Align Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized)
to candidate 5210149 Shew_2593 acyl-CoA synthetase (RefSeq)
Query= reanno::acidovorax_3H11:Ac3H11_3009 (578 letters) >FitnessBrowser__PV4:5210149 Length = 574 Score = 643 bits (1658), Expect = 0.0 Identities = 317/566 (56%), Positives = 400/566 (70%), Gaps = 7/566 (1%) Query: 6 AATNSAPLVDSHARGATDVPLIEQTIGAFFADMVARQPEREALVSVHQGRRYTYAQLQTE 65 A N PL S G T PLIEQTIG + M A P++ A+V HQG R++Y + Q+ Sbjct: 8 ATENQFPLQLSQFDGDTSTPLIEQTIGDYLDQMAASHPDQLAIVMHHQGIRWSYQEYQSH 67 Query: 66 AHRLASALLGMGLTPGDRVGIWSHNNAEWVLMQLATAQVGLVLVNINPAYRTAEVEYALN 125 LA+ LL +G+ PGDRVGIWS NN EW L Q ATA++G ++V INPAYR E++YALN Sbjct: 68 IDELAAGLLAIGIKPGDRVGIWSPNNIEWCLTQFATAKIGAIMVCINPAYRPEELQYALN 127 Query: 126 KVGCKLLVSMARFKTSDYLGMLRELAPEWQGQQPGHLQAAKLPQLKTVVWIDDEAGQGAD 185 VGC+ ++ +FK+S YL ML ELAPE + PG L++A LP L+ V+ + DEA Sbjct: 128 NVGCRAIICAEKFKSSHYLSMLYELAPELKQCLPGQLESANLPSLEFVIRMGDEAS---- 183 Query: 186 EPGLLRFTELIARGNAADPR-LAQVAAGLQATDPINIQFTSGTTGFPKGATLTHRNILNN 244 PG+L F L +D + L AA L D INIQFTSGTTG PKGATL+H NILNN Sbjct: 184 -PGMLNFNHLKRPLTESDRKALKDTAAQLSPFDAINIQFTSGTTGSPKGATLSHHNILNN 242 Query: 245 GFFIGECMKLTPADRLCIPVPLYHCFGMVLGNLACFTHGATIVYPNDGFDPLTVLQTVQD 304 G + + M+L DRLCIPVPLYHCFGMVLGNL+C + GA+ +YP+D FDPLT L+ V+ Sbjct: 243 GLLVAKAMRLGLEDRLCIPVPLYHCFGMVLGNLSCISVGASAIYPSDSFDPLTTLEVVEA 302 Query: 305 ERCTGLHGVPTMFIAELDHPRFAEFNLSTLRTGIMAGSPCPTEVMKRVVEQMNLREITIA 364 ERCT LHGVPTMFIA+L+HP F F+LS+LRTG+MAG+ CP EVM+RV + M ++E+ I Sbjct: 303 ERCTALHGVPTMFIAQLEHPEFKRFDLSSLRTGVMAGATCPEEVMRRVQDLMYMKEVLIG 362 Query: 365 YGMTETSPVSCQSSTDTPLSKRVSTVGQVQPHLEVKIVDPDTGAVVPIGQRGEFCTKGYS 424 YG TE SP++ + + L KRV+TVG+ H +VKIVD + G V+P+GQ GE C++GY Sbjct: 363 YGQTECSPINNMTEIGSSLEKRVTTVGRALAHTQVKIVD-EFGEVLPVGQPGEVCSRGYC 421 Query: 425 VMHGYWGDEAKTREAIDEGGWMHTGDLATMDAEGYVNIVGRIKDMVIRGGENIYPREIEE 484 VM YW D KT ID GW+H+GDL MD+EGYV IVGRIKDM+IRGGENIYPREIEE Sbjct: 422 VMQFYWNDAEKTAATIDSEGWLHSGDLGEMDSEGYVKIVGRIKDMIIRGGENIYPREIEE 481 Query: 485 FLYRHPQVQDVQVVGVPDQKYGEELCAWIIAKPGTQPTEDDIRAFCKGQIAHYKVPRYIR 544 LY HP VQD + GV +KYGEE+CAWI +PG TE++IR F + A++KVPRYI+ Sbjct: 482 KLYTHPDVQDAAIFGVKSEKYGEEVCAWIKVQPGASVTEEEIRHFLTEKFAYFKVPRYIK 541 Query: 545 FVTSFPMTVTGKIQKFKIRDEMKDQL 570 FV +PMTVTGKIQKFK+R+ M +L Sbjct: 542 FVEQYPMTVTGKIQKFKMREMMYQEL 567 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: 856 Number of extensions: 28 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: 574 Length adjustment: 36 Effective length of query: 542 Effective length of database: 538 Effective search space: 291596 Effective search space used: 291596 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 17 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