Query 020116
Match_columns 331
No_of_seqs 129 out of 284
Neff 6.0
Searched_HMMs 29240
Date Mon Mar 25 12:01:58 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/020116.a3m -d /work/01045/syshi/HHdatabase/pdb70.hhm -o /work/01045/syshi/hhsearch_pdb/020116hhsearch_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 2.1E-18 7.3E-23 138.6 10.7 93 189-311 4-96 (98)
2 1vbk_A Hypothetical protein PH 98.4 1.6E-06 5.3E-11 82.6 11.8 107 145-290 48-158 (307)
3 2c5s_A THII, probable thiamine 98.4 2.4E-06 8E-11 84.4 13.0 110 145-290 57-166 (413)
4 3tma_A Methyltransferase; thum 96.4 0.0044 1.5E-07 58.8 6.3 95 179-306 70-168 (354)
5 3k0b_A Predicted N6-adenine-sp 96.3 0.01 3.5E-07 57.9 8.6 95 180-306 64-165 (393)
6 3ldg_A Putative uncharacterize 95.8 0.0095 3.3E-07 58.0 5.7 96 179-306 53-158 (384)
7 3v97_A Ribosomal RNA large sub 95.3 0.06 2.1E-06 56.3 10.0 99 180-306 53-154 (703)
8 3tm4_A TRNA (guanine N2-)-meth 95.2 0.099 3.4E-06 50.1 10.3 95 179-306 72-181 (373)
9 3ldu_A Putative methylase; str 94.7 0.091 3.1E-06 50.9 8.6 95 180-306 57-159 (385)
10 1ydl_A TFIIH, general transcri 47.9 11 0.00038 28.6 2.6 24 36-64 11-34 (79)
11 3dgp_B RNA polymerase II trans 47.0 13 0.00043 27.7 2.7 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=99.76 E-value=2.1e-18 Score=138.62 Aligned_cols=93 Identities=17% Similarity=0.303 Sum_probs=84.7
Q ss_pred eeEeecCHHHHHHHHHHHHHhhcccccccCCCCceeEEEEcccCccccccCCCCCCCCccccccCChhHHHHHHHHHhhh
Q 020116 189 QATCVLKEKELQATVSKLVLQFVNDEQNKLSRPVKFAVGYNRRGFEEKQNKIPKDTKDSDVSALLDRNKCFTIVAAAVKE 268 (331)
Q Consensus 189 ~~tc~A~~~~i~~~~~~l~~~~F~~~~~~~~~p~tfaI~~~~Rn~~~~e~~~~~~n~~~~~~~~l~R~~vI~~VA~~V~~ 268 (331)
..+|.+++++|.+.|..++.++|+. .++.||+|++++|+ + +.|++++|++.||++|.+
T Consensus 4 ~~~~~~~~e~I~~~a~~~~~~~f~~-----~~~~TF~V~~kR~~-----------k------~~~~S~ei~~~vG~~i~~ 61 (98)
T 2dir_A 4 GSSGKAFLEDMKKYAETFLEPWFKA-----PNKGTFQIVYKSRN-----------N------SHVNREEVIRELAGIVCT 61 (98)
T ss_dssp CCCCCHHHHHHHHHHHHHHHHHHST-----TCCCEEEEEEECSS-----------C------CSSCHHHHHHHHHHHHHH
T ss_pred eEEEECCHHHHHHHHHHHHHHhcCc-----CCCceEEEEEEeCC-----------C------CCCCHHHHHHHHHHHHHh
Confidence 4789999999999999999999852 24469999999999 5 599999999999999998
Q ss_pred cCCCCeeeCCCCCeEEEEEEeeCCCCCCCccEEEEEeecCCcc
Q 020116 269 VVSDSAVDLKSPELSVLVELLPISGLPSELLVVGVSILPQKLV 311 (331)
Q Consensus 269 ~~~~hkVdLknPd~~IlVEV~k~~~~~~~~~v~giSVv~~y~~ 311 (331)
..++++|||+|||++|.|||.+ + .|||||+++|+.
