Align Aconitate-delta-isomerase 1; Itaconic acid/2-hydroxyparaconate biosynthesis cluster protein ADI1; EC 5.-.-.- (characterized)
to candidate AZOBR_RS26900 AZOBR_RS26900 hypothetical protein
Query= SwissProt::A0A0U2X0E4 (443 letters) >FitnessBrowser__azobra:AZOBR_RS26900 Length = 352 Score = 228 bits (582), Expect = 2e-64 Identities = 139/323 (43%), Positives = 185/323 (57%), Gaps = 12/323 (3%) Query: 11 RAGTSRGLYFLASDLPAEPSERDAALISIMGSGHPLQIDGMGGGNSLTSKVAIVSASTQR 70 R GTS+G YFLA DLP + RDA L+ +MGS QIDGMGG + LTSKVA+V S +R Sbjct: 11 RGGTSKGGYFLADDLPPGTAARDAFLLRVMGSPDSRQIDGMGGADPLTSKVAVVRRS-ER 69 Query: 71 SEFDVDYLFCQVGITERFVDTAPNCGNLMSGVAAFAIERGLVQPHPSDTTCLVRIFNLNS 130 DVDYLF QV + + V A NCGN+++GV FAIERGLV T V I N+ Sbjct: 70 PGVDVDYLFLQVFVDKAIVTDAQNCGNILAGVGPFAIERGLVPARDGVTP--VTIHMENT 127 Query: 131 RQASELVIPVYNGRVHYDD---IDDMHMQRPSARVGLRFLDTVGSCTGKLLPTGNASDWI 187 Q + +P G V Y ID + +A + + F DT GS G LLPTGN D I Sbjct: 128 GQVAVAAVPTPGGTVTYRGEARIDGV--PGTAAAIPIEFRDTAGSSCGALLPTGNVVDVI 185 Query: 188 DGLKVSIIDSAVPVVFIRQHDVGITGSEAPATLNANTALLDRLERVRLEAGRRMGLGDVS 247 DG+ V+ ID+ +PVV +R D+G+ G E L+ + AL RLE +RL+AG RM LGDV+ Sbjct: 186 DGVPVTCIDNGMPVVVLRAADLGVRGDETREELDGDAALKARLESIRLQAGPRMKLGDVT 245 Query: 248 GSVVPKLSLIGPGTETTTFTARYFTPKACHNAHAVTGAICTAGAAYIDGSVVCEILSSRA 307 VPK++L+ + R F P CH + V GA+ A A ++GS +S A Sbjct: 246 DKSVPKMTLVSAPANGGAVSTRTFIPHRCHASIGVLGAVSVATACALEGSPA----ASLA 301 Query: 308 SACSASQRRISIEHPSGVLEVGL 330 + + +S+EHP+G + V L Sbjct: 302 VVPDGAAKTLSVEHPTGEMTVVL 324 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: 403 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: 352 Length adjustment: 31 Effective length of query: 412 Effective length of database: 321 Effective search space: 132252 Effective search space used: 132252 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