Align aspartate transaminase (EC 2.6.1.1) (characterized)
to candidate WP_013684737.1 ARCVE_RS10425 LL-diaminopimelate aminotransferase
Query= BRENDA::Q8YTF2 (403 letters) >NCBI__GCF_000194625.1:WP_013684737.1 Length = 384 Score = 360 bits (923), Expect = e-104 Identities = 178/379 (46%), Positives = 255/379 (67%), Gaps = 3/379 (0%) Query: 9 ADRIQQLPPYVFARLDELKAKAREQGIDLIDLGMGNPDGATPQPVVDAAIQALQDPKNHG 68 A+R+Q+LPPY+FA LD +K K +G+ LID G+G+PD TP +V+A +A++ +N Sbjct: 5 AERLQRLPPYLFAELDAMKRKKLREGVKLIDFGVGDPDLPTPPHIVEAMKKAVEKVENQK 64 Query: 69 YPPFEGTASFRRAITNWYNRRYGVVLDPDSEALPLLGSKEGLSHLAIAYVNPGDVVLVPS 128 YP +EG SFR A+ ++Y RR GV LDP+ E + L+GSKEG++HL +AYVN GD+VL P Sbjct: 65 YPSYEGMLSFREAVADFYKRRKGVDLDPEKEVIALIGSKEGIAHLPLAYVNSGDIVLCPD 124 Query: 129 PAYPAHFRGPVIAGGTVHSLILKPENDWLIDLTAIPEEVARKAKILYFNYPSNPTGATAP 188 P YP + ++A G + + LK EN +L DL AIP++VARKAKI++ NYP+NPT + A Sbjct: 125 PGYPVYPSSAILADGKPYFMPLKKENGFLPDLQAIPDDVARKAKIMFLNYPNNPTASVAE 184 Query: 189 REFFEEIVAFARKYEILLVHDLCYAELAFDGYQPTSLLEIPGAKDIGVEFHTLSKTYNMA 248 ++F +E++ F +I+L HD Y+E+ FD Y+ S LE+ G + + +EF++LSKTYNM Sbjct: 185 KDFIKEVIEFCNDRKIVLAHDAAYSEITFD-YRARSFLEV-GIEGV-IEFNSLSKTYNMT 241 Query: 249 GWRVGFVVGNRHVIQGLRTLKTNLDYGIFAALQTAAETALQLPDIYLHEVQQRYRTRRDF 308 GWR+GF G V+ GL +KTN+D G+F A+Q AA AL D + E + Y+ RRD Sbjct: 242 GWRIGFAAGCPEVLAGLLKVKTNVDSGVFQAVQEAAIAALTGSDEVIDENNRIYKERRDT 301 Query: 309 LIQGLGELGWDVPKTKATMYLWVKCPVGMGSTDFALNLLQQTGVVVTPGNAFGVAGEGYV 368 LI+GL E+G + K KAT Y+W + P G S +F LL G++VTPG FG GEG+V Sbjct: 302 LIEGLKEVGLNAEKPKATFYVWCEVPEGYTSMEFTKKLLNDAGILVTPGIGFGEHGEGFV 361 Query: 369 RISLIADCDRLGEALDRIK 387 R +L D + EA++R+K Sbjct: 362 RFALTRDVGVIQEAVERLK 380 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: 461 Number of extensions: 17 Number of successful extensions: 2 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: 384 Length adjustment: 31 Effective length of query: 372 Effective length of database: 353 Effective search space: 131316 Effective search space used: 131316 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