Align arginine N-succinyltransferase; EC 2.3.1.109 (characterized)
to candidate AO356_01530 AO356_01530 arginine N-succinyltransferase
Query= CharProtDB::CH_107315 (338 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_01530 Length = 344 Score = 206 bits (525), Expect = 5e-58 Identities = 119/337 (35%), Positives = 192/337 (56%), Gaps = 3/337 (0%) Query: 2 LVMRPAQAADLPQVQRLAADSPVGVTSLPDDAERLRDKILASEASFAAEVSYNGEESYFF 61 +++RP DLP + LA + G TSLP + ERL ++ ++ +FA +V + Y F Sbjct: 1 MIVRPVALTDLPALLDLARCAGPGFTSLPANEERLAHRVRWAQRTFAGQVE-RADADYLF 59 Query: 62 VLEDSASGELVGCSAIVASAGFSEPFYSFRNETFVHASRSLSIHNKIHVLSLCHDLTGNS 121 VLED ++VG SA+ + G EP+Y++R V ++ L I +I L L ++++G S Sbjct: 60 VLEDD-DRQVVGISALTGAVGLREPWYNYRVGVTVSSAPELGIQRQIPTLFLNNEMSGQS 118 Query: 122 LLTSFYVQRDLVQSVYAELNSRGRLLFMASHPERFADAVVVEIVGYSDEQGESPFWNAVG 181 + S ++ + L S RLLF+A + F + ++ E+ G++DEQG SPFW+++G Sbjct: 119 EICSLFLHPEQRHGHNGRLLSLARLLFVAEFSQLFGEKLIAELRGHADEQGCSPFWDSLG 178 Query: 182 RNFFDLNYIEAEKLSGLKSRTFLAELMPHYPIYVPLLPDAAQESMGQVHPRAQITFDILM 241 R+FF ++ A++LSG+ +++F+AELMP P+Y LL + AQ +G+ HP + IL Sbjct: 179 RHFFQKDFSYADQLSGMGNKSFIAELMPRQPLYTCLLTEQAQAVIGKAHPNTEPALKILS 238 Query: 242 REGFETDNYIDIFDGGPTLHARTSGIRSIAQSRVVPVKIGEAPKSGRPYLVTNGQLQDFR 301 EGF YIDIFDGGP + A S IRS+ S+ + + IG + +L+ N +L++ R Sbjct: 239 AEGFSHRGYIDIFDGGPVIEAPVSKIRSVRDSQTLTLAIGTPDEQAPVWLIHNRRLENCR 298 Query: 302 AVVLDLDWAPGKPVALSVEAAEALGVGEGASVRLVAV 338 V G + + A+ L V G +VR VA+ Sbjct: 299 -VTSARARLHGNSLLVDRLTAKRLQVQPGDTVRAVAL 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: 287 Number of extensions: 19 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: 344 Length adjustment: 29 Effective length of query: 309 Effective length of database: 315 Effective search space: 97335 Effective search space used: 97335 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