Align ribose-phosphate diphosphokinase (EC 2.7.6.1) (characterized)
to candidate WP_024850401.1 N745_RS0101630 ribose-phosphate pyrophosphokinase
Query= BRENDA::P0A719 (315 letters) >NCBI__GCF_000526715.1:WP_024850401.1 Length = 321 Score = 373 bits (958), Expect = e-108 Identities = 190/312 (60%), Positives = 242/312 (77%), Gaps = 5/312 (1%) Query: 3 DMKLFAGNATPELAQRIANRLYTSLGDAAVGRFSDGEVSVQINENVRGGDIFIIQSTCAP 62 +++LFAGNA LA+ I++ + LG A VGRFSDGE+ VQINE+VRG D++++Q TC P Sbjct: 5 NVRLFAGNANVSLAENISSSIEIPLGKADVGRFSDGEIMVQINESVRGKDVYVLQPTCTP 64 Query: 63 TND-NLMELVVMVDALRRASAGRITAVIPYFGYARQDRRVRSARVPITAKVVADFLSSVG 121 NLMEL+VM+DAL+RASA RITAV+PY+G+ARQDRR SARVPITA++ AD ++ G Sbjct: 65 EPAVNLMELLVMIDALKRASAKRITAVVPYYGFARQDRRPHSARVPITARLAADMITVAG 124 Query: 122 VDRVLTVDLHAEQIQGFFDVPVDNVFGSPILLEDML---QLNLDNPIVVSPDIGGVVRAR 178 DRV+TVDLHA+QIQGFFD+PVDN++GSP L+ DM + D+ +VVSPD+GGVVRAR Sbjct: 125 ADRVITVDLHADQIQGFFDIPVDNIYGSPTLVADMRTSKHIVEDDMMVVSPDMGGVVRAR 184 Query: 179 AIAKLLNDTDMAIIDKRRPRANVSQVMHIIGDVAGRDCVLVDDMIDTGGTLCKAAEALKE 238 A+AK L DMAIIDKRRP+ANV+Q+M+IIGDV GRDC+LVDDM+DT GTLCKAA+AL E Sbjct: 185 AVAKALG-CDMAIIDKRRPKANVAQIMNIIGDVEGRDCILVDDMVDTAGTLCKAAQALIE 243 Query: 239 RGAKRVFAYATHPIFSGNAANNLRNSVIDEVVVCDTIPLSDEIKSLPNVRTLTLSGMLAE 298 GAK V AY H + SG A N+ NSV+ E+VV DTIPLS +R +T++ +L E Sbjct: 244 HGAKSVSAYVVHAVLSGPAVENINNSVLTELVVTDTIPLSAAAIDSDKIRQVTIAPVLGE 303 Query: 299 AIRRISNEESIS 310 IRR+ EES+S Sbjct: 304 TIRRVHQEESVS 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: 315 Number of extensions: 10 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: 321 Length adjustment: 27 Effective length of query: 288 Effective length of database: 294 Effective search space: 84672 Effective search space used: 84672 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_024850401.1 N745_RS0101630 (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.17605.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3e-119 383.5 4.7 3.4e-119 383.3 4.7 1.0 1 lcl|NCBI__GCF_000526715.1:WP_024850401.1 N745_RS0101630 ribose-phosphate Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000526715.1:WP_024850401.1 N745_RS0101630 ribose-phosphate pyrophosphokinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 383.3 4.7 3.4e-119 3.4e-119 2 308 .. 7 318 .. 6 319 .. 0.97 Alignments for each domain: == domain 1 score: 383.3 bits; conditional E-value: 3.4e-119 TIGR01251 2 kilsgssskelaekvaknlglelgdvevkkFadgElyvrieesvrgkdvfiivqstsapvndalmelll 70 ++++g+++ +lae+++ + +++lg+++v +F+dgE++v+i+esvrgkdv++++ ++ ++ +lmell+ lcl|NCBI__GCF_000526715.1:WP_024850401.1 7 RLFAGNANVSLAENISSSIEIPLGKADVGRFSDGEIMVQINESVRGKDVYVLQPTCTPEPAVNLMELLV 75 689*************************************************7777777889******* PP TIGR01251 71 lidalkrasaksvtaviPyygYaRqdkkak.srepisaklvaklleeaGadrvltvdlHseqiqgfFdv 138 +idalkrasak++tav+Pyyg+aRqd++ + r pi+a+l a++++ aGadrv+tvdlH++qiqgfFd+ lcl|NCBI__GCF_000526715.1:WP_024850401.1 76 MIDALKRASAKRITAVVPYYGFARQDRRPHsARVPITARLAADMITVAGADRVITVDLHADQIQGFFDI 144 ***************************97648************************************* PP TIGR01251 139 pvenlsaspklieelkkke...lknlvvvsPDkGaverakkvakklglelaiieKeRdskenevevtnl 204 pv+n+++sp+l+++++ + ++++vvsPD G+v ra++vak+lg+++aii+K+R+ k+n+++++n+ lcl|NCBI__GCF_000526715.1:WP_024850401.1 145 PVDNIYGSPTLVADMRTSKhivEDDMMVVSPDMGGVVRARAVAKALGCDMAIIDKRRP-KANVAQIMNI 212 **************998888899***********************************.899******* PP TIGR01251 205 lgdvegkdvvivDDiisTggTlvkaaelLkekGAkkvivaathgvfsgdAlerlaeagveevivtntil 273 +gdveg+d+++vDD+++T+gTl+kaa++L e+GAk+v ++++h+v+sg+A+e++++++++e++vt+ti+ lcl|NCBI__GCF_000526715.1:WP_024850401.1 213 IGDVEGRDCILVDDMVDTAGTLCKAAQALIEHGAKSVSAYVVHAVLSGPAVENINNSVLTELVVTDTIP 281 ********************************************************************* PP TIGR01251 274 v.ee.kklpkvseisvapliaeaiarihenesvsslf 308 +k++++++ap++ e+i+r+h++esvs+++ lcl|NCBI__GCF_000526715.1:WP_024850401.1 282 LsAAaIDSDKIRQVTIAPVLGETIRRVHQEESVSEIM 318 *6557999**************************985 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (309 nodes) Target sequences: 1 (321 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: 6.74 // [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