Query 020866
Match_columns 320
No_of_seqs 127 out of 269
Neff 6.1
Searched_HMMs 29240
Date Mon Mar 25 09:20:34 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/020866.a3m -d /work/01045/syshi/HHdatabase/pdb70.hhm -o /work/01045/syshi/hhsearch_pdb/020866hhsearch_pdb -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 2dir_A Thump domain-containing 99.8 1.6E-18 5.6E-23 138.4 10.7 94 178-301 4-97 (98)
2 1vbk_A Hypothetical protein PH 98.4 1.9E-06 6.6E-11 81.4 11.6 111 133-279 47-158 (307)
3 2c5s_A THII, probable thiamine 98.2 8.6E-06 2.9E-10 79.8 12.7 111 133-279 56-166 (413)
4 3tma_A Methyltransferase; thum 96.0 0.01 3.5E-07 55.9 6.5 95 168-295 70-168 (354)
5 3k0b_A Predicted N6-adenine-sp 95.7 0.01 3.5E-07 57.6 5.3 95 169-295 64-165 (393)
6 3ldg_A Putative uncharacterize 94.9 0.025 8.6E-07 54.7 5.2 95 169-295 54-158 (384)
7 3v97_A Ribosomal RNA large sub 94.9 0.39 1.3E-05 49.9 14.4 99 169-295 53-154 (703)
8 3tm4_A TRNA (guanine N2-)-meth 94.0 0.15 5.2E-06 48.5 8.4 96 168-295 72-181 (373)
9 3ldu_A Putative methylase; str 93.3 0.21 7.3E-06 48.0 8.2 95 169-295 57-159 (385)
10 1ydl_A TFIIH, general transcri 37.8 20 0.00067 27.0 2.5 24 37-65 12-35 (79)
11 3dgp_B RNA polymerase II trans 36.5 22 0.00077 26.1 2.6 22 38-64 4-25 (71)
No 1
>2dir_A Thump domain-containing protein 1; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.308.1.3
Probab=99.77 E-value=1.6e-18 Score=138.43 Aligned_cols=94 Identities=17% Similarity=0.289 Sum_probs=85.3
Q ss_pred eeeeecCHHHHHHHHHHHHHhhcccccccCCCCceEEEEEcccCccccccCCCCCCCCcccccCCChhHHHHHHHHhhhh
Q 020866 178 QATCVLKEKELQATVSKLVLQFVNDEQNKLSRPVKFAVGYNRRGFEEKQNKIPKDTKDSDVSALLDRNKCFTIVAAAVKE 257 (320)
Q Consensus 178 ~~tc~a~~~~i~~~~~~ll~~~F~~~~~~~~~~~tfaI~~~~Rn~~e~~~~~~~~~~~~~~~~~l~R~~vI~~VA~~V~~ 257 (320)
..+|.+++++|.+.|..++.++|+. .++.||+|.+++|+++ .|++++|+..|+++|.+
T Consensus 4 ~~~~~~~~e~I~~~a~~~~~~~f~~-----~~~~TF~V~~kR~~k~-----------------~~~S~ei~~~vG~~i~~ 61 (98)
T 2dir_A 4 GSSGKAFLEDMKKYAETFLEPWFKA-----PNKGTFQIVYKSRNNS-----------------HVNREEVIRELAGIVCT 61 (98)
T ss_dssp CCCCCHHHHHHHHHHHHHHHHHHST-----TCCCEEEEEEECSSCC-----------------SSCHHHHHHHHHHHHHH
T ss_pred eEEEECCHHHHHHHHHHHHHHhcCc-----CCCceEEEEEEeCCCC-----------------CCCHHHHHHHHHHHHHh
Confidence 4689999999999999999999863 2457999999999976 89999999999999987
Q ss_pred cCCCceeeCCCCCeEEEEEEeeCCCCCCCceEEEEEeeCCCccc
Q 020866 258 VVSDSAVDLKSPELSVLVELLPISGLPSELLVVGVSILPQKLVT 301 (320)
Q Consensus 258 ~~~~hkVdLknPd~vIlVEV~k~~~~~~~~~vcgiSVv~~y~~~ 301 (320)
..++++|||+|||++|.|||.+ + .|||||+++|+..
