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
P89105 UniProt NPD GO	CTR9_YEAST	RNA polymerase-associated protein CTR9 (Cln three-requiring protein 9) (Centromere-binding factor 1- ...	0.96	+	nuc	0	Nucleus; nucleoplasm	Cdc73/Paf1 complex [IPI] nucleus [IDA]			1077
Q6PD62 UniProt NPD GO	CTR9_HUMAN	RNA polymerase-associated protein CTR9 homolog (SH2 domain-binding protein 1)	0.96	+	nuc	0	Nucleus. Found in speckles (By similarity)		609366		1173
Q6DEU9 UniProt NPD GO	CTR9_XENTR	RNA polymerase-associated protein CTR9 homolog (SH2 domain-binding protein 1)	0.96	+	nuc	0					1172
P98175 UniProt NPD GO	RBM10_HUMAN	RNA-binding protein 10 (RNA-binding motif protein 10) (DXS8237E)	0.96	+	nuc	0	Nucleus (By similarity)	nucleus [NAS]	300080		929
Q4R5N1 UniProt NPD GO	RNPS1_MACFA	RNA-binding protein with serine-rich domain 1	0.96	+	nuc	0	Nucleus; nucleoplasm; nuclear speckle (By similarity). Cytoplasm (By similarity). Nucleocytoplasmic ...				305
Q99M28 UniProt NPD GO	RNPS1_MOUSE	RNA-binding protein with serine-rich domain 1	0.96	+	nuc	0	Nucleus; nucleoplasm; nuclear speckle (By similarity). Cytoplasm (By similarity). Nucleocytoplasmic ...				305
Q5NVM8 UniProt NPD GO	RNPS1_PONPY	RNA-binding protein with serine-rich domain 1	0.96	+	nuc	0	Nucleus; nucleoplasm; nuclear speckle (By similarity). Cytoplasm (By similarity). Nucleocytoplasmic ...				305
Q6AYK1 UniProt NPD GO	RNPS1_RAT	RNA-binding protein with serine-rich domain 1	0.96	+	nuc	0	Nucleus; nucleoplasm; nuclear speckle (By similarity). Cytoplasm (By similarity). Nucleocytoplasmic ...				305
Q15287 UniProt NPD GO	RNPS1_HUMAN	RNA-binding protein with serine-rich domain 1 (SR-related protein LDC2)	0.96	+	nuc	0	Nucleus; nucleoplasm; nuclear speckle. Cytoplasmic. Nucleocytoplasmic shuttling protein	nucleus [TAS]	606447		305
Q8VH51 UniProt NPD GO	RNPC2_MOUSE	RNA-binding region-containing protein 2 (Coactivator of activating protein 1 and estrogen receptors) ...	0.96	+	nuc	0	Nucleus (Probable)	nucleus [TAS]			530
Q8NFW9 UniProt NPD GO	MYRIP_HUMAN	Rab effector MyRIP (Myosin-VIIa- and Rab-interacting protein) (Exophilin-8) (Slp homolog lacking C2 ...	0.96	-	nuc	0	Cytoplasm (By similarity). In pre- and post-synaptic areas in photoreceptor cells and in the basal m ...				859
Q9PT60 UniProt NPD GO	RBP1A_XENLA	RalA-binding protein 1-A (RalBP1-A) (Ral-interacting protein 1-A) (XRLIP2) (XRLIP76-A) (RIP1-A)	0.96	+	nuc	0	Cytoplasm; cytosol. Cell membrane; peripheral membrane protein. Targeted to the plasma membrane thro ...	membrane [ISS]			654
P08638 UniProt NPD GO	LEUR_YEAST	Regulatory protein LEU3	0.96	-	nuc	0	Nucleus	nucleus [IDA]		2ERG	886
P35601 UniProt NPD GO	RFC1_MOUSE	Replication factor C subunit 1 (Replication factor C large subunit) (RF-C 140 kDa subunit) (Activato ...	0.96	+	nuc	0	Nucleus	nucleus [IDA]			1131
Q12192 UniProt NPD GO	RFM1_YEAST	Repression factor of MSEs protein 1	0.96	-	nuc	0	Nucleus	histone deacetylase complex [IPI] nucleus [IPI]			310
Q96RL1 UniProt NPD GO	RXINP_HUMAN	Retinoid X receptor-interacting protein 110 (Receptor-associated protein 80) (Nuclear zinc finger pr ...	0.96	+	nuc	0	Nucleus		609433		719
