Query 047634
Match_columns 82
No_of_seqs 110 out of 382
Neff 5.5
Searched_HMMs 29240
Date Mon Mar 25 23:20:50 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/047634.a3m -d /work/01045/syshi/HHdatabase/pdb70.hhm -o /work/01045/syshi/hhsearch_pdb/047634hhsearch_pdb -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 2ckz_B C25, DNA-directed RNA p 99.8 4.8E-20 1.6E-24 132.0 10.7 55 1-55 40-94 (218)
2 3ayh_B DNA-directed RNA polyme 99.8 4.5E-20 1.5E-24 130.2 8.8 55 1-55 40-94 (203)
3 3h0g_G DNA-directed RNA polyme 99.8 2.6E-19 8.9E-24 123.3 5.8 72 1-72 41-132 (172)
4 4ayb_E DNA-directed RNA polyme 99.7 5.9E-18 2E-22 116.3 8.4 55 1-55 40-94 (180)
5 2rf4_A DNA-directed RNA polyme 99.7 7.9E-18 2.7E-22 119.9 6.9 72 4-75 79-184 (214)
6 2c35_B Human RPB7, DNA-directe 99.7 3.5E-16 1.2E-20 106.9 10.0 75 1-75 40-132 (172)
7 1y14_B B16, RPB7, DNA-directed 99.6 3.5E-15 1.2E-19 102.2 8.2 73 1-73 40-132 (171)
8 2b8k_G B16, DNA-directed RNA p 99.6 2.3E-15 7.8E-20 107.6 7.3 75 1-75 40-134 (215)
9 1go3_E DNA-directed RNA polyme 99.5 6.4E-14 2.2E-18 96.5 11.2 54 2-55 41-94 (187)
10 2bh8_A 1B11; transcription, mo 92.6 0.11 3.8E-06 32.2 3.3 41 15-55 28-74 (101)
11 2cqo_A Nucleolar protein of 40 72.7 0.8 2.7E-05 29.0 0.2 24 32-55 12-35 (119)
12 2ja9_A Exosome complex exonucl 66.2 3.7 0.00012 27.9 2.4 18 38-55 3-20 (175)
13 2khi_A 30S ribosomal protein S 61.3 1.9 6.5E-05 26.8 0.2 25 31-55 19-43 (115)
14 2k52_A Uncharacterized protein 55.5 7.6 0.00026 22.3 2.2 17 39-55 2-18 (80)
15 2ba0_A Archeal exosome RNA bin 55.3 7.2 0.00025 27.2 2.4 18 38-55 53-70 (229)
16 3u7d_B Protein HEG homolog 1; 54.3 4.3 0.00015 19.7 0.8 16 62-77 6-21 (26)
17 2eqs_A ATP-dependent RNA helic 51.5 9.2 0.00032 23.1 2.2 19 37-55 7-25 (103)
18 2je6_I RRP4, exosome complex R 49.8 9.8 0.00034 26.9 2.4 19 37-55 69-87 (251)
19 2z0s_A Probable exosome comple 48.6 9.4 0.00032 26.6 2.1 18 38-55 62-79 (235)
20 1luz_A Protein K3, protein K2; 47.5 11 0.00038 22.3 2.1 16 39-55 8-23 (88)
21 2nn6_I 3'-5' exoribonuclease C 46.6 12 0.00041 25.7 2.4 18 38-55 77-94 (209)
22 4aid_A Polyribonucleotide nucl 41.4 1 3.5E-05 36.9 -4.3 45 11-55 604-650 (726)
23 2khj_A 30S ribosomal protein S 40.5 18 0.00062 21.8 2.3 18 38-55 27-44 (109)
24 3m7n_A Putative uncharacterize 39.6 17 0.0006 24.1 2.3 18 37-55 53-70 (179)
25 1kl9_A Eukaryotic translation 38.6 20 0.00069 24.2 2.5 16 40-55 13-28 (182)
26 1wi5_A RRP5 protein homolog; S 38.2 20 0.00069 21.9 2.3 17 39-55 18-34 (119)
27 3cdi_A Polynucleotide phosphor 34.0 8.6 0.00029 31.4 0.0 45 11-55 594-640 (723)
28 2nn6_H Exosome complex exonucl 31.3 14 0.00046 27.2 0.7 18 38-55 91-108 (308)
29 2a19_A EIF-2- alpha, eukaryoti 30.1 31 0.0011 23.0 2.3 16 40-55 13-28 (175)
30 3qk9_A Mitochondrial import in 29.8 29 0.00099 24.3 2.2 35 15-49 142-180 (222)
31 2k4k_A GSP13, general stress p 29.0 35 0.0012 21.4 2.3 17 39-55 4-20 (130)
No 1
