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
Q9LEM8 UniProt NPD GO	NAC2_CHLRE	PsbD mRNA maturation factor Nac2, chloroplast precursor	0.70	-	nuc	0	Plastid; chloroplast; chloroplast stroma				1385
Q99PU8 UniProt NPD GO	DHX30_MOUSE	Putative ATP-dependent RNA helicase DHX30 (EC 3.6.1.-) (DEAH box protein 30)	0.70	-	mit	0					1217
P34305 UniProt NPD GO	RHA2_CAEEL	Putative ATP-dependent RNA helicase rha-2 (EC 3.6.1.-)	0.70	-	mit	0					1148
Q9LRW1 UniProt NPD GO	LBD22_ARATH	Putative LOB domain-containing protein 22	0.70	-	mit	0					268
Q09769 UniProt NPD GO	LONM_SCHPO	Putative Lon protease homolog, mitochondrial precursor (EC 3.4.21.-)	0.70	-	nuc	0	Mitochondrion; mitochondrial matrix (Potential)				1067
Q9ZVH0 UniProt NPD GO	NAC9_ARATH	Putative NAC domain-containing protein 9 (ANAC009)	0.70	-	nuc	0	Nucleus (Potential)				418
Q9FIY7 UniProt NPD GO	SM3L3_ARATH	Putative SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member ...	0.70	-	cyt	0	Nucleus (By similarity)				1277
Q8INZ1 UniProt NPD GO	GR36D_DROME	Putative chemosensory receptor 36d	0.70	-	end	5 *	Membrane; multi-pass membrane protein (Potential)	integral to membrane [ISS]			410
O13799 UniProt NPD GO	YE02_SCHPO	Putative helicase C17H9.02 (EC 3.6.1.-)	0.70	-	nuc	0	Nucleus (Potential)				1030
P80235 UniProt NPD GO	CACM_YEAST	Putative mitochondrial carnitine O-acetyltransferase (EC 2.3.1.7)	0.70	-	mit	0	Mitochondrion; mitochondrial inner membrane; intermembrane side	mitochondrion [IDA]			687
Q9VQ79 UniProt NPD GO	PDCD8_DROME	Putative oxidoreductase CG7263, mitochondrial precursor (EC 1.-.-.-)	0.70	+	nuc	1	Mitochondrion; mitochondrial intermembrane space (By similarity)				739
Q9UVG6 UniProt NPD GO	VPS15_PICPA	Putative serine/threonine-protein kinase VPS15 (EC 2.7.11.1) (Vacuolar protein sorting protein 15)	0.70	-	nuc	0	Golgi apparatus; trans-Golgi network; trans-Golgi network membrane; lipid-anchor (By similarity). En ...				1339
O22928 UniProt NPD GO	PUSH_ARATH	Putative tRNA pseudouridine synthase (EC 5.4.99.-) (tRNA-uridine isomerase) (tRNA pseudouridylate sy ...	0.70	-	mit	0					510
Q9BZA5 UniProt NPD GO	CY15A_HUMAN	Putative testis protein CYorf15A	0.70	-	nuc	0			400031		182
Q9BR46 UniProt NPD GO	CT078_HUMAN	Putative uncharacterized protein C20orf78	0.70	-	nuc	0					151
O59669 UniProt NPD GO	YB85_SCHPO	Putative zinc-finger protein C29A3.05	0.70	+	nuc	0					139
Q5M7L6 UniProt NPD GO	RSPO2_XENTR	R-spondin-2 precursor (Roof plate-specific spondin-2)	0.70	+	nuc	0	Secreted protein (By similarity)				243
P48743 UniProt NPD GO	RFX1_YEAST	RFX-like DNA-binding protein RFX1	0.70	-	nuc	0		cytoplasm [IDA] nucleus [IDA]			811
Q99KR6 UniProt NPD GO	RNF34_MOUSE	RING finger protein 34 (RING finger protein RIFF) (Phafin-1)	0.70	-	exc	0	Nucleus; nucleoplasm; nuclear speckle (By similarity). Intracellular membrane; peripheral membrane p ...				376
Q8BI21 UniProt NPD GO	RNF38_MOUSE	RING finger protein 38	0.70	+	nuc	0					518
Q7M3S9 UniProt NPD GO	RNGB_DICDI	RING finger protein B (Protein rngB)	0.70	-	nuc	0	Cytoplasm				943
P38748 UniProt NPD GO	YHB0_YEAST	RING finger protein YHL010C	0.70	-	nuc	0					585
Q8CCI5 UniProt NPD GO	RYBP_MOUSE	RING1 and YY1-binding protein (Death effector domain-associated factor) (DED-associated factor)	0.70	+	nuc	0	Nucleus (By similarity). Cytoplasm (By similarity). Primarily found in the nucleus (By similarity)	nucleoplasm [IDA] nucleus [IDA]			228
O13745 UniProt NPD GO	TFB1_SCHPO	RNA polymerase II transcription factor B subunit 1 (RNA polymerase II transcription factor B p73 sub ...	0.70	-	nuc	0	Nucleus (By similarity)				477
Q75D20 UniProt NPD GO	TFB3_ASHGO	RNA polymerase II transcription factor B subunit 3 (RNA polymerase II transcription factor B p38 sub ...	0.70	-	cyt	0	Nucleus (By similarity)				318
Q6FMP4 UniProt NPD GO	TFB3_CANGA	RNA polymerase II transcription factor B subunit 3 (RNA polymerase II transcription factor B p38 sub ...	0.70	-	nuc	0	Nucleus (By similarity)				330
