Query 045123
Match_columns 219
No_of_seqs 189 out of 1363
Neff 6.2
Searched_HMMs 29240
Date Mon Mar 25 17:41:04 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/045123.a3m -d /work/01045/syshi/HHdatabase/pdb70.hhm -o /work/01045/syshi/hhsearch_pdb/045123hhsearch_pdb -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 3h0g_A DNA-directed RNA polyme 100.0 2.7E-53 9.4E-58 441.8 13.3 207 3-219 4-212 (1752)
2 3qqc_A DNA-directed RNA polyme 100.0 5.9E-50 2E-54 372.0 8.5 175 11-219 65-246 (436)
3 1twf_A B220, DNA-directed RNA 100.0 8.9E-47 3E-51 393.2 13.5 185 1-194 1-187 (1733)
4 4ayb_A DNA-directed RNA polyme 100.0 1.9E-36 6.5E-41 301.6 12.0 156 11-190 2-166 (880)
5 1hqm_D DNA-directed RNA polyme 99.9 3.9E-26 1.3E-30 232.5 1.4 104 13-116 3-137 (1265)
6 3lu0_D DNA-directed RNA polyme 99.6 5.3E-16 1.8E-20 157.8 4.4 104 10-113 12-139 (1407)
7 2a6h_D DNA-directed RNA polyme 99.5 3.4E-14 1.2E-18 146.1 5.6 102 14-115 4-136 (1524)
8 1ef4_A Subunit N, DNA-directed 47.0 7.4 0.00025 25.7 1.3 31 105-136 5-36 (55)
9 3hcj_A MSRB, peptide methionin 39.1 9.9 0.00034 30.2 1.1 25 53-84 89-113 (154)
10 3na7_A HP0958; flagellar bioge 38.4 9.6 0.00033 32.0 1.0 38 63-117 198-236 (256)
11 3e0o_A Peptide methionine sulf 36.5 9.3 0.00032 30.0 0.6 25 53-84 80-104 (144)
12 1twf_J DNA-directed RNA polyme 31.0 19 0.00066 24.8 1.4 31 103-134 4-36 (70)
13 4ayb_N DNA-directed RNA polyme 30.5 12 0.00042 25.5 0.3 13 104-116 5-17 (66)
14 2l1u_A MSRB2, methionine-R-sul 28.7 16 0.00056 28.5 0.8 29 53-88 83-111 (143)
15 1iym_A EL5; ring-H2 finger, ub 26.1 47 0.0016 20.0 2.6 48 61-112 3-52 (55)
16 2k8d_A Peptide methionine sulf 24.5 14 0.00046 29.3 -0.4 10 75-84 115-124 (151)
No 1
>3h0g_A DNA-directed RNA polymerase II subunit RPB1; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe}
Probab=100.00 E-value=2.7e-53 Score=441.83 Aligned_cols=207 Identities=42% Similarity=0.780 Sum_probs=178.1
Q ss_pred CCCCCCccccceeeeEEEEeCCHHHHhcCcccEEecCccccC--CCCCCCCCccCCCCCCCCCcccCCCCCCCCccCCcc
Q 045123 3 NCFTFSPFKVAKVRMVQFSILSPDEIRKMSVTEIDHGKTTER--GMPMAGGLSDLRLGTIDKRFKCETCSSNMGECPGHF 80 (219)
Q Consensus 3 ~~~~~~~~~~~~i~~i~F~~~s~eeI~~~Sv~ei~~~~~~~~--~~p~~~Gl~D~rlG~~~~~~~C~TC~~~~~~CpGHf 80 (219)
..|++|+++.++|++|+|++||+|||+++||++|+++++||. ++|+.|||+|||||++++...|.|||+++.+|||||
T Consensus 4 ~~~~~s~~~~~~i~~i~Fg~~S~eeI~~~Sv~~I~~~~~~d~~~~~P~~~Gl~D~rlG~~~~~~~C~TCg~~~~~CpGHF 83 (1752)
T 3h0g_A 4 IQFSPSSVPLRRVEEVQFGILSPEEIRSMSVAKIEFPETMDESGQRPRVGGLLDPRLGTIDRQFKCQTCGETMADCPGHF 83 (1752)
T ss_dssp CSSCCCSSCCCCCCCBEECCCCHHHHHHHCCCCCCCTTCTTCSSSSSCCSSSSSSSCCCSSSSCCCTTSCCSSSSCCCCC
T ss_pred ccCCCCcCcceeeeeEEEecCCHHHHHHhCeeEEecccccccccCCCCCCCCcCccccCCCCCCCCCCCCCCCCcCCCcc
Confidence 478999999999999999999999999999999999999996 499999999999999999999999999999999999
Q ss_pred eeeecccceeeeeehhhhhhhhhhhcccccccccCccCHHHHHHHHhcCchhHHHHHHHHhccccccCCCCcccccccCC
Q 045123 81 GHLELAKPMFHIGFMKTLLTIMRCVCFNCSKILADEEDDKFKLALKIRHPKSRLEQILCACKTKNKCEGGDEIDVLSLLG 160 (219)
Q Consensus 81 GhIeL~~Pv~h~~f~~~i~~iL~~vC~~C~rll~~~~~~~~~~~~~~~~~k~r~~~i~~~ck~~~~Ce~~~~~d~~~~~~ 160 (219)
|||||++||||||||+.|++||+|+|++|+||++++++++|+.+++++++++||++||++||++++|+.+...++++ +.
