Align arginine N-succinyltransferase (EC 2.3.1.109) (characterized)
to candidate WP_046157872.1 VL52_RS15515 arginine N-succinyltransferase
Query= BRENDA::P80358 (340 letters) >NCBI__GCF_000971335.1:WP_046157872.1 Length = 348 Score = 360 bits (925), Expect = e-104 Identities = 186/344 (54%), Positives = 239/344 (69%), Gaps = 6/344 (1%) Query: 1 MIVRPVTSADLPALIELARST---GTGLTTLPANEQRLQHRVSWAEKAFRGEAERGDADY 57 M +RPV DLP L+ELARS G GLT+LP NE RLQ R++ + +F GE +R D Y Sbjct: 2 MFIRPVEHKDLPGLMELARSAASGGVGLTSLPINEDRLQKRIARSVLSFSGELDRADHGY 61 Query: 58 LFVLED-DAGKVVGISAIAGAVGLREPWYNYRVGLTVSASQELNIHREIPTLFLANDLTG 116 +FVLED + GKV GI A+ AVGL+EPWYNYR+G V AS+EL ++ TLFL+ND TG Sbjct: 62 VFVLEDSENGKVAGICAVEAAVGLKEPWYNYRIGTIVHASEELGVYSRHETLFLSNDHTG 121 Query: 117 NSELCSLFLHADHRSGLNGKLLSRARFLFIAEFRHLFGDKLIAEMRGMSDEEGRSPFWES 176 SELC+L+LH D+R NG LLS++RFLF+A+F LFG ++AEMRG+SDE GRSPFWE+ Sbjct: 122 YSELCTLYLHPDYRVKRNGGLLSKSRFLFLAQFPQLFGKMVVAEMRGVSDENGRSPFWEA 181 Query: 177 LGRHFFKMEFSQADYLTGVGNKAFIAELMPKFPLYTCFLSEEARGVIGRVHPNTEPALAM 236 LGRHFF ++F++ADYLTG+G KAF+AELMPK P+Y FL EA+ VIG H T PA+AM Sbjct: 182 LGRHFFSIDFAEADYLTGIGQKAFVAELMPKHPVYVDFLEPEAQAVIGLTHEATRPAVAM 241 Query: 237 LKAEGFSYQGYVDIFDAGPAIEAETDKIRAIAESQNLVLAV--GTPGDDAEPYLIHNRKR 294 L++EGF Y+GYVDIFDAGP ++A T IRA+ ESQ L V P D E YL+ N Sbjct: 242 LESEGFRYEGYVDIFDAGPTVQAYTGDIRAVKESQRLPARVVDPLPDGDKECYLVCNDAL 301 Query: 295 EDCRITAAPARAAAGTLVVDPLTAKRLRLSAGASVRAVPLSAQK 338 +D R A + G + P A+ L++ G VR V L+ ++ Sbjct: 302 QDYRAVLAESVRPQGEFCLTPELARALKIKDGDHVRCVTLTPKE 345 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: 372 Number of extensions: 7 Number of successful extensions: 3 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: 348 Length adjustment: 29 Effective length of query: 311 Effective length of database: 319 Effective search space: 99209 Effective search space used: 99209 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