GenomeNet

Database: Pfam
Entry: RNA_pol_Rpo13
LinkDB: RNA_pol_Rpo13
Original site: RNA_pol_Rpo13 
#=GF ID   RNA_pol_Rpo13
#=GF AC   PF12136.9
#=GF DE   RNA polymerase Rpo13 subunit HTH domain
#=GF AU   Mistry J;0000-0003-2479-5322
#=GF AU   Gavin OL;
#=GF SE   pdb_2waq
#=GF GA   25.00 25.00;
#=GF TC   30.60 28.60;
#=GF NC   20.50 17.50;
#=GF BM   hmmbuild HMM.ann SEED.ann
#=GF SM   hmmsearch -Z 47079205 -E 1000 --cpu 4 HMM pfamseq
#=GF TP   Domain
#=GF RN   [1]
#=GF RM   19419240
#=GF RT   Evolution of Complex RNA Polymerases: The Complete Archaeal RNA
#=GF RT   Polymerase Structure.
#=GF RA   Korkhin Y, Unligil UM, Littlefield O, Nelson PJ, Stuart DI,
#=GF RA   Sigler PB, Bell SD, Abrescia NG;
#=GF RL   PLoS Biol. 2009;7:e102.
#=GF DR   INTERPRO; IPR021985;
#=GF DR   SO; 0000417; polypeptide_domain;
#=GF CC   This domain is found in archaea, and is about 40 amino acids in
#=GF CC   length. It has a single completely conserved residue E that may
#=GF CC   be functionally important. It is found in the archaeal DNA
#=GF CC   dependent RNA polymerase. The domain is a 'helix-turn-helix'
#=GF CC   (HTH) domain in the Rpo13 subunit of the RNA polymerase. This
#=GF CC   domain is involved in downstream DNA binding, and the entire
#=GF CC   subunit has also been implicated in contacting transcription
#=GF CC   factor II B.
#=GF SQ   15
#=GS Q975M1_SULTO/33-72     AC Q975M1.1
#=GS Q4JAJ6_SULAC/22-61     AC Q4JAJ6.1
#=GS E0SPY1_IGNAA/23-60     AC E0SPY1.1
#=GS A2BMA7_HYPBU/16-59     AC A2BMA7.1
#=GS Q980B8_SACS2/20-59     AC Q980B8.1
#=GS Q980B8_SACS2/20-59     DR PDB; 3HKZ Y; 38-59;
#=GS Q980B8_SACS2/20-59     DR PDB; 3HKZ Z; 38-59;
#=GS F4B7L2_ACIHW/5-54      AC F4B7L2.1
#=GS A3DN92_STAMF/11-54     AC A3DN92.1
#=GS A0A2U9IEQ3_9CREN/3-54  AC A0A2U9IEQ3.1
#=GS A0A031LJX8_9CREN/4-57  AC A0A031LJX8.1
#=GS A0A0V8RWB8_PYROC/7-50  AC A0A0V8RWB8.1
#=GS A0A348B172_9CREN/2-49  AC A0A348B172.1
#=GS W7L7R3_9CREN/14-54     AC W7L7R3.1
#=GS A8AB08_IGNH4/17-59     AC A8AB08.1
#=GS H2C6X8_9CREN/16-54     AC H2C6X8.1
#=GS A4YCS7_METS5/19-57     AC A4YCS7.1
Q975M1_SULTO/33-72                ........................HEEKVEA.....E....SEEEELPA---.LSVADIELLMKNTEIWDNLLNGKI
Q4JAJ6_SULAC/22-61                ........................EEISREE.....D....DEGGEFST---.VTISDIEMLLKDTEIWDKLLRNEL
E0SPY1_IGNAA/23-60                ......................ep--EYLAE.....E....EEES--VD---.LSPTDIELFLQRSEIWDKLVSNEI
A2BMA7_HYPBU/16-59                ........................VTITTAE.....E....EAEEEVVTVDIdVNAALLEAMVARTEIIEKLAKGEY
Q980B8_SACS2/20-59                ........................NEEKEVE.....E....TSEDEFPK---.LSIQDIELLMRNTEIWDNLLNGKI
#=GR Q980B8_SACS2/20-59     SS    ........................XXXXXXX.....X....XXXXXXXX---.XX---TTHHHHHHHHHHHTT--SS
F4B7L2_ACIHW/5-54                 .............yenkeeeepke------EkeektE....EEEEELPA---.LTLQDIELLMKNTEVWDELIAGKI
A3DN92_STAMF/11-54                ........................EEEYMEE.....E....EEETEEKTPPRlVRINYLEKFIKTTILWEKFVRGET
A0A2U9IEQ3_9CREN/3-54             ...............deynngeen-EETTSE.....EkeprEEDSEFPA---.VSLQDIELLMKNTEVWYELLNGKI
A0A031LJX8_9CREN/4-57             essyegkeeeektdseveersrgg-------.....-....--DDDLPA---.MSLQDIELLMKNTDVWYNLISGKI
A0A0V8RWB8_PYROC/7-50             .................eevseka---HESE.....E....EVEEEA----IdINAALLEAMVKRTEILEKYVKGEV
A0A348B172_9CREN/2-49             .............sedsereaeev-EAEDIE.....E....SDEG--GS---.VSIQEIETFVKRTQLWEQLLEGKI
W7L7R3_9CREN/14-54                ......................et-EEKVTE.....E....EEDSEFPA---.VSLQDIELLMKNTEIWHELLKGKI
A8AB08_IGNH4/17-59                ........................EEAPLVE.....E....EEGTKAPTTER.FPLEAYEISVELADLWDGAIEGKV
H2C6X8_9CREN/16-54                .......................a-EEIRGE.....D....EEEG-VPA---.MSLQDIELLSKNTEVWYKLISGKI
A4YCS7_METS5/19-57                ........................DEAGKVE.....E....DEEG-VPA---.MSLQDIELLTKNTEVWHRLMSGKI
#=GC SS_cons                      ........................XXXXXXX.....X....XXXXXXXX---.XX---TTHHHHHHHHHHHTT--SS
#=GC seq_cons                     .........................EtthsE.....E....EEEsEhPs....lSlpDIELLhKsTElW-cLlpGKI
//
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