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
P79184 UniProt NPD GO	CD4_MACFU	T-cell surface glycoprotein CD4 precursor (T-cell surface antigen T4/Leu-3)	0.51	-	end	1	Membrane; single-pass type I membrane protein	T cell receptor complex [ISS]			458
P16003 UniProt NPD GO	CD4_MACMU	T-cell surface glycoprotein CD4 precursor (T-cell surface antigen T4/Leu-3)	0.51	-	end	1	Membrane; single-pass type I membrane protein	T cell receptor complex [ISS]			458
P06332 UniProt NPD GO	CD4_MOUSE	T-cell surface glycoprotein CD4 precursor (T-cell surface antigen T4/Leu-3) (T-cell differentiation ...	0.51	-	end	1	Membrane; single-pass type I membrane protein	external side of plasma membrane [IDA] plasma membrane [IDA] T cell receptor complex [ISS]			457
P51882 UniProt NPD GO	CD5_RAT	T-cell surface glycoprotein CD5 precursor (Lymphocyte antigen Ly-1) (Lyt-1)	0.51	-	end	1 *	Membrane; single-pass type I membrane protein				491
P19238 UniProt NPD GO	CD5_BOVIN	T-cell surface glycoprotein CD5 precursor (Lymphocyte antigen T1/Leu-1)	0.51	-	exc	1	Membrane; single-pass type I membrane protein				495
P53360 UniProt NPD GO	TBP_MESAU	TATA-box-binding protein (TATA-box factor) (TATA-binding factor) (TATA sequence-binding protein) (Tr ...	0.51	+	nuc	0	Nucleus				318
Q3UKC1 UniProt NPD GO	TAXB1_MOUSE	Tax1-binding protein 1 homolog	0.51	-	nuc	0					814
Q9AXM6 UniProt NPD GO	T10H_TAXCU	Taxane 10-beta-hydroxylase (EC 1.14.13.76) (5-alpha-taxadienol-10-beta-hydroxylase) (Cytochrome P450 ...	0.51	-	end	1 *					497
Q95YE9 UniProt NPD GO	CLK2_CAEEL	Telomere length regulation protein clk-2 (Clock abnormal protein 2)	0.51	-	cyt	0	Nucleus (Potential)	cytoplasm [IDA]			877
Q9ER58 UniProt NPD GO	TICN2_MOUSE	Testican-2 precursor (SPARC/osteonectin, CWCV, and Kazal-like domains proteoglycan 2)	0.51	-	exc	0	Secreted protein; extracellular space; extracellular matrix (Probable)	extracellular matrix (sensu Metazoa) [ISS]			423
Q8K2L8 UniProt NPD GO	TTC15_MOUSE	Tetratricopeptide repeat protein 15 (TPR repeat protein 15)	0.51	-	nuc	0					797
Q5XHX6 UniProt NPD GO	TXND2_RAT	Thioredoxin domain-containing protein 2 (Spermatid-specific thioredoxin-1) (Sptrx-1)	0.51	-	nuc	0	Cytoplasm (By similarity)				550
P42705 UniProt NPD GO	TPO_CANFA	Thrombopoietin precursor (Megakaryocyte colony-stimulating factor) (C-MPL ligand) (ML) (Megakaryocyt ...	0.51	-	nuc	0	Secreted protein				352
P40238 UniProt NPD GO	TPOR_HUMAN	Thrombopoietin receptor precursor (TPO-R) (Myeloproliferative leukemia protein) (C-mpl) (CD110 antig ...	0.51	-	exc	1	Membrane; single-pass type I membrane protein	integral to plasma membrane [TAS]	604498		635
P20396 UniProt NPD GO	TRH_HUMAN	Thyroliberin precursor [Contains: Prothyroliberin; Thyroliberin (Thyrotropin-releasing hormone) (TRH ...	0.51	-	exc	0	Secreted protein	soluble fraction [TAS]	275120		242
