Query psy5332
Match_columns 287
No_of_seqs 222 out of 1023
Neff 7.2
Searched_HMMs 29240
Date Fri Aug 16 23:55:52 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy5332.a3m -d /work/01045/syshi/HHdatabase/pdb70.hhm -o /work/01045/syshi/hhsearch_pdb/5332hhsearch_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 3.4E-59 1.2E-63 425.8 18.0 214 1-223 43-267 (297)
2 1twf_C B44.5, DNA-directed RNA 100.0 7.5E-55 2.6E-59 401.9 20.7 216 1-223 44-266 (318)
3 2pa8_D DNA-directed RNA polyme 100.0 9.8E-52 3.4E-56 374.5 14.2 206 1-221 39-262 (265)
4 2a6h_A DNA-directed RNA polyme 100.0 9E-36 3.1E-40 274.4 12.6 213 1-262 51-279 (315)
5 1bdf_A RNA polymerase alpha su 100.0 6.9E-33 2.4E-37 246.1 14.9 169 1-216 54-232 (235)
6 3lu0_A DNA-directed RNA polyme 100.0 4.5E-31 1.6E-35 243.6 7.2 220 1-261 54-279 (329)
7 1twf_C B44.5, DNA-directed RNA 98.5 1.6E-07 5.6E-12 86.3 7.6 55 231-285 217-271 (318)
8 3h0g_C DNA-directed RNA polyme 98.5 1E-07 3.5E-12 86.7 5.9 50 230-279 217-266 (297)
9 2pa8_D DNA-directed RNA polyme 97.9 8.3E-06 2.8E-10 73.1 4.8 50 231-280 215-264 (265)
10 1bdf_A RNA polymerase alpha su 97.5 5.1E-05 1.8E-09 66.8 3.3 42 232-273 191-232 (235)
11 2a6h_A DNA-directed RNA polyme 97.2 0.00023 7.9E-09 65.2 4.7 38 236-273 189-226 (315)
12 2pa8_L DNA-directed RNA polyme 92.9 0.19 6.4E-06 37.5 5.6 39 182-220 50-88 (92)
13 2pa8_L DNA-directed RNA polyme 92.3 0.36 1.2E-05 35.9 6.4 44 237-280 48-91 (92)
14 3h0g_K DNA-directed RNA polyme 91.7 0.47 1.6E-05 37.2 6.7 46 237-282 65-110 (123)
15 3h0g_K DNA-directed RNA polyme 91.5 0.26 9E-06 38.7 5.1 42 181-222 66-107 (123)
16 1twf_K B13.6, DNA-directed RNA 90.7 0.42 1.4E-05 37.4 5.5 40 182-221 68-107 (120)
17 3lu0_A DNA-directed RNA polyme 90.1 0.23 8E-06 45.5 4.1 34 239-272 198-231 (329)
18 1twf_K B13.6, DNA-directed RNA 89.5 0.88 3E-05 35.5 6.5 42 237-278 66-107 (120)
19 1xpp_A TA1416, DNA-directed RN 88.3 0.88 3E-05 35.2 5.7 44 237-281 58-101 (115)
20 1xpp_A TA1416, DNA-directed RN 88.3 0.72 2.5E-05 35.7 5.2 40 182-222 60-99 (115)
21 3rfr_A PMOB; membrane, oxidore 32.5 84 0.0029 29.2 6.3 67 51-122 296-367 (419)
22 2vmh_A GH95CBM51, fibronectin 28.2 97 0.0033 24.5 5.4 26 108-133 120-146 (151)
23 2wnv_C C1Q chain C, complement 24.9 1.2E+02 0.004 23.1 5.2 25 102-126 90-114 (131)
24 1yew_A Particulate methane mon 23.3 1.5E+02 0.005 27.3 6.2 68 51-122 262-335 (382)
25 2wnv_B C1Q chain B, complement 22.1 1.5E+02 0.0051 22.7 5.4 42 102-145 92-133 (136)
26 2vng_A CPE0329; family 51 carb 21.0 2E+02 0.0068 23.6 6.1 27 107-133 141-168 (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=3.4e-59 Score=425.79 Aligned_cols=214 Identities=39% Similarity=0.791 Sum_probs=186.8
Q ss_pred CeeeEEEEeeCCCcchhhHhhhhcCccccccccccc----cceeccCCCCCCCCCCceEEEEEEEEeeCCCCceeEeCCc
Q psy5332 1 MAIDWVQLEANSTVLSDEFIASRIGLIPLTSDEVVD----RILYSRDCTCVDFCSECSVEFTLDVKCVDDQTRHVTTADL 76 (287)
Q Consensus 1 lAId~V~i~~NtSvl~DE~lAHRLGLIPl~s~~~~~----~~~~~~~c~~~~~c~~ctv~~~L~v~~~~~~~~~V~s~Dl 76 (287)
|||+.|+|++|||||+||+|||||||||+.+++..+ .|+|..+|.|.+.|+.|+++|+|+|+|+++.+++|||+||
T Consensus 43 ~AI~~V~I~~NtSvl~DE~laHrlglIP~v~edv~e~~~~~l~~k~~c~~~~~~~~~~v~l~L~v~g~~~~~~~Vta~Dl 122 (297)
T 3h0g_C 43 VAIDLVEINVNTSVMPDEFLAHRLGMIPLDSSNIDEPPPVGLEYTRNCDCDQYCPKCSVELFLNAKCTGEGTMEIYARDL 122 (297)
T ss_dssp EEEEEEEEEEECSSSCHHHHHHHHHHSCBCCTTCSSCSSSCCCCSSSCSSSSSCGGGSCEEEEEECCCCSSCEEEEGGGC
T ss_pred ceEEEEEEEeCCccccccceeeeeccCCcccccccccccceeEeccccccccCCCCceEEEEEEEEeccCCCceEEcccc
Confidence 699999999999999999999999999999986322 3899999999999999999999999999888999999999
Q ss_pred eeCCCe--eeeccCCCcccCCCCCCCCCCeEEEEeCCCCEEEEEEEEEeccccccceecccceeeeeecCCCCcccccCC
Q psy5332 77 KSTDAR--VVPVTSRNRDADMNEYGETDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTAGVCFEYDPDNSMRHTLFP 154 (287)
Q Consensus 77 ~s~d~~--v~P~~~~~~~~~~~~~~~~~dI~I~kL~pGQ~I~le~~a~kGiGk~HAKwsPV~~~~y~~~P~i~i~~~~~~ 154 (287)
++.+.. +.|+... ++++||+|+||+|||+|+|+|+|+||+||+|||||||++|+|||+|.|+|++..+|
T Consensus 123 ~~~~~~~~~~pv~~~---------~~n~di~IakL~~gq~l~le~~a~kG~G~~HAKwsPv~~~~y~~~P~i~l~~~~~~ 193 (297)
T 3h0g_C 123 VVSSNSSLGHPILAD---------PKSRGPLICKLRKEQEISLRCIAKKGIAKEHAKWSPTSAVAFEYDPWNKLQHTDYW 193 (297)
T ss_dssp BCCSCCSSCCBCCCS---------TTSCCSEEEEECSSCCEEEEEEEEEECGGGCTTSCCBCCCCCCSSSSCSSCCSCCC
T ss_pred cccCccccccccccc---------CCCCCeEEEEECCCCEEEEEEEEECCEeccccccCcceEEEEEeccceEEcccccc
Confidence 987643 3344311 36799999999999999999999999999999999999999999999999987654
Q ss_pred ----CCCCCCCCccCccccc-ccCCCCCcccCCCcEEEEeecCCccCHHHHHHHHHHHHHHHHHHHHHhhhccc
Q psy5332 155 ----KPDEWPKSEYSELDET-QHEAPYNWEAKPNKYFFNVESAGALKPENIVIMGVTVLKQKLSNLQTQLAHDR 223 (287)
Q Consensus 155 ----~~~~~~~~~~~~~~~~-~~~~~~~~~~~~d~fif~VEs~G~l~p~~iv~~A~~iLk~Kl~~l~~~l~~e~ 223 (287)
..++||++++...+.. .+...|+....+|||+|+|||+|+++|+++|.+|+++|++|++.|.+.|+++.
