Query 013712
Match_columns 437
No_of_seqs 217 out of 627
Neff 4.0
Searched_HMMs 29240
Date Mon Mar 25 15:42:10 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/013712.a3m -d /work/01045/syshi/HHdatabase/pdb70.hhm -o /work/01045/syshi/hhsearch_pdb/013712hhsearch_pdb -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 1s29_A LA protein; winged heli 100.0 5.9E-30 2E-34 214.0 8.1 81 170-250 7-91 (92)
2 2cqk_A C-MPL binding protein; 100.0 2.7E-30 9.3E-35 219.6 5.8 85 169-255 10-96 (101)
3 2voo_A Lupus LA protein; RNA-b 99.9 2.2E-25 7.5E-30 203.4 5.0 163 171-345 10-185 (193)
4 1wfx_A Probable RNA 2'-phospho 92.0 0.19 6.5E-06 46.5 5.5 52 200-252 24-79 (186)
5 3htx_A HEN1; HEN1, small RNA m 82.0 1.1 3.8E-05 50.4 4.8 87 169-255 103-211 (950)
6 2k9l_A RNA polymerase sigma fa 49.9 17 0.00057 28.5 4.0 54 174-232 15-70 (76)
7 2k9m_A RNA polymerase sigma fa 33.5 25 0.00085 30.4 2.8 61 172-237 4-66 (130)
8 2jo7_A Glycosylphosphatidylino 21.7 84 0.0029 29.7 4.2 52 170-232 4-59 (224)
9 2cpj_A Non-POU domain-containi 19.7 19 0.00063 27.9 -0.5 37 315-351 54-93 (99)
10 2dgv_A HnRNP M, heterogeneous 13.0 27 0.00092 26.3 -1.1 34 315-348 51-87 (92)
No 1
>1s29_A LA protein; winged helix-turn-helix, autoantigen, RNA-binding, RNA binding protein; 1.60A {Trypanosoma brucei} SCOP: a.4.5.46
Probab=99.96 E-value=5.9e-30 Score=214.03 Aligned_cols=81 Identities=36% Similarity=0.576 Sum_probs=76.6
Q ss_pred hHHHHHHHHhhhhhhcCCCCcCcchHHHHhh--ccCCcEehhhhhcchhhhhcCCCHHHHHHHHhcCCceEEcC--CEEe
Q 013712 170 TLALKANIVKQIEYYFSDENLQNDHYLISLM--DAQGWVPIAIIADFKRVKRMSTDLPFILDALQNSSTVEAQG--DKVR 245 (437)
Q Consensus 170 ~~~L~~~I~kQIEYYFSdeNL~kD~FLR~~M--DsdG~VPIslIasFnRVK~LT~D~~lI~eALr~S~~LEV~~--dKVR 245 (437)
.++++.+|++||||||||+||+||.||+++| ++||||||++|++|+|||+||.|+++|++||+.|+.|||++ ++||
T Consensus 7 ~~~~~~~I~~QvEyYFSd~NL~~D~fL~~~m~~~~~G~Vpl~~i~sF~r~k~lt~d~~~i~~al~~S~~lev~edg~~VR 86 (92)
T 1s29_A 7 SSENKQKLQKQVEFYFSDVNVQRDIFLKGKMAENAEGFVSLETLLTFKRVNSVTTDVKEVVEAIRPSEKLVLSEDGLMVR 86 (92)
T ss_dssp CHHHHHHHHHHHHHHTSHHHHTTCHHHHHHHTTSTTCCEEHHHHTTSHHHHTTCSCHHHHHHHHTTCSSEEECTTSSEEE
T ss_pred CHHHHHHHHHHHHhhcchhhhccCHHHHHHhccCCCCCEEhHHHhCChhHHHHcCCHHHHHHHHhhCCeEEEeCCCCEEe
Confidence 3689999999999999999999999999999 79999999999999999999999999999999999999984 4899
Q ss_pred eCCCC
Q 013712 246 RRDEW 250 (437)
Q Consensus 246 RR~~w 250 (437)
|+.+.
