Align Ribose-phosphate pyrophosphokinase; RPPK; 5-phospho-D-ribosyl alpha-1-diphosphate synthase; Phosphoribosyl diphosphate synthase; Phosphoribosyl pyrophosphate synthase; P-Rib-PP synthase; PRPP synthase; PRPPase; EC 2.7.6.1 (characterized)
to candidate WP_027457389.1 K420_RS0106660 ribose-phosphate pyrophosphokinase
Query= SwissProt::P0A1V6 (315 letters) >NCBI__GCF_000519045.1:WP_027457389.1 Length = 316 Score = 409 bits (1052), Expect = e-119 Identities = 201/310 (64%), Positives = 257/310 (82%), Gaps = 1/310 (0%) Query: 4 MKLFAGNATPELAQRIANRLYTSLGDAAVGRFSDGEVSVQINENVRGGDIFIIQSTCAPT 63 + +F GNA P+LA +A +L LG A VGRFSDGEVSV++ E+VRG DIF++QSTCAPT Sbjct: 6 LMVFTGNANPKLAADVAQQLNVDLGRANVGRFSDGEVSVELQEHVRGRDIFVLQSTCAPT 65 Query: 64 NDNLMELVVMVDALRRASAGRITAVIPYFGYARQDRRVRSARVPITAKVVADFLSSVGVD 123 NDNLME++VMVDAL+RASAGRITA IPYFGYARQDRR RS+RVPI AK+VA+ L + GVD Sbjct: 66 NDNLMEMLVMVDALKRASAGRITAAIPYFGYARQDRRSRSSRVPIAAKLVANMLVASGVD 125 Query: 124 RVLTVDLHAEQIQGFFDVPVDNVFGSPILLEDMLQLNLDNPIVVSPDIGGVVRARAIAKL 183 RVLT+DLHAEQIQGFFD+PVDN++ PILL+D+ + N +NP+VVSPD GGVVRAR++AK Sbjct: 126 RVLTMDLHAEQIQGFFDIPVDNIYALPILLDDIRKQNYENPLVVSPDHGGVVRARSLAKR 185 Query: 184 LNDTDMAIIDKRRPRANVSQVMHIIGDVAGRDCVLVDDMIDTGGTLCKAAEALKERGAKR 243 L + D+AIIDKRRP+ANVS+VM+IIG+V GR C+++DDM+DT GTLCKAA ALK GAK+ Sbjct: 186 L-ECDLAIIDKRRPKANVSEVMNIIGEVDGRTCIIMDDMVDTAGTLCKAATALKANGAKK 244 Query: 244 VFAYATHPIFSGNAANNLRNSVIDEVVVCDTIPLTDEIKALPNVRTLTLSGMLAEAIRRI 303 V AY THP+ SG A + +S +D +VV DTIPL D+ A P +R L+++ ++AE IRRI Sbjct: 245 VVAYCTHPVLSGPAVERVNSSDLDALVVTDTIPLRDDAAASPRIRQLSVAEIMAETIRRI 304 Query: 304 SNEESISAMF 313 SN++S+S++F Sbjct: 305 SNDDSVSSLF 314 Lambda K H 0.322 0.137 0.386 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: 305 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: 315 Length of database: 316 Length adjustment: 27 Effective length of query: 288 Effective length of database: 289 Effective search space: 83232 Effective search space used: 83232 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 (21.9 bits) S2: 48 (23.1 bits)
Align candidate WP_027457389.1 K420_RS0106660 (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.3846.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.1e-127 411.2 0.7 1.2e-127 411.0 0.7 1.0 1 lcl|NCBI__GCF_000519045.1:WP_027457389.1 K420_RS0106660 ribose-phosphate Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000519045.1:WP_027457389.1 K420_RS0106660 ribose-phosphate pyrophosphokinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 411.0 0.7 1.2e-127 1.2e-127 2 308 .. 7 314 .. 6 315 .. 0.98 Alignments for each domain: == domain 1 score: 411.0 bits; conditional E-value: 1.2e-127 TIGR01251 2 kilsgssskelaekvaknlglelgdvevkkFadgElyvrieesvrgkdvfiivqstsapvndalmelll 70 +++ g+++++la+ va++l+++lg+++v +F+dgE++v+++e+vrg+d+f++ qst+ap+nd+lme+l+ lcl|NCBI__GCF_000519045.1:WP_027457389.1 7 MVFTGNANPKLAADVAQQLNVDLGRANVGRFSDGEVSVELQEHVRGRDIFVL-QSTCAPTNDNLMEMLV 74 89**************************************************.**************** PP TIGR01251 71 lidalkrasaksvtaviPyygYaRqdkkak.srepisaklvaklleeaGadrvltvdlHseqiqgfFdv 138 ++dalkrasa+++ta iPy+gYaRqd++ + sr pi+aklva++l + G+drvlt+dlH+eqiqgfFd+ lcl|NCBI__GCF_000519045.1:WP_027457389.1 75 MVDALKRASAGRITAAIPYFGYARQDRRSRsSRVPIAAKLVANMLVASGVDRVLTMDLHAEQIQGFFDI 143 ***************************98768************************************* PP TIGR01251 139 pvenlsaspklieelkkkelknlvvvsPDkGaverakkvakklglelaiieKeRdskenevevtnllgd 207 pv+n++a p l+++++k++ +n++vvsPD+G+v ra+++ak+l+++laii+K+R+ k+n+ ev+n++g+ lcl|NCBI__GCF_000519045.1:WP_027457389.1 144 PVDNIYALPILLDDIRKQNYENPLVVSPDHGGVVRARSLAKRLECDLAIIDKRRP-KANVSEVMNIIGE 211 *******************************************************.899********** PP TIGR01251 208 vegkdvvivDDiisTggTlvkaaelLkekGAkkvivaathgvfsgdAlerlaeagveevivtntilv.e 275 v+g++++i+DD+++T+gTl+kaa++Lk +GAkkv++++th+v+sg+A+er++++ +++++vt+ti+ + lcl|NCBI__GCF_000519045.1:WP_027457389.1 212 VDGRTCIIMDDMVDTAGTLCKAATALKANGAKKVVAYCTHPVLSGPAVERVNSSDLDALVVTDTIPLrD 280 *******************************************************************87 PP TIGR01251 276 e.kklpkvseisvapliaeaiarihenesvsslf 308 + + p+++++sva+++ae+i+ri+++ svsslf lcl|NCBI__GCF_000519045.1:WP_027457389.1 281 DaAASPRIRQLSVAEIMAETIRRISNDDSVSSLF 314 78999****************************9 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 10.27 // [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