Align aromatic-amino-acid transaminase (EC 2.6.1.57) (characterized)
to candidate WP_083780753.1 BBTA_RS02905 aspartate/tyrosine/aromatic aminotransferase
Query= BRENDA::P04693 (397 letters) >NCBI__GCF_000015165.1:WP_083780753.1 Length = 399 Score = 323 bits (829), Expect = 4e-93 Identities = 174/386 (45%), Positives = 242/386 (62%), Gaps = 1/386 (0%) Query: 11 DPILTLMERFKEDPRSDKVNLSIGLYYNEDGIIPQLQAVAEAEARLNAQPHGASLYLPME 70 D ++ F EDPR KVNL IG+YY+E+G IPQL AV EA+ RL ++ YLP E Sbjct: 11 DAVMLAARLFAEDPRPHKVNLGIGMYYDEEGRIPQLAAVREADHRLRSRNRPWP-YLPAE 69 Query: 71 GLNCYRHAIAPLLFGADHPVLKQQRVATIQTLGGSGALKVGADFLKRYFPESGVWVSDPT 130 GL ++ P++FG D ++R A IQT+GG+GA+++GA+ + P++ +SDP+ Sbjct: 70 GLVDLKNKAMPVVFGEDQADDLRRRTAWIQTVGGTGAVRIGAELARAIAPDAMASISDPS 129 Query: 131 WENHVAIFAGAGFEVSTYPWYDEATNGVRFNDLLATLKTLPARSIVLLHPCCHNPTGADL 190 W NH AIF G VS+Y +YD + + + +L L LP ++V+LH CCHNPTG D Sbjct: 130 WPNHEAIFRAVGARVSSYRYYDVESCNIDVDGMLQDLGRLPRGTVVVLHGCCHNPTGFDP 189 Query: 191 TNDQWDAVIEILKARELIPFLDIAYQGFGAGMEEDAYAIRAIASAGLPALVSNSFSKIFS 250 T QW+ + ++L R LIPF+D+AYQGFG G+E DA ++R IA + VS SFSK FS Sbjct: 190 TPAQWNHIAQVLADRGLIPFIDLAYQGFGEGLEADAQSVRIIAQSCNLIFVSVSFSKSFS 249 Query: 251 LYGERVGGLSVMCEDAEAAGRVLGQLKATVRRNYSSPPNFGAQVVAAVLNDEALKASWLA 310 LYGERVG L V+ E A V + +A R YSS P+ GA ++A VL D LK +W+ Sbjct: 250 LYGERVGLLFVVTESEAQAALVGERARAVSRALYSSAPSNGALLIAEVLGDPQLKTTWID 309 Query: 311 EVEEMRTRILAMRQELVKVLSTEMPERNFDYLLNQRGMFSYTGLSAAQVDRLREEFGVYL 370 E++ MR RIL MR ELV L+ NF + QRG+FSY+GL+ +++RLR + V+ Sbjct: 310 ELDAMRRRILLMRAELVDQLAGGNRGANFAPIKAQRGLFSYSGLTRTEIERLRVDHAVHA 369 Query: 371 IASGRMCVAGLNTANVQRVAKAFAAV 396 +A GR+C+A LN N+ VA A V Sbjct: 370 VADGRICLAALNAGNLPSVAAAIRQV 395 Lambda K H 0.320 0.135 0.401 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: 388 Number of extensions: 13 Number of successful extensions: 2 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: 397 Length of database: 399 Length adjustment: 31 Effective length of query: 366 Effective length of database: 368 Effective search space: 134688 Effective search space used: 134688 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