Align Indole-3-glycerol phosphate synthase; Short=IGPS; EC 4.1.1.48 (characterized, see rationale)
to candidate WP_015739153.1 ADEG_RS05850 indole-3-glycerol phosphate synthase TrpC
Query= uniprot:A0A560BXT3 (262 letters) >NCBI__GCF_000024605.1:WP_015739153.1 Length = 266 Score = 183 bits (465), Expect = 3e-51 Identities = 106/258 (41%), Positives = 155/258 (60%), Gaps = 4/258 (1%) Query: 4 VLTRICDDKRALVQARKSARPLSAVEDAARAADPARGFIRALRRTVDGGRYGLIAEIKKA 63 +L +I KRA + RK P S +E + A P R F +ALR G+ +IAEIK+A Sbjct: 1 MLEKILTHKRAELSLRKKRCPQSQLEASLHLAPPPRPFAQALRFP---GKVRIIAEIKRA 57 Query: 64 SPSKGLIRPDFDPPSLARAYREGGATCLSVLTDEPYFQGCDDYLLAARAAVDLPVLRKDF 123 SP +G IRPD DP +AR Y+ GGA +SVL DE +F G +L R +DLP+L K+F Sbjct: 58 SP-RGPIRPDADPVKIARLYQRGGAAAVSVLVDERFFGGKPAFLRLVRWEIDLPLLYKEF 116 Query: 124 MVDPYQIAESRALGADCILIIMAALSDAQAAEIEGAAIAWGLDVLVEVHNREELDRALAL 183 ++DPYQ+ E+R LGAD +L+I L + ++ A + G+D LVEVH+R++L +ALA+ Sbjct: 117 VLDPYQVYEARLLGADAVLLIARLLRTEELRMLKELAASLGMDSLVEVHSRDDLQKALAV 176 Query: 184 KTPLLGVNNRNLKTLAVDIATTEELAAHVPADRMLVAESGLYSPADLSRMAAVGARCFLV 243 +G+NNR+L T V + TT L +P + ++V+ SG+ SP L+ + L+ Sbjct: 177 GAEFIGINNRDLATFRVSLQTTRLLRPLIPPEVVVVSASGISSPLALTCLREWKVDAALI 236 Query: 244 GESLMRQEDVTAATRALL 261 GE+LM D A R L+ Sbjct: 237 GEALMAAPDPEAKLRELV 254 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: 177 Number of extensions: 8 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: 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 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