C-terminal zinc ribbon domain of RPA12 subunit of RNA polymerase I; The C-terminal zinc ribbon domain (C-ribbon) of subunit A12 (Zn-ribbon_RPA12) in RNA polymerase (Pol) I is involved in intrinsic transcript cleavage. Eukaryote genomes are transcribed by three nuclear RNA polymerases (Pol I, II and III) that share some subunits. RPA12 in Pol I, RPB9 in Pol II, RPC11 in Pol III and TFS in archaea are distantly related to each other and to the TFIIS elongation factor of Pol II. RPA12 has two zinc-binding domains separated by a flexible linker.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 573027217 202 KEATIKEKCPGCGNDEMNFHTLQLRSADEGTTVFYDCPKCGYKFSQN 248
Cdd:cd10507    1 KGATIEEKCPKCGHDEMTYSTLQLRSADEGQTVFYECPKCGHRFSEN 47

C-terminal zinc ribbon domain of RPA12 subunit of RNA polymerase I; The C-terminal zinc ribbon domain (C-ribbon) of subunit A12 (Zn-ribbon_RPA12) in RNA polymerase (Pol) I is involved in intrinsic transcript cleavage. Eukaryote genomes are transcribed by three nuclear RNA polymerases (Pol I, II and III) that share some subunits. RPA12 in Pol I, RPB9 in Pol II, RPC11 in Pol III and TFS in archaea are distantly related to each other and to the TFIIS elongation factor of Pol II. RPA12 has two zinc-binding domains separated by a flexible linker.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 573027217 202 KEATIKEKCPGCGNDEMNFHTLQLRSADEGTTVFYDCPKCGYKFSQN 248
Cdd:cd10507    1 KGATIEEKCPKCGHDEMTYSTLQLRSADEGQTVFYECPKCGHRFSEN 47

Transcription factor S-II (TFIIS);

                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 573027217  209 KCPGCGNDEMNFHTLQLRSADEGTTVFYDCPKCGYKF 245
Cdd:pfam01096   2 KCPKCGNREAYFFQLQTRSADEPMTVFYVCTKCGHRW 38

C2C2 Zinc finger; Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.

                           10        20        30
                   ....*....|....*....|....*....|....*....
gi 573027217   209 KCPGCGNDEMNFHTLQLRSADEGTTVFYDCPKCGYKFSQ 247
Cdd:smart00440   2 ECPKCGNREATFYQLQTRSADEPMTVFYVCTKCGHHWRE 40

transcription elongation factor S-II; This model represents eukaryotic transcription elongation factor S-II. This protein allows stalled RNA transcription complexes to perform a cleavage of the nascent RNA and restart at the newly generated 3-prime end.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 573027217  209 KCPGCGNDEMNFHTLQLRSADEGTTVFYDCPKCG--YKFS 246
Cdd:TIGR01385 260 TCGKCKQKKCTYYQLQTRSADEPMTTFVTCEECGnrWKFC 299

C-terminal zinc ribbon domain of RPA12 subunit of RNA polymerase I; The C-terminal zinc ribbon domain (C-ribbon) of subunit A12 (Zn-ribbon_RPA12) in RNA polymerase (Pol) I is involved in intrinsic transcript cleavage. Eukaryote genomes are transcribed by three nuclear RNA polymerases (Pol I, II and III) that share some subunits. RPA12 in Pol I, RPB9 in Pol II, RPC11 in Pol III and TFS in archaea are distantly related to each other and to the TFIIS elongation factor of Pol II. RPA12 has two zinc-binding domains separated by a flexible linker.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 573027217 202 KEATIKEKCPGCGNDEMNFHTLQLRSADEGTTVFYDCPKCGYKFSQN 248
Cdd:cd10507    1 KGATIEEKCPKCGHDEMTYSTLQLRSADEGQTVFYECPKCGHRFSEN 47

Transcription factor S-II (TFIIS);

                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 573027217  209 KCPGCGNDEMNFHTLQLRSADEGTTVFYDCPKCGYKF 245
Cdd:pfam01096   2 KCPKCGNREAYFFQLQTRSADEPMTVFYVCTKCGHRW 38

transcription factor S, archaeal; This model describes archaeal 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. There has been an apparent duplication event in the Halobacteriaceae lineage (Haloarcula, Haloferax, Haloquadratum, Halobacterium and Natromonas). There appears to be a separate duplication in Methanosphaera stadtmanae. [Transcription, Transcription factors]

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 573027217  133 FCPNCGSLLdVPGDEDFiKCAPCGAVQNAKVYDNLSIVTRShpsafpsalrqKRQLVNTAASIGNDNKPKEATiKEKCPG 212
Cdd:TIGR01384   2 FCPKCGSLM-TPKNGVY-VCPSCGYEKEKKPEDDYKVTEKV-----------KHKIKETIIIREEDSETLPTT-RVECPK 67

                          90       100       110
                  ....*....|....*....|....*....|.
gi 573027217  213 CGNDEMNFHTLQLRSADEGTTVFYDCPKCGY 243
Cdd:TIGR01384  68 CGHKEAYYWLLQTRRADEPETRFYKCTKCGY 98

C-terminal zinc ribbon domain of archaeal Transcription Factor S (TFS); TFS is an archaeal protein that stimulates the intrinsic cleavage activity of archaeal RNA polymerase. TFS C-terminal domain shows sequence similarity to the homologous C-terminal zinc ribbon domain of subunits A12.2, Rpb9, and C11 in eukaryotic RNA Polymerases (Pol) I, II, and III, respectively and domain III of TFIIS. TFS is not a subunit of archaeal RNA polymerase even though its domains arrangement is similar to A12.2, Rpb9, and C1. TFS is a transcription factor with a similar function to eukaryotic TFIIS. TFS has external cleavage induction activity and improves the fidelity of transcription. TFS has two zinc-binding domains.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|
gi 573027217 205 TIKEKCPGCGNDEMNFHTLQLRSADEGTTVFYDCPKCGYK 244
Cdd:cd10511    4 TTKITCPKCGHDEAYWWMVQTRSADEPPTRFYKCTKCGHT 43

domain III/zinc ribbon domain of Transcription Factor IIS; TFIIS is a zinc-containing transcription factor. It has been shown in vitro to have distinct biochemical activities, including binding to RNA polymerases, stimulation of transcript elongation, and activation of a nascent RNA cleavage activity in the RNA polymerase II (Pol II) elongation complex. TFIIS consists of three domains. Domain II and III are sufficient for all known TFIIS activities. Domain III is a zinc ribbon that separated from domain II by a long linker and is indispensable for TFIIS function. The TFIIS homologs, subunits A12.2, B9, and C11, of Pol I, II, and III respectively, are required for RNA cleavage by the polymerases. In a single organism, there are tissue-specific TFIIS related proteins.

                         10        20        30
                 ....*....|....*....|....*....|....*..
gi 573027217 209 KCPGCGNDEMNFHTLQLRSADEGTTVFYDCPKCGYKF 245
Cdd:cd13749    9 KCGKCKKRKCTYYQLQTRSADEPMTTFVTCLNCGNRW 45

C4-type Zn-finger protein [General function prediction only];

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 573027217 202 KEATIKEKCPGCGNDEMNFHTLQLRSADEG----TTVFydCPKCGYKFS 246
Cdd:COG1779    4 KEEETEVKCPVCGGKTLKVIWQTYNIPYFGevliITGR--CSSCGYRFS 50