Align indole-3-glycerol-phosphate synthase (EC 4.1.1.48) (characterized)
to candidate WP_037581605.1 BS73_RS29020 indole-3-glycerol phosphate synthase TrpC
Query= BRENDA::A1KJ27 (272 letters) >NCBI__GCF_000744815.1:WP_037581605.1 Length = 269 Score = 320 bits (820), Expect = 2e-92 Identities = 167/263 (63%), Positives = 203/263 (77%), Gaps = 1/263 (0%) Query: 5 TVLDSILEGVRADVAAREASVSLSEIKAAAAAAPPPLDVMAALR-EPGIGVIAEVKRASP 63 +VLD I+EGVR D+A R+A VSL E+K AA AP D +AALR + G+ VI EVKR+SP Sbjct: 2 SVLDEIIEGVREDLAERQARVSLDELKEQAAKAPAAKDGVAALRGDDGVKVICEVKRSSP 61 Query: 64 SAGALATIADPAKLAQAYQDGGARIVSVVTEQRRFQGSLDDLDAVRASVSIPVLRKDFVV 123 S GALA IADPA LA Y+ GGA +SV+TEQRRF GSL DLDAVRA V + VLRKDF+V Sbjct: 62 SKGALAAIADPASLAADYEAGGAAAISVLTEQRRFGGSLADLDAVRAKVDVAVLRKDFIV 121 Query: 124 QPYQIHEARAHGADMLLLIVAALEQSVLVSMLDRTESLGMTALVEVHTEQEADRALKAGA 183 YQ+ EARAHGAD+ LLIVAAL+Q LVS+++R ES+G+T LVEVH E E RA+ AGA Sbjct: 122 TSYQLWEARAHGADIALLIVAALDQPALVSLIERAESIGLTPLVEVHDEDEVTRAVDAGA 181 Query: 184 KVIGVNARDLMTLDVDRDCFARIAPGLPSSVIRIAESGVRGTADLLAYAGAGADAVLVGE 243 ++IGVNAR+L TL V+RD FA +AP +P ++++AESGVRG DL+ YA GADAVLVGE Sbjct: 182 RIIGVNARNLKTLQVNRDTFAEVAPAIPKGIVKVAESGVRGPHDLITYANDGADAVLVGE 241 Query: 244 GLVTSGDPRAAVADLVTAGTHPS 266 LVT DP+ AVADLV AG HP+ Sbjct: 242 SLVTGRDPKTAVADLVAAGAHPA 264 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: 248 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: 272 Length of database: 269 Length adjustment: 25 Effective length of query: 247 Effective length of database: 244 Effective search space: 60268 Effective search space used: 60268 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 Jul 26 2024. The underlying query database was built on Jul 25 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