Align Aromatic-amino-acid aminotransferase (EC 2.6.1.57) (characterized)
to candidate N515DRAFT_3488 N515DRAFT_3488 aromatic-amino-acid transaminase
Query= reanno::Cup4G11:RR42_RS33490 (400 letters) >FitnessBrowser__Dyella79:N515DRAFT_3488 Length = 400 Score = 388 bits (997), Expect = e-112 Identities = 199/395 (50%), Positives = 262/395 (66%), Gaps = 2/395 (0%) Query: 2 FEHIDAYPGDPILSLNESFQLDPRTDKVNLSIGIYFDDEGRLPVMQAVREAEAALMADMG 61 F ++ PGDPIL L E++ D R KVNL +GIY+D++GR+P+++AV E E L + Sbjct: 4 FASVEMTPGDPILGLTEAYLADARPGKVNLGVGIYYDEQGRIPLLRAVHEVEQRLAQEAK 63 Query: 62 PRPYLPMAGFAAYRDAVQALVFGQPCQARAEGRIATVQTLGGSGALRVGADFLKRYFPDA 121 PR YLP+ G AY Q LVFG A GR+AT QT+GGSGALRVGAD LK+ P A Sbjct: 64 PRGYLPIDGLPAYTQGTQKLVFGAESPLLAAGRVATSQTIGGSGALRVGADVLKKALPKA 123 Query: 122 QVWISDPSWENHRVIFERTGFTVNTYPYYDDATGGLKFDAMLDALRLIPKRSIVLLHACC 181 ++ IS+PSWENHRV+F GF V Y YYD T GL F ML L + ++VLLHACC Sbjct: 124 KIAISNPSWENHRVVFIAAGFEVVEYTYYDPQTHGLDFAGMLADLGKLEPGTVVLLHACC 183 Query: 182 HNPTGVDLNHDQWRQLITLLKQHELLPFVDMAYQGFGAGLDDDAFAVRELVAQGVPC-LV 240 HNPTGVDLN QW+Q++ ++K+ +LLPF+DMAYQGF G+D DA AVR A G+ +V Sbjct: 184 HNPTGVDLNAAQWQQVVEVVKERQLLPFIDMAYQGFDQGIDADATAVRLFAASGIESFVV 243 Query: 241 ANSFSKNFSLYGERCGGLSVVCDSAEETGRVLGQLTGAVRANYSNPPTHGARVVARVLTT 300 +S++K+FSLYGER G L+ V +E RV + +R+ YS+P THG +VA VL + Sbjct: 244 TSSYAKSFSLYGERAGALTFVAADRDEALRVQSLVKRTIRSIYSSPSTHGGALVAGVLNS 303 Query: 301 PALRTIWERELAGKCERIAKMRAAIHKGLAAHVSGEALSRYLTQRGMFTYTGLTADQVDR 360 P LR +WE+EL ERI MRA + + LAAH + Q GMF+Y+GL+ QVDR Sbjct: 304 PELRAMWEQELGEMRERIHAMRAGMVEKLAAH-GAPQFAFIQQQAGMFSYSGLSKAQVDR 362 Query: 361 LRTEHGVYLLRSGRMCVAGLNERNVTQVAQAIASV 395 LR E+ +Y + +GR+CVA LN N+ VA A+A+V Sbjct: 363 LRDEYAIYAIGTGRICVAALNRSNLDTVAAAVAAV 397 Lambda K H 0.323 0.137 0.417 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: 422 Number of extensions: 20 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: 400 Length of database: 400 Length adjustment: 31 Effective length of query: 369 Effective length of database: 369 Effective search space: 136161 Effective search space used: 136161 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 (21.9 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
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