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_086510738.1 BZY95_RS15130 phosphoribosylpyrophosphate synthetase
Query= curated2:Q8TUT6 (291 letters) >NCBI__GCF_002151265.1:WP_086510738.1 Length = 297 Score = 153 bits (387), Expect = 4e-42 Identities = 106/279 (37%), Positives = 155/279 (55%), Gaps = 10/279 (3%) Query: 14 RRLAEELDAELAPVEEDRFPDGEQIVRVPP-ELDGTVVVVHSMSPPQDENLVKAIITLDA 72 +RLAE + E +E RFPD E +R+P EL +VV S++ P D+ LV+ ++ Sbjct: 16 QRLAEAVGIEALRMERHRFPDEELCLRLPDAELPECLVVYRSLNRPNDK-LVELMLLARH 74 Query: 73 ARENGAEEVIAIVPYMAYSRQDRRFEPGEPVSFRAVARAVSANADALITVD--LHEPGTL 130 ARE G ++ + PY+AY RQD F PGE VS R V ++ DALITVD LH L Sbjct: 75 ARERGVRRLVLVAPYLAYMRQDIAFRPGELVSQRLVGGFLAELFDALITVDPHLHRIERL 134 Query: 131 KYFDVP---AENVSAAEELGKYLAERFEGEDLVVIGPDEGARELAREVASICGVEYDHLE 187 + VP A +SAA L + +AER D +++GPD + + A G+ Y Sbjct: 135 EQA-VPLRQAVALSAAPALAEAIAER--RRDALLLGPDAESAQWVESAARATGLAYGVCT 191 Query: 188 KKRLSGDEVEIHPKELDVEGRTVVLVDDMIDTGGTMVEAARALRDQGAGTLYAACTHALL 247 K+R EVEI EL GR VVL+DD+ +G T+ +AAR + GA + A THAL Sbjct: 192 KQRHGDREVEIALPELAFAGRRVVLLDDIASSGRTLAQAARRVLAAGAAGVDVAVTHALF 251 Query: 248 TRNAATRLLASGFEDIIATDTVPNPFEKVSVAPPVAEAV 286 +A + + +G E++ +TD++P+ V +AP +A A+ Sbjct: 252 AGDALSVIRQAGVEEVWSTDSIPHQSNAVLLAPALAAAL 290 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: 184 Number of extensions: 8 Number of successful extensions: 2 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 WP_086510738.1 BZY95_RS15130 (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.1192.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.1e-58 182.1 0.0 7.2e-58 181.9 0.0 1.0 1 lcl|NCBI__GCF_002151265.1:WP_086510738.1 BZY95_RS15130 phosphoribosylpyro Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_002151265.1:WP_086510738.1 BZY95_RS15130 phosphoribosylpyrophosphate synthetase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 181.9 0.0 7.2e-58 7.2e-58 7 285 .. 9 280 .. 3 292 .. 0.91 Alignments for each domain: == domain 1 score: 181.9 bits; conditional E-value: 7.2e-58 TIGR01251 7 ssskelaekvaknlglelgdvevkkFadgElyvrieesvrgkdvfiivqstsapvndalmellllidal 75 +++ a+++a+++g+e +++e ++F+d+El+ r+ ++ ++ ++ s nd+l+el+ll+ + lcl|NCBI__GCF_002151265.1:WP_086510738.1 9 DEESPAAQRLAEAVGIEALRMERHRFPDEELCLRLPDAE-LPECLVVYRSLN-RPNDKLVELMLLARHA 75 5677889****************************9984.458999966655.79************** PP TIGR01251 76 krasaksvtaviPyygYaRqdkkaksrepisaklvaklleeaGadrvltvdlHseqiqgfFd.vpven. 142 ++ +++++ +v+Py++Y Rqd ++++e +s +lv+ +l+e+ d ++tvd H + i+ + vp+++ lcl|NCBI__GCF_002151265.1:WP_086510738.1 76 RERGVRRLVLVAPYLAYMRQDIAFRPGELVSQRLVGGFLAEL-FDALITVDPHLHRIERLEQaVPLRQa 143 ******************************************.**************999888876543 PP TIGR01251 143 ..lsaspklieelkkkelknlvvvsPDkGaverakkvakklglelaiieKeRdskenevevtnllgdve 209 lsa+p l+e ++++ ++ +++ PD+ ++++++++a++ gl + + K+R+ + eve+ ++ + lcl|NCBI__GCF_002151265.1:WP_086510738.1 144 vaLSAAPALAEAIAER-RRDALLLGPDAESAQWVESAARATGLAYGVCTKQRH-GDREVEIALPELAFA 210 33999*********97.999*********************************.666************ PP TIGR01251 210 gkdvvivDDiisTggTlvkaaelLkekGAkkvivaathgvfsgdAlerlaeagveevivtntilveekk 278 g+ vv++DDi s+g Tl++aa+ + +GA v va+th++f+gdAl+ +++agveev +t++i++ lcl|NCBI__GCF_002151265.1:WP_086510738.1 211 GRRVVLLDDIASSGRTLAQAARRVLAAGAAGVDVAVTHALFAGDALSVIRQAGVEEVWSTDSIPH---- 275 *****************************************************************.... PP TIGR01251 279 lpkvsei 285 + + + lcl|NCBI__GCF_002151265.1:WP_086510738.1 276 --QSNAV 280 ..44444 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: 00:00:00.01 # Mc/sec: 8.02 // [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