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_013820404.1 METME_RS19220 ribose-phosphate pyrophosphokinase
Query= SwissProt::P0A1V6 (315 letters) >NCBI__GCF_000214665.1:WP_013820404.1 Length = 317 Score = 417 bits (1071), Expect = e-121 Identities = 204/308 (66%), Positives = 255/308 (82%) Query: 6 LFAGNATPELAQRIANRLYTSLGDAAVGRFSDGEVSVQINENVRGGDIFIIQSTCAPTND 65 +F+GNA L++ I +L LG A+V RFSDGE+ V+I ENVRG D+F++Q TC+PTN+ Sbjct: 8 VFSGNANKALSEGIVRKLNMRLGMASVDRFSDGEIFVEIEENVRGRDVFVVQPTCSPTNE 67 Query: 66 NLMELVVMVDALRRASAGRITAVIPYFGYARQDRRVRSARVPITAKVVADFLSSVGVDRV 125 NLMEL+VM+DALRRASA RITAVIPY+GYARQDRR RSARVPITA++VAD + G DR Sbjct: 68 NLMELLVMIDALRRASAARITAVIPYYGYARQDRRSRSARVPITARLVADMIGHAGADRA 127 Query: 126 LTVDLHAEQIQGFFDVPVDNVFGSPILLEDMLQLNLDNPIVVSPDIGGVVRARAIAKLLN 185 LTVDLHA+QIQGFF +PVDNV+ SPILL D+ + +N IVVSPD+GGVVRARA+AK L Sbjct: 128 LTVDLHADQIQGFFGIPVDNVYASPILLGDVWRQEYENLIVVSPDVGGVVRARALAKRLG 187 Query: 186 DTDMAIIDKRRPRANVSQVMHIIGDVAGRDCVLVDDMIDTGGTLCKAAEALKERGAKRVF 245 D D+AIIDKRRPRANVS++MHIIGDV GR CV+VDD++DT GTLC AA ALK+ GA +V Sbjct: 188 DADLAIIDKRRPRANVSEIMHIIGDVDGRTCVMVDDLVDTAGTLCHAASALKKNGAVKVV 247 Query: 246 AYATHPIFSGNAANNLRNSVIDEVVVCDTIPLTDEIKALPNVRTLTLSGMLAEAIRRISN 305 AY THP+ SG AA+N+RNSV+DE+VV DTIPLTDE+KA+ +R L+++ MLAE IRRI+ Sbjct: 248 AYCTHPVLSGAAADNVRNSVLDELVVTDTIPLTDELKAIGKIRQLSVAEMLAETIRRIAV 307 Query: 306 EESISAMF 313 ES+S+++ Sbjct: 308 GESVSSLY 315 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: 350 Number of extensions: 7 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: 315 Length of database: 317 Length adjustment: 27 Effective length of query: 288 Effective length of database: 290 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 (21.9 bits) S2: 48 (23.1 bits)
Align candidate WP_013820404.1 METME_RS19220 (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.26257.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.2e-123 396.1 0.6 4.8e-123 396.0 0.6 1.0 1 lcl|NCBI__GCF_000214665.1:WP_013820404.1 METME_RS19220 ribose-phosphate p Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000214665.1:WP_013820404.1 METME_RS19220 ribose-phosphate pyrophosphokinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 396.0 0.6 4.8e-123 4.8e-123 1 308 [. 6 315 .. 6 316 .. 0.98 Alignments for each domain: == domain 1 score: 396.0 bits; conditional E-value: 4.8e-123 TIGR01251 1 lkilsgssskelaekvaknlglelgdvevkkFadgElyvrieesvrgkdvfiivqstsapvndalmell 69 ++++sg+++k+l+e + ++l+++lg ++v++F+dgE+ v+iee+vrg+dvf++ q t+ p+n++lmell lcl|NCBI__GCF_000214665.1:WP_013820404.1 6 IMVFSGNANKALSEGIVRKLNMRLGMASVDRFSDGEIFVEIEENVRGRDVFVV-QPTCSPTNENLMELL 73 589**************************************************.9************** PP TIGR01251 70 llidalkrasaksvtaviPyygYaRqdkkak.srepisaklvaklleeaGadrvltvdlHseqiqgfFd 137 ++idal+rasa ++taviPyygYaRqd++ + r pi+a+lva+++ +aGadr ltvdlH++qiqgfF lcl|NCBI__GCF_000214665.1:WP_013820404.1 74 VMIDALRRASAARITAVIPYYGYARQDRRSRsARVPITARLVADMIGHAGADRALTVDLHADQIQGFFG 142 ****************************98757************************************ PP TIGR01251 138 vpvenlsaspklieelkkkelknlvvvsPDkGaverakkvakklg.lelaiieKeRdskenevevtnll 205 +pv+n++asp l+ ++ ++e +nl+vvsPD G+v ra+++ak+lg ++laii+K+R+ ++n+ e+++++ lcl|NCBI__GCF_000214665.1:WP_013820404.1 143 IPVDNVYASPILLGDVWRQEYENLIVVSPDVGGVVRARALAKRLGdADLAIIDKRRP-RANVSEIMHII 210 *********************************************9***********.888******** PP TIGR01251 206 gdvegkdvvivDDiisTggTlvkaaelLkekGAkkvivaathgvfsgdAlerlaeagveevivtntilv 274 gdv+g+++v+vDD+++T+gTl++aa++Lk++GA kv++++th+v+sg A+ ++++++++e++vt+ti+ lcl|NCBI__GCF_000214665.1:WP_013820404.1 211 GDVDGRTCVMVDDLVDTAGTLCHAASALKKNGAVKVVAYCTHPVLSGAAADNVRNSVLDELVVTDTIPL 279 ********************************************************************* PP TIGR01251 275 .ee.kklpkvseisvapliaeaiarihenesvsslf 308 +e k++ k++++sva+++ae+i+ri+ +esvssl+ lcl|NCBI__GCF_000214665.1:WP_013820404.1 280 tDElKAIGKIRQLSVAEMLAETIRRIAVGESVSSLY 315 8779******************************98 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (309 nodes) Target sequences: 1 (317 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 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 8.86 // [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