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
O70239 UniProt NPD GO	AXN1_RAT	Axin-1 (Axis inhibition protein 1) (rAxin)	0.89	-	nuc	0	Cytoplasm (By similarity)	synapse [IDA]		1WSP	827
P57095 UniProt NPD GO	AXN2_BRARE	Axin-2 (Axis inhibition protein 2)	0.89	-	nuc	0	Cytoplasm (By similarity)				812
P52172 UniProt NPD GO	SRP_DROME	Box A-binding factor (ABF) (GATA-binding factor-B) (Transcription factor GATA-B) (dGATA-B) (Protein ...	0.89	-	nuc	0	Nucleus				1264
Q80ZF8 UniProt NPD GO	BAI3_MOUSE	Brain-specific angiogenesis inhibitor 3 precursor	0.89	-	end	8 *	Membrane; multi-pass membrane protein				1522
Q9HCU9 UniProt NPD GO	BRMS1_HUMAN	Breast cancer metastasis-suppressor 1	0.89	-	nuc	0			606259		246
Q3UQU0 UniProt NPD GO	BRD9_MOUSE	Bromodomain-containing protein 9	0.89	+	nuc	0					596
Q9S775 UniProt NPD GO	PKL_ARATH	CHD3-type chromatin remodeling factor PICKLE (EC 3.6.1.-) (Protein GYMNOS)	0.89	-	nuc	0	Nucleus				1384
Q8BRT1 UniProt NPD GO	CLAP2_MOUSE	CLIP-associating protein 2 (Cytoplasmic linker-associated protein 2)	0.89	-	nuc	0	Cytoplasm. Localizes to microtubule tips. Polarized accumulation is subject to regulation by positio ...	cytoplasmic microtubule [IDA] Golgi apparatus [IDA]			1286
Q99JD4 UniProt NPD GO	CLAP2_RAT	CLIP-associating protein 2 (Cytoplasmic linker-associated protein 2)	0.89	-	nuc	0	Cytoplasm. Localizes to microtubule tips. Polarized accumulation is subject to regulation by positio ...	microtubule [IDA]			1286
Q80TJ1 UniProt NPD GO	CAPS1_MOUSE	Calcium-dependent secretion activator 1 (Calcium-dependent activator protein for secretion 1) (CAPS- ...	0.89	-	nuc	0	Cytoplasmic vesicle. Membrane-associated to vesicles. Strongly enriched in synaptic fractions. May p ...	cytoplasmic vesicle [IDA]			1355
Q6GLR7 UniProt NPD GO	CAPS1_XENLA	Calcium-dependent secretion activator 1 (Calcium-dependent activator protein for secretion 1) (CAPS- ...	0.89	-	nuc	0	Cytoplasmic vesicle (By similarity). Membrane-associated to vesicles. Strongly enriched in synaptic ...				1299
Q64338 UniProt NPD GO	PDE1C_MOUSE	Calcium/calmodulin-dependent 3',5'-cyclic nucleotide phosphodiesterase 1C (EC 3.1.4.17) (Cam-PDE 1C) ...	0.89	+	nuc	0					706
Q6NPP4 UniProt NPD GO	CMTA2_ARATH	Calmodulin-binding transcription activator 2 (Signal-responsive protein 4) (Ethylene-induced calmodu ...	0.89	-	nuc	0	Nucleus				1050
Q9FYG2 UniProt NPD GO	CMTA4_ARATH	Calmodulin-binding transcription activator 4 (Signal-responsive protein 5) (Ethylene-induced calmodu ...	0.89	-	nuc	0	Nucleus				1016
Q8BQ86 UniProt NPD GO	CHST8_MOUSE	Carbohydrate sulfotransferase 8 (EC 2.8.2.-) (N-acetylgalactosamine-4-O-sulfotransferase 1) (GalNAc- ...	0.89	-	mit	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)	integral to membrane [ISS]			417
