Align acetylglutamate kinase (EC 2.7.2.8) (characterized)
to candidate AZOBR_RS03285 AZOBR_RS03285 acetylglutamate kinase
Query= BRENDA::Q9HTN2 (301 letters) >FitnessBrowser__azobra:AZOBR_RS03285 Length = 299 Score = 325 bits (834), Expect = 6e-94 Identities = 163/292 (55%), Positives = 215/292 (73%) Query: 4 SRDDAAQVAKVLSEALPYIRRFVGKTLVIKYGGNAMESEELKAGFARDVVLMKAVGINPV 63 +RD+ A+ LSEALPY+RR+ G+T VIKYGG+AM + L FARD+VL+K VGINPV Sbjct: 5 TRDEWLAKARTLSEALPYMRRYAGRTFVIKYGGHAMGDDSLAEKFARDIVLLKQVGINPV 64 Query: 64 VVHGGGPQIGDLLKRLSIESHFIDGMRVTDAATMDVVEMVLGGQVNKDIVNLINRHGGSA 123 VVHGGGPQIG +L+RL+I+S FIDG+RVTD T++VVEMVL G +NK IV IN GG A Sbjct: 65 VVHGGGPQIGQMLQRLAIKSSFIDGLRVTDKETVEVVEMVLAGSINKQIVAAINNAGGRA 124 Query: 124 IGLTGKDAELIRAKKLTVTRQTPEMTKPEIIDIGHVGEVTGVNVGLLNMLVKGDFIPVIA 183 +GL+GKD LI A+KL T++ P+ +++D+G VGE VN ++ L + D IPVIA Sbjct: 125 VGLSGKDGSLITARKLRRTQRDPDSNIEKVLDLGFVGEPYQVNPQIITSLAQSDIIPVIA 184 Query: 184 PIGVGSNGESYNINADLVAGKVAEALKAEKLMLLTNIAGLMDKQGQVLTGLSTEQVNELI 243 PIG NG++YNINAD AG VA AL A + LLT++AG++DK +++ +S +Q I Sbjct: 185 PIGFDRNGDTYNINADTAAGAVASALGATRFFLLTDVAGVLDKNKELVPRMSLDQARAAI 244 Query: 244 ADGTIYGGMLPKIRCALEAVQGGVTSAHIIDGRVPNAVLLEIFTDSGVGTLI 295 ADGT GGM+PKI ++AV+ GV +A I+DGRVP+A+LLEIFT+ G GTLI Sbjct: 245 ADGTATGGMIPKIETCIDAVEQGVDAAVILDGRVPHALLLEIFTEGGAGTLI 296 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: 281 Number of extensions: 10 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: 299 Length adjustment: 27 Effective length of query: 274 Effective length of database: 272 Effective search space: 74528 Effective search space used: 74528 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 AZOBR_RS03285 AZOBR_RS03285 (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.11856.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.3e-84 267.1 1.5 7.3e-84 266.9 1.5 1.0 1 lcl|FitnessBrowser__azobra:AZOBR_RS03285 AZOBR_RS03285 acetylglutamate ki Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__azobra:AZOBR_RS03285 AZOBR_RS03285 acetylglutamate kinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 266.9 1.5 7.3e-84 7.3e-84 1 231 [] 30 273 .. 30 273 .. 0.98 Alignments for each domain: == domain 1 score: 266.9 bits; conditional E-value: 7.3e-84 TIGR00761 1 tiViKiGGaais..elleelakdiaklrkegiklvivHGGgpeinelleklgievefvnglRvTdketl 67 t ViK+GG+a+ l e++a+di+ l+++gi++v+vHGGgp+i ++l++l+i+ f++glRvTdket+ lcl|FitnessBrowser__azobra:AZOBR_RS03285 30 TFVIKYGGHAMGddSLAEKFARDIVLLKQVGINPVVVHGGGPQIGQMLQRLAIKSSFIDGLRVTDKETV 98 57*********88889***************************************************** PP TIGR00761 68 evvemvligkvnkelvallekhgikavGltgkDgqlltaekldke............dlgyvGeikkvn 124 evvemvl+g++nk++va+++++g +avGl+gkDg+l+ta+kl + dlg+vGe +vn lcl|FitnessBrowser__azobra:AZOBR_RS03285 99 EVVEMVLAGSINKQIVAAINNAGGRAVGLSGKDGSLITARKLRRTqrdpdsniekvlDLGFVGEPYQVN 167 ****************************************8887778999******************* PP TIGR00761 125 kelleallkagiipviaslaldeegqllNvnaDtaAaelAaaleAekLvlLtdvaGilegdkkslisel 193 ++++ +l +++iipvia++++d +g+++N+naDtaA+++A+al+A + lLtdvaG+l++ +k+l+ ++ lcl|FitnessBrowser__azobra:AZOBR_RS03285 168 PQIITSLAQSDIIPVIAPIGFDRNGDTYNINADTAAGAVASALGATRFFLLTDVAGVLDK-NKELVPRM 235 ************************************************************.666***** PP TIGR00761 194 eleeieqlikqavikgGmipKveaalealesgvkkvvi 231 +l++++ i + ++gGmipK+e +++a+e+gv ++vi lcl|FitnessBrowser__azobra:AZOBR_RS03285 236 SLDQARAAIADGTATGGMIPKIETCIDAVEQGVDAAVI 273 **********************************9987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (231 nodes) Target sequences: 1 (299 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: 10.56 // [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