Align Putative [LysW]-aminoadipate semialdehyde/glutamate semialdehyde transaminase; EC 2.6.1.118; EC 2.6.1.124 (uncharacterized)
to candidate WP_006748314.1 THITH_RS09650 aspartate aminotransferase family protein
Query= curated2:Q5JFW3 (362 letters) >NCBI__GCF_000227685.2:WP_006748314.1 Length = 398 Score = 259 bits (661), Expect = 1e-73 Identities = 147/371 (39%), Positives = 216/371 (58%), Gaps = 22/371 (5%) Query: 13 GEGVYVWDEKGRRYLDLIAGIGVNVLGHAHPEWVLDMSRQLEKIVVAGPMFEHDEREEML 72 GEG ++WD +GRRYLD ++GI V LGHAHP+ ++ Q ++ ++ +E++ Sbjct: 19 GEGAWLWDTEGRRYLDALSGIAVCGLGHAHPKIAAAIAEQAHTLIHTSNLYRVPLQEQLA 78 Query: 73 EELSHWVDYEYVYMGNSGTEAVEAAIKFARL-----ATGRSEIVAMTNAFHGRTLGSLSA 127 L + + NSG EA EAAIK ARL R +IV M +FHGRTL +LSA Sbjct: 79 RRLCALAGMDQAFFCNSGAEANEAAIKLARLHGHRRGIARPKIVVMEGSFHGRTLATLSA 138 Query: 128 TWKKKYREGFGPLVPGFKHIPFNNVEAAKE-AITKETAAVIFEPIQGEGGIVPADEEFVK 186 T + + GF PLV GF +P+ + A E E AA++ EPI GEGGI +++ Sbjct: 139 TGNARIQNGFEPLVEGFIRVPYGDSAAVAELGGDPEIAAILVEPITGEGGIRLPPSGYLR 198 Query: 187 TLRDLTEDVGALLIADEVQSGL-RTGKFLAIEHYGVRPDIVTMGKGIGNGFPVSLTL--- 242 LR L LL+ DE+QSG+ RTG++ A +H + PD++++ KG+GNG P+ +L Sbjct: 199 ELRTLATRHHWLLMLDEIQSGIGRTGQWFAFQHEDIVPDVLSLAKGLGNGVPIGASLVSG 258 Query: 243 --TDLEIPRGKHGSTFGGNPLACRAVATTLRILRRDRLVEKA---GEKFMEFSGER---- 293 TDL P G HG+TFGGNPL CRA L +++ + L E+A G+ + ER Sbjct: 259 AATDLFTP-GSHGTTFGGNPLVCRAALAVLDVMQEEALGEQAARHGDMLLRLLQERLGSH 317 Query: 294 --VVKTRGRGLMIGIVLRRPAGNYVKALQERGILVNTAGNRVIRLLPPLIIEGDTLEEAR 351 V++ RG+GLM+GI L RPA V+ +RG+L+N RV+RLLPPLI + D + E Sbjct: 318 PEVIEIRGKGLMLGIELDRPATELVRQALDRGLLINVTAERVVRLLPPLITDDDQIAEIA 377 Query: 352 KEIEGVLNDIL 362 + +++ ++ Sbjct: 378 DTVADLVSRLI 388 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: 380 Number of extensions: 20 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: 398 Length adjustment: 30 Effective length of query: 332 Effective length of database: 368 Effective search space: 122176 Effective search space used: 122176 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