Query 039779
Match_columns 471
No_of_seqs 219 out of 615
Neff 3.8
Searched_HMMs 29240
Date Mon Mar 25 22:51:21 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/039779.a3m -d /work/01045/syshi/HHdatabase/pdb70.hhm -o /work/01045/syshi/hhsearch_pdb/039779hhsearch_pdb -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 2cqk_A C-MPL binding protein; 100.0 2.3E-31 7.9E-36 227.9 5.4 87 320-408 8-96 (101)
2 1s29_A LA protein; winged heli 100.0 1.4E-30 4.9E-35 219.4 7.5 82 322-403 6-91 (92)
3 2voo_A Lupus LA protein; RNA-b 99.9 1.3E-23 4.5E-28 192.8 8.7 111 323-438 9-134 (193)
4 1wfx_A Probable RNA 2'-phospho 91.4 0.17 6E-06 47.2 4.6 51 353-404 24-78 (186)
5 3htx_A HEN1; HEN1, small RNA m 85.6 0.58 2E-05 53.1 4.5 84 322-405 103-208 (950)
6 2k9l_A RNA polymerase sigma fa 70.5 4.9 0.00017 31.9 4.4 58 322-385 11-70 (76)
7 2k9m_A RNA polymerase sigma fa 46.2 9.6 0.00033 33.3 2.3 62 325-391 4-67 (130)
8 2jo7_A Glycosylphosphatidylino 20.9 65 0.0022 30.7 3.4 52 324-386 5-60 (224)
9 2h2m_A Protein MURR1, COMM dom 11.7 53 0.0018 28.6 0.2 34 337-373 24-58 (108)
10 3c18_A Nucleotidyltransferase- 11.1 1.3E+02 0.0046 29.9 2.9 70 324-393 202-272 (290)
No 1
>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=99.97 E-value=2.3e-31 Score=227.89 Aligned_cols=87 Identities=34% Similarity=0.615 Sum_probs=80.9
Q ss_pred CCCcHHHHHHHHhhhhhhcCCCCCCcchHHHHhhcCCCcEehhhhccccchhcccCCHHHHHHHHhhCCcEEEc--CCeE
Q 039779 320 PAPDPQLHSRIVTQIDYYFSNENLVKDTFLRQNMDDQGWVPIRLIAGFNKVSLLTDNIQLILDALRSSTVVEVQ--GDRI 397 (471)
Q Consensus 320 p~~d~~L~~~I~kQIEYYFSDeNL~kD~FLRs~MD~dG~VPIs~IasFnRVK~LT~D~~lI~eALr~S~~LEV~--gdkV 397 (471)
++.+++|+++|++||||||||+||+||.||+++||+||||||++|++|||||+||.|+++|++||+.|++|||+ +++|
T Consensus 8 ~~~~~~l~~~I~~QvEyYFSd~NL~~D~fL~~~md~~G~Vpl~~iasF~r~k~lt~d~~~i~~al~~S~~levsedg~kV 87 (101)
T 2cqk_A 8 AVSTEDLKECLKKQLEFCFSRENLSKDLYLISQMDSDQFIPIWTVANMEEIKKLTTDPDLILEVLRSSPMVQVDEKGEKV 87 (101)
T ss_dssp SCCHHHHHHHHHHHHHHHTSHHHHHHCHHHHHHSCTTSCEEHHHHHHCHHHHHHCCCHHHHHHHHHHSSSEEECSSSSEE
T ss_pred CCCHHHHHHHHHHHHHhhcchhhhccCHHHHHhhhcCCCEEhHHHhCChHHHHHcCCHHHHHHHHHhCCcEEEcCCCCee
Confidence 45778999999999999999999999999999999999999999999999999999999999999999999997 5699
Q ss_pred ecCCCCccccC
Q 039779 398 RKRNDWMRWIM 408 (471)
Q Consensus 398 RRR~~w~kwvl 408 (471)
||+.+ +|++
T Consensus 88 Rr~~~--~~i~ 96 (101)
T 2cqk_A 88 RPSHK--RCIS 96 (101)
T ss_dssp EECCS--CCCC
T ss_pred eeCCC--CCcC
