Query 026613
Match_columns 236
No_of_seqs 191 out of 1620
Neff 7.8
Searched_HMMs 46136
Date Fri Mar 29 10:19:12 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/026613.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/026613hhsearch_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 2.7E-44 5.9E-49 318.8 16.5 174 8-235 137-314 (317)
2 COG0564 RluA Pseudouridylate s 100.0 2.9E-44 6.2E-49 313.9 14.7 163 6-225 122-289 (289)
3 PRK11112 tRNA pseudouridine sy 100.0 5.6E-43 1.2E-47 301.9 15.8 175 8-235 47-235 (257)
4 PRK11180 rluD 23S rRNA pseudou 100.0 2.8E-42 6E-47 306.9 16.6 179 7-235 131-313 (325)
5 TIGR00005 rluA_subfam pseudour 100.0 6.6E-42 1.4E-46 301.2 17.2 176 7-234 119-298 (299)
6 TIGR01621 RluA-like pseudourid 100.0 8.9E-42 1.9E-46 287.7 16.2 156 7-230 43-202 (217)
7 cd02563 PseudoU_synth_TruC tRN 100.0 1.7E-41 3.8E-46 287.1 15.6 164 8-224 46-223 (223)
8 PRK10158 23S rRNA/tRNA pseudou 100.0 1.8E-41 3.8E-46 286.3 15.6 159 7-224 56-218 (219)
9 cd02558 PSRA_1 PSRA_1: Pseudou 100.0 4.8E-40 1E-44 282.0 15.0 159 7-224 82-245 (246)
10 cd02557 PseudoU_synth_ScRIB2 P 100.0 8.2E-39 1.8E-43 269.0 13.9 148 7-227 59-212 (213)
11 cd02869 PseudoU_synth_RluCD_li 100.0 2.4E-35 5.1E-40 241.6 13.4 126 6-140 38-167 (185)
12 cd02550 PseudoU_synth_Rsu_Rlu_ 100.0 6.9E-28 1.5E-32 192.9 10.8 113 7-132 34-148 (154)
13 TIGR00093 pseudouridine syntha 99.9 6.1E-28 1.3E-32 187.6 6.3 109 11-139 1-111 (128)
14 KOG1919 RNA pseudouridylate sy 99.9 1.3E-26 2.8E-31 207.1 14.0 127 7-139 149-283 (371)
15 cd02870 PseudoU_synth_RsuA_lik 99.9 1.2E-26 2.6E-31 184.2 6.1 107 6-132 32-140 (146)
16 PF00849 PseudoU_synth_2: RNA 99.9 1.3E-25 2.7E-30 180.7 11.2 115 5-124 38-164 (164)
17 cd02556 PseudoU_synth_RluB Pse 99.9 2.1E-26 4.6E-31 186.7 6.6 111 6-136 34-146 (167)
18 cd02553 PseudoU_synth_RsuA Pse 99.9 4.2E-26 9.1E-31 185.0 5.3 110 7-139 35-146 (167)
19 PRK10839 16S rRNA pseudouridyl 99.9 1.2E-25 2.6E-30 191.3 5.3 108 7-136 94-203 (232)
20 cd02566 PseudoU_synth_RluE Pse 99.9 4.4E-24 9.6E-29 173.3 6.4 123 7-136 32-158 (168)
21 cd02555 PSSA_1 PSSA_1: Pseudou 99.9 4.1E-23 8.9E-28 168.8 5.6 107 6-138 45-155 (177)
22 PRK11394 23S rRNA pseudouridin 99.9 1.6E-22 3.4E-27 169.6 6.2 126 6-140 70-201 (217)
23 PRK10700 23S rRNA pseudouridyl 99.8 3.8E-19 8.2E-24 155.9 6.3 110 7-136 102-213 (289)
24 cd02554 PseudoU_synth_RluF Pse 99.7 2.1E-18 4.6E-23 139.2 6.1 108 6-137 31-140 (164)
25 PRK10475 23S rRNA pseudouridin 99.7 5.3E-17 1.1E-21 142.2 5.9 106 7-136 99-206 (290)
26 COG1187 RsuA 16S rRNA uridine- 99.7 1.5E-16 3.3E-21 135.5 6.8 112 7-137 100-214 (248)
27 cd02868 PseudoU_synth_hTruB2_l 97.9 9E-06 2E-10 68.9 3.7 41 8-48 34-76 (226)
28 cd01291 PseudoU_synth PseudoU_ 96.7 0.0075 1.6E-07 43.2 6.6 28 6-48 24-51 (87)
29 PF01509 TruB_N: TruB family p 77.8 3.2 7E-05 32.9 3.8 42 7-48 8-49 (149)
30 cd02572 PseudoU_synth_hDyskeri 75.7 3.1 6.7E-05 34.1 3.2 40 9-48 32-71 (182)
31 KOG2559 Predicted pseudouridin 66.7 2.6 5.7E-05 36.1 0.9 20 8-27 91-110 (318)
32 cd00506 PseudoU_synth_TruB_lik 66.6 6 0.00013 33.2 3.0 41 8-48 29-69 (210)
33 PRK04099 truB tRNA pseudouridi 57.9 12 0.00026 32.8 3.4 41 8-48 31-71 (273)
34 PRK00989 truB tRNA pseudouridi 57.2 14 0.00031 31.5 3.7 41 8-48 38-79 (230)
35 TIGR00431 TruB tRNA pseudourid 56.9 12 0.00027 31.4 3.2 41 8-48 31-71 (209)
36 cd02573 PseudoU_synth_EcTruB P 54.4 15 0.00031 32.3 3.4 40 9-48 30-69 (277)
37 PRK00020 truB tRNA pseudouridi 53.0 16 0.00034 31.5 3.3 38 11-48 42-79 (244)
38 PRK02193 truB tRNA pseudouridi 47.4 22 0.00047 31.3 3.4 41 8-48 29-69 (279)
39 PRK14123 tRNA pseudouridine sy 46.6 23 0.00051 31.5 3.5 41 8-48 32-72 (305)
40 PRK02484 truB tRNA pseudouridi 46.3 24 0.00053 31.2 3.5 41 8-48 32-72 (294)
41 PRK04270 H/ACA RNA-protein com 45.6 23 0.0005 31.3 3.3 40 9-48 52-91 (300)
42 PRK03287 truB tRNA pseudouridi 45.4 23 0.0005 31.4 3.3 41 8-48 38-78 (298)
43 PRK05389 truB tRNA pseudouridi 44.2 26 0.00057 31.2 3.4 40 9-48 43-82 (305)
44 PRK14124 tRNA pseudouridine sy 42.8 26 0.00055 31.3 3.1 40 9-48 33-72 (308)
45 PRK01851 truB tRNA pseudouridi 42.0 28 0.00061 30.9 3.3 38 11-48 48-85 (303)
46 PRK14122 tRNA pseudouridine sy 40.4 31 0.00067 30.8 3.3 37 12-48 34-70 (312)
47 PRK14846 truB tRNA pseudouridi 39.8 31 0.00067 31.2 3.2 41 8-48 32-72 (345)
48 PRK00130 truB tRNA pseudouridi 39.5 34 0.00074 30.2 3.4 40 9-48 32-71 (290)
49 PRK01550 truB tRNA pseudouridi 39.4 34 0.00074 30.4 3.4 38 11-48 34-71 (304)
50 PRK05033 truB tRNA pseudouridi 38.9 34 0.00075 30.5 3.3 39 10-48 41-79 (312)
51 PRK02755 truB tRNA pseudouridi 37.5 40 0.00087 29.9 3.5 38 9-48 33-71 (295)
52 PRK01528 truB tRNA pseudouridi 34.5 41 0.0009 29.7 3.1 40 9-48 33-72 (292)
53 TIGR00425 CBF5 rRNA pseudourid 32.9 45 0.00097 29.9 3.1 37 12-48 67-103 (322)
54 COG0130 TruB Pseudouridine syn 29.9 53 0.0011 28.7 3.0 37 12-48 48-84 (271)
55 PRK04642 truB tRNA pseudouridi 26.0 76 0.0016 28.2 3.3 37 12-48 43-79 (300)
56 cd02867 PseudoU_synth_TruB_4 P 23.6 83 0.0018 28.1 3.1 42 7-48 57-98 (312)
57 PF08892 YqcI_YcgG: YqcI/YcgG 21.3 68 0.0015 27.1 2.0 33 115-149 169-204 (219)
No 1
>PRK11025 23S rRNA pseudouridylate synthase C; Provisional
Probab=100.00 E-value=2.7e-44 Score=318.79 Aligned_cols=174 Identities=28% Similarity=0.398 Sum_probs=140.5
Q ss_pred ccccccCCCCcceeeeeecccch----hhhhccCccccEEEEEEeCccCCCceEEEccceeeecCCCceeeEEEEeCCcc
Q 026613 8 SHVYEKCIAVSSGIITVERVMYK----DNDNEKRILQRWYWALVVGTPRCSKGVISAPLGKVVVDNGKSDRITVVNNDQI 83 (236)
Q Consensus 8 ~~~vhRLD~~TSGllLlak~~~~----~~~~~~~~v~K~Y~Alv~G~~~~~~g~i~~~l~~~~~~~~~~~~~~~~~~~~~ 83 (236)
+++|||||++||||||||||..+ +.+|.++.|+|+|+|+|.|.++...|+|+.||.+.....+ .++....
T Consensus 137 ~~~vhRLD~~TSGlll~Ak~~~a~~~l~~~~~~~~v~K~Y~a~v~G~~~~~~~~i~~~i~~~~~~~~--~~~~~~~---- 210 (317)
T PRK11025 137 LELVHRLDRDTSGVLLVAKKRSALRSLHEQLREKGMQKDYLALVRGQWQSHVKVVQAPLLKNILQSG--ERIVRVS---- 210 (317)
T ss_pred CceeCCCCCCCceEEEEEcCHHHHHHHHHHHHhCCccEEEEEEEeCcccCCCceEecccccCcccCC--ceEEecC----
Confidence 57899999999999999999543 3367899999999999999998778999999986532111 1221111
Q ss_pred ccccceeeeEEEeeeCCCceEEEEEEeCCCchhHHHHHHhhhCCCceecCCCCCCcccccccccCCCCCccCCCcccccc
Q 026613 84 MSAQHAVTRYQVIKPSCHGYTWLKLSPLTGRKHQLRVHCAEVLGTPIVGDYKYGWQTHRKWKQFHPSDLSKDSNEEIPKE 163 (236)
Q Consensus 84 ~~~k~a~T~~~~l~~~~~~~slv~~~~~TGR~HQIR~hla~~lG~PIlGD~~Yg~~~~~~~~~~~~~~~~~~~~~~~~~~ 163 (236)
.+++.|.|+|++++.. .++|||+|+|.||||||||+|||+ +||||+||.+||..... ..+.
T Consensus 211 ~~gk~a~T~~~~l~~~-~~~sLv~~~~~TGRtHQIRvhla~-lG~PIlGD~~Yg~~~~~---------------~~~~-- 271 (317)
T PRK11025 211 QEGKPSETRFKVEERY-AFATLVRASPVTGRTHQIRVHTQY-AGHPIAFDDRYGDREFD---------------QQLT-- 271 (317)
T ss_pred CCCccceEEEEEeEEc-CCcEEEEEEeCCCCHHHHHHHHHH-CCCCEECCcccCCcccc---------------hhhh--
Confidence 2479999999999987 789999999999999999999997 99999999999964210 0000
Q ss_pred cccccccccCcCcccccccccccccccccccCcchhhhhhhcccCCcCCCCceEEEEcCCcHHHHHHHHHhc
Q 026613 164 KTLHFGLDLESGSILEKQPRLHLHCKEMTLPNVSQAIQKVQLSSGCDVSKLETLKLVAPLPSHMQRSWDVLN 235 (236)
Q Consensus 164 ~~~~~~~~~~~~~~~~~~~~l~LHA~~l~~~~p~~~~~~~~~~~~~~~~~~~~~~~~aplP~~~~~~~~~l~ 235 (236)
.....+++|||++|.|+|| .+++.+.|+||+|++|..+++.|.
T Consensus 272 --------------~~~~~r~~LHa~~l~f~~P---------------~~~~~~~~~aplP~~~~~~l~~l~ 314 (317)
T PRK11025 272 --------------GTGLNRLFLHAAALKFTHP---------------GTGEVMRIEAPLDEQLKRCLQKLR 314 (317)
T ss_pred --------------ccCCcchhhhcCcceeeCC---------------CCCCeEEEEcCCCHHHHHHHHHHh
Confidence 0013579999999999998 689999999999999999988764
No 2
>COG0564 RluA Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=2.9e-44 Score=313.91 Aligned_cols=163 Identities=32% Similarity=0.484 Sum_probs=135.6
Q ss_pred ccccccccCCCCcceeeeeecccch----hhhhccCccccEEEEEEeCccCCCceEEEccceeeecCCCceeeEEEEeCC
Q 026613 6 TASHVYEKCIAVSSGIITVERVMYK----DNDNEKRILQRWYWALVVGTPRCSKGVISAPLGKVVVDNGKSDRITVVNND 81 (236)
Q Consensus 6 ~~~~~vhRLD~~TSGllLlak~~~~----~~~~~~~~v~K~Y~Alv~G~~~~~~g~i~~~l~~~~~~~~~~~~~~~~~~~ 81 (236)
..+++|||||++||||||+|||..+ +.+|+++.+.|+|+|+|.|.++..+|+|+.|+.+... ...++.+...+
T Consensus 122 ~~~~~vHRLDkdTSGlll~AK~~~a~~~l~~~f~~r~v~K~Y~Alv~G~~~~~~~~i~~pi~r~~~---~~~~~~v~~~~ 198 (289)
T COG0564 122 ERPGIVHRLDKDTSGLLLVAKNREAARELSEQFKQRKVKKTYLALVRGHLPEDEGTIDAPIGRDPK---NRKKMAVVKEG 198 (289)
T ss_pred CceeeeccCCCCCceEEEEECCHHHHHHHHHHHhcCcCcEEEEEEEECcccCCCCEEeeeeecCCc---CCceEEEeccC
Confidence 3588999999999999999999643 3478899999999999999999888999999998632 22233444332
Q ss_pred ccccccceeeeEEEeeeCCCc-eEEEEEEeCCCchhHHHHHHhhhCCCceecCCCCCCcccccccccCCCCCccCCCccc
Q 026613 82 QIMSAQHAVTRYQVIKPSCHG-YTWLKLSPLTGRKHQLRVHCAEVLGTPIVGDYKYGWQTHRKWKQFHPSDLSKDSNEEI 160 (236)
Q Consensus 82 ~~~~~k~a~T~~~~l~~~~~~-~slv~~~~~TGR~HQIR~hla~~lG~PIlGD~~Yg~~~~~~~~~~~~~~~~~~~~~~~ 160 (236)
+++.|+|.|+++++. .. +||++|+|.||||||||+||++ +||||+||++||.....
T Consensus 199 ---~gk~A~T~~~~l~~~-~~~~tlv~~~~~TGRTHQIRVHl~~-lghPI~GD~~Yg~~~~~------------------ 255 (289)
T COG0564 199 ---SGKPAITHYEVLERF-GDNYTLVELKPETGRTHQIRVHLAH-LGHPIVGDPLYGGKDKS------------------ 255 (289)
T ss_pred ---CCCceEEEEEehhcc-CCceEEEEEEeCCCCHhHHHHHHHH-CCCCeeCCcccCCchhh------------------
Confidence 179999999999998 55 6999999999999999999997 99999999999985200
Q ss_pred ccccccccccccCcCcccccccccccccccccccCcchhhhhhhcccCCcCCCCceEEEEcCCcH
Q 026613 161 PKEKTLHFGLDLESGSILEKQPRLHLHCKEMTLPNVSQAIQKVQLSSGCDVSKLETLKLVAPLPS 225 (236)
Q Consensus 161 ~~~~~~~~~~~~~~~~~~~~~~~l~LHA~~l~~~~p~~~~~~~~~~~~~~~~~~~~~~~~aplP~ 225 (236)
. .....|++|||++|.|+|| .+++.+.|+||+|.
