Align acetylglutamate kinase (EC 2.7.2.8) (characterized)
to candidate Ac3H11_1907 Acetylglutamate kinase (EC 2.7.2.8)
Query= BRENDA::Q9HTN2 (301 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1907 Length = 317 Score = 325 bits (833), Expect = 8e-94 Identities = 168/285 (58%), Positives = 212/285 (74%), Gaps = 5/285 (1%) Query: 12 AKVLSEALPYIRRFVGKTLVIKYGGNAMESEELKAGFARDVVLMKAVGINPVVVHGGGPQ 71 A++L++ALPYIR+F GKT+VIKYGGNAM L+A FA DVVL+K VG+NPVVVHGGGPQ Sbjct: 34 AEILAQALPYIRKFHGKTMVIKYGGNAMTDPALQADFAEDVVLLKLVGMNPVVVHGGGPQ 93 Query: 72 IGDLLKRLSIESHFIDGMRVTDAATMDVVEMVLGGQVNKDIVNLINRHGGSAIGLTGKDA 131 I L RL + FI GMRVTDA TM+VVE VL G+V +DIV LIN+ GG A+GLTG+D Sbjct: 94 IETALNRLGKKGEFIQGMRVTDAETMEVVEWVLAGEVQQDIVGLINQAGGKAVGLTGRDG 153 Query: 132 ELIRAKKL-TVTRQTPEMTKPEIIDIGHVGEVTGVNVGLLNMLVKGDFIPVIAPIGVGSN 190 +IRA+KL V + P + D+G VG++ ++ ++ L FIPVI+PIG G N Sbjct: 154 GMIRAQKLKMVDNKNPAIEH----DVGQVGDIVSIDPSVVKALQDDAFIPVISPIGFGEN 209 Query: 191 GESYNINADLVAGKVAEALKAEKLMLLTNIAGLMDKQGQVLTGLSTEQVNELIADGTIYG 250 ESYNINAD+VA K+AE LKAEKLMLLTN G++DK G +LT L+ +++EL ADGTI G Sbjct: 210 NESYNINADVVASKLAEVLKAEKLMLLTNTPGVLDKAGNLLTDLTARRIDELFADGTISG 269 Query: 251 GMLPKIRCALEAVQGGVTSAHIIDGRVPNAVLLEIFTDSGVGTLI 295 GMLPKI AL+A + GV + HIIDGRVP+A+LLEI T+ GT+I Sbjct: 270 GMLPKIAGALDAAKAGVNAVHIIDGRVPHAMLLEILTEQAYGTMI 314 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: 310 Number of extensions: 15 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: 317 Length adjustment: 27 Effective length of query: 274 Effective length of database: 290 Effective search space: 79460 Effective search space used: 79460 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 Ac3H11_1907 (Acetylglutamate kinase (EC 2.7.2.8))
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.30962.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-74 236.9 4.8 1.2e-74 236.7 4.8 1.0 1 lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1907 Acetylglutamate kinase (EC 2.7.2 Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1907 Acetylglutamate kinase (EC 2.7.2.8) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 236.7 4.8 1.2e-74 1.2e-74 1 231 [] 51 291 .. 51 291 .. 0.97 Alignments for each domain: == domain 1 score: 236.7 bits; conditional E-value: 1.2e-74 TIGR00761 1 tiViKiGGaais..elleelakdiaklrkegiklvivHGGgpeinelleklgievefvnglR 60 t+ViK+GG+a++ l+ ++a+d++ l+ +g+++v+vHGGgp+i+++l++lg + ef++g+R lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1907 51 TMVIKYGGNAMTdpALQADFAEDVVLLKLVGMNPVVVHGGGPQIETALNRLGKKGEFIQGMR 112 69**********9889********************************************** PP TIGR00761 61 vTdketlevvemvligkvnkelvallekhgikavGltgkDgqlltaekldke.........d 113 vTd+et+evve vl+g+v++ +v l++++g kavGltg Dg ++ a+kl+ d lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1907 113 VTDAETMEVVEWVLAGEVQQDIVGLINQAGGKAVGLTGRDGGMIRAQKLKMVdnknpaiehD 174 ***********************************************55444446999999* PP TIGR00761 114 lgyvGeikkvnkelleallkagiipviaslaldeegqllNvnaDtaAaelAaaleAekLvlL 175 +g vG+i ++++++++al + +ipvi+++++ e+++ +N+naD++A++lA++l+AekL+lL lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1907 175 VGQVGDIVSIDPSVVKALQDDAFIPVISPIGFGENNESYNINADVVASKLAEVLKAEKLMLL 236 ************************************************************** PP TIGR00761 176 tdvaGilegdkksliseleleeieqlikqavikgGmipKveaalealesgvkkvvi 231 t+++G+l++ + +l++ l++++i++l + i gGm pK++ al+a++ gv++v+i lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1907 237 TNTPGVLDK-AGNLLTDLTARRIDELFADGTISGGMLPKIAGALDAAKAGVNAVHI 291 *********.666*****************************************98 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (231 nodes) Target sequences: 1 (317 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: 10.18 // [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