Query psy12829
Match_columns 181
No_of_seqs 128 out of 1038
Neff 6.5
Searched_HMMs 29240
Date Fri Aug 16 20:53:31 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy12829.a3m -d /work/01045/syshi/HHdatabase/pdb70.hhm -o /work/01045/syshi/hhsearch_pdb/12829hhsearch_pdb -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 3h0g_C DNA-directed RNA polyme 100.0 3.5E-59 1.2E-63 399.1 10.8 168 5-181 3-176 (297)
2 2pa8_D DNA-directed RNA polyme 100.0 1.2E-57 4E-62 384.7 14.1 159 7-180 1-160 (265)
3 1twf_C B44.5, DNA-directed RNA 100.0 4.1E-58 1.4E-62 396.2 10.2 171 5-181 4-175 (318)
4 1bdf_A RNA polymerase alpha su 100.0 8.2E-42 2.8E-46 283.9 14.7 140 2-176 7-157 (235)
5 2a6h_A DNA-directed RNA polyme 100.0 2.1E-41 7.1E-46 291.8 12.7 140 6-178 8-157 (315)
6 3lu0_A DNA-directed RNA polyme 100.0 1.1E-35 3.8E-40 257.0 6.4 141 2-177 7-158 (329)
7 2pa8_L DNA-directed RNA polyme 97.0 0.00093 3.2E-08 47.4 4.7 45 7-52 1-45 (92)
8 1xpp_A TA1416, DNA-directed RN 96.9 0.0013 4.6E-08 48.5 4.9 48 4-52 8-55 (115)
9 1twf_K B13.6, DNA-directed RNA 96.1 0.0044 1.5E-07 46.0 3.8 45 5-50 17-61 (120)
10 3h0g_K DNA-directed RNA polyme 94.7 0.022 7.5E-07 42.4 3.2 34 8-41 19-52 (123)
11 3rfr_A PMOB; membrane, oxidore 54.5 25 0.00086 30.8 6.2 67 95-166 296-367 (419)
12 1yew_A Particulate methane mon 29.7 1.2E+02 0.0039 26.3 6.3 68 95-166 262-335 (382)
13 2vmh_A GH95CBM51, fibronectin 25.0 2E+02 0.007 21.1 6.4 26 152-177 120-146 (151)
14 2vb2_X Copper protein, cation 24.6 50 0.0017 22.4 2.6 29 143-172 52-80 (88)
15 2qcp_X Cation efflux system pr 23.9 53 0.0018 21.7 2.6 29 143-172 44-72 (80)
16 1xhj_A Nitrogen fixation prote 22.8 1.8E+02 0.0062 19.6 5.5 39 8-46 29-74 (88)
17 1ej5_A WAsp, wiskott-aldrich s 22.4 30 0.001 24.6 1.2 11 29-39 80-90 (107)
18 2l3b_A Conserved protein found 20.8 63 0.0022 23.8 2.6 25 152-176 23-47 (130)
19 2vng_A CPE0329; family 51 carb 20.4 2.7E+02 0.0092 21.3 6.4 27 151-177 141-168 (180)
No 1
>3h0g_C DNA-directed RNA polymerase II subunit RPB3; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe}
Probab=100.00 E-value=3.5e-59 Score=399.09 Aligned_cols=168 Identities=42% Similarity=0.773 Sum_probs=151.9
Q ss_pred CCCcEEEEEecCCeEEEEEEecCchhhHHHHHHHHhhCCcceEEEEEEeeCccccccceeeeeccCCccccccccc----
Q psy12829 5 NQPSVHITDLTDENVKFQVEDTELSVANSLRRVFIAETPTMAIDWVQLEANSTVLSDEFIASRIGLIPLTSDEVVD---- 80 (181)
Q Consensus 5 ~~~~i~i~~~~~~~~~F~l~g~~~siaNaLRRvLlsevPt~AI~~V~I~~NtSvl~DE~laHRlglIP~~~~~~~~---- 80 (181)
++|+|++.+.++++++|+++|+++|+||||||+|||||||+||+.|+|++|||+|+||+||||||||||+++++.+
T Consensus 3 ~~p~I~i~~~~~~~~~F~l~g~~~tiaNALRRiLLSeVPt~AI~~V~I~~NtSvl~DE~laHrlglIP~v~edv~e~~~~ 82 (297)
T 3h0g_C 3 SETHITIRNISKNSVDFVLTNTSLAVANSLRRVVLAEIPTVAIDLVEINVNTSVMPDEFLAHRLGMIPLDSSNIDEPPPV 82 (297)
T ss_dssp -CCSBCCCCBCSSEEEEEECSCCHHHHHHHHHHHHSSCCEEEEEEEEEEEECSSSCHHHHHHHHHHSCBCCTTCSSCSSS
T ss_pred CCCeEEEEEccCCEEEEEEECCChhHHHHHHHHHHHcCccceEEEEEEEeCCccccccceeeeeccCCcccccccccccc
Confidence 6799999999999999999999999999999999999999999999999999999999999999999999998643
Q ss_pred eEEEeecCCCcCCCCCceEEEEEEEEecCCCceeEEeccceeCCCe--eeeccccCcCCCCCCccCCCCeEEEEeCCCCE
Q psy12829 81 RILYSRDCTCVDFCSECSVEFTLDVKCVDDQTRHVTTADLKSTDAR--VVPVTSRNRDADMNEYGETDDILIVKLRKGQE 158 (181)
Q Consensus 81 ~~~~~~~~~~~~~~~~~~v~~~L~v~~~~~~~~~V~s~di~~~~~~--~~p~~~~~~~~~~~~~~~~~di~I~kL~~gq~ 158 (181)
.|+|+.+|.|.+.|+.|+++|+|+++|+.+.+++|||+||++.+.. +.|+.. .++||||+||||++||+
