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
O54826 UniProt NPD GO	AF10_MOUSE	Protein AF-10	0.87	+	nuc	0	Nucleus (Potential)				1068
Q9FMT4 UniProt NPD GO	Y5417_ARATH	Protein At5g14170	0.87	-	nuc	0				1V31	534
Q5W0B1 UniProt NPD GO	CM007_HUMAN	Protein C13orf7	0.87	-	nuc	0					726
Q5RD97 UniProt NPD GO	CM007_PONPY	Protein C13orf7 homolog	0.87	-	nuc	0					726
Q8K2H3 UniProt NPD GO	CE005_MOUSE	Protein C5orf5 homolog	0.87	-	nuc	0					851
Q9NXG0 UniProt NPD GO	CI039_HUMAN	Protein C9orf39	0.87	-	nuc	0					1084
Q6AYJ3 UniProt NPD GO	CI068_RAT	Protein C9orf68 homolog	0.87	-	nuc	0					398
Q9H8G2 UniProt NPD GO	CI082_HUMAN	Protein C9orf82	0.87	-	nuc	0					361
Q8VDY9 UniProt NPD GO	CI082_MOUSE	Protein C9orf82 homolog	0.87	-	nuc	0					356
Q6TFL3 UniProt NPD GO	CI093_HUMAN	Protein C9orf93	0.87	-	nuc	0					1326
Q9DBR2 UniProt NPD GO	FA13C_MOUSE	Protein FAM13C1	0.87	-	nuc	0					601
Q9WV03 UniProt NPD GO	FA50A_MOUSE	Protein FAM50A (XAP-5 protein)	0.87	+	nuc	0	Nucleus (Potential)				339
Q6DFY8 UniProt NPD GO	FAM5B_MOUSE	Protein FAM5B precursor	0.87	-	mit	1 *	Secreted protein (Potential)				783
Q8K1M8 UniProt NPD GO	FAM5B_RAT	Protein FAM5B precursor (BMP/retinoic acid-inducible neural-specific protein 2)	0.87	-	mit	1 *	Secreted protein (Potential)	cytoplasm [IMP]			783
Q70Z53 UniProt NPD GO	F10C1_HUMAN	Protein FRA10AC1	0.87	+	nuc	0	Nucleus		608866		315
Q6FUQ5 UniProt NPD GO	FYV7_CANGA	Protein FYV7	0.87	+	nuc	0	Nucleus; nucleolus (By similarity)				152
O43313 UniProt NPD GO	K0431_HUMAN	Protein KIAA0431	0.87	-	nuc	0					667
O94874 UniProt NPD GO	K0776_HUMAN	Protein KIAA0776	0.87	+	cyt	0					794
Q5F3F2 UniProt NPD GO	MYSM1_CHICK	Protein MYSM1 (Myb-like, SWIRM and MPN domain-containing protein 1)	0.87	-	nuc	0	Nucleus (Probable)				832
P32344 UniProt NPD GO	QRI5_YEAST	Protein QRI5	0.87	+	nuc	0		mitochondrion [IDA]			111
P53552 UniProt NPD GO	RLR1_YEAST	Protein RLR1 (Protein THO2)	0.87	-	nuc	0		nucleus [IC] THO complex [IMP]			1597
Q9H3C7 UniProt NPD GO	ZN403_HUMAN	Protein ZNF403 (Laryngeal carcinoma-related protein 1)	0.87	+	nuc	0	Cytoplasmic vesicle (By similarity). Associated with vesicular structures (By similarity)				697
Q24120 UniProt NPD GO	CAPU_DROME	Protein cappuccino	0.87	-	nuc	0					1059
Q24573 UniProt NPD GO	DRI_DROME	Protein dead ringer (Protein retained)	0.87	-	nuc	0	Nucleus	nucleus [IEP]		1KQQ	911
P13002 UniProt NPD GO	ELF1_DROME	Protein grainyhead (Protein grainy-head) (DNA-binding protein ELF-1) (Element I-binding activity) (T ...	0.87	+	nuc	0	Nucleus	nucleus [IDA]			1333
P14003 UniProt NPD GO	HAIR_DROME	Protein hairy	0.87	-	nuc	0	Nucleus				337
Q9NBL2 UniProt NPD GO	MSL3_DROVI	Protein male-specific lethal-3	0.87	+	nuc	0	Nucleus (By similarity)	dosage compensation complex (sensu Insecta) [ISS]			543
Q8VHQ3 UniProt NPD GO	PP16B_MOUSE	Protein phosphatase 1 regulatory inhibitor subunit 16B (TGF-beta-inhibited membrane-associated prote ...	0.87	+	nuc	0	Cell membrane; lipid-anchor (By similarity)	plasma membrane [ISS]			568
