Align [LysW]-aminoadipate semialdehyde/glutamate semialdehyde transaminase; EC 2.6.1.118; EC 2.6.1.124 (uncharacterized)
to candidate WP_011372920.1 SUDEN_RS06750 adenosylmethionine--8-amino-7-oxononanoate transaminase
Query= curated2:Q7SI94 (388 letters) >NCBI__GCF_000012965.1:WP_011372920.1 Length = 432 Score = 144 bits (363), Expect = 5e-39 Identities = 120/406 (29%), Positives = 194/406 (47%), Gaps = 43/406 (10%) Query: 13 IKIIKGEGQYVWDEKNNKYLDMHAGHGVAFLGHRNKVIIDHLKKQMEEISTLSLAFDTPI 72 I I K G Y+ D N Y+D + V GH N I + +K+Q++ + + LA T Sbjct: 30 IPIKKAYGVYLEDFDGNLYIDAISSWWVNIFGHTNSYINEKIKEQLDTLEHVILAGFTHE 89 Query: 73 REEMIKE-LDELKPEDLDNLFLLNSGSEAVELALKIARKITKRRK-----IVAFKNSFHG 126 + + E L +L P+ L+ F ++GS VE+ALK++ K + V+ NS+HG Sbjct: 90 QVVRLSERLVKLTPDGLEKCFYADNGSSGVEVALKMSFHTHKNNQKEKNIFVSLTNSYHG 149 Query: 127 RSMGALSVTWNKKYREPFEPLIGPVEFLEYNNVDSLKSITE--------------DTAAV 172 ++GALSV K Y++ ++PL+ S+++ E + +A+ Sbjct: 150 ETIGALSVGDVKLYKDTYKPLLIQSIQTPVPKDMSIEAAREAACEFEKLCEKRAKEISAI 209 Query: 173 IVEP-VQGEGGVIPAKKEFVKSLREVTEKVNALLIIDEVQTGFGRTGKIWAYQHFDIKPD 231 I+EP +QG G + KEF+ +RE+ + + LI DEV GFGR+G ++A + +I PD Sbjct: 210 ILEPLIQGAGYMHMYHKEFLILVREICNRYDIHLITDEVMVGFGRSGDMFACKSANITPD 269 Query: 232 ILTAGKAIGGGF-PVSAVFLPNWISEKI-------EEGDHGSTYGGNPLAAAAVTAACKV 283 L K + GG+ P+S V + I H +Y GN LA AA A + Sbjct: 270 FLILSKGLTGGYLPLSVVLTTDEIYTSFYCDYSENRAFLHSHSYTGNALACAAANATLDI 329 Query: 284 AKSEKIAEQAQKKGELFMRILKEKLEDFKIVREIRGLGLMIGIDLKVNPS---IAIKVLQ 340 ++E I E+ Q+ L K + K V IR G++ ++LK S I +KV + Sbjct: 330 FENENIIEKNQEIANYMAEELL-KFKTLKNVLSIRQTGMVCAVELKGYDSKDRIGLKVYE 388 Query: 341 DEKVLSLKAGLT------TIRFLPPYLITQSDMEWASDATRKGISE 380 LK G+ + F+PPY+IT +++ + I E Sbjct: 389 ----YGLKNGVLLRPLGHVVYFMPPYIITNDEIKKMMQVAYEAIKE 430 Lambda K H 0.317 0.136 0.386 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: 349 Number of extensions: 19 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: 388 Length of database: 432 Length adjustment: 31 Effective length of query: 357 Effective length of database: 401 Effective search space: 143157 Effective search space used: 143157 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Apr 10 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