P38165 UniProt NPD GO	RTG3_YEAST	Retrograde regulation protein 3	0.96	+	nuc	0	Nucleus (Probable)	cytoplasm [IDA] nucleus [IDA]			486
Q8R4H2 UniProt NPD GO	ARHGC_MOUSE	Rho guanine nucleotide exchange factor 12 (Leukemia-associated RhoGEF)	0.96	-	nuc	0	Cytoplasm (Probable). Membrane (Probable). Translocated to the membrane upon stimulation (Probable)				1543
O43182 UniProt NPD GO	RHG06_HUMAN	Rho-GTPase-activating protein 6 (Rho-type GTPase-activating protein RhoGAPX-1)	0.96	-	nuc	0	Cytoplasm	actin filament [NAS] cytoplasm [NAS]	300118		974
O54834 UniProt NPD GO	RHG06_MOUSE	Rho-GTPase-activating protein 6 (Rho-type GTPase-activating protein RhoGAPX-1)	0.96	-	nuc	0	Cytoplasm (Potential)	actin cytoskeleton [IDA]			986
Q9UTR5 UniProt NPD GO	RGF2_SCHPO	Rho1 guanine nucleotide exchange factor 2	0.96	-	nuc	0		barrier septum [IDA] cell cortex of cell tip [IDA]			1158
Q10362 UniProt NPD GO	SET3_SCHPO	SET domain-containing protein 3	0.96	-	nuc	0	Cytoplasm. Nucleus				859
O43295 UniProt NPD GO	SRGP2_HUMAN	SLIT-ROBO Rho GTPase-activating protein 3 (srGAP3) (srGAP2) (WAVE-associated Rac GTPase-activating p ...	0.96	-	nuc	0			606524		1099
Q812A2 UniProt NPD GO	SRGP2_MOUSE	SLIT-ROBO Rho GTPase-activating protein 3 (srGAP3) (srGAP2) (WAVE-associated Rac GTPase-activating p ...	0.96	-	nuc	0					1099
P02835 UniProt NPD GO	FTZ_DROME	Segmentation protein fushi tarazu	0.96	+	nuc	0	Nucleus			1FTZ	410
Q9VXE5 UniProt NPD GO	PAKM_DROME	Serine/threonine-protein kinase PAK mbt (EC 2.7.11.1) (p21-activated kinase-related protein) (Protei ...	0.96	-	nuc	0	Cell membrane; cell-cell junction; adherens junction; peripheral membrane protein. Apical membrane s ...	adherens junction [IDA]			639
Q6C3D7 UniProt NPD GO	STE20_YARLI	Serine/threonine-protein kinase STE20 (EC 2.7.11.1)	0.96	-	exc	0	Cytoplasm (By similarity). Nucleus (By similarity)				1125
Q9UL54 UniProt NPD GO	TAOK2_HUMAN	Serine/threonine-protein kinase TAO2 (EC 2.7.11.1) (Thousand and one amino acid protein 2) (Prostate ...	0.96	-	nuc	4	Cytoplasmic vesicle; cytoplasmic vesicle membrane; multi-pass membrane protein (Potential). Found to ...	cytoplasmic membrane-bound vesicle [IDA]			1235
Q6DD27 UniProt NPD GO	TAOK3_XENLA	Serine/threonine-protein kinase TAO3 (EC 2.7.11.1) (Thousand and one amino acid protein 3)	0.96	-	nuc	0	Cytoplasm (By similarity)				896
Q863C0 UniProt NPD GO	SRY_CERAL	Sex-determining region Y protein (Testis-determining factor)	0.96	+	nuc	0	Nucleus				229
Q5BDI1 UniProt NPD GO	SGO1_EMENI	Shugoshin	0.96	-	nuc	0	Nucleus (By similarity). Localizes to the centromere (By similarity)				479
Q8C0T5 UniProt NPD GO	SI1L1_MOUSE	Signal-induced proliferation-associated 1-like protein 1	0.96	-	nuc	0					1782
O35412 UniProt NPD GO	SI1L1_RAT	Signal-induced proliferation-associated 1-like protein 1 (SPA-1-like protein p1294)	0.96	-	nuc	0					1822
Q9HFF5 UniProt NPD GO	PDS5_SCHPO	Sister chromatid cohesion protein pds5 (Precocious dissociation of sisters protein 5)	0.96	+	nuc	0	Nucleus. Centromeric. Localized to chromatin throughout the cell cycle				1205
