Query 018524
Match_columns 354
No_of_seqs 346 out of 1760
Neff 8.4
Searched_HMMs 29240
Date Mon Mar 25 16:36:43 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/018524.a3m -d /work/01045/syshi/HHdatabase/pdb70.hhm -o /work/01045/syshi/hhsearch_pdb/018524hhsearch_pdb -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 1v9f_A Ribosomal large subunit 100.0 8.4E-57 2.9E-61 424.7 23.6 281 9-353 6-312 (325)
2 1v9k_A Ribosomal large subunit 100.0 1.1E-52 3.7E-57 377.5 22.2 216 85-353 3-225 (228)
3 2i82_A Ribosomal large subunit 100.0 1.8E-51 6.1E-56 366.8 19.9 203 84-342 12-216 (217)
4 1ksk_A Ribosomal small subunit 100.0 5E-43 1.7E-47 316.0 4.4 204 19-305 3-208 (234)
5 1vio_A Ribosomal small subunit 100.0 2.2E-42 7.6E-47 313.3 3.7 204 19-305 2-209 (243)
6 2oml_A Ribosomal large subunit 100.0 3.8E-39 1.3E-43 281.2 9.8 170 83-306 3-172 (189)
7 2olw_A Ribosomal large subunit 100.0 4.1E-39 1.4E-43 286.5 10.1 170 83-306 31-200 (217)
8 3dh3_A Ribosomal large subunit 100.0 1.4E-38 4.9E-43 293.5 2.4 201 17-304 4-207 (290)
9 2gml_A Ribosomal large subunit 100.0 2.5E-32 8.4E-37 243.5 8.2 142 89-303 12-153 (237)
10 1r3e_A TRNA pseudouridine synt 96.8 0.00058 2E-08 62.5 2.9 70 91-182 3-72 (309)
11 1k8w_A TRNA pseudouridine synt 96.8 0.00072 2.5E-08 62.4 3.4 70 91-182 25-94 (327)
12 1p9k_A ORF, hypothetical prote 96.7 0.00022 7.7E-09 52.0 -0.6 53 9-74 11-64 (79)
13 2aus_C Pseudouridine synthase; 96.6 0.00079 2.7E-08 62.7 2.9 73 88-182 43-115 (334)
14 1sgv_A TRNA pseudouridine synt 96.6 0.00079 2.7E-08 61.8 2.7 71 90-182 5-75 (316)
15 2apo_A Probable tRNA pseudouri 96.5 0.0011 3.7E-08 62.1 2.6 73 88-182 63-135 (357)
16 3u28_A H/ACA ribonucleoprotein 96.2 0.0025 8.5E-08 60.3 3.5 75 88-184 56-131 (400)
17 2k6p_A Uncharacterized protein 94.0 0.014 4.9E-07 43.5 1.0 34 20-65 1-35 (92)
18 2vqe_D 30S ribosomal protein S 93.7 0.00041 1.4E-08 60.3 -9.3 79 18-109 97-180 (209)
19 1c05_A Ribosomal protein S4 de 91.6 0.0034 1.2E-07 52.1 -6.0 78 18-110 49-131 (159)
20 2xzm_D Ribosomal protein S4 co 89.7 0.043 1.5E-06 46.2 -1.0 46 18-75 105-151 (181)
21 3r8n_D 30S ribosomal protein S 86.6 0.055 1.9E-06 46.5 -2.4 46 18-75 93-139 (205)
22 3j20_D 30S ribosomal protein S 86.2 0.027 9.1E-07 47.4 -4.4 45 19-75 102-147 (180)
23 3bbn_D Ribosomal protein S4; s 85.3 0.063 2.1E-06 46.0 -2.7 44 19-74 88-132 (201)
24 2cqj_A BRMS2, U3 small nucleol 84.4 0.013 4.5E-07 41.5 -6.1 45 18-74 6-51 (71)
25 3iz6_C 40S ribosomal protein S 79.7 0.21 7.3E-06 42.3 -1.4 46 18-75 107-153 (195)
26 3u5c_J 40S ribosomal protein S 78.9 0.14 4.6E-06 43.6 -2.9 46 18-75 105-151 (197)
27 1dm9_A Hypothetical 15.5 KD pr 76.2 0.13 4.6E-06 41.0 -3.5 42 18-72 7-49 (133)
28 3hp7_A Hemolysin, putative; st 75.1 0.086 2.9E-06 48.0 -5.6 36 19-66 6-44 (291)
No 1
>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=100.00 E-value=8.4e-57 Score=424.66 Aligned_cols=281 Identities=20% Similarity=0.254 Sum_probs=174.1
Q ss_pred CccccCCCCCCCcccccccccC-CCCCCCCCCCCCCccccCCCCCCCCCCcccccceeEEeecccccccccccC------
Q 018524 9 PTFTLTPKAVPRFRKTFFSLAS-MSNPTEPTSQNAPQTQQNYPTPLSPPLPAISKDIELTRAMSASSKSSLYKL------ 81 (354)
Q Consensus 9 ~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~v~~~~~~~~~~~~~~~~~------ 81 (354)
.++++++++.+||+|+||+... ..||..++++|..|.| .|||.++......+.+. +.+.+
T Consensus 6 ~~~~v~~~~~g~RLd~~L~~~~~~~SR~~~~~lI~~G~V------------~VNG~~v~~~~~~v~~g-D~I~v~~~~~~ 72 (325)
T 1v9f_A 6 LTATVSENQLGQRLDQALAEMFPDYSRSRIKEWILDQRV------------LVNGKVCDKPKEKVLGG-EQVAINAEIEE 72 (325)
T ss_dssp --------------------------------------------------------------------------------
T ss_pred EEEEECCccCCchHHHHHHhhccccCHHHHHHHHHCCCE------------EECCEEccCCCCEeCCC-CEEEEeccccc
Confidence 3577888889999999999886 7899999999999988 44444322222222221 11111
Q ss_pred --------CCccEEEeCCcEEEEECCCCCccccccccc-cccccccccccccCCCccccccccccccccccCCCCCceEE
Q 018524 82 --------SRSDVLYEDEWLVAVNKPQGVYCESVLASV-PCLLAGDSAESKSGRLSEGTKLNLLELHLANRLDRDTSGVM 152 (354)
Q Consensus 82 --------~~~~Ilyed~~~lvvnKP~Gl~~~~~~~~~-~~~~~~~~~~~~~~~l~~~~~~~~~~l~~vhRLDk~TSGll 152 (354)
.++.|+|||++|+|||||+|++||+..... .++++... ..+.... +...+++|||||++|||||
T Consensus 73 ~~~~~~~~~~~~ilyed~~~lvvnKP~G~~~~~~~~~~~~tl~~~l~-----~~~~~~~--~~~~~~~vhRLD~~TSGll 145 (325)
T 1v9f_A 73 EARFEPQDIPLDIVYEDEDIIIINKPRDLVVHPGAGNPDGTVLNALL-----HYYPPIA--DVPRAGIVHRLDKDTTGLM 145 (325)
T ss_dssp ---CCCCCCCCCEEEECSSEEEEEECSSCCSSCBTTBSSSSHHHHHH-----HHCGGGG--GSGGGGBCCCCCTTCEEEE
T ss_pred cccCCcccCCCeEEEECCCEEEEECCCCCeEecCCCCCCccHHHHHH-----HHHHhcC--CCCceeeecCCCCCCeeEE
Confidence 135799999999999999999999754321 22211110 0111110 1146899999999999999
Q ss_pred EEEeCHHHHHHHHHHhhcCccceEEEEEEeCCCCCCCceEEecCCCCCCCCceeEeeecCCccccCCCcccccceeeEEE
Q 018524 153 VITKSHKVASKLVKAFTDHKVSKTYIALCIGPAPKWKRITIISGHGRSKFGAWRVYAASDVGRVLPGGSVVRDMVTSFEV 232 (354)
Q Consensus 153 llAk~~~~a~~l~~~f~~~~v~K~Y~A~v~G~~~~~~~~~i~~~i~~~~~~~~~~~~~~~~~~~~~~g~~~~~a~t~~~v 232 (354)
|||||+++++.|+++|+++.++|+|+|+|.|.++. .+.|+.+++++.....+... ..+ .+.+.|+|++
T Consensus 146 l~ak~~~~~~~l~~~~~~~~v~K~Y~a~v~G~~~~--~g~i~~~i~~~~~~~~~~~v-------~~~---gk~a~t~~~v 213 (325)
T 1v9f_A 146 VVAKTVPAQTRLVESLQRREITREYEAVAIGHMTA--GGTVDEPISRHPTKRTHMAV-------HPM---GKPAVTHYRI 213 (325)
T ss_dssp EEESSHHHHHHHHHHHHTTCSEEEEEEEEESCCCC--CEEEECCEEECSSCTTCEEE-------CTT---SBCCEEEEEE
T ss_pred EEEcCHHHHHHHHHHHHcCCeeEEEEEEEeCCCCC--CCEEeeeeeECCCCCEEEEE-------CCC---CeeEEEEEEE
Confidence 99999999999999999999999999999999875 57888888776544333321 122 2678899999
Q ss_pred eeecCCCCCCCCcchhcccccceeeeeehhhccCCCCceEEEEEEeCCCchhHHHHHHhhcCCceecCCCCCCccccCC-
Q 018524 233 LSVNGEGSFKEPSELQEHEENNIVVEKKAVLDADAKKNEILVRAFPRSGRTHQIRLHCQYLGISIRGDVKYEGVYEWNG- 311 (354)
Q Consensus 233 l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~slv~~~~~TGR~HQIRvhla~lG~PIvGD~~Yg~~~~~~~- 311 (354)
+.. ..++++++|+|.|||+||||+||+++||||+||.+||+......
