Query 033231
Match_columns 124
No_of_seqs 103 out of 279
Neff 3.5
Searched_HMMs 29240
Date Mon Mar 25 18:54:45 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/033231.a3m -d /work/01045/syshi/HHdatabase/pdb70.hhm -o /work/01045/syshi/hhsearch_pdb/033231hhsearch_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 3.8E-37 1.3E-41 230.0 5.7 94 22-115 34-127 (127)
2 3h0g_F DNA-directed RNA polyme 100.0 6.2E-36 2.1E-40 226.9 4.6 81 32-112 62-142 (142)
3 1twf_F ABC23, DNA-directed RNA 100.0 3.5E-35 1.2E-39 225.3 7.7 85 31-115 71-155 (155)
4 4ayb_K DNA-directed RNA polyme 100.0 4.3E-31 1.5E-35 189.0 9.0 69 42-110 24-94 (95)
5 3lu0_E DNA-directed RNA polyme 99.3 2.1E-12 7.3E-17 91.1 3.2 50 46-96 15-65 (91)
6 2a6h_E RNA polymerase omega ch 99.2 4.1E-11 1.4E-15 85.3 5.7 48 46-93 15-76 (99)
7 2z3g_A Blasticidin-S deaminase 26.8 54 0.0018 23.0 3.2 39 76-118 86-127 (130)
8 3dmo_A Cytidine deaminase; str 26.5 47 0.0016 24.1 2.9 36 80-118 101-136 (138)
9 1uwz_A Cytidine deaminase; CDD 23.8 43 0.0015 23.7 2.2 36 80-118 91-126 (136)
10 2d30_A Cytidine deaminase; pur 20.3 66 0.0023 23.2 2.6 35 81-118 101-135 (141)
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=3.8e-37 Score=230.01 Aligned_cols=94 Identities=72% Similarity=1.097 Sum_probs=85.4
Q ss_pred CCCcchhHHHHHhHHhhhcCCccccHHHHHHHHHHHHHHHhhcCCceecCCCCCChHHHHHHHHHcCCccEEEEEecCCC
Q 033231 22 EPIETEEKEEQEQKEAARKTSKYMTKYERARILGTRALQISMNAPVMVELEGETDPLEIAMKELRERKIPFTIRRYLPDG 101 (124)
Q Consensus 22 ~~~~~~~~~~~~~~~~~r~T~~~LTKYElARIiG~RAlQLs~GApplVd~~~~~dPv~IA~~EL~eGkIpi~IrR~lpdg 101 (124)
+.+++.......+....|+|+|||||||+|||+|+||+||||||||||++++.+||+.||++||++|+|||+|||+||||
T Consensus 34 ~~~~~~~~~~~~~~~~~r~t~p~lTRYElARIiG~RAlQLs~GAppLVd~e~~~dPl~IAl~ElaeGkIpi~VrR~lPdg 113 (127)
T 1qkl_A 34 ENVEILPSGERPQANQKRITTPYMTKYERARVLGTRALQIAMCAPVMVELEGETDPLLIAMKELKARKIPIIIRRYLPDG 113 (127)
T ss_dssp CEEEEEESCCCTTTCCCSSCCSSCCHHHHHHHHHHHHHHHHHSCCSSSCSSSSCSSSHHHHHHHHHTCCCEEEEEEETTT
T ss_pred ccceeccccCcCCCccccccCCCcCHHHHHHHHHHHHHHHhcCCcceEcCCCCCCHHHHHHHHHHcCCCCeEEEEECCCC
Confidence 44455545556677889999999999999999999999999999999999877899999999999999999999999999
Q ss_pred cEEEeecceeeecc
Q 033231 102 SYEDWGVDELIVED 115 (124)
Q Consensus 102 ~yE~~~l~eL~i~~ 115 (124)
+||+|++++|+|++
T Consensus 114 ~yEd~~~~eL~i~~ 127 (127)
T 1qkl_A 114 SYEDWGVDELIITD 127 (127)
T ss_dssp EEEEESSSSSCSCC
T ss_pred CEEEeehhheeccC
Confidence 99999999999874
No 2
>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=6.2e-36 Score=226.86 Aligned_cols=81 Identities=74% Similarity=1.180 Sum_probs=77.0
Q ss_pred HHhHHhhhcCCccccHHHHHHHHHHHHHHHhhcCCceecCCCCCChHHHHHHHHHcCCccEEEEEecCCCcEEEeeccee
Q 033231 32 QEQKEAARKTSKYMTKYERARILGTRALQISMNAPVMVELEGETDPLEIAMKELRERKIPFTIRRYLPDGSYEDWGVDEL 111 (124)