T Consensus 62 ~~~~~kVdL~nPd~~I~VEI~~--~------~~~isv~~~y~~ 96 (98)
T 2dir_A 62 LNSENKVDLTNPQYTVVVEIIK--A------VCCLSVVKSGPS 96 (98)
T ss_dssp HCTTCEECSSSCSEEEEEEEET--T------EEEEEEEECCCT
T ss_pred hCCCCeeEcCCCCEEEEEEEeC--C------EEEEEEcccccc
Confidence 7778999999999999999999 8 999999999975
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=98.41 E-value=1.6e-06 Score=82.56 Aligned_cols=107 Identities=15% Similarity=0.125 Sum_probs=83.8
Q ss_pred cceEEEEeccCCCCCHHHHHHHHHHhhccCCcCCceeEEEeeeeeeEeecCHHHHHHHHHHHHHhhcccccccCCC-C--
Q 020116 145 NGLLLLTFPREHSPNTINIVSNIFQSLGSGSLKSPVWCHRIFPIQATCVLKEKELQATVSKLVLQFVNDEQNKLSR-P-- 221 (331)
Q Consensus 145 ~Gv~fi~f~~~~~~dP~~lv~~I~~dv~~~~~~~tRfi~Rl~PI~~tc~A~~~~i~~~~~~l~~~~F~~~~~~~~~-p-- 221 (331)
.|-+|+. . .++.+++.++ +..=-|+++.|+.. |..++++|.+.+..++..++. + .
T Consensus 48 ~gri~V~---~--~~~~~~~~~L---------~~vfGI~~~s~v~~-~~~dle~I~~~~~~~~~~~~~-------~~~~~ 105 (307)
T 1vbk_A 48 HGRIIVK---T--NSPKEAANVL---------VRVFGIVSISPAME-VEASLEKINRTALLMFRKKAK-------EVGKE 105 (307)
T ss_dssp TTEEEEE---C--SCHHHHHHHH---------TTSTTEEEEEEEEE-EECCHHHHHHHHHHHHHHHHH-------HHTCS
T ss_pred CCEEEEE---c--CCHHHHHHHH---------hhcCCeEEEEEEEE-eCCCHHHHHHHHHHHHHHhhc-------ccCCC
Confidence 6777774 2 2677655544 12345788899987 568999999999999877542 2 2
Q ss_pred -ceeEEEEcccCccccccCCCCCCCCccccccCChhHHHHHHHHHhhhcCCCCeeeCCCCCeEEEEEEee
Q 020116 222 -VKFAVGYNRRGFEEKQNKIPKDTKDSDVSALLDRNKCFTIVAAAVKEVVSDSAVDLKSPELSVLVELLP 290 (331)
Q Consensus 222 -~tfaI~~~~Rn~~~~e~~~~~~n~~~~~~~~l~R~~vI~~VA~~V~~~~~~hkVdLknPd~~IlVEV~k 290 (331)
.||+|+.++++. + -.++.+++-..|++.|.+.. +.+|||+|||++|.|||..
