Query 020949
Match_columns 319
No_of_seqs 189 out of 686
Neff 6.3
Searched_HMMs 46136
Date Fri Mar 29 06:25:57 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/020949.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/020949hhsearch_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-48 9.7E-53 366.4 23.0 246 7-312 3-248 (299)
2 KOG1105 Transcription elongati 100.0 2.3E-44 5.1E-49 337.0 19.9 243 8-317 2-245 (296)
3 smart00510 TFS2M Domain in the 100.0 9.7E-31 2.1E-35 212.2 9.2 101 191-298 1-101 (102)
4 PF07500 TFIIS_M: Transcriptio 99.9 1.8E-28 3.8E-33 202.8 5.2 110 189-307 1-110 (115)
5 smart00509 TFS2N Domain in the 99.7 1.6E-17 3.4E-22 127.7 5.3 74 8-87 1-74 (75)
6 cd00183 TFIIS_I N-terminal dom 99.6 1.4E-15 3.1E-20 117.1 5.3 72 10-87 5-76 (76)
7 KOG1634 Predicted transcriptio 99.5 8.2E-15 1.8E-19 151.7 4.6 85 224-308 268-353 (778)
8 PF08711 Med26: TFIIS helical 99.4 1.9E-13 4E-18 98.0 2.5 52 36-87 1-53 (53)
9 PF11467 LEDGF: Lens epitheliu 96.2 0.0045 9.7E-08 50.8 3.2 78 2-87 1-80 (106)
10 KOG2821 RNA polymerase II tran 96.0 0.0032 6.9E-08 62.8 1.6 57 31-89 24-80 (433)
11 KOG1793 Uncharacterized conser 95.9 0.009 1.9E-07 58.9 4.4 56 34-89 235-293 (417)
12 COG5139 Uncharacterized conser 94.9 0.035 7.7E-07 52.9 4.5 54 35-88 233-288 (397)
13 PLN02976 amine oxidase 86.0 0.93 2E-05 52.2 4.7 56 36-91 1305-1361(1713)
14 KOG1886 BAH domain proteins [T 56.2 3.7 8.1E-05 41.7 0.0 100 187-288 238-342 (464)
15 KOG4274 Positive cofactor 2 (P 51.9 19 0.00041 37.7 4.2 62 191-266 9-70 (742)
16 PF14726 RTTN_N: Rotatin, an a 44.5 20 0.00043 29.0 2.5 50 31-80 47-96 (98)
17 smart00099 btg1 tob/btg1 famil 30.7 39 0.00084 27.9 2.2 61 226-288 28-92 (108)
18 PF02172 KIX: KIX domain; Int 25.7 91 0.002 24.3 3.3 67 189-259 10-76 (81)
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-48 Score=366.38 Aligned_cols=246 Identities=27% Similarity=0.404 Sum_probs=176.0
Q ss_pred HHHHHHHHHHHHHHhccChhhHhhHHHHHHHHHHhhcCCCChhhhhcCCcceecccccCCCCHHHHHHHHHHHHHHHHHH
Q 020949 7 QLCEEAKRGAEAAVMAEGEAEKAWTAWCIDALDQLNKSDITCPLLVSTQLVRYLLPLTEHPTKKIQDFASDLIVSWRDMF 86 (319)
Q Consensus 7 ~l~~~a~k~~~~a~~~~~~~e~~~~~~~l~~L~~L~~~~it~~lL~~T~iGk~V~~Lrkh~~~~I~~~Ak~Lv~~WK~~v 86 (319)
|+...++ ++++++.+++ .+.|+++|++|+.++||.++|++|+||++||+||+|++++|+.+|+.||.+||++|
T Consensus 3 ei~~~~k-~L~k~~~~~~------~~~~l~~L~~L~~~~~t~~lL~~T~IG~~Vn~lrkh~~~~I~~lAk~li~~WK~~v 75 (299)
T TIGR01385 3 EVASHAK-ALDKNKSSKN------VEQCLDILHQLKEFPPTEELLQETKVGVKVNKLRKHPNEDISKLAKKIIKSWKKVV 75 (299)
T ss_pred HHHHHHH-HhhhhccCCC------HHHHHHHHHHHhcCCCcHHHHhhCchhHHHHHHHcCCcHHHHHHHHHHHHHHHHHH
Confidence 3444444 5788776432 45899999999999999999999999999999999999999999999999999999
Q ss_pred HhhcccccCCCCCCCCCCCCCcccccccCCchhhhhhccccccccccccCCCCCCCCccccchhhhhhcccccCCcccCC
Q 020949 87 LEQIRDEKKGSCTIPGDTEPAKIEKVDKRTSEECQEISGVGIVKVQKVDQNSTSSSSNVVRSEIVETEETNSADNVNVGN 166 (319)
Q Consensus 87 ~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~i~~~~~~~~~~~~~~~ 166 (319)
..++..+....+ +.... . ++++ ...+ ++. .+.+ . ......
