Align Indole-3-glycerol phosphate synthase; Short=IGPS; EC 4.1.1.48 (characterized, see rationale)
to candidate WP_004514652.1 GMET_RS12550 indole-3-glycerol phosphate synthase TrpC
Query= uniprot:A0A560BXT3 (262 letters) >NCBI__GCF_000012925.1:WP_004514652.1 Length = 266 Score = 253 bits (647), Expect = 2e-72 Identities = 139/260 (53%), Positives = 174/260 (66%), Gaps = 1/260 (0%) Query: 3 DVLTRICDDKRALVQARKSARPLSAVEDA-ARAADPARGFIRALRRTVDGGRYGLIAEIK 61 D+L +I + KR V A +SA PL+ ++ A D RGF RALR G +IAE+K Sbjct: 6 DILKKIVEHKRREVTAARSATPLAELKARIADLEDQPRGFERALRDCHASGWTAVIAEVK 65 Query: 62 KASPSKGLIRPDFDPPSLARAYREGGATCLSVLTDEPYFQGCDDYLLAARAAVDLPVLRK 121 K SPSKGLIRPDFDP +A Y + GA CLSVLTDE +F G YL R V LP+LRK Sbjct: 66 KGSPSKGLIRPDFDPLEIAETYEQNGAACLSVLTDEHFFLGNLRYLALIREQVRLPLLRK 125 Query: 122 DFMVDPYQIAESRALGADCILIIMAALSDAQAAEIEGAAIAWGLDVLVEVHNREELDRAL 181 DF+ DPYQ+ E+RA GAD IL+I A L Q E+ G A LDVL+EVH+ E++ AL Sbjct: 126 DFLFDPYQVFEARAAGADAILLIAAMLEREQIEELAGIARELSLDVLLEVHDEPEMETAL 185 Query: 182 ALKTPLLGVNNRNLKTLAVDIATTEELAAHVPADRMLVAESGLYSPADLSRMAAVGARCF 241 A L+G+NNRNL+T VD+ATTE+L VPADR +VAESG+ + AD+ R+ GAR F Sbjct: 186 ATNCALIGINNRNLRTFVVDLATTEQLLPMVPADRFVVAESGVNTRADILRLQTAGARGF 245 Query: 242 LVGESLMRQEDVTAATRALL 261 L+GESLMR+ED+ A R LL Sbjct: 246 LIGESLMREEDIGAKLRELL 265 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: 204 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: 262 Length of database: 266 Length adjustment: 25 Effective length of query: 237 Effective length of database: 241 Effective search space: 57117 Effective search space used: 57117 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