>2ckz_B C25, DNA-directed RNA polymerase III 25 KD polypeptide; multiprotein complex, nucleotidyltransferase, nuclear protein, hypothetical protein; 3.2A {Saccharomyces cerevisiae}
Probab=99.83 E-value=4.8e-20 Score=131.98 Aligned_cols=55 Identities=24% Similarity=0.469 Sum_probs=53.7
Q ss_pred CCeEEEEEEEeccEecceeEEcCCCceEEEEEEeEEEeeecCCCeEEEEEEEccC
Q 047634 1 GRHGFVVAIMGVESIGTGLIRDGIGFVTFPVRCQCIVFRPFRGEILGAAVTMVNK 55 (82)
Q Consensus 1 g~~GliV~v~di~~i~~G~I~~gdG~~~~~V~f~aivfrPf~gEVv~g~V~~v~~ 55 (82)
+++|||||++||.++++|+|.||||+++|+|+|+|++|||++||+++|+|++|++
T Consensus 40 ~~~Gl~I~v~di~~i~eG~I~~GdG~~~~~V~fk~~~f~p~vGEv~~G~Is~Vt~ 94 (218)
T 2ckz_B 40 PNVGLCITIYDLLTVEEGQLKPGDGSSYINVTFRAVVFKPFLGEIVTGWISKCTA 94 (218)
T ss_dssp TTTEEEEEEEEEEEECCCEECSSSSCEEEEEEEEEEEECCCTTCEEEEEEEEEET
T ss_pred CCccEEEEEEEeeeccCcEEeCCCCCEEEEEEEEEEEecCCCCCEEEEEEEEEcc
Confidence 4689999999999999999999999999999999999999999999999999999
No 2
>3ayh_B DNA-directed RNA polymerase III subunit RPC8; transcription; 2.19A {Schizosaccharomyces pombe}
Probab=99.82 E-value=4.5e-20 Score=130.23 Aligned_cols=55 Identities=29% Similarity=0.561 Sum_probs=53.7
Q ss_pred CCeEEEEEEEeccEecceeEEcCCCceEEEEEEeEEEeeecCCCeEEEEEEEccC
Q 047634 1 GRHGFVVAIMGVESIGTGLIRDGIGFVTFPVRCQCIVFRPFRGEILGAAVTMVNK 55 (82)
Q Consensus 1 g~~GliV~v~di~~i~~G~I~~gdG~~~~~V~f~aivfrPf~gEVv~g~V~~v~~ 55 (82)
+++|||||++|+.++++|+|.||||+++|+|+|||++|||++||+++|+|++|++
T Consensus 40 ~~~Gl~I~v~di~~i~~g~I~~GdG~~~~~V~fk~~~f~p~~GEv~~G~Vs~vt~ 94 (203)
T 3ayh_B 40 QNIGLAICVYDFLKIGEGIIKYGDGSSYMNVVFRLIIFRPFRGEVMLGKIKSCSE 94 (203)
T ss_dssp TTTEEEEEEEEEEEECCCEECTTTCCEEEEEEEEEEEECCCTTCEEEEEEEEEET
T ss_pred CCccEEEEEEEeeEecccEEeCCCCCEEEEEEEEEEEEccCCCCEEEEEEEEEec
Confidence 4689999999999999999999999999999999999999999999999999999
No 3
>3h0g_G DNA-directed RNA polymerase II subunit RPB7; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe}
Probab=99.77 E-value=2.6e-19 Score=123.33 Aligned_cols=72 Identities=39% Similarity=0.828 Sum_probs=63.8
Q ss_pred CCeEEEEEEE--eccEecceeEEcCCCceEEEEEEeEEEeeecCCCeEEEEEEEccC-----------------CCCCce
Q 047634 1 GRHGFVVAIM--GVESIGTGLIRDGIGFVTFPVRCQCIVFRPFRGEILGAAVTMVNK-----------------LIPDDM 61 (82)
Q Consensus 1 g~~GliV~v~--di~~i~~G~I~~gdG~~~~~V~f~aivfrPf~gEVv~g~V~~v~~-----------------~~p~d~ 61 (82)
++.|+||+++ ||.++++|+|.+|||+++|+|+|+|++|+|++||+++|+|+++++ .+++++
T Consensus 41 ~~~G~~I~i~~idi~~i~~G~I~~gdg~~~~~v~f~~ivf~p~~Gev~~G~V~~v~~fG~FV~l~~~~glVh~s~l~~~~ 120 (172)
T 3h0g_G 41 GQYGYIICVLDSNTIDIDKGRVVPGQGFAEFEVKYRAVLWRPFRGEVVDAIVTTVNKMGFFANIGPLNVFVSSHLVPPDM 120 (172)
T ss_dssp TTTEEEEEECTTTSEEECCCEECTTTCCEEEEEEEEEEEECCCTTCEEECCCCEEETTEEECCBTTBCCEEEGGGSCTTC
T ss_pred CCccEEEEEEeeeeeEeeCCEEECCCCcEEEEEEEEEeeeccCCCCEEEEEEEEEEcceEEEEeCCeEEEEEHHHCCCcc
Confidence 4679999999 999999999999999999999999999999999999999999999 567777
Q ss_pred EEcCCC-CCeEE
Q 047634 62 ELQTGD-LPNYT 72 (82)
Q Consensus 62 ~~~~~~-~p~~~ 72 (82)
.|++++ +++|.
