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
Q9W7E9 UniProt NPD GO	SMS2_PROAN	Somatostatin-2 precursor (Somatostatin II) (PSS2) [Contains: [Pro17]-somatostatin-29; [Pro2]-somatos ...	0.11	-	exc	0	Secreted protein				109
P21779 UniProt NPD GO	SMS_PETMA	Somatostatin-37 [Contains: Somatostatin-34; Somatostatin-14]	0.11	-	nuc	0	Secreted protein				37
P09537 UniProt NPD GO	SOMA_PAROL	Somatotropin precursor (Growth hormone)	0.11	-	exc	0	Secreted protein				190
Q92000 UniProt NPD GO	SHH_XENLA	Sonic hedgehog protein precursor (X-SHH) (VHH-1) [Contains: Sonic hedgehog protein N-product; Sonic ...	0.11	-	mit	0	Sonic hedgehog protein C-product: Secreted protein; extracellular space (By similarity). Sonic hedge ...				444
Q8N0X7 UniProt NPD GO	SPG20_HUMAN	Spartin (Trans-activated by hepatitis C virus core protein 1)	0.11	-	nuc	0			607111		666
Q99500 UniProt NPD GO	EDG3_HUMAN	Sphingosine 1-phosphate receptor Edg-3 (S1P receptor Edg-3) (Endothelial differentiation G-protein c ...	0.11	-	end	7 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS] plasma membrane [TAS]	601965		378
Q684M3 UniProt NPD GO	EDG8_PIG	Sphingosine 1-phosphate receptor Edg-8 (Endothelial differentiation sphingolipid G-protein-coupled r ...	0.11	-	end	7 *	Membrane; multi-pass membrane protein				398
Q9JI99 UniProt NPD GO	SGPP1_MOUSE	Sphingosine-1-phosphate phosphatase 1 (EC 3.1.3.-) (Sphingosine-1-phosphatase 1) (SPPase1) (SPP) (mS ...	0.11	+	end	7	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)	endoplasmic reticulum [IDA] membrane fraction [IDA]			430
Q56K13 UniProt NPD GO	SF3B5_BOVIN	Splicing factor 3B subunit 5 (SF3b5) (Pre-mRNA-splicing factor SF3b 10 kDa subunit)	0.11	-	nuc	0	Nucleus (By similarity)				86
Q9BWJ5 UniProt NPD GO	SF3B5_HUMAN	Splicing factor 3B subunit 5 (SF3b5) (Pre-mRNA-splicing factor SF3b 10 kDa subunit)	0.11	-	nuc	0	Nucleus (By similarity)				86
Q9WV75 UniProt NPD GO	SPON2_RAT	Spondin-2 precursor (Mindin)	0.11	-	mit	0	Secreted protein; extracellular space; extracellular matrix				330
P43647 UniProt NPD GO	STC_ONCKE	Stanniocalcin (STC) (Corpuscles of Stannius protein) (CS) (Hypocalcin) (Teleocalcin)	0.11	-	cyt	0	Secreted protein				179
Q04398 UniProt NPD GO	SPG3_YEAST	Stationary phase protein 3	0.11	-	mit	2 *	Membrane; multi-pass membrane protein (Potential)				127
O77760 UniProt NPD GO	SOAT1_CERAE	Sterol O-acyltransferase 1 (EC 2.3.1.26) (Cholesterol acyltransferase 1) (Acyl coenzyme A:cholestero ...	0.11	-	end	8	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein				550
P02814 UniProt NPD GO	SMR3B_HUMAN	Submaxillary gland androgen-regulated protein 3 homolog B precursor (Proline-rich protein 3) (Prolin ...	0.11	-	exc	0	Secreted protein	extracellular space [TAS]			79