P01152 UniProt NPD GO	TRHA_XENLA	Thyroliberin type A precursor [Contains: Prothyroliberin type A; Thyroliberin (Thyrotropin-releasing ...	0.51	-	exc	0	Secreted protein				227
Q27987 UniProt NPD GO	TSHR_BOVIN	Thyrotropin receptor precursor (TSH-R) (Thyroid-stimulating hormone receptor)	0.51	-	end	7	Membrane; multi-pass membrane protein				763
Q6QNU9 UniProt NPD GO	TLR12_MOUSE	Toll-like receptor 12 precursor	0.51	-	end	0	Membrane; single-pass type I membrane protein (By similarity)				906
Q5I2M7 UniProt NPD GO	TLR9_FELCA	Toll-like receptor 9 precursor (CD289 antigen)	0.51	-	end	0	Membrane; single-pass type I membrane protein (By similarity)				1031
Q9XSC9 UniProt NPD GO	TCO2_BOVIN	Transcobalamin-2 precursor (Transcobalamin II) (TCII) (TC II)	0.51	-	exc	0	Secreted protein			2BBC	432
P60002 UniProt NPD GO	ELOF1_HUMAN	Transcription elongation factor 1 homolog	0.51	+	nuc	0	Nucleus (By similarity)				83
P60003 UniProt NPD GO	ELOF1_MOUSE	Transcription elongation factor 1 homolog	0.51	+	nuc	0	Nucleus (By similarity)			1WII	83
Q06945 UniProt NPD GO	SOX4_HUMAN	Transcription factor SOX-4	0.51	-	nuc	0	Nucleus		184430		474
P49905 UniProt NPD GO	TAF12_DROME	Transcription initiation factor TFIID subunit 12 (Transcription initiation factor TFIID 28-alpha kDa ...	0.51	-	nuc	0	Nucleus				196
P11747 UniProt NPD GO	TAF13_YEAST	Transcription initiation factor TFIID subunit 13 (TBP-associated factor 13) (TBP-associated factor 1 ...	0.51	-	nuc	0	Nucleus	nucleus [IDA] transcription factor TFIID complex [IDA]			167
Q90701 UniProt NPD GO	TEAD3_CHICK	Transcriptional enhancer factor TEF-5 (TEA domain family member 3) (TEAD-3) (Cardiac-enriched TEA do ...	0.51	-	nuc	0	Nucleus (Potential)				433
Q99M85 UniProt NPD GO	SCRT1_MOUSE	Transcriptional repressor scratch 1 (Scratch homolog 1 zinc finger protein) (Scratch 1) (SCRT) (mScr ...	0.51	-	nuc	0	Nucleus (By similarity)				348
Q64280 UniProt NPD GO	TGFB4_MOUSE	Transforming growth factor beta-4 precursor (TGF-beta-4) (Lefty protein) (Lefty-1 protein) (STRA3 pr ...	0.51	-	vac	0	Secreted protein				368
O35433 UniProt NPD GO	TRPV1_RAT	Transient receptor potential cation channel subfamily V member 1 (TrpV1) (osm-9-like TRP channel 1) ...	0.51	-	end	6	Cell membrane; multi-pass membrane protein				838
Q9W0T5 UniProt NPD GO	PYX_DROME	Transient receptor potential channel pyrexia	0.51	-	end	5	Membrane; multi-pass membrane protein (Probable)	integral to membrane [IC]			956
O18412 UniProt NPD GO	FZO_DROME	Transmembrane GTPase fzo (EC 3.6.5.-) (Protein fuzzy onions)	0.51	-	nuc	1	Mitochondrion; mitochondrial outer membrane; multi-pass membrane protein	mitochondrial envelope [IDA]			718
Q7RTY8 UniProt NPD GO	TMPS7_HUMAN	Transmembrane protease, serine 7 precursor (EC 3.4.21.-)	0.51	-	nuc	0					572
Q8VDX6 UniProt NPD GO	TMEM5_MOUSE	Transmembrane protein 5	0.51	-	mit	1 *	Membrane; single-pass type II membrane protein (Potential)				444
