HHsearch alignment for GI: 254780766 and conserved domain: TIGR02169

>TIGR02169 SMC_prok_A chromosome segregation protein SMC; InterPro: IPR011891 The SMC (structural maintenance of chromosomes) family of proteins, exist in virtually all organisms including both bacteria and archaea. The SMC proteins are essential for successful chromosome transmission during replication and segregation of the genome in all organisms and form three types of heterodimer (SMC1SMC3, SMC2SMC4, SMC5SMC6), which are core components of large multiprotein complexes. The best known complexes are cohesin, which is responsible for sister-chromatid cohesion, and condensin, which is required for full chromosome condensation in mitosis. SMCs are generally present as single proteins in bacteria, and as at least six distinct proteins in eukaryotes. The proteins range in size from approximately 110 to 170 kDa, and share a five-domain structure, with globular N- and C-terminal (IPR003395 from INTERPRO) domains separated by a long (circa 100 nm or 900 residues) coiled coil segment in the centre of which is a globular ''hinge'' domain, characterised by a set of four highly conserved glycine residues that are typical of flexible regions in a protein. The amino-terminal domain contains a 'Walker A' nucleotide-binding domain (GxxGxGKS/T), which by mutational studies has been shown to be essential in several proteins. The carboxy-terminal domain contains a sequence (the DA-box) that resembles a 'Walker B' motif (XXXXD, where X is any hydrophobic residue), and a LSGG motif with homology to the signature sequence of the ATP-binding cassette (ABC) family of ATPases . All SMC proteins appear to form dimers, either forming homodimers with themselves, as in the case of prokaryotic SMC proteins, or heterodimers between different but related SMC proteins. The dimers are arranged in an antiparallel alignment. This orientation brings the N- and C-terminal globular domains (from either different or identical protamers) together, which unites an ATP binding site (Walker A motif) within the N-terminal domain with a Walker B motif (DA box) within the C-terminal domain, to form a potentially functional ATPase. Protein interaction and microscopy data suggest that SMC dimers form a ring-like structure which might embrace DNA molecules. Non-SMC subunits associate with the SMC amino- and carboxy-terminal domains. The sequence homology within the carboxy-terminal domain is relatively high within the SMC1-SMC4 group, whereas SMC5 and SMC6 show some divergence in both of these sequences. SMCs share not only sequence similarity but also structural similarity with ABC proteins. SMC proteins function together with other proteins in a range of chromosomal transactions, including chromosome condensation, sister-chromatid cohesion, recombination, DNA repair and epigenetic silencing of gene expression . This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by IPR011890 from INTERPRO. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent ..
Probab=98.75  E-value=2.7e-07  Score=66.86  Aligned_cols=174  Identities=15%  Similarity=0.198  Sum_probs=114.6

Q ss_pred             CCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHH-HHHHH---HHHHHHHHHHHHHHC
Q ss_conf             01000135846778887777666667988630565432100245653279999999-99999---999999999998531
Q gi|254780766|r  144 LDRMVFAIDPRHRRRMIDFERLMRGRNRLLTEGYFDSSWCSSIEAQMAELGVKINI-ARVEM---INALSSLIMEYVQKE  219 (375)
Q Consensus       144 lD~~i~~~~~~y~~~l~~y~K~LkqRN~lLk~~~~d~~~l~~~~~qla~~~~~I~~-~R~~~---l~~l~~~l~~~~~~~  219 (375)
T Consensus      1000 ~~~~~~~LepVNm~AI~eYe~~~~r~~eL-~~K---~~~L~~Er~~i~~rI~~~e~~Kr~~F~~aF~~IN~~f~~iF~~L 1075 (1202)
T TIGR02169      1000 VEEEIRALEPVNMLAIQEYEEVEKRLDEL-KEK---RAKLEEEREEILERIEEYEKKKREVFMEAFEAINENFKEIFAEL 1075 (1202)
T ss_pred             HHHHHHHHCCCCCCCHHHHHHHHHHHHHH-HHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             99998641430143322179999998769-999---99999989999999999887889999999999999999999853


Q ss_pred             C-CCCEEEEECCCCCCCCCCCHHHHHHHHHHHHHHCCCHHHCCEEECCCCCCEEEECCCCCCCHHH-HHCCCHHHHHHHH
Q ss_conf             6-4301122015666765589678888765455311100000000025732001100124551023-3122058999999
Q gi|254780766|r  220 N-FPHIKLSLTGFLDGKFDQSFCALKEEYAKKLFDGRKMDSMSRRTLIGPHRSDLIVDYCDKAITI-AHGSTGEQKVVLV  297 (375)
Q Consensus       220 ~-~~~~~~~l~~~~~~~~~~~~~~~~e~~~~~L~~~~~~d~~~~~t~~Gphr~d~~~~~~~~~~~~-~~~S~Gqqk~~~l  297 (375)
T Consensus      1076 SP~G~g~L~Le~-PdDPF~GGl-------------------------------~l~a~P~~K~vqrleAMSGGEKSLtAL 1123 (1202)
T TIGR02169      1076 SPGGTGELILEN-PDDPFAGGL-------------------------------ELKAKPKGKPVQRLEAMSGGEKSLTAL 1123 (1202)
T ss_pred             CCCCCEEEECCC-CCCCCCCCC-------------------------------EEEEEECCCCEEEHHHCCCCHHHHHHH
T ss_conf             889824654358-887436871-------------------------------788873788502022103838999999


Q ss_pred             HHHHHHHHHHHHHCCCCCEEEEECCHHCCCHHHHHHHHHHHHHC--CCCEEEEECCHHHHHHH
Q ss_conf             99999999999870899789980122015989999999997417--98099980696785432
Q gi|254780766|r  298 GIFLAHARLISNTTGFAPILLLDEISAHLDEDKRNALFRIVTDI--GSQIFMTGTDKSVFDSL  358 (375)
Q Consensus       298 ~l~La~~~~~~~~~~~~pilLiDdi~s~LD~~~~~~ll~~l~~~--~~Qv~iTt~~~~~~~~~  358 (375)
T Consensus      1124 sFIFA-----iQ~y~PsPFYafDEVDmfLD~~Nverva~li~~~s~~AQFIVvSLR~~m~~~A 1181 (1202)
T TIGR02169      1124 SFIFA-----IQRYKPSPFYAFDEVDMFLDGVNVERVAKLIKEKSKEAQFIVVSLRKPMIEAA 1181 (1202)
T ss_pred             HHHHH-----HHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCEEEEEEECCHHHHHHH
T ss_conf             99999-----96218985404446777751875999999998604863467776235899876