Align Ribose-phosphate pyrophosphokinase; RPPK; 5-phospho-D-ribosyl alpha-1-diphosphate synthase; Phosphoribosyl diphosphate synthase; Phosphoribosyl pyrophosphate synthase; P-Rib-PP synthase; PPRibP synthase; PRPP synthase; PRPPase; EC 2.7.6.1 (characterized)
to candidate Synpcc7942_2113 Synpcc7942_2113 ribose-phosphate pyrophosphokinase
Query= SwissProt::P14193 (317 letters) >FitnessBrowser__SynE:Synpcc7942_2113 Length = 331 Score = 347 bits (890), Expect = e-100 Identities = 173/309 (55%), Positives = 231/309 (74%), Gaps = 2/309 (0%) Query: 10 LKIFSLNSNPELAKEIADIVGVQLGKCSVTRFSDGEVQINIEESIRGCDCYIIQSTSDPV 69 L++FS +SN L++E++ +G+ LG RF+DGE+ + I+ESIRGCD Y++Q T PV Sbjct: 22 LRLFSGSSNSALSQEVSRYLGIDLGPMIRKRFADGELYVQIQESIRGCDVYLMQPTCWPV 81 Query: 70 NEHIMELLIMVDALKRASAKTINIVIPYYGYARQDRKARSREPITAKLFANLLETAGATR 129 N+H+MELLIM+DA +RASA+ I V+PYYGYAR DRK RE ITAKL ANL+ AGA R Sbjct: 82 NDHLMELLIMIDACRRASARQITAVLPYYGYARADRKTAGRESITAKLVANLITQAGANR 141 Query: 130 VIALDLHAPQIQGFFDIPIDHLMGVPILGEYFEGKNLEDIVIVSPDHGGVTRARKLADRL 189 V+A+DLH+ QIQG+FDIP DH+ G P+L +Y KNL D+V+VSPD GGV RAR A +L Sbjct: 142 VLAMDLHSAQIQGYFDIPFDHVYGSPVLIDYLRSKNLADLVVVSPDVGGVARARAFAKKL 201 Query: 190 -KAPIAIIDKRRPRPNVAEVMNIVGNIEGKTAILIDDIIDTAGTITLAANALVENGAKEV 248 AP+AIIDKRR NVAEV+N++G+++GKTA+L+DD+IDTAGTI A L + GA +V Sbjct: 202 DDAPLAIIDKRRQAHNVAEVLNVIGDVQGKTAVLVDDMIDTAGTICEGARLLRKQGASQV 261 Query: 249 YACCTHPVLSGPAVERINNSTI-KELVVTNSIKLPEEKKIERFKQLSVGPLLAEAIIRVH 307 YAC TH V S PA+ER++ S + +E++VTN+I +PEE + + LSV LL E I R+H Sbjct: 262 YACATHAVFSPPAIERLSASGLFEEVIVTNTIPIPEENRFPQLTILSVANLLGETIWRIH 321 Query: 308 EQQSVSYLF 316 E+ SVS +F Sbjct: 322 EESSVSSMF 330 Lambda K H 0.319 0.137 0.383 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: 263 Number of extensions: 13 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: 317 Length of database: 331 Length adjustment: 28 Effective length of query: 289 Effective length of database: 303 Effective search space: 87567 Effective search space used: 87567 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 (21.7 bits) S2: 48 (23.1 bits)
Align candidate Synpcc7942_2113 Synpcc7942_2113 (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.23632.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.2e-132 425.4 0.0 5.9e-132 425.2 0.0 1.0 1 lcl|FitnessBrowser__SynE:Synpcc7942_2113 Synpcc7942_2113 ribose-phosphate Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__SynE:Synpcc7942_2113 Synpcc7942_2113 ribose-phosphate pyrophosphokinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 425.2 0.0 5.9e-132 5.9e-132 2 309 .] 23 331 .] 22 331 .] 0.99 Alignments for each domain: == domain 1 score: 425.2 bits; conditional E-value: 5.9e-132 TIGR01251 2 kilsgssskelaekvaknlglelgdvevkkFadgElyvrieesvrgkdvfiivqstsapvndalmelll 70 +++sgss+++l+++v+++lg++lg++ k+FadgElyv+i+es+rg+dv+++ q t+ pvnd+lmell+ lcl|FitnessBrowser__SynE:Synpcc7942_2113 23 RLFSGSSNSALSQEVSRYLGIDLGPMIRKRFADGELYVQIQESIRGCDVYLM-QPTCWPVNDHLMELLI 90 689*************************************************.**************** PP TIGR01251 71 lidalkrasaksvtaviPyygYaRqdkkaksrepisaklvaklleeaGadrvltvdlHseqiqgfFdvp 139 +ida++rasa+++tav+PyygYaR d+k+ +re+i+aklva+l+++aGa+rvl++dlHs qiqg+Fd+p lcl|FitnessBrowser__SynE:Synpcc7942_2113 91 MIDACRRASARQITAVLPYYGYARADRKTAGRESITAKLVANLITQAGANRVLAMDLHSAQIQGYFDIP 159 ********************************************************************* PP TIGR01251 140 venlsaspklieelkkkelknlvvvsPDkGaverakkvakklg.lelaiieKeRdskenevevtnllgd 207 ++++++sp+li++l++k+l +lvvvsPD G+v+ra+++akkl+ ++laii+K+R+ ++n++ev n++gd lcl|FitnessBrowser__SynE:Synpcc7942_2113 160 FDHVYGSPVLIDYLRSKNLADLVVVSPDVGGVARARAFAKKLDdAPLAIIDKRRQ-AHNVAEVLNVIGD 227 *******************************************9***********.999********** PP TIGR01251 208 vegkdvvivDDiisTggTlvkaaelLkekGAkkvivaathgvfsgdAlerlaeag.veevivtntilv. 274 v+gk++v+vDD+i+T+gT++++a+lL+++GA++v+++ath+vfs +A+erl+ +g +eevivtnti++ lcl|FitnessBrowser__SynE:Synpcc7942_2113 228 VQGKTAVLVDDMIDTAGTICEGARLLRKQGASQVYACATHAVFSPPAIERLSASGlFEEVIVTNTIPIp 296 ****************************************************9998************9 PP TIGR01251 275 eekklpkvseisvapliaeaiarihenesvsslfd 309 ee+++p+++ +sva+l+ e+i+rihe++svss+f+ lcl|FitnessBrowser__SynE:Synpcc7942_2113 297 EENRFPQLTILSVANLLGETIWRIHEESSVSSMFR 331 99*******************************95 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (309 nodes) Target sequences: 1 (331 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: 9.56 // [ok]
This GapMind analysis is from Apr 09 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