Align N-succinylglutamate kinase (EC 2.7.2.-) (characterized)
to candidate 352922 BT3395 putative acetylglutamate kinase (NCBI ptt file)
Query= reanno::Btheta:352922 (257 letters) >FitnessBrowser__Btheta:352922 Length = 257 Score = 495 bits (1274), Expect = e-145 Identities = 257/257 (100%), Positives = 257/257 (100%) Query: 1 MREKLTVIKVGGKIVEEEATLLQLLNDFAAISGHKVLVHGGGRSATKIAAQLGIESKMVN 60 MREKLTVIKVGGKIVEEEATLLQLLNDFAAISGHKVLVHGGGRSATKIAAQLGIESKMVN Sbjct: 1 MREKLTVIKVGGKIVEEEATLLQLLNDFAAISGHKVLVHGGGRSATKIAAQLGIESKMVN 60 Query: 61 GRRITDAETLKVVTMVYGGLVNKNIVAGLQARGVNALGLTGADMNVIRSVKRPVKEVDYG 120 GRRITDAETLKVVTMVYGGLVNKNIVAGLQARGVNALGLTGADMNVIRSVKRPVKEVDYG Sbjct: 61 GRRITDAETLKVVTMVYGGLVNKNIVAGLQARGVNALGLTGADMNVIRSVKRPVKEVDYG 120 Query: 121 FVGDVEKVDASLLADLIHKGVVPVMAPLTHDGQGNMLNTNADTIAGETAKALSALFDVTL 180 FVGDVEKVDASLLADLIHKGVVPVMAPLTHDGQGNMLNTNADTIAGETAKALSALFDVTL Sbjct: 121 FVGDVEKVDASLLADLIHKGVVPVMAPLTHDGQGNMLNTNADTIAGETAKALSALFDVTL 180 Query: 181 VYCFEKKGVLRDENDDDSVIPEITRAEFEQYVADGVIQGGMIPKLENSFEAINAGVTEVV 240 VYCFEKKGVLRDENDDDSVIPEITRAEFEQYVADGVIQGGMIPKLENSFEAINAGVTEVV Sbjct: 181 VYCFEKKGVLRDENDDDSVIPEITRAEFEQYVADGVIQGGMIPKLENSFEAINAGVTEVV 240 Query: 241 ITLASAIKDNEGTRIKK 257 ITLASAIKDNEGTRIKK Sbjct: 241 ITLASAIKDNEGTRIKK 257 Lambda K H 0.316 0.135 0.366 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: 3 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: 257 Length of database: 257 Length adjustment: 24 Effective length of query: 233 Effective length of database: 233 Effective search space: 54289 Effective search space used: 54289 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 352922 BT3395 (putative acetylglutamate kinase (NCBI ptt file))
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.1179510.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8.2e-65 204.6 6.7 9.3e-65 204.4 6.7 1.0 1 FitnessBrowser__Btheta:352922 Domain annotation for each sequence (and alignments): >> FitnessBrowser__Btheta:352922 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 204.4 6.7 9.3e-65 9.3e-65 2 231 .] 6 241 .. 5 241 .. 0.94 Alignments for each domain: == domain 1 score: 204.4 bits; conditional E-value: 9.3e-65 TIGR00761 2 iViKiGGaaiselleelakdiaklrkegiklvivHGGgpeinelleklgievefvnglRvTdketlevvemvligkvnke 81 ViK+GG++++e +l++ + +++ + v+vHGGg+ ++++ +lgie ++vng R+Td+etl+vv+mv+ g vnk+ FitnessBrowser__Btheta:352922 6 TVIKVGGKIVEE-EATLLQLLNDFAAISGHKVLVHGGGRSATKIAAQLGIESKMVNGRRITDAETLKVVTMVYGGLVNKN 84 69*********7.677777777777776677************************************************* PP TIGR00761 82 lvallekhgikavGltgkDgqlltae..kldkedlgyvGeikkvnkelleallkagiipviaslaldeegqllNvnaDta 159 +va l+ +g++a+Gltg+D +++ +++ d+g+vG+++kv+++ll +l+++g++pv+a+l d +g++lN+naDt+ FitnessBrowser__Btheta:352922 85 IVAGLQARGVNALGLTGADMNVIRSVkrPVKEVDYGFVGDVEKVDASLLADLIHKGVVPVMAPLTHDGQGNMLNTNADTI 164 ***********************98855566669********************************************** PP TIGR00761 160 AaelAaaleAe...kLvlLtdvaGileg..dkksliseleleeieqlikqavikgGmipKveaalealesgvkkvvi 231 A+e A+al A Lv+ +++G+l++ d +s+i e++ +e eq++ +vi+gGmipK+e+ ea++ gv +vvi FitnessBrowser__Btheta:352922 165 AGETAKALSALfdvTLVYCFEKKGVLRDenDDDSVIPEITRAEFEQYVADGVIQGGMIPKLENSFEAINAGVTEVVI 241 **********64457***********99899999*****************************************98 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (231 nodes) Target sequences: 1 (257 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: 11.52 // [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