Align Putative [LysW]-aminoadipate semialdehyde/glutamate semialdehyde transaminase; EC 2.6.1.118; EC 2.6.1.124 (uncharacterized)
to candidate WP_012991510.1 THAL_RS02335 glutamate-1-semialdehyde 2,1-aminomutase
Query= curated2:Q5JFW3 (362 letters) >NCBI__GCF_000025605.1:WP_012991510.1 Length = 424 Score = 126 bits (316), Expect = 1e-33 Identities = 97/297 (32%), Positives = 143/297 (48%), Gaps = 25/297 (8%) Query: 14 EGVYVWDEKGRRYLDLIAGIGVNVLGHAHPEWVLDMSRQLEKIVVAG-PMFEHDEREEML 72 +G +WD +G+ Y+D + G +LGHAHP V ++ RQL + + G +E E++ Sbjct: 39 KGCRLWDVEGKEYIDFLMSWGPLILGHAHPYVVSEVERQLSRGMSYGLTCYEEIRLAELV 98 Query: 73 EELSHWVDYEYVYMGNSGTEAVEAAIKFARLATGRSEIVAMTNAFHGRTLGSLSATWKKK 132 +S E V +SGTEA +AI+ AR TGR +V +HG G L + Sbjct: 99 --VSSVPSVEMVRFVSSGTEATMSAIRLARGYTGRKFVVKFEGCYHGHYDGLLVSAGSGV 156 Query: 133 YREGFGPLVPGFKH--------IPFNNVEAAK---EAITKETAAVIFEPIQGEGGIVPAD 181 G P PG +P+N+ +A E ++ A VI EP+ G G+V Sbjct: 157 ATLGI-PGTPGVPEEIAGLTLVLPYNDTDAVLSTFERYGEDIACVIVEPVAGNMGVVLPS 215 Query: 182 EEFVKTLRDLTEDVGALLIADEVQSGLRTGKFLAIEHYGVRPDIVTMGKGIGNGFPVSLT 241 E F++ LR++T GA+LI DEV + R A E+Y + PDI MGK +G G P+ Sbjct: 216 EGFLEVLREVTRKYGAVLIFDEVITNFRLSVGGAQEYYAIDPDITCMGKILGGGMPLGAY 275 Query: 242 LTDLEI-----PRGK--HGSTFGGNPLAC---RAVATTLRILRRDRLVEKAGEKFME 288 EI P GK T GNP++ RA L L+ +L+E+ + E Sbjct: 276 GGKKEIMSHVAPEGKVYQAGTLSGNPVSVVCGRATLEELLRLKPYQLLEERTRRLAE 332 Lambda K H 0.320 0.140 0.410 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: 347 Number of extensions: 21 Number of successful extensions: 3 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: 362 Length of database: 424 Length adjustment: 31 Effective length of query: 331 Effective length of database: 393 Effective search space: 130083 Effective search space used: 130083 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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