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
Q53TS8 UniProt NPD GO	AL2SA_HUMAN	Amyotrophic lateral sclerosis 2 chromosomal region candidate gene 11 protein	0.71	-	nuc	0					623
P09798 UniProt NPD GO	CDC16_YEAST	Anaphase-promoting complex subunit CDC16 (Cell division control protein 16)	0.71	-	nuc	0	Nucleus	anaphase-promoting complex [TAS]			840
Q9D4H4 UniProt NPD GO	AMOL1_MOUSE	Angiomotin-like protein 1	0.71	-	nuc	0		tight junction [IDA]			882
Q63ZY3 UniProt NPD GO	ANR25_HUMAN	Ankyrin repeat domain-containing protein 25 (SRC-1-interacting protein) (SRC1-interacting protein)	0.71	-	nuc	0					851
Q16994 UniProt NPD GO	FMR2_ANTEL	Antho-RFamide neuropeptides type 2 precursor [Contains: Antho-RFamide]	0.71	-	vac	0	Secreted protein				429
Q7YRZ2 UniProt NPD GO	APTX_BOVIN	Aprataxin homolog (Forkhead-associated domain histidine triad-like protein) (FHA-HIT)	0.71	+	nuc	0	Nucleus (By similarity). Upon genotoxic stress, it colocalizes with XRCC1 at sites of DNA damage (By ...				356
P38714 UniProt NPD GO	SYRM_YEAST	Arginyl-tRNA synthetase, mitochondrial precursor (EC 6.1.1.19) (Arginine--tRNA ligase) (ArgRS)	0.71	-	cyt	0	Mitochondrion; mitochondrial matrix	mitochondrion [IDA]			643
O95260 UniProt NPD GO	ATE1_HUMAN	Arginyl-tRNA--protein transferase 1 (EC 2.3.2.8) (R-transferase 1) (Arginyltransferase 1) (Arginine- ...	0.71	-	nuc	0	Isoform ATE1-1: Nucleus (By similarity). Isoform ATE1-1, isoform ATE1-2: Cytoplasm (By similarity)	cytoplasm [IDA] nucleus [IDA]	607103		518
Q9Z2A5 UniProt NPD GO	ATE1_MOUSE	Arginyl-tRNA--protein transferase 1 (EC 2.3.2.8) (R-transferase 1) (Arginyltransferase 1) (Arginine- ...	0.71	-	nuc	0	Isoform ATE1-1: Nucleus. Isoform ATE1-1, isoform ATE1-2: Cytoplasm	cytoplasm [IDA] nucleus [IDA]			516
Q6BQ20 UniProt NPD GO	ATG13_DEBHA	Autophagy-related protein 13	0.71	-	nuc	0	Cytoplasm (By similarity). Membrane; peripheral membrane protein (By similarity)				837
Q51ZN8 UniProt NPD GO	ATG2_MAGGR	Autophagy-related protein 2	0.71	-	nuc	0	Perivacuolar compartment (By similarity)				2077
Q6FR93 UniProt NPD GO	ATG20_CANGA	Autophagy-related protein 20	0.71	-	nuc	0	Cytoplasm (By similarity). Membrane; peripheral membrane protein (By similarity). Endosome; endosoma ...				753
P20675 UniProt NPD GO	NGF_PRANA	Beta-nerve growth factor precursor (Beta-NGF)	0.71	-	exc	0	Secreted protein				241
O46382 UniProt NPD GO	BIG1_BOVIN	Brefeldin A-inhibited guanine nucleotide-exchange protein 1 (Brefeldin A-inhibited GEP 1) (p200 ARF- ...	0.71	-	nuc	0					1849
O75419 UniProt NPD GO	CC45L_HUMAN	CDC45-related protein (PORC-PI-1) (Cdc45)	0.71	-	cyt	0	Cytoplasm. Nucleus	nucleus [TAS]	603465		566
