Query 032987
Match_columns 129
No_of_seqs 112 out of 440
Neff 6.7
Searched_HMMs 29240
Date Mon Mar 25 13:35:42 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/032987.a3m -d /work/01045/syshi/HHdatabase/pdb70.hhm -o /work/01045/syshi/hhsearch_pdb/032987hhsearch_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 100.0 4.4E-41 1.5E-45 258.2 16.4 126 1-128 1-127 (218)
2 3ayh_B DNA-directed RNA polyme 100.0 3.9E-41 1.3E-45 255.7 14.1 125 1-127 1-125 (203)
3 4ayb_E DNA-directed RNA polyme 100.0 5.3E-39 1.8E-43 239.0 15.9 125 1-127 1-125 (180)
4 3h0g_G DNA-directed RNA polyme 100.0 7E-37 2.4E-41 226.9 10.9 122 1-125 1-125 (172)
5 1go3_E DNA-directed RNA polyme 100.0 4.5E-33 1.6E-37 207.8 15.9 124 1-126 1-124 (187)
6 2c35_B Human RPB7, DNA-directe 100.0 2.3E-31 7.9E-36 196.6 15.3 123 1-126 1-123 (172)
7 1y14_B B16, RPB7, DNA-directed 100.0 2.2E-30 7.4E-35 191.5 12.7 123 1-126 1-125 (171)
8 2b8k_G B16, DNA-directed RNA p 100.0 2.2E-30 7.7E-35 198.3 12.5 124 1-127 1-126 (215)
9 2rf4_A DNA-directed RNA polyme 100.0 7.8E-30 2.7E-34 195.1 14.0 121 1-123 37-171 (214)
10 2bh8_A 1B11; transcription, mo 97.6 3.6E-05 1.2E-09 51.7 2.8 59 54-112 28-93 (101)
11 2cqo_A Nucleolar protein of 40 96.9 0.00027 9.4E-09 48.6 1.2 43 71-113 12-56 (119)
12 2khi_A 30S ribosomal protein S 96.9 0.00065 2.2E-08 46.2 3.1 47 70-116 19-65 (115)
13 2eqs_A ATP-dependent RNA helic 96.9 0.0013 4.4E-08 43.9 4.4 39 76-115 7-49 (103)
14 2k52_A Uncharacterized protein 96.7 0.0023 7.7E-08 40.7 4.6 38 78-116 2-40 (80)
15 1wi5_A RRP5 protein homolog; S 96.7 0.00023 7.7E-09 48.7 -0.3 37 78-114 18-55 (119)
16 1luz_A Protein K3, protein K2; 96.6 0.0025 8.6E-08 41.5 4.3 33 78-111 8-43 (88)
17 1kl9_A Eukaryotic translation 96.5 0.0035 1.2E-07 46.2 4.8 35 79-113 13-50 (182)
18 3cdi_A Polynucleotide phosphor 96.4 0.00054 1.9E-08 60.1 0.0 73 38-113 585-660 (723)
19 2khj_A 30S ribosomal protein S 96.3 0.0054 1.9E-07 41.1 4.8 40 77-116 27-66 (109)
20 2a19_A EIF-2- alpha, eukaryoti 96.2 0.0067 2.3E-07 44.3 5.1 35 79-113 13-50 (175)
21 2k4k_A GSP13, general stress p 96.0 0.013 4.3E-07 40.7 5.3 37 78-115 4-41 (130)
22 1e3p_A Guanosine pentaphosphat 95.9 0.00032 1.1E-08 61.8 -4.0 92 9-113 600-700 (757)
23 2ba0_A Archeal exosome RNA bin 95.4 0.017 5.9E-07 43.8 4.6 37 77-113 53-90 (229)
24 2je6_I RRP4, exosome complex R 95.1 0.027 9.3E-07 43.3 4.8 37 76-112 69-106 (251)
25 2z0s_A Probable exosome comple 94.9 0.029 9.8E-07 42.6 4.5 36 77-112 62-98 (235)
26 4aid_A Polyribonucleotide nucl 94.9 0.00098 3.3E-08 58.5 -4.3 65 50-114 604-671 (726)
27 3aev_A Translation initiation 94.8 0.042 1.4E-06 42.8 5.4 36 78-113 8-46 (275)
28 2ja9_A Exosome complex exonucl 94.7 0.047 1.6E-06 39.9 5.1 38 77-115 3-42 (175)
29 2nn6_I 3'-5' exoribonuclease C 94.7 0.031 1.1E-06 41.8 4.1 38 77-114 77-123 (209)
30 1q8k_A Eukaryotic translation 94.4 0.039 1.3E-06 43.7 4.3 36 79-115 11-49 (308)
31 3cw2_C Translation initiation 94.2 0.045 1.5E-06 42.4 4.1 37 78-115 8-47 (266)
32 3m7n_A Putative uncharacterize 93.9 0.081 2.8E-06 38.5 4.8 27 76-103 53-79 (179)
33 3go5_A Multidomain protein wit 93.5 0.062 2.1E-06 42.0 3.8 37 80-116 68-106 (285)
34 3go5_A Multidomain protein wit 92.9 0.11 3.9E-06 40.5 4.4 37 79-116 4-40 (285)
35 1hh2_P NUSA, N utilization sub 92.8 0.15 5E-06 41.1 5.0 39 78-116 131-169 (344)
36 3bzc_A TEX; helix-turn-helix, 92.7 0.084 2.9E-06 46.7 3.8 39 79-117 652-690 (785)
37 2nn6_H Exosome complex exonucl 91.7 0.13 4.5E-06 40.7 3.6 33 77-109 91-124 (308)
38 3psi_A Transcription elongatio 90.0 0.64 2.2E-05 43.0 6.8 39 78-117 899-938 (1219)
39 1k0r_A NUSA; two component arr 89.8 0.27 9.1E-06 39.9 3.7 40 77-116 126-173 (366)
40 2id0_A Exoribonuclease 2; RNAs 89.7 0.15 5E-06 44.0 2.3 46 75-120 552-603 (644)
41 2asb_A Transcription elongatio 86.9 0.56 1.9E-05 36.2 3.7 40 77-116 3-50 (251)
42 2wp8_J Exosome complex exonucl 85.8 0.37 1.3E-05 43.5 2.5 48 75-126 881-933 (977)
43 3psf_A Transcription elongatio 77.8 0.45 1.5E-05 43.3 0.0 38 78-116 902-940 (1030)
44 2bx2_L Ribonuclease E, RNAse E 67.0 5.7 0.00019 33.5 4.2 52 63-114 27-80 (517)
45 2vnu_D Exosome complex exonucl 66.0 1.8 6.1E-05 38.0 1.0 46 77-126 666-716 (760)
46 2nn6_G Exosome complex exonucl 56.3 11 0.00038 29.3 3.9 39 77-115 123-161 (289)
47 2ovm_B NCOR, progesterone rece 29.6 38 0.0013 16.8 2.0 18 15-34 8-25 (26)
48 3d0f_A Penicillin-binding 1 tr 28.1 75 0.0026 20.2 3.9 37 79-115 31-67 (106)
49 3fhd_A ORF 37; enase like PD-( 25.0 35 0.0012 28.7 2.2 46 14-59 197-246 (508)
50 3ee1_A Effector protein VIRA; 23.5 90 0.0031 24.0 4.1 53 22-75 297-349 (400)
51 3eb8_A Cysteine protease-like 21.8 86 0.0029 23.8 3.6 54 22-76 255-308 (358)
52 2l55_A SILB,silver efflux prot 21.4 68 0.0023 19.9 2.6 22 85-106 6-27 (82)
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=100.00 E-value=4.4e-41 Score=258.21 Aligned_cols=126 Identities=41% Similarity=0.768 Sum_probs=122.8
Q ss_pred CeEEEEeeEEEEECCCCCCCCHHHHHHHHHHHHhcCeEeCCeeEEEEEEEeeeeeceeEEeCCCceEEEEEEEEEEeeec
Q 032987 1 MFYLSKIEHTLRLPPHLLRLPLNEAIKLELENVFLDKVIANLGLCISIYDIKEIEGGFVYPGEGASTHTVKFRLVVFRPF 80 (129)
Q Consensus 1 MF~~~~l~d~V~I~P~~~~~~~~~~i~~~L~~k~~gk~~~~~G~~I~v~~i~~i~~g~I~~gdG~~~~~V~F~alvfrP~ 80 (129)
||++++++|+|+|||++|+++++++|+++|+++|+||+++++|+|||++||.++++|+|.||||+++|+|+|+|++|||+
T Consensus 1 MF~l~~l~d~V~I~P~~f~~~l~~~i~~~L~~kyegkv~~~~Gl~I~v~di~~i~eG~I~~GdG~~~~~V~fk~~~f~p~ 80 (218)
T 2ckz_B 1 MFILSKIADLVRIPPDQFHRDTISAITHQLNNKFANKIIPNVGLCITIYDLLTVEEGQLKPGDGSSYINVTFRAVVFKPF 80 (218)
T ss_dssp CEEEEEEEEEEEECGGGTTSCHHHHHHHHHHHHHTTEEETTTEEEEEEEEEEEECCCEECSSSSCEEEEEEEEEEEECCC
T ss_pred CeEEEEEEEEEEECHHHcCchHHHHHHHHHHHHhcCcCcCCccEEEEEEEeeeccCcEEeCCCCCEEEEEEEEEEEecCC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCEEEEEEEEEccCceEEEe-CccceEEecCCCCCCCCCcCCCCCCCC
Q 032987 81 VGEIIAAKLKESDANGLRLSL-GFFEDIYVPSHLLPSPSRSEPDPYGRL 128 (129)
Q Consensus 81 ~~EVl~g~V~~v~~~Gi~v~~-G~~~~i~i~~~~lp~~~~f~~d~~~~~ 128 (129)
+||+++|+|++++++|+|+++ ||+++++||++.+|+++.| |++++.
