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
Q9NZ71 UniProt NPD GO	RTEL1_HUMAN	Regulator of telomere elongation helicase 1 (EC 3.6.1.-) (Helicase-like protein NHL)	0.71	+	nuc	0	Nucleus (Potential)				1400
P87323 UniProt NPD GO	MCS4_SCHPO	Response regulator mcs4 (Mitotic catastrophe suppressor 4)	0.71	-	nuc	0	Cytoplasm (Potential)				522
P10405 UniProt NPD GO	GAGY_DROME	Retrovirus-related Gag polyprotein from transposon gypsy	0.71	-	nuc	0					451
O94989 UniProt NPD GO	ARHGF_HUMAN	Rho guanine nucleotide exchange factor 15 (Vsm-RhoGEF)	0.71	-	nuc	0			608504		841
Q7TPD6 UniProt NPD GO	RAVR2_MOUSE	Ribonucleoprotein PTB-binding 2 (Protein raver-2)	0.71	-	nuc	0	Nucleus. Cytoplasm. May shuttle between the nucleus and the cytoplasm	nucleus [IDA]			673
Q80W87 UniProt NPD GO	ROBO4_RAT	Roundabout homolog 4 precursor	0.71	-	nuc	0					961
P30283 UniProt NPD GO	CGS5_YEAST	S-phase entry cyclin-5	0.71	-	nuc	0		nucleus [IDA]			435
Q9QZS8 UniProt NPD GO	SH2D3_MOUSE	SH2 domain-containing protein 3C (SH2 domain-containing Eph receptor-binding protein 1) (Cas/HEF1-as ...	0.71	-	nuc	0	Cytoplasm. Membrane; peripheral membrane protein. Associated with the membrane when EGF-stimulated. ...				854
Q99469 UniProt NPD GO	STAC_HUMAN	SH3 and cysteine-rich domain-containing protein (SRC homology 3 and cysteine-rich domain protein)	0.71	-	nuc	0	Cytoplasm	soluble fraction [TAS]	602317		402
Q810C0 UniProt NPD GO	SLIK2_MOUSE	SLIT and NTRK-like protein 2 precursor	0.71	-	end	1	Membrane; single-pass membrane protein (Potential)				846
P23499 UniProt NPD GO	SPRL1_COTJA	SPARC-like protein 1 precursor (QR1 protein)	0.71	-	exc	0	Secreted protein (Potential)				676
P40654 UniProt NPD GO	LG27_EUBMA	SRY-related protein LG27 (Fragment)	0.71	-	nuc	0	Nucleus (Potential)				71
O94864 UniProt NPD GO	ST65G_HUMAN	STAGA complex 65 subunit gamma (STAF65gamma) (SPTF-associated factor 65 gamma) (Suppressor of Ty 7-l ...	0.71	-	nuc	0	Nucleus	nucleus [NAS]			414
Q6GQ82 UniProt NPD GO	SNF5_XENLA	SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1	0.71	-	nuc	0	Nucleus (By similarity)				378
P40316 UniProt NPD GO	SECU_YEAST	Securin	0.71	-	nuc	0	Cytoplasm. Nucleus	nucleus [IDA] spindle [IDA]			373
Q9BCZ4 UniProt NPD GO	SELS_MOUSE	Selenoprotein S (VCP-interacting membrane protein) (Minor histocompatibility antigen H47)	0.71	-	nuc	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass membrane protein (By similarity)				190
Q8CHH9 UniProt NPD GO	SEPT8_MOUSE	Septin-8	0.71	-	mit	0					428
Q5Z987 UniProt NPD GO	ATR_ORYSA	Serine/threonine-protein kinase ATR (EC 2.7.11.1)	0.71	-	end	0	Nucleus (Probable)				2710
Q9FKS4 UniProt NPD GO	ATR_ARATH	Serine/threonine-protein kinase ATR (EC 2.7.11.1) (DNA-repair protein ATR) (AtATR) (Ataxia telangiec ...	0.71	+	end	0	Nucleus (Probable)				2702