T Consensus 106 ~~tF~Vr~kR~~k----------~------~~~~S~ei~r~vG~~i~~~~-~~~Vdl~~PD~~i~VEi~~ 158 (307)
T 1vbk_A 106 RPKFRVTARRITK----------E------FPLDSLEIQAKVGEYILNNE-NCEVDLKNYDIEIGIEIMQ 158 (307)
T ss_dssp SCEEEEEEEESSS----------C------SSSCHHHHHHHHHHHHHHHS-SCEECSSSCSEEEEEEEET
T ss_pred CceEEEEEEeCCC----------C------CCCChHHHHHHHHHHHHHHh-CCceeeeCCCEEEEEEEEc
Confidence 399999999992 2 56888999999999998765 7899999999999999998
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=98.39 E-value=2.4e-06 Score=84.36 Aligned_cols=110 Identities=13% Similarity=0.169 Sum_probs=86.0
Q ss_pred cceEEEEeccCCCCCHHHHHHHHHHhhccCCcCCceeEEEeeeeeeEeecCHHHHHHHHHHHHHhhcccccccCCCCcee
Q 020116 145 NGLLLLTFPREHSPNTINIVSNIFQSLGSGSLKSPVWCHRIFPIQATCVLKEKELQATVSKLVLQFVNDEQNKLSRPVKF 224 (331)
Q Consensus 145 ~Gv~fi~f~~~~~~dP~~lv~~I~~dv~~~~~~~tRfi~Rl~PI~~tc~A~~~~i~~~~~~l~~~~F~~~~~~~~~p~tf 224 (331)
.|.++|... ..++.+++.++ +..=-|+++.|+.. |..++++|.+.+..++...+ ....||
T Consensus 57 ~gri~v~~~---~~~~~~~~~~L---------~~vfGI~~~~~v~~-~~~dle~I~~~~~~~~~~~~-------~~~~tF 116 (413)
T 2c5s_A 57 HDRMYIQLN---GEDHEAVSERL---------KDVFGIHKFNLAMK-VPSELEDIKKGALAAFLQVK-------GDVKTF 116 (413)
T ss_dssp SSCEEEECT---TCCHHHHHHHH---------TTCTTEEEEEEEEE-EESSHHHHHHHHHHHHHTCC-------SCCCEE
T ss_pred CCEEEEEeC---CCCHHHHHHHH---------hhCCCeEEEEEEEE-ecCCHHHHHHHHHHHHHhhc-------cCCCcE
Confidence 577777542 23566654443 23345788899977 46899999999999888655 244699
Q ss_pred EEEEcccCccccccCCCCCCCCccccccCChhHHHHHHHHHhhhcCCCCeeeCCCCCeEEEEEEee
Q 020116 225 AVGYNRRGFEEKQNKIPKDTKDSDVSALLDRNKCFTIVAAAVKEVVSDSAVDLKSPELSVLVELLP 290 (331)
Q Consensus 225 aI~~~~Rn~~~~e~~~~~~n~~~~~~~~l~R~~vI~~VA~~V~~~~~~hkVdLknPd~~IlVEV~k 290 (331)
+|+.++++ . +-.++.++|-..|++.|....++.+|||+|||+.|.|||.+
T Consensus 117 ~V~~kR~~-----------k-----~f~~~S~ei~r~vG~~i~~~~~~~~Vdl~~Pdi~i~vEI~~ 166 (413)
T 2c5s_A 117 KITVHRSY-----------K-----HFPMRTMELLPEIGGHILENTEDITVDVHNPDVNVRVEIRS 166 (413)
T ss_dssp EEEEEECC-----------T-----TCSSCHHHHHHHHHHHHHTTSSSCEECSSSCSEEEEEEECS
T ss_pred EEEEEECC-----------C-----CCCCChHHHHHHHHHHHHHhCCCCeeccCCCCeEEEEEEEe
Confidence 99999999 2 23789999999999999887668899999999999999998
No 4
>3tma_A Methyltransferase; thump domain; 2.05A {Thermus thermophilus}
Probab=96.37 E-value=0.0044 Score=58.80 Aligned_cols=95 Identities=18% Similarity=0.148 Sum_probs=69.4
Q ss_pred ceeEEEeeeeeeEe--e-cC-HHHHHHHHHHHHHhhcccccccCCCCceeEEEEcccCccccccCCCCCCCCccccccCC
Q 020116 179 PVWCHRIFPIQATC--V-LK-EKELQATVSKLVLQFVNDEQNKLSRPVKFAVGYNRRGFEEKQNKIPKDTKDSDVSALLD 254 (331)
Q Consensus 179 tRfi~Rl~PI~~tc--~-A~-~~~i~~~~~~l~~~~F~~~~~~~~~p~tfaI~~~~Rn~~~~e~~~~~~n~~~~~~~~l~ 254 (331)
.|...|++-+-..+ . .+ +++|.+.+..+--..+ ....||+|..++.+ + ..++
T Consensus 70 lR~a~rvl~~~~~~~~~~~~~~~~L~~~~~~~~w~~~-------~~~~tF~V~~~~~~-----------~------~~f~ 125 (354)
