Align arginine N-succinyltransferase; EC 2.3.1.109 (characterized)
to candidate GFF3097 HP15_3040 arginine N-succinyltransferase subunit beta
Query= CharProtDB::CH_107315 (338 letters) >FitnessBrowser__Marino:GFF3097 Length = 366 Score = 205 bits (522), Expect = 1e-57 Identities = 118/340 (34%), Positives = 181/340 (53%), Gaps = 6/340 (1%) Query: 1 MLVMRPAQAADLPQVQRLAADSPVGVTSLPDDAERLRDKILASEASFAAEVSYNGEESYF 60 MLV+RP Q DL + +A + G+T+LP D E L+ KI + +F ++ Y Sbjct: 1 MLVIRPLQENDLDDLYAMAQSAGKGLTTLPADRELLQKKINHARETFNQRIAPEAG-LYL 59 Query: 61 FVLEDSASGELVGCSAIVASAGFSEPFYSFRNETFVHASRSLSIHNKIHVLSLCHDLTGN 120 F LED+ + VG S I A G E FY++R V+AS+ L +H + L L +D+T Sbjct: 60 FALEDTERKKTVGISGIQARVGLDEVFYNYRLSVTVNASKELGVHVRTPTLHLSNDMTDT 119 Query: 121 SLLTSFYVQRDLVQSVYAELNSRGRLLFMASHPERFADAVVVEIVGYSDEQGESPFWNAV 180 S + S + + L SR R +++ + F++ + E+ G SD G SP W+A+ Sbjct: 120 SEICSLLLSDEYKGGGSGLLLSRCRFMYLDEFRKHFSEKIFAEMRGVSDANGRSPLWDAL 179 Query: 181 GRNFFDLNYIEAEKLSGLKSRTFLAELMPHYPIYVPLLPDAAQESMGQVHPRAQITFDIL 240 G FFD+ + EA+ LSGL +++F+AELMP YPIY+ +LPD+A+ +G+VH +L Sbjct: 180 GTKFFDMEFSEADMLSGLGNKSFIAELMPKYPIYLSMLPDSARAVIGRVHDNTAPALRML 239 Query: 241 MREGFETDNYIDIFDGGPTLHARTSGIRSIAQSRVVPVKIGEAP-----KSGRPYLVTNG 295 EGF + +DIFDGGP + A +R++ + + P S +V+N Sbjct: 240 QSEGFNFNGLVDIFDGGPVVEAFVHNVRTVREGMNRHAMVTRKPVNLDVPSEERVMVSNR 299 Query: 296 QLQDFRAVVLDLDWAPGKPVALSVEAAEALGVGEGASVRL 335 +DFR + +D V+L E AEAL + G VRL Sbjct: 300 SFRDFRVTTVPIDCIGPDTVSLPPEVAEALQIESGDPVRL 339 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: 284 Number of extensions: 9 Number of successful extensions: 3 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: 366 Length adjustment: 29 Effective length of query: 309 Effective length of database: 337 Effective search space: 104133 Effective search space used: 104133 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