T Consensus 194 ~e~~~~~~~P~~~~~~~~~~~~~~~~~~~~~~~dkfif~VET~Gsl~p~eiv~~A~~iL~~kl~~f~~~L~~~~ 267 (297)
T 3h0g_C 194 FENDADAEWPKSKNADWEEPPREGEPFNFQEEPRRFYMDVESVGSIPPNEIMVQGLRILQEKLAVLVRDLDEEQ 267 (297)
T ss_dssp CSSCSTTTSCCCGGGTTCCCCSCCSCCCSSCCCCCEEEEEEBCSSSCTTTTTHHHHHHHHHHHHHHHHHHHCC-
T ss_pred ccchhHhhCCccccceeeccccccccccccccCCEEEEEEEEcCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence 3567899877654332 23456888899999999999999999999999999999999999999987653
No 2
>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=7.5e-55 Score=401.87 Aligned_cols=216 Identities=38% Similarity=0.663 Sum_probs=178.1
Q ss_pred CeeeEEEEeeCCCcchhhHhhhhcCccccccccccccceeccCCCCCCCCCCceEEEEEEEEeeCCCCceeEeCCceeCC
Q psy5332 1 MAIDWVQLEANSTVLSDEFIASRIGLIPLTSDEVVDRILYSRDCTCVDFCSECSVEFTLDVKCVDDQTRHVTTADLKSTD 80 (287)
Q Consensus 1 lAId~V~i~~NtSvl~DE~lAHRLGLIPl~s~~~~~~~~~~~~c~~~~~c~~ctv~~~L~v~~~~~~~~~V~s~Dl~s~d 80 (287)
|||+.|+|+.|||||+||||||||||||+.+.. ++.|.|..+|.|+++|+.|+++|+|+|+|++++++.|||+||.+..
T Consensus 44 ~AI~~V~I~~NTSvl~DE~vaHrlglIP~v~eD-vk~l~~~~~~~~~~~c~~~~v~l~L~v~c~~~g~~~Vta~Di~~~~ 122 (318)
T 1twf_C 44 LAIDSVEVETNTTVLADEFIAHRLGLIPLQSMD-IEQLEYSRDCFCEDHCDKCSVVLTLQAFGESESTTNVYSKDLVIVS 122 (318)
T ss_dssp EEEEEEEEEEECSSSCHHHHHHHHHTSCEEETT-GGGSCCTTTSSSSSCCTTTEEEEEEEEECCSSSCEEEEGGGEEECS
T ss_pred ceEEEEEEEeCCcccccceeEeecccCCCcccC-hhheEEeeccccccCCCCceEEEEEEEEecCCCCeeEEhHhccccC
Confidence 699999999999999999999999999999854 4889999999999999999999999999999999999999998643
Q ss_pred CeeeeccCCCcccCCCC-CCCCCCeEEEEeCCCCEEEEEEEEEeccccccceecccceeeeeecCCCCcccccCCCCCCC
Q psy5332 81 ARVVPVTSRNRDADMNE-YGETDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTAGVCFEYDPDNSMRHTLFPKPDEW 159 (287)
Q Consensus 81 ~~v~P~~~~~~~~~~~~-~~~~~dI~I~kL~pGQ~I~le~~a~kGiGk~HAKwsPV~~~~y~~~P~i~i~~~~~~~~~~~ 159 (287)
.. .+. +..++.. .++++||+|+||+|||+|+|+|+|+||+||+|||||||++++|+|+|.+++.+...+.. ..
T Consensus 123 ~~---~~~--~~~~p~v~ei~npdi~IakL~~gq~L~me~~a~kG~G~~hAk~sPva~~~y~~~P~~~~~~~~~~i~-~D 196 (318)
T 1twf_C 123 NL---MGR--NIGHPIIQDKEGNGVLICKLRKGQELKLTCVAKKGIAKEHAKWGPAAAIEFEYDPWNKLKHTDYWYE-QD 196 (318)
T ss_dssp CC---TTC--SEEEECCCSTTSCCSEEEEECTTCEEEEEEEEEEECTTTCGGGCCEEEEEEEECSSTTSCCSCCCCS-SC
T ss_pred cc---ccc--cccCCCccccCCCCeEEEEECCCCEEEEEEEEEcCcccccccccccccceecccccccccccccccc-cC
Confidence 10 110 0001111 15689999999999999999999999999999999999999999999998876332211 11
Q ss_pred CCCccCcccccc------cCCCCCcccCCCcEEEEeecCCccCHHHHHHHHHHHHHHHHHHHHHhhhccc
Q psy5332 160 PKSEYSELDETQ------HEAPYNWEAKPNKYFFNVESAGALKPENIVIMGVTVLKQKLSNLQTQLAHDR 223 (287)
Q Consensus 160 ~~~~~~~~~~~~------~~~~~~~~~~~d~fif~VEs~G~l~p~~iv~~A~~iLk~Kl~~l~~~l~~e~ 223 (287)
+.++|++..... ...++.+..++|||+|+|||+|+++|+++|.+|+++|++|++.|.+.|+...
T Consensus 197 ~~~~f~pv~~v~~~ve~~~~~rv~~~~d~dkfif~VET~Gsi~Peeav~~A~kIL~~kl~~f~~~l~~~~ 266 (318)
T 1twf_C 197 SAKEWPQSKNCEYEDPPNEGDPFDYKAQADTFYMNVESVGSIPVDQVVVRGIDTLQKKVASILLALTQMD 266 (318)
T ss_dssp HHHHSCCCGGGTTSCCCCSSSCCCTTCCCCCEEEEEEECSSSCHHHHHHHHHHHHHHHHHHHHHHHHHHS
T ss_pred chhhCCCCcceeEEecccccccccccccCCEEEEEEEecCCcCHHHHHHHHHHHHHHHHHHHHHHHHhhh
Confidence 224455443321 1256888899999999999999999999999999999999999999886653
No 3
>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=9.8e-52 Score=374.53 Aligned_cols=206 Identities=30% Similarity=0.532 Sum_probs=174.3
Q ss_pred CeeeEEEEeeCCCcchhhHhhhhcCccccccccccccceeccCC-CCCCCCCCceEEEEEEEEeeCCCCceeEeCCceeC
Q psy5332 1 MAIDWVQLEANSTVLSDEFIASRIGLIPLTSDEVVDRILYSRDC-TCVDFCSECSVEFTLDVKCVDDQTRHVTTADLKST 79 (287)
Q Consensus 1 lAId~V~i~~NtSvl~DE~lAHRLGLIPl~s~~~~~~~~~~~~c-~~~~~c~~ctv~~~L~v~~~~~~~~~V~s~Dl~s~ 79 (287)
|||+.|+|+.|||||+||||||||||||+.++..++.|.|..+| +|+++|+.|+++|+|+|+| +++|+.|||+||.+.
