Align acetylglutamate kinase (EC 2.7.2.8) (characterized)
to candidate WP_013009786.1 DACET_RS02235 acetylglutamate kinase
Query= BRENDA::Q9HTN2 (301 letters) >NCBI__GCF_000025725.1:WP_013009786.1 Length = 292 Score = 355 bits (912), Expect = e-103 Identities = 176/290 (60%), Positives = 232/290 (80%), Gaps = 1/290 (0%) Query: 6 DDAAQVAKVLSEALPYIRRFVGKTLVIKYGGNAMESEELKAGFARDVVLMKAVGINPVVV 65 ++ + A +L E+LPYI+ F G+T+VIKYGG+AM +ELK FARD+V+MK +G+NPV+V Sbjct: 2 EELIRKADILIESLPYIKEFYGETIVIKYGGHAMVDDELKFSFARDIVMMKYIGLNPVIV 61 Query: 66 HGGGPQIGDLLKRLSIESHFIDGMRVTDAATMDVVEMVLGGQVNKDIVNLINRHGGSAIG 125 HGGGPQIG++LK+L+IESHF+ GMRVTD TM++VEMVL G+VNKDIV+LIN +GG AIG Sbjct: 62 HGGGPQIGEMLKKLNIESHFVSGMRVTDKQTMNIVEMVLAGKVNKDIVSLININGGKAIG 121 Query: 126 LTGKDAELIRAKKLTVTRQTPEMTKPEIIDIGHVGEVTGVNVGLLNMLVKGDFIPVIAPI 185 L+GKD LI A+KL + + PEIID+GHVG V V+V +LN + K +FIPVIAP+ Sbjct: 122 LSGKDGNLITAEKLYLKEGDGFVVTPEIIDLGHVGSVKKVDVEVLNNISK-NFIPVIAPV 180 Query: 186 GVGSNGESYNINADLVAGKVAEALKAEKLMLLTNIAGLMDKQGQVLTGLSTEQVNELIAD 245 GVG + + YNINADLVAG +A ALKA KL+LLT++ G++DK+G +++ L+ E++ L D Sbjct: 181 GVGEDYQPYNINADLVAGSIATALKARKLILLTDVKGVLDKEGNLISTLTPEKIRMLKKD 240 Query: 246 GTIYGGMLPKIRCALEAVQGGVTSAHIIDGRVPNAVLLEIFTDSGVGTLI 295 GT+ GGM+PKI CAL+AVQ GV AHIIDGRV ++VLLEIFTDSG+GT I Sbjct: 241 GTLTGGMIPKIDCALDAVQNGVAKAHIIDGRVSHSVLLEIFTDSGIGTQI 290 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: 347 Number of extensions: 13 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: 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_013009786.1 DACET_RS02235 (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.28854.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1e-82 263.2 7.0 1.2e-82 263.0 7.0 1.0 1 lcl|NCBI__GCF_000025725.1:WP_013009786.1 DACET_RS02235 acetylglutamate ki Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000025725.1:WP_013009786.1 DACET_RS02235 acetylglutamate kinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 263.0 7.0 1.2e-82 1.2e-82 1 231 [] 25 267 .. 25 267 .. 0.97 Alignments for each domain: == domain 1 score: 263.0 bits; conditional E-value: 1.2e-82 TIGR00761 1 tiViKiGGaais..elleelakdiaklrkegiklvivHGGgpeinelleklgievefvnglRvTdketl 67 tiViK+GG+a+ el+ ++a+di+ ++ g+++vivHGGgp+i e+l+kl+ie +fv g+RvTdk+t+ lcl|NCBI__GCF_000025725.1:WP_013009786.1 25 TIVIKYGGHAMVddELKFSFARDIVMMKYIGLNPVIVHGGGPQIGEMLKKLNIESHFVSGMRVTDKQTM 93 69*********988999**************************************************** PP TIGR00761 68 evvemvligkvnkelvallekhgikavGltgkDgqlltaekldke............dlgyvGeikkvn 124 ++vemvl+gkvnk +v l++ +g ka+Gl+gkDg+l+taekl+ + dlg+vG++kkv+ lcl|NCBI__GCF_000025725.1:WP_013009786.1 94 NIVEMVLAGKVNKDIVSLININGGKAIGLSGKDGNLITAEKLYLKegdgfvvtpeiiDLGHVGSVKKVD 162 ****************************************77766679********************* PP TIGR00761 125 kelleallkagiipviaslaldeegqllNvnaDtaAaelAaaleAekLvlLtdvaGilegdkkslisel 193 e+l+++ k+ +ipvia++++ e+ q +N+naD +A+ +A+al+A kL+lLtdv+G+l++ + +lis l lcl|NCBI__GCF_000025725.1:WP_013009786.1 163 VEVLNNISKN-FIPVIAPVGVGEDYQPYNINADLVAGSIATALKARKLILLTDVKGVLDK-EGNLISTL 229 ****998777.9************************************************.555***** PP TIGR00761 194 eleeieqlikqavikgGmipKveaalealesgvkkvvi 231 ++e+i++l k + ++gGmipK+++al+a+++gv k++i lcl|NCBI__GCF_000025725.1:WP_013009786.1 230 TPEKIRMLKKDGTLTGGMIPKIDCALDAVQNGVAKAHI 267 ************************************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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 11.84 // [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