T Consensus 84 GHIELa~PVfHpgF~~~I~kILr~vC~~C~klll~~~~~~f~~~lrlrd~k~r~~~V~~~ck~k~~Ce~~~~~~~~~-~~ 162 (1752)
T 3h0g_A 84 GHIELAKPVFHIGFLSKIKKILECVCWNCGKLKIDSSNPKFNDTQRYRDPKNRLNAVWNVCKTKMVCDTGLSAGSDN-FD 162 (1752)
T ss_dssp EECCCCSCBCCHHHHHHHHHHSSSSCTTTCCCSCCSCSHHHHHHHHSSCTTTTHHHHHHHHHHCCCCCSSTTCCSSC-CC
T ss_pred eeeecccceEeehhhHHHHHHHHHHHHHhcccccccccHHHHHHHHccCHHHHHHHHHHHhccccccCCCCcccccc-hh
Confidence 99999999999999999999999999999999999988999999999999999999999999999998643322111 00
Q ss_pred CCCCCCCccCCCCCCCCCCeEEEeceEEEEEEccccccCCCCCCCCCCCCcccccCCCC
Q 045123 161 HDGEEPLRKRKSGCGALQPTLTIDGMNMIAEYKAQRKKNDDQGQLPEPVERKQTLTAER 219 (219)
Q Consensus 161 ~~~~~~~~~~~~gCG~~qP~irk~glkl~~~~k~~~~~~~~~~~~~~~~~~k~~ltae~ 219 (219)
.........|+|||+.||+|||+|++|+++|+..+++ +++ + +++.|||++
T Consensus 163 -~~~~~~~~~~~gCG~~qP~IRKeglkl~~~~k~~k~~--~~~--~----~k~~LtP~e 212 (1752)
T 3h0g_A 163 -LSNPSANMGHGGCGAAQPTIRKDGLRLWGSWKRGKDE--SDL--P----EKRLLSPLE 212 (1752)
T ss_dssp -SSCCCCCCSSCSSCCCCCCCEEETTEEECCBCCSSSS--CBC--S----SCCCCCHHH
T ss_pred -cccccccccCCCcCCcCCcEEeeccEEEEEEcccccc--ccc--c----cceecCHHH
Confidence 1111123457999999999999999999999853321 111 1 378888863
No 2
>3qqc_A DNA-directed RNA polymerase subunit B, DNA-direct polymerase subunit A', DNA-directed...; transcription, fusion protein, chimera protein, multiprotein; 3.30A {Pyrococcus furiosus}
Probab=100.00 E-value=5.9e-50 Score=371.98 Aligned_cols=175 Identities=34% Similarity=0.705 Sum_probs=141.9
Q ss_pred ccceeeeEEEEeCCHHHHhcCcccEEecCccccC-CCCCCCCCccCCCCCCCCCcccCCCCCCCCccCCcceeeecccce
Q 045123 11 KVAKVRMVQFSILSPDEIRKMSVTEIDHGKTTER-GMPMAGGLSDLRLGTIDKRFKCETCSSNMGECPGHFGHLELAKPM 89 (219)
Q Consensus 11 ~~~~i~~i~F~~~s~eeI~~~Sv~ei~~~~~~~~-~~p~~~Gl~D~rlG~~~~~~~C~TC~~~~~~CpGHfGhIeL~~Pv 89 (219)
..++|++|+||+||++||+++||++|+++++||. ++|++|||+|||||++++...|+|||+++.+||||||||+|+.||
T Consensus 65 ~~~~i~~i~F~~~s~eeI~~~Sv~~I~~~~~~d~~~~P~~gGl~D~rlG~~~~~~~C~TCg~~~~~CpGHfGhIeL~~PV 144 (436)
T 3qqc_A 65 GGKVIGSIEFGILSPQEIRKMSAVEVTVPDTYDDDGYPIEGGVMDKRMGVIDPGLRCETCGGRAGECPGHFGHIELARPV 144 (436)
T ss_dssp --CEEEEEECCBCCHHHHHHTEEEECCBCCCCC----CCCSBSSCSSSCCCSSCCCCSSSCCCSSSCCCCEEEEEEEEEE
T ss_pred ccceeeeeeeccCCHHHHHHhCCeEEecccccCCCCCccCCCccCccccCCCCCCCCCCCCCCCCcCCCCceeEeechHH
Confidence 4479999999999999999999999999999985 799999999999999999999999999999999999999999999
Q ss_pred eeeeehhhhhhhhhhhcccccccccCccC-HHHHHHHHhc-----CchhHHHHHHHHhccccccCCCCcccccccCCCCC
Q 045123 90 FHIGFMKTLLTIMRCVCFNCSKILADEED-DKFKLALKIR-----HPKSRLEQILCACKTKNKCEGGDEIDVLSLLGHDG 163 (219)
Q Consensus 90 ~h~~f~~~i~~iL~~vC~~C~rll~~~~~-~~~~~~~~~~-----~~k~r~~~i~~~ck~~~~Ce~~~~~d~~~~~~~~~ 163 (219)
|||+|++.|++||+|+|++|+|+++++++ ++|..+++.. +++.|+++||+.|+++++|
T Consensus 145 fh~gF~~~I~kILr~vC~~C~klll~~~~~~~f~~~lr~~~~~~~~~k~~~~~i~~~~k~~~~C---------------- 208 (436)
T 3qqc_A 145 IHVGFAKTIYRILESTCRECGRIKLTDEEIEEYMKKIELARNRRSEFNEIIKEIHKKAKERMVC---------------- 208 (436)
T ss_dssp ECGGGHHHHHHHHHHSCSTTCCCSSCHHHHHHHHHHHHHTSSCHHHHHHHHHHHHHHHHTCCSC----------------
T ss_pred HHHHHHHHHHHHHHHHHHHhcccccccccHHHHHHHHHhhhhccccHHHHHHHHHHHcccCCcC----------------
