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
P47029 UniProt NPD GO	YJI4_YEAST	Uncharacterized protein YJL084C	0.96	-	nuc	0		cytoplasm [IDA]			1046
Q03758 UniProt NPD GO	YML1_YEAST	Uncharacterized protein YML111W	0.96	-	nuc	0		cytoplasm [IDA] ubiquitin ligase complex [IMP]			920
P40343 UniProt NPD GO	VPS27_YEAST	Vacuolar protein sorting-associated protein VPS27	0.96	+	nuc	0		endosome [IDA]		1VFY	622
O60504 UniProt NPD GO	VINEX_HUMAN	Vinexin (Sorbin and SH3 domain-containing protein 3) (SH3-containing adapter molecule 1) (SCAM-1)	0.96	-	nuc	0	Isoform Alpha, isoform Beta: Cell membrane; cell-matrix junction (By similarity). Isoform Beta: Nucl ...			2CT3	671
Q8WVS4 UniProt NPD GO	WDR60_HUMAN	WD repeat protein 60	0.96	+	nuc	0					1066
Q9Y2W2 UniProt NPD GO	WBP11_HUMAN	WW domain-binding protein 11 (WBP-11) (SH3 domain-binding protein SNP70) (Npw38-binding protein) (Np ...	0.96	-	nuc	0	Nucleus. Cytoplasm. Predominantly located in the nucleus with granular heterogeneous distribution. E ...	nucleus [TAS]			641
Q14191 UniProt NPD GO	WRN_HUMAN	Werner syndrome ATP-dependent helicase (EC 3.6.1.-)	0.96	+	nuc	0	Nucleus; nucleolus	nucleus [TAS]	277700	2FC0	1432
Q01371 UniProt NPD GO	WC1_NEUCR	White collar 1 protein (WC1)	0.96	+	nuc	0	Nucleus				1167
Q96MU7 UniProt NPD GO	YTDC1_HUMAN	YTH domain-containing protein 1 (Putative splicing factor YT521)	0.96	+	nuc	0	Nucleus (By similarity). Localizes to a novel subnuclear structure, the YT bodies (By similarity)				727
Q9H869 UniProt NPD GO	YYAP1_HUMAN	YY1-associated protein 1 (Hepatocellular carcinoma susceptibility protein) (Hepatocellular carcinoma ...	0.96	-	nuc	0	Cytoplasm. Nucleus				796
Q9VNG1 UniProt NPD GO	ZN403_DROME	ZNF403-like protein	0.96	+	nuc	0					671
P61129 UniProt NPD GO	ZC3H6_HUMAN	Zinc finger CCCH domain-containing protein 6	0.96	+	nuc	0					1189
Q8TBK6 UniProt NPD GO	ZCH10_HUMAN	Zinc finger CCHC domain-containing protein 10	0.96	-	nuc	0					192
Q9H5U6 UniProt NPD GO	ZCHC4_HUMAN	Zinc finger CCHC domain-containing protein 4	0.96	+	nuc	0					513
Q5VYS8 UniProt NPD GO	ZCHC6_HUMAN	Zinc finger CCHC domain-containing protein 6	0.96	+	nuc	0					1495
Q5BLK4 UniProt NPD GO	ZCHC6_MOUSE	Zinc finger CCHC domain-containing protein 6	0.96	+	nuc	0					1491
Q9H0M4 UniProt NPD GO	ZCPW1_HUMAN	Zinc finger CW-type PWWP domain protein 1	0.96	+	nuc	0					494
Q14202 UniProt NPD GO	ZMYM3_HUMAN	Zinc finger MYM-type protein 3 (Zinc finger protein 261) (DXS6673E protein)	0.96	-	nuc	0	Nucleus (By similarity)		300061		1370
O95625 UniProt NPD GO	ZBT11_HUMAN	Zinc finger and BTB domain-containing protein 11	0.96	-	nuc	0	Nucleus (Potential)				1053
O43167 UniProt NPD GO	ZBT24_HUMAN	Zinc finger and BTB domain-containing protein 24 (Zinc finger protein 450)	0.96	-	nuc	0	Nucleus (Potential)				697
Q5EXX3 UniProt NPD GO	ZBT38_RAT	Zinc finger and BTB domain-containing protein 38 (Zinc finger protein expressed in neurons) (Zenon)	0.96	+	nuc	0	Nucleus	nucleus [IDA]			1203
O88466 UniProt NPD GO	ZF106_MOUSE	Zinc finger protein 106 (Zfp-106) (Zinc finger protein 474) (H3a minor histocompatibility antigen) ( ...	0.96	+	nuc	0	Isoform 3: Cytoplasm	cytosol [IDA] membrane fraction [IDA]			1888
Q3Y4E1 UniProt NPD GO	ZN148_BOVIN	Zinc finger protein 148 (Zinc finger DNA-binding protein 89) (Transcription factor ZBP-89)	0.96	+	nuc	0	Nucleus (By similarity)				794
Q9UQR1 UniProt NPD GO	ZN148_HUMAN	Zinc finger protein 148 (Zinc finger DNA-binding protein 89) (Transcription factor ZBP-89)	0.96	+	nuc	0	Nucleus	DNA-directed RNA polymerase II, core complex [TAS]	601897		794
Q62806 UniProt NPD GO	ZN148_RAT	Zinc finger protein 148 (Zinc finger DNA-binding protein 89) (Transcription factor ZBP-89)	0.96	+	nuc	0	Nucleus	nucleus [TAS]			794
Q61624 UniProt NPD GO	ZN148_MOUSE	Zinc finger protein 148 (Zinc finger DNA-binding protein 89) (Transcription factor ZBP-89) (G-rich b ...	0.96	+	nuc	0	Nucleus	nucleus [IDA]			794
