Query 023907
Match_columns 275
No_of_seqs 207 out of 1796
Neff 7.7
Searched_HMMs 46136
Date Fri Mar 29 07:31:40 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/023907.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/023907hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK11025 23S rRNA pseudouridyl 100.0 5.3E-45 1.1E-49 333.8 21.5 204 1-274 111-314 (317)
2 COG0564 RluA Pseudouridylate s 100.0 4.9E-45 1.1E-49 328.9 20.1 191 1-264 96-289 (289)
3 PRK11112 tRNA pseudouridine sy 100.0 8.7E-44 1.9E-48 316.8 20.6 206 1-274 20-235 (257)
4 PRK11180 rluD 23S rRNA pseudou 100.0 9E-43 2E-47 320.2 21.8 210 1-274 102-313 (325)
5 TIGR01621 RluA-like pseudourid 100.0 2E-42 4.3E-47 300.9 20.9 184 1-270 20-203 (217)
6 TIGR00005 rluA_subfam pseudour 100.0 2.5E-42 5.5E-47 313.8 22.5 208 1-274 90-299 (299)
7 cd02563 PseudoU_synth_TruC tRN 100.0 1.9E-42 4.1E-47 302.3 20.4 195 1-263 19-223 (223)
8 PRK10158 23S rRNA/tRNA pseudou 100.0 8E-42 1.7E-46 297.6 20.1 185 1-263 32-218 (219)
9 cd02558 PSRA_1 PSRA_1: Pseudou 100.0 6.7E-41 1.5E-45 296.5 19.6 187 1-263 57-245 (246)
10 cd02557 PseudoU_synth_ScRIB2 P 100.0 3.5E-40 7.5E-45 286.1 18.6 177 1-266 34-212 (213)
11 cd02869 PseudoU_synth_RluCD_li 100.0 2.2E-36 4.7E-41 255.7 19.2 156 1-179 10-167 (185)
12 KOG1919 RNA pseudouridylate sy 100.0 1.7E-29 3.8E-34 232.5 18.4 155 1-178 124-283 (371)
13 cd02550 PseudoU_synth_Rsu_Rlu_ 100.0 3.3E-29 7.2E-34 206.8 13.2 137 1-170 10-147 (154)
14 PF00849 PseudoU_synth_2: RNA 99.9 4E-27 8.8E-32 195.4 15.6 144 1-163 11-164 (164)
15 cd02553 PseudoU_synth_RsuA Pse 99.9 1.2E-27 2.6E-32 200.2 7.7 136 1-178 11-146 (167)
16 cd02556 PseudoU_synth_RluB Pse 99.9 1.1E-26 2.3E-31 194.4 9.8 131 1-171 11-142 (167)
17 TIGR00093 pseudouridine syntha 99.9 5.4E-27 1.2E-31 187.9 7.4 111 32-178 1-111 (128)
18 cd02870 PseudoU_synth_RsuA_lik 99.9 3.7E-27 8E-32 192.9 5.4 110 26-171 31-140 (146)
19 PRK10839 16S rRNA pseudouridyl 99.9 7.5E-26 1.6E-30 198.8 5.5 133 1-175 71-203 (232)
20 cd02566 PseudoU_synth_RluE Pse 99.9 1.2E-24 2.6E-29 182.1 7.4 145 1-175 10-158 (168)
21 cd02555 PSSA_1 PSSA_1: Pseudou 99.9 1.4E-23 3E-28 177.0 7.3 108 27-176 45-154 (177)
22 PRK11394 23S rRNA pseudouridin 99.9 3.4E-23 7.4E-28 179.0 6.7 126 27-178 70-200 (217)
23 cd02554 PseudoU_synth_RluF Pse 99.8 2.1E-19 4.5E-24 149.6 9.3 106 27-172 31-136 (164)
24 PRK10700 23S rRNA pseudouridyl 99.8 1.4E-19 3E-24 163.7 8.9 121 11-171 89-209 (289)
25 PRK10475 23S rRNA pseudouridin 99.8 1.6E-18 3.5E-23 156.6 7.6 124 1-170 78-201 (290)
26 COG1187 RsuA 16S rRNA uridine- 99.7 3.4E-17 7.3E-22 143.8 6.4 114 25-173 97-211 (248)
27 cd02868 PseudoU_synth_hTruB2_l 98.1 1E-05 2.2E-10 70.7 7.3 43 28-86 33-75 (226)
28 cd01291 PseudoU_synth PseudoU_ 96.6 0.0097 2.1E-07 44.0 6.7 22 25-46 22-43 (87)
29 cd02572 PseudoU_synth_hDyskeri 92.7 0.42 9E-06 40.5 6.7 56 14-87 16-71 (182)
30 cd00506 PseudoU_synth_TruB_lik 91.3 0.74 1.6E-05 39.9 6.7 56 14-87 14-69 (210)
31 PRK00989 truB tRNA pseudouridi 90.7 0.65 1.4E-05 40.8 5.9 57 14-87 23-79 (230)
32 TIGR00431 TruB tRNA pseudourid 89.1 1.3 2.8E-05 38.4 6.4 56 14-87 16-71 (209)
33 PRK00020 truB tRNA pseudouridi 88.1 1.7 3.7E-05 38.5 6.7 55 14-86 24-78 (244)
34 PF01509 TruB_N: TruB family p 87.2 0.66 1.4E-05 38.0 3.3 42 27-86 7-48 (149)
35 PRK04099 truB tRNA pseudouridi 87.1 2 4.3E-05 38.7 6.6 56 14-87 16-71 (273)
36 cd02573 PseudoU_synth_EcTruB P 85.8 2.6 5.7E-05 38.1 6.7 56 14-87 14-69 (277)
37 PRK02193 truB tRNA pseudouridi 85.7 2.6 5.6E-05 38.2 6.5 56 14-87 14-69 (279)
38 PRK02484 truB tRNA pseudouridi 84.4 3.2 7E-05 37.8 6.6 56 14-87 17-72 (294)
39 PRK14123 tRNA pseudouridine sy 84.0 3.4 7.4E-05 37.9 6.6 56 14-87 17-72 (305)
40 PRK14124 tRNA pseudouridine sy 84.0 4.1 8.8E-05 37.4 7.1 56 14-87 17-72 (308)
41 PRK03287 truB tRNA pseudouridi 83.8 3.4 7.4E-05 37.8 6.5 56 14-87 23-78 (298)
42 PRK14846 truB tRNA pseudouridi 83.2 4.2 9E-05 37.8 6.9 56 14-87 17-72 (345)
43 PRK00130 truB tRNA pseudouridi 83.0 4.2 9.1E-05 37.0 6.7 56 14-87 16-71 (290)
44 PRK05389 truB tRNA pseudouridi 82.2 4.2 9.1E-05 37.3 6.5 55 14-86 27-81 (305)
45 PRK04270 H/ACA RNA-protein com 82.2 4.1 8.9E-05 37.2 6.5 56 14-87 36-91 (300)
46 PRK01851 truB tRNA pseudouridi 80.5 6.1 0.00013 36.2 6.9 56 14-87 30-85 (303)
47 PRK01528 truB tRNA pseudouridi 79.6 6.6 0.00014 35.8 6.8 56 14-87 17-72 (292)
48 PRK14122 tRNA pseudouridine sy 79.3 6.2 0.00013 36.3 6.6 55 14-86 15-69 (312)
49 PRK05033 truB tRNA pseudouridi 78.7 7.1 0.00015 35.9 6.7 56 14-87 24-79 (312)
50 PRK01550 truB tRNA pseudouridi 78.4 7.5 0.00016 35.7 6.8 56 14-87 16-71 (304)
51 COG0130 TruB Pseudouridine syn 74.8 9.4 0.0002 34.4 6.3 56 14-87 29-84 (271)
52 KOG2559 Predicted pseudouridin 72.9 1.9 4.1E-05 38.1 1.3 23 27-49 89-111 (318)
53 PRK02755 truB tRNA pseudouridi 71.7 13 0.00027 34.1 6.4 54 14-86 17-70 (295)
54 TIGR00425 CBF5 rRNA pseudourid 68.4 14 0.0003 34.2 6.1 55 15-87 49-103 (322)
55 PRK04642 truB tRNA pseudouridi 65.1 21 0.00045 32.7 6.4 55 14-86 24-78 (300)
56 cd02867 PseudoU_synth_TruB_4 P 49.8 35 0.00076 31.4 5.3 43 27-87 56-98 (312)
57 PF13021 DUF3885: Domain of un 27.9 96 0.0021 19.3 3.1 24 38-61 5-28 (38)
No 1
>PRK11025 23S rRNA pseudouridylate synthase C; Provisional
Probab=100.00 E-value=5.3e-45 Score=333.82 Aligned_cols=204 Identities=32% Similarity=0.479 Sum_probs=160.9
Q ss_pred CCccCCCCCcCcHHHHHHHHhhcCCCCCCcccccCCCCCceEEEEEeCHHHHHHHHHHHHhccccccccccccccCCcce
Q 023907 1 MPVQGGIGIRRSIDELAATCLTYDYSEPPRLVHRLDRDSSGILVMGRTQTSATVLHSIFREKTFSASKEDNDNEKRILQR 80 (275)
Q Consensus 1 l~v~~g~~~~~sl~~l~~~~l~~~~~~~~~~vhRLD~~TSGllllAk~~~~a~~l~~~~~~~~~~~~~~~~~~~~~~v~K 80 (275)
|+||++.+...++.+.+..+. .....+++|||||++||||||||+|..+++.|+.+|+++. +.|
T Consensus 111 l~~~~~~~~~~~~~~~~~~~~--~~~~~~~~vhRLD~~TSGlll~Ak~~~a~~~l~~~~~~~~--------------v~K 174 (317)
T PRK11025 111 TAVHGGSGLSFGVIEGLRALR--PEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLREKG--------------MQK 174 (317)
T ss_pred CcCcCCCCCCccHHHHHHHhc--cCCCcCceeCCCCCCCceEEEEEcCHHHHHHHHHHHHhCC--------------ccE
Confidence 689988776555544443221 2234578999999999999999999999999999999877 999
Q ss_pred EEEEEEecccCCCccEEeccceeeeccCCceeeEEEecCCCCCCCcceEEEEEEeeecCCcEEEEEEEeCcCchhHHHHH
Q 023907 81 WYWALVVGTPRCSKGVISAPLGKVVVDNGKSDRITVVNNDQIMSAQHAVTRYQVIKPSCHGYTWLKLSPLTGRKHQLRVH 160 (275)
Q Consensus 81 ~Y~alv~G~~~~~~g~i~~~l~~~~~~~~~~~~~~~~~~~~~~~~k~a~t~~~~l~~~~~~~slv~~~~~TGR~HQIR~h 160 (275)
+|+|+|.|.++...|.|+.||.+.....+. .+.... ..++.|.|.|++++.. .++|||+|+|.||||||||+|
T Consensus 175 ~Y~a~v~G~~~~~~~~i~~~i~~~~~~~~~--~~~~~~----~~gk~a~T~~~~l~~~-~~~sLv~~~~~TGRtHQIRvh 247 (317)
T PRK11025 175 DYLALVRGQWQSHVKVVQAPLLKNILQSGE--RIVRVS----QEGKPSETRFKVEERY-AFATLVRASPVTGRTHQIRVH 247 (317)
T ss_pred EEEEEEeCcccCCCceEecccccCcccCCc--eEEecC----CCCccceEEEEEeEEc-CCcEEEEEEeCCCCHHHHHHH
Confidence 999999999988889999998764322211 111111 2478999999999987 789999999999999999999
Q ss_pred HHhcCCCceeCCCCCCCCccccccccCCCCCCcCCCcccccccccccccccCcCcccccccccccccceeeccCCchhhh
Q 023907 161 CAEVLGTPIVGDYKYGWQTHRKWKQFHPSDLSKDSNEEIPKEKTLHFGLDLESGSILEKQPRLHLHCKEMTLPNVSQAIQ 240 (275)
Q Consensus 161 la~~lG~PIvGD~~Yg~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~LHa~~l~f~~~~~~~~ 240 (275)
||+ +||||+||.+||.... +..+. .. ...+++|||++|.|++|
T Consensus 248 la~-lG~PIlGD~~Yg~~~~---------------~~~~~-----~~-----------~~~r~~LHa~~l~f~~P----- 290 (317)
T PRK11025 248 TQY-AGHPIAFDDRYGDREF---------------DQQLT-----GT-----------GLNRLFLHAAALKFTHP----- 290 (317)
T ss_pred HHH-CCCCEECCcccCCccc---------------chhhh-----cc-----------CCcchhhhcCcceeeCC-----
Confidence 997 9999999999996421 00000 00 13578999999999998
Q ss_pred hhhccCCCCCCCCccEEEEcCCchHHHHHHHHhc
Q 023907 241 KVQLSSGCDVSKLETLKLVAPLPSHMQRSWDVLN 274 (275)
Q Consensus 241 ~~~~~~~~~~~~~~~~~~~aplP~~f~~~~~~l~ 274 (275)
.+++.+.|.||+|++|..+++.|.
T Consensus 291 ----------~~~~~~~~~aplP~~~~~~l~~l~ 314 (317)
T PRK11025 291 ----------GTGEVMRIEAPLDEQLKRCLQKLR 314 (317)
T ss_pred ----------CCCCeEEEEcCCCHHHHHHHHHHh
Confidence 578999999999999999998775
No 2
>COG0564 RluA Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=4.9e-45 Score=328.88 Aligned_cols=191 Identities=35% Similarity=0.560 Sum_probs=153.3
Q ss_pred CCccCCCCCcCcHHHHHHHHhhcCC--CCCCcccccCCCCCceEEEEEeCHHHHHHHHHHHHhccccccccccccccCCc
Q 023907 1 MPVQGGIGIRRSIDELAATCLTYDY--SEPPRLVHRLDRDSSGILVMGRTQTSATVLHSIFREKTFSASKEDNDNEKRIL 78 (275)
Q Consensus 1 l~v~~g~~~~~sl~~l~~~~l~~~~--~~~~~~vhRLD~~TSGllllAk~~~~a~~l~~~~~~~~~~~~~~~~~~~~~~v 78 (275)
|+||||.+... ..++..++.... .+.+++||||||+||||||||||..++..|+.+|++++ +
T Consensus 96 l~vhp~~~~~~--~tl~~~l~~~~~~~~~~~~~vHRLDkdTSGlll~AK~~~a~~~l~~~f~~r~--------------v 159 (289)
T COG0564 96 LVVHPGGGHHE--GTLVNALLRHCQDGVERPGIVHRLDKDTSGLLLVAKNREAARELSEQFKQRK--------------V 159 (289)
T ss_pred CcCcCCCCCcc--HhHHHHHHHhccccCCceeeeccCCCCCceEEEEECCHHHHHHHHHHHhcCc--------------C
Confidence 68999855433 333332332211 67899999999999999999999999999999999977 9
Q ss_pred ceEEEEEEecccCCCccEEeccceeeeccCCceeeEEEecCCCCCCCcceEEEEEEeeecCCc-EEEEEEEeCcCchhHH
Q 023907 79 QRWYWALVVGTPRCSKGVISAPLGKVVVDNGKSDRITVVNNDQIMSAQHAVTRYQVIKPSCHG-YTWLKLSPLTGRKHQL 157 (275)
Q Consensus 79 ~K~Y~alv~G~~~~~~g~i~~~l~~~~~~~~~~~~~~~~~~~~~~~~k~a~t~~~~l~~~~~~-~slv~~~~~TGR~HQI 157 (275)
.|+|+|+|.|.++..+|.|+.|+.+..... ..+.+..... +++|+|.|++++.. .. +|+++|+|.|||||||
T Consensus 160 ~K~Y~Alv~G~~~~~~~~i~~pi~r~~~~~---~~~~v~~~~~---gk~A~T~~~~l~~~-~~~~tlv~~~~~TGRTHQI 232 (289)
T COG0564 160 KKTYLALVRGHLPEDEGTIDAPIGRDPKNR---KKMAVVKEGS---GKPAITHYEVLERF-GDNYTLVELKPETGRTHQI 232 (289)
T ss_pred cEEEEEEEECcccCCCCEEeeeeecCCcCC---ceEEEeccCC---CCceEEEEEehhcc-CCceEEEEEEeCCCCHhHH
Confidence 999999999999988899999998854222 2233333221 79999999999998 45 7999999999999999
Q ss_pred HHHHHhcCCCceeCCCCCCCCccccccccCCCCCCcCCCcccccccccccccccCcCcccccccccccccceeeccCCch
Q 023907 158 RVHCAEVLGTPIVGDYKYGWQTHRKWKQFHPSDLSKDSNEEIPKEKTLHFGLDLESGSILEKQPRLHLHCKEMTLPNVSQ 237 (275)
Q Consensus 158 R~hla~~lG~PIvGD~~Yg~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~LHa~~l~f~~~~~ 237 (275)
|+||++ +||||+||++||.... . ......+++|||+.|.|+||
T Consensus 233 RVHl~~-lghPI~GD~~Yg~~~~-~---------------------------------~~~~~~r~~LHA~~l~f~hp-- 275 (289)
T COG0564 233 RVHLAH-LGHPIVGDPLYGGKDK-S---------------------------------AGAGLKRQALHAYKLSFTHP-- 275 (289)
T ss_pred HHHHHH-CCCCeeCCcccCCchh-h---------------------------------cccCcchhhhhhceeEccCC--
Confidence 999996 9999999999997520 0 00014689999999999998
Q ss_pred hhhhhhccCCCCCCCCccEEEEcCCch
Q 023907 238 AIQKVQLSSGCDVSKLETLKLVAPLPS 264 (275)
Q Consensus 238 ~~~~~~~~~~~~~~~~~~~~~~aplP~ 264 (275)
.+++.+.|.||+|.
T Consensus 276 -------------~t~~~~~~~a~~p~ 289 (289)
T COG0564 276 -------------LTGEELEFEAPLPE 289 (289)
T ss_pred -------------CCCCEEEEecCCCC
Confidence 47899999999984
No 3
>PRK11112 tRNA pseudouridine synthase C; Provisional
Probab=100.00 E-value=8.7e-44 Score=316.84 Aligned_cols=206 Identities=30% Similarity=0.383 Sum_probs=153.3
Q ss_pred CCccCCCCCcCcHHHHHHHHhhcCCCCCCcccccCCCCCceEEEEEeCHHHHHHHHHHHHhccccccccccccccCCcce
Q 023907 1 MPVQGGIGIRRSIDELAATCLTYDYSEPPRLVHRLDRDSSGILVMGRTQTSATVLHSIFREKTFSASKEDNDNEKRILQR 80 (275)
Q Consensus 1 l~v~~g~~~~~sl~~l~~~~l~~~~~~~~~~vhRLD~~TSGllllAk~~~~a~~l~~~~~~~~~~~~~~~~~~~~~~v~K 80 (275)
|+||++.........++. ++.......+++|||||++||||||||||+.+++.|+++|+++. |.|
T Consensus 20 l~~~~~~~~~~~~~~~~~-~l~~~~~~~~~~VHRLDr~TSGlll~Ak~~~~~~~L~~~f~~~~--------------v~K 84 (257)
T PRK11112 20 WLVHRSWLDRHETVFVMQ-TVRDQIGQHVFTAHRLDRPTSGVLLMALSSEVARLLAQQFEQHQ--------------IQK 84 (257)
T ss_pred CeecCCCCCCCchHHHHH-HHHHHhCCCceeeccCCCCCeeEEEEECCHHHHHHHHHHHHhCC--------------cce
Confidence 578876422221111222 33323344688999999999999999999999999999999977 999
Q ss_pred EEEEEEecccCCCccEEeccceeeeccCCceeeEEEecCCCCCCCcceEEEEEEeeec----------CCcEEEEEEEeC
Q 023907 81 WYWALVVGTPRCSKGVISAPLGKVVVDNGKSDRITVVNNDQIMSAQHAVTRYQVIKPS----------CHGYTWLKLSPL 150 (275)
Q Consensus 81 ~Y~alv~G~~~~~~g~i~~~l~~~~~~~~~~~~~~~~~~~~~~~~k~a~t~~~~l~~~----------~~~~slv~~~~~ 150 (275)
+|+|+|.|.++ .++.++.|+....... .. .... ....++.|.|.|+++... ..++|||+|+|.
