Align indole-3-glycerol-phosphate synthase (EC 4.1.1.48) (characterized)
to candidate WP_058929284.1 AU252_RS01935 indole-3-glycerol phosphate synthase TrpC
Query= BRENDA::A1KJ27 (272 letters) >NCBI__GCF_001484605.1:WP_058929284.1 Length = 273 Score = 264 bits (674), Expect = 2e-75 Identities = 145/264 (54%), Positives = 182/264 (68%), Gaps = 5/264 (1%) Query: 4 ATVLDSILEGVRADVAAREASVSLSEIKAAAAAAPPPLDVMAAL-----REPGIGVIAEV 58 ATVLD I GV D+ AR+ VSL+++K AAAA P D +AL + + VIAE+ Sbjct: 2 ATVLDDINAGVWEDMEARKRLVSLADLKDLAAAAAPARDAWSALGGTAVQRDQLKVIAEI 61 Query: 59 KRASPSAGALATIADPAKLAQAYQDGGARIVSVVTEQRRFQGSLDDLDAVRASVSIPVLR 118 KR SPS G LA+I DPA LA+ Y DGGA ++SV+TEQRRF GSL DLDAVRA V +P+LR Sbjct: 62 KRRSPSKGDLASIVDPAALAEQYADGGAAVISVLTEQRRFNGSLADLDAVRARVDVPLLR 121 Query: 119 KDFVVQPYQIHEARAHGADMLLLIVAALEQSVLVSMLDRTESLGMTALVEVHTEQEADRA 178 KDF + YQI EARAHGAD++LLIVA+L S L + LGM LVE HTE+E +RA Sbjct: 122 KDFTLDEYQIWEARAHGADLILLIVASLSDSQLREFSALSRELGMNVLVETHTEEEIERA 181 Query: 179 LKAGAKVIGVNARDLMTLDVDRDCFARIAPGLPSSVIRIAESGVRGTADLLAYAGAGADA 238 + A A++IGVN R+L TLDVDR FA +A +P+ + IAESGVRG D+ YA GA+A Sbjct: 182 VAAEARIIGVNVRNLKTLDVDRSVFASLAGLIPAEALVIAESGVRGVDDVTHYAANGANA 241 Query: 239 VLVGEGLVTSGDPRAAVADLVTAG 262 +LVGE LV+ PR +A+ AG Sbjct: 242 ILVGEALVSDATPRDRIAEFTAAG 265 Lambda K H 0.317 0.131 0.358 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: 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: 272 Length of database: 273 Length adjustment: 25 Effective length of query: 247 Effective length of database: 248 Effective search space: 61256 Effective search space used: 61256 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