NucPred on Proteomes

Authors: Andrea Krings, Amine Heddad, Markus Brameier and Bob MacCallum, Stockholm Bioinformatics Center, Stockholm University, Sweden.

NucPred - predictions for eukaryotic proteomes

Species:

Note: All filters/tests are combined with AND unless otherwise stated

Show only the proteins with links to database(s):
OMIM - human disease genes
PDB - protein 3D structure
( AND OR combination )

Annotation filters (can be slow! - Perl regexps allowed: e.g. nucleus|nucleolus)

UniProt ID (e.g. "PK3B_")
UniProt description (e.g. "kinase")
UniProt subcellular location
AND
UniProt GO component
AND
AND the
AND the

Only show proteins where the PredictNLS prediction is:

positive
negative

Only show proteins where the PSORT II predicted location

is is not

Click here: to filter by NucPred score

exclude all transmembrane proteins predicted by TMHMM
don't exclude lone N-terminal predicted transmembrane helices
(these could be signal peptides)

export all ACs and IDs as text file

Show proteins (ordered by NucPred score ) from to (currently 98716 matches)

You can bookmark/save your search criteria with this link. You can also start again with default settings.

UniProt accession	UniProt ID	UniProt description	NucPred score	Predict- NLS	PSORT II	TMHMM #helices	UniProt annotation for subcellular location	Uniprot GO cellular component	OMIM	PDB	sequence length
Q09214 UniProt NPD GO	YP65_CAEEL	Hypothetical protein B0495.5	0.12	-	mit	0					729
Q11093 UniProt NPD GO	YWZ3_CAEEL	Hypothetical protein C02B8.3	0.12	-	nuc	0					133
Q10195 UniProt NPD GO	YBY6_SCHPO	Hypothetical protein C11C11.06c in chromosome II	0.12	-	nuc	0					178
Q09744 UniProt NPD GO	YB63_SCHPO	Hypothetical protein C12C2.03c in chromosome II	0.12	-	cyt	0					571
O94629 UniProt NPD GO	YGEB_SCHPO	Hypothetical protein C1347.11 in chromosome II	0.12	-	mit	0					106
P34330 UniProt NPD GO	YKZ3_CAEEL	Hypothetical protein C14B9.3	0.12	-	end	6					348
O13960 UniProt NPD GO	YIN3_SCHPO	Hypothetical protein C1705.03c precursor	0.12	-	exc	0	Secreted protein (Potential)				421
Q09238 UniProt NPD GO	YQ86_CAEEL	Hypothetical protein C18H9.6	0.12	-	cyt	0					211
Q09256 UniProt NPD GO	YQB3_CAEEL	Hypothetical protein C30G12.3	0.12	-	nuc	0					150
Q09283 UniProt NPD GO	YQIC_CAEEL	Hypothetical protein C45G9.12	0.12	-	mit	0					93
O14178 UniProt NPD GO	YDS2_SCHPO	Hypothetical protein C4F8.02c in chromosome I	0.12	-	nuc	0					279
Q09291 UniProt NPD GO	YQL2_CAEEL	Hypothetical protein C56G7.2	0.12	-	nuc	1					367
O14249 UniProt NPD GO	YE63_SCHPO	Hypothetical protein C6G10.03c in chromosome I	0.12	-	cyt	0					428
O74901 UniProt NPD GO	YCS1_SCHPO	Hypothetical protein CC613.01	0.12	-	end	12	Membrane; multi-pass membrane protein (Potential)	integral to membrane [NAS]			497
Q8ST67 UniProt NPD GO	Y109_ENCCU	Hypothetical protein ECU01_0090/ECU01_1520/ECU02_1550/ECU08_0020	0.12	-	end	7 *					276
Q8SVY6 UniProt NPD GO	Y410_ENCCU	Hypothetical protein ECU04_0100	0.12	-	end	7 *					276
Q8SUH8 UniProt NPD GO	Y808_ENCCU	Hypothetical protein ECU08_2080	0.12	-	end	7 *					276
Q8STK1 UniProt NPD GO	Y9K1_ENCCU	Hypothetical protein ECU09_2010	0.12	-	end	6 *					245
P34473 UniProt NPD GO	YMH6_CAEEL	Hypothetical protein F58A4.6	0.12	-	cyt	0					165
Q10046 UniProt NPD GO	YRT3_CAEEL	Hypothetical protein T07A5.3 in chromosome III	0.12	-	end	11 *	Membrane; multi-pass membrane protein (Potential)				544
Q10005 UniProt NPD GO	YRY1_CAEEL	Hypothetical protein T15H9.1	0.12	-	cyt	0					82
O02485 UniProt NPD GO	YDJ1_CAEEL	Hypothetical protein ZK1073.1 in chromosome X	0.12	-	nuc	0					325
Q9HGQ3 UniProt NPD GO	YLH3_SCHPO	Hypothetical transport protein C17D4.03c in chromosome I	0.12	-	end	13	Membrane; multi-pass membrane protein (Potential)				732
Q9U3Z3 UniProt NPD GO	CXIX_CONBE	I-superfamily conotoxin BtX precursor (Kappa-Btx)	0.12	-	exc	1 *	Secreted protein (Probable)				70
