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
P31319 UniProt NPD GO	KAPR_APLCA	cAMP-dependent protein kinase regulatory subunit (N4 subunit of protein kinase A)	0.45	-	cyt	0					377
P12367 UniProt NPD GO	KAP2_MOUSE	cAMP-dependent protein kinase type II-alpha regulatory subunit	0.45	-	cyt	0				1R2A	400
Q524Z5 UniProt NPD GO	PALC_MAGGR	pH-response regulator protein palC	0.45	-	nuc	0					507
Q6CTM7 UniProt NPD GO	PALF_KLULA	pH-response regulator protein palF/RIM8	0.45	-	nuc	0					572
Q8R2K7 UniProt NPD GO	SNPC5_MOUSE	snRNA-activating protein complex subunit 5 (SNAPc subunit 5) (snRNA-activating protein complex 19 kD ...	0.45	-	nuc	0	Nucleus (By similarity)				98
P41814 UniProt NPD GO	TRM6_YEAST	tRNA (adenine-N(1)-)-methyltransferase non-catalytic subunit TRM6 (tRNA(m1A58)-methyltransferase sub ...	0.45	-	nuc	0	Nucleus	nucleus [IDA]			478
Q6C1W9 UniProt NPD GO	TRM10_YARLI	tRNA (guanine-N(1)-)-methyltransferase (EC 2.1.1.31) (tRNA methyltransferase 10)	0.45	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				371
Q9BSV6 UniProt NPD GO	SEN34_HUMAN	tRNA-splicing endonuclease subunit Sen34 (EC 3.1.27.9) (tRNA-intron endonuclease Sen34) (HsSen34) (L ...	0.45	-	nuc	0	Nucleus. Nucleus; nucleolus. May be transiently localized in the nucleolus		608754		310
Q10287 UniProt NPD GO	BGS1_SCHPO	1,3-beta-glucan synthase component bgs1 (EC 2.4.1.34) (1,3-beta-D-glucan-UDP glucosyltransferase)	0.44	-	end	13	Membrane; multi-pass membrane protein (Potential)	cell septum surface [IDA]			1729
Q9XF62 UniProt NPD GO	DIP13_CHLRE	13 kDa deflagellation-inducible protein	0.44	-	nuc	0	Nucleus				111
O96436 UniProt NPD GO	1433_EIMTE	14-3-3 protein	0.44	-	nuc	0					277
P26203 UniProt NPD GO	P15B_RABIT	15 kDa protein B precursor (Protein P15B) (P15H)	0.44	-	vac	1 *	Secreted protein				137
Q29599 UniProt NPD GO	OAS1_PIG	2'-5'-oligoadenylate synthetase 1 (EC 2.7.7.-) ((2-5')oligo(A) synthetase 1) (2-5A synthetase 1) (p4 ...	0.44	-	nuc	0	Mitochondrion (By similarity). Nucleus (By similarity). Microsome (By similarity). Associated with d ...			1PX5	349
Q60597 UniProt NPD GO	ODO1_MOUSE	2-oxoglutarate dehydrogenase E1 component, mitochondrial precursor (EC 1.2.4.2) (Alpha-ketoglutarate ...	0.44	-	mit	0	Mitochondrion; mitochondrial matrix	mitochondrion [IDA]			1019
Q39604 UniProt NPD GO	IDLC_CHLRE	28 kDa inner dynein arm light chain, axonemal (p28)	0.44	-	nuc	0	Present along the entire length of the axoneme				253
Q8BJZ4 UniProt NPD GO	RT35_MOUSE	28S ribosomal protein S35, mitochondrial precursor (S35mt) (MRP-S35)	0.44	-	mit	0	Mitochondrion (By similarity)	mitochondrial small ribosomal subunit [ISS]			320
Q9H9J2 UniProt NPD GO	RM44_HUMAN	39S ribosomal protein L44, mitochondrial precursor (EC 3.1.26.-) (L44mt) (MRP-L44)	0.44	-	mit	0	Mitochondrion				332
Q9CY73 UniProt NPD GO	RM44_MOUSE	39S ribosomal protein L44, mitochondrial precursor (EC 3.1.26.-) (L44mt) (MRP-L44)	0.44	-	mit	0	Mitochondrion (By similarity)				333
P51404 UniProt NPD GO	RS13_CAEEL	40S ribosomal protein S13	0.44	-	nuc	0					150
P62299 UniProt NPD GO	RS13_BRUPA	40S ribosomal protein S13 (17.4K protein)	0.44	-	nuc	0					150
P62300 UniProt NPD GO	RS13_WUCBA	40S ribosomal protein S13 (40S ribosomal protein S15)	0.44	-	nuc	0					150
P31674 UniProt NPD GO	RS15_ORYSA	40S ribosomal protein S15	0.44	-	cyt	0					154
Q22054 UniProt NPD GO	RS16_CAEEL	40S ribosomal protein S16	0.44	-	cyt	0					143
O64650 UniProt NPD GO	RS27A_ARATH	40S ribosomal protein S27-1	0.44	-	nuc	0		cytosolic ribosome (sensu Eukaryota) [IDA]			84
P37165 UniProt NPD GO	RS27A_CAEEL	40S ribosomal protein S27a	0.44	+	nuc	0					93
