Align acetylglutamate kinase (EC 2.7.2.8) (characterized)
to candidate WP_013076224.1 BTUS_RS11390 acetylglutamate kinase
Query= BRENDA::Q6V1L5 (301 letters) >NCBI__GCF_000092905.1:WP_013076224.1 Length = 289 Score = 261 bits (667), Expect = 1e-74 Identities = 141/280 (50%), Positives = 186/280 (66%), Gaps = 4/280 (1%) Query: 12 DRVRILSEALPYLQQFAGRTVVVKYGGAAMKQEELKEAVMRDIVFLACVGMRPVVVHGGG 71 ++ +L EALPY+Q+FAG+ V+KYGG+AM + V+ DI++L VG+RPVVVHGGG Sbjct: 5 EKAAVLIEALPYIQRFAGKIFVIKYGGSAMGERFTD--VILDIIWLKQVGIRPVVVHGGG 62 Query: 72 PEINAWLGRVGIEPQFHNGLRVTDADTMEVVEMVLVGRVNKDIVSRINTTGGRAVGFCGT 131 EI A L R+G QF GLRVTD MEVVEMVL G VN +V+ N G AVG G Sbjct: 63 KEITAMLERLGHRAQFVEGLRVTDEAVMEVVEMVLSGAVNPRLVAAFNQHDGGAVGLSGA 122 Query: 132 DGRLV-LARPHDQEG-IGFVGEVNSVNSEVIEPLLERGYIPVISSVAADENGQSFNINAD 189 DG L+ +A+ H G IG+VGEV VN+ +IE LL+R IPVI+ V D G+ +N+NAD Sbjct: 123 DGMLLEVAKKHHPAGDIGYVGEVVHVNTALIEGLLDRHLIPVIAPVGVDREGRRYNVNAD 182 Query: 190 TVAGEIAAALNAEKLILLTDTRGILEDPKRPESLIPRLNIPQSRELIAQGIVGGGMIPKV 249 AG +A AL AEKL L+TD GIL + ++ ++ + R+L+ G + GGMIPKV Sbjct: 183 EAAGAVAGALGAEKLFLITDVPGILRRGPKGSEVVSKITAEEIRQLVEGGEIYGGMIPKV 242 Query: 250 DCCIRSLAQGVRAAHIIDGRIPHALLLEIFTDAGIGTMIV 289 C+ +L G + HII+G PHALLLE+FTD GIGTM++ Sbjct: 243 KACLTALEAGAKHVHIINGEDPHALLLEVFTDRGIGTMVL 282 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: 317 Number of extensions: 13 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: 301 Length of database: 289 Length adjustment: 26 Effective length of query: 275 Effective length of database: 263 Effective search space: 72325 Effective search space used: 72325 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_013076224.1 BTUS_RS11390 (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.8977.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.6e-85 272.3 1.5 1.9e-85 272.1 1.5 1.0 1 lcl|NCBI__GCF_000092905.1:WP_013076224.1 BTUS_RS11390 acetylglutamate kin Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000092905.1:WP_013076224.1 BTUS_RS11390 acetylglutamate kinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 272.1 1.5 1.9e-85 1.9e-85 2 231 .] 25 258 .. 24 258 .. 0.98 Alignments for each domain: == domain 1 score: 272.1 bits; conditional E-value: 1.9e-85 TIGR00761 2 iViKiGGaaiselleelakdiaklrkegiklvivHGGgpeinelleklgievefvnglRvTdketlevv 70 ViK+GG+a+ e ++++ di+ l+++gi++v+vHGGg+ei+++le+lg++ +fv+glRvTd++++evv lcl|NCBI__GCF_000092905.1:WP_013076224.1 25 FVIKYGGSAMGERFTDVILDIIWLKQVGIRPVVVHGGGKEITAMLERLGHRAQFVEGLRVTDEAVMEVV 93 69******************************************************************* PP TIGR00761 71 emvligkvnkelvallekhgikavGltgkDgqlltaekldke..dlgyvGeikkvnkelleallkagii 137 emvl g vn++lva++++h+ avGl+g+Dg ll++ k ++ d+gyvGe+ +vn++l+e ll+ + i lcl|NCBI__GCF_000092905.1:WP_013076224.1 94 EMVLSGAVNPRLVAAFNQHDGGAVGLSGADGMLLEVAKKHHPagDIGYVGEVVHVNTALIEGLLDRHLI 162 ***********************************996666557************************* PP TIGR00761 138 pviaslaldeegqllNvnaDtaAaelAaaleAekLvlLtdvaGileg..dkksliseleleeieqlikq 204 pvia++++d eg+ +NvnaD aA+++A al+AekL l+tdv+Gil++ ++++++s++++eei+ql++ lcl|NCBI__GCF_000092905.1:WP_013076224.1 163 PVIAPVGVDREGRRYNVNADEAAGAVAGALGAEKLFLITDVPGILRRgpKGSEVVSKITAEEIRQLVEG 231 ***********************************************9999****************** PP TIGR00761 205 avikgGmipKveaalealesgvkkvvi 231 + i+gGmipKv+a+l ale g k+v+i lcl|NCBI__GCF_000092905.1:WP_013076224.1 232 GEIYGGMIPKVKACLTALEAGAKHVHI 258 *************************98 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (231 nodes) Target sequences: 1 (289 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: 7.50 // [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