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 Echvi_3167 Echvi_3167 ribose-phosphate pyrophosphokinase
Query= curated2:Q8TUT6 (291 letters) >FitnessBrowser__Cola:Echvi_3167 Length = 297 Score = 138 bits (347), Expect = 2e-37 Identities = 90/284 (31%), Positives = 149/284 (52%), Gaps = 8/284 (2%) Query: 11 KLGRRLAEELDAELAPVEEDRFPDGEQIVRVPPEL-DGTVVVVHSMSPPQDENLVKAIIT 69 KL +A ++DAE+ FPDGE R+ ++ D VV+V ++ P DE L+ Sbjct: 13 KLTELMATKMDAEVGKATLRNFPDGESYTRILSDVKDKCVVLVCTLHEP-DEKLLPLYFL 71 Query: 70 LDAARENGAEEVIAIVPYMAYSRQDRRFEPGEPVSFRAVARAVSANADALITVD--LHEP 127 A+ GA + PY+AY RQD+ F GE V+ + +S AD++ TVD LH Sbjct: 72 SHTAKSLGAMCTCLVAPYLAYMRQDKVFNEGEGVTSGFFGKLISGFADSITTVDPHLHRI 131 Query: 128 GTL-KYFDVPAENVSAAEELGKYLAERFEGEDLVVIGPDEGARELAREVASICGVEYDHL 186 +L + + +P + + AA+ + ++ E E V+IGPD + + EVA G + L Sbjct: 132 SSLGEVYQIPNKVIHAADAISDWIKENIENP--VLIGPDSESEQWVSEVAKNAGAPFIVL 189 Query: 187 EKKRLSGDEVEIHPKELDV-EGRTVVLVDDMIDTGGTMVEAARALRDQGAGTLYAACTHA 245 +K R +VE+ ++D+ + T +LVDD+I T TM+E + L+ G HA Sbjct: 190 QKMRHGDRDVEVSVPDVDIYKDATPILVDDIISTARTMIETVQHLKKAGMKPPICVGIHA 249 Query: 246 LLTRNAATRLLASGFEDIIATDTVPNPFEKVSVAPPVAEAVENL 289 + + N+ LL SG E I+ +T+P+P + ++ +A+ V+ L Sbjct: 250 VFSGNSYKDLLGSGVEKIVTCNTIPHPSNGIDLSDIMAKEVKKL 293 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: 196 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: 297 Length adjustment: 26 Effective length of query: 265 Effective length of database: 271 Effective search space: 71815 Effective search space used: 71815 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 Echvi_3167 Echvi_3167 (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.19693.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.7e-62 197.1 0.0 1.9e-62 196.9 0.0 1.0 1 lcl|FitnessBrowser__Cola:Echvi_3167 Echvi_3167 ribose-phosphate pyro Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Cola:Echvi_3167 Echvi_3167 ribose-phosphate pyrophosphokinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 196.9 0.0 1.9e-62 1.9e-62 3 297 .. 5 292 .. 3 297 .] 0.92 Alignments for each domain: == domain 1 score: 196.9 bits; conditional E-value: 1.9e-62 TIGR01251 3 ilsgssskelaekvaknlglelgdvevkkFadgElyvrieesvrgkdvfiivqstsapvndalmellllidalk 76 ++s++ +++l e +a +++ e+g+++ ++F+dgE y+ri ++v++k v+++ t ++ +++l+ l +l ++k lcl|FitnessBrowser__Cola:Echvi_3167 5 LFSLPGNEKLTELMATKMDAEVGKATLRNFPDGESYTRILSDVKDKCVVLV--CTLHEPDEKLLPLYFLSHTAK 76 689999*************************************88555555..666789*************** PP TIGR01251 77 rasaksvtaviPyygYaRqdkkaksrepisaklvaklleeaGadrvltvdlHseqiq...gfFdvpvenlsasp 147 + +a +v+Py++Y Rqdk ++++e++++ ++kl++ ad++ tvd H + i+ +++++p + ++a+ lcl|FitnessBrowser__Cola:Echvi_3167 77 SLGAMCTCLVAPYLAYMRQDKVFNEGEGVTSGFFGKLISGF-ADSITTVDPHLHRISslgEVYQIPNKVIHAAD 149 *****************************************.***********99973336899********** PP TIGR01251 148 klieelkkkelknlvvvsPDkGaverakkvakklglelaiieKeRdskenevevtnllgdv.egkdvvivDDii 220 + +++k++ +n+v++ PD+ + +++++vak++g+++ +++K R+ + +vev ++d+ ++ + ++vDDii lcl|FitnessBrowser__Cola:Echvi_3167 150 AISDWIKEN-IENPVLIGPDSESEQWVSEVAKNAGAPFIVLQKMRH-GDRDVEVSVPDVDIyKDATPILVDDII 221 *******97.9***********************************.666**********9678999******* PP TIGR01251 221 sTggTlvkaaelLkekGAkkvivaathgvfsgdAlerlaeagveevivtntilveekklpkvseisvapliaea 294 sT+ T++++++ Lk++G k i++ +h+vfsg++++ l +gve+++ +nti++ + i++++++a+ lcl|FitnessBrowser__Cola:Echvi_3167 222 STARTMIETVQHLKKAGMKPPICVGIHAVFSGNSYKDLLGSGVEKIVTCNTIPH------PSNGIDLSDIMAKE 289 ******************************************************......55556666655555 PP TIGR01251 295 iar 297 +++ lcl|FitnessBrowser__Cola:Echvi_3167 290 VKK 292 544 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (309 nodes) Target sequences: 1 (297 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 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 10.89 // [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