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
P54828 UniProt NPD GO	TSHB_CANFA	Thyrotropin beta chain precursor (Thyroid-stimulating hormone beta subunit) (TSH-beta) (TSH-B)	0.02	-	vac	0	Secreted protein				138
Q28376 UniProt NPD GO	TSHB_HORSE	Thyrotropin beta chain precursor (Thyroid-stimulating hormone beta subunit) (TSH-beta) (TSH-B)	0.02	-	exc	0	Secreted protein				138
P79357 UniProt NPD GO	TSHB_LAMGL	Thyrotropin beta chain precursor (Thyroid-stimulating hormone beta subunit) (TSH-beta) (TSH-B)	0.02	-	end	0	Secreted protein				138
P04652 UniProt NPD GO	TSHB_RAT	Thyrotropin beta chain precursor (Thyroid-stimulating hormone beta subunit) (TSH-beta) (TSH-B)	0.02	-	exc	0	Secreted protein				138
P01223 UniProt NPD GO	TSHB_BOVIN	Thyrotropin beta chain precursor (Thyroid-stimulating hormone subunit beta) (TSH-beta) (TSH-B)	0.02	-	exc	0	Secreted protein				138
P12656 UniProt NPD GO	TSHB_MOUSE	Thyrotropin beta chain precursor (Thyroid-stimulating hormone subunit beta) (TSH-beta) (TSH-B)	0.02	-	exc	0	Secreted protein				138
P15223 UniProt NPD GO	SCX1_CENNO	Toxin 1 precursor (Toxin II.14) (Cn1)	0.02	-	exc	0	Secreted protein				86
P69944 UniProt NPD GO	AETX2_ANEER	Toxin AETX-2 (AETX II)	0.02	-	nuc	0	Secreted protein. Found in nematocyst				59
P69945 UniProt NPD GO	AETX3_ANEER	Toxin AETX-3 (AETX III)	0.02	-	nuc	0	Secreted protein. Found in nematocyst				59
P0C1F2 UniProt NPD GO	TXA21_ANTEL	Toxin APE 2-1	0.02	-	nuc	0	Secreted protein (Probable). Found in nematocyst (Probable)				47
P61789 UniProt NPD GO	TX5A_HETVE	Toxin AU5A	0.02	-	nuc	0	Secreted protein				37
P58608 UniProt NPD GO	ADO1_AGRDO	Toxin Ado1	0.02	-	nuc	0	Secreted protein			1LMR	35
P58604 UniProt NPD GO	TXC9_CUPSA	Toxin CSTX-9	0.02	-	nuc	0	Secreted protein				68
P59899 UniProt NPD GO	SC2B_CENLL	Toxin Cll 2b precursor (Cll2b) (Toxin II.6)	0.02	-	mit	0	Secreted protein				87
P08900 UniProt NPD GO	SCX2_CENSU	Toxin Css II (CssII)	0.02	-	nuc	0	Secreted protein				66
P60266 UniProt NPD GO	SCX4_CENSU	Toxin Css IV (CssIV)	0.02	-	cyt	0	Secreted protein				66
P60264 UniProt NPD GO	SC29_CENLL	Toxin II.9 (Fragment)	0.02	-	nuc	0	Secreted protein				29
P84679 UniProt NPD GO	SC33_TITCA	Toxin Tc33 (Fragment)	0.02	-		0	Secreted protein	extracellular region [IDA]			10
P84686 UniProt NPD GO	SC46_TITCA	Toxin Tc46 (Fragment)	0.02	-		0	Secreted protein	extracellular region [IDA]			10
P60212 UniProt NPD GO	SC48A_TITCA	Toxin Tc48a	0.02	-	nuc	0	Secreted protein	extracellular region [IDA]			65
P60213 UniProt NPD GO	SC49A_TITCA	Toxin Tc48b/Tc49a (Fragment)	0.02	-	nuc	0	Secreted protein	extracellular region [IDA]			39
P84691 UniProt NPD GO	SC61_TITCA	Toxin Tc61 (Fragment)	0.02	-		0	Secreted protein	extracellular region [IDA]			10
P84692 UniProt NPD GO	SC64_TITCA	Toxin Tc64 (Fragment)	0.02	-		0	Secreted protein	extracellular region [IDA]			10
P60263 UniProt NPD GO	SCX4_TITDI	Toxin TdII-4 (Fragment)	0.02	-	nuc	0	Secreted protein				27
P0C1G1 UniProt NPD GO	UP1_URTPI	Toxin Up-1 (UpI) (Fragment)	0.02	-	nuc	0	Secreted protein. Found in nematocyst				46
Q4LCS9 UniProt NPD GO	TXA22_ANDAU	Toxin-like peptide AaF1CA22 precursor (Neurotoxin KAaH2)	0.02	-	exc	0	Secreted protein	extracellular region [IDA]			80
Q4LCS8 UniProt NPD GO	TXA25_ANDAU	Toxin-like peptide AaF1CA25 precursor (Neurotoxin AaBTX-L1)	0.02	-	end	1 *	Secreted protein	extracellular region [IDA]			82
Q4LCS7 UniProt NPD GO	TXA26_ANDAU	Toxin-like peptide AaF1CA26 precursor	0.02	-	exc	1 *	Secreted protein (By similarity)	extracellular region [ISS]			80
