Align phosphoribosylanthranilate isomerase (EC 5.3.1.24) (characterized)
to candidate WP_015739153.1 ADEG_RS05850 indole-3-glycerol phosphate synthase TrpC
Query= BRENDA::P00909 (453 letters) >NCBI__GCF_000024605.1:WP_015739153.1 Length = 266 Score = 152 bits (383), Expect = 2e-41 Identities = 98/255 (38%), Positives = 148/255 (58%), Gaps = 6/255 (2%) Query: 5 VLAKIVADKAIWVEARKQQQPLASFQNEVQ--PSTRHFYDALQ-GARTAFILECKKASPS 61 +L KI+ K + RK++ P + + + P R F AL+ + I E K+ASP Sbjct: 1 MLEKILTHKRAELSLRKKRCPQSQLEASLHLAPPPRPFAQALRFPGKVRIIAEIKRASP- 59 Query: 62 KGVIRDDFDPARIAAIYKHY-ASAISVLTDEKYFQGSFNFLPIVSQIAPQPILCKDFIID 120 +G IR D DP +IA +Y+ A+A+SVL DE++F G FL +V P+L K+F++D Sbjct: 60 RGPIRPDADPVKIARLYQRGGAAAVSVLVDERFFGGKPAFLRLVRWEIDLPLLYKEFVLD 119 Query: 121 PYQIYLARYYQADACLLMLSVLDDDQYRQLAAVAHSLEMGVLTEVSNEEEQERAIALGAK 180 PYQ+Y AR ADA LL+ +L ++ R L +A SL M L EV + ++ ++A+A+GA+ Sbjct: 120 PYQVYEARLLGADAVLLIARLLRTEELRMLKELAASLGMDSLVEVHSRDDLQKALAVGAE 179 Query: 181 VVGINNRDLRDLSIDLNRTRELAPKLGHNVTVISESGINTYAQVRELSHF-ANGFLIGSA 239 +GINNRDL + L TR L P + V V+S SGI++ + L + + LIG A Sbjct: 180 FIGINNRDLATFRVSLQTTRLLRPLIPPEVVVVSASGISSPLALTCLREWKVDAALIGEA 239 Query: 240 LMAHDDLHAAVRRVL 254 LMA D A +R ++ Sbjct: 240 LMAAPDPEAKLRELV 254 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: 252 Number of extensions: 13 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: 266 Length adjustment: 29 Effective length of query: 424 Effective length of database: 237 Effective search space: 100488 Effective search space used: 100488 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