Query 031054
Match_columns 166
No_of_seqs 157 out of 1308
Neff 7.4
Searched_HMMs 46136
Date Fri Mar 29 08:32:55 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/031054.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/031054hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 cd02556 PseudoU_synth_RluB Pse 100.0 5.1E-43 1.1E-47 268.2 16.3 134 21-156 34-167 (167)
2 TIGR00093 pseudouridine syntha 100.0 7.3E-43 1.6E-47 256.8 15.4 128 26-156 1-128 (128)
3 cd02553 PseudoU_synth_RsuA Pse 100.0 1.4E-42 2.9E-47 265.9 16.5 133 21-159 34-167 (167)
4 cd02555 PSSA_1 PSSA_1: Pseudou 100.0 8.4E-42 1.8E-46 263.9 15.8 132 21-159 45-176 (177)
5 PRK10839 16S rRNA pseudouridyl 100.0 1.9E-41 4E-46 271.4 15.1 138 22-163 94-231 (232)
6 cd02554 PseudoU_synth_RluF Pse 100.0 5.4E-41 1.2E-45 256.4 16.0 133 21-160 31-163 (164)
7 PRK10700 23S rRNA pseudouridyl 100.0 1.9E-40 4.1E-45 273.6 18.1 141 21-163 101-241 (289)
8 COG1187 RsuA 16S rRNA uridine- 100.0 3.6E-40 7.9E-45 265.3 16.2 143 21-164 99-243 (248)
9 PRK10475 23S rRNA pseudouridin 100.0 1.5E-39 3.3E-44 268.1 16.2 136 21-163 98-233 (290)
10 PRK11394 23S rRNA pseudouridin 100.0 7.8E-39 1.7E-43 253.8 16.1 135 21-156 70-217 (217)
11 cd02566 PseudoU_synth_RluE Pse 100.0 5.4E-36 1.2E-40 229.5 15.1 125 21-146 31-168 (168)
12 cd02870 PseudoU_synth_RsuA_lik 100.0 1.2E-34 2.6E-39 217.1 13.3 115 21-137 32-146 (146)
13 cd02550 PseudoU_synth_Rsu_Rlu_ 100.0 2.2E-34 4.8E-39 217.4 12.2 115 21-137 33-154 (154)
14 cd02557 PseudoU_synth_ScRIB2 P 100.0 7.3E-31 1.6E-35 208.0 10.3 116 21-136 58-186 (213)
15 COG0564 RluA Pseudouridylate s 100.0 8.5E-31 1.8E-35 216.2 11.0 116 20-136 121-250 (289)
16 TIGR01621 RluA-like pseudourid 100.0 2.7E-30 5.9E-35 205.4 10.8 114 21-136 42-166 (217)
17 PRK10158 23S rRNA/tRNA pseudou 100.0 3.8E-30 8.3E-35 204.7 10.5 114 22-136 56-182 (219)
18 TIGR00005 rluA_subfam pseudour 100.0 2.3E-29 5.1E-34 207.9 11.4 114 21-136 118-245 (299)
19 cd02558 PSRA_1 PSRA_1: Pseudou 100.0 2.3E-29 4.9E-34 203.5 10.8 114 21-136 81-206 (246)
20 cd02869 PseudoU_synth_RluCD_li 100.0 3.6E-29 7.9E-34 192.3 10.9 115 20-136 37-164 (185)
21 PRK11112 tRNA pseudouridine sy 100.0 2.3E-29 4.9E-34 204.6 9.4 115 22-136 46-182 (257)
22 cd02563 PseudoU_synth_TruC tRN 100.0 4.3E-29 9.3E-34 199.0 9.6 115 22-136 45-181 (223)
23 PRK11180 rluD 23S rRNA pseudou 100.0 7.9E-29 1.7E-33 207.4 11.3 130 2-136 114-254 (325)
24 PRK11025 23S rRNA pseudouridyl 100.0 2.3E-28 5.1E-33 204.0 9.7 113 22-136 136-262 (317)
25 PF00849 PseudoU_synth_2: RNA 99.9 6.2E-25 1.3E-29 166.0 8.3 105 20-124 38-164 (164)
26 KOG1919 RNA pseudouridylate sy 99.9 1.2E-21 2.5E-26 165.9 8.5 115 21-137 148-282 (371)
27 cd02868 PseudoU_synth_hTruB2_l 98.6 4.1E-07 8.8E-12 73.0 10.9 122 23-148 34-214 (226)
28 cd01291 PseudoU_synth PseudoU_ 98.2 1.1E-05 2.4E-10 55.0 7.1 67 18-126 21-87 (87)
29 cd00506 PseudoU_synth_TruB_lik 97.5 0.00063 1.4E-08 54.1 8.6 135 2-146 12-205 (210)
30 PRK00989 truB tRNA pseudouridi 97.5 0.00048 1.1E-08 55.4 7.7 138 2-148 21-213 (230)
31 cd02572 PseudoU_synth_hDyskeri 97.3 0.004 8.7E-08 48.4 10.8 133 1-143 13-170 (182)
32 TIGR00431 TruB tRNA pseudourid 97.3 0.0032 6.9E-08 50.0 9.6 136 2-147 14-205 (209)
33 PRK00020 truB tRNA pseudouridi 97.1 0.0064 1.4E-07 49.4 10.4 131 2-144 22-213 (244)
34 cd02573 PseudoU_synth_EcTruB P 97.0 0.011 2.4E-07 48.9 10.8 133 2-144 12-203 (277)
35 PRK14123 tRNA pseudouridine sy 97.0 0.012 2.5E-07 49.4 10.9 135 2-146 15-213 (305)
36 PRK00130 truB tRNA pseudouridi 96.8 0.016 3.4E-07 48.3 9.9 133 2-146 14-205 (290)
37 PRK04099 truB tRNA pseudouridi 96.7 0.018 3.8E-07 47.6 9.8 130 2-143 14-201 (273)
38 PRK02193 truB tRNA pseudouridi 96.7 0.024 5.1E-07 47.0 10.5 132 2-143 12-202 (279)
39 PRK02484 truB tRNA pseudouridi 96.7 0.029 6.3E-07 46.8 11.0 133 2-144 15-211 (294)
40 cd02867 PseudoU_synth_TruB_4 P 96.7 0.033 7.2E-07 46.8 11.1 134 21-160 56-250 (312)
41 PRK14124 tRNA pseudouridine sy 96.6 0.018 4E-07 48.2 9.2 135 2-148 15-207 (308)
42 PRK01851 truB tRNA pseudouridi 96.6 0.026 5.6E-07 47.3 9.9 133 2-146 28-218 (303)
43 PRK14846 truB tRNA pseudouridi 96.5 0.033 7.1E-07 47.3 10.4 136 2-147 15-208 (345)
44 PRK03287 truB tRNA pseudouridi 96.5 0.02 4.3E-07 47.9 8.9 55 2-64 21-77 (298)
45 PRK02755 truB tRNA pseudouridi 96.5 0.047 1E-06 45.6 11.0 133 2-145 15-207 (295)
46 PRK04270 H/ACA RNA-protein com 96.5 0.028 6.2E-07 46.9 9.7 131 2-144 34-188 (300)
47 PRK05033 truB tRNA pseudouridi 96.5 0.048 1E-06 45.9 10.9 133 2-146 22-212 (312)
48 PRK01550 truB tRNA pseudouridi 96.4 0.053 1.2E-06 45.4 10.9 133 2-144 14-210 (304)
49 PRK01528 truB tRNA pseudouridi 96.2 0.072 1.6E-06 44.4 10.6 135 2-146 15-207 (292)
50 PRK05389 truB tRNA pseudouridi 96.2 0.05 1.1E-06 45.6 9.5 132 2-144 25-214 (305)
51 TIGR00425 CBF5 rRNA pseudourid 95.8 0.13 2.9E-06 43.4 10.6 130 2-143 46-199 (322)
52 PRK04642 truB tRNA pseudouridi 95.7 0.12 2.6E-06 43.2 9.8 131 2-144 22-211 (300)
53 PRK14122 tRNA pseudouridine sy 95.5 0.14 3.1E-06 43.0 9.6 55 2-64 13-69 (312)
54 KOG2559 Predicted pseudouridin 95.3 0.037 8E-07 45.0 5.1 50 102-151 206-261 (318)
55 PF01509 TruB_N: TruB family p 90.5 0.52 1.1E-05 35.5 4.5 40 21-64 7-48 (149)
56 COG0130 TruB Pseudouridine syn 89.9 1.6 3.4E-05 36.1 7.1 115 21-143 42-183 (271)
57 PF07530 PRE_C2HC: Associated 50.3 16 0.00034 23.7 2.2 24 115-138 1-24 (68)
58 PF07867 DUF1654: Protein of u 49.6 13 0.00028 24.7 1.8 33 1-33 2-36 (73)
59 cd07973 Spt4 Transcription elo 45.0 82 0.0018 22.0 5.3 45 33-77 47-92 (98)
60 smart00596 PRE_C2HC PRE_C2HC d 43.2 27 0.00058 22.9 2.5 25 115-139 1-25 (69)
61 PF00004 AAA: ATPase family as 32.8 47 0.001 22.7 2.7 26 110-135 7-32 (132)
62 PF14401 RLAN: RimK-like ATPgr 26.7 80 0.0017 23.7 3.1 46 116-162 102-148 (153)
63 KOG3490 Transcription elongati 22.0 2.3E+02 0.005 20.2 4.4 44 34-77 52-96 (111)
64 KOG2553 Pseudouridylate syntha 20.4 53 0.0011 28.8 1.2 23 102-125 263-288 (416)
No 1
>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=100.00 E-value=5.1e-43 Score=268.20 Aligned_cols=134 Identities=35% Similarity=0.581 Sum_probs=121.6
Q ss_pred CCeeecCCCCcCCceeeeeeCCHHHHHHhhcCCCCCCeEEEEEEecccChhhhhhhhcceeeCCcccceeEEEEcCCCCC
Q 031054 21 PRLFTVGRLDVATTGLIIVTNDGDFAQAVSHPSSKLQKEYIATIDGAVNKRHLIAISEGTVIEGTHCTPDVVELLPPQPD 100 (166)
Q Consensus 21 ~~l~~vhRLD~~TSGlll~ak~~~~~~~l~~~~~~i~K~Y~a~v~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 100 (166)
+++++|||||++||||||||||++++++|+++++.++|+|+|+|+|.++++.+..+..++..++++.+++.++++...
T Consensus 34 ~~~~~V~RLD~~TsGLll~ak~~~~~~~L~~~~~~i~K~Y~a~V~g~~~~~~~~~~~~gv~~~~~~~~~~~~~~~~~~-- 111 (167)
T cd02556 34 PRWISVGRLDLNTEGLLLFTNDGELANRLMHPSNEIEREYAVRVFGQVTDEQLKSLKKGVELEDGFAGFKSIQLEGGE-- 111 (167)
T ss_pred CceEEcCcCCCCCeeEEEEECCHHHHHHHhCCcCCCCeEEEEEECccCCHHHHHHHHcCCEECCCcCcceEEEEEecC--
Confidence 467999999999999999999999999999999999999999999999988887778888777777778888887542
Q ss_pred CCceEEEEEecCCchhHHHHHHHHcCCceeeeeeeEEeCeecCCCCCCCcEEEcCH
Q 031054 101 IPRPRIRIVVHEGRNHEVRELVKNAGLKLYSLKRLRIGGFRLPSDLGIGMHVELKQ 156 (166)
Q Consensus 101 ~~~~ll~~~l~tGR~HQIR~~l~~~G~pI~~l~R~~~g~~~l~~~l~~G~~r~l~~ 156 (166)
.++++++|+|.|||+||||+||+++||||+.|+|++||++.|.++|++|+||+|+|
T Consensus 112 ~~~sll~v~l~tGR~HQIR~~~a~~G~pV~~L~R~~ig~~~l~~~L~~G~~r~l~~ 167 (167)
T cd02556 112 GKNSWYRVTLREGRNREVRRLWEAFGLQVSRLIRIRYGPIFLPGNLKRGQWEELPP 167 (167)
T ss_pred CCcEEEEEEEEeCCCHHHHHHHHHcCCeEeEEEEEEECCcccCCCCCCCceEECCC
Confidence 24689999999999999999999999999999999999999965899999999986
No 2
>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=100.00 E-value=7.3e-43 Score=256.77 Aligned_cols=128 Identities=32% Similarity=0.580 Sum_probs=117.4
Q ss_pred cCCCCcCCceeeeeeCCHHHHHHhhcCCCCCCeEEEEEEecccChhhhhhhhcceeeCCcccceeEEEEcCCCCCCCceE
Q 031054 26 VGRLDVATTGLIIVTNDGDFAQAVSHPSSKLQKEYIATIDGAVNKRHLIAISEGTVIEGTHCTPDVVELLPPQPDIPRPR 105 (166)
Q Consensus 26 vhRLD~~TSGlll~ak~~~~~~~l~~~~~~i~K~Y~a~v~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l 105 (166)
|||||++||||||||||+++++.|++++++|+|+|+|+|+|.++++.+..+..++.++++..+++.++++... .+.++
T Consensus 1 v~RLD~~TSGlll~akd~~~~~~L~~~~~~i~K~Y~a~v~g~~~~~~~~~~~~g~~~~~~~~~~~~~~~l~~~--~~~~~ 78 (128)
T TIGR00093 1 AGRLDRDSEGLLLLTNDGELVHRLTHPGHHCEKTYLVTVEGPVTDEDLEALRKGVQLEDGPTKPAKLEVITEP--GFPTW 78 (128)
T ss_pred CCCCCCCCEEEEEEEeCHHHHHHHhCCCCCCCeEEEEEECCCCCHHHHHHHhCCeEECCcEEeeeEEEEEccC--CCceE
Confidence 7999999999999999999999999999999999999999999988887778888777777778889888643 23589
Q ss_pred EEEEecCCchhHHHHHHHHcCCceeeeeeeEEeCeecCCCCCCCcEEEcCH
Q 031054 106 IRIVVHEGRNHEVRELVKNAGLKLYSLKRLRIGGFRLPSDLGIGMHVELKQ 156 (166)
Q Consensus 106 l~~~l~tGR~HQIR~~l~~~G~pI~~l~R~~~g~~~l~~~l~~G~~r~l~~ 156 (166)
++|+|.|||+||||+||+++||||++|+|++||+++| ++||+|+||+|++
T Consensus 79 l~~~l~tGR~HQIR~~~~~lG~pI~g~~R~~~g~~~l-~~L~~G~~r~l~~ 128 (128)
T TIGR00093 79 LRITLSEGRNRQVRRMFAAVGFPVLRLHRVRIGDVSL-NGLPPGEWRPLTL 128 (128)
T ss_pred EEEEEeCCCCHHHHHHHHHcCCeEeEEEEEEECCEEc-CCCCCCCeEECCC
Confidence 9999999999999999999999999999999999999 5999999999985
No 3
>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=100.00 E-value=1.4e-42 Score=265.90 Aligned_cols=133 Identities=35% Similarity=0.652 Sum_probs=119.9
Q ss_pred CCeeecCCCCcCCceeeeeeCCHHHHHHhhcCCCCCCeEEEEEEecccChhhhhhhhcceeeCCc-ccceeEEEEcCCCC
Q 031054 21 PRLFTVGRLDVATTGLIIVTNDGDFAQAVSHPSSKLQKEYIATIDGAVNKRHLIAISEGTVIEGT-HCTPDVVELLPPQP 99 (166)
Q Consensus 21 ~~l~~vhRLD~~TSGlll~ak~~~~~~~l~~~~~~i~K~Y~a~v~g~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~ 99 (166)
+++++|||||++||||||||||+++++++.++++.++|+|+|+|+|.++++.+..+..++..+++ ...++.++++.
T Consensus 34 ~~~~~vhRLD~~TSGlll~ak~~~~~~~l~~~~~~i~K~Y~a~V~G~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--- 110 (167)
T cd02553 34 RDLFPVGRLDKDTTGLLLLTNDGQLAHRLTSPKKHVPKTYEVTLAGPLTEDDIEAFAEGVLLHDGYPTKPAKLEILS--- 110 (167)
T ss_pred CCeEEcccCCCCCEEEEEEEeCHHHHHHhhCCcCCCceEEEEEEccCCCHHHHHHHHCCeEEcCCCEeeeeEEEEeC---
Confidence 46899999999999999999999999999998899999999999999998888777777766554 45678888774
Q ss_pred CCCceEEEEEecCCchhHHHHHHHHcCCceeeeeeeEEeCeecCCCCCCCcEEEcCHHHH
Q 031054 100 DIPRPRIRIVVHEGRNHEVRELVKNAGLKLYSLKRLRIGGFRLPSDLGIGMHVELKQSDL 159 (166)
Q Consensus 100 ~~~~~ll~~~l~tGR~HQIR~~l~~~G~pI~~l~R~~~g~~~l~~~l~~G~~r~l~~~e~ 159 (166)
.++++|+|.|||+||||+||+++||||++++|++||+++|+++|++|+||+|+++|+
T Consensus 111 ---~sll~v~l~tGR~HQIR~hla~lG~pI~~~~R~~~g~~~l~~~l~~g~~r~l~~~e~ 167 (167)
T cd02553 111 ---PTTVRLTITEGKYHQVKRMFAAVGNKVVALHRIRIGGLELDDDLAPGEWRPLTEEEL 167 (167)
T ss_pred ---CcEEEEEEEeCCCHHHHHHHHHcCCeEEEEEEEEECCEecCCCCCCCceEECCHhhC
Confidence 289999999999999999999999999999999999999953599999999999985
No 4
>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=100.00 E-value=8.4e-42 Score=263.88 Aligned_cols=132 Identities=26% Similarity=0.509 Sum_probs=120.4
Q ss_pred CCeeecCCCCcCCceeeeeeCCHHHHHHhhcCCCCCCeEEEEEEecccChhhhhhhhcceeeCCcccceeEEEEcCCCCC
Q 031054 21 PRLFTVGRLDVATTGLIIVTNDGDFAQAVSHPSSKLQKEYIATIDGAVNKRHLIAISEGTVIEGTHCTPDVVELLPPQPD 100 (166)
Q Consensus 21 ~~l~~vhRLD~~TSGlll~ak~~~~~~~l~~~~~~i~K~Y~a~v~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 100 (166)
+++++|||||++||||||||||+++++.|+++++.|+|+|+|+|+|.++++.+..+..++.+++....++.+.+..
T Consensus 45 ~~l~~VgRLD~dTsGLLl~t~d~~~~~~L~~~~~~i~K~Y~v~v~g~~~~~~l~~l~~g~~~~~~~~~~~~~~~~~---- 120 (177)
T cd02555 45 ARLAPIGPLDKDASGLLVFSQDGRVLRKLIGDASRLEQEYLVEVRGELTAGGLERLNHGLTYDGRELPPAKVSWQN---- 120 (177)
T ss_pred CceeEecCCCCCCeeEEEEECCHHHHHHHhChhcCCCEEEEEEEcccCCHHHHHHHhcCcccCCeecceEEEEEcC----
Confidence 4689999999999999999999999999999999999999999999998887777888888877766666666532
Q ss_pred CCceEEEEEecCCchhHHHHHHHHcCCceeeeeeeEEeCeecCCCCCCCcEEEcCHHHH
Q 031054 101 IPRPRIRIVVHEGRNHEVRELVKNAGLKLYSLKRLRIGGFRLPSDLGIGMHVELKQSDL 159 (166)
Q Consensus 101 ~~~~ll~~~l~tGR~HQIR~~l~~~G~pI~~l~R~~~g~~~l~~~l~~G~~r~l~~~e~ 159 (166)
.++++++|.|||+||||+||+++||||++|+|++||+++| ++|++|+||+|+++|.
T Consensus 121 --~~~l~i~l~tGr~hQIR~~~~~~G~pV~~L~R~~ig~i~L-~~L~~G~~r~l~~~E~ 176 (177)
T cd02555 121 --EQRLRFALKEPQPGQIRRMCESVGLEVVALRRIRIGRVSL-GKLPLGQWRYLTTGER 176 (177)
T ss_pred --CCEEEEEEECCcChHHHHHHHHcCCeEEEEEEEEECCEEc-CCCCCCceEECCHHHC
Confidence 4799999999999999999999999999999999999999 5999999999999995
No 5
>PRK10839 16S rRNA pseudouridylate synthase A; Provisional
Probab=100.00 E-value=1.9e-41 Score=271.43 Aligned_cols=138 Identities=27% Similarity=0.528 Sum_probs=121.8
Q ss_pred CeeecCCCCcCCceeeeeeCCHHHHHHhhcCCCCCCeEEEEEEecccChhhhhhhhcceeeCCcccceeEEEEcCCCCCC
Q 031054 22 RLFTVGRLDVATTGLIIVTNDGDFAQAVSHPSSKLQKEYIATIDGAVNKRHLIAISEGTVIEGTHCTPDVVELLPPQPDI 101 (166)
Q Consensus 22 ~l~~vhRLD~~TSGlll~ak~~~~~~~l~~~~~~i~K~Y~a~v~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 101 (166)
++++|||||++||||||||||+.+++.|.++++.++|+|+|.+++++..+....+..++..+|.. +.+.+..+....
