Align arginine N-succinyltransferase; EC 2.3.1.109 (characterized)
to candidate WP_046157872.1 VL52_RS15515 arginine N-succinyltransferase
Query= CharProtDB::CH_107315 (338 letters) >NCBI__GCF_000971335.1:WP_046157872.1 Length = 348 Score = 240 bits (612), Expect = 4e-68 Identities = 135/343 (39%), Positives = 200/343 (58%), Gaps = 7/343 (2%) Query: 1 MLVMRPAQAADLP---QVQRLAADSPVGVTSLPDDAERLRDKILASEASFAAEVSYNGEE 57 M+ +RP + DLP ++ R AA VG+TSLP + +RL+ +I S SF+ E+ + Sbjct: 1 MMFIRPVEHKDLPGLMELARSAASGGVGLTSLPINEDRLQKRIARSVLSFSGELD-RADH 59 Query: 58 SYFFVLEDSASGELVGCSAIVASAGFSEPFYSFRNETFVHASRSLSIHNKIHVLSLCHDL 117 Y FVLEDS +G++ G A+ A+ G EP+Y++R T VHAS L ++++ L L +D Sbjct: 60 GYVFVLEDSENGKVAGICAVEAAVGLKEPWYNYRIGTIVHASEELGVYSRHETLFLSNDH 119 Query: 118 TGNSLLTSFYVQRDLVQSVYAELNSRGRLLFMASHPERFADAVVVEIVGYSDEQGESPFW 177 TG S L + Y+ D L S+ R LF+A P+ F VV E+ G SDE G SPFW Sbjct: 120 TGYSELCTLYLHPDYRVKRNGGLLSKSRFLFLAQFPQLFGKMVVAEMRGVSDENGRSPFW 179 Query: 178 NAVGRNFFDLNYIEAEKLSGLKSRTFLAELMPHYPIYVPLLPDAAQESMGQVHPRAQITF 237 A+GR+FF +++ EA+ L+G+ + F+AELMP +P+YV L AQ +G H + Sbjct: 180 EALGRHFFSIDFAEADYLTGIGQKAFVAELMPKHPVYVDFLEPEAQAVIGLTHEATRPAV 239 Query: 238 DILMREGFETDNYIDIFDGGPTLHARTSGIRSIAQSRVVPVKIGEAPKSG--RPYLVTNG 295 +L EGF + Y+DIFD GPT+ A T IR++ +S+ +P ++ + G YLV N Sbjct: 240 AMLESEGFRYEGYVDIFDAGPTVQAYTGDIRAVKESQRLPARVVDPLPDGDKECYLVCND 299 Query: 296 QLQDFRAVVLDLDWAPGKPVALSVEAAEALGVGEGASVRLVAV 338 LQD+RAV+ + P L+ E A AL + +G VR V + Sbjct: 300 ALQDYRAVLAE-SVRPQGEFCLTPELARALKIKDGDHVRCVTL 341 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: 265 Number of extensions: 9 Number of successful extensions: 4 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: 348 Length adjustment: 29 Effective length of query: 309 Effective length of database: 319 Effective search space: 98571 Effective search space used: 98571 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 24 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