Align Indole-3-glycerol phosphate synthase; Short=IGPS; EC 4.1.1.48 (characterized, see rationale)
to candidate WP_013135934.1 ARNIT_RS10630 indole-3-glycerol phosphate synthase TrpC
Query= uniprot:A0A166NT80_PSEFL (278 letters) >NCBI__GCF_000092245.1:WP_013135934.1 Length = 263 Score = 185 bits (469), Expect = 1e-51 Identities = 104/258 (40%), Positives = 156/258 (60%), Gaps = 3/258 (1%) Query: 6 VLENILARKVQEVAERSARVSLAEL-ENLAKAADAPRGFAKALIDQAKTKQPAVIAEIKK 64 +L+ I R +++V R + L L +L+ APR K + K + +IAE+KK Sbjct: 2 ILDEINKRTLEDVERRKKEIPLDLLGRSLSSNPYAPRD-VKPYLTSTKEEPIRIIAEVKK 60 Query: 65 ASPSKGVIRENFVPADIAKSYEKGGATCLSVLTDIDYFQGADAYLQQARAACKLPVIRKD 124 ASPSKG+I+E+F P IA+ Y K GA +SVLT+ YF+G YL Q R P++RKD Sbjct: 61 ASPSKGIIKEDFDPVSIAQEYSKNGANAISVLTEPHYFKGNLEYLTQIRRYVPTPLLRKD 120 Query: 125 FMIDPYQIVESRALGADCVLLIVSALDDVKMAELAAVAKSVGLDVLVEVHDGDELERALK 184 F++D YQIVE+ GAD +LLI +L + EL A +GL+VLVEVHD ++L +A+K Sbjct: 121 FILDKYQIVEALVYGADFILLIAKSLSTKDLKELYEYALHLGLEVLVEVHDKEDLTKAMK 180 Query: 185 TLDTPLVGVNNRNLHTFEVNLETTLDLLPRIPRDRLVITESGILNRADVELMEISDVYAF 244 ++G+N+RNL T E+++ L+P IP ++++ ESG+ N ++ + AF Sbjct: 181 -CGAHIIGINHRNLETMEMDMTLCERLIPMIPNGKIIVAESGVSNTEMIKNLSEIGADAF 239 Query: 245 LVGEAFMRAESPGTELQR 262 L+GE FMR S EL++ Sbjct: 240 LIGEHFMRVPSIEEELKK 257 Lambda K H 0.318 0.135 0.369 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: 180 Number of extensions: 11 Number of successful extensions: 2 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: 278 Length of database: 263 Length adjustment: 25 Effective length of query: 253 Effective length of database: 238 Effective search space: 60214 Effective search space used: 60214 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: 47 (22.7 bits)
This GapMind analysis is from Apr 10 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