Align arginine N-succinyltransferase; EC 2.3.1.109 (characterized)
to candidate Ga0059261_3996 Ga0059261_3996 arginine and ornithine succinyltransferase subunits
Query= CharProtDB::CH_107315 (338 letters) >FitnessBrowser__Korea:Ga0059261_3996 Length = 336 Score = 185 bits (470), Expect = 1e-51 Identities = 113/332 (34%), Positives = 173/332 (52%), Gaps = 3/332 (0%) Query: 3 VMRPAQAADLPQVQRLAADSPVGVTSLPDDAERLRDKILASEASFAAEVSYNGEESYFFV 62 ++RPA+ DL + +A + G T+LP + LR K+ S +F+ +E + V Sbjct: 4 LIRPAREDDLQALYEMAKLTGGGFTNLPPEKPALRAKLERSALAFSRTDDALKDELFVLV 63 Query: 63 LEDSASGELVGCSAIVASAGFSEPFYSFRNETFVHASRSLSIHNKIHVLSLCHDLTGNSL 122 LE+S + E+ G I G PFYS+R S +L+ + +LSL +DL G S Sbjct: 64 LENSETHEVRGTCQIFTQVGQRWPFYSYRLGIETKHSEALARTFRAEILSLTNDLEGCSE 123 Query: 123 LTSFYVQRDLVQSVYAELNSRGRLLFMASHPERFADAVVVEIVGYSDEQGESPFWNAVGR 182 + ++ L +R R LF+A H RF D V+ E+ G DE G SPFW+ V Sbjct: 124 VGGLFLHPGERAGGLGMLLARSRYLFIAMHRARFGDRVLAELRGVIDEAGGSPFWDGVAG 183 Query: 183 NFFDLNYIEAEKLSGLKSRTFLAELMPHYPIYVPLLPDAAQESMGQVHPRAQITFDILMR 242 FF +N+ +A++ + + F+A+LMP +PIY +L + A+ +G HP + +L + Sbjct: 184 RFFGMNFQQADEFNAIHGNQFIADLMPKHPIYTAMLTEGARSVIGLPHPSGRAAMRMLEQ 243 Query: 243 EGFETDNYIDIFDGGPTLHARTSGIRSIAQSRVVPVKIGEAPKSGRPYLVTNGQLQDFRA 302 EGF +NYIDIFDGGPT+ ART + ++ SR K+ + G ++ G L DFRA Sbjct: 244 EGFAFENYIDIFDGGPTMTARTDQVMTVRDSRT--DKVVDIADGGSASIIARGTLSDFRA 301 Query: 303 VVLDLDWAPGKPVALSVEAAEALGVGEGASVR 334 + + G V + +A LGV G VR Sbjct: 302 CHGRIGLSDG-GVTVDAMSASILGVEAGQEVR 332 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: 244 Number of extensions: 12 Number of successful extensions: 2 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: 336 Length adjustment: 28 Effective length of query: 310 Effective length of database: 308 Effective search space: 95480 Effective search space used: 95480 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