Query 031089
Match_columns 166
No_of_seqs 157 out of 1308
Neff 7.4
Searched_HMMs 29240
Date Mon Mar 25 14:17:38 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/031089.a3m -d /work/01045/syshi/HHdatabase/pdb70.hhm -o /work/01045/syshi/hhsearch_pdb/031089hhsearch_pdb -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 2gml_A Ribosomal large subunit 100.0 2.3E-43 7.9E-48 282.1 13.7 137 21-164 45-181 (237)
2 3dh3_A Ribosomal large subunit 100.0 4.7E-42 1.6E-46 282.1 16.0 137 21-164 98-234 (290)
3 1ksk_A Ribosomal small subunit 100.0 1.2E-41 4.1E-46 271.5 14.7 135 22-162 97-233 (234)
4 2oml_A Ribosomal large subunit 100.0 7.8E-41 2.7E-45 259.3 17.3 135 21-156 42-189 (189)
5 1vio_A Ribosomal small subunit 100.0 4.9E-41 1.7E-45 269.5 16.1 138 22-165 96-235 (243)
6 2olw_A Ribosomal large subunit 100.0 2.1E-40 7.2E-45 262.2 17.9 135 21-156 70-217 (217)
7 2i82_A Ribosomal large subunit 100.0 6.3E-32 2.2E-36 213.3 9.5 114 22-136 54-180 (217)
8 1v9k_A Ribosomal large subunit 100.0 5.5E-31 1.9E-35 209.3 10.2 114 21-136 44-171 (228)
9 1v9f_A Ribosomal large subunit 100.0 1.5E-30 5.2E-35 216.4 8.4 129 2-136 113-253 (325)
10 1r3e_A TRNA pseudouridine synt 96.8 0.01 3.4E-07 48.7 10.2 138 2-151 15-210 (309)
11 1k8w_A TRNA pseudouridine synt 96.7 0.014 4.6E-07 48.3 10.1 130 2-143 37-224 (327)
12 1sgv_A TRNA pseudouridine synt 96.6 0.014 4.8E-07 47.9 9.6 132 2-143 18-210 (316)
13 3u28_A H/ACA ribonucleoprotein 96.5 0.027 9.1E-07 47.7 10.8 132 2-143 71-227 (400)
14 2apo_A Probable tRNA pseudouri 96.3 0.021 7.1E-07 47.7 9.3 132 2-143 78-231 (357)
15 2aus_C Pseudouridine synthase; 96.3 0.018 6.3E-07 47.6 9.0 132 2-143 58-211 (334)
16 3h7h_A Transcription elongatio 26.1 1.2E+02 0.0042 20.9 4.9 44 34-77 61-105 (120)
No 1
>2gml_A Ribosomal large subunit pseudouridine synthase F; RLUF, ribosome, RNA modifying enzyme, isomerase; 2.60A {Escherichia coli}
Probab=100.00 E-value=2.3e-43 Score=282.14 Aligned_cols=137 Identities=28% Similarity=0.450 Sum_probs=128.5
Q ss_pred CCeeecCCCCcCCceeeeeeCCHHHHHHhhcCCCCCCeEEEEEEecccChhhhhhhhcceeeCCcccceeEEEEcCCCCC
Q 031089 21 PRLFTVGRLDVATTGLIIVTNDGDFAQAVSHPSSKLQKEYIATIDGAVNKRHLIAISEGTVIEGTHCTPDVVELLPPQPD 100 (166)
Q Consensus 21 ~~l~~vhRLD~~TSGlll~ak~~~~~~~l~~~~~~i~K~Y~a~v~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 100 (166)
.+++||||||++||||||||||++++++|+++.+.|+|+|+|+|+|.++++.+..+..|+.++++..+++.++++.
T Consensus 45 ~rl~~VgRLD~dTSGLLLlT~dg~~a~~L~~p~~~v~K~Y~a~V~G~~~~~~i~~l~~Gv~l~~~~~~~a~~~~l~---- 120 (237)
T 2gml_A 45 KRVFPIGRLDKDSQGLIFLTNHGDLVNKILRAGNDHEKEYLVTVDKPITEEFIRGMSAGVPILGTVTKKCKVKKEA---- 120 (237)
T ss_dssp SCCEEESCCCTTCEEEEEEESCHHHHHHHHHHHHHSCEEEEEEESSCCCHHHHHHHSSCCEETTEECCCCEEEEEE----
T ss_pred CCeeEecCCCCCCeeEEEEEcCHHHHHHHhCccCCCCEEEEEEEcccCCHHHHHHHHcCeEeCCcccccEEEEEeC----
Confidence 4689999999999999999999999999999988999999999999999988888888998888888889998874
Q ss_pred CCceEEEEEecCCchhHHHHHHHHcCCceeeeeeeEEeCeecCCCCCCCcEEEcCHHHHhhccc
Q 031089 101 IPRPRIRIVVHEGRNHEVRELVKNAGLKLYSLKRLRIGGFRLPSDLGIGMHVELKQSDLKLMGW 164 (166)
Q Consensus 101 ~~~~ll~~~l~tGR~HQIR~~l~~~G~pI~~l~R~~~g~~~l~~~l~~G~~r~l~~~e~~~l~~ 164 (166)
.++++|+|.|||+||||+||+++||||++|+|++||++.| ++|++|+||+|+++|+..|+.
T Consensus 121 --~s~l~i~L~tGR~HQIRr~~a~lG~pV~~L~R~~iG~l~L-~~L~~G~~R~Lt~~E~~~l~~ 181 (237)
T 2gml_A 121 --PFVFRITLVQGLNRQIRRMCEHFGYEVKKLERTRIMNVSL-SGIPLGEWRDLTDDELIDLFK 181 (237)
T ss_dssp --TTEEEEEECCCSTTHHHHHHHHTTCCEEEEEEEEETTEEC-TTCCTTCEEECCHHHHHHHHT
T ss_pred --CEEEEEEEecCCcHHHHHHHHHcCCCEeeeEEEEECCEec-CCCCCCCEEECCHHHHHHHHH
Confidence 4799999999999999999999999999999999999999 599999999999999998864
No 2
>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=100.00 E-value=4.7e-42 Score=282.12 Aligned_cols=137 Identities=28% Similarity=0.450 Sum_probs=128.9
Q ss_pred CCeeecCCCCcCCceeeeeeCCHHHHHHhhcCCCCCCeEEEEEEecccChhhhhhhhcceeeCCcccceeEEEEcCCCCC
Q 031089 21 PRLFTVGRLDVATTGLIIVTNDGDFAQAVSHPSSKLQKEYIATIDGAVNKRHLIAISEGTVIEGTHCTPDVVELLPPQPD 100 (166)
Q Consensus 21 ~~l~~vhRLD~~TSGlll~ak~~~~~~~l~~~~~~i~K~Y~a~v~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 100 (166)
.++++|||||++||||||||+|++++++|+++.+.++|+|+|+|+|.++++.+..+..|+.+++....++.+++..