Q8BVW3 UniProt NPD GO	TRI14_MOUSE	Tripartite motif-containing protein 14 (PU.1-binding protein)	0.51	-	cyt	0					440
O95361 UniProt NPD GO	TRI16_HUMAN	Tripartite motif-containing protein 16 (Estrogen-responsive B box protein)	0.51	-	nuc	0	Cytoplasm	cytoplasm [TAS]	609505		564
Q8C0E3 UniProt NPD GO	TRI47_MOUSE	Tripartite motif-containing protein 47	0.51	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				641
Q96LD4 UniProt NPD GO	TRI47_HUMAN	Tripartite motif-containing protein 47 (Gene overexpressed in astrocytoma protein) (RING finger prot ...	0.51	-	nuc	0	Cytoplasm. Nucleus				638
Q9GZ71 UniProt NPD GO	TPM_HALDV	Tropomyosin	0.51	-	nuc	0					284
P42638 UniProt NPD GO	TPM2_SCHMA	Tropomyosin 2 (TMII)	0.51	-	nuc	0					284
Q43691 UniProt NPD GO	IACX2_WHEAT	Trypsin/alpha-amylase inhibitor CMX2 precursor (ITRL-2)	0.51	-	exc	1 *	Secreted protein (Potential)				121
P32348 UniProt NPD GO	TBG_USTVI	Tubulin gamma chain (Gamma tubulin)	0.51	-	cyt	0					469
P07101 UniProt NPD GO	TY3H_HUMAN	Tyrosine 3-monooxygenase (EC 1.14.16.2) (Tyrosine 3-hydroxylase) (TH)	0.51	-	cyt	0			605407		528
Q62120 UniProt NPD GO	JAK2_MOUSE	Tyrosine-protein kinase JAK2 (EC 2.7.10.2) (Janus kinase 2) (JAK-2)	0.51	-	cyt	0	Intracytoplasmic membrane; peripheral membrane protein. Wholly intracellular, possibly membrane asso ...	cytoplasm [TAS]			1129
Q62137 UniProt NPD GO	JAK3_MOUSE	Tyrosine-protein kinase JAK3 (EC 2.7.10.2) (Janus kinase 3) (JAK-3)	0.51	-	mit	0	Intracytoplasmic membrane; peripheral membrane protein. Wholly intracellular, possibly membrane asso ...				1299
Q63272 UniProt NPD GO	JAK3_RAT	Tyrosine-protein kinase JAK3 (EC 2.7.10.2) (Janus kinase 3) (JAK-3)	0.51	-	cyt	0	Intracytoplasmic membrane; peripheral membrane protein. Wholly intracellular, possibly membrane asso ...				1100
Q641Z2 UniProt NPD GO	PTN9_RAT	Tyrosine-protein phosphatase non-receptor type 9 (EC 3.1.3.48)	0.51	-	cyt	0	Cytoplasm (Probable)				593
Q5BGW9 UniProt NPD GO	RU2A_EMENI	U2 small nuclear ribonucleoprotein A' (U2 snRNP-A')	0.51	-	nuc	0	Nucleus (By similarity)				230
P49955 UniProt NPD GO	SF3B1_YEAST	U2 snRNP component HSH155	0.51	-	cyt	0	Nucleus (By similarity)	snRNP U2 [IDA]			971
P38882 UniProt NPD GO	UTP9_YEAST	U3 small nucleolar RNA-associated protein 9 (U3 snoRNA-associated protein 9)	0.51	-	nuc	0	Nucleus; nucleolus	nucleolus [IDA] nucleus [IDA] small nucleolar ribonucleoprotein complex [IPI]			575
P53941 UniProt NPD GO	IMP4_YEAST	U3 small nucleolar ribonucleoprotein protein IMP4 (U3 snoRNP protein IMP4)	0.51	-	mit	0	Nucleus; nucleolus	small nuclear ribonucleoprotein complex [TAS] small nucleolar ribonucleoprotein complex [IPI]			290

You are viewing entries 24651 to 24700 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.)

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