Align ribose-phosphate diphosphokinase (EC 2.7.6.1) (characterized)
to candidate 350276 BT0748 ribose-phosphate pyrophosphokinase (NCBI ptt file)
Query= BRENDA::E7EAU9 (317 letters) >FitnessBrowser__Btheta:350276 Length = 305 Score = 266 bits (679), Expect = 6e-76 Identities = 142/302 (47%), Positives = 201/302 (66%), Gaps = 3/302 (0%) Query: 12 IFSLNSNPELAKEIADNVGVQLGKCSVTRFSDGEVQINIEESIRGCDCYIIQSTSAPVNE 71 +FS ++ LA++I ++ LG ++T F+DGE ++ EESIRG +++QST P ++ Sbjct: 2 VFSGTNSRYLAEKICASLNCPLGNMNITHFADGEFAVSYEESIRGAHVFLVQSTF-PNSD 60 Query: 72 HIMELLIMVDALKRASAKTINIVIPYYGYARQDRKARSREPITAKLFANLLETAGATRVI 131 ++MELL+M+DA KRASAK++ VIPY+G+ARQDRK + R I AKL A+LL AG R+I Sbjct: 61 NLMELLLMIDAAKRASAKSVVAVIPYFGWARQDRKDKPRVSIGAKLVADLLSVAGIDRLI 120 Query: 132 ALDLHAPQIQGFFDIPIDHLMGVPILGHYFEGKDLKDIVIVSPDHGGVTRARKLADRLKA 191 +DLHA QIQGFF+IP+DHL + Y + L+D+VI +PD GG RA + L Sbjct: 121 TMDLHADQIQGFFNIPVDHLYASAVFLPYIQSLKLEDLVIATPDVGGSKRASTFSKYLGV 180 Query: 192 PIAIIDKRRPRPNEVEVMNIVGNVEGKTAILIDDIIDTAGTITLAANALVENGAAEVYAC 251 P+ + +K R + NEV M I+G+V+ K +LIDDI+DTAGTIT AAN ++E GA V A Sbjct: 181 PLVLCNKSREKANEVASMQIIGDVKDKNVVLIDDIVDTAGTITKAANIMMEAGAKSVRAI 240 Query: 252 CTHPVLSGPAVERINNSKIKELVVTNSIKLPEEKKIERFKQLSVGPLLAEAIIRVHEKQS 311 +H V+S PA R+ S + E+V T+SI P KK + KQLS+ + AE I RV +S Sbjct: 241 ASHCVMSDPASFRVQESGLTEMVFTDSI--PYAKKCAKVKQLSIADMFAETIKRVMNNES 298 Query: 312 VS 313 +S Sbjct: 299 IS 300 Lambda K H 0.319 0.136 0.383 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: 196 Number of extensions: 4 Number of successful extensions: 3 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: 317 Length of database: 305 Length adjustment: 27 Effective length of query: 290 Effective length of database: 278 Effective search space: 80620 Effective search space used: 80620 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 (21.7 bits) S2: 48 (23.1 bits)
Align candidate 350276 BT0748 (ribose-phosphate pyrophosphokinase (NCBI ptt file))
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.19450.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.9e-111 356.5 1.1 5.6e-111 356.3 1.1 1.0 1 lcl|FitnessBrowser__Btheta:350276 BT0748 ribose-phosphate pyrophos Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Btheta:350276 BT0748 ribose-phosphate pyrophosphokinase (NCBI ptt file) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 356.3 1.1 5.6e-111 5.6e-111 2 306 .. 1 301 [. 1 304 [. 0.98 Alignments for each domain: == domain 1 score: 356.3 bits; conditional E-value: 5.6e-111 TIGR01251 2 kilsgssskelaekvaknlglelgdvevkkFadgElyvrieesvrgkdvfiivqstsapvndalmellllidalkr 77 +++sg++s+ laek++ +l+ +lg++++++FadgE+ v +ees+rg +vf++ qst p +d+lmelll+ida+kr lcl|FitnessBrowser__Btheta:350276 1 MVFSGTNSRYLAEKICASLNCPLGNMNITHFADGEFAVSYEESIRGAHVFLV-QSTF-PNSDNLMELLLMIDAAKR 74 689*************************************************.7777.79**************** PP TIGR01251 78 asaksvtaviPyygYaRqdkkaksrepisaklvaklleeaGadrvltvdlHseqiqgfFdvpvenlsaspklieel 153 asaksv aviPy+g+aRqd+k+k+r +i aklva+ll+ aG+dr++t+dlH++qiqgfF++pv++l+as +++ ++ lcl|FitnessBrowser__Btheta:350276 75 ASAKSVVAVIPYFGWARQDRKDKPRVSIGAKLVADLLSVAGIDRLITMDLHADQIQGFFNIPVDHLYASAVFLPYI 150 **************************************************************************** PP TIGR01251 154 kkkelknlvvvsPDkGaverakkvakklglelaiieKeRdskenevevtnllgdvegkdvvivDDiisTggTlvka 229 ++ +l++lv+ PD G+ +ra++++k lg++l++ +K R+ k+nev +++++gdv++k+vv++DDi++T+gT++ka lcl|FitnessBrowser__Btheta:350276 151 QSLKLEDLVIATPDVGGSKRASTFSKYLGVPLVLCNKSRE-KANEVASMQIIGDVKDKNVVLIDDIVDTAGTITKA 225 ****************************************.899******************************** PP TIGR01251 230 aelLkekGAkkvivaathgvfsgdAlerlaeagveevivtntilveekklpkvseisvapliaeaiarihenesvs 305 a+++ e+GAk+v ++a+h v+s++A r++e+g++e++ t++i+ kk+ kv+++s+a+++ae+i+r+ +nes+s lcl|FitnessBrowser__Btheta:350276 226 ANIMMEAGAKSVRAIASHCVMSDPASFRVQESGLTEMVFTDSIPY-AKKCAKVKQLSIADMFAETIKRVMNNESIS 300 *********************************************.99***************************9 PP TIGR01251 306 s 306 s lcl|FitnessBrowser__Btheta:350276 301 S 301 8 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (309 nodes) Target sequences: 1 (305 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: 7.73 // [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