Align ribose-phosphate diphosphokinase (EC 2.7.6.1) (characterized)
to candidate GFF703 PS417_03575 ribose-phosphate pyrophosphokinase
Query= BRENDA::P0A717 (315 letters) >lcl|FitnessBrowser__WCS417:GFF703 PS417_03575 ribose-phosphate pyrophosphokinase Length = 313 Score = 426 bits (1094), Expect = e-124 Identities = 210/313 (67%), Positives = 258/313 (82%), Gaps = 1/313 (0%) Query: 1 MPDMKLFAGNATPELAQRIANRLYTSLGDAAVGRFSDGEVSVQINENVRGGDIFIIQSTC 60 M M +F GNA P+LA+R+ +L+ LGD +VG+FSDGE++ +INENVRG D+FIIQ TC Sbjct: 1 MSKMMVFTGNANPDLARRVVRQLHIPLGDISVGKFSDGEITAEINENVRGKDVFIIQPTC 60 Query: 61 APTNDNLMELVVMVDALRRASAGRITAVIPYFGYARQDRRVRSARVPITAKVVADFLSSV 120 APTNDNLMELVVM DA RR+SA RITAVIPYFGYARQDRR RSARV I+AKVVAD L+ V Sbjct: 61 APTNDNLMELVVMADAFRRSSATRITAVIPYFGYARQDRRPRSARVAISAKVVADMLTVV 120 Query: 121 GVDRVLTVDLHAEQIQGFFDVPVDNVFGSPILLEDMLQLNLDNPIVVSPDIGGVVRARAI 180 G+DRVLTVDLHA+QIQGFFD+PVDN++GSP+L++D+ +N ++VSPDIGGVVRARA+ Sbjct: 121 GIDRVLTVDLHADQIQGFFDIPVDNIYGSPVLVDDIEDQRFENLMIVSPDIGGVVRARAV 180 Query: 181 AKLLNDTDMAIIDKRRPRANVSQVMHIIGDVAGRDCVLVDDMIDTGGTLCKAAEALKERG 240 AK L D+ IIDKRR +AN S+VMHIIGDV GR C+LVDDM+DT GTLC AA+ALKE G Sbjct: 181 AKSLG-VDLGIIDKRREKANHSEVMHIIGDVEGRTCILVDDMVDTAGTLCHAAKALKEHG 239 Query: 241 AKRVFAYATHPIFSGNAANNLRNSVIDEVVVCDTIPLSDEIKSLPNVRTLTLSGMLAEAI 300 A +VFAY THP+ SG A N+ NSV+DE+VV +TIPLS ++ +R L ++ ++AEA+ Sbjct: 240 AAKVFAYCTHPVLSGRAIENIENSVLDELVVTNTIPLSAAAQACARIRQLDIAPVVAEAV 299 Query: 301 RRISNEESISAMF 313 RRISNEESISAMF Sbjct: 300 RRISNEESISAMF 312 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: 359 Number of extensions: 11 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: 313 Length adjustment: 27 Effective length of query: 288 Effective length of database: 286 Effective search space: 82368 Effective search space used: 82368 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 GFF703 PS417_03575 (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.3123.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 9.4e-127 408.1 2.8 1.1e-126 407.9 2.8 1.0 1 lcl|FitnessBrowser__WCS417:GFF703 PS417_03575 ribose-phosphate pyr Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__WCS417:GFF703 PS417_03575 ribose-phosphate pyrophosphokinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 407.9 2.8 1.1e-126 1.1e-126 1 309 [] 4 313 .] 4 313 .] 0.98 Alignments for each domain: == domain 1 score: 407.9 bits; conditional E-value: 1.1e-126 TIGR01251 1 lkilsgssskelaekvaknlglelgdvevkkFadgElyvrieesvrgkdvfiivqstsapvndalmellllidalk 76 ++++ g+++++la++v ++l+++lgd++v kF+dgE+ +i+e+vrgkdvfii q t+ap+nd+lmel++++da++ lcl|FitnessBrowser__WCS417:GFF703 4 MMVFTGNANPDLARRVVRQLHIPLGDISVGKFSDGEITAEINENVRGKDVFII-QPTCAPTNDNLMELVVMADAFR 78 799**************************************************.********************** PP TIGR01251 77 rasaksvtaviPyygYaRqdkkak.srepisaklvaklleeaGadrvltvdlHseqiqgfFdvpvenlsaspklie 151 r+sa ++taviPy+gYaRqd++ + r +isak+va++l+ +G+drvltvdlH++qiqgfFd+pv+n+++sp+l++ lcl|FitnessBrowser__WCS417:GFF703 79 RSSATRITAVIPYFGYARQDRRPRsARVAISAKVVADMLTVVGIDRVLTVDLHADQIQGFFDIPVDNIYGSPVLVD 154 *********************97758************************************************** PP TIGR01251 152 elkkkelknlvvvsPDkGaverakkvakklglelaiieKeRdskenevevtnllgdvegkdvvivDDiisTggTlv 227 +++++ +nl++vsPD G+v ra++vak+lg++l ii+K+R+ k+n+ ev++++gdveg+++++vDD+++T+gTl+ lcl|FitnessBrowser__WCS417:GFF703 155 DIEDQRFENLMIVSPDIGGVVRARAVAKSLGVDLGIIDKRRE-KANHSEVMHIIGDVEGRTCILVDDMVDTAGTLC 229 ******************************************.899****************************** PP TIGR01251 228 kaaelLkekGAkkvivaathgvfsgdAlerlaeagveevivtntilv.ee.kklpkvseisvapliaeaiarihen 301 +aa++Lke+GA kv++++th+v+sg+A+e++++++++e++vtnti+ +++ +++++++ap++aea++ri+++ lcl|FitnessBrowser__WCS417:GFF703 230 HAAKALKEHGAAKVFAYCTHPVLSGRAIENIENSVLDELVVTNTIPLsAAaQACARIRQLDIAPVVAEAVRRISNE 305 ***********************************************65579************************ PP TIGR01251 302 esvsslfd 309 es+s++f+ lcl|FitnessBrowser__WCS417:GFF703 306 ESISAMFR 313 ******95 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (309 nodes) Target sequences: 1 (313 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: 6.57 // [ok]
This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.
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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code, or see changes to Amino acid biosynthesis since the publication.
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