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
P38789 UniProt NPD GO	SSF1_YEAST	Ribosome biogenesis protein SSF1	0.97	+	nuc	0	Nucleus; nucleolus	nucleolus [IDA]			453
Q12153 UniProt NPD GO	SSF2_YEAST	Ribosome biogenesis protein SSF2	0.97	+	nuc	0	Nucleus; nucleolus	nucleolus [IDA]			453
Q9QX47 UniProt NPD GO	SON_MOUSE	SON protein	0.97	+	nuc	0	Nucleus (By similarity)				2404
P18583 UniProt NPD GO	SON_HUMAN	SON protein (SON3) (Negative regulatory element-binding protein) (NRE-binding protein) (DBP-5) (Bax ...	0.97	+	nuc	0	Nucleus; nucleoplasm; nuclear speckle		182465		2426
Q9H4L7 UniProt NPD GO	SMRCD_HUMAN	SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A containing DEAD ...	0.97	+	nuc	0	Nucleus (By similarity)	nuclear matrix [NAS]			1026
Q6STE5 UniProt NPD GO	SMRD3_HUMAN	SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 3 (60 kD ...	0.97	-	nuc	0	Nucleus	nucleoplasm [TAS] nucleus [IDA] SWI/SNF complex [NAS]	601737		483
Q6P9Z1 UniProt NPD GO	SMRD3_MOUSE	SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 3 (60 kD ...	0.97	-	nuc	0	Nucleus (By similarity)				483
Q870Q1 UniProt NPD GO	SWC4_NEUCR	SWR1-complex protein 4	0.97	-	nuc	0	Nucleus (By similarity)				771
P53201 UniProt NPD GO	SWC4_YEAST	SWR1-complex protein 4 (ESA1-associated factor 2)	0.97	+	nuc	0	Nucleus	H4/H2A histone acetyltransferase complex [IPI] nucleus [IDA] SWR1 complex [IPI]			476
O95171 UniProt NPD GO	SCEL_HUMAN	Sciellin	0.97	-	nuc	0	Cytoplasm. Membrane. May become cross-linked to membrane proteins by transglutaminase	cornified envelope [TAS] cytoplasm [IDA]	604112		668
Q9EQG3 UniProt NPD GO	SCEL_MOUSE	Sciellin	0.97	-	nuc	0	Cytoplasm. Membrane. May become cross-linked to membrane proteins by transglutaminase	cornified envelope [ISS] cytoplasm [IDA]			652
O35314 UniProt NPD GO	SCG1_RAT	Secretogranin-1 precursor (Secretogranin-I) (SgI) (Chromogranin B) (CgB) (Glucagonoma peptide) [Cont ...	0.97	-	exc	0	Neuroendocrine and endocrine secretory granules (By similarity)	secretory granule [IDA]			675
Q9VYB0 UniProt NPD GO	BTHD_DROME	Selenoprotein BthD precursor (dSelM)	0.97	+	nuc	0	Cytoplasm. Secreted protein; salivary gland lumen	cytoplasm [IDA]			249
Q04172 UniProt NPD GO	SHE9_YEAST	Sensitive to high expression protein 9, mitochondrial precursor (Mitochondrial distribution and morp ...	0.97	-	end	1	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein	mitochondrial inner membrane [IDA]			456
Q03018 UniProt NPD GO	ESP1_YEAST	Separin (EC 3.4.22.49) (Separase)	0.97	+	nuc	0	Nucleus. Cytoplasm. Accumulates in the nucleus in G2 and is mobilized onto the spindle pole bodies a ...	cytoplasm [IDA] mitochondrion [IDA] nucleus [IDA] spindle [IDA]			1630
Q6PQD5 UniProt NPD GO	ATM_PIG	Serine-protein kinase ATM (EC 2.7.11.1) (Ataxia telangiectasia mutated homolog) (A-T, mutated homolo ...	0.97	-	end	0	Nucleus (By similarity). Cytoplasmic vesicle (By similarity). Primarily nuclear. Found also in endoc ...				3056
