Query 013857
Match_columns 435
No_of_seqs 131 out of 1268
Neff 3.0
Searched_HMMs 46136
Date Fri Mar 29 08:05:22 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/013857.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/013857hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 cd00506 PseudoU_synth_TruB_lik 100.0 1.1E-45 2.3E-50 344.7 12.2 125 310-434 1-125 (210)
2 PRK00020 truB tRNA pseudouridi 100.0 4.8E-45 1E-49 347.8 13.1 127 307-434 9-137 (244)
3 PRK02484 truB tRNA pseudouridi 100.0 5.4E-45 1.2E-49 354.4 12.6 127 307-434 2-129 (294)
4 PRK00130 truB tRNA pseudouridi 100.0 5.4E-45 1.2E-49 353.7 12.6 126 308-434 2-127 (290)
5 PRK01550 truB tRNA pseudouridi 100.0 5.9E-45 1.3E-49 355.5 12.6 126 308-434 2-128 (304)
6 TIGR00431 TruB tRNA pseudourid 100.0 7.4E-45 1.6E-49 339.4 12.7 125 308-434 2-126 (209)
7 PRK04642 truB tRNA pseudouridi 100.0 8.3E-45 1.8E-49 354.3 13.5 127 307-434 9-135 (300)
8 PRK02755 truB tRNA pseudouridi 100.0 6.8E-45 1.5E-49 354.0 12.8 126 307-434 2-127 (295)
9 PRK14123 tRNA pseudouridine sy 100.0 9.9E-45 2.1E-49 354.0 12.8 127 307-434 2-130 (305)
10 PRK03287 truB tRNA pseudouridi 100.0 1.1E-44 2.4E-49 353.0 12.6 127 307-434 8-134 (298)
11 PRK00989 truB tRNA pseudouridi 100.0 1.7E-44 3.7E-49 341.5 12.7 126 307-434 8-134 (230)
12 PRK05033 truB tRNA pseudouridi 100.0 2.1E-44 4.6E-49 352.9 13.2 126 307-434 9-134 (312)
13 cd02573 PseudoU_synth_EcTruB P 100.0 2.7E-44 5.7E-49 346.8 12.8 125 310-434 1-125 (277)
14 cd02867 PseudoU_synth_TruB_4 P 100.0 1.9E-44 4E-49 353.4 11.7 125 310-434 1-154 (312)
15 PRK14124 tRNA pseudouridine sy 100.0 2.6E-44 5.6E-49 351.7 12.6 126 307-434 2-127 (308)
16 PRK14122 tRNA pseudouridine sy 100.0 3.7E-44 8.1E-49 351.3 13.2 124 311-434 3-126 (312)
17 PRK01851 truB tRNA pseudouridi 100.0 7.5E-44 1.6E-48 347.9 14.5 126 307-434 15-140 (303)
18 PRK01528 truB tRNA pseudouridi 100.0 3.9E-44 8.6E-49 348.3 12.4 125 308-434 3-127 (292)
19 PRK05389 truB tRNA pseudouridi 100.0 5.6E-44 1.2E-48 348.9 12.9 126 307-434 12-137 (305)
20 PRK04099 truB tRNA pseudouridi 100.0 7E-44 1.5E-48 344.1 12.5 125 308-434 2-126 (273)
21 PRK02193 truB tRNA pseudouridi 100.0 6.8E-44 1.5E-48 344.9 12.2 125 310-434 1-125 (279)
22 PRK14846 truB tRNA pseudouridi 100.0 4.4E-43 9.5E-48 347.4 12.4 125 308-434 3-127 (345)
23 PF01509 TruB_N: TruB family p 100.0 9.8E-39 2.1E-43 284.0 9.3 105 330-434 1-105 (149)
24 COG0130 TruB Pseudouridine syn 100.0 5.7E-37 1.2E-41 295.8 10.7 109 302-428 6-117 (271)
25 cd02572 PseudoU_synth_hDyskeri 100.0 3E-36 6.5E-41 275.3 11.1 104 308-430 2-105 (182)
26 TIGR00425 CBF5 rRNA pseudourid 100.0 7.7E-35 1.7E-39 285.9 11.6 107 308-432 33-139 (322)
27 PRK04270 H/ACA RNA-protein com 100.0 3.4E-34 7.3E-39 278.0 11.4 105 307-430 21-125 (300)
28 cd02868 PseudoU_synth_hTruB2_l 100.0 8.5E-34 1.8E-38 267.2 11.2 125 310-434 1-132 (226)
29 KOG2529 Pseudouridine synthase 100.0 2.5E-31 5.4E-36 267.3 -0.8 364 13-389 8-392 (395)
30 KOG2529 Pseudouridine synthase 99.6 3.7E-15 7.9E-20 151.2 6.4 73 307-380 67-139 (395)
31 KOG2559 Predicted pseudouridin 99.5 7.9E-15 1.7E-19 142.7 5.1 115 303-430 6-172 (318)
32 cd01291 PseudoU_synth PseudoU_ 98.4 4.9E-07 1.1E-11 72.8 5.3 50 314-378 1-51 (87)
33 PRK10158 23S rRNA/tRNA pseudou 97.6 9.5E-05 2.1E-09 69.1 5.2 71 308-381 20-103 (219)
34 TIGR01621 RluA-like pseudourid 97.6 0.00011 2.3E-09 68.8 5.4 70 309-378 9-88 (217)
35 cd02553 PseudoU_synth_RsuA Pse 97.6 0.0001 2.2E-09 66.3 5.0 68 311-378 2-78 (167)
36 cd02557 PseudoU_synth_ScRIB2 P 97.5 0.00016 3.4E-09 67.2 5.7 73 308-381 22-106 (213)
37 cd02558 PSRA_1 PSRA_1: Pseudou 97.5 0.00019 4.1E-09 68.3 5.7 71 308-378 45-127 (246)
38 COG0564 RluA Pseudouridylate s 97.3 0.00038 8.3E-09 68.5 6.3 75 308-383 84-172 (289)
39 cd02566 PseudoU_synth_RluE Pse 97.3 0.00018 3.8E-09 64.7 3.2 66 311-378 1-75 (168)
40 cd02563 PseudoU_synth_TruC tRN 97.2 0.00064 1.4E-08 63.4 5.9 72 309-382 8-93 (223)
41 cd02550 PseudoU_synth_Rsu_Rlu_ 97.1 0.00057 1.2E-08 60.0 4.3 70 311-382 1-80 (154)
42 TIGR00005 rluA_subfam pseudour 97.1 0.00066 1.4E-08 65.3 4.9 71 310-381 80-166 (299)
43 PRK11112 tRNA pseudouridine sy 97.1 0.00087 1.9E-08 64.2 5.6 69 309-378 9-91 (257)
44 PF00849 PseudoU_synth_2: RNA 97.1 0.00013 2.9E-09 62.9 -0.1 79 311-389 2-96 (164)
45 PRK11180 rluD 23S rRNA pseudou 97.0 0.0008 1.7E-08 66.3 4.6 70 309-378 91-176 (325)
46 cd02556 PseudoU_synth_RluB Pse 96.9 0.0013 2.8E-08 59.1 4.7 67 311-378 2-78 (167)
47 PRK10475 23S rRNA pseudouridin 96.8 0.0023 5E-08 63.3 6.3 66 310-378 68-142 (290)
48 PRK11025 23S rRNA pseudouridyl 96.8 0.0019 4E-08 63.6 5.3 70 309-378 100-181 (317)
49 cd02869 PseudoU_synth_RluCD_li 96.7 0.0016 3.4E-08 57.1 4.0 68 311-378 1-84 (185)
50 PRK11394 23S rRNA pseudouridin 96.7 0.0011 2.4E-08 63.4 2.6 68 311-378 41-114 (217)
51 PRK10839 16S rRNA pseudouridyl 96.4 0.0014 3E-08 61.3 1.5 71 311-381 62-140 (232)
52 cd02555 PSSA_1 PSSA_1: Pseudou 96.4 0.0043 9.2E-08 57.0 4.5 70 311-383 6-93 (177)
53 PF08068 DKCLD: DKCLD (NUC011) 96.4 0.0021 4.5E-08 51.4 2.2 20 307-326 40-59 (59)
54 cd02554 PseudoU_synth_RluF Pse 96.3 0.0084 1.8E-07 54.8 6.2 68 311-378 2-75 (164)
55 PRK10700 23S rRNA pseudouridyl 96.0 0.0098 2.1E-07 58.6 5.2 67 311-378 69-145 (289)
56 cd02870 PseudoU_synth_RsuA_lik 96.0 0.0027 5.8E-08 55.5 1.1 67 312-378 2-76 (146)
57 KOG1919 RNA pseudouridylate sy 95.8 0.013 2.9E-07 60.3 5.4 77 306-382 110-199 (371)
58 COG1187 RsuA 16S rRNA uridine- 94.8 0.033 7.1E-07 54.7 4.3 67 311-378 65-143 (248)
59 TIGR01213 conserved hypothetic 83.6 1.6 3.5E-05 45.8 4.9 42 369-428 275-317 (388)
60 TIGR00093 pseudouridine syntha 79.3 1.9 4.1E-05 37.3 3.0 38 341-378 1-40 (128)
61 PRK14554 putative pseudouridyl 64.3 11 0.00024 40.1 5.1 60 351-428 287-350 (422)
62 TIGR00094 tRNA_TruD_broad tRNA 63.5 37 0.0008 34.9 8.5 47 311-358 45-93 (387)
63 cd02575 PseudoU_synth_EcTruD P 59.3 99 0.0021 30.9 10.4 100 311-413 28-135 (253)
64 PRK00984 truD tRNA pseudouridi 58.6 1E+02 0.0022 31.7 10.6 122 289-414 24-153 (341)
65 COG0585 Uncharacterized conser 57.6 45 0.00098 35.4 8.1 69 287-357 27-97 (406)
66 cd02577 PSTD1 PSTD1: Pseudouri 55.9 1.4E+02 0.0031 30.5 11.1 69 289-359 7-77 (319)
67 cd02552 PseudoU_synth_TruD_lik 53.3 58 0.0013 31.8 7.6 47 311-358 34-82 (232)
68 COG0575 CdsA CDP-diglyceride s 33.2 25 0.00053 34.3 1.6 25 323-347 217-247 (265)
69 PF08555 DUF1754: Eukaryotic f 29.3 27 0.00059 29.2 1.0 25 110-134 73-97 (98)
70 COG1258 Predicted pseudouridyl 25.7 94 0.002 33.3 4.4 38 368-423 279-317 (398)
71 PRK10719 eutA reactivating fac 24.5 1.3E+02 0.0028 33.0 5.2 65 349-413 146-225 (475)
No 1
>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=100.00 E-value=1.1e-45 Score=344.70 Aligned_cols=125 Identities=43% Similarity=0.731 Sum_probs=123.4
Q ss_pred eEEEEeCCCCCCHHHHHHHHHHhhccceeeccCCCCCCCCeEEEEEecCcccccchhcCCCcEEEEEEEECcccccCCCC
Q 013857 310 TMVLVNKPKGWTSFTVCGKLRRLVKVKKVGHAGTLDPMATGLLIVCVGKATKLVDRYQGMIKGYSGVFRLGEATSTWDAD 389 (435)
Q Consensus 310 gII~VyKPkGmTS~dVV~kIKRiLk~kKVGHaGTLDP~ASGVLVVgIGkATKLL~~Ll~~~KeYiatgqLG~aTDT~D~e 389 (435)
||++||||.|||||+||++||++++.+||||+|||||+||||||||+|+|||++++++..+|+|+++++||.+|||+|++
T Consensus 1 Gil~i~KP~g~tS~~vv~~ik~~~~~kKvGH~GTLDP~AsGvLiv~vG~aTkl~~~~~~~~K~Y~~~~~lG~~TdT~D~~ 80 (210)
T cd00506 1 GLFAVDKPQGPSSHDVVDTIRRIFLAEKVGHGGTLDPFATGVLVVGIGKATKLLKHLLAATKDYTAIGRLGQATDTFDAT 80 (210)
T ss_pred CEEEEEcCCCCCHHHHHHHHHHHhCccccCCCCcCCCcCeeEEEEEECHHHhhhHHHhcCCceEEEEEEECCcCCCCCCC
Confidence 49999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCeEeeccCCCCCHHHHHHHHHcCccceeeccccccccccCCeec
Q 013857 390 SPVIQREPWEHIKDEDIRKAAASFRGEIWQVPPMFSAIKVRVFHF 434 (435)
Q Consensus 390 GkVieksp~~hIT~EkLekaLssFqG~I~QiPP~YSAVKVnGkRL 434 (435)
|+|++++++.|+|.++|++++++|+|.++|+||+|||+|+||+|+
T Consensus 81 G~v~~~~~~~~it~e~l~~~l~~f~G~i~Q~pP~ySAvKv~G~ra 125 (210)
T cd00506 81 GQVIEETPYDHITHEQLERALETLTGDIQQVPPLYSAVKRQGQRA 125 (210)
T ss_pred CCEEEEeCCCCCCHHHHHHHHHHCCCeEEEeCCchheEEECCHhH
Confidence 999999999999999999999999999999999999999999986
No 2
>PRK00020 truB tRNA pseudouridine synthase B; Provisional
Probab=100.00 E-value=4.8e-45 Score=347.79 Aligned_cols=127 Identities=36% Similarity=0.631 Sum_probs=123.7
Q ss_pred CCceEEEEeCCCCCCHHHHHHHHHHhhccceeeccCCCCCCCCeEEEEEecCcccccchhcCCCcEEEEEEEECcccccC
Q 013857 307 PFGTMVLVNKPKGWTSFTVCGKLRRLVKVKKVGHAGTLDPMATGLLIVCVGKATKLVDRYQGMIKGYSGVFRLGEATSTW 386 (435)
Q Consensus 307 LnGgII~VyKPkGmTS~dVV~kIKRiLk~kKVGHaGTLDP~ASGVLVVgIGkATKLL~~Ll~~~KeYiatgqLG~aTDT~ 386 (435)
.+| |++||||.|||||+||++||++++.+||||+|||||+||||||||+|++||+++++++.+|+|+++++||.+|||+
T Consensus 9 ~~G-il~vdKP~G~TS~dvv~~vkr~~~~kKvGH~GTLDP~AtGvLiv~iG~aTKl~~~l~~~~K~Y~a~~~lG~~TdT~ 87 (244)
T PRK00020 9 LDG-VLLLDKPVGLSSNHALQRAKRTVDAAKAGHTGTLDPFATGLLVCCMGRATKISGRMLEADKTYQATLQFGEETDSG 87 (244)
T ss_pred CCe-EEEEecCCCCCHHHHHHHHHHHhCCCCCCcCCcCCCcCeeEEEEEECHHhhhhHHhccCCcEEEEEEEeCCcccCC
Confidence 567 9999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCCeEeecc--CCCCCHHHHHHHHHcCccceeeccccccccccCCeec
Q 013857 387 DADSPVIQREP--WEHIKDEDIRKAAASFRGEIWQVPPMFSAIKVRVFHF 434 (435)
Q Consensus 387 D~eGkVieksp--~~hIT~EkLekaLssFqG~I~QiPP~YSAVKVnGkRL 434 (435)
|++|+|+++.+ +.|+|.++|+++|++|+|.++|+||+|||+||||+|+
T Consensus 88 D~~G~v~~~~~~~~~~it~e~l~~~l~~f~G~i~Q~PP~ySAvKv~Gkra 137 (244)
T PRK00020 88 DLTGHIVARAPDGFAGVEEAALRDVLSRFVGTIEQIPPMYSALKRDGKPL 137 (244)
T ss_pred CCCCcEEEeccCccCCCCHHHHHHHHHhccCeEEEeCChhheEEECCeEH
Confidence 99999999987 5599999999999999999999999999999999996
No 3
>PRK02484 truB tRNA pseudouridine synthase B; Provisional
Probab=100.00 E-value=5.4e-45 Score=354.39 Aligned_cols=127 Identities=39% Similarity=0.627 Sum_probs=124.3
Q ss_pred CCceEEEEeCCCCCCHHHHHHHHHHhhccceeeccCCCCCCCCeEEEEEecCcccccchhcCCCcEEEEEEEECcccccC
Q 013857 307 PFGTMVLVNKPKGWTSFTVCGKLRRLVKVKKVGHAGTLDPMATGLLIVCVGKATKLVDRYQGMIKGYSGVFRLGEATSTW 386 (435)
Q Consensus 307 LnGgII~VyKPkGmTS~dVV~kIKRiLk~kKVGHaGTLDP~ASGVLVVgIGkATKLL~~Ll~~~KeYiatgqLG~aTDT~ 386 (435)
.|| |++||||.|||||+||+++|++++.+||||+|||||+|||||+||+|+|||+++++++.+|+|+++++||.+|||+
T Consensus 2 m~G-il~i~KP~G~TS~dvv~~vrr~l~~kKvGH~GTLDP~AtGvL~i~vG~aTkl~~~l~~~~K~Y~a~~~lG~~TdT~ 80 (294)
T PRK02484 2 ING-IINLKKEAGMTSHDAVFKLRKILQTKKIGHGGTLDPDVVGVLPIAVGKATRLIEYMTEAGKVYEGEITLGYSTTTE 80 (294)
T ss_pred cce-EEEEeCCCCCCHHHHHHHHHHHhCCCccccCCCCCCCCeeEEEEEEChhhhhhHHhccCCcEEEEEEEECCcccCC
Confidence 467 9999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCCeEeeccCCC-CCHHHHHHHHHcCccceeeccccccccccCCeec
Q 013857 387 DADSPVIQREPWEH-IKDEDIRKAAASFRGEIWQVPPMFSAIKVRVFHF 434 (435)
Q Consensus 387 D~eGkVieksp~~h-IT~EkLekaLssFqG~I~QiPP~YSAVKVnGkRL 434 (435)
|.+|+|+++.++.| ++.++|+++|++|+|.|+|+||+|||+||||+|+
T Consensus 81 D~~G~vi~~~~~~~~~~~~~l~~~l~~f~G~i~Q~PP~ySAvKv~Gkra 129 (294)
T PRK02484 81 DASGEVVAETPLTQPLTEEEVDQAMTSFTGKITQIPPMYSAVKVNGKKL 129 (294)
T ss_pred CCCCCEEEeccCCCCCCHHHHHHHHHhccCeEEEeCChhHeEeeCCHhH
Confidence 99999999999987 9999999999999999999999999999999986
No 4
>PRK00130 truB tRNA pseudouridine synthase B; Provisional
Probab=100.00 E-value=5.4e-45 Score=353.67 Aligned_cols=126 Identities=46% Similarity=0.764 Sum_probs=124.1
Q ss_pred CceEEEEeCCCCCCHHHHHHHHHHhhccceeeccCCCCCCCCeEEEEEecCcccccchhcCCCcEEEEEEEECcccccCC
Q 013857 308 FGTMVLVNKPKGWTSFTVCGKLRRLVKVKKVGHAGTLDPMATGLLIVCVGKATKLVDRYQGMIKGYSGVFRLGEATSTWD 387 (435)
Q Consensus 308 nGgII~VyKPkGmTS~dVV~kIKRiLk~kKVGHaGTLDP~ASGVLVVgIGkATKLL~~Ll~~~KeYiatgqLG~aTDT~D 387 (435)