Q75UG5 UniProt NPD GO	CCAP_PERAM	Cardioactive peptide precursor (CCAP) (Crustacean cardioactive peptide) (Cardioacceleratory peptide ...	0.89	-	nuc	0	Secreted protein (By similarity)	extracellular region [ISS]			171
Q15699 UniProt NPD GO	CART1_HUMAN	Cartilage homeoprotein 1 (CART-1)	0.89	+	nuc	0	Nucleus (Probable)		601527		326
Q6P9K8 UniProt NPD GO	CSKI1_MOUSE	Caskin-1 (CASK-interacting protein 1)	0.89	-	nuc	0	Cytoplasm (By similarity)				1431
Q8VHK2 UniProt NPD GO	CSKI1_RAT	Caskin-1 (CASK-interacting protein 1)	0.89	-	nuc	0	Cytoplasm	cytoplasm [IDA]			1430
Q8VHK1 UniProt NPD GO	CSKI2_MOUSE	Caskin-2	0.89	+	nuc	0	Cytoplasm (By similarity)				1201
Q03019 UniProt NPD GO	TWINE_DROME	Cdc25-like protein phosphatase twine (EC 3.1.3.48)	0.89	-	nuc	0					426
P50445 UniProt NPD GO	RUX_DROME	Cell cycle negative regulator roughex	0.89	-	nuc	0		nucleus [IDA]			335
P32562 UniProt NPD GO	CDC5_YEAST	Cell cycle serine/threonine-protein kinase CDC5/MSD2 (EC 2.7.11.21)	0.89	+	nuc	0		bud neck [IDA] nucleus [IDA] spindle pole [IDA]			705
Q94126 UniProt NPD GO	CES2_CAEEL	Cell death specification protein 2	0.89	+	exc	0	Nucleus				211
P40382 UniProt NPD GO	CDT1_SCHPO	Cell division cycle protein cdt1	0.89	-	nuc	0					444
P41412 UniProt NPD GO	RES2_SCHPO	Cell division cycle-related protein res2/pct1	0.89	-	nuc	0		MBF transcription complex [TAS]			657
Q3UHD9 UniProt NPD GO	CENG1_MOUSE	Centaurin-gamma 1 (ARF-GAP with GTP-binding protein-like, ankyrin repeat and pleckstrin homology dom ...	0.89	+	nuc	0	Cytoplasm. Nucleus (By similarity)				1186
Q8CGU4 UniProt NPD GO	CENG1_RAT	Centaurin-gamma 1 (ARF-GAP with GTP-binding protein-like, ankyrin repeat and pleckstrin homology dom ...	0.89	+	nuc	0	Cytoplasm. Nucleus	nucleus [IDA]			1186
Q99490 UniProt NPD GO	CENG1_HUMAN	Centaurin-gamma 1 (ARF-GAP with GTP-binding protein-like, ankyrin repeat and pleckstrin homology dom ...	0.89	+	nuc	0	Isoform 1, isoform 2: Cytoplasm. Isoform 1: Nucleus	nucleus [ISS]	605476	2BMJ	1192
Q4V7C8 UniProt NPD GO	CEP55_RAT	Centrosome protein 55	0.89	-	nuc	0	Centrosome (By similarity). Present at the centrosomes at interphase. A small portion is associated ...				462
Q96CF2 UniProt NPD GO	CHM4C_HUMAN	Charged multivesicular body protein 4c (Chromatin-modifying protein 4c) (CHMP4c) (Vacuolar protein s ...	0.89	-	nuc	0	Cytoplasm				233
Q10429 UniProt NPD GO	CND3_SCHPO	Condensin complex subunit 3 (p100) (CAPG homolog)	0.89	-	mit	0	Nucleus. Cytoplasm. In interphase cells, the majority of the condensin complex is found in the cytop ...	condensin complex [IDA] cytoplasm [IDA] nucleus [IDA]			875
Q9P0U4 UniProt NPD GO	CXCC1_HUMAN	CpG-binding protein (PHD finger and CXXC domain-containing protein 1) (CXXC finger protein 1)	0.89	-	nuc	0	Nucleus; nucleoplasm; nuclear speckle. Associated with euchromatin. During mitosis, excluded from co ...	nucleus [IDA]	609150		656
