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
P01495 UniProt NPD GO	SCX2_CENNO	Toxin 2 precursor (Toxin II.9.2.2) (Cn2) (Fragment)	0.03	-	cyt	0	Secreted protein			1CN2	84
P80076 UniProt NPD GO	SCX3_CENNO	Toxin 3 (Toxin II.9.2.3) (Cn3)	0.03	-	cyt	0	Secreted protein				66
P45665 UniProt NPD GO	SCXY_CENNO	Toxin CngtIV precursor	0.03	-	vac	1 *	Secreted protein				86
P56646 UniProt NPD GO	SCXM_CENSC	Toxin CsE M1 (CsEM1) (CsEIII)	0.03	-	cyt	0	Secreted protein				65
P01404 UniProt NPD GO	TXF8_DENAN	Toxin F-VIII precursor (Toxin TA2) (Toxin DaF8)	0.03	-	nuc	1 *	Secreted protein				81
P58912 UniProt NPD GO	TX60B_PHYSE	Toxin PsTX-60B (Fragment)	0.03	-	nuc	0	Secreted protein. Found in nematocyst				24
P58606 UniProt NPD GO	PTU1_PEITU	Toxin Ptu1	0.03	-	nuc	0	Secreted protein			1I26	34
P56610 UniProt NPD GO	SCX6_TITBA	Toxin TbTX-VI (Tb4) (Fragment)	0.03	-		0	Secreted protein				19
P84680 UniProt NPD GO	SC35_TITCA	Toxin Tc35 (Fragment)	0.03	-		0	Secreted protein	extracellular region [IDA]			10
P84683 UniProt NPD GO	SC40_TITCA	Toxin Tc40 (Fragment)	0.03	-		0	Secreted protein	extracellular region [IDA]			9
Q96RI8 UniProt NPD GO	TAAR6_HUMAN	Trace amine-associated receptor 6 (Trace amine receptor 4) (TaR-4)	0.03	-	end	7 *	Membrane; multi-pass membrane protein	integral to membrane [IC]	608923		345
Q5W8W0 UniProt NPD GO	TAAR6_PANTR	Trace amine-associated receptor 6 (Trace amine receptor 4) (TaR-4)	0.03	-	end	7 *	Membrane; multi-pass membrane protein (By similarity)				345
Q5QD11 UniProt NPD GO	TAA7B_MOUSE	Trace amine-associated receptor 7b	0.03	-	end	7 *	Membrane; multi-pass membrane protein				358
Q923X9 UniProt NPD GO	TAA8A_RAT	Trace amine-associated receptor 8a (Trace amine receptor 11) (TaR-11)	0.03	-	end	7 *	Membrane; multi-pass membrane protein				344
Q5QD06 UniProt NPD GO	TAA8B_MOUSE	Trace amine-associated receptor 8b	0.03	-	end	7 *	Membrane; multi-pass membrane protein				344
Q923Y3 UniProt NPD GO	TAA8B_RAT	Trace amine-associated receptor 8b (Trace amine receptor 7) (TaR-7)	0.03	-	end	7 *	Membrane; multi-pass membrane protein				344
Q3T086 UniProt NPD GO	TPC6A_BOVIN	Trafficking protein particle complex 6A	0.03	-	cyt	0	Golgi apparatus; cis-Golgi network (By similarity)				159
Q9Y296 UniProt NPD GO	TPPC4_HUMAN	Trafficking protein particle complex subunit 4 (Synbindin) (TRS23 homolog) (Hematopoietic stem/proge ...	0.03	-	cyt	0	Golgi apparatus; cis-Golgi network (By similarity)	dendrite [ISS] Golgi stack [ISS] synapse [ISS] synaptic vesicle [ISS]			219
Q2NL13 UniProt NPD GO	TPPC5_BOVIN	Trafficking protein particle complex subunit 5	0.03	-	mit	0	Golgi apparatus; cis-Golgi network (By similarity)				188
P80427 UniProt NPD GO	TALDO_CARMA	Transaldolase (EC 2.2.1.2) (Fragments)	0.03	-	nuc	0	Cytoplasm				75
Q9BZ99 UniProt NPD GO	TTY11_HUMAN	Transcript Y 11 protein	0.03	-	nuc	0					119
Q6FMX1 UniProt NPD GO	SPT4_CANGA	Transcription elongation factor SPT4 (Chromatin elongation factor SPT4)	0.03	-	cyt	0	Nucleus. Centromere and heterochromatin (By similarity)				102
P29055 UniProt NPD GO	TF2B_YEAST	Transcription initiation factor IIB (General transcription factor TFIIB) (Transcription factor E)	0.03	-	mit	0	Nucleus	nucleoplasm [IPI]			345
Q99376 UniProt NPD GO	TFR1_RAT	Transferrin receptor protein 1 (TfR1) (TR) (TfR) (Trfr) (CD71 antigen) (Fragment)	0.03	-	cyt	0	Membrane; single-pass type II membrane protein (By similarity)				622
P98138 UniProt NPD GO	TGFA_RABIT	Transforming growth factor alpha (TGF-alpha) (EGF-like TGF) (ETGF) (TGF type 1) (Fragment)	0.03	-	cyt	0					50
P98135 UniProt NPD GO	TGFA_SHEEP	Transforming growth factor alpha precursor (TGF-alpha) (EGF-like TGF) (ETGF) (TGF type 1) (Fragment) ...	0.03	-	end	1 *	Precursor form: Cell membrane; single-pass type I membrane protein. Mature form: Secreted protein; e ...				133
O11780 UniProt NPD GO	BGH3_PIG	Transforming growth factor-beta-induced protein ig-h3 precursor (Beta ig-h3) (Kerato-epithelin) (RGD ...	0.03	-	exc	0	Secreted protein; extracellular space. May be associated both with microfibrils and with the cell su ...				683
