Align Indole-3-glycerol phosphate synthase; Short=IGPS; EC 4.1.1.48 (characterized, see rationale)
to candidate WP_006746920.1 THITH_RS15380 indole-3-glycerol phosphate synthase TrpC
Query= uniprot:A0A166NT80_PSEFL (278 letters) >NCBI__GCF_000227685.2:WP_006746920.1 Length = 275 Score = 309 bits (791), Expect = 5e-89 Identities = 163/265 (61%), Positives = 199/265 (75%), Gaps = 1/265 (0%) Query: 3 VPTVLENILARKVQEVAERSARVSLAELENLAKAADAPRGFAKALIDQAKTKQPAVIAEI 62 VP +L+ ILARK +E+ RSA + L EL + A+ AD PRGF AL + + PAVIAEI Sbjct: 8 VPDILQRILARKQEEIRARSATLPLPELASRARDADPPRGFRAALAARIRRGLPAVIAEI 67 Query: 63 KKASPSKGVIRENFVPADIAKSYEKGGATCLSVLTDIDYFQGADAYLQQARAACKLPVIR 122 KKASPSKGV+R +F P IA SY + GA CLSVLTDID+FQGAD YLQ+ARAAC LPV+R Sbjct: 68 KKASPSKGVLRADFDPVAIAGSYARHGAACLSVLTDIDFFQGADGYLQKARAACDLPVLR 127 Query: 123 KDFMIDPYQIVESRALGADCVLLIVSALDDVKMAELAAVAKSVGLDVLVEVHDGDELERA 182 KDF++DPYQ+ E+RALGADC+LLIV+ALDD +M L +A +G+DVLVEVHD DEL RA Sbjct: 128 KDFVVDPYQVHEARALGADCILLIVAALDDEQMRALYRLALDLGMDVLVEVHDRDELGRA 187 Query: 183 LKTLDTPLVGVNNRNLHTFEVNLETTLDLLPRIPRDRLVITESGILNRADVELMEISDVY 242 L LD L+G+NNR+L +FE LETTLDL ++P L++TESGI +DV M + V Sbjct: 188 L-ALDAGLIGINNRDLRSFETRLETTLDLCAQVPEGVLLVTESGIHRPSDVARMRAAGVE 246 Query: 243 AFLVGEAFMRAESPGTELQRLFFPE 267 AFLVGEAFMRA PG L+RLF PE Sbjct: 247 AFLVGEAFMRAPDPGEALERLFGPE 271 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: 236 Number of extensions: 6 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: 275 Length adjustment: 25 Effective length of query: 253 Effective length of database: 250 Effective search space: 63250 Effective search space used: 63250 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 25 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