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
P61209 UniProt NPD GO	ARF1_DROME	ADP-ribosylation factor 1	0.05	-	cyt	0					181
P61210 UniProt NPD GO	ARF1_LOCMI	ADP-ribosylation factor 1 (lARF1)	0.05	-	cyt	0					181
P19146 UniProt NPD GO	ARF2_YEAST	ADP-ribosylation factor 2	0.05	-	cyt	0		cytosol [TAS] Golgi-associated vesicle [TAS]		1MR3	180
Q9H0F7 UniProt NPD GO	ARL6_HUMAN	ADP-ribosylation factor-like protein 6 (Bardet-Biedl syndrome 3 protein)	0.05	-	cyt	0	Cytoplasm (By similarity)	cytoplasm [ISS] membrane [ISS]	608845		186
Q09767 UniProt NPD GO	ARL_SCHPO	ADP-ribosylation factor-like protein alp41 (Altered polarity protein 41)	0.05	-	nuc	0					186
O46373 UniProt NPD GO	ADT1_RABIT	ADP/ATP translocase 1 (Adenine nucleotide translocator 1) (ANT 1) (ADP,ATP carrier protein 1) (Solut ...	0.05	-	cyt	3	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)				297
P12235 UniProt NPD GO	ADT1_HUMAN	ADP/ATP translocase 1 (Adenine nucleotide translocator 1) (ANT 1) (ADP,ATP carrier protein 1) (Solut ...	0.05	-	cyt	3	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein	integral to plasma membrane [TAS] mitochondrion [TAS]	609283		297
P48962 UniProt NPD GO	ADT1_MOUSE	ADP/ATP translocase 1 (Adenine nucleotide translocator 1) (ANT 1) (ADP,ATP carrier protein 1) (Solut ...	0.05	-	cyt	3	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein	mitochondrial inner membrane [IDA]			297
P12236 UniProt NPD GO	ADT3_HUMAN	ADP/ATP translocase 3 (Adenine nucleotide translocator 2) (ANT 3) (ADP,ATP carrier protein 3) (Solut ...	0.05	-	cyt	2	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein	mitochondrial inner membrane presequence tr... [TAS]	403000		297
Q3SYW1 UniProt NPD GO	AP1M2_BOVIN	AP-1 complex subunit mu-2 (Adaptor-related protein complex 1 mu-2 subunit) (Mu-adaptin 2) (Adaptor p ...	0.05	-	cyt	0	Component of the coat surrounding the cytoplasmic face of coated vesicles located at the Golgi compl ...				422
Q9Y6Q5 UniProt NPD GO	AP1M2_HUMAN	AP-1 complex subunit mu-2 (Adaptor-related protein complex 1 mu-2 subunit) (Mu-adaptin 2) (Adaptor p ...	0.05	-	cyt	0	Component of the coat surrounding the cytoplasmic face of coated vesicles located at the Golgi compl ...		607309		422
Q9WVP1 UniProt NPD GO	AP1M2_MOUSE	AP-1 complex subunit mu-2 (Adaptor-related protein complex 1 mu-2 subunit) (Mu-adaptin 2) (Adaptor p ...	0.05	-	cyt	0	Component of the coat surrounding the cytoplasmic face of coated vesicles located at the Golgi compl ...	Golgi trans face [TAS]			422
Q9Y7L6 UniProt NPD GO	AP2S_SCHPO	AP-2 complex subunit sigma (Clathrin assembly protein 2 small chain) (Adaptin small chain)	0.05	-	nuc	0	Component of the coat surrounding the cytoplasmic face of the plasma membrane coated vesicles (By si ...				143
Q9Y2T2 UniProt NPD GO	AP3M1_HUMAN	AP-3 complex subunit mu-1 (Adapter-related protein complex 3 mu-1 subunit) (Mu-adaptin 3A) (AP-3 ada ...	0.05	-	cyt	0		lysosome [TAS]			418
Q9JKC8 UniProt NPD GO	AP3M1_MOUSE	AP-3 complex subunit mu-1 (Adapter-related protein complex 3 mu-1 subunit) (Mu-adaptin 3A) (AP-3 ada ...	0.05	-	cyt	0					418
