Align aspartate transaminase (EC 2.6.1.1) (characterized)
to candidate WP_015932449.1 MNOD_RS28520 pyridoxal phosphate-dependent aminotransferase
Query= BRENDA::Q8YTF2 (403 letters) >NCBI__GCF_000022085.1:WP_015932449.1 Length = 406 Score = 318 bits (814), Expect = 2e-91 Identities = 165/392 (42%), Positives = 247/392 (63%), Gaps = 14/392 (3%) Query: 6 ITPADRIQQLPPYVFARLDELKAKAREQGIDLIDLGMGNPDGATPQPVVDAAIQALQDPK 65 +T RI++LPPYVF +++ +KA AR G D+IDLGMGNPD P+ V++ ++ P+ Sbjct: 1 MTDFHRIKRLPPYVFEQVNRIKAAARANGADIIDLGMGNPDLDAPRHVIEKLVETAGKPR 60 Query: 66 NHGYPPFEGTASFRRAITNWYNRRYGVVLDPDSEALPLLGSKEGLSHLAIAYVNPGDVVL 125 Y +G A RRA +Y RR+GV L+P+++ + LGSKEG +++A A PGDVVL Sbjct: 61 TDRYSASKGIAGLRRAQAGYYARRFGVTLNPETQVVATLGSKEGFANMAQAITAPGDVVL 120 Query: 126 VPSPAYPAHFRGPVIAGGTVHSLILKPENDWL-----IDLTAIPEEVARKAKILYFNYPS 180 VP+P+YP H G ++AGG + S+ +P + L +IP+ VA L YPS Sbjct: 121 VPNPSYPIHAFGFLMAGGVIRSVPAEPTPAFFPAVERAVLHSIPKPVA-----LVVCYPS 175 Query: 181 NPTGATAPREFFEEIVAFARKYEILLVHDLCYAELAF-DGYQPTSLLEIPGAKDIGVEFH 239 NPT A +F+ ++VAFA+K+E++L+ DL YAE+ F D P S+L++PGA D+ VEF Sbjct: 176 NPTAYVASLDFYRDLVAFAKKHELILLSDLAYAEVYFDDANPPPSVLQVPGAIDVTVEFT 235 Query: 240 TLSKTYNMAGWRVGFVVGNRHVIQGLRTLKTNLDYGIFAALQTAAETALQLPDIYLHEVQ 299 +LSKT++MAGWR+GF VGN ++ L +K+ LDYG F +Q AA AL P+ +HE++ Sbjct: 236 SLSKTFSMAGWRMGFAVGNERLLAALTRVKSYLDYGAFTPIQVAATAALNGPEACIHEMR 295 Query: 300 QRYRTRRDFLIQGLGELGWDVPKTKATMYLWVKCPV---GMGSTDFALNLLQQTGVVVTP 356 YR RRD L+ + GW +P A+M+ WV P +GS +F+ L+++ V V P Sbjct: 296 ATYRRRRDALVDSFQKCGWTIPVPSASMFAWVPIPEKFRSLGSLEFSKLLVEKADVAVAP 355 Query: 357 GNAFGVAGEGYVRISLIADCDRLGEALDRIKQ 388 G FG G+ +VRI+L+ + R+ +A I++ Sbjct: 356 GIGFGEHGDDFVRIALVENEQRIRQAARNIRR 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: 488 Number of extensions: 17 Number of successful extensions: 4 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: 406 Length adjustment: 31 Effective length of query: 372 Effective length of database: 375 Effective search space: 139500 Effective search space used: 139500 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