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
Q15696 UniProt NPD GO	U2AFM_HUMAN	U2 small nuclear ribonucleoprotein auxiliary factor 35 kDa subunit-related protein 2 (U2(RNU2) small ...	0.99	+	nuc	0	Nucleus (Potential)	minor (U12-dependent) spliceosome complex [IDA]	300028		482
Q04500 UniProt NPD GO	UTP14_YEAST	U3 small nucleolar RNA-associated protein 14 (U3 snoRNA-associated protein 14)	0.99	+	nuc	0	Nucleus; nucleolus	small nucleolar ribonucleoprotein complex [IPI]			899
O00566 UniProt NPD GO	MPP10_HUMAN	U3 small nucleolar ribonucleoprotein protein MPP10 (M phase phosphoprotein 10)	0.99	+	nuc	0	Nucleus; nucleolus. Fibrillar region of the nucleolus. After dissolution of the nucleolus in early M ...	nucleolus [IDA] small nucleolar ribonucleoprotein complex [NAS]	605503		681
Q810V0 UniProt NPD GO	MPP10_MOUSE	U3 small nucleolar ribonucleoprotein protein MPP10 (M phase phosphoprotein 10)	0.99	+	nuc	0	Nucleus; nucleolus (By similarity). Fibrillar region of the nucleolus. After dissolution of the nucl ...				681
Q10988 UniProt NPD GO	UVE1_SCHPO	UV-damage endonuclease (EC 3.-.-.-) (UVDE)	0.99	+	mit	0		mitochondrion [IDA] nucleus [IDA]			599
Q9BXU7 UniProt NPD GO	UBP26_HUMAN	Ubiquitin carboxyl-terminal hydrolase 26 (EC 3.1.2.15) (Ubiquitin thioesterase 26) (Ubiquitin-specif ...	0.99	+	nuc	0			300309		913
Q86T82 UniProt NPD GO	UBP37_HUMAN	Ubiquitin carboxyl-terminal hydrolase 37 (EC 3.1.2.15) (Ubiquitin thioesterase 37) (Ubiquitin-specif ...	0.99	-	nuc	0					979
Q70EK9 UniProt NPD GO	UBP51_HUMAN	Ubiquitin carboxyl-terminal hydrolase 51 (EC 3.1.2.15) (Ubiquitin thioesterase 51) (Ubiquitin-specif ...	0.99	+	nuc	0					711
Q80U87 UniProt NPD GO	UBP8_MOUSE	Ubiquitin carboxyl-terminal hydrolase 8 (EC 3.1.2.15) (Ubiquitin thioesterase 8) (Ubiquitin-specific ...	0.99	-	nuc	0		intracellular [IDA]			1080
P39967 UniProt NPD GO	UBP9_YEAST	Ubiquitin carboxyl-terminal hydrolase 9 (EC 3.1.2.15) (Ubiquitin thioesterase 9) (Ubiquitin-specific ...	0.99	-	nuc	0		cytoplasm [IC]			754
Q6UWE0 UniProt NPD GO	LRSM1_HUMAN	Ubiquitin ligase protein LRSAM1 (EC 6.3.2.-) (Leucine-rich repeat and sterile alpha motif-containing ...	0.99	-	nuc	0	Cytoplasm. Displays a punctuate distribution and localizes to a submembranal ring				723
Q80XC6 UniProt NPD GO	CN102_MOUSE	Uncharacterized protein C14orf102 homolog	0.99	+	nuc	0					1172
Q9NWQ4 UniProt NPD GO	CN118_HUMAN	Uncharacterized protein C14orf118	0.99	+	nuc	1					453
Q9CS00 UniProt NPD GO	CS029_MOUSE	Uncharacterized protein C19orf29 homolog	0.99	+	mit	0					772
Q7Z570 UniProt NPD GO	CB010_HUMAN	Uncharacterized protein C2orf10	0.99	+	nuc	0					1209