T Consensus 81 vGEv~~G~Is~Vt~fGifVeL~g~~eglv~~s~l~~d~~~f--d~~~~~ 127 (218)
T 2ckz_B 81 LGEIVTGWISKCTAEGIKVSLLGIFDDIFIPQNMLFEGCYY--TPEESA 127 (218)
T ss_dssp TTCEEEEEEEEEETTEEEEECTTSCCCEEEETTTSCTTCEE--ETTTTE
T ss_pred CCCEEEEEEEEEccCcEEEEccCccceEEEcHHHCCCCcEE--cCcCce
Confidence 999999999999999999999 9999999999999999999 766653
No 2
>3ayh_B DNA-directed RNA polymerase III subunit RPC8; transcription; 2.19A {Schizosaccharomyces pombe}
Probab=100.00 E-value=3.9e-41 Score=255.73 Aligned_cols=125 Identities=37% Similarity=0.737 Sum_probs=121.8
Q ss_pred CeEEEEeeEEEEECCCCCCCCHHHHHHHHHHHHhcCeEeCCeeEEEEEEEeeeeeceeEEeCCCceEEEEEEEEEEeeec
Q 032987 1 MFYLSKIEHTLRLPPHLLRLPLNEAIKLELENVFLDKVIANLGLCISIYDIKEIEGGFVYPGEGASTHTVKFRLVVFRPF 80 (129)
Q Consensus 1 MF~~~~l~d~V~I~P~~~~~~~~~~i~~~L~~k~~gk~~~~~G~~I~v~~i~~i~~g~I~~gdG~~~~~V~F~alvfrP~ 80 (129)
||++++++|+|+|||++|++++.++|+++|+++|+||+++++|+|||++|+.++++|+|.||||+++|+|+|+|++|||+
T Consensus 1 MF~l~~l~d~V~i~P~~f~~~~~~~i~~~L~~~~egkv~~~~Gl~I~v~di~~i~~g~I~~GdG~~~~~V~fk~~~f~p~ 80 (203)
T 3ayh_B 1 MFLLSRFSDIISIHPSNFWKPTKEALAEEIHKKYANKVIQNIGLAICVYDFLKIGEGIIKYGDGSSYMNVVFRLIIFRPF 80 (203)
T ss_dssp CEEEEEEEEEEEECGGGTTSCHHHHHHHHHHHHHTTEEETTTEEEEEEEEEEEECCCEECTTTCCEEEEEEEEEEEECCC
T ss_pred CeEEEEEEEEEEECHHHcCChHHHHHHHHhhhhhCCEEeCCccEEEEEEEeeEecccEEeCCCCCEEEEEEEEEEEEccC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCEEEEEEEEEccCceEEEeCccceEEecCCCCCCCCCcCCCCCCC
Q 032987 81 VGEIIAAKLKESDANGLRLSLGFFEDIYVPSHLLPSPSRSEPDPYGR 127 (129)
Q Consensus 81 ~~EVl~g~V~~v~~~Gi~v~~G~~~~i~i~~~~lp~~~~f~~d~~~~ 127 (129)
+||+++|+|++++++|+|+++||+++++||++.+|+++.| |++++
T Consensus 81 ~GEv~~G~Vs~vt~~GifV~lg~~eglv~~~~l~~d~~~f--d~~~~ 125 (203)
T 3ayh_B 81 RGEVMLGKIKSCSEEGIRVTISFFDDIFIPKDMLFDPCVF--RPDER 125 (203)
T ss_dssp TTCEEEEEEEEEETTEEEEECSSCCCEEEEGGGBCTTEEE--EGGGT
T ss_pred CCCEEEEEEEEEeccEEEEEEeCceEEEEcHHhCCCCceE--CccCc
Confidence 9999999999999999999999999999999999999999 65544
No 3
>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=100.00 E-value=5.3e-39 Score=238.96 Aligned_cols=125 Identities=28% Similarity=0.524 Sum_probs=121.7
Q ss_pred CeEEEEeeEEEEECCCCCCCCHHHHHHHHHHHHhcCeEeCCeeEEEEEEEeeeeeceeEEeCCCceEEEEEEEEEEeeec
Q 032987 1 MFYLSKIEHTLRLPPHLLRLPLNEAIKLELENVFLDKVIANLGLCISIYDIKEIEGGFVYPGEGASTHTVKFRLVVFRPF 80 (129)
Q Consensus 1 MF~~~~l~d~V~I~P~~~~~~~~~~i~~~L~~k~~gk~~~~~G~~I~v~~i~~i~~g~I~~gdG~~~~~V~F~alvfrP~ 80 (129)
||++++++|+|+|||++|++++++++.++|+++|+||++++.|+||+++||.++++|+|.+|||+++++|+|+|++|||+
T Consensus 1 Mf~l~~l~d~V~IpP~~f~~~~~~~i~~~L~~k~~~kv~~~~G~~I~v~di~~~~~g~I~~gdg~~~~~v~~~~iv~~p~ 80 (180)
T 4ayb_E 1 MYKLIKARSIVRIPPNEFGKPLNEIALNELRQQYQEKILKDLGLVLAILNVKTSEEGMLVFGDGATYHEVEFDMITYVPV 80 (180)
T ss_dssp CEEEEEEEEEEEECGGGTTSCHHHHHHHHHHHHTTTCBCSSSCEEEEEEEEEEEEEEEECSSCSSEEEEEEEEEEEECCC
T ss_pred CeEEEEEEEEEEECHHHhCccHHHHHHHHHHHHhcCeEcCCCcEEEEeeeEeecCceeEccCchHHHHHHhhheeeeecc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCEEEEEEEEEccCceEEEeCccceEEecCCCCCCCCCcCCCCCCC
Q 032987 81 VGEIIAAKLKESDANGLRLSLGFFEDIYVPSHLLPSPSRSEPDPYGR 127 (129)
Q Consensus 81 ~~EVl~g~V~~v~~~Gi~v~~G~~~~i~i~~~~lp~~~~f~~d~~~~ 127 (129)
+||+++|+|++++++|+|+++||+++++|+++.+++++.| |++++
T Consensus 81 ~Gev~~G~V~~v~~~G~fv~l~~~~glvh~s~l~~d~~~~--d~~~~ 125 (180)
T 4ayb_E 81 VQEVVEGEVLQVDNYGVFVNLGPMDGLVHISQITDDTLKY--DNVRG 125 (180)
T ss_dssp TTCEEEEEEEEEETTEEEEECSSSEEEEEGGGSCSSCEEE--CSSSC
T ss_pred CCCEEEEEEeeeccceEEEEECCccceEEeeecCCCcccc--chhcc
Confidence 9999999999999999999999999999999999999999 66554
No 4
>3h0g_G DNA-directed RNA polymerase II subunit RPB7; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe}
Probab=100.00 E-value=7e-37 Score=226.90 Aligned_cols=122 Identities=28% Similarity=0.499 Sum_probs=115.8
Q ss_pred CeEEEEeeE-EEEECCCCCCCCHHHHHHHHHHHHhcCeEeCCeeEEEEEE--EeeeeeceeEEeCCCceEEEEEEEEEEe
Q 032987 1 MFYLSKIEH-TLRLPPHLLRLPLNEAIKLELENVFLDKVIANLGLCISIY--DIKEIEGGFVYPGEGASTHTVKFRLVVF 77 (129)
Q Consensus 1 MF~~~~l~d-~V~I~P~~~~~~~~~~i~~~L~~k~~gk~~~~~G~~I~v~--~i~~i~~g~I~~gdG~~~~~V~F~alvf 77 (129)
||++.+++| +|++||++|++++.+++.++|+++|+|+|+++.|+||+++ ||.++++|+|.+|||+++++|+|+|++|
T Consensus 1 Mf~l~~l~d~~i~ipp~~~~~~~~~~i~~~l~~~~~g~vi~~~G~~I~i~~idi~~i~~G~I~~gdg~~~~~v~f~~ivf 80 (172)
T 3h0g_G 1 MPFFLKELSLTISLHPSYFGPRMQDYLKAKLLADVEGTCSGQYGYIICVLDSNTIDIDKGRVVPGQGFAEFEVKYRAVLW 80 (172)
T ss_dssp --CEEEEEEEEEECCGGGCTTTHHHHHHHHHHHHHTTCEETTTEEEEEECTTTSEEECCCEECTTTCCEEEEEEEEEEEE
T ss_pred CeEEEEEecCeEEeCHHHhCccHHHHHHHHHHHHhCCcCcCCccEEEEEEeeeeeEeeCCEEECCCCcEEEEEEEEEeee
Confidence 999999999 9999999999999999999999999999999999999999 9999999999999999999999999999
Q ss_pred eecCCCEEEEEEEEEccCceEEEeCccceEEecCCCCCCCCCcCCCCC
Q 032987 78 RPFVGEIIAAKLKESDANGLRLSLGFFEDIYVPSHLLPSPSRSEPDPY 125 (129)
Q Consensus 78 rP~~~EVl~g~V~~v~~~Gi~v~~G~~~~i~i~~~~lp~~~~f~~d~~ 125 (129)
+|++||+++|+|++++++|+|+.+||++ .+||.+.|++++.| |++
T Consensus 81 ~p~~Gev~~G~V~~v~~fG~FV~l~~~~-glVh~s~l~~~~~~--d~~ 125 (172)
T 3h0g_G 81 RPFRGEVVDAIVTTVNKMGFFANIGPLN-VFVSSHLVPPDMKF--DPT 125 (172)
T ss_dssp CCCTTCEEECCCCEEETTEEECCBTTBC-CEEEGGGSCTTCCC--BSS
T ss_pred ccCCCCEEEEEEEEEEcceEEEEeCCeE-EEEEHHHCCCcccc--Ccc
Confidence 9999999999999999999999999998 88888889999999 553
No 5
>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=100.00 E-value=4.5e-33 Score=207.84 Aligned_cols=124 Identities=25% Similarity=0.426 Sum_probs=119.4
Q ss_pred CeEEEEeeEEEEECCCCCCCCHHHHHHHHHHHHhcCeEeCCeeEEEEEEEeeeeeceeEEeCCCceEEEEEEEEEEeeec
Q 032987 1 MFYLSKIEHTLRLPPHLLRLPLNEAIKLELENVFLDKVIANLGLCISIYDIKEIEGGFVYPGEGASTHTVKFRLVVFRPF 80 (129)
Q Consensus 1 MF~~~~l~d~V~I~P~~~~~~~~~~i~~~L~~k~~gk~~~~~G~~I~v~~i~~i~~g~I~~gdG~~~~~V~F~alvfrP~ 80 (129)
||++++++++|+|||++|+..+.++|.+.|+++|+||+.++.|+||+++||.+.++|+|.++||.+++++.|++++|+|+
T Consensus 1 Mf~~~~l~~~i~I~P~~~~~~i~~~I~~~L~~~~~gk~~~~~G~~i~~idi~~~g~~~I~~~d~~~~~~~~~~~i~~~~~ 80 (187)
T 1go3_E 1 MYKILEIADVVKVPPEEFGKDLKETVKKILMEKYEGRLDKDVGFVLSIVDVKDIGEGKVVHGDGSAYHPVVFETLVYIPE 80 (187)
T ss_dssp CEEEEEEEEEEEECGGGTTSCHHHHHHHHHHHHHTTCEETTTEEEEEEEEEEEECCCBCCTTCCSEEEEEEEEEEEECCC
T ss_pred CcEEEEEEEEEEECHHHhCccHHHHHHHHHHHHhCCeEcCCccEEEEEEEEeeccCCEEeCCCccEEEEEEEEEEEEccC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCEEEEEEEEEccCceEEEeCccceEEecCCCCCCCCCcCCCCCC
Q 032987 81 VGEIIAAKLKESDANGLRLSLGFFEDIYVPSHLLPSPSRSEPDPYG 126 (129)
Q Consensus 81 ~~EVl~g~V~~v~~~Gi~v~~G~~~~i~i~~~~lp~~~~f~~d~~~ 126 (129)
.||+++|+|++++++|+||++||++++.++++.+++++.| |+.+
T Consensus 81 ~Gev~~G~V~~v~~~G~fV~l~~~eglvhis~l~~~~~~~--d~~~ 124 (187)
T 1go3_E 81 MYELIEGEVVDVVEFGSFVRLGPLDGLIHVSQIMDDYVSY--DPKR 124 (187)
T ss_dssp TTCEEEEEEEEEETTEEEEECSSSEEEEEGGGSCSSCEEE--CCC-
T ss_pred CCCEEEEEEEEEeCcEEEEEEcCccEEEEhHHhCCCcceE--CCcc
Confidence 9999999999999999999999999999999999988888 6544
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=99.97 E-value=2.3e-31 Score=196.59 Aligned_cols=123 Identities=29% Similarity=0.535 Sum_probs=117.9
Q ss_pred CeEEEEeeEEEEECCCCCCCCHHHHHHHHHHHHhcCeEeCCeeEEEEEEEeeeeeceeEEeCCCceEEEEEEEEEEeeec
Q 032987 1 MFYLSKIEHTLRLPPHLLRLPLNEAIKLELENVFLDKVIANLGLCISIYDIKEIEGGFVYPGEGASTHTVKFRLVVFRPF 80 (129)
Q Consensus 1 MF~~~~l~d~V~I~P~~~~~~~~~~i~~~L~~k~~gk~~~~~G~~I~v~~i~~i~~g~I~~gdG~~~~~V~F~alvfrP~ 80 (129)
||++.+++++|++||++|++++.+++..+|+.+|+|+++++.|+||+++||.++++|+|.+|||.++++++|+|++|+|+