T Consensus 39 ~AI~~V~i~~Ntsvl~DE~v~Hr~~~Ip~~~edv~k~~~~~~~~~~~~~~~~~~~~~~~l~~~~-~~g~~~V~a~Di~~~ 117 (265)
T 2pa8_D 39 MAVDDVYFIENNSPLYDEILAHRLALIPFMSEEALDTYRWPEECIECTENCEKCYTKIYIEAEA-PNEPRMIYSKDIKSE 117 (265)
T ss_dssp EEEEEEEEEEECSSSCHHHHHHHHTTSCBCCTTHHHHSCCGGGCTTCCSSCTTTEEEEEEEEEC-CSSCEEEEGGGCEES
T ss_pred ceEEEEEEEeCCCccccHHHHHhhcCCcCcccCchhhccccccccccccCCCCcEEEEEEEEEe-cCCCcEEEhhhcccC
Confidence 69999999999999999999999999999999655789999999 8999999999999999999 569999999999986
Q ss_pred CCeeeeccCCCcccCCCCCCCCCCeEEEEeCCCCEEEEEEEEEeccccccceecccceeeeeecCCCCcccccCCCCCCC
Q psy5332 80 DARVVPVTSRNRDADMNEYGETDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTAGVCFEYDPDNSMRHTLFPKPDEW 159 (287)
Q Consensus 80 d~~v~P~~~~~~~~~~~~~~~~~dI~I~kL~pGQ~I~le~~a~kGiGk~HAKwsPV~~~~y~~~P~i~i~~~~~~~~~~~ 159 (287)
++.++|+ ++||+|+||++||+|+|+|+|+||+||+||||+|+++++||++|.+.++..+..+.+.|
T Consensus 118 ~~~v~~~--------------~~~i~I~~L~~g~~l~~e~~~~~G~G~~~ak~~pv~t~~yr~~p~I~i~~~C~~C~~~C 183 (265)
T 2pa8_D 118 DPSVVPI--------------SGDIPIVLLGTNQKISLEARLRLGYGKEHAKFIPVSLSVVRYYPKVEILANCEKAVNVC 183 (265)
T ss_dssp STTCCBS--------------CSCCEEEEECTTCEEEEEEEEEEECTTTCGGGCCEEEEEEEEEEEEEECSCCTTHHHHC
T ss_pred CCCceec--------------CCCcEEEEeCCCCEEEEEEEEecCccccccCcccceeeeeccccchhhhhhHHHHHHhC
Confidence 6666654 49999999999999999999999999999999999999999999998871111122345
Q ss_pred CCCccCc------c-ccc----------ccCCCCCcccCCCcEEEEeecCCccCHHHHHHHHHHHHHHHHHHHHHhhhc
Q psy5332 160 PKSEYSE------L-DET----------QHEAPYNWEAKPNKYFFNVESAGALKPENIVIMGVTVLKQKLSNLQTQLAH 221 (287)
Q Consensus 160 ~~~~~~~------~-~~~----------~~~~~~~~~~~~d~fif~VEs~G~l~p~~iv~~A~~iLk~Kl~~l~~~l~~ 221 (287)
|...+.- + ... .+...+.+..++++|+|.|||+|+++|++++.+|+++|++|++.|.+.++.
T Consensus 184 P~g~I~id~~~~v~~d~~~C~~C~~C~~vCp~aI~~~~~~d~~i~~VEt~Gsl~Pee~v~~A~~iL~~~~~~~~~~l~~ 262 (265)
T 2pa8_D 184 PEGVFELKDGKLSVKNELSCTLCEECLRYCNGSIRISFVEDKYILEIESVGSLKPERILLEAGKSIIRKIEELEKKLVE 262 (265)
T ss_dssp TTCCEEEETTEEEESCGGGCCCCCHHHHHHTTSEEEEEEEEEEEEEEEECSSSCHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred cccCeEecCCeeEEeccccCCCchHHHHhCCCceEEEecCCeEEEEeccCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 6554320 0 000 112445667789999999999999999999999999999999999988754
No 4
>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=9e-36 Score=274.36 Aligned_cols=213 Identities=16% Similarity=0.183 Sum_probs=133.9
Q ss_pred CeeeEEEEeeCCCcchhhHhhhhcCccccccccc------cccceeccCCCCCCCCCCceEEEEEEEEeeCCCCceeEeC
Q psy5332 1 MAIDWVQLEANSTVLSDEFIASRIGLIPLTSDEV------VDRILYSRDCTCVDFCSECSVEFTLDVKCVDDQTRHVTTA 74 (287)
Q Consensus 1 lAId~V~i~~NtSvl~DE~lAHRLGLIPl~s~~~------~~~~~~~~~c~~~~~c~~ctv~~~L~v~~~~~~~~~V~s~ 74 (287)
+||+.|.|+. +|||+|+||+..... ++.+.|..+| |+.|+++++|+|+ ||+.|||+
T Consensus 51 ~AI~~V~I~~---------v~He~~~Ipgv~Edv~eIilNlk~i~~~~~~-----~~~~~~~~~L~v~----gp~~VtA~ 112 (315)
T 2a6h_A 51 TAVTSVYIED---------VLHEFSTIPGVKEDVVEIILNLKELVVRFLN-----PSLQTVTLLLKAE----GPKEVKAR 112 (315)
T ss_dssp EEEEEEEESS---------CCSTTCBCTTBSSBHHHHHHHHHTCCEEECS-----TTCSBCCEEEEEE----SSCEEEGG
T ss_pred eEEEEEEEec---------chhccCCCCCccCCHHHHhhhhheEEEeccc-----CCCCeEEEEEEEe----cCeeEEhh
Confidence 6999999976 999999999999542 4678888876 4578999999998 88999999
Q ss_pred CceeCCCeeeeccCCCcccCCCCCCCCCCeEEEEeCCCCEEEEEEEEEeccccccceecccceeeeeecCCCCcccccCC
Q psy5332 75 DLKSTDARVVPVTSRNRDADMNEYGETDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTAGVCFEYDPDNSMRHTLFP 154 (287)
Q Consensus 75 Dl~s~d~~v~P~~~~~~~~~~~~~~~~~dI~I~kL~pGQ~I~le~~a~kGiGk~HAKwsPV~~~~y~~~P~i~i~~~~~~ 154 (287)
||.+. +.+.| ++||++||+|++||+|+|+|+|++|+||+||||++ ...|.-.+
T Consensus 113 Di~~~-~~v~i--------------vnpd~~IatL~~g~~l~me~~~~kG~Gy~~ak~~~------~~~p~g~i------ 165 (315)
T 2a6h_A 113 DFLPV-ADVEI--------------MNPDLHIATLEEGGRLNMEVRVDRGVGYVPAEKHG------IKDRINAI------ 165 (315)
T ss_dssp GSCCC-TTEEE--------------SCTTCEEEEBCSSCEEEEEEEEEEEESEECHHHHC------CCSSTTCE------
T ss_pred hCCcC-CCcEE--------------cCCCeEEEEECCCCEEEEEEEEEecCCccccccCc------ccCCcceE------
Confidence 99843 33554 45999999999999999999999999999999997 11222111
Q ss_pred CCCCCCCCccCcccccc---cCCCCCcccCCCcEEEEeecCCccCHHHHHHHHHHHHHHHHHHHHHhhhccccc-c---c
Q psy5332 155 KPDEWPKSEYSELDETQ---HEAPYNWEAKPNKYFFNVESAGALKPENIVIMGVTVLKQKLSNLQTQLAHDRVF-Y---V 227 (287)
Q Consensus 155 ~~~~~~~~~~~~~~~~~---~~~~~~~~~~~d~fif~VEs~G~l~p~~iv~~A~~iLk~Kl~~l~~~l~~e~~~-e---~ 227 (287)
..++.|+++.... ...+++..+++|+|+|+|||+|+++|++++.+|+++|+++++.|.+.-.+.... + .
