Align Aconitate-delta-isomerase 1; Itaconic acid/2-hydroxyparaconate biosynthesis cluster protein ADI1; EC 5.-.-.- (characterized)
to candidate PP_2513 PP_2513 4-oxalomesaconate tautomerase
Query= SwissProt::A0A0U2X0E4 (443 letters) >FitnessBrowser__Putida:PP_2513 Length = 361 Score = 244 bits (624), Expect = 2e-69 Identities = 146/326 (44%), Positives = 194/326 (59%), Gaps = 10/326 (3%) Query: 5 IDTTIYRAGTSRGLYFLASDLPAEPSERDAALISIMGSGHPLQIDGMGGGNSLTSKVAIV 64 I + R GTS+G YFL DLPA RD L+++MGS QIDG+GG +SLTSKVAI+ Sbjct: 6 IPCLLMRGGTSKGAYFLHDDLPAPGPLRDRVLLAVMGSPDARQIDGIGGADSLTSKVAII 65 Query: 65 SASTQRSEFDVDYLFCQVGITERFVDTAPNCGNLMSGVAAFAIERGLVQPHPSDTTCLVR 124 AS QR + DVDYLF QV + E VD NCGN+++GV FA+ERGLV + T VR Sbjct: 66 RAS-QRDDADVDYLFAQVVVDEARVDYGQNCGNILAGVGPFALERGLVAASGASTP--VR 122 Query: 125 IFNLNSRQASELVIPVYNGRVHY--DDIDDMHMQRPSARVGLRFLDTVGSCTGKLLPTGN 182 IF N+ Q + +P +G+V Y D D R +A V + F D G+ G LLPTGN Sbjct: 123 IFMENTGQIAVAQVPTADGQVEYAGDTRIDGVPGRAAALV-VTFADVAGASCGALLPTGN 181 Query: 183 ASDWIDGLKVSIIDSAVPVVFIRQHDVGITGSEAPATLNANTALLDRLERVRLEAGRRMG 242 + D ++G++V+ ID+ +PVV + D+G+TG E TL A++AL RLE +RL+ G RM Sbjct: 182 SRDCVEGVEVTCIDNGMPVVLLCAEDLGVTGYEPCETLEADSALKTRLEAIRLQLGPRMN 241 Query: 243 LGDVSGSVVPKLSLIGPGTETTTFTARYFTPKACHNAHAVTGAICTAGAAYIDGSVVCEI 302 LGDVS VPK+ L+ T R F P CH + V GA+ A A I+GSV Sbjct: 242 LGDVSQRNVPKMCLLSAPRNGGTVNTRSFIPHRCHASIGVFGAVSVATACLIEGSVA--- 298 Query: 303 LSSRASACSASQRRISIEHPSGVLEV 328 AS ++R+++EHPSG V Sbjct: 299 -QGLASTSGGDRQRLAVEHPSGEFTV 323 Lambda K H 0.318 0.133 0.389 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: 397 Number of extensions: 12 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: 443 Length of database: 361 Length adjustment: 31 Effective length of query: 412 Effective length of database: 330 Effective search space: 135960 Effective search space used: 135960 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 50 (23.9 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