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
P32789 UniProt NPD GO	YBA9_YEAST	Hypothetical 76.4 kDa protein in SCT1-HIR1 intergenic region	0.86	-	nuc	0					676
P38456 UniProt NPD GO	YMF11_MARPO	Hypothetical 83.1 kDa protein in COB-ATPA intergenic region (ORF 732)	0.86	-	nuc	0					732
Q05050 UniProt NPD GO	YMS1_YEAST	Hypothetical 93.3 kDa protein in TAP42-CYK2 intergenic region	0.86	-	nuc	0		cytoplasm [IDA] mitochondrion [IDA]			843
Q10240 UniProt NPD GO	YD17_SCHPO	Hypothetical UPF0300 protein C4G9.07 in chromosome I	0.86	-	nuc	0					513
Q9M9F9 UniProt NPD GO	Y1843_ARATH	Hypothetical protein At1g78430	0.86	-	nuc	0					326
Q03564 UniProt NPD GO	YKD6_CAEEL	Hypothetical protein B0464.6	0.86	-	nuc	1					643
Q10366 UniProt NPD GO	YDBG_SCHPO	Hypothetical protein C22E12.16c in chromosome I	0.86	-	nuc	0					851
Q9UUN3 UniProt NPD GO	YQ86_SCHPO	Hypothetical protein C297.06c in chromosome III	0.86	-	nuc	0					230
O14342 UniProt NPD GO	YB3C_SCHPO	Hypothetical protein C2F12.12c in chromosome II	0.86	-	nuc	0					517
Q09287 UniProt NPD GO	YQK3_CAEEL	Hypothetical protein C56G2.3	0.86	-	nuc	0					318
Q09556 UniProt NPD GO	YQW3_CAEEL	Hypothetical protein F33H1.3	0.86	-	nuc	0					359
P34414 UniProt NPD GO	YLZ9_CAEEL	Hypothetical protein F42H10.9	0.86	-	nuc	1 *					309
P34564 UniProt NPD GO	YNV1_CAEEL	Hypothetical protein T16H12.1	0.86	-	nuc	0					344
Q3TES0 UniProt NPD GO	IQEC3_MOUSE	IQ motif and Sec7 domain-containing protein 3	0.86	-	nuc	0	Cytoplasm (Potential)				1195
Q76M68 UniProt NPD GO	IQEC3_RAT	IQ motif and Sec7 domain-containing protein 3 (Potential synaptic guanine nucleotide exchange factor ...	0.86	-	nuc	0	Cytoplasm (Potential)				1194
P03975 UniProt NPD GO	IGEB_MOUSE	IgE-binding protein	0.86	+	nuc	0					557
Q6CM45 UniProt NPD GO	TIM50_KLULA	Import inner membrane translocase subunit TIM50, mitochondrial precursor	0.86	-	mit	0	Mitochondrion; mitochondrial inner membrane; single-pass membrane protein (By similarity)				480
Q91615 UniProt NPD GO	IRS1A_XENLA	Insulin receptor substrate 1-A (IRS1-A) (xIRS-1-A) (XIRS-L)	0.86	-	nuc	0		cytoplasm [ISS] microsome [ISS] nucleus [ISS]			885
P15092 UniProt NPD GO	IFI4_MOUSE	Interferon-activable protein 204 (Ifi-204) (Interferon-inducible protein p204)	0.86	-	nuc	0	Nucleus. Nucleus; nucleolus. Primarily nucleolar				640
Q8UVC3 UniProt NPD GO	INVS_CHICK	Inversin	0.86	+	nuc	0	Cytoplasm (By similarity). Associates with the cytoskeleton (By similarity)				1106
P29375 UniProt NPD GO	JAD1A_HUMAN	Jumonji/ARID domain-containing protein 1A (Retinoblastoma-binding protein 2) (RBBP-2)	0.86	+	nuc	0	Nucleus (Potential)	nucleus [TAS]	180202		1722
Q86UP2 UniProt NPD GO	KTN1_HUMAN	Kinectin (Kinesin receptor) (CG-1 antigen)	0.86	+	nuc	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type II membrane protein. Vesicle ...	endoplasmic reticulum membrane [ISS]	600381		1357
Q86Z98 UniProt NPD GO	KINH_GIBMO	Kinesin heavy chain	0.86	-	nuc	0					931
Q8J1G7 UniProt NPD GO	CIN8_ASHGO	Kinesin-like protein CIN8	0.86	-	nuc	0	Spindle (By similarity). Spindle microtubules that lie between the poles (By similarity)				945
P27895 UniProt NPD GO	CIN8_YEAST	Kinesin-like protein CIN8 (Chromosome instability protein 8)	0.86	+	nuc	0	Spindle. Spindle microtubules that lie between the poles. Mitochondrion	condensed nuclear chromosome kinetochore [IDA] kinesin complex [TAS] mitochondrion [IDA] spindle microtubule [IDA]			1000
Q9BW19 UniProt NPD GO	KIFC1_HUMAN	Kinesin-like protein KIFC1 (Kinesin-like protein 2) (Kinesin-related protein HSET)	0.86	-	nuc	0		microtubule associated complex [NAS]	603763		673
Q9Y4X4 UniProt NPD GO	KLF12_HUMAN	Krueppel-like factor 12 (Transcriptional repressor AP-2rep)	0.86	-	nuc	0	Nucleus		607531		402
