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
P21217 UniProt NPD GO	FUT3_HUMAN	Galactoside 3(4)-L-fucosyltransferase (EC 2.4.1.65) (Blood group Lewis alpha-4-fucosyltransferase) ( ...	0.41	-	mit	0	Golgi apparatus; Golgi stack; Golgi stack membrane; single-pass type II membrane protein. Membrane-b ...	membrane fraction [TAS]	111100		361
P07316 UniProt NPD GO	CRGB_HUMAN	Gamma crystallin B (Gamma crystallin 1-2)	0.41	-	nuc	0			123670	1MZ3	174
P04344 UniProt NPD GO	CRGB_MOUSE	Gamma crystallin B (Gamma crystallin 3)	0.41	-	nuc	0					174
P07320 UniProt NPD GO	CRGD_HUMAN	Gamma crystallin D (Gamma crystallin 4)	0.41	-	nuc	0			115700	2G98	173
Q9BY60 UniProt NPD GO	GBRL3_HUMAN	Gamma-aminobutyric acid receptor-associated protein-like 3 (GABA(A) receptor-associated protein-like ...	0.41	-	nuc	0					117
P02667 UniProt NPD GO	CAS2_RAT	Gamma-casein precursor	0.41	-	exc	0	Secreted protein				179
P78347 UniProt NPD GO	GTF2I_HUMAN	General transcription factor II-I (GTFII-I) (TFII-I) (Bruton tyrosine kinase-associated protein 135) ...	0.41	-	cyt	0	Cytoplasm (Potential). Nucleus (Potential)		601679		998
O93829 UniProt NPD GO	BET4_CANAL	Geranylgeranyl transferase type-2 alpha subunit (EC 2.5.1.60) (Geranylgeranyl transferase type II al ...	0.41	-	nuc	0					371
P15590 UniProt NPD GO	GLB1_MAIZE	Globulin-1 S allele precursor (GLB1-S) (7S-like)	0.41	-	exc	1 *					573
P06883 UniProt NPD GO	GLUC_RAT	Glucagon precursor [Contains: Glicentin; Glicentin-related polypeptide (GRPP); Oxyntomodulin (OXY) ( ...	0.41	-	exc	0	Secreted protein				180
P41764 UniProt NPD GO	G6PD_EMENI	Glucose-6-phosphate 1-dehydrogenase (EC 1.1.1.49) (G6PD)	0.41	-	cyt	0					511
P41951 UniProt NPD GO	PQN25_CAEEL	Glutamine/asparagine-rich protein pqn-25	0.41	-	nuc	1 *					672
P14323 UniProt NPD GO	GLUB1_ORYSA	Glutelin type-B 1 precursor [Contains: Glutelin type-B 1 acidic chain; Glutelin type-B 1 basic chain ...	0.41	-	exc	0					499
Q9Z1E4 UniProt NPD GO	GYS1_MOUSE	Glycogen [starch] synthase, muscle (EC 2.4.1.11)	0.41	-	cyt	0					738
Q9WUB3 UniProt NPD GO	PYGM_MOUSE	Glycogen phosphorylase, muscle form (EC 2.4.1.1) (Myophosphorylase)	0.41	-	nuc	0					841
Q66PG4 UniProt NPD GO	LARG2_CHICK	Glycosyltransferase-like protein LARGE2 (EC 2.4.-.-) (Glycosyltransferase-like 1B)	0.41	-	exc	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)				739
Q6PA90 UniProt NPD GO	LRG2A_XENLA	Glycosyltransferase-like protein LARGE2-A (EC 2.4.-.-) (Glycosyltransferase-like 1B-A)	0.41	-	exc	0	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)				723
Q04451 UniProt NPD GO	SYG_BOMMO	Glycyl-tRNA synthetase (EC 6.1.1.14) (Glycine--tRNA ligase) (GlyRS)	0.41	-	cyt	0					680
O35166 UniProt NPD GO	GOSR2_MOUSE	Golgi SNAP receptor complex member 2 (27 kDa Golgi SNARE protein) (Membrin)	0.41	-	nuc	1	Golgi apparatus; Golgi membrane; single-pass type IV membrane protein (Potential)	endoplasmic reticulum membrane [IDA] Golgi membrane [IDA]			212
P09920 UniProt NPD GO	CSF3_MOUSE	Granulocyte colony-stimulating factor precursor (G-CSF)	0.41	-	exc	0	Secreted protein				208
Q5USV5 UniProt NPD GO	GDF8_ANTAM	Growth/differentiation factor 8 precursor (GDF-8) (Myostatin)	0.41	+	nuc	0	Secreted protein (By similarity)				375
P16378 UniProt NPD GO	GNAO_DROME	Guanine nucleotide-binding protein G(o) subunit alpha 47A	0.41	-	cyt	0					354
P16052 UniProt NPD GO	GNAS_CRILO	Guanine nucleotide-binding protein G(s) subunit alpha (Adenylate cyclase-stimulating G alpha protein ...	0.41	-	cyt	0	Cell membrane; lipid anchor (By similarity)				394
Q9BIG4 UniProt NPD GO	GPA10_CAEEL	Guanine nucleotide-binding protein alpha-10 subunit	0.41	-	cyt	0					356
P93163 UniProt NPD GO	GPA2_SOYBN	Guanine nucleotide-binding protein alpha-2 subunit (GP-alpha-2)	0.41	-	nuc	0					385
P87034 UniProt NPD GO	GPA3_USTMA	Guanine nucleotide-binding protein alpha-3 subunit	0.41	-	mit	0					354
P14433 UniProt NPD GO	HA1U_MOUSE	H-2 class I histocompatibility antigen, TLA(C) alpha chain precursor	0.41	-	end	1	Membrane; single-pass type I membrane protein			1NEZ	361
