GapMind for Amino acid biosynthesis

 

Aligments for a candidate for tyrB in Sphingomonas koreensis DSMZ 15582

Align aspartate aminotransferase (EC 2.6.1.1) (characterized)
to candidate Ga0059261_1688 Ga0059261_1688 Aspartate/tyrosine/aromatic aminotransferase

Query= metacyc::MONOMER-13012
         (397 letters)



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

 Score =  340 bits (871), Expect = 5e-98
 Identities = 171/392 (43%), Positives = 247/392 (63%), Gaps = 2/392 (0%)

Query: 1   MFSVLKPLPTDPILGLMAAYKQDTNPNKIDLGVGVYKDELGNTPVLKAVKKAEAFRLENE 60
           MF+ L   P DPILGL     QD +P+K+DLG+G+Y++E G  PVL  VK AE +  E +
Sbjct: 1   MFADLAEPPLDPILGLAQLLAQDKSPDKVDLGIGIYQNEHGEAPVLDCVKTAERWLAETQ 60

Query: 61  TSKSYIGLAGNLDYCQKMESLLLGEHKTLLANRVRTAQAPGGTGALRVAAEFIMRCNPKA 120
            SK Y+  AGN DY  +   LL G+     A R RT QAPGGTGALR+A++ + +  P+ 
Sbjct: 61  PSKRYLSSAGNADYNTQTRGLLFGKGSDGFA-RSRTIQAPGGTGALRLASDLLRKLRPEG 119

Query: 121 TVWVTTPTWANHISLFEAAGLTVKEYPYYDYENKDLLFDEMINTLKQVPKGDVVLLHACC 180
            V++  PTW NH  + +A+G  V  YPYYD     L FDEM+  L  +   D +LLH CC
Sbjct: 120 RVFIPGPTWPNHPGILKASGHEVVVYPYYDMAAGALRFDEMMAALADLGPRDTLLLHGCC 179

Query: 181 HNPSGMDLNEAQWKVVAELAKEVGFTPLVDIAYQGFGSSLEEDARGLRILADAVEELIIC 240
           HNP+G DL+  QW+ VA L  + G   LVD+AY G G  L EDA G+R+LA+ + E I+ 
Sbjct: 180 HNPTGADLDREQWRAVAGLVAKSGAAVLVDLAYLGLGDGLAEDAAGIRLLAEQIPEFIVA 239

Query: 241 SSCSKNFGLYRERIGACSLIAKDSATADISNSVLLSVVRSIYSMPPAHGADIVNTILSST 300
           SS SKNF LYRER+GA +++      A ++++  L V R+++SMPP HGA +V  +L   
Sbjct: 240 SSYSKNFALYRERVGALTVVGGSEKDAVLAHAHALPVARTLWSMPPDHGAAVVAKVLGDA 299

Query: 301 ELTQMWHQELDEMRSRINGLRTQIKETLATKDIAQDFSFIERQHGMFSFLGINKEQITRL 360
           EL ++W  EL  MR RIN +R ++   LA +   +D+ FI +Q GMF+ LGI  + +  L
Sbjct: 300 ELRRVWEGELTLMRGRINAMRERLATRLAAQG-TRDYGFIAKQRGMFTMLGIAPDAVETL 358

Query: 361 QKEYGIYIVGSSRVNVAGVSDANIEYFANAVA 392
           ++++ +++  S R+NVAG++  N++  A+A+A
Sbjct: 359 RRDHHVHLTSSGRINVAGLNANNVDRVADAIA 390


Lambda     K      H
   0.318    0.134    0.388 

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: 401
Number of extensions: 16
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 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 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