HHsearch alignment for GI: 254780382 and conserved domain: TIGR00348
>TIGR00348 hsdR type I site-specific deoxyribonuclease, HsdR family; InterPro: IPR004473 There are four classes of restriction endonucleases: types I, II,III and IV. All types of enzymes recognise specific short DNA sequences and carry out the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. They differ in their recognition sequence, subunit composition, cleavage position, and cofactor requirements , , as summarised below: Type I enzymes (3.1.21.3 from EC) cleave at sites remote from recognition site; require both ATP and S-adenosyl-L-methionine to function; multifunctional protein with both restriction and methylase (2.1.1.72 from EC) activities. Type II enzymes (3.1.21.4 from EC) cleave within or at short specific distances from recognition site; most require magnesium; single function (restriction) enzymes independent of methylase. Type III enzymes (3.1.21.5 from EC) cleave at sites a short distance from recognition site; require ATP (but doesn't hydrolyse it); S-adenosyl-L-methionine stimulates reaction but is not required; exists as part of a complex with a modification methylase methylase (2.1.1.72 from EC). Type IV enzymes target methylated DNA. Type I restriction endonucleases are components of prokaryotic DNA restriction-modification mechanisms that protects the organism against invading foreign DNA. Type I enzymes have three different subunits subunits - M (modification), S (specificity) and R (restriction) - that form multifunctional enzymes with restriction (3.1.21.3 from EC), methylase (2.1.1.72 from EC) and ATPase activities , . The S subunit is required for both restriction and modification and is responsible for recognition of the DNA sequence specific for the system. The M subunit is necessary for modification, and the R subunit is required for restriction. These enzymes use S-Adenosyl-L-methionine (AdoMet) as the methyl group donor in the methylation reaction, and have a requirement for ATP. They recognize asymmetric DNA sequences split into two domains of specific sequence, one 3-4 bp long and another 4-5 bp long, separated by a nonspecific spacer 6-8 bp in length. Cleavage occurs a considerable distance from the recognition sites, rarely less than 400 bp away and up to 7000 bp away. Adenosyl residues are methylated, one on each strand of the recognition sequence. These enzymes are widespread in eubacteria and archaea. In enteric bacteria they have been subdivide into four families: types IA, IB, IC and ID. This entry represents the R subunit (HsdR) of type I restriction endonucleases such as EcoRI (3.1.21.3 from EC), which recognises the DNA sequence 5'-GAATTC; the R protein (HsdR) is required for both nuclease and ATPase activity , , , .; GO: 0003677 DNA binding, 0005524 ATP binding, 0009035 Type I site-specific deoxyribonuclease activity, 0009307 DNA restriction-modification system.
Probab=98.41 E-value=7.6e-07 Score=63.03 Aligned_cols=297 Identities=17% Similarity=0.315 Sum_probs=151.2
Q ss_pred EEEECCCCCCHHHHHHHHHHHHHHCCCCCCCCCEEEEECCCHHHHHHHHHHHHHHC---CCCCCCCCCCCCCCCCCCCCC
Q ss_conf 99982798517899999999998606521478279998285899999999987410---233322100001222222222
Q gi|254780382|r 41 VCGIAQTGTGKTASFVLPMLTILEKGRARVRMPRTLILEPTRELAAQVADNFEKYG---KNYNLTVALLIGGIPFEAQNK 117 (465)
Q Consensus 41 vi~~apTGsGKT~~~~lp~l~~l~~~~~~~~~~~~lil~PtreLa~Qi~~~~~~~~---~~~~l~~~~~~gg~~~~~~~~ 117 (465)
T Consensus 326 G~iWHtQGSGKtlTm~f--~A~k~~~~~~~~~p~v~fvvDR~eLd~Ql~~~~~~~~~~~~~~~~~~------eS~~~Lk~ 397 (813)
T TIGR00348 326 GLIWHTQGSGKTLTMLF--LARKLRKQKELKNPKVFFVVDRRELDEQLYKEFSSLKDLIKDCAERI------ESIAELKE 397 (813)
T ss_pred CEEEEEECCCHHHHHHH--HHHHHHHHHHHCCCEEEEEEECHHHHHHHHHHHHHHHHHCHHHHHCC------CCHHHHHH
T ss_conf 44898507637889999--99999874652698499997272778899999987642010104206------78889999
Q ss_pred CCC-----------CHHHHHHCCCCHHHH----HHH----CCC--CCCCCCE-EECCCCCCCCCCCC-------------
Q ss_conf 221-----------011221022102333----320----000--0012100-10255100000001-------------
