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
Q8C827 UniProt NPD GO	ZFP62_MOUSE	Zinc finger protein 62 homolog (Zfp-62) (ZT3)	0.48	-	nuc	0	Nucleus (Potential)				914
Q03936 UniProt NPD GO	ZNF92_HUMAN	Zinc finger protein 92 (Zinc finger protein HTF12)	0.48	-	nuc	0	Nucleus (Probable)	nucleus [NAS]	603974		586
O82256 UniProt NPD GO	COL13_ARATH	Zinc finger protein CONSTANS-LIKE 13	0.48	-	nuc	0	Nucleus (Potential)				332
Q02799 UniProt NPD GO	LEE1_YEAST	Zinc finger protein LEE1	0.48	-	nuc	0					301
Q9BH11 UniProt NPD GO	ZP4_BOVIN	Zona pellucida sperm-binding protein 4 precursor (Zona pellucida sperm-binding protein B)	0.48	-	exc	1	Cell membrane; single-pass type I membrane protein. Processed form: Secreted protein; extracellular ...				534
Q5RAG3 UniProt NPD GO	ZYGBL_PONPY	Zyg-11 protein homolog (Zyg-11 homolog B-like)	0.48	-	cyt	0					766
Q7ZY18 UniProt NPD GO	MC6ZB_XENLA	Zygotic DNA replication licensing factor mcm6-B (Zygotic minichromosome maintenance protein 6-B) (zM ...	0.48	-	cyt	0	Nucleus. Associated with chromatin before the formation of nuclei and detaches from it as DNA replic ...	MCM complex [IPI]			825
O02623 UniProt NPD GO	PDK_ASCSU	[Pyruvate dehydrogenase [lipoamide]] kinase, mitochondrial precursor (EC 2.7.11.2) (Pyruvate dehydro ...	0.48	-	mit	0	Mitochondrion; mitochondrial matrix				399
P13861 UniProt NPD GO	KAP2_HUMAN	cAMP-dependent protein kinase type II-alpha regulatory subunit	0.48	-	cyt	0		cytoplasm [TAS] membrane fraction [TAS] plasma membrane [TAS]	176910		403
Q4IPA4 UniProt NPD GO	YTH1_GIBZE	mRNA 3'-end-processing protein YTH1	0.48	-	nuc	0	Nucleus (By similarity)				411
P78587 UniProt NPD GO	MCE1_CANAL	mRNA capping enzyme subunit alpha (mRNA guanylyltransferase) (EC 2.7.7.50) (GTP--RNA guanylyltransfe ...	0.48	-	cyt	0	Nucleus			1P16	449
Q754G2 UniProt NPD GO	PALF_ASHGO	pH-response regulator protein palF/RIM8	0.48	-	nuc	0					548
Q6FJT9 UniProt NPD GO	PALH_CANGA	pH-response regulator protein palH/RIM21	0.48	-	end	7	Cell membrane; multi-pass membrane protein (By similarity)				539
Q7SFN5 UniProt NPD GO	PALI_NEUCR	pH-response regulator protein palI/rim-9	0.48	-	nuc	5 *	Cell membrane; multi-pass membrane protein (By similarity)				705
O94396 UniProt NPD GO	PUS1_SCHPO	tRNA pseudouridine synthase 1 (EC 5.4.99.-) (tRNA-uridine isomerase 1) (tRNA pseudouridylate synthas ...	0.48	-	nuc	0	Nucleus	nucleus [IGI]			534
Q6B8L1 UniProt NPD GO	TILS_GRATL	tRNA(Ile)-lysidine synthase (EC 6.3.4.-) (tRNA(Ile)-lysidine synthetase) (tRNA(Ile)-2-lysyl-cytidine ...	0.48	-	nuc	0	Plastid; chloroplast				320
P23614 UniProt NPD GO	CP23_CHICK	23 kDa cortical cytoskeleton-associated protein (CAP-23)	0.47	-	nuc	0	Cytoskeleton. Cortical cytoskeleton	cortical cytoskeleton [TAS] cytoplasm [IDA] extrinsic to internal side of plasma membrane [IDA] growth cone [IDA] nucleus [IDA]			208
P53549 UniProt NPD GO	PRS10_YEAST	26S protease subunit RPT4 (26S protease subunit SUG2) (Proteasomal cap subunit)	0.47	-	cyt	0		nucleus [IDA] proteasome regulatory particle, base subcom... [IDA]			436
P59223 UniProt NPD GO	RS13A_ARATH	40S ribosomal protein S13-1	0.47	-	mit	0					151
P59224 UniProt NPD GO	RS13B_ARATH	40S ribosomal protein S13-2	0.47	-	mit	0					151
P30742 UniProt NPD GO	RS26_CRICR	40S ribosomal protein S26	0.47	-	nuc	0					114
Q9UT56 UniProt NPD GO	RS26A_SCHPO	40S ribosomal protein S26-A	0.47	-	nuc	0					120
O43105 UniProt NPD GO	RS7_NEUCR	40S ribosomal protein S7	0.47	-	nuc	0					202
P05755 UniProt NPD GO	RS9B_YEAST	40S ribosomal protein S9-B (S13) (YS11) (RP21) (YP28)	0.47	-	nuc	0		cytosolic small ribosomal subunit (sensu Eu... [TAS] small nucleolar ribonucleoprotein complex [IPI]			194
P54645 UniProt NPD GO	AAPK1_RAT	5'-AMP-activated protein kinase catalytic subunit alpha-1 (EC 2.7.11.1) (AMPK alpha-1 chain)	0.47	-	nuc	0		intracellular [ISS]			548
