Align ribose-phosphate diphosphokinase (EC 2.7.6.1) (characterized)
to candidate Ga0059261_2274 Ga0059261_2274 ribose-phosphate pyrophosphokinase
Query= BRENDA::P0A719 (315 letters) >FitnessBrowser__Korea:Ga0059261_2274 Length = 311 Score = 331 bits (848), Expect = 2e-95 Identities = 171/312 (54%), Positives = 231/312 (74%), Gaps = 2/312 (0%) Query: 4 MKLFAGNATPELAQRIANRLYTSLGDAAVGRFSDGEVSVQINENVRGGDIFIIQSTCAPT 63 MKL AGN+ LAQ IA+ L L A V RF+D E+ V+I ENVRG D+F++QST P Sbjct: 1 MKLMAGNSNLPLAQAIASYLEIPLTQANVRRFADEEIFVEILENVRGEDVFVLQSTAYPA 60 Query: 64 NDNLMELVVMVDALRRASAGRITAVIPYFGYARQDRRVRSARVPITAKVVADFLSSVGVD 123 NDNLMEL++M+DALRRASA RITAV+PYFGYARQDR+ R PI+AK+VA+ +++ G + Sbjct: 61 NDNLMELLIMIDALRRASAKRITAVLPYFGYARQDRKP-GPRTPISAKLVANLITTAGAN 119 Query: 124 RVLTVDLHAEQIQGFFDVPVDNVFGSPILLEDMLQLNLD-NPIVVSPDIGGVVRARAIAK 182 RVL+VDLHA QIQGFFD+P DN+F +P++ ED+ D N +VVSPD+GGVVRARA+AK Sbjct: 120 RVLSVDLHAGQIQGFFDIPTDNLFAAPVMSEDIKARFSDKNLMVVSPDVGGVVRARALAK 179 Query: 183 LLNDTDMAIIDKRRPRANVSQVMHIIGDVAGRDCVLVDDMIDTGGTLCKAAEALKERGAK 242 L + +AI+DKRR +A S+VM+IIGDV GR C+L+DD++D+ GTLC AA ALK GA+ Sbjct: 180 RLENAPLAIVDKRREKAGESEVMNIIGDVEGRFCILIDDIVDSAGTLCNAAAALKAAGAE 239 Query: 243 RVFAYATHPIFSGNAANNLRNSVIDEVVVCDTIPLSDEIKSLPNVRTLTLSGMLAEAIRR 302 V AY TH + SG A + S + E+V+ D+I + +R LT++ ++AEAIRR Sbjct: 240 GVVAYCTHGVLSGGAVARVDGSELSELVITDSIGNHAIVGEAQRIRHLTIAPLIAEAIRR 299 Query: 303 ISNEESISAMFE 314 I++E S+S++F+ Sbjct: 300 IADESSVSSLFD 311 Lambda K H 0.321 0.137 0.385 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: 301 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: 311 Length adjustment: 27 Effective length of query: 288 Effective length of database: 284 Effective search space: 81792 Effective search space used: 81792 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 Ga0059261_2274 Ga0059261_2274 (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.2799.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8e-118 378.8 0.1 8.9e-118 378.6 0.1 1.0 1 lcl|FitnessBrowser__Korea:Ga0059261_2274 Ga0059261_2274 ribose-phosphate Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Korea:Ga0059261_2274 Ga0059261_2274 ribose-phosphate pyrophosphokinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 378.6 0.1 8.9e-118 8.9e-118 1 309 [] 1 311 [] 1 311 [] 0.98 Alignments for each domain: == domain 1 score: 378.6 bits; conditional E-value: 8.9e-118 TIGR01251 1 lkilsgssskelaekvaknlglelgdvevkkFadgElyvrieesvrgkdvfiivqstsapvndalmell 69 +k+++g+s+ la+++a +l+++l++++v++Fad+E+ v+i e+vrg+dvf++ qst p nd+lmell lcl|FitnessBrowser__Korea:Ga0059261_2274 1 MKLMAGNSNLPLAQAIASYLEIPLTQANVRRFADEEIFVEILENVRGEDVFVL-QSTAYPANDNLMELL 68 7899*************************************************.99999********** PP TIGR01251 70 llidalkrasaksvtaviPyygYaRqdkkaksrepisaklvaklleeaGadrvltvdlHseqiqgfFdv 138 ++idal+rasak++tav+Py+gYaRqd+k +r+pisaklva+l+++aGa+rvl vdlH+ qiqgfFd+ lcl|FitnessBrowser__Korea:Ga0059261_2274 69 IMIDALRRASAKRITAVLPYFGYARQDRKPGPRTPISAKLVANLITTAGANRVLSVDLHAGQIQGFFDI 137 ********************************************************************* PP TIGR01251 139 pvenlsaspklieelkkke.lknlvvvsPDkGaverakkvakklg.lelaiieKeRdskenevevtnll 205 p +nl a+p++ e++k++ +knl+vvsPD G+v ra+++ak+l+ ++lai++K+R+ k+ e ev+n++ lcl|FitnessBrowser__Korea:Ga0059261_2274 138 PTDNLFAAPVMSEDIKARFsDKNLMVVSPDVGGVVRARALAKRLEnAPLAIVDKRRE-KAGESEVMNII 205 *****************999************************99***********.777******** PP TIGR01251 206 gdvegkdvvivDDiisTggTlvkaaelLkekGAkkvivaathgvfsgdAlerlaeagveevivtntilv 274 gdveg+ ++++DDi++++gTl++aa +Lk +GA+ v++++thgv+sg A+ r++ + ++e+++t++i lcl|FitnessBrowser__Korea:Ga0059261_2274 206 GDVEGRFCILIDDIVDSAGTLCNAAAALKAAGAEGVVAYCTHGVLSGGAVARVDGSELSELVITDSIGN 274 *******************************************************************99 PP TIGR01251 275 ee..kklpkvseisvapliaeaiarihenesvsslfd 309 + + ++++++++apliaeai+ri++++svsslfd lcl|FitnessBrowser__Korea:Ga0059261_2274 275 HAivGEAQRIRHLTIAPLIAEAIRRIADESSVSSLFD 311 5558999****************************96 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (309 nodes) Target sequences: 1 (311 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: 6.54 // [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