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_013840250.1 DESRU_RS00870 ribose-phosphate pyrophosphokinase
Query= SwissProt::P14193 (317 letters) >NCBI__GCF_000215085.1:WP_013840250.1 Length = 315 Score = 421 bits (1082), Expect = e-122 Identities = 207/312 (66%), Positives = 251/312 (80%) Query: 6 GDKNLKIFSLNSNPELAKEIADIVGVQLGKCSVTRFSDGEVQINIEESIRGCDCYIIQST 65 G K LKIF+ N+NP+LA+EI +GV +G V+RFSDGE++ +EES+RG D +IIQ T Sbjct: 4 GSKRLKIFAGNANPDLAREICQYLGVAMGASKVSRFSDGEIRAEVEESVRGADAFIIQPT 63 Query: 66 SDPVNEHIMELLIMVDALKRASAKTINIVIPYYGYARQDRKARSREPITAKLFANLLETA 125 S PVNEH+MELLIMVDAL+RASA+ I V+PYYGYARQDRK R+R PITAKL AN++ + Sbjct: 64 STPVNEHLMELLIMVDALRRASARRITAVVPYYGYARQDRKTRARAPITAKLVANIIIAS 123 Query: 126 GATRVIALDLHAPQIQGFFDIPIDHLMGVPILGEYFEGKNLEDIVIVSPDHGGVTRARKL 185 G R+I +DLHA QIQGFFDIP+DHL GVPIL EYF +D+V+VSPD GGVTRAR L Sbjct: 124 GCRRMITMDLHAGQIQGFFDIPVDHLPGVPILAEYFHQNLKDDVVVVSPDIGGVTRARDL 183 Query: 186 ADRLKAPIAIIDKRRPRPNVAEVMNIVGNIEGKTAILIDDIIDTAGTITLAANALVENGA 245 A+R+ AP+AIIDKRRP PNVAEV N++G+I+GKT I+IDDIIDTAGTIT A AL+E GA Sbjct: 184 AERIGAPLAIIDKRRPEPNVAEVTNVIGSIKGKTVIMIDDIIDTAGTITKGAAALMERGA 243 Query: 246 KEVYACCTHPVLSGPAVERINNSTIKELVVTNSIKLPEEKKIERFKQLSVGPLLAEAIIR 305 KE+ CCTH VLSGPA++R+ S IKE+VVTN+I LP EK I++ K LSV PLL EAIIR Sbjct: 244 KEIRVCCTHAVLSGPAIQRLQESVIKEVVVTNTIPLPPEKMIDKIKVLSVAPLLGEAIIR 303 Query: 306 VHEQQSVSYLFS 317 +HE SVS LFS Sbjct: 304 IHEDLSVSKLFS 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: 301 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: 315 Length adjustment: 27 Effective length of query: 290 Effective length of database: 288 Effective search space: 83520 Effective search space used: 83520 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_013840250.1 DESRU_RS00870 (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.2394375.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.3e-128 412.9 0.3 3.7e-128 412.7 0.3 1.0 1 NCBI__GCF_000215085.1:WP_013840250.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000215085.1:WP_013840250.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 412.7 0.3 3.7e-128 3.7e-128 2 309 .] 9 315 .] 8 315 .] 0.99 Alignments for each domain: == domain 1 score: 412.7 bits; conditional E-value: 3.7e-128 TIGR01251 2 kilsgssskelaekvaknlglelgdvevkkFadgElyvrieesvrgkdvfiivqstsapvndalmellllida 74 ki++g+++++la++++++lg+ +g ++v +F+dgE+ ++eesvrg d fii q ts+pvn++lmell+++da NCBI__GCF_000215085.1:WP_013840250.1 9 KIFAGNANPDLAREICQYLGVAMGASKVSRFSDGEIRAEVEESVRGADAFII-QPTSTPVNEHLMELLIMVDA 80 89**************************************************.******************** PP TIGR01251 75 lkrasaksvtaviPyygYaRqdkkaksrepisaklvaklleeaGadrvltvdlHseqiqgfFdvpvenlsasp 147 l+rasa+++tav+PyygYaRqd+k++ r pi+aklva+++ + G +r++t+dlH+ qiqgfFd+pv++l + p NCBI__GCF_000215085.1:WP_013840250.1 81 LRRASARRITAVVPYYGYARQDRKTRARAPITAKLVANIIIASGCRRMITMDLHAGQIQGFFDIPVDHLPGVP 153 ************************************************************************* PP TIGR01251 148 klieelkkkelknlvvvsPDkGaverakkvakklglelaiieKeRdskenevevtnllgdvegkdvvivDDii 220 l+e+++++ ++++vvvsPD G+v+ra+++a+++g++laii+K+R+ + n++evtn++g ++gk+v+++DDii NCBI__GCF_000215085.1:WP_013840250.1 154 ILAEYFHQNLKDDVVVVSPDIGGVTRARDLAERIGAPLAIIDKRRP-EPNVAEVTNVIGSIKGKTVIMIDDII 225 **********************************************.888*********************** PP TIGR01251 221 sTggTlvkaaelLkekGAkkvivaathgvfsgdAlerlaeagveevivtntilv.eekklpkvseisvaplia 292 +T+gT++k+a +L e+GAk++ v++th+v+sg+A++rl+e++++ev+vtnti+ ek ++k++++svapl+ NCBI__GCF_000215085.1:WP_013840250.1 226 DTAGTITKGAAALMERGAKEIRVCCTHAVLSGPAIQRLQESVIKEVVVTNTIPLpPEKMIDKIKVLSVAPLLG 298 ******************************************************999**************** PP TIGR01251 293 eaiarihenesvsslfd 309 eai+rihe+ svs+lf+ NCBI__GCF_000215085.1:WP_013840250.1 299 EAIIRIHEDLSVSKLFS 315 ***************95 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (309 nodes) Target sequences: 1 (315 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 12.81 // [ok]
This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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