Align acetylglutamate kinase (EC 2.7.2.8) (characterized)
to candidate WP_089322531.1 CHB58_RS02525 acetylglutamate kinase
Query= BRENDA::Q9HTN2 (301 letters) >NCBI__GCF_900188395.1:WP_089322531.1 Length = 292 Score = 348 bits (894), Expect = e-101 Identities = 176/285 (61%), Positives = 222/285 (77%) Query: 12 AKVLSEALPYIRRFVGKTLVIKYGGNAMESEELKAGFARDVVLMKAVGINPVVVHGGGPQ 71 A VL EALPYI+RF GKT+VIKYGGNAM +ELK FA DVVL+K +GINPV+VHGGGPQ Sbjct: 8 ASVLLEALPYIKRFYGKTVVIKYGGNAMVDDELKRSFAEDVVLLKYIGINPVIVHGGGPQ 67 Query: 72 IGDLLKRLSIESHFIDGMRVTDAATMDVVEMVLGGQVNKDIVNLINRHGGSAIGLTGKDA 131 IG+ LK+L I++ FI GMRVTD TM++VEMVL G+VNK+IV LIN HGG+A+GL+GKD Sbjct: 68 IGEFLKKLDIKTRFIGGMRVTDKETMNIVEMVLVGKVNKEIVKLINSHGGNAVGLSGKDG 127 Query: 132 ELIRAKKLTVTRQTPEMTKPEIIDIGHVGEVTGVNVGLLNMLVKGDFIPVIAPIGVGSNG 191 LI A+K+ + E+ EIID+G VGEV VN ++ L++ FIPVIAP+GVG + Sbjct: 128 NLIEARKIDYKKYLSEVKATEIIDLGFVGEVEKVNPAIVFKLLESKFIPVIAPVGVGKDY 187 Query: 192 ESYNINADLVAGKVAEALKAEKLMLLTNIAGLMDKQGQVLTGLSTEQVNELIADGTIYGG 251 E+YNINAD+VAG+VA ALKAEKL++LT+I G+ DK G +++ LS + + +LI DGTI GG Sbjct: 188 EAYNINADIVAGEVAAALKAEKLIMLTDIEGIKDKNGDLMSVLSKDDIPQLIEDGTISGG 247 Query: 252 MLPKIRCALEAVQGGVTSAHIIDGRVPNAVLLEIFTDSGVGTLIS 296 M+PK++ A+ GGV AHIIDGRV +AVLLEIFT GVGT IS Sbjct: 248 MIPKVKACQIALGGGVKKAHIIDGRVKHAVLLEIFTKEGVGTEIS 292 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: 327 Number of extensions: 9 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: 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_089322531.1 CHB58_RS02525 (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.1936.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-85 272.8 7.2 1.3e-85 272.6 7.2 1.0 1 lcl|NCBI__GCF_900188395.1:WP_089322531.1 CHB58_RS02525 acetylglutamate ki Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_900188395.1:WP_089322531.1 CHB58_RS02525 acetylglutamate kinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 272.6 7.2 1.3e-85 1.3e-85 1 231 [] 25 268 .. 25 268 .. 0.99 Alignments for each domain: == domain 1 score: 272.6 bits; conditional E-value: 1.3e-85 TIGR00761 1 tiViKiGGaais..elleelakdiaklrkegiklvivHGGgpeinelleklgievefvnglRvTdketl 67 t+ViK+GG+a+ el++++a+d++ l+ gi++vivHGGgp+i e l+kl+i+++f++g+RvTdket+ lcl|NCBI__GCF_900188395.1:WP_089322531.1 25 TVVIKYGGNAMVddELKRSFAEDVVLLKYIGINPVIVHGGGPQIGEFLKKLDIKTRFIGGMRVTDKETM 93 69*********9999****************************************************** PP TIGR00761 68 evvemvligkvnkelvallekhgikavGltgkDgqlltaekldke............dlgyvGeikkvn 124 ++vemvl+gkvnke+v+l++ hg +avGl+gkDg+l++a+k+d++ dlg+vGe++kvn lcl|NCBI__GCF_900188395.1:WP_089322531.1 94 NIVEMVLVGKVNKEIVKLINSHGGNAVGLSGKDGNLIEARKIDYKkylsevkateiiDLGFVGEVEKVN 162 ******************************************99999********************** PP TIGR00761 125 kelleallkagiipviaslaldeegqllNvnaDtaAaelAaaleAekLvlLtdvaGilegdkkslisel 193 ++++ +ll++ +ipvia++++ ++ +++N+naD +A+e+Aaal+AekL++Ltd++Gi +++++ l+s l lcl|NCBI__GCF_900188395.1:WP_089322531.1 163 PAIVFKLLESKFIPVIAPVGVGKDYEAYNINADIVAGEVAAALKAEKLIMLTDIEGIKDKNGD-LMSVL 230 ************************************************************666.***** PP TIGR00761 194 eleeieqlikqavikgGmipKveaalealesgvkkvvi 231 + ++i qli+ + i gGmipKv+a+ al +gvkk++i lcl|NCBI__GCF_900188395.1:WP_089322531.1 231 SKDDIPQLIEDGTISGGMIPKVKACQIALGGGVKKAHI 268 ************************************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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 10.12 // [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