Q Consensus 32 ~~~~~~~r~T~~~LTKYElARIiG~RAlQLs~GApplVd~~~~~dPv~IA~~EL~eGkIpi~IrR~lpdg~yE~~~l~eL 111 (124)
++.+..+|+|+|||||||+|||+|+||+||||||||||+++++++|++||++||++|+|||+|||++|||+||+|+|+||
T Consensus 62 ~~~~~~~R~T~pylTRYElARIiG~RAlQIsmGAp~LVd~~~~tdPl~IA~~EL~egkIPiiVrR~lPdgkyEdw~l~EL 141 (142)
T 3h0g_F 62 KAVAKEDRTTTPYMTKYERARILGTRALQISMNAPVLVDLEGETDPLQIAMKELAQKKIPLLVRRYLPDGSYEDWSVAEL 141 (142)
T ss_dssp CCCCTTSCCSCSSCCHHHHHHHHHHHHHHHHTCCCCCSCCCSCCCTTHHHHHHHHTTCCCCEEECCCSSSCCCEEETTTC
T ss_pred ccCCcccccCCCccCHHHHHHHHHHHHHHHHCCCCceEcCCCCCCHHHHHHHHHHcCCCceEEEEECCCCCEEEeEHHHc
Confidence 34557889999999999999999999999999999999998789999999999999999999999999999999999999
Q ss_pred e
Q 033231 112 I 112 (124)
Q Consensus 112 ~ 112 (124)
+
T Consensus 142 ~ 142 (142)
T 3h0g_F 142 I 142 (142)
T ss_dssp C
T ss_pred C
Confidence 6
No 3
>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=3.5e-35 Score=225.30 Aligned_cols=85 Identities=74% Similarity=1.149 Sum_probs=79.4
Q ss_pred HHHhHHhhhcCCccccHHHHHHHHHHHHHHHhhcCCceecCCCCCChHHHHHHHHHcCCccEEEEEecCCCcEEEeecce
Q 033231 31 EQEQKEAARKTSKYMTKYERARILGTRALQISMNAPVMVELEGETDPLEIAMKELRERKIPFTIRRYLPDGSYEDWGVDE 110 (124)
Q Consensus 31 ~~~~~~~~r~T~~~LTKYElARIiG~RAlQLs~GApplVd~~~~~dPv~IA~~EL~eGkIpi~IrR~lpdg~yE~~~l~e 110 (124)
.++++...|+|++||||||+|||+|+||+||||||||||++++.+||+.||++||++|+|||+|||+||||+||+|+|+|
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 34455678999999999999999999999999999999999877899999999999999999999999999999999999
Q ss_pred eeecc
Q 033231 111 LIVED 115 (124)
Q Consensus 111 L~i~~ 115 (124)
|+|++
T Consensus 151 L~~~~ 155 (155)
T 1twf_F 151 LIVDL 155 (155)
T ss_dssp SBCCC
T ss_pred hccCC
Confidence 99974
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=4.3e-31 Score=189.02 Aligned_cols=69 Identities=36% Similarity=0.659 Sum_probs=65.2
Q ss_pred CccccHHHHHHHHHHHHHHHhhcCCceecCCC--CCChHHHHHHHHHcCCccEEEEEecCCCcEEEeecce
Q 033231 42 SKYMTKYERARILGTRALQISMNAPVMVELEG--ETDPLEIAMKELRERKIPFTIRRYLPDGSYEDWGVDE 110 (124)
Q Consensus 42 ~~~LTKYElARIiG~RAlQLs~GApplVd~~~--~~dPv~IA~~EL~eGkIpi~IrR~lpdg~yE~~~l~e 110 (124)
.+.|||||+|||+|+||+||||||||||+++. .+||+.||++||.+|+|||+|||++|||+||+|+|+|
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 35699999999999999999999999999863 6899999999999999999999999999999999986
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=99.26 E-value=2.1e-12 Score=91.09 Aligned_cols=50 Identities=22% Similarity=0.294 Sum_probs=46.4
Q ss_pred cHHHHHHHHHHHHHHHhh-cCCceecCCCCCChHHHHHHHHHcCCccEEEEE
Q 033231 46 TKYERARILGTRALQISM-NAPVMVELEGETDPLEIAMKELRERKIPFTIRR 96 (124)
Q Consensus 46 TKYElARIiG~RAlQLs~-GApplVd~~~~~dPv~IA~~EL~eGkIpi~IrR 96 (124)
+||+++.++++||+||+. |++|+|+.+ +.+|+.||++||.+|+|.+.+..