|| |++||||.|||||+||+++|++++.+||||+|||||+|||||+||+|+|||++++++..+|+|+++++||.+|||+|
T Consensus 2 ~G-il~i~KP~G~tS~dvv~~vrr~~~~kKvGH~GTLDP~AtGvL~v~vG~aTkl~~~l~~~~K~Y~a~~~lG~~TdT~D 80 (290)
T PRK00130 2 DG-ILNILKPPGMTSFDVVRKIRKIAKIKKVGHTGTLDPLASGVLPVCLGKATKIVDYLMEGKKTYRAEIKLGVETDTYD 80 (290)
T ss_pred Ce-EEEEeCCCCCCHHHHHHHHHHHhCCCccCcCCCCCCCCeeEEEEEEChhhhhHHHhccCCcEEEEEEEECCcccCCC
Confidence 56 99999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCeEeeccCCCCCHHHHHHHHHcCccceeeccccccccccCCeec
Q 013857 388 ADSPVIQREPWEHIKDEDIRKAAASFRGEIWQVPPMFSAIKVRVFHF 434 (435)
Q Consensus 388 ~eGkVieksp~~hIT~EkLekaLssFqG~I~QiPP~YSAVKVnGkRL 434 (435)
++|+|++++++.|+|.++|+++|++|+|.|+|+||+|||+||||+|+
T Consensus 81 ~~G~i~~~~~~~~~t~~~l~~~l~~f~G~i~Q~PP~ySAvKv~Gkra 127 (290)
T PRK00130 81 REGEILKEKEVSHLTEEEIREAILSFQGEIDQVPPMYSALKINGKKL 127 (290)
T ss_pred CCCCEEEecCCCCCCHHHHHHHHHHccCeEEEECChHHeEecCCHhH
Confidence 99999999999999999999999999999999999999999999986
No 5
>PRK01550 truB tRNA pseudouridine synthase B; Provisional
Probab=100.00 E-value=5.9e-45 Score=355.48 Aligned_cols=126 Identities=44% Similarity=0.708 Sum_probs=123.5
Q ss_pred CceEEEEeCCCCCCHHHHHHHHHHhhccceeeccCCCCCCCCeEEEEEecCcccccchhcCCCcEEEEEEEECcccccCC
Q 013857 308 FGTMVLVNKPKGWTSFTVCGKLRRLVKVKKVGHAGTLDPMATGLLIVCVGKATKLVDRYQGMIKGYSGVFRLGEATSTWD 387 (435)
Q Consensus 308 nGgII~VyKPkGmTS~dVV~kIKRiLk~kKVGHaGTLDP~ASGVLVVgIGkATKLL~~Ll~~~KeYiatgqLG~aTDT~D 387 (435)
|| |++||||.|||||+||+++|++++.+||||+|||||+|||||+||+|+|||++++++..+|+|+++++||.+|||+|
T Consensus 2 ~G-il~i~KP~G~TS~dvv~~vrr~~~~kKvGH~GTLDP~AtGvL~i~vG~aTkl~~~l~~~~K~Y~a~~~lG~~TdT~D 80 (304)
T PRK01550 2 NG-VLLLHKPRGMTSHDCVFKLRKILRTKKVGHTGTLDPEVSGVLPICVGRATKIAEYLTDEGKTYEGEVTLGFSTTTED 80 (304)
T ss_pred Ce-EEEEECCCCCCHHHHHHHHHHHcCCCCcccCCCCCCcCeeEEEEEEChhhhhhHHhcCCCcEEEEEEEECCcccCCC
Confidence 56 99999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCeEeeccCCC-CCHHHHHHHHHcCccceeeccccccccccCCeec
Q 013857 388 ADSPVIQREPWEH-IKDEDIRKAAASFRGEIWQVPPMFSAIKVRVFHF 434 (435)
Q Consensus 388 ~eGkVieksp~~h-IT~EkLekaLssFqG~I~QiPP~YSAVKVnGkRL 434 (435)
++|+|+++.++.+ ++.++|+++|++|+|.|+|+||||||+||||+|+
T Consensus 81 ~~G~v~~~~~~~~~~~~~~i~~~l~~f~G~i~Q~PP~ySAvKv~Gkr~ 128 (304)
T PRK01550 81 ADGEVVETKPVDRPITREEIEAALASLTGTIEQIPPMYSAVKVNGKKL 128 (304)
T ss_pred CCCCEEeeccCCCCCCHHHHHHHHHhccceEEEeCChhHeEecCCHhH
Confidence 9999999999886 9999999999999999999999999999999986
No 6
>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=100.00 E-value=7.4e-45 Score=339.42 Aligned_cols=125 Identities=48% Similarity=0.752 Sum_probs=121.5
Q ss_pred CceEEEEeCCCCCCHHHHHHHHHHhhccceeeccCCCCCCCCeEEEEEecCcccccchhcCCCcEEEEEEEECcccccCC
Q 013857 308 FGTMVLVNKPKGWTSFTVCGKLRRLVKVKKVGHAGTLDPMATGLLIVCVGKATKLVDRYQGMIKGYSGVFRLGEATSTWD 387 (435)
Q Consensus 308 nGgII~VyKPkGmTS~dVV~kIKRiLk~kKVGHaGTLDP~ASGVLVVgIGkATKLL~~Ll~~~KeYiatgqLG~aTDT~D 387 (435)
|| |++||||.|||||+||++||++++.+||||+|||||+|||||+||+|+|||++++++..+|+|+++++||.+|||+|
T Consensus 2 ~G-~l~v~KP~g~tS~~vv~~vkk~~~~kKvGH~GTLDP~AsGvLiv~vG~~Tkl~~~~~~~~K~Y~~~~~~G~~TdT~D 80 (209)
T TIGR00431 2 NG-VLLLDKPQGMTSFDALAKVRRLLNVKKVGHTGTLDPFATGVLPILVGKATKLSPYLTDLDKEYRAEIRLGVRTDTLD 80 (209)
T ss_pred Ce-EEEEECCCCCCHHHHHHHHHHHhCCCcCCCCCCCCCcCceEEEEEEChHhhhhHHHcCCCCeEEEEEEECCcCCCCC
Confidence 56 99999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCeEeeccCCCCCHHHHHHHHHcCccceeeccccccccccCCeec
Q 013857 388 ADSPVIQREPWEHIKDEDIRKAAASFRGEIWQVPPMFSAIKVRVFHF 434 (435)
Q Consensus 388 ~eGkVieksp~~hIT~EkLekaLssFqG~I~QiPP~YSAVKVnGkRL 434 (435)
++|+|+++.++.+ +.++|+++|++|+|.++|+||+|||+||||+|+
T Consensus 81 ~~G~i~~~~~~~~-~~~~l~~~l~~f~G~~~Q~PP~ySA~Kv~G~ra 126 (209)
T TIGR00431 81 PDGQIVETRPVNP-TTEDVEAALPTFRGEIEQIPPMYSALKVNGKRL 126 (209)
T ss_pred CCCCEEEecCCCC-CHHHHHHHHHHccCcEEEECChhhEEeeCCHhH
Confidence 9999999999874 778999999999999999999999999999986
No 7
>PRK04642 truB tRNA pseudouridine synthase B; Provisional
Probab=100.00 E-value=8.3e-45 Score=354.33 Aligned_cols=127 Identities=37% Similarity=0.569 Sum_probs=124.7
Q ss_pred CCceEEEEeCCCCCCHHHHHHHHHHhhccceeeccCCCCCCCCeEEEEEecCcccccchhcCCCcEEEEEEEECcccccC
Q 013857 307 PFGTMVLVNKPKGWTSFTVCGKLRRLVKVKKVGHAGTLDPMATGLLIVCVGKATKLVDRYQGMIKGYSGVFRLGEATSTW 386 (435)
Q Consensus 307 LnGgII~VyKPkGmTS~dVV~kIKRiLk~kKVGHaGTLDP~ASGVLVVgIGkATKLL~~Ll~~~KeYiatgqLG~aTDT~ 386 (435)
.|| |++||||.|||||+||+++|++++.+||||+|||||+|||||+||+|+|||++++++..+|+|+++++||.+|||+
T Consensus 9 m~G-il~i~KP~G~TS~dvv~~vrr~~~~kKvGH~GTLDP~AtGvL~v~~G~aTkl~~~l~~~~K~Y~a~~~lG~~TdT~ 87 (300)
T PRK04642 9 LDG-ILLLDKPAGLSSNNALQAARRLLRAEKGGHTGSLDPLATGLLPLCFGEATKIAGLLLGSAKAYDAEIVLGVTTDTD 87 (300)
T ss_pred cCe-EEEEecCCCCCHHHHHHHHHHHhCCCcccCCCccCCcCeeeEEEEEChhhhhhHHhcCCCcEEEEEEEECccccCc
Confidence 567 9999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCCeEeeccCCCCCHHHHHHHHHcCccceeeccccccccccCCeec
Q 013857 387 DADSPVIQREPWEHIKDEDIRKAAASFRGEIWQVPPMFSAIKVRVFHF 434 (435)
Q Consensus 387 D~eGkVieksp~~hIT~EkLekaLssFqG~I~QiPP~YSAVKVnGkRL 434 (435)
|++|+|+++.++.+++.++|+++|++|+|.|+|+||||||+|+||+|+
T Consensus 88 D~~G~v~~~~~~~~~~~~~l~~~l~~f~G~i~Q~PP~ySAvKv~Gkrl 135 (300)
T PRK04642 88 DADGQVLRERPVPDLSAAALQAALAPLIGRIRQRAPIYSALKQGGEPL 135 (300)
T ss_pred CCCCCEEEecCCCCCCHHHHHHHHHHCCCcEEEeCCchHeEeECCeeH
Confidence 999999999999899999999999999999999999999999999997
No 8
>PRK02755 truB tRNA pseudouridine synthase B; Provisional
Probab=100.00 E-value=6.8e-45 Score=353.96 Aligned_cols=126 Identities=44% Similarity=0.741 Sum_probs=123.3
Q ss_pred CCceEEEEeCCCCCCHHHHHHHHHHhhccceeeccCCCCCCCCeEEEEEecCcccccchhcCCCcEEEEEEEECcccccC
Q 013857 307 PFGTMVLVNKPKGWTSFTVCGKLRRLVKVKKVGHAGTLDPMATGLLIVCVGKATKLVDRYQGMIKGYSGVFRLGEATSTW 386 (435)
Q Consensus 307 LnGgII~VyKPkGmTS~dVV~kIKRiLk~kKVGHaGTLDP~ASGVLVVgIGkATKLL~~Ll~~~KeYiatgqLG~aTDT~ 386 (435)
.|| |++||||.|||||+||+++|++++.+||||+|||||+|||||+||+|+|||+++++.. +|+|+++++||.+|||+
T Consensus 2 m~G-il~i~KP~G~TS~dvv~~vrr~~~~kKvGH~GTLDP~AtGvL~i~vG~aTkl~~~l~~-~K~Y~a~~~lG~~TdT~ 79 (295)
T PRK02755 2 MFG-FLNLDKPAGLTSHDCVARLRRLLRLKRVGHGGTLDPAATGVLPIALGKATRLLPYLPG-EKTYRGTIRFGVRTSTD 79 (295)
T ss_pred cce-EEEEeCCCCCCHHHHHHHHHHHhCCCccccCCCCCCcCeeEEEEEEChhhhhHHHhCC-CcEEEEEEEECCcccCC
Confidence 467 9999999999999999999999999999999999999999999999999999999997 99999999999999999
Q ss_pred CCCCCeEeeccCCCCCHHHHHHHHHcCccceeeccccccccccCCeec
Q 013857 387 DADSPVIQREPWEHIKDEDIRKAAASFRGEIWQVPPMFSAIKVRVFHF 434 (435)
Q Consensus 387 D~eGkVieksp~~hIT~EkLekaLssFqG~I~QiPP~YSAVKVnGkRL 434 (435)
|.+|+|+++.++.|++.++|+++|++|+|.|+|+||+|||+|+||+|+
T Consensus 80 D~~G~v~~~~~~~~~~~~~l~~~l~~f~G~i~Q~PP~ySAvKv~G~r~ 127 (295)
T PRK02755 80 DLQGEILSSQPWPHLSLAEIETALPQFRGKIEQRPPQYSAIQVDGERL 127 (295)
T ss_pred CCCCCEEEecCCCCCCHHHHHHHHHhccCeEEEeCChhheEeeCCHhH
Confidence 999999999999999999999999999999999999999999999996
No 9
>PRK14123 tRNA pseudouridine synthase B; Provisional
Probab=100.00 E-value=9.9e-45 Score=354.01 Aligned_cols=127 Identities=37% Similarity=0.605 Sum_probs=123.6
Q ss_pred CCceEEEEeCCCCCCHHHHHHHHHHhhccceeeccCCCCCCCCeEEEEEecCcccccchhcCCCcEEEEEEEECcccccC
Q 013857 307 PFGTMVLVNKPKGWTSFTVCGKLRRLVKVKKVGHAGTLDPMATGLLIVCVGKATKLVDRYQGMIKGYSGVFRLGEATSTW 386 (435)
Q Consensus 307 LnGgII~VyKPkGmTS~dVV~kIKRiLk~kKVGHaGTLDP~ASGVLVVgIGkATKLL~~Ll~~~KeYiatgqLG~aTDT~ 386 (435)
.|| |++||||.|||||+||+++|++++.+||||+|||||+|||||+||+|+|||++++++..+|+|+++++||.+|||+
T Consensus 2 m~G-il~i~KP~G~TS~dvv~~vrr~~~~kKvGH~GTLDP~AtGvL~v~vG~aTkl~~~l~~~~K~Y~~~~~lG~~TdT~ 80 (305)
T PRK14123 2 YNG-ILPVYKERGLTSHDVVFKLRKILKTKKIGHTGTLDPEVAGVLPVCIGNATRVSDYVMDMGKAYEATVSIGRSTTTE 80 (305)
T ss_pred cce-EEEEeCCCCCCHHHHHHHHHHHhCCCccccCcCCCCcCeeEEEEEEChhhhhHHHhcCCCcEEEEEEEECCcccCC
Confidence 467 9999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCCeEeeccCC--CCCHHHHHHHHHcCccceeeccccccccccCCeec
Q 013857 387 DADSPVIQREPWE--HIKDEDIRKAAASFRGEIWQVPPMFSAIKVRVFHF 434 (435)
Q Consensus 387 D~eGkVieksp~~--hIT~EkLekaLssFqG~I~QiPP~YSAVKVnGkRL 434 (435)
|++|+|+++.++. |+|.++|+++|++|+|+|+|+||||||+||||+|+
T Consensus 81 D~~G~vi~~~~~~~~~~~~~~l~~~l~~f~G~i~Q~PP~ySAvKv~Gkra 130 (305)
T PRK14123 81 DQTGDTLETKGVHSADFNKDDIDRLLEQFKGIIEQIPPMYSSVKVNGKKL 130 (305)
T ss_pred CCCCCEEEeccCCcCCCCHHHHHHHHHhccCceeecCChhheEeeCCHhH
Confidence 9999999999874 79999999999999999999999999999999986
No 10
>PRK03287 truB tRNA pseudouridine synthase B; Provisional
Probab=100.00 E-value=1.1e-44 Score=352.96 Aligned_cols=127 Identities=46% Similarity=0.631 Sum_probs=124.7
Q ss_pred CCceEEEEeCCCCCCHHHHHHHHHHhhccceeeccCCCCCCCCeEEEEEecCcccccchhcCCCcEEEEEEEECcccccC
Q 013857 307 PFGTMVLVNKPKGWTSFTVCGKLRRLVKVKKVGHAGTLDPMATGLLIVCVGKATKLVDRYQGMIKGYSGVFRLGEATSTW 386 (435)
Q Consensus 307 LnGgII~VyKPkGmTS~dVV~kIKRiLk~kKVGHaGTLDP~ASGVLVVgIGkATKLL~~Ll~~~KeYiatgqLG~aTDT~ 386 (435)
.|| |++||||.|||||+||+++|++++.+||||+|||||+|||||+||+|+|||+++++++.+|+|+++++||.+|||+
T Consensus 8 ~~G-il~i~KP~G~TS~dvv~~vrr~~~~kKvGH~GTLDP~AtGvL~i~vG~aTKl~~~l~~~~K~Y~a~~~lG~~TdT~ 86 (298)
T PRK03287 8 GSG-LVVVDKPAGMTSHDVVARCRRLFGTRKVGHAGTLDPMATGVLVLGVERATKLLGHLTLTDKSYTATIRLGQATTTD 86 (298)
T ss_pred cCe-EEEEeCCCCCCHHHHHHHHHHHhCCCCCCcCccCCCcceeEEEEEeChhhhhhHHHhcCCcEEEEEEEeCccccCC
Confidence 456 9999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCCeEeeccCCCCCHHHHHHHHHcCccceeeccccccccccCCeec
Q 013857 387 DADSPVIQREPWEHIKDEDIRKAAASFRGEIWQVPPMFSAIKVRVFHF 434 (435)
Q Consensus 387 D~eGkVieksp~~hIT~EkLekaLssFqG~I~QiPP~YSAVKVnGkRL 434 (435)
|++|+|+++.++.|+|.++|+++|++|+|.|+|+||+|||+|+||+|+
T Consensus 87 D~~G~v~~~~~~~~it~~~i~~~l~~f~G~i~Q~PP~ySAvKv~Gkr~ 134 (298)
T PRK03287 87 DAEGEVLASADASAVTDEAIAAAVAALTGEIMQVPSAVSAIKVDGKRA 134 (298)
T ss_pred CCCCCEEeecCCCCCCHHHHHHHHHhCcCeEEEeCChhHeEEECCHHH
Confidence 999999999999999999999999999999999999999999999986
No 11
>PRK00989 truB tRNA pseudouridine synthase B; Provisional
Probab=100.00 E-value=1.7e-44 Score=341.54 Aligned_cols=126 Identities=44% Similarity=0.666 Sum_probs=122.3
Q ss_pred CCceEEEEeCCCCCCHHHHHHHHHHhhccceeeccCCCCCCCCeEEEEEecC-cccccchhcCCCcEEEEEEEECccccc
Q 013857 307 PFGTMVLVNKPKGWTSFTVCGKLRRLVKVKKVGHAGTLDPMATGLLIVCVGK-ATKLVDRYQGMIKGYSGVFRLGEATST 385 (435)
Q Consensus 307 LnGgII~VyKPkGmTS~dVV~kIKRiLk~kKVGHaGTLDP~ASGVLVVgIGk-ATKLL~~Ll~~~KeYiatgqLG~aTDT 385 (435)
.|| |++||||.|||||+||++||++++.+||||+|||||+||||||||+|+ +||+++++++.+|+|+++++||.+|||
T Consensus 8 ~~G-~l~i~KP~g~TS~dvv~~ikk~~~~kKvGH~GTLDP~AtGvLiv~vG~~aTkl~~~~~~~~K~Y~~~~~~G~~TdT 86 (230)
T PRK00989 8 KEG-ILLVDKPQGRTSFSLIRSLTKLIGVKKIGHAGTLDPFATGVMVMLIGRKFTRLSDILLFEDKEYAAVAHLGTTTDS 86 (230)
T ss_pred CCE-EEEEeCCCCCCHHHHHHHHHHHhCCCcCCcCccCCCCCeeEEEEEECCchhhhHHHhcCCCcEEEEEEEECCcccC
Confidence 566 999999999999999999999999999999999999999999999999 799999999999999999999999999
Q ss_pred CCCCCCeEeeccCCCCCHHHHHHHHHcCccceeeccccccccccCCeec
Q 013857 386 WDADSPVIQREPWEHIKDEDIRKAAASFRGEIWQVPPMFSAIKVRVFHF 434 (435)
Q Consensus 386 ~D~eGkVieksp~~hIT~EkLekaLssFqG~I~QiPP~YSAVKVnGkRL 434 (435)
+|.+|+|+++.+. +++.++|+++|++|+|.++|+||+|||+|+||+|+
T Consensus 87 ~D~~G~vi~~~~~-~~~~~~i~~~l~~f~G~~~Q~PP~ySAvKv~Gkra 134 (230)
T PRK00989 87 YDCDGKIVGRSKK-IPTLEEVLSAASYFQGEIQQVPPMFSAKKVQGKKL 134 (230)
T ss_pred CCCCCcEEEecCC-CCCHHHHHHHHHhCcceEEeeCChhHeEEECCHhH
Confidence 9999999999884 78999999999999999999999999999999986
No 12
>PRK05033 truB tRNA pseudouridine synthase B; Provisional
Probab=100.00 E-value=2.1e-44 Score=352.93 Aligned_cols=126 Identities=40% Similarity=0.636 Sum_probs=123.6