T Consensus 166 ----~iDa~f~pv~~v~y~ve~~rv~~~~~~dkli~eIeT~Gsi~P~eal~~A~~iL~~~l~~f~~~~~~~~~~~~~~~~ 241 (315)
T 2a6h_A 166 ----PVDAVFSPVRRVAFQVEDTRLGQRTDLDKLTLRIWTDGSVTPLEALNQAVEILREHLTYFSNPQAAAVAAPEEAKE 241 (315)
T ss_dssp ----ECCEECCCEEEEEEEEEECCBTTBCCCEEEEEEEEECSSSCHHHHHHHHHHHHHHHHHTTCSCC------------
T ss_pred ----eecCCCCCceeEEEEeeeeeecccccccEEEEEEEEcCCCCHHHHHHHHHHHHHHHHHHHhhcccccccccccccc
Confidence 1233444443321 123456677899999999999999999999999999999999985421111000 0 0
Q ss_pred -ccCCCC--CcccCCCeEEEEEeecCCCChhhHHHHHH
Q psy5332 228 -INEAPY--NWEAKPNKYFFNVESAGALKPENIVIMGV 262 (287)
Q Consensus 228 -~~~~~i--~~~~~~d~f~f~veS~g~l~~~~i~~~a~ 262 (287)
..+..+ .+....|.+.|||||.+||+.++|...+-
T Consensus 242 ~~~~~~~~~~l~~~i~~L~LsvRs~NcLk~a~I~ti~d 279 (315)
T 2a6h_A 242 PEAPPEQEEELDLPLEELGLSTRVLHSLKEEGIESVRA 279 (315)
T ss_dssp --------------------------------------
T ss_pred ccccccccccccCcHHHccCcHHHHHHHHHcCCcCHHH
Confidence 001111 12367889999999999999999999883
No 5
>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=6.9e-33 Score=246.09 Aligned_cols=169 Identities=17% Similarity=0.224 Sum_probs=129.0
Q ss_pred CeeeEEEEeeCCCcchhhHhhhhcCccccccccc------cccceeccCCCCCCCCCCceEEEEEEEEeeCCCCceeEeC
Q psy5332 1 MAIDWVQLEANSTVLSDEFIASRIGLIPLTSDEV------VDRILYSRDCTCVDFCSECSVEFTLDVKCVDDQTRHVTTA 74 (287)
Q Consensus 1 lAId~V~i~~NtSvl~DE~lAHRLGLIPl~s~~~------~~~~~~~~~c~~~~~c~~ctv~~~L~v~~~~~~~~~V~s~ 74 (287)
+||+.|.| |.+|||+|+||+..... ++.+.|..++ .|+++++|+++ ||+.|||+
T Consensus 54 ~AI~~V~I---------e~v~He~~~Ipgv~Edv~~iilNlk~i~~~~~~-------~~~~~~~L~v~----gp~~VtA~ 113 (235)
T 1bdf_A 54 CAVTEVEI---------DGVLHEYSTKEGVQEDILEILLNLKGLAVRVQG-------KDEVILTLNKS----GIGPVTAA 113 (235)
T ss_dssp EEEEEEEE---------TTCCSTTCCCTTBSSCHHHHHHHHHTCCEECSS-------CSEEEEEEEEE----SSEEEEGG
T ss_pred eEEEEEEE---------cceeeccccCCCccCCHHHHhhchheeEEeccC-------CceEEEEEEEe----cCeEEEhH
Confidence 69999999 88999999999999542 3567777653 47899999998 88999999
Q ss_pred CceeCCCeeeeccCCCcccCCCCCCCCCCeEEEEeCC-CCEEEEEEEEEeccccccceecccceeeeeecCCCCcccccC
Q psy5332 75 DLKSTDARVVPVTSRNRDADMNEYGETDDILIVKLRK-GQELRLRAYAKKGFGKEHAKWNPTAGVCFEYDPDNSMRHTLF 153 (287)
Q Consensus 75 Dl~s~d~~v~P~~~~~~~~~~~~~~~~~dI~I~kL~p-GQ~I~le~~a~kGiGk~HAKwsPV~~~~y~~~P~i~i~~~~~ 153 (287)
||.. ++.++| ++||++||+|++ ||+|+|+|+|+||+||+|||||-... -...|.-.+
T Consensus 114 Di~~-~~~v~i--------------vnpd~~IatL~~~g~~l~~e~~~~kG~Gy~~ak~si~~~--~~~~~~g~i----- 171 (235)
T 1bdf_A 114 DITH-DGDVEI--------------VKPQHVICHLTDENASISMRIKVQRGRGYVPASTRIHSE--EDERPIGRL----- 171 (235)
T ss_dssp GBCC-CSSCEE--------------SCTTCEEEEECSTTCEEEEEEEEEECCSEECGGGTC-------CCCCSCC-----
T ss_pred hCCC-CCCCEE--------------cCCCeEEEEECCCCCEEEEEEEEEecccceecccccccc--cccCCCcEE-----
Confidence 9984 333554 459999999999 99999999999999999999951000 001111000
Q ss_pred CCCCCCCCCccCccccc---ccCCCCCcccCCCcEEEEeecCCccCHHHHHHHHHHHHHHHHHHHH
Q psy5332 154 PKPDEWPKSEYSELDET---QHEAPYNWEAKPNKYFFNVESAGALKPENIVIMGVTVLKQKLSNLQ 216 (287)
Q Consensus 154 ~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~d~fif~VEs~G~l~p~~iv~~A~~iLk~Kl~~l~ 216 (287)
..++.|+++.+. ....++++..++|+|+|+|||+|+++|++++.+|+++|++|++.|.
