Align acetylglutamate kinase (EC 2.7.2.8) (characterized)
to candidate WP_029621561.1 G7G_RS0100260 acetylglutamate kinase
Query= BRENDA::Q9HTN2 (301 letters) >NCBI__GCF_000192475.1:WP_029621561.1 Length = 287 Score = 281 bits (719), Expect = 1e-80 Identities = 147/289 (50%), Positives = 197/289 (68%), Gaps = 13/289 (4%) Query: 7 DAAQVAKVLSEALPYIRRFVGKTLVIKYGGNAMESEELKAGFARDVVLMKAVGINPVVVH 66 D A L+ ALPY++R+ G +VIK GG+AM S+E FARDVVLM+ VG+NPVVVH Sbjct: 9 DWIATAATLNSALPYLQRYDGAIVVIKLGGHAMGSDEAMESFARDVVLMRQVGVNPVVVH 68 Query: 67 GGGPQIGDLLKRLSIESHFIDGMRVTDAATMDVVEMVLGGQVNKDIVNLINRHGGSAIGL 126 GGGP I +L +L I+S F+ G RVTD AT++VVEMVL G VNK IV IN GGSA+GL Sbjct: 69 GGGPMINAMLGKLDIQSEFVGGKRVTDKATVEVVEMVLSGLVNKRIVQAINGQGGSAVGL 128 Query: 127 TGKDAELIRAKKLTVTRQTPEMTKPEIIDIGHVGEVTGVNVGLLNMLVKGDFIPVIAPIG 186 +GKDA L+ + T P +G VG + +N +L+ L D IPVIAP+G Sbjct: 129 SGKDANLM----------VCDQTDP---SLGFVGSPSKMNPKVLHDLFSHDVIPVIAPLG 175 Query: 187 VGSNGESYNINADLVAGKVAEALKAEKLMLLTNIAGLMDKQGQVLTGLSTEQVNELIADG 246 G NGE++N+N D AG +A ALKA++L+LLT+++G+ + G+V+T L Q+ E+ +G Sbjct: 176 AGQNGETFNVNGDTAAGAIASALKADRLLLLTDVSGVKNAAGEVVTELKAGQIREMTLEG 235 Query: 247 TIYGGMLPKIRCALEAVQGGVTSAHIIDGRVPNAVLLEIFTDSGVGTLI 295 TI GGM+PK AL+A+ GV + I+DGR PNAVLLE+FT+ G G+LI Sbjct: 236 TIAGGMIPKTETALDALHSGVRAVVILDGRAPNAVLLELFTEHGAGSLI 284 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: 286 Number of extensions: 12 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: 287 Length adjustment: 26 Effective length of query: 275 Effective length of database: 261 Effective search space: 71775 Effective search space used: 71775 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_029621561.1 G7G_RS0100260 (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.3823926.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 9.2e-80 253.5 5.3 1.1e-79 253.2 5.3 1.1 1 NCBI__GCF_000192475.1:WP_029621561.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000192475.1:WP_029621561.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 253.2 5.3 1.1e-79 1.1e-79 2 231 .] 32 261 .. 31 261 .. 0.99 Alignments for each domain: == domain 1 score: 253.2 bits; conditional E-value: 1.1e-79 TIGR00761 2 iViKiGGaais..elleelakdiaklrkegiklvivHGGgpeinelleklgievefvnglRvTdketlevvem 72 +ViK+GG+a+ e++e++a+d++ +r++g+++v+vHGGgp+in++l kl+i+ efv+g RvTdk+t+evvem NCBI__GCF_000192475.1:WP_029621561.1 32 VVIKLGGHAMGsdEAMESFARDVVLMRQVGVNPVVVHGGGPMINAMLGKLDIQSEFVGGKRVTDKATVEVVEM 104 8*********8889*********************************************************** PP TIGR00761 73 vligkvnkelvallekhgikavGltgkDgqlltaekldkedlgyvGeikkvnkelleallkagiipviaslal 145 vl g vnk++v++++ +g +avGl+gkD++l++ ++ d + lg+vG+ +k+n+++l++l +++ipvia+l++ NCBI__GCF_000192475.1:WP_029621561.1 105 VLSGLVNKRIVQAINGQGGSAVGLSGKDANLMVCDQTDPS-LGFVGSPSKMNPKVLHDLFSHDVIPVIAPLGA 176 ***************************************9.******************************** PP TIGR00761 146 deegqllNvnaDtaAaelAaaleAekLvlLtdvaGilegdkksliseleleeieqlikqavikgGmipKveaa 218 ++g+++Nvn+DtaA+++A+al+A++L+lLtdv+G+ + + ++++el++ +i+++ ++ i+gGmipK e a NCBI__GCF_000192475.1:WP_029621561.1 177 GQNGETFNVNGDTAAGAIASALKADRLLLLTDVSGVKNA-AGEVVTELKAGQIREMTLEGTIAGGMIPKTETA 248 ***************************************.777****************************** PP TIGR00761 219 lealesgvkkvvi 231 l+al+sgv++vvi NCBI__GCF_000192475.1:WP_029621561.1 249 LDALHSGVRAVVI 261 ***********98 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (231 nodes) Target sequences: 1 (287 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: 14.93 // [ok]
This GapMind analysis is from Jul 26 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