Align arginine N-succinyltransferase; EC 2.3.1.109 (characterized)
to candidate PP_4479 PP_4479 arginine N-succinyltransferase, subunit beta
Query= CharProtDB::CH_107315 (338 letters) >FitnessBrowser__Putida:PP_4479 Length = 342 Score = 226 bits (577), Expect = 5e-64 Identities = 123/336 (36%), Positives = 198/336 (58%), Gaps = 4/336 (1%) Query: 2 LVMRPAQAADLPQVQRLAADS-PVGVTSLPDDAERLRDKILASEASFAAEVSYNGEESYF 60 +++RP +++DLP + LA + G+T+LP + ERL ++ +E SF E G+ Y Sbjct: 1 MIVRPVRSSDLPALIELARSTGTTGLTTLPANEERLGHRVGWAEKSFRGEAE-RGDTDYL 59 Query: 61 FVLEDSASGELVGCSAIVASAGFSEPFYSFRNETFVHASRSLSIHNKIHVLSLCHDLTGN 120 FVLE+ G +VG SAI + G EP+Y++R V AS+ L I+ +I L L +DLTGN Sbjct: 60 FVLEND-EGLVVGISAIAGAVGLREPWYNYRVGLTVSASQELKIYREIPTLFLANDLTGN 118 Query: 121 SLLTSFYVQRDLVQSVYAELNSRGRLLFMASHPERFADAVVVEIVGYSDEQGESPFWNAV 180 S L S +++ D + L SR R+LF+A PE F ++ E+ G SDEQG SPFW ++ Sbjct: 119 SELCSLFLRSDYRSGLNGRLLSRARMLFIAEFPELFGKKIIAEMRGMSDEQGRSPFWESL 178 Query: 181 GRNFFDLNYIEAEKLSGLKSRTFLAELMPHYPIYVPLLPDAAQESMGQVHPRAQITFDIL 240 GR+FF + + +A+ L+G+ +++F+AELMP +P+Y L +AA+ +G+VH + +L Sbjct: 179 GRHFFKMEFSQADYLTGVGNKSFIAELMPKFPLYTCFLSEAARSVIGRVHKDTEPALAML 238 Query: 241 MREGFETDNYIDIFDGGPTLHARTSGIRSIAQSRVVPVKIGEAPKSGRPYLVTNGQLQDF 300 +EGF Y+DIFD GP + T+ IR++ +S+ + + +G P+++ N + D Sbjct: 239 KQEGFNYQGYVDIFDAGPAIECDTAKIRAVRESQTLVLAVGTPGDDATPFIIHNRKRDDC 298 Query: 301 RAVVLDLDWAPGKPVALSVEAAEALGVGEGASVRLV 336 R A G + + A+ L +G G +VR V Sbjct: 299 RITAAPARLAAG-TLVVDPLTAKRLRMGVGDNVRAV 333 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: 252 Number of extensions: 15 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: 342 Length adjustment: 28 Effective length of query: 310 Effective length of database: 314 Effective search space: 97340 Effective search space used: 97340 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