Align Indole-3-glycerol phosphate synthase; Short=IGPS; EC 4.1.1.48 (characterized, see rationale)
to candidate WP_011385240.1 AMB_RS14415 indole-3-glycerol phosphate synthase TrpC
Query= uniprot:A0A560BXT3 (262 letters) >NCBI__GCF_000009985.1:WP_011385240.1 Length = 271 Score = 292 bits (747), Expect = 6e-84 Identities = 148/259 (57%), Positives = 194/259 (74%) Query: 4 VLTRICDDKRALVQARKSARPLSAVEDAARAADPARGFIRALRRTVDGGRYGLIAEIKKA 63 +L RIC +KR V +KS RP+ + A+ P RGF +L R V +GLI EIKKA Sbjct: 7 ILDRICSEKRKQVAEQKSRRPIQELLKRAQDQAPPRGFAASLDRKVAEIGWGLITEIKKA 66 Query: 64 SPSKGLIRPDFDPPSLARAYREGGATCLSVLTDEPYFQGCDDYLLAARAAVDLPVLRKDF 123 SPS G+IR DF P LARAY+ GGA CLSVLTD+ +FQG D L AAR+A D+PVLRKDF Sbjct: 67 SPSAGIIRADFKPEFLARAYQRGGAACLSVLTDQKFFQGTDADLGAARSACDIPVLRKDF 126 Query: 124 MVDPYQIAESRALGADCILIIMAALSDAQAAEIEGAAIAWGLDVLVEVHNREELDRALAL 183 MVDPYQI E+RALGADCIL+I+A+L+DA+ +++E A+ +G+DVL+EVH+ EL+RAL L Sbjct: 127 MVDPYQIVEARALGADCILLIVASLTDAELSQMEDIALGYGMDVLIEVHDEAELERALKL 186 Query: 184 KTPLLGVNNRNLKTLAVDIATTEELAAHVPADRMLVAESGLYSPADLSRMAAVGARCFLV 243 K+PL+G+NNR+L+ + D+ATTE L +PA +++V+ESGL P DL RMAAVG + FL+ Sbjct: 187 KSPLIGINNRDLRIMKTDLATTERLVPLIPAGKVVVSESGLEGPGDLRRMAAVGVKRFLI 246 Query: 244 GESLMRQEDVTAATRALLA 262 GE+LMR+ DV A + LLA Sbjct: 247 GEALMRRPDVEQAVKVLLA 265 Lambda K H 0.321 0.135 0.382 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: 224 Number of extensions: 2 Number of successful extensions: 1 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: 262 Length of database: 271 Length adjustment: 25 Effective length of query: 237 Effective length of database: 246 Effective search space: 58302 Effective search space used: 58302 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 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