Align Ribose-phosphate pyrophosphokinase; RPPK; EC 2.7.6.1; 5-phospho-D-ribosyl alpha-1-diphosphate synthase; Phosphoribosyl diphosphate synthase; Phosphoribosyl pyrophosphate synthase; P-Rib-PP synthase; PRPP synthase; PRPPase (uncharacterized)
to candidate 201141 SO1980 phosphoribosyl transferase domain protein (NCBI ptt file)
Query= curated2:Q8ZU24 (284 letters) >FitnessBrowser__MR1:201141 Length = 301 Score = 87.8 bits (216), Expect = 3e-22 Identities = 65/208 (31%), Positives = 97/208 (46%), Gaps = 2/208 (0%) Query: 58 NLIKLFLTIDALNDAGASKIILVIPYMPYARQDRRFRPGEPISSKTVLKLLAHLNVFGII 117 ++++L L DAL GA +I L++PYMP ARQDR GE +S K L+ + Sbjct: 72 SIMQLLLLTDALRRNGAEQIDLLLPYMPGARQDRVCNVGEALSVKVYASLINQQQYASVS 131 Query: 118 TVDLHKGYVAEYAPRL-VIKNLYPAEEFAKALGGVDVVLSPDFGSVHRAEAVARLLQ-VP 175 D H A R+ VI N A L G V++SPD G+ + +A+ LQ +P Sbjct: 132 VFDPHSDVTAALLDRVQVIDNHSFVAAIAAQLTGELVLVSPDAGANKKVFGLAKALQGMP 191 Query: 176 YTYFEKYRDRSTGAITLIPRQDVDLRNKRVAIVDDILSTGGTLVDACKAAKTLGAAEVYA 235 +K+RD G I DL K IVDDI + G T ++ K A V Sbjct: 192 VIRADKHRDVVNGHIIATEVFCDDLSGKTCLIVDDICAGGRTFIELAIKLKQKRAQSVIL 251 Query: 236 AITHCQLLKDARERVRSCVDKIICTDTV 263 ++H + + +D++ CTD++ Sbjct: 252 IVSHYEDKASESALREAGIDRLFCTDSL 279 Lambda K H 0.323 0.140 0.398 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: 175 Number of extensions: 15 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: 284 Length of database: 301 Length adjustment: 26 Effective length of query: 258 Effective length of database: 275 Effective search space: 70950 Effective search space used: 70950 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.5 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (22.0 bits) S2: 48 (23.1 bits)
Align candidate 201141 SO1980 (phosphoribosyl transferase domain protein (NCBI ptt file))
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.23368.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.6e-42 130.8 0.0 3.2e-42 130.5 0.0 1.1 1 lcl|FitnessBrowser__MR1:201141 SO1980 phosphoribosyl transferas Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__MR1:201141 SO1980 phosphoribosyl transferase domain protein (NCBI ptt file) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 130.5 0.0 3.2e-42 3.2e-42 62 274 .. 70 281 .. 38 295 .. 0.89 Alignments for each domain: == domain 1 score: 130.5 bits; conditional E-value: 3.2e-42 TIGR01251 62 ndalmellllidalkrasaksvtaviPyygYaRqdkkaksrepisaklvaklleeaGadrvltvdlHseqiqgfFd.vp 139 ++++m+llll+dal+r++a+++ + +Py++ aRqd+ + +e++s+k+ a+l+++ + +v ++d Hs+ + d v+ lcl|FitnessBrowser__MR1:201141 70 DHSIMQLLLLTDALRRNGAEQIDLLLPYMPGARQDRVCNVGEALSVKVYASLINQQQYASVSVFDPHSDVTAALLDrVQ 148 899********************************************************************99998554 PP TIGR01251 140 venlsaspklieelkkkelknlvvvsPDkGaverakkvakklg.lelaiieKeRdskenevevtnl.lgdvegkdvviv 216 v + ++++++ ++++ +lv+vsPD+Ga + + +ak+l+ +++ +K+Rd + ++ t++ d+ gk+++iv lcl|FitnessBrowser__MR1:201141 149 VID---NHSFVAAIAAQLTGELVLVSPDAGANKKVFGLAKALQgMPVIRADKHRDVVNGHIIATEVfCDDLSGKTCLIV 224 443...35577788888899**********************999**********977777666651568********* PP TIGR01251 217 DDiisTggTlvkaaelLkekGAkkvivaathgvfsgdAle.rlaeagveevivtntilv 274 DDi + g T ++ a Lk+k A++vi +++h + ++A e l+eag+++++ t+++ v lcl|FitnessBrowser__MR1:201141 225 DDICAGGRTFIELAIKLKQKRAQSVILIVSH--YEDKASEsALREAGIDRLFCTDSLGV 281 *******************************..89988762699***********9876 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (309 nodes) Target sequences: 1 (301 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: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 7.80 // [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