Align Indole-3-glycerol phosphate synthase; IGPS; EC 4.1.1.48 (uncharacterized)
to candidate WP_069663042.1 BCR25_RS07715 indole-3-glycerol phosphate synthase TrpC
Query= curated2:Q8Y6Q4 (252 letters) >NCBI__GCF_001730305.1:WP_069663042.1 Length = 252 Score = 290 bits (743), Expect = 1e-83 Identities = 151/252 (59%), Positives = 188/252 (74%) Query: 1 MTFLEEILAQKEVEVAKMPLEQVAEKRKTYSFYEFLKANTNTMQLIAEVKRASPSKGEIN 60 M FLE+I+ +K+ E+ KMPLE++ R+T SFYE +K N + +I EVKRASPSKG IN Sbjct: 1 MDFLEKIITEKKQEIQKMPLEKLQPLRQTTSFYERVKKNPEKIHIIGEVKRASPSKGAIN 60 Query: 61 MGVNPVLQAKSYQAAGAGMISVLTDPVFFKGSIEDLREVAKNVGIPVLCKDFIISEKQLI 120 + VN + QAK+Y+ AG ISVLTDP FFKGSIEDLR+VA V IPVLCKDFII EKQLI Sbjct: 61 LSVNVIEQAKAYEKAGVTAISVLTDPTFFKGSIEDLRQVAAEVSIPVLCKDFIIDEKQLI 120 Query: 121 RARNAGATVVLLIISALTEEKLITLFEQALALDLEVLVEVHDQEELAVAQKIGAQLIGVN 180 RARNAGAT+VLLI+SAL+ +L L+EQA L LEVLVEVHD++E +A+++GA LIGVN Sbjct: 121 RARNAGATIVLLIVSALSRSRLKKLYEQARTLGLEVLVEVHDEQEQTIAEELGASLIGVN 180 Query: 181 NRNLHTFEVDIAVSERLASDFSSDACFISESGFRTAEDVARVSQKYDAVLVGEALMREAT 240 NRNL TF+V + VS+ L +DA +ISESGF A V +V KY A+LVGE LMR+ Sbjct: 181 NRNLKTFDVSLNVSQLLGEKQRTDAVYISESGFSDATQVEQVKDKYQAILVGEGLMRQTE 240 Query: 241 PEVAAKSLKVTR 252 P K L+V+R Sbjct: 241 PMDKVKELQVSR 252 Lambda K H 0.317 0.131 0.344 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: 204 Number of extensions: 7 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: 252 Length of database: 252 Length adjustment: 24 Effective length of query: 228 Effective length of database: 228 Effective search space: 51984 Effective search space used: 51984 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: 46 (22.3 bits)
This GapMind analysis is from Jul 26 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