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
Q76KJ5 UniProt NPD GO	PAF49_MOUSE	RNA polymerase I-associated factor PAF49 (Anti-sense to ERCC-1 protein) (ASE-1) (CD3-epsilon-associa ...	0.94	+	nuc	0	Nucleus. Accumulates in the nucleolus of exponentially growing cells	DNA-directed RNA polymerase I complex [IDA] nucleolus [IDA]			399
Q04712 UniProt NPD GO	RRN11_YEAST	RNA polymerase I-specific transcription initiation factor RRN11	0.94	-	nuc	0	Nucleus; nucleolus	RNA polymerase I transcription factor complex [TAS]			507
P54000 UniProt NPD GO	SUB1_YEAST	RNA polymerase II transcriptional coactivator SUB1	0.94	-	nuc	0	Nucleus (Probable)	nucleus [IC]			292
Q52KV5 UniProt NPD GO	LEO1_XENLA	RNA polymerase-associated protein LEO1	0.94	+	nuc	0	Nucleus (By similarity)				703
P38439 UniProt NPD GO	LEO1_YEAST	RNA polymerase-associated protein LEO1	0.94	+	nuc	0	Nucleus; nucleoplasm	Cdc73/Paf1 complex [IPI] nucleus [IDA]			464
P42696 UniProt NPD GO	RBM34_HUMAN	RNA-binding protein 34 (RNA-binding motif protein 34)	0.94	-	nuc	0	Nucleus; nucleolus				430
P25567 UniProt NPD GO	SRO9_YEAST	RNA-binding protein SRO9 (Suppressor of RHO3 protein 9)	0.94	-	nuc	0	Cytoplasm. Associates with translating ribosome	polysome [IDA]			434
P41885 UniProt NPD GO	RBF1_CAEEL	Rabphilin-1	0.94	-	nuc	0					1106
Q9H0H5 UniProt NPD GO	RGAP1_HUMAN	Rac GTPase-activating protein 1 (MgcRacGAP)	0.94	-	nuc	0	Nucleus. Cytoplasm. Spindle. During interphase, localized to the nucleus and cytoplasm along with mi ...	nucleus [IDA]	604980		632
Q60695 UniProt NPD GO	RGL1_MOUSE	Ral guanine nucleotide dissociation stimulator-like 1 (RalGDS-like 1)	0.94	-	nuc	0				1EF5	768
Q8TEU7 UniProt NPD GO	RPGF6_HUMAN	Rap guanine nucleotide exchange factor 6 (PDZ domain-containing guanine nucleotide exchange factor 2 ...	0.94	-	nuc	0	Cytoplasm. Cell membrane. Upon binding to M-Ras, it translocates to the plasma membrane	plasma membrane [IDA]			1601
P07248 UniProt NPD GO	ADR1_YEAST	Regulatory protein ADR1	0.94	-	end	0	Nucleus	nucleus [IDA]		2ADR	1323
P22697 UniProt NPD GO	CYS3_NEUCR	Regulatory protein cys-3	0.94	+	nuc	0	Nucleus				236
P35251 UniProt NPD GO	RFC1_HUMAN	Replication factor C subunit 1 (Replication factor C large subunit) (RF-C 140 kDa subunit) (Activato ...	0.94	+	nuc	0	Nucleus	DNA replication factor C complex [TAS]	102579		1148
P13405 UniProt NPD GO	RB_MOUSE	Retinoblastoma-associated protein (PP105) (RB)	0.94	-	nuc	0	Nucleus	nucleus [IDA] spindle [IDA] transcription factor complex [IDA]			921
P28749 UniProt NPD GO	RBL1_HUMAN	Retinoblastoma-like protein 1 (107 kDa retinoblastoma-associated protein) (PRB1) (P107)	0.94	-	nuc	0			116957	1H28	1068
Q9NZN5 UniProt NPD GO	ARHGC_HUMAN	Rho guanine nucleotide exchange factor 12 (Leukemia-associated RhoGEF)	0.94	-	nuc	0	Cytoplasm (Probable). Membrane (Probable). Translocated to the membrane upon stimulation (Probable)		604763	1X86	1544
O94653 UniProt NPD GO	BMS1_SCHPO	Ribosome biogenesis protein BMS1 homolog	0.94	+	nuc	0	Nucleus; nucleolus (By similarity)				1121
