Align acetylglutamate kinase (EC 2.7.2.8) (characterized)
to candidate WP_011317428.1 AVA_RS02805 acetylglutamate kinase
Query= BRENDA::Q6V1L5 (301 letters) >NCBI__GCF_000204075.1:WP_011317428.1 Length = 297 Score = 435 bits (1118), Expect = e-127 Identities = 215/290 (74%), Positives = 251/290 (86%) Query: 4 EFIEAGAADRVRILSEALPYLQQFAGRTVVVKYGGAAMKQEELKEAVMRDIVFLACVGMR 63 E+I A RV++LSEALPY+QQFAGRTVVVKYGGAAMK LK+ V+RDIVFL+CVG+R Sbjct: 7 EYIRQAEATRVQVLSEALPYIQQFAGRTVVVKYGGAAMKDSHLKDQVIRDIVFLSCVGLR 66 Query: 64 PVVVHGGGPEINAWLGRVGIEPQFHNGLRVTDADTMEVVEMVLVGRVNKDIVSRINTTGG 123 P++VHGGGPEIN+WL ++GIE QF NGLRVTDA TM+VVEMVLVGRVNK+IVS IN GG Sbjct: 67 PILVHGGGPEINSWLDKLGIEAQFKNGLRVTDAPTMDVVEMVLVGRVNKEIVSLINQAGG 126 Query: 124 RAVGFCGTDGRLVLARPHDQEGIGFVGEVNSVNSEVIEPLLERGYIPVISSVAADENGQS 183 AVG CG DG L+ ARP QEGIGFVGEV++VN +++E L GYIPV+SSVAAD++GQ+ Sbjct: 127 LAVGLCGKDGNLITARPQGQEGIGFVGEVSNVNIKILETLASNGYIPVVSSVAADDSGQA 186 Query: 184 FNINADTVAGEIAAALNAEKLILLTDTRGILEDPKRPESLIPRLNIPQSRELIAQGIVGG 243 +NINADTVAGEIAAAL AEKLILLTDTRGIL+D K P +LIP+++I ++RELI G+V G Sbjct: 187 YNINADTVAGEIAAALGAEKLILLTDTRGILKDYKDPGTLIPKVDIREARELINGGVVSG 246 Query: 244 GMIPKVDCCIRSLAQGVRAAHIIDGRIPHALLLEIFTDAGIGTMIVGSGY 293 GMIPKV CC+RSLAQGVRAAHIIDGRIPHALLLEIFTD GIGTMI+GS Y Sbjct: 247 GMIPKVTCCVRSLAQGVRAAHIIDGRIPHALLLEIFTDVGIGTMILGSQY 296 Lambda K H 0.320 0.139 0.406 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: 391 Number of extensions: 14 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: 301 Length of database: 297 Length adjustment: 27 Effective length of query: 274 Effective length of database: 270 Effective search space: 73980 Effective search space used: 73980 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: 48 (23.1 bits)
Align candidate WP_011317428.1 AVA_RS02805 (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.3443503.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.3e-90 289.0 1.4 1.6e-90 288.7 1.4 1.1 1 NCBI__GCF_000204075.1:WP_011317428.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000204075.1:WP_011317428.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 288.7 1.4 1.6e-90 1.6e-90 1 231 [] 34 268 .. 34 268 .. 0.99 Alignments for each domain: == domain 1 score: 288.7 bits; conditional E-value: 1.6e-90 TIGR00761 1 tiViKiGGaais..elleelakdiaklrkegiklvivHGGgpeinelleklgievefvnglRvTdketlevve 71 t+V+K+GGaa++ +l++++++di++l +g+++++vHGGgpein +l+klgie +f+nglRvTd+ t++vve NCBI__GCF_000204075.1:WP_011317428.1 34 TVVVKYGGAAMKdsHLKDQVIRDIVFLSCVGLRPILVHGGGPEINSWLDKLGIEAQFKNGLRVTDAPTMDVVE 106 69*********98899********************************************************* PP TIGR00761 72 mvligkvnkelvallekhgikavGltgkDgqlltaekldkedlgyvGeikkvnkelleallkagiipviasla 144 mvl+g+vnke+v l++++g avGl+gkDg+l+ta+ +e +g+vGe+++vn ++le+l +g+ipv++s+a NCBI__GCF_000204075.1:WP_011317428.1 107 MVLVGRVNKEIVSLINQAGGLAVGLCGKDGNLITARPQGQEGIGFVGEVSNVNIKILETLASNGYIPVVSSVA 179 ************************************999999******************************* PP TIGR00761 145 ldeegqllNvnaDtaAaelAaaleAekLvlLtdvaGileg..dkksliseleleeieqlikqavikgGmipKv 215 +d++gq++N+naDt+A+e+Aaal+AekL+lLtd++Gil++ d +li +++++e+++li+ +v+ gGmipKv NCBI__GCF_000204075.1:WP_011317428.1 180 ADDSGQAYNINADTVAGEIAAALGAEKLILLTDTRGILKDykDPGTLIPKVDIREARELINGGVVSGGMIPKV 252 ****************************************99999**************************** PP TIGR00761 216 eaalealesgvkkvvi 231 ++++++l++gv++++i NCBI__GCF_000204075.1:WP_011317428.1 253 TCCVRSLAQGVRAAHI 268 **************98 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (231 nodes) Target sequences: 1 (297 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: 13.05 // [ok]
This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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