Align Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized)
to candidate WP_010876295.1 MTH_RS03060 AMP-binding protein
Query= reanno::acidovorax_3H11:Ac3H11_3009 (578 letters) >NCBI__GCF_000008645.1:WP_010876295.1 Length = 548 Score = 572 bits (1473), Expect = e-167 Identities = 286/549 (52%), Positives = 380/549 (69%), Gaps = 7/549 (1%) Query: 28 EQTIGAFFADMVARQPEREALVSVHQGRRYTYAQLQTEAHRLASALLGMGLTPGDRVGIW 87 E TIG FF V R ++E +V + R+TY + + LA LL +G+ GD VGIW Sbjct: 5 EDTIGEFFEKQVERYADKEFIVYPDRDLRFTYREFNERVNLLAKGLLSIGIGKGDHVGIW 64 Query: 88 SHNNAEWVLMQLATAQVGLVLVNINPAYRTAEVEYALNKVGCKLLVSMARFKTSDYLGML 147 + N +W+ ATA++G VLV +N AY++ E+EY + + K L + F+ DY+ L Sbjct: 65 ATNVPDWLTFLFATAKIGAVLVTVNTAYKSHELEYVMKQSDMKALAIIDGFRDVDYVQTL 124 Query: 148 RELAPEWQGQQPGHLQAAKLPQLKTVVWIDDEAGQGADEPGLLRFTELIARG-NAADPRL 206 EL PE + + GHL++ + P+L++V++I + +G + EL+ G + D L Sbjct: 125 YELVPELKTHERGHLRSERFPELRSVIYIGAQKHRG-----MYNTNELMLLGKHVPDTEL 179 Query: 207 AQVAAGLQATDPINIQFTSGTTGFPKGATLTHRNILNNGFFIGECMKLTPADRLCIPVPL 266 V + L+ TD IN+Q+TSGTTGFPKG LTHRNILNNG++IGE + T DRLC+PVPL Sbjct: 180 RTVMSTLKNTDVINMQYTSGTTGFPKGVMLTHRNILNNGYYIGERQRFTEEDRLCLPVPL 239 Query: 267 YHCFGMVLGNLACFTHGATIVYPNDGFDPLTVLQTVQDERCTGLHGVPTMFIAELDHPRF 326 +HCFG+VLG LA THG T+V + FDPL VL V+ ERCT L+GVPTMFIAE HP F Sbjct: 240 FHCFGIVLGVLALLTHGGTLVMI-ELFDPLLVLAAVEKERCTALYGVPTMFIAEFTHPMF 298 Query: 327 AEFNLSTLRTGIMAGSPCPTEVMKRVVEQMNLREITIAYGMTETSPVSCQSSTDTPLSKR 386 F+LS+LRTGIMAGSPCP E MKRV+ MN++E+TIAYG+TE SPV Q+S D P+ KR Sbjct: 299 DMFDLSSLRTGIMAGSPCPIEAMKRVMNDMNMKEVTIAYGLTEASPVFTQTSVDDPIEKR 358 Query: 387 VSTVGQVQPHLEVKIVDPDTGAVVPIGQRGEFCTKGYSVMHGYWGDEAKTREAIDEGGWM 446 V TVG PH+EVKIVDP+TG + G+ GE C +GY+VM GY+ T EAIDE GW+ Sbjct: 359 VETVGTPLPHIEVKIVDPETGEELGPGEPGEICCRGYNVMKGYYKMPEMTAEAIDEDGWL 418 Query: 447 HTGDLATMDAEGYVNIVGRIKDMVIRGGENIYPREIEEFLYRHPQVQDVQVVGVPDQKYG 506 H+GDLA MD +GY +IVGRIKDM+IRGGENIYPREIEEFL+ P V+DVQVVG+PD+KYG Sbjct: 419 HSGDLAVMDEDGYYSIVGRIKDMIIRGGENIYPREIEEFLHTMPGVKDVQVVGIPDEKYG 478 Query: 507 EELCAWIIAKPGTQPTEDDIRAFCKGQIAHYKVPRYIRFVTSFPMTVTGKIQKFKIRDEM 566 E + A+II + G E+D+R + +IA YKVP+++ FV FP+T +GK+QKFK+R+ Sbjct: 479 EIVGAFIIREDGADILEEDVRDYAIQRIARYKVPKHVFFVDEFPLTASGKVQKFKLREMA 538 Query: 567 KDQLGLEEQ 575 + L +EQ Sbjct: 539 VELLKKKEQ 547 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: 836 Number of extensions: 30 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: 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