Align Putative [LysW]-aminoadipate semialdehyde/glutamate semialdehyde transaminase; EC 2.6.1.118; EC 2.6.1.124 (uncharacterized)
to candidate WP_083509450.1 APY04_RS02685 aspartate aminotransferase family protein
Query= curated2:Q5JFW3 (362 letters) >NCBI__GCF_001541235.1:WP_083509450.1 Length = 388 Score = 249 bits (636), Expect = 9e-71 Identities = 148/378 (39%), Positives = 213/378 (56%), Gaps = 21/378 (5%) Query: 5 RKRLRLVRGEGVYVWDEKGRRYLDLIAGIGVNVLGHAHPEWVLDMSRQLEKIVVAGPMFE 64 R+ L RGEGV++ G RYLDL +G+ VNVLGHAHP V ++ Q K+ ++ Sbjct: 6 RQNLVFERGEGVWLITVDGDRYLDLGSGVAVNVLGHAHPRLVAALNEQASKLWHTSNLYR 65 Query: 65 HDEREEMLEELSHWVDYEYVYMGNSGTEAVEAAIKFAR---LATGRSE---IVAMTNAFH 118 + +E + E L + V+ NSG EA EAAIK AR A G E I+ AFH Sbjct: 66 VEGQERLAERLVATTFADKVFFCNSGAEACEAAIKAARRYHFAGGEPERWRIITFNGAFH 125 Query: 119 GRTLGSLSATWKKKYREGFGPLVPGFKHIPFNNVEAAKEAITKETAAVIFEPIQGEGGIV 178 GRTL +++A +Y EGFG V GF +PF ++ A ++AI+ ETAA++ EP+QGEGG+ Sbjct: 126 GRTLATIAAGGNPRYLEGFGTPVAGFDQVPFGDLTATEKAISPETAAIMIEPVQGEGGVN 185 Query: 179 PADEEFVKTLRDLTEDVGALLIADEVQSGL-RTGKFLAIEHYGVRPDIVTMGKGIGNGFP 237 A EF++ LR L + G LL+ DEVQSG+ R+G+ + E G+ PD++ + KGIG GFP Sbjct: 186 VASAEFMQGLRALCDANGLLLVLDEVQSGIGRSGQLFSYELAGITPDLMAIAKGIGGGFP 245 Query: 238 VSLTLTDLEIPR----GKHGSTFGGNPLACRAVATTLRILRRDRLVEKAGEKFMEFSGER 293 + L R G HGSTFGGNPLA L ++ + +E K + Sbjct: 246 LGALLATENAARGLVPGTHGSTFGGNPLATAIGLEVLNAVQEEGFLESVRRKSLHIKQSL 305 Query: 294 ----------VVKTRGRGLMIGIVLRRPAGNYVKALQERGILVNTAGNRVIRLLPPLIIE 343 V + RG+GL++G+ L P + V A +E +L+ A + V+RLLPPL I Sbjct: 306 AAISDNYPGIVQEVRGQGLLVGLKLSVPPADLVAAAREEHLLLVGASDNVVRLLPPLNIT 365 Query: 344 GDTLEEARKEIEGVLNDI 361 + + EA + +E L+ + Sbjct: 366 DEEIAEAMQRLERALDRV 383 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: 377 Number of extensions: 15 Number of successful extensions: 5 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: 388 Length adjustment: 30 Effective length of query: 332 Effective length of database: 358 Effective search space: 118856 Effective search space used: 118856 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