Align acetylglutamate kinase (EC 2.7.2.8) (characterized)
to candidate YP_004139843.1 Mesci_0621 acetylglutamate kinase
Query= BRENDA::Q9HTN2 (301 letters) >NCBI__GCF_000185905.1:YP_004139843.1 Length = 297 Score = 283 bits (723), Expect = 4e-81 Identities = 140/295 (47%), Positives = 201/295 (68%) Query: 1 MTLSRDDAAQVAKVLSEALPYIRRFVGKTLVIKYGGNAMESEELKAGFARDVVLMKAVGI 60 MT A A +LS ALPY++R+ KT+V+KYGG+AM EL FARD+ L+K G+ Sbjct: 1 MTEITATAEMQAALLSRALPYMQRYEHKTVVVKYGGHAMGDIELGKAFARDIALLKQSGV 60 Query: 61 NPVVVHGGGPQIGDLLKRLSIESHFIDGMRVTDAATMDVVEMVLGGQVNKDIVNLINRHG 120 NP+VVHGGGPQIG +L ++ IES F G+RVTD T+++VEMVL G +NK+IV LIN G Sbjct: 61 NPIVVHGGGPQIGAMLAKMGIESKFEGGLRVTDQKTVEIVEMVLAGSINKEIVALINAEG 120 Query: 121 GSAIGLTGKDAELIRAKKLTVTRQTPEMTKPEIIDIGHVGEVTGVNVGLLNMLVKGDFIP 180 AIGL GKD ++ A+K T P+ ++D+G VGE V+ LL++L + + IP Sbjct: 121 EWAIGLCGKDGNMVFAEKARKTMIDPDSNIERVLDLGFVGEPVEVDRTLLDLLARSEMIP 180 Query: 181 VIAPIGVGSNGESYNINADLVAGKVAEALKAEKLMLLTNIAGLMDKQGQVLTGLSTEQVN 240 V+AP+ G +G +YNINAD AG +A A +A +L+ LT++ G++DK +++ L+ + Sbjct: 181 VLAPVAPGRDGHTYNINADTFAGAIAGACQATRLLFLTDVPGVLDKNKKLIDELTVAEAK 240 Query: 241 ELIADGTIYGGMLPKIRCALEAVQGGVTSAHIIDGRVPNAVLLEIFTDSGVGTLI 295 LI DGT+ GGM+PK+ +EA++ GV I++G+ P+AVLLE+FT+ G GTLI Sbjct: 241 ALIKDGTVSGGMIPKVETCIEAIERGVEGVVILNGKTPHAVLLELFTEHGAGTLI 295 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: 260 Number of extensions: 11 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: 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 YP_004139843.1 Mesci_0621 (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.29698.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.7e-79 252.6 1.7 2e-79 252.4 1.7 1.0 1 lcl|NCBI__GCF_000185905.1:YP_004139843.1 Mesci_0621 acetylglutamate kinas Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000185905.1:YP_004139843.1 Mesci_0621 acetylglutamate kinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 252.4 1.7 2e-79 2e-79 1 231 [] 29 272 .. 29 272 .. 0.97 Alignments for each domain: == domain 1 score: 252.4 bits; conditional E-value: 2e-79 TIGR00761 1 tiViKiGGaais..elleelakdiaklrkegiklvivHGGgpeinelleklgievefvnglRvTdketl 67 t+V+K+GG+a+ el +++a+dia l+++g+++++vHGGgp+i ++l k+gie +f +glRvTd++t+ lcl|NCBI__GCF_000185905.1:YP_004139843.1 29 TVVVKYGGHAMGdiELGKAFARDIALLKQSGVNPIVVHGGGPQIGAMLAKMGIESKFEGGLRVTDQKTV 97 69*********988999**************************************************** PP TIGR00761 68 evvemvligkvnkelvallekhgikavGltgkDgqlltaekldke............dlgyvGeikkvn 124 e+vemvl+g++nke+val++ +g a+Gl+gkDg+++ aek k dlg+vGe +v+ lcl|NCBI__GCF_000185905.1:YP_004139843.1 98 EIVEMVLAGSINKEIVALINAEGEWAIGLCGKDGNMVFAEKARKTmidpdsniervlDLGFVGEPVEVD 166 ****************************************8777778888******************* PP TIGR00761 125 kelleallkagiipviaslaldeegqllNvnaDtaAaelAaaleAekLvlLtdvaGilegdkkslisel 193 + ll+ l +++ipv+a++a +g+++N+naDt A+++A a +A +L++Ltdv+G+l++ +k+li+el lcl|NCBI__GCF_000185905.1:YP_004139843.1 167 RTLLDLLARSEMIPVLAPVAPGRDGHTYNINADTFAGAIAGACQATRLLFLTDVPGVLDK-NKKLIDEL 234 ************************************************************.566***** PP TIGR00761 194 eleeieqlikqavikgGmipKveaalealesgvkkvvi 231 +++e++ lik + + gGmipKve ++ea+e gv+ vvi lcl|NCBI__GCF_000185905.1:YP_004139843.1 235 TVAEAKALIKDGTVSGGMIPKVETCIEAIERGVEGVVI 272 **********************************9997 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: 8.36 // [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