Align aromatic-amino-acid transaminase (EC 2.6.1.57) (characterized)
to candidate N515DRAFT_3488 N515DRAFT_3488 aromatic-amino-acid transaminase
Query= BRENDA::P04693 (397 letters) >FitnessBrowser__Dyella79:N515DRAFT_3488 Length = 400 Score = 375 bits (964), Expect = e-109 Identities = 197/398 (49%), Positives = 266/398 (66%), Gaps = 7/398 (1%) Query: 2 FQKVDAYAGDPILTLMERFKEDPRSDKVNLSIGLYYNEDGIIPQLQAVAEAEARL--NAQ 59 F V+ GDPIL L E + D R KVNL +G+YY+E G IP L+AV E E RL A+ Sbjct: 4 FASVEMTPGDPILGLTEAYLADARPGKVNLGVGIYYDEQGRIPLLRAVHEVEQRLAQEAK 63 Query: 60 PHGASLYLPMEGLNCYRHAIAPLLFGADHPVLKQQRVATIQTLGGSGALKVGADFLKRYF 119 P G YLP++GL Y L+FGA+ P+L RVAT QT+GGSGAL+VGAD LK+ Sbjct: 64 PRG---YLPIDGLPAYTQGTQKLVFGAESPLLAAGRVATSQTIGGSGALRVGADVLKKAL 120 Query: 120 PESGVWVSDPTWENHVAIFAGAGFEVSTYPWYDEATNGVRFNDLLATLKTLPARSIVLLH 179 P++ + +S+P+WENH +F AGFEV Y +YD T+G+ F +LA L L ++VLLH Sbjct: 121 PKAKIAISNPSWENHRVVFIAAGFEVVEYTYYDPQTHGLDFAGMLADLGKLEPGTVVLLH 180 Query: 180 PCCHNPTGADLTNDQWDAVIEILKARELIPFLDIAYQGFGAGMEEDAYAIRAIASAGLPA 239 CCHNPTG DL QW V+E++K R+L+PF+D+AYQGF G++ DA A+R A++G+ + Sbjct: 181 ACCHNPTGVDLNAAQWQQVVEVVKERQLLPFIDMAYQGFDQGIDADATAVRLFAASGIES 240 Query: 240 -LVSNSFSKIFSLYGERVGGLSVMCEDAEAAGRVLGQLKATVRRNYSSPPNFGAQVVAAV 298 +V++S++K FSLYGER G L+ + D + A RV +K T+R YSSP G +VA V Sbjct: 241 FVVTSSYAKSFSLYGERAGALTFVAADRDEALRVQSLVKRTIRSIYSSPSTHGGALVAGV 300 Query: 299 LNDEALKASWLAEVEEMRTRILAMRQELVKVLSTEMPERNFDYLLNQRGMFSYTGLSAAQ 358 LN L+A W E+ EMR RI AMR +V+ L+ + F ++ Q GMFSY+GLS AQ Sbjct: 301 LNSPELRAMWEQELGEMRERIHAMRAGMVEKLAAHGAPQ-FAFIQQQAGMFSYSGLSKAQ 359 Query: 359 VDRLREEFGVYLIASGRMCVAGLNTANVQRVAKAFAAV 396 VDRLR+E+ +Y I +GR+CVA LN +N+ VA A AAV Sbjct: 360 VDRLRDEYAIYAIGTGRICVAALNRSNLDTVAAAVAAV 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: 420 Number of extensions: 18 Number of successful extensions: 4 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: 400 Length adjustment: 31 Effective length of query: 366 Effective length of database: 369 Effective search space: 135054 Effective search space used: 135054 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