T Consensus 76 ~~~k~~~~~~~~--~~~~~--~--~~~~------------~~~~---~~~--~~~~---~--------------~~~~~~ 115 (299)
T TIGR01385 76 DKNKSDHPGGNP--EDKTT--V--GESV------------NSVK---QEA--KSQS---D--------------KIEQPK 115 (299)
T ss_pred hhhcccCccccc--ccccc--c--CCCC------------CCCC---ccc--cCCc---c--------------cccCCC
Confidence 876332111100 00000 0 0000 0000 000 0000 0 000000
Q ss_pred CcccCCCCcccccccccCCCCCCChHHHHHHHHHHHHHHhhhhCCCchhhhhhhhccchHHHHHHHHHHHHHHhcCCChh
Q 020949 167 SITEEGEASGIILHKLSSSKIRCNDCFREVVREKVCDALSKVSGEADEEIRDEVNACDSVRVAIALESAMFEKWGRSDGP 246 (319)
Q Consensus 167 ~~~~~~~~~~~~~~~~~~~~~~t~d~vR~k~r~~L~~aL~~~~~e~~~~~~~~~~~~~~~~lA~~IE~~lf~~~~~~~~~ 246 (319)
.....++.. +.+.+ ..+.++|++|++||++||+||.....+.+ ..+++..+|.+||.+||..|+.++.+
T Consensus 116 ~~~~~~~~~--~~~~~--~~~~t~d~~Rdk~r~~L~~aL~~~~~~~~-------~~~~~~~lA~~iE~~~f~~~~~~~~~ 184 (299)
T TIGR01385 116 YVSSSPRNA--KNDFV--PTAVTNDKVRDKCRELLYDALAKDSDHPP-------QSIDPEAKAIQIEELKFNNLGTTEAA 184 (299)
T ss_pred CCCCccccc--CCCCC--CCccCCcHHHHHHHHHHHHHHhhcCCCCc-------cccCHHHHHHHHHHHHHHHcCCCcHH
Confidence 000011111 11222 23589999999999999999997543222 23467789999999999999988899
Q ss_pred hhhhhhhHhhccCCCCChhHHhhhhcCCcCccccccCChhhcCCHHHHHHHHHHHHHHHHHHHHHH
Q 020949 247 YKIKYRAVLGNLKDPKNPDFRRKVLFGQVKPETVVGMTAKEMASDEMLRSYQHEDEERARLWKEHT 312 (319)
Q Consensus 247 Yk~k~RSl~fNLKD~kNp~Lr~~Vl~G~I~p~~lv~Mt~eEMASdelk~e~~ki~e~r~~l~ke~~ 312 (319)
|+++||||+|||||++||+||++||+|+|+|++||.||++||||+++|+++++|.+ ++|+...+
T Consensus 185 Yk~k~Rsl~~NLKd~kNp~Lr~~vl~G~i~p~~lv~Ms~eEmas~e~k~~~e~~~k--e~l~~~~~ 248 (299)
T TIGR01385 185 YKARYRSIYSNLRDKNNPDLRHNVLTGEITPEKLATMTAEEMASAELKQEREEITK--ENLFEAQG 248 (299)
T ss_pred HHHHHHHHHHHccCCCCHHHHHHHHcCCCCHHHHhcCCHHHcCCHHHHHHHHHHHH--HHHHHHHh
Confidence 99999999999999999999999999999999999999999999999998888888 88876543
No 2
>KOG1105 consensus Transcription elongation factor TFIIS/Cofactor of enhancer-binding protein Sp1 [Transcription]
Probab=100.00 E-value=2.3e-44 Score=337.01 Aligned_cols=243 Identities=31% Similarity=0.440 Sum_probs=178.9
Q ss_pred HHHHHHHHHHHHHhccChhhHhhHHHHHHHHHHhhcCCCChhhhhcCCcceecc-cccCCCCHHHHHHHHHHHHHHHHHH
Q 020949 8 LCEEAKRGAEAAVMAEGEAEKAWTAWCIDALDQLNKSDITCPLLVSTQLVRYLL-PLTEHPTKKIQDFASDLIVSWRDMF 86 (319)
Q Consensus 8 l~~~a~k~~~~a~~~~~~~e~~~~~~~l~~L~~L~~~~it~~lL~~T~iGk~V~-~Lrkh~~~~I~~~Ak~Lv~~WK~~v 86 (319)
+||.+.++|++.....+.+. ++.++++|.+|++++||.++|++|+||+.|| .|++|+|++|.++|+.||+.||++|
T Consensus 2 ~~e~~~r~ak~l~~~~~~~n---~~~~ld~l~~L~~~pvt~ell~~Tr~g~~vn~~~Kk~~n~ev~~~ak~Lik~Wkk~~ 78 (296)
T KOG1105|consen 2 LEEEALRAAKALEKDKQSKN---VEAALDLLKRLKKIPVTLELLQETRTGMGVNEVLKKHKNEEVRSLAKKLIKSWKKLV 78 (296)
T ss_pred ccHHHHHHHHHHHhhccccc---HHHHHHHHHHHHhcccHHHHHHHhhHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHHh
Confidence 57777777777644334456 8899999999999999999999999999999 7888999999999999999999999
Q ss_pred HhhcccccCCCCCCCCCCCCCcccccccCCchhhhhhccccccccccccCCCCCCCCccccchhhhhhcccccCCcccCC
Q 020949 87 LEQIRDEKKGSCTIPGDTEPAKIEKVDKRTSEECQEISGVGIVKVQKVDQNSTSSSSNVVRSEIVETEETNSADNVNVGN 166 (319)
Q Consensus 87 ~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~i~~~~~~~~~~~~~~~ 166 (319)
+.. +....... .+...| ...+..+. ++ +.++.++. .+..
