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Expanding the Catalog of cas Genes with Metagenomes

Introduction

• This website deposites the Cas proteins predicted from complete/draft genomes and metagenomes.
• Please cite this paper: Quan Zhang, Thomas G. Doak and Yuzhen Ye. Expanding the catalog of cas genes with metagenomes, Nucleic Acids Research, doi: 10.1093/nar/gkt1262, 2013

Cas9

• The collection of 497 Cas9 sequences (90% non-redundant, with conserved active sites): multiple alignment used to produce Fig. 1 in our paper
• You may get unfiltered Cas9 sequences below (Download sequences of individual families -> Known Cas families -> choose TIGR01865:cas_Csn1 and TIGR03031:cas_csx12)

Models of 24 novel Cas families: alignments and HMMs

• The alignments of seed set in STOCKHOLM format (download)
• HMMs of 24 novel Cas families, each contains at least five sequences (download)
• The corresponding nucleotide sequences from 24 novel Cas families (download)
• Other datasets: 2,836 putative Cas protein sequences encoded by genes located in cas loci, but were not annotated as CRISPR-associated protein families (with 90% identity)(download); the sequences that were not clustered (called "singleton") (download)

Download sequences of individual families

>> Novel Cas protein family cmr7 cmr8 cmr9 cash1 cash2 cash3 cash4 cash5 cash6 cash7 cash8 cash9 cash10 cash11 cash12 cash13 cash14 cash15 cash16 cash17 cash18 cash19 cash20 cash21

>> Old families that are associated with CRISPR-Cas immune systems 23S_rRNA_IVP 2OG-FeII_Oxy_3 AAA_10 AAA_14 AAA_21 AAA_30 Antitoxin-MazE Arch_ATPase Bro-N DDE_3 DDE_Tnp_1 DEDD_Tnp_IS110 DUF1016 DUF1814 DUF1887 DUF2276 DUF262 DUF3990 DUF4143 DUF4433 DUF772 DUF86 DUF87 Fic Gar1 HTH_11 HTH_21 HTH_29 HTH_Tnp_1 IstB_IS21 KilA-N Metallophos_2 NTP_transf_2 NurA OrfB_IS605 PIN PhdYeFM_antitox Plasmid_stabil rve RVT_1 Radical_SAM SIR2_2 TIGR00040 TIGR01439 TIGR01552 TIGR02436 TIGR03698 Transposase_20 Transposase_mut Uma2 UvrD-helicase UvrD_C_2 VirE_N Virulence_RhuM WYL Y1_Tnp