P19850 UniProt NPD GO	TKNA_CHICK	Substance P	0.11	-		0	Secreted protein				11
P25103 UniProt NPD GO	NK1R_HUMAN	Substance-P receptor (SPR) (NK-1 receptor) (NK-1R) (Tachykinin receptor 1)	0.11	-	end	7 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS] plasma membrane [TAS]	162323		407
Q94523 UniProt NPD GO	DHSA_DROME	Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial precursor (EC 1.3.5.1) (FP) ...	0.11	-	mit	0	Mitochondrion; mitochondrial inner membrane (By similarity)				661
P31040 UniProt NPD GO	DHSA_HUMAN	Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial precursor (EC 1.3.5.1) (Fp) ...	0.11	-	mit	0	Mitochondrion; mitochondrial inner membrane	mitochondrion [IDA] respiratory chain complex II (sensu Eukaryota) [TAS]	600857		664
Q9Z2I9 UniProt NPD GO	SUCB1_MOUSE	Succinyl-CoA ligase [ADP-forming] beta-chain, mitochondrial precursor (EC 6.2.1.5) (Succinyl-CoA syn ...	0.11	-	mit	0	Mitochondrion	mitochondrion [IDA]			463
P53597 UniProt NPD GO	SUCA_HUMAN	Succinyl-CoA ligase [GDP-forming] subunit alpha, mitochondrial precursor (EC 6.2.1.4) (Succinyl-CoA ...	0.11	-	mit	0	Mitochondrion	mitochondrion [TAS]			333
P10691 UniProt NPD GO	SUS1_SOLTU	Sucrose synthase (EC 2.4.1.13) (Sucrose-UDP glucosyltransferase) (SS16)	0.11	-	mit	0					805
Q9FE59 UniProt NPD GO	SUC4_ARATH	Sucrose transport protein SUC4 (Sucrose permease 4) (Sucrose-proton symporter 4) (Sucrose transporte ...	0.11	-	end	12 *	Cell membrane; multi-pass membrane protein (Probable)				510
Q9Y872 UniProt NPD GO	MET3_CANAL	Sulfate adenylyltransferase (EC 2.7.7.4) (Sulfate adenylate transferase) (SAT) (ATP-sulfurylase)	0.11	-	nuc	0					527
Q12555 UniProt NPD GO	MET3_EMENI	Sulfate adenylyltransferase (EC 2.7.7.4) (Sulfate adenylate transferase) (SAT) (ATP-sulfurylase)	0.11	-	cyt	0					574
O04722 UniProt NPD GO	SUT21_ARATH	Sulfate transporter 2.1 (AST68)	0.11	-	end	10	Membrane; multi-pass membrane protein (Potential)				677
P92946 UniProt NPD GO	SUT22_ARATH	Sulfate transporter 2.2 (AST56) (AtH14)	0.11	-	end	10	Membrane; multi-pass membrane protein (Potential)				658
Q61207 UniProt NPD GO	SAP_MOUSE	Sulfated glycoprotein 1 precursor (SGP-1) (Prosaposin)	0.11	-	exc	0	Secreted protein; extracellular space	mitochondrion [IDA]			557
Q9R112 UniProt NPD GO	SQRD_MOUSE	Sulfide:quinone oxidoreductase, mitochondrial precursor (EC 1.-.-.-)	0.11	-	mit	0	Mitochondrion (Probable)	mitochondrial inner membrane [IDA] mitochondrion [IDA]			450
P52840 UniProt NPD GO	ST1A1_MOUSE	Sulfotransferase 1A1 (EC 2.8.2.1) (Aryl sulfotransferase) (Phenol sulfotransferase) (Sulfokinase) (P ...	0.11	-	cyt	0	Cytoplasm (By similarity)				291
Q6IMI4 UniProt NPD GO	ST6B1_HUMAN	Sulfotransferase 6B1 (EC 2.8.2.-)	0.11	-	cyt	0	Cytoplasm (By similarity)				265