T Consensus 94 ~~~~v~RLD~~TSGlll~ak~~~~~~~l~~~~~~i~K~Y~a~i~~~i~~~~~~~~~~~~~~~g~~-a~t~~~~~~~~~-- 170 (232)
T PRK10839 94 KLHAAGRLDIDTTGLVLMTDDGQWSHRITSPRHHCEKTYLVTLESPVADDTAEQFAKGVQLHNEK-DLTKPAVLEVIT-- 170 (232)
T ss_pred CceecCCCCCCceeEEEEecCHHHHHHHhCCCCCCCeEEEEEECCCCCHHHHHHHHCCeEECCCc-ccccccEEEEec--
Confidence 57899999999999999999999999999988899999999999999988877888888766542 344555554321
Q ss_pred CceEEEEEecCCchhHHHHHHHHcCCceeeeeeeEEeCeecCCCCCCCcEEEcCHHHHhhcc
Q 031054 102 PRPRIRIVVHEGRNHEVRELVKNAGLKLYSLKRLRIGGFRLPSDLGIGMHVELKQSDLKLMG 163 (166)
Q Consensus 102 ~~~ll~~~l~tGR~HQIR~~l~~~G~pI~~l~R~~~g~~~l~~~l~~G~~r~l~~~e~~~l~ 163 (166)
.++++|+|+|||+||||+||+++||||++|+|++||+++|+++|++|+||+|+++|++.|+
T Consensus 171 -~sll~~~l~tGRtHQIR~h~~~~G~pi~gl~R~~~g~~~l~~~l~~g~~r~l~~~e~~~l~ 231 (232)
T PRK10839 171 -PTQVRLTISEGRYHQVKRMFAAVGNHVVELHRERIGAITLDADLAPGEYRPLTEEEIASVG 231 (232)
T ss_pred -CCEEEEEEEcCcCHHHHHHHHHcCCeEeeEEEEEEcCEecCCCCCCCceeECCHHHHHhhc
Confidence 3899999999999999999999999999999999999999448999999999999999986
No 6
>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=100.00 E-value=5.4e-41 Score=256.38 Aligned_cols=133 Identities=36% Similarity=0.645 Sum_probs=124.7
Q ss_pred CCeeecCCCCcCCceeeeeeCCHHHHHHhhcCCCCCCeEEEEEEecccChhhhhhhhcceeeCCcccceeEEEEcCCCCC
Q 031054 21 PRLFTVGRLDVATTGLIIVTNDGDFAQAVSHPSSKLQKEYIATIDGAVNKRHLIAISEGTVIEGTHCTPDVVELLPPQPD 100 (166)
Q Consensus 21 ~~l~~vhRLD~~TSGlll~ak~~~~~~~l~~~~~~i~K~Y~a~v~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 100 (166)
.++++|||||++||||||||||++++++|++|.++++|+|+|.|+|+++++.+..+..|+.+++....++.++.++
T Consensus 31 ~~~~~vgRLD~~tsGlll~t~dg~~~~~L~~p~~~~~K~Y~V~v~~~l~~~~l~~l~~G~~~~~~~~~~~~v~~~~---- 106 (164)
T cd02554 31 PRIFPIGRLDKDSEGLILLTNDGDLVNKILHADNNHEKEYLVTVNKPITDEFIEGMSNGVVILGTVTKPCKVERLA---- 106 (164)
T ss_pred CCEEEccCCCCCCeeEEEEEcCHHHHHHHhhhhcCCCeEEEEEECCCCCHHHHHHHhCCCEECCeEEcceEEEECC----
Confidence 5689999999999999999999999999999999999999999999999999999999999988777788888763
Q ss_pred CCceEEEEEecCCchhHHHHHHHHcCCceeeeeeeEEeCeecCCCCCCCcEEEcCHHHHh
Q 031054 101 IPRPRIRIVVHEGRNHEVRELVKNAGLKLYSLKRLRIGGFRLPSDLGIGMHVELKQSDLK 160 (166)
Q Consensus 101 ~~~~ll~~~l~tGR~HQIR~~l~~~G~pI~~l~R~~~g~~~l~~~l~~G~~r~l~~~e~~ 160 (166)
.++++|++++||+||||+||+++|+||..|+|++||+++| ++|++|+||+|+++|++
T Consensus 107 --~~~l~i~l~eGr~~qIRrm~~~~G~~V~~L~Ri~iG~~~L-~~L~~G~~R~L~~~E~~ 163 (164)
T cd02554 107 --KDKFRIVLTQGLNRQIRRMCEALGYRVTDLKRVRIMNIEL-GDLAPGEWRPLTDAELF 163 (164)
T ss_pred --CCEEEEEEECCcCHHHHHHHHHcCCEEEEEEEEEECcEEc-CCCCCCCeEECCHHHhc
Confidence 1469999999999999999999999999999999999999 59999999999999986
No 7
>PRK10700 23S rRNA pseudouridylate synthase B; Provisional
Probab=100.00 E-value=1.9e-40 Score=273.65 Aligned_cols=141 Identities=31% Similarity=0.514 Sum_probs=127.3
Q ss_pred CCeeecCCCCcCCceeeeeeCCHHHHHHhhcCCCCCCeEEEEEEecccChhhhhhhhcceeeCCcccceeEEEEcCCCCC
Q 031054 21 PRLFTVGRLDVATTGLIIVTNDGDFAQAVSHPSSKLQKEYIATIDGAVNKRHLIAISEGTVIEGTHCTPDVVELLPPQPD 100 (166)
Q Consensus 21 ~~l~~vhRLD~~TSGlll~ak~~~~~~~l~~~~~~i~K~Y~a~v~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 100 (166)
.++++|||||++||||||||||+++++.|++++++|+|+|+|+|+|.++++.+..+..|+.++++...++.+++... .
T Consensus 101 ~~~~~VgRLD~dTsGLLLlTndg~~~~~L~~p~~~i~K~Y~v~V~G~~~~~~l~~l~~Gv~l~~~~~~~~~v~~~~~--~ 178 (289)
T PRK10700 101 ARWIAVGRLDVNTCGLLLFTTDGELANRLMHPSREVEREYAVRVFGQVDDAKLRQLSRGVQLEDGPAAFKTIKFSGG--E 178 (289)
T ss_pred CceeEccCCCCCCceEEEEEcCHHHHHHHhCccCCCCeEEEEEEccCCCHHHHHHHHcCCEeCCceeeeEEEEeccC--C
Confidence 35799999999999999999999999999999999999999999999999999889999999877666777766532 1
Q ss_pred CCceEEEEEecCCchhHHHHHHHHcCCceeeeeeeEEeCeecCCCCCCCcEEEcCHHHHhhcc
Q 031054 101 IPRPRIRIVVHEGRNHEVRELVKNAGLKLYSLKRLRIGGFRLPSDLGIGMHVELKQSDLKLMG 163 (166)
Q Consensus 101 ~~~~ll~~~l~tGR~HQIR~~l~~~G~pI~~l~R~~~g~~~l~~~l~~G~~r~l~~~e~~~l~ 163 (166)
...++++|+|++||+||||+||+++|+||+.|+|++||++.|+++|++|+||+|+++|++.|.
T Consensus 179 ~~~s~l~v~L~EGk~hQIRrm~~~lG~~V~~L~Ri~iG~l~L~~~L~~G~~R~L~~~E~~~l~ 241 (289)
T PRK10700 179 GINQWYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDIPLPKGLPRGGWTELDLAQTNYLR 241 (289)
T ss_pred CCceEEEEEEeCCccHHHHHHHHHcCCEEeEEEEEEEeeeEcCCCCCCCceEECCHHHHHHHH
Confidence 235799999999999999999999999999999999999999547999999999999998775
No 8
>COG1187 RsuA 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=3.6e-40 Score=265.28 Aligned_cols=143 Identities=35% Similarity=0.609 Sum_probs=127.9
Q ss_pred CCeeecCCCCcCCceeeeeeCCHHHHHHhhcCCCCCCeEEEEEEecccChhhhhhhhcceeeCCcccceeE-EEEcCCCC
Q 031054 21 PRLFTVGRLDVATTGLIIVTNDGDFAQAVSHPSSKLQKEYIATIDGAVNKRHLIAISEGTVIEGTHCTPDV-VELLPPQP 99 (166)
Q Consensus 21 ~~l~~vhRLD~~TSGlll~ak~~~~~~~l~~~~~~i~K~Y~a~v~g~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~ 99 (166)
.+++||||||+||||||||||||++++.|++|+++++|+|+|.|.|.++++.+..++.|+.++|+...++. ..+....
T Consensus 99 ~~~~pvGRLD~dTeGLLLLTnDG~la~rL~~P~~~~~K~Y~v~v~g~~~~~~l~~l~~Gv~l~d~~~~~~~~~~l~~~~- 177 (248)
T COG1187 99 KRLFPVGRLDKDTEGLLLLTNDGELAHRLMHPSSEVEKEYLVRVEGPVTEEDLEKLRKGVTLDDGETKPAKPASLEKEP- 177 (248)
T ss_pred cceeeccccCCCCeeEEEEeCCHHHHHHhcCCCCCCCEEEEEEEecCCCHHHHHHHhCCcEecCcccccceeEEEEecC-
Confidence 56999999999999999999999999999999999999999999999999999999999999998777776 3332221
Q ss_pred CCCceEEEEEecCCchhHHHHHHHHcCCceeeeeeeEEeCeecCC-CCCCCcEEEcCHHHHhhccc
Q 031054 100 DIPRPRIRIVVHEGRNHEVRELVKNAGLKLYSLKRLRIGGFRLPS-DLGIGMHVELKQSDLKLMGW 164 (166)
Q Consensus 100 ~~~~~ll~~~l~tGR~HQIR~~l~~~G~pI~~l~R~~~g~~~l~~-~l~~G~~r~l~~~e~~~l~~ 164 (166)
..+++|++++|.+||+||||+||+++|+|+++|+|++||+++|++ .+++|+||+|++.|++.|..
T Consensus 178 ~~~~s~~~itl~EGrnrQVRRm~~a~G~~V~~L~R~~iG~l~L~~L~l~~G~~R~L~~~E~~~l~~ 243 (248)
T COG1187 178 GKNNSWLRITLTEGRNRQVRRMFEAVGLEVLRLKRIRIGPLSLGDLPLPPGEWRELTLEEIAQLRK 243 (248)
T ss_pred CCCceEEEEEEeCCcCHHHHHHHHHcCCEEeEEEEEEEeeeEcCCCCCCCceeEECCHHHHHHHHH
Confidence 114789999999999999999999999999999999999999953 45559999999999998864
No 9
>PRK10475 23S rRNA pseudouridine synthase F; Provisional
Probab=100.00 E-value=1.5e-39 Score=268.10 Aligned_cols=136 Identities=28% Similarity=0.456 Sum_probs=126.3
Q ss_pred CCeeecCCCCcCCceeeeeeCCHHHHHHhhcCCCCCCeEEEEEEecccChhhhhhhhcceeeCCcccceeEEEEcCCCCC
Q 031054 21 PRLFTVGRLDVATTGLIIVTNDGDFAQAVSHPSSKLQKEYIATIDGAVNKRHLIAISEGTVIEGTHCTPDVVELLPPQPD 100 (166)
Q Consensus 21 ~~l~~vhRLD~~TSGlll~ak~~~~~~~l~~~~~~i~K~Y~a~v~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 100 (166)
.++++|||||++||||||||||+++++.|+++.+.++|+|+|+|+|+++++.+..+..|+.+++....++.++.+.
T Consensus 98 ~~l~~VgRLDrdTsGLLLlT~dg~~~~~L~~p~~~i~K~Y~v~V~g~~~~~~l~~l~~Gv~l~~~~~~~~~v~~~~---- 173 (290)
T PRK10475 98 KRVFPIGRLDKDSQGLIFLTNHGDLVNKILRAGNDHEKEYLVTVDKPITDEFIRGMGAGVPILGTVTKKCKVKKEA---- 173 (290)
T ss_pred ccccccccCCCCCcceEEEecCHHHHHHhhCcCCCCCeEEEEEECCCCCHHHHHHHhCCcEECCEEecceEEEecC----
Confidence 3579999999999999999999999999999999999999999999999999999999999988777777777652
Q ss_pred CCceEEEEEecCCchhHHHHHHHHcCCceeeeeeeEEeCeecCCCCCCCcEEEcCHHHHhhcc
Q 031054 101 IPRPRIRIVVHEGRNHEVRELVKNAGLKLYSLKRLRIGGFRLPSDLGIGMHVELKQSDLKLMG 163 (166)
Q Consensus 101 ~~~~ll~~~l~tGR~HQIR~~l~~~G~pI~~l~R~~~g~~~l~~~l~~G~~r~l~~~e~~~l~ 163 (166)
.++++|+|++||+||||+||+++|++|+.|+|++||++.| ++|++|+||+|+++|++.|.
T Consensus 174 --~~~~~i~l~eGk~rqIRrm~~~~G~~V~~L~R~~ig~l~L-~~L~~G~~r~Lt~~E~~~l~ 233 (290)
T PRK10475 174 --PFVFRITLVQGLNRQIRRMCEHFGYEVTKLERTRIMNVSL-SGIPLGEWRDLTDDELIDLF 233 (290)
T ss_pred --CcEEEEEEECCcCHHHHHHHHHcCCEEeEEEEEEECCEEc-CCCCCCCeEECCHHHHHHHH
Confidence 3689999999999999999999999999999999999999 59999999999999998774
No 10
>PRK11394 23S rRNA pseudouridine synthase E; Provisional
Probab=100.00 E-value=7.8e-39 Score=253.80 Aligned_cols=135 Identities=27% Similarity=0.518 Sum_probs=120.4
Q ss_pred CCeeecCCCCcCCceeeeeeCCHHHHHHhhcCCCCCCeEEEEEEecccChhhhhhhhcceeeCCcccceeEEEEcCCC--
Q 031054 21 PRLFTVGRLDVATTGLIIVTNDGDFAQAVSHPSSKLQKEYIATIDGAVNKRHLIAISEGTVIEGTHCTPDVVELLPPQ-- 98 (166)
Q Consensus 21 ~~l~~vhRLD~~TSGlll~ak~~~~~~~l~~~~~~i~K~Y~a~v~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-- 98 (166)
+++++|||||++||||||||+|++++++|.++++.++|+|+|.|+|.++++.+..+..|+.+++....++.++++...
T Consensus 70 ~~~~~vgRLD~~TsGllLlt~d~~~~~~L~~~~~~i~K~Y~~~v~g~~~~~~l~~l~~Gv~i~~~~~~p~~~~~i~~~~~ 149 (217)
T PRK11394 70 QGVYAAGRLDRDSEGLLVLTNNGALQARLTQPGKRTGKIYYVQVEGIPTQDALEALRNGVTLNDGPTLPAGAELVDEPAW 149 (217)
T ss_pred CCeEEecCCCCCCeeEEEEECCHHHHHHHhCcccCCCEEEEEEECCCCCHHHHHHHhCCeEECCccccccEEEEeccccc
Confidence 468999999999999999999999999999999999999999999999999898889999988776666666655321
Q ss_pred -----------CCCCceEEEEEecCCchhHHHHHHHHcCCceeeeeeeEEeCeecCCCCCCCcEEEcCH
Q 031054 99 -----------PDIPRPRIRIVVHEGRNHEVRELVKNAGLKLYSLKRLRIGGFRLPSDLGIGMHVELKQ 156 (166)
Q Consensus 99 -----------~~~~~~ll~~~l~tGR~HQIR~~l~~~G~pI~~l~R~~~g~~~l~~~l~~G~~r~l~~ 156 (166)
...+.++++|+|.|||+||||+||+++||||++|+||+||+++| ++|++|+||+|+.
T Consensus 150 ~~~~~~~~~~~~~~~~s~l~I~L~eGR~hQIRrm~a~lG~pVl~L~Ry~iG~l~L-~~L~~G~~R~L~~ 217 (217)
T PRK11394 150 LWPRNPPIRERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGDYSL-DNLANGEWREATD 217 (217)
T ss_pred ccccccccccccCCCceEEEEEEeCCCCHHHHHHHHHcCCeEeeeEEEEECCEEc-CCCCCCCeEeCCC
Confidence 11246899999999999999999999999999999999999999 5999999999973
No 11
>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=100.00 E-value=5.4e-36 Score=229.50 Aligned_cols=125 Identities=30% Similarity=0.564 Sum_probs=107.1
Q ss_pred CCeeecCCCCcCCceeeeeeCCHHHHHHhhcCCCCCCeEEEEEEecccChhhhhhhhcceeeCCcccceeEEEEcCC---
Q 031054 21 PRLFTVGRLDVATTGLIIVTNDGDFAQAVSHPSSKLQKEYIATIDGAVNKRHLIAISEGTVIEGTHCTPDVVELLPP--- 97 (166)
Q Consensus 21 ~~l~~vhRLD~~TSGlll~ak~~~~~~~l~~~~~~i~K~Y~a~v~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--- 97 (166)
+++++|||||++||||||||||+++++.|.++.+.++|+|+|+|+|.++++.+..+..|+.+++....++.+.....
T Consensus 31 ~~~~~v~RLD~~TsGlll~a~d~~~~~~l~~~~~~v~K~Y~a~v~g~~~~~~~~~l~~g~~~~~~~~~~~~v~~~~~~~~ 110 (168)
T cd02566 31 PGVYAAGRLDRDSEGLLLLTDDGRLQHRITDPSFKHPKTYYVQVEGVPTEDALEQLRNGVELGDGLTLPAKVEKVDEPPW 110 (168)
T ss_pred CCeEEccCCCCCCeEEEEEEeCHHHHHHHHCCCCCCCEEEEEEECCcCCHHHHHHHhCCcEECCeEecceEEEEeccccc
Confidence 46799999999999999999999999999999888999999999999998888777788877666555555554321
Q ss_pred ----------CCCCCceEEEEEecCCchhHHHHHHHHcCCceeeeeeeEEeCeecCCCC
Q 031054 98 ----------QPDIPRPRIRIVVHEGRNHEVRELVKNAGLKLYSLKRLRIGGFRLPSDL 146 (166)
Q Consensus 98 ----------~~~~~~~ll~~~l~tGR~HQIR~~l~~~G~pI~~l~R~~~g~~~l~~~l 146 (166)
....+.++++|+|.|||+||||+||+++||||+.|+|++||++.| ++|
T Consensus 111 ~~~~~~~~~~~~~~~~sll~v~l~tGR~HQIR~~la~lG~pV~~L~R~~~g~~~l-~~L 168 (168)
T cd02566 111 LWEREPPIRFRKNIPTSWIEITICEGKNRQVRRMTAAVGFPTLRLIRVSIGDIGL-DNL 168 (168)
T ss_pred ccccccccccccCCCccEEEEEEecCccHHHHHHHHHcCCeEeEEEEEEECCEEc-CCC
Confidence 112345799999999999999999999999999999999999999 465
No 12
>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=100.00 E-value=1.2e-34 Score=217.11 Aligned_cols=115 Identities=34% Similarity=0.652 Sum_probs=105.0
Q ss_pred CCeeecCCCCcCCceeeeeeCCHHHHHHhhcCCCCCCeEEEEEEecccChhhhhhhhcceeeCCcccceeEEEEcCCCCC
Q 031054 21 PRLFTVGRLDVATTGLIIVTNDGDFAQAVSHPSSKLQKEYIATIDGAVNKRHLIAISEGTVIEGTHCTPDVVELLPPQPD 100 (166)
Q Consensus 21 ~~l~~vhRLD~~TSGlll~ak~~~~~~~l~~~~~~i~K~Y~a~v~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 100 (166)
+++++|||||++||||||||||+++++.|.++++.++|+|+|+|.|.++++.+..+..++..++++.++++++++...
T Consensus 32 ~~~~~vhRLD~~TsGlll~ak~~~~~~~l~~~~~~i~K~Y~a~v~g~~~~~~~~~~~~~~~~~~~~~~~t~~~~l~~~-- 109 (146)
T cd02870 32 ERLFPVGRLDYDTEGLLLLTNDGELANRLTHPRYGVEKTYLVKVRGVPSEEELRRLRAGVELDDGKTAPAKVKVLSRD-- 109 (146)
T ss_pred CCEEECCCCCCCCeeEEEEeCCHHHHHHhhCccCCCCeEEEEEECCCCCHHHHHHHHCCeEeCCceEcceEEEEeccC--
Confidence 568999999999999999999999999999998899999999999999988887778888777777788999998653
Q ss_pred CCceEEEEEecCCchhHHHHHHHHcCCceeeeeeeEE
Q 031054 101 IPRPRIRIVVHEGRNHEVRELVKNAGLKLYSLKRLRI 137 (166)
Q Consensus 101 ~~~~ll~~~l~tGR~HQIR~~l~~~G~pI~~l~R~~~ 137 (166)
.+.++++|+|+|||+||||+||+++|+||+.++|++|
T Consensus 110 ~~~sll~~~l~tGR~HQIR~hla~~G~pI~~l~R~~~ 146 (146)
T cd02870 110 PKNTLLEVTLHEGRNRQVRRMFEAVGHPVLRLKRVRI 146 (146)
T ss_pred CCCcEEEEEEEeCCcHHHHHHHHHcCCcCCeEEEEEC
Confidence 2468999999999999999999999999999999986
No 13
>cd02550 PseudoU_synth_Rsu_Rlu_like PseudoU_synth_Rsu_Rlu: Pseudouridine synthase, Rsu/Rlu family. This group is comprised of eukaryotic, bacterial and archeal proteins similar to eight site specific Escherichia coli pseudouridine synthases: RsuA, RluA, RluB, RluC, RluD, RluE, RluF and TruA. Pseudouridine synthases catalyze the isomerization of specific uridines in a n RNA molecule to pseudouridines (5-ribosyluracil, psi) requiring no cofactors. E. coli RluC for example makes psi955, 2504 and 2580 in 23S RNA. Some psi sites such as psi1917 in 23S RNA made by RluD are universally conserved. Other psi sites occur in a more restricted fashion, for example psi2819 in 21S mitochondrial ribosomal RNA made by S. cerevisiae Pus5p is only found in mitochondrial large subunit rRNAs from some other species and in gram negative bacteria. The E. coli counterpart of this psi residue is psi2580 in 23S rRNA. psi2604in 23S RNA made by RluF has only been detected in E.coli.
Probab=100.00 E-value=2.2e-34 Score=217.36 Aligned_cols=115 Identities=30% Similarity=0.609 Sum_probs=99.3
Q ss_pred CCeeecCCCCcCCceeeeeeCCHHHHHHhhcCCCCCCeEEEEEEecccChhhhhhhh-------cceeeCCcccceeEEE
Q 031054 21 PRLFTVGRLDVATTGLIIVTNDGDFAQAVSHPSSKLQKEYIATIDGAVNKRHLIAIS-------EGTVIEGTHCTPDVVE 93 (166)
Q Consensus 21 ~~l~~vhRLD~~TSGlll~ak~~~~~~~l~~~~~~i~K~Y~a~v~g~~~~~~~~~~~-------~~~~~~~~~~~~~~~~ 93 (166)
+++++|||||++||||||||+|+++++.|+++++.++|+|+|+|+|.++++.+..+. .++..++++.+.+.++
T Consensus 33 ~~~~~vhRLD~~TSGlll~ak~~~~~~~l~~~~~~v~K~Y~a~v~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~t~~~ 112 (154)
T cd02550 33 PRVHAAGRLDKDTSGLLLLTNDGRLQRRLTEPRREIEKEYLVTVRGELDEEGIEDLATVRRGRLSGLVDEGVPLAVTKVR 112 (154)
T ss_pred CceeEeccCCCCCeeEEEEEcCHHHHHHHhhhhccCcEEEEEEEEeecCcchheeccccccCcceeEEcCCCcccceEEE
Confidence 568999999999999999999999999999998899999999999999866544333 3444455666788999
Q ss_pred EcCCCCCCCceEEEEEecCCchhHHHHHHHHcCCceeeeeeeEE
Q 031054 94 LLPPQPDIPRPRIRIVVHEGRNHEVRELVKNAGLKLYSLKRLRI 137 (166)
Q Consensus 94 ~~~~~~~~~~~ll~~~l~tGR~HQIR~~l~~~G~pI~~l~R~~~ 137 (166)
++... .++++++++|.|||+||||+||+++||||..|+|++|
T Consensus 113 ~l~~~--~~~sll~~~l~tGR~HQIR~hla~~G~pI~~l~R~~~ 154 (154)
T cd02550 113 VIGEH--GGTGRLRLTLKTGRTHQIRRHCAAVGFPVLRLHRVRI 154 (154)
T ss_pred EEEec--CCcEEEEEEEcCCCcHHHHHHHHHcCCcEEeEEEEeC
Confidence 88543 3468999999999999999999999999999999986
No 14
>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=99.97 E-value=7.3e-31 Score=208.02 Aligned_cols=116 Identities=20% Similarity=0.285 Sum_probs=93.3
Q ss_pred CCeeecCCCCcCCceeeeeeCCHHHHHHhhcC--CCCCCeEEEEEEecccChhhhh--------hhhcceee---CCccc
Q 031054 21 PRLFTVGRLDVATTGLIIVTNDGDFAQAVSHP--SSKLQKEYIATIDGAVNKRHLI--------AISEGTVI---EGTHC 87 (166)
Q Consensus 21 ~~l~~vhRLD~~TSGlll~ak~~~~~~~l~~~--~~~i~K~Y~a~v~g~~~~~~~~--------~~~~~~~~---~~~~~ 87 (166)
..+++|||||++||||||||+|++++++|+++ ++.++|+|+|+|+|.++.+... ....++.. .+++.
