Align arginine N-succinyltransferase (EC 2.3.1.109) (characterized)
to candidate H281DRAFT_06479 H281DRAFT_06479 arginine succinyltransferase
Query= BRENDA::P80358 (340 letters) >FitnessBrowser__Burk376:H281DRAFT_06479 Length = 352 Score = 197 bits (500), Expect = 4e-55 Identities = 117/339 (34%), Positives = 187/339 (55%), Gaps = 6/339 (1%) Query: 1 MIVRPVTSADLPALIELARSTGTGLTTLPANEQRLQHRVSWAEKAFRGEAE-RGDADYLF 59 + VRP ADL AL +AR+ L +LP + + L+ RV+ +E +FR E + G+ YLF Sbjct: 2 LFVRPGRLADLDALEHMARTAQPVLHSLPHDRRALEARVALSEDSFRAEVDFPGEEFYLF 61 Query: 60 VLED-DAGKVVGISAIAGAVGLREPWYNYRVGLTVSASQELNIHREIPTLFLANDLTGNS 118 VLED ++GK++G ++I A G +P+Y +R + AS+EL+++R+I L ++++LTG S Sbjct: 62 VLEDSESGKLMGTASIVAAAGYSDPFYAFRNDALIHASRELHVNRKIHALTMSHELTGKS 121 Query: 119 ELCSLFLHADHRSGLNGKLLSRARFLFIAEFRHLFGDKLIAEMRGMSDEEGRSPFWESLG 178 L ++ R L+SRAR ++IA R F ++ + + G++DE G SPFWE++G Sbjct: 122 RLAGYYIDPSLRGDAAAHLMSRARMMYIAANRKRFTPEVFSLLLGVTDENGVSPFWEAVG 181 Query: 179 RHFFKMEFSQADYLTGVGNKAFIAELMPKFPLYTCFLSEEARGVIGRVHPNTEPALAMLK 238 R FF F+ + +G ++ FIAE+MP +P+Y L E A+ V+G A + Sbjct: 182 RKFFGRNFADIEIESGGRSRTFIAEVMPTYPIYVPLLPEAAQRVLGEPDSKALLAYEIHL 241 Query: 239 AEGFSYQGYVDIFDAGPAIEAETDKIRAIAESQNLVLAVGTPGDDAEPYLIHNRKRED-- 296 EGF ++DIFDAGP + A+ D+ + ++ V G + YLI + + Sbjct: 242 EEGFETDRFIDIFDAGPVLTAQVDRSACVTLNETRVAHEAAAGANGSTYLIAHNGADGQF 301 Query: 297 -CRITAAPARAAAGTLVVDPLTAKRLRLSAGASVRAVPL 334 C + P G + P A L + G +VR VPL Sbjct: 302 RCVLGELPTARNEGAPLAQPARA-ALGVQDGDTVRCVPL 339 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: 289 Number of extensions: 11 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: 352 Length adjustment: 29 Effective length of query: 311 Effective length of database: 323 Effective search space: 100453 Effective search space used: 100453 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