Align acetylglutamate kinase (EC 2.7.2.8) (characterized)
to candidate WP_003556104.1 RLEG_RS00430 acetylglutamate kinase
Query= BRENDA::Q9HTN2 (301 letters) >NCBI__GCF_000023185.1:WP_003556104.1 Length = 295 Score = 293 bits (749), Expect = 4e-84 Identities = 141/293 (48%), Positives = 210/293 (71%) Query: 3 LSRDDAAQVAKVLSEALPYIRRFVGKTLVIKYGGNAMESEELKAGFARDVVLMKAVGINP 62 ++ ++ A++L++ALP+++R+ KT+V+KYGG+AM + EL FA D+ L+K G+NP Sbjct: 1 MNETESEMQARLLAKALPFMQRYENKTIVVKYGGHAMGNPELGKAFASDIALLKQSGVNP 60 Query: 63 VVVHGGGPQIGDLLKRLSIESHFIDGMRVTDAATMDVVEMVLGGQVNKDIVNLINRHGGS 122 +VVHGGGPQIG +L ++ IES F G+RVTD T+++VEMVL G +NK+IV LIN+ G Sbjct: 61 IVVHGGGPQIGAMLSKMGIESKFEGGLRVTDQKTVEIVEMVLAGSINKEIVALINQTGEW 120 Query: 123 AIGLTGKDAELIRAKKLTVTRQTPEMTKPEIIDIGHVGEVTGVNVGLLNMLVKGDFIPVI 182 AIGL GKD ++ A+K T + P+ ++D+G VGEV V+ LL++L + + IPVI Sbjct: 121 AIGLCGKDGNMVFAEKARKTIKDPDSNIERVLDLGFVGEVVEVDRTLLDLLARSEMIPVI 180 Query: 183 APIGVGSNGESYNINADLVAGKVAEALKAEKLMLLTNIAGLMDKQGQVLTGLSTEQVNEL 242 AP+ G +G +YNINAD AG +A AL A +L+ LT++ G++DK GQ++ LS + + L Sbjct: 181 APVAPGRDGATYNINADTFAGAIAGALNATRLLFLTDVPGVLDKNGQLIKELSVAEAHAL 240 Query: 243 IADGTIYGGMLPKIRCALEAVQGGVTSAHIIDGRVPNAVLLEIFTDSGVGTLI 295 IADGTI GGM+PK+ ++A++ GV I++G+ ++VLLEIFT+ GVGTLI Sbjct: 241 IADGTISGGMIPKVETCIDAIKAGVQGVVILNGKTAHSVLLEIFTEHGVGTLI 293 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: 259 Number of extensions: 13 Number of successful extensions: 1 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_003556104.1 RLEG_RS00430 (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.3353.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.1e-80 256.5 2.7 1.3e-80 256.3 2.7 1.0 1 lcl|NCBI__GCF_000023185.1:WP_003556104.1 RLEG_RS00430 acetylglutamate kin Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000023185.1:WP_003556104.1 RLEG_RS00430 acetylglutamate kinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 256.3 2.7 1.3e-80 1.3e-80 1 231 [] 27 270 .. 27 270 .. 0.98 Alignments for each domain: == domain 1 score: 256.3 bits; conditional E-value: 1.3e-80 TIGR00761 1 tiViKiGGaais..elleelakdiaklrkegiklvivHGGgpeinelleklgievefvnglRvTdketl 67 tiV+K+GG+a+ el +++a+dia l+++g+++++vHGGgp+i ++l+k+gie +f +glRvTd++t+ lcl|NCBI__GCF_000023185.1:WP_003556104.1 27 TIVVKYGGHAMGnpELGKAFASDIALLKQSGVNPIVVHGGGPQIGAMLSKMGIESKFEGGLRVTDQKTV 95 69*********9899****************************************************** PP TIGR00761 68 evvemvligkvnkelvallekhgikavGltgkDgqlltaekldke............dlgyvGeikkvn 124 e+vemvl+g++nke+val+++ g a+Gl+gkDg+++ aek k dlg+vGe+ +v+ lcl|NCBI__GCF_000023185.1:WP_003556104.1 96 EIVEMVLAGSINKEIVALINQTGEWAIGLCGKDGNMVFAEKARKTikdpdsniervlDLGFVGEVVEVD 164 ****************************************7777777799******************* PP TIGR00761 125 kelleallkagiipviaslaldeegqllNvnaDtaAaelAaaleAekLvlLtdvaGilegdkkslisel 193 + ll+ l +++ipvia++a +g ++N+naDt A+++A al+A +L++Ltdv+G+l+++++ li+el lcl|NCBI__GCF_000023185.1:WP_003556104.1 165 RTLLDLLARSEMIPVIAPVAPGRDGATYNINADTFAGAIAGALNATRLLFLTDVPGVLDKNGQ-LIKEL 232 ************************************************************666.***** PP TIGR00761 194 eleeieqlikqavikgGmipKveaalealesgvkkvvi 231 +++e++ li + i gGmipKve +++a++ gv+ vvi lcl|NCBI__GCF_000023185.1:WP_003556104.1 233 SVAEAHALIADGTISGGMIPKVETCIDAIKAGVQGVVI 270 **********************************9997 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 11.89 // [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