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
O02754 UniProt NPD GO	CEBPA_BOVIN	CCAAT/enhancer-binding protein alpha (C/EBP alpha)	0.44	+	nuc	0	Nucleus				353
P05554 UniProt NPD GO	CEBPA_RAT	CCAAT/enhancer-binding protein alpha (C/EBP alpha)	0.44	+	nuc	0	Nucleus	transcription factor complex [IDA]		1NWQ	358
Q8HY00 UniProt NPD GO	CD209_PONPY	CD209 antigen (Dendritic cell-specific ICAM-3-grabbing nonintegrin 1) (DC-SIGN1)	0.44	-	nuc	1 *	Membrane; single-pass type II membrane protein (By similarity)				404
Q9JLH5 UniProt NPD GO	CK5P2_RAT	CDK5 regulatory subunit-associated protein 2 (CDK5 activator-binding protein C48) (Fragment)	0.44	-	nuc	0	Centrosome (By similarity)	cytoskeleton [ISS]			218
Q8L8Q7 UniProt NPD GO	COBL2_ARATH	COBRA-like protein 2 precursor	0.44	-	exc	1	Cell membrane; lipid-anchor; GPI-anchor (Potential)				441
Q9N359 UniProt NPD GO	CSN4_CAEEL	COP9 signalosome complex subunit 4 (Signalosome subunit 4)	0.44	-	cyt	0	Cytoplasm. Nucleus				412
Q91ZF0 UniProt NPD GO	ZCSL3_MOUSE	CSL-type zinc finger-containing protein 3 (J-domain protein DjC7)	0.44	-	nuc	0				1WJZ	196
Q13634 UniProt NPD GO	CAD18_HUMAN	Cadherin-18 precursor (Cadherin-14)	0.44	-	end	1	Membrane; single-pass type I membrane protein		603019		790
P24005 UniProt NPD GO	ACTB_DICDI	Calcium-regulated actin-bundling protein (34 kDa actin-binding protein)	0.44	-	cyt	0					295
Q13939 UniProt NPD GO	CALI_HUMAN	Calicin	0.44	-	cyt	0	Calyx. Sperm head cytoskeletal structure tightly associated to the nucleus	cytoskeleton [NAS]	603960		588
Q9D805 UniProt NPD GO	CAN9_MOUSE	Calpain-9 (EC 3.4.22.-) (Digestive tract-specific calpain) (nCL-4)	0.44	-	cyt	0	Cytoplasm (By similarity)				690
Q7RZP7 UniProt NPD GO	PALB_NEUCR	Calpain-like protease palB/rim-13 (EC 3.4.22.-) (Cysteine protease rim-13)	0.44	-	cyt	0					986
Q6DBY9 UniProt NPD GO	CHST1_BRARE	Carbohydrate sulfotransferase 1 (EC 2.8.2.21) (Keratan sulfate Gal-6 sulfotransferase) (KSST) (KSGal ...	0.44	-	nuc	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)				420
Q9NRB3 UniProt NPD GO	CHSTC_HUMAN	Carbohydrate sulfotransferase 12 (EC 2.8.2.5) (Chondroitin 4-O-sulfotransferase 2) (Chondroitin 4-su ...	0.44	-	exc	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)	integral to Golgi membrane [NAS]			414
P08311 UniProt NPD GO	CATG_HUMAN	Cathepsin G precursor (EC 3.4.21.20) (CG)	0.44	-	exc	0			116830	1T32	255
O74772 UniProt NPD GO	CWF14_SCHPO	Cell cycle control protein cwf14	0.44	-	nuc	0	Nucleus (Probable)	spliceosome complex [IDA]			146
Q8BGZ4 UniProt NPD GO	CDC23_MOUSE	Cell division cycle protein 23 homolog (Anaphase-promoting complex subunit 8) (APC8) (Cyclosome subu ...	0.44	-	nuc	0					597
Q6NVL7 UniProt NPD GO	CHM2B_XENTR	Charged multivesicular body protein 2b (Chromatin-modifying protein 2b) (CHMP2b)	0.44	-	nuc	0	Cytoplasm; cytosol (By similarity)				214
Q6DD52 UniProt NPD GO	CHMP5_XENLA	Charged multivesicular body protein 5 (Chromatin-modifying protein 5)	0.44	-	nuc	0	Cytoplasm (By similarity)				219
Q64347 UniProt NPD GO	CLCN1_MOUSE	Chloride channel protein, skeletal muscle (Chloride channel protein 1) (ClC-1)	0.44	-	end	11	Membrane; multi-pass membrane protein				994
Q811Q2 UniProt NPD GO	CLIC6_RAT	Chloride intracellular channel 6	0.44	-	nuc	0	Cytoplasm (By similarity). Predominantly. Cell membrane (By similarity). Upon chloride ion efflux fr ...	plasma membrane [IDA]			612
Q85FJ0 UniProt NPD GO	RR11_ADICA	Chloroplast 30S ribosomal protein S11	0.44	-	nuc	0	Plastid; chloroplast				130
Q9MUP2 UniProt NPD GO	RR12_MESVI	Chloroplast 30S ribosomal protein S12	0.44	-	nuc	0	Plastid; chloroplast				122
