GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ptransferase in Sphingomonas koreensis DSMZ 15582

Align aspartate transaminase (EC 2.6.1.1); glutamate-prephenate aminotransferase (EC 2.6.1.79) (characterized)
to candidate Ga0059261_1558 Ga0059261_1558 Aspartate/tyrosine/aromatic aminotransferase

Query= BRENDA::Q02635
         (400 letters)



>FitnessBrowser__Korea:Ga0059261_1558
          Length = 389

 Score =  152 bits (385), Expect = 1e-41
 Identities = 110/372 (29%), Positives = 179/372 (48%), Gaps = 20/372 (5%)

Query: 27  KAKGRDVIGLGAGEPDFDTPDNIKKAAIDAIDRGETKYTPVSGIPELREAIAKKFKRENN 86
           +A+    I LG G PD +    + +AA DA+     +Y P++G+P LR+AIA  + R   
Sbjct: 23  RARAMGAINLGQGFPDGEGCVPVIRAAADALTTRSNQYPPMAGLPALRQAIATHYTRHQQ 82

Query: 87  LDYTAAQTIVGTGGKQILFNAFMATLNPGDEVVIPAPYWVSYPEMVALCGGTPVFVPTRQ 146
           LD +  + IV +G  + +  +F A + PGDEV++  P + +Y  +V   GG    +   +
Sbjct: 83  LDLSPEEVIVTSGATEAIAASFTALIAPGDEVILIQPLYDAYLPLVQRAGGV-ARLARLE 141

Query: 147 ENNFKLKAEDLDRAITPKTKWFVFNSPSNPSGAAYSHEELKALTDVLMKHPHVWVLTDDM 206
             +++L    L+ A  P+T+  V N+P NP+GA  SH EL  L    ++   +  + D++
Sbjct: 142 PGSWRLTPAALEAAAGPRTRLIVVNNPVNPAGAKLSHGELADLAAFCVERDLI-AICDEV 200

Query: 207 YEHLTYGDFRFATPVEVEPGLYERTLTMNGVSKAYAMTGWRIGYAAGPLHLIKAMDMIQG 266
           +EH+ Y   R   P+   PG+ +RT+ +    K +A+TGW++G+      L   +     
Sbjct: 201 WEHVVYDSARH-IPLIAMPGMRDRTVKIGSAGKIFALTGWKVGWMCAAAPLAAVLARAHQ 259

Query: 267 QQTSGAASIAQWAAVEALNGPQDFIGRNKEIFQGRRDLVVSMLNQAKGISCPTPEGAFYV 326
             T   A   QWA  E L     +I  +   FQ  RD + + L  A           + V
Sbjct: 260 FLTFSTAPNLQWAVAEGLETQDAWIADSIVGFQRSRDRLAAGLTAA----------GYRV 309

Query: 327 YPSCAG--LIGKTAPSGKVIETDEDFVSELLETEGVAVVHGSAF----GLGPNFRISYAT 380
            PS A   L    A SG  +  D  F   L+E  GVA +  SAF     +    R+ +A 
Sbjct: 310 LPSGATWFLSIDLAASGIALH-DAAFCDRLVEEIGVAAIPVSAFYAEAPVTHLARLCFAK 368

Query: 381 SEALLEEACRRI 392
           ++A+L+ A  R+
Sbjct: 369 ADAVLDTAIERM 380


Lambda     K      H
   0.318    0.134    0.402 

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: 363
Number of extensions: 18
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: 400
Length of database: 389
Length adjustment: 31
Effective length of query: 369
Effective length of database: 358
Effective search space:   132102
Effective search space used:   132102
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.

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