Align arginine N-succinyltransferase (EC 2.3.1.109) (characterized)
to candidate WP_046157873.1 VL52_RS15520 arginine/ornithine succinyltransferase subunit alpha
Query= BRENDA::P80358 (340 letters) >NCBI__GCF_000971335.1:WP_046157873.1 Length = 339 Score = 232 bits (592), Expect = 9e-66 Identities = 129/336 (38%), Positives = 198/336 (58%), Gaps = 7/336 (2%) Query: 3 VRPVTSADLPALIELARSTGTGLTTLPANEQRLQHRVSWAEKAFRGEAERGDAD---YLF 59 VRPV ++DLPA+ LA+++G G+T+LP+N ++L R+ + AF EA G+A Y+F Sbjct: 4 VRPVRTSDLPAIERLAQASGIGVTSLPSNREKLFERIQQSVSAFEHEAT-GEASRDYYMF 62 Query: 60 VLEDDAGKVVGISAIAGAVGLREPWYNYRVGLTVSASQELNIHREIPTLFLANDLTGNSE 119 LE G VVG ++I + G EP+Y+YR V AS+ L ++ + L + +DLTG + Sbjct: 63 ALEQ-GGAVVGTASICASAGFDEPFYSYRSETAVHASRALKVNNRVHVLNICHDLTGTVQ 121 Query: 120 LCSLFLHADHRSGLNGKLLSRARFLFIAEFRHLFGDKLIAEMRGMSDEEGRSPFWESLGR 179 LC F+ + + G+L+SRAR LFIA R FG ++IAEM+G+ D+ G+SPFW ++GR Sbjct: 122 LCGFFVDSG-LDAIAGELMSRARLLFIAGERERFGRRIIAEMQGVHDDAGQSPFWNAIGR 180 Query: 180 HFFKMEFSQADYLTGVGNKAFIAELMPKFPLYTCFLSEEARGVIGRVHPNTEPALAMLKA 239 FF ++F Q + +K FIAELMP +P+Y L +EA+ IG++HP+ E +L Sbjct: 181 RFFNLDFLQVEQAFVSHSKTFIAELMPSYPIYVPLLPDEAQQAIGQIHPHFERVCQLLCK 240 Query: 240 EGFSYQGYVDIFDAGPAIEAETDKIRAIAESQNLVLAV-GTPGDDAEPYLIHNRKREDCR 298 EGF Y+DIFD G + AE D+++ + S+ + + + A L+ N++ Sbjct: 241 EGFEADNYLDIFDGGAVLTAELDRLKTVEHSRAYPVEIQASLPAQASLQLVSNQRLAGFA 300 Query: 299 ITAAPARAAAGTLVVDPLTAKRLRLSAGASVRAVPL 334 TAA G ++P AK L +S+G VR L Sbjct: 301 ATAARVAVVDGVAFINPDAAKALGVSSGDRVRVAGL 336 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: 270 Number of extensions: 13 Number of successful extensions: 4 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 24 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