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
P01249 UniProt NPD GO	THP1_BOVIN	Thymopoietin-1 (Thymopoietin I)	0.04	-	cyt	0					49
P21753 UniProt NPD GO	TYB9_PIG	Thymosin beta-9	0.04	-	nuc	0	Cytoplasm				41
Q9I955 UniProt NPD GO	TYBA_CYPCA	Thymosin beta-a	0.04	-	nuc	0	Cytoplasm (By similarity)				45
Q9W6I9 UniProt NPD GO	THA_ONCMY	Thyroid hormone receptor alpha (Fragment)	0.04	-	cyt	0	Nucleus				218
Q95J88 UniProt NPD GO	TSHB_MONDO	Thyrotropin beta chain precursor (Thyroid-stimulating hormone beta subunit) (TSH-beta) (TSH-B)	0.04	-	exc	0	Secreted protein				138
P01224 UniProt NPD GO	TSHB_PIG	Thyrotropin beta chain precursor (Thyroid-stimulating hormone beta subunit) (TSH-beta) (TSH-B)	0.04	-	exc	0	Secreted protein				138
Q08127 UniProt NPD GO	TSHB_ANGAN	Thyrotropin beta chain precursor (Thyroid-stimulating hormone subunit beta) (TSH-beta) (TSH-B)	0.04	-	exc	0	Secreted protein				147
Q7ZZV4 UniProt NPD GO	TSHB_ANGJA	Thyrotropin beta chain precursor (Thyroid-stimulating hormone subunit beta) (TSH-beta) (TSH-B)	0.04	-	exc	0	Secreted protein (By similarity)				147
P21761 UniProt NPD GO	TRFR_MOUSE	Thyrotropin-releasing hormone receptor (TRH-R) (Thyroliberin receptor)	0.04	-	end	7 *	Membrane; multi-pass membrane protein				393
Q01717 UniProt NPD GO	TRFR_RAT	Thyrotropin-releasing hormone receptor (TRH-R) (Thyroliberin receptor)	0.04	-	end	7 *	Membrane; multi-pass membrane protein				412
P17726 UniProt NPD GO	TAP_ORNMO	Tick anticoagulant peptide (TAP)	0.04	-	nuc	0				1TCP	60
P82651 UniProt NPD GO	TIN1_HOPTI	Tigerinin-1	0.04	-		0	Secreted protein				11
O13226 UniProt NPD GO	TWHH_PSEPR	Tiggy-winkle hedgehog protein (Fragment)	0.04	-	nuc	0	The C-terminal peptide diffuses from the cell, while the N-terminal peptide remains associated with ...				53
Q9ER41 UniProt NPD GO	TOR1B_MOUSE	Torsin B precursor (Torsin family 1 member B)	0.04	-	mit	1 *	Endoplasmic reticulum; endoplasmic reticulum lumen (By similarity)	cytoplasm [IDA]			336
Q6AYR4 UniProt NPD GO	TOR2A_RAT	Torsin-2A precursor (Torsin family 2 member A)	0.04	-	exc	1 *	Secreted protein (Probable)				321
Q68F68 UniProt NPD GO	TOR2A_XENLA	Torsin-2A precursor (Torsin family 2 member A)	0.04	-	exc	0					314
Q5JU69 UniProt NPD GO	TOR2A_HUMAN	Torsin-2A precursor (Torsin family 2 member A) (Torsin-related protein 1)	0.04	-	exc	1 *	Secreted protein (Probable)		608052		321
P60976 UniProt NPD GO	CALA_CALS5	Toxic peptide A precursor	0.04	-	exc	0	Secreted protein				80
P01405 UniProt NPD GO	TX496_DENVI	Toxin 4.9.6	0.04	-	nuc	0	Secreted protein				60
P0C1F0 UniProt NPD GO	TXA11_ANTEL	Toxin APE 1-1	0.04	-	nuc	0	Secreted protein (Probable). Found in nematocyst (Probable)				47
P0C1F1 UniProt NPD GO	TXA12_ANTEL	Toxin APE 1-2	0.04	-	nuc	0	Secreted protein (Probable). Found in nematocyst (Probable)				47
P59897 UniProt NPD GO	SCX1_CENII	Toxin Cii 1 (Cii1)	0.04	-	cyt	0	Secreted protein				66
P59898 UniProt NPD GO	SCX2_CENLL	Toxin Cll 2 (Cll2)	0.04	-	cyt	0	Secreted protein				66
P58609 UniProt NPD GO	IOB1_ISYOB	Toxin Iob1	0.04	-	nuc	0	Secreted protein				36
P83480 UniProt NPD GO	TXPR1_THRPR	Toxin ProTx-1 (ProTx-I)	0.04	-	cyt	0	Secreted protein				35
Q8IAE2 UniProt NPD GO	ACTPA_PHYSE	Toxin PsTX-20A precursor (Pstx20)	0.04	-	mit	0	Secreted protein. Found in nematocyst				226
P01406 UniProt NPD GO	TX54_DENJA	Toxin S5C4	0.04	-	nuc	0	Secreted protein				60
P56855 UniProt NPD GO	TX1_SCOGR	Toxin SGTx1	0.04	-	cyt	0	Secreted protein			1LA4	34
P84631 UniProt NPD GO	SCX2_TITPA	Toxin Tpa2	0.04	-	nuc	0	Secreted protein				65
