Align Succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate Ga0059261_3205 Ga0059261_3205 transaminase, acetylornithine/succinylornithine family
Query= reanno::Koxy:BWI76_RS11670 (406 letters) >FitnessBrowser__Korea:Ga0059261_3205 Length = 398 Score = 324 bits (830), Expect = 3e-93 Identities = 173/393 (44%), Positives = 236/393 (60%), Gaps = 10/393 (2%) Query: 14 MMPVYAPAAFIPVRGEGSRLWDQQGKEYIDFAGGIAVNALGHAHPRLVKALTEQAGKFWH 73 +MPVY PVRGEG L ++G+ Y+DFA GIAVNALGH HP+ KA+ EQA H Sbjct: 6 LMPVYPRCEVRPVRGEGCYLIGERGERYLDFAAGIAVNALGHGHPQFTKAIAEQAATLMH 65 Query: 74 TGNGYTNEPVLRLAKQLIDATFADRVFFCNSGAEANEAALKLARKYAHDRFGSEKSGIVA 133 N Y + LA++++D +FAD VFF NSG EA E A+K AR+Y + ++ ++ Sbjct: 66 VSNLYGSPQGEALAQRIVDNSFADTVFFTNSGVEAIECAIKTARRYHYVNGNPQRHKLIT 125 Query: 134 FKNAFHGRTLFTVSAGGQPAYSQDFAPLPPQIQHAIYNDLDSAKALIDDNTCAVIVEPMQ 193 FKNAFHGR++ +SA QP F PL P + +NDL+ A A IDD T +VE +Q Sbjct: 126 FKNAFHGRSIGAISATDQPKMRDGFEPLLPGFDYVKFNDLEGAIAKIDDETAGFLVETVQ 185 Query: 194 GEGGVVPADADFLRGLRELCDAHNALLIFDEVQTGVGRTGELYAYMHYGVTPDLLSTAKA 253 GEGG+ +F++GLR+ CD H LLI DE+Q G GRTG+++AY HYG+TPD+L+ AK Sbjct: 186 GEGGMTAGTVEFIQGLRKACDEHGLLLILDEIQCGYGRTGKMWAYEHYGITPDILTAAKG 245 Query: 254 LGGGFPIGALLASERCASVMTVGTHGTTYGGNPLACAVAGEVFATINTREVLNGVKQRHQ 313 +G GFP+GA LA+E A MT GTHG+TYGGNPLA A AG+ + G + + Sbjct: 246 IGNGFPLGACLATEEAAKGMTFGTHGSTYGGNPLAMA-AGQAVLDVMLEP---GFFEHVE 301 Query: 314 WFCERLNA-----INARYGLFKEIRGLGLLIGCVLKDEYAGKAKAISNQAAEEGLMILIA 368 ERL A I LF EIRG GL++G LK E A +++ GL+ + A Sbjct: 302 KMGERLRAGFEQLIPNHDHLFDEIRGKGLMLGIKLK-EPAVSRDFVAHLRENHGLLTVAA 360 Query: 369 GANVVRFAPALIISEDEVNSGLDRFELACKRFL 401 G NV R P L+I E + +++ + ++ Sbjct: 361 GENVFRVLPPLVIEESHIAECIEKLSAGARSYV 393 Lambda K H 0.321 0.137 0.412 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: 469 Number of extensions: 20 Number of successful extensions: 4 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: 406 Length of database: 398 Length adjustment: 31 Effective length of query: 375 Effective length of database: 367 Effective search space: 137625 Effective search space used: 137625 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