Align aromatic-amino-acid transaminase (EC 2.6.1.57) (characterized)
to candidate BWI76_RS01925 BWI76_RS01925 aromatic amino acid aminotransferase
Query= BRENDA::P04693 (397 letters) >FitnessBrowser__Koxy:BWI76_RS01925 Length = 397 Score = 679 bits (1752), Expect = 0.0 Identities = 339/397 (85%), Positives = 360/397 (90%) Query: 1 MFQKVDAYAGDPILTLMERFKEDPRSDKVNLSIGLYYNEDGIIPQLQAVAEAEARLNAQP 60 MFQKVDAYAGDPIL+LMERFK+DPRSDKVNLSIGLYYNEDGIIPQLQ+VA AEARLNAQP Sbjct: 1 MFQKVDAYAGDPILSLMERFKDDPRSDKVNLSIGLYYNEDGIIPQLQSVAAAEARLNAQP 60 Query: 61 HGASLYLPMEGLNCYRHAIAPLLFGADHPVLKQQRVATIQTLGGSGALKVGADFLKRYFP 120 HGAS+YLPMEGLN YRHAIAPLLFGADH VL Q RVA+IQTLGGSGALKVGADFLKRYFP Sbjct: 61 HGASVYLPMEGLNTYRHAIAPLLFGADHQVLAQNRVASIQTLGGSGALKVGADFLKRYFP 120 Query: 121 ESGVWVSDPTWENHVAIFAGAGFEVSTYPWYDEATNGVRFNDLLATLKTLPARSIVLLHP 180 S VWVSDPTWENH+AIF GAGFEVSTYPW+DE TNGVRF L L +L R IVLLHP Sbjct: 121 GSRVWVSDPTWENHIAIFEGAGFEVSTYPWFDEKTNGVRFAAFLEKLNSLAERDIVLLHP 180 Query: 181 CCHNPTGADLTNDQWDAVIEILKARELIPFLDIAYQGFGAGMEEDAYAIRAIASAGLPAL 240 CCHNPTGADL+N QWD V+E+LKAR LIPFLDIAYQGFGAGMEEDAYAIRAIA+AG+P L Sbjct: 181 CCHNPTGADLSNAQWDQVVEVLKARNLIPFLDIAYQGFGAGMEEDAYAIRAIANAGMPML 240 Query: 241 VSNSFSKIFSLYGERVGGLSVMCEDAEAAGRVLGQLKATVRRNYSSPPNFGAQVVAAVLN 300 VSNSFSKIFSLYGERVGGLS++CEDAE A RVLGQLKATVRRNYSSPPNFGAQVVAAVL+ Sbjct: 241 VSNSFSKIFSLYGERVGGLSIVCEDAETAIRVLGQLKATVRRNYSSPPNFGAQVVAAVLS 300 Query: 301 DEALKASWLAEVEEMRTRILAMRQELVKVLSTEMPERNFDYLLNQRGMFSYTGLSAAQVD 360 D LKASWLAEVE MRTRILAMRQELV VL +P NFDYLL QRGMFSYTG S AQVD Sbjct: 301 DSELKASWLAEVEGMRTRILAMRQELVNVLKETVPGGNFDYLLKQRGMFSYTGFSLAQVD 360 Query: 361 RLREEFGVYLIASGRMCVAGLNTANVQRVAKAFAAVM 397 RLR+EFGVYLIASGRMCVAGLN+ NVQRVA+AFAAV+ Sbjct: 361 RLRDEFGVYLIASGRMCVAGLNSRNVQRVAQAFAAVI 397 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: 585 Number of extensions: 5 Number of successful extensions: 1 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: 397 Length adjustment: 31 Effective length of query: 366 Effective length of database: 366 Effective search space: 133956 Effective search space used: 133956 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 Jul 25 2024. The underlying query database was built on Jul 25 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