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
P00652 UniProt NPD GO	RNC2_ASPCL	Guanyl-specific ribonuclease C2 (EC 3.1.27.3) (RNase C-2)	0.02	-	cyt	0	Secreted protein				104
P10282 UniProt NPD GO	RNF1_GIBFU	Guanyl-specific ribonuclease F1 precursor (EC 3.1.27.3) (RNase F1)	0.02	-	exc	0				1RCL	131
Q9P6I5 UniProt NPD GO	KGUA_SCHPO	Guanylate kinase (EC 2.7.4.8) (GMP kinase)	0.02	-	cyt	0					202
P79897 UniProt NPD GO	GUC2A_PIG	Guanylin precursor (Guanylate cyclase activator 2A)	0.02	-	exc	0	Secreted protein				109
O73763 UniProt NPD GO	GCIP_RANPI	Guanylyl cyclase inhibitory protein	0.02	-	cyt	0					205
P43081 UniProt NPD GO	GUC1A_MOUSE	Guanylyl cyclase-activating protein 1 (GCAP 1) (Guanylate cyclase activator 1A)	0.02	-	cyt	0	Membrane; lipid-anchor				201
O95843 UniProt NPD GO	GUC1C_HUMAN	Guanylyl cyclase-activating protein 3 (GCAP 3) (Guanylate cyclase activator 1C)	0.02	-	cyt	0			605128		208
Q04456 UniProt NPD GO	EST1_CAEBR	Gut esterase 1 precursor (EC 3.1.1.1) (Non-specific carboxylesterase)	0.02	-	end	0	Endoplasmic reticulum; endoplasmic reticulum lumen				562
P20036 UniProt NPD GO	HA2Q_HUMAN	HLA class II histocompatibility antigen, DP alpha chain precursor (HLA-SB alpha chain) (MHC class II ...	0.02	-	end	1 *	Membrane; single-pass type I membrane protein (By similarity)	integral to plasma membrane [NAS]	142880		260
P13760 UniProt NPD GO	2B14_HUMAN	HLA class II histocompatibility antigen, DRB1-4 beta chain precursor (MHC class I antigen DRB1*4) (D ...	0.02	-	end	1 *	Membrane; single-pass type I membrane protein		142857	2SEB	266
Q5R611 UniProt NPD GO	HRSL3_PONPY	HRAS-like suppressor 3 (H-rev 107 protein homolog)	0.02	-	cyt	1					162
P53816 UniProt NPD GO	HRSL3_HUMAN	HRAS-like suppressor 3 (H-rev 107 protein homolog) (HREV107-3) (NY-REN-65 antigen)	0.02	-	cyt	1					162
Q9S760 UniProt NPD GO	HA22D_ARATH	HVA22-like protein d (AtHVA22d)	0.02	-	end	3 *	Membrane; multi-pass membrane protein (Potential)				135
P83464 UniProt NPD GO	TXHA3_SELHA	Hainantoxin-3 (Hainantoxin-III) (HnTx-III)	0.02	-	nuc	0	Secreted protein	extracellular region [NAS]			33
P50417 UniProt NPD GO	HPT_ATEGE	Haptoglobin precursor [Contains: Haptoglobin alpha chain; Haptoglobin beta chain]	0.02	-	exc	0	Secreted protein (By similarity)				347
P81672 UniProt NPD GO	HSP70_PINPS	Heat shock 70 kDa protein (Fragment)	0.02	-		0					11
P20147 UniProt NPD GO	HSP90_PLAFP	Heat shock 90 kDa protein homolog (Fragment)	0.02	-	nuc	0					193
P19882 UniProt NPD GO	HSP60_YEAST	Heat shock protein 60, mitochondrial precursor (Stimulator factor I 66 kDa component) (P66) (CPN60)	0.02	-	mit	0	Mitochondrion; mitochondrial matrix	mitochondrial nucleoid [IDA] mitochondrion [IDA]			572
P02244 UniProt NPD GO	HEMT_PHAGO	Hemerythrin	0.02	-	cyt	0				1I4Z	113
P23544 UniProt NPD GO	HEMTB_LINRE	Hemerythrin beta chain	0.02	-	cyt	0					117
Q10584 UniProt NPD GO	HCYB_MEGCR	Hemocyanin B chain (KLH-B) (Fragment)	0.02	-		0	Secreted protein; extracellular space				12
Q9NFL4 UniProt NPD GO	HCYG_EURCA	Hemocyanin G chain (HcG)	0.02	-	nuc	0	Secreted protein; extracellular space	extracellular space [ISS]			628
P83174 UniProt NPD GO	HCY1_CANPG	Hemocyanin subunit 1 (Fragment)	0.02	-	nuc	0	Secreted protein; extracellular space				23
