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
P62851 UniProt NPD GO	RS25_HUMAN	40S ribosomal protein S25	0.28	+	nuc	0		cytosolic small ribosomal subunit (sensu Eu... [IDA]	180465		125
P62852 UniProt NPD GO	RS25_MOUSE	40S ribosomal protein S25	0.28	+	nuc	0					125
P62853 UniProt NPD GO	RS25_RAT	40S ribosomal protein S25	0.28	+	nuc	0					125
Q6Q311 UniProt NPD GO	RS25_SHEEP	40S ribosomal protein S25	0.28	+	nuc	0					125
Q90YS2 UniProt NPD GO	RS3_ICTPU	40S ribosomal protein S3	0.28	-	mit	0					245
O60128 UniProt NPD GO	RS3_SCHPO	40S ribosomal protein S3	0.28	-	cyt	0					249
Q9NB21 UniProt NPD GO	RS7_CULQU	40S ribosomal protein S7	0.28	-	nuc	0					192
P14132 UniProt NPD GO	RS9_DICDI	40S ribosomal protein S9 (40S ribosomal protein 1024) (Vegetative-specific protein V12)	0.28	-	nuc	0					185
Q29197 UniProt NPD GO	RS9_PIG	40S ribosomal protein S9 (Fragment)	0.28	-	mit	0					130
Q9BRK5 UniProt NPD GO	CAB45_HUMAN	45 kDa calcium-binding protein precursor (Cab45) (Stromal cell-derived factor 4) (SDF-4)	0.28	-	vac	1 *	Golgi apparatus; Golgi lumen (By similarity)				362
Q09137 UniProt NPD GO	AAPK2_RAT	5'-AMP-activated protein kinase catalytic subunit alpha-2 (EC 2.7.11.1) (AMPK alpha-2 chain)	0.28	-	cyt	0		nucleus [TAS]			552
P41595 UniProt NPD GO	5HT2B_HUMAN	5-hydroxytryptamine 2B receptor (5-HT-2B) (Serotonin receptor 2B)	0.28	-	end	7	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	601122		481
Q06036 UniProt NPD GO	RK122_SECCE	50S ribosomal protein L12-2, chloroplast precursor (CL12-2)	0.28	-	mit	0	Plastid; chloroplast				174
P82195 UniProt NPD GO	RK18_SPIOL	50S ribosomal protein L18 alpha/beta, chloroplast (Fragment)	0.28	-	nuc	0	Plastid; chloroplast				29
O65037 UniProt NPD GO	RK27_ORYSA	50S ribosomal protein L27, chloroplast precursor	0.28	-	mit	0	Plastid; chloroplast				195
Q03215 UniProt NPD GO	K6PF1_KLULA	6-phosphofructokinase subunit alpha (EC 2.7.1.11) (Phosphofructokinase 1) (Phosphohexokinase) (6PF-1 ...	0.28	-	cyt	0	Cytoplasm (By similarity)				992
Q60HD9 UniProt NPD GO	K6PF_MACFA	6-phosphofructokinase, muscle type (EC 2.7.1.11) (Phosphofructokinase 1) (Phosphohexokinase) (Phosph ...	0.28	-	cyt	0					779
P47857 UniProt NPD GO	K6PF_MOUSE	6-phosphofructokinase, muscle type (EC 2.7.1.11) (Phosphofructokinase 1) (Phosphohexokinase) (Phosph ...	0.28	-	cyt	0		6-phosphofructokinase complex [ISS]			779
O22540 UniProt NPD GO	RL11_ORYSA	60S ribosomal protein L11	0.28	-	cyt	0	Cytoplasm				182
P26784 UniProt NPD GO	RL16A_YEAST	60S ribosomal protein L16-A (L13A) (RP22)	0.28	-	cyt	0		cytosolic large ribosomal subunit (sensu Eu... [TAS]		1K5Y	198
P47913 UniProt NPD GO	RL20_YEAST	60S ribosomal protein L20 (L18A)	0.28	-	nuc	0		cytosolic large ribosomal subunit (sensu Eu... [TAS]			174
P20280 UniProt NPD GO	RL21_RAT	60S ribosomal protein L21	0.28	-	mit	0					159
P50887 UniProt NPD GO	RL22_DROME	60S ribosomal protein L22	0.28	-	nuc	0					299
P35268 UniProt NPD GO	RL22_HUMAN	60S ribosomal protein L22 (Epstein-Barr virus small RNA-associated protein) (EBER-associated protein ...	0.28	-	nuc	0		cytosolic large ribosomal subunit (sensu Eu... [TAS]	180474		127
O94008 UniProt NPD GO	RL32_CANAL	60S ribosomal protein L32	0.28	-	nuc	0					131
P05745 UniProt NPD GO	RL36A_YEAST	60S ribosomal protein L36-A (L39A) (YL39)	0.28	-	nuc	0		cytosolic large ribosomal subunit (sensu Eu... [TAS]			99
O14455 UniProt NPD GO	RL36B_YEAST	60S ribosomal protein L36-B (L39B) (YL39)	0.28	-	nuc	0		cytosolic large ribosomal subunit (sensu Eu... [TAS]			99
P53368 UniProt NPD GO	8ODP_MOUSE	7,8-dihydro-8-oxoguanine triphosphatase (EC 3.1.6.-) (8-oxo-dGTPase) (Nucleoside diphosphate-linked ...	0.28	-	mit	0					156
P53369 UniProt NPD GO	8ODP_RAT	7,8-dihydro-8-oxoguanine triphosphatase (EC 3.1.6.-) (8-oxo-dGTPase) (Nucleoside diphosphate-linked ...	0.28	-	mit	0					156