Confidence 99864 4554
No 2
>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=1.4e-30 Score=219.41 Aligned_cols=82 Identities=24% Similarity=0.569 Sum_probs=78.0
Q ss_pred CcHHHHHHHHhhhhhhcCCCCCCcchHHHHhh--cCCCcEehhhhccccchhcccCCHHHHHHHHhhCCcEEEc--CCeE
Q 039779 322 PDPQLHSRIVTQIDYYFSNENLVKDTFLRQNM--DDQGWVPIRLIAGFNKVSLLTDNIQLILDALRSSTVVEVQ--GDRI 397 (471)
Q Consensus 322 ~d~~L~~~I~kQIEYYFSDeNL~kD~FLRs~M--D~dG~VPIs~IasFnRVK~LT~D~~lI~eALr~S~~LEV~--gdkV 397 (471)
.+++++++|++||||||||+||+||.||+++| |+||||||++|++|||||+||.|+++|++||+.|+.|||+ |++|
T Consensus 6 ~~~~~~~~I~~QvEyYFSd~NL~~D~fL~~~m~~~~~G~Vpl~~i~sF~r~k~lt~d~~~i~~al~~S~~lev~edg~~V 85 (92)
T 1s29_A 6 LSSENKQKLQKQVEFYFSDVNVQRDIFLKGKMAENAEGFVSLETLLTFKRVNSVTTDVKEVVEAIRPSEKLVLSEDGLMV 85 (92)
T ss_dssp CCHHHHHHHHHHHHHHTSHHHHTTCHHHHHHHTTSTTCCEEHHHHTTSHHHHTTCSCHHHHHHHHTTCSSEEECTTSSEE
T ss_pred CCHHHHHHHHHHHHhhcchhhhccCHHHHHHhccCCCCCEEhHHHhCChhHHHHcCCHHHHHHHHhhCCeEEEeCCCCEE
Confidence 67899999999999999999999999999999 7999999999999999999999999999999999999997 6799
Q ss_pred ecCCCC
Q 039779 398 RKRNDW 403 (471)
Q Consensus 398 RRR~~w 403 (471)
||+.++
T Consensus 86 RR~~Pl 91 (92)
T 1s29_A 86 RRRDPL 91 (92)
T ss_dssp EESSCC
T ss_pred eCCCCC
Confidence 999754
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=99.89 E-value=1.3e-23 Score=192.76 Aligned_cols=111 Identities=27% Similarity=0.560 Sum_probs=90.7
Q ss_pred cHHHHHHHHhhhhhhcCCCCCCcchHHHHhhc-CCCcEehhhhccccchhcccCCHHHHHHHHhhC--CcEEEcC--CeE
Q 039779 323 DPQLHSRIVTQIDYYFSNENLVKDTFLRQNMD-DQGWVPIRLIAGFNKVSLLTDNIQLILDALRSS--TVVEVQG--DRI 397 (471)
Q Consensus 323 d~~L~~~I~kQIEYYFSDeNL~kD~FLRs~MD-~dG~VPIs~IasFnRVK~LT~D~~lI~eALr~S--~~LEV~g--dkV 397 (471)
.++|+.+|++||||||||+||++|.||+++|+ ++|||+|++|++|+|||.|+.|.++|++||+.| ..|+|++ .+|
T Consensus 9 ~~~~~~~i~~q~e~yfs~~nl~~D~fl~~~~~~~~g~V~l~~i~sF~r~k~l~~d~~~I~~Al~~S~~~~lev~ed~~~v 88 (193)
T 2voo_A 9 MAALEAKICHQIEYYFGDFNLPRDKFLKEQIKLDEGWVPLEIMIKFNRLNRLTTDFNVIVEALSKSKAELMEISEDKTKI 88 (193)
T ss_dssp CHHHHHHHHHHHHHHTSTTTGGGCHHHHHHHHHTTTCEEHHHHTTSHHHHHHCCCHHHHHHHHHTCSSCCEEECTTSSEE
T ss_pred cHHHHHHHHHHhheecchhhcccCHHHHHHhcccCCcEEeHHHhhhhHHHHhcCCHHHHHHHHhhcccceEEEecccceE
Confidence 45899999999999999999999999999998 799999999999999999999999999999999 9999985 578
Q ss_pred ecCCCCccccCCCC----------CCCCCCCCCCCCCCcHHHHhhcccccc
Q 039779 398 RKRNDWMRWIMPPG----------KFSSLPSPQSQGKSGIDMLSAQVQSIS 438 (471)
