Query psy4559
Match_columns 336
No_of_seqs 247 out of 1338
Neff 4.4
Searched_HMMs 29240
Date Fri Aug 16 20:08:04 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy4559.a3m -d /work/01045/syshi/HHdatabase/pdb70.hhm -o /work/01045/syshi/hhsearch_pdb/4559hhsearch_pdb -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 1r3e_A TRNA pseudouridine synt 100.0 4E-52 1.4E-56 399.2 15.5 216 56-319 22-238 (309)
2 1k8w_A TRNA pseudouridine synt 100.0 8.7E-51 3E-55 392.5 13.0 223 56-319 44-273 (327)
3 1sgv_A TRNA pseudouridine synt 100.0 7.5E-51 2.6E-55 391.3 6.4 190 56-285 25-219 (316)
4 2apo_A Probable tRNA pseudouri 100.0 1.2E-36 4E-41 297.0 10.2 176 70-319 98-278 (357)
5 3u28_A H/ACA ribonucleoprotein 100.0 2.3E-36 8E-41 298.3 11.2 191 55-319 77-275 (400)
6 2aus_C Pseudouridine synthase; 100.0 2.4E-36 8.2E-41 292.2 10.7 175 70-318 78-258 (334)
7 2v9k_A Uncharacterized protein 98.4 7.3E-07 2.5E-11 91.2 9.9 88 153-269 423-519 (530)
8 1k8w_A TRNA pseudouridine synt 98.4 5.6E-08 1.9E-12 94.2 1.0 82 90-186 116-197 (327)
9 1r3e_A TRNA pseudouridine synt 98.4 5.6E-08 1.9E-12 93.6 0.7 83 90-187 94-176 (309)
10 1sgv_A TRNA pseudouridine synt 98.3 1.6E-07 5.3E-12 90.7 1.6 82 91-187 99-184 (316)
11 2aus_C Pseudouridine synthase; 85.4 0.48 1.6E-05 45.7 3.3 65 91-187 121-185 (334)
12 2apo_A Probable tRNA pseudouri 85.4 0.49 1.7E-05 46.2 3.4 64 91-186 141-204 (357)
13 3u28_A H/ACA ribonucleoprotein 81.4 0.49 1.7E-05 47.0 1.6 66 90-187 134-201 (400)
14 3dh3_A Ribosomal large subunit 74.4 4.8 0.00016 37.8 6.1 55 228-291 174-231 (290)
15 2gml_A Ribosomal large subunit 21.3 1.1E+02 0.0037 27.9 5.0 53 232-291 123-178 (237)
No 1
>1r3e_A TRNA pseudouridine synthase B; RNA modification, pseudouridylation, lyase-RNA complex; HET: FHU; 2.10A {Thermotoga maritima} SCOP: b.122.1.1 d.265.1.2 PDB: 1ze2_A* 2ab4_A* 1ze1_A
Probab=100.00 E-value=4e-52 Score=399.24 Aligned_cols=216 Identities=14% Similarity=0.180 Sum_probs=183.1
Q ss_pred hhhhhhcCcceeEEeeecCCCCccccccccccccCCcchHHHHHhhhhcCC-chhhhhhhccccCchhhhhhhhCCceee
Q psy4559 56 WLSYMKNKKNITVLVSLIDLFVPALLPWQETVTVPSIKPLQKVLKIIDNNN-CLFVHRQAGVRLNSQEAYDVACQGPIRP 134 (336)
Q Consensus 56 ~~~~~~~~~~~~~~~~~lDp~~~gvlP~~~~~~v~~~gkatrvl~~i~g~~-~~~~~~~sgi~tDt~daYe~Ar~G~~~~ 134 (336)
|+..+-+.|.+-- .--|||+|+||||+ |+|+|||+++++.+.. .|..+..+|..|||.|+. |++..
T Consensus 22 ~vrr~l~~kKvGH-~GTLDP~AtGvL~i-------~iG~aTKl~~~l~~~~K~Y~a~~~lG~~TdT~D~e-----G~v~~ 88 (309)
T 1r3e_A 22 EVRKKLKTRKVGH-GGTLDPFACGVLII-------GVNQGTRILEFYKDLKKVYWVKMRLGLITETFDIT-----GEVVE 88 (309)
T ss_dssp HHHHHTTCSCEEE-SSCCCTTCEEEEEE-------EEGGGGGGGGGGTTSCEEEEEEEEETEEESSSBTT-----SCEEE
T ss_pred HHHHHhccceecc-cccCCCCcceeEEE-------EECHHHhHHHHhCccCcEEEEEEEECCcccCCCCC-----CCEEE
Confidence 3333333343333 45689999999999 9999999999998755 677777899999999995 88764
Q ss_pred CCCCCceeecceeeeeCCCCCchhhhhhhccccccceeeecCccchhhhhhhccccccccCChHHHHHHHcCCCcCCCCC
Q psy4559 135 ALLKEPVVYGLKCVHFKPPDFTIGNLYSALLPWQEAVLKITDNNCLFVCLFVHRQAGVRLNSQEAYDIARQGPIRPALLK 214 (336)
Q Consensus 135 t~dreg~I~gielI~~~~~~~t~e~i~~~L~~f~G~i~QvPP~~~k~I~~imp~ySAvKv~GkraYeLAR~G~~ve~~~R 214 (336)
..+..++.++|++++..|+|+|+|+|| | |||+|+||||||||||+|++||+++|
T Consensus 89 ---------------~~~~~~t~~~i~~~l~~f~G~i~Q~PP---------~--~SAvKv~GkraYelAR~G~~ve~~~R 142 (309)
T 1r3e_A 89 ---------------ERECNVTEEEIREAIFSFVGEYDQVPP---------A--YSAKKYKGERLYKLAREGKIINLPPK 142 (309)
T ss_dssp ---------------ECCCCCCHHHHHHHHHSSSEEEEECCC---------S--SSSCEETTEEHHHHHHTTCCCCCCCE
T ss_pred ---------------EecCCCCHHHHHHHHHhccceEEEeCC---------h--HHhcccCCccHHHHHhCCCcccccce
Confidence 233348999999999999999999999 8 99999999999999999999999999
Q ss_pred cceEEEEEEeeecCCeeEEEEEEecCChhhHHHHHHHHHHHcCCceEeceeEEeeEecccCccccccccCChhHHHHHhh
Q psy4559 215 EPVVYGLKCVHFKPPDFTIEVHCIGEYEEFLIRLIYDLGTKLRSAAICTSIQCIRFAQFGLEHSLLRKHWRVQHVIENIA 294 (336)
Q Consensus 215 ~v~Iy~i~ll~~~~p~~~l~V~CSkG~~TYIRSL~~DIG~~LG~~Ahm~~LrRtr~G~F~le~Al~le~~~l~~I~~~i~ 294 (336)
+|+||+|++++|+.|.|+|+|+||+| |||||||||||++|||+|||++||||++|+|++++|+++++|....+.+.+.
