Align aspartate transaminase (EC 2.6.1.1) (characterized)
to candidate WP_041434028.1 THAL_RS00345 glutamate--pyruvate aminotransferase
Query= BRENDA::Q8YTF2 (403 letters) >NCBI__GCF_000025605.1:WP_041434028.1 Length = 395 Score = 343 bits (879), Expect = 7e-99 Identities = 172/384 (44%), Positives = 250/384 (65%), Gaps = 5/384 (1%) Query: 11 RIQQLPPYVFARLDELKAKAREQGIDLIDLGMGNPDGATPQPVVDAAIQALQDPKNHGYP 70 R+++LP YVFA ++ELK + R G D++DLGMGNPD +VD + + HGY Sbjct: 4 RVKKLPKYVFALVNELKYQMRRAGEDIVDLGMGNPDLPPAPHIVDKLCEVAKRDNVHGYS 63 Query: 71 PFEGTASFRRAITNWYNRRYGVVLDPDSEALPLLGSKEGLSHLAIAYVNPGDVVLVPSPA 130 G R+AI ++Y RRYGV LDPD+EA+ +G+KEG SHL +A + PGD V+VP+P Sbjct: 64 ASRGIPRLRKAICDFYERRYGVKLDPDTEAILTIGAKEGYSHLILAMIEPGDTVVVPNPT 123 Query: 131 YPAHFRGPVIAGGTVHSLILKPEN---DWLIDLTAIPEEVARKAKILYFNYPSNPTGATA 187 YP H+ P+IAGG S+ ++ EN ++L L I RK K + ++P NPT Sbjct: 124 YPIHYYAPIIAGGDAISVPIQEENFEENFLKSLHDIIRSSFRKPKAVVVSFPHNPTTQCV 183 Query: 188 PREFFEEIVAFARKYEILLVHDLCYAELAFDGYQPTSLLEIPGAKDIGVEFHTLSKTYNM 247 EFF+E+V A K E+ ++HD YA+L FDGY+P S+L++ GAK I VE +++SK ++M Sbjct: 184 SIEFFKELVNLALKEEVFVIHDFAYADLGFDGYEPPSILQVEGAKKIAVELYSMSKGFSM 243 Query: 248 AGWRVGFVVGNRHVIQGLRTLKTNLDYGIFAALQTAAETALQLPDIYLHEVQQRYRTRRD 307 AGWRV FV+GN +I+ L LK+ LDYG+F +Q A+ AL+ P + + + Y+ RRD Sbjct: 244 AGWRVAFVLGNEIMIKNLAHLKSYLDYGVFTPIQVASIIALESPYEIVQKNRDVYQKRRD 303 Query: 308 FLIQGLGELGWDVPKTKATMYLWVKCP--VGMGSTDFALNLLQQTGVVVTPGNAFGVAGE 365 L++GL +GW+V K K +M++W K P +GM S DFA+ LL++ V V+PG FG GE Sbjct: 304 VLVEGLRRIGWEVKKPKGSMFVWAKIPEWIGMNSLDFAMFLLKEAKVAVSPGIGFGEYGE 363 Query: 366 GYVRISLIADCDRLGEALDRIKQA 389 GYVR +L+ + R+ +A+ IK+A Sbjct: 364 GYVRFALVENEHRIRQAVRGIKRA 387 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: 463 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: 395 Length adjustment: 31 Effective length of query: 372 Effective length of database: 364 Effective search space: 135408 Effective search space used: 135408 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