P69735 UniProt NPD GO	RB3GP_RAT	Rab3 GTPase-activating protein catalytic subunit (RAB3 GTPase-activating protein 130 kDa subunit) (R ...	0.70	-	cyt	0	Cytoplasm. In neurons, it is enriched in the synaptic soluble fraction				774
P34892 UniProt NPD GO	KIN16_CAEEL	Receptor-like tyrosine-protein kinase kin-16 precursor (EC 2.7.10.1)	0.70	-	end	1					495
Q9LSM5 UniProt NPD GO	SGT1_ARATH	SGT1 protein homolog At5g65490	0.70	-	exc	0					643
Q9W032 UniProt NPD GO	SGT1_DROME	SGT1 protein homolog ecdysoneless	0.70	-	nuc	0	Cytoplasm				684
Q9NZQ3 UniProt NPD GO	SPN90_HUMAN	SH3 adapter protein SPIN90 (NCK-interacting protein with SH3 domain) (SH3 protein interacting with N ...	0.70	-	nuc	0	Nucleus. Colocalizes with DRF1 at membrane ruffles, and with Nck at Z-disks in mature cardiac myocyt ...	intermediate filament [NAS]			722
Q9Z131 UniProt NPD GO	3BP5_MOUSE	SH3 domain-binding protein 5 (SH3 domain-binding protein that preferentially associates with BTK)	0.70	-	nuc	0	Mitochondrion (By similarity)	cytoplasm [IC]			431
Q9S7P9 UniProt NPD GO	SNP33_ARATH	SNAP25 homologous protein SNAP33 (AtSNAP33) (Synaptosomal-associated protein SNAP25-like 1) (SNAP-25 ...	0.70	-	nuc	0	Membrane. Plasma membrane, some endomembrane compartment and cell plate in dividing cells				300
Q04890 UniProt NPD GO	SOX12_MOUSE	SOX-12 protein	0.70	-	nuc	0	Nucleus (Potential)				314
Q5U379 UniProt NPD GO	SNF5_BRARE	SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1	0.70	-	nuc	0	Nucleus (By similarity)				373
Q8MIZ3 UniProt NPD GO	DCPS_PIG	Scavenger mRNA decapping enzyme DcpS (EC 3.-.-.-) (DCS-1) (Hint-related 7meGMP-directed hydrolase) ( ...	0.70	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				337
P14150 UniProt NPD GO	HMEN_SCHAM	Segmentation polarity homeobox protein engrailed (G-EN) (Fragment)	0.70	+	nuc	0	Nucleus (Probable)				93
Q09883 UniProt NPD GO	SPN6_SCHPO	Septin homolog spn6	0.70	-	nuc	0	Cortices of developing spores				380
Q5R6R7 UniProt NPD GO	SEPT4_PONPY	Septin-4	0.70	-	nuc	0					478
Q91604 UniProt NPD GO	STK11_XENLA	Serine/threonine-protein kinase 11 (EC 2.7.11.1) (Serine/threonine-protein kinase XEEK1) (Egg and em ...	0.70	-	cyt	0	Cytoplasm				432
Q8WU08 UniProt NPD GO	ST32A_HUMAN	Serine/threonine-protein kinase 32A (EC 2.7.11.1) (YANK1)	0.70	+	nuc	0					396
Q9NRP7 UniProt NPD GO	STK36_HUMAN	Serine/threonine-protein kinase 36 (EC 2.7.11.1) (Fused homolog)	0.70	-	end	0	Cytoplasm. Nucleus. Low levels also present in the nucleus	cytoplasm [IDA] nucleus [IDA]	607652		1315
Q501V0 UniProt NPD GO	KPSH1_BRARE	Serine/threonine-protein kinase H1 homolog (EC 2.7.11.1)	0.70	-	nuc	0					422
P38970 UniProt NPD GO	HAL5_YEAST	Serine/threonine-protein kinase HAL5 (EC 2.7.11.1) (Halotolerence protein 5)	0.70	-	nuc	0					855
P38692 UniProt NPD GO	KIC1_YEAST	Serine/threonine-protein kinase KIC1 (EC 2.7.11.1) (Kinase that interacts with CDC31) (N-rich kinase ...	0.70	-	nuc	0		bud [IDA] cytoplasm [IDA] incipient bud site [IDA] mating projection tip [IDA]			1080
Q04899 UniProt NPD GO	PCTK3_MOUSE	Serine/threonine-protein kinase PCTAIRE-3 (EC 2.7.11.22) (PCTAIRE-motif protein kinase 3)	0.70	-	nuc	0					451
P23561 UniProt NPD GO	STE11_YEAST	Serine/threonine-protein kinase STE11 (EC 2.7.11.1)	0.70	-	nuc	0		cytoplasm [IDA]		1X9X	738
Q4WPF2 UniProt NPD GO	ATG1_ASPFU	Serine/threonine-protein kinase atg1 (EC 2.7.11.1) (Autophagy-related protein 1)	0.70	-	nuc	0	Cytoplasm (By similarity)				973
O74630 UniProt NPD GO	ATM_SCHPO	Serine/threonine-protein kinase tel1 (EC 2.7.11.1) (DNA-damage checkpoint kinase tel1) (Telomere len ...	0.70	-	end	0	Nucleus. Localizes to nuclear DNA repair foci with other DNA repair proteins in response to DNA doub ...				2812
Q23023 UniProt NPD GO	UNC51_CAEEL	Serine/threonine-protein kinase unc-51 (EC 2.7.11.1) (Uncoordinated protein 51)	0.70	-	nuc	0		nucleus [IDA]			856

You are viewing entries 13951 to 14000 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.