Align Ribose-phosphate pyrophosphokinase; RPPK; 5-phospho-D-ribosyl alpha-1-diphosphate synthase; Phosphoribosyl diphosphate synthase; Phosphoribosyl pyrophosphate synthase; P-Rib-PP synthase; PRPP synthase; PRPPase; EC 2.7.6.1 (characterized)
to candidate WP_009567132.1 AFE_RS12705 ribose-phosphate pyrophosphokinase
Query= SwissProt::P0A1V6 (315 letters) >NCBI__GCF_000021485.1:WP_009567132.1 Length = 315 Score = 371 bits (953), Expect = e-107 Identities = 190/311 (61%), Positives = 241/311 (77%), Gaps = 2/311 (0%) Query: 3 DMKLFAGNATPELAQRIANRLYTSLGDAAVGRFSDGEVSVQINENVRGGDIFIIQSTCAP 62 ++ +F+GNA P LA ++A L +G A V FSDGEV V+I ENVRG D+F++Q TC P Sbjct: 5 NLMVFSGNANPVLAAQVARFLQIPIGRAEVSAFSDGEVFVEILENVRGRDVFVLQPTCTP 64 Query: 63 TNDNLMELVVMVDALRRASAGRITAVIPYFGYARQDRRVRSARVPITAKVVADFLSSVGV 122 TND+LMEL+ M+DAL+RASA RITA +PYFGYARQDR+ RS R ITAK+VAD ++S G Sbjct: 65 TNDHLMELLTMIDALKRASANRITAAMPYFGYARQDRKSRS-RTAITAKLVADLITSAGA 123 Query: 123 DRVLTVDLHAEQIQGFFDVPVDNVFGSPILLEDMLQLNLDNPIVVSPDIGGVVRARAIAK 182 +RVLT+DLHA+QIQGFFDVPVDN++ SPILL D+ + + IVVSPD+GGVVRARAIAK Sbjct: 124 NRVLTMDLHADQIQGFFDVPVDNIYASPILLGDIWRQSYPELIVVSPDVGGVVRARAIAK 183 Query: 183 LLNDTDMAIIDKRRPRANVSQVMHIIGDVAGRDCVLVDDMIDTGGTLCKAAEALKERGAK 242 L + D+AIIDKRRPR N S VM+IIGDV GR CVLVDDM+DT TLC+AA ALK RGA Sbjct: 184 RL-EVDLAIIDKRRPRPNESVVMNIIGDVDGRTCVLVDDMVDTANTLCEAAHALKARGAV 242 Query: 243 RVFAYATHPIFSGNAANNLRNSVIDEVVVCDTIPLTDEIKALPNVRTLTLSGMLAEAIRR 302 +V AY THP+ SG A + S +DE+VV DTIPL + +A +R L+++ +LAE IRR Sbjct: 243 KVCAYCTHPVLSGPAMERIERSDLDELVVTDTIPLRPDARASSKIRVLSVAELLAETIRR 302 Query: 303 ISNEESISAMF 313 I+ E+S+S++F Sbjct: 303 IAEEDSVSSLF 313 Lambda K H 0.322 0.137 0.386 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: 312 Number of extensions: 10 Number of successful extensions: 3 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: 315 Length of database: 315 Length adjustment: 27 Effective length of query: 288 Effective length of database: 288 Effective search space: 82944 Effective search space used: 82944 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 (21.9 bits) S2: 48 (23.1 bits)
Align candidate WP_009567132.1 AFE_RS12705 (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.13180.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.4e-126 405.6 0.1 6.1e-126 405.4 0.1 1.0 1 lcl|NCBI__GCF_000021485.1:WP_009567132.1 AFE_RS12705 ribose-phosphate pyr Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000021485.1:WP_009567132.1 AFE_RS12705 ribose-phosphate pyrophosphokinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 405.4 0.1 6.1e-126 6.1e-126 2 308 .. 7 313 .. 6 314 .. 0.99 Alignments for each domain: == domain 1 score: 405.4 bits; conditional E-value: 6.1e-126 TIGR01251 2 kilsgssskelaekvaknlglelgdvevkkFadgElyvrieesvrgkdvfiivqstsapvndalmelll 70 +++sg++++ la++va+ l++++g++ev F+dgE+ v+i e+vrg+dvf++ q t++p+nd+lmell+ lcl|NCBI__GCF_000021485.1:WP_009567132.1 7 MVFSGNANPVLAAQVARFLQIPIGRAEVSAFSDGEVFVEILENVRGRDVFVL-QPTCTPTNDHLMELLT 74 89**************************************************.**************** PP TIGR01251 71 lidalkrasaksvtaviPyygYaRqdkkaksrepisaklvaklleeaGadrvltvdlHseqiqgfFdvp 139 +idalkrasa+++ta +Py+gYaRqd+k +sr++i+aklva+l+++aGa+rvlt+dlH++qiqgfFdvp lcl|NCBI__GCF_000021485.1:WP_009567132.1 75 MIDALKRASANRITAAMPYFGYARQDRKSRSRTAITAKLVADLITSAGANRVLTMDLHADQIQGFFDVP 143 ********************************************************************* PP TIGR01251 140 venlsaspklieelkkkelknlvvvsPDkGaverakkvakklglelaiieKeRdskenevevtnllgdv 208 v+n++asp l+ ++ ++ +l+vvsPD G+v ra+++ak+l+++laii+K+R+ + ne v+n++gdv lcl|NCBI__GCF_000021485.1:WP_009567132.1 144 VDNIYASPILLGDIWRQSYPELIVVSPDVGGVVRARAIAKRLEVDLAIIDKRRP-RPNESVVMNIIGDV 211 ******************************************************.899*********** PP TIGR01251 209 egkdvvivDDiisTggTlvkaaelLkekGAkkvivaathgvfsgdAlerlaeagveevivtntilv.ee 276 +g+++v+vDD+++T+ Tl++aa++Lk +GA kv++++th+v+sg+A+er++++ ++e++vt+ti+ + lcl|NCBI__GCF_000021485.1:WP_009567132.1 212 DGRTCVLVDDMVDTANTLCEAAHALKARGAVKVCAYCTHPVLSGPAMERIERSDLDELVVTDTIPLrPD 280 ******************************************************************855 PP TIGR01251 277 .kklpkvseisvapliaeaiarihenesvsslf 308 ++ +k++++sva+l+ae+i+ri+e+ svsslf lcl|NCBI__GCF_000021485.1:WP_009567132.1 281 aRASSKIRVLSVAELLAETIRRIAEEDSVSSLF 313 699*****************************9 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 10.05 // [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