O94885 UniProt NPD GO	SASH1_HUMAN	SAM and SH3 domain-containing protein 1 (Proline-glutamate repeat-containing protein)	0.94	-	nuc	0			607955		1247
P42948 UniProt NPD GO	SET4_YEAST	SET domain protein 4	0.94	-	nuc	0					560
Q52KW0 UniProt NPD GO	SHAN2_XENLA	SH3 and multiple ankyrin repeat domains protein 2 (Shank2)	0.94	-	nuc	0	Cytoplasm; postsynaptic density of neuronal cells (By similarity)				1292
Q9CSN1 UniProt NPD GO	SNW1_MOUSE	SNW domain-containing protein 1 (Nuclear protein SkiP) (Ski-interacting protein)	0.94	+	nuc	0	Nucleus (By similarity)				536
Q13573 UniProt NPD GO	SNW1_HUMAN	SNW domain-containing protein 1 (Nuclear protein SkiP) (Ski-interacting protein) (Nuclear receptor c ...	0.94	+	nuc	0	Nucleus	nucleus [TAS] spliceosome complex [IDA]	603055		536
Q9EQE1 UniProt NPD GO	SENP2_RAT	Sentrin-specific protease 2 (EC 3.4.22.-) (Sentrin/SUMO-specific protease SENP2) (Axin-associating m ...	0.94	-	nuc	0	Nucleus; nuclear envelope; nuclear pore complex; nucleoplasmic side (By similarity). Cytoplasm. Cyto ...	nuclear pore [ISS]			588
Q9HC62 UniProt NPD GO	SENP2_HUMAN	Sentrin-specific protease 2 (EC 3.4.22.-) (Sentrin/SUMO-specific protease SENP2) (SMT3-specific isop ...	0.94	-	nuc	0	Nucleus; nuclear envelope; nuclear pore complex; nucleoplasmic side	nuclear pore [IDA]	608261	1TH0	589
Q9H4L4 UniProt NPD GO	SENP3_HUMAN	Sentrin-specific protease 3 (EC 3.4.22.-) (Sentrin/SUMO-specific protease SENP3) (SUMO-1-specific pr ...	0.94	-	nuc	0	Nucleus; nucleolus (By similarity)				574
Q9UPZ9 UniProt NPD GO	ICK_HUMAN	Serine/threonine-protein kinase ICK (EC 2.7.11.22) (Intestinal cell kinase) (hICK) (MAK-related kina ...	0.94	-	nuc	0	Cytoplasm (By similarity)				632
Q7TT49 UniProt NPD GO	MRCKB_RAT	Serine/threonine-protein kinase MRCK beta (EC 2.7.11.1) (CDC42-binding protein kinase beta) (Myotoni ...	0.94	+	nuc	0	Cytoplasm (By similarity). Displays a dispersed punctate distribution and concentrates along the cel ...	intercellular junction [ISS] leading edge [ISS]			1713
Q9Z1J2 UniProt NPD GO	NEK4_MOUSE	Serine/threonine-protein kinase Nek4 (EC 2.7.11.1) (NimA-related protein kinase 4) (Serine/threonine ...	0.94	-	nuc	0	Nucleus (Probable)				792
Q03306 UniProt NPD GO	PKH3_YEAST	Serine/threonine-protein kinase PKH3 (EC 2.7.11.1) (Pkb-activating kinase homolog 3)	0.94	-	nuc	0					898
Q96SB4 UniProt NPD GO	SRPK1_HUMAN	Serine/threonine-protein kinase SRPK1 (EC 2.7.11.1) (Serine/arginine-rich protein-specific kinase 1) ...	0.94	+	nuc	0	Cytoplasm. Nucleus. Isoform 1 and isoform 2 are cytoplasmic and nuclear	cytoplasm [IDA] nucleus [IDA]	601939	1WBP	826
Q5RD27 UniProt NPD GO	SRPK1_PONPY	Serine/threonine-protein kinase SRPK1 (EC 2.7.11.1) (Serine/arginine-rich protein-specific kinase 1) ...	0.94	+	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)	cytoplasm [ISS] nucleus [ISS]			655