T Consensus 98 ~~~~~VhRLD~dTSGLllla~d~~~~~~L~~~~~~v~K~Y~a~V~G~~~~~~i~~l~~Gv~l~~~~~~~~~v~~~~---- 173 (290)
T 3dh3_A 98 KRVFPIGRLDKDSQGLIFLTNHGDLVNKILRAGNDHEKEYLVTVDKPITEEFIRGMSAGVPILGTVTKKCKVKKEA---- 173 (290)
T ss_dssp SCCEESSCCCTTCEEEEEEESCTTHHHHHHCGGGCCCEEEEEEESSCCCHHHHHHHHTCCBCSSSBCCCCEEEECS----
T ss_pred CceeeeccCCCCCcceEEEcCCHHHHHHHHHhhCCcCEEEEEEECCCCCHHHHHHHhcCcccCCcccceEEEEEcC----
Confidence 5789999999999999999999999999999999999999999999999999998999999998888888888753
Q ss_pred CCceEEEEEecCCchhHHHHHHHHcCCceeeeeeeEEeCeecCCCCCCCcEEEcCHHHHhhccc
Q 031089 101 IPRPRIRIVVHEGRNHEVRELVKNAGLKLYSLKRLRIGGFRLPSDLGIGMHVELKQSDLKLMGW 164 (166)
Q Consensus 101 ~~~~ll~~~l~tGR~HQIR~~l~~~G~pI~~l~R~~~g~~~l~~~l~~G~~r~l~~~e~~~l~~ 164 (166)
.++++|+|+|||+||||+||+++||||++|+|++||+++| ++|++|+||+|+++|++.|..
T Consensus 174 --~~~l~l~l~tGR~HQIR~~~~~lG~pV~~L~R~~iG~l~L-~~L~~G~~R~Lt~~Ei~~l~~ 234 (290)
T 3dh3_A 174 --PFVFRITLVQGLNRQIRRMCEHFGYEVKKLERTRIMNVSL-SGIPLGEWRDLTDDELIDLFK 234 (290)
T ss_dssp --SSEEEEEESCCCTTHHHHHHHHTTCCEEEEEEEEETTEEC-TTCCTTCEEECCHHHHHHHHH
T ss_pred --CeEEEEEEeCCCChHHHHHHHHcCCeEEEeEEEEECCEec-CCCCCCCcEECCHHHHHHHHH
Confidence 4799999999999999999999999999999999999999 599999999999999998864
No 3
>1ksk_A Ribosomal small subunit pseudouridine synthase A; RSUA, lyase; 2.00A {Escherichia coli} SCOP: d.265.1.3 d.66.1.5 PDB: 1ksl_A 1ksv_A*
Probab=100.00 E-value=1.2e-41 Score=271.47 Aligned_cols=135 Identities=29% Similarity=0.592 Sum_probs=121.8
Q ss_pred CeeecCCCCcCCceeeeeeCCHHHHHHhhcCCCCCCeEEEEEEecccChhhhhhhhcceeeCC--cccceeEEEEcCCCC
Q 031089 22 RLFTVGRLDVATTGLIIVTNDGDFAQAVSHPSSKLQKEYIATIDGAVNKRHLIAISEGTVIEG--THCTPDVVELLPPQP 99 (166)
Q Consensus 22 ~l~~vhRLD~~TSGlll~ak~~~~~~~l~~~~~~i~K~Y~a~v~g~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~ 99 (166)
++++|||||++||||||||||+++++++.++++.++|+|+|+|.|.++++.+..+..++.+++ ....++.+++++
T Consensus 97 ~~~~vhRLD~~TsGlll~ak~~~~~~~l~~~~~~v~K~Y~a~v~g~~~~~~i~~~~~g~~~~~~~~~~~~a~~~~~~--- 173 (234)
T 1ksk_A 97 KLHAAGRLDIDTTGLVLMTDDGQWSHRITSPRHHCEKTYLVTLESPVADDTAEQFAKGVQLHNEKDLTKPAVLEVIT--- 173 (234)
T ss_dssp GCEESSCCCTTCEEEEEEESCHHHHHHHHCTTSCCCEEEEEEESSCCCTTHHHHHHHCCCCTTCSSCCCCCEEEEEE---
T ss_pred CeeEcCCCCCCCeeEEEEEcCHHHHHHHhCCCCCCCeEEEEEEccCCCHHHHHHHHCCeEECCCCcccceEEEEEeC---
Confidence 579999999999999999999999999999999999999999999998887777777776644 245677788774
Q ss_pred CCCceEEEEEecCCchhHHHHHHHHcCCceeeeeeeEEeCeecCCCCCCCcEEEcCHHHHhhc
Q 031089 100 DIPRPRIRIVVHEGRNHEVRELVKNAGLKLYSLKRLRIGGFRLPSDLGIGMHVELKQSDLKLM 162 (166)
Q Consensus 100 ~~~~~ll~~~l~tGR~HQIR~~l~~~G~pI~~l~R~~~g~~~l~~~l~~G~~r~l~~~e~~~l 162 (166)
.++++|+|.|||+||||+||+++||||++|+||++|+++|+.+|++|+||+|+++|++.|
T Consensus 174 ---~s~~~~~l~tGR~HQIR~h~~~lG~pi~gd~ry~~g~~~l~~~L~~G~~r~l~~~e~~~l 233 (234)
T 1ksk_A 174 ---PTQVRLTISEGRYHQVKRMFAAVGNHVVELHRERIGGITLDADLAPGEYRPLTEEEIASV 233 (234)
T ss_dssp ---TTEEEEEESCCCTTHHHHHHHHTTCCEEEEEEEEETTEECCTTCCTTCEEECCHHHHTTC
T ss_pred ---CeEEEEEEccCCCHHHHHHHHHcCCeEeeeEEEEECCEecCCCCCCCceEECCHHHHHhh
Confidence 489999999999999999999999999999999999999933999999999999999876
No 4
>2oml_A Ribosomal large subunit pseudouridine synthase E; bifurcated beta sheet, thrombin-cleaved, isomerase; 1.20A {Escherichia coli}
Probab=100.00 E-value=7.8e-41 Score=259.27 Aligned_cols=135 Identities=27% Similarity=0.527 Sum_probs=116.2
Q ss_pred CCeeecCCCCcCCceeeeeeCCHHHHHHhhcCCCCCCeEEEEEEecccChhhhhhhhcceeeCCcccceeEEEEcCCCC-
Q 031089 21 PRLFTVGRLDVATTGLIIVTNDGDFAQAVSHPSSKLQKEYIATIDGAVNKRHLIAISEGTVIEGTHCTPDVVELLPPQP- 99 (166)
Q Consensus 21 ~~l~~vhRLD~~TSGlll~ak~~~~~~~l~~~~~~i~K~Y~a~v~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~- 99 (166)
+++++|||||++||||||||||++++++|+++++.|+|+|+|+|+|.++++.+..+..++..+++...++.+.+....+
