Align Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized)
to candidate 3609616 Dshi_2999 AMP-dependent synthetase and ligase (RefSeq)
Query= reanno::acidovorax_3H11:Ac3H11_3009 (578 letters) >FitnessBrowser__Dino:3609616 Length = 506 Score = 231 bits (590), Expect = 4e-65 Identities = 165/518 (31%), Positives = 247/518 (47%), Gaps = 46/518 (8%) Query: 54 GRRYTYAQLQTEAHRLASALLGMGLTPGDRVGIWSHNNAEWVLMQLATAQVGLVLVNINP 113 G T+ A R A+ L G+GL PGDR+ + + E + + Q G+V + +N Sbjct: 26 GDTLTHGGFVELAARYAATLTGLGLAPGDRLALQVEKSPEALAVYAGCVQAGIVFLPLNT 85 Query: 114 AYRTAEVEYALNKVGCKLLVSMARFKTSDYLGMLRELAPEWQGQQPGHLQAAKLPQLKTV 173 AY AE+ Y + G KL++ R + G P +A QL T+ Sbjct: 86 AYTPAEISYFVGNSGAKLVLCDPRAEA---------------GLTPVAAEAGA--QLLTL 128 Query: 174 VWIDDEAGQGADEPGLLRFTELIARGNAADPRLAQVAAGLQATDPINIQFTSGTTGFPKG 233 AD G F + A A +A+ L A +TSGTTG KG Sbjct: 129 A---------ADGTG--SFPDAAATAPATFETVARTEDDLAA-----FLYTSGTTGRSKG 172 Query: 234 ATLTHRNILNNGFFIGECMKLTPADRLCIPVPLYHCFGMVLG-NLACFTHGATIVYPNDG 292 A L+ RN+L+N + + + T D L +P++H G+ +G N+ G+ I P Sbjct: 173 AMLSQRNLLSNAEVLVDYWRFTDKDVLLHALPIFHTHGLFVGTNITLLAGGSMIFLPK-- 230 Query: 293 FDPLTVLQTVQDERCTGLHGVPTMFIAELDHPRFAEFNLSTLRTGIMAGSPCPTEVMKRV 352 FD VL + R T + GVPT + L RF ++ +R + +P E R Sbjct: 231 FDAEAVLANLP--RATTMMGVPTFYTRLLAEDRFDRDLVAHMRLFVSGSAPLLAET-HRE 287 Query: 353 VEQMNLREITIAYGMTETSPVSCQSSTDTPL--SKRVSTVGQVQPHLEVKIVDPDTGAVV 410 E I YGMTET+ +T P ++R TVG P +E+K+ DPDTGA + Sbjct: 288 FEARTGHRILERYGMTETN-----MNTSNPYDGARRAGTVGFPLPGVELKVCDPDTGAEL 342 Query: 411 PIGQRGEFCTKGYSVMHGYWGDEAKTREAIDEGGWMHTGDLATMDAEGYVNIVGRIKDMV 470 P G+ G+ +G +V GYW KT + G+ TGDL +D +GYV IVGR KD++ Sbjct: 343 PQGEIGQIEVRGPNVFQGYWQMPEKTAAELRADGFFITGDLGLIDDQGYVQIVGRGKDLI 402 Query: 471 IRGGENIYPREIEEFLYRHPQVQDVQVVGVPDQKYGEELCAWIIAKPGTQPTEDDIRAFC 530 I GG NIYP+E+E L P V + V+G P +GE + ++ +PG + + + A Sbjct: 403 ISGGYNIYPKEVELALDEAPGVLESAVIGAPHPDFGESVVGILVPQPGARIDTEAVAARL 462 Query: 531 KGQIAHYKVPRYIRFVTSFPMTVTGKIQKFKIRDEMKD 568 GQ+A +K PR + + + P GK+QK +R++ D Sbjct: 463 AGQLARFKQPRKLVVMDALPRNTMGKVQKNVLREQFAD 500 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: 696 Number of extensions: 30 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 578 Length of database: 506 Length adjustment: 35 Effective length of query: 543 Effective length of database: 471 Effective search space: 255753 Effective search space used: 255753 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 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