Q8BYR5 UniProt NPD GO	CAPS2_MOUSE	Calcium-dependent secretion activator 2 (Calcium-dependent activator protein for secretion 2) (CAPS- ...	0.71	-	nuc	0	Cytoplasmic vesicle. Membrane-associated to vesicles. Strongly enriched in synaptic fractions. Proba ...	cytoplasmic membrane-bound vesicle [IDA] postsynaptic membrane [IDA] presynaptic membrane [IDA]			1297
Q22036 UniProt NPD GO	CAN5_CAEEL	Calpain-5 (EC 3.4.22.-) (Sex-determining transformer protein 3)	0.71	-	cyt	0		membrane [TAS]			648
O19112 UniProt NPD GO	CILP1_PIG	Cartilage intermediate layer protein 1 (CILP-1) [Contains: Cartilage intermediate layer protein 1 C2 ...	0.71	-	nuc	0	Secreted protein; extracellular space; extracellular matrix (By similarity)				599
O74135 UniProt NPD GO	CKI3_SCHPO	Casein kinase I homolog 3 (EC 2.7.11.1)	0.71	-	nuc	0	Cytoplasm				439
Q9BXL6 UniProt NPD GO	CAR14_HUMAN	Caspase recruitment domain-containing protein 14 (CARD-containing MAGUK protein 2) (Carma 2)	0.71	-	nuc	0	Cytoplasm	plasma membrane [NAS]	607211		1004
Q86V15 UniProt NPD GO	CASZ1_HUMAN	Castor homolog 1 zinc finger protein (Castor-related protein) (Zinc finger protein 693)	0.71	-	nuc	0	Nucleus (Probable)				1044
Q9UU80 UniProt NPD GO	CWF18_SCHPO	Cell cycle control protein cwf18	0.71	-	nuc	0	Nucleus (Probable)	spliceosome complex [IDA]			142
P45436 UniProt NPD GO	CED3_CAEVU	Cell death protein 3 precursor (EC 3.4.22.-) [Contains: Cell death protein 3 subunit 1; Cell death p ...	0.71	-	nuc	0					496
O00311 UniProt NPD GO	CDC7_HUMAN	Cell division cycle 7-related protein kinase (EC 2.7.11.1) (CDC7-related kinase) (HsCdc7) (huCdc7)	0.71	-	nuc	0	Nucleus	cytoplasm [TAS] nucleus [TAS]	603311		574
P49336 UniProt NPD GO	CDK8_HUMAN	Cell division protein kinase 8 (EC 2.7.11.22) (EC 2.7.11.23) (Protein kinase K35)	0.71	-	nuc	0		mediator complex [IDA]	603184		464
Q64662 UniProt NPD GO	P53_SPEBE	Cellular tumor antigen p53 (Tumor suppressor p53) (Fragment)	0.71	+	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				314
Q63517 UniProt NPD GO	CENPI_RAT	Centromere protein I (CENP-I) (Follicle-stimulating hormone primary response protein) (FSH primary r ...	0.71	-	nuc	0					745
O43102 UniProt NPD GO	CBF5_ASPFU	Centromere/microtubule-binding protein cbf5 (Centromere-binding factor 5) (Small nucleolar RNP prote ...	0.71	+	nuc	0	Nucleus; nucleolus (By similarity)				487
Q99NF3 UniProt NPD GO	CEP41_MOUSE	Centrosomal protein of 41 kDa (Cep41 protein) (Testis-specific gene A14 protein)	0.71	-	nuc	0	Centrosome (By similarity)				373
Q5RCQ2 UniProt NPD GO	CEP68_PONPY	Centrosomal protein of 68 kDa (Cep68 protein)	0.71	-	nuc	0	Centrosome (By similarity)				751
Q9SDN0 UniProt NPD GO	DNJ20_ARATH	Chaperone protein dnaJ 20, chloroplast precursor (AtJ20) (AtDjC20)	0.71	-	mit	0	Plastid; chloroplast (Potential)				197
Q5ZHP5 UniProt NPD GO	CHM4B_CHICK	Charged multivesicular body protein 4b (Chromatin-modifying protein 4b) (CHMP4b)	0.71	-	nuc	0	Cytoplasm (By similarity)				227
