Align Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized)
to candidate 3607419 Dshi_0833 AMP-dependent synthetase and ligase (RefSeq)
Query= reanno::acidovorax_3H11:Ac3H11_3009 (578 letters) >FitnessBrowser__Dino:3607419 Length = 541 Score = 196 bits (498), Expect = 2e-54 Identities = 169/537 (31%), Positives = 241/537 (44%), Gaps = 43/537 (8%) Query: 43 PEREALVSVHQGRRYTYAQLQTEAHRLASALLGMGLTPGDRVGIWSHNNAEWVLMQLATA 102 P+REA+V + RR+TYA+ RLASAL G G+ PGD V N V Sbjct: 34 PDREAVV--YGARRFTYAEYHARVSRLASALAGAGIAPGDVVATLLPNIPAMVEAHFGVP 91 Query: 103 QVGLVLVNINPAYRTAEVEYALNKVGCKLLVSMARFKTSDYLGMLRELAPEWQGQQPGHL 162 G VL IN V Y L+ G K ++ S +L + E G P + Sbjct: 92 ACGAVLNTINIRLDVDTVAYILSHGGAKAVLV-----DSQFLPLAAEACERLDGPAPLLI 146 Query: 163 QAAKLPQLKTVVWIDDEAGQGADEPGLLRFTELIARGNAADPRLAQVAAGLQATDPINIQ 222 + A DD AG A G + + +A G+ P + + + + Sbjct: 147 EVA-----------DDAAGVHA-LGGYTEYEDFLAGGDPDFPWIMP----RDEWESLALN 190 Query: 223 FTSGTTGFPKGATLTHRN--ILNNGFFIGECMKLTPADRLCIPVPLYHCFGMVLGNLACF 280 +TSGTTG PKG HR ++ G I M L P R VPL+HC G + Sbjct: 191 YTSGTTGRPKGVVYHHRGAYLMTMGTVISWRMVLYP--RWLAIVPLFHCNGWNHSWMMPM 248 Query: 281 THGATIVYPNDGFDPLTVLQTVQDERCTGLHGVPTMFIAELDHPRFAEFNLSTLRTGIMA 340 G T+V D + + + T G P + ++ P A S A Sbjct: 249 L-GGTVVCCRD-VSAQAIYTAIAENGVTHFGGAPIVLNMIVNAPDAARRPFSHTVEVFTA 306 Query: 341 GSPCPTEVMKRVVEQMNLREITIAYGMTET--SPVSCQSSTD---TPLSKRVSTV---GQ 392 G+P P +E++ +T YG+TET C + D P ++R + G Sbjct: 307 GAP-PAAATLAAIEELGFN-VTQVYGLTETYGHVTECVWNPDWDTLPQAERAAIKARQGV 364 Query: 393 VQPHLE-VKIVDPDTGAVVPIGQR-GEFCTKGYSVMHGYWGDEAKTREAIDEGGWMHTGD 450 P +E + ++DP+ V G GE +G SVM GY+ + T EA GG+ H+GD Sbjct: 365 ALPQMEHITVMDPEMRQVPMDGATTGEVMMRGNSVMKGYYRNPDATAEAF-AGGYFHSGD 423 Query: 451 LATMDAEGYVNIVGRIKDMVIRGGENIYPREIEEFLYRHPQVQDVQVVGVPDQKYGEELC 510 +A +GY+ I R KD++I GGENI E+E L HP V VV PD +GE C Sbjct: 424 IALQHPDGYIQIADRAKDIIISGGENISSVEVEGALMHHPAVLLCAVVAKPDPTWGEVPC 483 Query: 511 AWIIAKPGTQPTEDDIRAFCKGQIAHYKVPRYIRFVTSFPMTVTGKIQKFKIRDEMK 567 A++ K G E +I AF + ++A +K P+ + F T P T TGKIQKF++R+ K Sbjct: 484 AFVELKDGKTAEEAEIIAFARERLAGFKTPKKVVF-TELPKTSTGKIQKFELRNRAK 539 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: 729 Number of extensions: 41 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: 541 Length adjustment: 36 Effective length of query: 542 Effective length of database: 505 Effective search space: 273710 Effective search space used: 273710 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