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
P47932 UniProt NPD GO	REL1_MOUSE	Prorelaxin 1 precursor [Contains: Relaxin B chain; Relaxin A chain]	0.68	-	exc	0	Secreted protein				185
Q9FHY1 UniProt NPD GO	ABIL4_ARATH	Protein ABIL4 (Abl interactor-like protein 4) (AtABIL4)	0.68	-	nuc	0					279
Q8C5R2 UniProt NPD GO	CJ047_MOUSE	Protein C10orf47 homolog	0.68	-	nuc	0					471
Q9NQ89 UniProt NPD GO	CL004_HUMAN	Protein C12orf4	0.68	-	nuc	0					552
Q91YN0 UniProt NPD GO	CL004_MOUSE	Protein C12orf4 homolog	0.68	-	nuc	0					552
Q5RD58 UniProt NPD GO	CL004_PONPY	Protein C12orf4 homolog	0.68	-	nuc	0					552
O13712 UniProt NPD GO	YDZ5_SCHPO	Protein C14C4.05c in chromosome I	0.68	-	nuc	2	Nucleus; nuclear membrane; multi-pass membrane protein	spindle pole body [IPI]			844
Q86U38 UniProt NPD GO	CN021_HUMAN	Protein C14orf21	0.68	+	nuc	0					636
Q8BMC4 UniProt NPD GO	CN021_MOUSE	Protein C14orf21 homolog	0.68	+	nuc	0					636
Q8IXS0 UniProt NPD GO	CF146_HUMAN	Protein C6orf146	0.68	-	nuc	0					508
Q66H24 UniProt NPD GO	CI040_RAT	Protein C9orf40 homolog	0.68	-	mit	0					166
Q9Y421 UniProt NPD GO	FA32A_HUMAN	Protein FAM32A	0.68	+	nuc	0					112
Q5R9E5 UniProt NPD GO	FA32A_PONPY	Protein FAM32A	0.68	+	nuc	0					112
Q5RCM2 UniProt NPD GO	FA35A_PONPY	Protein FAM35A	0.68	-	cyt	0					904
Q6IFS6 UniProt NPD GO	HSN2_MOUSE	Protein HSN2 precursor	0.68	-	nuc	0	Secreted protein (Potential)				433
P53604 UniProt NPD GO	MSO1_YEAST	Protein MSO1	0.68	+	nuc	0		microsome [IDA]			210
Q7RTT5 UniProt NPD GO	SSX7_HUMAN	Protein SSX7	0.68	-	nuc	0			300542		188
P38968 UniProt NPD GO	WEB1_YEAST	Protein WEB1 (Protein transport protein SEC31)	0.68	-	nuc	0		COPII vesicle coat [TAS]			1273
P40589 UniProt NPD GO	WNT4_DROME	Protein Wnt-4 precursor (dWnt-4)	0.68	-	exc	0	Secreted protein; extracellular space; extracellular matrix	extracellular region [NAS]			539
Q9VGX3 UniProt NPD GO	FAU_DROME	Protein anoxia up-regulated	0.68	-	nuc	0					619
Q8C7D2 UniProt NPD GO	CRBN_MOUSE	Protein cereblon (Protein PiL)	0.68	-	nuc	0					445
Q8AW93 UniProt NPD GO	DTX1_XENLA	Protein deltex-1 (xDtx1)	0.68	-	nuc	0					623
P13346 UniProt NPD GO	FOSB_MOUSE	Protein fosB	0.68	+	nuc	0	Nucleus				338
P12980 UniProt NPD GO	LYL1_HUMAN	Protein lyl-1 (Lymphoblastic leukemia-derived sequence 1)	0.68	-	nuc	0	Nucleus (Potential)		151440		267
P53031 UniProt NPD GO	2ABA_CANTR	Protein phosphatase PP2A regulatory subunit B (PR55) (Cell division control protein 55)	0.68	-	nuc	0					508
Q9UTE0 UniProt NPD GO	SEY1_SCHPO	Protein sey1	0.68	-	mit	1	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein. Nucleus; nuclear ...				762
O95487 UniProt NPD GO	SC24B_HUMAN	Protein transport protein Sec24B (SEC24-related protein B)	0.68	-	nuc	0	Cytoplasm. Cytoplasm; perinuclear region	membrane [TAS]	607184		1268
Q60992 UniProt NPD GO	VAV2_MOUSE	Protein vav-2	0.68	-	cyt	0		cytoplasm [IDA] plasma membrane [IDA]			868
Q5BGC4 UniProt NPD GO	VTS1_EMENI	Protein vts1	0.68	-	mit	0	Cytoplasm (By similarity)				611
P09089 UniProt NPD GO	ZEN1_DROME	Protein zerknuellt 1 (ZEN-1)	0.68	+	nuc	0	Nucleus			1KZ2	353
