Align Putative [LysW]-aminoadipate semialdehyde/glutamate semialdehyde transaminase; EC 2.6.1.118; EC 2.6.1.124 (uncharacterized)
to candidate Ga0059261_3205 Ga0059261_3205 transaminase, acetylornithine/succinylornithine family
Query= curated2:Q5JFW3 (362 letters) >FitnessBrowser__Korea:Ga0059261_3205 Length = 398 Score = 261 bits (666), Expect = 3e-74 Identities = 156/380 (41%), Positives = 223/380 (58%), Gaps = 27/380 (7%) Query: 1 MPLY-RKRLRLVRGEGVYVWDEKGRRYLDLIAGIGVNVLGHAHPEWVLDMSRQLEKIVVA 59 MP+Y R +R VRGEG Y+ E+G RYLD AGI VN LGH HP++ ++ Q ++ Sbjct: 7 MPVYPRCEVRPVRGEGCYLIGERGERYLDFAAGIAVNALGHGHPQFTKAIAEQAATLMHV 66 Query: 60 GPMFEHDEREEMLEELSHWVDYEYVYMGNSGTEAVEAAIKFAR---LATG---RSEIVAM 113 ++ + E + + + + V+ NSG EA+E AIK AR G R +++ Sbjct: 67 SNLYGSPQGEALAQRIVDNSFADTVFFTNSGVEAIECAIKTARRYHYVNGNPQRHKLITF 126 Query: 114 TNAFHGRTLGSLSATWKKKYREGFGPLVPGFKHIPFNNVEAAKEAITKETAAVIFEPIQG 173 NAFHGR++G++SAT + K R+GF PL+PGF ++ FN++E A I ETA + E +QG Sbjct: 127 KNAFHGRSIGAISATDQPKMRDGFEPLLPGFDYVKFNDLEGAIAKIDDETAGFLVETVQG 186 Query: 174 EGGIVPADEEFVKTLRDLTEDVGALLIADEVQSGL-RTGKFLAIEHYGVRPDIVTMGKGI 232 EGG+ EF++ LR ++ G LLI DE+Q G RTGK A EHYG+ PDI+T KGI Sbjct: 187 EGGMTAGTVEFIQGLRKACDEHGLLLILDEIQCGYGRTGKMWAYEHYGITPDILTAAKGI 246 Query: 233 GNGFPVSLTLTDLEIPR----GKHGSTFGGNPLACRAVATTLRILRRDRL---VEKAGEK 285 GNGFP+ L E + G HGST+GGNPLA A L ++ VEK GE+ Sbjct: 247 GNGFPLGACLATEEAAKGMTFGTHGSTYGGNPLAMAAGQAVLDVMLEPGFFEHVEKMGER 306 Query: 286 FMEFSGERVV--------KTRGRGLMIGIVLRRPA--GNYVKALQE-RGILVNTAGNRVI 334 + E+++ + RG+GLM+GI L+ PA ++V L+E G+L AG V Sbjct: 307 -LRAGFEQLIPNHDHLFDEIRGKGLMLGIKLKEPAVSRDFVAHLRENHGLLTVAAGENVF 365 Query: 335 RLLPPLIIEGDTLEEARKEI 354 R+LPPL+IE + E +++ Sbjct: 366 RVLPPLVIEESHIAECIEKL 385 Lambda K H 0.320 0.140 0.410 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: 431 Number of extensions: 30 Number of successful extensions: 7 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: 362 Length of database: 398 Length adjustment: 30 Effective length of query: 332 Effective length of database: 368 Effective search space: 122176 Effective search space used: 122176 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