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_085217580.1 B9N75_RS03680 ribose-phosphate pyrophosphokinase
Query= SwissProt::P0A1V6 (315 letters) >NCBI__GCF_900177405.1:WP_085217580.1 Length = 311 Score = 332 bits (850), Expect = 9e-96 Identities = 172/312 (55%), Positives = 230/312 (73%), Gaps = 2/312 (0%) Query: 4 MKLFAGNATPELAQRIANRLYTSLGDAAVGRFSDGEVSVQINENVRGGDIFIIQSTCAPT 63 MKL +GN+ L + IA L + DA+V RF+D EV V+I+ENVRG D+F+IQST P Sbjct: 1 MKLLSGNSNRPLVEAIAAYLEMPITDASVRRFADEEVFVEIHENVRGEDVFVIQSTAFPA 60 Query: 64 NDNLMELVVMVDALRRASAGRITAVIPYFGYARQDRRVRSARVPITAKVVADFLSSVGVD 123 NDNLMEL++ +DAL+RASA RITAV+PYFGYARQDR+ R PI+AK+VA+ ++ G D Sbjct: 61 NDNLMELLICIDALKRASAKRITAVLPYFGYARQDRKP-GPRTPISAKLVANLITVAGAD 119 Query: 124 RVLTVDLHAEQIQGFFDVPVDNVFGSPILLEDMLQLNLDNPI-VVSPDIGGVVRARAIAK 182 RVL+VDLHA QIQGFFD+P DN++ +P++ D+ PI VVSPD+GGVVRARA+AK Sbjct: 120 RVLSVDLHAGQIQGFFDIPTDNLYAAPVMSADIQARFAGKPITVVSPDVGGVVRARALAK 179 Query: 183 LLNDTDMAIIDKRRPRANVSQVMHIIGDVAGRDCVLVDDMIDTGGTLCKAAEALKERGAK 242 L++ +AI+DKRR R S+VM+IIGDV GR CVLVDD++D+ GTLC AA ALKE GA Sbjct: 180 RLDNAPLAIVDKRRERPGESEVMNIIGDVNGRFCVLVDDIVDSAGTLCNAAAALKEGGAT 239 Query: 243 RVFAYATHPIFSGNAANNLRNSVIDEVVVCDTIPLTDEIKALPNVRTLTLSGMLAEAIRR 302 V AY TH + SG A + S + E+V+ D+I D +A +R LT++ +LAEA+RR Sbjct: 240 DVVAYCTHGVLSGAAVPRVDKSELAELVITDSIATYDAAEASEKIRILTIAPLLAEAVRR 299 Query: 303 ISNEESISAMFE 314 I++E S+S++F+ Sbjct: 300 IADESSVSSLFD 311 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: 302 Number of extensions: 10 Number of successful extensions: 3 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 WP_085217580.1 B9N75_RS03680 (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.2178978.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.4e-118 379.1 0.1 7.2e-118 378.9 0.1 1.0 1 NCBI__GCF_900177405.1:WP_085217580.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_900177405.1:WP_085217580.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 378.9 0.1 7.2e-118 7.2e-118 1 309 [] 1 311 [] 1 311 [] 0.98 Alignments for each domain: == domain 1 score: 378.9 bits; conditional E-value: 7.2e-118 TIGR01251 1 lkilsgssskelaekvaknlglelgdvevkkFadgElyvrieesvrgkdvfiivqstsapvndalmellllid 73 +k+lsg+s++ l e++a +l+++++d++v++Fad+E+ v+i+e+vrg+dvf+i qst p nd+lmell+ id NCBI__GCF_900177405.1:WP_085217580.1 1 MKLLSGNSNRPLVEAIAAYLEMPITDASVRRFADEEVFVEIHENVRGEDVFVI-QSTAFPANDNLMELLICID 72 799**************************************************.9****************** PP TIGR01251 74 alkrasaksvtaviPyygYaRqdkkaksrepisaklvaklleeaGadrvltvdlHseqiqgfFdvpvenlsas 146 alkrasak++tav+Py+gYaRqd+k +r+pisaklva+l++ aGadrvl vdlH+ qiqgfFd+p +nl+a+ NCBI__GCF_900177405.1:WP_085217580.1 73 ALKRASAKRITAVLPYFGYARQDRKPGPRTPISAKLVANLITVAGADRVLSVDLHAGQIQGFFDIPTDNLYAA 145 ************************************************************************* PP TIGR01251 147 pklieelkkke.lknlvvvsPDkGaverakkvakklg.lelaiieKeRdskenevevtnllgdvegkdvvivD 217 p++ ++++++ k ++vvsPD G+v ra+++ak+l+ ++lai++K+R+ + e ev+n++gdv+g+ +v+vD NCBI__GCF_900177405.1:WP_085217580.1 146 PVMSADIQARFaGKPITVVSPDVGGVVRARALAKRLDnAPLAIVDKRRE-RPGESEVMNIIGDVNGRFCVLVD 217 *********99899999*******************99***********.777******************** PP TIGR01251 218 DiisTggTlvkaaelLkekGAkkvivaathgvfsgdAlerlaeagveevivtntilv.ee.kklpkvseisva 288 Di++++gTl++aa +Lke GA++v++++thgv+sg A+ r++++ + e+++t++i++ + ++ +k++ +++a NCBI__GCF_900177405.1:WP_085217580.1 218 DIVDSAGTLCNAAAALKEGGATDVVAYCTHGVLSGAAVPRVDKSELAELVITDSIATyDAaEASEKIRILTIA 290 *********************************************************7668999********* PP TIGR01251 289 pliaeaiarihenesvsslfd 309 pl+aea++ri++++svsslfd NCBI__GCF_900177405.1:WP_085217580.1 291 PLLAEAVRRIADESSVSSLFD 311 *******************96 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 16.18 // [ok]
This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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