Align aspartate transaminase (EC 2.6.1.1) (characterized)
to candidate WP_074201258.1 BUQ81_RS04875 alanine transaminase
Query= BRENDA::Q8YTF2 (403 letters) >NCBI__GCF_900141795.1:WP_074201258.1 Length = 398 Score = 352 bits (902), Expect = e-101 Identities = 177/380 (46%), Positives = 248/380 (65%), Gaps = 3/380 (0%) Query: 11 RIQQLPPYVFARLDELKAKAREQGIDLIDLGMGNPDGATPQPVVDAAIQALQDPKNHGYP 70 RI++LPPYVF + ELK AR +G D+ID GMGNPD TP+ +VD ++ Q P + Y Sbjct: 6 RIKRLPPYVFNIVGELKQAARRRGEDIIDFGMGNPDQDTPKHIVDKLVEVAQRPGVYRYS 65 Query: 71 PFEGTASFRRAITNWYNRRYGVVLDPDSEALPLLGSKEGLSHLAIAYVNPGDVVLVPSPA 130 +G R+AI NWY ++ V LD ++EA+ +GSKEGL+HLA+A + GD VLVP+PA Sbjct: 66 VSQGIPRLRKAICNWYRDKFDVELDYETEAVVTIGSKEGLAHLAMAICDQGDTVLVPNPA 125 Query: 131 YPAHFRGPVIAGGTVHSLILKPENDWLIDLTAIPEEVARKAKILYFNYPSNPTGATAPRE 190 YP H G VIAG + + + P+ D+ +L + K K+L N+PSNPT A Sbjct: 126 YPIHPYGFVIAGADIRHVPITPDVDFFAELEKAIRDSWPKPKVLLLNFPSNPTTDVADLA 185 Query: 191 FFEEIVAFARKYEILLVHDLCYAELAFDGYQPTSLLEIPGAKDIGVEFHTLSKTYNMAGW 250 FFE++VA AR++ I ++HDL YA++ FDGYQ S++++PGAKDI VEF+TLSK+YNM GW Sbjct: 186 FFEKVVAIAREHNIWVIHDLAYADIVFDGYQAPSIMQVPGAKDIAVEFYTLSKSYNMPGW 245 Query: 251 RVGFVVGNRHVIQGLRTLKTNLDYGIFAALQTAAETALQLPDIYLHEVQQRYRTRRDFLI 310 RVGF+VGN ++ L+ +K+ LDYG+F +Q AA TAL+ P + E++ Y+ RRD L Sbjct: 246 RVGFMVGNPTLVHALKRMKSYLDYGMFTPIQVAAITALEGPQDCVEEIRDMYKQRRDVLC 305 Query: 311 QGLGELGWDVPKTKATMYLWVKCPV---GMGSTDFALNLLQQTGVVVTPGNAFGVAGEGY 367 GL +GW V KATM++W P MGS +F+ LL+ V V+PG FG G+ + Sbjct: 306 SGLNSIGWTVTPPKATMFVWAPIPEPYREMGSLEFSKKLLKDAKVAVSPGIGFGEYGDDH 365 Query: 368 VRISLIADCDRLGEALDRIK 387 VR SLI + R +A+ I+ Sbjct: 366 VRFSLIENEHRTRQAIRGIR 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: 487 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: 398 Length adjustment: 31 Effective length of query: 372 Effective length of database: 367 Effective search space: 136524 Effective search space used: 136524 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