Align Ribose-phosphate pyrophosphokinase; RPPK; EC 2.7.6.1; 5-phospho-D-ribosyl alpha-1-diphosphate synthase; Phosphoribosyl diphosphate synthase; Phosphoribosyl pyrophosphate synthase; P-Rib-PP synthase; PRPP synthase; PRPPase (uncharacterized)
to candidate WP_013722688.1 ALIDE2_RS16725 phosphoribosylpyrophosphate synthetase
Query= curated2:Q973F3 (291 letters) >NCBI__GCF_000204645.1:WP_013722688.1 Length = 299 Score = 130 bits (326), Expect = 5e-35 Identities = 80/264 (30%), Positives = 143/264 (54%), Gaps = 11/264 (4%) Query: 32 FPDGESYIRIPQHITNQEILVVQSLYPPQDKHFVELLLILETLADMKNNKITAIVPYLAY 91 FPDGES +R+ + + +++ SL P D + LL + D+ ++ PYLAY Sbjct: 34 FPDGESLVRLDASVAGRTVVITCSLAKP-DAKTLPLLFAADAARDLGAARVVLAAPYLAY 92 Query: 92 SRQDRRFKEGEALSIKTILNAIARAGADVLIVIEPHKEEELSY---FGKEVKIADPMPEL 148 RQDRRF+ GEA++ KT ++ D L+ ++PH S + ++ P + Sbjct: 93 LRQDRRFRAGEAITSKTYARLLSDT-FDALVTVDPHLHRYHSLDEIYRIPSRVVHSAPLI 151 Query: 149 AKEVSKKVEKPFVLAPDRGALERAKRLAEQLNAEYSYIEKERDRDTGEVRIKNLPELR-L 207 A+ V +V++P ++ PD + + ++A A ++ ++K R D +V + +LP++ Sbjct: 152 AQWVKAQVDRPLLIGPDSESEQWVTQVAADAGAPFTVLQKIRHGDR-DVEV-SLPDVTPW 209 Query: 208 SGKDVIIVDDIISTGGTMIQATRAAYEHGARKVISVAVHSLFLDNAYEKLINSGVKEIVT 267 + ++VDDI+S+ TMIQA + + G + + VH+LF +AY +L+ SG +VT Sbjct: 210 LDRQPVLVDDIVSSARTMIQAVGSVRKVGLPTPVCIGVHALFAPDAYNELLASGAARVVT 269 Query: 268 TNTIPQDPSKVTVVDVSPAIARKI 291 NT+P + +DV+ A+AR + Sbjct: 270 CNTVPHASNG---IDVTEAMARAL 290 Lambda K H 0.316 0.135 0.366 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: 190 Number of extensions: 8 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: 291 Length of database: 299 Length adjustment: 26 Effective length of query: 265 Effective length of database: 273 Effective search space: 72345 Effective search space used: 72345 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 48 (23.1 bits)
Align candidate WP_013722688.1 ALIDE2_RS16725 (phosphoribosylpyrophosphate synthetase)
to HMM TIGR01251 (prs: ribose-phosphate diphosphokinase (EC 2.7.6.1))
# hmmsearch :: search profile(s) against a sequence database # HMMER 3.3.1 (Jul 2020); http://hmmer.org/ # Copyright (C) 2020 Howard Hughes Medical Institute. # Freely distributed under the BSD open source license. # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: ../tmp/path.aa/TIGR01251.hmm # target sequence database: /tmp/gapView.17032.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01251 [M=309] Accession: TIGR01251 Description: ribP_PPkin: ribose-phosphate diphosphokinase Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.5e-56 176.3 0.0 4.1e-56 176.1 0.0 1.0 1 lcl|NCBI__GCF_000204645.1:WP_013722688.1 ALIDE2_RS16725 phosphoribosylpyr Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000204645.1:WP_013722688.1 ALIDE2_RS16725 phosphoribosylpyrophosphate synthetase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 176.1 0.0 4.1e-56 4.1e-56 4 300 .. 6 295 .. 4 299 .] 0.91 Alignments for each domain: == domain 1 score: 176.1 bits; conditional E-value: 4.1e-56 TIGR01251 4 lsgssskelaekvaknlglelgdvevkkFadgElyvrieesvrgkdvfiivqstsapvndalmelllli 72 + ++ +++a+++a +l+ e ++F+dgE vr++ sv g ++i + a+ + + + ll+++ lcl|NCBI__GCF_000204645.1:WP_013722688.1 6 FHLPGDEDFADRLALALQAESAGLALHHFPDGESLVRLDASVAG-RTVVI-TCSLAKPDAKTLPLLFAA 72 66677889999*********************************.44555.4555679*********** PP TIGR01251 73 dalkrasaksvtaviPyygYaRqdkkaksrepisaklvaklleeaGadrvltvdlHseq...iqgfFdv 138 da+++ +a +v + +Py++Y Rqd++++ +e+i++k+ a+ll+ d ++tvd H + + +++++ lcl|NCBI__GCF_000204645.1:WP_013722688.1 73 DAARDLGAARVVLAAPYLAYLRQDRRFRAGEAITSKTYARLLSDT-FDALVTVDPHLHRyhsLDEIYRI 140 *********************************************.*********9876111567999* PP TIGR01251 139 pvenlsaspklieelkkkelknlvvvsPDkGaverakkvakklglelaiieKeRdskenevevt.nllg 206 p + ++++p +++++k++ ++ ++++ PD+ + +++++va+ +g+++ +++K R+ ++ +vev + ++ lcl|NCBI__GCF_000204645.1:WP_013722688.1 141 PSRVVHSAPLIAQWVKAQ-VDRPLLIGPDSESEQWVTQVAADAGAPFTVLQKIRHGDR-DVEVSlPDVT 207 ****************96.99999*******************************555.6666514445 PP TIGR01251 207 dvegkdvvivDDiisTggTlvkaaelLkekGAkkvivaathgvfsgdAlerlaeagveevivtntilve 275 +++ v+vDDi+s++ T+++a+ +++ G +++ +h++f+ dA++ l +g+ +v+ +nt+++ lcl|NCBI__GCF_000204645.1:WP_013722688.1 208 PWLDRQPVLVDDIVSSARTMIQAVGSVRKVGLPTPVCIGVHALFAPDAYNELLASGAARVVTCNTVPH- 275 567*****************************************************************. PP TIGR01251 276 ekklpkvseisvapliaeaiarihe 300 + + i+v++ +a+a+ + e lcl|NCBI__GCF_000204645.1:WP_013722688.1 276 -----ASNGIDVTEAMARALEQLME 295 .....9999*********9987766 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (309 nodes) Target sequences: 1 (299 residues searched) Passed MSV filter: 1 (1); expected 0.0 (0.02) Passed bias filter: 1 (1); expected 0.0 (0.02) Passed Vit filter: 1 (1); expected 0.0 (0.001) Passed Fwd filter: 1 (1); expected 0.0 (1e-05) Initial search space (Z): 1 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 7.83 // [ok]
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