Query 037910
Match_columns 235
No_of_seqs 165 out of 458
Neff 4.4
Searched_HMMs 46136
Date Fri Mar 29 05:38:39 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/037910.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/037910hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 TIGR01385 TFSII transcription 100.0 9.1E-29 2E-33 226.5 12.2 117 105-229 129-256 (299)
2 KOG1105 Transcription elongati 99.9 1.9E-26 4.2E-31 210.9 11.7 115 107-229 128-253 (296)
3 smart00510 TFS2M Domain in the 99.9 1.3E-26 2.8E-31 182.7 6.6 91 112-210 1-102 (102)
4 PF07500 TFIIS_M: Transcriptio 99.9 1.2E-26 2.6E-31 184.0 1.8 104 110-221 1-115 (115)
5 KOG1634 Predicted transcriptio 99.1 4.2E-11 9.1E-16 121.2 4.2 71 146-216 268-350 (778)
6 PF13943 WPP: WPP domain 23.7 2.6E+02 0.0056 22.5 5.6 51 108-161 5-55 (99)
7 PF02172 KIX: KIX domain; Int 17.3 1.3E+02 0.0029 23.1 2.7 52 108-163 8-59 (81)
8 PF09693 Phage_XkdX: Phage unc 14.3 52 0.0011 21.9 -0.2 26 173-198 14-39 (40)
9 TIGR00244 transcriptional regu 11.9 4.2E+02 0.0092 22.7 4.5 39 115-164 63-101 (147)
10 PF14237 DUF4339: Domain of un 11.5 1.5E+02 0.0032 19.6 1.3 20 175-194 17-36 (45)
No 1
>TIGR01385 TFSII 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.
Probab=99.96 E-value=9.1e-29 Score=226.47 Aligned_cols=117 Identities=29% Similarity=0.419 Sum_probs=105.6
Q ss_pred cccccCCchHHHHHHHHHHHHHHhhhccchhhHHhhhhhcCChHHHHHHHHHHHHHhhCCc-----------ccCCCCCC
Q 037910 105 AVEIKCSDATRTLIRERLAEAFSKVAGEVEEMEKKEQVRACDPVGVAVSVESVLFKNMCPF-----------LFNVKDPK 173 (235)
Q Consensus 105 ~~~~~t~D~vRdK~relL~~AL~~~~~e~~d~ik~~~~~~~d~~~lA~eIE~aLF~~~~~s-----------~fNLKD~K 173 (235)
++...++|++|++|+++||+||..+..+.+. .+++..+|.+||.+||..|+.+ +|||||++
T Consensus 129 ~~~~~t~d~~Rdk~r~~L~~aL~~~~~~~~~--------~~~~~~lA~~iE~~~f~~~~~~~~~Yk~k~Rsl~~NLKd~k 200 (299)
T TIGR01385 129 VPTAVTNDKVRDKCRELLYDALAKDSDHPPQ--------SIDPEAKAIQIEELKFNNLGTTEAAYKARYRSIYSNLRDKN 200 (299)
T ss_pred CCCccCCcHHHHHHHHHHHHHHhhcCCCCcc--------ccCHHHHHHHHHHHHHHHcCCCcHHHHHHHHHHHHHccCCC
Confidence 3567899999999999999999986543332 3577889999999999999865 99999999
Q ss_pred ChhhhhhhhcCCCCccccccCCcccCCcHHHHHHHHHHHHHHHHHHhccccccceE