P28007 UniProt NPD GO	GAR1_YEAST	H/ACA ribonucleoprotein complex subunit 1 (snoRNP protein GAR1)	0.41	-	mit	0	Nucleus; nucleolus	nucleolus [IDA] small nucleolar ribonucleoprotein complex [IDA]			205
P61569 UniProt NPD GO	ENK16_HUMAN	HERV-K_10p14 provirus ancestral Env polyprotein precursor (Envelope polyprotein) [Includes: Truncate ...	0.41	-	nuc	1					286
Q80WC7 UniProt NPD GO	HRBL_MOUSE	HIV-1 Rev-binding protein-like protein (Rev/Rex activation domain-binding protein related) (RAB-R)	0.41	-	nuc	0					479
P30512 UniProt NPD GO	1A29_HUMAN	HLA class I histocompatibility antigen, A-29 alpha chain precursor (MHC class I antigen A*29) (Aw-19 ...	0.41	-	end	1 *	Membrane; single-pass type I membrane protein		142800		365
P30453 UniProt NPD GO	1A34_HUMAN	HLA class I histocompatibility antigen, A-34 alpha chain precursor (MHC class I antigen A*34) (Aw-34 ...	0.41	-	end	1	Membrane; single-pass type I membrane protein		142800		365
Q29718 UniProt NPD GO	1B82_HUMAN	HLA class I histocompatibility antigen, B-82 alpha chain precursor (MHC class I antigen B*82)	0.41	-	end	1 *	Membrane; single-pass type I membrane protein		142830		362
Q9TNN7 UniProt NPD GO	1C05_HUMAN	HLA class I histocompatibility antigen, Cw-5 alpha chain precursor (MHC class I antigen Cw*5)	0.41	-	end	1	Membrane; single-pass type I membrane protein		142840		366
Q9Y5R4 UniProt NPD GO	HEMK1_HUMAN	HemK methyltransferase family member 1 (EC 2.1.1.-) (M.HsaHemKP)	0.41	-	mit	0					338
Q6PGH2 UniProt NPD GO	HN1L_MOUSE	Hematological and neurological expressed 1-like protein (HN1-like protein)	0.41	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				190
P14317 UniProt NPD GO	HCLS1_HUMAN	Hematopoietic lineage cell-specific protein (Hematopoietic cell-specific LYN substrate 1) (LckBP1) ( ...	0.41	+	nuc	0	Membrane; peripheral membrane protein (Probable). Cytoplasm (Probable). Mitochondrion (Probable)	cytoplasm [ISS] DNA-directed RNA polymerase II, core complex [TAS] nucleus [ISS]	601306		486
Q8N7M5 UniProt NPD GO	RGMC_RAT	Hemojuvelin precursor (Hemochromatosis type 2 protein homolog) (RGM domain family member C)	0.41	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor (By similarity)				422
O93336 UniProt NPD GO	HS2ST_XENLA	Heparan sulfate 2-O-sulfotransferase 1 (EC 2.8.2.-)	0.41	+	mit	0	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)				356
P48810 UniProt NPD GO	RB87F_DROME	Heterogeneous nuclear ribonucleoprotein 87F (HRP36.1 protein) (Protein P11)	0.41	-	cyt	0	Nucleus. Cytoplasm. Nuclear and/or cytoplasmic	chromatin [IDA] nucleoplasm [IDA] nucleus [IDA] omega speckle [IDA] polytene chromosome puff [IDA] ribonucleoprotein complex [IDA]			385
P19600 UniProt NPD GO	HNRPC_XENLA	Heterogeneous nuclear ribonucleoprotein C (hnRNP core protein C)	0.41	-	nuc	0	Nucleus. Component of ribonucleosomes				282
O94483 UniProt NPD GO	HOS3_SCHPO	High osmolarity sensitivity protein 3	0.41	-	mit	0		DASH complex [IDA]			94
Q9URQ5 UniProt NPD GO	HTL1_YEAST	High temperature lethal protein 1 (Chromatin structure remodeling complex protein HTL1)	0.41	-	nuc	0	Nucleus	nucleus [IDA] RSC complex [IDA]			78
Q28640 UniProt NPD GO	HRG_RABIT	Histidine-rich glycoprotein precursor (Histidine-proline-rich glycoprotein) (HPRG) (Fragment)	0.41	-	nuc	0	Secreted protein				526
P10412 UniProt NPD GO	H14_HUMAN	Histone H1.4 (Histone H1b)	0.41	+	nuc	0	Nucleus	nucleosome [NAS]	142220		218
P40274 UniProt NPD GO	H162_TRYCR	Histone H1.M6.2	0.41	+	nuc	0					90
Q9U7D1 UniProt NPD GO	H3_MASBA	Histone H3	0.41	-	nuc	0	Nucleus (By similarity)				135
P02309 UniProt NPD GO	H4_YEAST	Histone H4	0.41	-	cyt	0	Nucleus	nuclear nucleosome [TAS]		2FSB	102
Q41811 UniProt NPD GO	H43_MAIZE	Histone H4.3 (HM4)	0.41	-	cyt	0	Nucleus (By similarity)				102
Q14549 UniProt NPD GO	GBX1_HUMAN	Homeobox protein GBX-1 (Gastrulation and brain-specific homeobox protein 1) (Fragment)	0.41	+	nuc	0	Nucleus (By similarity)	nuclear chromosome [NAS]	603354		139

You are viewing entries 31101 to 31150 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.