T Consensus 214 l~~--------------------------------~~~~slv~~~l~TGR~HQIRvhla~lG~PI~GD~~Yg~~~~~~~~ 261 (325)
T 1v9f_A 214 MEH--------------------------------FRVHTRLRLRLETGRTHQIRVHMAHITHPLVGDPVYGGRPRPPKG 261 (325)
T ss_dssp EEE--------------------------------CSSEEEEEEEESCCCTTHHHHHHHHTTCCBTTCTTTTCCCCCCTT
T ss_pred eEE--------------------------------cCCeEEEEEEECCCCcHHHHHHHHhCCCceeCChhhCCccccccc
Confidence 875 24579999999999999999999999999999999997521000
Q ss_pred ---------CCCCCceeeeeeeEeeCCCCCCceEEEcCCChhHHHHHHhcc
Q 018524 312 ---------KRYDGHELHAESLSFDHPVTGCPVMVQAPLPLWGTEALQSSS 353 (354)
Q Consensus 312 ---------~~~~~~~LHa~~L~f~~P~~~~~~~~~aplP~~f~~~l~~l~ 353 (354)
....+++|||++|+|.||.+++.+.|+||+|.+|.++|+.|+
T Consensus 262 ~~~~~~~~~~~~~r~~LHA~~L~f~hP~~~~~~~~~aplp~~~~~~l~~l~ 312 (325)
T 1v9f_A 262 ASEAFISTLRKFDRQALHATMLRLYHPISGIEMEWHAPIPQDMVELIEVMR 312 (325)
T ss_dssp CCHHHHHHHHHCCSCSEEEEEEEEECTTTCCEEEEECCCCHHHHHHHHHHH
T ss_pred cchhhhhhccCCcChhhheeeeEeeCCCCCCEEEEEecCcHHHHHHHHHhc
Confidence 124689999999999999999999999999999999999875
No 2
>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=100.00 E-value=1.1e-52 Score=377.46 Aligned_cols=216 Identities=29% Similarity=0.349 Sum_probs=169.3
Q ss_pred cEEEeCCcEEEEECCCCCccccccccccccccccccccccCCCccccccccccccccccCCCCCceEEEEEeCHHHHHHH
Q 018524 85 DVLYEDEWLVAVNKPQGVYCESVLASVPCLLAGDSAESKSGRLSEGTKLNLLELHLANRLDRDTSGVMVITKSHKVASKL 164 (354)
Q Consensus 85 ~Ilyed~~~lvvnKP~Gl~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~l~~vhRLDk~TSGllllAk~~~~a~~l 164 (354)
.|+|||++|+|||||+|++||+......+++. .+..... ....+++|||||++||||||||||+++++.|
T Consensus 3 ~Ilyed~~~lvvnKP~G~~~~~~~~~~~~l~~---------~l~~~~~-~~~~~~~VhRLD~~TSGlll~ak~~~~~~~l 72 (228)
T 1v9k_A 3 VIMYEDDHILVLNKPSGTAVHGGSGLSFGVIE---------GLRALRP-EARFLELVHRLDRDTSGVLLVAKKRSALRSL 72 (228)
T ss_dssp CEEEECSSEEEEEECTTSCSSCCSSSBCCHHH---------HHHHHST-TCSCCEESSCCCTTCEEEEEEESSHHHHHHH
T ss_pred CEEEECCCEEEEECCCCCeEecCCChHHHHHH---------HHHHHcC-CCCccceEecCCCCCeEEEEEEeCHHHHHHH
Confidence 68999999999999999999975432222211 1111000 0135889999999999999999999999999
Q ss_pred HHHhhcCccceEEEEEEeCCCCCCCceEEecCCCCCC--CCceeEeeecCCccccCCCcccccceeeEEEeeecCCCCCC
Q 018524 165 VKAFTDHKVSKTYIALCIGPAPKWKRITIISGHGRSK--FGAWRVYAASDVGRVLPGGSVVRDMVTSFEVLSVNGEGSFK 242 (354)
Q Consensus 165 ~~~f~~~~v~K~Y~A~v~G~~~~~~~~~i~~~i~~~~--~~~~~~~~~~~~~~~~~~g~~~~~a~t~~~vl~~~~~~~~~ 242 (354)
+++|+++.|+|+|+|+|.|.+++ +.+.|+.++.++. .|...+.. ..+ .+.+.|.|+++..
T Consensus 73 ~~~~~~~~v~K~Y~a~v~G~~~~-~~~~i~~~l~~~~~~~g~~~~~~-------~~~---gk~a~t~~~vl~~------- 134 (228)
T 1v9k_A 73 HEQLREKGMQKDYLALVRGQWQS-HVKSVQAPLLKNILQSGERIVRV-------SQE---GKPSETRFKVEER------- 134 (228)
T ss_dssp HHHHHTTCSEEEEEEEEESCCCT-TCCEECCCEEEEECTTSCEEEEE-------CTT---SBCCCEEEEEEEE-------
T ss_pred HHHHHhCCeeEEEEEEEecccCC-CCCEEeCceeccCCCCCceEEEE-------CCC---CcEEEEEEEEEEE-------
Confidence 99999999999999999999875 4456776665432 22222211 112 2678899998865
Q ss_pred CCcchhcccccceeeeeehhhccCCCCceEEEEEEeCCCchhHHHHHHhhcCCceecCCCCCCcccc-----CCCCCCCc
Q 018524 243 EPSELQEHEENNIVVEKKAVLDADAKKNEILVRAFPRSGRTHQIRLHCQYLGISIRGDVKYEGVYEW-----NGKRYDGH 317 (354)
Q Consensus 243 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~slv~~~~~TGR~HQIRvhla~lG~PIvGD~~Yg~~~~~-----~~~~~~~~ 317 (354)
..++++++|+|.|||+||||+||+++||||+||.+||+.... ......++
T Consensus 135 -------------------------~~~~slv~~~l~TGR~HQIR~hla~lG~PI~gD~~YG~~~~~~~~~~~~~~~~r~ 189 (228)
T 1v9k_A 135 -------------------------YAFATLVRCSPVTGRTHQIRVHTQYAGHPIAFDDRYGDREFDRQLTEAGTGLNRL 189 (228)
T ss_dssp -------------------------CSSEEEEEEEESSCCTTHHHHHHHHTTCCBTTCTTTSCHHHHHHHHHTTCCCCSC
T ss_pred -------------------------cCCeEEEEEEECCCCchHHHHHHHHCCCcEecCcccCCccccchhhcccCCCCCh
Confidence 245799999999999999999999999999999999974210 11235689
Q ss_pred eeeeeeeEeeCCCCCCceEEEcCCChhHHHHHHhcc
Q 018524 318 ELHAESLSFDHPVTGCPVMVQAPLPLWGTEALQSSS 353 (354)
Q Consensus 318 ~LHa~~L~f~~P~~~~~~~~~aplP~~f~~~l~~l~ 353 (354)
+|||++|+|.||.+++.+.|+||+|.+|.++++.|+
T Consensus 190 ~LHa~~l~f~hP~t~~~~~~~aplp~~~~~~l~~l~ 225 (228)
T 1v9k_A 190 FLHAAALKFTHPGTGEVMRIEAPMDEGLKRCLQKMR 225 (228)
T ss_dssp CEEEEEEEEECTTTCCEEEEECCCCHHHHHHHHHHH
T ss_pred hhccceeEeeCCCCCCEEEEEeCCcHHHHHHHHHhh
Confidence 999999999999999999999999999999998875
No 3
>2i82_A Ribosomal large subunit pseudouridine synthase A; lyase/RNA complex; HET: FOU; 2.05A {Escherichia coli}
Probab=100.00 E-value=1.8e-51 Score=366.84 Aligned_cols=203 Identities=25% Similarity=0.296 Sum_probs=159.5
Q ss_pred ccEEEeCCcEEEEECCCCCccccccc--cccccccccccccccCCCccccccccccccccccCCCCCceEEEEEeCHHHH
Q 018524 84 SDVLYEDEWLVAVNKPQGVYCESVLA--SVPCLLAGDSAESKSGRLSEGTKLNLLELHLANRLDRDTSGVMVITKSHKVA 161 (354)
Q Consensus 84 ~~Ilyed~~~lvvnKP~Gl~~~~~~~--~~~~~~~~~~~~~~~~~l~~~~~~~~~~l~~vhRLDk~TSGllllAk~~~~a 161 (354)
++|+|||++|+|||||+|++||+... ...+ +...+.... ..+++|||||++||||||||||++++
T Consensus 12 ~~ilyed~~~lvvnKP~G~~~~~~~~~~~~~t---------l~~~l~~~~----~~~~~vhRLD~~TSGlll~ak~~~~~ 78 (217)
T 2i82_A 12 LVILYQDDHIMVVNKPSGLLSVPGRLEEHKDS---------VMTRIQRDY----PQAESVHRLDMATSGVIVVALTKAAE 78 (217)
T ss_dssp CCEEEECSSEEEEEECTTSBSSCCSSGGGCCB---------HHHHHHHHC----TTCEESSCCCTTCEEEEEEESSHHHH
T ss_pred ceEEEECCCEEEEECCCCCeEeCCCCCCchhH---------HHHHHHHHC----CCCceeecCCCCCeEEEEEEeCHHHH
Confidence 68999999999999999999997532 1112 222221111 35789999999999999999999999
Q ss_pred HHHHHHhhcCccceEEEEEEeCCCCCCCceEEecCCCCCCCCceeEeeecCCccccCCCcccccceeeEEEeeecCCCCC
Q 018524 162 SKLVKAFTDHKVSKTYIALCIGPAPKWKRITIISGHGRSKFGAWRVYAASDVGRVLPGGSVVRDMVTSFEVLSVNGEGSF 241 (354)
Q Consensus 162 ~~l~~~f~~~~v~K~Y~A~v~G~~~~~~~~~i~~~i~~~~~~~~~~~~~~~~~~~~~~g~~~~~a~t~~~vl~~~~~~~~ 241 (354)
+.|+++|+++.|+|+|+|+|.|.++. +.+.++.++.++..+...... ...+ .+.+.|+|+++...
