Align Ribose-phosphate pyrophosphokinase; RPPK; 5-phospho-D-ribosyl alpha-1-diphosphate synthase; Phosphoribosyl diphosphate synthase; Phosphoribosyl pyrophosphate synthase; P-Rib-PP synthase; PPRibP synthase; PRPP synthase; PRPPase; EC 2.7.6.1 (characterized)
to candidate WP_012991258.1 THAL_RS01060 ribose-phosphate pyrophosphokinase
Query= SwissProt::P14193 (317 letters) >NCBI__GCF_000025605.1:WP_012991258.1 Length = 309 Score = 335 bits (858), Expect = 1e-96 Identities = 171/309 (55%), Positives = 230/309 (74%), Gaps = 3/309 (0%) Query: 9 NLKIFSLNSNPELAKEIADIVGVQLGKCSVTRFSDGEVQINIEESIRGCDCYIIQSTSDP 68 ++K+ + NSNP LA+E+A+ +GV L VTRFSDGEV++ I ES+RG D +++QS P Sbjct: 4 SIKLLTGNSNPTLAREVAEYLGVPLTDMLVTRFSDGEVRVQINESLRGEDVFVLQSLCPP 63 Query: 69 VNEHIMELLIMVDALKRASAKTINIVIPYYGYARQDRKARSREPITAKLFANLLETAGAT 128 NE+IMELL+++DA+KRASA I VIPYY YARQDRK R R PI+A+L A+L+ TAGA Sbjct: 64 ANENIMELLLILDAIKRASAGRITAVIPYYAYARQDRKDRPRVPISARLLADLITTAGAQ 123 Query: 129 RVIALDLHAPQIQGFFDIPIDHLMGVPILGEYFEGKNLEDIVIVSPDHGGVTRARKLADR 188 RV+ +DLH+PQIQGFFDIP+D+L + +L +Y + +D V+VSPD GGV RAR LA++ Sbjct: 124 RVVVVDLHSPQIQGFFDIPVDNLYALQVLHQYLQEDAGKDTVVVSPDAGGVERARLLANK 183 Query: 189 LKAPIAIIDKRRPRPNVAEVMNIVGNIEGKTAILIDDIIDTAGTITLAANALVENGAKEV 248 L + IAII KRRP PNVAEV++I+G++EGK A+++DDIIDTAGT+ AA L+ GA V Sbjct: 184 LGSSIAIIYKRRPEPNVAEVLDIIGDVEGKRAVIVDDIIDTAGTVCAAAELLLARGATRV 243 Query: 249 YACCTHPVLSGPAVERINNSTIKELVVTNSIKLPEEKKIERFKQLSVGPLLAEAIIRVHE 308 TH + SGPAV+R+ S I+E+VVTN+I K + + +SV PLL EAI R+HE Sbjct: 244 DVVATHGIFSGPAVDRLMKSPIQEVVVTNTI---PPKDFPKLRVVSVAPLLGEAIKRIHE 300 Query: 309 QQSVSYLFS 317 +SVS LF+ Sbjct: 301 GESVSSLFT 309 Lambda K H 0.319 0.137 0.383 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: 5 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: 317 Length of database: 309 Length adjustment: 27 Effective length of query: 290 Effective length of database: 282 Effective search space: 81780 Effective search space used: 81780 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_012991258.1 THAL_RS01060 (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.1329.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.5e-129 417.3 0.0 1.6e-129 417.2 0.0 1.0 1 lcl|NCBI__GCF_000025605.1:WP_012991258.1 THAL_RS01060 ribose-phosphate py Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000025605.1:WP_012991258.1 THAL_RS01060 ribose-phosphate pyrophosphokinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 417.2 0.0 1.6e-129 1.6e-129 2 309 .] 6 309 .] 5 309 .] 0.99 Alignments for each domain: == domain 1 score: 417.2 bits; conditional E-value: 1.6e-129 TIGR01251 2 kilsgssskelaekvaknlglelgdvevkkFadgElyvrieesvrgkdvfiivqstsapvndalmelll 70 k+l g+s+++la++va++lg++l+d+ v++F+dgE+ v+i+es+rg+dvf++ qs ++p n+++melll lcl|NCBI__GCF_000025605.1:WP_012991258.1 6 KLLTGNSNPTLAREVAEYLGVPLTDMLVTRFSDGEVRVQINESLRGEDVFVL-QSLCPPANENIMELLL 73 7899***********************************************9.**************** PP TIGR01251 71 lidalkrasaksvtaviPyygYaRqdkkaksrepisaklvaklleeaGadrvltvdlHseqiqgfFdvp 139 ++da+krasa+++taviPyy+YaRqd+k+++r pisa+l+a+l+++aGa+rv++vdlHs+qiqgfFd+p lcl|NCBI__GCF_000025605.1:WP_012991258.1 74 ILDAIKRASAGRITAVIPYYAYARQDRKDRPRVPISARLLADLITTAGAQRVVVVDLHSPQIQGFFDIP 142 ********************************************************************* PP TIGR01251 140 venlsaspklieelkkkelknlvvvsPDkGaverakkvakklglelaiieKeRdskenevevtnllgdv 208 v+nl+a ++l ++l+++ k++vvvsPD+G+vera+ +a+klg+++aii+K+R+ + n++ev +++gdv lcl|NCBI__GCF_000025605.1:WP_012991258.1 143 VDNLYALQVLHQYLQEDAGKDTVVVSPDAGGVERARLLANKLGSSIAIIYKRRP-EPNVAEVLDIIGDV 210 ******************************************************.888*********** PP TIGR01251 209 egkdvvivDDiisTggTlvkaaelLkekGAkkvivaathgvfsgdAlerlaeagveevivtntilveek 277 egk +vivDDii+T+gT+++aaelL +GA++v v+athg+fsg+A+ rl ++ ++ev+vtnti+ k lcl|NCBI__GCF_000025605.1:WP_012991258.1 211 EGKRAVIVDDIIDTAGTVCAAAELLLARGATRVDVVATHGIFSGPAVDRLMKSPIQEVVVTNTIPP--K 277 ******************************************************************..9 PP TIGR01251 278 klpkvseisvapliaeaiarihenesvsslfd 309 +pk++++svapl+ eai+rihe+esvsslf+ lcl|NCBI__GCF_000025605.1:WP_012991258.1 278 DFPKLRVVSVAPLLGEAIKRIHEGESVSSLFT 309 9*****************************96 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (309 nodes) Target sequences: 1 (309 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 8.59 // [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