T Consensus 42 ~~~~~vhRLD~~TSGlll~ak~~~~~~~l~~~~~~v~K~Y~a~v~G~~~~~~~~~i~~~i~~~~~~~~~~~~~~~~~~~~ 121 (189)
T 2oml_A 42 QGVYAAGRLDRDSEGLLVLTNNGALQARLTQPGKRTGKIYYVQVEGIPTQDALEALRNGVTLNDGPTLPAGAELVDEPAW 121 (189)
T ss_dssp SSCEESSCCCTTCEEEEEEESCHHHHHHHHSTTSCCCEEEEEEEESCCCHHHHHHHHHCCEETTEECCCCEEEEECCCTT
T ss_pred CCceECCCCCCCCeeEEEEEcCHHHHHHHhCccCCCcEEEEEEEcCCCCHHHHHHHHcCceeCCceeeeeEEEEeccccc
Confidence 3679999999999999999999999999999989999999999999999877656777776655554455555443211
Q ss_pred ------------CCCceEEEEEecCCchhHHHHHHHHcCCceeeeeeeEEeCeecCCCCCCCcEEEcCH
Q 031089 100 ------------DIPRPRIRIVVHEGRNHEVRELVKNAGLKLYSLKRLRIGGFRLPSDLGIGMHVELKQ 156 (166)
Q Consensus 100 ------------~~~~~ll~~~l~tGR~HQIR~~l~~~G~pI~~l~R~~~g~~~l~~~l~~G~~r~l~~ 156 (166)
..++++++|+|.|||+||||+||+++||||++|+||++|++.| ++|++|+||+|++
T Consensus 122 ~~~t~~~v~~~~~~~~slv~~~l~TGR~HQIRvhla~lG~PI~gD~~Y~~g~~~l-~~L~~G~~r~L~~ 189 (189)
T 2oml_A 122 LWPRNPPIRERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGDYSL-DNLANGEWREVTD 189 (189)
T ss_dssp CCCCSSCCC-CTTSCEEEEEEEESCCCTTHHHHHHHHTTCCEEEEEEEEETTEEC-TTCCTTCEEECCC
T ss_pred ccccccccccccCCCcEEEEEEEeeCCCHHHHHHHHHcCCcCcceEEEEECCEEc-CCcCCCceEeCCC
Confidence 1257999999999999999999999999999999999999999 5999999999974
No 5
>1vio_A Ribosomal small subunit pseudouridine synthase A; structural genomics, lyase; 1.59A {Haemophilus influenzae} SCOP: d.265.1.3 d.66.1.5
Probab=100.00 E-value=4.9e-41 Score=269.49 Aligned_cols=138 Identities=30% Similarity=0.540 Sum_probs=122.6
Q ss_pred CeeecCCCCcCCceeeeeeCCHHHHHHhhcCCCCCCeEEEEEEecccChhhhhhhhcceeeCC--cccceeEEEEcCCCC
Q 031089 22 RLFTVGRLDVATTGLIIVTNDGDFAQAVSHPSSKLQKEYIATIDGAVNKRHLIAISEGTVIEG--THCTPDVVELLPPQP 99 (166)
Q Consensus 22 ~l~~vhRLD~~TSGlll~ak~~~~~~~l~~~~~~i~K~Y~a~v~g~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~ 99 (166)
++++|||||++||||||||+|+++++++.++++.|+|+|+|+|.|.++++.+..+..++.+++ ....++.++++.
T Consensus 96 ~~~~vhRLD~~TsGlll~ak~~~~a~~l~~~~~~v~K~Y~a~v~g~~~~~~i~~~~~g~~~~~~~~~~~~a~~~~l~--- 172 (243)
T 1vio_A 96 KLHSAGRLDVDTTGLVLLTDDGQWSHRITSPKHHCEKTYLVTLADPVEENYSAACAEGILLRGEKEPTKPAKLEILD--- 172 (243)
T ss_dssp GCEESSCCCTTCEEEEEEESCHHHHHHHHCTTSCCCEEEEEEESSCCCTTHHHHHHHCCCCTTCSSCCCCCEEEECS---
T ss_pred CEeEccCCCCCCeEEEEEEECHHHHHHHhCCCCCCCEEEEEEEeCCCCHHHHHHHhCCeEECCCCccceeEEEEEeC---
Confidence 579999999999999999999999999999999999999999999998887777776766543 245677788775
Q ss_pred CCCceEEEEEecCCchhHHHHHHHHcCCceeeeeeeEEeCeecCCCCCCCcEEEcCHHHHhhcccC
Q 031089 100 DIPRPRIRIVVHEGRNHEVRELVKNAGLKLYSLKRLRIGGFRLPSDLGIGMHVELKQSDLKLMGWK 165 (166)
Q Consensus 100 ~~~~~ll~~~l~tGR~HQIR~~l~~~G~pI~~l~R~~~g~~~l~~~l~~G~~r~l~~~e~~~l~~~ 165 (166)
.++++|+|.|||+||||+||+++||||++|+||+||++.|+.+|++|+||+|+++|++.|++.
T Consensus 173 ---~sl~~~~l~tGR~HQIR~hl~~lG~pI~gd~r~~~G~~~l~~~L~~G~~r~L~~~e~~~l~~~ 235 (243)
T 1vio_A 173 ---DYNVNLTISEGRYHQVKRMFAALGNKVVGLHRWKIGDVVLDESLEEGEYRPLTQSEIEKLVEG 235 (243)
T ss_dssp ---SSEEEEEESCCCTTHHHHHHHHTTCCEEEEEEEEETTEECCTTCCTTCEEECCHHHHHHTC--
T ss_pred ---CEEEEEEEccCCcHHHHHHHHHCCCeEcccEEEEECCEEcCCCCCCCceEECCHHHHHHHHhc
Confidence 589999999999999999999999999999999999999943999999999999999998753
No 6
>2olw_A Ribosomal large subunit pseudouridine synthase E; bifurcated beta sheet, isomerase; 1.60A {Escherichia coli}
Probab=100.00 E-value=2.1e-40 Score=262.20 Aligned_cols=135 Identities=27% Similarity=0.527 Sum_probs=117.9
Q ss_pred CCeeecCCCCcCCceeeeeeCCHHHHHHhhcCCCCCCeEEEEEEecccChhhhhhhhcceeeCCcccceeEEEEcCCCC-
Q 031089 21 PRLFTVGRLDVATTGLIIVTNDGDFAQAVSHPSSKLQKEYIATIDGAVNKRHLIAISEGTVIEGTHCTPDVVELLPPQP- 99 (166)
Q Consensus 21 ~~l~~vhRLD~~TSGlll~ak~~~~~~~l~~~~~~i~K~Y~a~v~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~- 99 (166)
+++++|||||++||||||||||+++++.|++++++|+|+|+|+|.|.++++.+..+..++..++++.+++.++++....
