Align acetylglutamate kinase (EC 2.7.2.8) (characterized)
to candidate Synpcc7942_1496 Synpcc7942_1496 acetylglutamate kinase
Query= BRENDA::Q6V1L5 (301 letters) >FitnessBrowser__SynE:Synpcc7942_1496 Length = 301 Score = 595 bits (1534), Expect = e-175 Identities = 301/301 (100%), Positives = 301/301 (100%) Query: 1 MSSEFIEAGAADRVRILSEALPYLQQFAGRTVVVKYGGAAMKQEELKEAVMRDIVFLACV 60 MSSEFIEAGAADRVRILSEALPYLQQFAGRTVVVKYGGAAMKQEELKEAVMRDIVFLACV Sbjct: 1 MSSEFIEAGAADRVRILSEALPYLQQFAGRTVVVKYGGAAMKQEELKEAVMRDIVFLACV 60 Query: 61 GMRPVVVHGGGPEINAWLGRVGIEPQFHNGLRVTDADTMEVVEMVLVGRVNKDIVSRINT 120 GMRPVVVHGGGPEINAWLGRVGIEPQFHNGLRVTDADTMEVVEMVLVGRVNKDIVSRINT Sbjct: 61 GMRPVVVHGGGPEINAWLGRVGIEPQFHNGLRVTDADTMEVVEMVLVGRVNKDIVSRINT 120 Query: 121 TGGRAVGFCGTDGRLVLARPHDQEGIGFVGEVNSVNSEVIEPLLERGYIPVISSVAADEN 180 TGGRAVGFCGTDGRLVLARPHDQEGIGFVGEVNSVNSEVIEPLLERGYIPVISSVAADEN Sbjct: 121 TGGRAVGFCGTDGRLVLARPHDQEGIGFVGEVNSVNSEVIEPLLERGYIPVISSVAADEN 180 Query: 181 GQSFNINADTVAGEIAAALNAEKLILLTDTRGILEDPKRPESLIPRLNIPQSRELIAQGI 240 GQSFNINADTVAGEIAAALNAEKLILLTDTRGILEDPKRPESLIPRLNIPQSRELIAQGI Sbjct: 181 GQSFNINADTVAGEIAAALNAEKLILLTDTRGILEDPKRPESLIPRLNIPQSRELIAQGI 240 Query: 241 VGGGMIPKVDCCIRSLAQGVRAAHIIDGRIPHALLLEIFTDAGIGTMIVGSGYHEAHQPW 300 VGGGMIPKVDCCIRSLAQGVRAAHIIDGRIPHALLLEIFTDAGIGTMIVGSGYHEAHQPW Sbjct: 241 VGGGMIPKVDCCIRSLAQGVRAAHIIDGRIPHALLLEIFTDAGIGTMIVGSGYHEAHQPW 300 Query: 301 Q 301 Q Sbjct: 301 Q 301 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: 525 Number of extensions: 13 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: 301 Length adjustment: 27 Effective length of query: 274 Effective length of database: 274 Effective search space: 75076 Effective search space used: 75076 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 Synpcc7942_1496 Synpcc7942_1496 (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.3798870.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.3e-89 284.9 0.1 2.7e-89 284.7 0.1 1.1 1 FitnessBrowser__SynE:Synpcc7942_1496 Domain annotation for each sequence (and alignments): >> FitnessBrowser__SynE:Synpcc7942_1496 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 284.7 0.1 2.7e-89 2.7e-89 1 231 [] 31 265 .. 31 265 .. 0.99 Alignments for each domain: == domain 1 score: 284.7 bits; conditional E-value: 2.7e-89 TIGR00761 1 tiViKiGGaais..elleelakdiaklrkegiklvivHGGgpeinelleklgievefvnglRvTdketlevve 71 t+V+K+GGaa++ el+e++++di++l+ +g+++v+vHGGgpein++l ++gie++f nglRvTd++t+evve FitnessBrowser__SynE:Synpcc7942_1496 31 TVVVKYGGAAMKqeELKEAVMRDIVFLACVGMRPVVVHGGGPEINAWLGRVGIEPQFHNGLRVTDADTMEVVE 103 69**********999********************************************************** PP TIGR00761 72 mvligkvnkelvallekhgikavGltgkDgqlltaekldkedlgyvGeikkvnkelleallkagiipviasla 144 mvl+g+vnk +v ++ g +avG +g Dg+l+ a+ d+e +g+vGe+++vn e++e ll+ g+ipvi+s+a FitnessBrowser__SynE:Synpcc7942_1496 104 MVLVGRVNKDIVSRINTTGGRAVGFCGTDGRLVLARPHDQEGIGFVGEVNSVNSEVIEPLLERGYIPVISSVA 176 ************************************************************************* PP TIGR00761 145 ldeegqllNvnaDtaAaelAaaleAekLvlLtdvaGileg..dkksliseleleeieqlikqavikgGmipKv 215 +de+gq +N+naDt+A+e+Aaal+AekL+lLtd++Gile+ +sli +l++ + ++li q+++ gGmipKv FitnessBrowser__SynE:Synpcc7942_1496 177 ADENGQSFNINADTVAGEIAAALNAEKLILLTDTRGILEDpkRPESLIPRLNIPQSRELIAQGIVGGGMIPKV 249 ****************************************987889*************************** PP TIGR00761 216 eaalealesgvkkvvi 231 ++++++l++gv++++i FitnessBrowser__SynE:Synpcc7942_1496 250 DCCIRSLAQGVRAAHI 265 **************98 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (231 nodes) Target sequences: 1 (301 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: 19.92 // [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