Query 038232
Match_columns 217
No_of_seqs 146 out of 507
Neff 5.4
Searched_HMMs 46136
Date Fri Mar 29 08:56:50 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/038232.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/038232hhsearch_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 4.5E-36 9.8E-41 270.4 16.2 181 2-216 53-236 (299)
2 smart00510 TFS2M Domain in the 100.0 2.9E-31 6.3E-36 205.6 9.4 102 109-217 1-102 (102)
3 KOG1105 Transcription elongati 100.0 2.7E-30 5.9E-35 231.6 14.5 176 2-216 56-233 (296)
4 PF07500 TFIIS_M: Transcriptio 99.9 2.2E-28 4.9E-33 191.6 6.3 104 107-217 1-104 (115)
5 KOG1634 Predicted transcriptio 99.4 3E-14 6.6E-19 140.8 3.3 76 141-216 267-343 (778)
6 smart00509 TFS2N Domain in the 96.7 0.0014 3E-08 48.1 2.8 24 2-25 51-74 (75)
7 PF08711 Med26: TFIIS helical 95.4 0.017 3.8E-07 39.0 3.0 22 3-24 30-52 (53)
8 KOG1886 BAH domain proteins [T 77.3 0.89 1.9E-05 44.1 0.5 102 103-206 236-342 (464)
9 KOG4274 Positive cofactor 2 (P 71.2 6.3 0.00014 39.5 4.6 61 108-182 8-68 (742)
10 smart00099 btg1 tob/btg1 famil 51.6 21 0.00045 28.2 3.5 61 144-206 28-92 (108)
11 PF02172 KIX: KIX domain; Int 51.0 29 0.00062 26.0 4.0 67 107-177 10-76 (81)
12 PF07742 BTG: BTG family; Int 29.1 75 0.0016 25.2 3.5 63 144-206 28-94 (118)
13 PF09606 Med15: ARC105 or Med1 26.7 67 0.0014 33.5 3.5 51 114-178 2-52 (799)
14 PF06254 DUF1019: Protein of u 23.0 39 0.00086 25.8 0.8 49 153-201 12-60 (89)
15 TIGR01669 phage_XkdX phage unc 20.8 44 0.00095 22.2 0.6 33 173-205 12-44 (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=100.00 E-value=4.5e-36 Score=270.36 Aligned_cols=181 Identities=28% Similarity=0.385 Sum_probs=129.3
Q ss_pred cccchHHHHHHHHHHHHHHHHHHHHHhhhccCCCccCCCCCCcchhhccccccccccccccccccccccccccccccCCC
Q 038232 2 KASSRKKIQDFASDLIVSWRNMSLEQMRDERKGSYTIPGDIEPAKIEKVDKRTSEECQEISGVGIVKVQKVDQNATSLSS 81 (217)
Q Consensus 2 ~~~~~~~i~~~A~~l~~~WKkvv~~e~~~~~~~~~~~~~~~~~~k~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~t~~~~ 81 (217)
++||+++|+++|++||..||++|.++..++... .++.+...++..... +.+..+++.
T Consensus 53 rkh~~~~I~~lAk~li~~WK~~v~~~k~~~~~~-------~~~~~~~~~~~~~~~--------------~~~~~~~~~-- 109 (299)
T TIGR01385 53 RKHPNEDISKLAKKIIKSWKKVVDKNKSDHPGG-------NPEDKTTVGESVNSV--------------KQEAKSQSD-- 109 (299)
T ss_pred HcCCcHHHHHHHHHHHHHHHHHHhhhcccCccc-------ccccccccCCCCCCC--------------CccccCCcc--
Confidence 589999999999999999999999984332211 011110000000000 000000000
Q ss_pred CCCCCCccccccCCCCC---CCCccccCCChHHHHHHHHHHHHHHhhhhCCCchhHhhhhhccchHHHHHHHHHHHHHhh
Q 038232 82 NVVRPESVVTEKTNSSD---NLSRSMIRCNDCFREVVREKVCDALSKVSGEADEEIRDEVNACDSVRVAIALESAMFEKW 158 (217)
Q Consensus 82 ~~~~~~~v~~e~~ss~~---~~~~s~~~~~d~~Rdk~r~~L~~aL~~~~~e~~~~~~~e~~~~~~~~lA~~IE~alf~~~ 158 (217)
.....+. .+++.. +.+.+++.++|++|++|+++||+||.....+.+ ..+++..+|.+||.+||..|
T Consensus 110 ---~~~~~~~-~~~~~~~~~~~~~~~~~t~d~~Rdk~r~~L~~aL~~~~~~~~-------~~~~~~~lA~~iE~~~f~~~ 178 (299)
