Align Indole-3-glycerol phosphate synthase; Short=IGPS; EC 4.1.1.48 (characterized, see rationale)
to candidate WP_012335095.1 M446_RS26050 indole-3-glycerol phosphate synthase TrpC
Query= uniprot:A0A560BXT3 (262 letters) >NCBI__GCF_000019365.1:WP_012335095.1 Length = 285 Score = 283 bits (724), Expect = 3e-81 Identities = 152/259 (58%), Positives = 183/259 (70%) Query: 3 DVLTRICDDKRALVQARKSARPLSAVEDAARAADPARGFIRALRRTVDGGRYGLIAEIKK 62 DVL I KR + K PL+ +E A ADP RGF A+R + GR LIAEIKK Sbjct: 20 DVLAHIEAYKRREIAEAKLRVPLAELERRAEKADPPRGFAEAIRADLAAGRPALIAEIKK 79 Query: 63 ASPSKGLIRPDFDPPSLARAYREGGATCLSVLTDEPYFQGCDDYLLAARAAVDLPVLRKD 122 ASPS+GLIR DFDPP+LARAY EGGATCLSVLTDEP F+G +YL AAR A LPVLRKD Sbjct: 80 ASPSRGLIRADFDPPALARAYAEGGATCLSVLTDEPSFKGRPEYLTAARQACPLPVLRKD 139 Query: 123 FMVDPYQIAESRALGADCILIIMAALSDAQAAEIEGAAIAWGLDVLVEVHNREELDRALA 182 F+ +PYQ+ E+RA GADCIL+IMA+L D +AA + A G+DVLVEVH+R EL+RAL Sbjct: 140 FLFEPYQVVEARAWGADCILVIMASLDDEEAAALVATAHDLGMDVLVEVHDRAELERALP 199 Query: 183 LKTPLLGVNNRNLKTLAVDIATTEELAAHVPADRMLVAESGLYSPADLSRMAAVGARCFL 242 L T ++G+NNR+L+T V + T L VP DR++V ESG+ AD R+A G R L Sbjct: 200 LGTRMIGINNRDLRTFEVSLETALALRPLVPEDRIVVGESGIAGHADAQRLARAGIRTLL 259 Query: 243 VGESLMRQEDVTAATRALL 261 VGESLMR+ DVTAATR LL Sbjct: 260 VGESLMREADVTAATRRLL 278 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: 257 Number of extensions: 5 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: 285 Length adjustment: 25 Effective length of query: 237 Effective length of database: 260 Effective search space: 61620 Effective search space used: 61620 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 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