Query 034463
Match_columns 94
No_of_seqs 105 out of 1045
Neff 5.7
Searched_HMMs 29240
Date Mon Mar 25 04:29:20 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/034463.a3m -d /work/01045/syshi/HHdatabase/pdb70.hhm -o /work/01045/syshi/hhsearch_pdb/034463hhsearch_pdb -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 3s6n_E Small nuclear ribonucle 99.9 1E-24 3.6E-29 142.2 3.1 74 4-93 18-91 (92)
2 1b34_B Protein (small nuclear 99.9 1.8E-23 6.3E-28 141.0 3.6 85 5-94 30-114 (118)
3 4emg_A Probable U6 snRNA-assoc 99.8 4.2E-21 1.4E-25 125.0 6.6 74 14-93 19-92 (93)
4 4emk_A U6 snRNA-associated SM- 99.8 7.7E-20 2.6E-24 119.6 8.9 69 5-93 23-91 (94)
5 3bw1_A SMX4 protein, U6 snRNA- 99.8 9.2E-20 3.1E-24 119.0 8.5 65 21-94 24-88 (96)
6 1d3b_B Protein (small nuclear 99.8 4.2E-19 1.5E-23 114.1 8.5 67 21-93 18-84 (91)
7 1ljo_A Archaeal SM-like protei 99.8 4.4E-20 1.5E-24 115.7 3.6 68 5-93 8-76 (77)
8 1i4k_A Putative snRNP SM-like 99.8 5.2E-19 1.8E-23 110.5 8.0 60 15-93 15-74 (77)
9 1n9r_A SMF, small nuclear ribo 99.8 5.5E-19 1.9E-23 115.1 8.1 68 7-93 22-92 (93)
10 2fwk_A U6 snRNA-associated SM- 99.8 1.6E-19 5.6E-24 122.2 5.3 70 22-93 41-113 (121)
11 1mgq_A SM-like protein; LSM, R 99.8 8.5E-19 2.9E-23 111.5 8.2 64 7-91 20-83 (83)
12 1h64_1 SnRNP SM-like protein; 99.8 9.9E-19 3.4E-23 108.9 8.3 57 21-93 18-74 (75)
13 4emk_C U6 snRNA-associated SM- 99.8 7.6E-19 2.6E-23 118.0 8.2 60 27-93 41-100 (113)
14 1i8f_A Putative snRNP SM-like 99.8 1.6E-18 5.4E-23 109.7 8.1 65 7-93 16-80 (81)
15 1th7_A SnRNP-2, small nuclear 99.8 1.9E-18 6.5E-23 109.2 8.0 57 21-93 23-79 (81)
16 3s6n_G Small nuclear ribonucle 99.8 1.6E-18 5.3E-23 108.7 7.3 57 23-93 18-74 (76)
17 3s6n_F Small nuclear ribonucle 99.8 5.7E-19 1.9E-23 113.3 5.2 61 14-93 16-76 (86)
18 3pgw_B SM B; protein-RNA compl 99.7 8.8E-18 3E-22 124.8 9.1 61 27-91 22-82 (231)
19 4emk_B U6 snRNA-associated SM- 99.7 4.5E-18 1.5E-22 106.2 6.0 57 21-93 18-74 (75)
20 1b34_A Protein (small nuclear 99.7 4.2E-18 1.4E-22 115.0 5.4 67 8-93 4-72 (119)
21 4emh_A Probable U6 snRNA-assoc 99.7 1.2E-17 4E-22 111.1 7.3 62 14-93 26-87 (105)
22 1d3b_A Protein (small nuclear 99.7 9.4E-17 3.2E-21 100.5 7.3 57 23-93 19-75 (75)
23 1m5q_A SMAP3, small nuclear ri 99.6 6.3E-16 2.2E-20 106.1 6.2 53 21-93 14-66 (130)
24 2y9a_D Small nuclear ribonucle 99.5 1.9E-14 6.7E-19 98.2 7.0 59 21-93 17-75 (126)
25 3sb2_A Protein HFQ; SM-like, R 95.8 0.0058 2E-07 38.4 2.7 33 9-46 15-47 (79)
26 1u1s_A HFQ protein; SM-like ba 95.8 0.0091 3.1E-07 37.8 3.5 35 10-49 15-49 (82)
27 2qtx_A Uncharacterized protein 95.7 0.011 3.8E-07 36.5 3.5 35 10-49 21-55 (71)
28 2ylb_A Protein HFQ; RNA-bindin 95.6 0.0059 2E-07 37.9 2.2 34 10-48 17-50 (74)
29 2y90_A Protein HFQ; RNA-bindin 95.3 0.011 3.8E-07 38.9 2.7 36 9-49 16-51 (104)
30 3ahu_A Protein HFQ; SM-like mo 95.1 0.024 8.3E-07 35.5 3.7 34 11-49 20-53 (78)
31 1kq1_A HFQ, HOST factor for Q 95.0 0.02 7E-07 35.7 3.2 37 9-50 14-50 (77)
32 1y96_A Gemin6, SIP2, GEM-assoc 92.4 0.24 8.2E-06 31.4 4.7 24 27-50 25-49 (86)
33 3hfo_A SSR3341 protein; HFQ, S 86.8 0.42 1.4E-05 29.2 2.4 35 9-48 16-50 (70)
34 3hfn_A ASL2047 protein; HFQ, S 83.2 1.1 3.8E-05 27.4 3.1 34 9-47 18-51 (72)
35 1x4r_A PARP14 protein; WWE dom 50.8 0.94 3.2E-05 29.3 -2.6 25 22-51 28-52 (99)
36 2fb7_A SM-like protein, LSM-14 35.0 86 0.003 19.9 6.7 63 21-88 21-84 (95)
37 1ycy_A Conserved hypothetical 23.1 1.3E+02 0.0044 18.0 4.3 27 27-54 24-50 (71)
38 1nvp_D Transcription initiatio 21.9 1.2E+02 0.004 19.5 3.8 25 28-52 53-80 (108)
No 1
>3s6n_E Small nuclear ribonucleoprotein E; SMN complex, SMN-gemin2 complex, U-rich snRNA, SM fold, SM C SNRNPS, snRNP biogenesis, PRE-mRNA splicing; 2.50A {Homo sapiens} PDB: 2y9b_E 2y9c_E 2y9d_E 3cw1_E 3pgw_E* 2y9a_E
Probab=99.90 E-value=1e-24 Score=142.17 Aligned_cols=74 Identities=20% Similarity=0.526 Sum_probs=66.0
Q ss_pred EEEEeeeeeCcceEEEEEEEEEecCCEEEEEEEeeecCeeceEeeceEEeeeecCCCCCCccccccceeeEeeCeEEEeC
Q 034463 4 IQIRFSFRNSQTTLMLFCFWALEFIVLQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRG 83 (94)
Q Consensus 4 ~~~~~~~~~~~~~i~~l~~~l~~~~~r~~~G~L~gfD~hmNLVL~d~~E~~~~~~~~~~~~~~~k~~~~~r~lG~v~iRG 83 (94)
++++++|++++.+| ++|+.+++||+++|+|+|||+||||+|+||+|++.. . .+++++|.++|||
T Consensus 18 l~lL~~~l~~~v~V---~l~~~~~~gr~~~G~L~gfD~~mNlvL~d~~E~~~~---~----------~~~~~lg~v~iRG 81 (92)
T 3s6n_E 18 INLIFRYLQNRSRI---QVWLYEQVNMRIEGCIIGFDEYMNLVLDDAEEIHSK---T----------KSRKQLGRIMLKG 81 (92)
T ss_dssp HHHHHHHHHHTCEE---EEEESSSCSSEEEEEEEEECTTCCEEEEEEEEECSS---S----------CCEEEEEEEEECG
T ss_pred HHHHHHHhCCCEEE---EEEEEecCCEEEEEEEEEEcCcCcEEEeeeEEEecC---C----------CceeEcCeEEEeC
Confidence 56789999999999 999999999999999999999999999999998642 1 1367899999999
Q ss_pred CeEEEEEeCC
Q 034463 84 DSVIIVLRNP 93 (94)
Q Consensus 84 dnVv~I~~~~ 93 (94)
+||++|+|.+
T Consensus 82 ~nV~~i~~~~ 91 (92)
T 3s6n_E 82 DNITLLQSVS 91 (92)
T ss_dssp GGEEEEEEC-
T ss_pred CEEEEEEeCC
Confidence 9999999986
No 2
>1b34_B Protein (small nuclear ribonucleoprotein SM D2); snRNP, splicing, spliceosome, core snRNP domain, systemi erythematosus, SLE, RNA binding protein; 2.50A {Homo sapiens} SCOP: b.38.1.1 PDB: 2y9a_C 2y9b_C 2y9c_C 2y9d_C 3cw1_C 3pgw_Y* 3s6n_B
Probab=99.87 E-value=1.8e-23 Score=141.02 Aligned_cols=85 Identities=65% Similarity=0.995 Sum_probs=58.8