T TIGR01385 110 ---KIEQPKY-VSSSPRNAKNDFVPTAVTNDKVRDKCRELLYDALAKDSDHPP-------QSIDPEAKAIQIEELKFNNL 178 (299)
T ss_pred ---cccCCCC-CCCcccccCCCCCCCccCCcHHHHHHHHHHHHHHhhcCCCCc-------cccCHHHHHHHHHHHHHHHc
Confidence 0000000 011111 225566789999999999999999997543332 23567799999999999999
Q ss_pred cCCChhhHHHHHHHHhhcCCCCChhhHhhhhcCCCCccccccCCcccCCCHHHHhhhh
Q 038232 159 DRYDGPYKIKYKAVLGNLKDPKNPDFRRNVHLGQVKPETIVGMTAKEMAGDKMLSCYQ 216 (217)
Q Consensus 159 ~~~~~~Yk~k~RSl~fNLKD~kNp~Lr~~VL~G~isp~~Lv~Ms~eEMASdelk~e~q 216 (217)
+.++..|+++||||+|||||++||+||++||+|+|+|++||.|+++||||+++|++++
T Consensus 179 ~~~~~~Yk~k~Rsl~~NLKd~kNp~Lr~~vl~G~i~p~~lv~Ms~eEmas~e~k~~~e 236 (299)
T TIGR01385 179 GTTEAAYKARYRSIYSNLRDKNNPDLRHNVLTGEITPEKLATMTAEEMASAELKQERE 236 (299)
T ss_pred CCCcHHHHHHHHHHHHHccCCCCHHHHHHHHcCCCCHHHHhcCCHHHcCCHHHHHHHH
Confidence 9888899999999999999999999999999999999999999999999999999875
No 2
>smart00510 TFS2M Domain in the central regions of transcription elongation factor S-II (and elsewhere).
Probab=99.97 E-value=2.9e-31 Score=205.56 Aligned_cols=102 Identities=35% Similarity=0.570 Sum_probs=93.0
Q ss_pred hHHHHHHHHHHHHHHhhhhCCCchhHhhhhhccchHHHHHHHHHHHHHhhcCCChhhHHHHHHHHhhcCCCCChhhHhhh
Q 038232 109 DCFREVVREKVCDALSKVSGEADEEIRDEVNACDSVRVAIALESAMFEKWDRYDGPYKIKYKAVLGNLKDPKNPDFRRNV 188 (217)
Q Consensus 109 d~~Rdk~r~~L~~aL~~~~~e~~~~~~~e~~~~~~~~lA~~IE~alf~~~~~~~~~Yk~k~RSl~fNLKD~kNp~Lr~~V 188 (217)
|++|++|+++|+++|...+...+. .+++..+|.+||.+||..|+..++.|++++|||+|||||++||+||++|
T Consensus 1 d~~R~~~~~~L~~al~~~~~~~~~-------~~~~~~lA~~IE~~lf~~~~~~~~~Yk~k~Rsl~fNLkd~kN~~Lr~~v 73 (102)
T smart00510 1 DKVRDKCQEMLYKALQKISDPEEI-------ELDPTELAVQIEAEMFSEFGTTDKKYKNKYRSLYFNLKDKKNPDLRRKV 73 (102)
T ss_pred ChHHHHHHHHHHHHHHhcCCCCcc-------cccHHHHHHHHHHHHHHHcCCCcHHHHHHHHHHHHHhcCCCCHHHHHHH
Confidence 689999999999999986554432 2456799999999999999988889999999999999999999999999
Q ss_pred hcCCCCccccccCCcccCCCHHHHhhhhC
Q 038232 189 HLGQVKPETIVGMTAKEMAGDKMLSCYQR 217 (217)
Q Consensus 189 L~G~isp~~Lv~Ms~eEMASdelk~e~q~ 217 (217)
|+|+|+|++||.||++||||+++|+++++
T Consensus 74 l~G~i~p~~lv~Ms~~ElAs~elk~~~e~ 102 (102)
T smart00510 74 LNGEITPEKLATMTAEELASAELKEKREK 102 (102)
T ss_pred HcCCCCHHHHhcCCHHHcCCHHHHHHHhC
Confidence 99999999999999999999999999875
No 3
>KOG1105 consensus Transcription elongation factor TFIIS/Cofactor of enhancer-binding protein Sp1 [Transcription]
Probab=99.97 E-value=2.7e-30 Score=231.60 Aligned_cols=176 Identities=30% Similarity=0.487 Sum_probs=125.8
Q ss_pred cccchHHHHHHHHHHHHHHHHHHHHH-hhhccCCC-ccCCCCCCcchhhccccccccccccccccccccccccccccccC
Q 038232 2 KASSRKKIQDFASDLIVSWRNMSLEQ-MRDERKGS-YTIPGDIEPAKIEKVDKRTSEECQEISGVGIVKVQKVDQNATSL 79 (217)
Q Consensus 2 ~~~~~~~i~~~A~~l~~~WKkvv~~e-~~~~~~~~-~~~~~~~~~~k~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~t~~ 79 (217)
|+||+++|.++|+.||..||++|.+. ...+.+.. ...|+.. ...++ +.. ..|.
