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
O35914 UniProt NPD GO	BNC1_MOUSE	Zinc finger protein basonuclin-1	0.85	+	nuc	0	Nucleus (By similarity). Cytoplasm (By similarity). Relocates to the midpiece of the flagellum durin ...				961
P78871 UniProt NPD GO	RST2_SCHPO	Zinc finger protein rst2	0.85	-	nuc	0	Nucleus (Probable)	cytoplasm [IDA] nucleus [IDA]			567
P57999 UniProt NPD GO	ZAN_RABIT	Zonadhesin (Fragment)	0.85	+	nuc	1	Cell membrane; single-pass type I membrane protein. Exclusively on the apical region of the sperm he ...				2282
Q7T3T8 UniProt NPD GO	ZAR1_BRARE	Zygote arrest 1 (Oocyte-specific maternal effect factor)	0.85	-	nuc	0	Cytoplasm (By similarity)				329
P15337 UniProt NPD GO	CREB1_RAT	cAMP response element-binding protein (CREB)	0.85	+	nuc	0	Nucleus	mitochondrion [IDA] nucleus [TAS]		1KDX	341
Q03061 UniProt NPD GO	CREM_RAT	cAMP-responsive element modulator	0.85	+	nuc	0	Nucleus				341
Q62865 UniProt NPD GO	PDE3A_RAT	cGMP-inhibited 3',5'-cyclic phosphodiesterase A (EC 3.1.4.17) (Cyclic GMP-inhibited phosphodiesteras ...	0.85	+	end	5	Membrane; peripheral membrane protein (Potential)				1141
Q9UW12 UniProt NPD GO	PALA_CANAL	pH-response regulator protein palA/RIM20	0.85	-	nuc	0					785
Q6CUM6 UniProt NPD GO	TRM10_KLULA	tRNA (guanine-N(1)-)-methyltransferase (EC 2.1.1.31) (tRNA methyltransferase 10)	0.85	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				298
Q62077 UniProt NPD GO	PLCG1_MOUSE	1-phosphatidylinositol-4,5-bisphosphate phosphodiesterase gamma 1 (EC 3.1.4.11) (Phosphoinositide ph ...	0.84	-	nuc	0					1302
Q8WXF0 UniProt NPD GO	SRR35_HUMAN	35 kDa SR repressor protein (SRrp35)	0.84	-	nuc	0	Nucleus (Probable)	cytoplasm [ISS] nucleoplasm [ISS]			261
P21771 UniProt NPD GO	RT28_YEAST	40S ribosomal protein S28, mitochondrial precursor	0.84	-	mit	0	Mitochondrion	mitochondrial small ribosomal subunit [IDA]			286
Q94624 UniProt NPD GO	RS6_MANSE	40S ribosomal protein S6	0.84	+	nuc	0					253
Q6P5L3 UniProt NPD GO	RL19_BRARE	60S ribosomal protein L19	0.84	+	nuc	0					196
Q8JIY1 UniProt NPD GO	ADA10_XENLA	ADAM 10 precursor (EC 3.4.24.81) (A disintegrin and metalloproteinase domain 10) (Kuzbanian protein ...	0.84	-	exc	1	Membrane; single-pass type I membrane protein	cell surface [ISS] cytoplasm [ISS] Golgi apparatus [ISS] Golgi-associated vesicle [ISS] nucleus [ISS]			749
Q9UKF5 UniProt NPD GO	ADA29_HUMAN	ADAM 29 precursor (A disintegrin and metalloproteinase domain 29)	0.84	+	end	1	Membrane; single-pass type I membrane protein	integral to plasma membrane [TAS]	604778		820
O09178 UniProt NPD GO	AMPD3_RAT	AMP deaminase 3 (EC 3.5.4.6) (AMP deaminase isoform E)	0.84	-	nuc	0					765
Q9H8U3 UniProt NPD GO	ZFAN3_HUMAN	AN1-type zinc finger protein 3 (Testis-expressed sequence 27)	0.84	-	nuc	0			607455	1X4W	227
