Align ribose-phosphate diphosphokinase (EC 2.7.6.1) (characterized)
to candidate BPHYT_RS02845 BPHYT_RS02845 ribose-phosphate pyrophosphokinase
Query= BRENDA::P0A719 (315 letters) >FitnessBrowser__BFirm:BPHYT_RS02845 Length = 318 Score = 403 bits (1036), Expect = e-117 Identities = 195/310 (62%), Positives = 249/310 (80%), Gaps = 1/310 (0%) Query: 4 MKLFAGNATPELAQRIANRLYTSLGDAAVGRFSDGEVSVQINENVRGGDIFIIQSTCAPT 63 + +F GNA P LAQ + L LG A V RFSDGE+ V+I ENVRG D+F++QSTCAP Sbjct: 7 LMVFTGNANPALAQEVVKILGIPLGKAMVSRFSDGEIQVEIQENVRGKDVFVLQSTCAPA 66 Query: 64 NDNLMELVVMVDALRRASAGRITAVIPYFGYARQDRRVRSARVPITAKVVADFLSSVGVD 123 NDNLMEL++MVDAL+RASAGRITA IPYFGYARQDRR RSARV I+AK+VA+ L GV+ Sbjct: 67 NDNLMELMIMVDALKRASAGRITAAIPYFGYARQDRRPRSARVAISAKIVANMLEIAGVE 126 Query: 124 RVLTVDLHAEQIQGFFDVPVDNVFGSPILLEDMLQLNLDNPIVVSPDIGGVVRARAIAKL 183 R++T+DLHA+QIQGFFD+PVDN++ +P+LL D+ + N +N +VVSPD+GGVVRARA+AK Sbjct: 127 RIITMDLHADQIQGFFDIPVDNIYATPVLLGDLRKQNYENLLVVSPDVGGVVRARALAKQ 186 Query: 184 LNDTDMAIIDKRRPRANVSQVMHIIGDVAGRDCVLVDDMIDTGGTLCKAAEALKERGAKR 243 LN D+AIIDKRRP+ANV++VM+IIG+V GR CV++DDM+DT GTLCKAA+ LKERGAK+ Sbjct: 187 LN-CDLAIIDKRRPKANVAEVMNIIGEVEGRTCVIMDDMVDTAGTLCKAAQVLKERGAKQ 245 Query: 244 VFAYATHPIFSGNAANNLRNSVIDEVVVCDTIPLSDEIKSLPNVRTLTLSGMLAEAIRRI 303 VFAYATHP+ SG A + S +D +VV DTIPL DE +S +R+LT +G+LAE RI Sbjct: 246 VFAYATHPVLSGGAGERIAASALDALVVTDTIPLGDEARSCAKIRSLTSAGLLAETFSRI 305 Query: 304 SNEESISAMF 313 +S+ ++F Sbjct: 306 RRGDSVMSLF 315 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: 311 Number of extensions: 10 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: 318 Length adjustment: 27 Effective length of query: 288 Effective length of database: 291 Effective search space: 83808 Effective search space used: 83808 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 BPHYT_RS02845 BPHYT_RS02845 (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.8593.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5e-125 402.5 0.3 5.6e-125 402.3 0.3 1.0 1 lcl|FitnessBrowser__BFirm:BPHYT_RS02845 BPHYT_RS02845 ribose-phosphate p Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__BFirm:BPHYT_RS02845 BPHYT_RS02845 ribose-phosphate pyrophosphokinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 402.3 0.3 5.6e-125 5.6e-125 2 308 .. 8 315 .. 7 316 .. 0.99 Alignments for each domain: == domain 1 score: 402.3 bits; conditional E-value: 5.6e-125 TIGR01251 2 kilsgssskelaekvaknlglelgdvevkkFadgElyvrieesvrgkdvfiivqstsapvndalmellll 71 +++ g+++++la++v k lg++lg++ v +F+dgE++v+i+e+vrgkdvf++ qst+ap nd+lmel+++ lcl|FitnessBrowser__BFirm:BPHYT_RS02845 8 MVFTGNANPALAQEVVKILGIPLGKAMVSRFSDGEIQVEIQENVRGKDVFVL-QSTCAPANDNLMELMIM 76 89**************************************************.***************** PP TIGR01251 72 idalkrasaksvtaviPyygYaRqdkkak.srepisaklvaklleeaGadrvltvdlHseqiqgfFdvpv 140 +dalkrasa+++ta iPy+gYaRqd++ + r +isak+va++le aG++r++t+dlH++qiqgfFd+pv lcl|FitnessBrowser__BFirm:BPHYT_RS02845 77 VDALKRASAGRITAAIPYFGYARQDRRPRsARVAISAKIVANMLEIAGVERIITMDLHADQIQGFFDIPV 146 **************************97758*************************************** PP TIGR01251 141 enlsaspklieelkkkelknlvvvsPDkGaverakkvakklglelaiieKeRdskenevevtnllgdveg 210 +n++a p+l+ +l+k++ +nl+vvsPD G+v ra+++ak+l+++laii+K+R+ k+n++ev+n++g+veg lcl|FitnessBrowser__BFirm:BPHYT_RS02845 147 DNIYATPVLLGDLRKQNYENLLVVSPDVGGVVRARALAKQLNCDLAIIDKRRP-KANVAEVMNIIGEVEG 215 *****************************************************.899************* PP TIGR01251 211 kdvvivDDiisTggTlvkaaelLkekGAkkvivaathgvfsgdAlerlaeagveevivtntilv.ee.kk 278 +++vi+DD+++T+gTl+kaa++Lke+GAk+v+++ath+v+sg A er+a + +++++vt+ti+ +e ++ lcl|FitnessBrowser__BFirm:BPHYT_RS02845 216 RTCVIMDDMVDTAGTLCKAAQVLKERGAKQVFAYATHPVLSGGAGERIAASALDALVVTDTIPLgDEaRS 285 ****************************************************************9888** PP TIGR01251 279 lpkvseisvapliaeaiarihenesvsslf 308 + k++ ++ a l+ae+ +ri+++ sv slf lcl|FitnessBrowser__BFirm:BPHYT_RS02845 286 CAKIRSLTSAGLLAETFSRIRRGDSVMSLF 315 *****************************9 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (309 nodes) Target sequences: 1 (318 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: 10.14 // [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