Align arginine N-succinyltransferase (EC 2.3.1.109) (characterized)
to candidate GFF3098 HP15_3041 arginine N-succinyltransferase, alpha chain
Query= BRENDA::P80358 (340 letters) >FitnessBrowser__Marino:GFF3098 Length = 339 Score = 204 bits (518), Expect = 3e-57 Identities = 129/338 (38%), Positives = 182/338 (53%), Gaps = 6/338 (1%) Query: 2 IVRPVTSADLPALIELARSTGTGLT-TLPANEQRLQHRVSWAEKAFRGE--AERGDADYL 58 +VRP DL ++ +A + L+ TLP L +++ + +F G AE +L Sbjct: 3 LVRPAEPDDLDQILAIAGTQCARLSSTLPKQGDALAYKIEQSLASFAGRISAEDDPPRFL 62 Query: 59 FVLED-DAGKVVGISAIAGAVGLREPWYNYRVGLTVSASQELNIHREIPTLFLANDLTGN 117 FVLED + G + G + I G +P+Y+YR + AS EL + R + L+ ++ LT Sbjct: 63 FVLEDTETGDIAGTAGIDAHAGNGQPFYSYRRDALIHASHELGVSRRVEVLYPSHSLTDV 122 Query: 118 SELCSLFLHADHRSGLNGKLLSRARFLFIAEFRHLFGDKLIAEMRGMSDEEGRSPFWESL 177 S LCS + + + +LLSRAR LFIA+ R F ++ E++G+ E+G PFW+SL Sbjct: 123 SLLCSFSIRPELQGTDAFELLSRARILFIADHREWFTQRMAVEIQGVQLEDGSVPFWDSL 182 Query: 178 GRHFFKMEFSQADYLTGVGNKAFIAELMPKFPLYTCFLSEEARGVIGRVHPNTEPALAML 237 GRHFF M+F AD +G +K FIAELMP P+Y LSE A+ +G+ H T P +L Sbjct: 183 GRHFFDMDFETADQYSGQLSKTFIAELMPPNPIYVTLLSEAAQKAMGQPHQITVPNFELL 242 Query: 238 KAEGFSYQGYVDIFDAGPAIEAETDKIRAIAESQNLVLAVGTPGDDAEPYLIHNRKREDC 297 + EGF Y+DIFDAGP +EA TD ++ + S L GT D E LI + E Sbjct: 243 QREGFQPGNYLDIFDAGPVLEARTDSLKTLVTSHPKELH-GTNEDTGETCLIAAGEGEQF 301 Query: 298 RITAAP-ARAAAGTLVVDPLTAKRLRLSAGASVRAVPL 334 R T P A + L V T L +AG VR PL Sbjct: 302 RCTLTPVAESLDDKLKVPVSTWNTLNRTAGDRVRIAPL 339 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: 280 Number of extensions: 13 Number of successful extensions: 1 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 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