P53676 UniProt NPD GO	AP3M1_RAT	AP-3 complex subunit mu-1 (Adapter-related protein complex 3 mu-1 subunit) (Mu-adaptin 3A) (AP-3 ada ...	0.05	-	cyt	0					418
P53677 UniProt NPD GO	AP3M2_HUMAN	AP-3 complex subunit mu-2 (Adapter-related protein complex 3 mu-2 subunit) (Clathrin coat assembly p ...	0.05	-	cyt	0		membrane coat adaptor complex [TAS]			418
P53678 UniProt NPD GO	AP3M2_RAT	AP-3 complex subunit mu-2 (Adapter-related protein complex 3 mu-2 subunit) (Clathrin coat assembly p ...	0.05	-	cyt	0	Component of the coat surrounding the cytoplasmic face of coated vesicles located at the Golgi compl ...				418
Q8R2R9 UniProt NPD GO	AP3M2_MOUSE	AP-3 complex subunit mu-2 (Adapter-related protein complex 3 mu-2 subunit) (Clathrin coat assembly p ...	0.05	-	cyt	0	Component of the coat surrounding the cytoplasmic face of coated vesicles located at the Golgi compl ...				418
Q9FT52 UniProt NPD GO	ATPQ_ARATH	ATP synthase D chain, mitochondrial (EC 3.6.3.14)	0.05	-	cyt	0	Mitochondrion				167
P48894 UniProt NPD GO	ATP6_FELCA	ATP synthase a chain (EC 3.6.3.14) (ATPase protein 6)	0.05	-	end	6 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				226
Q9ZZY6 UniProt NPD GO	ATP6_HIPAM	ATP synthase a chain (EC 3.6.3.14) (ATPase protein 6)	0.05	-	end	6 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				226
P48662 UniProt NPD GO	ATP6_HORSE	ATP synthase a chain (EC 3.6.3.14) (ATPase protein 6)	0.05	-	end	6 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				226
Q95706 UniProt NPD GO	ATP6_HYLLA	ATP synthase a chain (EC 3.6.3.14) (ATPase protein 6)	0.05	-	vac	5 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				226
O03169 UniProt NPD GO	ATP6_LATCH	ATP synthase a chain (EC 3.6.3.14) (ATPase protein 6)	0.05	-	end	5 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				220
P00848 UniProt NPD GO	ATP6_MOUSE	ATP synthase a chain (EC 3.6.3.14) (ATPase protein 6)	0.05	-	end	6 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				226
O63912 UniProt NPD GO	ATP6_MYXGL	ATP synthase a chain (EC 3.6.3.14) (ATPase protein 6)	0.05	-	end	6 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				228
Q9T9W9 UniProt NPD GO	ATP6_PANPA	ATP synthase a chain (EC 3.6.3.14) (ATPase protein 6)	0.05	-	end	6 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				226
P92695 UniProt NPD GO	ATP6_PONPA	ATP synthase a chain (EC 3.6.3.14) (ATPase protein 6)	0.05	-	end	5 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				226
O79406 UniProt NPD GO	ATP6_SCYCA	ATP synthase a chain (EC 3.6.3.14) (ATPase protein 6)	0.05	-	end	6 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				227
Q9ZZ49 UniProt NPD GO	ATP6_SQUAC	ATP synthase a chain (EC 3.6.3.14) (ATPase protein 6)	0.05	-	end	6 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				227
P00852 UniProt NPD GO	ATP6_EMENI	ATP synthase a chain precursor (EC 3.6.3.14) (ATPase protein 6)	0.05	-	end	6 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				256
P56525 UniProt NPD GO	ATPD_NEUCR	ATP synthase delta chain, mitochondrial precursor (EC 3.6.3.14)	0.05	-	mit	0	Mitochondrion				165
