Query 008506
Match_columns 563
No_of_seqs 217 out of 624
Neff 3.8
Searched_HMMs 29240
Date Mon Mar 25 05:09:25 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/008506.a3m -d /work/01045/syshi/HHdatabase/pdb70.hhm -o /work/01045/syshi/hhsearch_pdb/008506hhsearch_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 2.5E-29 8.5E-34 216.2 8.1 80 297-376 8-91 (92)
2 2cqk_A C-MPL binding protein; 100.0 1.4E-29 4.8E-34 221.3 5.9 85 295-381 10-96 (101)
3 2voo_A Lupus LA protein; RNA-b 99.9 9.8E-25 3.3E-29 204.9 4.8 159 297-468 10-179 (193)
4 1wfx_A Probable RNA 2'-phospho 90.3 0.34 1.2E-05 46.3 5.6 54 326-380 24-81 (186)
5 3htx_A HEN1; HEN1, small RNA m 83.6 1.7 5.7E-05 50.5 7.1 85 296-380 104-210 (950)
6 2k9l_A RNA polymerase sigma fa 50.4 16 0.00055 29.6 4.1 54 300-358 15-70 (76)
7 2k9m_A RNA polymerase sigma fa 34.8 24 0.00081 31.6 3.0 79 298-384 4-84 (130)
8 2jo7_A Glycosylphosphatidylino 17.4 1.4E+02 0.0048 29.1 4.9 52 296-358 4-59 (224)
9 1dfa_A PI-SCEI endonuclease; i 8.6 44 0.0015 35.0 -1.7 27 308-334 305-331 (454)
10 3c18_A Nucleotidyltransferase- 8.2 2.6E+02 0.009 28.4 3.8 69 298-366 203-272 (290)
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=2.5e-29 Score=216.24 Aligned_cols=80 Identities=36% Similarity=0.577 Sum_probs=76.3
Q ss_pred HHHHHHHHHHhhhhcCCCCcCcchHHHHhh--cCCCcEehhhhhcchhHhhhcCCHHHHHHHHhcCCceEEcC--Ceeec
Q 008506 297 LALKANIVKQIEYYFSDENLQNDHYLISLM--DAQGWVPIAIIADFKRVKRMSTDLPFILDALQNSSTVEAQG--DKVRR 372 (563)
Q Consensus 297 ~~L~~~I~kQIEYYFSDeNL~kD~FLRk~M--D~dG~VPIslIasFnRVK~LT~Di~lI~eALr~S~~VEV~~--dKVRR 372 (563)
++++++|++||||||||+||+||.||+++| ++||||||++|++|+|||+||.|+++|++||+.|+.|||++ ++|||
T Consensus 8 ~~~~~~I~~QvEyYFSd~NL~~D~fL~~~m~~~~~G~Vpl~~i~sF~r~k~lt~d~~~i~~al~~S~~lev~edg~~VRR 87 (92)
T 1s29_A 8 SENKQKLQKQVEFYFSDVNVQRDIFLKGKMAENAEGFVSLETLLTFKRVNSVTTDVKEVVEAIRPSEKLVLSEDGLMVRR 87 (92)
T ss_dssp HHHHHHHHHHHHHHTSHHHHTTCHHHHHHHTTSTTCCEEHHHHTTSHHHHTTCSCHHHHHHHHTTCSSEEECTTSSEEEE
T ss_pred HHHHHHHHHHHHhhcchhhhccCHHHHHHhccCCCCCEEhHHHhCChhHHHHcCCHHHHHHHHhhCCeEEEeCCCCEEeC
Confidence 589999999999999999999999999999 78999999999999999999999999999999999999985 48999
Q ss_pred CCCC
Q 008506 373 RDEW 376 (563)
Q Consensus 373 R~~w 376 (563)
|.++
T Consensus 88 ~~Pl 91 (92)