T Consensus 79 ~~~-~~~~k~~~-~~~~~p-~~~~~~~~---------s~----------~~~~~ks~---------------~~~~---- 117 (296)
T KOG1105|consen 79 DKS-PGREKSGD-NKSHDP-GEASSKSP---------SG----------AKQPEKSR---------------GDSK---- 117 (296)
T ss_pred hcc-cccccCcc-ccCCCC-CcCCcCCc---------cC----------CCCccccc---------------cccc----
Confidence 864 11111000 000000 00000000 00 00000000 0000
Q ss_pred CcccCCCCcccccccccCCCCCCChHHHHHHHHHHHHHHhhhhCCCchhhhhhhhccchHHHHHHHHHHHHHHhcCCChh
Q 020949 167 SITEEGEASGIILHKLSSSKIRCNDCFREVVREKVCDALSKVSGEADEEIRDEVNACDSVRVAIALESAMFEKWGRSDGP 246 (319)
Q Consensus 167 ~~~~~~~~~~~~~~~~~~~~~~t~d~vR~k~r~~L~~aL~~~~~e~~~~~~~~~~~~~~~~lA~~IE~~lf~~~~~~~~~ 246 (319)
.. +..+.. ...+.++|++|++|++|||+||.... +. ....+++..+|.+||.+||..++.++++
T Consensus 118 --~~-~~~~~~------~~~~~~~d~~r~k~~e~l~~al~~~~----~~---~~~~~~~~~~a~~iE~~~~~~~g~~~~k 181 (296)
T KOG1105|consen 118 --RD-KHSGSK------DPVPITNDPVRDKCRELLYAALTTED----DS---RVTGADPLELAVQIEEAIFEKLGNTDSK 181 (296)
T ss_pred --cc-cccCcC------CCCCCCCchHHHHHHHHHHHHhcccc----cc---cccCCCHHHHHHHHHHHHHHHhCCCcHH
Confidence 00 000000 11235689999999999999998321 11 1235677899999999999999999999
Q ss_pred hhhhhhhHhhccCCCCChhHHhhhhcCCcCccccccCChhhcCCHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 020949 247 YKIKYRAVLGNLKDPKNPDFRRKVLFGQVKPETVVGMTAKEMASDEMLRSYQHEDEERARLWKEHTRKYMQ 317 (319)
Q Consensus 247 Yk~k~RSl~fNLKD~kNp~Lr~~Vl~G~I~p~~lv~Mt~eEMASdelk~e~~ki~e~r~~l~ke~~r~~~~ 317 (319)
|+++|||++|||+|++||+||++||+|+|+|++|+.||++||||+++|+ +|++|++|+|++|+-
T Consensus 182 yK~r~RS~~~NLkd~~Np~LR~~vl~G~i~pe~la~mt~eEMaS~~lk~-------~~~k~~keal~~~q~ 245 (296)
T KOG1105|consen 182 YKNRYRSRVSNLKDKNNPDLRRNVLTGEISPERLATMTSEEMASEELKE-------ERQKLTKEALREHQM 245 (296)
T ss_pred HHHHHHHHhhccCCCCCHHHHHHHhcCCCCHHHhccCChhhhccHHHHH-------HHHHHHHHHHHHHhh
Confidence 9999999999999999999999999999999999999999999999999 999999999999974
No 3
>smart00510 TFS2M Domain in the central regions of transcription elongation factor S-II (and elsewhere).
Probab=99.97 E-value=9.7e-31 Score=212.21 Aligned_cols=101 Identities=42% Similarity=0.654 Sum_probs=91.0
Q ss_pred hHHHHHHHHHHHHHHhhhhCCCchhhhhhhhccchHHHHHHHHHHHHHHhcCCChhhhhhhhhHhhccCCCCChhHHhhh
Q 020949 191 DCFREVVREKVCDALSKVSGEADEEIRDEVNACDSVRVAIALESAMFEKWGRSDGPYKIKYRAVLGNLKDPKNPDFRRKV 270 (319)
Q Consensus 191 d~vR~k~r~~L~~aL~~~~~e~~~~~~~~~~~~~~~~lA~~IE~~lf~~~~~~~~~Yk~k~RSl~fNLKD~kNp~Lr~~V 270 (319)
|++|++|+++||++|.......+. .+++..+|.+||.+||..|+.++.+|++++|||+|||||++||+||++|
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 679999999999999976543321 2356789999999999999988889999999999999999999999999
Q ss_pred hcCCcCccccccCChhhcCCHHHHHHHH
Q 020949 271 LFGQVKPETVVGMTAKEMASDEMLRSYQ 298 (319)
Q Consensus 271 l~G~I~p~~lv~Mt~eEMASdelk~e~~ 298 (319)
|+|+|+|++||.||++||||+|+|++++
T Consensus 74 l~G~i~p~~lv~Ms~~ElAs~elk~~~e 101 (102)
T smart00510 74 LNGEITPEKLATMTAEELASAELKEKRE 101 (102)
T ss_pred HcCCCCHHHHhcCCHHHcCCHHHHHHHh
Confidence 9999999999999999999999999664
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=1.8e-28 Score=202.77 Aligned_cols=110 Identities=38% Similarity=0.648 Sum_probs=97.2
Q ss_pred CChHHHHHHHHHHHHHHhhhhCCCchhhhhhhhccchHHHHHHHHHHHHHHhcCCChhhhhhhhhHhhccCCCCChhHHh
Q 020949 189 CNDCFREVVREKVCDALSKVSGEADEEIRDEVNACDSVRVAIALESAMFEKWGRSDGPYKIKYRAVLGNLKDPKNPDFRR 268 (319)
Q Consensus 189 t~d~vR~k~r~~L~~aL~~~~~e~~~~~~~~~~~~~~~~lA~~IE~~lf~~~~~~~~~Yk~k~RSl~fNLKD~kNp~Lr~ 268 (319)
|++++|++|+++|+++|.....+ .+ ...++..+|.+||.+||..|+.++..|++++|+|+|||||++||+||.