Q gi|254780382|r 118 KLE-----------RGADVLICTPGRILD----HFN----RGK--LLMNNIE-ILVIDEADRMLDMG------------- 162 (465)
Q Consensus 118 ~l~-----------~~~~IiV~TP~rl~~----~l~----~~~--~~l~~~~-~lViDEah~l~~~g------------- 162 (465)
T Consensus 398 ~L~~~~~sennPn~~k~g~~~t~IqKF~~~~~~k~~e~~~~~~~~i~~~r~~vv~i~DEaHRs-qyG~tqklhnGkfqtG 476 (813)
T TIGR00348 398 LLEKNDESENNPNISKRGIIITTIQKFDDELLDKLKEEEEKFPESIIIDRKEVVVIIDEAHRS-QYGKTQKLHNGKFQTG 476 (813)
T ss_pred HHHHCCCCCCCCCCCCCCEEEEEEECCCHHHHHHHHHHHHCCCCEEEEEECCEEEEEECCCCC-CCCCCCCCCCCHHHHH
T ss_conf 875177645675535676799960010403445368887438736898716089997067555-3534110004413589
Q ss_pred CHHHHHHHHHHHCCCCCCCCCCCCCCC----C----CCCCC---CCCCCCCC-----------CCCCCCCCC------CC
Q ss_conf 003578875431022222333432112----2----22111---12222210-----------013444321------23
Q gi|254780382|r 163 FIPYIQNITSLVPFTRQTLLFSATMTD----E----LQKVS---ENFLQNPK-----------RIEVNTPSS------TA 214 (465)
Q Consensus 163 f~~~i~~i~~~~~~~~q~i~~SAT~~~----~----v~~l~---~~~l~~~~-----------~i~v~~~~~------~~ 214 (465)
T Consensus 477 la~~~~~---~lk-nA~f~gFTGTPI~~~d~~T~nP~~~fgy~~e~Ylh~Y~I~dai~Dg~V~~v~i~Y~~~~~~~~~~~ 552 (813)
T TIGR00348 477 LAKALKK---ALK-NASFFGFTGTPISKKDRDTFNPLEVFGYPFEKYLHRYFITDAIRDGKVVTVKIEYEARLVEDHLLK 552 (813)
T ss_pred HHHHHHH---HCH-HHHHHCCCCCCCCHHCCCCCCCCHHCCCCCCCEEEECCHHHHHHCCCEEEEEEEECCHHHHHHHHH
T ss_conf 9999987---431-120101224776532477666210026789864310321455207845788743210102454210
Q ss_pred -----CCCC----CCCCCC---------------------------CCCCCHHHHHH----HHCCCCC----------CC
Q ss_conf -----4642----111112---------------------------22211024443----2101223----------45
Q gi|254780382|r 215 -----ETIE----HCFVAT---------------------------YAQYSKKCALL----QQLLQSQ----------DT 244 (465)
Q Consensus 215 -----~~i~----~~~~~~---------------------------~~~~~~k~~~l----~~l~~~~----------~~ 244 (465)
T Consensus 553 ~etde~~~~~~~~~~~~~~~~~i~~~~~~~lk~~~~~~~~~fPG~~~~~~~~~~~~~~di~~h~~~~~~~~eE~anks~~ 632 (813)
T TIGR00348 553 SETDEEKLEAFLDEIFELLPERIREITKESLKEKLQKLKLSFPGKILENEDRLEEIAKDIAEHFAKFKELREEEANKSSF 632 (813)
T ss_pred CCCCCHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHCCCCHHHHHHCCCC
T ss_conf 02675678988766764124420547789999999762123587524698999999999999998331011234311464
Q ss_pred CCEEEEEECCCC-CCCCCCCCCCCC-----------CCC-----------------CCCCCCCCC---------------
Q ss_conf 650677621344-322222222223-----------322-----------------222345420---------------
Q gi|254780382|r 245 MKNGIIFCNQKK-NVVNLCHSLEKQ-----------GFS-----------------VCAIHGNID--------------- 280 (465)
Q Consensus 245 ~~k~iIF~~t~~-~~~~l~~~L~~~-----------g~~-----------------v~~lhg~l~--------------- 280 (465)
T Consensus 633 ~~kAMvVa~sr~n~c~~~~~~l~~~~~e~~~~~~~~~~~~~v~t~~~~d~s~~sYki~~Y~~~~~~k~~~~dekkaln~~ 712 (813)
T TIGR00348 633 KFKAMVVAISRKNACVEFKKALDEELNEKVADITEEEAIEIVMTGKKSDESEESYKIRDYNKHLRKKFEKSDEKKALNNV 712 (813)
T ss_pred CCCCEEEEECHHHHHHHHHHHHHHHCCCCCCCCCCCCCEEEEECCCCCCCHHHCCCHHHHHHHHHHCCCCCHHHHHHHHH
T ss_conf 56744886224789999999987417873100257764356313377741454058478888985205864478887544
Q ss_pred HHHHHHHHHHHCC--CCCEEEEEHHHHHHHHCCCCCCEEEEECCCCCHHHHHHHHHCCCC----CCC----CEEEEEEEC
Q ss_conf 3332344442013--552388884664644078876500200246778998875210245----888----539999778
Q gi|254780382|r 281 QRSRMKILSNFKE--GTIQLMVASDLAARGLDIPDVGHVFNFDVPNRAENYIHRIGRTGR----AGR----HGKAFTLVA 350 (465)
Q Consensus 281 ~~~R~~~~~~F~~--g~~~vLV~Td~~~~GiDip~v~~VI~~d~P~~~~~y~hR~GR~gR----~g~----~G~~i~~~~ 350 (465)
T Consensus 713 ~e~~~~~~~~F~~p~~~~k~LIV~dMlLTGFDAP~L~TlY-~DK~lK~H~L~QA~aR~NRPfv~d~k~~K~~GlIVDy~g 791 (813)
T TIGR00348 713 KEIYEKLLERFKDPEENLKLLIVVDMLLTGFDAPILNTLY-LDKPLKDHGLLQAIARVNRPFVLDAKDDKTFGLIVDYVG 791 (813)
T ss_pred HHHHHHHHHHHCCCCCCCCEEEEECCCCCCCCHHHHHHHH-CCCCHHCHHHHHHHHHHCCCEECCCCCCCCCCEEEEECC
T ss_conf 5577688987078888884798707702256611233230-121000002678887631560215544688741688403
Q ss_pred H
Q ss_conf 8
Q gi|254780382|r 351 K 351 (465)
Q Consensus 351 ~ 351 (465)
T Consensus 792 l 792 (813)
T TIGR00348 792 L 792 (813)
T ss_pred H
T ss_conf 1