T Consensus 56 Kk~~n~ev~~~ak~Lik~Wkk~~~~~~~~~k~~~~~~~~p~~~-----~~~~~---------s~~--~~~~--------- 110 (296)
T KOG1105|consen 56 KKHKNEEVRSLAKKLIKSWKKLVDKSPGREKSGDNKSHDPGEA-----SSKSP---------SGA--KQPE--------- 110 (296)
T ss_pred HhCCCHHHHHHHHHHHHHHHHHhhcccccccCccccCCCCCcC-----CcCCc---------cCC--CCcc---------
Confidence 79999999999999999999999985 11111110 1111111 00000 000 0000
Q ss_pred CCCCCCCCccccccCCCCCCCCccccCCChHHHHHHHHHHHHHHhhhhCCCchhHhhhhhccchHHHHHHHHHHHHHhhc
Q 038232 80 SSNVVRPESVVTEKTNSSDNLSRSMIRCNDCFREVVREKVCDALSKVSGEADEEIRDEVNACDSVRVAIALESAMFEKWD 159 (217)
Q Consensus 80 ~~~~~~~~~v~~e~~ss~~~~~~s~~~~~d~~Rdk~r~~L~~aL~~~~~e~~~~~~~e~~~~~~~~lA~~IE~alf~~~~ 159 (217)
.++.+....+-+++ ....+.++|++|++|+++||+||..... +....+++..+|.+||.+||..++
T Consensus 111 ---ks~~~~~~~~~~~~----~~~~~~~~d~~r~k~~e~l~~al~~~~~-------~~~~~~~~~~~a~~iE~~~~~~~g 176 (296)
T KOG1105|consen 111 ---KSRGDSKRDKHSGS----KDPVPITNDPVRDKCRELLYAALTTEDD-------SRVTGADPLELAVQIEEAIFEKLG 176 (296)
T ss_pred ---ccccccccccccCc----CCCCCCCCchHHHHHHHHHHHHhccccc-------ccccCCCHHHHHHHHHHHHHHHhC
Confidence 01111111110111 1334456999999999999999984211 122346778999999999999999
Q ss_pred CCChhhHHHHHHHHhhcCCCCChhhHhhhhcCCCCccccccCCcccCCCHHHHhhhh
Q 038232 160 RYDGPYKIKYKAVLGNLKDPKNPDFRRNVHLGQVKPETIVGMTAKEMAGDKMLSCYQ 216 (217)
Q Consensus 160 ~~~~~Yk~k~RSl~fNLKD~kNp~Lr~~VL~G~isp~~Lv~Ms~eEMASdelk~e~q 216 (217)
.+...|+.+|||++|||+|++||+||++||+|+|+|++|+.|+++||||+++|+.++
T Consensus 177 ~~~~kyK~r~RS~~~NLkd~~Np~LR~~vl~G~i~pe~la~mt~eEMaS~~lk~~~~ 233 (296)
T KOG1105|consen 177 NTDSKYKNRYRSRVSNLKDKNNPDLRRNVLTGEISPERLATMTSEEMASEELKEERQ 233 (296)
T ss_pred CCcHHHHHHHHHHhhccCCCCCHHHHHHHhcCCCCHHHhccCChhhhccHHHHHHHH
Confidence 999999999999999999999999999999999999999999999999999999886
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=99.95 E-value=2.2e-28 Score=191.62 Aligned_cols=104 Identities=35% Similarity=0.602 Sum_probs=93.3
Q ss_pred CChHHHHHHHHHHHHHHhhhhCCCchhHhhhhhccchHHHHHHHHHHHHHhhcCCChhhHHHHHHHHhhcCCCCChhhHh
Q 038232 107 CNDCFREVVREKVCDALSKVSGEADEEIRDEVNACDSVRVAIALESAMFEKWDRYDGPYKIKYKAVLGNLKDPKNPDFRR 186 (217)
Q Consensus 107 ~~d~~Rdk~r~~L~~aL~~~~~e~~~~~~~e~~~~~~~~lA~~IE~alf~~~~~~~~~Yk~k~RSl~fNLKD~kNp~Lr~ 186 (217)
|++++|++++++|+++|.....+ .+ ....+..+|.+||.+||..|+..+..|++++|+|+|||||++||+||.
