Align Indole-3-glycerol phosphate synthase; Short=IGPS; EC 4.1.1.48 (characterized, see rationale)
to candidate WP_028487310.1 B076_RS0110675 indole-3-glycerol phosphate synthase TrpC
Query= uniprot:E4PQZ8_MARAH (273 letters) >NCBI__GCF_000483485.1:WP_028487310.1 Length = 268 Score = 293 bits (751), Expect = 2e-84 Identities = 152/263 (57%), Positives = 194/263 (73%), Gaps = 2/263 (0%) Query: 9 TPTILRRIVDRKWEEIDERKRQVSIADLKAKARDQPAA--RGFANALRSRIEQQTPAVIA 66 TPTIL++I+ RK EEI E ++ + ++K KA + RGFA+AL+++++ AVIA Sbjct: 4 TPTILKKIIFRKLEEIQEGCERIPLREMKQKALMMTTSPTRGFADALQAKLDAGESAVIA 63 Query: 67 EIKKASPSKGILRDPFEPAVIAESYEKGGAACLSVLTDRDFFQGDEDYLVAARNACSLPV 126 EIKKASPSKG+LR+PF+P IA+SY+ GAACLSVLTD DFFQG +YL R A LP+ Sbjct: 64 EIKKASPSKGVLREPFDPVEIAKSYQAHGAACLSVLTDHDFFQGSNEYLQQVREAVDLPI 123 Query: 127 IRKDFMVAPYQVYESRAIGADCILLIAACLTKDQMQELEGIAHEIGLDVLVEVHDGEELD 186 IRKDF+V YQVYE+R IGADCILLIAA + Q+ EL A ++G+DVLVEVH+ EEL+ Sbjct: 124 IRKDFIVDDYQVYEARVIGADCILLIAAAIGDAQLYELTETALQLGMDVLVEVHNEEELE 183 Query: 187 DALTLTTPLVGINNRNLHTFDVSLDTTFDLHERISQDRLTITESGIMTRSDVEAMTARGI 246 AL L P++GINNR+LHTFDVSL+TT + +RI DR+ ITESGI+ DV M + Sbjct: 184 RALRLPLPMIGINNRDLHTFDVSLETTIRMLDRIPDDRIVITESGILGPEDVAKMREHHV 243 Query: 247 YGFLVGESFMRAEEPGQKLQELF 269 FLVGE+FMRAE PG+KL ELF Sbjct: 244 NSFLVGEAFMRAENPGEKLAELF 266 Lambda K H 0.320 0.136 0.387 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: 253 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: 273 Length of database: 268 Length adjustment: 25 Effective length of query: 248 Effective length of database: 243 Effective search space: 60264 Effective search space used: 60264 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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