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
Q91858 UniProt NPD GO	TAF12_XENLA	Transcription initiation factor TFIID subunit 12 (Transcription initiation factor TFIID 20/15 kDa su ...	0.35	-	mit	0	Nucleus				164
Q95GM2 UniProt NPD GO	IF1C_LEUFR	Translation initiation factor IF-1, chloroplast	0.35	-	nuc	0	Plastid; chloroplast				77
P33754 UniProt NPD GO	SEC66_YEAST	Translocation protein SEC66 (Sec62/63 complex 31.5 kDa subunit) (Protein HSS1)	0.35	-	nuc	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type II membrane protein	endoplasmic reticulum membrane [TAS] Sec62/Sec63 complex [IPI]			206
Q96PE5 UniProt NPD GO	TMM10_HUMAN	Transmembrane protein 10	0.35	-	nuc	1 *	Membrane; single-pass membrane protein				141
Q8VC04 UniProt NPD GO	T106A_MOUSE	Transmembrane protein 106A	0.35	-	nuc	1	Membrane; single-pass membrane protein (Potential)				261
Q92519 UniProt NPD GO	TRIB2_HUMAN	Tribbles homolog 2 (TRB-2)	0.35	-	mit	0	Cytoplasm (By similarity). May associate with the cytoskeleton (By similarity)	cytoplasm [ISS]	609462		343
Q27180 UniProt NPD GO	T1B_PARTE	Trichocyst matrix protein T1-B precursor (Secretory granule protein T1-B) (TMP 1-B) [Contains: Trich ...	0.35	-	exc	0	Trichocyst. These are architecturally complex secretory storage granules-docked at the plasma membra ...				369
O75382 UniProt NPD GO	TRIM3_HUMAN	Tripartite motif-containing protein 3 (RING finger protein 22) (Brain-expressed RING finger protein) ...	0.35	-	cyt	0	Cytoplasm (By similarity)	cytoplasm [TAS]	605493		744
Q9R1R2 UniProt NPD GO	TRIM3_MOUSE	Tripartite motif-containing protein 3 (RING finger protein 22) (RING finger protein HAC1)	0.35	-	cyt	0	Cytoplasm (By similarity)	cytoplasm [IDA]			744
Q9UB83 UniProt NPD GO	TPM_PERAM	Tropomyosin (Major allergen Per a 7)	0.35	-	nuc	0					284
P13104 UniProt NPD GO	TPM1_BRARE	Tropomyosin 1 alpha chain (Alpha-tropomyosin)	0.35	-	nuc	0					284
P13105 UniProt NPD GO	TPM1_RANTE	Tropomyosin 1 alpha chain (Alpha-tropomyosin)	0.35	-	nuc	0					284
P39921 UniProt NPD GO	TPM1_HYDAT	Tropomyosin-1 (Tropomyosin I)	0.35	+	nuc	0					253
P48776 UniProt NPD GO	T23O_MOUSE	Tryptophan 2,3-dioxygenase (EC 1.13.11.11) (TO) (Tryptophan pyrrolase) (Tryptophanase) (Tryptophan o ...	0.35	-	cyt	0					406
Q8J1R4 UniProt NPD GO	TBB2_SUIBO	Tubulin beta-2 chain (Beta-2 tubulin)	0.35	-	cyt	0					445
P38160 UniProt NPD GO	TTL_PIG	Tubulin--tyrosine ligase (EC 6.3.2.25) (TTL)	0.35	-	cyt	0					379
Q16890 UniProt NPD GO	TPD53_HUMAN	Tumor protein D53 (hD53) (Tumor protein D52-like 1)	0.35	-	nuc	0		cytoplasm [IDA] perinuclear region [IDA]	604069		204
Q6J9G1 UniProt NPD GO	STYK1_MOUSE	Tyrosine protein-kinase STYK1 (EC 2.7.10.2) (Serine/threonine/tyrosine kinase 1) (Novel oncogene wit ...	0.35	-	nuc	1 *	Cytoplasm				429
Q06805 UniProt NPD GO	TIE1_BOVIN	Tyrosine-protein kinase receptor Tie-1 precursor (EC 2.7.10.1)	0.35	-	end	0	Membrane; single-pass type I membrane protein				1136
P35590 UniProt NPD GO	TIE1_HUMAN	Tyrosine-protein kinase receptor Tie-1 precursor (EC 2.7.10.1)	0.35	-	end	1 *	Membrane; single-pass type I membrane protein	integral to plasma membrane [TAS]	600222		1138
P40567 UniProt NPD GO	MSL1_YEAST	U2 small nuclear ribonucleoprotein B''	0.35	-	nuc	0	Nucleus	snRNP U2 [IDA]			111
Q9UK45 UniProt NPD GO	LSM7_HUMAN	U6 snRNA-associated Sm-like protein LSm7	0.35	-	nuc	0	Nucleus (Potential)	nucleus [NAS]	607287		103
Q9VUX2 UniProt NPD GO	MIB_DROME	Ubiquitin ligase protein mind-bomb (EC 6.3.2.-) (Mind bomb homolog) (D-mib)	0.35	-	nuc	0	Cytoplasm; cell cortex. Localizes at the apical cortex of cells	apical cortex [IDA] cytoplasm [IDA]			1226
Q86MW9 UniProt NPD GO	SINA_SCHMA	Ubiquitin ligase sina (EC 6.3.2.-) (Seven in absentia homolog) (SmSINA)	0.35	-	nuc	0					371
P06104 UniProt NPD GO	UBC2_YEAST	Ubiquitin-conjugating enzyme E2 2 (EC 6.3.2.19) (Ubiquitin-protein ligase UBC2) (Ubiquitin carrier p ...	0.35	-	nuc	0	Cytoplasm. Nucleus	cytoplasm [IDA] nucleus [IDA] proteasome complex (sensu Eukaryota) [IPI]		1AYZ	172