Confidence 99999999999999999999999999765 4677666632 4788999999999999999
Q ss_pred CCCCccCCCCCCCCCCeEEEeceEEEEEEccccccCCCCCCCCCCCCcccccCCCC
Q 045123 164 EEPLRKRKSGCGALQPTLTIDGMNMIAEYKAQRKKNDDQGQLPEPVERKQTLTAER 219 (219)
Q Consensus 164 ~~~~~~~~~gCG~~qP~irk~glkl~~~~k~~~~~~~~~~~~~~~~~~k~~ltae~ 219 (219)
+|||+.||+||++|++++.+.. +. ++++ ++ ++.|||++
T Consensus 209 --------~gCG~~qp~Ir~e~~~~~~~~~--~~---~~~~-~~----k~~LtP~~ 246 (436)
T 3qqc_A 209 --------PHCGAPQYPIKFEKPTIYWEIR--KD---EQGN-EY----RHRLMPTE 246 (436)
T ss_dssp --------C-------CCCBCSSSCEEEEC--CC------C-CC----EEEECHHH
T ss_pred --------cccCCcCceEEEecceeeeecc--cc---cccc-cc----ccccCHHH
Confidence 6999999999999987654332 11 1111 22 78888863
No 3
>1twf_A B220, DNA-directed RNA polymerase II largest subunit; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: e.29.1.2 PDB: 1i3q_A 1i6h_A 1k83_A* 1nik_A 1nt9_A 1pqv_A 1r5u_A 1r9s_A* 1r9t_A* 1sfo_A* 1twa_A* 1twc_A* 1i50_A* 1twg_A* 1twh_A* 1wcm_A 1y1v_A 1y1w_A 1y1y_A 1y77_A* ...
Probab=100.00 E-value=8.9e-47 Score=393.16 Aligned_cols=185 Identities=39% Similarity=0.785 Sum_probs=166.4
Q ss_pred CCCCCCCCccccceeeeEEEEeCCHHHHhcCcccEEecCccccCC--CCCCCCCccCCCCCCCCCcccCCCCCCCCccCC
Q 045123 1 MENCFTFSPFKVAKVRMVQFSILSPDEIRKMSVTEIDHGKTTERG--MPMAGGLSDLRLGTIDKRFKCETCSSNMGECPG 78 (219)
Q Consensus 1 ~~~~~~~~~~~~~~i~~i~F~~~s~eeI~~~Sv~ei~~~~~~~~~--~p~~~Gl~D~rlG~~~~~~~C~TC~~~~~~CpG 78 (219)
|. .|++|+++.++|++|+|+++|+|||++||++||+++++||.+ +|..|||+|||||++++...|.|||.+..+|||
T Consensus 1 ~~-~~~~~~~~~~~i~~I~f~l~SpeeIr~~Sv~eI~~pet~~~~~~~P~~~GL~d~rlG~~~~~~~C~tCg~~~~~C~G 79 (1733)
T 1twf_A 1 MV-GQQYSSAPLRTVKEVQFGLFSPEEVRAISVAKIRFPETMDETQTRAKIGGLNDPRLGSIDRNLKCQTCQEGMNECPG 79 (1733)
T ss_dssp -C-CCSCCCSCBCCCCEEECCBCCHHHHHHTCCCCCCCSCCSCTTSCCSCCSSSSCSSSCCCTTCCCSSSCCCCTTSCCC
T ss_pred CC-CCCCCcCCccccceEEEEeCCHHHHHHhCeeEEecccccccccCCCCcCCCcCcccCcccCCCEeCCCCCCCCcCCC
Confidence 56 899999999999999999999999999999999999999976 999999999999999999999999999999999
Q ss_pred cceeeecccceeeeeehhhhhhhhhhhcccccccccCccCHHHHHHHHhcCchhHHHHHHHHhccccccCCCCccccccc
Q 045123 79 HFGHLELAKPMFHIGFMKTLLTIMRCVCFNCSKILADEEDDKFKLALKIRHPKSRLEQILCACKTKNKCEGGDEIDVLSL 158 (219)
Q Consensus 79 HfGhIeL~~Pv~h~~f~~~i~~iL~~vC~~C~rll~~~~~~~~~~~~~~~~~k~r~~~i~~~ck~~~~Ce~~~~~d~~~~ 158 (219)
|||||||++|||||+||+.++++|+++|++|+++++++.+++|.+++++++|++|+++||++|+++++|+.+...+.+
T Consensus 80 HfGHIELa~PV~HigF~k~i~kiLe~VC~~Cskllld~~~~~~~~~L~~~~pk~r~~~v~e~ck~k~~Ce~~~~~~~e-- 157 (1733)
T 1twf_A 80 HFGHIDLAKPVFHVGFIAKIKKVCECVCMHCGKLLLDEHNELMRQALAIKDSKKRFAAIWTLCKTKMVCETDVPSEDD-- 157 (1733)
T ss_dssp CCCCEEEEEEEECGGGHHHHHHHHHHBCTTTCCBSCCTTSHHHHHHHTCCSHHHHHHHHHHHHTTCCBCCSEECCSSC--
T ss_pred ccceeecccccccHHHHhhHHHHHHHHhHhcceeeeccchHHHHHHHHhcCHHHHHHHHHHHhcccccccccccchhc--
Confidence 999999999999999999999999999999999999988888888888889999999999999999999642111110
Q ss_pred CCCCCCCCCccCCCCCCCCCCeEEEeceEEEEEEcc
Q 045123 159 LGHDGEEPLRKRKSGCGALQPTLTIDGMNMIAEYKA 194 (219)
Q Consensus 159 ~~~~~~~~~~~~~~gCG~~qP~irk~glkl~~~~k~ 194 (219)
. .....|+|||+.||.||++||+++++|+.