T Consensus 143 ~v~I~~i~ll~~~~p~~~~~v~CskG--TYIRsL~~DiG~~Lg~~a~~~~LrRt~~G~f~~~~a~~l~~l~~~~l~~~l~ 220 (309)
T 1r3e_A 143 RVKIFKIWDVNIEGRDVSFRVEVSPG--TYIRSLCMDIGYKLGCGATAVELVRESVGPHTIEESLNVFEAAPEEIENRII 220 (309)
T ss_dssp EEEEEEEEEEEEETTEEEEEEEECTT--CCHHHHHHHHHHHTTSCEEEEEEEEEEETTEEGGGCBCTTTSCHHHHHHHCE
T ss_pred EEEEEEEEEEEeeCCEEEEEEEECCC--chHHHHHHHHHHHhCCCEEEEEEEEEEEcCCcHHHccCHHHHhhchhhcccc
Confidence 99999999999999999999999999 9999999999999999999999999999999999999999997543434455
Q ss_pred hhhhhhcccCCcCCCCceeeeCCCC
Q psy4559 295 HNETLVDKMDPMRPQLQSVNMTDSD 319 (336)
Q Consensus 295 ~~~~lL~~~p~~~~~l~~v~~~~~~ 319 (336)
+++.+|. .+|.+.++|++
T Consensus 221 p~~~~l~-------~~p~v~l~~~~ 238 (309)
T 1r3e_A 221 PLEKCLE-------WLPRVVVHQES 238 (309)
T ss_dssp EGGGSST-------TSCEEECCTTT
T ss_pred CHHHHhc-------CCCeEEeCHHH
Confidence 5555554 45566655543
No 2
>1k8w_A TRNA pseudouridine synthase B; protein-RNA complex, T stem-loop, lyase/RNA complex; HET: FHU; 1.85A {Escherichia coli} SCOP: b.122.1.1 d.265.1.2 PDB: 1zl3_A* 1r3f_A
Probab=100.00 E-value=8.7e-51 Score=392.46 Aligned_cols=223 Identities=20% Similarity=0.301 Sum_probs=184.1
Q ss_pred hhhhhhcCcceeEEeeecCCCCccccccccccccCCcchHHHHHhhhhcCC-chhhhhhhccccCchhhhhhhhCCceee
Q psy4559 56 WLSYMKNKKNITVLVSLIDLFVPALLPWQETVTVPSIKPLQKVLKIIDNNN-CLFVHRQAGVRLNSQEAYDVACQGPIRP 134 (336)
Q Consensus 56 ~~~~~~~~~~~~~~~~~lDp~~~gvlP~~~~~~v~~~gkatrvl~~i~g~~-~~~~~~~sgi~tDt~daYe~Ar~G~~~~ 134 (336)
|+..+-+.|.+- -.--|||+|+||||+ |+|++||+++++.+.. .|..+..+|..|||+|+. |++..
T Consensus 44 ~vr~~l~~kKvG-H~GTLDP~AtGvL~i-------~~G~aTKl~~~l~~~~K~Y~a~~~lG~~TdT~D~e-----G~v~~ 110 (327)
T 1k8w_A 44 KVKRIYNANRAG-HTGALDPLATGMLPI-------CLGEATKFSQYLLDSDKRYRVIARLGQRTDTSDAD-----GQIVE 110 (327)
T ss_dssp HHHHHTTCSCEE-ESSCCCTTCEEEEEE-------EEGGGGGGTHHHHTSCEEEEEEEEETEEESSSBTT-----SCEEE
T ss_pred HHHHhhccceec-cCCCCCCCCeeEEEE-------EECHHHhHHHHhccCCcEEEEEEEECCcccCCCCC-----CCEEe
Confidence 344443444443 356789999999999 9999999999998754 677777799999999995 88764
Q ss_pred CCCCCceeecceeeeeCCCCCchhhhhhhccccccceeeecCccchhhhhhhccccccccCChHHHHHHHcCCCcCCCCC
Q psy4559 135 ALLKEPVVYGLKCVHFKPPDFTIGNLYSALLPWQEAVLKITDNNCLFVCLFVHRQAGVRLNSQEAYDIARQGPIRPALLK 214 (336)
Q Consensus 135 t~dreg~I~gielI~~~~~~~t~e~i~~~L~~f~G~i~QvPP~~~k~I~~imp~ySAvKv~GkraYeLAR~G~~ve~~~R 214 (336)
..+..++.++|++++..|+|+|+|+|| | |||+|+||||||||||+|++||+++|
T Consensus 111 ---------------~~~~~~t~e~i~~~l~~f~G~i~Q~PP---------~--~SAvKv~GkraYelAR~G~~ve~~~R 164 (327)
T 1k8w_A 111 ---------------ERPVTFSAEQLAAALDTFRGDIEQIPS---------M--YSALKYQGKKLYEYARQGIEVPREAR 164 (327)
T ss_dssp ---------------ECCCCCCHHHHHHHHHTTSEEEEECCC---------S--SSCCEETTEEHHHHHHTTCCCCCCCE
T ss_pred ---------------ecCCCCCHHHHHHHHHhccceEEEeCC---------h--hheeccCCccHHHHHhCCCcccccce
Confidence 233358999999999999999999999 8 99999999999999999999999999
Q ss_pred cceEEEEEEeeecCCeeEEEEEEecCChhhHHHHHHHHHHHcCCceEeceeEEeeEecccCccccccccCChhHHHH-H-
Q psy4559 215 EPVVYGLKCVHFKPPDFTIEVHCIGEYEEFLIRLIYDLGTKLRSAAICTSIQCIRFAQFGLEHSLLRKHWRVQHVIE-N- 292 (336)
Q Consensus 215 ~v~Iy~i~ll~~~~p~~~l~V~CSkG~~TYIRSL~~DIG~~LG~~Ahm~~LrRtr~G~F~le~Al~le~~~l~~I~~-~- 292 (336)
+|+||+|++++|+.|.|+|+|+||+| |||||||+|||++|||+|||++||||++|+|++++|+++++|....-.+ .
T Consensus 165 ~v~I~~i~ll~~~~~~~~~~v~CskG--TYIRsL~~DiG~~Lg~~a~~~~LrRt~~G~F~~~~a~~l~~l~~~~~~~~~~ 242 (327)
T 1k8w_A 165 PITVYELLFIRHEGNELELEIHCSKG--TYIRTIIDDLGEKLGCGAHVIYLRRLAVSKYPVERMVTLEHLRELVEQAEQQ 242 (327)
T ss_dssp EEEEEEEEEEEEETTEEEEEEEECTT--CCHHHHHHHHHHHHTSCEEEEEEEEEEETTCCGGGCEEHHHHHHHHHHHHHT
T ss_pred EEEEEEEEEEEeeCCEEEEEEEEcCC--chHHHHHHHHHHHhCCCeEEEEEEEEEEcCCccccccCHHHHHHHHHhhhcc
Confidence 99999999999999999999999999 9999999999999999999999999999999999999888874211000 0
Q ss_pred ----hhhhhhhhcccCCcCCCCceeeeCCCC
Q psy4559 293 ----IAHNETLVDKMDPMRPQLQSVNMTDSD 319 (336)
Q Consensus 293 ----i~~~~~lL~~~p~~~~~l~~v~~~~~~ 319 (336)
-...++.+.+.+.....+|.+.++|++
T Consensus 243 ~~~~~~~l~~~l~p~~~~l~~lp~v~l~~~~ 273 (327)
T 1k8w_A 243 DIPAAELLDPLLMPMDSPASDYPVVNLPLTS 273 (327)
T ss_dssp TSCTHHHHGGGCBCTTGGGTTSCEEEECHHH
T ss_pred cccchhHHhhhccCHHHHHccCCEEEeCHHH
Confidence 011223344555566667777776643
No 3
>1sgv_A TRNA pseudouridine synthase B; hinged motion, tRNA modification, structural genomics, PSI, structure initiative; 1.90A {Mycobacterium tuberculosis} SCOP: b.122.1.1 d.265.1.2
Probab=100.00 E-value=7.5e-51 Score=391.34 Aligned_cols=190 Identities=15% Similarity=0.253 Sum_probs=139.5
Q ss_pred hhhhhhcCcceeEEeeecCCCCccccccccccccCCcchHHHHHhhhhcCC-chhhhhhhccccCchhhhhhhhCCceee
Q psy4559 56 WLSYMKNKKNITVLVSLIDLFVPALLPWQETVTVPSIKPLQKVLKIIDNNN-CLFVHRQAGVRLNSQEAYDVACQGPIRP 134 (336)
Q Consensus 56 ~~~~~~~~~~~~~~~~~lDp~~~gvlP~~~~~~v~~~gkatrvl~~i~g~~-~~~~~~~sgi~tDt~daYe~Ar~G~~~~ 134 (336)
|+..+-+.|.+- -.--|||+|+||||+ |+|+|||+++++.+.. .|..+..+|..|||+|+. |++..
