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
Q2QLE2 UniProt NPD GO	CAV2_PIG	Caveolin-2	0.01	-	end	2	Golgi apparatus; Golgi membrane; peripheral membrane protein; cytoplasmic side (By similarity). Memb ...				162
P83660 UniProt NPD GO	C146_CYPDO	Cd-146 peptide	0.01	-		0	Secreted protein	extracellular space [IDA]			16
P83403 UniProt NPD GO	CEC_GLOMR	Cecropin	0.01	-	cyt	0	Secreted protein				39
Q06589 UniProt NPD GO	CEC1_CERCA	Cecropin-1 precursor	0.01	-	mit	1 *	Secreted protein				63
P83413 UniProt NPD GO	CECA_HELVI	Cecropin-A	0.01	-	nuc	0	Secreted protein				35
Q27239 UniProt NPD GO	CECA_BOMMO	Cecropin-A precursor	0.01	-	end	1 *	Secreted protein				63
Q86PR6 UniProt NPD GO	CECA_CULPP	Cecropin-A precursor	0.01	-	end	1 *	Secreted protein (By similarity)				59
P50724 UniProt NPD GO	CECA_TRINI	Cecropin-A precursor	0.01	-	exc	1 *	Secreted protein				62
P01507 UniProt NPD GO	CECA_HYACE	Cecropin-A precursor (Cecropin-C)	0.01	-	end	1 *	Secreted protein			1F0H	64
Q9XZG9 UniProt NPD GO	CECA_SPOLT	Cecropin-A precursor (Fragment)	0.01	-	mit	0	Secreted protein (By similarity)				57
P82290 UniProt NPD GO	CECA_ANOGA	Cecropin-A precursor [Contains: Cecropin-A; Cecropin-A amidated isoform]	0.01	-	end	0	Secreted protein				58
P81685 UniProt NPD GO	CECA1_DROMA	Cecropin-A1 precursor	0.01	-	vac	1 *	Secreted protein	extracellular region [ISS]			63
P81688 UniProt NPD GO	CECA1_DROSE	Cecropin-A1 precursor	0.01	-	vac	1 *	Secreted protein	extracellular region [ISS]			63
O61272 UniProt NPD GO	CECA1_DROSI	Cecropin-A1 precursor	0.01	-	vac	1 *	Secreted protein	extracellular region [ISS]			63
P81417 UniProt NPD GO	CECA1_AEDAL	Cecropin-A1 precursor (Cecropin-A) (AalCecA)	0.01	-	exc	1 *	Secreted protein				59
Q963B0 UniProt NPD GO	CECA2_AEDAL	Cecropin-A2 precursor	0.01	-	exc	1 *	Secreted protein (By similarity)				59
P01509 UniProt NPD GO	CECB_ANTPE	Cecropin-B	0.01	-	cyt	0	Secreted protein				35
P83414 UniProt NPD GO	CECB_HELVI	Cecropin-B (Fragment)	0.01	-	cyt	0	Secreted protein				33
Q8MUF4 UniProt NPD GO	CECB_ANOGA	Cecropin-B precursor	0.01	-	end	1 *	Secreted protein (By similarity)				60
Q9XZH0 UniProt NPD GO	CECB_SPOLT	Cecropin-B precursor (Fragment)	0.01	-	mit	0	Secreted protein (By similarity)				58
P01508 UniProt NPD GO	CECB_HYACE	Cecropin-B precursor (Immune protein P9)	0.01	-	end	1 *	Secreted protein				62
P04142 UniProt NPD GO	CECB_BOMMO	Cecropin-B precursor (Lepidopteran-A/B)	0.01	-	end	1 *	Secreted protein				63
Q9Y0Y0 UniProt NPD GO	CECB1_AEDAL	Cecropin-B type 1 precursor (Cecropin-B1) [Contains: Cecropin-B (AalCecB); Cecropin-B amidated isofo ...	0.01	-	exc	1 *	Secreted protein				60
Q963A9 UniProt NPD GO	CECB2_AEDAL	Cecropin-B type 2 precursor (Cecropin-B2) [Contains: Cecropin-B (AalCecB); Cecropin-B amidated isofo ...	0.01	-	exc	1 *	Secreted protein				60
Q9Y0X9 UniProt NPD GO	CECC1_AEDAL	Cecropin-C type 1 precursor (Cecropin-C1) [Contains: Cecropin-C (AalCecC)]	0.01	-	exc	0	Secreted protein				59
Q963A8 UniProt NPD GO	CECC2_AEDAL	Cecropin-C type 2 precursor (Cecropin-C2) [Contains: Cecropin-C (AalCecC)]	0.01	-	exc	1 *	Secreted protein				59
O76146 UniProt NPD GO	CECD_BOMMO	Cecropin-D precursor	0.01	-	vac	1 *	Secreted protein				61
