Query 032288
Match_columns 143
No_of_seqs 139 out of 295
Neff 3.4
Searched_HMMs 29240
Date Mon Mar 25 19:44:30 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/032288.a3m -d /work/01045/syshi/HHdatabase/pdb70.hhm -o /work/01045/syshi/hhsearch_pdb/032288hhsearch_pdb -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 1qkl_A RPB6, DNA-directed RNA 100.0 1.5E-41 5.1E-46 259.2 8.0 127 1-134 1-127 (127)
2 1twf_F ABC23, DNA-directed RNA 100.0 1.9E-37 6.4E-42 242.9 8.8 85 50-134 71-155 (155)
3 3h0g_F DNA-directed RNA polyme 100.0 1.8E-37 6.1E-42 240.2 6.6 82 50-131 61-142 (142)
4 4ayb_K DNA-directed RNA polyme 100.0 2.9E-31 9.8E-36 194.0 9.1 69 61-129 24-94 (95)
5 3lu0_E DNA-directed RNA polyme 99.3 8.5E-13 2.9E-17 95.2 2.6 53 62-115 12-65 (91)
6 2a6h_E RNA polymerase omega ch 99.2 1.8E-11 6.3E-16 89.0 5.4 50 63-112 13-76 (99)
7 2kxh_B Peptide of FAR upstream 20.2 39 0.0013 20.0 1.1 9 74-82 14-22 (31)
8 2npt_A Dual specificity mitoge 17.8 84 0.0029 23.0 2.7 21 109-129 13-33 (106)
9 2wsc_D Photosystem I reaction 14.1 56 0.0019 26.5 1.0 16 108-123 151-166 (212)
10 2z3g_A Blasticidin-S deaminase 13.8 1.4E+02 0.0048 21.4 3.0 29 100-131 94-122 (130)
No 1
>1qkl_A RPB6, DNA-directed RNA polymerase II 14.4 KD polypeptide; transcription; NMR {Homo sapiens} SCOP: a.143.1.2
Probab=100.00 E-value=1.5e-41 Score=259.15 Aligned_cols=127 Identities=57% Similarity=0.837 Sum_probs=99.0
Q ss_pred CCcccccCCCCCCCCCCCCccccccchhhhcccCCCCCCCCCccchhhhHhhhhhhhhcCCccccHHHHHHHHHHHHHHH
Q 032288 1 MADEDYNDLDMGYEDEPPEPEIEEGAEEDAENINNDDINGEPIETEEKEEQEQKEAARKTSKYMTKYERARILGTRALQI 80 (143)
Q Consensus 1 m~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~t~~~lTKYElARIiG~RAlQL 80 (143)
|+|++|+.+++ +|++.+++. +.++-++..++.+.|++++... ...++..+|+|+||||||++|||+|+||+||
T Consensus 1 m~d~~~~~~~~--~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~r~t~p~lTRYElARIiG~RAlQL 73 (127)
T 1qkl_A 1 MSDNEDNFDGD--DFDDVEEDE--GLDDLENAEEEGQENVEILPSG---ERPQANQKRITTPYMTKYERARVLGTRALQI 73 (127)
T ss_dssp CCCCCCCSCCC--SSSSSCCCC--TTTTCCCSCCCCSCEEEEEESC---CCTTTCCCSSCCSSCCHHHHHHHHHHHHHHH
T ss_pred CCcccccCCCc--ccccccccc--CccccccccccCcccceecccc---CcCCCccccccCCCcCHHHHHHHHHHHHHHH
Confidence 88988833333 344332222 1111011123334678888642 3345789999999999999999999999999
Q ss_pred hhcCCceecCCCCCChHHHHHHHHHcCCCCeEEEeecCCCcEEEeecceeeecc
Q 032288 81 SMNAPVMVELEGETDPLEIAMKELRERKIPFTIRRYLPDGSYEDWGVDELIVED 134 (143)