T Consensus 85 ~Y~Alv~G~~~-~~~~i~~~l~~~~~~~---~~-~~~~--~~~~~k~a~T~~~~l~~~~~~~~~~~~~~~~~slv~i~~~ 157 (257)
T PRK11112 85 TYHAIVRGWLM-EEAVLDYPLKEELDKI---AD-KFAR--EDKAPQPAVTHYRGLATVEMPVATGRYPTTRYSLVELEPK 157 (257)
T ss_pred EEEEEEEeEeC-CCCeEeeeeeeccccc---ce-eecc--cCCCCeEeEEEEEEEEEecccccccccCCCCeEEEEEEcC
Confidence 99999999886 4578998886531111 01 1111 112478999999999763 135899999999
Q ss_pred cCchhHHHHHHHhcCCCceeCCCCCCCCccccccccCCCCCCcCCCcccccccccccccccCcCccccccccccccccee
Q 023907 151 TGRKHQLRVHCAEVLGTPIVGDYKYGWQTHRKWKQFHPSDLSKDSNEEIPKEKTLHFGLDLESGSILEKQPRLHLHCKEM 230 (275)
Q Consensus 151 TGR~HQIR~hla~~lG~PIvGD~~Yg~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~LHa~~l 230 (275)
||||||||+|||+ +||||+||.+||..... ..+. ..++ ..+++|||++|
T Consensus 158 TGRtHQIRvhla~-lG~PIvGD~~Yg~~~~~---------------~~~~----~~~~-----------~~rl~LHA~~L 206 (257)
T PRK11112 158 TGRKHQLRRHMAH-LRHPIIGDTKHGDLRQN---------------RSLA----EHFG-----------CSRLMLHASEL 206 (257)
T ss_pred CCChHHHHHHHHH-cCCCEeCCcccCCcccc---------------hhhh----hccC-----------CcchhHhhCcc
Confidence 9999999999996 99999999999964210 0000 0011 35799999999
Q ss_pred eccCCchhhhhhhccCCCCCCCCccEEEEcCCchHHHHHHHHhc
Q 023907 231 TLPNVSQAIQKVQLSSGCDVSKLETLKLVAPLPSHMQRSWDVLN 274 (275)
Q Consensus 231 ~f~~~~~~~~~~~~~~~~~~~~~~~~~~~aplP~~f~~~~~~l~ 274 (275)
.|+|| .+++.+.|.||+|++|+.+++.|+
T Consensus 207 ~F~hP---------------~t~e~~~~~a~~p~~~~~~~~~~~ 235 (257)
T PRK11112 207 SLTHP---------------FTGEPLTITAGLDETWQQLLSQFG 235 (257)
T ss_pred CccCC---------------CCCCEEEEEcCCCHHHHHHHHHcC
Confidence 99998 588999999999999999998774
No 4
>PRK11180 rluD 23S rRNA pseudouridine synthase D; Provisional
Probab=100.00 E-value=9e-43 Score=320.16 Aligned_cols=210 Identities=28% Similarity=0.410 Sum_probs=158.8
Q ss_pred CCccCCCCC-cCcHHHHHHHHhhc-CCCCCCcccccCCCCCceEEEEEeCHHHHHHHHHHHHhccccccccccccccCCc
Q 023907 1 MPVQGGIGI-RRSIDELAATCLTY-DYSEPPRLVHRLDRDSSGILVMGRTQTSATVLHSIFREKTFSASKEDNDNEKRIL 78 (275)
Q Consensus 1 l~v~~g~~~-~~sl~~l~~~~l~~-~~~~~~~~vhRLD~~TSGllllAk~~~~a~~l~~~~~~~~~~~~~~~~~~~~~~v 78 (275)
|+||++.+. ..++.+.+..++.. .....+++|||||++||||||||||..++..|+++|.++. +
T Consensus 102 l~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~vhRLD~~TSGlll~Ak~~~~~~~l~~~~~~~~--------------v 167 (325)
T PRK11180 102 LVVHPGAGNPDGTVLNALLHYYPPIADVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVEALQKRE--------------I 167 (325)
T ss_pred CeEeCCCCCCCCcHHHHHHHHhhhccCCcccceeccCCCCCceeEEEECCHHHHHHHHHHHHhCC--------------c
Confidence 578876543 34565555444432 2234688999999999999999999999999999999876 9
Q ss_pred ceEEEEEEecccCCCccEEeccceeeeccCCceeeEEEecCCCCCCCcceEEEEEEeeecCCcEEEEEEEeCcCchhHHH
Q 023907 79 QRWYWALVVGTPRCSKGVISAPLGKVVVDNGKSDRITVVNNDQIMSAQHAVTRYQVIKPSCHGYTWLKLSPLTGRKHQLR 158 (275)
Q Consensus 79 ~K~Y~alv~G~~~~~~g~i~~~l~~~~~~~~~~~~~~~~~~~~~~~~k~a~t~~~~l~~~~~~~slv~~~~~TGR~HQIR 158 (275)
.|+|+|+|.|.++ .+|.++.+|.... .....+.+. ..++.|.|.|+++... .++|+|+|+|.||||||||
T Consensus 168 ~K~Y~A~v~G~~~-~~~~i~~~l~~~~---~~~~~~~~~-----~~gk~a~T~~~~l~~~-~~~slv~~~~~TGRtHQIR 237 (325)
T PRK11180 168 TREYEAVAIGHMT-AGGTVDEPISRHP---TKRTHMAVH-----PMGKPAVTHYRIMEHF-RVHTRLRLRLETGRTHQIR 237 (325)
T ss_pred ceEEEEEEecCCC-CCCEEECceecCC---CcCcEEEeC-----CCCcEEeEEEEEeEEc-CCeEEEEEEeCCCCHHHHH
Confidence 9999999999986 4678999986532 111112121 2378999999999987 6889999999999999999
Q ss_pred HHHHhcCCCceeCCCCCCCCccccccccCCCCCCcCCCcccccccccccccccCcCcccccccccccccceeeccCCchh
Q 023907 159 VHCAEVLGTPIVGDYKYGWQTHRKWKQFHPSDLSKDSNEEIPKEKTLHFGLDLESGSILEKQPRLHLHCKEMTLPNVSQA 238 (275)
Q Consensus 159 ~hla~~lG~PIvGD~~Yg~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~LHa~~l~f~~~~~~ 238 (275)
+|||+ +||||+||.+||+..... +.....+... .....+++|||++|.|+||
T Consensus 238 vhla~-lG~PI~GD~~Yg~~~~~~----------~~~~~~~~~~--------------~~~~~r~~Lha~~l~f~hP--- 289 (325)
T PRK11180 238 VHMAH-ITHPLVGDQVYGGRPRPP----------KGASEEFIST--------------LRKFDRQALHATMLRLYHP--- 289 (325)
T ss_pred HHHHh-CCCCEeCccccCCCcccc----------cccchhhhhh--------------ccccchhhhhcceeEeeCC---
Confidence 99997 999999999999653100 0000000000 0013579999999999998
Q ss_pred hhhhhccCCCCCCCCccEEEEcCCchHHHHHHHHhc
Q 023907 239 IQKVQLSSGCDVSKLETLKLVAPLPSHMQRSWDVLN 274 (275)
Q Consensus 239 ~~~~~~~~~~~~~~~~~~~~~aplP~~f~~~~~~l~ 274 (275)
.+++.+.|.||+|++|..+++.|+
T Consensus 290 ------------~~~~~~~~~a~~p~~~~~~~~~l~ 313 (325)
T PRK11180 290 ------------ITGIEMEWHAPLPQDMVELIEALR 313 (325)
T ss_pred ------------CCCCeEEEECCChHHHHHHHHHhh
Confidence 478999999999999999998775
No 5
>TIGR01621 RluA-like pseudouridine synthase Rlu family protein, TIGR01621. This model represents a clade of sequences within the pseudouridine synthase superfamily (pfam00849). The superfamily includes E. coli proteins: RluA, RluB, RluC, RluD, and RsuA. The sequences modeled here are most closely related to RluA. Neisseria, among those species hitting this model, does not appear to have an RluA homolog. It is presumed that these sequences function as pseudouridine synthases, although perhaps with different specificity.
Probab=100.00 E-value=2e-42 Score=300.92 Aligned_cols=184 Identities=30% Similarity=0.433 Sum_probs=147.0
Q ss_pred CCccCCCCCcCcHHHHHHHHhhcCCCCCCcccccCCCCCceEEEEEeCHHHHHHHHHHHHhccccccccccccccCCcce
Q 023907 1 MPVQGGIGIRRSIDELAATCLTYDYSEPPRLVHRLDRDSSGILVMGRTQTSATVLHSIFREKTFSASKEDNDNEKRILQR 80 (275)
Q Consensus 1 l~v~~g~~~~~sl~~l~~~~l~~~~~~~~~~vhRLD~~TSGllllAk~~~~a~~l~~~~~~~~~~~~~~~~~~~~~~v~K 80 (275)
|+||++.+. .++.+.+... .....+++|||||++|||+||||+|+++++.|+++|.++. +.|
T Consensus 20 l~v~~~~~~-~~l~~~l~~~---~~~~~~~~VhRLDr~TSGlll~Ak~~~~~~~L~~~~~~~~--------------v~K 81 (217)
T TIGR01621 20 ISVHKDDGE-TGLLQEVATQ---LGVGQVWLVHRLDKMTSGILLLALNAESASELSQGFAKRK--------------IEK 81 (217)
T ss_pred CeECCCCCc-ChHHHHHHHh---cCCCCccEecCCCCCCceEEEEEcCHHHHHHHHHHHhcCC--------------ccE
Confidence 578876543 3444443322 2245789999999999999999999999999999999977 999
Q ss_pred EEEEEEecccCCCccEEeccceeeeccCCceeeEEEecCCCCCCCcceEEEEEEeeecCCcEEEEEEEeCcCchhHHHHH
Q 023907 81 WYWALVVGTPRCSKGVISAPLGKVVVDNGKSDRITVVNNDQIMSAQHAVTRYQVIKPSCHGYTWLKLSPLTGRKHQLRVH 160 (275)
Q Consensus 81 ~Y~alv~G~~~~~~g~i~~~l~~~~~~~~~~~~~~~~~~~~~~~~k~a~t~~~~l~~~~~~~slv~~~~~TGR~HQIR~h 160 (275)
+|+|+|.|.++..+|.|+.++.... .+. ..+... .++.|.|.|+++... +++++++|+|.|||+||||+|
T Consensus 82 ~YlAlV~g~~~~~~~~i~~~~~~~~--~~~---~~~~~~----~~k~a~t~~~~~~~~-~~~slv~~~~~TGR~HQIRvh 151 (217)
T TIGR01621 82 TYLALSSKKPKKKQGLICGDMEKSR--RGS---WKLVNS----QENPAITRFFSASAA-TGLRLFILKPHTGKTHQLRVA 151 (217)
T ss_pred EEEEEEeccccCCCCEEeCCcccCC--CCC---EEEeCC----CCCceeEEEEEEEEc-CCeEEEEEEeCCCCHHHHHHH
Confidence 9999999999888899998886421 221 122221 368899999999887 689999999999999999999
Q ss_pred HHhcCCCceeCCCCCCCCccccccccCCCCCCcCCCcccccccccccccccCcCcccccccccccccceeeccCCchhhh
Q 023907 161 CAEVLGTPIVGDYKYGWQTHRKWKQFHPSDLSKDSNEEIPKEKTLHFGLDLESGSILEKQPRLHLHCKEMTLPNVSQAIQ 240 (275)
Q Consensus 161 la~~lG~PIvGD~~Yg~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~LHa~~l~f~~~~~~~~ 240 (275)
||+ +||||+||.+||.... ..+++|||++|.|++
T Consensus 152 la~-lG~PIlGD~~Yg~~~~---------------------------------------~~~~~Lha~~l~f~~------ 185 (217)
T TIGR01621 152 MKS-LGSPILGDPLYGTTDE---------------------------------------SDRGYLHAFALRFDY------ 185 (217)
T ss_pred HHH-CCCceeCCcccCCCCC---------------------------------------ccCceeeeeEeEEEE------
Confidence 997 9999999999996320 236899999999997
Q ss_pred hhhccCCCCCCCCccEEEEcCCchHHHHHH
Q 023907 241 KVQLSSGCDVSKLETLKLVAPLPSHMQRSW 270 (275)
Q Consensus 241 ~~~~~~~~~~~~~~~~~~~aplP~~f~~~~ 270 (275)
+++.+.|.|| |++|..++
T Consensus 186 -----------~~~~~~~~~~-~~~~~~~~ 203 (217)
T TIGR01621 186 -----------QNEVIQWLCD-PRQFQKWH 203 (217)
T ss_pred -----------CCeEEEEEEC-cHHHHHHH
Confidence 3689999999 77675543
No 6
>TIGR00005 rluA_subfam pseudouridine synthase, RluA family. modifies uracil-65 in transfer RNAs to pseudouridine.
Probab=100.00 E-value=2.5e-42 Score=313.85 Aligned_cols=208 Identities=30% Similarity=0.404 Sum_probs=160.6
Q ss_pred CCccCCCCC-cCcHHHHHHHHhhc-CCCCCCcccccCCCCCceEEEEEeCHHHHHHHHHHHHhccccccccccccccCCc
Q 023907 1 MPVQGGIGI-RRSIDELAATCLTY-DYSEPPRLVHRLDRDSSGILVMGRTQTSATVLHSIFREKTFSASKEDNDNEKRIL 78 (275)
Q Consensus 1 l~v~~g~~~-~~sl~~l~~~~l~~-~~~~~~~~vhRLD~~TSGllllAk~~~~a~~l~~~~~~~~~~~~~~~~~~~~~~v 78 (275)
|+||++.+. ..++.+++..++.. .....+++|||||++||||||||+|..+++.++++|.++. +
T Consensus 90 ~~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~vhRLD~~TSGlll~ak~~~~~~~l~~~~~~~~--------------v 155 (299)
T TIGR00005 90 LVVHPGGGNPFGTVLNALLAHCPPIAGVERVGIVHRLDRDTSGLMVVAKTPLALRELQRQLKNRT--------------V 155 (299)
T ss_pred CeEeCCCCCCcccHHHHHHHhcccccCCCcCceECCCCCCCceEEEEEcCHHHHHHHHHHHHhCC--------------c
Confidence 577876543 34566665544321 1225789999999999999999999999999999999876 9
Q ss_pred ceEEEEEEecccCCCccEEeccceeeeccCCceeeEEEecCCCCCCCcceEEEEEEeeecCCcEEEEEEEeCcCchhHHH
Q 023907 79 QRWYWALVVGTPRCSKGVISAPLGKVVVDNGKSDRITVVNNDQIMSAQHAVTRYQVIKPSCHGYTWLKLSPLTGRKHQLR 158 (275)
Q Consensus 79 ~K~Y~alv~G~~~~~~g~i~~~l~~~~~~~~~~~~~~~~~~~~~~~~k~a~t~~~~l~~~~~~~slv~~~~~TGR~HQIR 158 (275)
.|+|+|+|.|.++...|.|+.||.......+ ...+... .++++|.|.|+++... .++|+++|+|.|||+||||
T Consensus 156 ~K~Y~a~v~g~~~~~~~~i~~~l~~~~~~~~---~~~~~~~---~~~k~a~t~~~~l~~~-~~~slv~~~l~tGR~HQIR 228 (299)
T TIGR00005 156 TKEYVALVHGQFDSGGGTVDAPLGRVPNNRG---LMAVHPS---SEGKPAVTHFRVLERF-GNASLVECELETGRTHQIR 228 (299)
T ss_pred ceEEEEEEeccccCCCCEEeCceecCCCCCc---eEEEecC---CCCCeeeEEEEEeEEc-CCeEEEEEEeCCCChHHHH
Confidence 9999999999998888999999876422111 1122221 1478999999999886 6889999999999999999
Q ss_pred HHHHhcCCCceeCCCCCCCCccccccccCCCCCCcCCCcccccccccccccccCcCcccccccccccccceeeccCCchh
Q 023907 159 VHCAEVLGTPIVGDYKYGWQTHRKWKQFHPSDLSKDSNEEIPKEKTLHFGLDLESGSILEKQPRLHLHCKEMTLPNVSQA 238 (275)
Q Consensus 159 ~hla~~lG~PIvGD~~Yg~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~LHa~~l~f~~~~~~ 238 (275)
+|||+ +||||+||.+||+.... ... .+. .....+++|||++|.|++|
T Consensus 229 ~hla~-lG~pI~gD~~Yg~~~~~--~~~--------~~~-------------------~~~~~r~~Lha~~l~f~~p--- 275 (299)
T TIGR00005 229 VHLQY-LGHPLAGDPLYGNKPVP--GNN--------LNG-------------------LLNFDRQALHAYELGFIHP--- 275 (299)
T ss_pred HHHHH-CCCcEeCccccCCcccc--ccc--------ccc-------------------ccCCcchhhccCeeeccCC---
Confidence 99997 99999999999974310 000 000 0013579999999999998
Q ss_pred hhhhhccCCCCCCCCccEEEEcCCchHHHHHHHHhc
Q 023907 239 IQKVQLSSGCDVSKLETLKLVAPLPSHMQRSWDVLN 274 (275)
Q Consensus 239 ~~~~~~~~~~~~~~~~~~~~~aplP~~f~~~~~~l~ 274 (275)
.+++.+.|.||+|++|..++..|+
T Consensus 276 ------------~~~~~~~~~a~~p~~~~~~~~~~~ 299 (299)
T TIGR00005 276 ------------ATGEILEFEAPLPADLVLLLEALR 299 (299)
T ss_pred ------------CCCCEEEEEcCChHHHHHHHHhhC
Confidence 478999999999999999987763
No 7
>cd02563 PseudoU_synth_TruC tRNA pseudouridine isomerase C: Pseudouridine synthases catalyze the isomerization of specific uridines in an tRNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. TruC makes psi65 in tRNAs. This psi residue is not universally conserved.
Probab=100.00 E-value=1.9e-42 Score=302.33 Aligned_cols=195 Identities=29% Similarity=0.382 Sum_probs=145.2
Q ss_pred CCccCCCCCcCcHHHHHHHHhhcCCCCCCcccccCCCCCceEEEEEeCHHHHHHHHHHHHhccccccccccccccCCcce
Q 023907 1 MPVQGGIGIRRSIDELAATCLTYDYSEPPRLVHRLDRDSSGILVMGRTQTSATVLHSIFREKTFSASKEDNDNEKRILQR 80 (275)
Q Consensus 1 l~v~~g~~~~~sl~~l~~~~l~~~~~~~~~~vhRLD~~TSGllllAk~~~~a~~l~~~~~~~~~~~~~~~~~~~~~~v~K 80 (275)
|+||++.+.......++. .+.......+++|||||++||||||||+|+.+++.|+++|+++. ++|
T Consensus 19 ~~~~~~~~~~~~~~~~~~-~l~~~~~~~~~~vhRLD~~TSGlll~Ak~~~~~~~l~~~f~~~~--------------v~K 83 (223)
T cd02563 19 LLVHRSELDRHETRFALQ-TLRDQLGQHVYPVHRLDRPTSGVLLFALSSEVARKLGEQFTEHR--------------VHK 83 (223)
T ss_pred CeEcCCCCCCCCcHHHHH-HHHHHcCCCcccccCCCCCCeEEEEEEECHHHHHHHHHHHhcCc--------------eeE
Confidence 578876533222122222 23323345788999999999999999999999999999999977 999
Q ss_pred EEEEEEecccCCCccEEeccceeeeccCCceeeEEEecCCCCCCCcceEEEEEEeeec----------CCcEEEEEEEeC
Q 023907 81 WYWALVVGTPRCSKGVISAPLGKVVVDNGKSDRITVVNNDQIMSAQHAVTRYQVIKPS----------CHGYTWLKLSPL 150 (275)
Q Consensus 81 ~Y~alv~G~~~~~~g~i~~~l~~~~~~~~~~~~~~~~~~~~~~~~k~a~t~~~~l~~~----------~~~~slv~~~~~ 150 (275)
+|+|+|.|.++. +|.|+.++...... .....+... ..++.|.|.|+++... ..++|||+|+|.
