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
Q99JY1 UniProt NPD GO	TIRAP_MOUSE	Toll-interleukin 1 receptor domain-containing adapter protein (TIR domain-containing adapter protein ...	0.39	-	nuc	0	Cytoplasm (By similarity)				241
Q9QUK6 UniProt NPD GO	TLR4_MOUSE	Toll-like receptor 4 precursor (CD284 antigen)	0.39	-	end	1	Membrane; single-pass type I membrane protein (By similarity)	lipopolysaccharide receptor complex [ISS]			835
Q76DT2 UniProt NPD GO	TX60A_ACTVL	Toxin AvTX-60A precursor	0.39	-	exc	0	Secreted protein. Found in the nematocyst				498
O13868 UniProt NPD GO	ELOF1_SCHPO	Transcription elongation factor 1 homolog	0.39	-	nuc	0	Nucleus (By similarity)				107
Q3T020 UniProt NPD GO	TCAL8_BOVIN	Transcription elongation factor A protein-like 8 (TCEA-like protein 8) (Transcription elongation fac ...	0.39	-	nuc	0	Nucleus (Probable)				117
Q8AVS4 UniProt NPD GO	PURBB_XENLA	Transcriptional activator protein Pur-beta-B (Purine-rich element-binding protein B-B)	0.39	-	nuc	0	Nucleus (By similarity)				327
Q3BAK2 UniProt NPD GO	IF1C_PHAAO	Translation initiation factor IF-1, chloroplast	0.39	-	nuc	0	Plastid; chloroplast				77
Q85G77 UniProt NPD GO	IF3C_CYAME	Translation initiation factor IF-3, chloroplast	0.39	-	nuc	0	Plastid; chloroplast				175
Q5E9B4 UniProt NPD GO	EI2BB_BOVIN	Translation initiation factor eIF-2B subunit beta (eIF-2B GDP-GTP exchange factor subunit beta)	0.39	-	cyt	0					351
Q8BU14 UniProt NPD GO	SEC62_MOUSE	Translocation protein SEC62 (Translocation protein 1) (TP-1)	0.39	+	end	2	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				398
O43280 UniProt NPD GO	TREA_HUMAN	Trehalase precursor (EC 3.2.1.28) (Alpha,alpha-trehalase) (Alpha,alpha-trehalose glucohydrolase)	0.39	-	mit	0	Cell membrane; lipid-anchor; GPI-anchor (By similarity)	anchored to plasma membrane [TAS] plasma membrane [TAS]	275360		583
Q96UB1 UniProt NPD GO	TMLH_NEUCR	Trimethyllysine dioxygenase (EC 1.14.11.8) (Epsilon-trimethyllysine 2-oxoglutarate dioxygenase) (TML ...	0.39	-	mit	0	Cytoplasm (Probable)				471
Q13049 UniProt NPD GO	TRI32_HUMAN	Tripartite motif-containing protein 32 (EC 6.3.2.-) (Zinc finger protein HT2A) (72 kDa Tat-interacti ...	0.39	-	cyt	0	Nucleus	nucleus [TAS]	254110	2CT2	653
Q9BYJ4 UniProt NPD GO	TRI34_HUMAN	Tripartite motif-containing protein 34 (Interferon-responsive finger protein 1) (RING finger protein ...	0.39	-	nuc	0			605684		488
Q5BIM1 UniProt NPD GO	TRI45_BOVIN	Tripartite motif-containing protein 45	0.39	-	mit	0					580
Q6PFY8 UniProt NPD GO	TRI45_MOUSE	Tripartite motif-containing protein 45	0.39	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				580
Q9NGB4 UniProt NPD GO	OSA_DROYA	Trithorax group protein osa (Protein eyelid) (Fragment)	0.39	-	nuc	0	Nucleus (By similarity)	nucleus [ISS]			324
O02389 UniProt NPD GO	TPM_CHLNI	Tropomyosin	0.39	-	nuc	0					284
Q25632 UniProt NPD GO	TPM_ONCVO	Tropomyosin (MOv-14) (Ov-tmy-1)	0.39	-	nuc	0					284
P21107 UniProt NPD GO	TPM3_MOUSE	Tropomyosin alpha-3 chain (Tropomyosin-3) (Tropomyosin gamma)	0.39	-	nuc	0					284
P67937 UniProt NPD GO	TPM4_PIG	Tropomyosin alpha-4 chain (Tropomyosin-4)	0.39	-	nuc	0					247
P02561 UniProt NPD GO	TPM4_HORSE	Tropomyosin alpha-4 chain (Tropomyosin-4) (Platelet beta tropomyosin)	0.39	-	nuc	0					247
P67936 UniProt NPD GO	TPM4_HUMAN	Tropomyosin alpha-4 chain (Tropomyosin-4) (TM30p1)	0.39	-	nuc	0			600317		247
Q22866 UniProt NPD GO	TPM1_CAEEL	Tropomyosin isoforms 1/2	0.39	-	nuc	0					284
P15846 UniProt NPD GO	TPMM_TRICO	Tropomyosin, muscle	0.39	-	nuc	0					284
P19237 UniProt NPD GO	TNNI1_HUMAN	Troponin I, slow skeletal muscle (Troponin I, slow-twitch isoform)	0.39	-	nuc	0		troponin complex [NAS]	191042		186
Q41874 UniProt NPD GO	TBG3_MAIZE	Tubulin gamma-3 chain (Gamma-3 tubulin) (Fragment)	0.39	-	cyt	0					421
