Align aspartate transaminase (EC 2.6.1.1) (characterized)
to candidate 8500663 DvMF_1411 aminotransferase class I and II (RefSeq)
Query= BRENDA::Q8YTF2 (403 letters) >FitnessBrowser__Miya:8500663 Length = 394 Score = 362 bits (930), Expect = e-105 Identities = 177/381 (46%), Positives = 250/381 (65%), Gaps = 3/381 (0%) Query: 11 RIQQLPPYVFARLDELKAKAREQGIDLIDLGMGNPDGATPQPVVDAAIQALQDPKNHGYP 70 R+ +LPPYVFA ++ELK + R Q +D++DLGMGNPD TPQ +VD ++A NH Y Sbjct: 6 RMHRLPPYVFATVNELKMQLRRQNVDIVDLGMGNPDIPTPQHIVDKLVEASGKGVNHRYS 65 Query: 71 PFEGTASFRRAITNWYNRRYGVVLDPDSEALPLLGSKEGLSHLAIAYVNPGDVVLVPSPA 130 G + R+AI +WY RR+GV LDPD+EA+ +G+KEGLSHL++A ++PGDVV P P Sbjct: 66 VSRGIPNLRKAICDWYMRRFGVYLDPDTEAVATMGAKEGLSHLSLAMLSPGDVVFAPDPT 125 Query: 131 YPAHFRGPVIAGGTVHSLILKPENDWLIDLTAIPEEVARKAKILYFNYPSNPTGATAPRE 190 YP H P+IAG V + + D+ DL + + K+L+ +YP NPT A E Sbjct: 126 YPIHTYAPIIAGADVRRIPIGRGRDFFEDLLVATRQTWPQPKLLFISYPHNPTCEIAAPE 185 Query: 191 FFEEIVAFARKYEILLVHDLCYAELAFDGYQPTSLLEIPGAKDIGVEFHTLSKTYNMAGW 250 FF+++V FA++++I ++HD YA+LAFDG+ P S ++ GAKD+GVEF ++SK+Y+MAGW Sbjct: 186 FFQKVVDFAKEHKIYVIHDFAYADLAFDGHMPPSFMQAEGAKDVGVEFFSMSKSYSMAGW 245 Query: 251 RVGFVVGNRHVIQGLRTLKTNLDYGIFAALQTAAETALQLPDIYLHEVQQRYRTRRDFLI 310 RVGF VGNR ++ L +K+ LDYG F +Q AA AL P + E+ YR RRD LI Sbjct: 246 RVGFCVGNRDLVYALTRIKSYLDYGHFQPIQIAATVALNGPQECVTEIVDTYRKRRDVLI 305 Query: 311 QGLGELGWDVPKTKATMYLWVKCPV---GMGSTDFALNLLQQTGVVVTPGNAFGVAGEGY 367 +GLG GW VP K TM++W + P MGS +F+ LL++ V V+PG FG G+ + Sbjct: 306 EGLGRAGWVVPPPKGTMFVWAQIPEEFRAMGSVEFSKLLLKEGHVAVSPGLGFGAHGDDH 365 Query: 368 VRISLIADCDRLGEALDRIKQ 388 VR +LI + R +A+ IK+ Sbjct: 366 VRFALIENEHRTKQAMKGIKK 386 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: 485 Number of extensions: 24 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: 394 Length adjustment: 31 Effective length of query: 372 Effective length of database: 363 Effective search space: 135036 Effective search space used: 135036 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