APRT(human)

RecName: Full=Adenine phosphoribosyltransferase

Fasta format

>gi|114074|sp|P07741.2|APT_HUMAN RecName: Full=Adenine phosphoribosyltransferase; Short=APRT

MADSELQLVEQRIRSFPDFPTPGVVFRDISPVLKDPASFRAAIGLLARHLKATHGGRIDYIAGLDSRGFL

FGPSLAQELGLGCVLIRKRGKLPGPTLWASYSLEYGKAELEIQKDALEPGQRVVVVDDLLATGGTMNAAC

ELLGRLQAEVLECVSLVELTSLKGREKLAPVPFFSLLQYE

Primary structure prediction

1. ProtParam

Physico-chemical parameters of a protein sequence (amino-acid and atomic compositions, isoelectric point, extinction coefficient, etc.

Number of amino acids: 180

Molecular weight: 19607.7

Amino acid composition:


Ala (A)  16      8.9%

Arg (R)  12      6.7%

Asn (N)   1      0.6%

Asp (D)   9      5.0%

Cys (C)   3      1.7%

Gln (Q)   7      3.9%

Glu (E)  13      7.2%

Gly (G)  17      9.4%

His (H)   2      1.1%

Ile (I)   7      3.9%

Leu (L)  29     16.1%

Lys (K)   8      4.4%

Met (M)   2      1.1%

Phe (F)   8      4.4%

Pro (P)  11      6.1%

Ser (S)  11      6.1%

Thr (T)   6      3.3%

Trp (W)   1      0.6%

Tyr (Y)   4      2.2%

Val (V)  13      7.2%

Pyl (O)   0      0.0%

Sec (U)   0      0.0%

 (B)   0         0.0%

 (Z)   0         0.0%

 (X)   0         0.0%

Total number of negatively charged residues (Asp + Glu): 22

Total number of positively charged residues (Arg + Lys): 20

Atomic composition:

Carbon      C         885

Hydrogen    H        1423

Nitrogen    N         237

Oxygen      O         254

Sulfur      S           5

Extinction coefficients:

Extinction coefficients are in units of M^-1 cm^-1, at 280 nm measured in water.

Ext. coefficient    11585

Abs 0.1% (=1 g/l)   0.591, assuming all pairs of Cys residues form cystines

Ext. coefficient    11460

Abs 0.1% (=1 g/l)   0.584, assuming all Cys residues are reduced

Instability index:

The instability index (II) is computed to be 39.29

This classifies the protein as stable.

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2.    Compute pI/Mw

Compute the theoretical isoelectric point (pI) and molecular weight (Mw) from a UniProt Knowledgebase entry or for a user sequence

Theoretical pI/Mw: 5.75 / 19607.77

3. ScanSitepI/Mw

Compute the theoretical pI and Mw, and multiple phosphorylation states

Protein: APRT (human)

# Phosphates	Molecular Weight	Isoelectric Point
0	19607.5431	5.78
1	19685.5071	5.49
2	19763.4711	5.29
3	19841.4351	5.12
4	19919.3991	4.99
5	19997.3631	4.87
6	20075.3271	4.77
7	20153.2911	4.68
8	20231.2551	4.59

Theoretical pI/Mw: 5.75 / 19607.77

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4.    ProtScale

Amino acid scale representation (Hydrophobicity, other conformational parameters

SEQUENCE LENGTH: 179

Using the scale Hphob. / Kyte& Doolittle, the individual values for the 20 amino acids are:

Ala: 1.800 Arg: -4.500 Asn: -3.500 Asp: -3.500 Cys: 2.500 Gln: -3.500

Glu: -3.500 Gly: -0.400 His: -3.200 Ile: 4.500 Leu: 3.800 Lys: -3.900

Met: 1.900 Phe: 2.800 Pro: -1.600 Ser: -0.800 Thr: -0.700 Trp: -0.900

Tyr: -1.300 Val: 4.200 : -3.500 : -3.500 : -0.490

Weights for window positions 1,..,9, using linear weight variation model:

1 2 3 4 5 6 7 8 9

1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00

edge center edge

Secondary structure prediction

1. CFSSP

Chou & Fasman Secondary Structure Prediction Server

Name of the sequence is gi|114074|sp|P07741.2|APT_HUMAN RecName: Full=Adenine phosphoribosyltransferase; Short=APRT.

Sequence consists of 180 amino acids.