Q Consensus 81 s~GApplVd~~~~~dPv~IA~~EL~eGkIpi~IrR~lPdg~yEdw~l~eL~~~~ 134 (143)
||||||||++++.+||+.||++||++|||||+|||+||||+||+|+|++|++++
T Consensus 74 s~GAppLVd~e~~~dPl~IAl~ElaeGkIpi~VrR~lPdg~yEd~~~~eL~i~~ 127 (127)
T 1qkl_A 74 AMCAPVMVELEGETDPLLIAMKELKARKIPIIIRRYLPDGSYEDWGVDELIITD 127 (127)
T ss_dssp HHSCCSSSCSSSSCSSSHHHHHHHHHTCCCEEEEEEETTTEEEEESSSSSCSCC
T ss_pred hcCCcceEcCCCCCCHHHHHHHHHHcCCCCeEEEEECCCCCEEEeehhheeccC
Confidence 999999999987789999999999999999999999999999999999999864
No 2
>1twf_F ABC23, DNA-directed RNA polymerases I, II, and III 23 KD polypeptide; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: a.143.1.2 PDB: 1i3q_F 1i6h_F 1k83_F* 1nik_F 1nt9_F 1pqv_F 1r5u_F 1r9s_F* 1r9t_F* 1sfo_F* 1twa_F* 1twc_F* 1i50_F* 1twg_F* 1twh_F* 1wcm_F 1y1v_F 1y1w_F 1y1y_F 1y77_F* ...
Probab=100.00 E-value=1.9e-37 Score=242.92 Aligned_cols=85 Identities=74% Similarity=1.149 Sum_probs=80.1
Q ss_pred HhhhhhhhhcCCccccHHHHHHHHHHHHHHHhhcCCceecCCCCCChHHHHHHHHHcCCCCeEEEeecCCCcEEEeecce
Q 032288 50 EQEQKEAARKTSKYMTKYERARILGTRALQISMNAPVMVELEGETDPLEIAMKELRERKIPFTIRRYLPDGSYEDWGVDE 129 (143)
Q Consensus 50 ~~~~~~~~r~t~~~lTKYElARIiG~RAlQLs~GApplVd~~~~~dPv~IA~~EL~eGkIpi~IrR~lPdg~yEdw~l~e 129 (143)
.++++..+|+|++||||||+|||+|+||+||||||||||++++.+||+.||++||++|||||+|||+||||+||+|+|+|
T Consensus 71 ~~~~~~~~r~t~p~lTRYElARIiG~RAlQLsmGAppLVd~e~~~dPl~IAl~ElaeGkIPl~IrR~lPdG~yEd~~v~e 150 (155)
T 1twf_F 71 EKAIPKDQRATTPYMTKYERARILGTRALQISMNAPVFVDLEGETDPLRIAMKELAEKKIPLVIRRYLPDGSFEDWSVEE 150 (155)
T ss_dssp -CCCCSSSCCSCSBCCHHHHHHHHHHHHHHHHTTCCCSSCCSSCCSHHHHHHHHHHTTCCCEEEEEECTTSCEEEEETTT
T ss_pred cccCCcccccCCCCcCHHHHHHHHHHHHHHHhcCCCcEEecCCCCCHHHHHHHHHHcCCCCeEEEEECCCCCEEEeeHHH
Confidence 45567889999999999999999999999999999999999877899999999999999999999999999999999999
Q ss_pred eeecc
Q 032288 130 LIVED 134 (143)
Q Consensus 130 L~~~~ 134 (143)
|++++
T Consensus 151 L~~~~ 155 (155)
T 1twf_F 151 LIVDL 155 (155)
T ss_dssp SBCCC
T ss_pred hccCC
Confidence 99864
No 3
>3h0g_F DNA-directed RNA polymerases I, II, and III subunit rpabc2; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe}
Probab=100.00 E-value=1.8e-37 Score=240.21 Aligned_cols=82 Identities=73% Similarity=1.162 Sum_probs=78.4
Q ss_pred HhhhhhhhhcCCccccHHHHHHHHHHHHHHHhhcCCceecCCCCCChHHHHHHHHHcCCCCeEEEeecCCCcEEEeecce
Q 032288 50 EQEQKEAARKTSKYMTKYERARILGTRALQISMNAPVMVELEGETDPLEIAMKELRERKIPFTIRRYLPDGSYEDWGVDE 129 (143)
