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
O54988 UniProt NPD GO	SLK_MOUSE	STE20-like serine/threonine-protein kinase (EC 2.7.11.1) (STE20-like kinase) (STE20-related serine/t ...	0.99	-	nuc	0	Cytoplasm				1233
O54941 UniProt NPD GO	SMCE1_MOUSE	SWI/SNF-related matrix-associated actin-dependent regulator chromatin subfamily E member 1 (BRG1-ass ...	0.99	-	mit	0	Nucleus (By similarity)				411
Q969G3 UniProt NPD GO	SMCE1_HUMAN	SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily E member 1 (BRG1- ...	0.99	-	mit	0	Nucleus	nuclear chromosome [TAS] transcriptional repressor complex [IPI]	603111		411
Q758T8 UniProt NPD GO	SWC3_ASHGO	SWR1-complex protein 3	0.99	+	nuc	0	Nucleus (By similarity)				688
P05060 UniProt NPD GO	SCG1_HUMAN	Secretogranin-1 precursor (Secretogranin I) (SgI) (Chromogranin B) (CgB) [Contains: GAWK peptide; CC ...	0.99	-	nuc	0	Neuroendocrine and endocrine secretory granules		118920		677
Q9BQF6 UniProt NPD GO	SENP7_HUMAN	Sentrin-specific protease 7 (EC 3.4.22.-) (Sentrin/SUMO-specific protease SENP7) (SUMO-1-specific pr ...	0.99	+	nuc	0		nucleus [ISS]			984
O61366 UniProt NPD GO	GPRS_DROME	Serine-enriched protein	0.99	-	nuc	0					1302
Q62388 UniProt NPD GO	ATM_MOUSE	Serine-protein kinase ATM (EC 2.7.11.1) (Ataxia telangiectasia mutated homolog) (A-T, mutated homolo ...	0.99	-	end	0	Nucleus (By similarity). Cytoplasmic vesicle (By similarity). Primarily nuclear. Found also in endoc ...	nucleus [TAS] spindle [IDA]			3066
Q5ZMJ9 UniProt NPD GO	SRRM1_CHICK	Serine/arginine repetitive matrix protein 1	0.99	+	nuc	0	Nucleus (By similarity)				888
Q5R5Q2 UniProt NPD GO	SRRM1_PONPY	Serine/arginine repetitive matrix protein 1	0.99	+	nuc	0	Nucleus; nucleoplasm; nuclear matrix (By similarity). Nucleus; nucleoplasm; nuclear speckle (By simi ...				917
Q52KI8 UniProt NPD GO	SRRM1_MOUSE	Serine/arginine repetitive matrix protein 1 (Plenty-of-prolines 101)	0.99	+	nuc	0	Nucleus; nucleoplasm; nuclear matrix (By similarity). Nucleus; nucleoplasm; nuclear speckle (By simi ...	spliceosome complex [IDA]			946
Q8IYB3 UniProt NPD GO	SRRM1_HUMAN	Serine/arginine repetitive matrix protein 1 (Ser/Arg-related nuclear matrix protein) (SR-related nuc ...	0.99	+	nuc	0	Nucleus; nucleoplasm; nuclear matrix. Nucleus; nucleoplasm; nuclear speckle		605975	1MP1	904
O55098 UniProt NPD GO	STK10_MOUSE	Serine/threonine-protein kinase 10 (EC 2.7.11.1) (Lymphocyte-oriented kinase)	0.99	-	nuc	0					966
Q75CH3 UniProt NPD GO	ATG1_ASHGO	Serine/threonine-protein kinase ATG1 (EC 2.7.11.1) (Autophagy-related protein 1)	0.99	-	nuc	0	Cytoplasm (By similarity)				972
Q8TF76 UniProt NPD GO	HASP_HUMAN	Serine/threonine-protein kinase Haspin (EC 2.7.11.1) (Haploid germ cell-specific nuclear protein kin ...	0.99	-	nuc	0	Nucleus	nucleus [IEP]			798
Q61136 UniProt NPD GO	PRP4B_MOUSE	Serine/threonine-protein kinase PRP4 homolog (EC 2.7.11.1) (PRP4 pre-mRNA-processing factor 4 homolo ...	0.99	+	nuc	0	Nucleus	chromosome [IDA]			1007
Q8C0V0 UniProt NPD GO	TLK1_MOUSE	Serine/threonine-protein kinase tousled-like 1 (EC 2.7.11.1) (Tousled-like kinase 1)	0.99	-	nuc	0	Nucleus (By similarity)	nucleus [ISS]			766