T Consensus 121 ~~d~~~~~~~~~ 132 (172)
T 3h0g_G 121 KFDPTANPPNYS 132 (172)
T ss_dssp CCBSSSSSCBEE
T ss_pred ccCcccccceEe
Confidence 777753 33553
No 4
>4ayb_E DNA-directed RNA polymerase; transferase, multi-subunit, transcription; 3.20A {Sulfolobus shibatae} PDB: 2y0s_E 4b1o_E 4b1p_T 2waq_E 2wb1_E 2pmz_E 3hkz_E
Probab=99.74 E-value=5.9e-18 Score=116.33 Aligned_cols=55 Identities=25% Similarity=0.391 Sum_probs=53.7
Q ss_pred CCeEEEEEEEeccEecceeEEcCCCceEEEEEEeEEEeeecCCCeEEEEEEEccC
Q 047634 1 GRHGFVVAIMGVESIGTGLIRDGIGFVTFPVRCQCIVFRPFRGEILGAAVTMVNK 55 (82)
Q Consensus 1 g~~GliV~v~di~~i~~G~I~~gdG~~~~~V~f~aivfrPf~gEVv~g~V~~v~~ 55 (82)
++.|+||+++||.++++|+|.+|||+++++++|+|++|+|++||+++|+|+++++
T Consensus 40 ~~~G~~I~v~di~~~~~g~I~~gdg~~~~~v~~~~iv~~p~~Gev~~G~V~~v~~ 94 (180)
T 4ayb_E 40 KDLGLVLAILNVKTSEEGMLVFGDGATYHEVEFDMITYVPVVQEVVEGEVLQVDN 94 (180)
T ss_dssp SSSCEEEEEEEEEEEEEEEECSSCSSEEEEEEEEEEEECCCTTCEEEEEEEEEET
T ss_pred CCCcEEEEeeeEeecCceeEccCchHHHHHHhhheeeeeccCCCEEEEEEeeecc
Confidence 4689999999999999999999999999999999999999999999999999999
No 5
>2rf4_A DNA-directed RNA polymerase I subunit RPA4; transferase DNA/RNA, DNA-binding, phosphorylation, POL I, POLI, rpoli, nuclear protein; 3.10A {Saccharomyces cerevisiae}
Probab=99.72 E-value=7.9e-18 Score=119.87 Aligned_cols=72 Identities=19% Similarity=0.266 Sum_probs=56.7
Q ss_pred EEEEEEEeccEecc------------eeEEcCCCceEEEEEEeEEEeeecCCCeEEEEEEEccC----------------
Q 047634 4 GFVVAIMGVESIGT------------GLIRDGIGFVTFPVRCQCIVFRPFRGEILGAAVTMVNK---------------- 55 (82)
Q Consensus 4 GliV~v~di~~i~~------------G~I~~gdG~~~~~V~f~aivfrPf~gEVv~g~V~~v~~---------------- 55 (82)
|+|+++.|+..+++ |+|.+|+|.++++|+|+++|||||+||+|+|+|+++++
T Consensus 79 Gv~la~~di~~~~~~~~~~d~~~~~~g~I~~~~g~~~~~V~~~~iVFrPf~GevL~G~V~~~s~~~Ig~~~~G~Fn~~Ip 158 (214)
T 2rf4_A 79 GVVLGYEGLKILDADPLSKEDTSEKLIKITPDTPFGFTWCHVNLYVWQPQVGDVLEGYIFIQSASHIGLLIHDAFNASIK 158 (214)
T ss_dssp EEEEEEEEEETTSCCC-----------------CCCEEEEEEEEEEECCCTTCEEEEEECCCCSSCEEEEETTTEEEEEC
T ss_pred EEEEEEECeEeccCCCcCccccccceeEEeCCCceEEEEEEEEEEEEecCCCCEEEEEEEEECCCcEEEEEeCCEEEEEc
Confidence 99999999976654 79999999999999999999999999999999999999
Q ss_pred --CCCCceEEcCCC---C-CeEECCC
Q 047634 56 --LIPDDMELQTGD---L-PNYTTSD 75 (82)
Q Consensus 56 --~~p~d~~~~~~~---~-p~~~~~d 75 (82)
.+|+++.|++++ . ++|.+++
T Consensus 159 ~~~ip~~~~f~~~~~~~~~~~wv~~~ 184 (214)
T 2rf4_A 159 KNNIPVDWTFVHNDGNRSLGHWVDSN 184 (214)
T ss_dssp STTSCSSCBCCCCSCC-CCCCCBCSS
T ss_pred HHHCCCcccccccccccCCCceEcCC
Confidence 788888888775 3 3787654
No 6
>2c35_B Human RPB7, DNA-directed RNA polymerase II 19 kDa polypeptide; transcription, nucleotidyltransferase; 2.70A {Homo sapiens} SCOP: b.40.4.5 d.230.1.1
Probab=99.67 E-value=3.5e-16 Score=106.93 Aligned_cols=75 Identities=49% Similarity=0.945 Sum_probs=67.8
Q ss_pred CCeEEEEEEEeccEecceeEEcCCCceEEEEEEeEEEeeecCCCeEEEEEEEccC-----------------CCCCceEE
Q 047634 1 GRHGFVVAIMGVESIGTGLIRDGIGFVTFPVRCQCIVFRPFRGEILGAAVTMVNK-----------------LIPDDMEL 63 (82)
Q Consensus 1 g~~GliV~v~di~~i~~G~I~~gdG~~~~~V~f~aivfrPf~gEVv~g~V~~v~~-----------------~~p~d~~~ 63 (82)
|+.|++|+++||.++++|++.+|||.++++++|++++|+|+.||+++|+|+++++ .+++++.|
T Consensus 40 ~~~G~~I~~~di~~i~~g~i~~~d~~~~~~~~~~~~~~~~~~Gev~~G~V~~v~~fG~fV~l~~~~glvhis~l~~~~~~ 119 (172)
T 2c35_B 40 GKYGFVIAVTTIDNIGAGVIQPGRGFVLYPVKYKAIVFRPFKGEVVDAVVTQVNKVGLFTEIGPMSCFISRHSIPSEMEF 119 (172)
T ss_dssp TTTEEEEEEEEEEEECCCBCCTTCSSEEEEEEEEEEEECCCTTCEEEEEEEEEETTEEEEEETTEEEEEEGGGSCTTEEE
T ss_pred CCceEEEEEEEeeecCCeEEeCCCCCEEEEEEEEEEEeeCCCCCEEEEEEEEEeCCEEEEEECCEEEEEEHHHCCCCcEE
Confidence 4679999999999999999999999999999999999999999999999999999 67778889
Q ss_pred cCCCCC-eEECCC
Q 047634 64 QTGDLP-NYTTSD 75 (82)
Q Consensus 64 ~~~~~p-~~~~~d 75 (82)
++.++| +|..++
T Consensus 120 d~~~~~~~~~~~~ 132 (172)
T 2c35_B 120 DPNSNPPCYKTMD 132 (172)
T ss_dssp ESSSSSCEEEETT
T ss_pred CCCCCccEEEeCC
Confidence 888765 666543
No 7
>1y14_B B16, RPB7, DNA-directed RNA polymerase II 19 kDa polypeptide; transferase; 2.30A {Saccharomyces cerevisiae} SCOP: b.40.4.5 d.230.1.1 PDB: 1nt9_G 1wcm_G 1pqv_G 1y1v_G 1y1w_G 1y1y_G 1y77_G* 2b63_G* 2ja5_G* 2ja6_G* 2ja7_G* 2ja8_G* 2r7z_G 2r92_G 2r93_G 2vum_G* 3fki_G 3h3v_H 3hou_G* 3hov_G* ...
