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
Q9D1Q6 UniProt NPD GO	TXND4_MOUSE	Thioredoxin domain-containing protein 4 precursor (Endoplasmic reticulum resident protein ERp44)	0.27	-	nuc	0	Endoplasmic reticulum; endoplasmic reticulum lumen	endoplasmic reticulum lumen [ISS] endoplasmic reticulum membrane [ISS]			406
Q9CQ79 UniProt NPD GO	TXND9_MOUSE	Thioredoxin domain-containing protein 9 (ATP-binding protein associated with cell differentiation)	0.27	-	cyt	0					226
P35440 UniProt NPD GO	TSP2_CHICK	Thrombospondin-2 precursor	0.27	-	exc	0					1178
Q99N42 UniProt NPD GO	TYPH_MOUSE	Thymidine phosphorylase (EC 2.4.2.4) (TdRPase) (TP)	0.27	-	nuc	0					471
P16473 UniProt NPD GO	TSHR_HUMAN	Thyrotropin receptor precursor (TSH-R) (Thyroid-stimulating hormone receptor)	0.27	-	end	7	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	275000	1XUM	764
P21463 UniProt NPD GO	TSHR_RAT	Thyrotropin receptor precursor (TSH-R) (Thyroid-stimulating hormone receptor)	0.27	-	end	7	Membrane; multi-pass membrane protein				764
Q04468 UniProt NPD GO	TCMO_HELTU	Trans-cinnamate 4-monooxygenase (EC 1.14.13.11) (Cinnamic acid 4-hydroxylase) (CA4H) (C4H) (P450C4H) ...	0.27	-	end	0					505
Q5RA91 UniProt NPD GO	TAF11_PONPY	Transcription initiation factor TFIID subunit 11 (Transcription initiation factor TFIID 28 kDa subun ...	0.27	-	nuc	0	Nucleus (By similarity)				211
Q3ZBY2 UniProt NPD GO	TAGL3_BOVIN	Transgelin-3	0.27	-	cyt	0					199
Q9R1Q8 UniProt NPD GO	TAGL3_MOUSE	Transgelin-3 (Neuronal protein NP25)	0.27	-	cyt	0					199
P37805 UniProt NPD GO	TAGL3_RAT	Transgelin-3 (Neuronal protein NP25)	0.27	-	cyt	0					219
Q9UI15 UniProt NPD GO	TAGL3_HUMAN	Transgelin-3 (Neuronal protein NP25) (Neuronal protein 22) (NP22)	0.27	-	cyt	0			607953		199
O20250 UniProt NPD GO	TKTC_SPIOL	Transketolase, chloroplast precursor (EC 2.2.1.1) (TK)	0.27	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane	thylakoid membrane (sensu Viridiplantae) [IDA]			741
Q95GM6 UniProt NPD GO	IF1C_HEDHE	Translation initiation factor IF-1, chloroplast	0.27	-	nuc	0	Plastid; chloroplast				77
Q68RX2 UniProt NPD GO	IF1C_PANGI	Translation initiation factor IF-1, chloroplast	0.27	-	nuc	0	Plastid; chloroplast				77
P08698 UniProt NPD GO	IF1C_SPIOL	Translation initiation factor IF-1, chloroplast	0.27	-	nuc	0	Plastid; chloroplast				77
P25038 UniProt NPD GO	IF2M_YEAST	Translation initiation factor IF-2, mitochondrial precursor (IF-2Mt) (IF-2(Mt))	0.27	-	mit	0	Mitochondrion	mitochondrion [IDA]			676
Q99LD9 UniProt NPD GO	EI2BB_MOUSE	Translation initiation factor eIF-2B subunit beta (eIF-2B GDP-GTP exchange factor subunit beta)	0.27	-	cyt	0					351
P49770 UniProt NPD GO	EI2BB_HUMAN	Translation initiation factor eIF-2B subunit beta (eIF-2B GDP-GTP exchange factor subunit beta) (S20 ...	0.27	-	cyt	0		eukaryotic translation initiation factor 2B... [NAS]	606454		351
Q7TNJ0 UniProt NPD GO	TM7S4_MOUSE	Transmembrane 7 superfamily member 4 (Dendritic cell-specific transmembrane protein) (DC-STAMP)	0.27	-	end	6 *	Cell membrane; multi-pass membrane protein (Potential). Localised to the cell surface of osteoclasts ...	cell surface [IDA] integral to membrane [NAS]			470
P57088 UniProt NPD GO	TMM33_HUMAN	Transmembrane protein 33 (DB83 protein)	0.27	-	end	3 *	Membrane; multi-pass membrane protein (Potential)				247
Q03630 UniProt NPD GO	BET5_YEAST	Transport protein particle 18 kDa subunit (TRAPP 18 kDa subunit)	0.27	-	nuc	0	Golgi apparatus; cis-Golgi network	TRAPP complex [IDA]			159
P27900 UniProt NPD GO	GL1_ARATH	Trichome differentiation protein GL1 (GLABROUS1 protein) (R2R3-MYB transcription factor GL1)	0.27	-	nuc	0	Nucleus (Probable)				228
P40939 UniProt NPD GO	ECHA_HUMAN	Trifunctional enzyme subunit alpha, mitochondrial precursor (TP-alpha) (78 kDa gastrin-binding prote ...	0.27	-	mit	0	Mitochondrion		609016		763
