Align aspartate transaminase (EC 2.6.1.1) (characterized)
to candidate WP_012566498.1 RC1_RS06235 LL-diaminopimelate aminotransferase
Query= BRENDA::Q8YTF2 (403 letters) >NCBI__GCF_000016185.1:WP_012566498.1 Length = 407 Score = 326 bits (835), Expect = 9e-94 Identities = 169/384 (44%), Positives = 243/384 (63%), Gaps = 10/384 (2%) Query: 11 RIQQLPPYVFARLDELKAKAREQGIDLIDLGMGNPDGATPQPVVDAAIQALQDPKNHGYP 70 RI++LPPYVFA ++ +KA+AR G D+IDLGMGNPD TP +V ++A+Q+PK H Y Sbjct: 8 RIKRLPPYVFAEVNAMKARARAAGEDIIDLGMGNPDQPTPPHIVAKLVEAVQNPKTHRYS 67 Query: 71 PFEGTASFRRAITNWYNRRYGVVLDPDSEALPLLGSKEGLSHLAIAYVNPGDVVLVPSPA 130 G R+AI+ +Y RR+ V +DP++EA+ +GSKEGL++LA A +PGDV+LVP+P+ Sbjct: 68 QSRGIPGLRKAISAYYKRRFDVDIDPETEAIVTIGSKEGLANLAQAITSPGDVILVPNPS 127 Query: 131 YPAHFRGPVIAGGTVHSLILKPENDWLIDLTAIPEEVAR----KAKILYFNYPSNPTGAT 186 YP H G ++AG + + P D L E R K L ++P+NPTG T Sbjct: 128 YPIHPFGFMLAGAALRHI---PVGDGLDGFVPALERAIRHSVPKPTALIVSFPANPTGQT 184 Query: 187 APREFFEEIVAFARKYEILLVHDLCYAELAFDGYQPTSLLEIPGAKDIGVEFHTLSKTYN 246 +F+ IV K+ I ++ D+ YAE+ F+G P S+L+IP A+ I VEF++LSKTYN Sbjct: 185 VTLDFYRPIVDLCLKHGIYILSDIAYAEIYFNGNPPPSVLQIPEARPITVEFNSLSKTYN 244 Query: 247 MAGWRVGFVVGNRHVIQGLRTLKTNLDYGIFAALQTAAETALQLPDIYLHEVQQRYRTRR 306 M GWRVGF VG++ +I L K+ +DYG F +Q AA AL P + E+++ YR RR Sbjct: 245 MPGWRVGFGVGSKKLIGALAKFKSYVDYGAFTPIQVAATAALNGPQDCVAEIREMYRQRR 304 Query: 307 DFLIQGLGELGWDVPKTKATMYLWVKCPV---GMGSTDFALNLLQQTGVVVTPGNAFGVA 363 D LI+GL + GW VP A+M++W + P +GS +FA LLQ+ V V+PG FG Sbjct: 305 DVLIEGLAQAGWKVPSPNASMFVWAEIPEPFRELGSLEFAKLLLQEAQVAVSPGIGFGEY 364 Query: 364 GEGYVRISLIADCDRLGEALDRIK 387 G+G+VR L+ + R+ +A I+ Sbjct: 365 GDGHVRFGLVENTQRIRQACRNIR 388 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: 514 Number of extensions: 24 Number of successful extensions: 3 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: 407 Length adjustment: 31 Effective length of query: 372 Effective length of database: 376 Effective search space: 139872 Effective search space used: 139872 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 09 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