Align acetylglutamate kinase (EC 2.7.2.8) (characterized)
to candidate GFF201 PGA1_c02050 acetylglutamate kinase ArgB
Query= BRENDA::Q9HTN2 (301 letters) >FitnessBrowser__Phaeo:GFF201 Length = 286 Score = 288 bits (737), Expect = 1e-82 Identities = 149/289 (51%), Positives = 202/289 (69%), Gaps = 13/289 (4%) Query: 7 DAAQVAKVLSEALPYIRRFVGKTLVIKYGGNAMESEELKAGFARDVVLMKAVGINPVVVH 66 D A+ LS ALPY++R+ G +V+K GG+AM S+E FARD+VL++ VG+NPV+VH Sbjct: 9 DWIATAETLSSALPYLQRYDGAIVVVKLGGHAMGSDEAMETFARDIVLLRQVGVNPVIVH 68 Query: 67 GGGPQIGDLLKRLSIESHFIDGMRVTDAATMDVVEMVLGGQVNKDIVNLINRHGGSAIGL 126 GGGP I +L++L I+S F++G RVTDAATM+VVEMVL G VNK IV INR GG+ +GL Sbjct: 69 GGGPMINAMLEKLQIKSDFVNGKRVTDAATMEVVEMVLSGVVNKRIVQAINRQGGAGVGL 128 Query: 127 TGKDAELIRAKKLTVTRQTPEMTKPEIIDIGHVGEVTGVNVGLLNMLVKGDFIPVIAPIG 186 +GKDA LI T T+ P D+G VG + ++ +L+ L + D IPVIAPIG Sbjct: 129 SGKDANLI-----TCTQADP--------DLGFVGTPSQMDPSVLHHLFEQDMIPVIAPIG 175 Query: 187 VGSNGESYNINADLVAGKVAEALKAEKLMLLTNIAGLMDKQGQVLTGLSTEQVNELIADG 246 G +GE++NIN D AG +A ALKA++L+LLT+++G+ + G+V+T L V + DG Sbjct: 176 AGPDGETFNINGDTAAGAIASALKADRLLLLTDVSGVKNGAGEVVTELKAADVEAMTRDG 235 Query: 247 TIYGGMLPKIRCALEAVQGGVTSAHIIDGRVPNAVLLEIFTDSGVGTLI 295 I GGM+PK AL AV+ GV + I+DGRVPNAVLLE+FTD G G++I Sbjct: 236 VIIGGMIPKTETALAAVRSGVRACTIVDGRVPNAVLLELFTDHGAGSMI 284 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: 283 Number of extensions: 10 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: 286 Length adjustment: 26 Effective length of query: 275 Effective length of database: 260 Effective search space: 71500 Effective search space used: 71500 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 GFF201 PGA1_c02050 (acetylglutamate kinase ArgB)
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.18215.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.6e-81 257.2 4.3 8e-81 256.9 4.3 1.1 1 lcl|FitnessBrowser__Phaeo:GFF201 PGA1_c02050 acetylglutamate kina Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Phaeo:GFF201 PGA1_c02050 acetylglutamate kinase ArgB # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 256.9 4.3 8e-81 8e-81 2 231 .] 32 261 .. 31 261 .. 0.98 Alignments for each domain: == domain 1 score: 256.9 bits; conditional E-value: 8e-81 TIGR00761 2 iViKiGGaais..elleelakdiaklrkegiklvivHGGgpeinelleklgievefvnglRvTdketlevvemvlig 76 +V+K+GG+a+ e++e++a+di+ lr++g+++vivHGGgp+in++lekl+i+ +fvng RvTd++t+evvemvl g lcl|FitnessBrowser__Phaeo:GFF201 32 VVVKLGGHAMGsdEAMETFARDIVLLRQVGVNPVIVHGGGPMINAMLEKLQIKSDFVNGKRVTDAATMEVVEMVLSG 108 8*********8889*************************************************************** PP TIGR00761 77 kvnkelvallekhgikavGltgkDgqlltaekldkedlgyvGeikkvnkelleallkagiipviaslaldeegqllN 153 vnk++v++++++g + vGl+gkD++l+t ++ d + lg+vG+ +++++++l++l ++++ipvia++++ +g+++N lcl|FitnessBrowser__Phaeo:GFF201 109 VVNKRIVQAINRQGGAGVGLSGKDANLITCTQADPD-LGFVGTPSQMDPSVLHHLFEQDMIPVIAPIGAGPDGETFN 184 ***********************************9.**************************************** PP TIGR00761 154 vnaDtaAaelAaaleAekLvlLtdvaGilegdkksliseleleeieqlikqavikgGmipKveaalealesgvkkvv 230 +n+DtaA+++A+al+A++L+lLtdv+G+ +g + ++++el+++++e + + +vi gGmipK e al+a++sgv++ lcl|FitnessBrowser__Phaeo:GFF201 185 INGDTAAGAIASALKADRLLLLTDVSGVKNG-AGEVVTELKAADVEAMTRDGVIIGGMIPKTETALAAVRSGVRACT 260 *******************************.777**************************************9877 PP TIGR00761 231 i 231 i lcl|FitnessBrowser__Phaeo:GFF201 261 I 261 6 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (231 nodes) Target sequences: 1 (286 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: 00:00:00.01 # Mc/sec: 5.30 // [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