Align arginine N-succinyltransferase; EC 2.3.1.109 (characterized)
to candidate 15865 b1747 arginine succinyltransferase (NCBI)
Query= CharProtDB::CH_107315 (338 letters) >FitnessBrowser__Keio:15865 Length = 344 Score = 224 bits (571), Expect = 2e-63 Identities = 128/337 (37%), Positives = 197/337 (58%), Gaps = 3/337 (0%) Query: 1 MLVMRPAQAADLPQVQRLAADSPVGVTSLPDDAERLRDKILASEASFAAEVSYNGEESYF 60 M+V+RP + +D+ + +LA+ + G+TSLP + L +I + ++ E+ E+ Y Sbjct: 1 MMVIRPVERSDVSALMQLASKTGGGLTSLPANEATLSARIERAIKTWQGELP-KSEQGYV 59 Query: 61 FVLEDSASGELVGCSAIVASAGFSEPFYSFRNETFVHASRSLSIHNKIHVLSLCHDLTGN 120 FVLEDS +G + G AI + G ++P+Y++R T VHAS+ L+++N + L L +D TG+ Sbjct: 60 FVLEDSETGTVAGICAIEVAVGLNDPWYNYRVGTLVHASKELNVYNALPTLFLSNDHTGS 119 Query: 121 SLLTSFYVQRDLVQSVYAELNSRGRLLFMASHPERFADAVVVEIVGYSDEQGESPFWNAV 180 S L + ++ D + L S+ R +FMA+ ++F D VV E+ G DE G SPFW ++ Sbjct: 120 SELCTLFLDPDWRKEGNGYLLSKSRFMFMAAFRDKFNDKVVAEMRGVIDEHGYSPFWQSL 179 Query: 181 GRNFFDLNYIEAEKLSGLKSRTFLAELMPHYPIYVPLLPDAAQESMGQVHPRAQITFDIL 240 G+ FF +++ A+ L G + F+AELMP +PIY L AQ+ +GQVHP+ +L Sbjct: 180 GKRFFSMDFSRADFLCGTGQKAFIAELMPKHPIYTHFLSQEAQDVIGQVHPQTAPARAVL 239 Query: 241 MREGFETDNYIDIFDGGPTLHARTSGIRSIAQSRVVPVKIGEAPKSGRP-YLVTNGQLQD 299 +EGF NYIDIFDGGPTL +R+I +SR+V V G+ + P LV N Sbjct: 240 EKEGFRYRNYIDIFDGGPTLECDIDRVRAIRKSRLVEVAEGQPAQGDFPACLVANENYHH 299 Query: 300 FRAVVLDLDWAPGKPVALSVEAAEALGVGEGASVRLV 336 FR V++ D A + + L+ +AL G VRLV Sbjct: 300 FRVVLVRTDPATER-LILTAAQLDALKCHAGDRVRLV 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: 267 Number of extensions: 13 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