Align aspartate transaminase (EC 2.6.1.1) (characterized)
to candidate WP_092483207.1 BM299_RS08760 LL-diaminopimelate aminotransferase
Query= BRENDA::Q8YTF2 (403 letters) >NCBI__GCF_900115975.1:WP_092483207.1 Length = 392 Score = 392 bits (1007), Expect = e-114 Identities = 182/380 (47%), Positives = 259/380 (68%) Query: 9 ADRIQQLPPYVFARLDELKAKAREQGIDLIDLGMGNPDGATPQPVVDAAIQALQDPKNHG 68 A RI+ LPPY+FAR+++L A+ + G+D+I LG+G+PD TP+ +++ + P NH Sbjct: 6 AQRIKNLPPYLFARIEKLVAEKKAAGVDIISLGIGDPDMPTPEHIIEELQKQAAVPVNHQ 65 Query: 69 YPPFEGTASFRRAITNWYNRRYGVVLDPDSEALPLLGSKEGLSHLAIAYVNPGDVVLVPS 128 YP G SFR+A+ +WY +R GV LDP +E + L+GSKEG++H++ Y+NPGD VLVP Sbjct: 66 YPSSVGMLSFRQAVADWYRKRSGVELDPATEVVSLIGSKEGIAHISWCYLNPGDTVLVPD 125 Query: 129 PAYPAHFRGPVIAGGTVHSLILKPENDWLIDLTAIPEEVARKAKILYFNYPSNPTGATAP 188 P YP + G ++AG + + L EN +L DL AIP EVARKAK+++ NYP+NPTGA A Sbjct: 126 PGYPVYSGGAILAGAEPYYMPLTAENKFLPDLNAIPAEVARKAKMMFINYPNNPTGAVAG 185 Query: 189 REFFEEIVAFARKYEILLVHDLCYAELAFDGYQPTSLLEIPGAKDIGVEFHTLSKTYNMA 248 EF+ ++ FA++Y IL+ HD Y ++AFDGY+P S L+ PGAKD+G+EF ++SKTYNM Sbjct: 186 EEFYLAVIDFAKEYNILVCHDAAYCDMAFDGYKPPSFLQFPGAKDVGIEFLSVSKTYNMT 245 Query: 249 GWRVGFVVGNRHVIQGLRTLKTNLDYGIFAALQTAAETALQLPDIYLHEVQQRYRTRRDF 308 GWR+G+ G+ V+ L LK+N+D G F A+Q AA L P + +Q+ YR RRD Sbjct: 246 GWRIGWAAGHPGVVDALGRLKSNIDSGQFQAIQYAAMKGLTGPQDSVERMQKVYRERRDI 305 Query: 309 LIQGLGELGWDVPKTKATMYLWVKCPVGMGSTDFALNLLQQTGVVVTPGNAFGVAGEGYV 368 L+ L +GW + K KAT Y+W P G S FA +L + GV++TPGN +G GEG+ Sbjct: 306 LVDALNSMGWQLEKPKATFYVWAPVPAGYTSASFAEMVLDKCGVIITPGNGYGENGEGFF 365 Query: 369 RISLIADCDRLGEALDRIKQ 388 RI+L + DR+ EALDR+K+ Sbjct: 366 RIALTVEKDRMMEALDRMKK 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: 508 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