Align arginine N-succinyltransferase; EC 2.3.1.109 (characterized)
to candidate BPHYT_RS07700 BPHYT_RS07700 arginine N-succinyltransferase
Query= CharProtDB::CH_107315 (338 letters) >FitnessBrowser__BFirm:BPHYT_RS07700 Length = 352 Score = 287 bits (734), Expect = 3e-82 Identities = 155/339 (45%), Positives = 214/339 (63%), Gaps = 5/339 (1%) Query: 1 MLVMRPAQAADLPQVQRLAADSPVGVTSLPDDAERLRDKILASEASFAAEVSYNGEESYF 60 ML +RP + ADL ++ +A + + SLP D L ++ SE SF AEV + GEE Y Sbjct: 1 MLFVRPGRLADLDALEHMARTAQPVLHSLPHDRRALEARVALSEDSFRAEVDFPGEEFYL 60 Query: 61 FVLEDSASGELVGCSAIVASAGFSEPFYSFRNETFVHASRSLSIHNKIHVLSLCHDLTGN 120 FVLEDS SG+L+G ++IVA+AG+S+PFY+FRN+ +HASR L ++ KIH L++ H+LTG Sbjct: 61 FVLEDSESGKLMGTASIVAAAGYSDPFYAFRNDALIHASRELHVNRKIHALTMSHELTGK 120 Query: 121 SLLTSFYVQRDLVQSVYAELNSRGRLLFMASHPERFADAVVVEIVGYSDEQGESPFWNAV 180 S L +Y+ L A L SR R++++A++ +RF V ++G +DE G SPFW AV Sbjct: 121 SRLAGYYIDPSLRGDAAAHLMSRARMMYIAANRKRFTPEVFSLLLGVTDENGVSPFWEAV 180 Query: 181 GRNFFDLNYIEAEKLSGLKSRTFLAELMPHYPIYVPLLPDAAQESMGQVHPRAQITFDIL 240 GR FF N+ + E SG +SRTF+AE+MP YPIYVPLLP+AAQ +G+ +A + +DI Sbjct: 181 GRKFFGRNFADIEIESGGRSRTFIAEVMPTYPIYVPLLPEAAQRVLGEPDSKALLAYDIH 240 Query: 241 MREGFETDNYIDIFDGGPTLHARTSGIRSIAQSRVVPVKIGEAPKSGRPYLVT-NGQLQD 299 + EGFETD YIDIFD GP L A+ + ++ V A G YL+ NG + Sbjct: 241 LEEGFETDRYIDIFDAGPVLTAQVDRSACVTRNETRVVHENNASADGSTYLIAHNGADGE 300 Query: 300 FRAVVLDLDWAPGKPVALSV--EAAEALGVGEGASVRLV 336 FR V+ +L A GK S+ A ALGV EG +VR V Sbjct: 301 FRCVLGEL--AAGKEAGASLPHAAGAALGVEEGDTVRCV 337 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: 344 Number of extensions: 10 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: 352 Length adjustment: 29 Effective length of query: 309 Effective length of database: 323 Effective search space: 99807 Effective search space used: 99807 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