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
Q13620 UniProt NPD GO	CUL4B_HUMAN	Cullin-4B (CUL-4B)	0.96	-	nuc	0			300304		895
P52958 UniProt NPD GO	CTF1A_FUSSO	Cutinase transcription factor 1 alpha	0.96	-	nuc	0	Nucleus (Potential)				909
Q9UK58 UniProt NPD GO	CCNL1_HUMAN	Cyclin-L1 (Cyclin-L)	0.96	+	nuc	0	Nucleus; nucleoplasm; nuclear speckle (By similarity). More specifically found in nuclear intrachrom ...				526
Q52KE7 UniProt NPD GO	CCNL1_MOUSE	Cyclin-L1 (Cyclin-L) (Cyclin Ania-6a)	0.96	+	nuc	0	Nucleus; nucleoplasm; nuclear speckle. More specifically found in nuclear intrachromatin granules cl ...				532
Q9R1Q2 UniProt NPD GO	CCNL1_RAT	Cyclin-L1 (Cyclin-L) (Cyclin Ania-6a)	0.96	+	nuc	0	Nucleus; nucleoplasm; nuclear speckle. More specifically found in nuclear intrachromatin granules cl ...	nuclear speck [IDA]			527
Q5BKF8 UniProt NPD GO	CCNL2_XENTR	Cyclin-L2	0.96	-	nuc	0	Nucleus (By similarity)				497
Q96S94 UniProt NPD GO	CCNL2_HUMAN	Cyclin-L2 (Paneth cell-enhanced expression protein)	0.96	+	nuc	0	Nucleus; nucleoplasm; nuclear speckle				520
Q93Y39 UniProt NPD GO	RH13_ARATH	DEAD-box ATP-dependent RNA helicase 13 (EC 3.6.1.-)	0.96	+	nuc	0					832
Q9Z330 UniProt NPD GO	DNMT1_RAT	DNA (cytosine-5)-methyltransferase 1 (EC 2.1.1.37) (Dnmt1) (DNA methyltransferase I) (DNA MTase RnoI ...	0.96	-	nuc	0	Nucleus	nucleus [IDA]			1622
Q5QJC4 UniProt NPD GO	DCR1A_CHICK	DNA cross-link repair 1A protein (chSNM1A)	0.96	+	nuc	0	Nucleus (By similarity)				972
Q6PJP8 UniProt NPD GO	DCR1A_HUMAN	DNA cross-link repair 1A protein (hSNM1) (hSNM1A)	0.96	+	nuc	0	Nucleus. In some cells it may be found in typically 1 or 2 discrete nuclear aggregates of unknown fu ...		609682		1040
O48653 UniProt NPD GO	DPOLA_ORYSA	DNA polymerase alpha catalytic subunit (EC 2.7.7.7)	0.96	-	nuc	0	Nucleus (By similarity)	nucleus [IDA]			1534
Q753V5 UniProt NPD GO	RAD5_ASHGO	DNA repair protein RAD5 (EC 3.6.1.-)	0.96	+	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				1085
Q5ACX1 UniProt NPD GO	RAD5_CANAL	DNA repair protein RAD5 (EC 3.6.1.-)	0.96	+	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				1084
Q6BIP2 UniProt NPD GO	RAD5_DEBHA	DNA repair protein RAD5 (EC 3.6.1.-)	0.96	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				1153
O44199 UniProt NPD GO	RAD50_CAEEL	DNA repair protein rad-50 (EC 3.6.-.-)	0.96	-	nuc	0	Nucleus (By similarity)				1298
P87235 UniProt NPD GO	RHP42_SCHPO	DNA repair protein rhp42	0.96	+	nuc	0	Nucleus (Potential)				686
P47027 UniProt NPD GO	DPB11_YEAST	DNA replication regulator DPB11	0.96	+	nuc	0	Nucleus	replication fork [IDA]			764
Q9DEI1 UniProt NPD GO	PRKDC_XENLA	DNA-dependent protein kinase catalytic subunit (EC 2.7.11.1) (DNA-PK catalytic subunit) (DNA-PKcs)	0.96	-	end	0	Nucleus				4146
P97313 UniProt NPD GO	PRKDC_MOUSE	DNA-dependent protein kinase catalytic subunit (EC 2.7.11.1) (DNA-PK catalytic subunit) (DNA-PKcs) ( ...	0.96	-	nuc	0	Nucleus	nucleus [IDA]			4128