Q 037910 174 NPDFWRKVLLGEVKPETLVTALPEEMASDERQSRNKQIREDALAKIRDHSVVGEKE 229 (235)
Q Consensus 174 Np~Lr~~VL~GeIsP~~Lv~MSseEMASdELK~ereki~eeAL~eaq~a~~~ge~~ 229 (235)
||+||++|++|+|+|++||.||++||||+|+|++|+++.+++|++||+++..|..+
T Consensus 201 Np~Lr~~vl~G~i~p~~lv~Ms~eEmas~e~k~~~e~~~ke~l~~~~~~~~~~~~t 256 (299)
T TIGR01385 201 NPDLRHNVLTGEITPEKLATMTAEEMASAELKQEREEITKENLFEAQGAKIQKAVT 256 (299)
T ss_pred CHHHHHHHHcCCCCHHHHhcCCHHHcCCHHHHHHHHHHHHHHHHHHHhhhhhcCCc
Confidence 99999999999999999999999999999999999999999999999999887654
No 2
>KOG1105 consensus Transcription elongation factor TFIIS/Cofactor of enhancer-binding protein Sp1 [Transcription]
Probab=99.94 E-value=1.9e-26 Score=210.86 Aligned_cols=115 Identities=32% Similarity=0.495 Sum_probs=104.8
Q ss_pred cccCCchHHHHHHHHHHHHHHhhhccchhhHHhhhhhcCChHHHHHHHHHHHHHhhCCc-----------ccCCCCCCCh
Q 037910 107 EIKCSDATRTLIRERLAEAFSKVAGEVEEMEKKEQVRACDPVGVAVSVESVLFKNMCPF-----------LFNVKDPKNP 175 (235)
Q Consensus 107 ~~~t~D~vRdK~relL~~AL~~~~~e~~d~ik~~~~~~~d~~~lA~eIE~aLF~~~~~s-----------~fNLKD~KNp 175 (235)
.+.++|++|++|+++||+||.... ...+.++++..+|.+||.+||..++++ +|||+|++||
T Consensus 128 ~~~~~d~~r~k~~e~l~~al~~~~--------~~~~~~~~~~~~a~~iE~~~~~~~g~~~~kyK~r~RS~~~NLkd~~Np 199 (296)
T KOG1105|consen 128 VPITNDPVRDKCRELLYAALTTED--------DSRVTGADPLELAVQIEEAIFEKLGNTDSKYKNRYRSRVSNLKDKNNP 199 (296)
T ss_pred CCCCCchHHHHHHHHHHHHhcccc--------cccccCCCHHHHHHHHHHHHHHHhCCCcHHHHHHHHHHhhccCCCCCH
Confidence 455789999999999999999432 123446788999999999999998876 9999999999
Q ss_pred hhhhhhhcCCCCccccccCCcccCCcHHHHHHHHHHHHHHHHHHhccccccceE
Q 037910 176 DFWRKVLLGEVKPETLVTALPEEMASDERQSRNKQIREDALAKIRDHSVVGEKE 229 (235)
Q Consensus 176 ~Lr~~VL~GeIsP~~Lv~MSseEMASdELK~ereki~eeAL~eaq~a~~~ge~~ 229 (235)
+||++||+|+|+|++|+.||++||||++||++|+++.++||++||++.++|+.|
T Consensus 200 ~LR~~vl~G~i~pe~la~mt~eEMaS~~lk~~~~k~~keal~~~q~~~~~gt~t 253 (296)
T KOG1105|consen 200 DLRRNVLTGEISPERLATMTSEEMASEELKEERQKLTKEALREHQMAKIQGTQT 253 (296)
T ss_pred HHHHHHhcCCCCHHHhccCChhhhccHHHHHHHHHHHHHHHHHHhhcccccccc
Confidence 999999999999999999999999999999999999999999999999999876
No 3
>smart00510 TFS2M Domain in the central regions of transcription elongation factor S-II (and elsewhere).
