Align aromatic-amino-acid transaminase TyrB; EC 2.6.1.57 (characterized)
to candidate Dsui_1904 Dsui_1904 aspartate/tyrosine/aromatic aminotransferase
Query= CharProtDB::CH_004054 (397 letters) >FitnessBrowser__PS:Dsui_1904 Length = 398 Score = 525 bits (1353), Expect = e-154 Identities = 268/397 (67%), Positives = 307/397 (77%), Gaps = 1/397 (0%) Query: 1 MFQKVDAYAGDPILTLMERFKEDPRSDKVNLSIGLYYNEDGIIPQLQAVAEAEARLNAQP 60 MF+ VDAYAGDPILTL+E F +D R+ KVNL IGLYY+E G IP L +V +AEA + A P Sbjct: 1 MFEHVDAYAGDPILTLVETFHKDSRTTKVNLGIGLYYDEQGRIPLLGSVRQAEAAIAAAP 60 Query: 61 HGASLYLPMEGLNCYRHAIAPLLFGADHPVLKQQRVATIQTLGGSGALKVGADFLKRYFP 120 S YLPMEG YR + LLFGAD LK R+ATIQTLGGSGALKVGAD LKRYFP Sbjct: 61 APRS-YLPMEGAADYRAVVQKLLFGADSAALKAGRIATIQTLGGSGALKVGADLLKRYFP 119 Query: 121 ESGVWVSDPTWENHVAIFAGAGFEVSTYPWYDEATNGVRFNDLLATLKTLPARSIVLLHP 180 +S WVS+PTW+NH +IF GAG V YP+YD T GV F ++A LK LP +SIVLLHP Sbjct: 120 KSEAWVSNPTWDNHRSIFEGAGIAVHDYPYYDANTGGVDFTGMVACLKGLPEQSIVLLHP 179 Query: 181 CCHNPTGADLTNDQWDAVIEILKARELIPFLDIAYQGFGAGMEEDAYAIRAIASAGLPAL 240 CCHNPTG DL+ +QW VI I+ R+LIPFLDIAYQGFG G++EDAYAIRA+A +GLP L Sbjct: 180 CCHNPTGVDLSREQWQQVIAIVAERKLIPFLDIAYQGFGDGLDEDAYAIRALADSGLPFL 239 Query: 241 VSNSFSKIFSLYGERVGGLSVMCEDAEAAGRVLGQLKATVRRNYSSPPNFGAQVVAAVLN 300 VSNSFSK S YGERVGGLSV+C+DAE AGRVLGQLK TVRRNYSSPP G V V+N Sbjct: 240 VSNSFSKNLSFYGERVGGLSVVCKDAEEAGRVLGQLKFTVRRNYSSPPIHGELVTTIVMN 299 Query: 301 DEALKASWLAEVEEMRTRILAMRQELVKVLSTEMPERNFDYLLNQRGMFSYTGLSAAQVD 360 D AL A W+ EV EMRTRI AMRQ+L +VL+ +P ++F Y QRGMFSYTGLS AQVD Sbjct: 300 DAALHAEWVKEVTEMRTRIQAMRQKLYEVLTARVPGKDFSYFTKQRGMFSYTGLSPAQVD 359 Query: 361 RLREEFGVYLIASGRMCVAGLNTANVQRVAKAFAAVM 397 RLREEFGVYL+ SGRMCVAGLNT NV VA+A AAV+ Sbjct: 360 RLREEFGVYLVRSGRMCVAGLNTGNVAYVAEAMAAVL 396 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: 489 Number of extensions: 11 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: 398 Length adjustment: 31 Effective length of query: 366 Effective length of database: 367 Effective search space: 134322 Effective search space used: 134322 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