Align Indole-3-glycerol phosphate synthase; Short=IGPS; EC 4.1.1.48 (characterized, see rationale)
to candidate WP_010527322.1 GQW_RS0107180 indole-3-glycerol phosphate synthase TrpC
Query= uniprot:TRPC_BACTN (260 letters) >NCBI__GCF_000220155.1:WP_010527322.1 Length = 264 Score = 226 bits (575), Expect = 5e-64 Identities = 121/253 (47%), Positives = 175/253 (69%), Gaps = 1/253 (0%) Query: 3 DILSEIIANKRFEVDLQKQAISIEQLQEGINEVPASRSMKRALA-SSDSGIIAEFKRRSP 61 +IL I+A K+ E+ K+ +S+++LQ + S+K++LA +++ IIAEFKR+SP Sbjct: 2 NILDTIVAQKKKELQEIKEKVSVKELQYYRHFSSPVTSLKKSLAENTEFPIIAEFKRKSP 61 Query: 62 SKGWIKQEARPEEIVPSYLAAGASALSILTDEKFFGGSLKDIRTARPLVDVPIIRKDFII 121 SKG I +A +++V Y AG S +S+LTD +FFGGS +D+ AR L VPI+RK+FII Sbjct: 62 SKGNIHIDANIKDVVKGYQLAGVSGISVLTDTQFFGGSNEDLSDARDLTSVPILRKEFII 121 Query: 122 DEYQLYQAKIVGADAVLLIAAALKQEKCQELAEQAHELGLEVLLEIHSAEELPYINSKID 181 D YQ+Y+AK +GA A+LLIAA L +E+ ++LA A+ LGLEVL+EIH +E+ +NS +D Sbjct: 122 DPYQVYEAKAIGAGAILLIAAILTKEEARDLAALANYLGLEVLMEIHDMQEVEKLNSYVD 181 Query: 182 MIGINNRNLGTFFTDVENSFRLAGQLPQDAVLVSESGISDPEVVKRLRTAGFRGFLIGET 241 M+GINNRNL TF ++E++ LA LP D + ++ESGI + L+ AGF+GFLIGE Sbjct: 182 MVGINNRNLKTFEVNLEHAATLASALPDDILPIAESGIHSARDILFLKEAGFKGFLIGEY 241 Query: 242 FMKTPQPGETLQN 254 FMK P + N Sbjct: 242 FMKHDHPEKACMN 254 Lambda K H 0.317 0.135 0.368 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: 226 Number of extensions: 12 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: 260 Length of database: 264 Length adjustment: 25 Effective length of query: 235 Effective length of database: 239 Effective search space: 56165 Effective search space used: 56165 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 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