T Consensus 256 -------~---------~~~~~r~~LHA~~l~f~hp---------------~t~~~~~~~a~~p~ 289 (289)
T COG0564 256 -------A---------GAGLKRQALHAYKLSFTHP---------------LTGEELEFEAPLPE 289 (289)
T ss_pred -------c---------ccCcchhhhhhceeEccCC---------------CCCCEEEEecCCCC
Confidence 0 0115789999999999998 58999999999984
No 3
>PRK11112 tRNA pseudouridine synthase C; Provisional
Probab=100.00 E-value=5.6e-43 Score=301.94 Aligned_cols=175 Identities=29% Similarity=0.387 Sum_probs=137.0
Q ss_pred ccccccCCCCcceeeeeecccch----hhhhccCccccEEEEEEeCccCCCceEEEccceeeecCCCceeeEEEEeCCcc
Q 026613 8 SHVYEKCIAVSSGIITVERVMYK----DNDNEKRILQRWYWALVVGTPRCSKGVISAPLGKVVVDNGKSDRITVVNNDQI 83 (236)
Q Consensus 8 ~~~vhRLD~~TSGllLlak~~~~----~~~~~~~~v~K~Y~Alv~G~~~~~~g~i~~~l~~~~~~~~~~~~~~~~~~~~~ 83 (236)
+++|||||++||||||||||... ..+|+++.|+|+|+|+|.|.++ .+++++.|+....... ...+ ... .
T Consensus 47 ~~~VHRLDr~TSGlll~Ak~~~~~~~L~~~f~~~~v~K~Y~Alv~G~~~-~~~~i~~~l~~~~~~~--~~~~-~~~---~ 119 (257)
T PRK11112 47 VFTAHRLDRPTSGVLLMALSSEVARLLAQQFEQHQIQKTYHAIVRGWLM-EEAVLDYPLKEELDKI--ADKF-ARE---D 119 (257)
T ss_pred ceeeccCCCCCeeEEEEECCHHHHHHHHHHHHhCCcceEEEEEEEeEeC-CCCeEeeeeeeccccc--ceee-ccc---C
Confidence 57899999999999999999543 3367899999999999999886 4689999987632111 1111 111 2
Q ss_pred ccccceeeeEEEeeeC----------CCceEEEEEEeCCCchhHHHHHHhhhCCCceecCCCCCCcccccccccCCCCCc
Q 026613 84 MSAQHAVTRYQVIKPS----------CHGYTWLKLSPLTGRKHQLRVHCAEVLGTPIVGDYKYGWQTHRKWKQFHPSDLS 153 (236)
Q Consensus 84 ~~~k~a~T~~~~l~~~----------~~~~slv~~~~~TGR~HQIR~hla~~lG~PIlGD~~Yg~~~~~~~~~~~~~~~~ 153 (236)
..++.|.|.|++++.. ..+++|++|+|.||||||||+|||+ +||||+||.+||.....+
T Consensus 120 ~~~k~a~T~~~~l~~~~~~~~~~~~~~~~~slv~i~~~TGRtHQIRvhla~-lG~PIvGD~~Yg~~~~~~---------- 188 (257)
T PRK11112 120 KAPQPAVTHYRGLATVEMPVATGRYPTTRYSLVELEPKTGRKHQLRRHMAH-LRHPIIGDTKHGDLRQNR---------- 188 (257)
T ss_pred CCCeEeEEEEEEEEEecccccccccCCCCeEEEEEEcCCCChHHHHHHHHH-cCCCEeCCcccCCcccch----------
Confidence 3478999999999753 1358999999999999999999997 999999999999742110
Q ss_pred cCCCcccccccccccccccCcCcccccccccccccccccccCcchhhhhhhcccCCcCCCCceEEEEcCCcHHHHHHHHH
Q 026613 154 KDSNEEIPKEKTLHFGLDLESGSILEKQPRLHLHCKEMTLPNVSQAIQKVQLSSGCDVSKLETLKLVAPLPSHMQRSWDV 233 (236)
Q Consensus 154 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~LHA~~l~~~~p~~~~~~~~~~~~~~~~~~~~~~~~aplP~~~~~~~~~ 233 (236)
.+. ..++ ..+++|||++|.|+|| .+++.++|+||+|++|+.+++.
T Consensus 189 -----~~~----~~~~-----------~~rl~LHA~~L~F~hP---------------~t~e~~~~~a~~p~~~~~~~~~ 233 (257)
T PRK11112 189 -----SLA----EHFG-----------CSRLMLHASELSLTHP---------------FTGEPLTITAGLDETWQQLLSQ 233 (257)
T ss_pred -----hhh----hccC-----------CcchhHhhCccCccCC---------------CCCCEEEEEcCCCHHHHHHHHH
Confidence 000 0011 3689999999999998 6899999999999999999987
Q ss_pred hc
Q 026613 234 LN 235 (236)
Q Consensus 234 l~ 235 (236)
++
T Consensus 234 ~~ 235 (257)
T PRK11112 234 FG 235 (257)
T ss_pred cC
Confidence 75
No 4
>PRK11180 rluD 23S rRNA pseudouridine synthase D; Provisional
Probab=100.00 E-value=2.8e-42 Score=306.94 Aligned_cols=179 Identities=27% Similarity=0.393 Sum_probs=139.3
Q ss_pred cccccccCCCCcceeeeeecccch----hhhhccCccccEEEEEEeCccCCCceEEEccceeeecCCCceeeEEEEeCCc
Q 026613 7 ASHVYEKCIAVSSGIITVERVMYK----DNDNEKRILQRWYWALVVGTPRCSKGVISAPLGKVVVDNGKSDRITVVNNDQ 82 (236)
Q Consensus 7 ~~~~vhRLD~~TSGllLlak~~~~----~~~~~~~~v~K~Y~Alv~G~~~~~~g~i~~~l~~~~~~~~~~~~~~~~~~~~ 82 (236)
.+++|||||++||||||+|||... ..+|.++.|.|+|+|+|.|.++ .+|+|+.||.+.. ....++.+ .
T Consensus 131 ~~~~vhRLD~~TSGlll~Ak~~~~~~~l~~~~~~~~v~K~Y~A~v~G~~~-~~~~i~~~l~~~~---~~~~~~~~-~--- 202 (325)
T PRK11180 131 RAGIVHRLDKDTTGLMVVAKTVPAQTRLVEALQKREITREYEAVAIGHMT-AGGTVDEPISRHP---TKRTHMAV-H--- 202 (325)
T ss_pred ccceeccCCCCCceeEEEECCHHHHHHHHHHHHhCCcceEEEEEEecCCC-CCCEEECceecCC---CcCcEEEe-C---
Confidence 467999999999999999999433 3367889999999999999986 4689999997532 11112222 1
Q ss_pred cccccceeeeEEEeeeCCCceEEEEEEeCCCchhHHHHHHhhhCCCceecCCCCCCcccccccccCCCCCccCCCccccc
Q 026613 83 IMSAQHAVTRYQVIKPSCHGYTWLKLSPLTGRKHQLRVHCAEVLGTPIVGDYKYGWQTHRKWKQFHPSDLSKDSNEEIPK 162 (236)
Q Consensus 83 ~~~~k~a~T~~~~l~~~~~~~slv~~~~~TGR~HQIR~hla~~lG~PIlGD~~Yg~~~~~~~~~~~~~~~~~~~~~~~~~ 162 (236)
+.++.|.|.|+++... .++++++|+|+||||||||+|||+ +||||+||.+||..... .+....++..
T Consensus 203 -~~gk~a~T~~~~l~~~-~~~slv~~~~~TGRtHQIRvhla~-lG~PI~GD~~Yg~~~~~----------~~~~~~~~~~ 269 (325)
T PRK11180 203 -PMGKPAVTHYRIMEHF-RVHTRLRLRLETGRTHQIRVHMAH-ITHPLVGDQVYGGRPRP----------PKGASEEFIS 269 (325)
T ss_pred -CCCcEEeEEEEEeEEc-CCeEEEEEEeCCCCHHHHHHHHHh-CCCCEeCccccCCCccc----------ccccchhhhh
Confidence 2378999999999987 789999999999999999999998 99999999999975310 0000111100
Q ss_pred ccccccccccCcCcccccccccccccccccccCcchhhhhhhcccCCcCCCCceEEEEcCCcHHHHHHHHHhc
Q 026613 163 EKTLHFGLDLESGSILEKQPRLHLHCKEMTLPNVSQAIQKVQLSSGCDVSKLETLKLVAPLPSHMQRSWDVLN 235 (236)
Q Consensus 163 ~~~~~~~~~~~~~~~~~~~~~l~LHA~~l~~~~p~~~~~~~~~~~~~~~~~~~~~~~~aplP~~~~~~~~~l~ 235 (236)
. .....+++|||++|+|+|| .+++.+.|.||+|++|..+++.|.
T Consensus 270 ~--------------~~~~~r~~Lha~~l~f~hP---------------~~~~~~~~~a~~p~~~~~~~~~l~ 313 (325)
T PRK11180 270 T--------------LRKFDRQALHATMLRLYHP---------------ITGIEMEWHAPLPQDMVELIEALR 313 (325)
T ss_pred h--------------ccccchhhhhcceeEeeCC---------------CCCCeEEEECCChHHHHHHHHHhh
Confidence 0 0013589999999999998 589999999999999999998765
No 5
>TIGR00005 rluA_subfam pseudouridine synthase, RluA family. modifies uracil-65 in transfer RNAs to pseudouridine.
Probab=100.00 E-value=6.6e-42 Score=301.25 Aligned_cols=176 Identities=27% Similarity=0.374 Sum_probs=140.7
Q ss_pred cccccccCCCCcceeeeeecccch----hhhhccCccccEEEEEEeCccCCCceEEEccceeeecCCCceeeEEEEeCCc
Q 026613 7 ASHVYEKCIAVSSGIITVERVMYK----DNDNEKRILQRWYWALVVGTPRCSKGVISAPLGKVVVDNGKSDRITVVNNDQ 82 (236)
Q Consensus 7 ~~~~vhRLD~~TSGllLlak~~~~----~~~~~~~~v~K~Y~Alv~G~~~~~~g~i~~~l~~~~~~~~~~~~~~~~~~~~ 82 (236)
..++|||||++||||||||||... ..+|+++.|+|+|+|+|.|.++.++|+|+.||.+.... ...+.+...
T Consensus 119 ~~~~vhRLD~~TSGlll~ak~~~~~~~l~~~~~~~~v~K~Y~a~v~g~~~~~~~~i~~~l~~~~~~---~~~~~~~~~-- 193 (299)
T TIGR00005 119 RVGIVHRLDRDTSGLMVVAKTPLALRELQRQLKNRTVTKEYVALVHGQFDSGGGTVDAPLGRVPNN---RGLMAVHPS-- 193 (299)
T ss_pred cCceECCCCCCCceEEEEEcCHHHHHHHHHHHHhCCcceEEEEEEeccccCCCCEEeCceecCCCC---CceEEEecC--
Confidence 578999999999999999999543 33678999999999999999988889999999764211 112222221
Q ss_pred cccccceeeeEEEeeeCCCceEEEEEEeCCCchhHHHHHHhhhCCCceecCCCCCCcccccccccCCCCCccCCCccccc
Q 026613 83 IMSAQHAVTRYQVIKPSCHGYTWLKLSPLTGRKHQLRVHCAEVLGTPIVGDYKYGWQTHRKWKQFHPSDLSKDSNEEIPK 162 (236)
Q Consensus 83 ~~~~k~a~T~~~~l~~~~~~~slv~~~~~TGR~HQIR~hla~~lG~PIlGD~~Yg~~~~~~~~~~~~~~~~~~~~~~~~~ 162 (236)
.+++.|.|+|+++... .++++++|+|.|||+||||+||++ +||||+||.+||..... .+. .+.
T Consensus 194 -~~~k~a~t~~~~l~~~-~~~slv~~~l~tGR~HQIR~hla~-lG~pI~gD~~Yg~~~~~--~~~--------~~~---- 256 (299)
T TIGR00005 194 -SEGKPAVTHFRVLERF-GNASLVECELETGRTHQIRVHLQY-LGHPLAGDPLYGNKPVP--GNN--------LNG---- 256 (299)
T ss_pred -CCCCeeeEEEEEeEEc-CCeEEEEEEeCCCChHHHHHHHHH-CCCcEeCccccCCcccc--ccc--------ccc----
Confidence 2478999999999886 788999999999999999999998 99999999999974310 000 000
Q ss_pred ccccccccccCcCcccccccccccccccccccCcchhhhhhhcccCCcCCCCceEEEEcCCcHHHHHHHHHh
Q 026613 163 EKTLHFGLDLESGSILEKQPRLHLHCKEMTLPNVSQAIQKVQLSSGCDVSKLETLKLVAPLPSHMQRSWDVL 234 (236)
Q Consensus 163 ~~~~~~~~~~~~~~~~~~~~~l~LHA~~l~~~~p~~~~~~~~~~~~~~~~~~~~~~~~aplP~~~~~~~~~l 234 (236)
.....+++|||++|+|+|| .+++.+.|+||+|++|..+++.|
T Consensus 257 ---------------~~~~~r~~Lha~~l~f~~p---------------~~~~~~~~~a~~p~~~~~~~~~~ 298 (299)
T TIGR00005 257 ---------------LLNFDRQALHAYELGFIHP---------------ATGEILEFEAPLPADLVLLLEAL 298 (299)
T ss_pred ---------------ccCCcchhhccCeeeccCC---------------CCCCEEEEEcCChHHHHHHHHhh
Confidence 0014689999999999998 58999999999999999998765
No 6
>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=8.9e-42 Score=287.67 Aligned_cols=156 Identities=27% Similarity=0.412 Sum_probs=129.4
Q ss_pred cccccccCCCCcceeeeeecccch----hhhhccCccccEEEEEEeCccCCCceEEEccceeeecCCCceeeEEEEeCCc
Q 026613 7 ASHVYEKCIAVSSGIITVERVMYK----DNDNEKRILQRWYWALVVGTPRCSKGVISAPLGKVVVDNGKSDRITVVNNDQ 82 (236)
Q Consensus 7 ~~~~vhRLD~~TSGllLlak~~~~----~~~~~~~~v~K~Y~Alv~G~~~~~~g~i~~~l~~~~~~~~~~~~~~~~~~~~ 82 (236)
.+++|||||++||||||||||... ..+|+++.|+|+|+|+|.|.++..+|+|+.++.+.. .+ ...+..
T Consensus 43 ~~~~VhRLDr~TSGlll~Ak~~~~~~~L~~~~~~~~v~K~YlAlV~g~~~~~~~~i~~~~~~~~--~~---~~~~~~--- 114 (217)
T TIGR01621 43 QVWLVHRLDKMTSGILLLALNAESASELSQGFAKRKIEKTYLALSSKKPKKKQGLICGDMEKSR--RG---SWKLVN--- 114 (217)
T ss_pred CccEecCCCCCCceEEEEEcCHHHHHHHHHHHhcCCccEEEEEEEeccccCCCCEEeCCcccCC--CC---CEEEeC---
Confidence 578999999999999999999543 336889999999999999999888899999986531 11 122222
Q ss_pred cccccceeeeEEEeeeCCCceEEEEEEeCCCchhHHHHHHhhhCCCceecCCCCCCcccccccccCCCCCccCCCccccc
Q 026613 83 IMSAQHAVTRYQVIKPSCHGYTWLKLSPLTGRKHQLRVHCAEVLGTPIVGDYKYGWQTHRKWKQFHPSDLSKDSNEEIPK 162 (236)
Q Consensus 83 ~~~~k~a~T~~~~l~~~~~~~slv~~~~~TGR~HQIR~hla~~lG~PIlGD~~Yg~~~~~~~~~~~~~~~~~~~~~~~~~ 162 (236)
..++.+.|+|+++... .++++++|+|.|||+||||+||++ +||||+||.+||....