T Consensus 70 ~~~~~VhRLDr~TSGllllAk~~~~~~~L~~~~~~v~K~Y~A~V~G~~~~~~~~~i~~~i~~~~g~~~~~~~~~~~~~~~ 149 (217)
T 2olw_A 70 QGVYAAGRLDRDSEGLLVLTNNGALQARLTQPGKRTGKIYYVQVEGIPTQDALEALRNGVTLNDGPTLPAGAELVDEPAW 149 (217)
T ss_dssp CSCEESSCCCTTCEEEEEEESCHHHHHHHHCTTCCCCEEEEEEEESCCCHHHHHHHHHCCEETTEECCCCEEEEECCCTT
T ss_pred CCceECCCCCCCCeeEEEEEcCHHHHHHHHcccccCCEEEEEEEccCCCHHHHHHHhCCEEeCCCcccceEEEEecCCcc
Confidence 3679999999999999999999999999999999999999999999999877666777777666666667776653211
Q ss_pred ------------CCCceEEEEEecCCchhHHHHHHHHcCCceeeeeeeEEeCeecCCCCCCCcEEEcCH
Q 031089 100 ------------DIPRPRIRIVVHEGRNHEVRELVKNAGLKLYSLKRLRIGGFRLPSDLGIGMHVELKQ 156 (166)
Q Consensus 100 ------------~~~~~ll~~~l~tGR~HQIR~~l~~~G~pI~~l~R~~~g~~~l~~~l~~G~~r~l~~ 156 (166)
..+.++++|+|.|||+||||+||+++||||++|+||++|++.| ++|++|+||+|++
T Consensus 150 ~~~~~~~v~~~~~~~~slv~~~l~TGRtHQIRvhla~lG~PIvgD~rY~~g~l~L-~~L~~G~~r~L~~ 217 (217)
T 2olw_A 150 LWPRNPPIRERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGDYSL-DNLANGEWREVTD 217 (217)
T ss_dssp CCCCSSCCC-CCSSCEEEEEEEESCCCTTHHHHHHHHTTCCEEEEEEEEETTEEC-TTCCTTCEEECC-
T ss_pred ccccccceeccCCCCcEEEEEEECcCCCHHHHHHHHHCCCcEeCCEEEEECCeec-CCCCCcceEeCCC
Confidence 1357999999999999999999999999999999999999999 5999999999985
No 7
>2i82_A Ribosomal large subunit pseudouridine synthase A; lyase/RNA complex; HET: FOU; 2.05A {Escherichia coli}
Probab=99.97 E-value=6.3e-32 Score=213.31 Aligned_cols=114 Identities=19% Similarity=0.224 Sum_probs=95.0
Q ss_pred CeeecCCCCcCCceeeeeeCCHHHHHHhhc--CCCCCCeEEEEEEecccChhhh--hh-----h----hcceeeCCcccc
Q 031089 22 RLFTVGRLDVATTGLIIVTNDGDFAQAVSH--PSSKLQKEYIATIDGAVNKRHL--IA-----I----SEGTVIEGTHCT 88 (166)
Q Consensus 22 ~l~~vhRLD~~TSGlll~ak~~~~~~~l~~--~~~~i~K~Y~a~v~g~~~~~~~--~~-----~----~~~~~~~~~~~~ 88 (166)
++++|||||++||||||||||++++++|++ +++.|+|+|+|+|.|.++++.. .. . ..++..++++.+
T Consensus 54 ~~~~vhRLD~~TSGlll~ak~~~~~~~l~~~f~~~~v~K~Y~a~v~G~~~~~~g~i~~~l~~~~~~~~~~~v~~~~gk~a 133 (217)
T 2i82_A 54 QAESVHRLDMATSGVIVVALTKAAERELKRQFREREPKKQYVARVWGHPSPAEGLVDLPLICDWPNRPKQKVCYETGKPA 133 (217)
T ss_dssp TCEESSCCCTTCEEEEEEESSHHHHHHHHHHHHTTCSEEEEEEEEESCCSSSEEEEECCEEECGGGTTCEEECTTTCBCC
T ss_pred CCceeecCCCCCeEEEEEEeCHHHHHHHHHHHHhCCeeEEEEEEEecccCCCCcEEecceeecCCCCcEEEEeCCCCcEE
Confidence 468999999999999999999999999998 7899999999999999876542 11 1 122333566778
Q ss_pred eeEEEEcCCCCCCCceEEEEEecCCchhHHHHHHHHcCCceeeeeeeE
Q 031089 89 PDVVELLPPQPDIPRPRIRIVVHEGRNHEVRELVKNAGLKLYSLKRLR 136 (166)
Q Consensus 89 ~~~~~~~~~~~~~~~~ll~~~l~tGR~HQIR~~l~~~G~pI~~l~R~~ 136 (166)
.+.++++..... ..++++|+|.|||+||||+||+++||||++|.+|.
T Consensus 134 ~t~~~vl~~~~~-~~slv~~~l~TGR~HQIR~hla~lG~PIvGD~~Yg 180 (217)
T 2i82_A 134 QTEYEVVEYAAD-NTARVVLKPITGRSHQLRVHMLALGHPILGDRFYA 180 (217)
T ss_dssp EEEEEEEEEETT-TEEEEEEEESSCCTTHHHHHHHHTTCCBTTCTTTS
T ss_pred EEEEEEEEECCC-CeEEEEEEECCCCcHHHHHHHHHCCCcEECccccC
Confidence 899999875421 26999999999999999999999999999999985
No 8
>1v9k_A Ribosomal large subunit pseudouridine synthase C; pseudouridine syntase, RNA binding, lyase; 2.00A {Escherichia coli} SCOP: d.265.1.3 PDB: 1xpi_A
Probab=99.97 E-value=5.5e-31 Score=209.32 Aligned_cols=114 Identities=19% Similarity=0.243 Sum_probs=95.2
Q ss_pred CCeeecCCCCcCCceeeeeeCCHHHHHHhhc--CCCCCCeEEEEEEecccChhhhh---hh-----hcc---eee-CCcc
Q 031089 21 PRLFTVGRLDVATTGLIIVTNDGDFAQAVSH--PSSKLQKEYIATIDGAVNKRHLI---AI-----SEG---TVI-EGTH 86 (166)
Q Consensus 21 ~~l~~vhRLD~~TSGlll~ak~~~~~~~l~~--~~~~i~K~Y~a~v~g~~~~~~~~---~~-----~~~---~~~-~~~~ 86 (166)
.++++|||||++||||||||||+++++.|++ +++.|+|+|+|+|.|.++++... .+ ..| +.+ ++++
T Consensus 44 ~~~~~VhRLD~~TSGlll~ak~~~~~~~l~~~~~~~~v~K~Y~a~v~G~~~~~~~~i~~~l~~~~~~~g~~~~~~~~~gk 123 (228)
T 1v9k_A 44 RFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLREKGMQKDYLALVRGQWQSHVKSVQAPLLKNILQSGERIVRVSQEGK 123 (228)
T ss_dssp SCCEESSCCCTTCEEEEEEESSHHHHHHHHHHHHTTCSEEEEEEEEESCCCTTCCEECCCEEEEECTTSCEEEEECTTSB
T ss_pred CccceEecCCCCCeEEEEEEeCHHHHHHHHHHHHhCCeeEEEEEEEecccCCCCCEEeCceeccCCCCCceEEEECCCCc
Confidence 4679999999999999999999999999987 47899999999999998865432 11 122 333 4567
Q ss_pred cceeEEEEcCCCCCCCceEEEEEecCCchhHHHHHHHHcCCceeeeeeeE
Q 031089 87 CTPDVVELLPPQPDIPRPRIRIVVHEGRNHEVRELVKNAGLKLYSLKRLR 136 (166)
Q Consensus 87 ~~~~~~~~~~~~~~~~~~ll~~~l~tGR~HQIR~~l~~~G~pI~~l~R~~ 136 (166)
.+.+.++++... .+.++++|+|.|||+||||+||+++||||++|.+|.