T Consensus 62 ~~~~~kVdL~nPd~~I~VEI~~--~------~~~isv~~~y~~~ 97 (98)
T 2dir_A 62 LNSENKVDLTNPQYTVVVEIIK--A------VCCLSVVKSGPSS 97 (98)
T ss_dssp HCTTCEECSSSCSEEEEEEEET--T------EEEEEEEECCCTT
T ss_pred hCCCCeeEcCCCCEEEEEEEeC--C------EEEEEEccccccC
Confidence 6678999999999999999999 8 9999999999753
No 2
>1vbk_A Hypothetical protein PH1313; structural genomics, riken structural genomics/proteomics initiative, RSGI, NPPSFA; 1.90A {Pyrococcus horikoshii} SCOP: c.26.2.6 d.308.1.1
Probab=98.38 E-value=1.9e-06 Score=81.40 Aligned_cols=111 Identities=16% Similarity=0.154 Sum_probs=85.7
Q ss_pred CcceEEEEccCCCCCCHHHHHHHHHHHHcCCCCCCCceEEeeeeeeeeeecCHHHHHHHHHHHHHhhccc-ccccCCCCc
Q 020866 133 RNGLLLLTFPREHSPNTINIVSNIFQSLGSGSLKSPVWCHRIFPIQATCVLKEKELQATVSKLVLQFVND-EQNKLSRPV 211 (320)
Q Consensus 133 ~~gv~fi~f~~~~~~dP~~lv~~I~~d~~~~~~~~tR~i~RliPI~~tc~a~~~~i~~~~~~ll~~~F~~-~~~~~~~~~ 211 (320)
..|.+||. . .++.++++++ +..=-|+++.|+.. |..++++|.+.+..++..++.. + ....
T Consensus 47 ~~gri~V~--~---~~~~~~~~~L---------~~vfGI~~~s~v~~-~~~dle~I~~~~~~~~~~~~~~~~----~~~~ 107 (307)
T 1vbk_A 47 RHGRIIVK--T---NSPKEAANVL---------VRVFGIVSISPAME-VEASLEKINRTALLMFRKKAKEVG----KERP 107 (307)
T ss_dssp ETTEEEEE--C---SCHHHHHHHH---------TTSTTEEEEEEEEE-EECCHHHHHHHHHHHHHHHHHHHT----CSSC
T ss_pred ECCEEEEE--c---CCHHHHHHHH---------hhcCCeEEEEEEEE-eCCCHHHHHHHHHHHHHHhhcccC----CCCc
Confidence 46788886 2 2777755554 22356788899987 5689999999999998875421 0 1124
Q ss_pred eEEEEEcccCccccccCCCCCCCCcccccCCChhHHHHHHHHhhhhcCCCceeeCCCCCeEEEEEEee
Q 020866 212 KFAVGYNRRGFEEKQNKIPKDTKDSDVSALLDRNKCFTIVAAAVKEVVSDSAVDLKSPELSVLVELLP 279 (320)
Q Consensus 212 tfaI~~~~Rn~~e~~~~~~~~~~~~~~~~~l~R~~vI~~VA~~V~~~~~~hkVdLknPd~vIlVEV~k 279 (320)
||+|..++++.+ -.++..++-..|++.|.+.. +.+|||+|||++|.|||..
