Align acetylglutamate kinase (EC 2.7.2.8) (characterized)
to candidate WP_012282523.1 HM1_RS06540 acetylglutamate kinase
Query= BRENDA::Q6V1L5 (301 letters) >NCBI__GCF_000019165.1:WP_012282523.1 Length = 295 Score = 320 bits (819), Expect = 3e-92 Identities = 160/291 (54%), Positives = 208/291 (71%), Gaps = 11/291 (3%) Query: 10 AADRVRILSEALPYLQQFAGRTVVVKYGGAAMKQEELKEAVMRDIVFLACVGMRPVVVHG 69 A ++ IL EALPY+++F+G+TVV+KYGGAAM ++LKEAV+ D++ + VG+ PVVVHG Sbjct: 4 ALEKAGILVEALPYIKKFSGKTVVIKYGGAAMVNDQLKEAVIMDVILMKLVGIHPVVVHG 63 Query: 70 GGPEINAWLGRVGIEPQFHNGLRVTDADTMEVVEMVLVGRVNKDIVSRINTTGGRAVGFC 129 GGPEIN L R+G++ F GLRVTD TMEVVEMVL G+VNK+IV+ I GG+AVG C Sbjct: 64 GGPEINGMLDRLGLKSHFIQGLRVTDESTMEVVEMVLAGKVNKEIVALIQRFGGKAVGLC 123 Query: 130 GTDGRLVLARPHDQ----EG-------IGFVGEVNSVNSEVIEPLLERGYIPVISSVAAD 178 G DG L+ A+ + EG IGFVG+V + ++ L +RGYIPVI+ + Sbjct: 124 GKDGGLIQAKKRFELVKNEGGARVPTDIGFVGDVVKIEPGLVRELADRGYIPVIAPIGVG 183 Query: 179 ENGQSFNINADTVAGEIAAALNAEKLILLTDTRGILEDPKRPESLIPRLNIPQSRELIAQ 238 E G+S+NINADT AGE+A AL A+KL+LLTD GIL D K P SLI L I L+ + Sbjct: 184 EKGESYNINADTAAGELAQALKADKLVLLTDVEGILRDRKDPSSLISSLRIDDVPALVEE 243 Query: 239 GIVGGGMIPKVDCCIRSLAQGVRAAHIIDGRIPHALLLEIFTDAGIGTMIV 289 G++ GGMIPKV CC+ +L GV HIIDGR+PH+LLLE+FTD GIGTM++ Sbjct: 244 GVISGGMIPKVACCVEALQGGVGQTHIIDGRLPHSLLLEVFTDKGIGTMVL 294 Lambda K H 0.320 0.139 0.406 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: 350 Number of extensions: 15 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: 295 Length adjustment: 26 Effective length of query: 275 Effective length of database: 269 Effective search space: 73975 Effective search space used: 73975 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 48 (23.1 bits)
Align candidate WP_012282523.1 HM1_RS06540 (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.24539.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.4e-86 273.9 3.1 6.3e-86 273.6 3.1 1.0 1 lcl|NCBI__GCF_000019165.1:WP_012282523.1 HM1_RS06540 acetylglutamate kina Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000019165.1:WP_012282523.1 HM1_RS06540 acetylglutamate kinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 273.6 3.1 6.3e-86 6.3e-86 1 231 [] 25 270 .. 25 270 .. 0.97 Alignments for each domain: == domain 1 score: 273.6 bits; conditional E-value: 6.3e-86 TIGR00761 1 tiViKiGGaais..elleelakdiaklrkegiklvivHGGgpeinelleklgievefvnglRvTdketl 67 t+ViK+GGaa+ +l+e+++ d++ ++ +gi++v+vHGGgpein +l++lg++ +f++glRvTd++t+ lcl|NCBI__GCF_000019165.1:WP_012282523.1 25 TVVIKYGGAAMVndQLKEAVIMDVILMKLVGIHPVVVHGGGPEINGMLDRLGLKSHFIQGLRVTDESTM 93 69*********9889****************************************************** PP TIGR00761 68 evvemvligkvnkelvallekhgikavGltgkDgqlltae....kldke.......dlgyvGeikkvnk 125 evvemvl+gkvnke+val+++ g kavGl+gkDg l++a+ +++e d+g+vG++ k+++ lcl|NCBI__GCF_000019165.1:WP_012282523.1 94 EVVEMVLAGKVNKEIVALIQRFGGKAVGLCGKDGGLIQAKkrfeLVKNEggarvptDIGFVGDVVKIEP 162 ****************************************8884444449******************* PP TIGR00761 126 elleallkagiipviaslaldeegqllNvnaDtaAaelAaaleAekLvlLtdvaGileg..dkkslise 192 l+++l + g+ipvia++++ e+g+ +N+naDtaA+elA+al+A+kLvlLtdv+Gil++ d +slis+ lcl|NCBI__GCF_000019165.1:WP_012282523.1 163 GLVRELADRGYIPVIAPIGVGEKGESYNINADTAAGELAQALKADKLVLLTDVEGILRDrkDPSSLISS 231 **********************************************************99999****** PP TIGR00761 193 leleeieqlikqavikgGmipKveaalealesgvkkvvi 231 l+++++ l++++vi gGmipKv++++eal++gv + +i lcl|NCBI__GCF_000019165.1:WP_012282523.1 232 LRIDDVPALVEEGVISGGMIPKVACCVEALQGGVGQTHI 270 ***********************************9998 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (231 nodes) Target sequences: 1 (295 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: 6.87 // [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