Q6IV72 UniProt NPD GO	ZN425_HUMAN	Zinc finger protein 425	0.96	-	nuc	0	Nucleus (Probable)				752
Q8R2V3 UniProt NPD GO	ZN445_MOUSE	Zinc finger protein 445	0.96	-	nuc	0	Nucleus (Potential)				986
P51815 UniProt NPD GO	ZNF75_HUMAN	Zinc finger protein 75	0.96	+	nuc	0	Nucleus (Potential)	nucleus [NAS]	314997		289
P46974 UniProt NPD GO	ZMS1_YEAST	Zinc finger protein ZMS1	0.96	-	nuc	0	Nucleus (Potential)	nucleus [IDA]			1380
Q925H1 UniProt NPD GO	TRPS1_MOUSE	Zinc finger transcription factor Trps1	0.96	-	nuc	0	Nucleus	nucleus [IC]			1281
Q90ZS6 UniProt NPD GO	TRPS1_XENLA	Zinc finger transcription factor Trps1	0.96	-	nuc	0	Nucleus				1271
Q9UHF7 UniProt NPD GO	TRPS1_HUMAN	Zinc finger transcription factor Trps1 (Zinc finger protein GC79) (Tricho-rhino-phalangeal syndrome ...	0.96	-	nuc	0	Nucleus (By similarity)		604386		1281
P58268 UniProt NPD GO	REQU_CHICK	Zinc-finger protein ubi-d4 (Requiem) (Apoptosis response zinc finger protein)	0.96	+	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				405
Q5KCH0 UniProt NPD GO	PACC_CRYNE	pH-response transcription factor pacC/RIM101	0.96	+	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				917
Q12339 UniProt NPD GO	UTP23_YEAST	rRNA-processing protein UTP23 (U3-associated protein 23)	0.96	+	nuc	0	Mitochondrion. Nucleus; nucleolus	mitochondrion [IDA] nucleolus [IDA]			254
Q5M954 UniProt NPD GO	SEN2_RAT	tRNA-splicing endonuclease subunit Sen2 (EC 3.1.27.9) (tRNA-intron endonuclease Sen2)	0.96	-	nuc	0	Nucleus (By similarity). Nucleus; nucleolus (By similarity). May be transiently localized in the nuc ...				463
Q01970 UniProt NPD GO	PLCB3_HUMAN	1-phosphatidylinositol-4,5-bisphosphate phosphodiesterase beta 3 (EC 3.1.4.11) (Phosphoinositide pho ...	0.95	+	nuc	0	Membrane; peripheral membrane protein		600230		1234
Q9UPN4 UniProt NPD GO	AZI1_HUMAN	5-azacytidine-induced protein 1 (Pre-acrosome localization protein 1) (Centrosomal protein of 131 kD ...	0.95	-	nuc	0	Centrosome				1083
Q9WUU9 UniProt NPD GO	MCM3A_MOUSE	80 kDa MCM3-associated protein (GANP protein)	0.95	+	nuc	0	Cytoplasm. Nucleus	cytoplasm [IDA] nucleus [IDA]			1971
O54931 UniProt NPD GO	AKAP2_MOUSE	A-kinase anchor protein 2 (Protein kinase A-anchoring protein 2) (PRKA2) (AKAP-2) (AKAP expressed in ...	0.95	+	nuc	0	Proximal to tubules in nephrons				885
Q13023 UniProt NPD GO	AKAP6_HUMAN	A-kinase anchor protein 6 (Protein kinase A-anchoring protein 6) (PRKA6) (A-kinase anchor protein 10 ...	0.95	-	nuc	0	Sarcoplasmic reticulum. Nucleus; nuclear membrane. In heart muscle. Participation of multiple target ...	nuclear envelope [IDA] sarcoplasmic reticulum [IDA]	604691		2319
O88573 UniProt NPD GO	AFF1_MOUSE	AF4/FMR2 family member 1 (Protein AF-4) (Proto-oncogene AF4)	0.95	+	nuc	0	Nucleus (Potential)				1217
P51825 UniProt NPD GO	AFF1_HUMAN	AF4/FMR2 family member 1 (Protein AF-4) (Proto-oncogene AF4) (Protein FEL)	0.95	+	nuc	0	Nucleus (Potential)		159557		1210
Q9ESC8 UniProt NPD GO	AFF4_MOUSE	AF4/FMR2 family member 4	0.95	-	nuc	0	Nucleus (By similarity)	nucleus [IDA]			1160
Q865S1 UniProt NPD GO	AP3D1_BOVIN	AP-3 complex subunit delta-1 (Adapter-related protein complex 3 subunit delta-1) (Delta-adaptin 3) ( ...	0.95	+	nuc	0					1207
O54774 UniProt NPD GO	AP3D1_MOUSE	AP-3 complex subunit delta-1 (Adapter-related protein complex 3 subunit delta-1) (Delta-adaptin 3) ( ...	0.95	+	nuc	0		Golgi trans face [TAS]			1199
P12954 UniProt NPD GO	SRS2_YEAST	ATP-dependent DNA helicase SRS2 (EC 3.6.1.-)	0.95	-	nuc	0	Nucleus				1174
Q757U8 UniProt NPD GO	DBP10_ASHGO	ATP-dependent RNA helicase DBP10 (EC 3.6.1.-)	0.95	+	nuc	0	Nucleus; nucleolus (By similarity)				960
Q8TDD1 UniProt NPD GO	DDX54_HUMAN	ATP-dependent RNA helicase DDX54 (EC 3.6.1.-) (DEAD box protein 54) (ATP-dependent RNA helicase DP97 ...	0.95	+	nuc	0	Nucleus; nucleolus	nucleolus [IDA] nucleus [IDA]			881

You are viewing entries 1701 to 1750 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.)

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