T Consensus 58 ~~~~~vhRLD~~TSGllllak~~~~~~~l~~~f~~~~v~K~Y~a~v~G~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~ 137 (213)
T cd02557 58 TELRPCHRLDRLTSGLLLFAKTSQTASRLQQQIRSREVKKEYLARVKGEFPDGEVVVDQPIGLVSPKGGLRNDVDEKGKD 137 (213)
T ss_pred CCccCccCCCCCCceEEEEECCHHHHHHHHHHHHcCCccEEEEEEEeCcCCCCCeEEecceeccCcCCceeeccCCCCce
Confidence 35789999999999999999999999999985 7789999999999998754421 11223211 23345
Q ss_pred ceeEEEEcCCCCCCCceEEEEEecCCchhHHHHHHHHcCCceeeeeeeE
Q 031054 88 TPDVVELLPPQPDIPRPRIRIVVHEGRNHEVRELVKNAGLKLYSLKRLR 136 (166)
Q Consensus 88 ~~~~~~~~~~~~~~~~~ll~~~l~tGR~HQIR~~l~~~G~pI~~l~R~~ 136 (166)
+.+.++++...+..+.++++|+|.|||+||||+||+++||||++|.+|+
T Consensus 138 a~t~~~~~~~~~~~~~slv~v~~~TGR~HQIR~hla~lG~PIlGD~~Yg 186 (213)
T cd02557 138 ARTIFKRLSYNGDLNTSVVLCKPITGRTHQIRVHLQYLGHPIVNDPIYN 186 (213)
T ss_pred eeEEEEEEEEcCCCCeEEEEEEeCCCCHHHHHHHHHHCCCCCcCccccC
Confidence 5678887765432357999999999999999999999999999999985
No 15
>COG0564 RluA Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]
Probab=99.97 E-value=8.5e-31 Score=216.16 Aligned_cols=116 Identities=24% Similarity=0.277 Sum_probs=94.4
Q ss_pred CCCeeecCCCCcCCceeeeeeCCHHHHHHhhcC--CCCCCeEEEEEEecccChhhh--hh---------hhcceeeCC-c
Q 031054 20 RPRLFTVGRLDVATTGLIIVTNDGDFAQAVSHP--SSKLQKEYIATIDGAVNKRHL--IA---------ISEGTVIEG-T 85 (166)
Q Consensus 20 ~~~l~~vhRLD~~TSGlll~ak~~~~~~~l~~~--~~~i~K~Y~a~v~g~~~~~~~--~~---------~~~~~~~~~-~ 85 (166)
..++++|||||++|||||||||+..++..|+.+ ++.+.|+|+|+|.|.+.++.. .. ....+...+ +
T Consensus 121 ~~~~~~vHRLDkdTSGlll~AK~~~a~~~l~~~f~~r~v~K~Y~Alv~G~~~~~~~~i~~pi~r~~~~~~~~~v~~~~~g 200 (289)
T COG0564 121 VERPGIVHRLDKDTSGLLLVAKNREAARELSEQFKQRKVKKTYLALVRGHLPEDEGTIDAPIGRDPKNRKKMAVVKEGSG 200 (289)
T ss_pred CCceeeeccCCCCCceEEEEECCHHHHHHHHHHHhcCcCcEEEEEEEECcccCCCCEEeeeeecCCcCCceEEEeccCCC
Confidence 367899999999999999999999999998774 668999999999999876532 11 011122233 5
Q ss_pred ccceeEEEEcCCCCCCCceEEEEEecCCchhHHHHHHHHcCCceeeeeeeE
Q 031054 86 HCTPDVVELLPPQPDIPRPRIRIVVHEGRNHEVRELVKNAGLKLYSLKRLR 136 (166)
Q Consensus 86 ~~~~~~~~~~~~~~~~~~~ll~~~l~tGR~HQIR~~l~~~G~pI~~l~R~~ 136 (166)
+.+.|.|+++.+.... .++++|+|.||||||||+||+++||||++|..|.
T Consensus 201 k~A~T~~~~l~~~~~~-~tlv~~~~~TGRTHQIRVHl~~lghPI~GD~~Yg 250 (289)
T COG0564 201 KPAITHYEVLERFGDN-YTLVELKPETGRTHQIRVHLAHLGHPIVGDPLYG 250 (289)
T ss_pred CceEEEEEehhccCCc-eEEEEEEeCCCCHhHHHHHHHHCCCCeeCCcccC
Confidence 6778899999875321 5999999999999999999999999999999985
No 16
>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=99.97 E-value=2.7e-30 Score=205.37 Aligned_cols=114 Identities=18% Similarity=0.253 Sum_probs=92.0
Q ss_pred CCeeecCCCCcCCceeeeeeCCHHHHHHhhc--CCCCCCeEEEEEEecccChhh------hhhhhccee-e--CCcccce
Q 031054 21 PRLFTVGRLDVATTGLIIVTNDGDFAQAVSH--PSSKLQKEYIATIDGAVNKRH------LIAISEGTV-I--EGTHCTP 89 (166)
Q Consensus 21 ~~l~~vhRLD~~TSGlll~ak~~~~~~~l~~--~~~~i~K~Y~a~v~g~~~~~~------~~~~~~~~~-~--~~~~~~~ 89 (166)
+.+++|||||++||||||||+|++++++|++ +++.|+|+|+|+|+|.++.+. +.....+.. . ..++.+.
T Consensus 42 ~~~~~VhRLDr~TSGlll~Ak~~~~~~~L~~~~~~~~v~K~YlAlV~g~~~~~~~~i~~~~~~~~~~~~~~~~~~~k~a~ 121 (217)
T TIGR01621 42 GQVWLVHRLDKMTSGILLLALNAESASELSQGFAKRKIEKTYLALSSKKPKKKQGLICGDMEKSRRGSWKLVNSQENPAI 121 (217)
T ss_pred CCccEecCCCCCCceEEEEEcCHHHHHHHHHHHhcCCccEEEEEEEeccccCCCCEEeCCcccCCCCCEEEeCCCCCcee
Confidence 4679999999999999999999999999987 688999999999999986542 222222211 1 1234456
Q ss_pred eEEEEcCCCCCCCceEEEEEecCCchhHHHHHHHHcCCceeeeeeeE
Q 031054 90 DVVELLPPQPDIPRPRIRIVVHEGRNHEVRELVKNAGLKLYSLKRLR 136 (166)
Q Consensus 90 ~~~~~~~~~~~~~~~ll~~~l~tGR~HQIR~~l~~~G~pI~~l~R~~ 136 (166)
++++++... .++++++|+|.|||+||||+||+++||||++|..|+
T Consensus 122 t~~~~~~~~--~~~slv~~~~~TGR~HQIRvhla~lG~PIlGD~~Yg 166 (217)
T TIGR01621 122 TRFFSASAA--TGLRLFILKPHTGKTHQLRVAMKSLGSPILGDPLYG 166 (217)
T ss_pred EEEEEEEEc--CCeEEEEEEeCCCCHHHHHHHHHHCCCceeCCcccC
Confidence 778777653 347999999999999999999999999999999985
No 17
>PRK10158 23S rRNA/tRNA pseudouridine synthase A; Provisional
Probab=99.96 E-value=3.8e-30 Score=204.72 Aligned_cols=114 Identities=18% Similarity=0.220 Sum_probs=92.0
Q ss_pred CeeecCCCCcCCceeeeeeCCHHHHHHhhcC--CCCCCeEEEEEEecccChhhhh-----------hhhcceeeCCcccc
Q 031054 22 RLFTVGRLDVATTGLIIVTNDGDFAQAVSHP--SSKLQKEYIATIDGAVNKRHLI-----------AISEGTVIEGTHCT 88 (166)
Q Consensus 22 ~l~~vhRLD~~TSGlll~ak~~~~~~~l~~~--~~~i~K~Y~a~v~g~~~~~~~~-----------~~~~~~~~~~~~~~ 88 (166)
++++|||||++||||||||++.+++..|.+. .+.|.|+|+|+|.|.++.+... ....++..++++.+
T Consensus 56 ~~~~vhRLDr~TSGlll~Akt~~~~~~l~~~f~~~~v~K~Yla~v~G~~~~~~~~i~~~i~~~~~~~~~~~~~~~~gk~a 135 (219)
T PRK10158 56 QAESVHRLDMATSGVIVVALTKAAERELKRQFREREPKKQYVARVWGHPSPAEGLVDLPLICDWPNRPKQKVCYETGKPA 135 (219)
T ss_pred CCCEECCCCCCCceEEEEECCHHHHHHHHHHHHhCCccEEEEEEEecccCCCCcEEecceecCCCCCceEEecCCCCcee
Confidence 4689999999999999999999999888773 7789999999999998755321 11222223445667
Q ss_pred eeEEEEcCCCCCCCceEEEEEecCCchhHHHHHHHHcCCceeeeeeeE
Q 031054 89 PDVVELLPPQPDIPRPRIRIVVHEGRNHEVRELVKNAGLKLYSLKRLR 136 (166)
Q Consensus 89 ~~~~~~~~~~~~~~~~ll~~~l~tGR~HQIR~~l~~~G~pI~~l~R~~ 136 (166)
.+.++++.... ...++++|+|+|||+||||+||+++||||++|..|.
T Consensus 136 ~t~~~~l~~~~-~~~sll~~~~~TGRtHQIR~hla~lG~PIvGD~~Yg 182 (219)
T PRK10158 136 QTEYEVVEYAA-DNTARVVLKPITGRSHQLRVHMLALGHPILGDRFYA 182 (219)
T ss_pred eEEEEEEEEcC-CCCEEEEEEeCCCCHHHHHHHHHHCCCcEECCcccC
Confidence 88888886542 224799999999999999999999999999999985
No 18
>TIGR00005 rluA_subfam pseudouridine synthase, RluA family. modifies uracil-65 in transfer RNAs to pseudouridine.
Probab=99.96 E-value=2.3e-29 Score=207.93 Aligned_cols=114 Identities=19% Similarity=0.220 Sum_probs=91.1
Q ss_pred CCeeecCCCCcCCceeeeeeCCHHHHHHhhc--CCCCCCeEEEEEEecccChhhh------hh--hhccee-e-C--Ccc
Q 031054 21 PRLFTVGRLDVATTGLIIVTNDGDFAQAVSH--PSSKLQKEYIATIDGAVNKRHL------IA--ISEGTV-I-E--GTH 86 (166)
Q Consensus 21 ~~l~~vhRLD~~TSGlll~ak~~~~~~~l~~--~~~~i~K~Y~a~v~g~~~~~~~------~~--~~~~~~-~-~--~~~ 86 (166)
..+++|||||++||||||||+|+++++.+.+ +++.|+|+|+|+|.|.++++.. .. ...+.. + . +++
T Consensus 118 ~~~~~vhRLD~~TSGlll~ak~~~~~~~l~~~~~~~~v~K~Y~a~v~g~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~k 197 (299)
T TIGR00005 118 ERVGIVHRLDRDTSGLMVVAKTPLALRELQRQLKNRTVTKEYVALVHGQFDSGGGTVDAPLGRVPNNRGLMAVHPSSEGK 197 (299)
T ss_pred CcCceECCCCCCCceEEEEEcCHHHHHHHHHHHHhCCcceEEEEEEeccccCCCCEEeCceecCCCCCceEEEecCCCCC
Confidence 4689999999999999999999998888876 4778999999999999875541 11 111211 1 1 245
Q ss_pred cceeEEEEcCCCCCCCceEEEEEecCCchhHHHHHHHHcCCceeeeeeeE
Q 031054 87 CTPDVVELLPPQPDIPRPRIRIVVHEGRNHEVRELVKNAGLKLYSLKRLR 136 (166)
Q Consensus 87 ~~~~~~~~~~~~~~~~~~ll~~~l~tGR~HQIR~~l~~~G~pI~~l~R~~ 136 (166)
.+.+.++++... .++++++|+|.|||+||||+||+++||||++|++|.
T Consensus 198 ~a~t~~~~l~~~--~~~slv~~~l~tGR~HQIR~hla~lG~pI~gD~~Yg 245 (299)
T TIGR00005 198 PAVTHFRVLERF--GNASLVECELETGRTHQIRVHLQYLGHPLAGDPLYG 245 (299)
T ss_pred eeeEEEEEeEEc--CCeEEEEEEeCCCChHHHHHHHHHCCCcEeCccccC
Confidence 566778887643 347899999999999999999999999999999985
No 19
>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=99.96 E-value=2.3e-29 Score=203.47 Aligned_cols=114 Identities=21% Similarity=0.245 Sum_probs=92.1
Q ss_pred CCeeecCCCCcCCceeeeeeCCHHHHHHhhc--CCCCCCeEEEEEEecccChhhh---h-hh------hcceeeCCcccc
Q 031054 21 PRLFTVGRLDVATTGLIIVTNDGDFAQAVSH--PSSKLQKEYIATIDGAVNKRHL---I-AI------SEGTVIEGTHCT 88 (166)
Q Consensus 21 ~~l~~vhRLD~~TSGlll~ak~~~~~~~l~~--~~~~i~K~Y~a~v~g~~~~~~~---~-~~------~~~~~~~~~~~~ 88 (166)
+.+++|||||++||||||||||++++..++. +.+.++|+|+|+|+|.++.+.. . .+ ..+...++++.+
T Consensus 81 ~~~~~vhRLD~~TSGlll~Ak~~~~~~~l~~~~~~~~v~K~YlA~v~G~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~a 160 (246)
T cd02558 81 PDLTPAHRLDRLTAGLVLFSKRPETRGAYQTLFARREVSKTYEAVAPYVPALTFPLTVRSRIVKGRGFFQAREVEGEPNA 160 (246)
T ss_pred CcccccccCCCCceeEEEEEcCHHHHHHHHHHHHcCCccEEEEEEEecCCCCCCCcceeccccccCCcceeeccCCCCCc
Confidence 4678999999999999999999999988866 5788999999999998763321 1 11 111223455667
Q ss_pred eeEEEEcCCCCCCCceEEEEEecCCchhHHHHHHHHcCCceeeeeeeE
Q 031054 89 PDVVELLPPQPDIPRPRIRIVVHEGRNHEVRELVKNAGLKLYSLKRLR 136 (166)
Q Consensus 89 ~~~~~~~~~~~~~~~~ll~~~l~tGR~HQIR~~l~~~G~pI~~l~R~~ 136 (166)
.+.|+++... .+.++++|+|.|||+||||+||+++||||++|..|.
T Consensus 161 ~T~~~~l~~~--~~~slv~~~l~TGRtHQIRvhla~lG~PIvGD~~Yg 206 (246)
T cd02558 161 ETRIELLARR--GGWGLYRLSPHTGKTHQLRVHMAALGVPILNDPFYP 206 (246)
T ss_pred eEEEEEEEec--CCeEEEEEEeCCCCHHHHHHHHHHCCCcccCCccCC
Confidence 8899988653 347999999999999999999999999999999984
No 20
>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=99.96 E-value=3.6e-29 Score=192.35 Aligned_cols=115 Identities=22% Similarity=0.269 Sum_probs=94.6
Q ss_pred CCCeeecCCCCcCCceeeeeeCCHHHHHHhhcC--CCCCCeEEEEEEecccChhhhhh---hhc-----c---eeeCCcc
Q 031054 20 RPRLFTVGRLDVATTGLIIVTNDGDFAQAVSHP--SSKLQKEYIATIDGAVNKRHLIA---ISE-----G---TVIEGTH 86 (166)
Q Consensus 20 ~~~l~~vhRLD~~TSGlll~ak~~~~~~~l~~~--~~~i~K~Y~a~v~g~~~~~~~~~---~~~-----~---~~~~~~~ 86 (166)
...+++|||||++||||||||+|+++++.|.++ ++.++|+|+|+|.|.++.+.... +.. . ...++.+
T Consensus 37 ~~~~~~v~RLD~~tsGlll~ak~~~~~~~l~~~~~~~~~~K~Y~a~v~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 116 (185)
T cd02869 37 EFRPGLVHRLDKDTSGLLLVAKNKKAAAKLSKQFKERKVKKTYLALVDGKPPEDEGTIDAPLGRKKRKKRARVVVSEDGK 116 (185)
T ss_pred CCcCceecccCCCCceEEEEEcCHHHHHHHHHHHhcCceeEEEEEEEeCCCCCCccEEecccccCCccCceEEEECCCCe
Confidence 356899999999999999999999999999987 88999999999999987654321 110 1 1224456
Q ss_pred cceeEEEEcCCCCCCCceEEEEEecCCchhHHHHHHHHcCCceeeeeeeE
Q 031054 87 CTPDVVELLPPQPDIPRPRIRIVVHEGRNHEVRELVKNAGLKLYSLKRLR 136 (166)
Q Consensus 87 ~~~~~~~~~~~~~~~~~~ll~~~l~tGR~HQIR~~l~~~G~pI~~l~R~~ 136 (166)
.+.+.++++... .++++++|+|.|||+||||+||+++|+||++|..|.
T Consensus 117 ~~~t~~~~l~~~--~~~s~~~~~l~tGR~HQIR~hl~~~G~pIvGD~~Yg 164 (185)
T cd02869 117 PAITHYKVLERF--GNVTLVELQLETGRTHQIRVHLASIGHPIVGDPKYG 164 (185)
T ss_pred EEEEEEEEEEEc--CCcEEEEEEeCcCCccHHHHHHHHCCCCEeCccccC
Confidence 667788887643 257999999999999999999999999999999985
No 21
>PRK11112 tRNA pseudouridine synthase C; Provisional
Probab=99.96 E-value=2.3e-29 Score=204.64 Aligned_cols=115 Identities=17% Similarity=0.280 Sum_probs=90.0
Q ss_pred CeeecCCCCcCCceeeeeeCCHHHHHHhhc--CCCCCCeEEEEEEecccChhhhhhh---------hcceee--CCcccc
Q 031054 22 RLFTVGRLDVATTGLIIVTNDGDFAQAVSH--PSSKLQKEYIATIDGAVNKRHLIAI---------SEGTVI--EGTHCT 88 (166)
Q Consensus 22 ~l~~vhRLD~~TSGlll~ak~~~~~~~l~~--~~~~i~K~Y~a~v~g~~~~~~~~~~---------~~~~~~--~~~~~~ 88 (166)
.+++|||||++||||||||+|+++++.|++ +.+.|+|+|+|+|.|.++++..... ...... .+++.+
T Consensus 46 ~~~~VHRLDr~TSGlll~Ak~~~~~~~L~~~f~~~~v~K~Y~Alv~G~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~k~a 125 (257)
T PRK11112 46 HVFTAHRLDRPTSGVLLMALSSEVARLLAQQFEQHQIQKTYHAIVRGWLMEEAVLDYPLKEELDKIADKFAREDKAPQPA 125 (257)
T ss_pred CceeeccCCCCCeeEEEEECCHHHHHHHHHHHHhCCcceEEEEEEEeEeCCCCeEeeeeeecccccceeecccCCCCeEe
Confidence 478999999999999999999999999988 5889999999999998764431100 011111 134455
Q ss_pred eeEEEEcCCC---------CCCCceEEEEEecCCchhHHHHHHHHcCCceeeeeeeE
Q 031054 89 PDVVELLPPQ---------PDIPRPRIRIVVHEGRNHEVRELVKNAGLKLYSLKRLR 136 (166)
Q Consensus 89 ~~~~~~~~~~---------~~~~~~ll~~~l~tGR~HQIR~~l~~~G~pI~~l~R~~ 136 (166)
.+.++++... ...+.++++|+|.|||+||||+||+++||||++|..|.
T Consensus 126 ~T~~~~l~~~~~~~~~~~~~~~~~slv~i~~~TGRtHQIRvhla~lG~PIvGD~~Yg 182 (257)
T PRK11112 126 VTHYRGLATVEMPVATGRYPTTRYSLVELEPKTGRKHQLRRHMAHLRHPIIGDTKHG 182 (257)
T ss_pred EEEEEEEEEecccccccccCCCCeEEEEEEcCCCChHHHHHHHHHcCCCEeCCcccC
Confidence 6777776532 12357999999999999999999999999999999984
No 22
>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=99.96 E-value=4.3e-29 Score=199.01 Aligned_cols=115 Identities=18% Similarity=0.333 Sum_probs=89.5
Q ss_pred CeeecCCCCcCCceeeeeeCCHHHHHHhhc--CCCCCCeEEEEEEecccChhhhhh--h----h--c--ceee-CCcccc
Q 031054 22 RLFTVGRLDVATTGLIIVTNDGDFAQAVSH--PSSKLQKEYIATIDGAVNKRHLIA--I----S--E--GTVI-EGTHCT 88 (166)
Q Consensus 22 ~l~~vhRLD~~TSGlll~ak~~~~~~~l~~--~~~~i~K~Y~a~v~g~~~~~~~~~--~----~--~--~~~~-~~~~~~ 88 (166)
++++|||||++||||||||+|+++++.|++ .++.++|+|+|+|.|.++.+.... + . . .+.. .+++.+
T Consensus 45 ~~~~vhRLD~~TSGlll~Ak~~~~~~~l~~~f~~~~v~K~Y~alv~G~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~a 124 (223)
T cd02563 45 HVYPVHRLDRPTSGVLLFALSSEVARKLGEQFTEHRVHKTYLAVVRGYVPESGTIDYPLSEELDKLADKFASDDKAPQAA 124 (223)
T ss_pred CcccccCCCCCCeEEEEEEECHHHHHHHHHHHhcCceeEEEEEEEECccCCCCeEEEeeeeCCCccceEEeecCCCCcee
Confidence 578999999999999999999999999988 578899999999999886532110 0 0 0 0111 223445
Q ss_pred eeEEEEcCCC---------CCCCceEEEEEecCCchhHHHHHHHHcCCceeeeeeeE
Q 031054 89 PDVVELLPPQ---------PDIPRPRIRIVVHEGRNHEVRELVKNAGLKLYSLKRLR 136 (166)
Q Consensus 89 ~~~~~~~~~~---------~~~~~~ll~~~l~tGR~HQIR~~l~~~G~pI~~l~R~~ 136 (166)
.+.++++... ...++++++|+|.|||+||||+||+++||||++|..|.
