Align Ribose-phosphate pyrophosphokinase; RPPK; 5-phospho-D-ribosyl alpha-1-diphosphate synthase; Phosphoribosyl diphosphate synthase; Phosphoribosyl pyrophosphate synthase; P-Rib-PP synthase; PPRibP synthase; PRPP synthase; PRPPase; EC 2.7.6.1 (characterized)
to candidate WP_028950806.1 Q385_RS0106030 ribose-phosphate pyrophosphokinase
Query= SwissProt::P14193 (317 letters) >NCBI__GCF_000619805.1:WP_028950806.1 Length = 311 Score = 336 bits (861), Expect = 5e-97 Identities = 166/309 (53%), Positives = 230/309 (74%), Gaps = 1/309 (0%) Query: 8 KNLKIFSLNSNPELAKEIADIVGVQLGKCSVTRFSDGEVQINIEESIRGCDCYIIQSTSD 67 K LK+ S N+N LA+EI++ + L +TRFSDGE+++ I E++RG D ++IQ+ S Sbjct: 3 KVLKLISGNANKSLAREISEYLETPLVDVLLTRFSDGEIRVQINENVRGADVFVIQTLSY 62 Query: 68 PVNEHIMELLIMVDALKRASAKTINIVIPYYGYARQDRKARSREPITAKLFANLLETAGA 127 PVN+HIMELL+++DALKR+S I VIPY+ YARQDRK + R PI+AKL A++++ AGA Sbjct: 63 PVNDHIMELLLLLDALKRSSTHRITAVIPYFAYARQDRKDKPRVPISAKLLADIIQKAGA 122 Query: 128 TRVIALDLHAPQIQGFFDIPIDHLMGVPILGEYFEGKNLEDIVIVSPDHGGVTRARKLAD 187 RV+ +DLH+ QIQGFFD P+D++ +P++ EY + KN++D+VIVSPD GGV RAR L + Sbjct: 123 DRVLTVDLHSAQIQGFFDCPVDNIYALPVIYEYLKAKNIKDLVIVSPDAGGVERARMLQN 182 Query: 188 RLKAPIAIIDKRRPRPNVAEVMNIVGNIEGKTAILIDDIIDTAGTITLAANALVENGAKE 247 RL +AII K+RP PNV E ++++G++EGK A++IDDIIDTAGTI AA L GAK Sbjct: 183 RLGGNLAIIYKKRPAPNVVETLDVIGDVEGKNAVIIDDIIDTAGTIVAAAEMLKSKGAKS 242 Query: 248 VYACCTHPVLSGPAVERINNSTIKELVVTNSIKLPEEKKIERFKQLSVGPLLAEAIIRVH 307 V A CTHPV SGPA+ER+ NS I+E++ TN+I L E K+ ++ LSV L+ EAI R++ Sbjct: 243 VIAACTHPVFSGPAIERLINSEIEEVIATNTIPL-EGKEFDKLTVLSVAELIGEAIKRIN 301 Query: 308 EQQSVSYLF 316 + SVS LF Sbjct: 302 IESSVSSLF 310 Lambda K H 0.319 0.137 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: 263 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: 317 Length of database: 311 Length adjustment: 27 Effective length of query: 290 Effective length of database: 284 Effective search space: 82360 Effective search space used: 82360 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 WP_028950806.1 Q385_RS0106030 (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.14280.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.9e-132 425.2 1.2 6.6e-132 425.0 1.2 1.0 1 lcl|NCBI__GCF_000619805.1:WP_028950806.1 Q385_RS0106030 ribose-phosphate Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000619805.1:WP_028950806.1 Q385_RS0106030 ribose-phosphate pyrophosphokinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 425.0 1.2 6.6e-132 6.6e-132 2 308 .. 6 310 .. 5 311 .] 0.99 Alignments for each domain: == domain 1 score: 425.0 bits; conditional E-value: 6.6e-132 TIGR01251 2 kilsgssskelaekvaknlglelgdvevkkFadgElyvrieesvrgkdvfiivqstsapvndalmelll 70 k++sg+++k+la++++++l+++l+dv ++F+dgE+ v+i+e+vrg dvf+i q+ s pvnd++melll lcl|NCBI__GCF_000619805.1:WP_028950806.1 6 KLISGNANKSLAREISEYLETPLVDVLLTRFSDGEIRVQINENVRGADVFVI-QTLSYPVNDHIMELLL 73 799*************************************************.99999*********** PP TIGR01251 71 lidalkrasaksvtaviPyygYaRqdkkaksrepisaklvaklleeaGadrvltvdlHseqiqgfFdvp 139 l+dalkr+s +++taviPy++YaRqd+k+k+r pisakl+a+++++aGadrvltvdlHs qiqgfFd p lcl|NCBI__GCF_000619805.1:WP_028950806.1 74 LLDALKRSSTHRITAVIPYFAYARQDRKDKPRVPISAKLLADIIQKAGADRVLTVDLHSAQIQGFFDCP 142 ********************************************************************* PP TIGR01251 140 venlsaspklieelkkkelknlvvvsPDkGaverakkvakklglelaiieKeRdskenevevtnllgdv 208 v+n++a p+++e+lk+k+ k+lv+vsPD+G+vera+ + ++lg +laii+K+R+ + n+ve+ +++gdv lcl|NCBI__GCF_000619805.1:WP_028950806.1 143 VDNIYALPVIYEYLKAKNIKDLVIVSPDAGGVERARMLQNRLGGNLAIIYKKRP-APNVVETLDVIGDV 210 ******************************************************.999*********** PP TIGR01251 209 egkdvvivDDiisTggTlvkaaelLkekGAkkvivaathgvfsgdAlerlaeagveevivtntilveek 277 egk++vi+DDii+T+gT+v+aae+Lk+kGAk+vi+a+th+vfsg+A+erl ++ +eevi+tnti+ e k lcl|NCBI__GCF_000619805.1:WP_028950806.1 211 EGKNAVIIDDIIDTAGTIVAAAEMLKSKGAKSVIAACTHPVFSGPAIERLINSEIEEVIATNTIPLEGK 279 ******************************************************************88* PP TIGR01251 278 klpkvseisvapliaeaiarihenesvsslf 308 +++k++++sva+li eai+ri+ ++svsslf lcl|NCBI__GCF_000619805.1:WP_028950806.1 280 EFDKLTVLSVAELIGEAIKRINIESSVSSLF 310 ******************************9 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (309 nodes) Target sequences: 1 (311 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 7.41 // [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