Q ss_pred CCceEEEEeCCCCCCHHHHHHHHHHhhccceeeccCCCCCCCCeEEEEEecCcccccchhcCCCcEEEEEEEECcccccC
Q 013857 307 PFGTMVLVNKPKGWTSFTVCGKLRRLVKVKKVGHAGTLDPMATGLLIVCVGKATKLVDRYQGMIKGYSGVFRLGEATSTW 386 (435)
Q Consensus 307 LnGgII~VyKPkGmTS~dVV~kIKRiLk~kKVGHaGTLDP~ASGVLVVgIGkATKLL~~Ll~~~KeYiatgqLG~aTDT~ 386 (435)
.+| |++||||.|||||+||+++|++++.+||||+|||||+|||||+||+|+|||++++++..+|+|+++++||.+|||+
T Consensus 9 ~~G-il~i~KP~G~TS~dvv~~vrr~l~~kKvGH~GTLDP~AtGvL~v~vG~aTkl~~~~~~~~K~Y~a~~~lG~~TdT~ 87 (312)
T PRK05033 9 ING-VLLLDKPQGMSSNDALQKVKRLFNANKAGHTGALDPLATGMLPICLGEATKFSQYLLDSDKRYRVTARLGQRTDTS 87 (312)
T ss_pred CCe-EEEEeCCCCCCHHHHHHHHHHHhCCCCCCCCCcCCCcCeeEEEEEECHHhhhhHHhcCCCcEEEEEEEECCcccCC
Confidence 567 9999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCCeEeeccCCCCCHHHHHHHHHcCccceeeccccccccccCCeec
Q 013857 387 DADSPVIQREPWEHIKDEDIRKAAASFRGEIWQVPPMFSAIKVRVFHF 434 (435)
Q Consensus 387 D~eGkVieksp~~hIT~EkLekaLssFqG~I~QiPP~YSAVKVnGkRL 434 (435)
|++|+|+++.++ |+|.++|+++|++|+|.|+|+||+|||+||||+|+
T Consensus 88 D~~G~v~~~~~~-~~t~~~l~~~l~~f~G~i~Q~PP~ySAvKv~Gkra 134 (312)
T PRK05033 88 DADGEVVEERPV-TLSAEQLEAALEKFRGDIEQVPSMYSALKYQGQPL 134 (312)
T ss_pred CCCCCEEEeecC-CCCHHHHHHHHHHCcCcEEEeCChhHeEeeCCeEH
Confidence 999999999998 89999999999999999999999999999999996
No 13
>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=100.00 E-value=2.7e-44 Score=346.81 Aligned_cols=125 Identities=47% Similarity=0.709 Sum_probs=123.2
Q ss_pred eEEEEeCCCCCCHHHHHHHHHHhhccceeeccCCCCCCCCeEEEEEecCcccccchhcCCCcEEEEEEEECcccccCCCC
Q 013857 310 TMVLVNKPKGWTSFTVCGKLRRLVKVKKVGHAGTLDPMATGLLIVCVGKATKLVDRYQGMIKGYSGVFRLGEATSTWDAD 389 (435)
Q Consensus 310 gII~VyKPkGmTS~dVV~kIKRiLk~kKVGHaGTLDP~ASGVLVVgIGkATKLL~~Ll~~~KeYiatgqLG~aTDT~D~e 389 (435)
||++||||.|||||+||+++|++++.+||||+|||||+|||||+||+|+|||++++++..+|+|+++++||.+|||+|++
T Consensus 1 Gil~i~KP~G~tS~~vv~~vr~~~~~kKvGH~GTLDP~AtGvL~v~vG~aTkl~~~l~~~~K~Y~~~~~~G~~TdT~D~~ 80 (277)
T cd02573 1 GILLLDKPAGLTSHDVVQKVRRLLGTKKVGHTGTLDPLATGVLPIALGEATKLSQYLLDADKTYRATVRLGEATDTDDAE 80 (277)
T ss_pred CEEEEECCCCCCHHHHHHHHHHHhCcCccCCCCCCCCcCeEEEEEEEChHHhhHHHhcCCCcEEEEEEEECCcccCCCCC
Confidence 49999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCeEeeccCCCCCHHHHHHHHHcCccceeeccccccccccCCeec
Q 013857 390 SPVIQREPWEHIKDEDIRKAAASFRGEIWQVPPMFSAIKVRVFHF 434 (435)
Q Consensus 390 GkVieksp~~hIT~EkLekaLssFqG~I~QiPP~YSAVKVnGkRL 434 (435)
|+|++++++.|+|.++|+++|++|+|.++|+||+|||+||||+|+
T Consensus 81 G~v~~~~~~~~~~~~~i~~~l~~f~G~i~Q~PP~ySAvkv~G~ra 125 (277)
T cd02573 81 GEIIETSPPPRLTEEEIEAALKAFTGEIEQVPPMYSAVKVNGKRL 125 (277)
T ss_pred CCEEEecCCCCCCHHHHHHHHHHccCcEEeeCChhHeEeeCCccH
Confidence 999999999999999999999999999999999999999999996
No 14
>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=100.00 E-value=1.9e-44 Score=353.42 Aligned_cols=125 Identities=41% Similarity=0.687 Sum_probs=122.3
Q ss_pred eEEEEeCCCCCCHHHHHHHHHHhhcc-----------------------------ceeeccCCCCCCCCeEEEEEecCcc
Q 013857 310 TMVLVNKPKGWTSFTVCGKLRRLVKV-----------------------------KKVGHAGTLDPMATGLLIVCVGKAT 360 (435)
Q Consensus 310 gII~VyKPkGmTS~dVV~kIKRiLk~-----------------------------kKVGHaGTLDP~ASGVLVVgIGkAT 360 (435)
|||+||||.|||||+||++||++|+. +||||+|||||+||||||||||+||
T Consensus 1 Gil~i~KP~G~TS~~vv~~lk~~l~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~KiGH~GTLDPlAsGVLvvgvG~aT 80 (312)
T cd02867 1 GVFAINKPSGITSAQVLNDLKPLFLNSALFKDKIQRAVAKRGKKARRRKGRKRSKLKIGHGGTLDPLATGVLVVGVGAGT 80 (312)
T ss_pred CeEEEeCCCCCCHHHHHHHHHHHhcccccccchhhhhhhhhhhhhhhhccccccccccccccccCCccceeEEEEECcHH
Confidence 49999999999999999999999875 7999999999999999999999999
Q ss_pred cccchhcCCCcEEEEEEEECcccccCCCCCCeEeeccCCCCCHHHHHHHHHcCccceeeccccccccccCCeec
Q 013857 361 KLVDRYQGMIKGYSGVFRLGEATSTWDADSPVIQREPWEHIKDEDIRKAAASFRGEIWQVPPMFSAIKVRVFHF 434 (435)
Q Consensus 361 KLL~~Ll~~~KeYiatgqLG~aTDT~D~eGkVieksp~~hIT~EkLekaLssFqG~I~QiPP~YSAVKVnGkRL 434 (435)
|++++++.++|+|+++++||.+|||+|++|+|+++.++.|||.++|+++|++|+|.|+|+||+|||+|+||+||
T Consensus 81 K~l~~~l~~~K~Y~~~~~lG~~TdT~D~eG~Ii~~~~~~~it~e~i~~~l~~F~G~i~Q~PP~ySAvKv~Gkrl 154 (312)
T cd02867 81 KQLQDYLSCSKTYEATGLFGASTTTYDREGKILKKKPYSHITREDIEEVLAKFRGDIKQVPPLYSALKMDGKRL 154 (312)
T ss_pred HHHHHHhcCCceEEEEEEeCCcccCCCCCCCEEEecCCCCCCHHHHHHHHHhcceeeeeeCcchheeeeCCHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999987
No 15
>PRK14124 tRNA pseudouridine synthase B; Provisional
Probab=100.00 E-value=2.6e-44 Score=351.73 Aligned_cols=126 Identities=44% Similarity=0.631 Sum_probs=123.3
Q ss_pred CCceEEEEeCCCCCCHHHHHHHHHHhhccceeeccCCCCCCCCeEEEEEecCcccccchhcCCCcEEEEEEEECcccccC
Q 013857 307 PFGTMVLVNKPKGWTSFTVCGKLRRLVKVKKVGHAGTLDPMATGLLIVCVGKATKLVDRYQGMIKGYSGVFRLGEATSTW 386 (435)
Q Consensus 307 LnGgII~VyKPkGmTS~dVV~kIKRiLk~kKVGHaGTLDP~ASGVLVVgIGkATKLL~~Ll~~~KeYiatgqLG~aTDT~ 386 (435)
.|| |++||||.|||||+||+++|++++.+||||+|||||+|||||+||+|+|||++++++..+|+|+++++||.+|||+
T Consensus 2 m~G-il~i~KP~G~TS~dvv~~vrr~l~~kKvGH~GTLDP~AtGvL~v~vG~aTkl~~~l~~~~K~Y~a~~~lG~~TdT~ 80 (308)
T PRK14124 2 KHG-FLVAYKPKGPTSHDVVDEVRKKLKTRKVGHAGTLDPFATGVLIVGVNKATRLLEYLKNEKKVYYVKMRLGLITETF 80 (308)
T ss_pred Cce-EEEEECCCCCCHHHHHHHHHHHcCCCccCcCcCCCCCCcEEEEEEEChHHhhhHHHhcCCceEEEEEEeCccccCC
Confidence 467 9999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCCeEeeccCCCCCHHHHHHHHHcCccceeeccccccccccCCeec
Q 013857 387 DADSPVIQREPWEHIKDEDIRKAAASFRGEIWQVPPMFSAIKVRVFHF 434 (435)
Q Consensus 387 D~eGkVieksp~~hIT~EkLekaLssFqG~I~QiPP~YSAVKVnGkRL 434 (435)
|++|+|++++++ ++|.++|+++|++|+|.++|+||+|||+|+||+|+
T Consensus 81 D~~G~vi~~~~~-~~~~~~i~~~l~~f~G~i~Q~PP~ySAvKv~Gkra 127 (308)
T PRK14124 81 DITGEVVEEREC-NVTEEEIREAIFSFVGEYKQVPPAYSAKKYKGERL 127 (308)
T ss_pred CCCCCEEEecCC-CCCHHHHHHHHHhCcCeEEEeCCchHeEEECChhH
Confidence 999999999998 89999999999999999999999999999999986
No 16
>PRK14122 tRNA pseudouridine synthase B; Provisional
Probab=100.00 E-value=3.7e-44 Score=351.29 Aligned_cols=124 Identities=39% Similarity=0.614 Sum_probs=122.8
Q ss_pred EEEEeCCCCCCHHHHHHHHHHhhccceeeccCCCCCCCCeEEEEEecCcccccchhcCCCcEEEEEEEECcccccCCCCC
Q 013857 311 MVLVNKPKGWTSFTVCGKLRRLVKVKKVGHAGTLDPMATGLLIVCVGKATKLVDRYQGMIKGYSGVFRLGEATSTWDADS 390 (435)
Q Consensus 311 II~VyKPkGmTS~dVV~kIKRiLk~kKVGHaGTLDP~ASGVLVVgIGkATKLL~~Ll~~~KeYiatgqLG~aTDT~D~eG 390 (435)
|++||||.|||||+||+++|++++.+||||+|||||+|||||+||+|+|||++++++..+|+|+++++||.+|||+|++|
T Consensus 3 il~idKP~G~TS~dvv~~vrr~l~~kKvGH~GTLDP~AtGvL~i~iG~aTKl~~~l~~~~K~Y~a~~~lG~~TdT~D~eG 82 (312)
T PRK14122 3 VYAVDKPLGLTSHDVVNRARRALGTRRVGHTGTLDPLATGVLVLCTDDSTKLVPFLSAEDKEYLAWVSFGATTPTLDAEG 82 (312)
T ss_pred EEEEECCCCCCHHHHHHHHHHHhCCCCCCCCCCCCCcCeeeEEEEEChhhhhhHHhcCCCceEEEEEEECCcCCCCCCCC
Confidence 79999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CeEeeccCCCCCHHHHHHHHHcCccceeeccccccccccCCeec
Q 013857 391 PVIQREPWEHIKDEDIRKAAASFRGEIWQVPPMFSAIKVRVFHF 434 (435)
Q Consensus 391 kVieksp~~hIT~EkLekaLssFqG~I~QiPP~YSAVKVnGkRL 434 (435)
+|+++.++.|++.++|+++|++|+|.|+|+||+|||+||||+|+
T Consensus 83 ~i~~~~~~~~~~~~~l~~~l~~f~G~i~Q~PP~ySAvKv~Gkra 126 (312)
T PRK14122 83 PISEEAPVSPLDEKDLEAALPGFLGLTEQVPPQYSAIKVGGVRA 126 (312)
T ss_pred CEEEecCCCCCCHHHHHHHHHhCcCeEEEeCChHHeEEECCeEH
Confidence 99999999999999999999999999999999999999999996
No 17
>PRK01851 truB tRNA pseudouridine synthase B; Provisional
Probab=100.00 E-value=7.5e-44 Score=347.94 Aligned_cols=126 Identities=42% Similarity=0.639 Sum_probs=123.4
Q ss_pred CCceEEEEeCCCCCCHHHHHHHHHHhhccceeeccCCCCCCCCeEEEEEecCcccccchhcCCCcEEEEEEEECcccccC
Q 013857 307 PFGTMVLVNKPKGWTSFTVCGKLRRLVKVKKVGHAGTLDPMATGLLIVCVGKATKLVDRYQGMIKGYSGVFRLGEATSTW 386 (435)
Q Consensus 307 LnGgII~VyKPkGmTS~dVV~kIKRiLk~kKVGHaGTLDP~ASGVLVVgIGkATKLL~~Ll~~~KeYiatgqLG~aTDT~ 386 (435)
.+| |++||||.|||||+||+++|++++.+||||+|||||+|||||+||+|+|||++++++..+|+|+++++||.+|||+
T Consensus 15 ~~G-il~i~KP~G~TS~dvv~~vrr~l~~kKvGH~GTLDP~AtGvL~v~vG~aTkl~~~l~~~~K~Y~~~~~lG~~TdT~ 93 (303)
T PRK01851 15 VDG-VLLLDKPLGLSSNDALQRAKRLLRAKKAGHTGTLDPLATGLLPLCFGEATKFSQDLLDADKTYEATLRLGVRTSTG 93 (303)
T ss_pred CCe-EEEEeCCCCCCHHHHHHHHHHHhCcccCCCCCCCCCCCceEEEEEECHHHhhhHHhcccCeEEEEEEEECCccCCC
Confidence 467 9999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCCeEeeccCCCCCHHHHHHHHHcCccceeeccccccccccCCeec
Q 013857 387 DADSPVIQREPWEHIKDEDIRKAAASFRGEIWQVPPMFSAIKVRVFHF 434 (435)
Q Consensus 387 D~eGkVieksp~~hIT~EkLekaLssFqG~I~QiPP~YSAVKVnGkRL 434 (435)
|++|+|+++.++. +|.++|+++|++|+|.|+|+||+|||+||||+|+
T Consensus 94 D~~G~v~~~~~~~-~t~~~i~~~l~~f~G~i~Q~PP~ySAvKv~Gkra 140 (303)
T PRK01851 94 DAEGEVLATRPVD-CDPAALEAALARFTGEIRQVPPMYSALKKDGKPL 140 (303)
T ss_pred CCCCCEEeecCCC-CCHHHHHHHHHhccCeeeeeCCchheEeeCCeeH
Confidence 9999999999986 9999999999999999999999999999999996
No 18
>PRK01528 truB tRNA pseudouridine synthase B; Provisional
Probab=100.00 E-value=3.9e-44 Score=348.34 Aligned_cols=125 Identities=33% Similarity=0.452 Sum_probs=122.1
Q ss_pred CceEEEEeCCCCCCHHHHHHHHHHhhccceeeccCCCCCCCCeEEEEEecCcccccchhcCCCcEEEEEEEECcccccCC
Q 013857 308 FGTMVLVNKPKGWTSFTVCGKLRRLVKVKKVGHAGTLDPMATGLLIVCVGKATKLVDRYQGMIKGYSGVFRLGEATSTWD 387 (435)
Q Consensus 308 nGgII~VyKPkGmTS~dVV~kIKRiLk~kKVGHaGTLDP~ASGVLVVgIGkATKLL~~Ll~~~KeYiatgqLG~aTDT~D 387 (435)
|| |++||||.|||||+||+++|++++.+||||+|||||+|||||+||+|+|||+++++++.+|+|+++++||.+|||+|
T Consensus 3 ~G-iL~i~KP~G~TS~dvv~~vrk~~~~kKvGH~GTLDP~AtGvL~v~vG~aTKl~~~l~~~~K~Y~~~~~lG~~TdT~D 81 (292)
T PRK01528 3 NY-WLNIYKPRGISSAKLVSIVKKILGKVKIGHAGTLDVEAEGVLPLAVGEATKLVQLLIDAKKTYIFTVKFGKQTDSGD 81 (292)
T ss_pred CE-EEEEeCCCCCCHHHHHHHHHHHcCCCccCcCccCCCcCceEEEEEEChHhhhhHHHhcCCceEEEEEEECCcccCCC
Confidence 45 99999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCeEeeccCCCCCHHHHHHHHHcCccceeeccccccccccCCeec
Q 013857 388 ADSPVIQREPWEHIKDEDIRKAAASFRGEIWQVPPMFSAIKVRVFHF 434 (435)
Q Consensus 388 ~eGkVieksp~~hIT~EkLekaLssFqG~I~QiPP~YSAVKVnGkRL 434 (435)
++|+|+++.++. ++.++|+++|++|+|.|+|+||+|||+||||+|+
T Consensus 82 ~~G~v~~~~~~~-~~~e~l~~~l~~f~G~i~Q~PP~ySAvKv~G~ra 127 (292)
T PRK01528 82 YAGKVIATKDYI-PSKEEAYAVCSKFIGNITQIPPAFSALKVNGVRA 127 (292)
T ss_pred CCCCEEEecCCC-CCHHHHHHHHHhccceEEeeCChhHeEEECCHhH
Confidence 999999999987 5999999999999999999999999999999986
No 19
>PRK05389 truB tRNA pseudouridine synthase B; Provisional
Probab=100.00 E-value=5.6e-44 Score=348.86 Aligned_cols=126 Identities=40% Similarity=0.542 Sum_probs=122.7
Q ss_pred CCceEEEEeCCCCCCHHHHHHHHHHhhccceeeccCCCCCCCCeEEEEEecCcccccchhcCCCcEEEEEEEECcccccC
Q 013857 307 PFGTMVLVNKPKGWTSFTVCGKLRRLVKVKKVGHAGTLDPMATGLLIVCVGKATKLVDRYQGMIKGYSGVFRLGEATSTW 386 (435)
Q Consensus 307 LnGgII~VyKPkGmTS~dVV~kIKRiLk~kKVGHaGTLDP~ASGVLVVgIGkATKLL~~Ll~~~KeYiatgqLG~aTDT~ 386 (435)
.|| |++||||.|||||+||++||++++.+||||+|||||+|||||+||+|+|||++++++..+|+|+++++||.+|||+
T Consensus 12 ~~G-il~i~KP~G~TS~dvv~~vrk~~~~kKvGH~GTLDP~AtGvL~v~vG~aTkl~~~l~~~~K~Y~a~~~lG~~TdT~ 90 (305)
T PRK05389 12 ISG-WLILDKPAGMTSTEAVSKVKWLFDAQKAGHAGTLDPLASGVLPIALGEATKTVPYVMDGTKRYRFTVAWGEERDTD 90 (305)
T ss_pred CCe-EEEEeCCCCCCHHHHHHHHHHHhcccccCCcccCCCCCceEEEEEEChhhhhhHHhccCCcEEEEEEEECCcccCC
Confidence 567 9999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCCeEeeccCCCCCHHHHHHHHHcCccceeeccccccccccCCeec
Q 013857 387 DADSPVIQREPWEHIKDEDIRKAAASFRGEIWQVPPMFSAIKVRVFHF 434 (435)
Q Consensus 387 D~eGkVieksp~~hIT~EkLekaLssFqG~I~QiPP~YSAVKVnGkRL 434 (435)
|++|+|+++.++ +++.++|+++|++|+|+|+|+||+|||+|+||+|+
T Consensus 91 D~~G~v~~~~~~-~~~~~~i~~~l~~f~G~i~Q~PP~ySAvKv~Gkra 137 (305)