Q Consensus 50 ~~~~~~~~r~t~~~lTKYElARIiG~RAlQLs~GApplVd~~~~~dPv~IA~~EL~eGkIpi~IrR~lPdg~yEdw~l~e 129 (143)
..+.+..+|+|+|||||||+|||+|+||+||||||||||+++++++|+.||++||++|||||+|||++|||+||+|+|+|
T Consensus 61 ~~~~~~~~R~T~pylTRYElARIiG~RAlQIsmGAp~LVd~~~~tdPl~IA~~EL~egkIPiiVrR~lPdgkyEdw~l~E 140 (142)
T 3h0g_F 61 GKAVAKEDRTTTPYMTKYERARILGTRALQISMNAPVLVDLEGETDPLQIAMKELAQKKIPLLVRRYLPDGSYEDWSVAE 140 (142)
T ss_dssp CCCCCTTSCCSCSSCCHHHHHHHHHHHHHHHHTCCCCCSCCCSCCCTTHHHHHHHHTTCCCCEEECCCSSSCCCEEETTT
T ss_pred cccCCcccccCCCccCHHHHHHHHHHHHHHHHCCCCceEcCCCCCCHHHHHHHHHHcCCCceEEEEECCCCCEEEeEHHH
Confidence 34567999999999999999999999999999999999999878999999999999999999999999999999999999
Q ss_pred ee
Q 032288 130 LI 131 (143)
Q Consensus 130 L~ 131 (143)
|+
T Consensus 141 L~ 142 (142)
T 3h0g_F 141 LI 142 (142)
T ss_dssp CC
T ss_pred cC
Confidence 96
No 4
>4ayb_K DNA-directed RNA polymerase; transferase, multi-subunit, transcription; 3.20A {Sulfolobus shibatae} PDB: 2y0s_I 4b1o_K 4b1p_I 2waq_K 2wb1_I 2pmz_K 3hkz_K
Probab=99.97 E-value=2.9e-31 Score=193.95 Aligned_cols=69 Identities=36% Similarity=0.659 Sum_probs=65.2
Q ss_pred CccccHHHHHHHHHHHHHHHhhcCCceecCC--CCCChHHHHHHHHHcCCCCeEEEeecCCCcEEEeecce
Q 032288 61 SKYMTKYERARILGTRALQISMNAPVMVELE--GETDPLEIAMKELRERKIPFTIRRYLPDGSYEDWGVDE 129 (143)
Q Consensus 61 ~~~lTKYElARIiG~RAlQLs~GApplVd~~--~~~dPv~IA~~EL~eGkIpi~IrR~lPdg~yEdw~l~e 129 (143)
.+.|||||+|||+|+||+||||||||||+++ +.+||+.||++||.+|+|||+|||+||||+||+|+|+|
T Consensus 24 ~~kLTKYEkaRIiG~RA~Qis~GA~~~I~~~~~~~~Dp~~IA~~EL~~~kiP~iIrR~lPnG~~E~~~l~e 94 (95)
T 4ayb_K 24 QNKLTRYEIARVISARALQLAMGAPALIDINNISSTDVISIAEEEFKRGVLPITIRRRLPNGKIILLSLRK 94 (95)
T ss_dssp TSSCCHHHHHHHHHHHHHHHHTCCCCSSCTTTSCSSCTHHHHHHHHHTTCCCEEEEEECTTSCEEEECCCC
T ss_pred cccccHHHHHHHHHHHHHHHHCCCCceEeCCCCCCCCHHHHHHHHHHcCCCCEEEEEeCCCCCEEEEEecc
Confidence 3569999999999999999999999999986 36899999999999999999999999999999999986
No 5
>3lu0_E DNA-directed RNA polymerase subunit omega; E. coli RNA polymerase, nucleotidyltransferase, transcription, transferase; 11.20A {Escherichia coli} PDB: 3iyd_E*
Probab=99.29 E-value=8.5e-13 Score=95.16 Aligned_cols=53 Identities=23% Similarity=0.271 Sum_probs=47.8
Q ss_pred ccccHHHHHHHHHHHHHHHhh-cCCceecCCCCCChHHHHHHHHHcCCCCeEEEe
Q 032288 62 KYMTKYERARILGTRALQISM-NAPVMVELEGETDPLEIAMKELRERKIPFTIRR 115 (143)
Q Consensus 62 ~~lTKYElARIiG~RAlQLs~-GApplVd~~~~~dPv~IA~~EL~eGkIpi~IrR 115 (143)
.+.+||+|+.++++||+||+. |++|+|+.. +.||+.||++||.+|+|.+.+-.
