Protein Overview: LCD1

General Information:
Name(s) found:	LCD1 / YDR499W [SGD]
Description(s) found: SHOW ONLY BEST	gi\|927769\|gb\|AAB64941.1\| Ydr499wp; CAI: 0.12 [Saccharomyces cerevisiae] [NCBI NR] gi\|74583474\|sp\|Q04377.1\|LCD1_YEAST RecName: Full=DNA damage checkpoint protein LCD1; AltName: Full=Lethal, checkpoint-defective, DNA damage-sensitive protein 1; AltName: Full=DNA damage checkpoint protein 2 [NCBI NR] gi\|6320707\|ref\|NP_010787.1\| Essential protein required for the DNA integrity checkpoint pathways; interacts physically with Mec1p; putative homolog of S. pombe Rad26 and human ATRIP; Lcd1p [Saccharomyces cerevisiae] [NCBI NR] pir\|\|S69557 hypothetical protein YDR499w - yeast (Saccharomyces cerevisiae) [NCBI NR] DNA damage checkpoint protein LCD1 OS=Saccharomyces cerevisiae GN=LCD1 PE=1 SV=1 [Swiss-Prot] LCD1 Cell cycle checkpoint protein [mips] Essential protein required for the DNA integrity checkpoint pathways; interacts physically with Mec1p; putative homolog of S. pombe Rad26 and human ATRIP [SGD] LCD1, Chr IV from 1447833-1450076 [yeast_orfs2] Chr IV from 1447833-1450076 [yeastorf3.fasta] Chr IV from 1447816-1450059 [yeastorf4.fasta] Chr IV from 1447818-1450061 [yeastorf5.fasta] >Q04377 (Q04377) D9719.5P [4932.FASTACCERV.txt] LCD1 SGDID:S0002907, Chr IV from 1447818-1450061, Verified ORF [yeastflysequest.fasta] LCD1 SGDID:S0002907, Chr IV from 1447820-1450063, Verified ORF [10112005cervSGD.fasta] Essential protein required for the DNA integrity checkpoint pathways; interacts physically with Mec1p; putative homolog of S. pombe Rad26 and human ATRIP [Saccharomyces cerevisiae]gi\|927769\|gb\|AAB64941.1\| Ydr499wp; CAI: 0.12 [Saccharomyces cerevisiae]gi [nrdb_11152004_Chlamydomonas] (Q04377) Ydr499wp [cerv4932.FASTAC] LCD1 SGDID:S000002907, Chr IV from 1447820-1450063, Verified ORF, "Essential protein required for the DNA integrity checkpoint pathways; interacts physically with Mec1p; putative homolog of S. pombe Rad26 and human ATRIP" [SGD_S-cerevisiae_na_12-16-2005_con_reversed.fasta] LCD1 SGDID:S000002907, Chr IV from 1447822-1450065, Verified ORF, "Essential protein required for the DNA integrity checkpoint pathways; interacts physically with Mec1p; putative homolog of S. pombe Rad26 and human ATRIP" [yeast-contam.fasta] LCD1 SGDID:S000002907, Chr IV from 1447823-1450066, Verified ORF, "Essential protein required for the DNA integrity checkpoint pathways; interacts physically with Mec1p; putative homolog of S. pombe Rad26 and human ATRIP" [SGD_S-cerevisiae_na_08-19-2008_con_reversed.fasta] DNA damage checkpoint protein LCD1 (Lethal, checkpoint-defective, DNA damage sensitive protein 1) (DNA damage checkpoint protein 2) [nr-271106-contam.fasta] Essential protein required for the DNA integrity checkpoint pathways; interacts physically with Mec1p; putative homolog of S. pombe Rad26 and human ATRIP; Lcd1p [Saccharomyces cerevisiae] [nr-271106-contam.fasta] Ydr499wp; CAI: 0.12 [Saccharomyces cerevisiae] [nr-271106-contam.fasta] [chemostatdb.fasta] DNA damage checkpoint protein LCD1 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=LCD1 PE=1 SV=1 [UniProt_S_cerevisiae_20120516_05-16-2012_reversed.fasta] LCD1 SGDID:S000002907, Chr IV from 1447830-1450073, Genome Release 64-1-1, Verified ORF, "Essential protein required for the DNA integrity checkpoint pathways; interacts physically with Mec1p; putative homolog of S. pombe Rad26 and human ATRIP" [yeast-030211-contam.fasta] LCD1 SGDID:S000002907, Chr IV from 1447830-1450073, Genome Release 64-2-1, Verified ORF, "Essential protein required for the DNA integrity checkpoint pathways; interacts physically with Mec1p; putative homolog of S. pombe Rad26 and human ATRIP; forms nuclear foci upon DNA replication stress" [20141208_orf_trans.fasta] YDR499W SGDID:S000002907, Chr IV from 1447830-1450073, Genome Release 64-1-1, Verified ORF, "Essential protein required for the DNA integrity checkpoint pathways; interacts physically with Mec1p; putative homolog of S. pombe Rad26 and human ATRIP" [2016-01-SGD_Yeast_Contam_Riffle_20140507-Ska-Hec-110-tubulin.fasta] ID=asmbl_1183\|g.712 ORF ID=asmbl_1183\|g.712 ID=asmbl_1183\|m.712 type:complete len:748 (+) ID=asmbl_1183:5-2248(+) [Y12_quiver_Trinity_v2_2_0_PASA_2June2016-contam.fasta]
Organism:	Saccharomyces cerevisiae
Length:	747 amino acids
Gene Ontology:
Cellular Component:	nuclear chromosome [IDA]
Biological Process:	establishment of protein localization [IDA][IMP] DNA damage checkpoint [IMP][IPI] telomere maintenance via telomerase [IMP]
Molecular Function:	protein binding [IDA] damaged DNA binding [IDA]

