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