P38321 UniProt NPD GO	YB75_YEAST	Uncharacterized protein YBR225W	0.99	-	nuc	0					900
P36115 UniProt NPD GO	YKZ9_YEAST	Uncharacterized protein YKR019C	0.99	+	nuc	0		mitochondrion [IDA]			615
Q867B5 UniProt NPD GO	RAG1_PIG	V(D)J recombination-activating protein 1 (RAG-1)	0.99	+	nuc	0	Nucleus (By similarity)				1043
P41846 UniProt NPD GO	WBS14_CAEEL	WBSCR14 protein homolog (Mlx interactor)	0.99	-	nuc	0	Nucleus (By similarity)				1009
Q96KN7 UniProt NPD GO	RPGR1_HUMAN	X-linked retinitis pigmentosa GTPase regulator-interacting protein 1 (RPGR-interacting protein 1)	0.99	-	nuc	0	Situated between the axonemal microtubules and the plasma membrane (By similarity)		608194		1286
Q9EPQ2 UniProt NPD GO	RPGR1_MOUSE	X-linked retinitis pigmentosa GTPase regulator-interacting protein 1 (RPGR-interacting protein 1)	0.99	-	nuc	0	Situated between the axonemal microtubules and the plasma membrane	axoneme [IDA] cilium [IDA]			1331
Q5T200 UniProt NPD GO	ZC313_HUMAN	Zinc finger CCCH domain-containing protein 13	0.99	+	nuc	0					1668
Q8BYK8 UniProt NPD GO	ZC3H6_MOUSE	Zinc finger CCCH domain-containing protein 6	0.99	+	nuc	0					1177
Q5TAX3 UniProt NPD GO	ZCH11_HUMAN	Zinc finger CCHC domain-containing protein 11	0.99	-	nuc	0					1644
Q99PP2 UniProt NPD GO	ZN318_MOUSE	Zinc finger protein 318 (Testicular zinc finger protein)	0.99	+	nuc	0	Nucleus	nucleus [IDA]			2025
Q14966 UniProt NPD GO	ZN638_HUMAN	Zinc finger protein 638 (Nuclear protein 220) (Zinc-finger matrin-like protein) (Cutaneous T-cell ly ...	0.99	+	nuc	0	Nucleus; nucleoplasm; nuclear speckle	cytoplasm [TAS] nucleoplasm [TAS]			1978
Q9H582 UniProt NPD GO	ZN644_HUMAN	Zinc finger protein 644 (Zinc finger motif enhancer-binding protein 2) (Zep-2)	0.99	+	nuc	0	Nucleus				1327
P55200 UniProt NPD GO	HRX_MOUSE	Zinc finger protein HRX (ALL-1) (Fragment)	0.99	+	nuc	0	Nucleus (By similarity)	nucleus [IDA]			3866
Q03164 UniProt NPD GO	HRX_HUMAN	Zinc finger protein HRX (ALL-1) (Trithorax-like protein)	0.99	+	nuc	0	Nucleus	nucleus [IDA]	159555	2AGH	3969
P33748 UniProt NPD GO	MSN2_YEAST	Zinc finger protein MSN2 (Multicopy suppressor of SNF1 protein 2)	0.99	-	nuc	0	Cytoplasm. Nucleus	cytosol [IDA] nucleus [IDA]			704
Q8WW38 UniProt NPD GO	FOG2_HUMAN	Zinc finger protein ZFPM2 (Zinc finger protein multitype 2) (Friend of GATA protein 2) (FOG-2) (hFOG ...	0.99	-	nuc	0	Nucleus (By similarity)		603693		1151
Q9VXG1 UniProt NPD GO	HANG_DROME	Zinc finger protein hangover	0.99	-	nuc	0	Nucleus. In neurons	nucleus [IDA]			1913
O62255 UniProt NPD GO	DCP2_CAEEL	mRNA decapping enzyme 2 (EC 3.6.1.-) (Nudix hydrolase 5)	0.99	+	nuc	1 *					809
