Align Arginine N-succinyltransferase (EC 2.3.1.109) (characterized)
to candidate Pf1N1B4_5856 Arginine N-succinyltransferase, alpha subunit (EC 2.3.1.109)
Query= reanno::Marino:GFF3098 (339 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5856 Length = 343 Score = 198 bits (504), Expect = 1e-55 Identities = 116/281 (41%), Positives = 160/281 (56%), Gaps = 2/281 (0%) Query: 1 MWLVRPAEPDDLDQILAIAGTQCARLSSTLPKQGDALAYKIEQSLASFAGRISAEDDPPR 60 M ++RP E DL Q+ +A ++S LP + L KI S ASF + P Sbjct: 1 MLVLRPVELTDLPQLQQLARDSLVGVTS-LPDDTERLREKILASCASFEKDVQGHG-PEN 58 Query: 61 FLFVLEDTETGDIAGTAGIDAHAGNGQPFYSYRRDALIHASHELGVSRRVEVLYPSHSLT 120 + FVLE+ T +AG + I A AG +PFYS R AS EL + V L H L+ Sbjct: 59 YFFVLENLTTRRLAGCSEILATAGFNEPFYSLRNRHFTSASRELNIEHGVPALSLCHDLS 118 Query: 121 DVSLLCSFSIRPELQGTDAFELLSRARILFIADHREWFTQRMAVEIQGVQLEDGSVPFWD 180 +LL F I L+ T ELLSRAR+LFIA H F + + EI G E G PFWD Sbjct: 119 GHTLLRGFHIDAALERTRFSELLSRARLLFIAAHTARFAEAVITEIVGYSDEQGQSPFWD 178 Query: 181 SLGRHFFDMDFETADQYSGQLSKTFIAELMPPNPIYVTLLSEAAQKAMGQPHQITVPNFE 240 +LG+HFFD+ + A++ G S+TF+AELMP PIYV +L AAQ +G+ H F+ Sbjct: 179 ALGKHFFDLPYVEAERLCGLQSRTFLAELMPQYPIYVPMLPPAAQACIGRIHPDGQEAFD 238 Query: 241 LLQREGFQPGNYLDIFDAGPVLEARTDSLKTLVTSHPKELH 281 +L+REGF+ +Y+D+FDAGP L ART +++++ S +H Sbjct: 239 ILEREGFETNSYIDLFDAGPTLYARTSNIRSIAQSQIGTVH 279 Lambda K H 0.319 0.135 0.403 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: 299 Number of extensions: 14 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: 339 Length of database: 343 Length adjustment: 29 Effective length of query: 310 Effective length of database: 314 Effective search space: 97340 Effective search space used: 97340 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 (21.7 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