Align aspartate transaminase (EC 2.6.1.1) (characterized)
to candidate WP_011386083.1 AMB_RS18860 pyridoxal phosphate-dependent aminotransferase
Query= BRENDA::Q8YTF2 (403 letters) >NCBI__GCF_000009985.1:WP_011386083.1 Length = 410 Score = 333 bits (854), Expect = 5e-96 Identities = 165/380 (43%), Positives = 241/380 (63%), Gaps = 3/380 (0%) Query: 11 RIQQLPPYVFARLDELKAKAREQGIDLIDLGMGNPDGATPQPVVDAAIQALQDPKNHGYP 70 RI++LPPYVFA ++ +KA+AR G D+ID GMGNPD TP +VD ++A ++P+ H Y Sbjct: 9 RIKRLPPYVFAEVNAMKARARAAGEDIIDFGMGNPDQPTPAHIVDKLVEAARNPRAHRYS 68 Query: 71 PFEGTASFRRAITNWYNRRYGVVLDPDSEALPLLGSKEGLSHLAIAYVNPGDVVLVPSPA 130 G R+A++ +Y RR+ V +DP++E + LGSKEGL++LA A +PGD+VLVP+P+ Sbjct: 69 MSRGIPGLRKALSGYYQRRFAVDIDPETECIVTLGSKEGLANLANAITSPGDIVLVPNPS 128 Query: 131 YPAHFRGPVIAGGTVHSLILKPENDWLIDLTAIPEEVARKAKILYFNYPSNPTGATAPRE 190 YP H G +IAGG+ + + P+ ++L L K L NYPSNPT A + Sbjct: 129 YPIHPYGFIIAGGSCRFVPVTPDAEFLKALDRAVRHSVPKPIALVLNYPSNPTALLADLD 188 Query: 191 FFEEIVAFARKYEILLVHDLCYAELAFDGYQPTSLLEIPGAKDIGVEFHTLSKTYNMAGW 250 F+ ++V F R + I ++ DL Y+E+ FD P S+L+IPGAK+I VEF ++SKTYNM GW Sbjct: 189 FYGQVVEFCRHHGIWILSDLAYSEIYFDVAPPPSILQIPGAKEIAVEFTSMSKTYNMPGW 248 Query: 251 RVGFVVGNRHVIQGLRTLKTNLDYGIFAALQTAAETALQLPDIYLHEVQQRYRTRRDFLI 310 R+GF GN+ +I L +K+ LDYG F +Q AA AL P + +++ Y+ RRD LI Sbjct: 249 RIGFAAGNKTLIAALGRIKSYLDYGAFTPIQVAATAALNGPQDCVDDIRALYKGRRDALI 308 Query: 311 QGLGELGWDVPKTKATMYLWVKCP---VGMGSTDFALNLLQQTGVVVTPGNAFGVAGEGY 367 +GL GW++P ATM+ W P +GS +F+ L+++ V V PG FG G+ + Sbjct: 309 EGLSAAGWEIPSPPATMFAWAPIPKAFAHLGSLEFSKLLMREAQVAVAPGIGFGEYGDSH 368 Query: 368 VRISLIADCDRLGEALDRIK 387 VRI L+ + R +A+ IK Sbjct: 369 VRIGLVENVQRTRQAVRNIK 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: 484 Number of extensions: 25 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: 410 Length adjustment: 31 Effective length of query: 372 Effective length of database: 379 Effective search space: 140988 Effective search space used: 140988 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