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
P56856 UniProt NPD GO	CLD18_HUMAN	Claudin-18	0.02	-	end	4 *	Cell membrane; cell-cell junction; tight junction; multi-pass membrane protein	integral to membrane [ISS] tight junction [ISS]	609210		261
Q8N6F1 UniProt NPD GO	CLD19_HUMAN	Claudin-19	0.02	-	end	4 *	Cell membrane; cell-cell junction; tight junction; multi-pass membrane protein	integral to membrane [ISS] tight junction [ISS]			224
Q765P1 UniProt NPD GO	CLD2_BOVIN	Claudin-2	0.02	-	end	4 *	Cell membrane; cell-cell junction; tight junction; multi-pass membrane protein (By similarity)				230
O88552 UniProt NPD GO	CLD2_MOUSE	Claudin-2	0.02	-	end	4 *	Cell membrane; cell-cell junction; tight junction; multi-pass membrane protein	integral to membrane [NAS] tight junction [IDA]			230
Q765N9 UniProt NPD GO	CLD3_BOVIN	Claudin-3	0.02	-	end	4 *	Cell membrane; cell-cell junction; tight junction; multi-pass membrane protein (By similarity)				219
Q95KM5 UniProt NPD GO	CLD3_CANFA	Claudin-3	0.02	-	end	4 *	Cell membrane; cell-cell junction; tight junction; multi-pass membrane protein (By similarity)	integral to membrane [ISS] tight junction [ISS]			218
Q9Z0G9 UniProt NPD GO	CLD3_MOUSE	Claudin-3 (Clostridium perfringens enterotoxin receptor 2) (CPE-receptor 2) (CPE-R 2)	0.02	-	end	4 *	Cell membrane; cell-cell junction; tight junction; multi-pass membrane protein	integral to membrane [NAS] tight junction [IDA]			219
Q63400 UniProt NPD GO	CLD3_RAT	Claudin-3 (Ventral prostate.1 protein) (RVP1)	0.02	-	end	4 *	Cell membrane; cell-cell junction; tight junction; multi-pass membrane protein (By similarity)	integral to membrane [ISS] tight junction [ISS]			219
Q9Z261 UniProt NPD GO	CLD7_MOUSE	Claudin-7	0.02	-	end	4 *	Cell membrane; cell-cell junction; tight junction; multi-pass membrane protein	integral to membrane [NAS] tight junction [IDA]			211
O95471 UniProt NPD GO	CLD7_HUMAN	Claudin-7 (CLDN-7)	0.02	-	end	4 *	Cell membrane; cell-cell junction; tight junction; multi-pass membrane protein	integral to membrane [ISS] tight junction [ISS]	609131		211
P56748 UniProt NPD GO	CLD8_HUMAN	Claudin-8	0.02	-	end	4 *	Cell membrane; cell-cell junction; tight junction; multi-pass membrane protein (By similarity)	integral to membrane [ISS] tight junction [ISS]			225
Q9YH92 UniProt NPD GO	CLDX_BRARE	Claudin-like protein ZF4A22 (Claudin-7)	0.02	-	end	4 *	Membrane; multi-pass membrane protein				215
P16295 UniProt NPD GO	FA9_CAVPO	Coagulation factor IX (EC 3.4.21.22) (Christmas factor) (Fragment)	0.02	-	ves	0	Secreted protein				285
P16292 UniProt NPD GO	FA9_RABIT	Coagulation factor IX (EC 3.4.21.22) (Christmas factor) (Fragment)	0.02	-	cyt	0	Secreted protein				275
Q4PRD1 UniProt NPD GO	LC1_DABRU	Coagulation factor X-activating enzyme light chain 1 precursor (RVV-X light chain 1) (Coagulation fa ...	0.02	-	end	0	Secreted protein				146
Q7T045 UniProt NPD GO	LC1_VIPLE	Coagulation factor X-activating enzyme light chain 1 precursor (VLFXA light chain 1) [Contains: Coag ...	0.02	-	exc	0	Secreted protein				146
Q4PRD2 UniProt NPD GO	LC2_DABRU	Coagulation factor X-activating enzyme light chain 2 precursor (RVV-X light chain 1) (Coagulation fa ...	0.02	-	exc	0	Secreted protein				158
P84785 UniProt NPD GO	COCIN_PHACN	Coccinin (Fragment)	0.02	-		0					10
O43405 UniProt NPD GO	COCH_HUMAN	Cochlin precursor (COCH-5B2)	0.02	-	vac	0	Secreted protein; extracellular space; extracellular matrix		156000	1JBI	550
P02456 UniProt NPD GO	CO1A1_RABIT	Collagen alpha-1(I) chain (Fragment)	0.02	-	nuc	0					53
