Align indole-3-glycerol-phosphate synthase (EC 4.1.1.48) (characterized)
to candidate WP_012853204.1 TCUR_RS14185 indole-3-glycerol phosphate synthase TrpC
Query= BRENDA::A1KJ27 (272 letters) >NCBI__GCF_000024385.1:WP_012853204.1 Length = 268 Score = 342 bits (877), Expect = 5e-99 Identities = 177/262 (67%), Positives = 213/262 (81%) Query: 5 TVLDSILEGVRADVAAREASVSLSEIKAAAAAAPPPLDVMAALREPGIGVIAEVKRASPS 64 +VL+ ILEGVRAD+A R+A+V L +K AAAAPPP D +AALR G+ VIAEVKR+SPS Sbjct: 2 SVLEEILEGVRADLAERQAAVPLDALKEKAAAAPPPRDAIAALRSDGVSVIAEVKRSSPS 61 Query: 65 AGALATIADPAKLAQAYQDGGARIVSVVTEQRRFQGSLDDLDAVRASVSIPVLRKDFVVQ 124 GALA IADPA LA+ Y+ GGA+++SV+TE+RRF GSL DL VRA+V +P+LRKDF+V Sbjct: 62 KGALAAIADPAALARDYEAGGAKVISVLTERRRFGGSLADLAEVRANVDVPLLRKDFIVT 121 Query: 125 PYQIHEARAHGADMLLLIVAALEQSVLVSMLDRTESLGMTALVEVHTEQEADRALKAGAK 184 YQ+ EARA+GAD+ LLIVAALEQ LVS+++R ES+G+ LVEVHTE+E RAL+AGAK Sbjct: 122 SYQLWEARAYGADLALLIVAALEQDALVSLVERAESIGLVPLVEVHTEEELARALEAGAK 181 Query: 185 VIGVNARDLMTLDVDRDCFARIAPGLPSSVIRIAESGVRGTADLLAYAGAGADAVLVGEG 244 VIGVNARDL TL VDR FAR+AP +P V+++AESGVRG DLLAYA AGADAVLVGE Sbjct: 182 VIGVNARDLKTLQVDRGVFARLAPLIPRDVVKVAESGVRGPHDLLAYASAGADAVLVGES 241 Query: 245 LVTSGDPRAAVADLVTAGTHPS 266 LVT DPR AVADLV AG HP+ Sbjct: 242 LVTGRDPRTAVADLVAAGAHPA 263 Lambda K H 0.317 0.131 0.358 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: 267 Number of extensions: 9 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: 272 Length of database: 268 Length adjustment: 25 Effective length of query: 247 Effective length of database: 243 Effective search space: 60021 Effective search space used: 60021 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