Align Indole-3-glycerol phosphate synthase; Short=IGPS; EC 4.1.1.48 (characterized, see rationale)
to candidate WP_077244750.1 B1A74_RS11895 indole-3-glycerol phosphate synthase TrpC
Query= uniprot:A0A166NT80_PSEFL (278 letters) >NCBI__GCF_001995255.1:WP_077244750.1 Length = 269 Score = 267 bits (682), Expect = 2e-76 Identities = 143/261 (54%), Positives = 180/261 (68%), Gaps = 1/261 (0%) Query: 4 PTVLENILARKVQEVAERSARVSLAELENLAKAADAPRGFAKALIDQAKTKQPAVIAEIK 63 P +LE IL RK +E+ ERS L EL +A+ PRGF AL + AVIAEIK Sbjct: 6 PDILERILERKREELIERSDVQPLRELRGWLTSAEEPRGFRAALQADIDAGRAAVIAEIK 65 Query: 64 KASPSKGVIRENFVPADIAKSYEKGGATCLSVLTDIDYFQGADAYLQQARAACKLPVIRK 123 KASPSKG I NF P A+SY + GATCLSVLTD+ +F+G D L+ A AC LP++RK Sbjct: 66 KASPSKGQISPNFNPDAFARSYAEHGATCLSVLTDVSFFKGRDGDLRAAHVACDLPILRK 125 Query: 124 DFMIDPYQIVESRALGADCVLLIVSALDDVKMAELAAVAKSVGLDVLVEVHDGDELERAL 183 DF+ID YQ+ E+R LGAD VLLI + LDD + EL + + +G+D LVEVHD +ELERA+ Sbjct: 126 DFVIDLYQVYEARVLGADAVLLIAAVLDDTNLGELIFLTRELGMDPLVEVHDAEELERAV 185 Query: 184 KTLDTPLVGVNNRNLHTFEVNLETTLDLLPRIPRDRLVITESGILNRADVELMEISDVYA 243 + L L+G+NNR+L +FE LETTL+LL R+P D L++TESGI + DV+ M + V A Sbjct: 186 R-LGADLIGINNRDLRSFETRLETTLELLDRLPEDVLLVTESGIHSVEDVQRMRDAGVNA 244 Query: 244 FLVGEAFMRAESPGTELQRLF 264 FLVGEAFMR E PG L RLF Sbjct: 245 FLVGEAFMREEDPGAALGRLF 265 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: 215 Number of extensions: 7 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: 269 Length adjustment: 25 Effective length of query: 253 Effective length of database: 244 Effective search space: 61732 Effective search space used: 61732 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