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
Q7L8S5 UniProt NPD GO	OTU6A_HUMAN	OTU domain-containing protein 6A	0.92	-	nuc	0					288
P54788 UniProt NPD GO	ORC1_KLULA	Origin recognition complex subunit 1	0.92	+	nuc	0	Nucleus				886
P25456 UniProt NPD GO	P43_XENLA	P43 5S RNA-binding protein (42S P43) (Thesaurin-B)	0.92	-	nuc	0					365
Q99JF8 UniProt NPD GO	PSIP1_MOUSE	PC4 and SFRS1-interacting protein (Lens epithelium-derived growth factor) (mLEDGF)	0.92	+	nuc	0	Nucleus (By similarity)				528
Q96BD5 UniProt NPD GO	PF21A_HUMAN	PHD finger protein 21A (BRAF35-HDAC complex protein BHC80) (BHC80a)	0.92	-	nuc	0	Nucleus (By similarity)		608325		680
Q96EK2 UniProt NPD GO	PF21B_HUMAN	PHD finger protein 21B	0.92	-	nuc	0					531
Q8C966 UniProt NPD GO	PF21B_MOUSE	PHD finger protein 21B	0.92	-	nuc	0					487
Q90482 UniProt NPD GO	POU50_BRARE	POU domain protein ZP-50	0.92	+	nuc	0	Nucleus				368
P15143 UniProt NPD GO	PO2F1_CHICK	POU domain, class 2, transcription factor 1 (Octamer-binding transcription factor 1) (Oct-1) (OTF-1) ...	0.92	+	nuc	0	Nucleus				739
Q29076 UniProt NPD GO	PO2F1_PIG	POU domain, class 2, transcription factor 1 (Octamer-binding transcription factor 1) (Oct-1) (OTF-1) ...	0.92	+	nuc	0	Nucleus (By similarity)				745
P57071 UniProt NPD GO	PRD15_HUMAN	PR domain zinc finger protein 15 (PR domain-containing protein 15) (Zinc finger protein 298)	0.92	+	nuc	0	Nucleus (Potential)	nucleus [NAS]			1507
Q9NQX1 UniProt NPD GO	PRDM5_HUMAN	PR domain zinc finger protein 5 (PR domain-containing protein 5)	0.92	+	nuc	0	Nucleus (Potential)				630
O94312 UniProt NPD GO	YH57_SCHPO	PWWP domain protein C215.07c	0.92	-	nuc	0				1H3Z	568
Q9BMQ6 UniProt NPD GO	MYSP_OPIFE	Paramyosin (Fragment)	0.92	-	nuc	0	Thick filaments of the myofibrils				638
P58073 UniProt NPD GO	PTHR_BOVIN	Parathyroid hormone-related protein precursor (PTH-rP) (PTHrP) [Contains: Osteostatin]	0.92	+	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity). Secreted protein (By similarity)				177
Q5AUG9 UniProt NPD GO	CWC27_EMENI	Peptidyl-prolyl isomerase cwc27 (EC 5.2.1.8)	0.92	+	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				558
O15055 UniProt NPD GO	PER2_HUMAN	Period circadian protein 2	0.92	+	nuc	0	Nucleus (Potential)		603426		1255
Q865B6 UniProt NPD GO	PRGC1_PIG	Peroxisome proliferator-activated receptor gamma coactivator 1-alpha (PPAR gamma coactivator 1-alpha ...	0.92	-	nuc	0	Nucleus (By similarity)	DNA-directed RNA polymerase II, core complex [ISS] nucleus [ISS]			796
Q8VHJ7 UniProt NPD GO	PRGC2_MOUSE	Peroxisome proliferator-activated receptor gamma coactivator 1-beta (PPAR gamma coactivator-1beta pr ...	0.92	+	nuc	0		nucleus [ISS]			1014
O70173 UniProt NPD GO	P3C2G_RAT	Phosphatidylinositol-4-phosphate 3-kinase C2 domain-containing gamma polypeptide (EC 2.7.1.154) (Pho ...	0.92	-	nuc	0	Membrane; peripheral membrane protein (By similarity)	Golgi apparatus [IDA] nuclear envelope [IDA] plasma membrane [IDA]			1505
Q6INI0 UniProt NPD GO	PI3R5_XENLA	Phosphoinositide 3-kinase regulatory subunit 5 (PI3-kinase regulatory subunit 5)	0.92	-	nuc	0	Nucleus (By similarity). Cytoplasm (By similarity). Membrane; peripheral membrane protein (By simila ...				879
Q9CZX5 UniProt NPD GO	PINX1_MOUSE	Pin2-interacting protein X1 (TRF1-interacting protein 1) (Liver-related putative tumor suppressor) ( ...	0.92	+	nuc	0	Nucleus (By similarity). Nucleus; nucleolus (By similarity). In nucleoli and at telomere speckles (B ...	chromosome, telomeric region [IDA] nucleolus [IDA]			332
O93385 UniProt NPD GO	PITX2_CHICK	Pituitary homeobox 2 (cPITX2)	0.92	+	nuc	0	Nucleus				333
Q00286 UniProt NPD GO	PIT1_MOUSE	Pituitary-specific positive transcription factor 1 (Pit-1) (Growth hormone factor 1) (GHF-1)	0.92	+	nuc	0	Nucleus	nucleus [IDA] transcription factor complex [IC]			291
Q61183 UniProt NPD GO	PAPOA_MOUSE	Poly(A) polymerase alpha (EC 2.7.7.19) (PAP) (Polynucleotide adenylyltransferase)	0.92	+	nuc	0	Nucleus (By similarity)				738