T Consensus 25 ~vrr~l~~kKvG-H~GTLDP~AtGvL~i-------~iG~aTKl~~~l~~~~K~Y~~~~~lG~~TdT~D~e-----G~v~~ 91 (316)
T 1sgv_A 25 RCRRIFATRRVG-HAGTLDPMATGVLVI-------GIERATKILGLLTAAPKSYAATIRLGQTTSTEDAE-----GQVLQ 91 (316)
T ss_dssp HHHHHTTCSCEE-ESSCCCTTCEEEEEE-------EEGGGGGGGGGTTTSCEEEEEEEEETEEETTSBTT-----SCEEE
T ss_pred HHHHHhcccccc-ccccCCCCCeEEEEE-------EECHHHhHHHHhCcCCcEEEEEEEECCccCCCCCC-----CCEEE
Confidence 344443444443 345689999999999 9999999999998754 677777899999999995 88764
Q ss_pred CCCCCceeecceeeeeCCCCCchhhhhhhccccccceeeecCccchhhhhhhccccccccCChHHHHHHHcCCCcCCCCC
Q psy4559 135 ALLKEPVVYGLKCVHFKPPDFTIGNLYSALLPWQEAVLKITDNNCLFVCLFVHRQAGVRLNSQEAYDIARQGPIRPALLK 214 (336)
Q Consensus 135 t~dreg~I~gielI~~~~~~~t~e~i~~~L~~f~G~i~QvPP~~~k~I~~imp~ySAvKv~GkraYeLAR~G~~ve~~~R 214 (336)
+ .+..+++.++|++++..|+|+|+|+|| | |||+|+||||||||||+|++||+++|
T Consensus 92 ~--------------~~~~~~t~~~i~~~l~~f~G~i~Q~PP---------~--ySAvKv~GkrlYelAR~G~~ve~~~R 146 (316)
T 1sgv_A 92 S--------------VPAKHLTIEAIDAAMERLRGEIRQVPS---------S--VSAIKVGGRRAYRLARQGRSVQLEAR 146 (316)
T ss_dssp E--------------CCCTTCCHHHHHHHHHHTCEEC---------------------------------------CCCC
T ss_pred e--------------cCCCCCCHHHHHHHHHhccccEEEeCC---------H--HHhcccCChhHHHHHhCCCcccccce
Confidence 2 222358999999999999999999999 8 99999999999999999999999999
Q ss_pred cceEEEEEEeeec----CCeeEEEEEEecCChhhHHHHHHHHHHHcCCceEeceeEEeeEecccCccccccccCC
Q psy4559 215 EPVVYGLKCVHFK----PPDFTIEVHCIGEYEEFLIRLIYDLGTKLRSAAICTSIQCIRFAQFGLEHSLLRKHWR 285 (336)
Q Consensus 215 ~v~Iy~i~ll~~~----~p~~~l~V~CSkG~~TYIRSL~~DIG~~LG~~Ahm~~LrRtr~G~F~le~Al~le~~~ 285 (336)
+|+||+|++++|+ .|.++|+|+|||| |||||||||||++|||+|||++||||++|+|++++|+++++|.
T Consensus 147 ~v~I~~i~ll~~~~~~~~p~~~~~v~CskG--TYIRsLa~DiG~~Lg~~a~~~~LrRt~~G~F~~~~a~tl~~l~ 219 (316)
T 1sgv_A 147 PIRIDRFELLAARRRDQLIDIDVEIDCSSG--TYIRALARDLGDALGVGGHVTALRRTRVGRFELDQARSLDDLA 219 (316)
T ss_dssp CCEEEEEEEEEEEEETTEEEEEEEEEESCC--TTHHHHHHHHHHHHTSCEEEEEEEEEEETTEEGGGCBCHHHHH
T ss_pred EEEEEEEEEEEeeccCCCceEEEEEEECCC--CcHHHHHHHHHHHhCCCEEEeeEEEEEEccCcHHHccCHHHHh
Confidence 9999999999985 3899999999999 9999999999999999999999999999999999998877764
No 4
>2apo_A Probable tRNA pseudouridine synthase B; protein-protein complex, box H/ACA, snoRNP, pseudouridine synthase, RNA modification; 1.95A {Methanocaldococcus jannaschii} SCOP: b.122.1.1 d.265.1.2
Probab=100.00 E-value=1.2e-36 Score=296.99 Aligned_cols=176 Identities=14% Similarity=0.166 Sum_probs=130.0
Q ss_pred eeecCCCCccccccccccccCCcchHHHHHhhhhcCC-chhhhhhhccccCchhhhhhhhCCceeeCCCCCceeecceee
Q psy4559 70 VSLIDLFVPALLPWQETVTVPSIKPLQKVLKIIDNNN-CLFVHRQAGVRLNSQEAYDVACQGPIRPALLKEPVVYGLKCV 148 (336)
Q Consensus 70 ~~~lDp~~~gvlP~~~~~~v~~~gkatrvl~~i~g~~-~~~~~~~sgi~tDt~daYe~Ar~G~~~~t~dreg~I~gielI 148 (336)
.--|||+|+||||+ |+|+|||+++++.+.. .+.....+| .
T Consensus 98 ~GTLDP~AtGvL~v-------~~G~aTk~~~~l~~~~K~Y~~~~~lG---------------~----------------- 138 (357)
T 2apo_A 98 GGTLDPKVTGVLPV-------ALERATKTIPMWHIPPKEYVCLMHLH---------------R----------------- 138 (357)
T ss_dssp SSCCCTTCEEEEEE-------EEGGGGGGGGGTTSSCEEEEEEEEES---------------S-----------------
T ss_pred ccccCCCceeEEEE-------EeCHHHhHHHHhccCCcEEEEEEEEC---------------C-----------------
Confidence 45689999999999 9999999999998643 344332232 1
Q ss_pred eeCCCCCchhhhhhhccccccceeeecCccchhhhhhhccccccccCChHHHHHHHcCCCcCCCCCcceEEEEEEeeecC
Q psy4559 149 HFKPPDFTIGNLYSALLPWQEAVLKITDNNCLFVCLFVHRQAGVRLNSQEAYDIARQGPIRPALLKEPVVYGLKCVHFKP 228 (336)
Q Consensus 149 ~~~~~~~t~e~i~~~L~~f~G~i~QvPP~~~k~I~~imp~ySAvKv~GkraYeLAR~G~~ve~~~R~v~Iy~i~ll~~~~ 228 (336)
.++.++|++++..|+|+|.|+|| | |||+| +++|+++||+|++++|+.
