Align aspartate transaminase (EC 2.6.1.1) (characterized)
to candidate WP_012505537.1 PAES_RS04825 pyridoxal phosphate-dependent aminotransferase
Query= BRENDA::Q8YTF2 (403 letters) >NCBI__GCF_000020625.1:WP_012505537.1 Length = 404 Score = 340 bits (872), Expect = 4e-98 Identities = 165/389 (42%), Positives = 246/389 (63%), Gaps = 10/389 (2%) Query: 10 DRIQQLPPYVFARLDELKAKAREQGIDLIDLGMGNPDGATPQPVVDAAIQALQDPKNHGY 69 ++I++LP YVFA ++ELK R +G D+ID MGNPDG TPQ ++D ++++Q P+ HGY Sbjct: 8 EKIKRLPKYVFAAVNELKMAERRKGEDVIDFSMGNPDGPTPQHIIDKLVESVQKPRTHGY 67 Query: 70 PPFEGTASFRRAITNWYNRRYGVVLDPDSEALPLLGSKEGLSHLAIAYVNPGDVVLVPSP 129 +G R AI WY +YGV LD D+E + +GSKEG +L A NPGD+ +VP P Sbjct: 68 SVSKGIYKLRLAICGWYRDKYGVELDADTEVVASMGSKEGYVNLVQAITNPGDIAMVPDP 127 Query: 130 AYPAHFRGPVIAGGTVHSLILKPENDWLIDLTAI-------PEEVARKAKILYFNYPSNP 182 YP H + ++AGG VH L+ + ++ +D A E + K K L N+P+NP Sbjct: 128 CYPIHSQAFILAGGNVHRFKLEMDEEYRLDEEAFFRNIETAMRESSPKPKYLVVNFPNNP 187 Query: 183 TGATAPREFFEEIVAFARKYEILLVHDLCYAELAFDGYQPTSLLEIPGAKDIGVEFHTLS 242 T AT R F+E +V AR+ ++ D+ YAE+ +DGYQ S+L++PGAKD+ VE +TLS Sbjct: 188 TTATVERSFYERLVETARRERFYIISDIAYAEITYDGYQSPSILQVPGAKDVAVESYTLS 247 Query: 243 KTYNMAGWRVGFVVGNRHVIQGLRTLKTNLDYGIFAALQTAAETALQLPDIYLHEVQQRY 302 KTYNMAGWRVGF+VGN ++ L +K+ LDYG+F +Q A+ AL + E++ Y Sbjct: 248 KTYNMAGWRVGFLVGNPKLVGALMRIKSWLDYGMFTPIQVASTIALNSDQSCVAEIRDTY 307 Query: 303 RTRRDFLIQGLGELGWDVPKTKATMYLWVKCPVGM---GSTDFALNLLQQTGVVVTPGNA 359 R RRD +++ GW++ +A+M+LW + P + GS +F+ LL++ V V+PG Sbjct: 308 RKRRDVMLKSFANAGWEIRAPRASMFLWARIPEPLRQVGSLEFSKMLLREAKVAVSPGIG 367 Query: 360 FGVAGEGYVRISLIADCDRLGEALDRIKQ 388 FG G+ YVRI+LI + +R+ +A I++ Sbjct: 368 FGPNGDEYVRIALIENEERIRQAARNIRK 396 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: 416 Number of extensions: 16 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: 404 Length adjustment: 31 Effective length of query: 372 Effective length of database: 373 Effective search space: 138756 Effective search space used: 138756 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