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_066921978.1 ACG33_RS13470 phosphoribosylpyrophosphate synthetase
Query= curated2:B0R7B4 (281 letters) >NCBI__GCF_001579945.1:WP_066921978.1 Length = 304 Score = 122 bits (307), Expect = 7e-33 Identities = 89/288 (30%), Positives = 136/288 (47%), Gaps = 10/288 (3%) Query: 1 MLLSGSSSQSLAAALAAATGERLGDVTYDSFPDGEQLVTVPPAVDGERAVIVASTPTSDA 60 +L+ S LA +A R+ V + FPDGE LVT+ + G I+AS ++DA Sbjct: 4 VLMPFPSDAVLAGTIAQPLQARISPVAWRHFPDGESLVTLDDTLAGADVAILASLRSADA 63 Query: 61 HIEVLQLQD-AARDAGASEIITVLPYMGYARQDDAFDPGQPVSARAVARAISTGTDRVLT 119 L+ AR+ GA + + PY+GY RQD F G+ VS A+ + D ++T Sbjct: 64 LALPLRFAALTAREFGARSVGLIAPYLGYMRQDTRFHRGEAVSTPLFAQYLEEAFDWLVT 123 Query: 120 VNPH---EDGVLECFDVPAAGVDAAPQLAAPLPADLTDPVFLSPDHGATDLATSVRDAYG 176 V+PH + + + +P V A P +A + + D + + PD + + G Sbjct: 124 VDPHLHRVERLQSLYRIPTGHVSATPAVADWIAKTVPDAILIGPDSESEQWVAGIAARSG 183 Query: 177 TGVTDHFQKVRHSGSDVTVE-PSEIQTAGRDVVVTDDIVATGTTMSEAITALDD---PAR 232 K RH DV V P AGR V+ DDIV++G T+ E + L PA Sbjct: 184 MPY-QVLAKERHGDYDVRVSLPDPAAVAGRTPVLIDDIVSSGHTILETLAHLRQLSLPAP 242 Query: 233 VFVATVHPLLAGSARLKLARAGVEAVYGTDTIECAVSEVSAAPAIADA 280 + VA +HP+ AG A +L AG+ + TDTI + ++ +A A Sbjct: 243 MLVA-IHPVFAGDAYARLQEAGLARIVSTDTIAHPSNAIALGADLAAA 289 Lambda K H 0.314 0.130 0.362 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: 224 Number of extensions: 16 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: 281 Length of database: 304 Length adjustment: 26 Effective length of query: 255 Effective length of database: 278 Effective search space: 70890 Effective search space used: 70890 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_066921978.1 ACG33_RS13470 (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.4777.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.7e-55 172.3 0.0 7.2e-55 172.0 0.0 1.0 1 lcl|NCBI__GCF_001579945.1:WP_066921978.1 ACG33_RS13470 phosphoribosylpyro Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_001579945.1:WP_066921978.1 ACG33_RS13470 phosphoribosylpyrophosphate synthetase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 172.0 0.0 7.2e-55 7.2e-55 8 274 .. 10 275 .. 4 290 .. 0.92 Alignments for each domain: == domain 1 score: 172.0 bits; conditional E-value: 7.2e-55 TIGR01251 8 sskelaekvaknlglelgdvevkkFadgElyvrieesvrgkdvfiivqstsapvndalmellllidalk 76 s la +a+ l+ ++ +v ++F+dgE v++++++ g dv+i+ s + + + l +++ +++ lcl|NCBI__GCF_001579945.1:WP_066921978.1 10 SDAVLAGTIAQPLQARISPVAWRHFPDGESLVTLDDTLAGADVAIL-ASLR-SADALALPLRFAALTAR 76 55678999**************************************.5554.68999999999999*** PP TIGR01251 77 rasaksvtaviPyygYaRqdkkaksrepisaklvaklleeaGadrvltvdlHseqi...qgfFdvpven 142 + +a+sv +++Py+gY Rqd +++++e++s l+a+ leea d ++tvd H + + q+ +++p + lcl|NCBI__GCF_001579945.1:WP_066921978.1 77 EFGARSVGLIAPYLGYMRQDTRFHRGEAVSTPLFAQYLEEA-FDWLVTVDPHLHRVerlQSLYRIPTGH 144 *****************************************.**********8655222789******* PP TIGR01251 143 lsaspklieelkkkelknlvvvsPDkGaverakkvakklglelaiieKeRdskenevevt.nllgdveg 210 +sa p ++++++k+ + + +++ PD+ + +++ +a++ g++++++ KeR+ + +v+v + v+g lcl|NCBI__GCF_001579945.1:WP_066921978.1 145 VSATPAVADWIAKT-VPDAILIGPDSESEQWVAGIAARSGMPYQVLAKERHGDY-DVRVSlPDPAAVAG 211 ************96.999*********************************555.66665156689*** PP TIGR01251 211 kdvvivDDiisTggTlvkaaelLkekGAkkvivaathgvfsgdAlerlaeagveevivtntilv 274 ++ v++DDi+s+g+T++++ L++ + +a+h+vf+gdA+ rl+eag+ ++++t+ti++ lcl|NCBI__GCF_001579945.1:WP_066921978.1 212 RTPVLIDDIVSSGHTILETLAHLRQLSLPAPMLVAIHPVFAGDAYARLQEAGLARIVSTDTIAH 275 **************************************************************99 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (309 nodes) Target sequences: 1 (304 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 7.67 // [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