Align arginine N-succinyltransferase (EC 2.3.1.109) (characterized)
to candidate WP_053935843.1 WG78_RS00585 arginine N-succinyltransferase
Query= BRENDA::P80358 (340 letters) >NCBI__GCF_001294205.1:WP_053935843.1 Length = 338 Score = 341 bits (875), Expect = 1e-98 Identities = 178/338 (52%), Positives = 231/338 (68%), Gaps = 2/338 (0%) Query: 1 MIVRPVTSADLPALIELARSTGTGLTTLPANEQRLQHRVSWAEKAFRGEAERGDADYLFV 60 M +R + +DL L+ LA++ G G+TTL A+ QRL R++ + ++ G + DA Y FV Sbjct: 1 MRIRFLQDSDLDGLLALAQAAGVGVTTLSADPQRLAARIAASTQSVEGSPDLADASYFFV 60 Query: 61 LEDDA-GKVVGISAIAGAVGLREPWYNYRVGLTVSASQELNIHREIPTLFLANDLTGNSE 119 LED+ G +VG S I A+G+ + WYNYRVGL V AS+EL I++++ TLFL +DLTG SE Sbjct: 61 LEDETTGTLVGTSGIEAAIGMHDTWYNYRVGLAVHASRELEIYKQLTTLFLNSDLTGASE 120 Query: 120 LCSLFLHADHRSGLNGKLLSRARFLFIAEFRHLFGDKLIAEMRGMSDEEGRSPFWESLGR 179 LCSLFL D R NG LLSR RFLF+AEF F +++IAEMRG+SDE GRSPFWESLGR Sbjct: 121 LCSLFLLPDWRKDGNGSLLSRCRFLFMAEFPERFSERVIAEMRGVSDENGRSPFWESLGR 180 Query: 180 HFFKMEFSQADYLTGVGNKAFIAELMPKFPLYTCFLSEEARGVIGRVHPNTEPALAMLKA 239 HFFKM+F++AD+L+ VG+K+FIAELMP +P+YTC LSEEA+ IG VHP T PA +L+ Sbjct: 181 HFFKMDFARADFLSYVGDKSFIAELMPSYPIYTCLLSEEAQAAIGEVHPGTRPARKLLEG 240 Query: 240 EGFSYQGYVDIFDAGPAIEAETDKIRAIAESQ-NLVLAVGTPGDDAEPYLIHNRKREDCR 298 EGF Y GYVDIFDAGP++E+ IRAI +S+ LAV P+L+ NRK + Sbjct: 241 EGFRYSGYVDIFDAGPSLESPLKDIRAIRDSRLYQALAVNAEPKGGVPWLVSNRKLGSFK 300 Query: 299 ITAAPARAAAGTLVVDPLTAKRLRLSAGASVRAVPLSA 336 A R +L + RL + G VRAVPLSA Sbjct: 301 CALAQTRPLEDSLPLTAAVLARLDIEDGDVVRAVPLSA 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: 339 Number of extensions: 12 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: 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 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