T Consensus 87 R~~Pl 91 (92)
T 1s29_A 87 RRDPL 91 (92)
T ss_dssp ESSCC
T ss_pred CCCCC
Confidence 99864
No 2
>2cqk_A C-MPL binding protein; LA domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: a.4.5.46
Probab=99.96 E-value=2.7e-30 Score=219.58 Aligned_cols=85 Identities=39% Similarity=0.631 Sum_probs=79.3
Q ss_pred chHHHHHHHHhhhhhhcCCCCcCcchHHHHhhccCCcEehhhhhcchhhhhcCCCHHHHHHHHhcCCceEEcC--CEEee
Q 013712 169 ETLALKANIVKQIEYYFSDENLQNDHYLISLMDAQGWVPIAIIADFKRVKRMSTDLPFILDALQNSSTVEAQG--DKVRR 246 (437)
Q Consensus 169 e~~~L~~~I~kQIEYYFSdeNL~kD~FLR~~MDsdG~VPIslIasFnRVK~LT~D~~lI~eALr~S~~LEV~~--dKVRR 246 (437)
..++++++|++||||||||+||+||.||+++|++||||||++|++|+|||+||.|+++|++||+.|+.|||++ +||||
T Consensus 10 ~~~~l~~~I~~QvEyYFSd~NL~~D~fL~~~md~~G~Vpl~~iasF~r~k~lt~d~~~i~~al~~S~~levsedg~kVRr 89 (101)
T 2cqk_A 10 STEDLKECLKKQLEFCFSRENLSKDLYLISQMDSDQFIPIWTVANMEEIKKLTTDPDLILEVLRSSPMVQVDEKGEKVRP 89 (101)
T ss_dssp CHHHHHHHHHHHHHHHTSHHHHHHCHHHHHHSCTTSCEEHHHHHHCHHHHHHCCCHHHHHHHHHHSSSEEECSSSSEEEE
T ss_pred CHHHHHHHHHHHHHhhcchhhhccCHHHHHhhhcCCCEEhHHHhCChHHHHHcCCHHHHHHHHHhCCcEEEcCCCCeeee
Confidence 4578999999999999999999999999999999999999999999999999999999999999999999985 48998
Q ss_pred CCCCCcccc
Q 013712 247 RDEWSKWIP 255 (437)
Q Consensus 247 R~~w~kwv~ 255 (437)
+ +++|++
T Consensus 90 ~--~~~~i~ 96 (101)
T 2cqk_A 90 S--HKRCIS 96 (101)
T ss_dssp C--CSCCCC
T ss_pred C--CCCCcC
Confidence 6 457774
No 3
>2voo_A Lupus LA protein; RNA-binding protein, RNA recognition motif, systemic lupus erythematosus, phosphoprotein, RNA maturation; 1.8A {Homo sapiens} SCOP: a.4.5.46 d.58.7.1 PDB: 2von_A 2vod_A 2vop_A 1zh5_A 1yty_A 1s7a_A
Probab=99.91 E-value=2.2e-25 Score=203.41 Aligned_cols=163 Identities=23% Similarity=0.327 Sum_probs=112.5
Q ss_pred HHHHHHHHhhhhhhcCCCCcCcchHHHHhhc-cCCcEehhhhhcchhhhhcCCCHHHHHHHHhcC--CceEEcCC--EEe
