Align Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized)
to candidate Dsui_2069 Dsui_2069 acyl-CoA synthetase (AMP-forming)/AMP-acid ligase II
Query= reanno::acidovorax_3H11:Ac3H11_3009 (578 letters) >FitnessBrowser__PS:Dsui_2069 Length = 529 Score = 194 bits (494), Expect = 6e-54 Identities = 168/537 (31%), Positives = 243/537 (45%), Gaps = 45/537 (8%) Query: 43 PEREALVSVHQG--------RRYTYAQLQTEAHRLASALLGMGLTPGDRVGIWSHNNAEW 94 P++ AL++ G R +TYAQL E +R A ALL +G+ GD V + +N + Sbjct: 19 PDKPALIAWEGGDHDTPAQRRVWTYAQLNAEVNRHAHALLALGVQKGDVVAAFLYNTPAF 78 Query: 95 VLMQLATAQVGLVLVNINPAYRTAEVEYALNKVGCKLLVSMARFKTSDYLGMLRELAPEW 154 V LA A+VG V IN YR A E A F D G + L E Sbjct: 79 VFSLLAAARVGAVFNPIN--YRLAAQELA--------------FILED--GQAKVLLFEK 120 Query: 155 QGQQPGHLQAAKLPQLKTVVWIDDEAGQGADEPGLLRFTELIARGNAADPRLAQVAAGLQ 214 +G + ++ A+ + T WI ++ A R +L+ A P + ++ Sbjct: 121 EGCEV--VEKAREHGVPTAHWIYADS-DAAPAFATARLDQLVRHQPATLPPVI-----VE 172 Query: 215 ATDPINIQFTSGTTGFPKGATLTHRNILNNGFFIGECMKLTPADRLCIPVPLYHCFGMVL 274 D + +TSGTTG PKG THR+ L + + + M L+ D PL H + Sbjct: 173 ENDNCILMYTSGTTGRPKGVLHTHRSKLAHNAMMHQAMTLSREDVGLAVAPLNHTAELHT 232 Query: 275 GNLACFTHGATIVYPNDGFDPLTVLQTVQDERCTGLHGVPTMFIAELDHPRFAEFNLSTL 334 L GAT V FD + + E+ T PTM L HP A +LS+L Sbjct: 233 SFLPRLQLGATQVLLRR-FDAGEAWRLTEVEKVTHFFAAPTMVTLLLHHPDVASRDLSSL 291 Query: 335 RTGIMAGSPCPTEVMKRVVEQMNLREITIAYGMTETSPVSCQSSTDTPLSKRVST-VGQV 393 R G+ +++ +++ + I YG TE P LS S + + Sbjct: 292 RLVEYGGASMAPHLIREWDKKVGAGLVQI-YGTTEMGPCMSVLYPHEQLSHAGSAGLPSL 350 Query: 394 QPHLEVKIVDPDTGAVVPIG-----QRGEFCTKGYSVMHGYWGDEAKTREAIDEGGWMHT 448 L V V D P + GE +G +M GY A+ GW HT Sbjct: 351 NHDLLVARVKADGSPSDPADLAAPDEVGEILVRGPCMMGGYLNRPEANARAL-AFGWYHT 409 Query: 449 GDLATMDAEGYVNIVGRIKDMVIRGGENIYPREIEEFLYRHPQVQDVQVVGVPDQKYGEE 508 GDL ++D EGY+ I RI M+ G EN+YPRE+E+ L HP V +V VVG PD +G+ Sbjct: 410 GDLGSLDKEGYLWIRDRIDHMINSGAENVYPREVEDALVEHPGVLEVAVVGEPDDTWGQV 469 Query: 509 LCAWIIAKPGTQPTEDDIRAFC--KGQIAHYKVPRYIRFVTSFPMTVTGKIQKFKIR 563 + A ++AKPG T++ + F ++AHYK PR F+ + P T +GKIQK +R Sbjct: 470 VAAHVVAKPGATLTQEALDHFLLEGDRLAHYKRPRRYHFIEALPKTTSGKIQKHLLR 526 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: 702 Number of extensions: 34 Number of successful extensions: 5 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: 529 Length adjustment: 36 Effective length of query: 542 Effective length of database: 493 Effective search space: 267206 Effective search space used: 267206 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