Align Indole-3-glycerol phosphate synthase; Short=IGPS; EC 4.1.1.48 (characterized, see rationale)
to candidate SMc00236 SMc00236 Indole-3-glycerol phosphate synthase
Query= uniprot:A0A560BXT3 (262 letters) >FitnessBrowser__Smeli:SMc00236 Length = 271 Score = 290 bits (742), Expect = 2e-83 Identities = 158/263 (60%), Positives = 191/263 (72%), Gaps = 4/263 (1%) Query: 1 MSDVLTRICDDKRALVQARKSARPLSAVEDAARAADPA--RGFIRALRRTVDGGRYGLIA 58 M+D+L RI KR + A K+ PL ++ ARAAD + RGF AL D G +GLIA Sbjct: 1 MTDILRRIEAYKREEIAAAKARVPLEELK--ARAADQSAPRGFHAALAARRDKGEFGLIA 58 Query: 59 EIKKASPSKGLIRPDFDPPSLARAYREGGATCLSVLTDEPYFQGCDDYLLAARAAVDLPV 118 EIKKASPSKGLIRPDFDPP LA+AY GGA CLSVLTD P FQG ++L AR A LP Sbjct: 59 EIKKASPSKGLIRPDFDPPELAKAYAAGGAACLSVLTDAPSFQGAPEFLTKAREACPLPA 118 Query: 119 LRKDFMVDPYQIAESRALGADCILIIMAALSDAQAAEIEGAAIAWGLDVLVEVHNREELD 178 LRKDFM D YQ+ E+RA GADCIL+IMA+L D A +E AA A G+DVLVEVH+ EE++ Sbjct: 119 LRKDFMFDTYQVFEARAWGADCILLIMASLGDNDARRLEEAAFALGMDVLVEVHDAEEME 178 Query: 179 RALALKTPLLGVNNRNLKTLAVDIATTEELAAHVPADRMLVAESGLYSPADLSRMAAVGA 238 RAL L +PL+G+NNRNL+T VD+A +E LAA V ADR+LV ESG+++ D R+ G Sbjct: 179 RALRLSSPLVGINNRNLRTFEVDLAVSERLAAMVSADRLLVGESGVFTHEDCRRLEKSGI 238 Query: 239 RCFLVGESLMRQEDVTAATRALL 261 FLVGESLMR++DV AATRALL Sbjct: 239 TTFLVGESLMRKDDVEAATRALL 261 Lambda K H 0.321 0.135 0.382 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: 225 Number of extensions: 4 Number of successful extensions: 1 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: 262 Length of database: 271 Length adjustment: 25 Effective length of query: 237 Effective length of database: 246 Effective search space: 58302 Effective search space used: 58302 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 bits) S2: 47 (22.7 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
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