Align ribose-phosphate diphosphokinase (EC 2.7.6.1) (characterized)
to candidate WP_013554179.1 NITSA_RS06260 ribose-phosphate pyrophosphokinase
Query= BRENDA::P0A719 (315 letters) >NCBI__GCF_000186245.1:WP_013554179.1 Length = 311 Score = 348 bits (892), Expect = e-100 Identities = 176/313 (56%), Positives = 229/313 (73%), Gaps = 5/313 (1%) Query: 1 MPDMKLFAGNATPELAQRIANRLYTSLGDAAVGRFSDGEVSVQINENVRGGDIFIIQSTC 60 M + LF+G A P L+Q IA+ L L A + RFSDGE++VQI E+VRG D+FIIQ TC Sbjct: 1 MSNYMLFSGTANPPLSQAIADYLEMPLSGATINRFSDGEINVQIAESVRGKDVFIIQPTC 60 Query: 61 APTNDNLMELVVMVDALRRASAGRITAVIPYFGYARQDRRVRSARVPITAKVVADFLSSV 120 AP N NLMEL++M DAL+R+SA ITAV+PY+GYARQDR+ + RVPITAK+VAD + Sbjct: 61 APANANLMELLIMTDALKRSSAKSITAVVPYYGYARQDRKA-APRVPITAKLVADMMEKA 119 Query: 121 GVDRVLTVDLHAEQIQGFFDVPVDNVFGSPILLEDMLQLNLDNPIVVSPDIGGVVRARAI 180 G+ RV+TVDLHA QIQGFFD+PVDN++GS + ++ + N NPI+ SPDIGGV RAR Sbjct: 120 GITRVVTVDLHASQIQGFFDIPVDNLYGSILFIDYIRSKNFANPIIASPDIGGVARARYF 179 Query: 181 AKLLNDTDMAIIDKRRPRANVSQVMHIIGDVAGRDCVLVDDMIDTGGTLCKAAEALKERG 240 A L DM I+DKRR +ANV++VM+IIGDV GRD +L+DDM+DT GT+ K A ALKE G Sbjct: 180 ASRLG-MDMVIVDKRREKANVAEVMNIIGDVRGRDVILIDDMVDTAGTMVKGAAALKEAG 238 Query: 241 AKRVFAYATHPIFSGNAANNLRNSVIDEVVVCDTIPLSDEIKSLPNVRTLTLSGMLAEAI 300 A V A THP+ SG A + +R+ +DE+VV DTIPL E K ++ L+ + ML E I Sbjct: 239 ATSVMACCTHPVLSGPAIDRIRDGALDELVVSDTIPLKAECK---KIKVLSTAQMLGEVI 295 Query: 301 RRISNEESISAMF 313 RR+ N ES++++F Sbjct: 296 RRVQNNESVNSLF 308 Lambda K H 0.321 0.137 0.385 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: 260 Number of extensions: 11 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 315 Length of database: 311 Length adjustment: 27 Effective length of query: 288 Effective length of database: 284 Effective search space: 81792 Effective search space used: 81792 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 (21.9 bits) S2: 48 (23.1 bits)
Align candidate WP_013554179.1 NITSA_RS06260 (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.8944.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.8e-128 412.4 0.6 5.5e-128 412.2 0.6 1.0 1 lcl|NCBI__GCF_000186245.1:WP_013554179.1 NITSA_RS06260 ribose-phosphate p Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000186245.1:WP_013554179.1 NITSA_RS06260 ribose-phosphate pyrophosphokinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 412.2 0.6 5.5e-128 5.5e-128 1 308 [. 4 308 .. 4 309 .. 0.99 Alignments for each domain: == domain 1 score: 412.2 bits; conditional E-value: 5.5e-128 TIGR01251 1 lkilsgssskelaekvaknlglelgdvevkkFadgElyvrieesvrgkdvfiivqstsapvndalmell 69 ++++sg++++ l++++a++l+++l +++++F+dgE++v+i+esvrgkdvfii q t+ap n +lmell lcl|NCBI__GCF_000186245.1:WP_013554179.1 4 YMLFSGTANPPLSQAIADYLEMPLSGATINRFSDGEINVQIAESVRGKDVFII-QPTCAPANANLMELL 71 589**************************************************.*************** PP TIGR01251 70 llidalkrasaksvtaviPyygYaRqdkkaksrepisaklvaklleeaGadrvltvdlHseqiqgfFdv 138 +++dalkr+saks+tav+PyygYaRqd+ka +r pi+aklva+++e+aG++rv+tvdlH++qiqgfFd+ lcl|NCBI__GCF_000186245.1:WP_013554179.1 72 IMTDALKRSSAKSITAVVPYYGYARQDRKAAPRVPITAKLVADMMEKAGITRVVTVDLHASQIQGFFDI 140 ********************************************************************* PP TIGR01251 139 pvenlsaspklieelkkkelknlvvvsPDkGaverakkvakklglelaiieKeRdskenevevtnllgd 207 pv+nl++s +i+++++k+ n+++ sPD G+v+ra+ +a++lg++++i++K+R+ k+n++ev+n++gd lcl|NCBI__GCF_000186245.1:WP_013554179.1 141 PVDNLYGSILFIDYIRSKNFANPIIASPDIGGVARARYFASRLGMDMVIVDKRRE-KANVAEVMNIIGD 208 *******************************************************.899********** PP TIGR01251 208 vegkdvvivDDiisTggTlvkaaelLkekGAkkvivaathgvfsgdAlerlaeagveevivtntilvee 276 v g+dv+++DD+++T+gT+vk+a +Lke+GA++v++++th+v+sg+A+ r++ ++e++v++ti+ + lcl|NCBI__GCF_000186245.1:WP_013554179.1 209 VRGRDVILIDDMVDTAGTMVKGAAALKEAGATSVMACCTHPVLSGPAIDRIRDGALDELVVSDTIPL-K 276 *******************************************************************.8 PP TIGR01251 277 kklpkvseisvapliaeaiarihenesvsslf 308 +++k++++s a+++ e+i+r+++nesv+slf lcl|NCBI__GCF_000186245.1:WP_013554179.1 277 AECKKIKVLSTAQMLGEVIRRVQNNESVNSLF 308 99*****************************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: 00:00:00.00 # Mc/sec: 9.64 // [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