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
P22987 UniProt NPD GO	KIN1_SCHPO	Protein kinase kin1 (EC 2.7.11.1)	0.86	-	nuc	0	Cytoplasm. Localized to the cell tips except during mitosis	cell tip [IDA] cytoplasm [IDA]			891
Q8K3F4 UniProt NPD GO	PP14D_RAT	Protein phosphatase 1 regulatory subunit 14D (Gastrointestinal and brain-specific PP1-inhibitory pro ...	0.86	-	nuc	0	Cytoplasm (Probable)				146
O13791 UniProt NPD GO	SLT1_SCHPO	Protein slt1	0.86	-	nuc	0					433
P07332 UniProt NPD GO	FES_HUMAN	Proto-oncogene tyrosine-protein kinase Fes/Fps (EC 2.7.10.2) (C-Fes)	0.86	-	nuc	0			190030	1WQU	822
Q03099 UniProt NPD GO	YMN3_YEAST	Putative ATP-dependent helicase YML133C (EC 3.6.1.-)	0.86	+	nuc	0		mitochondrion [IDA]			1374
Q923W1 UniProt NPD GO	NC6IP_MOUSE	Putative RNA methyltransferase NCOA6IP (EC 2.1.1.-) (Nuclear receptor coactivator 6-interacting prot ...	0.86	+	nuc	0	Nucleus				853
Q93348 UniProt NPD GO	IRX1_CAEEL	Putative iroquois-class homeobox protein irx-1	0.86	+	nuc	0	Nucleus (Probable)				356
P32742 UniProt NPD GO	YNH4_CAEEL	Putative serine/threonine-protein kinase R107.4 (EC 2.7.11.1)	0.86	-	nuc	0					820
Q8BFU0 UniProt NPD GO	RSPO2_MOUSE	R-spondin-2 precursor (Roof plate-specific spondin-2) (Cysteine-rich and single thrombospondin domai ...	0.86	+	nuc	0	Secreted protein				243
Q8IZ40 UniProt NPD GO	RCOR2_HUMAN	REST corepressor 2	0.86	-	nuc	0	Nucleus (By similarity)				523
Q5FWT8 UniProt NPD GO	RCOR2_RAT	REST corepressor 2	0.86	-	nuc	0	Nucleus (By similarity)				523
Q8C796 UniProt NPD GO	RCOR2_MOUSE	REST corepressor 2 (M-CoREST)	0.86	-	nuc	0	Nucleus (By similarity)	nucleus [IDA]			523
Q924T7 UniProt NPD GO	RNF31_MOUSE	RING finger protein 31	0.86	-	nuc	0		cytosol [IDA] internal side of plasma membrane [IDA]			1066
Q96EP0 UniProt NPD GO	RNF31_HUMAN	RING finger protein 31 (Zinc in-between-RING-finger ubiquitin-associated domain protein)	0.86	+	nuc	0				2CT7	1072
Q925F4 UniProt NPD GO	RNF37_MOUSE	RING finger protein 37 (Ubiquitin-conjugating enzyme 7-interacting protein 5) (UbcM4-interacting pro ...	0.86	+	nuc	0	Nucleus				539
Q80VR2 UniProt NPD GO	ELL3_MOUSE	RNA polymerase II elongation factor ELL3	0.86	-	nuc	0	Nucleus (By similarity)				395
P40993 UniProt NPD GO	RMRP_YEAST	RNase MRP protein component SNM1	0.86	+	nuc	0		ribonuclease MRP complex [TAS]			198
Q92565 UniProt NPD GO	RPGF5_HUMAN	Rap guanine nucleotide exchange factor 5 (Guanine nucleotide exchange factor for Rap1) (Related to E ...	0.86	-	nuc	0	Nucleus	nucleus [IDA]	609527	1WGY	580
Q60790 UniProt NPD GO	RASA3_MOUSE	Ras GTPase-activating protein 3 (GAP1(IP4BP)) (Ins P4-binding protein) (GapIII)	0.86	+	nuc	0					834