T Consensus 108 tF~Vr~kR~~k~----------------~~~~S~ei~r~vG~~i~~~~-~~~Vdl~~PD~~i~VEi~~ 158 (307)
T 1vbk_A 108 KFRVTARRITKE----------------FPLDSLEIQAKVGEYILNNE-NCEVDLKNYDIEIGIEIMQ 158 (307)
T ss_dssp EEEEEEEESSSC----------------SSSCHHHHHHHHHHHHHHHS-SCEECSSSCSEEEEEEEET
T ss_pred eEEEEEEeCCCC----------------CCCChHHHHHHHHHHHHHHh-CCceeeeCCCEEEEEEEEc
Confidence 999999999832 27999999999999998654 6799999999999999988
No 3
>2c5s_A THII, probable thiamine biosynthesis protein THII; RNA-binding protein, RNA binding protein, tRNA modification, 4-thiouridine synthase; HET: AMP; 2.5A {Bacillus anthracis} SCOP: c.26.2.6 d.308.1.1
Probab=98.23 E-value=8.6e-06 Score=79.85 Aligned_cols=111 Identities=13% Similarity=0.159 Sum_probs=87.2
Q ss_pred CcceEEEEccCCCCCCHHHHHHHHHHHHcCCCCCCCceEEeeeeeeeeeecCHHHHHHHHHHHHHhhcccccccCCCCce
Q 020866 133 RNGLLLLTFPREHSPNTINIVSNIFQSLGSGSLKSPVWCHRIFPIQATCVLKEKELQATVSKLVLQFVNDEQNKLSRPVK 212 (320)
Q Consensus 133 ~~gv~fi~f~~~~~~dP~~lv~~I~~d~~~~~~~~tR~i~RliPI~~tc~a~~~~i~~~~~~ll~~~F~~~~~~~~~~~t 212 (320)
..|.+||..+ ..++.+++.++ +..=-|+++.|+.. |..++++|.+.+..++...+. +..|
T Consensus 56 ~~gri~v~~~---~~~~~~~~~~L---------~~vfGI~~~~~v~~-~~~dle~I~~~~~~~~~~~~~-------~~~t 115 (413)
T 2c5s_A 56 THDRMYIQLN---GEDHEAVSERL---------KDVFGIHKFNLAMK-VPSELEDIKKGALAAFLQVKG-------DVKT 115 (413)
T ss_dssp CSSCEEEECT---TCCHHHHHHHH---------TTCTTEEEEEEEEE-EESSHHHHHHHHHHHHHTCCS-------CCCE
T ss_pred ECCEEEEEeC---CCCHHHHHHHH---------hhCCCeEEEEEEEE-ecCCHHHHHHHHHHHHHhhcc-------CCCc
Confidence 3588888732 22666655543 23356788999987 568899999999998887652 4459
Q ss_pred EEEEEcccCccccccCCCCCCCCcccccCCChhHHHHHHHHhhhhcCCCceeeCCCCCeEEEEEEee
Q 020866 213 FAVGYNRRGFEEKQNKIPKDTKDSDVSALLDRNKCFTIVAAAVKEVVSDSAVDLKSPELSVLVELLP 279 (320)
Q Consensus 213 faI~~~~Rn~~e~~~~~~~~~~~~~~~~~l~R~~vI~~VA~~V~~~~~~hkVdLknPd~vIlVEV~k 279 (320)
|+|..++++.. -.++..++-..|++.|.+..++.+|||+|||+.|-|||.+
T Consensus 116 F~V~~kR~~k~----------------f~~~S~ei~r~vG~~i~~~~~~~~Vdl~~Pdi~i~vEI~~ 166 (413)
T 2c5s_A 116 FKITVHRSYKH----------------FPMRTMELLPEIGGHILENTEDITVDVHNPDVNVRVEIRS 166 (413)
T ss_dssp EEEEEEECCTT----------------CSSCHHHHHHHHHHHHHTTSSSCEECSSSCSEEEEEEECS
T ss_pred EEEEEEECCCC----------------CCCChHHHHHHHHHHHHHhCCCCeeccCCCCeEEEEEEEe
Confidence 99999999842 2789999999999999876567899999999999999988
No 4
>3tma_A Methyltransferase; thump domain; 2.05A {Thermus thermophilus}