T Consensus 115 -~~~k~a~t~~~~~~~~-~~~slv~~~~~TGR~HQIRvhla~-lG~PIlGD~~Yg~~~~--------------------- 170 (217)
T TIGR01621 115 -SQENPAITRFFSASAA-TGLRLFILKPHTGKTHQLRVAMKS-LGSPILGDPLYGTTDE--------------------- 170 (217)
T ss_pred -CCCCceeEEEEEEEEc-CCeEEEEEEeCCCCHHHHHHHHHH-CCCceeCCcccCCCCC---------------------
Confidence 1368899999999987 789999999999999999999997 9999999999996320
Q ss_pred ccccccccccCcCcccccccccccccccccccCcchhhhhhhcccCCcCCCCceEEEEcCCcHHHHHH
Q 026613 163 EKTLHFGLDLESGSILEKQPRLHLHCKEMTLPNVSQAIQKVQLSSGCDVSKLETLKLVAPLPSHMQRS 230 (236)
Q Consensus 163 ~~~~~~~~~~~~~~~~~~~~~l~LHA~~l~~~~p~~~~~~~~~~~~~~~~~~~~~~~~aplP~~~~~~ 230 (236)
..+++|||++|.|++ +++.+.|.|| |++|...
T Consensus 171 ------------------~~~~~Lha~~l~f~~-----------------~~~~~~~~~~-~~~~~~~ 202 (217)
T TIGR01621 171 ------------------SDRGYLHAFALRFDY-----------------QNEVIQWLCD-PRQFQKW 202 (217)
T ss_pred ------------------ccCceeeeeEeEEEE-----------------CCeEEEEEEC-cHHHHHH
Confidence 247999999999997 4789999999 6666554
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=1.7e-41 Score=287.08 Aligned_cols=164 Identities=27% Similarity=0.347 Sum_probs=127.8
Q ss_pred ccccccCCCCcceeeeeecccch----hhhhccCccccEEEEEEeCccCCCceEEEccceeeecCCCceeeEEEEeCCcc
Q 026613 8 SHVYEKCIAVSSGIITVERVMYK----DNDNEKRILQRWYWALVVGTPRCSKGVISAPLGKVVVDNGKSDRITVVNNDQI 83 (236)
Q Consensus 8 ~~~vhRLD~~TSGllLlak~~~~----~~~~~~~~v~K~Y~Alv~G~~~~~~g~i~~~l~~~~~~~~~~~~~~~~~~~~~ 83 (236)
.++|||||++||||||||||... ..+|+++.|+|+|+|+|.|.++. +|+|+.++.+... ......+...
T Consensus 46 ~~~vhRLD~~TSGlll~Ak~~~~~~~l~~~f~~~~v~K~Y~alv~G~~~~-~~~i~~~l~~~~~---~~~~~~~~~~--- 118 (223)
T cd02563 46 VYPVHRLDRPTSGVLLFALSSEVARKLGEQFTEHRVHKTYLAVVRGYVPE-SGTIDYPLSEELD---KLADKFASDD--- 118 (223)
T ss_pred cccccCCCCCCeEEEEEEECHHHHHHHHHHHhcCceeEEEEEEEECccCC-CCeEEEeeeeCCC---ccceEEeecC---
Confidence 67899999999999999999543 33678999999999999999876 7899999876421 1111112111
Q ss_pred ccccceeeeEEEeeeC----------CCceEEEEEEeCCCchhHHHHHHhhhCCCceecCCCCCCcccccccccCCCCCc
Q 026613 84 MSAQHAVTRYQVIKPS----------CHGYTWLKLSPLTGRKHQLRVHCAEVLGTPIVGDYKYGWQTHRKWKQFHPSDLS 153 (236)
Q Consensus 84 ~~~k~a~T~~~~l~~~----------~~~~slv~~~~~TGR~HQIR~hla~~lG~PIlGD~~Yg~~~~~~~~~~~~~~~~ 153 (236)
..++.+.|.|++++.. ..+++|++|+|.||||||||+|||+ +||||+||.+||......
T Consensus 119 ~~~~~a~t~~~~l~~~~~~~~~~~~~~~~~slv~~~~~TGR~HQIRvhla~-lG~PIvGD~~Yg~~~~~~---------- 187 (223)
T cd02563 119 KAPQAATTHYRLLAVEELPVVVGKYPTSRYSLVELTPHTGRKHQLRRHLAH-IRHPIIGDTTHGDGRHNR---------- 187 (223)
T ss_pred CCCceeEEEEEEeeecccccccccCCCCCeEEEEEEeCCCCHHHHHHHHHH-cCCCeeCCcccCCcccCh----------
Confidence 2478999999999752 1358999999999999999999997 999999999999753110
Q ss_pred cCCCcccccccccccccccCcCcccccccccccccccccccCcchhhhhhhcccCCcCCCCceEEEEcCCc
Q 026613 154 KDSNEEIPKEKTLHFGLDLESGSILEKQPRLHLHCKEMTLPNVSQAIQKVQLSSGCDVSKLETLKLVAPLP 224 (236)
Q Consensus 154 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~LHA~~l~~~~p~~~~~~~~~~~~~~~~~~~~~~~~aplP 224 (236)
.+. ..+ ...+++|||++|.|+|| .+++.+.|+||+|
T Consensus 188 -----~~~----~~~-----------~~~rl~Lha~~L~F~hP---------------~t~~~~~~~a~~~ 223 (223)
T cd02563 188 -----FFR----EHF-----------GCHRLLLAATRLEFTHP---------------VTGERLLIEAPLD 223 (223)
T ss_pred -----hHH----hhc-----------CCccceeecCeeEeeCC---------------CCCCeEEEEccCC
Confidence 000 001 14689999999999998 6999999999987
No 8
>PRK10158 23S rRNA/tRNA pseudouridine synthase A; Provisional
Probab=100.00 E-value=1.8e-41 Score=286.28 Aligned_cols=159 Identities=28% Similarity=0.399 Sum_probs=129.1
Q ss_pred cccccccCCCCcceeeeeecccch----hhhhccCccccEEEEEEeCccCCCceEEEccceeeecCCCceeeEEEEeCCc
Q 026613 7 ASHVYEKCIAVSSGIITVERVMYK----DNDNEKRILQRWYWALVVGTPRCSKGVISAPLGKVVVDNGKSDRITVVNNDQ 82 (236)
Q Consensus 7 ~~~~vhRLD~~TSGllLlak~~~~----~~~~~~~~v~K~Y~Alv~G~~~~~~g~i~~~l~~~~~~~~~~~~~~~~~~~~ 82 (236)
.+++|||||++||||||+|||... ..+|.++.|+|+|+|+|.|.++..+++++.|+..... ...++.+..
T Consensus 56 ~~~~vhRLDr~TSGlll~Akt~~~~~~l~~~f~~~~v~K~Yla~v~G~~~~~~~~i~~~i~~~~~---~~~~~~~~~--- 129 (219)
T PRK10158 56 QAESVHRLDMATSGVIVVALTKAAERELKRQFREREPKKQYVARVWGHPSPAEGLVDLPLICDWP---NRPKQKVCY--- 129 (219)
T ss_pred CCCEECCCCCCCceEEEEECCHHHHHHHHHHHHhCCccEEEEEEEecccCCCCcEEecceecCCC---CCceEEecC---
Confidence 467999999999999999999443 3467899999999999999998888999999876421 111222221
Q ss_pred cccccceeeeEEEeeeCCCceEEEEEEeCCCchhHHHHHHhhhCCCceecCCCCCCcccccccccCCCCCccCCCccccc
Q 026613 83 IMSAQHAVTRYQVIKPSCHGYTWLKLSPLTGRKHQLRVHCAEVLGTPIVGDYKYGWQTHRKWKQFHPSDLSKDSNEEIPK 162 (236)
Q Consensus 83 ~~~~k~a~T~~~~l~~~~~~~slv~~~~~TGR~HQIR~hla~~lG~PIlGD~~Yg~~~~~~~~~~~~~~~~~~~~~~~~~ 162 (236)
.+++.+.|.|++++......++++|+|+||||||||+||++ +||||+||.+||.....
T Consensus 130 -~~gk~a~t~~~~l~~~~~~~sll~~~~~TGRtHQIR~hla~-lG~PIvGD~~Yg~~~~~-------------------- 187 (219)
T PRK10158 130 -ETGKPAQTEYEVVEYAADNTARVVLKPITGRSHQLRVHMLA-LGHPILGDRFYASPEAR-------------------- 187 (219)
T ss_pred -CCCceeeEEEEEEEEcCCCCEEEEEEeCCCCHHHHHHHHHH-CCCcEECCcccCCcccc--------------------
Confidence 24789999999999863345899999999999999999997 99999999999964210
Q ss_pred ccccccccccCcCcccccccccccccccccccCcchhhhhhhcccCCcCCCCceEEEEcCCc
Q 026613 163 EKTLHFGLDLESGSILEKQPRLHLHCKEMTLPNVSQAIQKVQLSSGCDVSKLETLKLVAPLP 224 (236)
Q Consensus 163 ~~~~~~~~~~~~~~~~~~~~~l~LHA~~l~~~~p~~~~~~~~~~~~~~~~~~~~~~~~aplP 224 (236)
...++++|||++|.|+|| .+++.++|.||.|
T Consensus 188 ----------------~~~~r~~Lha~~l~f~~P---------------~~~~~~~~~a~~~ 218 (219)
T PRK10158 188 ----------------AMAPRLLLHAEMLTITHP---------------AYGNSMTFKAPAD 218 (219)
T ss_pred ----------------ccccchhhhhCccCccCC---------------CCCCeEEEEeCCC
Confidence 003579999999999998 5899999999976
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=4.8e-40 Score=282.01 Aligned_cols=159 Identities=21% Similarity=0.233 Sum_probs=124.2
Q ss_pred cccccccCCCCcceeeeeecccch----hhhhccCccccEEEEEEeCccCCCce-EEEccceeeecCCCceeeEEEEeCC
Q 026613 7 ASHVYEKCIAVSSGIITVERVMYK----DNDNEKRILQRWYWALVVGTPRCSKG-VISAPLGKVVVDNGKSDRITVVNND 81 (236)
Q Consensus 7 ~~~~vhRLD~~TSGllLlak~~~~----~~~~~~~~v~K~Y~Alv~G~~~~~~g-~i~~~l~~~~~~~~~~~~~~~~~~~ 81 (236)
..++|||||++||||||||||... +.+|++++|+|+|+|+|.|.++...+ .++.++.+.. ...++...
T Consensus 82 ~~~~vhRLD~~TSGlll~Ak~~~~~~~l~~~~~~~~v~K~YlA~v~G~~~~~~~~~~~~~i~~~~----~~~~~~~~--- 154 (246)
T cd02558 82 DLTPAHRLDRLTAGLVLFSKRPETRGAYQTLFARREVSKTYEAVAPYVPALTFPLTVRSRIVKGR----GFFQAREV--- 154 (246)
T ss_pred cccccccCCCCceeEEEEEcCHHHHHHHHHHHHcCCccEEEEEEEecCCCCCCCcceeccccccC----Ccceeecc---
Confidence 467899999999999999999543 34688999999999999998865444 4666665421 11122111
Q ss_pred ccccccceeeeEEEeeeCCCceEEEEEEeCCCchhHHHHHHhhhCCCceecCCCCCCcccccccccCCCCCccCCCcccc
Q 026613 82 QIMSAQHAVTRYQVIKPSCHGYTWLKLSPLTGRKHQLRVHCAEVLGTPIVGDYKYGWQTHRKWKQFHPSDLSKDSNEEIP 161 (236)
Q Consensus 82 ~~~~~k~a~T~~~~l~~~~~~~slv~~~~~TGR~HQIR~hla~~lG~PIlGD~~Yg~~~~~~~~~~~~~~~~~~~~~~~~ 161 (236)
.+++.+.|+|++++.. .++++++|+|.|||+||||+|||+ +||||+||.+||...... .
T Consensus 155 --~~~~~a~T~~~~l~~~-~~~slv~~~l~TGRtHQIRvhla~-lG~PIvGD~~Yg~~~~~~-------------~---- 213 (246)
T cd02558 155 --EGEPNAETRIELLARR-GGWGLYRLSPHTGKTHQLRVHMAA-LGVPILNDPFYPVLLDKD-------------P---- 213 (246)
T ss_pred --CCCCCceEEEEEEEec-CCeEEEEEEeCCCCHHHHHHHHHH-CCCcccCCccCCCCCccc-------------c----
Confidence 1257899999999987 789999999999999999999997 999999999998642100 0
Q ss_pred cccccccccccCcCcccccccccccccccccccCcchhhhhhhcccCCcCCCCceEEEEcCCc
Q 026613 162 KEKTLHFGLDLESGSILEKQPRLHLHCKEMTLPNVSQAIQKVQLSSGCDVSKLETLKLVAPLP 224 (236)
Q Consensus 162 ~~~~~~~~~~~~~~~~~~~~~~l~LHA~~l~~~~p~~~~~~~~~~~~~~~~~~~~~~~~aplP 224 (236)
. ....+++|||++|.|+|| .+++.+.|+||+|
T Consensus 214 -------------~---~~~~~~~Lha~~l~f~hP---------------~t~~~~~~~~~~~ 245 (246)
T cd02558 214 -------------D---DFSRPLQLLAKELEFTDP---------------LTGRPRRFESGRS 245 (246)
T ss_pred -------------c---ccccCchhhhcccCccCC---------------CCCCEEEEecCCC
Confidence 0 001358999999999998 6899999999997
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=8.2e-39 Score=268.98 Aligned_cols=148 Identities=23% Similarity=0.286 Sum_probs=122.7
Q ss_pred cccccccCCCCcceeeeeecccch----hhhhccCccccEEEEEEeCccCCCceEEEccceeeecCCCceeeEEEEeCCc
Q 026613 7 ASHVYEKCIAVSSGIITVERVMYK----DNDNEKRILQRWYWALVVGTPRCSKGVISAPLGKVVVDNGKSDRITVVNNDQ 82 (236)
Q Consensus 7 ~~~~vhRLD~~TSGllLlak~~~~----~~~~~~~~v~K~Y~Alv~G~~~~~~g~i~~~l~~~~~~~~~~~~~~~~~~~~ 82 (236)
...+|||||++||||||||||... ..+|.++.++|+|+|+|.|.++..+++++.|+.+..... .+....