Q12280 UniProt NPD GO	IQG1_YEAST	Ras GTPase-activating-like protein IQG1 (IQGAP-related protein 1) (Cytokinesis protein 1)	0.86	-	nuc	0	Bud neck. Forms a ring at the bud neck in a MLC1-dependent manner, which contracts at the end of cyt ...	contractile ring (sensu Saccharomyces) [IDA]			1495
Q3SZJ2 UniProt NPD GO	RIPK2_BOVIN	Receptor-interacting serine/threonine-protein kinase 2 (EC 2.7.11.1)	0.86	-	nuc	0	Cytoplasm (Probable)				540
P31266 UniProt NPD GO	SUH_MOUSE	Recombining binding protein suppressor of hairless (J kappa-recombination signal-binding protein) (R ...	0.86	-	nuc	0	Nucleus				526
Q99NE5 UniProt NPD GO	RIMS1_MOUSE	Regulating synaptic membrane exocytosis protein 1 (Rab3-interacting molecule 1) (RIM 1) (Rab3-intera ...	0.86	-	nuc	0		presynaptic membrane [ISS]			388
O54829 UniProt NPD GO	RGS7_MOUSE	Regulator of G-protein signaling 7 (RGS7)	0.86	-	nuc	0					469
P04386 UniProt NPD GO	GAL4_YEAST	Regulatory protein GAL4	0.86	+	nuc	0	Nucleus	nucleus [TAS]		1HBW	881
Q00798 UniProt NPD GO	RBP1_PLAVB	Reticulocyte-binding protein 1 precursor	0.86	-	exc	0	Membrane; peripheral membrane protein				2833
Q9UR07 UniProt NPD GO	RT23_SCHPO	Retrotransposable element Tf2 155 kDa protein type 3	0.86	-	nuc	0					1333
P04323 UniProt NPD GO	POL3_DROME	Retrovirus-related Pol polyprotein from transposon 17.6 [Includes: Protease (EC 3.4.23.-); Reverse t ...	0.86	+	nuc	0					1058
Q8K4I3 UniProt NPD GO	ARHG6_MOUSE	Rho guanine nucleotide exchange factor 6 (Rac/Cdc42 guanine nucleotide exchange factor 6)	0.86	-	nuc	0				1V61	771
P97433 UniProt NPD GO	RGNEF_MOUSE	Rho-guanine nucleotide exchange factor (Rho-interacting protein 2) (RhoGEF) (RIP2)	0.86	-	nuc	0					1693
Q07844 UniProt NPD GO	RIX7_YEAST	Ribosome biogenesis ATPase RIX7	0.86	-	nuc	0	Nucleus; nucleolus	nucleolus [IDA] nucleus [IDA]			837
Q6FS36 UniProt NPD GO	RLP7_CANGA	Ribosome biogenesis protein RLP7	0.86	-	nuc	0	Nucleus; nucleolus (By similarity)				317
Q5TZA2 UniProt NPD GO	CROCC_HUMAN	Rootletin (Ciliary rootlet coiled-coil protein)	0.86	-	nuc	0	Centrosome. In ciliated cells, associated with ciliary rootlets. In non-ciliated cellS, localized be ...	centriole [ISS] ciliary rootlet [ISS]			2017
Q9UN79 UniProt NPD GO	SOX13_HUMAN	SOX-13 protein (Type 1 diabetes autoantigen ICA12) (Islet cell antigen 12)	0.86	-	end	2	Nucleus (Potential)		604748		889
Q56UN5 UniProt NPD GO	YSK4_HUMAN	SPS1/STE20-related protein kinase YSK4 (EC 2.7.11.1) (Regulated in COPD, protein kinase)	0.86	-	nuc	0					1328
Q9WUD1 UniProt NPD GO	STUB1_MOUSE	STIP1 homology and U box-containing protein 1 (EC 6.3.2.-) (STIP1 homology and U-box-containing prot ...	0.86	-	nuc	0	Cytoplasm	ubiquitin conjugating enzyme complex [TAS]		2C2V	304