T 1s29_A 88 RDPL 91 (92)
T ss_dssp SSCC
T ss_pred CCCC
Confidence 9864
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=99.95 E-value=1.4e-29 Score=221.30 Aligned_cols=85 Identities=39% Similarity=0.636 Sum_probs=79.0
Q ss_pred hHHHHHHHHHHHhhhhcCCCCcCcchHHHHhhcCCCcEehhhhhcchhHhhhcCCHHHHHHHHhcCCceEEcC--Ceeec
Q 008506 295 ETLALKANIVKQIEYYFSDENLQNDHYLISLMDAQGWVPIAIIADFKRVKRMSTDLPFILDALQNSSTVEAQG--DKVRR 372 (563)
Q Consensus 295 e~~~L~~~I~kQIEYYFSDeNL~kD~FLRk~MD~dG~VPIslIasFnRVK~LT~Di~lI~eALr~S~~VEV~~--dKVRR 372 (563)
..++++++|++||||||||+||++|.||+++|++||||||++|++|+|||+||+|+++|++||+.|+.|||++ +||||
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 3578999999999999999999999999999999999999999999999999999999999999999999985 48998
Q ss_pred CCCCCcccc
Q 008506 373 RDEWSKWIP 381 (563)
Q Consensus 373 R~~w~kwv~ 381 (563)
|. ++|++
T Consensus 90 ~~--~~~i~ 96 (101)
T 2cqk_A 90 SH--KRCIS 96 (101)
T ss_dssp CC--SCCCC
T ss_pred CC--CCCcC
Confidence 74 56764
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=99.90 E-value=9.8e-25 Score=204.86 Aligned_cols=159 Identities=23% Similarity=0.313 Sum_probs=111.6
Q ss_pred HHHHHHHHHHhhhhcCCCCcCcchHHHHhhc-CCCcEehhhhhcchhHhhhcCCHHHHHHHHhcC--CceEEcCC--eee
Q 008506 297 LALKANIVKQIEYYFSDENLQNDHYLISLMD-AQGWVPIAIIADFKRVKRMSTDLPFILDALQNS--STVEAQGD--KVR 371 (563)
Q Consensus 297 ~~L~~~I~kQIEYYFSDeNL~kD~FLRk~MD-~dG~VPIslIasFnRVK~LT~Di~lI~eALr~S--~~VEV~~d--KVR 371 (563)
++|+.+|++||||||||+||++|.||+++|+ ++|||+|++|++|+|||+|+.|+++|++||+.| ..|+++++ +||
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 cCCCCC--cccccccccccCCc----ccCccccccccccccccCCCCCCCCCCCCCcccccccCCCCcccCCCCCCCccc
Q 008506 372 RRDEWS--KWIPASVEQTMSST----AQTSQSQSAENPVDSIGNGDINKDNKREMPKENVGFSSNTGNLMENVPPSFDSV 445 (563)
Q Consensus 372 RR~~w~--kwv~~s~e~~~~S~----~~~~~~~pieev~~~f~n~~~~~~n~~~~~~~~~efa~n~~~~~~~~~~~~~~~ 445 (563)
|+.... .+-.... .....+ ..++.+...++.+.+|+.-- ...+|....+.+ ....--+|++|
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-NDVKNRSVYIKGFPTDATLDDIKEWLEDKG---------QVLNIQMRRTLH--KAFKGSIFVVF 157 (193)
T ss_dssp ECTTSCCCCCCHHHH-HHHHHTEEEEECCCTTCCHHHHHHHHTTSC---------CEEEEEEEECTT--CCEEEEEEEEE
T ss_pred ecccCCCcccchhhh-hccccCEEEecCCCCcCCHHHHHHHHhcCC---------CEEEEEEEECCC--CCcccEEEEEE
