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
Q6NRG6 UniProt NPD GO	SAS6_XENLA	Spindle assembly abnormal protein 6 homolog	0.64	-	nuc	0	Centrosome. Component of the centrosome (By similarity)				668
O43077 UniProt NPD GO	MDE3_SCHPO	Sporulation protein kinase mde3 (EC 2.7.11.1) (Mei4-dependent protein 3)	0.64	-	nuc	0					559
Q06134 UniProt NPD GO	SPO77_YEAST	Sporulation-specific protein 77	0.64	-	nuc	0	Diffuse location throughout the cell at all stages of sporulation	intracellular [IDA]			477
Q6NYK3 UniProt NPD GO	SPRE2_BRARE	Sprouty-related, EVH1 domain-containing protein 2 (Spred-2)	0.64	-	nuc	0	Membrane; peripheral membrane protein (By similarity)				413
P84285 UniProt NPD GO	ARE2_CANAL	Sterol O-acyltransferase 2 (EC 2.3.1.26) (Sterol-ester synthase) (ASAT)	0.64	+	end	8	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein	endoplasmic reticulum membrane [IDA]			609
Q9WTN3 UniProt NPD GO	SRBP1_MOUSE	Sterol regulatory element-binding protein 1 (SREBP-1) (Sterol regulatory element-binding transcripti ...	0.64	+	nuc	2	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein. Golgi apparatus; ...	nucleus [IDA]			1134
P70483 UniProt NPD GO	STRN_RAT	Striatin	0.64	-	nuc	0	Cytoplasm. Membrane; peripheral membrane protein	membrane [IDA]			780
Q5EA00 UniProt NPD GO	SMP1L_BOVIN	Stromal membrane-associated protein 1-like	0.64	-	nuc	0	Cytoplasm. Detected in multiple foci throughout the cytoplasm and in juxtanuclear structures (By sim ...				429
O22060 UniProt NPD GO	SPS1_CITUN	Sucrose-phosphate synthase 1 (EC 2.4.1.14) (UDP-glucose-fructose-phosphate glucosyltransferase 1)	0.64	-	nuc	0					1057
O70441 UniProt NPD GO	SYN3_RAT	Synapsin-3 (Synapsin III)	0.64	-	nuc	0	Synapse. Peripheral membrane protein localized to the cytoplasmic surface of synaptic vesicles	synaptic vesicle [IDA]			579
Q24547 UniProt NPD GO	STX1A_DROME	Syntaxin-1A (dSynt1)	0.64	-	nuc	1	Membrane; single-pass type IV membrane protein	plasma membrane [NAS]			291
Q15531 UniProt NPD GO	STX1B_HUMAN	Syntaxin-1B1 (Syntaxin 1B)	0.64	-	gol	1	Membrane; single-pass type IV membrane protein (Potential)	integral to plasma membrane [TAS]	601485		288
Q7KVY7 UniProt NPD GO	STX4_DROME	Syntaxin-4	0.64	-	nuc	1	Membrane; single-pass type IV membrane protein (Potential)	cytoplasm [ISS] plasma membrane [ISS]			333
Q6ZWJ1 UniProt NPD GO	STXB4_HUMAN	Syntaxin-binding protein 4 (Syntaxin 4-interacting protein) (Synip)	0.64	-	nuc	0	Cytoplasm (By similarity)				553
Q94890 UniProt NPD GO	H15_DROME	T-box protein H15	0.64	-	nuc	0	Nucleus (Potential)				660
Q861Q9 UniProt NPD GO	TBX4_CANFA	T-box transcription factor TBX4 (T-box protein 4)	0.64	-	nuc	0	Nucleus (Potential)				554
P29020 UniProt NPD GO	CD3H_MOUSE	T-cell surface glycoprotein CD3 eta chain precursor (T-cell receptor T3 eta chain)	0.64	-	exc	1 *	Membrane; single-pass type I membrane protein	alpha-beta T cell receptor complex [IDA]			206
Q15573 UniProt NPD GO	TAF1A_HUMAN	TATA box-binding protein-associated factor RNA polymerase I subunit A (TATA box-binding protein-asso ...	0.64	-	cyt	0	Nucleus		604903		450
Q9CXF4 UniProt NPD GO	TBC15_MOUSE	TBC1 domain family member 15	0.64	-	nuc	0		mitochondrion [IDA]			671
Q96BZ9 UniProt NPD GO	TBC20_HUMAN	TBC1 domain family member 20	0.64	-	end	2	Membrane; multi-pass membrane protein (Potential)				403
Q8IZP1 UniProt NPD GO	TBCD3_HUMAN	TBC1 domain family member 3 (Rab GTPase-activating protein PRC17) (Prostate cancer gene 17 protein) ...	0.64	-	nuc	0			607741		549
Q9JIB4 UniProt NPD GO	TF2H2_MOUSE	TFIIH basal transcription factor complex p44 subunit (Basic transcription factor 2 44 kDa subunit) ( ...	0.64	-	nuc	0	Nucleus				396
Q9JJD0 UniProt NPD GO	THA11_MOUSE	THAP domain-containing protein 11	0.64	+	nuc	0	Nucleus (By similarity)				305
Q21986 UniProt NPD GO	YNQA_CAEEL	TPR repeat-containing protein R13F6.10	0.64	-	cyt	0					958
P70347 UniProt NPD GO	TANK_MOUSE	TRAF family member-associated NF-kappa-B activator (TRAF-interacting protein) (I-TRAF)	0.64	-	nuc	0	Cytoplasm				448
P97516 UniProt NPD GO	TEF_PHOSU	Thyrotroph embryonic factor (Fragment)	0.64	+	nuc	0	Nucleus (By similarity)				221
