Align Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized)
to candidate WP_058931641.1 AU252_RS16370 AMP-binding protein
Query= reanno::acidovorax_3H11:Ac3H11_3009 (578 letters) >NCBI__GCF_001484605.1:WP_058931641.1 Length = 558 Score = 572 bits (1473), Expect = e-167 Identities = 296/569 (52%), Positives = 378/569 (66%), Gaps = 25/569 (4%) Query: 16 SHARGATDVPLIEQTIGAFFADMVARQPEREALVSVH-----QGRRYTYAQLQTEAHRLA 70 ++ G TDVPL+E+TIG F +VAR P +AL+ RR++Y ++ + RLA Sbjct: 3 AYTAGDTDVPLLEETIGQNFERVVARFPFHDALIEAAPVPGADARRWSYTKMNDDVDRLA 62 Query: 71 SALLGMGLTPGDRVGIWSHNNAEWVLMQLATAQVGLVLVNINPAYRTAEVEYALNKVGCK 130 ALL G+ GDRVGIWS N AEW L+Q ATA+ G +LVN+NPAYR+ E+E+ + + G + Sbjct: 63 RALLASGVAKGDRVGIWSPNCAEWTLLQYATAKAGAILVNVNPAYRSHELEFVVKQNGMR 122 Query: 131 LLVSMARFKTSDYLGMLRELAPEWQGQQPGHLQAAKLPQLKTVVWIDDEAGQGADEPGL- 189 +LV+ + SDY+GM R+ A P L+ +V++ D G D G Sbjct: 123 MLVAAPSDRNSDYVGMARQAL-------------AGCPDLRELVFLPDYGMDGLDAGGPQ 169 Query: 190 ----LRFTELIARGNAADPR-LAQVAAGLQATDPINIQFTSGTTGFPKGATLTHRNILNN 244 L + EL+ R +A L A L DPIN+Q+TSGTTGFPKGATLTH NILNN Sbjct: 170 SDAELTYAELLKRADAVGHSGLKARMAELDPHDPINLQYTSGTTGFPKGATLTHHNILNN 229 Query: 245 GFFIGECMKLTPADRLCIPVPLYHCFGMVLGNLACFTHGATIVYPNDGFDPLTVLQTVQD 304 G+ IGE + T DR+ IPVP YHCFGMV+GNLA +HGA + P GF P L+ VQD Sbjct: 230 GYSIGELLGYTEHDRVVIPVPFYHCFGMVIGNLAALSHGAATIIPGRGFTPAAALEAVQD 289 Query: 305 ERCTGLHGVPTMFIAELDHPRFAEFNLSTLRTGIMAGSPCPTEVMKRVVEQMNLREITIA 364 T L+GVPTMFIAEL P F+ ++L+TLRTG+MAGS CP +VM RV+ +M++ ++ I Sbjct: 290 FGGTSLYGVPTMFIAELALPDFSSYDLATLRTGVMAGSVCPIDVMNRVISEMHMVDVAIC 349 Query: 365 YGMTETSPVSCQSSTDTPLSKRVSTVGQVQPHLEVKIVDPDTGAVVPIGQRGEFCTKGYS 424 YGMTETSPVS + L R TVG+ P LE +IVDP TG V+ G+ GE CT+GY+ Sbjct: 350 YGMTETSPVSTMTRNGDTLQHRTETVGRTMPRLENQIVDPGTGEVLERGEIGELCTRGYA 409 Query: 425 VMHGYWGDEAKTREAIDEGGWMHTGDLATMDAEGYVNIVGRIKDMVIRGGENIYPREIEE 484 VM GYW T EAID WMHTGDLA MD EGYV I GRIKD+VIRGGENIYPREIEE Sbjct: 410 VMAGYWDQPETTAEAIDTDRWMHTGDLARMDDEGYVVIEGRIKDLVIRGGENIYPREIEE 469 Query: 485 FLYRHPQVQDVQVVGVPDQKYGEELCAWIIAKPGTQPTE-DDIRAFCKGQIAHYKVPRYI 543 FLY HP +QDVQV+GVPD +YGEEL A II G +P + + FC+G++AHYK+PRY+ Sbjct: 470 FLYSHPSIQDVQVIGVPDARYGEELMACIILTAGAEPLDAAAVAEFCRGKLAHYKIPRYV 529 Query: 544 RFVTSFPMTVTGKIQKFKIRDEMKDQLGL 572 SFPMTV+GKI+K ++R+E +LGL Sbjct: 530 DVRESFPMTVSGKIRKVEMREEAVARLGL 558 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: 874 Number of extensions: 39 Number of successful extensions: 4 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: 558 Length adjustment: 36 Effective length of query: 542 Effective length of database: 522 Effective search space: 282924 Effective search space used: 282924 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