GapMind for Amino acid biosynthesis

 

Alignments 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)



>FitnessBrowser__Korea:Ga0059261_1688
          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 Jul 25 2024. The underlying query database was built on Jul 25 2024.

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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