Query 000469
Match_columns 1472
No_of_seqs 174 out of 228
Neff 7.0
Searched_HMMs 29240
Date Tue Mar 26 16:30:26 2013
Command hhsearch -i /local_scratch/syshi/lefta3m/000469.a3m -d /local_scratch/syshi/pdb70.hhm -v 0 -o /local_scratch/syshi/H1_248-252//hhsearch_pdb/000469hhsearch_pdb
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 1vdy_A Hypothetical protein (R 1.0 1 1 9.8 10.1 88 553-672 45-132 (140)
2 1xqr_A HSPBP1 protein; armadil 1.0 1 1 9.5 5.9 15 1039-1053 204-218 (296)
3 2db0_A 253AA long hypothetical 1.0 1 1 9.4 5.0 72 171-259 71-143 (253)
4 1sz9_A PCF11 protein; RNA poly 1.0 1 1 9.2 2.4 16 203-218 99-114 (144)
5 3e98_A GAF domain of unknown f 1.0 1 1 9.1 3.2 24 590-614 31-54 (252)
6 3d23_B 3C-like proteinase; mai 1.0 1 1 8.4 2.3 80 40-143 206-296 (302)
7 2zze_A Alanyl-tRNA synthetase; 1.0 1 1 8.3 -4.4 23 77-99 143-174 (752)
8 3d9j_A RNA-binding protein 16; 1.0 1 1 8.2 2.8 35 995-1029 37-71 (145)
9 1lrr_A SEQA protein; protein-D 1.0 1 1 8.1 0.8 22 29-50 33-54 (131)
10 1j3e_A SEQA protein; protein-D 1.0 1 1 8.0 0.8 22 29-50 17-38 (115)
No 1
>1vdy_A Hypothetical protein (RAFL09-17-B18); structural genomics, riken structural genomics/proteomics initiative, RSGI, unknown function; NMR {Arabidopsis thaliana} PDB: 2dcp_A
Probab=1.00 E-value=1 Score=9.83 Aligned_cols=88 Identities=13% Similarity=0.160 Sum_probs=54.1
Q ss_pred CHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHCCCCCCHHHHHHHHCCCCCHHHHHHHHCCCCCCCCCCCCHHHHHHH
Q ss_conf 41999999998417999741479999999999422999848889999413010499843010788999999842688999
Q 000469 553 SCLKIILEILEKVSKPDVNALLHEFGFQLLYELCLDPLTCGPTMDLLSNKKYQFFVKHLDAIGVAPLPKRNSNQALRISS 632 (1472)
Q Consensus 553 ScLhsIL~lL~~~~~~~~~p~L~e~~~~LL~~Lc~~p~TS~~tLr~LR~~~~dff~~~L~~~~i~~lp~~~~~~~~~~s~ 632 (1472)
+.++-|.+.|.+.+. +..|+.+-+|++||-.||.+- |+.+.+.+|.+- ...+.+..-.-.|.|... ...
T Consensus 45 ~~~~eim~~L~kRL~-~k~~~vk~KaL~lL~yL~~~G--s~~f~~~~r~~~--~~Ik~l~~F~g~~dp~~G-~d~----- 113 (140)
T 1vdy_A 45 SIVKEFSEFILKRLD-NKSPIVKQKALRLIKYAVGKS--GSEFRREMQRNS--VAVRNLFHYKGHPDPLKG-DAL----- 113 (140)
T ss_dssp HHHHHHHHHHHHHHT-SSSHHHHHHHHHHHHHHTTTS--CHHHHHHHHHTT--HHHHTTTTCCCCCCTTTS-SCH-----
T ss_pred HHHHHHHHHHHHHHC-CCCCCEEEHHHHHHHHHHHHC--CHHHHHHHHHHH--HHHHHHHHCCCCCCCCCC-CCH-----
T ss_conf 589999999999965-899652004999999999719--899999999809--999999965899974466-425-----
Q ss_pred HHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHCCCC
Q ss_conf 9999999999999998312998601478999999631898
Q 000469 633 LHQRAWLLKLLAIELHAGYGSSSTHQEACQTILAHLFGRD 672 (1472)
Q Consensus 633 L~~rs~lL~~~AlEL~~~s~~~s~~~~~~~~ll~~L~g~~ 672 (1472)
+..-|...+.++++|++..
