Align Indole-3-glycerol phosphate synthase; Short=IGPS; EC 4.1.1.48 (characterized, see rationale)
to candidate WP_004322777.1 C665_RS16190 indole-3-glycerol phosphate synthase TrpC
Query= uniprot:A0A166NT80_PSEFL (278 letters) >NCBI__GCF_000310185.1:WP_004322777.1 Length = 266 Score = 280 bits (715), Expect = 3e-80 Identities = 151/262 (57%), Positives = 189/262 (72%), Gaps = 4/262 (1%) Query: 6 VLENILARKVQEVAERSARVSLAELENLAKAADAPRGFAKALIDQAKTKQPAVIAEIKKA 65 +L+ I A KV+EVA +A + A A R F A+ + ++PAVIAEIKKA Sbjct: 4 ILQKICAVKVEEVAAAAAARPQCLVREDAAAQPPARDFVGAIRAKHAARRPAVIAEIKKA 63 Query: 66 SPSKGVIRENFVPADIAKSYEKGGATCLSVLTDIDYFQGADAYLQQARAACKLPVIRKDF 125 SPSKGVIR +F PA+IA YE+ GA CLSVLTD +FQGA YLQ ARAAC LPV+RKDF Sbjct: 64 SPSKGVIRPDFHPAEIAADYERAGAACLSVLTDRGFFQGAPEYLQAARAACHLPVLRKDF 123 Query: 126 MIDPYQIVESRALGADCVLLIVSALDDVKMAELAAVAKSVGLDVLVEVHDGDELERALKT 185 ++DPYQ+ E+RA+GAD +LLI + LD +M ++ +A +G+ VLVEVHD ELE AL+ Sbjct: 124 LVDPYQVFEARAMGADAILLIAACLDLARMRDMEQLAVELGMAVLVEVHDAAELEHALQ- 182 Query: 186 LDTPLVGVNNRNLHTFEVNLETTLDLLPRI---PRDRLVITESGILNRADVELMEISDVY 242 LDTPL+G+NNRNL +FEV+L+TTLDLLPRI R+V+TESGIL DV LM+ + V+ Sbjct: 183 LDTPLIGINNRNLRSFEVSLQTTLDLLPRIASGAAGRIVVTESGILKPEDVALMQANAVH 242 Query: 243 AFLVGEAFMRAESPGTELQRLF 264 FLVGEAFMRA PG ELQ LF Sbjct: 243 TFLVGEAFMRAPHPGAELQALF 264 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: 226 Number of extensions: 9 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: 278 Length of database: 266 Length adjustment: 25 Effective length of query: 253 Effective length of database: 241 Effective search space: 60973 Effective search space used: 60973 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 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