T Consensus 139 -----~~~~~~i~~~l~~f~G~i~Q~PP---------~--~SAvK-----------------~~~R~v~I~~~~l~~~~~ 185 (357)
T 2apo_A 139 -----DASEEDILRVFKEFTGRIYQRPP---------L--KAAVK-----------------RRLRIRKIHELELLDKDG 185 (357)
T ss_dssp -----CCCHHHHHHHHHHHSEEEECC---------------------------------------CEEEEEEEEEEEEET
T ss_pred -----CCCHHHHHHHHHhCcccEEEeCC---------c--hhhcc-----------------ccccceeEEEEEEEEeeC
Confidence 25789999999999999999999 8 99999 357999999999999999
Q ss_pred CeeEEEEEEecCChhhHHHHHHHHHHHcCCceEeceeEEeeEecccCccccccccCChhH-HHHH---hhhhhhhhcccC
Q psy4559 229 PDFTIEVHCIGEYEEFLIRLIYDLGTKLRSAAICTSIQCIRFAQFGLEHSLLRKHWRVQH-VIEN---IAHNETLVDKMD 304 (336)
Q Consensus 229 p~~~l~V~CSkG~~TYIRSL~~DIG~~LG~~Ahm~~LrRtr~G~F~le~Al~le~~~l~~-I~~~---i~~~~~lL~~~p 304 (336)
|.++|+|+||+| |||||||+|||.+|||+|||++||||++|+|++++|++++++.... +..+ -...++++.+.+
T Consensus 186 ~~~~~~v~cs~G--TYIRsL~~DiG~~LG~~a~~~~LrRt~~G~f~~~~a~tl~~l~~~~~~~~~~g~~~~l~~~l~P~e 263 (357)
T 2apo_A 186 KDVLFRVKCQSG--TYIRKLCEDIGEALGTSAHMQELRRTKSGCFEEKDAVYLQDLLDAYVFWKEDGDEEELRRVIKPME 263 (357)
T ss_dssp TEEEEEEEECTT--CCHHHHHHHHHHHTTSCEEEEEEEEEEETTEEGGGCBCHHHHHHHHHHHHTSCCCHHHHHHEEEGG
T ss_pred CEEEEEEEECCC--chHHHHHHHHHHhhCCCEEEEEEEEEEEccCcHHHccCHHHHHhhhhhhhccCchhhHhhheeChh
Confidence 999999999999 9999999999999999999999999999999999998766653110 0000 001223344445
Q ss_pred CcCCCCceeeeCCCC
Q psy4559 305 PMRPQLQSVNMTDSD 319 (336)
Q Consensus 305 ~~~~~l~~v~~~~~~ 319 (336)
.....+|.|.++|++
T Consensus 264 ~~l~~lP~v~l~~~~ 278 (357)
T 2apo_A 264 YGLRHLKKVVVKDSA 278 (357)
T ss_dssp GGGTTSEEEEECHHH
T ss_pred HhhccCcEEEECHHH
Confidence 555567777776654
No 5
>3u28_A H/ACA ribonucleoprotein complex subunit 4; pseudouridine synthase, pseudouridylation, H/ACA RNA; 1.90A {Saccharomyces cerevisiae} PDB: 3uai_A
Probab=100.00 E-value=2.3e-36 Score=298.33 Aligned_cols=191 Identities=12% Similarity=0.127 Sum_probs=138.7
Q ss_pred hhhhhhhcCcceeEEeeecCCCCccccccccccccCCcchHHHHHhhhhcCC-chhhhhhhccccCchhhhhhhhCCcee
Q psy4559 55 GWLSYMKNKKNITVLVSLIDLFVPALLPWQETVTVPSIKPLQKVLKIIDNNN-CLFVHRQAGVRLNSQEAYDVACQGPIR 133 (336)
Q Consensus 55 ~~~~~~~~~~~~~~~~~~lDp~~~gvlP~~~~~~v~~~gkatrvl~~i~g~~-~~~~~~~sgi~tDt~daYe~Ar~G~~~ 133 (336)
.|+..+-+.+.+- -.--|||+|+||||+ |+|+|||+++++.+.. .+..+..+| ..
T Consensus 77 ~~vrr~l~~kKvG-H~GTLDP~AtGvL~v-------~iG~aTKl~~~l~~~~K~Y~a~~~lG---------------~~- 132 (400)
T 3u28_A 77 AWIKRILRCEKTG-HSGTLDPKVTGCLIV-------CIDRATRLVKSQQGAGKEYVCIVRLH---------------DA- 132 (400)
T ss_dssp HHHHHHHTCSCEE-ESSCCCTTCEEEEEE-------EEGGGGGGHHHHHHSCEEEEEEEEES---------------SC-
T ss_pred HHHHHHhCcCccc-ccCCCCCCCeEEEEE-------EEChHHhHhHHhcCCCcEEEEEEEeC---------------CC-
Confidence 3444444444332 235699999999999 9999999999998644 344443233 21
Q ss_pred eCCCCCceeecceeeeeCCCCCchhhhhhhccccccceeeecCccchhhhhhhccccccccCChHHHHHHHcCCCcCCCC
Q psy4559 134 PALLKEPVVYGLKCVHFKPPDFTIGNLYSALLPWQEAVLKITDNNCLFVCLFVHRQAGVRLNSQEAYDIARQGPIRPALL 213 (336)
Q Consensus 134 ~t~dreg~I~gielI~~~~~~~t~e~i~~~L~~f~G~i~QvPP~~~k~I~~imp~ySAvKv~GkraYeLAR~G~~ve~~~ 213 (336)
..+.++|++++..|+|+|.|+|| | |||+|++ +
T Consensus 133 --------------------~~~~~~i~~~l~~f~G~i~Q~PP---------~--ySAvK~~-----------------~ 164 (400)
T 3u28_A 133 --------------------LKDEKDLGRSLENLTGALFQRPP---------L--ISAVKRQ-----------------L 164 (400)
T ss_dssp --------------------CSSTTHHHHHHHHTCEEEEECCC----------------CCC-----------------C
T ss_pred --------------------CCCHHHHHHHHHhCcCceEEECC---------c--eecccCC-----------------c
Confidence 12678999999999999999999 8 9999953 6
Q ss_pred CcceEEEEEEeeecC--CeeEEEEEEecCChhhHHHHHHHHHHHcCCceEeceeEEeeEecccCccc-cccccCChh-HH
Q psy4559 214 KEPVVYGLKCVHFKP--PDFTIEVHCIGEYEEFLIRLIYDLGTKLRSAAICTSIQCIRFAQFGLEHS-LLRKHWRVQ-HV 289 (336)
Q Consensus 214 R~v~Iy~i~ll~~~~--p~~~l~V~CSkG~~TYIRSL~~DIG~~LG~~Ahm~~LrRtr~G~F~le~A-l~le~~~l~-~I 289 (336)
|+++||+|++++|+. |.++|+|+||+| |||||||||||.+|||+|||++||||++|+|++++| ++++++... ..
