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
P97492 UniProt NPD GO	RGS14_MOUSE	Regulator of G-protein signaling 14 (RGS14) (RAP1/RAP2-interacting protein)	0.74	+	nuc	0		nucleus [IDA] spindle [IDA]		1WFY	547
O00287 UniProt NPD GO	RFXAP_HUMAN	Regulatory factor X-associated protein (RFX DNA-binding complex 36 kDa subunit) (RFX-associated prot ...	0.74	-	nuc	0	Nucleus		601861		272
Q5TJF7 UniProt NPD GO	RXRB_CANFA	Retinoic acid receptor RXR-beta (Retinoid X receptor beta)	0.74	+	nuc	0	Nucleus (By similarity)				533
P18911 UniProt NPD GO	RARG1_MOUSE	Retinoic acid receptor gamma-A (RAR-gamma-A)	0.74	+	nuc	0	Nucleus	nucleus [IDA] transcription factor complex [IDA]			458
P20787 UniProt NPD GO	RARG2_MOUSE	Retinoic acid receptor gamma-B (RAR-gamma-B)	0.74	+	nuc	0	Nucleus	nucleus [IDA] transcription factor complex [IDA]			447
O15013 UniProt NPD GO	ARHGA_HUMAN	Rho guanine nucleotide exchange factor 10	0.74	-	nuc	0			608236		1369
Q8MKW7 UniProt NPD GO	RNZ_DROME	Ribonuclease Z, mitochondrial precursor (EC 3.1.26.11) (RNase Z) (tRNase Z) (tRNA 3 endonuclease) (D ...	0.74	-	nuc	0	Nucleus (Probable). Mitochondrion (Probable)	mitochondrion [NAS] nucleus [NAS]			766
Q5R4K3 UniProt NPD GO	KS6A5_PONPY	Ribosomal protein S6 kinase alpha-5 (EC 2.7.11.1)	0.74	+	cyt	0	Nucleus (By similarity)				802
Q96S38 UniProt NPD GO	KS6C1_HUMAN	Ribosomal protein S6 kinase delta-1 (EC 2.7.11.1) (52 kDa ribosomal protein S6 kinase) (Ribosomal S6 ...	0.74	-	nuc	0	Cytoplasm. Membrane. Also found in some small dot-like or ring-shaped early endosome structures				1066
Q6C818 UniProt NPD GO	RSA3_YARLI	Ribosome assembly protein 3	0.74	+	nuc	0	Nucleus; nucleolus (By similarity)				159
P38805 UniProt NPD GO	RPF1_YEAST	Ribosome production factor 1 (Ribosome biogenesis protein RPF1)	0.74	-	cyt	0	Nucleus; nucleolus	nucleolus [IDA]			295
Q8WZ75 UniProt NPD GO	ROBO4_HUMAN	Roundabout homolog 4 precursor (Magic roundabout)	0.74	-	nuc	0		integral to membrane [TAS]	607528		1007
P98167 UniProt NPD GO	SSPO_BOVIN	SCO-spondin precursor	0.74	-	nuc	0	Secreted protein; extracellular space				5146
P59622 UniProt NPD GO	SLAP1_RAT	SRC-like-adapter (Src-like-adapter protein 1)	0.74	-	nuc	0	Cytoplasm (By similarity). Endosome (By similarity). Colocalizes with endosomes (By similarity)				312
Q63ZM7 UniProt NPD GO	STABP_XENLA	STAM-binding protein-like (EC 3.1.2.15)	0.74	-	nuc	0					416
Q6FML0 UniProt NPD GO	SWC5_CANGA	SWR1-complex protein 5	0.74	+	nuc	0	Nucleus (By similarity)				299
Q9ER74 UniProt NPD GO	SALL1_MOUSE	Sal-like protein 1 (Zinc finger protein Spalt-3) (Sal-3) (MSal-3)	0.74	-	nuc	0	Nucleus	nucleus [IDA]			1322
Q5U7N0 UniProt NPD GO	SEMG2_MACFA	Semenogelin-2 precursor (Semenogelin II) (SGII)	0.74	-	nuc	0	Secreted protein (By similarity)				582
P18296 UniProt NPD GO	CUT1_SCHPO	Separin (EC 3.4.22.49) (Separase) (Cell untimely torn protein 1)	0.74	+	nuc	0	Cytoplasm. Nucleus				1828
