HHsearch alignment for GI: 254780766 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=98.99 E-value=4.3e-08 Score=72.05 Aligned_cols=164 Identities=16% Similarity=0.227 Sum_probs=109.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHCCCCCC-CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCC-EEEEECCC
Q ss_conf 677888777766666798863056543-2100245653279999999999999999999999985316430-11220156
Q gi|254780766|r 154 RHRRRMIDFERLMRGRNRLLTEGYFDS-SWCSSIEAQMAELGVKINIARVEMINALSSLIMEYVQKENFPH-IKLSLTGF 231 (375)
Q Consensus 154 ~y~~~l~~y~K~LkqRN~lLk~~~~d~-~~l~~~~~qla~~~~~I~~~R~~~l~~l~~~l~~~~~~~~~~~-~~~~l~~~ 231 (375)
T Consensus 999 VNL~AieEy~-~~~eR~~fL~~Q~~DL~~A~~~L~~~I~~iD~e~~~rF~~tF~~vn~~F~~~F~~LFgGG~A~L~LTd- 1076 (1191)
T TIGR02168 999 VNLAAIEEYE-ELKERYDFLSAQKEDLTEAKETLEEAIEEIDKETRERFKDTFDQVNENFQRVFPKLFGGGEAELRLTD- 1076 (1191)
T ss_pred CCHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEEEEC-
T ss_conf 5855899999-99999999999999999999999999999989999999999999998886685864899878988656-
Q ss_pred CCCCCCCCHHHHHHHHHHHHHHCCCHHHCCEEECCCCCCEEEECCCCCC-CHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 6676558967888876545531110000000002573200110012455-102331220589999999999999999987
Q gi|254780766|r 232 LDGKFDQSFCALKEEYAKKLFDGRKMDSMSRRTLIGPHRSDLIVDYCDK-AITIAHGSTGEQKVVLVGIFLAHARLISNT 310 (375)
Q Consensus 232 ~~~~~~~~~~~~~e~~~~~L~~~~~~d~~~~~t~~Gphr~d~~~~~~~~-~~~~~~~S~Gqqk~~~l~l~La~~~~~~~~ 310 (375)
T Consensus 1077 ~~d~Lea----------------------------Gi---eI~A~PPGKk~~~l~LLSGGEKALTA~ALlFAIf~~---- 1121 (1191)
T TIGR02168 1077 PEDLLEA----------------------------GI---EIMAQPPGKKNQNLSLLSGGEKALTALALLFAIFKV---- 1121 (1191)
T ss_pred CCCCCCC----------------------------CC---EEEEECCCCCCCCCCCCCCHHHHHHHHHHHHHHHCC----
T ss_conf 8774337----------------------------75---678527639876643020157999999999999600----
Q ss_pred CCCCCEEEEECCHHCCCHHHHHHHHHHHHHC--CCCEEEEECCHHHH
Q ss_conf 0899789980122015989999999997417--98099980696785
Q gi|254780766|r 311 TGFAPILLLDEISAHLDEDKRNALFRIVTDI--GSQIFMTGTDKSVF 355 (375)
Q Consensus 311 ~~~~pilLiDdi~s~LD~~~~~~ll~~l~~~--~~Qv~iTt~~~~~~ 355 (375)
T Consensus 1122 -~P~PFC~LDEVDAPLDdaNV~RF~~ll~~~~~~tQFI~iTHnk~TM 1167 (1191)
T TIGR02168 1122 -KPAPFCILDEVDAPLDDANVERFANLLKEMSKKTQFIVITHNKGTM 1167 (1191)
T ss_pred -CCCCEEEECCCCCCCCHHHHHHHHHHHHHHHHCCCEEEEECCHHHH
T ss_conf -7887263212336798266999999999985189278886784899