Align ribose-phosphate diphosphokinase (EC 2.7.6.1) (characterized)
to candidate WP_013134556.1 ARNIT_RS03720 ribose-phosphate pyrophosphokinase
Query= BRENDA::P0A719 (315 letters) >NCBI__GCF_000092245.1:WP_013134556.1 Length = 311 Score = 340 bits (873), Expect = 2e-98 Identities = 175/314 (55%), Positives = 231/314 (73%), Gaps = 6/314 (1%) Query: 1 MPDMKLFAGNATPELAQRIANRLYTSLGDAAVGRFSDGEVSVQINENVRGGDIFIIQSTC 60 M +LF G+A PE A+++A L + A + +FSDGE+SV+I E+VRG D+FIIQ TC Sbjct: 1 MRGYRLFTGSANPEFAKKVAKYLNIEISPAKLTKFSDGEISVKITESVRGMDVFIIQPTC 60 Query: 61 APTNDNLMELVVMVDALRRASAGRITAVIPYFGYARQDRRVRSARVPITAKVVADFLSSV 120 APTNDNLMEL++MVDAL+R+SA I+AVIPY+GYARQDR+ + RVPITAK+VAD L + Sbjct: 61 APTNDNLMELLIMVDALKRSSAKSISAVIPYYGYARQDRKA-APRVPITAKLVADLLEAA 119 Query: 121 GVDRVLTVDLHAEQIQGFFDVPVDNVFGSPILLEDMLQLNLDNPIVVSPDIGGVVRARAI 180 G+ RV+T+DLHA QIQGFF++P DN+FGS + ++ + L NPI+ SPDIGGV RAR+ Sbjct: 120 GISRVITIDLHAAQIQGFFNIPADNLFGSIMFIDYIKSKKLANPIIASPDIGGVARARSY 179 Query: 181 AKLLNDTDMAIIDKRRPRANVSQVMHIIGDVAGRDCVLVDDMIDTGGTLCKAAEALKERG 240 A+ LN D+ I+DKRR +AN S+VM+IIGDV+G+D +LVDDM+DT GTL KAAE LK +G Sbjct: 180 AEKLN-YDLVIVDKRREKANESEVMNIIGDVSGKDIILVDDMVDTAGTLVKAAEVLKNKG 238 Query: 241 AKRVFAYATHPIFSGNAANNLRN-SVIDEVVVCDTIPLSDEIKSLPNVRTLTLSGMLAEA 299 A V A TH + SG A L N +DE+V+ DTIPL E + LT S ++ E Sbjct: 239 ANSVMACCTHGVLSGPAYERLENGEALDELVISDTIPLKQE---HDKITVLTASNIIGET 295 Query: 300 IRRISNEESISAMF 313 IRRI N ES++++F Sbjct: 296 IRRIHNNESVNSIF 309 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: 281 Number of extensions: 11 Number of successful extensions: 5 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 WP_013134556.1 ARNIT_RS03720 (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.27049.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.9e-126 406.1 1.8 4.3e-126 405.9 1.8 1.0 1 lcl|NCBI__GCF_000092245.1:WP_013134556.1 ARNIT_RS03720 ribose-phosphate p Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000092245.1:WP_013134556.1 ARNIT_RS03720 ribose-phosphate pyrophosphokinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 405.9 1.8 4.3e-126 4.3e-126 2 308 .. 5 309 .. 4 310 .. 0.99 Alignments for each domain: == domain 1 score: 405.9 bits; conditional E-value: 4.3e-126 TIGR01251 2 kilsgssskelaekvaknlglelgdvevkkFadgElyvrieesvrgkdvfiivqstsapvndalmelll 70 +++ gs+++e+a+kvak+l++e+ +++ +kF+dgE++v+i esvrg dvfii q t+ap+nd+lmell+ lcl|NCBI__GCF_000092245.1:WP_013134556.1 5 RLFTGSANPEFAKKVAKYLNIEISPAKLTKFSDGEISVKITESVRGMDVFII-QPTCAPTNDNLMELLI 72 789*************************************************.**************** PP TIGR01251 71 lidalkrasaksvtaviPyygYaRqdkkaksrepisaklvaklleeaGadrvltvdlHseqiqgfFdvp 139 ++dalkr+saks++aviPyygYaRqd+ka +r pi+aklva+lle+aG++rv+t+dlH+ qiqgfF++p lcl|NCBI__GCF_000092245.1:WP_013134556.1 73 MVDALKRSSAKSISAVIPYYGYARQDRKAAPRVPITAKLVADLLEAAGISRVITIDLHAAQIQGFFNIP 141 ********************************************************************* PP TIGR01251 140 venlsaspklieelkkkelknlvvvsPDkGaverakkvakklglelaiieKeRdskenevevtnllgdv 208 ++nl +s +i+++k+k+l n+++ sPD G+v+ra+++a+kl+ +l+i++K+R+ k+ne ev+n++gdv lcl|NCBI__GCF_000092245.1:WP_013134556.1 142 ADNLFGSIMFIDYIKSKKLANPIIASPDIGGVARARSYAEKLNYDLVIVDKRRE-KANESEVMNIIGDV 209 ******************************************************.899*********** PP TIGR01251 209 egkdvvivDDiisTggTlvkaaelLkekGAkkvivaathgvfsgdAlerlaeag.veevivtntilvee 276 gkd+++vDD+++T+gTlvkaae+Lk+kGA++v++++thgv+sg+A+erl++ ++e+++++ti+ + lcl|NCBI__GCF_000092245.1:WP_013134556.1 210 SGKDIILVDDMVDTAGTLVKAAEVLKNKGANSVMACCTHGVLSGPAYERLENGEaLDELVISDTIPL-K 277 ***************************************************99879***********.7 PP TIGR01251 277 kklpkvseisvapliaeaiarihenesvsslf 308 ++ +k+++++ +++i e+i+rih+nesv+s+f lcl|NCBI__GCF_000092245.1:WP_013134556.1 278 QEHDKITVLTASNIIGETIRRIHNNESVNSIF 309 7899**************************99 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 9.91 // [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