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 57999999999999999987544 11 123567999999999999998888999999999999999999999999
Q ss_pred hhhcCCcCccccccCChhhcCCHHHHHHHHHHHHHHHHH
Q 020949 269 KVLFGQVKPETVVGMTAKEMASDEMLRSYQHEDEERARL 307 (319)
Q Consensus 269 ~Vl~G~I~p~~lv~Mt~eEMASdelk~e~~ki~e~r~~l 307 (319)
+||+|+|+|.+||.||++||||+++|++++++.+ +++
T Consensus 74 ~il~g~i~p~~lv~ms~~Elas~e~k~~~e~~~~--~~l 110 (115)
T PF07500_consen 74 RILSGEISPEELVTMSPEELASEELKEEREKIRK--ESL 110 (115)
T ss_dssp HHHHSSSTTCHHHHCTTTTTTTSCCCCCHCCHHH--HHH
T ss_pred HHHcCCCCHHHHhcCCHHHhCCHHHHHHHHHHHH--HHH
Confidence 9999999999999999999999999997777776 554
No 5
>smart00509 TFS2N Domain in the N-terminus of transcription elongation factor S-II (and elsewhere).
Probab=99.70 E-value=1.6e-17 Score=127.75 Aligned_cols=74 Identities=31% Similarity=0.468 Sum_probs=64.4
Q ss_pred HHHHHHHHHHHHHhccChhhHhhHHHHHHHHHHhhcCCCChhhhhcCCcceecccccCCCCHHHHHHHHHHHHHHHHHHH
Q 020949 8 LCEEAKRGAEAAVMAEGEAEKAWTAWCIDALDQLNKSDITCPLLVSTQLVRYLLPLTEHPTKKIQDFASDLIVSWRDMFL 87 (319)
Q Consensus 8 l~~~a~k~~~~a~~~~~~~e~~~~~~~l~~L~~L~~~~it~~lL~~T~iGk~V~~Lrkh~~~~I~~~Ak~Lv~~WK~~v~ 87 (319)
||+.+++..+.+.. +++ ++.|+++|++|+.++||.++|++|+||+.|+.||+|++++|+.+|+.||+.||++|+
T Consensus 1 ~~~~~k~~~k~~~~---~~~---~~~~l~~L~~L~~~~~t~~~L~~T~iG~~v~~Lrkh~~~~I~~~A~~Li~~WK~~v~ 74 (75)
T smart00509 1 LLRAAKKLDKVANN---GKE---VSRCLDILKKLKKLPITVDLLEETRIGKKVNGLRKHKNEEIRKLAKKLIKSWKKLVY 74 (75)
T ss_pred ChHHHHHHHHHhcC---CCC---HHHHHHHHHHHhcCCCCHHHHHHCcHHHHHHHHHcCCcHHHHHHHHHHHHHHHHHhc
Confidence 46777775555532 235 678999999999999999999999999999999999999999999999999999985
No 6
>cd00183 TFIIS_I N-terminal domain (domain I) of transcription elongation factor S-II (TFIIS); similar to a domain found in elongin A and CRSP70; likely to be involved in transcription; domain I from TFIIS interacts with RNA polymerase II holoenzyme
Probab=99.59 E-value=1.4e-15 Score=117.06 Aligned_cols=72 Identities=28% Similarity=0.380 Sum_probs=62.1
Q ss_pred HHHHHHHHHHHhccChhhHhhHHHHHHHHHHhhcCCCChhhhhcCCcceecccccCCCCHHHHHHHHHHHHHHHHHHH
Q 020949 10 EEAKRGAEAAVMAEGEAEKAWTAWCIDALDQLNKSDITCPLLVSTQLVRYLLPLTEHPTKKIQDFASDLIVSWRDMFL 87 (319)
Q Consensus 10 ~~a~k~~~~a~~~~~~~e~~~~~~~l~~L~~L~~~~it~~lL~~T~iGk~V~~Lrkh~~~~I~~~Ak~Lv~~WK~~v~ 87 (319)
..++++++....+ ++ .+.|+++|+.|+.++||.++|++|+||+.||+||+|++++|+.+|+.||.+||+.|+
T Consensus 5 ~r~~~~l~~~~~~---~~---~~~~~~~L~~L~~~~it~~~L~~T~iG~~V~~Lrkh~~~~i~~~A~~Lv~~Wk~~v~ 76 (76)
T cd00183 5 LRAKKKLEKKDSN---EE---VSRLLDLLRLLKKLPLTVEILKETRIGKKVNSLRKHSNEKIRKLAKALIKSWKKLVD 76 (76)
T ss_pred HHHHHHhhccccC---CC---HHHHHHHHHHHhcCCCCHHHHHHCCHHHHHHHHHcCCcHHHHHHHHHHHHHHHHhcC
Confidence 3445556665532 24 678999999999999999999999999999999999999999999999999999873
No 7
