Align aspartate transaminase (EC 2.6.1.1) (characterized)
to candidate WP_013554781.1 NITSA_RS09335 pyridoxal phosphate-dependent aminotransferase
Query= BRENDA::Q8YTF2 (403 letters) >NCBI__GCF_000186245.1:WP_013554781.1 Length = 424 Score = 328 bits (842), Expect = 1e-94 Identities = 170/394 (43%), Positives = 242/394 (61%), Gaps = 18/394 (4%) Query: 10 DRIQQLPPYVFARLDELKAKAREQGIDLIDLGMGNPDGATPQPVVDAAIQALQDPKNHGY 69 ++I +LP YVFA ++ELK R G D+ID MGNPDG +PV++ +++ + P HGY Sbjct: 8 NKINRLPKYVFAVVNELKMAERRAGADVIDFSMGNPDGPAFEPVIEKLVESARKPHTHGY 67 Query: 70 PPFEGTASFRRAITNWYNRRYGVVLDPDSEALPLLGSKEGLSHLAIAYVNPGDVVLVPSP 129 +G R AI NWY R+Y VVLDP++EA+ +GSKEG HL A NPGDV +VP P Sbjct: 68 SASKGIYKLRLAICNWYLRKYNVVLDPETEAVATMGSKEGYVHLVQAITNPGDVAIVPDP 127 Query: 130 AYPAHFRGPVIAGGTVHSLILK--------PENDWLIDLTAIPEEVARKAKILYFNYPSN 181 YP H V+AGG V + L E + DL + K K L N+P N Sbjct: 128 TYPIHSYAFVLAGGNVEKMELTFDEESFEVDEERFFSDLERALKNSVPKPKFLVVNFPHN 187 Query: 182 PTGATAPREFFEEIVAFARKYEILLVHDLCYAELAFDGYQPTSLLEIPGAKDIGVEFHTL 241 PT AT +F+E++VA AR+ ++ D+ YA++ FDGY+ S+L++ GAKD+ VE TL Sbjct: 188 PTTATVGLDFYEKLVAIARRERFYIISDIAYADITFDGYKTPSILQVEGAKDVAVESFTL 247 Query: 242 SKTYNMAGWRVGFVVGNRHVIQGLRTLKTNLDYGIFAALQTAAETALQLPDIYLHEVQQ- 300 SK+YNMAGWRVGF+VGN ++ L+ +K+ LDYG+F +Q AA AL D Y H V++ Sbjct: 248 SKSYNMAGWRVGFIVGNPKLVGALQKIKSWLDYGMFTPIQVAATVAL---DEYEHLVEEI 304 Query: 301 ---RYRTRRDFLIQGLGELGWDVPKTKATMYLWVK---CPVGMGSTDFALNLLQQTGVVV 354 +Y+ RRD L+ + GW+V K +A+M++W + C +GS +F+ LL + V V Sbjct: 305 VIPKYQKRRDVLVDAFAKAGWEVGKPRASMFVWARIPECARHLGSLEFSKELLLKAHVAV 364 Query: 355 TPGNAFGVAGEGYVRISLIADCDRLGEALDRIKQ 388 +PG FG G+ YVRI+LI + R+ +A IK+ Sbjct: 365 SPGIGFGEYGDRYVRIALIENEKRIRQAAKNIKR 398 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: 462 Number of extensions: 17 Number of successful extensions: 4 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 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