P59913 UniProt NPD GO	PCMD1_MOUSE	Protein-L-isoaspartate O-methyltransferase domain-containing protein 1	0.68	+	cyt	0	Cytoplasm (By similarity)				357
Q9Z2Q8 UniProt NPD GO	FOS_CRIGR	Proto-oncogene protein c-fos (Cellular oncogene fos)	0.68	-	nuc	0	Nucleus				381
P27870 UniProt NPD GO	VAV_MOUSE	Proto-oncogene vav (p95vav)	0.68	-	mit	0				1K1Z	845
Q9NPG4 UniProt NPD GO	PCD12_HUMAN	Protocadherin-12 precursor (Vascular cadherin-2) (Vascular endothelial cadherin-2) (VE-cadherin-2) ( ...	0.68	-	nuc	1	Membrane; single-pass type I membrane protein	integral to plasma membrane [TAS] plasma membrane [TAS]	605622		1184
Q5BJS0 UniProt NPD GO	DHX30_RAT	Putative ATP-dependent RNA helicase DHX30 (EC 3.6.1.-) (DEAH box protein 30)	0.68	-	mit	0					1194
O80792 UniProt NPD GO	RH33_ARATH	Putative DEAD-box ATP-dependent RNA helicase 33 (EC 3.6.1.-)	0.68	-	nuc	0					845
Q60YA8 UniProt NPD GO	DKC1_CAEBR	Putative H/ACA ribonucleoprotein complex subunit 4 (EC 5.4.99.-)	0.68	-	nuc	0	Nucleus; nucleolus (By similarity)				445
Q9VPT5 UniProt NPD GO	PEX12_DROME	Putative peroxisome assembly protein 12 (Peroxin-12)	0.68	-	nuc	0	Peroxisome; peroxisomal membrane; multi-pass membrane protein (Potential)				297
Q09595 UniProt NPD GO	YRL5_CAEEL	Putative serine/threonine-protein kinase R03D7.5 (EC 2.7.11.1)	0.68	+	nuc	0					410
Q9M9B3 UniProt NPD GO	COL8_ARATH	Putative zinc finger protein CONSTANS-LIKE 8	0.68	-	nuc	0	Nucleus (Potential)				313
P07272 UniProt NPD GO	PPR1_YEAST	Pyrimidine pathway regulatory protein 1	0.68	-	nuc	0	Nucleus	nucleus [TAS]		1PYI	904
Q9NVW2 UniProt NPD GO	RNF12_HUMAN	RING finger protein 12 (LIM domain-interacting RING finger protein) (RING finger LIM domain-binding ...	0.68	-	nuc	0		transcriptional repressor complex [NAS]	300379		624
Q5E9J6 UniProt NPD GO	RNF34_BOVIN	RING finger protein 34	0.68	-	exc	0	Nucleus; nucleoplasm; nuclear speckle (By similarity). Intracellular membrane; peripheral membrane p ...				375
Q6AYH3 UniProt NPD GO	RNF34_RAT	RING finger protein 34 (RING finger protein MOMO)	0.68	-	exc	0	Nucleus; nucleoplasm; nuclear speckle (By similarity). Intracellular membrane; peripheral membrane p ...				381
Q9H0F5 UniProt NPD GO	RNF38_HUMAN	RING finger protein 38	0.68	+	nuc	0				1X4J	515
Q9VL31 UniProt NPD GO	RIP_DROME	RIP-like protein (RIP-alpha)	0.68	-	nuc	0					197
P29558 UniProt NPD GO	RBMS1_HUMAN	RNA-binding motif, single-stranded-interacting protein 1 (Single-stranded DNA-binding protein MSSP-1 ...	0.68	-	nuc	0	Nucleus		602310	1X5O	406
Q15434 UniProt NPD GO	RBMS2_HUMAN	RNA-binding motif, single-stranded-interacting protein 2 (Suppressor of CDC2 with RNA-binding motif ...	0.68	-	nuc	0	Nucleus (Potential)		602387	1X4E	407
Q8WXA3 UniProt NPD GO	RUFY2_HUMAN	RUN and FYVE domain-containing protein 2 (Rab4-interacting protein related)	0.68	-	nuc	0	Nucleus (By similarity)				655
Q9QZD5 UniProt NPD GO	RAE2_MOUSE	Rab proteins geranylgeranyltransferase component A 2 (Rab escort protein 2) (REP-2) (Choroideraemia- ...	0.68	-	nuc	0					621

You are viewing entries 14901 to 14950 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.