Align [LysW]-aminoadipate semialdehyde/glutamate semialdehyde transaminase; EC 2.6.1.118; EC 2.6.1.124 (uncharacterized)
to candidate WP_011372884.1 SUDEN_RS06570 aspartate aminotransferase family protein
Query= curated2:Q7SI94 (388 letters) >NCBI__GCF_000012965.1:WP_011372884.1 Length = 394 Score = 204 bits (520), Expect = 3e-57 Identities = 138/392 (35%), Positives = 210/392 (53%), Gaps = 27/392 (6%) Query: 4 LLKFYQDRGIKIIKGEGQYVWDEKNNKYLDMHAGHGVAFLGHRNKVIIDHLKKQMEEIST 63 +L Y ++ + G V D KY+D +G V +GH NK + D + KQ+ I+ Sbjct: 12 VLPTYARADVEFVSGNNAIVVDANGKKYIDFASGIAVCSVGHANKRVNDAICKQLSNITH 71 Query: 64 LSLAFDTPIREEMIKELDELKPEDLDNLFLLNSGSEAVELALKIARKI------TKRRKI 117 S + + + +++ E D+ F NSG+EA E A+KIARK KR K+ Sbjct: 72 TSNLYYIAPQAKAAQKIVEASGYDM-KCFFGNSGAEANEGAIKIARKFGEKDGELKRYKV 130 Query: 118 VAFKNSFHGRSMGALSVTWNKKYREPFEPLIGPVEFLEYNNVDSLKSITED-TAAVIVEP 176 + ++SFHGR++ + T +K F P P F+ +N+D + S+ +D T AV++E Sbjct: 131 ITLQHSFHGRTITTVKATGQEKMHNYFGPY--PDGFVYADNIDHVASLVDDHTCAVMIEL 188 Query: 177 VQGEGGVIPAKKEFVKSLREVTEKVNALLIIDEVQTGFGRTGKIWAYQHFDIKPDILTAG 236 VQGEGGV P ++ V+ L + ++ N LLIIDEVQTG RTGK A ++DIKPD++T Sbjct: 189 VQGEGGVQPLDRDSVQKLAKFLKEKNVLLIIDEVQTGIYRTGKFLASNYYDIKPDVVTLA 248 Query: 237 KAIGGGFPVSAVFLPNWISEKIEEGDHGSTYGGNPLAAAAVTAACKVAKSEKIAEQAQKK 296 K +GGG P+ V + + GDHGST+GGN L + TAAC+V I + + Sbjct: 249 KGLGGGVPIGVVM--TTLKDVFGAGDHGSTFGGNFL---STTAACEVV---DILNEMNES 300 Query: 297 GELFMRI--LKEKLEDF-----KIVREIRGLGLMIGIDLKVNPSIA--IKVLQDEKVLSL 347 GEL I +LE F I G+G+M G+ +K ++ I ++E V+ L Sbjct: 301 GELQKGIDYFDSELEKFYNAHRDIFTSKVGIGMMCGLRVKDGDTLTKIISNAREEGVIVL 360 Query: 348 KAGLTTIRFLPPYLITQSDMEWASDATRKGIS 379 KAG T+R LP IT+ +++ + + IS Sbjct: 361 KAGRDTLRLLPALTITKEEIDEGFTSLNRTIS 392 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: 350 Number of extensions: 15 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: 394 Length adjustment: 31 Effective length of query: 357 Effective length of database: 363 Effective search space: 129591 Effective search space used: 129591 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