T Consensus 124 ~a~t~~~vl~~~--~~~slv~~~l~TGR~HQIR~hla~lG~PI~gD~~YG 171 (228)
T 1v9k_A 124 PSETRFKVEERY--AFATLVRCSPVTGRTHQIRVHTQYAGHPIAFDDRYG 171 (228)
T ss_dssp CCCEEEEEEEEC--SSEEEEEEEESSCCTTHHHHHHHHTTCCBTTCTTTS
T ss_pred EEEEEEEEEEEc--CCeEEEEEEECCCCchHHHHHHHHCCCcEecCcccC
Confidence 788999998764 347999999999999999999999999999999863
No 9
>1v9f_A Ribosomal large subunit pseudouridine synthase D; RNA binding, lyase; 1.70A {Escherichia coli} SCOP: d.265.1.3 PDB: 2ist_A 1qyu_A 1prz_A
Probab=99.96 E-value=1.5e-30 Score=216.39 Aligned_cols=129 Identities=18% Similarity=0.194 Sum_probs=102.2
Q ss_pred cchHHHHHHHhhcCCCCCCCCeeecCCCCcCCceeeeeeCCHHHHHHhhc--CCCCCCeEEEEEEecccChhh-------
Q 031089 2 SLFDDYLKSWDKRNPGLPRPRLFTVGRLDVATTGLIIVTNDGDFAQAVSH--PSSKLQKEYIATIDGAVNKRH------- 72 (166)
Q Consensus 2 sl~d~~~~~~~~~~~~~~~~~l~~vhRLD~~TSGlll~ak~~~~~~~l~~--~~~~i~K~Y~a~v~g~~~~~~------- 72 (166)
|++|.+..++..... .+++++|||||++||||||||||+++++.|++ +++.++|+|+|+|.|.++++.
T Consensus 113 tl~~~l~~~~~~~~~---~~~~~~vhRLD~~TSGlll~ak~~~~~~~l~~~~~~~~v~K~Y~a~v~G~~~~~g~i~~~i~ 189 (325)
T 1v9f_A 113 TVLNALLHYYPPIAD---VPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQRREITREYEAVAIGHMTAGGTVDEPIS 189 (325)
T ss_dssp SHHHHHHHHCGGGGG---SGGGGBCCCCCTTCEEEEEEESSHHHHHHHHHHHHTTCSEEEEEEEEESCCCCCEEEECCEE
T ss_pred cHHHHHHHHHHhcCC---CCceeeecCCCCCCeeEEEEEcCHHHHHHHHHHHHcCCeeEEEEEEEeCCCCCCCEEeeeee
Confidence 566766655532211 24689999999999999999999999999987 688999999999999987621
Q ss_pred ---hhhhhcceeeCCcccceeEEEEcCCCCCCCceEEEEEecCCchhHHHHHHHHcCCceeeeeeeE
Q 031089 73 ---LIAISEGTVIEGTHCTPDVVELLPPQPDIPRPRIRIVVHEGRNHEVRELVKNAGLKLYSLKRLR 136 (166)
Q Consensus 73 ---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~~l~tGR~HQIR~~l~~~G~pI~~l~R~~ 136 (166)
...++.++. .+++.+.+.++++... .++++++|+|.|||+||||+||+++||||++|.+|.
T Consensus 190 ~~~~~~~~~~v~-~~gk~a~t~~~vl~~~--~~~slv~~~l~TGR~HQIRvhla~lG~PI~GD~~Yg 253 (325)
T 1v9f_A 190 RHPTKRTHMAVH-PMGKPAVTHYRIMEHF--RVHTRLRLRLETGRTHQIRVHMAHITHPLVGDPVYG 253 (325)
T ss_dssp ECSSCTTCEEEC-TTSBCCEEEEEEEEEC--SSEEEEEEEESCCCTTHHHHHHHHTTCCBTTCTTTT
T ss_pred ECCCCCEEEEEC-CCCeeEEEEEEEeEEc--CCeEEEEEEECCCCcHHHHHHHHhCCCceeCChhhC
Confidence 112233333 3556778889888754 247999999999999999999999999999999985
No 10
>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=96.80 E-value=0.01 Score=48.67 Aligned_cols=138 Identities=17% Similarity=0.196 Sum_probs=83.2
Q ss_pred cchHHHHHHHhhcCCCCCCCCeeecCCCCcCCceeeeeeCCH--HHHHHhhcCCCCCCeEEEEEEe-c------------
Q 031089 2 SLFDDYLKSWDKRNPGLPRPRLFTVGRLDVATTGLIIVTNDG--DFAQAVSHPSSKLQKEYIATID-G------------ 66 (166)
Q Consensus 2 sl~d~~~~~~~~~~~~~~~~~l~~vhRLD~~TSGlll~ak~~--~~~~~l~~~~~~i~K~Y~a~v~-g------------ 66 (166)
|..| +...+++.+. ..++...|-||-.+||+|+++-.. ++...|. ...|+|.|.+. |
T Consensus 15 TS~~-vv~~vrr~l~---~kKvGH~GTLDP~AtGvL~i~iG~aTKl~~~l~----~~~K~Y~a~~~lG~~TdT~D~eG~v 86 (309)
T 1r3e_A 15 TSHD-VVDEVRKKLK---TRKVGHGGTLDPFACGVLIIGVNQGTRILEFYK----DLKKVYWVKMRLGLITETFDITGEV 86 (309)
T ss_dssp CHHH-HHHHHHHHTT---CSCEEESSCCCTTCEEEEEEEEGGGGGGGGGGT----TSCEEEEEEEEETEEESSSBTTSCE
T ss_pred CHHH-HHHHHHHHhc---cceecccccCCCCcceeEEEEECHHHhHHHHhC----ccCcEEEEEEEECCcccCCCCCCCE
Confidence 4455 4445555443 357899999999999999987653 2333333 35899999875 3
Q ss_pred ------ccChhhhhhh----h----------cceeeCCc-----------------ccceeEEEEcCCCCCCCceEEEEE
Q 031089 67 ------AVNKRHLIAI----S----------EGTVIEGT-----------------HCTPDVVELLPPQPDIPRPRIRIV 109 (166)
Q Consensus 67 ------~~~~~~~~~~----~----------~~~~~~~~-----------------~~~~~~~~~~~~~~~~~~~ll~~~ 109 (166)
.++.+.+... . ..+.++|. ......+++++.. .+...+++.
T Consensus 87 ~~~~~~~~t~~~i~~~l~~f~G~i~Q~PP~~SAvKv~GkraYelAR~G~~ve~~~R~v~I~~i~ll~~~--~p~~~~~v~ 164 (309)
T 1r3e_A 87 VEERECNVTEEEIREAIFSFVGEYDQVPPAYSAKKYKGERLYKLAREGKIINLPPKRVKIFKIWDVNIE--GRDVSFRVE 164 (309)
T ss_dssp EEECCCCCCHHHHHHHHHSSSEEEEECCCSSSSCEETTEEHHHHHHTTCCCCCCCEEEEEEEEEEEEEE--TTEEEEEEE
T ss_pred EEEecCCCCHHHHHHHHHhccceEEEeCChHHhcccCCccHHHHHhCCCcccccceEEEEEEEEEEEee--CCEEEEEEE
Confidence 1344443321 0 01122221 1111234444332 235667777
Q ss_pred ecCCchhHHHHHHHHcCC------ceeeeeeeEEeCeecCCCCCCCcE
Q 031089 110 VHEGRNHEVRELVKNAGL------KLYSLKRLRIGGFRLPSDLGIGMH 151 (166)
Q Consensus 110 l~tGR~HQIR~~l~~~G~------pI~~l~R~~~g~~~l~~~l~~G~~ 151 (166)
--.| --||..+.-+|. .+..|.|++.|+|+++..+..-+|
T Consensus 165 CskG--TYIRsL~~DiG~~Lg~~a~~~~LrRt~~G~f~~~~a~~l~~l 210 (309)
T 1r3e_A 165 VSPG--TYIRSLCMDIGYKLGCGATAVELVRESVGPHTIEESLNVFEA 210 (309)
T ss_dssp ECTT--CCHHHHHHHHHHHTTSCEEEEEEEEEEETTEEGGGCBCTTTS
T ss_pred ECCC--chHHHHHHHHHHHhCCCEEEEEEEEEEEcCCcHHHccCHHHH
Confidence 7777 489998876654 569999999999999655544444
No 11
>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=96.67 E-value=0.014 Score=48.25 Aligned_cols=130 Identities=19% Similarity=0.252 Sum_probs=79.9
Q ss_pred cchHHHHHHHhhcCCCCCCCCeeecCCCCcCCceeeeeeCC--HHHHHHhhcCCCCCCeEEEEEEe-cc-----------
Q 031089 2 SLFDDYLKSWDKRNPGLPRPRLFTVGRLDVATTGLIIVTND--GDFAQAVSHPSSKLQKEYIATID-GA----------- 67 (166)
Q Consensus 2 sl~d~~~~~~~~~~~~~~~~~l~~vhRLD~~TSGlll~ak~--~~~~~~l~~~~~~i~K~Y~a~v~-g~----------- 67 (166)
|..| +...+++.+. ..++...|.||-.+||+|+++-. ..+...|.. ..|+|.|.+. |.