T Consensus 1 ~~~~~R~k~~~~L~~~l~~~~~~-~~------~~~~~~~lA~~IE~~lf~~~~~~~~~Y~~k~Rsl~~NLkd~~N~~L~~ 73 (115)
T PF07500_consen 1 TNDKVRDKARKLLYKALQKRSDE-QD------DPEDAKELAKEIEEALFDKFGSTSKKYKQKFRSLMFNLKDPKNPDLRR 73 (115)
T ss_dssp -TCHHHHHHHHHHHHHHHHCCCC-CC------CTCCHHHHHHHHHHHHHHHHTSTSHHHHHHHHHHHHHHCSSTTCCHHH
T ss_pred CCcHHHHHHHHHHHHHHHhcCcc-cc------chhHHHHHHHHHHHHHHHHHccCcHHHHHHHHHHHHHhccCCcHHHHH
Confidence 68999999999999999986544 11 234667999999999999998888999999999999999999999999
Q ss_pred hhhcCCCCccccccCCcccCCCHHHHhhhhC
Q 038232 187 NVHLGQVKPETIVGMTAKEMAGDKMLSCYQR 217 (217)
Q Consensus 187 ~VL~G~isp~~Lv~Ms~eEMASdelk~e~q~ 217 (217)
+||+|+|+|.+||.|+++||||+++|+++++
T Consensus 74 ~il~g~i~p~~lv~ms~~Elas~e~k~~~e~ 104 (115)
T PF07500_consen 74 RILSGEISPEELVTMSPEELASEELKEEREK 104 (115)
T ss_dssp HHHHSSSTTCHHHHCTTTTTTTSCCCCCHCC
T ss_pred HHHcCCCCHHHHhcCCHHHhCCHHHHHHHHH
Confidence 9999999999999999999999999988753
No 5
>KOG1634 consensus Predicted transcription factor DATF1, contains PHD and TFS2M domains [Transcription]
Probab=99.45 E-value=3e-14 Score=140.80 Aligned_cols=76 Identities=29% Similarity=0.454 Sum_probs=70.7
Q ss_pred cchHHHHHHHHHHHHHhhc-CCChhhHHHHHHHHhhcCCCCChhhHhhhhcCCCCccccccCCcccCCCHHHHhhhh
Q 038232 141 CDSVRVAIALESAMFEKWD-RYDGPYKIKYKAVLGNLKDPKNPDFRRNVHLGQVKPETIVGMTAKEMAGDKMLSCYQ 216 (217)
Q Consensus 141 ~~~~~lA~~IE~alf~~~~-~~~~~Yk~k~RSl~fNLKD~kNp~Lr~~VL~G~isp~~Lv~Ms~eEMASdelk~e~q 216 (217)
.++.-++..||..||..|+ +.+..|+.|+|+|+|||||++||.||.+|+.|+|++++||.|+++|||+.++.+.++
T Consensus 267 ~d~~ll~~~ie~el~~~fG~gvnkkY~ek~RsL~fNlKDkkN~~lre~v~~~ei~~e~Lv~msaeelAs~eL~~~rE 343 (778)
T KOG1634|consen 267 QDPNLLLEKIEHELFVLFGLGVNKKYPEKLRSLLFNLKDKKNPELRERVMSGEISAERLVNMSAEELASPELAEWRE 343 (778)
T ss_pred cchhhHhhhhhhhceeccCCcccccchhhhhhhhhccccccchHHHHHHhhcccCHhhhccCCchhhcCchHHHHHH
Confidence 3555778899999999999 778999999999999999999999999999999999999999999999999988765
No 6
>smart00509 TFS2N Domain in the N-terminus of transcription elongation factor S-II (and elsewhere).
Probab=96.69 E-value=0.0014 Score=48.08 Aligned_cols=24 Identities=25% Similarity=0.610 Sum_probs=22.3
Q ss_pred cccchHHHHHHHHHHHHHHHHHHH
Q 038232 2 KASSRKKIQDFASDLIVSWRNMSL 25 (217)
Q Consensus 2 ~~~~~~~i~~~A~~l~~~WKkvv~ 25 (217)
.+|++++|+.+|++||..||++|.