>KOG1634 consensus Predicted transcription factor DATF1, contains PHD and TFS2M domains [Transcription]
Probab=99.51 E-value=8.2e-15 Score=151.73 Aligned_cols=85 Identities=33% Similarity=0.504 Sum_probs=75.6
Q ss_pred chHHHHHHHHHHHHHHhc-CCChhhhhhhhhHhhccCCCCChhHHhhhhcCCcCccccccCChhhcCCHHHHHHHHHHHH
Q 020949 224 DSVRVAIALESAMFEKWG-RSDGPYKIKYRAVLGNLKDPKNPDFRRKVLFGQVKPETVVGMTAKEMASDEMLRSYQHEDE 302 (319)
Q Consensus 224 ~~~~lA~~IE~~lf~~~~-~~~~~Yk~k~RSl~fNLKD~kNp~Lr~~Vl~G~I~p~~lv~Mt~eEMASdelk~e~~ki~e 302 (319)
++.-++..||..+|..|| +.+.+|++|+|||+|||||++||.||.+|+.|+|+|++||.|+++||||.++.+.+++..+
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 445677799999999999 7889999999999999999999999999999999999999999999999999997777666
Q ss_pred HHHHHH
Q 020949 303 ERARLW 308 (319)
Q Consensus 303 ~r~~l~ 308 (319)
+=..|+
T Consensus 348 e~~~mv 353 (778)
T KOG1634|consen 348 EMNEMV 353 (778)
T ss_pred HHHhhh
Confidence 333333
No 8
>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=99.38 E-value=1.9e-13 Score=98.00 Aligned_cols=52 Identities=31% Similarity=0.455 Sum_probs=47.4
Q ss_pred HHHHHhhcCCCChhhhhcCCcceecccccCC-CCHHHHHHHHHHHHHHHHHHH
Q 020949 36 DALDQLNKSDITCPLLVSTQLVRYLLPLTEH-PTKKIQDFASDLIVSWRDMFL 87 (319)
Q Consensus 36 ~~L~~L~~~~it~~lL~~T~iGk~V~~Lrkh-~~~~I~~~Ak~Lv~~WK~~v~ 87 (319)
++|+.|..+|||.++|++|+||++|+.|++| .+++|++.|+.||.+||+.|+
T Consensus 1 ~iL~~L~~l~it~~~L~~T~IGk~V~~l~k~~~~~~i~~~A~~Li~~Wk~~v~ 53 (53)
T PF08711_consen 1 EILKVLEKLPITVELLKSTGIGKAVNKLRKHSENPEIRKLAKELIKKWKRIVD 53 (53)
T ss_dssp HHHHHHHCSS-SHHHHHHHSHHHHHHHHHHCTS-HHHHHHHHHHHHHHHHHH-
T ss_pred CHHHHhhcCCCCHHHHHhCChhHHHHHHHcCCCCHHHHHHHHHHHHHHhHhcC
Confidence 5899999999999999999999999999999 999999999999999999874
No 9
>PF11467 LEDGF: Lens epithelium-derived growth factor (LEDGF) ; InterPro: IPR021567 LEDGF is a chromatin-associated protein that protects cells from stress-induced apoptosis. It is the binding partner of HIV-1 integrase in human cells. The integrase binding domain (IBD) of LEDGF is a compact right-handed bundle composed of five alpha-helices. The residues essential for the interaction with the integrase are present in the inter-helical loop regions of the bundle structure. ; PDB: 3F9K_K 3HPG_G 3U88_C 3HPH_H 2B4J_D 1Z9E_A.
Probab=96.18 E-value=0.0045 Score=50.76 Aligned_cols=78 Identities=23% Similarity=0.442 Sum_probs=55.5
Q ss_pred hhHHHHHHHHHHHHHHHHHhccChhhHhhHHHHHHHHHHhhcCCCChhhhh-cCCcceecccccCC-CCHHHHHHHHHHH
Q 020949 2 EKKVMQLCEEAKRGAEAAVMAEGEAEKAWTAWCIDALDQLNKSDITCPLLV-STQLVRYLLPLTEH-PTKKIQDFASDLI 79 (319)
Q Consensus 2 e~~~~~l~~~a~k~~~~a~~~~~~~e~~~~~~~l~~L~~L~~~~it~~lL~-~T~iGk~V~~Lrkh-~~~~I~~~Ak~Lv 79 (319)
|..|.+|.-. +..+-.-+ .|. +.+|+++|.+|..++||.-+|+ .+.+-.++.+||+. .|..|.+.|..|.
