Align Indole-3-glycerol phosphate synthase; Short=IGPS; EC 4.1.1.48 (characterized, see rationale)
to candidate Ga0059261_0930 Ga0059261_0930 indole-3-glycerol phosphate synthase (EC 4.1.1.48)
Query= uniprot:A0A560BXT3 (262 letters) >FitnessBrowser__Korea:Ga0059261_0930 Length = 260 Score = 292 bits (748), Expect = 4e-84 Identities = 161/259 (62%), Positives = 188/259 (72%), Gaps = 1/259 (0%) Query: 3 DVLTRICDDKRALVQARKSARPLSAVEDAARAADPARGFIRALRRTVDGGRYGLIAEIKK 62 + L +I D KR V RK+A L+ ++ A A P RGF AL G YGLIAEIKK Sbjct: 2 NTLDKILDVKRREVAERKAATALADLQARALAQTPPRGFRAALDAKAATG-YGLIAEIKK 60 Query: 63 ASPSKGLIRPDFDPPSLARAYREGGATCLSVLTDEPYFQGCDDYLLAARAAVDLPVLRKD 122 ASPSKGLIR DFDPP+ ARAY GGA CLSVLTD +FQG +DYL+AARAA LPV+RKD Sbjct: 61 ASPSKGLIRADFDPPAHARAYEAGGAACLSVLTDAEFFQGHEDYLIAARAACALPVIRKD 120 Query: 123 FMVDPYQIAESRALGADCILIIMAALSDAQAAEIEGAAIAWGLDVLVEVHNREELDRALA 182 FM+DP+Q E+R++GAD ILII+AAL DAQ AEIE AAI G+DVLVEVH+ ELDRALA Sbjct: 121 FMIDPWQALEARSIGADAILIIVAALEDAQMAEIEDAAIGLGMDVLVEVHDEAELDRALA 180 Query: 183 LKTPLLGVNNRNLKTLAVDIATTEELAAHVPADRMLVAESGLYSPADLSRMAAVGARCFL 242 L++ L+GVNNRNLK +V T EL P VAESGL + ADL MA G RCFL Sbjct: 181 LRSRLIGVNNRNLKDFSVSFDRTYELVGRAPEGCTFVAESGLTARADLDAMAEHGVRCFL 240 Query: 243 VGESLMRQEDVTAATRALL 261 +GESLMRQ+DV AATRAL+ Sbjct: 241 IGESLMRQDDVEAATRALV 259 Lambda K H 0.321 0.135 0.382 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: 238 Number of extensions: 8 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: 262 Length of database: 260 Length adjustment: 25 Effective length of query: 237 Effective length of database: 235 Effective search space: 55695 Effective search space used: 55695 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 (21.9 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