Q9ZPS9 UniProt NPD GO	BRL2_ARATH	Serine/threonine-protein kinase BRI1-like 2 precursor (EC 2.7.11.1) (BRASSINOSTEROID INSENSITIVE 1-l ...	0.71	-	nuc	1	Cell membrane; single-pass type I membrane protein				1143
P23293 UniProt NPD GO	BUR1_YEAST	Serine/threonine-protein kinase BUR1 (EC 2.7.11.22) (EC 2.7.11.23) (Suppressor of GPA1-Vall50 mutati ...	0.71	-	nuc	0	Nucleus	nucleus [IPI]			657
P84199 UniProt NPD GO	NEK1_CAEEL	Serine/threonine-protein kinase D1044.8 (EC 2.7.11.1)	0.71	-	nuc	0					959
Q9JLM8 UniProt NPD GO	DCAK1_MOUSE	Serine/threonine-protein kinase DCAMKL1 (EC 2.7.11.1) (Doublecortin-like and CAM kinase-like 1)	0.71	-	nuc	0					756
Q7TSJ6 UniProt NPD GO	LATS2_MOUSE	Serine/threonine-protein kinase LATS2 (EC 2.7.11.1) (Large tumor suppressor homolog 2) (Serine/threo ...	0.71	-	nuc	0	Centrosome. Cytoplasm. Co-localizes with STK6 at the centrosomes during interphase, early prophase a ...	spindle pole [IDA]		2COS	1042
Q8NG66 UniProt NPD GO	NEK11_HUMAN	Serine/threonine-protein kinase Nek11 (EC 2.7.11.1) (NimA-related protein kinase 11) (Never in mitos ...	0.71	-	nuc	0	Nucleus. Nucleus; nucleolus. Nuclear during interphase but moves to the polar microtubules during pr ...	nucleolus [IDA]	609779		645
O88643 UniProt NPD GO	PAK1_MOUSE	Serine/threonine-protein kinase PAK 1 (EC 2.7.11.1) (p21-activated kinase 1) (PAK-1) (P65-PAK) (Alph ...	0.71	+	nuc	0		axon [IDA] cytoplasm [IDA] focal adhesion [TAS] growth cone [IDA] nucleus [IDA]			545
P22216 UniProt NPD GO	RAD53_YEAST	Serine/threonine-protein kinase RAD53 (EC 2.7.11.1) (Serine-protein kinase 1)	0.71	-	nuc	0	Nucleus	nucleus [IDA]		2A0T	821
P49657 UniProt NPD GO	MNB_DROME	Serine/threonine-protein kinase minibrain (EC 2.7.12.1)	0.71	+	nuc	0	Nucleus (Potential)				908
P36876 UniProt NPD GO	2ABA_RAT	Serine/threonine-protein phosphatase 2A 55 kDa regulatory subunit B alpha isoform (PP2A, subunit B, ...	0.71	-	nuc	0					447
Q7SEF9 UniProt NPD GO	PTPA2_NEUCR	Serine/threonine-protein phosphatase 2A activator 2 (EC 5.2.1.8) (Peptidyl-prolyl cis-trans isomeras ...	0.71	+	cyt	0	Cytoplasm (By similarity)				449
Q66H98 UniProt NPD GO	SDPR_RAT	Serum deprivation-response protein (Phosphatidylserine-binding protein)	0.71	-	nuc	0	Cytoplasm; cytosol (By similarity). Colocalizes with CAV1 to caveolae	cytosol [ISS]			416
P34691 UniProt NPD GO	FEM3_CAEEL	Sex-determination protein fem-3 (Feminization of XX and XO animals protein 3) (Ce-FEM-3)	0.71	-	nuc	0					388
P52633 UniProt NPD GO	STAT6_MOUSE	Signal transducer and transcription activator 6	0.71	-	nuc	0	Cytoplasm. Nucleus. Translocated into the nucleus in response to phosphorylation	cytoplasm [IDA] nucleus [IDA]			837