Confidence 874211 1100000 001111 12667777788888887321 111222211111 11222389999
Q ss_pred ccCCCCCcccccccccccCCCCc
Q 008506 446 EIEPDNGEEHCDEFLLLDDGKPA 468 (563)
Q Consensus 446 ~~~~da~~~~~~~~~~~~~~kp~ 468 (563)
+..++|.+|+..... ...|+++
T Consensus 158 ~~~e~A~~A~~~~~~-~~~Gr~l 179 (193)
T 2voo_A 158 DSIESAKKFVETPGQ-KYKETDL 179 (193)
T ss_dssp SSHHHHHHHHHCTTC-EETTEEC
T ss_pred CCHHHHHHHHHhCCC-eECCEEE
Confidence 999999999865322 4445443
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=90.35 E-value=0.34 Score=46.30 Aligned_cols=54 Identities=15% Similarity=0.207 Sum_probs=40.7
Q ss_pred hcCCCcEehhhhhcchhHh--hhcCCHHHHHHHHhcCCc--eEEcCCeeecCCCCCccc
Q 008506 326 MDAQGWVPIAIIADFKRVK--RMSTDLPFILDALQNSST--VEAQGDKVRRRDEWSKWI 380 (563)
Q Consensus 326 MD~dG~VPIslIasFnRVK--~LT~Di~lI~eALr~S~~--VEV~~dKVRRR~~w~kwv 380 (563)
||++|||+|..|+. -+.+ ....+.+.|.+++++.+. .++++++||.+....--|
T Consensus 24 ld~~G~v~v~~LL~-~~~~~~~~~~t~~~l~~vV~~~~K~Rf~l~~~~IRA~qGHSi~V 81 (186)
T 1wfx_A 24 LTREGWARVSEVVE-GLRKAGWSWVEEWHIVGVALHDPKGRYELRNGEIRARYGHSIPV 81 (186)
T ss_dssp CCTTCCEEHHHHHH-HHHHTTCTTCCHHHHHHHHHHCSSCCEEEETTEEEESSCCSSCC
T ss_pred cCCCCCEEHHHHHh-hhhhcccCCCCHHHHHHHHhcCCCCceEeeccEEEeccCCCCcc
Confidence 58999999999998 4433 334567889999887764 788899999887654433
No 5
>3htx_A HEN1; HEN1, small RNA methyltransferase, protein-RNA complex; HET: SAH; 3.10A {Arabidopsis thaliana}
Probab=83.57 E-value=1.7 Score=50.48 Aligned_cols=85 Identities=25% Similarity=0.439 Sum_probs=64.5
Q ss_pred HHHHHHHHHHHhhhhcCCCCcCcchHHHHhh--------cCCCcEehhhhhcch-hHhhhcC--------C----HHHHH
Q 008506 296 TLALKANIVKQIEYYFSDENLQNDHYLISLM--------DAQGWVPIAIIADFK-RVKRMST--------D----LPFIL 354 (563)
Q Consensus 296 ~~~L~~~I~kQIEYYFSDeNL~kD~FLRk~M--------D~dG~VPIslIasFn-RVK~LT~--------D----i~lI~ 354 (563)
.++..+.|+.+|+|.|||+=|.-..=|..++ +--|.||+++|+.+. ||-.+++ | +.+|.
T Consensus 104 ~~~~~~~~~~~~~~~f~~e~~~~~~pl~~h~~~~~~r~~~~~~~~p~~~~~~~d~k~~~~ck~~~~~~e~~p~~~~~~~~ 183 (950)
T 3htx_A 104 VDEARDEIVGRIKYIFSDEFLSAEHPLGAHLRAALRRDGERCGSVPVSVIATVDAKINSRCKIINPSVESDPFLAISYVM 183 (950)
T ss_dssp HHHHHHHHHHHHHHHTSTGGGGCSSTHHHHHHHHHTSCGGGTTEECHHHHHHTCHHHHHHHHHHCTHHHHCTHHHHHHHH
T ss_pred hhhHHHHHHHHHHHHhhhhhhhccCchHHHHHHHHhhcCccccccchhhheehhhhhhhhhhhcCcccccChHHHHHHHH