T Consensus 59 ~~~~vhRLD~~TSGllllak~~~~~~~l~~~f~~~~v~K~Y~a~v~G~~~~~~~~i~~~l~~~~~~~----~~~~~~--- 131 (213)
T cd02557 59 ELRPCHRLDRLTSGLLLFAKTSQTASRLQQQIRSREVKKEYLARVKGEFPDGEVVVDQPIGLVSPKG----GLRNDV--- 131 (213)
T ss_pred CccCccCCCCCCceEEEEECCHHHHHHHHHHHHcCCccEEEEEEEeCcCCCCCeEEecceeccCcCC----ceeecc---
Confidence 467899999999999999999543 235678899999999999999888899999997642211 111111
Q ss_pred cccccceeeeEEEeeeCCC--ceEEEEEEeCCCchhHHHHHHhhhCCCceecCCCCCCcccccccccCCCCCccCCCccc
Q 026613 83 IMSAQHAVTRYQVIKPSCH--GYTWLKLSPLTGRKHQLRVHCAEVLGTPIVGDYKYGWQTHRKWKQFHPSDLSKDSNEEI 160 (236)
Q Consensus 83 ~~~~k~a~T~~~~l~~~~~--~~slv~~~~~TGR~HQIR~hla~~lG~PIlGD~~Yg~~~~~~~~~~~~~~~~~~~~~~~ 160 (236)
...++.|.|.|+++... . +++|++|+|.|||+||||+||++ +||||+||.+||.
T Consensus 132 ~~~~~~a~t~~~~~~~~-~~~~~slv~v~~~TGR~HQIR~hla~-lG~PIlGD~~Yg~---------------------- 187 (213)
T cd02557 132 DEKGKDARTIFKRLSYN-GDLNTSVVLCKPITGRTHQIRVHLQY-LGHPIVNDPIYNN---------------------- 187 (213)
T ss_pred CCCCceeeEEEEEEEEc-CCCCeEEEEEEeCCCCHHHHHHHHHH-CCCCCcCccccCC----------------------
Confidence 12478999999999886 4 78999999999999999999997 9999999999985
Q ss_pred ccccccccccccCcCcccccccccccccccccccCcchhhhhhhcccCCcCCCCceEEEEcCCcHHH
Q 026613 161 PKEKTLHFGLDLESGSILEKQPRLHLHCKEMTLPNVSQAIQKVQLSSGCDVSKLETLKLVAPLPSHM 227 (236)
Q Consensus 161 ~~~~~~~~~~~~~~~~~~~~~~~l~LHA~~l~~~~p~~~~~~~~~~~~~~~~~~~~~~~~aplP~~~ 227 (236)
.+++|||++|.|+ .++|++|+|.+|
T Consensus 188 ---------------------~~l~Lha~~l~f~---------------------~~~~~~~~p~~~ 212 (213)
T cd02557 188 ---------------------LGIYLHALRYEGP---------------------DWSYETELPDWA 212 (213)
T ss_pred ---------------------cChhhhhccCcCc---------------------cEEEEeCCCccc
Confidence 1489999999995 569999999876
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=2.4e-35 Score=241.63 Aligned_cols=126 Identities=34% Similarity=0.496 Sum_probs=102.3
Q ss_pred ccccccccCCCCcceeeeeecccchh----hhhccCccccEEEEEEeCccCCCceEEEccceeeecCCCceeeEEEEeCC
Q 026613 6 TASHVYEKCIAVSSGIITVERVMYKD----NDNEKRILQRWYWALVVGTPRCSKGVISAPLGKVVVDNGKSDRITVVNND 81 (236)
Q Consensus 6 ~~~~~vhRLD~~TSGllLlak~~~~~----~~~~~~~v~K~Y~Alv~G~~~~~~g~i~~~l~~~~~~~~~~~~~~~~~~~ 81 (236)
...++|||||++||||||||+|.... ..|+++.++|+|+|+|.|.++...+.++.++.... ..........
T Consensus 38 ~~~~~v~RLD~~tsGlll~ak~~~~~~~l~~~~~~~~~~K~Y~a~v~g~~~~~~~~~~~~~~~~~---~~~~~~~~~~-- 112 (185)
T cd02869 38 FRPGLVHRLDKDTSGLLLVAKNKKAAAKLSKQFKERKVKKTYLALVDGKPPEDEGTIDAPLGRKK---RKKRARVVVS-- 112 (185)
T ss_pred CcCceecccCCCCceEEEEEcCHHHHHHHHHHHhcCceeEEEEEEEeCCCCCCccEEecccccCC---ccCceEEEEC--
Confidence 45789999999999999999995432 24668899999999999999888888888886531 1111111111
Q ss_pred ccccccceeeeEEEeeeCCCceEEEEEEeCCCchhHHHHHHhhhCCCceecCCCCCCcc
Q 026613 82 QIMSAQHAVTRYQVIKPSCHGYTWLKLSPLTGRKHQLRVHCAEVLGTPIVGDYKYGWQT 140 (236)
Q Consensus 82 ~~~~~k~a~T~~~~l~~~~~~~slv~~~~~TGR~HQIR~hla~~lG~PIlGD~~Yg~~~ 140 (236)
.+++.+.|+|+++... .++++++|+|.|||+||||+||++ +||||+||.+||...
T Consensus 113 --~~~~~~~t~~~~l~~~-~~~s~~~~~l~tGR~HQIR~hl~~-~G~pIvGD~~Yg~~~ 167 (185)
T cd02869 113 --EDGKPAITHYKVLERF-GNVTLVELQLETGRTHQIRVHLAS-IGHPIVGDPKYGGKA 167 (185)
T ss_pred --CCCeEEEEEEEEEEEc-CCcEEEEEEeCcCCccHHHHHHHH-CCCCEeCccccCCcc
Confidence 2368999999999886 688999999999999999999997 999999999999754
No 12
>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=99.95 E-value=6.9e-28 Score=192.88 Aligned_cols=113 Identities=26% Similarity=0.333 Sum_probs=88.5
Q ss_pred cccccccCCCCcceeeeeecccchh--hhhccCccccEEEEEEeCccCCCceEEEccceeeecCCCceeeEEEEeCCccc
Q 026613 7 ASHVYEKCIAVSSGIITVERVMYKD--NDNEKRILQRWYWALVVGTPRCSKGVISAPLGKVVVDNGKSDRITVVNNDQIM 84 (236)
Q Consensus 7 ~~~~vhRLD~~TSGllLlak~~~~~--~~~~~~~v~K~Y~Alv~G~~~~~~g~i~~~l~~~~~~~~~~~~~~~~~~~~~~ 84 (236)
..++|||||++||||||||+|.... +...++.++|+|+|+|.|.++. ++.++.++... . .... +.. .
T Consensus 34 ~~~~vhRLD~~TSGlll~ak~~~~~~~l~~~~~~v~K~Y~a~v~g~~~~-~~~~~~~~~~~----~-~~~~-~~~----~ 102 (154)
T cd02550 34 RVHAAGRLDKDTSGLLLLTNDGRLQRRLTEPRREIEKEYLVTVRGELDE-EGIEDLATVRR----G-RLSG-LVD----E 102 (154)
T ss_pred ceeEeccCCCCCeeEEEEEcCHHHHHHHhhhhccCcEEEEEEEEeecCc-chheecccccc----C-ccee-EEc----C
Confidence 4678999999999999999995433 3334788999999999999874 56666665441 1 1111 121 2
Q ss_pred cccceeeeEEEeeeCCCceEEEEEEeCCCchhHHHHHHhhhCCCceec
Q 026613 85 SAQHAVTRYQVIKPSCHGYTWLKLSPLTGRKHQLRVHCAEVLGTPIVG 132 (236)
Q Consensus 85 ~~k~a~T~~~~l~~~~~~~slv~~~~~TGR~HQIR~hla~~lG~PIlG 132 (236)
+++.+.|+|++++.. .++++++|+|.|||+||||+|||+ +||||.-
T Consensus 103 ~~~~~~t~~~~l~~~-~~~sll~~~l~tGR~HQIR~hla~-~G~pI~~ 148 (154)
T cd02550 103 GVPLAVTKVRVIGEH-GGTGRLRLTLKTGRTHQIRRHCAA-VGFPVLR 148 (154)
T ss_pred CCcccceEEEEEEec-CCcEEEEEEEcCCCcHHHHHHHHH-cCCcEEe
Confidence 367899999999876 678999999999999999999997 9999974
No 13
>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=6.1e-28 Score=187.60 Aligned_cols=109 Identities=17% Similarity=0.222 Sum_probs=84.6
Q ss_pred cccCCCCcceeeeeecccch--hhhhccCccccEEEEEEeCccCCCceEEEccceeeecCCCceeeEEEEeCCccccccc
Q 026613 11 YEKCIAVSSGIITVERVMYK--DNDNEKRILQRWYWALVVGTPRCSKGVISAPLGKVVVDNGKSDRITVVNNDQIMSAQH 88 (236)
Q Consensus 11 vhRLD~~TSGllLlak~~~~--~~~~~~~~v~K~Y~Alv~G~~~~~~g~i~~~l~~~~~~~~~~~~~~~~~~~~~~~~k~ 88 (236)
|||||++||||||||+|... .+..+++.|+|+|+|+|.|.++.+. ++ ++. .+ +.+ + +++.
T Consensus 1 v~RLD~~TSGlll~akd~~~~~~L~~~~~~i~K~Y~a~v~g~~~~~~--~~-~~~-----~g----~~~-~-----~~~~ 62 (128)
T TIGR00093 1 AGRLDRDSEGLLLLTNDGELVHRLTHPGHHCEKTYLVTVEGPVTDED--LE-ALR-----KG----VQL-E-----DGPT 62 (128)
T ss_pred CCCCCCCCEEEEEEEeCHHHHHHHhCCCCCCCeEEEEEECCCCCHHH--HH-HHh-----CC----eEE-C-----CcEE
Confidence 79999999999999999543 3345788899999999999886532 11 111 11 111 1 1456
Q ss_pred eeeeEEEeeeCCCceEEEEEEeCCCchhHHHHHHhhhCCCceecCCCCCCc
Q 026613 89 AVTRYQVIKPSCHGYTWLKLSPLTGRKHQLRVHCAEVLGTPIVGDYKYGWQ 139 (236)
Q Consensus 89 a~T~~~~l~~~~~~~slv~~~~~TGR~HQIR~hla~~lG~PIlGD~~Yg~~ 139 (236)
+.+.|++++.. .+.++++|+|.|||+||||+||++ +||||+||..+.-.
T Consensus 63 ~~~~~~~l~~~-~~~~~l~~~l~tGR~HQIR~~~~~-lG~pI~g~~R~~~g 111 (128)
T TIGR00093 63 KPAKLEVITEP-GFPTWLRITLSEGRNRQVRRMFAA-VGFPVLRLHRVRIG 111 (128)
T ss_pred eeeEEEEEccC-CCceEEEEEEeCCCCHHHHHHHHH-cCCeEeEEEEEEEC
Confidence 77889999765 567899999999999999999998 99999999988644
No 14
>KOG1919 consensus RNA pseudouridylate synthases [RNA processing and modification]
Probab=99.94 E-value=1.3e-26 Score=207.08 Aligned_cols=127 Identities=28% Similarity=0.396 Sum_probs=99.9
Q ss_pred cccccccCCCCcceeeeeecccch----hhhhccCccccEE-EEEEeCccC-CCceEEEccceeeecCCCceeeEEEEeC
Q 026613 7 ASHVYEKCIAVSSGIITVERVMYK----DNDNEKRILQRWY-WALVVGTPR-CSKGVISAPLGKVVVDNGKSDRITVVNN 80 (236)
Q Consensus 7 ~~~~vhRLD~~TSGllLlak~~~~----~~~~~~~~v~K~Y-~Alv~G~~~-~~~g~i~~~l~~~~~~~~~~~~~~~~~~ 80 (236)
-++.+||||+.|||||+|||+... ..++.+++++|.| .|-|.|.++ ...-++..++.... . ..++.+...
T Consensus 149 ~~~~~hRLDr~tSGllvlAkt~~~~~~~~~~~r~~~~~k~Y~v~~v~g~fp~~~~~~i~~~~~~~~---~-~~~~~l~~~ 224 (371)
T KOG1919|consen 149 GLRPCHRLDRLTSGLLVLAKTKEAADKFHEVLRKRTVKKEYVVARVEGPFPVVGEVEIKEPIGEEE---R-PLRMGLNAV 224 (371)
T ss_pred ccccccccCccccceEEEEechhHhHHHHHHHhcccceeEEEEEEEeccCCCCceEEeCCCccccc---c-ccceEeeec
Confidence 378999999999999999999543 2357888999999 799999987 33445666665431 1 123333322
Q ss_pred Cc--cccccceeeeEEEeeeCCCceEEEEEEeCCCchhHHHHHHhhhCCCceecCCCCCCc
Q 026613 81 DQ--IMSAQHAVTRYQVIKPSCHGYTWLKLSPLTGRKHQLRVHCAEVLGTPIVGDYKYGWQ 139 (236)
Q Consensus 81 ~~--~~~~k~a~T~~~~l~~~~~~~slv~~~~~TGR~HQIR~hla~~lG~PIlGD~~Yg~~ 139 (236)
.. ...++.|.|.|++++.. +..++|+|+|+||||||||+||+. +|+||+||.+|++.
T Consensus 225 ~~~~~~~~k~a~T~~~~~~~~-~~ss~V~~~PlTGRtHQIRvHlq~-lG~PI~gD~~Y~~~ 283 (371)
T KOG1919|consen 225 GVRDEVAAKDAKTLFKVLSYD-GGSSLVECRPLTGRTHQIRVHLQY-LGHPIAGDPKYGNH 283 (371)
T ss_pred ccccccccccceeEEEEcccC-CceEEEEeeccCCcHHHHHHHHHH-hCCCcCCCcccccc
Confidence 21 13479999999999998 899999999999999999999996 99999999999874
No 15
>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=1.2e-26 Score=184.15 Aligned_cols=107 Identities=14% Similarity=0.166 Sum_probs=83.5
Q ss_pred ccccccccCCCCcceeeeeecccch--hhhhccCccccEEEEEEeCccCCCceEEEccceeeecCCCceeeEEEEeCCcc
Q 026613 6 TASHVYEKCIAVSSGIITVERVMYK--DNDNEKRILQRWYWALVVGTPRCSKGVISAPLGKVVVDNGKSDRITVVNNDQI 83 (236)
Q Consensus 6 ~~~~~vhRLD~~TSGllLlak~~~~--~~~~~~~~v~K~Y~Alv~G~~~~~~g~i~~~l~~~~~~~~~~~~~~~~~~~~~ 83 (236)
....+|||||++||||||||+|... .+..+++.++|+|+|+|.|.++.+.. ... .. .+ ...
T Consensus 32 ~~~~~vhRLD~~TsGlll~ak~~~~~~~l~~~~~~i~K~Y~a~v~g~~~~~~~--~~~------~~----~~-~~~---- 94 (146)
T cd02870 32 ERLFPVGRLDYDTEGLLLLTNDGELANRLTHPRYGVEKTYLVKVRGVPSEEEL--RRL------RA----GV-ELD---- 94 (146)
T ss_pred CCEEECCCCCCCCeeEEEEeCCHHHHHHhhCccCCCCeEEEEEECCCCCHHHH--HHH------HC----Ce-EeC----
Confidence 3568899999999999999999543 33446778999999999999865331 110 01 11 111
Q ss_pred ccccceeeeEEEeeeCCCceEEEEEEeCCCchhHHHHHHhhhCCCceec
Q 026613 84 MSAQHAVTRYQVIKPSCHGYTWLKLSPLTGRKHQLRVHCAEVLGTPIVG 132 (236)
Q Consensus 84 ~~~k~a~T~~~~l~~~~~~~slv~~~~~TGR~HQIR~hla~~lG~PIlG 132 (236)
+++.+.|+|++++.. .++++++|+|.|||+||||+||++ +||||+-
T Consensus 95 -~~~~~~t~~~~l~~~-~~~sll~~~l~tGR~HQIR~hla~-~G~pI~~ 140 (146)
T cd02870 95 -DGKTAPAKVKVLSRD-PKNTLLEVTLHEGRNRQVRRMFEA-VGHPVLR 140 (146)
T ss_pred -CceEcceEEEEeccC-CCCcEEEEEEEeCCcHHHHHHHHH-cCCcCCe
Confidence 267889999999876 678999999999999999999998 9999974
No 16
>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=99.93 E-value=1.3e-25 Score=180.67 Aligned_cols=115 Identities=30% Similarity=0.386 Sum_probs=85.4
Q ss_pred cccccccccCCCCcceeeeeecccch----hhhhccCccccEEEEEEeCccCCCceEEEccceeeecCCCceeeEEEEeC
Q 026613 5 ITASHVYEKCIAVSSGIITVERVMYK----DNDNEKRILQRWYWALVVGTPRCSKGVISAPLGKVVVDNGKSDRITVVNN 80 (236)
Q Consensus 5 ~~~~~~vhRLD~~TSGllLlak~~~~----~~~~~~~~v~K~Y~Alv~G~~~~~~g~i~~~l~~~~~~~~~~~~~~~~~~ 80 (236)
....++|||||++||||||||+|... ..+|+++.++|+|+|+|.|.+...++.++.++............. ..