Q8N6G6 UniProt NPD GO	ATL1_HUMAN	ADAMTS-like protein 1 precursor (ADAMTSL-1) (Punctin-1)	0.28	-	exc	0	Secreted protein; extracellular space; extracellular matrix		609198		525
Q94177 UniProt NPD GO	ADRL_CAEEL	ADIPOR-like receptor C43G2.1	0.28	-	end	7	Membrane; multi-pass membrane protein (Potential)	integral to membrane [ISS]			434
Q7TN05 UniProt NPD GO	AP1S3_MOUSE	AP-1 complex subunit sigma-3 (Adapter-related protein complex 1 sigma-1C subunit) (Sigma-adaptin 1C) ...	0.28	-	nuc	0	Component of the coat surrounding the cytoplasmic face of coated vesicles located at the Golgi compl ...				154
Q9JKC7 UniProt NPD GO	AP4M1_MOUSE	AP-4 complex subunit mu-1 (Adapter-related protein complex 4 mu-1 subunit) (Mu subunit of AP-4) (AP- ...	0.28	-	nuc	0	Golgi apparatus; trans-Golgi network (By similarity). Associated with the trans-Golgi network. Found ...	Golgi trans face [TAS]			449
P35011 UniProt NPD GO	ATPF_GALSU	ATP synthase B chain (EC 3.6.3.14) (ATPase subunit I)	0.28	-	nuc	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein				176
Q6ENH8 UniProt NPD GO	ATPF_ORYNI	ATP synthase B chain (EC 3.6.3.14) (ATPase subunit I)	0.28	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane				183
P12087 UniProt NPD GO	ATPF_ORYSA	ATP synthase B chain (EC 3.6.3.14) (ATPase subunit I)	0.28	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein				183
O01666 UniProt NPD GO	ATPG_DROME	ATP synthase gamma chain, mitochondrial precursor (EC 3.6.3.14)	0.28	-	mit	0	Mitochondrion				297
Q5RBS9 UniProt NPD GO	ATPG_PONPY	ATP synthase gamma chain, mitochondrial precursor (EC 3.6.3.14)	0.28	-	mit	0	Mitochondrion (By similarity)				297
P05495 UniProt NPD GO	ATPAM_NICPL	ATP synthase subunit alpha, mitochondrial (EC 3.6.3.14)	0.28	-	cyt	0	Mitochondrion				509
P05492 UniProt NPD GO	ATPAM_OENBI	ATP synthase subunit alpha, mitochondrial (EC 3.6.3.14)	0.28	-	cyt	0	Mitochondrion				511
Q63563 UniProt NPD GO	ABCC9_RAT	ATP-binding cassette transporter sub-family C member 9 (Sulfonylurea receptor 2)	0.28	-	end	12 *	Membrane; multi-pass membrane protein (Potential)	ATP-sensitive potassium channel complex [TAS]			1545
P35100 UniProt NPD GO	CLPC_PEA	ATP-dependent Clp protease ATP-binding subunit clpC homolog, chloroplast precursor	0.28	-	mit	0	Plastid; chloroplast				922
Q6BY27 UniProt NPD GO	DBP2_DEBHA	ATP-dependent RNA helicase DBP2 (EC 3.6.1.-)	0.28	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				536
Q6CJU1 UniProt NPD GO	DBP5_KLULA	ATP-dependent RNA helicase DBP5 (EC 3.6.1.-)	0.28	-	cyt	0	Cytoplasm. Nucleus; nuclear envelope; nuclear pore complex; cytoplasmic side. Nuclear pore complex c ...				469
Q8VDW0 UniProt NPD GO	DDX39_MOUSE	ATP-dependent RNA helicase DDX39 (EC 3.6.1.-) (DEAD box protein 39)	0.28	-	cyt	0	Nucleus (By similarity)				427
Q5U216 UniProt NPD GO	DDX39_RAT	ATP-dependent RNA helicase DDX39 (EC 3.6.1.-) (DEAD box protein 39) (Nuclear RNA helicase, DECD vari ...	0.28	-	cyt	0	Nucleus (By similarity)				427
Q59S59 UniProt NPD GO	MRH4_CANAL	ATP-dependent RNA helicase MRH4, mitochondrial precursor (EC 3.6.1.-)	0.28	-	mit	0	Mitochondrion (By similarity)				555
Q6CDV4 UniProt NPD GO	IF4A_YARLI	ATP-dependent RNA helicase eIF4A (EC 3.6.1.-) (Eukaryotic initiation factor 4A) (eIF-4A) (Translatio ...	0.28	-	cyt	0	Cytoplasm (By similarity)				395
O88967 UniProt NPD GO	YMEL1_MOUSE	ATP-dependent metalloprotease YME1L1 (EC 3.4.24.-) (YME1-like protein 1) (ATP-dependent metalloprote ...	0.28	-	mit	0	Mitochondrion (By similarity)				715
P49655 UniProt NPD GO	IRK10_RAT	ATP-sensitive inward rectifier potassium channel 10 (Potassium channel, inwardly rectifying subfamil ...	0.28	-	mit	2	Membrane; multi-pass membrane protein				379

You are viewing entries 41951 to 42000 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.