Probab=99.93 E-value=1.3e-26 Score=182.73 Aligned_cols=91 Identities=40% Similarity=0.584 Sum_probs=82.0
Q ss_pred chHHHHHHHHHHHHHHhhhccchhhHHhhhhhcCChHHHHHHHHHHHHHhhCCc-----------ccCCCCCCChhhhhh
Q 037910 112 DATRTLIRERLAEAFSKVAGEVEEMEKKEQVRACDPVGVAVSVESVLFKNMCPF-----------LFNVKDPKNPDFWRK 180 (235)
Q Consensus 112 D~vRdK~relL~~AL~~~~~e~~d~ik~~~~~~~d~~~lA~eIE~aLF~~~~~s-----------~fNLKD~KNp~Lr~~ 180 (235)
|++|++|+++||+||.......+. .+++..+|.+||.+||..|+.+ +|||||++||+||++
T Consensus 1 d~~R~~~~~~L~~al~~~~~~~~~--------~~~~~~lA~~IE~~lf~~~~~~~~~Yk~k~Rsl~fNLkd~kN~~Lr~~ 72 (102)
T smart00510 1 DKVRDKCQEMLYKALQKISDPEEI--------ELDPTELAVQIEAEMFSEFGTTDKKYKNKYRSLYFNLKDKKNPDLRRK 72 (102)
T ss_pred ChHHHHHHHHHHHHHHhcCCCCcc--------cccHHHHHHHHHHHHHHHcCCCcHHHHHHHHHHHHHhcCCCCHHHHHH
Confidence 689999999999999997654432 3467889999999999998854 999999999999999
Q ss_pred hhcCCCCccccccCCcccCCcHHHHHHHHH
Q 037910 181 VLLGEVKPETLVTALPEEMASDERQSRNKQ 210 (235)
Q Consensus 181 VL~GeIsP~~Lv~MSseEMASdELK~erek 210 (235)
||+|+|+|++||.||++||||+|||++|++
T Consensus 73 vl~G~i~p~~lv~Ms~~ElAs~elk~~~e~ 102 (102)
T smart00510 73 VLNGEITPEKLATMTAEELASAELKEKREK 102 (102)
T ss_pred HHcCCCCHHHHhcCCHHHcCCHHHHHHHhC
Confidence 999999999999999999999999999873
No 4
>PF07500 TFIIS_M: Transcription factor S-II (TFIIS), central domain; InterPro: IPR003618 Transcription factor S-II (TFIIS) is a eukaryotic protein which induces mRNA cleavage by enhancing the intrinsic nuclease activity of RNA polymerase (Pol) II, past template-encoded pause sites. TFIIS shows DNA-binding activity only in the presence of RNA polymerase II []. It is widely distributed being found in mammals, Drosophila, yeast and in the archaebacteria Sulfolobus acidocaldarius []. S-II proteins have a relatively conserved C-terminal region but variable N-terminal region, and some members of this family are expressed in a tissue-specific manner [, ]. TFIIS is a modular factor that comprises an N-terminal domain I, a central domain II, and a C-terminal domain III []. The weakly conserved domain I forms a four-helix bundle and is not required for TFIIS activity. Domain II forms a three-helix bundle, and domain III adopts a zinc-ribbon fold with a thin protruding beta-hairpin. Domain II and the linker between domains II and III are required for Pol II binding, whereas domain III is essential for stimulation of RNA cleavage. TFIIS extends from the polymerase surface via a pore to the internal active site, spanning a distance of 100 Angstroms. Two essential and invariant acidic residues in a TFIIS loop complement the Pol II active site and could position a metal ion and a water molecule for hydrolytic RNA cleavage. TFIIS also induces extensive structural changes in Pol II that would realign nucleic acids in the active centre. This domain is found in the central region of transcription elongation factor S-II and in several hypothetical proteins.; GO: 0006351 transcription, DNA-dependent; PDB: 3PO3_S 1ENW_A 3GTM_S 1Y1V_S 3NDQ_A 2DME_A.