P24813 UniProt NPD GO	YAP2_YEAST	AP-1-like transcription activator YAP2 (Transcription factor CAD1) (Cadmium resistance protein 1)	0.84	-	nuc	0	Cytoplasm. Nucleus	cytoplasm [IDA] nucleus [IDA]			409
Q13367 UniProt NPD GO	AP3B2_HUMAN	AP-3 complex subunit beta-2 (Adapter-related protein complex 3 beta-2 subunit) (Beta3B-adaptin) (Ada ...	0.84	-	nuc	0	Component of the coat surrounding the cytoplasmic face of coated vesicles located at the Golgi compl ...	COPI-coated vesicle [TAS]	602166		1082
Q9UMZ2 UniProt NPD GO	SYNG_HUMAN	AP1 subunit gamma-binding protein 1 (Gamma-synergin)	0.84	+	nuc	0	Cytoplasm (By similarity). Golgi apparatus; trans-Golgi network; trans-Golgi network membrane; perip ...	AP-1 adaptor complex [TAS] cytoplasm [TAS] Golgi apparatus [TAS]	607291		1314
Q62431 UniProt NPD GO	ARI3A_MOUSE	AT-rich interactive domain-containing protein 3A (ARID domain-containing protein 3A) (Dead ringer-li ...	0.84	-	nuc	0	Nucleus	nucleus [IDA]			601
Q6P542 UniProt NPD GO	ABCF1_MOUSE	ATP-binding cassette sub-family F member 1	0.84	+	nuc	0					837
Q767L0 UniProt NPD GO	ABCF1_PIG	ATP-binding cassette sub-family F member 1	0.84	+	nuc	0					807
Q7YR37 UniProt NPD GO	ABCF1_PANTR	ATP-binding cassette sub-family F member 1 (ATP-binding cassette 50)	0.84	+	nuc	0					807
Q23976 UniProt NPD GO	KU70_DROME	ATP-dependent DNA helicase 2 subunit 1 (EC 3.6.1.-) (Yolk protein factor 1 subunit beta) (ATP-depend ...	0.84	-	cyt	0	Nucleus				631
Q8K363 UniProt NPD GO	DDX18_MOUSE	ATP-dependent RNA helicase DDX18 (EC 3.6.1.-) (DEAD box protein 18)	0.84	+	nuc	0					660
Q5ACK7 UniProt NPD GO	DRS1_CANAL	ATP-dependent RNA helicase DRS1 (EC 3.6.1.-)	0.84	+	nuc	0	Nucleus; nucleolus (By similarity)				613
Q6FW42 UniProt NPD GO	DRS1_CANGA	ATP-dependent RNA helicase DRS1 (EC 3.6.1.-)	0.84	+	nuc	0	Nucleus; nucleolus (By similarity)				725
Q6BTL5 UniProt NPD GO	DRS1_DEBHA	ATP-dependent RNA helicase DRS1 (EC 3.6.1.-)	0.84	-	nuc	0	Nucleus; nucleolus (By similarity)				771
Q75AE1 UniProt NPD GO	ROK1_ASHGO	ATP-dependent RNA helicase ROK1 (EC 3.6.1.-)	0.84	+	cyt	0	Nucleus; nucleolus (By similarity)				569
P45818 UniProt NPD GO	ROK1_YEAST	ATP-dependent RNA helicase ROK1 (EC 3.6.1.-) (Rescuer of KEM1 protein 1)	0.84	+	nuc	0	Nucleus; nucleolus	nucleolus [TAS]			564
Q2UQI6 UniProt NPD GO	DRS1_ASPOR	ATP-dependent RNA helicase drs1 (EC 3.6.1.-)	0.84	+	nuc	0	Nucleus; nucleolus (By similarity)				820
Q4WQM4 UniProt NPD GO	HAS1_ASPFU	ATP-dependent RNA helicase has1 (EC 3.6.1.-)	0.84	+	nuc	0	Nucleus; nucleolus (By similarity)				622
Q4X1X0 UniProt NPD GO	MRH4_ASPFU	ATP-dependent RNA helicase mrh4, mitochondrial precursor (EC 3.6.1.-)	0.84	-	mit	0	Mitochondrion (By similarity)				631