T Consensus 172 -----~iD~~f~pv~~v~y~ve~~~v~~~~~~d~li~eIeT~Gsi~P~eal~~A~~iL~~~~~~f~ 232 (235)
T 1bdf_A 172 -----LVDACYSPVERIAYNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFV 232 (235)
T ss_dssp -----BCCEECCSEEEEEEECCBCCCSSCSSEEEEEEEEEECSSSCHHHHHHHHHHHHHHHGGGGC
T ss_pred -----EECCCCCcEEEEEEEccCccccccccCcEEEEEEEecCCCCHHHHHHHHHHHHHHHHHHHh
Confidence 123344444332 1234566778899999999999999999999999999999998765
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=99.96 E-value=4.5e-31 Score=243.59 Aligned_cols=220 Identities=17% Similarity=0.209 Sum_probs=128.4
Q ss_pred CeeeEEEEeeCCCcchhhHhhhhcCccccccccccccceeccCCCCCCCCCCceEEEEEEEEeeCCCCceeEeCCceeCC
Q psy5332 1 MAIDWVQLEANSTVLSDEFIASRIGLIPLTSDEVVDRILYSRDCTCVDFCSECSVEFTLDVKCVDDQTRHVTTADLKSTD 80 (287)
Q Consensus 1 lAId~V~i~~NtSvl~DE~lAHRLGLIPl~s~~~~~~~~~~~~c~~~~~c~~ctv~~~L~v~~~~~~~~~V~s~Dl~s~d 80 (287)
+||+.|.| +| ++||+|+||...+...+-+-..++|.|.. |..|+++++|+++ ||+.|||+||.+ +
T Consensus 54 ~AIt~V~I-~g--------v~Hefs~Ipgv~Edv~eiilNlK~i~~k~-~~~~~~~~~L~~~----Gp~~VtA~DI~~-~ 118 (329)
T 3lu0_A 54 CAVTEVEI-DG--------VLHEYSTKEGVQEDILEILLNLKGLAVRV-QGKDEVILTLNKS----GIGPVTAADITH-D 118 (329)
T ss_dssp EEEEEEEE-SS--------CSSTTCCCTTBSSCHHHHHHHHHSCCCEE-SSCSCEEEEECCC----SSSCEETTSSCC-C
T ss_pred eEEEEEEE-eC--------ccccccccccccCCHHHHHhhhccceEec-CCCceEEEEEEEe----CCeEEEeeeecc-C
Confidence 59999999 34 89999999998875433233345565532 4678899999985 899999999986 3
Q ss_pred CeeeeccCCCcccCCCCCCCCCCeEEEEeC-CCCEEEEEEEEEeccccccceecccceeeeeecCCCCcccccCCCCCCC
Q psy5332 81 ARVVPVTSRNRDADMNEYGETDDILIVKLR-KGQELRLRAYAKKGFGKEHAKWNPTAGVCFEYDPDNSMRHTLFPKPDEW 159 (287)
Q Consensus 81 ~~v~P~~~~~~~~~~~~~~~~~dI~I~kL~-pGQ~I~le~~a~kGiGk~HAKwsPV~~~~y~~~P~i~i~~~~~~~~~~~ 159 (287)
+.++ +++|+++||+|+ +||+|+|+++|++|+||.+|.+.-.. + ...-.++. -.
T Consensus 119 ~~ve--------------ivnpd~~IatL~~~~~~L~me~~i~~G~GY~~a~~~~~~----~-~~~~~ig~-------i~ 172 (329)
T 3lu0_A 119 GDVE--------------IVKPQHVICHLTDENASISMRIKVQRGRGYVPASTRIHS----E-EDERPIGR-------LL 172 (329)
T ss_dssp SSEE--------------CSCTTCEEECBCSSCCCCCEEEEEEEESSEECTTTSCCC----S-TTSSSCCC-------EE
T ss_pred CCCE--------------EeCCCcEEEEEccCCcEEEEEEEEECcccceechhcccc----c-cccCcCce-------Ee
Confidence 3455 456999999999 99999999999999999887653110 0 00000000 01
Q ss_pred CCCccCcccccc---cCCCCCcccCCCcEEEEeecCCccCHHHHHHHHHHHHHHHHHHHHHhhhcccccccccCCCC--C
Q psy5332 160 PKSEYSELDETQ---HEAPYNWEAKPNKYFFNVESAGALKPENIVIMGVTVLKQKLSNLQTQLAHDRVFYVINEAPY--N 234 (287)
Q Consensus 160 ~~~~~~~~~~~~---~~~~~~~~~~~d~fif~VEs~G~l~p~~iv~~A~~iLk~Kl~~l~~~l~~e~~~e~~~~~~i--~ 234 (287)
.++.|+++.... ...+++...++|+++|+|||+|+++|++++.+|+++|++++..|.+.-.............+ .
T Consensus 173 iDa~fsPV~~Vny~Ve~~rvgq~td~dkL~leI~TdGsi~P~eAl~~Aa~iL~~~l~~f~~~~~~~~~~~~~~~~~~~~~ 252 (329)
T 3lu0_A 173 VDACYSPVERIAYNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFVDLRDVRQPEVKEEKPEFDPI 252 (329)
T ss_dssp CCEECCCEEEEEEEEEEECCSSCSCEEEEEEEEEECSSSCHHHHHHHHHHHHHHHTTTSSSCC-----------------
T ss_pred eCCCCCceeeEEEEEeccccCCCcccceEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHhccccccccccccccchhhhh
Confidence 334455544321 12345566778999999999999999999999999999999887642111100000000011 1
Q ss_pred cccCCCeEEEEEeecCCCChhhHHHHH
Q psy5332 235 WEAKPNKYFFNVESAGALKPENIVIMG 261 (287)
Q Consensus 235 ~~~~~d~f~f~veS~g~l~~~~i~~~a 261 (287)
+....|.+.|||||.+||+..+|...+
T Consensus 253 l~~~I~eLeLsvRs~NCLKra~I~tv~ 279 (329)
T 3lu0_A 253 LLRPVDDLELTVRSANCLKAEAIHYIG 279 (329)
T ss_dssp ---------------------------
T ss_pred hhhhHHhhcCCHHHHHHHHHcCCcCHH
Confidence 235689999999999999999998877
No 7
>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=98.51 E-value=1.6e-07 Score=86.30 Aligned_cols=55 Identities=22% Similarity=0.559 Sum_probs=48.0
Q ss_pred CCCCcccCCCeEEEEEeecCCCChhhHHHHHHHHHHHHHHHHHHHHhhhhccccc
Q psy5332 231 APYNWEAKPNKYFFNVESAGALKPENIVIMGVTVLKQKLSNLQTQLAHELSHDAL 285 (287)
Q Consensus 231 ~~i~~~~~~d~f~f~veS~g~l~~~~i~~~a~~~l~~k~~~l~~~l~~~~~~~~~ 285 (287)
..|....+.|+|+|+|||+|+|+|++++.+|+++|++||+.|...|+++.+.+.+
T Consensus 217 ~rv~~~~d~dkfif~VET~Gsi~Peeav~~A~kIL~~kl~~f~~~l~~~~~~~~~ 271 (318)
T 1twf_C 217 DPFDYKAQADTFYMNVESVGSIPVDQVVVRGIDTLQKKVASILLALTQMDQDKVN 271 (318)
T ss_dssp SCCCTTCCCCCEEEEEEECSSSCHHHHHHHHHHHHHHHHHHHHHHHHHHSCC---
T ss_pred ccccccccCCEEEEEEEecCCcCHHHHHHHHHHHHHHHHHHHHHHHHhhhccccc
Confidence 3567778899999999999999999999999999999999999999988776654
No 8
>3h0g_C DNA-directed RNA polymerase II subunit RPB3; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe}
Probab=98.50 E-value=1e-07 Score=86.69 Aligned_cols=50 Identities=32% Similarity=0.790 Sum_probs=46.8
Q ss_pred CCCCCcccCCCeEEEEEeecCCCChhhHHHHHHHHHHHHHHHHHHHHhhh
Q psy5332 230 EAPYNWEAKPNKYFFNVESAGALKPENIVIMGVTVLKQKLSNLQTQLAHE 279 (287)
Q Consensus 230 ~~~i~~~~~~d~f~f~veS~g~l~~~~i~~~a~~~l~~k~~~l~~~l~~~ 279 (287)
...+++.+++|+|+|+|||+|+|+|++|+..|+++|++|++.|...|+++
T Consensus 217 ~~~~~~~~~~dkfif~VET~Gsl~p~eiv~~A~~iL~~kl~~f~~~L~~~ 266 (297)
T 3h0g_C 217 GEPFNFQEEPRRFYMDVESVGSIPPNEIMVQGLRILQEKLAVLVRDLDEE 266 (297)
T ss_dssp CSCCCSSCCCCCEEEEEEBCSSSCTTTTTHHHHHHHHHHHHHHHHHHHCC
T ss_pred cccccccccCCEEEEEEEEcCCCCHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 44688899999999999999999999999999999999999999999875
No 9
>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=97.90 E-value=8.3e-06 Score=73.14 Aligned_cols=50 Identities=26% Similarity=0.473 Sum_probs=45.7
Q ss_pred CCCCcccCCCeEEEEEeecCCCChhhHHHHHHHHHHHHHHHHHHHHhhhh
Q psy5332 231 APYNWEAKPNKYFFNVESAGALKPENIVIMGVTVLKQKLSNLQTQLAHEL 280 (287)
Q Consensus 231 ~~i~~~~~~d~f~f~veS~g~l~~~~i~~~a~~~l~~k~~~l~~~l~~~~ 280 (287)
..+.+....|+|+|.|||+|+++|++++..|+++|++|++.|.+.|+++.