Q Consensus 398 RRR~~w~kwvlp~~----------~~~~v~gp~s~~~~Sid~Lae~f~~It 438 (471)
||+.. ..+++. +...+.++ + ...+.+.|.+.|...+
T Consensus 89 rR~~~---~p~p~~~~~~~~~~~~~~l~V~nL-p-~~~t~~~L~~~F~~~G 134 (193)
T 2voo_A 89 RRSPS---KPLPEVTDEYKNDVKNRSVYIKGF-P-TDATLDDIKEWLEDKG 134 (193)
T ss_dssp EECTT---SCCCCCCHHHHHHHHHTEEEEECC-C-TTCCHHHHHHHHTTSC
T ss_pred Eeccc---CCCcccchhhhhccccCEEEecCC-C-CcCCHHHHHHHHhcCC
Confidence 88732 222221 22233333 2 4578888988887654
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=91.41 E-value=0.17 Score=47.19 Aligned_cols=51 Identities=14% Similarity=0.166 Sum_probs=40.1
Q ss_pred hcCCCcEehhhhccccchh--cccCCHHHHHHHHhhCCc--EEEcCCeEecCCCCc
Q 039779 353 MDDQGWVPIRLIAGFNKVS--LLTDNIQLILDALRSSTV--VEVQGDRIRKRNDWM 404 (471)
Q Consensus 353 MD~dG~VPIs~IasFnRVK--~LT~D~~lI~eALr~S~~--LEV~gdkVRRR~~w~ 404 (471)
||.+|||+|+.|+. -+.+ ....+.+.|.++++..++ .|+++++||.+....
T Consensus 24 ld~~G~v~v~~LL~-~~~~~~~~~~t~~~l~~vV~~~~K~Rf~l~~~~IRA~qGHS 78 (186)
T 1wfx_A 24 LTREGWARVSEVVE-GLRKAGWSWVEEWHIVGVALHDPKGRYELRNGEIRARYGHS 78 (186)
T ss_dssp CCTTCCEEHHHHHH-HHHHTTCTTCCHHHHHHHHHHCSSCCEEEETTEEEESSCCS
T ss_pred cCCCCCEEHHHHHh-hhhhcccCCCCHHHHHHHHhcCCCCceEeeccEEEeccCCC
Confidence 68999999999998 3333 344578899999988754 778899999987654
No 5
>3htx_A HEN1; HEN1, small RNA methyltransferase, protein-RNA complex; HET: SAH; 3.10A {Arabidopsis thaliana}
Probab=85.59 E-value=0.58 Score=53.07 Aligned_cols=84 Identities=23% Similarity=0.368 Sum_probs=64.6
Q ss_pred CcHHHHHHHHhhhhhhcCCCCCCcchHHHHhh--------cCCCcEehhhhccc-cchhcccC--------C----HHHH
Q 039779 322 PDPQLHSRIVTQIDYYFSNENLVKDTFLRQNM--------DDQGWVPIRLIAGF-NKVSLLTD--------N----IQLI 380 (471)
Q Consensus 322 ~d~~L~~~I~kQIEYYFSDeNL~kD~FLRs~M--------D~dG~VPIs~IasF-nRVK~LT~--------D----~~lI 380 (471)
..++-.+.|+.+|+|.|||+=|.-+.=|..|+ |--|.||+.+|+.+ -||-.+++ | +.+|
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 45788899999999999999998888777776 24589999999999 45555442 2 4678
Q ss_pred HHHHhhC-CcEEEcCCeEecCCCCcc
Q 039779 381 LDALRSS-TVVEVQGDRIRKRNDWMR 405 (471)
Q Consensus 381 ~eALr~S-~~LEV~gdkVRRR~~w~k 405 (471)
..|.+.+ ..+..++..|||++++.-
T Consensus 183 ~~a~~~~~~~~~~~~~~~~~~~~~~~ 208 (950)
T 3htx_A 183 MKAAAKLADYIVASPHGLRRKNAYPS 208 (950)
T ss_dssp HHHHHHCCSSEEEETTEEEESSCCCH
T ss_pred HHHhhcCCCcEEeCCcccccCCCCCH
Confidence 8888777 455456679999987653
No 6
>2k9l_A RNA polymerase sigma factor RPON; protein, transcription; NMR {Aquifex aeolicus}
