Align acetylglutamate kinase (EC 2.7.2.8) (characterized)
to candidate WP_084056755.1 B9A12_RS04085 acetylglutamate kinase
Query= BRENDA::Q9HTN2 (301 letters) >NCBI__GCF_900176285.1:WP_084056755.1 Length = 303 Score = 345 bits (884), Expect = e-99 Identities = 171/290 (58%), Positives = 226/290 (77%), Gaps = 1/290 (0%) Query: 12 AKVLSEALPYIRRFVGKTLVIKYGGNAMESEELKAGFARDVVLMKAVGINPVVVHGGGPQ 71 A +L EALPYIR F GKT+VIKYGG+AM+ E LK FA+DVVLMK +GI+PVVVHGGGPQ Sbjct: 5 ASLLIEALPYIRHFSGKTIVIKYGGHAMKDEALKESFAKDVVLMKYIGIHPVVVHGGGPQ 64 Query: 72 IGDLLKRLSIESHFIDGMRVTDAATMDVVEMVLGGQVNKDIVNLINRHGGSAIGLTGKDA 131 IG +L R+ +S F GMRVTD TMDVVEMVL G+VNK+IV INRHGG AIGL+GKD Sbjct: 65 IGRMLDRVGKKSDFRAGMRVTDQDTMDVVEMVLAGKVNKEIVAFINRHGGRAIGLSGKDG 124 Query: 132 ELIRAKKLTVTRQTPEMTKPEIIDIGHVGEVTGVNVGLLNMLVKGDFIPVIAPIGVGSNG 191 +LI A+K+ + R + PEIIDIG VGEV +N +L +L + IPVIAP+GVG++G Sbjct: 125 QLIEARKMHIYRYQGDDQPPEIIDIGLVGEVQRINAEILKVLEQSRVIPVIAPVGVGTDG 184 Query: 192 ESYNINADLVAGKVAEALKAEKLMLLTNIAGLMDKQGQVLTGLSTEQVNELIADGTIYGG 251 E+YNINADLVAGKVA AL AEKL+L+T++ G++D+ G++++ ++ + +L+ D T+ GG Sbjct: 185 ETYNINADLVAGKVASALNAEKLILMTDVPGVLDRSGELISTMTASEAADLMQDETLKGG 244 Query: 252 MLPKIRCALEAVQGGVTSAHIIDGRVPNAVLLEIFTDSGVGT-LISNRKR 300 M+PK++CA++AVQ GV I+DGR+P+ VLLE+FTDSG+GT ++ R R Sbjct: 245 MIPKVQCAIDAVQAGVHKVAIVDGRIPHCVLLELFTDSGIGTEIVGTRTR 294 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: 341 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: 303 Length adjustment: 27 Effective length of query: 274 Effective length of database: 276 Effective search space: 75624 Effective search space used: 75624 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_084056755.1 B9A12_RS04085 (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.16933.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.1e-84 267.7 6.0 4.8e-84 267.5 6.0 1.0 1 lcl|NCBI__GCF_900176285.1:WP_084056755.1 B9A12_RS04085 acetylglutamate ki Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_900176285.1:WP_084056755.1 B9A12_RS04085 acetylglutamate kinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 267.5 6.0 4.8e-84 4.8e-84 1 231 [] 22 265 .. 22 265 .. 0.97 Alignments for each domain: == domain 1 score: 267.5 bits; conditional E-value: 4.8e-84 TIGR00761 1 tiViKiGGaais..elleelakdiaklrkegiklvivHGGgpeinelleklgievefvnglRvTdketl 67 tiViK+GG+a++ l+e++akd++ ++ gi++v+vHGGgp+i ++l+++g + +f g+RvTd++t+ lcl|NCBI__GCF_900176285.1:WP_084056755.1 22 TIVIKYGGHAMKdeALKESFAKDVVLMKYIGIHPVVVHGGGPQIGRMLDRVGKKSDFRAGMRVTDQDTM 90 69**********98899**************************************************** PP TIGR00761 68 evvemvligkvnkelvallekhgikavGltgkDgqlltaekldke............dlgyvGeikkvn 124 +vvemvl+gkvnke+va++++hg +a+Gl+gkDgql++a+k++ d+g+vGe++++n lcl|NCBI__GCF_900176285.1:WP_084056755.1 91 DVVEMVLAGKVNKEIVAFINRHGGRAIGLSGKDGQLIEARKMHIYryqgddqppeiiDIGLVGEVQRIN 159 ****************************************666555678899***************** PP TIGR00761 125 kelleallkagiipviaslaldeegqllNvnaDtaAaelAaaleAekLvlLtdvaGilegdkkslisel 193 +e+l+ l ++ +ipvia++++ +g+++N+naD +A+++A+al+AekL+l+tdv+G+l++ + +lis + lcl|NCBI__GCF_900176285.1:WP_084056755.1 160 AEILKVLEQSRVIPVIAPVGVGTDGETYNINADLVAGKVASALNAEKLILMTDVPGVLDR-SGELISTM 227 ************************************************************.555***** PP TIGR00761 194 eleeieqlikqavikgGmipKveaalealesgvkkvvi 231 +++e+++l++ + +kgGmipKv++a++a++ gv+kv i lcl|NCBI__GCF_900176285.1:WP_084056755.1 228 TASEAADLMQDETLKGGMIPKVQCAIDAVQAGVHKVAI 265 ***********************************987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (231 nodes) Target sequences: 1 (303 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: 00:00:00.01 # Mc/sec: 6.74 // [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