Q ss_pred EEEeeeeeCcceEEEEEEEEEecCCEEEEEEEeeecCeeceEeeceEEeeeecCCCCCCccccccceeeEeeCeEEEeCC
Q 034463 5 QIRFSFRNSQTTLMLFCFWALEFIVLQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGD 84 (94)
Q Consensus 5 ~~~~~~~~~~~~i~~l~~~l~~~~~r~~~G~L~gfD~hmNLVL~d~~E~~~~~~~~~~~~~~~k~~~~~r~lG~v~iRGd 84 (94)
++++++++++.+| .+++ ++||++.|+|+|||+||||||+||+|++...+++.++.+..+..+++|++|+++||||
T Consensus 30 ~lL~~~~~~~k~V---~V~L--k~gr~~~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~ 104 (118)
T 1b34_B 30 SVLTQSVKNNTQV---LINC--RNNKKLLGRVKAFDRHCNMVLENVKEMWTEVPKSGKGKKKSKPVNKDRYISKMFLRGD 104 (118)
T ss_dssp HHHHHHHHHTCEE---EEEE--TTSCEEEEEEEEECTTCCEEEEEEEEC-------------------CEEEEEEEECGG
T ss_pred HHHHHHhcCCcEE---EEEE--CCCcEEEEEEEEeCCceEEEEeCEEEEEecccccccccccccccccccCcCeEEEcCC
Confidence 3455666667788 8888 8899999999999999999999999998654332222111122334688999999999
Q ss_pred eEEEEEeCCC
Q 034463 85 SVIIVLRNPK 94 (94)
Q Consensus 85 nVv~I~~~~~ 94 (94)
||++|+++|+
T Consensus 105 nVv~I~~~~~ 114 (118)
T 1b34_B 105 SVIVVLRNPL 114 (118)
T ss_dssp GEEEEEECCC
T ss_pred EEEEEEeCch
Confidence 9999999874
No 3
>4emg_A Probable U6 snRNA-associated SM-like protein LSM3; SM fold, mRNA decay, LSM proteins, RNA binding protein; 2.70A {Schizosaccharomyces pombe}
Probab=99.84 E-value=4.2e-21 Score=124.96 Aligned_cols=74 Identities=27% Similarity=0.341 Sum_probs=53.5
Q ss_pred cceEEEEEEEEEecCCEEEEEEEeeecCeeceEeeceEEeeeecCCCCCCccccccceeeEeeCeEEEeCCeEEEEEeCC
Q 034463 14 QTTLMLFCFWALEFIVLQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVLRNP 93 (94)
Q Consensus 14 ~~~i~~l~~~l~~~~~r~~~G~L~gfD~hmNLVL~d~~E~~~~~~~~~~~~~~~k~~~~~r~lG~v~iRGdnVv~I~~~~ 93 (94)
+.++ .+.+ ++||++.|+|+|||+||||+|+||+|++...+++++..+ .+...++|++|+++||||||++|+|+.
T Consensus 19 ~~~V---~V~l--~~gr~~~G~L~~~D~~mNlvL~d~~E~~~~~~~~~~~~~-~~~~~~~r~lG~v~iRG~nVv~I~p~~ 92 (93)
T 4emg_A 19 DEIV---YVKL--RGDRELNGRLHAYDEHLNMVLGDAEEIVTIFDDEETDKD-KALKTIRKHYEMLFVRGDSVILIAPPR 92 (93)
T ss_dssp TSEE---EEEE--TTTEEEEEEEEEECTTCCEEEEEEEEEEC---------------CEEEEEEEEEECGGGEEEEECCC
T ss_pred CCEE---EEEE--CCCcEEEEEEEEECCcccEEeecEEEEEeccccCCcccc-ccccccEeEeceEEECCCeEEEEEecC
Confidence 4566 6666 889999999999999999999999999876443321100 001124689999999999999999974
No 4
>4emk_A U6 snRNA-associated SM-like protein LSM5; SM fold, mRNA decay and PRE-mRNA splicing, LSM proteins, RNA protein; 2.30A {Schizosaccharomyces pombe} PDB: 3swn_A
Probab=99.81 E-value=7.7e-20 Score=119.62 Aligned_cols=69 Identities=23% Similarity=0.318 Sum_probs=56.5
Q ss_pred EEEeeeeeCcceEEEEEEEEEecCCEEEEEEEeeecCeeceEeeceEEeeeecCCCCCCccccccceeeEeeCeEEEeCC
Q 034463 5 QIRFSFRNSQTTLMLFCFWALEFIVLQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGD 84 (94)
Q Consensus 5 ~~~~~~~~~~~~i~~l~~~l~~~~~r~~~G~L~gfD~hmNLVL~d~~E~~~~~~~~~~~~~~~k~~~~~r~lG~v~iRGd 84 (94)
+++++|+++ ++|+..++||+++|+|+|||+||||+|+||+|++.. . .+++.+|+++|||+
T Consensus 23 ~lL~~~l~k-------~V~V~Lk~gr~~~G~L~gfD~~mNlvL~d~~E~~~~---~----------~~~~~lg~v~IRG~ 82 (94)
T 4emk_A 23 ELIDKCIGS-------NLWVIMKSEREFAGTLVGFDDYVNIVLKDVTEYDTV---T----------GVTEKHSEMLLNGN 82 (94)
T ss_dssp HHHHHTTTS-------EEEEEESSSEEEEEEEEEECTTCCEEEEEEEEEETT---T----------CCEEEEEEEEECST
T ss_pred HHHHHHcCC-------eEEEEECCCcEEEEEEEEEcccCCeEeeeEEEEecC---C----------CcEeEcCEEEEcCC
Confidence 455666664 456666999999999999999999999999998731 1 13678999999999
Q ss_pred eEEEEEeCC
Q 034463 85 SVIIVLRNP 93 (94)
Q Consensus 85 nVv~I~~~~ 93 (94)
||++|+|..
T Consensus 83 nI~~i~p~~ 91 (94)
T 4emk_A 83 GMCMLIPGG 91 (94)
T ss_dssp TEEEEEECC
T ss_pred EEEEEEeCC
Confidence 999999975
No 5
>3bw1_A SMX4 protein, U6 snRNA-associated SM-like protein LSM3; RNA-binding protein, SM protein, ring, HOMO octamer, mRNA processing; 2.50A {Saccharomyces cerevisiae}
Probab=99.81 E-value=9.2e-20 Score=119.02 Aligned_cols=65 Identities=28% Similarity=0.447 Sum_probs=52.7
Q ss_pred EEEEEecCCEEEEEEEeeecCeeceEeeceEEeeeecCCCCCCccccccceeeEeeCeEEEeCCeEEEEEeCCC
Q 034463 21 CFWALEFIVLQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVLRNPK 94 (94)
Q Consensus 21 ~~~l~~~~~r~~~G~L~gfD~hmNLVL~d~~E~~~~~~~~~~~~~~~k~~~~~r~lG~v~iRGdnVv~I~~~~~ 94 (94)
.+.+ ++||++.|+|+|||+||||||+||+|++...++++. ...+|.+|+++|||+||++|+|++.
T Consensus 24 ~V~L--k~gr~~~G~L~~fD~~mNlVL~d~~E~~~~~~~~~~-------~~~~r~lG~v~IRG~nVv~I~~~d~ 88 (96)
T 3bw1_A 24 YIKL--RGARTLVGTLQAFDSHCNIVLSDAVETIYQLNNEEL-------SESERRCEMVFIRGDTVTLISTPSE 88 (96)
T ss_dssp EEEE--GGGCEEEEEEEEECTTCCEEEEEEEEEEECCSTTCC-------CEEEEEEEEEEECGGGEEEEECCC-
T ss_pred EEEE--CCCcEEEEEEEEECCCCcEEEcCEEEEecccccccc-------CcceeEcCEEEECCCEEEEEEecCc
Confidence 4444 889999999999999999999999999875432211 1246899999999999999999863
No 6
>1d3b_B Protein (small nuclear ribonucleoprotein associat B); snRNP, splicing, core snRNP domain, systemic lupus eryth SLE, RNA binding protein; HET: CIT; 2.00A {Homo sapiens} SCOP: b.38.1.1 PDB: 2y9a_A 2y9b_A 2y9c_A 2y9d_A
Probab=99.79 E-value=4.2e-19 Score=114.10 Aligned_cols=67 Identities=22% Similarity=0.347 Sum_probs=51.8
Q ss_pred EEEEEecCCEEEEEEEeeecCeeceEeeceEEeeeecCCCCCCccccccceeeEeeCeEEEeCCeEEEEEeCC
Q 034463 21 CFWALEFIVLQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVLRNP 93 (94)
Q Consensus 21 ~~~l~~~~~r~~~G~L~gfD~hmNLVL~d~~E~~~~~~~~~~~~~~~k~~~~~r~lG~v~iRGdnVv~I~~~~ 93 (94)
.+.+ ++||++.|+|+|||+||||+|+||+|++...+.+.+. +...++|.+|+++|||+||++|+++.
