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
Q94526 UniProt NPD GO	ORK1_DROME	Open rectifier potassium channel protein 1 (Two pore domain potassium channel Ork1)	0.93	-	nuc	6 *	Membrane; multi-pass membrane protein (Potential)				1001
O16810 UniProt NPD GO	ORC1_DROME	Origin recognition complex subunit 1 (DmORC1)	0.93	-	nuc	0	Nucleus (By similarity)	nuclear origin of replication recognition c... [IDA]			924
Q9JK30 UniProt NPD GO	ORC3_MOUSE	Origin recognition complex subunit 3 (Origin recognition complex subunit Latheo)	0.93	-	nuc	0	Nucleus				715
Q9H4L5 UniProt NPD GO	OSBL3_HUMAN	Oxysterol-binding protein-related protein 3 (OSBP-related protein 3) (ORP-3)	0.93	+	nuc	0			606732		887
Q68ED3 UniProt NPD GO	PAD5_MOUSE	PAP-associated domain-containing protein 5 (EC 2.7.7.-) (Topoisomerase-related function protein 4-2) ...	0.93	+	nuc	0	Nucleus (Probable)				633
Q8K2W6 UniProt NPD GO	PHF13_MOUSE	PHD finger protein 13	0.93	+	nuc	0					296
O75151 UniProt NPD GO	PHF2_HUMAN	PHD finger protein 2 (GRC5)	0.93	+	nuc	0	Nucleus (Potential)	nucleus [TAS]	604351		1101
P16143 UniProt NPD GO	PO2F1_XENLA	POU domain, class 2, transcription factor 1 (Octamer-binding transcription factor 1) (Oct-1) (OTF-1) ...	0.93	+	nuc	0	Nucleus				760
P42571 UniProt NPD GO	PO2F3_RAT	POU domain, class 2, transcription factor 3 (Octamer-binding transcription factor 11) (Oct-11) (Tran ...	0.93	+	nuc	0	Nucleus				430
O75182 UniProt NPD GO	SIN3B_HUMAN	Paired amphipathic helix protein Sin3b (Transcriptional corepressor Sin3b) (Histone deacetylase comp ...	0.93	-	nuc	0	Nucleus (By similarity)		607777		1162
Q09750 UniProt NPD GO	PST1_SCHPO	Paired amphipathic helix protein pst1 (SIN3 homolog 1)	0.93	-	nuc	0	Nucleus	centric heterochromatin [IDA] histone deacetylase complex [IDA]			1522
Q17353 UniProt NPD GO	PAR3_CAEEL	Partitioning defective protein 3 (Abnormal embryonic partitioning of cytoplasm protein 3)	0.93	-	nuc	0	Cytoplasm. Cytoplasmic and cell periphery	apical part of cell [IDA] basal part of cell [IDA] cytoplasm [IDA] integral to membrane [IDA]			1379
Q4IPB3 UniProt NPD GO	CWC27_GIBZE	Peptidyl-prolyl isomerase CWC27 (EC 5.2.1.8)	0.93	+	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				548
Q9P7Q7 UniProt NPD GO	MAK1_SCHPO	Peroxide stress-activated histidine kinase mak1 (EC 2.7.13.3) (Mcs4-associated kinase 1) (His-Asp ph ...	0.93	+	nuc	0	Cytoplasm (Potential)				1639
Q9UBK2 UniProt NPD GO	PRGC1_HUMAN	Peroxisome proliferator-activated receptor gamma coactivator 1-alpha (PPAR gamma coactivator 1-alpha ...	0.93	+	nuc	0	Nucleus	DNA-directed RNA polymerase II, core complex [TAS] nucleus [TAS]	604517		798
Q9C0D0 UniProt NPD GO	PHAR1_HUMAN	Phosphatase and actin regulator 1	0.93	+	nuc	0	Cytoplasm (By similarity). Enriched at synapses (By similarity)		608723		580
