Align acetylglutamate kinase (EC 2.7.2.8) (characterized)
to candidate WP_092054505.1 BQ4888_RS05155 acetylglutamate kinase
Query= BRENDA::Q9HTN2 (301 letters) >NCBI__GCF_900111775.1:WP_092054505.1 Length = 292 Score = 355 bits (910), Expect = e-103 Identities = 180/289 (62%), Positives = 224/289 (77%), Gaps = 1/289 (0%) Query: 7 DAAQVAKVLSEALPYIRRFVGKTLVIKYGGNAMESEELKAGFARDVVLMKAVGINPVVVH 66 D A VL EALPY++RF G T+VIKYGG+AM E+LK FARDVVL+K +G+NPV+VH Sbjct: 3 DLINKANVLMEALPYLKRFAGTTIVIKYGGHAMADEKLKESFARDVVLLKYIGLNPVIVH 62 Query: 67 GGGPQIGDLLKRLSIESHFIDGMRVTDAATMDVVEMVLGGQVNKDIVNLINRHGGSAIGL 126 GGGPQI + LK+ I S F+ GMRVTDAATM VVEMVL GQVNK++V LINRHGG A+GL Sbjct: 63 GGGPQINETLKKYGIVSEFVRGMRVTDAATMGVVEMVLVGQVNKEVVGLINRHGGRAVGL 122 Query: 127 TGKDAELIRAKKLTVTRQTPEMTKPEIIDIGHVGEVTGVNVGLLNMLVKGDFIPVIAPIG 186 +GKD EL+ A+K+ + E E +DIG VG+V VN L++ L +G FIPVIAP+G Sbjct: 123 SGKDGELLLAEKM-LQEVRQEDGSVEQVDIGFVGDVIHVNQALIDTLEQGKFIPVIAPVG 181 Query: 187 VGSNGESYNINADLVAGKVAEALKAEKLMLLTNIAGLMDKQGQVLTGLSTEQVNELIADG 246 VG+ GESYNINAD+VAG+VA ALKAEKL+LLT++ G+ DKQG +LTG+S ++ LI+D Sbjct: 182 VGAGGESYNINADVVAGRVAAALKAEKLILLTDVQGVKDKQGNLLTGISVGEMRRLISDE 241 Query: 247 TIYGGMLPKIRCALEAVQGGVTSAHIIDGRVPNAVLLEIFTDSGVGTLI 295 +I GGM+PK+ C +A+ GGV AHIIDGRV +AVLLEIFTD GVGT I Sbjct: 242 SIVGGMIPKVECCADALAGGVKKAHIIDGRVEHAVLLEIFTDKGVGTEI 290 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: 335 Number of extensions: 11 Number of successful extensions: 2 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: 292 Length adjustment: 26 Effective length of query: 275 Effective length of database: 266 Effective search space: 73150 Effective search space used: 73150 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_092054505.1 BQ4888_RS05155 (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.9882.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.1e-80 256.5 7.9 1.3e-80 256.2 7.9 1.0 1 lcl|NCBI__GCF_900111775.1:WP_092054505.1 BQ4888_RS05155 acetylglutamate k Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_900111775.1:WP_092054505.1 BQ4888_RS05155 acetylglutamate kinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 256.2 7.9 1.3e-80 1.3e-80 1 231 [] 25 267 .. 25 267 .. 0.98 Alignments for each domain: == domain 1 score: 256.2 bits; conditional E-value: 1.3e-80 TIGR00761 1 tiViKiGGaais..elleelakdiaklrkegiklvivHGGgpeinelleklgievefvnglRvTdketl 67 tiViK+GG+a+ +l+e++a+d++ l+ g+++vivHGGgp+ine l+k gi efv g+RvTd++t+ lcl|NCBI__GCF_900111775.1:WP_092054505.1 25 TIVIKYGGHAMAdeKLKESFARDVVLLKYIGLNPVIVHGGGPQINETLKKYGIVSEFVRGMRVTDAATM 93 69*********9989****************************************************** PP TIGR00761 68 evvemvligkvnkelvallekhgikavGltgkDgqlltaekldke...........dlgyvGeikkvnk 125 vvemvl+g+vnke+v l+++hg +avGl+gkDg+ll aek+ +e d+g+vG++ +vn+ lcl|NCBI__GCF_900111775.1:WP_092054505.1 94 GVVEMVLVGQVNKEVVGLINRHGGRAVGLSGKDGELLLAEKMLQEvrqedgsveqvDIGFVGDVIHVNQ 162 ****************************************9988889999******************* PP TIGR00761 126 elleallkagiipviaslaldeegqllNvnaDtaAaelAaaleAekLvlLtdvaGilegdkkslisele 194 +l+++l + +ipvia++++ + g+ +N+naD++A+ +Aaal+AekL+lLtdv+G+ ++ + +l++ ++ lcl|NCBI__GCF_900111775.1:WP_092054505.1 163 ALIDTLEQGKFIPVIAPVGVGAGGESYNINADVVAGRVAAALKAEKLILLTDVQGVKDK-QGNLLTGIS 230 ***********************************************************.555****** PP TIGR00761 195 leeieqlikqavikgGmipKveaalealesgvkkvvi 231 + e+++li+ + i gGmipKve++++al++gvkk++i lcl|NCBI__GCF_900111775.1:WP_092054505.1 231 VGEMRRLISDESIVGGMIPKVECCADALAGGVKKAHI 267 ***********************************98 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (231 nodes) Target sequences: 1 (292 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: 9.56 // [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