T Consensus 114 ---------------------g~~VR~~AkEl~~ll~d~~ 132 (140)
T 1vdy_A 114 ---------------------NKAVRETAHETISAIFSEE 132 (140)
T ss_dssp ---------------------HHHHHHHHHHHHHHHTCCS
T ss_pred ---------------------HHHHHHHHHHHHHHHHCCC
T ss_conf ---------------------0899999999999971868
No 2
>1xqr_A HSPBP1 protein; armadillo repeat, superhelical twist, chaperone; 2.10A {Homo sapiens} SCOP: a.118.1.21 PDB: 1xqs_A*
Probab=1.00 E-value=1 Score=9.53 Aligned_cols=15 Identities=27% Similarity=0.308 Sum_probs=5.3
Q ss_pred HHHHCCCHHHHHHHH
Q ss_conf 997119399999983
Q 000469 1039 QLQSRGFLRSCLMNV 1053 (1472)
Q Consensus 1039 ~L~~~g~L~~li~sl 1053 (1472)
.+...|.+..++.-+
T Consensus 204 ~vv~~g~i~~Lv~LL 218 (296)
T 1xqr_A 204 TLCSMGMVQQLVALV 218 (296)
T ss_dssp HHHHTTHHHHHHHHH
T ss_pred HHHHCCCHHHHHHHH
T ss_conf 999868799999987
No 3
>2db0_A 253AA long hypothetical protein; heat repeats, helical structure, structural genomics; 2.20A {Pyrococcus horikoshii}
Probab=1.00 E-value=1 Score=9.44 Aligned_cols=72 Identities=18% Similarity=0.323 Sum_probs=30.8
Q ss_pred HHHHHHHCCCCCCCHHHHHHHHHHHHHHHHCCHHHHHHH-HHHHHHCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHH
Q ss_conf 288997615899895499999999997420392459999-9998622688755667788877677720107999999864
Q 000469 171 IEPLFKLLSYENVPPYLKGALRNAIAACIHVSLVMKDNI-WRLLEQYDLPVVVGTHVGNTAQPIAGQVYDMQFELNEIEA 249 (1472)
Q Consensus 171 i~~Lf~Ll~~~~Vp~~LKa~il~tLaal~~~s~~~a~~i-W~~Ld~~~i~~~~~~~~~~~~~~~~~~~~gi~~el~eiE~ 249 (1472)
+.-||.++. .+=..+|.-+|=++++.+++..|+.-+.+ =-....+-+ |+ .....++.+.+++|
T Consensus 71 ~~kL~vm~~-ksEaIpltqeIa~a~G~la~i~Pe~v~~vVp~lfanyri--------gd-----~kikIn~~yaLeeI-- 134 (253)
T 2db0_A 71 LKKLFSLLK-KSEAIPLTQEIAKAFGQMAKEKPELVKSMIPVLFANYRI--------GD-----EKTKINVSYALEEI-- 134 (253)
T ss_dssp HHHHHHHHH-HCCSHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHSCC--------CS-----HHHHHHHHHHHHHH--
T ss_pred HHHHHHHHH-HCCCCCHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHC--------CC-----CCCEECHHHHHHHH--
T ss_conf 999999984-103585388988987589871899887658999988751--------78-----41102299999999--
Q ss_pred HCCCCCCHHH
Q ss_conf 1047864599
Q 000469 250 RREQYPSTIS 259 (1472)
Q Consensus 250 ~~~~Yp~t~a 259 (1472)
...||+..+
T Consensus 135 -aranP~l~~ 143 (253)
T 2db0_A 135 -AKANPMLMA 143 (253)
T ss_dssp -HHHCHHHHH
T ss_pred -HHHCHHHHH
T ss_conf -986967789
No 4
>1sz9_A PCF11 protein; RNA polymerase II CTD interacting domain, arm repeats, transcription; 2.10A {Saccharomyces cerevisiae} SCOP: a.118.9.4 PDB: 1sza_A* 2bf0_X
Probab=1.00 E-value=1 Score=9.20 Aligned_cols=16 Identities=0% Similarity=0.059 Sum_probs=6.5
Q ss_pred HHHHHHHHHHHHHCCC
Q ss_conf 2459999999862268
Q 000469 203 LVMKDNIWRLLEQYDL 218 (1472)
Q Consensus 203 ~~~a~~iW~~Ld~~~i 218 (1472)
+..+.+|...++.|.-
T Consensus 99 ~~~r~k~~rL~~~W~~ 114 (144)
T 1sz9_A 99 NTTRTKLINMFKLWLN 114 (144)
T ss_dssp HHHHHHHHHHHHHHTS
T ss_pred HHHHHHHHHHHHHHHC
T ss_conf 9999999999999837
No 5
>3e98_A GAF domain of unknown function; structural genomics, joint center for structural genomics, JCSG, protein structure initiative, PSI-2; HET: MSE; 2.43A {Pseudomonas aeruginosa}
Probab=1.00 E-value=1 Score=9.15 Aligned_cols=24 Identities=33% Similarity=0.517 Sum_probs=13.0
Q ss_pred CCCHHHHHHHHCCCCCHHHHHHHHC
Q ss_conf 9848889999413010499843010
Q 000469 590 LTCGPTMDLLSNKKYQFFVKHLDAI 614 (1472)
Q Consensus 590 ~TS~~tLr~LR~~~~dff~~~L~~~ 614 (1472)
.|..-|..||+.++ |||.+|-...
