Align acetylglutamate kinase (EC 2.7.2.8) (characterized)
to candidate 5207681 Shew_0203 acetylglutamate kinase (RefSeq)
Query= BRENDA::A0A140NEG9 (258 letters) >FitnessBrowser__PV4:5207681 Length = 261 Score = 237 bits (605), Expect = 2e-67 Identities = 126/253 (49%), Positives = 171/253 (67%), Gaps = 1/253 (0%) Query: 5 LIIKLGGVLLDSEEALERLFSALVNYRESHQRPLVIVHGGGCVVDELMKGLNLPVKKKNG 64 L++K+GG L+ E L RL ++ N +S Q +++VHGGGC+VDE +K + K +G Sbjct: 8 LVLKVGGALMQCEMGLARLMASAANIIKSGQS-VILVHGGGCLVDEQLKANGMETVKLDG 66 Query: 65 LRVTPADQIDIITGALAGTANKTLLAWAKKHQIAAVGLFLGDGDSVKVTQLDEELGHVGL 124 LRVTP +Q+ I+ GALAGT+NK L A A K I +VG+ L DG V + DE+LG VG Sbjct: 67 LRVTPEEQVPIVVGALAGTSNKILQASAIKAGITSVGMSLCDGAIVNGSIKDEQLGFVGE 126 Query: 125 AQPGSPKLINSLLENGYLPVVSSIGVTDEGQLMNVNADQAATALAATLGADLILLSDVSG 184 P P +N LL G++P+VSSI V D G L+NVNADQAAT +A + L+LLSDVSG Sbjct: 127 VSPNDPTYLNFLLAQGWMPIVSSIAVDDAGNLLNVNADQAATVIAKLVEGQLVLLSDVSG 186 Query: 185 ILDGKGQRIAEMTAAKAEQLIEQGIITDGMIVKVNAALDAARTLGRPVDIASWRHAEQLP 244 +LDGKGQ I + A A++L + G+I GM VKV AAL+ A+ +G+PV +ASWR AEQL Sbjct: 187 VLDGKGQLIKTLDKAHADELTKLGVIEKGMKVKVEAALEVAQWMGQPVQVASWRDAEQLS 246 Query: 245 ALFNGMPMGTRIL 257 AL G +GT+++ Sbjct: 247 ALEKGESIGTQVM 259 Lambda K H 0.317 0.136 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: 217 Number of extensions: 8 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: 258 Length of database: 261 Length adjustment: 24 Effective length of query: 234 Effective length of database: 237 Effective search space: 55458 Effective search space used: 55458 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 (21.6 bits) S2: 47 (22.7 bits)
Align candidate 5207681 Shew_0203 (acetylglutamate kinase (RefSeq))
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.7366.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.9e-60 190.3 6.6 2.2e-60 190.1 6.6 1.0 1 lcl|FitnessBrowser__PV4:5207681 Shew_0203 acetylglutamate kinase Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__PV4:5207681 Shew_0203 acetylglutamate kinase (RefSeq) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 190.1 6.6 2.2e-60 2.2e-60 1 228 [. 7 233 .. 7 236 .. 0.95 Alignments for each domain: == domain 1 score: 190.1 bits; conditional E-value: 2.2e-60 TIGR00761 1 tiViKiGGaais..elleelakdiaklrkegiklvivHGGgpeinelleklgievefvnglRvTdketlevvemvlig 76 t+V+K+GGa+++ l +l++ +a++ k+g+++++vHGGg+ ++e l++ g+e+ +++glRvT +e++ +v +l+g lcl|FitnessBrowser__PV4:5207681 7 TLVLKVGGALMQceMGLARLMASAANIIKSGQSVILVHGGGCLVDEQLKANGMETVKLDGLRVTPEEQVPIVVGALAG 84 589*********9555899*********************************************************** PP TIGR00761 77 kvnkelvallekhgikavGltgkDgqlltaekldkedlgyvGeikkvnkelleallkagiipviaslaldeegqllNv 154 + nk l a k+gi vG++ Dg ++ + d++ lg+vGe++ ++ l+ ll++g +p+++s+a+d++g+llNv lcl|FitnessBrowser__PV4:5207681 85 TSNKILQASAIKAGITSVGMSLCDGAIVNGSIKDEQ-LGFVGEVSPNDPTYLNFLLAQGWMPIVSSIAVDDAGNLLNV 161 **************************9999766665.***************************************** PP TIGR00761 155 naDtaAaelAaaleAekLvlLtdvaGilegdkksliseleleeieqlikqavikgGmipKveaalealesgvkk 228 naD+aA+ +A+ +e + LvlL+dv+G+l+g+++ li+ l+ +++++l k +vi++Gm+ Kveaale ++ + lcl|FitnessBrowser__PV4:5207681 162 NADQAATVIAKLVEGQ-LVLLSDVSGVLDGKGQ-LIKTLDKAHADELTKLGVIEKGMKVKVEAALEVAQWMGQP 233 ***************9.*************555.*******************************998866655 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (231 nodes) Target sequences: 1 (261 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: 7.38 // [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