T Consensus 37 TS~d-vv~~vr~~l~---~kKvGH~GTLDP~AtGvL~i~~G~aTKl~~~l~~----~~K~Y~a~~~lG~~TdT~D~eG~v 108 (327)
T 1k8w_A 37 SSND-ALQKVKRIYN---ANRAGHTGALDPLATGMLPICLGEATKFSQYLLD----SDKRYRVIARLGQRTDTSDADGQI 108 (327)
T ss_dssp CHHH-HHHHHHHHTT---CSCEEESSCCCTTCEEEEEEEEGGGGGGTHHHHT----SCEEEEEEEEETEEESSSBTTSCE
T ss_pred CHHH-HHHHHHHhhc---cceeccCCCCCCCCeeEEEEEECHHHhHHHHhcc----CCcEEEEEEEECCcccCCCCCCCE
Confidence 4455 4455555443 35789999999999999998554 345666663 4799999874 32
Q ss_pred -------cChhhhhhh----h----------cceeeCCcc-----------------cceeEEEEcCCCCCCCceEEEEE
Q 031089 68 -------VNKRHLIAI----S----------EGTVIEGTH-----------------CTPDVVELLPPQPDIPRPRIRIV 109 (166)
Q Consensus 68 -------~~~~~~~~~----~----------~~~~~~~~~-----------------~~~~~~~~~~~~~~~~~~ll~~~ 109 (166)
++.+.+... . ..+.++|.. ...-.+++++.. .+...++|.
T Consensus 109 ~~~~~~~~t~e~i~~~l~~f~G~i~Q~PP~~SAvKv~GkraYelAR~G~~ve~~~R~v~I~~i~ll~~~--~~~~~~~v~ 186 (327)
T 1k8w_A 109 VEERPVTFSAEQLAAALDTFRGDIEQIPSMYSALKYQGKKLYEYARQGIEVPREARPITVYELLFIRHE--GNELELEIH 186 (327)
T ss_dssp EEECCCCCCHHHHHHHHHTTSEEEEECCCSSSCCEETTEEHHHHHHTTCCCCCCCEEEEEEEEEEEEEE--TTEEEEEEE
T ss_pred EeecCCCCCHHHHHHHHHhccceEEEeCChhheeccCCccHHHHHhCCCcccccceEEEEEEEEEEEee--CCEEEEEEE
Confidence 344444321 0 011122211 111233444321 235667777
Q ss_pred ecCCchhHHHHHHHHcCC------ceeeeeeeEEeCeecC
Q 031089 110 VHEGRNHEVRELVKNAGL------KLYSLKRLRIGGFRLP 143 (166)
Q Consensus 110 l~tGR~HQIR~~l~~~G~------pI~~l~R~~~g~~~l~ 143 (166)
--.| --||..+.-+|. .+..|.|++.|+|.++
T Consensus 187 CskG--TYIRsL~~DiG~~Lg~~a~~~~LrRt~~G~F~~~ 224 (327)
T 1k8w_A 187 CSKG--TYIRTIIDDLGEKLGCGAHVIYLRRLAVSKYPVE 224 (327)
T ss_dssp ECTT--CCHHHHHHHHHHHHTSCEEEEEEEEEEETTCCGG
T ss_pred EcCC--chHHHHHHHHHHHhCCCeEEEEEEEEEEcCCccc
Confidence 7777 489998876654 5699999999999996
No 12
>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=96.59 E-value=0.014 Score=47.93 Aligned_cols=132 Identities=23% Similarity=0.344 Sum_probs=77.0
Q ss_pred cchHHHHHHHhhcCCCCCCCCeeecCCCCcCCceeeeeeCCH--HHHHHhhcCCCCCCeEEEEEEe-c------------
Q 031089 2 SLFDDYLKSWDKRNPGLPRPRLFTVGRLDVATTGLIIVTNDG--DFAQAVSHPSSKLQKEYIATID-G------------ 66 (166)
Q Consensus 2 sl~d~~~~~~~~~~~~~~~~~l~~vhRLD~~TSGlll~ak~~--~~~~~l~~~~~~i~K~Y~a~v~-g------------ 66 (166)
|..| +...+++.+.. .++...|-||-.+||+|+++-.. ++...|. ...|+|.+.+. |
T Consensus 18 TS~d-vv~~vrr~l~~---kKvGH~GTLDP~AtGvL~i~iG~aTKl~~~l~----~~~K~Y~~~~~lG~~TdT~D~eG~v 89 (316)
T 1sgv_A 18 TSHD-VVGRCRRIFAT---RRVGHAGTLDPMATGVLVIGIERATKILGLLT----AAPKSYAATIRLGQTTSTEDAEGQV 89 (316)
T ss_dssp CHHH-HHHHHHHHTTC---SCEEESSCCCTTCEEEEEEEEGGGGGGGGGTT----TSCEEEEEEEEETEEETTSBTTSCE
T ss_pred CHHH-HHHHHHHHhcc---ccccccccCCCCCeEEEEEEECHHHhHHHHhC----cCCcEEEEEEEECCccCCCCCCCCE
Confidence 4455 44555554532 57899999999999999987653 2333333 45899999874 3
Q ss_pred -------ccChhhhhh----hh----------cceeeCCc-----------------ccceeEEEEcCCCC--CCCceEE
Q 031089 67 -------AVNKRHLIA----IS----------EGTVIEGT-----------------HCTPDVVELLPPQP--DIPRPRI 106 (166)
Q Consensus 67 -------~~~~~~~~~----~~----------~~~~~~~~-----------------~~~~~~~~~~~~~~--~~~~~ll 106 (166)
.++.+.+.. +. ..+.++|. ....-.+++++... ..+...+
T Consensus 90 ~~~~~~~~~t~~~i~~~l~~f~G~i~Q~PP~ySAvKv~GkrlYelAR~G~~ve~~~R~v~I~~i~ll~~~~~~~~p~~~~ 169 (316)
T 1sgv_A 90 LQSVPAKHLTIEAIDAAMERLRGEIRQVPSSVSAIKVGGRRAYRLARQGRSVQLEARPIRIDRFELLAARRRDQLIDIDV 169 (316)
T ss_dssp EEECCCTTCCHHHHHHHHHHTCEEC----------------------------CCCCCCEEEEEEEEEEEEETTEEEEEE
