GapMind for Amino acid biosynthesis

 

Aligments for a candidate for ilvE in Dyella japonica UNC79MFTsu3.2

Align aromatic-amino-acid transaminase TyrB; EC 2.6.1.57 (characterized)
to candidate N515DRAFT_3488 N515DRAFT_3488 aromatic-amino-acid transaminase

Query= CharProtDB::CH_004054
         (397 letters)



>lcl|FitnessBrowser__Dyella79:N515DRAFT_3488 N515DRAFT_3488
           aromatic-amino-acid transaminase
          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 Aug 03 2021. The underlying query database was built on Aug 03 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code, or see changes to Amino acid biosynthesis since the publication.

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