Align acetylglutamate kinase (EC 2.7.2.8) (characterized)
to candidate WP_029133645.1 A3GO_RS0112310 acetylglutamate kinase
Query= BRENDA::Q9HTN2 (301 letters) >NCBI__GCF_000428045.1:WP_029133645.1 Length = 298 Score = 423 bits (1087), Expect = e-123 Identities = 213/298 (71%), Positives = 253/298 (84%) Query: 1 MTLSRDDAAQVAKVLSEALPYIRRFVGKTLVIKYGGNAMESEELKAGFARDVVLMKAVGI 60 M+L+ + A VA VL+EALPYI+RF GKT+VIKYGGNAM +LK GFARDVVLMK VGI Sbjct: 1 MSLTPESAHNVAHVLTEALPYIQRFRGKTVVIKYGGNAMTEADLKDGFARDVVLMKLVGI 60 Query: 61 NPVVVHGGGPQIGDLLKRLSIESHFIDGMRVTDAATMDVVEMVLGGQVNKDIVNLINRHG 120 NPVVVHGGGPQIG+LL RL ES F+ GMRVTD+ TMDVVEMVLGGQVNK+IVNL+N+HG Sbjct: 61 NPVVVHGGGPQIGNLLGRLGKESEFVQGMRVTDSETMDVVEMVLGGQVNKEIVNLLNQHG 120 Query: 121 GSAIGLTGKDAELIRAKKLTVTRQTPEMTKPEIIDIGHVGEVTGVNVGLLNMLVKGDFIP 180 GSA+GLTGKD LI A+KL + R +PE+ PEIID+GHVGEV +N +++MLV G+FIP Sbjct: 121 GSAVGLTGKDGGLIHARKLMLKRTSPELQAPEIIDVGHVGEVASINKAVVDMLVSGNFIP 180 Query: 181 VIAPIGVGSNGESYNINADLVAGKVAEALKAEKLMLLTNIAGLMDKQGQVLTGLSTEQVN 240 VIAPIGVG +G SYNINADLVAGK+AE L+AEKL+LLTN AGL+DKQG +LTGL+ +V+ Sbjct: 181 VIAPIGVGEDGRSYNINADLVAGKMAEVLQAEKLILLTNTAGLLDKQGGLLTGLTAGRVD 240 Query: 241 ELIADGTIYGGMLPKIRCALEAVQGGVTSAHIIDGRVPNAVLLEIFTDSGVGTLISNR 298 ELIADGTI+GGMLPKIRCAL+AV GV S+ I+DGRV +AVLLE+FTD G+GTLI R Sbjct: 241 ELIADGTIHGGMLPKIRCALDAVNAGVNSSVIVDGRVKHAVLLELFTDQGIGTLIKCR 298 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: 401 Number of extensions: 16 Number of successful extensions: 1 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: 298 Length adjustment: 27 Effective length of query: 274 Effective length of database: 271 Effective search space: 74254 Effective search space used: 74254 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_029133645.1 A3GO_RS0112310 (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.32084.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3e-79 251.8 6.4 3.6e-79 251.5 6.4 1.0 1 lcl|NCBI__GCF_000428045.1:WP_029133645.1 A3GO_RS0112310 acetylglutamate k Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000428045.1:WP_029133645.1 A3GO_RS0112310 acetylglutamate kinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 251.5 6.4 3.6e-79 3.6e-79 1 231 [] 29 272 .. 29 272 .. 0.97 Alignments for each domain: == domain 1 score: 251.5 bits; conditional E-value: 3.6e-79 TIGR00761 1 tiViKiGGaais..elleelakdiaklrkegiklvivHGGgpeinelleklgievefvnglRvTdketl 67 t+ViK+GG+a++ +l++ +a+d++ ++ +gi++v+vHGGgp+i +ll +lg e efv+g+RvTd et+ lcl|NCBI__GCF_000428045.1:WP_029133645.1 29 TVVIKYGGNAMTeaDLKDGFARDVVLMKLVGINPVVVHGGGPQIGNLLGRLGKESEFVQGMRVTDSETM 97 69**********999****************************************************** PP TIGR00761 68 evvemvligkvnkelvallekhgikavGltgkDgqlltaekldke............dlgyvGeikkvn 124 +vvemvl g+vnke+v+ll++hg +avGltgkDg l+ a+kl + d+g+vGe+ ++n lcl|NCBI__GCF_000428045.1:WP_029133645.1 98 DVVEMVLGGQVNKEIVNLLNQHGGSAVGLTGKDGGLIHARKLMLKrtspelqapeiiDVGHVGEVASIN 166 ****************************************6665557999******************* PP TIGR00761 125 kelleallkagiipviaslaldeegqllNvnaDtaAaelAaaleAekLvlLtdvaGilegdkkslisel 193 k++++ l+ ++ipvia++++ e+g+ +N+naD +A+++A++l+AekL+lLt++aG+l++++ l++ l lcl|NCBI__GCF_000428045.1:WP_029133645.1 167 KAVVDMLVSGNFIPVIAPIGVGEDGRSYNINADLVAGKMAEVLQAEKLILLTNTAGLLDKQGG-LLTGL 234 ************************************************************555.***** PP TIGR00761 194 eleeieqlikqavikgGmipKveaalealesgvkkvvi 231 ++ ++++li + i+gGm pK+++al+a++ gv+++vi lcl|NCBI__GCF_000428045.1:WP_029133645.1 235 TAGRVDELIADGTIHGGMLPKIRCALDAVNAGVNSSVI 272 **********************************9987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (231 nodes) Target sequences: 1 (298 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: 10.97 // [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