P12465 UniProt NPD GO	RPOC2_CHLVU	DNA-directed RNA polymerase beta'' chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase beta'' s ...	0.96	+	nuc	0	Plastid; chloroplast				1562
Q3ZJ90 UniProt NPD GO	RPOC2_PSEAK	DNA-directed RNA polymerase beta'' chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase beta'' s ...	0.96	+	nuc	0	Plastid; chloroplast				3462
P51612 UniProt NPD GO	XPC_MOUSE	DNA-repair protein complementing XP-C cells homolog (Xeroderma pigmentosum group C-complementing pro ...	0.96	+	nuc	0	Nucleus (Probable)	nucleus [IDA]			930
P28706 UniProt NPD GO	RAD13_SCHPO	DNA-repair protein rad13	0.96	-	nuc	0	Nucleus				1112
Q925Q8 UniProt NPD GO	DACH2_MOUSE	Dachshund homolog 2 (Dach2)	0.96	-	nuc	0	Nucleus (Probable)				634
Q9UER7 UniProt NPD GO	DAXX_HUMAN	Death domain-associated protein 6 (Daxx) (hDaxx) (Fas death domain-associated protein) (ETS1-associa ...	0.96	+	nuc	0	Nucleus. Cytoplasm. Dispersed throughout the nucleoplasm, in PML/POD/ND10 nuclear bodies, and in nuc ...	cytoplasm [TAS] nucleus [IDA]	603186		740
P18171 UniProt NPD GO	DEC13_DROME	Defective chorion-1 protein, FC177 isoform precursor	0.96	+	exc	0	Secreted protein	chorion [IDA] extracellular region [IDA]			1590
Q8BPM0 UniProt NPD GO	DAAM1_MOUSE	Disheveled-associated activator of morphogenesis 1	0.96	+	nuc	0					1071
Q80U19 UniProt NPD GO	DAAM2_MOUSE	Disheveled-associated activator of morphogenesis 2	0.96	-	nuc	0					1068
P97839 UniProt NPD GO	DLGP4_RAT	Disks large-associated protein 4 (DAP-4) (SAP90/PSD-95-associated protein 4) (SAPAP4) (PSD-95/SAP90- ...	0.96	+	nuc	0	Membrane; peripheral membrane protein (By similarity)	membrane fraction [IDA] postsynaptic membrane [IDA]			992
Q96KC8 UniProt NPD GO	DNJC1_HUMAN	DnaJ homolog subfamily C member 1	0.96	+	end	1	Nucleus; nuclear membrane; multi-pass membrane protein. Microsome; microsomal membrane; multi-pass m ...	endoplasmic reticulum [ISS] endoplasmic reticulum lumen [ISS] integral to membrane [ISS] microsome [ISS] nucleus [ISS]		2CQR	554
Q61712 UniProt NPD GO	DNJC1_MOUSE	DnaJ homolog subfamily C member 1 (DnaJ protein homolog MTJ1)	0.96	+	nuc	1	Nucleus; nuclear membrane; multi-pass membrane protein. Microsome; microsomal membrane; multi-pass m ...	endoplasmic reticulum [IDA] endoplasmic reticulum lumen [TAS] integral to membrane [TAS] microsome [TAS] nucleus [TAS]			552
P33981 UniProt NPD GO	TTK_HUMAN	Dual specificity protein kinase TTK (EC 2.7.12.1) (Phosphotyrosine picked threonine-protein kinase) ...	0.96	-	nuc	0		spindle [TAS]	604092		841
P14680 UniProt NPD GO	YAK1_YEAST	Dual specificity protein kinase YAK1 (EC 2.7.12.1)	0.96	-	nuc	0	Cytoplasm. Nucleus. Shuttles between both compartments in response to glucose	cytoplasm [IDA] nucleus [IDA]			807
Q6XZF7 UniProt NPD GO	DNMBP_HUMAN	Dynamin-binding protein (Scaffold protein Tuba)	0.96	-	nuc	0	Cytoplasm (By similarity). Golgi apparatus; Golgi stack (By similarity). Localized to synapses and G ...			1UHC	1577
