Align aspartate transaminase (EC 2.6.1.1) (characterized)
to candidate WP_007475111.1 CMTB2_RS07105 LL-diaminopimelate aminotransferase
Query= BRENDA::Q8YTF2 (403 letters) >NCBI__GCF_000170735.1:WP_007475111.1 Length = 403 Score = 332 bits (851), Expect = 1e-95 Identities = 167/388 (43%), Positives = 243/388 (62%), Gaps = 10/388 (2%) Query: 10 DRIQQLPPYVFARLDELKAKAREQGIDLIDLGMGNPDGATPQPVVDAAIQALQDPKNHGY 69 +RI++LP Y+FA +++LK +AR G D+ID MGNPDG TP+P+VD I+A + PKNH Y Sbjct: 5 ERIERLPNYIFAVINDLKLQARRAGEDIIDFSMGNPDGPTPKPIVDKLIEAAKKPKNHRY 64 Query: 70 PPFEGTASFRRAITNWYNRRYGVVLDPDSEALPLLGSKEGLSHLAIAYVNPGDVVLVPSP 129 +G R AI NWY RRYGV L+P++EA+ +GSKEG HL A N GDV +VP P Sbjct: 65 SISKGIYKLREAICNWYARRYGVTLNPETEAVVTMGSKEGYVHLTQAITNVGDVAIVPDP 124 Query: 130 AYPAHFRGPVIAGGTVHSLILK-------PENDWLIDLTAIPEEVARKAKILYFNYPSNP 182 YP H ++AG +V + L ++++ +L E K K L N+P NP Sbjct: 125 TYPIHSYAFMLAGASVRKVKLTYNEKYELNQDEFFKELHQAMIESVPKPKFLVLNFPHNP 184 Query: 183 TGATAPREFFEEIVAFARKYEILLVHDLCYAELAFDGYQPTSLLEIPGAKDIGVEFHTLS 242 T T +EF+++ V FA+K + ++ D+ YA++ FDGY+ S+ E+ GAK++ VE TLS Sbjct: 185 TTVTVDKEFYKKAVDFAKKEGLYIISDIAYADITFDGYKTPSIFEVEGAKEVAVESFTLS 244 Query: 243 KTYNMAGWRVGFVVGNRHVIQGLRTLKTNLDYGIFAALQTAAETALQLPDIYLHEVQQRY 302 K+YNMAGWRVGF+VGN +I L+ K+ +DYG+F +Q AA AL+ + + ++ Y Sbjct: 245 KSYNMAGWRVGFMVGNPTLIGALQKYKSWIDYGMFTPIQVAATVALRDYNHLVKDIVDTY 304 Query: 303 RTRRDFLIQGLGELGWDVPKTKATMYLWVKCP---VGMGSTDFALNLLQQTGVVVTPGNA 359 + RRD LI+ GW++ K ATM++W K P +GS +F+ LL + + V+PG Sbjct: 305 KKRRDVLIESFANAGWEIEKPTATMFVWAKIPEVAKHLGSLEFSKRLLTEAHIAVSPGIG 364 Query: 360 FGVAGEGYVRISLIADCDRLGEALDRIK 387 FG G+ YVRI+LI + R+ +A IK Sbjct: 365 FGAYGDEYVRIALIENEKRIRQAAKNIK 392 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: 474 Number of extensions: 21 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: 403 Length adjustment: 31 Effective length of query: 372 Effective length of database: 372 Effective search space: 138384 Effective search space used: 138384 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