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
Q9R0I7 UniProt NPD GO	YLPM1_MOUSE	YLP motif-containing protein 1 (Nuclear protein ZAP3)	0.94	-	nuc	0	Nucleus; nucleoplasm; nuclear speckle	nucleus [IDA]			1386
Q5ZJJ1 UniProt NPD GO	ZC11A_CHICK	Zinc finger CCCH domain-containing protein 11A	0.94	-	nuc	0					723
Q6NZF1 UniProt NPD GO	ZC11A_MOUSE	Zinc finger CCCH domain-containing protein 11A	0.94	-	nuc	0					792
Q9CX48 UniProt NPD GO	ZCH10_MOUSE	Zinc finger CCHC domain-containing protein 10	0.94	+	nuc	0					178
Q9JLM4 UniProt NPD GO	ZMYM3_MOUSE	Zinc finger MYM-type protein 3 (Zinc finger protein 261) (DXHXS6673E protein)	0.94	-	nuc	0	Nucleus				1370
P28875 UniProt NPD GO	CZF1_CANAL	Zinc finger protein 1	0.94	-	nuc	0	Nucleus (Probable)				388
Q9H116 UniProt NPD GO	ZN336_HUMAN	Zinc finger protein 336 (Zinc finger and BTB domain-containing protein 23)	0.94	-	nuc	0	Nucleus (Probable)				711
Q8N895 UniProt NPD GO	ZN366_HUMAN	Zinc finger protein 366	0.94	+	nuc	0	Nucleus (Probable)				744
Q8TF68 UniProt NPD GO	ZN384_HUMAN	Zinc finger protein 384 (Nuclear matrix transcription factor 4) (Nuclear matrix protein 4) (CAG repe ...	0.94	-	nuc	0	Nucleus (By similarity)		609951		576
Q9EQJ4 UniProt NPD GO	ZN384_RAT	Zinc finger protein 384 (Nuclear matrix transcription factor 4) (Nuclear matrix protein 4) (Cas-asso ...	0.94	-	nuc	0	Nucleus	focal adhesion [IDA] nucleus [IDA]			579
Q6DFC8 UniProt NPD GO	ZN395_XENLA	Zinc finger protein 395	0.94	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity). May shuttle between nucleus and cytoplasm (By si ...				498
Q7TS63 UniProt NPD GO	ZN406_MOUSE	Zinc finger protein 406	0.94	-	nuc	0	Nucleus (Potential)				1219
Q9Y4E5 UniProt NPD GO	ZN451_HUMAN	Zinc finger protein 451 (Coactivator for steroid receptors)	0.94	-	nuc	0	Nucleus (Potential)				1061
Q95JV5 UniProt NPD GO	ZN512_MACFA	Zinc finger protein 512	0.94	+	nuc	0	Nucleus (Potential)				565
Q9UID6 UniProt NPD GO	ZN639_HUMAN	Zinc finger protein 639 (Zinc finger protein ZASC1) (Zinc finger protein ANC_2H01)	0.94	+	nuc	0	Nucleus				485
Q62511 UniProt NPD GO	ZFP91_MOUSE	Zinc finger protein 91 (Zfp-91) (Zinc finger protein PZF) (Penta Zf protein)	0.94	+	nuc	0	Nucleus (Probable)				455
Q3SWY8 UniProt NPD GO	CF113_BOVIN	Zinc finger protein C6orf113 homolog	0.94	-	nuc	0					579
P10071 UniProt NPD GO	GLI3_HUMAN	Zinc finger protein GLI3	0.94	-	nuc	0	Nucleus	cytoplasm [TAS] nucleus [TAS]	200990		1580
Q5IS56 UniProt NPD GO	GLI3_PANTR	Zinc finger protein GLI3	0.94	-	nuc	0	Nucleus				1580
Q91660 UniProt NPD GO	GLI3_XENLA	Zinc finger protein GLI3 (Neural-specific DNA-binding protein xGLI3) (xGLI-3)	0.94	-	nuc	0	Nucleus (Potential)				1569
Q13129 UniProt NPD GO	RLF_HUMAN	Zinc finger protein Rlf (Rearranged L-myc fusion gene protein) (Zn-15-related protein)	0.94	+	nuc	0	Nucleus (Probable)		180610		1914
P70121 UniProt NPD GO	ZHX1_MOUSE	Zinc fingers and homeoboxes protein 1	0.94	+	exc	0	Nucleus (By similarity)				873
P58270 UniProt NPD GO	DPF3_CHICK	Zinc-finger protein DPF3 (cer-d4)	0.94	-	nuc	0	Cytoplasm (Potential). Nucleus (Potential)				427
P58269 UniProt NPD GO	DPF3_MOUSE	Zinc-finger protein Dpf3 (cer-d4)	0.94	+	nuc	0	Cytoplasm (Potential). Nucleus (Potential)				356
Q61103 UniProt NPD GO	REQU_MOUSE	Zinc-finger protein ubi-d4 (Requiem) (Apoptosis response zinc finger protein) (D4, zinc and double P ...	0.94	+	nuc	0	Cytoplasm. Nucleus				391
Q6BSZ4 UniProt NPD GO	PACC_DEBHA	pH-response transcription factor pacC/RIM101	0.94	+	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				617
P36049 UniProt NPD GO	EBP2_YEAST	rRNA-processing protein EBP2 (EBNA1-binding protein homolog)	0.94	+	nuc	0	Nucleus; nucleolus	nucleolus [IDA]			427
O14214 UniProt NPD GO	TRM10_SCHPO	tRNA (guanine-N(1)-)-methyltransferase (EC 2.1.1.31) (tRNA methyltransferase 10)	0.94	+	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				304