Sequence:

Sequence:
[PDR BLAST]
[ProtParam]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MRRETVGEFS SDDDDDILLE LGTRPPRFTQ IPPSSAALQT QIPTTLEVTT TTLNNKQSKN  60
   61 DNQLVNQLNK AQGEASMLRD KINFLNIERE KEKNIQAVKV NELQVKHLQE LAKLKQELQK 120
  121 LEDEKKFLQM EARGKSKREV ITNVKPPSTT LSTNTNTITP DSSSVAIEAK PQSPQSKKRK 180
  181 ISDNLLKKNM VPLNPNRIIP DETSLFLESI LLHQIIGADL STIEILNRLK LDYITEFKFK 240
  241 NFVIAKGAPI GKSIVSLLLR CKKTLTLDRF IDTLLEDIAV LIKEISVHPN ESKLAVPFLV 300
  301 ALMYQIVQFR PSATHNLALK DCFLFICDLI RIYHHVLKVP IHESNMNLHV EPQIFQYELI 360
  361 DYLIISYSFD LLEGILRVLQ SHPKQTYMEF FDENILKSFE FVYKLALTIS YKPMVNVIFS 420
  421 AVEVVNIITS IILNMDNSSD LKSLISGSWW RDCITRLYAL LEKEIKSGDV YNENVDTTTL 480
  481 HMSKYHDFFG LIRNIGDNEL GGLISKLIYT DRLQSVPRVI SKEDIGMDSD KFTAPIIGYK 540
  541 MEKWLLKLKD EVLNIFENLL MIYGDDATIV NGEMLIHSSK FLSREQALMI ERYVGQDSPN 600
  601 LDLRCHLIEH TLTIIYRLWK DHFKQLREEQ IKQVESQLIM SLWRFLVCQT ETVTANEREM 660
  661 RDHRHLVDSL HDLTIKDQAS YYEDAFEDLP EYIEEELKMQ LNKRTGRIMQ VKYDEKFQEM 720
  721 ARTILESKSF DLTTLEEADS LYISMGL

Protein Complex Data

	PUBLICATION	TOPOLOGY	COCOMPLEXED PROTEINS
View Details	Krogan NJ, et al. (2006)		LCD1 VAC17
View Details	Gavin AC, et al. (2002)		CMR1 DNA2 HDA1 HDA2 HDA3 HSC82 KAP95 LCD1 MEC1 MGM101 MLH1 MPH1 MSH2 MSH3 MSH6 OLA1 PGK1 PMS1 PRO2 RAD16 RAD52 RFA1 RFA2 RFA3 RIM1 RNH1 RSC8 RVB2 SGS1 SHS1 TIF1, TIF2 TOP3 VAS1 VPS1 YHR122W
View Details	Ho Y, et al. (2002)		ADH2 ADH5 HEM15 HHF1, HHF2 ILV5 LCD1 RNQ1