Probab=95.96 E-value=0.01 Score=55.92 Aligned_cols=95 Identities=18% Similarity=0.139 Sum_probs=68.2
Q ss_pred CceEEeeeeeeeee--e-cC-HHHHHHHHHHHHHhhcccccccCCCCceEEEEEcccCccccccCCCCCCCCcccccCCC
Q 020866 168 PVWCHRIFPIQATC--V-LK-EKELQATVSKLVLQFVNDEQNKLSRPVKFAVGYNRRGFEEKQNKIPKDTKDSDVSALLD 243 (320)
Q Consensus 168 tR~i~RliPI~~tc--~-a~-~~~i~~~~~~ll~~~F~~~~~~~~~~~tfaI~~~~Rn~~e~~~~~~~~~~~~~~~~~l~ 243 (320)
+|...|+.-+-..+ . .+ .++|.+.+..+--..+ .+..||+|..++.+.. .++
T Consensus 70 lR~a~rvl~~~~~~~~~~~~~~~~L~~~~~~~~w~~~-------~~~~tF~V~~~~~~~~-----------------~f~ 125 (354)
T 3tma_A 70 LRLAHHLVLFRARLLLSREDPLGALERAALALPWPEL-------EGAGSFRVEARREGEH-----------------PFT 125 (354)
T ss_dssp CSSCSCEEEEEEEEECCSSSHHHHHHHHHHTSCCTTH-------HHHCCEEEEEEEESCC-----------------SSC
T ss_pred cCCccEEEEEeeeccCCchhhHHHHHHHHHhCchhhc-------CCCCCEEEEEEEcCCC-----------------CCC
Confidence 56666766555555 3 35 6777777765421111 1346999999887743 788
Q ss_pred hhHHHHHHHHhhhhcCCCceeeCCCCCeEEEEEEeeCCCCCCCceEEEEEee
Q 020866 244 RNKCFTIVAAAVKEVVSDSAVDLKSPELSVLVELLPISGLPSELLVVGVSIL 295 (320)
Q Consensus 244 R~~vI~~VA~~V~~~~~~hkVdLknPd~vIlVEV~k~~~~~~~~~vcgiSVv 295 (320)
..+|-+.|++.+.+.. +.+||+++||+.|.|++.+ + .|.+++-
T Consensus 126 s~~vk~~i~~~l~~~~-g~~v~~~~pd~~i~v~i~~--d------~~~l~~d 168 (354)
T 3tma_A 126 SPEVERRVGEALHRAY-GVPVDLKRPAVRVRVDVRG--E------EAFLGVQ 168 (354)
T ss_dssp HHHHHHHHHHHHHHHH-CCCBCSSSCSEEEEEEEET--T------EEEEEEE
T ss_pred HHHHHHHHHHHHHHhh-CCcccCCCCCEEEEEEEEC--C------EEEEEEE
Confidence 9999999999887532 4569999999999999999 7 7777764
No 5
>3k0b_A Predicted N6-adenine-specific DNA methylase; methylase,PF01170, putative RNA methylase, PSI,MCSG, structu genomics; 1.50A {Listeria monocytogenes str}
Probab=95.69 E-value=0.01 Score=57.55 Aligned_cols=95 Identities=17% Similarity=0.127 Sum_probs=64.7
Q ss_pred ceEEeeeeeeeeeec-CHHHHHHHHHHH-HHhhcccccccCCCCceEEEEEcccCccccccCCCCCCCCcccccCCChhH
Q 020866 169 VWCHRIFPIQATCVL-KEKELQATVSKL-VLQFVNDEQNKLSRPVKFAVGYNRRGFEEKQNKIPKDTKDSDVSALLDRNK 246 (320)
Q Consensus 169 R~i~RliPI~~tc~a-~~~~i~~~~~~l-l~~~F~~~~~~~~~~~tfaI~~~~Rn~~e~~~~~~~~~~~~~~~~~l~R~~ 246 (320)
|-..|++-+-..+.+ +.++|-+.+..+ ...||+ ...||+|..++.++. .++..+
T Consensus 64 R~a~RVl~~l~~f~a~~~~~L~~~~~~i~w~~~l~-------~~~tF~V~~~~~~s~-----------------~fss~~ 119 (393)
T 3k0b_A 64 RVADRVKIVVGVFKATTFDELFEKTKALPWEDYLP-------LDAQFPVAGKSVKST-----------------LYSVPD 119 (393)
T ss_dssp SSCSCEEEEEEEEECSSHHHHHHHHHTSCGGGTCC-------TTCBCCEEEEEESSS-----------------CCCHHH