T Consensus 18 ~V~l--~~gr~~~G~L~~~D~~mNlvL~d~~E~~~~~~~~~~~----~~~~~~~~lg~v~iRG~~I~~i~~~~ 84 (91)
T 1d3b_B 18 RCIL--QDGRIFIGTFKAFDKHMNLILCDCDEFRKIKPKNSKQ----AEREEKRVLGLVLLRGENLVSMTVEG 84 (91)
T ss_dssp EEEE--TTCCEEEEEEEECCTTCCEEEEEEEEEEEECCSSTTS----CCEEEEEEEEEEEECGGGEEEEEEEE
T ss_pred EEEE--CCCeEEEEEEEEECCCCeEEecCEEEEeecccccccc----ccCccEeECCEEEECCCeEEEEEcCC
Confidence 4444 8899999999999999999999999987543321110 01235789999999999999998753
No 7
>1ljo_A Archaeal SM-like protein AF-SM2; snRNP, core snRNP domain, RNA binding protein, unknown F; 1.95A {Archaeoglobus fulgidus} SCOP: b.38.1.1
Probab=99.79 E-value=4.4e-20 Score=115.65 Aligned_cols=68 Identities=25% Similarity=0.282 Sum_probs=54.2
Q ss_pred EEEeeeeeCcceEEEEEEEEEecCC-EEEEEEEeeecCeeceEeeceEEeeeecCCCCCCccccccceeeEeeCeEEEeC
Q 034463 5 QIRFSFRNSQTTLMLFCFWALEFIV-LQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRG 83 (94)
Q Consensus 5 ~~~~~~~~~~~~i~~l~~~l~~~~~-r~~~G~L~gfD~hmNLVL~d~~E~~~~~~~~~~~~~~~k~~~~~r~lG~v~iRG 83 (94)
+.++++++++ + .+.+ +.| +++.|+|.|||+|||++|+||+|++.. .+++++|.++|||
T Consensus 8 ~~L~~~~~~~--v---~V~l--k~g~~~~~G~L~~~D~~mNlvL~d~~e~~~~--------------~~~~~lg~v~iRG 66 (77)
T 1ljo_A 8 QMVKSMVGKI--I---RVEM--KGEENQLVGKLEGVDDYMNLYLTNAMECKGE--------------EKVRSLGEIVLRG 66 (77)
T ss_dssp HHHHHTTTSE--E---EEEE--TTCSSEEEEEEEEECTTCCEEEEEEEEEETT--------------EEEEEEEEEEECG
T ss_pred HHHHHHCCCE--E---EEEE--eCCCEEEEEEEEEECCcceEEEeeEEEEecC--------------CcEeECCeEEEeC
Confidence 3455566543 3 3344 889 999999999999999999999998731 1467899999999
Q ss_pred CeEEEEEeCC
Q 034463 84 DSVIIVLRNP 93 (94)
Q Consensus 84 dnVv~I~~~~ 93 (94)
+||++|+++.
T Consensus 67 ~nI~~i~~~d 76 (77)
T 1ljo_A 67 NNVVLIQPQE 76 (77)
T ss_dssp GGEEEEEEC-
T ss_pred CeEEEEEeCC
Confidence 9999999975
No 8
>1i4k_A Putative snRNP SM-like protein; core snRNP domain, RNA binding protein; HET: CIT; 2.50A {Archaeoglobus fulgidus} SCOP: b.38.1.1 PDB: 1i5l_A*
Probab=99.78 E-value=5.2e-19 Score=110.51 Aligned_cols=60 Identities=23% Similarity=0.358 Sum_probs=52.2
Q ss_pred ceEEEEEEEEEecCCEEEEEEEeeecCeeceEeeceEEeeeecCCCCCCccccccceeeEeeCeEEEeCCeEEEEEeCC
Q 034463 15 TTLMLFCFWALEFIVLQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVLRNP 93 (94)
Q Consensus 15 ~~i~~l~~~l~~~~~r~~~G~L~gfD~hmNLVL~d~~E~~~~~~~~~~~~~~~k~~~~~r~lG~v~iRGdnVv~I~~~~ 93 (94)
.++ .+++ ++|+++.|+|.|||+|||++|+||+|++.. .+++++|+++|||+||++|++++
T Consensus 15 ~~V---~V~L--~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~--------------~~~~~lg~v~iRG~~I~~i~~~d 74 (77)
T 1i4k_A 15 SPV---IVRL--KGGREFRGTLDGYDIHMNLVLLDAEEIQNG--------------EVVRKVGSVVIRGDTVVFVSPAP 74 (77)
T ss_dssp SEE---EEEE--TTSCEEEEEEEEECTTCCEEEEEEEEEETT--------------EEEEEEEEEEECGGGEEEEEECC
T ss_pred CEE---EEEE--cCCCEEEEEEEEEcCCCCeEEeeEEEEecC--------------CcEeECCEEEECCCEEEEEEeCC
Confidence 455 6777 779999999999999999999999998742 14678999999999999999976
No 9
>1n9r_A SMF, small nuclear ribonucleoprotein F, snRNP-F, SM protein F; heptamer, translation; 2.80A {Saccharomyces cerevisiae} SCOP: b.38.1.1 PDB: 1n9s_A
Probab=99.78 E-value=5.5e-19 Score=115.07 Aligned_cols=68 Identities=15% Similarity=0.204 Sum_probs=54.7
Q ss_pred EeeeeeC--cceEEEEEEEEEecCC-EEEEEEEeeecCeeceEeeceEEeeeecCCCCCCccccccceeeEeeCeEEEeC
Q 034463 7 RFSFRNS--QTTLMLFCFWALEFIV-LQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRG 83 (94)
Q Consensus 7 ~~~~~~~--~~~i~~l~~~l~~~~~-r~~~G~L~gfD~hmNLVL~d~~E~~~~~~~~~~~~~~~k~~~~~r~lG~v~iRG 83 (94)
..+||++ +.+| .+++ +.| +++.|+|.|||+|||++|+||+|++.. .+++++|.++|||
T Consensus 22 P~~~L~~~i~k~V---~V~L--k~g~~~~~G~L~~~D~~MNlvL~d~~E~~~~--------------~~~~~lg~v~IRG 82 (93)
T 1n9r_A 22 PKPFLKGLVNHRV---GVKL--KFNSTEYRGTLVSTDNYFNLQLNEAEEFVAG--------------VSHGTLGEIFIRC 82 (93)
T ss_dssp ----CGGGTTSEE---EEEE--SSTTEEEEEEEEECCTTTCEEEEEEEEEETT--------------EEEEECCSEEECG
T ss_pred hHHHHHHhCCCEE---EEEE--cCCCEEEEEEEEEEccccEEEEeeEEEEcCC--------------CeEeEcCEEEEcC
Confidence 3455555 5677 7888 678 999999999999999999999998621 1357899999999
Q ss_pred CeEEEEEeCC
Q 034463 84 DSVIIVLRNP 93 (94)
Q Consensus 84 dnVv~I~~~~ 93 (94)
+||++|++++
T Consensus 83 ~nI~~I~~~~ 92 (93)
T 1n9r_A 83 NNVLYIRELP 92 (93)
T ss_dssp GGEEEEEECC
T ss_pred CeEEEEEeCC
Confidence 9999999976
No 10
>2fwk_A U6 snRNA-associated SM-like protein LSM5; structural genomics, structural genomics consortium, SGC, DNA binding protein; 2.14A {Cryptosporidium parvum} SCOP: b.38.1.1 PDB: 3pgg_A
Probab=99.78 E-value=1.6e-19 Score=122.18 Aligned_cols=70 Identities=23% Similarity=0.305 Sum_probs=51.1
Q ss_pred EEEEecCCEEEEEEEeeecCeeceEeeceEEeeeecCCCC---CCccccccceeeEeeCeEEEeCCeEEEEEeCC
Q 034463 22 FWALEFIVLQLLGRVRAFDRHCNMVLENVREMWTELPKTG---KGKKKALPVNKDRFISKMFLRGDSVIIVLRNP 93 (94)
Q Consensus 22 ~~l~~~~~r~~~G~L~gfD~hmNLVL~d~~E~~~~~~~~~---~~~~~~k~~~~~r~lG~v~iRGdnVv~I~~~~ 93 (94)
+|+.-++||++.|+|+|||+||||||+||+|++...++++ ++.+ +..+++|.+|+++|||+||++|++.+
T Consensus 41 V~V~Lk~Gr~~~G~L~~fD~~mNlVL~d~~E~~~~~~~~~~~~~g~~--~~~~~~r~lG~v~IRG~nVv~I~~~~ 113 (121)
T 2fwk_A 41 IYVVMKGDKEFSGVLRGFDEYVNMVLDDVQEYGFKADEEDISGGNKK--LKRVMVNRLETILLSGNNVAMLVPGG 113 (121)
T ss_dssp CEEEETTTEEECCEEEEECTTCCEEEESCCEEEC-----------------CEECCCCSEEEECGGGEEEEESSS
T ss_pred EEEEECCCcEEEEEEEEEcccCCeEeceEEEEEeccccccccccCcc--cccccceEcceEEECCCEEEEEEecC
Confidence 4556699999999999999999999999999986422111 1100 00122678999999999999999875
No 11
>1mgq_A SM-like protein; LSM, RNA-binding, archea, RNA binding protein; 1.70A {Methanothermobacterthermautotrophicus} SCOP: b.38.1.1 PDB: 1i81_A 1loj_A* 1jbm_A 1jri_A
Probab=99.78 E-value=8.5e-19 Score=111.48 Aligned_cols=64 Identities=20% Similarity=0.294 Sum_probs=53.3
Q ss_pred EeeeeeCcceEEEEEEEEEecCCEEEEEEEeeecCeeceEeeceEEeeeecCCCCCCccccccceeeEeeCeEEEeCCeE
Q 034463 7 RFSFRNSQTTLMLFCFWALEFIVLQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSV 86 (94)
Q Consensus 7 ~~~~~~~~~~i~~l~~~l~~~~~r~~~G~L~gfD~hmNLVL~d~~E~~~~~~~~~~~~~~~k~~~~~r~lG~v~iRGdnV 86 (94)
