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
Q9N0L8 UniProt NPD GO	WAP_MACEU	Whey acidic protein precursor (tWAP)	0.46	-	exc	0	Secreted protein			1TWP	191
Q9DCD2 UniProt NPD GO	XAB2_MOUSE	XPA-binding protein 2	0.46	-	cyt	0	Nucleus (By similarity). Detected in the splicing complex carrying pre-mRNA (By similarity)	nucleus [IC]			855
Q99PK0 UniProt NPD GO	XAB2_RAT	XPA-binding protein 2 (Adapter protein ATH-55)	0.46	-	cyt	0	Nucleus. Detected in the splicing complex carrying pre-mRNA	nucleus [ISS]			855
Q9HCS7 UniProt NPD GO	XAB2_HUMAN	XPA-binding protein 2 (HCNP protein)	0.46	-	cyt	0	Nucleus (By similarity). Detected in the splicing complex carrying pre-mRNA (By similarity)	nucleus [IC]			855
Q5RDU9 UniProt NPD GO	YJDC_PONPY	YjeF domain-containing protein 1	0.46	-	nuc	0	Cytoplasm (By similarity). Processing bodies (PB) (By similarity)				508
Q99ML0 UniProt NPD GO	ZMY10_MOUSE	Zinc finger MYND domain-containing protein 10 (BLu protein)	0.46	-	cyt	0					440
Q07230 UniProt NPD GO	ZSCA2_MOUSE	Zinc finger and SCAN domain-containing protein 2 (Zinc finger protein 29) (Zfp-29)	0.46	-	nuc	0	Nucleus				614
P52742 UniProt NPD GO	ZN135_HUMAN	Zinc finger protein 135	0.46	-	nuc	0	Nucleus (Potential)	nucleus [NAS]	604077		469
Q2M3W8 UniProt NPD GO	ZN181_HUMAN	Zinc finger protein 181 (HHZ181)	0.46	-	nuc	0	Nucleus (Probable)		606741		571
Q9BRH9 UniProt NPD GO	ZN251_HUMAN	Zinc finger protein 251 (Fragment)	0.46	-	nuc	0	Nucleus (Probable)				293
Q9UL40 UniProt NPD GO	ZN346_HUMAN	Zinc finger protein 346 (Just another zinc finger protein)	0.46	-	nuc	0	Nucleus; nucleolus. Cytoplasm. Nuclear at steady state, primarily in the nucleolus. Shuttles between ...	nucleolus [TAS] nucleus [TAS]	605308		294
Q9BWM5 UniProt NPD GO	ZN416_HUMAN	Zinc finger protein 416	0.46	-	nuc	0	Nucleus (Probable)				594
P22227 UniProt NPD GO	ZFP42_MOUSE	Zinc finger protein 42 (Zfp-42) (REX-1 protein) (Reduced expression protein 1)	0.46	-	nuc	0					288
Q9C0F3 UniProt NPD GO	ZN436_HUMAN	Zinc finger protein 436	0.46	-	nuc	0	Nucleus (Potential)				470
Q8BPP0 UniProt NPD GO	ZN436_MOUSE	Zinc finger protein 436 (Zinc finger protein 46)	0.46	-	nuc	0	Nucleus (Potential)				452
Q39265 UniProt NPD GO	ZFP6_ARATH	Zinc finger protein 6	0.46	+	nuc	0					197
Q8NB50 UniProt NPD GO	ZFP62_HUMAN	Zinc finger protein 62 homolog (Zfp-62)	0.46	-	nuc	0	Nucleus (Potential)				694
Q6ZNG0 UniProt NPD GO	ZN620_HUMAN	Zinc finger protein 620	0.46	-	nuc	0	Nucleus (Probable)				422
Q5EBL2 UniProt NPD GO	ZN628_HUMAN	Zinc finger protein 628	0.46	-	nuc	0	Nucleus (By similarity)				1048
Q8IYX0 UniProt NPD GO	ZN679_HUMAN	Zinc finger protein 679	0.46	-	nuc	0	Nucleus (Potential)				411
Q21388 UniProt NPD GO	NAS10_CAEEL	Zinc metalloproteinase nas-10 (EC 3.4.24.21) (Nematode astacin 10)	0.46	-	nuc	0					560
P16905 UniProt NPD GO	KAPR1_DROME	cAMP-dependent protein kinase type I regulatory subunit (DRI class I to class IV)	0.46	-	cyt	0					376
Q10294 UniProt NPD GO	PAC2_SCHPO	cAMP-independent regulatory protein pac2	0.46	-	nuc	0					235
Q5KMN5 UniProt NPD GO	YTH1_CRYNE	mRNA 3'-end-processing protein YTH1	0.46	-	nuc	0	Nucleus (By similarity)				332
Q756C5 UniProt NPD GO	PALA_ASHGO	pH-response regulator protein palA/RIM20	0.46	-	cyt	0					631
P38238 UniProt NPD GO	TRM7_YEAST	tRNA (uridine-2'-O-)-methyltransferase TRM7 (EC 2.1.1.-)	0.46	-	nuc	0	Cytoplasm	cytoplasm [IDA]			310