Q9BXJ4 UniProt NPD GO	C1QT3_HUMAN	Complement C1q tumor necrosis factor-related protein 3 precursor (Secretory protein CORS26)	0.02	-	exc	0	Secreted protein (Potential)				246
Q9ES30 UniProt NPD GO	C1QT3_MOUSE	Complement C1q tumor necrosis factor-related protein 3 precursor (Secretory protein CORS26)	0.02	-	exc	0	Secreted protein (Potential)	extracellular region [IDA]			246
Q8CFG8 UniProt NPD GO	CS1B_MOUSE	Complement C1s-B subcomponent precursor (EC 3.4.21.42) (C1 esterase) [Contains: Complement C1s-B sub ...	0.02	-	exc	0					688
P17684 UniProt NPD GO	CXKT_CONTU	Conantokin-T (Con-T)	0.02	-	nuc	0	Secreted protein			1ONT	21
P58922 UniProt NPD GO	CXG6_CONTE	Conotoxin Gla(1)-TxVI	0.02	-	nuc	0	Secreted protein				31
P58841 UniProt NPD GO	CX3A_CONQU	Conotoxin QcIIIA	0.02	-		0	Secreted protein				15
Q5K0B8 UniProt NPD GO	CXO1_CONIM	Conotoxin-1 precursor	0.02	+	end	0	Secreted protein (By similarity)				78
Q5K0D2 UniProt NPD GO	CXO9_CONST	Conotoxin-9 precursor	0.02	-	exc	0	Secreted protein (By similarity)				82
P82981 UniProt NPD GO	VSP2_AGKCO	Contortrixobin (EC 3.4.21.-)	0.02	-	cyt	0	Secreted protein (Potential)				234
P83047 UniProt NPD GO	COW_CONVE	Contryphan-Vn	0.02	-		0	Secreted protein			1NXN	9
O93426 UniProt NPD GO	CVXA_CRODU	Convulxin alpha precursor (CVX alpha)	0.02	-	exc	1 *				1UOS	158
O93427 UniProt NPD GO	CVXB_CRODU	Convulxin beta precursor (CVX beta)	0.02	-	exc	0				1UOS	148
O35372 UniProt NPD GO	CNIH_MOUSE	Cornichon homolog	0.02	-	end	3 *	Membrane; multi-pass membrane protein (Potential)				144
Q5BJU5 UniProt NPD GO	CNIH2_RAT	Cornichon homolog 2	0.02	-	end	3 *	Membrane; multi-pass membrane protein (Potential)				160
Q6PI25 UniProt NPD GO	CNIH2_HUMAN	Cornichon homolog 2 (Cornichon-like protein)	0.02	-	end	3 *	Membrane; multi-pass membrane protein (Potential)	integral to membrane [ISS]			160
O35089 UniProt NPD GO	CNIH2_MOUSE	Cornichon homolog 2 (Cornichon-like protein)	0.02	-	end	3 *	Membrane; multi-pass membrane protein (Potential)				160
P60606 UniProt NPD GO	CTXN1_HUMAN	Cortexin-1	0.02	-	nuc	1 *			600135		82
P50451 UniProt NPD GO	CBG_SAISC	Corticosteroid-binding globulin precursor (CBG) (Transcortin) (Serpin A6)	0.02	-	end	0	Secreted protein				406
Q12127 UniProt NPD GO	CCW12_YEAST	Covalently-linked cell wall protein 12 precursor (Protein Alpha0.6)	0.02	-	mit	0	Cell membrane; lipid-anchor; GPI-anchor (Potential)	cell wall (sensu Fungi) [IDA]			133
P09037 UniProt NPD GO	ANGT_CRIGE	Crinia-angiotensin-2 (Crinia-angiotensin II)	0.02	-		0	Secreted protein				11
P59685 UniProt NPD GO	CHH_LITSH	Crustacean hyperglycemic hormone (CHH)	0.02	-	cyt	0	Secreted protein				72
O97387 UniProt NPD GO	CHH5_PENMO	Crustacean hyperglycemic hormones 5 precursor (Pm-SGP-V) [Contains: CHH precursor-related peptide 5 ...	0.02	-	vac	0	Secreted protein				122
P45667 UniProt NPD GO	SCXR_CENLL	Crustacean-specific toxin 1 (Cll1)	0.02	-	nuc	0	Secreted protein				66
P83994 UniProt NPD GO	CU18A_LOCMI	Cuticle protein 18.6, isoform A (LM-18.6A) (LM-ACP 18.6A)	0.02	-	mit	0					185
P83995 UniProt NPD GO	CU18B_LOCMI	Cuticle protein 18.6, isoform B (LM-18.6B) (LM-ACP 18.6B)	0.02	-	mit	0					185
P82119 UniProt NPD GO	CUO6_BLACR	Cuticle protein 6 (BcNCP14.9)	0.02	-	cyt	0					139
P45584 UniProt NPD GO	CU63_LOCMI	Cuticle protein 63 (LM-63) (LM-ACP 63)	0.02	-	end	3 *					157
P11739 UniProt NPD GO	CU64_LOCMI	Cuticle protein 64 (LM-64) (LM-ACP 64)	0.02	-	end	4 *					152
P45585 UniProt NPD GO	CU65_LOCMI	Cuticle protein 65 (LM-65) (LM-ACP 65)	0.02	-	end	3 *					145
P81579 UniProt NPD GO	CUPA5_CANPG	Cuticle protein AM1274 (CPAM1274)	0.02	-	cyt	0					116

You are viewing entries 82851 to 82900 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.