+.+++. .++ .+++ ++|+++.|+|.|||+|||++|+||+|++.. .+.+++|+++|||+||
T Consensus 20 L~~~~~--~~V---~V~L--k~g~~~~G~L~~~D~~mNlvL~d~~e~~~~--------------~~~~~lg~v~IRG~~I 78 (83)
T 1mgq_A 20 LGNSLN--SPV---IIKL--KGDREFRGVLKSFDLHMNLVLNDAEELEDG--------------EVTRRLGTVLIRGDNI 78 (83)
T ss_dssp HHHTTT--SEE---EEEE--TTTEEEEEEEEEECTTCCEEEEEEEEEETT--------------EEEEEEEEEEECGGGE
T ss_pred HHHhCC--CEE---EEEE--cCCcEEEEEEEEECCCceeEEccEEEEecC--------------CcccCCCEEEECCCEE
Confidence 344553 356 7777 779999999999999999999999998742 1468899999999999
Q ss_pred EEEEe
Q 034463 87 IIVLR 91 (94)
Q Consensus 87 v~I~~ 91 (94)
++|+|
T Consensus 79 ~~i~p 83 (83)
T 1mgq_A 79 VYISP 83 (83)
T ss_dssp EEEEC
T ss_pred EEEEC
Confidence 99987
No 12
>1h64_1 SnRNP SM-like protein; SM fold, spliceosome, snRNP core; 1.9A {Pyrococcus abyssi} SCOP: b.38.1.1 PDB: 1m8v_A*
Probab=99.78 E-value=9.9e-19 Score=108.86 Aligned_cols=57 Identities=21% Similarity=0.308 Sum_probs=49.5
Q ss_pred EEEEEecCCEEEEEEEeeecCeeceEeeceEEeeeecCCCCCCccccccceeeEeeCeEEEeCCeEEEEEeCC
Q 034463 21 CFWALEFIVLQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVLRNP 93 (94)
Q Consensus 21 ~~~l~~~~~r~~~G~L~gfD~hmNLVL~d~~E~~~~~~~~~~~~~~~k~~~~~r~lG~v~iRGdnVv~I~~~~ 93 (94)
.+.+ ++|+++.|+|.|||+|||++|+||+|++.. .+++++|+++|||+||++|++++
T Consensus 18 ~V~l--~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~--------------~~~~~lg~v~iRG~~I~~i~~~~ 74 (75)
T 1h64_1 18 LVIL--KKGFEFRGRLIGYDIHLNVVLADAEMIQDG--------------EVVKRYGKIVIRGDNVLAISPTE 74 (75)
T ss_dssp EEEE--TTSEEEEEEEEEECTTCCEEEEEEEEEETT--------------EEEEEEEEEEECGGGEEEEEEC-
T ss_pred EEEE--CCCCEEEEEEEEEeCCCCeEEeeEEEEeeC--------------CceeECCEEEECCCEEEEEEeCC
Confidence 5555 889999999999999999999999998742 14688999999999999999975
No 13
>4emk_C U6 snRNA-associated SM-like protein LSM7; SM fold, mRNA decay and PRE-mRNA splicing, LSM proteins, RNA protein; 2.30A {Schizosaccharomyces pombe} PDB: 3swn_C
Probab=99.77 E-value=7.6e-19 Score=118.05 Aligned_cols=60 Identities=20% Similarity=0.279 Sum_probs=47.5
Q ss_pred cCCEEEEEEEeeecCeeceEeeceEEeeeecCCCCCCccccccceeeEeeCeEEEeCCeEEEEEeCC
Q 034463 27 FIVLQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVLRNP 93 (94)
Q Consensus 27 ~~~r~~~G~L~gfD~hmNLVL~d~~E~~~~~~~~~~~~~~~k~~~~~r~lG~v~iRGdnVv~I~~~~ 93 (94)
++||++.|+|+|||+||||||+||+|++...... +....+|.+|+++|||+||++|+|..
T Consensus 41 ~dGr~~~G~L~~fD~~mNLVL~d~~E~~~~~~~~-------~~~~~~r~lG~v~IRG~nIv~I~~~d 100 (113)
T 4emk_C 41 TGGRQITGILKGFDQLMNLVLDDVEEQLRNPEDG-------KLTGAIRKLGLVVVRGTTLVLIAPMD 100 (113)
T ss_dssp TTSCEEEEEEEEECTTCCEEEEEEEEEC----------------CCEEEEEEEEECTTTEEEEEECC
T ss_pred eCCeEEEEEEEEEcCcccEEEeeEEEEEcCCCCc-------ccccceeEccEEEECCCeEEEEEecC
Confidence 8899999999999999999999999998642110 01124689999999999999999864
No 14
>1i8f_A Putative snRNP SM-like protein; beta barrel-like SMAP monomers form 35-stranded beta-sheet I heptamer, structural genomics; 1.75A {Pyrobaculum aerophilum} SCOP: b.38.1.1 PDB: 1lnx_A*
Probab=99.77 E-value=1.6e-18 Score=109.69 Aligned_cols=65 Identities=22% Similarity=0.320 Sum_probs=54.2
Q ss_pred EeeeeeCcceEEEEEEEEEecCCEEEEEEEeeecCeeceEeeceEEeeeecCCCCCCccccccceeeEeeCeEEEeCCeE
Q 034463 7 RFSFRNSQTTLMLFCFWALEFIVLQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSV 86 (94)
Q Consensus 7 ~~~~~~~~~~i~~l~~~l~~~~~r~~~G~L~gfD~hmNLVL~d~~E~~~~~~~~~~~~~~~k~~~~~r~lG~v~iRGdnV 86 (94)
+.+++. .++ .+++ ++|+++.|+|.|||+|||++|+||+|+ .. .+++++|+++|||+||
T Consensus 16 L~~~~~--~~V---~V~l--~~g~~~~G~L~~~D~~mNlvL~d~~e~-~~--------------~~~~~lg~v~iRG~~I 73 (81)
T 1i8f_A 16 LQDSIG--KQV---LVKL--RDSHEIRGILRSFDQHVNLLLEDAEEI-ID--------------GNVYKRGTMVVRGENV 73 (81)
T ss_dssp HHTTTT--SEE---EEEE--GGGEEEEEEEEEECTTCCEEEEEEEEE-ET--------------TEEEEEEEEEECGGGE
T ss_pred HHHHCC--CeE---EEEE--cCCcEEEEEEEEEcCCCeeEEccEEEE-cC--------------CcccCCCEEEECCCEE
Confidence 445554 366 7777 679999999999999999999999998 21 1368899999999999
Q ss_pred EEEEeCC
Q 034463 87 IIVLRNP 93 (94)
Q Consensus 87 v~I~~~~ 93 (94)
++|+|++
T Consensus 74 ~~i~~~d 80 (81)
T 1i8f_A 74 LFISPVP 80 (81)
T ss_dssp EEEEECC
T ss_pred EEEEeCC
Confidence 9999975
No 15
>1th7_A SnRNP-2, small nuclear riboprotein protein; archaea, SM protein, SM fold, SS-SM1, RNA binding protein; 1.68A {Sulfolobus solfataricus} SCOP: b.38.1.1
Probab=99.76 E-value=1.9e-18 Score=109.19 Aligned_cols=57 Identities=23% Similarity=0.399 Sum_probs=49.3
Q ss_pred EEEEEecCCEEEEEEEeeecCeeceEeeceEEeeeecCCCCCCccccccceeeEeeCeEEEeCCeEEEEEeCC
Q 034463 21 CFWALEFIVLQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVLRNP 93 (94)
Q Consensus 21 ~~~l~~~~~r~~~G~L~gfD~hmNLVL~d~~E~~~~~~~~~~~~~~~k~~~~~r~lG~v~iRGdnVv~I~~~~ 93 (94)
.+.+ ++|+++.|+|.|||+|||++|+||+|++.. .+.+++|+++|||+||++|++++
T Consensus 23 ~V~l--~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~--------------~~~~~lg~v~iRG~~I~~i~~~~ 79 (81)
T 1th7_A 23 LVKL--KGNKEVRGMLRSYDQHMNLVLSDSEEIQSD--------------GSGKKLGTIVIRGDNVILISPLQ 79 (81)
T ss_dssp EEEE--TTTEEEEEEEEEECTTCCEEEEEEEEECSS--------------SCEEEEEEEEECGGGEEEEEEC-
T ss_pred EEEE--cCCcEEEEEEEEEcCCCCEEEccEEEEecC--------------CceeECCEEEECCCEEEEEEecC
Confidence 5555 889999999999999999999999998742 13578999999999999999875
No 16
>3s6n_G Small nuclear ribonucleoprotein G; SMN complex, SMN-gemin2 complex, U-rich snRNA, SM fold, SM C SNRNPS, snRNP biogenesis, PRE-mRNA splicing; 2.50A {Homo sapiens} PDB: 2y9b_G 2y9c_G 2y9d_G 3cw1_G 3pgw_G* 2y9a_G
Probab=99.76 E-value=1.6e-18 Score=108.66 Aligned_cols=57 Identities=25% Similarity=0.288 Sum_probs=46.0
Q ss_pred EEEecCCEEEEEEEeeecCeeceEeeceEEeeeecCCCCCCccccccceeeEeeCeEEEeCCeEEEEEeCC
Q 034463 23 WALEFIVLQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVLRNP 93 (94)
Q Consensus 23 ~l~~~~~r~~~G~L~gfD~hmNLVL~d~~E~~~~~~~~~~~~~~~k~~~~~r~lG~v~iRGdnVv~I~~~~ 93 (94)
++.-++|++++|+|.|||+|||++|+||+|++.. .+++++|.++|||+||++++|..
