Query 000935
Match_columns 1219
No_of_seqs 27 out of 29
Neff 1.7
Searched_HMMs 29240
Date Tue Mar 26 16:17:33 2013
Command hhsearch -i /local_scratch/syshi/lefta3m/000935.a3m -d /local_scratch/syshi/pdb70.hhm -v 0 -o /local_scratch/syshi/H1_704-707//hhsearch_pdb/000935hhsearch_pdb
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 1r9f_A Core protein P19; prote 1.0 1 1 18.1 -1.4 22 456-477 5-27 (136)
2 1rpu_A 19 kDa protein; RNAI, p 1.0 1 1 17.8 -1.4 21 456-476 27-48 (172)
3 4gga_A P55CDC, cell division c 1.0 1 1 14.9 7.3 81 88-188 96-178 (420)
4 3m6c_A 60 kDa chaperonin 1; ch 1.0 1 1 14.7 -0.6 18 642-659 166-184 (194)
5 2fc6_A Nuclear, target of EGR1 1.0 1 1 14.6 -1.0 21 91-113 19-39 (50)
6 2dyd_A Poly(A)-binding protein 1.0 1 1 14.2 -2.7 53 694-747 10-62 (85)
7 3ut4_A CTHE_2751, putative unc 1.0 1 1 14.1 2.4 29 359-387 40-68 (134)
8 2we8_A Xanthine dehydrogenase; 1.0 1 1 13.7 -0.2 11 772-782 338-348 (386)
9 3on5_A BH1974 protein; structu 1.0 1 1 13.5 -0.2 28 904-931 195-222 (362)
10 3s8s_A Histone-lysine N-methyl 1.0 1 1 13.3 -1.0 62 496-558 1-62 (110)
No 1
>1r9f_A Core protein P19; protein-RNA complex, dimer, double helix, viral protein/RNA complex; 1.85A {Tomato bushy stunt virus} SCOP: d.255.1.1
Probab=1.00 E-value=1 Score=18.11 Aligned_cols=22 Identities=50% Similarity=0.885 Sum_probs=15.1
Q ss_pred CCCC-CCCCCCCCCEEEEEEECC
Q ss_conf 3999-999999632035875205
Q 000935 456 MSPY-DPDEGPSITGWRVQRWES 477 (1219)
Q Consensus 456 MSPy-dPdeGPsiTGWRvqrWES 477 (1219)
.+|+ -|||.|+.+.||++.=|.
T Consensus 5 ~sPFklpDESPs~~EWRlH~~e~ 27 (136)
T 1r9f_A 5 TSPFKLPDESPSWTEWRLHNDET 27 (136)
T ss_dssp CCSCSSCCCCCCHHHHHHHHHHC
T ss_pred CCCCCCCCCCCCHHHHHCCCCCC
T ss_conf 58751788999703530015556
No 2
>1rpu_A 19 kDa protein; RNAI, protein-RNA complex, RNA double helix, RNA length recognition, RNA binding protein/RNA complex; 2.50A {Carnation italian ringspot virus} SCOP: d.255.1.1
Probab=1.00 E-value=1 Score=17.84 Aligned_cols=21 Identities=52% Similarity=0.857 Sum_probs=15.5
Q ss_pred CCCC-CCCCCCCCCEEEEEEEC
Q ss_conf 3999-99999963203587520
Q 000935 456 MSPY-DPDEGPSITGWRVQRWE 476 (1219)
Q Consensus 456 MSPy-dPdeGPsiTGWRvqrWE 476 (1219)
.+|+ -|||.|+.+.||++.=|
T Consensus 27 ~sPFklpDESPs~~EWRlh~~e 48 (172)
T 1rpu_A 27 TSPFKLPDESPSWTEWRLYNDE 48 (172)
T ss_dssp CCSBSSCCCCCCHHHHHHHTTC
T ss_pred CCCCCCCCCCCCHHHHHHCCCC
T ss_conf 5875078889870353101455
No 3
>4gga_A P55CDC, cell division cycle protein 20 homolog; cell cycle, mitosis, securin, ubiquitination, WD40; 2.04A {Homo sapiens} PDB: 4ggd_A
Probab=1.00 E-value=1 Score=14.92 Aligned_cols=81 Identities=15% Similarity=0.338 Sum_probs=53.2
Q ss_pred CCCHHHHHHCC--CHHHHHCCCCCEECCCCCCCCCCCCCCCCCCEEEEEEECCCCCCCEEEEEEECCCCCCCEEEEEECC
Q ss_conf 35845753136--3023300011100012213457999999982034888227997420378961279978548976368
Q 000935 88 KMSVPELCRNF--SAVAWCGKLNAIACASETCARIPSSNANTPFWIPIHIVIPERPTECAVFNVIADCPRDSVQFIEWSP 165 (1219)
Q Consensus 88 Km~vpElcRnF--savawc~klN~iaca~eTCarip~S~~np~FWiPihIviPerPtE~avfnv~adsp~d~vq~ieWSp 165 (1219)