Q75B88 UniProt NPD GO	EME1_ASHGO	Crossover junction endonuclease EME1 (EC 3.1.22.-)	0.89	-	nuc	0	Nucleus (By similarity)				714
P38257 UniProt NPD GO	MMS4_YEAST	Crossover junction endonuclease MMS4 (EC 3.1.22.-)	0.89	-	nuc	0	Nucleus				691
Q754C9 UniProt NPD GO	MUS81_ASHGO	Crossover junction endonuclease MUS81 (EC 3.1.22.-)	0.89	-	nuc	0	Nucleus (By similarity)				604
Q7SXA9 UniProt NPD GO	MUS81_BRARE	Crossover junction endonuclease MUS81 (EC 3.1.22.-)	0.89	-	nuc	0	Nucleus (By similarity)				604
Q5R9C9 UniProt NPD GO	ATF7_PONPY	Cyclic AMP-dependent transcription factor ATF-7 (Activating transcription factor 7) (Transcription f ...	0.89	+	nuc	0	Nucleus (By similarity)				483
O96433 UniProt NPD GO	CCNT_DROME	Cyclin-T	0.89	+	nuc	0		nucleus [IDA] polytene chromosome puff [IDA] transcription elongation factor complex b [IPI]			1097
Q6T8E9 UniProt NPD GO	CCNT1_BOVIN	Cyclin-T1 (CycT1)	0.89	-	nuc	0	Nucleus (By similarity)				727
O19002 UniProt NPD GO	CDN1A_FELCA	Cyclin-dependent kinase inhibitor 1 (p21) (CDK-interacting protein 1)	0.89	+	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				163
Q3V1H1 UniProt NPD GO	CKAP2_MOUSE	Cytoskeleton-associated protein 2	0.89	-	nuc	0	Cytoplasm. Colocalizes with microtubules throughout the cell cycle				664
Q4QQM1 UniProt NPD GO	PA24B_MOUSE	Cytosolic phospholipase A2 beta (EC 3.1.1.4) (cPLA2-beta) (Phospholipase A2 group IVB)	0.89	-	cyt	0	Cytoplasm; cytosol. Translocates to membrane vesicles in a calcium-dependent fashion (By similarity) ...				1012
Q2KN94 UniProt NPD GO	CYTSA_FUGRU	Cytospin-A	0.89	-	nuc	0					1118
Q8NEU8 UniProt NPD GO	DP13B_HUMAN	DCC-interacting protein 13 beta (Dip13 beta) (Adapter protein containing PH domain, PTB domain and l ...	0.89	-	nuc	0	Endosome; early endosome; early endosomal membrane; peripheral membrane protein. Nucleus. Early endo ...	cytoplasm [IC] endosome membrane [IDA] nucleus [IDA]	606232		664
O44424 UniProt NPD GO	DGC14_DROME	DGCR14 protein homolog (ES2 protein) (dES2)	0.89	-	nuc	0	Nucleus (By similarity)	nucleus [ISS]			501
Q9JHY8 UniProt NPD GO	DNL1_RAT	DNA ligase 1 (EC 6.5.1.1) (DNA ligase I) (Polydeoxyribonucleotide synthase [ATP] 1)	0.89	+	nuc	0	Nucleus				918
Q08387 UniProt NPD GO	DNL4_YEAST	DNA ligase 4 (EC 6.5.1.1) (DNA ligase IV) (Polydeoxyribonucleotide synthase [ATP] 4) (DNA ligase II) ...	0.89	+	nuc	0	Nucleus (Potential)	nucleus [TAS]		1Z56	944
P54280 UniProt NPD GO	PMS1_SCHPO	DNA mismatch repair protein pms1	0.89	-	nuc	0					794
Q07864 UniProt NPD GO	DPOE1_HUMAN	DNA polymerase epsilon, catalytic subunit A (EC 2.7.7.7) (DNA polymerase II subunit A)	0.89	+	nuc	0	Nucleus		174762		2286

You are viewing entries 4551 to 4600 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.