Align [LysW]-aminoadipate semialdehyde/glutamate semialdehyde transaminase; EC 2.6.1.118; EC 2.6.1.124 (uncharacterized)
to candidate WP_084276125.1 B8779_RS08250 aspartate aminotransferase family protein
Query= curated2:Q7SI94 (388 letters) >NCBI__GCF_900176045.1:WP_084276125.1 Length = 396 Score = 212 bits (540), Expect = 1e-59 Identities = 135/376 (35%), Positives = 213/376 (56%), Gaps = 17/376 (4%) Query: 4 LLKFYQDRGIKIIKGEGQYVWDEKNNKYLDMHAGHGVAFLGHRNKVIIDHLKKQMEEIST 63 +L Y + +KG+ ++DE+ +++D +G GV +GH NK + D + Q ++I Sbjct: 11 VLHTYARNYVNFVKGKNAKLYDERGKEFIDFTSGIGVVSVGHGNKRLADAICDQAQKIIH 70 Query: 64 LSLAFDTPIREEMIKELDELKPEDLDNLFLLNSGSEAVELALKIARKI------TKRRKI 117 +S + + + K + EL D+ LF NSG+EA E A+KIARK KR KI Sbjct: 71 ISNLYLIEPQALLAKRIVELSSYDM-RLFFANSGAEANEGAIKIARKYGEVDGKVKRYKI 129 Query: 118 VAFKNSFHGRSMGALSVTWNKKYREPFEPLIGPVEFLEYNNVDSLKSITED-TAAVIVEP 176 + K+SFHGR++ AL T + F P P F+ +++D + + +D T AV++E Sbjct: 130 ITLKHSFHGRTITALKATGQEAMHTYFGPF--PDGFVYADSIDQIPDLIDDHTVAVMIEL 187 Query: 177 VQGEGGVIPAKKEFVKSLREVTEKVNALLIIDEVQTGFGRTGKIWAYQHFDIKPDILTAG 236 +QGEGGV P KE V++L ++ ++ + LLIIDEVQTG RTG+ A ++I+PDI+T Sbjct: 188 IQGEGGVEPQDKEAVQNLAKLLKQKDVLLIIDEVQTGIYRTGEFLASNLYEIEPDIITLA 247 Query: 237 KAIGGGFPVSAVFLPNWISEKIEEGDHGSTYGGNPLAAAAVTAACKVAKSEKIAEQAQKK 296 K +GGG P+ AV + + + GDHGST+GGN L+ A + + K + + + Sbjct: 248 KGLGGGVPIGAVM--TRLKDIFKPGDHGSTFGGNYLSTRAALEVIAILEELKASGKLDEH 305 Query: 297 GELFMRILKEKLEDFKIVREIR-GLGLMIGIDLKVNPSIAIKVLQD---EKVLSLKAGLT 352 F LKE + + + E G G+M G+ K + I K++++ E +L LKAG Sbjct: 306 FIYFEERLKEIAKKYAALFEKEVGFGMMRGLRAK-SAEIQGKIIEEAFNEGLLVLKAGRN 364 Query: 353 TIRFLPPYLITQSDME 368 T+RFLPP IT+ +M+ Sbjct: 365 TVRFLPPLTITKEEMD 380 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: 370 Number of extensions: 18 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: 396 Length adjustment: 31 Effective length of query: 357 Effective length of database: 365 Effective search space: 130305 Effective search space used: 130305 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