-+..|+|.-.| +.++|- ..|.||.+...+.+ |-..+.-.-...+ ......++|.++.|||
T Consensus 96 ~l~ap~~~~d~y~~~l~wS-~~n~lAvgld~tV~---------------lWd~~tg~~~~~~--~~~~~~~~V~sv~fsp 157 (420)
T 4gga_A 96 ILDAPEIRNDYYLNLVDWS-SGNVLAVALDNSVY---------------LWSASSGDILQLL--QMEQPGEYISSVAWIK 157 (420)
T ss_dssp EEECTTCCCCTTCBCEEEC-TTSEEEEEETTEEE---------------EEETTTCCEEEEE--ECCSTTCCEEEEEECT
T ss_pred EEECCCCCCCCCCEEEEEC-CCCEEEEEECCEEE---------------EEECCCCCEEEEE--EECCCCCCEEEEEECC
T ss_conf 8789887566335248787-99999999699999---------------9989999789999--8148998489999979
Q ss_pred CCCCCEEEEEECCCEEEEEECCC
Q ss_conf 98863477873043099973589
Q 000935 166 TSCPRALLIANFYGRVTIWTQPS 188 (1219)
Q Consensus 166 ~~cpRALLiAnf~GRvtIWtQPs 188 (1219)
.+ +-|+++...|.|.||.-.+
T Consensus 158 dg--~~lasgs~Dg~v~iWd~~~ 178 (420)
T 4gga_A 158 EG--NYLAVGTSSAEVQLWDVQQ 178 (420)
T ss_dssp TS--SEEEEEETTSCEEEEETTT
T ss_pred CC--CEEEEEECCCEEEEEECCC
T ss_conf 99--9999998998299998689
No 4
>3m6c_A 60 kDa chaperonin 1; chaperone, ATP-binding, nucleotide-binding; 2.20A {Mycobacterium tuberculosis}
Probab=1.00 E-value=1 Score=14.75 Aligned_cols=18 Identities=28% Similarity=0.829 Sum_probs=8.7
Q ss_pred CCCCCCHHHHHHH-HHHHH
Q ss_conf 4322331468999-99887
Q 000935 642 SQVKANSSTWERA-IAERF 659 (1219)
Q Consensus 642 ~q~ka~ss~wera-iaeRf 659 (1219)
.|....+|.++|. +.||.
T Consensus 166 ~~ie~t~s~ydkEKLqERl 184 (194)
T 3m6c_A 166 AEIDKSDSDWDREKLGERL 184 (194)
T ss_dssp HHHHTCCCHHHHHHHHHHH
T ss_pred HHHHHCCCHHHHHHHHHHH
T ss_conf 9988559988999999999
No 5
>2fc6_A Nuclear, target of EGR1, member 1; structure genomics, ZF-CCCH domain, member 1(nuclear), structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.66.1.1
Probab=1.00 E-value=1 Score=14.63 Aligned_cols=21 Identities=38% Similarity=0.933 Sum_probs=15.1
Q ss_pred HHHHHHCCCHHHHHCCCCCEECC
Q ss_conf 45753136302330001110001
Q 000935 91 VPELCRNFSAVAWCGKLNAIACA 113 (1219)
Q Consensus 91 vpElcRnFsavawc~klN~iaca 113 (1219)
.-.+|++|||--||-+ .+-|-
T Consensus 19 ~~~iC~~FSayGwCp~--G~~Cp 39 (50)
T 2fc6_A 19 PTSICDNFSAYGWCPL--GPQCP 39 (50)
T ss_dssp CSCBCSHHHHTCCCTT--GGGCS
T ss_pred CCCHHHHCCCCCCCCC--CCCCC
T ss_conf 2203020012552788--88788
No 6
>2dyd_A Poly(A)-binding protein; alpha helical protein, RNA binding protein; NMR {Triticum aestivum}
Probab=1.00 E-value=1 Score=14.15 Aligned_cols=53 Identities=26% Similarity=0.387 Sum_probs=40.3
Q ss_pred ECCCCCCCCCHHHHHHCCCCCCCEEEEECCCCCHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 325677897311131208975623365426861578999888768999999730
Q 000935 694 LDADFHSLPSIQHRQQYGPSLDRIKCRLLEGTNAQEVRAMVLDMQARLLLDMLG 747 (1219)
Q Consensus 694 lDaDFHsLps~QhRqqy~p~lDrIkCrlLeG~nAqeVRamVLDMQaRllLDMLG 747 (1219)
.-+++-+.|.-|+||.-|-.|--.--+ ++-..|..+-.|.|+|..--+|.||-
T Consensus 10 ~as~La~~~p~~Qkq~LGE~LyplV~~-~~p~~AgKITGMLLEmd~~Ell~Lle 62 (85)
T 2dyd_A 10 LASALANSPPETQRMMLGENLYPLVDQ-LEHDQAAKVTGMLLEMDQTEVLHLLE 62 (85)
T ss_dssp SCHHHHCCCHHHHHHHHHHHHHHHHCC-SCHHHHHHHHHHHHHHCHHHHHHHTT
T ss_pred HHHHHHCCCHHHHHHHHHHHHHHHHHH-HCCCCCCHHHHHHHCCCHHHHHHHHC