Q9H501 UniProt NPD GO	ABTAP_HUMAN	ABT1-associated protein	0.98	+	nuc	0	Nucleus; nucleolus (By similarity). Nucleus; nucleoplasm (By similarity)				851
Q01663 UniProt NPD GO	AP1_SCHPO	AP-1-like transcription factor (Caffeine resistance protein 3)	0.98	+	nuc	0	Nucleus	cytoplasm [IDA] nucleus [IDA]		1GD2	552
Q8WYP5 UniProt NPD GO	AHTF1_HUMAN	AT-hook-containing transcription factor 1 (Embryonic large molecule derived from yolk sac)	0.98	+	nuc	0	Nucleus; nuclear matrix. Cytoplasm (By similarity)				2275
Q8CJF7 UniProt NPD GO	AHTF1_MOUSE	AT-hook-containing transcription factor 1 (Embryonic large molecule derived from yolk sac)	0.98	-	nuc	0	Nucleus; nuclear matrix. Cytoplasm				2243
Q6CRF4 UniProt NPD GO	DBP4_KLULA	ATP-dependent RNA helicase DBP4 (EC 3.6.1.-)	0.98	+	nuc	0	Nucleus; nucleolus (By similarity)				770
Q8CDM1 UniProt NPD GO	ATAD2_MOUSE	ATPase family AAA domain-containing protein 2	0.98	+	nuc	0					1040
Q9NQW6 UniProt NPD GO	ANLN_HUMAN	Actin-binding protein anillin	0.98	-	nuc	0	Nucleus. Mainly found in the nucleus during interphase. Colocalizes with cortical F-actin upon nucle ...	actin cytoskeleton [IDA] contractile ring [IDA]			1124
Q801E2 UniProt NPD GO	ANLN_XENLA	Actin-binding protein anillin	0.98	-	nuc	0	Nucleus. Mainly found in the nucleus during interphase. Colocalizes with cortical F-actin upon nucle ...				1116
Q9UPS8 UniProt NPD GO	ANR26_HUMAN	Ankyrin repeat domain-containing protein 26	0.98	-	nuc	0					1709
Q96GY3 UniProt NPD GO	ANTOL_HUMAN	Antolefinin	0.98	+	nuc	0					246
Q9D8N6 UniProt NPD GO	ANTOL_MOUSE	Antolefinin (Antolefinine)	0.98	+	nuc	0					246
Q9UKV3 UniProt NPD GO	ACINU_HUMAN	Apoptotic chromatin condensation inducer in the nucleus (Acinus)	0.98	+	nuc	0	Nucleus	nucleus [IDA]	604562		1341
Q9JIX8 UniProt NPD GO	ACINU_MOUSE	Apoptotic chromatin condensation inducer in the nucleus (Acinus)	0.98	+	nuc	0	Nucleus (By similarity)	nucleolus [IDA] nucleus [ISS]			1338
Q9P2R6 UniProt NPD GO	RERE_HUMAN	Arginine-glutamic acid dipeptide repeats protein (Atrophin-1-like protein) (Atrophin-1-related prote ...	0.98	+	nuc	0	Nucleus. Localized in nuclear bodies of variables size. Colocalized with PML and BAX in nuclear PODs ...	nucleus [NAS]	605226		1566
Q9DBU6 UniProt NPD GO	RSRC1_MOUSE	Arginine/serine-rich coiled coil protein 1	0.98	+	nuc	0					334
Q9P203 UniProt NPD GO	BTBD7_HUMAN	BTB/POZ domain-containing protein 7	0.98	+	nuc	0					1132
Q8CFE5 UniProt NPD GO	BTBD7_MOUSE	BTB/POZ domain-containing protein 7	0.98	+	nuc	0					1130

You are viewing entries 501 to 550 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.