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_009871053.1 AMB_RS03050 ribose-phosphate pyrophosphokinase
Query= SwissProt::P0A1V6 (315 letters) >NCBI__GCF_000009985.1:WP_009871053.1 Length = 310 Score = 335 bits (858), Expect = 1e-96 Identities = 171/312 (54%), Positives = 235/312 (75%), Gaps = 3/312 (0%) Query: 4 MKLFAGNATPELAQRIANRLYTSLGDAAVGRFSDGEVSVQINENVRGGDIFIIQSTCAPT 63 MK+ A N+ LA+ IA L S+ A + RFSD EV V+I+ENVRG D+F+IQST P Sbjct: 1 MKILACNSNRPLAEAIAEYLTMSITKAVIRRFSDNEVFVEIHENVRGEDVFVIQSTSYPA 60 Query: 64 NDNLMELVVMVDALRRASAGRITAVIPYFGYARQDRRVRSARVPITAKVVADFLSSVGVD 123 NDNLMEL+V +DALRR SA RITAVIPYFGYARQDR+ S R PI+AK+VA+ +++ G D Sbjct: 61 NDNLMELLVTLDALRRGSARRITAVIPYFGYARQDRK-SSPRSPISAKLVANLITTAGAD 119 Query: 124 RVLTVDLHAEQIQGFFDVPVDNVFGSPILLEDM-LQLNLDNPIVVSPDIGGVVRARAIAK 182 RV+T+DLH+ QIQGFFD+P+DN++ +P+ D+ + D+ +VVSPD+GGVVRARAIA Sbjct: 120 RVVTLDLHSGQIQGFFDIPLDNLYAAPVFTNDIRARYQGDDVMVVSPDVGGVVRARAIAS 179 Query: 183 LLNDTDMAIIDKRRPRANVSQVMHIIGDVAGRDCVLVDDMIDTGGTLCKAAEALKERGAK 242 + D D+AIIDKRR +A VS+VM+IIGDV GR C++VDD++D+ GTLC AAEAL + GA Sbjct: 180 RI-DADLAIIDKRREKAGVSEVMNIIGDVRGRRCIMVDDIVDSAGTLCNAAEALMKAGAV 238 Query: 243 RVFAYATHPIFSGNAANNLRNSVIDEVVVCDTIPLTDEIKALPNVRTLTLSGMLAEAIRR 302 V A+ TH + SG A + S ++E+V+ D+IP T+ +K N+R +T++ ++AE+I R Sbjct: 239 SVAAFVTHGVLSGGAVARVTASPLEELVITDSIPATEAVKMARNIRQVTIAPLMAESISR 298 Query: 303 ISNEESISAMFE 314 IS E S+S++F+ Sbjct: 299 ISEERSVSSLFD 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: 284 Number of extensions: 10 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 WP_009871053.1 AMB_RS03050 (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.13515.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8.2e-121 388.6 2.4 9.2e-121 388.4 2.4 1.0 1 lcl|NCBI__GCF_000009985.1:WP_009871053.1 AMB_RS03050 ribose-phosphate pyr Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000009985.1:WP_009871053.1 AMB_RS03050 ribose-phosphate pyrophosphokinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 388.4 2.4 9.2e-121 9.2e-121 1 309 [] 1 310 [] 1 310 [] 0.98 Alignments for each domain: == domain 1 score: 388.4 bits; conditional E-value: 9.2e-121 TIGR01251 1 lkilsgssskelaekvaknlglelgdvevkkFadgElyvrieesvrgkdvfiivqstsapvndalmell 69 +kil+++s++ lae++a++l ++++++ +++F+d+E+ v+i+e+vrg+dvf+i qsts p nd+lmell lcl|NCBI__GCF_000009985.1:WP_009871053.1 1 MKILACNSNRPLAEAIAEYLTMSITKAVIRRFSDNEVFVEIHENVRGEDVFVI-QSTSYPANDNLMELL 68 79***************************************************.99999********** PP TIGR01251 70 llidalkrasaksvtaviPyygYaRqdkkaksrepisaklvaklleeaGadrvltvdlHseqiqgfFdv 138 +++dal+r sa+++taviPy+gYaRqd+k ++r+pisaklva+l+++aGadrv+t+dlHs qiqgfFd+ lcl|NCBI__GCF_000009985.1:WP_009871053.1 69 VTLDALRRGSARRITAVIPYFGYARQDRKSSPRSPISAKLVANLITTAGADRVVTLDLHSGQIQGFFDI 137 ********************************************************************* PP TIGR01251 139 pvenlsaspklieelkkke.lknlvvvsPDkGaverakkvakklglelaiieKeRdskenevevtnllg 206 p++nl+a+p++++++++++ ++++vvsPD G+v ra+++a++++++laii+K+R+ k+ + ev+n++g lcl|NCBI__GCF_000009985.1:WP_009871053.1 138 PLDNLYAAPVFTNDIRARYqGDDVMVVSPDVGGVVRARAIASRIDADLAIIDKRRE-KAGVSEVMNIIG 205 *****************998999*********************************.777********* PP TIGR01251 207 dvegkdvvivDDiisTggTlvkaaelLkekGAkkvivaathgvfsgdAlerlaeagveevivtntilv. 274 dv g+ +++vDDi++++gTl++aae+L ++GA +v + +thgv+sg A+ r++ + +ee+++t++i+ lcl|NCBI__GCF_000009985.1:WP_009871053.1 206 DVRGRRCIMVDDIVDSAGTLCNAAEALMKAGAVSVAAFVTHGVLSGGAVARVTASPLEELVITDSIPAt 274 ********************************************************************5 PP TIGR01251 275 ee.kklpkvseisvapliaeaiarihenesvsslfd 309 e k +++++++apl+ae i+ri+e++svsslfd lcl|NCBI__GCF_000009985.1:WP_009871053.1 275 EAvKMARNIRQVTIAPLMAESISRISEERSVSSLFD 310 559999****************************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: 00:00:00.01 # Mc/sec: 8.14 // [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