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