Align acetylglutamate kinase (EC 2.7.2.8) (characterized)
to candidate WP_011386705.1 AMB_RS22045 acetylglutamate kinase
Query= BRENDA::Q9HTN2 (301 letters) >NCBI__GCF_000009985.1:WP_011386705.1 Length = 300 Score = 275 bits (703), Expect = 9e-79 Identities = 138/263 (52%), Positives = 193/263 (73%), Gaps = 5/263 (1%) Query: 12 AKVLSEALPYIRRFVGKTLVIKYGGNAMESEELKAGFARDVVLMKAVGINPVVVHGGGPQ 71 AK LSEALP++R+F +TLVIK+GG+AMES++L FARDVVL+K VGINPVVVHGGGPQ Sbjct: 20 AKTLSEALPFMRQFNDETLVIKFGGHAMESDDLARLFARDVVLLKQVGINPVVVHGGGPQ 79 Query: 72 IGDLLKRLSIESHFIDGMRVTDAATMDVVEMVLGGQVNKDIVNLINRHGGSAIGLTGKDA 131 I +LKRL I++ +DG+R TD AT++VVEM+L G++NK IV+ IN GG A+GL+GKD Sbjct: 80 IDAMLKRLDIQTPRVDGLRFTDEATVEVVEMILAGKINKQIVSAINEAGGFAVGLSGKDG 139 Query: 132 ELIRAKKLTVTRQTPEMTKPEIIDIGHVGEVTGVNVGLLNMLVKGDFIPVIAPIGVGSNG 191 LIRA+KL T++ P+ +++D+G VGE +N +L+ K D IPVIAP+G+G G Sbjct: 140 HLIRARKLRRTKKDPDSNIEKVLDLGFVGEPAEINPHILDQFKKSDTIPVIAPVGMGGAG 199 Query: 192 ESYNINADLVAGKVAEALKAEKLMLLTNIAGLMDKQGQVLTGLSTEQVNELIADGTIYGG 251 E+YNINAD AG +A A A++L++LT++AG++DK G ++ ++ QV+ IADGTI GG Sbjct: 200 ETYNINADTAAGAIAGATNAKRLLMLTDVAGVLDKSGNLIPEMTAAQVHAYIADGTISGG 259 Query: 252 MLPKIRCA-----LEAVQGGVTS 269 M+ ++ + V G VT+ Sbjct: 260 MIRPLQYLALIYHIRGVHGAVTA 282 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: 293 Number of extensions: 7 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: 300 Length adjustment: 27 Effective length of query: 274 Effective length of database: 273 Effective search space: 74802 Effective search space used: 74802 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_011386705.1 AMB_RS22045 (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.6070.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8e-72 227.5 1.1 9.6e-72 227.2 1.1 1.0 1 lcl|NCBI__GCF_000009985.1:WP_011386705.1 AMB_RS22045 acetylglutamate kina Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000009985.1:WP_011386705.1 AMB_RS22045 acetylglutamate kinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 227.2 1.1 9.6e-72 9.6e-72 1 216 [. 37 265 .. 37 277 .. 0.96 Alignments for each domain: == domain 1 score: 227.2 bits; conditional E-value: 9.6e-72 TIGR00761 1 tiViKiGGaais..elleelakdiaklrkegiklvivHGGgpeinelleklgievefvnglRvTdketl 67 t+ViK GG+a++ +l + +a+d++ l+++gi++v+vHGGgp+i+++l++l+i++ v+glR Td++t+ lcl|NCBI__GCF_000009985.1:WP_011386705.1 37 TLVIKFGGHAMEsdDLARLFARDVVLLKQVGINPVVVHGGGPQIDAMLKRLDIQTPRVDGLRFTDEATV 105 68*********999999**************************************************** PP TIGR00761 68 evvemvligkvnkelvallekhgikavGltgkDgqlltaekldke............dlgyvGeikkvn 124 evvem+l+gk+nk++v +++++g avGl+gkDg+l+ a+kl + dlg+vGe ++n lcl|NCBI__GCF_000009985.1:WP_011386705.1 106 EVVEMILAGKINKQIVSAINEAGGFAVGLSGKDGHLIRARKLRRTkkdpdsniekvlDLGFVGEPAEIN 174 ****************************************7766666799******************* PP TIGR00761 125 kelleallkagiipviaslaldeegqllNvnaDtaAaelAaaleAekLvlLtdvaGilegdkkslisel 193 +++l+++ k++ ipvia++++ +g+++N+naDtaA+++A a +A++L++LtdvaG+l+++++ li e+ lcl|NCBI__GCF_000009985.1:WP_011386705.1 175 PHILDQFKKSDTIPVIAPVGMGGAGETYNINADTAAGAIAGATNAKRLLMLTDVAGVLDKSGN-LIPEM 242 ************************************************************666.***** PP TIGR00761 194 eleeieqlikqavikgGmipKve 216 ++++++ +i + i gGmi+ ++ lcl|NCBI__GCF_000009985.1:WP_011386705.1 243 TAAQVHAYIADGTISGGMIRPLQ 265 *******************8765 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (231 nodes) Target sequences: 1 (300 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: 9.81 // [ok]
This GapMind analysis is from Apr 09 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