T Consensus 84 ~Y~alv~G~~~~-~~~i~~~l~~~~~~---~~~~~~~~~---~~~~~a~t~~~~l~~~~~~~~~~~~~~~~~slv~~~~~ 156 (223)
T cd02563 84 TYLAVVRGYVPE-SGTIDYPLSEELDK---LADKFASDD---KAPQAATTHYRLLAVEELPVVVGKYPTSRYSLVELTPH 156 (223)
T ss_pred EEEEEEECccCC-CCeEEEeeeeCCCc---cceEEeecC---CCCceeEEEEEEeeecccccccccCCCCCeEEEEEEeC
Confidence 999999999876 78999988663211 111112111 2468899999999752 135899999999
Q ss_pred cCchhHHHHHHHhcCCCceeCCCCCCCCccccccccCCCCCCcCCCcccccccccccccccCcCccccccccccccccee
Q 023907 151 TGRKHQLRVHCAEVLGTPIVGDYKYGWQTHRKWKQFHPSDLSKDSNEEIPKEKTLHFGLDLESGSILEKQPRLHLHCKEM 230 (275)
Q Consensus 151 TGR~HQIR~hla~~lG~PIvGD~~Yg~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~LHa~~l 230 (275)
|||+||||+|||+ +||||+||.+||+.... ..+.+ .+ ...+++|||++|
T Consensus 157 TGR~HQIRvhla~-lG~PIvGD~~Yg~~~~~---------------~~~~~----~~-----------~~~rl~Lha~~L 205 (223)
T cd02563 157 TGRKHQLRRHLAH-IRHPIIGDTTHGDGRHN---------------RFFRE----HF-----------GCHRLLLAATRL 205 (223)
T ss_pred CCCHHHHHHHHHH-cCCCeeCCcccCCcccC---------------hhHHh----hc-----------CCccceeecCee
Confidence 9999999999997 99999999999965310 00000 01 135799999999
Q ss_pred eccCCchhhhhhhccCCCCCCCCccEEEEcCCc
Q 023907 231 TLPNVSQAIQKVQLSSGCDVSKLETLKLVAPLP 263 (275)
Q Consensus 231 ~f~~~~~~~~~~~~~~~~~~~~~~~~~~~aplP 263 (275)
.|++| .+++.+.|+||+|
T Consensus 206 ~F~hP---------------~t~~~~~~~a~~~ 223 (223)
T cd02563 206 EFTHP---------------VTGERLLIEAPLD 223 (223)
T ss_pred EeeCC---------------CCCCeEEEEccCC
Confidence 99998 5899999999997
No 8
>PRK10158 23S rRNA/tRNA pseudouridine synthase A; Provisional
Probab=100.00 E-value=8e-42 Score=297.56 Aligned_cols=185 Identities=30% Similarity=0.417 Sum_probs=145.5
Q ss_pred CCccCCCC--CcCcHHHHHHHHhhcCCCCCCcccccCCCCCceEEEEEeCHHHHHHHHHHHHhccccccccccccccCCc
Q 023907 1 MPVQGGIG--IRRSIDELAATCLTYDYSEPPRLVHRLDRDSSGILVMGRTQTSATVLHSIFREKTFSASKEDNDNEKRIL 78 (275)
Q Consensus 1 l~v~~g~~--~~~sl~~l~~~~l~~~~~~~~~~vhRLD~~TSGllllAk~~~~a~~l~~~~~~~~~~~~~~~~~~~~~~v 78 (275)
|+||++.. ...++.+.+...+ ..+++|||||++||||||||+|.++++.|+++|+++. +
T Consensus 32 l~~~~~~~~~~~~sl~~~l~~~~-----~~~~~vhRLDr~TSGlll~Akt~~~~~~l~~~f~~~~--------------v 92 (219)
T PRK10158 32 LLSVPGRLEEHKDSVMTRIQRDY-----PQAESVHRLDMATSGVIVVALTKAAERELKRQFRERE--------------P 92 (219)
T ss_pred CcEeCCCCCccchhHHHHHHHhC-----CCCCEECCCCCCCceEEEEECCHHHHHHHHHHHHhCC--------------c
Confidence 57887653 2334444443221 2578999999999999999999999999999999876 9
Q ss_pred ceEEEEEEecccCCCccEEeccceeeeccCCceeeEEEecCCCCCCCcceEEEEEEeeecCCcEEEEEEEeCcCchhHHH
Q 023907 79 QRWYWALVVGTPRCSKGVISAPLGKVVVDNGKSDRITVVNNDQIMSAQHAVTRYQVIKPSCHGYTWLKLSPLTGRKHQLR 158 (275)
Q Consensus 79 ~K~Y~alv~G~~~~~~g~i~~~l~~~~~~~~~~~~~~~~~~~~~~~~k~a~t~~~~l~~~~~~~slv~~~~~TGR~HQIR 158 (275)
.|+|+|+|.|.++..++.++.|+..... ......+.. .+++.+.|.|++++......++|+|+|+|||+||||
T Consensus 93 ~K~Yla~v~G~~~~~~~~i~~~i~~~~~---~~~~~~~~~----~~gk~a~t~~~~l~~~~~~~sll~~~~~TGRtHQIR 165 (219)
T PRK10158 93 KKQYVARVWGHPSPAEGLVDLPLICDWP---NRPKQKVCY----ETGKPAQTEYEVVEYAADNTARVVLKPITGRSHQLR 165 (219)
T ss_pred cEEEEEEEecccCCCCcEEecceecCCC---CCceEEecC----CCCceeeEEEEEEEEcCCCCEEEEEEeCCCCHHHHH
Confidence 9999999999998888999999865321 111122221 236899999999998634458999999999999999
Q ss_pred HHHHhcCCCceeCCCCCCCCccccccccCCCCCCcCCCcccccccccccccccCcCcccccccccccccceeeccCCchh
Q 023907 159 VHCAEVLGTPIVGDYKYGWQTHRKWKQFHPSDLSKDSNEEIPKEKTLHFGLDLESGSILEKQPRLHLHCKEMTLPNVSQA 238 (275)
Q Consensus 159 ~hla~~lG~PIvGD~~Yg~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~LHa~~l~f~~~~~~ 238 (275)
+||++ +||||+||.+||..... . ..++++|||++|.|++|
T Consensus 166 ~hla~-lG~PIvGD~~Yg~~~~~---------------~---------------------~~~r~~Lha~~l~f~~P--- 205 (219)
T PRK10158 166 VHMLA-LGHPILGDRFYASPEAR---------------A---------------------MAPRLLLHAEMLTITHP--- 205 (219)
T ss_pred HHHHH-CCCcEECCcccCCcccc---------------c---------------------cccchhhhhCccCccCC---
Confidence 99996 99999999999964210 0 03469999999999998
Q ss_pred hhhhhccCCCCCCCCccEEEEcCCc
Q 023907 239 IQKVQLSSGCDVSKLETLKLVAPLP 263 (275)
Q Consensus 239 ~~~~~~~~~~~~~~~~~~~~~aplP 263 (275)
.+++.++|.||.|
T Consensus 206 ------------~~~~~~~~~a~~~ 218 (219)
T PRK10158 206 ------------AYGNSMTFKAPAD 218 (219)
T ss_pred ------------CCCCeEEEEeCCC
Confidence 4789999999986
No 9
>cd02558 PSRA_1 PSRA_1: Pseudouridine synthase, a subgroup of the RluA family. This group is comprised of bacterial proteins assigned to the RluA family of pseudouridine synthases. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. The RluA family is comprised of proteins related to Escherichia coli RluA.
Probab=100.00 E-value=6.7e-41 Score=296.48 Aligned_cols=187 Identities=22% Similarity=0.288 Sum_probs=140.9
Q ss_pred CCccCCCCC-cCcHHHHHHHHhhcCCCCCCcccccCCCCCceEEEEEeCHHHHHHHHHHHHhccccccccccccccCCcc
Q 023907 1 MPVQGGIGI-RRSIDELAATCLTYDYSEPPRLVHRLDRDSSGILVMGRTQTSATVLHSIFREKTFSASKEDNDNEKRILQ 79 (275)
Q Consensus 1 l~v~~g~~~-~~sl~~l~~~~l~~~~~~~~~~vhRLD~~TSGllllAk~~~~a~~l~~~~~~~~~~~~~~~~~~~~~~v~ 79 (275)
|+||++.+. ..++.+.+...+ ....+++|||||++|||+||||||+++++.++.+|+++. ++
T Consensus 57 l~~~~~~~~~~~t~~~~l~~~~---~~~~~~~vhRLD~~TSGlll~Ak~~~~~~~l~~~~~~~~--------------v~ 119 (246)
T cd02558 57 LPVTPRGRYVTETLLVRLRRQT---GNPDLTPAHRLDRLTAGLVLFSKRPETRGAYQTLFARRE--------------VS 119 (246)
T ss_pred CccCCCCcchhhhHHHHHHHHh---CCCcccccccCCCCceeEEEEEcCHHHHHHHHHHHHcCC--------------cc
Confidence 678876443 234444433222 234678999999999999999999999999999999876 99
Q ss_pred eEEEEEEecccCCCcc-EEeccceeeeccCCceeeEEEecCCCCCCCcceEEEEEEeeecCCcEEEEEEEeCcCchhHHH
Q 023907 80 RWYWALVVGTPRCSKG-VISAPLGKVVVDNGKSDRITVVNNDQIMSAQHAVTRYQVIKPSCHGYTWLKLSPLTGRKHQLR 158 (275)
Q Consensus 80 K~Y~alv~G~~~~~~g-~i~~~l~~~~~~~~~~~~~~~~~~~~~~~~k~a~t~~~~l~~~~~~~slv~~~~~TGR~HQIR 158 (275)
|+|+|+|.|.++...+ .++.++... .+ ....... .+++.|.|.|++++.. .++|+++|+|.|||+||||
T Consensus 120 K~YlA~v~G~~~~~~~~~~~~~i~~~---~~-~~~~~~~-----~~~~~a~T~~~~l~~~-~~~slv~~~l~TGRtHQIR 189 (246)
T cd02558 120 KTYEAVAPYVPALTFPLTVRSRIVKG---RG-FFQAREV-----EGEPNAETRIELLARR-GGWGLYRLSPHTGKTHQLR 189 (246)
T ss_pred EEEEEEEecCCCCCCCcceecccccc---CC-cceeecc-----CCCCCceEEEEEEEec-CCeEEEEEEeCCCCHHHHH
Confidence 9999999998865443 355555432 11 1111111 2357899999999886 6899999999999999999
Q ss_pred HHHHhcCCCceeCCCCCCCCccccccccCCCCCCcCCCcccccccccccccccCcCcccccccccccccceeeccCCchh
Q 023907 159 VHCAEVLGTPIVGDYKYGWQTHRKWKQFHPSDLSKDSNEEIPKEKTLHFGLDLESGSILEKQPRLHLHCKEMTLPNVSQA 238 (275)
Q Consensus 159 ~hla~~lG~PIvGD~~Yg~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~LHa~~l~f~~~~~~ 238 (275)
+|||+ +||||+||.+||...... .. . ...+++|||++|.|+||
T Consensus 190 vhla~-lG~PIvGD~~Yg~~~~~~-------------~~-----------------~---~~~~~~Lha~~l~f~hP--- 232 (246)
T cd02558 190 VHMAA-LGVPILNDPFYPVLLDKD-------------PD-----------------D---FSRPLQLLAKELEFTDP--- 232 (246)
T ss_pred HHHHH-CCCcccCCccCCCCCccc-------------cc-----------------c---cccCchhhhcccCccCC---
Confidence 99996 999999999999642100 00 0 01348999999999998
Q ss_pred hhhhhccCCCCCCCCccEEEEcCCc
Q 023907 239 IQKVQLSSGCDVSKLETLKLVAPLP 263 (275)
Q Consensus 239 ~~~~~~~~~~~~~~~~~~~~~aplP 263 (275)
.+++.+.|.||+|
T Consensus 233 ------------~t~~~~~~~~~~~ 245 (246)
T cd02558 233 ------------LTGRPRRFESGRS 245 (246)
T ss_pred ------------CCCCEEEEecCCC
Confidence 5889999999998
No 10
>cd02557 PseudoU_synth_ScRIB2 PseudoU_synth_ScRIB2_like: Pseudouridine synthase, Saccharomyces cerevisiae RIB2_like. This group is comprised of eukaryotic and bacterial proteins similar to Saccharomyces cerevisiae RIB2, S. cerevisiae Pus6p and human hRPUDSD2. S. cerevisiae RIB2 displays two distinct catalytic activities. The N-terminal domain of RIB2 is RNA:psi-synthase which makes psi32 on cytoplasmic tRNAs. Psi32 is highly phylogenetically conserved. The C-terminal domain of RIB2 has a DRAP deaminase activity which catalyses the formation of 5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione 5'-phosphate from 2,5-diamino-6-ribitylamino-4(3H)-pyrimidinone 5'-phosphate during riboflavin biosynthesis. S. cerevisiae Pus6p makes the psi31 of cytoplasmic and mitochondrial tRNAs.
Probab=100.00 E-value=3.5e-40 Score=286.15 Aligned_cols=177 Identities=27% Similarity=0.352 Sum_probs=142.8
Q ss_pred CCccCCCC-CcCcHHHHHHHHhhcCCCCCCcccccCCCCCceEEEEEeCHHHHHHHHHHHHhccccccccccccccCCcc
Q 023907 1 MPVQGGIG-IRRSIDELAATCLTYDYSEPPRLVHRLDRDSSGILVMGRTQTSATVLHSIFREKTFSASKEDNDNEKRILQ 79 (275)
Q Consensus 1 l~v~~g~~-~~~sl~~l~~~~l~~~~~~~~~~vhRLD~~TSGllllAk~~~~a~~l~~~~~~~~~~~~~~~~~~~~~~v~ 79 (275)
|+||++.. ...++.+++...+ ....+++|||||++||||||||+|+++++.|+++|+++. ++
T Consensus 34 l~~~~~~~~~~~sl~~~l~~~~---~~~~~~~vhRLD~~TSGllllak~~~~~~~l~~~f~~~~--------------v~ 96 (213)
T cd02557 34 IPVHPTGRYRYNTVTEILKSEY---GLTELRPCHRLDRLTSGLLLFAKTSQTASRLQQQIRSRE--------------VK 96 (213)
T ss_pred CcCCCCCCCCcChHHHHHHHHc---CCCCccCccCCCCCCceEEEEECCHHHHHHHHHHHHcCC--------------cc
Confidence 57786543 3456666665322 124688999999999999999999999999999999876 99
Q ss_pred eEEEEEEecccCCCccEEeccceeeeccCCceeeEEEecCCCCCCCcceEEEEEEeeecC-CcEEEEEEEeCcCchhHHH
Q 023907 80 RWYWALVVGTPRCSKGVISAPLGKVVVDNGKSDRITVVNNDQIMSAQHAVTRYQVIKPSC-HGYTWLKLSPLTGRKHQLR 158 (275)
Q Consensus 80 K~Y~alv~G~~~~~~g~i~~~l~~~~~~~~~~~~~~~~~~~~~~~~k~a~t~~~~l~~~~-~~~slv~~~~~TGR~HQIR 158 (275)
|+|+|+|.|.++...+.++.||.......+ +.... ...++.|.|.|+++.... .++++|+|+|.|||+||||
T Consensus 97 K~Y~a~v~G~~~~~~~~i~~~l~~~~~~~~----~~~~~---~~~~~~a~t~~~~~~~~~~~~~slv~v~~~TGR~HQIR 169 (213)
T cd02557 97 KEYLARVKGEFPDGEVVVDQPIGLVSPKGG----LRNDV---DEKGKDARTIFKRLSYNGDLNTSVVLCKPITGRTHQIR 169 (213)
T ss_pred EEEEEEEeCcCCCCCeEEecceeccCcCCc----eeecc---CCCCceeeEEEEEEEEcCCCCeEEEEEEeCCCCHHHHH
Confidence 999999999998888999999876432221 11111 124688999999998862 2789999999999999999
Q ss_pred HHHHhcCCCceeCCCCCCCCccccccccCCCCCCcCCCcccccccccccccccCcCcccccccccccccceeeccCCchh
Q 023907 159 VHCAEVLGTPIVGDYKYGWQTHRKWKQFHPSDLSKDSNEEIPKEKTLHFGLDLESGSILEKQPRLHLHCKEMTLPNVSQA 238 (275)
Q Consensus 159 ~hla~~lG~PIvGD~~Yg~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~LHa~~l~f~~~~~~ 238 (275)
+|||+ +||||+||.+||.. +++|||++|.|+
T Consensus 170 ~hla~-lG~PIlGD~~Yg~~-------------------------------------------~l~Lha~~l~f~----- 200 (213)
T cd02557 170 VHLQY-LGHPIVNDPIYNNL-------------------------------------------GIYLHALRYEGP----- 200 (213)
T ss_pred HHHHH-CCCCCcCccccCCc-------------------------------------------ChhhhhccCcCc-----
Confidence 99996 99999999999951 379999999984
Q ss_pred hhhhhccCCCCCCCCccEEEEcCCchHH
Q 023907 239 IQKVQLSSGCDVSKLETLKLVAPLPSHM 266 (275)
Q Consensus 239 ~~~~~~~~~~~~~~~~~~~~~aplP~~f 266 (275)
.+.|.||+|.||
T Consensus 201 ----------------~~~~~~~~p~~~ 212 (213)
T cd02557 201 ----------------DWSYETELPDWA 212 (213)
T ss_pred ----------------cEEEEeCCCccc
Confidence 688999999987
No 11
>cd02869 PseudoU_synth_RluCD_like PseudoU_synth_RsuA/RluD: Pseudouridine synthase, RsuA/RluD family. This group is comprised of eukaryotic, bacterial and archeal proteins similar to eight site specific Escherichia coli pseudouridine synthases: RsuA, RluA, RluB, RluC, RluD, RluE, RluF and TruA. Pseudouridine synthases catalyze the isomerization of specific uridines in a n RNA molecule to pseudouridines (5-ribosyluracil, psi) requiring no cofactors. E. coli RluC for example makes psi955, 2504 and 2580 in 23S RNA. Some psi sites such as psi1917 in 23S RNA made by RluD are universally conserved. Other psi sites occur in a more restricted fashion, for example psi2819 in 21S mitochondrial ribosomal RNA made by S. cerevisiae Pus5p is only found in mitochondrial large subunit rRNAs from some other species and in gram negative bacteria. The E. coli counterpart of this psi residue is psi2580 in 23S rRNA. psi2604in 23S RNA made by RluF has only been detected in E.coli.
Probab=100.00 E-value=2.2e-36 Score=255.75 Aligned_cols=156 Identities=38% Similarity=0.595 Sum_probs=121.3
Q ss_pred CCccCCCCC-cCcHHHHHHH-HhhcCCCCCCcccccCCCCCceEEEEEeCHHHHHHHHHHHHhccccccccccccccCCc
Q 023907 1 MPVQGGIGI-RRSIDELAAT-CLTYDYSEPPRLVHRLDRDSSGILVMGRTQTSATVLHSIFREKTFSASKEDNDNEKRIL 78 (275)
Q Consensus 1 l~v~~g~~~-~~sl~~l~~~-~l~~~~~~~~~~vhRLD~~TSGllllAk~~~~a~~l~~~~~~~~~~~~~~~~~~~~~~v 78 (275)
++||++... ..++.+++.. .........+++|||||++|||+||||+|+++++.|.++|+++. +
T Consensus 10 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~RLD~~tsGlll~ak~~~~~~~l~~~~~~~~--------------~ 75 (185)
T cd02869 10 LPVHPGPGHLTGTLVNALLKLLLLLGEEFRPGLVHRLDKDTSGLLLVAKNKKAAAKLSKQFKERK--------------V 75 (185)
T ss_pred CeeecCCCCCCCCHHHHHHHHHhhcCCCCcCceecccCCCCceEEEEEcCHHHHHHHHHHHhcCc--------------e
Confidence 467765443 3444544321 12233456799999999999999999999999999999998866 9
Q ss_pred ceEEEEEEecccCCCccEEeccceeeeccCCceeeEEEecCCCCCCCcceEEEEEEeeecCCcEEEEEEEeCcCchhHHH
Q 023907 79 QRWYWALVVGTPRCSKGVISAPLGKVVVDNGKSDRITVVNNDQIMSAQHAVTRYQVIKPSCHGYTWLKLSPLTGRKHQLR 158 (275)
Q Consensus 79 ~K~Y~alv~G~~~~~~g~i~~~l~~~~~~~~~~~~~~~~~~~~~~~~k~a~t~~~~l~~~~~~~slv~~~~~TGR~HQIR 158 (275)
.|+|+|+|.|.++...+.++.++.... .......... .+++.+.|+|+++... .++++++|+|.|||+||||
T Consensus 76 ~K~Y~a~v~g~~~~~~~~~~~~~~~~~---~~~~~~~~~~----~~~~~~~t~~~~l~~~-~~~s~~~~~l~tGR~HQIR 147 (185)
T cd02869 76 KKTYLALVDGKPPEDEGTIDAPLGRKK---RKKRARVVVS----EDGKPAITHYKVLERF-GNVTLVELQLETGRTHQIR 147 (185)
T ss_pred eEEEEEEEeCCCCCCccEEecccccCC---ccCceEEEEC----CCCeEEEEEEEEEEEc-CCcEEEEEEeCcCCccHHH
Confidence 999999999999988888888775420 0011111111 2368899999999886 6889999999999999999
Q ss_pred HHHHhcCCCceeCCCCCCCCc
Q 023907 159 VHCAEVLGTPIVGDYKYGWQT 179 (275)
Q Consensus 159 ~hla~~lG~PIvGD~~Yg~~~ 179 (275)
+||++ +||||+||.+||...
