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 N515DRAFT_2463 N515DRAFT_2463 ribose-phosphate pyrophosphokinase
Query= curated2:Q8TUT6 (291 letters) >FitnessBrowser__Dyella79:N515DRAFT_2463 Length = 293 Score = 127 bits (319), Expect = 3e-34 Identities = 90/290 (31%), Positives = 143/290 (49%), Gaps = 8/290 (2%) Query: 2 IVLATSEGVKLGRRLAEELDAELAPVEEDRFPDGEQIVRV-PPELDGTVVVVHSMSPPQD 60 +V A +L LA +E RFPDGE +VRV P + ++V ++ P D Sbjct: 4 VVYAMPGNQELADALAHRRRMARLALELHRFPDGEGLVRVEEPPVGAEAIIVCTLDRP-D 62 Query: 61 ENLVKAIITLDAARENGAEEVIAIVPYMAYSRQDRRFEPGEPVSFRAVARAVSANADALI 120 E + ++ D RE GA V + PY+AY RQD RF PGE VS R ++ + D + Sbjct: 63 EKTLPLLMAADTLRELGAGSVGLVAPYLAYLRQDARFRPGEAVSSGIFGRLLAEHFDWQV 122 Query: 121 TVD--LHEPGTLKYFDVP-AENVSAAEELGKYLAERFEGEDLVVIGPDEGARELAREVAS 177 T+D LH +L +P +SAA L +L ER E ++IGPDE + VA+ Sbjct: 123 TIDPHLHRLRSLTEAGMPQGRAISAAPALAGWLRERVELP--LLIGPDEESAPWVESVAA 180 Query: 178 ICGVEYDHLEKKRLSGDEVEIHPKEL-DVEGRTVVLVDDMIDTGGTMVEAARALRDQGAG 236 + K+R +V++ +L + G VL+DD+I +G T++++ LR G Sbjct: 181 LMSAPAVVATKRRFGDRKVQVQLPDLSNWPGHNPVLLDDIISSGHTLLKSIEGLRALGMP 240 Query: 237 TLYAACTHALLTRNAATRLLASGFEDIIATDTVPNPFEKVSVAPPVAEAV 286 + H L NA RL +G ++ T++VP ++ ++ +A A+ Sbjct: 241 APWCVAVHGLFADNALERLRVAGVAGVVTTNSVPGETARIDLSELLAAAL 290 Lambda K H 0.314 0.134 0.370 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: 178 Number of extensions: 8 Number of successful extensions: 3 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: 291 Length of database: 293 Length adjustment: 26 Effective length of query: 265 Effective length of database: 267 Effective search space: 70755 Effective search space used: 70755 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (22.0 bits) S2: 48 (23.1 bits)
Align candidate N515DRAFT_2463 N515DRAFT_2463 (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.31276.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.7e-52 162.8 0.0 5.3e-52 162.6 0.0 1.0 1 lcl|FitnessBrowser__Dyella79:N515DRAFT_2463 N515DRAFT_2463 ribose-phosphate Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Dyella79:N515DRAFT_2463 N515DRAFT_2463 ribose-phosphate pyrophosphokinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 162.6 0.0 5.3e-52 5.3e-52 5 295 .. 7 290 .. 3 293 .] 0.93 Alignments for each domain: == domain 1 score: 162.6 bits; conditional E-value: 5.3e-52 TIGR01251 5 sgssskelaekvaknlglelgdvevkkFadgElyvrieesvrgkdvfiivqstsapvndalmelll 70 + + ++ela+++a++ + + e ++F+dgE vr+ee g + +i+ t +++ + ll+ lcl|FitnessBrowser__Dyella79:N515DRAFT_2463 7 AMPGNQELADALAHRRRMARLALELHRFPDGEGLVRVEEPPVGAEAIIV--CTLDRPDEKTLPLLM 70 56789**************************************999999..677789********* PP TIGR01251 71 lidalkrasaksvtaviPyygYaRqdkkaksrepisaklvaklleeaGadrvltvdlHseqiqgfF 136 ++d+l++ +a+sv +v+Py++Y Rqd +++++e++s+ ++++ll+e d +t+d H + +++ lcl|FitnessBrowser__Dyella79:N515DRAFT_2463 71 AADTLRELGAGSVGLVAPYLAYLRQDARFRPGEAVSSGIFGRLLAEH-FDWQVTIDPHLHRLRSLT 135 ***********************************************.************999999 PP TIGR01251 137 d...vpvenlsaspklieelkkkelknlvvvsPDkGaverakkvakklglelaiieKeRdskenev 199 + + + +sa+p l+ +l+++ ++ ++++ PD+ ++ ++++va+ + ++ ++ K+R ++ +v lcl|FitnessBrowser__Dyella79:N515DRAFT_2463 136 EagmPQGRAISAAPALAGWLRER-VELPLLIGPDEESAPWVESVAALMSAPAVVATKRRFGDR-KV 199 843124477999*********97.9999********************************555.77 PP TIGR01251 200 evt.nllgdvegkdvvivDDiisTggTlvkaaelLkekGAkkvivaathgvfsgdAlerlaeagve 264 +v+ + l + g + v++DDiis+g+Tl+k++e L+ G ++a+hg+f+++Alerl+ agv lcl|FitnessBrowser__Dyella79:N515DRAFT_2463 200 QVQlPDLSNWPGHNPVLLDDIISSGHTLLKSIEGLRALGMPAPWCVAVHGLFADNALERLRVAGVA 265 7762556799******************************************************** PP TIGR01251 265 evivtntilveekklpkvseisvapliaeai 295 v+ tn+++ + +i++++l+a a+ lcl|FitnessBrowser__Dyella79:N515DRAFT_2463 266 GVVTTNSVPG------ETARIDLSELLAAAL 290 **********......889999999999887 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (309 nodes) Target sequences: 1 (293 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: 6.31 // [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