Align Indole-3-glycerol phosphate synthase; Short=IGPS; EC 4.1.1.48 (characterized, see rationale)
to candidate WP_041100205.1 SUTH_RS14350 indole-3-glycerol phosphate synthase TrpC
Query= uniprot:A0A166NT80_PSEFL (278 letters) >NCBI__GCF_000828635.1:WP_041100205.1 Length = 268 Score = 284 bits (727), Expect = 1e-81 Identities = 153/262 (58%), Positives = 193/262 (73%), Gaps = 1/262 (0%) Query: 6 VLENILARKVQEVAERSARVSLAELENLAKAADAPRGFAKALIDQAKTKQPAVIAEIKKA 65 +L ILA K +EVA SA LA + +A+A R F A+ + + A+IAEIKKA Sbjct: 4 ILNRILAVKREEVAAASAAKPLAGIRAVAEALAPTRDFVGAMKARVGAGETAIIAEIKKA 63 Query: 66 SPSKGVIRENFVPADIAKSYEKGGATCLSVLTDIDYFQGADAYLQQARAACKLPVIRKDF 125 SPSKGVIR +F P +IA YEK GATCLSVLTD +FQG++AYL++ARAAC LPV+RKDF Sbjct: 64 SPSKGVIRPDFHPTEIAADYEKHGATCLSVLTDRQFFQGSEAYLREARAACSLPVLRKDF 123 Query: 126 MIDPYQIVESRALGADCVLLIVSALDDVKMAELAAVAKSVGLDVLVEVHDGDELERALKT 185 ++D YQ+ E+RA+GAD +LLIV+AL +M E+ A+A S+G+ VLVE HD EL+ AL+ Sbjct: 124 LVDNYQVYEARAMGADAILLIVAALSLAQMQEMEAIAHSLGMAVLVESHDAAELDVALQ- 182 Query: 186 LDTPLVGVNNRNLHTFEVNLETTLDLLPRIPRDRLVITESGILNRADVELMEISDVYAFL 245 L TPL+G+NNRNL +FEV+L+TTL L RIP DR+V+TESGI+ DV L+ V AFL Sbjct: 183 LKTPLIGINNRNLRSFEVSLDTTLSQLDRIPADRIVVTESGIVTPDDVALLRGRGVNAFL 242 Query: 246 VGEAFMRAESPGTELQRLFFPE 267 VGEAFMRA SPG EL RLF PE Sbjct: 243 VGEAFMRAPSPGAELARLFSPE 264 Lambda K H 0.318 0.135 0.369 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: 241 Number of extensions: 8 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: 278 Length of database: 268 Length adjustment: 25 Effective length of query: 253 Effective length of database: 243 Effective search space: 61479 Effective search space used: 61479 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 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