T Consensus 165 R~v~I~~i~ll~~~~~~~~~~~~V~CskG--TYIRsL~~DiG~~LG~gahm~~LrRt~~G~F~~~~a~vtL~~l~~~~~~ 242 (400)
T 3u28_A 165 RVRTIYESNLIEFDNKRNLGVFWASCEAG--TYMRTLCVHLGMLLGVGGHMQELRRVRSGALSENDNMVTLHDVMDAQWV 242 (400)
T ss_dssp EEEEEEEEEEEEEETTTTEEEEEEEECTT--CCHHHHHHHHHHHHSSCEEEEEEEEEEETTEETTSSCBCHHHHHHHHHH
T ss_pred eeEEEEEEEEEEEcCCCceEEEEEEECCC--CCHHHHHHHHHHHHCCCEEEEEEEEEEEcCcchhhhcCCHHHHHHhhhh
Confidence 899999999999976 789999999999 999999999999999999999999999999999986 565554211 00
Q ss_pred HHHhh---hhhhhhcccCCcCCCCceeeeCCCC
Q psy4559 290 IENIA---HNETLVDKMDPMRPQLQSVNMTDSD 319 (336)
Q Consensus 290 ~~~i~---~~~~lL~~~p~~~~~l~~v~~~~~~ 319 (336)
.++.. ..++++.+.+.....+|.|.+.|++
T Consensus 243 ~~~~~~~~~l~~~l~P~e~~l~~lp~V~L~dea 275 (400)
T 3u28_A 243 YDNTRDESYLRSIIQPLETLLVGYKRIVVKDSA 275 (400)
T ss_dssp HHHHCCCHHHHHHCEEGGGGGTTSCEEEECHHH
T ss_pred hhcccchhhHhhhcCCHHHHHhhCCccccCHHH
Confidence 11111 1233454555566667777776654
No 6
>2aus_C Pseudouridine synthase; isomerase, structural protein, isomerase-structural protein; 2.10A {Pyrococcus abyssi} PDB: 3lwr_A 3lwo_A* 3lwq_A* 3lwp_A 3lwv_A 3hax_A* 2hvy_A* 3hay_A* 2ey4_A 2rfk_A 3mqk_A 3hjw_A* 3hjy_A
Probab=100.00 E-value=2.4e-36 Score=292.22 Aligned_cols=175 Identities=13% Similarity=0.167 Sum_probs=127.1
Q ss_pred eeecCCCCccccccccccccCCcchHHHHHhhhhcCC-chhhhhhhccccCchhhhhhhhCCceeeCCCCCceeecceee
Q psy4559 70 VSLIDLFVPALLPWQETVTVPSIKPLQKVLKIIDNNN-CLFVHRQAGVRLNSQEAYDVACQGPIRPALLKEPVVYGLKCV 148 (336)
Q Consensus 70 ~~~lDp~~~gvlP~~~~~~v~~~gkatrvl~~i~g~~-~~~~~~~sgi~tDt~daYe~Ar~G~~~~t~dreg~I~gielI 148 (336)
.--|||+|+||||+ |+|+|||+++++.+.. .+.....+| .
T Consensus 78 ~GTLDP~atGvL~v-------~~g~aTk~~~~l~~~~K~Y~~~~~lg---------------~----------------- 118 (334)
T 2aus_C 78 GGTLDPKVSGVLPV-------ALERATRVVQALLPAGKEYVALMHLH---------------G----------------- 118 (334)
T ss_dssp SSCCCTTCEEEEEE-------EEGGGGGGGGGGTTCCEEEEEEEEES---------------S-----------------
T ss_pred ccccCCccceeEEE-------EeChhhhhHHHhcccCcEEEEEEEEC---------------C-----------------
Confidence 45689999999999 9999999999998643 343332222 1
Q ss_pred eeCCCCCchhhhhhhccccccceeeecCccchhhhhhhccccccccCChHHHHHHHcCCCcCCCCCcceEEEEEEeeecC
Q psy4559 149 HFKPPDFTIGNLYSALLPWQEAVLKITDNNCLFVCLFVHRQAGVRLNSQEAYDIARQGPIRPALLKEPVVYGLKCVHFKP 228 (336)
Q Consensus 149 ~~~~~~~t~e~i~~~L~~f~G~i~QvPP~~~k~I~~imp~ySAvKv~GkraYeLAR~G~~ve~~~R~v~Iy~i~ll~~~~ 228 (336)
+++.++|++++..|+|+|+|+|| | |||+| +++|+++||+|++++|+.
T Consensus 119 -----~~~~~~i~~~l~~f~G~i~Q~pP---------~--~SA~k-----------------~~~R~v~I~~~~~~~~~~ 165 (334)
T 2aus_C 119 -----DVPEDKIRAVMKEFEGEIIQRPP---------L--RSAVK-----------------RRLRTRKVYYIEILEIDG 165 (334)
T ss_dssp -----CCCHHHHHHHHHHTSEEEECC----------------------------------------EEEEEEEEEEEEET
T ss_pred -----CCCHHHHHHHHHhCcCeEEEeCC---------c--cccCc-----------------CCcCCEEEEEEEEEEeeC
Confidence 25789999999999999999999 8 99999 357999999999999999
Q ss_pred CeeEEEEEEecCChhhHHHHHHHHHHHcCCceEeceeEEeeEecccCcc-ccccccCChhH-HHHH---hhhhhhhhccc
Q psy4559 229 PDFTIEVHCIGEYEEFLIRLIYDLGTKLRSAAICTSIQCIRFAQFGLEH-SLLRKHWRVQH-VIEN---IAHNETLVDKM 303 (336)
Q Consensus 229 p~~~l~V~CSkG~~TYIRSL~~DIG~~LG~~Ahm~~LrRtr~G~F~le~-Al~le~~~l~~-I~~~---i~~~~~lL~~~ 303 (336)
|.++|+|+||+| |||||||||||.+|||+|||++||||++|+|++++ |++++++.... ..+. -...++++.+.
T Consensus 166 ~~~~~~v~cs~G--TYIRsL~~Dig~~Lg~~a~~~~LrRt~~g~f~~~~~~~~l~~l~~~~~~~~~~~~~~~~~~~l~p~ 243 (334)
T 2aus_C 166 RDVLFRVGVEAG--TYIRSLIHHIGLALGVGAHMAELRRTRSGPFKEDETLVTLHDLVDYYHFWKEDGIEEYIRKAIQPM 243 (334)
T ss_dssp TEEEEEEEECTT--CCHHHHHHHHHHHHSSCEEEEEEEEEEETTEESSTTEECHHHHHHHHHHHHTTCCCHHHHHHSEEG
T ss_pred CeEEEEEEECCC--cHHHHHHHHHHHHhCCCEEEeEEEEEEEccCchhhcccCHHHHHhhhhhhccccchhhhhhhccCh
Confidence 999999999999 99999999999999999999999999999999999 68766653110 0000 00112233344
Q ss_pred CCcCCCCceeeeCCC
Q psy4559 304 DPMRPQLQSVNMTDS 318 (336)
Q Consensus 304 p~~~~~l~~v~~~~~ 318 (336)
+.....+|.|.+++.
