Align aromatic-amino-acid transaminase TyrB; EC 2.6.1.57 (characterized)
to candidate Ga0059261_1688 Ga0059261_1688 Aspartate/tyrosine/aromatic aminotransferase
Query= CharProtDB::CH_004054 (397 letters) >FitnessBrowser__Korea:Ga0059261_1688 Length = 395 Score = 271 bits (694), Expect = 2e-77 Identities = 160/385 (41%), Positives = 217/385 (56%), Gaps = 4/385 (1%) Query: 11 DPILTLMERFKEDPRSDKVNLSIGLYYNEDGIIPQLQAVAEAEARLNAQPHGASLYLPME 70 DPIL L + +D DKV+L IG+Y NE G P L V AE L A+ + YL Sbjct: 11 DPILGLAQLLAQDKSPDKVDLGIGIYQNEHGEAPVLDCVKTAERWL-AETQPSKRYLSSA 69 Query: 71 GLNCYRHAIAPLLFGADHPVLKQQRVATIQTLGGSGALKVGADFLKRYFPESGVWVSDPT 130 G Y LLFG + R TIQ GG+GAL++ +D L++ PE V++ PT Sbjct: 70 GNADYNTQTRGLLFGKGSDGFARSR--TIQAPGGTGALRLASDLLRKLRPEGRVFIPGPT 127 Query: 131 WENHVAIFAGAGFEVSTYPWYDEATNGVRFNDLLATLKTLPARSIVLLHPCCHNPTGADL 190 W NH I +G EV YP+YD A +RF++++A L L R +LLH CCHNPTGADL Sbjct: 128 WPNHPGILKASGHEVVVYPYYDMAAGALRFDEMMAALADLGPRDTLLLHGCCHNPTGADL 187 Query: 191 TNDQWDAVIEILKARELIPFLDIAYQGFGAGMEEDAYAIRAIASAGLPALVSNSFSKIFS 250 +QW AV ++ +D+AY G G G+ EDA IR +A +V++S+SK F+ Sbjct: 188 DREQWRAVAGLVAKSGAAVLVDLAYLGLGDGLAEDAAGIRLLAEQIPEFIVASSYSKNFA 247 Query: 251 LYGERVGGLSVMCEDAEAAGRVLGQLKATVRRNYSSPPNFGAQVVAAVLNDEALKASWLA 310 LY ERVG L+V+ + A R +S PP+ GA VVA VL D L+ W Sbjct: 248 LYRERVGALTVVGGSEKDAVLAHAHALPVARTLWSMPPDHGAAVVAKVLGDAELRRVWEG 307 Query: 311 EVEEMRTRILAMRQELVKVLSTEMPERNFDYLLNQRGMFSYTGLSAAQVDRLREEFGVYL 370 E+ MR RI AMR+ L L+ + R++ ++ QRGMF+ G++ V+ LR + V+L Sbjct: 308 ELTLMRGRINAMRERLATRLAAQ-GTRDYGFIAKQRGMFTMLGIAPDAVETLRRDHHVHL 366 Query: 371 IASGRMCVAGLNTANVQRVAKAFAA 395 +SGR+ VAGLN NV RVA A AA Sbjct: 367 TSSGRINVAGLNANNVDRVADAIAA 391 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: 411 Number of extensions: 19 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: 397 Length of database: 395 Length adjustment: 31 Effective length of query: 366 Effective length of database: 364 Effective search space: 133224 Effective search space used: 133224 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 Aug 03 2021. The underlying query database was built on Aug 03 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