Q99MB1 UniProt NPD GO	TLR3_MOUSE	Toll-like receptor 3 precursor (CD283 antigen)	0.64	-	exc	1 *	Membrane; single-pass type I membrane protein (By similarity)	membrane [ISS]			905
Q9QVN7 UniProt NPD GO	TCEA2_MOUSE	Transcription elongation factor A protein 2 (Transcription elongation factor S-II protein 2) (Testis ...	0.64	-	nuc	0	Nucleus				299
P05549 UniProt NPD GO	AP2A_HUMAN	Transcription factor AP-2 alpha (AP2-alpha) (Activating enhancer-binding protein 2 alpha) (AP-2 tran ...	0.64	-	nuc	0	Nucleus	nucleus [IMP]	107580		437
P21677 UniProt NPD GO	TFE2_RAT	Transcription factor E2-alpha (Immunoglobulin enhancer-binding factor E12/E47) (Transcription factor ...	0.64	-	nuc	0	Nucleus				649
Q08369 UniProt NPD GO	GATA4_MOUSE	Transcription factor GATA-4 (GATA-binding factor 4)	0.64	-	nuc	0	Nucleus	nucleus [NAS]			440
P17433 UniProt NPD GO	SPI1_MOUSE	Transcription factor PU.1 (31 kDa transforming protein) (SFFV proviral integration 1 protein)	0.64	+	nuc	0	Nucleus	nucleus [IDA] transcription factor complex [IC]		1PUE	272
Q86T24 UniProt NPD GO	KAISO_HUMAN	Transcriptional regulator Kaiso (Zinc finger and BTB domain-containing protein 33)	0.64	-	nuc	0	Nucleus. Cytoplasm. Also cytoplasmic in cells grown at high densities		300329		672
Q9Y6A5 UniProt NPD GO	TACC3_HUMAN	Transforming acidic coiled-coil-containing protein 3 (ERIC-1)	0.64	-	nuc	0	Cytoplasm (By similarity)		605303		838
P09531 UniProt NPD GO	TGFB1_CHICK	Transforming growth factor beta-1 precursor (TGF-beta-1) [Contains: Latency-associated peptide (LAP) ...	0.64	-	nuc	0	Secreted protein				373
P10600 UniProt NPD GO	TGFB3_HUMAN	Transforming growth factor beta-3 precursor (TGF-beta-3)	0.64	-	mit	1 *	Secreted protein		190230	1TGK	412
Q6B8S2 UniProt NPD GO	IF2C_GRATL	Translation initiation factor IF-2, chloroplast	0.64	+	nuc	0	Plastid; chloroplast				744
Q9UI10 UniProt NPD GO	EI2BD_HUMAN	Translation initiation factor eIF-2B subunit delta (eIF-2B GDP-GTP exchange factor subunit delta)	0.64	-	nuc	0		eukaryotic translation initiation factor 2B... [NAS]	606687		523
Q969W9 UniProt NPD GO	TMEPA_HUMAN	Transmembrane prostate androgen-induced protein (Solid tumor-associated 1 protein)	0.64	-	nuc	1 *	Cell membrane; single-pass membrane protein (Potential)	integral to membrane [NAS]	606564		287
Q9NW97 UniProt NPD GO	TMM51_HUMAN	Transmembrane protein 51	0.64	+	nuc	2 *	Membrane; multi-pass membrane protein (Potential)				253
Q13061 UniProt NPD GO	TRDN_HUMAN	Triadin	0.64	-	nuc	1 *	Sarcoplasmic reticulum; sarcoplasmic reticulum membrane; single-pass type II membrane protein	integral to membrane [TAS]	603283		728
Q6MFY8 UniProt NPD GO	TRI40_RAT	Tripartite motif-containing protein 40 (RING finger protein 35)	0.64	-	nuc	0					247
Q27249 UniProt NPD GO	TPM3_CAEEL	Tropomyosin isoform 3	0.64	-	nuc	0					256
P05547 UniProt NPD GO	TNNI_PONLE	Troponin I (TnI)	0.64	+	nuc	0					201
Q8CIW5 UniProt NPD GO	PEO1_MOUSE	Twinkle protein, mitochondrial precursor (EC 3.6.1.-) (T7 gp4-like protein with intramitochondrial n ...	0.64	-	mit	0	Mitochondrion (By similarity). Colocalizes with mtDNA in mitochondrial nucleoids, a nucleoproteins c ...	mitochondrion [IDA]			685
P18412 UniProt NPD GO	TEC1_YEAST	Ty transcription activator TEC1	0.64	-	nuc	0	Nucleus	nucleus [IC]			486
P18031 UniProt NPD GO	PTN1_HUMAN	Tyrosine-protein phosphatase non-receptor type 1 (EC 3.1.3.48) (Protein-tyrosine phosphatase 1B) (PT ...	0.64	-	nuc	1	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein; cytoplasmic side ...		176885	2HNQ	435
Q10038 UniProt NPD GO	VHP1_CAEEL	Tyrosine-protein phosphatase vhp-1 (EC 3.1.3.48) (Vh1 dual specificity phosphatase family protein 1) ...	0.64	-	nuc	0					657
P52479 UniProt NPD GO	UBP10_MOUSE	Ubiquitin carboxyl-terminal hydrolase 10 (EC 3.1.2.15) (Ubiquitin thioesterase 10) (Ubiquitin-specif ...	0.64	+	nuc	0					792
Q9Z1F9 UniProt NPD GO	ULE1B_MOUSE	Ubiquitin-like 1-activating enzyme E1B (SUMO-1-activating enzyme subunit 2) (Anthracycline-associate ...	0.64	-	mit	0					638

You are viewing entries 17151 to 17200 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.