Align [LysW]-aminoadipate semialdehyde/glutamate semialdehyde transaminase; EC 2.6.1.118; EC 2.6.1.124 (uncharacterized)
to candidate WP_012674835.1 SULAZ_RS03325 aspartate aminotransferase family protein
Query= curated2:Q7SI94 (388 letters) >NCBI__GCF_000021545.1:WP_012674835.1 Length = 386 Score = 248 bits (633), Expect = 2e-70 Identities = 141/368 (38%), Positives = 224/368 (60%), Gaps = 16/368 (4%) Query: 17 KGEGQYVWDEKNNKYLDMHAGHGVAFLGHRNKVIIDHLKKQMEEISTLSLAFDTPIREEM 76 KGEG Y++D+K KYLDM +G V LG+ + + + +Q +I +S F + E+ Sbjct: 22 KGEGCYLYDDKGKKYLDMLSGIAVNALGYNHPKLTKAICEQASKIIHISNLFYIKPQIEV 81 Query: 77 IKELDELKPEDLDNLFLLNSGSEAVELALKIAR-----KITKRRKIVAFKNSFHGRSMGA 131 K L E +F NSG+E+ E +K+ R K +R +I+ F+ SFHGR++ Sbjct: 82 AKILSENSFGG--KVFFCNSGAESNEALIKLVRRYFYDKKQERYEIITFEGSFHGRTLAT 139 Query: 132 LSVTWNKKYREPFEPLIGPVEFLEYNNVDSLKS-ITEDTAAVIVEPVQGEGGVIPAKKEF 190 ++ T KY E F PL+ ++ ++N++DS+K+ IT+ TAA+++E VQGEGGV PA KEF Sbjct: 140 VTATAQPKYHEGFYPLVEGFKYAKFNDIDSVKNLITDKTAAILIELVQGEGGVNPANKEF 199 Query: 191 VKSLREVTEKVNALLIIDEVQTGFGRTGKIWAYQHFDIKPDILTAGKAIGGGFPVSAVFL 250 +K L ++ ++ + L +DEVQTG GRTGK++AYQHFDI+PDI++ K +GGG P+ A+ Sbjct: 200 IKELYKLCKENDILFTVDEVQTGIGRTGKLFAYQHFDIQPDIISLAKGLGGGVPIGAIIA 259 Query: 251 PNWISEKIEEGDHGSTYGGNPLAAAAVTAACKVAKSEKIAEQAQKKGELFMRILKEKLED 310 + I++ G H ST+GGN L+ A + SE ++ QK GE LKE L+ Sbjct: 260 KDDIAKSFVPGTHASTFGGNYLSTVAAKVVLEEVLSEGFLDRVQKVGE----YLKEALKI 315 Query: 311 FKIVREIRGLGLMIGIDL--KVNPSIAIKVLQDEKVLSLKAGLTTIRFLPPYLITQSDME 368 F ++GLGLM+G+DL ++ +K ++ ++ AG T+RF+PP +IT+ +++ Sbjct: 316 FGY--PVKGLGLMVGMDLPQSISAKEVMKKTLEKGLIVGTAGENTLRFVPPLIITEKEVD 373 Query: 369 WASDATRK 376 A D ++ Sbjct: 374 EAVDILKE 381 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: 360 Number of extensions: 12 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: 388 Length of database: 386 Length adjustment: 30 Effective length of query: 358 Effective length of database: 356 Effective search space: 127448 Effective search space used: 127448 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