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
Q5ZLP2 UniProt NPD GO	APIP_CHICK	APAF1-interacting protein homolog	0.02	-	mit	0	Cytoplasm (By similarity)				242
Q6NU29 UniProt NPD GO	APIP_XENLA	APAF1-interacting protein homolog	0.02	-	cyt	0	Cytoplasm (By similarity)				239
Q6CID6 UniProt NPD GO	HIS1_KLULA	ATP phosphoribosyltransferase (EC 2.4.2.17) (ATP-PRTase) (ATP-PRT)	0.02	-	cyt	0	Cytoplasm (By similarity)				297
Q5JCK5 UniProt NPD GO	ATP6_AEDAL	ATP synthase a chain (EC 3.6.3.14) (ATPase protein 6)	0.02	-	end	5 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				226
P50363 UniProt NPD GO	ATP6_ALLAR	ATP synthase a chain (EC 3.6.3.14) (ATPase protein 6)	0.02	-	end	6 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				262
P50364 UniProt NPD GO	ATP6_ALLMA	ATP synthase a chain (EC 3.6.3.14) (ATPase protein 6)	0.02	-	end	6 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				262
Q37708 UniProt NPD GO	ATP6_ARTSF	ATP synthase a chain (EC 3.6.3.14) (ATPase protein 6)	0.02	-	end	6 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				219
P24876 UniProt NPD GO	ATP6_ASCSU	ATP synthase a chain (EC 3.6.3.14) (ATPase protein 6)	0.02	-	end	5 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				199
Q33823 UniProt NPD GO	ATP6_ASTPE	ATP synthase a chain (EC 3.6.3.14) (ATPase protein 6)	0.02	-	end	6 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				230
Q9MIY5 UniProt NPD GO	ATP6_BRARE	ATP synthase a chain (EC 3.6.3.14) (ATPase protein 6)	0.02	-	end	6 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				227
Q7IV55 UniProt NPD GO	ATP6_DROMA	ATP synthase a chain (EC 3.6.3.14) (ATPase protein 6)	0.02	-	end	6 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein	mitochondrion [ISS]			224
P00850 UniProt NPD GO	ATP6_DROME	ATP synthase a chain (EC 3.6.3.14) (ATPase protein 6)	0.02	-	end	6 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein	mitochondrion [NAS]			224
Q7IV45 UniProt NPD GO	ATP6_DROSE	ATP synthase a chain (EC 3.6.3.14) (ATPase protein 6)	0.02	-	end	6 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				224
P50269 UniProt NPD GO	ATP6_DROSI	ATP synthase a chain (EC 3.6.3.14) (ATPase protein 6)	0.02	-	end	6 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				224
P00851 UniProt NPD GO	ATP6_DROYA	ATP synthase a chain (EC 3.6.3.14) (ATPase protein 6)	0.02	-	end	6 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				224
P55778 UniProt NPD GO	ATP6_GADMO	ATP synthase a chain (EC 3.6.3.14) (ATPase protein 6)	0.02	-	end	6 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				227
P07925 UniProt NPD GO	ATP6_MAIZE	ATP synthase a chain (EC 3.6.3.14) (ATPase protein 6)	0.02	-	end	4 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				291
Q38PR7 UniProt NPD GO	ATP6_MAMPR	ATP synthase a chain (EC 3.6.3.14) (ATPase protein 6)	0.02	-	end	6 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				222
Q00224 UniProt NPD GO	ATP6_MYTED	ATP synthase a chain (EC 3.6.3.14) (ATPase protein 6)	0.02	-	end	5 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				238
P00849 UniProt NPD GO	ATP6_XENLA	ATP synthase a chain (EC 3.6.3.14) (ATPase protein 6)	0.02	-	end	6 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				226
P37212 UniProt NPD GO	ATP6_NEUCR	ATP synthase a chain precursor (EC 3.6.3.14) (ATPase protein 6)	0.02	-	end	6 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				252
Q36918 UniProt NPD GO	ATP6_PENCH	ATP synthase a chain precursor (EC 3.6.3.14) (ATPase protein 6)	0.02	-	end	6 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				257
Q36258 UniProt NPD GO	ATP6_YARLI	ATP synthase a chain precursor (EC 3.6.3.14) (ATPase protein 6)	0.02	-	end	6 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				255
P93298 UniProt NPD GO	ATP61_ARATH	ATP synthase a chain precursor 1 (EC 3.6.3.14) (ATPase protein 6) (P6-1)	0.02	-	end	7	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				385
Q9TM27 UniProt NPD GO	ATPD_CYACA	ATP synthase delta chain, chloroplast (EC 3.6.3.14)	0.02	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane				183
Q09544 UniProt NPD GO	ATPD_CAEEL	ATP synthase delta chain, mitochondrial precursor (EC 3.6.3.14)	0.02	-	mit	0	Mitochondrion				163
Q95312 UniProt NPD GO	ATPD_PIG	ATP synthase delta chain, mitochondrial precursor (EC 3.6.3.14) (Fragment)	0.02	-	mit	0	Mitochondrion				80