P56804 UniProt NPD GO	RR14_ARATH	Chloroplast 30S ribosomal protein S14	0.71	-	nuc	0	Plastid; chloroplast				100
P06370 UniProt NPD GO	RR14_MARPO	Chloroplast 30S ribosomal protein S14	0.71	-	nuc	0	Plastid; chloroplast				100
Q95H62 UniProt NPD GO	RR14_WHEAT	Chloroplast 30S ribosomal protein S14	0.71	-	nuc	0	Plastid; chloroplast				103
Q32S00 UniProt NPD GO	RR15_STAPU	Chloroplast 30S ribosomal protein S15	0.71	-	nuc	0	Plastid; chloroplast				111
P42342 UniProt NPD GO	RR7_SPIMX	Chloroplast 30S ribosomal protein S7	0.71	-	mit	0	Plastid; chloroplast				155
P51269 UniProt NPD GO	RK20_PORPU	Chloroplast 50S ribosomal protein L20	0.71	+	nuc	0	Plastid; chloroplast				115
Q4WPW2 UniProt NPD GO	EAF3_ASPFU	Chromatin modification-related protein eaf3	0.71	-	nuc	0	Nucleus (By similarity)				330
O42934 UniProt NPD GO	CHP2_SCHPO	Chromo domain protein 2	0.71	+	nuc	0	Nucleus (By similarity)	centric heterochromatin [TAS] mating-type region heterochromatin [TAS] nuclear telomeric heterochromatin [TAS]			380
Q96DT5 UniProt NPD GO	DYH11_HUMAN	Ciliary dynein heavy chain 11 (Axonemal beta dynein heavy chain 11)	0.71	+	cyt	0		axonemal dynein complex [NAS]	603339		4523
Q10568 UniProt NPD GO	CPSF2_BOVIN	Cleavage and polyadenylation specificity factor 100 kDa subunit (CPSF 100 kDa subunit)	0.71	-	cyt	0	Nucleus (Potential)				782
Q7ZVC2 UniProt NPD GO	CLUA1_BRARE	Clusterin-associated protein 1 homolog	0.71	-	nuc	0	Nucleus (By similarity)				427
Q8HZ57 UniProt NPD GO	CCHCR_PANPA	Coiled-coil alpha-helical rod protein 1 (Alpha helical coiled-coil rod protein)	0.71	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				782
Q8HZ60 UniProt NPD GO	CCHCR_PANTR	Coiled-coil alpha-helical rod protein 1 (Alpha helical coiled-coil rod protein)	0.71	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				782
Q9TSV3 UniProt NPD GO	CCHCR_PIG	Coiled-coil alpha-helical rod protein 1 (Alpha helical coiled-coil rod protein) (Fragment)	0.71	-	mit	0	Cytoplasm (By similarity). Nucleus (By similarity)				427
Q8TD31 UniProt NPD GO	CCHCR_HUMAN	Coiled-coil alpha-helical rod protein 1 (Alpha helical coiled-coil rod protein) (Putative gene 8 pro ...	0.71	-	nuc	0	Cytoplasm. Nucleus		605310		782
Q6P1N0 UniProt NPD GO	CCD1A_HUMAN	Coiled-coil and C2 domain-containing protein 1A (Five repressor element under dual repression-bindin ...	0.71	-	nuc	0	Cytoplasm. Nucleus		610055		951
P08649 UniProt NPD GO	CO4_RAT	Complement C4 precursor [Contains: Complement C4 beta chain; Complement C4 alpha chain; C4a anaphyla ...	0.71	+	end	0		extracellular region [IDA]			1737
P01029 UniProt NPD GO	CO4B_MOUSE	Complement C4-B precursor [Contains: Complement C4 beta chain; Complement C4 alpha chain; C4a anaphy ...	0.71	+	mit	0					1738

You are viewing entries 13151 to 13200 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.