T Consensus 1 E~~L~~l~~~----Ik~~L~~~-~~D---v~kcL~~LdeL~~l~vT~~mL~kn~e~V~TlkklRrY~gn~~Ir~KA~~lY 72 (106)
T PF11467_consen 1 ERRLQELHSE----IKSSLKVD-NPD---VKKCLKALDELKSLQVTSLMLQKNPECVETLKKLRRYKGNQQIRKKATELY 72 (106)
T ss_dssp HHHHHHHHHH----HHHTCETT-EE----HHHHHHHHHHHHTS---HHHHTTTHHHHHHHHHHTT-TT-HHHHHHHHHHH
T ss_pred ChhHHHHHHH----HHHHHcCC-CCC---HHHHHHHHHHHhccCCCHHHHHhCHHHHHHHHHHHHhhccHHHHHHHHHHH
Confidence 4566666653 33332111 235 7899999999999999986655 67788888999998 5588999999999
Q ss_pred HHHHHHHH
Q 020949 80 VSWRDMFL 87 (319)
Q Consensus 80 ~~WK~~v~ 87 (319)
.+.|.++.
T Consensus 73 nkfK~~f~ 80 (106)
T PF11467_consen 73 NKFKSLFL 80 (106)
T ss_dssp HHHHHHHH
T ss_pred HHHHHHhC
Confidence 99999986
No 10
>KOG2821 consensus RNA polymerase II transcription elongation factor Elongin/SIII, subunit elongin A [Transcription]
Probab=95.97 E-value=0.0032 Score=62.83 Aligned_cols=57 Identities=19% Similarity=0.295 Sum_probs=52.6
Q ss_pred HHHHHHHHHHhhcCCCChhhhhcCCcceecccccCCCCHHHHHHHHHHHHHHHHHHHhh
Q 020949 31 TAWCIDALDQLNKSDITCPLLVSTQLVRYLLPLTEHPTKKIQDFASDLIVSWRDMFLEQ 89 (319)
Q Consensus 31 ~~~~l~~L~~L~~~~it~~lL~~T~iGk~V~~Lrkh~~~~I~~~Ak~Lv~~WK~~v~~~ 89 (319)
..+.+..|..|.++|++.++|.+|.+|+.|+.|++|. .+..+|..|+..||+.|...
T Consensus 24 pkR~lk~I~~ls~lP~~~k~l~Et~~~k~l~~L~k~~--~~g~~~~Dl~~~WK~~v~~d 80 (433)
T KOG2821|consen 24 PKRLLKRIQKLSNLPHLFKHLLETGKGKTLNSLRKIS--HVGKLAFDLVALWKDLVLVD 80 (433)
T ss_pred HHHHHHHHHHhccchHHHHHHHHhhhhHHHHHHHHhh--cccccccchHHHHHHhcccc
Confidence 3489999999999999999999999999999999999 69999999999999999543
No 11
>KOG1793 consensus Uncharacterized conserved protein [Function unknown]
Probab=95.92 E-value=0.009 Score=58.85 Aligned_cols=56 Identities=25% Similarity=0.328 Sum_probs=49.4
Q ss_pred HHHHHHHhhcCCCCh-hhhhcCCcceecccccCCCC--HHHHHHHHHHHHHHHHHHHhh
Q 020949 34 CIDALDQLNKSDITC-PLLVSTQLVRYLLPLTEHPT--KKIQDFASDLIVSWRDMFLEQ 89 (319)
Q Consensus 34 ~l~~L~~L~~~~it~-~lL~~T~iGk~V~~Lrkh~~--~~I~~~Ak~Lv~~WK~~v~~~ 89 (319)
=..+|..|.+++|-. +.|...+||++|=.|.+|+. ..++.+|..||..|-.-|+..
T Consensus 235 r~~ll~iL~dlpi~~~E~Lk~SGlGkvVmflsks~ket~~nkrlA~kLI~eWsRpI~~~ 293 (417)
T KOG1793|consen 235 RKSLLDILNDLPIDKREHLKESGLGKVVMFLSKSPKETKENKRLANKLINEWSRPIFKL 293 (417)
T ss_pred HHHHHHHHhcCCcchHHHHHhcCCCeEEEEEecCCccchHHHHHHHHHHHHhhccccCC
Confidence 345778888899998 99999999999999999966 779999999999999988643
No 12
>COG5139 Uncharacterized conserved protein [Function unknown]
Probab=94.88 E-value=0.035 Score=52.91 Aligned_cols=54 Identities=22% Similarity=0.280 Sum_probs=45.9
Q ss_pred HHHHHHhhcCCCChhhhhcCCcceecccccCC--CCHHHHHHHHHHHHHHHHHHHh
Q 020949 35 IDALDQLNKSDITCPLLVSTQLVRYLLPLTEH--PTKKIQDFASDLIVSWRDMFLE 88 (319)
Q Consensus 35 l~~L~~L~~~~it~~lL~~T~iGk~V~~Lrkh--~~~~I~~~Ak~Lv~~WK~~v~~ 88 (319)
-.+|..|+.+||-.++|.+.+||+.|=+.... ..++|+..|+.||..|-.-|..
