Align Aconitate-delta-isomerase 1; Itaconic acid/2-hydroxyparaconate biosynthesis cluster protein ADI1; EC 5.-.-.- (characterized)
to candidate WP_011382697.1 AMB_RS01270 4-oxalomesaconate tautomerase
Query= SwissProt::A0A0U2X0E4 (443 letters) >NCBI__GCF_000009985.1:WP_011382697.1 Length = 363 Score = 246 bits (628), Expect = 8e-70 Identities = 145/347 (41%), Positives = 203/347 (58%), Gaps = 18/347 (5%) Query: 1 MLHPIDTTIYRAGTSRGLYFLASDLPAEPSERDAALISIMGSGHPLQIDGMGGGNSLTSK 60 M PI R GTSRG +FL SDLPA+ + RD L+++MGS H QIDG+GGG+ LTSK Sbjct: 1 MQTPIPCLFMRGGTSRGPFFLESDLPADMALRDKVLLAVMGSPHARQIDGLGGGHPLTSK 60 Query: 61 VAIVSASTQRSEFDVDYLFCQVGITERFVDTAPNCGNLMSGVAAFAIERGLVQPHPSDTT 120 V IV ST D+D+LF Q+ VDT PNCGN+++ V FA+ERG+V+P TT Sbjct: 61 VGIVRPSTTPG-VDLDFLFAQLQPDRETVDTTPNCGNMLAAVVPFALERGIVRPQGDTTT 119 Query: 121 CLVRIFNLNSRQASELVIPVYNGRVHYDD---IDDMHMQRPSARVGLRFLDTVGS-CTGK 176 +R+ LN+ ++ + GR+ Y ID + ++ + + FLDT GS CTG Sbjct: 120 --LRVLTLNTDMQCDITVRTPGGRMEYQGEARIDGV--PGTASPIAINFLDTAGSVCTG- 174 Query: 177 LLPTGNASDWIDGLKVSIIDSAVPVVFIRQHDVGITGSEAPATLNANTALLDRLERVRLE 236 LLPTG D IDGL+V+ ID+ +P+V R D+G TG+E+ TLNA+T L R+E +RL+ Sbjct: 175 LLPTGRTRDVIDGLEVTCIDNGMPMVLFRAADLGRTGAESVETLNADTELKARIETLRLK 234 Query: 237 AGRRMGLGDVSGSVVPKLSLIGPGTETTTFTARYFTPKACHNAHAVTGAICTAGAAYIDG 296 AG MGLGDV PK+ L+ P + R F P CH+A V A+ A A ++G Sbjct: 235 AGHLMGLGDVGPKNYPKMCLVAPPSAGGALGTRCFIPHVCHDAIGVLAAVTVATACVLEG 294 Query: 297 SVVCEILSSRASACSASQRRISIEHPSG----VLEVGLVPPENAAQS 339 SV A+ + + I++EHP+G LE+ L P+ ++ Sbjct: 295 SVT----EGLANVPGGAVKTIAVEHPTGEFSVELELDLADPQKVVRA 337 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: 416 Number of extensions: 15 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: 363 Length adjustment: 31 Effective length of query: 412 Effective length of database: 332 Effective search space: 136784 Effective search space used: 136784 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