Align Indole-3-glycerol phosphate synthase; Short=IGPS; EC 4.1.1.48 (characterized, see rationale)
to candidate BPHYT_RS17405 BPHYT_RS17405 indole-3-glycerol phosphate synthase
Query= uniprot:A0A166NT80_PSEFL (278 letters) >FitnessBrowser__BFirm:BPHYT_RS17405 Length = 261 Score = 296 bits (757), Expect = 4e-85 Identities = 155/260 (59%), Positives = 197/260 (75%), Gaps = 2/260 (0%) Query: 6 VLENILARKVQEVAERSARVSLAELENLAKAADAPRGFAKALIDQAKTKQPAVIAEIKKA 65 +L+ I+A K +EV L EL A + D R F AL + AVI+E+KKA Sbjct: 4 ILDRIIAVKREEVRAAEQSAPLEELRLEASSRDI-RDFVGALRAKHTAGLAAVISEVKKA 62 Query: 66 SPSKGVIRENFVPADIAKSYEKGGATCLSVLTDIDYFQGADAYLQQARAACKLPVIRKDF 125 SPSKGV+RE+FVPA+IA+SYEK GA CLSVLTD+ +FQG+ AYL++ARAAC LPV+RKDF Sbjct: 63 SPSKGVLREHFVPAEIARSYEKHGAACLSVLTDVQFFQGSVAYLEEARAACNLPVLRKDF 122 Query: 126 MIDPYQIVESRALGADCVLLIVSALDDVKMAELAAVAKSVGLDVLVEVHDGDELERALKT 185 ++DPYQIVE+RA+GAD +LLI +AL+ +M +L A+A S+GL VLVEVHD DEL +L T Sbjct: 123 IVDPYQIVEARAMGADAILLIAAALETSQMQDLEALAHSLGLAVLVEVHDHDELMESL-T 181 Query: 186 LDTPLVGVNNRNLHTFEVNLETTLDLLPRIPRDRLVITESGILNRADVELMEISDVYAFL 245 L TPL+G+NNRNL TFE ++ETT+ +L IP DR+V+TESGIL+RADVE + DV+ FL Sbjct: 182 LKTPLIGINNRNLRTFETSIETTIGMLEAIPDDRIVVTESGILSRADVERLRAMDVHTFL 241 Query: 246 VGEAFMRAESPGTELQRLFF 265 VGEAFMRA PG EL R+FF Sbjct: 242 VGEAFMRANEPGVELARMFF 261 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: 225 Number of extensions: 7 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: 261 Length adjustment: 25 Effective length of query: 253 Effective length of database: 236 Effective search space: 59708 Effective search space used: 59708 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 Aug 03 2021. The underlying query database was built on Aug 03 2021.
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