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_066922443.1 ACG33_RS15105 ribose-phosphate pyrophosphokinase
Query= curated2:Q8RHM2 (316 letters) >NCBI__GCF_001579945.1:WP_066922443.1 Length = 331 Score = 179 bits (453), Expect = 1e-49 Identities = 107/315 (33%), Positives = 174/315 (55%), Gaps = 15/315 (4%) Query: 7 VKIFSGNSNLELAKKIAEKAGLQLGKAEIQRFKDGEVYIEIEETVRGRDVFVVQS----T 62 +KIF+ N++ E IA G++L E + F+DGE + E+VR VFV Q+ Sbjct: 1 MKIFALNTSREFGAAIAATVGIELTAHEEREFEDGEFKVRTLESVRNERVFVCQTLHGDA 60 Query: 63 SEPVNENLMELLIFVDALKRASAKTINVIIPYYGYARQDRKSKPREPITSKLVANLLTTA 122 ++ N+ L LL F+ ALK A+A + V++PY YAR+DR++KPR+P+T++ +A L Sbjct: 61 TQSTNDKLCRLLFFIGALKDAAAADVTVVVPYLAYARKDRRTKPRDPVTTRYLAALFEAV 120 Query: 123 GVNRVVAMDLH-ADQIQGFFDIPLDHMQALPLMARYFKEKGFKGDEVVVVSPDVGGVKRA 181 G++ +V MD+H + F +H++A PL+ R+F + G +VV++PD GGVKRA Sbjct: 121 GLDAIVTMDVHNIAAFENAFRCRKEHLEAAPLIVRHFHHRIEIGRRIVVLAPDAGGVKRA 180 Query: 182 RKLAEKL------DCKIAIIDKRRPKPNMSEVMNLIGEVEGKIAIFIDDMIDTAGTITNG 235 + AE ++A ++K+R + +++ G+V I +DD+ T T+ Sbjct: 181 KAFAELFADSAGRAVELAFMEKQRSEGHVTG-SAFAGDVCAAAVIIVDDLASTGTTLARA 239 Query: 236 ADAIAQRGAKEVYACCTHAVFSDPAIERLEKSVLKEIVITDSIALPERK---KIDKIKIL 292 A +RGA EVYA TH +F A E L + + IV TD+I R+ K+ +L Sbjct: 240 ARMCRERGAAEVYAAVTHGIFGFGAAEALGSTDIDGIVTTDTIGDVCRRCPALAPKLAVL 299 Query: 293 SVDSVFANAIDRITN 307 +FA A+ R+ + Sbjct: 300 ETAPLFAEAVRRMAH 314 Lambda K H 0.319 0.136 0.372 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: 163 Number of extensions: 6 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: 316 Length of database: 331 Length adjustment: 28 Effective length of query: 288 Effective length of database: 303 Effective search space: 87264 Effective search space used: 87264 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 (21.7 bits) S2: 48 (23.1 bits)
Align candidate WP_066922443.1 ACG33_RS15105 (ribose-phosphate pyrophosphokinase)
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.28731.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.9e-79 251.7 0.2 4.8e-79 251.4 0.2 1.0 1 lcl|NCBI__GCF_001579945.1:WP_066922443.1 ACG33_RS15105 ribose-phosphate p Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_001579945.1:WP_066922443.1 ACG33_RS15105 ribose-phosphate pyrophosphokinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 251.4 0.2 4.8e-79 4.8e-79 1 300 [. 1 314 [. 1 319 [. 0.92 Alignments for each domain: == domain 1 score: 251.4 bits; conditional E-value: 4.8e-79 TIGR01251 1 lkilsgssskelaekvaknlglelgdvevkkFadgElyvrieesvrgkdvfiiv...qstsapvndalm 66 +ki+++++s+e+ +++a +g+el+ e ++F dgE++vr esvr++ vf+ + +++nd+l lcl|NCBI__GCF_001579945.1:WP_066922443.1 1 MKIFALNTSREFGAAIAATVGIELTAHEEREFEDGEFKVRTLESVRNERVFVCQtlhGDATQSTNDKLC 69 79*********************************************8888876666445678****** PP TIGR01251 67 ellllidalkrasaksvtaviPyygYaRqdkkaksrepisaklvaklleeaGadrvltvdlHs.eqiqg 134 ll+ i alk+a a vt+v+Py++YaR+d+++k+r+p++ + +a l+e++G d ++t+d+H+ + ++ lcl|NCBI__GCF_001579945.1:WP_066922443.1 70 RLLFFIGALKDAAAADVTVVVPYLAYARKDRRTKPRDPVTTRYLAALFEAVGLDAIVTMDVHNiAAFEN 138 **************************************************************945689* PP TIGR01251 135 fFdvpvenlsaspklieelkkke..lknlvvvsPDkGaverakkvak....klg..lelaiieKeRdsk 195 +F+ + e+l+a+p +++++++++ + +vv++PD+G+v+rak++a+ ++g +ela++eK+R + lcl|NCBI__GCF_001579945.1:WP_066922443.1 139 AFRCRKEHLEAAPLIVRHFHHRIeiGRRIVVLAPDAGGVKRAKAFAElfadSAGraVELAFMEKQRSEG 207 *********************999999***************9986522216666689*********44 PP TIGR01251 196 enevevtnllgdvegkdvvivDDiisTggTlvkaaelLkekGAkkvivaathgvfsgdAlerlaeagve 264 +v+ + gdv v+ivDD+ sTg+Tl++aa++ +e+GA +v++a+thg+f A+e l + ++ lcl|NCBI__GCF_001579945.1:WP_066922443.1 208 --HVTGSAFAGDVCAAAVIIVDDLASTGTTLARAARMCRERGAAEVYAAVTHGIFGFGAAEALGSTDID 274 ..6****************************************************************** PP TIGR01251 265 evivtntilv..ee..kklpkvseisvapliaeaiarihe 300 ++ t+ti + pk+ +++ apl+aea++r+++ lcl|NCBI__GCF_001579945.1:WP_066922443.1 275 GIVTTDTIGDvcRRcpALAPKLAVLETAPLFAEAVRRMAH 314 ********7643335677899**************99876 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (309 nodes) Target sequences: 1 (331 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: 9.91 // [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