T Consensus 148 ~hl~~-~G~pIvGD~~Yg~~~ 167 (185)
T cd02869 148 VHLAS-IGHPIVGDPKYGGKA 167 (185)
T ss_pred HHHHH-CCCCEeCccccCCcc
Confidence 99997 999999999999754
No 12
>KOG1919 consensus RNA pseudouridylate synthases [RNA processing and modification]
Probab=99.97 E-value=1.7e-29 Score=232.53 Aligned_cols=155 Identities=34% Similarity=0.500 Sum_probs=121.2
Q ss_pred CCccC-CCCCcCcHHHHHHHHhhcCCCCCCcccccCCCCCceEEEEEeCHHHHHHHHHHHHhccccccccccccccCCcc
Q 023907 1 MPVQG-GIGIRRSIDELAATCLTYDYSEPPRLVHRLDRDSSGILVMGRTQTSATVLHSIFREKTFSASKEDNDNEKRILQ 79 (275)
Q Consensus 1 l~v~~-g~~~~~sl~~l~~~~l~~~~~~~~~~vhRLD~~TSGllllAk~~~~a~~l~~~~~~~~~~~~~~~~~~~~~~v~ 79 (275)
||||+ |.-..+++..++... ...+.+++|||||+.|||+||||+++.++..+++.|++++ +.
T Consensus 124 ipVhp~g~~~~n~i~~~l~~~---~~~~~~~~~hRLDr~tSGllvlAkt~~~~~~~~~~~r~~~--------------~~ 186 (371)
T KOG1919|consen 124 IPVHPTGRYRENTITKILAAL---HKVEGLRPCHRLDRLTSGLLVLAKTKEAADKFHEVLRKRT--------------VK 186 (371)
T ss_pred CceeccCccccccchHHHHHh---ccccccccccccCccccceEEEEechhHhHHHHHHHhccc--------------ce
Confidence 68994 444455555554422 3567799999999999999999999999999999999977 99
Q ss_pred eEE-EEEEecccC-CCccEEeccceeeeccCCceeeEEEecCCC--CCCCcceEEEEEEeeecCCcEEEEEEEeCcCchh
Q 023907 80 RWY-WALVVGTPR-CSKGVISAPLGKVVVDNGKSDRITVVNNDQ--IMSAQHAVTRYQVIKPSCHGYTWLKLSPLTGRKH 155 (275)
Q Consensus 80 K~Y-~alv~G~~~-~~~g~i~~~l~~~~~~~~~~~~~~~~~~~~--~~~~k~a~t~~~~l~~~~~~~slv~~~~~TGR~H 155 (275)
|.| .|-|.|.++ .....+..++..... ..++.+..... ...++.|.|.|+++... ++.++|+|.|+|||||
T Consensus 187 k~Y~v~~v~g~fp~~~~~~i~~~~~~~~~----~~~~~l~~~~~~~~~~~k~a~T~~~~~~~~-~~ss~V~~~PlTGRtH 261 (371)
T KOG1919|consen 187 KEYVVARVEGPFPVVGEVEIKEPIGEEER----PLRMGLNAVGVRDEVAAKDAKTLFKVLSYD-GGSSLVECRPLTGRTH 261 (371)
T ss_pred eEEEEEEEeccCCCCceEEeCCCcccccc----ccceEeeecccccccccccceeEEEEcccC-CceEEEEeeccCCcHH
Confidence 999 688999887 444556666654321 11222222211 13479999999999998 8999999999999999
Q ss_pred HHHHHHHhcCCCceeCCCCCCCC
Q 023907 156 QLRVHCAEVLGTPIVGDYKYGWQ 178 (275)
Q Consensus 156 QIR~hla~~lG~PIvGD~~Yg~~ 178 (275)
|||+||+. +|+||+||.+|+..
T Consensus 262 QIRvHlq~-lG~PI~gD~~Y~~~ 283 (371)
T KOG1919|consen 262 QIRVHLQY-LGHPIAGDPKYGNH 283 (371)
T ss_pred HHHHHHHH-hCCCcCCCcccccc
Confidence 99999996 99999999999763
No 13
>cd02550 PseudoU_synth_Rsu_Rlu_like PseudoU_synth_Rsu_Rlu: Pseudouridine synthase, Rsu/Rlu family. This group is comprised of eukaryotic, bacterial and archeal proteins similar to eight site specific Escherichia coli pseudouridine synthases: RsuA, RluA, RluB, RluC, RluD, RluE, RluF and TruA. Pseudouridine synthases catalyze the isomerization of specific uridines in a n RNA molecule to pseudouridines (5-ribosyluracil, psi) requiring no cofactors. E. coli RluC for example makes psi955, 2504 and 2580 in 23S RNA. Some psi sites such as psi1917 in 23S RNA made by RluD are universally conserved. Other psi sites occur in a more restricted fashion, for example psi2819 in 21S mitochondrial ribosomal RNA made by S. cerevisiae Pus5p is only found in mitochondrial large subunit rRNAs from some other species and in gram negative bacteria. The E. coli counterpart of this psi residue is psi2580 in 23S rRNA. psi2604in 23S RNA made by RluF has only been detected in E.coli.
Probab=99.96 E-value=3.3e-29 Score=206.81 Aligned_cols=137 Identities=24% Similarity=0.316 Sum_probs=103.3
Q ss_pred CCccCCCCC-cCcHHHHHHHHhhcCCCCCCcccccCCCCCceEEEEEeCHHHHHHHHHHHHhccccccccccccccCCcc
Q 023907 1 MPVQGGIGI-RRSIDELAATCLTYDYSEPPRLVHRLDRDSSGILVMGRTQTSATVLHSIFREKTFSASKEDNDNEKRILQ 79 (275)
Q Consensus 1 l~v~~g~~~-~~sl~~l~~~~l~~~~~~~~~~vhRLD~~TSGllllAk~~~~a~~l~~~~~~~~~~~~~~~~~~~~~~v~ 79 (275)
++||++.+. ..++.+.+ .......+++|||||++||||||||+|+++++.|+++ ++. +.
T Consensus 10 ~~~~~~~~~~~~~~~~~l----~~~~~~~~~~vhRLD~~TSGlll~ak~~~~~~~l~~~--~~~--------------v~ 69 (154)
T cd02550 10 LVCHPTDRDRDPTVVVRL----DKLHGPRVHAAGRLDKDTSGLLLLTNDGRLQRRLTEP--RRE--------------IE 69 (154)
T ss_pred CEEecCCCCCCCcHHHhh----hcccCCceeEeccCCCCCeeEEEEEcCHHHHHHHhhh--hcc--------------Cc
Confidence 467766543 23443332 2233467899999999999999999999999999998 433 99
Q ss_pred eEEEEEEecccCCCccEEeccceeeeccCCceeeEEEecCCCCCCCcceEEEEEEeeecCCcEEEEEEEeCcCchhHHHH
Q 023907 80 RWYWALVVGTPRCSKGVISAPLGKVVVDNGKSDRITVVNNDQIMSAQHAVTRYQVIKPSCHGYTWLKLSPLTGRKHQLRV 159 (275)
Q Consensus 80 K~Y~alv~G~~~~~~g~i~~~l~~~~~~~~~~~~~~~~~~~~~~~~k~a~t~~~~l~~~~~~~slv~~~~~TGR~HQIR~ 159 (275)
|+|+|+|.|.+++ ++.+..++.. .+.. .. +.. .+++.+.|.|++++.. .++++++|+|.|||+||||+
T Consensus 70 K~Y~a~v~g~~~~-~~~~~~~~~~----~~~~-~~-~~~----~~~~~~~t~~~~l~~~-~~~sll~~~l~tGR~HQIR~ 137 (154)
T cd02550 70 KEYLVTVRGELDE-EGIEDLATVR----RGRL-SG-LVD----EGVPLAVTKVRVIGEH-GGTGRLRLTLKTGRTHQIRR 137 (154)
T ss_pred EEEEEEEEeecCc-chheeccccc----cCcc-ee-EEc----CCCcccceEEEEEEec-CCcEEEEEEEcCCCcHHHHH
Confidence 9999999999864 4556665543 1111 11 111 2367889999999876 67899999999999999999
Q ss_pred HHHhcCCCcee
Q 023907 160 HCAEVLGTPIV 170 (275)
Q Consensus 160 hla~~lG~PIv 170 (275)
|||+ +||||.
T Consensus 138 hla~-~G~pI~ 147 (154)
T cd02550 138 HCAA-VGFPVL 147 (154)
T ss_pred HHHH-cCCcEE
Confidence 9997 999997
No 14
>PF00849 PseudoU_synth_2: RNA pseudouridylate synthase This Prosite family is a subset of the Pfam family. This Prosite family is a subset of the Pfam family.; InterPro: IPR006145 Pseudouridine synthases catalyse the isomerisation of uridine to pseudouridine (Psi) in a variety of RNA molecules, and may function as RNA chaperones. Pseudouridine is the most abundant modified nucleotide found in all cellular RNAs. There are four distinct families of pseudouridine synthases that share no global sequence similarity, but which do share the same fold of their catalytic domain(s) and uracil-binding site and are descended from a common molecular ancestor. The catalytic domain consists of two subdomains, each of which has an alpha+beta structure that has some similarity to the ferredoxin-like fold (note: some pseudouridine synthases contain additional domains). The active site is the most conserved structural region of the superfamily and is located between the two homologous domains. These families are []: Pseudouridine synthase I, TruA. Pseudouridine synthase II, TruB, which contains and additional C-terminal PUA domain. Pseudouridine synthase RsuA (ribosomal small subunit) and RluC/RluD (ribosomal large subunits), both of which contain an additional N-terminal alpha-L RNA-binding motif. Pseudouridine synthase TruD, which has a natural circular permutation in the catalytic domain, as well as an insertion of a family-specific alpha+beta subdomain. This entry represents several different pseudouridine synthases from family 3, including: RsuA (acts on small ribosomal subunit), RluA, RluB, RluC, RluD, RluE and RluF (act on large ribosomal subunit). RsuA from Escherichia coli catalyses formation of pseudouridine at position 516 in 16S rRNA during assembly of the 30S ribosomal subunit [, ]. RsuA consists of an N-terminal domain connected by an extended linker to the central and C-terminal domains. Uracil and UMP bind in a cleft between the central and C-terminal domains near the catalytic residue Asp 102. The N-terminal domain shows structural similarity to the ribosomal protein S4. Despite only 15% amino acid identity, the other two domains are structurally similar to those of the tRNA-specific psi-synthase TruA, including the position of the catalytic Asp. Our results suggest that all four families of pseudouridine synthases share the same fold of their catalytic domain(s) and uracil-binding site. RluB, RluC, RluD, RluE and RluF are homologous enzymes which each convert specific uridine bases in E. coli ribosomal 23S RNA to pseudouridine: RluB modifies uracil-2605. RluC modifies uracil-955, U-2504, and U-2580. RluD modifies uracil-1911, U-1915, and U-1917. RluE modifies uracil-3457. RluF modifies uracil-2604, and to a lesser extent U-2605. RluD also possesses a second function related to proper assembly of the 50S ribosomal subunit that is independent of Psi-synthesis [, ]. Both RluC and RluD have an N-terminal S4 RNA binding domain. Despite the conserved topology shared by RluC and RluD, the surface shape and charge distribution are very different. ; GO: 0003723 RNA binding, 0009982 pseudouridine synthase activity, 0001522 pseudouridine synthesis, 0009451 RNA modification; PDB: 2GML_A 3DH3_B 1VIO_A 2I82_B 1XPI_B 1V9K_B 1PRZ_A 1V9F_A 2IST_A 1QYU_A ....
Probab=99.95 E-value=4e-27 Score=195.41 Aligned_cols=144 Identities=35% Similarity=0.517 Sum_probs=103.7
Q ss_pred CCccCCCC-CcCcHHHHHHH-HhhcCCCCCCcccccCCCCCceEEEEEeCHHHHHHHHHHHHhccccccccccccccCCc
Q 023907 1 MPVQGGIG-IRRSIDELAAT-CLTYDYSEPPRLVHRLDRDSSGILVMGRTQTSATVLHSIFREKTFSASKEDNDNEKRIL 78 (275)
Q Consensus 1 l~v~~g~~-~~~sl~~l~~~-~l~~~~~~~~~~vhRLD~~TSGllllAk~~~~a~~l~~~~~~~~~~~~~~~~~~~~~~v 78 (275)
|++|+..+ ........... .........+++|||||++||||||||+|+++++.|+++|..+. +
T Consensus 11 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~RLD~~TsGlll~a~~~~~~~~l~~~f~~~~--------------~ 76 (164)
T PF00849_consen 11 VPVHPSDGNESKSVKELPALSLKRGDDPPELYPVHRLDRDTSGLLLFAKDKEAAAKLSKQFPKRK--------------V 76 (164)
T ss_dssp SBSSSSSTBSSSSHHCHHHHHHHHCTTSGGGEESS---TT-EEEEEEESSHHHHHHHHHHHHTTC--------------S
T ss_pred CeEecCCCCCcccccchhhhhhhhccCCCceEECCCCCccccCCeeccCCcccccccccccccCC--------------C
Confidence 46666552 22233333332 33445677899999999999999999999999999999999866 9
Q ss_pred ceEEEEEEecccCCCccEEeccceeeeccCCceeeEEEecCCCCCCCcceEEEEEEeeec--------CCcEEEEEEEeC
Q 023907 79 QRWYWALVVGTPRCSKGVISAPLGKVVVDNGKSDRITVVNNDQIMSAQHAVTRYQVIKPS--------CHGYTWLKLSPL 150 (275)
Q Consensus 79 ~K~Y~alv~G~~~~~~g~i~~~l~~~~~~~~~~~~~~~~~~~~~~~~k~a~t~~~~l~~~--------~~~~slv~~~~~ 150 (275)
+|+|+|+|.|.+....+.++.++............. .. ...++.+.|.|+++... ..+.++++|+|.
T Consensus 77 ~K~Y~a~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~----~~~~~~~~t~~~~l~~~~~~~~~~~~~~~s~v~~~l~ 151 (164)
T PF00849_consen 77 EKTYLALVEGGPVEEEGKINSPLGKDVGKNKSSNKD-PP----GRDGKPAITRYRVLRSGSRTPSKDENAGCSLVECELI 151 (164)
T ss_dssp EEEEEEEECSSSSTTCEEEESHEEE-EECSSCTCCE-EE----TTTSBTSEEEEEEEEEETT---EECCSSEEEEEEEES
T ss_pred cEEEEEeEcccccccceeeeccccccccccccceee-ee----cccccccceeeeeeccccccccccccCCCEEEEEEEC
Confidence 999999999877788899999987632112111111 11 12478899999999875 357899999999
Q ss_pred cCchhHHHHHHHh
Q 023907 151 TGRKHQLRVHCAE 163 (275)
Q Consensus 151 TGR~HQIR~hla~ 163 (275)
|||+||||+|||+
T Consensus 152 tGr~HQIR~hla~ 164 (164)
T PF00849_consen 152 TGRTHQIRVHLAH 164 (164)
T ss_dssp S-STTHHHHHHHH
T ss_pred cCCCHHHHHHhcC
Confidence 9999999999984
No 15
>cd02553 PseudoU_synth_RsuA PseudoU_synth_RsuA: Pseudouridine synthase, Escherichia coli RsuA like. This group is comprised of eukaryotic and bacterial proteins similar to Escherichia coli RsuA. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. E.coli RsuA makes psi516 in 16S RNA. Psi at this position is not generally conserved in other organisms.
Probab=99.94 E-value=1.2e-27 Score=200.16 Aligned_cols=136 Identities=18% Similarity=0.181 Sum_probs=96.6
Q ss_pred CCccCCCCCcCcHHHHHHHHhhcCCCCCCcccccCCCCCceEEEEEeCHHHHHHHHHHHHhccccccccccccccCCcce
Q 023907 1 MPVQGGIGIRRSIDELAATCLTYDYSEPPRLVHRLDRDSSGILVMGRTQTSATVLHSIFREKTFSASKEDNDNEKRILQR 80 (275)
Q Consensus 1 l~v~~g~~~~~sl~~l~~~~l~~~~~~~~~~vhRLD~~TSGllllAk~~~~a~~l~~~~~~~~~~~~~~~~~~~~~~v~K 80 (275)
|+||++.....++.+++..++ ....+++|||||++||||||||+|..+++.+... .+ .++|
T Consensus 11 ~~~~~~~~~~~tl~~~l~~~~---~~~~~~~vhRLD~~TSGlll~ak~~~~~~~l~~~--~~--------------~i~K 71 (167)
T cd02553 11 VVCATKDPHHPTVIDLLPEPD---RRRDLFPVGRLDKDTTGLLLLTNDGQLAHRLTSP--KK--------------HVPK 71 (167)
T ss_pred CEeCCCCCCCCcHHHHhhhhc---ccCCeEEcccCCCCCEEEEEEEeCHHHHHHhhCC--cC--------------CCce
Confidence 467766665667766665433 2346899999999999999999999988877653 32 3999
Q ss_pred EEEEEEecccCCCccEEeccceeeeccCCceeeEEEecCCCCCCCcceEEEEEEeeecCCcEEEEEEEeCcCchhHHHHH
Q 023907 81 WYWALVVGTPRCSKGVISAPLGKVVVDNGKSDRITVVNNDQIMSAQHAVTRYQVIKPSCHGYTWLKLSPLTGRKHQLRVH 160 (275)
Q Consensus 81 ~Y~alv~G~~~~~~g~i~~~l~~~~~~~~~~~~~~~~~~~~~~~~k~a~t~~~~l~~~~~~~slv~~~~~TGR~HQIR~h 160 (275)
+|+|+|.|.++.... .... .+ +.. .+. .+...+.+++++ .++++|+|.|||+||||+|
T Consensus 72 ~Y~a~V~G~~~~~~~--~~~~------~~----~~~-~~~----~~~~~~~~~~~~-----~sll~v~l~tGR~HQIR~h 129 (167)
T cd02553 72 TYEVTLAGPLTEDDI--EAFA------EG----VLL-HDG----YPTKPAKLEILS-----PTTVRLTITEGKYHQVKRM 129 (167)
T ss_pred EEEEEEccCCCHHHH--HHHH------CC----eEE-cCC----CEeeeeEEEEeC-----CcEEEEEEEeCCCHHHHHH
Confidence 999999998865432 1111 11 111 110 122334555553 2899999999999999999
Q ss_pred HHhcCCCceeCCCCCCCC
Q 023907 161 CAEVLGTPIVGDYKYGWQ 178 (275)
Q Consensus 161 la~~lG~PIvGD~~Yg~~ 178 (275)
||+ +||||++|..++-.
T Consensus 130 la~-lG~pI~~~~R~~~g 146 (167)
T cd02553 130 FAA-VGNKVVALHRIRIG 146 (167)
T ss_pred HHH-cCCeEEEEEEEEEC
Confidence 997 99999999887643
No 16
>cd02556 PseudoU_synth_RluB PseudoU_synth_RluB: Pseudouridine synthase, Escherichia coli RluB like. This group is comprised of bacterial and eukaryotic proteins similar to E. coli RluB. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. E.coli RluB makes psi2605 in 23S RNA. psi2605 has been detected in eubacteria but, not in eukarya and archea despite the presence of a precursor U at that site.
Probab=99.94 E-value=1.1e-26 Score=194.36 Aligned_cols=131 Identities=17% Similarity=0.205 Sum_probs=96.2
Q ss_pred CCccCCC-CCcCcHHHHHHHHhhcCCCCCCcccccCCCCCceEEEEEeCHHHHHHHHHHHHhccccccccccccccCCcc
Q 023907 1 MPVQGGI-GIRRSIDELAATCLTYDYSEPPRLVHRLDRDSSGILVMGRTQTSATVLHSIFREKTFSASKEDNDNEKRILQ 79 (275)
Q Consensus 1 l~v~~g~-~~~~sl~~l~~~~l~~~~~~~~~~vhRLD~~TSGllllAk~~~~a~~l~~~~~~~~~~~~~~~~~~~~~~v~ 79 (275)
+++|+.. ....++.+++..+ ....+++|||||++||||||||+|+++++.|.. .++. +.
