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= CharProtDB::CH_107315 (338 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5856 Length = 343 Score = 398 bits (1023), Expect = e-115 Identities = 201/343 (58%), Positives = 262/343 (76%), Gaps = 5/343 (1%) Query: 1 MLVMRPAQAADLPQVQRLAADSPVGVTSLPDDAERLRDKILASEASFAAEVSYNGEESYF 60 MLV+RP + DLPQ+Q+LA DS VGVTSLPDD ERLR+KILAS ASF +V +G E+YF Sbjct: 1 MLVLRPVELTDLPQLQQLARDSLVGVTSLPDDTERLREKILASCASFEKDVQGHGPENYF 60 Query: 61 FVLEDSASGELVGCSAIVASAGFSEPFYSFRNETFVHASRSLSIHNKIHVLSLCHDLTGN 120 FVLE+ + L GCS I+A+AGF+EPFYS RN F ASR L+I + + LSLCHDL+G+ Sbjct: 61 FVLENLTTRRLAGCSEILATAGFNEPFYSLRNRHFTSASRELNIEHGVPALSLCHDLSGH 120 Query: 121 SLLTSFYVQRDLVQSVYAELNSRGRLLFMASHPERFADAVVVEIVGYSDEQGESPFWNAV 180 +LL F++ L ++ ++EL SR RLLF+A+H RFA+AV+ EIVGYSDEQG+SPFW+A+ Sbjct: 121 TLLRGFHIDAALERTRFSELLSRARLLFIAAHTARFAEAVITEIVGYSDEQGQSPFWDAL 180 Query: 181 GRNFFDLNYIEAEKLSGLKSRTFLAELMPHYPIYVPLLPDAAQESMGQVHPRAQITFDIL 240 G++FFDL Y+EAE+L GL+SRTFLAELMP YPIYVP+LP AAQ +G++HP Q FDIL Sbjct: 181 GKHFFDLPYVEAERLCGLQSRTFLAELMPQYPIYVPMLPPAAQACIGRIHPDGQEAFDIL 240 Query: 241 MREGFETDNYIDIFDGGPTLHARTSGIRSIAQSRVVPVKIGEAPKSG-----RPYLVTNG 295 REGFET++YID+FD GPTL+ARTS IRSIAQS++ V A + YLV+N Sbjct: 241 EREGFETNSYIDLFDAGPTLYARTSNIRSIAQSQIGTVHPDSATDARGSSLVSNYLVSND 300 Query: 296 QLQDFRAVVLDLDWAPGKPVALSVEAAEALGVGEGASVRLVAV 338 L+D+RA+V +LD+ G+PVALS E AL V + +++RL+A+ Sbjct: 301 SLKDYRAIVAELDYHAGQPVALSAEMCAALNVTDASAIRLIAL 343 Lambda K H 0.319 0.135 0.387 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: 356 Number of extensions: 12 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: 338 Length of database: 343 Length adjustment: 28 Effective length of query: 310 Effective length of database: 315 Effective search space: 97650 Effective search space used: 97650 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