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
P53692 UniProt NPD GO	SMC6_SCHPO	Structural maintenance of chromosome 6 (DNA repair protein rad18)	0.96	-	nuc	0	Nucleus	Smc5-Smc6 complex [IDA]			1140
P34228 UniProt NPD GO	SEF1_YEAST	Suppressor protein SEF1	0.96	+	nuc	0	Nucleus (Probable)				1057
O75683 UniProt NPD GO	SURF6_HUMAN	Surfeit locus protein 6	0.96	+	nuc	0	Nucleus; nucleoplasm (By similarity). Granular component of the nucleolus (By similarity)	granular component [ISS] nucleolus [TAS]	185642		361
O57594 UniProt NPD GO	SURF6_FUGRU	Surfeit locus protein 6 homolog	0.96	+	nuc	0	Nucleus; nucleolus (By similarity)				359
Q15431 UniProt NPD GO	SYCP1_HUMAN	Synaptonemal complex protein 1 (SCP-1)	0.96	+	nuc	0	Nucleus (By similarity). In tripartite segments of synaptonemal complexes, between lateral elements ...	lateral element [ISS]	602162		976
Q60563 UniProt NPD GO	SYCP1_MESAU	Synaptonemal complex protein 1 (SCP-1) (Meiotic chromosome synaptic protein) (Fragment)	0.96	+	nuc	0	Nucleus. In tripartite segments of synaptonemal complexes, between lateral elements in the nucleus. ...				845
Q8CGA2 UniProt NPD GO	TBC14_MOUSE	TBC1 domain family member 14	0.96	+	nuc	0					679
P17214 UniProt NPD GO	EST1_YEAST	Telomere elongation protein EST1 (EC 2.7.7.-) (Ever shorter telomeres protein 1)	0.96	+	cyt	0	Nucleus	nucleolus [IDA] nucleus [IDA] telomerase holoenzyme complex [IDA]			699
Q5UIP0 UniProt NPD GO	RIF1_HUMAN	Telomere-associated protein RIF1 (Rap1-interacting factor 1 homolog)	0.96	-	nuc	0	Nucleus. Exhibits ATM- and TP53BP1-dependent localization to uncapped or aberrant telomeres and to D ...		608952		2472
Q14241 UniProt NPD GO	ELOA1_HUMAN	Transcription elongation factor B polypeptide 3 (RNA polymerase II transcription factor SIII subunit ...	0.96	+	nuc	0	Nucleus (Probable)		600786		772
Q75EP8 UniProt NPD GO	SPT6_ASHGO	Transcription elongation factor SPT6 (Chromatin elongation factor SPT6)	0.96	-	nuc	0	Nucleus (By similarity)				1432
Q6FLB1 UniProt NPD GO	SPT6_CANGA	Transcription elongation factor SPT6 (Chromatin elongation factor SPT6)	0.96	+	nuc	0	Nucleus (By similarity)				1449
Q6CVK3 UniProt NPD GO	SPT6_KLULA	Transcription elongation factor SPT6 (Chromatin elongation factor SPT6)	0.96	-	nuc	0	Nucleus (By similarity)				1460
Q800Q5 UniProt NPD GO	T7L1B_BRARE	Transcription factor 7-like 1-B (HMG box transcription factor 3-B) (TCF-3-B)	0.96	+	nuc	0	Nucleus (By similarity)				551
Q924A0 UniProt NPD GO	TF7L2_MOUSE	Transcription factor 7-like 2 (HMG box transcription factor 4) (T-cell-specific transcription factor ...	0.96	+	nuc	0	Nucleus	nucleus [IDA] transcription factor complex [IDA]			459
P39933 UniProt NPD GO	TF3A_YEAST	Transcription factor IIIA (TFIIIA)	0.96	+	nuc	0	Nucleus	transcription factor complex [IPI]			429
Q00312 UniProt NPD GO	RBF1_CANAL	Transcription factor RBF1 (RPG-box-binding factor) (Repressor-activator protein 1)	0.96	-	nuc	0	Nucleus. Predominantly				527
Q7YRJ7 UniProt NPD GO	SOX9_CANFA	Transcription factor SOX-9	0.96	+	nuc	0	Nucleus (Potential)				513
P52890 UniProt NPD GO	ATF1_SCHPO	Transcription factor atf1 (Transcription factor mts1) (Protein sss1)	0.96	-	nuc	0	Nucleus				566
Q5BEG5 UniProt NPD GO	IWS1_EMENI	Transcription factor iws1	0.96	+	nuc	0	Nucleus (By similarity)				429
Q8IZX4 UniProt NPD GO	TAF1L_HUMAN	Transcription initiation factor TFIID 210 kDa subunit (TBP-associated factor 210 kDa) (TAF(II)210) ( ...	0.96	+	nuc	0	Nucleus (By similarity)	nucleus [ISS] transcription factor TFIID complex [ISS]	607798		1826
Q24325 UniProt NPD GO	TAF2_DROME	Transcription initiation factor TFIID subunit 2 (Transcription initiation factor TFIID 150 kDa subun ...	0.96	+	nuc	0	Nucleus				1221
P32257 UniProt NPD GO	GAL11_KLULA	Transcription regulatory protein GAL11	0.96	+	nuc	0					1034
Q04052 UniProt NPD GO	ARO80_YEAST	Transcriptional activator ARO80	0.96	+	nuc	0	Nucleus	nucleus [IC]			950