P0C016 UniProt NPD GO	RS27A_SCHPO	40S ribosomal protein S27a	0.44	+	nuc	0					74
O94438 UniProt NPD GO	RS3B_SCHPO	40S ribosomal protein S3aE-B (S1-A)	0.44	-	nuc	0					251
Q8VCE6 UniProt NPD GO	NT5M_MOUSE	5'(3')-deoxyribonucleotidase, mitochondrial precursor (EC 3.1.3.-) (5',3'-nucleotidase, mitochondria ...	0.44	-	mit	0	Mitochondrion (By similarity)				220
P49145 UniProt NPD GO	5HT1D_RABIT	5-hydroxytryptamine 1D receptor (5-HT-1D) (Serotonin receptor 1D) (5-HT-1D-alpha)	0.44	-	end	7 *	Membrane; multi-pass membrane protein				377
P30155 UniProt NPD GO	RK27_TOBAC	50S ribosomal protein L27, chloroplast precursor (CL27)	0.44	-	nuc	0	Plastid; chloroplast				179
P49872 UniProt NPD GO	F261_BOVIN	6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 1 (6PF-2-K/Fru-2,6-P2ASE liver isozyme) [Include ...	0.44	-	cyt	0		6-phosphofructo-2-kinase/fructose-2,6-bipho... [ISS]			471
Q7ZYS8 UniProt NPD GO	RL10A_XENLA	60S ribosomal protein L10a	0.44	+	nuc	0					217
Q92366 UniProt NPD GO	RL29_SCHPO	60S ribosomal protein L29 (L43)	0.44	-	nuc	0					60
P17094 UniProt NPD GO	RL31_ARATH	60S ribosomal protein L3-1 (Protein EMBRYO DEFECTIVE 2207)	0.44	-	nuc	0	Cytoplasm				388
Q9U332 UniProt NPD GO	RL31_CAEEL	60S ribosomal protein L31	0.44	-	nuc	0					122
P14063 UniProt NPD GO	RM31_YEAST	60S ribosomal protein L31, mitochondrial precursor (YmL31)	0.44	-	nuc	0	Mitochondrion	mitochondrial large ribosomal subunit [IPI]			131
Q90YT6 UniProt NPD GO	RL32_ICTPU	60S ribosomal protein L32	0.44	-	nuc	0					135
P40525 UniProt NPD GO	RL34B_YEAST	60S ribosomal protein L34-B	0.44	-	mit	0		cytosolic large ribosomal subunit (sensu Eu... [TAS]			121
Q06678 UniProt NPD GO	RM35_YEAST	60S ribosomal protein L35, mitochondrial precursor (YmL35)	0.44	-	mit	0	Mitochondrion	mitochondrial large ribosomal subunit [IPI]			367
P32429 UniProt NPD GO	RL7A_CHICK	60S ribosomal protein L7a	0.44	-	nuc	0					265
Q8LPK0 UniProt NPD GO	ATH7_ARATH	ABC2 homolog 7	0.44	-	end	7 *	Membrane; multi-pass membrane protein (Potential)				901
Q3T0M9 UniProt NPD GO	ARL4A_BOVIN	ADP-ribosylation factor-like protein 4A	0.44	+	mit	0	Nucleus (By similarity)				200
P40617 UniProt NPD GO	ARL4A_HUMAN	ADP-ribosylation factor-like protein 4A	0.44	+	mit	0	Nucleus	nucleus [TAS]	604786		200
P61213 UniProt NPD GO	ARL4A_MOUSE	ADP-ribosylation factor-like protein 4A	0.44	+	mit	0	Nucleus (By similarity)				200
P61214 UniProt NPD GO	ARL4A_RAT	ADP-ribosylation factor-like protein 4A	0.44	+	mit	0	Nucleus (By similarity)				200
Q99P81 UniProt NPD GO	ABCG3_MOUSE	ATP-binding cassette sub-family G member 3	0.44	+	end	5	Membrane; multi-pass membrane protein (Probable)				650
Q9H221 UniProt NPD GO	ABCG8_HUMAN	ATP-binding cassette sub-family G member 8 (Sterolin-2)	0.44	-	end	5	Membrane; multi-pass membrane protein (Probable)		605460		673
Q9DBM0 UniProt NPD GO	ABCG8_MOUSE	ATP-binding cassette sub-family G member 8 (Sterolin-2)	0.44	-	end	6	Membrane; multi-pass membrane protein (Probable)				673
Q09428 UniProt NPD GO	ABCC8_HUMAN	ATP-binding cassette transporter sub-family C member 8 (Sulfonylurea receptor 1)	0.44	-	end	16 *	Membrane; multi-pass membrane protein		602485		1580
P20449 UniProt NPD GO	DBP5_YEAST	ATP-dependent RNA helicase DBP5 (EC 3.6.1.-) (DEAD box protein 5) (Helicase CA5/6) (Ribonucleic acid ...	0.44	-	cyt	0	Cytoplasm. Nucleus; nuclear envelope; nuclear pore complex; cytoplasmic side. Nuclear pore complex c ...	cytoplasm [IDA] nuclear pore [IPI] nucleus [IDA]			482

You are viewing entries 28751 to 28800 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.