T Consensus 83 ~l~~k~~c~~~~~~~~~~v~l~L~v~g~~~~~~~Vta~Dl~~~~~~~~~~pv~~---------~~~n~di~IakL~~gq~ 153 (297)
T 3h0g_C 83 GLEYTRNCDCDQYCPKCSVELFLNAKCTGEGTMEIYARDLVVSSNSSLGHPILA---------DPKSRGPLICKLRKEQE 153 (297)
T ss_dssp CCCCSSSCSSSSSCGGGSCEEEEEECCCCSSCEEEEGGGCBCCSCCSSCCBCCC---------STTSCCSEEEEECSSCC
T ss_pred eeEeccccccccCCCCceEEEEEEEEeccCCCceEEcccccccCcccccccccc---------cCCCCCeEEEEECCCCE
Confidence 4889999999999999999999999998888999999999975432 223221 13689999999999999
Q ss_pred EEEEEEEEeccccccceeccCCC
Q psy12829 159 LRLRAYAKKGFGKEHAKWNPTAG 181 (181)
Q Consensus 159 i~~e~~~~kG~G~~HAKw~pv~~ 181 (181)
|+|+|+|+|||||+|||||||++
T Consensus 154 l~le~~a~kG~G~~HAKwsPv~~ 176 (297)
T 3h0g_C 154 ISLRCIAKKGIAKEHAKWSPTSA 176 (297)
T ss_dssp EEEEEEEEEECGGGCTTSCCBCC
T ss_pred EEEEEEEECCEeccccccCcceE
Confidence 99999999999999999999984
No 2
>2pa8_D DNA-directed RNA polymerase subunit D; ferredoxin-like Fe-S binding motif, platform for RNA polymer assembly, transferase; 1.76A {Sulfolobus solfataricus} PDB: 2pmz_D 3hkz_D 2waq_D 2wb1_D 2y0s_D
Probab=100.00 E-value=1.2e-57 Score=384.68 Aligned_cols=159 Identities=32% Similarity=0.567 Sum_probs=149.1
Q ss_pred CcEEEEEecCCeEEEEEEecCchhhHHHHHHHHhhCCcceEEEEEEeeCccccccceeeeeccCCccccccccceEEEee
Q psy12829 7 PSVHITDLTDENVKFQVEDTELSVANSLRRVFIAETPTMAIDWVQLEANSTVLSDEFIASRIGLIPLTSDEVVDRILYSR 86 (181)
Q Consensus 7 ~~i~i~~~~~~~~~F~l~g~~~siaNaLRRvLlsevPt~AI~~V~I~~NtSvl~DE~laHRlglIP~~~~~~~~~~~~~~ 86 (181)
++|++.+.++++++|.++|+++|+||||||+|||||||+||+.|+|++|||+|+||+++||||||||+++|+.|++.|+.
T Consensus 1 ~~i~i~~~~~~~~~f~l~g~~~t~~NalRRills~vp~~AI~~V~i~~Ntsvl~DE~v~Hr~~~Ip~~~edv~k~~~~~~ 80 (265)
T 2pa8_D 1 MSINLLHKDDTRIDLVFEGYPLEFVNAIRRASMLYVPIMAVDDVYFIENNSPLYDEILAHRLALIPFMSEEALDTYRWPE 80 (265)
T ss_dssp -CEEEEEECSSEEEEEEESSCHHHHHHHHHHHHHSCCEEEEEEEEEEEECSSSCHHHHHHHHTTSCBCCTTHHHHSCCGG
T ss_pred CeEEEEEcCCCEEEEEEeCCCHHHHHHHHHHHHHcCccceEEEEEEEeCCCccccHHHHHhhcCCcCcccCchhhccccc
Confidence 46889999999999999999999999999999999999999999999999999999999999999999999889999999
Q ss_pred cC-CCcCCCCCceEEEEEEEEecCCCceeEEeccceeCCCeeeeccccCcCCCCCCccCCCCeEEEEeCCCCEEEEEEEE
Q psy12829 87 DC-TCVDFCSECSVEFTLDVKCVDDQTRHVTTADLKSTDARVVPVTSRNRDADMNEYGETDDILIVKLRKGQELRLRAYA 165 (181)
Q Consensus 87 ~~-~~~~~~~~~~v~~~L~v~~~~~~~~~V~s~di~~~~~~~~p~~~~~~~~~~~~~~~~~di~I~kL~~gq~i~~e~~~ 165 (181)
+| .|+++|++|+++|+|+++| ++||+.|||+||++.+..++ ++||||+|+||++||+|+|+++|
T Consensus 81 ~~~~~~~~~~~~~~~~~l~~~~-~~g~~~V~a~Di~~~~~~v~--------------~~~~~i~I~~L~~g~~l~~e~~~ 145 (265)
T 2pa8_D 81 ECIECTENCEKCYTKIYIEAEA-PNEPRMIYSKDIKSEDPSVV--------------PISGDIPIVLLGTNQKISLEARL 145 (265)
T ss_dssp GCTTCCSSCTTTEEEEEEEEEC-CSSCEEEEGGGCEESSTTCC--------------BSCSCCEEEEECTTCEEEEEEEE
T ss_pred cccccccCCCCcEEEEEEEEEe-cCCCcEEEhhhcccCCCCce--------------ecCCCcEEEEeCCCCEEEEEEEE
Confidence 98 7899999999999999999 67999999999997444444 67899999999999999999999
Q ss_pred EeccccccceeccCC
Q psy12829 166 KKGFGKEHAKWNPTA 180 (181)
Q Consensus 166 ~kG~G~~HAKw~pv~ 180 (181)
+||+||+||||+|++
T Consensus 146 ~~G~G~~~ak~~pv~ 160 (265)
T 2pa8_D 146 RLGYGKEHAKFIPVS 160 (265)
T ss_dssp EEECTTTCGGGCCEE
T ss_pred ecCccccccCcccce
Confidence 999999999999985
No 3
>1twf_C B44.5, DNA-directed RNA polymerase II 45 kDa polypeptide; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: d.74.3.1 d.181.1.1 PDB: 1i3q_C 1i6h_C 1k83_C* 1nik_C 1nt9_C 1pqv_C 1r5u_C 1r9s_C* 1r9t_C* 1sfo_C* 1twa_C* 1twc_C* 1i50_C* 1twg_C* 1twh_C* 1wcm_C 1y1v_C 1y1w_C 1y1y_C 1y77_C* ...
