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 WP_038212599.1 Q392_RS22290 phosphoribosylpyrophosphate synthetase
Query= curated2:Q8TUT6 (291 letters) >NCBI__GCF_000745855.1:WP_038212599.1 Length = 306 Score = 151 bits (382), Expect = 2e-41 Identities = 102/276 (36%), Positives = 140/276 (50%), Gaps = 7/276 (2%) Query: 15 RLAEELDAELAPVEEDRFPDGEQIVRVPPELDGTVVVVHSMSPPQDENLVKAIITLDAAR 74 RLAE AEL +E RFPDGE VR+ + G V + D ++ DAAR Sbjct: 17 RLAEAAGAELGRLETRRFPDGESYVRLLADPAGRAVDLVCTLADPDAGFLRLAFAADAAR 76 Query: 75 ENGAEEVIAIVPYMAYSRQDRRFEPGEPVSFRAVARAVSANADALITVDLH---EPGTLK 131 + GA EV + PY+AY RQDRRF GE VS R AR VS D ++TVD H P Sbjct: 77 DLGAAEVNLVAPYLAYMRQDRRFLDGESVSSRTFARLVSCTFDRVVTVDPHLHRHPALQG 136 Query: 132 YFDVPAENVSAAEELGKYLAERFEGEDLVVIGPDEGARELAREVASICGVEYDHLEKKRL 191 + VP + AA L ++A +++GPDE + + A +A G + L K R Sbjct: 137 LYTVPTATLHAAPLLADWIAAHVRAP--LIVGPDEESEQWAGAIARRIGAPHAVLRKTRH 194 Query: 192 SGDEVEIHPKELDV-EGRTVVLVDDMIDTGGTMVEAARALRDQGAGTLYAACTHALLTRN 250 V++ +L RT VLVDD+ +G T+ AA+ L QG HAL ++ Sbjct: 195 GDRSVDVAAPDLSAWRERTPVLVDDIASSGRTLAAAAQQLAAQGLPPAECVVVHALFAQD 254 Query: 251 AATRLLASGFEDIIATDTVPNPFEKVSVAPPVAEAV 286 A + LA F II+TDTVP+ + +AP A+A+ Sbjct: 255 AWAQ-LAPHFARIISTDTVPHRSNGIGLAPLAADAL 289 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: 9 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: 306 Length adjustment: 27 Effective length of query: 264 Effective length of database: 279 Effective search space: 73656 Effective search space used: 73656 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 WP_038212599.1 Q392_RS22290 (phosphoribosylpyrophosphate synthetase)
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.12748.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.8e-58 183.8 0.0 2.3e-58 183.5 0.0 1.0 1 lcl|NCBI__GCF_000745855.1:WP_038212599.1 Q392_RS22290 phosphoribosylpyrop Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000745855.1:WP_038212599.1 Q392_RS22290 phosphoribosylpyrophosphate synthetase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 183.5 0.0 2.3e-58 2.3e-58 5 297 .. 7 291 .. 4 295 .. 0.93 Alignments for each domain: == domain 1 score: 183.5 bits; conditional E-value: 2.3e-58 TIGR01251 5 sgssskelaekvaknlglelgdvevkkFadgElyvrieesvrgkdvfiivqstsapvndalmellllid 73 ++ ++ +a+++a+++g elg+ e+++F+dgE yvr+ + g+ v ++ t a+ + + l +++d lcl|NCBI__GCF_000745855.1:WP_038212599.1 7 PLPGNEGFAARLAEAAGAELGRLETRRFPDGESYVRLLADPAGRAVDLV--CTLADPDAGFLRLAFAAD 73 56778999***********************************999999..677789************ PP TIGR01251 74 alkrasaksvtaviPyygYaRqdkkaksrepisaklvaklleeaGadrvltvdlH...seqiqgfFdvp 139 a+++ +a +v++v+Py++Y Rqd+++ +e++s++++a+l++ drv+tvd H ++++qg ++vp lcl|NCBI__GCF_000745855.1:WP_038212599.1 74 AARDLGAAEVNLVAPYLAYMRQDRRFLDGESVSSRTFARLVSCT-FDRVVTVDPHlhrHPALQGLYTVP 141 *******************************************9.********994444679******* PP TIGR01251 140 venlsaspklieelkkkelknlvvvsPDkGaverakkvakklglelaiieKeRdskenevevtnllg.d 207 ++l+a+p l+++++++ ++ +++v PD+ + ++a ++a+++g++ a+++K+R+ ++ v+v + ++ lcl|NCBI__GCF_000745855.1:WP_038212599.1 142 TATLHAAPLLADWIAAH-VRAPLIVGPDEESEQWAGAIARRIGAPHAVLRKTRHGDR-SVDVAAPDLsA 208 ***************96.999*********************************666.77777666515 PP TIGR01251 208 vegkdvvivDDiisTggTlvkaaelLkekGAkkvivaathgvfsgdAlerlaeagveevivtntilvee 276 +++ v+vDDi s+g Tl++aa+ L +G ++++h++f++dA +la + ++i+t+t+++ lcl|NCBI__GCF_000745855.1:WP_038212599.1 209 WRERTPVLVDDIASSGRTLAAAAQQLAAQGLPPAECVVVHALFAQDAWAQLAPH-FARIISTDTVPH-- 274 69**************************************************99.9***********.. PP TIGR01251 277 kklpkvseisvapliaeaiar 297 + + i +apl a+a++r lcl|NCBI__GCF_000745855.1:WP_038212599.1 275 ----RSNGIGLAPLAADALLR 291 ....78888899998888865 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (309 nodes) Target sequences: 1 (306 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: 00:00:00.01 # Mc/sec: 8.88 // [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