T 3tma_A 70 LRLAHHLVLFRARLLLSREDPLGALERAALALPWPEL-------EGAGSFRVEARREG-----------E------HPFT 125 (354)
T ss_dssp CSSCSCEEEEEEEEECCSSSHHHHHHHHHHTSCCTTH-------HHHCCEEEEEEEES-----------C------CSSC
T ss_pred cCCccEEEEEeeeccCCchhhHHHHHHHHHhCchhhc-------CCCCCEEEEEEEcC-----------C------CCCC
Confidence 67777776666666 4 36 7888887765411111 12359999999877 3 5677
Q ss_pred hhHHHHHHHHHhhhcCCCCeeeCCCCCeEEEEEEeeCCCCCCCccEEEEEee
Q 020116 255 RNKCFTIVAAAVKEVVSDSAVDLKSPELSVLVELLPISGLPSELLVVGVSIL 306 (331)
Q Consensus 255 R~~vI~~VA~~V~~~~~~hkVdLknPd~~IlVEV~k~~~~~~~~~v~giSVv 306 (331)
..+|-+.|++.+.... +.+||+++||+.|.|++.+ + .|.+++-
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 8889899998887642 4569999999999999999 8 7877774
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=96.30 E-value=0.01 Score=57.86 Aligned_cols=95 Identities=17% Similarity=0.151 Sum_probs=65.9
Q ss_pred eeEEEeeeeeeEeec-CHHHHHHHHHHH-HHhhcccccccCCCCceeEEEEcccCccccccCCCCCCCCccccccCChhH
Q 020116 180 VWCHRIFPIQATCVL-KEKELQATVSKL-VLQFVNDEQNKLSRPVKFAVGYNRRGFEEKQNKIPKDTKDSDVSALLDRNK 257 (331)
Q Consensus 180 Rfi~Rl~PI~~tc~A-~~~~i~~~~~~l-~~~~F~~~~~~~~~p~tfaI~~~~Rn~~~~e~~~~~~n~~~~~~~~l~R~~ 257 (331)
|-..|++-+-..+.+ +.++|...+..+ +..||+ ...||+|..++++ + ..++..+
T Consensus 64 R~a~RVl~~l~~f~a~~~~~L~~~~~~i~w~~~l~-------~~~tF~V~~~~~~-----------s------~~fss~~ 119 (393)
T 3k0b_A 64 RVADRVKIVVGVFKATTFDELFEKTKALPWEDYLP-------LDAQFPVAGKSVK-----------S------TLYSVPD 119 (393)
T ss_dssp SSCSCEEEEEEEEECSSHHHHHHHHHTSCGGGTCC-------TTCBCCEEEEEES-----------S------SCCCHHH
T ss_pred cceeeEEEEEEEEecCCHHHHHHHHHhCCHHHhCC-------CCCeEEEEEEEec-----------C------CCCCHHH
Confidence 555666655556655 899999988887 567773 4569999987766 3 4555544
Q ss_pred HHHHHHHHh----hhcC-CCCeeeCCCCCeEEEEEEeeCCCCCCCccEEEEEee
Q 020116 258 CFTIVAAAV----KEVV-SDSAVDLKSPELSVLVELLPISGLPSELLVVGVSIL 306 (331)
Q Consensus 258 vI~~VA~~V----~~~~-~~hkVdLknPd~~IlVEV~k~~~~~~~~~v~giSVv 306 (331)
+-..|.++| +... ....||+++||+.|.|++.. + .|-+++=
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 444444444 3321 12379999999999999999 8 8888875
No 6
>3ldg_A Putative uncharacterized protein SMU.472; YPSC, methyltransferase, transferase; HET: SAH; 1.96A {Streptococcus mutans}
Probab=95.81 E-value=0.0095 Score=58.01 Aligned_cols=96 Identities=16% Similarity=0.121 Sum_probs=64.8
Q ss_pred ceeEEEeeeeeeEeec-CHHHHHHHHHHH-HHhhcccccccCCCCceeEE-EEcccCccccccCCCCCCCCccccccCCh
Q 020116 179 PVWCHRIFPIQATCVL-KEKELQATVSKL-VLQFVNDEQNKLSRPVKFAV-GYNRRGFEEKQNKIPKDTKDSDVSALLDR 255 (331)
Q Consensus 179 tRfi~Rl~PI~~tc~A-~~~~i~~~~~~l-~~~~F~~~~~~~~~p~tfaI-~~~~Rn~~~~e~~~~~~n~~~~~~~~l~R 255 (331)
+|-..|++-+-..+.+ +.++|...+..+ +..||+ ...||+| ..++.+ + ..++.