Probab=100.00 E-value=4.1e-58 Score=396.24 Aligned_cols=171 Identities=47% Similarity=0.748 Sum_probs=152.4
Q ss_pred CCCcEEEEEecCCeEEEEEEecCchhhHHHHHHHHhhCCcceEEEEEEeeCccccccceeeeeccCCccccccccceEEE
Q psy12829 5 NQPSVHITDLTDENVKFQVEDTELSVANSLRRVFIAETPTMAIDWVQLEANSTVLSDEFIASRIGLIPLTSDEVVDRILY 84 (181)
Q Consensus 5 ~~~~i~i~~~~~~~~~F~l~g~~~siaNaLRRvLlsevPt~AI~~V~I~~NtSvl~DE~laHRlglIP~~~~~~~~~~~~ 84 (181)
++|+|++.+.++++++|+|+|+++||||||||+|||||||+||+.|+|++|||+|+||+|+||||||||+++|+ |++.|
T Consensus 4 ~~p~I~i~~~~~~~~kF~leG~~~tlaNALRRiLLSevPg~AI~~V~I~~NTSvl~DE~vaHrlglIP~v~eDv-k~l~~ 82 (318)
T 1twf_C 4 EGPQVKIREASKDNVDFILSNVDLAMANSLRRVMIAEIPTLAIDSVEVETNTTVLADEFIAHRLGLIPLQSMDI-EQLEY 82 (318)
T ss_dssp CSSBCCCSCCCSSEECCEEBSSCHHHHHHHHHHHHHCCCEEEEEEEEEEEECSSSCHHHHHHHHHTSCEEETTG-GGSCC
T ss_pred cCCeEEEEEecCCEEEEEEEccChhHHHHHHHHHHHcCccceEEEEEEEeCCcccccceeEeecccCCCcccCh-hheEE
Confidence 56789999999999999999999999999999999999999999999999999999999999999999999984 89999
Q ss_pred eecCCCcCCCCCceEEEEEEEEecCCCceeEEeccceeCCCeeeeccccCcCCCCCC-ccCCCCeEEEEeCCCCEEEEEE
Q psy12829 85 SRDCTCVDFCSECSVEFTLDVKCVDDQTRHVTTADLKSTDARVVPVTSRNRDADMNE-YGETDDILIVKLRKGQELRLRA 163 (181)
Q Consensus 85 ~~~~~~~~~~~~~~v~~~L~v~~~~~~~~~V~s~di~~~~~~~~p~~~~~~~~~~~~-~~~~~di~I~kL~~gq~i~~e~ 163 (181)
+.+|.|+++|++|+++|+|+++|+.++++.|||+||++.+.. .+. +..++.. .++||||+||||++||+|+|+|
T Consensus 83 ~~~~~~~~~c~~~~v~l~L~v~c~~~g~~~Vta~Di~~~~~~---~~~--~~~~p~v~ei~npdi~IakL~~gq~L~me~ 157 (318)
T 1twf_C 83 SRDCFCEDHCDKCSVVLTLQAFGESESTTNVYSKDLVIVSNL---MGR--NIGHPIIQDKEGNGVLICKLRKGQELKLTC 157 (318)
T ss_dssp TTTSSSSSCCTTTEEEEEEEEECCSSSCEEEEGGGEEECSCC---TTC--SEEEECCCSTTSCCSEEEEECTTCEEEEEE
T ss_pred eeccccccCCCCceEEEEEEEEecCCCCeeEEhHhccccCcc---ccc--cccCCCccccCCCCeEEEEECCCCEEEEEE
Confidence 999999999999999999999999999999999999863310 010 0011122 2679999999999999999999
Q ss_pred EEEeccccccceeccCCC
Q psy12829 164 YAKKGFGKEHAKWNPTAG 181 (181)
Q Consensus 164 ~~~kG~G~~HAKw~pv~~ 181 (181)
+|+||+||+|||||||++
T Consensus 158 ~a~kG~G~~hAk~sPva~ 175 (318)
T 1twf_C 158 VAKKGIAKEHAKWGPAAA 175 (318)
T ss_dssp EEEEECTTTCGGGCCEEE
T ss_pred EEEcCccccccccccccc
Confidence 999999999999999863
No 4
>1bdf_A RNA polymerase alpha subunit; nucleotidyltransferase, assemble; 2.50A {Escherichia coli} SCOP: d.74.3.1 d.181.1.1
Probab=100.00 E-value=8.2e-42 Score=283.94 Aligned_cols=140 Identities=18% Similarity=0.258 Sum_probs=126.2
Q ss_pred CCCCCCcEEEEEecCCeEEEEEE----ecCchhhHHHHHHHHhhCCcceEEEEEEeeCccccccceeeeeccCCcccccc
Q psy12829 2 PYANQPSVHITDLTDENVKFQVE----DTELSVANSLRRVFIAETPTMAIDWVQLEANSTVLSDEFIASRIGLIPLTSDE 77 (181)
Q Consensus 2 ~~~~~~~i~i~~~~~~~~~F~l~----g~~~siaNaLRRvLlsevPt~AI~~V~I~~NtSvl~DE~laHRlglIP~~~~~ 77 (181)
.|..+.+|++.+.++++++|.++ |++.|+||||||+||||+||+||+.|+|++ ++||||+|||+.||
T Consensus 7 ~~~~p~~i~i~~~~~~~~~F~l~Ple~G~~~tlgNaLRRiLLsevpg~AI~~V~Ie~---------v~He~~~Ipgv~Ed 77 (235)
T 1bdf_A 7 EFLKPRLVDIEQVSSTHAKVTLEPLERGFGHTLGNALRAILLSSMPGCAVTEVEIDG---------VLHEYSTKEGVQED 77 (235)
T ss_dssp CSCCCCEEEEEESSSSEEEEEEEEEETTHHHHHHHHHHHHHTTSCCCEEEEEEEETT---------CCSTTCCCTTBSSC