Q3ZJ80 UniProt NPD GO	IF1C_PSEAK	Translation initiation factor IF-1, chloroplast	0.03	-	cyt	0	Plastid; chloroplast				109
Q75AA8 UniProt NPD GO	TMA20_ASHGO	Translation machinery-associated protein 20	0.03	-	nuc	0	Cytoplasm (By similarity)				181
Q4PLZ3 UniProt NPD GO	TCTP_IXOSC	Translationally-controlled tumor protein homolog (TCTP)	0.03	-	cyt	0	Cytoplasm (By similarity)				173
P28014 UniProt NPD GO	TCTP_MEDSA	Translationally-controlled tumor protein homolog (TCTP)	0.03	-	cyt	0	Cytoplasm (By similarity)				167
Q4XFJ8 UniProt NPD GO	TCTP_PLACH	Translationally-controlled tumor protein homolog (TCTP)	0.03	-	cyt	0	Cytoplasm (By similarity)				171
Q8I3Z5 UniProt NPD GO	TCTP_PLAF7	Translationally-controlled tumor protein homolog (TCTP)	0.03	-	cyt	0	Cytoplasm (By similarity)				171
Q9XYU2 UniProt NPD GO	TCTP_PLAYO	Translationally-controlled tumor protein homolog (TCTP)	0.03	-	cyt	0	Cytoplasm (By similarity)				171
Q9ZRX0 UniProt NPD GO	TCTP_PSEMZ	Translationally-controlled tumor protein homolog (TCTP)	0.03	-	cyt	0	Cytoplasm (By similarity)				167
P82008 UniProt NPD GO	SEC63_CANFA	Translocation protein SEC63 homolog (Fragments)	0.03	-	cyt	0	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein				33
Q62186 UniProt NPD GO	SSRD_MOUSE	Translocon-associated protein subunit delta precursor (TRAP-delta) (Signal sequence receptor subunit ...	0.03	-	exc	1	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type I membrane protein (By simil ...				172
Q07984 UniProt NPD GO	SSRD_RAT	Translocon-associated protein subunit delta precursor (TRAP-delta) (Signal sequence receptor subunit ...	0.03	-	exc	1	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type I membrane protein	endoplasmic reticulum [TAS] translocon complex [IDA]			173
P49111 UniProt NPD GO	T4S1_MESAU	Transmembrane 4 L6 family member 1 (Tumor-associated antigen L6 homolog) (MM3)	0.03	-	end	4 *	Membrane; multi-pass membrane protein				202
Q9NS93 UniProt NPD GO	TM7S3_HUMAN	Transmembrane 7 superfamily member 3 precursor (Seven span transmembrane protein)	0.03	-	end	7	Cell membrane; multi-pass membrane protein		605181		570
P58021 UniProt NPD GO	TM9S2_MOUSE	Transmembrane 9 superfamily protein member 2 precursor	0.03	-	end	9	Endosome; endosomal membrane; multi-pass membrane protein (Probable)				662
Q8VCA5 UniProt NPD GO	TMPS4_MOUSE	Transmembrane protease, serine 4 (EC 3.4.21.-) (Channel-activating protease 2) (mCAP2)	0.03	-	cyt	1 *	Membrane; single-pass type II membrane protein (Potential)				435
Q8C581 UniProt NPD GO	TMM91_MOUSE	Transmembrane protein 91	0.03	-	end	2	Membrane; multi-pass membrane protein (Potential)				172
Q5NVS2 UniProt NPD GO	TTHY_PONPY	Transthyretin precursor (Prealbumin)	0.03	-	end	0	Secreted protein (By similarity)				147
P34499 UniProt NPD GO	YMS3_CAEEL	Transthyretin-like protein K03H1.3 precursor	0.03	-	exc	0	Secreted protein (Potential)				148
Q09030 UniProt NPD GO	TFF2_RAT	Trefoil factor 2 precursor (Spasmolytic polypeptide) (SP)	0.03	-	exc	0	Secreted protein				129
P53007 UniProt NPD GO	TXTP_HUMAN	Tricarboxylate transport protein, mitochondrial precursor (Citrate transport protein) (CTP) (Tricarb ...	0.03	-	end	0	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein	mitochondrial inner membrane [TAS]	190315		311
P11869 UniProt NPD GO	TPT_SPIOL	Triose phosphate/phosphate translocator, chloroplast precursor (cTPT) (p36) (E29)	0.03	-	end	9	Plastid; chloroplast; chloroplast membrane; multi-pass membrane protein. Located in zones of contact ...				404
P21727 UniProt NPD GO	TPT_PEA	Triose phosphate/phosphate translocator, chloroplast precursor (cTPT) (p36) (E30)	0.03	-	end	9	Plastid; chloroplast; chloroplast membrane; multi-pass membrane protein. Located in zones of contact ...				402
Q750Y8 UniProt NPD GO	TPIS_ASHGO	Triosephosphate isomerase (EC 5.3.1.1) (TIM) (Triose-phosphate isomerase)	0.03	-	cyt	0					248

You are viewing entries 81851 to 81900 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.