O13290 UniProt NPD GO	DYHC_SCHPO	Dynein heavy chain, cytosolic (DYHC)	0.96	-	nuc	0	Cytoplasm. Localized at the astral microtubules and the spindle pole body (SPB) during nuclear movem ...	cortical microtubule cytoskeleton [IDA] spindle pole body [IDA]			4196
Q6PH08 UniProt NPD GO	ERC2_MOUSE	ERC protein 2 (CAZ-associated structural protein 1) (CAST1)	0.96	-	nuc	0	Cytoplasm. Localized to the active zone of presynaptic density	endoplasmic reticulum [ISS] growth cone [ISS] presynaptic membrane [ISS] synapse [ISS]			957
Q5AAG1 UniProt NPD GO	EPL1_CANAL	Enhancer of polycomb-like protein 1	0.96	-	nuc	0	Nucleus (By similarity)				753
Q6BNX0 UniProt NPD GO	EPL1_DEBHA	Enhancer of polycomb-like protein 1	0.96	+	nuc	0	Nucleus (By similarity)				1016
P43572 UniProt NPD GO	EPL1_YEAST	Enhancer of polycomb-like protein 1	0.96	+	nuc	0	Nucleus	H4/H2A histone acetyltransferase complex [IPI]			832
Q61188 UniProt NPD GO	EZH2_MOUSE	Enhancer of zeste homolog 2 (ENX-1)	0.96	-	nuc	0	Nucleus (Probable)	pronucleus [IDA]			746
Q92817 UniProt NPD GO	EVPL_HUMAN	Envoplakin (210 kDa paraneoplastic pemphigus antigen) (p210) (210 kDa cornified envelope precursor p ...	0.96	-	nuc	0	Cell membrane; cell-cell junction; desmosome. Colocalized with DSP at desmosomes and along intermedi ...	cornified envelope [IDA] plasmodesma [TAS]	601590		2033
Q9QZ05 UniProt NPD GO	E2AK4_MOUSE	Eukaryotic translation initiation factor 2-alpha kinase 4 (EC 2.7.11.1) (GCN2-like protein) (mGCN2)	0.96	-	nuc	0		cytosolic ribosome (sensu Eukaryota) [ISS]		1UKX	1648
P38249 UniProt NPD GO	IF3A_YEAST	Eukaryotic translation initiation factor 3 110 kDa subunit (eIF3 p110) (Translation initiation facto ...	0.96	-	nuc	0		cytoplasm [IDA] eukaryotic translation initiation factor 3 ... [IDA] incipient bud site [IDA] ribosome [TAS]			964
Q40554 UniProt NPD GO	IF3A_TOBAC	Eukaryotic translation initiation factor 3 subunit 10 (eIF-3 theta) (Eukaryotic translation initiati ...	0.96	+	nuc	0					958
Q7S8B6 UniProt NPD GO	EXO84_NEUCR	Exocyst complex component EXO84	0.96	-	nuc	0	Secretory vesicle (By similarity). Cell periphery. The polarization of EXO84 requires actin cables ( ...				621
P38167 UniProt NPD GO	ECM21_YEAST	Extracellular matrix protein 21	0.96	-	nuc	0	Cytoplasm	cytoplasm [IDA]			1117
Q8IWU6 UniProt NPD GO	SULF1_HUMAN	Extracellular sulfatase Sulf-1 precursor (EC 3.1.6.-) (HSulf-1)	0.96	+	nuc	0	Endoplasmic reticulum (By similarity). Golgi apparatus; Golgi stack (By similarity). Cell surface (B ...	cell surface [IDA] extracellular space [NAS]			871
O94267 UniProt NPD GO	SPT16_SCHPO	FACT complex subunit spt16 (Facilitates chromatin transcription complex subunit spt16)	0.96	+	cyt	0	Nucleus (By similarity)				1019
Q5RAB8 UniProt NPD GO	FARP1_PONPY	FERM, RhoGEF and pleckstrin domain-containing protein 1	0.96	-	nuc	0					1045

You are viewing entries 1351 to 1400 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.