T ss_pred cceeeEEEEEEEEecCCHHHHHHHHHhCCHHHhCC-------CCCeEEEEEEEecCC-----------------CCCHHH
Confidence 444454444444544 689998888876 556664 556999998776643 667666
Q ss_pred HHHHHHHhhh----hcC-CCceeeCCCCCeEEEEEEeeCCCCCCCceEEEEEee
Q 020866 247 CFTIVAAAVK----EVV-SDSAVDLKSPELSVLVELLPISGLPSELLVVGVSIL 295 (320)
Q Consensus 247 vI~~VA~~V~----~~~-~~hkVdLknPd~vIlVEV~k~~~~~~~~~vcgiSVv 295 (320)
+-..|-++|- ... ..-.||+++||+.|.|++.. + .|-+++=
T Consensus 120 ~~~~vkdAI~d~~~~~~~~rp~vd~~~Pd~~i~v~l~~--~------~~~~~ld 165 (393)
T 3k0b_A 120 CQAIVKKAIVNRVSEKYRRSGRLMETGALFKLEVSILK--D------EVTLTID 165 (393)
T ss_dssp HHHHHHHHHHHHHHHHTTTCTTCCSCSSBCCEEEEEET--T------EEEEEEE
T ss_pred HHHHHHHHHHHHHHHhhCCCCCCCCCCCCEEEEEEEEC--C------EEEEEEe
Confidence 6555555553 211 12369999999999999999 8 7888875
No 6
>3ldg_A Putative uncharacterized protein SMU.472; YPSC, methyltransferase, transferase; HET: SAH; 1.96A {Streptococcus mutans}
Probab=94.88 E-value=0.025 Score=54.66 Aligned_cols=95 Identities=18% Similarity=0.134 Sum_probs=62.6
Q ss_pred ceEEeeeeeeeeeec-CHHHHHHHHHHH-HHhhcccccccCCCCceEEE-EEcccCccccccCCCCCCCCcccccCCChh
Q 020866 169 VWCHRIFPIQATCVL-KEKELQATVSKL-VLQFVNDEQNKLSRPVKFAV-GYNRRGFEEKQNKIPKDTKDSDVSALLDRN 245 (320)
Q Consensus 169 R~i~RliPI~~tc~a-~~~~i~~~~~~l-l~~~F~~~~~~~~~~~tfaI-~~~~Rn~~e~~~~~~~~~~~~~~~~~l~R~ 245 (320)
|-..|++-+-..+.+ +.++|-+.+..+ ...||+ +..||+| ..++.++. .++..
T Consensus 54 R~a~RVl~~l~~f~a~~~~~Ly~~~~~i~W~~~l~-------~~~tf~V~~~~~~~s~-----------------~~~s~ 109 (384)
T 3ldg_A 54 RSADRIKIVVGEFPARTFEELFQGVYALDWENYLP-------LGCQFPVAKAKSVKSK-----------------LHNEP 109 (384)
T ss_dssp SSCSEEEEEEEEEECSSHHHHHHHHHHSCGGGTCC-------TTCBCCBCCCEEESCS-----------------CCCHH
T ss_pred ccceeEEEEEEEEecCCHHHHHHHHHcCCHHHhCC-------CCCeEEEEeeeecCCC-----------------CCCHH
Confidence 555555555555655 689998888876 567764 5568999 75555432 45555
Q ss_pred HHHHHHHHhh----hhcC---CCceeeCCCCCeEEEEEEeeCCCCCCCceEEEEEee
Q 020866 246 KCFTIVAAAV----KEVV---SDSAVDLKSPELSVLVELLPISGLPSELLVVGVSIL 295 (320)
Q Consensus 246 ~vI~~VA~~V----~~~~---~~hkVdLknPd~vIlVEV~k~~~~~~~~~vcgiSVv 295 (320)
++-..|-++| .... |...||+++||+.|.|.+.+ + .|-||+=
T Consensus 110 ~~~~~vkdAi~d~~~~~~~~r~~~~v~~~~pd~~i~v~~~~--~------~~~~~ld 158 (384)
T 3ldg_A 110 SIQGITKKAIVKKLQHYFHRPDSVPLPENGPEFKIEISLLK--D------QARVMID 158 (384)
T ss_dssp HHHHHHHHHHHHHHHHHTTCCTTSCCCCCSCBCEEEEEEET--T------EEEEEEE
T ss_pred HHHHHHHHHHHHHHHHhhCCCCccccCCCCCCEEEEEEEEC--C------EEEEEEe
