Align acetylglutamate kinase (EC 2.7.2.8) (characterized)
to candidate 6936060 Sama_0257 acetylglutamate kinase (RefSeq)
Query= BRENDA::A0A140NEG9 (258 letters) >FitnessBrowser__SB2B:6936060 Length = 262 Score = 224 bits (571), Expect = 1e-63 Identities = 117/252 (46%), Positives = 167/252 (66%), Gaps = 1/252 (0%) Query: 5 LIIKLGGVLLDSEEALERLFSALVNYRESHQRPLVIVHGGGCVVDELMKGLNLPVKKKNG 64 L++K+GG LL E + RL E ++ +V+VHGGGC+VDE +K + K +G Sbjct: 8 LVLKVGGALLQCEMGMARLMDTARQLLEKGEQ-VVLVHGGGCLVDEQLKANGMETVKLDG 66 Query: 65 LRVTPADQIDIITGALAGTANKTLLAWAKKHQIAAVGLFLGDGDSVKVTQLDEELGHVGL 124 LRVTPA+Q+ II GALAGT+NK L A K + ++G+ L D + V DE LG VG Sbjct: 67 LRVTPAEQMPIIAGALAGTSNKLLQGAAAKAGVVSMGMSLCDANMVTAVIKDERLGMVGE 126 Query: 125 AQPGSPKLINSLLENGYLPVVSSIGVTDEGQLMNVNADQAATALAATLGADLILLSDVSG 184 P K + +L G+LP++SSI + ++G+L+NVNADQAA+ LA LG L+LLSDVSG Sbjct: 127 VSPKDAKALEFILAQGWLPIISSIAMGEDGELLNVNADQAASVLAKLLGGKLVLLSDVSG 186 Query: 185 ILDGKGQRIAEMTAAKAEQLIEQGIITDGMIVKVNAALDAARTLGRPVDIASWRHAEQLP 244 +LDGKG+ I + + + ++L++ G+I GM VKV AAL+ A+ LG+PV +ASWR + Q+ Sbjct: 187 VLDGKGKLIPSLNSQEIDELVKLGVIEKGMKVKVEAALEVAQWLGQPVQVASWRDSGQMA 246 Query: 245 ALFNGMPMGTRI 256 AL G +GT+I Sbjct: 247 ALIKGEAVGTQI 258 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: 218 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: 262 Length adjustment: 24 Effective length of query: 234 Effective length of database: 238 Effective search space: 55692 Effective search space used: 55692 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 6936060 Sama_0257 (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.30123.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.5e-61 191.8 5.9 7.5e-61 191.6 5.9 1.0 1 lcl|FitnessBrowser__SB2B:6936060 Sama_0257 acetylglutamate kinase Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__SB2B:6936060 Sama_0257 acetylglutamate kinase (RefSeq) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 191.6 5.9 7.5e-61 7.5e-61 2 229 .. 8 234 .. 7 236 .. 0.95 Alignments for each domain: == domain 1 score: 191.6 bits; conditional E-value: 7.5e-61 TIGR00761 2 iViKiGGaais..elleelakdiaklrkegiklvivHGGgpeinelleklgievefvnglRvTdketlevvemvlig 76 +V+K+GGa+++ + +l++ + +l ++g ++v+vHGGg+ ++e l++ g+e+ +++glRvT +e++ ++ +l+g lcl|FitnessBrowser__SB2B:6936060 8 LVLKVGGALLQceMGMARLMDTARQLLEKGEQVVLVHGGGCLVDEQLKANGMETVKLDGLRVTPAEQMPIIAGALAG 84 79*********944478999********************************************************* PP TIGR00761 77 kvnkelvallekhgikavGltgkDgqlltaekldkedlgyvGeikkvnkelleallkagiipviaslaldeegqllN 153 + nk l + +k+g+ +G++ D++++ta d+ +lg+vGe++ ++++le +l++g +p+i+s+a+ e+g+llN lcl|FitnessBrowser__SB2B:6936060 85 TSNKLLQGAAAKAGVVSMGMSLCDANMVTAVIKDE-RLGMVGEVSPKDAKALEFILAQGWLPIISSIAMGEDGELLN 160 ***************************99976555.5**************************************** PP TIGR00761 154 vnaDtaAaelAaaleAekLvlLtdvaGilegdkksliseleleeieqlikqavikgGmipKveaalealesgvkkv 229 vnaD+aA+ lA+ l+ + LvlL+dv+G+l+g k +li +l+ +ei++l+k +vi++Gm+ Kveaale ++ + + v lcl|FitnessBrowser__SB2B:6936060 161 VNADQAASVLAKLLGGK-LVLLSDVSGVLDG-KGKLIPSLNSQEIDELVKLGVIEKGMKVKVEAALEVAQWLGQPV 234 ***************99.*************.666********************************998777666 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (231 nodes) Target sequences: 1 (262 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 0.01s 00:00:00.02 Elapsed: 00:00:00.00 # Mc/sec: 7.35 // [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