Align ribose-phosphate diphosphokinase (EC 2.7.6.1) (characterized)
to candidate GFF727 HP15_707 ribose-phosphate pyrophosphokinase
Query= BRENDA::P0A719 (315 letters) >FitnessBrowser__Marino:GFF727 Length = 290 Score = 422 bits (1085), Expect = e-123 Identities = 204/289 (70%), Positives = 247/289 (85%) Query: 27 LGDAAVGRFSDGEVSVQINENVRGGDIFIIQSTCAPTNDNLMELVVMVDALRRASAGRIT 86 +G A VGRFSDGE +V+INENVRG D+FIIQ TC PTNDNLMEL+VM DALRRASA R+T Sbjct: 1 MGQATVGRFSDGETTVEINENVRGHDVFIIQPTCYPTNDNLMELIVMADALRRASATRVT 60 Query: 87 AVIPYFGYARQDRRVRSARVPITAKVVADFLSSVGVDRVLTVDLHAEQIQGFFDVPVDNV 146 AVIPY+GYARQDRRVRS RV I+AKVVAD +SS+GVDRVLTVDLHA+QIQGFFD+PVDN+ Sbjct: 61 AVIPYYGYARQDRRVRSTRVAISAKVVADMISSIGVDRVLTVDLHADQIQGFFDIPVDNI 120 Query: 147 FGSPILLEDMLQLNLDNPIVVSPDIGGVVRARAIAKLLNDTDMAIIDKRRPRANVSQVMH 206 + +P++LED+ + +N +VVSPD+GGVVRARA+AK L+D D+AIIDKRRP+ANVSQVMH Sbjct: 121 YATPVMLEDIFKQRFENFVVVSPDVGGVVRARAVAKRLDDADLAIIDKRRPKANVSQVMH 180 Query: 207 IIGDVAGRDCVLVDDMIDTGGTLCKAAEALKERGAKRVFAYATHPIFSGNAANNLRNSVI 266 IIGDV + C+LVDD+IDT GTLCKAA ALKE GA RV AY THP+ SG A +N+ S + Sbjct: 181 IIGDVKDKTCILVDDIIDTAGTLCKAANALKEHGAARVVAYITHPVLSGPAIDNINASQL 240 Query: 267 DEVVVCDTIPLSDEIKSLPNVRTLTLSGMLAEAIRRISNEESISAMFEH 315 DE+VVCDTIPL D+ + +R L ++G+LAE+IRR+SNEESISAMFE+ Sbjct: 241 DELVVCDTIPLGDKAHNCDRIRVLGMAGLLAESIRRVSNEESISAMFEN 289 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: 314 Number of extensions: 6 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: 290 Length adjustment: 27 Effective length of query: 288 Effective length of database: 263 Effective search space: 75744 Effective search space used: 75744 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 GFF727 HP15_707 (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.26992.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.9e-119 384.1 4.9 2.1e-119 384.0 4.9 1.0 1 lcl|FitnessBrowser__Marino:GFF727 HP15_707 ribose-phosphate pyroph Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Marino:GFF727 HP15_707 ribose-phosphate pyrophosphokinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 384.0 4.9 2.1e-119 2.1e-119 25 309 .] 2 288 .. 1 288 [. 0.98 Alignments for each domain: == domain 1 score: 384.0 bits; conditional E-value: 2.1e-119 TIGR01251 25 gdvevkkFadgElyvrieesvrgkdvfiivqstsapvndalmellllidalkrasaksvtaviPyygYaRqdkkak 100 g+++v +F+dgE+ v+i+e+vrg+dvfii q t+ p+nd+lmel++++dal+rasa +vtaviPyygYaRqd++++ lcl|FitnessBrowser__Marino:GFF727 2 GQATVGRFSDGETTVEINENVRGHDVFII-QPTCYPTNDNLMELIVMADALRRASATRVTAVIPYYGYARQDRRVR 76 78999************************.99999***************************************98 PP TIGR01251 101 .srepisaklvaklleeaGadrvltvdlHseqiqgfFdvpvenlsaspklieelkkkelknlvvvsPDkGaverak 175 r +isak+va++++++G+drvltvdlH++qiqgfFd+pv+n++a p+++e++ k+ +n+vvvsPD G+v ra+ lcl|FitnessBrowser__Marino:GFF727 77 sTRVAISAKVVADMISSIGVDRVLTVDLHADQIQGFFDIPVDNIYATPVMLEDIFKQRFENFVVVSPDVGGVVRAR 152 579************************************************************************* PP TIGR01251 176 kvakklg.lelaiieKeRdskenevevtnllgdvegkdvvivDDiisTggTlvkaaelLkekGAkkvivaathgvf 250 +vak+l+ ++laii+K+R+ k+n+ +v++++gdv++k++++vDDii+T+gTl+kaa++Lke+GA +v++++th+v+ lcl|FitnessBrowser__Marino:GFF727 153 AVAKRLDdADLAIIDKRRP-KANVSQVMHIIGDVKDKTCILVDDIIDTAGTLCKAANALKEHGAARVVAYITHPVL 227 *******9***********.899***************************************************** PP TIGR01251 251 sgdAlerlaeagveevivtntilv.ee.kklpkvseisvapliaeaiarihenesvsslfd 309 sg+A+ +++ ++++e++v++ti+ ++ +++++++++ +a l+ae i+r++++es+s++f+ lcl|FitnessBrowser__Marino:GFF727 228 SGPAIDNINASQLDELVVCDTIPLgDKaHNCDRIRVLGMAGLLAESIRRVSNEESISAMFE 288 ************************98889******************************96 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (309 nodes) Target sequences: 1 (290 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: 00:00:00.00 # Mc/sec: 10.94 // [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