T Consensus 38 ~~~~~~v~RLD~~TsGlll~a~~~~~~~~l~~~f~~~~~~K~Y~a~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~-- 114 (164)
T PF00849_consen 38 PPELYPVHRLDRDTSGLLLFAKDKEAAAKLSKQFPKRKVEKTYLALVEGGPVEEEGKINSPLGKDVGKNKSSNKD-PP-- 114 (164)
T ss_dssp SGGGEESS---TT-EEEEEEESSHHHHHHHHHHHHTTCSEEEEEEEECSSSSTTCEEEESHEEE-EECSSCTCCE-EE--
T ss_pred CCceEECCCCCccccCCeeccCCcccccccccccccCCCcEEEEEeEcccccccceeeeccccccccccccceee-ee--
Confidence 45678999999999999999999443 235788999999999999777778999999998732112211111 22
Q ss_pred CccccccceeeeEEEeeeC--------CCceEEEEEEeCCCchhHHHHHHhh
Q 026613 81 DQIMSAQHAVTRYQVIKPS--------CHGYTWLKLSPLTGRKHQLRVHCAE 124 (236)
Q Consensus 81 ~~~~~~k~a~T~~~~l~~~--------~~~~slv~~~~~TGR~HQIR~hla~ 124 (236)
...++.+.|.|++++.. ..++++++|+|.|||+||||+|||+
T Consensus 115 --~~~~~~~~t~~~~l~~~~~~~~~~~~~~~s~v~~~l~tGr~HQIR~hla~ 164 (164)
T PF00849_consen 115 --GRDGKPAITRYRVLRSGSRTPSKDENAGCSLVECELITGRTHQIRVHLAH 164 (164)
T ss_dssp --TTTSBTSEEEEEEEEEETT---EECCSSEEEEEEEESS-STTHHHHHHHH
T ss_pred --cccccccceeeeeeccccccccccccCCCEEEEEEECcCCCHHHHHHhcC
Confidence 23478999999999975 3689999999999999999999985
No 17
>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=99.93 E-value=2.1e-26 Score=186.72 Aligned_cols=111 Identities=10% Similarity=0.106 Sum_probs=86.1
Q ss_pred ccccccccCCCCcceeeeeecccch--hhhhccCccccEEEEEEeCccCCCceEEEccceeeecCCCceeeEEEEeCCcc
Q 026613 6 TASHVYEKCIAVSSGIITVERVMYK--DNDNEKRILQRWYWALVVGTPRCSKGVISAPLGKVVVDNGKSDRITVVNNDQI 83 (236)
Q Consensus 6 ~~~~~vhRLD~~TSGllLlak~~~~--~~~~~~~~v~K~Y~Alv~G~~~~~~g~i~~~l~~~~~~~~~~~~~~~~~~~~~ 83 (236)
...++|||||++||||||||+|... .+..+++.++|+|+|+|.|.++++. ++ .. .. .+. ..
T Consensus 34 ~~~~~V~RLD~~TsGLll~ak~~~~~~~L~~~~~~i~K~Y~a~V~g~~~~~~--~~----~~--~~----gv~-~~---- 96 (167)
T cd02556 34 PRWISVGRLDLNTEGLLLFTNDGELANRLMHPSNEIEREYAVRVFGQVTDEQ--LK----SL--KK----GVE-LE---- 96 (167)
T ss_pred CceEEcCcCCCCCeeEEEEECCHHHHHHHhCCcCCCCeEEEEEECccCCHHH--HH----HH--Hc----CCE-EC----
Confidence 3467899999999999999999543 3456788899999999999986532 11 10 01 111 11
Q ss_pred ccccceeeeEEEeeeCCCceEEEEEEeCCCchhHHHHHHhhhCCCceecCCCC
Q 026613 84 MSAQHAVTRYQVIKPSCHGYTWLKLSPLTGRKHQLRVHCAEVLGTPIVGDYKY 136 (236)
Q Consensus 84 ~~~k~a~T~~~~l~~~~~~~slv~~~~~TGR~HQIR~hla~~lG~PIlGD~~Y 136 (236)
+++.+.|+|++++.. .++++++|+|.|||+||||+||++ +||||+-=...
T Consensus 97 -~~~~~~~~~~~~~~~-~~~sll~v~l~tGR~HQIR~~~a~-~G~pV~~L~R~ 146 (167)
T cd02556 97 -DGFAGFKSIQLEGGE-GKNSWYRVTLREGRNREVRRLWEA-FGLQVSRLIRI 146 (167)
T ss_pred -CCcCcceEEEEEecC-CCcEEEEEEEEeCCCHHHHHHHHH-cCCeEeEEEEE
Confidence 257788999999765 577999999999999999999998 99999876554
No 18
>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=99.92 E-value=4.2e-26 Score=184.98 Aligned_cols=110 Identities=12% Similarity=0.119 Sum_probs=80.1
Q ss_pred cccccccCCCCcceeeeeecccc--hhhhhccCccccEEEEEEeCccCCCceEEEccceeeecCCCceeeEEEEeCCccc
Q 026613 7 ASHVYEKCIAVSSGIITVERVMY--KDNDNEKRILQRWYWALVVGTPRCSKGVISAPLGKVVVDNGKSDRITVVNNDQIM 84 (236)
Q Consensus 7 ~~~~vhRLD~~TSGllLlak~~~--~~~~~~~~~v~K~Y~Alv~G~~~~~~g~i~~~l~~~~~~~~~~~~~~~~~~~~~~ 84 (236)
.+++|||||++||||||||||.. ..+..+++.++|+|+|+|.|.+++++. +.+. . .+. ..++
T Consensus 35 ~~~~vhRLD~~TSGlll~ak~~~~~~~l~~~~~~i~K~Y~a~V~G~~~~~~~--~~~~------~----~~~-~~~~--- 98 (167)
T cd02553 35 DLFPVGRLDKDTTGLLLLTNDGQLAHRLTSPKKHVPKTYEVTLAGPLTEDDI--EAFA------E----GVL-LHDG--- 98 (167)
T ss_pred CeEEcccCCCCCEEEEEEEeCHHHHHHhhCCcCCCceEEEEEEccCCCHHHH--HHHH------C----CeE-EcCC---
Confidence 46899999999999999999953 233446788999999999999865432 1110 1 111 1111
Q ss_pred cccceeeeEEEeeeCCCceEEEEEEeCCCchhHHHHHHhhhCCCceecCCCCCCc
Q 026613 85 SAQHAVTRYQVIKPSCHGYTWLKLSPLTGRKHQLRVHCAEVLGTPIVGDYKYGWQ 139 (236)
Q Consensus 85 ~~k~a~T~~~~l~~~~~~~slv~~~~~TGR~HQIR~hla~~lG~PIlGD~~Yg~~ 139 (236)
.+...+.+++++ .++++|+|.|||+||||+||++ +||||++|..++-.
T Consensus 99 -~~~~~~~~~~~~-----~sll~v~l~tGR~HQIR~hla~-lG~pI~~~~R~~~g 146 (167)
T cd02553 99 -YPTKPAKLEILS-----PTTVRLTITEGKYHQVKRMFAA-VGNKVVALHRIRIG 146 (167)
T ss_pred -CEeeeeEEEEeC-----CcEEEEEEEeCCCHHHHHHHHH-cCCeEEEEEEEEEC
Confidence 123345566553 2899999999999999999998 99999999888654
No 19
>PRK10839 16S rRNA pseudouridylate synthase A; Provisional
Probab=99.92 E-value=1.2e-25 Score=191.26 Aligned_cols=108 Identities=14% Similarity=0.090 Sum_probs=82.7
Q ss_pred cccccccCCCCcceeeeeecccchh--hhhccCccccEEEEEEeCccCCCceEEEccceeeecCCCceeeEEEEeCCccc
Q 026613 7 ASHVYEKCIAVSSGIITVERVMYKD--NDNEKRILQRWYWALVVGTPRCSKGVISAPLGKVVVDNGKSDRITVVNNDQIM 84 (236)
Q Consensus 7 ~~~~vhRLD~~TSGllLlak~~~~~--~~~~~~~v~K~Y~Alv~G~~~~~~g~i~~~l~~~~~~~~~~~~~~~~~~~~~~ 84 (236)
.+++|||||++||||||||||.... +..+++.++|+|+|.+.+.+..+. +. .. +..+..
T Consensus 94 ~~~~v~RLD~~TSGlll~ak~~~~~~~l~~~~~~i~K~Y~a~i~~~i~~~~------~~-------~~-~~~~~~----- 154 (232)
T PRK10839 94 KLHAAGRLDIDTTGLVLMTDDGQWSHRITSPRHHCEKTYLVTLESPVADDT------AE-------QF-AKGVQL----- 154 (232)
T ss_pred CceecCCCCCCceeEEEEecCHHHHHHHhCCCCCCCeEEEEEECCCCCHHH------HH-------HH-HCCeEE-----
Confidence 4679999999999999999996533 334678899999998877664321 00 00 011111
Q ss_pred cccceeeeEEEeeeCCCceEEEEEEeCCCchhHHHHHHhhhCCCceecCCCC
Q 026613 85 SAQHAVTRYQVIKPSCHGYTWLKLSPLTGRKHQLRVHCAEVLGTPIVGDYKY 136 (236)
Q Consensus 85 ~~k~a~T~~~~l~~~~~~~slv~~~~~TGR~HQIR~hla~~lG~PIlGD~~Y 136 (236)
+++.+.|+|.+++.. + .++++|+|.||||||||+||++ +||||+|=...
T Consensus 155 ~g~~a~t~~~~~~~~-~-~sll~~~l~tGRtHQIR~h~~~-~G~pi~gl~R~ 203 (232)
T PRK10839 155 HNEKDLTKPAVLEVI-T-PTQVRLTISEGRYHQVKRMFAA-VGNHVVELHRE 203 (232)
T ss_pred CCCcccccccEEEEe-c-CCEEEEEEEcCcCHHHHHHHHH-cCCeEeeEEEE
Confidence 267789999999886 3 3899999999999999999997 99999998765
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=99.90 E-value=4.4e-24 Score=173.27 Aligned_cols=123 Identities=15% Similarity=0.140 Sum_probs=81.3
Q ss_pred cccccccCCCCcceeeeeecccchhhhh--ccCccccEEEEEEeCccCCCceE-EEccceeeecCCCceeeEEEEeCCcc
Q 026613 7 ASHVYEKCIAVSSGIITVERVMYKDNDN--EKRILQRWYWALVVGTPRCSKGV-ISAPLGKVVVDNGKSDRITVVNNDQI 83 (236)
Q Consensus 7 ~~~~vhRLD~~TSGllLlak~~~~~~~~--~~~~v~K~Y~Alv~G~~~~~~g~-i~~~l~~~~~~~~~~~~~~~~~~~~~ 83 (236)
...+|||||++||||||||+|......+ +++.++|+|+|+|.|.++.+... +...+. .+++......+...+
T Consensus 32 ~~~~v~RLD~~TsGlll~a~d~~~~~~l~~~~~~v~K~Y~a~v~g~~~~~~~~~l~~g~~---~~~~~~~~~~v~~~~-- 106 (168)
T cd02566 32 GVYAAGRLDRDSEGLLLLTDDGRLQHRITDPSFKHPKTYYVQVEGVPTEDALEQLRNGVE---LGDGLTLPAKVEKVD-- 106 (168)
T ss_pred CeEEccCCCCCCeEEEEEEeCHHHHHHHHCCCCCCCEEEEEEECCcCCHHHHHHHhCCcE---ECCeEecceEEEEec--
Confidence 4578999999999999999996554433 44569999999999998653210 001110 011111111121111
Q ss_pred ccccceeeeEEEeeeC-CCceEEEEEEeCCCchhHHHHHHhhhCCCceecCCCC
Q 026613 84 MSAQHAVTRYQVIKPS-CHGYTWLKLSPLTGRKHQLRVHCAEVLGTPIVGDYKY 136 (236)
Q Consensus 84 ~~~k~a~T~~~~l~~~-~~~~slv~~~~~TGR~HQIR~hla~~lG~PIlGD~~Y 136 (236)
.+....|.|+++... ..+.++++|+|.|||+||||+||++ +||||+.....
T Consensus 107 -~~~~~~~~~~~~~~~~~~~~sll~v~l~tGR~HQIR~~la~-lG~pV~~L~R~ 158 (168)
T cd02566 107 -EPPWLWEREPPIRFRKNIPTSWIEITICEGKNRQVRRMTAA-VGFPTLRLIRV 158 (168)
T ss_pred -ccccccccccccccccCCCccEEEEEEecCccHHHHHHHHH-cCCeEeEEEEE
Confidence 122345556666542 1456899999999999999999997 99999987665
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=99.88 E-value=4.1e-23 Score=168.81 Aligned_cols=107 Identities=14% Similarity=0.132 Sum_probs=76.6
Q ss_pred ccccccccCCCCcceeeeeecccch--hhhhccCccccEEEEEEeCccCCCceE--EEccceeeecCCCceeeEEEEeCC
Q 026613 6 TASHVYEKCIAVSSGIITVERVMYK--DNDNEKRILQRWYWALVVGTPRCSKGV--ISAPLGKVVVDNGKSDRITVVNND 81 (236)
Q Consensus 6 ~~~~~vhRLD~~TSGllLlak~~~~--~~~~~~~~v~K~Y~Alv~G~~~~~~g~--i~~~l~~~~~~~~~~~~~~~~~~~ 81 (236)
...++|||||++||||||||+|... .+..+++.|+|+|+|+|.|.+++. +. ++..+. .+..