Confidence 5433343443 3211 11239999999999999999 8 8888876
No 7
>3v97_A Ribosomal RNA large subunit methyltransferase L; YCBY, RNA methyltransferase, ribosome RNA, SAH, RLML; HET: SAH OSU; 2.20A {Escherichia coli} PDB: 3v8v_A*
Probab=94.86 E-value=0.39 Score=49.86 Aligned_cols=99 Identities=17% Similarity=0.174 Sum_probs=64.5
Q ss_pred ceEEeeeeeeeeeec-CHHHHHHHHHHH-HHhhcccccccCCCCceEEEEEcccCccccccCCCCCCCCcccccCCChhH
Q 020866 169 VWCHRIFPIQATCVL-KEKELQATVSKL-VLQFVNDEQNKLSRPVKFAVGYNRRGFEEKQNKIPKDTKDSDVSALLDRNK 246 (320)
Q Consensus 169 R~i~RliPI~~tc~a-~~~~i~~~~~~l-l~~~F~~~~~~~~~~~tfaI~~~~Rn~~e~~~~~~~~~~~~~~~~~l~R~~ 246 (320)
|-..|++=.-..+.+ +.++|-+.+..+ ...||+ +..||+|.++.++.. -.++.+.-..
T Consensus 53 R~a~Rvl~~l~~f~~~~~~~L~~~~~~~~w~~~~~-------~~~tf~V~~~~~~~~-------------~~~~~~~~~~ 112 (703)
T 3v97_A 53 RLASRIMLPLGECKVYSDLDLYLGVQAINWTEMFN-------PGATFAVHFSGLNDT-------------IRNSQYGAMK 112 (703)
T ss_dssp SSCSEEEEEEEEEECSSHHHHHHHHHTSCHHHHBC-------TTCCEEEEEECCCSS-------------CCSHHHHHHH
T ss_pred CceeEEEEEEEEEecCCHHHHHHHHHcCCHHHhCC-------CCceEEEEEEEecCC-------------cCChHHHHHH
Confidence 445555544455554 689999888876 677774 566999999877632 0001111223
Q ss_pred HHHHHHHhhhhcC-CCceeeCCCCCeEEEEEEeeCCCCCCCceEEEEEee
Q 020866 247 CFTIVAAAVKEVV-SDSAVDLKSPELSVLVELLPISGLPSELLVVGVSIL 295 (320)
Q Consensus 247 vI~~VA~~V~~~~-~~hkVdLknPd~vIlVEV~k~~~~~~~~~vcgiSVv 295 (320)
|-++|.+.+.... ..-.||+++||+.|.|.+.+ + .|-+|+=
T Consensus 113 vk~ai~d~~~~~~g~rp~v~~~~pd~~i~v~l~~--~------~~~l~ld 154 (703)
T 3v97_A 113 VKDAIVDAFTRKNLPRPNVDRDAPDIRVNVWLHK--E------TASIALD 154 (703)
T ss_dssp HHHHHHHHHHTTTCCCCCBCSSSCSEEEEEEEET--T------EEEEEEE
T ss_pred HHHHHHHHHHHhhCCCCCCCCCCCCEEEEEEEEC--C------EEEEEEe
Confidence 4445555554321 12369999999999999999 8 8888885
No 8
>3tm4_A TRNA (guanine N2-)-methyltransferase TRM14; rossmann fold, thump domain, tRNA methyltransferase; HET: SAM; 1.95A {Pyrococcus furiosus} PDB: 3tlj_A* 3tm5_A*
Probab=93.97 E-value=0.15 Score=48.47 Aligned_cols=96 Identities=27% Similarity=0.241 Sum_probs=64.8
Q ss_pred CceEEeeeeeeeeeec----------CHHHHHHHHHHH-HHhhcccccccCCCCceEEEEEcccCccccccCCCCCCCCc
Q 020866 168 PVWCHRIFPIQATCVL----------KEKELQATVSKL-VLQFVNDEQNKLSRPVKFAVGYNRRGFEEKQNKIPKDTKDS 236 (320)
Q Consensus 168 tR~i~RliPI~~tc~a----------~~~~i~~~~~~l-l~~~F~~~~~~~~~~~tfaI~~~~Rn~~e~~~~~~~~~~~~ 236 (320)
+|...|++-+-..+.+ +.++|-+.+..+ ...|| .+..||+|..++.+..
