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
P25302 UniProt NPD GO	SWI4_YEAST	Regulatory protein SWI4 (Cell-cycle box factor subunit SWI4) (Protein ART1)	1.00	+	nuc	0		nucleus [IDA]			1093
Q96T23 UniProt NPD GO	RSF1_HUMAN	Remodeling and spacing factor 1 (Rsf-1) (Hepatitis B virus X-associated protein) (HBV pX-associated ...	1.00	+	nuc	0	Nucleus	nucleus [IDA] RSF complex [IPI]	608522		1431
Q99708 UniProt NPD GO	RBBP8_HUMAN	Retinoblastoma-binding protein 8 (RBBP-8) (CtBP-interacting protein) (CtIP) (Retinoblastoma-interact ...	1.00	-	nuc	0	Nucleus. Predominantly	nucleus [TAS]	604124		897
Q5U5Q9 UniProt NPD GO	RXINP_MOUSE	Retinoid X receptor-interacting protein 110	1.00	+	nuc	0	Nucleus (By similarity)				727
Q7Z6B7 UniProt NPD GO	SRGP1_HUMAN	SLIT-ROBO Rho GTPase-activating protein 1 (srGAP1) (Rho-GTPase-activating protein 13)	1.00	-	nuc	0			606523		1085
O94421 UniProt NPD GO	SNF22_SCHPO	SNF2-family ATP-dependent chromatin remodeling factor snf22 (EC 3.6.1.-) (ATP-dependent helicase snf ...	1.00	+	nuc	0	Nucleus (Probable)				1680
O55092 UniProt NPD GO	SLK_CAVPO	STE20-like serine/threonine-protein kinase (EC 2.7.11.1) (STE20-like kinase) (STE20-related serine/t ...	1.00	-	nuc	0	Cytoplasm (By similarity)				1231
Q9H2G2 UniProt NPD GO	SLK_HUMAN	STE20-like serine/threonine-protein kinase (EC 2.7.11.1) (STE20-like kinase) (STE20-related serine/t ...	1.00	-	nuc	0	Cytoplasm (By similarity)				1235
Q6FRS1 UniProt NPD GO	SWC3_CANGA	SWR1-complex protein 3	1.00	+	nuc	0	Nucleus (By similarity)				659
Q6CKU6 UniProt NPD GO	SWC3_KLULA	SWR1-complex protein 3	1.00	+	nuc	0	Nucleus (By similarity)				758
P31376 UniProt NPD GO	SWC3_YEAST	SWR1-complex protein 3	1.00	+	nuc	0	Nucleus	mitochondrion [IDA] nucleus [IDA] SWR1 complex [IPI]			625
P48590 UniProt NPD GO	FTZ_DROHY	Segmentation protein fushi tarazu	1.00	+	nuc	0	Nucleus				456
P59110 UniProt NPD GO	SENP1_MOUSE	Sentrin-specific protease 1 (EC 3.4.22.-) (Sentrin/SUMO-specific protease SENP1)	1.00	+	nuc	0	Nucleus (By similarity)				640
O94804 UniProt NPD GO	STK10_HUMAN	Serine/threonine-protein kinase 10 (EC 2.7.11.1) (Lymphocyte-oriented kinase)	1.00	-	nuc	0			603919		968
Q12263 UniProt NPD GO	GIN4_YEAST	Serine/threonine-protein kinase GIN4 (EC 2.7.11.1)	1.00	-	nuc	0		bud neck [IDA]			1142
Q9Z0R0 UniProt NPD GO	HASP_MOUSE	Serine/threonine-protein kinase Haspin (EC 2.7.11.1) (Haploid germ cell-specific nuclear protein kin ...	1.00	+	nuc	0	Nucleus	nucleus [IEP]			754
Q96PY6 UniProt NPD GO	NEK1_HUMAN	Serine/threonine-protein kinase Nek1 (EC 2.7.11.1) (NimA-related protein kinase 1) (NY-REN-55 antige ...	1.00	+	nuc	0	Nucleus (Probable)	cytoplasm [IDA] nucleus [IDA]	604588		1258
Q9VPC0 UniProt NPD GO	KP58_DROME	Serine/threonine-protein kinase PITSLRE (EC 2.7.11.22) (Cell division cycle 2-like)	1.00	+	nuc	0	Nucleus (Potential)				952
Q6CXI9 UniProt NPD GO	SGO1_KLULA	Shugoshin	1.00	+	nuc	0	Nucleus (By similarity). Localizes to the centromere (By similarity)				594