Probab=70.50 E-value=4.9 Score=31.87 Aligned_cols=58 Identities=9% Similarity=0.182 Sum_probs=40.2
Q ss_pred CcHHHHHHHHhhhhhhcCCCCCCcchHHHHhhcCCCcE--ehhhhccccchhcccCCHHHHHHHHh
Q 039779 322 PDPQLHSRIVTQIDYYFSNENLVKDTFLRQNMDDQGWV--PIRLIAGFNKVSLLTDNIQLILDALR 385 (471)
Q Consensus 322 ~d~~L~~~I~kQIEYYFSDeNL~kD~FLRs~MD~dG~V--PIs~IasFnRVK~LT~D~~lI~eALr 385 (471)
..+. .+.|..||...|++.-..==.||...+|++||+ ++..|+. .|..+.+.|.++|+
T Consensus 11 ~~~e-~ehL~~Ql~~~~~~~~~~Ia~~iI~~LD~~GYL~~~l~eia~-----~l~~~~~eve~vL~ 70 (76)
T 2k9l_A 11 TPSE-LEELQQNIKLELEGKEQELALELLNYLNEKGFLSKSVEEISD-----VLRCSVEELEKVRQ 70 (76)
T ss_dssp CHHH-HHHHHHHHHHHCCTTSHHHHHHHHHHCTTSSTTCCCHHHHHH-----HHTSCHHHHHHHHH
T ss_pred CCch-HHHHHHHHcccCCHHHHHHHHHHHHhcCCCCCCCCCHHHHHH-----HcCCCHHHHHHHHH
Confidence 3344 888999999556665544457899999999996 5666663 23356677777665
No 7
>2k9m_A RNA polymerase sigma factor RPON; core binding domain, transcription; NMR {Aquifex aeolicus}
Probab=46.18 E-value=9.6 Score=33.33 Aligned_cols=62 Identities=10% Similarity=0.155 Sum_probs=41.8
Q ss_pred HHHHHHHhhhhhhcCCCCCCcchHHHHhhcCCCcE--ehhhhccccchhcccCCHHHHHHHHhhCCcEE
Q 039779 325 QLHSRIVTQIDYYFSNENLVKDTFLRQNMDDQGWV--PIRLIAGFNKVSLLTDNIQLILDALRSSTVVE 391 (471)
Q Consensus 325 ~L~~~I~kQIEYYFSDeNL~kD~FLRs~MD~dG~V--PIs~IasFnRVK~LT~D~~lI~eALr~S~~LE 391 (471)
.|.+.|..||...|++.-..==.||...+|++||+ ++..|+. .|..+.+.|.++|+.-..+|
T Consensus 4 sL~e~L~~Ql~~~~~~~~~~ia~~iI~~LD~~GYL~~~l~eia~-----~l~~~~~eve~vL~~iQ~~d 67 (130)
T 2k9m_A 4 SELEELQQNIKLELEGKEQELALELLNYLNEKGFLSKSVEEISD-----VLRCSVEELEKVRQKVLRLE 67 (130)
T ss_dssp CHHHHHHHHHHHHCCSHHHHHHHHHTTSBCTTSSBSSCHHHHHH-----HTTCCHHHHHHHHHHHHTSS
T ss_pred CHHHHHHHHHcccCCHHHHHHHHHHHHhcCCCCCCCCCHHHHHH-----HcCCCHHHHHHHHHHHhcCC
Confidence 57889999999556654433346788888999997 5566653 23457777777776544443
No 8
>2jo7_A Glycosylphosphatidylinositol-anchored merozoite surface protein; surface antigen, GPI-anchored protein, recombinant vaccine; NMR {Babesia divergens}
Probab=20.89 E-value=65 Score=30.74 Aligned_cols=52 Identities=19% Similarity=0.241 Sum_probs=42.7
Q ss_pred HHHHHHHHhhhhhhcCCCCCCcchHHHHhhcCCCcEehhhhccccchhc----ccCCHHHHHHHHhh
Q 039779 324 PQLHSRIVTQIDYYFSNENLVKDTFLRQNMDDQGWVPIRLIAGFNKVSL----LTDNIQLILDALRS 386 (471)
Q Consensus 324 ~~L~~~I~kQIEYYFSDeNL~kD~FLRs~MD~dG~VPIs~IasFnRVK~----LT~D~~lI~eALr~ 386 (471)
++|+..++.|=| +||.+.|++||-.-|--|..|=||.. |..|-+.|.+|-+.
