Align acetylglutamate kinase (EC 2.7.2.8) (characterized)
to candidate WP_027457587.1 K420_RS0107980 acetylglutamate kinase
Query= BRENDA::Q9HTN2 (301 letters) >NCBI__GCF_000519045.1:WP_027457587.1 Length = 295 Score = 362 bits (930), Expect = e-105 Identities = 181/286 (63%), Positives = 229/286 (80%), Gaps = 3/286 (1%) Query: 12 AKVLSEALPYIRRFVGKTLVIKYGGNAMESEELKAGFARDVVLMKAVGINPVVVHGGGPQ 71 A VL+EALPYI+RF GKT+V+KYGGNAM E LK FARDVVL++ +G N VVVHGGGPQ Sbjct: 12 AAVLAEALPYIKRFHGKTIVVKYGGNAMTDEHLKNCFARDVVLLELIGFNIVVVHGGGPQ 71 Query: 72 IGDLLKRLSIESHFIDGMRVTDAATMDVVEMVLGGQVNKDIVNLINRHGGSAIGLTGKDA 131 I +LL R+ + F+ GMRVTDA TM+VVEMVLGGQVNKDIVNLIN+HGG A+GLTGKD Sbjct: 72 IENLLTRVGKKGEFVQGMRVTDAETMEVVEMVLGGQVNKDIVNLINQHGGKAVGLTGKDG 131 Query: 132 ELIRAKKLTVTRQTPEMTKPEIIDIGHVGEVTGVNVGLLNMLVKGDFIPVIAPIGVGSNG 191 IRA+KL + + ++ID+G VGE+T V+ L++ L KG FIPVIAPIGVG NG Sbjct: 132 NCIRARKLMLENKE---NPGDLIDVGQVGEITQVDPSLIDHLDKGAFIPVIAPIGVGENG 188 Query: 192 ESYNINADLVAGKVAEALKAEKLMLLTNIAGLMDKQGQVLTGLSTEQVNELIADGTIYGG 251 E+YNINAD+VAGK+AE LKAEKL+LLTN G++DK+G+++TG++ +Q++E++ DGT+ GG Sbjct: 189 ETYNINADVVAGKIAEVLKAEKLVLLTNTPGVLDKEGKLITGITPKQIDEMVEDGTLSGG 248 Query: 252 MLPKIRCALEAVQGGVTSAHIIDGRVPNAVLLEIFTDSGVGTLISN 297 MLPKI AL+A + GV HIIDGRV +A+LLEI TD GVGT+I + Sbjct: 249 MLPKIGSALDAARNGVKGVHIIDGRVEHALLLEILTDHGVGTMIKS 294 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: 357 Number of extensions: 17 Number of successful extensions: 3 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: 295 Length adjustment: 26 Effective length of query: 275 Effective length of database: 269 Effective search space: 73975 Effective search space used: 73975 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_027457587.1 K420_RS0107980 (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.5564.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.2e-80 253.8 6.7 8.7e-80 253.6 6.7 1.1 1 lcl|NCBI__GCF_000519045.1:WP_027457587.1 K420_RS0107980 acetylglutamate k Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000519045.1:WP_027457587.1 K420_RS0107980 acetylglutamate kinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 253.6 6.7 8.7e-80 8.7e-80 1 231 [] 29 269 .. 29 269 .. 0.97 Alignments for each domain: == domain 1 score: 253.6 bits; conditional E-value: 8.7e-80 TIGR00761 1 tiViKiGGaais..elleelakdiaklrkegiklvivHGGgpeinelleklgievefvnglRvTdketl 67 tiV+K+GG+a++ +l++ +a+d++ l+ g ++v+vHGGgp+i++ll+++g + efv+g+RvTd+et+ lcl|NCBI__GCF_000519045.1:WP_027457587.1 29 TIVVKYGGNAMTdeHLKNCFARDVVLLELIGFNIVVVHGGGPQIENLLTRVGKKGEFVQGMRVTDAETM 97 69*********98788999************************************************** PP TIGR00761 68 evvemvligkvnkelvallekhgikavGltgkDgqlltaekldke.........dlgyvGeikkvnkel 127 evvemvl g+vnk +v+l+++hg kavGltgkDg+ + a+kl e d+g vGei++v+++l lcl|NCBI__GCF_000519045.1:WP_027457587.1 98 EVVEMVLGGQVNKDIVNLINQHGGKAVGLTGKDGNCIRARKLMLEnkenpgdliDVGQVGEITQVDPSL 166 ****************************************665555689******************** PP TIGR00761 128 leallkagiipviaslaldeegqllNvnaDtaAaelAaaleAekLvlLtdvaGilegdkksliselele 196 +++l k +ipvia++++ e+g+++N+naD++A+++A++l+AekLvlLt+++G+l++ + +li+ ++++ lcl|NCBI__GCF_000519045.1:WP_027457587.1 167 IDHLDKGAFIPVIAPIGVGENGETYNINADVVAGKIAEVLKAEKLVLLTNTPGVLDK-EGKLITGITPK 234 *********************************************************.666******** PP TIGR00761 197 eieqlikqavikgGmipKveaalealesgvkkvvi 231 +i+++++ + + gGm pK+ +al+a+++gvk v+i lcl|NCBI__GCF_000519045.1:WP_027457587.1 235 QIDEMVEDGTLSGGMLPKIGSALDAARNGVKGVHI 269 *********************************98 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (231 nodes) Target sequences: 1 (295 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: 8.09 // [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