T Consensus 125 ~t~~~~l~~~~~~~~~~~~~~~~~slv~~~~~TGR~HQIRvhla~lG~PIvGD~~Yg 181 (223)
T cd02563 125 TTHYRLLAVEELPVVVGKYPTSRYSLVELTPHTGRKHQLRRHLAHIRHPIIGDTTHG 181 (223)
T ss_pred EEEEEEeeecccccccccCCCCCeEEEEEEeCCCCHHHHHHHHHHcCCCeeCCcccC
Confidence 6777776531 12347999999999999999999999999999999985
No 23
>PRK11180 rluD 23S rRNA pseudouridine synthase D; Provisional
Probab=99.96 E-value=7.9e-29 Score=207.41 Aligned_cols=130 Identities=18% Similarity=0.219 Sum_probs=98.0
Q ss_pred cchHHHHHHHhhcCCCCCCCCeeecCCCCcCCceeeeeeCCHHHHHHhhc--CCCCCCeEEEEEEecccChhhh-h-hh-
Q 031054 2 SLFDDYLKSWDKRNPGLPRPRLFTVGRLDVATTGLIIVTNDGDFAQAVSH--PSSKLQKEYIATIDGAVNKRHL-I-AI- 76 (166)
Q Consensus 2 sl~d~~~~~~~~~~~~~~~~~l~~vhRLD~~TSGlll~ak~~~~~~~l~~--~~~~i~K~Y~a~v~g~~~~~~~-~-~~- 76 (166)
|+++.+...+... ...+++.+|||||++||||||||+|.+++..|++ ..+.|+|+|+|+|.|.++++.. . .+
T Consensus 114 tl~~~l~~~~~~~---~~~~~~~~vhRLD~~TSGlll~Ak~~~~~~~l~~~~~~~~v~K~Y~A~v~G~~~~~~~i~~~l~ 190 (325)
T PRK11180 114 TVLNALLHYYPPI---ADVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVEALQKREITREYEAVAIGHMTAGGTVDEPIS 190 (325)
T ss_pred cHHHHHHHHhhhc---cCCcccceeccCCCCCceeEEEECCHHHHHHHHHHHHhCCcceEEEEEEecCCCCCCEEECcee
Confidence 4556555444221 1134678999999999999999999999999987 5788999999999999865431 0 01
Q ss_pred hc-----ceee-CCcccceeEEEEcCCCCCCCceEEEEEecCCchhHHHHHHHHcCCceeeeeeeE
Q 031054 77 SE-----GTVI-EGTHCTPDVVELLPPQPDIPRPRIRIVVHEGRNHEVRELVKNAGLKLYSLKRLR 136 (166)
Q Consensus 77 ~~-----~~~~-~~~~~~~~~~~~~~~~~~~~~~ll~~~l~tGR~HQIR~~l~~~G~pI~~l~R~~ 136 (166)
+. .+.. ++++.+.+.|+++... .+.++++|+|.|||+||||+||+++||||++|..|.
T Consensus 191 ~~~~~~~~~~~~~~gk~a~T~~~~l~~~--~~~slv~~~~~TGRtHQIRvhla~lG~PI~GD~~Yg 254 (325)
T PRK11180 191 RHPTKRTHMAVHPMGKPAVTHYRIMEHF--RVHTRLRLRLETGRTHQIRVHMAHITHPLVGDQVYG 254 (325)
T ss_pred cCCCcCcEEEeCCCCcEEeEEEEEeEEc--CCeEEEEEEeCCCCHHHHHHHHHhCCCCEeCccccC
Confidence 00 0111 2345567888888653 347999999999999999999999999999999984
No 24
>PRK11025 23S rRNA pseudouridylate synthase C; Provisional
Probab=99.95 E-value=2.3e-28 Score=203.98 Aligned_cols=113 Identities=20% Similarity=0.264 Sum_probs=90.9
Q ss_pred CeeecCCCCcCCceeeeeeCCHHHHHHhhc--CCCCCCeEEEEEEecccChhh--hhh-h-----hcc--e-ee-CCccc
Q 031054 22 RLFTVGRLDVATTGLIIVTNDGDFAQAVSH--PSSKLQKEYIATIDGAVNKRH--LIA-I-----SEG--T-VI-EGTHC 87 (166)
Q Consensus 22 ~l~~vhRLD~~TSGlll~ak~~~~~~~l~~--~~~~i~K~Y~a~v~g~~~~~~--~~~-~-----~~~--~-~~-~~~~~ 87 (166)
.+++|||||++||||||||+|..+++.|.. ..+.++|+|+|+|.|.+..+. +.. + ..+ + .. ++++.
T Consensus 136 ~~~~vhRLD~~TSGlll~Ak~~~a~~~l~~~~~~~~v~K~Y~a~v~G~~~~~~~~i~~~i~~~~~~~~~~~~~~~~~gk~ 215 (317)
T PRK11025 136 FLELVHRLDRDTSGVLLVAKKRSALRSLHEQLREKGMQKDYLALVRGQWQSHVKVVQAPLLKNILQSGERIVRVSQEGKP 215 (317)
T ss_pred cCceeCCCCCCCceEEEEEcCHHHHHHHHHHHHhCCccEEEEEEEeCcccCCCceEecccccCcccCCceEEecCCCCcc
Confidence 468999999999999999999999988877 377899999999999876432 110 0 011 1 11 24566
Q ss_pred ceeEEEEcCCCCCCCceEEEEEecCCchhHHHHHHHHcCCceeeeeeeE
Q 031054 88 TPDVVELLPPQPDIPRPRIRIVVHEGRNHEVRELVKNAGLKLYSLKRLR 136 (166)
Q Consensus 88 ~~~~~~~~~~~~~~~~~ll~~~l~tGR~HQIR~~l~~~G~pI~~l~R~~ 136 (166)
+.|.|+++... .+.++++|.|.|||+||||+||+++||||++|..|.
T Consensus 216 a~T~~~~l~~~--~~~sLv~~~~~TGRtHQIRvhla~lG~PIlGD~~Yg 262 (317)
T PRK11025 216 SETRFKVEERY--AFATLVRASPVTGRTHQIRVHTQYAGHPIAFDDRYG 262 (317)
T ss_pred ceEEEEEeEEc--CCcEEEEEEeCCCCHHHHHHHHHHCCCCEECCcccC
Confidence 78889888754 347999999999999999999999999999999985
No 25
>PF00849 PseudoU_synth_2: RNA pseudouridylate synthase This Prosite family is a subset of the Pfam family. This Prosite family is a subset of the Pfam family.; InterPro: IPR006145 Pseudouridine synthases catalyse the isomerisation of uridine to pseudouridine (Psi) in a variety of RNA molecules, and may function as RNA chaperones. Pseudouridine is the most abundant modified nucleotide found in all cellular RNAs. There are four distinct families of pseudouridine synthases that share no global sequence similarity, but which do share the same fold of their catalytic domain(s) and uracil-binding site and are descended from a common molecular ancestor. The catalytic domain consists of two subdomains, each of which has an alpha+beta structure that has some similarity to the ferredoxin-like fold (note: some pseudouridine synthases contain additional domains). The active site is the most conserved structural region of the superfamily and is located between the two homologous domains. These families are []: Pseudouridine synthase I, TruA. Pseudouridine synthase II, TruB, which contains and additional C-terminal PUA domain. Pseudouridine synthase RsuA (ribosomal small subunit) and RluC/RluD (ribosomal large subunits), both of which contain an additional N-terminal alpha-L RNA-binding motif. Pseudouridine synthase TruD, which has a natural circular permutation in the catalytic domain, as well as an insertion of a family-specific alpha+beta subdomain. This entry represents several different pseudouridine synthases from family 3, including: RsuA (acts on small ribosomal subunit), RluA, RluB, RluC, RluD, RluE and RluF (act on large ribosomal subunit). RsuA from Escherichia coli catalyses formation of pseudouridine at position 516 in 16S rRNA during assembly of the 30S ribosomal subunit [, ]. RsuA consists of an N-terminal domain connected by an extended linker to the central and C-terminal domains. Uracil and UMP bind in a cleft between the central and C-terminal domains near the catalytic residue Asp 102. The N-terminal domain shows structural similarity to the ribosomal protein S4. Despite only 15% amino acid identity, the other two domains are structurally similar to those of the tRNA-specific psi-synthase TruA, including the position of the catalytic Asp. Our results suggest that all four families of pseudouridine synthases share the same fold of their catalytic domain(s) and uracil-binding site. RluB, RluC, RluD, RluE and RluF are homologous enzymes which each convert specific uridine bases in E. coli ribosomal 23S RNA to pseudouridine: RluB modifies uracil-2605. RluC modifies uracil-955, U-2504, and U-2580. RluD modifies uracil-1911, U-1915, and U-1917. RluE modifies uracil-3457. RluF modifies uracil-2604, and to a lesser extent U-2605. RluD also possesses a second function related to proper assembly of the 50S ribosomal subunit that is independent of Psi-synthesis [, ]. Both RluC and RluD have an N-terminal S4 RNA binding domain. Despite the conserved topology shared by RluC and RluD, the surface shape and charge distribution are very different. ; GO: 0003723 RNA binding, 0009982 pseudouridine synthase activity, 0001522 pseudouridine synthesis, 0009451 RNA modification; PDB: 2GML_A 3DH3_B 1VIO_A 2I82_B 1XPI_B 1V9K_B 1PRZ_A 1V9F_A 2IST_A 1QYU_A ....
Probab=99.92 E-value=6.2e-25 Score=165.98 Aligned_cols=105 Identities=23% Similarity=0.384 Sum_probs=77.2
Q ss_pred CCCeeecCCCCcCCceeeeeeCCHHHHHHhhc--CCCCCCeEEEEEEeccc-Chhhhhh--hhc----------ceeeCC
Q 031054 20 RPRLFTVGRLDVATTGLIIVTNDGDFAQAVSH--PSSKLQKEYIATIDGAV-NKRHLIA--ISE----------GTVIEG 84 (166)
Q Consensus 20 ~~~l~~vhRLD~~TSGlll~ak~~~~~~~l~~--~~~~i~K~Y~a~v~g~~-~~~~~~~--~~~----------~~~~~~ 84 (166)
.+.+++|||||++||||||||+|++++++|++ +.++++|+|+|+|.|.+ .++.... +.. .....+
T Consensus 38 ~~~~~~v~RLD~~TsGlll~a~~~~~~~~l~~~f~~~~~~K~Y~a~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 117 (164)
T PF00849_consen 38 PPELYPVHRLDRDTSGLLLFAKDKEAAAKLSKQFPKRKVEKTYLALVEGGPVEEEGKINSPLGKDVGKNKSSNKDPPGRD 117 (164)
T ss_dssp SGGGEESS---TT-EEEEEEESSHHHHHHHHHHHHTTCSEEEEEEEECSSSSTTCEEEESHEEE-EECSSCTCCEEETTT
T ss_pred CCceEECCCCCccccCCeeccCCcccccccccccccCCCcEEEEEeEcccccccceeeeccccccccccccceeeeeccc
Confidence 47899999999999999999999999999999 68899999999999544 3322110 100 111133
Q ss_pred cccceeEEEEcCCC-------CCCCceEEEEEecCCchhHHHHHHHH
Q 031054 85 THCTPDVVELLPPQ-------PDIPRPRIRIVVHEGRNHEVRELVKN 124 (166)
Q Consensus 85 ~~~~~~~~~~~~~~-------~~~~~~ll~~~l~tGR~HQIR~~l~~ 124 (166)
.+.+.+.++++... ...+.++++|+|.|||+||||+|||+
T Consensus 118 ~~~~~t~~~~l~~~~~~~~~~~~~~~s~v~~~l~tGr~HQIR~hla~ 164 (164)
T PF00849_consen 118 GKPAITRYRVLRSGSRTPSKDENAGCSLVECELITGRTHQIRVHLAH 164 (164)
T ss_dssp SBTSEEEEEEEEEETT---EECCSSEEEEEEEESS-STTHHHHHHHH
T ss_pred ccccceeeeeeccccccccccccCCCEEEEEEECcCCCHHHHHHhcC
Confidence 55667888888765 45678999999999999999999986
No 26
>KOG1919 consensus RNA pseudouridylate synthases [RNA processing and modification]
Probab=99.85 E-value=1.2e-21 Score=165.87 Aligned_cols=115 Identities=17% Similarity=0.258 Sum_probs=91.5
Q ss_pred CCeeecCCCCcCCceeeeeeCCHHHHHHhhcC--CCCCCeEE-EEEEecccChh-hhh--------h--hhccee---eC
Q 031054 21 PRLFTVGRLDVATTGLIIVTNDGDFAQAVSHP--SSKLQKEY-IATIDGAVNKR-HLI--------A--ISEGTV---IE 83 (166)
Q Consensus 21 ~~l~~vhRLD~~TSGlll~ak~~~~~~~l~~~--~~~i~K~Y-~a~v~g~~~~~-~~~--------~--~~~~~~---~~ 83 (166)
..+.++||||+.|||||+||++.+.+..+.+. ++.+.|.| ++.|.|.++.. .+. . .+.++. ..
T Consensus 148 ~~~~~~hRLDr~tSGllvlAkt~~~~~~~~~~~r~~~~~k~Y~v~~v~g~fp~~~~~~i~~~~~~~~~~~~~~l~~~~~~ 227 (371)
T KOG1919|consen 148 EGLRPCHRLDRLTSGLLVLAKTKEAADKFHEVLRKRTVKKEYVVARVEGPFPVVGEVEIKEPIGEEERPLRMGLNAVGVR 227 (371)
T ss_pred cccccccccCccccceEEEEechhHhHHHHHHHhcccceeEEEEEEEeccCCCCceEEeCCCccccccccceEeeecccc
Confidence 45799999999999999999999999998874 66999999 79999998832 211 0 111111 11
Q ss_pred ---CcccceeEEEEcCCCCCCCceEEEEEecCCchhHHHHHHHHcCCceeeeeeeEE
Q 031054 84 ---GTHCTPDVVELLPPQPDIPRPRIRIVVHEGRNHEVRELVKNAGLKLYSLKRLRI 137 (166)
Q Consensus 84 ---~~~~~~~~~~~~~~~~~~~~~ll~~~l~tGR~HQIR~~l~~~G~pI~~l~R~~~ 137 (166)
..+.+.+.|+.+.+. ...+++++.|.|||+||||+||+++|+||+++.-|+-
T Consensus 228 ~~~~~k~a~T~~~~~~~~--~~ss~V~~~PlTGRtHQIRvHlq~lG~PI~gD~~Y~~ 282 (371)
T KOG1919|consen 228 DEVAAKDAKTLFKVLSYD--GGSSLVECRPLTGRTHQIRVHLQYLGHPIAGDPKYGN 282 (371)
T ss_pred cccccccceeEEEEcccC--CceEEEEeeccCCcHHHHHHHHHHhCCCcCCCccccc
Confidence 135667888888875 5689999999999999999999999999999999843
No 27
>cd02868 PseudoU_synth_hTruB2_like PseudoU_synth_ hTRUB2_Like: Pseudouridine synthase, humanTRUB2_like. This group consists of eukaryotic pseudouridine synthases similar to human TruB pseudouridine synthase homolog 2 (TRUB2). Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi).
Probab=98.64 E-value=4.1e-07 Score=72.98 Aligned_cols=122 Identities=19% Similarity=0.230 Sum_probs=72.1
Q ss_pred eeecCCCCcCCceeeeeeCCHHHHHHhhc--CCCCCCeEEEEEEe-----------cc---------cChhhhh----hh
Q 031054 23 LFTVGRLDVATTGLIIVTNDGDFAQAVSH--PSSKLQKEYIATID-----------GA---------VNKRHLI----AI 76 (166)
Q Consensus 23 l~~vhRLD~~TSGlll~ak~~~~~~~l~~--~~~~i~K~Y~a~v~-----------g~---------~~~~~~~----~~ 76 (166)
.++|||||++|||||+|+.+... ++.. ..+.+.|+|++... |. ++.+.+. .+
T Consensus 34 ~~~vhrLD~~aSGvl~~a~~~~t--kl~~~~~~~~~~K~Y~~~~~lg~~TdT~D~~G~v~~~~~~~~it~~~i~~~l~~f 111 (226)
T cd02868 34 LVGVHRLDAFSSGVLVLGVNHGN--KLLSHLYSNHPTRVYTIRGLLGKATENFFHTGRVIEKTTYDHITREKIERLLAVI 111 (226)
T ss_pred eeEccccCCCCceEEEEEeChhH--hHHHHHHhcCCCeEEEEEEEEccccCCCCCCCCEEEecCCCCCCHHHHHHHHHHh
Confidence 57889999999999999999765 3433 24568999997542 11 1112221 11
Q ss_pred hcc----------eeeCCc-----------------ccceeEEEEcCCCCCCCceEEEEEecCCchhHHHHHHHHcCC--
Q 031054 77 SEG----------TVIEGT-----------------HCTPDVVELLPPQPDIPRPRIRIVVHEGRNHEVRELVKNAGL-- 127 (166)
Q Consensus 77 ~~~----------~~~~~~-----------------~~~~~~~~~~~~~~~~~~~ll~~~l~tGR~HQIR~~l~~~G~-- 127 (166)
..+ +.++|. ....-.++++... .+...+++.--.|----||..+..+|.
T Consensus 112 ~g~~~q~~p~~sa~kv~GkraYelAR~G~~ve~~~r~v~I~~i~l~~~~--~p~~~~~v~cskGT~~YIRsL~~Dig~~L 189 (226)
T cd02868 112 QSGHQQKAFELCSVDDQSQQAAELAARGLIRPADKSPPIIYGIRLLEFR--PPEFTLEVQCINETQEYLRKLIHEIGLEL 189 (226)
T ss_pred hCCceEECCceEEEeeCCHHHHHHHHCCCccCCCCcceEEEEEEEEEec--CCeEEEEEEEECCCHHHHHHHHHHHHHHh
Confidence 111 111111 1111233333321 234445555555543589988887775
Q ss_pred ----ceeeeeeeEEeCeecCCCCCC
Q 031054 128 ----KLYSLKRLRIGGFRLPSDLGI 148 (166)
Q Consensus 128 ----pI~~l~R~~~g~~~l~~~l~~ 148 (166)
.+..|.|+++|+|++++.+..
T Consensus 190 g~~a~~~~L~R~~~G~f~~~~a~~~ 214 (226)
T cd02868 190 RSSAVCTQVRRTRDGPFTVDDALLR 214 (226)
T ss_pred CCcEEEEEEEeeEECCCCHHHcccH
Confidence 569999999999999755543
No 28
>cd01291 PseudoU_synth PseudoU_synth: Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). Pseudouridine synthases contains the RsuA/RluD, TruA, TruB and TruD families. This group consists of eukaryotic, bacterial and archeal pseudouridine synthases. Some psi sites such as psi55,13,38 and 39 in tRNA are highly conserved, being in the same position in eubacteria, archeabacteria and eukaryotes. Other psi sites occur in a more restricted fashion, for example psi2604in 23S RNA made by E.coli RluF has only been detected in E.coli. Human dyskerin with the help of guide RNAs makes the hundreds of psueudouridnes present in rRNA and small nuclear RNAs (snRNAs). Mutations in human dyskerin cause X-linked dyskeratosis congenitas. Missense mutation in human PUS1 causes mitochondrial myopathy and sideroblastic anemia (MLASA).
Probab=98.15 E-value=1.1e-05 Score=54.98 Aligned_cols=67 Identities=16% Similarity=0.237 Sum_probs=49.5
Q ss_pred CCCCCeeecCCCCcCCceeeeeeCCHHHHHHhhcCCCCCCeEEEEEEecccChhhhhhhhcceeeCCcccceeEEEEcCC
Q 031054 18 LPRPRLFTVGRLDVATTGLIIVTNDGDFAQAVSHPSSKLQKEYIATIDGAVNKRHLIAISEGTVIEGTHCTPDVVELLPP 97 (166)
Q Consensus 18 ~~~~~l~~vhRLD~~TSGlll~ak~~~~~~~l~~~~~~i~K~Y~a~v~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 97 (166)
.+..++..+|++|+.++|+++++ ++|.++++ ..+..+.....
T Consensus 21 ~~~~~i~~aG~kDk~a~t~q~v~-----------------n~f~i~~r---------------------~~~~~~~~~~~ 62 (87)
T cd01291 21 IPPKRVGYAGRKDKRAVTTQLVS-----------------NRFTITLR---------------------VKPLNLKWPEE 62 (87)
T ss_pred CChheEEECccCCCCeeEEEEEc-----------------ccEEEEEE---------------------EecceeEEccc
Confidence 34568999999999999999999 89999988 11122222111
Q ss_pred CCCCCceEEEEEecCCchhHHHHHHHHcC
Q 031054 98 QPDIPRPRIRIVVHEGRNHEVRELVKNAG 126 (166)
Q Consensus 98 ~~~~~~~ll~~~l~tGR~HQIR~~l~~~G 126 (166)
. ....+++++| |+.||+|.+++.+|
T Consensus 63 ~--~~~~~l~f~l--~~~~yat~~l~el~ 87 (87)
T cd01291 63 R--KRALVLEFTL--PRGSYATMLLRELG 87 (87)
T ss_pred c--cceEEEEEEc--CCcchHHHHHHHhC
Confidence 0 1246788888 99999999999875
No 29
>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=97.53 E-value=0.00063 Score=54.06 Aligned_cols=135 Identities=20% Similarity=0.285 Sum_probs=76.5
Q ss_pred cchHHHHHHHhhcCCCCCCCCeeecCCCCcCCceeeeeeCCH--HHHHHhhcCCCCCCeEEEEEEe-cc-----------
Q 031054 2 SLFDDYLKSWDKRNPGLPRPRLFTVGRLDVATTGLIIVTNDG--DFAQAVSHPSSKLQKEYIATID-GA----------- 67 (166)
Q Consensus 2 sl~d~~~~~~~~~~~~~~~~~l~~vhRLD~~TSGlll~ak~~--~~~~~l~~~~~~i~K~Y~a~v~-g~----------- 67 (166)
|..| +...+++.+. ..++...|-||-.+||||+++-.. .+...+. ...|+|.|.+. |.
T Consensus 12 tS~~-vv~~ik~~~~---~kKvGH~GTLDP~AsGvLiv~vG~aTkl~~~~~----~~~K~Y~~~~~lG~~TdT~D~~G~v 83 (210)
T cd00506 12 SSHD-VVDTIRRIFL---AEKVGHGGTLDPFATGVLVVGIGKATKLLKHLL----AATKDYTAIGRLGQATDTFDATGQV 83 (210)
T ss_pred CHHH-HHHHHHHHhC---ccccCCCCcCCCcCeeEEEEEECHHHhhhHHHh----cCCceEEEEEEECCcCCCCCCCCCE
Confidence 4455 3444444333 247889999999999999987663 2344444 38899999764 21
Q ss_pred --------cChhhhhh----hhc----------ceeeCCc-----------------ccceeEEEEcCCCCCCCceEEEE
Q 031054 68 --------VNKRHLIA----ISE----------GTVIEGT-----------------HCTPDVVELLPPQPDIPRPRIRI 108 (166)
Q Consensus 68 --------~~~~~~~~----~~~----------~~~~~~~-----------------~~~~~~~~~~~~~~~~~~~ll~~ 108 (166)
++.+.+.. +.. .+.++|. ......++++......+...++|
T Consensus 84 ~~~~~~~~it~e~l~~~l~~f~G~i~Q~pP~ySAvKv~G~raYelAR~G~~v~~~~r~v~I~~i~ll~~~~~~~~~~~~v 163 (210)
T cd00506 84 IEETPYDHITHEQLERALETLTGDIQQVPPLYSAVKRQGQRAYELARRGLLVPDEARPPTIYELLCIRFNPPHFLLEVEV 163 (210)
T ss_pred EEEeCCCCCCHHHHHHHHHHCCCeEEEeCCchheEEECCHhHHHHHHCCCccccCcEeEEEEEEEEEEEcCCCcEEEEEE
Confidence 22222221 100 1112221 11112334443321112334555
Q ss_pred EecCCchhHHHHHHHHcCC------ceeeeeeeEEeCeecCCCC
Q 031054 109 VVHEGRNHEVRELVKNAGL------KLYSLKRLRIGGFRLPSDL 146 (166)
Q Consensus 109 ~l~tGR~HQIR~~l~~~G~------pI~~l~R~~~g~~~l~~~l 146 (166)
.--.| -.||..+..+|. .+..|.|+++|+|.+++.+
T Consensus 164 ~cs~G--TYIRsL~~Dig~~Lg~~a~l~~L~R~~~G~f~~~~a~ 205 (210)
T cd00506 164 VCETG--TYIRTLIHDLGLELGVGAHVTELRRTRVGPFKVENAV 205 (210)
T ss_pred EECCC--cCHHHHHHHHHHHhCCcEEEEEEEEEEECCCchhhcc
Confidence 55555 779988877765 4588999999999996444
No 30
>PRK00989 truB tRNA pseudouridine synthase B; Provisional
Probab=97.51 E-value=0.00048 Score=55.37 Aligned_cols=138 Identities=20% Similarity=0.268 Sum_probs=80.2
Q ss_pred cchHHHHHHHhhcCCCCCCCCeeecCCCCcCCceeeeeeCCHHHHHHhhcCCCCCCeEEEEEEe-c----------c---
Q 031054 2 SLFDDYLKSWDKRNPGLPRPRLFTVGRLDVATTGLIIVTNDGDFAQAVSHPSSKLQKEYIATID-G----------A--- 67 (166)
Q Consensus 2 sl~d~~~~~~~~~~~~~~~~~l~~vhRLD~~TSGlll~ak~~~~~~~l~~~~~~i~K~Y~a~v~-g----------~--- 67 (166)
|..| +...+++.+. ..++...|-||..+||||+++-... +-+|.+--....|+|.+.+. | .
