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
Q01896 UniProt NPD GO	ATN2_YEAST	Sodium transport ATPase 2 (EC 3.6.3.7)	0.29	-	end	10	Cell membrane; multi-pass membrane protein	mitochondrion [IDA] plasma membrane [IDA]			1091
P09572 UniProt NPD GO	AT1A1_CHICK	Sodium/potassium-transporting ATPase alpha-1 chain precursor (EC 3.6.3.9) (Sodium pump 1) (Na+/K+ AT ...	0.29	-	end	8	Membrane; multi-pass membrane protein	sodium:potassium-exchanging ATPase complex [ISS]			1021
Q24048 UniProt NPD GO	ATPB2_DROME	Sodium/potassium-transporting ATPase subunit beta-2 (Sodium/potassium-dependent ATPase beta-2 subuni ...	0.29	-	nuc	1	Membrane; single-pass type II membrane protein (Probable)				323
Q8R3L5 UniProt NPD GO	SO3A1_MOUSE	Solute carrier organic anion transporter family member 3A1 (Solute carrier family 21 member 11) (Sod ...	0.29	-	end	12 *	Membrane; multi-pass membrane protein				710
P87385 UniProt NPD GO	SMS2_RANRI	Somatostatin 2 precursor (PSS2) [Contains: [Pro2,Met13]-somatostatin-14 (S-2) (SS2)]	0.29	-	exc	0	Secreted protein				103
P49670 UniProt NPD GO	SMS_CANFA	Somatostatin precursor [Contains: Somatostatin-28; Somatostatin-14]	0.29	-	exc	0	Secreted protein				116
P33094 UniProt NPD GO	SMS_CHICK	Somatostatin precursor [Contains: Somatostatin-28; Somatostatin-14]	0.29	-	exc	0	Secreted protein				116
Q8HYE5 UniProt NPD GO	SOMA_AILME	Somatotropin precursor (Growth hormone)	0.29	-	mit	0	Secreted protein				216
P11228 UniProt NPD GO	SOMA_ANAPL	Somatotropin precursor (Growth hormone)	0.29	-	exc	0	Secreted protein				216
Q8MI73 UniProt NPD GO	SOMA_DELDE	Somatotropin precursor (Growth hormone)	0.29	-	exc	0	Secreted protein				216
Q7YQB8 UniProt NPD GO	SOMA_HIPAM	Somatotropin precursor (Growth hormone)	0.29	-	exc	0	Secreted protein				216
Q9GL60 UniProt NPD GO	SOMA_MONDO	Somatotropin precursor (Growth hormone)	0.29	-	exc	1 *	Secreted protein				215
P69162 UniProt NPD GO	SOMA_PANGG	Somatotropin precursor (Growth hormone)	0.29	-	mit	0	Secreted protein				200
P69161 UniProt NPD GO	SOMA_PANPG	Somatotropin precursor (Growth hormone)	0.29	-	mit	0	Secreted protein				200
P01248 UniProt NPD GO	SOMA_PIG	Somatotropin precursor (Growth hormone)	0.29	-	exc	0	Secreted protein				216
Q9UMY4 UniProt NPD GO	SNX12_HUMAN	Sorting nexin-12	0.29	-	cyt	0				2CSK	172
Q1RMH8 UniProt NPD GO	SNX3_BOVIN	Sorting nexin-3	0.29	-	cyt	0					161
Q5R5V1 UniProt NPD GO	SNX3_PONPY	Sorting nexin-3	0.29	-	cyt	0					161
O60493 UniProt NPD GO	SNX3_HUMAN	Sorting nexin-3 (Protein SDP3)	0.29	-	cyt	0			605930		161
O70492 UniProt NPD GO	SNX3_MOUSE	Sorting nexin-3 (SDP3 protein)	0.29	-	cyt	0					161
P53353 UniProt NPD GO	ASPX_VULVU	Sperm acrosomal protein FSA-ACR.1 precursor (Fragment)	0.29	-	nuc	0	Acrosome. Intracellular acrosomal compartment of sperm				349
P19623 UniProt NPD GO	SPEE_HUMAN	Spermidine synthase (EC 2.5.1.16) (Putrescine aminopropyltransferase) (SPDSY)	0.29	-	cyt	0			182891		302
Q13242 UniProt NPD GO	SFRS9_HUMAN	Splicing factor, arginine/serine-rich 9 (Pre-mRNA-splicing factor SRp30C)	0.29	-	nuc	0	Nucleus. Cellular stresses such as heat shock may induce localization to discrete nuclear bodies ter ...		601943		221
Q9PTL1 UniProt NPD GO	SPY1_CHICK	Sprouty homolog 1 (Spry-1) (Fragment)	0.29	-	nuc	0	Cytoplasm. Membrane; peripheral membrane protein. Found in the cytoplasm in unstimulated cells but i ...				76
Q66X93 UniProt NPD GO	SND1_RAT	Staphylococcal nuclease domain-containing protein 1 (p100 co-activator) (100 kDa coactivator) (SND p ...	0.29	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity). In IL-4 stimulated cells colocalizes with STAT6 ...				909
Q876L3 UniProt NPD GO	ARE1_SACBA	Sterol O-acyltransferase 1 (EC 2.3.1.26) (Sterol-ester synthase 1)	0.29	-	end	9	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				623
