GapMind for Amino acid biosynthesis

 

Alignments 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)



>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 Aug 03 2021. The underlying query database was built on Aug 03 2021.

Links

Downloads

Related tools

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 (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:

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. 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