Align arginine N-succinyltransferase (EC 2.3.1.109) (characterized)
to candidate WP_086508152.1 BZY95_RS01055 arginine N-succinyltransferase
Query= BRENDA::P80358 (340 letters) >NCBI__GCF_002151265.1:WP_086508152.1 Length = 348 Score = 286 bits (731), Expect = 7e-82 Identities = 157/343 (45%), Positives = 217/343 (63%), Gaps = 12/343 (3%) Query: 1 MIVRPVTSADLPALIELARSTGTGLTTLPANEQRLQHRVSWAEKAFRGEAERGDADYLFV 60 M +RP+ DL L ++AR TG G T+LP N + L +++ A AF +Y FV Sbjct: 1 MRIRPIAEGDLDELQKIARETGVGFTSLPDNREFLAAKIAAAVAAFEQRTPADRRNYFFV 60 Query: 61 LEDD-AGKVVGISAIAGAVGLREPWYNYRVGLTVSASQELNIHREIPTLFLANDLTGNSE 119 LED+ +G++ G AI G VG P+Y+YR+G +S +L++HR I TLFL++D TG++E Sbjct: 61 LEDEESGELAGCCAIEGQVGREVPFYHYRLGTLAHSSVQLDLHRTIDTLFLSSDHTGDAE 120 Query: 120 LCSLFLHADHRSG-----LNGKLLSRARFLFIAEFRHLFGDKLIAEMRGMSDEEGRSPFW 174 + SLFL R NG LLS R+LF+AEFR F DK++AEMRG+ DE G+SPFW Sbjct: 121 VASLFLRPGFRGKERAHQRNGALLSMVRWLFMAEFRDQFPDKVLAEMRGVFDERGKSPFW 180 Query: 175 ESLGRHFFKMEFSQADYLTGVGNKAFIAELMPKFPLYTCFLSEEARGVIGRVHPNTEPAL 234 E LG HFF ++F +AD LTG+G K+FI ELMPKFP+YT FLS+EAR IG+VH +T PAL Sbjct: 181 ECLGSHFFPLDFDEADRLTGLGQKSFIGELMPKFPIYTPFLSDEARACIGQVHHDTRPAL 240 Query: 235 AMLKAEGFSYQGYVDIFDAGPAIEAETDKIRAIAESQNLVLAVGTPGDDAEP----YLIH 290 AMLK EG ++GY+DIFD GP +EA D +RA+ +S + + + G D P +L Sbjct: 241 AMLKKEGLRWEGYIDIFDGGPTVEAYIDDVRAVRKSHCCRVEIRS-GSDTPPARPRWLAA 299 Query: 291 NRKREDCRIT-AAPARAAAGTLVVDPLTAKRLRLSAGASVRAV 332 + + R A GTL + A+RL ++AG S+R + Sbjct: 300 STTMAEFRAAWVACGPDEEGTLTLSETEAQRLGVAAGDSLRVL 342 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: 336 Number of extensions: 18 Number of successful extensions: 4 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