Probab=99.59 E-value=3.5e-15 Score=102.16 Aligned_cols=73 Identities=29% Similarity=0.717 Sum_probs=50.4
Q ss_pred CCeEEEEEEEecc--EecceeEEcCCCceEEEEEEeEEEeeecCCCeEEEEEEEccC-----------------CCCCce
Q 047634 1 GRHGFVVAIMGVE--SIGTGLIRDGIGFVTFPVRCQCIVFRPFRGEILGAAVTMVNK-----------------LIPDDM 61 (82)
Q Consensus 1 g~~GliV~v~di~--~i~~G~I~~gdG~~~~~V~f~aivfrPf~gEVv~g~V~~v~~-----------------~~p~d~ 61 (82)
|+.|++|+++||. ++++|+|.+|||.+++++.|++++|+|+.||+++|+|+++++ .+++++
T Consensus 40 g~~G~~I~~~di~~~di~~g~i~~~d~~~~~~~~~~~~~~~~~~Gev~~G~V~~v~~fG~FV~l~~~dglvhis~l~~~~ 119 (171)
T 1y14_B 40 GKFGYILCVLDYDNIDIQRGRILPTDGSAEFNVKYRAVVFKPFKGEVVDGTVVSCSQHGFEVQVGPMKVFVTKHLMPQDL 119 (171)
T ss_dssp TTTEEEEEECCGGGCBCC------------CEEEEEEEEECCCTTCEEEEEEEEEETTEEEEEETTEEEEEEGGGSCTTC
T ss_pred CCceEEEEEEEecccccCccEEeCCCCCEEEEEEEEEEEccCCCCCEEEEEEEEEecCEEEEEecCeEEEEEHHHCCCCc
Confidence 5789999999999 999999999999999999999999999999999999999999 566666
Q ss_pred EEcCCCCC-eEEC
Q 047634 62 ELQTGDLP-NYTT 73 (82)
Q Consensus 62 ~~~~~~~p-~~~~ 73 (82)
.|++.+.| +|..
T Consensus 120 ~~d~~~~~~~~~~ 132 (171)
T 1y14_B 120 TFNAGSNPPSYQS 132 (171)
T ss_dssp EECC-----CEEC
T ss_pred eECcccCceEEec
Confidence 77776654 5544
No 8
>2b8k_G B16, DNA-directed RNA polymerase II 19 kDa polypeptide; DNA-dependent RNA polymerase, cellular RNA polymerase; 4.15A {Saccharomyces cerevisiae} SCOP: b.40.4.5 d.230.1.1
Probab=99.59 E-value=2.3e-15 Score=107.58 Aligned_cols=75 Identities=29% Similarity=0.720 Sum_probs=64.9
Q ss_pred CCeEEEEEEEecc--EecceeEEcCCCceEEEEEEeEEEeeecCCCeEEEEEEEccC-----------------CCCCce
Q 047634 1 GRHGFVVAIMGVE--SIGTGLIRDGIGFVTFPVRCQCIVFRPFRGEILGAAVTMVNK-----------------LIPDDM 61 (82)
Q Consensus 1 g~~GliV~v~di~--~i~~G~I~~gdG~~~~~V~f~aivfrPf~gEVv~g~V~~v~~-----------------~~p~d~ 61 (82)
|+.|+||+++||. ++++|+|.+|||.++++++|++++|+|++||+++|+|+++++ .+++.+
T Consensus 40 g~~G~vI~~~dI~~~di~dG~I~~gdg~~~~~v~~~~i~~~p~vGev~~G~V~~vt~fG~FVelg~~dGlVhiS~l~d~~ 119 (215)
T 2b8k_G 40 GKFGYILCVLDYDNIDIQRGRILPTDGSAEFNVKYRAVVFKPFKGEVVDGTVVSCSQHGFEVQVGPMKVFVTKHLMPQDL 119 (215)
T ss_dssp TTTEEEEEECCSTTCBCCCEEECSSSCCEEEEEECCEEEECCCTTEEEEEEEEEEETTEEEEECTTSEEEEEGGGSCSSC
T ss_pred CCCCEEEEEEEeeecccccceEeCCCHHHHHHHHhhhheeccCCCCEEEEEEEEEecceEEEEecCcEEEEEHHHCCccc
Confidence 5689999999999 999999999999999999999999999999999999999999 455556
Q ss_pred EEcCCCCC-eEECCC
Q 047634 62 ELQTGDLP-NYTTSD 75 (82)
Q Consensus 62 ~~~~~~~p-~~~~~d 75 (82)
.|++...| +|..++
T Consensus 120 ~~d~~~~~w~~~~~~ 134 (215)
T 2b8k_G 120 TFNAGSNPPSYQSSE 134 (215)
T ss_dssp CCBSSCSSCEEECSS
T ss_pred eeccccccceeeccc
Confidence 66666555 565443
No 9
>1go3_E DNA-directed RNA polymerase subunit E; transferase, transferase, transcription; 1.75A {Methanococcus jannaschii} SCOP: b.40.4.5 d.230.1.1
Probab=99.55 E-value=6.4e-14 Score=96.48 Aligned_cols=54 Identities=31% Similarity=0.480 Sum_probs=52.7
Q ss_pred CeEEEEEEEeccEecceeEEcCCCceEEEEEEeEEEeeecCCCeEEEEEEEccC
Q 047634 2 RHGFVVAIMGVESIGTGLIRDGIGFVTFPVRCQCIVFRPFRGEILGAAVTMVNK 55 (82)
Q Consensus 2 ~~GliV~v~di~~i~~G~I~~gdG~~~~~V~f~aivfrPf~gEVv~g~V~~v~~ 55 (82)
++|+||+++||.++++|+|.++||+++++++|++++|+|++||+++|+|+++++
T Consensus 41 ~~G~~i~~idi~~~g~~~I~~~d~~~~~~~~~~~i~~~~~~Gev~~G~V~~v~~ 94 (187)
T 1go3_E 41 DVGFVLSIVDVKDIGEGKVVHGDGSAYHPVVFETLVYIPEMYELIEGEVVDVVE 94 (187)
T ss_dssp TTEEEEEEEEEEEECCCBCCTTCCSEEEEEEEEEEEECCCTTCEEEEEEEEEET