T Consensus 1 mfil~~m~~~I~~~p~~~~~~~~~~i~~~l~~~~~~~vi~~~G~~I~~~di~~i~~g~i~~~d~~~~~~~~~~~~~~~~~ 80 (172)
T 2c35_B 1 MFYHISLEHEILLHPRYFGPNLLNTVKQKLFTEVEGTCTGKYGFVIAVTTIDNIGAGVIQPGRGFVLYPVKYKAIVFRPF 80 (172)
T ss_dssp CEEEEEEEEEEEECGGGCCSCHHHHHHHHHHHHHTTCEETTTEEEEEEEEEEEECCCBCCTTCSSEEEEEEEEEEEECCC
T ss_pred CcEEEEEeEEEEECHHHhCChHHHHHHHHHHHHHcCcCcCCceEEEEEEEeeecCCeEEeCCCCCEEEEEEEEEEEeeCC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCEEEEEEEEEccCceEEEeCccceEEecCCCCCCCCCcCCCCCC
Q 032987 81 VGEIIAAKLKESDANGLRLSLGFFEDIYVPSHLLPSPSRSEPDPYG 126 (129)
Q Consensus 81 ~~EVl~g~V~~v~~~Gi~v~~G~~~~i~i~~~~lp~~~~f~~d~~~ 126 (129)
.||+++|+|++++++|+||.+||++ .+||.+.|++++.| |+.+
T Consensus 81 ~Gev~~G~V~~v~~fG~fV~l~~~~-glvhis~l~~~~~~--d~~~ 123 (172)
T 2c35_B 81 KGEVVDAVVTQVNKVGLFTEIGPMS-CFISRHSIPSEMEF--DPNS 123 (172)
T ss_dssp TTCEEEEEEEEEETTEEEEEETTEE-EEEEGGGSCTTEEE--ESSS
T ss_pred CCCEEEEEEEEEeCCEEEEEECCEE-EEEEHHHCCCCcEE--CCCC
Confidence 9999999999999999999999998 88888899988888 5544
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=99.97 E-value=2.2e-30 Score=191.47 Aligned_cols=123 Identities=23% Similarity=0.528 Sum_probs=104.8
Q ss_pred CeEEEEeeEEEEECCCCCCCCHHHHHHHHHHHHhcCeEeCCeeEEEEEEEee--eeeceeEEeCCCceEEEEEEEEEEee
Q 032987 1 MFYLSKIEHTLRLPPHLLRLPLNEAIKLELENVFLDKVIANLGLCISIYDIK--EIEGGFVYPGEGASTHTVKFRLVVFR 78 (129)
Q Consensus 1 MF~~~~l~d~V~I~P~~~~~~~~~~i~~~L~~k~~gk~~~~~G~~I~v~~i~--~i~~g~I~~gdG~~~~~V~F~alvfr 78 (129)
||++.+++++|++||++|+++..+++..+|+.+|+|+++.+.|+||+++||. ++++|+|.+|||.+++++.|++++|+
T Consensus 1 mfil~~m~~~i~~pp~~l~~~~p~~i~~~i~~~~i~~vig~~G~~I~~~di~~~di~~g~i~~~d~~~~~~~~~~~~~~~ 80 (171)
T 1y14_B 1 MFFIKDLSLNITLHPSFFGPRMKQYLKTKLLEEVEGSCTGKFGYILCVLDYDNIDIQRGRILPTDGSAEFNVKYRAVVFK 80 (171)
T ss_dssp CEEEEEEEEECCCCTTSCSTTHHHHHHHHHHHHHTTEEETTTEEEEEECCGGGCBCC------------CEEEEEEEEEC
T ss_pred CeEEEEEEEEEEECHHHhCChHHHHHHHHHHHHHcCcCcCCceEEEEEEEecccccCccEEeCCCCCEEEEEEEEEEEcc
Confidence 9999999999999999999999999999999999999999999999999999 99999999999999999999999999
Q ss_pred ecCCCEEEEEEEEEccCceEEEeCccceEEecCCCCCCCCCcCCCCCC
Q 032987 79 PFVGEIIAAKLKESDANGLRLSLGFFEDIYVPSHLLPSPSRSEPDPYG 126 (129)
Q Consensus 79 P~~~EVl~g~V~~v~~~Gi~v~~G~~~~i~i~~~~lp~~~~f~~d~~~ 126 (129)
|+.||+++|+|++++++|+|+.+|| .+.+++.+.|++++.| |+.+
T Consensus 81 ~~~Gev~~G~V~~v~~fG~FV~l~~-~dglvhis~l~~~~~~--d~~~ 125 (171)
T 1y14_B 81 PFKGEVVDGTVVSCSQHGFEVQVGP-MKVFVTKHLMPQDLTF--NAGS 125 (171)
T ss_dssp CCTTCEEEEEEEEEETTEEEEEETT-EEEEEEGGGSCTTCEE--CC--
T ss_pred CCCCCEEEEEEEEEecCEEEEEecC-eEEEEEHHHCCCCceE--Cccc
Confidence 9999999999999999999999999 5688888899988888 5543
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=99.97 E-value=2.2e-30 Score=198.34 Aligned_cols=124 Identities=23% Similarity=0.524 Sum_probs=118.0
Q ss_pred CeEEEEeeEEEEECCCCCCCCHHHHHHHHHHHHhcCeEeCCeeEEEEEEEee--eeeceeEEeCCCceEEEEEEEEEEee
Q 032987 1 MFYLSKIEHTLRLPPHLLRLPLNEAIKLELENVFLDKVIANLGLCISIYDIK--EIEGGFVYPGEGASTHTVKFRLVVFR 78 (129)
Q Consensus 1 MF~~~~l~d~V~I~P~~~~~~~~~~i~~~L~~k~~gk~~~~~G~~I~v~~i~--~i~~g~I~~gdG~~~~~V~F~alvfr 78 (129)
||++.+++++|++||++|++++.+++..+|+.+|+|+|+.+.|+||+++||. ++++|+|.||||.+++++.|++++|+
T Consensus 1 MfiL~~m~~~I~ipp~~~~~~~p~~i~~~I~~~~ig~vIg~~G~vI~~~dI~~~di~dG~I~~gdg~~~~~v~~~~i~~~ 80 (215)
T 2b8k_G 1 MFFIKDLSLNITLHPSFFGPRMKQYLKTKLLEEVEGSCTGKFGYILCVLDYDNIDIQRGRILPTDGSAEFNVKYRAVVFK 80 (215)
T ss_dssp CEEEECCEEEEEECGGGCSSSHHHHHHHHHHHSSTTCEETTTEEEEEECCSTTCBCCCEEECSSSCCEEEEEECCEEEEC
T ss_pred CEEeHHHHhhhhcCHHHHChhHhHHHHhcCCHHHCCeEcCCCCEEEEEEEeeecccccceEeCCCHHHHHHHHhhhheec
Confidence 9999999999999999999999999999999999999999999999999999 99999999999999999999999999
Q ss_pred ecCCCEEEEEEEEEccCceEEEeCccceEEecCCCCCCCCCcCCCCCCC
Q 032987 79 PFVGEIIAAKLKESDANGLRLSLGFFEDIYVPSHLLPSPSRSEPDPYGR 127 (129)
Q Consensus 79 P~~~EVl~g~V~~v~~~Gi~v~~G~~~~i~i~~~~lp~~~~f~~d~~~~ 127 (129)
|+.||+++|+|++++++|+||.+|| .+.+|+.+.|++++.| |+.++
T Consensus 81 p~vGev~~G~V~~vt~fG~FVelg~-~dGlVhiS~l~d~~~~--d~~~~ 126 (215)
T 2b8k_G 81 PFKGEVVDGTVVSCSQHGFEVQVGP-MKVFVTKHLMPQDLTF--NAGSN 126 (215)
T ss_dssp CCTTEEEEEEEEEEETTEEEEECTT-SEEEEEGGGSCSSCCC--BSSCS
T ss_pred cCCCCEEEEEEEEEecceEEEEecC-cEEEEEHHHCCcccee--ccccc
Confidence 9999999999999999999999999 5688888899988888 55543
No 9
>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=99.97 E-value=7.8e-30 Score=195.07 Aligned_cols=121 Identities=17% Similarity=0.227 Sum_probs=104.2
Q ss_pred CeEEEEeeEEEEECCCCCCCCHHHHHHHHHHHHhcCeEeCCe-eEEEEEEEeeeeec------------eeEEeCCCceE
Q 032987 1 MFYLSKIEHTLRLPPHLLRLPLNEAIKLELENVFLDKVIANL-GLCISIYDIKEIEG------------GFVYPGEGAST 67 (129)
Q Consensus 1 MF~~~~l~d~V~I~P~~~~~~~~~~i~~~L~~k~~gk~~~~~-G~~I~v~~i~~i~~------------g~I~~gdG~~~ 67 (129)
||++++++++|+|||++|+++++.++.+.|+.+ .+|+.++. |+|+++.++..+++ |+|.+|+|.++
T Consensus 37 mF~l~~~~~~V~L~P~~f~~~~~~i~~~~L~~l-l~ky~~~~~Gv~la~~di~~~~~~~~~~d~~~~~~g~I~~~~g~~~ 115 (214)
T 2rf4_A 37 CIVRVPIALYVSLAPMYLENPLQGVMKQHLNPL-VMKYNNKVGGVVLGYEGLKILDADPLSKEDTSEKLIKITPDTPFGF 115 (214)
T ss_dssp CEEEEEEEEEEECCGGGTTCHHHHHHHHHHHHH-BTSEETTTTEEEEEEEEEETTSCCC-----------------CCCE
T ss_pred cEEEEEEEEEEEECHHHhCChhHHHHHHHHHHH-HhcccCCCCEEEEEEECeEeccCCCcCccccccceeEEeCCCceEE
Confidence 999999999999999999998888877888886 77888887 89999999976654 79999999999
Q ss_pred EEEEEEEEEeeecCCCEEEEEEEEEccCceEE-EeCccceEEecCCCCCCCCCcCCC
Q 032987 68 HTVKFRLVVFRPFVGEIIAAKLKESDANGLRL-SLGFFEDIYVPSHLLPSPSRSEPD 123 (129)
Q Consensus 68 ~~V~F~alvfrP~~~EVl~g~V~~v~~~Gi~v-~~G~~~~i~i~~~~lp~~~~f~~d 123 (129)
++|+|+|+|||||+||+|+|+|+++++.|+.+ .+|||+ ++||++.||+++.|+++
T Consensus 116 ~~V~~~~iVFrPf~GevL~G~V~~~s~~~Ig~~~~G~Fn-~~Ip~~~ip~~~~f~~~ 171 (214)
T 2rf4_A 116 TWCHVNLYVWQPQVGDVLEGYIFIQSASHIGLLIHDAFN-ASIKKNNIPVDWTFVHN 171 (214)
T ss_dssp EEEEEEEEEECCCTTCEEEEEECCCCSSCEEEEETTTEE-EEECSTTSCSSCBCCCC
T ss_pred EEEEEEEEEEecCCCCEEEEEEEEECCCcEEEEEeCCEE-EEEcHHHCCCccccccc
Confidence 99999999999999999999999999999998 569997 89999999999999544
No 10
>2bh8_A 1B11; transcription, molecular evolution, unique architecture, transcription regulation, phosphorylation; 1.9A {Escherichia coli}
Probab=97.57 E-value=3.6e-05 Score=51.72 Aligned_cols=59 Identities=24% Similarity=0.345 Sum_probs=50.7
Q ss_pred eeceeEEeCCCceEEEEEEEEEE---e---eecCCCEEEEEEEEEccCceEEEe-CccceEEecCC
Q 032987 54 IEGGFVYPGEGASTHTVKFRLVV---F---RPFVGEIIAAKLKESDANGLRLSL-GFFEDIYVPSH 112 (129)
Q Consensus 54 i~~g~I~~gdG~~~~~V~F~alv---f---rP~~~EVl~g~V~~v~~~Gi~v~~-G~~~~i~i~~~ 112 (129)
.+-|.|.+.+|...+-|.++++. | +|..||+++++|++++++|+|+.+ +..+++.+.++
T Consensus 28 kGfGFI~~~~gg~dvfvH~s~l~~~~~~~~~l~~Ge~V~g~V~~i~~fG~fv~l~~~~eGlvhis~ 93 (101)
T 2bh8_A 28 KGFGFITPDDGSKDVFVHFSAGSSGAAVRGNPQQGDRVEGKIKSITDFGIFIGLDGGIDGLVHLSD 93 (101)
T ss_dssp GTEEEEEESSSSCEEEEECCCSCSSSCCCCCCCTTCEEEEEEEECCSEEEEECTTSCEEEEEEEEE
T ss_pred CCCEEEEeCCCCcEEEEEEEEEecCCccccCCCCCCEEEEEEEEeCCcEEEEEcCCCceEEEEHHH
Confidence 36789999999999999999998 3 799999999999999999999999 55676665544
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=96.87 E-value=0.00027 Score=48.65 Aligned_cols=43 Identities=9% Similarity=0.059 Sum_probs=34.6
Q ss_pred EEEEEEeeecCCCEEEEEEEEEccCceEEEeCc--cceEEecCCC
Q 032987 71 KFRLVVFRPFVGEIIAAKLKESDANGLRLSLGF--FEDIYVPSHL 113 (129)
Q Consensus 71 ~F~alvfrP~~~EVl~g~V~~v~~~Gi~v~~G~--~~~i~i~~~~ 113 (129)
.++.+.+.|..|+++.|+|+++.++|+||.++. .+++.+.++.
