Align arginine N-succinyltransferase; EC 2.3.1.109 (characterized)
to candidate H281DRAFT_06480 H281DRAFT_06480 arginine succinyltransferase
Query= CharProtDB::CH_107315 (338 letters) >FitnessBrowser__Burk376:H281DRAFT_06480 Length = 345 Score = 215 bits (548), Expect = 1e-60 Identities = 124/346 (35%), Positives = 191/346 (55%), Gaps = 14/346 (4%) Query: 1 MLVMRPAQAADLPQVQRLAADSPVGVTSLPDDAERLRDKILASEASFAAEVSYNGEESYF 60 M+V+R Q D+ + RLA ++ G+T+ D + L ++ + + + + E YF Sbjct: 1 MIVVRVVQRGDVDALMRLAQETGPGLTTFKPDRDALAARVERARRTMEDKAEPH-EAGYF 59 Query: 61 FVLEDSASGELVGCSAIVASAGFSEPFYSFRNETFVHASRSLSIHNKIHVLSLCHDLTGN 120 FV+ED+A+G++ G I + G +PFY++R T VHAS+ L I ++ L++ HDLTG Sbjct: 60 FVMEDTATGDVAGVCGIETAVGLQQPFYNYRVSTVVHASQDLGIWTRMRALNISHDLTGY 119 Query: 121 SLLTSFYVQRDLVQSVYAELNSRGRLLFMASHPERFADAVVVEIVGYSDEQGESPFWNAV 180 + + S ++ S L SR R +F+A ERF + E+ G+ D +G SPFW AV Sbjct: 120 AEVCSLFLSPRYRTSGVGGLLSRSRFMFLAQFRERFPQRLCAELRGHFDAEGTSPFWRAV 179 Query: 181 GRNFFDLNYIEAEKLSGLKSRTFLAELMPHYPIYVPLLPDAAQESMGQVHPRAQITFDIL 240 G +F+ +++ A+ LS + FLAELMP YP+YV LLP AQE +G H +L Sbjct: 180 GSHFYQIDFNAADYLSSHGRKAFLAELMPRYPVYVELLPQEAQECVGLTHNDTIPARRML 239 Query: 241 MREGFETDNYIDIFDGGPTLHARTSGIRSIAQSRVVPVKIGEAPKSGRP----YLVTNGQ 296 EG +N++DIFD GP L S +R++ +S +VPV+I + P+ +V+N Sbjct: 240 EAEGLRYENHVDIFDAGPVLECHISDLRTVRESVLVPVEIADVPEGAAQDAPRSMVSNTS 299 Query: 297 LQDFRAVVLDLDWAPGKP----VALSVEAAEALGVGEGASVRLVAV 338 L DFR V A G P ++ A ALGV G VR++A+ Sbjct: 300 LGDFRVGV-----AAGVPQDGVFRMNATEAAALGVKAGDPVRVLAL 340 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: 273 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: 345 Length adjustment: 29 Effective length of query: 309 Effective length of database: 316 Effective search space: 97644 Effective search space used: 97644 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