>> Known Cas families

PF01867.11:Cas_Cas1(gene,protein)	PF03787.10:RAMPs(gene,protein)	PF08798.6:CRISPR_assoc(gene,protein)
PF09455.5:Cas_DxTHG(gene,protein)	PF09481.5:CRISPR_Cse1(gene,protein)	PF09484.5:Cas_TM1802(gene,protein)
PF09485.5:CRISPR_Cse2(gene,protein)	PF09559.5:Cas6(gene,protein)	PF09609.5:Cas_GSU0054(gene,protein)
PF09611.5:Cas_Csy1(gene,protein)	PF09614.5:Cas_Csy2(gene,protein)	PF09615.5:Cas_Csy3(gene,protein)
PF09617.5:Cas_GSU0053(gene,protein)	PF09618.5:Cas_Csy4(gene,protein)	PF09620.5:Cas_csx3(gene,protein)
PF09623.5:Cas_NE0113(gene,protein)	PF09651.5:Cas_APE2256(gene,protein)	PF09652.5:Cas_VVA1548(gene,protein)
PF09657.5:Cas_Csx8(gene,protein)	PF09658.5:Cas_Csx9(gene,protein)	PF09659.5:Cas_Csm6(gene,protein)
PF09670.5:Cas_Cas02710(gene,protein)	PF09700.5:Cas_Cmr3(gene,protein)	PF09701.5:Cas_Cmr5(gene,protein)
PF09702.5:Cas_Csa5(gene,protein)	PF09703.5:Cas_Csa4(gene,protein)	PF09704.5:Cas_Cas5d(gene,protein)
PF09706.5:Cas_CXXC_CXXC(gene,protein)	PF09707.5:Cas_Cas2CT1978(gene,protein)	PF09709.5:Cas_Csd1(gene,protein)
PF09711.5:Cas_Csn2(gene,protein)	TIGR00287:cas1(gene,protein)	TIGR00372:cas4(gene,protein)
TIGR01573:cas2(gene,protein)	TIGR01587:cas3_core(gene,protein)	TIGR01595:cas_CT1132(gene,protein)
TIGR01596:cas3_HD(gene,protein)	TIGR01863:cas_Csd1(gene,protein)	TIGR01865:cas_Csn1(gene,protein)
TIGR01866:cas_Csn2(gene,protein)	TIGR01868:casD_Cas5e(gene,protein)	TIGR01869:casC_Cse4(gene,protein)
TIGR01870:cas_TM1810_Csm2(gene,protein)	TIGR01873:cas_CT1978(gene,protein)	TIGR01874:cas_cas5a(gene,protein)
TIGR01875:cas_MJ0381(gene,protein)	TIGR01876:cas_Cas5d(gene,protein)	TIGR01877:cas_cas6(gene,protein)
TIGR01878:cas_Csa5(gene,protein)	TIGR01881:cas_Cmr5(gene,protein)	TIGR01884:cas_HTH(gene,protein)
TIGR01888:cas_cmr3(gene,protein)	TIGR01894:cas_TM1795_cmr1(gene,protein)	TIGR01895:cas_Cas5t(gene,protein)
TIGR01896:cas_AF1879(gene,protein)	TIGR01897:cas_MJ1666(gene,protein)	TIGR01898:cas_TM1791_cmr6(gene,protein)
TIGR01899:cas_TM1807_csm5(gene,protein)	TIGR01903:cas_TM1808_csm4(gene,protein)	TIGR01907:casE_Cse3(gene,protein)
TIGR01908:cas_CXXC_CXXC(gene,protein)	TIGR01914:cas_Csa4(gene,protein)	TIGR02165:cas_GSU0054(gene,protein)
TIGR02221:cas_TM1812(gene,protein)	TIGR02547:casA_cse1(gene,protein)	TIGR02548:casB_cse2(gene,protein)
TIGR02549:CRISPR_DxTHG(gene,protein)	TIGR02556:cas_TM1802(gene,protein)	TIGR02562:cas3_yersinia(gene,protein)
TIGR02563:cas_Csy4(gene,protein)	TIGR02564:cas_Csy1(gene,protein)	TIGR02565:cas_Csy2(gene,protein)
TIGR02566:cas_Csy3(gene,protein)	TIGR02570:cas_GSU0053(gene,protein)	TIGR02577:cas_TM1794_Cmr2(gene,protein)
TIGR02578:cas_TM1811_Csm1(gene,protein)	TIGR02579:cas_csx3(gene,protein)	TIGR02580:cas_RAMP_Cmr4(gene,protein)
TIGR02581:cas_cyan_RAMP(gene,protein)	TIGR02582:cas_TM1809(gene,protein)	TIGR02583:DevR_archaea(gene,protein)
TIGR02584:cas_NE0113(gene,protein)	TIGR02585:cas_Cst2_DevR(gene,protein)	TIGR02586:cas_devS(gene,protein)
TIGR02589:cas_Csd2(gene,protein)	TIGR02590:cas_Csh2(gene,protein)	TIGR02591:cas_Csh1(gene,protein)
TIGR02592:cas_Cas5h(gene,protein)	TIGR02593:CRISPR_cas5(gene,protein)	TIGR02619:TIGR02619(gene,protein)
TIGR02620:cas_VVA1548(gene,protein)	TIGR02621:cas3_GSU0051(gene,protein)	TIGR02670:cas_csx8(gene,protein)
TIGR02672:cas_csm6(gene,protein)	TIGR02674:cas_cyan_RAMP_2(gene,protein)	TIGR02682:cas_csx11(gene,protein)
TIGR02710:TIGR02710(gene,protein)	TIGR02807:cas6_var(gene,protein)	TIGR03031:cas_csx12(gene,protein)
TIGR03114:cas_csf1(gene,protein)	TIGR03115:cas_csf2(gene,protein)	TIGR03116:cas_csf3(gene,protein)
TIGR03117:cas_csf4(gene,protein)	TIGR03157:cas_Csc2(gene,protein)	TIGR03158:cas3_cyano(gene,protein)
TIGR03159:cas_Csc1(gene,protein)	TIGR03174:cas_Csc3(gene,protein)	TIGR03485:cas_csx13_N(gene,protein)
TIGR03486:cas_csx13_C(gene,protein)	TIGR03487:cas_csp2(gene,protein)	TIGR03488:cas_Cas5p(gene,protein)
TIGR03489:cas_csp1(gene,protein)	TIGR03637:cas1_YPEST(gene,protein)	TIGR03638:cas1_ECOLI(gene,protein)
TIGR03639:cas1_NMENI(gene,protein)	TIGR03640:cas1_DVULG(gene,protein)	TIGR03641:cas1_HMARI(gene,protein)
TIGR03642:cas_csx14(gene,protein)	TIGR03876:cas_csaX(gene,protein)	TIGR03983:cas1_MYXAN(gene,protein)
TIGR03984:TIGR03984(gene,protein)	TIGR03985:TIGR03985(gene,protein)	TIGR03986:TIGR03986(gene,protein)
TIGR04093:cas1_CYANO(gene,protein)	TIGR04106:cas_GSU0052(gene,protein)	TIGR04113:cas_csx17(gene,protein)
TIGR04328:cas4_PREFRAN(gene,protein)	TIGR04329:cas1_PREFRAN(gene,protein)	TIGR04330:cas_Cpf1(gene,protein)