T Consensus 12 ~~~~~~~~~~vG~iv~G~V~~I~~fGaFV~l~g~~~~Glvhisel 56 (119)
T 2cqo_A 12 RPETMENLPALYTIFQGEVAMVTDYGAFIKIPGCRKQGLVHRTHM 56 (119)
T ss_dssp CCCCSCCSCCTTCEEEEEEEEEETTEEEEECTTCSSCEEEEHHHH
T ss_pred chhhhhcccCCCCEEEEEEEEEeCceEEEEECCCcEEEEEEHHHC
Confidence 456677899999999999999999999999955 4655555443
No 12
>2khi_A 30S ribosomal protein S1; acetylation, phosphoprotein, ribonucleoprotein, RNA-binding; NMR {Escherichia coli}
Probab=96.86 E-value=0.00065 Score=46.22 Aligned_cols=47 Identities=9% Similarity=-0.026 Sum_probs=35.9
Q ss_pred EEEEEEEeeecCCCEEEEEEEEEccCceEEEeCccceEEecCCCCCC
Q 032987 70 VKFRLVVFRPFVGEIIAAKLKESDANGLRLSLGFFEDIYVPSHLLPS 116 (129)
Q Consensus 70 V~F~alvfrP~~~EVl~g~V~~v~~~Gi~v~~G~~~~i~i~~~~lp~ 116 (129)
..|..+..+|..|++++|+|++++++|+||.++.--.-+++.+.|..
T Consensus 19 ~p~~~~~~~~~~G~~~~G~V~~v~~~G~FV~l~~~~~Glvhisel~~ 65 (115)
T 2khi_A 19 SHWVAIAKRYPEGTKLTGRVTNLTDYGCFVEIEEGVEGLVHVSEMDW 65 (115)
T ss_dssp --CCCSSCSSCSSCEEEEEEEEEETTEEEEECSTTCEEEEETTSSSC
T ss_pred CCHHHHhhcCCCCCEEEEEEEEEECCEEEEEECCCCEEEEEHHHCCc
Confidence 34555667899999999999999999999999753345666666643
No 13
>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=96.85 E-value=0.0013 Score=43.92 Aligned_cols=39 Identities=21% Similarity=0.181 Sum_probs=31.2
Q ss_pred EeeecCCCEEEEEEEEEccCceEEEeC----ccceEEecCCCCC
Q 032987 76 VFRPFVGEIIAAKLKESDANGLRLSLG----FFEDIYVPSHLLP 115 (129)
Q Consensus 76 vfrP~~~EVl~g~V~~v~~~Gi~v~~G----~~~~i~i~~~~lp 115 (129)
...|..|++++|+|+++.++|+||.++ ..+++.+ .+.|+
T Consensus 7 ~~~~~vG~i~~G~V~~v~~fG~FV~l~~~~~~~~Glvh-isel~ 49 (103)
T 2eqs_A 7 GEEPTIGDIYNGKVTSIMQFGCFVQLEGLRKRWEGLVH-ISELR 49 (103)
T ss_dssp CSSCCTTCEEEEEEEEECSSCEEEEECSSSSCCEEEEC-GGGTS
T ss_pred cccCCCCCEEEEEEEEEeccEEEEEEcCCCCCeEEEEE-HHHCC
Confidence 457889999999999999999999998 4665444 44553
No 14
>2k52_A Uncharacterized protein MJ1198; metal-binding, zinc, zinc-finger, structural genomics, PSI-2, protein structure initiative; NMR {Methanocaldococcus jannaschii}
Probab=96.72 E-value=0.0023 Score=40.66 Aligned_cols=38 Identities=11% Similarity=0.038 Sum_probs=30.3
Q ss_pred eecCCCEEEEEEEEEccCceEEEeC-ccceEEecCCCCCC
Q 032987 78 RPFVGEIIAAKLKESDANGLRLSLG-FFEDIYVPSHLLPS 116 (129)
Q Consensus 78 rP~~~EVl~g~V~~v~~~Gi~v~~G-~~~~i~i~~~~lp~ 116 (129)
.|..|++++|+|+++.++|+|+.++ ..+ -+++.+.+..
T Consensus 2 ~~~~G~iv~G~V~~v~~~G~fV~l~~~~~-Gllh~sel~~ 40 (80)
T 2k52_A 2 DVEPGKFYKGVVTRIEKYGAFINLNEQVR-GLLRPRDMIS 40 (80)
T ss_dssp CCCTTCEEEEEEEEEETTEEEEEEETTEE-EEECGGGCSS
T ss_pred CCCCCCEEEEEEEEEeCCEEEEEECCCCE-EEEEHHHCCc
Confidence 4778999999999999999999998 454 4555555643
No 15
>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=96.70 E-value=0.00023 Score=48.72 Aligned_cols=37 Identities=11% Similarity=0.177 Sum_probs=30.9
Q ss_pred eecCCCEEEEEEEEEccCceEEEeC-ccceEEecCCCC
Q 032987 78 RPFVGEIIAAKLKESDANGLRLSLG-FFEDIYVPSHLL 114 (129)
Q Consensus 78 rP~~~EVl~g~V~~v~~~Gi~v~~G-~~~~i~i~~~~l 114 (129)
.+..|++++|+|+++.++|+||.+| .-.+.+|+++.+
T Consensus 18 ~l~~G~i~~G~V~~v~~fG~fV~l~~~~~~~l~~~~~~ 55 (119)
T 1wi5_A 18 ALKPGMLLTGTVSSLEDHGYLVDIGVDGTRAFLPLLKA 55 (119)
T ss_dssp TCCTTCEEEEEEEEECSSEEEEECCCSSCEEEEEHHHH
T ss_pred cCCCCCEEEEEEEEEeCceEEEEECCCCeEEEEEEecc
Confidence 4678999999999999999999999 345677777654
No 16
>1luz_A Protein K3, protein K2; stranded anti-parallel beta barrel, viral protein; 1.80A {Vaccinia virus} SCOP: b.40.4.5
Probab=96.61 E-value=0.0025 Score=41.52 Aligned_cols=33 Identities=27% Similarity=0.392 Sum_probs=27.4
Q ss_pred eecCCCEEEEEEEEEccCceEEEeC---ccceEEecC
Q 032987 78 RPFVGEIIAAKLKESDANGLRLSLG---FFEDIYVPS 111 (129)
Q Consensus 78 rP~~~EVl~g~V~~v~~~Gi~v~~G---~~~~i~i~~ 111 (129)
.|..|++++|+|+ ++++|+|+.++ -.+++.+.+
T Consensus 8 ~~~vG~~~~G~V~-v~~fG~FVel~~~~~~eGLvhis 43 (88)
T 1luz_A 8 LPNAGDVIKGRVY-EKDYALYIYLFDYPHFEAILAES 43 (88)
T ss_dssp CCCTTCEEEEEEE-EETTEEEEEETTCTTSEEEEGGG
T ss_pred CCCCCCEEEEEEE-EEccEEEEEECCCCCeEEEEEee
Confidence 4889999999999 99999999995 366655544
No 17
>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=96.46 E-value=0.0035 Score=46.22 Aligned_cols=35 Identities=23% Similarity=0.357 Sum_probs=30.3
Q ss_pred ecCCCEEEEEEEEEccCceEEEe---CccceEEecCCC
Q 032987 79 PFVGEIIAAKLKESDANGLRLSL---GFFEDIYVPSHL 113 (129)
Q Consensus 79 P~~~EVl~g~V~~v~~~Gi~v~~---G~~~~i~i~~~~ 113 (129)
|..|+++.|+|++++++|+||.+ +..+++.+.++.
T Consensus 13 p~~G~iv~G~V~~I~~fGaFV~L~e~~g~eGLvhiSel 50 (182)
T 1kl9_A 13 PEVEDVVMVNVRSIAEMGAYVSLLEYNNIEGMILLSEL 50 (182)
T ss_dssp CCTTCEEEEEEEEECSSEEEEEETTTTTEEEEEEGGGC
T ss_pred CCCCCEEEEEEEEEeccEEEEEEccCCCcEEEEEHHHC
Confidence 68899999999999999999999 678877666554
No 18
>3cdi_A Polynucleotide phosphorylase; mRNA turnover, RNAse, RNA degradation, kinase, transferase; 2.60A {Escherichia coli} PDB: 1sro_A
Probab=96.38 E-value=0.00054 Score=60.07 Aligned_cols=73 Identities=15% Similarity=0.179 Sum_probs=0.0
Q ss_pred EeCCeeEEEEEEEeeeeeceeEEeCCCceEEEE--EEEEEEeeecCCCEEEEEEEEEccCceEEEeCc-cceEEecCCC
Q 032987 38 VIANLGLCISIYDIKEIEGGFVYPGEGASTHTV--KFRLVVFRPFVGEIIAAKLKESDANGLRLSLGF-FEDIYVPSHL 113 (129)
Q Consensus 38 ~~~~~G~~I~v~~i~~i~~g~I~~gdG~~~~~V--~F~alvfrP~~~EVl~g~V~~v~~~Gi~v~~G~-~~~i~i~~~~ 113 (129)
+..+.|.-| ||.+-+...|...++...-+. .++.++..|..|++++|+|+++.++|+||.+++ .+++.|.++.