P29835 UniProt NPD GO	GL19_ORYSA	19 kDa globulin precursor (Alpha-globulin)	0.45	-	nuc	1 *					186
P54658 UniProt NPD GO	HS32_DICDI	32 kDa heat shock protein (4-1 protein)	0.45	-	nuc	0					281
P12686 UniProt NPD GO	RT13_YEAST	40S ribosomal protein S13, mitochondrial precursor (YmS-A)	0.45	-	mit	0	Mitochondrion	mitochondrial small ribosomal subunit [IDA]			339
P52820 UniProt NPD GO	RS15_HELLU	40S ribosomal protein S15 (Fragment)	0.45	-	cyt	0					37
P34737 UniProt NPD GO	RS15_PODAN	40S ribosomal protein S15 (S12)	0.45	+	nuc	0					152
O94715 UniProt NPD GO	RS15A_SCHPO	40S ribosomal protein S15-A	0.45	-	cyt	0					153
P49171 UniProt NPD GO	RS26_PIG	40S ribosomal protein S26	0.45	-	nuc	0					114
Q3T0B7 UniProt NPD GO	RS27L_BOVIN	40S ribosomal protein S27-like protein	0.45	+	nuc	0					83
P15357 UniProt NPD GO	RS27A_DROME	40S ribosomal protein S27a	0.45	+	nuc	0					80
P28286 UniProt NPD GO	5HT2B_DROME	5-hydroxytryptamine receptor 2B (5-HT receptor) (Serotonin receptor 2B)	0.45	-	end	7	Membrane; multi-pass membrane protein				617
P26285 UniProt NPD GO	F262_BOVIN	6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 2 (6PF-2-K/Fru-2,6-P2ASE heart-type isozyme) (PF ...	0.45	-	nuc	0					530
Q04599 UniProt NPD GO	RM01_YEAST	60S ribosomal protein L1, mitochondrial precursor	0.45	-	nuc	0	Mitochondrion	mitochondrial large ribosomal subunit [IPI]			285
P36520 UniProt NPD GO	RM10_YEAST	60S ribosomal protein L10, mitochondrial precursor (YmL10/YmL18)	0.45	-	mit	0	Mitochondrion	mitochondrial large ribosomal subunit [TAS]			322
P24558 UniProt NPD GO	RL18_SALSA	60S ribosomal protein L18	0.45	-	nuc	0					179
Q8SQP8 UniProt NPD GO	RL39_ENCCU	60S ribosomal protein L39	0.45	-	nuc	0					52
P48536 UniProt NPD GO	RL39_KLUMA	60S ribosomal protein L39 (L46)	0.45	-	mit	0					50
P49165 UniProt NPD GO	RL4_URECA	60S ribosomal protein L4 (L1)	0.45	-	nuc	0					386
O13672 UniProt NPD GO	RL8_SCHPO	60S ribosomal protein L8 (L7A) (L4)	0.45	-	mit	0					258
Q02981 UniProt NPD GO	YP109_YEAST	ABC1 family protein YPL109C, mitochondrial precursor	0.45	-	end	0	Mitochondrion	mitochondrion [IDA]			657
P58459 UniProt NPD GO	ATS10_MOUSE	ADAMTS-10 (EC 3.4.24.-) (A disintegrin and metalloproteinase with thrombospondin motifs 10) (ADAM-TS ...	0.45	-	nuc	0	Secreted protein; extracellular space; extracellular matrix (By similarity)				450
Q10588 UniProt NPD GO	BST1_HUMAN	ADP-ribosyl cyclase 2 precursor (EC 3.2.2.5) (Cyclic ADP-ribose hydrolase 2) (cADPr hydrolase 2) (Bo ...	0.45	-	nuc	1 *	Cell membrane; lipid-anchor; GPI-anchor	extrinsic to membrane [TAS]	600387	1ISM	318
P36000 UniProt NPD GO	AP1B1_YEAST	AP-1 complex subunit beta-1 (Beta(1)-adaptin) (Clathrin assembly protein large beta-1 chain) (Clathr ...	0.45	-	cyt	0	Component of the coat surrounding the cytoplasmic face of coated vesicles in the plasma membrane	AP-1 adaptor complex [IPI]			726
P17427 UniProt NPD GO	AP2A2_MOUSE	AP-2 complex subunit alpha-2 (Adapter-related protein complex 2 alpha-2 subunit) (Alpha-adaptin C) ( ...	0.45	-	cyt	0	Component of the coat surrounding the cytoplasmic face of coated vesicles in the plasma membrane	membrane coat [IDA] secretory granule [TAS]		1QTS	938
Q9FH50 UniProt NPD GO	APO3_ARATH	APO protein 3, mitochondrial precursor	0.45	-	mit	0	Mitochondrion (Potential)				402

You are viewing entries 28051 to 28100 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.