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
Q6PIJ6 UniProt NPD GO	FBX38_HUMAN	F-box only protein 38 (Modulator of KLF7 activity homolog) (MoKA)	0.94	+	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)		608533		1188
Q8AXF4 UniProt NPD GO	FBX43_XENLA	F-box only protein 43 (Emi1-related protein 1) (Xerp1) (Early mitotic inhibitor 2) (F-box protein 26 ...	0.94	-	nuc	0					651
Q6PB97 UniProt NPD GO	FXL19_MOUSE	F-box/LRR-repeat protein 19 (F-box and leucine-rich repeat protein 19)	0.94	-	nuc	0					674
Q5A1D5 UniProt NPD GO	SPT16_CANAL	FACT complex subunit SPT16 (Facilitates chromatin transcription complex subunit SPT16) (Cell divisio ...	0.94	+	nuc	0	Nucleus (By similarity)				1060
Q4H2R2 UniProt NPD GO	SSRP1_CIOIN	FACT complex subunit SSRP1 (Facilitates chromatin transcription complex subunit SSRP1) (Structure-sp ...	0.94	+	nuc	0	Nucleus (By similarity)				704
Q8BGE5 UniProt NPD GO	FANCM_MOUSE	Fanconi anemia group M protein homolog (EC 3.6.1.-) (ATP-dependent RNA helicase FANCM) (Protein FACM ...	0.94	-	nuc	1	Nucleus (By similarity)				2021
Q60688 UniProt NPD GO	FOXD4_MOUSE	Forkhead box protein D4 (Forkhead-related protein FKHL9) (Forkhead-related transcription factor 5) ( ...	0.94	-	nuc	0	Nucleus				444
O94532 UniProt NPD GO	FOR3_SCHPO	Formin-3	0.94	-	nuc	0	Cell membrane; peripheral membrane protein. Found at the cell periphery and the growing tips of inte ...	cell cortex of cell tip [IDA]			1461
Q9NW75 UniProt NPD GO	GPTC2_HUMAN	G patch domain-containing protein 2	0.94	-	nuc	0					528
P36417 UniProt NPD GO	GBF_DICDI	G-box-binding factor (GBF)	0.94	-	nuc	0	Nucleus (Potential)				708
Q9JHZ4 UniProt NPD GO	GRAP1_RAT	GRIP1-associated protein 1 (GRASP-1)	0.94	-	nuc	0					837
P34288 UniProt NPD GO	GAP_CAEEL	GTPase-activating protein GAP (CeGAP)	0.94	-	nuc	0	Cytoplasm (By similarity)	cytoplasm [NAS]			1317
Q13439 UniProt NPD GO	GOGA4_HUMAN	Golgin subfamily A member 4 (Trans-Golgi p230) (256 kDa golgin) (Golgin-245) (Protein 72.1)	0.94	-	nuc	0	Cytoplasm. Golgi apparatus; Golgi membrane; peripheral membrane protein	Golgi trans face [TAS]	602509	1UPT	2230
O77086 UniProt NPD GO	C3G_DROME	Guanine nucleotide-releasing factor 2 (CRK SH3-binding GNRP)	0.94	-	nuc	0					1571
Q75EZ7 UniProt NPD GO	HDA2_ASHGO	HDA1 complex subunit 2 (Histone deacetylase complex 1 subunit 2)	0.94	-	nuc	0	Nucleus (By similarity)				665
P41151 UniProt NPD GO	HSF1_ARATH	Heat shock factor protein 1 (HSF 1) (Heat shock transcription factor 1) (HSTF 1)	0.94	-	nuc	0	Nucleus				495
Q32L62 UniProt NPD GO	HEMGN_BOVIN	Hemogen (Hemopoietic gene protein)	0.94	+	nuc	0	Nucleus (By similarity)				447
Q09599 UniProt NPD GO	SLBP_CAEEL	Histone RNA hairpin-binding protein (Histone stem-loop-binding protein)	0.94	-	nuc	0					367
Q9TYU5 UniProt NPD GO	TIP60_CAEEL	Histone acetyltransferase Tip60 homolog (EC 2.3.1.48) (Myst family histone acetyltransferase-like pr ...	0.94	-	nuc	0	Nucleus (By similarity)				458
Q9FNE9 UniProt NPD GO	ATXR6_ARATH	Histone-lysine N-methyltransferase ATXR6 (EC 2.1.1.43) (Trithorax-related protein 6) (TRX-related pr ...	0.94	+	nuc	0	Nucleus (By similarity)				349
P45975 UniProt NPD GO	SUV9_DROME	Histone-lysine N-methyltransferase, H3 lysine-9 specific (EC 2.1.1.43) (Histone H3-K9 methyltransfer ...	0.94	-	nuc	0	Nucleus. Associates with centromeric heterochromatin				635
Q91685 UniProt NPD GO	MIX2_XENLA	Homeobox protein MIX.2	0.94	+	nuc	0	Nucleus (Probable)				369
Q23175 UniProt NPD GO	HM32_CAEEL	Homeobox protein ceh-32	0.94	-	nuc	0	Nucleus	nucleus [IDA]			439
P53546 UniProt NPD GO	GSCB_XENLA	Homeobox protein goosecoid isoform B	0.94	+	nuc	0	Nucleus				243