T PRK05389 91 DLEGEVTATSDV-RPTDEEIRAALPAFTGEIMQVPPQFSAIKIDGERA 137 (305)
T ss_pred CCCCCEEEecCC-CCCHHHHHHHHHhccceEEEeCCchheEEECCHhH
Confidence 999999999886 48999999999999999999999999999999996
No 20
>PRK04099 truB tRNA pseudouridine synthase B; Provisional
Probab=100.00 E-value=7e-44 Score=344.15 Aligned_cols=125 Identities=34% Similarity=0.475 Sum_probs=122.4
Q ss_pred CceEEEEeCCCCCCHHHHHHHHHHhhccceeeccCCCCCCCCeEEEEEecCcccccchhcCCCcEEEEEEEECcccccCC
Q 013857 308 FGTMVLVNKPKGWTSFTVCGKLRRLVKVKKVGHAGTLDPMATGLLIVCVGKATKLVDRYQGMIKGYSGVFRLGEATSTWD 387 (435)
Q Consensus 308 nGgII~VyKPkGmTS~dVV~kIKRiLk~kKVGHaGTLDP~ASGVLVVgIGkATKLL~~Ll~~~KeYiatgqLG~aTDT~D 387 (435)
|| |++||||.|||||+||++||++++.+||||+|||||+|||||+||+|+|||++++++..+|+|+++++||.+|||+|
T Consensus 2 ng-il~vdKP~g~tS~~vv~~ikk~~~~kKvGH~GTLDP~AtGvLiv~iG~aTKl~~~l~~~~K~Y~a~~~lG~~TdT~D 80 (273)
T PRK04099 2 NR-LFVANKPAGMSSNAFLSRLKRKYGVKKAGFSGTLDPFAKGVLIVAFGQYTKLFRFLKKTPKTYRATLWLGASSPSLD 80 (273)
T ss_pred Ce-EEEEeCCCCCCHHHHHHHHHHHhCCCccccCccCCCCCeeEEEEEEChHhhhHHHhccCCceEEEEEEECCcccCCC
Confidence 56 99999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCeEeeccCCCCCHHHHHHHHHcCccceeeccccccccccCCeec
Q 013857 388 ADSPVIQREPWEHIKDEDIRKAAASFRGEIWQVPPMFSAIKVRVFHF 434 (435)
Q Consensus 388 ~eGkVieksp~~hIT~EkLekaLssFqG~I~QiPP~YSAVKVnGkRL 434 (435)
.+| |++..++.+++.++|+++|++|+|+++|+||+|||+|+||+|+
T Consensus 81 ~e~-i~~~~~~~~~~~~~i~~~l~~f~G~i~Q~PP~ySAvKv~Gkra 126 (273)
T PRK04099 81 IEN-IESIQIIKPFDKDLIEKILKSLQGEISYTPPKFSAKKINGKRA 126 (273)
T ss_pred Ccc-eEEeccCCCCCHHHHHHHHHhCcceEEEeCChhhEEeeCCHhH
Confidence 998 8899999999999999999999999999999999999999986
No 21
>PRK02193 truB tRNA pseudouridine synthase B; Provisional
Probab=100.00 E-value=6.8e-44 Score=344.87 Aligned_cols=125 Identities=34% Similarity=0.550 Sum_probs=122.5
Q ss_pred eEEEEeCCCCCCHHHHHHHHHHhhccceeeccCCCCCCCCeEEEEEecCcccccchhcCCCcEEEEEEEECcccccCCCC
Q 013857 310 TMVLVNKPKGWTSFTVCGKLRRLVKVKKVGHAGTLDPMATGLLIVCVGKATKLVDRYQGMIKGYSGVFRLGEATSTWDAD 389 (435)
Q Consensus 310 gII~VyKPkGmTS~dVV~kIKRiLk~kKVGHaGTLDP~ASGVLVVgIGkATKLL~~Ll~~~KeYiatgqLG~aTDT~D~e 389 (435)
.|++||||.|||||+||+++|++++.+||||+|||||+|||||+||+|+|||++++++..+|+|+++++||.+|||+|.+
T Consensus 1 ~il~i~KP~G~tS~dvv~~vrr~~~~kKvGH~GTLDP~AtGvL~v~vG~aTkl~~~l~~~~K~Y~a~~~lG~~TdT~D~~ 80 (279)
T PRK02193 1 MIKLLYKPKGISSFKFIKNFAKTNNIKKIGHTGTLDPLASGLLLVATDEDTKLIDYLDQKDKTYIAKIKFGFISTTYDSE 80 (279)
T ss_pred CEEEEECCCCCCHHHHHHHHHHHcCCCccccCccCCCcCeeEEEEEEChhhhhhHHhccCCcEEEEEEEeCCcccCCCCC
Confidence 48999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCeEeeccCCCCCHHHHHHHHHcCccceeeccccccccccCCeec
Q 013857 390 SPVIQREPWEHIKDEDIRKAAASFRGEIWQVPPMFSAIKVRVFHF 434 (435)
Q Consensus 390 GkVieksp~~hIT~EkLekaLssFqG~I~QiPP~YSAVKVnGkRL 434 (435)
|+|+++.++.+++.++|+++|++|+|.|+|+||+|||+||||+|+
T Consensus 81 G~i~~~~~~~~~~~~~l~~~l~~f~G~i~Q~PP~ySAvKv~Gkra 125 (279)
T PRK02193 81 GQIINVSQNIKVTKENLEEALNNLVGSQKQVPPVFSAKKVNGKRA 125 (279)
T ss_pred CCEEeecCCCCCCHHHHHHHHHhCcCeEEEeCChHHeEeeCCHhH
Confidence 999998888899999999999999999999999999999999986
No 22
>PRK14846 truB tRNA pseudouridine synthase B; Provisional
Probab=100.00 E-value=4.4e-43 Score=347.40 Aligned_cols=125 Identities=31% Similarity=0.437 Sum_probs=121.7
Q ss_pred CceEEEEeCCCCCCHHHHHHHHHHhhccceeeccCCCCCCCCeEEEEEecCcccccchhcCCCcEEEEEEEECcccccCC
Q 013857 308 FGTMVLVNKPKGWTSFTVCGKLRRLVKVKKVGHAGTLDPMATGLLIVCVGKATKLVDRYQGMIKGYSGVFRLGEATSTWD 387 (435)
Q Consensus 308 nGgII~VyKPkGmTS~dVV~kIKRiLk~kKVGHaGTLDP~ASGVLVVgIGkATKLL~~Ll~~~KeYiatgqLG~aTDT~D 387 (435)
|| |++||||.|||||+||+++|++++.+||||+|||||+||||||||+|+|||+++++++.+|+|+++++||.+|||+|
T Consensus 3 nG-iL~idKP~G~TS~dvv~~vrk~l~~kKVGH~GTLDP~AtGVL~i~vG~aTKl~~~l~~~~K~Y~a~~~lG~~TDT~D 81 (345)
T PRK14846 3 NY-WLNIYKPRGISSAQLVSIVKKILGKTKIGHAGTLDVEAEGILPFAVGEATKLIHLLIDARKTYIFTVKFGMQTNSGD 81 (345)
T ss_pred Ce-EEEEeCCCCCCHHHHHHHHHHHhCCCcCCcCccCCCcCceEEEEEEChhhhhhHHHhcCCceEEEEEEECCccCCCC
Confidence 45 99999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCeEeeccCCCCCHHHHHHHHHcCccceeeccccccccccCCeec
Q 013857 388 ADSPVIQREPWEHIKDEDIRKAAASFRGEIWQVPPMFSAIKVRVFHF 434 (435)
Q Consensus 388 ~eGkVieksp~~hIT~EkLekaLssFqG~I~QiPP~YSAVKVnGkRL 434 (435)
++|+|+++.++. ++.++|+++|++|+|.|+|+||||||+|+||+|+
T Consensus 82 ~eG~ii~~~~~~-~~~e~l~~~L~~f~G~i~Q~PP~ySAvKv~Gkra 127 (345)
T PRK14846 82 CAGKVIATKDCI-PSQEEAYAVCSKFIGNVTQIPPAFSALKVNGVRA 127 (345)
T ss_pred CCCCEEEecCCC-CCHHHHHHHHHhCcceEEeeCChhheEeECChhH
Confidence 999999998875 7899999999999999999999999999999986
No 23
>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=100.00 E-value=9.8e-39 Score=284.02 Aligned_cols=105 Identities=50% Similarity=0.808 Sum_probs=95.5
Q ss_pred HHhhccceeeccCCCCCCCCeEEEEEecCcccccchhcCCCcEEEEEEEECcccccCCCCCCeEeeccCCCCCHHHHHHH
Q 013857 330 RRLVKVKKVGHAGTLDPMATGLLIVCVGKATKLVDRYQGMIKGYSGVFRLGEATSTWDADSPVIQREPWEHIKDEDIRKA 409 (435)
Q Consensus 330 KRiLk~kKVGHaGTLDP~ASGVLVVgIGkATKLL~~Ll~~~KeYiatgqLG~aTDT~D~eGkVieksp~~hIT~EkLeka 409 (435)
|++++.+||||+|||||+|||||+||+|+|||+++++++.+|+|+++++||.+|||+|++|+|+++.++.|+|.++|+++
T Consensus 1 r~~~~~~KvGH~GTLDP~AsGvL~v~vg~~Tkl~~~l~~~~K~Y~~~~~lG~~TdT~D~~G~v~~~~~~~~it~e~l~~~ 80 (149)
T PF01509_consen 1 RRILGIKKVGHGGTLDPFASGVLVVGVGKATKLLSYLQNSDKEYVATIRLGVETDTYDIEGEVTETKPYDHITEEDLEKV 80 (149)
T ss_dssp HHHTTBSSEEESS-SSTT-EEEEEEEEGGGGGGHHHHTTSEEEEEEEEEESSEETTSBTTSSEEEE---TT--HHHHHHH
T ss_pred CcccCcceeccccccCCcceEEEEEEECCcchHHHHhhccCCEEEEEEEEEEEeCCcceeeeEEEeeccccCCHHHHHHH
Confidence 68899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHcCccceeeccccccccccCCeec
Q 013857 410 AASFRGEIWQVPPMFSAIKVRVFHF 434 (435)
Q Consensus 410 LssFqG~I~QiPP~YSAVKVnGkRL 434 (435)
|++|+|+++|+||+|||+|+||+|+
T Consensus 81 l~~f~G~~~Q~pP~ySAvki~G~ra 105 (149)
T PF01509_consen 81 LAKFQGEIEQVPPMYSAVKINGKRA 105 (149)
T ss_dssp HHHTSEEEEES-SSSSSSECTTCEH
T ss_pred HHhCcCCEeeeCchheeEcCCCccH
Confidence 9999999999999999999999996
No 24
>COG0130 TruB Pseudouridine synthase [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=5.7e-37 Score=295.82 Aligned_cols=109 Identities=46% Similarity=0.770 Sum_probs=103.9
Q ss_pred CCcCCCC---ceEEEEeCCCCCCHHHHHHHHHHhhccceeeccCCCCCCCCeEEEEEecCcccccchhcCCCcEEEEEEE
Q 013857 302 PTWDGPF---GTMVLVNKPKGWTSFTVCGKLRRLVKVKKVGHAGTLDPMATGLLIVCVGKATKLVDRYQGMIKGYSGVFR 378 (435)
Q Consensus 302 ~~wd~Ln---GgII~VyKPkGmTS~dVV~kIKRiLk~kKVGHaGTLDP~ASGVLVVgIGkATKLL~~Ll~~~KeYiatgq 378 (435)
+..+..+ | |++||||.|||||+|++|+|++|+.+|+||+|||||+|||||+||+|+|||++++++...|+|+|+++
T Consensus 6 ~~~~~i~~~~G-il~ldKP~G~tS~~~v~~vkkil~~~K~GH~GTLDP~atGvLpi~ig~aTKl~~~l~~~~K~Y~a~~~ 84 (271)
T COG0130 6 PEKRPIEIYIG-VINLDKPPGPTSHEVVAWVKRILGVEKAGHGGTLDPLATGVLPICLGEATKLVQYLLDADKEYVATVR 84 (271)
T ss_pred ccccccccccc-eEEeeCCCCCCHHHHHHHHHHHhCccccccccccCCcccceEEEEechhHhHHHHHhhCCcEEEEEEE
Confidence 3444455 7 99999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ECcccccCCCCCCeEeeccCCCCCHHHHHHHHHcCccceeeccccccccc
Q 013857 379 LGEATSTWDADSPVIQREPWEHIKDEDIRKAAASFRGEIWQVPPMFSAIK 428 (435)
Q Consensus 379 LG~aTDT~D~eGkVieksp~~hIT~EkLekaLssFqG~I~QiPP~YSAVK 428 (435)
||.+|| +.++|+++|..|+|.|+|+||||||+|
T Consensus 85 lG~~t~-----------------~~e~i~~~l~~F~G~I~Q~PP~~SAvK 117 (271)
T COG0130 85 LGDQTD-----------------SEEEVRAALEAFTGEIYQIPPMFSAVK 117 (271)
T ss_pred eCCcCC-----------------CHHHHHHHHHhcceeeEecCCchhhcc
Confidence 999998 689999999999999999999999999
No 25
>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=100.00 E-value=3e-36 Score=275.26 Aligned_cols=104 Identities=40% Similarity=0.725 Sum_probs=100.4
Q ss_pred CceEEEEeCCCCCCHHHHHHHHHHhhccceeeccCCCCCCCCeEEEEEecCcccccchhcCCCcEEEEEEEECcccccCC
Q 013857 308 FGTMVLVNKPKGWTSFTVCGKLRRLVKVKKVGHAGTLDPMATGLLIVCVGKATKLVDRYQGMIKGYSGVFRLGEATSTWD 387 (435)
Q Consensus 308 nGgII~VyKPkGmTS~dVV~kIKRiLk~kKVGHaGTLDP~ASGVLVVgIGkATKLL~~Ll~~~KeYiatgqLG~aTDT~D 387 (435)
|| |++||||.|||||+||+++|++++.+||||+|||||+||||||||+|+|||++++++..+|+|+++++||..
T Consensus 2 ~g-~l~i~Kp~g~tS~~~v~~~k~~~~~kkvGH~GTLDp~A~GvLiv~~g~~Tk~~~~~~~~~K~Y~a~v~~g~~----- 75 (182)
T cd02572 2 YG-VINLDKPSGPSSHEVVAWIKRILGVEKTGHSGTLDPKVTGCLPVCIDRATRLVKSQQEAGKEYVCVMRLHDD----- 75 (182)
T ss_pred Ce-EEEEecCCCCCHHHHHHHHHHHhCCCccCcCCCCCCcCeeEEEEEECHHhhhhHHHhCCCCEEEEEEEECCc-----
Confidence 45 999999999999999999999999999999999999999999999999999999999999999999999964
Q ss_pred CCCCeEeeccCCCCCHHHHHHHHHcCccceeeccccccccccC
Q 013857 388 ADSPVIQREPWEHIKDEDIRKAAASFRGEIWQVPPMFSAIKVR 430 (435)
Q Consensus 388 ~eGkVieksp~~hIT~EkLekaLssFqG~I~QiPP~YSAVKVn 430 (435)
||.++|+++|++|+|+|+|+||+|||+|++
T Consensus 76 -------------it~e~l~~~l~~f~G~i~Q~pP~~SA~K~~ 105 (182)
T cd02572 76 -------------VDEEKVRRVLEEFTGAIFQRPPLISAVKRQ 105 (182)
T ss_pred -------------CCHHHHHHHHHHCCCcEEeeCCHhheecCC
Confidence 789999999999999999999999999965
No 26
>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=100.00 E-value=7.7e-35 Score=285.87 Aligned_cols=107 Identities=41% Similarity=0.634 Sum_probs=101.4
Q ss_pred CceEEEEeCCCCCCHHHHHHHHHHhhccceeeccCCCCCCCCeEEEEEecCcccccchhcCCCcEEEEEEEECcccccCC
Q 013857 308 FGTMVLVNKPKGWTSFTVCGKLRRLVKVKKVGHAGTLDPMATGLLIVCVGKATKLVDRYQGMIKGYSGVFRLGEATSTWD 387 (435)
Q Consensus 308 nGgII~VyKPkGmTS~dVV~kIKRiLk~kKVGHaGTLDP~ASGVLVVgIGkATKLL~~Ll~~~KeYiatgqLG~aTDT~D 387 (435)
.+||++||||.|||||+||++||++++.+||||+|||||+|||||+||+|+|||++++++..+|+|+++++||.
T Consensus 33 ~~G~l~i~KP~g~tS~~~v~~vr~~~~~kkvGH~GTLDP~A~GvL~v~~G~aTkl~~~~~~~~K~Y~~~v~lG~------ 106 (322)
T TIGR00425 33 SYGVVNLDKPSGPSSHEVVAWVRRILNVEKTGHGGTLDPKVTGVLPVCIERATRLVKSLQEAPKEYVCLMRLHR------ 106 (322)
T ss_pred CCCEEEEeCCCCCCHHHHHHHHHHHhcccccCCCCCCCCCCceEEEEEEChHhhccHHhccCCCEEEEEEEECC------
Confidence 34499999999999999999999999999999999999999999999999999999999999999999999994
Q ss_pred CCCCeEeeccCCCCCHHHHHHHHHcCccceeeccccccccccCCe
Q 013857 388 ADSPVIQREPWEHIKDEDIRKAAASFRGEIWQVPPMFSAIKVRVF 432 (435)
Q Consensus 388 ~eGkVieksp~~hIT~EkLekaLssFqG~I~QiPP~YSAVKVnGk 432 (435)
.++.++|+++|++|+|.|+|+||+|||+|++-.
T Consensus 107 ------------~~~~~~l~~~l~~f~g~i~Q~pP~~SA~k~~~r 139 (322)
T TIGR00425 107 ------------DAKEEDILRVLKEFTGRIFQRPPLKSAVKRQLR 139 (322)
T ss_pred ------------CCCHHHHHHHHHHcCCcEEeeCChheEEeccCe
Confidence 368999999999999999999999999998643
No 27
>PRK04270 H/ACA RNA-protein complex component Cbf5p; Reviewed
Probab=100.00 E-value=3.4e-34 Score=278.00 Aligned_cols=105 Identities=47% Similarity=0.688 Sum_probs=100.9
Q ss_pred CCceEEEEeCCCCCCHHHHHHHHHHhhccceeeccCCCCCCCCeEEEEEecCcccccchhcCCCcEEEEEEEECcccccC
Q 013857 307 PFGTMVLVNKPKGWTSFTVCGKLRRLVKVKKVGHAGTLDPMATGLLIVCVGKATKLVDRYQGMIKGYSGVFRLGEATSTW 386 (435)
Q Consensus 307 LnGgII~VyKPkGmTS~dVV~kIKRiLk~kKVGHaGTLDP~ASGVLVVgIGkATKLL~~Ll~~~KeYiatgqLG~aTDT~ 386 (435)
.+| |++||||.|||||+||+++|++++.+||||+|||||+|||||+||+|+|||++++++..+|+|+++++||.
T Consensus 21 ~~g-~l~i~Kp~g~tS~~~v~~~r~~~~~kkvGH~GTLDp~A~GvL~v~~g~atk~~~~~~~~~K~Y~~~~~~g~----- 94 (300)
T PRK04270 21 KFG-VVNLDKPPGPTSHEVAAWVRDILGVEKAGHGGTLDPKVTGVLPVALGKATKVVQALLESGKEYVCVMHLHG----- 94 (300)
T ss_pred CCC-EEEEECCCCCCHHHHHHHHHHHhccccccCCCCCCCcCeEEEEEEEChHhhhhHHhccCCcEEEEEEEECC-----
Confidence 456 99999999999999999999999999999999999999999999999999999999999999999999994
Q ss_pred CCCCCeEeeccCCCCCHHHHHHHHHcCccceeeccccccccccC
Q 013857 387 DADSPVIQREPWEHIKDEDIRKAAASFRGEIWQVPPMFSAIKVR 430 (435)
Q Consensus 387 D~eGkVieksp~~hIT~EkLekaLssFqG~I~QiPP~YSAVKVn 430 (435)
++|.++|+++|++|+|+|+|+||||||+|+.
