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 47087087  76 QGPVVDRRCSRCGHEGMAYYTRQMRSADEGQTVFYTCINCKFQEKED 122
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 47087087  76 QGPVVDRRCSRCGHEGMAYYTRQMRSADEGQTVFYTCINCKFQEKED 122
Cdd:cd10507   1 KGATIEEKCPKCGHDEMTYSTLQLRSADEGQTVFYECPKCGHRFSEN 47

Transcription factor S-II (TFIIS);

                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 47087087    83 RCSRCGHEGMAYYTRQMRSADEGQTVFYTCINCKFQEK 120
Cdd:pfam01096   2 KCPKCGNREAYFFQLQTRSADEPMTVFYVCTKCGHRWR 39

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

                           10        20        30
                   ....*....|....*....|....*....|....*...
gi 47087087     84 CSRCGHEGMAYYTRQMRSADEGQTVFYTCINCKFQEKE 121
Cdd:smart00440   3 CPKCGNREATFYQLQTRSADEPMTVFYVCTKCGHHWRE 40

Putative transposase DNA-binding domain; This putative domain is found at the C-terminus of a large number of transposase proteins. This domain contains four conserved cysteines suggestive of a zinc binding domain. Given the need for transposases to bind DNA as well as the large number of DNA-binding zinc fingers we hypothesize this domain is DNA-binding.

                          10        20        30
                  ....*....|....*....|....*....|
gi 47087087    17 CPDCGSVLPLPGVQDTVICPRCGFSIDvRD 46
Cdd:pfam07282  31 CSVCGHKNKESLSGRTFVCPNCGFVAD-RD 59

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 47087087  76 QGPVVDRRCSRCGHEGMAYYTRQMRSADEGQTVFYTCINCKFQEKED 122
Cdd:cd10507   1 KGATIEEKCPKCGHDEMTYSTLQLRSADEGQTVFYECPKCGHRFSEN 47

C-terminal zinc ribbon domain of RNA polymerase intrinsic transcript cleavage subunit; The homologous C-terminal zinc ribbon domains of subunits A12.2, Rpb9, and C11 in RNA Polymerases (Pol) I, II, and III, respectively are required for intrinsic transcript cleavage. TFS is a related archaeal protein that is involved in RNA cleavage by archaeal polymerase. These proteins have two zinc-binding beta-ribbon domains, N-terminal zinc ribbon (N-ribbon) and C-terminal zinc ribbon (C-ribbon). Transcription Factor IIS (TFIIS) domain III is homologous to the C-ribbon domain that stimulates the weak cleavage activity of Rpb9 for Pol II.

                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*
gi 47087087  76 QGPVVDRRCSRCGHEGMAYYTRQMRSADEGQTVFYTCINCKFQEK 120
Cdd:cd00656   1 TLPTTDRTCPKCGHDEAYWWMLQTRSADEPPTRFYKCTKCGHTWR 45

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 47087087    16 FCPDCGSV-LPLPGVqdtVICPRCGFSIDVRDFGGKVVKTSVVFNKLGTVIPMSVDEGPEsqgPVVDRRCSRCGHEGMAY 94
Cdd:TIGR01384   2 FCPKCGSLmTPKNGV---YVCPSCGYEKEKKPEDDYKVTEKVKHKIKETIIIREEDSETL---PTTRVECPKCGHKEAYY 75

                          90       100
                  ....*....|....*....|....*..
gi 47087087    95 YTRQMRSADEGQTVFYTCINCKFQEKE 121
Cdd:TIGR01384  76 WLLQTRRADEPETRFYKCTKCGYVWRE 102

C-terminal zinc ribbon domain of RPC11 subunit of RNA polymerase III; The C-terminal zinc ribbon domain (C-ribbon) of subunit C11 (Zn-ribbon_RPC11) in RNA polymerase (Pol) III is required for intrinsic transcript cleavage. RPC11 is also involved in Pol III termination. Eukaryote genomes are transcribed by three nuclear RNA polymerases (Pol I, II and III) that share some subunits. RPC11 has strong homology to RPB9 of Pol II and RPA12 of Pol I. Zn-ribbon_RPC11 is homologous to Pol II elongation factor TFIIS domain III. C11 has two zinc-binding domains separated by a flexible linker.

                        10        20        30        40
                ....*....|....*....|....*....|....*....|..
gi 47087087  80 VDRRCSRCGHEGMAYYTRQMRSADEGQTVFYTCINCKFQEKE 121
Cdd:cd10509   5 TEATCPKCGHNRAYFMQIQTRSADEPMTTFYKCCKCGHQWRE 46

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 47087087    71 EGPESQGPVVDR-RCSRCGHEGMAYYTRQMRSADEGQTVFYTCINC 115
Cdd:TIGR01385 247 QGAKIQKAVTDLfTCGKCKQKKCTYYQLQTRSADEPMTTFVTCEEC 292

C-terminal zinc ribbon domain of RPB9 subunit of RNA polymerase II; The C-terminal zinc ribbon domain (C-ribbon) of subunit B9 (Zn-ribbon_RPB9) in RNA polymerase (Pol) II is involved in intrinsic transcript cleavage. Eukaryote genomes are transcribed by three nuclear RNA polymerases (Pol I, II and III) that share some subunits. RPB9 have strong homology to RPA12 of Pol I and RPC11 of Pol III subunits but its intrinsic cleavage activity is weaker for Pol II. Zn-ribbon_RPB9 is homologous to Pol II elongation factor TFIIS domain III. The very weak cleavage activity of Pol II is stimulated by TFIIS. RPB9 has two zinc-binding domains separated by a flexible linker.

                        10        20        30
                ....*....|....*....|....*....|....*
gi 47087087  81 DRRCSRCGHEGMAYYTRQMRSADEGQTVFYTCINC 115
Cdd:cd10508  10 DHPCPKCGHNEAVFFQSQSRRAEEGMTLFYVCTNC 44

DNA topoisomerase I, ssDNA-binding Zn-finger and Zn-ribbon domains [Replication, recombination and repair];

                        10        20        30
                ....*....|....*....|....*....|....
gi 47087087   7 CSNFqsdldfcPDCGSVLPLPGVQDT-VICPRCG 39
Cdd:COG0551 609 CSNY-------PECKYTKPLPKPEVTgVKCPKCG 635