P30159 UniProt NPD GO	ATPE_DICDH	ATP synthase epsilon chain (EC 3.6.3.14) (ATP synthase F1 sector epsilon subunit)	0.02	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				139
Q08808 UniProt NPD GO	ATPE_GALSU	ATP synthase epsilon chain (EC 3.6.3.14) (ATP synthase F1 sector epsilon subunit)	0.02	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				138
Q6B8S5 UniProt NPD GO	ATPE_GRATL	ATP synthase epsilon chain (EC 3.6.3.14) (ATP synthase F1 sector epsilon subunit)	0.02	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				134
Q9MUT4 UniProt NPD GO	ATPE_MESVI	ATP synthase epsilon chain (EC 3.6.3.14) (ATP synthase F1 sector epsilon subunit)	0.02	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				133
Q9TJR8 UniProt NPD GO	ATPE_PROWI	ATP synthase epsilon chain (EC 3.6.3.14) (ATP synthase F1 sector epsilon subunit)	0.02	-	cyt	0	Plastid; plastid membrane; peripheral membrane protein (By similarity)				134
Q96253 UniProt NPD GO	ATP5E_ARATH	ATP synthase epsilon chain, mitochondrial (EC 3.6.3.14)	0.02	-	nuc	0	Mitochondrion				69
P29418 UniProt NPD GO	ATP5E_RAT	ATP synthase epsilon chain, mitochondrial (EC 3.6.3.14)	0.02	-	mit	0	Mitochondrion				50
Q3ZC75 UniProt NPD GO	AT5G3_BOVIN	ATP synthase lipid-binding protein, mitochondrial precursor (EC 3.6.3.14) (ATP synthase proteolipid ...	0.02	-	nuc	2	Mitochondrion; mitochondrial membrane; multi-pass membrane protein (By similarity)				141
Q08076 UniProt NPD GO	ATP8_ALBTU	ATP synthase protein 8 (EC 3.6.3.14) (ATPase subunit 8) (A6L)	0.02	-	mit	1 *	Mitochondrion; mitochondrial membrane; single-pass membrane protein				52
O47427 UniProt NPD GO	ATP8_BRAFL	ATP synthase protein 8 (EC 3.6.3.14) (ATPase subunit 8) (A6L)	0.02	-	exc	1 *	Mitochondrion; mitochondrial membrane; single-pass membrane protein				54
O21003 UniProt NPD GO	ATP8_BRALA	ATP synthase protein 8 (EC 3.6.3.14) (ATPase subunit 8) (A6L)	0.02	-	exc	1 *	Mitochondrion; mitochondrial membrane; single-pass membrane protein				54
P24948 UniProt NPD GO	ATP8_CYPCA	ATP synthase protein 8 (EC 3.6.3.14) (ATPase subunit 8) (A6L)	0.02	-	mit	1 *	Mitochondrion; mitochondrial membrane; single-pass membrane protein				54
Q36362 UniProt NPD GO	ATP8_DICLA	ATP synthase protein 8 (EC 3.6.3.14) (ATPase subunit 8) (A6L)	0.02	-	nuc	1 *	Mitochondrion; mitochondrial membrane; single-pass membrane protein				55
Q00608 UniProt NPD GO	ATP8_KLULA	ATP synthase protein 8 (EC 3.6.3.14) (ATPase subunit 8) (A6L)	0.02	-	pox	1 *	Mitochondrion; mitochondrial membrane; single-pass membrane protein				48
P15997 UniProt NPD GO	ATP8_STRPU	ATP synthase protein 8 (EC 3.6.3.14) (ATPase subunit 8) (A6L)	0.02	-	nuc	1 *	Mitochondrion; mitochondrial membrane; single-pass membrane protein				55
Q75EZ3 UniProt NPD GO	ATPO_ASHGO	ATP synthase subunit 5, mitochondrial precursor (EC 3.6.3.14) (Oligomycin sensitivity conferral prot ...	0.02	-	mit	0	Mitochondrion				207
P62626 UniProt NPD GO	ATPB_AEGCO	ATP synthase subunit beta (EC 3.6.3.14) (ATPase subunit beta) (ATP synthase F1 sector subunit beta)	0.02	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				498
P62614 UniProt NPD GO	ATPB_AEGCR	ATP synthase subunit beta (EC 3.6.3.14) (ATPase subunit beta) (ATP synthase F1 sector subunit beta)	0.02	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				498
P19366 UniProt NPD GO	ATPB_ARATH	ATP synthase subunit beta (EC 3.6.3.14) (ATPase subunit beta) (ATP synthase F1 sector subunit beta)	0.02	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				498
Q8S8W8 UniProt NPD GO	ATPB_ATRBE	ATP synthase subunit beta (EC 3.6.3.14) (ATPase subunit beta) (ATP synthase F1 sector subunit beta)	0.02	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				498
P30399 UniProt NPD GO	ATPB_CUSRE	ATP synthase subunit beta (EC 3.6.3.14) (ATPase subunit beta) (ATP synthase F1 sector subunit beta)	0.02	-	cyt	0	Plastid; plastid thylakoid membrane; peripheral membrane protein (By similarity)				490
Q9TM41 UniProt NPD GO	ATPB_CYACA	ATP synthase subunit beta (EC 3.6.3.14) (ATPase subunit beta) (ATP synthase F1 sector subunit beta)	0.02	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				490
O78491 UniProt NPD GO	ATPB_GUITH	ATP synthase subunit beta (EC 3.6.3.14) (ATPase subunit beta) (ATP synthase F1 sector subunit beta)	0.02	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				475

You are viewing entries 82251 to 82300 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.