Align Arginine N-succinyltransferase subunit beta; EC 2.3.1.109; AOST; AST; ARUAII (uncharacterized)
to candidate WP_086508151.1 BZY95_RS01050 arginine N-succinyltransferase
Query= curated2:P80358 (340 letters) >NCBI__GCF_002151265.1:WP_086508151.1 Length = 357 Score = 244 bits (623), Expect = 2e-69 Identities = 138/345 (40%), Positives = 202/345 (58%), Gaps = 5/345 (1%) Query: 1 MIVRPVTSADLPALIELARSTGTGLTTLPANEQRLQHRVSWAEKAFRGEAE-RGDADYLF 59 M+VRPV ADLPAL LA LT LPA+ RL+ R++ + ++F E + GD Y F Sbjct: 2 MVVRPVRPADLPALERLAGLATPSLTNLPAHRDRLEERIARSRQSFGREVDFPGDEHYTF 61 Query: 60 VLED-DAGKVVGISAIAGAVGLREPWYNYRVGLTVSASQELNIHREIPTLFLANDLTGNS 118 VLED + +VVG + + G RE +Y YR + ASQ+LN+ RE+ TL L+++++ + Sbjct: 62 VLEDLERDEVVGTATLRAEAGAREAYYTYRQETLIHASQQLNVRREVQTLSLSHEVSETT 121 Query: 119 ELCSLFLHADHRSGLNGKLLSRARFLFIAEFRHLFGDKLIAEMRGMSDEEGRSPFWESLG 178 +LC+L L +R LL R+R +FIA++ F + L G DE+G SPFW S+G Sbjct: 122 QLCALSLDPRYRGTSAESLLRRSRLMFIAQYPERFAEVLAMAFPGYLDEQGESPFWNSVG 181 Query: 179 RHFFKMEFSQADYLTGVGNKAFIAELMPKFPLYTCFLSEEARGVIGRVHPNTEPALAMLK 238 RHFF ++ +YL GV +K+FIAE+MP+FPLY L+ +AR IGR HP E A+A + Sbjct: 182 RHFFVRDYHDINYLAGVRSKSFIAEVMPQFPLYLALLTPQARAAIGREHPAHEAAMAEML 241 Query: 239 AEGFSYQGYVDIFDAGPAIEAETDKIRAIAESQNLVLAVGTPG--DDAEPYLIHNRKRED 296 AEGF +VD+FDAGP I+ E +++ + + V DAEP ++ N++ D Sbjct: 242 AEGFMRSRHVDLFDAGPVIKGERNRLHTFRHAAWHPVRVRPAHALPDAEPAMVANQRLAD 301 Query: 297 CR-ITAAPARAAAGTLVVDPLTAKRLRLSAGASVRAVPLSAQKRG 340 R + A A + G L++ P A+ L G +V A PL+ G Sbjct: 302 FRCVVARYALSPTGQLMLSPEHAELLGAEEGRAVLAAPLTLPSNG 346 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: 316 Number of extensions: 12 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: 357 Length adjustment: 29 Effective length of query: 311 Effective length of database: 328 Effective search space: 102008 Effective search space used: 102008 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