T ss_pred CccEEEEEEEEeeccCCEEeCCCccEEEEEEEEEEEEccCCCCEEEEEEEEEeC
Confidence 569999999999999999999999999999999999999999999999999999
No 10
>2bh8_A 1B11; transcription, molecular evolution, unique architecture, transcription regulation, phosphorylation; 1.9A {Escherichia coli}
Probab=92.58 E-value=0.11 Score=32.25 Aligned_cols=41 Identities=17% Similarity=0.209 Sum_probs=37.2
Q ss_pred ecceeEEcCCCceEEEEEEeEEE---e---eecCCCeEEEEEEEccC
Q 047634 15 IGTGLIRDGIGFVTFPVRCQCIV---F---RPFRGEILGAAVTMVNK 55 (82)
Q Consensus 15 i~~G~I~~gdG~~~~~V~f~aiv---f---rPf~gEVv~g~V~~v~~ 55 (82)
.+-|.|.+.+|....-|.+++|. | +|..||++++.|+++++
T Consensus 28 kGfGFI~~~~gg~dvfvH~s~l~~~~~~~~~l~~Ge~V~g~V~~i~~ 74 (101)
T 2bh8_A 28 KGFGFITPDDGSKDVFVHFSAGSSGAAVRGNPQQGDRVEGKIKSITD 74 (101)
T ss_dssp GTEEEEEESSSSCEEEEECCCSCSSSCCCCCCCTTCEEEEEEEECCS
T ss_pred CCCEEEEeCCCCcEEEEEEEEEecCCccccCCCCCCEEEEEEEEeCC
Confidence 46789999999999999999998 3 78999999999999997
No 11
>2cqo_A Nucleolar protein of 40 kDa; S1 domain, OB-fold, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}
Probab=72.71 E-value=0.8 Score=29.00 Aligned_cols=24 Identities=25% Similarity=0.214 Sum_probs=21.6
Q ss_pred EEeEEEeeecCCCeEEEEEEEccC
Q 047634 32 RCQCIVFRPFRGEILGAAVTMVNK 55 (82)
Q Consensus 32 ~f~aivfrPf~gEVv~g~V~~v~~ 55 (82)
+++.+.+.|..|+++.|+|+++.+
T Consensus 12 ~~~~~~~~~~vG~iv~G~V~~I~~ 35 (119)
T 2cqo_A 12 RPETMENLPALYTIFQGEVAMVTD 35 (119)
T ss_dssp CCCCSCCSCCTTCEEEEEEEEEET
T ss_pred chhhhhcccCCCCEEEEEEEEEeC
Confidence 466778899999999999999999
No 12
>2ja9_A Exosome complex exonuclease RRP40; RNA-binding protein, RNA, S1 domain, KH domain, hydrolase, RNA-binding, nuclear protein; 2.20A {Saccharomyces cerevisiae} SCOP: b.40.4.5 d.51.1.1
Probab=66.20 E-value=3.7 Score=27.85 Aligned_cols=18 Identities=6% Similarity=0.067 Sum_probs=17.2
Q ss_pred eeecCCCeEEEEEEEccC
Q 047634 38 FRPFRGEILGAAVTMVNK 55 (82)
Q Consensus 38 frPf~gEVv~g~V~~v~~ 55 (82)
|.|..|+++.|+|+++..
T Consensus 3 Y~P~~gDvViG~V~~v~~ 20 (175)
T 2ja9_A 3 YIPSVNDFVIGVIIGTFS 20 (175)
T ss_dssp CCCCTTCEEEEEEEEECS
T ss_pred ccCCCcCEEEEEEEEEEC
Confidence 789999999999999987
No 13
>2khi_A 30S ribosomal protein S1; acetylation, phosphoprotein, ribonucleoprotein, RNA-binding; NMR {Escherichia coli}
Probab=61.34 E-value=1.9 Score=26.79 Aligned_cols=25 Identities=24% Similarity=0.139 Sum_probs=20.4
Q ss_pred EEEeEEEeeecCCCeEEEEEEEccC
Q 047634 31 VRCQCIVFRPFRGEILGAAVTMVNK 55 (82)
Q Consensus 31 V~f~aivfrPf~gEVv~g~V~~v~~ 55 (82)
..|..+..+|..|++++|+|+++++
T Consensus 19 ~p~~~~~~~~~~G~~~~G~V~~v~~ 43 (115)
T 2khi_A 19 SHWVAIAKRYPEGTKLTGRVTNLTD 43 (115)
T ss_dssp --CCCSSCSSCSSCEEEEEEEEEET
T ss_pred CCHHHHhhcCCCCCEEEEEEEEEEC
Confidence 3456667789999999999999998
No 14
>2k52_A Uncharacterized protein MJ1198; metal-binding, zinc, zinc-finger, structural genomics, PSI-2, protein structure initiative; NMR {Methanocaldococcus jannaschii}
Probab=55.52 E-value=7.6 Score=22.27 Aligned_cols=17 Identities=24% Similarity=0.253 Sum_probs=15.4
Q ss_pred eecCCCeEEEEEEEccC
Q 047634 39 RPFRGEILGAAVTMVNK 55 (82)
Q Consensus 39 rPf~gEVv~g~V~~v~~ 55 (82)
.|..|++++|+|+++.+
T Consensus 2 ~~~~G~iv~G~V~~v~~ 18 (80)
T 2k52_A 2 DVEPGKFYKGVVTRIEK 18 (80)
T ss_dssp CCCTTCEEEEEEEEEET
T ss_pred CCCCCCEEEEEEEEEeC
Confidence 46789999999999998
No 15
>2ba0_A Archeal exosome RNA binding protein RRP4; RNAse PH, RNA degradation, exoribonuclease, S1domain, KH domain, archaeal; 2.70A {Archaeoglobus fulgidus} SCOP: b.40.4.5 b.84.4.2 d.51.1.1
