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
Q5RFH5 UniProt NPD GO	SPT4H_PONPY	Transcription elongation factor SPT4 (DRB sensitivity-inducing factor small subunit) (DSIF small sub ...	0.01	-	mit	0	Nucleus (By similarity)				117
P63272 UniProt NPD GO	SPT4H_HUMAN	Transcription elongation factor SPT4 (hSPT4) (DRB sensitivity-inducing factor small subunit) (DSIF s ...	0.01	-	mit	0	Nucleus	nucleus [IDA]	603555		117
P63271 UniProt NPD GO	SPT41_MOUSE	Transcription elongation factor SPT4 1 (DRB sensitivity-inducing factor small subunit 1) (DSIF small ...	0.01	-	mit	0	Nucleus (By similarity)				117
Q9Z199 UniProt NPD GO	SPT42_MOUSE	Transcription elongation factor SPT4 2 (DRB sensitivity-inducing factor small subunit 2) (DSIF small ...	0.01	-	nuc	0	Nucleus (By similarity)				117
P52656 UniProt NPD GO	T2AG_DROME	Transcription initiation factor IIA gamma chain (TFIIA P14 subunit) (TFIIA-14) (dTFIIA-S) (TFIIA-gam ...	0.01	-	cyt	0	Nucleus				106
Q95VY2 UniProt NPD GO	TCTP_BRABE	Translationally-controlled tumor protein (TCTP)	0.01	-	cyt	0	Cytoplasm (By similarity)				169
P61288 UniProt NPD GO	TCTP_PIG	Translationally-controlled tumor protein (TCTP)	0.01	-	cyt	0	Cytoplasm (By similarity)				172
P43348 UniProt NPD GO	TCTP_RABIT	Translationally-controlled tumor protein (TCTP)	0.01	-	cyt	0	Cytoplasm (By similarity)				172
P13693 UniProt NPD GO	TCTP_HUMAN	Translationally-controlled tumor protein (TCTP) (p23) (Histamine-releasing factor) (HRF) (Fortilin)	0.01	-	cyt	0	Cytoplasm	cytoplasm [IDA] extracellular space [IDA] multivesicular body [IDA]	600763	1YZ1	172
P31265 UniProt NPD GO	TCTP_ARATH	Translationally-controlled tumor protein homolog (TCTP)	0.01	-	cyt	0	Cytoplasm (By similarity)				168
Q944W6 UniProt NPD GO	TCTP_BRAOL	Translationally-controlled tumor protein homolog (TCTP)	0.01	-	cyt	0	Cytoplasm (By similarity)				168
P35681 UniProt NPD GO	TCTP_ORYSA	Translationally-controlled tumor protein homolog (TCTP)	0.01	-	cyt	0	Cytoplasm (By similarity)				168
P91800 UniProt NPD GO	TCTP_SCHJA	Translationally-controlled tumor protein homolog (TCTP)	0.01	-	cyt	0	Cytoplasm (By similarity)				169
Q9XHL7 UniProt NPD GO	TCTP_TOBAC	Translationally-controlled tumor protein homolog (TCTP)	0.01	-	cyt	0	Cytoplasm (By similarity)				168
P35691 UniProt NPD GO	TCTP_YEAST	Translationally-controlled tumor protein homolog (TCTP)	0.01	-	cyt	0	Cytoplasm (By similarity)	cytoplasm [IDA]			167
P50906 UniProt NPD GO	TCTP_PEA	Translationally-controlled tumor protein homolog (TCTP) (23 kDa callus protein) (p23) (PsRCI22-3)	0.01	-	cyt	0	Cytoplasm (By similarity)				167
Q95WA2 UniProt NPD GO	TCTP_SCHMA	Translationally-controlled tumor protein homolog (TCTP) (Histamine-releasing factor) (Fragment)	0.01	-	cyt	0	Cytoplasm (By similarity)				166
P82009 UniProt NPD GO	SEC62_CANFA	Translocation protein SEC62 (Translocation protein 1) (TP-1) (Fragments)	0.01	-	cyt	0	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein				39
Q96DZ7 UniProt NPD GO	T4S19_HUMAN	Transmembrane 4 L6 family 19	0.01	-	end	4 *	Membrane; multi-pass membrane protein (Potential)				209
Q91XD3 UniProt NPD GO	T4S4_MOUSE	Transmembrane 4 L6 family member 4	0.01	-	end	4 *	Membrane; multi-pass membrane protein (By similarity)				202
Q9DA39 UniProt NPD GO	TMBI4_MOUSE	Transmembrane BAX inhibitor motif-containing protein 4 (Z-protein)	0.01	-	end	6 *	Membrane; multi-pass membrane protein (Potential)				238
P49020 UniProt NPD GO	TMED2_CRIGR	Transmembrane emp24 domain-containing protein 2 precursor (COPI-coated vesicle membrane protein p24) ...	0.01	-	end	1	Type I membrane protein. Golgi-derived coatomer-coated vesicles				196
Q15363 UniProt NPD GO	TMED2_HUMAN	Transmembrane emp24 domain-containing protein 2 precursor (Membrane protein p24A)	0.01	-	end	2 *	Type I membrane protein. Golgi-derived coatomer-coated vesicles	ER-Golgi intermediate compartment [IDA] integral to membrane [ISS] microsome [ISS] plasma membrane [TAS] zymogen granule membrane [ISS]			201