T Consensus 215 ~aI~~~~~~d~~i~~VEt~Gsl~Pee~v~~A~~iL~~~~~~~~~~l~~~~ 264 (265)
T 2pa8_D 215 GSIRISFVEDKYILEIESVGSLKPERILLEAGKSIIRKIEELEKKLVEVV 264 (265)
T ss_dssp TSEEEEEEEEEEEEEEEECSSSCHHHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_pred CceEEEecCCeEEEEeccCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 45677788999999999999999999999999999999999999998764
No 10
>1bdf_A RNA polymerase alpha subunit; nucleotidyltransferase, assemble; 2.50A {Escherichia coli} SCOP: d.74.3.1 d.181.1.1
Probab=97.48 E-value=5.1e-05 Score=66.83 Aligned_cols=42 Identities=19% Similarity=0.377 Sum_probs=37.0
Q ss_pred CCCcccCCCeEEEEEeecCCCChhhHHHHHHHHHHHHHHHHH
Q psy5332 232 PYNWEAKPNKYFFNVESAGALKPENIVIMGVTVLKQKLSNLQ 273 (287)
Q Consensus 232 ~i~~~~~~d~f~f~veS~g~l~~~~i~~~a~~~l~~k~~~l~ 273 (287)
.+....+.|+|+|+|||+|+++|++++.+|+++|++|++.|.
T Consensus 191 ~v~~~~~~d~li~eIeT~Gsi~P~eal~~A~~iL~~~~~~f~ 232 (235)
T 1bdf_A 191 RVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFV 232 (235)
T ss_dssp CCSSCSSEEEEEEEEEECSSSCHHHHHHHHHHHHHHHGGGGC
T ss_pred cccccccCcEEEEEEEecCCCCHHHHHHHHHHHHHHHHHHHh
Confidence 344456789999999999999999999999999999998764
No 11
>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=97.24 E-value=0.00023 Score=65.22 Aligned_cols=38 Identities=16% Similarity=0.347 Sum_probs=35.2
Q ss_pred ccCCCeEEEEEeecCCCChhhHHHHHHHHHHHHHHHHH
Q psy5332 236 EAKPNKYFFNVESAGALKPENIVIMGVTVLKQKLSNLQ 273 (287)
Q Consensus 236 ~~~~d~f~f~veS~g~l~~~~i~~~a~~~l~~k~~~l~ 273 (287)
..+.|+|+|+|||+|+++|++++..|+++|++|+..|.
T Consensus 189 ~~~~dkli~eIeT~Gsi~P~eal~~A~~iL~~~l~~f~ 226 (315)
T 2a6h_A 189 RTDLDKLTLRIWTDGSVTPLEALNQAVEILREHLTYFS 226 (315)
T ss_dssp BCCCEEEEEEEEECSSSCHHHHHHHHHHHHHHHHHTTC
T ss_pred cccccEEEEEEEEcCCCCHHHHHHHHHHHHHHHHHHHh
Confidence 45789999999999999999999999999999999873
No 12
>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=92.91 E-value=0.19 Score=37.46 Aligned_cols=39 Identities=10% Similarity=0.353 Sum_probs=35.7
Q ss_pred CCcEEEEeecCCccCHHHHHHHHHHHHHHHHHHHHHhhh
Q psy5332 182 PNKYFFNVESAGALKPENIVIMGVTVLKQKLSNLQTQLA 220 (287)
Q Consensus 182 ~d~fif~VEs~G~l~p~~iv~~A~~iLk~Kl~~l~~~l~ 220 (287)
.+++.|.|.|+|..+|.+++.+|++-|.+.++.|.+.+.
T Consensus 50 ~~~~~lrIqT~~~~~p~~al~~a~~~l~~~~~~~~~~f~ 88 (92)
T 2pa8_L 50 SDKIIVKILTDGSITPKDALLKAIENIRGMTSHYIDEIK 88 (92)
T ss_dssp SCCEEEEEEECSSSCHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred CCceEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 578999999999999999999999999999999987664
No 13
>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=92.29 E-value=0.36 Score=35.92 Aligned_cols=44 Identities=9% Similarity=0.258 Sum_probs=39.8
Q ss_pred cCCCeEEEEEeecCCCChhhHHHHHHHHHHHHHHHHHHHHhhhh
Q psy5332 237 AKPNKYFFNVESAGALKPENIVIMGVTVLKQKLSNLQTQLAHEL 280 (287)
Q Consensus 237 ~~~d~f~f~veS~g~l~~~~i~~~a~~~l~~k~~~l~~~l~~~~ 280 (287)
.-.+++.|.|.++|..+|.+.+..|++-|.+.|+.+.+.++...
T Consensus 48 Pl~~~~~lrIqT~~~~~p~~al~~a~~~l~~~~~~~~~~f~~~~ 91 (92)
T 2pa8_L 48 PLSDKIIVKILTDGSITPKDALLKAIENIRGMTSHYIDEIKGLT 91 (92)
T ss_dssp TTSCCEEEEEEECSSSCHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred CCCCceEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 44788999999999999999999999999999999999887643
No 14
>3h0g_K DNA-directed RNA polymerase II subunit RPB11; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe}
Probab=91.69 E-value=0.47 Score=37.23 Aligned_cols=46 Identities=11% Similarity=0.314 Sum_probs=41.6
Q ss_pred cCCCeEEEEEeecCCCChhhHHHHHHHHHHHHHHHHHHHHhhhhcc
Q psy5332 237 AKPNKYFFNVESAGALKPENIVIMGVTVLKQKLSNLQTQLAHELSH 282 (287)
Q Consensus 237 ~~~d~f~f~veS~g~l~~~~i~~~a~~~l~~k~~~l~~~l~~~~~~ 282 (287)
.-.++++|.|.++|..+|.+.+..|++-|...|+.|.+.++.+.+.