Q6FKS8 UniProt NPD GO	SPB4_CANGA	ATP-dependent rRNA helicase SPB4 (EC 3.6.1.-)	0.84	+	cyt	0	Nucleus; nucleolus (By similarity)				617
Q96S55 UniProt NPD GO	WRIP1_HUMAN	ATPase WRNIP1 (Werner helicase-interacting protein 1)	0.84	+	nuc	0	Nucleus (By similarity). Colocalizes with WRN in granular structures in the nucleus (By similarity)	nucleus [ISS]	608196		665
O14639 UniProt NPD GO	ABLM1_HUMAN	Actin-binding LIM protein 1 (Actin-binding LIM protein family member 1) (abLIM-1) (Actin-binding dou ...	0.84	-	nuc	0	Cytoplasm (By similarity). Cytoskeleton (By similarity). Associated with the cytoskeleton (By simila ...	actin cytoskeleton [TAS]	602330		778
Q9ULW3 UniProt NPD GO	ABT1_HUMAN	Activator of basal transcription 1 (hABT1) (Basal transcriptional activator)	0.84	-	nuc	0	Nucleus (By similarity). Nucleus; nucleolus (By similarity)	nucleus [TAS]			272
P25582 UniProt NPD GO	SPB1_YEAST	AdoMet-dependent rRNA methyltransferase SPB1 (EC 2.1.1.-) (2'-O-ribose RNA methyltransferase) (S-ade ...	0.84	+	nuc	0	Nucleus; nucleolus	nucleolus [IDA] nucleus [IDA]			841
O42832 UniProt NPD GO	SPB1_SCHPO	AdoMet-dependent rRNA methyltransferase spb1 (EC 2.1.1.-) (2'-O-ribose RNA methyltransferase) (S-ade ...	0.84	-	nuc	0	Nucleus; nucleolus (By similarity)				802
Q6PAM1 UniProt NPD GO	TXLNA_MOUSE	Alpha-taxilin	0.84	-	nuc	0					554
Q8TEW8 UniProt NPD GO	PAR3L_HUMAN	Amyotrophic lateral sclerosis 2 chromosome region candidate gene 19 protein (Partitioning-defective ...	0.84	+	nuc	0	Intracytoplasmic membrane. Cell membrane; cell-cell junction. Partially localized along the cell-cel ...				1205
P10275 UniProt NPD GO	ANDR_HUMAN	Androgen receptor (Dihydrotestosterone receptor)	0.84	+	nuc	0	Nucleus	cytoplasm [IDA] nucleus [IDA]	300068	2AXA	919
O97775 UniProt NPD GO	ANDR_PANTR	Androgen receptor (Dihydrotestosterone receptor)	0.84	+	nuc	0	Nucleus			1T7T	911
Q94546 UniProt NPD GO	ATU_DROME	Another transcription unit protein	0.84	+	nuc	0					725
Q8K4J0 UniProt NPD GO	DCR1C_MOUSE	Artemis protein (EC 3.1.-.-) (DNA cross-link repair 1C protein) (mArt protein) (SNM1-like protein)	0.84	-	nuc	0	Nucleus (By similarity)	nucleus [IC]			705
Q67C55 UniProt NPD GO	ATG11_PICAN	Autophagy-related protein 11 (Peroxisome degradation deficient protein 18)	0.84	+	nuc	0	Vacuole; vacuolar membrane; peripheral membrane protein (By similarity). Vacuolar and perivacuolar p ...				1299
Q5A1Z5 UniProt NPD GO	ATG13_CANAL	Autophagy-related protein 13	0.84	-	nuc	0	Cytoplasm (By similarity). Membrane; peripheral membrane protein (By similarity)				761
Q6BZE1 UniProt NPD GO	ATG20_DEBHA	Autophagy-related protein 20	0.84	-	nuc	0	Cytoplasm (By similarity). Membrane; peripheral membrane protein (By similarity). Endosome; endosoma ...				625

You are viewing entries 6851 to 6900 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.