Q 013712 171 LALKANIVKQIEYYFSDENLQNDHYLISLMD-AQGWVPIAIIADFKRVKRMSTDLPFILDALQNS--STVEAQGD--KVR 245 (437)
Q Consensus 171 ~~L~~~I~kQIEYYFSdeNL~kD~FLR~~MD-sdG~VPIslIasFnRVK~LT~D~~lI~eALr~S--~~LEV~~d--KVR 245 (437)
++|+.+|++||||||||+||++|.||+++|+ ++|||||++|++|+|||+|+.|.++|++||+.| ..|+++++ +||
T Consensus 10 ~~~~~~i~~q~e~yfs~~nl~~D~fl~~~~~~~~g~V~l~~i~sF~r~k~l~~d~~~I~~Al~~S~~~~lev~ed~~~vr 89 (193)
T 2voo_A 10 AALEAKICHQIEYYFGDFNLPRDKFLKEQIKLDEGWVPLEIMIKFNRLNRLTTDFNVIVEALSKSKAELMEISEDKTKIR 89 (193)
T ss_dssp HHHHHHHHHHHHHHTSTTTGGGCHHHHHHHHHTTTCEEHHHHTTSHHHHHHCCCHHHHHHHHHTCSSCCEEECTTSSEEE
T ss_pred HHHHHHHHHHhheecchhhcccCHHHHHHhcccCCcEEeHHHhhhhHHHHhcCCHHHHHHHHhhcccceEEEecccceEE
Confidence 5899999999999999999999999999997 799999999999999999999999999999999 89999865 788
Q ss_pred eCCCCC--ccccccccccCCCCc----cCcccccccccccccCCCCCCCCCCCCCCcccccccCCCCcccCCCCCCCccc
Q 013712 246 RRDEWS--KWIPASVEQTMSSTA----QTSQSQSAENPVDSIGNGDINKDNKREMPKENVGFSSNTGNLMENVPPSFDSV 319 (437)
Q Consensus 246 RR~~w~--kwv~~~~e~~~~s~t----~t~~~~~ve~~~~~~~n~~~~~~n~~~~~~~~~~f~~n~~~~~~~~~~~~~t~ 319 (437)
|+.... .+-.... ....+++ ..+.+...++....|..- + ...+|....+.+ ....--+||+|
T Consensus 90 R~~~~p~p~~~~~~~-~~~~~~~l~V~nLp~~~t~~~L~~~F~~~----G-----~v~~v~i~~~~~--~~~kG~aFVeF 157 (193)
T 2voo_A 90 RSPSKPLPEVTDEYK-NDVKNRSVYIKGFPTDATLDDIKEWLEDK----G-----QVLNIQMRRTLH--KAFKGSIFVVF 157 (193)
T ss_dssp ECTTSCCCCCCHHHH-HHHHHTEEEEECCCTTCCHHHHHHHHTTS----C-----CEEEEEEEECTT--CCEEEEEEEEE
T ss_pred ecccCCCcccchhhh-hccccCEEEecCCCCcCCHHHHHHHHhcC----C-----CEEEEEEEECCC--CCcccEEEEEE
Confidence 873211 1100000 0001111 133444445555555521 1 111121111100 11122399999
Q ss_pred ccCCCCCcccc--cccccCCCCcccccC
Q 013712 320 EIEPDNGEEHC--DEFLLLDDGKPAFSA 345 (437)
Q Consensus 320 ~~~~Da~~~~~--~~~~~~~~~~~~~~~ 345 (437)
+..++|.+|.. ..+|.|+.+++..+.