T Consensus 11 ~~~~~~~~~~~~tl~~~l~~~----~~~~~~~V~RLD~~TsGLll~ak~~~~~~~L~~--~~~~--------------i~ 70 (167)
T cd02556 11 LICTRKDPKGRPTVFDLLPKL----GIPRWISVGRLDLNTEGLLLFTNDGELANRLMH--PSNE--------------IE 70 (167)
T ss_pred cEECccCCCCCccHHHhhhhh----ccCceEEcCcCCCCCeeEEEEECCHHHHHHHhC--CcCC--------------CC
Confidence 3566532 2345555554422 235678999999999999999999999999975 3433 99
Q ss_pred eEEEEEEecccCCCccEEeccceeeeccCCceeeEEEecCCCCCCCcceEEEEEEeeecCCcEEEEEEEeCcCchhHHHH
Q 023907 80 RWYWALVVGTPRCSKGVISAPLGKVVVDNGKSDRITVVNNDQIMSAQHAVTRYQVIKPSCHGYTWLKLSPLTGRKHQLRV 159 (275)
Q Consensus 80 K~Y~alv~G~~~~~~g~i~~~l~~~~~~~~~~~~~~~~~~~~~~~~k~a~t~~~~l~~~~~~~slv~~~~~TGR~HQIR~ 159 (275)
|+|+|+|.|.++... +.. + ..| +.. .+++.+.|.|+++... .++++++|+|.|||+||||+
T Consensus 71 K~Y~a~V~g~~~~~~--~~~-~-----~~g----v~~------~~~~~~~~~~~~~~~~-~~~sll~v~l~tGR~HQIR~ 131 (167)
T cd02556 71 REYAVRVFGQVTDEQ--LKS-L-----KKG----VEL------EDGFAGFKSIQLEGGE-GKNSWYRVTLREGRNREVRR 131 (167)
T ss_pred eEEEEEECccCCHHH--HHH-H-----HcC----CEE------CCCcCcceEEEEEecC-CCcEEEEEEEEeCCCHHHHH
Confidence 999999999886543 110 0 111 111 1256788999999765 56799999999999999999
Q ss_pred HHHhcCCCceeC
Q 023907 160 HCAEVLGTPIVG 171 (275)
Q Consensus 160 hla~~lG~PIvG 171 (275)
||++ +||||+-
T Consensus 132 ~~a~-~G~pV~~ 142 (167)
T cd02556 132 LWEA-FGLQVSR 142 (167)
T ss_pred HHHH-cCCeEeE
Confidence 9997 9999985
No 17
>TIGR00093 pseudouridine synthase. This model identifies panels of pseudouridine synthase enzymes that RNA modifications involved in maturing the protein translation apparatus. Counts per genome vary: two in Staphylococcus aureus, three in Pseudomonas putida, four in E. coli, etc.
Probab=99.94 E-value=5.4e-27 Score=187.90 Aligned_cols=111 Identities=23% Similarity=0.356 Sum_probs=86.9
Q ss_pred cccCCCCCceEEEEEeCHHHHHHHHHHHHhccccccccccccccCCcceEEEEEEecccCCCccEEeccceeeeccCCce
Q 023907 32 VHRLDRDSSGILVMGRTQTSATVLHSIFREKTFSASKEDNDNEKRILQRWYWALVVGTPRCSKGVISAPLGKVVVDNGKS 111 (275)
Q Consensus 32 vhRLD~~TSGllllAk~~~~a~~l~~~~~~~~~~~~~~~~~~~~~~v~K~Y~alv~G~~~~~~g~i~~~l~~~~~~~~~~ 111 (275)
|||||++||||||||+|+++++.|.+ .++ .+.|+|+|+|.|.++... ++ ++. .+
T Consensus 1 v~RLD~~TSGlll~akd~~~~~~L~~--~~~--------------~i~K~Y~a~v~g~~~~~~--~~-~~~-----~g-- 54 (128)
T TIGR00093 1 AGRLDRDSEGLLLLTNDGELVHRLTH--PGH--------------HCEKTYLVTVEGPVTDED--LE-ALR-----KG-- 54 (128)
T ss_pred CCCCCCCCEEEEEEEeCHHHHHHHhC--CCC--------------CCCeEEEEEECCCCCHHH--HH-HHh-----CC--
Confidence 79999999999999999999999987 233 399999999999886532 11 111 11
Q ss_pred eeEEEecCCCCCCCcceEEEEEEeeecCCcEEEEEEEeCcCchhHHHHHHHhcCCCceeCCCCCCCC
Q 023907 112 DRITVVNNDQIMSAQHAVTRYQVIKPSCHGYTWLKLSPLTGRKHQLRVHCAEVLGTPIVGDYKYGWQ 178 (275)
Q Consensus 112 ~~~~~~~~~~~~~~k~a~t~~~~l~~~~~~~slv~~~~~TGR~HQIR~hla~~lG~PIvGD~~Yg~~ 178 (275)
+.. . +++.+.+.|+++... .+.++++|+|.|||+||||+||++ +||||+||..+.-.
T Consensus 55 --~~~-~-----~~~~~~~~~~~l~~~-~~~~~l~~~l~tGR~HQIR~~~~~-lG~pI~g~~R~~~g 111 (128)
T TIGR00093 55 --VQL-E-----DGPTKPAKLEVITEP-GFPTWLRITLSEGRNRQVRRMFAA-VGFPVLRLHRVRIG 111 (128)
T ss_pred --eEE-C-----CcEEeeeEEEEEccC-CCceEEEEEEeCCCCHHHHHHHHH-cCCeEeEEEEEEEC
Confidence 111 1 135567888988765 557899999999999999999997 99999999988543
No 18
>cd02870 PseudoU_synth_RsuA_like Pseudouridine synthases are responsible for the synthesis of pseudouridine from uracil in ribosomal RNA. The RsuA subfamily includes Pseudouridine Synthase similar to Ribosomal small subunit pseudouridine 516 synthase. Most of the proteins in this family are bacterial proteins.
Probab=99.93 E-value=3.7e-27 Score=192.95 Aligned_cols=110 Identities=23% Similarity=0.312 Sum_probs=87.3
Q ss_pred CCCCcccccCCCCCceEEEEEeCHHHHHHHHHHHHhccccccccccccccCCcceEEEEEEecccCCCccEEeccceeee
Q 023907 26 SEPPRLVHRLDRDSSGILVMGRTQTSATVLHSIFREKTFSASKEDNDNEKRILQRWYWALVVGTPRCSKGVISAPLGKVV 105 (275)
Q Consensus 26 ~~~~~~vhRLD~~TSGllllAk~~~~a~~l~~~~~~~~~~~~~~~~~~~~~~v~K~Y~alv~G~~~~~~g~i~~~l~~~~ 105 (275)
...+++|||||++|||+||||+|+++++.|... ++. +.|+|+|+|.|.+..... ...
T Consensus 31 ~~~~~~vhRLD~~TsGlll~ak~~~~~~~l~~~--~~~--------------i~K~Y~a~v~g~~~~~~~--~~~----- 87 (146)
T cd02870 31 GERLFPVGRLDYDTEGLLLLTNDGELANRLTHP--RYG--------------VEKTYLVKVRGVPSEEEL--RRL----- 87 (146)
T ss_pred CCCEEECCCCCCCCeeEEEEeCCHHHHHHhhCc--cCC--------------CCeEEEEEECCCCCHHHH--HHH-----
Confidence 456899999999999999999999999998763 323 999999999998864331 110
Q ss_pred ccCCceeeEEEecCCCCCCCcceEEEEEEeeecCCcEEEEEEEeCcCchhHHHHHHHhcCCCceeC
Q 023907 106 VDNGKSDRITVVNNDQIMSAQHAVTRYQVIKPSCHGYTWLKLSPLTGRKHQLRVHCAEVLGTPIVG 171 (275)
Q Consensus 106 ~~~~~~~~~~~~~~~~~~~~k~a~t~~~~l~~~~~~~slv~~~~~TGR~HQIR~hla~~lG~PIvG 171 (275)
..+ +. . .+++.+.|+|++++.. .++++++|+|.|||+||||+||++ +|+||+.
T Consensus 88 -~~~----~~-~-----~~~~~~~t~~~~l~~~-~~~sll~~~l~tGR~HQIR~hla~-~G~pI~~ 140 (146)
T cd02870 88 -RAG----VE-L-----DDGKTAPAKVKVLSRD-PKNTLLEVTLHEGRNRQVRRMFEA-VGHPVLR 140 (146)
T ss_pred -HCC----eE-e-----CCceEcceEEEEeccC-CCCcEEEEEEEeCCcHHHHHHHHH-cCCcCCe
Confidence 011 11 1 1257789999999876 578999999999999999999997 9999973
No 19
>PRK10839 16S rRNA pseudouridylate synthase A; Provisional
Probab=99.92 E-value=7.5e-26 Score=198.78 Aligned_cols=133 Identities=16% Similarity=0.140 Sum_probs=93.4
Q ss_pred CCccCCCCCcCcHHHHHHHHhhcCCCCCCcccccCCCCCceEEEEEeCHHHHHHHHHHHHhccccccccccccccCCcce
Q 023907 1 MPVQGGIGIRRSIDELAATCLTYDYSEPPRLVHRLDRDSSGILVMGRTQTSATVLHSIFREKTFSASKEDNDNEKRILQR 80 (275)
Q Consensus 1 l~v~~g~~~~~sl~~l~~~~l~~~~~~~~~~vhRLD~~TSGllllAk~~~~a~~l~~~~~~~~~~~~~~~~~~~~~~v~K 80 (275)
|+||+......++.+++ .......+++|||||++||||||||+|+.++..|.. ..+ .+.|
T Consensus 71 ~~~~~~~~~~~tl~~~l----~~~~~~~~~~v~RLD~~TSGlll~ak~~~~~~~l~~--~~~--------------~i~K 130 (232)
T PRK10839 71 YVCSTDDPDHPTVLYFL----DEPVAYKLHAAGRLDIDTTGLVLMTDDGQWSHRITS--PRH--------------HCEK 130 (232)
T ss_pred eEecccCCCCCeEEEec----ccccccCceecCCCCCCceeEEEEecCHHHHHHHhC--CCC--------------CCCe
Confidence 45676543333433332 222234688999999999999999999999888875 333 3999
Q ss_pred EEEEEEecccCCCccEEeccceeeeccCCceeeEEEecCCCCCCCcceEEEEEEeeecCCcEEEEEEEeCcCchhHHHHH
Q 023907 81 WYWALVVGTPRCSKGVISAPLGKVVVDNGKSDRITVVNNDQIMSAQHAVTRYQVIKPSCHGYTWLKLSPLTGRKHQLRVH 160 (275)
Q Consensus 81 ~Y~alv~G~~~~~~g~i~~~l~~~~~~~~~~~~~~~~~~~~~~~~k~a~t~~~~l~~~~~~~slv~~~~~TGR~HQIR~h 160 (275)
+|+|.+.+.+..... .. + ..+ +.. .++.|.|.|.+++.. + .++++|+|.||||||||+|
T Consensus 131 ~Y~a~i~~~i~~~~~--~~-~-----~~~------~~~-----~g~~a~t~~~~~~~~-~-~sll~~~l~tGRtHQIR~h 189 (232)
T PRK10839 131 TYLVTLESPVADDTA--EQ-F-----AKG------VQL-----HNEKDLTKPAVLEVI-T-PTQVRLTISEGRYHQVKRM 189 (232)
T ss_pred EEEEEECCCCCHHHH--HH-H-----HCC------eEE-----CCCcccccccEEEEe-c-CCEEEEEEEcCcCHHHHHH
Confidence 999987776543210 00 0 011 111 256788999999875 3 3899999999999999999
Q ss_pred HHhcCCCceeCCCCC
Q 023907 161 CAEVLGTPIVGDYKY 175 (275)
Q Consensus 161 la~~lG~PIvGD~~Y 175 (275)
|++ +||||+|=...
T Consensus 190 ~~~-~G~pi~gl~R~ 203 (232)
T PRK10839 190 FAA-VGNHVVELHRE 203 (232)
T ss_pred HHH-cCCeEeeEEEE
Confidence 997 99999986543
No 20
>cd02566 PseudoU_synth_RluE PseudoU_synth_RluE: Pseudouridine synthase, Escherichia coli RluE. This group is comprised of bacterial proteins similar to E. coli RluE. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. Escherichia coli RluE makes psi2457 in 23S RNA. psi2457 is not universally conserved.
Probab=99.91 E-value=1.2e-24 Score=182.15 Aligned_cols=145 Identities=17% Similarity=0.193 Sum_probs=92.3
Q ss_pred CCccCCCC--CcCcHHHHHHHHhhcCCCCCCcccccCCCCCceEEEEEeCHHHHHHHHHHHHhccccccccccccccCCc
Q 023907 1 MPVQGGIG--IRRSIDELAATCLTYDYSEPPRLVHRLDRDSSGILVMGRTQTSATVLHSIFREKTFSASKEDNDNEKRIL 78 (275)
Q Consensus 1 l~v~~g~~--~~~sl~~l~~~~l~~~~~~~~~~vhRLD~~TSGllllAk~~~~a~~l~~~~~~~~~~~~~~~~~~~~~~v 78 (275)
+++|++.. ...++.+.+. ...+++|||||++||||||||+|+.+++.|.+... .+
T Consensus 10 ~~~~~~~~~~~~~~l~~~l~-------~~~~~~v~RLD~~TsGlll~a~d~~~~~~l~~~~~----------------~v 66 (168)
T cd02566 10 VLSQFTDESEKHKTLKDYID-------DPGVYAAGRLDRDSEGLLLLTDDGRLQHRITDPSF----------------KH 66 (168)
T ss_pred CEEecCCCcCCCccHHHHcC-------cCCeEEccCCCCCCeEEEEEEeCHHHHHHHHCCCC----------------CC
Confidence 45675432 3345544432 14678999999999999999999998888766522 29
Q ss_pred ceEEEEEEecccCCCccE-EeccceeeeccCCceeeEEEecCCCCCCCcceEEEEEEeeec-CCcEEEEEEEeCcCchhH
Q 023907 79 QRWYWALVVGTPRCSKGV-ISAPLGKVVVDNGKSDRITVVNNDQIMSAQHAVTRYQVIKPS-CHGYTWLKLSPLTGRKHQ 156 (275)
Q Consensus 79 ~K~Y~alv~G~~~~~~g~-i~~~l~~~~~~~~~~~~~~~~~~~~~~~~k~a~t~~~~l~~~-~~~~slv~~~~~TGR~HQ 156 (275)
+|+|+|+|.|.++..... +...+. .+++......+.... ......|.|.++... ....++++|+|.|||+||
T Consensus 67 ~K~Y~a~v~g~~~~~~~~~l~~g~~---~~~~~~~~~~v~~~~---~~~~~~~~~~~~~~~~~~~~sll~v~l~tGR~HQ 140 (168)
T cd02566 67 PKTYYVQVEGVPTEDALEQLRNGVE---LGDGLTLPAKVEKVD---EPPWLWEREPPIRFRKNIPTSWIEITICEGKNRQ 140 (168)
T ss_pred CEEEEEEECCcCCHHHHHHHhCCcE---ECCeEecceEEEEec---ccccccccccccccccCCCccEEEEEEecCccHH
Confidence 999999999998643210 000010 011111111111110 112344555556532 135689999999999999
Q ss_pred HHHHHHhcCCCceeCCCCC
Q 023907 157 LRVHCAEVLGTPIVGDYKY 175 (275)
Q Consensus 157 IR~hla~~lG~PIvGD~~Y 175 (275)
||+||++ +||||+.....
T Consensus 141 IR~~la~-lG~pV~~L~R~ 158 (168)
T cd02566 141 VRRMTAA-VGFPTLRLIRV 158 (168)
T ss_pred HHHHHHH-cCCeEeEEEEE
Confidence 9999997 99999976654
No 21
>cd02555 PSSA_1 PSSA_1: Pseudouridine synthase, a subgroup of the RsuA family. This group is comprised of bacterial proteins assigned to the RsuA family of pseudouridine synthases. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. The TruA family is comprised of proteins related to Escherichia coli RsuA.
Probab=99.89 E-value=1.4e-23 Score=176.96 Aligned_cols=108 Identities=19% Similarity=0.258 Sum_probs=81.5
Q ss_pred CCCcccccCCCCCceEEEEEeCHHHHHHHHHHHHhccccccccccccccCCcceEEEEEEecccCCCccE--Eeccceee
Q 023907 27 EPPRLVHRLDRDSSGILVMGRTQTSATVLHSIFREKTFSASKEDNDNEKRILQRWYWALVVGTPRCSKGV--ISAPLGKV 104 (275)
Q Consensus 27 ~~~~~vhRLD~~TSGllllAk~~~~a~~l~~~~~~~~~~~~~~~~~~~~~~v~K~Y~alv~G~~~~~~g~--i~~~l~~~ 104 (275)
.++++|||||++||||||||+|+.+++.|.+++.. +.|+|+|+|.|.+++. +. +...+.
T Consensus 45 ~~l~~VgRLD~dTsGLLl~t~d~~~~~~L~~~~~~----------------i~K~Y~v~v~g~~~~~-~l~~l~~g~~-- 105 (177)
T cd02555 45 ARLAPIGPLDKDASGLLVFSQDGRVLRKLIGDASR----------------LEQEYLVEVRGELTAG-GLERLNHGLT-- 105 (177)
T ss_pred CceeEecCCCCCCeeEEEEECCHHHHHHHhChhcC----------------CCEEEEEEEcccCCHH-HHHHHhcCcc--
Confidence 46889999999999999999999999999987543 9999999999988653 21 111110
Q ss_pred eccCCceeeEEEecCCCCCCCcceEEEEEEeeecCCcEEEEEEEeCcCchhHHHHHHHhcCCCceeCCCCCC
Q 023907 105 VVDNGKSDRITVVNNDQIMSAQHAVTRYQVIKPSCHGYTWLKLSPLTGRKHQLRVHCAEVLGTPIVGDYKYG 176 (275)
Q Consensus 105 ~~~~~~~~~~~~~~~~~~~~~k~a~t~~~~l~~~~~~~slv~~~~~TGR~HQIR~hla~~lG~PIvGD~~Yg 176 (275)
+ .+. ..+.+.+.+ .+.++++++|.|||+||||+||++ +||||+|+....
T Consensus 106 -----------~-~~~---~~~~~~~~~-------~~~~~l~i~l~tGr~hQIR~~~~~-~G~pV~~L~R~~ 154 (177)
T cd02555 106 -----------Y-DGR---ELPPAKVSW-------QNEQRLRFALKEPQPGQIRRMCES-VGLEVVALRRIR 154 (177)
T ss_pred -----------c-CCe---ecceEEEEE-------cCCCEEEEEEECCcChHHHHHHHH-cCCeEEEEEEEE
Confidence 0 000 012233322 134799999999999999999997 999999998874
No 22
>PRK11394 23S rRNA pseudouridine synthase E; Provisional
Probab=99.88 E-value=3.4e-23 Score=179.00 Aligned_cols=126 Identities=25% Similarity=0.382 Sum_probs=83.8
Q ss_pred CCCcccccCCCCCceEEEEEeCHHHHHHHHHHHHhccccccccccccccCCcceEEEEEEecccCCCccEEecccee-ee
Q 023907 27 EPPRLVHRLDRDSSGILVMGRTQTSATVLHSIFREKTFSASKEDNDNEKRILQRWYWALVVGTPRCSKGVISAPLGK-VV 105 (275)
Q Consensus 27 ~~~~~vhRLD~~TSGllllAk~~~~a~~l~~~~~~~~~~~~~~~~~~~~~~v~K~Y~alv~G~~~~~~g~i~~~l~~-~~ 105 (275)
.++++|||||++||||||||+|+.+++.|.++ ++. +.|+|+|+|.|.+....... +.. ..
T Consensus 70 ~~~~~vgRLD~~TsGllLlt~d~~~~~~L~~~--~~~--------------i~K~Y~~~v~g~~~~~~l~~---l~~Gv~ 130 (217)
T PRK11394 70 QGVYAAGRLDRDSEGLLVLTNNGALQARLTQP--GKR--------------TGKIYYVQVEGIPTQDALEA---LRNGVT 130 (217)
T ss_pred CCeEEecCCCCCCeeEEEEECCHHHHHHHhCc--ccC--------------CCEEEEEEECCCCCHHHHHH---HhCCeE
Confidence 46899999999999999999999999999986 322 99999999999986543211 100 00
Q ss_pred ccCCce--eeEEEecCC-CCCCCcceEEEEEEeee-cCCcEEEEEEEeCcCchhHHHHHHHhcCCCceeCCCCCCCC
Q 023907 106 VDNGKS--DRITVVNND-QIMSAQHAVTRYQVIKP-SCHGYTWLKLSPLTGRKHQLRVHCAEVLGTPIVGDYKYGWQ 178 (275)
Q Consensus 106 ~~~~~~--~~~~~~~~~-~~~~~k~a~t~~~~l~~-~~~~~slv~~~~~TGR~HQIR~hla~~lG~PIvGD~~Yg~~ 178 (275)
..++.. ..+...... ... ..+..+.. ...+.++++|+|.|||+||||+||++ +||||+||.+|+-.
T Consensus 131 i~~~~~~p~~~~~i~~~~~~~------~~~~~~~~~~~~~~s~l~I~L~eGR~hQIRrm~a~-lG~pVl~L~Ry~iG 200 (217)
T PRK11394 131 LNDGPTLPAGAELVDEPAWLW------PRNPPIRERKSIPTSWLKITLYEGRNRQVRRMTAH-VGFPTLRLIRYAMG 200 (217)
T ss_pred ECCccccccEEEEeccccccc------ccccccccccCCCceEEEEEEeCCCCHHHHHHHHH-cCCeEeeeEEEEEC
Confidence 011110 000000000 000 00111111 11357899999999999999999997 99999999999754
No 23
>cd02554 PseudoU_synth_RluF PseudoU_synth_RluF_like: Pseudouridine synthase, Escherichia coli RluF like. This group is comprised of bacterial proteins similar to Escherichia coli RluF. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. E.coli RluF makes psi2604 in 23S RNA. psi2604 has only been detected in E. coli. It is absent from other eubacteria despite a precursor U at that site and from eukarya and archea which lack a precursor U at that site.