T Consensus 244 ~~~l~~~p~V~L~de 258 (334)
T 2aus_C 244 EKAVEHLPKIWIKDS 258 (334)
T ss_dssp GGGGTTSCEEEECHH
T ss_pred hHhcccccEEEECHH
Confidence 455555667766654
No 7
>2v9k_A Uncharacterized protein FLJ32312; pseudouridine synthase, PUS10, RNA modification, thump domai; HET: EPE; 2.0A {Homo sapiens}
Probab=98.41 E-value=7.3e-07 Score=91.17 Aligned_cols=88 Identities=11% Similarity=0.151 Sum_probs=72.1
Q ss_pred CCCchhhhhhhcccccc-ceeeecCccchhhhhhhccccccccCChHHHHHHHcCCCcCCCCCcceEEEEEEeeecCCee
Q psy4559 153 PDFTIGNLYSALLPWQE-AVLKITDNNCLFVCLFVHRQAGVRLNSQEAYDIARQGPIRPALLKEPVVYGLKCVHFKPPDF 231 (336)
Q Consensus 153 ~~~t~e~i~~~L~~f~G-~i~QvPP~~~k~I~~imp~ySAvKv~GkraYeLAR~G~~ve~~~R~v~Iy~i~ll~~~~p~~ 231 (336)
..++.++++++.. |.| .|.|-|| . + ++. | +....|.=+||++++..++...|
T Consensus 423 ~~v~~e~l~~~~~-l~~l~I~QrtP---------~-R-V~h-----------R----R~~~~R~R~I~~i~~~~~~~~~~ 475 (530)
T 2v9k_A 423 KAIQKKDIEFLND-IKDLKIDQKTP---------L-R-VLH-----------R----RPLAVRARVIHFMETQYVDEHHF 475 (530)
T ss_dssp SCCCHHHHGGGGG-CCSEEEEEECC---------G-G-GTT-----------T----SCCCEEEEEEEEEEEEEEETTEE
T ss_pred CCCCHHHHHHHHh-cCCceeeccCC---------e-E-EEE-----------e----cCCCccceEEEEEEEEEecCCEE
Confidence 3578899988877 999 8999999 2 0 111 1 22234777899999999999999
Q ss_pred EEEEEEecCChhhHHHHHH-H-------HHHHcCCceEeceeEEee
Q psy4559 232 TIEVHCIGEYEEFLIRLIY-D-------LGTKLRSAAICTSIQCIR 269 (336)
Q Consensus 232 ~l~V~CSkG~~TYIRSL~~-D-------IG~~LG~~Ahm~~LrRtr 269 (336)
.++|.|..| ||||.||| | ||..||++|+|.+|==+.
T Consensus 476 ~l~i~~eaG--tYIKelvhGD~GRT~Psl~~lLg~~a~i~eLDV~~ 519 (530)
T 2v9k_A 476 RLHLKTQAG--TYIKEFVHGDFGRTKPNIGSLMNVTADILELDVES 519 (530)
T ss_dssp EEEEEECTT--CCHHHHHHCTTTTEESCHHHHHTSCEEEEEEEEEE
T ss_pred EEEEEecCC--CEEEEEEcCCCCCcCCcHHHHhCCCcEEEEeEEeE
Confidence 999999999 99999999 7 999999999999986443
No 8
>1k8w_A TRNA pseudouridine synthase B; protein-RNA complex, T stem-loop, lyase/RNA complex; HET: FHU; 1.85A {Escherichia coli} SCOP: b.122.1.1 d.265.1.2 PDB: 1zl3_A* 1r3f_A
Probab=98.38 E-value=5.6e-08 Score=94.20 Aligned_cols=82 Identities=13% Similarity=0.180 Sum_probs=74.2
Q ss_pred CCcchHHHHHhhhhcCCchhhhhhhccccCchhhhhhhhCCceeeCCCCCceeecceeeeeCCCCCchhhhhhhcccccc
Q psy4559 90 PSIKPLQKVLKIIDNNNCLFVHRQAGVRLNSQEAYDVACQGPIRPALLKEPVVYGLKCVHFKPPDFTIGNLYSALLPWQE 169 (336)
Q Consensus 90 ~~~gkatrvl~~i~g~~~~~~~~~sgi~tDt~daYe~Ar~G~~~~t~dreg~I~gielI~~~~~~~t~e~i~~~L~~f~G 169 (336)
+..+++++++..|+|..+|.+|+|||++.+|+++|++||+|+..+...|+..|++++++++..+.++.+
T Consensus 116 ~t~e~i~~~l~~f~G~i~Q~PP~~SAvKv~GkraYelAR~G~~ve~~~R~v~I~~i~ll~~~~~~~~~~----------- 184 (327)
T 1k8w_A 116 FSAEQLAAALDTFRGDIEQIPSMYSALKYQGKKLYEYARQGIEVPREARPITVYELLFIRHEGNELELE----------- 184 (327)
T ss_dssp CCHHHHHHHHHTTSEEEEECCCSSSCCEETTEEHHHHHHTTCCCCCCCEEEEEEEEEEEEEETTEEEEE-----------
T ss_pred CCHHHHHHHHHhccceEEEeCChhheeccCCccHHHHHhCCCcccccceEEEEEEEEEEEeeCCEEEEE-----------
Confidence 367899999999999999999999999999999999999999999999999999999999987766665
Q ss_pred ceeeecCccchhhhhhh
Q psy4559 170 AVLKITDNNCLFVCLFV 186 (336)
Q Consensus 170 ~i~QvPP~~~k~I~~im 186 (336)
+.+. .++||+++.
T Consensus 185 -v~Cs---kGTYIRsL~ 197 (327)
T 1k8w_A 185 -IHCS---KGTYIRTII 197 (327)
T ss_dssp -EEEC---TTCCHHHHH
T ss_pred -EEEc---CCchHHHHH
Confidence 6665 678999997
No 9
>1r3e_A TRNA pseudouridine synthase B; RNA modification, pseudouridylation, lyase-RNA complex; HET: FHU; 2.10A {Thermotoga maritima} SCOP: b.122.1.1 d.265.1.2 PDB: 1ze2_A* 2ab4_A* 1ze1_A
Probab=98.37 E-value=5.6e-08 Score=93.55 Aligned_cols=83 Identities=10% Similarity=0.075 Sum_probs=74.2
Q ss_pred CCcchHHHHHhhhhcCCchhhhhhhccccCchhhhhhhhCCceeeCCCCCceeecceeeeeCCCCCchhhhhhhcccccc
Q psy4559 90 PSIKPLQKVLKIIDNNNCLFVHRQAGVRLNSQEAYDVACQGPIRPALLKEPVVYGLKCVHFKPPDFTIGNLYSALLPWQE 169 (336)
Q Consensus 90 ~~~gkatrvl~~i~g~~~~~~~~~sgi~tDt~daYe~Ar~G~~~~t~dreg~I~gielI~~~~~~~t~e~i~~~L~~f~G 169 (336)
+..+++++++..|+|..+|.+|+||+++.+|+++|++||+|+..+...|+..|++++++++..+.++.+
T Consensus 94 ~t~~~i~~~l~~f~G~i~Q~PP~~SAvKv~GkraYelAR~G~~ve~~~R~v~I~~i~ll~~~~p~~~~~----------- 162 (309)
T 1r3e_A 94 VTEEEIREAIFSFVGEYDQVPPAYSAKKYKGERLYKLAREGKIINLPPKRVKIFKIWDVNIEGRDVSFR----------- 162 (309)
T ss_dssp CCHHHHHHHHHSSSEEEEECCCSSSSCEETTEEHHHHHHTTCCCCCCCEEEEEEEEEEEEEETTEEEEE-----------
T ss_pred CCHHHHHHHHHhccceEEEeCChHHhcccCCccHHHHHhCCCcccccceEEEEEEEEEEEeeCCEEEEE-----------
Confidence 367899999999999999999999999999999999999999999999999999999999987766665
Q ss_pred ceeeecCccchhhhhhhc
Q psy4559 170 AVLKITDNNCLFVCLFVH 187 (336)
Q Consensus 170 ~i~QvPP~~~k~I~~imp 187 (336)
+.+. .++||+++..
