Align aspartate transaminase (EC 2.6.1.1) (characterized)
to candidate 353461 BT3935 aminotransferase (NCBI ptt file)
Query= BRENDA::Q8YTF2 (403 letters) >FitnessBrowser__Btheta:353461 Length = 393 Score = 276 bits (705), Expect = 1e-78 Identities = 143/384 (37%), Positives = 222/384 (57%), Gaps = 3/384 (0%) Query: 6 ITPADRIQQLPPYVFARLDELKAKAREQGIDLIDLGMGNPDGATPQPVVDAAIQALQDPK 65 I PA+R+ + Y F++ + A+ +G D+I LG+G+PD + ++ DP Sbjct: 10 IAPAERLASVSEYYFSKKLKEVAQMNAEGKDVISLGIGSPDMPPSKVTIETLCNNAHDPN 69 Query: 66 NHGYPPFEGTASFRRAITNWYNRRYGVVLDPDSEALPLLGSKEGLSHLAIAYVNPGDVVL 125 HGY P+ G R+ WY R YGV L+P++E PL+GSKEG+ H+ +A+VNPG+ VL Sbjct: 70 GHGYQPYVGIPELRKGFAAWYQRWYGVELNPNTEIQPLIGSKEGILHVTLAFVNPGEQVL 129 Query: 126 VPSPAYPAHFRGPVIAGGTVHSLILKPENDWLIDLTAIPEEVARKAKILYFNYPSNPTGA 185 VP+P YP + I G V S LK E+ W+ D A+ + + K+++ NYP+ PTGA Sbjct: 130 VPNPGYPTYTSLSKILGAEVISYDLKEEDGWMPDFEALEKMDLNRVKLMWTNYPNMPTGA 189 Query: 186 TAPREFFEEIVAFARKYEILLVHDLCYAELAFDGYQPTSLLEIPGAKDIGVEFHTLSKTY 245 A E +E +V FAR+ I++V+D Y+ + + +P S+L +PGAK+ +EF+++SK++ Sbjct: 190 NATPELYERLVDFARRKNIVIVNDNPYSFILNE--KPISILSVPGAKECCIEFNSMSKSH 247 Query: 246 NMAGWRVGFVVGNRHVIQGLRTLKTNLDYGIFAALQTAAETALQLPDIYLHEVQQRYRTR 305 NM GWR+G + N +Q + +K+N+D G+F A+Q AA TAL+ + YR R Sbjct: 248 NMPGWRIGMLASNAEFVQWILKVKSNIDSGMFRAMQLAAATALEAEADWYEGNNHNYRGR 307 Query: 306 RDFLIQGLGELGWDVPKTKATMYLWVKCPVGMGST-DFALNLLQQTGVVVTPGNAFGVAG 364 R + + LG + + M+LW K P + +L Q V +TPG FG G Sbjct: 308 RHLAGEIMKTLGCTYDENQVGMFLWGKIPASCKDVEELTEKVLHQARVFITPGFIFGSNG 367 Query: 365 EGYVRISLIADCDRLGEALDRIKQ 388 ++RISL +L EAL+RIK+ Sbjct: 368 ARFIRISLCCKDAKLAEALERIKK 391 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: 420 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: 393 Length adjustment: 31 Effective length of query: 372 Effective length of database: 362 Effective search space: 134664 Effective search space used: 134664 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