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
P42681 UniProt NPD GO	TXK_HUMAN	Tyrosine-protein kinase TXK (EC 2.7.10.2)	0.62	-	mit	0	Cytoplasm (Probable)		600058		527
P35831 UniProt NPD GO	PTN12_MOUSE	Tyrosine-protein phosphatase non-receptor type 12 (EC 3.1.3.48) (Protein-tyrosine phosphatase P19) ( ...	0.62	-	nuc	0	Cytoplasm	cytosol [IDA]			775
Q62189 UniProt NPD GO	SNRPA_MOUSE	U1 small nuclear ribonucleoprotein A (U1 snRNP protein A) (U1A protein) (U1-A)	0.62	+	nuc	0	Nucleus (By similarity)				286
O43818 UniProt NPD GO	U3IP2_HUMAN	U3 small nucleolar RNA-interacting protein 2 (U3 small nucleolar ribonucleoprotein-associated 55 kDa ...	0.62	+	mit	0	Nucleus; nucleolus	small nuclear ribonucleoprotein complex [TAS] small nucleolar ribonucleoprotein complex [TAS]			475
Q96LJ8 UniProt NPD GO	UBXD3_HUMAN	UBX domain-containing protein 3	0.62	-	nuc	0					280
Q9JLA3 UniProt NPD GO	UGGG1_RAT	UDP-glucose:glycoprotein glucosyltransferase 1 precursor (EC 2.4.1.-) (UDP-glucose ceramide glucosyl ...	0.62	-	end	0	Endoplasmic reticulum; endoplasmic reticulum lumen. Endoplasmic reticulum-Golgi intermediate compart ...	endoplasmic reticulum [TAS] endoplasmic reticulum lumen [IDA] ER-Golgi intermediate compartment [IDA]			1527
Q5ZJT1 UniProt NPD GO	DC12_CHICK	UPF0361 protein DC12 homolog	0.62	-	mit	0					336
Q6P7N4 UniProt NPD GO	DC12_XENTR	UPF0361 protein DC12 homolog	0.62	-	nuc	0					335
P87167 UniProt NPD GO	BUT2_SCHPO	Uba3-binding protein but2	0.62	-	nuc	0					390
Q9BQL6 UniProt NPD GO	URP1_HUMAN	Unc-112-related protein 1 (Kindlin-1) (Kindlerin) (Kindlin syndrome protein)	0.62	-	cyt	0	Cytoplasm. Colocalizes with filamentous actin. Cell membrane; cell-matrix junction; focal adhesion. ...		607900		677
Q5R8D5 UniProt NPD GO	CA037_PONPY	Uncharacterized protein C1orf37 homolog	0.62	-	nuc	1					387
Q9D2X8 UniProt NPD GO	CH076_MOUSE	Uncharacterized protein C8orf76 homolog	0.62	-	nuc	0					372
P40002 UniProt NPD GO	YEA7_YEAST	Uncharacterized protein YEL007W	0.62	-	nuc	0		cytoplasm [IDA] nucleus [IDA]			666
P40022 UniProt NPD GO	YEM4_YEAST	Uncharacterized protein YER034W	0.62	+	nuc	0		cytoplasm [IDA] nucleus [IDA]			185
P46951 UniProt NPD GO	YG4B_YEAST	Uncharacterized protein YGR198W	0.62	-	cyt	0		cytoplasm [IDA] plasma membrane [IDA]			817
Q03653 UniProt NPD GO	YM62_YEAST	Uncharacterized protein YMR212C	0.62	-	nuc	0		mitochondrion [IDA]			782
Q12232 UniProt NPD GO	YO154_YEAST	Uncharacterized protein YOR154W precursor	0.62	-	exc	2 *	Membrane; single-pass type I membrane protein (Potential)				587
P37806 UniProt NPD GO	UNC87_CAEEL	Uncoordinated protein 87 (Protein unc-87)	0.62	-	nuc	0					576
P22674 UniProt NPD GO	UNG2_HUMAN	Uracil-DNA glycosylase 2 (EC 3.2.2.-) (UDG 2)	0.62	-	nuc	0	Nucleus	nucleoplasm [IDA]	607752		326
Q96LB4 UniProt NPD GO	VATG3_HUMAN	Vacuolar ATP synthase subunit G 3 (EC 3.6.3.14) (V-ATPase G subunit 3) (Vacuolar proton pump G subun ...	0.62	+	nuc	0					118
Q63616 UniProt NPD GO	VP33B_RAT	Vacuolar protein sorting 33B (r-vps33b)	0.62	-	cyt	0	Late endosome; late endosomal membrane; peripheral membrane protein (By similarity). Lysosome; lysos ...				617
Q5VIR6 UniProt NPD GO	VPS53_HUMAN	Vacuolar protein sorting protein 53	0.62	-	cyt	0	Golgi apparatus; trans-Golgi network; trans-Golgi network membrane; peripheral membrane protein. End ...				699
Q5R5J4 UniProt NPD GO	VPS53_PONPY	Vacuolar protein sorting protein 53	0.62	-	cyt	0	Golgi apparatus; trans-Golgi network; trans-Golgi network membrane; peripheral membrane protein (By ...				699