T Consensus 51 rkh~~~~I~~~A~~Li~~WK~~v~ 74 (75)
T smart00509 51 RKHKNEEIRKLAKKLIKSWKKLVY 74 (75)
T ss_pred HcCCcHHHHHHHHHHHHHHHHHhc
Confidence 579999999999999999999984
No 7
>PF08711 Med26: TFIIS helical bundle-like domain; InterPro: IPR017923 Transcription factor IIS (TFIIS) is a transcription elongation factor that increases the overall transcription rate of RNA polymerase II by reactivating transcription elongation complexes that have arrested transcription. The three structural domains of TFIIS are conserved from yeast to human. The 80 or so N-terminal residues form a protein interaction domain containing a conserved motif, which has been called the LW motif because of the invariant leucine and tryptophan residues it contains. Although the N-terminal domain is not needed for transcriptional activity, a similar sequence has been identified in other transcription factors and proteins that are predominantly nuclear localized [, ]: MED26 (also known as CRSP70 and ARC70), a subunit of the Mediator complex, which is required for the activity of the enhancer-binding protein Sp1. Elongin A, a subunit of a transcription elongation factor previously known as SIII. It increases the rate of transcription by suppressing transient pausing of the elongation complex. PPP1R10, a nuclear regulatory subunit of protein phosphatase 1 that was previously known as p99, FB19 or PNUTS. PIBP, a small hypothetical protein that could be a phosphoinositide binding protein. IWS1, which is thought to function in both transcription initiation and elongation. The TFIIS N-terminal domain is a compact four-helix bundle. The hydrophobic core residues of helices 2, 3, and 4 are well conserved among TFIIS domains, although helix 1 is less conserved []. ; GO: 0003677 DNA binding, 0006351 transcription, DNA-dependent, 0005634 nucleus; PDB: 1EO0_A 3OAK_A 3NFQ_B 3O8Z_A 1WJT_A 2XPL_A 2XPO_A 2XPP_A 2XPN_A.
Probab=95.37 E-value=0.017 Score=39.02 Aligned_cols=22 Identities=23% Similarity=0.588 Sum_probs=19.6
Q ss_pred cc-chHHHHHHHHHHHHHHHHHH
Q 038232 3 AS-SRKKIQDFASDLIVSWRNMS 24 (217)
Q Consensus 3 ~~-~~~~i~~~A~~l~~~WKkvv 24 (217)
+| ++.+|+..|++||..||++|
T Consensus 30 k~~~~~~i~~~A~~Li~~Wk~~v 52 (53)
T PF08711_consen 30 KHSENPEIRKLAKELIKKWKRIV 52 (53)
T ss_dssp HCTS-HHHHHHHHHHHHHHHHHH
T ss_pred cCCCCHHHHHHHHHHHHHHhHhc
Confidence 56 99999999999999999987
No 8
>KOG1886 consensus BAH domain proteins [Transcription]
Probab=77.28 E-value=0.89 Score=44.06 Aligned_cols=102 Identities=17% Similarity=0.058 Sum_probs=75.3
Q ss_pred cccCCChHHHHHHHHHHHHHHhhhhCCCchh--Hhhh--hhccchHHHHHHHHHHHHHhhcCCChhhHHHHHHHHhhcCC
Q 038232 103 SMIRCNDCFREVVREKVCDALSKVSGEADEE--IRDE--VNACDSVRVAIALESAMFEKWDRYDGPYKIKYKAVLGNLKD 178 (217)
Q Consensus 103 s~~~~~d~~Rdk~r~~L~~aL~~~~~e~~~~--~~~e--~~~~~~~~lA~~IE~alf~~~~~~~~~Yk~k~RSl~fNLKD 178 (217)
....+++.-|++++.-++++....++-.... -.+. ....+.+..+..||...|+.+......|..+.+.|.++|+
T Consensus 236 ~~~~t~~~~~~k~~g~~~~~v~~~~~~~s~~~~~~~~~~~~p~~~v~~~~~le~~s~~s~a~d~~~~~~~~~~l~~~~k- 314 (464)
T KOG1886|consen 236 FDLLTGRSDRDKVLGKLLEVVWQNSCSTSEAKPAGDQGSLWPNPSVSPCGALEQPSHASLAKDLESYLGLRETLVLLLK- 314 (464)
T ss_pred CCCCCCcccccccccccchhhccccccccccCCCcccccCCCCcccchhhhhhhhhhhhHhhhhhhhhhhhhHHHhhhc-
Confidence 3466889999999999999985443322110 0000 0112356889999999999998777899999999999999
Q ss_pred CCChhhHhhhhcCC-CCccccccCCcccC
Q 038232 179 PKNPDFRRNVHLGQ-VKPETIVGMTAKEM 206 (217)
Q Consensus 179 ~kNp~Lr~~VL~G~-isp~~Lv~Ms~eEM 206 (217)
.---|+.+.++|. +.|+.++.|.+=++
T Consensus 315 -~~~~l~~~~ln~~~~~~e~~~~l~~p~~ 342 (464)
T KOG1886|consen 315 -GQALLKPEPLNPGETKPEPKQELHPPSF 342 (464)
T ss_pred -chhhhccccCCCcccCchhhhhccCCCC
Confidence 5578889999995 88988888866443
No 9
>KOG4274 consensus Positive cofactor 2 (PC2), subunit of a multiprotein coactivator of RNA polymerase II [Transcription]
Probab=71.15 E-value=6.3 Score=39.51 Aligned_cols=61 Identities=23% Similarity=0.248 Sum_probs=47.6
Q ss_pred ChHHHHHHHHHHHHHHhhhhCCCchhHhhhhhccchHHHHHHHHHHHHHhhcCCChhhHHHHHHHHhhcCCCCCh
Q 038232 108 NDCFREVVREKVCDALSKVSGEADEEIRDEVNACDSVRVAIALESAMFEKWDRYDGPYKIKYKAVLGNLKDPKNP 182 (217)
Q Consensus 108 ~d~~Rdk~r~~L~~aL~~~~~e~~~~~~~e~~~~~~~~lA~~IE~alf~~~~~~~~~Yk~k~RSl~fNLKD~kNp 182 (217)
.-++|++++..|.+.|....- +...-|..+|+++|.++. +..+|-..+--|+..++|..|.
