Align Arginine N-succinyltransferase; AST; AOST; EC 2.3.1.109 (characterized)
to candidate Ga0059261_3996 Ga0059261_3996 arginine and ornithine succinyltransferase subunits
Query= SwissProt::Q8ZPV1 (344 letters) >FitnessBrowser__Korea:Ga0059261_3996 Length = 336 Score = 232 bits (592), Expect = 9e-66 Identities = 139/335 (41%), Positives = 192/335 (57%), Gaps = 10/335 (2%) Query: 3 VIRPVEHADIAALMQLAGKTGGGLTSLPANEATLAARIERALKTWSG-ELPKGEQGYVFV 61 +IRP D+ AL ++A TGGG T+LP + L A++ER+ +S + ++ +V V Sbjct: 4 LIRPAREDDLQALYEMAKLTGGGFTNLPPEKPALRAKLERSALAFSRTDDALKDELFVLV 63 Query: 62 LEDSETGEVGGICAIEVAVGLNDPWYNYRVGTLVHASKELNVYNALPTLFLSNDHTGSSE 121 LE+SET EV G C I VG P+Y+YR+G S+ L L L+ND G SE Sbjct: 64 LENSETHEVRGTCQIFTQVGQRWPFYSYRLGIETKHSEALARTFRAEILSLTNDLEGCSE 123 Query: 122 LCTLFLDPEWRKEGNGYLLSKSRFMFMAAFRDKFNEKVVAEMRGVIDEHGYSPFWQSLGK 181 + LFL P R G G LL++SR++F+A R +F ++V+AE+RGVIDE G SPFW + Sbjct: 124 VGGLFLHPGERAGGLGMLLARSRYLFIAMHRARFGDRVLAELRGVIDEAGGSPFWDGVAG 183 Query: 182 RFFSMDFSRADFLCGTGQKAFIAELMPKHPIYTHFLSEEAQAVIGEVHPQTAPARAVLEK 241 RFF M+F +AD FIA+LMPKHPIYT L+E A++VIG HP A +LE+ Sbjct: 184 RFFGMNFQQADEFNAIHGNQFIADLMPKHPIYTAMLTEGARSVIGLPHPSGRAAMRMLEQ 243 Query: 242 EGFRYRHYIDIFDGGPTLECDIDRVRAIRKSR---LVEVAEGQPAPGDYPACLVANENYH 298 EGF + +YIDIFDGGPT+ D+V +R SR +V++A+G A ++A Sbjct: 244 EGFAFENYIDIFDGGPTMTARTDQVMTVRDSRTDKVVDIADGG------SASIIARGTLS 297 Query: 299 HFRAALVRADPQTSRLVLTAAQLDALKCRAGDHVR 333 FRA R + + A L AG VR Sbjct: 298 DFRACHGRIGLSDGGVTVDAMSASILGVEAGQEVR 332 Lambda K H 0.321 0.137 0.416 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: 283 Number of extensions: 7 Number of successful extensions: 2 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: 344 Length of database: 336 Length adjustment: 28 Effective length of query: 316 Effective length of database: 308 Effective search space: 97328 Effective search space used: 97328 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