Q9JMK8 UniProt NPD GO	VPS54_RAT	Vacuolar protein sorting protein 54 (Vps54-like protein)	0.62	-	nuc	0					965
Q5YF90 UniProt NPD GO	NGFV1_NAJSP	Venom nerve growth factor 1 precursor (vNGF-1) (Nerve growth factor I)	0.62	-	exc	0	Secreted protein				243
O94484 UniProt NPD GO	YC73_SCHPO	Very hypothetical protein C417.03 in chromosome III	0.62	-	nuc	0					100
P18948 UniProt NPD GO	VIT6_CAEEL	Vitellogenin-6 precursor	0.62	-	exc	0	Secreted protein				1650
O13286 UniProt NPD GO	SRW1_SCHPO	WD repeat-containing protein srw1 (Suppressor of rad/wee1)	0.62	-	nuc	0					556
Q8WYQ9 UniProt NPD GO	ZCH14_HUMAN	Zinc finger CCHC domain-containing protein 14 (BDG-29)	0.62	-	nuc	0					949
Q9H7M6 UniProt NPD GO	ZSWM4_HUMAN	Zinc finger SWIM domain-containing protein 4	0.62	-	cyt	0					989
Q80TB7 UniProt NPD GO	ZSWM6_MOUSE	Zinc finger SWIM domain-containing protein 6 (Fragment)	0.62	-	cyt	0					1017
Q15916 UniProt NPD GO	ZN482_HUMAN	Zinc finger and BTB domain-containing protein 6 (Zinc finger protein 482) (Zinc finger protein with ...	0.62	-	nuc	0	Nucleus	nucleus [TAS]	605976		424
Q8NAP8 UniProt NPD GO	ZBTB8_HUMAN	Zinc finger and BTB domain-containing protein 8	0.62	-	nuc	0	Nucleus (Potential)				512
Q8NAM6 UniProt NPD GO	ZSCA4_HUMAN	Zinc finger and SCAN domain-containing protein 4 (Zinc finger protein 494)	0.62	-	nuc	0	Nucleus (Potential)				433
P17013 UniProt NPD GO	ZN11A_HUMAN	Zinc finger protein 11A (Zinc finger protein KOX2) (Fragments)	0.62	-	nuc	0	Nucleus (Potential)	nucleus [NAS]	194521		301
P17017 UniProt NPD GO	ZNF14_HUMAN	Zinc finger protein 14 (Zinc finger protein KOX6) (Gonadotropin-inducible transcription repressor 4) ...	0.62	-	nuc	0	Nucleus (Probable)		194556		642
Q9HCL3 UniProt NPD GO	ZFP14_HUMAN	Zinc finger protein 14 homolog (Zfp-14)	0.62	-	nuc	0	Nucleus (Probable)				533
Q9Y473 UniProt NPD GO	ZN175_HUMAN	Zinc finger protein 175 (Zinc finger protein OTK18)	0.62	-	nuc	0	Cytoplasm. Nucleus		601139		711
Q5R9S5 UniProt NPD GO	ZN182_PONPY	Zinc finger protein 182 (Zinc finger protein 21)	0.62	-	nuc	0	Nucleus (Potential)				620
P17030 UniProt NPD GO	ZNF25_HUMAN	Zinc finger protein 25 (Zinc finger protein KOX19)	0.62	-	nuc	0	Nucleus (Potential)		194528		456
Q9ERR8 UniProt NPD GO	ZN319_MOUSE	Zinc finger protein 319	0.62	-	nuc	0	Nucleus (Probable)	nucleus [IDA]			581
O70524 UniProt NPD GO	ZN330_CRIGR	Zinc finger protein 330 (Nucleolar cysteine-rich protein) (Nucleolar autoantigen 36)	0.62	-	nuc	0	Nucleus (By similarity). Nucleus; nucleolus (By similarity). Predominantly expressed in nucleolus. I ...				317
Q5PPH4 UniProt NPD GO	ZN414_RAT	Zinc finger protein 414	0.62	-	nuc	0	Nucleus (Probable)				299
Q8N9F8 UniProt NPD GO	ZN454_HUMAN	Zinc finger protein 454	0.62	-	nuc	0	Nucleus (Potential)				522
Q8TA94 UniProt NPD GO	ZN563_HUMAN	Zinc finger protein 563	0.62	-	nuc	0	Nucleus (Potential)				476
Q969W8 UniProt NPD GO	ZN566_HUMAN	Zinc finger protein 566	0.62	-	nuc	0	Nucleus (Probable)				418
Q9GM03 UniProt NPD GO	ZN575_MACFA	Zinc finger protein 575	0.62	-	nuc	0	Nucleus (Potential)				260
Q8N8J6 UniProt NPD GO	ZN615_HUMAN	Zinc finger protein 615	0.62	-	nuc	0	Nucleus (Potential)				555
Q86XU0 UniProt NPD GO	ZN677_HUMAN	Zinc finger protein 677	0.62	-	nuc	0	Nucleus (Probable)				584
Q5VV52 UniProt NPD GO	ZN691_HUMAN	Zinc finger protein 691	0.62	-	nuc	0	Nucleus (Probable)				312

You are viewing entries 18251 to 18300 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.