Probab=55.34 E-value=7.2 Score=27.21 Aligned_cols=18 Identities=17% Similarity=0.385 Sum_probs=17.3
Q ss_pred eeecCCCeEEEEEEEccC
Q 047634 38 FRPFRGEILGAAVTMVNK 55 (82)
Q Consensus 38 frPf~gEVv~g~V~~v~~ 55 (82)
|.|..|+++.|+|+++++
T Consensus 53 y~p~~GDiV~G~V~~v~~ 70 (229)
T 2ba0_A 53 YTPSVGDVVIGIIREVAA 70 (229)
T ss_dssp CCCCTTCEEEEEEEEECS
T ss_pred ccCCCCCEEEEEEEEEeC
Confidence 789999999999999998
No 16
>3u7d_B Protein HEG homolog 1; FERM domain, RAP1 effector, membrane protein cytoplasmic TAI protein binding; 2.49A {Homo sapiens}
Probab=54.29 E-value=4.3 Score=19.66 Aligned_cols=16 Identities=6% Similarity=0.191 Sum_probs=12.7
Q ss_pred EEcCCCCCeEECCCCc
Q 047634 62 ELQTGDLPNYTTSDGS 77 (82)
Q Consensus 62 ~~~~~~~p~~~~~d~~ 77 (82)
.||...+|+|.++|.+
T Consensus 6 iypgqynpsfisddsr 21 (26)
T 3u7d_B 6 IFPGQYNPSFISDESR 21 (26)
T ss_pred cccCccCcccccCcch
Confidence 4777789999988864
No 17
>2eqs_A ATP-dependent RNA helicase DHX8; S1 domain, OB-fold, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}
Probab=51.46 E-value=9.2 Score=23.11 Aligned_cols=19 Identities=26% Similarity=0.298 Sum_probs=17.0
Q ss_pred EeeecCCCeEEEEEEEccC
Q 047634 37 VFRPFRGEILGAAVTMVNK 55 (82)
Q Consensus 37 vfrPf~gEVv~g~V~~v~~ 55 (82)
...|..|++++|+|+++.+
T Consensus 7 ~~~~~vG~i~~G~V~~v~~ 25 (103)
T 2eqs_A 7 GEEPTIGDIYNGKVTSIMQ 25 (103)
T ss_dssp CSSCCTTCEEEEEEEEECS
T ss_pred cccCCCCCEEEEEEEEEec
Confidence 4568899999999999998
No 18
>2je6_I RRP4, exosome complex RNA-binding protein 1; nuclease, hydrolase, exonuclease, phosphorolytic, exoribonuclease, RNA degradation; HET: 1PE; 1.6A {Sulfolobus solfataricus} SCOP: b.40.4.5 b.84.4.2 d.51.1.1 PDB: 2jea_I* 2jeb_I* 3l7z_C
Probab=49.79 E-value=9.8 Score=26.94 Aligned_cols=19 Identities=21% Similarity=0.203 Sum_probs=17.5
Q ss_pred EeeecCCCeEEEEEEEccC
Q 047634 37 VFRPFRGEILGAAVTMVNK 55 (82)
Q Consensus 37 vfrPf~gEVv~g~V~~v~~ 55 (82)
.|.|..|+++.|+|+++++
T Consensus 69 ~y~p~~GDiV~G~V~~v~~ 87 (251)
T 2je6_I 69 FYYPKINDIVIGLVEDVEI 87 (251)
T ss_dssp CCCCCTTCEEEEEEEEECS
T ss_pred ccCCCCCCEEEEEEEEEeC
Confidence 4789999999999999998
No 19
>2z0s_A Probable exosome complex RNA-binding protein 1; alpha/beta protein, cytoplasm, structural genomics, NPPSFA; 3.20A {Aeropyrum pernix} SCOP: b.40.4.5 d.51.1.1
Probab=48.63 E-value=9.4 Score=26.58 Aligned_cols=18 Identities=17% Similarity=0.370 Sum_probs=17.2
Q ss_pred eeecCCCeEEEEEEEccC
Q 047634 38 FRPFRGEILGAAVTMVNK 55 (82)
Q Consensus 38 frPf~gEVv~g~V~~v~~ 55 (82)
|.|..|+++.|+|+++++
T Consensus 62 y~p~~GDiV~G~V~~v~~ 79 (235)
T 2z0s_A 62 YVPQAGDVVIGLIQSVGI 79 (235)
T ss_dssp CCCCTTCCEEEEEEEECS
T ss_pred cCCCCCCEEEEEEEEEeC
Confidence 789999999999999998
No 20
>1luz_A Protein K3, protein K2; stranded anti-parallel beta barrel, viral protein; 1.80A {Vaccinia virus} SCOP: b.40.4.5
Probab=47.49 E-value=11 Score=22.34 Aligned_cols=16 Identities=19% Similarity=0.347 Sum_probs=14.7
Q ss_pred eecCCCeEEEEEEEccC
Q 047634 39 RPFRGEILGAAVTMVNK 55 (82)
Q Consensus 39 rPf~gEVv~g~V~~v~~ 55 (82)
.|..|++++|+|+ +++
T Consensus 8 ~~~vG~~~~G~V~-v~~ 23 (88)
T 1luz_A 8 LPNAGDVIKGRVY-EKD 23 (88)
T ss_dssp CCCTTCEEEEEEE-EET
T ss_pred CCCCCCEEEEEEE-EEc
Confidence 3889999999999 998
No 21
>2nn6_I 3'-5' exoribonuclease CSL4 homolog; RNA, exosome, PM/SCL, phosphorolytic, hydrolase/transferase complex; 3.35A {Homo sapiens} SCOP: b.40.4.5 b.84.4.2