T ss_pred hhcCCceEEEEEccCCEEEEEEEecCCCCchHHHHHHHHHHHhcCCceEEEEEEEcc---------eeeccccCCCccCC
Confidence 46666679999999999999998 999999999999999999999999999954 99999999999998
Q ss_pred c------cceEEEeecCCCcCCCCCceEEEEEEEEecCCCceeEEeccceeCCCeeeeccccCcCCCCCCccCCCCeEEE
Q psy12829 78 V------VDRILYSRDCTCVDFCSECSVEFTLDVKCVDDQTRHVTTADLKSTDARVVPVTSRNRDADMNEYGETDDILIV 151 (181)
Q Consensus 78 ~------~~~~~~~~~~~~~~~~~~~~v~~~L~v~~~~~~~~~V~s~di~~~~~~~~p~~~~~~~~~~~~~~~~~di~I~ 151 (181)
+ +|++.|+.++ .|++.++|+++ ||+.|||+||+. +..++ ++|||++||
T Consensus 78 v~~iilNlk~i~~~~~~-------~~~~~~~L~v~----gp~~VtA~Di~~-~~~v~--------------ivnpd~~Ia 131 (235)
T 1bdf_A 78 ILEILLNLKGLAVRVQG-------KDEVILTLNKS----GIGPVTAADITH-DGDVE--------------IVKPQHVIC 131 (235)
T ss_dssp HHHHHHHHHTCCEECSS-------CSEEEEEEEEE----SSEEEEGGGBCC-CSSCE--------------ESCTTCEEE
T ss_pred HHHHhhchheeEEeccC-------CceEEEEEEEe----cCeEEEhHhCCC-CCCCE--------------EcCCCeEEE
Confidence 6 5788888653 47899999998 999999999984 33243 678999999
Q ss_pred EeCC-CCEEEEEEEEEecccccccee
Q psy12829 152 KLRK-GQELRLRAYAKKGFGKEHAKW 176 (181)
Q Consensus 152 kL~~-gq~i~~e~~~~kG~G~~HAKw 176 (181)
||++ ||+|+|+|+|.||+||+||||
T Consensus 132 tL~~~g~~l~~e~~~~kG~Gy~~ak~ 157 (235)
T 1bdf_A 132 HLTDENASISMRIKVQRGRGYVPAST 157 (235)
T ss_dssp EECSTTCEEEEEEEEEECCSEECGGG
T ss_pred EECCCCCEEEEEEEEEecccceeccc
Confidence 9999 999999999999999999999
No 5
>2a6h_A DNA-directed RNA polymerase alpha chain; RNA polymerase holoenzyme, streptolydigin, antibiotic, transcription regulation; HET: STD; 2.40A {Thermus thermophilus} SCOP: d.74.3.1 d.181.1.1 PDB: 1smy_A* 1zyr_A* 1iw7_A* 2a69_A* 2a6e_A 2a68_A* 2be5_A* 2cw0_A 2o5i_A 2o5j_A* 2ppb_A* 3aoh_A* 3aoi_A* 3dxj_A* 3eql_A* 1i6v_A* 1ynj_A* 1l9z_A 1l9u_A* 1ynn_A* ...
Probab=100.00 E-value=2.1e-41 Score=291.76 Aligned_cols=140 Identities=21% Similarity=0.300 Sum_probs=127.7
Q ss_pred CCcEEEEEecCCeEEEEEE----ecCchhhHHHHHHHHhhCCcceEEEEEEeeCccccccceeeeeccCCccccccc---
Q psy12829 6 QPSVHITDLTDENVKFQVE----DTELSVANSLRRVFIAETPTMAIDWVQLEANSTVLSDEFIASRIGLIPLTSDEV--- 78 (181)
Q Consensus 6 ~~~i~i~~~~~~~~~F~l~----g~~~siaNaLRRvLlsevPt~AI~~V~I~~NtSvl~DE~laHRlglIP~~~~~~--- 78 (181)
+|+|++.+.++++++|.++ |++.|+||||||+|||||||+||+.|+|++ ++||||+|||+.||+
T Consensus 8 ~p~i~i~~~~~~~~~F~l~Ple~G~~~TlgNaLRRiLLsevpg~AI~~V~I~~---------v~He~~~Ipgv~Edv~eI 78 (315)
T 2a6h_A 8 APVFTVRTQGREYGEFVLEPLERGFGVTLGNPLRRILLSSIPGTAVTSVYIED---------VLHEFSTIPGVKEDVVEI 78 (315)
T ss_dssp CCEEEEEEETTTEEEEEEEEECTTCHHHHHHHHHHHHHHTCEEEEEEEEEESS---------CCSTTCBCTTBSSBHHHH
T ss_pred CCeEEEEEccCCEEEEEEEccCCCchhHHHHHHHHHHHhcCCceEEEEEEEec---------chhccCCCCCccCCHHHH
Confidence 4779999999999999997 999999999999999999999999999998 999999999999986
Q ss_pred ---cceEEEeecCCCcCCCCCceEEEEEEEEecCCCceeEEeccceeCCCeeeeccccCcCCCCCCccCCCCeEEEEeCC
Q psy12829 79 ---VDRILYSRDCTCVDFCSECSVEFTLDVKCVDDQTRHVTTADLKSTDARVVPVTSRNRDADMNEYGETDDILIVKLRK 155 (181)
Q Consensus 79 ---~~~~~~~~~~~~~~~~~~~~v~~~L~v~~~~~~~~~V~s~di~~~~~~~~p~~~~~~~~~~~~~~~~~di~I~kL~~ 155 (181)
+|++.|+.+| |+.|++.++|+++ ||+.|||+||+. +..++ ++|||++||||++
T Consensus 79 ilNlk~i~~~~~~-----~~~~~~~~~L~v~----gp~~VtA~Di~~-~~~v~--------------ivnpd~~IatL~~ 134 (315)