P10894 UniProt NPD GO	PLCB1_BOVIN	1-phosphatidylinositol-4,5-bisphosphate phosphodiesterase beta 1 (EC 3.1.4.11) (Phosphoinositide pho ...	0.93	+	nuc	0					1216
O89040 UniProt NPD GO	PLCB2_RAT	1-phosphatidylinositol-4,5-bisphosphate phosphodiesterase beta 2 (EC 3.1.4.11) (Phospholipase C-beta ...	0.93	-	nuc	0					1183
P25455 UniProt NPD GO	PIP1_DROME	1-phosphatidylinositol-4,5-bisphosphate phosphodiesterase classes I and II (EC 3.1.4.11) (Phosphoino ...	0.93	-	nuc	0					1312
Q9Y1J3 UniProt NPD GO	PDPK1_CAEEL	3-phosphoinositide-dependent protein kinase 1 (EC 2.7.11.1) (Pdk-class protein kinase protein 1)	0.93	-	nuc	0	Cytoplasm (By similarity)				636
P97789 UniProt NPD GO	XRN1_MOUSE	5'-3' exoribonuclease 1 (EC 3.1.11.-) (mXRN1) (Strand-exchange protein 1 homolog) (Protein Dhm2)	0.93	-	nuc	0	Cytoplasm. Discrete foci at the inner surface of the cell membrane				1719
P40848 UniProt NPD GO	XRN2_SCHPO	5'-3' exoribonuclease 2 (EC 3.1.11.-) (Protein dhp1)	0.93	+	nuc	0	Nucleus				991
Q9WVC7 UniProt NPD GO	AKAP6_RAT	A-kinase anchor protein 6 (Protein kinase A-anchoring protein 6) (PRKA6) (mAKAP)	0.93	-	nuc	0	Sarcoplasmic reticulum. Nucleus; nuclear membrane. In heart muscle. Participation of multiple target ...	nuclear envelope [IDA] sarcoplasmic reticulum [IDA]			2314
Q3V1V3 UniProt NPD GO	ABTAP_MOUSE	ABT1-associated protein	0.93	+	nuc	0	Nucleus; nucleolus (By similarity). Nucleus; nucleoplasm (By similarity)				845
Q76MT4 UniProt NPD GO	ABTAP_RAT	ABT1-associated protein	0.93	+	nuc	0	Nucleus; nucleolus. Nucleus; nucleoplasm. Is concomitantly relocalized into discrete nuclear bodies ...				842
Q69Z28 UniProt NPD GO	ATS16_MOUSE	ADAMTS-16 precursor (EC 3.4.24.-) (A disintegrin and metalloproteinase with thrombospondin motifs 16 ...	0.93	+	end	0	Secreted protein; extracellular space; extracellular matrix (By similarity)				1222
Q9JLQ2 UniProt NPD GO	GIT2_MOUSE	ARF GTPase-activating protein GIT2 (G protein-coupled receptor kinase-interactor 2) (Cool-interactin ...	0.93	-	nuc	0					708
Q14161 UniProt NPD GO	GIT2_HUMAN	ARF GTPase-activating protein GIT2 (G protein-coupled receptor kinase-interactor 2) (GRK-interacting ...	0.93	-	nuc	0		nucleoplasm [IDA]	608564		759
Q14865 UniProt NPD GO	ARI5B_HUMAN	AT-rich interactive domain-containing protein 5B (ARID domain-containing protein 5B) (Mrf1-like) (Mo ...	0.93	-	nuc	0	Nucleus (By similarity)	nucleus [IC]	608538	1IG6	1188
Q6BKH3 UniProt NPD GO	DBP7_DEBHA	ATP-dependent RNA helicase DBP7 (EC 3.6.1.-)	0.93	-	nuc	0	Nucleus; nucleolus (By similarity)				798
Q5KCY8 UniProt NPD GO	SPB4_CRYNE	ATP-dependent rRNA helicase SPB4 (EC 3.6.1.-)	0.93	+	nuc	0	Nucleus; nucleolus (By similarity)				748
Q38694 UniProt NPD GO	AGL9_ARADE	Agamous-like MADS-box protein AGL9 homolog (OM1)	0.93	-	nuc	0	Nucleus (By similarity)				250
Q9WU39 UniProt NPD GO	SCNNG_MOUSE	Amiloride-sensitive sodium channel gamma-subunit (Epithelial Na+ channel subunit gamma) (Gamma ENaC) ...	0.93	-	nuc	2	Cell membrane; apical cell membrane; multi-pass membrane protein (By similarity). Apical membrane of ...	integral to membrane [IDA]			655
P19091 UniProt NPD GO	ANDR_MOUSE	Androgen receptor (Dihydrotestosterone receptor)	0.93	+	nuc	0	Nucleus	cytoplasm [ISS] nucleus [ISS]			899
P15207 UniProt NPD GO	ANDR_RAT	Androgen receptor (Dihydrotestosterone receptor)	0.93	+	nuc	0	Nucleus	axon [IDA] cytoplasm [TAS] dendrite [IDA] nucleus [IDA]		1XNN	902
Q9BXX3 UniProt NPD GO	AN30A_HUMAN	Ankyrin repeat domain-containing protein 30A (NY-BR-1 antigen)	0.93	-	nuc	0		nucleus [NAS]			1341
Q9Y2G4 UniProt NPD GO	ANKR6_HUMAN	Ankyrin repeat domain-containing protein 6	0.93	-	nuc	0					692
Q01613 UniProt NPD GO	APX_XENLA	Apical protein (APX)	0.93	+	nuc	0	Membrane; peripheral membrane protein				1420

You are viewing entries 2651 to 2700 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.