Align ribose-phosphate diphosphokinase (EC 2.7.6.1) (characterized)
to candidate 15329 b1207 ribose-phosphate pyrophosphokinase (NCBI)
Query= BRENDA::P0A719 (315 letters) >FitnessBrowser__Keio:15329 Length = 315 Score = 610 bits (1574), Expect = e-179 Identities = 315/315 (100%), Positives = 315/315 (100%) Query: 1 MPDMKLFAGNATPELAQRIANRLYTSLGDAAVGRFSDGEVSVQINENVRGGDIFIIQSTC 60 MPDMKLFAGNATPELAQRIANRLYTSLGDAAVGRFSDGEVSVQINENVRGGDIFIIQSTC Sbjct: 1 MPDMKLFAGNATPELAQRIANRLYTSLGDAAVGRFSDGEVSVQINENVRGGDIFIIQSTC 60 Query: 61 APTNDNLMELVVMVDALRRASAGRITAVIPYFGYARQDRRVRSARVPITAKVVADFLSSV 120 APTNDNLMELVVMVDALRRASAGRITAVIPYFGYARQDRRVRSARVPITAKVVADFLSSV Sbjct: 61 APTNDNLMELVVMVDALRRASAGRITAVIPYFGYARQDRRVRSARVPITAKVVADFLSSV 120 Query: 121 GVDRVLTVDLHAEQIQGFFDVPVDNVFGSPILLEDMLQLNLDNPIVVSPDIGGVVRARAI 180 GVDRVLTVDLHAEQIQGFFDVPVDNVFGSPILLEDMLQLNLDNPIVVSPDIGGVVRARAI Sbjct: 121 GVDRVLTVDLHAEQIQGFFDVPVDNVFGSPILLEDMLQLNLDNPIVVSPDIGGVVRARAI 180 Query: 181 AKLLNDTDMAIIDKRRPRANVSQVMHIIGDVAGRDCVLVDDMIDTGGTLCKAAEALKERG 240 AKLLNDTDMAIIDKRRPRANVSQVMHIIGDVAGRDCVLVDDMIDTGGTLCKAAEALKERG Sbjct: 181 AKLLNDTDMAIIDKRRPRANVSQVMHIIGDVAGRDCVLVDDMIDTGGTLCKAAEALKERG 240 Query: 241 AKRVFAYATHPIFSGNAANNLRNSVIDEVVVCDTIPLSDEIKSLPNVRTLTLSGMLAEAI 300 AKRVFAYATHPIFSGNAANNLRNSVIDEVVVCDTIPLSDEIKSLPNVRTLTLSGMLAEAI Sbjct: 241 AKRVFAYATHPIFSGNAANNLRNSVIDEVVVCDTIPLSDEIKSLPNVRTLTLSGMLAEAI 300 Query: 301 RRISNEESISAMFEH 315 RRISNEESISAMFEH Sbjct: 301 RRISNEESISAMFEH 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: 477 Number of extensions: 3 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: 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 15329 b1207 (ribose-phosphate pyrophosphokinase (NCBI))
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.5051.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.4e-131 422.7 0.4 3.8e-131 422.6 0.4 1.0 1 lcl|FitnessBrowser__Keio:15329 b1207 ribose-phosphate pyrophosp Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Keio:15329 b1207 ribose-phosphate pyrophosphokinase (NCBI) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 422.6 0.4 3.8e-131 3.8e-131 1 309 [] 4 314 .. 4 314 .. 0.99 Alignments for each domain: == domain 1 score: 422.6 bits; conditional E-value: 3.8e-131 TIGR01251 1 lkilsgssskelaekvaknlglelgdvevkkFadgElyvrieesvrgkdvfiivqstsapvndalmellllidalkras 79 +k+++g++++ela+++a++l ++lgd+ v +F+dgE++v+i+e+vrg d+fii qst+ap+nd+lmel++++dal+ras lcl|FitnessBrowser__Keio:15329 4 MKLFAGNATPELAQRIANRLYTSLGDAAVGRFSDGEVSVQINENVRGGDIFII-QSTCAPTNDNLMELVVMVDALRRAS 81 799**************************************************.************************* PP TIGR01251 80 aksvtaviPyygYaRqdkkak.srepisaklvaklleeaGadrvltvdlHseqiqgfFdvpvenlsaspklieelkkke 157 a+++taviPy+gYaRqd++++ r pi+ak+va++l+++G+drvltvdlH+eqiqgfFdvpv+n+ +sp l+e++ + + lcl|FitnessBrowser__Keio:15329 82 AGRITAVIPYFGYARQDRRVRsARVPITAKVVADFLSSVGVDRVLTVDLHAEQIQGFFDVPVDNVFGSPILLEDMLQLN 160 *******************9857******************************************************** PP TIGR01251 158 lknlvvvsPDkGaverakkvakklg.lelaiieKeRdskenevevtnllgdvegkdvvivDDiisTggTlvkaaelLke 235 l+n++vvsPD G+v ra+++ak l+ +++aii+K+R+ ++n+ +v++++gdv+g+d+v+vDD+i+TggTl+kaae+Lke lcl|FitnessBrowser__Keio:15329 161 LDNPIVVSPDIGGVVRARAIAKLLNdTDMAIIDKRRP-RANVSQVMHIIGDVAGRDCVLVDDMIDTGGTLCKAAEALKE 238 *************************9***********.888************************************** PP TIGR01251 236 kGAkkvivaathgvfsgdAlerlaeagveevivtntilv.ee.kklpkvseisvapliaeaiarihenesvsslfd 309 +GAk+v+++ath++fsg+A+++l++++++ev+v++ti+ +e k+lp+v++++++ ++aeai+ri+++es+s++f+ lcl|FitnessBrowser__Keio:15329 239 RGAKRVFAYATHPIFSGNAANNLRNSVIDEVVVCDTIPLsDEiKSLPNVRTLTLSGMLAEAIRRISNEESISAMFE 314 ***************************************8889*******************************96 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 6.60 // [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