T Consensus 233 ksL~dvL~~lpI~tEHL~eSgvGrIV~FYtiskk~e~~v~r~A~~LV~eWtrpIik 288 (397)
T COG5139 233 KSLLDVLKTLPIHTEHLVESGVGRIVYFYTISKKEEKEVRRSAKALVQEWTRPIIK 288 (397)
T ss_pred HHHHHHHhhCCchHHHhhhcCCceEEEEEecCCcccHHHHHHHHHHHHHhhccccC
Confidence 34677888899999999999999999766554 6688999999999999988753
No 13
>PLN02976 amine oxidase
Probab=86.04 E-value=0.93 Score=52.21 Aligned_cols=56 Identities=14% Similarity=0.233 Sum_probs=46.5
Q ss_pred HHHHHhhcCCCChhhhhcCCcceec-ccccCCCCHHHHHHHHHHHHHHHHHHHhhcc
Q 020949 36 DALDQLNKSDITCPLLVSTQLVRYL-LPLTEHPTKKIQDFASDLIVSWRDMFLEQIR 91 (319)
Q Consensus 36 ~~L~~L~~~~it~~lL~~T~iGk~V-~~Lrkh~~~~I~~~Ak~Lv~~WK~~v~~~~~ 91 (319)
.+|+-|=-++..+..|+..+||++| +++--|.+++|+.+|.+|+..|...+..++.
T Consensus 1305 ~~~~ll~~~~~d~~a~r~sg~~~~~k~~~~~h~~~~~r~~a~~~~~~w~~~~~~~~~ 1361 (1713)
T PLN02976 1305 HCVRLLVLVSTDLLAVRLSGIGKTVKEKVCVHTSRDIRAIASQLVSVWLEVFRREKA 1361 (1713)
T ss_pred HHHHHHhhcchhHHHHHhccchHHHHhhhhhcccHHHHHHHHHHHHHHHHHHHHhhh
Confidence 3444444456667778899999999 9999999999999999999999999977644
No 14
>KOG1886 consensus BAH domain proteins [Transcription]
Probab=56.15 E-value=3.7 Score=41.74 Aligned_cols=100 Identities=18% Similarity=0.107 Sum_probs=71.8
Q ss_pred CCCChHHHHHHHHHHHHHHhhhhCCCchhhh--hh--hhccchHHHHHHHHHHHHHHhcCCChhhhhhhhhHhhccCCCC
Q 020949 187 IRCNDCFREVVREKVCDALSKVSGEADEEIR--DE--VNACDSVRVAIALESAMFEKWGRSDGPYKIKYRAVLGNLKDPK 262 (319)
Q Consensus 187 ~~t~d~vR~k~r~~L~~aL~~~~~e~~~~~~--~~--~~~~~~~~lA~~IE~~lf~~~~~~~~~Yk~k~RSl~fNLKD~k 262 (319)
..+++.-|++|+.-++..+...++-....-. +. ....+....-..||...|+.+..+...|..+.+.+.++|| .
T Consensus 238 ~~t~~~~~~k~~g~~~~~v~~~~~~~s~~~~~~~~~~~~p~~~v~~~~~le~~s~~s~a~d~~~~~~~~~~l~~~~k--~ 315 (464)
T KOG1886|consen 238 LLTGRSDRDKVLGKLLEVVWQNSCSTSEAKPAGDQGSLWPNPSVSPCGALEQPSHASLAKDLESYLGLRETLVLLLK--G 315 (464)
T ss_pred CCCCcccccccccccchhhccccccccccCCCcccccCCCCcccchhhhhhhhhhhhHhhhhhhhhhhhhHHHhhhc--c
Confidence 5788999999999999998544321111100 00 0111245677899999999998777899999999999998 5
Q ss_pred ChhHHhhhhcCC-cCccccccCChhhc
Q 020949 263 NPDFRRKVLFGQ-VKPETVVGMTAKEM 288 (319)
Q Consensus 263 Np~Lr~~Vl~G~-I~p~~lv~Mt~eEM 288 (319)
---|+.+.++|. +.|+-.+.|..=+.
