Align arginine N-succinyltransferase (EC 2.3.1.109) (characterized)
to candidate GFF2696 HP15_2640 arginine/ornithine succinyltransferase
Query= BRENDA::P80358 (340 letters) >FitnessBrowser__Marino:GFF2696 Length = 379 Score = 195 bits (496), Expect = 1e-54 Identities = 105/272 (38%), Positives = 155/272 (56%), Gaps = 2/272 (0%) Query: 1 MIVRPVTSADLPALIELARSTGTGLTTLPANEQRLQHRVSWAEKAF-RGEAERGDADYLF 59 MI+RP+T DL AL+++A +G G T+L + L ++ + ++F R GD YLF Sbjct: 7 MIIRPITPKDLDALMQIAVESGPGFTSLMPDRDALSRKIDHSVESFARTVTTPGDEHYLF 66 Query: 60 VLEDDA-GKVVGISAIAGAVGLREPWYNYRVGLTVSASQELNIHREIPTLFLANDLTGNS 118 VLED A G+++G + I A GL P ++R + ++ +L TG + Sbjct: 67 VLEDSATGQIMGTTGIEAAAGLSRPLVHFRRNAVIHHEEDPRKRHAEESLTRCQHYTGCT 126 Query: 119 ELCSLFLHADHRSGLNGKLLSRARFLFIAEFRHLFGDKLIAEMRGMSDEEGRSPFWESLG 178 E+CSL+L R GKLLSR RFLF+A F D +IAEMRG+SD GRSPFW+ L Sbjct: 127 EVCSLYLRPGFRRANAGKLLSRVRFLFMALHPERFADTVIAEMRGVSDHAGRSPFWDWLK 186 Query: 179 RHFFKMEFSQADYLTGVGNKAFIAELMPKFPLYTCFLSEEARGVIGRVHPNTEPALAMLK 238 H ++F A L G F+ +P PL+T +++ AR VIG+VH +T PA ML+ Sbjct: 187 HHVADLDFMSATQLACCGQSGFVERFIPATPLFTRQMTDAARAVIGQVHEDTRPARHMLE 246 Query: 239 AEGFSYQGYVDIFDAGPAIEAETDKIRAIAES 270 EGF ++G+VD+ D GP +E I ++ ++ Sbjct: 247 REGFRHRGFVDLLDGGPTLECARSDIASVRDT 278 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: 315 Number of extensions: 6 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: 379 Length adjustment: 29 Effective length of query: 311 Effective length of database: 350 Effective search space: 108850 Effective search space used: 108850 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