T Consensus 21 TS~d-vv~~ikk~~~---~kKvGH~GTLDP~AtGvLiv~vG~~-aTkl~~~~~~~~K~Y~~~~~~G~~TdT~D~~G~vi~ 95 (230)
T PRK00989 21 TSFS-LIRSLTKLIG---VKKIGHAGTLDPFATGVMVMLIGRK-FTRLSDILLFEDKEYAAVAHLGTTTDSYDCDGKIVG 95 (230)
T ss_pred CHHH-HHHHHHHHhC---CCcCCcCccCCCCCeeEEEEEECCc-hhhhHHHhcCCCcEEEEEEEECCcccCCCCCCcEEE
Confidence 4455 3444544443 2478999999999999999876531 12222222247899999875 1 1
Q ss_pred -----cChhhhhh----hh----------cceeeCCcc--------------ccee--EEEEcCCCCCCCceEEEEEecC
Q 031054 68 -----VNKRHLIA----IS----------EGTVIEGTH--------------CTPD--VVELLPPQPDIPRPRIRIVVHE 112 (166)
Q Consensus 68 -----~~~~~~~~----~~----------~~~~~~~~~--------------~~~~--~~~~~~~~~~~~~~ll~~~l~t 112 (166)
++.+.+.. +. ..+.++|.. .... .++++... .+...+++.--.
T Consensus 96 ~~~~~~~~~~i~~~l~~f~G~~~Q~PP~ySAvKv~GkraYelAR~G~~ve~~~r~v~i~~~ll~~~--~p~~~~~v~cs~ 173 (230)
T PRK00989 96 RSKKIPTLEEVLSAASYFQGEIQQVPPMFSAKKVQGKKLYEYARQGLSIERRPSTVQVHLQLTKYE--YPLLHFVVQCSK 173 (230)
T ss_pred ecCCCCCHHHHHHHHHhCcceEEeeCChhHeEEECCHhHHHHHhCCCccccCcEEEEEEEEEEEee--CCeEEEEEEEcC
Confidence 12222221 10 011222211 1111 12333322 245677777777
Q ss_pred CchhHHHHHHHHcCC------ceeeeeeeEEeCeecCCCCCC
Q 031054 113 GRNHEVRELVKNAGL------KLYSLKRLRIGGFRLPSDLGI 148 (166)
Q Consensus 113 GR~HQIR~~l~~~G~------pI~~l~R~~~g~~~l~~~l~~ 148 (166)
|- .||..+..+|. .+..|.|+++|+|.+++.++.
T Consensus 174 GT--YIRSL~~DiG~~Lg~~a~~~~LrRt~~G~f~l~~a~~l 213 (230)
T PRK00989 174 GT--YIRSIAHELGNMLGCGAYLEELRRLRSGSFSIDQCIDG 213 (230)
T ss_pred CC--cHHHHHHHHHHHHCCCEEEEEEEeEEECCCcHHHcCCH
Confidence 75 89999888775 568999999999999644443
No 31
>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=97.34 E-value=0.004 Score=48.40 Aligned_cols=133 Identities=20% Similarity=0.182 Sum_probs=75.3
Q ss_pred CcchHHHHHHHhhcCCCCCCCCeeecCCCCcCCceeeeeeCCH--HHHHHhhcCCCCCCeEEEEEEec--ccChhhhhhh
Q 031054 1 MSLFDDYLKSWDKRNPGLPRPRLFTVGRLDVATTGLIIVTNDG--DFAQAVSHPSSKLQKEYIATIDG--AVNKRHLIAI 76 (166)
Q Consensus 1 ~sl~d~~~~~~~~~~~~~~~~~l~~vhRLD~~TSGlll~ak~~--~~~~~l~~~~~~i~K~Y~a~v~g--~~~~~~~~~~ 76 (166)
+|..|.+ ...++.+. ..++...|-||..+||||+++-.. .+...+. .-.|+|.|.+.- .++++++...
T Consensus 13 ~tS~~~v-~~~k~~~~---~kkvGH~GTLDp~A~GvLiv~~g~~Tk~~~~~~----~~~K~Y~a~v~~g~~it~e~l~~~ 84 (182)
T cd02572 13 PSSHEVV-AWIKRILG---VEKTGHSGTLDPKVTGCLPVCIDRATRLVKSQQ----EAGKEYVCVMRLHDDVDEEKVRRV 84 (182)
T ss_pred CCHHHHH-HHHHHHhC---CCccCcCCCCCCcCeeEEEEEECHHhhhhHHHh----CCCCEEEEEEEECCcCCHHHHHHH
Confidence 3556644 44544333 247899999999999999987663 2334444 345999987643 3455555321
Q ss_pred -hc--c-e-eeC---------CcccceeEEEEcCCCCCCCceEEEEEecCCchhHHHHHHHHcC------CceeeeeeeE
Q 031054 77 -SE--G-T-VIE---------GTHCTPDVVELLPPQPDIPRPRIRIVVHEGRNHEVRELVKNAG------LKLYSLKRLR 136 (166)
Q Consensus 77 -~~--~-~-~~~---------~~~~~~~~~~~~~~~~~~~~~ll~~~l~tGR~HQIR~~l~~~G------~pI~~l~R~~ 136 (166)
.. | + ... ........++.+......+...+++.-..| --||.....+| ..+..|+|++
T Consensus 85 l~~f~G~i~Q~pP~~SA~K~~~R~v~I~~i~l~~~~~~~~~~~~~v~cs~G--TYIRsL~~dlg~~Lg~~a~l~~L~R~~ 162 (182)
T cd02572 85 LEEFTGAIFQRPPLISAVKRQLRVRTIYESKLLEYDGERRLVLFRVSCEAG--TYIRTLCVHIGLLLGVGAHMQELRRTR 162 (182)
T ss_pred HHHCCCcEEeeCCHhheecCCceEEEEEEEEEEEEcCCCcEEEEEEEECCC--cCHHHHHHHHHHHHCCCeEEEEEEeEE
Confidence 11 1 1 000 011111233333332211334455555556 56887776655 3468999999
Q ss_pred EeCe-ecC
Q 031054 137 IGGF-RLP 143 (166)
Q Consensus 137 ~g~~-~l~ 143 (166)
+|+| .++
T Consensus 163 ~G~f~~~~ 170 (182)
T cd02572 163 SGPFSEED 170 (182)
T ss_pred EcCcCchh
Confidence 9999 774
No 32
>TIGR00431 TruB tRNA pseudouridine 55 synthase. TruB, the tRNA pseudouridine 55 synthase, converts uracil to pseudouridine in the T loop (not the anticodon loop - beware mis-annotation in Swiss-Prot) of most tRNAs of all three domains of life. This model is built on a seed alignment of bacterial proteins only. Saccharomyces cerevisiae protein YNL292w (Pus4) has been shown to be the pseudouridine 55 synthase of both cytosolic and mitochondrial compartments, active at no other position on tRNA and the only enzyme active at that position in the species. A distinct yeast protein YLR175w, (centromere/microtubule-binding protein CBF5) is an rRNA pseudouridine synthase, and the archaeal set is much more similar to CBF5 than to Pus4. It is unclear whether the archaeal proteins found by this model are tRNA pseudouridine 55 synthases like TruB, rRNA pseudouridine synthases like CBF5, or (as suggested by the absence of paralogs in the Archaea) both. CBF5 likely has additional, eukaryotic-specific
Probab=97.26 E-value=0.0032 Score=50.04 Aligned_cols=136 Identities=22% Similarity=0.290 Sum_probs=79.8
Q ss_pred cchHHHHHHHhhcCCCCCCCCeeecCCCCcCCceeeeeeCCHHHHHHhhcCCCCCCeEEEEEEe-ccc------------
Q 031054 2 SLFDDYLKSWDKRNPGLPRPRLFTVGRLDVATTGLIIVTNDGDFAQAVSHPSSKLQKEYIATID-GAV------------ 68 (166)
Q Consensus 2 sl~d~~~~~~~~~~~~~~~~~l~~vhRLD~~TSGlll~ak~~~~~~~l~~~~~~i~K~Y~a~v~-g~~------------ 68 (166)
|..| +...+++.+.. .++...|-||-.+||||+++-.... ++.+--....|+|.|.+. |.-
T Consensus 14 tS~~-vv~~vkk~~~~---kKvGH~GTLDP~AsGvLiv~vG~~T--kl~~~~~~~~K~Y~~~~~~G~~TdT~D~~G~i~~ 87 (209)
T TIGR00431 14 TSFD-ALAKVRRLLNV---KKVGHTGTLDPFATGVLPILVGKAT--KLSPYLTDLDKEYRAEIRLGVRTDTLDPDGQIVE 87 (209)
T ss_pred CHHH-HHHHHHHHhCC---CcCCCCCCCCCcCceEEEEEEChHh--hhhHHHcCCCCeEEEEEEECCcCCCCCCCCCEEE
Confidence 3444 44555554432 4678899999999999999777432 232222367899999763 211
Q ss_pred ------Chhhhhh----hh----------cceeeCCc-----------------ccceeEEEEcCCCCCCCceEEEEEec
Q 031054 69 ------NKRHLIA----IS----------EGTVIEGT-----------------HCTPDVVELLPPQPDIPRPRIRIVVH 111 (166)
Q Consensus 69 ------~~~~~~~----~~----------~~~~~~~~-----------------~~~~~~~~~~~~~~~~~~~ll~~~l~ 111 (166)
+.+.++. +. ..+.++|. +.....++++... .+...+++.--
T Consensus 88 ~~~~~~~~~~l~~~l~~f~G~~~Q~PP~ySA~Kv~G~raYelAR~g~~v~~~~r~v~I~~i~ll~~~--~~~~~~~v~cs 165 (209)
T TIGR00431 88 TRPVNPTTEDVEAALPTFRGEIEQIPPMYSALKVNGKRLYEYARQGIEVERKARPVTVYDLQFLKYE--GPELTLEVHCS 165 (209)
T ss_pred ecCCCCCHHHHHHHHHHccCcEEEECChhhEEeeCCHhHHHHHHCCCccccCcceeEEEEEEEEEEc--CCcEEEEEEEC
Confidence 1112211 10 01112221 1112234444332 23566777777
Q ss_pred CCchhHHHHHHHHcCC------ceeeeeeeEEeCeecCCCCC
Q 031054 112 EGRNHEVRELVKNAGL------KLYSLKRLRIGGFRLPSDLG 147 (166)
Q Consensus 112 tGR~HQIR~~l~~~G~------pI~~l~R~~~g~~~l~~~l~ 147 (166)
.|- .||....-+|. .+..|.|+++|+|.+++.++
T Consensus 166 ~GT--YIRsL~~Dig~~L~~~a~l~~L~Rt~~G~f~~~~a~~ 205 (209)
T TIGR00431 166 KGT--YIRTLARDLGEKLGCGAYVSHLRRTAVGDFPLDQSVT 205 (209)
T ss_pred CCC--CHHHHHHHHHHHHCCCEEEEEEEeEEECCCcHHHcCC
Confidence 775 89988877775 56899999999999964443
No 33
>PRK00020 truB tRNA pseudouridine synthase B; Provisional
Probab=97.15 E-value=0.0064 Score=49.36 Aligned_cols=131 Identities=24% Similarity=0.317 Sum_probs=78.7
Q ss_pred cchHHHHHHHhhcCCCCCCCCeeecCCCCcCCceeeeeeCCH--HHHHHhhcCCCCCCeEEEEEEe-----------cc-
Q 031054 2 SLFDDYLKSWDKRNPGLPRPRLFTVGRLDVATTGLIIVTNDG--DFAQAVSHPSSKLQKEYIATID-----------GA- 67 (166)
Q Consensus 2 sl~d~~~~~~~~~~~~~~~~~l~~vhRLD~~TSGlll~ak~~--~~~~~l~~~~~~i~K~Y~a~v~-----------g~- 67 (166)
|..| +...+++.+. ..++...|-||..+||||+++-.. .+...+. ...|+|.|.+. |.
T Consensus 22 TS~d-vv~~vkr~~~---~kKvGH~GTLDP~AtGvLiv~iG~aTKl~~~l~----~~~K~Y~a~~~lG~~TdT~D~~G~v 93 (244)
T PRK00020 22 SSNH-ALQRAKRTVD---AAKAGHTGTLDPFATGLLVCCMGRATKISGRML----EADKTYQATLQFGEETDSGDLTGHI 93 (244)
T ss_pred CHHH-HHHHHHHHhC---CCCCCcCCcCCCcCeeEEEEEECHHhhhhHHhc----cCCcEEEEEEEeCCcccCCCCCCcE
Confidence 4555 4455555443 247889999999999999987663 3344443 35699999752 11
Q ss_pred ----------cChhhhhh----hh----------cceeeCCc-----------------ccceeEEEEcCCCCCCCceEE
Q 031054 68 ----------VNKRHLIA----IS----------EGTVIEGT-----------------HCTPDVVELLPPQPDIPRPRI 106 (166)
Q Consensus 68 ----------~~~~~~~~----~~----------~~~~~~~~-----------------~~~~~~~~~~~~~~~~~~~ll 106 (166)
++.+.+.. +. ..+.++|. ......+++++.. .+...+
T Consensus 94 ~~~~~~~~~~it~e~l~~~l~~f~G~i~Q~PP~ySAvKv~GkraYelAR~G~~ve~~~r~v~I~~i~ll~~~--~~~~~~ 171 (244)
T PRK00020 94 VARAPDGFAGVEEAALRDVLSRFVGTIEQIPPMYSALKRDGKPLYEYARAGIELDRPPRQVTIRHIELLSFS--GMQAQI 171 (244)
T ss_pred EEeccCccCCCCHHHHHHHHHhccCeEEEeCChhheEEECCeEHHHHHhCCcccccCCeeEEEEEEEEEEEe--CCEEEE
Confidence 22222221 10 01122221 1112234444432 235567
Q ss_pred EEEecCCchhHHHHHHHHcCC------ceeeeeeeEEeCeecCC
Q 031054 107 RIVVHEGRNHEVRELVKNAGL------KLYSLKRLRIGGFRLPS 144 (166)
Q Consensus 107 ~~~l~tGR~HQIR~~l~~~G~------pI~~l~R~~~g~~~l~~ 144 (166)
++.--.| --||..+..+|. .+..|+|+++|+|++++
T Consensus 172 ~v~cSkG--TYIRSL~~DiG~~Lg~~a~l~~LrRt~~G~f~l~~ 213 (244)
T PRK00020 172 DVACSKG--TYIRTLAQDIGRALGCHAHLAALRRTHVGPFSLDR 213 (244)
T ss_pred EEEECCC--cCHHHHHHHHHHHHCCCEEEEEEEeeEECCCChHH
Confidence 7777677 589999888875 56999999999999963
No 34
>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=97.00 E-value=0.011 Score=48.86 Aligned_cols=133 Identities=23% Similarity=0.376 Sum_probs=78.4
Q ss_pred cchHHHHHHHhhcCCCCCCCCeeecCCCCcCCceeeeeeCCH--HHHHHhhcCCCCCCeEEEEEEe-c----------c-
Q 031054 2 SLFDDYLKSWDKRNPGLPRPRLFTVGRLDVATTGLIIVTNDG--DFAQAVSHPSSKLQKEYIATID-G----------A- 67 (166)
Q Consensus 2 sl~d~~~~~~~~~~~~~~~~~l~~vhRLD~~TSGlll~ak~~--~~~~~l~~~~~~i~K~Y~a~v~-g----------~- 67 (166)
|..| +...+++.+.. .++...|-||-.+||||+++-.. .+...+. ...|+|.|.+. | .
T Consensus 12 tS~~-vv~~vr~~~~~---kKvGH~GTLDP~AtGvL~v~vG~aTkl~~~l~----~~~K~Y~~~~~~G~~TdT~D~~G~v 83 (277)
T cd02573 12 TSHD-VVQKVRRLLGT---KKVGHTGTLDPLATGVLPIALGEATKLSQYLL----DADKTYRATVRLGEATDTDDAEGEI 83 (277)
T ss_pred CHHH-HHHHHHHHhCc---CccCCCCCCCCcCeEEEEEEEChHHhhHHHhc----CCCcEEEEEEEECCcccCCCCCCCE
Confidence 4455 44455444432 46788999999999999987663 2333343 36899999874 2 1
Q ss_pred --------cChhhhhh----hh----------cceeeCCc-----------------ccceeEEEEcCCCCCCCceEEEE
Q 031054 68 --------VNKRHLIA----IS----------EGTVIEGT-----------------HCTPDVVELLPPQPDIPRPRIRI 108 (166)
Q Consensus 68 --------~~~~~~~~----~~----------~~~~~~~~-----------------~~~~~~~~~~~~~~~~~~~ll~~ 108 (166)
++.+.+.. +. ..+.++|. ......++++......+...+++
T Consensus 84 ~~~~~~~~~~~~~i~~~l~~f~G~i~Q~PP~ySAvkv~G~raYelAR~G~~ve~~~r~v~I~~i~ll~~~~~~~~~~~~v 163 (277)
T cd02573 84 IETSPPPRLTEEEIEAALKAFTGEIEQVPPMYSAVKVNGKRLYELARAGEEVERPPRKVTIYSLELLSFDPENPEADFEV 163 (277)
T ss_pred EEecCCCCCCHHHHHHHHHHccCcEEeeCChhHeEeeCCccHHHHHhCCCccccCCeeEEEEEEEEEEecCCCCeEEEEE
Confidence 22222221 10 01122221 11112334443321114566777
Q ss_pred EecCCchhHHHHHHHHcCC------ceeeeeeeEEeCeecCC
Q 031054 109 VVHEGRNHEVRELVKNAGL------KLYSLKRLRIGGFRLPS 144 (166)
Q Consensus 109 ~l~tGR~HQIR~~l~~~G~------pI~~l~R~~~g~~~l~~ 144 (166)
.--.| --||..+..+|. .+..|.|+++|+|.+++
T Consensus 164 ~cs~G--TYIRsL~~Dig~~Lg~~a~~~~L~Rt~~G~f~~~~ 203 (277)
T cd02573 164 ECSKG--TYIRSLARDLGKALGCGAHLSALRRTRSGPFTLED 203 (277)
T ss_pred EECCC--CcHHHHHHHHHHHHCCCeEEEEEEEEEECCccHHH
Confidence 77677 489988877764 57999999999999963
No 35
>PRK14123 tRNA pseudouridine synthase B; Provisional
Probab=96.99 E-value=0.012 Score=49.38 Aligned_cols=135 Identities=21% Similarity=0.333 Sum_probs=78.0
Q ss_pred cchHHHHHHHhhcCCCCCCCCeeecCCCCcCCceeeeeeCCHH--HHHHhhcCCCCCCeEEEEEEe-c------------
Q 031054 2 SLFDDYLKSWDKRNPGLPRPRLFTVGRLDVATTGLIIVTNDGD--FAQAVSHPSSKLQKEYIATID-G------------ 66 (166)
Q Consensus 2 sl~d~~~~~~~~~~~~~~~~~l~~vhRLD~~TSGlll~ak~~~--~~~~l~~~~~~i~K~Y~a~v~-g------------ 66 (166)
|..| +...+++.+. ..++...|-||-.+||||+++-... +...+. ...|+|.|.+. |
T Consensus 15 TS~d-vv~~vrr~~~---~kKvGH~GTLDP~AtGvL~v~vG~aTkl~~~l~----~~~K~Y~~~~~lG~~TdT~D~~G~v 86 (305)
T PRK14123 15 TSHD-VVFKLRKILK---TKKIGHTGTLDPEVAGVLPVCIGNATRVSDYVM----DMGKAYEATVSIGRSTTTEDQTGDT 86 (305)
T ss_pred CHHH-HHHHHHHHhC---CCccccCcCCCCcCeeEEEEEEChhhhhHHHhc----CCCcEEEEEEEECCcccCCCCCCCE
Confidence 4455 4445545443 2478899999999999999876642 333333 37899999763 1
Q ss_pred ---------ccChhhhhh----hh----------cceeeCCc-----------------ccceeEEEEcC---CCCCCCc
Q 031054 67 ---------AVNKRHLIA----IS----------EGTVIEGT-----------------HCTPDVVELLP---PQPDIPR 103 (166)
Q Consensus 67 ---------~~~~~~~~~----~~----------~~~~~~~~-----------------~~~~~~~~~~~---~~~~~~~ 103 (166)
.++.+.+.. +. ..+.++|. ......+++++ .....+.
T Consensus 87 i~~~~~~~~~~~~~~l~~~l~~f~G~i~Q~PP~ySAvKv~GkraYelAR~G~~ve~~~r~v~I~~i~~~~~~~~~~~~~~ 166 (305)
T PRK14123 87 LETKGVHSADFNKDDIDRLLEQFKGIIEQIPPMYSSVKVNGKKLYEYARNNETVERPKRKVNIKDIGRISELDFKENECH 166 (305)
T ss_pred EEeccCCcCCCCHHHHHHHHHhccCceeecCChhheEeeCCHhHHHHHhCCCcccCCceEEEEEEEEEeecccccCCCce
Confidence 123333221 10 01112221 11122334332 1111134
Q ss_pred eEEEEEecCCchhHHHHHHHHcCC------ceeeeeeeEEeCeecCCCC
Q 031054 104 PRIRIVVHEGRNHEVRELVKNAGL------KLYSLKRLRIGGFRLPSDL 146 (166)
Q Consensus 104 ~ll~~~l~tGR~HQIR~~l~~~G~------pI~~l~R~~~g~~~l~~~l 146 (166)
..+++.--.|- .||..+.-+|. .+..|.|++.|+|++++.+
T Consensus 167 ~~~~v~cskGT--YIRsL~~DiG~~Lg~~a~~~~LrRt~~G~f~l~~a~ 213 (305)
T PRK14123 167 FKIRVICGKGT--YIRTLATDIGVKLGFPAHMSKLTRIESGGFVLKDSL 213 (305)
T ss_pred EEEEEEeCCCc--CHHHHHHHHHHHHCCCEEEEEEEeEEECCCchHHcC
Confidence 45666666664 89999887775 5689999999999996444
No 36
>PRK00130 truB tRNA pseudouridine synthase B; Provisional
Probab=96.78 E-value=0.016 Score=48.31 Aligned_cols=133 Identities=20% Similarity=0.312 Sum_probs=78.2
Q ss_pred cchHHHHHHHhhcCCCCCCCCeeecCCCCcCCceeeeeeCCH--HHHHHhhcCCCCCCeEEEEEEe-cc-----------
Q 031054 2 SLFDDYLKSWDKRNPGLPRPRLFTVGRLDVATTGLIIVTNDG--DFAQAVSHPSSKLQKEYIATID-GA----------- 67 (166)
Q Consensus 2 sl~d~~~~~~~~~~~~~~~~~l~~vhRLD~~TSGlll~ak~~--~~~~~l~~~~~~i~K~Y~a~v~-g~----------- 67 (166)
|..| +...+++.+.. .++...|-||-.+||+|+++-.. .+...+. .-.|+|.|.+. |.
