Align phosphoribosylanthranilate isomerase (EC 5.3.1.24) (characterized)
to candidate WP_029910639.1 P166_RS0107530 indole-3-glycerol phosphate synthase TrpC
Query= BRENDA::P00909 (453 letters) >NCBI__GCF_000711315.1:WP_029910639.1 Length = 267 Score = 167 bits (422), Expect = 5e-46 Identities = 104/251 (41%), Positives = 143/251 (56%), Gaps = 12/251 (4%) Query: 5 VLAKIVADKAIWVEARKQQQPLASFQNE--VQPSTRHFYDALQG----ARTAFILECKKA 58 +L KI+ K ++ ++ L + + + P + F DALQ ++A I E KKA Sbjct: 9 ILKKIIFRKLEEIQEGCEKISLREMKQKAMMMPQPKGFADALQAKLDEGKSAVIAEIKKA 68 Query: 59 SPSKGVIRDDFDPARIAAIYK-HYASAISVLTDEKYFQGSFNFLPIVSQIAPQPILCKDF 117 SPSKGV+RD F+P IA Y+ H A+ +SVLTD +FQG+ +L V + PI+ KDF Sbjct: 69 SPSKGVLRDPFEPVEIAKSYQEHGAACLSVLTDRDFFQGANEYLQAVREAVDLPIIRKDF 128 Query: 118 IIDPYQIYLARYYQADACLLMLSVLDDDQYRQLAAVAHSLEMGVLTEVSNEEEQERAIAL 177 I+D YQ+Y AR AD LL+ + + D Q +L A L M VL EV NEEE ERA+ L Sbjct: 129 IVDDYQVYEARAIGADCILLIAAAIGDAQMYELTQTALQLGMDVLVEVHNEEEMERALQL 188 Query: 178 GAKVVGINNRDLRDLSIDLNRTRELAPKLGHNVTVISESGI---NTYAQVRELSHFANGF 234 ++GINNRDL + L T + + N VI+ESGI + AQ+RE H N F Sbjct: 189 PLPMIGINNRDLHTFDVSLETTFRMLEMIPDNRIVITESGILAPSDVAQMRE--HNVNSF 246 Query: 235 LIGSALMAHDD 245 L+G A M D+ Sbjct: 247 LVGEAFMRADN 257 Lambda K H 0.320 0.135 0.389 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: 259 Number of extensions: 14 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: 453 Length of database: 267 Length adjustment: 29 Effective length of query: 424 Effective length of database: 238 Effective search space: 100912 Effective search space used: 100912 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 (21.8 bits) S2: 49 (23.5 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