Align N-acetylglutamate synthase; N-acetylglutamate kinase (EC 2.3.1.1; EC 2.7.2.8) (characterized)
to candidate N515DRAFT_3768 N515DRAFT_3768 N-acetylglutamate kinase
Query= reanno::Dyella79:N515DRAFT_3768 (438 letters) >FitnessBrowser__Dyella79:N515DRAFT_3768 Length = 438 Score = 860 bits (2221), Expect = 0.0 Identities = 438/438 (100%), Positives = 438/438 (100%) Query: 1 MEAHKHTRKTIVRLLSSMGSAKEIQQYLKRFSQLDAKRFAVVKVGGAVLRDDLPALTSSL 60 MEAHKHTRKTIVRLLSSMGSAKEIQQYLKRFSQLDAKRFAVVKVGGAVLRDDLPALTSSL Sbjct: 1 MEAHKHTRKTIVRLLSSMGSAKEIQQYLKRFSQLDAKRFAVVKVGGAVLRDDLPALTSSL 60 Query: 61 TFLQQVGLTPIVLHGAGPQLDEELSAAGIQKQTVNGLRVTSPKALAIVRKVFQEQNLRLV 120 TFLQQVGLTPIVLHGAGPQLDEELSAAGIQKQTVNGLRVTSPKALAIVRKVFQEQNLRLV Sbjct: 61 TFLQQVGLTPIVLHGAGPQLDEELSAAGIQKQTVNGLRVTSPKALAIVRKVFQEQNLRLV 120 Query: 121 EALQGMDTRATSVPSGVFTSEYLDRDVYGLVGKVSSINLAPIEASLRAGSIPVIASLGET 180 EALQGMDTRATSVPSGVFTSEYLDRDVYGLVGKVSSINLAPIEASLRAGSIPVIASLGET Sbjct: 121 EALQGMDTRATSVPSGVFTSEYLDRDVYGLVGKVSSINLAPIEASLRAGSIPVIASLGET 180 Query: 181 AEGQILNINADFAANELVRVLQPYKIVFLTGTGGLLDDKGRIIDSINLSTEYEHLMAQPW 240 AEGQILNINADFAANELVRVLQPYKIVFLTGTGGLLDDKGRIIDSINLSTEYEHLMAQPW Sbjct: 181 AEGQILNINADFAANELVRVLQPYKIVFLTGTGGLLDDKGRIIDSINLSTEYEHLMAQPW 240 Query: 241 INGGMRVKIEQIADLLSSLPLTSSVSITQPSELAKELFTHKGSGTLVRRGEKVLRYESWE 300 INGGMRVKIEQIADLLSSLPLTSSVSITQPSELAKELFTHKGSGTLVRRGEKVLRYESWE Sbjct: 241 INGGMRVKIEQIADLLSSLPLTSSVSITQPSELAKELFTHKGSGTLVRRGEKVLRYESWE 300 Query: 301 GIDLARMRELIESSFGRKVVADYFERTRPYRIYVSENYRAAMILTQEEGLAYLDKFAVLD 360 GIDLARMRELIESSFGRKVVADYFERTRPYRIYVSENYRAAMILTQEEGLAYLDKFAVLD Sbjct: 301 GIDLARMRELIESSFGRKVVADYFERTRPYRIYVSENYRAAMILTQEEGLAYLDKFAVLD 360 Query: 361 DAQGEGLGRAVWQVMREENPQLFWRSRHGNQVNIFYYAESDGCFKQERWKVFWYGLKNFG 420 DAQGEGLGRAVWQVMREENPQLFWRSRHGNQVNIFYYAESDGCFKQERWKVFWYGLKNFG Sbjct: 361 DAQGEGLGRAVWQVMREENPQLFWRSRHGNQVNIFYYAESDGCFKQERWKVFWYGLKNFG 420 Query: 421 EIERCVAHCAVRPATLMD 438 EIERCVAHCAVRPATLMD Sbjct: 421 EIERCVAHCAVRPATLMD 438 Lambda K H 0.319 0.135 0.389 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: 712 Number of extensions: 16 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: 438 Length of database: 438 Length adjustment: 32 Effective length of query: 406 Effective length of database: 406 Effective search space: 164836 Effective search space used: 164836 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: 51 (24.3 bits)
Align candidate N515DRAFT_3768 N515DRAFT_3768 (N-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.2121.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.4e-60 190.8 0.0 1.8e-60 190.3 0.0 1.1 1 lcl|FitnessBrowser__Dyella79:N515DRAFT_3768 N515DRAFT_3768 N-acetylglutamate Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Dyella79:N515DRAFT_3768 N515DRAFT_3768 N-acetylglutamate kinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 190.3 0.0 1.8e-60 1.8e-60 1 225 [. 39 259 .. 39 266 .. 0.97 Alignments for each domain: == domain 1 score: 190.3 bits; conditional E-value: 1.8e-60 TIGR00761 1 tiViKiGGaaiselleelakdiaklrkegiklvivHGGgpeinelleklgievefvnglRvTdket 66 ++V+K+GGa++++ l +l + + +l+++g+ ++++HG gp+ +e l++ gi+ ++vnglRvT ++ lcl|FitnessBrowser__Dyella79:N515DRAFT_3768 39 FAVVKVGGAVLRDDLPALTSSLTFLQQVGLTPIVLHGAGPQLDEELSAAGIQKQTVNGLRVTSPKA 104 58**************************************************************** PP TIGR00761 67 levvemvligkvnkelvallekhgikavGltgkDgqlltaekldkedlgyvGeikkvnkelleall 132 l++v++v+ + +n +lv++l+ + +a + ++ ++t e+ld++ +g+vG+++++n + +ea+l lcl|FitnessBrowser__Dyella79:N515DRAFT_3768 105 LAIVRKVFQE-QNLRLVEALQGMDTRATSVPSG---VFTSEYLDRDVYGLVGKVSSINLAPIEASL 166 ********99.9****************99999...****************************** PP TIGR00761 133 kagiipviaslaldeegqllNvnaDtaAaelAaaleAekLvlLtdvaGilegdkksliselel.ee 197 ag ipviasl+ ++egq+lN+naD aA el ++l++ k+v+Lt + G+l++ k ++i++++l e lcl|FitnessBrowser__Dyella79:N515DRAFT_3768 167 RAGSIPVIASLGETAEGQILNINADFAANELVRVLQPYKIVFLTGTGGLLDD-KGRIIDSINLsTE 231 ***************************************************9.666*******889 PP TIGR00761 198 ieqlikqavikgGmipKveaalealesg 225 +e+l+ q +i+gGm K+e++++ l+s+ lcl|FitnessBrowser__Dyella79:N515DRAFT_3768 232 YEHLMAQPWINGGMRVKIEQIADLLSSL 259 **********************999876 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (231 nodes) Target sequences: 1 (438 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: 10.29 // [ok]
This GapMind analysis is from Apr 09 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