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_012978320.1 AZL_RS31030 ribose-phosphate pyrophosphokinase
Query= curated2:Q8TUT6 (291 letters) >NCBI__GCF_000010725.1:WP_012978320.1 Length = 308 Score = 144 bits (364), Expect = 2e-39 Identities = 98/288 (34%), Positives = 142/288 (49%), Gaps = 7/288 (2%) Query: 8 EGVKLGRRLAEELDAELAPVEEDRFPDGEQIVRVPPELDGTVVVVHSMSPPQDENLVKAI 67 E RRLA L E RFPDGE +VR+P ++ +V S+ P D+ LV+ Sbjct: 21 ESADAARRLAAALGIPCHIAELHRFPDGESLVRLPEPVE-RAIVYRSLDRPNDK-LVELT 78 Query: 68 ITLDAARENGAEEVIAIVPYMAYSRQDRRFEPGEPVSFRAVARAVSANADALITVDLHEP 127 + R GA ++ + PYMAY RQD F PGEPVS V + D + V+ H Sbjct: 79 LAASVLRRQGATDLCLVAPYMAYMRQDAIFRPGEPVSQTVVGDWLGRCFDRFVCVEPHLH 138 Query: 128 GTLKYFDV----PAENVSAAEELGKYLAERFEGEDLVVIGPDEGARELAREVASICGVEY 183 T + +V P+ +S A + +L D V++GPDE + L VA G+ Sbjct: 139 RTHRLDEVFVGRPSVALSGAAPIADHLRAAGVTPDTVIVGPDEESAPLVEAVAGPLGLTG 198 Query: 184 DHLEKKRLSGDEVEIH-PKELDVEGRTVVLVDDMIDTGGTMVEAARALRDQGAGTLYAAC 242 K+R +V + P + + GR VV+VDD+I +G T+ ARA R GA L Sbjct: 199 IVGRKERRGDRDVTVALPPDAPIHGRPVVIVDDVISSGETIFSCARAARILGADELRVYG 258 Query: 243 THALLTRNAATRLLASGFEDIIATDTVPNPFEKVSVAPPVAEAVENLS 290 HAL A R A G E ++ D VP+P +S++ +A+A+ +LS Sbjct: 259 VHALFGEAVAGRFAAEGLEPPLSCDGVPHPTNALSLSGLIADAIRSLS 306 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: 211 Number of extensions: 13 Number of successful extensions: 4 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: 308 Length adjustment: 27 Effective length of query: 264 Effective length of database: 281 Effective search space: 74184 Effective search space used: 74184 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_012978320.1 AZL_RS31030 (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.19642.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 9.3e-49 151.9 0.0 1.1e-48 151.7 0.0 1.0 1 lcl|NCBI__GCF_000010725.1:WP_012978320.1 AZL_RS31030 ribose-phosphate pyr Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000010725.1:WP_012978320.1 AZL_RS31030 ribose-phosphate pyrophosphokinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 151.7 0.0 1.1e-48 1.1e-48 8 298 .. 21 305 .. 16 308 .] 0.93 Alignments for each domain: == domain 1 score: 151.7 bits; conditional E-value: 1.1e-48 TIGR01251 8 sskelaekvaknlglelgdvevkkFadgElyvrieesvrgkdvfiivqstsapvndalmellllidalk 76 +s + a+++a +lg++ +e ++F+dgE vr+ e v +++i+ s nd+l+el l+++ l+ lcl|NCBI__GCF_000010725.1:WP_012978320.1 21 ESADAARRLAAALGIPCHIAELHRFPDGESLVRLPEPV---ERAIVYRSLD-RPNDKLVELTLAASVLR 85 56788999*****************************9...6799966666.69*************** PP TIGR01251 77 rasaksvtaviPyygYaRqdkkaksrepisaklvaklleeaGadrvltvdlHseqiq...gfFd.vpve 141 r++a + +v+Py++Y Rqd ++++ep+s +v++ l dr + v+ H + ++ ++F p lcl|NCBI__GCF_000010725.1:WP_012978320.1 86 RQGATDLCLVAPYMAYMRQDAIFRPGEPVSQTVVGDWLGRC-FDRFVCVEPHLHRTHrldEVFVgRPSV 153 *****************************************.********9987664222788878999 PP TIGR01251 142 nlsaspklieelkkke.lknlvvvsPDkGaverakkvakklglelaiieKeRdskenevevtnllgdve 209 ls++ ++++l++ ++v+v PD+ ++ +++va lgl + +KeR ++ + + + + lcl|NCBI__GCF_000010725.1:WP_012978320.1 154 ALSGAAPIADHLRAAGvTPDTVIVGPDEESAPLVEAVAGPLGLTGIVGRKERRGDRDVTVALPPDAPIH 222 *************988899************************999******988877777899***** PP TIGR01251 210 gkdvvivDDiisTggTlvkaaelLkekGAkkvivaathgvfsgdAlerlaeagveevivtntilveekk 278 g+ vvivDD+is+g T+ a++++ GA + v+ +h++f + + r+a g+e ++++ +++ lcl|NCBI__GCF_000010725.1:WP_012978320.1 223 GRPVVIVDDVISSGETIFSCARAARILGADELRVYGVHALFGEAVAGRFAAEGLEPPLSCDGVPH---- 287 *****************************************************************.... PP TIGR01251 279 lpkvseisvapliaeaiari 298 + +s++ lia+ai++ lcl|NCBI__GCF_000010725.1:WP_012978320.1 288 --PTNALSLSGLIADAIRSL 305 ..999************864 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (309 nodes) Target sequences: 1 (308 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 11.73 // [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