Q5RC51 UniProt NPD GO	PARN_PONPY	Poly(A)-specific ribonuclease PARN (EC 3.1.13.4) (Polyadenylate-specific ribonuclease)	0.92	+	nuc	0	Nucleus (By similarity). Cytoplasm (By similarity). Some nuclear fraction is nucleolar (By similarit ...				639
P93831 UniProt NPD GO	CLF_ARATH	Polycomb group protein CURLY LEAF (Protein INCURVATA 1) (Protein photoperiod insensitive flowering) ...	0.92	+	nuc	0	Nucleus				902
Q8W5B1 UniProt NPD GO	VRN2_ARATH	Polycomb group protein VERNALIZATION 2	0.92	-	nuc	0	Nucleus				440
Q9V727 UniProt NPD GO	ASX_DROME	Polycomb protein Asx (Additional sex combs)	0.92	-	nuc	0	Nucleus. Associated with chromatin. Colocalizes with many PcG sites on polytene chromosomes. It also ...	chromatin [IEP] nucleus [IDA]			1669
Q9QXK2 UniProt NPD GO	RAD18_MOUSE	Postreplication repair protein RAD18 (mRAD18Sc)	0.92	+	nuc	0	Nucleus	chromatin [IDA] nucleus [IDA]			509
Q6FPI4 UniProt NPD GO	RAD18_CANGA	Postreplication repair ubiquitin-protein ligase E3 RAD18 (EC 6.-.-.-)	0.92	-	nuc	0	Nucleus (By similarity)				411
Q6BLM3 UniProt NPD GO	RAD18_DEBHA	Postreplication repair ubiquitin-protein ligase E3 RAD18 (EC 6.-.-.-)	0.92	-	nuc	0	Nucleus (By similarity)				491
Q02398 UniProt NPD GO	RAD18_EMENI	Postreplication repair ubiquitin-protein ligase E3 rad18 (EC 6.-.-.-)	0.92	-	nuc	0	Nucleus (By similarity)				443
Q95167 UniProt NPD GO	KCNB2_CANFA	Potassium voltage-gated channel subfamily B member 2 (Voltage-gated potassium channel subunit Kv2.2) ...	0.92	-	nuc	4	Membrane; multi-pass membrane protein				809
Q6CCZ1 UniProt NPD GO	PRP5_YARLI	Pre-mRNA-processing ATP-dependent RNA helicase PRP5 (EC 3.6.1.-)	0.92	+	nuc	0	Nucleus (By similarity)				974
Q5AED6 UniProt NPD GO	CLF1_CANAL	Pre-mRNA-splicing factor CLF1	0.92	-	mit	0	Nucleus (By similarity)				758
Q59XY0 UniProt NPD GO	CWC22_CANAL	Pre-mRNA-splicing factor CWC22	0.92	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				648
Q5KM20 UniProt NPD GO	CWC26_CRYNE	Pre-mRNA-splicing factor CWC26	0.92	+	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				331
P53277 UniProt NPD GO	SYF2_YEAST	Pre-mRNA-splicing factor SYF2 (Synthetic lethal with CDC40 protein 2) (PRP19 complex protein 31)	0.92	-	nuc	0	Nucleus	spliceosome complex [IDA]			215
Q9P6R8 UniProt NPD GO	CWC24_SCHPO	Pre-mRNA-splicing factor cwc24 (Complexed with cdc5 protein 24) (Cell cycle control protein cwf24)	0.92	+	nuc	0	Nucleus (By similarity)	spliceosome complex [IDA]			533
Q5B0I1 UniProt NPD GO	CWC25_EMENI	Pre-mRNA-splicing factor cwc25	0.92	+	nuc	0	Nucleus (By similarity)				415
Q9VUM0 UniProt NPD GO	MSH6_DROME	Probable DNA mismatch repair protein MSH6	0.92	+	nuc	0					1190
Q6PCP7 UniProt NPD GO	GP156_MOUSE	Probable G-protein coupled receptor 156 (GABAB-related G-protein coupled receptor)	0.92	-	end	7 *	Membrane; multi-pass membrane protein	plasma membrane [IDA]			798
P34339 UniProt NPD GO	IF3A_CAEEL	Probable eukaryotic translation initiation factor 3 subunit 10 (eIF-3 theta) (eIF3a) (Egg-laying def ...	0.92	+	nuc	0					1076
P42694 UniProt NPD GO	HELZ_HUMAN	Probable helicase with zinc-finger domain (EC 3.6.1.-)	0.92	-	nuc	0	Nucleus (Probable)		606699		1942
Q9NH52 UniProt NPD GO	MES4_CAEEL	Probable histone methyltransferase mes-4 (Maternal-effect sterile protein 4)	0.92	-	nuc	0	Nucleus. Specifically associated with the autosomes. Colocalizes with methylated Lys-4 of histone H3 ...	nuclear chromosome [IEP]			898
Q2UL45 UniProt NPD GO	NDC80_ASPOR	Probable kinetochore protein ndc80	0.92	-	nuc	0	Nucleus (By similarity). Associated with kinetochores (By similarity)				736
Q6FNV1 UniProt NPD GO	NOP14_CANGA	Probable nucleolar complex protein 14	0.92	+	nuc	0	Nucleus; nucleolus (By similarity)				799
P53739 UniProt NPD GO	KN8R_YEAST	Probable serine/threonine-protein kinase YNR047W (EC 2.7.11.1)	0.92	-	nuc	0		cytoplasm [IDA]			893
P53749 UniProt NPD GO	YN92_YEAST	Probable transcriptional regulatory protein YNR063W	0.92	+	mit	0	Nucleus (Probable)				607

You are viewing entries 3351 to 3400 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.