Q08490 UniProt NPD GO	SGO1_YEAST	Shugoshin	1.00	-	nuc	0	Nucleus. Localizes to the centromere during S and M phases. Colocalizes with kinetochores. Associate ...	kinetochore [IDA] nucleus [IDA]			590
Q4QSC8 UniProt NPD GO	SGO1_MAIZE	Shugoshin-1 (ZmSGO1)	1.00	+	nuc	0	Nucleus. Localizes to the centromere during meiosis I. REC8 is required for centromeric localization ...				474
Q7TSY8 UniProt NPD GO	SGOL2_MOUSE	Shugoshin-like 2	1.00	-	nuc	0	Nucleus (By similarity). Localizes to the centromere (By similarity)				1164
Q562F6 UniProt NPD GO	SGOL2_HUMAN	Shugoshin-like 2 (Tripin)	1.00	+	nuc	0	Nucleus (By similarity). Localizes to the centromere (By similarity)				1265
Q563C3 UniProt NPD GO	CCA5A_XENLA	Sororin (Cell division cycle-associated protein 5-A) (Xp35)	1.00	+	nuc	0	Nucleus (By similarity). Nuclear in interphase cells. During mitosis, it localizes throughout the cy ...				269
Q9HB58 UniProt NPD GO	SP110_HUMAN	Sp110 nuclear body protein (Speckled 110 kDa) (Transcriptional coactivator Sp110) (Interferon-induce ...	1.00	+	nuc	0	Nucleus. Found in the nuclear body	nucleus [TAS]	604457		689
Q09003 UniProt NPD GO	SPH1_XENLA	Sphere organelles protein SPH-1 (Sphere protein 1)	1.00	+	nuc	0	Nucleus. Sphere organelles				536
P32908 UniProt NPD GO	SMC1_YEAST	Structural maintenance of chromosome 1 (DA-box protein SMC1)	1.00	-	nuc	0	Nucleus. Associates with chromatin. Before prophase it is scattered along chromosome arms. At anapha ...	nuclear cohesin complex [IDA]		1W1W	1225
O95425 UniProt NPD GO	SVIL_HUMAN	Supervillin (Archvillin) (p205/p250)	1.00	+	nuc	0	Cell membrane; peripheral membrane protein; cytoplasmic side. Cytoskeleton. Tightly associated with ...	actin cytoskeleton [NAS] costamere [IDA] cytoplasm [IDA] nucleus [IDA] plasma membrane [IDA]	604126		2214
Q9VWF2 UniProt NPD GO	SAYP_DROME	Supporter of activation of yellow protein (Protein enhancer of yellow 3)	1.00	-	nuc	0	Nucleus. On polytene chromosomes, it mainly localizes to transcriptionally active euchromatin sites ...	euchromatin [IDA] heterochromatin [IDA] nucleus [IDA] polytene chromosome chromocenter [IDA]			2006
P46676 UniProt NPD GO	SUM1_YEAST	Suppressor of mar1-1 protein (SUM1-1 protein)	1.00	+	nuc	0	Nucleus	histone deacetylase complex [IDA] nucleus [IDA]			1062
P40340 UniProt NPD GO	TBP7_YEAST	TAT-binding homolog 7	1.00	+	nuc	0		nucleus [IDA]			1379
Q8BYJ6 UniProt NPD GO	TBCD4_MOUSE	TBC1 domain family member 4 (Akt substrate of 160 kDa) (AS160)	1.00	-	nuc	0					1307
P61406 UniProt NPD GO	EST1A_MOUSE	Telomerase-binding protein EST1A (Ever shorter telomeres 1A) (Telomerase subunit EST1A) (EST1-like p ...	1.00	-	nuc	0	Nucleus; nucleolus. Particularly enriched in the nucleolus (By similarity)	cytoplasm [ISS] nucleus [ISS] telomerase holoenzyme complex [ISS]			1418
Q9BXT5 UniProt NPD GO	TEX15_HUMAN	Testis-expressed sequence 15 protein	1.00	+	nuc	0			605795		2789
P53840 UniProt NPD GO	TOF1_YEAST	Topoisomerase 1-associated factor 1	1.00	+	nuc	0	Nucleus. Associated with chromatin during S phase	nuclear chromosome [IPI]			1238
