Align [LysW]-aminoadipate semialdehyde/glutamate semialdehyde transaminase; EC 2.6.1.118; EC 2.6.1.124 (uncharacterized)
to candidate WP_010965684.1 CA_RS12260 aspartate aminotransferase family protein
Query= curated2:Q7SI94 (388 letters) >NCBI__GCF_000008765.1:WP_010965684.1 Length = 387 Score = 286 bits (731), Expect = 9e-82 Identities = 154/378 (40%), Positives = 237/378 (62%), Gaps = 16/378 (4%) Query: 4 LLKFYQDRGIKIIKGEGQYVWDEKNNKYLDMHAGHGVAFLGHRNKVIIDHLKKQMEEIST 63 L+ Y + KGEG ++D+ N+Y+D +G V LGH N I+ +++Q ++ Sbjct: 6 LMNTYGRFNVTFDKGEGTKLYDKDGNEYIDFVSGVAVNCLGHCNPSIVKAIEEQSSKLMH 65 Query: 64 LSLAFDTPIREEMIKELDEL--KPEDLDNLFLLNSGSEAVELALKIARKIT------KRR 115 +S + E EL E+ K + D +F+ NSG+EA+E LK+ARK ++ Sbjct: 66 VSNYY----WNENAMELTEILCKNSEFDKVFMCNSGTEAIEAGLKLARKYALLHGDENKK 121 Query: 116 KIVAFKNSFHGRSMGALSVTWNKKYREPFEPLIGPVEFLEYNNVDSLKS-ITEDTAAVIV 174 +I+ NSFHGR+MGALSVT KY+E F+PLIG V+ +++N++D +K I+ TAAVIV Sbjct: 122 EIIYMDNSFHGRTMGALSVTGQPKYQESFKPLIGAVKSVKFNDLDDIKQKISSKTAAVIV 181 Query: 175 EPVQGEGGVIPAKKEFVKSLREVTEKVNALLIIDEVQTGFGRTGKIWAYQHFDIKPDILT 234 EP+QGEGG+IPAKKE++K LR++ ++ NALLI DEVQ G GR G ++AYQ F++ PDI+ Sbjct: 182 EPIQGEGGIIPAKKEYLKLLRDLCDENNALLIFDEVQCGMGRVGSLFAYQKFEVVPDIVC 241 Query: 235 AGKAIGGGFPVSAVFLPNWISEKIEEGDHGSTYGGNPLAAAAVTAACKVAKSEKIAE--Q 292 KA+GGGFP+ A+ ++ GDHG+TYGGNPLA A A K +K+ E Sbjct: 242 IAKALGGGFPIGAMLAKESVASSFVPGDHGNTYGGNPLACAVAIAVLKELVDKKVVEINV 301 Query: 293 AQKKGELFMRILKEKLEDFKIVREIRGLGLMIGIDLKVNPSIAIKVLQDEKVLSLKAGLT 352 +K LF +++ K E +K++ ++RG+GL+IG+++ + I + K+L + AG Sbjct: 302 NEKSKYLFDKLMTLK-EKYKVINDVRGMGLLIGVEVACDVKKIINKCFESKLLLITAGKN 360 Query: 353 TIRFLPPYLITQSDMEWA 370 +RFLPP ++ +++ A Sbjct: 361 VVRFLPPLNVSFEEIDKA 378 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: 395 Number of extensions: 14 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: 387 Length adjustment: 30 Effective length of query: 358 Effective length of database: 357 Effective search space: 127806 Effective search space used: 127806 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 Jul 25 2024. The underlying query database was built on Jul 25 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