Q8LK56 UniProt NPD GO	DME_ARATH	Transcriptional activator DEMETER (EC 3.2.2.-) (DNA glycosylase-related protein DME)	0.96	+	nuc	0	Nucleus				1987
P08153 UniProt NPD GO	SWI5_YEAST	Transcriptional factor SWI5	0.96	-	nuc	0	Nucleus. Cytoplasm. Nuclear in G1, cytoplasmic in S, G2 and M cell cycle phases	cytoplasm [IDA] nucleus [IDA]		1ZFD	709
Q9VJJ7 UniProt NPD GO	TRPG_DROME	Transient receptor potential-gamma protein (TRPgamma)	0.96	+	end	6	Membrane; multi-pass membrane protein (Probable)	rhabdomere [IDA]			1128
P47024 UniProt NPD GO	YJL3_YEAST	Transposon Ty4 207.7 kDa hypothetical protein	0.96	+	nuc	0		mitochondrion [IDA]			1803
Q07283 UniProt NPD GO	TRHY_HUMAN	Trichohyalin	0.96	+	nuc	0		cytoskeleton [NAS]	190370		1898
O75962 UniProt NPD GO	TRIO_HUMAN	Triple functional domain protein (PTPRF-interacting protein)	0.96	-	nuc	0			601893	1NTY	3038
P50607 UniProt NPD GO	TUB_HUMAN	Tubby protein homolog	0.96	+	nuc	0		cytoplasm [TAS] nucleus [TAS]	601197	1S31	506
Q8CHB8 UniProt NPD GO	TTLL5_MOUSE	Tubulin--tyrosine ligase-like protein 5	0.96	+	nuc	0					1328
P29352 UniProt NPD GO	PTN22_MOUSE	Tyrosine-protein phosphatase non-receptor type 22 (EC 3.1.3.48) (Hematopoietic cell protein-tyrosine ...	0.96	-	nuc	0	Cytoplasm			1JEG	802
Q9BVJ6 UniProt NPD GO	UT14A_HUMAN	U3 small nucleolar RNA-associated protein 14 homolog A (Antigen NY-CO-16)	0.96	+	nuc	0	Nucleus; nucleolus		300508		771
P36026 UniProt NPD GO	UBP11_YEAST	Ubiquitin carboxyl-terminal hydrolase 11 (EC 3.1.2.15) (Ubiquitin thioesterase 11) (Ubiquitin-specif ...	0.96	-	nuc	0					717
Q5ZID5 UniProt NPD GO	UBP28_CHICK	Ubiquitin carboxyl-terminal hydrolase 28 (EC 3.1.2.15) (Ubiquitin thioesterase 28) (Ubiquitin-specif ...	0.96	-	nuc	0					1047
Q96RU2 UniProt NPD GO	UBP28_HUMAN	Ubiquitin carboxyl-terminal hydrolase 28 (EC 3.1.2.15) (Ubiquitin thioesterase 28) (Ubiquitin-specif ...	0.96	+	nuc	0					1077
Q9ES63 UniProt NPD GO	UBP29_MOUSE	Ubiquitin carboxyl-terminal hydrolase 29 (EC 3.1.2.15) (Ubiquitin thioesterase 29) (Ubiquitin-specif ...	0.96	+	nuc	0					869
O42957 UniProt NPD GO	ULP1_SCHPO	Ubiquitin-like-specific protease 1 (EC 3.4.22.-)	0.96	+	nuc	0		nucleus [IDA]			568
Q00987 UniProt NPD GO	MDM2_HUMAN	Ubiquitin-protein ligase E3 Mdm2 (EC 6.3.2.-) (p53-binding protein Mdm2) (Oncoprotein Mdm2) (Double ...	0.96	-	nuc	0	Nucleus; nucleoplasm. Cytoplasm. Expressed predominantly in the nucleoplasm. Nucleus; nucleolus. Int ...	nucleolus [IDA] nucleoplasm [IDA]	164785	2F1Y	491
Q07963 UniProt NPD GO	UBR2_YEAST	Ubiquitin-protein ligase E3 UBR2 (EC 6.-.-.-) (Ubiquitin-protein ligase E3 component N-recognin-1 ho ...	0.96	+	nuc	0	Cytoplasm	cytoplasm [IDA]			1872
P19812 UniProt NPD GO	UBR1_YEAST	Ubiquitin-protein ligase E3 component N-recognin-1 (EC 6.-.-.-) (N-end-recognizing protein)	0.96	+	cyt	0		proteasome complex (sensu Eukaryota) [IPI]			1950
O14795 UniProt NPD GO	UN13B_HUMAN	Unc-13 homolog B (Munc13-2) (munc13)	0.96	-	nuc	0	Cytoplasm (By similarity). Membrane; peripheral membrane protein (By similarity). Cell membrane (By ...	cytoplasm [TAS] Golgi apparatus [TAS]	605836		1591
Q8K0T7 UniProt NPD GO	UN13C_MOUSE	Unc-13 homolog C (Munc13-3) (Fragment)	0.96	-	nuc	0	Cytoplasm (By similarity). Membrane; peripheral membrane protein (By similarity). Localized to presy ...				1430
Q8N7W2 UniProt NPD GO	CJ030_HUMAN	Uncharacterized protein C10orf30	0.96	-	nuc	0					519
Q8BSV3 UniProt NPD GO	CJ030_MOUSE	Uncharacterized protein C10orf30 homolog	0.96	-	nuc	0					434
Q9USN8 UniProt NPD GO	YJY1_SCHPO	Uncharacterized protein C132.01c	0.96	+	nuc	0					1021
Q9H7Z3 UniProt NPD GO	CN102_HUMAN	Uncharacterized protein C14orf102	0.96	+	nuc	0					1164
Q96MY7 UniProt NPD GO	CN044_HUMAN	Uncharacterized protein C14orf44	0.96	-	nuc	0					647
P39732 UniProt NPD GO	YAD1_YEAST	Uncharacterized protein YAL031C	0.96	-	mit	0		cytoplasm [IDA]			760

You are viewing entries 1651 to 1700 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.