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_093395382.1 BM091_RS09785 ribose-phosphate diphosphokinase
Query= SwissProt::P0A1V6 (315 letters) >NCBI__GCF_900114975.1:WP_093395382.1 Length = 315 Score = 236 bits (601), Expect = 7e-67 Identities = 130/310 (41%), Positives = 195/310 (62%), Gaps = 5/310 (1%) Query: 3 DMKLFAGNATPELAQRIANRLYTSLGDAAVGRFSDGEVSVQINENVRGGDIFIIQSTCAP 62 + ++F+GNA P LA+ + L LG A V F+DGE+ V+I ENVRG D++++QS C P Sbjct: 5 EFRIFSGNANPALAEAVCGELGVELGRALVTTFADGEIRVEIEENVRGRDVYVVQSLCCP 64 Query: 63 TNDNLMELVVMVDALRRASAGRITAVIPYFGYARQDRRVRSARVPITAKVVADFLSSVGV 122 N ++EL++M+DAL+RASA R+TAVIPY+ Y R+D++ + RVPIT +++A+ L GV Sbjct: 65 VNSYVIELLLMIDALKRASADRVTAVIPYYAYGRRDKKDK-PRVPITGRMLANLLEEAGV 123 Query: 123 DRVLTVDLHAEQIQGFFDVPVDNVFGSPILLEDMLQLNLDNPIVVSPDIGGVVRARAIAK 182 D V+ +D H+ Q GFF VPVD+V + +E + + IVV+PD GV RAR+ A Sbjct: 124 DHVVALDFHSGQTMGFFKVPVDHVTALNVFVEHARKNLPEGSIVVAPDAAGVRRARSFAT 183 Query: 183 LLNDTDMAIIDKRRPRANVSQVMHIIGDVAGRDCVLVDDMIDTGGTLCKAAEALKERGAK 242 LN +MAI+D+R A I+GDV + VL DD++DTG T+ + +EA GA Sbjct: 184 ALN-LEMAIMDERDMGAPWEP--RIVGDVRDKYVVLFDDIVDTGRTIERVSEAAHRAGAL 240 Query: 243 RVFAYATHPIFSGNAANNLRNSVIDEVVVCDT-IPLTDEIKALPNVRTLTLSGMLAEAIR 301 V AY+ H IFS LR S + +VV D+ +P T+ + ++++G+LA+AIR Sbjct: 241 SVMAYSVHGIFSAGCEERLRRSALKCLVVTDSVVPYTNPDTLGVPIEYVSVAGVLAKAIR 300 Query: 302 RISNEESISA 311 + E++ A Sbjct: 301 ALHCGETLEA 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: 245 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: 315 Length adjustment: 27 Effective length of query: 288 Effective length of database: 288 Effective search space: 82944 Effective search space used: 82944 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_093395382.1 BM091_RS09785 (ribose-phosphate diphosphokinase)
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.4023131.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.6e-96 306.8 0.0 7.8e-96 306.6 0.0 1.0 1 NCBI__GCF_900114975.1:WP_093395382.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_900114975.1:WP_093395382.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 306.6 0.0 7.8e-96 7.8e-96 2 304 .. 7 308 .. 6 312 .. 0.95 Alignments for each domain: == domain 1 score: 306.6 bits; conditional E-value: 7.8e-96 TIGR01251 2 kilsgssskelaekvaknlglelgdvevkkFadgElyvrieesvrgkdvfiivqstsapvndalmellllida 74 +i+sg+++++lae+v+ +lg+elg++ v++FadgE+ v+iee+vrg+dv+++ qs + pvn ++elll+ida NCBI__GCF_900114975.1:WP_093395382.1 7 RIFSGNANPALAEAVCGELGVELGRALVTTFADGEIRVEIEENVRGRDVYVV-QSLCCPVNSYVIELLLMIDA 78 69**************************************************.89999*************** PP TIGR01251 75 lkrasaksvtaviPyygYaRqdkkaksrepisaklvaklleeaGadrvltvdlHseqiqgfFdvpvenlsasp 147 lkrasa++vtaviPyy+Y+R dkk+k+r pi+ +++a+lleeaG+d+v+++d+Hs q+ gfF+vpv++++a + NCBI__GCF_900114975.1:WP_093395382.1 79 LKRASADRVTAVIPYYAYGRRDKKDKPRVPITGRMLANLLEEAGVDHVVALDFHSGQTMGFFKVPVDHVTALN 151 ************************************************************************* PP TIGR01251 148 klieelkkkelknlvvvsPDkGaverakkvakklglelaiieKeRdskenevevtnllgdvegkdvvivDDii 220 +++e+ +k+ + +vv+PD+ +v+ra+++a++l+le+ai++ Rd + +++gdv +k vv++DDi+ NCBI__GCF_900114975.1:WP_093395382.1 152 VFVEHARKNLPEGSIVVAPDAAGVRRARSFATALNLEMAIMDE-RDMGA--PWEPRIVGDVRDKYVVLFDDIV 221 *****************************************95.56333..466789**************** PP TIGR01251 221 sTggTlvkaaelLkekGAkkvivaathgvfsgdAlerlaeagveevivtntilv.ee..kklpkvseisvapl 290 +Tg T+ + +e+++++GA +v+++ +hg+fs erl+++ ++ ++vt+++ ++ + ++ +sva + NCBI__GCF_900114975.1:WP_093395382.1 222 DTGRTIERVSEAAHRAGALSVMAYSVHGIFSAGCEERLRRSALKCLVVTDSVVPyTNpdTLGVPIEYVSVAGV 294 ***************************************************99866665666799******** PP TIGR01251 291 iaeaiarihenesv 304 +a+ai++ h +e++ NCBI__GCF_900114975.1:WP_093395382.1 295 LAKAIRALHCGETL 308 ******99987766 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (309 nodes) Target sequences: 1 (315 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: 15.97 // [ok]
This GapMind analysis is from Jul 25 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