HHsearch alignment for GI: 254780601 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=96.45  E-value=0.063  Score=32.13  Aligned_cols=140  Identities=19%  Similarity=0.228  Sum_probs=76.7

Q ss_pred             CEEEECCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCCEEEEECCCHHHHHHHHHHHHHHHHHCCCEEEEEECCCCHHHHH
Q ss_conf             69999289874689999999998610421225568827999849989999999999998544698799998899879999
Q gi|254780601|r   39 DVLVSAQTGSGKTVAFGLALASTLLAENDRFSPASAPLALAIAPTRELAVQVGRELEWLYAKTGVVVAVCIGGVSVHRER  118 (573)
Q Consensus        39 d~i~~a~TGsGKT~af~lp~l~~l~~~~~~~~~~~~~~~lil~PTrELa~Qv~~~~~~l~~~~~~~v~~~~gg~~~~~q~  118 (573)
T Consensus       326 G~iWH-tQGSGKtlTm~f~A~k-~~~~~----~~~~p~v~fvvDR~eLd~Ql~~~~~~~~~~--~-~~~~~~~eS~~~Lk  396 (813)
T TIGR00348       326 GLIWH-TQGSGKTLTMLFLARK-LRKQK----ELKNPKVFFVVDRRELDEQLYKEFSSLKDL--I-KDCAERIESIAELK  396 (813)
T ss_pred             CEEEE-EECCCHHHHHHHHHHH-HHHHH----HHCCCEEEEEEECHHHHHHHHHHHHHHHHH--C-HHHHHCCCCHHHHH
T ss_conf             44898-5076378899999999-98746----526984999972727788999999876420--1-01042067888999


Q ss_pred             HHHCC------C-----CEEEEECCCCHHH--------HHHCCC----CCCCCCEEEEEECCCCC--------CCCHHHH
Q ss_conf             96128------9-----7599822310133--------210001----22464318999613110--------0100123
Q gi|254780601|r  119 RDLQN------G-----AHIVVGTPGRLCD--------HIRGKG----LNISHLKAVVLDEADEM--------LDLGFRD  167 (573)
Q Consensus       119 ~~l~~------~-----~~iiv~TPgrl~d--------~~~~~~----l~l~~v~~lVlDEaD~m--------l~~gf~~  167 (573)
T Consensus       397 ~~L~~~~~sennPn~~k~g~~~t~IqKF~~~~~~k~~e~~~~~~~~i~~~r~~v-v~i~DEaHRsqyG~tqklhnGkfqt  475 (813)
T TIGR00348       397 ELLEKNDESENNPNISKRGIIITTIQKFDDELLDKLKEEEEKFPESIIIDRKEV-VVIIDEAHRSQYGKTQKLHNGKFQT  475 (813)
T ss_pred             HHHHHCCCCCCCCCCCCCCEEEEEEECCCHHHHHHHHHHHHCCCCEEEEEECCE-EEEEECCCCCCCCCCCCCCCCHHHH
T ss_conf             987517764567553567679996001040344536888743873689871608-9997067555353411000441358


Q ss_pred             HHHHHHHHCCCCCCEEEEECC
Q ss_conf             578887521433422563111
Q gi|254780601|r  168 DIEFILDSSPKKRRMLMFSAT  188 (573)
Q Consensus       168 ~i~~i~~~~p~~~q~~l~SAT  188 (573)
T Consensus       476 Gla~~~~~~lknA~f~gFTGT  496 (813)
T TIGR00348       476 GLAKALKKALKNASFFGFTGT  496 (813)
T ss_pred             HHHHHHHHHCHHHHHHCCCCC
T ss_conf             999999874311201012247