Probab=46.64 E-value=12 Score=25.72 Aligned_cols=18 Identities=28% Similarity=0.423 Sum_probs=17.2
Q ss_pred eeecCCCeEEEEEEEccC
Q 047634 38 FRPFRGEILGAAVTMVNK 55 (82)
Q Consensus 38 frPf~gEVv~g~V~~v~~ 55 (82)
|.|..|+++.|+|+++++
T Consensus 77 y~p~vGDvV~G~V~~v~~ 94 (209)
T 2nn6_I 77 LLPDVGAIVTCKVSSINS 94 (209)
T ss_dssp CCCCTTCEEEEEEEEECS
T ss_pred CCCCCCCEEEEEEEEEEC
Confidence 789999999999999998
No 22
>4aid_A Polyribonucleotide nucleotidyltransferase; transferase-peptide complex; 2.60A {Caulobacter vibrioides} PDB: 4aim_A 4am3_A
Probab=41.45 E-value=1 Score=36.94 Aligned_cols=45 Identities=16% Similarity=0.048 Sum_probs=6.4
Q ss_pred eccEecceeEEcCCCceEEE--EEEeEEEeeecCCCeEEEEEEEccC
Q 047634 11 GVESIGTGLIRDGIGFVTFP--VRCQCIVFRPFRGEILGAAVTMVNK 55 (82)
Q Consensus 11 di~~i~~G~I~~gdG~~~~~--V~f~aivfrPf~gEVv~g~V~~v~~ 55 (82)
||.+-|..+|...++.+.-. -.++.++..|..|++++|+|+++.+
T Consensus 604 di~ddG~v~I~~~~~~~~~~A~~~i~~i~~~~~vG~v~~G~V~~I~~ 650 (726)
T 4aid_A 604 DINDDGVVKVSASDGAKIKAAIDWIKSITDEAEVGKIYDGKVVKVVD 650 (726)
T ss_dssp ----------CCSCHHHHHHHHHC-----------------------
T ss_pred eEECCceEEEEeCCHHHHHHHHHHHHHHhhhhcCCcEEEEEEEEEec
Confidence 44555555565666555544 3588899999999999999999998
No 23
>2khj_A 30S ribosomal protein S1; OB fold, acetylation, phosphoprotein, ribonucleoprotein, RNA-binding; NMR {Escherichia coli}
Probab=40.54 E-value=18 Score=21.83 Aligned_cols=18 Identities=28% Similarity=0.294 Sum_probs=15.8
Q ss_pred eeecCCCeEEEEEEEccC
Q 047634 38 FRPFRGEILGAAVTMVNK 55 (82)
Q Consensus 38 frPf~gEVv~g~V~~v~~ 55 (82)
..+..|+++.|+|+++++
T Consensus 27 ~~~~~G~iv~G~V~~v~~ 44 (109)
T 2khj_A 27 ALNKKGAIVTGKVTAVDA 44 (109)
T ss_dssp TTCCSSSEEEEEEEEECS
T ss_pred hcCCCCCEEEEEEEEEEC
Confidence 356789999999999998
No 24
>3m7n_A Putative uncharacterized protein AF_0206; exosome, RNA, exonuclease, hydrolase, nuclease, hydrolase-RN; 2.40A {Archaeoglobus fulgidus} PDB: 2ba1_A 3m85_A
Probab=39.58 E-value=17 Score=24.13 Aligned_cols=18 Identities=11% Similarity=-0.001 Sum_probs=16.2
Q ss_pred EeeecCCCeEEEEEEEccC
Q 047634 37 VFRPFRGEILGAAVTMVNK 55 (82)
Q Consensus 37 vfrPf~gEVv~g~V~~v~~ 55 (82)
-|.|. |+++.|+|+++.+
T Consensus 53 ~y~p~-GdiV~G~V~~V~~ 70 (179)
T 3m7n_A 53 PEIVK-GDVVLGRVVDLRN 70 (179)
T ss_dssp CCCCT-TCEEEEEEEEECS
T ss_pred cccCC-CCEEEEEEEEEeC
Confidence 46788 9999999999998
No 25
>1kl9_A Eukaryotic translation initiation factor 2 subuni; OB fold, helical domain; 1.90A {Homo sapiens} SCOP: a.60.14.1 b.40.4.5
Probab=38.55 E-value=20 Score=24.16 Aligned_cols=16 Identities=13% Similarity=0.223 Sum_probs=15.2
Q ss_pred ecCCCeEEEEEEEccC
Q 047634 40 PFRGEILGAAVTMVNK 55 (82)
Q Consensus 40 Pf~gEVv~g~V~~v~~ 55 (82)
|..|+++.|+|+++++
T Consensus 13 p~~G~iv~G~V~~I~~ 28 (182)
T 1kl9_A 13 PEVEDVVMVNVRSIAE 28 (182)
T ss_dssp CCTTCEEEEEEEEECS
T ss_pred CCCCCEEEEEEEEEec
Confidence 6889999999999999
No 26
>1wi5_A RRP5 protein homolog; S1 domain, OB-fold, structural genomics, riken structural genomics/proteomics initiative, RSGI, unknown function; NMR {Homo sapiens} SCOP: b.40.4.5
Probab=38.19 E-value=20 Score=21.94 Aligned_cols=17 Identities=18% Similarity=0.218 Sum_probs=15.2
Q ss_pred eecCCCeEEEEEEEccC
Q 047634 39 RPFRGEILGAAVTMVNK 55 (82)
Q Consensus 39 rPf~gEVv~g~V~~v~~ 55 (82)
.+..|++++|+|+++.+
T Consensus 18 ~l~~G~i~~G~V~~v~~ 34 (119)