P01864 UniProt NPD GO	GCAB_MOUSE	Ig gamma-2A chain C region secreted form (B allele)	0.12	-	nuc	0	Secreted protein (Potential)			1HI6	335
P23084 UniProt NPD GO	HVC1_HETFR	Ig heavy chain C region (Clone 6125) (Fragment)	0.12	-	nuc	0					370
P01683 UniProt NPD GO	KV02_RABIT	Ig kappa chain V region 3315	0.12	-	nuc	0					115
P01613 UniProt NPD GO	KV1U_HUMAN	Ig kappa chain V-I region Ni	0.12	-	nuc	0		extracellular region [NAS]			112
P01606 UniProt NPD GO	KV1N_HUMAN	Ig kappa chain V-I region OU	0.12	-	nuc	0		extracellular region [NAS]			108
P01669 UniProt NPD GO	KV3Q_MOUSE	Ig kappa chain V-III region PC 7769	0.12	-	nuc	0					111
P01672 UniProt NPD GO	KV3T_MOUSE	Ig kappa chain V-III region PC 7940	0.12	-	mit	0					111
P01678 UniProt NPD GO	KV6D_MOUSE	Ig kappa chain V-VI region SAPC 10	0.12	-	nuc	0					107
P01676 UniProt NPD GO	KV6B_MOUSE	Ig kappa chain V-VI region XRPC 24	0.12	-	nuc	0					107
P01704 UniProt NPD GO	LV2A_HUMAN	Ig lambda chain V-II region TOG	0.12	-	nuc	0		extracellular region [NAS]			111
P01712 UniProt NPD GO	LV2I_HUMAN	Ig lambda chain V-II region WIN	0.12	-	nuc	0		extracellular region [NAS]			111
P01714 UniProt NPD GO	LV3A_HUMAN	Ig lambda chain V-III region SH	0.12	-	nuc	0		extracellular region [NAS]			108
P83742 UniProt NPD GO	IGW1_HETFR	IgW chain C region, secreted form 1/3 (Fragment)	0.12	-	nuc	0	Secreted protein				144
P20764 UniProt NPD GO	IGLL1_MOUSE	Immunoglobulin lambda-like polypeptide 1 precursor (Ig lambda-5) (CD179b antigen)	0.12	-	exc	0	Secreted protein (Potential)				209
O94618 UniProt NPD GO	TIM21_SCHPO	Import inner membrane translocase subunit TIM21, mitochondrial precursor	0.12	-	mit	1	Mitochondrion; mitochondrial inner membrane; single-pass membrane protein (By similarity)				223
Q6CAQ9 UniProt NPD GO	TIM21_YARLI	Import inner membrane translocase subunit TIM21, mitochondrial precursor	0.12	-	mit	1	Mitochondrion; mitochondrial inner membrane; single-pass membrane protein (By similarity)				269
Q14623 UniProt NPD GO	IHH_HUMAN	Indian hedgehog protein precursor (IHH) (HHG-2) [Contains: Indian hedgehog protein N-product; Indian ...	0.12	-	mit	1 *	The C-terminal peptide diffuses from the cell, while the N-terminal peptide remains associated with ...	extracellular region [NAS]	607778		411
Q9S735 UniProt NPD GO	PHT19_ARATH	Inorganic phosphate transporter 1-9 (AtPht1;9) (H(+)/Pi cotransporter)	0.12	-	end	12 *	Cell membrane; multi-pass membrane protein (By similarity)				532
Q91VM9 UniProt NPD GO	IPYR2_MOUSE	Inorganic pyrophosphatase 2, mitochondrial precursor (EC 3.6.1.1) (PPase 2)	0.12	-	mit	0	Mitochondrion (Potential)	mitochondrion [IDA]			330
P21150 UniProt NPD GO	SIX4_ANDAU	Insect toxin 4 (Insect toxin AaH IT4) (AaHIT4) (AaIT4)	0.12	-	cyt	0	Secreted protein				65
Q5NKU6 UniProt NPD GO	ICAM3_PANTR	Intercellular adhesion molecule 3 precursor (ICAM-3) (CD50 antigen)	0.12	-	end	1	Membrane; single-pass type I membrane protein (By similarity)				547
Q5NKT8 UniProt NPD GO	ICAM4_PANTR	Intercellular adhesion molecule 4 precursor (ICAM-4) (CD242 antigen) (Fragment)	0.12	-	end	1	Membrane; single-pass type I membrane protein (By similarity)				269
Q9NZH6 UniProt NPD GO	IL1F7_HUMAN	Interleukin-1 family member 7 precursor (IL-1F7) (Interleukin-1 zeta) (IL-1 zeta) (FIL1 zeta) (Inter ...	0.12	-	nuc	0	Secreted protein	extracellular region [TAS]	605510		218
Q9NZH8 UniProt NPD GO	IL1F9_HUMAN	Interleukin-1 family member 9 (IL-1F9) (Interleukin-1 homolog 1) (IL-1H1) (Interleukin-1 epsilon) (I ...	0.12	-	cyt	0	Secreted protein		605542		169
Q9NPH3 UniProt NPD GO	IL1AP_HUMAN	Interleukin-1 receptor accessory protein precursor (IL-1 receptor accessory protein) (IL-1RAcP)	0.12	-	mit	1	Isoform 1: Cell membrane; single-pass type I membrane protein. Isoform 2, isoform 3, isoform 4: Secr ...	integral to plasma membrane [TAS]	602626		570
Q28374 UniProt NPD GO	IL10_HORSE	Interleukin-10 precursor (IL-10) (Cytokine synthesis inhibitory factor) (CSIF)	0.12	-	end	0	Secreted protein	extracellular region [ISS]			178

