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
P38186 UniProt NPD GO	YBH0_YEAST	Very hypothetical protein YBL070C	0.03	-	nuc	2 *	Membrane; multi-pass membrane protein (Potential)				106
P38168 UniProt NPD GO	YBK0_YEAST	Very hypothetical protein YBL100C	0.03	-	mit	1					104
Q2NKV8 UniProt NPD GO	GOT1A_BOVIN	Vesicle transport protein GOT1A (Golgi transport 1 homolog A)	0.03	-	end	4 *	Golgi apparatus; Golgi membrane; multi-pass membrane protein (By similarity)				132
Q6ZVE7 UniProt NPD GO	GOT1A_HUMAN	Vesicle transport protein GOT1A (Golgi transport 1 homolog A) (hGOT1b)	0.03	-	end	4 *	Golgi apparatus; Golgi membrane; multi-pass membrane protein (By similarity)				132
Q5SSN7 UniProt NPD GO	SFT2A_MOUSE	Vesicle transport protein SFT2A (SFT2 domain-containing protein 1)	0.03	-	end	4 *	Membrane; multi-pass membrane protein (Potential)				159
Q5U3Y5 UniProt NPD GO	SFT2A_RAT	Vesicle transport protein SFT2A (SFT2 domain-containing protein 1)	0.03	-	end	4 *	Membrane; multi-pass membrane protein (Potential)				159
O95562 UniProt NPD GO	SFT2B_HUMAN	Vesicle transport protein SFT2B (SFT2 domain-containing protein 2)	0.03	-	end	4 *	Membrane; multi-pass membrane protein (Potential)				160
Q4FZV2 UniProt NPD GO	SFT2B_RAT	Vesicle transport protein SFT2B (SFT2 domain-containing protein 2)	0.03	-	end	4 *	Membrane; multi-pass membrane protein (Potential)				157
P25803 UniProt NPD GO	CYSEP_PHAVU	Vignain precursor (EC 3.4.22.-) (Bean endopeptidase) (Cysteine proteinase EP-C1)	0.03	-	end	0	Endoplasmic reticulum; endoplasmic reticulum lumen				362
P12412 UniProt NPD GO	CYSEP_VIGMU	Vignain precursor (EC 3.4.22.-) (Bean endopeptidase) (Cysteine proteinase) (Sulfhydryl-endopeptidase ...	0.03	-	end	0	Endoplasmic reticulum; endoplasmic reticulum lumen. Protein body				362
P51473 UniProt NPD GO	OPSV_XENLA	Violet-sensitive opsin (Violet cone photoreceptor pigment) (Violet cone opsin)	0.03	-	end	7 *	Membrane; multi-pass membrane protein				347
Q8N0U8 UniProt NPD GO	VKORL_HUMAN	Vitamin K epoxide reductase complex subunit 1-like protein 1 (VKORC1-like protein 1)	0.03	-	end	2 *	Membrane; multi-pass membrane protein (Potential)		608838		176
Q6TEK5 UniProt NPD GO	VKORL_MOUSE	Vitamin K epoxide reductase complex subunit 1-like protein 1 (VKORC1-like protein 1)	0.03	-	end	4 *	Membrane; multi-pass membrane protein (Potential)				176
Q6TEK3 UniProt NPD GO	VKORL_RAT	Vitamin K epoxide reductase complex subunit 1-like protein 1 (VKORC1-like protein 1)	0.03	-	end	4 *	Membrane; multi-pass membrane protein (Potential)				176
Q28315 UniProt NPD GO	PROC_CAPHI	Vitamin K-dependent protein C (EC 3.4.21.69) (Autoprothrombin IIA) (Anticoagulant protein C) (Blood ...	0.03	-	cyt	0					157
