Align arginine N-succinyltransferase (EC 2.3.1.109) (characterized)
to candidate CCNA_00617 CCNA_00617 arginine N-succinyltransferase, beta chain
Query= BRENDA::P80358 (340 letters) >FitnessBrowser__Caulo:CCNA_00617 Length = 347 Score = 213 bits (542), Expect = 6e-60 Identities = 108/285 (37%), Positives = 170/285 (59%), Gaps = 2/285 (0%) Query: 2 IVRPVTSADLPALIELARSTGTGLTTLPANEQRLQHRVSWAEKAFRGEAERGDADYLFVL 61 +VRP DL L+ LAR+ G+T LPA+ L R++ +E+A R ++++ Sbjct: 16 LVRPARRGDLDGLLALARAADAGMTNLPADRAALDDRLAASEQALIDPETRNAGAAVYLV 75 Query: 62 EDDAGKVVGISAIAGAVGLREPWYNYRVGLTVSASQELNIHREIPTLFLANDLTGNSELC 121 + G+V+G + + +G+ +P+Y+YRV S +L E+ L L NDLT +E+ Sbjct: 76 LERQGRVIGAACVFARIGVAQPFYSYRVTRLTQLSPDLGKRVEMSVLTLVNDLTDQAEVG 135 Query: 122 SLFLHADHRSGLNGKLLSRARFLFIAEFRHLFGDKLIAEMRGMSDEEGRSPFWESLGRHF 181 LF+ D R G G+L++R+R+LF+A R FG+++IA++RG+ D +GRSP W++LG HF Sbjct: 136 GLFVAPDARKGQAGRLMARSRYLFMARHRDWFGEQVIADLRGVQDADGRSPVWDALGAHF 195 Query: 182 FKMEFSQADYLTGVGNKAFIAELMPKFPLYTCFLSEEARGVIGRVHPNTEPALAMLKAEG 241 + M+F+ AD + FI++L PK+P+Y L A+ +G+ H + A +L+ EG Sbjct: 196 YAMDFAAADRACALSGTRFISDLGPKYPIYVGLLPPAAQAALGKPHQDGVGAERLLREEG 255 Query: 242 FSYQGYVDIFDAGPAIEAETDKIRAIAESQNLVLA--VGTPGDDA 284 F GYVDIFD GP + A D ++AI E++ LA TP DDA Sbjct: 256 FVSDGYVDIFDGGPTLRARIDDLKAIREARRAPLAGLTDTPTDDA 300 Lambda K H 0.320 0.136 0.398 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: 299 Number of extensions: 13 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 340 Length of database: 347 Length adjustment: 29 Effective length of query: 311 Effective length of database: 318 Effective search space: 98898 Effective search space used: 98898 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