Align arginine N-succinyltransferase (EC 2.3.1.109) (characterized)
to candidate Pf6N2E2_2180 Arginine N-succinyltransferase, alpha subunit (EC 2.3.1.109)
Query= BRENDA::P80358 (340 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2180 Length = 338 Score = 209 bits (531), Expect = 1e-58 Identities = 120/337 (35%), Positives = 185/337 (54%), Gaps = 3/337 (0%) Query: 1 MIVRPVTSADLPALIELARSTGTGLTTLPANEQRLQHRVSWAEKAFRGEAER-GDADYLF 59 + +RPV DLP L +LAR + G+T+LP + RL+ ++ + +F + + G +Y F Sbjct: 2 LALRPVQLTDLPQLQQLARDSLVGVTSLPDDTARLEEKILDSCASFEADVQGPGAENYFF 61 Query: 60 VLED-DAGKVVGISAIAGAVGLREPWYNYRVGLTVSASQELNIHREIPTLFLANDLTGNS 118 VLED ++ ++VG S I + G EP+Y+ R S S+ELNI +P L L DL G + Sbjct: 62 VLEDLESRRLVGCSEILSSTGYNEPFYSLRNRPFSSESRELNIQHGVPALSLCQDLNGQT 121 Query: 119 ELCSLFLHADHRSGLNGKLLSRARFLFIAEFRHLFGDKLIAEMRGMSDEEGRSPFWESLG 178 L + A+ +LLSRAR +FIA F + +I E+ G S E+G+SPFW+++G Sbjct: 122 LLRGFHIDAERVRTPESELLSRARLMFIAAHPQRFAESVITEIVGFSSEDGQSPFWDAIG 181 Query: 179 RHFFKMEFSQADYLTGVGNKAFIAELMPKFPLYTCFLSEEARGVIGRVHPNTEPALAMLK 238 +HFF + + +A+ L G+ ++ F+AELMP++P+Y L A+ IGRVHP+ + A +L Sbjct: 182 QHFFDLPYVEAERLCGLQSRTFLAELMPQYPIYVPMLPPAAQACIGRVHPDGQEAFDILA 241 Query: 239 AEGFSYQGYVDIFDAGPAIEAETDKIRAIAESQNLVLAVGTPGDDAEPYLIHNRKREDCR 298 EGF YVDIFD GP + A +R I +S++ D YL+ N + + R Sbjct: 242 REGFETNNYVDIFDGGPTLHARIANVRTITQSRSATARQSLQIDARGRYLVSNDRLGNYR 301 Query: 299 ITAAPARA-AAGTLVVDPLTAKRLRLSAGASVRAVPL 334 A G + + P L + G +R V L Sbjct: 302 AIVAELDVNDEGPVALSPDMLAALGVMDGERIRVVAL 338 Lambda K H 0.320 0.136 0.398 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: 266 Number of extensions: 15 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: 340 Length of database: 338 Length adjustment: 28 Effective length of query: 312 Effective length of database: 310 Effective search space: 96720 Effective search space used: 96720 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