Probab=99.92 E-value=1.2e-26 Score=183.99 Aligned_cols=104 Identities=38% Similarity=0.598 Sum_probs=93.5
Q ss_pred CCchHHHHHHHHHHHHHHhhhccchhhHHhhhhhcCChHHHHHHHHHHHHHhhCCc-----------ccCCCCCCChhhh
Q 037910 110 CSDATRTLIRERLAEAFSKVAGEVEEMEKKEQVRACDPVGVAVSVESVLFKNMCPF-----------LFNVKDPKNPDFW 178 (235)
Q Consensus 110 t~D~vRdK~relL~~AL~~~~~e~~d~ik~~~~~~~d~~~lA~eIE~aLF~~~~~s-----------~fNLKD~KNp~Lr 178 (235)
|++++|++|+++|+++|...... .+. ..++..+|.+||.+||..|+.. +|||||++||+||
T Consensus 1 ~~~~~R~k~~~~L~~~l~~~~~~-~~~-------~~~~~~lA~~IE~~lf~~~~~~~~~Y~~k~Rsl~~NLkd~~N~~L~ 72 (115)
T PF07500_consen 1 TNDKVRDKARKLLYKALQKRSDE-QDD-------PEDAKELAKEIEEALFDKFGSTSKKYKQKFRSLMFNLKDPKNPDLR 72 (115)
T ss_dssp -TCHHHHHHHHHHHHHHHHCCCC-CCC-------TCCHHHHHHHHHHHHHHHHTSTSHHHHHHHHHHHHHHCSSTTCCHH
T ss_pred CCcHHHHHHHHHHHHHHHhcCcc-ccc-------hhHHHHHHHHHHHHHHHHHccCcHHHHHHHHHHHHHhccCCcHHHH
Confidence 67999999999999999998654 221 3567899999999999999644 9999999999999
Q ss_pred hhhhcCCCCccccccCCcccCCcHHHHHHHHHHHHHHHHHHhc
Q 037910 179 RKVLLGEVKPETLVTALPEEMASDERQSRNKQIREDALAKIRD 221 (235)
Q Consensus 179 ~~VL~GeIsP~~Lv~MSseEMASdELK~ereki~eeAL~eaq~ 221 (235)
.+|++|+|+|.+||.||++||||+++|++++++.+++++++|+
T Consensus 73 ~~il~g~i~p~~lv~ms~~Elas~e~k~~~e~~~~~~l~~~~~ 115 (115)
T PF07500_consen 73 RRILSGEISPEELVTMSPEELASEELKEEREKIRKESLKQSQM 115 (115)
T ss_dssp HHHHHSSSTTCHHHHCTTTTTTTSCCCCCHCCHHHHHHHHTB-
T ss_pred HHHHcCCCCHHHHhcCCHHHhCCHHHHHHHHHHHHHHHHHhhC
Confidence 9999999999999999999999999999999999999999985
No 5
>KOG1634 consensus Predicted transcription factor DATF1, contains PHD and TFS2M domains [Transcription]
Probab=99.11 E-value=4.2e-11 Score=121.20 Aligned_cols=71 Identities=35% Similarity=0.450 Sum_probs=65.3
Q ss_pred ChHHHHHHHHHHHHHhhCCc------------ccCCCCCCChhhhhhhhcCCCCccccccCCcccCCcHHHHHHHHHHHH
Q 037910 146 DPVGVAVSVESVLFKNMCPF------------LFNVKDPKNPDFWRKVLLGEVKPETLVTALPEEMASDERQSRNKQIRE 213 (235)
Q Consensus 146 d~~~lA~eIE~aLF~~~~~s------------~fNLKD~KNp~Lr~~VL~GeIsP~~Lv~MSseEMASdELK~ereki~e 213 (235)
++.-++..||..||..||.. +|||||+|||.||.+|+.|+|+|++||.|+++||||.||++||++..+
T Consensus 268 d~~ll~~~ie~el~~~fG~gvnkkY~ek~RsL~fNlKDkkN~~lre~v~~~ei~~e~Lv~msaeelAs~eL~~~rEek~e 347 (778)
T KOG1634|consen 268 DPNLLLEKIEHELFVLFGLGVNKKYPEKLRSLLFNLKDKKNPELRERVMSGEISAERLVNMSAEELASPELAEWREEKAE 347 (778)
T ss_pred chhhHhhhhhhhceeccCCcccccchhhhhhhhhccccccchHHHHHHhhcccCHhhhccCCchhhcCchHHHHHHHHHH
Confidence 45567779999999999933 999999999999999999999999999999999999999999999988
Q ss_pred HHH
Q 037910 214 DAL 216 (235)
Q Consensus 214 eAL 216 (235)
