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
Q60953 UniProt NPD GO	PML_MOUSE	Probable transcription factor PML	0.81	-	nuc	0	Nucleus. Localized in PML nuclear bodies	nucleus [IDA] PML body [IMP]			808
Q09931 UniProt NPD GO	UBPY_CAEEL	Probable ubiquitin carboxyl-terminal hydrolase K02C4.3 (EC 3.1.2.15) (Ubiquitin thioesterase) (Ubiqu ...	0.81	-	vac	0					1302
Q63449 UniProt NPD GO	PRGR_RAT	Progesterone receptor (PR)	0.81	+	nuc	0	Nucleus				923
Q9PS27 UniProt NPD GO	PRT_DICLA	Protamine	0.81	+	nuc	0	Nucleus				34
P29629 UniProt NPD GO	PRT_PERFV	Protamine	0.81	+	nuc	0	Nucleus				34
P19782 UniProt NPD GO	PRM2_BOVIN	Protamine-2 (Protamine-P2) (Sperm histone P2)	0.81	+	nuc	0	Nucleus				112
Q28337 UniProt NPD GO	PRM2_CALJA	Protamine-2 (Protamine-P2) (Sperm histone P2)	0.81	+	nuc	0	Nucleus				104
P69010 UniProt NPD GO	PRTZ_CLUHA	Protamine-Z (Clupeine-Z)	0.81	+	nuc	0	Nucleus			7INS	31
P69011 UniProt NPD GO	PRTZ_CLUPA	Protamine-Z (Clupeine-Z)	0.81	+	nuc	0	Nucleus				31
P25327 UniProt NPD GO	PRTZ1_SAROR	Protamine-Z1/Z2 (Sardaine-Z1/Z2)	0.81	+	nuc	0	Nucleus				34
Q07660 UniProt NPD GO	BRE4_YEAST	Protein BRE4 (Brefeldin A-sensitivity protein 4)	0.81	-	end	9	Membrane; multi-pass membrane protein (Potential)				1125
Q8WNU5 UniProt NPD GO	CJ068_MACFA	Protein C10orf68 homolog	0.81	+	nuc	0					618
Q80ST9 UniProt NPD GO	CF152_MOUSE	Protein C6orf152 homolog	0.81	-	nuc	0					704
O43439 UniProt NPD GO	MTG8R_HUMAN	Protein CBFA2T2 (MTG8-like protein) (MTG8-related protein 1) (Myeloid translocation-related protein ...	0.81	-	nuc	0	Nucleus (Probable)		603672		604
Q29RM2 UniProt NPD GO	FA53C_BOVIN	Protein FAM53C	0.81	-	nuc	0					392
Q9NYF3 UniProt NPD GO	FA53C_HUMAN	Protein FAM53C	0.81	-	nuc	0			609372		392
Q8BXQ8 UniProt NPD GO	FA53C_MOUSE	Protein FAM53C	0.81	-	nuc	0					393
Q5R815 UniProt NPD GO	FA53C_PONPY	Protein FAM53C	0.81	-	nuc	0					392
Q7ZZR3 UniProt NPD GO	FAM5A_CHICK	Protein FAM5A precursor (BMP/retinoic acid-inducible neural-specific protein 1)	0.81	-	exc	0	Secreted protein (Potential)				761
Q6DEE7 UniProt NPD GO	FA76B_XENLA	Protein FAM76B	0.81	-	nuc	0					337
Q566M1 UniProt NPD GO	FA76B_XENTR	Protein FAM76B	0.81	-	nuc	0					337
Q84JK2 UniProt NPD GO	FD_ARATH	Protein FD (BZIP transcription factor 14) (AtbZIP14)	0.81	-	nuc	0	Nucleus				285
O15063 UniProt NPD GO	K0355_HUMAN	Protein KIAA0355	0.81	-	nuc	0					1070
Q6PEE2 UniProt NPD GO	K0427_MOUSE	Protein KIAA0427 homolog	0.81	+	nuc	0					623
Q5DTU0 UniProt NPD GO	K1914_MOUSE	Protein KIAA1914	0.81	-	nuc	0					825
P32266 UniProt NPD GO	MGM1_YEAST	Protein MGM1, mitochondrial precursor [Contains: Protein MGM1 isoform 1; Protein MGM1 isoform 2]	0.81	-	mit	0	Mitochondrion; mitochondrial intermembrane space	mitochondrial intermembrane space [IDA]			881
P52918 UniProt NPD GO	MSN5_YEAST	Protein MSN5	0.81	-	end	0		nucleus [IDA]			1224
Q69Z66 UniProt NPD GO	MYSM1_MOUSE	Protein MYSM1 (Myb-like, SWIRM and MPN domain-containing protein 1)	0.81	-	nuc	0	Nucleus (Probable)				819
P08468 UniProt NPD GO	PT111_YEAST	Protein PET111, mitochondrial precursor	0.81	-	mit	0	Mitochondrion; mitochondrial matrix	mitochondrial inner membrane [IDA]			800
