Align arginine N-succinyltransferase; EC 2.3.1.109 (characterized)
to candidate WP_086508152.1 BZY95_RS01055 arginine N-succinyltransferase
Query= CharProtDB::CH_107315 (338 letters) >NCBI__GCF_002151265.1:WP_086508152.1 Length = 348 Score = 224 bits (571), Expect = 2e-63 Identities = 128/341 (37%), Positives = 192/341 (56%), Gaps = 9/341 (2%) Query: 4 MRPAQAADLPQVQRLAADSPVGVTSLPDDAERLRDKILASEASFAAEVSYNGEESYFFVL 63 +RP DL ++Q++A ++ VG TSLPD+ E L KI A+ A+F + +YFFVL Sbjct: 3 IRPIAEGDLDELQKIARETGVGFTSLPDNREFLAAKIAAAVAAFEQRTPAD-RRNYFFVL 61 Query: 64 EDSASGELVGCSAIVASAGFSEPFYSFRNETFVHASRSLSIHNKIHVLSLCHDLTGNSLL 123 ED SGEL GC AI G PFY +R T H+S L +H I L L D TG++ + Sbjct: 62 EDEESGELAGCCAIEGQVGREVPFYHYRLGTLAHSSVQLDLHRTIDTLFLSSDHTGDAEV 121 Query: 124 TSFYVQ-----RDLVQSVYAELNSRGRLLFMASHPERFADAVVVEIVGYSDEQGESPFWN 178 S +++ ++ L S R LFMA ++F D V+ E+ G DE+G+SPFW Sbjct: 122 ASLFLRPGFRGKERAHQRNGALLSMVRWLFMAEFRDQFPDKVLAEMRGVFDERGKSPFWE 181 Query: 179 AVGRNFFDLNYIEAEKLSGLKSRTFLAELMPHYPIYVPLLPDAAQESMGQVHPRAQITFD 238 +G +FF L++ EA++L+GL ++F+ ELMP +PIY P L D A+ +GQVH + Sbjct: 182 CLGSHFFPLDFDEADRLTGLGQKSFIGELMPKFPIYTPFLSDEARACIGQVHHDTRPALA 241 Query: 239 ILMREGFETDNYIDIFDGGPTLHARTSGIRSIAQSRVVPVKI---GEAPKSGRPYLVTNG 295 +L +EG + YIDIFDGGPT+ A +R++ +S V+I + P + +L + Sbjct: 242 MLKKEGLRWEGYIDIFDGGPTVEAYIDDVRAVRKSHCCRVEIRSGSDTPPARPRWLAAST 301 Query: 296 QLQDFRAVVLDLDWAPGKPVALSVEAAEALGVGEGASVRLV 336 + +FRA + + LS A+ LGV G S+R++ Sbjct: 302 TMAEFRAAWVACGPDEEGTLTLSETEAQRLGVAAGDSLRVL 342 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: 293 Number of extensions: 12 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: 348 Length adjustment: 29 Effective length of query: 309 Effective length of database: 319 Effective search space: 98571 Effective search space used: 98571 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