Align arginine N-succinyltransferase (EC 2.3.1.109) (characterized)
to candidate Ga0059261_3996 Ga0059261_3996 arginine and ornithine succinyltransferase subunits
Query= BRENDA::P80358 (340 letters) >FitnessBrowser__Korea:Ga0059261_3996 Length = 336 Score = 223 bits (569), Expect = 4e-63 Identities = 131/334 (39%), Positives = 187/334 (55%), Gaps = 4/334 (1%) Query: 2 IVRPVTSADLPALIELARSTGTGLTTLPANEQRLQHRVSWAEKAF-RGEAERGDADYLFV 60 ++RP DL AL E+A+ TG G T LP + L+ ++ + AF R + D ++ V Sbjct: 4 LIRPAREDDLQALYEMAKLTGGGFTNLPPEKPALRAKLERSALAFSRTDDALKDELFVLV 63 Query: 61 LED-DAGKVVGISAIAGAVGLREPWYNYRVGLTVSASQELNIHREIPTLFLANDLTGNSE 119 LE+ + +V G I VG R P+Y+YR+G+ S+ L L L NDL G SE Sbjct: 64 LENSETHEVRGTCQIFTQVGQRWPFYSYRLGIETKHSEALARTFRAEILSLTNDLEGCSE 123 Query: 120 LCSLFLHADHRSGLNGKLLSRARFLFIAEFRHLFGDKLIAEMRGMSDEEGRSPFWESLGR 179 + LFLH R+G G LL+R+R+LFIA R FGD+++AE+RG+ DE G SPFW+ + Sbjct: 124 VGGLFLHPGERAGGLGMLLARSRYLFIAMHRARFGDRVLAELRGVIDEAGGSPFWDGVAG 183 Query: 180 HFFKMEFSQADYLTGVGNKAFIAELMPKFPLYTCFLSEEARGVIGRVHPNTEPALAMLKA 239 FF M F QAD + FIA+LMPK P+YT L+E AR VIG HP+ A+ ML+ Sbjct: 184 RFFGMNFQQADEFNAIHGNQFIADLMPKHPIYTAMLTEGARSVIGLPHPSGRAAMRMLEQ 243 Query: 240 EGFSYQGYVDIFDAGPAIEAETDKIRAIAESQNLVLAVGTPGDDAEPYLIHNRKREDCRI 299 EGF+++ Y+DIFD GP + A TD++ + +S+ + G A +I D R Sbjct: 244 EGFAFENYIDIFDGGPTMTARTDQVMTVRDSRTDKVVDIADGGSAS--IIARGTLSDFRA 301 Query: 300 TAAPARAAAGTLVVDPLTAKRLRLSAGASVRAVP 333 + G + VD ++A L + AG VR P Sbjct: 302 CHGRIGLSDGGVTVDAMSASILGVEAGQEVRHAP 335 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: 9 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: 336 Length adjustment: 28 Effective length of query: 312 Effective length of database: 308 Effective search space: 96096 Effective search space used: 96096 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