T Consensus 79 ~~l~~~f~~~~v~K~Y~a~v~G~~~~-~~g~i~~~l~~~~~~~~~~~v------~~~~---gk~a~t~~~vl~~~----- 143 (217)
T 2i82_A 79 RELKRQFREREPKKQYVARVWGHPSP-AEGLVDLPLICDWPNRPKQKV------CYET---GKPAQTEYEVVEYA----- 143 (217)
T ss_dssp HHHHHHHHTTCSEEEEEEEEESCCSS-SEEEEECCEEECGGGTTCEEE------CTTT---CBCCEEEEEEEEEE-----
T ss_pred HHHHHHHHhCCeeEEEEEEEecccCC-CCcEEecceeecCCCCcEEEE------eCCC---CcEEEEEEEEEEEC-----
Confidence 99999999999999999999999875 456777777554322111111 1122 26788999988652
Q ss_pred CCCcchhcccccceeeeeehhhccCCCCceEEEEEEeCCCchhHHHHHHhhcCCceecCCCCCCccccCCCCCCCceeee
Q 018524 242 KEPSELQEHEENNIVVEKKAVLDADAKKNEILVRAFPRSGRTHQIRLHCQYLGISIRGDVKYEGVYEWNGKRYDGHELHA 321 (354)
Q Consensus 242 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~slv~~~~~TGR~HQIRvhla~lG~PIvGD~~Yg~~~~~~~~~~~~~~LHa 321 (354)
...+++++|+|.|||+||||+||+++||||+||.+||+.... ....+++|||
T Consensus 144 --------------------------~~~~slv~~~l~TGR~HQIR~hla~lG~PIvGD~~Yg~~~~~--~~~~r~~LHa 195 (217)
T 2i82_A 144 --------------------------ADNTARVVLKPITGRSHQLRVHMLALGHPILGDRFYASPEAR--AMAPRLLLHA 195 (217)
T ss_dssp --------------------------TTTEEEEEEEESSCCTTHHHHHHHHTTCCBTTCTTTSCHHHH--HTCSSCCEEE
T ss_pred --------------------------CCCeEEEEEEECCCCcHHHHHHHHHCCCcEECccccCCcccc--CCCCCceeee
Confidence 122689999999999999999999999999999999975321 1236899999
Q ss_pred eeeEeeCCCCCCceEEEcCCC
Q 018524 322 ESLSFDHPVTGCPVMVQAPLP 342 (354)
Q Consensus 322 ~~L~f~~P~~~~~~~~~aplP 342 (354)
++|+|.||.+++.+.|+||+|
T Consensus 196 ~~l~f~hP~~~~~~~~~ap~p 216 (217)
T 2i82_A 196 EMLTITHPAYGNSMTFKAPAD 216 (217)
T ss_dssp EEEEEECTTTCCEEEEECCCC
T ss_pred eEeEEcCCCCCCEEEEEecCC
Confidence 999999999999999999998
No 4
>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=5e-43 Score=316.02 Aligned_cols=204 Identities=19% Similarity=0.187 Sum_probs=154.0
Q ss_pred CCcccccccccCCCCCCCCCCCCCCccccCCCCCCCCCCcccccceeEEeecccccccccccCCCccEEEe-CCcEEEEE
Q 018524 19 PRFRKTFFSLASMSNPTEPTSQNAPQTQQNYPTPLSPPLPAISKDIELTRAMSASSKSSLYKLSRSDVLYE-DEWLVAVN 97 (354)
Q Consensus 19 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~v~~~~~~~~~~~~~~~~~~~~~Ilye-d~~~lvvn 97 (354)
+||+|+|++.....||..+.+++..|.| .+||..+......+.+. +.+.+.+..|+|| |++|+|||
T Consensus 3 ~~RLd~~L~~~~~~SR~~~~~li~~G~V------------~VNG~~v~~~~~~v~~g-D~I~v~~~~i~~e~d~~~lvvn 69 (234)
T 1ksk_A 3 HMRLDKFIAQQLGVSRAIAGREIRGNRV------------TVDGEIVRNAAFKLLPE-HDVAYDGNPLAQQHGPRYFMLN 69 (234)
T ss_dssp CEEHHHHHHHHHTCCHHHHHHHHHTTCE------------EETTEECCCTTCEECTT-CCEEETTEEECCCCCCCEEEEE
T ss_pred cccHHHHHHHcCCCCHHHHHHHHHcCeE------------EECCEEeCCCCCCCCCC-CEEEEeCeEeecCCCCEEEEEE
Confidence 6899999998888899999999999999 88887665455556554 5677777789999 99999999
Q ss_pred CCCCCccccccccccccccccccccccCCCccccccccccccccccCCCCCceEEEEEeCHHHHHHHHHHhhcCccceEE
Q 018524 98 KPQGVYCESVLASVPCLLAGDSAESKSGRLSEGTKLNLLELHLANRLDRDTSGVMVITKSHKVASKLVKAFTDHKVSKTY 177 (354)
Q Consensus 98 KP~Gl~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~l~~vhRLDk~TSGllllAk~~~~a~~l~~~f~~~~v~K~Y 177 (354)
||+|++||+......+ +.+.+..... ..+++|||||++||||||||||+++++.+.+ +++.++|+|
T Consensus 70 KP~G~~~~~~~~~~~t---------l~~~l~~~~~---~~~~~vhRLD~~TsGlll~ak~~~~~~~l~~--~~~~v~K~Y 135 (234)
T 1ksk_A 70 KPQGYVCSTDDPDHPT---------VLYFLDEPVA---WKLHAAGRLDIDTTGLVLMTDDGQWSHRITS--PRHHCEKTY 135 (234)
T ss_dssp ECTTCBSSSSCSSSCB---------GGGGCCCTTG---GGCEESSCCCTTCEEEEEEESCHHHHHHHHC--TTSCCCEEE
T ss_pred CCCCCEeCCCCCCCCc---------HHHHhhhhhc---CCeeEcCCCCCCCeeEEEEEcCHHHHHHHhC--CCCCCCeEE
Confidence 9999999976543222 2223322221 3689999999999999999999999999987 789999999
Q ss_pred EEEEeCCCCCCCceEEecCCCCCCCCceeEeeecCCccccC-CCcccccceeeEEEeeecCCCCCCCCcchhccccccee
Q 018524 178 IALCIGPAPKWKRITIISGHGRSKFGAWRVYAASDVGRVLP-GGSVVRDMVTSFEVLSVNGEGSFKEPSELQEHEENNIV 256 (354)
Q Consensus 178 ~A~v~G~~~~~~~~~i~~~i~~~~~~~~~~~~~~~~~~~~~-~g~~~~~a~t~~~vl~~~~~~~~~~~~~~~~~~~~~~~ 256 (354)
+|+|.|.++.+. ++... .|. .+. ++...+++ .++++.
T Consensus 136 ~a~v~g~~~~~~---i~~~~----~g~-----------~~~~~~~~~~~a--~~~~~~---------------------- 173 (234)
T 1ksk_A 136 LVTLESPVADDT---AEQFA----KGV-----------QLHNEKDLTKPA--VLEVIT---------------------- 173 (234)
T ss_dssp EEEESSCCCTTH---HHHHH----HCC-----------CCTTCSSCCCCC--EEEEEE----------------------
T ss_pred EEEEccCCCHHH---HHHHH----CCe-----------EECCCCcccceE--EEEEeC----------------------
Confidence 999999987632 11110 000 010 11112233 244331
Q ss_pred eeeehhhccCCCCceEEEEEEeCCCchhHHHHHHhhcCCceecCCCCCC
Q 018524 257 VEKKAVLDADAKKNEILVRAFPRSGRTHQIRLHCQYLGISIRGDVKYEG 305 (354)
Q Consensus 257 ~~~~~~~~~~~~~~~slv~~~~~TGR~HQIRvhla~lG~PIvGD~~Yg~ 305 (354)
.++++|+|.|||+||||+||+++||||+||.+|+.
T Consensus 174 --------------~s~~~~~l~tGR~HQIR~h~~~lG~pi~gd~ry~~ 208 (234)
T 1ksk_A 174 --------------PTQVRLTISEGRYHQVKRMFAAVGNHVVELHRERI 208 (234)
T ss_dssp --------------TTEEEEEESCCCTTHHHHHHHHTTCCEEEEEEEEE
T ss_pred --------------CeEEEEEEccCCCHHHHHHHHHcCCeEeeeEEEEE
Confidence 36899999999999999999999999999999974
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=2.2e-42 Score=313.33 Aligned_cols=204 Identities=20% Similarity=0.232 Sum_probs=152.2
Q ss_pred CCcccccccccCCCCCCCCCCCCCCccccCCCCCCCCCCcccccceeEEeecccccccccccCCCccEEEeCCc-EEEEE
Q 018524 19 PRFRKTFFSLASMSNPTEPTSQNAPQTQQNYPTPLSPPLPAISKDIELTRAMSASSKSSLYKLSRSDVLYEDEW-LVAVN 97 (354)
Q Consensus 19 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~v~~~~~~~~~~~~~~~~~~~~~Ilyed~~-~lvvn 97 (354)
.||+|+||+.....||..+.+++..|.| .|||.++......+.+. +.+.+.+..|+|||++ |+|||
T Consensus 2 ~~RLd~~L~~~~~~SR~~~~~lI~~G~V------------~VNG~~v~~~~~~v~~g-D~I~v~~~~i~~ed~~~~lvvn 68 (243)
T 1vio_A 2 SLRLDKFIAENVGLTRSQATKAIRQSAV------------KINGEIVKSGSVQISQE-DEIYFEDELLTWIEEGQYFMLN 68 (243)
T ss_dssp CEEHHHHHHHHHTCCHHHHHHHHHTTCE------------EETTEECCCTTCEECTT-SCEEETTEECCSSCCCCEEEEE
T ss_pred CccHHHHHHHcCCCCHHHHHHHHHcCcE------------EECCEEeCCCCCCcCCC-CEEEEeccccccCCCCEEEEEE
Confidence 5899999998888899999999999999 88888765555555554 4677777889999999 99999
Q ss_pred CCCCCccccccccccccccccccccccCCCccccccccccccccccCCCCCceEEEEEeCHHHHHHHHHHhhcCccceEE
Q 018524 98 KPQGVYCESVLASVPCLLAGDSAESKSGRLSEGTKLNLLELHLANRLDRDTSGVMVITKSHKVASKLVKAFTDHKVSKTY 177 (354)
Q Consensus 98 KP~Gl~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~l~~vhRLDk~TSGllllAk~~~~a~~l~~~f~~~~v~K~Y 177 (354)
||+|++|++......+ +.+.+..... ..+++|||||++||||||||||+++++.+.. +++.++|+|
T Consensus 69 KP~G~~~~~~~~~~~t---------l~~~l~~~~~---~~~~~vhRLD~~TsGlll~ak~~~~a~~l~~--~~~~v~K~Y 134 (243)
T 1vio_A 69 KPQGCVCSNDDGDYPT---------IYQFFDYPLA---GKLHSAGRLDVDTTGLVLLTDDGQWSHRITS--PKHHCEKTY 134 (243)
T ss_dssp ECTTCBSSCCC--CCB---------GGGGSCTTGG---GGCEESSCCCTTCEEEEEEESCHHHHHHHHC--TTSCCCEEE
T ss_pred CCCCCEeCCCCCCCCc---------HHHHHhHHhc---CCEeEccCCCCCCeEEEEEEECHHHHHHHhC--CCCCCCEEE
Confidence 9999999976542222 2223322221 3589999999999999999999999888876 789999999
Q ss_pred EEEEeCCCCCCCceEEecCCCCCCCCceeEeeecCCcccc-CCCcccccceeeEEEeeecCCCCCCCCcchhccccccee
Q 018524 178 IALCIGPAPKWKRITIISGHGRSKFGAWRVYAASDVGRVL-PGGSVVRDMVTSFEVLSVNGEGSFKEPSELQEHEENNIV 256 (354)
Q Consensus 178 ~A~v~G~~~~~~~~~i~~~i~~~~~~~~~~~~~~~~~~~~-~~g~~~~~a~t~~~vl~~~~~~~~~~~~~~~~~~~~~~~ 256 (354)
+|+|.|.++++. ++... .|. .+ .+|...+++ .++++
T Consensus 135 ~a~v~g~~~~~~---i~~~~----~g~-----------~~~~~~~~~~~a--~~~~l----------------------- 171 (243)
T 1vio_A 135 LVTLADPVEENY---SAACA----EGI-----------LLRGEKEPTKPA--KLEIL----------------------- 171 (243)
T ss_dssp EEEESSCCCTTH---HHHHH----HCC-----------CCTTCSSCCCCC--EEEEC-----------------------
T ss_pred EEEEeCCCCHHH---HHHHh----CCe-----------EECCCCccceeE--EEEEe-----------------------
Confidence 999999987632 11110 000 01 111122333 23332
Q ss_pred eeeehhhccCCCCceEEEEEEeCCCchhHHHHHHhhcCCceecCC--CCCC
Q 018524 257 VEKKAVLDADAKKNEILVRAFPRSGRTHQIRLHCQYLGISIRGDV--KYEG 305 (354)
Q Consensus 257 ~~~~~~~~~~~~~~~slv~~~~~TGR~HQIRvhla~lG~PIvGD~--~Yg~ 305 (354)
..++++|+|.|||+||||+||+++||||+||. .||.
