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 SMc02686 SMc02686 ribose-phosphate pyrophosphokinase
Query= SwissProt::P0A1V6 (315 letters) >FitnessBrowser__Smeli:SMc02686 Length = 310 Score = 338 bits (868), Expect = 7e-98 Identities = 172/312 (55%), Positives = 235/312 (75%), Gaps = 3/312 (0%) Query: 4 MKLFAGNATPELAQRIANRLYTSLGDAAVGRFSDGEVSVQINENVRGGDIFIIQSTCAPT 63 MK+FAGN+ LA+ I N L LG A V RF+D E+ V+I ENVRG D+FI+QST PT Sbjct: 1 MKVFAGNSNRLLAEAICNYLNLPLGKATVRRFADQEIFVEIGENVRGEDVFIVQSTSFPT 60 Query: 64 NDNLMELVVMVDALRRASAGRITAVIPYFGYARQDRRVRSARVPITAKVVADFLSSVGVD 123 ND+LMEL++M+DA+RR+SA RITAV+PYFGYARQDR+ R PI+AK+VA+ ++ G D Sbjct: 61 NDHLMELLIMIDAVRRSSARRITAVLPYFGYARQDRKP-GPRTPISAKLVANLITEAGAD 119 Query: 124 RVLTVDLHAEQIQGFFDVPVDNVFGSPILLEDMLQ-LNLDNPIVVSPDIGGVVRARAIAK 182 RVLT+DLHA QIQGFFD+P DN++ PIL D+ + NL N +VVSPD+GGVVRARA+AK Sbjct: 120 RVLTLDLHAGQIQGFFDIPTDNLYAIPILARDVKENYNLKNVMVVSPDVGGVVRARALAK 179 Query: 183 LLNDTDMAIIDKRRPRANVSQVMHIIGDVAGRDCVLVDDMIDTGGTLCKAAEALKERGAK 242 L D +AI+DKRR R S+VM++IG+V G+DC+L+DD++D+GGTLC AAEAL + GA Sbjct: 180 RL-DCLLAIVDKRRDRPGESEVMNVIGEVNGKDCLLIDDIVDSGGTLCNAAEALLKNGAT 238 Query: 243 RVFAYATHPIFSGNAANNLRNSVIDEVVVCDTIPLTDEIKALPNVRTLTLSGMLAEAIRR 302 V AY TH + SG A + +S++ E+V+ D+I T +++ N+R ++ + +L EAI R Sbjct: 239 SVTAYITHGVLSGGAVARVTSSMLKELVITDSIQPTTAVQSAHNIRVISTAALLGEAISR 298 Query: 303 ISNEESISAMFE 314 S EES+S++F+ Sbjct: 299 TSQEESVSSLFD 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: 292 Number of extensions: 12 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: 310 Length adjustment: 27 Effective length of query: 288 Effective length of database: 283 Effective search space: 81504 Effective search space used: 81504 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 SMc02686 SMc02686 (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.4644.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.8e-122 392.2 0.1 7.6e-122 392.0 0.1 1.0 1 lcl|FitnessBrowser__Smeli:SMc02686 SMc02686 ribose-phosphate pyroph Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Smeli:SMc02686 SMc02686 ribose-phosphate pyrophosphokinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 392.0 0.1 7.6e-122 7.6e-122 1 309 [] 1 310 [] 1 310 [] 0.99 Alignments for each domain: == domain 1 score: 392.0 bits; conditional E-value: 7.6e-122 TIGR01251 1 lkilsgssskelaekvaknlglelgdvevkkFadgElyvrieesvrgkdvfiivqstsapvndalmellllidal 75 +k+++g+s++ lae+++++l+l+lg+++v++Fad+E+ v+i e+vrg+dvfi+ qsts p+nd+lmell++ida+ lcl|FitnessBrowser__Smeli:SMc02686 1 MKVFAGNSNRLLAEAICNYLNLPLGKATVRRFADQEIFVEIGENVRGEDVFIV-QSTSFPTNDHLMELLIMIDAV 74 79***************************************************.********************* PP TIGR01251 76 krasaksvtaviPyygYaRqdkkaksrepisaklvaklleeaGadrvltvdlHseqiqgfFdvpvenlsaspkli 150 +r+sa+++tav+Py+gYaRqd+k +r+pisaklva+l++eaGadrvlt+dlH+ qiqgfFd+p +nl+a p l+ lcl|FitnessBrowser__Smeli:SMc02686 75 RRSSARRITAVLPYFGYARQDRKPGPRTPISAKLVANLITEAGADRVLTLDLHAGQIQGFFDIPTDNLYAIPILA 149 *************************************************************************** PP TIGR01251 151 eelkkke.lknlvvvsPDkGaverakkvakklglelaiieKeRdskenevevtnllgdvegkdvvivDDiisTgg 224 +++k+++ lkn++vvsPD G+v ra+++ak+l++ lai++K+Rd + e ev+n++g+v+gkd++++DDi+++gg lcl|FitnessBrowser__Smeli:SMc02686 150 RDVKENYnLKNVMVVSPDVGGVVRARALAKRLDCLLAIVDKRRD-RPGESEVMNVIGEVNGKDCLLIDDIVDSGG 223 *****999************************************.777*************************** PP TIGR01251 225 TlvkaaelLkekGAkkvivaathgvfsgdAlerlaeagveevivtntilv.ee.kklpkvseisvapliaeaiar 297 Tl++aae+L ++GA++v++++thgv+sg A+ r+++++++e+++t++i+ + ++ +++++is a l+ eai+r lcl|FitnessBrowser__Smeli:SMc02686 224 TLCNAAEALLKNGATSVTAYITHGVLSGGAVARVTSSMLKELVITDSIQPtTAvQSAHNIRVISTAALLGEAISR 298 ************************************************99666899******************* PP TIGR01251 298 ihenesvsslfd 309 ++++esvsslfd lcl|FitnessBrowser__Smeli:SMc02686 299 TSQEESVSSLFD 310 **********96 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (309 nodes) Target sequences: 1 (310 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: 10.35 // [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