Align acetylornithine transaminase (EC 2.6.1.11); 4-aminobutyrate-2-oxoglutarate transaminase (EC 2.6.1.19) (characterized)
to candidate Dsui_3250 Dsui_3250 acetylornithine/succinylornithine aminotransferase
Query= BRENDA::B1XNF8 (418 letters) >FitnessBrowser__PS:Dsui_3250 Length = 390 Score = 339 bits (870), Expect = 7e-98 Identities = 185/395 (46%), Positives = 251/395 (63%), Gaps = 15/395 (3%) Query: 23 YVMHTYGRFPVAIAKGEGCRLWDTEGKSYLDFVAGIATCTLGHAHPALIQAVSAQIQKLH 82 ++M+TY R PVA + GEG R++DT+GK YLD ++GIA TLGH HP L+ A+++Q ++ Sbjct: 3 HLMNTYARLPVAFSHGEGNRIYDTDGKCYLDALSGIAVNTLGHNHPKLVNAIASQAARVL 62 Query: 83 HISNLYYIPEQGALAQWIVEHSCADKVFFCNSGAEANEAAIKLVRKYAHTVSDFLEQPVI 142 H SNLY IP Q LA + S ++VFFCNSG EANEAAIKL R + H ++ PVI Sbjct: 63 HTSNLYRIPLQEELADRLAGLSRMEEVFFCNSGCEANEAAIKLARFFGHQKG--VDAPVI 120 Query: 143 LSAKSSFHGRTLATITATGQPKYQKHFDPLPDGFAYVPYNDIRALEEAITDIDEGNRRVA 202 + + +FHGRTLAT++ATG K Q F+PL GF VPYND+ A+ A E N V Sbjct: 121 IVMEKAFHGRTLATLSATGNRKAQAGFEPLVSGFVRVPYNDLDAIRAAA----ELNPNVV 176 Query: 203 AIMLEALQGEGGVRPGDVEYFKAVRRICDENGILLVLDEVQVGVGRTGKYWGYENLGIEP 262 A++LE +QGEGG+ D E+ + +R +CDE LL+ DEVQ G+GRTG ++G+++ GI P Sbjct: 177 AVLLEMVQGEGGIHVADPEFQRGLRSLCDEKDWLLMCDEVQCGMGRTGTWFGFQHAGILP 236 Query: 263 DIFTSAKGLAGGIPIGAMMCKDSCA-VFNPGEHASTFGGNPFSCAAALAVVETLEQENLL 321 D+ T AKGL G+PIGA M A +F PG H STFGGNP +CAAAL + +E+E L Sbjct: 237 DVATLAKGLGSGVPIGACMTAGKAAGLFKPGNHGSTFGGNPLACAAALTTIACIEEEKLR 296 Query: 322 ENVNARGEQLRAGLKTLAEKYPYFSDVRGWGLINGMEIKADLELTSIEVVKAAMEKGLLL 381 EN A+GE +R GL ++RG GL+ G+E L+ E+V +E GLL+ Sbjct: 297 ENAVAQGEAIRRGLSEALAGVGGLVEIRGKGLMLGIE----LDRPCGELVAKGLEAGLLI 352 Query: 382 APAGPKVLRFVPPLIVSAAEINEAIALLDQTLAAM 416 KV+R +P L SAA+ E + Q LAA+ Sbjct: 353 NVTAEKVVRLLPALTFSAADTQELV----QRLAAL 383 Lambda K H 0.319 0.136 0.406 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: 417 Number of extensions: 21 Number of successful extensions: 5 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: 418 Length of database: 390 Length adjustment: 31 Effective length of query: 387 Effective length of database: 359 Effective search space: 138933 Effective search space used: 138933 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: 50 (23.9 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
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