T Consensus 95 -------------~~~~~~~~~~l~~~~g~i~Q~pP~~SA~k~~ 125 (300)
T PRK04270 95 -------------DVPEEDIRKVFKEFTGEIYQKPPLKSAVKRR 125 (300)
T ss_pred -------------CCCHHHHHHHHHHCCCcEEeECCHHHhccCC
Confidence 4789999999999999999999999999965
No 28
>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=100.00 E-value=8.5e-34 Score=267.19 Aligned_cols=125 Identities=22% Similarity=0.249 Sum_probs=118.4
Q ss_pred eEEEEeCCCCCCHHHHHHHHHH----hhccceeecc-CCCCCCCCeEEEEEecCcccccchhcC--CCcEEEEEEEECcc
Q 013857 310 TMVLVNKPKGWTSFTVCGKLRR----LVKVKKVGHA-GTLDPMATGLLIVCVGKATKLVDRYQG--MIKGYSGVFRLGEA 382 (435)
Q Consensus 310 gII~VyKPkGmTS~dVV~kIKR----iLk~kKVGHa-GTLDP~ASGVLVVgIGkATKLL~~Ll~--~~KeYiatgqLG~a 382 (435)
||++||||+||+|+++++.+++ .++.+|+||+ |||||+|||||++|+|++||++++++. ..|+|+++++||.+
T Consensus 1 GilvvnKP~Gi~s~~~~~~~~~~l~~~~~~~k~~~~vhrLD~~aSGvl~~a~~~~tkl~~~~~~~~~~K~Y~~~~~lg~~ 80 (226)
T cd02868 1 GLFAVYKPPGVHWKHVRDTIESNLLKYFPEDKVLVGVHRLDAFSSGVLVLGVNHGNKLLSHLYSNHPTRVYTIRGLLGKA 80 (226)
T ss_pred CEEEEEcCCCCChhHHHHHHHHHHHHHccccceeeEccccCCCCceEEEEEeChhHhHHHHHHhcCCCeEEEEEEEEccc
Confidence 4999999999999999998776 3567889999 999999999999999999999999998 47999999999999
Q ss_pred cccCCCCCCeEeeccCCCCCHHHHHHHHHcCccceeeccccccccccCCeec
Q 013857 383 TSTWDADSPVIQREPWEHIKDEDIRKAAASFRGEIWQVPPMFSAIKVRVFHF 434 (435)
Q Consensus 383 TDT~D~eGkVieksp~~hIT~EkLekaLssFqG~I~QiPP~YSAVKVnGkRL 434 (435)
|||+|++|+|++++++.|||.++|+++|.+|+|.++|.||+|||+|+||+|+
T Consensus 81 TdT~D~~G~v~~~~~~~~it~~~i~~~l~~f~g~~~q~~p~~sa~kv~Gkra 132 (226)
T cd02868 81 TENFFHTGRVIEKTTYDHITREKIERLLAVIQSGHQQKAFELCSVDDQSQQA 132 (226)
T ss_pred cCCCCCCCCEEEecCCCCCCHHHHHHHHHHhhCCceEECCceEEEeeCCHHH
Confidence 9999999999999999999999999999999999999999999999999986
No 29
>KOG2529 consensus Pseudouridine synthase [Translation, ribosomal structure and biogenesis]
Probab=99.96 E-value=2.5e-31 Score=267.29 Aligned_cols=364 Identities=21% Similarity=0.183 Sum_probs=300.2
Q ss_pred ccceeecccCCcccccc-cccceeEeeecccccccCCCCCcceeeeeeeCCCCCCCCccccCCCCCCCCCCCCCCCCCCC
Q 013857 13 SSRTLSLLLPPPLKDNF-IKKNVYLLSTKAFSSSITSTPYPLQYDMIINNPTQPQQSQTRRRPARVNSTNSDENQNPDGE 91 (435)
Q Consensus 13 ~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 91 (435)
+|+...+.+.|-+...- +-.++.-+--+.|--++++|-||.+ +|++++|.+..-.++++.+.-+. ...+ ...++|
T Consensus 8 ss~~~~~~~kp~~~~a~~~~~~~~~~ll~~~~~~~v~t~~~t~-~~~~~splk~~i~~~~~sgv~~i--~kpa-~pss~e 83 (395)
T KOG2529|consen 8 SSPQFMFMTKPALETAQKFDASIWALLLANMDKLLVRTGHYTP-SAAGVSPLKRGIKEYSRSGVINI--DKPA-NPSSHE 83 (395)
T ss_pred cccccccccCccccccccchhhhhHHHHHHHHhhhhhhcCcCc-hhhhcCHHHHhHHhHhhcCceec--cCCC-CCchHH
Confidence 34444455555544433 4445554445556678899999999 99999999998888888876666 2222 223344
Q ss_pred CCcchhhhHHhHHhhhhcCCCCCchhhhHHHHHHHHHhhccccCCCCCcccCCCCCcceeecceeeecccccccccceec
Q 013857 92 LGFDSWVDKKLEKEAKTRQPGSDNAEMTKSMRKYYNKRRQRMYGTDSEDEYGKNDDGFVELKPEVVEFNRLHKREEELYF 171 (435)
Q Consensus 92 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~ly~ 171 (435)
+.+||+++|. .++++|+|..|++|+++++.|+.++++++++++|.++.- .+|++|+|+|.++..+|++.|.||+
T Consensus 84 --~~swvk~iL~-~ek~Gh~gTlDP~vtg~l~v~~~~~tr~~~s~~s~gk~y---vg~~~lt~~v~~~~k~~~~~e~l~g 157 (395)
T KOG2529|consen 84 --VVSWVKNILR-VEKTGHSGTLDPEVTGCLIVCIDRATRLLKSQQSAGKEY---VGIGKLTPEVEDALKLHQKLEHLYG 157 (395)
T ss_pred --HHHHHHHHhh-HHHhCCCCCCCccccceEEEEeecccccccchhccCcEE---EEEEecCcchhhhhhhccchhhhhh
Confidence 9999999999 889999999999999999999999999999999986644 9999999999999999999999999
Q ss_pred cccccCcCccc-chhHHHHHHhhccCCcccccccccCCCCc----hhHHHhhhh------cCCCcccccCC-----ccCC
Q 013857 172 YDTFAYPWEKD-KHYKMVYQLEKKYFPDQCLDKAFLDPSAD----QNVKKMRKK------AGGKSEEKKYN-----KEDD 235 (435)
Q Consensus 172 ~~~~~~pwek~-~~~~~~~~le~kyfp~~~~d~a~~~~~~~----~~~~~~~~~------~~~~~~~~~~~-----~~~~ 235 (435)
++.+++||+.+ +|+.||++|+..+++++|.|++|+.++.+ ...+.+... -+++..+++-. ++.+
T Consensus 158 ~l~~~~pl~~~~kr~~~v~~~y~s~~ie~d~~~~l~~f~~~~~~~t~~rt~~~~lg~ll~~g~k~~E~~r~r~~~~~E~~ 237 (395)
T KOG2529|consen 158 ALFQRPPLISAVKRVLRVRTLYESKIIEYDRDYPLLRFGVSCEAGTYKRTMCVHLGLLLGFGGKMQELRRVRSGICSEED 237 (395)
T ss_pred hhccCCchhhhccceeEeechhhhhcccccccchhccccccccccchHHHHHHhhhhHhhhcchhhhhhhcccccccccc
Confidence 99999999999 99999999999999999999999999986 222222222 45555555432 3466
Q ss_pred cceeeecccccccccccccccccCcccccchhhHHHHHHHhccCCCCC---CCCCCCccccccCCCCCCCCcCCCCceEE
Q 013857 236 KRLVFFDDQEKKSEKDSILGEDVNVKGEVSEKKVEEFFKCLKKVPNKE---NEVGSGEPYIVSRSTELPPTWDGPFGTMV 312 (435)
Q Consensus 236 ~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~k~~~~~---~~~~~~~~~~~~~~~~~p~~wd~LnGgII 312 (435)
..|+++|+++...+.++.. +. -..-.....||.++...+++.++. +.+.-|.++.++.....++.|+..++.++
T Consensus 238 ~~~t~~d~~~~q~~~d~~~--d~-~~~r~~~~~les~l~~~~~vv~kd~~v~~~cyg~k~~v~~~~r~~~~i~~~~e~v~ 314 (395)
T KOG2529|consen 238 DMLTEHDEQDAQFEYDTER--DE-SYLRRVKKPLESLLTGYKRVVVKDSTVNAPCYGAKLLVPGLLRYSDDIDGPFEVVD 314 (395)
T ss_pred cccccccchhhhhhhcccc--Cc-ceeeeeeeccccccccceeeecccchhcCccccceeeeccccccCccccCceeEEE
Confidence 7899999888777766622 22 234556789999999999999998 55667899999999999999999999999
Q ss_pred EEeCCCCCCHHHHHHHHHHhhccceeeccCCCCC-CCCeEEEEEecCcccccchhcCCCcEEEEEEEECcccccCCCC
Q 013857 313 LVNKPKGWTSFTVCGKLRRLVKVKKVGHAGTLDP-MATGLLIVCVGKATKLVDRYQGMIKGYSGVFRLGEATSTWDAD 389 (435)
Q Consensus 313 ~VyKPkGmTS~dVV~kIKRiLk~kKVGHaGTLDP-~ASGVLVVgIGkATKLL~~Ll~~~KeYiatgqLG~aTDT~D~e 389 (435)
...|+-++.++-+....+.......++|++++++ |+.+|.+.|+|.+++.++..+...+.|.-....|.+|.+.|..
T Consensus 315 ~t~k~e~~~~~i~~~~~~~~~s~dh~~~a~~k~~~me~d~~~~~~g~~~~~~~~~e~~~~g~~~~~~~~~~~t~~~~~ 392 (395)
T KOG2529|consen 315 MTTKGEAIASKIAEMSLRQVASCDHGVVAKTKRVIMEADVYERCWGLGPKASPGKEAKAEGKLDKFGKGNETTPKDWI 392 (395)
T ss_pred EeecchhhhhhhhhhhhhhhceeeeeeecccccccccccccceeeccCcccCchHHHHHhhhhhhccCCCCCChhHhc
Confidence 9999999999999999999999999999999999 9999999999999999999998888888888888888876654
No 30
>KOG2529 consensus Pseudouridine synthase [Translation, ribosomal structure and biogenesis]
Probab=99.56 E-value=3.7e-15 Score=151.18 Aligned_cols=73 Identities=38% Similarity=0.650 Sum_probs=68.2
Q ss_pred CCceEEEEeCCCCCCHHHHHHHHHHhhccceeeccCCCCCCCCeEEEEEecCcccccchhcCCCcEEEEEEEEC
Q 013857 307 PFGTMVLVNKPKGWTSFTVCGKLRRLVKVKKVGHAGTLDPMATGLLIVCVGKATKLVDRYQGMIKGYSGVFRLG 380 (435)
Q Consensus 307 LnGgII~VyKPkGmTS~dVV~kIKRiLk~kKVGHaGTLDP~ASGVLVVgIGkATKLL~~Ll~~~KeYiatgqLG 380 (435)
..| +++|+||++.+||++++|++++|...|.||.|||||.+||+|++|++++||++...+...|+|++.+.+.
T Consensus 67 ~sg-v~~i~kpa~pss~e~~swvk~iL~~ek~Gh~gTlDP~vtg~l~v~~~~~tr~~~s~~s~gk~yvg~~~lt 139 (395)
T KOG2529|consen 67 RSG-VINIDKPANPSSHEVVSWVKNILRVEKTGHSGTLDPEVTGCLIVCIDRATRLLKSQQSAGKEYVGIGKLT 139 (395)
T ss_pred hcC-ceeccCCCCCchHHHHHHHHHHhhHHHhCCCCCCCccccceEEEEeecccccccchhccCcEEEEEEecC
Confidence 345 9999999999999999999999999999999999999999999999999999999999999997766543
No 31
>KOG2559 consensus Predicted pseudouridine synthase [Translation, ribosomal structure and biogenesis]
Probab=99.52 E-value=7.9e-15 Score=142.68 Aligned_cols=115 Identities=21% Similarity=0.328 Sum_probs=103.0
Q ss_pred CcCCCCceEEEEeCCCCCCHHHHHHHHHHhhc------------------------------------------------
Q 013857 303 TWDGPFGTMVLVNKPKGWTSFTVCGKLRRLVK------------------------------------------------ 334 (435)
Q Consensus 303 ~wd~LnGgII~VyKPkGmTS~dVV~kIKRiLk------------------------------------------------ 334 (435)
.|+ ++| |+|||||+||+|..+++.|-+.+.
T Consensus 6 i~k-l~G-vl~VYKpsGik~khlr~~i~~~i~k~~~~~~~~s~~q~~~~~~g~~eg~e~~~~~~~~~sV~~~~nhPlv~g 83 (318)
T KOG2559|consen 6 IWK-LSG-VLCVYKPSGIKSKHLRKLITRKIAKSVSDIESTSRIQLPLISIGVIEGHEKSLVVVGRNSVADYRNHPLVSG 83 (318)
T ss_pred hhh-hcc-eeEEecCCCccHHHHHHHHHHHHHhhhcccCCCcccccceEeecccccccceeeeecccchhhhccCCcccC
Confidence 577 899 999999999999999998765430
Q ss_pred ----cceeeccCCCCCCCCeEEEEEecCcccccchhcCCCcEEEEEEEECcccccCCCCCCeEeeccCCCCCHHHHHHHH
Q 013857 335 ----VKKVGHAGTLDPMATGLLIVCVGKATKLVDRYQGMIKGYSGVFRLGEATSTWDADSPVIQREPWEHIKDEDIRKAA 410 (435)
Q Consensus 335 ----~kKVGHaGTLDP~ASGVLVVgIGkATKLL~~Ll~~~KeYiatgqLG~aTDT~D~eGkVieksp~~hIT~EkLekaL 410 (435)
..+|+-...||-.|||||++|||.||+++. .+.+|.+|+.|-+||.|++..+++|||+++|+++|
T Consensus 84 ~s~~~~~V~v~h~l~~~~sgvl~~gVghgc~~i~-----------~~mlg~aT~~~r~Dgri~~~~n~dhVs~~ri~~vl 152 (318)
T KOG2559|consen 84 RSIRQEDVQVVHVLPLATSGVLLFGVGHGCESIP-----------ELMLGSATNVYRIDGRIKKSENIDHVSKHRIEKVL 152 (318)
T ss_pred cchhhcceeeEEeecccccceEEEecCcchhhhh-----------hhhhccchhccCccceEeeecccchhhHHHHHHHH
Confidence 146777888999999999999999999998 56799999999999999999999999999999999
Q ss_pred HcCccceeeccccccccccC
Q 013857 411 ASFRGEIWQVPPMFSAIKVR 430 (435)
Q Consensus 411 ssFqG~I~QiPP~YSAVKVn 430 (435)
+.++|+++-.--+||++-++
T Consensus 153 a~lq~shq~a~f~~~nvDl~ 172 (318)
T KOG2559|consen 153 ARLQSSHQSASFRHANVDLE 172 (318)
T ss_pred HHHHHHHHHHHHHhcCCCch
Confidence 99999999888888887654
No 32
>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=98.39 E-value=4.9e-07 Score=72.76 Aligned_cols=50 Identities=26% Similarity=0.240 Sum_probs=45.1
Q ss_pred EeCCCCCCHHHHHHHHH-HhhccceeeccCCCCCCCCeEEEEEecCcccccchhcCCCcEEEEEEE
Q 013857 314 VNKPKGWTSFTVCGKLR-RLVKVKKVGHAGTLDPMATGLLIVCVGKATKLVDRYQGMIKGYSGVFR 378 (435)
Q Consensus 314 VyKPkGmTS~dVV~kIK-RiLk~kKVGHaGTLDP~ASGVLVVgIGkATKLL~~Ll~~~KeYiatgq 378 (435)
|+||-+.|++.+....+ ..+..+++||+|++|+.|+|+++|| |+|.++++
T Consensus 1 l~K~~~~t~~~~~~~~~~~~~~~~~i~~aG~kDk~a~t~q~v~---------------n~f~i~~r 51 (87)
T cd01291 1 LYKPGGDTMEAARQLAKLLGIPPKRVGYAGRKDKRAVTTQLVS---------------NRFTITLR 51 (87)
T ss_pred CCCCCCChHHHHHHHHHHhCCChheEEECccCCCCeeEEEEEc---------------ccEEEEEE
Confidence 68999999998888886 4578899999999999999999999 99999988
No 33
>PRK10158 23S rRNA/tRNA pseudouridine synthase A; Provisional
Probab=97.58 E-value=9.5e-05 Score=69.08 Aligned_cols=71 Identities=25% Similarity=0.401 Sum_probs=54.2
Q ss_pred CceEEEEeCCCCCCHH---------HHHHHHHHhhccceeeccCCCCCCCCeEEEEEecCccc--ccchhcC--CCcEEE
Q 013857 308 FGTMVLVNKPKGWTSF---------TVCGKLRRLVKVKKVGHAGTLDPMATGLLIVCVGKATK--LVDRYQG--MIKGYS 374 (435)
Q Consensus 308 nGgII~VyKPkGmTS~---------dVV~kIKRiLk~kKVGHaGTLDP~ASGVLVVgIGkATK--LL~~Ll~--~~KeYi 374 (435)
+..+++||||.|+.++ .+.+.+...+ .+++..|.||-.+||||++|.++... +...+.. -.|+|.
T Consensus 20 d~~~lvvnKPaGl~~~~~~~~~~~~sl~~~l~~~~--~~~~~vhRLDr~TSGlll~Akt~~~~~~l~~~f~~~~v~K~Yl 97 (219)
T PRK10158 20 DEHIMVVNKPSGLLSVPGRLEEHKDSVMTRIQRDY--PQAESVHRLDMATSGVIVVALTKAAERELKRQFREREPKKQYV 97 (219)
T ss_pred CCCEEEEECCCCCcEeCCCCCccchhHHHHHHHhC--CCCCEECCCCCCCceEEEEECCHHHHHHHHHHHHhCCccEEEE
Confidence 4448999999999665 2344444433 35889999999999999999988666 7777765 679999
Q ss_pred EEEEECc
Q 013857 375 GVFRLGE 381 (435)
Q Consensus 375 atgqLG~ 381 (435)
|.+. |.
T Consensus 98 a~v~-G~ 103 (219)
T PRK10158 98 ARVW-GH 103 (219)
T ss_pred EEEe-cc
Confidence 9887 54
No 34
>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=97.57 E-value=0.00011 Score=68.77 Aligned_cols=70 Identities=19% Similarity=0.292 Sum_probs=53.6
Q ss_pred ceEEEEeCCCCCCHH------HHHHHHHHhhccceeeccCCCCCCCCeEEEEEecCc-ccc-cchhcC--CCcEEEEEEE
Q 013857 309 GTMVLVNKPKGWTSF------TVCGKLRRLVKVKKVGHAGTLDPMATGLLIVCVGKA-TKL-VDRYQG--MIKGYSGVFR 378 (435)
Q Consensus 309 GgII~VyKPkGmTS~------dVV~kIKRiLk~kKVGHaGTLDP~ASGVLVVgIGkA-TKL-L~~Ll~--~~KeYiatgq 378 (435)
.-+++||||.|+.++ .+...+...++..++...|.||-.+||||+++-+.. ++. ...+.. ..|+|.|.+.
T Consensus 9 ~~~lvvnKP~Gl~v~~~~~~~~l~~~l~~~~~~~~~~~VhRLDr~TSGlll~Ak~~~~~~~L~~~~~~~~v~K~YlAlV~ 88 (217)
T TIGR01621 9 PDFLLINKHPGISVHKDDGETGLLQEVATQLGVGQVWLVHRLDKMTSGILLLALNAESASELSQGFAKRKIEKTYLALSS 88 (217)
T ss_pred CCEEEEECCCCCeECCCCCcChHHHHHHHhcCCCCccEecCCCCCCceEEEEEcCHHHHHHHHHHHhcCCccEEEEEEEe
Confidence 448999999999875 445555555555679999999999999999998764 444 444444 6799999987
No 35
>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=97.56 E-value=0.0001 Score=66.25 Aligned_cols=68 Identities=26% Similarity=0.327 Sum_probs=50.7
Q ss_pred EEEEeCCCCCCHH-------HHHHHHHHhhccceeeccCCCCCCCCeEEEEEecC--cccccchhcCCCcEEEEEEE
Q 013857 311 MVLVNKPKGWTSF-------TVCGKLRRLVKVKKVGHAGTLDPMATGLLIVCVGK--ATKLVDRYQGMIKGYSGVFR 378 (435)
Q Consensus 311 II~VyKPkGmTS~-------dVV~kIKRiLk~kKVGHaGTLDP~ASGVLVVgIGk--ATKLL~~Ll~~~KeYiatgq 378 (435)
+++||||.|+.++ .+.+.+...+...+++..|.||..+||+|+++-+. +.+++..-....|+|.|.+.
