Align arginine N-succinyltransferase (EC 2.3.1.109) (characterized)
to candidate Pf1N1B4_5857 Arginine N-succinyltransferase (EC 2.3.1.109)
Query= BRENDA::P80358 (340 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5857 Length = 344 Score = 456 bits (1174), Expect = e-133 Identities = 221/334 (66%), Positives = 269/334 (80%) Query: 1 MIVRPVTSADLPALIELARSTGTGLTTLPANEQRLQHRVSWAEKAFRGEAERGDADYLFV 60 MI+RPV DLPAL++L + G G TTLPA+E+RL HRV WA++ F + ER DADYLFV Sbjct: 1 MIIRPVQVTDLPALLDLVQRAGPGFTTLPASEERLTHRVRWAQRTFAEQVERADADYLFV 60 Query: 61 LEDDAGKVVGISAIAGAVGLREPWYNYRVGLTVSASQELNIHREIPTLFLANDLTGNSEL 120 LEDD +VVG+SA+ GAVGLREPWYNYRVGLTVS+S +L I R++PTLFL N++TG SE+ Sbjct: 61 LEDDDQQVVGVSALVGAVGLREPWYNYRVGLTVSSSPDLGIARQLPTLFLNNEMTGQSEI 120 Query: 121 CSLFLHADHRSGLNGKLLSRARFLFIAEFRHLFGDKLIAEMRGMSDEEGRSPFWESLGRH 180 CSLFL D R G NG+LLS R LF+AEF HLFGDKLIAE+RG +DE+G SPFW+SLGRH Sbjct: 121 CSLFLRHDQRHGNNGRLLSLGRLLFVAEFPHLFGDKLIAELRGSADEQGCSPFWDSLGRH 180 Query: 181 FFKMEFSQADYLTGVGNKAFIAELMPKFPLYTCFLSEEARGVIGRVHPNTEPALAMLKAE 240 FFKM+FS AD+L+G+G+KAFIAELMP+ PLYTC L+E+A+ VIG+ HPNTEPAL +L AE Sbjct: 181 FFKMDFSHADHLSGLGSKAFIAELMPRQPLYTCLLTEQAQAVIGKPHPNTEPALKILTAE 240 Query: 241 GFSYQGYVDIFDAGPAIEAETDKIRAIAESQNLVLAVGTPGDDAEPYLIHNRKREDCRIT 300 GFS++GY+DIFDAGP IEA KIR + +SQ L LA+GT D A +LIHNR+ E+CRIT Sbjct: 241 GFSHKGYIDIFDAGPVIEAPVSKIRTVRDSQRLELAIGTLDDQAPIWLIHNRRLENCRIT 300 Query: 301 AAPARAAAGTLVVDPLTAKRLRLSAGASVRAVPL 334 A AR +L+VD LTAKRL+L G SVRAVPL Sbjct: 301 TAQARLVGNSLIVDRLTAKRLQLQPGNSVRAVPL 334 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: 391 Number of extensions: 15 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: 344 Length adjustment: 29 Effective length of query: 311 Effective length of database: 315 Effective search space: 97965 Effective search space used: 97965 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