T Consensus 158 ~~~e~A~~A~~~~~~~~~Gr~l~V~~~~ 185 (193)
T 2voo_A 158 DSIESAKKFVETPGQKYKETDLLILFKD 185 (193)
T ss_dssp SSHHHHHHHHHCTTCEETTEECEEEETT
T ss_pred CCHHHHHHHHHhCCCeECCEEEEEEEhH
Confidence 99999999933 368999998888763
No 4
>1wfx_A Probable RNA 2'-phosphotransferase; tRNA splicing, NAD, structural GE riken structural genomics/proteomics initiative, RSGI; 2.80A {Aeropyrum pernix} SCOP: d.166.1.5
Probab=91.97 E-value=0.19 Score=46.54 Aligned_cols=52 Identities=15% Similarity=0.228 Sum_probs=40.1
Q ss_pred hccCCcEehhhhhcchhhh--hcCCCHHHHHHHHhcCCc--eEEcCCEEeeCCCCCc
Q 013712 200 MDAQGWVPIAIIADFKRVK--RMSTDLPFILDALQNSST--VEAQGDKVRRRDEWSK 252 (437)
Q Consensus 200 MDsdG~VPIslIasFnRVK--~LT~D~~lI~eALr~S~~--LEV~~dKVRRR~~w~k 252 (437)
||++|||+|..|+. -+.+ ....+.+.|.++++.++. .++++++||.++...-
T Consensus 24 ld~~G~v~v~~LL~-~~~~~~~~~~t~~~l~~vV~~~~K~Rf~l~~~~IRA~qGHSi 79 (186)
T 1wfx_A 24 LTREGWARVSEVVE-GLRKAGWSWVEEWHIVGVALHDPKGRYELRNGEIRARYGHSI 79 (186)
T ss_dssp CCTTCCEEHHHHHH-HHHHTTCTTCCHHHHHHHHHHCSSCCEEEETTEEEESSCCSS
T ss_pred cCCCCCEEHHHHHh-hhhhcccCCCCHHHHHHHHhcCCCCceEeeccEEEeccCCCC
Confidence 68999999999998 4433 344577889999987764 7888999998876543
No 5
>3htx_A HEN1; HEN1, small RNA methyltransferase, protein-RNA complex; HET: SAH; 3.10A {Arabidopsis thaliana}
Probab=82.01 E-value=1.1 Score=50.45 Aligned_cols=87 Identities=24% Similarity=0.418 Sum_probs=66.3
Q ss_pred chHHHHHHHHhhhhhhcCCCCcCcchHHHHhh--------ccCCcEehhhhhcc-hhhhhcCC--------C----HHHH
Q 013712 169 ETLALKANIVKQIEYYFSDENLQNDHYLISLM--------DAQGWVPIAIIADF-KRVKRMST--------D----LPFI 227 (437)
Q Consensus 169 e~~~L~~~I~kQIEYYFSdeNL~kD~FLR~~M--------DsdG~VPIslIasF-nRVK~LT~--------D----~~lI 227 (437)
..++.-+.|+.+|+|.|||+=|.-.+=|..++ +--|.||+++|+.+ -||-.+++ | +.+|
T Consensus 103 ~~~~~~~~~~~~~~~~f~~e~~~~~~pl~~h~~~~~~r~~~~~~~~p~~~~~~~d~k~~~~ck~~~~~~e~~p~~~~~~~ 182 (950)
T 3htx_A 103 TVDEARDEIVGRIKYIFSDEFLSAEHPLGAHLRAALRRDGERCGSVPVSVIATVDAKINSRCKIINPSVESDPFLAISYV 182 (950)
T ss_dssp CHHHHHHHHHHHHHHHTSTGGGGCSSTHHHHHHHHHTSCGGGTTEECHHHHHHTCHHHHHHHHHHCTHHHHCTHHHHHHH
T ss_pred chhhHHHHHHHHHHHHhhhhhhhccCchHHHHHHHHhhcCccccccchhhheehhhhhhhhhhhcCcccccChHHHHHHH
Confidence 44788999999999999999999988887776 24689999999999 45655553 2 4678
Q ss_pred HHHHhcCCceEE-cCCEEeeCCCCCcccc
Q 013712 228 LDALQNSSTVEA-QGDKVRRRDEWSKWIP 255 (437)
Q Consensus 228 ~eALr~S~~LEV-~~dKVRRR~~w~kwv~ 255 (437)
..|...++-+-+ ++.-|||+++..-=+.
