Align Ribose-phosphate pyrophosphokinase; RPPK; EC 2.7.6.1; 5-phospho-D-ribosyl alpha-1-diphosphate synthase; Phosphoribosyl diphosphate synthase; Phosphoribosyl pyrophosphate synthase; P-Rib-PP synthase; PRPP synthase; PRPPase (uncharacterized)
to candidate WP_010960970.1 MCA_RS08445 phosphoribosylpyrophosphate synthetase
Query= curated2:Q8TUT6 (291 letters) >NCBI__GCF_000008325.1:WP_010960970.1 Length = 289 Score = 154 bits (390), Expect = 2e-42 Identities = 101/284 (35%), Positives = 157/284 (55%), Gaps = 9/284 (3%) Query: 8 EGVKLGRRLAEELDAELAPVEEDRFPDGEQIVRVPPELDGTVVVVHSMSPPQDENLVKAI 67 E + + LA L +E RFPDGE VRVPP++ GT VV S+ P D+ LV+ + Sbjct: 5 ETLTQSQELAGALGCPWRAIEVHRFPDGESRVRVPPDVRGTGVVHRSLDRPNDK-LVELV 63 Query: 68 ITLDAARENGAEEVIAIVPYMAYSRQDRRFEPGEPVSFRAVARAVSANADALITVD--LH 125 + + R G + ++ + PY+ Y RQD F+ GE VS + V ++ DALITVD LH Sbjct: 64 LAAETLRGQGCDRLVLVAPYLCYMRQDIAFQAGEAVSQKVVGNLLARYFDALITVDPHLH 123 Query: 126 EPGTLKYFDVPAE---NVSAAEELGKYLAERFEGEDLVVIGPDEGARELAREVASICGVE 182 L+ VP + +VS+A + +YLA + ++ +++GPD+ +R+ +A+ G+ Sbjct: 124 RIDRLEQA-VPLKRVLSVSSATLVSRYLAT--DRKEWLLLGPDQESRQWVEAIAAQAGLP 180 Query: 183 YDHLEKKRLSGDEVEIHPKELDVEGRTVVLVDDMIDTGGTMVEAARALRDQGAGTLYAAC 242 K+RL EV I + + VVLVDD+ TG T+ E AR L G + Sbjct: 181 CAVASKRRLGDREVGISLPQEAGAFKGVVLVDDIASTGTTLAETARLLARAGVARIDVIV 240 Query: 243 THALLTRNAATRLLASGFEDIIATDTVPNPFEKVSVAPPVAEAV 286 THAL T +A +RL +G I +TD++ +P ++ +AP +A+AV Sbjct: 241 THALFTGDAWSRLKQAGVGAIASTDSISHPTNRMCLAPLLADAV 284 Lambda K H 0.314 0.134 0.370 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: 157 Number of extensions: 8 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: 291 Length of database: 289 Length adjustment: 26 Effective length of query: 265 Effective length of database: 263 Effective search space: 69695 Effective search space used: 69695 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (22.0 bits) S2: 48 (23.1 bits)
Align candidate WP_010960970.1 MCA_RS08445 (phosphoribosylpyrophosphate synthetase)
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.16992.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.5e-58 184.1 0.0 2e-58 183.7 0.0 1.0 1 lcl|NCBI__GCF_000008325.1:WP_010960970.1 MCA_RS08445 phosphoribosylpyroph Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000008325.1:WP_010960970.1 MCA_RS08445 phosphoribosylpyrophosphate synthetase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 183.7 0.0 2e-58 2e-58 13 297 .. 10 286 .. 3 288 .. 0.90 Alignments for each domain: == domain 1 score: 183.7 bits; conditional E-value: 2e-58 TIGR01251 13 aekvaknlglelgdvevkkFadgElyvrieesvrgkdvfiivqstsapvndalmellllidalkrasak 81 ++++a +lg + +ev++F+dgE vr+ +vrg ++ + nd+l+el+l++++l+ ++ + lcl|NCBI__GCF_000008325.1:WP_010960970.1 10 SQELAGALGCPWRAIEVHRFPDGESRVRVPPDVRG--TGVV-HRSLDRPNDKLVELVLAAETLRGQGCD 75 6889999999*************************..6777.5556679******************** PP TIGR01251 82 svtaviPyygYaRqdkkaksrepisaklvaklleeaGadrvltvdlHseqiqgfFd.vpvenlsa..sp 147 ++ +v+Py+ Y Rqd ++ +e++s k+v++ll+ + d ++tvd H + i + vp++ + + s lcl|NCBI__GCF_000008325.1:WP_010960970.1 76 RLVLVAPYLCYMRQDIAFQAGEAVSQKVVGNLLARY-FDALITVDPHLHRIDRLEQaVPLKRVLSvsSA 143 ************************************.**************999888988876431144 PP TIGR01251 148 klieelkkkelknlvvvsPDkGaverakkvakklglelaiieKeRdskenevevtnllgdvegkdvviv 216 +l+ ++ ++ k+ +++ PD+ + ++++++a+++gl++a+ K+R + ev + + + k vv+v lcl|NCBI__GCF_000008325.1:WP_010960970.1 144 TLVSRYLATDRKEWLLLGPDQESRQWVEAIAAQAGLPCAVASKRRLG-DREVGISLPQEAGAFKGVVLV 211 56666666669***********************************5.54887777777777777**** PP TIGR01251 217 DDiisTggTlvkaaelLkekGAkkvivaathgvfsgdAlerlaeagveevivtntilveekklpkvsei 285 DDi sTg+Tl+++a+lL ++G ++ v++th++f+gdA +rl++agv ++++t++i + +++ lcl|NCBI__GCF_000008325.1:WP_010960970.1 212 DDIASTGTTLAETARLLARAGVARIDVIVTHALFTGDAWSRLKQAGVGAIASTDSISH------PTNRM 274 **********************************************************......88999 PP TIGR01251 286 svapliaeaiar 297 +apl+a+a+++ lcl|NCBI__GCF_000008325.1:WP_010960970.1 275 CLAPLLADAVRK 286 999999999875 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (309 nodes) Target sequences: 1 (289 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: 7.36 // [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