P19009 UniProt NPD GO	VITA1_XENLA	Vitellogenin-A1 precursor (VTG A1) (Fragment)	0.03	-	exc	0					71
P19011 UniProt NPD GO	VITB2_XENLA	Vitellogenin-B2 precursor (VTG B2) (Fragment)	0.03	-	exc	0					71
P83840 UniProt NPD GO	VITA_VIOAR	Vitri peptide A	0.03	-	nuc	0					30
P21796 UniProt NPD GO	VDAC1_HUMAN	Voltage-dependent anion-selective channel protein 1 (VDAC-1) (hVDAC1) (Outer mitochondrial membrane ...	0.03	-	cyt	0	Mitochondrion; mitochondrial outer membrane. Cell membrane	mitochondrial outer membrane [TAS] mitochondrion [TAS]	604492		282
Q9MZ15 UniProt NPD GO	VDAC2_PIG	Voltage-dependent anion-selective channel protein 2	0.03	-	cyt	0	Mitochondrion; mitochondrial outer membrane (By similarity)				294
P68003 UniProt NPD GO	VDAC2_RABIT	Voltage-dependent anion-selective channel protein 2 (Outer mitochondrial membrane protein porin 2)	0.03	-	cyt	0	Mitochondrion; mitochondrial outer membrane (By similarity)				294
P82013 UniProt NPD GO	VDAC2_MELGA	Voltage-dependent anion-selective channel protein 2 (VDAC-2) (Outer mitochondrial membrane protein p ...	0.03	-	nuc	0	Mitochondrion; mitochondrial outer membrane (By similarity)				282
Q29380 UniProt NPD GO	VDAC3_PIG	Voltage-dependent anion-selective channel protein 3 (VDAC-3) (Outer mitochondrial membrane protein p ...	0.03	-	cyt	0	Mitochondrion; mitochondrial outer membrane				283
P97707 UniProt NPD GO	CCG1_RAT	Voltage-dependent calcium channel gamma-1 subunit (Dihydropyridine-sensitive L-type, skeletal muscle ...	0.03	-	end	4 *	Membrane; multi-pass membrane protein				223
Q8MI69 UniProt NPD GO	WFDC2_PIG	WAP four-disulfide core domain protein 2 precursor (Epididymal secretory protein E4)	0.03	-	exc	1 *	Secreted protein (Potential)				123
Q9W5Z5 UniProt NPD GO	WSB1_FUGRU	WD repeat and SOCS box-containing protein 1 (WSB-1)	0.03	-	cyt	0					427
O75083 UniProt NPD GO	WDR1_HUMAN	WD repeat protein 1 (Actin-interacting protein 1) (AIP1) (NORI-1)	0.03	-	cyt	0			604734		605
P61964 UniProt NPD GO	WDR5_HUMAN	WD repeat protein 5 (BMP2-induced 3-kb gene protein)	0.03	-	nuc	0			609012	2GNQ	334
P61965 UniProt NPD GO	WDR5_MOUSE	WD repeat protein 5 (BMP2-induced 3-kb gene protein) (WD repeat protein BIG-3)	0.03	-	nuc	0		intracellular [IDA]			334
P53196 UniProt NPD GO	YGA4_YEAST	WD repeat protein YGL004C	0.03	-	cyt	0		cytoplasm [IDA]			417
O22466 UniProt NPD GO	MSI1_LYCES	WD-40 repeat protein MSI1	0.03	-	cyt	0	Nucleus				424
Q969T9 UniProt NPD GO	WBP2_HUMAN	WW domain-binding protein 2 (WBP-2)	0.03	-	nuc	0			606962		261
P97765 UniProt NPD GO	WBP2_MOUSE	WW domain-binding protein 2 (WBP-2)	0.03	-	nuc	0					261
