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
P98012 UniProt NPD GO	COX2_BETVU	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.05	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				260
Q8HEC3 UniProt NPD GO	COX2_CAEBR	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.05	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein	mitochondrial inner membrane [ISS]			231
P24894 UniProt NPD GO	COX2_CAEEL	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.05	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein	mitochondrial inner membrane [NAS]			231
P98027 UniProt NPD GO	COX2_CHEME	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.05	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				227
P50684 UniProt NPD GO	COX2_COTJA	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.05	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				227
P50662 UniProt NPD GO	COX2_CRACA	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.05	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				227
P00405 UniProt NPD GO	COX2_MOUSE	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.05	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				227
O47675 UniProt NPD GO	COX2_NYCPR	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.05	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				227
P98046 UniProt NPD GO	COX2_TARSY	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.05	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				227
O48276 UniProt NPD GO	COX2_UROCI	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.05	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				227
O47673 UniProt NPD GO	COX2_VULZE	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.05	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				227
Q8SEM9 UniProt NPD GO	COX2_CAERE	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II) (Fragment)	0.05	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein	mitochondrial inner membrane [ISS]			230
Q7YFV7 UniProt NPD GO	COX2_ASHGO	Cytochrome c oxidase subunit 2 precursor (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.05	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				248
P41312 UniProt NPD GO	COX3_DIDMA	Cytochrome c oxidase subunit 3 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide III)	0.05	-	end	7 *					281
P20609 UniProt NPD GO	COXE_DICDI	Cytochrome c oxidase subunit 7e (EC 1.9.3.1) (Cytochrome c oxidase polypeptide VIIe)	0.05	-	cyt	1 *	Mitochondrion; mitochondrial inner membrane				52
O60397 UniProt NPD GO	COX7S_HUMAN	Cytochrome c oxidase subunit VIIa 3, mitochondrial precursor	0.05	-	mit	0	Mitochondrion (By similarity)		123997		106
P80976 UniProt NPD GO	COX6B_THUOB	Cytochrome c oxidase subunit VIb (EC 1.9.3.1) (COX VIb) (Fragments)	0.05	-	nuc	0					34
P80430 UniProt NPD GO	CX6B1_RAT	Cytochrome c oxidase subunit VIb isoform 1 (EC 1.9.3.1) (COX VIb-1) (Fragment)	0.05	-		0	Mitochondrion; mitochondrial intermembrane space (By similarity)				8
P62897 UniProt NPD GO	CYC_MOUSE	Cytochrome c, somatic	0.05	-	cyt	0	Mitochondrion; mitochondrial matrix	cytosol [IDA] mitochondrion [IDA] soluble fraction [IDA]			104
P62898 UniProt NPD GO	CYC_RAT	Cytochrome c, somatic	0.05	-	cyt	0	Mitochondrion; mitochondrial matrix				104
Q9TLW2 UniProt NPD GO	CY550_CYACA	Cytochrome c-550 precursor (Cytochrome c550)	0.05	-	mit	0	Plastid; chloroplast				164
P08197 UniProt NPD GO	CYC6_CHLRE	Cytochrome c6, chloroplast precursor (Soluble cytochrome f) (Cytochrome c553) (Cytochrome c-553) (Cy ...	0.05	-	mit	0	Plastid; chloroplast; chloroplast thylakoid lumen			1CYJ	148
Q8WWM9 UniProt NPD GO	CYGB_HUMAN	Cytoglobin (Histoglobin) (HGb) (Stellate cell activation-associated protein)	0.05	-	cyt	0	Cytoplasm (By similarity)	cytoplasm [NAS]	608759	2DC3	190
Q9FUJ2 UniProt NPD GO	CKX4_ARATH	Cytokinin dehydrogenase 4 precursor (EC 1.5.99.12) (Cytokinin oxidase 4) (CKO 4) (AtCKX4)	0.05	-	mit	1 *	Secreted protein; extracellular space				524
P0C1F8 UniProt NPD GO	ACTS2_RADMA	Cytolysin RTX-S-2 (RTX-S II) (Fragment)	0.05	-	cyt	0	Secreted protein. Found in nematocyst				147