Q6BNF3 UniProt NPD GO	STE20_DEBHA	Serine/threonine-protein kinase STE20 (EC 2.7.11.1)	0.94	+	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				1079
Q6NU21 UniProt NPD GO	TAO1A_XENLA	Serine/threonine-protein kinase TAO1-A (EC 2.7.11.1) (Thousand and one amino acid protein 1-A)	0.94	-	nuc	0	Cytoplasm (By similarity)				1001
Q9JLS3 UniProt NPD GO	TAOK2_RAT	Serine/threonine-protein kinase TAO2 (EC 2.7.11.1) (Thousand and one amino acid protein 2)	0.94	-	nuc	4	Cytoplasmic vesicle; cytoplasmic vesicle membrane; multi-pass membrane protein (By similarity). Foun ...			1U5R	1235
Q8BYC6 UniProt NPD GO	TAOK3_MOUSE	Serine/threonine-protein kinase TAO3 (EC 2.7.11.1) (Thousand and one amino acid protein 3)	0.94	-	nuc	0	Cytoplasm (By similarity)				898
Q5R4F3 UniProt NPD GO	TAOK3_PONPY	Serine/threonine-protein kinase TAO3 (EC 2.7.11.1) (Thousand and one amino acid protein 3)	0.94	-	nuc	0	Cytoplasm (By similarity)				898
Q53UA7 UniProt NPD GO	TAOK3_RAT	Serine/threonine-protein kinase TAO3 (EC 2.7.11.1) (Thousand and one amino acid protein 3) (Jun kina ...	0.94	-	nuc	0	Cytoplasm (By similarity)				898
Q9H4A3 UniProt NPD GO	WNK1_HUMAN	Serine/threonine-protein kinase WNK1 (EC 2.7.11.1) (Protein kinase with no lysine 1) (Protein kinase ...	0.94	-	nuc	0	Cytoplasm	cytoplasm [IDA]	605232		2382
Q9HGN1 UniProt NPD GO	GCN2_SCHPO	Serine/threonine-protein kinase gcn2 (EC 2.7.11.1)	0.94	+	nuc	0					1576
O94235 UniProt NPD GO	MPH1_SCHPO	Serine/threonine-protein kinase mph1 (EC 2.7.12.2)	0.94	-	nuc	0					678
P32361 UniProt NPD GO	IRE1_YEAST	Serine/threonine-protein kinase/endoribonuclease IRE1 precursor (Endoplasmic reticulum-to-nucleus si ...	0.94	-	exc	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type I membrane protein	endoplasmic reticulum membrane [TAS] nuclear envelope [TAS]		2BE1	1115
Q86SQ7 UniProt NPD GO	SDCG8_HUMAN	Serologically defined colon cancer antigen 8 (Centrosomal colon cancer autoantigen protein) (hCCCAP) ...	0.94	+	nuc	0	Centrosome				713
Q863D9 UniProt NPD GO	SRY_ALCAC	Sex-determining region Y protein (Testis-determining factor)	0.94	+	nuc	0	Nucleus				229
O60292 UniProt NPD GO	SI1L3_HUMAN	Signal-induced proliferation-associated 1-like protein 3 (SPA-1-like protein 3)	0.94	-	nuc	0					1781
Q9H7L9 UniProt NPD GO	SDS3_HUMAN	Sin3 histone deacetylase corepressor complex component SDS3 (Suppressor of defective silencing 3 pro ...	0.94	+	nuc	0		Sin3 complex [ISS]	608250		328
Q8BR65 UniProt NPD GO	SDS3_MOUSE	Sin3 histone deacetylase corepressor complex component SDS3 (Suppressor of defective silencing 3 pro ...	0.94	+	nuc	0		Sin3 complex [IDA]			328
P12755 UniProt NPD GO	SKI_HUMAN	Ski oncogene (C-ski)	0.94	+	nuc	0	Nucleus	nucleus [NAS]	164780	1SBX	728
Q60698 UniProt NPD GO	SKI_MOUSE	Ski oncogene (C-ski)	0.94	+	nuc	0	Nucleus	cytoplasm [IDA] nucleus [IDA] transcriptional repressor complex [IDA]			725
Q02225 UniProt NPD GO	SKI_XENLA	Ski oncogene (C-ski)	0.94	-	nuc	0	Nucleus				717

You are viewing entries 2501 to 2550 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.