T Consensus 31 l~~~~V~~yL~~~P-dFf~~~~~Ll 54 (252)
T 3e98_A 31 LDAEQVAAYLSQHP-EFFVEHDELI 54 (252)
T ss_dssp -------------------------
T ss_pred CCHHHHHHHHHHCC-HHHHHCHHHH
T ss_conf 99999999999697-7876299999
No 6
>3d23_B 3C-like proteinase; main protease, ATP-binding, endonuclease, exonuclease, helic hydrolase, membrane, metal-binding, nuclease; HET: 3IH; 2.50A {Human coronavirus}
Probab=1.00 E-value=1 Score=8.38 Aligned_cols=80 Identities=19% Similarity=0.256 Sum_probs=0.0
Q ss_pred HHHHHHCCCCCCCCCCCCCC----------HHHHHHCCCCCCCCHHHHHHHHHHHHCCCHHHHHHHHHHHHCCCCCCCCH
Q ss_conf 99999147945533465220----------27855101478800399999999882089123999999850699985358
Q 000469 40 FVSEIYQKEPELLSGNDVLW----------TFVVFAGEDHTNFQTLVAFLKMLSTLASSQEGASKVYELLQGKAFRSIGW 109 (1472)
Q Consensus 40 ~ia~~Y~~~P~~~~~~~~fW----------gFi~wa~~~~~~~~~~~afl~ML~sLa~g~~~A~~~~~lL~~~~~~~iSW 109 (1472)
.+|.+|+ +-+|..=| .|=.||... ...+-.+..+|..|..+ .-+|-
T Consensus 206 VvA~LYA-----Ailng~~Wf~~~~~~s~~~fN~WA~~n-----------------gft~~~~~~~~~~Laa~--TgVsV 261 (302)
T 3d23_B 206 VIAWLYA-----AILNNCAWFVQNDVCSTEDFNVWAMAN-----------------GFSQVKADLVLDALASM--TGVSI 261 (302)
T ss_dssp HHHHHHH-----HHHTTCCTTCCSCCCCHHHHHHHHHHH-----------------TBCCCCCCHHHHHHHHH--HSCCH
T ss_pred HHHHHHH-----HHHCCCCEEECCCEECHHHHHHHHHHC-----------------CCCCCCCHHHHHHHHHH--HCCCH
T ss_conf 9999999-----997588546323466388978889757-----------------96524411577887877--48769
Q ss_pred HHHHHHHHHHHHHHHH-CCCCCCCCCCCCCHHHHH
Q ss_conf 9999999999999410-014689989999930499
Q 000469 110 RTLFDCLSIYDEKFKQ-SLQTGGALLPDFQEGDAK 143 (1472)
Q Consensus 110 ~~iF~~L~~Y~~~l~~-~~~~~~~~~~~l~~ee~~ 143 (1472)
.++..+++.-...+.- .+-...+...|++|+|+.