Q8HYP5 UniProt NPD GO	CCL21_MACMU	Small inducible cytokine A21 precursor (CCL21)	0.71	-	exc	0	Secreted protein (By similarity)				131
Q14524 UniProt NPD GO	SCN5A_HUMAN	Sodium channel protein type 5 subunit alpha (Sodium channel protein type V subunit alpha) (Voltage-g ...	0.71	-	end	21	Membrane; multi-pass membrane protein		608567		2016
Q9CPY3 UniProt NPD GO	CDCA5_MOUSE	Sororin (Cell division cycle-associated protein 5)	0.71	-	mit	0	Nucleus (By similarity). Nuclear in interphase cells. During mitosis, it localizes throughout the cy ...	cytoplasm [IDA] nucleus [IDA]			264
O60749 UniProt NPD GO	SNX2_HUMAN	Sorting nexin-2 (Transformation-related gene 9 protein)	0.71	-	nuc	0			605929		519
O14243 UniProt NPD GO	SNX4_SCHPO	Sorting nexin-4 (Autophagy-related protein 24)	0.71	-	nuc	0	Cytoplasm (By similarity). Membrane; peripheral membrane protein (By similarity). Endosome; endosoma ...				401
Q4R5U9 UniProt NPD GO	SNX7_MACFA	Sorting nexin-7	0.71	-	cyt	0					387
Q96R06 UniProt NPD GO	SPAG5_HUMAN	Sperm-associated antigen 5 (Astrin) (Mitotic spindle-associated protein p126) (MAP126) (Deepest)	0.71	-	nuc	0	Cytoplasm. In a punctate pattern in interphase cells. During mitosis, detected at spindle poles duri ...				1193
Q20010 UniProt NPD GO	SAS5_CAEEL	Spindle assembly abnormal protein 5	0.71	-	nuc	0	Cytoplasm. Centriole. Localizes to centrioles. Shuttles between centrioles and the cytoplasm through ...				404
Q6BSY1 UniProt NPD GO	MAD1_DEBHA	Spindle assembly checkpoint component MAD1 (Mitotic arrest deficient protein 1)	0.71	-	nuc	0	Nucleus (By similarity)				669
Q94535 UniProt NPD GO	U2AF1_DROME	Splicing factor U2af 38 kDa subunit (U2 auxiliary factor 38 kDa subunit) (U2 snRNP auxiliary factor ...	0.71	+	nuc	0	Nucleus	nucleus [IC] snRNP U2 [TAS]			264
Q12508 UniProt NPD GO	RMD5_YEAST	Sporulation protein RMD5 (Glucose-induced degradation protein 2)	0.71	+	nuc	1	Cytoplasm	cytosol [IDA]			421
Q08646 UniProt NPD GO	SSP2_YEAST	Sporulation-specific protein 2	0.71	-	nuc	0	Spore wall	spore wall (sensu Fungi) [IDA]			371
Q38740 UniProt NPD GO	SBP2_ANTMA	Squamosa promoter-binding protein 2	0.71	-	nuc	0	Nucleus				171
Q60864 UniProt NPD GO	STIP1_MOUSE	Stress-induced-phosphoprotein 1 (STI1) (Hsc70/Hsp90-organizing protein) (Hop) (mSTI1)	0.71	-	nuc	0	Cytoplasm. Nucleus				543
Q43845 UniProt NPD GO	SPS_SOLTU	Sucrose-phosphate synthase (EC 2.4.1.14) (UDP-glucose-fructose-phosphate glucosyltransferase)	0.71	-	cyt	0					1053
O76808 UniProt NPD GO	SUH_CIOIN	Suppressor of hairless homolog (Su(H))	0.71	-	nuc	0					554
O14222 UniProt NPD GO	FSV1_SCHPO	Syntaxin-like protein fsv1	0.71	-	nuc	0	Membrane-bound. Associated with the Golgi and prevacuolar membrane				247

You are viewing entries 13501 to 13550 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.