Q92429 UniProt NPD GO	SODM_GANMI	Superoxide dismutase [Mn], mitochondrial precursor (EC 1.15.1.1) (Mn-SOD)	0.11	-	cyt	0	Mitochondrion; mitochondrial matrix (By similarity)				200
Q18864 UniProt NPD GO	SURF4_CAEEL	Surfeit locus protein 4 homolog	0.11	-	end	5	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				277
Q9NZ01 UniProt NPD GO	GPSN2_HUMAN	Synaptic glycoprotein SC2	0.11	-	cyt	4	Membrane; multi-pass membrane protein (Potential)				308
Q9WVJ4 UniProt NPD GO	SYJ2B_RAT	Synaptojanin-2-binding protein (Mitochondrial outer membrane protein 25) (NPW16)	0.11	-	cyt	1	Mitochondrion; mitochondrial outer membrane				206
Q9JHZ9 UniProt NPD GO	S38A3_RAT	System N amino acid transporter 1 (SN1) (N-system amino acid transporter 1) (Solute carrier family 3 ...	0.11	-	end	11	Cell membrane; multi-pass membrane protein	integral to plasma membrane [IDA]			504
Q99ME7 UniProt NPD GO	TBX19_MOUSE	T-box transcription factor TBX19 (T-box protein 19) (T-box factor, pituitary)	0.11	-	nuc	0	Nucleus (Potential)				446
P04212 UniProt NPD GO	TVB4_MOUSE	T-cell receptor beta chain V region LB2 precursor	0.11	-	exc	0					136
P47209 UniProt NPD GO	TCPE_CAEEL	T-complex protein 1 subunit epsilon (TCP-1-epsilon) (CCT-epsilon)	0.11	-	cyt	0	Cytoplasm				542
P80313 UniProt NPD GO	TCPH_MOUSE	T-complex protein 1 subunit eta (TCP-1-eta) (CCT-eta)	0.11	-	cyt	0	Cytoplasm	chaperonin-containing T-complex [IDA]			544
P54409 UniProt NPD GO	TCPH_TETPY	T-complex protein 1 subunit eta (TCP-1-eta) (CCT-eta)	0.11	-	nuc	0	Cytoplasm				558
P47828 UniProt NPD GO	TCPQ_CANAL	T-complex protein 1 subunit theta (TCP-1-theta) (CCT-theta)	0.11	-	cyt	0	Cytoplasm (By similarity)				540
P56845 UniProt NPD GO	TCLB5_MOUSE	TCL1B5 protein	0.11	-	cyt	0					121
Q6YCH2 UniProt NPD GO	TDPZ4_MOUSE	TD and POZ domain-containing protein 4	0.11	-	cyt	0					370
Q8I6S2 UniProt NPD GO	TKN2_OCTVU	Tachykinin-2 precursor (Tachykinin II) (OctTK-II)	0.11	-	nuc	0	Secreted protein				92
Q7LZE4 UniProt NPD GO	IVBTI_OXYSC	Taicatoxin, serine protease inhibitor component (TCX)	0.11	-	nuc	0	Secreted protein				62
Q9BN12 UniProt NPD GO	TMTX_MESTA	Tamulustoxin (TmTX)	0.11	-	nuc	0	Secreted protein				35
Q717C1 UniProt NPD GO	TS1R3_GORGO	Taste receptor type 1 member 3 precursor (Sweet taste receptor T1R3)	0.11	-	end	7	Membrane; multi-pass membrane protein				852
Q923K1 UniProt NPD GO	TS1R3_RAT	Taste receptor type 1 member 3 precursor (Sweet taste receptor T1R3)	0.11	-	end	6	Membrane; multi-pass membrane protein	integral to membrane [IC]			858
Q9NYV7 UniProt NPD GO	T2R16_HUMAN	Taste receptor type 2 member 16 (T2R16)	0.11	-	end	7 *	Membrane; multi-pass membrane protein	integral to membrane [IC]	604867		291

You are viewing entries 63551 to 63600 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.