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
O75069 UniProt NPD GO	TMCC2_HUMAN	Transmembrane and coiled-coil domains protein 2 (Cerebral protein 11)	0.91	-	end	2	Membrane; multi-pass membrane protein (Potential)				709
Q7M3K2 UniProt NPD GO	PELET_DROME	Transposable element P transposase (P-element transposase)	0.91	+	nuc	0					751
P25384 UniProt NPD GO	YCB9_YEAST	Transposon Ty2 protein B (Ty1-17 protein B)	0.91	-	nuc	0					1770
Q9QZ47 UniProt NPD GO	TNNT3_MOUSE	Troponin T, fast skeletal muscle (TnTf) (Fast skeletal muscle troponin T) (fTnT)	0.91	-	nuc	0					271
P09739 UniProt NPD GO	TNNT3_RAT	Troponin T, fast skeletal muscle (TnTf) (Fast skeletal muscle troponin T) (fTnT)	0.91	-	nuc	0		troponin complex [TAS]			258
P06398 UniProt NPD GO	TNNT3_COTJA	Troponin T, fast skeletal muscle isoforms	0.91	+	nuc	0					252
P08621 UniProt NPD GO	RU17_HUMAN	U1 small nuclear ribonucleoprotein 70 kDa (U1 snRNP 70 kDa) (snRNP70) (U1-70K)	0.91	+	nuc	0		spliceosome complex [IDA]	180740		437
Q8WVK2 UniProt NPD GO	SNUT3_HUMAN	U4/U6.U5 tri-snRNP-associated protein 3 (U4/U6.U5 tri-snRNP-associated 27 kDa protein) (27K) (Nuclei ...	0.91	+	nuc	0	Nucleus (Potential)				155
O13773 UniProt NPD GO	UCP7_SCHPO	UBA domain-containing protein 7	0.91	-	nuc	0					697
Q9VK07 UniProt NPD GO	UVRAG_DROME	UVRAG-like protein	0.91	-	nuc	0					696
O94782 UniProt NPD GO	UBP1_HUMAN	Ubiquitin carboxyl-terminal hydrolase 1 (EC 3.1.2.15) (Ubiquitin thioesterase 1) (Ubiquitin-specific ...	0.91	-	nuc	0	Nucleus		603478		785
Q9UHP3 UniProt NPD GO	UBP25_HUMAN	Ubiquitin carboxyl-terminal hydrolase 25 (EC 3.1.2.15) (Ubiquitin thioesterase 25) (Ubiquitin-specif ...	0.91	-	nuc	0			604736		1087
Q9NVE5 UniProt NPD GO	UBP40_HUMAN	Ubiquitin carboxyl-terminal hydrolase 40 (EC 3.1.2.15) (Ubiquitin thioesterase 40) (Ubiquitin-specif ...	0.91	+	nuc	0					1235
P51592 UniProt NPD GO	HYD_DROME	Ubiquitin--protein ligase hyd (EC 6.3.2.-) (Protein hyperplastic discs)	0.91	+	nuc	0	Nucleus (Potential)	cytoplasm [IDA] nucleus [IDA]			2885
P40028 UniProt NPD GO	YEN1_YEAST	Uncharacterized protein YER041W	0.91	-	nuc	0					759
P40085 UniProt NPD GO	YEX0_YEAST	Uncharacterized protein YER140W	0.91	+	end	5	Membrane; multi-pass membrane protein (Potential)	mitochondrion [IDA]			556
P43587 UniProt NPD GO	YFH3_YEAST	Uncharacterized protein YFR003C	0.91	+	nuc	0					155
P38809 UniProt NPD GO	YHP7_YEAST	Uncharacterized protein YHR097C	0.91	-	nuc	0		cytoplasm [IDA] nucleus [IDA]			366
P40473 UniProt NPD GO	YIM2_YEAST	Uncharacterized protein YIL122W	0.91	-	nuc	0		nucleus [IDA]			351
Q04279 UniProt NPD GO	YMX6_YEAST	Uncharacterized protein YMR086W	0.91	-	nuc	0		cytoplasm [IDA]			960
Q9BZF9 UniProt NPD GO	UACA_HUMAN	Uveal autoantigen with coiled-coil domains and ankyrin repeats protein	0.91	-	nuc	0	Nucleus. Cytoplasm. Expressed diffusely in cytoplasm	extracellular region [NAS]			1416
Q12071 UniProt NPD GO	VPS54_YEAST	Vacuolar protein sorting protein 54 (CPF1 genetically-interacting protein 1) (Temperature-sensitive ...	0.91	-	nuc	0	Golgi apparatus; trans-Golgi network; trans-Golgi network membrane; peripheral membrane protein. End ...	GARP complex [IPI] Golgi apparatus [IDA] mitochondrion [IDA]			889
P70460 UniProt NPD GO	VASP_MOUSE	Vasodilator-stimulated phosphoprotein (VASP)	0.91	-	nuc	0	Cytoplasm. Targeted to stress fibers and focal adhesions through interaction with a number of protei ...	filopodium [IDA] focal adhesion [IDA] lamellipodium [IDA]			374
Q9I9A3 UniProt NPD GO	VSX2_ORYLA	Visual system homeobox 2 (Transcription factor VSX2)	0.91	+	nuc	0	Nucleus (By similarity)				393
