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
Q86U06 UniProt NPD GO	RBM23_HUMAN	Probable RNA-binding protein 23 (RNA-binding motif protein 23) (RNA-binding region-containing protei ...	0.89	+	nuc	0	Nucleus (Potential)			2CQ4	439
Q8GWF1 UniProt NPD GO	WRK38_ARATH	Probable WRKY transcription factor 38 (WRKY DNA-binding protein 38)	0.89	-	nuc	0	Nucleus (Probable)				289
Q20678 UniProt NPD GO	EXOC1_CAEEL	Probable exocyst complex component 1 (Exocyst complex component Sec3)	0.89	-	nuc	0					848
Q9VNH6 UniProt NPD GO	EXOC4_DROME	Probable exocyst complex component 4 (Exocyst complex component Sec8)	0.89	-	nuc	0					985
O23372 UniProt NPD GO	ATXR3_ARATH	Probable histone-lysine N-methyltransferase ATXR3 (EC 2.1.1.43) (Trithorax-related protein 3) (TRX-r ...	0.89	+	nuc	0	Nucleus (By similarity)				2351
O60312 UniProt NPD GO	AT10A_HUMAN	Probable phospholipid-transporting ATPase VA (EC 3.6.3.1) (ATPVA) (Aminophospholipid translocase VA) ...	0.89	-	end	10	Membrane; multi-pass membrane protein (By similarity)	integral to membrane [NAS]	605855		1499
Q20822 UniProt NPD GO	SRP68_CAEEL	Probable signal recognition particle 68 kDa protein (SRP68)	0.89	-	nuc	0	Cytoplasm (By similarity)				622
O77459 UniProt NPD GO	KEN_DROME	Probable transcription factor Ken (Protein Ken and Barbie)	0.89	-	nuc	0	Nucleus (Probable)	nucleus [IMP]			601
Q9P7V9 UniProt NPD GO	UBP9_SCHPO	Probable ubiquitin carboxyl-terminal hydrolase 9 (EC 3.1.2.15) (Ubiquitin thioesterase 9) (Ubiquitin ...	0.89	+	nuc	0					585
Q12796 UniProt NPD GO	PNRC1_HUMAN	Proline-rich nuclear receptor coactivator 1 (Proline-rich protein 2) (B4-2 protein)	0.89	+	nuc	0	Nucleus (Potential)	nucleus [TAS]	606714		327
P11248 UniProt NPD GO	PRM2_RAT	Protamine-2 (Protamine-P2) (Sperm histone P2)	0.89	+	nuc	0	Nucleus				104
P11171 UniProt NPD GO	41_HUMAN	Protein 4.1 (Band 4.1) (P4.1) (EPB4.1) (4.1R)	0.89	+	nuc	0	Cytoplasm. Nucleus	plasma membrane [TAS] spectrin [TAS]	130500	1GG3	864
Q9VM95 UniProt NPD GO	AATF_DROME	Protein AATF-like	0.89	+	nuc	0	Nucleus (By similarity)	nucleus [ISS]			488
Q06604 UniProt NPD GO	BSP1_YEAST	Protein BSP1 (Binding of synaptojanin polyphosphoinositide phosphatase domain protein 1)	0.89	-	nuc	0	Cell membrane; peripheral membrane protein. Actin patches. Peripheral membrane protein in a PtdIns(4 ...	actin cortical patch [IDA] bud neck [IDA] bud tip [IDA] membrane fraction [IDA]			576
Q5R939 UniProt NPD GO	CJ084_PONPY	Protein C10orf84 homolog	0.89	+	nuc	0					233
Q9NZP6 UniProt NPD GO	CO002_HUMAN	Protein C15orf2	0.89	-	nuc	0					1156
O95447 UniProt NPD GO	CU013_HUMAN	Protein C21orf13	0.89	-	nuc	0					670
Q8CDN1 UniProt NPD GO	CC020_MOUSE	Protein C3orf20 homolog	0.89	-	nuc	1	Membrane; single-pass membrane protein (Potential)				933
Q6AXS3 UniProt NPD GO	DEK_RAT	Protein DEK	0.89	-	nuc	0	Nucleus (Potential)				378
Q6PNC0 UniProt NPD GO	DMXL1_MOUSE	Protein DmX-like 1 (X-like 1 protein)	0.89	-	nuc	0					3013
Q8BP78 UniProt NPD GO	F10C1_MOUSE	Protein FRA10AC1 homolog	0.89	+	nuc	0	Nucleus (By similarity)				315
Q5FVF1 UniProt NPD GO	F10C1_RAT	Protein FRA10AC1 homolog	0.89	+	nuc	0	Nucleus (By similarity)				315
Q5VT52 UniProt NPD GO	K0460_HUMAN	Protein KIAA0460	0.89	+	nuc	0					1461
Q75RY2 UniProt NPD GO	PAIR1_ORYSA	Protein PAIR1 (HOMOLOGOUS PAIRING ABERRATION IN RICE MEIOSIS 1 protein)	0.89	+	nuc	0	Nucleus	nucleus [IDA]			492
P43606 UniProt NPD GO	PTR3_YEAST	Protein PTR3 (Protein SSY3)	0.89	-	nuc	0		extrinsic to plasma membrane [IDA]			678
P35208 UniProt NPD GO	SPT10_YEAST	Protein SPT10	0.89	-	nuc	0		nucleus [TAS]			640