T 1wi5_A 18 ALKPGMLLTGTVSSLED 34 (119)
T ss_dssp TCCTTCEEEEEEEEECS
T ss_pred cCCCCCEEEEEEEEEeC
Confidence 35689999999999998
No 27
>3cdi_A Polynucleotide phosphorylase; mRNA turnover, RNAse, RNA degradation, kinase, transferase; 2.60A {Escherichia coli} PDB: 1sro_A
Probab=33.99 E-value=8.6 Score=31.40 Aligned_cols=45 Identities=22% Similarity=0.094 Sum_probs=0.0
Q ss_pred eccEecceeEEcCCCceEEEE--EEeEEEeeecCCCeEEEEEEEccC
Q 047634 11 GVESIGTGLIRDGIGFVTFPV--RCQCIVFRPFRGEILGAAVTMVNK 55 (82)
Q Consensus 11 di~~i~~G~I~~gdG~~~~~V--~f~aivfrPf~gEVv~g~V~~v~~ 55 (82)
||.+-+.-.|...+....... .++.++..|..|++++|+|+++.+
T Consensus 594 dI~~dg~v~I~~~~~~~~~~a~~~i~~i~~~~~vG~i~~G~V~~i~~ 640 (723)
T 3cdi_A 594 EIEDDGTVKIAATDGEKAKHAIRRIEEITAEIEVGRVYTGKVTRIVD 640 (723)
T ss_dssp -----------------------------------------------
T ss_pred EecCCccEEEecCCHHHHHHHHHHHHHHhhhhhcCcEEEEEEEEEec
Confidence 455444444544555554433 477788999999999999999999
No 28
>2nn6_H Exosome complex exonuclease RRP4; RNA, exosome, PM/SCL, phosphorolytic, hydrolase/transferase complex; 3.35A {Homo sapiens} SCOP: b.40.4.5 b.84.4.2 d.51.1.1
Probab=31.30 E-value=14 Score=27.21 Aligned_cols=18 Identities=22% Similarity=0.300 Sum_probs=17.3
Q ss_pred eeecCCCeEEEEEEEccC
Q 047634 38 FRPFRGEILGAAVTMVNK 55 (82)
Q Consensus 38 frPf~gEVv~g~V~~v~~ 55 (82)
|.|..|+++.|+|+++.+
T Consensus 91 Y~P~vGDvViG~Vt~V~~ 108 (308)
T 2nn6_H 91 YIGEVGDIVVGRITEVQQ 108 (308)
T ss_dssp CCCCSSBCCCEEEEEEET
T ss_pred cCCCCCCEEEEEEEEEeC
Confidence 789999999999999998
No 29
>2a19_A EIF-2- alpha, eukaryotic translation initiation factor 2 alpha; transferase, protein biosynthesis, protein synthesis transferase complex; HET: TPO ANP; 2.50A {Saccharomyces cerevisiae} PDB: 2a1a_A* 1q46_A
Probab=30.05 E-value=31 Score=22.99 Aligned_cols=16 Identities=19% Similarity=0.264 Sum_probs=14.7
Q ss_pred ecCCCeEEEEEEEccC
Q 047634 40 PFRGEILGAAVTMVNK 55 (82)
Q Consensus 40 Pf~gEVv~g~V~~v~~ 55 (82)
|-.|+++.|+|+++.+
T Consensus 13 p~~G~iv~G~V~~i~~ 28 (175)
T 2a19_A 13 PEIDDIVMVNVQQIAE 28 (175)
T ss_dssp CCTTCEEEEEEEEEET
T ss_pred CCCCCEEEEEEEEEec
Confidence 5689999999999998
No 30
>3qk9_A Mitochondrial import inner membrane translocase S TIM44; mitochondrion, protein transport; 3.10A {Saccharomyces cerevisiae} PDB: 2fxt_A
Probab=29.75 E-value=29 Score=24.25 Aligned_cols=35 Identities=20% Similarity=0.299 Sum_probs=25.4
Q ss_pred ecceeEEcCCCceEEEEEEeE---EEeee-cCCCeEEEE
Q 047634 15 IGTGLIRDGIGFVTFPVRCQC---IVFRP-FRGEILGAA 49 (82)
Q Consensus 15 i~~G~I~~gdG~~~~~V~f~a---ivfrP-f~gEVv~g~ 49 (82)
+-++++....+.+++.|+|++ -+.|= -.|||++|-
T Consensus 142 I~~a~~~~~~~~p~itV~f~aq~i~~~rd~k~GeVVeGd 180 (222)
T 3qk9_A 142 IVSAKLLAPQDIPVLVVGCRAQEINLYRKKKTGEIAAGD 180 (222)
T ss_dssp EEEEEECSSSCCEEEEEEEEEEEECCEEESTTCCCSSSC
T ss_pred EEEEEEecCCCceEEEEEEEEEEEEEEEeCCCCccccCC
Confidence 456677654567999999986 34555 789999874
No 31
>2k4k_A GSP13, general stress protein 13; cytoplasm, stress response, RNA binding protein; NMR {Bacillus subtilis}
Probab=29.01 E-value=35 Score=21.40 Aligned_cols=17 Identities=18% Similarity=0.128 Sum_probs=15.2
Q ss_pred eecCCCeEEEEEEEccC
Q 047634 39 RPFRGEILGAAVTMVNK 55 (82)
Q Consensus 39 rPf~gEVv~g~V~~v~~ 55 (82)
.+..|+++.|+|+++++
T Consensus 4 ~~~vG~iv~G~V~~i~~ 20 (130)
T 2k4k_A 4 KFEVGSVYTGKVTGLQA 20 (130)
T ss_dssp CCCTTCEEEEEEEEEET
T ss_pred cCCCCCEEEEEEEEEeC
Confidence 46789999999999998
Done!