Align arginine N-succinyltransferase; EC 2.3.1.109 (characterized)
to candidate 5208067 Shew_0579 arginine N-succinyltransferase (RefSeq)
Query= CharProtDB::CH_107315 (338 letters) >FitnessBrowser__PV4:5208067 Length = 339 Score = 256 bits (653), Expect = 8e-73 Identities = 132/339 (38%), Positives = 209/339 (61%), Gaps = 1/339 (0%) Query: 1 MLVMRPAQAADLPQVQRLAADSPVGVTSLPDDAERLRDKILASEASFAAEVSYNGEESYF 60 ML++RP +++D + ++A +S G TSLP + E LR+KI EASF E+ +E Y Sbjct: 1 MLIIRPIRSSDFDALYQIAIESGHGFTSLPVNEELLRNKIARVEASFVKEIEKPFDEGYL 60 Query: 61 FVLEDSASGELVGCSAIVASAGFSEPFYSFRNETFVHASRSLSIHNKIHVLSLCHDLTGN 120 VLED+ +GE+VG + A+ G + FY +R T V+ S + + N++ L+LCHD TG Sbjct: 61 MVLEDTETGEVVGTCGLEAAVGMVDAFYHYRLGTEVYYSEQIDVRNEVETLTLCHDYTGA 120 Query: 121 SLLTSFYVQRDLVQSVYAELNSRGRLLFMASHPERFADAVVVEIVGYSDEQGESPFWNAV 180 + L + +++ ++ + SR R LF+A H ERF D V+ E+ G SD +G SPF+ + Sbjct: 121 AELCTLFLRDTYRKNNNGRMLSRSRFLFLAQHAERFGDTVIAEMRGESDAEGNSPFYGWL 180 Query: 181 GRNFFDLNYIEAEKLSGLKSRTFLAELMPHYPIYVPLLPDAAQESMGQVHPRAQITFDIL 240 +NF +++++A+ LSGL + F+AE+MP +YV LLP+ AQ+ +G+VH + ++L Sbjct: 181 QKNFLGIDFVQADYLSGLGQKAFMAEMMPKNSVYVCLLPEEAQKVIGEVHTNTRPALNLL 240 Query: 241 MREGFETDNYIDIFDGGPTLHARTSGIRSIAQSRVVPVKIGEAPKSGRPYLVTNGQLQDF 300 EGF Y+DIFDGGPT+ + IRS+ +SR++ VK+GE P S ++++N L + Sbjct: 241 QAEGFRCRGYVDIFDGGPTVECNLNDIRSVRESRLLTVKVGEMPVSSSSFIISNTLLAGY 300 Query: 301 RAVVLDLDWA-PGKPVALSVEAAEALGVGEGASVRLVAV 338 RA +L + V LS E A AL V EG +R++A+ Sbjct: 301 RATSANLMVSDETDEVILSPELAGALLVAEGEQIRVLAM 339 Lambda K H 0.319 0.135 0.387 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: 272 Number of extensions: 10 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: 338 Length of database: 339 Length adjustment: 28 Effective length of query: 310 Effective length of database: 311 Effective search space: 96410 Effective search space used: 96410 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: 49 (23.5 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
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