P18709 UniProt NPD GO	VITA2_XENLA	Vitellogenin-A2 precursor (VTG A2) [Contains: Lipovitellin I; Lipovitellin II; Phosvitin]	0.91	-	exc	0					1807
Q96DN5 UniProt NPD GO	WDR67_HUMAN	WD repeat protein 67	0.91	-	nuc	0					1066
Q6NXY1 UniProt NPD GO	WDR67_MOUSE	WD repeat protein 67 (Protein 4-B-3)	0.91	-	cyt	0					996
Q65Z40 UniProt NPD GO	WAPL_MOUSE	Wings apart-like protein homolog (Dioxin-inducible factor 2) (DIF-2)	0.91	+	nuc	0					1200
Q5REG6 UniProt NPD GO	ZC11A_PONPY	Zinc finger CCCH domain-containing protein 11A	0.91	-	nuc	0					811
Q5SVZ6 UniProt NPD GO	ZMYM1_HUMAN	Zinc finger MYM-type protein 1	0.91	-	nuc	0					1142
Q8R5C8 UniProt NPD GO	ZMY11_MOUSE	Zinc finger MYND domain-containing protein 11	0.91	-	nuc	0	Nucleus (By similarity)				562
Q9CU65 UniProt NPD GO	ZN198_MOUSE	Zinc finger protein 198 (Fragment)	0.91	-	nuc	0	Nucleus (Potential)				988
Q9ERU2 UniProt NPD GO	ZNF22_RAT	Zinc finger protein 22 (Krueppel-type zinc finger protein Krox-25)	0.91	+	nuc	0	Nucleus	nucleus [IDA]			237
Q9ERU3 UniProt NPD GO	ZNF22_MOUSE	Zinc finger protein 22 (Zinc finger protein 422) (Krox-25 protein) (Krox-26 protein)	0.91	+	nuc	0	Nucleus (By similarity)	nucleus [ISS]			237
Q9H4Z2 UniProt NPD GO	ZN335_HUMAN	Zinc finger protein 335	0.91	-	nuc	0	Nucleus (Probable)				1342
Q61751 UniProt NPD GO	TCF17_MOUSE	Zinc finger protein 354A (Transcription factor 17) (Renal transcription factor Kid-1) (Kidney, ische ...	0.91	-	nuc	0	Nucleus				572
Q7Z4V0 UniProt NPD GO	ZN438_HUMAN	Zinc finger protein 438	0.91	+	nuc	0	Nucleus (Probable)				828
Q8C0P7 UniProt NPD GO	ZN451_MOUSE	Zinc finger protein 451	0.91	-	nuc	0	Nucleus (Potential)				1056
Q7TSH3 UniProt NPD GO	ZN516_MOUSE	Zinc finger protein 516	0.91	-	nuc	0	Nucleus (Probable)				1157
O15015 UniProt NPD GO	ZN646_HUMAN	Zinc finger protein 646	0.91	-	nuc	0	Nucleus (Probable)				1829
P47976 UniProt NPD GO	CTH1_YEAST	Zinc finger protein CTH1	0.91	+	nuc	0	Nucleus (Potential)	nucleus [IC]			325
Q92785 UniProt NPD GO	REQU_HUMAN	Zinc-finger protein ubi-d4 (Requiem) (Apoptosis response zinc finger protein) (D4, zinc and double P ...	0.91	+	nuc	0	Nucleus. 30%. Cytoplasm. 70%		601671		391
Q9W638 UniProt NPD GO	REQUA_XENLA	Zinc-finger protein ubi-d4 A (Requiem A) (xReq A) (Apoptosis response zinc finger protein A)	0.91	+	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				388
P32023 UniProt NPD GO	KGP25_DROME	cGMP-dependent protein kinase, isozyme 2 forms cD5/T2 (EC 2.7.11.12) (CGK) (Foraging protein)	0.91	-	nuc	0					934
P79020 UniProt NPD GO	PALA_EMENI	pH-response regulator protein palA/RIM20	0.91	-	nuc	0					847
Q6FV94 UniProt NPD GO	PACC_CANGA	pH-response transcription factor pacC/RIM101	0.91	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				584
Q8K0S9 UniProt NPD GO	SNPC1_MOUSE	snRNA-activating protein complex subunit 1 (SNAPc subunit 1) (snRNA-activating protein complex 43 kD ...	0.91	-	nuc	0	Nucleus (By similarity)				389
Q8CE96 UniProt NPD GO	TRM6_MOUSE	tRNA (adenine-N(1)-)-methyltransferase non-catalytic subunit TRM6 (tRNA(m1A58)-methyltransferase sub ...	0.91	-	nuc	0	Nucleus (By similarity)				497
P40977 UniProt NPD GO	PLC1_SCHPO	1-phosphatidylinositol-4,5-bisphosphate phosphodiesterase 1 (EC 3.1.4.11) (PLC-1) (Phospholipase C-1 ...	0.90	-	nuc	0					899
P32383 UniProt NPD GO	PLC1_YEAST	1-phosphatidylinositol-4,5-bisphosphate phosphodiesterase 1 (EC 3.1.4.11) (Phosphoinositide phosphol ...	0.90	-	nuc	0		condensed nuclear chromosome kinetochore [IDA] nucleus [IDA]			869

You are viewing entries 4001 to 4050 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.