Align phosphoribosylanthranilate isomerase (EC 5.3.1.24) (characterized)
to candidate WP_006746920.1 THITH_RS15380 indole-3-glycerol phosphate synthase TrpC
Query= BRENDA::P00909 (453 letters) >NCBI__GCF_000227685.2:WP_006746920.1 Length = 275 Score = 161 bits (407), Expect = 3e-44 Identities = 103/257 (40%), Positives = 144/257 (56%), Gaps = 8/257 (3%) Query: 5 VLAKIVADKAIWVEARKQQQPLASFQNEVQPST--RHFYDALQG----ARTAFILECKKA 58 +L +I+A K + AR PL + + + R F AL A I E KKA Sbjct: 11 ILQRILARKQEEIRARSATLPLPELASRARDADPPRGFRAALAARIRRGLPAVIAEIKKA 70 Query: 59 SPSKGVIRDDFDPARIAAIY-KHYASAISVLTDEKYFQGSFNFLPIVSQIAPQPILCKDF 117 SPSKGV+R DFDP IA Y +H A+ +SVLTD +FQG+ +L P+L KDF Sbjct: 71 SPSKGVLRADFDPVAIAGSYARHGAACLSVLTDIDFFQGADGYLQKARAACDLPVLRKDF 130 Query: 118 IIDPYQIYLARYYQADACLLMLSVLDDDQYRQLAAVAHSLEMGVLTEVSNEEEQERAIAL 177 ++DPYQ++ AR AD LL+++ LDD+Q R L +A L M VL EV + +E RA+AL Sbjct: 131 VVDPYQVHEARALGADCILLIVAALDDEQMRALYRLALDLGMDVLVEVHDRDELGRALAL 190 Query: 178 GAKVVGINNRDLRDLSIDLNRTRELAPKLGHNVTVISESGINTYAQV-RELSHFANGFLI 236 A ++GINNRDLR L T +L ++ V +++ESGI+ + V R + FL+ Sbjct: 191 DAGLIGINNRDLRSFETRLETTLDLCAQVPEGVLLVTESGIHRPSDVARMRAAGVEAFLV 250 Query: 237 GSALMAHDDLHAAVRRV 253 G A M D A+ R+ Sbjct: 251 GEAFMRAPDPGEALERL 267 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: 255 Number of extensions: 15 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: 275 Length adjustment: 29 Effective length of query: 424 Effective length of database: 246 Effective search space: 104304 Effective search space used: 104304 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