T Consensus 183 ~~a~~~~~~~~~~~~~~~~~~~~~~~~~~ 211 (950)
T 3htx_A 183 MKAAAKLADYIVASPHGLRRKNAYPSEIV 211 (950)
T ss_dssp HHHHHHCCSSEEEETTEEEESSCCCHHHH
T ss_pred HHHhhcCCCcEEeCCcccccCCCCCHHHH
Confidence 888877754445 4568999988764443
No 6
>2k9l_A RNA polymerase sigma factor RPON; protein, transcription; NMR {Aquifex aeolicus}
Probab=49.94 E-value=17 Score=28.49 Aligned_cols=54 Identities=11% Similarity=0.232 Sum_probs=37.0
Q ss_pred HHHHHhhhhhhcCCCCcCcchHHHHhhccCCcE--ehhhhhcchhhhhcCCCHHHHHHHHh
Q 013712 174 KANIVKQIEYYFSDENLQNDHYLISLMDAQGWV--PIAIIADFKRVKRMSTDLPFILDALQ 232 (437)
Q Consensus 174 ~~~I~kQIEYYFSdeNL~kD~FLR~~MDsdG~V--PIslIasFnRVK~LT~D~~lI~eALr 232 (437)
.+.|..||...||+.-..==.||...+|++||+ ++..|+. .|..+.+.|.+||+
T Consensus 15 ~ehL~~Ql~~~~~~~~~~Ia~~iI~~LD~~GYL~~~l~eia~-----~l~~~~~eve~vL~ 70 (76)
T 2k9l_A 15 LEELQQNIKLELEGKEQELALELLNYLNEKGFLSKSVEEISD-----VLRCSVEELEKVRQ 70 (76)
T ss_dssp HHHHHHHHHHHCCTTSHHHHHHHHHHCTTSSTTCCCHHHHHH-----HHTSCHHHHHHHHH
T ss_pred HHHHHHHHcccCCHHHHHHHHHHHHhcCCCCCCCCCHHHHHH-----HcCCCHHHHHHHHH
Confidence 888999998556655544457888889999996 5555653 23356666666665
No 7
>2k9m_A RNA polymerase sigma factor RPON; core binding domain, transcription; NMR {Aquifex aeolicus}
Probab=33.45 E-value=25 Score=30.39 Aligned_cols=61 Identities=10% Similarity=0.193 Sum_probs=39.5
Q ss_pred HHHHHHHhhhhhhcCCCCcCcchHHHHhhccCCcE--ehhhhhcchhhhhcCCCHHHHHHHHhcCCce
Q 013712 172 ALKANIVKQIEYYFSDENLQNDHYLISLMDAQGWV--PIAIIADFKRVKRMSTDLPFILDALQNSSTV 237 (437)
Q Consensus 172 ~L~~~I~kQIEYYFSdeNL~kD~FLR~~MDsdG~V--PIslIasFnRVK~LT~D~~lI~eALr~S~~L 237 (437)
.|.+.+..||...||+.-..==.||...+|++||+ ++..|+. .+..+.+.|.+||+.-..+
T Consensus 4 sL~e~L~~Ql~~~~~~~~~~ia~~iI~~LD~~GYL~~~l~eia~-----~l~~~~~eve~vL~~iQ~~ 66 (130)
T 2k9m_A 4 SELEELQQNIKLELEGKEQELALELLNYLNEKGFLSKSVEEISD-----VLRCSVEELEKVRQKVLRL 66 (130)
T ss_dssp CHHHHHHHHHHHHCCSHHHHHHHHHTTSBCTTSSBSSCHHHHHH-----HTTCCHHHHHHHHHHHHTS
T ss_pred CHHHHHHHHHcccCCHHHHHHHHHHHHhcCCCCCCCCCHHHHHH-----HcCCCHHHHHHHHHHHhcC
Confidence 57888999998555554433335677778999996 4555653 2346677777777644333
No 8
>2jo7_A Glycosylphosphatidylinositol-anchored merozoite surface protein; surface antigen, GPI-anchored protein, recombinant vaccine; NMR {Babesia divergens}
