Align arginine N-succinyltransferase; EC 2.3.1.109 (characterized)
to candidate WP_053935843.1 WG78_RS00585 arginine N-succinyltransferase
Query= CharProtDB::CH_107315 (338 letters) >NCBI__GCF_001294205.1:WP_053935843.1 Length = 338 Score = 223 bits (569), Expect = 4e-63 Identities = 136/338 (40%), Positives = 194/338 (57%), Gaps = 11/338 (3%) Query: 4 MRPAQAADLPQVQRLAADSPVGVTSLPDDAERLRDKILASEASFAAEVSYNGEESYFFVL 63 +R Q +DL + LA + VGVT+L D +RL +I AS S + SYFFVL Sbjct: 3 IRFLQDSDLDGLLALAQAAGVGVTTLSADPQRLAARIAASTQSVEGSPDL-ADASYFFVL 61 Query: 64 EDSASGELVGCSAIVASAGFSEPFYSFRNETFVHASRSLSIHNKIHVLSLCHDLTGNSLL 123 ED +G LVG S I A+ G + +Y++R VHASR L I+ ++ L L DLTG S L Sbjct: 62 EDETTGTLVGTSGIEAAIGMHDTWYNYRVGLAVHASRELEIYKQLTTLFLNSDLTGASEL 121 Query: 124 TSFYVQRDLVQSVYAELNSRGRLLFMASHPERFADAVVVEIVGYSDEQGESPFWNAVGRN 183 S ++ D + L SR R LFMA PERF++ V+ E+ G SDE G SPFW ++GR+ Sbjct: 122 CSLFLLPDWRKDGNGSLLSRCRFLFMAEFPERFSERVIAEMRGVSDENGRSPFWESLGRH 181 Query: 184 FFDLNYIEAEKLSGLKSRTFLAELMPHYPIYVPLLPDAAQESMGQVHPRAQITFDILMRE 243 FF +++ A+ LS + ++F+AELMP YPIY LL + AQ ++G+VHP + +L E Sbjct: 182 FFKMDFARADFLSYVGDKSFIAELMPSYPIYTCLLSEEAQAAIGEVHPGTRPARKLLEGE 241 Query: 244 GFETDNYIDIFDGGPTLHARTSGIRSIAQSRVV-PVKIGEAPKSGRPYLVTNGQLQDFRA 302 GF Y+DIFD GP+L + IR+I SR+ + + PK G P+LV+N +L F+ Sbjct: 242 GFRYSGYVDIFDAGPSLESPLKDIRAIRDSRLYQALAVNAEPKGGVPWLVSNRKLGSFKC 301 Query: 303 VVLDLDWAPGKPVALSVEAAEA----LGVGEGASVRLV 336 + A +P+ S+ A L + +G VR V Sbjct: 302 AL-----AQTRPLEDSLPLTAAVLARLDIEDGDVVRAV 334 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: 282 Number of extensions: 13 Number of successful extensions: 3 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