Align N-succinylornithine aminotransferase (EC 2.6.1.81) (characterized)
to candidate CA265_RS18530 CA265_RS18530 aspartate aminotransferase family protein
Query= reanno::Btheta:353284 (373 letters) >FitnessBrowser__Pedo557:CA265_RS18530 Length = 382 Score = 451 bits (1161), Expect = e-131 Identities = 217/375 (57%), Positives = 290/375 (77%), Gaps = 2/375 (0%) Query: 1 MKLFDVYPLYDINIVKGQGCKVWDENGTEYLDLYGGHAVISIGHAHPHYVEMISNQVATL 60 M+LFDVYPL DI I K G VWD N +YLDLYGGHAVISIGH +PHYV +++Q+ + Sbjct: 1 MQLFDVYPLNDIEITKAAGSNVWDANDQQYLDLYGGHAVISIGHTNPHYVNRLTDQLNKV 60 Query: 61 GFYSNSVINKLQQQVAERLGKISGYEDYSLFLINSGAEANENALKLASFYNGRTKVISFS 120 GFYSNSV LQ Q+AE+LG++SG +D+ LFL NSGAEANENALKLASFYNGR KVI+F+ Sbjct: 61 GFYSNSVKIPLQVQLAEKLGEVSGKKDFQLFLCNSGAEANENALKLASFYNGRKKVIAFT 120 Query: 121 KAFHGRTSLAVEATNNPTIIAPINNNGHVTYLPLNDIEAMKQEL-AKG-DVCAVIIEGIQ 178 AFHGRTSLAV T+NP I+AP+N +V +LP N+ A+++ A+G ++ AVIIEGIQ Sbjct: 121 GAFHGRTSLAVAVTDNPKIVAPVNQTENVIFLPFNNEIALEETFKAQGNEISAVIIEGIQ 180 Query: 179 GVGGIKIPTTEFMQELRKVCTETGTILILDEIQSGYGRSGKFFAHQYNHIQPDIITVAKG 238 GVGGIK + F+Q++R +C E + I D +Q GYGR+G F++H Y+ ++ D+ T+AKG Sbjct: 181 GVGGIKEASKSFLQKIRSLCDEYNAVYIADSVQCGYGRTGSFYSHDYSGVEADVYTMAKG 240 Query: 239 IGNGFPMAGVLISPMFKPVYGQLGTTFGGNHLACSAALAVMDVIEQDNLVENAKAVGDYL 298 +GNGFP+AG+ I+ FKP +G+LGTTFGGNHLAC+AALAV++V+E+DNL++NA+ VG+YL Sbjct: 241 MGNGFPVAGISIASKFKPWHGELGTTFGGNHLACAAALAVLEVMEKDNLIKNAEEVGNYL 300 Query: 299 LEELKKFPQIKEVRGRGLMIGLEFEEPIKELRSRLIYDEHVFTGASGTNVLRLLPPLCLS 358 + ELKKF Q+ EVRGRGLMIG+E + ++ L++ H+FTG + NV+RLLP L L+ Sbjct: 301 IAELKKFEQVVEVRGRGLMIGIELPAELAHVKKELLFTHHIFTGEAKPNVIRLLPALNLT 360 Query: 359 MEEADEFLARFKRVL 373 ADEFLA F++ + Sbjct: 361 KAHADEFLAAFEKAV 375 Lambda K H 0.320 0.139 0.403 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: 416 Number of extensions: 16 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: 373 Length of database: 382 Length adjustment: 30 Effective length of query: 343 Effective length of database: 352 Effective search space: 120736 Effective search space used: 120736 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 Jul 25 2024. The underlying query database was built on Jul 25 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