T Consensus 585 I~~~~G~~I---dI~~dg~v~I~~~~~~~~~~a~~~i~~i~~~~~vG~i~~G~V~~i~~fGaFVel~~g~eGLvHiSel 660 (723)
T 3cdi_A 585 LTEETGTTI---EIEDDGTVKIAATDGEKAKHAIRRIEEITAEIEVGRVYTGKVTRIVDFGAFVAIGGGKEGLVHISQI 660 (723)
T ss_dssp -------------------------------------------------------------------------------
T ss_pred eehhhCceE---EecCCccEEEecCCHHHHHHHHHHHHHHhhhhhcCcEEEEEEEEEecceEEEEeCCCceEEEEHHHc
Confidence 345566443 555545555655555554333 577888999999999999999999999999965 5555555544
No 19
>2khj_A 30S ribosomal protein S1; OB fold, acetylation, phosphoprotein, ribonucleoprotein, RNA-binding; NMR {Escherichia coli}
Probab=96.33 E-value=0.0054 Score=41.07 Aligned_cols=40 Identities=20% Similarity=0.173 Sum_probs=31.3
Q ss_pred eeecCCCEEEEEEEEEccCceEEEeCccceEEecCCCCCC
Q 032987 77 FRPFVGEIIAAKLKESDANGLRLSLGFFEDIYVPSHLLPS 116 (129)
Q Consensus 77 frP~~~EVl~g~V~~v~~~Gi~v~~G~~~~i~i~~~~lp~ 116 (129)
..+..|+++.|+|++++++|+||.++.--+-++|.+.+.+
T Consensus 27 ~~~~~G~iv~G~V~~v~~~G~fV~l~~~~~Gll~~sel~~ 66 (109)
T 2khj_A 27 ALNKKGAIVTGKVTAVDAKGATVELADGVEGYLRASEASR 66 (109)
T ss_dssp TTCCSSSEEEEEEEEECSSCEEEECSTTCBCCBCTTCCCS
T ss_pred hcCCCCCEEEEEEEEEECCeEEEEECCCCEEEEEHHHcCc
Confidence 3577899999999999999999999852235566666653
No 20
>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=96.20 E-value=0.0067 Score=44.34 Aligned_cols=35 Identities=20% Similarity=0.351 Sum_probs=27.9
Q ss_pred ecCCCEEEEEEEEEccCceEEEe---CccceEEecCCC
Q 032987 79 PFVGEIIAAKLKESDANGLRLSL---GFFEDIYVPSHL 113 (129)
Q Consensus 79 P~~~EVl~g~V~~v~~~Gi~v~~---G~~~~i~i~~~~ 113 (129)
|..|+++.|+|+++.++|+||.+ +..+++.+.++.
T Consensus 13 p~~G~iv~G~V~~i~~fGaFV~L~e~~gveGLvhiSel 50 (175)
T 2a19_A 13 PEIDDIVMVNVQQIAEMGAYVKLLEYDNIEGMILLSEL 50 (175)
T ss_dssp CCTTCEEEEEEEEEETTEEEEEETTTTTCEEEEECC--
T ss_pred CCCCCEEEEEEEEEecceEEEEEcCCCCcEEEEEHHHc
Confidence 55899999999999999999999 567766555443
No 21
>2k4k_A GSP13, general stress protein 13; cytoplasm, stress response, RNA binding protein; NMR {Bacillus subtilis}
Probab=95.96 E-value=0.013 Score=40.67 Aligned_cols=37 Identities=16% Similarity=0.125 Sum_probs=29.2
Q ss_pred eecCCCEEEEEEEEEccCceEEEe-CccceEEecCCCCC
Q 032987 78 RPFVGEIIAAKLKESDANGLRLSL-GFFEDIYVPSHLLP 115 (129)
Q Consensus 78 rP~~~EVl~g~V~~v~~~Gi~v~~-G~~~~i~i~~~~lp 115 (129)
.+..|+++.|+|++++++|+||.+ +..+++.+ .+.|.
T Consensus 4 ~~~vG~iv~G~V~~i~~~G~FV~l~~~~~Glih-isel~ 41 (130)
T 2k4k_A 4 KFEVGSVYTGKVTGLQAYGAFVALDEETQGLVH-ISEVT 41 (130)
T ss_dssp CCCTTCEEEEEEEEEETTEEEEEEETTEEEEEE-GGGTS
T ss_pred cCCCCCEEEEEEEEEeCCeEEEEECCCcEEEEE-HHHCC
Confidence 467899999999999999999999 45655544 44454
No 22
>1e3p_A Guanosine pentaphosphate synthetase; polyribonucleotide transferase, ATP-GTP diphosphotransferase RNA processing, RNA degradation; 2.5A {Streptomyces antibioticus} SCOP: a.4.9.1 b.40.4.5 d.14.1.4 d.14.1.4 d.52.3.1 d.101.1.1 d.101.1.1 PDB: 1e3h_A
Probab=95.87 E-value=0.00032 Score=61.80 Aligned_cols=92 Identities=16% Similarity=0.207 Sum_probs=27.6
Q ss_pred EEEEECCCCCCCCHHHHHHHHHHHHhcCeE----eCCeeEEEEEEEeeeeeceeEEeCCCceEEEE--EEEEEE--eeec
Q 032987 9 HTLRLPPHLLRLPLNEAIKLELENVFLDKV----IANLGLCISIYDIKEIEGGFVYPGEGASTHTV--KFRLVV--FRPF 80 (129)
Q Consensus 9 d~V~I~P~~~~~~~~~~i~~~L~~k~~gk~----~~~~G~~I~v~~i~~i~~g~I~~gdG~~~~~V--~F~alv--frP~ 80 (129)
.+++|||+..+.-+.. -||+ ..+.|..|.+ .+-+.-.|...++...-.. ..+.++ ..|.
T Consensus 600 ~~~~I~~~ki~~vIG~----------gGk~Ik~I~~~~G~~IdI---~~dG~v~Is~~~~~~~~~a~~~i~~i~~p~~~~ 666 (757)
T 1e3p_A 600 ITVKIPVDKIGEVIGP----------KRQMINQIQEDTGAEITI---EDDGTIYIGAADGPAAEAARATINGIANPTSPE 666 (757)
T ss_dssp CCC----------------------------CTTCCCCCSCC-----------CCCBSSHHHHCC---------------
T ss_pred EEEEEChHHeehcccc----------cceeeehhhHhhCCEEEe---cCCceEEEecCCHHHHHHHHHHHHHhcchhhcc
Confidence 3677888877654433 2333 3466766543 3323333333333222111 356677 8999
Q ss_pred CCCEEEEEEEEEccCceEEEeCc-cceEEecCCC
Q 032987 81 VGEIIAAKLKESDANGLRLSLGF-FEDIYVPSHL 113 (129)
Q Consensus 81 ~~EVl~g~V~~v~~~Gi~v~~G~-~~~i~i~~~~ 113 (129)
.|++++|+|+++.++|+||.+.+ .+++.|.++.
T Consensus 667 vG~i~~G~V~~i~~fGaFV~l~~g~eGLvHiSel 700 (757)
T 1e3p_A 667 VGERILGSVVKTTTFGAFVSLLPGKDGLLHISQI 700 (757)
T ss_dssp ------CBEEECC-CSCEECCC---CCCCC----
T ss_pred cccEEEEEEEEccccEEEEEEcCCcEEEEEhHHh
Confidence 99999999999999999999955 6656555544
No 23
>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=95.43 E-value=0.017 Score=43.79 Aligned_cols=37 Identities=22% Similarity=0.418 Sum_probs=31.6
Q ss_pred eeecCCCEEEEEEEEEccCceEEEeC-ccceEEecCCC
Q 032987 77 FRPFVGEIIAAKLKESDANGLRLSLG-FFEDIYVPSHL 113 (129)
Q Consensus 77 frP~~~EVl~g~V~~v~~~Gi~v~~G-~~~~i~i~~~~ 113 (129)
|.|..|+++.|+|++++++|++|.+| +++++...++.
T Consensus 53 y~p~~GDiV~G~V~~v~~~~a~V~I~~~~~g~l~isev 90 (229)
T 2ba0_A 53 YTPSVGDVVIGIIREVAANGWAVDIYSPYQAFLPVSEN 90 (229)
T ss_dssp CCCCTTCEEEEEEEEECSSEEEEECSSSSCEEEEGGGC
T ss_pred ccCCCCCEEEEEEEEEeCCeEEEEeCCCeEEEEEHHHc
Confidence 78999999999999999999999998 78766544443
No 24
>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=95.08 E-value=0.027 Score=43.31 Aligned_cols=37 Identities=11% Similarity=0.318 Sum_probs=31.8
Q ss_pred EeeecCCCEEEEEEEEEccCceEEEeC-ccceEEecCC
Q 032987 76 VFRPFVGEIIAAKLKESDANGLRLSLG-FFEDIYVPSH 112 (129)
Q Consensus 76 vfrP~~~EVl~g~V~~v~~~Gi~v~~G-~~~~i~i~~~ 112 (129)
.|.|..|+++.|+|++++++|+||.+| +++++.+.++
T Consensus 69 ~y~p~~GDiV~G~V~~v~~~ga~VdI~~~~~GlL~ise 106 (251)
T 2je6_I 69 FYYPKINDIVIGLVEDVEIYGWVVDIKAPYKAYLPASN 106 (251)
T ss_dssp CCCCCTTCEEEEEEEEECSSEEEEECSSSSCEEEEHHH
T ss_pred ccCCCCCCEEEEEEEEEeCceEEEEcCCCeEEEEEHHH
Confidence 478999999999999999999999998 6876665443
No 25
>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=94.90 E-value=0.029 Score=42.60 Aligned_cols=36 Identities=6% Similarity=0.223 Sum_probs=31.1
Q ss_pred eeecCCCEEEEEEEEEccCceEEEeC-ccceEEecCC
Q 032987 77 FRPFVGEIIAAKLKESDANGLRLSLG-FFEDIYVPSH 112 (129)
Q Consensus 77 frP~~~EVl~g~V~~v~~~Gi~v~~G-~~~~i~i~~~ 112 (129)
|.|..|+++.|+|++++++|+||.+| +++++.+.++
T Consensus 62 y~p~~GDiV~G~V~~v~~~~~~V~I~~~~~g~l~ise 98 (235)
T 2z0s_A 62 YVPQAGDVVIGLIQSVGIMNWFVDINSPYVAVLSVQD 98 (235)
T ss_dssp CCCCTTCCEEEEEEEECSSEEEEECSSSSCEEEEHHH
T ss_pred cCCCCCCEEEEEEEEEeCCeEEEEeCCCeEEEEEHHH
Confidence 78999999999999999999999998 7876654433
No 26
>4aid_A Polyribonucleotide nucleotidyltransferase; transferase-peptide complex; 2.60A {Caulobacter vibrioides} PDB: 4aim_A 4am3_A
Probab=94.85 E-value=0.00098 Score=58.51 Aligned_cols=65 Identities=17% Similarity=0.068 Sum_probs=6.3
Q ss_pred EeeeeeceeEEeCCCceEEE--EEEEEEEeeecCCCEEEEEEEEEccCceEEEeCc-cceEEecCCCC
Q 032987 50 DIKEIEGGFVYPGEGASTHT--VKFRLVVFRPFVGEIIAAKLKESDANGLRLSLGF-FEDIYVPSHLL 114 (129)
Q Consensus 50 ~i~~i~~g~I~~gdG~~~~~--V~F~alvfrP~~~EVl~g~V~~v~~~Gi~v~~G~-~~~i~i~~~~l 114 (129)
||.+-+..+|...|+.+.-. -.++.++..|..|++++|+|+++.++|+||.+.+ .+++.|.++.-
T Consensus 604 di~ddG~v~I~~~~~~~~~~A~~~i~~i~~~~~vG~v~~G~V~~I~~fGaFVel~~g~eGLvHiSels 671 (726)
T 4aid_A 604 DINDDGVVKVSASDGAKIKAAIDWIKSITDEAEVGKIYDGKVVKVVDFGAFVNFFGAKDGLVHVSQIS 671 (726)
T ss_dssp ----------CCSCHHHHHHHHHC--------------------------------------------
T ss_pred eEECCceEEEEeCCHHHHHHHHHHHHHHhhhhcCCcEEEEEEEEEeccEEEEEECCCcEEEEEHHHcC
Confidence 34444555666555554443 4688889999999999999999999999999965 66655555443
No 27
>3aev_A Translation initiation factor 2 subunit alpha; proteins-rRNA complex, 16S rRNA, RNA-binding; 2.80A {Pyrococcus horikoshii} PDB: 1yz6_A
Probab=94.84 E-value=0.042 Score=42.82 Aligned_cols=36 Identities=28% Similarity=0.234 Sum_probs=29.2
Q ss_pred eecCCCEEEEEEEEEccCceEEEeC---ccceEEecCCC
Q 032987 78 RPFVGEIIAAKLKESDANGLRLSLG---FFEDIYVPSHL 113 (129)
Q Consensus 78 rP~~~EVl~g~V~~v~~~Gi~v~~G---~~~~i~i~~~~ 113 (129)
.|..|+++.|+|+++.++|+||.++ ..+++.+.++.