T Consensus 18 ~V~Lk~gr~~~G~L~~~D~~mNlvL~~~~e~~~~--------------~~~~~lg~v~iRG~~I~~i~~~d 74 (76)
T 3s6n_G 18 SLKLNGGRHVQGILRGFDPFMNLVIDECVEMATS--------------GQQNNIGMVVIRGNSIIMLEALE 74 (76)
T ss_dssp EEEETTTEEEEEEEEEECTTCCEEEEEEEECCCC------------------CBSSEEECSSSEEEEEC--
T ss_pred EEEECCCcEEEEEEEEECCcceEEEeceEEEccC--------------CcEeEcCEEEECCCeEEEEEecc
Confidence 3344889999999999999999999999998642 12578999999999999999864
No 17
>3s6n_F Small nuclear ribonucleoprotein F; SMN complex, SMN-gemin2 complex, U-rich snRNA, SM fold, SM C SNRNPS, snRNP biogenesis, PRE-mRNA splicing; 2.50A {Homo sapiens} PDB: 2y9b_F 2y9c_F 2y9d_F 3cw1_F 3pgw_F* 2y9a_F
Probab=99.76 E-value=5.7e-19 Score=113.33 Aligned_cols=61 Identities=15% Similarity=0.154 Sum_probs=52.1
Q ss_pred cceEEEEEEEEEecCCEEEEEEEeeecCeeceEeeceEEeeeecCCCCCCccccccceeeEeeCeEEEeCCeEEEEEeCC
Q 034463 14 QTTLMLFCFWALEFIVLQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVLRNP 93 (94)
Q Consensus 14 ~~~i~~l~~~l~~~~~r~~~G~L~gfD~hmNLVL~d~~E~~~~~~~~~~~~~~~k~~~~~r~lG~v~iRGdnVv~I~~~~ 93 (94)
+.+| .+++ +.|+++.|+|+|||+|||++|+||+|.... .+.+++|.++|||+||++|++++
T Consensus 16 ~k~V---~V~L--k~g~~~~G~L~~~D~~mNlvL~d~~e~~~g--------------~~~~~lg~v~IRG~nI~~i~~~d 76 (86)
T 3s6n_F 16 GKPV---MVKL--KWGMEYKGYLVSVDGYMNMQLANTEEYIDG--------------ALSGHLGEVLIRCNNVLYIRGVE 76 (86)
T ss_dssp TSEE---EEEE--TTSCEEEEEEEEECTTCCEEEEEEEEEETT--------------EEEEEESSEEECGGGEEEEEECC
T ss_pred CCeE---EEEE--cCCeEEEEEEEEEcCceEEEEeeEEEEcCC--------------ceeeEccEEEEeCCeEEEEEeCC
Confidence 4566 6777 779999999999999999999999997521 13578999999999999999986
No 18
>3pgw_B SM B; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 3cw1_A
Probab=99.73 E-value=8.8e-18 Score=124.81 Aligned_cols=61 Identities=25% Similarity=0.418 Sum_probs=48.9
Q ss_pred cCCEEEEEEEeeecCeeceEeeceEEeeeecCCCCCCccccccceeeEeeCeEEEeCCeEEEEEe
Q 034463 27 FIVLQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVLR 91 (94)
Q Consensus 27 ~~~r~~~G~L~gfD~hmNLVL~d~~E~~~~~~~~~~~~~~~k~~~~~r~lG~v~iRGdnVv~I~~ 91 (94)
+++|+++|+|+|||+||||||+||+|++...+++.+. ...+++|++|+++||||||++|+.
T Consensus 22 kdGRel~GtLkgFDq~MNLVL~Da~E~~~ik~k~~k~----~~~~~~R~LGlV~IRGdnIV~Isv 82 (231)
T 3pgw_B 22 QDGRIFIGTFKAFDKHMNLILCDCDEFRKIKPKNSKQ----AEREEKRVLGLVLLRGENLVSMTV 82 (231)
T ss_pred CCCcEEEEEEEEEcccccEEecCEEEEEeccCccccc----ccccceeEeceEEECCCcEEEEEe
Confidence 8899999999999999999999999997643322111 112357899999999999999984
No 19
>4emk_B U6 snRNA-associated SM-like protein LSM6; SM fold, mRNA decay and PRE-mRNA splicing, LSM proteins, RNA protein; 2.30A {Schizosaccharomyces pombe} PDB: 3swn_B
Probab=99.73 E-value=4.5e-18 Score=106.23 Aligned_cols=57 Identities=21% Similarity=0.261 Sum_probs=48.7
Q ss_pred EEEEEecCCEEEEEEEeeecCeeceEeeceEEeeeecCCCCCCccccccceeeEeeCeEEEeCCeEEEEEeCC
Q 034463 21 CFWALEFIVLQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVLRNP 93 (94)
Q Consensus 21 ~~~l~~~~~r~~~G~L~gfD~hmNLVL~d~~E~~~~~~~~~~~~~~~k~~~~~r~lG~v~iRGdnVv~I~~~~ 93 (94)
.+.+ +.|+++.|+|.|||+|||++|+||+|.... .+.+++|.++|||+||++++|.+
T Consensus 18 ~V~L--k~g~~~~G~L~~~D~~mNlvL~d~~e~~~~--------------~~~~~lg~v~iRG~~I~~i~~~~ 74 (75)
T 4emk_B 18 LIRL--SSGVDYKGILSCLDGYMNLALERTEEYVNG--------------KKTNVYGDAFIRGNNVLYVSALD 74 (75)
T ss_dssp EEEC--TTSCEEEEEEEEECTTCEEEEEEEEEEETT--------------EEEEEEEEEEEEGGGSSEEEEC-
T ss_pred EEEE--cCCcEEEEEEEEEcCcceEEEccEEEEecC--------------CcccEecEEEEcCCeEEEEEecC
Confidence 5555 789999999999999999999999998531 13578999999999999999864
No 20
>1b34_A Protein (small nuclear ribonucleoprotein SM D1); snRNP, splicing, spliceosome, core snRNP domain, systemi erythematosus, SLE, RNA binding protein; 2.50A {Homo sapiens} SCOP: b.38.1.1 PDB: 2y9a_B 2y9b_B 2y9c_B 2y9d_B 3cw1_B 3pgw_X* 3s6n_A
Probab=99.72 E-value=4.2e-18 Score=115.03 Aligned_cols=67 Identities=15% Similarity=0.140 Sum_probs=55.1
Q ss_pred eeeeeCc--ceEEEEEEEEEecCCEEEEEEEeeecCeeceEeeceEEeeeecCCCCCCccccccceeeEeeCeEEEeCCe
Q 034463 8 FSFRNSQ--TTLMLFCFWALEFIVLQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDS 85 (94)
Q Consensus 8 ~~~~~~~--~~i~~l~~~l~~~~~r~~~G~L~gfD~hmNLVL~d~~E~~~~~~~~~~~~~~~k~~~~~r~lG~v~iRGdn 85 (94)
|+||++- .+| .++| +.++++.|+|.|||+||||+|+||+|+... + +.+++|.++|||+|
T Consensus 4 ~~~L~~~~gk~V---~V~L--k~g~~~~G~L~~~D~~MNlvL~d~~e~~~~------~--------~~~~lg~v~IRG~n 64 (119)
T 1b34_A 4 VRFLMKLSHETV---TIEL--KNGTQVHGTITGVDVSMNTHLKAVKMTLKN------R--------EPVQLETLSIRGNN 64 (119)
T ss_dssp HHHHHTCTTCEE---EEEE--TTCCEEEEEEEEECTTCCEEEEEEEEECTT------S--------CCEEEEEEEECGGG
T ss_pred HHHHHHhCCCEE---EEEE--cCCCEEEEEEEEEcccceEEeccEEEecCC------C--------ceeEcceEEEcCCe
Confidence 4555544 466 7777 789999999999999999999999997421 1 24689999999999
Q ss_pred EEEEEeCC
Q 034463 86 VIIVLRNP 93 (94)
Q Consensus 86 Vv~I~~~~ 93 (94)
|++|++++
T Consensus 65 I~~I~~pd 72 (119)
T 1b34_A 65 IRYFILPD 72 (119)
T ss_dssp EEEEECCT
T ss_pred EEEEEecc
Confidence 99999875
No 21