T Consensus 12 kV~nRY~LV~~AAKRARQL~~~G~~plv~~~-~~Kpv~iALrEIa~GkV~~~~l~ 65 (91)
T 3lu0_E 12 KIGNRFDLVLVAARRARQMQVGGKDPLVPEE-NDKTTVIALREIEEGLINNQILD 65 (91)
T ss_dssp HSSSHHHHHHHHHHHHHHHHHTCCCSCCSSS-CCCSSCCSHHHHHSSSCEEESSS
T ss_pred HcCCHhHHHHHHHHHHHHHHhcCCCCccCCC-CCChHHHHHHHHHcCCCceeeCC
Confidence 355999999999999999998 999999976 78999999999999999987533
No 6
>2a6h_E RNA polymerase omega chain; RNA polymerase holoenzyme, streptolydigin, antibiotic, transcription regulation; HET: STD; 2.40A {Thermus thermophilus} SCOP: a.143.1.1 PDB: 1smy_E* 1zyr_E* 1iw7_E* 2a69_E* 2a6e_E 2a68_E* 2be5_E* 2cw0_E 3dxj_E* 2o5i_E 2o5j_E* 2ppb_E* 3aoh_E* 3aoi_E* 3eql_E* 1ynj_K* 1i6v_E* 1l9u_E 1l9z_E 1hqm_E* ...
Probab=99.19 E-value=1.8e-11 Score=88.99 Aligned_cols=50 Identities=24% Similarity=0.278 Sum_probs=43.0
Q ss_pred cccHHHHHHHHHHHHHHHhhcC--CceecC---CCCC---------ChHHHHHHHHHcCCCCeE
Q 032288 63 YMTKYERARILGTRALQISMNA--PVMVEL---EGET---------DPLEIAMKELRERKIPFT 112 (143)
Q Consensus 63 ~lTKYElARIiG~RAlQLs~GA--pplVd~---~~~~---------dPv~IA~~EL~eGkIpi~ 112 (143)
+.+||+++.++++||+||+.|+ .|+++. ..+. ||+.||++||.+|+|.|.
T Consensus 13 v~nrY~LV~~aAKRARQI~~g~~k~~lv~~l~~~~~~~l~e~~~~~Kpv~iAL~EI~~Gki~~~ 76 (99)
T 2a6h_E 13 VDSKYRLTVVVAKRAQQLLRHGFKNTVLEPEERPKMQTLEGLFDDPNAETWAMKELLTGRLVFG 76 (99)
T ss_dssp SSSHHHHHHHHHHHHHHHHHTCTTCCSCCSSSCCCCSSSSGGGTSSCSHHHHHHHHTTTCCEEE
T ss_pred cCCHhHHHHHHHHHHHHHHcCCccccchhhhhhcccccccccccCCCHHHHHHHHHHcCCeeec
Confidence 5689999999999999999999 999872 1123 999999999999998763
No 7
>2kxh_B Peptide of FAR upstream element-binding protein 1; RRM, FIR, FBP, protein-protein complex, protein binding; NMR {Homo sapiens}
Probab=20.24 E-value=39 Score=19.95 Aligned_cols=9 Identities=44% Similarity=0.283 Sum_probs=6.7
Q ss_pred HHHHHHHhh
Q 032288 74 GTRALQISM 82 (143)
Q Consensus 74 G~RAlQLs~ 82 (143)
-.||+||+.