T 2a6h_A 79 ILNLKELVVRFLN-----PSLQTVTLLLKAE----GPKEVKARDFLP-VADVE--------------IMNPDLHIATLEE 134 (315)
T ss_dssp HHHHHTCCEEECS-----TTCSBCCEEEEEE----SSCEEEGGGSCC-CTTEE--------------ESCTTCEEEEBCS
T ss_pred hhhhheEEEeccc-----CCCCeEEEEEEEe----cCeeEEhhhCCc-CCCcE--------------EcCCCeEEEEECC
Confidence 5889998875 3468899999999 999999999985 33344 6789999999999
Q ss_pred CCEEEEEEEEEeccccccceecc
Q psy12829 156 GQELRLRAYAKKGFGKEHAKWNP 178 (181)
Q Consensus 156 gq~i~~e~~~~kG~G~~HAKw~p 178 (181)
||+|+|+|+|.+|+||+||||++
T Consensus 135 g~~l~me~~~~kG~Gy~~ak~~~ 157 (315)
T 2a6h_A 135 GGRLNMEVRVDRGVGYVPAEKHG 157 (315)
T ss_dssp SCEEEEEEEEEEEESEECHHHHC
T ss_pred CCEEEEEEEEEecCCccccccCc
Confidence 99999999999999999999985
No 6
>3lu0_A DNA-directed RNA polymerase subunit alpha; E. coli RNA polymerase, nucleotidyltransferase, transcription, transferase; 11.20A {Escherichia coli} PDB: 3iyd_A
Probab=100.00 E-value=1.1e-35 Score=257.04 Aligned_cols=141 Identities=18% Similarity=0.269 Sum_probs=122.5
Q ss_pred CCCCCCcEEEEEecCCeEEEEEE----ecCchhhHHHHHHHHhhCCcceEEEEEEeeCccccccceeeeeccCCcccccc
Q psy12829 2 PYANQPSVHITDLTDENVKFQVE----DTELSVANSLRRVFIAETPTMAIDWVQLEANSTVLSDEFIASRIGLIPLTSDE 77 (181)
Q Consensus 2 ~~~~~~~i~i~~~~~~~~~F~l~----g~~~siaNaLRRvLlsevPt~AI~~V~I~~NtSvl~DE~laHRlglIP~~~~~ 77 (181)
.|..+..+++.+.++.+++|.++ |++.|+||||||+||||+||+||+.|+|++ ++||||+|||+.||
T Consensus 7 ~~~~p~~~~v~~~~~~~~kF~l~PlerG~g~TlgNaLRRvLLssvpg~AIt~V~I~g---------v~Hefs~Ipgv~Ed 77 (329)
T 3lu0_A 7 EFLKPRLVDIEQVSSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDG---------VLHEYSTKEGVQED 77 (329)
T ss_dssp TSSSCCCCCEEECTTSEEEEEECCCCTTCHHHHHHHHHHHTTTSSCEEEEEEEEESS---------CSSTTCCCTTBSSC
T ss_pred hccCCceEEEEEcCCCEEEEEEEecCCCChhHHHHHHHHHHHhcCCceEEEEEEEeC---------ccccccccccccCC
Confidence 36677788898899999999999 999999999999999999999999999976 99999999999998
Q ss_pred cc------ceEEEeecCCCcCCCCCceEEEEEEEEecCCCceeEEeccceeCCCeeeeccccCcCCCCCCccCCCCeEEE
Q psy12829 78 VV------DRILYSRDCTCVDFCSECSVEFTLDVKCVDDQTRHVTTADLKSTDARVVPVTSRNRDADMNEYGETDDILIV 151 (181)
Q Consensus 78 ~~------~~~~~~~~~~~~~~~~~~~v~~~L~v~~~~~~~~~V~s~di~~~~~~~~p~~~~~~~~~~~~~~~~~di~I~ 151 (181)
+. |++.++. |..|++.++|+++ ||+.|||+||.+ +..++ ++||+++||
T Consensus 78 v~eiilNlK~i~~k~-------~~~~~~~~~L~~~----Gp~~VtA~DI~~-~~~ve--------------ivnpd~~Ia 131 (329)
T 3lu0_A 78 ILEILLNLKGLAVRV-------QGKDEVILTLNKS----GIGPVTAADITH-DGDVE--------------IVKPQHVIC 131 (329)
T ss_dssp HHHHHHHHHSCCCEE-------SSCSCEEEEECCC----SSSCEETTSSCC-CSSEE--------------CSCTTCEEE
T ss_pred HHHHHhhhccceEec-------CCCceEEEEEEEe----CCeEEEeeeecc-CCCCE--------------EeCCCcEEE
Confidence 73 3443332 2457889999986 999999999986 33344 778999999
Q ss_pred EeC-CCCEEEEEEEEEeccccccceec
Q psy12829 152 KLR-KGQELRLRAYAKKGFGKEHAKWN 177 (181)
Q Consensus 152 kL~-~gq~i~~e~~~~kG~G~~HAKw~ 177 (181)
||+ +||+|+|++++.+|+||++|.++
T Consensus 132 tL~~~~~~L~me~~i~~G~GY~~a~~~ 158 (329)
T 3lu0_A 132 HLTDENASISMRIKVQRGRGYVPASTR 158 (329)
T ss_dssp CBCSSCCCCCEEEEEEEESSEECTTTS
T ss_pred EEccCCcEEEEEEEEECcccceechhc
Confidence 999 99999999999999999988754
