HHsearch alignment for GI: 254780386 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=94.13 E-value=0.00071 Score=44.20 Aligned_cols=198 Identities=17% Similarity=0.229 Sum_probs=0.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHHHHCCCCCCCCC
Q ss_conf 99888999874343323321001233332221145554223568888776554678865433--3655420011222112
Q gi|254780386|r 91 ETTDLIDLKKVSIKNLRCHIDTEKSALDFLNNKYDVLEKAFESREEQLLDFLGKYHSTCSKV--FNYGISSVYRSLKMKL 168 (440)
Q Consensus 91 ~~~~~l~~~~~~l~~l~~~l~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~ 168 (440)
T Consensus 295 ~~~~~i~~le~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~ 374 (1191)
T TIGR02168 295 ELKAEISRLEQQIQILKERLENLEQQLEELEEQLEELESKLDELEEELAELEEKLEELKEEVESLEAELEELEAELEELE 374 (1191)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 99999999999999999999989888999999999988748999999999999999999999999999999999999999
Q ss_pred CCCHHHHHHCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCC
Q ss_conf 21002232101122322222210233332221012222221110000111002466653101223322222222222100
Q gi|254780386|r 169 TRMRSIYLNRLDLENKSSLLRALLSSHQKDLTMMKNLFEKNAVSQNDLNQQERIVYKSTLELRENIHEQKNMLRHINELY 248 (440)
Q Consensus 169 ~~~~~~~~~~~~l~~~~~~l~~~~~~~~~el~~~~~l~~~~~~~~~~l~~~~~~~~~~~~el~~~~~~~~~~~~~l~~~~ 248 (440)
T Consensus 375 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~l 454 (1191)
T TIGR02168 375 SRLEELEEELETLRSEVAELEEQLASLNNELERLEARLERLEERRERLQQEIEELLKKLEEAEAELKELQEELAELEEEL 454 (1191)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 89999999999999999999999999999999999999999999999999999998769999999999997788999999
Q ss_pred CCCCCCCCCCCCC---CCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf 0122333211233---222122222222122233221222221
Q gi|254780386|r 249 DEANLEFANYLKE---ISRDLEQNQRTFADEMSKLTILEKTRE 288 (440)
Q Consensus 249 ~~~~~~~~~~~~e---~~~~l~e~~~~l~~~~~~l~~l~~~l~ 288 (440)
T Consensus 455 ~~l~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~l~~~~~r~~ 497 (1191)
T TIGR02168 455 EELQEELERLEEALEELREELEEAEQALDAAKRELAQLQARLD 497 (1191)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 9999999999999999999999999999999999999999999