Align acetylglutamate kinase (EC 2.7.2.8) (characterized)
to candidate HSERO_RS21495 HSERO_RS21495 acetylglutamate kinase
Query= BRENDA::Q9HTN2 (301 letters) >FitnessBrowser__HerbieS:HSERO_RS21495 Length = 297 Score = 335 bits (860), Expect = 6e-97 Identities = 164/285 (57%), Positives = 218/285 (76%), Gaps = 5/285 (1%) Query: 12 AKVLSEALPYIRRFVGKTLVIKYGGNAMESEELKAGFARDVVLMKAVGINPVVVHGGGPQ 71 A++L+EALPYIR+F GKT+V+KYGGNAM E LK GFARDV+L+K VG+NPVVVHGGGPQ Sbjct: 14 AEILAEALPYIRKFHGKTIVVKYGGNAMTEESLKHGFARDVILLKLVGMNPVVVHGGGPQ 73 Query: 72 IGDLLKRLSIESHFIDGMRVTDAATMDVVEMVLGGQVNKDIVNLINRHGGSAIGLTGKDA 131 I LK++ + F+ GMR+TD TM+VVE VLGG+V +DIV LIN +GG A+GLTGKD Sbjct: 74 IDAALKKIGKQGTFVQGMRITDEETMEVVEWVLGGEVQQDIVMLINHYGGQAVGLTGKDG 133 Query: 132 ELIRAKKLTVTRQTPEMTKP-EIIDIGHVGEVTGVNVGLLNMLVKGDFIPVIAPIGVGSN 190 LIRA+K+ Q P+ P +DIG+VGE+ +N ++ L FIP+I+PIG G + Sbjct: 134 GLIRARKM----QMPDKEHPGAFLDIGYVGEIEAINPAVVKALQDDAFIPIISPIGFGDD 189 Query: 191 GESYNINADLVAGKVAEALKAEKLMLLTNIAGLMDKQGQVLTGLSTEQVNELIADGTIYG 250 G++YNINAD+VAGK+AE L AEKL+++TNIAG+ DK G +LT LS +++E+ ADGTI G Sbjct: 190 GQAYNINADVVAGKIAEILHAEKLIMMTNIAGVQDKAGNLLTDLSAREIDEMFADGTISG 249 Query: 251 GMLPKIRCALEAVQGGVTSAHIIDGRVPNAVLLEIFTDSGVGTLI 295 GMLPKI AL+A + GV + HIIDGR+ +++LLE+ T+ GT+I Sbjct: 250 GMLPKISSALDAAKSGVNTVHIIDGRIEHSLLLEVLTEQAFGTMI 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: 338 Number of extensions: 11 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: 297 Length adjustment: 27 Effective length of query: 274 Effective length of database: 270 Effective search space: 73980 Effective search space used: 73980 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 HSERO_RS21495 HSERO_RS21495 (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.931129.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.1e-76 242.5 4.1 2.5e-76 242.2 4.1 1.1 1 FitnessBrowser__HerbieS:HSERO_RS21495 Domain annotation for each sequence (and alignments): >> FitnessBrowser__HerbieS:HSERO_RS21495 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 242.2 4.1 2.5e-76 2.5e-76 1 231 [] 31 271 .. 31 271 .. 0.97 Alignments for each domain: == domain 1 score: 242.2 bits; conditional E-value: 2.5e-76 TIGR00761 1 tiViKiGGaais..elleelakdiaklrkegiklvivHGGgpeinelleklgievefvnglRvTdketlevv 70 tiV+K+GG+a++ l++ +a+d++ l+ +g+++v+vHGGgp+i+++l+k+g + fv+g+R+Td+et+evv FitnessBrowser__HerbieS:HSERO_RS21495 31 TIVVKYGGNAMTeeSLKHGFARDVILLKLVGMNPVVVHGGGPQIDAALKKIGKQGTFVQGMRITDEETMEVV 102 69*********988899******************************************************* PP TIGR00761 71 emvligkvnkelvallekhgikavGltgkDgqlltaekldke.........dlgyvGeikkvnkelleallk 133 e vl g+v++ +v l+++ g +avGltgkDg l+ a+k++ d+gyvGei+++n+++++al + FitnessBrowser__HerbieS:HSERO_RS21495 103 EWVLGGEVQQDIVMLINHYGGQAVGLTGKDGGLIRARKMQMPdkehpgaflDIGYVGEIEAINPAVVKALQD 174 *************************************77655568*************************** PP TIGR00761 134 agiipviaslaldeegqllNvnaDtaAaelAaaleAekLvlLtdvaGilegdkksliseleleeieqlikqa 205 +ip+i+++++ ++gq++N+naD++A+++A+ l+AekL+++t++aG+ ++ + +l++ l+++ei+++ + FitnessBrowser__HerbieS:HSERO_RS21495 175 DAFIPIISPIGFGDDGQAYNINADVVAGKIAEILHAEKLIMMTNIAGVQDK-AGNLLTDLSAREIDEMFADG 245 **************************************************9.666***************** PP TIGR00761 206 vikgGmipKveaalealesgvkkvvi 231 i gGm pK+++al+a++sgv+ v+i FitnessBrowser__HerbieS:HSERO_RS21495 246 TISGGMLPKISSALDAAKSGVNTVHI 271 ************************98 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (231 nodes) Target sequences: 1 (297 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: 11.15 // [ok]
This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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