Probab=21.67 E-value=84 Score=29.69 Aligned_cols=52 Identities=17% Similarity=0.249 Sum_probs=41.1
Q ss_pred hHHHHHHHHhhhhhhcCCCCcCcchHHHHhhccCCcEehhhhhcchhhhh----cCCCHHHHHHHHh
Q 013712 170 TLALKANIVKQIEYYFSDENLQNDHYLISLMDAQGWVPIAIIADFKRVKR----MSTDLPFILDALQ 232 (437)
Q Consensus 170 ~~~L~~~I~kQIEYYFSdeNL~kD~FLR~~MDsdG~VPIslIasFnRVK~----LT~D~~lI~eALr 232 (437)
.++|+..++.|= .+||...|++||-.-|.-|..|=||.. |..|-+.|.+|=+
T Consensus 4 Le~lR~Elk~qR-----------E~~Ls~Ii~sdGp~tIlQLid~LRiidtDlLlkVD~~~V~kAG~ 59 (224)
T 2jo7_A 4 LDVLRGELRGQR-----------EAFLSEIIKSDGPFTILQLVGYLRVVDTDLLLKVDSTKVDEAGK 59 (224)
T ss_dssp HHHHHHHHHHHH-----------HHHHHHHHHCCSCCCTTHHHHHHHHHHHHTTTCCCHHHHHHHHH
T ss_pred HHHHHHHHHHHH-----------HHHHHHHHccCCCeeHHHHHHHHHHhccchhhccCHHHHHHHHH
Confidence 467888888885 589999999999999999999999875 3356666655543
No 9
>2cpj_A Non-POU domain-containing octamer-binding protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1
Probab=19.74 E-value=19 Score=27.88 Aligned_cols=37 Identities=11% Similarity=-0.015 Sum_probs=28.3
Q ss_pred CCcccccCCCCCccc---ccccccCCCCcccccCCCCCCc
Q 013712 315 SFDSVEIEPDNGEEH---CDEFLLLDDGKPAFSAENGDSR 351 (437)
Q Consensus 315 ~~~t~~~~~Da~~~~---~~~~~~~~~~~~~~~~~~~~~~ 351 (437)
=|++|+..++|.+|. ....+.|+.+++++......++
T Consensus 54 afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a~~~~~~~ 93 (99)
T 2cpj_A 54 GFIRLETRTLAEIAKVELDNMPLRGKQLRVRFACHSASLT 93 (99)
T ss_dssp EEEECSSSHHHHHHHHHHTTCCBTTBCCEEEESSCCSCCC
T ss_pred EEEEECCHHHHHHHHHHhCCCEeCCceEEEEEcCCCCCCC
Confidence 489999999999883 3477899999988875555433
No 10
>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A
Probab=13.00 E-value=27 Score=26.32 Aligned_cols=34 Identities=6% Similarity=-0.172 Sum_probs=26.3
Q ss_pred CCcccccCCCCCccc---ccccccCCCCcccccCCCC
Q 013712 315 SFDSVEIEPDNGEEH---CDEFLLLDDGKPAFSAENG 348 (437)
Q Consensus 315 ~~~t~~~~~Da~~~~---~~~~~~~~~~~~~~~~~~~ 348 (437)
=|++|+..+||.+|. ....+.|+.+++++.....
T Consensus 51 afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a~~~~ 87 (92)
T 2dgv_A 51 GVVKFESPEVAERACRMMNGMKLSGREIDVRIDRNAS 87 (92)
T ss_dssp EEEEESSHHHHHHHHHHHTTCCBTTBCCCCEECSCCS
T ss_pred EEEEECCHHHHHHHHHHhCCCEECCcEEEEEEcCCCC
Confidence 489999999999883 3477899999888874433
Done!