Tutorial #1 - Identification of Proteins

Example of 45 known proteins

Uwe Hobohm, Tony Houthaeve and Chris Sander (1994) Analytical Biochemistry 222, pp. 202-209.

Example of Probability of Correct Identification

Uwe Hobohm, Tony Houthaeve and Chris Sander (1994) Analytical Biochemistry 222, pp. 202-209.

PROPSEARCH: Database Query Using Amino Acid Analysis Data

PROPSEARCH database query

http://www.embl-heidelberg.de/aaa.html

Enter AAA data as Mole % Example: PTC-AAA data, Bovine Serum Albumin

1.7 g analyzed, n=1, Compositional Error = 8.7%

Hydrolysis data outlen=100:

AA	%AA		WEIGHT	AA	%AA		WEIGHT
Arg	4.23	4.23	1.0	Met	0.75	0.75	1.0
Glx	14.96	14.96	1.0	Ile	1.98	1.98	1.0
Ser	5.06	5.06	1.0	Leu	12.26	12.26	1.0
His	3.12	3.12	1.0	Phe	5.31	5.31	1.0
Gly	3.63	3.63	1.0	Lys	7.32	7.32	1.0
Thr	5.89	5.89	1.0	Asx	10.67	10.67	1.0
Ala	8.74	8.74	1.0	sum	100.01	100.00
Pro	5.53	5.53	1.0
Tyr	4.13	4.13	1.0
Val	6.43	6.43	1.0

Results from PROPSEARCH

Fragment search: OFF (POS1 and POS2 are begin and end of sequence)

Rank	ID	DIST*	LEN2	POS1	POS2	pI	DE 1
1	albu_bovin	1.32	607	1	607	6.04	serum albumin precursor
2	albu_sheep	1.33	607	1	607	6.08	serum albumin precursor
3	albu_rat	1.40	608	1	608	6.44	serum albumin precursor
4	albu_mouse	1.55	438	1	438	5.30	serum albumin (fragments)
5	albu_human	1.60	609	1	609	6.23	serum albumin precursor
6	albu_pig	1.63	605	1	605	6.25	serum albumin precursor
7	albu_horse	1.65	607	1	607	6.30	serum albumin precursor
8	>f1;s37157	1.69	590	1	590	4.96	NADPH-ferrihemoprotein reductase
9	afam_rat	1.77	608	1	608	6.14	AFAMIN precursor
10	mepd_rat	1.77	686	1	686	5.64	thimet oligopeptidase

*smaller=better
1.5 less reliable
2.5 unreliable

Uwe Hobohm, Tony Houthaeve and Chris Sander (1994) Analytical Biochemistry 222, 202-209.

ExPASy Amino Acid Composition Similarity Search

ExPASy database query

http://expasy.hcuge.ch/ch2d/aacompi.html

Enter AAA data as Mole %

Example: PTC-AAA data, Human Cellular Retinaldehyde

Binding Protein, 1.9 g analyzed, n=1

Compositional Error = 6.9%

AMINO ACID COMPOSITION FOR UNKNOWN PROTEIN

Asx:	7.37	Glx:	17.32	Ser:	4.62	OPTIONS
His:	1.72	Gly:	7.46	Thr:	4.84
Ala:	8.22	Pro:	4.32	Tyr:	2.86	max. number of proteins: 20
Arg:	7.07	Val:	6.09	Met:	2.05	pI range: 0.25
Ile:	3.31	Leu:	10.31	Phe:	7.44	Mw range: 20%
Lys:	5.01
						Tagging: No_Tag
						pI: 0.00 Range: (-0.25, 0.25)
						Mw: 36000 Range: (28800, 43200)

Results from ExPASy Computer Search

The closet SWISS-PROT entries for the species HUMAN:

Rank Score* Protein (pI Mw) Description
1 6 CRAL_HUMAN 4.98 36343 cellular retinaldehyde-binding protein
2 31 RO52_HUMAN 5.98 54169 52 kd RO protein (Sjogren syndrome type)
3 32 GRK6_HUMAN 8.33 65968 G protein-coupled receptor kinase GRK6
4 32 RYNR_HUMAN 5.19 564429 Ryanodine receptor, skeletal
5 36 CP27_HUMAN 8.43 56908 sterol 26-hydroxylase
6 37 SYD_HUMUM 6.20 57192 aspartyl-TRNA synthetase
7 38 VAV_HUMAN 6.20 98354 Vav Oncogene
8 38 STA5_HUMAN 5.98 90646 signal transducer
9 38 RFP_HUMAN 5.83 58489 transforming protein RFP
10 38 RTC1_HUMAN 6.34 23294 ras-like protein TC21

* smaller = better
0-25 is good
25-50 less reliable
>50 unreliable

Reference
Ron Appel at Ron.Appel@dim.hucge.ch

Return to Table of Contents.

Rank	Score*	Protein	(pI Mw)	Description
1	6	CRAL_HUMAN	4.98	36343 cellular retinaldehyde-binding protein
2	31	RO52_HUMAN	5.98	54169 52 kd RO protein (Sjogren syndrome type)
3	32	GRK6_HUMAN	8.33	65968 G protein-coupled receptor kinase GRK6
4	32	RYNR_HUMAN	5.19	564429 Ryanodine receptor, skeletal
5	36	CP27_HUMAN	8.43	56908 sterol 26-hydroxylase
6	37	SYD_HUMUM	6.20	57192 aspartyl-TRNA synthetase
7	38	VAV_HUMAN	6.20	98354 Vav Oncogene
8	38	STA5_HUMAN	5.98	90646 signal transducer
9	38	RFP_HUMAN	5.83	58489 transforming protein RFP
10	38	RTC1_HUMAN	6.34	23294 ras-like protein TC21