T Consensus 8 S~kFRq~vIsried~l~~n~q-------------~~~k~a~~mE~hVF~K~~-tkDEYl~lvAkli~h~~d~s~~ 68 (742)
T KOG4274|consen 8 SPKFRQHVISRIEDELRKNGQ-------------AHSKSAKDMESHVFLKAK-TKDEYLSLVAKLIIHFRDISNK 68 (742)
T ss_pred cHHHHHHHHHHhhhhhhhhhh-------------ccCcchHHHHHHHHHhhh-hHHHHHHHHHHHHHHHHhhhhh
Confidence 357899999999999986321 112557899999999875 4678999999999999987764
No 10
>smart00099 btg1 tob/btg1 family. The tob/btg1 is a family of proteins that inhibit cell proliferation.
Probab=51.61 E-value=21 Score=28.23 Aligned_cols=61 Identities=15% Similarity=0.139 Sum_probs=48.5
Q ss_pred HHHHHHHHHHHHHhhcCC----ChhhHHHHHHHHhhcCCCCChhhHhhhhcCCCCccccccCCcccC
Q 038232 144 VRVAIALESAMFEKWDRY----DGPYKIKYKAVLGNLKDPKNPDFRRNVHLGQVKPETIVGMTAKEM 206 (217)
Q Consensus 144 ~~lA~~IE~alf~~~~~~----~~~Yk~k~RSl~fNLKD~kNp~Lr~~VL~G~isp~~Lv~Ms~eEM 206 (217)
..++..++..|.+.|.+. +...-+-||.|.-| .+-.|.|.+.-..--|..++|..+=|.||
T Consensus 28 ~~F~~~L~~~L~~~y~~HWyP~~P~kGqayRCIrIn--~~~Dp~l~~Aa~~sGl~~~~l~~~LP~el 92 (108)
T smart00099 28 EIFAEKLTRLLKEKYKNHWYPEKPYKGSGFRCIRIN--QKVDPVIEQACKESGLDIDDLGGNLPKEL 92 (108)
T ss_pred HHHHHHHHHHHHHHHhcCCCCCCCCCCcceEEEEEC--CcCCHHHHHHHHHhCCCHHHHHHhCCccc
Confidence 489999999999999753 34567889999999 55789888877777788888877666665
No 11
>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=50.97 E-value=29 Score=26.01 Aligned_cols=67 Identities=13% Similarity=0.164 Sum_probs=44.2
Q ss_pred CChHHHHHHHHHHHHHHhhhhCCCchhHhhhhhccchHHHHHHHHHHHHHhhcCCChhhHHHHHHHHhhcC
Q 038232 107 CNDCFREVVREKVCDALSKVSGEADEEIRDEVNACDSVRVAIALESAMFEKWDRYDGPYKIKYKAVLGNLK 177 (217)
Q Consensus 107 ~~d~~Rdk~r~~L~~aL~~~~~e~~~~~~~e~~~~~~~~lA~~IE~alf~~~~~~~~~Yk~k~RSl~fNLK 177 (217)
-...+|+..+..|..++..... +... ......+....|..||..||+... +-.+|-..+--.+++++
T Consensus 10 vt~~lR~hlV~KLv~aI~P~pd--p~a~-~d~rm~~l~~yarkvE~~~fe~A~-sreeYY~llA~kiy~iq 76 (81)
T PF02172_consen 10 VTPDLRNHLVHKLVQAIFPTPD--PNAM-NDPRMKNLIEYARKVEKDMFETAQ-SREEYYHLLAEKIYKIQ 76 (81)
T ss_dssp T-HHHHHHHHHHHHHHHS-SSS--CCCC-CSHHHHHHHHHHHHHHHHHHHC-S-SHHHHHHHHHHHHHHHH
T ss_pred cCHHHHHHHHHHHHHhhCCCCC--hhhh-hhHHHHHHHHHHHHHHHHHHHHhc-cHHHHHHHHHHHHHHHH
Confidence 4578999999999998875311 1100 011112456899999999999764 24689888888888875
No 12
>PF07742 BTG: BTG family; InterPro: IPR002087 Anti-proliferative proteins have been shown to include mammalian and avian protein BTG1 (which appears to be involved in negative regulation of cell proliferation) and rat/mouse NGF-inducible protein PC3/TIS21 (BTG2) [, , ]. These proteins have from 158 to 363 amino acid residues, that are highly similar and include 3 conserved cysteine residues. BTG2 seems to have a signal sequence; while the other proteins may lack such a domain. The sequence of the N-terminal half of these proteins is well conserved.; PDB: 3DJU_B 3E9V_A 2Z15_D 2D5R_B 3DJN_B.