T Consensus 14 tS~d-vv~~vrr~~~~---kKvGH~GTLDP~AtGvL~v~vG~aTkl~~~l~----~~~K~Y~a~~~lG~~TdT~D~~G~i 85 (290)
T PRK00130 14 TSFD-VVRKIRKIAKI---KKVGHTGTLDPLASGVLPVCLGKATKIVDYLM----EGKKTYRAEIKLGVETDTYDREGEI 85 (290)
T ss_pred CHHH-HHHHHHHHhCC---CccCcCCCCCCCCeeEEEEEEChhhhhHHHhc----cCCcEEEEEEEECCcccCCCCCCCE
Confidence 4455 44555554432 47889999999999999987663 2333333 35899999764 21
Q ss_pred --------cChhhhhh----hh----------cceeeCCc-----------------ccceeEEEEcCCCCCCCceEEEE
Q 031054 68 --------VNKRHLIA----IS----------EGTVIEGT-----------------HCTPDVVELLPPQPDIPRPRIRI 108 (166)
Q Consensus 68 --------~~~~~~~~----~~----------~~~~~~~~-----------------~~~~~~~~~~~~~~~~~~~ll~~ 108 (166)
++.+.+.. +. ..+.++|. ....-.+++++.. .+...+++
T Consensus 86 ~~~~~~~~~t~~~l~~~l~~f~G~i~Q~PP~ySAvKv~GkraYelAR~G~~ve~~~r~v~I~~i~l~~~~--~~~~~~~v 163 (290)
T PRK00130 86 LKEKEVSHLTEEEIREAILSFQGEIDQVPPMYSALKINGKKLYELARQGIEVEREARKITIYDIEILEID--LPYVIFDV 163 (290)
T ss_pred EEecCCCCCCHHHHHHHHHHccCeEEEECChHHeEecCCHhHHHHHHCCCccccCceEEEEEEEEEEEEe--CCeEEEEE
Confidence 22332221 10 01112221 1111233444332 23455666
Q ss_pred EecCCchhHHHHHHHHcCC------ceeeeeeeEEeCeecCCCC
Q 031054 109 VVHEGRNHEVRELVKNAGL------KLYSLKRLRIGGFRLPSDL 146 (166)
Q Consensus 109 ~l~tGR~HQIR~~l~~~G~------pI~~l~R~~~g~~~l~~~l 146 (166)
.--.| --||..+.-+|. .+..|.|+++|+|++++.+
T Consensus 164 ~cskG--TYIRsL~~Dig~~Lg~~a~~~~LrRt~~G~f~~~~a~ 205 (290)
T PRK00130 164 KCSKG--TYIRSLCFDIGEKLNCGAYMWNLIRTETGPFNIENSI 205 (290)
T ss_pred EECCC--CCHHHHHHHHHHHHCCCEEEEEEEeEEECCCCHHHcC
Confidence 66666 489998887764 5699999999999996443
No 37
>PRK04099 truB tRNA pseudouridine synthase B; Provisional
Probab=96.74 E-value=0.018 Score=47.56 Aligned_cols=130 Identities=26% Similarity=0.259 Sum_probs=76.5
Q ss_pred cchHHHHHHHhhcCCCCCCCCeeecCCCCcCCceeeeeeCCHH--HHHHhhcCCCCCCeEEEEEEe-cc-----------
Q 031054 2 SLFDDYLKSWDKRNPGLPRPRLFTVGRLDVATTGLIIVTNDGD--FAQAVSHPSSKLQKEYIATID-GA----------- 67 (166)
Q Consensus 2 sl~d~~~~~~~~~~~~~~~~~l~~vhRLD~~TSGlll~ak~~~--~~~~l~~~~~~i~K~Y~a~v~-g~----------- 67 (166)
|..| +...+++.+.. .++...|-||-.+||||+++-... +...+. ...|+|.|.+. |.
T Consensus 14 tS~~-vv~~ikk~~~~---kKvGH~GTLDP~AtGvLiv~iG~aTKl~~~l~----~~~K~Y~a~~~lG~~TdT~D~e~i~ 85 (273)
T PRK04099 14 SSNA-FLSRLKRKYGV---KKAGFSGTLDPFAKGVLIVAFGQYTKLFRFLK----KTPKTYRATLWLGASSPSLDIENIE 85 (273)
T ss_pred CHHH-HHHHHHHHhCC---CccccCccCCCCCeeEEEEEEChHhhhHHHhc----cCCceEEEEEEECCcccCCCCcceE
Confidence 4455 45555554432 478899999999999999977643 233333 35899999763 21
Q ss_pred -------cChhhhhh----hhc----------ceeeCCc-----------------ccceeEEEEcCCCCCCCceEEEEE
Q 031054 68 -------VNKRHLIA----ISE----------GTVIEGT-----------------HCTPDVVELLPPQPDIPRPRIRIV 109 (166)
Q Consensus 68 -------~~~~~~~~----~~~----------~~~~~~~-----------------~~~~~~~~~~~~~~~~~~~ll~~~ 109 (166)
++.+.+.. +.. .+.++|. ....-.+++++.. .+...+++.
T Consensus 86 ~~~~~~~~~~~~i~~~l~~f~G~i~Q~PP~ySAvKv~GkraYelAR~G~~ve~~~r~v~I~~~~ll~~~--~p~~~f~v~ 163 (273)
T PRK04099 86 SIQIIKPFDKDLIEKILKSLQGEISYTPPKFSAKKINGKRAYELARKGEEFELKPITMEIFDCKLLSYN--HPFLTFEIT 163 (273)
T ss_pred EeccCCCCCHHHHHHHHHhCcceEEEeCChhhEEeeCCHhHHHHHhCCcccccCceeEEEEEEEEEEEe--CCEEEEEEE
Confidence 22222221 100 1112221 1111233444432 234556666
Q ss_pred ecCCchhHHHHHHHHcCC------ceeeeeeeEEeCeecC
Q 031054 110 VHEGRNHEVRELVKNAGL------KLYSLKRLRIGGFRLP 143 (166)
Q Consensus 110 l~tGR~HQIR~~l~~~G~------pI~~l~R~~~g~~~l~ 143 (166)
--.| --||..+..+|. .+..|.|++.|+|.++
T Consensus 164 cs~G--TYIRSL~~Dig~~Lg~~a~m~~LrRt~~G~f~~~ 201 (273)
T PRK04099 164 VSEG--AYIRSLGELIAKKLGVNGTLSSLERLSEGKFVYE 201 (273)
T ss_pred ECCC--CCHHHHHHHHHHHHCCCEEEEEEEeEEECCCcHH
Confidence 6566 669988887765 4599999999999995
No 38
>PRK02193 truB tRNA pseudouridine synthase B; Provisional
Probab=96.72 E-value=0.024 Score=46.98 Aligned_cols=132 Identities=27% Similarity=0.429 Sum_probs=75.9
Q ss_pred cchHHHHHHHhhcCCCCCCCCeeecCCCCcCCceeeeeeCCH--HHHHHhhcCCCCCCeEEEEEEe-c----------c-
Q 031054 2 SLFDDYLKSWDKRNPGLPRPRLFTVGRLDVATTGLIIVTNDG--DFAQAVSHPSSKLQKEYIATID-G----------A- 67 (166)
Q Consensus 2 sl~d~~~~~~~~~~~~~~~~~l~~vhRLD~~TSGlll~ak~~--~~~~~l~~~~~~i~K~Y~a~v~-g----------~- 67 (166)
|..| +...+++.+.. .++...|-||-.+||+|+++-.. .+...+ ....|+|.|.+. | .
T Consensus 12 tS~d-vv~~vrr~~~~---kKvGH~GTLDP~AtGvL~v~vG~aTkl~~~l----~~~~K~Y~a~~~lG~~TdT~D~~G~i 83 (279)
T PRK02193 12 SSFK-FIKNFAKTNNI---KKIGHTGTLDPLASGLLLVATDEDTKLIDYL----DQKDKTYIAKIKFGFISTTYDSEGQI 83 (279)
T ss_pred CHHH-HHHHHHHHcCC---CccccCccCCCcCeeEEEEEEChhhhhhHHh----ccCCcEEEEEEEeCCcccCCCCCCCE
Confidence 4555 44555554432 47899999999999999987663 233334 357899999762 2 1
Q ss_pred --------cChhhhhh----hh----------cceeeCCc-----------------ccceeEEEEcCCCCCCCceEEEE
Q 031054 68 --------VNKRHLIA----IS----------EGTVIEGT-----------------HCTPDVVELLPPQPDIPRPRIRI 108 (166)
Q Consensus 68 --------~~~~~~~~----~~----------~~~~~~~~-----------------~~~~~~~~~~~~~~~~~~~ll~~ 108 (166)
++.+.+.. +. ..+.++|. +.....++++......+...++|
T Consensus 84 ~~~~~~~~~~~~~l~~~l~~f~G~i~Q~PP~ySAvKv~GkraYelAR~G~~ve~~~r~v~I~~i~ll~~~~~~~~~~~~v 163 (279)
T PRK02193 84 INVSQNIKVTKENLEEALNNLVGSQKQVPPVFSAKKVNGKRAYDLARQGKQIELKPIEIKISKIELLNFDEKLQNCVFMW 163 (279)
T ss_pred EeecCCCCCCHHHHHHHHHhCcCeEEEeCChHHeEeeCCHhHHHHHhCCceeccCCeeEEEEEEEEEEEcCCCceEEEEE
Confidence 12222211 10 01112221 11122344444321112334555
Q ss_pred EecCCchhHHHHHHHHcCC------ceeeeeeeEEeCeecC
Q 031054 109 VVHEGRNHEVRELVKNAGL------KLYSLKRLRIGGFRLP 143 (166)
Q Consensus 109 ~l~tGR~HQIR~~l~~~G~------pI~~l~R~~~g~~~l~ 143 (166)
.--.| -.||..+.-+|. .+..|.|+++|+++++
T Consensus 164 ~cskG--TYIRsL~~DiG~~Lg~~a~~~~LrRt~~G~f~~~ 202 (279)
T PRK02193 164 VVSRG--TYIRSLIHDLGKMLKTGAYMSDLERTKIGNLDKN 202 (279)
T ss_pred EECCC--cCHHHHHHHHHHHHCCCEEEEEEEeEEECCcCHH
Confidence 55455 789998887765 5689999999999984
No 39
>PRK02484 truB tRNA pseudouridine synthase B; Provisional
Probab=96.69 E-value=0.029 Score=46.79 Aligned_cols=133 Identities=18% Similarity=0.217 Sum_probs=77.8
Q ss_pred cchHHHHHHHhhcCCCCCCCCeeecCCCCcCCceeeeeeCCH--HHHHHhhcCCCCCCeEEEEEEe-cc-----------
Q 031054 2 SLFDDYLKSWDKRNPGLPRPRLFTVGRLDVATTGLIIVTNDG--DFAQAVSHPSSKLQKEYIATID-GA----------- 67 (166)
Q Consensus 2 sl~d~~~~~~~~~~~~~~~~~l~~vhRLD~~TSGlll~ak~~--~~~~~l~~~~~~i~K~Y~a~v~-g~----------- 67 (166)
|..| +...+++.+.. .++...|-||-.+||+|+++-.. .+...+. ...|+|.|.+. |.
T Consensus 15 TS~d-vv~~vrr~l~~---kKvGH~GTLDP~AtGvL~i~vG~aTkl~~~l~----~~~K~Y~a~~~lG~~TdT~D~~G~v 86 (294)
T PRK02484 15 TSHD-AVFKLRKILQT---KKIGHGGTLDPDVVGVLPIAVGKATRLIEYMT----EAGKVYEGEITLGYSTTTEDASGEV 86 (294)
T ss_pred CHHH-HHHHHHHHhCC---CccccCCCCCCCCeeEEEEEEChhhhhhHHhc----cCCcEEEEEEEECCcccCCCCCCCE
Confidence 4455 44445444432 47899999999999999987663 3344444 35599999874 11
Q ss_pred ---------cChhhhhh----hh----------cceeeCCc-----------------ccceeEEEEcC---CCC-CCCc
Q 031054 68 ---------VNKRHLIA----IS----------EGTVIEGT-----------------HCTPDVVELLP---PQP-DIPR 103 (166)
Q Consensus 68 ---------~~~~~~~~----~~----------~~~~~~~~-----------------~~~~~~~~~~~---~~~-~~~~ 103 (166)
++.+.+.. +. ..+.++|. +.....+++++ ... ..+.
T Consensus 87 i~~~~~~~~~~~~~l~~~l~~f~G~i~Q~PP~ySAvKv~GkraYelAR~G~~ve~~~r~v~I~~i~l~~~~~~~~~~~~~ 166 (294)
T PRK02484 87 VAETPLTQPLTEEEVDQAMTSFTGKITQIPPMYSAVKVNGKKLYEYARAGEEVERPKRQVTIYQFERTSPLSFDEDGLCR 166 (294)
T ss_pred EEeccCCCCCCHHHHHHHHHhccCeEEEeCChhHeEeeCCHhHHHHHHCCCccccCceEEEEEEEEEeccccccccCCce
Confidence 23333221 10 01112221 11122344432 111 1234
Q ss_pred eEEEEEecCCchhHHHHHHHHcCC------ceeeeeeeEEeCeecCC
Q 031054 104 PRIRIVVHEGRNHEVRELVKNAGL------KLYSLKRLRIGGFRLPS 144 (166)
Q Consensus 104 ~ll~~~l~tGR~HQIR~~l~~~G~------pI~~l~R~~~g~~~l~~ 144 (166)
..+++.--.|- .||..+.-+|. .+..|.|+++|+|.+++
T Consensus 167 ~~~~v~cskGT--YIRsL~~DiG~~Lg~~a~~~~L~Rt~~G~f~l~~ 211 (294)
T PRK02484 167 FSFRVACSKGT--YVRTLAVDLGEKLGYAAHMSFLTRTASAGLTLEQ 211 (294)
T ss_pred EEEEEEeCCCC--CHHHHHHHHHHHHCCCEEEEEEEeEEECCCcHHH
Confidence 56777776674 89998887765 56899999999999964
No 40
>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=96.65 E-value=0.033 Score=46.78 Aligned_cols=134 Identities=16% Similarity=0.074 Sum_probs=78.0
Q ss_pred CCeeecCCCCcCCceeeeeeCCH--HHHHHhhcCCCCCCeEEEEEEe-----------c---------ccChhhhhh---
Q 031054 21 PRLFTVGRLDVATTGLIIVTNDG--DFAQAVSHPSSKLQKEYIATID-----------G---------AVNKRHLIA--- 75 (166)
Q Consensus 21 ~~l~~vhRLD~~TSGlll~ak~~--~~~~~l~~~~~~i~K~Y~a~v~-----------g---------~~~~~~~~~--- 75 (166)
.++...|-||-.+||||+++-.. .+...+.+ ..|+|.+... | .++.+.+..
T Consensus 56 ~KiGH~GTLDPlAsGVLvvgvG~aTK~l~~~l~----~~K~Y~~~~~lG~~TdT~D~eG~Ii~~~~~~~it~e~i~~~l~ 131 (312)
T cd02867 56 LKIGHGGTLDPLATGVLVVGVGAGTKQLQDYLS----CSKTYEATGLFGASTTTYDREGKILKKKPYSHITREDIEEVLA 131 (312)
T ss_pred cccccccccCCccceeEEEEECcHHHHHHHHhc----CCceEEEEEEeCCcccCCCCCCCEEEecCCCCCCHHHHHHHHH
Confidence 57899999999999999986653 33444442 8999999763 2 123333321
Q ss_pred -h-------------------------hcceeeCCc----ccceeEEEEcCCCCCCCceEEEEEecCCchhHHHHHHHHc
Q 031054 76 -I-------------------------SEGTVIEGT----HCTPDVVELLPPQPDIPRPRIRIVVHEGRNHEVRELVKNA 125 (166)
Q Consensus 76 -~-------------------------~~~~~~~~~----~~~~~~~~~~~~~~~~~~~ll~~~l~tGR~HQIR~~l~~~ 125 (166)
+ ++|..++-. ......++++......+...+++.-..| -.||..+..+
T Consensus 132 ~F~G~i~Q~PP~ySAvKv~GkrlYeyAR~G~~v~~~~~~R~V~I~~~~l~~~~~~~~~~~~~v~cskG--TYIRsL~~Di 209 (312)
T cd02867 132 KFRGDIKQVPPLYSALKMDGKRLYEYAREGKPLPRPIERRQVVVSELLVKDWIEPGPLFTRTVEEEGK--QYERSVVKML 209 (312)
T ss_pred hcceeeeeeCcchheeeeCCHHHHHHHhCCccccCCCCCceEEEEEEEEEeccCCCCeEEEEEEeCCc--CCHHHHHHHH
Confidence 1 111111110 0111123333322112334455554444 5789988877
Q ss_pred CC------ceeeeeeeEEeCeecCCCCCCCcEEEcCHHHHh
Q 031054 126 GL------KLYSLKRLRIGGFRLPSDLGIGMHVELKQSDLK 160 (166)
Q Consensus 126 G~------pI~~l~R~~~g~~~l~~~l~~G~~r~l~~~e~~ 160 (166)
|. .+..|.|++.|++.++........+.+.+.|-.
T Consensus 210 g~~Lg~~a~~~~L~Rt~~g~f~~~~~~~~~~~~~~~~~~~~ 250 (312)
T cd02867 210 GKELKTFAEVTELTATAEGDPVEEVEATHEESKRKSEVEEE 250 (312)
T ss_pred HHHhCCCeEEEEEEeeeecCcccccccccCCCcccChhhhc
Confidence 75 468999999999998534555556666666544
No 41
>PRK14124 tRNA pseudouridine synthase B; Provisional
Probab=96.60 E-value=0.018 Score=48.25 Aligned_cols=135 Identities=19% Similarity=0.300 Sum_probs=78.6
Q ss_pred cchHHHHHHHhhcCCCCCCCCeeecCCCCcCCceeeeeeCCH--HHHHHhhcCCCCCCeEEEEEEe-----------cc-
Q 031054 2 SLFDDYLKSWDKRNPGLPRPRLFTVGRLDVATTGLIIVTNDG--DFAQAVSHPSSKLQKEYIATID-----------GA- 67 (166)
Q Consensus 2 sl~d~~~~~~~~~~~~~~~~~l~~vhRLD~~TSGlll~ak~~--~~~~~l~~~~~~i~K~Y~a~v~-----------g~- 67 (166)
|..| +...+++.+.. .++...|-||-.+||+|+++-.. .+...+.+ -.|+|.|.+. |.
T Consensus 15 TS~d-vv~~vrr~l~~---kKvGH~GTLDP~AtGvL~v~vG~aTkl~~~l~~----~~K~Y~a~~~lG~~TdT~D~~G~v 86 (308)
T PRK14124 15 TSHD-VVDEVRKKLKT---RKVGHAGTLDPFATGVLIVGVNKATRLLEYLKN----EKKVYYVKMRLGLITETFDITGEV 86 (308)
T ss_pred CHHH-HHHHHHHHcCC---CccCcCcCCCCCCcEEEEEEEChHHhhhHHHhc----CCceEEEEEEeCccccCCCCCCCE
Confidence 4455 44555554432 46789999999999999986663 34444443 4899999874 11
Q ss_pred -------cChhhhhh----hh----------cceeeCCc-----------------ccceeEEEEcCCCCCCCceEEEEE
Q 031054 68 -------VNKRHLIA----IS----------EGTVIEGT-----------------HCTPDVVELLPPQPDIPRPRIRIV 109 (166)
Q Consensus 68 -------~~~~~~~~----~~----------~~~~~~~~-----------------~~~~~~~~~~~~~~~~~~~ll~~~ 109 (166)
++.+.+.. +. ..+.++|. ......++++... .+...+++.
T Consensus 87 i~~~~~~~~~~~i~~~l~~f~G~i~Q~PP~ySAvKv~GkraYelAR~G~~ve~~~r~v~I~~i~ll~~~--~~~~~~~v~ 164 (308)
T PRK14124 87 VEERECNVTEEEIREAIFSFVGEYKQVPPAYSAKKYKGERLYKLAREGKIINLPPKEVKIYEIWDISIE--GPDVSFRVE 164 (308)
T ss_pred EEecCCCCCHHHHHHHHHhCcCeEEEeCCchHeEEECChhHHHHHhCCCccccCceeeEEEEEEEEEEe--CCeEEEEEE
Confidence 22222221 10 01122221 1111233444332 234556666
Q ss_pred ecCCchhHHHHHHHHcCC------ceeeeeeeEEeCeecCCCCCC
Q 031054 110 VHEGRNHEVRELVKNAGL------KLYSLKRLRIGGFRLPSDLGI 148 (166)
Q Consensus 110 l~tGR~HQIR~~l~~~G~------pI~~l~R~~~g~~~l~~~l~~ 148 (166)
--.| --||..+..+|. .+..|.|+++|+|+++..+..
T Consensus 165 cskG--TYIRsL~~DiG~~Lg~~a~m~~LrRt~~G~f~l~~a~~l 207 (308)
T PRK14124 165 VSPG--TYIRSLCMDIGYKLGCGATAVELVRLSVGKFSIEDSINV 207 (308)
T ss_pred ECCC--CCHHHHHHHHHHHHCCCEEEEEEEeEEECCCcHHHccCH
Confidence 6566 668888776654 469999999999999644443
No 42
>PRK01851 truB tRNA pseudouridine synthase B; Provisional
Probab=96.58 E-value=0.026 Score=47.28 Aligned_cols=133 Identities=26% Similarity=0.381 Sum_probs=78.2
Q ss_pred cchHHHHHHHhhcCCCCCCCCeeecCCCCcCCceeeeeeCCH--HHHHHhhcCCCCCCeEEEEEEe-cc-----------
Q 031054 2 SLFDDYLKSWDKRNPGLPRPRLFTVGRLDVATTGLIIVTNDG--DFAQAVSHPSSKLQKEYIATID-GA----------- 67 (166)
Q Consensus 2 sl~d~~~~~~~~~~~~~~~~~l~~vhRLD~~TSGlll~ak~~--~~~~~l~~~~~~i~K~Y~a~v~-g~----------- 67 (166)
|..| +...+++.+.. .++...|-||-.+||||+++-.. .+...+. ...|+|.|.+. |.
