Align ribose-phosphate diphosphokinase (EC 2.7.6.1) (characterized)
to candidate CCNA_00520 CCNA_00520 ribose-phosphate pyrophosphokinase
Query= BRENDA::P0A719 (315 letters) >FitnessBrowser__Caulo:CCNA_00520 Length = 312 Score = 331 bits (849), Expect = 1e-95 Identities = 175/313 (55%), Positives = 229/313 (73%), Gaps = 3/313 (0%) Query: 4 MKLFAGNATPELAQRIANRLYTSLGDAAVGRFSDGEVSVQINENVRGGDIFIIQSTCAPT 63 MKL +GN+ L+Q IA L L A V RF+D EV V I+ENVRG D+F+IQST P Sbjct: 1 MKLLSGNSNRPLSQAIAEYLDMPLTRAQVRRFADLEVFVTIDENVRGEDVFVIQSTSYPA 60 Query: 64 NDNLMELVVMVDALRRASAGRITAVIPYFGYARQDRRVRSARVPITAKVVADFLSSVGVD 123 NDNLMEL++ +DAL+RAS RITAVIPYFGYARQDR+ R PI+AK+VA+ ++ G D Sbjct: 61 NDNLMELLICIDALKRASGKRITAVIPYFGYARQDRKT-GGRTPISAKLVANLITRSGAD 119 Query: 124 RVLTVDLHAEQIQGFFDVPVDNVFGSPILLEDMLQLNL--DNPIVVSPDIGGVVRARAIA 181 RVLT+DLHA QIQGFFD+P DN+ S ++ ED+ + D+ +VVSPD+GGVVRARA+A Sbjct: 120 RVLTMDLHAGQIQGFFDIPTDNLLPSRLMAEDIRRHYPMGDDLMVVSPDVGGVVRARALA 179 Query: 182 KLLNDTDMAIIDKRRPRANVSQVMHIIGDVAGRDCVLVDDMIDTGGTLCKAAEALKERGA 241 K L+D D+AI+DKRR S+VM+IIGDV R C+L DD+ D+ GTLC AA+AL GA Sbjct: 180 KRLDDADLAIVDKRRSGPGQSEVMNIIGDVKDRRCILFDDIADSAGTLCNAAQALMAHGA 239 Query: 242 KRVFAYATHPIFSGNAANNLRNSVIDEVVVCDTIPLSDEIKSLPNVRTLTLSGMLAEAIR 301 K V AY TH + SG AA+ + NSV+ E+VV D+I SD K+ P +R ++ + ++ EAIR Sbjct: 240 KSVSAYITHGVLSGAAADRVANSVLTELVVTDSIEASDPAKACPKIRYVSCAPLIGEAIR 299 Query: 302 RISNEESISAMFE 314 RI+NEES+S +F+ Sbjct: 300 RIANEESVSKLFD 312 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: 277 Number of extensions: 9 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: 312 Length adjustment: 27 Effective length of query: 288 Effective length of database: 285 Effective search space: 82080 Effective search space used: 82080 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 CCNA_00520 CCNA_00520 (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.9644.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.7e-118 379.9 0.0 4.2e-118 379.7 0.0 1.0 1 lcl|FitnessBrowser__Caulo:CCNA_00520 CCNA_00520 ribose-phosphate pyro Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Caulo:CCNA_00520 CCNA_00520 ribose-phosphate pyrophosphokinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 379.7 0.0 4.2e-118 4.2e-118 1 309 [] 1 312 [] 1 312 [] 0.98 Alignments for each domain: == domain 1 score: 379.7 bits; conditional E-value: 4.2e-118 TIGR01251 1 lkilsgssskelaekvaknlglelgdvevkkFadgElyvrieesvrgkdvfiivqstsapvndalmellllid 73 +k+lsg+s++ l++++a++l+++l++++v++Fad E+ v+i+e+vrg+dvf+i qsts p nd+lmell+ id lcl|FitnessBrowser__Caulo:CCNA_00520 1 MKLLSGNSNRPLSQAIAEYLDMPLTRAQVRRFADLEVFVTIDENVRGEDVFVI-QSTSYPANDNLMELLICID 72 799**************************************************.99999************** PP TIGR01251 74 alkrasaksvtaviPyygYaRqdkkaksrepisaklvaklleeaGadrvltvdlHseqiqgfFdvpvenlsas 146 alkras k++taviPy+gYaRqd+k+ +r+pisaklva+l++ Gadrvlt+dlH+ qiqgfFd+p +nl s lcl|FitnessBrowser__Caulo:CCNA_00520 73 ALKRASGKRITAVIPYFGYARQDRKTGGRTPISAKLVANLITRSGADRVLTMDLHAGQIQGFFDIPTDNLLPS 145 ************************************************************************* PP TIGR01251 147 pklieelkkke..lknlvvvsPDkGaverakkvakklg.lelaiieKeRdskenevevtnllgdvegkdvviv 216 + ++e++++++ ++l+vvsPD G+v ra+++ak+l+ ++lai++K+R + ev+n++gdv+++ ++++ lcl|FitnessBrowser__Caulo:CCNA_00520 146 RLMAEDIRRHYpmGDDLMVVSPDVGGVVRARALAKRLDdADLAIVDKRRS-GPGQSEVMNIIGDVKDRRCILF 217 *********99999************************9***********.667******************* PP TIGR01251 217 DDiisTggTlvkaaelLkekGAkkvivaathgvfsgdAlerlaeagveevivtntilv.ee.kklpkvseisv 287 DDi +++gTl++aa++L +GAk+v +++thgv+sg A+ r+a+++++e++vt++i+ + k++pk++ +s lcl|FitnessBrowser__Caulo:CCNA_00520 218 DDIADSAGTLCNAAQALMAHGAKSVSAYITHGVLSGAAADRVANSVLTELVVTDSIEAsDPaKACPKIRYVSC 290 **********************************************************5449*********** PP TIGR01251 288 apliaeaiarihenesvsslfd 309 apli eai+ri+++esvs+lfd lcl|FitnessBrowser__Caulo:CCNA_00520 291 APLIGEAIRRIANEESVSKLFD 312 ********************96 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (309 nodes) Target sequences: 1 (312 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: 7.06 // [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