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 AZOBR_RS31185 AZOBR_RS31185 ribose-phosphate pyrophosphokinase
Query= SwissProt::P0A1V6 (315 letters) >FitnessBrowser__azobra:AZOBR_RS31185 Length = 311 Score = 323 bits (828), Expect = 3e-93 Identities = 167/312 (53%), Positives = 228/312 (73%), Gaps = 4/312 (1%) Query: 4 MKLFAGNATPELAQRIANRLYTSLGDAAVGRFSDGEVSVQINENVRGGDIFIIQSTCAPT 63 MK+ AGN+ LA+ I+ L L A++ RFSD EV V+I ENVRG D+F++QST P Sbjct: 1 MKVLAGNSNRPLAEAISTCLGVPLTKASIRRFSDMEVFVEILENVRGEDVFVVQSTSFPA 60 Query: 64 NDNLMELVVMVDALRRASAGRITAVIPYFGYARQDRRVRSARVPITAKVVADFLSSVGVD 123 NDNLMEL+V +DALRR SA RITAV+PY+GYARQDR+ R PI+AK+VA+ ++ G + Sbjct: 61 NDNLMELLVTIDALRRGSARRITAVLPYYGYARQDRKT-GPRTPISAKLVANLITQAGAN 119 Query: 124 RVLTVDLHAEQIQGFFDVPVDNVFGSPILLEDMLQL--NLDNPIVVSPDIGGVVRARAIA 181 RVLT+DLHA QIQGFFD+P DN+ +P+ +D+ ++ +VSPD+GGVVRAR++A Sbjct: 120 RVLTMDLHAGQIQGFFDIPTDNLMAAPVFEKDIRATFEDIGEVTMVSPDVGGVVRARSLA 179 Query: 182 KLLNDTDMAIIDKRRPRANVSQVMHIIGDVAGRDCVLVDDMIDTGGTLCKAAEALKERGA 241 K L D D+AIIDKRR RA VS+VM+IIGDV R C+L+DD++D+GGTLC AA AL + GA Sbjct: 180 KRL-DADLAIIDKRRERAGVSEVMNIIGDVKNRRCILLDDIVDSGGTLCNAAVALMDAGA 238 Query: 242 KRVFAYATHPIFSGNAANNLRNSVIDEVVVCDTIPLTDEIKALPNVRTLTLSGMLAEAIR 301 K V AY TH + SG A + S ++++V D+I T+ ++ N+R LT++ +LA+AI Sbjct: 239 KSVHAYCTHGVLSGGAVARVAVSPLEQLVTTDSIQATEAVRVSRNIRQLTIAPLLADAIT 298 Query: 302 RISNEESISAMF 313 RIS E S+S++F Sbjct: 299 RISEERSVSSLF 310 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: 290 Number of extensions: 14 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: 315 Length of database: 311 Length adjustment: 27 Effective length of query: 288 Effective length of database: 284 Effective search space: 81792 Effective search space used: 81792 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 AZOBR_RS31185 AZOBR_RS31185 (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.2785.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.2e-116 374.9 0.3 1.3e-116 374.8 0.3 1.0 1 lcl|FitnessBrowser__azobra:AZOBR_RS31185 AZOBR_RS31185 ribose-phosphate p Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__azobra:AZOBR_RS31185 AZOBR_RS31185 ribose-phosphate pyrophosphokinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 374.8 0.3 1.3e-116 1.3e-116 1 309 [] 1 311 [] 1 311 [] 0.98 Alignments for each domain: == domain 1 score: 374.8 bits; conditional E-value: 1.3e-116 TIGR01251 1 lkilsgssskelaekvaknlglelgdvevkkFadgElyvrieesvrgkdvfiivqstsapvndalmell 69 +k+l+g+s++ lae+++ lg++l+++++++F+d E+ v+i e+vrg+dvf++ qsts p nd+lmell lcl|FitnessBrowser__azobra:AZOBR_RS31185 1 MKVLAGNSNRPLAEAISTCLGVPLTKASIRRFSDMEVFVEILENVRGEDVFVV-QSTSFPANDNLMELL 68 799**************************************************.*************** PP TIGR01251 70 llidalkrasaksvtaviPyygYaRqdkkaksrepisaklvaklleeaGadrvltvdlHseqiqgfFdv 138 ++idal+r sa+++tav+PyygYaRqd+k+ +r+pisaklva+l+++aGa+rvlt+dlH+ qiqgfFd+ lcl|FitnessBrowser__azobra:AZOBR_RS31185 69 VTIDALRRGSARRITAVLPYYGYARQDRKTGPRTPISAKLVANLITQAGANRVLTMDLHAGQIQGFFDI 137 ********************************************************************* PP TIGR01251 139 pvenlsaspklieelkkke..lknlvvvsPDkGaverakkvakklglelaiieKeRdskenevevtnll 205 p +nl+a+p++ ++++++ ++++vsPD G+v ra+++ak+l+++laii+K+R+ ++ + ev+n++ lcl|FitnessBrowser__azobra:AZOBR_RS31185 138 PTDNLMAAPVFEKDIRATFedIGEVTMVSPDVGGVVRARSLAKRLDADLAIIDKRRE-RAGVSEVMNII 205 *****************99888899********************************.666******** PP TIGR01251 206 gdvegkdvvivDDiisTggTlvkaaelLkekGAkkvivaathgvfsgdAlerlaeagveevivtntilv 274 gdv+++ ++++DDi+++ggTl++aa +L ++GAk+v +++thgv+sg A+ r+a + +e+++ t++i+ lcl|FitnessBrowser__azobra:AZOBR_RS31185 206 GDVKNRRCILLDDIVDSGGTLCNAAVALMDAGAKSVHAYCTHGVLSGGAVARVAVSPLEQLVTTDSIQA 274 ********************************************************************* PP TIGR01251 275 .ee.kklpkvseisvapliaeaiarihenesvsslfd 309 e + +++++++apl+a+ai+ri+e++svsslf+ lcl|FitnessBrowser__azobra:AZOBR_RS31185 275 tEAvRVSRNIRQLTIAPLLADAITRISEERSVSSLFS 311 55588899***************************95 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (309 nodes) Target sequences: 1 (311 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: 00:00:00.01 # Mc/sec: 8.39 // [ok]
This GapMind analysis is from Apr 09 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