No 7
>2pa8_L DNA-directed RNA polymerase subunit L; ferredoxin-like Fe-S binding motif, platform for RNA polymer assembly, transferase; 1.76A {Sulfolobus solfataricus} PDB: 2pmz_L 3hkz_L 2waq_L 2wb1_L 2y0s_L
Probab=96.97 E-value=0.00093 Score=47.36 Aligned_cols=45 Identities=7% Similarity=0.111 Sum_probs=37.2
Q ss_pred CcEEEEEecCCeEEEEEEecCchhhHHHHHHHHhhCCcceEEEEEE
Q psy12829 7 PSVHITDLTDENVKFQVEDTELSVANSLRRVFIAETPTMAIDWVQL 52 (181)
Q Consensus 7 ~~i~i~~~~~~~~~F~l~g~~~siaNaLRRvLlsevPt~AI~~V~I 52 (181)
+++++.+.+++.++|.+.|=|+||||+||-.|+.. |..-+-...|
T Consensus 1 Meikvi~k~~n~~~f~i~~EDHTLgN~Lr~~L~~~-p~V~fagY~v 45 (92)
T 2pa8_L 1 MEIRILKSESNYLELEIEGEDHTLGNLIAGTLRRI-SGVSFASYYQ 45 (92)
T ss_dssp CEEEEEEEETTEEEEEEETCCHHHHHHHHHHHHTS-TTEEEEEEEC
T ss_pred CceEEEecCCCeEEEEEecCchhHHHHHHHHHhcC-CCeeEEEeec
Confidence 46899999999999999999999999999998874 6655444433
No 8
>1xpp_A TA1416, DNA-directed RNA polymerase subunit L; structural genomics, protein structure initiative, MCSG; 1.60A {Thermoplasma acidophilum} SCOP: d.74.3.2
Probab=96.86 E-value=0.0013 Score=48.48 Aligned_cols=48 Identities=4% Similarity=0.144 Sum_probs=38.8
Q ss_pred CCCCcEEEEEecCCeEEEEEEecCchhhHHHHHHHHhhCCcceEEEEEE
Q psy12829 4 ANQPSVHITDLTDENVKFQVEDTELSVANSLRRVFIAETPTMAIDWVQL 52 (181)
Q Consensus 4 ~~~~~i~i~~~~~~~~~F~l~g~~~siaNaLRRvLlsevPt~AI~~V~I 52 (181)
.+++++++.+.+++.+.|.+.|=|+||||+||-.|+.. |..-+-...|
T Consensus 8 ~~kmeiki~~k~~n~~~f~i~~EDHTLgNlLr~~Llkd-p~V~fAgY~v 55 (115)
T 1xpp_A 8 TAESSLRVISKEKNSITVEMINYDNTLLRTLVEEILKD-DQVDEARYYI 55 (115)
T ss_dssp -CCCEEEEEEECSSEEEEEEESCCHHHHHHHHHHHTTC-TTEEEEEEEC
T ss_pred ccceEEEEEcCCCCEEEEEEeCCCchhHHHHHHHHhcC-CCeEEEEeec
Confidence 35688999999999999999999999999999998765 6554444433
No 9
>1twf_K B13.6, DNA-directed RNA polymerase II 13.6 kDa polypepti; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: d.74.3.2 PDB: 1i3q_K 1i6h_K 1k83_K* 1nik_K 1nt9_K 1pqv_K 1r5u_K 1r9s_K* 1r9t_K* 1sfo_K* 1twa_K* 1twc_K* 1i50_K* 1twg_K* 1twh_K* 1wcm_K 1y1v_K 1y1w_K 1y1y_K 1y77_K* ...
Probab=96.13 E-value=0.0044 Score=45.99 Aligned_cols=45 Identities=9% Similarity=0.153 Sum_probs=36.0
Q ss_pred CCCcEEEEEecCCeEEEEEEecCchhhHHHHHHHHhhCCcceEEEE
Q psy12829 5 NQPSVHITDLTDENVKFQVEDTELSVANSLRRVFIAETPTMAIDWV 50 (181)
Q Consensus 5 ~~~~i~i~~~~~~~~~F~l~g~~~siaNaLRRvLlsevPt~AI~~V 50 (181)
+++.+++.+.+++.++|.+.|=|+||||+||-.|+.. |..-+-..
T Consensus 17 ~K~~~~~~~k~~n~~~f~i~~EDHTLgNlLr~~Llk~-p~V~fAgY 61 (120)
T 1twf_K 17 SKLKIDPDTKAPNAVVITFEKEDHTLGNLIRAELLND-RKVLFAAY 61 (120)
T ss_dssp CSCCEEECSSSTTEEEEEEESCCHHHHHHHHHHHTTC-TTEEEEEE
T ss_pred ceEEEEeccCCCCeEEEEEeCCCchHHHHHHHHHhhC-CCeeEEee
Confidence 4567777777889999999999999999999998864 65444443
No 10
>3h0g_K DNA-directed RNA polymerase II subunit RPB11; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe}
Probab=94.68 E-value=0.022 Score=42.37 Aligned_cols=34 Identities=12% Similarity=0.270 Sum_probs=28.0
Q ss_pred cEEEEEecCCeEEEEEEecCchhhHHHHHHHHhh
Q psy12829 8 SVHITDLTDENVKFQVEDTELSVANSLRRVFIAE 41 (181)
Q Consensus 8 ~i~i~~~~~~~~~F~l~g~~~siaNaLRRvLlse 41 (181)
.++.....++.+.|.+.|=|+||||+||-.|+..
