Align acetylglutamate kinase (EC 2.7.2.8) (characterized)
to candidate WP_026605792.1 METAC_RS0102300 acetylglutamate kinase
Query= BRENDA::Q9HTN2 (301 letters) >NCBI__GCF_000427445.1:WP_026605792.1 Length = 294 Score = 273 bits (698), Expect = 3e-78 Identities = 136/292 (46%), Positives = 200/292 (68%), Gaps = 8/292 (2%) Query: 5 RDDAAQVAKVLSEALPYIRRFVGKTLVIKYGGNAMESEELKAGFARDVVLMKAVGINPVV 64 ++ A + A +L +ALP++ + +V+KYGG+AM +++ FARD+VL++ G+NPVV Sbjct: 10 QERAQEQAAILMQALPHMLHYDEAIVVVKYGGHAMGDDKVGRDFARDMVLLEQSGVNPVV 69 Query: 65 VHGGGPQIGDLLKRLSIESHFIDGMRVTDAATMDVVEMVLGGQVNKDIVNLINRHGGSAI 124 VHGGGPQIG +L +L I+S F DG+R+TD AT+++VEMVL G +NK IV IN GG AI Sbjct: 70 VHGGGPQIGAMLAKLGIKSAFADGLRITDRATIEIVEMVLAGSINKQIVGFINAEGGRAI 129 Query: 125 GLTGKDAELIRAKKLTVTRQTPEMTKPEIIDIGHVGEVTGVNVGLLNMLVKGDFIPVIAP 184 GL GKD ++ A K T ID+G VGE V+ +L+ ++ + IPV+AP Sbjct: 130 GLCGKDGNMVIANKAAPTSGA--------IDLGFVGEPAKVDTTVLDQVLGRELIPVLAP 181 Query: 185 IGVGSNGESYNINADLVAGKVAEALKAEKLMLLTNIAGLMDKQGQVLTGLSTEQVNELIA 244 I G +GE+YN+NAD AG +A ALKA++L+ LT++ G++DK ++ L +Q++ LIA Sbjct: 182 IAQGVDGETYNVNADTFAGAIAGALKAKRLLFLTDVPGVLDKNKDLIKELRVDQIHALIA 241 Query: 245 DGTIYGGMLPKIRCALEAVQGGVTSAHIIDGRVPNAVLLEIFTDSGVGTLIS 296 DGTI GGM+PK+ + A++ GV I+DG+ P+AVL+E+ TD G GTLI+ Sbjct: 242 DGTITGGMIPKVETCIYALEQGVEGVVILDGKTPHAVLVELLTDHGAGTLIT 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: 289 Number of extensions: 8 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: 294 Length adjustment: 26 Effective length of query: 275 Effective length of database: 268 Effective search space: 73700 Effective search space used: 73700 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_026605792.1 METAC_RS0102300 (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.2671.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.6e-81 258.1 4.1 4.5e-81 257.8 4.1 1.1 1 lcl|NCBI__GCF_000427445.1:WP_026605792.1 METAC_RS0102300 acetylglutamate Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000427445.1:WP_026605792.1 METAC_RS0102300 acetylglutamate kinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 257.8 4.1 4.5e-81 4.5e-81 2 231 .] 35 269 .. 34 269 .. 0.98 Alignments for each domain: == domain 1 score: 257.8 bits; conditional E-value: 4.5e-81 TIGR00761 2 iViKiGGaais..elleelakdiaklrkegiklvivHGGgpeinelleklgievefvnglRvTdketle 68 +V+K+GG+a+ ++ +++a+d++ l+++g+++v+vHGGgp+i ++l klgi+ f +glR+Td++t+e lcl|NCBI__GCF_000427445.1:WP_026605792.1 35 VVVKYGGHAMGddKVGRDFARDMVLLEQSGVNPVVVHGGGPQIGAMLAKLGIKSAFADGLRITDRATIE 103 8*********888899***************************************************** PP TIGR00761 69 vvemvligkvnkelvallekhgikavGltgkDgqlltaekldke....dlgyvGeikkvnkelleallk 133 +vemvl+g++nk++v +++ +g +a+Gl+gkDg++++a+k dlg+vGe kv++ +l+++l lcl|NCBI__GCF_000427445.1:WP_026605792.1 104 IVEMVLAGSINKQIVGFINAEGGRAIGLCGKDGNMVIANKAAPTsgaiDLGFVGEPAKVDTTVLDQVLG 172 ***************************************888877899********************* PP TIGR00761 134 agiipviaslaldeegqllNvnaDtaAaelAaaleAekLvlLtdvaGilegdkksliseleleeieqli 202 + ipv+a++a +g+++NvnaDt A+++A al+A++L++Ltdv+G+l+++k+ li+el++++i+ li lcl|NCBI__GCF_000427445.1:WP_026605792.1 173 RELIPVLAPIAQGVDGETYNVNADTFAGAIAGALKAKRLLFLTDVPGVLDKNKD-LIKELRVDQIHALI 240 ***************************************************666.************** PP TIGR00761 203 kqavikgGmipKveaalealesgvkkvvi 231 + i+gGmipKve ++ ale+gv+ vvi lcl|NCBI__GCF_000427445.1:WP_026605792.1 241 ADGTITGGMIPKVETCIYALEQGVEGVVI 269 *************************9997 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (231 nodes) Target sequences: 1 (294 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 0.01s 00:00:00.02 Elapsed: 00:00:00.00 # Mc/sec: 7.53 // [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