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
P80054 UniProt NPD GO	PR39_PIG	Antibacterial protein PR-39 precursor	0.48	-	mit	1 *	Secreted protein				172
P50489 UniProt NPD GO	AMA1_PLAFC	Apical membrane antigen 1 precursor (Merozoite surface antigen)	0.48	-	nuc	1	Membrane; single-pass type I membrane protein				622
Q9QUH3 UniProt NPD GO	APOA5_RAT	Apolipoprotein A-V precursor (Apolipoprotein A5) (ApoAV) (ApoA-V) (Regeneration-associated protein 3 ...	0.48	-	nuc	0	Secreted protein				367
P23529 UniProt NPD GO	APOE_CAVPO	Apolipoprotein E precursor (Apo-E)	0.48	-	exc	0	Secreted protein				298
P04802 UniProt NPD GO	SYDC_YEAST	Aspartyl-tRNA synthetase, cytoplasmic (EC 6.1.1.12) (Aspartate--tRNA ligase) (AspRS)	0.48	-	cyt	0	Cytoplasm			1EOV	556
Q12797 UniProt NPD GO	ASPH_HUMAN	Aspartyl/asparaginyl beta-hydroxylase (EC 1.14.11.16) (Aspartate beta-hydroxylase) (ASP beta-hydroxy ...	0.48	-	mit	1	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type II membrane protein	endoplasmic reticulum [TAS] endoplasmic reticulum membrane [TAS]	600582		757
Q9WU60 UniProt NPD GO	ATRN_MOUSE	Attractin precursor (Mahogany protein)	0.48	-	mit	1	Membrane; single-pass type I membrane protein				1428
P40344 UniProt NPD GO	ATG3_YEAST	Autophagy-related protein 3 (Autophagy-related E2-like conjugation enzyme ATG3)	0.48	-	mit	0	Cytoplasm	cytoplasm [IDA] cytosol [IDA]			310
Q4VC05 UniProt NPD GO	BCL7A_HUMAN	B-cell CLL/lymphoma 7 protein family member A	0.48	-	nuc	0			601406		210
Q6NWJ0 UniProt NPD GO	BCL7B_BRARE	B-cell CLL/lymphoma 7 protein family member B	0.48	-	nuc	0					203
P21854 UniProt NPD GO	CD72_HUMAN	B-cell differentiation antigen CD72 (Lyb-2)	0.48	-	nuc	1	Membrane; single-pass type II membrane protein	integral to plasma membrane [IDA]	107272		359
Q6PBE2 UniProt NPD GO	BCAS2_XENTR	BCAS2 protein homolog	0.48	-	nuc	0	Nucleus (By similarity)				223
Q9XUM6 UniProt NPD GO	BAT34_CAEEL	BTB and MATH domain-containing protein 34	0.48	-	nuc	0					384
P08725 UniProt NPD GO	BAR2_CHIPA	Balbiani ring protein 2 (Giant secretory protein I-B) (GSP-IB) (Fragment)	0.48	+	nuc	0	Secreted protein				162
Q8IWZ6 UniProt NPD GO	BBS7_HUMAN	Bardet-Biedl syndrome 7 protein (BBS2-like protein 1)	0.48	-	cyt	0			607590		715
O54918 UniProt NPD GO	BIM_MOUSE	Bcl-2-like protein 11 (Bcl2-interacting mediator of cell death)	0.48	-	nuc	0	Membrane; peripheral membrane protein. Associated with intracytoplasmic membranes			1PQ1	196
Q07422 UniProt NPD GO	DRTS_TOXGO	Bifunctional dihydrofolate reductase-thymidylate synthase (DHFR-TS) [Includes: Dihydrofolate reducta ...	0.48	-	cyt	0					610
P98069 UniProt NPD GO	BMPH_STRPU	Bone morphogenetic protein 1 homolog precursor (EC 3.4.24.-) (SUBMP)	0.48	-	cyt	0					639
P34820 UniProt NPD GO	BMP8B_HUMAN	Bone morphogenetic protein 8B precursor (BMP-8B) (BMP-8) (Osteogenic protein 2) (OP-2)	0.48	-	exc	0	Secreted protein		602284		402
