Align Ribose-phosphate pyrophosphokinase; RPPK; 5-phospho-D-ribosyl alpha-1-diphosphate synthase; Phosphoribosyl diphosphate synthase; Phosphoribosyl pyrophosphate synthase; P-Rib-PP synthase; PPRibP synthase; PRPP synthase; PRPPase; EC 2.7.6.1 (characterized)
to candidate WP_013074142.1 BTUS_RS00375 ribose-phosphate diphosphokinase
Query= SwissProt::P14193 (317 letters) >NCBI__GCF_000092905.1:WP_013074142.1 Length = 316 Score = 443 bits (1139), Expect = e-129 Identities = 217/314 (69%), Positives = 263/314 (83%) Query: 4 QYGDKNLKIFSLNSNPELAKEIADIVGVQLGKCSVTRFSDGEVQINIEESIRGCDCYIIQ 63 +Y D LK+F+ NSNP L +E+ + VGV+LG+ VTRFSDGE+Q+ IEES+RGCD +++Q Sbjct: 2 RYRDAKLKVFTGNSNPALVREVVEHVGVELGRSRVTRFSDGEIQVKIEESVRGCDVFVVQ 61 Query: 64 STSDPVNEHIMELLIMVDALKRASAKTINIVIPYYGYARQDRKARSREPITAKLFANLLE 123 STS P+NE++MELLIMVDALKRASAK IN+V+PYYGYARQDRKAR REPITAKL ANL+E Sbjct: 62 STSAPINENLMELLIMVDALKRASAKRINVVMPYYGYARQDRKARPREPITAKLVANLIE 121 Query: 124 TAGATRVIALDLHAPQIQGFFDIPIDHLMGVPILGEYFEGKNLEDIVIVSPDHGGVTRAR 183 TAGA RVIA+DLHA QIQGFFDIP+DHL+ PIL YF+ K L+D+V+VSPD GGVTRAR Sbjct: 122 TAGAHRVIAMDLHAGQIQGFFDIPVDHLLAQPILASYFQDKGLKDVVVVSPDMGGVTRAR 181 Query: 184 KLADRLKAPIAIIDKRRPRPNVAEVMNIVGNIEGKTAILIDDIIDTAGTITLAANALVEN 243 +A RL A IAIIDKRRP PNVAE+MNI+G+I+GKTA++IDDIIDTAGTIT A AL+E Sbjct: 182 GMAQRLGASIAIIDKRRPEPNVAEIMNIIGDIDGKTAVMIDDIIDTAGTITQGAKALLER 241 Query: 244 GAKEVYACCTHPVLSGPAVERINNSTIKELVVTNSIKLPEEKKIERFKQLSVGPLLAEAI 303 GAKEVYACCTH VLSGPA+ER+ S I+E+VVTN+I L E +++ LSV PL+ +AI Sbjct: 242 GAKEVYACCTHAVLSGPAMERLRESEIREVVVTNTIPLKESPVLDKLVVLSVAPLIGDAI 301 Query: 304 IRVHEQQSVSYLFS 317 IRVHE SVS LF+ Sbjct: 302 IRVHEDLSVSTLFN 315 Lambda K H 0.319 0.137 0.383 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: 323 Number of extensions: 8 Number of successful extensions: 1 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: 317 Length of database: 316 Length adjustment: 27 Effective length of query: 290 Effective length of database: 289 Effective search space: 83810 Effective search space used: 83810 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 (21.7 bits) S2: 48 (23.1 bits)
Align candidate WP_013074142.1 BTUS_RS00375 (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.30636.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.2e-131 422.8 0.6 3.7e-131 422.6 0.6 1.0 1 lcl|NCBI__GCF_000092905.1:WP_013074142.1 BTUS_RS00375 ribose-phosphate di Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000092905.1:WP_013074142.1 BTUS_RS00375 ribose-phosphate diphosphokinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 422.6 0.6 3.7e-131 3.7e-131 2 309 .] 9 315 .. 8 315 .. 0.99 Alignments for each domain: == domain 1 score: 422.6 bits; conditional E-value: 3.7e-131 TIGR01251 2 kilsgssskelaekvaknlglelgdvevkkFadgElyvrieesvrgkdvfiivqstsapvndalmelll 70 k++ g+s+++l ++v +++g+elg+++v++F+dgE++v+ieesvrg+dvf++ qstsap+n++lmell+ lcl|NCBI__GCF_000092905.1:WP_013074142.1 9 KVFTGNSNPALVREVVEHVGVELGRSRVTRFSDGEIQVKIEESVRGCDVFVV-QSTSAPINENLMELLI 76 89**************************************************.**************** PP TIGR01251 71 lidalkrasaksvtaviPyygYaRqdkkaksrepisaklvaklleeaGadrvltvdlHseqiqgfFdvp 139 ++dalkrasak++++v+PyygYaRqd+ka++repi+aklva+l+e+aGa+rv+++dlH+ qiqgfFd+p lcl|NCBI__GCF_000092905.1:WP_013074142.1 77 MVDALKRASAKRINVVMPYYGYARQDRKARPREPITAKLVANLIETAGAHRVIAMDLHAGQIQGFFDIP 145 ********************************************************************* PP TIGR01251 140 venlsaspklieelkkkelknlvvvsPDkGaverakkvakklglelaiieKeRdskenevevtnllgdv 208 v++l a+p l+ ++++k lk++vvvsPD G+v+ra+ +a++lg+++aii+K+R+ + n++e++n++gd+ lcl|NCBI__GCF_000092905.1:WP_013074142.1 146 VDHLLAQPILASYFQDKGLKDVVVVSPDMGGVTRARGMAQRLGASIAIIDKRRP-EPNVAEIMNIIGDI 213 ******************************************************.888*********** PP TIGR01251 209 egkdvvivDDiisTggTlvkaaelLkekGAkkvivaathgvfsgdAlerlaeagveevivtntilvee. 276 +gk++v++DDii+T+gT++++a++L e+GAk+v++++th+v+sg+A+erl+e+ ++ev+vtnti+ +e lcl|NCBI__GCF_000092905.1:WP_013074142.1 214 DGKTAVMIDDIIDTAGTITQGAKALLERGAKEVYACCTHAVLSGPAMERLRESEIREVVVTNTIPLKEs 282 ******************************************************************554 PP TIGR01251 277 kklpkvseisvapliaeaiarihenesvsslfd 309 l+k+ ++svapli +ai+r+he+ svs+lf+ lcl|NCBI__GCF_000092905.1:WP_013074142.1 283 PVLDKLVVLSVAPLIGDAIIRVHEDLSVSTLFN 315 999****************************95 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (309 nodes) Target sequences: 1 (316 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: 00:00:00.01 # Mc/sec: 6.62 // [ok]
This GapMind analysis is from Apr 10 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