Q2M3X8 UniProt NPD GO	PHAR1_MOUSE	Phosphatase and actin regulator 1	0.93	+	nuc	0	Cytoplasm (By similarity). Enriched at synapses (By similarity)				580
P62024 UniProt NPD GO	PHAR1_RAT	Phosphatase and actin regulator 1	0.93	+	nuc	0	Cytoplasm. Enriched at synapses				580
O48963 UniProt NPD GO	PHOT1_ARATH	Phototropin-1 (EC 2.7.11.1) (Non-phototropic hypocotyl protein 1) (Root phototropism protein 1)	0.93	-	nuc	0	Cell membrane; peripheral membrane protein. Cytoplasm				996
Q28503 UniProt NPD GO	PIT1_MACMU	Pituitary-specific positive transcription factor 1 (Pit-1) (Growth hormone factor 1) (GHF-1)	0.93	+	nuc	0	Nucleus				291
P48561 UniProt NPD GO	TRF5_YEAST	Poly(A) RNA polymerase protein 1 (EC 2.7.7.-) (Topoisomerase 1-related protein TRF5)	0.93	-	nuc	0	Nucleus; nucleolus	nucleolus [IDA]			625
Q8VDG3 UniProt NPD GO	PARN_MOUSE	Poly(A)-specific ribonuclease PARN (EC 3.1.13.4) (Polyadenylate-specific ribonuclease)	0.93	+	nuc	0	Nucleus. Cytoplasm. Some nuclear fraction is nucleolar			1WHV	624
O95453 UniProt NPD GO	PARN_HUMAN	Poly(A)-specific ribonuclease PARN (EC 3.1.13.4) (Polyadenylate-specific ribonuclease) (Deadenylatin ...	0.93	+	nuc	0	Nucleus. Cytoplasm. Some nuclear fraction is nucleolar	cytoplasm [TAS] nucleus [TAS]	604212	2A1S	639
Q6CTZ8 UniProt NPD GO	RAD18_KLULA	Postreplication repair ubiquitin-protein ligase E3 RAD18 (EC 6.-.-.-)	0.93	-	nuc	0	Nucleus (By similarity)				427
Q63099 UniProt NPD GO	KCNB2_RAT	Potassium voltage-gated channel subfamily B member 2 (Voltage-gated potassium channel subunit Kv2.2) ...	0.93	-	nuc	4	Membrane; multi-pass membrane protein				907
Q9ER47 UniProt NPD GO	KCNH7_MOUSE	Potassium voltage-gated channel subfamily H member 7 (Voltage-gated potassium channel subunit Kv11.3 ...	0.93	-	nuc	4	Membrane; multi-pass membrane protein				1195
O54852 UniProt NPD GO	KCNH7_RAT	Potassium voltage-gated channel subfamily H member 7 (Voltage-gated potassium channel subunit Kv11.3 ...	0.93	-	nuc	4	Membrane; multi-pass membrane protein				1195
Q9NS40 UniProt NPD GO	KCNH7_HUMAN	Potassium voltage-gated channel subfamily H member 7 (Voltage-gated potassium channel subunit Kv11.3 ...	0.93	-	nuc	4	Membrane; multi-pass membrane protein		608169		1196
Q99NE9 UniProt NPD GO	PBX4_MOUSE	Pre-B-cell leukemia transcription factor 4 (Homeobox protein PBX4)	0.93	-	nuc	0	Nucleus (Potential)	nucleus [IMP]			378
Q4WPE9 UniProt NPD GO	PRP28_ASPFU	Pre-mRNA-splicing ATP-dependent RNA helicase prp28 (EC 3.6.1.-)	0.93	+	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				796
Q52G60 UniProt NPD GO	CEF1_MAGGR	Pre-mRNA-splicing factor CEF1	0.93	+	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				773
