Align Arginine N-succinyltransferase (EC 2.3.1.109) (characterized)
to candidate GFF2696 HP15_2640 arginine/ornithine succinyltransferase
Query= reanno::SB2B:6938907 (339 letters) >FitnessBrowser__Marino:GFF2696 Length = 379 Score = 276 bits (705), Expect = 8e-79 Identities = 146/334 (43%), Positives = 201/334 (60%), Gaps = 8/334 (2%) Query: 2 LIIRPIRASDFDALYRIAVESGHGFTSLPVNEDLLRRKIARSEASFQKVVETPYDEGYLM 61 +IIRPI D DAL +IAVESG GFTSL + D L RKI S SF + V TP DE YL Sbjct: 7 MIIRPITPKDLDALMQIAVESGPGFTSLMPDRDALSRKIDHSVESFARTVTTPGDEHYLF 66 Query: 62 VLEDTQTQEVVGTCALEAAVGMEDAFYHYRLGTEVYHSQQINVRNEVETLTLCHDYTGAA 121 VLED+ T +++GT +EAA G+ H+R ++H + R+ E+LT C YTG Sbjct: 67 VLEDSATGQIMGTTGIEAAAGLSRPLVHFRRNAVIHHEEDPRKRHAEESLTRCQHYTGCT 126 Query: 122 ELCTLFLRGAYRKDNNGRMLSRSRFLFLAQHANRFGETVIAEMRGVSDENGNSPFYGWLQ 181 E+C+L+LR +R+ N G++LSR RFLF+A H RF +TVIAEMRGVSD G SPF+ WL+ Sbjct: 127 EVCSLYLRPGFRRANAGKLLSRVRFLFMALHPERFADTVIAEMRGVSDHAGRSPFWDWLK 186 Query: 182 KHFLGIDFVEADYLSGLGRKAFMAEMMPRNPVYVCLLPEEAQKVIGEVHTNTRPALSLLR 241 H +DF+ A L+ G+ F+ +P P++ + + A+ VIG+VH +TRPA +L Sbjct: 187 HHVADLDFMSATQLACCGQSGFVERFIPATPLFTRQMTDAARAVIGQVHEDTRPARHMLE 246 Query: 242 AEGFRCRGYVDIFDGGPTVECNLQDIRGVRESRLLTVRIGEMPASD--------DSFILS 293 EGFR RG+VD+ DGGPT+EC DI VR++ L R+ + S S I++ Sbjct: 247 REGFRHRGFVDLLDGGPTLECARSDIASVRDTLLTRARLQKGNRSSWNIAGNTVGSAIVA 306 Query: 294 NTQLVDYRATSVELMVSSDSDEVILSPELAAGLL 327 N +RAT E ++ + + PE A L Sbjct: 307 NAGCSGFRATVTEQVLPNPDANSLSVPEQLANEL 340 Lambda K H 0.321 0.137 0.397 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: 301 Number of extensions: 10 Number of successful extensions: 1 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: 339 Length of database: 379 Length adjustment: 29 Effective length of query: 310 Effective length of database: 350 Effective search space: 108500 Effective search space used: 108500 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 (21.9 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