Confidence 4789999999999999999999888787777 246899999999984 4444442 1 46788
Q ss_pred HHHhcCCceEE-cCCeeecCCCCCccc
Q 008506 355 DALQNSSTVEA-QGDKVRRRDEWSKWI 380 (563)
Q Consensus 355 eALr~S~~VEV-~~dKVRRR~~w~kwv 380 (563)
.|...++-+-+ ++.-|||+++..-=+
T Consensus 184 ~a~~~~~~~~~~~~~~~~~~~~~~~~~ 210 (950)
T 3htx_A 184 KAAAKLADYIVASPHGLRRKNAYPSEI 210 (950)
T ss_dssp HHHHHCCSSEEEETTEEEESSCCCHHH
T ss_pred HHhhcCCCcEEeCCcccccCCCCCHHH
Confidence 88887754445 456899998765433
No 6
>2k9l_A RNA polymerase sigma factor RPON; protein, transcription; NMR {Aquifex aeolicus}
Probab=50.37 E-value=16 Score=29.57 Aligned_cols=54 Identities=11% Similarity=0.232 Sum_probs=36.4
Q ss_pred HHHHHHHhhhhcCCCCcCcchHHHHhhcCCCcE--ehhhhhcchhHhhhcCCHHHHHHHHh
Q 008506 300 KANIVKQIEYYFSDENLQNDHYLISLMDAQGWV--PIAIIADFKRVKRMSTDLPFILDALQ 358 (563)
Q Consensus 300 ~~~I~kQIEYYFSDeNL~kD~FLRk~MD~dG~V--PIslIasFnRVK~LT~Di~lI~eALr 358 (563)
.+.|..||...|++.-..==.||...+|++||+ ++..|+. .|..+.+.|..+|+
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 888999998445555443456888888999996 5555653 23356666666654
No 7
>2k9m_A RNA polymerase sigma factor RPON; core binding domain, transcription; NMR {Aquifex aeolicus}
Probab=34.79 E-value=24 Score=31.58 Aligned_cols=79 Identities=10% Similarity=0.185 Sum_probs=46.2
Q ss_pred HHHHHHHHHhhhhcCCCCcCcchHHHHhhcCCCcE--ehhhhhcchhHhhhcCCHHHHHHHHhcCCceEEcCCeeecCCC
Q 008506 298 ALKANIVKQIEYYFSDENLQNDHYLISLMDAQGWV--PIAIIADFKRVKRMSTDLPFILDALQNSSTVEAQGDKVRRRDE 375 (563)
Q Consensus 298 ~L~~~I~kQIEYYFSDeNL~kD~FLRk~MD~dG~V--PIslIasFnRVK~LT~Di~lI~eALr~S~~VEV~~dKVRRR~~ 375 (563)
.|.+.|..||...||+.-..==.||...+|++||+ ++..|+. .+..+.+.|..+|+.--.++= -.|=.| +
T Consensus 4 sL~e~L~~Ql~~~~~~~~~~ia~~iI~~LD~~GYL~~~l~eia~-----~l~~~~~eve~vL~~iQ~~dP--~GVgAr-d 75 (130)
T 2k9m_A 4 SELEELQQNIKLELEGKEQELALELLNYLNEKGFLSKSVEEISD-----VLRCSVEELEKVRQKVLRLEP--LGVCSK-D 75 (130)
T ss_dssp CHHHHHHHHHHHHCCSHHHHHHHHHTTSBCTTSSBSSCHHHHHH-----HTTCCHHHHHHHHHHHHTSSS--CCTTTS-C
T ss_pred CHHHHHHHHHcccCCHHHHHHHHHHHHhcCCCCCCCCCHHHHHH-----HcCCCHHHHHHHHHHHhcCCC--CccccC-C
Confidence 57888999998445554333335677777999996 4555653 234566677776664333322 223222 4
Q ss_pred CCccccccc
Q 008506 376 WSKWIPASV 384 (563)
Q Consensus 376 w~kwv~~s~ 384 (563)
...|+.+-.
