Align arginine N-succinyltransferase (EC 2.3.1.109) (characterized)
to candidate AO356_18735 AO356_18735 arginine N-succinyltransferase
Query= BRENDA::P80358 (340 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_18735 Length = 341 Score = 585 bits (1509), Expect = e-172 Identities = 291/338 (86%), Positives = 315/338 (93%) Query: 1 MIVRPVTSADLPALIELARSTGTGLTTLPANEQRLQHRVSWAEKAFRGEAERGDADYLFV 60 MIVRPV S+DLPALI LARSTGTGLTTLPANE+RL HRV WAEK FRGEA RGDADYLFV Sbjct: 1 MIVRPVRSSDLPALIALARSTGTGLTTLPANEERLAHRVGWAEKTFRGEAGRGDADYLFV 60 Query: 61 LEDDAGKVVGISAIAGAVGLREPWYNYRVGLTVSASQELNIHREIPTLFLANDLTGNSEL 120 LEDD G+VVGISAIAGAVGLREPWYN+RVGLTVSASQELNI+REIPTLFLANDLTGNSEL Sbjct: 61 LEDDDGRVVGISAIAGAVGLREPWYNFRVGLTVSASQELNIYREIPTLFLANDLTGNSEL 120 Query: 121 CSLFLHADHRSGLNGKLLSRARFLFIAEFRHLFGDKLIAEMRGMSDEEGRSPFWESLGRH 180 CSLFLHAD+RSGLNG++L++AR LFIAEF LFG+K+IAEMRGMSD+ GRSPFWESLGRH Sbjct: 121 CSLFLHADYRSGLNGRMLAKARLLFIAEFPQLFGNKIIAEMRGMSDDNGRSPFWESLGRH 180 Query: 181 FFKMEFSQADYLTGVGNKAFIAELMPKFPLYTCFLSEEARGVIGRVHPNTEPALAMLKAE 240 FFKMEFSQADYLTGVGNKAFIAELMPKFPLYTCFLSE AR VIG+VHP+TEPAL+MLK+E Sbjct: 181 FFKMEFSQADYLTGVGNKAFIAELMPKFPLYTCFLSEGARAVIGQVHPDTEPALSMLKSE 240 Query: 241 GFSYQGYVDIFDAGPAIEAETDKIRAIAESQNLVLAVGTPGDDAEPYLIHNRKREDCRIT 300 GFSYQGYVDIFDAGPA+E ET KIRAI +SQ LVLA+GTPGDDA P+LIHNRKREDCRIT Sbjct: 241 GFSYQGYVDIFDAGPAVECETGKIRAIRDSQALVLAIGTPGDDATPFLIHNRKREDCRIT 300 Query: 301 AAPARAAAGTLVVDPLTAKRLRLSAGASVRAVPLSAQK 338 AAPAR AAGTLVVDPLTAKRL+L+AG VRAV LSA + Sbjct: 301 AAPARFAAGTLVVDPLTAKRLQLNAGDQVRAVALSAAR 338 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: 485 Number of extensions: 16 Number of successful extensions: 1 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: 340 Length of database: 341 Length adjustment: 28 Effective length of query: 312 Effective length of database: 313 Effective search space: 97656 Effective search space used: 97656 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