Align ribose-phosphate diphosphokinase (EC 2.7.6.1) (characterized)
to candidate WP_015817076.1 TERTU_RS17075 ribose-phosphate pyrophosphokinase
Query= BRENDA::P0A719 (315 letters) >NCBI__GCF_000023025.1:WP_015817076.1 Length = 315 Score = 442 bits (1138), Expect = e-129 Identities = 218/313 (69%), Positives = 269/313 (85%), Gaps = 1/313 (0%) Query: 1 MPDMKLFAGNATPELAQRIANRLYTSLGDAAVGRFSDGEVSVQINENVRGGDIFIIQSTC 60 +PD+ +F+GNA PELA+++ +L LGD V +FSDGE+ V++ +NVRG D+F+IQ TC Sbjct: 3 VPDLMVFSGNANPELAEKVCAKLGIPLGDVTVDKFSDGEILVELKQNVRGSDVFVIQPTC 62 Query: 61 APTNDNLMELVVMVDALRRASAGRITAVIPYFGYARQDRRVRSARVPITAKVVADFLSSV 120 APTNDN+MEL+V+VDALRR+SAGRITAV+PYFGYARQDRRVRSARVPITAKVVAD L +V Sbjct: 63 APTNDNIMELMVIVDALRRSSAGRITAVVPYFGYARQDRRVRSARVPITAKVVADMLVTV 122 Query: 121 GVDRVLTVDLHAEQIQGFFDVPVDNVFGSPILLEDMLQLNLDNPIVVSPDIGGVVRARAI 180 GVDRVLTVDLHAEQIQGFFDVPVDNV+GSP+LL D+ + + ++ +VVSPDIGGVVRARA+ Sbjct: 123 GVDRVLTVDLHAEQIQGFFDVPVDNVYGSPVLLADIEKQSFEDLVVVSPDIGGVVRARAV 182 Query: 181 AKLLNDTDMAIIDKRRPRANVSQVMHIIGDVAGRDCVLVDDMIDTGGTLCKAAEALKERG 240 AK L D ++AIIDKRRP+ANV++VMH+IG++ R C+LVDDM+DT GTLC AA+ALK+RG Sbjct: 183 AKQL-DIELAIIDKRRPKANVAEVMHLIGEIENRTCLLVDDMVDTAGTLCNAAQALKDRG 241 Query: 241 AKRVFAYATHPIFSGNAANNLRNSVIDEVVVCDTIPLSDEIKSLPNVRTLTLSGMLAEAI 300 AK+V AYATHP+ SG A L NSV+DE+VV D+IPLS E K+ +R LTLS MLAEA+ Sbjct: 242 AKKVIAYATHPVLSGPAIERLNNSVLDELVVTDSIPLSKEGKNCKVIRQLTLSNMLAEAM 301 Query: 301 RRISNEESISAMF 313 RRISNEES+SAMF Sbjct: 302 RRISNEESLSAMF 314 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: 357 Number of extensions: 6 Number of successful extensions: 2 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: 315 Length adjustment: 27 Effective length of query: 288 Effective length of database: 288 Effective search space: 82944 Effective search space used: 82944 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_015817076.1 TERTU_RS17075 (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.503.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.3e-128 412.2 1.3 5.9e-128 412.1 1.3 1.0 1 lcl|NCBI__GCF_000023025.1:WP_015817076.1 TERTU_RS17075 ribose-phosphate p Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000023025.1:WP_015817076.1 TERTU_RS17075 ribose-phosphate pyrophosphokinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 412.1 1.3 5.9e-128 5.9e-128 2 309 .] 7 315 .] 6 315 .] 0.99 Alignments for each domain: == domain 1 score: 412.1 bits; conditional E-value: 5.9e-128 TIGR01251 2 kilsgssskelaekvaknlglelgdvevkkFadgElyvrieesvrgkdvfiivqstsapvndalmelll 70 +++sg++++elaekv+ +lg++lgdv+v+kF+dgE+ v+++++vrg+dvf+i q t+ap+nd++mel++ lcl|NCBI__GCF_000023025.1:WP_015817076.1 7 MVFSGNANPELAEKVCAKLGIPLGDVTVDKFSDGEILVELKQNVRGSDVFVI-QPTCAPTNDNIMELMV 74 89**************************************************.**************** PP TIGR01251 71 lidalkrasaksvtaviPyygYaRqdkkak.srepisaklvaklleeaGadrvltvdlHseqiqgfFdv 138 ++dal+r+sa+++tav+Py+gYaRqd++++ r pi+ak+va++l ++G+drvltvdlH+eqiqgfFdv lcl|NCBI__GCF_000023025.1:WP_015817076.1 75 IVDALRRSSAGRITAVVPYFGYARQDRRVRsARVPITAKVVADMLVTVGVDRVLTVDLHAEQIQGFFDV 143 ****************************9857************************************* PP TIGR01251 139 pvenlsaspklieelkkkelknlvvvsPDkGaverakkvakklglelaiieKeRdskenevevtnllgd 207 pv+n+++sp+l+++++k+ ++lvvvsPD G+v ra++vak+l+ elaii+K+R+ k+n++ev++l+g+ lcl|NCBI__GCF_000023025.1:WP_015817076.1 144 PVDNVYGSPVLLADIEKQSFEDLVVVSPDIGGVVRARAVAKQLDIELAIIDKRRP-KANVAEVMHLIGE 211 *******************************************************.899********** PP TIGR01251 208 vegkdvvivDDiisTggTlvkaaelLkekGAkkvivaathgvfsgdAlerlaeagveevivtntilv.e 275 +e++++++vDD+++T+gTl++aa++Lk++GAkkvi++ath+v+sg+A+erl++++++e++vt++i+ + lcl|NCBI__GCF_000023025.1:WP_015817076.1 212 IENRTCLLVDDMVDTAGTLCNAAQALKDRGAKKVIAYATHPVLSGPAIERLNNSVLDELVVTDSIPLsK 280 *******************************************************************88 PP TIGR01251 276 e.kklpkvseisvapliaeaiarihenesvsslfd 309 e k+++ ++++++++++aea++ri+++es+s++f+ lcl|NCBI__GCF_000023025.1:WP_015817076.1 281 EgKNCKVIRQLTLSNMLAEAMRRISNEESLSAMFS 315 89*******************************95 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (309 nodes) Target sequences: 1 (315 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: 00:00:00.00 # Mc/sec: 11.52 // [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