Q63ZG9 UniProt NPD GO	ZN403_XENLA	Protein ZNF403	0.89	+	nuc	0	Cytoplasm (By similarity)				664
O42632 UniProt NPD GO	KPC1_COCHE	Protein kinase C-like (EC 2.7.11.13)	0.89	-	nuc	0					1174
P91664 UniProt NPD GO	MAX_DROME	Protein max (Myc-associated factor X) (dMax)	0.89	+	nuc	0	Nucleus	nucleus [IC]			161
Q76I79 UniProt NPD GO	SSH1_MOUSE	Protein phosphatase Slingshot homolog 1 (EC 3.1.3.48) (EC 3.1.3.16) (SSH-1L) (mSSH-1L)	0.89	-	nuc	0	Localized to the cleavage furrow and the midbody during cytokinesis (By similarity). Cytoplasmic. Al ...				1042
P13368 UniProt NPD GO	7LESS_DROME	Protein sevenless (EC 2.7.10.1)	0.89	+	end	1		plasma membrane [IDA]			2554
Q06698 UniProt NPD GO	YL419_YEAST	Putative ATP-dependent RNA helicase YLR419W (EC 3.6.1.-)	0.89	+	nuc	0	Cytoplasm	mitochondrion [IDA]			1435
Q6PHZ5 UniProt NPD GO	RB15B_MOUSE	Putative RNA-binding protein 15B (RNA-binding motif protein 15B)	0.89	-	nuc	0	Nucleus (Probable)			1WHY	564
O60231 UniProt NPD GO	DHX16_HUMAN	Putative pre-mRNA-splicing factor ATP-dependent RNA helicase DHX16 (EC 3.6.1.-) (DEAH-box protein 16 ...	0.89	+	nuc	0	Nucleus	nucleus [TAS]	603405		1041
Q7YR39 UniProt NPD GO	DHX16_PANTR	Putative pre-mRNA-splicing factor ATP-dependent RNA helicase DHX16 (EC 3.6.1.-) (DEAH-box protein 16 ...	0.89	+	nuc	0	Nucleus				1044
Q5JKN2 UniProt NPD GO	ABIL2_ORYSA	Putative protein ABIL2 (Abl interactor-like protein 2)	0.89	-	nuc	0					323
Q12152 UniProt NPD GO	YP150_YEAST	Putative serine/threonine-protein kinase YPL150W (EC 2.7.11.1)	0.89	-	nuc	0					901
Q08471 UniProt NPD GO	YO066_YEAST	Putative transcriptional activator YOR066W	0.89	+	nuc	0					629
O42926 UniProt NPD GO	VP132_SCHPO	Putative vacuolar protein sorting-associated protein vps1302	0.89	-	nuc	0					3131
P10563 UniProt NPD GO	QUTA_EMENI	Quinic acid utilization activator	0.89	-	nuc	0	Nucleus				825
Q8C551 UniProt NPD GO	R51A1_MOUSE	RAD51-associated protein 1 (RAD51-interacting protein) (RAB22)	0.89	-	nuc	0	Nucleus. Colocalizes with RAD51 to multiple nuclear foci	nucleus [IDA]			337
Q92766 UniProt NPD GO	RREB1_HUMAN	RAS-responsive element-binding protein 1 (RREB-1) (Raf-responsive zinc finger protein LZ321)	0.89	-	nuc	0	Nucleus		602209		755
Q63068 UniProt NPD GO	RNUXA_RAT	RNA U small nuclear RNA export adapter protein (Phosphorylated adapter RNA export protein) (Resinife ...	0.89	-	nuc	0	Nucleus (By similarity). Nucleus; nucleoplasm (By similarity). Nucleus; nucleoplasm; Cajal body (By ...				385
Q9Y388 UniProt NPD GO	RBMX2_HUMAN	RNA-binding motif protein, X-linked 2	0.89	+	nuc	0					322
Q9NW13 UniProt NPD GO	RBM28_HUMAN	RNA-binding protein 28 (RNA-binding motif protein 28)	0.89	+	nuc	0	Nucleus; nucleolus				758
Q09100 UniProt NPD GO	RNP24_SCHPO	RNA-binding protein rnp24	0.89	+	nuc	0	Nucleus				369
Q8K3I4 UniProt NPD GO	MYRIP_MOUSE	Rab effector MyRIP (Myosin-VIIa- and Rab-interacting protein) (Exophilin-8) (Slp homolog lacking C2 ...	0.89	-	nuc	0	Cytoplasm. In pre- and post-synaptic areas in photoreceptor cells and in the basal microvilli of ret ...	actin cytoskeleton [IDA] synapse [IDA]			856
Q14644 UniProt NPD GO	RASA3_HUMAN	Ras GTPase-activating protein 3 (GAP1(IP4BP)) (Ins P4-binding protein)	0.89	+	nuc	0	Cell membrane	plasma membrane [TAS]	605182		834
Q18563 UniProt NPD GO	RGS6_CAEEL	Regulator of G-protein signaling rgs-6	0.89	-	nuc	0					737
P27705 UniProt NPD GO	MIG1_YEAST	Regulatory protein MIG1 (Regulatory protein CAT4)	0.89	-	nuc	0	Nucleus	cytoplasm [IDA] nucleus [IDA]			504

You are viewing entries 4801 to 4850 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.