GapMind for Amino acid biosynthesis

 

Aligments for a candidate for ilvE in Sphingomonas koreensis DSMZ 15582

Align aromatic-amino-acid transaminase TyrB; EC 2.6.1.57 (characterized)
to candidate Ga0059261_1688 Ga0059261_1688 Aspartate/tyrosine/aromatic aminotransferase

Query= CharProtDB::CH_004054
         (397 letters)



>lcl|FitnessBrowser__Korea:Ga0059261_1688 Ga0059261_1688
           Aspartate/tyrosine/aromatic aminotransferase
          Length = 395

 Score =  271 bits (694), Expect = 2e-77
 Identities = 160/385 (41%), Positives = 217/385 (56%), Gaps = 4/385 (1%)

Query: 11  DPILTLMERFKEDPRSDKVNLSIGLYYNEDGIIPQLQAVAEAEARLNAQPHGASLYLPME 70
           DPIL L +   +D   DKV+L IG+Y NE G  P L  V  AE  L A+   +  YL   
Sbjct: 11  DPILGLAQLLAQDKSPDKVDLGIGIYQNEHGEAPVLDCVKTAERWL-AETQPSKRYLSSA 69

Query: 71  GLNCYRHAIAPLLFGADHPVLKQQRVATIQTLGGSGALKVGADFLKRYFPESGVWVSDPT 130
           G   Y      LLFG       + R  TIQ  GG+GAL++ +D L++  PE  V++  PT
Sbjct: 70  GNADYNTQTRGLLFGKGSDGFARSR--TIQAPGGTGALRLASDLLRKLRPEGRVFIPGPT 127

Query: 131 WENHVAIFAGAGFEVSTYPWYDEATNGVRFNDLLATLKTLPARSIVLLHPCCHNPTGADL 190
           W NH  I   +G EV  YP+YD A   +RF++++A L  L  R  +LLH CCHNPTGADL
Sbjct: 128 WPNHPGILKASGHEVVVYPYYDMAAGALRFDEMMAALADLGPRDTLLLHGCCHNPTGADL 187

Query: 191 TNDQWDAVIEILKARELIPFLDIAYQGFGAGMEEDAYAIRAIASAGLPALVSNSFSKIFS 250
             +QW AV  ++        +D+AY G G G+ EDA  IR +A      +V++S+SK F+
Sbjct: 188 DREQWRAVAGLVAKSGAAVLVDLAYLGLGDGLAEDAAGIRLLAEQIPEFIVASSYSKNFA 247

Query: 251 LYGERVGGLSVMCEDAEAAGRVLGQLKATVRRNYSSPPNFGAQVVAAVLNDEALKASWLA 310
           LY ERVG L+V+    + A           R  +S PP+ GA VVA VL D  L+  W  
Sbjct: 248 LYRERVGALTVVGGSEKDAVLAHAHALPVARTLWSMPPDHGAAVVAKVLGDAELRRVWEG 307

Query: 311 EVEEMRTRILAMRQELVKVLSTEMPERNFDYLLNQRGMFSYTGLSAAQVDRLREEFGVYL 370
           E+  MR RI AMR+ L   L+ +   R++ ++  QRGMF+  G++   V+ LR +  V+L
Sbjct: 308 ELTLMRGRINAMRERLATRLAAQ-GTRDYGFIAKQRGMFTMLGIAPDAVETLRRDHHVHL 366

Query: 371 IASGRMCVAGLNTANVQRVAKAFAA 395
            +SGR+ VAGLN  NV RVA A AA
Sbjct: 367 TSSGRINVAGLNANNVDRVADAIAA 391


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: 411
Number of extensions: 19
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: 395
Length adjustment: 31
Effective length of query: 366
Effective length of database: 364
Effective search space:   133224
Effective search space used:   133224
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 (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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 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