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_026596222.1 H035_RS0103305 ribose-phosphate pyrophosphokinase
Query= SwissProt::P0A1V6 (315 letters) >NCBI__GCF_000421465.1:WP_026596222.1 Length = 316 Score = 378 bits (971), Expect = e-110 Identities = 188/308 (61%), Positives = 247/308 (80%), Gaps = 1/308 (0%) Query: 6 LFAGNATPELAQRIANRLYTSLGDAAVGRFSDGEVSVQINENVRGGDIFIIQSTCAPTND 65 +FAGN+ LA+ +A L LG A+V RFSDGE++V+I E+VRG +IF++QST P ++ Sbjct: 8 IFAGNSNLPLARDVAENLNMRLGLASVDRFSDGEIAVEIEEHVRGREIFVLQSTQMP-HE 66 Query: 66 NLMELVVMVDALRRASAGRITAVIPYFGYARQDRRVRSARVPITAKVVADFLSSVGVDRV 125 NLMEL+V++DAL+R+SAG +TAVIPYFGYARQDRR RSARVPITAK+VA ++S G DRV Sbjct: 67 NLMELLVIIDALKRSSAGTVTAVIPYFGYARQDRRPRSARVPITAKLVAKMITSAGADRV 126 Query: 126 LTVDLHAEQIQGFFDVPVDNVFGSPILLEDMLQLNLDNPIVVSPDIGGVVRARAIAKLLN 185 LTVDLHA+Q+QGFFD+PVDNV+ SP+LL D+ + + IVVSPD+GGVVRARA+AK L Sbjct: 127 LTVDLHADQVQGFFDIPVDNVYASPLLLGDIWRRKYPDQIVVSPDVGGVVRARALAKRLG 186 Query: 186 DTDMAIIDKRRPRANVSQVMHIIGDVAGRDCVLVDDMIDTGGTLCKAAEALKERGAKRVF 245 D D+AIIDKRRPRAN +QVM++IGDVAGR C+LVDD++DT GTLC+AA ALK+ GA RV Sbjct: 187 DADLAIIDKRRPRANETQVMNLIGDVAGRTCILVDDLVDTAGTLCQAANALKDHGAVRVV 246 Query: 246 AYATHPIFSGNAANNLRNSVIDEVVVCDTIPLTDEIKALPNVRTLTLSGMLAEAIRRISN 305 +Y THP+ SG A N+ S +DE+VV +TIPL + A +R L+++ M+AE IRRI+ Sbjct: 247 SYCTHPVLSGPAVENISRSALDELVVTNTIPLQPKALACGKIRQLSIAEMMAETIRRIAV 306 Query: 306 EESISAMF 313 ES+S+++ Sbjct: 307 GESVSSLY 314 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: 319 Number of extensions: 9 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: 316 Length adjustment: 27 Effective length of query: 288 Effective length of database: 289 Effective search space: 83232 Effective search space used: 83232 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_026596222.1 H035_RS0103305 (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.23579.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.1e-119 382.7 0.0 5.8e-119 382.5 0.0 1.0 1 lcl|NCBI__GCF_000421465.1:WP_026596222.1 H035_RS0103305 ribose-phosphate Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000421465.1:WP_026596222.1 H035_RS0103305 ribose-phosphate pyrophosphokinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 382.5 0.0 5.8e-119 5.8e-119 2 308 .. 7 314 .. 6 315 .. 0.97 Alignments for each domain: == domain 1 score: 382.5 bits; conditional E-value: 5.8e-119 TIGR01251 2 kilsgssskelaekvaknlglelgdvevkkFadgElyvrieesvrgkdvfiivqstsapvndalmelll 70 +i++g+s+ la+ va+nl+++lg ++v++F+dgE+ v+iee+vrg+++f++ qst + ++lmell+ lcl|NCBI__GCF_000421465.1:WP_026596222.1 7 MIFAGNSNLPLARDVAENLNMRLGLASVDRFSDGEIAVEIEEHVRGREIFVL-QSTQM-PHENLMELLV 73 79**************************************************.77775.689******* PP TIGR01251 71 lidalkrasaksvtaviPyygYaRqdkkak.srepisaklvaklleeaGadrvltvdlHseqiqgfFdv 138 +idalkr+sa++vtaviPy+gYaRqd++ + r pi+aklvak++++aGadrvltvdlH++q+qgfFd+ lcl|NCBI__GCF_000421465.1:WP_026596222.1 74 IIDALKRSSAGTVTAVIPYFGYARQDRRPRsARVPITAKLVAKMITSAGADRVLTVDLHADQVQGFFDI 142 ***************************97758************************************* PP TIGR01251 139 pvenlsaspklieelkkkelknlvvvsPDkGaverakkvakklg.lelaiieKeRdskenevevtnllg 206 pv+n++asp l+ ++ +++ + +vvsPD G+v ra+++ak+lg ++laii+K+R+ ++ne +v+nl+g lcl|NCBI__GCF_000421465.1:WP_026596222.1 143 PVDNVYASPLLLGDIWRRKYPDQIVVSPDVGGVVRARALAKRLGdADLAIIDKRRP-RANETQVMNLIG 210 ********************************************9***********.889********* PP TIGR01251 207 dvegkdvvivDDiisTggTlvkaaelLkekGAkkvivaathgvfsgdAlerlaeagveevivtntilv. 274 dv+g+++++vDD+++T+gTl++aa++Lk++GA +v+ ++th+v+sg+A+e+++++ ++e++vtnti+ lcl|NCBI__GCF_000421465.1:WP_026596222.1 211 DVAGRTCILVDDLVDTAGTLCQAANALKDHGAVRVVSYCTHPVLSGPAVENISRSALDELVVTNTIPLq 279 ********************************************************************5 PP TIGR01251 275 ee.kklpkvseisvapliaeaiarihenesvsslf 308 + ++ k++++s+a+++ae+i+ri+ +esvssl+ lcl|NCBI__GCF_000421465.1:WP_026596222.1 280 PKaLACGKIRQLSIAEMMAETIRRIAVGESVSSLY 314 345899***************************98 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (309 nodes) Target sequences: 1 (316 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: 6.56 // [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