P20700 UniProt NPD GO	LMNB1_HUMAN	Lamin-B1	0.86	-	nuc	0	Nucleus; nuclear inner membrane; lipid-anchor; nucleoplasmic side	lamin filament [TAS]	150340		585
P09010 UniProt NPD GO	LAML1_XENLA	Lamin-L(I)	0.86	-	nuc	0	Nucleus; nuclear inner membrane; lipid-anchor; nucleoplasmic side				583
P42166 UniProt NPD GO	LAP2A_HUMAN	Lamina-associated polypeptide 2 isoform alpha (Thymopoietin isoform alpha) (TP alpha) (Thymopoietin- ...	0.86	+	nuc	0	Nucleus. Expressed diffusely throughout the nucleus	nuclear envelope [TAS] nucleus [TAS]	188380	1H9F	693
Q91YK0 UniProt NPD GO	LRC49_MOUSE	Leucine-rich repeat-containing protein 49	0.86	-	nuc	0					686
Q92539 UniProt NPD GO	LPIN2_HUMAN	Lipin-2	0.86	+	nuc	0	Nucleus (Potential)		609628		896
Q8ND30 UniProt NPD GO	LIPB2_HUMAN	Liprin-beta-2 (Protein tyrosine phosphatase receptor type f polypeptide-interacting protein-binding ...	0.86	-	nuc	0		intracellular [TAS]	603142		876
Q9JLB2 UniProt NPD GO	MPP5_MOUSE	MAGUK p55 subfamily member 5 (Protein associated with Lin-7 1)	0.86	+	nuc	0	Cell membrane; peripheral membrane protein. Intracellular membrane; peripheral membrane protein. Loc ...	plasma membrane [IDA]		1VF6	675
Q9BXY0 UniProt NPD GO	RBM13_HUMAN	MAK16-like protein RBM13 (RNA-binding motif protein 13) (NNP78)	0.86	+	nuc	0	Nucleus; nucleolus				300
P49739 UniProt NPD GO	MCM3M_XENLA	Maternal DNA replication licensing factor mcm3 (Maternal minichromosome maintenance protein 3) (mMCM ...	0.86	-	nuc	0	Nucleus. Associated with chromatin before the formation of nuclei and detaches from it as DNA replic ...	chromatin [IDA] MCM complex [IDA]			807
P26359 UniProt NPD GO	SWI4_SCHPO	Mating-type switching protein swi4	0.86	+	cyt	0					993
Q9UW22 UniProt NPD GO	MTAL2_CANAL	Mating-type-like protein ALPHA2 (MTLalpha2 protein)	0.86	+	nuc	0	Nucleus (By similarity)				186
Q52TG1 UniProt NPD GO	MATK_CALOL	Maturase K (Intron maturase)	0.86	+	cyt	0	Plastid; chloroplast				549
Q70CZ6 UniProt NPD GO	MATK_CESEL	Maturase K (Intron maturase)	0.86	-	cyt	0	Plastid; chloroplast				510
Q5D873 UniProt NPD GO	MATK_LYCCR	Maturase K (Intron maturase)	0.86	-	mit	0	Plastid; chloroplast				517
Q5I6K1 UniProt NPD GO	MATK_MIMAU	Maturase K (Intron maturase)	0.86	-	pox	0	Plastid; chloroplast				511
Q85XY6 UniProt NPD GO	MATK_OCIBA	Maturase K (Intron maturase)	0.86	-	nuc	0	Plastid; chloroplast				506
Q8SM04 UniProt NPD GO	MATK_PENHE	Maturase K (Intron maturase)	0.86	-	nuc	0	Plastid; chloroplast				510
P29467 UniProt NPD GO	MEI4_YEAST	Meiosis-specific protein MEI4	0.86	-	end	0					408
P21651 UniProt NPD GO	MER2_YEAST	Meiotic recombination 2 protein	0.86	+	nuc	0					314
P78395 UniProt NPD GO	MAPE_HUMAN	Melanoma antigen preferentially expressed in tumors (Preferentially expressed antigen of melanoma) ( ...	0.86	+	mit	0			606021		509
Q9HBD1 UniProt NPD GO	MNAB_HUMAN	Membrane-associated nucleic acid-binding protein (RING finger protein 164)	0.86	-	nuc	0	Cytoplasm; perinuclear region. Intracytoplasmic membrane. Membrane-associated. Primarily localizes t ...	cell surface [IDA] membrane fraction [IDA]			1191
P35240 UniProt NPD GO	MERL_HUMAN	Merlin (Moesin-ezrin-radixin-like protein) (Neurofibromin-2) (Schwannomin) (Schwannomerlin)	0.86	-	mit	0	In a fibroblastic cell line, isoforms 1 and 10 are found homogeneously distributed over the entire c ...	cytoskeleton [TAS] nucleus [IDA] plasma membrane [IDA]	101000	1H4R	595
Q14872 UniProt NPD GO	MTF1_HUMAN	Metal-regulatory transcription factor 1 (Transcription factor MTF-1) (MRE-binding transcription fact ...	0.86	-	nuc	0	Nucleus (Potential)	nucleus [TAS]	600172		753

You are viewing entries 6101 to 6150 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.