Q9UKI8 UniProt NPD GO	TLK1_HUMAN	Serine/threonine-protein kinase tousled-like 1 (EC 2.7.11.1) (Tousled-like kinase 1) (PKU-beta)	0.99	-	nuc	0	Nucleus. Isoform 3: Cytoplasm (Probable)	nucleus [IEP]	608438		766
Q6FMT2 UniProt NPD GO	SGO1_CANGA	Shugoshin	0.99	+	nuc	0	Nucleus (By similarity). Localizes to the centromere (By similarity)				603
Q872U8 UniProt NPD GO	SGO1_NEUCR	Shugoshin	0.99	-	nuc	0	Nucleus (By similarity). Localizes to the centromere (By similarity)				774
O13734 UniProt NPD GO	SGO2_SCHPO	Shugoshin-2	0.99	-	nuc	0	Nucleus. Localizes to the centromere. Bub1 is required for centromeric localization. During anaphase ...	condensed nuclear chromosome, pericentric r... [IDA] heterochromatin [IDA] kinetochore [IDA]			647
Q8NEV8 UniProt NPD GO	SLC2B_HUMAN	Slp homolog lacking C2 domains b (Exophilin-5)	0.99	-	nuc	0					1989
Q62245 UniProt NPD GO	SOS1_MOUSE	Son of sevenless homolog 1 (SOS-1) (mSOS-1)	0.99	+	nuc	0				4GBQ	1319
Q59S66 UniProt NPD GO	IPL1_CANAL	Spindle assembly checkpoint kinase (EC 2.7.11.1) (Aurora kinase)	0.99	+	nuc	0	Nucleus (By similarity). Associates with the mitotic spindle and on elongated and disassembling spin ...				530
Q8TF01 UniProt NPD GO	SFR17_HUMAN	Splicing factor, arginine/serine-rich 130 (Serine-arginine-rich-splicing regulatory protein 130) (SR ...	0.99	+	nuc	0	Nucleus; nucleoplasm; nuclear speckle				805
Q20060 UniProt NPD GO	SMC4_CAEEL	Structural maintenance of chromosome 4 (Protein smc-4)	0.99	-	nuc	0	Nucleus. Cytoplasm. In interphase cells, the majority of the condensin complex is found in the cytop ...				1549
Q17768 UniProt NPD GO	SPR3_CAEEL	Suppressor of presenilin protein 3	0.99	+	nuc	0	Nucleus				684
P46675 UniProt NPD GO	STU2_YEAST	Suppressor of tubulin STU2	0.99	-	nuc	0	Spindle. Localizes primarily to the spindle pole body (SPB) and to a lesser extent along spindle mic ...	cell cortex [IDA] condensed nuclear chromosome kinetochore [IDA] kinetochore [IDA] spindle microtubule [IDA] spindle pole body [IDA]			888
Q62209 UniProt NPD GO	SYCP1_MOUSE	Synaptonemal complex protein 1 (SCP-1)	0.99	+	nuc	0	Nucleus (By similarity). In tripartite segments of synaptonemal complexes, between lateral elements ...	central element [IDA] lateral element [TAS] transverse filament [IDA]			993
Q9BX26 UniProt NPD GO	SYCP2_HUMAN	Synaptonemal complex protein 2 (SCP-2) (Synaptonemal complex lateral element protein) (hsSCP2)	0.99	-	nuc	0	Nucleus (By similarity). In axial/lateral elements of the tripartite segments of synaptonemal comple ...	nucleus [NAS] synaptonemal complex [NAS]	604105		1530
P54816 UniProt NPD GO	TBP7_CAEEL	TAT-binding homolog 7 (Lin-48 expression abnormal protein 1)	0.99	-	nuc	0					1242
Q8LKW0 UniProt NPD GO	TERT_ORYSA	Telomerase reverse transcriptase (EC 2.7.7.49) (OsTERT)	0.99	+	nuc	0	Nucleus (By similarity)				1261
Q5RAK6 UniProt NPD GO	EST1A_PONPY	Telomerase-binding protein EST1A (Ever shorter telomeres 1A) (Telomerase subunit EST1A) (EST1-like p ...	0.99	-	nuc	0	Nucleus; nucleolus. Particularly enriched in the nucleolus (By similarity)				1419
Q86US8 UniProt NPD GO	EST1A_HUMAN	Telomerase-binding protein EST1A (Ever shorter telomeres 1A) (Telomerase subunit EST1A) (EST1-like p ...	0.99	-	nuc	0	Nucleus; nucleolus. Particularly enriched in the nucleolus	cytoplasm [IDA] nucleus [IDA] telomerase holoenzyme complex [TAS]			1419
