Align acetylglutamate kinase (EC 2.7.2.8) (characterized)
to candidate WP_092344194.1 BLU87_RS01680 acetylglutamate kinase
Query= BRENDA::Q9HTN2 (301 letters) >NCBI__GCF_900107645.1:WP_092344194.1 Length = 296 Score = 362 bits (929), Expect = e-105 Identities = 175/289 (60%), Positives = 229/289 (79%) Query: 12 AKVLSEALPYIRRFVGKTLVIKYGGNAMESEELKAGFARDVVLMKAVGINPVVVHGGGPQ 71 A +L E LP+I+RF GKT+VIKYGGNAM E LK GFARD+++MK +G+NPVVVHGGGPQ Sbjct: 8 ANILMETLPWIKRFYGKTIVIKYGGNAMVEEHLKKGFARDIIMMKYIGMNPVVVHGGGPQ 67 Query: 72 IGDLLKRLSIESHFIDGMRVTDAATMDVVEMVLGGQVNKDIVNLINRHGGSAIGLTGKDA 131 IG +L+ + IES FI GMRVTD+ TMDVVEMVLGG+VNK+IV IN HGG+A+G+TGKD Sbjct: 68 IGKVLEAMHIESQFIQGMRVTDSETMDVVEMVLGGKVNKEIVTNINLHGGNAVGITGKDG 127 Query: 132 ELIRAKKLTVTRQTPEMTKPEIIDIGHVGEVTGVNVGLLNMLVKGDFIPVIAPIGVGSNG 191 L++A+KL +T P+ PEIIDIG VGEV V+ ++ L + +FIPVIAPIG G NG Sbjct: 128 GLLKARKLEMTAINPDTLTPEIIDIGMVGEVESVDPSIIQGLKENNFIPVIAPIGGGLNG 187 Query: 192 ESYNINADLVAGKVAEALKAEKLMLLTNIAGLMDKQGQVLTGLSTEQVNELIADGTIYGG 251 E++NINADLVAGK+A ALKAEKL+LLT+I G+ DKQG++++ + ++V +LI +GTI GG Sbjct: 188 ETFNINADLVAGKIAGALKAEKLILLTDIEGVKDKQGKLISTIDVQRVPDLINNGTISGG 247 Query: 252 MLPKIRCALEAVQGGVTSAHIIDGRVPNAVLLEIFTDSGVGTLISNRKR 300 M+PK+ C +EA+ GV HIIDGR+ +A LLE+FTD G+GT ++ K+ Sbjct: 248 MIPKVNCCVEAIDAGVAKTHIIDGRMEHACLLEMFTDKGIGTAVARYKK 296 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: 360 Number of extensions: 15 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: 296 Length adjustment: 27 Effective length of query: 274 Effective length of database: 269 Effective search space: 73706 Effective search space used: 73706 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_092344194.1 BLU87_RS01680 (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.13109.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 9.0 4.2e-81 257.9 9.0 1.0 1 lcl|NCBI__GCF_900107645.1:WP_092344194.1 BLU87_RS01680 acetylglutamate ki Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_900107645.1:WP_092344194.1 BLU87_RS01680 acetylglutamate kinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 257.9 9.0 4.2e-81 4.2e-81 1 231 [] 25 268 .. 25 268 .. 0.98 Alignments for each domain: == domain 1 score: 257.9 bits; conditional E-value: 4.2e-81 TIGR00761 1 tiViKiGGaais..elleelakdiaklrkegiklvivHGGgpeinelleklgievefvnglRvTdketl 67 tiViK+GG+a+ +l++ +a+di+ ++ g+++v+vHGGgp+i ++le++ ie +f++g+RvTd et+ lcl|NCBI__GCF_900107645.1:WP_092344194.1 25 TIVIKYGGNAMVeeHLKKGFARDIIMMKYIGMNPVVVHGGGPQIGKVLEAMHIESQFIQGMRVTDSETM 93 69*********98889999************************************************** PP TIGR00761 68 evvemvligkvnkelvallekhgikavGltgkDgqlltaekldke............dlgyvGeikkvn 124 +vvemvl gkvnke+v+ ++ hg +avG+tgkDg ll+a+kl+ d+g+vGe+++v+ lcl|NCBI__GCF_900107645.1:WP_092344194.1 94 DVVEMVLGGKVNKEIVTNINLHGGNAVGITGKDGGLLKARKLEMTainpdtltpeiiDIGMVGEVESVD 162 ****************************************8888888999******************* PP TIGR00761 125 kelleallkagiipviaslaldeegqllNvnaDtaAaelAaaleAekLvlLtdvaGilegdkkslisel 193 +++++ l ++++ipvia+++ +g+++N+naD +A+++A al+AekL+lLtd++G+ ++ + +lis + lcl|NCBI__GCF_900107645.1:WP_092344194.1 163 PSIIQGLKENNFIPVIAPIGGGLNGETFNINADLVAGKIAGALKAEKLILLTDIEGVKDK-QGKLISTI 230 ***********************************************************9.666***** PP TIGR00761 194 eleeieqlikqavikgGmipKveaalealesgvkkvvi 231 +++++ +li+++ i gGmipKv++++ea++ gv k +i lcl|NCBI__GCF_900107645.1:WP_092344194.1 231 DVQRVPDLINNGTISGGMIPKVNCCVEAIDAGVAKTHI 268 **********************************9998 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (231 nodes) Target sequences: 1 (296 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 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 9.49 // [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