T Consensus 2 ~ivvnKP~G~~~~~~~~~~~tl~~~l~~~~~~~~~~~vhRLD~~TSGlll~ak~~~~~~~l~~~~~~i~K~Y~a~V~ 78 (167)
T cd02553 2 YLMLNKPAGVVCATKDPHHPTVIDLLPEPDRRRDLFPVGRLDKDTTGLLLLTNDGQLAHRLTSPKKHVPKTYEVTLA 78 (167)
T ss_pred EEEEECCCCCEeCCCCCCCCcHHHHhhhhcccCCeEEcccCCCCCEEEEEEEeCHHHHHHhhCCcCCCceEEEEEEc
Confidence 5789999998775 24555555554567899999999999999999876 23333333347799999986
No 36
>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=97.51 E-value=0.00016 Score=67.23 Aligned_cols=73 Identities=23% Similarity=0.394 Sum_probs=55.7
Q ss_pred CceEEEEeCCCCCCHH--------HHHHHHHHhhccceeeccCCCCCCCCeEEEEEecC-c-ccccchhcC--CCcEEEE
Q 013857 308 FGTMVLVNKPKGWTSF--------TVCGKLRRLVKVKKVGHAGTLDPMATGLLIVCVGK-A-TKLVDRYQG--MIKGYSG 375 (435)
Q Consensus 308 nGgII~VyKPkGmTS~--------dVV~kIKRiLk~kKVGHaGTLDP~ASGVLVVgIGk-A-TKLL~~Ll~--~~KeYia 375 (435)
++.+++||||.|+-++ .+...+...++..++...|.||..+||||+++-+. + .++...+.. ..|+|+|
T Consensus 22 d~~~ivvnKP~Gl~~~~~~~~~~~sl~~~l~~~~~~~~~~~vhRLD~~TSGllllak~~~~~~~l~~~f~~~~v~K~Y~a 101 (213)
T cd02557 22 DDDLLVVDKPSGIPVHPTGRYRYNTVTEILKSEYGLTELRPCHRLDRLTSGLLLFAKTSQTASRLQQQIRSREVKKEYLA 101 (213)
T ss_pred CCCEEEEECCCCCcCCCCCCCCcChHHHHHHHHcCCCCccCccCCCCCCceEEEEECCHHHHHHHHHHHHcCCccEEEEE
Confidence 3448999999998763 46667776666567889999999999999999876 3 444454444 6799999
Q ss_pred EEEECc
Q 013857 376 VFRLGE 381 (435)
Q Consensus 376 tgqLG~ 381 (435)
.+. |.
T Consensus 102 ~v~-G~ 106 (213)
T cd02557 102 RVK-GE 106 (213)
T ss_pred EEe-Cc
Confidence 887 54
No 37
>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=97.46 E-value=0.00019 Score=68.32 Aligned_cols=71 Identities=21% Similarity=0.266 Sum_probs=55.6
Q ss_pred CceEEEEeCCCCCCHH--------HHHHHHHHhhccceeeccCCCCCCCCeEEEEEecCccc--ccchhcC--CCcEEEE
Q 013857 308 FGTMVLVNKPKGWTSF--------TVCGKLRRLVKVKKVGHAGTLDPMATGLLIVCVGKATK--LVDRYQG--MIKGYSG 375 (435)
Q Consensus 308 nGgII~VyKPkGmTS~--------dVV~kIKRiLk~kKVGHaGTLDP~ASGVLVVgIGkATK--LL~~Ll~--~~KeYia 375 (435)
++-+++||||.|+.++ .++..++..++...+...+.||-.+||||++|-+.... +...+.. ..|+|.|
T Consensus 45 d~~~lvvnKPaGl~~~~~~~~~~~t~~~~l~~~~~~~~~~~vhRLD~~TSGlll~Ak~~~~~~~l~~~~~~~~v~K~YlA 124 (246)
T cd02558 45 DEHLLVADKPHFLPVTPRGRYVTETLLVRLRRQTGNPDLTPAHRLDRLTAGLVLFSKRPETRGAYQTLFARREVSKTYEA 124 (246)
T ss_pred cCCEEEEECCCCCccCCCCcchhhhHHHHHHHHhCCCcccccccCCCCceeEEEEEcCHHHHHHHHHHHHcCCccEEEEE
Confidence 4558999999999985 36677776666667888999999999999999987443 4444433 7799999
Q ss_pred EEE
Q 013857 376 VFR 378 (435)
Q Consensus 376 tgq 378 (435)
.+.
T Consensus 125 ~v~ 127 (246)
T cd02558 125 VAP 127 (246)
T ss_pred EEe
Confidence 986
No 38
>COG0564 RluA Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]
Probab=97.34 E-value=0.00038 Score=68.48 Aligned_cols=75 Identities=29% Similarity=0.461 Sum_probs=61.2
Q ss_pred CceEEEEeCCCCCCH--------HHHHHHHHHhhc--cceeeccCCCCCCCCeEEEEEecC--cccccchhcC--CCcEE
Q 013857 308 FGTMVLVNKPKGWTS--------FTVCGKLRRLVK--VKKVGHAGTLDPMATGLLIVCVGK--ATKLVDRYQG--MIKGY 373 (435)
Q Consensus 308 nGgII~VyKPkGmTS--------~dVV~kIKRiLk--~kKVGHaGTLDP~ASGVLVVgIGk--ATKLL~~Ll~--~~KeY 373 (435)
+.-|++||||+||.+ ..+++.+...++ ..+++-...||-..||||++|-+. +..|...+.. ..|+|
T Consensus 84 D~~llVvnKP~Gl~vhp~~~~~~~tl~~~l~~~~~~~~~~~~~vHRLDkdTSGlll~AK~~~a~~~l~~~f~~r~v~K~Y 163 (289)
T COG0564 84 DEDLLVVNKPAGLVVHPGGGHHEGTLVNALLRHCQDGVERPGIVHRLDKDTSGLLLVAKNREAARELSEQFKQRKVKKTY 163 (289)
T ss_pred cCCEEEEECCCCCcCcCCCCCccHhHHHHHHHhccccCCceeeeccCCCCCceEEEEECCHHHHHHHHHHHhcCcCcEEE
Confidence 344899999999998 677888877665 578999999999999999999998 5566666655 57999
Q ss_pred EEEEEECccc
Q 013857 374 SGVFRLGEAT 383 (435)
Q Consensus 374 iatgqLG~aT 383 (435)
.|.+. |.-.
T Consensus 164 ~Alv~-G~~~ 172 (289)
T COG0564 164 LALVR-GHLP 172 (289)
T ss_pred EEEEE-Cccc
Confidence 99998 7544
No 39
>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=97.30 E-value=0.00018 Score=64.70 Aligned_cols=66 Identities=29% Similarity=0.312 Sum_probs=48.1
Q ss_pred EEEEeCCCCCCHHH-----HHHHHHHhhccceeeccCCCCCCCCeEEEEEecCcccccchhcC----CCcEEEEEEE
Q 013857 311 MVLVNKPKGWTSFT-----VCGKLRRLVKVKKVGHAGTLDPMATGLLIVCVGKATKLVDRYQG----MIKGYSGVFR 378 (435)
Q Consensus 311 II~VyKPkGmTS~d-----VV~kIKRiLk~kKVGHaGTLDP~ASGVLVVgIGkATKLL~~Ll~----~~KeYiatgq 378 (435)
+++||||.|+-|+. -...+...+...++...|.||-.+||||+++-+. ++...+.. ..|+|.|.+.
T Consensus 1 ~lv~nKP~G~~~~~~~~~~~~~~l~~~l~~~~~~~v~RLD~~TsGlll~a~d~--~~~~~l~~~~~~v~K~Y~a~v~ 75 (168)
T cd02566 1 LILFNKPYGVLSQFTDESEKHKTLKDYIDDPGVYAAGRLDRDSEGLLLLTDDG--RLQHRITDPSFKHPKTYYVQVE 75 (168)
T ss_pred CEEEECCCCCEEecCCCcCCCccHHHHcCcCCeEEccCCCCCCeEEEEEEeCH--HHHHHHHCCCCCCCEEEEEEEC
Confidence 47899999986661 2234555555567889999999999999998765 24444433 6799999875
No 40
>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=97.20 E-value=0.00064 Score=63.40 Aligned_cols=72 Identities=24% Similarity=0.400 Sum_probs=51.1
Q ss_pred ceEEEEeCCCCCCHHH----------HHHHHHHhhccceeeccCCCCCCCCeEEEEEecCc-cccc-chhcC--CCcEEE
Q 013857 309 GTMVLVNKPKGWTSFT----------VCGKLRRLVKVKKVGHAGTLDPMATGLLIVCVGKA-TKLV-DRYQG--MIKGYS 374 (435)
Q Consensus 309 GgII~VyKPkGmTS~d----------VV~kIKRiLk~kKVGHaGTLDP~ASGVLVVgIGkA-TKLL-~~Ll~--~~KeYi 374 (435)
+-+++||||.|+.++- ++..++..++ .++...+.||..+||||+++-+.. .+.+ ..+.. ..|+|+
T Consensus 8 ~~~lvvnKP~G~~~~~~~~~~~~~~~~~~~l~~~~~-~~~~~vhRLD~~TSGlll~Ak~~~~~~~l~~~f~~~~v~K~Y~ 86 (223)
T cd02563 8 EHLVAINKPSGLLVHRSELDRHETRFALQTLRDQLG-QHVYPVHRLDRPTSGVLLFALSSEVARKLGEQFTEHRVHKTYL 86 (223)
T ss_pred CCEEEEECCCCCeEcCCCCCCCCcHHHHHHHHHHcC-CCcccccCCCCCCeEEEEEEECHHHHHHHHHHHhcCceeEEEE
Confidence 3489999999997652 2233444333 468899999999999999998663 4444 43443 579999
Q ss_pred EEEEECcc
Q 013857 375 GVFRLGEA 382 (435)
Q Consensus 375 atgqLG~a 382 (435)
|.+. |.-
T Consensus 87 alv~-G~~ 93 (223)
T cd02563 87 AVVR-GYV 93 (223)
T ss_pred EEEE-Ccc
Confidence 9886 543
No 41
>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=97.10 E-value=0.00057 Score=60.03 Aligned_cols=70 Identities=30% Similarity=0.472 Sum_probs=49.0
Q ss_pred EEEEeCCCCCCHHH--------HHHHHHHhhccceeeccCCCCCCCCeEEEEEecCc--ccccchhcCCCcEEEEEEEEC
Q 013857 311 MVLVNKPKGWTSFT--------VCGKLRRLVKVKKVGHAGTLDPMATGLLIVCVGKA--TKLVDRYQGMIKGYSGVFRLG 380 (435)
Q Consensus 311 II~VyKPkGmTS~d--------VV~kIKRiLk~kKVGHaGTLDP~ASGVLVVgIGkA--TKLL~~Ll~~~KeYiatgqLG 380 (435)
+++||||.|+.++. +...+... ...++...|.||-.+||||+++-+.. .++...-....|+|.|.+. |
T Consensus 1 ~ivvnKP~G~~~~~~~~~~~~~~~~~l~~~-~~~~~~~vhRLD~~TSGlll~ak~~~~~~~l~~~~~~v~K~Y~a~v~-g 78 (154)
T cd02550 1 ILVLNKPSGLVCHPTDRDRDPTVVVRLDKL-HGPRVHAAGRLDKDTSGLLLLTNDGRLQRRLTEPRREIEKEYLVTVR-G 78 (154)
T ss_pred CEEEECCCCCEEecCCCCCCCcHHHhhhcc-cCCceeEeccCCCCCeeEEEEEcCHHHHHHHhhhhccCcEEEEEEEE-e
Confidence 47899999987652 22222221 23578899999999999999998764 3444443348899999986 5
Q ss_pred cc
Q 013857 381 EA 382 (435)
Q Consensus 381 ~a 382 (435)
.-
T Consensus 79 ~~ 80 (154)
T cd02550 79 EL 80 (154)
T ss_pred ec
Confidence 43
No 42
>TIGR00005 rluA_subfam pseudouridine synthase, RluA family. modifies uracil-65 in transfer RNAs to pseudouridine.
Probab=97.08 E-value=0.00066 Score=65.25 Aligned_cols=71 Identities=25% Similarity=0.437 Sum_probs=52.7
Q ss_pred eEEEEeCCCCCCHH--------HHHHHHHHhhcc----ceeeccCCCCCCCCeEEEEEecC-ccccc-chhcC--CCcEE
Q 013857 310 TMVLVNKPKGWTSF--------TVCGKLRRLVKV----KKVGHAGTLDPMATGLLIVCVGK-ATKLV-DRYQG--MIKGY 373 (435)
Q Consensus 310 gII~VyKPkGmTS~--------dVV~kIKRiLk~----kKVGHaGTLDP~ASGVLVVgIGk-ATKLL-~~Ll~--~~KeY 373 (435)
.+++||||.|+-++ .+++.+...+.. .++...|.||-.+||||+++-+. +.+.+ ..+.. -.|+|
T Consensus 80 ~~lvvnKP~g~~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~vhRLD~~TSGlll~ak~~~~~~~l~~~~~~~~v~K~Y 159 (299)
T TIGR00005 80 DIIVINKPSGLVVHPGGGNPFGTVLNALLAHCPPIAGVERVGIVHRLDRDTSGLMVVAKTPLALRELQRQLKNRTVTKEY 159 (299)
T ss_pred CEEEEECCCCCeEeCCCCCCcccHHHHHHHhcccccCCCcCceECCCCCCCceEEEEEcCHHHHHHHHHHHHhCCcceEE
Confidence 38999999998765 366666665543 56889999999999999999875 33334 33333 77999
Q ss_pred EEEEEECc
Q 013857 374 SGVFRLGE 381 (435)
Q Consensus 374 iatgqLG~ 381 (435)
.|.+. |.
T Consensus 160 ~a~v~-g~ 166 (299)
T TIGR00005 160 VALVH-GQ 166 (299)
T ss_pred EEEEe-cc
Confidence 99886 43
No 43
>PRK11112 tRNA pseudouridine synthase C; Provisional
Probab=97.08 E-value=0.00087 Score=64.24 Aligned_cols=69 Identities=28% Similarity=0.494 Sum_probs=49.5
Q ss_pred ceEEEEeCCCCCCHHH----------HHHHHHHhhccceeeccCCCCCCCCeEEEEEecCc-c-cccchhcC--CCcEEE
Q 013857 309 GTMVLVNKPKGWTSFT----------VCGKLRRLVKVKKVGHAGTLDPMATGLLIVCVGKA-T-KLVDRYQG--MIKGYS 374 (435)
Q Consensus 309 GgII~VyKPkGmTS~d----------VV~kIKRiLk~kKVGHaGTLDP~ASGVLVVgIGkA-T-KLL~~Ll~--~~KeYi 374 (435)
..+++||||.|+.++. +...++..++ .++...+.||..+||||++|-+.. . +|...+.. -.|+|.
T Consensus 9 ~~~lvvnKPaGl~~~~~~~~~~~~~~~~~~l~~~~~-~~~~~VHRLDr~TSGlll~Ak~~~~~~~L~~~f~~~~v~K~Y~ 87 (257)
T PRK11112 9 EWLVAVNKPAGWLVHRSWLDRHETVFVMQTVRDQIG-QHVFTAHRLDRPTSGVLLMALSSEVARLLAQQFEQHQIQKTYH 87 (257)
T ss_pred CCEEEEECCCCCeecCCCCCCCchHHHHHHHHHHhC-CCceeeccCCCCCeeEEEEECCHHHHHHHHHHHHhCCcceEEE
Confidence 4489999999997753 2233433333 257789999999999999999773 3 34454443 779999
Q ss_pred EEEE
Q 013857 375 GVFR 378 (435)
Q Consensus 375 atgq 378 (435)
|.+.
T Consensus 88 Alv~ 91 (257)
T PRK11112 88 AIVR 91 (257)
T ss_pred EEEE
Confidence 9876
No 44
>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=97.06 E-value=0.00013 Score=62.91 Aligned_cols=79 Identities=23% Similarity=0.302 Sum_probs=51.0
Q ss_pred EEEEeCCCCCCHHHHH-----------HH-HHHhhccceeeccCCCCCCCCeEEEEEecCc--ccccchh--cCCCcEEE
Q 013857 311 MVLVNKPKGWTSFTVC-----------GK-LRRLVKVKKVGHAGTLDPMATGLLIVCVGKA--TKLVDRY--QGMIKGYS 374 (435)
Q Consensus 311 II~VyKPkGmTS~dVV-----------~k-IKRiLk~kKVGHaGTLDP~ASGVLVVgIGkA--TKLL~~L--l~~~KeYi 374 (435)
+|+||||.||-++..- .. ........+++-.|.||..+||||+++.... -++...+ ....|+|.
T Consensus 2 ~ivvnKP~G~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~RLD~~TsGlll~a~~~~~~~~l~~~f~~~~~~K~Y~ 81 (164)
T PF00849_consen 2 LIVVNKPAGVPVHPSDGNESKSVKELPALSLKRGDDPPELYPVHRLDRDTSGLLLFAKDKEAAAKLSKQFPKRKVEKTYL 81 (164)
T ss_dssp EEEEEE-TTSBSSSSSTBSSSSHHCHHHHHHHHCTTSGGGEESS---TT-EEEEEEESSHHHHHHHHHHHHTTCSEEEEE
T ss_pred EEEEECCCCCeEecCCCCCcccccchhhhhhhhccCCCceEECCCCCccccCCeeccCCcccccccccccccCCCcEEEE
Confidence 6899999998765443 11 1112356799999999999999999998653 4455544 34889999
Q ss_pred EEEEECcccccCCCC
Q 013857 375 GVFRLGEATSTWDAD 389 (435)
Q Consensus 375 atgqLG~aTDT~D~e 389 (435)
|.+.-|...+...++
T Consensus 82 a~v~~~~~~~~~~~~ 96 (164)
T PF00849_consen 82 ALVEGGPVEEEGKIN 96 (164)
T ss_dssp EEECSSSSTTCEEEE
T ss_pred EeEcccccccceeee
Confidence 999866655544433
No 45
>PRK11180 rluD 23S rRNA pseudouridine synthase D; Provisional
Probab=96.98 E-value=0.0008 Score=66.25 Aligned_cols=70 Identities=29% Similarity=0.428 Sum_probs=52.8
Q ss_pred ceEEEEeCCCCCCHH--------HHHHHHHHhhc----cceeeccCCCCCCCCeEEEEEecC--cccccchhcC--CCcE
Q 013857 309 GTMVLVNKPKGWTSF--------TVCGKLRRLVK----VKKVGHAGTLDPMATGLLIVCVGK--ATKLVDRYQG--MIKG 372 (435)
Q Consensus 309 GgII~VyKPkGmTS~--------dVV~kIKRiLk----~kKVGHaGTLDP~ASGVLVVgIGk--ATKLL~~Ll~--~~Ke 372 (435)
..+++||||.|+.++ .+++.+...+. ..+++..+.||-.+||||+++-+. +..+...+.. ..|+
T Consensus 91 ~~~lvvnKP~gl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~vhRLD~~TSGlll~Ak~~~~~~~l~~~~~~~~v~K~ 170 (325)
T PRK11180 91 DDILVINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVEALQKREITRE 170 (325)
T ss_pred CCEEEEECCCCCeEeCCCCCCCCcHHHHHHHHhhhccCCcccceeccCCCCCceeEEEECCHHHHHHHHHHHHhCCcceE
Confidence 348999999999776 35666655442 246789999999999999999874 3455555554 6799
Q ss_pred EEEEEE
Q 013857 373 YSGVFR 378 (435)
Q Consensus 373 Yiatgq 378 (435)
|.|.+.
T Consensus 171 Y~A~v~ 176 (325)
T PRK11180 171 YEAVAI 176 (325)
T ss_pred EEEEEe
Confidence 999876
No 46
>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=96.89 E-value=0.0013 Score=59.15 Aligned_cols=67 Identities=19% Similarity=0.262 Sum_probs=46.1
Q ss_pred EEEEeCCCCCCHHH--------HHHHHHHhhccceeeccCCCCCCCCeEEEEEecCc-ccccch-hcCCCcEEEEEEE
Q 013857 311 MVLVNKPKGWTSFT--------VCGKLRRLVKVKKVGHAGTLDPMATGLLIVCVGKA-TKLVDR-YQGMIKGYSGVFR 378 (435)
Q Consensus 311 II~VyKPkGmTS~d--------VV~kIKRiLk~kKVGHaGTLDP~ASGVLVVgIGkA-TKLL~~-Ll~~~KeYiatgq 378 (435)
+++||||.|+-|+. +.+.+... ...+++..|.||-.+||||+++-+.. .+.+.. =....|+|.|.+.
T Consensus 2 ~lvvnKP~G~~~~~~~~~~~~tl~~~l~~~-~~~~~~~V~RLD~~TsGLll~ak~~~~~~~L~~~~~~i~K~Y~a~V~ 78 (167)
T cd02556 2 VLIYHKPEGLICTRKDPKGRPTVFDLLPKL-GIPRWISVGRLDLNTEGLLLFTNDGELANRLMHPSNEIEREYAVRVF 78 (167)
T ss_pred EEEEECCCCcEECccCCCCCccHHHhhhhh-ccCceEEcCcCCCCCeeEEEEECCHHHHHHHhCCcCCCCeEEEEEEC
Confidence 78999999985552 33333322 13467899999999999999987553 333332 1126799999886
No 47
>PRK10475 23S rRNA pseudouridine synthase F; Provisional
Probab=96.84 E-value=0.0023 Score=63.28 Aligned_cols=66 Identities=24% Similarity=0.297 Sum_probs=46.8
Q ss_pred eEEEEeCCCCCCHHH-------HHHHHHHhhccceeeccCCCCCCCCeEEEEEecCc--ccccchhcCCCcEEEEEEE
Q 013857 310 TMVLVNKPKGWTSFT-------VCGKLRRLVKVKKVGHAGTLDPMATGLLIVCVGKA--TKLVDRYQGMIKGYSGVFR 378 (435)
Q Consensus 310 gII~VyKPkGmTS~d-------VV~kIKRiLk~kKVGHaGTLDP~ASGVLVVgIGkA--TKLL~~Ll~~~KeYiatgq 378 (435)
-++++|||.|+.|+. +++.+.. ..++...|.||-.+||||+++-+.. .+|+.--....|+|.|++.