P48001 UniProt NPD GO	KNAT4_ARATH	Homeobox protein knotted-1-like 4 (KNAT4)	0.94	-	nuc	0	Nucleus (Probable)				393
Q09685 UniProt NPD GO	HGP1_SCHPO	Hyphal growth protein 1	0.94	-	nuc	0					411
Q85B66 UniProt NPD GO	YCF1B_ANTFO	Hypothetical 121 kDa protein ycf1 (ORF1031)	0.94	+	end	6 *	Plastid; chloroplast				1031
Q05024 UniProt NPD GO	YM74_YEAST	Hypothetical 26.5 kDa protein in FUS2-RNH1 intergenic region	0.94	+	nuc	0		cytoplasm [IDA] nucleolus [IDA] nucleus [IDA]			226
P40210 UniProt NPD GO	YM20_YEAST	Hypothetical 55.9 kDa protein in MDS1-RPL13B intergenic region	0.94	-	nuc	0		cytoplasm [IPI]			489
P47112 UniProt NPD GO	YJ16_YEAST	Hypothetical 68.4 kDa protein in SSC1-HYP1 intergenic region	0.94	-	nuc	0		cytoplasm [IDA] nucleus [IDA] pre-replicative complex [IMP]			604
P40522 UniProt NPD GO	YIF6_YEAST	Hypothetical 71.4 kDa protein in SNP1-GPP1 intergenic region	0.94	+	nuc	0		cytoplasm [IDA] nucleus [IDA]			640
Q03825 UniProt NPD GO	YM38_YEAST	Hypothetical 85.0 kDa protein in HLJ1-SMP2 intergenic region	0.94	-	nuc	0		nucleus [IC]			758
P50089 UniProt NPD GO	YG51_YEAST	Hypothetical 89.2 kDa protein in YHB1-PFK1 intergenic region	0.94	+	nuc	0		cytoplasm [IDA]			785
Q09268 UniProt NPD GO	YQDA_CAEEL	Hypothetical RING finger protein C32D5.10 in chromosome II	0.94	-	nuc	0					610
Q09713 UniProt NPD GO	YA36_SCHPO	Hypothetical protein C18B11.06 in chromosome I	0.94	+	nuc	0					327
Q09799 UniProt NPD GO	YAA5_SCHPO	Hypothetical protein C22G7.05 in chromosome I	0.94	-	nuc	0					598
Q09733 UniProt NPD GO	YA4G_SCHPO	Hypothetical protein C31A2.16 in chromosome I	0.94	-	nuc	0					1101
Q09280 UniProt NPD GO	YQI8_CAEEL	Hypothetical protein C45G9.8	0.94	+	mit	0					465
P87136 UniProt NPD GO	YDM5_SCHPO	Hypothetical protein C57A7.05 in chromosome I	0.94	+	end	11	Membrane; multi-pass membrane protein (Potential)				1337
P34433 UniProt NPD GO	YL53_CAEEL	Hypothetical protein F44E2.3	0.94	+	nuc	0					244
Q09575 UniProt NPD GO	YRD6_CAEEL	Hypothetical protein K02A2.6	0.94	-	nuc	0					1268
P34544 UniProt NPD GO	YNCA_CAEEL	Hypothetical protein R05D3.11 in chromosome III	0.94	-	nuc	0					1327
Q09350 UniProt NPD GO	YRU4_CAEEL	Hypothetical protein T09B9.4	0.94	-	nuc	0					528
Q16665 UniProt NPD GO	HIF1A_HUMAN	Hypoxia-inducible factor 1 alpha (HIF-1 alpha) (HIF1 alpha) (ARNT-interacting protein) (Member of PA ...	0.94	+	nuc	0	Cytoplasm. Nucleus. Cytoplasmic in normoxia, nuclear translocation in response to hypoxia	nucleus [IDA]	603348	1LQB	826
Q15051 UniProt NPD GO	IQCB1_HUMAN	IQ calmodulin-binding motif-containing protein 1 (Nephrocystin-5)	0.94	+	cyt	0			609254		598
Q02776 UniProt NPD GO	TIM50_YEAST	Import inner membrane translocase subunit TIM50, mitochondrial precursor	0.94	-	mit	0	Mitochondrion; mitochondrial inner membrane; single-pass membrane protein	mitochondrial inner membrane presequence tr... [IDA]			476
P33314 UniProt NPD GO	BUD2_YEAST	Inhibitory regulator protein BUD2/CLA2	0.94	+	nuc	0		intracellular [TAS]			1104
P87227 UniProt NPD GO	MIS6_SCHPO	Inner centromere protein mis6	0.94	-	cyt	0	Nucleus. Nuclear, centromeric	Mis6-Sim4 complex [TAS]			672
Q8QHJ9 UniProt NPD GO	I17RD_BRARE	Interleukin-17 receptor D precursor (IL-17 receptor D) (IL-17RD) (Interleukin-17D receptor) (IL-17D ...	0.94	-	exc	1 *	Membrane; single-pass type I membrane protein				745
O42287 UniProt NPD GO	ITSN1_XENLA	Intersectin-1	0.94	+	nuc	0	Intracytoplasmic membrane (By similarity). Synaptosome (By similarity). Enriched in synaptosomes (By ...				1270

You are viewing entries 2301 to 2350 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.