T Consensus 19 ~~~~dtk~~n~~~f~i~~EDHTLgNlLr~~Llk~ 52 (123)
T 3h0g_K 19 TYELDSKSPNAAVVTLEKEDHTLANMLANQLLSD 52 (123)
T ss_dssp CEEECSSSTTEEEEEEESCCSSHHHHHHHTGGGS
T ss_pred EEecCCCCCceEEEEEeCCCcchHHHHHHHHhcC
Confidence 3333455788999999999999999999998874
No 11
>3rfr_A PMOB; membrane, oxidoreductase; 2.68A {Methylocystis SP} PDB: 3chx_A
Probab=54.53 E-value=25 Score=30.81 Aligned_cols=67 Identities=15% Similarity=0.128 Sum_probs=38.1
Q ss_pred CCceEEEEEEEEecCCCc---eeEEeccceeCCCeeeeccc--cCcCCCCCCccCCCCeEEEEeCCCCEEEEEEEEE
Q psy12829 95 SECSVEFTLDVKCVDDQT---RHVTTADLKSTDARVVPVTS--RNRDADMNEYGETDDILIVKLRKGQELRLRAYAK 166 (181)
Q Consensus 95 ~~~~v~~~L~v~~~~~~~---~~V~s~di~~~~~~~~p~~~--~~~~~~~~~~~~~~di~I~kL~~gq~i~~e~~~~ 166 (181)
+..+++++|+|+|+.+.+ ++.+++.+..-++.+.+..- ......+.. .-+++ + +.||+.=.+++.+.
T Consensus 296 pgR~l~~~~~VtN~g~~pvrlgeF~tA~vrFlnp~v~~~~~~~p~~l~a~~G-L~s~~-p---I~PGETrt~~V~a~ 367 (419)
T 3rfr_A 296 PGRELTINVKVKNGTSQPVRLGEYTAAGLRFLNPTVFTQKPDFPDYLLADRG-LSNDD-V---IAPGESKEIVVKIQ 367 (419)
T ss_dssp SSSEEEEEEEEECCSSSCBEEEEEECSSCEEECTTTCSSCCCCCTTTEESCC-CCCCC-C---BCTTCEEEEEEEEE
T ss_pred CCcEEEEEEEEecCCCCceEEeeEEEccEEEeCcccccCCCCCchhhhhccC-CCCCC-C---cCCCcceEEEEEee
Confidence 347899999999998887 45666666653332221110 000000000 11344 4 58999988887775
No 12
>1yew_A Particulate methane monooxygenase, B subunit; membrane protein, beta barrel, oxidoreductase; 2.80A {Methylococcus capsulatus} PDB: 3rgb_A
Probab=29.67 E-value=1.2e+02 Score=26.35 Aligned_cols=68 Identities=13% Similarity=0.117 Sum_probs=38.1
Q ss_pred CCceEEEEEEEEecCCCc---eeEEeccceeCCCee---eeccccCcCCCCCCccCCCCeEEEEeCCCCEEEEEEEEE
Q psy12829 95 SECSVEFTLDVKCVDDQT---RHVTTADLKSTDARV---VPVTSRNRDADMNEYGETDDILIVKLRKGQELRLRAYAK 166 (181)
Q Consensus 95 ~~~~v~~~L~v~~~~~~~---~~V~s~di~~~~~~~---~p~~~~~~~~~~~~~~~~~di~I~kL~~gq~i~~e~~~~ 166 (181)
+..+++++++|+|+.+.+ +..+++++..-++.+ .+..-+ ..-.+..--++++-+ ++||++=.+++.|.
T Consensus 262 pgR~l~~~~~VtN~g~~pvrlgeF~tA~vrFln~~~~~~~~~~P~-~lla~~gL~vsd~~p---I~PGETr~~~v~a~ 335 (382)
T 1yew_A 262 PGRAMRMKLTITNHGNSPIRLGEFYTASVRFLDSDVYKDTTGYPE-DLLAEDGLSVSDNSP---LAPGETRTVDVTAS 335 (382)
T ss_dssp SCSEEEEEEEEEECSSSCEEEEEEECSSCEEECTTTCCCCSCCCG-GGEETTCEEESCCSC---BCTTCEEEEEEEEE
T ss_pred CCcEEEEEEEEEcCCCCceEeeeEEeccEEEeCCcccccCCCChH-HhhccCCceeCCCCC---cCCCceeEEEEEee
Confidence 347999999999998887 466777765433211 000000 000000012244444 48999988887775
No 13
>2vmh_A GH95CBM51, fibronectin type III domain protein; carbohydrate-binding module, sugar-binding protein, galactose, fucosidase; 1.50A {Clostridium perfringens} SCOP: b.18.1.33 PDB: 2vmi_A 2vmg_A*
Probab=24.99 E-value=2e+02 Score=21.10 Aligned_cols=26 Identities=15% Similarity=0.330 Sum_probs=20.3
Q ss_pred EeCCCCEEEEEEEEEe-ccccccceec
Q psy12829 152 KLRKGQELRLRAYAKK-GFGKEHAKWN 177 (181)
Q Consensus 152 kL~~gq~i~~e~~~~k-G~G~~HAKw~ 177 (181)
-|.--+.|+|.+..-- |.+++||-|-
T Consensus 120 dv~G~~~L~L~v~~~gd~~~~dha~Wa 146 (151)
T 2vmh_A 120 PIAGKNTLKLVVKDGGDSIGSDHGSFG 146 (151)
T ss_dssp ECTTCCEEEEEEECTTSCCTTCEEEEE
T ss_pred ecCCCeEEEEEEEeCCCCCCCCEEEEE
Confidence 4666788888887743 6899999995
No 14
>2vb2_X Copper protein, cation efflux system protein CUSF; cation PI, metal-binding, metal transport, copper tolerance, transport; 1.70A {Escherichia coli} PDB: 2vb3_X
Probab=24.59 E-value=50 Score=22.35 Aligned_cols=29 Identities=7% Similarity=0.080 Sum_probs=22.2
Q ss_pred cCCCCeEEEEeCCCCEEEEEEEEEeccccc
Q psy12829 143 GETDDILIVKLRKGQELRLRAYAKKGFGKE 172 (181)
Q Consensus 143 ~~~~di~I~kL~~gq~i~~e~~~~kG~G~~ 172 (181)
.+.++..+..|++|+++++++.-..| ||.
