Align Indole-3-glycerol phosphate synthase; Short=IGPS; EC 4.1.1.48 (characterized, see rationale)
to candidate H281DRAFT_05712 H281DRAFT_05712 indole-3-glycerol phosphate synthase
Query= uniprot:A0A166NT80_PSEFL (278 letters) >FitnessBrowser__Burk376:H281DRAFT_05712 Length = 265 Score = 297 bits (760), Expect = 2e-85 Identities = 157/261 (60%), Positives = 196/261 (75%), Gaps = 2/261 (0%) Query: 6 VLENILARKVQEVAERSARVSLAELENLAKAADAPRGFAKALIDQAKTKQPAVIAEIKKA 65 +L+ I+A K +EV L EL A + D R F AL + AVIAE+KKA Sbjct: 4 ILDRIIAVKREEVRAAEQSAPLEELRLEASSRDI-RDFVGALRAKHAAGLAAVIAEVKKA 62 Query: 66 SPSKGVIRENFVPADIAKSYEKGGATCLSVLTDIDYFQGADAYLQQARAACKLPVIRKDF 125 SPSKGV+RENFVPA IA+SYE GA CLSVLTD+ +F+G+ AYL+QARAAC+LPV+RKDF Sbjct: 63 SPSKGVLRENFVPAQIARSYETHGAACLSVLTDVQFFKGSVAYLEQARAACQLPVLRKDF 122 Query: 126 MIDPYQIVESRALGADCVLLIVSALDDVKMAELAAVAKSVGLDVLVEVHDGDELERALKT 185 ++DPYQIVE+RA+GAD +LLI +AL+ +M +L A+A S+GL VLVEVHD DEL +AL T Sbjct: 123 IVDPYQIVEARAMGADAILLIAAALETSEMQDLEALAHSLGLAVLVEVHDSDELMQAL-T 181 Query: 186 LDTPLVGVNNRNLHTFEVNLETTLDLLPRIPRDRLVITESGILNRADVELMEISDVYAFL 245 L TPL+GVNNRNL TFE ++E T+ +L IP DR+V+TESGIL+R DVE + DV FL Sbjct: 182 LKTPLIGVNNRNLRTFETSIENTIGMLEAIPDDRIVVTESGILSRVDVERLRAMDVNTFL 241 Query: 246 VGEAFMRAESPGTELQRLFFP 266 VGEAFMRA+ PG EL R+FFP Sbjct: 242 VGEAFMRADEPGVELARMFFP 262 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: 232 Number of extensions: 5 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: 265 Length adjustment: 25 Effective length of query: 253 Effective length of database: 240 Effective search space: 60720 Effective search space used: 60720 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