Align Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized)
to candidate WP_011868799.1 MMARC5_RS05260 AMP-binding protein
Query= reanno::acidovorax_3H11:Ac3H11_3009 (578 letters) >NCBI__GCF_000016125.1:WP_011868799.1 Length = 549 Score = 531 bits (1367), Expect = e-155 Identities = 271/534 (50%), Positives = 357/534 (66%), Gaps = 7/534 (1%) Query: 30 TIGAFFADMVARQPEREALVSVHQGRRYTYAQLQTEAHRLASALLGMGLTPGDRVGIWSH 89 T+G F V + PERE +V + R TY + + LA LL +G+T GD VGIW+ Sbjct: 7 TLGELFEKQVRKDPEREFMVYPDRNLRLTYKEFDDRVNMLAKGLLEIGITKGDHVGIWAK 66 Query: 90 NNAEWVLMQLATAQVGLVLVNINPAYRTAEVEYALNKVGCKLLVSMARFKTSDYLGMLRE 149 N +W+ ATA++G VLV +N AY++ E+ Y L + K L + F+ + Y+ +L E Sbjct: 67 NVPDWLTFMFATAKIGAVLVTVNTAYKSHELAYVLKQSDMKALAIIDGFRDTSYIDILYE 126 Query: 150 LAPEWQGQQPGHLQAAKLPQLKTVVWIDDEAGQGADEPGLLRFTELIARG-NAADPRLAQ 208 L PE + Q G L +++ P LK+V+++ E +G + EL+ G + D L + Sbjct: 127 LVPELKTCQRGGLNSSEFPFLKSVIYVGQEKHRG-----MYNTNELMLLGKHQPDDELLR 181 Query: 209 VAAGLQATDPINIQFTSGTTGFPKGATLTHRNILNNGFFIGECMKLTPADRLCIPVPLYH 268 + L + D IN+Q+TSGTTGFPKG LTH+NILNNGF+IG+ K T DRLCI VPL+H Sbjct: 182 IKKELDSDDVINMQYTSGTTGFPKGVMLTHKNILNNGFYIGDRQKFTKEDRLCITVPLFH 241 Query: 269 CFGMVLGNLACFTHGATIVYPNDGFDPLTVLQTVQDERCTGLHGVPTMFIAELDHPRFAE 328 CFG+VL +A THG T+V + FDPL VL VQ E+CT L+GVPTMFIAE HP F Sbjct: 242 CFGIVLAVMAILTHGGTMVMV-ELFDPLLVLAAVQKEKCTALYGVPTMFIAEYSHPMFDM 300 Query: 329 FNLSTLRTGIMAGSPCPTEVMKRVVEQMNLREITIAYGMTETSPVSCQSSTDTPLSKRVS 388 F+LS+LRTGIMAGS P EVMK+VV+ M + IT YG+TE SP Q+S D L KRV Sbjct: 301 FDLSSLRTGIMAGSTPPIEVMKKVVKDMYMTGITSVYGLTEGSPGFTQTSIDDSLEKRVQ 360 Query: 389 TVGQVQPHLEVKIVDPDTGAVVPIGQRGEFCTKGYSVMHGYWGDEAKTREAIDEGGWMHT 448 TVG+ P EVK+VDP+TG V G+ GE C KGY+VM GY+ KT+E IDE GW+H+ Sbjct: 361 TVGRKLPECEVKLVDPETGETVGPGEIGEICCKGYNVMKGYYKMPEKTKEVIDEDGWLHS 420 Query: 449 GDLATMDAEGYVNIVGRIKDMVIRGGENIYPREIEEFLYRHPQVQDVQVVGVPDQKYGEE 508 GDLAT+D EGY +IVGRIK+M+IRGGENIYPREIEEFLY P + D QV+G+PD+KYGE Sbjct: 421 GDLATVDEEGYYSIVGRIKEMIIRGGENIYPREIEEFLYTMPGINDAQVIGIPDEKYGEI 480 Query: 509 LCAWIIAKPGTQPTEDDIRAFCKGQIAHYKVPRYIRFVTSFPMTVTGKIQKFKI 562 + A++I K E+D+R + +IA YKVP+++ V FPMT +GKIQKFK+ Sbjct: 481 VGAFVIPKEDYDIREEDVRDYAIDKIARYKVPKHVFVVKEFPMTASGKIQKFKL 534 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: 801 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: 549 Length adjustment: 36 Effective length of query: 542 Effective length of database: 513 Effective search space: 278046 Effective search space used: 278046 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