Q7TT52 UniProt NPD GO	PP14D_MOUSE	Protein phosphatase 1 regulatory subunit 14D (Gastrointestinal and brain-specific PP1-inhibitory pro ...	0.87	-	nuc	0	Cytoplasm (Probable)				146
Q9GYI4 UniProt NPD GO	PTDSR_CAEEL	Protein psr-1 (Phosphatidylserine receptor 1)	0.87	+	nuc	0	Nucleus (By similarity)	nucleus [ISS]			400
P40380 UniProt NPD GO	RUM1_SCHPO	Protein rum1 (p25-rum1)	0.87	-	nuc	0					230
Q6FY22 UniProt NPD GO	SEC9_CANGA	Protein transport protein SEC9	0.87	+	nuc	0					694
P10627 UniProt NPD GO	TWIST_DROME	Protein twist	0.87	+	nuc	0	Nucleus	nucleus [IDA]			490
P46064 UniProt NPD GO	RECQ1_CAEEL	Putative ATP-dependent DNA helicase Q1 (EC 3.6.1.-)	0.87	-	mit	0	Nucleus (By similarity)				892
P40562 UniProt NPD GO	YIS2_YEAST	Putative ATP-dependent RNA helicase YIR002C (EC 3.6.1.-)	0.87	+	nuc	0		nucleus [IDA]			993
Q19802 UniProt NPD GO	FKH5_CAEEL	Putative forkhead-related transcription factor fkh-5	0.87	-	mit	0	Nucleus (Potential)				461
P53249 UniProt NPD GO	YG2G_YEAST	Putative uncharacterized protein YGR079W precursor	0.87	-	nuc	1 *					370
Q9JJT9 UniProt NPD GO	RNUXA_MOUSE	RNA U small nuclear RNA export adapter protein (Phosphorylated adapter RNA export protein)	0.87	-	nuc	0	Nucleus (By similarity). Nucleus; nucleoplasm (By similarity). Nucleus; nucleoplasm; Cajal body (By ...	cytoplasm [IDA] nucleus [IDA]			385
P36070 UniProt NPD GO	RRN3_YEAST	RNA polymerase I-specific transcription initiation factor RRN3	0.87	-	nuc	0	Nucleus (Potential)	RNA polymerase I transcription factor complex [TAS]			627
Q9HB65 UniProt NPD GO	ELL3_HUMAN	RNA polymerase II elongation factor ELL3	0.87	-	nuc	0	Nucleus	nucleus [IDA] transcription elongation factor complex [NAS]	609885		397
P32259 UniProt NPD GO	MED16_YEAST	RNA polymerase II mediator complex subunit 16 (Global transcriptional regulator SIN4) (YGP1 expressi ...	0.87	-	nuc	0	Nucleus	mediator complex [IDA]			974
Q5R4D6 UniProt NPD GO	LEO1_PONPY	RNA polymerase-associated protein LEO1	0.87	-	nuc	0	Nucleus (By similarity)				666
Q641X2 UniProt NPD GO	LEO1_RAT	RNA polymerase-associated protein LEO1	0.87	-	nuc	0	Nucleus (By similarity)				678
Q8WVC0 UniProt NPD GO	LEO1_HUMAN	RNA polymerase-associated protein LEO1 (Replicative senescence down-regulated leo1-like protein)	0.87	-	nuc	0	Nucleus				666
Q8BG26 UniProt NPD GO	RUSC1_MOUSE	RUN and SH3 domain-containing protein 1	0.87	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity). Translocated to the nuclear envelope upon stimul ...				893
Q6IQ26 UniProt NPD GO	RA6I1_HUMAN	Rab6-interacting protein 1 (Rab6IP1)	0.87	-	cyt	0					1287
Q28013 UniProt NPD GO	RASA3_BOVIN	Ras GTPase-activating protein 3 (GAP1(IP4BP)) (Ins P4-binding protein)	0.87	+	nuc	0					834
Q4VSN2 UniProt NPD GO	RIPK5_FUGRU	Receptor-interacting serine/threonine-protein kinase 5 (EC 2.7.11.1) (Dusty protein kinase) (Dusty P ...	0.87	-	nuc	0	Cytoplasm (Probable)				921
P13785 UniProt NPD GO	FLP_ZYGRO	Recombinase Flp protein	0.87	-	nuc	0					490
P49802 UniProt NPD GO	RGS7_HUMAN	Regulator of G-protein signaling 7 (RGS7)	0.87	-	nuc	0			602517	2A72	495

You are viewing entries 5751 to 5800 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.