T Consensus 8 ~p~~Gdiv~G~V~~I~~fGaFV~L~e~~gieGlIhiSel 46 (275)
T 3aev_A 8 YPEEGEFVVATVKRIHNYGAFLELDEYPGKEAFMHISEV 46 (275)
T ss_dssp CCCTTCEEEEEEEEEETTEEEEEETTSTTCEEEEEGGGS
T ss_pred CCCCCCEEEEEEEEEECcEEEEEECCCCCeEEEEEHHHc
Confidence 4678999999999999999999996 56655555443
No 28
>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=94.74 E-value=0.047 Score=39.92 Aligned_cols=38 Identities=13% Similarity=0.259 Sum_probs=32.1
Q ss_pred eeecCCCEEEEEEEEEccCceEEEeCc--cceEEecCCCCC
Q 032987 77 FRPFVGEIIAAKLKESDANGLRLSLGF--FEDIYVPSHLLP 115 (129)
Q Consensus 77 frP~~~EVl~g~V~~v~~~Gi~v~~G~--~~~i~i~~~~lp 115 (129)
|.|..|+++.|+|+++...+.++.+|+ ++ .++|....+
T Consensus 3 Y~P~~gDvViG~V~~v~~~~~~VdI~~~~~~-a~L~~s~~~ 42 (175)
T 2ja9_A 3 YIPSVNDFVIGVIIGTFSDSYKVSLQNFSSS-VSLSYMAFP 42 (175)
T ss_dssp CCCCTTCEEEEEEEEECSSEEEEESSTTSCC-EEEETTSST
T ss_pred ccCCCcCEEEEEEEEEECcEEEEEECCCCcc-EEEEHHHCC
Confidence 789999999999999999999999998 54 555555554
No 29
>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=94.65 E-value=0.031 Score=41.84 Aligned_cols=38 Identities=16% Similarity=0.225 Sum_probs=31.2
Q ss_pred eeecCCCEEEEEEEEEccCceEEEeC---------ccceEEecCCCC
Q 032987 77 FRPFVGEIIAAKLKESDANGLRLSLG---------FFEDIYVPSHLL 114 (129)
Q Consensus 77 frP~~~EVl~g~V~~v~~~Gi~v~~G---------~~~~i~i~~~~l 114 (129)
+.|..|+++.|+|++++++|+||.++ .++++.+.++.-
T Consensus 77 y~p~vGDvV~G~V~~v~~~~a~V~I~~v~~~~L~~~~~GlIhisei~ 123 (209)
T 2nn6_I 77 LLPDVGAIVTCKVSSINSRFAKVHILYVGSMPLKNSFRGTIRKEDVR 123 (209)
T ss_dssp CCCCTTCEEEEEEEEECSSEEEEEEEESSSSCCCCSSCSCEEEEGGG
T ss_pred CCCCCCCEEEEEEEEEECceEEEEECccccccccCCceeEEEHHHcc
Confidence 68999999999999999999999985 566666544433
No 30
>1q8k_A Eukaryotic translation initiation factor 2 subunit 1; NMR {Homo sapiens} SCOP: a.60.14.1 b.40.4.5 d.58.51.1
Probab=94.40 E-value=0.039 Score=43.75 Aligned_cols=36 Identities=19% Similarity=0.230 Sum_probs=28.6
Q ss_pred ecCCCEEEEEEEEEccCceEEEeC---ccceEEecCCCCC
Q 032987 79 PFVGEIIAAKLKESDANGLRLSLG---FFEDIYVPSHLLP 115 (129)
Q Consensus 79 P~~~EVl~g~V~~v~~~Gi~v~~G---~~~~i~i~~~~lp 115 (129)
|..|+++.|+|+++.++|+||.++ ..+++.+. +.|.
T Consensus 11 ~~vG~iv~G~V~~I~~fGaFV~L~ey~gveGLvhi-Sels 49 (308)
T 1q8k_A 11 PEVEDVVMVNVRSIQEMGAYVSLLEYNNIEGMIHL-SELS 49 (308)
T ss_dssp CSSCCEEEEEEEEEETTEEEEESCTTTSCCEEECG-GGTS
T ss_pred CCCCCEEEEEEEEEeCcEEEEEECCCCCeEEEEEh-HHcC
Confidence 568999999999999999999995 56655444 4453
No 31
>3cw2_C Translation initiation factor 2 subunit alpha; AIF2, intact AIF2, initiation factor 2 alpha subunit, initiation factor 2 beta subunit; 2.80A {Sulfolobus solfataricus} PDB: 2aho_B 3v11_B*
Probab=94.17 E-value=0.045 Score=42.41 Aligned_cols=37 Identities=27% Similarity=0.309 Sum_probs=29.1
Q ss_pred eecCCCEEEEEEEEEccCceEEEeC---ccceEEecCCCCC
Q 032987 78 RPFVGEIIAAKLKESDANGLRLSLG---FFEDIYVPSHLLP 115 (129)
Q Consensus 78 rP~~~EVl~g~V~~v~~~Gi~v~~G---~~~~i~i~~~~lp 115 (129)
.|..|+++.|+|+++.++|+||.++ ..+++ ++.+.|.
T Consensus 8 ~~~vG~iv~G~V~~I~~~GaFV~l~e~~~~~Gl-ihiSels 47 (266)
T 3cw2_C 8 LPSEGEILIATVKQVFDYGSYVSLDEYGGLQAF-LPWSEVS 47 (266)
T ss_dssp SCCTTCEEEEEEEECCSSSBEEEETTTTSEECB-BCGGGSS
T ss_pred cCCCCCEEEEEEEEEeccEEEEEEcCCCCeEEE-EEhHHcC
Confidence 4788999999999999999999995 45544 4444554
No 32
>3m7n_A Putative uncharacterized protein AF_0206; exosome, RNA, exonuclease, hydrolase, nuclease, hydrolase-RN; 2.40A {Archaeoglobus fulgidus} PDB: 2ba1_A 3m85_A
Probab=93.88 E-value=0.081 Score=38.46 Aligned_cols=27 Identities=4% Similarity=0.000 Sum_probs=24.6
Q ss_pred EeeecCCCEEEEEEEEEccCceEEEeCc
Q 032987 76 VFRPFVGEIIAAKLKESDANGLRLSLGF 103 (129)
Q Consensus 76 vfrP~~~EVl~g~V~~v~~~Gi~v~~G~ 103 (129)
-+.|. |+++.|+|+++.++|+|+.++.
T Consensus 53 ~y~p~-GdiV~G~V~~V~~~ga~V~I~~ 79 (179)
T 3m7n_A 53 PEIVK-GDVVLGRVVDLRNSIALIEVSS 79 (179)
T ss_dssp CCCCT-TCEEEEEEEEECSSEEEEEEEE
T ss_pred cccCC-CCEEEEEEEEEeCCcEEEEEcc
Confidence 46788 9999999999999999999974
No 33
>3go5_A Multidomain protein with S1 RNA-binding domains; structural genomics, joint center for structural genomics, JCSG; HET: MSE; 1.40A {Streptococcus pneumoniae}
Probab=93.49 E-value=0.062 Score=42.03 Aligned_cols=37 Identities=19% Similarity=0.262 Sum_probs=31.4
Q ss_pred cCCCEEEEEEEEEc-cCceEEEeCc-cceEEecCCCCCC
Q 032987 80 FVGEIIAAKLKESD-ANGLRLSLGF-FEDIYVPSHLLPS 116 (129)
Q Consensus 80 ~~~EVl~g~V~~v~-~~Gi~v~~G~-~~~i~i~~~~lp~ 116 (129)
..|+++.|+|++++ ++|+|+.+|. --+.|+|.+.|+.
T Consensus 68 ~~G~~~~g~V~~v~~~~GaFVdiG~~~~d~lvp~sel~~ 106 (285)
T 3go5_A 68 TQDQFGWGRVTEVRKDLGVFVDTGLPDKEIVVSLDILPE 106 (285)
T ss_dssp CSSSCEEEEEEEEETTTEEEEECSCTTCCEEEEGGGSCS
T ss_pred cCCCEEEEEEEEEccCceEEEEECCCCcEEEEEHHHCCc
Confidence 46999999999999 7999999996 2358999888764
No 34
>3go5_A Multidomain protein with S1 RNA-binding domains; structural genomics, joint center for structural genomics, JCSG; HET: MSE; 1.40A {Streptococcus pneumoniae}
Probab=92.85 E-value=0.11 Score=40.51 Aligned_cols=37 Identities=3% Similarity=-0.096 Sum_probs=32.3
Q ss_pred ecCCCEEEEEEEEEccCceEEEeCccceEEecCCCCCC
Q 032987 79 PFVGEIIAAKLKESDANGLRLSLGFFEDIYVPSHLLPS 116 (129)
Q Consensus 79 P~~~EVl~g~V~~v~~~Gi~v~~G~~~~i~i~~~~lp~ 116 (129)
...|++++|+|++++++|+|+.+|- .+.++|.+.+|+
T Consensus 4 ~~~G~~v~g~V~~~~~~G~fv~~~g-~egllp~se~~~ 40 (285)
T 3go5_A 4 TNLASFIVGLIIDENDRFYFVQKDG-QTYALAKEEGQH 40 (285)
T ss_dssp TTTTEEEEEEEEEECSSEEEEEETT-EEEEEEGGGCCC
T ss_pred ccCCCEEEEEEEEEECCEEEEEcCC-eEEEEEHHHCcc
Confidence 3579999999999999999999984 468999988875
No 35
>1hh2_P NUSA, N utilization substance protein A; transcription regulation, termination; 2.1A {Thermotoga maritima} SCOP: b.40.4.5 d.52.3.1 d.52.3.1 d.202.1.1 PDB: 1l2f_A
Probab=92.76 E-value=0.15 Score=41.11 Aligned_cols=39 Identities=13% Similarity=0.215 Sum_probs=32.6
Q ss_pred eecCCCEEEEEEEEEccCceEEEeCccceEEecCCCCCC
Q 032987 78 RPFVGEIIAAKLKESDANGLRLSLGFFEDIYVPSHLLPS 116 (129)
Q Consensus 78 rP~~~EVl~g~V~~v~~~Gi~v~~G~~~~i~i~~~~lp~ 116 (129)
+...||++.|+|.++++.|+++.+|=.+++...++++|.