Assorted functions associated with the CRISPR–Cas immune system

• The list of phylogenetic tree of top 21 assorted functions associated with the CRISPR-Cas immune system (download)
• The functions that can be assigned to at least ten proteins encoded by genes located in cas loci

Function name (Pfam id or TIGRFAM id)	# of sequences assigned	Description
WYL(PF13280)(gene,protein)	25	transcriptional regulation function by binding to an unknown ligand
rve(gene,protein)	24	an enzyme produced by a retrovirus
AAA_21(gene,protein)	22	ATPases Associated with diverse cellular Activities;They share a common conserved module of approximately 230 amino acid residues
DDE_Tnp_1(PF01609)(gene,protein)	20	Transposase
RVT_1(PF00078)(gene,protein)	19	Reverse transcriptase
DUF2276(PF10040)(gene,protein)	19	unchararized
Uma2(PF05685)(gene,protein)	18	Restriction endonuclease
TIGR02436/23S_rRNA_IVP(PF05635)(gene,protein)	18	23S rRNA-intervening sequence protein
PIN(PF01850)(gene,protein)	16	nuclease enzymes that cleave single stranded RNA
HTH_Tnp_1(PF01527)(gene,protein)	16	helix-turn-helix (HTH); a major structural motif capable of binding DNA
Transposase_mut(PF00872)(gene,protein)	14	Transposase
Transposase_20(PF02371)(gene,protein)	13	Transposase
HTH_21(PF13276)(gene,protein)	13	helix-turn-helix (HTH); a major structural motif capable of binding DNA
DUF772(PF05598)(gene,protein)	13	This presumed domain is found at the N-terminus of many proteins found in transposons
DEDD_Tnp_IS110(PF01548)(gene,protein)	13	Transposase
VirE_N(PF08800)(gene,protein)	12	N-terminus of VirE proteins
Virulence_RhuM(PF13310)(gene,protein)	11	no experimental data for members of this group or their homologues. However, these proteins are implicated in virulence/pathogenicity
NTP_transf_2(PF01909)(gene,protein)	11	Nucleotidyltransferase domain
Plasmid_stabil(PF05016)(gene,protein)	10	toxin
Fic(PF02661)(gene,protein)	10	toxin




• For questions or comments contact: Quan Zhang (quzhang@indiana.edu); Yuzhen Ye (yye@indiana.edu)

Last modified on October 21, 2013