Probab=29.13 E-value=75 Score=25.22 Aligned_cols=63 Identities=16% Similarity=0.228 Sum_probs=41.0
Q ss_pred HHHHHHHHHHHHHhhcCC----ChhhHHHHHHHHhhcCCCCChhhHhhhhcCCCCccccccCCcccC
Q 038232 144 VRVAIALESAMFEKWDRY----DGPYKIKYKAVLGNLKDPKNPDFRRNVHLGQVKPETIVGMTAKEM 206 (217)
Q Consensus 144 ~~lA~~IE~alf~~~~~~----~~~Yk~k~RSl~fNLKD~kNp~Lr~~VL~G~isp~~Lv~Ms~eEM 206 (217)
..++..++..|...|.+. +...-+-||.|..|=..+--|.|.+.-..-.|..++|...=|.||
T Consensus 28 ~~F~~~L~~~L~~ry~~HW~P~~P~kGsayRcIrin~~~~~Dp~l~~Aa~~sgl~~~~l~~~LP~el 94 (118)
T PF07742_consen 28 DRFAEELENLLCERYKGHWYPENPSKGSAYRCIRINPGHKMDPVLEQAAKESGLSYEDLRSLLPREL 94 (118)
T ss_dssp HHHHHHHHHHHHHHHTTS--TTSTTTTHHHH-EEES--SSB-HHHHHHHHHTT--HHHHHHHS-TTE
T ss_pred HHHHHHHHHHHHHHHhCCCCCCCCCCCCceEEEEEcCCCCCCHHHHHHHHHhCCCHHHHHHhcchhc
Confidence 489999999999999764 245567799998885444668888776666677666654444443
No 13
>PF09606 Med15: ARC105 or Med15 subunit of Mediator complex non-fungal; InterPro: IPR019087 The Mediator complex is a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. The Mediator complex, having a compact conformation in its free form, is recruited to promoters by direct interactions with regulatory proteins and serves for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. On recruitment the Mediator complex unfolds to an extended conformation and partially surrounds RNA polymerase II, specifically interacting with the unphosphorylated form of the C-terminal domain (CTD) of RNA polymerase II. The Mediator complex dissociates from the RNA polymerase II holoenzyme and stays at the promoter when transcriptional elongation begins. The Mediator complex is composed of at least 31 subunits: MED1, MED4, MED6, MED7, MED8, MED9, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED17, MED18, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, MED27, MED29, MED30, MED31, CCNC, CDK8 and CDC2L6/CDK11. The subunits form at least three structurally distinct submodules. The head and the middle modules interact directly with RNA polymerase II, whereas the elongated tail module interacts with gene-specific regulatory proteins. Mediator containing the CDK8 module is less active than Mediator lacking this module in supporting transcriptional activation. The head module contains: MED6, MED8, MED11, SRB4/MED17, SRB5/MED18, ROX3/MED19, SRB2/MED20 and SRB6/MED22. The middle module contains: MED1, MED4, NUT1/MED5, MED7, CSE2/MED9, NUT2/MED10, SRB7/MED21 and SOH1/MED31. CSE2/MED9 interacts directly with MED4. The tail module contains: MED2, PGD1/MED3, RGR1/MED14, GAL11/MED15 and SIN4/MED16. The CDK8 module contains: MED12, MED13, CCNC and CDK8. Individual preparations of the Mediator complex lacking one or more distinct subunits have been variously termed ARC, CRSP, DRIP, PC2, SMCC and TRAP. The proteins in this entry represent subunit Med15 of the Mediator complex. They contain a single copy of the approximately 70 residue ARC105 domain. The ARC105 domain of the ARC-Mediator co-activator is a three-helix bundle with marked similarity to the KIX domain. The sterol regulatory element binding protein (SREBP) family of transcription activators use the ARC105 subunit to activate target genes in the regulation of cholesterol and fatty acid homeostasis. In addition, ARC105 is a critical transducer of gene activation signals that control early metazoan development []. ; GO: 0001104 RNA polymerase II transcription cofactor activity, 0006357 regulation of transcription from RNA polymerase II promoter, 0016592 mediator complex; PDB: 2GUT_A.
