Align arginine N-succinyltransferase; EC 2.3.1.109 (characterized)
to candidate BWI76_RS11675 BWI76_RS11675 arginine N-succinyltransferase
Query= CharProtDB::CH_107315 (338 letters) >FitnessBrowser__Koxy:BWI76_RS11675 Length = 344 Score = 231 bits (589), Expect = 2e-65 Identities = 131/337 (38%), Positives = 196/337 (58%), Gaps = 3/337 (0%) Query: 1 MLVMRPAQAADLPQVQRLAADSPVGVTSLPDDAERLRDKILASEASFAAEVSYNGEESYF 60 M+V+RP + DLP + LA ++ G+TSLP D L +I S+ ++ E+ E+ Y Sbjct: 1 MMVIRPVEKGDLPGLLTLAGETGGGLTSLPADEATLAARIERSQMTWRGELP-KSEQGYV 59 Query: 61 FVLEDSASGELVGCSAIVASAGFSEPFYSFRNETFVHASRSLSIHNKIHVLSLCHDLTGN 120 FVLED ASG + G AI + G ++P+Y++R T VHAS+ L+++N + L L +D TG+ Sbjct: 60 FVLEDCASGAVAGICAIEVAVGLNDPWYNYRVGTQVHASKELNVYNALPTLFLSNDHTGS 119 Query: 121 SLLTSFYVQRDLVQSVYAELNSRGRLLFMASHPERFADAVVVEIVGYSDEQGESPFWNAV 180 S L + ++ + L S+ R LFMA+ ERF + VV E+ G DE G SPFW ++ Sbjct: 120 SELCTLFLDPKWRKEGNGYLLSKSRFLFMAAFRERFNEKVVAEMRGVIDEHGYSPFWESL 179 Query: 181 GRNFFDLNYIEAEKLSGLKSRTFLAELMPHYPIYVPLLPDAAQESMGQVHPRAQITFDIL 240 G+ FF + + A+ L G + F+A LMP +P+Y+ L D A+ +G+VHP+ +L Sbjct: 180 GKRFFAMEFSRADYLCGTGQKAFIAALMPKHPLYIDFLSDEARAVIGEVHPQTAPARAVL 239 Query: 241 MREGFETDNYIDIFDGGPTLHARTSGIRSIAQSRVVPVKIGEAPKSGRP-YLVTNGQLQD 299 +EGF NY+DIFDGGPTL +R+I +SR+V V G+ + P LV N Q Q Sbjct: 240 EKEGFRYLNYVDIFDGGPTLECEIDRVRAIRKSRLVTVAEGQPVQGEWPACLVANEQYQQ 299 Query: 300 FRAVVLDLDWAPGKPVALSVEAAEALGVGEGASVRLV 336 FRA+++ D + LS +AL G +RLV Sbjct: 300 FRAMLVHAD-PESDRLVLSARELDALKCHPGDQIRLV 335 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: 277 Number of extensions: 11 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: 344 Length adjustment: 29 Effective length of query: 309 Effective length of database: 315 Effective search space: 97335 Effective search space used: 97335 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