Align arginine N-succinyltransferase (EC 2.3.1.109) (characterized)
to candidate CCNA_01678 CCNA_01678 arginine N-succinyltransferase, beta chain
Query= BRENDA::P80358 (340 letters) >FitnessBrowser__Caulo:CCNA_01678 Length = 334 Score = 223 bits (568), Expect = 5e-63 Identities = 128/333 (38%), Positives = 192/333 (57%), Gaps = 6/333 (1%) Query: 1 MIVRPVTSADLPALIELARSTGTGLTTLPANEQRLQHRVSWAEKAFRGEAERGDADYLFV 60 ++VRP SAD AL+ELA +G G T+LP +E L+ R++ +E +F+ +A Y + Sbjct: 2 LVVRPAGSADFEALMELAVLSGRGFTSLPEDEPTLRSRLALSEASFQAGVAPPEAWYTLM 61 Query: 61 LED-DAGKVVGISAIAGAVGLREPWYNYRVGLTVSASQELNIHREIPTLFLANDLTGNSE 119 LED + G V G++ + VGL+ P++++RV +S L + + L L N+ G SE Sbjct: 62 LEDLETGTVEGVAGVKAGVGLKRPFFSFRVVTLAQSSPTLEMRFDHKALVLVNECAGWSE 121 Query: 120 LCSLFLHADHRSGLNGKLLSRARFLFIAEFRHLFGDKLIAEMRGMSDEEGRSPFWESLGR 179 + SLFL + R G G+LL+++R++ I F + ++AE+RG DE+GR PFWE + Sbjct: 122 VGSLFLRPEKRKGGAGRLLAQSRYMLIGIEPQRFAEMVLAELRGWFDEDGRCPFWEHVSH 181 Query: 180 HFFKMEFSQADYLTGVGNKAFIAELMPKFPLYTCFLSEEARGVIGRVHPNTEPALAMLKA 239 FF+++F QAD ++ + FI +L P+ P+YT L EEAR VIGRVH + E A AML+ Sbjct: 182 KFFRLDFDQADLMSASTDGQFILDLAPRHPIYTELLPEEARDVIGRVHRDGEAARAMLER 241 Query: 240 EGFSYQGYVDIFDAGPAIEAETDKIRAIAESQNLVLAVGTPGDDA--EPYLIHNRKREDC 297 EGF YQG VD+FDAGP + D IR + +++ L + V G+DA E LI + Sbjct: 242 EGFRYQGLVDLFDAGPTVACPRDDIRTVRDARRLRVKV---GEDAYGEEALISTGEVSRF 298 Query: 298 RITAAPARAAAGTLVVDPLTAKRLRLSAGASVR 330 R AP T ++ L + G VR Sbjct: 299 RAVRAPVLIDGETAILGRDAMDALGVGEGEVVR 331 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: 262 Number of extensions: 8 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: 334 Length adjustment: 28 Effective length of query: 312 Effective length of database: 306 Effective search space: 95472 Effective search space used: 95472 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