P82302 UniProt NPD GO	HCY1_MAISQ	Hemocyanin subunit 1 (Fragment)	0.02	-	cyt	0	Secreted protein; extracellular space				21
P84619 UniProt NPD GO	HCYA_CONCC	Hemocyanin subunit A (CCH-A) (Fragment)	0.02	-		0	Secreted protein; extracellular space				11
P82311 UniProt NPD GO	HCYIB_PANJA	Hemocyanin subunit Ib (Fragment)	0.02	-		0	Secreted protein; extracellular space				20
P83134 UniProt NPD GO	HBAD_ALDEL	Hemoglobin D subunit alpha (Hemoglobin D alpha chain)	0.02	-	cyt	0				1WMU	141
P80945 UniProt NPD GO	HBAA_ANGAN	Hemoglobin anodic subunit alpha (Hemoglobin anodic alpha chain)	0.02	-	cyt	0					142
P84203 UniProt NPD GO	HBAC_GYMUN	Hemoglobin cathodic subunit alpha (Hemoglobin cathodic alpha chain)	0.02	-	cyt	0					143
P11896 UniProt NPD GO	HBA3_PLEWA	Hemoglobin larval subunit alpha (Hemoglobin alpha-chain, larval) (Alpha-globin, larval)	0.02	-	cyt	0					142
P01971 UniProt NPD GO	HBA_ALCAA	Hemoglobin subunit alpha (Hemoglobin alpha chain) (Alpha-globin)	0.02	-	cyt	0					141
P14387 UniProt NPD GO	HBA_ANTPA	Hemoglobin subunit alpha (Hemoglobin alpha chain) (Alpha-globin)	0.02	-	cyt	0					141
P67817 UniProt NPD GO	HBA_ATEGE	Hemoglobin subunit alpha (Hemoglobin alpha chain) (Alpha-globin)	0.02	-	cyt	0					141
P01969 UniProt NPD GO	HBA_BOSGF	Hemoglobin subunit alpha (Hemoglobin alpha chain) (Alpha-globin)	0.02	-	cyt	0					141
P01966 UniProt NPD GO	HBA_BOVIN	Hemoglobin subunit alpha (Hemoglobin alpha chain) (Alpha-globin)	0.02	-	cyt	0				1HDA	141
P18972 UniProt NPD GO	HBA_CALAR	Hemoglobin subunit alpha (Hemoglobin alpha chain) (Alpha-globin)	0.02	-	cyt	0					141
P63105 UniProt NPD GO	HBA_CAMBA	Hemoglobin subunit alpha (Hemoglobin alpha chain) (Alpha-globin)	0.02	-	cyt	0					141
P63106 UniProt NPD GO	HBA_CAMDR	Hemoglobin subunit alpha (Hemoglobin alpha chain) (Alpha-globin)	0.02	-	cyt	0					141
P01928 UniProt NPD GO	HBA_CEBAP	Hemoglobin subunit alpha (Hemoglobin alpha chain) (Alpha-globin)	0.02	-	cyt	0					141
P07421 UniProt NPD GO	HBA_CEBCA	Hemoglobin subunit alpha (Hemoglobin alpha chain) (Alpha-globin)	0.02	-	cyt	0					141
P01926 UniProt NPD GO	HBA_CERAE	Hemoglobin subunit alpha (Hemoglobin alpha chain) (Alpha-globin)	0.02	-	cyt	0					141
P01933 UniProt NPD GO	HBA_CERTO	Hemoglobin subunit alpha (Hemoglobin alpha chain) (Alpha-globin)	0.02	-	cyt	0					141
Q7M2Y4 UniProt NPD GO	HBA_CHAMP	Hemoglobin subunit alpha (Hemoglobin alpha chain) (Alpha-globin)	0.02	-	cyt	0					141
P01930 UniProt NPD GO	HBA_COLBA	Hemoglobin subunit alpha (Hemoglobin alpha chain) (Alpha-globin)	0.02	-	cyt	0					141
P02016 UniProt NPD GO	HBA_CYPCA	Hemoglobin subunit alpha (Hemoglobin alpha chain) (Alpha-globin)	0.02	-	cyt	0					142
P01964 UniProt NPD GO	HBA_DASNO	Hemoglobin subunit alpha (Hemoglobin alpha chain) (Alpha-globin)	0.02	-	cyt	0					141
P01959 UniProt NPD GO	HBA_EQUAS	Hemoglobin subunit alpha (Hemoglobin alpha chain) (Alpha-globin)	0.02	-	cyt	0				1S0H	141
P01960 UniProt NPD GO	HBA_EQUZE	Hemoglobin subunit alpha (Hemoglobin alpha chain) (Alpha-globin)	0.02	-	cyt	0					141
P01949 UniProt NPD GO	HBA_ERIEU	Hemoglobin subunit alpha (Hemoglobin alpha chain) (Alpha-globin)	0.02	-	cyt	0					141
P01936 UniProt NPD GO	HBA_EULFU	Hemoglobin subunit alpha (Hemoglobin alpha chain) (Alpha-globin)	0.02	-	cyt	0					141

You are viewing entries 83701 to 83750 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.