T Consensus 68 ~~lvlnKP~G~~~~~~~~~~~tv~~~l~~---~~~l~~VgRLDrdTsGLLLlT~dg~~~~~L~~p~~~i~K~Y~v~V~ 142 (290)
T PRK10475 68 VLIALNKPVGIVSTTEDGERDNIVDFVNH---SKRVFPIGRLDKDSQGLIFLTNHGDLVNKILRAGNDHEKEYLVTVD 142 (290)
T ss_pred eEEEEECCCCCCcCCCCCCCCcHHHHhhc---cccccccccCCCCCcceEEEecCHHHHHHhhCcCCCCCeEEEEEEC
Confidence 378999999997763 3333321 2467899999999999999987542 3333322347899999986
No 48
>PRK11025 23S rRNA pseudouridylate synthase C; Provisional
Probab=96.79 E-value=0.0019 Score=63.64 Aligned_cols=70 Identities=26% Similarity=0.401 Sum_probs=50.6
Q ss_pred ceEEEEeCCCCCCHH-------HHHHHHHHhhc-cceeeccCCCCCCCCeEEEEEecCcc--cccchhcC--CCcEEEEE
Q 013857 309 GTMVLVNKPKGWTSF-------TVCGKLRRLVK-VKKVGHAGTLDPMATGLLIVCVGKAT--KLVDRYQG--MIKGYSGV 376 (435)
Q Consensus 309 GgII~VyKPkGmTS~-------dVV~kIKRiLk-~kKVGHaGTLDP~ASGVLVVgIGkAT--KLL~~Ll~--~~KeYiat 376 (435)
..+++||||.|+.++ .+++.+..... ...++..+.||-.+||||+++-+..+ .+...+.. ..|+|.|.
T Consensus 100 ~~~lvvnKP~gl~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TSGlll~Ak~~~a~~~l~~~~~~~~v~K~Y~a~ 179 (317)
T PRK11025 100 DHILVLNKPSGTAVHGGSGLSFGVIEGLRALRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLREKGMQKDYLAL 179 (317)
T ss_pred CCEEEEECCCCCcCcCCCCCCccHHHHHHHhccCCCcCceeCCCCCCCceEEEEEcCHHHHHHHHHHHHhCCccEEEEEE
Confidence 338999999999875 34555544322 23467899999999999999998743 34444443 77999998
Q ss_pred EE
Q 013857 377 FR 378 (435)
Q Consensus 377 gq 378 (435)
+.
T Consensus 180 v~ 181 (317)
T PRK11025 180 VR 181 (317)
T ss_pred Ee
Confidence 76
No 49
>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=96.74 E-value=0.0016 Score=57.14 Aligned_cols=68 Identities=29% Similarity=0.431 Sum_probs=47.9
Q ss_pred EEEEeCCCCCCHHH--------HHHHH----HHhhccceeeccCCCCCCCCeEEEEEecC-c-ccccchh--cCCCcEEE
Q 013857 311 MVLVNKPKGWTSFT--------VCGKL----RRLVKVKKVGHAGTLDPMATGLLIVCVGK-A-TKLVDRY--QGMIKGYS 374 (435)
Q Consensus 311 II~VyKPkGmTS~d--------VV~kI----KRiLk~kKVGHaGTLDP~ASGVLVVgIGk-A-TKLL~~L--l~~~KeYi 374 (435)
+++||||.|+.++. +...+ ........+...|.||-.+||||+++-+. + .++...+ ....|+|.
T Consensus 1 ~lvvnKP~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~RLD~~tsGlll~ak~~~~~~~l~~~~~~~~~~K~Y~ 80 (185)
T cd02869 1 LLVVNKPAGLPVHPGPGHLTGTLVNALLKLLLLLGEEFRPGLVHRLDKDTSGLLLVAKNKKAAAKLSKQFKERKVKKTYL 80 (185)
T ss_pred CEEEECCCCCeeecCCCCCCCCHHHHHHHHHhhcCCCCcCceecccCCCCceEEEEEcCHHHHHHHHHHHhcCceeEEEE
Confidence 47899999986553 23332 11223467889999999999999999855 3 4444543 33789999
Q ss_pred EEEE
Q 013857 375 GVFR 378 (435)
Q Consensus 375 atgq 378 (435)
|.+.
T Consensus 81 a~v~ 84 (185)
T cd02869 81 ALVD 84 (185)
T ss_pred EEEe
Confidence 9986
No 50
>PRK11394 23S rRNA pseudouridine synthase E; Provisional
Probab=96.66 E-value=0.0011 Score=63.44 Aligned_cols=68 Identities=24% Similarity=0.218 Sum_probs=49.5
Q ss_pred EEEEeCCCCCCHHHH----HHHHHHhhccceeeccCCCCCCCCeEEEEEecC-cccccchhc-CCCcEEEEEEE
Q 013857 311 MVLVNKPKGWTSFTV----CGKLRRLVKVKKVGHAGTLDPMATGLLIVCVGK-ATKLVDRYQ-GMIKGYSGVFR 378 (435)
Q Consensus 311 II~VyKPkGmTS~dV----V~kIKRiLk~kKVGHaGTLDP~ASGVLVVgIGk-ATKLL~~Ll-~~~KeYiatgq 378 (435)
++++|||.|+-|+.- ...+...+...++..+|.||..+||||+++-+. +++.+.... .-.|+|.|.+.
T Consensus 41 ylllnKP~G~l~~~~d~~~~~tl~d~l~~~~~~~vgRLD~~TsGllLlt~d~~~~~~L~~~~~~i~K~Y~~~v~ 114 (217)
T PRK11394 41 VILFNKPYDVLPQFTDEAGRKTLKEFIPVQGVYAAGRLDRDSEGLLVLTNNGALQARLTQPGKRTGKIYYVQVE 114 (217)
T ss_pred EEEEECCCCCEEeeCCccCCcchHHhcccCCeEEecCCCCCCeeEEEEECCHHHHHHHhCcccCCCEEEEEEEC
Confidence 789999999977621 223444444457889999999999999998854 444444333 37799999886
No 51
>PRK10839 16S rRNA pseudouridylate synthase A; Provisional
Probab=96.41 E-value=0.0014 Score=61.32 Aligned_cols=71 Identities=21% Similarity=0.254 Sum_probs=45.8
Q ss_pred EEEEeCCCCCCHHHH---HHHHHHhh---ccceeeccCCCCCCCCeEEEEEecCc--ccccchhcCCCcEEEEEEEECc
Q 013857 311 MVLVNKPKGWTSFTV---CGKLRRLV---KVKKVGHAGTLDPMATGLLIVCVGKA--TKLVDRYQGMIKGYSGVFRLGE 381 (435)
Q Consensus 311 II~VyKPkGmTS~dV---V~kIKRiL---k~kKVGHaGTLDP~ASGVLVVgIGkA--TKLL~~Ll~~~KeYiatgqLG~ 381 (435)
+++||||+||-++-- -..+-..+ ...++...|.||-.+||||+++-+.. .++..--....|+|.|++.--.
T Consensus 62 ~lvvnKP~G~~~~~~~~~~~tl~~~l~~~~~~~~~~v~RLD~~TSGlll~ak~~~~~~~l~~~~~~i~K~Y~a~i~~~i 140 (232)
T PRK10839 62 YFMLNKPQGYVCSTDDPDHPTVLYFLDEPVAYKLHAAGRLDIDTTGLVLMTDDGQWSHRITSPRHHCEKTYLVTLESPV 140 (232)
T ss_pred EEEEECCCCeEecccCCCCCeEEEecccccccCceecCCCCCCceeEEEEecCHHHHHHHhCCCCCCCeEEEEEECCCC
Confidence 899999999955521 00111111 12357789999999999999988762 3333322247899999765433
No 52
>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=96.39 E-value=0.0043 Score=57.01 Aligned_cols=70 Identities=26% Similarity=0.338 Sum_probs=47.1
Q ss_pred EEEEeCCCCCCHH-H---------------HHHHHHHhhccceeeccCCCCCCCCeEEEEEecC-cccc-cchhcCCCcE
Q 013857 311 MVLVNKPKGWTSF-T---------------VCGKLRRLVKVKKVGHAGTLDPMATGLLIVCVGK-ATKL-VDRYQGMIKG 372 (435)
Q Consensus 311 II~VyKPkGmTS~-d---------------VV~kIKRiLk~kKVGHaGTLDP~ASGVLVVgIGk-ATKL-L~~Ll~~~Ke 372 (435)
.+++|||.|+-|+ . +...+...+ .++...|.||-.+||||+++-.. +++. ..-.....|+
T Consensus 6 y~llnKP~G~l~s~~d~~~~~g~~~~~~~~~~~~l~~~~--~~l~~VgRLD~dTsGLLl~t~d~~~~~~L~~~~~~i~K~ 83 (177)
T cd02555 6 TLLLHKPAGMVSEQALALLGPGQRSAADRSGRRPLKGHF--ARLAPIGPLDKDASGLLVFSQDGRVLRKLIGDASRLEQE 83 (177)
T ss_pred EEEEECCCceEecCCCcccccccccccccchhhhhhhcC--CceeEecCCCCCCeeEEEEECCHHHHHHHhChhcCCCEE
Confidence 4789999997542 1 112222222 36889999999999999998744 4433 3333447899
Q ss_pred EEEEEEECccc
Q 013857 373 YSGVFRLGEAT 383 (435)
Q Consensus 373 YiatgqLG~aT 383 (435)
|.|.+. |.-+
T Consensus 84 Y~v~v~-g~~~ 93 (177)
T cd02555 84 YLVEVR-GELT 93 (177)
T ss_pred EEEEEc-ccCC
Confidence 999987 6543
No 53
>PF08068 DKCLD: DKCLD (NUC011) domain; InterPro: IPR012960 This is an N-terminal domain of dyskerin-like proteins, which is often associated with the TruB N-terminal(IPR002501 from INTERPRO) and PUA(IPR002478 from INTERPRO) domains [].; PDB: 3ZV0_D 3UAI_A 3U28_A 2AUS_C 2RFK_A 3LWV_A 3HJY_A 3HAX_A 3LWO_A 3HAY_A ....
Probab=96.38 E-value=0.0021 Score=51.36 Aligned_cols=20 Identities=30% Similarity=0.253 Sum_probs=15.4
Q ss_pred CCceEEEEeCCCCCCHHHHH
Q 013857 307 PFGTMVLVNKPKGWTSFTVC 326 (435)
Q Consensus 307 LnGgII~VyKPkGmTS~dVV 326 (435)
++-|||+||||+|+|||+||
T Consensus 40 i~~GvinlDKP~gPtSHeVv 59 (59)
T PF08068_consen 40 IKYGVINLDKPSGPTSHEVV 59 (59)
T ss_dssp HHTEEEEEEE-SSS-HHHHH
T ss_pred HhCCcEEeeCCCCCCccccC
Confidence 44459999999999999996
No 54
>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=96.34 E-value=0.0084 Score=54.83 Aligned_cols=68 Identities=19% Similarity=0.231 Sum_probs=45.4
Q ss_pred EEEEeCCCCCCHHHH---HHHHHHhhc-cceeeccCCCCCCCCeEEEEEecC-c-ccccchhcCCCcEEEEEEE
Q 013857 311 MVLVNKPKGWTSFTV---CGKLRRLVK-VKKVGHAGTLDPMATGLLIVCVGK-A-TKLVDRYQGMIKGYSGVFR 378 (435)
Q Consensus 311 II~VyKPkGmTS~dV---V~kIKRiLk-~kKVGHaGTLDP~ASGVLVVgIGk-A-TKLL~~Ll~~~KeYiatgq 378 (435)
.+++|||.|+-|+.- ...+...+. ..++-..|.||-.+||||+++-.. . .+|..-.....|+|.+++.
T Consensus 2 y~~lnKP~G~l~s~~~~~~~tv~~~l~~~~~~~~vgRLD~~tsGlll~t~dg~~~~~L~~p~~~~~K~Y~V~v~ 75 (164)
T cd02554 2 YIAYNKPVGIDCTLERADEDNIIDFVNPPPRIFPIGRLDKDSEGLILLTNDGDLVNKILHADNNHEKEYLVTVN 75 (164)
T ss_pred EEEEECCCCcEeecCCCCCCcHHHHhcCcCCEEEccCCCCCCeeEEEEEcCHHHHHHHhhhhcCCCeEEEEEEC
Confidence 467999999844421 112333333 256888999999999999997643 3 3343334447899999954
No 55
>PRK10700 23S rRNA pseudouridylate synthase B; Provisional
Probab=96.01 E-value=0.0098 Score=58.56 Aligned_cols=67 Identities=21% Similarity=0.268 Sum_probs=46.4
Q ss_pred EEEEeCCCCCCHH--------HHHHHHHHhhccceeeccCCCCCCCCeEEEEEe-cCcccccch-hcCCCcEEEEEEE
Q 013857 311 MVLVNKPKGWTSF--------TVCGKLRRLVKVKKVGHAGTLDPMATGLLIVCV-GKATKLVDR-YQGMIKGYSGVFR 378 (435)
Q Consensus 311 II~VyKPkGmTS~--------dVV~kIKRiLk~kKVGHaGTLDP~ASGVLVVgI-GkATKLL~~-Ll~~~KeYiatgq 378 (435)
++++|||.|+-|+ .|++.+.. +...++...|.||-.+||||+++- |..++.+.. =....|+|.|++.
T Consensus 69 ylvlnKP~G~~~s~~d~~~~~tv~d~l~~-~~~~~~~~VgRLD~dTsGLLLlTndg~~~~~L~~p~~~i~K~Y~v~V~ 145 (289)
T PRK10700 69 VLAYYKPEGELCTRNDPEGRPTVFDRLPK-LRGARWIAVGRLDVNTCGLLLFTTDGELANRLMHPSREVEREYAVRVF 145 (289)
T ss_pred EEEEECCCCCEeecCCCCCCccHHHHhhh-hcCCceeEccCCCCCCceEEEEEcCHHHHHHHhCccCCCCeEEEEEEc
Confidence 7889999998555 24444433 222457789999999999999876 334444332 2237899999985
No 56
>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=95.99 E-value=0.0027 Score=55.47 Aligned_cols=67 Identities=27% Similarity=0.315 Sum_probs=43.8
Q ss_pred EEEeCCCCCCHHHHHH----HHHHhh--ccceeeccCCCCCCCCeEEEEEecCc--ccccchhcCCCcEEEEEEE
Q 013857 312 VLVNKPKGWTSFTVCG----KLRRLV--KVKKVGHAGTLDPMATGLLIVCVGKA--TKLVDRYQGMIKGYSGVFR 378 (435)
Q Consensus 312 I~VyKPkGmTS~dVV~----kIKRiL--k~kKVGHaGTLDP~ASGVLVVgIGkA--TKLL~~Ll~~~KeYiatgq 378 (435)
++||||.|+-++.--. .+...+ ...+++..|.||-.+||||+++-... .++...-....|+|.|.+.
T Consensus 2 ivvnKP~G~~~~~~~~~~~~~l~~~l~~~~~~~~~vhRLD~~TsGlll~ak~~~~~~~l~~~~~~i~K~Y~a~v~ 76 (146)
T cd02870 2 LLLNKPRGVVSTVRDPEGRPTVLDLLKDVGERLFPVGRLDYDTEGLLLLTNDGELANRLTHPRYGVEKTYLVKVR 76 (146)
T ss_pred EEEECCCCcEecccCCCCCCEEeeeccccCCCEEECCCCCCCCeeEEEEeCCHHHHHHhhCccCCCCeEEEEEEC
Confidence 6799999996652111 111111 12468999999999999999997552 2232221236799999986
No 57
>KOG1919 consensus RNA pseudouridylate synthases [RNA processing and modification]
Probab=95.83 E-value=0.013 Score=60.35 Aligned_cols=77 Identities=25% Similarity=0.248 Sum_probs=57.0
Q ss_pred CCCceEEEEeCCCCCCHHHH--------HHHHHHhhccceeeccCCCCCCCCeEEEEEec--Ccccccchhc--CCCcEE
Q 013857 306 GPFGTMVLVNKPKGWTSFTV--------CGKLRRLVKVKKVGHAGTLDPMATGLLIVCVG--KATKLVDRYQ--GMIKGY 373 (435)
Q Consensus 306 ~LnGgII~VyKPkGmTS~dV--------V~kIKRiLk~kKVGHaGTLDP~ASGVLVVgIG--kATKLL~~Ll--~~~KeY 373 (435)
..+..+|+||||.|+.+|-+ ...+....+..-..-+..||+..||||+++-+ .+..+.+.|. ...|.|
T Consensus 110 ~ed~~~vVvnKP~gipVhp~g~~~~n~i~~~l~~~~~~~~~~~~hRLDr~tSGllvlAkt~~~~~~~~~~~r~~~~~k~Y 189 (371)
T KOG1919|consen 110 FEDKDYVVVNKPHGIPVHPTGRYRENTITKILAALHKVEGLRPCHRLDRLTSGLLVLAKTKEAADKFHEVLRKRTVKKEY 189 (371)
T ss_pred EecCCEEEEeCCCCCceeccCccccccchHHHHHhccccccccccccCccccceEEEEechhHhHHHHHHHhcccceeEE
Confidence 45666999999999999921 11222222445567788999999999999999 5788889998 588999
Q ss_pred -EEEEEECcc
Q 013857 374 -SGVFRLGEA 382 (435)
Q Consensus 374 -iatgqLG~a 382 (435)
++.+....-
T Consensus 190 ~v~~v~g~fp 199 (371)
T KOG1919|consen 190 VVARVEGPFP 199 (371)
T ss_pred EEEEEeccCC
Confidence 666665543
No 58
>COG1187 RsuA 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]
Probab=94.82 E-value=0.033 Score=54.74 Aligned_cols=67 Identities=27% Similarity=0.373 Sum_probs=48.3
Q ss_pred EEEEeCCCCCCHHHH----HHHHHHhhc-----cceeeccCCCCCCCCeEEEEEecCc---ccccchhcCCCcEEEEEEE
Q 013857 311 MVLVNKPKGWTSFTV----CGKLRRLVK-----VKKVGHAGTLDPMATGLLIVCVGKA---TKLVDRYQGMIKGYSGVFR 378 (435)
Q Consensus 311 II~VyKPkGmTS~dV----V~kIKRiLk-----~kKVGHaGTLDP~ASGVLVVgIGkA---TKLL~~Ll~~~KeYiatgq 378 (435)
.+++|||.|+-|..- ..++...+. ..++-+.|.||-.++|+|++ +|+| .+|++==....|+|.+++.
T Consensus 65 y~llnKP~G~v~s~~D~~gr~tv~D~lp~~~~~~~~~~pvGRLD~dTeGLLLL-TnDG~la~rL~~P~~~~~K~Y~v~v~ 143 (248)
T COG1187 65 YLLLNKPRGYVSSTEDDEGRPTVFDLLPERLPRKKRLFPVGRLDKDTEGLLLL-TNDGELAHRLMHPSSEVEKEYLVRVE 143 (248)
T ss_pred EEEEECCCCeEecccCCCCCceeeeecccccccccceeeccccCCCCeeEEEE-eCCHHHHHHhcCCCCCCCEEEEEEEe
Confidence 789999999755443 333443343 23588999999999999887 6664 4455444558999999986
No 59
>TIGR01213 conserved hypothetical protein TIGR01213. Members of this family show twilight-zone similarity to several predicted RNA pseudouridine synthases. All trusted members of this family are archaeal. Several eukaryotic homologs lack N-terminal homology including two CXXC motifs.