T Consensus 72 ~R~a~rv~~~~~~~~~~~~~~~~~~~~~~~L~~~v~~~~w~~~l-------~~~~tF~V~~~~~~~~------------- 131 (373)
T 3tm4_A 72 SRLLHRVIIEIASEKFNGIEKDESEEALKRIKDFVSSLPVEQFV-------KVSETFAVRSFRKGDH------------- 131 (373)
T ss_dssp CSSCSEEEEEEEEEECTTTTTSCHHHHHHHHHHHHHTSCGGGGS-------CTTSEEEEEEEEESSC-------------
T ss_pred hhhHhheEEEEEEeEeccccccccCCCHHHHHHHHHhCCHHHhC-------CCCCcEEEEEEECCCC-------------
Confidence 4777777776666654 366666665553 33344 3566999999887643
Q ss_pred ccccCCChhHHHHHHHHhhhhcC--CC-ceeeCCCCCeEEEEEEeeCCCCCCCceEEEEEee
Q 020866 237 DVSALLDRNKCFTIVAAAVKEVV--SD-SAVDLKSPELSVLVELLPISGLPSELLVVGVSIL 295 (320)
Q Consensus 237 ~~~~~l~R~~vI~~VA~~V~~~~--~~-hkVdLknPd~vIlVEV~k~~~~~~~~~vcgiSVv 295 (320)
.++..++-..|.++|-+.- -+ ..||+++||+.|.|.+.+ + .|-+++=
T Consensus 132 ----~~~s~~~~~~vk~aIvd~~~~~g~~~v~~~~p~~~i~~~~~~--d------~~~~~ld 181 (373)
T 3tm4_A 132 ----NITSIDIARTVGEAIFERLSRFGTPLVNLDHPAVIFRAELIK--D------VFFLGID 181 (373)
T ss_dssp ----SSCHHHHHHHHHHHHHHHHHTTSCCEECSSSCSEEEEEEEET--T------EEEEEEE
T ss_pred ----cCCHHHHHHHHHHHHHHHHHHhCCCcccCCCCCeEEEEEEEC--C------EEEEEEE
Confidence 6677666666666664210 11 589999999999999998 7 6777764
No 9
>3ldu_A Putative methylase; structural genomics, PSI-2, protein structure initiative, midwest center for structural genomics, MCSG; HET: MSE GTP; 1.70A {Clostridium difficile}
Probab=93.31 E-value=0.21 Score=47.97 Aligned_cols=95 Identities=16% Similarity=0.155 Sum_probs=62.8
Q ss_pred ceEEeeeeeeeeee-cCHHHHHHHHHHH-HHhhcccccccCCCCceEEEE-EcccCccccccCCCCCCCCcccccCCChh
Q 020866 169 VWCHRIFPIQATCV-LKEKELQATVSKL-VLQFVNDEQNKLSRPVKFAVG-YNRRGFEEKQNKIPKDTKDSDVSALLDRN 245 (320)
Q Consensus 169 R~i~RliPI~~tc~-a~~~~i~~~~~~l-l~~~F~~~~~~~~~~~tfaI~-~~~Rn~~e~~~~~~~~~~~~~~~~~l~R~ 245 (320)
|-..|++=+-..+. .+.++|-+.+..+ ...||+ +..||+|. .+++++. .++..