T Consensus 28 TS~d-vv~~vrr~l~~---kKvGH~GTLDP~AtGvL~v~vG~aTkl~~~l~----~~~K~Y~~~~~lG~~TdT~D~~G~v 99 (303)
T PRK01851 28 SSND-ALQRAKRLLRA---KKAGHTGTLDPLATGLLPLCFGEATKFSQDLL----DADKTYEATLRLGVRTSTGDAEGEV 99 (303)
T ss_pred CHHH-HHHHHHHHhCc---ccCCCCCCCCCCCceEEEEEECHHHhhhHHhc----ccCeEEEEEEEECCccCCCCCCCCE
Confidence 4555 44555554432 46788999999999999987663 3344444 35599999763 21
Q ss_pred -------cChhhhhh----hhc----------ceeeCCc-----------------ccceeEEEEcCCCCCCCceEEEEE
Q 031054 68 -------VNKRHLIA----ISE----------GTVIEGT-----------------HCTPDVVELLPPQPDIPRPRIRIV 109 (166)
Q Consensus 68 -------~~~~~~~~----~~~----------~~~~~~~-----------------~~~~~~~~~~~~~~~~~~~ll~~~ 109 (166)
++.+.+.. +.. .+.++|. ......++++... .+...+++.
T Consensus 100 ~~~~~~~~t~~~i~~~l~~f~G~i~Q~PP~ySAvKv~GkraYelAR~G~~ve~~~R~v~I~~i~ll~~~--~~~~~~~v~ 177 (303)
T PRK01851 100 LATRPVDCDPAALEAALARFTGEIRQVPPMYSALKKDGKPLYEYARAGITVEREARDVTIHALDLLACD--LPDVTIRVT 177 (303)
T ss_pred EeecCCCCCHHHHHHHHHhccCeeeeeCCchheEeeCCeeHHHHHhCCCccccCCcceEEEEEEEEEEe--CCEEEEEEE
Confidence 12222211 100 1112221 1112234444432 234566666
Q ss_pred ecCCchhHHHHHHHHcCC------ceeeeeeeEEeCeecCCCC
Q 031054 110 VHEGRNHEVRELVKNAGL------KLYSLKRLRIGGFRLPSDL 146 (166)
Q Consensus 110 l~tGR~HQIR~~l~~~G~------pI~~l~R~~~g~~~l~~~l 146 (166)
--.| --||..+.-+|. .+..|.|+++|+|.+++.+
T Consensus 178 cskG--TYIRsL~~DiG~~Lg~~a~~~~LrRt~~G~f~~~~a~ 218 (303)
T PRK01851 178 CSKG--TYIRTLAEDIGEALGCGAHLTALRRTGVGGLTLEQAV 218 (303)
T ss_pred ECCC--CCHHHHHHHHHHHHCCCEEEEEEEeEEECCCchHHcC
Confidence 6666 489998887765 4699999999999996433
No 43
>PRK14846 truB tRNA pseudouridine synthase B; Provisional
Probab=96.54 E-value=0.033 Score=47.32 Aligned_cols=136 Identities=18% Similarity=0.232 Sum_probs=76.8
Q ss_pred cchHHHHHHHhhcCCCCCCCCeeecCCCCcCCceeeeeeCCH--HHHHHhhcCCCCCCeEEEEEEe-c----------c-
Q 031054 2 SLFDDYLKSWDKRNPGLPRPRLFTVGRLDVATTGLIIVTNDG--DFAQAVSHPSSKLQKEYIATID-G----------A- 67 (166)
Q Consensus 2 sl~d~~~~~~~~~~~~~~~~~l~~vhRLD~~TSGlll~ak~~--~~~~~l~~~~~~i~K~Y~a~v~-g----------~- 67 (166)
|..| +...+++.+. ..++...|-||..+||||+++-.. .+...+. ...|+|.|.+. | .
T Consensus 15 TS~d-vv~~vrk~l~---~kKVGH~GTLDP~AtGVL~i~vG~aTKl~~~l~----~~~K~Y~a~~~lG~~TDT~D~eG~i 86 (345)
T PRK14846 15 SSAQ-LVSIVKKILG---KTKIGHAGTLDVEAEGILPFAVGEATKLIHLLI----DARKTYIFTVKFGMQTNSGDCAGKV 86 (345)
T ss_pred CHHH-HHHHHHHHhC---CCcCCcCccCCCcCceEEEEEEChhhhhhHHHh----cCCceEEEEEEECCccCCCCCCCCE
Confidence 4455 4455555443 247889999999999999986653 3444444 46788999763 2 1
Q ss_pred -------cChhhhhh----hh----------cceeeCCc-----------------ccceeEEEEcCCCCCCCceEEEEE
Q 031054 68 -------VNKRHLIA----IS----------EGTVIEGT-----------------HCTPDVVELLPPQPDIPRPRIRIV 109 (166)
Q Consensus 68 -------~~~~~~~~----~~----------~~~~~~~~-----------------~~~~~~~~~~~~~~~~~~~ll~~~ 109 (166)
++.+++.. +. ..+.++|. ......+++++.....+...++|.
T Consensus 87 i~~~~~~~~~e~l~~~L~~f~G~i~Q~PP~ySAvKv~GkraYelARkG~~Vel~~R~V~I~~i~ll~f~~~~~~~~~~v~ 166 (345)
T PRK14846 87 IATKDCIPSQEEAYAVCSKFIGNVTQIPPAFSALKVNGVRAYKLAREGKKVELKPRNITIYDLKCLNFDEKNATATYYTE 166 (345)
T ss_pred EEecCCCCCHHHHHHHHHhCcceEEeeCChhheEeECChhHHHHHhCCCccccCceeEEEEEEEEEEEcCCCcEEEEEEE
Confidence 11122211 10 01112221 111123344433211123345555
Q ss_pred ecCCchhHHHHHHHHcCC------ceeeeeeeEEeCeecCCCCC
Q 031054 110 VHEGRNHEVRELVKNAGL------KLYSLKRLRIGGFRLPSDLG 147 (166)
Q Consensus 110 l~tGR~HQIR~~l~~~G~------pI~~l~R~~~g~~~l~~~l~ 147 (166)
--.| -.||..+.-+|. .+..|.|+++|++.+++.++
T Consensus 167 CSkG--TYIRSLa~DIG~~Lg~~A~l~~LrRtr~G~F~l~~ai~ 208 (345)
T PRK14846 167 CSKG--TYIRTLAEDLALSLQSLGFVIELRRTQVGIFKEENAIR 208 (345)
T ss_pred ECCC--CcHHHHHHHHHHHHCCCEEEeEEEeEEECCCcHHHcCC
Confidence 5555 779988877665 56999999999999964443
No 44
>PRK03287 truB tRNA pseudouridine synthase B; Provisional
Probab=96.54 E-value=0.02 Score=47.88 Aligned_cols=55 Identities=20% Similarity=0.279 Sum_probs=37.3
Q ss_pred cchHHHHHHHhhcCCCCCCCCeeecCCCCcCCceeeeeeCCH--HHHHHhhcCCCCCCeEEEEEE
Q 031054 2 SLFDDYLKSWDKRNPGLPRPRLFTVGRLDVATTGLIIVTNDG--DFAQAVSHPSSKLQKEYIATI 64 (166)
Q Consensus 2 sl~d~~~~~~~~~~~~~~~~~l~~vhRLD~~TSGlll~ak~~--~~~~~l~~~~~~i~K~Y~a~v 64 (166)
|..| +...+++.+.. .++...|-||-.+||||+++-.. .+...+. ...|+|.|.+
T Consensus 21 TS~d-vv~~vrr~~~~---kKvGH~GTLDP~AtGvL~i~vG~aTKl~~~l~----~~~K~Y~a~~ 77 (298)
T PRK03287 21 TSHD-VVARCRRLFGT---RKVGHAGTLDPMATGVLVLGVERATKLLGHLT----LTDKSYTATI 77 (298)
T ss_pred CHHH-HHHHHHHHhCC---CCCCcCccCCCcceeEEEEEeChhhhhhHHHh----cCCcEEEEEE
Confidence 4455 44455454432 47889999999999999987663 3344444 3589999976
No 45
>PRK02755 truB tRNA pseudouridine synthase B; Provisional
Probab=96.50 E-value=0.047 Score=45.58 Aligned_cols=133 Identities=23% Similarity=0.322 Sum_probs=77.6
Q ss_pred cchHHHHHHHhhcCCCCCCCCeeecCCCCcCCceeeeeeCCHH--HHHHhhcCCCCCCeEEEEEEe-cc-----------
Q 031054 2 SLFDDYLKSWDKRNPGLPRPRLFTVGRLDVATTGLIIVTNDGD--FAQAVSHPSSKLQKEYIATID-GA----------- 67 (166)
Q Consensus 2 sl~d~~~~~~~~~~~~~~~~~l~~vhRLD~~TSGlll~ak~~~--~~~~l~~~~~~i~K~Y~a~v~-g~----------- 67 (166)
|..| +...+++.+.. .++...|-||-.+||+|+++-... +...|. . .|+|.|.+. |.
T Consensus 15 TS~d-vv~~vrr~~~~---kKvGH~GTLDP~AtGvL~i~vG~aTkl~~~l~----~-~K~Y~a~~~lG~~TdT~D~~G~v 85 (295)
T PRK02755 15 TSHD-CVARLRRLLRL---KRVGHGGTLDPAATGVLPIALGKATRLLPYLP----G-EKTYRGTIRFGVRTSTDDLQGEI 85 (295)
T ss_pred CHHH-HHHHHHHHhCC---CccccCCCCCCcCeeEEEEEEChhhhhHHHhC----C-CcEEEEEEEECCcccCCCCCCCE
Confidence 4455 44555554432 478899999999999999876632 333332 3 699999762 21
Q ss_pred --------cChhhhhh----hh----------cceeeCCc-----------------ccceeEEEEcCCCC-CCCceEEE
Q 031054 68 --------VNKRHLIA----IS----------EGTVIEGT-----------------HCTPDVVELLPPQP-DIPRPRIR 107 (166)
Q Consensus 68 --------~~~~~~~~----~~----------~~~~~~~~-----------------~~~~~~~~~~~~~~-~~~~~ll~ 107 (166)
++.+.+.. +. ..+.++|. +.....+++++... ..+...++
T Consensus 86 ~~~~~~~~~~~~~l~~~l~~f~G~i~Q~PP~ySAvKv~G~r~Y~lAR~G~~ve~~~r~v~I~~~~l~~~~~~~~~~~~~~ 165 (295)
T PRK02755 86 LSSQPWPHLSLAEIETALPQFRGKIEQRPPQYSAIQVDGERLYALARRGETMELPARTVTIFRLQLLDWRPGDQPELDLE 165 (295)
T ss_pred EEecCCCCCCHHHHHHHHHhccCeEEEeCChhheEeeCCHhHHHHHHCCCccccCceEEEEEEEEEEEEcCCCCceEEEE
Confidence 22222221 10 01122221 11122344444321 12345566
Q ss_pred EEecCCchhHHHHHHHHcCC------ceeeeeeeEEeCeecCCC
Q 031054 108 IVVHEGRNHEVRELVKNAGL------KLYSLKRLRIGGFRLPSD 145 (166)
Q Consensus 108 ~~l~tGR~HQIR~~l~~~G~------pI~~l~R~~~g~~~l~~~ 145 (166)
+.--.| --||..+.-+|. .+..|.|++.|+|++++.
T Consensus 166 v~cskG--TYIRsL~~DiG~~Lg~~a~m~~LrRt~~G~f~~~~a 207 (295)
T PRK02755 166 IHCGAG--TYIRSLARDLGAVLGTGGTLAALRRTQSLGFHLAQS 207 (295)
T ss_pred EEECCC--cCHHHHHHHHHHHHCCCEEEEEEEeEEECCCcHHHc
Confidence 666667 679988887764 579999999999999643
No 46
>PRK04270 H/ACA RNA-protein complex component Cbf5p; Reviewed
Probab=96.49 E-value=0.028 Score=46.92 Aligned_cols=131 Identities=21% Similarity=0.209 Sum_probs=74.5
Q ss_pred cchHHHHHHHhhcCCCCCCCCeeecCCCCcCCceeeeeeCCH--HHHHHhhcCCCCCCeEEEEEEe-c-ccChhhhhhh-
Q 031054 2 SLFDDYLKSWDKRNPGLPRPRLFTVGRLDVATTGLIIVTNDG--DFAQAVSHPSSKLQKEYIATID-G-AVNKRHLIAI- 76 (166)
Q Consensus 2 sl~d~~~~~~~~~~~~~~~~~l~~vhRLD~~TSGlll~ak~~--~~~~~l~~~~~~i~K~Y~a~v~-g-~~~~~~~~~~- 76 (166)
|..| +....++.+. ..++...|-||..+||+|+++-.. .+...+. ...|+|.|.+. | .++.+.+...
T Consensus 34 tS~~-~v~~~r~~~~---~kkvGH~GTLDp~A~GvL~v~~g~atk~~~~~~----~~~K~Y~~~~~~g~~~~~~~~~~~l 105 (300)
T PRK04270 34 TSHE-VAAWVRDILG---VEKAGHGGTLDPKVTGVLPVALGKATKVVQALL----ESGKEYVCVMHLHGDVPEEDIRKVF 105 (300)
T ss_pred CHHH-HHHHHHHHhc---cccccCCCCCCCcCeEEEEEEEChHhhhhHHhc----cCCcEEEEEEEECCCCCHHHHHHHH
Confidence 4455 3444444333 246789999999999999986653 3344444 35599998764 3 3455544321
Q ss_pred hc--ce--ee---------CCcccceeEEEEcCCCCCCCceEEEEEecCCchhHHHHHHHHcC------CceeeeeeeEE
Q 031054 77 SE--GT--VI---------EGTHCTPDVVELLPPQPDIPRPRIRIVVHEGRNHEVRELVKNAG------LKLYSLKRLRI 137 (166)
Q Consensus 77 ~~--~~--~~---------~~~~~~~~~~~~~~~~~~~~~~ll~~~l~tGR~HQIR~~l~~~G------~pI~~l~R~~~ 137 (166)
.. |. +. .........++++... .+...+++.-..| --||..+.-+| ..+..|.|+++
T Consensus 106 ~~~~g~i~Q~pP~~SA~k~~~r~v~I~~i~~~~~~--~~~~~~~v~cs~G--tYIRsl~~dig~~Lg~~a~~~~L~R~~~ 181 (300)
T PRK04270 106 KEFTGEIYQKPPLKSAVKRRLRVRTIYELEILEID--GRDVLFRVRCESG--TYIRKLCHDIGLALGTGAHMQELRRTRT 181 (300)
T ss_pred HHCCCcEEeECCHHHhccCCceEEEEEEEEEEEec--CCEEEEEEEECCc--eEHHHHHHHHHHHHCCCeEEEEEEeEEE
Confidence 11 10 11 0111111233444322 1234455554444 67888776655 34689999999
Q ss_pred eCeecCC
Q 031054 138 GGFRLPS 144 (166)
Q Consensus 138 g~~~l~~ 144 (166)
|+|++++
T Consensus 182 g~f~~~~ 188 (300)
T PRK04270 182 GPFTEED 188 (300)
T ss_pred CCCCcch
Confidence 9999963
No 47
>PRK05033 truB tRNA pseudouridine synthase B; Provisional
Probab=96.47 E-value=0.048 Score=45.88 Aligned_cols=133 Identities=21% Similarity=0.254 Sum_probs=78.4
Q ss_pred cchHHHHHHHhhcCCCCCCCCeeecCCCCcCCceeeeeeCCH--HHHHHhhcCCCCCCeEEEEEEe-cc-----------
Q 031054 2 SLFDDYLKSWDKRNPGLPRPRLFTVGRLDVATTGLIIVTNDG--DFAQAVSHPSSKLQKEYIATID-GA----------- 67 (166)
Q Consensus 2 sl~d~~~~~~~~~~~~~~~~~l~~vhRLD~~TSGlll~ak~~--~~~~~l~~~~~~i~K~Y~a~v~-g~----------- 67 (166)
|..| +...+++.+. ..++...|-||-.+||||+++-.. .+...+. .-.|+|.|.+. |.
T Consensus 22 TS~d-vv~~vrr~l~---~kKvGH~GTLDP~AtGvL~v~vG~aTkl~~~~~----~~~K~Y~a~~~lG~~TdT~D~~G~v 93 (312)
T PRK05033 22 SSND-ALQKVKRLFN---ANKAGHTGALDPLATGMLPICLGEATKFSQYLL----DSDKRYRVTARLGQRTDTSDADGEV 93 (312)
T ss_pred CHHH-HHHHHHHHhC---CCCCCCCCcCCCcCeeEEEEEECHHhhhhHHhc----CCCcEEEEEEEECCcccCCCCCCCE
Confidence 4556 4445555443 247788999999999999987663 2333333 35899999763 21
Q ss_pred -------cChhhhhh----hh----------cceeeCCc-----------------ccceeEEEEcCCCCCCCceEEEEE
Q 031054 68 -------VNKRHLIA----IS----------EGTVIEGT-----------------HCTPDVVELLPPQPDIPRPRIRIV 109 (166)
Q Consensus 68 -------~~~~~~~~----~~----------~~~~~~~~-----------------~~~~~~~~~~~~~~~~~~~ll~~~ 109 (166)
++.+.+.. +. ..+.++|. ......++++... .+...+++.
T Consensus 94 ~~~~~~~~t~~~l~~~l~~f~G~i~Q~PP~ySAvKv~GkraYelAR~G~~ve~~~r~v~I~~i~ll~~~--~~~~~~~v~ 171 (312)
T PRK05033 94 VEERPVTLSAEQLEAALEKFRGDIEQVPSMYSALKYQGQPLYEYARQGIEVEREARPITIYELELIRFE--GDELELEVH 171 (312)
T ss_pred EEeecCCCCHHHHHHHHHHCcCcEEEeCChhHeEeeCCeEHHHHHhCCcccccCceeEEEEEEEEeeEe--CCEEEEEEE
Confidence 22323221 10 01122221 1112234444432 234556666
Q ss_pred ecCCchhHHHHHHHHcCC------ceeeeeeeEEeCeecCCCC
Q 031054 110 VHEGRNHEVRELVKNAGL------KLYSLKRLRIGGFRLPSDL 146 (166)
Q Consensus 110 l~tGR~HQIR~~l~~~G~------pI~~l~R~~~g~~~l~~~l 146 (166)
--.| --||..+.-+|. .+..|.|+++|+|++++.+
T Consensus 172 cs~G--TYIRsL~~Dig~~Lg~~a~~~~LrRt~~G~f~~~~a~ 212 (312)
T PRK05033 172 CSKG--TYIRTLVDDLGEKLGCGAHVIYLRRTQVAPYPLERMV 212 (312)
T ss_pred ECCC--CCHHHHHHHHHHHHCCCEEEEEEEeEEECCccccccc
Confidence 6666 489998887765 5699999999999996433
No 48
>PRK01550 truB tRNA pseudouridine synthase B; Provisional
Probab=96.42 E-value=0.053 Score=45.45 Aligned_cols=133 Identities=21% Similarity=0.314 Sum_probs=78.1
Q ss_pred cchHHHHHHHhhcCCCCCCCCeeecCCCCcCCceeeeeeCCH--HHHHHhhcCCCCCCeEEEEEEe-c----------c-
Q 031054 2 SLFDDYLKSWDKRNPGLPRPRLFTVGRLDVATTGLIIVTNDG--DFAQAVSHPSSKLQKEYIATID-G----------A- 67 (166)
Q Consensus 2 sl~d~~~~~~~~~~~~~~~~~l~~vhRLD~~TSGlll~ak~~--~~~~~l~~~~~~i~K~Y~a~v~-g----------~- 67 (166)
|..| +...+++.+. ..++...|-||-.+||||+++-.. .++..+. .-.|+|.|.+. | .
T Consensus 14 TS~d-vv~~vrr~~~---~kKvGH~GTLDP~AtGvL~i~vG~aTkl~~~l~----~~~K~Y~a~~~lG~~TdT~D~~G~v 85 (304)
T PRK01550 14 TSHD-CVFKLRKILR---TKKVGHTGTLDPEVSGVLPICVGRATKIAEYLT----DEGKTYEGEVTLGFSTTTEDADGEV 85 (304)
T ss_pred CHHH-HHHHHHHHcC---CCCcccCCCCCCcCeeEEEEEEChhhhhhHHhc----CCCcEEEEEEEECCcccCCCCCCCE
Confidence 4555 4445545443 247889999999999999987663 3344444 35899999764 1 1
Q ss_pred ---------cChhhhhh----hh----------cceeeCCc-----------------ccceeEEEEcCCC----CCCCc
Q 031054 68 ---------VNKRHLIA----IS----------EGTVIEGT-----------------HCTPDVVELLPPQ----PDIPR 103 (166)
Q Consensus 68 ---------~~~~~~~~----~~----------~~~~~~~~-----------------~~~~~~~~~~~~~----~~~~~ 103 (166)
++.+.+.. +. ..+.++|. ......+++++.. ...+.
T Consensus 86 ~~~~~~~~~~~~~~i~~~l~~f~G~i~Q~PP~ySAvKv~Gkr~YelAR~G~~ve~~~r~v~I~~i~ll~~~~~~~~~~~~ 165 (304)
T PRK01550 86 VETKPVDRPITREEIEAALASLTGTIEQIPPMYSAVKVNGKKLYEYARAGIEVERPVRQITIHEFVLLDSREDFEGETQS 165 (304)
T ss_pred EeeccCCCCCCHHHHHHHHHhccceEEEeCChhHeEecCCHhHHHHHHCCCccccCCcceEEEEEEEEeeccccccCCce
Confidence 23333221 10 01111221 1112234444310 11234
Q ss_pred eEEEEEecCCchhHHHHHHHHcCC------ceeeeeeeEEeCeecCC
Q 031054 104 PRIRIVVHEGRNHEVRELVKNAGL------KLYSLKRLRIGGFRLPS 144 (166)
Q Consensus 104 ~ll~~~l~tGR~HQIR~~l~~~G~------pI~~l~R~~~g~~~l~~ 144 (166)
..+++.--.|- .||..+.-+|. .+..|.|++.|+|.+++
T Consensus 166 ~~~~v~cskGT--YIRsL~~Dig~~Lg~~a~~~~L~Rt~~G~f~~~~ 210 (304)
T PRK01550 166 FRFRVTCSKGT--YVRTLAVMIGEKLGYPAHMSHLVRTASGGFTLED 210 (304)
T ss_pred EEEEEEECCCC--CHHHHHHHHHHHHCCCEEEEEEEeEEECCCCHHH
Confidence 55666666674 69999887765 56999999999999963
No 49
>PRK01528 truB tRNA pseudouridine synthase B; Provisional
Probab=96.23 E-value=0.072 Score=44.43 Aligned_cols=135 Identities=19% Similarity=0.243 Sum_probs=76.7
Q ss_pred cchHHHHHHHhhcCCCCCCCCeeecCCCCcCCceeeeeeCCH--HHHHHhhcCCCCCCeEEEEEEe-ccc----------
Q 031054 2 SLFDDYLKSWDKRNPGLPRPRLFTVGRLDVATTGLIIVTNDG--DFAQAVSHPSSKLQKEYIATID-GAV---------- 68 (166)
Q Consensus 2 sl~d~~~~~~~~~~~~~~~~~l~~vhRLD~~TSGlll~ak~~--~~~~~l~~~~~~i~K~Y~a~v~-g~~---------- 68 (166)
|..| +...+++.+. ..++...|-||-.+||+|+++-.. .+...+. ...|+|.|.+. |.-
T Consensus 15 TS~d-vv~~vrk~~~---~kKvGH~GTLDP~AtGvL~v~vG~aTKl~~~l~----~~~K~Y~~~~~lG~~TdT~D~~G~v 86 (292)
T PRK01528 15 SSAK-LVSIVKKILG---KVKIGHAGTLDVEAEGVLPLAVGEATKLVQLLI----DAKKTYIFTVKFGKQTDSGDYAGKV 86 (292)
T ss_pred CHHH-HHHHHHHHcC---CCccCcCccCCCcCceEEEEEEChHhhhhHHHh----cCCceEEEEEEECCcccCCCCCCCE
Confidence 4455 4455555443 247889999999999999986653 3444454 35689999763 211
Q ss_pred --------Chhhhhh----hh----------cceeeCCc-----------------ccceeEEEEcCCCCCCCceEEEEE
Q 031054 69 --------NKRHLIA----IS----------EGTVIEGT-----------------HCTPDVVELLPPQPDIPRPRIRIV 109 (166)
Q Consensus 69 --------~~~~~~~----~~----------~~~~~~~~-----------------~~~~~~~~~~~~~~~~~~~ll~~~ 109 (166)
+.+.+.. +. ..+.++|. ......++++......+...+++.
