Align aromatic-amino-acid transaminase (EC 2.6.1.57) (characterized)
to candidate Dsui_2433 Dsui_2433 aspartate/tyrosine/aromatic aminotransferase
Query= BRENDA::P04693 (397 letters) >FitnessBrowser__PS:Dsui_2433 Length = 402 Score = 407 bits (1045), Expect = e-118 Identities = 208/398 (52%), Positives = 272/398 (68%), Gaps = 3/398 (0%) Query: 1 MFQKVDAYAGDPILTLMERFKEDPRSDKVNLSIGLYYNEDGIIPQLQAVAEAE-ARLNAQ 59 +F V+ DPIL L E F D R+ KVNL +G+YY+++G IP L AV AE ARL Sbjct: 5 IFASVEMAPRDPILGLTEAFNADTRATKVNLGVGVYYDDNGKIPLLAAVKAAEKARLETM 64 Query: 60 PHGASLYLPMEGLNCYRHAIAPLLFGADHPVLKQQRVATIQTLGGSGALKVGADFLKRYF 119 P Y P+EGLN Y A+ LLFGA +L RV T + LGG+GALK+GADFLKR Sbjct: 65 PPRG--YQPIEGLNAYNQAVQNLLFGAGSELLAAGRVITAEALGGTGALKIGADFLKRIS 122 Query: 120 PESGVWVSDPTWENHVAIFAGAGFEVSTYPWYDEATNGVRFNDLLATLKTLPARSIVLLH 179 P + V++SDP+WENH A+F AGF V YP+YD AT GV F + + L+ L A SI++LH Sbjct: 123 PNAKVYISDPSWENHRALFESAGFVVENYPYYDAATRGVNFAGMKSFLEGLAAGSIIILH 182 Query: 180 PCCHNPTGADLTNDQWDAVIEILKARELIPFLDIAYQGFGAGMEEDAYAIRAIASAGLPA 239 CCHNPTGADL++ QW V+++ KA+ L+PFLD+AYQGF G++ DA A+RA +++GL Sbjct: 183 ACCHNPTGADLSDAQWQEVVDVCKAKGLVPFLDMAYQGFADGIDADAVAVRAFSASGLQF 242 Query: 240 LVSNSFSKIFSLYGERVGGLSVMCEDAEAAGRVLGQLKATVRRNYSSPPNFGAQVVAAVL 299 VS+SFSK FSLYGERVG LSV+ E + RVL Q+K +R NYS+PP G VVAAVL Sbjct: 243 FVSSSFSKSFSLYGERVGALSVVTASKEESARVLSQVKRVIRTNYSNPPTHGGAVVAAVL 302 Query: 300 NDEALKASWLAEVEEMRTRILAMRQELVKVLSTEMPERNFDYLLNQRGMFSYTGLSAAQV 359 + L+ W E+ MR RI AMR LV L + ++F +++ QRGMFSYTGL++AQV Sbjct: 303 STPELRQMWEDELAGMRDRIRAMRVALVDKLKAKGVAQDFSFVVKQRGMFSYTGLTSAQV 362 Query: 360 DRLREEFGVYLIASGRMCVAGLNTANVQRVAKAFAAVM 397 D LR EFG+Y + +GR+C+A LN+ N+ V A AAV+ Sbjct: 363 DVLRNEFGIYAVGTGRICLAALNSKNIDAVVDAIAAVL 400 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: 441 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: 402 Length adjustment: 31 Effective length of query: 366 Effective length of database: 371 Effective search space: 135786 Effective search space used: 135786 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