Align ribose-phosphate diphosphokinase (EC 2.7.6.1) (characterized)
to candidate WP_019866389.1 METMI_RS0111210 ribose-phosphate pyrophosphokinase
Query= BRENDA::P0A719 (315 letters) >NCBI__GCF_000384075.1:WP_019866389.1 Length = 317 Score = 390 bits (1001), Expect = e-113 Identities = 193/310 (62%), Positives = 247/310 (79%) Query: 4 MKLFAGNATPELAQRIANRLYTSLGDAAVGRFSDGEVSVQINENVRGGDIFIIQSTCAPT 63 + +F+GNA L++ I +L LG AAVGRFSDGE++V+I ENVRG D+F+IQ TC+PT Sbjct: 6 LMVFSGNANLALSEGIVKKLNMRLGMAAVGRFSDGEIAVEIEENVRGKDVFVIQPTCSPT 65 Query: 64 NDNLMELVVMVDALRRASAGRITAVIPYFGYARQDRRVRSARVPITAKVVADFLSSVGVD 123 N+NLMEL+VM+DAL+RASA RITAV+PY+GY+RQDRR RSARVPI+AK+VA + G Sbjct: 66 NENLMELLVMIDALKRASASRITAVMPYYGYSRQDRRSRSARVPISAKLVAKMIEQAGAS 125 Query: 124 RVLTVDLHAEQIQGFFDVPVDNVFGSPILLEDMLQLNLDNPIVVSPDIGGVVRARAIAKL 183 R+LTVDLHA+QIQGFFD+PVDNV+ SPILL D+ + + IVVSPD+GGVVRARA+AK Sbjct: 126 RLLTVDLHADQIQGFFDIPVDNVYASPILLGDIWRQQYKDLIVVSPDVGGVVRARALAKR 185 Query: 184 LNDTDMAIIDKRRPRANVSQVMHIIGDVAGRDCVLVDDMIDTGGTLCKAAEALKERGAKR 243 LND D+AIIDKRR +ANV++VMHIIGDV GR C+L+DD++DT GTLC AA ALK+ GA R Sbjct: 186 LNDADLAIIDKRRLKANVAEVMHIIGDVDGRTCILIDDIVDTAGTLCHAAAALKKHGAVR 245 Query: 244 VFAYATHPIFSGNAANNLRNSVIDEVVVCDTIPLSDEIKSLPNVRTLTLSGMLAEAIRRI 303 V AY TH + SG+A NL S +DE+VV DTIPL+ E +R L+++ MLAE IRRI Sbjct: 246 VLAYCTHAVLSGSAMKNLTGSSLDELVVTDTIPLNQEAIDCGKIRQLSVAEMLAETIRRI 305 Query: 304 SNEESISAMF 313 + ES+S+++ Sbjct: 306 AVGESVSSLY 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: 316 Number of extensions: 7 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: 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 WP_019866389.1 METMI_RS0111210 (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.30412.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-124 399.5 1.0 4.4e-124 399.3 1.0 1.0 1 lcl|NCBI__GCF_000384075.1:WP_019866389.1 METMI_RS0111210 ribose-phosphate Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000384075.1:WP_019866389.1 METMI_RS0111210 ribose-phosphate pyrophosphokinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 399.3 1.0 4.4e-124 4.4e-124 2 308 .. 7 315 .. 6 316 .. 0.98 Alignments for each domain: == domain 1 score: 399.3 bits; conditional E-value: 4.4e-124 TIGR01251 2 kilsgssskelaekvaknlglelgdvevkkFadgElyvrieesvrgkdvfiivqstsapvndalmelll 70 +++sg+++ +l+e + k+l+++lg + v +F+dgE+ v+iee+vrgkdvf+i q t+ p+n++lmell+ lcl|NCBI__GCF_000384075.1:WP_019866389.1 7 MVFSGNANLALSEGIVKKLNMRLGMAAVGRFSDGEIAVEIEENVRGKDVFVI-QPTCSPTNENLMELLV 74 89**************************************************.9*************** PP TIGR01251 71 lidalkrasaksvtaviPyygYaRqdkkak.srepisaklvaklleeaGadrvltvdlHseqiqgfFdv 138 +idalkrasa+++tav+PyygY+Rqd++ + r pisaklvak++e+aGa+r+ltvdlH++qiqgfFd+ lcl|NCBI__GCF_000384075.1:WP_019866389.1 75 MIDALKRASASRITAVMPYYGYSRQDRRSRsARVPISAKLVAKMIEQAGASRLLTVDLHADQIQGFFDI 143 ***************************98757************************************* PP TIGR01251 139 pvenlsaspklieelkkkelknlvvvsPDkGaverakkvakklg.lelaiieKeRdskenevevtnllg 206 pv+n++asp l+ ++ +++ k+l+vvsPD G+v ra+++ak+l+ ++laii+K+R k+n++ev++++g lcl|NCBI__GCF_000384075.1:WP_019866389.1 144 PVDNVYASPILLGDIWRQQYKDLIVVSPDVGGVVRARALAKRLNdADLAIIDKRRL-KANVAEVMHIIG 211 ********************************************9***********.899********* PP TIGR01251 207 dvegkdvvivDDiisTggTlvkaaelLkekGAkkvivaathgvfsgdAlerlaeagveevivtntilv. 274 dv+g++++++DDi++T+gTl++aa +Lk++GA +v++++th+v+sg+A+++l+ + ++e++vt+ti+ lcl|NCBI__GCF_000384075.1:WP_019866389.1 212 DVDGRTCILIDDIVDTAGTLCHAAAALKKHGAVRVLAYCTHAVLSGSAMKNLTGSSLDELVVTDTIPLn 280 ********************************************************************7 PP TIGR01251 275 ee.kklpkvseisvapliaeaiarihenesvsslf 308 +e + k++++sva+++ae+i+ri+ +esvssl+ lcl|NCBI__GCF_000384075.1:WP_019866389.1 281 QEaIDCGKIRQLSVAEMLAETIRRIAVGESVSSLY 315 66899****************************98 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 8.34 // [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