P83775 UniProt NPD GO	CAP2_CANAL	Cytoplasmic antigenic protein 2 (Fragments)	0.05	-		0	Cytoplasm				19
Q9MYX7 UniProt NPD GO	CTLA4_PIG	Cytotoxic T-lymphocyte protein 4 precursor (Cytotoxic T-lymphocyte-associated antigen 4) (CTLA-4) (C ...	0.05	-	end	1	Membrane; single-pass type I membrane protein				223
P01527 UniProt NPD GO	CXA3_CERLA	Cytotoxin A-III (Cytolysin A-III)	0.05	-	nuc	0	Secreted protein				95
O43175 UniProt NPD GO	SERA_HUMAN	D-3-phosphoglycerate dehydrogenase (EC 1.1.1.95) (3-PGDH)	0.05	-	cyt	0			606879		532
Q60HD7 UniProt NPD GO	SERA_MACFA	D-3-phosphoglycerate dehydrogenase (EC 1.1.1.95) (3-PGDH)	0.05	-	cyt	0					532
Q5R7M2 UniProt NPD GO	SERA_PONPY	D-3-phosphoglycerate dehydrogenase (EC 1.1.1.95) (3-PGDH)	0.05	-	cyt	0					532
P00371 UniProt NPD GO	OXDA_PIG	D-amino-acid oxidase (EC 1.4.3.3) (DAMOX) (DAO) (DAAO)	0.05	-	mit	0	Peroxisome			1VE9	347
Q99042 UniProt NPD GO	OXDA_TRIVR	D-amino-acid oxidase (EC 1.4.3.3) (DAMOX) (DAO) (DAAO)	0.05	-	cyt	0					356
P50166 UniProt NPD GO	ARDH_CANTR	D-arabinitol 2-dehydrogenase [ribulose-forming] (EC 1.1.1.250) (ARDH)	0.05	-	mit	0					282
Q6FT39 UniProt NPD GO	DTD_CANGA	D-tyrosyl-tRNA(Tyr) deacylase (EC 3.1.-.-)	0.05	-	mit	0	Cytoplasm (By similarity)				149
Q07648 UniProt NPD GO	DTD_YEAST	D-tyrosyl-tRNA(Tyr) deacylase (EC 3.1.-.-)	0.05	-	cyt	0	Cytoplasm (Probable)	cytoplasm [IDA]			150
O43036 UniProt NPD GO	RPA4_SCHPO	DNA-dependent RNA polymerase 19 kDa polypeptide (EC 2.7.7.6) (A43)	0.05	-	cyt	0	Nucleus (By similarity)				173
Q9P1U0 UniProt NPD GO	RPA12_HUMAN	DNA-directed RNA polymerase I subunit 12 (EC 2.7.7.6) (Nuclear RNA polymerase I small-specific subun ...	0.05	-	cyt	0	Nucleus (Potential)				126
Q5TM50 UniProt NPD GO	RPA12_MACMU	DNA-directed RNA polymerase I subunit 12 (EC 2.7.7.6) (Nuclear RNA polymerase I small-specific subun ...	0.05	-	cyt	0	Nucleus (Potential)				126
Q1XHV8 UniProt NPD GO	RPA12_PANTR	DNA-directed RNA polymerase I subunit 12 (EC 2.7.7.6) (Nuclear RNA polymerase I small-specific subun ...	0.05	-	cyt	0	Nucleus (Potential)				126
Q6DRI4 UniProt NPD GO	RPO1D_BRARE	DNA-directed RNA polymerase I subunit D (EC 2.7.7.6)	0.05	-	cyt	0	Nucleus (By similarity)				112
Q39212 UniProt NPD GO	RPB3B_ARATH	DNA-directed RNA polymerase II 36 kDa polypeptide B (EC 2.7.7.6) (RNA polymerase II subunit 3)	0.05	-	cyt	0	Nucleus				319
Q9SYA6 UniProt NPD GO	RPB10_ARATH	DNA-directed RNA polymerase II 8.2 kDa polypeptide (EC 2.7.7.6) (RPB10) (RP10) (ABC10)	0.05	-	cyt	0	Nucleus				71
Q39290 UniProt NPD GO	RPB10_BRANA	DNA-directed RNA polymerase II 8.2 kDa polypeptide (EC 2.7.7.6) (RPB10) (RP10) (ABC10)	0.05	-	cyt	0	Nucleus				71
P19587 UniProt NPD GO	RPOA_SCEOB	DNA-directed RNA polymerase alpha chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase subunit a ...	0.05	-	cyt	0	Plastid; chloroplast				129
P36595 UniProt NPD GO	RPB6_SCHPO	DNA-directed RNA polymerases I, II, and III 15 kDa polypeptide (EC 2.7.7.6) (RPABC6)	0.05	-	cyt	0	Nucleus	DNA-directed RNA polymerase I complex [IGI] DNA-directed RNA polymerase II, holoenzyme [IGI] DNA-directed RNA polymerase III complex [IGI]			142
Q7M458 UniProt NPD GO	DGP_HELAS	Dart gland peptide	0.05	-	nuc	0	Secreted protein				21
Q9BTZ2 UniProt NPD GO	DHRS4_HUMAN	Dehydrogenase/reductase SDR family member 4 (EC 1.1.1.184) (NADPH-dependent carbonyl reductase/NADP- ...	0.05	-	cyt	0	Peroxisome	mitochondrion [ISS]			260
Q8HYR6 UniProt NPD GO	DHRS9_BOVIN	Dehydrogenase/reductase SDR family member 9 precursor (EC 1.1.-.-) (3-alpha hydroxysteroid dehydroge ...	0.05	+	mit	0	Cytoplasm (By similarity). Microsome; microsomal membrane (By similarity). Associated with microsoma ...	integral to endoplasmic reticulum membrane [ISS] microsome [ISS]			319
O76062 UniProt NPD GO	ERG24_HUMAN	Delta(14)-sterol reductase (EC 1.3.1.70) (C-14 sterol reductase) (Sterol C14-reductase) (Delta14-SR) ...	0.05	-	end	7 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein	endoplasmic reticulum [TAS] integral to plasma membrane [TAS]	603414		418

You are viewing entries 74251 to 74300 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.