T Consensus 172 -------------~~sl~~~~l~tGR~HQIR~hl~~lG~pI~gd~r~~~G~ 209 (243)
T 1vio_A 172 -------------DDYNVNLTISEGRYHQVKRMFAALGNKVVGLHRWKIGD 209 (243)
T ss_dssp -------------SSSEEEEEESCCCTTHHHHHHHHTTCCEEEEEEEEETT
T ss_pred -------------CCEEEEEEEccCCcHHHHHHHHHCCCeEcccEEEEECC
Confidence 14799999999999999999999999999999 5564
No 6
>2oml_A Ribosomal large subunit pseudouridine synthase E; bifurcated beta sheet, thrombin-cleaved, isomerase; 1.20A {Escherichia coli}
Probab=100.00 E-value=3.8e-39 Score=281.22 Aligned_cols=170 Identities=16% Similarity=0.160 Sum_probs=112.1
Q ss_pred CccEEEeCCcEEEEECCCCCccccccccccccccccccccccCCCccccccccccccccccCCCCCceEEEEEeCHHHHH
Q 018524 83 RSDVLYEDEWLVAVNKPQGVYCESVLASVPCLLAGDSAESKSGRLSEGTKLNLLELHLANRLDRDTSGVMVITKSHKVAS 162 (354)
Q Consensus 83 ~~~Ilyed~~~lvvnKP~Gl~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~l~~vhRLDk~TSGllllAk~~~~a~ 162 (354)
...|+|||++|+|||||+|++||+....... ++.+.+. . ..+++|||||++||||||||||+++++
T Consensus 3 ~~~ilyed~~~lvvnKP~G~~~~~~~~~~~~--------tl~~~l~--~----~~~~~vhRLD~~TSGlll~ak~~~~~~ 68 (189)
T 2oml_A 3 RRKPENQPTRVILFNKPYDVLPQFTDEAGRK--------TLKEFIP--V----QGVYAAGRLDRDSEGLLVLTNNGALQA 68 (189)
T ss_dssp -----CCCCCEEEEEECTTBCSCSSCCTTCB--------CGGGTCC--C----SSCEESSCCCTTCEEEEEEESCHHHHH
T ss_pred ccccccCCCeEEEEECCCCCEecCCCCCCCC--------CHHHHcC--C----CCceECCCCCCCCeeEEEEEcCHHHHH
Confidence 3469999999999999999999975432111 1222232 1 358999999999999999999999999
Q ss_pred HHHHHhhcCccceEEEEEEeCCCCCCCceEEecCCCCCCCCceeEeeecCCccccCCCcccccceeeEEEeeecCCCCCC
Q 018524 163 KLVKAFTDHKVSKTYIALCIGPAPKWKRITIISGHGRSKFGAWRVYAASDVGRVLPGGSVVRDMVTSFEVLSVNGEGSFK 242 (354)
Q Consensus 163 ~l~~~f~~~~v~K~Y~A~v~G~~~~~~~~~i~~~i~~~~~~~~~~~~~~~~~~~~~~g~~~~~a~t~~~vl~~~~~~~~~ 242 (354)
.|+++ ++.++|+|+|+|.|.++++....+..++... +| ...++ .+.++.....
T Consensus 69 ~l~~~--~~~v~K~Y~a~v~G~~~~~~~~~i~~~i~~~------------------~~-~~~~~--~~~~~~~~~~---- 121 (189)
T 2oml_A 69 RLTQP--GKRTGKIYYVQVEGIPTQDALEALRNGVTLN------------------DG-PTLPA--GAELVDEPAW---- 121 (189)
T ss_dssp HHHST--TSCCCEEEEEEEESCCCHHHHHHHHHCCEET------------------TE-ECCCC--EEEEECCCTT----
T ss_pred HHhCc--cCCCcEEEEEEEcCCCCHHHHHHHHcCceeC------------------Cc-eeeee--EEEEeccccc----
Confidence 99995 7899999999999998753222344443211 11 00111 1222111000
Q ss_pred CCcchhcccccceeeeeehhhccCCCCceEEEEEEeCCCchhHHHHHHhhcCCceecCCCCCCc
Q 018524 243 EPSELQEHEENNIVVEKKAVLDADAKKNEILVRAFPRSGRTHQIRLHCQYLGISIRGDVKYEGV 306 (354)
Q Consensus 243 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~slv~~~~~TGR~HQIRvhla~lG~PIvGD~~Yg~~ 306 (354)
...+.+.+.+ . ...++++++|+|.|||+||||+||+++||||+||.+||..
T Consensus 122 -------~~~t~~~v~~-----~-~~~~~slv~~~l~TGR~HQIRvhla~lG~PI~gD~~Y~~g 172 (189)
T 2oml_A 122 -------LWPRNPPIRE-----R-KSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMG 172 (189)
T ss_dssp -------CCCCSSCCC------C-TTSCEEEEEEEESCCCTTHHHHHHHHTTCCEEEEEEEEET
T ss_pred -------cccccccccc-----c-cCCCcEEEEEEEeeCCCHHHHHHHHHcCCcCcceEEEEEC
Confidence 0001111110 0 0136899999999999999999999999999999999854
No 7
>2olw_A Ribosomal large subunit pseudouridine synthase E; bifurcated beta sheet, isomerase; 1.60A {Escherichia coli}
Probab=100.00 E-value=4.1e-39 Score=286.46 Aligned_cols=170 Identities=16% Similarity=0.152 Sum_probs=112.3
Q ss_pred CccEEEeCCcEEEEECCCCCccccccccccccccccccccccCCCccccccccccccccccCCCCCceEEEEEeCHHHHH
Q 018524 83 RSDVLYEDEWLVAVNKPQGVYCESVLASVPCLLAGDSAESKSGRLSEGTKLNLLELHLANRLDRDTSGVMVITKSHKVAS 162 (354)
Q Consensus 83 ~~~Ilyed~~~lvvnKP~Gl~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~l~~vhRLDk~TSGllllAk~~~~a~ 162 (354)
...|+|||++|+|||||+|++||+...... .++.+.+.. ..+++|||||++||||||||||+++++
T Consensus 31 ~~~Ilyed~~~lvvnKP~Gl~~~~~~~~~~--------~tl~~~l~~------~~~~~VhRLDr~TSGllllAk~~~~~~ 96 (217)
T 2olw_A 31 RRKPENQPTRVILFNKPYDVLPQFTDEAGR--------KTLKEFIPV------QGVYAAGRLDRDSEGLLVLTNNGALQA 96 (217)
T ss_dssp ------CCCCEEEEEECTTBCSCSSCCTTS--------BCGGGTCCC------CSCEESSCCCTTCEEEEEEESCHHHHH
T ss_pred cCceEeeCCcEEEEECCCCCEeccCCCCCC--------ccHHHHhCc------CCceECCCCCCCCeeEEEEEcCHHHHH
Confidence 567999999999999999999997543211 122223321 358999999999999999999999999
Q ss_pred HHHHHhhcCccceEEEEEEeCCCCCCCceEEecCCCCCCCCceeEeeecCCccccCCCcccccceeeEEEeeecCCCCCC
Q 018524 163 KLVKAFTDHKVSKTYIALCIGPAPKWKRITIISGHGRSKFGAWRVYAASDVGRVLPGGSVVRDMVTSFEVLSVNGEGSFK 242 (354)
Q Consensus 163 ~l~~~f~~~~v~K~Y~A~v~G~~~~~~~~~i~~~i~~~~~~~~~~~~~~~~~~~~~~g~~~~~a~t~~~vl~~~~~~~~~ 242 (354)
.|+++ .++|+|+|+|+|.|.++++....+..++.. .+| +...+.++++.....
T Consensus 97 ~L~~~--~~~v~K~Y~A~V~G~~~~~~~~~i~~~i~~------------------~~g---~~~~~~~~~~~~~~~---- 149 (217)
T 2olw_A 97 RLTQP--GKRTGKIYYVQVEGIPTQDALEALRNGVTL------------------NDG---PTLPAGAELVDEPAW---- 149 (217)
T ss_dssp HHHCT--TCCCCEEEEEEEESCCCHHHHHHHHHCCEE------------------TTE---ECCCCEEEEECCCTT----
T ss_pred HHHcc--cccCCEEEEEEEccCCCHHHHHHHhCCEEe------------------CCC---cccceEEEEecCCcc----
Confidence 99994 788999999999999875321233333311 111 112223443321100
Q ss_pred CCcchhcccccceeeeeehhhccCCCCceEEEEEEeCCCchhHHHHHHhhcCCceecCCCCCCc
Q 018524 243 EPSELQEHEENNIVVEKKAVLDADAKKNEILVRAFPRSGRTHQIRLHCQYLGISIRGDVKYEGV 306 (354)
Q Consensus 243 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~slv~~~~~TGR~HQIRvhla~lG~PIvGD~~Yg~~ 306 (354)
..+.+.. +. .....++++++|+|.|||+||||+||+++||||+||.+||..
