Align acetylglutamate kinase (EC 2.7.2.8) (characterized)
to candidate WP_013834834.1 THICY_RS01430 acetylglutamate kinase
Query= BRENDA::Q9HTN2 (301 letters) >NCBI__GCF_000214825.1:WP_013834834.1 Length = 304 Score = 439 bits (1129), Expect = e-128 Identities = 212/298 (71%), Positives = 259/298 (86%) Query: 1 MTLSRDDAAQVAKVLSEALPYIRRFVGKTLVIKYGGNAMESEELKAGFARDVVLMKAVGI 60 M L++D A +A VL+EALPYI+RF GKT+V+KYGGNAM + L A FARD+VLMK VG+ Sbjct: 7 MNLNKDQAQNIASVLAEALPYIQRFAGKTIVVKYGGNAMTEDHLMASFARDIVLMKLVGM 66 Query: 61 NPVVVHGGGPQIGDLLKRLSIESHFIDGMRVTDAATMDVVEMVLGGQVNKDIVNLINRHG 120 NPVVVHGGGPQIGDLLKR+ ES F+ GMRVTD TMD+VEMVLGG VNK+IVNLI++HG Sbjct: 67 NPVVVHGGGPQIGDLLKRVGKESEFVQGMRVTDTETMDIVEMVLGGLVNKEIVNLIHQHG 126 Query: 121 GSAIGLTGKDAELIRAKKLTVTRQTPEMTKPEIIDIGHVGEVTGVNVGLLNMLVKGDFIP 180 G+++GLTGKD LI AKKL VT+ TP+M +PEIIDIGHVGEV+ +N G+++ML++GDFIP Sbjct: 127 GNSVGLTGKDGNLIMAKKLKVTKHTPDMDEPEIIDIGHVGEVSRINTGVIDMLIQGDFIP 186 Query: 181 VIAPIGVGSNGESYNINADLVAGKVAEALKAEKLMLLTNIAGLMDKQGQVLTGLSTEQVN 240 VIAP+GV G SYNINADLVAGKVAEAL+AEKLMLLTN GL+++QG++LTGL+ + V+ Sbjct: 187 VIAPVGVDEEGHSYNINADLVAGKVAEALQAEKLMLLTNTPGLLNQQGELLTGLNAKMVD 246 Query: 241 ELIADGTIYGGMLPKIRCALEAVQGGVTSAHIIDGRVPNAVLLEIFTDSGVGTLISNR 298 ELIADGTIYGGMLPKI+CAL+AVQGGV +AHI+DGRV +AV+LE+FTD GVGTLI+ R Sbjct: 247 ELIADGTIYGGMLPKIQCALDAVQGGVKAAHIVDGRVDHAVMLEVFTDEGVGTLITAR 304 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: 377 Number of extensions: 16 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: 304 Length adjustment: 27 Effective length of query: 274 Effective length of database: 277 Effective search space: 75898 Effective search space used: 75898 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_013834834.1 THICY_RS01430 (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.18160.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.3e-80 255.5 8.1 2.3e-80 255.5 8.1 1.7 2 lcl|NCBI__GCF_000214825.1:WP_013834834.1 THICY_RS01430 acetylglutamate ki Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000214825.1:WP_013834834.1 THICY_RS01430 acetylglutamate kinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? -0.4 0.0 0.035 0.035 150 172 .. 5 25 .. 2 33 .. 0.67 2 ! 255.5 8.1 2.3e-80 2.3e-80 1 231 [] 35 278 .. 35 278 .. 0.98 Alignments for each domain: == domain 1 score: -0.4 bits; conditional E-value: 0.035 TIGR00761 150 qllNvnaDtaAaelAaaleAekL 172 +++N+n D+ A ++A++l Ae+L lcl|NCBI__GCF_000214825.1:WP_013834834.1 5 KTMNLNKDQ-AQNIASVL-AEAL 25 789***998.45566555.3333 PP == domain 2 score: 255.5 bits; conditional E-value: 2.3e-80 TIGR00761 1 tiViKiGGaais..elleelakdiaklrkegiklvivHGGgpeinelleklgievefvnglRvTdketl 67 tiV+K+GG+a++ +l+ ++a+di+ ++ +g+++v+vHGGgp+i ll+++g e efv+g+RvTd et+ lcl|NCBI__GCF_000214825.1:WP_013834834.1 35 TIVVKYGGNAMTedHLMASFARDIVLMKLVGMNPVVVHGGGPQIGDLLKRVGKESEFVQGMRVTDTETM 103 69*********988899**************************************************** PP TIGR00761 68 evvemvligkvnkelvallekhgikavGltgkDgqlltaekldke............dlgyvGeikkvn 124 ++vemvl g vnke+v+l+++hg + vGltgkDg+l+ a+kl++ d+g+vGe++++n lcl|NCBI__GCF_000214825.1:WP_013834834.1 104 DIVEMVLGGLVNKEIVNLIHQHGGNSVGLTGKDGNLIMAKKLKVTkhtpdmdepeiiDIGHVGEVSRIN 172 ****************************************877777799******************** PP TIGR00761 125 kelleallkagiipviaslaldeegqllNvnaDtaAaelAaaleAekLvlLtdvaGilegdkkslisel 193 + +++ l++ ++ipvia++++deeg+ +N+naD +A+++A+al+AekL+lLt+++G+l++ + +l++ l lcl|NCBI__GCF_000214825.1:WP_013834834.1 173 TGVIDMLIQGDFIPVIAPVGVDEEGHSYNINADLVAGKVAEALQAEKLMLLTNTPGLLNQ-QGELLTGL 240 ************************************************************.666***** PP TIGR00761 194 eleeieqlikqavikgGmipKveaalealesgvkkvvi 231 +++ +++li + i+gGm pK+++al+a+++gvk+++i lcl|NCBI__GCF_000214825.1:WP_013834834.1 241 NAKMVDELIADGTIYGGMLPKIQCALDAVQGGVKAAHI 278 ************************************98 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (231 nodes) Target sequences: 1 (304 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: 10.89 // [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