Align acetylglutamate kinase (EC 2.7.2.8) (characterized)
to candidate WP_038216199.1 Q392_RS27375 acetylglutamate kinase
Query= BRENDA::Q9HTN2 (301 letters) >NCBI__GCF_000745855.1:WP_038216199.1 Length = 297 Score = 331 bits (848), Expect = 1e-95 Identities = 169/288 (58%), Positives = 216/288 (75%), Gaps = 5/288 (1%) Query: 12 AKVLSEALPYIRRFVGKTLVIKYGGNAMESEELKAGFARDVVLMKAVGINPVVVHGGGPQ 71 A++L++ALPYIR++ GKT+VIKYGGNAM L+A FA DVVL+K VGINPVVVHGGGPQ Sbjct: 14 AEILAQALPYIRKYHGKTMVIKYGGNAMTDPALQADFAEDVVLLKLVGINPVVVHGGGPQ 73 Query: 72 IGDLLKRLSIESHFIDGMRVTDAATMDVVEMVLGGQVNKDIVNLINRHGGSAIGLTGKDA 131 I L +L + HFI GMRVTDA TM+VVE VL G+V +DIV LIN+ GG A+GLTG+D Sbjct: 74 IEAALNKLGKKGHFIQGMRVTDAETMEVVEWVLAGEVQQDIVGLINQAGGKAVGLTGRDG 133 Query: 132 ELIRAKKLTVT-RQTPEMTKPEIIDIGHVGEVTGVNVGLLNMLVKGDFIPVIAPIGVGSN 190 LIRA+KL + R P + + D+G VG++ ++ G++ L FIPV++PIG G Sbjct: 134 GLIRAQKLKMADRNDPAL----MHDVGQVGDIVSIDPGVVQALQDDAFIPVVSPIGFGEE 189 Query: 191 GESYNINADLVAGKVAEALKAEKLMLLTNIAGLMDKQGQVLTGLSTEQVNELIADGTIYG 250 ESYNINAD+VAGK+A LKAEKL+LLTN G++DK GQ+LT LS ++++L ADGTI G Sbjct: 190 NESYNINADVVAGKLATVLKAEKLVLLTNTPGVLDKNGQLLTNLSAREIDDLFADGTISG 249 Query: 251 GMLPKIRCALEAVQGGVTSAHIIDGRVPNAVLLEIFTDSGVGTLISNR 298 GMLPKI AL+A + GV + HIIDGRVP+++LLEI TD GT+I R Sbjct: 250 GMLPKIEGALDAAKSGVNAVHIIDGRVPHSMLLEILTDQAYGTMIRAR 297 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: 321 Number of extensions: 15 Number of successful extensions: 3 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 WP_038216199.1 Q392_RS27375 (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.2606696.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.4e-77 244.7 4.1 5.2e-77 244.5 4.1 1.0 1 NCBI__GCF_000745855.1:WP_038216199.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000745855.1:WP_038216199.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 244.5 4.1 5.2e-77 5.2e-77 1 231 [] 31 271 .. 31 271 .. 0.98 Alignments for each domain: == domain 1 score: 244.5 bits; conditional E-value: 5.2e-77 TIGR00761 1 tiViKiGGaais..elleelakdiaklrkegiklvivHGGgpeinelleklgievefvnglRvTdketlevve 71 t+ViK+GG+a++ l+ ++a+d++ l+ +gi++v+vHGGgp+i+++l+klg + +f++g+RvTd+et+evve NCBI__GCF_000745855.1:WP_038216199.1 31 TMVIKYGGNAMTdpALQADFAEDVVLLKLVGINPVVVHGGGPQIEAALNKLGKKGHFIQGMRVTDAETMEVVE 103 69**********9889********************************************************* PP TIGR00761 72 mvligkvnkelvallekhgikavGltgkDgqlltaekldke.........dlgyvGeikkvnkelleallkag 135 vl+g+v++ +v l++++g kavGltg Dg l+ a+kl+ + d+g vG+i ++++ +++al + NCBI__GCF_000745855.1:WP_038216199.1 104 WVLAGEVQQDIVGLINQAGGKAVGLTGRDGGLIRAQKLKMAdrndpalmhDVGQVGDIVSIDPGVVQALQDDA 176 ************************************88777779***************************** PP TIGR00761 136 iipviaslaldeegqllNvnaDtaAaelAaaleAekLvlLtdvaGilegdkksliseleleeieqlikqavik 208 +ipv++++++ ee++ +N+naD++A++lA++l+AekLvlLt+++G+l+++++ l+++l+++ei++l + i NCBI__GCF_000745855.1:WP_038216199.1 177 FIPVVSPIGFGEENESYNINADVVAGKLATVLKAEKLVLLTNTPGVLDKNGQ-LLTNLSAREIDDLFADGTIS 248 *************************************************666.******************** PP TIGR00761 209 gGmipKveaalealesgvkkvvi 231 gGm pK+e al+a++sgv++v+i NCBI__GCF_000745855.1:WP_038216199.1 249 GGMLPKIEGALDAAKSGVNAVHI 271 *********************98 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 17.51 // [ok]
This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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