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 AZOBR_RS06995 AZOBR_RS06995 ribose-phosphate pyrophosphokinase
Query= curated2:Q8TUT6 (291 letters) >FitnessBrowser__azobra:AZOBR_RS06995 Length = 297 Score = 142 bits (357), Expect = 1e-38 Identities = 99/278 (35%), Positives = 140/278 (50%), Gaps = 7/278 (2%) Query: 14 RRLAEELDAELAPVEEDRFPDGEQIVRVPPELDGTVVVVHSMSPPQDENLVKAIITLDAA 73 RRLAE L+ E RFPDGE +VR+P ++ VV S+ P D+ LV+ + Sbjct: 18 RRLAEALNVPCHIAELHRFPDGESLVRLPEAVE-RAVVYRSLDRPNDK-LVELTLAASVL 75 Query: 74 RENGAEEVIAIVPYMAYSRQDRRFEPGEPVSFRAVARAVSANADALITVD--LHEPGTLK 131 R +GA E+ + PYMAY RQD F PGEPVS V + D + V+ LH TL Sbjct: 76 RRHGATELCLVAPYMAYMRQDAVFRPGEPVSQAVVGDWLGRLFDRFVCVEPHLHRTHTLD 135 Query: 132 YFDV--PAENVSAAEELGKYLAERFEGEDLVVIGPDEGARELAREVASICGVEYDHLEKK 189 V P+ +S A + + L D V++GPDE A L VA G+ K+ Sbjct: 136 EVFVGRPSVCLSGAGAIAERLRRDGTAPDAVIVGPDEEAAPLVEVVAGPLGLTALVGRKE 195 Query: 190 RLSGDEVEIH-PKELDVEGRTVVLVDDMIDTGGTMVEAARALRDQGAGTLYAACTHALLT 248 R +V + P + + GR VV+VDD+I +G T+ ARA R GA ++ HAL Sbjct: 196 RRGDRDVTVTLPADAPLAGRPVVIVDDVISSGETIFSCARAARAAGAASVRVFGVHALFD 255 Query: 249 RNAATRLLASGFEDIIATDTVPNPFEKVSVAPPVAEAV 286 A R A G ++ D VP+P + +A +A+A+ Sbjct: 256 AAVAARFAAEGLGTPLSCDGVPHPSNDLPLARLIADAL 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: 201 Number of extensions: 14 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: 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 AZOBR_RS06995 AZOBR_RS06995 (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.3125.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.6e-49 154.5 0.0 1.9e-49 154.2 0.0 1.0 1 lcl|FitnessBrowser__azobra:AZOBR_RS06995 AZOBR_RS06995 ribose-phosphate p Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__azobra:AZOBR_RS06995 AZOBR_RS06995 ribose-phosphate pyrophosphokinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 154.2 0.0 1.9e-49 1.9e-49 10 296 .. 14 294 .. 7 296 .. 0.92 Alignments for each domain: == domain 1 score: 154.2 bits; conditional E-value: 1.9e-49 TIGR01251 10 kelaekvaknlglelgdvevkkFadgElyvrieesvrgkdvfiivqstsapvndalmellllidalkra 78 + a+++a++l+++ +e ++F+dgE vr+ e+v +++++ s nd+l+el l+++ l+r lcl|FitnessBrowser__azobra:AZOBR_RS06995 14 ADGARRLAEALNVPCHIAELHRFPDGESLVRLPEAV---ERAVVYRSLD-RPNDKLVELTLAASVLRRH 78 5668999****************************9...6699966666.69***************** PP TIGR01251 79 saksvtaviPyygYaRqdkkaksrepisaklvaklleeaGadrvltvdlHseqiq...gfFd.vpvenl 143 +a ++ +v+Py++Y Rqd ++++ep+s +v++ l + dr + v+ H + ++ ++F p l lcl|FitnessBrowser__azobra:AZOBR_RS06995 79 GATELCLVAPYMAYMRQDAVFRPGEPVSQAVVGDWLGRL-FDRFVCVEPHLHRTHtldEVFVgRPSVCL 146 ***************************************.********99776542227787689999* PP TIGR01251 144 saspklieelkkke.lknlvvvsPDkGaverakkvakklglelaiieKeRdskenevevtnllgdvegk 211 s++ ++e+l+++ + + v+v PD+ a+ ++ va lgl + +KeR ++ + + + + ++g+ lcl|FitnessBrowser__azobra:AZOBR_RS06995 147 SGAGAIAERLRRDGtAPDAVIVGPDEEAAPLVEVVAGPLGLTALVGRKERRGDRDVTVTLPADAPLAGR 215 ***********998899**********************************888677778999****** PP TIGR01251 212 dvvivDDiisTggTlvkaaelLkekGAkkvivaathgvfsgdAlerlaeagveevivtntilveekklp 280 vvivDD+is+g T+ a++++ +GA +v v +h++f + r+a g+ + ++++ +++ lcl|FitnessBrowser__azobra:AZOBR_RS06995 216 PVVIVDDVISSGETIFSCARAARAAGAASVRVFGVHALFDAAVAARFAAEGLGTPLSCDGVPH------ 278 ***************************************************************...... PP TIGR01251 281 kvseisvapliaeaia 296 +++ +a lia+a++ lcl|FitnessBrowser__azobra:AZOBR_RS06995 279 PSNDLPLARLIADALL 294 7888889999998875 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: 10.29 // [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