Align Putative [LysW]-aminoadipate semialdehyde/glutamate semialdehyde transaminase; EC 2.6.1.118; EC 2.6.1.124 (uncharacterized)
to candidate WP_012386123.1 BIND_RS16295 aminotransferase class III-fold pyridoxal phosphate-dependent enzyme
Query= curated2:Q5JFW3 (362 letters) >NCBI__GCF_000019845.1:WP_012386123.1 Length = 477 Score = 209 bits (532), Expect = 1e-58 Identities = 151/399 (37%), Positives = 213/399 (53%), Gaps = 57/399 (14%) Query: 13 GEGVYVWDEKGRRYLDLIAGIGVNVLGHAHPEWVLDMSRQLEKIVVAGPMFEHDEREE-- 70 G+G Y++D RYLDL++G GV +G HP + R+ V+A + + + Sbjct: 59 GQGQYLFDRNDARYLDLLSGWGVFAIGRNHP-----LLRETLTSVLASDLPNLVQMDVSV 113 Query: 71 ----MLEELSHWVDY-EYVYMGNSGTEAVEAAIKFARLATGRSEIVAMTNAFHGRTLGSL 125 + E L +V + + V+ NSGTEAVEAAIKFAR ATGR IV +AFHG + GSL Sbjct: 114 LAGLLAERLLGFVPFLDKVFFCNSGTEAVEAAIKFARRATGRPGIVYCEHAFHGLSYGSL 173 Query: 126 SATWKKKYREGFGPLVPGFKHIPFNNVEAAKEAITK-ETAAVIFEPIQGEGGIVPADEEF 184 S + +REGFG +PG +PFN++ A ++A+ K + AA I EP+QG+G +P D+ + Sbjct: 174 SLNGDQIFREGFGDTLPGCHAVPFNDLAALEKALAKHDIAAFIVEPVQGKGVNLP-DDGY 232 Query: 185 VKTLRDLTEDVGALLIADEVQSGL-RTGKFLAIEHYGVRPDIVTMGKGIGNG-FPVSLTL 242 + ++ L G L +ADE+Q+GL RTGKFLAIEH+GV PD+V + K + G PV L Sbjct: 233 LAGVQALCRKYGTLFVADEIQTGLGRTGKFLAIEHWGVEPDMVLVAKALSGGHVPVGAVL 292 Query: 243 TDLEI---------PRGKHGSTFGGNPLACRAVATTLRILRRDRLVEKA---GEKFMEF- 289 + I HGSTF N LA A TL ++ R++LVEKA GE+ + F Sbjct: 293 SRKGIFEKVFSRMDRAVVHGSTFAKNDLAMAAGLATLEVIEREQLVEKAARNGERLLTFF 352 Query: 290 -----SGERVVKTRGRGLMIGIVLRRPAGNYVKA---------------------LQERG 323 E V RG+GLMIGI P +KA +E Sbjct: 353 QGLADRYELVRTVRGKGLMIGIEFGAPRSLKLKASWTLLETVNTGLFCQLITIPLFKEHK 412 Query: 324 ILVNTAG--NRVIRLLPPLIIEGDTLEEARKEIEGVLND 360 ILV AG + ++LLP L+I+ + + E V+ D Sbjct: 413 ILVQVAGHASHTVKLLPTLVIDDGDCDWIERAFETVIAD 451 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: 427 Number of extensions: 20 Number of successful extensions: 7 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: 477 Length adjustment: 31 Effective length of query: 331 Effective length of database: 446 Effective search space: 147626 Effective search space used: 147626 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