HHsearch alignment for GI: 254780619 and conserved domain: TIGR01384

>TIGR01384 TFS_arch transcription factor S; InterPro: IPR006288 DNA-directed RNA polymerases from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length . The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kD, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. These sequences are the archaeal DNA-directed RNA polymerase, subunit M (also known as transcription factor S), a protein related in size and sequence to certain eukaryotic RNA polymerase small subunits, and in sequence and function to the much larger eukaryotic transcription factor IIS (TFIIS). Although originally suggested to be a subunit of the archaeal RNA polymerase, it elutes separately from active polymerase in gel filtration experiments and acts, like TFIIs, as an induction factor for RNA cleavage by RNA polymerase . ; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0003899 DNA-directed RNA polymerase activity, 0006350 transcription.
Probab=90.96  E-value=0.085  Score=32.83  Aligned_cols=30  Identities=23%  Similarity=0.664  Sum_probs=26.0

Q ss_conf             014652012113578--320000210244655
Q gi|254780619|r  448 CLHCSCWLVEHRSKK--KLYCHQCGHSAIYSQ  477 (731)
Q Consensus       448 C~~C~~~l~~h~~~~--~l~Ch~Cg~~~~~~~  477 (731)
T Consensus         3 CPKCgs~M~P~K~~Gkn~~~C~~CGYE~~~T~   34 (111)
T ss_conf             78669715854306950116288887330466