T Consensus 150 --------~~~~~~~----v~-~~~~~~~slv~~~l~TGRtHQIRvhla~lG~PIvgD~rY~~g 200 (217)
T 2olw_A 150 --------LWPRNPP----IR-ERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMG 200 (217)
T ss_dssp --------CCCCSSC----CC--CCSSCEEEEEEEESCCCTTHHHHHHHHTTCCEEEEEEEEET
T ss_pred --------ccccccc----ee-ccCCCCcEEEEEEECcCCCHHHHHHHHHCCCcEeCCEEEEEC
Confidence 0000000 00 001246799999999999999999999999999999999854
No 8
>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=1.4e-38 Score=293.50 Aligned_cols=201 Identities=16% Similarity=0.216 Sum_probs=152.6
Q ss_pred CCCCcccccccccCCCCCCCCCCCCCCccccCCCCCCCCCCcccccceeEEeecccccccccccCCCccEE---EeCCcE
Q 018524 17 AVPRFRKTFFSLASMSNPTEPTSQNAPQTQQNYPTPLSPPLPAISKDIELTRAMSASSKSSLYKLSRSDVL---YEDEWL 93 (354)
Q Consensus 17 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~v~~~~~~~~~~~~~~~~~~~~~Il---yed~~~ 93 (354)
..+||+|+||+.++.+||.+++.+|..|.| .|||.++ .....+.+. +.+.+++..|. |||++|
T Consensus 4 ~~g~RLdk~La~~g~~SR~~a~~lI~~G~V------------~VNG~~v-~~~~~V~~g-D~I~v~~~~i~~~~~ed~~~ 69 (290)
T 3dh3_A 4 DSSVRLNKYISESGICSRREADRYIEQGNV------------FLNGKRA-TIGDQVKPG-DVVKVNGQLIEPREAEDLVL 69 (290)
T ss_dssp CCCEEHHHHHHTTTSSCHHHHHHHHHTTCE------------EETTEEC-CTTCEECTT-CCEEETTEEECCCCGGGCCE
T ss_pred ccchHHHHHHHhCCCCCHHHHHHHHHCCCE------------EECCEEc-cCCcCcCCC-CEEEeccccccccccccceE
Confidence 357999999999999999999999999999 8898876 666666663 66777665554 489999
Q ss_pred EEEECCCCCccccccccccccccccccccccCCCccccccccccccccccCCCCCceEEEEEeCHHHHHHHHHHhhcCcc
Q 018524 94 VAVNKPQGVYCESVLASVPCLLAGDSAESKSGRLSEGTKLNLLELHLANRLDRDTSGVMVITKSHKVASKLVKAFTDHKV 173 (354)
Q Consensus 94 lvvnKP~Gl~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~l~~vhRLDk~TSGllllAk~~~~a~~l~~~f~~~~v 173 (354)
||+|||+|++||+......+++ +.+.. . ..+++|||||++||||||||+|+++++.|.+ +.+.+
T Consensus 70 lvvnKP~G~~~~~~~~~~~tl~---------~~l~~--~---~~~~~VhRLD~dTSGLllla~d~~~~~~L~~--~~~~v 133 (290)
T 3dh3_A 70 IALNKPVGIVSTTEDGERDNIV---------DFVNH--S---KRVFPIGRLDKDSQGLIFLTNHGDLVNKILR--AGNDH 133 (290)
T ss_dssp EEEEECTTCBCCCCSSCTTBHH---------HHHTC--S---SCCEESSCCCTTCEEEEEEESCTTHHHHHHC--GGGCC
T ss_pred EEEECCCccccCCCCCCCCcHH---------HHhhc--c---CceeeeccCCCCCcceEEEcCCHHHHHHHHH--hhCCc
Confidence 9999999999997654322322 22222 1 5799999999999999999999999999998 68889
Q ss_pred ceEEEEEEeCCCCCCCceEEecCCCCCCCCceeEeeecCCccccCCCcccccceeeEEEeeecCCCCCCCCcchhccccc
Q 018524 174 SKTYIALCIGPAPKWKRITIISGHGRSKFGAWRVYAASDVGRVLPGGSVVRDMVTSFEVLSVNGEGSFKEPSELQEHEEN 253 (354)
Q Consensus 174 ~K~Y~A~v~G~~~~~~~~~i~~~i~~~~~~~~~~~~~~~~~~~~~~g~~~~~a~t~~~vl~~~~~~~~~~~~~~~~~~~~ 253 (354)
+|+|+|+|.|.++++....+..|+ .+ +|...+++ .++.
T Consensus 134 ~K~Y~a~V~G~~~~~~i~~l~~Gv------------------~l-~~~~~~~~--~v~~--------------------- 171 (290)
T 3dh3_A 134 EKEYLVTVDKPITEEFIRGMSAGV------------------PI-LGTVTKKC--KVKK--------------------- 171 (290)
T ss_dssp CEEEEEEESSCCCHHHHHHHHTCC------------------BC-SSSBCCCC--EEEE---------------------
T ss_pred CEEEEEEECCCCCHHHHHHHhcCc------------------cc-CCcccceE--EEEE---------------------
Confidence 999999999998763222122221 01 11111222 2221
Q ss_pred ceeeeeehhhccCCCCceEEEEEEeCCCchhHHHHHHhhcCCceecCCCCC
Q 018524 254 NIVVEKKAVLDADAKKNEILVRAFPRSGRTHQIRLHCQYLGISIRGDVKYE 304 (354)
Q Consensus 254 ~~~~~~~~~~~~~~~~~~slv~~~~~TGR~HQIRvhla~lG~PIvGD~~Yg 304 (354)
.+.++++|+|.|||+||||+||+++||||+++..|.
T Consensus 172 ---------------~~~~~l~l~l~tGR~HQIR~~~~~lG~pV~~L~R~~ 207 (290)
T 3dh3_A 172 ---------------EAPFVFRITLVQGLNRQIRRMCEHFGYEVKKLERTR 207 (290)
T ss_dssp ---------------CSSSEEEEEESCCCTTHHHHHHHHTTCCEEEEEEEE
T ss_pred ---------------cCCeEEEEEEeCCCChHHHHHHHHcCCeEEEeEEEE
Confidence 123689999999999999999999999999998775
No 9
>2gml_A Ribosomal large subunit pseudouridine synthase F; RLUF, ribosome, RNA modifying enzyme, isomerase; 2.60A {Escherichia coli}
Probab=99.97 E-value=2.5e-32 Score=243.54 Aligned_cols=142 Identities=18% Similarity=0.263 Sum_probs=103.2
Q ss_pred eCCcEEEEECCCCCccccccccccccccccccccccCCCccccccccccccccccCCCCCceEEEEEeCHHHHHHHHHHh
Q 018524 89 EDEWLVAVNKPQGVYCESVLASVPCLLAGDSAESKSGRLSEGTKLNLLELHLANRLDRDTSGVMVITKSHKVASKLVKAF 168 (354)
Q Consensus 89 ed~~~lvvnKP~Gl~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~l~~vhRLDk~TSGllllAk~~~~a~~l~~~f 168 (354)
.+++|||+|||+|++|++......+ +.+.+... ..+++|||||++||||||||+|++++++|.+
T Consensus 12 ~~~~~lvlnKPaG~vs~~~~~~~~t---------v~dll~~~-----~rl~~VgRLD~dTSGLLLlT~dg~~a~~L~~-- 75 (237)
T 2gml_A 12 SDLVLIALNKPVGIVSTTEDGERDN---------IVDFVNHS-----KRVFPIGRLDKDSQGLIFLTNHGDLVNKILR-- 75 (237)
T ss_dssp -CCCEEEEEECTTCBCCSSSSCSSB---------HHHHSCCS-----SCCEEESCCCTTCEEEEEEESCHHHHHHHHH--
T ss_pred CCCEEEEEECCCCCEeCCCCCCCCC---------HHHHhhcc-----CCeeEecCCCCCCeeEEEEEcCHHHHHHHhC--
Confidence 3567999999999999875432222 22233221 4689999999999999999999999999998
Q ss_pred hcCccceEEEEEEeCCCCCCCceEEecCCCCCCCCceeEeeecCCccccCCCcccccceeeEEEeeecCCCCCCCCcchh
Q 018524 169 TDHKVSKTYIALCIGPAPKWKRITIISGHGRSKFGAWRVYAASDVGRVLPGGSVVRDMVTSFEVLSVNGEGSFKEPSELQ 248 (354)
Q Consensus 169 ~~~~v~K~Y~A~v~G~~~~~~~~~i~~~i~~~~~~~~~~~~~~~~~~~~~~g~~~~~a~t~~~vl~~~~~~~~~~~~~~~ 248 (354)
+++.|+|+|+|+|.|.++++....+..++ .+. +. ..+.+.++++.
T Consensus 76 p~~~v~K~Y~a~V~G~~~~~~i~~l~~Gv------------------~l~-~~--~~~~a~~~~l~-------------- 120 (237)
T 2gml_A 76 AGNDHEKEYLVTVDKPITEEFIRGMSAGV------------------PIL-GT--VTKKCKVKKEA-------------- 120 (237)
T ss_dssp HHHHSCEEEEEEESSCCCHHHHHHHSSCC------------------EET-TE--ECCCCEEEEEE--------------
T ss_pred ccCCCCEEEEEEEcccCCHHHHHHHHcCe------------------EeC-Cc--ccccEEEEEeC--------------
Confidence 78899999999999998753211111111 011 11 11223344331
Q ss_pred cccccceeeeeehhhccCCCCceEEEEEEeCCCchhHHHHHHhhcCCceecCCCC
Q 018524 249 EHEENNIVVEKKAVLDADAKKNEILVRAFPRSGRTHQIRLHCQYLGISIRGDVKY 303 (354)
Q Consensus 249 ~~~~~~~~~~~~~~~~~~~~~~~slv~~~~~TGR~HQIRvhla~lG~PIvGD~~Y 303 (354)
.++++|+|.|||+||||+||+++||||+||..|
T Consensus 121 ----------------------~s~l~i~L~tGR~HQIRr~~a~lG~pV~~L~R~ 153 (237)
T 2gml_A 121 ----------------------PFVFRITLVQGLNRQIRRMCEHFGYEVKKLERT 153 (237)
T ss_dssp ----------------------TTEEEEEECCCSTTHHHHHHHHTTCCEEEEEEE
T ss_pred ----------------------CEEEEEEEecCCcHHHHHHHHHcCCCEeeeEEE
Confidence 268999999999999999999999999999775
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=96.77 E-value=0.00058 Score=62.52 Aligned_cols=70 Identities=20% Similarity=0.315 Sum_probs=50.0
Q ss_pred CcEEEEECCCCCccccccccccccccccccccccCCCccccccccccccccccCCCCCceEEEEEeCHHHHHHHHHHhhc
Q 018524 91 EWLVAVNKPQGVYCESVLASVPCLLAGDSAESKSGRLSEGTKLNLLELHLANRLDRDTSGVMVITKSHKVASKLVKAFTD 170 (354)
Q Consensus 91 ~~~lvvnKP~Gl~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~l~~vhRLDk~TSGllllAk~~~~a~~l~~~f~~ 170 (354)
+.+|+||||+|+.||.....+...+ +...+.-.+-||-..||||+++-... -++...+.+
T Consensus 3 ~Gil~vdKP~G~TS~~vv~~vrr~l------------------~~kKvGH~GTLDP~AtGvL~i~iG~a--TKl~~~l~~ 62 (309)
T 1r3e_A 3 HGILVAYKPKGPTSHDVVDEVRKKL------------------KTRKVGHGGTLDPFACGVLIIGVNQG--TRILEFYKD 62 (309)
T ss_dssp CEEEEEEECSSSCHHHHHHHHHHHT------------------TCSCEEESSCCCTTCEEEEEEEEGGG--GGGGGGGTT
T ss_pred CeEEEEECCCCCCHHHHHHHHHHHh------------------ccceecccccCCCCcceeEEEEECHH--HhHHHHhCc
Confidence 4699999999998875433322211 11457779999999999999999763 345554443
Q ss_pred CccceEEEEEEe
Q 018524 171 HKVSKTYIALCI 182 (354)
Q Consensus 171 ~~v~K~Y~A~v~ 182 (354)
..|+|.|.+.