>4emh_A Probable U6 snRNA-associated SM-like protein LSM4; SM fold, mRNA decay, PRE-mRNA splicing, LSM proteins, RNA BI protein; 2.20A {Schizosaccharomyces pombe}
Probab=99.72 E-value=1.2e-17 Score=111.14 Aligned_cols=62 Identities=15% Similarity=0.167 Sum_probs=50.2
Q ss_pred cceEEEEEEEEEecCCEEEEEEEeeecCeeceEeeceEEeeeecCCCCCCccccccceeeEeeCeEEEeCCeEEEEEeCC
Q 034463 14 QTTLMLFCFWALEFIVLQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVLRNP 93 (94)
Q Consensus 14 ~~~i~~l~~~l~~~~~r~~~G~L~gfD~hmNLVL~d~~E~~~~~~~~~~~~~~~k~~~~~r~lG~v~iRGdnVv~I~~~~ 93 (94)
+.+| .+++ +.|+++.|+|.|||+||||+|+||+|.... + ++.+++|.++|||+||.+|++++
T Consensus 26 gk~V---~V~L--k~G~~~~G~L~~~D~~MNlvL~d~~e~~~d------g-------~~~~~lg~v~IRG~nI~~I~~pd 87 (105)
T 4emh_A 26 GRPI---LVEL--KNGETFNGHLENCDNYMNLTLREVIRTMPD------G-------DKFFRLPECYIRGNNIKYLRIQD 87 (105)
T ss_dssp CCEE---EEEE--TTSCEEEEEEEEECTTCCEEEEEEEEECTT------S-------CEEEEEEEEEECGGGEEEEEC--
T ss_pred CCEE---EEEE--CCCCEEEEEEEEEcCCceEEEEEEEEEccC------C-------ceeeEcCeEEEeCCeEEEEecCH
Confidence 3455 6666 779999999999999999999999998531 1 13578999999999999999875
No 22
>1d3b_A Protein (small nuclear ribonucleoprotein SM D3); snRNP, splicing, core snRNP domain, systemic lupus eryth SLE, RNA binding protein; HET: CIT; 2.00A {Homo sapiens} SCOP: b.38.1.1
Probab=99.68 E-value=9.4e-17 Score=100.46 Aligned_cols=57 Identities=11% Similarity=0.194 Sum_probs=48.2
Q ss_pred EEEecCCEEEEEEEeeecCeeceEeeceEEeeeecCCCCCCccccccceeeEeeCeEEEeCCeEEEEEeCC
Q 034463 23 WALEFIVLQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVLRNP 93 (94)
Q Consensus 23 ~l~~~~~r~~~G~L~gfD~hmNLVL~d~~E~~~~~~~~~~~~~~~k~~~~~r~lG~v~iRGdnVv~I~~~~ 93 (94)
++.-+.|++++|+|.|||+|||++|+||+|.... + +.+++|.++|||+||.+|+.|+
T Consensus 19 ~VeLk~g~~~~G~L~~~D~~MNl~L~~~~e~~~~------~--------~~~~lg~v~IRG~nI~~i~lPd 75 (75)
T 1d3b_A 19 TCETNTGEVYRGKLIEAEDNMNCQMSNITVTYRD------G--------RVAQLEQVYIRGCKIRFLILPD 75 (75)
T ss_dssp EEEETTSCEEEEEEEEECTTCCEEEEEEEEECTT------S--------CEEEEEEEEECGGGEEEEEECC
T ss_pred EEEECCCcEEEEEEEEEccceeEEEEeEEEECCC------C--------cEEEcCeEEEeCCEEEEEEcCC
Confidence 3344889999999999999999999999998521 1 2578999999999999999874
No 23
>1m5q_A SMAP3, small nuclear ribonucleoprotein homolog, SM-like P; OB-like fold, B-sheet toroid, 14-MER, cadmium-binding site, translation; 2.00A {Pyrobaculum aerophilum} SCOP: b.38.1.1
Probab=99.61 E-value=6.3e-16 Score=106.11 Aligned_cols=53 Identities=15% Similarity=0.092 Sum_probs=47.1
Q ss_pred EEEEEecCCEEEEEEEeeecCeeceEeeceEEeeeecCCCCCCccccccceeeEeeCeEEEeCCeEEEEEeCC
Q 034463 21 CFWALEFIVLQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVLRNP 93 (94)
Q Consensus 21 ~~~l~~~~~r~~~G~L~gfD~hmNLVL~d~~E~~~~~~~~~~~~~~~k~~~~~r~lG~v~iRGdnVv~I~~~~ 93 (94)
.++| +.|+++.|+|.|||+||||+|+||+|.. .+++|.++|||+||++|++++
T Consensus 14 ~V~L--k~G~~~~G~L~~~D~~MNlvL~d~~E~~------------------~~~lg~v~IRG~nI~~I~~~d 66 (130)
T 1m5q_A 14 QVVL--SNGEVYKGVLHAVDNQLNIVLANASNKA------------------GEKFNRVFIMYRYIVHIDSTE 66 (130)
T ss_dssp EEEE--TTSCEEEEEEEEECTTCCEEEEEEECTT------------------CCEEEEEEECGGGEEEEEECC
T ss_pred EEEE--CCCcEEEEEEEEEcccceeEEeeEEEEc------------------CCEeceEEEeCCeEEEEEcCC
Confidence 6777 7799999999999999999999999961 146999999999999999875
No 24
>2y9a_D Small nuclear ribonucleoprotein SM D3; splicing-RNA complex, PRE-mRNA splicing, spliceosome, snRNP biogenesis, SM site, SM fold, heteromeric heptameric ring; 3.60A {Homo sapiens} PDB: 2y9b_D 2y9c_D 2y9d_D 3pgw_Z* 3cw1_D
Probab=99.53 E-value=1.9e-14 Score=98.23 Aligned_cols=59 Identities=10% Similarity=0.202 Sum_probs=49.0
Q ss_pred EEEEEecCCEEEEEEEeeecCeeceEeeceEEeeeecCCCCCCccccccceeeEeeCeEEEeCCeEEEEEeCC
Q 034463 21 CFWALEFIVLQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVLRNP 93 (94)
Q Consensus 21 ~~~l~~~~~r~~~G~L~gfD~hmNLVL~d~~E~~~~~~~~~~~~~~~k~~~~~r~lG~v~iRGdnVv~I~~~~ 93 (94)
.+++.-+.++++.|+|.+||.|||++|+||+|+... + +..++|.++|||+||.+|++++
T Consensus 17 ~V~VeLknG~~~~G~L~~~D~~MNi~L~dv~e~~~~------g--------~~~~l~~v~IRGnnI~~I~lpd 75 (126)
T 2y9a_D 17 IVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTYRD------G--------RVAQLEQVYIRGSKIRFLILPD 75 (126)
T ss_dssp EEEEEESSCCEEEEEEEEECTTSCEEEEEEEEECTT------S--------CCEEEEEEEECGGGEEEEECCS
T ss_pred EEEEEECCCcEEEEEEEEEcCceEEEEeeEEEEcCC------C--------cEeecccEEEeCCEEEEEEccc
Confidence 344455889999999999999999999999997421 1 2468999999999999999765
No 25
>3sb2_A Protein HFQ; SM-like, RNA chaperone, chaperone; 2.63A {Herbaspirillum seropedicae} SCOP: b.38.1.2
Probab=95.79 E-value=0.0058 Score=38.42 Aligned_cols=33 Identities=18% Similarity=0.426 Sum_probs=28.1
Q ss_pred eeeeCcceEEEEEEEEEecCCEEEEEEEeeecCeeceE
Q 034463 9 SFRNSQTTLMLFCFWALEFIVLQLLGRVRAFDRHCNMV 46 (94)
Q Consensus 9 ~~~~~~~~i~~l~~~l~~~~~r~~~G~L~gfD~hmNLV 46 (94)
++.+++.++ .++| ..|.++.|.+.|||+|+=++
T Consensus 15 ~lrk~k~~V---tI~L--vnG~~L~G~I~~fD~f~VlL 47 (79)
T 3sb2_A 15 ALRKEHVPV---SIYL--VNGIKLQGHVESFDQYVVLL 47 (79)
