Align arginine N-succinyltransferase (EC 2.3.1.109) (characterized)
to candidate GFF4237 PS417_21705 arginine N-succinyltransferase
Query= BRENDA::P80358 (340 letters) >FitnessBrowser__WCS417:GFF4237 Length = 339 Score = 224 bits (570), Expect = 3e-63 Identities = 126/336 (37%), Positives = 193/336 (57%), Gaps = 4/336 (1%) Query: 1 MIVRPVTSADLPALIELARSTGTGLTTLPANEQRLQHRVSWAEKAFRGEAE-RGDADYLF 59 +++RP ADL + LA + G+T+LP + +RL +++ +E +F E G+ Y F Sbjct: 2 LVMRPAQMADLGEVQRLAADSPIGVTSLPDDVERLSDKIAASEASFAAEVSFNGEESYFF 61 Query: 60 VLED-DAGKVVGISAIAGAVGLREPWYNYRVGLTVSASQELNIHREIPTLFLANDLTGNS 118 VLED + GK+ G SAI + G EP+Y++R V AS+EL IH +I L +DLTGNS Sbjct: 62 VLEDTETGKLAGCSAIVASAGYSEPFYSFRNETFVHASRELKIHNKIHVLSQCHDLTGNS 121 Query: 119 ELCSLFLHADHRSGLNGKLLSRARFLFIAEFRHLFGDKLIAEMRGMSDEEGRSPFWESLG 178 L S ++ + +L SR R LF+A F D ++ E+ G SDE G SPFW+++G Sbjct: 122 LLTSFYVVPELVGSPWSELNSRGRLLFVASHPERFADSVVTEIVGYSDENGDSPFWDAIG 181 Query: 179 RHFFKMEFSQADYLTGVGNKAFIAELMPKFPLYTCFLSEEARGVIGRVHPNTEPALAMLK 238 R+FF + ++ A+ L G+ ++ F+AELMP +P+Y L +EA+ +G+VHP + +L Sbjct: 182 RNFFDLNYAAAERLCGLKSRTFLAELMPHYPIYVPLLPDEAQEAMGQVHPRAQITFDILM 241 Query: 239 AEGFSYQGYVDIFDAGPAIEAETDKIRAIAESQNLVLAVGTPGDD-AEPYLIHNRKREDC 297 EGF Y+DIFD GP + A IR+IA+S+ + + +G YL+ N + +D Sbjct: 242 REGFETDHYIDIFDGGPTLHARVSGIRSIAQSRVVPVKIGEMVKGVGRQYLVSNAQLQDY 301 Query: 298 RITAAPARAAAG-TLVVDPLTAKRLRLSAGASVRAV 332 R A G + +D A+ L + GASVR V Sbjct: 302 RAVMLELDYAPGKPVTLDLAAAEALGVGEGASVRLV 337 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: 295 Number of extensions: 18 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: 339 Length adjustment: 28 Effective length of query: 312 Effective length of database: 311 Effective search space: 97032 Effective search space used: 97032 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