Align acetylglutamate kinase (EC 2.7.2.8) (characterized)
to candidate WP_006746951.1 THITH_RS15215 acetylglutamate kinase
Query= BRENDA::Q9HTN2 (301 letters) >NCBI__GCF_000227685.2:WP_006746951.1 Length = 292 Score = 345 bits (885), Expect = e-100 Identities = 182/297 (61%), Positives = 223/297 (75%), Gaps = 9/297 (3%) Query: 3 LSRDDAAQVAKVLSEALPYIRRFVGKTLVIKYGGNAMESEELKAGFARDVVLMKAVGINP 62 + + A VA VL EALPYI+RF GKT+VIKYGGNAM E LK+GFARDVVL+K VG+NP Sbjct: 1 MDKTTAQSVAHVLIEALPYIQRFAGKTIVIKYGGNAMTEEHLKSGFARDVVLLKQVGVNP 60 Query: 63 VVVHGGGPQIGDLLKRLSIESHFIDGMRVTDAATMDVVEMVLGGQVNKDIVNLINRHGGS 122 VVVHGGGPQIG+LLKRL S FI G+RVTD TMDVV+MVLGG VN++IV LINR GG Sbjct: 61 VVVHGGGPQIGNLLKRLGKTSEFIHGLRVTDRETMDVVQMVLGGLVNQEIVALINRFGGR 120 Query: 123 AIGLTGKDAELIRAKKLTVTRQTPEMTKPE---IIDIGHVGEVTGVNVGLLNMLVKGDFI 179 A+GLTGKD +LIRA+ L E+ PE +D+G VGEV GV+ +++ L FI Sbjct: 121 AVGLTGKDGQLIRARPLR------EINGPEGLTAVDLGLVGEVEGVDPDIVHTLDHSAFI 174 Query: 180 PVIAPIGVGSNGESYNINADLVAGKVAEALKAEKLMLLTNIAGLMDKQGQVLTGLSTEQV 239 PVIAPIG NG +YNINAD A K+A L AEKL LLTN G++D QGQ+L LS +V Sbjct: 175 PVIAPIGFDHNGNAYNINADTAAEKLAVVLDAEKLFLLTNTPGVLDAQGQLLPRLSAAEV 234 Query: 240 NELIADGTIYGGMLPKIRCALEAVQGGVTSAHIIDGRVPNAVLLEIFTDSGVGTLIS 296 ++L G I+GGM+PKI+CAL+AV+ GVT+ HI+DGRV +AVLLE+ T+ GVGTLI+ Sbjct: 235 DDLTRTGVIHGGMIPKIQCALDAVRSGVTATHIVDGRVEHAVLLELLTNEGVGTLIT 291 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: 318 Number of extensions: 13 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_006746951.1 THITH_RS15215 (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.17526.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 9.2e-81 256.8 0.9 1.1e-80 256.5 0.9 1.1 1 lcl|NCBI__GCF_000227685.2:WP_006746951.1 THITH_RS15215 acetylglutamate ki Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000227685.2:WP_006746951.1 THITH_RS15215 acetylglutamate kinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 256.5 0.9 1.1e-80 1.1e-80 1 231 [] 27 267 .. 27 267 .. 0.97 Alignments for each domain: == domain 1 score: 256.5 bits; conditional E-value: 1.1e-80 TIGR00761 1 tiViKiGGaais..elleelakdiaklrkegiklvivHGGgpeinelleklgievefvnglRvTdketl 67 tiViK+GG+a++ +l+ +a+d++ l+++g+++v+vHGGgp+i +ll++lg ef++glRvTd+et+ lcl|NCBI__GCF_000227685.2:WP_006746951.1 27 TIVIKYGGNAMTeeHLKSGFARDVVLLKQVGVNPVVVHGGGPQIGNLLKRLGKTSEFIHGLRVTDRETM 95 69**********8889999************************************************** PP TIGR00761 68 evvemvligkvnkelvallekhgikavGltgkDgqlltaekldke.........dlgyvGeikkvnkel 127 +vv+mvl g vn+e+val+++ g +avGltgkDgql+ a+ l + dlg+vGe++ v++++ lcl|NCBI__GCF_000227685.2:WP_006746951.1 96 DVVQMVLGGLVNQEIVALINRFGGRAVGLTGKDGQLIRARPLREIngpegltavDLGLVGEVEGVDPDI 164 ****************************************66665667888888*************** PP TIGR00761 128 leallkagiipviaslaldeegqllNvnaDtaAaelAaaleAekLvlLtdvaGilegdkksliselele 196 +++l ++ +ipvia++++d++g+++N+naDtaA +lA +l+AekL lLt+++G+l+ +++ l+ +l+++ lcl|NCBI__GCF_000227685.2:WP_006746951.1 165 VHTLDHSAFIPVIAPIGFDHNGNAYNINADTAAEKLAVVLDAEKLFLLTNTPGVLDAQGQ-LLPRLSAA 232 *********************************************************555.******** PP TIGR00761 197 eieqlikqavikgGmipKveaalealesgvkkvvi 231 e+++l +++vi+gGmipK+++al+a++sgv + +i lcl|NCBI__GCF_000227685.2:WP_006746951.1 233 EVDDLTRTGVIHGGMIPKIQCALDAVRSGVTATHI 267 ******************************99987 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 9.33 // [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