Align Aconitate-delta-isomerase 1; Itaconic acid/2-hydroxyparaconate biosynthesis cluster protein ADI1; EC 5.-.-.- (characterized)
to candidate WP_012402542.1 BPHY_RS16305 4-oxalomesaconate tautomerase
Query= SwissProt::A0A0U2X0E4 (443 letters) >NCBI__GCF_000020045.1:WP_012402542.1 Length = 369 Score = 217 bits (552), Expect = 6e-61 Identities = 131/336 (38%), Positives = 179/336 (53%), Gaps = 13/336 (3%) Query: 1 MLHPIDTTIYRAGTSRGLYFLASDLPAEPSERDAALISIMGSGHPLQIDGMGGGNSLTSK 60 M PI R GTSRG +F A DLP + S RD L+ +MGS P QIDG+GG + LTSK Sbjct: 1 MQRPIPCLFMRGGTSRGPFFRAEDLPTDLSTRDRVLLDVMGSPDPRQIDGLGGAHPLTSK 60 Query: 61 VAIVSASTQRSEFDVDYLFCQVGITERFVDTAPNCGNLMSGVAAFAIERGLVQPHPSDTT 120 V IV + R + D+++LF Q+ VDT PNCGN+++ V FA+E GL+ P TT Sbjct: 61 VGIVRRGS-RPDIDLEFLFAQLQPDADTVDTTPNCGNMLAAVVPFALEVGLLAPRGRQTT 119 Query: 121 CLVRIFNLNSRQASELVIPVYNGRVHYDDIDDMH-MQRPSARVGLRFLDTVGSCTGKLLP 179 R+ LN+ + ++ + GR YD + + +A V + FLDT GS +LP Sbjct: 120 A--RVLTLNTGMSCDITVDTPEGRPEYDGSARIDGVPGTAAPVSINFLDTAGSVCSAMLP 177 Query: 180 TGNASDWID-----GLKVSIIDSAVPVVFIRQHDVGITGSEAPATLNANTALLDRLERVR 234 TG D ID L V+ ID+ +P+V + + TG E+ A LNA+ L LE +R Sbjct: 178 TGRVRDRIDLGDGRTLDVTCIDNGMPMVLVPAEALDRTGRESVADLNADIELKAELEALR 237 Query: 235 LEAGRRMGLGDVSGSVVPKLSLIGPGTETTTFTARYFTPKACHNAHAVTGAICTAGAAYI 294 MGLGD S PK+ L+ + R F P CH+A V A+ A A + Sbjct: 238 RRCSEAMGLGDTSSKNYPKMCLVSRPVAGGALSTRCFIPHVCHDAIGVLAAVTVATACVL 297 Query: 295 DGSVVCEILSSRASACSASQRRISIEHPSGVLEVGL 330 DGSV ++ AS S +++SIEHPSG V L Sbjct: 298 DGSVAHDL----ASTSSGVVKQVSIEHPSGEFSVEL 329 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: 444 Number of extensions: 16 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: 369 Length adjustment: 31 Effective length of query: 412 Effective length of database: 338 Effective search space: 139256 Effective search space used: 139256 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 24 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