Align acetylglutamate kinase (EC 2.7.2.8) (characterized)
to candidate WP_013840421.1 DESRU_RS01820 acetylglutamate kinase
Query= BRENDA::Q9HTN2 (301 letters) >NCBI__GCF_000215085.1:WP_013840421.1 Length = 285 Score = 311 bits (798), Expect = 9e-90 Identities = 158/289 (54%), Positives = 220/289 (76%), Gaps = 15/289 (5%) Query: 12 AKVLSEALPYIRRFVGKTLVIKYGGNAMESEELKAGFARDVVLMKAVGINPVVVHGGGPQ 71 A VL EALPYI++F GKT+VIKYGG+AM +++LK D+VLMK VGI+PVVVHGGGP+ Sbjct: 7 AGVLVEALPYIKKFYGKTVVIKYGGHAMINDQLKQAVVTDLVLMKFVGIHPVVVHGGGPE 66 Query: 72 IGDLLKRLSIESHFIDGMRVTDAATMDVVEMVLGGQVNKDIVNLINRHGGSAIGLTGKDA 131 I +LKRL IES F+ G+RVTD+ TM+VVEMVL G++NK+I +LINR GG +GL+GKDA Sbjct: 67 ITGMLKRLGIESQFVGGLRVTDSPTMEVVEMVL-GKLNKEITSLINRLGGRGVGLSGKDA 125 Query: 132 EL-IRAKKLTVTRQTPEMTKPEIIDIGHVGEVTGVNVGLLNMLVKGDFIPVIAPIGVGSN 190 L I AKKL +Q DIG VGEVT +N GL+ ++K +IP+I+P+GVG + Sbjct: 126 NLIIAAKKLGGEQQ----------DIGFVGEVTEINPGLVETVLKEGYIPIISPVGVGRD 175 Query: 191 GESYNINADLVAGKVAEALKAEKLMLLTNIAGLMDKQ---GQVLTGLSTEQVNELIADGT 247 GESYNINAD VAG +A+ALKA+KL++LT++ G+++ + +L+ + + + L+ G Sbjct: 176 GESYNINADYVAGAMAKALKADKLIILTDVEGILENRHDPSSLLSTIKVQDIPALVDRGV 235 Query: 248 IYGGMLPKIRCALEAVQGGVTSAHIIDGRVPNAVLLEIFTDSGVGTLIS 296 + GGMLPK+ C +EA++GGV S HI+DGRVP+++LLE+FTD G+GT+++ Sbjct: 236 LQGGMLPKVDCCVEAIRGGVNSTHILDGRVPHSILLEVFTDQGIGTMVA 284 Lambda K H 0.318 0.138 0.381 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: 310 Number of extensions: 14 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: 301 Length of database: 285 Length adjustment: 26 Effective length of query: 275 Effective length of database: 259 Effective search space: 71225 Effective search space used: 71225 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 48 (23.1 bits)
Align candidate WP_013840421.1 DESRU_RS01820 (acetylglutamate kinase)
to HMM TIGR00761 (argB: acetylglutamate kinase (EC 2.7.2.8))
# 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/TIGR00761.hmm # target sequence database: /tmp/gapView.20864.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00761 [M=231] Accession: TIGR00761 Description: argB: acetylglutamate kinase 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-81 257.7 3.2 5.5e-81 257.5 3.2 1.0 1 lcl|NCBI__GCF_000215085.1:WP_013840421.1 DESRU_RS01820 acetylglutamate ki Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000215085.1:WP_013840421.1 DESRU_RS01820 acetylglutamate kinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 257.5 3.2 5.5e-81 5.5e-81 1 231 [] 24 260 .. 24 260 .. 0.97 Alignments for each domain: == domain 1 score: 257.5 bits; conditional E-value: 5.5e-81 TIGR00761 1 tiViKiGGaais..elleelakdiaklrkegiklvivHGGgpeinelleklgievefvnglRvTdketl 67 t+ViK+GG+a+ +l+++++ d++ ++ +gi++v+vHGGgpei+ +l++lgie +fv+glRvTd t+ lcl|NCBI__GCF_000215085.1:WP_013840421.1 24 TVVIKYGGHAMIndQLKQAVVTDLVLMKFVGIHPVVVHGGGPEITGMLKRLGIESQFVGGLRVTDSPTM 92 69*********9889****************************************************** PP TIGR00761 68 evvemvligkvnkelvallekhgikavGltgkDgqlltae...kldkedlgyvGeikkvnkelleallk 133 evvemvl + nke++ l+++ g + vGl+gkD++l++a +++d+g+vGe++++n+ l+e++lk lcl|NCBI__GCF_000215085.1:WP_013840421.1 93 EVVEMVLGK-LNKEITSLINRLGGRGVGLSGKDANLIIAAkklGGEQQDIGFVGEVTEINPGLVETVLK 160 ******966.***************************999633335669******************** PP TIGR00761 134 agiipviaslaldeegqllNvnaDtaAaelAaaleAekLvlLtdvaGileg..dkksliseleleeieq 200 +g+ip+i+++++ +g+ +N+naD +A+++A+al+A+kL++Ltdv+Gile+ d +sl+s +++++i lcl|NCBI__GCF_000215085.1:WP_013840421.1 161 EGYIPIISPVGVGRDGESYNINADYVAGAMAKALKADKLIILTDVEGILENrhDPSSLLSTIKVQDIPA 229 **************************************************9999*************** PP TIGR00761 201 likqavikgGmipKveaalealesgvkkvvi 231 l+ +v++gGm pKv++++ea+++gv++ +i lcl|NCBI__GCF_000215085.1:WP_013840421.1 230 LVDRGVLQGGMLPKVDCCVEAIRGGVNSTHI 260 ***************************9998 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (231 nodes) Target sequences: 1 (285 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: 11.31 // [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