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
P29540 UniProt NPD GO	T2EB_XENLA	Transcription initiation factor IIE subunit beta (TFIIE-beta)	0.85	-	nuc	0	Nucleus				288
Q9UNY4 UniProt NPD GO	TTF2_HUMAN	Transcription termination factor 2 (EC 3.6.1.-) (RNA polymerase II termination factor) (Transcriptio ...	0.85	-	nuc	0	Cytoplasm. Nucleus. Cytoplasmic during interphase. Relocates to the nucleus as cells enter mitosis		604718		1162
Q8I8U7 UniProt NPD GO	TRA1_DROME	Transcription-associated protein 1 (dTRA1)	0.85	+	nuc	0	Nucleus (Probable)	TIP60 histone acetyltransferase complex [IDA]			3805
P53768 UniProt NPD GO	HAP2_KLULA	Transcriptional activator HAP2	0.85	+	nuc	0	Nucleus				300
P15315 UniProt NPD GO	ACE1_YEAST	Transcriptional activator protein ACE1 (Copper-fist transcription factor)	0.85	-	nuc	0	Nucleus	nucleus [IDA]			225
Q8CHY6 UniProt NPD GO	P66A_MOUSE	Transcriptional repressor p66 alpha (GATA zinc finger domain-containing protein 2A)	0.85	-	nuc	0	Nucleus; nucleoplasm; nuclear speckle (By similarity)	nucleus [ISS] NuRD complex [ISS]			629
P16047 UniProt NPD GO	TGFB3_CHICK	Transforming growth factor beta-3 precursor (TGF-beta-3)	0.85	-	exc	1 *	Secreted protein				412
Q923J1 UniProt NPD GO	TRPM7_MOUSE	Transient receptor potential cation channel subfamily M member 7 (EC 2.7.11.1) (Long transient recep ...	0.85	+	end	6	Membrane; multi-pass membrane protein (Probable)			1IAJ	1863
Q8MIF3 UniProt NPD GO	TWST1_EULFU	Twist-related protein 1	0.85	-	nuc	0	Nucleus (By similarity)				198
Q7JGP2 UniProt NPD GO	TWST1_MACTO	Twist-related protein 1	0.85	-	nuc	0	Nucleus (By similarity)				201
Q8MIB9 UniProt NPD GO	TWST1_PONPY	Twist-related protein 1	0.85	-	nuc	0	Nucleus (By similarity)				203
P18475 UniProt NPD GO	TOR_DROME	Tyrosine-protein kinase receptor torso precursor (EC 2.7.10.1)	0.85	-	mit	0	Membrane; single-pass type I membrane protein	plasma membrane [NAS]			923
Q16825 UniProt NPD GO	PTN21_HUMAN	Tyrosine-protein phosphatase non-receptor type 21 (EC 3.1.3.48) (Protein-tyrosine phosphatase D1)	0.85	-	nuc	0		cytoskeleton [TAS]	603271		1174
Q9Y2R2 UniProt NPD GO	PTN22_HUMAN	Tyrosine-protein phosphatase non-receptor type 22 (EC 3.1.3.48) (Hematopoietic cell protein-tyrosine ...	0.85	-	nuc	0	Cytoplasm (By similarity)		600716		807
Q05900 UniProt NPD GO	RU1C_YEAST	U1 small nuclear ribonucleoprotein C homolog (U1 snRNP protein C) (U1-C)	0.85	+	nuc	0	Nucleus	commitment complex [IPI] snRNP U1 [IDA]			231
Q10187 UniProt NPD GO	UCP6_SCHPO	UBA domain-containing protein 6	0.85	+	nuc	0	Membrane; multi-pass membrane protein (Potential)				612
Q6GQ69 UniProt NPD GO	UBX8B_XENLA	UBX domain-containing protein 8-B	0.85	+	cyt	0	Cytoplasm (By similarity)				445
Q9BZE7 UniProt NPD GO	EVG1_HUMAN	UPF0193 protein EVG1	0.85	-	nuc	0					217
Q9P2Y5 UniProt NPD GO	UVRAG_HUMAN	UV radiation resistance-associated gene protein (p63)	0.85	-	nuc	0	Cytoplasm	cytoplasm [TAS]	602493		699
P35125 UniProt NPD GO	UBP6_HUMAN	Ubiquitin carboxyl-terminal hydrolase 6 (EC 3.1.2.15) (Ubiquitin thioesterase 6) (Ubiquitin-specific ...	0.85	-	nuc	0		lysosome [TAS]	604334		1406
Q61068 UniProt NPD GO	UBPW_MOUSE	Ubiquitin carboxyl-terminal hydrolase DUB-1 (EC 3.1.2.15) (Ubiquitin thioesterase DUB-1) (Ubiquitin- ...	0.85	+	nuc	0					526
Q9VB08 UniProt NPD GO	RING1_DROME	Ubiquitin ligase protein RING1 (EC 6.3.2.-) (dRING1) (dRING protein) (Sex comb extra protein)	0.85	-	nuc	0	Nucleus. Colocalizes with ubiquitinated histone H2A. Colocalizes with Pc, Pcl, Psc, ph at many sites ...	cohesin complex [IDA]			435
Q5A4X0 UniProt NPD GO	BRE1_CANAL	Ubiquitin-protein ligase BRE1 (EC 6.3.2.-)	0.85	-	nuc	0	Nucleus (By similarity)				681
