Align Aconitate-delta-isomerase 1; Itaconic acid/2-hydroxyparaconate biosynthesis cluster protein ADI1; EC 5.-.-.- (characterized)
to candidate RR42_RS23050 RR42_RS23050 4-oxalomesaconate tautomerase
Query= SwissProt::A0A0U2X0E4 (443 letters) >FitnessBrowser__Cup4G11:RR42_RS23050 Length = 359 Score = 273 bits (697), Expect = 8e-78 Identities = 159/340 (46%), Positives = 205/340 (60%), Gaps = 9/340 (2%) Query: 1 MLHPIDTTIYRAGTSRGLYFLASDLPAEPSERDAALISIMGSGHPLQIDGMGGGNSLTSK 60 M I + R GTSRG F A LP +P+ RD L+S MGS H LQ+DG+GGG+SLTSK Sbjct: 1 MSKDIPCVLMRGGTSRGPLFRADWLPDDPARRDQVLLSAMGSPHALQVDGLGGGSSLTSK 60 Query: 61 VAIVSASTQRSEFDVDYLFCQVGITERFVDTAPNCGNLMSGVAAFAIERGLVQPHPSDTT 120 AIVS S +R D+DYLF QV + + VDT PNCGN+++ VA FAIE GLV+ TT Sbjct: 61 AAIVSCS-RRPGCDIDYLFAQVAVDKHRVDTRPNCGNMLAAVAPFAIEEGLVRAGQCATT 119 Query: 121 CLVRIFNLNSRQASELVIPVYNGRVHYDDIDDMH-MQRPSARVGLRFLDTVGSCTGKLLP 179 +RIFN+N+ E V+ G+V Y + + +A + L FLD G TG + P Sbjct: 120 --LRIFNVNTSSVVEAVVQTPGGQVTYAGATRIDGVAGTAAPIMLNFLDAWGRVTGAMFP 177 Query: 180 TGNASDWIDGLKVSIIDSAVPVVFIRQHDVGITGSEAPATLNANTALLDRLERVRLEAGR 239 TGN D ID + V+ ID+A+P+V + +G+ G E PA L+AN +L RLE VR +AGR Sbjct: 178 TGNTIDVIDAVPVTCIDAAMPLVVVHAASLGVRGDETPAALDANREMLARLESVRRQAGR 237 Query: 240 RMGLGDVSGSVVPKLSLIGPGTETTTFTARYFTPKACHNAHAVTGAICTAGAAYIDGSVV 299 RMGLGDVS SV+PK L+ T+RYFTP CH AHAVTGA+ A AAY V Sbjct: 238 RMGLGDVSHSVIPKPVLVSGCGRANEITSRYFTPLRCHTAHAVTGAVGIA-AAYCTPGTV 296 Query: 300 CEILSSRASACSASQRRISIEHPSGVLEVGLVPPENAAQS 339 L+S S Q RI + HP+G +EV + P + S Sbjct: 297 ANGLASTPS----PQGRIVVRHPAGSIEVHVEPERDGGPS 332 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: 421 Number of extensions: 18 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: 443 Length of database: 359 Length adjustment: 31 Effective length of query: 412 Effective length of database: 328 Effective search space: 135136 Effective search space used: 135136 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