Q63524 UniProt NPD GO	TMED2_RAT	Transmembrane emp24 domain-containing protein 2 precursor (Membrane protein p24A) (RNP21.4)	0.01	-	end	2 *	Type I membrane protein. Golgi-derived coatomer-coated vesicles	integral to membrane [IDA] microsome [IDA] zymogen granule membrane [IDA]			201
Q9R0Q3 UniProt NPD GO	TMED2_MOUSE	Transmembrane emp24 domain-containing protein 2 precursor (Membrane protein p24A) (Sid 394)	0.01	-	end	2 *	Type I membrane protein. Golgi-derived coatomer-coated vesicles (By similarity)	integral to membrane [ISS] microsome [ISS] zymogen granule membrane [ISS]			201
Q9NUH8 UniProt NPD GO	TM14B_HUMAN	Transmembrane protein 14B	0.01	-	exc	4 *	Membrane; multi-pass membrane protein (Potential)				114
Q9P0S9 UniProt NPD GO	TM14C_HUMAN	Transmembrane protein 14C	0.01	-	cyt	4 *	Membrane; multi-pass membrane protein (Potential)				112
Q9CQN6 UniProt NPD GO	TM14C_MOUSE	Transmembrane protein 14C	0.01	-	nuc	4 *	Membrane; multi-pass membrane protein (Potential)	mitochondrion [IDA]			114
Q3UP23 UniProt NPD GO	TMM26_MOUSE	Transmembrane protein 26	0.01	-	end	5 *	Membrane; multi-pass membrane protein (Potential)				366
O95807 UniProt NPD GO	TM50A_HUMAN	Transmembrane protein 50A (Small membrane protein 1)	0.01	-	end	4 *	Membrane; multi-pass membrane protein (Potential)		605348		157
Q9CXL1 UniProt NPD GO	TM50A_MOUSE	Transmembrane protein 50A (Small membrane protein 1)	0.01	-	end	4 *	Membrane; multi-pass membrane protein (Potential)	cytoplasm [IDA]			157
Q9D1X9 UniProt NPD GO	TM50B_MOUSE	Transmembrane protein 50B	0.01	-	end	4 *	Membrane; multi-pass membrane protein (Potential)				158
Q3ZCD2 UniProt NPD GO	TMM54_BOVIN	Transmembrane protein 54	0.01	-	end	4 *	Membrane; multi-pass membrane protein (Potential)				222
Q9D7S1 UniProt NPD GO	TMM54_MOUSE	Transmembrane protein 54	0.01	-	end	3 *	Membrane; multi-pass membrane protein (Potential)				219
Q494T4 UniProt NPD GO	TMM54_RAT	Transmembrane protein 54	0.01	-	end	4 *	Membrane; multi-pass membrane protein (Potential)				216
Q3T0W0 UniProt NPD GO	TM86B_BOVIN	Transmembrane protein 86B	0.01	-	end	6 *	Membrane; multi-pass membrane protein (Potential)				224
Q9HC07 UniProt NPD GO	TPARL_HUMAN	Transmembrane protein TPARL (Transmembrane protein PT27)	0.01	-	end	7 *	Membrane; multi-pass membrane protein (Potential)				324
P36149 UniProt NPD GO	BET3_YEAST	Transport protein particle 22 kDa subunit (TRAPP 22 kDa subunit)	0.01	-	cyt	0	Golgi apparatus; cis-Golgi network	Golgi apparatus [IDA] TRAPP complex [IDA]			193
O46375 UniProt NPD GO	TTHY_BOVIN	Transthyretin precursor (Prealbumin)	0.01	-	end	0	Secreted protein				147
Q9MYN8 UniProt NPD GO	TTHY_ERIEU	Transthyretin precursor (Prealbumin)	0.01	-	end	0	Secreted protein				145
Q8HXW1 UniProt NPD GO	TTHY_MACFA	Transthyretin precursor (Prealbumin)	0.01	-	exc	0	Secreted protein (By similarity)				147
P12303 UniProt NPD GO	TTHY_SHEEP	Transthyretin precursor (Prealbumin)	0.01	-	end	0	Secreted protein				147
P31779 UniProt NPD GO	TTHY_RANCA	Transthyretin precursor (Prealbumin) (Tadpole T3-binding protein) (T-T3BP) (THBP)	0.01	-	end	0	Secreted protein			1LJB	153
Q03575 UniProt NPD GO	YLF5_CAEEL	Transthyretin-like protein C40H1.5 precursor	0.01	-	exc	0	Secreted protein (Potential)				139
P34500 UniProt NPD GO	YMS4_CAEEL	Transthyretin-like protein K03H1.4 precursor	0.01	-	vac	0	Secreted protein (Potential)				148
P04155 UniProt NPD GO	TFF1_HUMAN	Trefoil factor 1 precursor (pS2 protein) (HP1.A) (Breast cancer estrogen-inducible protein) (PNR-2)	0.01	-	exc	0	Secreted protein		113710	1PS2	84
Q03191 UniProt NPD GO	TFF3_RAT	Trefoil factor 3 precursor (Intestinal trefoil factor) (Polypeptide P1.B)	0.01	-	exc	0	Secreted protein				81
P19986 UniProt NPD GO	ITHA_PERAM	Trehalase inhibitor (Fragment)	0.01	-		0					19
Q27049 UniProt NPD GO	TRIA_TRIPA	Triabin precursor	0.01	-	mit	0	Secreted protein			1AVG	160
Q27176 UniProt NPD GO	T4C_PARTE	Trichocyst matrix protein T4-C (Secretory granule protein T4-C) (TMP 4-C) (Fragment)	0.01	-	cyt	0	Trichocyst. These are architecturally complex secretory storage granules-docked at the plasma membra ...				27

You are viewing entries 91801 to 91850 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.