Q02208 UniProt NPD GO	TOF2_YEAST	Topoisomerase 1-associated factor 2	1.00	+	nuc	0	Nucleus (Probable)	mitochondrion [IDA]			771
Q9EPQ8 UniProt NPD GO	TCF20_MOUSE	Transcription factor 20 (Stromelysin 1 PDGF-responsive element-binding protein) (SPRE-binding protei ...	1.00	+	nuc	0	Nucleus	nucleus [ISS]			1983
Q6BQ49 UniProt NPD GO	IWS1_DEBHA	Transcription factor IWS1	1.00	+	nuc	0	Nucleus (By similarity)				404
Q06505 UniProt NPD GO	IWS1_YEAST	Transcription factor IWS1 (Interacts with SPT6 protein 1) (Suppresses postrecruitment functions prot ...	1.00	+	nuc	0	Nucleus	transcription elongation factor complex [IPI]			410
P51123 UniProt NPD GO	TAF1_DROME	Transcription initiation factor TFIID subunit 1 (EC 2.7.11.1) (Transcription initiation factor TFIID ...	1.00	+	nuc	0	Nucleus			1TBA	2129
Q7YQM4 UniProt NPD GO	ATRX_PANTR	Transcriptional regulator ATRX (EC 3.6.1.-) (ATP-dependent helicase ATRX) (X-linked helicase II) (X- ...	1.00	+	nuc	0	Nucleus. Associated with pericentromeric heterochromatin during interphase and mitosis, probably by ...				2492
Q7YQM3 UniProt NPD GO	ATRX_PONPY	Transcriptional regulator ATRX (EC 3.6.1.-) (ATP-dependent helicase ATRX) (X-linked helicase II) (X- ...	1.00	+	nuc	0	Nucleus. Associated with pericentromeric heterochromatin during interphase and mitosis, probably by ...				2492
P46100 UniProt NPD GO	ATRX_HUMAN	Transcriptional regulator ATRX (EC 3.6.1.-) (ATP-dependent helicase ATRX) (X-linked helicase II) (X- ...	1.00	+	nuc	0	Nucleus. Associated with pericentromeric heterochromatin during interphase and mitosis, probably by ...	nuclear heterochromatin [TAS] nucleus [TAS]	309580		2492
Q61687 UniProt NPD GO	ATRX_MOUSE	Transcriptional regulator ATRX (EC 3.6.1.-) (ATP-dependent helicase ATRX) (X-linked nuclear protein) ...	1.00	+	nuc	0	Nucleus. Associated with pericentromeric heterochromatin during interphase and mitosis, probably by ...	heterochromatin [IDA] nuclear chromosome [IDA]			2476
Q9GQN5 UniProt NPD GO	ATRX_DROME	Transcriptional regulator ATRX homolog (EC 3.6.1.-) (ATP-dependent helicase XNP) (X-linked nuclear p ...	1.00	+	nuc	0	Nucleus				1311
Q9U7E0 UniProt NPD GO	ATRX_CAEEL	Transcriptional regulator ATRX homolog (EC 3.6.1.-) (ATP-dependent helicase xnp-1) (X-linked nuclear ...	1.00	+	nuc	0	Nucleus				1359
Q93971 UniProt NPD GO	TRPG_CAEEL	Transient receptor potential channel (Abnormal gonad development protein 2)	1.00	+	end	5	Membrane; multi-pass membrane protein (Potential)	integral to membrane [ISS]			2032
Q6ZT98 UniProt NPD GO	TTLL7_HUMAN	Tubulin--tyrosine ligase-like protein 7 (Protein NYD-SP30)	1.00	+	nuc	0					887
P18106 UniProt NPD GO	FPS_DROME	Tyrosine-protein kinase Fps85D (EC 2.7.10.2) (dFer)	1.00	+	nuc	0	Membrane; peripheral membrane protein	plasma membrane [IDA]			1325
Q15695 UniProt NPD GO	U2AFL_HUMAN	U2 small nuclear ribonucleoprotein auxiliary factor 35 kDa subunit-related protein 1 (U2(RNU2) small ...	1.00	+	nuc	0	Nucleus (Potential)	nucleus [NAS]	601079		479

You are viewing entries 151 to 200 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.