Q5PQK1 UniProt NPD GO	SEP10_RAT	Septin-10	0.74	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				456
Q13043 UniProt NPD GO	STK4_HUMAN	Serine/threonine-protein kinase 4 (EC 2.7.11.1) (STE20-like kinase MST1) (MST-1) (Mammalian STE20-li ...	0.74	-	nuc	0	Cytoplasm. The caspase-cleaved form cycles between the nucleus and cytoplasm		604965		487
P59241 UniProt NPD GO	STK6_RAT	Serine/threonine-protein kinase 6 (EC 2.7.11.1) (Aurora-A) (ratAurA)	0.74	-	nuc	0	Centrosome (By similarity). Spindle (By similarity). Localizes on centrosomes in interphase cells an ...	centrosome [IDA] spindle [IDA]			397
P97477 UniProt NPD GO	STK6_MOUSE	Serine/threonine-protein kinase 6 (EC 2.7.11.1) (Aurora-family kinase 1) (Aurora/IPL1-related kinase ...	0.74	-	nuc	0	Centrosome (By similarity). Spindle (By similarity). Localizes on centrosomes in interphase cells an ...				395
P49762 UniProt NPD GO	DOA_DROME	Serine/threonine-protein kinase Doa (EC 2.7.12.1) (Protein darkener of apricot)	0.74	-	nuc	0	Isoform C: Cytoplasm; cytosol. Isoform A: Nucleus. Isoform A is mainly nuclear with only low levels ...	cytoplasm [IDA] nucleus [IDA]			832
Q00537 UniProt NPD GO	PCTK2_HUMAN	Serine/threonine-protein kinase PCTAIRE-2 (EC 2.7.11.22) (PCTAIRE-motif protein kinase 2)	0.74	-	mit	0			603440		523
Q8K0D0 UniProt NPD GO	PCTK2_MOUSE	Serine/threonine-protein kinase PCTAIRE-2 (EC 2.7.11.22) (PCTAIRE-motif protein kinase 2)	0.74	-	mit	0					523
Q07832 UniProt NPD GO	PLK1_MOUSE	Serine/threonine-protein kinase PLK1 (EC 2.7.11.21) (Polo-like kinase 1) (PLK-1) (Serine/threonine-p ...	0.74	-	cyt	0	Nucleus				603
P25390 UniProt NPD GO	SSK22_YEAST	Serine/threonine-protein kinase SSK22 (EC 2.7.11.1) (MAP kinase kinase kinase SSK22) (Suppressor of ...	0.74	-	nuc	0					1331
Q8IYT8 UniProt NPD GO	ULK2_HUMAN	Serine/threonine-protein kinase ULK2 (EC 2.7.11.1) (Unc-51-like kinase 2)	0.74	-	nuc	0			608650		1036
Q9QY01 UniProt NPD GO	ULK2_MOUSE	Serine/threonine-protein kinase ULK2 (EC 2.7.11.1) (Unc-51-like kinase 2) (Serine/threonine-protein ...	0.74	-	nuc	0					1037
Q61151 UniProt NPD GO	2A5E_MOUSE	Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit epsilon isoform (PP2A, B subunit, ...	0.74	-	cyt	0	Cytoplasm (By similarity)	cytoplasm [TAS]			467
Q8TF05 UniProt NPD GO	PP4R1_HUMAN	Serine/threonine-protein phosphatase 4 regulatory subunit 1	0.74	-	nuc	0		soluble fraction [NAS]	604908		950
Q63918 UniProt NPD GO	SDPR_MOUSE	Serum deprivation-response protein (Phosphatidylserine-binding protein)	0.74	-	nuc	0	Cytoplasm; cytosol. Colocalizes with CAV1 to caveolae (By similarity)	cytosol [ISS]			417
Q9UQR0 UniProt NPD GO	SCML2_HUMAN	Sex comb on midleg-like protein 2	0.74	-	nuc	0	Nucleus (Probable)		300208	2BIV	700
Q8I8W7 UniProt NPD GO	FEM3_CAERE	Sex-determination protein fem-3 (Cr-FEM-3)	0.74	+	nuc	0					439
