Align indole-3-glycerol-phosphate synthase (EC 4.1.1.48) (characterized)
to candidate WP_011973824.1 MAEO_RS05625 indole-3-glycerol phosphate synthase TrpC
Query= BRENDA::Q9YGB5 (227 letters) >NCBI__GCF_000017185.1:WP_011973824.1 Length = 228 Score = 279 bits (713), Expect = 4e-80 Identities = 138/214 (64%), Positives = 173/214 (80%) Query: 14 KNAIIAELKVYSPKYGDLLKGRNPFEILRAYERAGAVGISYITDPKYFRGSFEFLRKLCR 73 KN IIAE+KV+SPKYGD++ R+ +IL+ YE AGA GISYITD ++F G FE +K+C+ Sbjct: 15 KNPIIAEIKVHSPKYGDMINRRDEMDILKIYENAGASGISYITDKEHFNGDFEMYKKICK 74 Query: 74 ETELPVLRKDFIASKEEVERTAEAGASAVLLITRLLKEELPEFVDFAKEHGLDTLVEVHS 133 TELPVLRKDFI +K+E+E+TAE A+LLI RLLKEE EFVD+A EHGLDTLVEVH+ Sbjct: 75 NTELPVLRKDFITTKDEIEKTAEVEGGAILLIARLLKEETAEFVDYALEHGLDTLVEVHN 134 Query: 134 EEELAIALQTDSTMIGINNRDIGKLELDDGNVSLTEKLAPLIPKRYVKVSESGIAGTEDL 193 +EE+ IA +T+STMIG+NNRDI KLELDDG VSLTE+LAPLIPK V VSESGI EDL Sbjct: 135 KEEIDIAKETNSTMIGVNNRDITKLELDDGTVSLTEQLAPLIPKNMVFVSESGIGTIEDL 194 Query: 194 KRALRHADAALIGTALMKTPDPEEFLRKLVEVEV 227 + AL++ADAALIGT+ MK + EEF++ V+ ++ Sbjct: 195 RMALKYADAALIGTSFMKAKNIEEFVKSFVDAKL 228 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: 208 Number of extensions: 1 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: 227 Length of database: 228 Length adjustment: 22 Effective length of query: 205 Effective length of database: 206 Effective search space: 42230 Effective search space used: 42230 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 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