T Consensus 15 nRY~LV~~AAKRARQL~~~G~~plv~~~-~~Kpv~iALrEIa~GkV~~~~l~ 65 (91)
T 3lu0_E 15 NRFDLVLVAARRARQMQVGGKDPLVPEE-NDKTTVIALREIEEGLINNQILD 65 (91)
T ss_dssp SHHHHHHHHHHHHHHHHHTCCCSCCSSS-CCCSSCCSHHHHHSSSCEEESSS
T ss_pred CHhHHHHHHHHHHHHHHhcCCCCccCCC-CCChHHHHHHHHHcCCCceeeCC
Confidence 899999999999999998 999999976 79999999999999999987543
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=99.15 E-value=4.1e-11 Score=85.26 Aligned_cols=48 Identities=25% Similarity=0.317 Sum_probs=41.8
Q ss_pred cHHHHHHHHHHHHHHHhhcC--CceecC---CCCC---------ChHHHHHHHHHcCCccEE
Q 033231 46 TKYERARILGTRALQISMNA--PVMVEL---EGET---------DPLEIAMKELRERKIPFT 93 (124)
Q Consensus 46 TKYElARIiG~RAlQLs~GA--pplVd~---~~~~---------dPv~IA~~EL~eGkIpi~ 93 (124)
+||+++.++++||+||+.|+ .++++. ..+. +|+.||++||.+|+|.|.
T Consensus 15 nrY~LV~~aAKRARQI~~g~~k~~lv~~l~~~~~~~l~e~~~~~Kpv~iAL~EI~~Gki~~~ 76 (99)
T 2a6h_E 15 SKYRLTVVVAKRAQQLLRHGFKNTVLEPEERPKMQTLEGLFDDPNAETWAMKELLTGRLVFG 76 (99)
T ss_dssp SHHHHHHHHHHHHHHHHHTCTTCCSCCSSSCCCCSSSSGGGTSSCSHHHHHHHHTTTCCEEE
T ss_pred CHhHHHHHHHHHHHHHHcCCccccchhhhhhcccccccccccCCCHHHHHHHHHHcCCeeec
Confidence 79999999999999999999 999872 1123 999999999999999763
No 7
>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=26.79 E-value=54 Score=23.04 Aligned_cols=39 Identities=21% Similarity=0.261 Sum_probs=25.9
Q ss_pred ChHHH---HHHHHHcCCccEEEEEecCCCcEEEeecceeeecchhh
Q 033231 76 DPLEI---AMKELRERKIPFTIRRYLPDGSYEDWGVDELIVEDSWK 118 (124)
Q Consensus 76 dPv~I---A~~EL~eGkIpi~IrR~lpdg~yE~~~l~eL~i~~~~~ 118 (124)
.|.-+ ++.|+. ..++++ -..++|.+...+|++|+ |.+|.