P23566 UniProt NPD GO	UBC2_SCHPO	Ubiquitin-conjugating enzyme E2 2 (EC 6.3.2.19) (Ubiquitin-protein ligase ubc2) (Ubiquitin carrier p ...	0.35	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				151
P33296 UniProt NPD GO	UBC6_YEAST	Ubiquitin-conjugating enzyme E2 6 (EC 6.3.2.19) (Ubiquitin-protein ligase UBC6) (Ubiquitin carrier p ...	0.35	-	nuc	1	Endoplasmic reticulum; endoplasmic reticulum membrane	endoplasmic reticulum membrane [IDA]			250
Q4KN68 UniProt NPD GO	CT062_HUMAN	Uncharacterized protein C20orf62	0.35	-	nuc	0					170
Q8K158 UniProt NPD GO	CB024_MOUSE	Uncharacterized protein C2orf24 homolog	0.35	-	cyt	0					407
Q6UXB0 UniProt NPD GO	CC040_HUMAN	Uncharacterized protein C3orf40 precursor	0.35	-	exc	0	Secreted protein (Potential)				335
Q8N112 UniProt NPD GO	CC045_HUMAN	Uncharacterized protein C3orf45	0.35	-	nuc	1	Membrane; single-pass membrane protein (Potential)				164
Q8IWN6 UniProt NPD GO	CX052_HUMAN	Uncharacterized protein CXorf52 (SPCX)	0.35	-	nuc	0					122
Q12121 UniProt NPD GO	YD211_YEAST	Uncharacterized protein YDL211C	0.35	-	nuc	1	Vacuole; vacuolar membrane; single-pass membrane protein (Potential)	vacuole (sensu Fungi) [IDA]			372
P53073 UniProt NPD GO	YGY1_YEAST	Uncharacterized protein YGL231C	0.35	-	nuc	2	Membrane; multi-pass membrane protein (Potential)	endoplasmic reticulum [IDA]			190
P38732 UniProt NPD GO	YHD9_YEAST	Uncharacterized protein YHL039W	0.35	-	cyt	0	Cytoplasm	cytoplasm [IDA]			585
Q3E795 UniProt NPD GO	YL361_YEAST	Uncharacterized protein YLR361C-A	0.35	-	nuc	0					98
Q03079 UniProt NPD GO	YP041_YEAST	Uncharacterized protein YPL041C	0.35	-	cyt	2	Membrane; multi-pass membrane protein				207
Q08984 UniProt NPD GO	YP272_YEAST	Uncharacterized protein YPL272C	0.35	-	cyt	0					517
P21784 UniProt NPD GO	RAG2_MOUSE	V(D)J recombination-activating protein 2 (RAG-2)	0.35	-	cyt	0	Nucleus			2A23	527
Q39258 UniProt NPD GO	VATE_ARATH	Vacuolar ATP synthase subunit E (EC 3.6.3.14) (V-ATPase E subunit) (Vacuolar proton pump E subunit)	0.35	-	cyt	0					230
P36095 UniProt NPD GO	VPS24_YEAST	Vacuolar protein sorting protein 24 (DOA4-independent degradation protein 3)	0.35	-	nuc	0	Endosome; endosomal membrane; peripheral membrane protein. Intracellular membrane; peripheral membra ...	cytoplasm [IDA] ESCRT III complex [IDA]			224
P0C0A1 UniProt NPD GO	VPS25_RAT	Vacuolar protein sorting protein 25 (ELL-associated protein of 20 kDa)	0.35	-	mit	0	Cytoplasm (By similarity). Nucleus (By similarity). Distributes diffusely throughout the cytoplasm a ...				176
P06015 UniProt NPD GO	VSA1_TRYBB	Variant surface glycoprotein AnTaT 1.1 precursor (VSG) (Expression-linked copy) (ELC)	0.35	-	nuc	0	Cell membrane; lipid-anchor; GPI-anchor. A soluble form is released from ruptured cells by the actio ...				503
Q9WTV8 UniProt NPD GO	V1AR_MICMA	Vasopressin V1a receptor (V1aR) (Vascular/hepatic-type arginine vasopressin receptor) (Antidiuretic ...	0.35	-	end	7	Membrane; multi-pass membrane protein				420
P01186 UniProt NPD GO	NEU2_RAT	Vasopressin-neurophysin 2-copeptin precursor (AVP-NPII) [Contains: Arg-vasopressin; Neurophysin 2 (N ...	0.35	-	nuc	1 *	Secreted protein				168
O42499 UniProt NPD GO	NEUV_FUGRU	Vasotocin-neurophysin VT 1 precursor [Contains: Vasotocin (VT); Neurophysin VT 1]	0.35	-	exc	0	Secreted protein				153
Q9P7Q4 UniProt NPD GO	SEC18_SCHPO	Vesicular-fusion protein SEC18 homolog	0.35	-	cyt	0	Cytoplasm (By similarity)				792
P57672 UniProt NPD GO	VESP_VESMC	Vespulakinin-1 [Contains: Vespulakinin-2]	0.35	-		0	Secreted protein. Venom reservoirs				17
P48672 UniProt NPD GO	VIM2_CARAU	Vimentin A2 (Fragment)	0.35	-	nuc	0					243
Q9EQ48 UniProt NPD GO	VN1A8_MOUSE	Vomeronasal type-1 receptor A8	0.35	-	end	7 *	Membrane; multi-pass membrane protein (Potential)				279

You are viewing entries 36301 to 36350 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.