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
P07304 UniProt NPD GO	TBA1_STYLE	Tubulin alpha-1 chain	0.12	-	cyt	0					445
P68360 UniProt NPD GO	TBA1_MERUN	Tubulin alpha-1 chain (Alpha-tubulin 1)	0.12	-	cyt	0					451
P68370 UniProt NPD GO	TBA1_RAT	Tubulin alpha-1 chain (Alpha-tubulin 1)	0.12	-	cyt	0					451
P68361 UniProt NPD GO	TBA1_CRIGR	Tubulin alpha-1 chain (Alpha-tubulin 1) (Alpha-tubulin I)	0.12	-	cyt	0					451
P68369 UniProt NPD GO	TBA1_MOUSE	Tubulin alpha-1 chain (Alpha-tubulin 1) (Alpha-tubulin isotype M-alpha-1)	0.12	-	cyt	0					451
P02552 UniProt NPD GO	TBA1_CHICK	Tubulin alpha-1 chain (Fragment)	0.12	-	cyt	0					412
P34690 UniProt NPD GO	TBA2_CAEEL	Tubulin alpha-2 chain	0.12	-	cyt	0					448
P09205 UniProt NPD GO	TBA2_CHLRE	Tubulin alpha-2 chain	0.12	-	cyt	0					451
P06604 UniProt NPD GO	TBA2_DROME	Tubulin alpha-2 chain	0.12	-	cyt	0					449
Q40832 UniProt NPD GO	TBA2_PELFA	Tubulin alpha-2 chain	0.12	-	cyt	0					453
Q6P9V9 UniProt NPD GO	TBA2_RAT	Tubulin alpha-2 chain (Alpha-tubulin 2)	0.12	-	cyt	0					451
P68362 UniProt NPD GO	TBA2_CRIGR	Tubulin alpha-2 chain (Alpha-tubulin 2) (Alpha-tubulin II)	0.12	-	cyt	0					451
P05213 UniProt NPD GO	TBA2_MOUSE	Tubulin alpha-2 chain (Alpha-tubulin 2) (Alpha-tubulin isotype M-alpha-2)	0.12	-	cyt	0		microtubule [IDA]			451
P41383 UniProt NPD GO	TBA2_PATVU	Tubulin alpha-2/alpha-4 chain	0.12	-	cyt	0					452
P11480 UniProt NPD GO	TBAE_PHYPO	Tubulin alpha-2B chain (Tubulin alpha-E chain)	0.12	-	cyt	0	Spindle. Mitosis in the slime mold Plasmodium differs from the process in many eukaryotes. The tubul ...				449
Q94572 UniProt NPD GO	TBA3_HOMAM	Tubulin alpha-3 chain (Alpha-III tubulin)	0.12	-	cyt	0					451
Q71U36 UniProt NPD GO	TBA3_HUMAN	Tubulin alpha-3 chain (Alpha-tubulin 3) (Tubulin B-alpha-1)	0.12	-	cyt	0			602529		451
Q9NY65 UniProt NPD GO	TBA8_HUMAN	Tubulin alpha-8 chain (Alpha-tubulin 8)	0.12	-	cyt	0			605742		449
Q9JJZ2 UniProt NPD GO	TBA8_MOUSE	Tubulin alpha-8 chain (Alpha-tubulin 8)	0.12	-	cyt	0					449
Q6AY56 UniProt NPD GO	TBA8_RAT	Tubulin alpha-8 chain (Alpha-tubulin 8)	0.12	-	cyt	0					449
P09645 UniProt NPD GO	TBA8_CHICK	Tubulin alpha-8 chain (Fragment)	0.12	-	cyt	0					324
P38669 UniProt NPD GO	TBA2_NEUCR	Tubulin alpha-B chain	0.12	-	cyt	0					449
P68363 UniProt NPD GO	TBAK_HUMAN	Tubulin alpha-ubiquitous chain (Alpha-tubulin ubiquitous) (Tubulin K-alpha-1)	0.12	-	cyt	0			602529		451
Q5R1W4 UniProt NPD GO	TBAK_PANTR	Tubulin alpha-ubiquitous chain (Alpha-tubulin ubiquitous) (Tubulin K-alpha-1)	0.12	-	cyt	0					451
P11482 UniProt NPD GO	TBB1_VOLCA	Tubulin beta chain (Beta tubulin)	0.12	-	cyt	0					443
P41799 UniProt NPD GO	TBB_PHANO	Tubulin beta chain (Beta tubulin)	0.12	-	cyt	0					447
Q25009 UniProt NPD GO	TBB1_HOMAM	Tubulin beta-1 chain (Beta-I tubulin)	0.12	-	cyt	0					451
Q9NFZ7 UniProt NPD GO	TBB1_ECHMU	Tubulin beta-1 chain (Beta-tubulin 1)	0.12	-	cyt	0					448
P04690 UniProt NPD GO	TBB_CHLRE	Tubulin beta-1/beta-2 chain	0.12	-	cyt	0					443
Q40106 UniProt NPD GO	TBB2_LUPAL	Tubulin beta-2 chain (Beta-2 tubulin)	0.12	-	cyt	0					448