Q8R478 UniProt NPD GO	WBP2_RAT	WW domain-binding protein 2 (WBP-2)	0.03	-	nuc	0					262
Q09022 UniProt NPD GO	XEN1_XENLA	Xenoxin-1 precursor	0.03	-	exc	0	Secreted protein	extracellular region [IDA]			84
Q7GCM7 UniProt NPD GO	XIP1_ORYSA	Xylanase inhibitor protein 1 precursor (Class III chitinase homolog a) (RIXI protein)	0.03	-	exc	1 *	Secreted protein (Potential)				304
Q53NL5 UniProt NPD GO	XIP2_ORYSA	Xylanase inhibitor protein 2 precursor (Class III chitinase homolog h)	0.03	-	exc	0	Secreted protein (Potential)				290
Q8VDQ1 UniProt NPD GO	ZADH1_MOUSE	Zinc-binding alcohol dehydrogenase domain-containing protein 1 (EC 1.-.-.-)	0.03	-	cyt	0	Cytoplasm (By similarity)			1VJ1	351
Q32KR8 UniProt NPD GO	ADPRH_BOVIN	[Protein ADP-ribosylarginine] hydrolase (EC 3.2.2.19) (ADP-ribosylarginine hydrolase) (ADP-ribose-L- ...	0.03	-	nuc	0					353
P54922 UniProt NPD GO	ADPRH_HUMAN	[Protein ADP-ribosylarginine] hydrolase (EC 3.2.2.19) (ADP-ribosylarginine hydrolase) (ADP-ribose-L- ...	0.03	-	cyt	0			603081		357
P84673 UniProt NPD GO	KNL3_PHYSA	[Val1,Thr6]-bradykinin	0.03	-		0	Secreted protein				9
P47058 UniProt NPD GO	TAD2_YEAST	tRNA-specific adenosine deaminase subunit TAD2 (EC 3.5.4.-) (tRNA-specific adenosine-34 deaminase su ...	0.03	-	mit	0		cytoplasm [IDA] nucleus [IDA]			250
P39714 UniProt NPD GO	BDH1_YEAST	(R,R)-butanediol dehydrogenase (EC 1.1.1.4)	0.02	-	mit	0		cytoplasm [IDA]			382
Q9LEL6 UniProt NPD GO	6OMT_COPJA	(RS)-norcoclaurine 6-O-methyltransferase (EC 2.1.1.128) (S-adenosyl-L-methionine:norcoclaurine 6-O-m ...	0.02	-	mit	0					347
Q8K3K7 UniProt NPD GO	PLCB_MOUSE	1-acyl-sn-glycerol-3-phosphate acyltransferase beta (EC 2.3.1.51) (1-AGP acyltransferase 2) (1-AGPAT ...	0.02	-	vac	3 *	Membrane; multi-pass membrane protein (Potential)	endoplasmic reticulum [IDA]			278
Q06588 UniProt NPD GO	ACCO1_ARATH	1-aminocyclopropane-1-carboxylate oxidase (EC 1.14.17.4) (ACC oxidase) (Ethylene-forming enzyme) (EF ...	0.02	-	cyt	0					323
Q8S932 UniProt NPD GO	ACCO_DIOKA	1-aminocyclopropane-1-carboxylate oxidase (EC 1.14.17.4) (ACC oxidase) (Ethylene-forming enzyme) (EF ...	0.02	-	cyt	0					318
P31239 UniProt NPD GO	ACCO_PEA	1-aminocyclopropane-1-carboxylate oxidase (EC 1.14.17.4) (ACC oxidase) (Ethylene-forming enzyme) (EF ...	0.02	-	cyt	0					317
Q00985 UniProt NPD GO	ACCO1_MALDO	1-aminocyclopropane-1-carboxylate oxidase 1 (EC 1.14.17.4) (ACC oxidase 1) (Ethylene-forming enzyme) ...	0.02	-	cyt	0					314
Q08508 UniProt NPD GO	ACCO4_PETHY	1-aminocyclopropane-1-carboxylate oxidase 4 (EC 1.14.17.4) (ACC oxidase 4) (Ethylene-forming enzyme) ...	0.02	-	cyt	0					319

You are viewing entries 82051 to 82100 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.