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_013706806.1 DESAC_RS09270 ribose-phosphate pyrophosphokinase
Query= SwissProt::P14193 (317 letters) >NCBI__GCF_000195295.1:WP_013706806.1 Length = 316 Score = 332 bits (851), Expect = 7e-96 Identities = 168/308 (54%), Positives = 225/308 (73%), Gaps = 1/308 (0%) Query: 10 LKIFSLNSNPELAKEIADIVGVQLGKCSVTRFSDGEVQINIEESIRGCDCYIIQSTSDPV 69 LKIF+ NSNP+LA EI + + + LGK V FSDGE+++ + E++RG D ++IQST PV Sbjct: 5 LKIFAGNSNPDLALEICNCLSMPLGKAFVGTFSDGEIRVEVGENVRGKDVFVIQSTCHPV 64 Query: 70 NEHIMELLIMVDALKRASAKTINIVIPYYGYARQDRKARSREPITAKLFANLLETAGATR 129 N +IMELLI++DALKRASA+ I VIPYYGYARQDRK R PI+AKL A+LL +AGA R Sbjct: 65 NNNIMELLIIIDALKRASARRITAVIPYYGYARQDRKVAPRVPISAKLVADLLTSAGANR 124 Query: 130 VIALDLHAPQIQGFFDIPIDHLMGVPILGEYFEGKNLEDIVIVSPDHGGVTRARKLADRL 189 ++ +DLH QIQGFF+IP+D+L ++ Y + +D V+VSPD GGV RAR A RL Sbjct: 125 ILTMDLHVGQIQGFFNIPVDNLYASSVMMPYIKANFRDDPVMVSPDAGGVPRARAYAKRL 184 Query: 190 KAPIAIIDKRRPRPNVAEVMNIVGNIEGKTAILIDDIIDTAGTITLAANALVENGAKEVY 249 +A +A IDKRR P A+ M+I+G ++ + A+++DDIIDT GT++ AA L+E GA VY Sbjct: 185 EANLAFIDKRRDAPGKAKAMHIIGEVKDRVAVILDDIIDTGGTLSEAAKVLLEKGASAVY 244 Query: 250 ACCTHPVLSGPAVERINNSTIKELVVTNSIKLPEEK-KIERFKQLSVGPLLAEAIIRVHE 308 ACC+HPVLSGPAVERI S +K LVVT++I L E + ++ QLSV PL +AI +H+ Sbjct: 245 ACCSHPVLSGPAVERIQESPLKGLVVTDTIPLRENALQCKKIHQLSVAPLFCKAITGIHK 304 Query: 309 QQSVSYLF 316 + S+S LF Sbjct: 305 EDSISSLF 312 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: 230 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: 316 Length adjustment: 27 Effective length of query: 290 Effective length of database: 289 Effective search space: 83810 Effective search space used: 83810 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_013706806.1 DESAC_RS09270 (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.28170.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.7e-127 409.1 0.0 5.3e-127 408.9 0.0 1.0 1 lcl|NCBI__GCF_000195295.1:WP_013706806.1 DESAC_RS09270 ribose-phosphate p Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000195295.1:WP_013706806.1 DESAC_RS09270 ribose-phosphate pyrophosphokinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 408.9 0.0 5.3e-127 5.3e-127 2 309 .] 6 313 .. 5 313 .. 0.99 Alignments for each domain: == domain 1 score: 408.9 bits; conditional E-value: 5.3e-127 TIGR01251 2 kilsgssskelaekvaknlglelgdvevkkFadgElyvrieesvrgkdvfiivqstsapvndalmelll 70 ki++g+s+++la ++++ l+++lg++ v +F+dgE+ v++ e+vrgkdvf+i qst++pvn+++mell+ lcl|NCBI__GCF_000195295.1:WP_013706806.1 6 KIFAGNSNPDLALEICNCLSMPLGKAFVGTFSDGEIRVEVGENVRGKDVFVI-QSTCHPVNNNIMELLI 73 89**************************************************.99************** PP TIGR01251 71 lidalkrasaksvtaviPyygYaRqdkkaksrepisaklvaklleeaGadrvltvdlHseqiqgfFdvp 139 +idalkrasa+++taviPyygYaRqd+k+ +r pisaklva+ll++aGa+r+lt+dlH qiqgfF++p lcl|NCBI__GCF_000195295.1:WP_013706806.1 74 IIDALKRASARRITAVIPYYGYARQDRKVAPRVPISAKLVADLLTSAGANRILTMDLHVGQIQGFFNIP 142 ********************************************************************* PP TIGR01251 140 venlsaspklieelkkkelknlvvvsPDkGaverakkvakklglelaiieKeRdskenevevtnllgdv 208 v+nl+as +++ ++k++ +++v+vsPD+G+v ra+++ak+l+++la+i+K+Rd + +++ ++++g+v lcl|NCBI__GCF_000195295.1:WP_013706806.1 143 VDNLYASSVMMPYIKANFRDDPVMVSPDAGGVPRARAYAKRLEANLAFIDKRRD-APGKAKAMHIIGEV 210 ******************************************************.777*********** PP TIGR01251 209 egkdvvivDDiisTggTlvkaaelLkekGAkkvivaathgvfsgdAlerlaeagveevivtntilv.ee 276 +++ +vi+DDii+TggTl +aa++L ekGA+ v+++++h+v+sg+A+er++e+ ++ ++vt+ti+ e+ lcl|NCBI__GCF_000195295.1:WP_013706806.1 211 KDRVAVILDDIIDTGGTLSEAAKVLLEKGASAVYACCSHPVLSGPAVERIQESPLKGLVVTDTIPLrEN 279 ******************************************************************766 PP TIGR01251 277 .kklpkvseisvapliaeaiarihenesvsslfd 309 +++k++++svapl+++ai+ ih++ s+sslfd lcl|NCBI__GCF_000195295.1:WP_013706806.1 280 aLQCKKIHQLSVAPLFCKAITGIHKEDSISSLFD 313 899*****************************96 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (309 nodes) Target sequences: 1 (316 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 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 10.04 // [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