P08841 UniProt NPD GO	TBB3_DROME	Tubulin beta-3 chain (Beta-3 tubulin)	0.12	-	cyt	0		microtubule [IDA]			454
Q922F4 UniProt NPD GO	TBB6_MOUSE	Tubulin beta-6 chain	0.12	-	cyt	0					447
Q6VAF6 UniProt NPD GO	TBB6_GOSHI	Tubulin beta-6 chain (Beta-6 tubulin)	0.12	-	cyt	0					450
Q9BXT4 UniProt NPD GO	TDRD1_HUMAN	Tudor domain-containing protein 1	0.12	-	nuc	0			605796		777
O43557 UniProt NPD GO	TNF14_HUMAN	Tumor necrosis factor ligand superfamily member 14 (Herpesvirus entry mediator-ligand) (HVEM-L) (CD2 ...	0.12	-	mit	1 *	Isoform 1: Cell membrane; single-pass type II membrane protein. Processed isoform 1: Secreted protei ...		604520		240
O02765 UniProt NPD GO	TNFL4_RABIT	Tumor necrosis factor ligand superfamily member 4 (OX40 ligand) (OX40L) (CD252 antigen)	0.12	-	mit	0	Membrane; single-pass type II membrane protein				187
Q92813 UniProt NPD GO	IOD2_HUMAN	Type II iodothyronine deiodinase (EC 1.97.1.10) (Type-II 5'deiodinase) (DIOII) (Type 2 DI) (5DII)	0.12	-	end	0		membrane [IC]	601413		265
P28202 UniProt NPD GO	PTP10_STYPL	Tyrosine-protein phosphatase 10 (EC 3.1.3.48) (Fragment)	0.12	-	cyt	0					116
P28214 UniProt NPD GO	PTP22_STYPL	Tyrosine-protein phosphatase 22 (EC 3.1.3.48) (Fragment)	0.12	-	cyt	0					115
Q10256 UniProt NPD GO	MUD1_SCHPO	UBA-domain protein mud1 (UBA-domain-containing protein 1) (DNA-damage-inducible protein DDI1 homolog ...	0.12	-	nuc	0				1Z96	332
Q12520 UniProt NPD GO	HUT1_YEAST	UDP-galactose transporter homolog 1 (Multicopy suppressor of leflunomide-sensitivity protein 6)	0.12	-	end	8 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein				339
O75795 UniProt NPD GO	UDB17_HUMAN	UDP-glucuronosyltransferase 2B17 precursor (EC 2.4.1.17) (UDPGT) (C19-steroid-specific UDP-glucurono ...	0.12	-	nuc	1	Microsome	membrane fraction [TAS]	601903		530
P21624 UniProt NPD GO	UTS1_PLAFE	UI precursor [Contains: Urophysin; Urotensin-1 (Urotensin I)] (Fragments)	0.12	-	nuc	0	Secreted protein				60
P04560 UniProt NPD GO	UTS2A_CYPCA	UII alpha precursor [Contains: Urophysin alpha; Urotensin II-alpha (UII-alpha) (U-II-alpha)]	0.12	-	exc	0	Secreted protein				125
O13890 UniProt NPD GO	YE35_SCHPO	UPF0061 protein C20G4.05c	0.12	-	cyt	0					568
Q93VG8 UniProt NPD GO	CG146_ARATH	UPF0326 protein At4g17486	0.12	-	nuc	0					224
Q9R0P9 UniProt NPD GO	UCHL1_MOUSE	Ubiquitin carboxyl-terminal hydrolase isozyme L1 (EC 3.4.19.12) (EC 6.-.-.-) (UCH-L1) (Ubiquitin thi ...	0.12	-	mit	0	Cytoplasm	axon [IDA] cell soma [IDA] cytoplasm [IDA] cytosol [IDA]			223
Q00981 UniProt NPD GO	UCHL1_RAT	Ubiquitin carboxyl-terminal hydrolase isozyme L1 (EC 3.4.19.12) (EC 6.-.-.-) (UCH-L1) (Ubiquitin thi ...	0.12	-	mit	0	Cytoplasm				223
O42915 UniProt NPD GO	UFD1_SCHPO	Ubiquitin fusion degradation protein 1 (UB fusion protein 1)	0.12	-	cyt	0					342
Q9VTF9 UniProt NPD GO	UFD1_DROME	Ubiquitin fusion degradation protein 1 homolog (UB fusion protein 1)	0.12	-	cyt	0					316

You are viewing entries 62051 to 62100 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.