Q6BV06 UniProt NPD GO	BUR1_DEBHA	Serine/threonine-protein kinase BUR1 (EC 2.7.11.22) (EC 2.7.11.23)	0.97	-	nuc	0	Nucleus (By similarity)				608
Q5VT25 UniProt NPD GO	MRCKA_HUMAN	Serine/threonine-protein kinase MRCK alpha (EC 2.7.11.1) (CDC42-binding protein kinase alpha) (Myoto ...	0.97	+	nuc	0	Cytoplasm (By similarity). Displays a dispersed punctate distribution and concentrates along the cel ...	intercellular junction [ISS] leading edge [ISS]	603412		1732
Q9NQU5 UniProt NPD GO	PAK6_HUMAN	Serine/threonine-protein kinase PAK 6 (EC 2.7.11.1) (p21-activated kinase 6) (PAK-6) (PAK-5)	0.97	+	nuc	0			608110	2C30	681
Q6ZQ29 UniProt NPD GO	TAOK2_MOUSE	Serine/threonine-protein kinase TAO2 (EC 2.7.11.1) (Thousand and one amino acid protein 2)	0.97	-	nuc	0	Cytoplasm; perinuclear region (By similarity). Cytoplasmic vesicle (By similarity). Found to be peri ...				1055
Q6GPK9 UniProt NPD GO	TAOK2_XENLA	Serine/threonine-protein kinase TAO2 (EC 2.7.11.1) (Thousand and one amino acid protein 2)	0.97	-	nuc	0					1025
Q86UE8 UniProt NPD GO	TLK2_HUMAN	Serine/threonine-protein kinase tousled-like 2 (EC 2.7.11.1) (Tousled-like kinase 2) (PKU-alpha)	0.97	-	nuc	0	Nucleus	nucleus [IEP]	608439		772
P34709 UniProt NPD GO	TRA2_CAEEL	Sex-determining transformer protein 2 precursor (Ce-Tra-2)	0.97	-	end	10 *	Membrane; multi-pass membrane protein	integral to membrane [IDA]			1475
Q759Q5 UniProt NPD GO	SGO1_ASHGO	Shugoshin	0.97	-	nuc	0	Nucleus (By similarity). Localizes to the centromere (By similarity)				648
Q9CXH7 UniProt NPD GO	SGOL1_MOUSE	Shugoshin-like 1	0.97	+	nuc	0	Nucleus (By similarity). Localizes to the centromere. BUB1 is required for centromeric localization. ...				517
P49965 UniProt NPD GO	SRP72_SCHMA	Signal recognition particle 72 kDa protein (SRP72)	0.97	-	nuc	0	Cytoplasm				707
P91240 UniProt NPD GO	SRP72_CAEEL	Signal recognition particle 72 kDa protein homolog (SRP72)	0.97	-	nuc	0	Cytoplasm				694
O43166 UniProt NPD GO	SI1L1_HUMAN	Signal-induced proliferation-associated 1-like protein 1 (High-risk human papilloma viruses E6 oncop ...	0.97	-	nuc	0					1803
Q9FQ20 UniProt NPD GO	SCC12_ARATH	Sister chromatid cohesion 1 protein 2 (SCC1 homolog 2) (AtRAD21-1)	0.97	-	nuc	0	Nucleus				810
Q9FQ19 UniProt NPD GO	SCC13_ARATH	Sister chromatid cohesion 1 protein 3 (SCC1 homolog 3) (AtRAD21-2)	0.97	+	nuc	0	Nucleus				693
Q02384 UniProt NPD GO	SOS2_MOUSE	Son of sevenless homolog 2 (SOS-2) (mSOS-2) (Fragment)	0.97	+	nuc	0					1297
Q5XG21 UniProt NPD GO	CCA5B_XENLA	Sororin-B (Cell division cycle-associated protein 5-B)	0.97	-	nuc	0	Nucleus (By similarity)				275
P91870 UniProt NPD GO	SPD2_CAEEL	Spindle-defective protein 2	0.97	-	nuc	0	Centrosome. Component of the centrosome. Localizes to the centriole throughout the cell cycle and ac ...	centriole [IDA] pericentriolar material [IDA]			824
