Align aspartate transaminase (EC 2.6.1.1) (characterized)
to candidate WP_018125202.1 B149_RS0110945 LL-diaminopimelate aminotransferase
Query= BRENDA::Q8YTF2 (403 letters) >NCBI__GCF_000375485.1:WP_018125202.1 Length = 388 Score = 369 bits (947), Expect = e-107 Identities = 177/381 (46%), Positives = 256/381 (67%), Gaps = 1/381 (0%) Query: 9 ADRIQQLPPYVFARLDELKAKAREQGIDLIDLGMGNPDGATPQPVVDAAIQALQDPKNHG 68 ADR+ LPPY+FA +D+ KA+ QGID+I LG+G+PD TP+ ++DA + + P NH Sbjct: 7 ADRLATLPPYLFAAIDKAKAEVAAQGIDIISLGIGDPDLPTPEFIIDALHEGAKKPVNHQ 66 Query: 69 YPPFEGTASFRRAITNWYNRRYGVVLDPDSEALPLLGSKEGLSHLAIAYVNPGDVVLVPS 128 YP + G +R A+ +WY +R+ V LDP+SE + L+GSKEG++H +AYVNPGD+VLV + Sbjct: 67 YPSYVGMLEYRTAVADWYRQRFNVELDPESEVVSLIGSKEGIAHFPLAYVNPGDLVLVAT 126 Query: 129 PAYPAHFRGPVIAGGTVHSLILKPENDWLIDLTAIPEEVARKAKILYFNYPSNPTGATAP 188 P YP + AGG V L L END+L+DL A+ ++ +AK+++ YP+NPT ATA Sbjct: 127 PNYPVYPAATGFAGGEVQFLPLLEENDFLVDLDAVDDDTWARAKMIFVCYPNNPTAATAT 186 Query: 189 REFFEEIVAFARKYEILLVHDLCYAELAFD-GYQPTSLLEIPGAKDIGVEFHTLSKTYNM 247 +EF+E +V A+++ +++V DL Y+E+ +D +P S+LE+ G KD+ +EFH+LSKTYNM Sbjct: 187 KEFYERLVQKAKEFNVIVVSDLAYSEIYYDPSNKPLSILEVEGGKDVAIEFHSLSKTYNM 246 Query: 248 AGWRVGFVVGNRHVIQGLRTLKTNLDYGIFAALQTAAETALQLPDIYLHEVQQRYRTRRD 307 GWRV VGN +I GL +K N+D GIF A+Q A AL+ + + + + Y+ RRD Sbjct: 247 TGWRVAMAVGNEQLIAGLGKIKENVDSGIFQAVQEAGIAALRHGEPHAEKFRAIYKERRD 306 Query: 308 FLIQGLGELGWDVPKTKATMYLWVKCPVGMGSTDFALNLLQQTGVVVTPGNAFGVAGEGY 367 + + L ++G +A+ Y+W K P G S DF N+L+QTGVV+TPGN FG GEGY Sbjct: 307 VVCKALSDIGIQHRVPEASFYVWAKVPEGNTSADFVTNVLKQTGVVLTPGNGFGTPGEGY 366 Query: 368 VRISLIADCDRLGEALDRIKQ 388 RISL + D L EA+ RI + Sbjct: 367 FRISLTVNNDLLKEAVSRISK 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: 494 Number of extensions: 18 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: 388 Length adjustment: 31 Effective length of query: 372 Effective length of database: 357 Effective search space: 132804 Effective search space used: 132804 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