T Consensus 158 ----~--~~~~~~~gCGa~qp~irk~gl~l~~e~k~ 187 (1733)
T 1twf_A 158 ----P--TQLVSRGGCGNTQPTIRKDGLKLVGSWKK 187 (1733)
T ss_dssp ----T--TSCEECCSCCCBCCCCEECSSCEEEEECS
T ss_pred ----c--ccccccCCCCCccHHHHhcCCceEEeecc
Confidence 0 11223689999999999999999999974
No 4
>4ayb_A DNA-directed RNA polymerase; transferase, multi-subunit, transcription; 3.20A {Sulfolobus shibatae} PDB: 2wb1_A 2y0s_A 2waq_A 4b1o_A 4b1p_W 2pmz_A 3hkz_A
Probab=100.00 E-value=1.9e-36 Score=301.58 Aligned_cols=156 Identities=35% Similarity=0.736 Sum_probs=130.1
Q ss_pred ccceeeeEEEEeCCHHHHhcCcccEEecCccccC-CCCCCCCCccCCCCCCCCCcccCCCCCCCCccCCcceeeecccce
Q 045123 11 KVAKVRMVQFSILSPDEIRKMSVTEIDHGKTTER-GMPMAGGLSDLRLGTIDKRFKCETCSSNMGECPGHFGHLELAKPM 89 (219)
Q Consensus 11 ~~~~i~~i~F~~~s~eeI~~~Sv~ei~~~~~~~~-~~p~~~Gl~D~rlG~~~~~~~C~TC~~~~~~CpGHfGhIeL~~Pv 89 (219)
..++|++|+||++|||||++||++||++|++||. |.|+.|||+|||||+.++...|+|||.++.+||||||||+|+.||
T Consensus 2 ~~k~i~~I~f~l~SpeeIr~~S~~eV~~p~t~n~~g~p~~ggl~D~~lG~~~~~~~C~tCg~~~~~c~ghfGhIeLa~PV 81 (880)
T 4ayb_A 2 SEKNIKGIKFGILSPDEIRKMSVTAIITPDVYDEDGTPIEGSVMDPRLGVIEPGQKCPTCGNTLGNCPGHFGHIELVRPV 81 (880)
T ss_dssp -CEEEEEEEEECCCHHHHHHHTCSCBCCSCCCBSSSSSBCSSSSCGGGCCCSSSCCCTTTCCCGGGCCCCCEEEEEEEEE
T ss_pred CCceeceEEEEeCCHHHHHHhcceEEeCcceECCCCCccCCCCCChhhCCCCCCCCCCCCCCCCCCCCCCCeeecccccc
Confidence 3578999999999999999999999999999985 899999999999999999999999999999999999999999999
Q ss_pred eeeeehhhhhhhhhhhcccccccccCccCHH-HHHHHH---hcCc--hhHH-HHHHHHhccccccCCCCcccccccCCCC
Q 045123 90 FHIGFMKTLLTIMRCVCFNCSKILADEEDDK-FKLALK---IRHP--KSRL-EQILCACKTKNKCEGGDEIDVLSLLGHD 162 (219)
Q Consensus 90 ~h~~f~~~i~~iL~~vC~~C~rll~~~~~~~-~~~~~~---~~~~--k~r~-~~i~~~ck~~~~Ce~~~~~d~~~~~~~~ 162 (219)
|||+|++.|.++|+++|++|+|+++++++.+ +..... .+.+ .+++ +.+.+.+.+...|
T Consensus 82 ~h~~f~~~i~~lL~~~c~~C~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~c--------------- 146 (880)
T 4ayb_A 82 IHVGFVKHVYEFLKATCRRCGRVKISEDEIEKYSRIYNAIKKRWPSAARRLTEYVKKTAMKAQVC--------------- 146 (880)
T ss_dssp ECGGGTTHHHHHHHTSCTTSSCCCSSCCHHHHHHHHHHHHGGGCHHHHHHHHHHHHHHHTTCSSC---------------
T ss_pred cchhHHHHHHHHHhCccccccCCcCCHHHHHHHHHHHHHhhccChHHHHHHHHHHHHHhcccccc---------------
Confidence 9999999999999999999999999865432 222222 1222 1223 4455666777777
Q ss_pred CCCCCccCCCCCCCCCCeEEEec-eEEEE
Q 045123 163 GEEPLRKRKSGCGALQPTLTIDG-MNMIA 190 (219)
Q Consensus 163 ~~~~~~~~~~gCG~~qP~irk~g-lkl~~ 190 (219)
++||+.||+|++++ +++..