O43508 UniProt NPD GO	TNF12_HUMAN	Tumor necrosis factor ligand superfamily member 12 (TNF-related weak inducer of apoptosis) (TWEAK) ( ...	0.39	+	mit	1 *	Cell membrane; single-pass type II membrane protein. Processed form: Secreted protein	integral to plasma membrane [TAS] perinuclear region [IDA]	602695		249
Q92956 UniProt NPD GO	TNR14_HUMAN	Tumor necrosis factor receptor superfamily member 14 precursor (Herpesvirus entry mediator A) (Tumor ...	0.39	-	nuc	1	Membrane; single-pass type I membrane protein (Probable)	integral to plasma membrane [IC]	602746	2AW2	283
Q8CHM3 UniProt NPD GO	T53I2_RAT	Tumor protein p53-inducible nuclear protein 2 (Fragment)	0.39	-	nuc	0	Nucleus (By similarity)				199
O80366 UniProt NPD GO	ARR9_ARATH	Two-component response regulator ARR9 (Response reactor 4)	0.39	-	nuc	0	Nucleus (Probable)				234
P55073 UniProt NPD GO	IOD3_HUMAN	Type III iodothyronine deiodinase (EC 1.97.1.11) (Type-III 5'deiodinase) (DIOIII) (Type 3 DI) (5DIII ...	0.39	-	nuc	0	Cell membrane; single-pass type II membrane protein. Endosome; endosomal membrane; single-pass type ...		601038		278
O02213 UniProt NPD GO	SER2_CAEEL	Tyramine receptor 2	0.39	-	end	7	Membrane; multi-pass membrane protein	integral to membrane [IDA]			455
P22270 UniProt NPD GO	OAR_DROME	Tyramine/octopamine receptor precursor (Tyr/Oct-Dro)	0.39	-	end	8 *	Membrane; multi-pass membrane protein				601
Q92396 UniProt NPD GO	TYRO_PODAN	Tyrosinase (EC 1.14.18.1) (Monophenol monooxygenase)	0.39	-	nuc	0					574
Q9V9J3 UniProt NPD GO	SRC42_DROME	Tyrosine-protein kinase Src42A (EC 2.7.10.2) (Dsrc41)	0.39	-	nuc	0					517
P38590 UniProt NPD GO	MSG5_YEAST	Tyrosine-protein phosphatase MSG5 (EC 3.1.3.48)	0.39	-	nuc	0		cytoplasm [IDA]			489
P35235 UniProt NPD GO	PTN11_MOUSE	Tyrosine-protein phosphatase non-receptor type 11 (EC 3.1.3.48) (Protein-tyrosine phosphatase SYP) ( ...	0.39	-	mit	0	Cytoplasm			1AYD	597
Q99952 UniProt NPD GO	PTN18_HUMAN	Tyrosine-protein phosphatase non-receptor type 18 (EC 3.1.3.48) (Brain-derived phosphatase)	0.39	-	mit	0	Nucleus (By similarity). Cytoplasm (By similarity)		606587		458
Q03369 UniProt NPD GO	RU1C_XENLA	U1 small nuclear ribonucleoprotein C (U1 snRNP protein C) (U1C protein) (U1-C)	0.39	-	nuc	0	Nucleus				159
Q4WV66 UniProt NPD GO	RU2A_ASPFU	U2 small nuclear ribonucleoprotein A' (U2 snRNP-A')	0.39	-	nuc	0	Nucleus (By similarity)				253
Q6C804 UniProt NPD GO	IMP4_YARLI	U3 small nucleolar ribonucleoprotein protein IMP4 (U3 snoRNP protein IMP4)	0.39	-	mit	0	Nucleus; nucleolus (By similarity)				283
Q5A5N6 UniProt NPD GO	ALG14_CANAL	UDP-N-acetylglucosamine transferase subunit ALG14 (EC 2.4.1.-) (Asparagine linked glycosylation prot ...	0.39	-	end	3 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				219
Q95YI5 UniProt NPD GO	US74C_DROME	UDP-sugar transporter UST74c (Protein fringe connection)	0.39	-	end	8	Golgi apparatus; Golgi membrane; multi-pass membrane protein				373
Q07953 UniProt NPD GO	YL022_YEAST	UPF0023 protein YLR022C	0.39	-	nuc	0		cytoplasm [IDA] nucleus [IDA]			250
Q9DB07 UniProt NPD GO	U360_MOUSE	UPF0360 protein (Protein C11orf2)	0.39	-	nuc	0					301
P54726 UniProt NPD GO	RD23A_MOUSE	UV excision repair protein RAD23 homolog A (mHR23A)	0.39	-	nuc	0	Nucleus (Probable)				363
P48502 UniProt NPD GO	UCR6_SOLTU	Ubiquinol-cytochrome c reductase complex 14 kDa protein (EC 1.10.2.2) (CR14)	0.39	-	mit	0	Mitochondrion; mitochondrial inner membrane				123
Q92353 UniProt NPD GO	UBP6_SCHPO	Ubiquitin carboxyl-terminal hydrolase 6 (EC 3.1.2.15) (Ubiquitin thiolesterase 6) (Ubiquitin-specifi ...	0.39	-	nuc	0	Nucleus				467
Q9XSJ0 UniProt NPD GO	UCHL5_BOVIN	Ubiquitin carboxyl-terminal hydrolase isozyme L5 (EC 3.4.19.12) (UCH-L5) (Ubiquitin thioesterase L5) ...	0.39	-	nuc	0					328

You are viewing entries 33051 to 33100 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.