Align aspartate transaminase (EC 2.6.1.1) (characterized)
to candidate AZOBR_RS07830 AZOBR_RS07830 aminotransferase
Query= BRENDA::Q8YTF2 (403 letters) >FitnessBrowser__azobra:AZOBR_RS07830 Length = 424 Score = 340 bits (872), Expect = 5e-98 Identities = 173/388 (44%), Positives = 244/388 (62%), Gaps = 10/388 (2%) Query: 11 RIQQLPPYVFARLDELKAKAREQGIDLIDLGMGNPDGATPQPVVDAAIQALQDPKNHGYP 70 RI++LPPYVFA ++ +KA+AR G D+IDLGMGNPD TPQ +VD I+A++DPK H Y Sbjct: 8 RIKRLPPYVFAEVNAMKARARAAGEDIIDLGMGNPDQPTPQHIVDKLIEAVRDPKTHRYS 67 Query: 71 PFEGTASFRRAITNWYNRRYGVVLDPDSEALPLLGSKEGLSHLAIAYVNPGDVVLVPSPA 130 G R+A +Y RR+ V +DP+SE + +GSKEGL++LA A +PGD++LVP+P+ Sbjct: 68 NSRGIPGLRKAHAAYYKRRFNVDVDPESECIVTIGSKEGLANLAQAITSPGDIILVPNPS 127 Query: 131 YPAHFRGPVIAGGTVHSLILKPENDWLIDLTAIPEEVAR-------KAKILYFNYPSNPT 183 YP H G ++AG +V L + N D+ + + R K L NYPSNPT Sbjct: 128 YPIHPFGFILAGASVRHLPVGQANGTSTDIDSFMIMLERAVRHSVPKPLALVLNYPSNPT 187 Query: 184 GATAPREFFEEIVAFARKYEILLVHDLCYAELAFDGYQPTSLLEIPGAKDIGVEFHTLSK 243 +F+ IV F RK+ I ++ DL YAE+ FDG P S+LEIP A+++ VEF ++SK Sbjct: 188 AEVVGLDFYRPIVEFCRKHGIYILSDLAYAEVFFDGEPPPSILEIPEAREVAVEFTSMSK 247 Query: 244 TYNMAGWRVGFVVGNRHVIQGLRTLKTNLDYGIFAALQTAAETALQLPDIYLHEVQQRYR 303 TY+MAGWR+GF GN+ +I L +K+ LDYG F +Q AA AL P + +V+ YR Sbjct: 248 TYSMAGWRIGFATGNKKLITALARIKSYLDYGAFTPIQVAATAALNGPQECVEQVRTMYR 307 Query: 304 TRRDFLIQGLGELGWDVPKTKATMYLWVKCP---VGMGSTDFALNLLQQTGVVVTPGNAF 360 RRD +I+GL GW VP A+M+ W P +GS +F+ LLQ+ V V PG F Sbjct: 308 QRRDVMIEGLASAGWTVPSPSASMFAWAPIPEPFAHLGSLEFSKLLLQEAKVAVAPGIGF 367 Query: 361 GVAGEGYVRISLIADCDRLGEALDRIKQ 388 G G+G+VR++L+ + R+ +A IK+ Sbjct: 368 GEYGDGHVRLALVENVHRIRQATRNIKE 395 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: 483 Number of extensions: 21 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: 424 Length adjustment: 31 Effective length of query: 372 Effective length of database: 393 Effective search space: 146196 Effective search space used: 146196 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 Aug 03 2021. The underlying query database was built on Aug 03 2021.
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