Q9V6K1 UniProt NPD GO	TPP2_DROME	Tripeptidyl-peptidase 2 (EC 3.4.14.10) (Tripeptidyl-peptidase II) (TPP-II) (Tripeptidyl aminopeptida ...	0.27	-	mit	0	Cytoplasm (Probable)	cytoplasm [ISS]			1441
Q6X2E0 UniProt NPD GO	DMAW1_CLAPU	Tryptophan dimethylallyltransferase 1 (EC 2.5.1.34) (DMATS 1) (All-trans-hexaprenyl-diphosphate synt ...	0.27	-	cyt	0					448
Q8WUA8 UniProt NPD GO	TSK_HUMAN	Tsukushi precursor (Leucine-rich repeat-containing protein 54) (E2-induced gene 4 protein)	0.27	-	exc	0	Secreted protein (Potential)		608015		353
Q4R7T7 UniProt NPD GO	TBD_MACFA	Tubulin delta chain (Delta tubulin)	0.27	-	cyt	0	Centrosome (By similarity). Associated with centrioles. Cytoplasm (By similarity). Nucleus (By simil ...				453
Q5U378 UniProt NPD GO	TBCE_BRARE	Tubulin-specific chaperone E (Tubulin-folding cofactor E)	0.27	-	nuc	0					521
Q9BDN0 UniProt NPD GO	TNR6_MACNE	Tumor necrosis factor receptor superfamily member 6 precursor (FASLG receptor) (Apoptosis-mediating ...	0.27	-	nuc	0	Membrane; single-pass type I membrane protein (By similarity)				331
P35234 UniProt NPD GO	PTN5_RAT	Tyrosine-protein phosphatase non-receptor type 5 (EC 3.1.3.48) (Protein-tyrosine phosphatase striatu ...	0.27	-	cyt	0					369
P40565 UniProt NPD GO	IST3_YEAST	U2 snRNP component IST3 (U2 snRNP protein SNU17) (Increased sodium tolerance protein 3)	0.27	-	nuc	0	Nucleus	snRNP U2 [IDA]			148
Q7ZXZ2 UniProt NPD GO	UTP15_XENLA	U3 small nucleolar RNA-associated protein 15 homolog	0.27	-	cyt	0	Nucleus; nucleolus (By similarity)				515
P53088 UniProt NPD GO	YGW1_YEAST	UPF0021 protein YGL211W	0.27	-	nuc	0		mitochondrion [IDA]			317
P47085 UniProt NPD GO	YJX8_YEAST	UPF0103 protein YJR008W	0.27	-	nuc	0		cytoplasm [IDA] nucleus [IDA]			338
Q9U516 UniProt NPD GO	U139_MANSE	UPF0139 protein pMsmaA27	0.27	-	nuc	0					108
Q3ZCB6 UniProt NPD GO	CT149_BOVIN	UPF0362 protein C20orf149 homolog	0.27	-	nuc	0					116
P51133 UniProt NPD GO	UCRI3_TOBAC	Ubiquinol-cytochrome c reductase iron-sulfur subunit 3, mitochondrial precursor (EC 1.10.2.2) (Riesk ...	0.27	-	mit	1	Mitochondrion; mitochondrial inner membrane				268
P37841 UniProt NPD GO	UCRI_SOLTU	Ubiquinol-cytochrome c reductase iron-sulfur subunit, mitochondrial precursor (EC 1.10.2.2) (Rieske ...	0.27	-	mit	0	Mitochondrion; mitochondrial inner membrane				265
Q9CXI0 UniProt NPD GO	COQ5_MOUSE	Ubiquinone biosynthesis methyltransferase COQ5, mitochondrial precursor (EC 2.1.1.-)	0.27	-	mit	0	Mitochondrion (By similarity)				327
Q18486 UniProt NPD GO	COQ8_CAEEL	Ubiquinone biosynthesis protein coq-8	0.27	-	cyt	0					755
Q8IUQ4 UniProt NPD GO	SIAH1_HUMAN	Ubiquitin ligase SIAH1 (EC 6.3.2.-) (Seven in absentia homolog 1) (Siah-1) (Siah-1a)	0.27	-	mit	0	Cytoplasm. Predominantly. Nucleus. Partially	cytoplasm [TAS]	602212	2A25	282
P31252 UniProt NPD GO	UBE13_WHEAT	Ubiquitin-activating enzyme E1 3	0.27	-	nuc	0					1053
P41226 UniProt NPD GO	UBE1L_HUMAN	Ubiquitin-activating enzyme E1 homolog (D8)	0.27	-	cyt	0			191325		1011
Q4PFA5 UniProt NPD GO	UBC2_USTMA	Ubiquitin-conjugating enzyme E2 2 (EC 6.3.2.19) (Ubiquitin-protein ligase UBC2) (Ubiquitin carrier p ...	0.27	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				185
Q3ZCF7 UniProt NPD GO	UB2D3_BOVIN	Ubiquitin-conjugating enzyme E2 D3 (EC 6.3.2.19) (Ubiquitin-protein ligase D3) (Ubiquitin carrier pr ...	0.27	-	nuc	0					147
O14933 UniProt NPD GO	UB2L6_HUMAN	Ubiquitin-conjugating enzyme E2 L6 (EC 6.3.2.19) (Ubiquitin-protein ligase L6) (Ubiquitin carrier pr ...	0.27	-	nuc	0			603890	1WZW	152
P28263 UniProt NPD GO	UBC8_YEAST	Ubiquitin-conjugating enzyme E2-24 kDa (EC 6.3.2.19) (Ubiquitin-protein ligase) (Ubiquitin carrier p ...	0.27	-	nuc	0	Cytoplasm	cytoplasm [IDA]			218
O13351 UniProt NPD GO	PMT3_SCHPO	Ubiquitin-like protein pmt3/smt3 precursor	0.27	-	nuc	0	Nucleus	nucleus [IDA]			117
Q9BY42 UniProt NPD GO	CT043_HUMAN	Uncharacterized protein C20orf43	0.27	-	nuc	0					306

You are viewing entries 43751 to 43800 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.