Align phosphoribosylanthranilate isomerase (EC 5.3.1.24) (characterized)
to candidate WP_018232677.1 THITHI_RS0108595 indole-3-glycerol phosphate synthase TrpC
Query= BRENDA::P00909 (453 letters) >NCBI__GCF_000378965.1:WP_018232677.1 Length = 265 Score = 155 bits (393), Expect = 1e-42 Identities = 100/251 (39%), Positives = 140/251 (55%), Gaps = 12/251 (4%) Query: 5 VLAKIVADKAIWVEARKQQQPLASFQN--EVQPSTRHFYDALQ----GARTAFILECKKA 58 +LA+I+ K + R + L + + P+ R F AL+ G R+A I E KKA Sbjct: 7 ILARILDRKREEIAERMLRTSLEDLRGFIDAAPAVRPFLAALEARIEGGRSAVIAEIKKA 66 Query: 59 SPSKGVIRDDFDPARIAAIYKHYASA-ISVLTDEKYFQGSFNFLPIVSQIAPQPILCKDF 117 SPS+GV+R+DFDPA IA Y+ +A +SVLTD +FQG+ L + P+L KDF Sbjct: 67 SPSRGVLREDFDPASIARSYEAGGAACLSVLTDRDFFQGADVHLEDARAASSLPVLRKDF 126 Query: 118 IIDPYQIYLARYYQADACLLMLSVLDDDQYRQLAAVAHSLEMGVLTEVSNEEEQERAIAL 177 I+D YQ+Y AR AD LL+ + L+D + + L + H L M L E+ E ER + L Sbjct: 127 IVDAYQVYEARVMGADCVLLIAAALEDARLQDLLMLTHELGMNALIEIHEARELERVLKL 186 Query: 178 GAKVVGINNRDLRDLSIDLNRTRELAPKLGHNVTVISESGINT---YAQVRELSHFANGF 234 A ++GINNRDLR L T +L + N VI+ESGI+T A++RE + F Sbjct: 187 DAALIGINNRDLRTFETRLETTLDLVKMIPGNRMVITESGIHTREDVARMREAG--VHAF 244 Query: 235 LIGSALMAHDD 245 L+G A M D Sbjct: 245 LVGEAFMTAAD 255 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: 262 Number of extensions: 9 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: 453 Length of database: 265 Length adjustment: 29 Effective length of query: 424 Effective length of database: 236 Effective search space: 100064 Effective search space used: 100064 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 Jul 25 2024. The underlying query database was built on Jul 25 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