Probab=99.80 E-value=2.1e-19 Score=149.59 Aligned_cols=106 Identities=17% Similarity=0.180 Sum_probs=77.2
Q ss_pred CCCcccccCCCCCceEEEEEeCHHHHHHHHHHHHhccccccccccccccCCcceEEEEEEecccCCCccEEeccceeeec
Q 023907 27 EPPRLVHRLDRDSSGILVMGRTQTSATVLHSIFREKTFSASKEDNDNEKRILQRWYWALVVGTPRCSKGVISAPLGKVVV 106 (275)
Q Consensus 27 ~~~~~vhRLD~~TSGllllAk~~~~a~~l~~~~~~~~~~~~~~~~~~~~~~v~K~Y~alv~G~~~~~~g~i~~~l~~~~~ 106 (275)
.++++|||||++|||+||||+|..+++.|+.+... +.|+|+|.|.|.+.+... .. .
T Consensus 31 ~~~~~vgRLD~~tsGlll~t~dg~~~~~L~~p~~~----------------~~K~Y~V~v~~~l~~~~l--~~------l 86 (164)
T cd02554 31 PRIFPIGRLDKDSEGLILLTNDGDLVNKILHADNN----------------HEKEYLVTVNKPITDEFI--EG------M 86 (164)
T ss_pred CCEEEccCCCCCCeeEEEEEcCHHHHHHHhhhhcC----------------CCeEEEEEECCCCCHHHH--HH------H
Confidence 57999999999999999999999999999887776 899999999998865311 00 0
Q ss_pred cCCceeeEEEecCCCCCCCcceEEEEEEeeecCCcEEEEEEEeCcCchhHHHHHHHhcCCCceeCC
Q 023907 107 DNGKSDRITVVNNDQIMSAQHAVTRYQVIKPSCHGYTWLKLSPLTGRKHQLRVHCAEVLGTPIVGD 172 (275)
Q Consensus 107 ~~~~~~~~~~~~~~~~~~~k~a~t~~~~l~~~~~~~slv~~~~~TGR~HQIR~hla~~lG~PIvGD 172 (275)
..|. .. . .+.|....+... +. +.++|.+.+||+||||+||++ +|+||+-=
T Consensus 87 ~~G~----~~-~--------~~~~~~~~v~~~-~~-~~l~i~l~eGr~~qIRrm~~~-~G~~V~~L 136 (164)
T cd02554 87 SNGV----VI-L--------GTVTKPCKVERL-AK-DKFRIVLTQGLNRQIRRMCEA-LGYRVTDL 136 (164)
T ss_pred hCCC----EE-C--------CeEEcceEEEEC-CC-CEEEEEEECCcCHHHHHHHHH-cCCEEEEE
Confidence 1111 11 1 112222222222 12 359999999999999999997 99999853
No 24
>PRK10700 23S rRNA pseudouridylate synthase B; Provisional
Probab=99.80 E-value=1.4e-19 Score=163.70 Aligned_cols=121 Identities=17% Similarity=0.216 Sum_probs=82.2
Q ss_pred CcHHHHHHHHhhcCCCCCCcccccCCCCCceEEEEEeCHHHHHHHHHHHHhccccccccccccccCCcceEEEEEEeccc
Q 023907 11 RSIDELAATCLTYDYSEPPRLVHRLDRDSSGILVMGRTQTSATVLHSIFREKTFSASKEDNDNEKRILQRWYWALVVGTP 90 (275)
Q Consensus 11 ~sl~~l~~~~l~~~~~~~~~~vhRLD~~TSGllllAk~~~~a~~l~~~~~~~~~~~~~~~~~~~~~~v~K~Y~alv~G~~ 90 (275)
.++.+++..+ ....+++|||||++||||||||+|.++++.|... .+ .+.|+|+|+|.|.+
T Consensus 89 ~tv~d~l~~~----~~~~~~~VgRLD~dTsGLLLlTndg~~~~~L~~p--~~--------------~i~K~Y~v~V~G~~ 148 (289)
T PRK10700 89 PTVFDRLPKL----RGARWIAVGRLDVNTCGLLLFTTDGELANRLMHP--SR--------------EVEREYAVRVFGQV 148 (289)
T ss_pred ccHHHHhhhh----cCCceeEccCCCCCCceEEEEEcCHHHHHHHhCc--cC--------------CCCeEEEEEEccCC
Confidence 4555555431 2346789999999999999999999999999763 32 39999999999988
Q ss_pred CCCccEEeccceeeeccCCceeeEEEecCCCCCCCcceEEEEEEeeecCCcEEEEEEEeCcCchhHHHHHHHhcCCCcee
Q 023907 91 RCSKGVISAPLGKVVVDNGKSDRITVVNNDQIMSAQHAVTRYQVIKPSCHGYTWLKLSPLTGRKHQLRVHCAEVLGTPIV 170 (275)
Q Consensus 91 ~~~~g~i~~~l~~~~~~~~~~~~~~~~~~~~~~~~k~a~t~~~~l~~~~~~~slv~~~~~TGR~HQIR~hla~~lG~PIv 170 (275)
++... .. + ..| +.+ .+ .......++.+... ...++++|++.+||+||||+||++ +|+||+
T Consensus 149 ~~~~l--~~-l-----~~G----v~l-~~-----~~~~~~~v~~~~~~-~~~s~l~v~L~EGk~hQIRrm~~~-lG~~V~ 208 (289)
T PRK10700 149 DDAKL--RQ-L-----SRG----VQL-ED-----GPAAFKTIKFSGGE-GINQWYNVTLTEGRNREVRRLWEA-VGVQVS 208 (289)
T ss_pred CHHHH--HH-H-----HcC----CEe-CC-----ceeeeEEEEeccCC-CCceEEEEEEeCCccHHHHHHHHH-cCCEEe
Confidence 65321 11 1 112 111 11 11111222222211 245899999999999999999997 999998
Q ss_pred C
Q 023907 171 G 171 (275)
Q Consensus 171 G 171 (275)
.
T Consensus 209 ~ 209 (289)
T PRK10700 209 R 209 (289)
T ss_pred E
Confidence 3
No 25
>PRK10475 23S rRNA pseudouridine synthase F; Provisional
Probab=99.75 E-value=1.6e-18 Score=156.56 Aligned_cols=124 Identities=15% Similarity=0.196 Sum_probs=83.7
Q ss_pred CCccCCCCCcCcHHHHHHHHhhcCCCCCCcccccCCCCCceEEEEEeCHHHHHHHHHHHHhccccccccccccccCCcce
Q 023907 1 MPVQGGIGIRRSIDELAATCLTYDYSEPPRLVHRLDRDSSGILVMGRTQTSATVLHSIFREKTFSASKEDNDNEKRILQR 80 (275)
Q Consensus 1 l~v~~g~~~~~sl~~l~~~~l~~~~~~~~~~vhRLD~~TSGllllAk~~~~a~~l~~~~~~~~~~~~~~~~~~~~~~v~K 80 (275)
+++|.......++.+++.. ...+++|||||++||||||||+|.++++.|.++... +.|
T Consensus 78 ~~~~~~~~~~~tv~~~l~~------~~~l~~VgRLDrdTsGLLLlT~dg~~~~~L~~p~~~----------------i~K 135 (290)
T PRK10475 78 IVSTTEDGERDNIVDFVNH------SKRVFPIGRLDKDSQGLIFLTNHGDLVNKILRAGND----------------HEK 135 (290)
T ss_pred CCcCCCCCCCCcHHHHhhc------cccccccccCCCCCcceEEEecCHHHHHHhhCcCCC----------------CCe
Confidence 3456554444555555442 246889999999999999999999999999775443 999
Q ss_pred EEEEEEecccCCCccEEeccceeeeccCCceeeEEEecCCCCCCCcceEEEEEEeeecCCcEEEEEEEeCcCchhHHHHH
Q 023907 81 WYWALVVGTPRCSKGVISAPLGKVVVDNGKSDRITVVNNDQIMSAQHAVTRYQVIKPSCHGYTWLKLSPLTGRKHQLRVH 160 (275)
Q Consensus 81 ~Y~alv~G~~~~~~g~i~~~l~~~~~~~~~~~~~~~~~~~~~~~~k~a~t~~~~l~~~~~~~slv~~~~~TGR~HQIR~h 160 (275)
+|+|+|.|.+.+. .+... ..|. .+ .+.. .+++. +..+ ..++++|++.+||+||||+|
T Consensus 136 ~Y~v~V~g~~~~~--~l~~l------~~Gv----~l-~~~~---~~~~~--v~~~-----~~~~~~i~l~eGk~rqIRrm 192 (290)
T PRK10475 136 EYLVTVDKPITDE--FIRGM------GAGV----PI-LGTV---TKKCK--VKKE-----APFVFRITLVQGLNRQIRRM 192 (290)
T ss_pred EEEEEECCCCCHH--HHHHH------hCCc----EE-CCEE---ecceE--EEec-----CCcEEEEEEECCcCHHHHHH
Confidence 9999999988543 22111 1121 11 0000 01111 1111 13579999999999999999
Q ss_pred HHhcCCCcee
Q 023907 161 CAEVLGTPIV 170 (275)
Q Consensus 161 la~~lG~PIv 170 (275)
|++ +|+||+
T Consensus 193 ~~~-~G~~V~ 201 (290)
T PRK10475 193 CEH-FGYEVT 201 (290)
T ss_pred HHH-cCCEEe
Confidence 997 999997
No 26
>COG1187 RsuA 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]
Probab=99.68 E-value=3.4e-17 Score=143.85 Aligned_cols=114 Identities=19% Similarity=0.280 Sum_probs=81.6
Q ss_pred CCCCCcccccCCCCCceEEEEEeCHHHHHHHHHHHHhccccccccccccccCCcceEEEEEEecccCCCccEEeccceee
Q 023907 25 YSEPPRLVHRLDRDSSGILVMGRTQTSATVLHSIFREKTFSASKEDNDNEKRILQRWYWALVVGTPRCSKGVISAPLGKV 104 (275)
Q Consensus 25 ~~~~~~~vhRLD~~TSGllllAk~~~~a~~l~~~~~~~~~~~~~~~~~~~~~~v~K~Y~alv~G~~~~~~g~i~~~l~~~ 104 (275)
...++++|+|||++|+|+|||++|++.++.|.++-.+ +.|+|+|.|.|.+.+.. ++.-
T Consensus 97 ~~~~~~pvGRLD~dTeGLLLLTnDG~la~rL~~P~~~----------------~~K~Y~v~v~g~~~~~~--l~~l---- 154 (248)
T COG1187 97 RKKRLFPVGRLDKDTEGLLLLTNDGELAHRLMHPSSE----------------VEKEYLVRVEGPVTEED--LEKL---- 154 (248)
T ss_pred cccceeeccccCCCCeeEEEEeCCHHHHHHhcCCCCC----------------CCEEEEEEEecCCCHHH--HHHH----
Confidence 4456999999999999999999999999999887766 99999999999776432 1110
Q ss_pred eccCCceeeEEEecCCCCCCCcceEEEEEEeeecCC-cEEEEEEEeCcCchhHHHHHHHhcCCCceeCCC
Q 023907 105 VVDNGKSDRITVVNNDQIMSAQHAVTRYQVIKPSCH-GYTWLKLSPLTGRKHQLRVHCAEVLGTPIVGDY 173 (275)
Q Consensus 105 ~~~~~~~~~~~~~~~~~~~~~k~a~t~~~~l~~~~~-~~slv~~~~~TGR~HQIR~hla~~lG~PIvGD~ 173 (275)
..| +.+. ++....+....+..... ..+++++.|.+||+||||.||++ +|+|++.=.
T Consensus 155 --~~G----v~l~------d~~~~~~~~~~l~~~~~~~~s~~~itl~EGrnrQVRRm~~a-~G~~V~~L~ 211 (248)
T COG1187 155 --RKG----VTLD------DGETKPAKPASLEKEPGKNNSWLRITLTEGRNRQVRRMFEA-VGLEVLRLK 211 (248)
T ss_pred --hCC----cEec------CcccccceeEEEEecCCCCceEEEEEEeCCcCHHHHHHHHH-cCCEEeEEE
Confidence 011 1111 11222223222222212 57999999999999999999997 999998533
No 27
>cd02868 PseudoU_synth_hTruB2_like PseudoU_synth_ hTRUB2_Like: Pseudouridine synthase, humanTRUB2_like. This group consists of eukaryotic pseudouridine synthases similar to human TruB pseudouridine synthase homolog 2 (TRUB2). Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi).
Probab=98.08 E-value=1e-05 Score=70.74 Aligned_cols=43 Identities=35% Similarity=0.286 Sum_probs=36.8
Q ss_pred CCcccccCCCCCceEEEEEeCHHHHHHHHHHHHhccccccccccccccCCcceEEEEEE
Q 023907 28 PPRLVHRLDRDSSGILVMGRTQTSATVLHSIFREKTFSASKEDNDNEKRILQRWYWALV 86 (275)
Q Consensus 28 ~~~~vhRLD~~TSGllllAk~~~~a~~l~~~~~~~~~~~~~~~~~~~~~~v~K~Y~alv 86 (275)
..++|||||++|||||+||+++.+ ++.+.|.++. +.|+|+|..
T Consensus 33 ~~~~vhrLD~~aSGvl~~a~~~~t--kl~~~~~~~~--------------~~K~Y~~~~ 75 (226)
T cd02868 33 VLVGVHRLDAFSSGVLVLGVNHGN--KLLSHLYSNH--------------PTRVYTIRG 75 (226)
T ss_pred eeeEccccCCCCceEEEEEeChhH--hHHHHHHhcC--------------CCeEEEEEE
Confidence 367889999999999999999876 5888898865 899999644
No 28
>cd01291 PseudoU_synth PseudoU_synth: Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). Pseudouridine synthases contains the RsuA/RluD, TruA, TruB and TruD families. This group consists of eukaryotic, bacterial and archeal pseudouridine synthases. Some psi sites such as psi55,13,38 and 39 in tRNA are highly conserved, being in the same position in eubacteria, archeabacteria and eukaryotes. Other psi sites occur in a more restricted fashion, for example psi2604in 23S RNA made by E.coli RluF has only been detected in E.coli. Human dyskerin with the help of guide RNAs makes the hundreds of psueudouridnes present in rRNA and small nuclear RNAs (snRNAs). Mutations in human dyskerin cause X-linked dyskeratosis congenitas. Missense mutation in human PUS1 causes mitochondrial myopathy and sideroblastic anemia (MLASA).
Probab=96.57 E-value=0.0097 Score=43.96 Aligned_cols=22 Identities=9% Similarity=0.060 Sum_probs=19.6
Q ss_pred CCCCCcccccCCCCCceEEEEE
Q 023907 25 YSEPPRLVHRLDRDSSGILVMG 46 (275)
Q Consensus 25 ~~~~~~~vhRLD~~TSGllllA 46 (275)
...+++.++++|+.++|+++++
T Consensus 22 ~~~~i~~aG~kDk~a~t~q~v~ 43 (87)
T cd01291 22 PPKRVGYAGRKDKRAVTTQLVS 43 (87)
T ss_pred ChheEEECccCCCCeeEEEEEc
Confidence 3457899999999999999999
No 29
>cd02572 PseudoU_synth_hDyskerin PseudoU_synth_hDyskerin_Like: Pseudouridine synthase, human dyskerin like. This group consists of eukaryotic and archeal pseudouridine synthases similar to human dyskerin, Saccharomyces cerevisiae Cbf5, and Drosophila melanogaster Mfl (minifly protein). Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactor is required. S. cerevisiae Cbf5 and human dyskerin are nucleolar proteins that, with the help of guide RNAs, make the hundreds of psueudouridnes present in rRNA and small nuclear RNAs (snRNAs). Cbf5/Dyskerin is the catalytic subunit of eukaryotic box H/ACA small nucleolar ribonucleoprotein (snoRNP) particles. D. melanogaster mfl hosts in its fourth intron, a box H/AC snoRNA gene. In addition dyskerin is likely to have a structural role in the telomerase complex. Mutations in human dyskerin cause X-linked dyskeratosis congenitas. Mutations in Drosophila Mfl r
Probab=92.70 E-value=0.42 Score=40.51 Aligned_cols=56 Identities=20% Similarity=0.072 Sum_probs=40.1
Q ss_pred HHHHHHHhhcCCCCCCcccccCCCCCceEEEEEeCHHHHHHHHHHHHhccccccccccccccCCcceEEEEEEe
Q 023907 14 DELAATCLTYDYSEPPRLVHRLDRDSSGILVMGRTQTSATVLHSIFREKTFSASKEDNDNEKRILQRWYWALVV 87 (275)
Q Consensus 14 ~~l~~~~l~~~~~~~~~~vhRLD~~TSGllllAk~~~~a~~l~~~~~~~~~~~~~~~~~~~~~~v~K~Y~alv~ 87 (275)
.+.+...-+.....++...+-||-..||||+++-+.. .++.+.+.+ -.|+|.|.+.
T Consensus 16 ~~~v~~~k~~~~~kkvGH~GTLDp~A~GvLiv~~g~~--Tk~~~~~~~----------------~~K~Y~a~v~ 71 (182)
T cd02572 16 HEVVAWIKRILGVEKTGHSGTLDPKVTGCLPVCIDRA--TRLVKSQQE----------------AGKEYVCVMR 71 (182)
T ss_pred HHHHHHHHHHhCCCccCcCCCCCCcCeeEEEEEECHH--hhhhHHHhC----------------CCCEEEEEEE
Confidence 3344433333344689999999999999999999973 445556655 5799998774
No 30
>cd00506 PseudoU_synth_TruB_like PseudoU_synth_TruB: Pseudouridine synthase, TruB family. This group consists of eukaryotic, bacterial and archeal pseudouridine synthases similar to Escherichia coli TruB, Saccharomyces cerevisiae Pus4, M. tuberculosis TruB, S. cerevisiae Cbf5 and human dyskerin. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. E. coli TruB, M. tuberculosis TruB and S. cerevisiae Pus4, make psi55 in the T loop of tRNAs. Pus4 catalyses the formation of psi55 in both cytoplasmic and mitochondrial tRNAs. Psi55 is almost universally conserved. S. cerevisiae Cbf5 and human dyskerin are nucleolar proteins that, with the help of guide RNAs, make the hundreds of psueudouridnes present in rRNA and small nuclear RNAs (snRNAs). Cbf5/Dyskerin is the catalytic subunit of eukaryotic box H/ACA small nucleolar ribonucleoprotein (snoRNP) particles. Mutations in human dysker
Probab=91.27 E-value=0.74 Score=39.92 Aligned_cols=56 Identities=21% Similarity=0.144 Sum_probs=40.6
Q ss_pred HHHHHHHhhcCCCCCCcccccCCCCCceEEEEEeCHHHHHHHHHHHHhccccccccccccccCCcceEEEEEEe
Q 023907 14 DELAATCLTYDYSEPPRLVHRLDRDSSGILVMGRTQTSATVLHSIFREKTFSASKEDNDNEKRILQRWYWALVV 87 (275)
Q Consensus 14 ~~l~~~~l~~~~~~~~~~vhRLD~~TSGllllAk~~~~a~~l~~~~~~~~~~~~~~~~~~~~~~v~K~Y~alv~ 87 (275)
.+.+....+.....++...+-||-..||||+++-+.. .++...+.+ ..|+|.|.+.
T Consensus 14 ~~vv~~ik~~~~~kKvGH~GTLDP~AsGvLiv~vG~a--Tkl~~~~~~----------------~~K~Y~~~~~ 69 (210)
T cd00506 14 HDVVDTIRRIFLAEKVGHGGTLDPFATGVLVVGIGKA--TKLLKHLLA----------------ATKDYTAIGR 69 (210)
T ss_pred HHHHHHHHHHhCccccCCCCcCCCcCeeEEEEEECHH--HhhhHHHhc----------------CCceEEEEEE
Confidence 3344434333345689999999999999999999974 445556665 6899999763
No 31
>PRK00989 truB tRNA pseudouridine synthase B; Provisional
Probab=90.69 E-value=0.65 Score=40.77 Aligned_cols=57 Identities=19% Similarity=0.044 Sum_probs=41.2
Q ss_pred HHHHHHHhhcCCCCCCcccccCCCCCceEEEEEeCHHHHHHHHHHHHhccccccccccccccCCcceEEEEEEe
Q 023907 14 DELAATCLTYDYSEPPRLVHRLDRDSSGILVMGRTQTSATVLHSIFREKTFSASKEDNDNEKRILQRWYWALVV 87 (275)
Q Consensus 14 ~~l~~~~l~~~~~~~~~~vhRLD~~TSGllllAk~~~~a~~l~~~~~~~~~~~~~~~~~~~~~~v~K~Y~alv~ 87 (275)
.+.+...-+.....++...+.||-..||||+++-.. .+.++.+.+.+ ..|+|.|.+.