T Consensus 63 --~~K~Y~a~~~ 72 (309)
T 1r3e_A 63 --LKKVYWVKMR 72 (309)
T ss_dssp --SCEEEEEEEE
T ss_pred --cCcEEEEEEE
Confidence 4899999886
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=96.76 E-value=0.00072 Score=62.37 Aligned_cols=70 Identities=21% Similarity=0.300 Sum_probs=49.5
Q ss_pred CcEEEEECCCCCccccccccccccccccccccccCCCccccccccccccccccCCCCCceEEEEEeCHHHHHHHHHHhhc
Q 018524 91 EWLVAVNKPQGVYCESVLASVPCLLAGDSAESKSGRLSEGTKLNLLELHLANRLDRDTSGVMVITKSHKVASKLVKAFTD 170 (354)
Q Consensus 91 ~~~lvvnKP~Gl~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~l~~vhRLDk~TSGllllAk~~~~a~~l~~~f~~ 170 (354)
+.+|+||||+|+.++.....+... + +...+.-.+.||-..||+|+++-.... ++...+.+
T Consensus 25 ~Gil~vdKP~G~TS~dvv~~vr~~------------l------~~kKvGH~GTLDP~AtGvL~i~~G~aT--Kl~~~l~~ 84 (327)
T 1k8w_A 25 NGVLLLDKPQGMSSNDALQKVKRI------------Y------NANRAGHTGALDPLATGMLPICLGEAT--KFSQYLLD 84 (327)
T ss_dssp CEEEEEEECTTCCHHHHHHHHHHH------------T------TCSCEEESSCCCTTCEEEEEEEEGGGG--GGTHHHHT
T ss_pred CeEEEEECCCCCCHHHHHHHHHHh------------h------ccceeccCCCCCCCCeeEEEEEECHHH--hHHHHhcc
Confidence 569999999999876543222221 1 114577799999999999999987642 35554543
Q ss_pred CccceEEEEEEe
Q 018524 171 HKVSKTYIALCI 182 (354)
Q Consensus 171 ~~v~K~Y~A~v~ 182 (354)
-.|+|.|.+.
T Consensus 85 --~~K~Y~a~~~ 94 (327)
T 1k8w_A 85 --SDKRYRVIAR 94 (327)
T ss_dssp --SCEEEEEEEE
T ss_pred --CCcEEEEEEE
Confidence 3899999886
No 12
>1p9k_A ORF, hypothetical protein; alfal motif, RNA-binding protein, E.coli, montreal-kingston structural genomics initiative, BSGI; NMR {Escherichia coli} SCOP: d.66.1.6
Probab=96.66 E-value=0.00022 Score=51.98 Aligned_cols=53 Identities=13% Similarity=0.083 Sum_probs=41.4
Q ss_pred CccccCCCCCCCcccccccccCCC-CCCCCCCCCCCccccCCCCCCCCCCcccccceeEEeeccccc
Q 018524 9 PTFTLTPKAVPRFRKTFFSLASMS-NPTEPTSQNAPQTQQNYPTPLSPPLPAISKDIELTRAMSASS 74 (354)
Q Consensus 9 ~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~v~~~~~~~~~~ 74 (354)
|.+++.. +.+||+|+||+.++.+ ||.+++.+|..|.| .|||.++......+.+
T Consensus 11 ~~~~v~~-~~~~RLdk~L~~~g~~~SR~~a~~lI~~G~V------------~VNG~~v~~~~~~v~~ 64 (79)
T 1p9k_A 11 ATFSLGK-HPHVELCDLLKLEGWSESGAQAKIAIAEGQV------------KVDGAVETRKRCKIVA 64 (79)
T ss_dssp CEEECCS-CSCCCHHHHHHHHTSCSSSSTTSHHHHHHHH------------EETTBCCCCSSCCCCS
T ss_pred cEEEECC-CCCchHHHHHHHCCCCCCHHHHHHHHHCCEE------------EECCEEecCCCCCCCC
Confidence 4466652 3449999999999876 99999999999999 8999877665555543
No 13
>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=96.64 E-value=0.00079 Score=62.68 Aligned_cols=73 Identities=26% Similarity=0.371 Sum_probs=51.9
Q ss_pred EeCCcEEEEECCCCCccccccccccccccccccccccCCCccccccccccccccccCCCCCceEEEEEeCHHHHHHHHHH
Q 018524 88 YEDEWLVAVNKPQGVYCESVLASVPCLLAGDSAESKSGRLSEGTKLNLLELHLANRLDRDTSGVMVITKSHKVASKLVKA 167 (354)
Q Consensus 88 yed~~~lvvnKP~Gl~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~l~~vhRLDk~TSGllllAk~~~~a~~l~~~ 167 (354)
|-.+.+|+||||.|+.||.....+...+ +...+.-.+-||-..||||+++-.. + .++.+.
T Consensus 43 ~~~~Gil~vdKP~g~tS~~vv~~vr~~~------------------~~~KvGH~GTLDP~atGvL~v~~g~-a-Tk~~~~ 102 (334)
T 2aus_C 43 HIQYGVINLDKPPGPTSHEVVAWIKRIL------------------NLEKAGHGGTLDPKVSGVLPVALER-A-TRVVQA 102 (334)
T ss_dssp HHHTEEEEEEECSSSCHHHHHHHHHHHT------------------TCSCEEESSCCCTTCEEEEEEEEGG-G-GGGGGG
T ss_pred hccCcEEEEECCCCCCHHHHHHHHHHHh------------------CcceeccccccCCccceeEEEEeCh-h-hhhHHH
Confidence 4467899999999998775433222211 1145778999999999999999964 3 355554
Q ss_pred hhcCccceEEEEEEe
Q 018524 168 FTDHKVSKTYIALCI 182 (354)
Q Consensus 168 f~~~~v~K~Y~A~v~ 182 (354)
+.+ ..|+|.|.+.
T Consensus 103 l~~--~~K~Y~~~~~ 115 (334)
T 2aus_C 103 LLP--AGKEYVALMH 115 (334)
T ss_dssp GTT--CCEEEEEEEE
T ss_pred hcc--cCcEEEEEEE
Confidence 444 4899999886
No 14
>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=96.63 E-value=0.00079 Score=61.75 Aligned_cols=71 Identities=24% Similarity=0.355 Sum_probs=50.5
Q ss_pred CCcEEEEECCCCCccccccccccccccccccccccCCCccccccccccccccccCCCCCceEEEEEeCHHHHHHHHHHhh
Q 018524 90 DEWLVAVNKPQGVYCESVLASVPCLLAGDSAESKSGRLSEGTKLNLLELHLANRLDRDTSGVMVITKSHKVASKLVKAFT 169 (354)
Q Consensus 90 d~~~lvvnKP~Gl~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~l~~vhRLDk~TSGllllAk~~~~a~~l~~~f~ 169 (354)
.+.+|+||||.|+.|+.....+...+ +...+.-.+-||-..||||+++-... -++...+.
T Consensus 5 ~~Gil~vdKP~G~TS~dvv~~vrr~l------------------~~kKvGH~GTLDP~AtGvL~i~iG~a--TKl~~~l~ 64 (316)
T 1sgv_A 5 GPGIVVIDKPAGMTSHDVVGRCRRIF------------------ATRRVGHAGTLDPMATGVLVIGIERA--TKILGLLT 64 (316)
T ss_dssp CSEEEEEEECTTCCHHHHHHHHHHHT------------------TCSCEEESSCCCTTCEEEEEEEEGGG--GGGGGGTT
T ss_pred CCeEEEEECCCCCCHHHHHHHHHHHh------------------ccccccccccCCCCCeEEEEEEECHH--HhHHHHhC
Confidence 45799999999998875433222211 11457789999999999999999764 24545443
Q ss_pred cCccceEEEEEEe
Q 018524 170 DHKVSKTYIALCI 182 (354)
Q Consensus 170 ~~~v~K~Y~A~v~ 182 (354)
+ ..|+|.|.+.
T Consensus 65 ~--~~K~Y~~~~~ 75 (316)
T 1sgv_A 65 A--APKSYAATIR 75 (316)
T ss_dssp T--SCEEEEEEEE
T ss_pred c--CCcEEEEEEE
Confidence 3 4899999886
No 15
>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=96.47 E-value=0.0011 Score=62.08 Aligned_cols=73 Identities=25% Similarity=0.301 Sum_probs=52.0
Q ss_pred EeCCcEEEEECCCCCccccccccccccccccccccccCCCccccccccccccccccCCCCCceEEEEEeCHHHHHHHHHH
Q 018524 88 YEDEWLVAVNKPQGVYCESVLASVPCLLAGDSAESKSGRLSEGTKLNLLELHLANRLDRDTSGVMVITKSHKVASKLVKA 167 (354)
Q Consensus 88 yed~~~lvvnKP~Gl~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~l~~vhRLDk~TSGllllAk~~~~a~~l~~~ 167 (354)
|-.+.+|+||||.|+.|+.....+...+ +...+.-.+-||-..||||+++-.. +. ++...
T Consensus 63 ~~~~Gil~vdKP~G~TS~~vv~~vr~~l------------------~~~KvGH~GTLDP~AtGvL~v~~G~-aT-k~~~~ 122 (357)
T 2apo_A 63 LIKYGVVVVDKPRGPTSHEVSTWVKKIL------------------NLDKAGHGGTLDPKVTGVLPVALER-AT-KTIPM 122 (357)
T ss_dssp HHHTEEEEEEECSSSCHHHHHHHHHHHT------------------TCSCEEESSCCCTTCEEEEEEEEGG-GG-GGGGG
T ss_pred hccCcEEEEECCCCCCHHHHHHHHHHHh------------------CccccccccccCCCceeEEEEEeCH-HH-hHHHH
Confidence 4567899999999998774333222211 1146778999999999999999964 33 45554
Q ss_pred hhcCccceEEEEEEe
Q 018524 168 FTDHKVSKTYIALCI 182 (354)
Q Consensus 168 f~~~~v~K~Y~A~v~ 182 (354)
+.+ ..|+|.|.+.
T Consensus 123 l~~--~~K~Y~~~~~ 135 (357)
T 2apo_A 123 WHI--PPKEYVCLMH 135 (357)
T ss_dssp TTS--SCEEEEEEEE
T ss_pred hcc--CCcEEEEEEE
Confidence 443 6899999886
No 16
>3u28_A H/ACA ribonucleoprotein complex subunit 4; pseudouridine synthase, pseudouridylation, H/ACA RNA; 1.90A {Saccharomyces cerevisiae} PDB: 3uai_A
Probab=96.21 E-value=0.0025 Score=60.26 Aligned_cols=75 Identities=19% Similarity=0.330 Sum_probs=52.0
Q ss_pred EeCCcEEEEECCCCCccccccccccccccccccccccCCCccccccccccccccccCCCCCceEEEEEeCHHHHHHHHHH
Q 018524 88 YEDEWLVAVNKPQGVYCESVLASVPCLLAGDSAESKSGRLSEGTKLNLLELHLANRLDRDTSGVMVITKSHKVASKLVKA 167 (354)
Q Consensus 88 yed~~~lvvnKP~Gl~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~l~~vhRLDk~TSGllllAk~~~~a~~l~~~ 167 (354)
|-.+.+|+||||.|+.||.....+...+ +...+.-.+-||-..||||+++-.. +. ++...