T Consensus 163 -v~Cs---kGTYIRsL~~ 176 (309)
T 1r3e_A 163 -VEVS---PGTYIRSLCM 176 (309)
T ss_dssp -EEEC---TTCCHHHHHH
T ss_pred -EEEC---CCchHHHHHH
Confidence 6665 6789998873
No 10
>1sgv_A TRNA pseudouridine synthase B; hinged motion, tRNA modification, structural genomics, PSI, structure initiative; 1.90A {Mycobacterium tuberculosis} SCOP: b.122.1.1 d.265.1.2
Probab=98.28 E-value=1.6e-07 Score=90.73 Aligned_cols=82 Identities=9% Similarity=0.135 Sum_probs=43.3
Q ss_pred CcchHHHHHhhhhcCCchhhhhhhccccCchhhhhhhhCCceeeCCCCCceeecceeeeeCC----CCCchhhhhhhccc
Q psy4559 91 SIKPLQKVLKIIDNNNCLFVHRQAGVRLNSQEAYDVACQGPIRPALLKEPVVYGLKCVHFKP----PDFTIGNLYSALLP 166 (336)
Q Consensus 91 ~~gkatrvl~~i~g~~~~~~~~~sgi~tDt~daYe~Ar~G~~~~t~dreg~I~gielI~~~~----~~~t~e~i~~~L~~ 166 (336)
..+++++++..|+|..+|.+|+||+++.||+++|++||+|+..+...|+..|++++++++.. +.++.+
T Consensus 99 t~~~i~~~l~~f~G~i~Q~PP~ySAvKv~GkrlYelAR~G~~ve~~~R~v~I~~i~ll~~~~~~~~p~~~~~-------- 170 (316)
T 1sgv_A 99 TIEAIDAAMERLRGEIRQVPSSVSAIKVGGRRAYRLARQGRSVQLEARPIRIDRFELLAARRRDQLIDIDVE-------- 170 (316)
T ss_dssp CHHHHHHHHHHTCEEC----------------------------CCCCCCEEEEEEEEEEEEETTEEEEEEE--------
T ss_pred CHHHHHHHHHhccccEEEeCCHHHhcccCChhHHHHHhCCCcccccceEEEEEEEEEEEeeccCCCceEEEE--------
Confidence 57899999999999999999999999999999999999999999999999999999999852 233333
Q ss_pred cccceeeecCccchhhhhhhc
Q psy4559 167 WQEAVLKITDNNCLFVCLFVH 187 (336)
Q Consensus 167 f~G~i~QvPP~~~k~I~~imp 187 (336)
+.+. .++|||++..
T Consensus 171 ----v~Cs---kGTYIRsLa~ 184 (316)
T 1sgv_A 171 ----IDCS---SGTYIRALAR 184 (316)
T ss_dssp ----EEES---CCTTHHHHHH
T ss_pred ----EEEC---CCCcHHHHHH
Confidence 6665 6789998874
No 11
>2aus_C Pseudouridine synthase; isomerase, structural protein, isomerase-structural protein; 2.10A {Pyrococcus abyssi} PDB: 3lwr_A 3lwo_A* 3lwq_A* 3lwp_A 3lwv_A 3hax_A* 2hvy_A* 3hay_A* 2ey4_A 2rfk_A 3mqk_A 3hjw_A* 3hjy_A
Probab=85.38 E-value=0.48 Score=45.67 Aligned_cols=65 Identities=14% Similarity=0.157 Sum_probs=43.0
Q ss_pred CcchHHHHHhhhhcCCchhhhhhhccccCchhhhhhhhCCceeeCCCCCceeecceeeeeCCCCCchhhhhhhccccccc
Q psy4559 91 SIKPLQKVLKIIDNNNCLFVHRQAGVRLNSQEAYDVACQGPIRPALLKEPVVYGLKCVHFKPPDFTIGNLYSALLPWQEA 170 (336)
Q Consensus 91 ~~gkatrvl~~i~g~~~~~~~~~sgi~tDt~daYe~Ar~G~~~~t~dreg~I~gielI~~~~~~~t~e~i~~~L~~f~G~ 170 (336)
..+++++++..|+|..+|.+|+||+++. . .|+..|++++++++..+.++.+
T Consensus 121 ~~~~i~~~l~~f~G~i~Q~pP~~SA~k~------------~-----~R~v~I~~~~~~~~~~~~~~~~------------ 171 (334)
T 2aus_C 121 PEDKIRAVMKEFEGEIIQRPPLRSAVKR------------R-----LRTRKVYYIEILEIDGRDVLFR------------ 171 (334)
T ss_dssp CHHHHHHHHHHTSEEEECC-----------------------------EEEEEEEEEEEEETTEEEEE------------
T ss_pred CHHHHHHHHHhCcCeEEEeCCccccCcC------------C-----cCCEEEEEEEEEEeeCCeEEEE------------
Confidence 5789999999999999999999999992 1 2456899999999976655554
Q ss_pred eeeecCccchhhhhhhc
Q psy4559 171 VLKITDNNCLFVCLFVH 187 (336)
Q Consensus 171 i~QvPP~~~k~I~~imp 187 (336)
+.+. .++||+++..
T Consensus 172 v~cs---~GTYIRsL~~ 185 (334)
T 2aus_C 172 VGVE---AGTYIRSLIH 185 (334)
T ss_dssp EEEC---TTCCHHHHHH
T ss_pred EEEC---CCcHHHHHHH
Confidence 5555 6788888873
No 12
>2apo_A Probable tRNA pseudouridine synthase B; protein-protein complex, box H/ACA, snoRNP, pseudouridine synthase, RNA modification; 1.95A {Methanocaldococcus jannaschii} SCOP: b.122.1.1 d.265.1.2
Probab=85.37 E-value=0.49 Score=46.20 Aligned_cols=64 Identities=14% Similarity=0.063 Sum_probs=42.6
Q ss_pred CcchHHHHHhhhhcCCchhhhhhhccccCchhhhhhhhCCceeeCCCCCceeecceeeeeCCCCCchhhhhhhccccccc
Q psy4559 91 SIKPLQKVLKIIDNNNCLFVHRQAGVRLNSQEAYDVACQGPIRPALLKEPVVYGLKCVHFKPPDFTIGNLYSALLPWQEA 170 (336)
Q Consensus 91 ~~gkatrvl~~i~g~~~~~~~~~sgi~tDt~daYe~Ar~G~~~~t~dreg~I~gielI~~~~~~~t~e~i~~~L~~f~G~ 170 (336)
..+++++++..|+|...|.+|+||+++. . .|+.+|++++++++..+.++.+
T Consensus 141 ~~~~i~~~l~~f~G~i~Q~PP~~SAvK~------------~-----~R~v~I~~~~l~~~~~~~~~~~------------ 191 (357)
T 2apo_A 141 SEEDILRVFKEFTGRIYQRPPLKAAVKR------------R-----LRIRKIHELELLDKDGKDVLFR------------ 191 (357)
T ss_dssp CHHHHHHHHHHHSEEEECC----------------------------CEEEEEEEEEEEEETTEEEEE------------
T ss_pred CHHHHHHHHHhCcccEEEeCCchhhccc------------c-----ccceeEEEEEEEEeeCCEEEEE------------
Confidence 5788999999999999999999999992 1 2456899999999976655544
Q ss_pred eeeecCccchhhhhhh
Q psy4559 171 VLKITDNNCLFVCLFV 186 (336)
Q Consensus 171 i~QvPP~~~k~I~~im 186 (336)
+.+. .++||+++.