+.+
T Consensus 348 e~~ 350 (778)
T KOG1634|consen 348 EMN 350 (778)
T ss_pred HHH
Confidence 765
No 6
>PF13943 WPP: WPP domain
Probab=23.66 E-value=2.6e+02 Score=22.52 Aligned_cols=51 Identities=20% Similarity=0.158 Sum_probs=30.6
Q ss_pred ccCCchHHHHHHHHHHHHHHhhhccchhhHHhhhhhcCChHHHHHHHHHHHHHh
Q 037910 108 IKCSDATRTLIRERLAEAFSKVAGEVEEMEKKEQVRACDPVGVAVSVESVLFKN 161 (235)
Q Consensus 108 ~~t~D~vRdK~relL~~AL~~~~~e~~d~ik~~~~~~~d~~~lA~eIE~aLF~~ 161 (235)
=.+....|+-++.-|.+-|..-+--.. +.......++...|..||...|..
T Consensus 5 WPpsq~tR~~vv~Rm~~nLss~s~~s~---ryg~l~~eeA~~~Ak~IEe~AF~~ 55 (99)
T PF13943_consen 5 WPPSQRTRDAVVERMTENLSSPSILSK---RYGTLPKEEAEEAAKRIEEEAFAA 55 (99)
T ss_pred CCCCchHHHHHHHHHHHhhhhhHHHHH---HcCCCCHHHHHHHHHHHHHHHHHH
Confidence 344577788888888877765320000 000111223578999999999974
No 7
>PF02172 KIX: KIX domain; InterPro: IPR003101 The nuclear factor CREB activates transcription of target genes in part through direct interactions with the KIX domain of the coactivator CBP in a phosphorylation-dependent manner []. This provides a model for activator:coactivator interactions. The KIX domain of CBP also binds to transactivation domains of other nuclear factors including Myb and Jun.; GO: 0003712 transcription cofactor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 2KWF_A 1KDX_A 2LQH_A 2LQI_A 1SB0_A 2AGH_B.
Probab=17.28 E-value=1.3e+02 Score=23.12 Aligned_cols=52 Identities=15% Similarity=0.141 Sum_probs=32.2
Q ss_pred ccCCchHHHHHHHHHHHHHHhhhccchhhHHhhhhhcCChHHHHHHHHHHHHHhhC
Q 037910 108 IKCSDATRTLIRERLAEAFSKVAGEVEEMEKKEQVRACDPVGVAVSVESVLFKNMC 163 (235)
Q Consensus 108 ~~t~D~vRdK~relL~~AL~~~~~e~~d~ik~~~~~~~d~~~lA~eIE~aLF~~~~ 163 (235)
..-+..+|+..+.-|..|+........ . .......+...|..||..+|..-.
T Consensus 8 ~~vt~~lR~hlV~KLv~aI~P~pdp~a--~--~d~rm~~l~~yarkvE~~~fe~A~ 59 (81)
T PF02172_consen 8 SSVTPDLRNHLVHKLVQAIFPTPDPNA--M--NDPRMKNLIEYARKVEKDMFETAQ 59 (81)
T ss_dssp CCT-HHHHHHHHHHHHHHHS-SSSCCC--C--CSHHHHHHHHHHHHHHHHHHHC-S
T ss_pred HHcCHHHHHHHHHHHHHhhCCCCChhh--h--hhHHHHHHHHHHHHHHHHHHHHhc
Confidence 344578999999999999886421110 0 000112357899999999998643
No 8
>PF09693 Phage_XkdX: Phage uncharacterised protein (Phage_XkdX); InterPro: IPR010022 This entry is represented by Bacteriophage 69, Orf86. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry identifies a family of small (about 50 amino acid) phage proteins, found in at least 12 different phage and prophage regions of Gram-positive bacteria. In a number of these phage, the gene for this protein is found near the holin and endolysin genes.
