Align Indole-3-glycerol phosphate synthase; Short=IGPS; EC 4.1.1.48 (characterized, see rationale)
to candidate WP_057509111.1 ABB28_RS13460 indole-3-glycerol phosphate synthase TrpC
Query= uniprot:A0A166NT80_PSEFL (278 letters) >NCBI__GCF_001431535.1:WP_057509111.1 Length = 264 Score = 323 bits (828), Expect = 2e-93 Identities = 167/262 (63%), Positives = 211/262 (80%), Gaps = 5/262 (1%) Query: 6 VLENILARKVQEVAERSARVSLAELENLAKAADAP--RGFAKALIDQAKTKQPAVIAEIK 63 +L+ ILARK +EVA+R A V L +L+ A+ ADAP RGF +AL PAVIAE+K Sbjct: 4 ILQTILARKAEEVAQRRAAVPLEQLQ--ARLADAPPVRGFVRALQAAIANGDPAVIAEVK 61 Query: 64 KASPSKGVIRENFVPADIAKSYEKGGATCLSVLTDIDYFQGADAYLQQARAACKLPVIRK 123 KASPSKGVIR +F PADIA SYE GGA+CLSVLTD+D+FQG+DAYLQQAR AC LPV+RK Sbjct: 62 KASPSKGVIRPDFHPADIAVSYEFGGASCLSVLTDVDFFQGSDAYLQQAREACTLPVLRK 121 Query: 124 DFMIDPYQIVESRALGADCVLLIVSALDDVKMAELAAVAKSVGLDVLVEVHDGDELERAL 183 DF++DPYQ+VE+R LGADC+LLIV+AL+D ++A L+ +A S+G+DVLVEVHD DELERAL Sbjct: 122 DFVVDPYQVVEARVLGADCILLIVAALEDAQLAALSELAISLGMDVLVEVHDIDELERAL 181 Query: 184 KTLDTPLVGVNNRNLHTFEVNLETTLDLLPRIPRDRLVITESGILNRADVELMEISDVYA 243 + + P++G+NNRNL TFEV+L+TTLD+ +P+DRL++TESGIL DV LM + + A Sbjct: 182 Q-VPAPMIGINNRNLRTFEVSLQTTLDMRSAVPKDRLLVTESGILGPQDVGLMRDAGINA 240 Query: 244 FLVGEAFMRAESPGTELQRLFF 265 FLVGEAFMR E PG L++LFF Sbjct: 241 FLVGEAFMRVEEPGEGLRQLFF 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: 244 Number of extensions: 13 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: 264 Length adjustment: 25 Effective length of query: 253 Effective length of database: 239 Effective search space: 60467 Effective search space used: 60467 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 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