Q923Y8 UniProt NPD GO	TAAR1_MOUSE	Trace amine-associated receptor 1 (Trace amine receptor 1) (TaR-1)	0.04	-	end	6 *	Membrane; multi-pass membrane protein	integral to membrane [IC]			332
Q923X8 UniProt NPD GO	TAA7B_RAT	Trace amine-associated receptor 7b (Trace amine receptor 12) (TaR-12)	0.04	-	end	6 *	Membrane; multi-pass membrane protein				358
Q5QD09 UniProt NPD GO	TAA7E_MOUSE	Trace amine-associated receptor 7e	0.04	-	end	6 *	Membrane; multi-pass membrane protein				358
Q5QD08 UniProt NPD GO	TAA7F_MOUSE	Trace amine-associated receptor 7f	0.04	-	end	7 *	Membrane; multi-pass membrane protein				358
Q8IUR0 UniProt NPD GO	TPPC5_HUMAN	Trafficking protein particle complex subunit 5	0.04	-	mit	0	Golgi apparatus; cis-Golgi network (By similarity)				188
Q9D289 UniProt NPD GO	TPC6B_MOUSE	Trafficking protein particle complex subunit 6B	0.04	-	cyt	0	Golgi apparatus; cis-Golgi network (By similarity)				158
Q6BHA5 UniProt NPD GO	SPT4_DEBHA	Transcription elongation factor SPT4 (Chromatin elongation factor SPT4)	0.04	-	cyt	0	Nucleus. Centromere and heterochromatin (By similarity)				112
P32774 UniProt NPD GO	TOA2_YEAST	Transcription initiation factor IIA small subunit (TFIIA 13.5 kDa subunit)	0.04	-	cyt	0	Nucleus	transcription factor TFIIA complex [IDA]		1YTF	122
P01135 UniProt NPD GO	TGFA_HUMAN	Transforming growth factor alpha precursor (TGF-alpha) (EGF-like TGF) (ETGF) (TGF type 1)	0.04	-	end	1	Precursor form: Cell membrane; single-pass type I membrane protein. Mature form: Secreted protein; e ...	plasma membrane [NAS]	190170	4TGF	160
Q06922 UniProt NPD GO	TGFA_PIG	Transforming growth factor alpha precursor (TGF-alpha) (EGF-like TGF) (ETGF) (TGF type 1)	0.04	-	end	1	Precursor form: Cell membrane; single-pass type I membrane protein. Mature form: Secreted protein; e ...				160
P19966 UniProt NPD GO	TAGL_CHICK	Transgelin (Smooth muscle protein 22-alpha) (SM22-alpha)	0.04	-	nuc	0	Cytoplasm (Probable)				199
Q8WHY8 UniProt NPD GO	IF1C_PSINU	Translation initiation factor IF-1, chloroplast	0.04	-	cyt	0	Plastid; chloroplast				80
P87163 UniProt NPD GO	EI2BE_CANAL	Translation initiation factor eIF-2B subunit epsilon (eIF-2B GDP-GTP exchange factor subunit epsilon ...	0.04	-	cyt	0					189
Q66HG5 UniProt NPD GO	TM9S2_RAT	Transmembrane 9 superfamily protein member 2 precursor	0.04	-	end	9	Endosome; endosomal membrane; multi-pass membrane protein (Probable)				663
Q9ET30 UniProt NPD GO	TM9S3_MOUSE	Transmembrane 9 superfamily protein member 3 precursor	0.04	-	end	9	Membrane; multi-pass membrane protein (Probable)				587
Q92544 UniProt NPD GO	TM9S4_HUMAN	Transmembrane 9 superfamily protein member 4	0.04	-	end	9	Membrane; multi-pass membrane protein (Probable)				625
Q96A25 UniProt NPD GO	T106A_HUMAN	Transmembrane protein 106A	0.04	-	mit	1	Membrane; single-pass membrane protein (Potential)				262
Q2M3R5 UniProt NPD GO	TMM20_HUMAN	Transmembrane protein 20	0.04	-	end	10	Membrane; multi-pass membrane protein (Potential)				365
Q9H2L4 UniProt NPD GO	TMM60_HUMAN	Transmembrane protein 60	0.04	-	end	4 *	Membrane; multi-pass membrane protein (Potential)				133
Q8K174 UniProt NPD GO	TMM60_MOUSE	Transmembrane protein 60	0.04	-	end	4 *	Membrane; multi-pass membrane protein (Potential)				133
Q6ZNR0 UniProt NPD GO	TMM91_HUMAN	Transmembrane protein 91	0.04	-	end	2	Membrane; multi-pass membrane protein (Potential)				172

You are viewing entries 78601 to 78650 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.