T Consensus 147 ---------~~cg~~~~~i~~~~~~~~~~ 166 (880)
T 4ayb_A 147 ---------PHCGEKQFKIKLEKPYNFYE 166 (880)
T ss_dssp ---------TTTTCCCCCCEEEETTEEEE
T ss_pred ---------hhccchhhhhhhcCcCCHHH
Confidence 58999999999886 34433
No 5
>1hqm_D DNA-directed RNA polymerase; transferase, transcription, 3D- structure; 3.30A {Thermus aquaticus} SCOP: i.8.1.1 PDB: 1i6v_D* 2gho_D
Probab=99.91 E-value=3.9e-26 Score=232.55 Aligned_cols=104 Identities=33% Similarity=0.501 Sum_probs=77.7
Q ss_pred ceeeeEEEEeCCHHHHhcCcccEEecCcccc--CCCCCCCCCccCCC-CCCC--------------CCcccCCCCCCCCc
Q 045123 13 AKVRMVQFSILSPDEIRKMSVTEIDHGKTTE--RGMPMAGGLSDLRL-GTID--------------KRFKCETCSSNMGE 75 (219)
Q Consensus 13 ~~i~~i~F~~~s~eeI~~~Sv~ei~~~~~~~--~~~p~~~Gl~D~rl-G~~~--------------~~~~C~TC~~~~~~ 75 (219)
++|++|+|+++|||+|++||+.||++|++|+ +++|..+||+|+|| |+.. +...|.|||..+.+
T Consensus 3 ~~~~~i~~gl~Spe~Ir~~S~geV~~pet~ny~t~kP~~~GLfd~rifGp~k~~~C~Cgkyk~~~~~~~~C~~Cg~~~~~ 82 (1265)
T 1hqm_D 3 KEVRKVRIALASPEKIRSWSYGEVEKPETINYRTLKPERDGLFDERIFGPIKDYECACGKYKRQRFEGKVCERCGVEVTR 82 (1265)
T ss_dssp CCBCCCCCCCCCTTTHHHHTTTCCCCCCC-------------------------------------CCSCSSSSSSSSCC
T ss_pred cccceEEEecCCHHHHHHhhEEEEcchhheecCCCcccCCCCcCccccCCCccceecCCCccccCCCCCCCCCCCCcccc
Confidence 4689999999999999999999999999998 37999999999999 7653 67899999999999
Q ss_pred c---CCcceeeecccceeeeeehhh-----------hhhhhhhhcccccccccCc
Q 045123 76 C---PGHFGHLELAKPMFHIGFMKT-----------LLTIMRCVCFNCSKILADE 116 (219)
Q Consensus 76 C---pGHfGhIeL~~Pv~h~~f~~~-----------i~~iL~~vC~~C~rll~~~ 116 (219)
| |||||||+|+.||||+||++. +.+.|+++|++|+++++++
T Consensus 83 ~~vrrg~~GhIeLa~PV~Hi~y~k~~~s~l~~lL~~~~k~le~v~y~~s~v~~~~ 137 (1265)
T 1hqm_D 83 SIVRRYRMGHIELATPAAHIWFVKDVPSKIGTLLDLFATELEQVLYFNKYIVLDP 137 (1265)
T ss_dssp SSSCCCSCCCCCCCSCCCSTTSTTHHHHTTTCTTTHHHHTTSSSCCCCSCCCCSS
T ss_pred cccccCccceEEecCceeeeeecccchHHHHHHhcCCHHhhccEeeecceEeecC
Confidence 9 899999999999999999996 4577889999999988764
No 6
>3lu0_D DNA-directed RNA polymerase subunit beta'; E. coli RNA polymerase, nucleotidyltransferase, transcription, transferase; 11.20A {Escherichia coli} PDB: 3iyd_D*
Probab=99.58 E-value=5.3e-16 Score=157.82 Aligned_cols=104 Identities=28% Similarity=0.470 Sum_probs=91.8
Q ss_pred cccceeeeEEEEeCCHHHHhcCcccEEecCccccC--CCCCCCCCccCCC-CCCC--------------CCcccCCCCCC
Q 045123 10 FKVAKVRMVQFSILSPDEIRKMSVTEIDHGKTTER--GMPMAGGLSDLRL-GTID--------------KRFKCETCSSN 72 (219)
Q Consensus 10 ~~~~~i~~i~F~~~s~eeI~~~Sv~ei~~~~~~~~--~~p~~~Gl~D~rl-G~~~--------------~~~~C~TC~~~ 72 (219)
.+...+++|++++.||++|++||..||++|++++. .+|..+||+++|+ |+.. +...|.+||..