T Consensus 131 ~~~~GeIV~G~V~ri~~~~v~VDlGk~EgiLp~sE~ip~ 169 (344)
T 1hh2_P 131 SELKGTVTTAEVIRVMGEWADIRIGKLETRLPKKEWIPG 169 (344)
T ss_dssp TCCTTCEEEEEEEEECSSEEEEEETTEEEEEEGGGSCTT
T ss_pred hhcCCCEEEEEEEEEecCcEEEEeCCeEEEEeHHHcCCC
Confidence 355799999999999999999999987766666667764
No 36
>3bzc_A TEX; helix-turn-helix, helix-hairpin-helix, S1 domain, YQGF domain, transcription, RNA binding protein; 2.27A {Pseudomonas aeruginosa} SCOP: a.60.2.6 a.60.2.6 a.294.1.1 b.40.4.5 c.55.3.13 PDB: 3bzk_A 2oce_A
Probab=92.69 E-value=0.084 Score=46.73 Aligned_cols=39 Identities=15% Similarity=0.166 Sum_probs=31.6
Q ss_pred ecCCCEEEEEEEEEccCceEEEeCccceEEecCCCCCCC
Q 032987 79 PFVGEIIAAKLKESDANGLRLSLGFFEDIYVPSHLLPSP 117 (129)
Q Consensus 79 P~~~EVl~g~V~~v~~~Gi~v~~G~~~~i~i~~~~lp~~ 117 (129)
...|++++|+|++++++|+||.+|.-.+=+|+.+.|.+.
T Consensus 652 l~vG~iv~G~V~~V~~fGaFV~l~~~~eGLVhiS~Lsd~ 690 (785)
T 3bzc_A 652 LKPGMVLEGVVTNVTNFGAFVDIGVHQDGLVHISALSEK 690 (785)
T ss_dssp CCTTCBCCCEEEEEETTEEEEECSSSSEEEEETTTSCSS
T ss_pred cCCCCEEEEEEEEEecCCeEEEeCCCcEEEEEHHHcCcc
Confidence 568999999999999999999999754455566667653
No 37
>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=91.73 E-value=0.13 Score=40.72 Aligned_cols=33 Identities=12% Similarity=0.368 Sum_probs=29.6
Q ss_pred eeecCCCEEEEEEEEEccCceEEEeC-ccceEEe
Q 032987 77 FRPFVGEIIAAKLKESDANGLRLSLG-FFEDIYV 109 (129)
Q Consensus 77 frP~~~EVl~g~V~~v~~~Gi~v~~G-~~~~i~i 109 (129)
|.|..|+++.|+|+++++.|++|.+| +.+...+
T Consensus 91 Y~P~vGDvViG~Vt~V~~~~a~VdI~s~~~~~l~ 124 (308)
T 2nn6_H 91 YIGEVGDIVVGRITEVQQKRWKVETNSRLDSVLL 124 (308)
T ss_dssp CCCCSSBCCCEEEEEEETTEEEEECSSSSCEEEE
T ss_pred cCCCCCCEEEEEEEEEeCceEEEEECCCcCCcee
Confidence 78999999999999999999999999 7776543
No 38
>3psi_A Transcription elongation factor SPT6; nucleus; 3.30A {Saccharomyces cerevisiae}
Probab=90.04 E-value=0.64 Score=43.04 Aligned_cols=39 Identities=18% Similarity=0.170 Sum_probs=29.8
Q ss_pred eecCCCEEEEEEEEEccCceEEEeCc-cceEEecCCCCCCC
Q 032987 78 RPFVGEIIAAKLKESDANGLRLSLGF-FEDIYVPSHLLPSP 117 (129)
Q Consensus 78 rP~~~EVl~g~V~~v~~~Gi~v~~G~-~~~i~i~~~~lp~~ 117 (129)
....|+++.|+|++++++|+||.++. .+++ |+.+.|.+.
T Consensus 899 ~l~~G~iv~G~V~~V~~fGaFV~L~~gveGL-VHiSelsd~ 938 (1219)
T 3psi_A 899 TFFKGSIIPVRVERFWHNDIICTTNSEVECV-VNAQRHAGA 938 (1219)
T ss_dssp TSCTTCEEEEEEEEECSSCEEEECTTSCEEE-ECTTSSSST
T ss_pred hCCCCCEEEEEEEEEecceEEEEeCCCceEE-EEHHHcCCC
Confidence 45689999999999999999999864 4444 445556543
No 39
>1k0r_A NUSA; two component arrangement, S1 domain, two K-homology domains., structural genomics, PSI, protein structure initiative; 1.70A {Mycobacterium tuberculosis} SCOP: b.40.4.5 d.52.3.1 d.52.3.1 d.202.1.1
Probab=89.79 E-value=0.27 Score=39.94 Aligned_cols=40 Identities=20% Similarity=0.344 Sum_probs=34.3
Q ss_pred eeecCCCEEEEEEEE----EccCceEEEeCc----cceEEecCCCCCC
Q 032987 77 FRPFVGEIIAAKLKE----SDANGLRLSLGF----FEDIYVPSHLLPS 116 (129)
Q Consensus 77 frP~~~EVl~g~V~~----v~~~Gi~v~~G~----~~~i~i~~~~lp~ 116 (129)
|+...||++.|+|.. ++..++++.+|- .+++.-+++++|.
T Consensus 126 f~~r~GeIVtG~V~r~~~~v~~~~v~VdLG~~~~k~EgiLP~~EqiP~ 173 (366)
T 1k0r_A 126 FSTREGEIVAGVIQRDSRANARGLVVVRIGTETKASEGVIPAAEQVPG 173 (366)
T ss_dssp -CCCTTCEEEEEEECCHHHHHTTCEEEEECCSSSCEEEEECGGGSCTT
T ss_pred HHhcCCCEEEEEEEEccccccCCeEEEEeCCCccceEEEEcHHHcCCC
Confidence 567899999999999 999999999998 8877777777774
No 40
>2id0_A Exoribonuclease 2; RNAse, exonuclease, hydrolyase, mRNA decay, RNR family, hydrolase; 2.35A {Escherichia coli} SCOP: b.40.4.5 b.40.4.5 b.40.4.5 b.40.4.16 PDB: 2ix0_A* 2ix1_A
Probab=89.65 E-value=0.15 Score=43.97 Aligned_cols=46 Identities=17% Similarity=0.237 Sum_probs=34.5
Q ss_pred EEeeecCCC--EEEEEEEEEccCceEEEeC-ccceEEecCCCCC---CCCCc
Q 032987 75 VVFRPFVGE--IIAAKLKESDANGLRLSLG-FFEDIYVPSHLLP---SPSRS 120 (129)
Q Consensus 75 lvfrP~~~E--Vl~g~V~~v~~~Gi~v~~G-~~~~i~i~~~~lp---~~~~f 120 (129)
..+++..|| +.+|+|++++++|+||.+. +--+-+|+.+.|. +.+.|
T Consensus 552 ~~l~~~vGe~~~f~g~V~~V~~~G~fV~L~~~gieGlVhis~l~~~~d~~~~ 603 (644)
T 2id0_A 552 RFLKDKAGTDTRFAAEIVDISRGGMRVRLVDNGAIAFIPAPFLHAVRDELVC 603 (644)
T ss_dssp HHHGGGTTSCCCEEEEEEEEETTEEEEEETTTCCEEEEEGGGTCSCGGGEEE
T ss_pred HHhhhccCCCceEEEEEEEEeCCceEEEEcCCcEEEEEEchhccCcCceeEE
Confidence 345788899 9999999999999999993 3224666666775 34455
No 41
>2asb_A Transcription elongation protein NUSA; protein-RNA complex, transcription/RNA complex; 1.50A {Mycobacterium tuberculosis} SCOP: b.40.4.5 d.52.3.1 d.52.3.1 PDB: 2atw_A
Probab=86.95 E-value=0.56 Score=36.17 Aligned_cols=40 Identities=20% Similarity=0.344 Sum_probs=31.9
Q ss_pred eeecCCCEEEEEEEE----EccCceEEEeCc----cceEEecCCCCCC
Q 032987 77 FRPFVGEIIAAKLKE----SDANGLRLSLGF----FEDIYVPSHLLPS 116 (129)
Q Consensus 77 frP~~~EVl~g~V~~----v~~~Gi~v~~G~----~~~i~i~~~~lp~ 116 (129)
|+...||++.|+|.. +++..+++.+|- .+++.=+++++|.
T Consensus 3 ~~~r~GeIVtG~V~r~~~~v~~~~ViVdlG~~~~k~EgiLP~~Eqip~ 50 (251)
T 2asb_A 3 FSTREGEIVAGVIQRDSRANARGLVVVRIGTETKASEGVIPAAEQVPG 50 (251)
T ss_dssp -CCCTTCEEEEEEECCHHHHHTTCEEEEECSSSSCEEEEECGGGSCTT
T ss_pred hhhcCCCEEEEEEEEccccccCCeEEEEeCCCCcceEEEEcHHHcCCC
Confidence 778899999999999 899999999997 6655555556654
No 42
>2wp8_J Exosome complex exonuclease DIS3; nucleus, hydrolase, RNA-binding, exonucle binding, mitochondrion, rRNA processing; 3.00A {Saccharomyces cerevisiae}
Probab=85.82 E-value=0.37 Score=43.54 Aligned_cols=48 Identities=15% Similarity=0.064 Sum_probs=34.7
Q ss_pred EEeeecCCCEEEEEEEEEccCceEEEeCc--cceEEecCCCCC---CCCCcCCCCCC
Q 032987 75 VVFRPFVGEIIAAKLKESDANGLRLSLGF--FEDIYVPSHLLP---SPSRSEPDPYG 126 (129)
Q Consensus 75 lvfrP~~~EVl~g~V~~v~~~Gi~v~~G~--~~~i~i~~~~lp---~~~~f~~d~~~ 126 (129)
..+++. ||+.+|+|+.++++|+||.+.. +++ +|+-+.|. +.+.| |+..
T Consensus 881 ~~l~~~-ge~~~g~V~~V~~~G~fV~L~~~giEG-lVhis~L~~~~d~y~f--de~~ 933 (977)
T 2wp8_J 881 QVMRNN-ESTETGYVIKVFNNGIVVLVPKFGVEG-LIRLDNLTEDPNSAAF--DEVE 933 (977)
T ss_dssp HHHHHT-TCEEEEEEEEECSSEEEEECTTTCCEE-EEEGGGTCSCGGGCEE--ETTT
T ss_pred hhhccc-ceEEEEEEEEEcCCeEEEEEcCCCeEE-EEEeccccCCCceeEE--cccc
Confidence 345666 9999999999999999999975 454 44445553 45667 6544
No 43
>3psf_A Transcription elongation factor SPT6; nucleus; 2.59A {Saccharomyces cerevisiae}
Probab=77.79 E-value=0.45 Score=43.29 Aligned_cols=38 Identities=16% Similarity=0.121 Sum_probs=0.0
Q ss_pred eecCCCEEEEEEEEEccCceEEEeCc-cceEEecCCCCCC
Q 032987 78 RPFVGEIIAAKLKESDANGLRLSLGF-FEDIYVPSHLLPS 116 (129)
Q Consensus 78 rP~~~EVl~g~V~~v~~~Gi~v~~G~-~~~i~i~~~~lp~ 116 (129)
....|+++.|+|++++++|+||.++. .+++.+ .+.|.+
T Consensus 902 ~l~~G~iv~G~V~~V~~fGaFV~L~~gveGLVH-iSelsd 940 (1030)
T 3psf_A 902 TFFKGSIIPVRVERFWHNDIICTTNSEVECVVN-AQRHAG 940 (1030)
T ss_dssp ----------------------------------------
T ss_pred HhcCCCEEEEEEEEEccCeEEEEeCCCcEEEEE-HHHcCC
Confidence 44679999999999999999998863 344444 445544
No 44
>2bx2_L Ribonuclease E, RNAse E; RNA-binding, RNA turnover, RNA processing, hydrolase, endonu nuclease; 2.85A {Escherichia coli} PDB: 2c0b_L 2c4r_L 2vmk_A 2vrt_A 1slj_A 1smx_A 1sn8_A
Probab=67.04 E-value=5.7 Score=33.50 Aligned_cols=52 Identities=10% Similarity=0.121 Sum_probs=36.1
Q ss_pred CCceEEEEEEEEEEeeecCCCEEEEEEEEEccC--ceEEEeCccceEEecCCCC
Q 032987 63 EGASTHTVKFRLVVFRPFVGEIIAAKLKESDAN--GLRLSLGFFEDIYVPSHLL 114 (129)
Q Consensus 63 dG~~~~~V~F~alvfrP~~~EVl~g~V~~v~~~--Gi~v~~G~~~~i~i~~~~l 114 (129)
+|.........---=++..|.|..|+|+++.+. |+||.+|+=.+-|++.+.+
T Consensus 27 e~~~L~el~iE~~~~~~~vGnIY~GkV~rv~p~~~aAFVdiG~gk~gfLhisei 80 (517)
T 2bx2_L 27 DGQRLYDLDIESPGHEQKKANIYKGKITRIEPSLEAAFVDYGAERHGFLPLKEI 80 (517)
T ss_dssp ETTEEEEEEEECSSSCCCTTCEEEEEEEEEETTTTEEEEESSSSSCEEEEGGGS
T ss_pred eCCEEEEEEEecCCCcCCCCCEEEEEEEEeccCCceEEEEeCCCcEEEEEHHHc
Confidence 344444444333333567899999999999999 9999999765555554444
No 45
>2vnu_D Exosome complex exonuclease RRP44; hydrolase-RNA complex, RNA degradation, RNA-binding, RNA Pro; HET: 1PE; 2.30A {Saccharomyces cerevisiae} SCOP: b.40.4.5 b.40.4.5 b.40.4.5 b.40.4.16
Probab=66.04 E-value=1.8 Score=37.98 Aligned_cols=46 Identities=15% Similarity=0.099 Sum_probs=32.1
Q ss_pred eeecCCCEEEEEEEEEccCceEEEeCc--cceEEecCCCC---CCCCCcCCCCCC
Q 032987 77 FRPFVGEIIAAKLKESDANGLRLSLGF--FEDIYVPSHLL---PSPSRSEPDPYG 126 (129)
Q Consensus 77 frP~~~EVl~g~V~~v~~~Gi~v~~G~--~~~i~i~~~~l---p~~~~f~~d~~~ 126 (129)
++... |+.+|+|+++.++|+||.+.. +++ +|+-+.| .+.+.| |+..
