Align Putative [LysW]-aminoadipate semialdehyde/glutamate semialdehyde transaminase; EC 2.6.1.118; EC 2.6.1.124 (uncharacterized)
to candidate WP_025272511.1 HALAL_RS0102620 aspartate aminotransferase family protein
Query= curated2:Q5JFW3 (362 letters) >NCBI__GCF_000527155.1:WP_025272511.1 Length = 417 Score = 214 bits (545), Expect = 3e-60 Identities = 142/399 (35%), Positives = 209/399 (52%), Gaps = 50/399 (12%) Query: 2 PLYRKRLRLV--RGEGVYVWDEKGRRYLDLIAGIGVNVLGHAHPEWVLDMSRQLEKIVVA 59 PL ++ +V GEGVY++D GRRYLD AGIGV GH HP V Q+ K++ Sbjct: 6 PLLKQATPVVADHGEGVYLYDADGRRYLDFTAGIGVTSTGHCHPHVVQAAQEQVGKLIHG 65 Query: 60 G-PMFEHDEREEMLEELSHWV--DYEYVYMGNSGTEAVEAAIKFARLATGRSEIVAMTNA 116 H E+ L + + ++ NSG+EAVEAA++ +R ATGR IV Sbjct: 66 QYTTVMHQPLLELTRRLGDVLPAGLDSLFFSNSGSEAVEAALRLSRQATGRPNIVVFQGG 125 Query: 117 FHGRTLGSLSATWK-KKYREGFGPLVPGFKHIPF--------NNVEAAKEAITK------ 161 FHGRT+ + + T ++ G PL+ G PF + A + A+ + Sbjct: 126 FHGRTVATATLTTSGTRFSAGISPLMSGVHMAPFPYAYRYGWDESTATEFALRELDYLFA 185 Query: 162 ------ETAAVIFEPIQGEGGIVPADEEFVKTLRDLTEDVGALLIADEVQSGL-RTGKFL 214 ETAA EP+ GEGG VPA+ EF+ LR ++ G LL+ DE+Q+G RTGKF Sbjct: 186 TVTSPAETAAFFIEPVLGEGGYVPANPEFLAGLRQRADEHGILLVLDEIQTGFGRTGKFW 245 Query: 215 AIEHYGVRPDIVTMGKGIGNGFPVSLTLTDLEIPR----GKHGSTFGGNPLACRAVATTL 270 +H+GV PD+V + KG+ +GFP+S T E+ G G T+GGN +AC A TL Sbjct: 246 GHDHFGVHPDVVLIAKGLASGFPLSGMATSEELMSQAWPGSQGGTYGGNAVACAAAVATL 305 Query: 271 RILRRDRLVEKA---GEKFMEFS---GER---VVKTRGRGLMIGIVLRRPAGN------- 314 +++R+ LV+ A G + +E + GE+ + RG GLM+G P G Sbjct: 306 DVIQREGLVDNAADRGRQLLEGARHIGEKTPLIGDVRGLGLMVGSEFTTPDGQPDTATAQ 365 Query: 315 -YVKALQERGILVNTAG--NRVIRLLPPLIIEGDTLEEA 350 K RG+++ T G V+R++PPL+++ ++EA Sbjct: 366 AAQKEAAARGLMLLTCGAHMNVVRMIPPLVVDAAQVDEA 404 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: 396 Number of extensions: 27 Number of successful extensions: 6 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: 417 Length adjustment: 30 Effective length of query: 332 Effective length of database: 387 Effective search space: 128484 Effective search space used: 128484 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