Align phosphoribosylanthranilate isomerase (EC 5.3.1.24) (characterized)
to candidate WP_009544995.1 CCE_RS10910 indole-3-glycerol-phosphate synthase
Query= BRENDA::P00909 (453 letters) >NCBI__GCF_000017845.1:WP_009544995.1 Length = 294 Score = 165 bits (417), Expect = 2e-45 Identities = 106/258 (41%), Positives = 148/258 (57%), Gaps = 12/258 (4%) Query: 5 VLAKIVADKAIWVEARKQQQPLASFQNEVQ--PSTRHFYDALQGART--AFILECKKASP 60 +L +IV K VE + + L + + Q P + F A+ +T A I E KKASP Sbjct: 31 ILEEIVWHKEKEVERMRDRLSLLDLRKQEQSAPPAKDFLGAISQGKTQPALIAEVKKASP 90 Query: 61 SKGVIRDDFDPARIAAIY-KHYASAISVLTDEKYFQGSFNFLPIVSQIAPQPILCKDFII 119 SKGVIR+DF+P IA Y + AS +SVLTD K+FQGSF+ L +V Q P+LCK+FII Sbjct: 91 SKGVIREDFEPVAIAQAYVQGGASCLSVLTDSKFFQGSFDNLALVRQAVDIPLLCKEFII 150 Query: 120 DPYQIYLARYYQADACLLMLSVLDDDQYRQLAAVAHSLEMGVLTEVSNEEEQERAIAL-G 178 PYQIYLAR ADA LL+ ++L D + L + H L M L EV + E +R +A+ G Sbjct: 151 YPYQIYLARVKGADAILLIAAILKDSDLQYLIKIIHGLGMTPLVEVHSLAELDRVLAIEG 210 Query: 179 AKVVGINNRDLRDLSIDLNRTRELAPK-----LGHNVTVISESGINTYAQVRELSHF-AN 232 +VGINNR+L + L T L + ++SESGI+T +++++ AN Sbjct: 211 VSLVGINNRNLETFEVSLETTTNLITARQDEIKERGIYIVSESGIHTPQHLQQVTEAGAN 270 Query: 233 GFLIGSALMAHDDLHAAV 250 LIG +L+ DD A+ Sbjct: 271 AVLIGESLVKQDDPTQAI 288 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: 276 Number of extensions: 12 Number of successful extensions: 4 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: 294 Length adjustment: 29 Effective length of query: 424 Effective length of database: 265 Effective search space: 112360 Effective search space used: 112360 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