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_042614861.1 ABB28_RS08010 ribose-phosphate pyrophosphokinase
Query= SwissProt::P0A1V6 (315 letters) >NCBI__GCF_001431535.1:WP_042614861.1 Length = 319 Score = 378 bits (970), Expect = e-109 Identities = 189/313 (60%), Positives = 242/313 (77%), Gaps = 1/313 (0%) Query: 2 PDMKLFAGNATPELAQRIANRLYTSLGDAAVGRFSDGEVSVQINENVRGGDIFIIQSTCA 61 P++ +F+GNA LAQ I L G A V FSDGEV V+I ENVR D+F+IQ T A Sbjct: 5 PNLLVFSGNANKRLAQNICKELGVRPGKALVSHFSDGEVQVEIEENVRKQDVFVIQPTSA 64 Query: 62 PTNDNLMELVVMVDALRRASAGRITAVIPYFGYARQDRRVRSARVPITAKVVADFLSSVG 121 P+ +NLMEL+V++DAL+RAS +TAV+PYFGY+RQDRR+RS+RVPITAK+ A S+ G Sbjct: 65 PSAENLMELLVLIDALKRASVASVTAVVPYFGYSRQDRRMRSSRVPITAKLAAKMFSTAG 124 Query: 122 VDRVLTVDLHAEQIQGFFDVPVDNVFGSPILLEDMLQ-LNLDNPIVVSPDIGGVVRARAI 180 DRVLTVDLHA+QIQGFFD+PVDNV+ SP+LL D+ + +N IVVSPD+GGVVRARA+ Sbjct: 125 ADRVLTVDLHADQIQGFFDIPVDNVYASPLLLADIWRAYGTENLIVVSPDVGGVVRARAV 184 Query: 181 AKLLNDTDMAIIDKRRPRANVSQVMHIIGDVAGRDCVLVDDMIDTGGTLCKAAEALKERG 240 AK L+D D+AIIDKRRPRANVS VM+IIGDV G+ CV+VDD++DT GTLC AA ALK RG Sbjct: 185 AKRLDDADLAIIDKRRPRANVSTVMNIIGDVEGKTCVMVDDIVDTAGTLCAAAAALKARG 244 Query: 241 AKRVFAYATHPIFSGNAANNLRNSVIDEVVVCDTIPLTDEIKALPNVRTLTLSGMLAEAI 300 A +V AY TH + SG A +N+ NS +DE+VV DTIPL D + +R L+++ MLAE + Sbjct: 245 ALKVAAYCTHAVLSGPAVDNITNSQLDELVVTDTIPLKDAARVCSKIRQLSVAEMLAETM 304 Query: 301 RRISNEESISAMF 313 RRI+ ES+S+++ Sbjct: 305 RRIAFGESVSSLY 317 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: 306 Number of extensions: 8 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: 319 Length adjustment: 27 Effective length of query: 288 Effective length of database: 292 Effective search space: 84096 Effective search space used: 84096 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_042614861.1 ABB28_RS08010 (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.15342.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.6e-119 384.4 1.6 1.8e-119 384.2 1.6 1.0 1 lcl|NCBI__GCF_001431535.1:WP_042614861.1 ABB28_RS08010 ribose-phosphate p Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_001431535.1:WP_042614861.1 ABB28_RS08010 ribose-phosphate pyrophosphokinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 384.2 1.6 1.8e-119 1.8e-119 3 308 .. 9 317 .. 7 318 .. 0.98 Alignments for each domain: == domain 1 score: 384.2 bits; conditional E-value: 1.8e-119 TIGR01251 3 ilsgssskelaekvaknlglelgdvevkkFadgElyvrieesvrgkdvfiivqstsapvndalmellll 71 ++sg+++k+la++++k+lg++ g++ v +F+dgE++v+iee+vr +dvf+i q tsap ++lmell+l lcl|NCBI__GCF_001431535.1:WP_042614861.1 9 VFSGNANKRLAQNICKELGVRPGKALVSHFSDGEVQVEIEENVRKQDVFVI-QPTSAPSAENLMELLVL 76 89*************************************************.***************** PP TIGR01251 72 idalkrasaksvtaviPyygYaRqdkkak.srepisaklvaklleeaGadrvltvdlHseqiqgfFdvp 139 idalkras+ svtav+Py+gY+Rqd++++ sr pi+akl ak++++aGadrvltvdlH++qiqgfFd+p lcl|NCBI__GCF_001431535.1:WP_042614861.1 77 IDALKRASVASVTAVVPYFGYSRQDRRMRsSRVPITAKLAAKMFSTAGADRVLTVDLHADQIQGFFDIP 145 ***************************9868************************************** PP TIGR01251 140 venlsaspklieelkkke.lknlvvvsPDkGaverakkvakklg.lelaiieKeRdskenevevtnllg 206 v+n++asp l++++ + + +nl+vvsPD G+v ra++vak+l+ ++laii+K+R+ ++n+ +v+n++g lcl|NCBI__GCF_001431535.1:WP_042614861.1 146 VDNVYASPLLLADIWRAYgTENLIVVSPDVGGVVRARAVAKRLDdADLAIIDKRRP-RANVSTVMNIIG 213 **************99999*************************9***********.888********* PP TIGR01251 207 dvegkdvvivDDiisTggTlvkaaelLkekGAkkvivaathgvfsgdAlerlaeagveevivtntilv. 274 dvegk++v+vDDi++T+gTl++aa +Lk +GA kv +++th+v+sg+A+ ++++++++e++vt+ti+ lcl|NCBI__GCF_001431535.1:WP_042614861.1 214 DVEGKTCVMVDDIVDTAGTLCAAAAALKARGALKVAAYCTHAVLSGPAVDNITNSQLDELVVTDTIPLk 282 ********************************************************************5 PP TIGR01251 275 ee.kklpkvseisvapliaeaiarihenesvsslf 308 + + ++k++++sva+++ae+++ri+ +esvssl+ lcl|NCBI__GCF_001431535.1:WP_042614861.1 283 DAaRVCSKIRQLSVAEMLAETMRRIAFGESVSSLY 317 44899****************************98 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (309 nodes) Target sequences: 1 (319 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: 00:00:00.00 # Mc/sec: 11.43 // [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