HHsearch alignment for GI: 254780229 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=97.22  E-value=0.034  Score=37.84  Aligned_cols=77  Identities=30%  Similarity=0.402  Sum_probs=45.5

Q ss_pred             CCCE-EEECCCCCCCHHHHHHHHHHHHH-----------------CC-----C----------EEEEEECCHH-H-----
Q ss_conf             8955-99428787703899999999996-----------------79-----8----------2899601058-9-----
Q gi|254780229|r  419 GKNL-IIEGPPGTGKSQTITNIIAAAML-----------------HG-----K----------KILFCAQKMA-A-----  459 (1775)
Q Consensus       419 g~~~-vi~GPPGTGKSQTIaNlIa~~la-----------------~G-----k----------~VLfVaeK~a-A-----  459 (1775)
T Consensus        23 ~~GFtvIsGPNGSGKS-NI~DaiLFaLGl~s~k~~RAe~LsDLi~~gahe~~~~~~~~~ea~V~v~F~nd~~~~prsqvt  101 (1202)
T ss_conf             8888478888888645-599999997664102342221052224487422235688996898988872278758731000

Q ss_conf             ----------9--99998644358441-3-654026611089999999999
Q gi|254780229|r  460 ----------I--EVVRHRLEKAGLGE-F-CLELHSHKVHKRAILDDLRKR  496 (1775)
Q Consensus       460 ----------L--dVV~~RL~~~gLg~-~-cleLHs~ka~k~~vl~~L~~~  496 (1775)
T Consensus       102 taaGsenv~~vde~~v~Rr~kv~~~~~yySyY~lNG~~~~l~ei~d~L~~~  152 (1202)
T ss_conf             022444444224358998888737984688888708203576689999861