Q5KII3 UniProt NPD GO	SLU7_CRYNE	Pre-mRNA-splicing factor SLU7	0.93	+	nuc	0	Nucleus (By similarity)				574
Q6BVE0 UniProt NPD GO	SYF2_DEBHA	Pre-mRNA-splicing factor SYF2	0.93	+	nuc	0	Nucleus (By similarity)				231
Q7RX84 UniProt NPD GO	CWC22_NEUCR	Pre-mRNA-splicing factor cwc-22	0.93	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				1010
O14161 UniProt NPD GO	CWC21_SCHPO	Pre-mRNA-splicing factor cwc21 (Complexed with cdc5 protein 21) (Cell cycle control protein cwf21)	0.93	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)	spliceosome complex [IDA]			293
Q09882 UniProt NPD GO	PRP45_SCHPO	Pre-mRNA-splicing factor prp45 (Complexed with cdc5 protein 13) (Cell cycle control protein cwf13) ( ...	0.93	-	nuc	0	Nucleus (Probable)				557
Q5B3U2 UniProt NPD GO	SLU7_EMENI	Pre-mRNA-splicing factor slu7 (Splicing factor sluA)	0.93	-	nuc	0	Nucleus (By similarity)				466
P39521 UniProt NPD GO	FHL1_YEAST	Pre-rRNA-processing protein FHL1	0.93	-	nuc	0	Nucleus (Probable)	nucleolus [IDA] nucleus [IDA]			936
Q8VHK9 UniProt NPD GO	DHX36_MOUSE	Probable ATP-dependent RNA helicase DHX36 (EC 3.6.1.-) (DEAH box protein 36) (MLE-like protein 1) (R ...	0.93	-	mit	0	Nucleus (By similarity)				1001
Q10332 UniProt NPD GO	YBMA_SCHPO	Probable ATP-dependent helicase C582.10c in chromosome II (EC 3.6.1.-)	0.93	-	nuc	0	Nucleus				830
Q9C6I8 UniProt NPD GO	NOG1_ARATH	Probable nucleolar GTP-binding protein 1	0.93	-	nuc	0	Nucleus; nucleolus (By similarity)				671
Q6CT09 UniProt NPD GO	NOP14_KLULA	Probable nucleolar complex protein 14	0.93	+	nuc	0	Nucleus; nucleolus (By similarity)				837
P36004 UniProt NPD GO	KKQ8_YEAST	Probable serine/threonine-protein kinase YKL168C (EC 2.7.11.1)	0.93	-	nuc	0		cytoplasm [IDA]			734
P40467 UniProt NPD GO	YIN0_YEAST	Probable transcriptional regulatory protein YIL130W	0.93	+	nuc	0	Nucleus (Probable)	nucleus [IDA]			964
P81299 UniProt NPD GO	CDC14_CAEEL	Probable tyrosine-protein phosphatase cdc-14 (EC 3.1.3.48) (Cell division cycle-related protein 14)	0.93	-	nuc	0					1063
Q12446 UniProt NPD GO	LAS17_YEAST	Proline-rich protein LAS17	0.93	+	nuc	0		actin cortical patch [IDA] cytoplasm [IDA]			633
P19884 UniProt NPD GO	RELX_MACMU	Prorelaxin precursor [Contains: Relaxin B chain; Relaxin A chain]	0.93	-	exc	0	Secreted protein				185
P35299 UniProt NPD GO	PRM2_PANPA	Protamine-2 (Protamine-P2) (Sperm histone P2)	0.93	+	nuc	0	Nucleus				102
P35300 UniProt NPD GO	PRM2_PANTR	Protamine-2 (Protamine-P2) (Sperm histone P2)	0.93	+	nuc	0	Nucleus				102
Q91VE1 UniProt NPD GO	PRM2_RATFU	Protamine-2 (Protamine-P2) (Sperm histone P2)	0.93	+	nuc	0	Nucleus				105

You are viewing entries 2901 to 2950 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.