GapMind for Amino acid biosynthesis

 

Alignments 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)



>FitnessBrowser__Korea:Ga0059261_1688
          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:

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