Align aspartate transaminase (EC 2.6.1.1) (characterized)
to candidate WP_027178113.1 G496_RS0103805 aminotransferase class I/II-fold pyridoxal phosphate-dependent enzyme
Query= BRENDA::Q8YTF2 (403 letters) >NCBI__GCF_000429985.1:WP_027178113.1 Length = 389 Score = 343 bits (881), Expect = 4e-99 Identities = 167/380 (43%), Positives = 238/380 (62%), Gaps = 3/380 (0%) Query: 11 RIQQLPPYVFARLDELKAKAREQGIDLIDLGMGNPDGATPQPVVDAAIQALQDPKNHGYP 70 R+ +LPPYVFA ++ELK + R QG D+IDLGMGNPD TP+ +VD ++A Q P NH Y Sbjct: 6 RVHRLPPYVFATVNELKMQMRHQGEDIIDLGMGNPDIPTPKHIVDKLVEAAQKPVNHRYS 65 Query: 71 PFEGTASFRRAITNWYNRRYGVVLDPDSEALPLLGSKEGLSHLAIAYVNPGDVVLVPSPA 130 +G RR + WY RYGV LD D E + +G+KEGL+HLA+ ++PGDVV P P+ Sbjct: 66 ASKGIKGLRREMAKWYRNRYGVELDYDQEVVVTMGAKEGLAHLALVMLSPGDVVFAPDPS 125 Query: 131 YPAHFRGPVIAGGTVHSLILKPENDWLIDLTAIPEEVARKAKILYFNYPSNPTGATAPRE 190 YP H +IAG V + + + D++ DL + K K+L N+P NPTG T Sbjct: 126 YPIHPYACIIAGADVRRIPMAHDRDFIEDLELAMRQTWPKPKLLIINFPHNPTGITTDLA 185 Query: 191 FFEEIVAFARKYEILLVHDLCYAELAFDGYQPTSLLEIPGAKDIGVEFHTLSKTYNMAGW 250 FF+ IV FA++ ++ ++HDL YA+ FDGY+ S L+ GAKD+GVEF +LSK+Y+M GW Sbjct: 186 FFQRIVDFAKENDLKVIHDLAYADFTFDGYEAPSFLQAKGAKDVGVEFFSLSKSYSMPGW 245 Query: 251 RVGFVVGNRHVIQGLRTLKTNLDYGIFAALQTAAETALQLPDIYLHEVQQRYRTRRDFLI 310 RVGF GN ++Q L +K+ LDYG+F +Q AA AL P + E+ Y RRD L Sbjct: 246 RVGFCCGNVEMVQALTRIKSYLDYGLFQPIQIAASVALSGPQECVREIMDVYEDRRDALC 305 Query: 311 QGLGELGWDVPKTKATMYLWVKCP---VGMGSTDFALNLLQQTGVVVTPGNAFGVAGEGY 367 +GL +GW V KAT ++W + P +GS +F+ +L++ V V PG FG G+ + Sbjct: 306 EGLNRIGWPVTPPKATQFVWAEIPDEFKKLGSVEFSKLMLRECKVAVAPGLGFGHYGDHH 365 Query: 368 VRISLIADCDRLGEALDRIK 387 VR +L+ + R+ +A+ +K Sbjct: 366 VRFALVENRQRINQAIRGMK 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: 436 Number of extensions: 19 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: 389 Length adjustment: 31 Effective length of query: 372 Effective length of database: 358 Effective search space: 133176 Effective search space used: 133176 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