T Consensus 52 ~v~~~~~l~~lk~Gd~V~F~~~~~~~-~~~ 80 (88)
T 2vb2_X 52 TITPQTKMSEIKTGDKVAFNFVQQGN-LSL 80 (88)
T ss_dssp ECCTTCEECCCCTTCEEEEEEEEETT-EEE
T ss_pred EcCChhhhhcCCCCCEEEEEEEEeCC-EEE
Confidence 34577888999999999999975543 454
No 15
>2qcp_X Cation efflux system protein CUSF; silver-binding, copper-binding, beta barrel, OB-fold, metall metal resistance, metal-binding; 1.00A {Escherichia coli str} PDB: 1zeq_X 3e6z_X
Probab=23.85 E-value=53 Score=21.74 Aligned_cols=29 Identities=7% Similarity=0.080 Sum_probs=22.1
Q ss_pred cCCCCeEEEEeCCCCEEEEEEEEEeccccc
Q psy12829 143 GETDDILIVKLRKGQELRLRAYAKKGFGKE 172 (181)
Q Consensus 143 ~~~~di~I~kL~~gq~i~~e~~~~kG~G~~ 172 (181)
.+.++..+..|++|+++++++.-..| ||.
T Consensus 44 ~v~~~~~l~~lk~Gd~V~F~~~~~~~-~~~ 72 (80)
T 2qcp_X 44 TITPQTKMSEIKTGDKVAFNFVQQGN-LSL 72 (80)
T ss_dssp ECCTTCEECCCCTTCEEEEEEEEETT-EEE
T ss_pred EccChhhhhcCCCCCEEEEEEEEeCC-EEE
Confidence 34577888999999999999975443 454
No 16
>1xhj_A Nitrogen fixation protein NIFU; alpha-beta, NIFU-like, structural genomics, protein structur initiative, NESG, PSI; NMR {Staphylococcus epidermidis} SCOP: d.52.8.1
Probab=22.77 E-value=1.8e+02 Score=19.62 Aligned_cols=39 Identities=21% Similarity=0.417 Sum_probs=31.5
Q ss_pred cEEEEEecCCeEEEEEEec----C---chhhHHHHHHHHhhCCcce
Q psy12829 8 SVHITDLTDENVKFQVEDT----E---LSVANSLRRVFIAETPTMA 46 (181)
Q Consensus 8 ~i~i~~~~~~~~~F~l~g~----~---~siaNaLRRvLlsevPt~A 46 (181)
.|++...++..++..|.|- . .|+-+++.+.|...+|.+.
T Consensus 29 dvelv~v~~g~V~V~L~GaC~gCpss~~TLk~gIE~~L~~~vPev~ 74 (88)
T 1xhj_A 29 DCTLVDVEDGIVKLQLHGACGTCPSSTITLKAGIERALHEEVPGVI 74 (88)
T ss_dssp EEEEEECCSSEEEEEEESSCCSSCHHHHHHHHHHHHHHHHHSTTCC
T ss_pred eEEEEEEECCEEEEEEeecCCCCcchHHHHHHHHHHHHHHhCCCce
Confidence 5788888788889999843 2 4789999999999999753
No 17
>1ej5_A WAsp, wiskott-aldrich syndrome protein; alpha helix, beta-hairpin turn, blood clotting; NMR {Homo sapiens} SCOP: a.68.1.1 PDB: 1t84_A* 2k42_A
Probab=22.44 E-value=30 Score=24.62 Aligned_cols=11 Identities=18% Similarity=0.299 Sum_probs=9.3
Q ss_pred hhhHHHHHHHH
Q psy12829 29 SVANSLRRVFI 39 (181)
Q Consensus 29 siaNaLRRvLl 39 (181)
.+++||||+|-
T Consensus 80 ~~~~al~~~~~ 90 (107)
T 1ej5_A 80 GLVGALMHVMQ 90 (107)
T ss_dssp THHHHHHHHGG
T ss_pred hHHHHHHHHHH
Confidence 59999999963
No 18
>2l3b_A Conserved protein found in conjugate transposon; beta, structural genomics, PSI-biology; NMR {Bacteroides thetaiotaomicron}
Probab=20.82 E-value=63 Score=23.77 Aligned_cols=25 Identities=24% Similarity=0.355 Sum_probs=21.1
Q ss_pred EeCCCCEEEEEEEEEecccccccee
Q psy12829 152 KLRKGQELRLRAYAKKGFGKEHAKW 176 (181)
Q Consensus 152 kL~~gq~i~~e~~~~kG~G~~HAKw 176 (181)
+|.+||..+++|++++.=-|.-|+|
T Consensus 23 ~I~~GeTvEIR~~L~reG~f~~t~Y 47 (130)
T 2l3b_A 23 KLKVGETAEIRCQLHRDGRFEETKY 47 (130)
T ss_dssp SCCTTCEEEEEEEEECSSCCSSCCC
T ss_pred ccCCCCeEEEEEEEecCceecccEE
Confidence 4789999999999998877777765
No 19
>2vng_A CPE0329; family 51 carbohydrate binding module, family 98 glycoside hydrolase, A-trisaccharide, blood group antigen, hydrolase; HET: A2G GAL FUC; 1.4A {Clostridium perfringens} SCOP: b.18.1.33 PDB: 2vno_A* 2vnr_A
Probab=20.43 E-value=2.7e+02 Score=21.30 Aligned_cols=27 Identities=15% Similarity=0.349 Sum_probs=21.5
Q ss_pred EEeC-CCCEEEEEEEEEeccccccceec
Q psy12829 151 VKLR-KGQELRLRAYAKKGFGKEHAKWN 177 (181)
Q Consensus 151 ~kL~-~gq~i~~e~~~~kG~G~~HAKw~ 177 (181)
+.|. --+.|+|.+.+-.|.+++||-|-
T Consensus 141 vdv~~G~k~L~Lvv~~g~~~~~DhadWa 168 (180)
T 2vng_A 141 LNIPENAKRLQLKSYAGEKTWGDEVVYA 168 (180)
T ss_dssp EECCTTCCEEEEEEECTTCCTTCEEEEE
T ss_pred EEccCCceEEEEEEeCCCCCccceeEec
Confidence 4576 56788888887778899999994
Done!