T Consensus 53 ~R~a~RVl~~l~~f~a~~~~~Ly~~~~~i~W~~~l~-------~~~tf~V~~~~~~~-----------s------~~~~s 108 (384)
T 3ldg_A 53 LRSADRIKIVVGEFPARTFEELFQGVYALDWENYLP-------LGCQFPVAKAKSVK-----------S------KLHNE 108 (384)
T ss_dssp CSSCSEEEEEEEEEECSSHHHHHHHHHHSCGGGTCC-------TTCBCCBCCCEEES-----------C------SCCCH
T ss_pred cccceeEEEEEEEEecCCHHHHHHHHHcCCHHHhCC-------CCCeEEEEeeeecC-----------C------CCCCH
Confidence 3566666666666755 899999998887 677773 4569999 765555 2 33443
Q ss_pred hHHH----HHHHHHhhhcC-CCCe--eeCCCCCeEEEEEEeeCCCCCCCccEEEEEee
Q 020116 256 NKCF----TIVAAAVKEVV-SDSA--VDLKSPELSVLVELLPISGLPSELLVVGVSIL 306 (331)
Q Consensus 256 ~~vI----~~VA~~V~~~~-~~hk--VdLknPd~~IlVEV~k~~~~~~~~~v~giSVv 306 (331)
.++- ++|.+.+.... .... ||+++||+.|.|.+.+ + .|-||+=
T Consensus 109 ~~~~~~vkdAi~d~~~~~~~~r~~~~v~~~~pd~~i~v~~~~--~------~~~~~ld 158 (384)
T 3ldg_A 109 PSIQGITKKAIVKKLQHYFHRPDSVPLPENGPEFKIEISLLK--D------QARVMID 158 (384)
T ss_dssp HHHHHHHHHHHHHHHHHHTTCCTTSCCCCCSCBCEEEEEEET--T------EEEEEEE
T ss_pred HHHHHHHHHHHHHHHHHhhCCCCccccCCCCCCEEEEEEEEC--C------EEEEEEe
Confidence 3332 33444444321 1112 9999999999999999 8 8888885
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=95.32 E-value=0.06 Score=56.34 Aligned_cols=99 Identities=17% Similarity=0.195 Sum_probs=68.7
Q ss_pred eeEEEeeeeeeEeec-CHHHHHHHHHHH-HHhhcccccccCCCCceeEEEEcccCccccccCCCCCCCCccccccCChhH
Q 020116 180 VWCHRIFPIQATCVL-KEKELQATVSKL-VLQFVNDEQNKLSRPVKFAVGYNRRGFEEKQNKIPKDTKDSDVSALLDRNK 257 (331)
Q Consensus 180 Rfi~Rl~PI~~tc~A-~~~~i~~~~~~l-~~~~F~~~~~~~~~p~tfaI~~~~Rn~~~~e~~~~~~n~~~~~~~~l~R~~ 257 (331)
|-..|++=.-..+.+ +.++|...+..+ +..||+ ...||+|.++.++ + ...++.+.-..