Q05519 UniProt NPD GO	SFR11_HUMAN	Splicing factor arginine/serine-rich 11 (Arginine-rich 54 kDa nuclear protein) (p54)	0.97	+	nuc	0	Nucleus. Colocalizes with spliceosome components	nucleus [TAS]	602010		484
Q12872 UniProt NPD GO	SFRS8_HUMAN	Splicing factor, arginine/serine-rich 8 (Suppressor of white apricot protein homolog)	0.97	+	nuc	0	Nucleus (Potential)		601945		951
Q9S7P5 UniProt NPD GO	SPL12_ARATH	Squamosa promoter-binding-like protein 12	0.97	+	nuc	1	Nucleus (Probable)			1WJ0	927
Q8RY95 UniProt NPD GO	SPL14_ARATH	Squamosa promoter-binding-like protein 14 (SPL1-related protein 2)	0.97	-	nuc	1	Nucleus (Probable)				1035
Q700C2 UniProt NPD GO	SPL16_ARATH	Squamosa promoter-binding-like protein 16 (SPL1-related protein 3)	0.97	+	nuc	1	Nucleus (Probable)				988
O17582 UniProt NPD GO	SPR4_CAEEL	Suppressor of presenilin protein 4	0.97	+	nuc	0	Nucleus (Probable)				1311
Q9I8B0 UniProt NPD GO	SURF6_XENLA	Surfeit locus protein 6 homolog	0.97	+	nuc	0	Nucleus; nucleolus (By similarity)				341
Q03410 UniProt NPD GO	SYCP1_RAT	Synaptonemal complex protein 1 (SCP-1)	0.97	+	nuc	0	Nucleus. In tripartite segments of synaptonemal complexes, between lateral elements in the nucleus. ...				997
Q9HCH5 UniProt NPD GO	SYTL2_HUMAN	Synaptotagmin-like protein 2 (Exophilin-4)	0.97	-	nuc	0	Intracytoplasmic membrane; peripheral membrane protein (By similarity). Bound to melanosomes (By sim ...	extrinsic to plasma membrane [ISS] melanosome [ISS] membrane fraction [ISS]			895
Q13009 UniProt NPD GO	TIAM1_HUMAN	T-lymphoma invasion and metastasis-inducing protein 1 (TIAM-1 protein)	0.97	-	nuc	0			600687		1591
O13339 UniProt NPD GO	TERT_SCHPO	Telomerase reverse transcriptase (EC 2.7.7.49) (Telomerase catalytic subunit)	0.97	+	nuc	0	Nucleus				988
O77448 UniProt NPD GO	TERT_TETTH	Telomerase reverse transcriptase (EC 2.7.7.49) (Telomerase catalytic subunit) (Telomerase subunit P1 ...	0.97	-	nuc	0	Nucleus			2B2A	1117
Q7M6U3 UniProt NPD GO	TEX14_MOUSE	Testis-expressed protein 14 (Testis-expressed sequence 14)	0.97	-	nuc	0	Cytoplasm. Detected in the intercellular bridges that connect male germ cell daughter cells after ce ...				1450
O42668 UniProt NPD GO	TPR1_SCHPO	Tetratricopeptide repeat protein 1	0.97	-	nuc	0					1039
Q96N46 UniProt NPD GO	TTC14_HUMAN	Tetratricopeptide repeat protein 14 (TPR repeat protein 14)	0.97	+	nuc	0					770
Q15643 UniProt NPD GO	TRIPB_HUMAN	Thyroid receptor-interacting protein 11 (TRIP-11) (Golgi-associated microtubule-binding protein 210) ...	0.97	-	nuc	0	Golgi apparatus; cis-Golgi network; cis-Golgi network membrane; peripheral membrane protein. Associa ...		604505		1979
Q6GL68 UniProt NPD GO	TF7L1_XENTR	Transcription factor 7-like 1 (HMG box transcription factor 3) (TCF-3)	0.97	+	nuc	0	Nucleus (By similarity)				553

You are viewing entries 1201 to 1250 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.