T Consensus 76 L~ECLllQL 84 (130)
T 2k9m_A 76 VWEFLELQI 84 (130)
T ss_dssp TTHHHHHHH
T ss_pred HHHHHHHHH
Confidence 555555444
No 8
>2jo7_A Glycosylphosphatidylinositol-anchored merozoite surface protein; surface antigen, GPI-anchored protein, recombinant vaccine; NMR {Babesia divergens}
Probab=17.42 E-value=1.4e+02 Score=29.10 Aligned_cols=52 Identities=17% Similarity=0.249 Sum_probs=41.6
Q ss_pred HHHHHHHHHHHhhhhcCCCCcCcchHHHHhhcCCCcEehhhhhcchhHhh----hcCCHHHHHHHHh
Q 008506 296 TLALKANIVKQIEYYFSDENLQNDHYLISLMDAQGWVPIAIIADFKRVKR----MSTDLPFILDALQ 358 (563)
Q Consensus 296 ~~~L~~~I~kQIEYYFSDeNL~kD~FLRk~MD~dG~VPIslIasFnRVK~----LT~Di~lI~eALr 358 (563)
.++|+..++-|= .+||...|++||-.-|.-|..|=||-. |..|-..|.+|-+
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 357888888886 589999999999999999999999986 3356666665544
No 9
>1dfa_A PI-SCEI endonuclease; intein, homing endonuclease, hydrolase; 2.00A {Saccharomyces cerevisiae} SCOP: b.86.1.2 d.95.2.2 d.95.2.2 PDB: 1lws_A 1lwt_A 1vde_A 1ef0_A 1um2_A 1jva_A
Probab=8.59 E-value=44 Score=35.01 Aligned_cols=27 Identities=22% Similarity=0.463 Sum_probs=23.1
Q ss_pred hhhcCCCCcCcchHHHHhhcCCCcEeh
Q 008506 308 EYYFSDENLQNDHYLISLMDAQGWVPI 334 (563)
Q Consensus 308 EYYFSDeNL~kD~FLRk~MD~dG~VPI 334 (563)
++||....-.+=.||+..+|.||+|.-
T Consensus 305 ~~i~~~~~~~~~~fL~Glfd~DG~v~~ 331 (454)
T 1dfa_A 305 SFLSTDNIGTRETFLAGLIDSDGYVTD 331 (454)
T ss_dssp GGGGTSCHHHHHHHHHHHHHHHCCEEC
T ss_pred HHHHcCCHHHHHHHHHHHccCCCceec
Confidence 678887777788999999999999864
No 10
>3c18_A Nucleotidyltransferase-like protein; ZP_00538802.1, structur genomics, joint center for structural genomics, JCSG; 1.90A {Exiguobacterium sibiricum}
Probab=8.20 E-value=2.6e+02 Score=28.45 Aligned_cols=69 Identities=13% Similarity=0.171 Sum_probs=50.8
Q ss_pred HHHHHHHHHhhhhcCCCCcCcchHHHHhhc-CCCcEehhhhhcchhHhhhcCCHHHHHHHHhcCCceEEc
Q 008506 298 ALKANIVKQIEYYFSDENLQNDHYLISLMD-AQGWVPIAIIADFKRVKRMSTDLPFILDALQNSSTVEAQ 366 (563)
Q Consensus 298 ~L~~~I~kQIEYYFSDeNL~kD~FLRk~MD-~dG~VPIslIasFnRVK~LT~Di~lI~eALr~S~~VEV~ 366 (563)
+..+.+.--+||+....=-.-=.+|.+.|. .+++..+.-|..-..++.++-|+..|++=|-....|+++
T Consensus 203 krielllla~Ef~I~sk~~~~~~~Ll~~m~ek~~~wS~~Ei~~~p~~~~~~idle~iL~~Lv~k~lI~~~ 272 (290)
T 3c18_A 203 QRIHLALIGLEHLLQSKVLSGGKYLFEVMRERDRPWTMHELMEESRLTELKVDLGSLVDFFIRKGLIRIS 272 (290)
T ss_dssp HHHHHHHHHHHHHHHHTHHHHHHHHHHHHTTSSSCEEHHHHHHCGGGGGGHHHHHHHHHHHHHTTSEEEE
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHhcCcccccccCCHHHHHHHHHHcCCeEEe
Confidence 444444445555443222222356777775 678999999999999999999999999999999988876
Done!