T Consensus 666 l~~~~-~~~~g~V~~V~~~G~fV~l~~~giEG-lVhis~L~~~~d~~~f--d~~~ 716 (760)
T 2vnu_D 666 MRNNE-STETGYVIKVFNNGIVVLVPKFGVEG-LIRLDNLTEDPNSAAF--DEVE 716 (760)
T ss_dssp HHTCC-SEEEEEEEEEETTEEEEEETTTTEEE-EEEHHHHCSCGGGCEE--ETTT
T ss_pred hhcCc-eEEEEEEEEEECCeEEEEEeCCCcEE-EEEeccccCCCceeEE--cccc
Confidence 34555 899999999999999999975 454 4444455 335566 5543
No 46
>2nn6_G Exosome complex exonuclease RRP40; 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=56.31 E-value=11 Score=29.30 Aligned_cols=39 Identities=10% Similarity=0.198 Sum_probs=31.3
Q ss_pred eeecCCCEEEEEEEEEccCceEEEeCccceEEecCCCCC
Q 032987 77 FRPFVGEIIAAKLKESDANGLRLSLGFFEDIYVPSHLLP 115 (129)
Q Consensus 77 frP~~~EVl~g~V~~v~~~Gi~v~~G~~~~i~i~~~~lp 115 (129)
|.|..|.++.|+|++++.....|.++.-....+|...++
T Consensus 123 YiP~vGDiVIG~Vt~v~~~~~~VdI~s~~~a~L~~~~f~ 161 (289)
T 2nn6_G 123 YVPVKGDHVIGIVTAKSGDIFKVDVGGSEPASLSYLSFE 161 (289)
T ss_dssp CCCCSSEEEEEEEEEEETTEEEEECSSSSCCCEESCSSS
T ss_pred CCCCCCCEEEEEEEEEeCcEEEEEECCCceeEEehhhcC
Confidence 789999999999999999999999975434455555444
No 47
>2ovm_B NCOR, progesterone receptor; nuclear receptor, steroid receptor, CO-repressor, asoprisnil, transcription; HET: AS0; 2.60A {Homo sapiens}
Probab=29.55 E-value=38 Score=16.75 Aligned_cols=18 Identities=28% Similarity=0.370 Sum_probs=12.8
Q ss_pred CCCCCCCHHHHHHHHHHHHh
Q 032987 15 PHLLRLPLNEAIKLELENVF 34 (129)
Q Consensus 15 P~~~~~~~~~~i~~~L~~k~ 34 (129)
++.+| ++..|.+.|.-+|
T Consensus 8 ~~~~g--leaiirkalmg~y 25 (26)
T 2ovm_B 8 ASNLG--LEDIIRKALMGSF 25 (26)
T ss_pred ccccC--HHHHHHHHHhhcc
Confidence 34444 8888888887766
No 48
>3d0f_A Penicillin-binding 1 transmembrane protein MRCA; BIG_1156.2, STR genomics, PSI-2, protein structure initiative; 1.64A {Nitrosomonas europaea atcc 19718}
Probab=28.15 E-value=75 Score=20.21 Aligned_cols=37 Identities=16% Similarity=0.044 Sum_probs=28.1
Q ss_pred ecCCCEEEEEEEEEccCceEEEeCccceEEecCCCCC
Q 032987 79 PFVGEIIAAKLKESDANGLRLSLGFFEDIYVPSHLLP 115 (129)
Q Consensus 79 P~~~EVl~g~V~~v~~~Gi~v~~G~~~~i~i~~~~lp 115 (129)
|-.++..-|.|+++++.++.+.++-=+.+.+|.+.|.
T Consensus 31 ~~~~~~~~AvV~~v~~~~~~v~~~~g~~~~l~~~~~~ 67 (106)
T 3d0f_A 31 GNSDDILAAVVLSATPGAVEAFRKNGETIRITGDGLK 67 (106)
T ss_dssp CTTTTCEEEEEEEEETTEEEEEETTSCEEEECGGGGS
T ss_pred CccCCeEEEEEEEeCCCeEEEEEcCCCeEEEcHHHCh
Confidence 4457888999999999999988854345677776654
No 49
>3fhd_A ORF 37; enase like PD-(D/E)XK superfamily, hydrolase; 1.85A {Human herpesvirus 8 type M} PDB: 3pov_A*
Probab=25.00 E-value=35 Score=28.71 Aligned_cols=46 Identities=17% Similarity=0.139 Sum_probs=25.6
Q ss_pred CCCCCCCCHHHHHHHHHHHHhc--CeEeCCeeEEEEEE-Eeeeee-ceeE
Q 032987 14 PPHLLRLPLNEAIKLELENVFL--DKVIANLGLCISIY-DIKEIE-GGFV 59 (129)
Q Consensus 14 ~P~~~~~~~~~~i~~~L~~k~~--gk~~~~~G~~I~v~-~i~~i~-~g~I 59 (129)
+|-.+|...+..+++.+.+.++ +..+.++|+.+.-. .+.-.| ||.+
T Consensus 197 ~AM~fG~~~E~~AK~li~~~i~~~~~~V~dCGL~Isp~~Gl~GASPD~l~ 246 (508)
T 3fhd_A 197 GPLAFGLRCEEVVKTLLATLLHPDETNCLDYGFMQSPQNGIFGVSLDFAA 246 (508)
T ss_dssp -----CHHHHHHHHHHHHHHTCTTSCEECCCCCEECTTTSSEEECCSEEE
T ss_pred HHHHHhHhhHHHHHHHHHHHhhcCCCeeeeeeeeEeCCCCcceEcCCeEE
Confidence 5677888888888775555443 23456799988765 444432 4444
No 50
>3ee1_A Effector protein VIRA; beta barrels, six-stranded beta barrel, hydrolase, protease, secreted, thiol protease, virulence; 3.01A {Shigella flexneri}
Probab=23.52 E-value=90 Score=23.96 Aligned_cols=53 Identities=21% Similarity=0.241 Sum_probs=28.9
Q ss_pred HHHHHHHHHHHHhcCeEeCCeeEEEEEEEeeeeeceeEEeCCCceEEEEEEEEE
Q 032987 22 LNEAIKLELENVFLDKVIANLGLCISIYDIKEIEGGFVYPGEGASTHTVKFRLV 75 (129)
Q Consensus 22 ~~~~i~~~L~~k~~gk~~~~~G~~I~v~~i~~i~~g~I~~gdG~~~~~V~F~al 75 (129)
+.+.|..+|+-.=+-|++.++|-+|.+..+.--.+-.|. .+|+--|+|.=..+
T Consensus 297 msenienrlnfmpeqrvinncghiikinavvpkndtais-asggrayevsssil 349 (400)
T 3ee1_A 297 MSENIENRLNFMPEQRVINNCGHIIKINAVVPKNDTAIS-ASGGRAYEVSSSIL 349 (400)
T ss_dssp HHHHHHHHHHHCCC----CCCCEEEEEEEECC-----------CCEEEEEEEEC
T ss_pred HHHhHHhhhccChHhhhhhcCCceEEEeeeecCCCceee-ccCCceeeeecccc
Confidence 345677777777788999999999999888766666664 45666667765544
No 51
>3eb8_A Cysteine protease-like VIRA; beta sheet, alpha helix, hydrolase, secreted, THIO protease, virulence; 2.40A {Shigella flexneri} PDB: 4fmb_A*
Probab=21.84 E-value=86 Score=23.77 Aligned_cols=54 Identities=20% Similarity=0.225 Sum_probs=30.9
Q ss_pred HHHHHHHHHHHHhcCeEeCCeeEEEEEEEeeeeeceeEEeCCCceEEEEEEEEEE
Q 032987 22 LNEAIKLELENVFLDKVIANLGLCISIYDIKEIEGGFVYPGEGASTHTVKFRLVV 76 (129)
Q Consensus 22 ~~~~i~~~L~~k~~gk~~~~~G~~I~v~~i~~i~~g~I~~gdG~~~~~V~F~alv 76 (129)
+.+.|..+|+-.=+-+++.++|-+|.+..+.--.+-.|. .+|+--|+|.=..+-
T Consensus 255 msenienrlnfmpeqrvinncghiikinavvpkndtais-asggrayevsssilp 308 (358)
T 3eb8_A 255 MSENIENRLNFMPEQRVINNCGHIIKINAVVPKNDTAIS-ASGGRAYEVSSSILP 308 (358)
T ss_dssp HHHHHHHHHHHCSSCCCCSEEEEEEEEEEC--------------CCEEEEEEEEE
T ss_pred HHHhHHhhhccChHhhhhhcCCceEEEeeeecCCCceee-ccCCceEeeeccccc
Confidence 345677777777788999999999999888766666664 455555666655543
No 52
>2l55_A SILB,silver efflux protein, MFP component of the components proton antiporter metal...; APO form, AG(I)-binding site; NMR {Cupriavidus metallidurans}
Probab=21.41 E-value=68 Score=19.93 Aligned_cols=22 Identities=5% Similarity=0.116 Sum_probs=19.3
Q ss_pred EEEEEEEEccCceEEEeCccce
Q 032987 85 IAAKLKESDANGLRLSLGFFED 106 (129)
Q Consensus 85 l~g~V~~v~~~Gi~v~~G~~~~ 106 (129)
..|+|.+++...+.++-||+.+
T Consensus 6 ~~G~V~~vd~~~iTi~H~pI~~ 27 (82)
T 2l55_A 6 AVGRIQSIGERSLIIAHEAIPS 27 (82)
T ss_dssp EEEEEEECCSSEEEEEECCCTT
T ss_pred EeEEEEEEccccEEEecCCccc
Confidence 4899999999999899999864
Done!