P51256 UniProt NPD GO	RR18_PORPU	Chloroplast 30S ribosomal protein S18	0.44	-	nuc	0	Plastid; chloroplast				70
P41605 UniProt NPD GO	RR2_PINTH	Chloroplast 30S ribosomal protein S2	0.44	-	mit	0	Plastid; chloroplast				234
P59144 UniProt NPD GO	RR4_HYPFI	Chloroplast 30S ribosomal protein S4	0.44	-	mit	0	Plastid; chloroplast				202
Q9MTP1 UniProt NPD GO	RR4_OENHO	Chloroplast 30S ribosomal protein S4	0.44	-	mit	0	Plastid; chloroplast				203
Q3BAN8 UniProt NPD GO	RR4_PHAAO	Chloroplast 30S ribosomal protein S4	0.44	-	mit	0	Plastid; chloroplast				201
Q9FS90 UniProt NPD GO	RR4_SPLSP	Chloroplast 30S ribosomal protein S4	0.44	-	mit	0	Plastid; chloroplast				202
O20106 UniProt NPD GO	RR4_CYPSP	Chloroplast 30S ribosomal protein S4 (Fragment)	0.44	-	mit	0	Plastid; chloroplast				194
O36051 UniProt NPD GO	RR4_NEOSP	Chloroplast 30S ribosomal protein S4 (Fragment)	0.44	-	mit	0	Plastid; chloroplast				182
O20291 UniProt NPD GO	RR4_TRISA	Chloroplast 30S ribosomal protein S4 (Fragment)	0.44	-	mit	0	Plastid; chloroplast				194
Q3V4Z6 UniProt NPD GO	RK16_ACOCL	Chloroplast 50S ribosomal protein L16	0.44	-	mit	0	Plastid; chloroplast				135
Q8S8V6 UniProt NPD GO	RK16_ATRBE	Chloroplast 50S ribosomal protein L16	0.44	-	nuc	0	Plastid; chloroplast				134
Q9TL21 UniProt NPD GO	RK16_NEPOL	Chloroplast 50S ribosomal protein L16	0.44	-	mit	0	Plastid; chloroplast				134
Q33BZ5 UniProt NPD GO	RK16_NICTO	Chloroplast 50S ribosomal protein L16	0.44	-	nuc	0	Plastid; chloroplast				134
P24283 UniProt NPD GO	RK22_PELHO	Chloroplast 50S ribosomal protein L22	0.44	-	nuc	0	Plastid; chloroplast				137
Q5SD01 UniProt NPD GO	RK32_HUPLU	Chloroplast 50S ribosomal protein L32	0.44	-	nuc	0	Plastid; chloroplast				56
P23362 UniProt NPD GO	CCKN_MACFA	Cholecystokinins precursor (CCK) [Contains: Cholecystokinin 58 (CCK58); Cholecystokinin 39 (CCK39); ...	0.44	-	exc	0					115
Q90ZD5 UniProt NPD GO	CRDL1_CHICK	Chordin-like protein 1 precursor (Neuralin) (Ventroptin)	0.44	-	exc	0	Secreted protein				456
P30387 UniProt NPD GO	1C04_GORGO	Class I histocompatibility antigen, GOGO-C0203 alpha chain precursor	0.44	-	end	1	Membrane; single-pass type I membrane protein				366
O88947 UniProt NPD GO	FA10_MOUSE	Coagulation factor X precursor (EC 3.4.21.6) (Stuart factor) [Contains: Factor X light chain; Factor ...	0.44	-	mit	0					481
P20909 UniProt NPD GO	COBA1_RAT	Collagen alpha-1(XI) chain precursor (Fragment)	0.44	-	nuc	0					482
P15989 UniProt NPD GO	CO6A3_CHICK	Collagen alpha-3(VI) chain precursor	0.44	-	nuc	0					3137
Q8SQ74 UniProt NPD GO	CO2_PANTR	Complement C2 precursor (EC 3.4.21.43) (C3/C5 convertase) [Contains: Complement C2b fragment; Comple ...	0.44	-	exc	0	Secreted protein				752
Q90X85 UniProt NPD GO	CO8B_ONCMY	Complement component C8 beta chain precursor (Complement component 8 subunit beta)	0.44	-	exc	1 *					587
P0C1N7 UniProt NPD GO	CXM35_CONTE	Conotoxin Tx3.5 precursor	0.44	-	exc	0	Secreted protein (By similarity)				64
P25308 UniProt NPD GO	CRF2_CATCO	Corticoliberin-2 precursor (Corticotropin-releasing factor 2) (CRF 2) (Corticotropin-releasing hormo ...	0.44	-	exc	0	Secreted protein				162
Q9I8Q3 UniProt NPD GO	CFC1_CHICK	Cryptic protein precursor (Cripto-related factor 1)	0.44	-	nuc	0					193
Q38JU2 UniProt NPD GO	CRYD_LYCES	Cryptochrome DASH, chloroplast/mitochondrial precursor (Cryptochrome-3)	0.44	-	mit	0	Plastid; chloroplast (By similarity). Mitochondrion (By similarity)				577

You are viewing entries 28851 to 28900 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.