Q5KG22 UniProt NPD GO	SWC4_CRYNE	SWR1-complex protein 4	0.86	-	nuc	0	Nucleus (By similarity)				463
P21135 UniProt NPD GO	SECU_SCHPO	Securin (Protein Cut2) (Cell untimely torn protein 2)	0.86	-	mit	0	Cytoplasm. Nucleus	nucleus [IDA] spindle [IDA]			301
Q92997 UniProt NPD GO	DVL3_HUMAN	Segment polarity protein dishevelled homolog DVL-3 (Dishevelled-3) (DSH homolog 3)	0.86	+	nuc	0	Cytoplasm (By similarity)		601368		716
Q61062 UniProt NPD GO	DVL3_MOUSE	Segment polarity protein dishevelled homolog DVL-3 (Dishevelled-3) (DSH homolog 3)	0.86	+	nuc	0	Cytoplasm (By similarity)				716
Q8WP32 UniProt NPD GO	SENP5_MACFA	Sentrin-specific protease 5 (EC 3.4.22.-) (Sentrin/SUMO-specific protease SENP5)	0.86	-	nuc	0					755
Q9Z0G2 UniProt NPD GO	STK23_MOUSE	Serine/threonine-protein kinase 23 (EC 2.7.11.1) (Muscle-specific serine kinase 1) (MSSK-1)	0.86	-	nuc	0					565
Q15139 UniProt NPD GO	KPCD1_HUMAN	Serine/threonine-protein kinase D1 (EC 2.7.11.13) (nPKC-D1) (Protein kinase D) (Protein kinase C mu ...	0.86	-	nuc	0		cytosol [TAS] integral to plasma membrane [TAS] plasma membrane [TAS]	605435		912
O94806 UniProt NPD GO	KPCD3_HUMAN	Serine/threonine-protein kinase D3 (EC 2.7.11.13) (Protein kinase C nu type) (nPKC-nu) (Protein kina ...	0.86	-	mit	0			607077		890
Q04859 UniProt NPD GO	MAK_MOUSE	Serine/threonine-protein kinase MAK (EC 2.7.11.22) (Male germ cell-associated kinase) (Protein kinas ...	0.86	-	nuc	0					622
Q6FX42 UniProt NPD GO	ATR_CANGA	Serine/threonine-protein kinase MEC1 (EC 2.7.11.1) (DNA-damage checkpoint kinase MEC1) (Mitosis entr ...	0.86	-	nuc	0	Nucleus. Localizes to nuclear DNA repair foci in response to DNA double strand breaks (By similarity ...				2379
Q6CT34 UniProt NPD GO	ATR_KLULA	Serine/threonine-protein kinase MEC1 (EC 2.7.11.1) (DNA-damage checkpoint kinase MEC1) (Mitosis entr ...	0.86	-	end	0	Nucleus. Localizes to nuclear DNA repair foci in response to DNA double strand breaks (By similarity ...				2287
P54199 UniProt NPD GO	MPS1_YEAST	Serine/threonine-protein kinase MPS1 (EC 2.7.12.2) (Regulatory cell proliferation kinase 1)	0.86	-	nuc	0		condensed nuclear chromosome kinetochore [IDA] spindle pole body [IDA]			764
Q8BTW9 UniProt NPD GO	PAK4_MOUSE	Serine/threonine-protein kinase PAK 4 (EC 2.7.11.1) (p21-activated kinase 4) (PAK-4)	0.86	-	nuc	0					593
P78362 UniProt NPD GO	SRPK2_HUMAN	Serine/threonine-protein kinase SRPK2 (EC 2.7.11.1) (Serine/arginine-rich protein-specific kinase 2) ...	0.86	+	nuc	0	Cytoplasm. Nucleus	cytoplasm [IDA] nucleus [IDA]	602980		688

You are viewing entries 6251 to 6300 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.