T Consensus 53 R~a~Rvl~~l~~f~~~~~~~L~~~~~~~~w~~~~~-------~~~tf~V~~~~~~-----------~--~~~~~~~~~~~ 112 (703)
T 3v97_A 53 RLASRIMLPLGECKVYSDLDLYLGVQAINWTEMFN-------PGATFAVHFSGLN-----------D--TIRNSQYGAMK 112 (703)
T ss_dssp SSCSEEEEEEEEEECSSHHHHHHHHHTSCHHHHBC-------TTCCEEEEEECCC-----------S--SCCSHHHHHHH
T ss_pred CceeEEEEEEEEEecCCHHHHHHHHHcCCHHHhCC-------CCceEEEEEEEec-----------C--CcCChHHHHHH
Confidence 556666666666755 899999988887 777883 5569999998877 1 00012222234
Q ss_pred HHHHHHHHhhhcC-CCCeeeCCCCCeEEEEEEeeCCCCCCCccEEEEEee
Q 020116 258 CFTIVAAAVKEVV-SDSAVDLKSPELSVLVELLPISGLPSELLVVGVSIL 306 (331)
Q Consensus 258 vI~~VA~~V~~~~-~~hkVdLknPd~~IlVEV~k~~~~~~~~~v~giSVv 306 (331)
|-++|.+.+.... ....||+++||+.|.|.+.+ + .|-+|+=
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 4456666655431 12369999999999999999 8 8999985
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=95.15 E-value=0.099 Score=50.10 Aligned_cols=95 Identities=26% Similarity=0.248 Sum_probs=65.1
Q ss_pred ceeEEEeeeeeeEeec----------CHHHHHHHHHHH-HHhhcccccccCCCCceeEEEEcccCccccccCCCCCCCCc
Q 020116 179 PVWCHRIFPIQATCVL----------KEKELQATVSKL-VLQFVNDEQNKLSRPVKFAVGYNRRGFEEKQNKIPKDTKDS 247 (331)
Q Consensus 179 tRfi~Rl~PI~~tc~A----------~~~~i~~~~~~l-~~~~F~~~~~~~~~p~tfaI~~~~Rn~~~~e~~~~~~n~~~ 247 (331)
+|..+|++-+-..+.+ +.++|...+..+ +..|| ....||+|..++.+ +
T Consensus 72 ~R~a~rv~~~~~~~~~~~~~~~~~~~~~~~L~~~v~~~~w~~~l-------~~~~tF~V~~~~~~-----------~--- 130 (373)
T 3tm4_A 72 SRLLHRVIIEIASEKFNGIEKDESEEALKRIKDFVSSLPVEQFV-------KVSETFAVRSFRKG-----------D--- 130 (373)
T ss_dssp CSSCSEEEEEEEEEECTTTTTSCHHHHHHHHHHHHHTSCGGGGS-------CTTSEEEEEEEEES-----------S---
T ss_pred hhhHhheEEEEEEeEeccccccccCCCHHHHHHHHHhCCHHHhC-------CCCCcEEEEEEECC-----------C---
Confidence 4777787777666644 577777766654 44455 34569999998877 2
Q ss_pred cccccCChhHHHHHHHHHhh----hcCCCCeeeCCCCCeEEEEEEeeCCCCCCCccEEEEEee
Q 020116 248 DVSALLDRNKCFTIVAAAVK----EVVSDSAVDLKSPELSVLVELLPISGLPSELLVVGVSIL 306 (331)
Q Consensus 248 ~~~~~l~R~~vI~~VA~~V~----~~~~~hkVdLknPd~~IlVEV~k~~~~~~~~~v~giSVv 306 (331)
..++..++-..|.++|. ..+. ..||+++||+.|.|.+.+ + .+-+++-
T Consensus 131 ---~~~~s~~~~~~vk~aIvd~~~~~g~-~~v~~~~p~~~i~~~~~~--d------~~~~~ld 181 (373)
T 3tm4_A 131 ---HNITSIDIARTVGEAIFERLSRFGT-PLVNLDHPAVIFRAELIK--D------VFFLGID 181 (373)
T ss_dssp ---CSSCHHHHHHHHHHHHHHHHHTTSC-CEECSSSCSEEEEEEEET--T------EEEEEEE
T ss_pred ---CcCCHHHHHHHHHHHHHHHHHHhCC-CcccCCCCCeEEEEEEEC--C------EEEEEEE
Confidence 34555455455555543 3222 589999999999999999 8 7777774
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=94.69 E-value=0.091 Score=50.91 Aligned_cols=95 Identities=14% Similarity=0.161 Sum_probs=63.9
Q ss_pred eeEEEeeeeeeEeec-CHHHHHHHHHHH-HHhhcccccccCCCCceeEEE-EcccCccccccCCCCCCCCccccccCChh
Q 020116 180 VWCHRIFPIQATCVL-KEKELQATVSKL-VLQFVNDEQNKLSRPVKFAVG-YNRRGFEEKQNKIPKDTKDSDVSALLDRN 256 (331)
Q Consensus 180 Rfi~Rl~PI~~tc~A-~~~~i~~~~~~l-~~~~F~~~~~~~~~p~tfaI~-~~~Rn~~~~e~~~~~~n~~~~~~~~l~R~ 256 (331)
|...|++-+-..+.+ +.++|...+..+ +..||+ ...||+|. .++++ + ..++..
