Align Putative [LysW]-aminoadipate semialdehyde/glutamate semialdehyde transaminase; EC 2.6.1.118; EC 2.6.1.124 (uncharacterized)
to candidate WP_006746091.1 THITH_RS02435 glutamate-1-semialdehyde-2,1-aminomutase
Query= curated2:Q5JFW3 (362 letters) >NCBI__GCF_000227685.2:WP_006746091.1 Length = 425 Score = 126 bits (317), Expect = 9e-34 Identities = 103/282 (36%), Positives = 133/282 (47%), Gaps = 24/282 (8%) Query: 12 RGEGVYVWDEKGRRYLDLIAGIGVNVLGHAHPEWVLDMSRQLEKIVVAGPMFEHDEREE- 70 R EG Y++D G+RY+D I G V GHAHP+ V+D R+ + G F E Sbjct: 38 RAEGAYMYDADGKRYIDYIGSWGPMVAGHAHPQ-VIDAVREA---CLNGLSFGCPTSLEV 93 Query: 71 -MLEELSHWV-DYEYVYMGNSGTEAVEAAIKFARLATGRSEIVAMTNAFHGR------TL 122 M E++ V E V M +SGTEA +AI+ AR TGR IV +HG Sbjct: 94 AMAEKVCDLVPSIEMVRMTSSGTEATMSAIRLARGFTGRERIVKFEGNYHGHGDALLVKA 153 Query: 123 GSLSATWKKKYREG----FGPLVPGFKHIPFNNVEAAKEAITKETAAVIFEPIQGEGGIV 178 GS + T + G L + + V A +ETA VI EPI G + Sbjct: 154 GSGALTLGQPSSPGVPASLAMLTTTLNYNDSDGVRAWFAEHGEETACVIVEPIAGNMNCI 213 Query: 179 PADEEFVKTLRDLTEDVGALLIADEVQSGLRTGKFLAIEHYGVRPDIVTMGKGIGNGFPV 238 P F++TLR++ + GA+LI DEV +G R A YGV PD+ T+GK IG G PV Sbjct: 214 PPQPGFLETLREVCDQSGAVLIFDEVMTGFRVAAGCAQALYGVAPDMTTLGKIIGGGMPV 273 Query: 239 SLTLTDLEI-----PRGK--HGSTFGGNPLACRAVATTLRIL 273 EI P G T GNP+A A TL IL Sbjct: 274 GAFGGRREIMEHLAPVGPVYQAGTLSGNPIAMTAGLQTLEIL 315 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: 382 Number of extensions: 23 Number of successful extensions: 4 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: 425 Length adjustment: 31 Effective length of query: 331 Effective length of database: 394 Effective search space: 130414 Effective search space used: 130414 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 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