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 207025 DVU1575 ribose-phosphate pyrophosphokinase
Query= SwissProt::P0A1V6 (315 letters) >MicrobesOnline__882:207025 Length = 312 Score = 337 bits (864), Expect = 2e-97 Identities = 167/311 (53%), Positives = 228/311 (73%), Gaps = 3/311 (0%) Query: 3 DMKLFAGNATPELAQRIANRLYTSLGDAAVGRFSDGEVSVQINENVRGGDIFIIQSTCAP 62 D+K+ G + PELA+ I N L + A FSDGE+ ++I +NVRG D+F++Q+TCAP Sbjct: 4 DLKILTGTSNPELAKAICNHLGCQITPALCETFSDGEIRIEIGDNVRGDDVFVVQATCAP 63 Query: 63 TNDNLMELVVMVDALRRASAGRITAVIPYFGYARQDRRVRSARVPITAKVVADFLSSVGV 122 N NLM+L +M+DAL+RASAGR+TAV+PY+GYARQDR+V S R PI+AK+VADFL++ G Sbjct: 64 VNFNLMQLFLMLDALKRASAGRVTAVMPYYGYARQDRKV-SPRAPISAKLVADFLTTAGT 122 Query: 123 DRVLTVDLHAEQIQGFFDVPVDNVFGSPILLEDMLQLNLDNPIVVSPDIGGVVRARAIAK 182 DRV+TVDLHA QIQGFF+ PVDN++ +P++L+ + Q+ ++VSPD GGV RARA AK Sbjct: 123 DRVVTVDLHAGQIQGFFNSPVDNLYAAPVILDYLRQVE-GEIVIVSPDAGGVERARAYAK 181 Query: 183 LLNDTDMAIIDKRRPRANVSQVMHIIGDVAGRDCVLVDDMIDTGGTLCKAAEALKERGAK 242 LN +AI+DKRR + N +Q MH+IGDV + ++VDDMIDT GTLC A E L + GA+ Sbjct: 182 RLN-AGLAIVDKRRDKPNQAQAMHVIGDVRDKVAIVVDDMIDTAGTLCAAGEVLLKNGAR 240 Query: 243 RVFAYATHPIFSGNAANNLRNSVIDEVVVCDTIPLTDEIKALPNVRTLTLSGMLAEAIRR 302 V A ATHP+ SG A L NS +V+V DT+PL D++ A P + L+++G+LA+AI Sbjct: 241 EVMACATHPVLSGPAIERLCNSPFKQVIVTDTVPLGDKLNACPKLHVLSVAGLLAKAIHN 300 Query: 303 ISNEESISAMF 313 I E S+S +F Sbjct: 301 IHTESSVSVLF 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: 306 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: 312 Length adjustment: 27 Effective length of query: 288 Effective length of database: 285 Effective search space: 82080 Effective search space used: 82080 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 207025 DVU1575 (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.8477.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.5e-124 400.8 0.0 1.7e-124 400.7 0.0 1.0 1 lcl|MicrobesOnline__882:207025 DVU1575 ribose-phosphate pyropho Domain annotation for each sequence (and alignments): >> lcl|MicrobesOnline__882:207025 DVU1575 ribose-phosphate pyrophosphokinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 400.7 0.0 1.7e-124 1.7e-124 2 308 .. 6 311 .. 5 312 .] 0.99 Alignments for each domain: == domain 1 score: 400.7 bits; conditional E-value: 1.7e-124 TIGR01251 2 kilsgssskelaekvaknlglelgdvevkkFadgElyvrieesvrgkdvfiivqstsapvndalmellllidalkrasa 80 kil g+s++ela++++++lg +++++ ++F+dgE+ ++i ++vrg dvf++ q t+apvn +lm+l l++dalkrasa lcl|MicrobesOnline__882:207025 6 KILTGTSNPELAKAICNHLGCQITPALCETFSDGEIRIEIGDNVRGDDVFVV-QATCAPVNFNLMQLFLMLDALKRASA 83 899*******************************************999999.************************** PP TIGR01251 81 ksvtaviPyygYaRqdkkaksrepisaklvaklleeaGadrvltvdlHseqiqgfFdvpvenlsaspklieelkkkelk 159 ++vtav+PyygYaRqd+k+++r pisaklva++l++aG+drv+tvdlH+ qiqgfF+ pv+nl+a+p+++++l++ + lcl|MicrobesOnline__882:207025 84 GRVTAVMPYYGYARQDRKVSPRAPISAKLVADFLTTAGTDRVVTVDLHAGQIQGFFNSPVDNLYAAPVILDYLRQ-VEG 161 **************************************************************************8.599 PP TIGR01251 160 nlvvvsPDkGaverakkvakklglelaiieKeRdskenevevtnllgdvegkdvvivDDiisTggTlvkaaelLkekGA 238 ++v+vsPD+G+vera+++ak+l++ lai++K+Rd k n+++ ++++gdv +k +++vDD+i+T+gTl++a e+L ++GA lcl|MicrobesOnline__882:207025 162 EIVIVSPDAGGVERARAYAKRLNAGLAIVDKRRD-KPNQAQAMHVIGDVRDKVAIVVDDMIDTAGTLCAAGEVLLKNGA 239 **********************************.999***************************************** PP TIGR01251 239 kkvivaathgvfsgdAlerlaeagveevivtntilv.ee.kklpkvseisvapliaeaiarihenesvsslf 308 ++v+++ath+v+sg+A+erl ++ +++vivt+t++ ++ +++pk++++sva l+a+ai +ih+++svs lf lcl|MicrobesOnline__882:207025 240 REVMACATHPVLSGPAIERLCNSPFKQVIVTDTVPLgDKlNACPKLHVLSVAGLLAKAIHNIHTESSVSVLF 311 ************************************9889******************************99 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (309 nodes) Target sequences: 1 (312 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: 6.72 // [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