Q96252 UniProt NPD GO	ATP4_ARATH	ATP synthase delta' chain, mitochondrial precursor (EC 3.6.3.14)	0.05	-	mit	0	Mitochondrion				203
Q41000 UniProt NPD GO	ATP4_PEA	ATP synthase delta' chain, mitochondrial precursor (EC 3.6.3.14)	0.05	-	mit	0	Mitochondrion				197
P32979 UniProt NPD GO	ATPE_CHLVU	ATP synthase epsilon chain (EC 3.6.3.14) (ATP synthase F1 sector epsilon subunit)	0.05	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				134
Q9TM40 UniProt NPD GO	ATPE_CYACA	ATP synthase epsilon chain (EC 3.6.3.14) (ATP synthase F1 sector epsilon subunit)	0.05	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				133
Q6ENG8 UniProt NPD GO	ATPE_ORYNI	ATP synthase epsilon chain (EC 3.6.3.14) (ATP synthase F1 sector epsilon subunit)	0.05	-	nuc	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				137
P12086 UniProt NPD GO	ATPE_ORYSA	ATP synthase epsilon chain (EC 3.6.3.14) (ATP synthase F1 sector epsilon subunit)	0.05	-	nuc	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				137
P84559 UniProt NPD GO	ATPE_POPEU	ATP synthase epsilon chain (EC 3.6.3.14) (ATP synthase F1 sector epsilon subunit) (Fragment)	0.05	-		0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				11
O94377 UniProt NPD GO	ATPK_SCHPO	ATP synthase f chain, mitochondrial precursor (EC 3.6.3.14)	0.05	-	nuc	0					96
Q5JCK6 UniProt NPD GO	ATP8_AEDAL	ATP synthase protein 8 (EC 3.6.3.14) (ATPase subunit 8) (A6L)	0.05	-	mit	1 *	Mitochondrion; mitochondrial membrane; single-pass membrane protein				53
Q32643 UniProt NPD GO	ATP8_CAPHI	ATP synthase protein 8 (EC 3.6.3.14) (ATPase subunit 8) (A6L)	0.05	-	nuc	1 *	Mitochondrion; mitochondrial membrane; single-pass membrane protein				65
P07513 UniProt NPD GO	ATP8_OENBE	ATP synthase protein 8 (EC 3.6.3.14) (ATPase subunit 8) (A6L)	0.05	-	cyt	0	Mitochondrion; mitochondrial membrane; single-pass membrane protein				59
Q9T9D5 UniProt NPD GO	ATP8_PAROL	ATP synthase protein 8 (EC 3.6.3.14) (ATPase subunit 8) (A6L)	0.05	-	mit	1 *	Mitochondrion; mitochondrial membrane; single-pass membrane protein				55
Q95912 UniProt NPD GO	ATP8_POLOR	ATP synthase protein 8 (EC 3.6.3.14) (ATPase subunit 8) (A6L)	0.05	-	nuc	1 *	Mitochondrion; mitochondrial membrane; single-pass membrane protein				55
Q9XN35 UniProt NPD GO	ATP8_SALFO	ATP synthase protein 8 (EC 3.6.3.14) (ATPase subunit 8) (A6L)	0.05	-	vac	1 *	Mitochondrion; mitochondrial membrane; single-pass membrane protein				55
Q9ZZ50 UniProt NPD GO	ATP8_SQUAC	ATP synthase protein 8 (EC 3.6.3.14) (ATPase subunit 8) (A6L)	0.05	-	nuc	1 *	Mitochondrion; mitochondrial membrane; single-pass membrane protein				55
O74190 UniProt NPD GO	ATPO_KLULA	ATP synthase subunit 5, mitochondrial precursor (EC 3.6.3.14) (Oligomycin sensitivity conferral prot ...	0.05	-	mit	0	Mitochondrion				206
Q08807 UniProt NPD GO	ATPB_GALSU	ATP synthase subunit beta (EC 3.6.3.14) (ATPase subunit beta) (ATP synthase F1 sector subunit beta)	0.05	-	nuc	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				476

You are viewing entries 73651 to 73700 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.