T Consensus 12 ~~~~~~~~i~i~laSpe~I~~ws~GEV~kpetinyrt~kPe~dGLFcerIFGp~kd~eC~Cgkyk~~~~~g~~C~~Cgve 91 (1407)
T 3lu0_D 12 TKTEEFDAIKIALASPDMIRSWSFGEVKKPETINYRTFKPERDGLFCARIFGPVKDYECLCGKYKRLKHRGVICEKCGVE 91 (1407)
T ss_dssp --CCCCCCEEECCCCHHHHHHHBCSCCCSCCCCCSSCCSCCSSSSSCTTTTCCSSSSCCSSCSCCSTTCSSSCCSSSCCC
T ss_pred cccCccceEEEEeCCHHHHHhhcCeEECCccccccCCCCCCCCCccchhhcCCCcCcEEeCccccccccCCCCCCCCCCc
Confidence 45678999999999999999999999999999985 6999999999999 9873 45789999999
Q ss_pred CCccC---Ccceeeecccceeeeeehhhh----hhhhhhhcccccccc
Q 045123 73 MGECP---GHFGHLELAKPMFHIGFMKTL----LTIMRCVCFNCSKIL 113 (219)
Q Consensus 73 ~~~Cp---GHfGhIeL~~Pv~h~~f~~~i----~~iL~~vC~~C~rll 113 (219)
...|. .|||||+|+.||.|++||+.+ -.+|...+..+.+++
T Consensus 92 vt~~~vRr~rmGhI~La~PV~Hiwy~k~~ps~i~~lL~~~~k~le~vi 139 (1407)
T 3lu0_D 92 VTQTKVRRERMGHIELASPTAHIWFLKSLPSRIGLLLDMPLRDIERVL 139 (1407)
T ss_dssp CCCTTHHHHCBCEEEEEEEECCTHHHHSSSCTTTTTTTSCSSTTHHHH
T ss_pred cccCcchhhhcceeeecCceeEeeeccCCchHHHHHhCCCHHHhhhhe
Confidence 99997 999999999999999999987 567777877776654
No 7
>2a6h_D DNA-directed RNA polymerase beta' chain; RNA polymerase holoenzyme, streptolydigin, antibiotic, transcription regulation; HET: STD; 2.40A {Thermus thermophilus} SCOP: e.29.1.2 PDB: 1smy_D* 1zyr_D* 1iw7_D* 2a69_D* 2a6e_D 2a68_D* 2be5_D* 2cw0_D 2o5i_D 2o5j_D* 2ppb_D* 3aoh_D* 3aoi_D* 3dxj_D* 3eql_D* 1ynj_D* 1l9z_D 1l9u_D* 1ynn_D* 2auj_D
Probab=99.45 E-value=3.4e-14 Score=146.14 Aligned_cols=102 Identities=33% Similarity=0.511 Sum_probs=87.7
Q ss_pred eeeeEEEEeCCHHHHhcCcccEEecCccccC--CCCCCCCCccCCC-CCCC--------------CCcccCCCCCCCCcc
Q 045123 14 KVRMVQFSILSPDEIRKMSVTEIDHGKTTER--GMPMAGGLSDLRL-GTID--------------KRFKCETCSSNMGEC 76 (219)
Q Consensus 14 ~i~~i~F~~~s~eeI~~~Sv~ei~~~~~~~~--~~p~~~Gl~D~rl-G~~~--------------~~~~C~TC~~~~~~C 76 (219)
.+..|++++.||++|++||+.||++|++.+. .+|..+||++.|. |+.. ....|..||..+.++
T Consensus 4 ~~~~i~i~laSP~~I~~ws~GeV~~peTiny~t~kPe~~GLFcerIFGp~~~~~C~Cgkyk~~~~~~~~C~~Cgve~t~s 83 (1524)
T 2a6h_D 4 EVRKVRIALASPEKIRSWSYGEVEKPETINYRTLKPERDGLFDERIFGPIKDYECACGKYKRQRFEGKVCERCGVEVTKS 83 (1524)
T ss_dssp CCCEEEEECCCHHHHHHHEEEECCSCCCBCTTSCSBCSSSTTCTTTTCCSSSSCCSSCSSCSSTTTTCCCSSSCCCCSST
T ss_pred ccceEEEEecCHHHHHHhhcceecCcccccccCCCCCCCCcccchhcCccccceEcCccccccCcCCCCCCCCCCccccc
Confidence 5678999999999999999999999999884 6999999999999 9875 223466677666666
Q ss_pred C---Ccceeeecccceeeeeehhhh-----------hhhhhhhcccccccccC
Q 045123 77 P---GHFGHLELAKPMFHIGFMKTL-----------LTIMRCVCFNCSKILAD 115 (219)
Q Consensus 77 p---GHfGhIeL~~Pv~h~~f~~~i-----------~~iL~~vC~~C~rll~~ 115 (219)
. .+||||+|+.||.|++|++.+ .+.|+.++++++.+.+.