T ss_dssp HHHHTTCCE---EEEE--TTSCEEEEEEEEECSSEEEE
T ss_pred HHHhcCCeE---EEEE--eCCCEEEEEEEEECCcEEEE
Confidence 355778888 8888 67999999999999999665
No 26
>1u1s_A HFQ protein; SM-like bacterial protein, riken structural genomics/proteomics initiative, RSGI, structural genomics, RNA binding protein; 1.60A {Pseudomonas aeruginosa} SCOP: b.38.1.2 PDB: 1u1t_A 3qui_A* 3m4g_A 3inz_A
Probab=95.76 E-value=0.0091 Score=37.82 Aligned_cols=35 Identities=14% Similarity=0.408 Sum_probs=28.3
Q ss_pred eeeCcceEEEEEEEEEecCCEEEEEEEeeecCeeceEeec
Q 034463 10 FRNSQTTLMLFCFWALEFIVLQLLGRVRAFDRHCNMVLEN 49 (94)
Q Consensus 10 ~~~~~~~i~~l~~~l~~~~~r~~~G~L~gfD~hmNLVL~d 49 (94)
..+++.++ .++| ..|.++.|.+.|||+|+=|+-++
T Consensus 15 lrk~~~~V---tv~L--~NG~~l~G~I~~fD~ftVlL~~~ 49 (82)
T 1u1s_A 15 LRKERVPV---SIYL--VNGIKLQGQIESFDQFVILLKNT 49 (82)
T ss_dssp HHHTTCCE---EEEE--TTSCEEEEEEEEECSSEEEEESS
T ss_pred HHHcCCcE---EEEE--eCCcEEEEEEEEEcceEEEEecC
Confidence 34567888 8888 57999999999999999766533
No 27
>2qtx_A Uncharacterized protein MJ1435; HFQ, SM, RNA-binding protein, sRNA, translational regulation, RNA binding protein; 2.50A {Methanocaldococcus jannaschii}
Probab=95.67 E-value=0.011 Score=36.47 Aligned_cols=35 Identities=14% Similarity=-0.102 Sum_probs=28.6
Q ss_pred eeeCcceEEEEEEEEEecCCEEEEEEEeeecCeeceEeec
Q 034463 10 FRNSQTTLMLFCFWALEFIVLQLLGRVRAFDRHCNMVLEN 49 (94)
Q Consensus 10 ~~~~~~~i~~l~~~l~~~~~r~~~G~L~gfD~hmNLVL~d 49 (94)
-.+++.++ .++| ..|.++.|.+.|||+|+=++-.+
T Consensus 21 ~r~~~~~V---tv~L--~NG~~l~G~I~~fD~ftVll~~~ 55 (71)
T 2qtx_A 21 RRLNGKKV---KIFL--RNGEVLDAEVTGVSNYEIMVKVG 55 (71)
T ss_dssp GGGTTCEE---EEEE--TTSCEEEEEEEEECSSEEEEEET
T ss_pred HHHcCCcE---EEEE--eCCeEEEEEEEEEcceEEEEEeC
Confidence 36677888 8888 57999999999999999766443
No 28
>2ylb_A Protein HFQ; RNA-binding protein, LSM protein, RNA chaperone; 1.15A {Salmonella enterica subsp} PDB: 2yht_A 1hk9_A 2ylc_A* 3gib_A* 3rer_A* 3qo3_A* 3res_A*
Probab=95.63 E-value=0.0059 Score=37.86 Aligned_cols=34 Identities=15% Similarity=0.410 Sum_probs=28.0
Q ss_pred eeeCcceEEEEEEEEEecCCEEEEEEEeeecCeeceEee
Q 034463 10 FRNSQTTLMLFCFWALEFIVLQLLGRVRAFDRHCNMVLE 48 (94)
Q Consensus 10 ~~~~~~~i~~l~~~l~~~~~r~~~G~L~gfD~hmNLVL~ 48 (94)
+.+++.++ .++| ..|.++.|.+.+||+|+=++-+
T Consensus 17 lrk~k~~V---ti~L--~nG~~l~G~I~~fD~f~vlL~~ 50 (74)
T 2ylb_A 17 LRRERVPV---SIYL--VNGIKLQGQIESFDQFVILLKN 50 (74)
T ss_dssp HHHHTCCE---EEEE--TTSCEEEEEEEEECSSEEEEES
T ss_pred HHhcCCcE---EEEE--eCCCEEEEEEEEECCcEEEEEC
Confidence 45668888 8888 5799999999999999966543
No 29
>2y90_A Protein HFQ; RNA-binding protein, SM-like, RNA chaperone; 2.25A {Escherichia coli} PDB: 3qhs_A
Probab=95.25 E-value=0.011 Score=38.91 Aligned_cols=36 Identities=14% Similarity=0.402 Sum_probs=29.8
Q ss_pred eeeeCcceEEEEEEEEEecCCEEEEEEEeeecCeeceEeec
Q 034463 9 SFRNSQTTLMLFCFWALEFIVLQLLGRVRAFDRHCNMVLEN 49 (94)
Q Consensus 9 ~~~~~~~~i~~l~~~l~~~~~r~~~G~L~gfD~hmNLVL~d 49 (94)
++.+++.+| .++| ..|.++.|++.+||+|+=++-++
T Consensus 16 ~lrk~k~~V---tI~L--vNG~~L~G~I~~fD~f~VlL~~~ 51 (104)
T 2y90_A 16 ALRRERVPV---SIYL--VNGIKLQGQIESFDQFVILLKNT 51 (104)
T ss_dssp HHHHTTCCE---EEEE--TTSCEEEEEEEEECSSEEEEESS
T ss_pred HHHhcCCcE---EEEE--eCCCEEEEEEEEECCcEEEEECC
Confidence 456778888 8888 57999999999999999766544
No 30
>3ahu_A Protein HFQ; SM-like motif, protein-RNA complex, translation-RNA complex; 2.20A {Bacillus subtilis} PDB: 3hsb_A
Probab=95.06 E-value=0.024 Score=35.48 Aligned_cols=34 Identities=24% Similarity=0.393 Sum_probs=27.7
Q ss_pred eeCcceEEEEEEEEEecCCEEEEEEEeeecCeeceEeec
Q 034463 11 RNSQTTLMLFCFWALEFIVLQLLGRVRAFDRHCNMVLEN 49 (94)
Q Consensus 11 ~~~~~~i~~l~~~l~~~~~r~~~G~L~gfD~hmNLVL~d 49 (94)
.+++.++ .++| ..|.++.|.+.|||+|+=++-.+
T Consensus 20 rk~~~~V---tv~L--~nG~~l~G~I~~fD~f~VlL~~~ 53 (78)
T 3ahu_A 20 RKENTYV---TVFL--LNGFQLRGQVKGFDNFTVLLESE 53 (78)
T ss_dssp HHHTCCE---EEEE--TTSCEEEEEEEEECSSEEEEESS
T ss_pred HHcCCcE---EEEE--eCCeEEEEEEEEEcceEEEEEEC
Confidence 4567788 8888 67999999999999999766433
No 31
>1kq1_A HFQ, HOST factor for Q beta; hexamer, RNA binding protein, translational regulator, SM motif; 1.55A {Staphylococcus aureus} SCOP: b.38.1.2 PDB: 1kq2_A
Probab=94.97 E-value=0.02 Score=35.65 Aligned_cols=37 Identities=16% Similarity=0.285 Sum_probs=29.8
Q ss_pred eeeeCcceEEEEEEEEEecCCEEEEEEEeeecCeeceEeece
Q 034463 9 SFRNSQTTLMLFCFWALEFIVLQLLGRVRAFDRHCNMVLENV 50 (94)
Q Consensus 9 ~~~~~~~~i~~l~~~l~~~~~r~~~G~L~gfD~hmNLVL~d~ 50 (94)
++.+++.++ .++| ..|.++.|.+.|||+|+=++-++-
T Consensus 14 ~lrk~k~~V---tI~L--~nG~~l~G~I~~fD~f~VlL~~~g 50 (77)
T 1kq1_A 14 NFKANQTEV---TVFF--LNGFQMKGVIEEYDKYVVSLNSQG 50 (77)
T ss_dssp HHHHHTCEE---EEEE--TTSCEEEEEEEEECSSEEEEEETT
T ss_pred HHHhcCCeE---EEEE--eCCCEEEEEEEEECCcEEEEEECC
Confidence 345678888 8888 579999999999999997765443
No 32
>1y96_A Gemin6, SIP2, GEM-associated protein 6; SM fold, protein complex, RNA binding protein; 2.00A {Homo sapiens}
Probab=92.36 E-value=0.24 Score=31.36 Aligned_cols=24 Identities=29% Similarity=0.178 Sum_probs=22.7
