Align Aconitate-delta-isomerase 1; Itaconic acid/2-hydroxyparaconate biosynthesis cluster protein ADI1; EC 5.-.-.- (characterized)
to candidate AZOBR_RS28105 AZOBR_RS28105 hypothetical protein
Query= SwissProt::A0A0U2X0E4 (443 letters) >FitnessBrowser__azobra:AZOBR_RS28105 Length = 374 Score = 266 bits (680), Expect = 8e-76 Identities = 161/354 (45%), Positives = 215/354 (60%), Gaps = 21/354 (5%) Query: 5 IDTTIYRAGTSRGLYFLASDLPAEPSERDAALISIMGSGHPLQIDGMGGGNSLTSKVAIV 64 I + R GTSRG +FLASDLPA P+ERDA L+S+MG+G+ L IDG+GGGN LTSKVAIV Sbjct: 11 IPCVMMRGGTSRGPFFLASDLPASPAERDALLLSVMGAGNDLGIDGIGGGNPLTSKVAIV 70 Query: 65 SASTQRSEFDVDYLFCQVGITERFVDTAPNCGNLMSGVAAFAIERGLVQPHPSDTTCLVR 124 +T DVDYLF QV + E VDT+PNCGN+++ VA FAIE GLV +D +VR Sbjct: 71 GPATLAGA-DVDYLFAQVRVQEGIVDTSPNCGNMLAAVAPFAIEAGLVPA--TDGVTVVR 127 Query: 125 IFNLNSRQASELVIPVYNGRVHYDD---IDDMHMQRPSARVGLRFLDTVGSCTGKLLPTG 181 I N+N+ + E + +GRV Y+ ID + +A + L FLD G+ TG+LLPTG Sbjct: 128 IHNVNTGKLIEARVQTPDGRVTYEGEAVIDGV--PGTAAPIHLAFLDAAGANTGRLLPTG 185 Query: 182 NASDWI------DGLKVSIIDSAVPVVFIRQHDVGITGSEAPATLNANTALLDRLERVRL 235 D I DG++VS ID+A+PV+ +R D+G TG E + + + RLE +R+ Sbjct: 186 APVDRIIGIDGTDGIEVSCIDAAIPVMLVRAADLGKTGHEPMDSYRLDRVFMARLEALRV 245 Query: 236 EAGRRMGLGDVSGSVVPKLSLIGPGTETTTFTARYFTPKACHNAHAVTGAICTAGAAYID 295 EAGRRMG + +G V+PK L+ P T T RYF P CH A A+TGA+ TA A I Sbjct: 246 EAGRRMGFPNAAGMVIPKPVLLAPPTRGGTLAVRYFMPHDCHRAMAITGAVATATACTIP 305 Query: 296 GSVVCEILSSRASACSASQRRISIEHPSGVLEVGLVPPENAAQSLVDVAVVERS 349 G+V +S + A ++ EHP+G L V L P A QS +++ S Sbjct: 306 GTV-----ASALAGRMALPGDVTFEHPAGRLTVRLDP--GAGQSAPTASILRTS 352 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: 464 Number of extensions: 27 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: 374 Length adjustment: 31 Effective length of query: 412 Effective length of database: 343 Effective search space: 141316 Effective search space used: 141316 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