Align acetylglutamate kinase (EC 2.7.2.8) (characterized)
to candidate WP_013684120.1 ARCVE_RS07250 acetylglutamate kinase
Query= BRENDA::Q9X2A4 (282 letters) >NCBI__GCF_000194625.1:WP_013684120.1 Length = 290 Score = 294 bits (752), Expect = 2e-84 Identities = 148/289 (51%), Positives = 207/289 (71%), Gaps = 13/289 (4%) Query: 3 IDTVNVLLEALPYIKEFYGKTFVIKFGGSAMKQENAKKAFIQDIILLKYTGIKPIIVHGG 62 ++ V ++EALP+IKEF+G VIK GG AM E+ + I+DI+LL + GIKP+++HGG Sbjct: 1 MEKVEAIVEALPFIKEFHGSCMVIKIGGHAMVSEDVLEKTIRDILLLYFVGIKPVVIHGG 60 Query: 63 GPAISQMMKDLGIEPVFKNGHRVTDEKTMEIVEMVLVGKINKEIVMNLNLHGGRAVGICG 122 GP I++ M+ LGI+P F +G RVTD++TMEIVEMVL GKIN +IV +GG+AVG+ G Sbjct: 61 GPEITEKMERLGIKPKFVDGLRVTDKETMEIVEMVLDGKINSKIVTTFIKNGGKAVGLSG 120 Query: 123 KDSKLIVAEKETKHG---------DIGYVGKVKKVNPEILHALIENDYIPVIAPVGIGED 173 KD L+VA+K+ K D+GYVG+ + VNPEIL LIE +IPV++PV + Sbjct: 121 KDGLLVVAKKKVKKKKEGDREIIIDLGYVGETEYVNPEILQILIEKGFIPVVSPVAADLE 180 Query: 174 GHSYNINADTAAAEIAKSLMAEKLILLTDVDGVLKD----GKLISTLTPDEAEELIRDGT 229 G+ YN+NAD A IA +L A+KLI+LTDV G+L D LI+ + DE E+++++G Sbjct: 181 GNCYNLNADLVAGNIAAALKAKKLIMLTDVPGILSDLSDKASLITRIRADELEQMLKEGK 240 Query: 230 VTGGMIPKVECAVSAVRGGVGAVHIINGGLEHAILLEIFSRKGIGTMIK 278 + GGM+PKVE ++A+RGGV HII+G EH+ILLE+F+RKGIGTM++ Sbjct: 241 LRGGMVPKVEAVLTALRGGVERAHIIDGSREHSILLELFTRKGIGTMVE 289 Lambda K H 0.318 0.140 0.393 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: 324 Number of extensions: 16 Number of successful extensions: 3 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: 282 Length of database: 290 Length adjustment: 26 Effective length of query: 256 Effective length of database: 264 Effective search space: 67584 Effective search space used: 67584 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 WP_013684120.1 ARCVE_RS07250 (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.24713.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2e-90 288.4 5.1 2.4e-90 288.1 5.1 1.1 1 lcl|NCBI__GCF_000194625.1:WP_013684120.1 ARCVE_RS07250 acetylglutamate ki Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000194625.1:WP_013684120.1 ARCVE_RS07250 acetylglutamate kinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 288.1 5.1 2.4e-90 2.4e-90 2 231 .] 22 265 .. 21 265 .. 0.97 Alignments for each domain: == domain 1 score: 288.1 bits; conditional E-value: 2.4e-90 TIGR00761 2 iViKiGGaais..elleelakdiaklrkegiklvivHGGgpeinelleklgievefvnglRvTdketle 68 +ViKiGG+a+ ++le++++di l+ +gik+v++HGGgpei+e +e+lgi+++fv+glRvTdket+e lcl|NCBI__GCF_000194625.1:WP_013684120.1 22 MVIKIGGHAMVseDVLEKTIRDILLLYFVGIKPVVIHGGGPEITEKMERLGIKPKFVDGLRVTDKETME 90 8*********9999******************************************************* PP TIGR00761 69 vvemvligkvnkelvallekhgikavGltgkDgqlltae.kldke.........dlgyvGeikkvnkel 127 +vemvl gk+n+++v+++ k+g kavGl+gkDg l++a+ k++k+ dlgyvGe++ vn+e+ lcl|NCBI__GCF_000194625.1:WP_013684120.1 91 IVEMVLDGKINSKIVTTFIKNGGKAVGLSGKDGLLVVAKkKVKKKkegdreiiiDLGYVGETEYVNPEI 159 ***************************************644444789********************* PP TIGR00761 128 leallkagiipviaslaldeegqllNvnaDtaAaelAaaleAekLvlLtdvaGileg..dkkslisele 194 l+ l+++g+ipv++++a+d eg+++N+naD +A+++Aaal+A+kL++Ltdv+Gil++ dk+sli++++ lcl|NCBI__GCF_000194625.1:WP_013684120.1 160 LQILIEKGFIPVVSPVAADLEGNCYNLNADLVAGNIAAALKAKKLIMLTDVPGILSDlsDKASLITRIR 228 ********************************************************************* PP TIGR00761 195 leeieqlikqavikgGmipKveaalealesgvkkvvi 231 ++e+eq++k++ ++gGm+pKvea+l al++gv++++i lcl|NCBI__GCF_000194625.1:WP_013684120.1 229 ADELEQMLKEGKLRGGMVPKVEAVLTALRGGVERAHI 265 ***********************************98 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (231 nodes) Target sequences: 1 (290 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 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 7.59 // [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