T Consensus 14 ~~RaRQIaA 22 (31)
T 2kxh_B 14 LQRARQIAA 22 (31)
T ss_dssp HHHHHHHHH
T ss_pred HHHHHHHHH
Confidence 369999953
No 8
>2npt_A Dual specificity mitogen-activated protein kinase; MAP2K5, MEK5, MKK PRKMK5, MAP kinase kinase 5, PHOX, PHOX-domain; 1.75A {Homo sapiens} SCOP: d.15.2.2 PDB: 2o2v_A 1wi0_A
Probab=17.84 E-value=84 Score=23.00 Aligned_cols=21 Identities=29% Similarity=0.534 Sum_probs=18.7
Q ss_pred CCeEEEeecCCCcEEEeecce
Q 032288 109 IPFTIRRYLPDGSYEDWGVDE 129 (143)
Q Consensus 109 Ipi~IrR~lPdg~yEdw~l~e 129 (143)
-+|+||=..|+|.-.||+|+-
T Consensus 13 ~~lVIRIk~p~~g~vDwaV~~ 33 (106)
T 2npt_A 13 QVLVIRIKIPNSGAVDWTVHS 33 (106)
T ss_dssp CCEEEEEEETTTEEEEEEECC
T ss_pred CceEEEEECCCCCccccccCC
Confidence 478999999999999999983
No 9
>2wsc_D Photosystem I reaction center subunit II, chloroplastic; photosynthesis, electron transfer, membrane proteins, large complexes; HET: CL1 PQN BCR LMU LMG SUC UNL; 3.30A {Spinacia oleracea} PDB: 2wse_D* 2wsf_D* 2o01_D* 3lw5_D*
Probab=14.12 E-value=56 Score=26.51 Aligned_cols=16 Identities=31% Similarity=0.667 Sum_probs=0.0
Q ss_pred CCCeEEEeecCCCcEE
Q 032288 108 KIPFTIRRYLPDGSYE 123 (143)
Q Consensus 108 kIpi~IrR~lPdg~yE 123 (143)
||.|.|.|.+|+|..+
T Consensus 151 KIdykiYRifP~Ge~q 166 (212)
T 2wsc_D 151 KIKYQFYRVFPSGEVQ 166 (212)
T ss_dssp CSCCEEECCCSSCCSC
T ss_pred ccccceEeecCCCceE
No 10
>2z3g_A Blasticidin-S deaminase; hydrolase, cytidine deaminase family, zinc, tetramer; HET: TRE; 1.50A {Aspergillus terreus} SCOP: c.97.1.1 PDB: 1wn6_A* 1wn5_A* 2z3h_A* 2z3j_A 2z3i_A*
Probab=13.78 E-value=1.4e+02 Score=21.37 Aligned_cols=29 Identities=24% Similarity=0.434 Sum_probs=0.0
Q ss_pred HHHHHHcCCCCeEEEeecCCCcEEEeecceee
Q 032288 100 AMKELRERKIPFTIRRYLPDGSYEDWGVDELI 131 (143)
Q Consensus 100 A~~EL~eGkIpi~IrR~lPdg~yEdw~l~eL~ 131 (143)
++.|+. ..+++++.. ++|.+...+|++|+
T Consensus 94 ~l~e~~-~~~~v~~~~--~~g~~~~~~l~eLL 122 (130)
T 2z3g_A 94 VLLDLH-PGIKAIVKD--SDGQPTAVGIRELL 122 (130)
T ss_dssp HHHHHC-TTCEEEEEC--TTSCEEEEEGGGGS
T ss_pred HHHHhC-CCCEEEEEC--CCCCEEEEEHHHhC
Done!