Q07987 UniProt NPD GO	DAN2_YEAST	Cell wall protein DAN2 precursor	0.01	-	cyt	1 *					124
P52755 UniProt NPD GO	QID3_TRIHA	Cell wall protein qid3 precursor	0.01	-	nuc	0	Cell wall (Potential)				143
O42386 UniProt NPD GO	RABP1_FUGRU	Cellular retinoic acid-binding protein 1 (Cellular retinoic acid-binding protein I) (CRABP-I) (Retin ...	0.01	-	nuc	0	Cytoplasm				136
Q5R2J5 UniProt NPD GO	RABP1_TRISI	Cellular retinoic acid-binding protein 1 (Cellular retinoic acid-binding protein I) (CRABP-I) (Retin ...	0.01	-	nuc	0	Cytoplasm (By similarity)				136
P22935 UniProt NPD GO	RABP2_MOUSE	Cellular retinoic acid-binding protein 2 (Cellular retinoic acid-binding protein II) (CRABP-II) (Ret ...	0.01	-	cyt	0	Cytoplasm				137
P51673 UniProt NPD GO	RABP2_RAT	Cellular retinoic acid-binding protein 2 (Cellular retinoic acid-binding protein II) (CRABP-II) (Ret ...	0.01	-	cyt	0	Cytoplasm	cytoplasm [IDA]			138
P80027 UniProt NPD GO	OXYT_OCTVU	Cephalotocin	0.01	-		0	Secreted protein				9
Q8IUK8 UniProt NPD GO	CBLN2_HUMAN	Cerebellin-2 precursor	0.01	-	mit	0	Secreted protein (Potential)		600433		224
Q8BGU2 UniProt NPD GO	CBLN2_MOUSE	Cerebellin-2 precursor	0.01	-	vac	0	Secreted protein (Potential)				224
P98087 UniProt NPD GO	CBLN2_RAT	Cerebellin-2 precursor (Cerebellin-like protein)	0.01	-	exc	0	Secreted protein (Potential)				224
Q10998 UniProt NPD GO	CP1_APLCA	Cerebral peptide 1 (CP1)	0.01	-		0					13
Q08704 UniProt NPD GO	CFI_MAIZE	Chalcone--flavonone isomerase (EC 5.5.1.6) (Chalcone isomerase)	0.01	-	mit	0					231
P11650 UniProt NPD GO	CFIA_PETHY	Chalcone--flavonone isomerase A (EC 5.5.1.6) (Chalcone isomerase A)	0.01	-	cyt	0					241
P11651 UniProt NPD GO	CFIB_PETHY	Chalcone--flavonone isomerase B (EC 5.5.1.6) (Chalcone isomerase B)	0.01	-	cyt	0					220
Q75ZH0 UniProt NPD GO	CCRL2_PIG	Chemokine C-C motif receptor-like 2	0.01	-	end	7 *	Membrane; multi-pass membrane protein (By similarity)				350
P97468 UniProt NPD GO	CML1_MOUSE	Chemokine receptor-like 1 (G-protein coupled receptor DEZ)	0.01	-	end	7 *	Membrane; multi-pass membrane protein				371
P42718 UniProt NPD GO	CHEP_PARID	Chemotactic peptide	0.01	-		0					13
O13842 UniProt NPD GO	CDA1_SCHPO	Chitin deacetylase 1 (EC 3.5.1.41)	0.01	-	cyt	0		spore wall (sensu Fungi) [TAS]			320
P30577 UniProt NPD GO	CHS2_AJECA	Chitin synthase 2 (EC 2.4.1.16) (Chitin-UDP acetyl-glucosaminyl transferase 2) (Class-III chitin syn ...	0.01	-	mit	0	Cell membrane; multi-pass membrane protein				194
P30587 UniProt NPD GO	CHS3_EXOJE	Chitin synthase 3 (EC 2.4.1.16) (Chitin-UDP acetyl-glucosaminyl transferase 3) (Class-III chitin syn ...	0.01	-	cyt	0	Cell membrane; multi-pass membrane protein				197
Q9WUB7 UniProt NPD GO	CLCKA_MOUSE	Chloride channel protein ClC-Ka (Chloride channel Ka) (ClC-K1)	0.01	-	end	10 *	Membrane; multi-pass membrane protein				687
Q06393 UniProt NPD GO	CLCKA_RAT	Chloride channel protein ClC-Ka (Chloride channel Ka) (ClC-K1)	0.01	-	end	8 *	Membrane; multi-pass membrane protein				687
P14584 UniProt NPD GO	CB21_RAPSA	Chlorophyll a-b binding of LHCII type 1 protein (Chlorophyll a-b binding of LHCII type I protein) (C ...	0.01	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				124

You are viewing entries 87051 to 87100 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.