Probab=14.28 E-value=52 Score=21.87 Aligned_cols=26 Identities=19% Similarity=0.096 Sum_probs=22.5
Q ss_pred CChhhhhhhhcCCCCccccccCCccc
Q 037910 173 KNPDFWRKVLLGEVKPETLVTALPEE 198 (235)
Q Consensus 173 KNp~Lr~~VL~GeIsP~~Lv~MSseE 198 (235)
.+.+|+.-|-.|-||++++-.+|-++
T Consensus 14 t~~~v~~~V~~g~IT~eey~eITGe~ 39 (40)
T PF09693_consen 14 TKEDVKNFVEAGWITKEEYKEITGED 39 (40)
T ss_pred CHHHHHHHhhcCeECHHHHHHhhCCC
Confidence 56789999999999999998888764
No 9
>TIGR00244 transcriptional regulator NrdR. Members of this almost entirely bacterial family contain an ATP cone domain (PFAM:PF03477). There is never more than one member per genome. Common gene symbols given include nrdR, ybaD, ribX and ytcG. The member from Streptomyces coelicolor is found upstream in the operon of the class II oxygen-independent ribonucleotide reductase gene nrdJ and was shown to repress nrdJ expression. Many members of this family are found near genes for riboflavin biosynthesis in Gram-negative bacteria, suggesting a role in that pathway. However, a phylogenetic profiling study associates members of this family with the presence of a palindromic signal with consensus acaCwAtATaTwGtgt, termed the NrdR-box, an upstream element for most operons for ribonucleotide reductase of all three classes in bacterial genomes.
Probab=11.87 E-value=4.2e+02 Score=22.73 Aligned_cols=39 Identities=13% Similarity=-0.055 Sum_probs=29.5
Q ss_pred HHHHHHHHHHHHHhhhccchhhHHhhhhhcCChHHHHHHHHHHHHHhhCC
Q 037910 115 RTLIRERLAEAFSKVAGEVEEMEKKEQVRACDPVGVAVSVESVLFKNMCP 164 (235)
Q Consensus 115 RdK~relL~~AL~~~~~e~~d~ik~~~~~~~d~~~lA~eIE~aLF~~~~~ 164 (235)
|+|++.-|..|+.++- -..+. ...++..||..|++....
T Consensus 63 r~Kl~~gl~~Ac~KRp-Vs~e~----------ie~~v~~Ie~~l~~~~~~ 101 (147)
T TIGR00244 63 REKLLRGMVRACEKRP-VSFDD----------LEHAINHIEAQLRAQGER 101 (147)
T ss_pred HHHHHHHHHHHhcCCC-CCHHH----------HHHHHHHHHHHHHHcCCC
Confidence 8999999999999863 11222 367899999999987654
No 10
>PF14237 DUF4339: Domain of unknown function (DUF4339)
Probab=11.45 E-value=1.5e+02 Score=19.58 Aligned_cols=20 Identities=30% Similarity=0.518 Sum_probs=17.0
Q ss_pred hhhhhhhhcCCCCccccccC
Q 037910 175 PDFWRKVLLGEVKPETLVTA 194 (235)
Q Consensus 175 p~Lr~~VL~GeIsP~~Lv~M 194 (235)
..|++-+-.|.|+++.||-.
T Consensus 17 ~el~~l~~~g~i~~~tlvw~ 36 (45)
T PF14237_consen 17 EELRQLISSGEIDPDTLVWK 36 (45)
T ss_pred HHHHHHHHcCCCCCCCeEeC
Confidence 47899999999999998743
Done!