Target Sequence:

MADSELQLVE QRIRSFPDFP TPGVVFRDIS PVLKDPASFR AAIGLLARHL KATHGGRIDY IAGLDSRGFL

FGPSLAQELG LGCVLIRKRG KLPGPTLWAS YSLEYGKAEL EIQKDALEPG QRVVVVDDLL ATGGTMNAAC

ELLGRLQAEV LECVSLVELT SLKGREKLAP VPFFSLLQYE

Secondary Structure:

* * * * *

Query 1 MADSELQLVEQRIRSFPDFPTPGVVFRDISPVLKDPASFRAAIGLLARHLKATHGGRIDY 60

Helix 1 HHHHHHHHHHHHH HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH 60

Sheet 1 EEEEEEEE EEEEEE 60

Turns 1 T TTTT 60

* * * * *

Query 61 IAGLDSRGFLFGPSLAQELGLGCVLIRKRGKLPGPTLWASYSLEYGKAELEIQKDALEPG 120

Helix 61 HHHHHHHHHHHHH HHHHHHHHHHHHHHHHHHHHHH 120

Sheet 61 EEEEEEEE EEE 120

Turns 61 TT T TTT TT T TT 120

* * * * *

Query 121 QRVVVVDDLLATGGTMNAACELLGRLQAEVLECVSLVELTSLKGREKLAPVPFFSLLQYE 180

Helix 121 HHHHHHHHHH HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH 180

Sheet 121 EEEEEEEEEE EEEEEEEEEEEEEEEEEEEEE EEEEEEEE 180

Turns 121 T TTTT 180

Total Residues: H: 132 E: 64 T: 21

Percent: H: 73.3 E: 35.6 T: 11.7

2. GOR

Garnier et al, 1996

        10        20        30        40        50        60        70

         |         |         |         |         |         |         |

MADSELQLVEQRIRSFPDFPTPGVVFRDISPVLKDPASFRAAIGLLARHLKATHGGRIDYIAGLDSRGFL

ccccchhhhhhhhcccccccccceeeeccccccccchhhhhhhhhhhhhhhhccccceeeeecccccccc

FGPSLAQELGLGCVLIRKRGKLPGPTLWASYSLEYGKAELEIQKDALEPGQRVVVVDDLLATGGTMNAAC

ccchhhhhhcchhhhhhcccccccceeceeechhhhhhhhhhhhhhhcccceeeeeeeeecccchhhhhh

ELLGRLQAEVLECVSLVELTSLKGREKLAPVPFFSLLQYE

Hhhhhhhhhhhhhhhhhhhhccccccccccccccccccee

Sequence length :   180

GOR4 :

   Alpha helix     (Hh) :    77 is  42.78%

3₁₀ helix       (Gg) :     0 is   0.00%

   Pi helix        (Ii) :     0 is   0.00%

   Beta bridge     (Bb) :     0 is   0.00%

   Extended strand (Ee) :    25 is  13.89%

   Beta turn       (Tt) :     0 is   0.00%

   Bend region     (Ss) :     0 is   0.00%

   Random coil     (Cc) :    78 is  43.33%

Ambiguous states (?)  :     0 is   0.00%

   Other states         :     0 is   0.00%

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3. Jpred

A consensus method for protein secondary structure prediction at University of Dundee

PDB	Chain	Description	Blast E-value
1zn9	B	Adenine phosphoribosyltransferase	2e-98

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4. PSIpred

Various protein structure prediction methods at Bloomsbury Centre for Bioinformatics

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5. SOPMA

Geourjon and Delage, 1995

10 20 30 40 50 60 70

| | | | | | |

MADSELQLVEQRIRSFPDFPTPGVVFRDISPVLKDPASFRAAIGLLARHLKATHGGRIDYIAGLDSRGFL

hhhhhhhhhhhhhtccccccccceeeeccccccccchhhhhhhhhhhhhhhhtttcceeeeeecccttce

FGPSLAQELGLGCVLIRKRGKLPGPTLWASYSLEYGKAELEIQKDALEPGQRVVVVDDLLATGGTMNAAC

ecchhhhhhtcceeeeettccccccccehhhhhhhtchhhhhhhhhccttceeeeeehhhhttcchhhhh

ELLGRLQAEVLECVSLVELTSLKGREKLAPVPFFSLLQYE

hhhhhhhhhhhhhhhhhhhhhccccccccccceeeeehhc

Sequence length : 180

SOPMA :

Alpha helix (Hh) : 83 is 46.11%

3₁₀ helix (Gg) : 0 is 0.00%

Pi helix (Ii) : 0 is 0.00%

Beta bridge (Bb) : 0 is 0.00%

Extended strand (Ee) : 29 is 16.11%

Beta turn (Tt) : 14 is 7.78%

Bend region (Ss) : 0 is 0.00%

Random coil (Cc) : 54 is 30.00%

Ambiguous states (?) : 0 is 0.00%

Other states : 0 is 0.00%

Parameters :

Window width : 17

Similarity threshold : 8

Number of states : 4

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Saturday 27 June 2015

primary and secondary structure prediction for APRT (human) protein sequence

1. ProtParam

Physico-chemical parameters of a protein sequence (amino-acid and atomic compositions, isoelectric point, extinction coefficient, etc.

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