HHsearch alignment for GI: 254781172 and conserved domain: TIGR00574

>TIGR00574 dnl1 DNA ligase I, ATP-dependent (dnl1); InterPro: IPR000977 DNA ligase (polydeoxyribonucleotide synthase) is the enzyme that joins two DNA fragments by catalysing the formation of an internucleotide ester bond between phosphate and deoxyribose. It is active during DNA replication, DNA repair and DNA recombination. There are two forms of DNA ligase, one requires ATP (6.5.1.1 from EC), the other NAD (6.5.1.2 from EC), the latter being restricted to eubacteria. Eukaryotic, archaebacterial, viral and some eubacterial DNA ligases are ATP-dependent. The first step in the ligation reaction is the formation of a covalent enzyme-AMP complex. The co-factor ATP is cleaved to pyrophosphate and AMP, with the AMP being covalently joined to a highly conserved lysine residue in the active site of the ligase. The activated AMP residue is then transferred to the 5'phosphate of the nick, before the nick is sealed by phosphodiester-bond formation and AMP elimination ,. Vertebrate cells encode three well-characterised DNA ligases (DNA ligases I, III and IV), all of which are related in structure and sequence. With the exception of the atypically small PBCV-1 viral enzyme, two regions of primary sequence are common to all members of the family. The catalytic region comprises six conserved sequence motifs (I, III, IIIa, IV, V-VI), motif I includes the lysine residue that is adenylated in the first step of the ligation reaction. The function of the second, less well-conserved region is unknown. When folded, each protein comprises of two distinct sub-domains: a large amino-terminal sub-domain ('domain 1') and a smaller carboxy-terminal sub-domain ('domain 2'). The ATP-binding site of the enzyme lies in the cleft between the two sub-domains. Domain 1 consists of two antiparallel beta sheets flanked by alpha helices, whereas domain 2 consists of a five-stranded beta barrel and a single alpha helix, which form the oligonucleotide-binding fold , . ; GO: 0003910 DNA ligase (ATP) activity, 0005524 ATP binding, 0006260 DNA replication, 0006281 DNA repair, 0006310 DNA recombination.
Probab=96.83  E-value=0.038  Score=35.75  Aligned_cols=221  Identities=18%  Similarity=0.145  Sum_probs=123.1

Q ss_pred             CCCCCCHHHCCCHHHHHHHHHHHH-------HHHCCCCCCCCEEEEEEECCEEEEEEEE-ECCEEEEEEECCCCHHHHHH
Q ss_conf             664257021599999999999999-------8612467776119999415818999998-59989988865986556669
Q gi|254781172|r   92 SIPTLSLEKIWNIEDLRKFITRIY-------RFWQKKDDNSIFFTLEPKIDGTMITIRY-EKGKFVYAALRGDGHSGEDV  163 (731)
Q Consensus        92 ~~pMlSL~k~~~~~el~~w~~~~~-------~~~~~~~~~~~~~~vepKiDG~sisl~Y-~~G~L~~a~TRGdG~~GeDV  163 (731)
T Consensus       196 ~kPMLA~~~~~~~e~l~~~~~RkhemDPPYekkfqeLGL-e~~~~~E~KYDGeR~Q~Hkl~Gd~-~~~FSR----rlen~  269 (705)
T TIGR00574       196 LKPMLAERAKSIEEALKKLGNRKHEMDPPYEKKFQELGL-EDKFLVEYKYDGERVQIHKLDGDE-VKIFSR----RLENI  269 (705)
T ss_pred             CCCHHHHHCCCHHHHHHHCCCCCCCCCCCHHHHHHHCCC-CCCEEEEEECCCHHEEEEEEECCE-EEEEEE----CCCCH
T ss_conf             662047445774799984588724688853234655177-451587640451010012331884-899873----78640


Q ss_pred             HHHHHHHC----C--CCCCCCCCCCCEEEEEEEEEEECHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHCC-C-----HHH
Q ss_conf             99775310----2--4322335445504899999985202123455643148543342345677775234-5-----555
Q gi|254781172|r  164 SACIRAIP----T--IPRVLSLNIPEIIEVRGEVYISKNDFLALNDEMIAVGRKPYANPRNAASGILRRL-N-----PTD  231 (731)
Q Consensus       164 T~n~~~i~----~--iP~~l~~~~~~~ieiRGEv~m~~~~F~~lN~~~~~~g~~~f~NpRN~aaG~lr~~-d-----~~~  231 (731)
T Consensus       270 T~~~p~~~~~s~~~~~~~a~~~~-~~~~IldGE~va~D~~~----------g~~l---PFq~l~~r~~~k~dRqftt~~~  335 (705)
T TIGR00574       270 TYQYPEILSESLTEFIKKAFPGD-IKSCILDGEMVAIDPET----------GKIL---PFQTLLTRAKRKYDRQFTTIDS  335 (705)
T ss_pred             HHHCCCHHHHHHHHHHHHHCCCC-CCEEEEEEEEEEECCCC----------CCCC---CCCHHHHHHHHHHHHHHHHHHH
T ss_conf             22304214564488899745888-66179714678731145----------8216---6413301311112001355676


Q ss_pred             --HHCCCEEE-EEEECCCCCCC--CCCCHHHHHHHHHCCCCCCC-CE-----EEE-ECCCCHHHHHHHHHHHHCCCCCCC
Q ss_conf             --30111056-64102454332--10000368999975996654-14-----887-403211345566553100112343
Q gi|254781172|r  232 --ITRYLNFF-VHGLGKTSEIF--AKGQYEMLQKMRCLGFPVNN-GV-----RQA-NTFHGIVSYYNEMKSIRSTLPYDI  299 (731)
Q Consensus       232 --~~r~L~f~-ay~~~~~~~~~--~~~~~e~l~~L~~~GF~v~~-~~-----~~~-~~~~~~~~~~~~~~~~r~~l~y~i  299 (731)
T Consensus       336 ~~~~~~~~~fl~FD~LY~ng~~L~~~pL~~RR~~L~~i~~~~~nWr~~~~~~~~~~~~~ee~~~~l~~a------i~~g~  409 (705)
T TIGR00574       336 MEKKVPVCLFLVFDILYLNGESLIDEPLIERREILESIVKPIPNWRIEIAEMIDVSDNVEELEKFLNEA------ISEGC  409 (705)
T ss_pred             HHHHCCCEEEEEEEEEEECCCCCCCCCHHHHHHHHHHHCCCCCCEEEEEEEEEECCCCHHHHHHHHHHH------HHCCC
T ss_conf             752014024444656232780355677388999988753528881799974463127989999999999------96389


Q ss_pred             CCEEEEECC---HHCCCCCCCCCCCCCCEEEECCCCCEEEEEEEEEE
Q ss_conf             763777311---00011158765686631231145621589987889
Q gi|254781172|r  300 DGLVYKVDE---FSLQKQLGERARSPRWMISHKFAEKQASTRLLDID  343 (731)
Q Consensus       300 DGiVikvn~---~~~q~~lG~ts~~PrwaiA~Kf~~e~~~T~v~~I~  343 (731)
T Consensus       410 EGlm~K~~~p~~~~Y~p----g~R~~~w-~K~K~~Y~~~~~d~LDLv  451 (705)
T TIGR00574       410 EGLMVKDLEPDEAIYEP----GKRGWLW-LKFKPDYLEGMGDTLDLV  451 (705)
T ss_pred             CEEEECCCCCCCCCCCC----CCCCCCC-EEEECCCCCCCCCEEEEE
T ss_conf             73897046879863147----7778875-033002366567510168