Align aspartate transaminase (EC 2.6.1.1) (characterized)
to candidate WP_013842324.1 DESRU_RS11730 LL-diaminopimelate aminotransferase
Query= BRENDA::Q8YTF2 (403 letters) >NCBI__GCF_000215085.1:WP_013842324.1 Length = 392 Score = 389 bits (998), Expect = e-112 Identities = 181/380 (47%), Positives = 262/380 (68%) Query: 9 ADRIQQLPPYVFARLDELKAKAREQGIDLIDLGMGNPDGATPQPVVDAAIQALQDPKNHG 68 A RI+ LPPY+FAR++++ A+ +E GID+I LG+G+PD TPQ ++ + P+NH Sbjct: 6 AQRIKNLPPYLFARIEKVIAEKKEAGIDVISLGIGDPDIPTPQHIITELQKQALVPENHQ 65 Query: 69 YPPFEGTASFRRAITNWYNRRYGVVLDPDSEALPLLGSKEGLSHLAIAYVNPGDVVLVPS 128 YP G S+R+A+ ++YNRR+ V LDP SE + L+GSKEG++H++ Y+NPGD+VLVP Sbjct: 66 YPSSVGMLSYRQAVADFYNRRFQVQLDPKSEVVALIGSKEGIAHISWCYLNPGDLVLVPD 125 Query: 129 PAYPAHFRGPVIAGGTVHSLILKPENDWLIDLTAIPEEVARKAKILYFNYPSNPTGATAP 188 P YP + G ++AG + + L +L D +AIPE+ ARKAK+++ NYP+NPTGA A Sbjct: 126 PGYPVYSGGAILAGAEPYYMPLTAARGFLPDFSAIPEDAARKAKMMFLNYPNNPTGAVAD 185 Query: 189 REFFEEIVAFARKYEILLVHDLCYAELAFDGYQPTSLLEIPGAKDIGVEFHTLSKTYNMA 248 +F+ E +AFA+KYEIL+ HD Y+E++FDGY P S ++IPGAK++G+EF ++SK YNM Sbjct: 186 EKFYREAIAFAQKYEILICHDNAYSEVSFDGYSPLSFMQIPGAKEVGIEFSSVSKAYNMT 245 Query: 249 GWRVGFVVGNRHVIQGLRTLKTNLDYGIFAALQTAAETALQLPDIYLHEVQQRYRTRRDF 308 GWR+G+ VGN VI+ L K+N+D G F A+Q AA L P + + YR RRD Sbjct: 246 GWRIGWAVGNAEVIEALGRFKSNIDSGQFQAVQYAAMAGLSGPQDAVTANNEIYRERRDI 305 Query: 309 LIQGLGELGWDVPKTKATMYLWVKCPVGMGSTDFALNLLQQTGVVVTPGNAFGVAGEGYV 368 ++ GL +GW++ K KAT Y+W P G S FA ++ + GVV+TPGN +G GEGY Sbjct: 306 VVDGLNAMGWNLEKPKATFYIWAPVPKGFTSASFAEFVIDKAGVVITPGNGYGEQGEGYF 365 Query: 369 RISLIADCDRLGEALDRIKQ 388 RIS+ +R+ EAL+R+K+ Sbjct: 366 RISITMPKERIVEALERMKK 385 Lambda K H 0.321 0.140 0.427 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: 488 Number of extensions: 19 Number of successful extensions: 1 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: 403 Length of database: 392 Length adjustment: 31 Effective length of query: 372 Effective length of database: 361 Effective search space: 134292 Effective search space used: 134292 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