Align phosphoribosylanthranilate isomerase (EC 5.3.1.24) (characterized)
to candidate WP_092344860.1 BLU87_RS03720 indole-3-glycerol phosphate synthase TrpC
Query= BRENDA::P00909 (453 letters) >NCBI__GCF_900107645.1:WP_092344860.1 Length = 261 Score = 178 bits (452), Expect = 2e-49 Identities = 109/259 (42%), Positives = 153/259 (59%), Gaps = 11/259 (4%) Query: 5 VLAKIVADKAIWVEARKQQQPLASFQNE------VQPSTRHF-YDALQGARTAFILECKK 57 +L +I+ K + + A + +QPL + + V+ RH +L G TA I E KK Sbjct: 2 ILDQILQTKRVEIAADRLRQPLRELKKKLATVDPVRGFARHLRQSSLSG--TAVIAEVKK 59 Query: 58 ASPSKGVIRDDFDPARIAAIYKHY-ASAISVLTDEKYFQGSFNFLPIVSQIAPQPILCKD 116 SPSKG+IR+DFDP IA Y+ AS +SVLTD +YF GS ++L ++ + P+L KD Sbjct: 60 GSPSKGIIREDFDPVDIARSYERSGASCLSVLTDFEYFYGSLDYLGMIRRQVDLPLLRKD 119 Query: 117 FIIDPYQIYLARYYQADACLLMLSVLDDDQYRQLAAVAHSLEMGVLTEVSNEEEQERAIA 176 FI+DPYQIY AR ADA LL+ + LDD + +LA +A LE+ L EV N E ERA+ Sbjct: 120 FIVDPYQIYQARVAGADAILLIAAALDDGRLLELAELATELELDTLLEVHNGAELERALQ 179 Query: 177 LGAKVVGINNRDLRDLSIDLNRTRELAPKLGHNVTVISESGINTYAQVRELSHF-ANGFL 235 L ++GINNR+L++ DL T LA K+ ++ESGI+ A + L A FL Sbjct: 180 LPVDLIGINNRNLKNFVTDLGVTESLAGKIPRQQVAVAESGIHNRADIERLQRSGAGAFL 239 Query: 236 IGSALMAHDDLHAAVRRVL 254 IG +LM D+ A +R +L Sbjct: 240 IGESLMREKDIEAKLRSLL 258 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: 246 Number of extensions: 10 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: 261 Length adjustment: 29 Effective length of query: 424 Effective length of database: 232 Effective search space: 98368 Effective search space used: 98368 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