You are viewing entries 61301 to 61350 of 98716. You can see more proteins by changing the limits in the form at the top of this page, or click here for the next page of proteins .

If you find NucPred useful, please cite this paper:

NucPred - Predicting Nuclear Localization of Proteins. Brameier M, Krings A, Maccallum RM. Bioinformatics, 2007. PubMed id: 17332022

The authors also look forward to your comments and suggestions.

What does the NucPred score mean?

You have to decide on a NucPred score threshold. Sequences which score greater than or equal to this threshold are predicted to spend some time in the nucleus. Higher thresholds yield fewer predicted nuclear proteins, but these predictions are more accurate (you can have higher confidence in them). The table below gives more details of the performance of NucPred estimated using the sequences it was trained on (by cross-validation). Another benchmark is available in the Bioinformatics 2007 paper.

NucPred score threshold	Specificity	Sensitivity
see above	fraction of proteins predicted to be nuclear that actually are nuclear	fraction of true nuclear proteins that are predicted (coverage)
0.10	0.45	0.88
0.20	0.52	0.83
0.30	0.57	0.77
0.40	0.63	0.69
0.50	0.70	0.62
0.60	0.71	0.53
0.70	0.81	0.44
0.80	0.84	0.32
0.90	0.88	0.21
1.00	1.00	0.02

Sequences which score >= 0.8 with NucPred and which are predicted by PredictNLS to contain an NLS have been shown to be 93% correct with a coverage of 16%. (PredictNLS by itself is 87% correct with 26% coverage on the same data.)

Go back to the NucPred Home Page.