Align arginine N-succinyltransferase; EC 2.3.1.109 (characterized)
to candidate WP_090447413.1 BLS63_RS19265 arginine N-succinyltransferase
Query= CharProtDB::CH_107315 (338 letters) >NCBI__GCF_900100495.1:WP_090447413.1 Length = 338 Score = 230 bits (586), Expect = 4e-65 Identities = 125/335 (37%), Positives = 195/335 (58%), Gaps = 3/335 (0%) Query: 2 LVMRPAQAADLPQVQRLAADSPVGVTSLPDDAERLRDKILASEASFAAEVSYNGEESYFF 61 +++RP ++ADLP + LA + G+T+LP + ERL ++ +E +F + + + Y F Sbjct: 1 MIVRPVRSADLPALIDLARSTGAGLTTLPANEERLAHRVGWAEKAFRGDAA-RADADYLF 59 Query: 62 VLEDSASGELVGCSAIVASAGFSEPFYSFRNETFVHASRSLSIHNKIHVLSLCHDLTGNS 121 VLED A G +VG SA+ + G EP+Y++R V AS+ L+IH +I L L +DLTGNS Sbjct: 60 VLEDDA-GAVVGISAVAGAVGLREPWYNYRVGLTVCASQELNIHRQIPTLFLANDLTGNS 118 Query: 122 LLTSFYVQRDLVQSVYAELNSRGRLLFMASHPERFADAVVVEIVGYSDEQGESPFWNAVG 181 L S +++ D + L S+ R LF+A E F D V+ E+ G SDE G SPFW ++G Sbjct: 119 ELCSLFLRADQRTGLNGRLLSKARFLFIAEFRELFGDKVIAEMRGMSDESGRSPFWESLG 178 Query: 182 RNFFDLNYIEAEKLSGLKSRTFLAELMPHYPIYVPLLPDAAQESMGQVHPRAQITFDILM 241 R+FF + + +A+ L+G+ ++ F+AELMP +P+Y L + A+ +G+VHP + +L Sbjct: 179 RHFFKMEFSQADYLTGVGNKAFIAELMPKFPLYTCFLSEEARAVIGRVHPDTEPALAMLK 238 Query: 242 REGFETDNYIDIFDGGPTLHARTSGIRSIAQSRVVPVKIGEAPKSGRPYLVTNGQLQDFR 301 EGF Y+DIFD GP + A T+ IR++ S+ + + IG PYL+ N + +D R Sbjct: 239 AEGFSYQGYVDIFDAGPAIEAETAKIRAVQASQALVLAIGTPGDDATPYLIHNRKREDCR 298 Query: 302 AVVLDLDWAPGKPVALSVEAAEALGVGEGASVRLV 336 A G + + A+ L + G VR V Sbjct: 299 ITAAPARLAAG-TLVVDPLTAKRLQLSAGDQVRAV 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: 255 Number of extensions: 14 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: 338 Length adjustment: 28 Effective length of query: 310 Effective length of database: 310 Effective search space: 96100 Effective search space used: 96100 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 24 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