O54825 UniProt NPD GO	BYST_MOUSE	Bystin	0.48	-	nuc	0	Cytoplasm				436
Q6UXN8 UniProt NPD GO	CLC9A_HUMAN	C-type lectin domain family 9 member A	0.48	-	nuc	1 *	Membrane; single-pass type II membrane protein (Potential)				241
Q5BJ41 UniProt NPD GO	CNOT6_XENLA	CCR4-NOT transcription complex subunit 6 (EC 3.1.-.-) (Cytoplasmic deadenylase)	0.48	-	nuc	0	Cytoplasm (Probable). Nucleus (Probable)				552
O95400 UniProt NPD GO	CD2B2_HUMAN	CD2 antigen cytoplasmic tail-binding protein 2 (CD2 cytoplasmic domain-binding protein) (CD2 tail-bi ...	0.48	-	cyt	0	Cytoplasm	cytoplasm [TAS]	604470	1SYX	341
Q9CWK3 UniProt NPD GO	CD2B2_MOUSE	CD2 antigen cytoplasmic tail-binding protein 2 (CD2 cytoplasmic domain-binding protein) (CD2 tail-bi ...	0.48	-	cyt	0	Cytoplasm (By similarity)				342
Q8HY01 UniProt NPD GO	CD209_HYLCO	CD209 antigen (Dendritic cell-specific ICAM-3-grabbing nonintegrin 1) (DC-SIGN1)	0.48	-	nuc	1 *	Membrane; single-pass type II membrane protein (By similarity)				404
Q8HY02 UniProt NPD GO	CD209_HYLSY	CD209 antigen (Dendritic cell-specific ICAM-3-grabbing nonintegrin 1) (DC-SIGN1)	0.48	-	nuc	1 *	Membrane; single-pass type II membrane protein (By similarity)				381
Q8HXZ7 UniProt NPD GO	CD209_PANTR	CD209 antigen (Dendritic cell-specific ICAM-3-grabbing nonintegrin 1) (DC-SIGN1)	0.48	-	nuc	0	Membrane; single-pass type II membrane protein (By similarity)				427
Q64685 UniProt NPD GO	SIAT1_MOUSE	CMP-N-acetylneuraminate-beta-galactosamide-alpha-2,6-sialyltransferase (EC 2.4.99.1) (Beta-galactosi ...	0.48	-	cyt	1 *	Golgi apparatus; Golgi stack; Golgi stack membrane; single-pass type II membrane protein. Membrane-b ...				403
Q94JU3 UniProt NPD GO	CSN7_ARATH	COP9 signalosome complex subunit 7 (CSN complex subunit 7) (FUSCA protein 5) (FUSCA5)	0.48	-	cyt	0	Cytoplasm. Nucleus				260
P10589 UniProt NPD GO	COT1_HUMAN	COUP transcription factor 1 (COUP-TF1) (COUP-TF I) (V-ERBA-related protein EAR-3)	0.48	-	nuc	0	Nucleus (Potential)		132890		423
Q90733 UniProt NPD GO	COT2_CHICK	COUP transcription factor 2 (COUP-TF2) (COUP-TF II)	0.48	-	nuc	0	Nucleus				410
P10288 UniProt NPD GO	CADH2_CHICK	Cadherin-2 precursor (Neural-cadherin) (N-cadherin)	0.48	-	end	1	Membrane; single-pass type I membrane protein				912
P10092 UniProt NPD GO	CALCB_HUMAN	Calcitonin gene-related peptide 2 precursor (Calcitonin gene-related peptide II) (CGRP-II) (Beta-typ ...	0.48	-	exc	0	Secreted protein	soluble fraction [TAS]	114160		127
Q8AYS8 UniProt NPD GO	KCMA1_CHICK	Calcium-activated potassium channel subunit alpha 1 (Calcium-activated potassium channel, subfamily ...	0.48	-	end	6 *	Membrane; multi-pass membrane protein (By similarity)				1137
Q9VT65 UniProt NPD GO	CANB_DROME	Calpain B (EC 3.4.22.-) (Calcium-activated neutral proteinase B) (CANP B) [Contains: Calpain B catal ...	0.48	-	cyt	0	Cytoplasm. Membrane. Translocates to intracellular membranes when calcium levels are increased	cytoplasm [IDA]			925