P49140 UniProt NPD GO	SKI_CHICK	Ski oncogene (C-ski)	0.96	-	nuc	0	Nucleus				750
Q8BIZ6 UniProt NPD GO	SNIP1_MOUSE	Smad nuclear-interacting protein 1	0.96	-	nuc	0	Nucleus (By similarity)	nucleus [IDA]			383
Q04003 UniProt NPD GO	SAS4_YEAST	Something about silencing protein 4	0.96	-	nuc	0	Nucleus	nuclear chromatin [IDA] nuclear chromosome, telomeric region [IC]			481
Q01082 UniProt NPD GO	SPTB2_HUMAN	Spectrin beta chain, brain 1 (Spectrin, non-erythroid beta chain 1) (Beta-II spectrin) (Fodrin beta ...	0.96	+	nuc	0		spectrin [TAS]	182790	1BKR	2364
Q09821 UniProt NPD GO	STP4_PIG	Spermatid nuclear transition protein 4 (STP-4) (TP-4) (TP4)	0.96	-	mit	0	Nucleus				138
Q6FS63 UniProt NPD GO	MAD1_CANGA	Spindle assembly checkpoint component MAD1 (Mitotic arrest deficient protein 1)	0.96	-	nuc	0	Nucleus (By similarity)				657
P87169 UniProt NPD GO	MAD1_SCHPO	Spindle assembly checkpoint component mad1 (Mitotic arrest deficient protein 1)	0.96	+	nuc	0	Nucleus (By similarity)				689
Q8N2M8 UniProt NPD GO	SFR16_HUMAN	Splicing factor, arginine/serine-rich 16 (Suppressor of white-apricot homolog 2)	0.96	+	nuc	0	Nucleus (By similarity)				659
Q8CFC7 UniProt NPD GO	SFR16_MOUSE	Splicing factor, arginine/serine-rich 16 (Suppressor of white-apricot homolog 2) (Clk4-associating S ...	0.96	+	nuc	0	Nucleus. Located in nuclear dots. Isoform 2: Nucleus; nucleoplasm				653
Q8S9G8 UniProt NPD GO	SPL7_ARATH	Squamosa promoter-binding-like protein 7	0.96	-	nuc	1	Nucleus (Probable)			1UL5	801
Q05958 UniProt NPD GO	ECM22_YEAST	Sterol regulatory element-binding protein ECM22 (Extracellular matrix protein 22)	0.96	+	nuc	0	Cytoplasm. Nucleus	nucleus [IPI]			814
O93308 UniProt NPD GO	SMC1A_XENLA	Structural maintenance of chromosome 1 protein (xSMC1)	0.96	+	nuc	0	Nucleus. Associates with chromatin. Before prophase it is scattered along chromosome arms. During pr ...	cohesin core heterodimer [ISS] kinetochore [ISS] nucleus [ISS]			1232
Q8NDV3 UniProt NPD GO	SM1L2_HUMAN	Structural maintenance of chromosome 1-like 2 protein (SMC1beta protein)	0.96	-	nuc	0	Nucleus. Associates with chromatin. In prophase I stage of meiosis, localizes along the AE of synapt ...		608685		1235
P41003 UniProt NPD GO	SMC2_SCHPO	Structural maintenance of chromosome 2 (Chromosome segregation protein cut14) (Cell untimely torn pr ...	0.96	-	nuc	0	Nucleus. Cytoplasm. In interphase cells, the majority of the condensin complex is found in the cytop ...	condensin complex [IDA] cytoplasm [IDA] nucleus [IDA]			1172
P41004 UniProt NPD GO	SMC4_SCHPO	Structural maintenance of chromosome 4 (Chromosome segregation protein cut3) (Cell untimely torn pro ...	0.96	-	nuc	0	Nucleus. Cytoplasm. In interphase cells, the majority of the condensin complex is found in the cytop ...	condensin complex [IDA] cytoplasm [IDA] nucleus [IDA]			1324
Q12749 UniProt NPD GO	SMC6_YEAST	Structural maintenance of chromosome 6 (DNA repair protein RHC18) (Rad18 homolog)	0.96	+	nuc	0	Nucleus	mitochondrion [IDA] nucleus [IDA] Smc5-Smc6 complex [IPI]			1114

You are viewing entries 1601 to 1650 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.