Align Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized)
to candidate WP_156962857.1 N800_RS03285 AMP-binding protein
Query= reanno::acidovorax_3H11:Ac3H11_3009 (578 letters) >NCBI__GCF_000768355.1:WP_156962857.1 Length = 504 Score = 191 bits (486), Expect = 5e-53 Identities = 145/537 (27%), Positives = 239/537 (44%), Gaps = 44/537 (8%) Query: 29 QTIGAFFADMVARQPEREALVSVHQGRRYTYAQLQTEAHRLASALLGMGLTPGDRVGIWS 88 Q++ + A P++ A+V R+ +Y A A L GL GDRV I Sbjct: 2 QSLASTVAMWAHSTPDKPAIVDAT--RQVSYRDFMAHAAGFAGQLARHGLRHGDRVAIVL 59 Query: 89 HNNAEWVLMQLATAQVGLVLVNINPAYRTAEVEYALNKVGCKLLVSMARFKTSDYLGMLR 148 N E + T G V V +N R ++ L G + +V +D + Sbjct: 60 PNRIEAAVACYGTWLAGGVAVPLNAQARARDIAPWLVHCGARFIVHEPG--NNDVASAME 117 Query: 149 ELAPEWQGQQPGHLQAAKLPQLKTVVWIDDEAGQGADEPGLLRFTELIARGNAADPRLAQ 208 LA P V D + PG L AR D LA Sbjct: 118 TLAS---------------PPFPFTVPEDQPICPPSPLPG---DALLSARAPGPDGDLAL 159 Query: 209 VAAGLQATDPINIQFTSGTTGFPKGATLTHRNILNNGFFIGECMKLTPADRLCIPVPLYH 268 + +TSGTTG PKG L+H N++ N + + L P+D + +P Y+ Sbjct: 160 IL------------YTSGTTGAPKGVMLSHANLMANATAVAAYLALDPSDSVLCVLPFYY 207 Query: 269 CFGMVLGNLACFTHGATIVYPNDGFDPLTVLQTVQDERCTGLHGVPTMFIAELDHPRFAE 328 +G + + + GAT+ P +++ + R TG GVP+ F L H Sbjct: 208 AYGASVVHTHLIS-GATLHLAGSLVFPNLIVEALATRRITGFSGVPSTFALLLSHGALDR 266 Query: 329 FNLSTLRTGIMAGSPCPTEVMKRVVEQMNLREITIAYGMTETSPVSCQSSTDTP---LSK 385 +LSTLR AG P + ++ + ++ + YG TE + T P L Sbjct: 267 HDLSTLRYVTQAGGPMSPSLTAQLRAALPGPQLFVMYGQTEAT----SRLTFLPPGQLDA 322 Query: 386 RVSTVGQVQPHLEVKIVDPDTGAVVPIGQRGEFCTKGYSVMHGYWGDEAKTREAIDEGGW 445 + +VG + ++IV + G G+ G+ +G +VM GYW + TR + +G W Sbjct: 323 KAGSVGIPVDGVSIRIVREE-GVPAAAGETGDVWVRGPNVMLGYWRNAEATRATLKDG-W 380 Query: 446 MHTGDLATMDAEGYVNIVGRIKDMVIRGGENIYPREIEEFLYRHPQVQDVQVVGVPDQKY 505 + TGD+ +D +GY+ +VGR DM+ G ++P ++E+ + V +V VVGV D Sbjct: 381 LKTGDMGHLDDDGYLYLVGRRSDMIKTGAHRVHPVDVEQAIAEMAGVIEVAVVGVDDDVL 440 Query: 506 GEELCAWIIAKPGTQPTEDDIRAFCKGQIAHYKVPRYIRFVTSFPMTVTGKIQKFKI 562 G+ L A+++ + T D+I+A C+ + YK+P+++ FV++ P T +GK+Q+ ++ Sbjct: 441 GQVLKAFVVVERVTTRLTDEIKAHCRAHLPPYKIPKHVEFVSTLPRTASGKVQRTQL 497 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: 683 Number of extensions: 23 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: 504 Length adjustment: 35 Effective length of query: 543 Effective length of database: 469 Effective search space: 254667 Effective search space used: 254667 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: 52 (24.6 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