Mass Spectrometry Data

The following runs contain data for this protein:

	BAIT	COMMENTS	PUBLICATION
View Run	MLP2	#29 Asynchronous Prep5-TiO2 Flowthrough	Keck JM, et al. (2011)

Yeast Two-Hybrid Data

The following interactions contain this protein:

SHOWING SINGLE HITS. [ Hide Single Hits ]

[View our yeast two-hybrid interpretation guidelines.]

	BAIT	PREY	HITS	PUBLICATION
View Screen	HRT1	LCD1	1	Unpublished Fields Lab Data

Microscopy / Localization Data

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	PROTEIN(S)	PUBLICATION
View Data	LCD1	Huh WK, et al. (2003)

Protein Structure Data

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[View Top Sequence Alignments] [Show Ginzu Version Information]

Domains predicted:

#		Region(s)	Method	Confidence	Match Description
1	View Details	[1..194]	deduced	N/A	No confident structure predictions are available.
2	View Details	[195..284]	ORFEUS	8.0	CBP80, 80KDa nuclear cap-binding protein
3	View Details	[285..566]	ORFEUS	8.0	CBP80, 80KDa nuclear cap-binding protein
4	View Details	[567..747]	ORFEUS	7.09	Hemolysin E (HlyE, ClyA, SheA)

Functions predicted (by domain):

Gene Ontology predictions

No functions predicted.

Term	Confidence	Notes
binding	2.96084803796407	bayes_pls_golite062009
protein transporter activity	2.47190066960729	bayes_pls_golite062009
nucleic acid binding	1.67566088591721	bayes_pls_golite062009
protein binding	1.61131270705552	bayes_pls_golite062009
transcription regulator activity	0.845665181662967	bayes_pls_golite062009
DNA binding	0.806448013051712	bayes_pls_golite062009
protein transmembrane transporter activity	0.795583320946118	bayes_pls_golite062009
cytoskeletal protein binding	0.66737572008694	bayes_pls_golite062009
substrate-specific transporter activity	0.65168535727044	bayes_pls_golite062009
structure-specific DNA binding	0.384349606267362	bayes_pls_golite062009
structural molecule activity	0.279533827088985	bayes_pls_golite062009
transcription factor activity	0.131703572961748	bayes_pls_golite062009

Term	Confidence	Notes
binding	2.96084803796407	bayes_pls_golite062009
protein transporter activity	2.47190066960729	bayes_pls_golite062009
nucleic acid binding	1.67566088591721	bayes_pls_golite062009
protein binding	1.61131270705552	bayes_pls_golite062009
transcription regulator activity	0.845665181662967	bayes_pls_golite062009
DNA binding	0.806448013051712	bayes_pls_golite062009
protein transmembrane transporter activity	0.795583320946118	bayes_pls_golite062009
cytoskeletal protein binding	0.66737572008694	bayes_pls_golite062009
substrate-specific transporter activity	0.65168535727044	bayes_pls_golite062009
structure-specific DNA binding	0.384349606267362	bayes_pls_golite062009
structural molecule activity	0.279533827088985	bayes_pls_golite062009
transcription factor activity	0.131703572961748	bayes_pls_golite062009

No functions predicted.

Reference: Malmström L, et al. (2007) Superfamily assignments for the yeast proteome through integration of structure prediction with the gene ontology. PLoS Biol 5(4): e76. doi:10.1371/journal.pbio.0050076

Philius Transmembrane Prediction:

Protein predicted to be:	GLOBULAR (No transmembrane regions or signal peptide)
Confidence of classification:	0.98

Source: Reynolds et al. (2008)

TMHMM	2.0c	PSIPRED	v2.61
SignalP	3.0	COILS	1999
DISOPRED	v0.1	NCBI nr	06/2007
PSI-BLAST	2.2.18	FFAS	ffas03
PDB	06/2007	Pfam	22
HMMER	2.3.2