Align ribose-phosphate diphosphokinase (EC 2.7.6.1) (characterized)
to candidate RR42_RS02015 RR42_RS02015 ribose-phosphate pyrophosphokinase
Query= BRENDA::P0A719 (315 letters) >FitnessBrowser__Cup4G11:RR42_RS02015 Length = 317 Score = 397 bits (1019), Expect = e-115 Identities = 198/310 (63%), Positives = 247/310 (79%), Gaps = 1/310 (0%) Query: 4 MKLFAGNATPELAQRIANRLYTSLGDAAVGRFSDGEVSVQINENVRGGDIFIIQSTCAPT 63 + +F GNA P+LA+ + L LG A VGRFSDGEV V+I ENVRG + ++QSTCAPT Sbjct: 6 LMVFTGNANPKLAEAVVQHLGIPLGKAQVGRFSDGEVQVEIQENVRGKHVIVLQSTCAPT 65 Query: 64 NDNLMELVVMVDALRRASAGRITAVIPYFGYARQDRRVRSARVPITAKVVADFLSSVGVD 123 NDNLMEL+VMVDAL+RASA ITA +PYFGYARQDRR RSARV I+AKVVA+ L GV+ Sbjct: 66 NDNLMELMVMVDALKRASARSITAAMPYFGYARQDRRPRSARVAISAKVVANMLEVAGVE 125 Query: 124 RVLTVDLHAEQIQGFFDVPVDNVFGSPILLEDMLQLNLDNPIVVSPDIGGVVRARAIAKL 183 RVLT+DLHA+QIQGFFD+PVDN++ SP+LL D+ + N N +VVSPD+GGVVRARA+AK Sbjct: 126 RVLTMDLHADQIQGFFDIPVDNIYASPVLLGDLREKNYGNLLVVSPDVGGVVRARALAKQ 185 Query: 184 LNDTDMAIIDKRRPRANVSQVMHIIGDVAGRDCVLVDDMIDTGGTLCKAAEALKERGAKR 243 LN D+AIIDKRRP+ANV++VM+IIG+V GR+CV++DDMIDTGGTLCKAA+ LKERGA + Sbjct: 186 LN-CDLAIIDKRRPKANVAEVMNIIGEVDGRNCVIMDDMIDTGGTLCKAAQVLKERGALK 244 Query: 244 VFAYATHPIFSGNAANNLRNSVIDEVVVCDTIPLSDEIKSLPNVRTLTLSGMLAEAIRRI 303 VFAY THP+ SG AA + +S +DEVVVCDTIPL D+ +R L+ + +LAE RI Sbjct: 245 VFAYCTHPVLSGGAAARIADSELDEVVVCDTIPLRDDAIQSGKIRQLSTASLLAETFTRI 304 Query: 304 SNEESISAMF 313 +SI ++F Sbjct: 305 VKGDSIMSLF 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: 306 Number of extensions: 9 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: 317 Length adjustment: 27 Effective length of query: 288 Effective length of database: 290 Effective search space: 83520 Effective search space used: 83520 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 RR42_RS02015 RR42_RS02015 (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.4326.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.7e-124 400.7 0.3 1.9e-124 400.6 0.3 1.0 1 lcl|FitnessBrowser__Cup4G11:RR42_RS02015 RR42_RS02015 ribose-phosphate py Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Cup4G11:RR42_RS02015 RR42_RS02015 ribose-phosphate pyrophosphokinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 400.6 0.3 1.9e-124 1.9e-124 2 308 .. 7 314 .. 6 315 .. 0.98 Alignments for each domain: == domain 1 score: 400.6 bits; conditional E-value: 1.9e-124 TIGR01251 2 kilsgssskelaekvaknlglelgdvevkkFadgElyvrieesvrgkdvfiivqstsapvndalmelll 70 +++ g+++++lae+v ++lg++lg+++v +F+dgE++v+i+e+vrgk+v+++ qst+ap+nd+lmel++ lcl|FitnessBrowser__Cup4G11:RR42_RS02015 7 MVFTGNANPKLAEAVVQHLGIPLGKAQVGRFSDGEVQVEIQENVRGKHVIVL-QSTCAPTNDNLMELMV 74 89********************************************888888.**************** PP TIGR01251 71 lidalkrasaksvtaviPyygYaRqdkkak.srepisaklvaklleeaGadrvltvdlHseqiqgfFdv 138 ++dalkrasa+s+ta +Py+gYaRqd++ + r +isak+va++le aG++rvlt+dlH++qiqgfFd+ lcl|FitnessBrowser__Cup4G11:RR42_RS02015 75 MVDALKRASARSITAAMPYFGYARQDRRPRsARVAISAKVVANMLEVAGVERVLTMDLHADQIQGFFDI 143 ***************************97758************************************* PP TIGR01251 139 pvenlsaspklieelkkkelknlvvvsPDkGaverakkvakklglelaiieKeRdskenevevtnllgd 207 pv+n++asp+l+ +l++k+ nl+vvsPD G+v ra+++ak+l+++laii+K+R+ k+n++ev+n++g+ lcl|FitnessBrowser__Cup4G11:RR42_RS02015 144 PVDNIYASPVLLGDLREKNYGNLLVVSPDVGGVVRARALAKQLNCDLAIIDKRRP-KANVAEVMNIIGE 211 *******************************************************.899********** PP TIGR01251 208 vegkdvvivDDiisTggTlvkaaelLkekGAkkvivaathgvfsgdAlerlaeagveevivtntilv.e 275 v+g+++vi+DD+i+TggTl+kaa++Lke+GA kv++++th+v+sg A+ r+a + ++ev+v++ti+ + lcl|FitnessBrowser__Cup4G11:RR42_RS02015 212 VDGRNCVIMDDMIDTGGTLCKAAQVLKERGALKVFAYCTHPVLSGGAAARIADSELDEVVVCDTIPLrD 280 *******************************************************************87 PP TIGR01251 276 e.kklpkvseisvapliaeaiarihenesvsslf 308 + + k++++s a l+ae+ +ri ++ s+ slf lcl|FitnessBrowser__Cup4G11:RR42_RS02015 281 DaIQSGKIRQLSTASLLAETFTRIVKGDSIMSLF 314 78999****************************9 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (309 nodes) Target sequences: 1 (317 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: 6.58 // [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