Align ribose-phosphate diphosphokinase (EC 2.7.6.1) (characterized)
to candidate WP_029134777.1 A3GO_RS0119195 ribose-phosphate pyrophosphokinase
Query= BRENDA::P0A719 (315 letters) >NCBI__GCF_000428045.1:WP_029134777.1 Length = 317 Score = 393 bits (1009), Expect = e-114 Identities = 193/315 (61%), Positives = 252/315 (80%), Gaps = 2/315 (0%) Query: 1 MPD--MKLFAGNATPELAQRIANRLYTSLGDAAVGRFSDGEVSVQINENVRGGDIFIIQS 58 MPD M +F+GN+ PEL I +RL G A VGRFSDGE +I E+VRG D+++IQS Sbjct: 1 MPDSHMMVFSGNSNPELVSEITSRLSLRTGRAVVGRFSDGEAMAEIQESVRGRDVYVIQS 60 Query: 59 TCAPTNDNLMELVVMVDALRRASAGRITAVIPYFGYARQDRRVRSARVPITAKVVADFLS 118 T PTNDNLMEL+V++DALR ASA RITAVIPYFGYARQDRR RSARVPITA++VA ++ Sbjct: 61 TSQPTNDNLMELLVLIDALRWASAERITAVIPYFGYARQDRRPRSARVPITARLVAKQIA 120 Query: 119 SVGVDRVLTVDLHAEQIQGFFDVPVDNVFGSPILLEDMLQLNLDNPIVVSPDIGGVVRAR 178 + G DRV+TVDLHA+QIQGFFD+PVDN++ P+LL D+ + N +VVSPD+GGVVRAR Sbjct: 121 AAGADRVVTVDLHADQIQGFFDIPVDNIYALPVLLGDVWRQKYPNLMVVSPDVGGVVRAR 180 Query: 179 AIAKLLNDTDMAIIDKRRPRANVSQVMHIIGDVAGRDCVLVDDMIDTGGTLCKAAEALKE 238 A+AK L+D D+AIIDKRRP+AN +QVM+IIGDV GR CVL+DDM+DT GTLCKAA+ALK+ Sbjct: 181 ALAKQLDDADLAIIDKRRPKANDAQVMNIIGDVKGRTCVLIDDMVDTAGTLCKAAQALKD 240 Query: 239 RGAKRVFAYATHPIFSGNAANNLRNSVIDEVVVCDTIPLSDEIKSLPNVRTLTLSGMLAE 298 RGA++V AY THP+ SG A +N+ NSV+D++VV +TI L +E + +R + ++ +LAE Sbjct: 241 RGAEQVIAYCTHPVLSGPAIHNIENSVLDQLVVSNTIQLHEEARHCTRIRQICIAELLAE 300 Query: 299 AIRRISNEESISAMF 313 +RRI+ ES++++F Sbjct: 301 TMRRIALNESVTSLF 315 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: 311 Number of extensions: 6 Number of successful extensions: 1 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: 317 Length adjustment: 27 Effective length of query: 288 Effective length of database: 290 Effective search space: 83520 Effective search space used: 83520 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_029134777.1 A3GO_RS0119195 (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.28166.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.7e-121 389.7 0.3 4.2e-121 389.6 0.3 1.0 1 lcl|NCBI__GCF_000428045.1:WP_029134777.1 A3GO_RS0119195 ribose-phosphate Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000428045.1:WP_029134777.1 A3GO_RS0119195 ribose-phosphate pyrophosphokinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 389.6 0.3 4.2e-121 4.2e-121 1 308 [. 6 315 .. 6 316 .. 0.98 Alignments for each domain: == domain 1 score: 389.6 bits; conditional E-value: 4.2e-121 TIGR01251 1 lkilsgssskelaekvaknlglelgdvevkkFadgElyvrieesvrgkdvfiivqstsapvndalmell 69 ++++sg+s++el +++ +l+l+ g++ v +F+dgE + +i+esvrg+dv++i qsts+p+nd+lmell lcl|NCBI__GCF_000428045.1:WP_029134777.1 6 MMVFSGNSNPELVSEITSRLSLRTGRAVVGRFSDGEAMAEIQESVRGRDVYVI-QSTSQPTNDNLMELL 73 79***************************************************.*************** PP TIGR01251 70 llidalkrasaksvtaviPyygYaRqdkkak.srepisaklvaklleeaGadrvltvdlHseqiqgfFd 137 +lidal+ asa+++taviPy+gYaRqd++ + r pi+a+lvak +++aGadrv+tvdlH++qiqgfFd lcl|NCBI__GCF_000428045.1:WP_029134777.1 74 VLIDALRWASAERITAVIPYFGYARQDRRPRsARVPITARLVAKQIAAAGADRVVTVDLHADQIQGFFD 142 ****************************97758************************************ PP TIGR01251 138 vpvenlsaspklieelkkkelknlvvvsPDkGaverakkvakklg.lelaiieKeRdskenevevtnll 205 +pv+n++a p+l+ ++ +++ nl+vvsPD G+v ra+++ak+l+ ++laii+K+R+ k+n+++v+n++ lcl|NCBI__GCF_000428045.1:WP_029134777.1 143 IPVDNIYALPVLLGDVWRQKYPNLMVVSPDVGGVVRARALAKQLDdADLAIIDKRRP-KANDAQVMNII 210 *********************************************9***********.899******** PP TIGR01251 206 gdvegkdvvivDDiisTggTlvkaaelLkekGAkkvivaathgvfsgdAlerlaeagveevivtntilv 274 gdv+g+++v++DD+++T+gTl+kaa++Lk++GA++vi+++th+v+sg+A+++++++++++++v+nti+ lcl|NCBI__GCF_000428045.1:WP_029134777.1 211 GDVKGRTCVLIDDMVDTAGTLCKAAQALKDRGAEQVIAYCTHPVLSGPAIHNIENSVLDQLVVSNTIQL 279 ********************************************************************9 PP TIGR01251 275 .ee.kklpkvseisvapliaeaiarihenesvsslf 308 ee +++ ++++i +a+l+ae+++ri+ nesv+slf lcl|NCBI__GCF_000428045.1:WP_029134777.1 280 hEEaRHCTRIRQICIAELLAETMRRIALNESVTSLF 315 7778*******************************9 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (309 nodes) Target sequences: 1 (317 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: 00:00:00.01 # Mc/sec: 7.56 // [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