T Consensus 56 ~~~~Gil~ldKP~G~TS~dvv~~vrr~l------------------~~kKvGH~GTLDP~AtGvL~v~iG~-aT-Kl~~~ 115 (400)
T 3u28_A 56 YISSGVINLDKPSNPSSHEVVAWIKRIL------------------RCEKTGHSGTLDPKVTGCLIVCIDR-AT-RLVKS 115 (400)
T ss_dssp HHHTEEEEEEECSSSCHHHHHHHHHHHH------------------TCSCEEESSCCCTTCEEEEEEEEGG-GG-GGHHH
T ss_pred hccCcEEEEECCCCCCHHHHHHHHHHHh------------------CcCcccccCCCCCCCeEEEEEEECh-HH-hHhHH
Confidence 5567899999999998875433222211 1146778999999999999999864 33 33343
Q ss_pred hhcCccceEEEEEEe-CC
Q 018524 168 FTDHKVSKTYIALCI-GP 184 (354)
Q Consensus 168 f~~~~v~K~Y~A~v~-G~ 184 (354)
+.. -.|+|.|.+. |.
T Consensus 116 l~~--~~K~Y~a~~~lG~ 131 (400)
T 3u28_A 116 QQG--AGKEYVCIVRLHD 131 (400)
T ss_dssp HHH--SCEEEEEEEEESS
T ss_pred hcC--CCcEEEEEEEeCC
Confidence 333 4899999875 44
No 17
>2k6p_A Uncharacterized protein HP_1423; alpha-L motif, RNA-binding, unknown function; NMR {Helicobacter pylori}
Probab=94.03 E-value=0.014 Score=43.45 Aligned_cols=34 Identities=6% Similarity=-0.054 Sum_probs=28.2
Q ss_pred CcccccccccCCC-CCCCCCCCCCCccccCCCCCCCCCCccccccee
Q 018524 20 RFRKTFFSLASMS-NPTEPTSQNAPQTQQNYPTPLSPPLPAISKDIE 65 (354)
Q Consensus 20 ~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~v~ 65 (354)
||+|+||+..... +|..+++++..|.| .|||.+.
T Consensus 1 ~RLD~~L~~~~~~~sR~~~~~li~~G~V------------~VNg~~~ 35 (92)
T 2k6p_A 1 MRIDKFLQSVGLVKRRVLATDMCNVGAV------------WLNGSCA 35 (92)
T ss_dssp CBHHHHSTTTTSCCCCCSSCCHHHHTCC------------EETTEEC
T ss_pred ChHHHHHHHCCCCCCHHHHHHHHHCCcE------------EECCEEc
Confidence 6999999987654 78889999999988 7787653
No 18
>2vqe_D 30S ribosomal protein S4; tRNA-binding, rRNA-binding, metal-binding, zinc-finger, translation; HET: TM2 PAR; 2.5A {Thermus thermophilus} SCOP: d.66.1.2 PDB: 1hnw_D* 1hnx_D* 1hnz_D* 1ibk_D* 1fka_D* 1ibm_D 1xmo_D* 1ibl_D* 1xnq_D* 1xnr_D* 1yl4_G 2b64_D* 2b9m_D* 2b9o_D* 2hgi_G 2hgp_G 2hgr_G 2hhh_D* 1xmq_D* 2j02_D* ...
Probab=93.71 E-value=0.00041 Score=60.30 Aligned_cols=79 Identities=4% Similarity=-0.145 Sum_probs=53.9
Q ss_pred CCCcccccccccCCC-CCCCCCCCCCCccccCCCCCCCCCCcccccceeEEeecccccccccccCCCccEEEeC-CcEEE
Q 018524 18 VPRFRKTFFSLASMS-NPTEPTSQNAPQTQQNYPTPLSPPLPAISKDIELTRAMSASSKSSLYKLSRSDVLYED-EWLVA 95 (354)
Q Consensus 18 ~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~v~~~~~~~~~~~~~~~~~~~~~Ilyed-~~~lv 95 (354)
..||+|+|++.++.+ ||.++..+|..|.| .|||.++..++..+.+. +.+.+.+....+.. ..++.
T Consensus 97 le~RLD~~L~~~g~~~SR~~arqLI~~G~V------------~VNG~~v~~ps~~V~~g-D~I~V~~~~r~~~~~~~~l~ 163 (209)
T 2vqe_D 97 LESRLDNVVYRLGFAVSRRQARQLVRHGHI------------TVNGRRVDLPSYRVRPG-DEIAVAEKSRNLELIRQNLE 163 (209)
T ss_dssp HHTBHHHHHHHTTSSSSHHHHHHHHHTTCE------------EETTEECCCTTCBCCTT-CEEEECGGGTTCHHHHHHHH
T ss_pred HHHHHHHHHHHhcCcCCHHHHHHHHHCCCE------------EECCEEeCcCCcCcCCC-CEEEEcCcccchHHHHHHHH
Confidence 358999999988765 99999999999999 88888776666666653 44444332221111 13455
Q ss_pred EE---CCCCCccccccc
Q 018524 96 VN---KPQGVYCESVLA 109 (354)
Q Consensus 96 vn---KP~Gl~~~~~~~ 109 (354)
.| ||+|++|...+.
T Consensus 164 ~~~~~kp~g~l~~d~~~ 180 (209)
T 2vqe_D 164 AMKGRKVGPWLSLDVEG 180 (209)
T ss_dssp HTTTCCCCTTCCEETTT
T ss_pred hcCCCCCCCeEEEeccc
Confidence 56 899998765443
No 19
>1c05_A Ribosomal protein S4 delta 41; two subdomains, unique topology, possible helix-turn-helix motif, ribosome; NMR {Geobacillus stearothermophilus} SCOP: d.66.1.2 PDB: 1c06_A 1eg0_A 1qd7_C
Probab=91.64 E-value=0.0034 Score=52.06 Aligned_cols=78 Identities=1% Similarity=-0.181 Sum_probs=51.7
Q ss_pred CCCcccccccccCCC-CCCCCCCCCCCccccCCCCCCCCCCcccccceeEEeecccccccccccCCCccEEEeC----Cc
Q 018524 18 VPRFRKTFFSLASMS-NPTEPTSQNAPQTQQNYPTPLSPPLPAISKDIELTRAMSASSKSSLYKLSRSDVLYED----EW 92 (354)
Q Consensus 18 ~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~v~~~~~~~~~~~~~~~~~~~~~Ilyed----~~ 92 (354)
..||+|++++..+.+ ||.++.++|..|.| .|||.++..++..+.+. +.+.+.+..+-+.. -.
T Consensus 49 le~RLD~~L~~~g~~~SR~~ar~lI~~G~V------------~VNG~~v~~ps~~V~~g-D~I~V~~~~~~~~kl~~al~ 115 (159)
T 1c05_A 49 LESRLDNLVYRLGLARTRRQARQLVTHGHI------------LVDGSRVNIPSYRVKPG-QTIAVREKSRNLQVIKEALE 115 (159)
T ss_dssp HHHBHHHHHHHTTSCSSHHHHHHHHHTTCE------------EETTEECCCSSCBCCTT-CEEEECGGGSSCHHHHHHHH
T ss_pred HHHHHHHHHHHcCCcCCHHHHHHHHHCCCE------------EECCEEeCcCCcEeCCC-CEEEEeCceehHHHHHHHHH
Confidence 358999999988865 99999999999999 78888766666666553 34443332221100 00
Q ss_pred EEEEECCCCCcccccccc
Q 018524 93 LVAVNKPQGVYCESVLAS 110 (354)
Q Consensus 93 ~lvvnKP~Gl~~~~~~~~ 110 (354)
++ +||+|..|......
T Consensus 116 ~~--~~~~g~v~~d~~~~ 131 (159)
T 1c05_A 116 AN--NYIPDYLSFDPEKM 131 (159)
T ss_dssp TC--CCCCSSEEEETTTT
T ss_pred Hh--CCCCCeEEEecCCC
Confidence 12 89999988654433
No 20
>2xzm_D Ribosomal protein S4 containing protein; ribosome, translation; 3.93A {Tetrahymena thermophila} PDB: 2xzn_D
Probab=89.71 E-value=0.043 Score=46.24 Aligned_cols=46 Identities=7% Similarity=0.005 Sum_probs=40.2
Q ss_pred CCCcccccccccCCC-CCCCCCCCCCCccccCCCCCCCCCCcccccceeEEeecccccc
Q 018524 18 VPRFRKTFFSLASMS-NPTEPTSQNAPQTQQNYPTPLSPPLPAISKDIELTRAMSASSK 75 (354)
Q Consensus 18 ~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~v~~~~~~~~~~~ 75 (354)
..||+|.++...+.+ ||.++..+|..|.| .|||.++..++..+.+.
T Consensus 105 le~RLD~vL~~~G~a~SR~~Ar~LI~~G~V------------~VNg~~V~~Ps~~V~~~ 151 (181)
T 2xzm_D 105 MERRLQTRVFKLNLANSIHHSRVLIRQRHI------------KVGKNLVNVPSFMVRTD 151 (181)
T ss_dssp HTTBHHHHHHHTTCSSSTTHHHHHTTTTCC------------EETTEECCCSCCBCCST
T ss_pred hccchhHHHHhccccCCHHHHHHHHHCCEE------------EECCEEECCCCcCCCCC
Confidence 358999999999888 99999999999999 99999888777777654
No 21
>3r8n_D 30S ribosomal protein S4; protein biosynthesis, RNA, tRNA, transfer RNA, 16S ribosomal subunit, RRF; 3.00A {Escherichia coli} PDB: 1p6g_D 1p87_D 2aw7_D 2avy_D 2i2u_D 2i2p_D* 2qan_D* 2qb9_D* 2qbb_D* 2qbd_D 2qbf_D 2qbh_D* 2qbj_D* 2qou_D* 2qow_D* 2qoy_D* 2qp0_D* 2vho_D 2vhp_D 2wwl_D* ...
Probab=86.60 E-value=0.055 Score=46.49 Aligned_cols=46 Identities=4% Similarity=-0.014 Sum_probs=37.7
Q ss_pred CCCcccccccccCCC-CCCCCCCCCCCccccCCCCCCCCCCcccccceeEEeecccccc
Q 018524 18 VPRFRKTFFSLASMS-NPTEPTSQNAPQTQQNYPTPLSPPLPAISKDIELTRAMSASSK 75 (354)
Q Consensus 18 ~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~v~~~~~~~~~~~ 75 (354)
..||+|.|++.++.+ ||.++..+|..|.| .|||.++..++..+.+.