T ss_conf 699987489799999888888999998-58310020666452688899999976
No 7
>3ut4_A CTHE_2751, putative uncharacterized protein; non PFAM singleton, helical fold, unknown function; 2.03A {Clostridium thermocellum} PDB: 3ut8_A 3ut7_A
Probab=1.00 E-value=1 Score=14.12 Aligned_cols=29 Identities=10% Similarity=0.109 Sum_probs=25.3
Q ss_pred CCCCCCCCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf 99998778512356655679999888530
Q 000935 359 LSPPKWAGFAPLAAYLFSWQEYLLSEAKQ 387 (1219)
Q Consensus 359 l~pp~W~GFaPLaAYLfswq~yl~se~~q 387 (1219)
|+-.||+++.+++.+|-..+++++-..++
T Consensus 40 LQD~NWPvA~~i~~~L~~~~~~l~p~I~~ 68 (134)
T 3ut4_A 40 LQDYNWPIAKDILPVVVLHQSIAMPHILT 68 (134)
T ss_dssp GSCTTSTTHHHHHHHHHHTHHHHHHHHHH
T ss_pred HHCCCCCCHHHHHHHHHHCCHHHHHHHHH
T ss_conf 82178832787999999755755899999
No 8
>2we8_A Xanthine dehydrogenase; oxidoreductase; 2.30A {Mycobacterium smegmatis} PDB: 2we7_A
Probab=1.00 E-value=1 Score=13.72 Aligned_cols=11 Identities=55% Similarity=0.758 Sum_probs=4.2
Q ss_pred CCCCCCCCCCC
Q ss_conf 45889864001
Q 000935 772 LSGIDPEAMAV 782 (1219)
Q Consensus 772 ls~i~pe~maV 782 (1219)
+.+-.|++.||
T Consensus 338 IGa~tPeEIAv 348 (386)
T 2we8_A 338 LGGRTPEETAV 348 (386)
T ss_dssp CCCCSHHHHHH
T ss_pred CCCCCHHHHHH
T ss_conf 89989899999
No 9
>3on5_A BH1974 protein; structural genomics, joint center for structural genomics, J protein structure initiative, PSI-biology, oxidoreductase; 2.80A {Bacillus halodurans}
Probab=1.00 E-value=1 Score=13.47 Aligned_cols=28 Identities=7% Similarity=-0.016 Sum_probs=20.2
Q ss_pred CCCCCCCEEEECCHHHHHHHHHHHHHHH
Q ss_conf 7889862165221145788789988876
Q 000935 904 TFPGTPAVRLIGDCHFLHRLCQLLLFCF 931 (1219)
Q Consensus 904 TFPGTPAVRLIgDCHFLhRLCQLLlFCf 931 (1219)
.|.-.|-+-++|--|+-.-|++++-+.=
T Consensus 195 ~~~p~~~L~I~GaGhva~aLa~la~~lg 222 (362)
T 3on5_A 195 IYSPKERLIIFGAGPDVPPLVTFASNVG 222 (362)
T ss_dssp EECCCEEEEEECCSTTHHHHHHHHHHHT
T ss_pred ECCCCCEEEEECCCHHHHHHHHHHHHCC
T ss_conf 6389978999898889999999997789
No 10
>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens}
Probab=1.00 E-value=1 Score=13.35 Aligned_cols=62 Identities=16% Similarity=0.154 Sum_probs=38.3
Q ss_pred CCCCCCEEEEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEECCCCCCCCCCHH
Q ss_conf 999991258985200146898743333345898656665445333345400049999960055
Q 000935 496 GGQAPMQTVWVSKVDTSIPTSNFKIHQLAAAGPTCDVWKTTDSGLEKSKIVSFDPFDLPSDIR 558 (1219)
Q Consensus 496 gGqpPmqTvW~skvd~SIpptdfkn~q~~~~~~~~d~~~~s~~~~dksk~v~FdpfdlP~dvr 558 (1219)
||+||..+++++..+.++...+++.. +-..|...+++-..|....+++..-|=-|+-+.+..
T Consensus 1 Gg~~p~~~lfV~nL~~~~te~~L~~~-F~~~G~i~~v~i~~d~~tg~~rG~aFV~f~~~~~A~ 62 (110)
T 3s8s_A 1 GGQIPLKEVTFARLNDNVRETFLKDM-CRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAK 62 (110)
T ss_dssp -CCSCCCEEEEESCCTTCCHHHHHHH-HTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHH
T ss_pred CCCCCCCEEEEECCCCCCCHHHHHHH-HHHCCCEEEEEEEECCCCCCEEEEEEEEECCHHHHH
T ss_conf 98899838999799999999999999-985697448999777999946069999989799999
Done!