Q9ESK3 UniProt NPD GO	CAN10_MOUSE	Calpain-10 (EC 3.4.22.-) (Calcium-activated neutral proteinase 10) (CANP 10)	0.48	-	mit	0					666
P43367 UniProt NPD GO	CAN2_PIG	Calpain-2 catalytic subunit (EC 3.4.22.53) (Calpain-2 large subunit) (Calcium-activated neutral prot ...	0.48	-	cyt	0	Cytoplasm (By similarity). Cell membrane (By similarity). Translocates to the plasma membrane upon C ...				324
Q8R4C0 UniProt NPD GO	CAN5_RAT	Calpain-5 (EC 3.4.22.-)	0.48	-	nuc	0					640
Q9ZNY3 UniProt NPD GO	CALR_EUGGR	Calreticulin precursor	0.48	-	end	0	Endoplasmic reticulum; endoplasmic reticulum lumen (By similarity)				401
P06782 UniProt NPD GO	SNF1_YEAST	Carbon catabolite derepressing protein kinase (EC 2.7.11.1)	0.48	-	nuc	0	Nucleus; nuclear membrane; peripheral membrane protein	cytoplasm [IPI] mitochondrion [IDA] nucleus [IPI] vacuole (sensu Fungi) [IPI]		2FH9	633
P32825 UniProt NPD GO	SXA2_SCHPO	Carboxypeptidase sxa2 precursor (EC 3.4.16.-)	0.48	-	mit	0	Secreted protein				507
P23786 UniProt NPD GO	CPT2_HUMAN	Carnitine O-palmitoyltransferase 2, mitochondrial precursor (EC 2.3.1.21) (Carnitine palmitoyltransf ...	0.48	-	mit	0	Mitochondrion; mitochondrial inner membrane	mitochondrial inner membrane [NAS]	608836		658
O54833 UniProt NPD GO	CSK22_MOUSE	Casein kinase II subunit alpha' (EC 2.7.11.1) (CK II)	0.48	-	cyt	0		protein kinase CK2 complex [TAS]			350
Q9XYF4 UniProt NPD GO	ICENC_DROME	Caspase Nc precursor (EC 3.4.22.-) (NEDD2-like caspase DRONC) [Contains: Caspase Nc subunit 1; Caspa ...	0.48	-	nuc	0	Cytoplasm (By similarity)	cytoplasm [IDA]		2FP3	450
Q5ZKN1 UniProt NPD GO	CDK9_CHICK	Cell division protein kinase 9 (EC 2.7.11.22) (EC 2.7.11.23) (Cyclin-dependent kinase 9)	0.48	-	cyt	0	Nucleus (By similarity)				372
Q84JA6 UniProt NPD GO	CESA4_ARATH	Cellulose synthase A catalytic subunit 4 [UDP-forming] (EC 2.4.1.12) (AtCesA-4) (Irregular xylem pro ...	0.48	+	end	8	Cell membrane; multi-pass membrane protein (Probable)				1049
O15182 UniProt NPD GO	CETN3_HUMAN	Centrin-3	0.48	-	nuc	0	Centrosome. Centrosome of interphase and mitotic cells	centriole [TAS]	602907		167
Q8TCT0 UniProt NPD GO	CERK1_HUMAN	Ceramide kinase (EC 2.7.1.138) (Acylsphingosine kinase) (hCERK) (Lipid kinase 4) (LK4)	0.48	-	cyt	0	Cytoplasm. Membrane; peripheral membrane protein	integral to membrane of membrane fraction [IDA]			537
P30573 UniProt NPD GO	CHS3_CANAL	Chitin synthase 3 (EC 2.4.1.16) (Chitin-UDP acetyl-glucosaminyl transferase 3) (Class-IV chitin synt ...	0.48	-	end	6	Cell membrane; multi-pass membrane protein				1213
Q92197 UniProt NPD GO	CHSC_ASPFU	Chitin synthase C (EC 2.4.1.16) (Chitin-UDP acetyl-glucosaminyl transferase C) (Class-III chitin syn ...	0.48	-	end	8	Cell membrane; multi-pass membrane protein				893

You are viewing entries 26101 to 26150 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.