Q9H857 UniProt NPD GO	NT5D2_HUMAN	5'-nucleotidase domain-containing protein 2	0.47	-	cyt	0					520
Q6PC69 UniProt NPD GO	RL10A_BRARE	60S ribosomal protein L10a	0.47	+	nuc	0					216
Q90YV8 UniProt NPD GO	RL10A_ICTPU	60S ribosomal protein L10a	0.47	-	nuc	0					216
P42922 UniProt NPD GO	RL11_LEICH	60S ribosomal protein L11	0.47	+	cyt	0					188
P51417 UniProt NPD GO	RL15_CHICK	60S ribosomal protein L15 (L10) (Fragment)	0.47	-	mit	0					165
P47832 UniProt NPD GO	RL26_CHICK	60S ribosomal protein L26 (Fragment)	0.47	-	nuc	0					128
Q92901 UniProt NPD GO	RL3L_HUMAN	60S ribosomal protein L3-like	0.47	-	mit	0		ribosome [TAS]			406
O42846 UniProt NPD GO	RL34A_SCHPO	60S ribosomal protein L34-A	0.47	-	mit	0					112
Q9URT8 UniProt NPD GO	RL34B_SCHPO	60S ribosomal protein L34-B (60S ribosomal protein L34-2)	0.47	-	mit	0					111
Q6CW22 UniProt NPD GO	RL39_KLULA	60S ribosomal protein L39	0.47	-	mit	0					50
P14794 UniProt NPD GO	RL40_DICDI	60S ribosomal protein L40 (CEP52)	0.47	-	nuc	0					52
P52809 UniProt NPD GO	RL44_PICJA	60S ribosomal protein L44 (60S ribosomal protein L41)	0.47	-	nuc	0					105
P40858 UniProt NPD GO	RN49_YEAST	60S ribosomal protein L49, mitochondrial precursor (YmL49)	0.47	-	mit	0	Mitochondrion	mitochondrial large ribosomal subunit [IPI]			161
P46223 UniProt NPD GO	RL7A_DROME	60S ribosomal protein L7a	0.47	-	nuc	0					271
P97793 UniProt NPD GO	ALK_MOUSE	ALK tyrosine kinase receptor precursor (EC 2.7.10.1) (Anaplastic lymphoma kinase) (CD246 antigen)	0.47	-	end	0	Membrane; single-pass type I membrane protein (Probable)				1621
O75843 UniProt NPD GO	AP1G2_HUMAN	AP-1 complex subunit gamma-2 (Adapter-related protein complex 1 gamma-2 subunit) (Gamma2-adaptin) (A ...	0.47	-	nuc	0	Component of the coat surrounding the cytoplasmic face of coated vesicles located at the Golgi compl ...	AP-1 adaptor complex [TAS] Golgi apparatus [TAS] Golgi-associated vesicle [IDA] membrane [IDA] transport vesicle [IDA]	603534		785
P18484 UniProt NPD GO	AP2A2_RAT	AP-2 complex subunit alpha-2 (Adapter-related protein complex 2 alpha-2 subunit) (Alpha-adaptin C) ( ...	0.47	-	cyt	0	Component of the coat surrounding the cytoplasmic face of coated vesicles in the plasma membrane			1W80	937
Q8R420 UniProt NPD GO	ABCA3_MOUSE	ATP-binding cassette sub-family A member 3	0.47	-	end	9 *					1704
Q4GZT4 UniProt NPD GO	ABCG2_BOVIN	ATP-binding cassette sub-family G member 2	0.47	-	end	6	Cell membrane; multi-pass membrane protein				655
Q8MIB3 UniProt NPD GO	ABCG2_PIG	ATP-binding cassette sub-family G member 2 (Brain multidrug resistance protein)	0.47	-	end	5	Cell membrane; multi-pass membrane protein (By similarity)				656
Q6BZR4 UniProt NPD GO	DBP9_YARLI	ATP-dependent RNA helicase DBP9 (EC 3.6.1.-)	0.47	+	nuc	0	Nucleus; nucleolus (By similarity)				544
Q5KJI2 UniProt NPD GO	DHH1_CRYNE	ATP-dependent RNA helicase DHH1 (EC 3.6.1.-)	0.47	-	nuc	0	Cytoplasm. Is concentrated in several cytoplasmic foci called P bodies (or cytoplasmic processing bo ...				625
Q6CSZ7 UniProt NPD GO	DHH1_KLULA	ATP-dependent RNA helicase DHH1 (EC 3.6.1.-)	0.47	-	nuc	0	Cytoplasm. Is concentrated in several cytoplasmic foci called P bodies (or cytoplasmic processing bo ...				514
P39517 UniProt NPD GO	DHH1_YEAST	ATP-dependent RNA helicase DHH1 (EC 3.6.1.-) (DExD/H-box helicase 1)	0.47	-	nuc	0	Cytoplasm. Is concentrated in several cytoplasmic foci called P bodies (or cytoplasmic processing bo ...	cytoplasm [IDA] cytoplasmic mRNA processing body [IDA]		1S2M	506
Q6FJJ8 UniProt NPD GO	MRH4_CANGA	ATP-dependent RNA helicase MRH4, mitochondrial precursor (EC 3.6.1.-)	0.47	-	nuc	0	Mitochondrion (By similarity)				568

You are viewing entries 26701 to 26750 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.