T Consensus 23 ~dvv~~ikk~~~~kKvGH~GTLDP~AtGvLiv~vG~-~aTkl~~~~~~----------------~~K~Y~~~~~ 79 (230)
T PRK00989 23 FSLIRSLTKLIGVKKIGHAGTLDPFATGVMVMLIGR-KFTRLSDILLF----------------EDKEYAAVAH 79 (230)
T ss_pred HHHHHHHHHHhCCCcCCcCccCCCCCeeEEEEEECC-chhhhHHHhcC----------------CCcEEEEEEE
Confidence 344443433334568999999999999999999886 34456666655 6799999764
No 32
>TIGR00431 TruB tRNA pseudouridine 55 synthase. TruB, the tRNA pseudouridine 55 synthase, converts uracil to pseudouridine in the T loop (not the anticodon loop - beware mis-annotation in Swiss-Prot) of most tRNAs of all three domains of life. This model is built on a seed alignment of bacterial proteins only. Saccharomyces cerevisiae protein YNL292w (Pus4) has been shown to be the pseudouridine 55 synthase of both cytosolic and mitochondrial compartments, active at no other position on tRNA and the only enzyme active at that position in the species. A distinct yeast protein YLR175w, (centromere/microtubule-binding protein CBF5) is an rRNA pseudouridine synthase, and the archaeal set is much more similar to CBF5 than to Pus4. It is unclear whether the archaeal proteins found by this model are tRNA pseudouridine 55 synthases like TruB, rRNA pseudouridine synthases like CBF5, or (as suggested by the absence of paralogs in the Archaea) both. CBF5 likely has additional, eukaryotic-specific
Probab=89.09 E-value=1.3 Score=38.36 Aligned_cols=56 Identities=16% Similarity=0.102 Sum_probs=40.7
Q ss_pred HHHHHHHhhcCCCCCCcccccCCCCCceEEEEEeCHHHHHHHHHHHHhccccccccccccccCCcceEEEEEEe
Q 023907 14 DELAATCLTYDYSEPPRLVHRLDRDSSGILVMGRTQTSATVLHSIFREKTFSASKEDNDNEKRILQRWYWALVV 87 (275)
Q Consensus 14 ~~l~~~~l~~~~~~~~~~vhRLD~~TSGllllAk~~~~a~~l~~~~~~~~~~~~~~~~~~~~~~v~K~Y~alv~ 87 (275)
.+++...-+.....++...+-||-..||||+++-+... ++...+.+ -.|+|.|.+.
T Consensus 16 ~~vv~~vkk~~~~kKvGH~GTLDP~AsGvLiv~vG~~T--kl~~~~~~----------------~~K~Y~~~~~ 71 (209)
T TIGR00431 16 FDALAKVRRLLNVKKVGHTGTLDPFATGVLPILVGKAT--KLSPYLTD----------------LDKEYRAEIR 71 (209)
T ss_pred HHHHHHHHHHhCCCcCCCCCCCCCcCceEEEEEEChHh--hhhHHHcC----------------CCCeEEEEEE
Confidence 34444333333446789999999999999999999754 56666665 6899998763
No 33
>PRK00020 truB tRNA pseudouridine synthase B; Provisional
Probab=88.12 E-value=1.7 Score=38.46 Aligned_cols=55 Identities=16% Similarity=0.106 Sum_probs=40.4
Q ss_pred HHHHHHHhhcCCCCCCcccccCCCCCceEEEEEeCHHHHHHHHHHHHhccccccccccccccCCcceEEEEEE
Q 023907 14 DELAATCLTYDYSEPPRLVHRLDRDSSGILVMGRTQTSATVLHSIFREKTFSASKEDNDNEKRILQRWYWALV 86 (275)
Q Consensus 14 ~~l~~~~l~~~~~~~~~~vhRLD~~TSGllllAk~~~~a~~l~~~~~~~~~~~~~~~~~~~~~~v~K~Y~alv 86 (275)
.+++...-+.....++...+-||-..||||+++-... .++...+.+ ..|+|.|.+
T Consensus 24 ~dvv~~vkr~~~~kKvGH~GTLDP~AtGvLiv~iG~a--TKl~~~l~~----------------~~K~Y~a~~ 78 (244)
T PRK00020 24 NHALQRAKRTVDAAKAGHTGTLDPFATGLLVCCMGRA--TKISGRMLE----------------ADKTYQATL 78 (244)
T ss_pred HHHHHHHHHHhCCCCCCcCCcCCCcCeeEEEEEECHH--hhhhHHhcc----------------CCcEEEEEE
Confidence 4455544443445689999999999999999999973 445555555 579999976
No 34
>PF01509 TruB_N: TruB family pseudouridylate synthase (N terminal domain); InterPro: IPR002501 Pseudouridine synthases catalyse the isomerisation of uridine to pseudouridine (Psi) in a variety of RNA molecules, and may function as RNA chaperones. Pseudouridine is the most abundant modified nucleotide found in all cellular RNAs. There are four distinct families of pseudouridine synthases that share no global sequence similarity, but which do share the same fold of their catalytic domain(s) and uracil-binding site and are descended from a common molecular ancestor. The catalytic domain consists of two subdomains, each of which has an alpha+beta structure that has some similarity to the ferredoxin-like fold (note: some pseudouridine synthases contain additional domains). The active site is the most conserved structural region of the superfamily and is located between the two homologous domains. These families are []: Pseudouridine synthase I, TruA. Pseudouridine synthase II, TruB, which contains and additional C-terminal PUA domain. Pseudouridine synthase RsuA (ribosomal small subunit) and RluC/RluD (ribosomal large subunits), both of which contain an additional N-terminal alpha-L RNA-binding motif. Pseudouridine synthase TruD, which has a natural circular permutation in the catalytic domain, as well as an insertion of a family-specific alpha+beta subdomain. TruB is responsible for the pseudouridine residue present in the T loops of virtually all tRNAs. TruB recognises the preformed 3-D structure of the T loop primarily through shape complementarity. It accesses its substrate uridyl residue by flipping out the nucleotide and disrupts the tertiary structure of tRNA []. This entry represents pseudouridine synthase TruB, as well as Cbf5p that modifies rRNA [].; GO: 0006396 RNA processing; PDB: 1SGV_B 2AUS_C 3UAI_A 3U28_A 2RFK_A 3LWV_A 3HJY_A 3HAX_A 3LWO_A 3HAY_A ....
Probab=87.16 E-value=0.66 Score=37.98 Aligned_cols=42 Identities=29% Similarity=0.298 Sum_probs=31.7
Q ss_pred CCCcccccCCCCCceEEEEEeCHHHHHHHHHHHHhccccccccccccccCCcceEEEEEE
Q 023907 27 EPPRLVHRLDRDSSGILVMGRTQTSATVLHSIFREKTFSASKEDNDNEKRILQRWYWALV 86 (275)
Q Consensus 27 ~~~~~vhRLD~~TSGllllAk~~~~a~~l~~~~~~~~~~~~~~~~~~~~~~v~K~Y~alv 86 (275)
.++...+.||-..||||+++-+.. .++.+.+.+ ..|+|.|..
T Consensus 7 ~KvGH~GTLDP~AsGvL~v~vg~~--Tkl~~~l~~----------------~~K~Y~~~~ 48 (149)
T PF01509_consen 7 KKVGHGGTLDPFASGVLVVGVGKA--TKLLSYLQN----------------SDKEYVATI 48 (149)
T ss_dssp SSEEESS-SSTT-EEEEEEEEGGG--GGGHHHHTT----------------SEEEEEEEE
T ss_pred ceeccccccCCcceEEEEEEECCc--chHHHHhhc----------------cCCEEEEEE
Confidence 467889999999999999999873 336666665 679999965
No 35
>PRK04099 truB tRNA pseudouridine synthase B; Provisional
Probab=87.15 E-value=2 Score=38.73 Aligned_cols=56 Identities=16% Similarity=0.151 Sum_probs=41.1
Q ss_pred HHHHHHHhhcCCCCCCcccccCCCCCceEEEEEeCHHHHHHHHHHHHhccccccccccccccCCcceEEEEEEe
Q 023907 14 DELAATCLTYDYSEPPRLVHRLDRDSSGILVMGRTQTSATVLHSIFREKTFSASKEDNDNEKRILQRWYWALVV 87 (275)
Q Consensus 14 ~~l~~~~l~~~~~~~~~~vhRLD~~TSGllllAk~~~~a~~l~~~~~~~~~~~~~~~~~~~~~~v~K~Y~alv~ 87 (275)
.+.+..+-+.....+....+-||-..||||+++-... .++.+.+.+ -.|+|.|.+.
T Consensus 16 ~~vv~~ikk~~~~kKvGH~GTLDP~AtGvLiv~iG~a--TKl~~~l~~----------------~~K~Y~a~~~ 71 (273)
T PRK04099 16 NAFLSRLKRKYGVKKAGFSGTLDPFAKGVLIVAFGQY--TKLFRFLKK----------------TPKTYRATLW 71 (273)
T ss_pred HHHHHHHHHHhCCCccccCccCCCCCeeEEEEEEChH--hhhHHHhcc----------------CCceEEEEEE
Confidence 4455544443345689999999999999999999975 336666655 5799998763
No 36
>cd02573 PseudoU_synth_EcTruB PseudoU_synth_EcTruB: Pseudouridine synthase, Escherichia coli TruB like. This group consists of bacterial pseudouridine synthases similar to E. coli TruB and Mycobacterium tuberculosis TruB. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). E. coli TruB and M. tuberculosis TruB make psi55 in the T loop of tRNAs. Psi55 is nearly universally conserved. E. coli TruB is not inhibited by RNA containing 5-fluorouridine.
Probab=85.78 E-value=2.6 Score=38.08 Aligned_cols=56 Identities=16% Similarity=0.150 Sum_probs=40.7
Q ss_pred HHHHHHHhhcCCCCCCcccccCCCCCceEEEEEeCHHHHHHHHHHHHhccccccccccccccCCcceEEEEEEe
Q 023907 14 DELAATCLTYDYSEPPRLVHRLDRDSSGILVMGRTQTSATVLHSIFREKTFSASKEDNDNEKRILQRWYWALVV 87 (275)
Q Consensus 14 ~~l~~~~l~~~~~~~~~~vhRLD~~TSGllllAk~~~~a~~l~~~~~~~~~~~~~~~~~~~~~~v~K~Y~alv~ 87 (275)
.+.+...-+.....++...+-||-..||||+++-+.. .++...+.+ ..|+|.|.+.
T Consensus 14 ~~vv~~vr~~~~~kKvGH~GTLDP~AtGvL~v~vG~a--Tkl~~~l~~----------------~~K~Y~~~~~ 69 (277)
T cd02573 14 HDVVQKVRRLLGTKKVGHTGTLDPLATGVLPIALGEA--TKLSQYLLD----------------ADKTYRATVR 69 (277)
T ss_pred HHHHHHHHHHhCcCccCCCCCCCCcCeEEEEEEEChH--HhhHHHhcC----------------CCcEEEEEEE
Confidence 3444433333344579999999999999999999974 346666665 6799999764
No 37
>PRK02193 truB tRNA pseudouridine synthase B; Provisional
Probab=85.65 E-value=2.6 Score=38.17 Aligned_cols=56 Identities=16% Similarity=0.146 Sum_probs=40.2
Q ss_pred HHHHHHHhhcCCCCCCcccccCCCCCceEEEEEeCHHHHHHHHHHHHhccccccccccccccCCcceEEEEEEe
Q 023907 14 DELAATCLTYDYSEPPRLVHRLDRDSSGILVMGRTQTSATVLHSIFREKTFSASKEDNDNEKRILQRWYWALVV 87 (275)
Q Consensus 14 ~~l~~~~l~~~~~~~~~~vhRLD~~TSGllllAk~~~~a~~l~~~~~~~~~~~~~~~~~~~~~~v~K~Y~alv~ 87 (275)
.+.+...-+.....++...+-||-..||||+++-... .++.+.+.+ ..|+|.|.+.
T Consensus 14 ~dvv~~vrr~~~~kKvGH~GTLDP~AtGvL~v~vG~a--Tkl~~~l~~----------------~~K~Y~a~~~ 69 (279)
T PRK02193 14 FKFIKNFAKTNNIKKIGHTGTLDPLASGLLLVATDED--TKLIDYLDQ----------------KDKTYIAKIK 69 (279)
T ss_pred HHHHHHHHHHcCCCccccCccCCCcCeeEEEEEEChh--hhhhHHhcc----------------CCcEEEEEEE
Confidence 4444433333344689999999999999999999974 345555554 6799999763
No 38
>PRK02484 truB tRNA pseudouridine synthase B; Provisional
Probab=84.40 E-value=3.2 Score=37.84 Aligned_cols=56 Identities=16% Similarity=0.091 Sum_probs=40.6
Q ss_pred HHHHHHHhhcCCCCCCcccccCCCCCceEEEEEeCHHHHHHHHHHHHhccccccccccccccCCcceEEEEEEe
Q 023907 14 DELAATCLTYDYSEPPRLVHRLDRDSSGILVMGRTQTSATVLHSIFREKTFSASKEDNDNEKRILQRWYWALVV 87 (275)
Q Consensus 14 ~~l~~~~l~~~~~~~~~~vhRLD~~TSGllllAk~~~~a~~l~~~~~~~~~~~~~~~~~~~~~~v~K~Y~alv~ 87 (275)
.+.+...-+.....++...+.||-..||||+++-... .++.+.+.+ -.|+|.|.+.
T Consensus 17 ~dvv~~vrr~l~~kKvGH~GTLDP~AtGvL~i~vG~a--Tkl~~~l~~----------------~~K~Y~a~~~ 72 (294)
T PRK02484 17 HDAVFKLRKILQTKKIGHGGTLDPDVVGVLPIAVGKA--TRLIEYMTE----------------AGKVYEGEIT 72 (294)
T ss_pred HHHHHHHHHHhCCCccccCCCCCCCCeeEEEEEEChh--hhhhHHhcc----------------CCcEEEEEEE
Confidence 4455533333345689999999999999999999974 335555655 5799999764
No 39
>PRK14123 tRNA pseudouridine synthase B; Provisional
Probab=84.04 E-value=3.4 Score=37.89 Aligned_cols=56 Identities=13% Similarity=0.105 Sum_probs=40.7
Q ss_pred HHHHHHHhhcCCCCCCcccccCCCCCceEEEEEeCHHHHHHHHHHHHhccccccccccccccCCcceEEEEEEe
Q 023907 14 DELAATCLTYDYSEPPRLVHRLDRDSSGILVMGRTQTSATVLHSIFREKTFSASKEDNDNEKRILQRWYWALVV 87 (275)
Q Consensus 14 ~~l~~~~l~~~~~~~~~~vhRLD~~TSGllllAk~~~~a~~l~~~~~~~~~~~~~~~~~~~~~~v~K~Y~alv~ 87 (275)
.+.+...-+.....++...+-||-..||||+++-.+.+ ++.+.+.. ..|+|.|.+.
T Consensus 17 ~dvv~~vrr~~~~kKvGH~GTLDP~AtGvL~v~vG~aT--kl~~~l~~----------------~~K~Y~~~~~ 72 (305)
T PRK14123 17 HDVVFKLRKILKTKKIGHTGTLDPEVAGVLPVCIGNAT--RVSDYVMD----------------MGKAYEATVS 72 (305)
T ss_pred HHHHHHHHHHhCCCccccCcCCCCcCeeEEEEEEChhh--hhHHHhcC----------------CCcEEEEEEE
Confidence 34444333333456899999999999999999999754 45666655 6799999763
No 40
>PRK14124 tRNA pseudouridine synthase B; Provisional
Probab=84.00 E-value=4.1 Score=37.42 Aligned_cols=56 Identities=14% Similarity=0.221 Sum_probs=40.9
Q ss_pred HHHHHHHhhcCCCCCCcccccCCCCCceEEEEEeCHHHHHHHHHHHHhccccccccccccccCCcceEEEEEEe
Q 023907 14 DELAATCLTYDYSEPPRLVHRLDRDSSGILVMGRTQTSATVLHSIFREKTFSASKEDNDNEKRILQRWYWALVV 87 (275)
Q Consensus 14 ~~l~~~~l~~~~~~~~~~vhRLD~~TSGllllAk~~~~a~~l~~~~~~~~~~~~~~~~~~~~~~v~K~Y~alv~ 87 (275)
.+.+...-+.....++...+-||-..||||+++-... .++.+.+.. -.|+|.|.+.
T Consensus 17 ~dvv~~vrr~l~~kKvGH~GTLDP~AtGvL~v~vG~a--Tkl~~~l~~----------------~~K~Y~a~~~ 72 (308)
T PRK14124 17 HDVVDEVRKKLKTRKVGHAGTLDPFATGVLIVGVNKA--TRLLEYLKN----------------EKKVYYVKMR 72 (308)
T ss_pred HHHHHHHHHHcCCCccCcCcCCCCCCcEEEEEEEChH--HhhhHHHhc----------------CCceEEEEEE
Confidence 4455544343345689999999999999999999974 335566665 5799999763
No 41
>PRK03287 truB tRNA pseudouridine synthase B; Provisional
Probab=83.84 E-value=3.4 Score=37.76 Aligned_cols=56 Identities=21% Similarity=0.254 Sum_probs=40.0
Q ss_pred HHHHHHHhhcCCCCCCcccccCCCCCceEEEEEeCHHHHHHHHHHHHhccccccccccccccCCcceEEEEEEe
Q 023907 14 DELAATCLTYDYSEPPRLVHRLDRDSSGILVMGRTQTSATVLHSIFREKTFSASKEDNDNEKRILQRWYWALVV 87 (275)
Q Consensus 14 ~~l~~~~l~~~~~~~~~~vhRLD~~TSGllllAk~~~~a~~l~~~~~~~~~~~~~~~~~~~~~~v~K~Y~alv~ 87 (275)
.+.+...-+.....++...+-||-..||||+++-... .++.+.+.+ -.|+|.|.+.
T Consensus 23 ~dvv~~vrr~~~~kKvGH~GTLDP~AtGvL~i~vG~a--TKl~~~l~~----------------~~K~Y~a~~~ 78 (298)
T PRK03287 23 HDVVARCRRLFGTRKVGHAGTLDPMATGVLVLGVERA--TKLLGHLTL----------------TDKSYTATIR 78 (298)
T ss_pred HHHHHHHHHHhCCCCCCcCccCCCcceeEEEEEeChh--hhhhHHHhc----------------CCcEEEEEEE
Confidence 4444433333345689999999999999999999963 445555655 5799999763
No 42
>PRK14846 truB tRNA pseudouridine synthase B; Provisional
Probab=83.22 E-value=4.2 Score=37.80 Aligned_cols=56 Identities=18% Similarity=0.143 Sum_probs=40.1
Q ss_pred HHHHHHHhhcCCCCCCcccccCCCCCceEEEEEeCHHHHHHHHHHHHhccccccccccccccCCcceEEEEEEe
Q 023907 14 DELAATCLTYDYSEPPRLVHRLDRDSSGILVMGRTQTSATVLHSIFREKTFSASKEDNDNEKRILQRWYWALVV 87 (275)
Q Consensus 14 ~~l~~~~l~~~~~~~~~~vhRLD~~TSGllllAk~~~~a~~l~~~~~~~~~~~~~~~~~~~~~~v~K~Y~alv~ 87 (275)
.+.+...-+.....++...+-||-..||||+++-... .++...+.+ ..|+|.|.+.
T Consensus 17 ~dvv~~vrk~l~~kKVGH~GTLDP~AtGVL~i~vG~a--TKl~~~l~~----------------~~K~Y~a~~~ 72 (345)
T PRK14846 17 AQLVSIVKKILGKTKIGHAGTLDVEAEGILPFAVGEA--TKLIHLLID----------------ARKTYIFTVK 72 (345)
T ss_pred HHHHHHHHHHhCCCcCCcCccCCCcCceEEEEEEChh--hhhhHHHhc----------------CCceEEEEEE
Confidence 3444433333345689999999999999999999974 445555555 6799998763
No 43
>PRK00130 truB tRNA pseudouridine synthase B; Provisional
Probab=82.97 E-value=4.2 Score=37.03 Aligned_cols=56 Identities=16% Similarity=0.074 Sum_probs=40.5
Q ss_pred HHHHHHHhhcCCCCCCcccccCCCCCceEEEEEeCHHHHHHHHHHHHhccccccccccccccCCcceEEEEEEe
Q 023907 14 DELAATCLTYDYSEPPRLVHRLDRDSSGILVMGRTQTSATVLHSIFREKTFSASKEDNDNEKRILQRWYWALVV 87 (275)
Q Consensus 14 ~~l~~~~l~~~~~~~~~~vhRLD~~TSGllllAk~~~~a~~l~~~~~~~~~~~~~~~~~~~~~~v~K~Y~alv~ 87 (275)
.+.+...-+.....++...+-||-..||||+++-... .++.+.+.+ -.|+|.|.+.
