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_013403879.1 CALKRO_RS10070 ribose-phosphate diphosphokinase
Query= SwissProt::P14193 (317 letters) >NCBI__GCF_000166775.1:WP_013403879.1 Length = 325 Score = 406 bits (1043), Expect = e-118 Identities = 200/310 (64%), Positives = 250/310 (80%), Gaps = 1/310 (0%) Query: 8 KNLKIFSLNSNPELAKEIADIVGVQLGKCSVTRFSDGEVQINIEESIRGCDCYIIQSTSD 67 K +KIF+ NSN ELA+EIA +G +LG + RFSDGE+ + I E++RG D +++QST Sbjct: 6 KEIKIFTGNSNKELAEEIASHLGKKLGDAEIGRFSDGEISVRINETVRGADVFVVQSTCH 65 Query: 68 PVNEHIMELLIMVDALKRASAKTINIVIPYYGYARQDRKARSREPITAKLFANLLETAGA 127 PVNE++MELLIM+DA KRASA I VIPYYGYARQDRKAR+R+PITAKL ANL+ +AGA Sbjct: 66 PVNENLMELLIMIDAFKRASAGRITAVIPYYGYARQDRKARARDPITAKLVANLITSAGA 125 Query: 128 TRVIALDLHAPQIQGFFDIPIDHLMGVPILGEYF-EGKNLEDIVIVSPDHGGVTRARKLA 186 RV+ +DLHAPQIQGFFDIP+DHL+GVPIL +YF E NLE+ V+VSPD G VTRAR A Sbjct: 126 DRVLTMDLHAPQIQGFFDIPLDHLIGVPILAKYFMENVNLENAVVVSPDLGSVTRARNFA 185 Query: 187 DRLKAPIAIIDKRRPRPNVAEVMNIVGNIEGKTAILIDDIIDTAGTITLAANALVENGAK 246 +L P+AI+DKRRP+ NVAE+MNI+G+++ KT +++DD+IDTAGTI AA AL++ GAK Sbjct: 186 TKLDLPLAIVDKRRPKANVAEIMNIIGDVKDKTCLMVDDMIDTAGTIVAAAQALMDYGAK 245 Query: 247 EVYACCTHPVLSGPAVERINNSTIKELVVTNSIKLPEEKKIERFKQLSVGPLLAEAIIRV 306 EVYACCTHPVLSGPAVERI S IKELVV N+I LP EK+I++ K LSV L AEAI R+ Sbjct: 246 EVYACCTHPVLSGPAVERIQQSPIKELVVLNTIPLPPEKRIDKIKVLSVASLFAEAITRI 305 Query: 307 HEQQSVSYLF 316 +E ++S LF Sbjct: 306 YEDVAISTLF 315 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: 305 Number of extensions: 10 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: 325 Length adjustment: 28 Effective length of query: 289 Effective length of database: 297 Effective search space: 85833 Effective search space used: 85833 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_013403879.1 CALKRO_RS10070 (ribose-phosphate diphosphokinase)
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.2018066.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.2e-133 429.9 0.7 2.4e-133 429.7 0.7 1.0 1 NCBI__GCF_000166775.1:WP_013403879.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000166775.1:WP_013403879.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 429.7 0.7 2.4e-133 2.4e-133 1 309 [] 8 316 .. 8 316 .. 0.99 Alignments for each domain: == domain 1 score: 429.7 bits; conditional E-value: 2.4e-133 TIGR01251 1 lkilsgssskelaekvaknlglelgdvevkkFadgElyvrieesvrgkdvfiivqstsapvndalmellllid 73 +ki+ g+s+kelae++a +lg +lgd+e+ +F+dgE++vri+e+vrg dvf++ qst++pvn++lmell++id NCBI__GCF_000166775.1:WP_013403879.1 8 IKIFTGNSNKELAEEIASHLGKKLGDAEIGRFSDGEISVRINETVRGADVFVV-QSTCHPVNENLMELLIMID 79 589**************************************************.9****************** PP TIGR01251 74 alkrasaksvtaviPyygYaRqdkkaksrepisaklvaklleeaGadrvltvdlHseqiqgfFdvpvenlsas 146 a+krasa+++taviPyygYaRqd+ka+ r+pi+aklva+l+++aGadrvlt+dlH++qiqgfFd+p+++l + NCBI__GCF_000166775.1:WP_013403879.1 80 AFKRASAGRITAVIPYYGYARQDRKARARDPITAKLVANLITSAGADRVLTMDLHAPQIQGFFDIPLDHLIGV 152 ************************************************************************* PP TIGR01251 147 pklieelkkke.lknlvvvsPDkGaverakkvakklglelaiieKeRdskenevevtnllgdvegkdvvivDD 218 p l++++ +++ l+n vvvsPD G+v+ra+++a+kl+l+lai++K+R+ k+n++e++n++gdv++k++++vDD NCBI__GCF_000166775.1:WP_013403879.1 153 PILAKYFMENVnLENAVVVSPDLGSVTRARNFATKLDLPLAIVDKRRP-KANVAEIMNIIGDVKDKTCLMVDD 224 *********999************************************.899********************* PP TIGR01251 219 iisTggTlvkaaelLkekGAkkvivaathgvfsgdAlerlaeagveevivtntilv.eekklpkvseisvapl 290 +i+T+gT+v+aa++L + GAk+v++++th+v+sg+A+er++++ ++e++v nti+ ek+++k++++sva l NCBI__GCF_000166775.1:WP_013403879.1 225 MIDTAGTIVAAAQALMDYGAKEVYACCTHPVLSGPAVERIQQSPIKELVVLNTIPLpPEKRIDKIKVLSVASL 297 ********************************************************999************** PP TIGR01251 291 iaeaiarihenesvsslfd 309 +aeai+ri+e+ ++s+lfd NCBI__GCF_000166775.1:WP_013403879.1 298 FAEAITRIYEDVAISTLFD 316 *****************96 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (309 nodes) Target sequences: 1 (325 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: 22.44 // [ok]
This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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