Align Indole-3-glycerol phosphate synthase; IGPS; EC 4.1.1.48 (uncharacterized)
to candidate WP_034994810.1 DL88_RS08730 indole-3-glycerol phosphate synthase TrpC
Query= curated2:Q8R9M7 (256 letters) >NCBI__GCF_000745425.1:WP_034994810.1 Length = 278 Score = 152 bits (384), Expect = 7e-42 Identities = 82/192 (42%), Positives = 122/192 (63%), Gaps = 2/192 (1%) Query: 44 GKVAIIGEIKRASPSKGIIREEFDLVEIAKTYEKAEVDAISVLTEKRFFKGEGGYIPQVK 103 GK II +I+ +SP R D++++A+ Y A A+S ++RFF+G + K Sbjct: 59 GKPGIIADIRGSSPVSKSTRSRLDVMDMAEDYRDAGAAAVSASPDRRFFRGSIADLATAK 118 Query: 104 KLTTKPVLRKDFVIDEYQIYESKFLGADAVLLIVAILEDKLKGFCDIAKQIGLDVLVEVH 163 + P+L D V+D YQ+YE+++ GADA LLI +IL D+LK F A+ I LD LVEV Sbjct: 119 A-SNLPILANDIVVDLYQVYEARYAGADASLLIASILGDQLKEFVARAQSIALDPLVEVR 177 Query: 164 EEEELETALKAGCDIIGINNRDLKTFKVDIKTTERLIKNIPKDKIV-VSESGIKTPEDVL 222 E EL AL+AG ++I +NNRDL+T +VD ERL+ IP+D ++ ++ GIKT ED+ Sbjct: 178 NEAELAMALEAGANLIAVNNRDLETLEVDPTVCERLLPKIPQDSVLAIASGGIKTQEDIE 237 Query: 223 YLSSLGVKAVLI 234 +++LG KAV + Sbjct: 238 KVAALGAKAVRV 249 Lambda K H 0.317 0.139 0.374 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: 146 Number of extensions: 8 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: 256 Length of database: 278 Length adjustment: 25 Effective length of query: 231 Effective length of database: 253 Effective search space: 58443 Effective search space used: 58443 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 (21.6 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