Align aspartate transaminase (EC 2.6.1.1) (characterized)
to candidate WP_028489058.1 Q394_RS0109350 alanine transaminase
Query= BRENDA::Q8YTF2 (403 letters) >NCBI__GCF_000621325.1:WP_028489058.1 Length = 397 Score = 350 bits (898), Expect = e-101 Identities = 173/381 (45%), Positives = 247/381 (64%), Gaps = 3/381 (0%) Query: 11 RIQQLPPYVFARLDELKAKAREQGIDLIDLGMGNPDGATPQPVVDAAIQALQDPKNHGYP 70 RI +LP YVF D LK +AR +G D+ID GMGNPD TP+ +VD ++A Q H Y Sbjct: 7 RINRLPTYVFKITDALKREARAKGEDIIDFGMGNPDQPTPKHIVDKLVEAAQRGDTHRYS 66 Query: 71 PFEGTASFRRAITNWYNRRYGVVLDPDSEALPLLGSKEGLSHLAIAYVNPGDVVLVPSPA 130 G R+AI+NWY R++ V +DP++EA+ +GSKEGL+HLA+A ++ GD VLVP+PA Sbjct: 67 MSRGIPRLRKAISNWYKRKFDVDIDPETEAIVTIGSKEGLAHLALATLSRGDTVLVPNPA 126 Query: 131 YPAHFRGPVIAGGTVHSLILKPENDWLIDLTAIPEEVARKAKILYFNYPSNPTGATAPRE 190 YP H G +IA + + L D+ +L A + K K+L N+P+NPTG E Sbjct: 127 YPIHPYGSIIADADIRHVPLVEGKDFFEELEAAIKNSWPKPKMLIINFPANPTGQCVDLE 186 Query: 191 FFEEIVAFARKYEILLVHDLCYAELAFDGYQPTSLLEIPGAKDIGVEFHTLSKTYNMAGW 250 FFE ++ A+++++ ++HD+ Y E+ FDGY+ S+L++PGAKDI VEF++LSKTYNM GW Sbjct: 187 FFERVIKVAKEHDVWVIHDIAYGEICFDGYEAPSILQVPGAKDIAVEFYSLSKTYNMPGW 246 Query: 251 RVGFVVGNRHVIQGLRTLKTNLDYGIFAALQTAAETALQLPDIYLHEVQQRYRTRRDFLI 310 RVGF+ GN +++ L +K+ LDYG+FA +Q AA AL+ P + E+ Y +RR+ L Sbjct: 247 RVGFMCGNPVLVKALERIKSYLDYGMFAPIQIAAIAALEGPQDCVKEISAMYESRRNVLC 306 Query: 311 QGLGELGWDVPKTKATMYLWVKCP---VGMGSTDFALNLLQQTGVVVTPGNAFGVAGEGY 367 GL GW V + KA+M++W K P MGS +FA LL++ V V+PG FG G+ + Sbjct: 307 DGLNAAGWAVERPKASMFVWAKIPEHYAAMGSLEFAKKLLKEAQVAVSPGIGFGEYGDDH 366 Query: 368 VRISLIADCDRLGEALDRIKQ 388 VR SLI + R +A+ IKQ Sbjct: 367 VRFSLIENEHRTRQAIRNIKQ 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: 461 Number of extensions: 21 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: 397 Length adjustment: 31 Effective length of query: 372 Effective length of database: 366 Effective search space: 136152 Effective search space used: 136152 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