Align aspartate transaminase (EC 2.6.1.1) (characterized)
to candidate WP_012170375.1 AZC_RS09575 pyridoxal phosphate-dependent aminotransferase
Query= BRENDA::Q8YTF2 (403 letters) >NCBI__GCF_000010525.1:WP_012170375.1 Length = 405 Score = 313 bits (801), Expect = 7e-90 Identities = 154/387 (39%), Positives = 243/387 (62%), Gaps = 4/387 (1%) Query: 6 ITPADRIQQLPPYVFARLDELKAKAREQGIDLIDLGMGNPDGATPQPVVDAAIQALQDPK 65 +T RI++LPPYVF +++ +KA AR G+D+IDLGMGNPD P V++ + + P+ Sbjct: 1 MTDFHRIRRLPPYVFEQVNRVKAAARNNGVDIIDLGMGNPDLDAPAHVIEKLKETIGKPR 60 Query: 66 NHGYPPFEGTASFRRAITNWYNRRYGVVLDPDSEALPLLGSKEGLSHLAIAYVNPGDVVL 125 Y +G RRA +Y RR+GV L+P+++ + LGSKEG +++A A PGDV+L Sbjct: 61 TDRYSASKGIPGLRRAQAAYYERRFGVKLNPETQVVATLGSKEGFANMAQAITAPGDVIL 120 Query: 126 VPSPAYPAHFRGPVIAGGTVHSLILKPENDWLIDLTAIPEEVARKAKILYFNYPSNPTGA 185 P+P+YP H G ++AGG + S+ ++P+ + + + K + YPSNPT Sbjct: 121 TPNPSYPIHAFGFLMAGGVIRSVPVEPDAQFFHAMERAVQHSIPKPIAVVVCYPSNPTAT 180 Query: 186 TAPREFFEEIVAFARKYEILLVHDLCYAELAFDGYQ-PTSLLEIPGAKDIGVEFHTLSKT 244 A +F++++VAFA+K +++++ DL YAEL FD + P S+L++PGA D+ VEF ++SKT Sbjct: 181 VANLDFYKDVVAFAKKNDLIVLSDLAYAELYFDDNEPPPSVLQVPGAMDVTVEFTSMSKT 240 Query: 245 YNMAGWRVGFVVGNRHVIQGLRTLKTNLDYGIFAALQTAAETALQLPDIYLHEVQQRYRT 304 ++MAGWR+GF VGN +I L +K+ LDYG + +Q AA AL P + E+++ Y+ Sbjct: 241 FSMAGWRMGFAVGNERLIAALARVKSYLDYGAYTPIQVAATAALNGPQECIAEMRETYKR 300 Query: 305 RRDFLIQGLGELGWDVPKTKATMYLWVKCPV---GMGSTDFALNLLQQTGVVVTPGNAFG 361 RRD ++ G GW +P KA+M+ W P MGS +F+ L+++ V V PG FG Sbjct: 301 RRDAMVDSFGRAGWTIPVPKASMFAWAPIPEPFRAMGSVEFSKLLIEKAEVAVAPGVGFG 360 Query: 362 VAGEGYVRISLIADCDRLGEALDRIKQ 388 G+ YVRI+++ + R+ +A I++ Sbjct: 361 EHGDEYVRIAVVENEQRIRQAARNIRR 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: 449 Number of extensions: 18 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: 405 Length adjustment: 31 Effective length of query: 372 Effective length of database: 374 Effective search space: 139128 Effective search space used: 139128 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