Align Aconitate-delta-isomerase 1; Itaconic acid/2-hydroxyparaconate biosynthesis cluster protein ADI1; EC 5.-.-.- (characterized)
to candidate WP_012968968.1 KVAR_RS21770 4-oxalomesaconate tautomerase
Query= SwissProt::A0A0U2X0E4 (443 letters) >NCBI__GCF_000025465.1:WP_012968968.1 Length = 351 Score = 257 bits (656), Expect = 5e-73 Identities = 149/348 (42%), Positives = 203/348 (58%), Gaps = 20/348 (5%) Query: 5 IDTTIYRAGTSRGLYFLASDLPAEPSERDAALISIMGSGHPLQIDGMGGGNSLTSKVAIV 64 I + R GTS+G + LA DLP + +R+ AL++IMGSGH L+IDG+GGG+ TSKVAIV Sbjct: 4 IPCALMRGGTSKGAFLLADDLPEDTQKRNEALLTIMGSGHELEIDGIGGGSPQTSKVAIV 63 Query: 65 SASTQRSEFDVDYLFCQVGITERFVDTAPNCGNLMSGVAAFAIERGLVQPHPSDTTCLVR 124 S ST + + DVDYLF QV + ER VDT PNCGN++ V FAIE+GLV T +R Sbjct: 64 SQSTSQ-QADVDYLFVQVIVNERRVDTTPNCGNMLCAVGGFAIEKGLVAATSPVTRVRIR 122 Query: 125 IFNLNSRQASELVIP----VYNGRVHYDDIDDMHMQRPSARVGLRFLDTVGSCTGKLLPT 180 N N+ +++ P VY G H D + +A VGL FL+ G+ +G+L PT Sbjct: 123 NVNTNTFVDADIQTPNGQVVYEGGTHIDGVPGQ-----AAPVGLTFLNAAGAKSGQLFPT 177 Query: 181 GNASDWIDGLKVSIIDSAVPVVFIRQHDVGITGSEAPATLNANTALLDRLERVRLEAGRR 240 GN D D ++V+ ID A+P+V I +G TG E+ + L+ + RLE +R +AG Sbjct: 178 GNRVDIFDSIRVTCIDMAMPMVIIPAQSLGKTGYESASELDQDKGFFQRLESIRKQAGAA 237 Query: 241 MGLGDVSGSVVPKLSLIGPGTETTTFTARYFTPKACHNAHAVTGAICTAGAAYIDGSVVC 300 MG GDVS V+PK L+ P T T RYF P +CH + A+TGAI A + I +VV Sbjct: 238 MGFGDVSNMVIPKPVLVAPPQHGGTLTVRYFMPHSCHKSLAITGAIGLASSCIIADTVVN 297 Query: 301 EILSSRASACSASQRRISIEHPSGVLEVGLV----PPENAAQSLVDVA 344 E+ A I++EHPSG ++V L PEN S++ A Sbjct: 298 EMTR------MAGDGLINVEHPSGSIDVSLSNTHGQPENICASVIRTA 339 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: 365 Number of extensions: 14 Number of successful extensions: 3 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: 351 Length adjustment: 31 Effective length of query: 412 Effective length of database: 320 Effective search space: 131840 Effective search space used: 131840 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