T Consensus 45 ~~l~~VgRLD~dTsGLLl~t~d~~~~~~L~~~~~~i~K~Y~v~v~g~~~~~-~l~~l~~g~~--------------~~~~ 109 (177)
T cd02555 45 ARLAPIGPLDKDASGLLVFSQDGRVLRKLIGDASRLEQEYLVEVRGELTAG-GLERLNHGLT--------------YDGR 109 (177)
T ss_pred CceeEecCCCCCCeeEEEEECCHHHHHHHhChhcCCCEEEEEEEcccCCHH-HHHHHhcCcc--------------cCCe
Confidence 3567999999999999999999544 334467889999999999998652 21 111110 0100
Q ss_pred ccccccceeeeEEEeeeCCCceEEEEEEeCCCchhHHHHHHhhhCCCceecCCCCCC
Q 026613 82 QIMSAQHAVTRYQVIKPSCHGYTWLKLSPLTGRKHQLRVHCAEVLGTPIVGDYKYGW 138 (236)
Q Consensus 82 ~~~~~k~a~T~~~~l~~~~~~~slv~~~~~TGR~HQIR~hla~~lG~PIlGD~~Yg~ 138 (236)
..+++.+.+ .+.++++++|.|||+||||+||++ +||||+|+....-
T Consensus 110 ---~~~~~~~~~-------~~~~~l~i~l~tGr~hQIR~~~~~-~G~pV~~L~R~~i 155 (177)
T cd02555 110 ---ELPPAKVSW-------QNEQRLRFALKEPQPGQIRRMCES-VGLEVVALRRIRI 155 (177)
T ss_pred ---ecceEEEEE-------cCCCEEEEEEECCcChHHHHHHHH-cCCeEEEEEEEEE
Confidence 012233322 134799999999999999999998 9999999988743
No 22
>PRK11394 23S rRNA pseudouridine synthase E; Provisional
Probab=99.87 E-value=1.6e-22 Score=169.57 Aligned_cols=126 Identities=19% Similarity=0.254 Sum_probs=80.4
Q ss_pred ccccccccCCCCcceeeeeecccch--hhhhccCccccEEEEEEeCccCCCceEEEcccee-eecCCCc--eeeEEEEeC
Q 026613 6 TASHVYEKCIAVSSGIITVERVMYK--DNDNEKRILQRWYWALVVGTPRCSKGVISAPLGK-VVVDNGK--SDRITVVNN 80 (236)
Q Consensus 6 ~~~~~vhRLD~~TSGllLlak~~~~--~~~~~~~~v~K~Y~Alv~G~~~~~~g~i~~~l~~-~~~~~~~--~~~~~~~~~ 80 (236)
...++|||||++||||||||+|... .+..+++.++|+|+|+|.|.++.+... . +.. ....++. ...+.+...
T Consensus 70 ~~~~~vgRLD~~TsGllLlt~d~~~~~~L~~~~~~i~K~Y~~~v~g~~~~~~l~--~-l~~Gv~i~~~~~~p~~~~~i~~ 146 (217)
T PRK11394 70 QGVYAAGRLDRDSEGLLVLTNNGALQARLTQPGKRTGKIYYVQVEGIPTQDALE--A-LRNGVTLNDGPTLPAGAELVDE 146 (217)
T ss_pred CCeEEecCCCCCCeeEEEEECCHHHHHHHhCcccCCCEEEEEEECCCCCHHHHH--H-HhCCeEECCccccccEEEEecc
Confidence 3568999999999999999999544 334567789999999999998653321 1 110 0000110 001111110
Q ss_pred CccccccceeeeEEEeee-CCCceEEEEEEeCCCchhHHHHHHhhhCCCceecCCCCCCcc
Q 026613 81 DQIMSAQHAVTRYQVIKP-SCHGYTWLKLSPLTGRKHQLRVHCAEVLGTPIVGDYKYGWQT 140 (236)
Q Consensus 81 ~~~~~~k~a~T~~~~l~~-~~~~~slv~~~~~TGR~HQIR~hla~~lG~PIlGD~~Yg~~~ 140 (236)
.. .-...+..+.. ...+.++++|+|.|||+||||+||++ +||||+||.+|+-..
T Consensus 147 ~~-----~~~~~~~~~~~~~~~~~s~l~I~L~eGR~hQIRrm~a~-lG~pVl~L~Ry~iG~ 201 (217)
T PRK11394 147 PA-----WLWPRNPPIRERKSIPTSWLKITLYEGRNRQVRRMTAH-VGFPTLRLIRYAMGD 201 (217)
T ss_pred cc-----cccccccccccccCCCceEEEEEEeCCCCHHHHHHHHH-cCCeEeeeEEEEECC
Confidence 00 00000111111 11357899999999999999999997 999999999997653
No 23
>PRK10700 23S rRNA pseudouridylate synthase B; Provisional
Probab=99.77 E-value=3.8e-19 Score=155.86 Aligned_cols=110 Identities=14% Similarity=0.140 Sum_probs=75.8
Q ss_pred cccccccCCCCcceeeeeecccc--hhhhhccCccccEEEEEEeCccCCCceEEEccceeeecCCCceeeEEEEeCCccc
Q 026613 7 ASHVYEKCIAVSSGIITVERVMY--KDNDNEKRILQRWYWALVVGTPRCSKGVISAPLGKVVVDNGKSDRITVVNNDQIM 84 (236)
Q Consensus 7 ~~~~vhRLD~~TSGllLlak~~~--~~~~~~~~~v~K~Y~Alv~G~~~~~~g~i~~~l~~~~~~~~~~~~~~~~~~~~~~ 84 (236)
..++|||||++||||||||+|.. ..+..+++.|+|+|+|+|.|.++++.. +. +. .+ +.+ ++
T Consensus 102 ~~~~VgRLD~dTsGLLLlTndg~~~~~L~~p~~~i~K~Y~v~V~G~~~~~~l--~~-l~-----~G----v~l-~~---- 164 (289)
T PRK10700 102 RWIAVGRLDVNTCGLLLFTTDGELANRLMHPSREVEREYAVRVFGQVDDAKL--RQ-LS-----RG----VQL-ED---- 164 (289)
T ss_pred ceeEccCCCCCCceEEEEEcCHHHHHHHhCccCCCCeEEEEEEccCCCHHHH--HH-HH-----cC----CEe-CC----
Confidence 35789999999999999999944 344568889999999999998864321 11 11 11 111 11
Q ss_pred cccceeeeEEEeeeCCCceEEEEEEeCCCchhHHHHHHhhhCCCceecCCCC
Q 026613 85 SAQHAVTRYQVIKPSCHGYTWLKLSPLTGRKHQLRVHCAEVLGTPIVGDYKY 136 (236)
Q Consensus 85 ~~k~a~T~~~~l~~~~~~~slv~~~~~TGR~HQIR~hla~~lG~PIlGD~~Y 136 (236)
+......++.+... ...++++|++++||+||||.||++ +|+||+.=...
T Consensus 165 -~~~~~~~v~~~~~~-~~~s~l~v~L~EGk~hQIRrm~~~-lG~~V~~L~Ri 213 (289)
T PRK10700 165 -GPAAFKTIKFSGGE-GINQWYNVTLTEGRNREVRRLWEA-VGVQVSRLIRV 213 (289)
T ss_pred -ceeeeEEEEeccCC-CCceEEEEEEeCCccHHHHHHHHH-cCCEEeEEEEE
Confidence 11112222222211 345899999999999999999997 99999876544
No 24
>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=99.74 E-value=2.1e-18 Score=139.21 Aligned_cols=108 Identities=14% Similarity=0.096 Sum_probs=75.6
Q ss_pred ccccccccCCCCcceeeeeecccc--hhhhhccCccccEEEEEEeCccCCCceEEEccceeeecCCCceeeEEEEeCCcc
Q 026613 6 TASHVYEKCIAVSSGIITVERVMY--KDNDNEKRILQRWYWALVVGTPRCSKGVISAPLGKVVVDNGKSDRITVVNNDQI 83 (236)
Q Consensus 6 ~~~~~vhRLD~~TSGllLlak~~~--~~~~~~~~~v~K~Y~Alv~G~~~~~~g~i~~~l~~~~~~~~~~~~~~~~~~~~~ 83 (236)
...++|||||++||||||||+|.. ..+.++.+.++|+|+|.+.|.+.++. +... ..| +.+ .
T Consensus 31 ~~~~~vgRLD~~tsGlll~t~dg~~~~~L~~p~~~~~K~Y~V~v~~~l~~~~------l~~l--~~G----~~~-~---- 93 (164)
T cd02554 31 PRIFPIGRLDKDSEGLILLTNDGDLVNKILHADNNHEKEYLVTVNKPITDEF------IEGM--SNG----VVI-L---- 93 (164)
T ss_pred CCEEEccCCCCCCeeEEEEEcCHHHHHHHhhhhcCCCeEEEEEECCCCCHHH------HHHH--hCC----CEE-C----
Confidence 357889999999999999999943 44567888899999999999886531 1110 011 111 1
Q ss_pred ccccceeeeEEEeeeCCCceEEEEEEeCCCchhHHHHHHhhhCCCceecCCCCC
Q 026613 84 MSAQHAVTRYQVIKPSCHGYTWLKLSPLTGRKHQLRVHCAEVLGTPIVGDYKYG 137 (236)
Q Consensus 84 ~~~k~a~T~~~~l~~~~~~~slv~~~~~TGR~HQIR~hla~~lG~PIlGD~~Yg 137 (236)
...|....++.. .. +.++|.+.+||+||||+||++ +|+||+-=..+.
T Consensus 94 ----~~~~~~~~v~~~-~~-~~l~i~l~eGr~~qIRrm~~~-~G~~V~~L~Ri~ 140 (164)
T cd02554 94 ----GTVTKPCKVERL-AK-DKFRIVLTQGLNRQIRRMCEA-LGYRVTDLKRVR 140 (164)
T ss_pred ----CeEEcceEEEEC-CC-CEEEEEEECCcCHHHHHHHHH-cCCEEEEEEEEE
Confidence 112333333332 22 359999999999999999997 999998766553
No 25
>PRK10475 23S rRNA pseudouridine synthase F; Provisional
Probab=99.67 E-value=5.3e-17 Score=142.18 Aligned_cols=106 Identities=11% Similarity=0.059 Sum_probs=72.3
Q ss_pred cccccccCCCCcceeeeeecccch--hhhhccCccccEEEEEEeCccCCCceEEEccceeeecCCCceeeEEEEeCCccc
Q 026613 7 ASHVYEKCIAVSSGIITVERVMYK--DNDNEKRILQRWYWALVVGTPRCSKGVISAPLGKVVVDNGKSDRITVVNNDQIM 84 (236)
Q Consensus 7 ~~~~vhRLD~~TSGllLlak~~~~--~~~~~~~~v~K~Y~Alv~G~~~~~~g~i~~~l~~~~~~~~~~~~~~~~~~~~~~ 84 (236)
..++|||||++||||||||+|... .+..+.+.++|+|+|+|.|.+.++ .++... .| +.+ +..
T Consensus 99 ~l~~VgRLDrdTsGLLLlT~dg~~~~~L~~p~~~i~K~Y~v~V~g~~~~~--~l~~l~------~G----v~l-~~~--- 162 (290)
T PRK10475 99 RVFPIGRLDKDSQGLIFLTNHGDLVNKILRAGNDHEKEYLVTVDKPITDE--FIRGMG------AG----VPI-LGT--- 162 (290)
T ss_pred cccccccCCCCCcceEEEecCHHHHHHhhCcCCCCCeEEEEEECCCCCHH--HHHHHh------CC----cEE-CCE---
Confidence 467999999999999999999543 345577789999999999988542 121111 11 111 110
Q ss_pred cccceeeeEEEeeeCCCceEEEEEEeCCCchhHHHHHHhhhCCCceecCCCC
Q 026613 85 SAQHAVTRYQVIKPSCHGYTWLKLSPLTGRKHQLRVHCAEVLGTPIVGDYKY 136 (236)
Q Consensus 85 ~~k~a~T~~~~l~~~~~~~slv~~~~~TGR~HQIR~hla~~lG~PIlGD~~Y 136 (236)
..+++ .+..+ ..++++|++.+||+||||.||++ +|++|+-=...
T Consensus 163 ~~~~~--~v~~~-----~~~~~~i~l~eGk~rqIRrm~~~-~G~~V~~L~R~ 206 (290)
T PRK10475 163 VTKKC--KVKKE-----APFVFRITLVQGLNRQIRRMCEH-FGYEVTKLERT 206 (290)
T ss_pred Eecce--EEEec-----CCcEEEEEEECCcCHHHHHHHHH-cCCEEeEEEEE
Confidence 01111 11111 12579999999999999999997 99999865443
No 26
>COG1187 RsuA 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]
Probab=99.65 E-value=1.5e-16 Score=135.50 Aligned_cols=112 Identities=11% Similarity=0.188 Sum_probs=79.6
Q ss_pred cccccccCCCCcceeeeeecc--cchhhhhccCccccEEEEEEeCccCCCceEEEccceeeecCCCceeeEEEEeCCccc
Q 026613 7 ASHVYEKCIAVSSGIITVERV--MYKDNDNEKRILQRWYWALVVGTPRCSKGVISAPLGKVVVDNGKSDRITVVNNDQIM 84 (236)
Q Consensus 7 ~~~~vhRLD~~TSGllLlak~--~~~~~~~~~~~v~K~Y~Alv~G~~~~~~g~i~~~l~~~~~~~~~~~~~~~~~~~~~~ 84 (236)
..+.|.|||+||||||||++| ....+..++..++|+|+|.|.|.++.+. ++.. ..| + ..++
T Consensus 100 ~~~pvGRLD~dTeGLLLLTnDG~la~rL~~P~~~~~K~Y~v~v~g~~~~~~--l~~l------~~G----v-~l~d---- 162 (248)
T COG1187 100 RLFPVGRLDKDTEGLLLLTNDGELAHRLMHPSSEVEKEYLVRVEGPVTEED--LEKL------RKG----V-TLDD---- 162 (248)
T ss_pred ceeeccccCCCCeeEEEEeCCHHHHHHhcCCCCCCCEEEEEEEecCCCHHH--HHHH------hCC----c-EecC----
Confidence 378999999999999999999 4456688999999999999999876431 1110 011 1 1111
Q ss_pred cccceeeeEEEeeeCCC-ceEEEEEEeCCCchhHHHHHHhhhCCCceecCCCCC
Q 026613 85 SAQHAVTRYQVIKPSCH-GYTWLKLSPLTGRKHQLRVHCAEVLGTPIVGDYKYG 137 (236)
Q Consensus 85 ~~k~a~T~~~~l~~~~~-~~slv~~~~~TGR~HQIR~hla~~lG~PIlGD~~Yg 137 (236)
+....+....+..... +.+++++++.+||+||||.++++ .|+|++.=..+.
T Consensus 163 -~~~~~~~~~~l~~~~~~~~s~~~itl~EGrnrQVRRm~~a-~G~~V~~L~R~~ 214 (248)
T COG1187 163 -GETKPAKPASLEKEPGKNNSWLRITLTEGRNRQVRRMFEA-VGLEVLRLKRIR 214 (248)
T ss_pred -cccccceeEEEEecCCCCceEEEEEEeCCcCHHHHHHHHH-cCCEEeEEEEEE
Confidence 2222333222222212 57999999999999999999997 999998876653
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=97.92 E-value=9e-06 Score=68.94 Aligned_cols=41 Identities=15% Similarity=-0.070 Sum_probs=33.5
Q ss_pred ccccccCCCCcceeeeeecccchhh--hhccCccccEEEEEEe
Q 026613 8 SHVYEKCIAVSSGIITVERVMYKDN--DNEKRILQRWYWALVV 48 (236)
Q Consensus 8 ~~~vhRLD~~TSGllLlak~~~~~~--~~~~~~v~K~Y~Alv~ 48 (236)
.|.|||||.+|||||+||++....+ .+.++.+.|+|+|...
T Consensus 34 ~~~vhrLD~~aSGvl~~a~~~~tkl~~~~~~~~~~K~Y~~~~~ 76 (226)
T cd02868 34 LVGVHRLDAFSSGVLVLGVNHGNKLLSHLYSNHPTRVYTIRGL 76 (226)
T ss_pred eeEccccCCCCceEEEEEeChhHhHHHHHHhcCCCeEEEEEEE
Confidence 5788999999999999999965544 4677778999996553
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=96.68 E-value=0.0075 Score=43.20 Aligned_cols=28 Identities=4% Similarity=-0.193 Sum_probs=23.7
Q ss_pred ccccccccCCCCcceeeeeecccchhhhhccCccccEEEEEEe
Q 026613 6 TASHVYEKCIAVSSGIITVERVMYKDNDNEKRILQRWYWALVV 48 (236)
Q Consensus 6 ~~~~~vhRLD~~TSGllLlak~~~~~~~~~~~~v~K~Y~Alv~ 48 (236)
...+..+++|+..+|+++++ +.|..++.
