Align arginine N-succinyltransferase (EC 2.3.1.109) (characterized)
to candidate 7023381 Shewana3_0611 arginine succinyltransferase (RefSeq)
Query= BRENDA::P80358 (340 letters) >FitnessBrowser__ANA3:7023381 Length = 339 Score = 283 bits (723), Expect = 6e-81 Identities = 146/338 (43%), Positives = 222/338 (65%), Gaps = 4/338 (1%) Query: 1 MIVRPVTSADLPALIELARSTGTGLTTLPANEQRLQHRVSWAEKAFRGEAERG-DADYLF 59 +I+RP+ + D +L ++A +G G T+LP N L+H+++ AE +F ++ D YL Sbjct: 2 LIIRPIQAGDFESLYQIAEESGHGFTSLPVNADLLRHKIARAEASFVKVIDKPFDEGYLM 61 Query: 60 VLEDDAGK-VVGISAIAGAVGLREPWYNYRVGLTVSASQELNIHREIPTLFLANDLTGNS 118 VLED A + VVG AI AVG+ + +Y+YR+G V S+++ + E+ TL L +D TG + Sbjct: 62 VLEDTATREVVGTCAIEAAVGMEDAFYHYRLGTEVYHSEQIEVRNEVETLTLCHDYTGAA 121 Query: 119 ELCSLFLHADHRSGLNGKLLSRARFLFIAEFRHLFGDKLIAEMRGMSDEEGRSPFWESLG 178 ELC+LFL +R G NG++LSR+RFLF+A+ FG+ +IAEMRG+SD +G SPF+ L Sbjct: 122 ELCTLFLREGYRKGNNGRMLSRSRFLFLAQHAKRFGETVIAEMRGVSDSDGNSPFYCWLQ 181 Query: 179 RHFFKMEFSQADYLTGVGNKAFIAELMPKFPLYTCFLSEEARGVIGRVHPNTEPALAMLK 238 ++F ++F QADYL+G+G KAF+AE+MP+ P+Y C L EEA+ VIG VH NT PAL++L+ Sbjct: 182 KNFLGIDFIQADYLSGLGKKAFMAEMMPRNPVYVCLLPEEAQKVIGEVHTNTRPALSLLQ 241 Query: 239 AEGFSYQGYVDIFDAGPAIEAETDKIRAIAESQNLVLAVGTPGDDAEPYLIHNRKREDCR 298 AEGF +GYVDIFD GP +E IRA+ ES+ L + +G + + +++ N + + R Sbjct: 242 AEGFRCRGYVDIFDGGPTVECRLTDIRAVRESRLLTVDIGEMPESDKQFIVSNTQLANYR 301 Query: 299 ITAAPARAAAGT--LVVDPLTAKRLRLSAGASVRAVPL 334 T+A T +V+ P A+ L L+ G +R + + Sbjct: 302 ATSACLAVDDKTEQVVISPELAEGLLLAKGDQIRILAM 339 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: 314 Number of extensions: 16 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: 339 Length adjustment: 28 Effective length of query: 312 Effective length of database: 311 Effective search space: 97032 Effective search space used: 97032 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