Q ss_pred cCCEEEEEEEeeec-CeeceEeece
Q 034463 27 FIVLQLLGRVRAFD-RHCNMVLENV 50 (94)
Q Consensus 27 ~~~r~~~G~L~gfD-~hmNLVL~d~ 50 (94)
..|+.++|.|.+|| .-.|++|.++
T Consensus 25 ~dg~~y~G~l~tvDp~s~sIvL~n~ 49 (86)
T 1y96_A 25 SEKNEYKGWVLTTDPVSANIVLVNF 49 (86)
T ss_dssp TTTEEEEEEEEEECTTTCCEEEEEE
T ss_pred cCCCEEEEEEEEECCCceEEEEeec
Confidence 66999999999999 9999999998
No 33
>3hfo_A SSR3341 protein; HFQ, SM, RNA-binding protein, sRNA, translational regulation binding protein; 1.30A {Synechocystis SP}
Probab=86.79 E-value=0.42 Score=29.20 Aligned_cols=35 Identities=17% Similarity=0.099 Sum_probs=29.0
Q ss_pred eeeeCcceEEEEEEEEEecCCEEEEEEEeeecCeeceEee
Q 034463 9 SFRNSQTTLMLFCFWALEFIVLQLLGRVRAFDRHCNMVLE 48 (94)
Q Consensus 9 ~~~~~~~~i~~l~~~l~~~~~r~~~G~L~gfD~hmNLVL~ 48 (94)
+|.+++.++ ++.| -.|-+++|.+.-||.|+=.+-+
T Consensus 16 ~~ik~k~~V---~I~L--~tG~~l~G~i~WQD~~cl~L~~ 50 (70)
T 3hfo_A 16 LLIKDQTPV---EIKL--LTGDSLFGTIRWQDTDGLGLVD 50 (70)
T ss_dssp HHHHHTCEE---EEEE--TTSCEEEEEEEEECSSEEEEEC
T ss_pred HHHhhCceE---EEEe--cCCCEEEEEEEEeCCCEEEEEc
Confidence 567888999 8888 5699999999999999855543
No 34
>3hfn_A ASL2047 protein; HFQ, SM, RNA-binding protein, sRNA, translational regulation binding protein; 2.31A {Nostoc SP}
Probab=83.15 E-value=1.1 Score=27.42 Aligned_cols=34 Identities=15% Similarity=0.107 Sum_probs=28.5
Q ss_pred eeeeCcceEEEEEEEEEecCCEEEEEEEeeecCeeceEe
Q 034463 9 SFRNSQTTLMLFCFWALEFIVLQLLGRVRAFDRHCNMVL 47 (94)
Q Consensus 9 ~~~~~~~~i~~l~~~l~~~~~r~~~G~L~gfD~hmNLVL 47 (94)
+|.+++.++ ++.| -.|.+++|.+.-+|.|+=.+-
T Consensus 18 ~~Ik~k~~V---~I~L--~tGd~l~G~i~WQD~~cl~L~ 51 (72)
T 3hfn_A 18 NLIKQAAPV---EIKL--VTGDAITGRVLWQDPTCVCIA 51 (72)
T ss_dssp HHHSSCCEE---EEEE--TTSCEEEEEEEEECSSEEEEE
T ss_pred HHHhhCceE---EEEe--cCCCEEEEEEEEECCCEEEEE
Confidence 577889999 8888 569999999999999985444
No 35
>1x4r_A PARP14 protein; WWE domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}
Probab=50.76 E-value=0.94 Score=29.31 Aligned_cols=25 Identities=28% Similarity=0.317 Sum_probs=19.8
Q ss_pred EEEEecCCEEEEEEEeeecCeeceEeeceE
Q 034463 22 FWALEFIVLQLLGRVRAFDRHCNMVLENVR 51 (94)
Q Consensus 22 ~~l~~~~~r~~~G~L~gfD~hmNLVL~d~~ 51 (94)
-|-++.. |++..||+-.||.|++|.
T Consensus 28 eWqY~d~-----~~~~~FDk~TNl~LEeA~ 52 (99)
T 1x4r_A 28 EWQYIDK-----NITQCFDKMTNMKLEVAW 52 (99)
T ss_dssp EEEEECS-----SCEEECCTTHHHHHHHHH
T ss_pred EEEEeCC-----CeEeechHHHHHHHHHHH
Confidence 3555543 568999999999999986
No 36
>2fb7_A SM-like protein, LSM-14_N (RAP55); DR.13312, BC055387, AAH55387, stronGly BENT five-stranded antiparallel beta- sheet, structural genomics, PSI; NMR {Danio rerio} SCOP: b.38.1.5 PDB: 2vxf_A
Probab=35.03 E-value=86 Score=19.86 Aligned_cols=63 Identities=19% Similarity=0.223 Sum_probs=39.8
Q ss_pred EEEEEecCCEEEEEEEeeecCe-eceEeeceEEeeeecCCCCCCccccccceeeEeeCeEEEeCCeEEE
Q 034463 21 CFWALEFIVLQLLGRVRAFDRH-CNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVII 88 (94)
Q Consensus 21 ~~~l~~~~~r~~~G~L~gfD~h-mNLVL~d~~E~~~~~~~~~~~~~~~k~~~~~r~lG~v~iRGdnVv~ 88 (94)
+++|..+.+.+++|+|..-|.. .-+.|.+|..+-++-..... ...+. ..-...++.||.-|--
T Consensus 21 ~ISLISk~dIRYeGiL~~In~~~sTiaL~nVRsfGTEgR~~~~---~ipp~--~~vyeyIvFrGsDIKD 84 (95)
T 2fb7_A 21 KISLISKAEIRYEGILYTIDTENSTVALAKVRSFGTEDRPTDR---PIAPR--DETFEYIIFRGSDIKD 84 (95)
T ss_dssp EEEEEETTTEEEEEEEEEEETTTTEEEEESCCCCSCCSSSCSS---CCCSC--CCCSSCEEECSTTEEE
T ss_pred eEEEEECCCceEEEEEecccCccCEEEEEeeeEecccCCCCCC---ccCCC--CcceeEEEEcCCCcce
Confidence 4577788999999999998853 44667777665443211110 01111 2236899999998743
No 37
>1ycy_A Conserved hypothetical protein; structural genomics, southeast collaboratory for structural genomics, secsg, protein structure initiative; 2.80A {Pyrococcus furiosus} SCOP: b.38.1.4
Probab=23.09 E-value=1.3e+02 Score=17.96 Aligned_cols=27 Identities=19% Similarity=0.283 Sum_probs=18.6
Q ss_pred cCCEEEEEEEeeecCeeceEeeceEEee
Q 034463 27 FIVLQLLGRVRAFDRHCNMVLENVREMW 54 (94)
Q Consensus 27 ~~~r~~~G~L~gfD~hmNLVL~d~~E~~ 54 (94)
.+...|+|.|.-||+-. +.|.|+..+.
T Consensus 24 g~ehSFtGiledFDeEv-iLL~dV~D~~ 50 (71)
T 1ycy_A 24 GGDHSFTGTLEDFDEEV-ILLKDVVDVI 50 (71)
T ss_dssp C----CEEEEEEECSSE-EEEEEEEETT
T ss_pred cCcceeeeehhhcCcce-eehhhHHHHh
Confidence 33566999999999976 5678888764
No 38
>1nvp_D Transcription initiation factor IIA gamma chain; transcription regulation, DNA, complex, transcription/DNA complex; 2.10A {Homo sapiens} SCOP: a.32.1.1 b.56.1.1
Probab=21.89 E-value=1.2e+02 Score=19.49 Aligned_cols=25 Identities=20% Similarity=0.272 Sum_probs=18.9
Q ss_pred CCEEEEEEEee---ecCeeceEeeceEE
Q 034463 28 IVLQLLGRVRA---FDRHCNMVLENVRE 52 (94)
Q Consensus 28 ~~r~~~G~L~g---fD~hmNLVL~d~~E 52 (94)
....+.|.|.- -|..|.++|.|++=
T Consensus 53 sk~sfKG~L~tYrfcDnVWTf~lkd~~f 80 (108)
T 1nvp_D 53 NRVNFRGSLNTYRFCDNVWTFVLNDVEF 80 (108)
T ss_dssp CEEEEEEEEEEEEEETTEEEEEEEEEEE
T ss_pred cCCeEeeccCCccccCcEEEEEEeceEE
Confidence 34567787744 59999999999873
Done!