Q9D939 UniProt NPD GO	ST1C2_MOUSE	Sulfotransferase 1C2 (EC 2.8.2.-)	0.29	-	cyt	0	Lysosome (By similarity)				296
Q9WUW9 UniProt NPD GO	S1C2A_RAT	Sulfotransferase 1C2A (EC 2.8.2.-) (Sulfotransferase K2) (rSULT1C2A)	0.29	-	cyt	0	Lysosome				296
O88582 UniProt NPD GO	SOCS2_RAT	Suppressor of cytokine signaling 2 (SOCS-2) (Cytokine-inducible SH2 protein 2)	0.29	-	nuc	0		cytoplasm [ISS]			198
Q5NVG5 UniProt NPD GO	SNP25_PONPY	Synaptosomal-associated protein 25 (SNAP-25) (Synaptosomal-associated 25 kDa protein)	0.29	-	nuc	0					206
Q8IV01 UniProt NPD GO	SYT12_HUMAN	Synaptotagmin-12 (Synaptotagmin XII) (SytXII)	0.29	-	nuc	1 *	Synaptic vesicle; synaptic vesicle membrane; multi-pass membrane protein (By similarity)		606436		421
Q58DD4 UniProt NPD GO	SDC2_BOVIN	Syndecan-2 precursor (SYND2)	0.29	-	end	1	Membrane; single-pass type I membrane protein (By similarity)				202
P09564 UniProt NPD GO	CD7_HUMAN	T-cell antigen CD7 precursor (GP40) (T-cell leukemia antigen) (TP41) (Leu-9)	0.29	-	exc	1	Membrane; single-pass type I membrane protein	integral to membrane [TAS] membrane fraction [TAS] plasma membrane [TAS]	186820		240
P29329 UniProt NPD GO	CD3Z_SHEEP	T-cell surface glycoprotein CD3 zeta chain precursor (T-cell receptor T3 zeta chain)	0.29	-	nuc	2 *	Membrane; single-pass type I membrane protein				166
Q5NVF9 UniProt NPD GO	TCPG_PONPY	T-complex protein 1 subunit gamma (TCP-1-gamma) (CCT-gamma)	0.29	-	cyt	0	Cytoplasm (By similarity)				545
O74341 UniProt NPD GO	TCPG_SCHPO	T-complex protein 1 subunit gamma (TCP-1-gamma) (CCT-gamma)	0.29	-	nuc	0	Cytoplasm (Potential)				528
Q27896 UniProt NPD GO	TRF_DROME	TBP-related factor	0.29	-	cyt	0	Nucleus	polytene chromosome [IDA] transcription factor TFIID complex [ISS]			224
O88393 UniProt NPD GO	TGBR3_MOUSE	TGF-beta receptor type III precursor (TGFR-3) (Transforming growth factor beta receptor III) (Betagl ...	0.29	-	end	1	Cell membrane; single-pass type I membrane protein (By similarity). Secreted protein; serum (By simi ...				850
Q3B7D3 UniProt NPD GO	TECT2_RAT	Tectonic-2 precursor	0.29	-	end	0	Membrane; single-pass type I membrane protein (Potential)				700
Q9JKL5 UniProt NPD GO	TESC_MOUSE	Tescalcin (TSC)	0.29	-	cyt	0		cytoplasm [IDA] lamellipodium [IDA] nucleus [IDA] ruffle [IDA]			214
Q9BXU0 UniProt NPD GO	TEX12_HUMAN	Testis-expressed sequence 12 protein	0.29	-	nuc	0			605791		123
Q9H489 UniProt NPD GO	TSYL3_HUMAN	Testis-specific Y-encoded-like protein 3 (TSPY-like 3)	0.29	-	cyt	0					355
Q6SA08 UniProt NPD GO	TSSK4_HUMAN	Testis-specific serine/threonine-protein kinase 4 (EC 2.7.11.1) (TSSK-4) (Testis-specific kinase 4) ...	0.29	-	nuc	0					328
Q95YJ5 UniProt NPD GO	TXND3_CIOIN	Thioredoxin domain-containing protein 3 homolog (Dynein intermediate chain 3)	0.29	-	cyt	0					653
Q8LCT3 UniProt NPD GO	TRXL6_ARATH	Thioredoxin-like 6, chloroplast precursor	0.29	-	mit	0	Plastid; chloroplast (Potential)				236
P35441 UniProt NPD GO	TSP1_MOUSE	Thrombospondin-1 precursor	0.29	-	exc	0		extracellular space [IDA]			1170
P35448 UniProt NPD GO	TSP1_XENLA	Thrombospondin-1 precursor	0.29	-	exc	0					1173
P20062 UniProt NPD GO	TCO2_HUMAN	Transcobalamin-2 precursor (Transcobalamin II) (TCII) (TC II)	0.29	-	exc	0	Secreted protein	extracellular space [TAS]	275350	2BB5	427
Q05959 UniProt NPD GO	TF2B_KLULA	Transcription initiation factor IIB (General transcription factor TFIIB)	0.29	-	nuc	0	Nucleus				357
Q99JX1 UniProt NPD GO	TAF11_MOUSE	Transcription initiation factor TFIID subunit 11 (Transcription initiation factor TFIID 28 kDa subun ...	0.29	-	nuc	0	Nucleus (By similarity)				211

You are viewing entries 41801 to 41850 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.