T ss_pred EEecCCCCCCHHHHHHHHHhccccEEEeCCHHHhcccCChhHHHHHhCCCcccccceEEEEEEEEEEEeeccCCCceEEE
Confidence 123333321 10 01111211 11122344443210 1123556
Q ss_pred EEEecCCchhHHHHHHHHcCC------ceeeeeeeEEeCeecC
Q 031089 107 RIVVHEGRNHEVRELVKNAGL------KLYSLKRLRIGGFRLP 143 (166)
Q Consensus 107 ~~~l~tGR~HQIR~~l~~~G~------pI~~l~R~~~g~~~l~ 143 (166)
++.--.| --||..+.-+|. .+..|.|++.|+|+++
T Consensus 170 ~v~CskG--TYIRsLa~DiG~~Lg~~a~~~~LrRt~~G~F~~~ 210 (316)
T 1sgv_A 170 EIDCSSG--TYIRALARDLGDALGVGGHVTALRRTRVGRFELD 210 (316)
T ss_dssp EEEESCC--TTHHHHHHHHHHHHTSCEEEEEEEEEEETTEEGG
T ss_pred EEEECCC--CcHHHHHHHHHHHhCCCEEEeeEEEEEEccCcHH
Confidence 6666677 479999887654 5699999999999996
No 13
>3u28_A H/ACA ribonucleoprotein complex subunit 4; pseudouridine synthase, pseudouridylation, H/ACA RNA; 1.90A {Saccharomyces cerevisiae} PDB: 3uai_A
Probab=96.46 E-value=0.027 Score=47.69 Aligned_cols=132 Identities=17% Similarity=0.151 Sum_probs=78.8
Q ss_pred cchHHHHHHHhhcCCCCCCCCeeecCCCCcCCceeeeeeCC--HHHHHHhhcCCCCCCeEEEEEEe-ccc--Chhhhhh-
Q 031089 2 SLFDDYLKSWDKRNPGLPRPRLFTVGRLDVATTGLIIVTND--GDFAQAVSHPSSKLQKEYIATID-GAV--NKRHLIA- 75 (166)
Q Consensus 2 sl~d~~~~~~~~~~~~~~~~~l~~vhRLD~~TSGlll~ak~--~~~~~~l~~~~~~i~K~Y~a~v~-g~~--~~~~~~~- 75 (166)
|..| +...+++.+. ..++...|-||-.+||+|+++-. ..+...+.. -.|+|.|.+. |.. +.+.+..
T Consensus 71 TS~d-vv~~vrr~l~---~kKvGH~GTLDP~AtGvL~v~iG~aTKl~~~l~~----~~K~Y~a~~~lG~~~~~~~~i~~~ 142 (400)
T 3u28_A 71 SSHE-VVAWIKRILR---CEKTGHSGTLDPKVTGCLIVCIDRATRLVKSQQG----AGKEYVCIVRLHDALKDEKDLGRS 142 (400)
T ss_dssp CHHH-HHHHHHHHHT---CSCEEESSCCCTTCEEEEEEEEGGGGGGHHHHHH----SCEEEEEEEEESSCCSSTTHHHHH
T ss_pred CHHH-HHHHHHHHhC---cCcccccCCCCCCCeEEEEEEEChHHhHhHHhcC----CCcEEEEEEEeCCCCCCHHHHHHH
Confidence 4445 3344444332 25789999999999999998544 355666664 5799999874 332 2344432
Q ss_pred ---hhcc----------eeeCCcccceeEEEEcCCCCCCCceEEEEEecCCchhHHHHHHHHcC------CceeeeeeeE
Q 031089 76 ---ISEG----------TVIEGTHCTPDVVELLPPQPDIPRPRIRIVVHEGRNHEVRELVKNAG------LKLYSLKRLR 136 (166)
Q Consensus 76 ---~~~~----------~~~~~~~~~~~~~~~~~~~~~~~~~ll~~~l~tGR~HQIR~~l~~~G------~pI~~l~R~~ 136 (166)
+... +.........-.++++......+...++|.--.|- -||..+..+| ..+..|.|++
T Consensus 143 l~~f~G~i~Q~PP~ySAvK~~~R~v~I~~i~ll~~~~~~~~~~~~V~CskGT--YIRsL~~DiG~~LG~gahm~~LrRt~ 220 (400)
T 3u28_A 143 LENLTGALFQRPPLISAVKRQLRVRTIYESNLIEFDNKRNLGVFWASCEAGT--YMRTLCVHLGMLLGVGGHMQELRRVR 220 (400)
T ss_dssp HHHTCEEEEECCC-----CCCCEEEEEEEEEEEEEETTTTEEEEEEEECTTC--CHHHHHHHHHHHHSSCEEEEEEEEEE
T ss_pred HHhCcCceEEECCceecccCCceeEEEEEEEEEEEcCCCceEEEEEEECCCC--CHHHHHHHHHHHHCCCEEEEEEEEEE
Confidence 1111 11111111122334443322223455666666664 7999988775 4568999999
Q ss_pred EeCeecC
Q 031089 137 IGGFRLP 143 (166)
Q Consensus 137 ~g~~~l~ 143 (166)
.|+|+++
T Consensus 221 ~G~F~~~ 227 (400)
T 3u28_A 221 SGALSEN 227 (400)
T ss_dssp ETTEETT
T ss_pred EcCcchh
Confidence 9999995
No 14
>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=96.33 E-value=0.021 Score=47.68 Aligned_cols=132 Identities=17% Similarity=0.156 Sum_probs=79.0
Q ss_pred cchHHHHHHHhhcCCCCCCCCeeecCCCCcCCceeeeeeCCHHHHHHhhcCCCCCCeEEEEEEe-c-ccChhhhhhh---
Q 031089 2 SLFDDYLKSWDKRNPGLPRPRLFTVGRLDVATTGLIIVTNDGDFAQAVSHPSSKLQKEYIATID-G-AVNKRHLIAI--- 76 (166)
Q Consensus 2 sl~d~~~~~~~~~~~~~~~~~l~~vhRLD~~TSGlll~ak~~~~~~~l~~~~~~i~K~Y~a~v~-g-~~~~~~~~~~--- 76 (166)
|..| +...+++.+. ..++...|-||-.+||+|+++-. ++. ++.+.-....|+|.|.+. | .++++.+...
