Align Aconitate-delta-isomerase 1; Itaconic acid/2-hydroxyparaconate biosynthesis cluster protein ADI1; EC 5.-.-.- (characterized)
to candidate WP_037577835.1 BS73_RS31830 hypothetical protein
Query= SwissProt::A0A0U2X0E4 (443 letters) >NCBI__GCF_000744815.1:WP_037577835.1 Length = 379 Score = 197 bits (501), Expect = 5e-55 Identities = 134/334 (40%), Positives = 178/334 (53%), Gaps = 20/334 (5%) Query: 9 IYRAGTSRGLYFLASDLPAEPSERDAALISIMGSGHPLQIDGMGGGNSLTSKVAIVSAST 68 + R GTS+G YFLA DLPA+P+ER+A L+ IMGS P QIDG+GG + LTSKVA+VSAS Sbjct: 14 LMRGGTSKGGYFLAGDLPADPAERNALLLRIMGSPDPRQIDGLGGAHPLTSKVAVVSASA 73 Query: 69 QRSEFDVDYLFCQVGITERFVDTAPNCGNLMSGVAAFAIERGLVQPHPSDTTCLVRIFNL 128 + DVDYLF QV + V A NCGNL++GV FAIERGLV +T VRI L Sbjct: 74 DPAA-DVDYLFLQVAVDAPDVSDAQNCGNLLAGVGPFAIERGLVAAEEGETP--VRIRML 130 Query: 129 NSRQASELVIPVYNGRVHY-DDIDDMHMQRPSARVGLRFLDTV------GSCTGKLLPTG 181 N+ Q + I RV Y D + +A V L F D+ G LLPTG Sbjct: 131 NTGQLATARIRTPGRRVRYAGDTTTPGVPGTAAPVVLEFGDSAADSPHSADAGGGLLPTG 190 Query: 182 NASD-WIDGLKVSIIDSAVPVVFIRQHD---VGITGSEAPATLNANTALLDRLERVRLEA 237 N D + G++ +++D+ +PVV + D G+ G E P L A+ L R+ +R A Sbjct: 191 NVVDELLPGVRATLVDAGMPVVLLDVEDFAEFGLRGDETPEQLEADEKLAARIAALRSAA 250 Query: 238 GRRMGLGDVSGSVVPKLSLIG-PGTETTTFTARYFTPKACHNAHAVTGAICTAGAAYIDG 296 MGL + + VPKL+L+ P T T R F P H A V A+ A + G Sbjct: 251 MPLMGLDPATATTVPKLTLVSPPRTPGGTVATRSFIPVRAHAAIGVVAAVSVASGLLLKG 310 Query: 297 SVVCEILSSRASACSASQRRISIEHPSGVLEVGL 330 S R + S + +EHP+G L+V + Sbjct: 311 ST-----GRRHAEFPPSGEPLRLEHPTGHLDVAI 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: 462 Number of extensions: 20 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: 379 Length adjustment: 31 Effective length of query: 412 Effective length of database: 348 Effective search space: 143376 Effective search space used: 143376 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