Q4PEQ0 UniProt NPD GO	SEY1_USTMA	Protein SEY1	0.81	-	nuc	1	Membrane; multi-pass membrane protein (Potential)				912
P36085 UniProt NPD GO	STB6_YEAST	Protein STB6	0.81	-	nuc	0					766
Q02457 UniProt NPD GO	TBF1_YEAST	Protein TBF1 (TTAGGG repeat-binding factor 1) (TBF alpha)	0.81	-	nuc	0	Nucleus	nuclear chromosome [IPI] nuclear chromosome, telomeric region [TAS] nucleus [IDA]			562
Q99107 UniProt NPD GO	TSD2_USTMA	Protein TSD2	0.81	-	nuc	0	Nucleus (Potential)				845
Q7S6P8 UniProt NPD GO	BFR2_NEUCR	Protein bfr-2	0.81	-	nuc	0	Nucleus; nucleolus (By similarity)				636
Q8TDB6 UniProt NPD GO	DTX3L_HUMAN	Protein deltex 3-like protein (B-lymphoma- and BAL-associated protein) (Rhysin-2) (Rhysin2)	0.81	-	nuc	0					740
Q07436 UniProt NPD GO	EXPA_DROME	Protein expanded	0.81	-	nuc	0	Cell membrane; apical cell membrane. Apical surface of disk cells	apical plasma membrane [TAS] zonula adherens [TAS]			1427
P07247 UniProt NPD GO	KRUP_DROME	Protein krueppel	0.81	-	nuc	0	Nucleus. Chromatin associated				502
P08970 UniProt NPD GO	SUHW_DROME	Protein suppressor of hairy wing	0.81	-	nuc	0	Nucleus. Colocalizes with other elements of the gypsy chromatin insulator complex at multiple sites ...	nucleus [IDA]			941
Q24331 UniProt NPD GO	TID_DROVI	Protein tumorous imaginal discs, mitochondrial precursor (Protein lethal(2)tumorous imaginal discs) ...	0.81	-	mit	0	Mitochondrion; mitochondrial outer membrane (By similarity)				529
P16591 UniProt NPD GO	FER_HUMAN	Proto-oncogene tyrosine-protein kinase FER (EC 2.7.10.2) (p94-FER) (c-FER)	0.81	-	nuc	0	Cytoplasm. Nucleus. Associated with the chromatin		176942		822
P47077 UniProt NPD GO	YJB0_YEAST	Pumilio domain-containing protein YJL010C	0.81	-	nuc	0		nucleolus [IDA] nucleus [IDA]			666
P32644 UniProt NPD GO	ECM32_YEAST	Putative ATP-dependent RNA helicase ECM32 (EC 3.6.1.-) (Extracellular matrix protein 32) (Helicase 1 ...	0.81	-	nuc	0	Cytoplasm. Associated with polyribosomes	polysome [IDA]			1121
Q96RS0 UniProt NPD GO	NC6IP_HUMAN	Putative RNA methyltransferase NCOA6IP (EC 2.1.1.-) (Nuclear receptor coactivator 6-interacting prot ...	0.81	+	nuc	0	Nucleus		606461		853
Q8VY05 UniProt NPD GO	SMCL_ARATH	Putative SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily C member ...	0.81	-	nuc	0	Nucleus (By similarity)				985
Q961G1 UniProt NPD GO	COG3_DROME	Putative conserved oligomeric Golgi complex component 3	0.81	-	nuc	0	Golgi apparatus (By similarity)				905
Q9QZ09 UniProt NPD GO	PHTF1_MOUSE	Putative homeodomain transcription factor 1	0.81	+	end	6	Nucleus (Potential)				761
Q11177 UniProt NPD GO	DHS27_CAEEL	Putative oxidoreductase dhs-27 (EC 1.-.-.-)	0.81	-	end	2	Membrane; multi-pass membrane protein (Potential)				816
O13612 UniProt NPD GO	YNH2_SCHPO	Putative thiol protease C32H8.02c (EC 3.4.22.-)	0.81	-	nuc	0	Cytoplasm	cytoplasm [IDA]			415
P38900 UniProt NPD GO	YH19_YEAST	Putative uncharacterized protein YHR219W	0.81	+	nuc	0					624
Q9Y3Y4 UniProt NPD GO	PYGO1_HUMAN	Pygopus homolog 1	0.81	-	nuc	0	Nucleus (Probable)		606902		419

You are viewing entries 8501 to 8550 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.