T Consensus 86 ~PCG~Crq~l~e~~-~~~~v~--~~~~~g~~~~~~l~eLL-P~~f~ 127 (130)
T 2z3g_A 86 SPCGRCRQVLLDLH-PGIKAI--VKDSDGQPTAVGIRELL-PSGYV 127 (130)
T ss_dssp CCCHHHHHHHHHHC-TTCEEE--EECTTSCEEEEEGGGGS-CC---
T ss_pred CcCHHHHHHHHHhC-CCCEEE--EECCCCCEEEEEHHHhC-cCCCC
Confidence 35454 888886 445544 44688899999999997 67775
No 8
>3dmo_A Cytidine deaminase; structural genomics, seattle structural genomics center for infectious disease, ssgcid, hydrolase; 1.60A {Burkholderia pseudomallei}
Probab=26.48 E-value=47 Score=24.14 Aligned_cols=36 Identities=17% Similarity=0.216 Sum_probs=26.8
Q ss_pred HHHHHHHcCCccEEEEEecCCCcEEEeecceeeecchhh
Q 033231 80 IAMKELRERKIPFTIRRYLPDGSYEDWGVDELIVEDSWK 118 (124)
Q Consensus 80 IA~~EL~eGkIpi~IrR~lpdg~yE~~~l~eL~i~~~~~ 118 (124)
=.+.|+....+++++ ..++|.+...+|++|+ |.+|.
T Consensus 101 Q~l~Ef~~~~~~V~~--~~~~g~~~~~tl~eLL-P~~F~ 136 (138)
T 3dmo_A 101 QVMIELGKPTLEVVL--TNMQGDVRVTSAGDLL-PDAFY 136 (138)
T ss_dssp HHHHHHHCTTCEEEE--ECSSSCEEEEEHHHHS-TTCCC
T ss_pred HHHHHhCCCCcEEEE--ECCCCCEEEeEHHHhC-cCccC
Confidence 357788766666665 4678999999999987 66664
No 9
>1uwz_A Cytidine deaminase; CDD, tetramer, zinc binding, pyrimidine metabolism, salvage, hydrolase; HET: THU; 1.99A {Bacillus subtilis} SCOP: c.97.1.1 PDB: 1ux0_A* 1jtk_A* 1ux1_A*
Probab=23.81 E-value=43 Score=23.74 Aligned_cols=36 Identities=17% Similarity=0.343 Sum_probs=26.8
Q ss_pred HHHHHHHcCCccEEEEEecCCCcEEEeecceeeecchhh
Q 033231 80 IAMKELRERKIPFTIRRYLPDGSYEDWGVDELIVEDSWK 118 (124)
Q Consensus 80 IA~~EL~eGkIpi~IrR~lpdg~yE~~~l~eL~i~~~~~ 118 (124)
=++.|+....+++++- .++|.+...+|++|+ |.+|.
T Consensus 91 q~l~e~~~~~~~v~~~--~~~g~~~~~~l~eLL-P~~f~ 126 (136)
T 1uwz_A 91 QVISELCTKDVIVVLT--NLQGQIKEMTVEELL-PGAFS 126 (136)
T ss_dssp HHHHHHSCTTCEEEEE--CSSSCEEEEEHHHHS-TTCCC
T ss_pred HHHHHcCCCCcEEEEE--CCCCCEEEEEHHHhC-CCCCC
Confidence 3788886555665554 578999999999997 66664
No 10
>2d30_A Cytidine deaminase; purines, pyrimidines, nucleosides, nucleotides, salvage of nucleosides and nucleotides, structural genomics; 2.40A {Bacillus anthracis} SCOP: c.97.1.1
Probab=20.29 E-value=66 Score=23.18 Aligned_cols=35 Identities=20% Similarity=0.251 Sum_probs=24.8
Q ss_pred HHHHHHcCCccEEEEEecCCCcEEEeecceeeecchhh
Q 033231 81 AMKELRERKIPFTIRRYLPDGSYEDWGVDELIVEDSWK 118 (124)
Q Consensus 81 A~~EL~eGkIpi~IrR~lpdg~yE~~~l~eL~i~~~~~ 118 (124)
.+.|+....+++++ ..++|.+...+|++|+ |.+|.
T Consensus 101 ~l~E~~~~~~~V~~--~~~~g~~~~~~l~eLL-P~~F~ 135 (141)
T 2d30_A 101 VMVELCKQDTKVYL--SNLHGDVQETTVGELL-PGAFL 135 (141)
T ss_dssp HHHHHSCTTCEEEE--ECSSSCEEEEEHHHHS-TTC--
T ss_pred HHHHhcCCCeEEEE--ECCCCCEEEEEHHHhC-CCCCC
Confidence 67888655555555 4578999999999997 66664
Done!