HHsearch alignment for GI: 255764514 and conserved domain: TIGR02168
>TIGR02168 SMC_prok_B chromosome segregation protein SMC; InterPro: IPR011890 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 . The smc gene is often associated with scpB (IPR005234 from INTERPRO) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle , , .; GO: 0005515 protein binding, 0005524 ATP binding, 0005694 chromosome.
Probab=97.94 E-value=0.0019 Score=41.63 Aligned_cols=171 Identities=19% Similarity=0.270 Sum_probs=138.6
Q ss_pred CCEEEEECCEEE-EEEEEECCCCEEEEECCCCCCHHHHHHHHHHHHCCCC------C--CCCCCCCCC------EEEEEE
Q ss_conf 925999422789-9998873898189988999788899999998714732------5--331128972------589999
Q gi|255764514|r 1 MTRLSIYNIVLI-ESLDIDFSAGLSILSGDTGSGKSILLDALILVTGGRG------D--GGLVRRHAE------KGQVVA 65 (554)
Q Consensus 1 L~~L~i~Nf~~i-~~~~i~f~~Gl~vItGetGaGKS~ildAl~~~lG~r~------~--~~~Ir~g~~------~a~Ve~ 65 (554)
T Consensus 2 Lk~l~l~GFKSFaD~t~i~F~~g~TgiVGPNGcGKSNi~DAiRWVLGEqSak~LRg~~M~DVIF~Gs~~Rkp~~~AeV~L 81 (1191)
T TIGR02168 2 LKKLELAGFKSFADPTTINFDKGITGIVGPNGCGKSNIVDAIRWVLGEQSAKALRGGKMEDVIFNGSETRKPLSLAEVEL 81 (1191)
T ss_pred CCEEEECCCCCCCCCEEEEECCCEEEEECCCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCEEECCCCCCCCCCEEEEEE
T ss_conf 61357612101353047861785279862799870018999998600334777346899955634887776577006898
Q ss_pred EEECCCCHHHHHHHHHCCCCCCCCEEEEEEEEC-CCCEEEEECCEEEECHHHHHH------HHHHHCCCCCCCHHHHH--
Q ss_conf 997289737888887478988883899999943-897799999988410112221------11000001220000000--
Q gi|255764514|r 66 VFEISHLPALEILFAEANLTLEKHVILRRVQFP-DGRTKAYVNDQVVSVNFMRAV------GSLLIEIHSQHADRSLL-- 136 (554)
Q Consensus 66 ~F~~~~~~~~~~~~~~~~~~~~~~~iirR~i~~-~GkS~~~INg~~v~~~~L~~l------~~~lidi~gQ~e~~~Ll-- 136 (554)
T Consensus 82 ~fdN~d~~l~~~y------~~y~Ei~itRr~~Rg~GeSeY~iN~~~cRLkDI~dLF~dtGlG~~sysII~QG~I~~i~~a 155 (1191)
T TIGR02168 82 VFDNSDGLLPGQY------ADYSEISITRRLYRGDGESEYFINGQPCRLKDIQDLFLDTGLGKRSYSIIEQGKISEIIEA 155 (1191)
T ss_pred EEECCCCCCHHHH------CCCCEEEEEEEEEECCCCCEEEECCCCCHHHHHHHHHHHCCCCCCCCEEECCCCHHHHHCC
T ss_conf 8855888351211------3677178998887458644045577501377799887322788654323034305565249
Q ss_pred HHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 03678777766300001389999999999999988877665
Q gi|255764514|r 137 DVQGHRKILDSYADIDLSLCELGTLYRHWCCTADALKKYQE 177 (554)
Q Consensus 137 ~~~~q~~lLD~~~~~~~~~~~~~~~~~~~~~~~~~l~~l~~ 177 (554)
T Consensus 156 KPeerR~i~EEAAGisKYK~Rk~Et~~kL~~t~~NL~Rl~D 196 (1191)
T TIGR02168 156 KPEERRAIFEEAAGISKYKERKKETERKLERTRENLERLED 196 (1191)
T ss_pred CHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 96899999887213578887799999989999985999999