T Consensus 57 R~a~RVl~~l~~f~~~~~~~L~~~~~~i~w~~~~~-------~~~tf~V~~~~~~~s~-----------------~~~~~ 112 (385)
T 3ldu_A 57 RCAERVHLKIAEFEAKSFDELFENTKRINWSRYIP-------YGAQFPISKASSIKSK-----------------LYSTP 112 (385)
T ss_dssp SSCSCCEEEEEEEECSSHHHHHHHHHTSCGGGTSC-------TTCBCCEEEEEEESSS-----------------CCCHH
T ss_pred CceeEEEEEeeeEecCCHHHHHHHHHhCCHHHhCC-------CCceEEEEeecccCCC-----------------cCcHH
Confidence 44444443333454 4689998888876 566664 55699999 7666643 56665
Q ss_pred HHHHHHHHhh----hhcC-CCceeeCCCCCeEEEEEEeeCCCCCCCceEEEEEee
Q 020866 246 KCFTIVAAAV----KEVV-SDSAVDLKSPELSVLVELLPISGLPSELLVVGVSIL 295 (320)
Q Consensus 246 ~vI~~VA~~V----~~~~-~~hkVdLknPd~vIlVEV~k~~~~~~~~~vcgiSVv 295 (320)
++-..|-++| .... ..-.||+.+||+.|.|.+.+ + .|-+++=
T Consensus 113 ~~~~~vkdAIvd~~~~~~~~rp~v~~~~p~~~i~~~i~~--~------~~~~~lD 159 (385)
T 3ldu_A 113 DVQAIVKKAIVESLKKSYLEDGLLKEDKEKYPIFVFIHK--D------KVTISID 159 (385)
T ss_dssp HHHHHHHHHHHHHHHHHTTCCSCCCCCSCBCCEEEEEET--T------EEEEEEE
T ss_pred HHHHHHHHHHHHHHHHhhCCCCCCCCCCCCEEEEEEEEC--C------EEEEEEe
Confidence 5554444444 2211 12369999999999999999 8 7888875
No 10
>1ydl_A TFIIH, general transcription factor IIH, polypeptide 5; alpha-beta protein, structural genomics, PSI, protein structure initiative; 2.30A {Homo sapiens} SCOP: d.295.1.1 PDB: 2jnj_A
Probab=37.81 E-value=20 Score=27.00 Aligned_cols=24 Identities=25% Similarity=0.457 Sum_probs=20.5
Q ss_pred CCceEEEEcCCChhhHHHHHHHHHHHHhh
Q 020866 37 SHSGFLLTCTIKREKSATKEAISILHKRL 65 (320)
Q Consensus 37 g~~G~lvTC~~~rEk~A~~E~~~lL~e~~ 65 (320)
-..|+||+|+. |+++++--||+..
T Consensus 12 ~~kGvLI~CDp-----a~Kq~Il~lde~~ 35 (79)
T 1ydl_A 12 TRKGMLIECDP-----AMKQFLLYLDESN 35 (79)
T ss_dssp CCCCEEEECCH-----HHHHHHHHHHHTT
T ss_pred cccceEEEeCH-----HHHHHHHHHhccC
Confidence 46899999997 8999999998843
No 11
>3dgp_B RNA polymerase II transcription factor B subunit; protein-protein complex, beta-alpha-beta spilt, heterodimer, damage, DNA excision; 1.80A {Saccharomyces cerevisiae} SCOP: d.295.1.0 PDB: 3dom_B
Probab=36.54 E-value=22 Score=26.11 Aligned_cols=22 Identities=23% Similarity=0.421 Sum_probs=19.8
Q ss_pred CceEEEEcCCChhhHHHHHHHHHHHHh
Q 020866 38 HSGFLLTCTIKREKSATKEAISILHKR 64 (320)
Q Consensus 38 ~~G~lvTC~~~rEk~A~~E~~~lL~e~ 64 (320)
..|+||+|+- |++.++--||+.
T Consensus 4 ~kGvLi~CDp-----a~Kq~il~lde~ 25 (71)
T 3dgp_B 4 RKGALVQCDP-----SIKALILQIDAK 25 (71)
T ss_dssp EEEEEEECCH-----HHHHHHHHHHHH
T ss_pred eeEEEEEcCH-----HHHHHHHHHcCC
Confidence 4799999997 899999999996
Done!