Align Putative [LysW]-aminoadipate semialdehyde/glutamate semialdehyde transaminase; EC 2.6.1.118; EC 2.6.1.124 (uncharacterized)
to candidate WP_012991318.1 THAL_RS01365 aspartate aminotransferase family protein
Query= curated2:Q5JFW3 (362 letters) >NCBI__GCF_000025605.1:WP_012991318.1 Length = 379 Score = 260 bits (665), Expect = 4e-74 Identities = 148/371 (39%), Positives = 225/371 (60%), Gaps = 15/371 (4%) Query: 5 RKRLRLVRGEGVYVWDEKGRRYLDLIAGIGVNVLGHAHPEWVLDMSRQLEKIVVAGPMFE 64 R +R V+G+GVY++DEKG+RYLDL++GI VN LG+ + V + Q +K++ +FE Sbjct: 9 RLPVRFVKGKGVYLYDEKGKRYLDLVSGIAVNALGYGDRDQVKAICHQAKKLIHVSNLFE 68 Query: 65 HDEREEMLEELSH--WVDYEYVYMGNSGTEAVEAAIKFARL-----ATGRSEIVAMTNAF 117 + +E++ + L W V+ NSGTEA EAAIK R R I+ N+F Sbjct: 69 NPWQEKLAKLLVERFWTKGR-VFFCNSGTEANEAAIKLVRRYFRLRGEDRYRIITFQNSF 127 Query: 118 HGRTLGSLSATWKKKYREGFGPLVPGFKHIPFNNVEAAKEAITKETAAVIFEPIQGEGGI 177 HGRT GS+SAT +KK + GF PL+ GF + FN++ + ++ IT +TAAV+ E +QGEGG+ Sbjct: 128 HGRTFGSMSATAQKKIQTGFEPLLEGFDYAIFNDISSVEKLITDKTAAVMLEIVQGEGGV 187 Query: 178 VPADEEFVKTLRDLTEDVGALLIADEVQSGL-RTGKFLAIEHYGVRPDIVTMGKGIGNGF 236 AD +F++ L+ L + G LL+ DEVQ+G+ RTGKF A +H+ + PDI+T+ KG+G G Sbjct: 188 RVADRQFLEDLQKLCRERGLLLLLDEVQTGIGRTGKFYAYQHFQLEPDIITLAKGLGGGV 247 Query: 237 PVSLTLTDLEIPR----GKHGSTFGGNPLAC-RAVATTLRILRRDRLVEKAGEKFME-FS 290 P+ L E+ + G HGSTFGGNPLAC A+ ++ V + GE FME + Sbjct: 248 PIGALLAREEVAKAFDAGSHGSTFGGNPLACASALVVVEKVSELLDHVREVGEYFMERLA 307 Query: 291 GERVVKTRGRGLMIGIVLRRPAGNYVKALQERGILVNTAGNRVIRLLPPLIIEGDTLEEA 350 + RG GLM+ + L V E+G+++N +V+R +PPLI++ ++ A Sbjct: 308 ALGRGEVRGMGLMLALELESNCKEVVLKALEKGLVINCTAKKVLRFVPPLILQKRHVDIA 367 Query: 351 RKEIEGVLNDI 361 + + VL ++ Sbjct: 368 VRILRRVLEEV 378 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: 363 Number of extensions: 18 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: 379 Length adjustment: 30 Effective length of query: 332 Effective length of database: 349 Effective search space: 115868 Effective search space used: 115868 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: 49 (23.5 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