Probab=26.69 E-value=67 Score=33.53 Aligned_cols=51 Identities=20% Similarity=0.262 Sum_probs=34.8
Q ss_pred HHHHHHHHHHhhhhCCCchhHhhhhhccchHHHHHHHHHHHHHhhcCCChhhHHHHHHHHhhcCC
Q 038232 114 VVREKVCDALSKVSGEADEEIRDEVNACDSVRVAIALESAMFEKWDRYDGPYKIKYKAVLGNLKD 178 (217)
Q Consensus 114 k~r~~L~~aL~~~~~e~~~~~~~e~~~~~~~~lA~~IE~alf~~~~~~~~~Yk~k~RSl~fNLKD 178 (217)
+++..|.++|........ +=|.++|.++|.+.. +..+|-..+--|+..++|
T Consensus 2 ~vi~~ie~a~~~~~~~~~-------------k~a~emE~hvF~Ka~-tkdEYl~~varli~h~r~ 52 (799)
T PF09606_consen 2 KVISKIEEAMRKNGQNTP-------------KSAREMENHVFQKAK-TKDEYLSLVARLILHIRD 52 (799)
T ss_dssp HHHHHHHHHHHHH----S-------------S-HHHHHHHHHHH-S-SHHHHHHHHHHHHHHHHH
T ss_pred cHHHHHHHHHHHhCCCCC-------------CCHHHHHHHHHHhhc-cHHHHHHHHHHHHHHHHH
Confidence 566677777776432222 447899999999875 357999988888888875
No 14
>PF06254 DUF1019: Protein of unknown function (DUF1019); InterPro: IPR009364 This entry is represented by Bacteriophage phi-80, CII. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.; PDB: 3C4R_C.
Probab=23.04 E-value=39 Score=25.78 Aligned_cols=49 Identities=14% Similarity=0.170 Sum_probs=22.5
Q ss_pred HHHHhhcCCChhhHHHHHHHHhhcCCCCChhhHhhhhcCCCCccccccC
Q 038232 153 AMFEKWDRYDGPYKIKYKAVLGNLKDPKNPDFRRNVHLGQVKPETIVGM 201 (217)
Q Consensus 153 alf~~~~~~~~~Yk~k~RSl~fNLKD~kNp~Lr~~VL~G~isp~~Lv~M 201 (217)
-||..+.+.+..|+.+++.|.--+-..==+++|.+|..|.=....|+.+
T Consensus 12 ~iFRwl~~ds~~~~~~~~~L~PAI~aAlP~E~rarl~~~~~~~~~la~~ 60 (89)
T PF06254_consen 12 KIFRWLDNDSPAYREKIMQLSPAILAALPPERRARLSSGDSTMYLLASA 60 (89)
T ss_dssp HHHHHHH--SHHHHHHHHHHHHHHHHHS-HHHHHHHHCTT-HHH-----
T ss_pred HHHHHHhCCCHHHHHHHHHHHHHHHHhCCHHHHhhccCCCCchhhhhHh
Confidence 4555555555666666666554444333356666666555444444433
No 15
>TIGR01669 phage_XkdX phage uncharacterized protein, XkdX family. This model represents 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=20.75 E-value=44 Score=22.19 Aligned_cols=33 Identities=15% Similarity=0.008 Sum_probs=26.9
Q ss_pred HhhcCCCCChhhHhhhhcCCCCccccccCCccc
Q 038232 173 LGNLKDPKNPDFRRNVHLGQVKPETIVGMTAKE 205 (217)
Q Consensus 173 ~fNLKD~kNp~Lr~~VL~G~isp~~Lv~Ms~eE 205 (217)
.|+...=.|.+|+.-|-.|-|+++++-.++.++
T Consensus 12 ~Y~~g~~t~e~v~~~V~~~~IT~eey~eITG~~ 44 (45)
T TIGR01669 12 YYLWGYYSNEDVNKFVEKKLITREQYKVITGEK 44 (45)
T ss_pred HHHcCCCCHHHHHHHhhcCccCHHHHHHHhCCC
Confidence 456666678899999999999999998777654
Done!