180 LEAKKTFDSDDVVCMQYTSGTTGFPKGVMLTHKNIINNGYYIGENLKYTAEDRLCLTVPM 239 Query: 267 YHCFGMVLGNLACFTHGATIVYPNDGFDPLTVLQTVQDERCTGLHGVPTMFIAELDHPRF 326 +HCFG+ LG +A +THG T+V FDPL VL VQ E+CT L+GVPTMFIAE HP F Sbjct: 240 FHCFGVTLGLMAMYTHGGTLVMLEQ-FDPLMVLAAVQKEKCTALYGVPTMFIAEYSHPMF 298 Query: 327 AEFNLSTLRTGIMAGSPCPTEVMKRVVEQMNLREITIAYGMTETSPVSCQSSTDTPLSKR 386 F+LS+LRTGIMAGS CP E MK+VV MN+ EIT YG+TE SP Q+S D PL R Sbjct: 299 EMFDLSSLRTGIMAGSTCPIEAMKKVVNDMNMTEITSVYGLTEGSPGFTQTSVDDPLELR 358 Query: 387 VSTVGQVQPHLEVKIVDPDTGAVVPIGQRGEFCTKGYSVMHGYWGDEAKTREAIDEGGWM 446 V TVG+ P+ E+K+VDP+TG V G+ GE C++GY+VM GY+ KT EAIDE GW+ Sbjct: 359 VETVGRKLPNCEIKVVDPETGKTVGPGEVGEICSRGYNVMKGYYKMPDKTAEAIDEDGWL 418 Query: 447 HTGDLATMDAEGYVNIVGRIKDMVIRGGENIYPREIEEFLYRHPQVQDVQVVGVPDQKYG 506 H+GDL T D GY +VGRIKDM+IRGGENIYPREIEEF Y P ++DVQVVG+PD KYG Sbjct: 419 HSGDLVTYDENGYYTVVGRIKDMIIRGGENIYPREIEEFYYTMPGIKDVQVVGIPDDKYG 478 Query: 507 EELCAWIIAKPGTQPTEDDIRAFCKGQIAHYKVPRYIRFVTSFPMTVTGKIQKFKIRDEM 566 E + A+II + G +E+D+R F +IA YKVP++ FV FP+T +GKIQKF +RD+ Sbjct: 479 EIVGAFIILEEGADISEEDVRDFGLERIARYKVPKHAFFVEEFPLTASGKIQKFIMRDQA 538 Query: 567 KDQL 570 + L Sbjct: 539 VELL 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: 833 Number of extensions: 35 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: 553 Length adjustment: 36 Effective length of query: 542 Effective length of database: 517 Effective search space: 280214 Effective search space used: 280214 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