T Consensus 5 e~lR~Elk~qRE-----------~~Ls~Ii~sdGp~tIlQLid~LRiidtDlLlkVD~~~V~kAG~k 60 (224)
T 2jo7_A 5 DVLRGELRGQRE-----------AFLSEIIKSDGPFTILQLVGYLRVVDTDLLLKVDSTKVDEAGKK 60 (224)
T ss_dssp HHHHHHHHHHHH-----------HHHHHHHHCCSCCCTTHHHHHHHHHHHHTTTCCCHHHHHHHHHH
T ss_pred HHHHHHHHHHHH-----------HHHHHHHccCCCeeHHHHHHHHHHhccchhhccCHHHHHHHHHH
Confidence 578888888855 89999999999999999999999875 44677777777553
No 9
>2h2m_A Protein MURR1, COMM domain-containing protein 1; all alpha-helical, metal transport; NMR {Homo sapiens}
Probab=11.68 E-value=53 Score=28.57 Aligned_cols=34 Identities=18% Similarity=0.359 Sum_probs=24.9
Q ss_pred hcCCCCCCcchHHHHhhcCCCcEehhhhccc-cchhcc
Q 039779 337 YFSNENLVKDTFLRQNMDDQGWVPIRLIAGF-NKVSLL 373 (471)
Q Consensus 337 YFSDeNL~kD~FLRs~MD~dG~VPIs~IasF-nRVK~L 373 (471)
||.++-+ .|.||++++=+| |++..+..| +||+.|
T Consensus 24 y~~~~~I-tee~L~~~lypd--vt~eef~~~~~K~~~l 58 (108)
T 2h2m_A 24 FHGYPGI-TEELLRSQLYPE--VPPEEFRPFLAKMRGI 58 (108)
T ss_dssp SSCCSSC-CHHHHHHHHCSS--SCSSTHHHHHTTTSTT
T ss_pred HcCCccc-cHHHHHHHHcCC--CCHHHHHHHHHHHHHH
Confidence 5566666 999999999776 777776655 566655
No 10
>3c18_A Nucleotidyltransferase-like protein; ZP_00538802.1, structur genomics, joint center for structural genomics, JCSG; 1.90A {Exiguobacterium sibiricum}
Probab=11.14 E-value=1.3e+02 Score=29.86 Aligned_cols=70 Identities=9% Similarity=0.110 Sum_probs=0.0
Q ss_pred HHHHHHHHhhhhhhcCCCCCCcchHHHHhhc-CCCcEehhhhccccchhcccCCHHHHHHHHhhCCcEEEc
Q 039779 324 PQLHSRIVTQIDYYFSNENLVKDTFLRQNMD-DQGWVPIRLIAGFNKVSLLTDNIQLILDALRSSTVVEVQ 393 (471)
Q Consensus 324 ~~L~~~I~kQIEYYFSDeNL~kD~FLRs~MD-~dG~VPIs~IasFnRVK~LT~D~~lI~eALr~S~~LEV~ 393 (471)
++-.+.+.--+||+.-..=-.-=.+|.+.|. .+++..+.-|..-..++.+..|++.|++=|-+-..|++.
T Consensus 202 ekrielllla~Ef~I~sk~~~~~~~Ll~~m~ek~~~wS~~Ei~~~p~~~~~~idle~iL~~Lv~k~lI~~~ 272 (290)
T 3c18_A 202 EQRIHLALIGLEHLLQSKVLSGGKYLFEVMRERDRPWTMHELMEESRLTELKVDLGSLVDFFIRKGLIRIS 272 (290)
T ss_dssp HHHHHHHHHHHHHHHHHTHHHHHHHHHHHHTTSSSCEEHHHHHHCGGGGGGHHHHHHHHHHHHHTTSEEEE
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHhcCcccccccCCHHHHHHHHHHcCCeEEe
Done!