T Consensus 84 ~VRR~rmG~I~La~PV~HiWylk~~PS~l~~LLd~s~k~le~i~yf~~y~v~~ 136 (1524)
T 2a6h_D 84 IVRRYRMGHIELATPAAHIWFVKDVPSKIGTLLDLSATELEQVLYFSKYIVLD 136 (1524)
T ss_dssp HHHHHCEEEEEEEEEEECHHHHSSSSCHHHHHTTSCTTHHHHHHHHSCCEEEC
T ss_pred hHHhhhcCeeeecCceeehhhhcCCchHHHHHhcCCHHHHhHhhcceeeEeec
Confidence 4 999999999999999999988 78899999998776554
No 8
>1ef4_A Subunit N, DNA-directed RNA polymerase; three helix bundle, zinc binding, structural genomics, PSI; NMR {Methanothermobacterthermautotrophicus} SCOP: a.4.11.1
Probab=47.05 E-value=7.4 Score=25.68 Aligned_cols=31 Identities=19% Similarity=0.460 Sum_probs=18.3
Q ss_pred hcccccccccCccCHHHHHHHH-hcCchhHHHH
Q 045123 105 VCFNCSKILADEEDDKFKLALK-IRHPKSRLEQ 136 (219)
Q Consensus 105 vC~~C~rll~~~~~~~~~~~~~-~~~~k~r~~~ 136 (219)
-|++|++++.+.- .+|...++ -.+|...|++
T Consensus 5 RCFTCGkvi~~~w-e~y~~~~~~~~~~~~~LD~ 36 (55)
T 1ef4_A 5 RCLSCGKPVSAYF-NEYQRRVADGEDPKDVLDD 36 (55)
T ss_dssp SCSCTTSCCHHHH-HHHHHHHHHTCCHHHHHHH
T ss_pred ecCCCCCChhHHH-HHHHHHHHcCCCHHHHHHH
Confidence 5999999987643 34544333 2455554444
No 9
>3hcj_A MSRB, peptide methionine sulfoxide reductase; methionine sulfoxide reductase B, oxidized form, oxidoreductase; 1.66A {Xanthomonas campestris PV} PDB: 3hci_A*
Probab=39.06 E-value=9.9 Score=30.18 Aligned_cols=25 Identities=32% Similarity=0.713 Sum_probs=15.1
Q ss_pred ccCCCCCCCCCcccCCCCCCCCccCCcceeee
Q 045123 53 SDLRLGTIDKRFKCETCSSNMGECPGHFGHLE 84 (219)
Q Consensus 53 ~D~rlG~~~~~~~C~TC~~~~~~CpGHfGhIe 84 (219)
-|..+|..--...|.. |-||.||+=
T Consensus 89 ~D~s~gm~RtEV~C~~-------Cg~HLGHVF 113 (154)
T 3hcj_A 89 RDTSYGMIRTEIVCAR-------CDSHLGHVF 113 (154)
T ss_dssp CCTTTTTSCEEEEETT-------TCCEEEEEE
T ss_pred ecCCCCceEEEEEeCC-------CCCccCCcc
Confidence 4566664433355655 558999973
No 10
>3na7_A HP0958; flagellar biogenesis, flagellum export, C4 Zn-ribbon, coiled post-transcriptional, gene regulation, chaperone; HET: EPE; 2.20A {Helicobacter pylori}
Probab=38.39 E-value=9.6 Score=32.01 Aligned_cols=38 Identities=26% Similarity=0.418 Sum_probs=23.7
Q ss_pred CcccCCCCCCCCccCCcceeeecccceeeeeehhhhhhh-hhhhcccccccccCcc
Q 045123 63 RFKCETCSSNMGECPGHFGHLELAKPMFHIGFMKTLLTI-MRCVCFNCSKILADEE 117 (219)
Q Consensus 63 ~~~C~TC~~~~~~CpGHfGhIeL~~Pv~h~~f~~~i~~i-L~~vC~~C~rll~~~~ 117 (219)
+..|.-|+.. | .|..+..|.+= =-..|.+|+|+|+...
T Consensus 198 ~~~C~GC~~~------------l-----ppq~~~~i~~~~~Iv~Cp~CgRIL~~~~ 236 (256)
T 3na7_A 198 KQACGGCFIR------------L-----NDKIYTEVLTSGDMITCPYCGRILYAEG 236 (256)
T ss_dssp TTBCTTTCCB------------C-----CHHHHHHHHHSSSCEECTTTCCEEECSC
T ss_pred CCccCCCCee------------e-----CHHHHHHHHCCCCEEECCCCCeeEEeCc
Confidence 4578887643 3 34445555431 0168999999998764
No 11
>3e0o_A Peptide methionine sulfoxide reductase MSRB; oxidoreductase; 2.60A {Bacillus subtilis} SCOP: b.88.1.3 PDB: 1xm0_A 2kzn_A
Probab=36.45 E-value=9.3 Score=30.01 Aligned_cols=25 Identities=28% Similarity=0.453 Sum_probs=14.7
Q ss_pred ccCCCCCCCCCcccCCCCCCCCccCCcceeee
Q 045123 53 SDLRLGTIDKRFKCETCSSNMGECPGHFGHLE 84 (219)
Q Consensus 53 ~D~rlG~~~~~~~C~TC~~~~~~CpGHfGhIe 84 (219)
-|..+|..--...|.. |-||.||+=
T Consensus 80 ~D~s~gm~RtEV~C~~-------Cg~HLGHVF 104 (144)
T 3e0o_A 80 LDTSHGMIRTEVRSRT-------ADSHLGHVF 104 (144)
T ss_dssp EECCTTSCEEEEEETT-------TCCEEEEEE
T ss_pred ecCCCCceEEEEEcCC-------CCCccCCcc
Confidence 3555564322345655 458999974
No 12
>1twf_J DNA-directed RNA polymerases I, II, and III 8.3 K polypeptide; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: a.4.11.1 PDB: 1i3q_J 1i6h_J 1k83_J* 1nik_J 1nt9_J 1pqv_J 1r5u_J 1r9s_J* 1r9t_J* 1sfo_J* 1twa_J* 1twc_J* 1i50_J* 1twg_J* 1twh_J* 1wcm_J 1y1v_J 1y1w_J 1y1y_J 1y77_J* ...