Q4LCT2 UniProt NPD GO	TXA5_ANDAU	Toxin-like peptide AaF1CA5 precursor	0.02	-	end	0	Secreted protein (By similarity)	extracellular region [ISS]			81
Q4LCT1 UniProt NPD GO	TXA7_ANDAU	Toxin-like peptide AaF1CA7 precursor	0.02	-	exc	1 *	Secreted protein (By similarity)	extracellular region [ISS]			75
Q4LCT0 UniProt NPD GO	TXA8_ANDAU	Toxin-like peptide AaF1CA8 precursor (Neurotoxin KAaH1)	0.02	-	end	0	Secreted protein	extracellular region [IDA]			80
Q923Y9 UniProt NPD GO	TAAR1_RAT	Trace amine-associated receptor 1 (Trace amine receptor 1) (TaR-1)	0.02	-	end	7 *	Membrane; multi-pass membrane protein				332
Q5QD17 UniProt NPD GO	TAAR2_MOUSE	Trace amine-associated receptor 2 (G-protein coupled receptor 58)	0.02	-	end	6 *	Membrane; multi-pass membrane protein				339
Q5QD25 UniProt NPD GO	TAAR2_RAT	Trace amine-associated receptor 2 (G-protein coupled receptor 58)	0.02	-	end	7 *	Membrane; multi-pass membrane protein				339
Q5QD15 UniProt NPD GO	TAAR4_MOUSE	Trace amine-associated receptor 4	0.02	-	end	7 *	Membrane; multi-pass membrane protein				347
Q5QD28 UniProt NPD GO	TAAR5_PANTR	Trace amine-associated receptor 5	0.02	-	end	7 *	Membrane; multi-pass membrane protein				337
O14804 UniProt NPD GO	TAAR5_HUMAN	Trace amine-associated receptor 5 (Putative neurotransmitter receptor)	0.02	-	end	7 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	607405		337
Q96RI9 UniProt NPD GO	TAAR9_HUMAN	Trace amine-associated receptor 9 (Trace amine receptor 3) (TaR-3)	0.02	-	end	7 *	Membrane; multi-pass membrane protein	integral to membrane [IC]	608282		348
P25068 UniProt NPD GO	TAP_BOVIN	Tracheal antimicrobial peptide precursor (TAP)	0.02	-	end	0	Secreted protein				64
Q5ZI57 UniProt NPD GO	TPPC3_CHICK	Trafficking protein particle complex subunit 3	0.02	-	cyt	0	Golgi apparatus; cis-Golgi network (By similarity)				180
Q5U1Z2 UniProt NPD GO	TPPC3_RAT	Trafficking protein particle complex subunit 3	0.02	-	cyt	0	Golgi apparatus; cis-Golgi network (By similarity)				180
O43617 UniProt NPD GO	TPPC3_HUMAN	Trafficking protein particle complex subunit 3 (BET3 homolog)	0.02	-	cyt	0	Golgi apparatus; cis-Golgi network (By similarity)			2C0J	180
O55013 UniProt NPD GO	TPPC3_MOUSE	Trafficking protein particle complex subunit 3 (BET3 homolog)	0.02	-	cyt	0	Golgi apparatus; cis-Golgi network (By similarity)	cytosol [IDA] Golgi membrane [IDA]		1WC9	180
Q5F359 UniProt NPD GO	TPPC5_CHICK	Trafficking protein particle complex subunit 5	0.02	-	cyt	0	Golgi apparatus; cis-Golgi network (By similarity)				188
P34214 UniProt NPD GO	TAL1_KLULA	Transaldolase (EC 2.2.1.2)	0.02	-	cyt	0					333
P15019 UniProt NPD GO	TAL1_YEAST	Transaldolase (EC 2.2.1.2)	0.02	-	mit	0					334
Q9BZ97 UniProt NPD GO	TTY13_HUMAN	Transcript Y 13 protein	0.02	-	nuc	1 *					58
Q752J8 UniProt NPD GO	SPT4_ASHGO	Transcription elongation factor SPT4 (Chromatin elongation factor SPT4)	0.02	-	cyt	0	Nucleus. Centromere and heterochromatin (By similarity)				102
P81205 UniProt NPD GO	SPT4_KLULA	Transcription elongation factor SPT4 (Chromatin elongation factor SPT4)	0.02	-	nuc	0	Nucleus (By similarity). Centromere and heterochromatin (By similarity)				102
P32914 UniProt NPD GO	SPT4_YEAST	Transcription elongation factor SPT4 (Chromatin elongation factor SPT4)	0.02	-	cyt	0	Nucleus. Centromere and heterochromatin	DSIF complex [IPI] kinetochore [IDA] nuclear chromosome, telomeric region [IDA] nucleus [IPI]			102

You are viewing entries 85951 to 86000 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.