T Consensus 65 Ple~~~~lrIqT~~~~~p~eaL~~al~~L~~~~~~l~~~F~~~~~~ 110 (123)
T 3h0g_K 65 PLNHNFILRVQTVEDCSPKQVIVDAAKSLITHLEEIKVNFMREWEL 110 (123)
T ss_dssp TTSCEEEEEEECCSSSCSHHHHHHHHHHHHHHHHHHHHHHHHHTTT
T ss_pred CCCCceEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 4578999999999999999999999999999999999999886443
No 15
>3h0g_K DNA-directed RNA polymerase II subunit RPB11; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe}
Probab=91.49 E-value=0.26 Score=38.71 Aligned_cols=42 Identities=10% Similarity=0.353 Sum_probs=37.8
Q ss_pred CCCcEEEEeecCCccCHHHHHHHHHHHHHHHHHHHHHhhhcc
Q psy5332 181 KPNKYFFNVESAGALKPENIVIMGVTVLKQKLSNLQTQLAHD 222 (287)
Q Consensus 181 ~~d~fif~VEs~G~l~p~~iv~~A~~iLk~Kl~~l~~~l~~e 222 (287)
..++++|.|.|+|..+|.+++.+|++-|.+.++.|.+.+..+
T Consensus 66 le~~~~lrIqT~~~~~p~eaL~~al~~L~~~~~~l~~~F~~~ 107 (123)
T 3h0g_K 66 LNHNFILRVQTVEDCSPKQVIVDAAKSLITHLEEIKVNFMRE 107 (123)
T ss_dssp TSCEEEEEEECCSSSCSHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred CCCceEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 357999999999999999999999999999999998877654
No 16
>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=90.67 E-value=0.42 Score=37.35 Aligned_cols=40 Identities=13% Similarity=0.306 Sum_probs=36.7
Q ss_pred CCcEEEEeecCCccCHHHHHHHHHHHHHHHHHHHHHhhhc
Q psy5332 182 PNKYFFNVESAGALKPENIVIMGVTVLKQKLSNLQTQLAH 221 (287)
Q Consensus 182 ~d~fif~VEs~G~l~p~~iv~~A~~iLk~Kl~~l~~~l~~ 221 (287)
.+++.+.|.|+|..+|.+++.+|++-|.+.++.+.+.+..
T Consensus 68 ~~~~~lrIqT~~~~~p~eaL~~a~~~L~~~~~~l~~~f~~ 107 (120)
T 1twf_K 68 FARFKLRIQTTEGYDPKDALKNACNSIINKLGALKTNFET 107 (120)
T ss_dssp SCEEEEEEEECTTCCHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred CCccEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4789999999999999999999999999999999887754
No 17
>3lu0_A DNA-directed RNA polymerase subunit alpha; E. coli RNA polymerase, nucleotidyltransferase, transcription, transferase; 11.20A {Escherichia coli} PDB: 3iyd_A
Probab=90.10 E-value=0.23 Score=45.47 Aligned_cols=34 Identities=24% Similarity=0.503 Sum_probs=31.3
Q ss_pred CCeEEEEEeecCCCChhhHHHHHHHHHHHHHHHH
Q psy5332 239 PNKYFFNVESAGALKPENIVIMGVTVLKQKLSNL 272 (287)
Q Consensus 239 ~d~f~f~veS~g~l~~~~i~~~a~~~l~~k~~~l 272 (287)
-|+++|.|+|.|++.|++.+..|.++|++.+..|
T Consensus 198 ~dkL~leI~TdGsi~P~eAl~~Aa~iL~~~l~~f 231 (329)
T 3lu0_A 198 LDKLVIEMETNGTIDPEEAIRRAATILAEQLEAF 231 (329)
T ss_dssp EEEEEEEEEECSSSCHHHHHHHHHHHHHHHTTTS
T ss_pred cceEEEEEEECCCCCHHHHHHHHHHHHHHHHHHH
Confidence 4799999999999999999999999999988654
No 18
>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=89.50 E-value=0.88 Score=35.49 Aligned_cols=42 Identities=12% Similarity=0.268 Sum_probs=39.5
Q ss_pred cCCCeEEEEEeecCCCChhhHHHHHHHHHHHHHHHHHHHHhh
Q psy5332 237 AKPNKYFFNVESAGALKPENIVIMGVTVLKQKLSNLQTQLAH 278 (287)
Q Consensus 237 ~~~d~f~f~veS~g~l~~~~i~~~a~~~l~~k~~~l~~~l~~ 278 (287)
.-.++++|.|.++|..+|.+.+..|++-|.+.|+.+.+.++.
T Consensus 66 Pl~~~~~lrIqT~~~~~p~eaL~~a~~~L~~~~~~l~~~f~~ 107 (120)
T 1twf_K 66 PFFARFKLRIQTTEGYDPKDALKNACNSIINKLGALKTNFET 107 (120)
T ss_dssp TTSCEEEEEEEECTTCCHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred CCCCccEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 447899999999999999999999999999999999999988
No 19
>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=88.31 E-value=0.88 Score=35.24 Aligned_cols=44 Identities=18% Similarity=0.207 Sum_probs=39.2
Q ss_pred cCCCeEEEEEeecCCCChhhHHHHHHHHHHHHHHHHHHHHhhhhc
Q psy5332 237 AKPNKYFFNVESAGALKPENIVIMGVTVLKQKLSNLQTQLAHELS 281 (287)
Q Consensus 237 ~~~d~f~f~veS~g~l~~~~i~~~a~~~l~~k~~~l~~~l~~~~~ 281 (287)
.-.++++|.|.++|.. |.+.+..|++-|...|+.|.+.++...+
T Consensus 58 Ple~~~~lrIqT~~~~-p~eaL~~al~~L~~~~~~l~~~f~~a~~ 101 (115)
T 1xpp_A 58 PVIDNPQIYVRVKSGK-PQSAIKRAVRKLSKLYEDLGTQFQKEFQ 101 (115)
T ss_dssp TTTSCCEEEEEESSSC-HHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred CCCCccEEEEEeCCCC-hHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4478899999999988 9999999999999999999998887544
No 20
>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=88.28 E-value=0.72 Score=35.74 Aligned_cols=40 Identities=18% Similarity=0.214 Sum_probs=35.6
Q ss_pred CCcEEEEeecCCccCHHHHHHHHHHHHHHHHHHHHHhhhcc
Q psy5332 182 PNKYFFNVESAGALKPENIVIMGVTVLKQKLSNLQTQLAHD 222 (287)
Q Consensus 182 ~d~fif~VEs~G~l~p~~iv~~A~~iLk~Kl~~l~~~l~~e 222 (287)
.+++.|.|.|+|.. |.+++.+|++-|.+.++.|.+.+...
T Consensus 60 e~~~~lrIqT~~~~-p~eaL~~al~~L~~~~~~l~~~f~~a 99 (115)
T 1xpp_A 60 IDNPQIYVRVKSGK-PQSAIKRAVRKLSKLYEDLGTQFQKE 99 (115)
T ss_dssp TSCCEEEEEESSSC-HHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred CCccEEEEEeCCCC-hHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 47889999999998 99999999999999999998877543
No 21
>3rfr_A PMOB; membrane, oxidoreductase; 2.68A {Methylocystis SP} PDB: 3chx_A
Probab=32.51 E-value=84 Score=29.21 Aligned_cols=67 Identities=16% Similarity=0.133 Sum_probs=38.8
Q ss_pred CCceEEEEEEEEeeCCCCc---eeEeCCceeCCCeeeeccCCCc--ccCCCCCCCCCCeEEEEeCCCCEEEEEEEEE
Q psy5332 51 SECSVEFTLDVKCVDDQTR---HVTTADLKSTDARVVPVTSRNR--DADMNEYGETDDILIVKLRKGQELRLRAYAK 122 (287)
Q Consensus 51 ~~ctv~~~L~v~~~~~~~~---~V~s~Dl~s~d~~v~P~~~~~~--~~~~~~~~~~~dI~I~kL~pGQ~I~le~~a~ 122 (287)
+.-+++++|+|+++++.+. ..++..+.--++.+.|...... ...+.... .++ +| .||+.=.+++.|.