Probab=83.64 E-value=1.6 Score=45.79 Aligned_cols=42 Identities=21% Similarity=0.395 Sum_probs=35.8
Q ss_pred CCcEEEEEEEECcccccCCCCCCeEeeccCCCCCHHHHHHHHHcCcc-ceeeccccccccc
Q 013857 369 MIKGYSGVFRLGEATSTWDADSPVIQREPWEHIKDEDIRKAAASFRG-EIWQVPPMFSAIK 428 (435)
Q Consensus 369 ~~KeYiatgqLG~aTDT~D~eGkVieksp~~hIT~EkLekaLssFqG-~I~QiPP~YSAVK 428 (435)
..|+|+|.+.+.. .|+.++|+++++.|+| .|+|.+|.=++.+
T Consensus 275 ~~K~Y~alV~~~~------------------~v~~e~L~~~~~~l~g~~I~QrTP~RV~hR 317 (388)
T TIGR01213 275 HRKVYRALVEVDG------------------PVSDEDLEELCKELEGATIYQRTPLRVLHR 317 (388)
T ss_pred CceEEEEEEEECC------------------CCCHHHHHHHHHhccCCEEEccCCceEEEe
Confidence 6799999999863 5788999999999999 8999999766543
No 60
>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=79.33 E-value=1.9 Score=37.34 Aligned_cols=38 Identities=24% Similarity=0.212 Sum_probs=27.8
Q ss_pred cCCCCCCCCeEEEEEecC-cccc-cchhcCCCcEEEEEEE
Q 013857 341 AGTLDPMATGLLIVCVGK-ATKL-VDRYQGMIKGYSGVFR 378 (435)
Q Consensus 341 aGTLDP~ASGVLVVgIGk-ATKL-L~~Ll~~~KeYiatgq 378 (435)
.|.||-.+||||+++-.. +.+. ...-....|+|.|.+.
T Consensus 1 v~RLD~~TSGlll~akd~~~~~~L~~~~~~i~K~Y~a~v~ 40 (128)
T TIGR00093 1 AGRLDRDSEGLLLLTNDGELVHRLTHPGHHCEKTYLVTVE 40 (128)
T ss_pred CCCCCCCCEEEEEEEeCHHHHHHHhCCCCCCCeEEEEEEC
Confidence 488999999999998755 3333 3322236899999986
No 61
>PRK14554 putative pseudouridylate synthase; Provisional
Probab=64.33 E-value=11 Score=40.12 Aligned_cols=60 Identities=22% Similarity=0.277 Sum_probs=42.6
Q ss_pred EEEEEecCcccc-cchhcC--CCcEEEEEEEECcccccCCCCCCeEeeccCCCCCHHHHHHHHHcCccc-eeeccccccc
Q 013857 351 LLIVCVGKATKL-VDRYQG--MIKGYSGVFRLGEATSTWDADSPVIQREPWEHIKDEDIRKAAASFRGE-IWQVPPMFSA 426 (435)
Q Consensus 351 VLVVgIGkATKL-L~~Ll~--~~KeYiatgqLG~aTDT~D~eGkVieksp~~hIT~EkLekaLssFqG~-I~QiPP~YSA 426 (435)
|-+..+.-+++- +..+.. ..|+|+|.+.+.. .|+.+++.+++..|+|. |+|.+|.=++
T Consensus 287 V~v~~l~~~~~~~~~~ik~~~~~K~YralV~~~~------------------~v~~e~l~~~~~~l~~~~I~QrTP~RV~ 348 (422)
T PRK14554 287 VEVENLRFATRKEVERIKEEKASKTYRALVESDE------------------PVSEEELEKLLDELSGATIEQRTPRRVK 348 (422)
T ss_pred EEEEEEEEEcHHHHHHHhcCCCceEEEEEEEECC------------------CCCHHHHHHHHHhccCcEeeccCcHhhh
Confidence 455545444332 233332 5599999999753 57889999999999997 9999997665
Q ss_pred cc
Q 013857 427 IK 428 (435)
Q Consensus 427 VK 428 (435)
.+
T Consensus 349 hR 350 (422)
T PRK14554 349 HR 350 (422)
T ss_pred hh
Confidence 44
No 62
>TIGR00094 tRNA_TruD_broad tRNA pseudouridine synthase, TruD family. MJ11364 is a strong partial match from 50 to 230 aa.
Probab=63.48 E-value=37 Score=34.87 Aligned_cols=47 Identities=28% Similarity=0.428 Sum_probs=39.8
Q ss_pred EEEEeCCCCCCHHHHHHHHHHhhc--cceeeccCCCCCCCCeEEEEEecC
Q 013857 311 MVLVNKPKGWTSFTVCGKLRRLVK--VKKVGHAGTLDPMATGLLIVCVGK 358 (435)
Q Consensus 311 II~VyKPkGmTS~dVV~kIKRiLk--~kKVGHaGTLDP~ASGVLVVgIGk 358 (435)
++.|.| .|++..++++.|.+.++ .+.||.+|+=|-.|-=.=-|++..
T Consensus 45 ~~~l~K-~~~~T~~a~~~iar~l~i~~~~i~yAG~KDk~AvT~Q~~s~~~ 93 (387)
T TIGR00094 45 HIRVEK-EGCNTLEVARVLAKFLGVSRREIGFAGTKDKRAVTEQWVCLRV 93 (387)
T ss_pred EEEEEE-CCcCHHHHHHHHHHHhCCChhheeecccccccceeEEEEEecc
Confidence 788888 99999999999999987 479999999999996555556643
No 63
>cd02575 PseudoU_synth_EcTruD PseudoU_synth_EcTruD: Pseudouridine synthase, TruD family. This group consists of bacterial pseudouridine synthases similar to Escherichia coli TruD. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). E. coli TruD makes the highly phylogenetically conserved psi13 in tRNAs.
Probab=59.34 E-value=99 Score=30.90 Aligned_cols=100 Identities=14% Similarity=0.159 Sum_probs=59.1
Q ss_pred EEEEeCCCCCCHHHHHHHHHHhhcc--ceeeccCCCCCCCCeEEEEEecCcccccchhcC-CCcEEEEEEEECccc---c
Q 013857 311 MVLVNKPKGWTSFTVCGKLRRLVKV--KKVGHAGTLDPMATGLLIVCVGKATKLVDRYQG-MIKGYSGVFRLGEAT---S 384 (435)
Q Consensus 311 II~VyKPkGmTS~dVV~kIKRiLk~--kKVGHaGTLDP~ASGVLVVgIGkATKLL~~Ll~-~~KeYiatgqLG~aT---D 384 (435)
++.|.| .||+.++++..|.+.+++ +.||.+|+=|-.|-=.=-|+|-...+....+.. ..+. +-...+|... -
T Consensus 28 ~~~l~K-~~~~T~~ai~~LAr~lgi~~~~igyAGlKDk~AvT~Q~~sv~~~~~~~~~~~~~~~~~-i~i~~~~~~~~kL~ 105 (253)
T cd02575 28 LLHIRK-TGLNTREVAKELAKALGVKERDVGYAGLKDRHAVTTQWFSVHLPGKEAPDLSALQLEG-VKILEVTRHNRKLR 105 (253)
T ss_pred EEEEEE-CCCCHHHHHHHHHHHhCCChhheeecccccCceeeEEEEEEEcCccCchhHHhccCCC-eEEEEEEecCCCcC
Confidence 555666 899999999999999875 699999999999976666666332121111211 1111 1223333333 3
Q ss_pred cCCCCCCeEe--eccCCCCCHHHHHHHHHcC
Q 013857 385 TWDADSPVIQ--REPWEHIKDEDIRKAAASF 413 (435)
Q Consensus 385 T~D~eGkVie--ksp~~hIT~EkLekaLssF 413 (435)
..|..|..-. -.... ...+.|+++++.+
T Consensus 106 ~G~L~GNrF~I~lR~v~-~~~~~l~~~l~~i 135 (253)
T cd02575 106 RGHLKGNRFVIRLRGVS-GNADKLEQRLETI 135 (253)
T ss_pred CCcccCCEEEEEEecCC-CCHHHHHHHHHHH
Confidence 4666774322 22222 2356677777654
No 64
>PRK00984 truD tRNA pseudouridine synthase D; Reviewed
Probab=58.57 E-value=1e+02 Score=31.70 Aligned_cols=122 Identities=17% Similarity=0.292 Sum_probs=70.4
Q ss_pred CccccccCCCCCCCCcCCCCceEEEEeCCCCCCHHHHHHHHHHhhcc--ceeeccCCCCCCCCeEEEEEecCcccccchh
Q 013857 289 GEPYIVSRSTELPPTWDGPFGTMVLVNKPKGWTSFTVCGKLRRLVKV--KKVGHAGTLDPMATGLLIVCVGKATKLVDRY 366 (435)
Q Consensus 289 ~~~~~~~~~~~~p~~wd~LnGgII~VyKPkGmTS~dVV~kIKRiLk~--kKVGHaGTLDP~ASGVLVVgIGkATKLL~~L 366 (435)
++=|.|..-...++.++..+= ++.|.| .|++..+++..|.+.+++ +.||.+|+=|-.|-=.=-|+|-...+....+
T Consensus 24 peDF~V~E~~~~~~~~~G~~~-~~~l~K-~~~~T~~~~~~lar~l~i~~~~i~yAG~KDk~AvT~Q~~si~~~~~~~~~~ 101 (341)
T PRK00984 24 PEDFVVREILGFEPSGEGEHL-LVRIRK-RGWNTLFVARALAKFLGISLRDVGYAGLKDRHAVTTQWFSIHLPGKEEPDL 101 (341)
T ss_pred ccceeEEeccCCCCCCCcCEE-EEEEEE-CCCCHHHHHHHHHHHhCCChhheeecccCcCCeeeEEEEEEECCCCChhhH
Confidence 344455554444455554444 566666 799999999999999875 6899999999999777777773311111111
Q ss_pred cC-CCcEEEEEEEECccc---ccCCCCCCeEe--eccCCCCCHHHHHHHHHcCc
Q 013857 367 QG-MIKGYSGVFRLGEAT---STWDADSPVIQ--REPWEHIKDEDIRKAAASFR 414 (435)
Q Consensus 367 l~-~~KeYiatgqLG~aT---DT~D~eGkVie--ksp~~hIT~EkLekaLssFq 414 (435)
.. ..+. .-...+|... -..|..|.--. -..... ..+.|++.|+.+.
T Consensus 102 ~~~~~~~-~~i~~~~~~~~~l~~G~l~GN~F~I~lR~~~~-~~~~~~~~l~~l~ 153 (341)
T PRK00984 102 SAFQLEG-LEILELGRHNRKLRLGDLKGNRFTIRLREVSK-DRDKVEQRLEEIA 153 (341)
T ss_pred hhcccCC-eEEEEEEccCCCCCCCcCCCCEEEEEEecCCC-CHHHHHHHHHHHH
Confidence 11 1111 1222344333 34666674322 223332 4677777776653
No 65
>COG0585 Uncharacterized conserved protein [Function unknown]
Probab=57.57 E-value=45 Score=35.37 Aligned_cols=69 Identities=26% Similarity=0.474 Sum_probs=50.2
Q ss_pred CCCccccccCCCCCCCCcCCCCceEEEEeCCCCCCHHHHHHHHHHhhcc--ceeeccCCCCCCCCeEEEEEec
Q 013857 287 GSGEPYIVSRSTELPPTWDGPFGTMVLVNKPKGWTSFTVCGKLRRLVKV--KKVGHAGTLDPMATGLLIVCVG 357 (435)
Q Consensus 287 ~~~~~~~~~~~~~~p~~wd~LnGgII~VyKPkGmTS~dVV~kIKRiLk~--kKVGHaGTLDP~ASGVLVVgIG 357 (435)
..++=+.|......++..+..+= +|.|.| .||+..+++..|.+.|++ +.||.|||=|-.|-=.=-|||-
T Consensus 27 ~~pedF~V~Ei~~~~~~~~G~~~-~~~l~K-~~~dT~~a~~~iak~lgv~~r~v~yAGlKDk~AVT~Q~vsi~ 97 (406)
T COG0585 27 AEPEDFIVEEILGYEPSGDGEYL-LFLLRK-RGWDTLDAAREIAKRLGVPRRRVGYAGLKDKRAVTTQYVSIP 97 (406)
T ss_pred eCCCccEEEeecCcCCCCCCCEE-EEEEEE-cCCChHHHHHHHHHHhCCChhhcccccccccceeeEEEEEEE
Confidence 34445566655555555443333 555555 799999999999999987 8999999999999666666665
No 66
>cd02577 PSTD1 PSTD1: Pseudouridine synthase, a subgroup of the TruD family. This group consists of several hypothetical archeal pseudouridine synthases assigned to the TruD family of psuedouridine synthases. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). The TruD family is comprised of proteins related to Escherichia coli TruD.
Probab=55.91 E-value=1.4e+02 Score=30.46 Aligned_cols=69 Identities=23% Similarity=0.402 Sum_probs=50.9
Q ss_pred CccccccCCCCCCCCcCCCCceEEEEeCCCCCCHHHHHHHHHHhhcc--ceeeccCCCCCCCCeEEEEEecCc
Q 013857 289 GEPYIVSRSTELPPTWDGPFGTMVLVNKPKGWTSFTVCGKLRRLVKV--KKVGHAGTLDPMATGLLIVCVGKA 359 (435)
Q Consensus 289 ~~~~~~~~~~~~p~~wd~LnGgII~VyKPkGmTS~dVV~kIKRiLk~--kKVGHaGTLDP~ASGVLVVgIGkA 359 (435)
++-|.|..-...+..+....- ++.+.| .||+..++++.|.+.+++ ..+|.|||=|-.|-=.=.|+|-..
T Consensus 7 peDF~V~Ei~~~~~~~~g~y~-~f~l~K-~n~dT~~ai~~lar~l~i~~~~i~~AG~KDk~AvT~Q~vsv~~~ 77 (319)
T cd02577 7 PEDFIVEEITPFDIGKKGKYL-IYLLEK-KNWDTLDAVRRIAKALGISRKRIGYAGTKDKHAVTTQYISIFDP 77 (319)
T ss_pred CCceEEEEecCCCCCCCCCEE-EEEEEE-CCCCHHHHHHHHHHHhCCChhheeeccccccccceEEEEEeecc
Confidence 344555555555555555444 666666 799999999999999875 689999999999977777777443
No 67
>cd02552 PseudoU_synth_TruD_like PseudoU_synth_TruD_like: Pseudouridine synthase, TruD family. This group consists of eukaryotic, bacterial and archeal pseudouridine synthases similar to Escherichia coli TruD and Saccharomyces cerevisiae Pus7. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). E. coli TruD and S. cerevisiae Pus7 make psi13 in cytoplasmic tRNAs. In addition S. cerevisiae Pus7 makes psi35 in U2 small nuclear RNA (U2 snRNA) and psi35 in pre-tRNATyr. Psi35 in U2 snRNA and psi13 in tRNAs are highly phylogenetically conserved. Psi34 is the mammalian U2 snRNA counterpart of yeast U2 snRNA psi35.
Probab=53.31 E-value=58 Score=31.81 Aligned_cols=47 Identities=23% Similarity=0.257 Sum_probs=38.5
Q ss_pred EEEEeCCCCCCHHHHHHHHHHhhcc--ceeeccCCCCCCCCeEEEEEecC
Q 013857 311 MVLVNKPKGWTSFTVCGKLRRLVKV--KKVGHAGTLDPMATGLLIVCVGK 358 (435)
Q Consensus 311 II~VyKPkGmTS~dVV~kIKRiLk~--kKVGHaGTLDP~ASGVLVVgIGk 358 (435)
++.|.| .|++..+++..|.+.+++ +.||++|+-|-.|-=.=-|+|-.
T Consensus 34 ~~~l~K-~~~~T~~a~~~la~~l~i~~~~i~yAG~KDk~AvT~Q~~sv~~ 82 (232)
T cd02552 34 HFTLYK-ENKDTMEALREIAKALGVPPRDIGYAGTKDKRAVTTQRVSVHK 82 (232)
T ss_pred EEEEEE-CCCCHHHHHHHHHHHcCCCHHHEeEcccccCceeeEEEEEEEC
Confidence 555666 799999999999999875 68999999999996666666643
No 68
>COG0575 CdsA CDP-diglyceride synthetase [Lipid metabolism]
Probab=33.18 E-value=25 Score=34.33 Aligned_cols=25 Identities=32% Similarity=0.562 Sum_probs=20.9
Q ss_pred HHHHH-HHHHhhcccee-----eccCCCCCC
Q 013857 323 FTVCG-KLRRLVKVKKV-----GHAGTLDPM 347 (435)
Q Consensus 323 ~dVV~-kIKRiLk~kKV-----GHaGTLDP~ 347 (435)
+|+++ .+||.++.|.. ||+|-||.+
T Consensus 217 GDL~eS~iKR~~gvKDsg~liPGHGGilDR~ 247 (265)
T COG0575 217 GDLFESYIKRLLGIKDSGWLIPGHGGILDRF 247 (265)
T ss_pred hhHHHHHHHHccCCCCcCCCCCCcCcccccH
Confidence 57777 88999988776 999999975
No 69
>PF08555 DUF1754: Eukaryotic family of unknown function (DUF1754); InterPro: IPR013865 This is a eukaryotic protein of unknown function.
Probab=29.25 E-value=27 Score=29.17 Aligned_cols=25 Identities=20% Similarity=0.367 Sum_probs=20.9
Q ss_pred CCCCCchhhhHHHHHHHHHhhcccc
Q 013857 110 QPGSDNAEMTKSMRKYYNKRRQRMY 134 (435)
Q Consensus 110 ~~~~~~~~~~~~~~~~~~~~~~~~~ 134 (435)
.....++.|+.|.|+|-..||+|++
T Consensus 73 ~~~~~~~~kTeAErrfee~q~KRl~ 97 (98)
T PF08555_consen 73 EDESYDDGKTEAERRFEEAQRKRLM 97 (98)
T ss_pred ccccccCCCCHHHHHHHHHHHHHHc
Confidence 3445678899999999999999985
No 70
>COG1258 Predicted pseudouridylate synthase [Translation, ribosomal structure and biogenesis]
Probab=25.65 E-value=94 Score=33.33 Aligned_cols=38 Identities=24% Similarity=0.323 Sum_probs=32.9
Q ss_pred CCCcEEEEEEEECcccccCCCCCCeEeeccCCCCCHHHHHHHHHcCcc-ceeecccc
Q 013857 368 GMIKGYSGVFRLGEATSTWDADSPVIQREPWEHIKDEDIRKAAASFRG-EIWQVPPM 423 (435)
Q Consensus 368 ~~~KeYiatgqLG~aTDT~D~eGkVieksp~~hIT~EkLekaLssFqG-~I~QiPP~ 423 (435)
...|.|.|.+.+.. .|+.++++.++.++.| .|.|.-|.
T Consensus 279 ~~rK~YrAlV~~~~------------------~v~~e~l~~~~~~L~g~~I~QrTP~ 317 (398)
T COG1258 279 RHRKVYRALVYSDR------------------PVSDEKLEEVLGSLEGKTIRQRTPR 317 (398)
T ss_pred ccceeEEEEEEECC------------------CcCHHHHHHHHhhccCcEEeecChH
Confidence 47899999998763 6889999999999999 78888875
No 71
>PRK10719 eutA reactivating factor for ethanolamine ammonia lyase; Provisional
Probab=24.49 E-value=1.3e+02 Score=33.00 Aligned_cols=65 Identities=14% Similarity=0.147 Sum_probs=55.5
Q ss_pred CeEEEEEecCcccccchhcCCCcEEEEEEEECcccccCCCCCCeEeeccC---------------CCCCHHHHHHHHHcC
Q 013857 349 TGLLIVCVGKATKLVDRYQGMIKGYSGVFRLGEATSTWDADSPVIQREPW---------------EHIKDEDIRKAAASF 413 (435)
Q Consensus 349 SGVLVVgIGkATKLL~~Ll~~~KeYiatgqLG~aTDT~D~eGkVieksp~---------------~hIT~EkLekaLssF 413 (435)
.||++|=+|.+|--+..+.+..=.|...+-+|-.-=|.|.+|+|+.-++- +.++.++|.+++..|
T Consensus 146 ~gVa~IDIGgGTT~iaVf~~G~l~~T~~l~vGG~~IT~D~~~~i~yis~~~~~l~~~~~~~~~~G~~~~~~~L~~i~~~M 225 (475)
T PRK10719 146 TRVLNIDIGGGTANYALFDAGKVIDTACLNVGGRLIETDSQGRVTYISPPGQMILDELGLAITDGRSLTGEQLQQVTRRM 225 (475)
T ss_pred CceEEEEeCCCceEEEEEECCEEEEEEEEecccceEEECCCCCEEEEChHHHHHHHHcCCCccccccCCHHHHHHHHHHH
Confidence 58999999999999999999999999999999999999999999877542 345777777776654
Done!