O13731 UniProt NPD GO	UBR11_SCHPO	Ubiquitin-protein ligase E3 component N-recognin-11 (EC 6.-.-.-) (N-end-recognizing protein 11)	0.85	-	end	0					2052
P38266 UniProt NPD GO	YBV8_YEAST	Uncharacterized protein YBR108W	0.85	-	nuc	0					947
P38282 UniProt NPD GO	YB02_YEAST	Uncharacterized protein YBR152W	0.85	-	mit	0		U4/U6 x U5 tri-snRNP complex [IDA]			291
Q12066 UniProt NPD GO	YDL89_YEAST	Uncharacterized protein YDL089W	0.85	-	end	2					484
P39970 UniProt NPD GO	YEN5_YEAST	Uncharacterized protein YER045C	0.85	-	nuc	0	Nucleus (Potential)	nucleus [IPI]			489
P43597 UniProt NPD GO	YFI6_YEAST	Uncharacterized protein YFR016C	0.85	-	nuc	0		bud [IDA] cytoplasm [IDA]			1233
P36076 UniProt NPD GO	YKI8_YEAST	Uncharacterized protein YKL088W	0.85	-	nuc	0		cytoplasm [IDA]			571
P48564 UniProt NPD GO	YN35_YEAST	Uncharacterized protein YNL295W	0.85	-	nuc	0					524
Q08223 UniProt NPD GO	YO053_YEAST	Uncharacterized protein YOL053W	0.85	-	nuc	1	Membrane; single-pass membrane protein (Potential)				395
Q08236 UniProt NPD GO	YO078_YEAST	Uncharacterized protein YOL078W	0.85	-	nuc	0		cytoplasm [IPI] TORC 2 complex [IPI]			1176
Q12219 UniProt NPD GO	YORA4_YEAST	Uncharacterized protein YOR114W	0.85	-	mit	0					294
Q91187 UniProt NPD GO	RAG1_ONCMY	V(D)J recombination-activating protein 1 (RAG-1)	0.85	+	nuc	0	Nucleus				1073
Q22639 UniProt NPD GO	VPS54_CAEEL	Vacuolar protein sorting protein 54	0.85	-	nuc	0					1058
Q03433 UniProt NPD GO	VPS71_YEAST	Vacuolar protein sorting protein 71 (SWR complex protein 6)	0.85	-	nuc	0	Nucleus	nucleus [IDA] SWR1 complex [IPI]			280
P32913 UniProt NPD GO	VPS17_YEAST	Vacuolar protein sorting-associated protein VPS17	0.85	+	nuc	0	Membrane; peripheral membrane protein; cytoplasmic side. Membrane-associated on the cytoplasmic side ...	endosome [IPI] retromer complex [TAS]			551
Q91V10 UniProt NPD GO	VSX1_MOUSE	Visual system homeobox 1 (Transcription factor VSX1) (Retinal inner nuclear layer homeobox protein) ...	0.85	+	nuc	0	Nucleus (By similarity)	nucleus [IDA]			363
Q9MZL5 UniProt NPD GO	CACB2_BOVIN	Voltage-dependent L-type calcium channel subunit beta-2 (CAB2) (Calcium channel voltage-dependent su ...	0.85	-	nuc	0	Sarcolemma; sarcolemmal membrane; peripheral membrane protein; cytoplasmic side (By similarity)				603
Q08281 UniProt NPD GO	YO128_YEAST	WD repeat protein YOL138C	0.85	-	nuc	0	Vacuole	vacuole (sensu Fungi) [IDA]			1341
Q5SXA9 UniProt NPD GO	WWC1_MOUSE	WW domain-containing protein 1 (Kidney and brain protein) (KIBRA)	0.85	-	nuc	0					1104
Q99PT3 UniProt NPD GO	ZNHI4_MOUSE	Zinc finger HIT domain-containing protein 4 (PAP-1-associated protein 1) (PAPA-1) (High mobility gro ...	0.85	+	nuc	0	Nucleus; nucleolus				345
Q96MP5 UniProt NPD GO	ZSWM3_HUMAN	Zinc finger SWIM domain-containing protein 3	0.85	-	nuc	0					696
Q8CFL8 UniProt NPD GO	ZSWM3_MOUSE	Zinc finger SWIM domain-containing protein 3	0.85	-	nuc	0					695
Q9UL36 UniProt NPD GO	ZN236_HUMAN	Zinc finger protein 236	0.85	-	nuc	0	Nucleus (Probable)	nucleus [NAS]	604760		1845
P17141 UniProt NPD GO	ZFP37_MOUSE	Zinc finger protein 37 (Zfp-37) (Male germ cell-specific zinc finger protein)	0.85	+	nuc	0	Nucleus (Probable)				594
Q8WTR7 UniProt NPD GO	ZN473_HUMAN	Zinc finger protein 473 (Zinc finger protein 100 homolog) (Zfp-100)	0.85	-	nuc	0	Nucleus (Probable)				871
Q96CS4 UniProt NPD GO	ZN689_HUMAN	Zinc finger protein 689	0.85	-	nuc	0	Nucleus (Probable)				500
Q4R4A2 UniProt NPD GO	CF113_MACFA	Zinc finger protein C6orf113 homolog	0.85	-	nuc	0					578

You are viewing entries 6801 to 6850 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.