T Consensus 57 R~a~RVl~~l~~f~~~~~~~L~~~~~~i~w~~~~~-------~~~tf~V~~~~~~~-----------s------~~~~~~ 112 (385)
T 3ldu_A 57 RCAERVHLKIAEFEAKSFDELFENTKRINWSRYIP-------YGAQFPISKASSIK-----------S------KLYSTP 112 (385)
T ss_dssp SSCSCCEEEEEEEECSSHHHHHHHHHTSCGGGTSC-------TTCBCCEEEEEEES-----------S------SCCCHH
T ss_pred CceeEEEEEeeeEecCCHHHHHHHHHhCCHHHhCC-------CCceEEEEeecccC-----------C------CcCcHH
Confidence 555555544455655 899999988877 667773 55699999 77766 3 444443
Q ss_pred HHHHH----HHHHhhhcC-CCCeeeCCCCCeEEEEEEeeCCCCCCCccEEEEEee
Q 020116 257 KCFTI----VAAAVKEVV-SDSAVDLKSPELSVLVELLPISGLPSELLVVGVSIL 306 (331)
Q Consensus 257 ~vI~~----VA~~V~~~~-~~hkVdLknPd~~IlVEV~k~~~~~~~~~v~giSVv 306 (331)
++-.. |.+.+.... ....||+++||+.|.|.+.+ + .|-+++=
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 33333 333333321 22379999999999999999 8 8888875
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=47.93 E-value=11 Score=28.62 Aligned_cols=24 Identities=25% Similarity=0.461 Sum_probs=20.4
Q ss_pred CCCceEEEEeCCChhhhHHHHHHHHHHHh
Q 020116 36 RSHSGFLLTCTIKREKSATKEAISILHKY 64 (331)
Q Consensus 36 ~G~~GilvTC~~grEk~A~~E~~~LLne~ 64 (331)
.-.+|+||+|+. |+++++--||+-
T Consensus 11 ~~~kGvLI~CDp-----a~Kq~Il~lde~ 34 (79)
T 1ydl_A 11 GTRKGMLIECDP-----AMKQFLLYLDES 34 (79)
T ss_dssp CCCCCEEEECCH-----HHHHHHHHHHHT
T ss_pred ccccceEEEeCH-----HHHHHHHHHhcc
Confidence 347899999997 899999888885
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=47.01 E-value=13 Score=27.74 Aligned_cols=22 Identities=23% Similarity=0.348 Sum_probs=19.8
Q ss_pred CceEEEEeCCChhhhHHHHHHHHHHHh
Q 020116 38 HSGFLLTCTIKREKSATKEAISILHKY 64 (331)
Q Consensus 38 ~~GilvTC~~grEk~A~~E~~~LLne~ 64 (331)
.+|+||+|+. |++.++--||+.
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 899999999997
Done!