Align indole-3-glycerol-phosphate synthase (EC 4.1.1.48) (characterized)
to candidate WP_092052720.1 BQ4888_RS01475 indole-3-glycerol-phosphate synthase
Query= BRENDA::Q9YGB5 (227 letters) >NCBI__GCF_900111775.1:WP_092052720.1 Length = 236 Score = 160 bits (405), Expect = 2e-44 Identities = 94/200 (47%), Positives = 126/200 (63%), Gaps = 2/200 (1%) Query: 17 IIAELKVYSPKYGDLLKGRNPFEILRAYERAGAVGISYITDPKYFRGSFEFLRKLCRETE 76 +I ++K SPK GDLL+GR+P + + RAGA +S +T+ K F GS E LR+L + T Sbjct: 20 VIPDIKCISPKEGDLLRGRDPLAVAQLLARAGAPALSVVTETKDFGGSLELLRQLAKNTT 79 Query: 77 LPVLRKDFIASKEEVERTAEAGASAVLLITRL-LKEELPEFVDFAKEHGLDTLVEVHSEE 135 LP+LRKDFI S E++ + E GA A+LLI L + L + A + GL+ LVE H+EE Sbjct: 80 LPILRKDFITSCEDMTLSRECGAQAILLICALHTLDSLTTLYNEALKIGLEPLVEAHTEE 139 Query: 136 ELAIALQTDSTMIGINNRDIGKLELDDGNVSLTEKLAPLIPKRYVKVSESGIAGTEDLKR 195 EL A + + ++GINNRDI KLE DDG VS TE LA PK + +SES I + + Sbjct: 140 ELGWAGKIGAKLVGINNRDILKLEKDDGTVSATELLASHKPKNAILISESSIRTPAEGQA 199 Query: 196 ALR-HADAALIGTALMKTPD 214 A+R AD LIGTAL + D Sbjct: 200 AIRAGADVLLIGTALWQADD 219 Lambda K H 0.317 0.137 0.372 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: 145 Number of extensions: 7 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: 227 Length of database: 236 Length adjustment: 23 Effective length of query: 204 Effective length of database: 213 Effective search space: 43452 Effective search space used: 43452 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: 46 (22.3 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