T Consensus 316 ~~~l~~~~ln~~~~~~e~~~~l~~p~~ 342 (464)
T KOG1886|consen 316 QALLKPEPLNPGETKPEPKQELHPPSF 342 (464)
T ss_pred hhhhccccCCCcccCchhhhhccCCCC
Confidence 577888888885 77888777765433
No 15
>KOG4274 consensus Positive cofactor 2 (PC2), subunit of a multiprotein coactivator of RNA polymerase II [Transcription]
Probab=51.91 E-value=19 Score=37.72 Aligned_cols=62 Identities=23% Similarity=0.234 Sum_probs=47.5
Q ss_pred hHHHHHHHHHHHHHHhhhhCCCchhhhhhhhccchHHHHHHHHHHHHHHhcCCChhhhhhhhhHhhccCCCCChhH
Q 020949 191 DCFREVVREKVCDALSKVSGEADEEIRDEVNACDSVRVAIALESAMFEKWGRSDGPYKIKYRAVLGNLKDPKNPDF 266 (319)
Q Consensus 191 d~vR~k~r~~L~~aL~~~~~e~~~~~~~~~~~~~~~~lA~~IE~~lf~~~~~~~~~Yk~k~RSl~fNLKD~kNp~L 266 (319)
-++|.+++.-|.+.|+...... ..=|..+|+++|..+. +..+|-..+--||..++|-.|..-
T Consensus 9 ~kFRq~vIsried~l~~n~q~~-------------~k~a~~mE~hVF~K~~-tkDEYl~lvAkli~h~~d~s~~ks 70 (742)
T KOG4274|consen 9 PKFRQHVISRIEDELRKNGQAH-------------SKSAKDMESHVFLKAK-TKDEYLSLVAKLIIHFRDISNKKS 70 (742)
T ss_pred HHHHHHHHHHhhhhhhhhhhcc-------------CcchHHHHHHHHHhhh-hHHHHHHHHHHHHHHHHhhhhhhh
Confidence 4789999999999998642111 1457899999998875 356899999999999998776443
No 16
>PF14726 RTTN_N: Rotatin, an armadillo repeat protein, centriole functioning
Probab=44.48 E-value=20 Score=28.95 Aligned_cols=50 Identities=20% Similarity=0.207 Sum_probs=42.6
Q ss_pred HHHHHHHHHHhhcCCCChhhhhcCCcceecccccCCCCHHHHHHHHHHHH
Q 020949 31 TAWCIDALDQLNKSDITCPLLVSTQLVRYLLPLTEHPTKKIQDFASDLIV 80 (319)
Q Consensus 31 ~~~~l~~L~~L~~~~it~~lL~~T~iGk~V~~Lrkh~~~~I~~~Ak~Lv~ 80 (319)
.+.++++|.+|-+.+....+|+.-+.-..+++||++-++..+...-.|++
T Consensus 47 ~~~VL~Ll~~L~~~~~a~~~l~~iG~~~fL~klr~~~~~~~~~~id~il~ 96 (98)
T PF14726_consen 47 KEEVLALLLRLLKSPYAAQILRDIGAVRFLSKLRPNVEPNLQAEIDEILD 96 (98)
T ss_pred HHHHHHHHHHHHhCcHHHHHHHHccHHHHHHHHHhcCCHHHHHHHHHHHh
Confidence 78999999999999999999997776667899999988877777766654
No 17
>smart00099 btg1 tob/btg1 family. The tob/btg1 is a family of proteins that inhibit cell proliferation.
Probab=30.66 E-value=39 Score=27.86 Aligned_cols=61 Identities=16% Similarity=0.125 Sum_probs=48.2
Q ss_pred HHHHHHHHHHHHHHhcCC----ChhhhhhhhhHhhccCCCCChhHHhhhhcCCcCccccccCChhhc
Q 020949 226 VRVAIALESAMFEKWGRS----DGPYKIKYRAVLGNLKDPKNPDFRRKVLFGQVKPETVVGMTAKEM 288 (319)
Q Consensus 226 ~~lA~~IE~~lf~~~~~~----~~~Yk~k~RSl~fNLKD~kNp~Lr~~Vl~G~I~p~~lv~Mt~eEM 288 (319)
..++.+++..|.+.|.+. ++..-+-+|.|.-| .+-.|.|.+.-..--|+.++|..+=+.||
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 579999999999998653 35677889999988 67889998887777788777766555555
No 18
>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=25.68 E-value=91 Score=24.33 Aligned_cols=67 Identities=15% Similarity=0.162 Sum_probs=42.1
Q ss_pred CChHHHHHHHHHHHHHHhhhhCCCchhhhhhhhccchHHHHHHHHHHHHHHhcCCChhhhhhhhhHhhccC
Q 020949 189 CNDCFREVVREKVCDALSKVSGEADEEIRDEVNACDSVRVAIALESAMFEKWGRSDGPYKIKYRAVLGNLK 259 (319)
Q Consensus 189 t~d~vR~k~r~~L~~aL~~~~~e~~~~~~~~~~~~~~~~lA~~IE~~lf~~~~~~~~~Yk~k~RSl~fNLK 259 (319)
-...+|+..++.|..++..... +....+ ..-.+....|..||..+|+.... -.+|-..+--.+++++
T Consensus 10 vt~~lR~hlV~KLv~aI~P~pd--p~a~~d-~rm~~l~~yarkvE~~~fe~A~s-reeYY~llA~kiy~iq 76 (81)
T PF02172_consen 10 VTPDLRNHLVHKLVQAIFPTPD--PNAMND-PRMKNLIEYARKVEKDMFETAQS-REEYYHLLAEKIYKIQ 76 (81)
T ss_dssp T-HHHHHHHHHHHHHHHS-SSS--CCCCCS-HHHHHHHHHHHHHHHHHHHC-SS-HHHHHHHHHHHHHHHH
T ss_pred cCHHHHHHHHHHHHHhhCCCCC--hhhhhh-HHHHHHHHHHHHHHHHHHHHhcc-HHHHHHHHHHHHHHHH
Confidence 3478999999999999875321 111100 00113468899999999986532 3578777777777663
Done!