T Consensus 78 TS~~-vv~~vr~~l~---~~KvGH~GTLDP~AtGvL~v~~G-~aT-k~~~~l~~~~K~Y~~~~~lG~~~~~~~i~~~l~~ 151 (357)
T 2apo_A 78 TSHE-VSTWVKKILN---LDKAGHGGTLDPKVTGVLPVALE-RAT-KTIPMWHIPPKEYVCLMHLHRDASEEDILRVFKE 151 (357)
T ss_dssp CHHH-HHHHHHHHTT---CSCEEESSCCCTTCEEEEEEEEG-GGG-GGGGGTTSSCEEEEEEEEESSCCCHHHHHHHHHH
T ss_pred CHHH-HHHHHHHHhC---ccccccccccCCCceeEEEEEeC-HHH-hHHHHhccCCcEEEEEEEECCCCCHHHHHHHHHh
Confidence 4445 4445555443 25789999999999999999775 332 333322347899999875 2 3455554422
Q ss_pred -hccee-e---------CCcccceeEEEEcCCCCCCCceEEEEEecCCchhHHHHHHHHcCC------ceeeeeeeEEeC
Q 031089 77 -SEGTV-I---------EGTHCTPDVVELLPPQPDIPRPRIRIVVHEGRNHEVRELVKNAGL------KLYSLKRLRIGG 139 (166)
Q Consensus 77 -~~~~~-~---------~~~~~~~~~~~~~~~~~~~~~~ll~~~l~tGR~HQIR~~l~~~G~------pI~~l~R~~~g~ 139 (166)
...+. . .......-.+++++.. .+...+++.--.| --||..+.-+|. .+..|.|++.|+
T Consensus 152 f~G~i~Q~PP~~SAvK~~~R~v~I~~~~l~~~~--~~~~~~~v~cs~G--TYIRsL~~DiG~~LG~~a~~~~LrRt~~G~ 227 (357)
T 2apo_A 152 FTGRIYQRPPLKAAVKRRLRIRKIHELELLDKD--GKDVLFRVKCQSG--TYIRKLCEDIGEALGTSAHMQELRRTKSGC 227 (357)
T ss_dssp HSEEEECC-----------CEEEEEEEEEEEEE--TTEEEEEEEECTT--CCHHHHHHHHHHHTTSCEEEEEEEEEEETT
T ss_pred CcccEEEeCCchhhccccccceeEEEEEEEEee--CCEEEEEEEECCC--chHHHHHHHHHHhhCCCEEEEEEEEEEEcc
Confidence 11110 0 0011111233333321 2345566666666 589988877653 579999999999
Q ss_pred eecC
Q 031089 140 FRLP 143 (166)
Q Consensus 140 ~~l~ 143 (166)
|.++
T Consensus 228 f~~~ 231 (357)
T 2apo_A 228 FEEK 231 (357)
T ss_dssp EEGG
T ss_pred CcHH
Confidence 9995
No 15
>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=96.33 E-value=0.018 Score=47.57 Aligned_cols=132 Identities=19% Similarity=0.210 Sum_probs=78.1
Q ss_pred cchHHHHHHHhhcCCCCCCCCeeecCCCCcCCceeeeeeCCHHHHHHhhcCCCCCCeEEEEEEe-c-ccChhhhhhh---
Q 031089 2 SLFDDYLKSWDKRNPGLPRPRLFTVGRLDVATTGLIIVTNDGDFAQAVSHPSSKLQKEYIATID-G-AVNKRHLIAI--- 76 (166)
Q Consensus 2 sl~d~~~~~~~~~~~~~~~~~l~~vhRLD~~TSGlll~ak~~~~~~~l~~~~~~i~K~Y~a~v~-g-~~~~~~~~~~--- 76 (166)
|..| +...+++.+. ..++...|-||-.+||+|+++-.. +. ++.+.-....|+|.|.+. | .++++.+...
T Consensus 58 tS~~-vv~~vr~~~~---~~KvGH~GTLDP~atGvL~v~~g~-aT-k~~~~l~~~~K~Y~~~~~lg~~~~~~~i~~~l~~ 131 (334)
T 2aus_C 58 TSHE-VVAWIKRILN---LEKAGHGGTLDPKVSGVLPVALER-AT-RVVQALLPAGKEYVALMHLHGDVPEDKIRAVMKE 131 (334)
T ss_dssp CHHH-HHHHHHHHTT---CSCEEESSCCCTTCEEEEEEEEGG-GG-GGGGGGTTCCEEEEEEEEESSCCCHHHHHHHHHH
T ss_pred CHHH-HHHHHHHHhC---cceeccccccCCccceeEEEEeCh-hh-hhHHHhcccCcEEEEEEEECCCCCHHHHHHHHHh
Confidence 4445 4445555443 257899999999999999987652 22 333322236899999874 2 3455555432
Q ss_pred -hccee-e---------CCcccceeEEEEcCCCCCCCceEEEEEecCCchhHHHHHHHHcC------CceeeeeeeEEeC
Q 031089 77 -SEGTV-I---------EGTHCTPDVVELLPPQPDIPRPRIRIVVHEGRNHEVRELVKNAG------LKLYSLKRLRIGG 139 (166)
Q Consensus 77 -~~~~~-~---------~~~~~~~~~~~~~~~~~~~~~~ll~~~l~tGR~HQIR~~l~~~G------~pI~~l~R~~~g~ 139 (166)
...+. . .........+++++.. .+...+++.-..| --||..+.-+| ..+..|.|++.|+
T Consensus 132 f~G~i~Q~pP~~SA~k~~~R~v~I~~~~~~~~~--~~~~~~~v~cs~G--TYIRsL~~Dig~~Lg~~a~~~~LrRt~~g~ 207 (334)
T 2aus_C 132 FEGEIIQRPPLRSAVKRRLRTRKVYYIEILEID--GRDVLFRVGVEAG--TYIRSLIHHIGLALGVGAHMAELRRTRSGP 207 (334)
T ss_dssp TSEEEECC------------EEEEEEEEEEEEE--TTEEEEEEEECTT--CCHHHHHHHHHHHHSSCEEEEEEEEEEETT
T ss_pred CcCeEEEeCCccccCcCCcCCEEEEEEEEEEee--CCeEEEEEEECCC--cHHHHHHHHHHHHhCCCEEEeEEEEEEEcc
Confidence 11110 0 0011111233333321 2345566666666 58998887765 3679999999999
Q ss_pred eecC
Q 031089 140 FRLP 143 (166)
Q Consensus 140 ~~l~ 143 (166)
|+++
T Consensus 208 f~~~ 211 (334)
T 2aus_C 208 FKED 211 (334)
T ss_dssp EESS
T ss_pred Cchh
Confidence 9995
No 16
>3h7h_A Transcription elongation factor SPT4; helices surrounding beta sheet, activator, ME binding, nucleus, repressor, transcription regulation; 1.55A {Homo sapiens}
Probab=26.14 E-value=1.2e+02 Score=20.93 Aligned_cols=44 Identities=11% Similarity=0.207 Sum_probs=30.8
Q ss_pred ceeeeeeCCH-HHHHHhhcCCCCCCeEEEEEEecccChhhhhhhh
Q 031089 34 TGLIIVTNDG-DFAQAVSHPSSKLQKEYIATIDGAVNKRHLIAIS 77 (166)
Q Consensus 34 SGlll~ak~~-~~~~~l~~~~~~i~K~Y~a~v~g~~~~~~~~~~~ 77 (166)
+|+|++.+-. ....+.+.-...+.=.|-+.|.|.++++.+..++
T Consensus 61 ~G~I~i~dP~~SwVAk~~~i~~~vPG~YAlkV~g~lp~~i~~~le 105 (120)
T 3h7h_A 61 DGIIAMMSPEDSWVSKWQRVSNFKPGVYAVSVTGRLPQGIVRELK 105 (120)
T ss_dssp EEEEEESCGGGCHHHHHTTCTTSCSEEEEEEECCCCCHHHHHHHH
T ss_pred ceEEEEeCCcHHHHHHHhccCCCCCCeEEEEecCcCCHHHHHHHH
Confidence 6999886533 3333444445567889999999999988766553
Done!