T Consensus 296 pgR~l~~~~~VtN~g~~pvrlgeF~tA~vrFlnp~v~~~~~~~p~~l~a~~GL~-s~~-pI---~PGETrt~~V~a~ 367 (419)
T 3rfr_A 296 PGRELTINVKVKNGTSQPVRLGEYTAAGLRFLNPTVFTQKPDFPDYLLADRGLS-NDD-VI---APGESKEIVVKIQ 367 (419)
T ss_dssp SSSEEEEEEEEECCSSSCBEEEEEECSSCEEECTTTCSSCCCCCTTTEESCCCC-CCC-CB---CTTCEEEEEEEEE
T ss_pred CCcEEEEEEEEecCCCCceEEeeEEEccEEEeCcccccCCCCCchhhhhccCCC-CCC-Cc---CCCcceEEEEEee
Confidence 4568999999999887774 3345555443333322221100 01111223 455 55 7999999988775
No 22
>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=28.21 E-value=97 Score=24.52 Aligned_cols=26 Identities=15% Similarity=0.330 Sum_probs=20.7
Q ss_pred EeCCCCEEEEEEEEEe-ccccccceec
Q psy5332 108 KLRKGQELRLRAYAKK-GFGKEHAKWN 133 (287)
Q Consensus 108 kL~pGQ~I~le~~a~k-GiGk~HAKws 133 (287)
-|.--+.|+|.+..-- |.+.+||-|-
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 5566688999888754 7899999995
No 23
>2wnv_C C1Q chain C, complement C1Q subcomponent subunit C; immune system, secreted, collagen, recognition, disulfide bond, innate immunity; HET: NAG; 1.25A {Homo sapiens} PDB: 2jg8_C 2wnu_C* 2jg9_C* 1pk6_C
Probab=24.88 E-value=1.2e+02 Score=23.09 Aligned_cols=25 Identities=16% Similarity=0.230 Sum_probs=20.1
Q ss_pred CCeEEEEeCCCCEEEEEEEEEeccc
Q psy5332 102 DDILIVKLRKGQELRLRAYAKKGFG 126 (287)
Q Consensus 102 ~dI~I~kL~pGQ~I~le~~a~kGiG 126 (287)
..-.+..|.+|+++-+++....|+.
T Consensus 90 S~~~~L~L~~GD~V~v~~~~~~~~~ 114 (131)
T 2wnv_C 90 SGGVLLRLQVGEEVWLAVNDYYDMV 114 (131)
T ss_dssp EEEEEEEECTTCEEEEEEEEEECCC
T ss_pred eeeEEEEECCCCEEEEEEeCCceEe
Confidence 3566889999999999997766653
No 24
>1yew_A Particulate methane monooxygenase, B subunit; membrane protein, beta barrel, oxidoreductase; 2.80A {Methylococcus capsulatus} PDB: 3rgb_A
Probab=23.27 E-value=1.5e+02 Score=27.28 Aligned_cols=68 Identities=12% Similarity=0.104 Sum_probs=38.8
Q ss_pred CCceEEEEEEEEeeCCCCc---eeEeCCceeCCCee---eeccCCCcccCCCCCCCCCCeEEEEeCCCCEEEEEEEEE
Q psy5332 51 SECSVEFTLDVKCVDDQTR---HVTTADLKSTDARV---VPVTSRNRDADMNEYGETDDILIVKLRKGQELRLRAYAK 122 (287)
Q Consensus 51 ~~ctv~~~L~v~~~~~~~~---~V~s~Dl~s~d~~v---~P~~~~~~~~~~~~~~~~~dI~I~kL~pGQ~I~le~~a~ 122 (287)
+.-+++++|+|+++++.+. ..++..+.--++.+ .|.+.+ ..-......++++-|| .||+.=.+++.|.
T Consensus 262 pgR~l~~~~~VtN~g~~pvrlgeF~tA~vrFln~~~~~~~~~~P~-~lla~~gL~vsd~~pI---~PGETr~~~v~a~ 335 (382)
T 1yew_A 262 PGRAMRMKLTITNHGNSPIRLGEFYTASVRFLDSDVYKDTTGYPE-DLLAEDGLSVSDNSPL---APGETRTVDVTAS 335 (382)
T ss_dssp SCSEEEEEEEEEECSSSCEEEEEEECSSCEEECTTTCCCCSCCCG-GGEETTCEEESCCSCB---CTTCEEEEEEEEE
T ss_pred CCcEEEEEEEEEcCCCCceEeeeEEeccEEEeCCcccccCCCChH-HhhccCCceeCCCCCc---CCCceeEEEEEee
Confidence 4568999999999988774 34555554322222 111100 0001112334666665 7999999888775
No 25
>2wnv_B C1Q chain B, complement C1Q subcomponent subunit B; immune system, secreted, collagen, recognition, disulfide bond, innate immunity; HET: NAG; 1.25A {Homo sapiens} PDB: 2jg8_B 2wnu_B* 2jg9_B* 1pk6_B
Probab=22.10 E-value=1.5e+02 Score=22.66 Aligned_cols=42 Identities=21% Similarity=0.205 Sum_probs=27.5
Q ss_pred CCeEEEEeCCCCEEEEEEEEEeccccccceecccceeeeeecCC
Q psy5332 102 DDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTAGVCFEYDPD 145 (287)
Q Consensus 102 ~dI~I~kL~pGQ~I~le~~a~kGiGk~HAKwsPV~~~~y~~~P~ 145 (287)
..-.+.+|.+|+++-+++....|+--.+..|+ .-..|.+.|+
T Consensus 92 S~~~~L~L~~GD~V~v~~~~~~~~~~~~~~~s--tFsGfLl~~~ 133 (136)
T 2wnv_B 92 TGGMVLKLEQGENVFLQATDKNSLLGMEGANS--IFSGFLLFPD 133 (136)
T ss_dssp EEEEEEEECTTCEEEEEEEEEECCBCBTTBCC--EEEEEEEEEC
T ss_pred eeeEEEEECCCCEEEEEEeCCceEEcCCCCCE--EEEEEEeccc
Confidence 35678899999999999976655433333444 2334665554
No 26
>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=20.98 E-value=2e+02 Score=23.56 Aligned_cols=27 Identities=15% Similarity=0.349 Sum_probs=22.1
Q ss_pred EEeC-CCCEEEEEEEEEeccccccceec
Q psy5332 107 VKLR-KGQELRLRAYAKKGFGKEHAKWN 133 (287)
Q Consensus 107 ~kL~-pGQ~I~le~~a~kGiGk~HAKws 133 (287)
+.|. --|.|+|.+.+--|.+.+||-|-
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 4676 55899999987778899999994
Done!