Align arginine N-succinyltransferase; EC 2.3.1.109 (characterized)
to candidate WP_086508151.1 BZY95_RS01050 arginine N-succinyltransferase
Query= CharProtDB::CH_107315 (338 letters) >NCBI__GCF_002151265.1:WP_086508151.1 Length = 357 Score = 246 bits (627), Expect = 8e-70 Identities = 126/335 (37%), Positives = 200/335 (59%), Gaps = 2/335 (0%) Query: 1 MLVMRPAQAADLPQVQRLAADSPVGVTSLPDDAERLRDKILASEASFAAEVSYNGEESYF 60 M+V+RP + ADLP ++RLA + +T+LP +RL ++I S SF EV + G+E Y Sbjct: 1 MMVVRPVRPADLPALERLAGLATPSLTNLPAHRDRLEERIARSRQSFGREVDFPGDEHYT 60 Query: 61 FVLEDSASGELVGCSAIVASAGFSEPFYSFRNETFVHASRSLSIHNKIHVLSLCHDLTGN 120 FVLED E+VG + + A AG E +Y++R ET +HAS+ L++ ++ LSL H+++ Sbjct: 61 FVLEDLERDEVVGTATLRAEAGAREAYYTYRQETLIHASQQLNVRREVQTLSLSHEVSET 120 Query: 121 SLLTSFYVQRDLVQSVYAELNSRGRLLFMASHPERFADAVVVEIVGYSDEQGESPFWNAV 180 + L + + + L R RL+F+A +PERFA+ + + GY DEQGESPFWN+V Sbjct: 121 TQLCALSLDPRYRGTSAESLLRRSRLMFIAQYPERFAEVLAMAFPGYLDEQGESPFWNSV 180 Query: 181 GRNFFDLNYIEAEKLSGLKSRTFLAELMPHYPIYVPLLPDAAQESMGQVHPRAQITFDIL 240 GR+FF +Y + L+G++S++F+AE+MP +P+Y+ LL A+ ++G+ HP + + Sbjct: 181 GRHFFVRDYHDINYLAGVRSKSFIAEVMPQFPLYLALLTPQARAAIGREHPAHEAAMAEM 240 Query: 241 MREGFETDNYIDIFDGGPTLHARTSGIRSIAQSRVVPVKI--GEAPKSGRPYLVTNGQLQ 298 + EGF ++D+FD GP + + + + + PV++ A P +V N +L Sbjct: 241 LAEGFMRSRHVDLFDAGPVIKGERNRLHTFRHAAWHPVRVRPAHALPDAEPAMVANQRLA 300 Query: 299 DFRAVVLDLDWAPGKPVALSVEAAEALGVGEGASV 333 DFR VV +P + LS E AE LG EG +V Sbjct: 301 DFRCVVARYALSPTGQLMLSPEHAELLGAEEGRAV 335 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: 330 Number of extensions: 12 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: 357 Length adjustment: 29 Effective length of query: 309 Effective length of database: 328 Effective search space: 101352 Effective search space used: 101352 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