T Consensus 192 v~cs---~GTYIRsL~ 204 (357)
T 2apo_A 192 VKCQ---SGTYIRKLC 204 (357)
T ss_dssp EEEC---TTCCHHHHH
T ss_pred EEEC---CCchHHHHH
Confidence 5554 678888887
No 13
>3u28_A H/ACA ribonucleoprotein complex subunit 4; pseudouridine synthase, pseudouridylation, H/ACA RNA; 1.90A {Saccharomyces cerevisiae} PDB: 3uai_A
Probab=81.36 E-value=0.49 Score=46.99 Aligned_cols=66 Identities=11% Similarity=0.007 Sum_probs=45.6
Q ss_pred CCcchHHHHHhhhhcCCchhhhhhhccccCchhhhhhhhCCceeeCCCCCceeecceeeeeCCC--CCchhhhhhhcccc
Q psy4559 90 PSIKPLQKVLKIIDNNNCLFVHRQAGVRLNSQEAYDVACQGPIRPALLKEPVVYGLKCVHFKPP--DFTIGNLYSALLPW 167 (336)
Q Consensus 90 ~~~gkatrvl~~i~g~~~~~~~~~sgi~tDt~daYe~Ar~G~~~~t~dreg~I~gielI~~~~~--~~t~e~i~~~L~~f 167 (336)
+..+++++++..|+|.+.|.+|+|||++.+ .|...|+.++++++..+ .++.+
T Consensus 134 ~~~~~i~~~l~~f~G~i~Q~PP~ySAvK~~-----------------~R~v~I~~i~ll~~~~~~~~~~~~--------- 187 (400)
T 3u28_A 134 KDEKDLGRSLENLTGALFQRPPLISAVKRQ-----------------LRVRTIYESNLIEFDNKRNLGVFW--------- 187 (400)
T ss_dssp SSTTHHHHHHHHTCEEEEECCC-----CCC-----------------CEEEEEEEEEEEEEETTTTEEEEE---------
T ss_pred CCHHHHHHHHHhCcCceEEECCceecccCC-----------------ceeEEEEEEEEEEEcCCCceEEEE---------
Confidence 368999999999999999999999999953 12357999999998753 23332
Q ss_pred ccceeeecCccchhhhhhhc
Q psy4559 168 QEAVLKITDNNCLFVCLFVH 187 (336)
Q Consensus 168 ~G~i~QvPP~~~k~I~~imp 187 (336)
+.+. .++|||++..
T Consensus 188 ---V~Cs---kGTYIRsL~~ 201 (400)
T 3u28_A 188 ---ASCE---AGTYMRTLCV 201 (400)
T ss_dssp ---EEEC---TTCCHHHHHH
T ss_pred ---EEEC---CCCCHHHHHH
Confidence 5554 6788888873
No 14
>3dh3_A Ribosomal large subunit pseudouridine synthase F; protein-RNA complex, S4 domain, alpha/beta protein, isomerase, RNA-binding, rRNA processing; HET: FHU; 3.00A {Escherichia coli}
Probab=74.45 E-value=4.8 Score=37.78 Aligned_cols=55 Identities=16% Similarity=0.224 Sum_probs=41.3
Q ss_pred CCeeEEEEEEecCChhhHHHHHHHHHHHcCCceEeceeEEeeEecccCccccccccC---ChhHHHH
Q psy4559 228 PPDFTIEVHCIGEYEEFLIRLIYDLGTKLRSAAICTSIQCIRFAQFGLEHSLLRKHW---RVQHVIE 291 (336)
Q Consensus 228 ~p~~~l~V~CSkG~~TYIRSL~~DIG~~LG~~Ahm~~LrRtr~G~F~le~Al~le~~---~l~~I~~ 291 (336)
...+.+.++.++- .-||-.+..+|. .+..|.|+++|++.+++ +..-+| +.+++..
T Consensus 174 ~~~l~l~l~tGR~--HQIR~~~~~lG~------pV~~L~R~~iG~l~L~~-L~~G~~R~Lt~~Ei~~ 231 (290)
T 3dh3_A 174 PFVFRITLVQGLN--RQIRRMCEHFGY------EVKKLERTRIMNVSLSG-IPLGEWRDLTDDELID 231 (290)
T ss_dssp SSEEEEEESCCCT--THHHHHHHHTTC------CEEEEEEEEETTEECTT-CCTTCEEECCHHHHHH
T ss_pred CeEEEEEEeCCCC--hHHHHHHHHcCC------eEEEeEEEEECCEecCC-CCCCCcEECCHHHHHH
Confidence 3456666666666 999999886654 38899999999999985 877777 4555543
No 15
>2gml_A Ribosomal large subunit pseudouridine synthase F; RLUF, ribosome, RNA modifying enzyme, isomerase; 2.60A {Escherichia coli}
Probab=21.31 E-value=1.1e+02 Score=27.87 Aligned_cols=53 Identities=11% Similarity=0.257 Sum_probs=36.8
Q ss_pred EEEEEEecCChhhHHHHHHHHHHHcCCceEeceeEEeeEecccCccccccccC---ChhHHHH
Q psy4559 232 TIEVHCIGEYEEFLIRLIYDLGTKLRSAAICTSIQCIRFAQFGLEHSLLRKHW---RVQHVIE 291 (336)
Q Consensus 232 ~l~V~CSkG~~TYIRSL~~DIG~~LG~~Ahm~~LrRtr~G~F~le~Al~le~~---~l~~I~~ 291 (336)
.++|+.-.|----||-.+..+|. -+..|.|+++|++.+++ |..-+| +.+++..
T Consensus 123 ~l~i~L~tGR~HQIRr~~a~lG~------pV~~L~R~~iG~l~L~~-L~~G~~R~Lt~~E~~~ 178 (237)
T 2gml_A 123 VFRITLVQGLNRQIRRMCEHFGY------EVKKLERTRIMNVSLSG-IPLGEWRDLTDDELID 178 (237)
T ss_dssp EEEEEECCCSTTHHHHHHHHTTC------CEEEEEEEEETTEECTT-CCTTCEEECCHHHHHH
T ss_pred EEEEEEecCCcHHHHHHHHHcCC------CEeeeEEEEECCEecCC-CCCCCEEECCHHHHHH
Confidence 35555555633778888766553 46789999999999974 777776 4555543
Done!