Align acetylglutamate kinase (EC 2.7.2.8) (characterized)
to candidate WP_011886331.1 acetylglutamate kinase
Query= BRENDA::Q9HTN2 (301 letters) >NCBI__GCF_000016205.1:WP_011886331.1 Length = 299 Score = 332 bits (852), Expect = 5e-96 Identities = 172/285 (60%), Positives = 211/285 (74%), Gaps = 5/285 (1%) Query: 12 AKVLSEALPYIRRFVGKTLVIKYGGNAMESEELKAGFARDVVLMKAVGINPVVVHGGGPQ 71 A++L+EALPYIRR+ GKT+VIKYGGNAM E LK GFARDV+L+K VGINPV+VHGGGPQ Sbjct: 16 AEILAEALPYIRRYHGKTVVIKYGGNAMTEERLKQGFARDVILLKLVGINPVIVHGGGPQ 75 Query: 72 IGDLLKRLSIESHFIDGMRVTDAATMDVVEMVLGGQVNKDIVNLINRHGGSAIGLTGKDA 131 I LK++ FI GMRVTD TM+VVE VLGG+V +DIV LIN GG A+GLTGKD Sbjct: 76 IDHALKKIGKAGTFIQGMRVTDEETMEVVEWVLGGEVQQDIVMLINHFGGHAVGLTGKDG 135 Query: 132 ELIRAKKLTVTRQTPEMTKP-EIIDIGHVGEVTGVNVGLLNMLVKGDFIPVIAPIGVGSN 190 LI A+KL + P+ P + IDIG VGEV +N ++ L FIPVI+PIG G + Sbjct: 136 GLIHARKLLM----PDRDNPGQYIDIGQVGEVEAINPAVVKALQDDAFIPVISPIGFGED 191 Query: 191 GESYNINADLVAGKVAEALKAEKLMLLTNIAGLMDKQGQVLTGLSTEQVNELIADGTIYG 250 G SYNINADLVAGK+A L AEKL+++TNI G+MDK G +LT LS +++ L DGTI G Sbjct: 192 GLSYNINADLVAGKLATVLNAEKLLMMTNIPGVMDKDGNLLTDLSAREIDALFEDGTISG 251 Query: 251 GMLPKIRCALEAVQGGVTSAHIIDGRVPNAVLLEIFTDSGVGTLI 295 GMLPKI AL+A + GV S HI+DGR+ ++VLLEI TD GT+I Sbjct: 252 GMLPKISSALDAAKSGVKSVHIVDGRIEHSVLLEILTDQPFGTMI 296 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: 322 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: 299 Length adjustment: 27 Effective length of query: 274 Effective length of database: 272 Effective search space: 74528 Effective search space used: 74528 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_011886331.1 (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.697267.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.3e-75 239.9 1.9 1.5e-75 239.7 1.9 1.1 1 NCBI__GCF_000016205.1:WP_011886331.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000016205.1:WP_011886331.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 239.7 1.9 1.5e-75 1.5e-75 1 231 [] 33 273 .. 33 273 .. 0.97 Alignments for each domain: == domain 1 score: 239.7 bits; conditional E-value: 1.5e-75 TIGR00761 1 tiViKiGGaais..elleelakdiaklrkegiklvivHGGgpeinelleklgievefvnglRvTdketlevve 71 t+ViK+GG+a++ +l++ +a+d++ l+ +gi++vivHGGgp+i+++l+k+g f++g+RvTd+et+evve NCBI__GCF_000016205.1:WP_011886331.1 33 TVVIKYGGNAMTeeRLKQGFARDVILLKLVGINPVIVHGGGPQIDHALKKIGKAGTFIQGMRVTDEETMEVVE 105 69*********998999******************************************************** PP TIGR00761 72 mvligkvnkelvallekhgikavGltgkDgqlltaekldke.........dlgyvGeikkvnkelleallkag 135 vl g+v++ +v l+++ g +avGltgkDg l+ a+kl d+g vGe++++n+++++al + NCBI__GCF_000016205.1:WP_011886331.1 106 WVLGGEVQQDIVMLINHFGGHAVGLTGKDGGLIHARKLLMPdrdnpgqyiDIGQVGEVEAINPAVVKALQDDA 178 ************************************5543336899*************************** PP TIGR00761 136 iipviaslaldeegqllNvnaDtaAaelAaaleAekLvlLtdvaGilegdkksliseleleeieqlikqavik 208 +ipvi+++++ e+g +N+naD +A++lA++l+AekL+++t+++G++++d++ l++ l+++ei+ l + + i NCBI__GCF_000016205.1:WP_011886331.1 179 FIPVISPIGFGEDGLSYNINADLVAGKLATVLNAEKLLMMTNIPGVMDKDGN-LLTDLSAREIDALFEDGTIS 250 *************************************************888.******************** PP TIGR00761 209 gGmipKveaalealesgvkkvvi 231 gGm pK+++al+a++sgvk+v+i NCBI__GCF_000016205.1:WP_011886331.1 251 GGMLPKISSALDAAKSGVKSVHI 273 *********************98 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (231 nodes) Target sequences: 1 (299 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: 26.61 // [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