Align arginine N-succinyltransferase; EC 2.3.1.109 (characterized)
to candidate CCNA_00617 CCNA_00617 arginine N-succinyltransferase, beta chain
Query= CharProtDB::CH_107315 (338 letters) >FitnessBrowser__Caulo:CCNA_00617 Length = 347 Score = 184 bits (466), Expect = 4e-51 Identities = 111/331 (33%), Positives = 171/331 (51%), Gaps = 4/331 (1%) Query: 3 VMRPAQAADLPQVQRLAADSPVGVTSLPDDAERLRDKILASEASFAAEVSYNGEESYFFV 62 ++RPA+ DL + LA + G+T+LP D L D++ ASE + + N + + V Sbjct: 16 LVRPARRGDLDGLLALARAADAGMTNLPADRAALDDRLAASEQALIDPETRNAGAAVYLV 75 Query: 63 LEDSASGELVGCSAIVASAGFSEPFYSFRNETFVHASRSLSIHNKIHVLSLCHDLTGNSL 122 LE G ++G + + A G ++PFYS+R S L ++ VL+L +DLT + Sbjct: 76 LE--RQGRVIGAACVFARIGVAQPFYSYRVTRLTQLSPDLGKRVEMSVLTLVNDLTDQAE 133 Query: 123 LTSFYVQRDLVQSVYAELNSRGRLLFMASHPERFADAVVVEIVGYSDEQGESPFWNAVGR 182 + +V D + L +R R LFMA H + F + V+ ++ G D G SP W+A+G Sbjct: 134 VGGLFVAPDARKGQAGRLMARSRYLFMARHRDWFGEQVIADLRGVQDADGRSPVWDALGA 193 Query: 183 NFFDLNYIEAEKLSGLKSRTFLAELMPHYPIYVPLLPDAAQESMGQVHPRAQITFDILMR 242 +F+ +++ A++ L F+++L P YPIYV LLP AAQ ++G+ H +L Sbjct: 194 HFYAMDFAAADRACALSGTRFISDLGPKYPIYVGLLPPAAQAALGKPHQDGVGAERLLRE 253 Query: 243 EGFETDNYIDIFDGGPTLHARTSGIRSIAQSRVVPVKIGEAPKSGRPYLVTNGQLQDFRA 302 EGF +D Y+DIFDGGPTL AR +++I ++R P+ G LV G FR Sbjct: 254 EGFVSDGYVDIFDGGPTLRARIDDLKAIREARRAPL-AGLTDTPTDDALVCAGAGAAFRV 312 Query: 303 VVLDLDWAPGKPVALSVEAAEALGVGEGASV 333 V L A V ALG+ G + Sbjct: 313 VRGGLS-AGDDGVRAEASLINALGLAPGQEI 342 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: 239 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: 347 Length adjustment: 29 Effective length of query: 309 Effective length of database: 318 Effective search space: 98262 Effective search space used: 98262 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