Align ribose-phosphate diphosphokinase (EC 2.7.6.1) (characterized)
to candidate WP_011373254.1 SUDEN_RS08525 ribose-phosphate pyrophosphokinase
Query= BRENDA::P0A719 (315 letters) >NCBI__GCF_000012965.1:WP_011373254.1 Length = 308 Score = 325 bits (834), Expect = 7e-94 Identities = 166/313 (53%), Positives = 226/313 (72%), Gaps = 6/313 (1%) Query: 1 MPDMKLFAGNATPELAQRIANRLYTSLGDAAVGRFSDGEVSVQINENVRGGDIFIIQSTC 60 M K+FAG+A+ E A+ + L L A V +FSDGE+SVQI E+VRG D+FIIQST Sbjct: 1 MRGYKIFAGSASVEFAKEVCQILDVPLAKATVKKFSDGEISVQIAESVRGRDVFIIQSTG 60 Query: 61 APTNDNLMELVVMVDALRRASAGRITAVIPYFGYARQDRRVRSARVPITAKVVADFLSSV 120 AP+NDNLMEL++M DALRR+SA ITAV+PY+GYARQDR+ + RVPITA++VAD + Sbjct: 61 APSNDNLMELLIMTDALRRSSASSITAVVPYYGYARQDRKA-APRVPITARLVADMYEAA 119 Query: 121 GVDRVLTVDLHAEQIQGFFDVPVDNVFGSPILLEDMLQLNLDNPIVVSPDIGGVVRARAI 180 G+DRV+T+DLHA QIQGFF++PVDN++GS + NL NPI+ SPDIGGV RAR Sbjct: 120 GIDRVVTIDLHAGQIQGFFNIPVDNLYGSVTFENYIRSKNLKNPIIASPDIGGVARARYF 179 Query: 181 AKLLNDTDMAIIDKRRPRANVSQVMHIIGDVAGRDCVLVDDMIDTGGTLCKAAEALKERG 240 A + DM I+DKRR +AN S+VM+IIG+V G+D +++DDM+DT GT+ KAA ALK +G Sbjct: 180 ASRMG-LDMVIVDKRREKANESEVMNIIGNVEGKDVIMIDDMVDTAGTMIKAATALKNKG 238 Query: 241 AKRVFAYATHPIFSGNAANNLRNSVIDEVVVCDTIPLSDEIKSLPNVRTLTLSGMLAEAI 300 A V A ATH + SG A N+ N +DE+++ +T+ E K + LT++ + AE I Sbjct: 239 ASSVMACATHAVLSGKAYENIENGELDELIITNTL----ESKPHKKIIVLTVAPLFAEVI 294 Query: 301 RRISNEESISAMF 313 RR+ + ES++++F Sbjct: 295 RRVYHNESVNSLF 307 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: 269 Number of extensions: 11 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: 315 Length of database: 308 Length adjustment: 27 Effective length of query: 288 Effective length of database: 281 Effective search space: 80928 Effective search space used: 80928 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_011373254.1 SUDEN_RS08525 (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.24653.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.9e-126 407.1 3.4 2.1e-126 407.0 3.4 1.0 1 lcl|NCBI__GCF_000012965.1:WP_011373254.1 SUDEN_RS08525 ribose-phosphate p Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000012965.1:WP_011373254.1 SUDEN_RS08525 ribose-phosphate pyrophosphokinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 407.0 3.4 2.1e-126 2.1e-126 1 308 [. 4 307 .. 4 308 .] 0.99 Alignments for each domain: == domain 1 score: 407.0 bits; conditional E-value: 2.1e-126 TIGR01251 1 lkilsgssskelaekvaknlglelgdvevkkFadgElyvrieesvrgkdvfiivqstsapvndalmell 69 +ki++gs+s e+a++v++ l+++l +++vkkF+dgE++v+i+esvrg+dvfii qst ap nd+lmell lcl|NCBI__GCF_000012965.1:WP_011373254.1 4 YKIFAGSASVEFAKEVCQILDVPLAKATVKKFSDGEISVQIAESVRGRDVFII-QSTGAPSNDNLMELL 71 589**************************************************.99999********** PP TIGR01251 70 llidalkrasaksvtaviPyygYaRqdkkaksrepisaklvaklleeaGadrvltvdlHseqiqgfFdv 138 +++dal+r+sa+s+tav+PyygYaRqd+ka +r pi+a+lva+++e+aG+drv+t+dlH+ qiqgfF++ lcl|NCBI__GCF_000012965.1:WP_011373254.1 72 IMTDALRRSSASSITAVVPYYGYARQDRKAAPRVPITARLVADMYEAAGIDRVVTIDLHAGQIQGFFNI 140 ********************************************************************* PP TIGR01251 139 pvenlsaspklieelkkkelknlvvvsPDkGaverakkvakklglelaiieKeRdskenevevtnllgd 207 pv+nl++s ++ +++++k+lkn+++ sPD G+v+ra+ +a+++gl+++i++K+R+ k+ne ev+n++g+ lcl|NCBI__GCF_000012965.1:WP_011373254.1 141 PVDNLYGSVTFENYIRSKNLKNPIIASPDIGGVARARYFASRMGLDMVIVDKRRE-KANESEVMNIIGN 208 *******************************************************.899********** PP TIGR01251 208 vegkdvvivDDiisTggTlvkaaelLkekGAkkvivaathgvfsgdAlerlaeagveevivtntilvee 276 vegkdv+++DD+++T+gT++kaa++Lk+kGA++v+++ath+v+sg+A+e++++ ++e+i+tnt+++ lcl|NCBI__GCF_000012965.1:WP_011373254.1 209 VEGKDVIMIDDMVDTAGTMIKAATALKNKGASSVMACATHAVLSGKAYENIENGELDELIITNTLES-- 275 *******************************************************************.. PP TIGR01251 277 kklpkvseisvapliaeaiarihenesvsslf 308 k +k+ +++vapl+ae+i+r+++nesv+slf lcl|NCBI__GCF_000012965.1:WP_011373254.1 276 KPHKKIIVLTVAPLFAEVIRRVYHNESVNSLF 307 8899***************************9 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 8.57 // [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