T Consensus 16 ~dvv~~vrr~~~~kKvGH~GTLDP~AtGvL~v~vG~a--Tkl~~~l~~----------------~~K~Y~a~~~ 71 (290)
T PRK00130 16 FDVVRKIRKIAKIKKVGHTGTLDPLASGVLPVCLGKA--TKIVDYLME----------------GKKTYRAEIK 71 (290)
T ss_pred HHHHHHHHHHhCCCccCcCCCCCCCCeeEEEEEEChh--hhhHHHhcc----------------CCcEEEEEEE
Confidence 3444433333344689999999999999999999974 336666665 5799999764
No 44
>PRK05389 truB tRNA pseudouridine synthase B; Provisional
Probab=82.25 E-value=4.2 Score=37.30 Aligned_cols=55 Identities=16% Similarity=0.068 Sum_probs=39.5
Q ss_pred HHHHHHHhhcCCCCCCcccccCCCCCceEEEEEeCHHHHHHHHHHHHhccccccccccccccCCcceEEEEEE
Q 023907 14 DELAATCLTYDYSEPPRLVHRLDRDSSGILVMGRTQTSATVLHSIFREKTFSASKEDNDNEKRILQRWYWALV 86 (275)
Q Consensus 14 ~~l~~~~l~~~~~~~~~~vhRLD~~TSGllllAk~~~~a~~l~~~~~~~~~~~~~~~~~~~~~~v~K~Y~alv 86 (275)
.+.+...-+.....++...+-||-..||||+++-... .++.+.+.+ -.|+|.|.+
T Consensus 27 ~dvv~~vrk~~~~kKvGH~GTLDP~AtGvL~v~vG~a--Tkl~~~l~~----------------~~K~Y~a~~ 81 (305)
T PRK05389 27 TEAVSKVKWLFDAQKAGHAGTLDPLASGVLPIALGEA--TKTVPYVMD----------------GTKRYRFTV 81 (305)
T ss_pred HHHHHHHHHHhcccccCCcccCCCCCceEEEEEEChh--hhhhHHhcc----------------CCcEEEEEE
Confidence 4444433333344678999999999999999999973 445555554 579999976
No 45
>PRK04270 H/ACA RNA-protein complex component Cbf5p; Reviewed
Probab=82.23 E-value=4.1 Score=37.23 Aligned_cols=56 Identities=20% Similarity=0.110 Sum_probs=39.8
Q ss_pred HHHHHHHhhcCCCCCCcccccCCCCCceEEEEEeCHHHHHHHHHHHHhccccccccccccccCCcceEEEEEEe
Q 023907 14 DELAATCLTYDYSEPPRLVHRLDRDSSGILVMGRTQTSATVLHSIFREKTFSASKEDNDNEKRILQRWYWALVV 87 (275)
Q Consensus 14 ~~l~~~~l~~~~~~~~~~vhRLD~~TSGllllAk~~~~a~~l~~~~~~~~~~~~~~~~~~~~~~v~K~Y~alv~ 87 (275)
.+.+...-+.....+....+-||-..||||+++-... .++.+.+.+ -.|+|.|.+.
T Consensus 36 ~~~v~~~r~~~~~kkvGH~GTLDp~A~GvL~v~~g~a--tk~~~~~~~----------------~~K~Y~~~~~ 91 (300)
T PRK04270 36 HEVAAWVRDILGVEKAGHGGTLDPKVTGVLPVALGKA--TKVVQALLE----------------SGKEYVCVMH 91 (300)
T ss_pred HHHHHHHHHHhccccccCCCCCCCcCeEEEEEEEChH--hhhhHHhcc----------------CCcEEEEEEE
Confidence 3344433332334578999999999999999999874 445566655 5799998763
No 46
>PRK01851 truB tRNA pseudouridine synthase B; Provisional
Probab=80.47 E-value=6.1 Score=36.21 Aligned_cols=56 Identities=13% Similarity=0.083 Sum_probs=40.1
Q ss_pred HHHHHHHhhcCCCCCCcccccCCCCCceEEEEEeCHHHHHHHHHHHHhccccccccccccccCCcceEEEEEEe
Q 023907 14 DELAATCLTYDYSEPPRLVHRLDRDSSGILVMGRTQTSATVLHSIFREKTFSASKEDNDNEKRILQRWYWALVV 87 (275)
Q Consensus 14 ~~l~~~~l~~~~~~~~~~vhRLD~~TSGllllAk~~~~a~~l~~~~~~~~~~~~~~~~~~~~~~v~K~Y~alv~ 87 (275)
.+.+...-+.....++...+-||-..||||+++-... .++.+.+.+ -.|+|.|.+.
T Consensus 30 ~dvv~~vrr~l~~kKvGH~GTLDP~AtGvL~v~vG~a--Tkl~~~l~~----------------~~K~Y~~~~~ 85 (303)
T PRK01851 30 NDALQRAKRLLRAKKAGHTGTLDPLATGLLPLCFGEA--TKFSQDLLD----------------ADKTYEATLR 85 (303)
T ss_pred HHHHHHHHHHhCcccCCCCCCCCCCCceEEEEEECHH--HhhhHHhcc----------------cCeEEEEEEE
Confidence 3444433333345678999999999999999999974 335566655 5799999763
No 47
>PRK01528 truB tRNA pseudouridine synthase B; Provisional
Probab=79.65 E-value=6.6 Score=35.79 Aligned_cols=56 Identities=16% Similarity=0.134 Sum_probs=39.5
Q ss_pred HHHHHHHhhcCCCCCCcccccCCCCCceEEEEEeCHHHHHHHHHHHHhccccccccccccccCCcceEEEEEEe
Q 023907 14 DELAATCLTYDYSEPPRLVHRLDRDSSGILVMGRTQTSATVLHSIFREKTFSASKEDNDNEKRILQRWYWALVV 87 (275)
Q Consensus 14 ~~l~~~~l~~~~~~~~~~vhRLD~~TSGllllAk~~~~a~~l~~~~~~~~~~~~~~~~~~~~~~v~K~Y~alv~ 87 (275)
.+.+...-+.....++...+-||-..||||+++-... .++.+.+.+ ..|+|.|.+.
T Consensus 17 ~dvv~~vrk~~~~kKvGH~GTLDP~AtGvL~v~vG~a--TKl~~~l~~----------------~~K~Y~~~~~ 72 (292)
T PRK01528 17 AKLVSIVKKILGKVKIGHAGTLDVEAEGVLPLAVGEA--TKLVQLLID----------------AKKTYIFTVK 72 (292)
T ss_pred HHHHHHHHHHcCCCccCcCccCCCcCceEEEEEEChH--hhhhHHHhc----------------CCceEEEEEE
Confidence 3444433333345689999999999999999999974 345555554 5799998763
No 48
>PRK14122 tRNA pseudouridine synthase B; Provisional
Probab=79.30 E-value=6.2 Score=36.28 Aligned_cols=55 Identities=16% Similarity=0.168 Sum_probs=40.4
Q ss_pred HHHHHHHhhcCCCCCCcccccCCCCCceEEEEEeCHHHHHHHHHHHHhccccccccccccccCCcceEEEEEE
Q 023907 14 DELAATCLTYDYSEPPRLVHRLDRDSSGILVMGRTQTSATVLHSIFREKTFSASKEDNDNEKRILQRWYWALV 86 (275)
Q Consensus 14 ~~l~~~~l~~~~~~~~~~vhRLD~~TSGllllAk~~~~a~~l~~~~~~~~~~~~~~~~~~~~~~v~K~Y~alv 86 (275)
.+.+...-+.....++...+-||-..||||+++-...+ ++.+.+.+ ..|+|.|.+
T Consensus 15 ~dvv~~vrr~l~~kKvGH~GTLDP~AtGvL~i~iG~aT--Kl~~~l~~----------------~~K~Y~a~~ 69 (312)
T PRK14122 15 HDVVNRARRALGTRRVGHTGTLDPLATGVLVLCTDDST--KLVPFLSA----------------EDKEYLAWV 69 (312)
T ss_pred HHHHHHHHHHhCCCCCCCCCCCCCcCeeeEEEEEChhh--hhhHHhcC----------------CCceEEEEE
Confidence 34444333333456889999999999999999999743 36666655 689999976
No 49
>PRK05033 truB tRNA pseudouridine synthase B; Provisional
Probab=78.70 E-value=7.1 Score=35.91 Aligned_cols=56 Identities=9% Similarity=0.090 Sum_probs=40.2
Q ss_pred HHHHHHHhhcCCCCCCcccccCCCCCceEEEEEeCHHHHHHHHHHHHhccccccccccccccCCcceEEEEEEe
Q 023907 14 DELAATCLTYDYSEPPRLVHRLDRDSSGILVMGRTQTSATVLHSIFREKTFSASKEDNDNEKRILQRWYWALVV 87 (275)
Q Consensus 14 ~~l~~~~l~~~~~~~~~~vhRLD~~TSGllllAk~~~~a~~l~~~~~~~~~~~~~~~~~~~~~~v~K~Y~alv~ 87 (275)
.+.+...-+.....++...+-||-..||||+++-...+ ++.+.+.+ -.|+|.|.+.
T Consensus 24 ~dvv~~vrr~l~~kKvGH~GTLDP~AtGvL~v~vG~aT--kl~~~~~~----------------~~K~Y~a~~~ 79 (312)
T PRK05033 24 NDALQKVKRLFNANKAGHTGALDPLATGMLPICLGEAT--KFSQYLLD----------------SDKRYRVTAR 79 (312)
T ss_pred HHHHHHHHHHhCCCCCCCCCcCCCcCeeEEEEEECHHh--hhhHHhcC----------------CCcEEEEEEE
Confidence 34444333323456899999999999999999999753 36666665 5799999763
No 50
>PRK01550 truB tRNA pseudouridine synthase B; Provisional
Probab=78.39 E-value=7.5 Score=35.65 Aligned_cols=56 Identities=13% Similarity=0.086 Sum_probs=40.6
Q ss_pred HHHHHHHhhcCCCCCCcccccCCCCCceEEEEEeCHHHHHHHHHHHHhccccccccccccccCCcceEEEEEEe
Q 023907 14 DELAATCLTYDYSEPPRLVHRLDRDSSGILVMGRTQTSATVLHSIFREKTFSASKEDNDNEKRILQRWYWALVV 87 (275)
Q Consensus 14 ~~l~~~~l~~~~~~~~~~vhRLD~~TSGllllAk~~~~a~~l~~~~~~~~~~~~~~~~~~~~~~v~K~Y~alv~ 87 (275)
.+.+...-+.....++...+-||-..||||+++-...+ ++.+.+.+ -.|+|.|.+.
T Consensus 16 ~dvv~~vrr~~~~kKvGH~GTLDP~AtGvL~i~vG~aT--kl~~~l~~----------------~~K~Y~a~~~ 71 (304)
T PRK01550 16 HDCVFKLRKILRTKKVGHTGTLDPEVSGVLPICVGRAT--KIAEYLTD----------------EGKTYEGEVT 71 (304)
T ss_pred HHHHHHHHHHcCCCCcccCCCCCCcCeeEEEEEEChhh--hhhHHhcC----------------CCcEEEEEEE
Confidence 44445343333456789999999999999999999743 35566665 5799999763
No 51
>COG0130 TruB Pseudouridine synthase [Translation, ribosomal structure and biogenesis]
Probab=74.76 E-value=9.4 Score=34.43 Aligned_cols=56 Identities=23% Similarity=0.102 Sum_probs=41.5
Q ss_pred HHHHHHHhhcCCCCCCcccccCCCCCceEEEEEeCHHHHHHHHHHHHhccccccccccccccCCcceEEEEEEe
Q 023907 14 DELAATCLTYDYSEPPRLVHRLDRDSSGILVMGRTQTSATVLHSIFREKTFSASKEDNDNEKRILQRWYWALVV 87 (275)
Q Consensus 14 ~~l~~~~l~~~~~~~~~~vhRLD~~TSGllllAk~~~~a~~l~~~~~~~~~~~~~~~~~~~~~~v~K~Y~alv~ 87 (275)
.+.+...-+.....+....+-||-..||+|+++-. + |.++.+.+.. -.|+|.|.+.
T Consensus 29 ~~~v~~vkkil~~~K~GH~GTLDP~atGvLpi~ig-~-aTKl~~~l~~----------------~~K~Y~a~~~ 84 (271)
T COG0130 29 HEVVAWVKRILGVEKAGHGGTLDPLATGVLPICLG-E-ATKLVQYLLD----------------ADKEYVATVR 84 (271)
T ss_pred HHHHHHHHHHhCccccccccccCCcccceEEEEec-h-hHhHHHHHhh----------------CCcEEEEEEE
Confidence 45555444444567889999999999999999999 3 3445555555 5799999874
No 52
>KOG2559 consensus Predicted pseudouridine synthase [Translation, ribosomal structure and biogenesis]
Probab=72.89 E-value=1.9 Score=38.09 Aligned_cols=23 Identities=35% Similarity=0.553 Sum_probs=20.7
Q ss_pred CCCcccccCCCCCceEEEEEeCH
Q 023907 27 EPPRLVHRLDRDSSGILVMGRTQ 49 (275)
Q Consensus 27 ~~~~~vhRLD~~TSGllllAk~~ 49 (275)
+.+.++||||-.||||+||+-+.
T Consensus 89 ~~V~v~h~l~~~~sgvl~~gVgh 111 (318)
T KOG2559|consen 89 EDVQVVHVLPLATSGVLLFGVGH 111 (318)
T ss_pred cceeeEEeecccccceEEEecCc
Confidence 56889999999999999999874
No 53
>PRK02755 truB tRNA pseudouridine synthase B; Provisional
Probab=71.71 E-value=13 Score=34.05 Aligned_cols=54 Identities=13% Similarity=0.111 Sum_probs=38.4
Q ss_pred HHHHHHHhhcCCCCCCcccccCCCCCceEEEEEeCHHHHHHHHHHHHhccccccccccccccCCcceEEEEEE
Q 023907 14 DELAATCLTYDYSEPPRLVHRLDRDSSGILVMGRTQTSATVLHSIFREKTFSASKEDNDNEKRILQRWYWALV 86 (275)
Q Consensus 14 ~~l~~~~l~~~~~~~~~~vhRLD~~TSGllllAk~~~~a~~l~~~~~~~~~~~~~~~~~~~~~~v~K~Y~alv 86 (275)
.+.+...-+.....++...+-||-..||||+++-...+ ++.+.+.. .|+|.|.+
T Consensus 17 ~dvv~~vrr~~~~kKvGH~GTLDP~AtGvL~i~vG~aT--kl~~~l~~-----------------~K~Y~a~~ 70 (295)
T PRK02755 17 HDCVARLRRLLRLKRVGHGGTLDPAATGVLPIALGKAT--RLLPYLPG-----------------EKTYRGTI 70 (295)
T ss_pred HHHHHHHHHHhCCCccccCCCCCCcCeeEEEEEEChhh--hhHHHhCC-----------------CcEEEEEE
Confidence 44445333333446899999999999999999999754 35554432 59999876
No 54
>TIGR00425 CBF5 rRNA pseudouridine synthase, putative. This family, found in archaea and eukaryotes, includes the only archaeal proteins markedly similar to bacterial TruB, the tRNA pseudouridine 55 synthase. However, among two related yeast proteins, the archaeal set matches yeast YLR175w far better than YNL292w. The first, termed centromere/microtubule binding protein 5 (CBF5), is an apparent rRNA pseudouridine synthase, while the second is the exclusive tRNA pseudouridine 55 synthase for both cytosolic and mitochondrial compartments. It is unclear whether archaeal proteins found by this model modify tRNA, rRNA, or both.
Probab=68.42 E-value=14 Score=34.16 Aligned_cols=55 Identities=22% Similarity=0.149 Sum_probs=39.5
Q ss_pred HHHHHHhhcCCCCCCcccccCCCCCceEEEEEeCHHHHHHHHHHHHhccccccccccccccCCcceEEEEEEe
Q 023907 15 ELAATCLTYDYSEPPRLVHRLDRDSSGILVMGRTQTSATVLHSIFREKTFSASKEDNDNEKRILQRWYWALVV 87 (275)
Q Consensus 15 ~l~~~~l~~~~~~~~~~vhRLD~~TSGllllAk~~~~a~~l~~~~~~~~~~~~~~~~~~~~~~v~K~Y~alv~ 87 (275)
+.+...-+.....++...+=||-..||||+++-... .++.+.+.+ -.|+|.|.+.
T Consensus 49 ~~v~~vr~~~~~kkvGH~GTLDP~A~GvL~v~~G~a--Tkl~~~~~~----------------~~K~Y~~~v~ 103 (322)
T TIGR00425 49 EVVAWVRRILNVEKTGHGGTLDPKVTGVLPVCIERA--TRLVKSLQE----------------APKEYVCLMR 103 (322)
T ss_pred HHHHHHHHHhcccccCCCCCCCCCCceEEEEEEChH--hhccHHhcc----------------CCCEEEEEEE
Confidence 344433332334688999999999999999999874 445566665 6899998763
No 55
>PRK04642 truB tRNA pseudouridine synthase B; Provisional
Probab=65.12 E-value=21 Score=32.71 Aligned_cols=55 Identities=15% Similarity=0.095 Sum_probs=40.1
Q ss_pred HHHHHHHhhcCCCCCCcccccCCCCCceEEEEEeCHHHHHHHHHHHHhccccccccccccccCCcceEEEEEE
Q 023907 14 DELAATCLTYDYSEPPRLVHRLDRDSSGILVMGRTQTSATVLHSIFREKTFSASKEDNDNEKRILQRWYWALV 86 (275)
Q Consensus 14 ~~l~~~~l~~~~~~~~~~vhRLD~~TSGllllAk~~~~a~~l~~~~~~~~~~~~~~~~~~~~~~v~K~Y~alv 86 (275)
.+.+...-+.....++...+=||-..||||+++-... .++.+.+.+ -.|+|.|.+
T Consensus 24 ~dvv~~vrr~~~~kKvGH~GTLDP~AtGvL~v~~G~a--Tkl~~~l~~----------------~~K~Y~a~~ 78 (300)
T PRK04642 24 NNALQAARRLLRAEKGGHTGSLDPLATGLLPLCFGEA--TKIAGLLLG----------------SAKAYDAEI 78 (300)
T ss_pred HHHHHHHHHHhCCCcccCCCccCCcCeeeEEEEEChh--hhhhHHhcC----------------CCcEEEEEE
Confidence 4455533333345678999999999999999999874 445566655 679999977
No 56
>cd02867 PseudoU_synth_TruB_4 PseudoU_synth_TruB_4: Pseudouridine synthase homolog 4. This group consists of Eukaryotic TruB proteins similar to Saccharomyces cerevisiae Pus4. S. cerevisiae Pus4, makes psi55 in the T loop of both cytoplasmic and mitochondrial tRNAs. Psi55 is almost universally conserved. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi).
Probab=49.80 E-value=35 Score=31.41 Aligned_cols=43 Identities=21% Similarity=0.136 Sum_probs=32.8
Q ss_pred CCCcccccCCCCCceEEEEEeCHHHHHHHHHHHHhccccccccccccccCCcceEEEEEEe
Q 023907 27 EPPRLVHRLDRDSSGILVMGRTQTSATVLHSIFREKTFSASKEDNDNEKRILQRWYWALVV 87 (275)
Q Consensus 27 ~~~~~vhRLD~~TSGllllAk~~~~a~~l~~~~~~~~~~~~~~~~~~~~~~v~K~Y~alv~ 87 (275)
.++...+-||-..||||+++-... .+.+ ..+.. ..|+|.+...
T Consensus 56 ~KiGH~GTLDPlAsGVLvvgvG~a-TK~l-~~~l~----------------~~K~Y~~~~~ 98 (312)
T cd02867 56 LKIGHGGTLDPLATGVLVVGVGAG-TKQL-QDYLS----------------CSKTYEATGL 98 (312)
T ss_pred cccccccccCCccceeEEEEECcH-HHHH-HHHhc----------------CCceEEEEEE
Confidence 478889999999999999999864 3334 34443 5799998763
No 57
>PF13021 DUF3885: Domain of unknown function (DUF3885)
Probab=27.90 E-value=96 Score=19.25 Aligned_cols=24 Identities=17% Similarity=0.281 Sum_probs=20.5
Q ss_pred CCceEEEEEeCHHHHHHHHHHHHh
Q 023907 38 DSSGILVMGRTQTSATVLHSIFRE 61 (275)
Q Consensus 38 ~TSGllllAk~~~~a~~l~~~~~~ 61 (275)
+-.|+-|+|+|++..+.+-..+.+
T Consensus 5 DDRGcdvia~~~~~i~~ly~~y~~ 28 (38)
T PF13021_consen 5 DDRGCDVIANNKERIRPLYEKYND 28 (38)
T ss_pred cCCCcEEeeCCHHHHHHHHHHHHH
Confidence 457999999999999988887765
Done!