P10827 UniProt NPD GO	THA_HUMAN	Thyroid hormone receptor alpha (C-erbA-alpha) (c-erbA-1) (EAR-7) (EAR7)	0.99	+	nuc	0	Nucleus		190120	1NAV	490
Q14669 UniProt NPD GO	TRIPC_HUMAN	Thyroid receptor-interacting protein 12 (TRIP12)	0.99	-	nuc	0			604506		1992
Q9W420 UniProt NPD GO	SPT6H_DROME	Transcription elongation factor SPT6	0.99	+	nuc	0	Nucleus. Recruited to sites of active transcription where it colocalizes with the elongating form of ...	nuclear exosome (RNase complex) [IPI] polytene chromosome interband [IDA] polytene chromosome puff [IDA] transcription elongation factor complex [IPI]			1831
P23615 UniProt NPD GO	SPT6_YEAST	Transcription elongation factor SPT6 (Chromatin elongation factor SPT6)	0.99	+	nuc	0	Nucleus. Colocalizes with RNA polymerase II on chromatin. Recruited to the active transcribed loci	mitochondrion [IDA] nucleus [IPI] transcription elongation factor complex [IPI]			1451
Q9UGU0 UniProt NPD GO	TCF20_HUMAN	Transcription factor 20 (Stromelysin 1 PDGF-responsive element-binding protein) (SPRE-binding protei ...	0.99	+	nuc	0	Nucleus	nucleus [NAS]	603107		1960
P37275 UniProt NPD GO	TCF8_HUMAN	Transcription factor 8 (NIL-2-A zinc finger protein) (Negative regulator of IL2)	0.99	+	nuc	0	Nucleus		189909		1124
Q64318 UniProt NPD GO	TCF8_MOUSE	Transcription factor 8 (Zinc finger homeobox protein 1a) (MEB1) (Delta EF1)	0.99	+	nuc	0	Nucleus	nucleus [IDA]			1117
P50875 UniProt NPD GO	SPT20_YEAST	Transcription factor SPT20	0.99	-	nuc	0	Nucleus (Probable)	SAGA complex [IDA] SLIK (SAGA-like) complex [IPI]			604
P21675 UniProt NPD GO	TAF1_HUMAN	Transcription initiation factor TFIID subunit 1 (EC 2.7.11.1) (Transcription initiation factor TFIID ...	0.99	+	nuc	0	Nucleus	nucleus [TAS] transcription factor TFIID complex [TAS]	313650	1EQF	1872
P22082 UniProt NPD GO	SNF2_YEAST	Transcription regulatory protein SNF2 (EC 3.6.1.-) (ATP-dependent helicase SNF2) (SWI/SNF complex co ...	0.99	+	nuc	0	Nucleus	SWI/SNF complex [TAS]			1703
P70486 UniProt NPD GO	ATRX_RAT	Transcriptional regulator ATRX (EC 3.6.1.-) (ATP-dependent helicase ATRX) (X-linked nuclear protein) ...	0.99	+	nuc	0	Nucleus (By similarity). Associated with pericentromeric heterochromatin during interphase and mitos ...				527
O15016 UniProt NPD GO	TRI66_HUMAN	Tripartite motif-containing protein 66	0.99	-	nuc	0					1214
Q924W6 UniProt NPD GO	TRI66_MOUSE	Tripartite motif-containing protein 66	0.99	-	nuc	0					1209
Q6EEF3 UniProt NPD GO	TTLL5_CERAE	Tubulin--tyrosine ligase-like protein 5 (SRC1 and TIF2-associated modulatory protein)	0.99	+	nuc	0					1295
Q9D361 UniProt NPD GO	CF151_MOUSE	U11/U12 snRNP 48 kDa protein	0.99	+	nuc	0	Nucleus (By similarity)	minor (U12-dependent) spliceosome complex [ISS]			337
Q62377 UniProt NPD GO	U2AFM_MOUSE	U2 small nuclear ribonucleoprotein auxiliary factor 35 kDa subunit-related protein 2 (U2(RNU2) small ...	0.99	+	nuc	0	Nucleus (Potential)	minor (U12-dependent) spliceosome complex [ISS] nucleolus [IDA]			462

You are viewing entries 451 to 500 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.