Align aromatic-amino-acid transaminase (EC 2.6.1.57) (characterized)
to candidate WP_011951610.1 SWIT_RS03890 aspartate/tyrosine/aromatic aminotransferase
Query= BRENDA::P04693 (397 letters) >NCBI__GCF_000016765.1:WP_011951610.1 Length = 401 Score = 289 bits (740), Expect = 9e-83 Identities = 161/396 (40%), Positives = 234/396 (59%), Gaps = 10/396 (2%) Query: 1 MFQKVDAYAGDPILTLMERFKEDPRSDKVNLSIGLYYNEDGIIPQLQAVAEAEARLNAQP 60 +F +++ D +L L+ + DPR+ K++L +G+Y +E G P AV AEA+L A+ Sbjct: 15 LFGRLELQPSDSLLALIGLYAADPRASKIDLGVGVYKDEAGHTPVFAAVKAAEAKLLAE- 73 Query: 61 HGASLYLPMEGLNCYRHAIAPLLFGADHPVLKQQRVATIQTLGGSGALKVGADFLKRYFP 120 Y+ EG + +AP++FG P + R+A +QT GG+GAL++GA+ + R P Sbjct: 74 QPTKAYVGPEGDIGFFEGLAPIVFGDAAP---RARLAGLQTPGGTGALRLGAELIARNNP 130 Query: 121 ESGVWVSDPTWENHVAIFAGAGFEVSTYPWYDEATNGVRFNDLLATLKTLPARSIVLLHP 180 ++ + V PTW NH IFA A + + D T + F+D+LA L+T +VLLH Sbjct: 131 DAVIHVGGPTWPNHAPIFAAARLALRQHRHIDLTTQELCFDDVLAALQTAVPGDVVLLHG 190 Query: 181 CCHNPTGADLTNDQWDAVIEILKARELIPFLDIAYQGFGAGMEEDAYAIRAIASAGLPAL 240 CCHNPTGAD T DQW+A+ ++ R L+PF+D+AYQG GA M+EDA +R +A L Sbjct: 191 CCHNPTGADFTADQWEALGALMAKRGLLPFIDLAYQGLGASMDEDAEGVRIVARHCPEML 250 Query: 241 VSNSFSKIFSLYGERVGGLSVMCEDAEAAGRVLGQLKATVRRNYSSPPNFGAQVVAAVLN 300 V+ S K F LY ERVG L ++ + EAA V L + R N+S PP+ GA VV +L Sbjct: 251 VAYSCDKNFGLYRERVGALFILAAEPEAAAVVQSNLLSLARANWSMPPDHGAAVVRLILE 310 Query: 301 DEALKASWLAEVEEMRTRILAMRQELVKVLSTEMPERNFDYLLNQRGMFSYTGLSAAQVD 360 L+A WLAE++E+R RI AMR L + + ++ Q+GMFS LS QV Sbjct: 311 SAELRAQWLAELDEVRARIAAMRAGLAAL------DPALAFIGRQKGMFSTLPLSPDQVK 364 Query: 361 RLREEFGVYLIASGRMCVAGLNTANVQRVAKAFAAV 396 +RE + +Y+ SGR+ +AGL A + +A AFAAV Sbjct: 365 AMRERYAIYMAGSGRINIAGLTPAKLAPLAAAFAAV 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: 393 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: 397 Length of database: 401 Length adjustment: 31 Effective length of query: 366 Effective length of database: 370 Effective search space: 135420 Effective search space used: 135420 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