O15389 UniProt NPD GO	SIGL5_HUMAN	Sialic acid-binding Ig-like lectin 5 precursor (Siglec-5) (Obesity-binding protein 2) (OB-binding pr ...	0.74	-	end	1	Membrane; single-pass type I membrane protein		604200		551
Q80W37 UniProt NPD GO	SPN1_MOUSE	Snurportin-1 (RNA U transporter 1)	0.74	-	nuc	0	Nucleus (By similarity). Cytoplasm (By similarity). Nucleoplasmic shuttling protein. Its nuclear imp ...				358
Q68FP5 UniProt NPD GO	SPN1_RAT	Snurportin-1 (RNA U transporter 1)	0.74	-	nuc	0	Nucleus (By similarity). Cytoplasm (By similarity). Nucleoplasmic shuttling protein. Its nuclear imp ...				358
Q9UI33 UniProt NPD GO	SC11A_HUMAN	Sodium channel protein type 11 subunit alpha (Sodium channel protein type XI subunit alpha) (Voltage ...	0.74	-	end	21	Membrane; multi-pass membrane protein (By similarity)		604385		1791
Q3ZBM5 UniProt NPD GO	SNX5_BOVIN	Sorting nexin-5	0.74	-	cyt	0					404
Q66QC7 UniProt NPD GO	HSP1_EQUAS	Sperm protamine P1	0.74	+	mit	0	Nucleus (By similarity)				49
P83214 UniProt NPD GO	HSP1_OCTVU	Sperm protamine P1 (Po1) [Contains: Sperm protamine P2 (Po2) (Main protamine)]	0.74	+	mit	0	Nucleus	nucleosome [NAS] nucleus [NAS]			56
Q7ZVT3 UniProt NPD GO	SAS6_BRARE	Spindle assembly abnormal protein 6 homolog	0.74	-	nuc	0	Centrosome. Component of the centrosome (By similarity)				627
Q9VAC8 UniProt NPD GO	SAS6_DROME	Spindle assembly abnormal protein 6 homolog	0.74	-	nuc	0	Centrosome. Component of the centrosome (By similarity)	centrosome [ISS]			472
Q6UVJ0 UniProt NPD GO	SAS6_HUMAN	Spindle assembly abnormal protein 6 homolog (HsSAS-6)	0.74	-	nuc	0	Centrosome. Component of the centrosome	centrosome [IDA]	609321		657
Q5A950 UniProt NPD GO	ATG26_CANAL	Sterol 3-beta-glucosyltransferase (EC 2.4.1.173) (Autophagy-related protein 26) (UDP-glycosyltransfe ...	0.74	-	nuc	0	Cytoplasm (By similarity). Membrane; peripheral membrane protein (By similarity)				1513
P36956 UniProt NPD GO	SRBP1_HUMAN	Sterol regulatory element-binding protein 1 (SREBP-1) (Sterol regulatory element-binding transcripti ...	0.74	+	nuc	0	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein. Golgi apparatus; ...	endoplasmic reticulum membrane [TAS] nuclear envelope [TAS] nucleus [TAS]	184756	1AM9	1147
Q91880 UniProt NPD GO	SUH_XENLA	Suppressor of hairless protein homolog (X-Su(H))	0.74	-	nuc	0					501
O18964 UniProt NPD GO	SYNJ1_BOVIN	Synaptojanin-1 (EC 3.1.3.36) (Synaptic inositol-1,4,5-trisphosphate 5-phosphatase 1) (p150) (Fragmen ...	0.74	-	nuc	0	Cytoplasm; perinuclear region. Predominantly				1324
Q9NX95 UniProt NPD GO	SYBU_HUMAN	Syntabulin (Syntaxin-1-binding protein) (Golgi-localized syntaphilin-related protein)	0.74	-	nuc	0	Isoform 3, isoform 4 and isoform 5: Golgi apparatus; Golgi membrane; single-pass membrane protein. I ...				663

You are viewing entries 12051 to 12100 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.