Align acetylglutamate kinase (EC 2.7.2.8) (characterized)
to candidate 206911 DVU1466 acetylglutamate kinase
Query= BRENDA::Q9HTN2 (301 letters) >MicrobesOnline__882:206911 Length = 308 Score = 332 bits (850), Expect = 9e-96 Identities = 167/294 (56%), Positives = 226/294 (76%), Gaps = 2/294 (0%) Query: 6 DDAAQVAKVLSEALPYIRRFVGKTLVIKYGGNAMESEELKAGFARDVVLMKAVGINPVVV 65 ++A +KVL E+LPY+R+F G+T+VIKYGG+AM+ E LK FA +V L+K VGINPV+V Sbjct: 5 ENARLQSKVLIESLPYLRQFHGETVVIKYGGHAMKDEALKKAFALNVALLKLVGINPVIV 64 Query: 66 HGGGPQIGDLLKRLSIESHFIDGMRVTDAATMDVVEMVLGGQVNKDIVNLINRHGGSAIG 125 HGGGPQIG +L++L+I+SHF +G+RVTD ATMDVVEMVL G+VNK+IVN +N G A+G Sbjct: 65 HGGGPQIGKMLEQLNIQSHFREGLRVTDDATMDVVEMVLVGKVNKEIVNQMNLAGAKAVG 124 Query: 126 LTGKDAELIRAKKLTVTRQTPEMTKPEIIDIGHVGEVTGVNVGLLNMLVKGDFIPVIAPI 185 L+GKD LIRA+K+ + + E PEIID+G VGEV GVN LL L + F+PVIAP+ Sbjct: 125 LSGKDGMLIRARKMEMV-ISKEAQAPEIIDLGKVGEVMGVNTTLLRSLERDGFVPVIAPV 183 Query: 186 GVGSNGESYNINADLVAGKVAEALKAEKLMLLTNIAGLMDKQGQVLTGLSTEQVNELIAD 245 GV NGE+YNINAD VAG VA ALKA++L+LLT++AG++D +++ ++ + L +D Sbjct: 184 GVDDNGETYNINADAVAGAVAAALKAKRLLLLTDVAGILDHDKKLIRSVNMREAVNLFSD 243 Query: 246 GTIYGGMLPKIRCALEAVQGGVTSAHIIDGRVPNAVLLEIFTDSGVGT-LISNR 298 GT+ GGM+PK++C LEA++ GV A IIDGR N +LLE+ TD GVGT ++S+R Sbjct: 244 GTLTGGMIPKVKCCLEALEEGVEKAMIIDGRTENCILLELLTDKGVGTEIVSDR 297 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: 304 Number of extensions: 9 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: 308 Length adjustment: 27 Effective length of query: 274 Effective length of database: 281 Effective search space: 76994 Effective search space used: 76994 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 206911 DVU1466 (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.8653.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5e-82 260.9 8.8 5.9e-82 260.7 8.8 1.0 1 lcl|MicrobesOnline__882:206911 DVU1466 acetylglutamate kinase Domain annotation for each sequence (and alignments): >> lcl|MicrobesOnline__882:206911 DVU1466 acetylglutamate kinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 260.7 8.8 5.9e-82 5.9e-82 1 231 [] 28 270 .. 28 270 .. 0.97 Alignments for each domain: == domain 1 score: 260.7 bits; conditional E-value: 5.9e-82 TIGR00761 1 tiViKiGGaais..elleelakdiaklrkegiklvivHGGgpeinelleklgievefvnglRvTdketlevvemvligk 77 t+ViK+GG+a++ l++++a ++a l+ +gi++vivHGGgp+i ++le+l+i+ +f +glRvTd +t++vvemvl+gk lcl|MicrobesOnline__882:206911 28 TVVIKYGGHAMKdeALKKAFALNVALLKLVGINPVIVHGGGPQIGKMLEQLNIQSHFREGLRVTDDATMDVVEMVLVGK 106 69**********97899999*********************************************************** PP TIGR00761 78 vnkelvallekhgikavGltgkDgqlltaekldke...........dlgyvGeikkvnkelleallkagiipviaslal 145 vnke+v++++ +g+kavGl+gkDg l+ a+k++ dlg vGe+ vn+ ll++l g++pvia++++ lcl|MicrobesOnline__882:206911 107 VNKEIVNQMNLAGAKAVGLSGKDGMLIRARKMEMViskeaqapeiiDLGKVGEVMGVNTTLLRSLERDGFVPVIAPVGV 185 ******************************66555556699************************************** PP TIGR00761 146 deegqllNvnaDtaAaelAaaleAekLvlLtdvaGilegdkksliseleleeieqlikqavikgGmipKveaaleales 224 d++g+++N+naD +A+++Aaal+A++L+lLtdvaGil++dkk li++++++e+ +l + + ++gGmipKv+++leale+ lcl|MicrobesOnline__882:206911 186 DDNGETYNINADAVAGAVAAALKAKRLLLLTDVAGILDHDKK-LIRSVNMREAVNLFSDGTLTGGMIPKVKCCLEALEE 263 ***************************************777.************************************ PP TIGR00761 225 gvkkvvi 231 gv+k++i lcl|MicrobesOnline__882:206911 264 GVEKAMI 270 *****98 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (231 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: 00:00:00.00 # Mc/sec: 10.29 // [ok]
This GapMind analysis is from Apr 09 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