Align Indole-3-glycerol phosphate synthase; Short=IGPS; EC 4.1.1.48 (characterized, see rationale)
to candidate 3608400 Dshi_1800 Indole-3-glycerol-phosphate synthase (RefSeq)
Query= uniprot:A0A560BXT3 (262 letters) >FitnessBrowser__Dino:3608400 Length = 271 Score = 325 bits (833), Expect = 6e-94 Identities = 169/259 (65%), Positives = 198/259 (76%), Gaps = 1/259 (0%) Query: 4 VLTRICDDKRALVQARKSARPLSAVEDAARAADPARGFIRALRRTVDGGRYGLIAEIKKA 63 +L RI K V ARK+ARPL+ VE AAR A P R F ALR G Y LIAE+KKA Sbjct: 5 ILDRIKAYKLEEVAARKAARPLAEVEAAARQASPVRPFAGALRAAAQNG-YALIAEVKKA 63 Query: 64 SPSKGLIRPDFDPPSLARAYREGGATCLSVLTDEPYFQGCDDYLLAARAAVDLPVLRKDF 123 SPSKGLIR DFDPP++ARAY GGA CLSVLTD P FQG +DYL+AARAA LPVLRKDF Sbjct: 64 SPSKGLIRADFDPPAIARAYAAGGAACLSVLTDAPSFQGHEDYLVAARAACALPVLRKDF 123 Query: 124 MVDPYQIAESRALGADCILIIMAALSDAQAAEIEGAAIAWGLDVLVEVHNREELDRALAL 183 M DPYQ+ E+RA+GADCILIIMA++SDAQA E+E AA +WG+D L+EVH+ +ELDRAL L Sbjct: 124 MYDPYQVPEARAMGADCILIIMASVSDAQAVELEDAATSWGMDALIEVHDGDELDRALRL 183 Query: 184 KTPLLGVNNRNLKTLAVDIATTEELAAHVPADRMLVAESGLYSPADLSRMAAVGARCFLV 243 +PL+G+NNRNLKT + TT LA +P DRM+VAESGL P +L+ +A GAR FL+ Sbjct: 184 NSPLMGINNRNLKTFETTLDTTRTLAPRIPGDRMIVAESGLSGPTELADLAGYGARTFLI 243 Query: 244 GESLMRQEDVTAATRALLA 262 GESLMRQ DV ATRALLA Sbjct: 244 GESLMRQADVAEATRALLA 262 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: 256 Number of extensions: 7 Number of successful extensions: 3 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: 271 Length adjustment: 25 Effective length of query: 237 Effective length of database: 246 Effective search space: 58302 Effective search space used: 58302 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