Probab=30.99 E-value=19 Score=24.79 Aligned_cols=31 Identities=23% Similarity=0.507 Sum_probs=18.1
Q ss_pred hhhcccccccccCccCHHHHHHHHh-c-CchhHH
Q 045123 103 RCVCFNCSKILADEEDDKFKLALKI-R-HPKSRL 134 (219)
Q Consensus 103 ~~vC~~C~rll~~~~~~~~~~~~~~-~-~~k~r~ 134 (219)
-..|++|++++.+.- .+|...++. . +|+..|
T Consensus 4 PVRCFTCGkvi~~~w-e~y~~~~~~g~l~~~~~L 36 (70)
T 1twf_J 4 PVRCFSCGKVVGDKW-ESYLNLLQEDELDEGTAL 36 (70)
T ss_dssp CSBCTTTCCBCTTCH-HHHHHHHHTSCCCHHHHH
T ss_pred CeecCCCCCChHHHH-HHHHHHHHcCCCCHHHHH
Confidence 346999999987642 345444433 3 444433
No 13
>4ayb_N DNA-directed RNA polymerase; transferase, multi-subunit, transcription; 3.20A {Sulfolobus shibatae} PDB: 2wb1_N 2y0s_N 2waq_N 4b1o_N 4b1p_O 2pmz_N 3hkz_N
Probab=30.55 E-value=12 Score=25.50 Aligned_cols=13 Identities=38% Similarity=1.071 Sum_probs=10.5
Q ss_pred hhcccccccccCc
Q 045123 104 CVCFNCSKILADE 116 (219)
Q Consensus 104 ~vC~~C~rll~~~ 116 (219)
.-||+|++++.+.
T Consensus 5 VRCFTCGkvi~~k 17 (66)
T 4ayb_N 5 IRCFTCGSLIADK 17 (66)
T ss_dssp SBCTTTCCBCHHH
T ss_pred cccCCCcHhHHHH
Confidence 3599999998874
No 14
>2l1u_A MSRB2, methionine-R-sulfoxide reductase B2, mitochondria; methionine sulfoxide reductase, oxidoreductase; NMR {Mus musculus}
Probab=28.74 E-value=16 Score=28.53 Aligned_cols=29 Identities=31% Similarity=0.602 Sum_probs=16.6
Q ss_pred ccCCCCCCCCCcccCCCCCCCCccCCcceeeecccc
Q 045123 53 SDLRLGTIDKRFKCETCSSNMGECPGHFGHLELAKP 88 (219)
Q Consensus 53 ~D~rlG~~~~~~~C~TC~~~~~~CpGHfGhIeL~~P 88 (219)
-|..+|..--...|..| -||.||+=---|
T Consensus 83 ~D~s~gm~RtEV~C~~C-------g~HLGHVF~DGP 111 (143)
T 2l1u_A 83 LDTSLGCPRMEVVCKQC-------EAHLGHVFPDGP 111 (143)
T ss_dssp EECTTSSCEEEEEESSS-------CCCCEEEECCSS
T ss_pred ecccCCceEEEEEECCC-------CCcCCcccCCCC
Confidence 35555544334567655 589999744333
No 15
>1iym_A EL5; ring-H2 finger, ubiquitin ligase, DNA binding protein; NMR {Oryza sativa} SCOP: g.44.1.1
Probab=26.11 E-value=47 Score=20.05 Aligned_cols=48 Identities=19% Similarity=0.335 Sum_probs=22.8
Q ss_pred CCCcccCCCCCCCCccCCcceeeecc--cceeeeeehhhhhhhhhhhccccccc
Q 045123 61 DKRFKCETCSSNMGECPGHFGHLELA--KPMFHIGFMKTLLTIMRCVCFNCSKI 112 (219)
Q Consensus 61 ~~~~~C~TC~~~~~~CpGHfGhIeL~--~Pv~h~~f~~~i~~iL~~vC~~C~rl 112 (219)
+....|..|...+.+-.. .+.|+ .-+||..-+....+- +..|+.|.+.
T Consensus 3 ~~~~~C~IC~~~~~~~~~---~~~~~~C~H~f~~~Ci~~w~~~-~~~CP~Cr~~ 52 (55)
T 1iym_A 3 DDGVECAVCLAELEDGEE---ARFLPRCGHGFHAECVDMWLGS-HSTCPLCRLT 52 (55)
T ss_dssp CCSCCCTTTCCCCCTTSC---CEECSSSCCEECTTHHHHTTTT-CCSCSSSCCC
T ss_pred CCCCcCccCCccccCCCc---eEECCCCCCcccHHHHHHHHHc-CCcCcCCCCE
Confidence 445678888766543100 01111 113555444333322 4678888763
No 16
>2k8d_A Peptide methionine sulfoxide reductase MSRB; thermophilic, Zn binding, metal-binding, oxidoreductase; NMR {Methanothermobacter thermautotrophicusorganism_taxid}
Probab=24.45 E-value=14 Score=29.29 Aligned_cols=10 Identities=40% Similarity=1.006 Sum_probs=7.4
Q ss_pred ccCCcceeee
Q 045123 75 ECPGHFGHLE 84 (219)
Q Consensus 75 ~CpGHfGhIe 84 (219)
.|-||.||+=
T Consensus 115 ~Cg~HLGHVF 124 (151)
T 2k8d_A 115 RCDAHLGHVF 124 (151)
T ss_dssp TEEEEEEEEE
T ss_pred CCCCcCCccc
Confidence 4558999974
Done!