T Consensus 24 ~~i~~aG~kDk~a~t~q~v~---------------n~f~i~~r 51 (87)
T cd01291 24 KRVGYAGRKDKRAVTTQLVS---------------NRFTITLR 51 (87)
T ss_pred heEEECccCCCCeeEEEEEc---------------ccEEEEEE
Confidence 34677899999999999999 77888776
No 29
>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=77.84 E-value=3.2 Score=32.90 Aligned_cols=42 Identities=12% Similarity=-0.092 Sum_probs=27.0
Q ss_pred cccccccCCCCcceeeeeecccchhhhhccCccccEEEEEEe
Q 026613 7 ASHVYEKCIAVSSGIITVERVMYKDNDNEKRILQRWYWALVV 48 (236)
Q Consensus 7 ~~~~vhRLD~~TSGllLlak~~~~~~~~~~~~v~K~Y~Alv~ 48 (236)
..+=.+.||-..||||+++-+..-.+...-....|+|.|...
T Consensus 8 KvGH~GTLDP~AsGvL~v~vg~~Tkl~~~l~~~~K~Y~~~~~ 49 (149)
T PF01509_consen 8 KVGHGGTLDPFASGVLVVGVGKATKLLSYLQNSDKEYVATIR 49 (149)
T ss_dssp SEEESS-SSTT-EEEEEEEEGGGGGGHHHHTTSEEEEEEEEE
T ss_pred eeccccccCCcceEEEEEEECCcchHHHHhhccCCEEEEEEE
Confidence 344567899999999999887544332111234499999874
No 30
>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=75.68 E-value=3.1 Score=34.14 Aligned_cols=40 Identities=8% Similarity=-0.115 Sum_probs=27.1
Q ss_pred cccccCCCCcceeeeeecccchhhhhccCccccEEEEEEe
Q 026613 9 HVYEKCIAVSSGIITVERVMYKDNDNEKRILQRWYWALVV 48 (236)
Q Consensus 9 ~~vhRLD~~TSGllLlak~~~~~~~~~~~~v~K~Y~Alv~ 48 (236)
+=.+-||-..||||+++-+..-.+..--..-.|+|.|.+.
T Consensus 32 GH~GTLDp~A~GvLiv~~g~~Tk~~~~~~~~~K~Y~a~v~ 71 (182)
T cd02572 32 GHSGTLDPKVTGCLPVCIDRATRLVKSQQEAGKEYVCVMR 71 (182)
T ss_pred CcCCCCCCcCeeEEEEEECHHhhhhHHHhCCCCEEEEEEE
Confidence 3457899999999999887544332111123499999876
No 31
>KOG2559 consensus Predicted pseudouridine synthase [Translation, ribosomal structure and biogenesis]
Probab=66.68 E-value=2.6 Score=36.14 Aligned_cols=20 Identities=15% Similarity=0.084 Sum_probs=17.7
Q ss_pred ccccccCCCCcceeeeeecc
Q 026613 8 SHVYEKCIAVSSGIITVERV 27 (236)
Q Consensus 8 ~~~vhRLD~~TSGllLlak~ 27 (236)
..++||||-.|||++||.-+
T Consensus 91 V~v~h~l~~~~sgvl~~gVg 110 (318)
T KOG2559|consen 91 VQVVHVLPLATSGVLLFGVG 110 (318)
T ss_pred eeeEEeecccccceEEEecC
Confidence 67899999999999999554
No 32
>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=66.56 E-value=6 Score=33.24 Aligned_cols=41 Identities=10% Similarity=-0.122 Sum_probs=29.0
Q ss_pred ccccccCCCCcceeeeeecccchhhhhccCccccEEEEEEe
Q 026613 8 SHVYEKCIAVSSGIITVERVMYKDNDNEKRILQRWYWALVV 48 (236)
Q Consensus 8 ~~~vhRLD~~TSGllLlak~~~~~~~~~~~~v~K~Y~Alv~ 48 (236)
.+=.+-||-..||||+++-+..-.+..--....|+|.|...
T Consensus 29 vGH~GTLDP~AsGvLiv~vG~aTkl~~~~~~~~K~Y~~~~~ 69 (210)
T cd00506 29 VGHGGTLDPFATGVLVVGIGKATKLLKHLLAATKDYTAIGR 69 (210)
T ss_pred cCCCCcCCCcCeeEEEEEECHHHhhhHHHhcCCceEEEEEE
Confidence 34457899999999999888544332112227799999885
No 33
>PRK04099 truB tRNA pseudouridine synthase B; Provisional
Probab=57.92 E-value=12 Score=32.75 Aligned_cols=41 Identities=12% Similarity=0.013 Sum_probs=29.4
Q ss_pred ccccccCCCCcceeeeeecccchhhhhccCccccEEEEEEe
Q 026613 8 SHVYEKCIAVSSGIITVERVMYKDNDNEKRILQRWYWALVV 48 (236)
Q Consensus 8 ~~~vhRLD~~TSGllLlak~~~~~~~~~~~~v~K~Y~Alv~ 48 (236)
.+-.+-||-..||||+++-+..-.+..--..-.|+|.|.+.
T Consensus 31 vGH~GTLDP~AtGvLiv~iG~aTKl~~~l~~~~K~Y~a~~~ 71 (273)
T PRK04099 31 AGFSGTLDPFAKGVLIVAFGQYTKLFRFLKKTPKTYRATLW 71 (273)
T ss_pred cccCccCCCCCeeEEEEEEChHhhhHHHhccCCceEEEEEE
Confidence 45567899999999999888554442222224799999875
No 34
>PRK00989 truB tRNA pseudouridine synthase B; Provisional
Probab=57.16 E-value=14 Score=31.47 Aligned_cols=41 Identities=7% Similarity=-0.040 Sum_probs=28.6
Q ss_pred ccccccCCCCcceeeeeeccc-chhhhhccCccccEEEEEEe
Q 026613 8 SHVYEKCIAVSSGIITVERVM-YKDNDNEKRILQRWYWALVV 48 (236)
Q Consensus 8 ~~~vhRLD~~TSGllLlak~~-~~~~~~~~~~v~K~Y~Alv~ 48 (236)
.+=.+.||-..||||+++-+. .-.+..--....|+|.|.+.
T Consensus 38 vGH~GTLDP~AtGvLiv~vG~~aTkl~~~~~~~~K~Y~~~~~ 79 (230)
T PRK00989 38 IGHAGTLDPFATGVMVMLIGRKFTRLSDILLFEDKEYAAVAH 79 (230)
T ss_pred CCcCccCCCCCeeEEEEEECCchhhhHHHhcCCCcEEEEEEE
Confidence 444578999999999998775 33332111226799999986
No 35
>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=56.88 E-value=12 Score=31.36 Aligned_cols=41 Identities=10% Similarity=-0.052 Sum_probs=28.7
Q ss_pred ccccccCCCCcceeeeeecccchhhhhccCccccEEEEEEe
Q 026613 8 SHVYEKCIAVSSGIITVERVMYKDNDNEKRILQRWYWALVV 48 (236)
Q Consensus 8 ~~~vhRLD~~TSGllLlak~~~~~~~~~~~~v~K~Y~Alv~ 48 (236)
.+=.+-||-..||||+++-+..-.+..--..-.|+|.|.+.
T Consensus 31 vGH~GTLDP~AsGvLiv~vG~~Tkl~~~~~~~~K~Y~~~~~ 71 (209)
T TIGR00431 31 VGHTGTLDPFATGVLPILVGKATKLSPYLTDLDKEYRAEIR 71 (209)
T ss_pred CCCCCCCCCcCceEEEEEEChHhhhhHHHcCCCCeEEEEEE
Confidence 34457899999999999887543331111246799999875
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=54.39 E-value=15 Score=32.30 Aligned_cols=40 Identities=10% Similarity=-0.039 Sum_probs=28.1
Q ss_pred cccccCCCCcceeeeeecccchhhhhccCccccEEEEEEe
Q 026613 9 HVYEKCIAVSSGIITVERVMYKDNDNEKRILQRWYWALVV 48 (236)
Q Consensus 9 ~~vhRLD~~TSGllLlak~~~~~~~~~~~~v~K~Y~Alv~ 48 (236)
+=.+-||-..||||+++-+..-.+..--..-.|+|.|.+.
T Consensus 30 GH~GTLDP~AtGvL~v~vG~aTkl~~~l~~~~K~Y~~~~~ 69 (277)
T cd02573 30 GHTGTLDPLATGVLPIALGEATKLSQYLLDADKTYRATVR 69 (277)
T ss_pred CCCCCCCCcCeEEEEEEEChHHhhHHHhcCCCcEEEEEEE
Confidence 3356799999999999887544332222225799999986
No 37
>PRK00020 truB tRNA pseudouridine synthase B; Provisional
Probab=52.96 E-value=16 Score=31.46 Aligned_cols=38 Identities=8% Similarity=-0.053 Sum_probs=26.7
Q ss_pred cccCCCCcceeeeeecccchhhhhccCccccEEEEEEe
Q 026613 11 YEKCIAVSSGIITVERVMYKDNDNEKRILQRWYWALVV 48 (236)
Q Consensus 11 vhRLD~~TSGllLlak~~~~~~~~~~~~v~K~Y~Alv~ 48 (236)
.+-||-..||||+++-+..-.+..--..-.|+|.|.+.
T Consensus 42 ~GTLDP~AtGvLiv~iG~aTKl~~~l~~~~K~Y~a~~~ 79 (244)
T PRK00020 42 TGTLDPFATGLLVCCMGRATKISGRMLEADKTYQATLQ 79 (244)
T ss_pred CCcCCCcCeeEEEEEECHHhhhhHHhccCCcEEEEEEE
Confidence 45699999999999887544332222234499999875
No 38
>PRK02193 truB tRNA pseudouridine synthase B; Provisional
Probab=47.38 E-value=22 Score=31.26 Aligned_cols=41 Identities=12% Similarity=-0.051 Sum_probs=28.8
Q ss_pred ccccccCCCCcceeeeeecccchhhhhccCccccEEEEEEe
Q 026613 8 SHVYEKCIAVSSGIITVERVMYKDNDNEKRILQRWYWALVV 48 (236)
Q Consensus 8 ~~~vhRLD~~TSGllLlak~~~~~~~~~~~~v~K~Y~Alv~ 48 (236)
.+=.+.||-..||||+++-+..-.+..--....|+|.|.+.
T Consensus 29 vGH~GTLDP~AtGvL~v~vG~aTkl~~~l~~~~K~Y~a~~~ 69 (279)
T PRK02193 29 IGHTGTLDPLASGLLLVATDEDTKLIDYLDQKDKTYIAKIK 69 (279)
T ss_pred cccCccCCCcCeeEEEEEEChhhhhhHHhccCCcEEEEEEE
Confidence 44567899999999999887543331111345699999875
No 39
>PRK14123 tRNA pseudouridine synthase B; Provisional
Probab=46.59 E-value=23 Score=31.46 Aligned_cols=41 Identities=12% Similarity=-0.106 Sum_probs=28.4
Q ss_pred ccccccCCCCcceeeeeecccchhhhhccCccccEEEEEEe
Q 026613 8 SHVYEKCIAVSSGIITVERVMYKDNDNEKRILQRWYWALVV 48 (236)
Q Consensus 8 ~~~vhRLD~~TSGllLlak~~~~~~~~~~~~v~K~Y~Alv~ 48 (236)
.+=.+-||-..||||+++-+..-.+..--....|+|.|.+.
T Consensus 32 vGH~GTLDP~AtGvL~v~vG~aTkl~~~l~~~~K~Y~~~~~ 72 (305)
T PRK14123 32 IGHTGTLDPEVAGVLPVCIGNATRVSDYVMDMGKAYEATVS 72 (305)
T ss_pred cccCcCCCCcCeeEEEEEEChhhhhHHHhcCCCcEEEEEEE
Confidence 34457899999999999887543332111226699999885
No 40
>PRK02484 truB tRNA pseudouridine synthase B; Provisional
Probab=46.25 E-value=24 Score=31.19 Aligned_cols=41 Identities=5% Similarity=-0.191 Sum_probs=28.1
Q ss_pred ccccccCCCCcceeeeeecccchhhhhccCccccEEEEEEe
Q 026613 8 SHVYEKCIAVSSGIITVERVMYKDNDNEKRILQRWYWALVV 48 (236)
Q Consensus 8 ~~~vhRLD~~TSGllLlak~~~~~~~~~~~~v~K~Y~Alv~ 48 (236)
.+=.+.||-..||||+++-+..-.+..--..-.|+|.|.+.
T Consensus 32 vGH~GTLDP~AtGvL~i~vG~aTkl~~~l~~~~K~Y~a~~~ 72 (294)
T PRK02484 32 IGHGGTLDPDVVGVLPIAVGKATRLIEYMTEAGKVYEGEIT 72 (294)
T ss_pred cccCCCCCCCCeeEEEEEEChhhhhhHHhccCCcEEEEEEE
Confidence 34457899999999999887544332111123499999886
No 41
>PRK04270 H/ACA RNA-protein complex component Cbf5p; Reviewed
Probab=45.63 E-value=23 Score=31.35 Aligned_cols=40 Identities=8% Similarity=-0.129 Sum_probs=26.9
Q ss_pred cccccCCCCcceeeeeecccchhhhhccCccccEEEEEEe
Q 026613 9 HVYEKCIAVSSGIITVERVMYKDNDNEKRILQRWYWALVV 48 (236)
Q Consensus 9 ~~vhRLD~~TSGllLlak~~~~~~~~~~~~v~K~Y~Alv~ 48 (236)
+=.+-||-..||||+++-+..-.+..--..-.|+|.|.+.
T Consensus 52 GH~GTLDp~A~GvL~v~~g~atk~~~~~~~~~K~Y~~~~~ 91 (300)
T PRK04270 52 GHGGTLDPKVTGVLPVALGKATKVVQALLESGKEYVCVMH 91 (300)
T ss_pred cCCCCCCCcCeEEEEEEEChHhhhhHHhccCCcEEEEEEE
Confidence 3456799999999999887543332111123499998875
No 42
>PRK03287 truB tRNA pseudouridine synthase B; Provisional
Probab=45.42 E-value=23 Score=31.39 Aligned_cols=41 Identities=7% Similarity=-0.014 Sum_probs=27.7
Q ss_pred ccccccCCCCcceeeeeecccchhhhhccCccccEEEEEEe
Q 026613 8 SHVYEKCIAVSSGIITVERVMYKDNDNEKRILQRWYWALVV 48 (236)
Q Consensus 8 ~~~vhRLD~~TSGllLlak~~~~~~~~~~~~v~K~Y~Alv~ 48 (236)
.+=.+-||-..||||+++-+..-.+..--..-.|+|.|.+.
T Consensus 38 vGH~GTLDP~AtGvL~i~vG~aTKl~~~l~~~~K~Y~a~~~ 78 (298)
T PRK03287 38 VGHAGTLDPMATGVLVLGVERATKLLGHLTLTDKSYTATIR 78 (298)
T ss_pred CCcCccCCCcceeEEEEEeChhhhhhHHHhcCCcEEEEEEE
Confidence 34456799999999999887543331111123799999875
No 43
>PRK05389 truB tRNA pseudouridine synthase B; Provisional
Probab=44.19 E-value=26 Score=31.15 Aligned_cols=40 Identities=10% Similarity=-0.080 Sum_probs=27.1
Q ss_pred cccccCCCCcceeeeeecccchhhhhccCccccEEEEEEe
Q 026613 9 HVYEKCIAVSSGIITVERVMYKDNDNEKRILQRWYWALVV 48 (236)
Q Consensus 9 ~~vhRLD~~TSGllLlak~~~~~~~~~~~~v~K~Y~Alv~ 48 (236)
+=.+-||-..||||+++-+..-.+..--..-.|+|.|.+.