T Consensus 93 le~RLD~~L~r~g~~~SR~~ArqLI~~G~V------------~VNG~~V~~ps~~Vk~G 139 (205)
T 3r8n_D 93 LEGRLDNVVYRMGFGATRAEARQLVSHKAI------------MVNGRVVNIASYQVSPN 139 (205)
T ss_dssp HHTBTTHHHHTTSSCSSHHHHHHHHHTTCC------------BSSSSBCCCTTCBCCTT
T ss_pred hHhhHHHHHHHhcchhHHHHHHHHHHCCCE------------EECCEEEccCCcCcCCC
Confidence 358999999988765 99999999999999 89998776666666553
No 22
>3j20_D 30S ribosomal protein S4P; archaea, archaeal, KINK-turn, protein synthe ribosome; 6.60A {Pyrococcus furiosus}
Probab=86.19 E-value=0.027 Score=47.41 Aligned_cols=45 Identities=7% Similarity=-0.022 Sum_probs=39.3
Q ss_pred CCcccccccccCCC-CCCCCCCCCCCccccCCCCCCCCCCcccccceeEEeecccccc
Q 018524 19 PRFRKTFFSLASMS-NPTEPTSQNAPQTQQNYPTPLSPPLPAISKDIELTRAMSASSK 75 (354)
Q Consensus 19 ~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~v~~~~~~~~~~~ 75 (354)
.||+|+++..++.+ ||.++..+|..|.| .|||.++..++..+.+.
T Consensus 102 e~RLD~~L~~~G~a~SR~~Ar~LI~~G~V------------~VNg~~V~~Ps~~V~~~ 147 (180)
T 3j20_D 102 ERRLQTIVYKKGLARTMRQARQLIVHGHI------------EVNGQIIRSPSYLVLKE 147 (180)
T ss_dssp HTSHHHHHHHHTSSSSHHHHHHHHHHTCC------------EESSSBCCCSSCCCCTG
T ss_pred hhhhhheeecCcccCcHHHHHHHHHcCCe------------EECCEEeCCCCcccCCC
Confidence 48999999999888 99999999999999 89999888777666653
No 23
>3bbn_D Ribosomal protein S4; small ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea}
Probab=85.25 E-value=0.063 Score=46.01 Aligned_cols=44 Identities=5% Similarity=-0.093 Sum_probs=35.6
Q ss_pred CCcccccccccCCC-CCCCCCCCCCCccccCCCCCCCCCCcccccceeEEeeccccc
Q 018524 19 PRFRKTFFSLASMS-NPTEPTSQNAPQTQQNYPTPLSPPLPAISKDIELTRAMSASS 74 (354)
Q Consensus 19 ~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~v~~~~~~~~~~ 74 (354)
.||+|+|++..+.+ ||.++..+|..|.| .|||.++..++..+.+
T Consensus 88 e~RLD~~L~r~g~a~SR~~ArqLI~~G~V------------~VNG~~V~~pS~~V~~ 132 (201)
T 3bbn_D 88 EMRLDNILFRLGMAPTIPGARQLVNHRHI------------LVNGRIVDIPSYRCKP 132 (201)
T ss_dssp HSBTTTTTTTTTSSSSSHHHHHHHHTTCE------------EETTEECCCTTCBCCT
T ss_pred HHHHHHHHHHcCCcCCHHHHHHHHhCCcE------------EeCCEEEeecceecCC
Confidence 48999999999876 99999999999999 8888766555544443
No 24
>2cqj_A BRMS2, U3 small nucleolar ribonucleoprotein protein IMP3 homolog; S4 domain, structural genomics, NPPSFA; NMR {Homo sapiens}
Probab=84.44 E-value=0.013 Score=41.49 Aligned_cols=45 Identities=11% Similarity=0.020 Sum_probs=38.2
Q ss_pred CCCcccccccccCCC-CCCCCCCCCCCccccCCCCCCCCCCcccccceeEEeeccccc
Q 018524 18 VPRFRKTFFSLASMS-NPTEPTSQNAPQTQQNYPTPLSPPLPAISKDIELTRAMSASS 74 (354)
Q Consensus 18 ~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~v~~~~~~~~~~ 74 (354)
..+|+|+++...+.+ ||.++..+|..|.| .|||.++..++..+.+
T Consensus 6 l~~RLD~~l~~~gla~SR~~A~~lI~~G~V------------~Vng~~v~kps~~V~~ 51 (71)
T 2cqj_A 6 SGRRLPTVLLKLRMAQHLQAAVAFVEQGHV------------RVGPDVVTDPAFLVTR 51 (71)
T ss_dssp CEEEHHHHHHHTTCSSSHHHHHHHHHTTCE------------EETTBCCCCTTCEEEH
T ss_pred HHHHHHHHHHHhCCcCCHHHHHHHHHCCcE------------EECCEEECCCCCCCCC
Confidence 346999999999888 99999999999999 8999877766666654
No 25
>3iz6_C 40S ribosomal protein S9 (S4P); eukaryotic ribosome,homology modeling,de novo modeling,ribos proteins,novel ribosomal proteins, ribosome; 5.50A {Triticum aestivum}
Probab=79.72 E-value=0.21 Score=42.33 Aligned_cols=46 Identities=11% Similarity=0.060 Sum_probs=41.3
Q ss_pred CCCcccccccccCCC-CCCCCCCCCCCccccCCCCCCCCCCcccccceeEEeecccccc
Q 018524 18 VPRFRKTFFSLASMS-NPTEPTSQNAPQTQQNYPTPLSPPLPAISKDIELTRAMSASSK 75 (354)
Q Consensus 18 ~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~v~~~~~~~~~~~ 75 (354)
..+|||+++..++.+ ||.++..+|..|.| .|||.++..++..+.+.
T Consensus 107 le~RLD~~L~r~G~a~SR~~ArqlI~~GhV------------~VNG~~V~~Ps~~V~~g 153 (195)
T 3iz6_C 107 LARRLQTLVFKAGMAKSIHHARVLIRQRHI------------RVGRQIVNIPSFMVRVE 153 (195)
T ss_dssp TTSCCCSSCCCCCCHHHHSCTTSHHHHHST------------TTSCCCCCCCCCCCSSS
T ss_pred HHhhhhHHHHhccccCCHHHHHHHHHcCCE------------EECCEEeCCCCcCcCCC
Confidence 458999999999998 99999999999999 89999988888888764
No 26
>3u5c_J 40S ribosomal protein S9-A; translation, ribosome, ribosomal, ribosomal R ribosomal protein, eukaryotic ribosome, RNA-protein C; 3.00A {Saccharomyces cerevisiae} PDB: 3izb_C 3o30_E 3o2z_E 3u5g_J 1s1h_D 3jyv_D*
Probab=78.87 E-value=0.14 Score=43.62 Aligned_cols=46 Identities=11% Similarity=0.017 Sum_probs=39.9
Q ss_pred CCCcccccccccCCC-CCCCCCCCCCCccccCCCCCCCCCCcccccceeEEeecccccc
Q 018524 18 VPRFRKTFFSLASMS-NPTEPTSQNAPQTQQNYPTPLSPPLPAISKDIELTRAMSASSK 75 (354)
Q Consensus 18 ~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~v~~~~~~~~~~~ 75 (354)
..+|||+++..++.+ ||.++..+|..|.| .|||.++..++..+.+.
T Consensus 105 le~RLD~~L~r~G~a~Sr~~ArqLI~~GhV------------~VNG~~V~~Ps~~V~~g 151 (197)
T 3u5c_J 105 LERRLQTQVYKLGLAKSVHHARVLITQRHI------------AVGKQIVNIPSFMVRLD 151 (197)
T ss_dssp HTTSHHHHHHHSSTTSSHHHHHHHHHTSCC------------BSSSCBCCCTTCCCCST
T ss_pred HHHHHHHHHHHccccCCHHHHHHHHHcCCE------------EECCEEeCCCccccCCC
Confidence 348999999999888 99999999999999 89999888777777664
No 27
>1dm9_A Hypothetical 15.5 KD protein in MRCA-PCKA intergenic region; heat shock proteins, protein-RNA interactions, ribosome, structural genomics; 2.00A {Escherichia coli} SCOP: d.66.1.3 PDB: 3bbu_A
Probab=76.21 E-value=0.13 Score=40.98 Aligned_cols=42 Identities=5% Similarity=-0.129 Sum_probs=32.8
Q ss_pred CCCcccccccccC-CCCCCCCCCCCCCccccCCCCCCCCCCcccccceeEEeeccc
Q 018524 18 VPRFRKTFFSLAS-MSNPTEPTSQNAPQTQQNYPTPLSPPLPAISKDIELTRAMSA 72 (354)
Q Consensus 18 ~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~v~~~~~~~~ 72 (354)
.+||+|+||+.+. ..||..+..++..|.| .|||.+. ..+..+
T Consensus 7 ~~~RLDk~L~~~~~~~SRs~a~~li~~G~V------------~VNG~~v-k~s~~V 49 (133)
T 1dm9_A 7 VEVRLDKWLWAARFYKTRALAREMIEGGKV------------HYNGQRS-KPSKIV 49 (133)
T ss_dssp TCCBHHHHHHHTTSSSSHHHHHHHHHTTCE------------EETTEEC-CTTCBC
T ss_pred cchhHHHHHHHCCCCCCHHHHHHHHHCCcE------------EECCEEc-CCCCEe
Confidence 4699999999874 4699999999999999 8898753 334333
No 28
>3hp7_A Hemolysin, putative; structural genomics, APC64019, PSI-2, protein STR initiative, midwest center for structural genomics, MCSG; HET: MSE; 1.53A {Streptococcus thermophilus}
Probab=75.15 E-value=0.086 Score=47.99 Aligned_cols=36 Identities=0% Similarity=-0.272 Sum_probs=31.1
Q ss_pred CCcccccccccCCC-CCCCCCCCCCCccccCCCCCCCCCCccccc-c-eeE
Q 018524 19 PRFRKTFFSLASMS-NPTEPTSQNAPQTQQNYPTPLSPPLPAISK-D-IEL 66 (354)
Q Consensus 19 ~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~-~-v~~ 66 (354)
.||+|+||+..+.. ||.+++.+|..|.| .||| . ++.
T Consensus 6 ~~RLD~~L~~~g~~~SR~~a~~lI~~G~V------------~Vng~~~~v~ 44 (291)
T 3hp7_A 6 KERVDVLAYKQGLFETREQAKRGVMAGLV------------VNVINGERYD 44 (291)
T ss_dssp EEEHHHHHHHTTSSSSHHHHHHHHHTTCE------------EETTTCCBCC
T ss_pred hhhHHHHHHHcCCcccHHHHHHHHHCCeE------------EECCeEEEEc
Confidence 58999999988776 99999999999999 8888 5 444
Done!