Align Indole-3-glycerol phosphate synthase; Short=IGPS; EC 4.1.1.48 (characterized, see rationale)
to candidate WP_012473989.1 CPHAMN1_RS02710 indole-3-glycerol phosphate synthase TrpC
Query= uniprot:E4PQZ8_MARAH (273 letters) >NCBI__GCF_000020545.1:WP_012473989.1 Length = 258 Score = 192 bits (489), Expect = 5e-54 Identities = 111/249 (44%), Positives = 150/249 (60%), Gaps = 2/249 (0%) Query: 11 TILRRIVDRKWEEIDERKRQVSIADLKAKARDQPAARGFANALRSRIEQQTPAVIAEIKK 70 T L +I+D K E+D+ K+Q + + A D AR FA AL++ +Q + +IAE+KK Sbjct: 3 TYLTKILDYKSSEVDQLKQQDPASRYRDAASDLMPARDFAGALKN--DQGSVKLIAEVKK 60 Query: 71 ASPSKGILRDPFEPAVIAESYEKGGAACLSVLTDRDFFQGDEDYLVAARNACSLPVIRKD 130 ASPS+G++ + F P IA Y GA+ SVLTDR FFQG YL + LPV+RKD Sbjct: 61 ASPSRGVMVEDFNPLDIARRYAGIGASAFSVLTDRHFFQGSNQYLQQVSASFDLPVLRKD 120 Query: 131 FMVAPYQVYESRAIGADCILLIAACLTKDQMQELEGIAHEIGLDVLVEVHDGEELDDALT 190 F++ Q+YE+R IGAD ILLI A L ++++ +A IGL VLVEVHD ELD AL Sbjct: 121 FIIDESQIYEARLIGADAILLIVAALDTFRLKDYLQLAAGIGLGVLVEVHDRSELDCALD 180 Query: 191 LTTPLVGINNRNLHTFDVSLDTTFDLHERISQDRLTITESGIMTRSDVEAMTARGIYGFL 250 +VG+NNRNL F VSLDT+ L I D +++ ESG+ SDV M L Sbjct: 181 AGATVVGVNNRNLKDFSVSLDTSLLLRPAIPDDVISVAESGLKKISDVSLMQDASFDAVL 240 Query: 251 VGESFMRAE 259 +GE + +E Sbjct: 241 IGEGLLSSE 249 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: 213 Number of extensions: 10 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: 258 Length adjustment: 25 Effective length of query: 248 Effective length of database: 233 Effective search space: 57784 Effective search space used: 57784 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