T Consensus 43 GH~GTLDP~AtGvL~v~vG~aTkl~~~l~~~~K~Y~a~~~ 82 (305)
T PRK05389 43 GHAGTLDPLASGVLPIALGEATKTVPYVMDGTKRYRFTVA 82 (305)
T ss_pred CCcccCCCCCceEEEEEEChhhhhhHHhccCCcEEEEEEE
Confidence 3456799999999999887443331111123799999875
No 44
>PRK14124 tRNA pseudouridine synthase B; Provisional
Probab=42.81 E-value=26 Score=31.27 Aligned_cols=40 Identities=8% Similarity=-0.037 Sum_probs=27.1
Q ss_pred cccccCCCCcceeeeeecccchhhhhccCccccEEEEEEe
Q 026613 9 HVYEKCIAVSSGIITVERVMYKDNDNEKRILQRWYWALVV 48 (236)
Q Consensus 9 ~~vhRLD~~TSGllLlak~~~~~~~~~~~~v~K~Y~Alv~ 48 (236)
+=.+-||-..||||+++-+..-.+..--..-.|+|.|.+.
T Consensus 33 GH~GTLDP~AtGvL~v~vG~aTkl~~~l~~~~K~Y~a~~~ 72 (308)
T PRK14124 33 GHAGTLDPFATGVLIVGVNKATRLLEYLKNEKKVYYVKMR 72 (308)
T ss_pred CcCcCCCCCCcEEEEEEEChHHhhhHHHhcCCceEEEEEE
Confidence 3346799999999999887443331111123799999885
No 45
>PRK01851 truB tRNA pseudouridine synthase B; Provisional
Probab=41.97 E-value=28 Score=30.92 Aligned_cols=38 Identities=8% Similarity=-0.051 Sum_probs=25.9
Q ss_pred cccCCCCcceeeeeecccchhhhhccCccccEEEEEEe
Q 026613 11 YEKCIAVSSGIITVERVMYKDNDNEKRILQRWYWALVV 48 (236)
Q Consensus 11 vhRLD~~TSGllLlak~~~~~~~~~~~~v~K~Y~Alv~ 48 (236)
-.-||-..||||+++-+..-.+..--..-.|+|.|.+.
T Consensus 48 ~GTLDP~AtGvL~v~vG~aTkl~~~l~~~~K~Y~~~~~ 85 (303)
T PRK01851 48 TGTLDPLATGLLPLCFGEATKFSQDLLDADKTYEATLR 85 (303)
T ss_pred CCCCCCCCceEEEEEECHHHhhhHHhcccCeEEEEEEE
Confidence 35699999999999887443332111123499999885
No 46
>PRK14122 tRNA pseudouridine synthase B; Provisional
Probab=40.37 E-value=31 Score=30.79 Aligned_cols=37 Identities=11% Similarity=-0.029 Sum_probs=26.1
Q ss_pred ccCCCCcceeeeeecccchhhhhccCccccEEEEEEe
Q 026613 12 EKCIAVSSGIITVERVMYKDNDNEKRILQRWYWALVV 48 (236)
Q Consensus 12 hRLD~~TSGllLlak~~~~~~~~~~~~v~K~Y~Alv~ 48 (236)
.-||-..||||+++-+..-.+..--..-.|+|.|.+.
T Consensus 34 GTLDP~AtGvL~i~iG~aTKl~~~l~~~~K~Y~a~~~ 70 (312)
T PRK14122 34 GTLDPLATGVLVLCTDDSTKLVPFLSAEDKEYLAWVS 70 (312)
T ss_pred CCCCCcCeeeEEEEEChhhhhhHHhcCCCceEEEEEE
Confidence 5699999999999877443332112345699999885
No 47
>PRK14846 truB tRNA pseudouridine synthase B; Provisional
Probab=39.83 E-value=31 Score=31.22 Aligned_cols=41 Identities=10% Similarity=-0.178 Sum_probs=28.4
Q ss_pred ccccccCCCCcceeeeeecccchhhhhccCccccEEEEEEe
Q 026613 8 SHVYEKCIAVSSGIITVERVMYKDNDNEKRILQRWYWALVV 48 (236)
Q Consensus 8 ~~~vhRLD~~TSGllLlak~~~~~~~~~~~~v~K~Y~Alv~ 48 (236)
.+=.+.||-..||||+++-+..-.+..--..-.|+|.|.+.
T Consensus 32 VGH~GTLDP~AtGVL~i~vG~aTKl~~~l~~~~K~Y~a~~~ 72 (345)
T PRK14846 32 IGHAGTLDVEAEGILPFAVGEATKLIHLLIDARKTYIFTVK 72 (345)
T ss_pred CCcCccCCCcCceEEEEEEChhhhhhHHHhcCCceEEEEEE
Confidence 34457899999999999887544332222234589999875
No 48
>PRK00130 truB tRNA pseudouridine synthase B; Provisional
Probab=39.47 E-value=34 Score=30.19 Aligned_cols=40 Identities=13% Similarity=-0.085 Sum_probs=27.5
Q ss_pred cccccCCCCcceeeeeecccchhhhhccCccccEEEEEEe
Q 026613 9 HVYEKCIAVSSGIITVERVMYKDNDNEKRILQRWYWALVV 48 (236)
Q Consensus 9 ~~vhRLD~~TSGllLlak~~~~~~~~~~~~v~K~Y~Alv~ 48 (236)
+=.+-||-..||||+++-+..-.+..--..-.|+|.|.+.
T Consensus 32 GH~GTLDP~AtGvL~v~vG~aTkl~~~l~~~~K~Y~a~~~ 71 (290)
T PRK00130 32 GHTGTLDPLASGVLPVCLGKATKIVDYLMEGKKTYRAEIK 71 (290)
T ss_pred CcCCCCCCCCeeEEEEEEChhhhhHHHhccCCcEEEEEEE
Confidence 3356799999999999887543331111123799999886
No 49
>PRK01550 truB tRNA pseudouridine synthase B; Provisional
Probab=39.43 E-value=34 Score=30.42 Aligned_cols=38 Identities=11% Similarity=-0.130 Sum_probs=26.1
Q ss_pred cccCCCCcceeeeeecccchhhhhccCccccEEEEEEe
Q 026613 11 YEKCIAVSSGIITVERVMYKDNDNEKRILQRWYWALVV 48 (236)
Q Consensus 11 vhRLD~~TSGllLlak~~~~~~~~~~~~v~K~Y~Alv~ 48 (236)
..-||-..||||+++-+..-.+..--..-.|+|.|.+.
T Consensus 34 ~GTLDP~AtGvL~i~vG~aTkl~~~l~~~~K~Y~a~~~ 71 (304)
T PRK01550 34 TGTLDPEVSGVLPICVGRATKIAEYLTDEGKTYEGEVT 71 (304)
T ss_pred CCCCCCcCeeEEEEEEChhhhhhHHhcCCCcEEEEEEE
Confidence 35699999999999887543332111123699999885
No 50
>PRK05033 truB tRNA pseudouridine synthase B; Provisional
Probab=38.90 E-value=34 Score=30.52 Aligned_cols=39 Identities=5% Similarity=-0.103 Sum_probs=26.7
Q ss_pred ccccCCCCcceeeeeecccchhhhhccCccccEEEEEEe
Q 026613 10 VYEKCIAVSSGIITVERVMYKDNDNEKRILQRWYWALVV 48 (236)
Q Consensus 10 ~vhRLD~~TSGllLlak~~~~~~~~~~~~v~K~Y~Alv~ 48 (236)
=-+-||-..||||+++-+..-.+..--..-.|+|.|.+.
T Consensus 41 H~GTLDP~AtGvL~v~vG~aTkl~~~~~~~~K~Y~a~~~ 79 (312)
T PRK05033 41 HTGALDPLATGMLPICLGEATKFSQYLLDSDKRYRVTAR 79 (312)
T ss_pred CCCcCCCcCeeEEEEEECHHhhhhHHhcCCCcEEEEEEE
Confidence 346799999999999887443331111124799999885
No 51
>PRK02755 truB tRNA pseudouridine synthase B; Provisional
Probab=37.55 E-value=40 Score=29.86 Aligned_cols=38 Identities=5% Similarity=-0.081 Sum_probs=26.4
Q ss_pred cccccCCCCcceeeeeecccchhh-hhccCccccEEEEEEe
Q 026613 9 HVYEKCIAVSSGIITVERVMYKDN-DNEKRILQRWYWALVV 48 (236)
Q Consensus 9 ~~vhRLD~~TSGllLlak~~~~~~-~~~~~~v~K~Y~Alv~ 48 (236)
+=.+-||-..||||+++-+..-.+ .+-. . .|+|.|.+.
T Consensus 33 GH~GTLDP~AtGvL~i~vG~aTkl~~~l~-~-~K~Y~a~~~ 71 (295)
T PRK02755 33 GHGGTLDPAATGVLPIALGKATRLLPYLP-G-EKTYRGTIR 71 (295)
T ss_pred ccCCCCCCcCeeEEEEEEChhhhhHHHhC-C-CcEEEEEEE
Confidence 334679999999999987744332 1112 3 699999875
No 52
>PRK01528 truB tRNA pseudouridine synthase B; Provisional
Probab=34.45 E-value=41 Score=29.72 Aligned_cols=40 Identities=8% Similarity=-0.158 Sum_probs=27.4
Q ss_pred cccccCCCCcceeeeeecccchhhhhccCccccEEEEEEe
Q 026613 9 HVYEKCIAVSSGIITVERVMYKDNDNEKRILQRWYWALVV 48 (236)
Q Consensus 9 ~~vhRLD~~TSGllLlak~~~~~~~~~~~~v~K~Y~Alv~ 48 (236)
+=.+-||-..||||+++-+..-.+..--..-.|+|.|.+.
T Consensus 33 GH~GTLDP~AtGvL~v~vG~aTKl~~~l~~~~K~Y~~~~~ 72 (292)
T PRK01528 33 GHAGTLDVEAEGVLPLAVGEATKLVQLLIDAKKTYIFTVK 72 (292)
T ss_pred CcCccCCCcCceEEEEEEChHhhhhHHHhcCCceEEEEEE
Confidence 3457799999999999887543332111234599999875
No 53
>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=32.90 E-value=45 Score=29.89 Aligned_cols=37 Identities=11% Similarity=-0.035 Sum_probs=25.6
Q ss_pred ccCCCCcceeeeeecccchhhhhccCccccEEEEEEe
Q 026613 12 EKCIAVSSGIITVERVMYKDNDNEKRILQRWYWALVV 48 (236)
Q Consensus 12 hRLD~~TSGllLlak~~~~~~~~~~~~v~K~Y~Alv~ 48 (236)
.=||-.-||||+++-...-.+..--..-.|+|.|.+.
T Consensus 67 GTLDP~A~GvL~v~~G~aTkl~~~~~~~~K~Y~~~v~ 103 (322)
T TIGR00425 67 GTLDPKVTGVLPVCIERATRLVKSLQEAPKEYVCLMR 103 (322)
T ss_pred CCCCCCCceEEEEEEChHhhccHHhccCCCEEEEEEE
Confidence 4589999999999887544332111235699998875
No 54
>COG0130 TruB Pseudouridine synthase [Translation, ribosomal structure and biogenesis]
Probab=29.93 E-value=53 Score=28.74 Aligned_cols=37 Identities=11% Similarity=-0.068 Sum_probs=26.5
Q ss_pred ccCCCCcceeeeeecccchhhhhccCccccEEEEEEe
Q 026613 12 EKCIAVSSGIITVERVMYKDNDNEKRILQRWYWALVV 48 (236)
Q Consensus 12 hRLD~~TSGllLlak~~~~~~~~~~~~v~K~Y~Alv~ 48 (236)
.-||-..||+|.++-+..-.+..--..-.|+|.|.+.
T Consensus 48 GTLDP~atGvLpi~ig~aTKl~~~l~~~~K~Y~a~~~ 84 (271)
T COG0130 48 GTLDPLATGVLPICLGEATKLVQYLLDADKEYVATVR 84 (271)
T ss_pred cccCCcccceEEEEechhHhHHHHHhhCCcEEEEEEE
Confidence 5699999999999888444332222234599999986
No 55
>PRK04642 truB tRNA pseudouridine synthase B; Provisional
Probab=26.00 E-value=76 Score=28.21 Aligned_cols=37 Identities=11% Similarity=-0.079 Sum_probs=25.2
Q ss_pred ccCCCCcceeeeeecccchhhhhccCccccEEEEEEe
Q 026613 12 EKCIAVSSGIITVERVMYKDNDNEKRILQRWYWALVV 48 (236)
Q Consensus 12 hRLD~~TSGllLlak~~~~~~~~~~~~v~K~Y~Alv~ 48 (236)
.=||-.-||||+++-...-.+..---.-.|+|.|.+.
T Consensus 43 GTLDP~AtGvL~v~~G~aTkl~~~l~~~~K~Y~a~~~ 79 (300)
T PRK04642 43 GSLDPLATGLLPLCFGEATKIAGLLLGSAKAYDAEIV 79 (300)
T ss_pred CccCCcCeeeEEEEEChhhhhhHHhcCCCcEEEEEEE
Confidence 4589999999999877443332111234699999884
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=23.55 E-value=83 Score=28.11 Aligned_cols=42 Identities=10% Similarity=-0.078 Sum_probs=28.5
Q ss_pred cccccccCCCCcceeeeeecccchhhhhccCccccEEEEEEe
Q 026613 7 ASHVYEKCIAVSSGIITVERVMYKDNDNEKRILQRWYWALVV 48 (236)
Q Consensus 7 ~~~~vhRLD~~TSGllLlak~~~~~~~~~~~~v~K~Y~Alv~ 48 (236)
-++=.+-||=..||||+++-+..-.....-..-.|+|.|...
T Consensus 57 KiGH~GTLDPlAsGVLvvgvG~aTK~l~~~l~~~K~Y~~~~~ 98 (312)
T cd02867 57 KIGHGGTLDPLATGVLVVGVGAGTKQLQDYLSCSKTYEATGL 98 (312)
T ss_pred ccccccccCCccceeEEEEECcHHHHHHHHhcCCceEEEEEE
Confidence 445567899999999999877443221111116799999875
No 57
>PF08892 YqcI_YcgG: YqcI/YcgG family; InterPro: IPR014988 This group of proteins are functionally uncharacterised. They include YqcI and YcgG from Bacillus subtilis. The alignment contains a conserved FPC motif at the N terminus and CPF at the C terminus.
Probab=21.27 E-value=68 Score=27.07 Aligned_cols=33 Identities=30% Similarity=0.605 Sum_probs=26.1
Q ss_pred hhHHHHHHhhhCC---CceecCCCCCCcccccccccCC
Q 026613 115 KHQLRVHCAEVLG---TPIVGDYKYGWQTHRKWKQFHP 149 (236)
Q Consensus 115 ~HQIR~hla~~lG---~PIlGD~~Yg~~~~~~~~~~~~ 149 (236)
+.+||.-+..+-| ||-+|| ||......|.|.+.
T Consensus 169 r~~IR~R~~~ydg~~~~p~L~~--yG~~~~~EwkQY~l 204 (219)
T PF08892_consen 169 REKIRKRDEAYDGIPIHPDLGD--YGDPENSEWKQYFL 204 (219)
T ss_pred HHHHHHHHHHhcCCCCCchhhh--cCCCCcchhHhhcc
Confidence 7899999998788 788887 99776666766653
Done!