T Consensus 262 e~lLaaI~~L~~gf~G~~IlG~~~leDE~Tp~~V~ 296 (302)
T 3d23_B 262 ETLLAAIKRLYMGFQGRQILGSCTFEDELAPSDVY 296 (302)
T ss_dssp HHHHHHHHHHHTCCTTCCBTTBSSCCCSSCHHHHH
T ss_pred HHHHHHHHHHHCCCCCCEEECCCCCCCCCCHHHHH
T ss_conf 99999999996187984650554344658999999
No 7
>2zze_A Alanyl-tRNA synthetase; ligase, hydrolase; HET: MLY; 2.16A {Pyrococcus horikoshii} PDB: 2zzf_A 2zzg_A*
Probab=1.00 E-value=1 Score=8.26 Aligned_cols=23 Identities=17% Similarity=0.374 Sum_probs=0.0
Q ss_pred HHHHHHHHHCCC---------HHHHHHHHHHH
Q ss_conf 999999882089---------12399999985
Q 000469 77 AFLKMLSTLASS---------QEGASKVYELL 99 (1472)
Q Consensus 77 afl~ML~sLa~g---------~~~A~~~~~lL 99 (1472)
+|++||+.-|.| +++-..||+||
T Consensus 143 TfFEMlGnfSFg~~~~~dYfK~eaI~~awe~l 174 (752)
T 2zze_A 143 TIFEMMAHHAFNYPGXPIYWMDETVELAFEFF 174 (752)
T ss_dssp SEEEEEEEEEEECTTCCCCCHHHHHHHHHHHH
T ss_pred HHHHHCCCCEECCCCHHHHHHHHHHHHHHHHH
T ss_conf 67885754230797167778888999999997
No 8
>3d9j_A RNA-binding protein 16; SCAF8, RNA polymerase II CTD interacting domain, arm repeats phospho-CTD, phosphoprotein, transcription; 1.60A {Homo sapiens} PDB: 3d9k_A* 3d9l_A* 3d9m_A* 3d9n_A* 3d9p_A* 3d9i_A 3d9o_A* 2diw_A
Probab=1.00 E-value=1 Score=8.22 Aligned_cols=35 Identities=20% Similarity=0.171 Sum_probs=0.0
Q ss_pred HHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHH
Q ss_conf 86133678987302458996059999999999980
Q 000469 995 RKEAQAILDLFIKDATQGSEPGKTLSLYVLDALIC 1029 (1472)
Q Consensus 995 ~~~~~~LidvIc~DA~~G~~~~r~~Al~lLd~Lv~ 1029 (1472)
..+...+++++.+-.-.....-|..+|+++|++++
T Consensus 37 ~~~~~~IV~~~~~~i~k~~~~~KL~~LYL~DsIvr 71 (145)
T 3d9j_A 37 IKFYKHVVQSVEKFIQKCKPEYKVPGLYVIDSIVR 71 (145)
T ss_dssp GGGHHHHHHHHHHHHHHSCGGGHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHCCCCCEEEHHHHHHHHHH
T ss_conf 99899999999999972896453303241189999
No 9
>1lrr_A SEQA protein; protein-DNA complex, replication, methylated GATC, replication inhibitor/DNA complex; HET: 6MA; 2.65A {Escherichia coli} SCOP: d.228.1.1
Probab=1.00 E-value=1 Score=8.08 Aligned_cols=22 Identities=9% Similarity=0.196 Sum_probs=0.0
Q ss_pred CCCCCHHHHHHHHHHHHCCCCC
Q ss_conf 7886589999999999147945
Q 000469 29 IGPLPFVSLLEFVSEIYQKEPE 50 (1472)
Q Consensus 29 ~~~~~lE~fll~ia~~Y~~~P~ 50 (1472)
.+...-.|||.+.+.+|..+|+
T Consensus 33 ~q~kaV~RFl~iLs~Ly~~~p~ 54 (131)
T 1lrr_A 33 EQKRAVNRFMLLLSTLYSLDAQ 54 (131)
T ss_dssp HCCSHHHHHHHHHHHHHHHCHH
T ss_pred HHHHHHHHHHHHHHHHHHHCHH
T ss_conf 8670699999999999987999
No 10
>1j3e_A SEQA protein; protein-DNA complex, recognition of hemimethylated DNA, mismatched DNA, replication; HET: 6MA; 2.50A {Escherichia coli} SCOP: d.228.1.1 PDB: 1iu3_C
Probab=1.00 E-value=1 Score=8.00 Aligned_cols=22 Identities=9% Similarity=0.196 Sum_probs=0.0
Q ss_pred CCCCCHHHHHHHHHHHHCCCCC
Q ss_conf 7886589999999999147945
Q 000469 29 IGPLPFVSLLEFVSEIYQKEPE 50 (1472)
Q Consensus 29 ~~~~~lE~fll~ia~~Y~~~P~ 50 (1472)
.+...-.|||.+.+.+|..+|+
T Consensus 17 ~q~kaV~RFl~iLs~Ly~~~p~ 38 (115)
T 1j3e_A 17 EQKRAVNRFMLLLSTLYSLDAQ 38 (115)
T ss_dssp HCCSHHHHHHHHHHHHHHHCHH
T ss_pred HHHHHHHHHHHHHHHHHHHCHH
T ss_conf 8670699999999999987989
Done!