T Consensus 87 ~~~~~~~~~~e~l~~~l~~f~G~i~Q~PP~ySAvKv~G~raYelAR~G~~vel~~r~v~I~~i~ll~~~~~~~~~~~~v~ 166 (292)
T PRK01528 87 IATKDYIPSKEEAYAVCSKFIGNITQIPPAFSALKVNGVRAYKLAREGKEVELKPRNITIYDLKCLNFDEKNATATYYTE 166 (292)
T ss_pred EEecCCCCCHHHHHHHHHhccceEEeeCChhHeEEECCHhHHHHHhCCcccccCceeEEEEEEEEEEEcCCCcEEEEEEE
Confidence 1222211 10 01112221 111123344433211122344455
Q ss_pred ecCCchhHHHHHHHHcCC------ceeeeeeeEEeCeecCCCC
Q 031054 110 VHEGRNHEVRELVKNAGL------KLYSLKRLRIGGFRLPSDL 146 (166)
Q Consensus 110 l~tGR~HQIR~~l~~~G~------pI~~l~R~~~g~~~l~~~l 146 (166)
--.| --||..+.-+|. .+..|.|++.|+|+++..+
T Consensus 167 cskG--TYIRsL~~DiG~~Lg~~a~~~~LrRt~~G~f~~~~a~ 207 (292)
T PRK01528 167 CSKG--TYIRTLAEDLALSLQSLGFVIELRRTQVGIFKEENAI 207 (292)
T ss_pred ECCC--ccHHHHHHHHHHHHCCceEEeEEEeEEECCccHHHcC
Confidence 5556 779998887775 5699999999999986444
No 50
>PRK05389 truB tRNA pseudouridine synthase B; Provisional
Probab=96.20 E-value=0.05 Score=45.64 Aligned_cols=132 Identities=19% Similarity=0.253 Sum_probs=77.3
Q ss_pred cchHHHHHHHhhcCCCCCCCCeeecCCCCcCCceeeeeeCCH--HHHHHhhcCCCCCCeEEEEEEe-cc-----------
Q 031054 2 SLFDDYLKSWDKRNPGLPRPRLFTVGRLDVATTGLIIVTNDG--DFAQAVSHPSSKLQKEYIATID-GA----------- 67 (166)
Q Consensus 2 sl~d~~~~~~~~~~~~~~~~~l~~vhRLD~~TSGlll~ak~~--~~~~~l~~~~~~i~K~Y~a~v~-g~----------- 67 (166)
|..| +...+++.+.. .++...|-||..+||||+++-.. .+...+. .-.|+|.|.+. |.
T Consensus 25 TS~d-vv~~vrk~~~~---kKvGH~GTLDP~AtGvL~v~vG~aTkl~~~l~----~~~K~Y~a~~~lG~~TdT~D~~G~v 96 (305)
T PRK05389 25 TSTE-AVSKVKWLFDA---QKAGHAGTLDPLASGVLPIALGEATKTVPYVM----DGTKRYRFTVAWGEERDTDDLEGEV 96 (305)
T ss_pred CHHH-HHHHHHHHhcc---cccCCcccCCCCCceEEEEEEChhhhhhHHhc----cCCcEEEEEEEECCcccCCCCCCCE
Confidence 4455 44445444432 46788999999999999986653 3444444 35899999763 21
Q ss_pred -------cChhhhhh----hh----------cceeeCCc-----------------ccceeEEEEcCCCCCCCceEEEEE
Q 031054 68 -------VNKRHLIA----IS----------EGTVIEGT-----------------HCTPDVVELLPPQPDIPRPRIRIV 109 (166)
Q Consensus 68 -------~~~~~~~~----~~----------~~~~~~~~-----------------~~~~~~~~~~~~~~~~~~~ll~~~ 109 (166)
++.+.+.. +. ..+.++|. ......++++... ..+...+++.
T Consensus 97 ~~~~~~~~~~~~i~~~l~~f~G~i~Q~PP~ySAvKv~GkraYelAR~G~~ve~~~r~v~I~~i~ll~~~-~~~~~~~~v~ 175 (305)
T PRK05389 97 TATSDVRPTDEEIRAALPAFTGEIMQVPPQFSAIKIDGERAYDLAREGETVELPARPVEIDRLTLVERP-DADHAVFEVE 175 (305)
T ss_pred EEecCCCCCHHHHHHHHHhccceEEEeCCchheEEECCHhHHHHHHCCCccccCceEEEEEEEEEEEec-CCCeEEEEEE
Confidence 12222211 10 01112221 1112234444431 1234566666
Q ss_pred ecCCchhHHHHHHHHcCC------ceeeeeeeEEeCeecCC
Q 031054 110 VHEGRNHEVRELVKNAGL------KLYSLKRLRIGGFRLPS 144 (166)
Q Consensus 110 l~tGR~HQIR~~l~~~G~------pI~~l~R~~~g~~~l~~ 144 (166)
--.| --||..+.-+|. .+..|.|+++|+|++++
T Consensus 176 cskG--TYIRsL~~DiG~~Lg~~a~~~~LrRt~~G~f~~~~ 214 (305)
T PRK05389 176 CGKG--TYVRSLARDLGRALGCYGHIAALRRTRVGPFTEED 214 (305)
T ss_pred eCCC--CCHHHHHHHHHHHHCCCeEEEEEEeEEECCCcHHH
Confidence 6666 489998887764 56999999999999963
No 51
>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=95.82 E-value=0.13 Score=43.36 Aligned_cols=130 Identities=20% Similarity=0.240 Sum_probs=73.9
Q ss_pred cchHHHHHHHhhcCCCCCCCCeeecCCCCcCCceeeeeeCCH--HHHHHhhcCCCCCCeEEEEEEe-c-ccChhhhhh-h
Q 031054 2 SLFDDYLKSWDKRNPGLPRPRLFTVGRLDVATTGLIIVTNDG--DFAQAVSHPSSKLQKEYIATID-G-AVNKRHLIA-I 76 (166)
Q Consensus 2 sl~d~~~~~~~~~~~~~~~~~l~~vhRLD~~TSGlll~ak~~--~~~~~l~~~~~~i~K~Y~a~v~-g-~~~~~~~~~-~ 76 (166)
|..| +...+++.+. ..++...|=||-.++|||+++-.. .+...+. .-.|+|.|.+. | .++++++.. +
T Consensus 46 tS~~-~v~~vr~~~~---~kkvGH~GTLDP~A~GvL~v~~G~aTkl~~~~~----~~~K~Y~~~v~lG~~~~~~~l~~~l 117 (322)
T TIGR00425 46 SSHE-VVAWVRRILN---VEKTGHGGTLDPKVTGVLPVCIERATRLVKSLQ----EAPKEYVCLMRLHRDAKEEDILRVL 117 (322)
T ss_pred CHHH-HHHHHHHHhc---ccccCCCCCCCCCCceEEEEEEChHhhccHHhc----cCCCEEEEEEEECCCCCHHHHHHHH
Confidence 4455 3444444443 246788999999999999987663 2333333 57899998763 3 345555422 2
Q ss_pred hc--c-e-ee---------CCcccceeEEEEcCCCCCCCceEEEEEecCCchhHHHHHHHHcC------CceeeeeeeEE
Q 031054 77 SE--G-T-VI---------EGTHCTPDVVELLPPQPDIPRPRIRIVVHEGRNHEVRELVKNAG------LKLYSLKRLRI 137 (166)
Q Consensus 77 ~~--~-~-~~---------~~~~~~~~~~~~~~~~~~~~~~ll~~~l~tGR~HQIR~~l~~~G------~pI~~l~R~~~ 137 (166)
.+ | + +. .........++++.... +...+++.--.| --||..+..+| ..+..|.|+++
T Consensus 118 ~~f~g~i~Q~pP~~SA~k~~~r~v~I~~~~l~~~~~--~~~~~~v~cskG--TYIRsL~~Dig~~Lg~~a~~~~L~R~~~ 193 (322)
T TIGR00425 118 KEFTGRIFQRPPLKSAVKRQLRVRTIYESELLEKDG--KDVLFRVSCEAG--TYIRKLCVDIGEALGTGAHMQELRRTRS 193 (322)
T ss_pred HHcCCcEEeeCChheEEeccCeEEEEEEEEEEEecC--CeEEEEEEeCCC--cChHHHHHHHHHHHCCCEEEEEeEeEEE
Confidence 11 1 1 00 11111112333333221 223344444445 66888776654 34689999999
Q ss_pred eCeecC
Q 031054 138 GGFRLP 143 (166)
Q Consensus 138 g~~~l~ 143 (166)
|+++++
T Consensus 194 g~f~~~ 199 (322)
T TIGR00425 194 GCFGED 199 (322)
T ss_pred CCcccc
Confidence 999996
No 52
>PRK04642 truB tRNA pseudouridine synthase B; Provisional
Probab=95.73 E-value=0.12 Score=43.23 Aligned_cols=131 Identities=25% Similarity=0.314 Sum_probs=76.1
Q ss_pred cchHHHHHHHhhcCCCCCCCCeeecCCCCcCCceeeeeeCCH--HHHHHhhcCCCCCCeEEEEEEe-----------cc-
Q 031054 2 SLFDDYLKSWDKRNPGLPRPRLFTVGRLDVATTGLIIVTNDG--DFAQAVSHPSSKLQKEYIATID-----------GA- 67 (166)
Q Consensus 2 sl~d~~~~~~~~~~~~~~~~~l~~vhRLD~~TSGlll~ak~~--~~~~~l~~~~~~i~K~Y~a~v~-----------g~- 67 (166)
|..| +...+++.+.. .++...|=||-.+||||+++-.. .+...+. .-.|+|.|.+. |.
T Consensus 22 TS~d-vv~~vrr~~~~---kKvGH~GTLDP~AtGvL~v~~G~aTkl~~~l~----~~~K~Y~a~~~lG~~TdT~D~~G~v 93 (300)
T PRK04642 22 SSNN-ALQAARRLLRA---EKGGHTGSLDPLATGLLPLCFGEATKIAGLLL----GSAKAYDAEIVLGVTTDTDDADGQV 93 (300)
T ss_pred CHHH-HHHHHHHHhCC---CcccCCCccCCcCeeeEEEEEChhhhhhHHhc----CCCcEEEEEEEECccccCcCCCCCE
Confidence 4455 44555554432 47788999999999999986653 3344443 46799999872 11
Q ss_pred --------cChhhhhh----hhc----------ceeeCCc-----------------ccceeEEEEcCCCCCCCceEEEE
Q 031054 68 --------VNKRHLIA----ISE----------GTVIEGT-----------------HCTPDVVELLPPQPDIPRPRIRI 108 (166)
Q Consensus 68 --------~~~~~~~~----~~~----------~~~~~~~-----------------~~~~~~~~~~~~~~~~~~~ll~~ 108 (166)
++.+++.. +.. .+.++|. ......+++++.. .+...+++
T Consensus 94 ~~~~~~~~~~~~~l~~~l~~f~G~i~Q~PP~ySAvKv~GkrlY~lAR~G~~ve~~~R~v~I~~~~ll~~~--~~~~~~~v 171 (300)
T PRK04642 94 LRERPVPDLSAAALQAALAPLIGRIRQRAPIYSALKQGGEPLYAKARRGEVIEAPVREVEVHAIEVLGYA--APRLRLRV 171 (300)
T ss_pred EEecCCCCCCHHHHHHHHHHCCCcEEEeCCchHeEeECCeeHHHHHhCCCccccCcEEEEEEEEEEEEEe--CCEEEEEE
Confidence 22232221 100 1112221 1112233444332 12344555
Q ss_pred EecCCchhHHHHHHHHcCC------ceeeeeeeEEeCeecCC
Q 031054 109 VVHEGRNHEVRELVKNAGL------KLYSLKRLRIGGFRLPS 144 (166)
Q Consensus 109 ~l~tGR~HQIR~~l~~~G~------pI~~l~R~~~g~~~l~~ 144 (166)
.--.| --||..+.-+|. .+..|.|+++|+|++++
T Consensus 172 ~cskG--TYIRSL~~Dig~~Lg~~a~m~~L~Rt~~G~f~~~~ 211 (300)
T PRK04642 172 TCGSG--TYIRSLARDLGEVLGCGAHIAALRRLWVEPFRAPQ 211 (300)
T ss_pred EeCCC--cCHHHHHHHHHHHhCCCEEEEEeEeeEECCcchHH
Confidence 55555 679988877764 56999999999999963
No 53
>PRK14122 tRNA pseudouridine synthase B; Provisional
Probab=95.53 E-value=0.14 Score=43.02 Aligned_cols=55 Identities=24% Similarity=0.341 Sum_probs=37.8
Q ss_pred cchHHHHHHHhhcCCCCCCCCeeecCCCCcCCceeeeeeCCH--HHHHHhhcCCCCCCeEEEEEE
Q 031054 2 SLFDDYLKSWDKRNPGLPRPRLFTVGRLDVATTGLIIVTNDG--DFAQAVSHPSSKLQKEYIATI 64 (166)
Q Consensus 2 sl~d~~~~~~~~~~~~~~~~~l~~vhRLD~~TSGlll~ak~~--~~~~~l~~~~~~i~K~Y~a~v 64 (166)
|..| +...+++.+. ..++...|-||-.+||+|+++-.. .+...+ ....|+|.|.+
T Consensus 13 TS~d-vv~~vrr~l~---~kKvGH~GTLDP~AtGvL~i~iG~aTKl~~~l----~~~~K~Y~a~~ 69 (312)
T PRK14122 13 TSHD-VVNRARRALG---TRRVGHTGTLDPLATGVLVLCTDDSTKLVPFL----SAEDKEYLAWV 69 (312)
T ss_pred CHHH-HHHHHHHHhC---CCCCCCCCCCCCcCeeeEEEEEChhhhhhHHh----cCCCceEEEEE
Confidence 4555 4455555443 247788999999999999987663 233333 35789999976
No 54
>KOG2559 consensus Predicted pseudouridine synthase [Translation, ribosomal structure and biogenesis]
Probab=95.30 E-value=0.037 Score=45.03 Aligned_cols=50 Identities=26% Similarity=0.365 Sum_probs=38.3
Q ss_pred CceEEEEEecCCchhHHHHHHHHcCCce------eeeeeeEEeCeecCCCCCCCcE
Q 031054 102 PRPRIRIVVHEGRNHEVRELVKNAGLKL------YSLKRLRIGGFRLPSDLGIGMH 151 (166)
Q Consensus 102 ~~~ll~~~l~tGR~HQIR~~l~~~G~pI------~~l~R~~~g~~~l~~~l~~G~~ 151 (166)
+...+++.-..--...+|....++|..+ ..+.|.++|+|.+++.|-.-+|
T Consensus 206 P~F~le~qc~~Etqe~Lr~LVh~igl~L~T~a~c~qlrr~r~g~F~~d~aLLr~qw 261 (318)
T KOG2559|consen 206 PKFSLETQCSGETQEMLRQLVHHIGLNLGTEATCIQLRRQRFGPFGSDNALLRKQW 261 (318)
T ss_pred CccEEEEeeccccHHHHHHHHHHHhhcccceeeeeeeeeeccCCCCccHHHHHHhh
Confidence 3456777665555677888888898865 7899999999999766666665
No 55
>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=90.52 E-value=0.52 Score=35.47 Aligned_cols=40 Identities=28% Similarity=0.410 Sum_probs=28.7
Q ss_pred CCeeecCCCCcCCceeeeeeCC--HHHHHHhhcCCCCCCeEEEEEE
Q 031054 21 PRLFTVGRLDVATTGLIIVTND--GDFAQAVSHPSSKLQKEYIATI 64 (166)
Q Consensus 21 ~~l~~vhRLD~~TSGlll~ak~--~~~~~~l~~~~~~i~K~Y~a~v 64 (166)
.++...|.||-.+||||+++=. -.+...+. ...|+|.|..
T Consensus 7 ~KvGH~GTLDP~AsGvL~v~vg~~Tkl~~~l~----~~~K~Y~~~~ 48 (149)
T PF01509_consen 7 KKVGHGGTLDPFASGVLVVGVGKATKLLSYLQ----NSDKEYVATI 48 (149)
T ss_dssp SSEEESS-SSTT-EEEEEEEEGGGGGGHHHHT----TSEEEEEEEE
T ss_pred ceeccccccCCcceEEEEEEECCcchHHHHhh----ccCCEEEEEE
Confidence 5789999999999999998654 34455555 3559999975
No 56
>COG0130 TruB Pseudouridine synthase [Translation, ribosomal structure and biogenesis]
Probab=89.89 E-value=1.6 Score=36.15 Aligned_cols=115 Identities=22% Similarity=0.277 Sum_probs=68.1
Q ss_pred CCeeecCCCCcCCceeeeeeCCH--HHHHHhhcCCCCCCeEEEEEEe-cccC--hhhhhh----hhccee-eC-------
Q 031054 21 PRLFTVGRLDVATTGLIIVTNDG--DFAQAVSHPSSKLQKEYIATID-GAVN--KRHLIA----ISEGTV-IE------- 83 (166)
Q Consensus 21 ~~l~~vhRLD~~TSGlll~ak~~--~~~~~l~~~~~~i~K~Y~a~v~-g~~~--~~~~~~----~~~~~~-~~------- 83 (166)
.++...|-||-..||+|+++-.. .++..|. .-.|+|.|.+. |.-+ .+++.. +...+. +.
T Consensus 42 ~K~GH~GTLDP~atGvLpi~ig~aTKl~~~l~----~~~K~Y~a~~~lG~~t~~~e~i~~~l~~F~G~I~Q~PP~~SAvK 117 (271)
T COG0130 42 EKAGHGGTLDPLATGVLPICLGEATKLVQYLL----DADKEYVATVRLGDQTDSEEEVRAALEAFTGEIYQIPPMFSAVK 117 (271)
T ss_pred cccccccccCCcccceEEEEechhHhHHHHHh----hCCcEEEEEEEeCCcCCCHHHHHHHHHhcceeeEecCCchhhcc
Confidence 56788899999999999987772 3444444 47899999874 3333 333322 111110 00
Q ss_pred ----CcccceeEEEEcCCCCCCCceEEEEEecCCchhHHHHHHHHcC------CceeeeeeeEEeCeecC
Q 031054 84 ----GTHCTPDVVELLPPQPDIPRPRIRIVVHEGRNHEVRELVKNAG------LKLYSLKRLRIGGFRLP 143 (166)
Q Consensus 84 ----~~~~~~~~~~~~~~~~~~~~~ll~~~l~tGR~HQIR~~l~~~G------~pI~~l~R~~~g~~~l~ 143 (166)
-.......+..++.. .+...+++.- ++=--||..+..+| -.+..|+|++.|+++++
T Consensus 118 ~~v~~R~V~i~~l~~~~~~--~~~~~~~v~C--skGTYIRtL~~DlG~~LG~gahm~~LrRt~~g~f~~~ 183 (271)
T COG0130 118 REVERRKITIYDLLELDFD--RNLVTLRVEC--SKGTYIRTLARDLGEALGCGAHMSELRRTRVGPFSEE 183 (271)
T ss_pred ceEeeEEEEEEEeeeccCC--CceEEEEEEE--ecCcCHHHHHHHHHHHHCCccchhhhccccccccccc
Confidence 011111122222221 1233444444 44477999888765 45699999999999995
No 57
>PF07530 PRE_C2HC: Associated with zinc fingers; InterPro: IPR006579 This domain is present in proteins found exclusively in the arthropods, including a number of Drosophila species, the silk moth and the gypsy moth. These proteins are possibly involved in RNA binding or single strand DNA binding.
Probab=50.34 E-value=16 Score=23.72 Aligned_cols=24 Identities=17% Similarity=0.350 Sum_probs=21.8
Q ss_pred hhHHHHHHHHcCCceeeeeeeEEe
Q 031054 115 NHEVRELVKNAGLKLYSLKRLRIG 138 (166)
Q Consensus 115 ~HQIR~~l~~~G~pI~~l~R~~~g 138 (166)
+.+|+.-|+..||+++..+|...+
T Consensus 1 ~~~I~~~L~~~G~~v~~i~~~~~~ 24 (68)
T PF07530_consen 1 CEEIKEELKDQGHPVRNIHNMHSR 24 (68)
T ss_pred CHHHHHHHHHcCCceEEEEccccC
Confidence 368999999999999999998877
No 58
>PF07867 DUF1654: Protein of unknown function (DUF1654); InterPro: IPR012449 This entry is represented by Bacteriophage F116 (Pseudomonas phage F116), Orf28. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family consists of proteins from the Pseudomonadaceae.
Probab=49.62 E-value=13 Score=24.68 Aligned_cols=33 Identities=21% Similarity=0.360 Sum_probs=22.6
Q ss_pred CcchHHHHHHHhh--cCCCCCCCCeeecCCCCcCC
Q 031054 1 MSLFDDYLKSWDK--RNPGLPRPRLFTVGRLDVAT 33 (166)
Q Consensus 1 ~sl~d~~~~~~~~--~~~~~~~~~l~~vhRLD~~T 33 (166)
||-++.|..+..+ ..|.+...+...|||||-++
T Consensus 2 mt~ye~L~~Rvq~~Insp~AQ~~r~v~I~R~~~e~ 36 (73)
T PF07867_consen 2 MTAYERLGLRVQRMINSPKAQKQRWVTIHRLDDES 36 (73)
T ss_pred CCHHHHHHHHHHHHHcChHhhheeEEEEEECCCCC
Confidence 5667777666655 45666667778888888754
No 59
>cd07973 Spt4 Transcription elongation factor Spt4. Spt4 is a transcription elongation factor. Three transcription-elongation factors Spt4, Spt5, and Spt6, are conserved among eukaryotes and are essential for transcription via the modulation of chromatin structure. It is known that Spt4, Spt5, and Spt6 are general transcription-elongation factors, controlling transcription both positively and negatively in important regulatory and developmental roles. Spt4 functions entirely in the context of the Spt4-Spt5 heterodimer and it has been found only as a complex to Spt5 in Yeast and Human. Spt4 is a small protein that has zinc finger at the N-terminus. Spt5 is a large protein that has several interesting structural features of an acidic N-terminus, a single NGN domain, five or six KOW domains, and a set of simple C-termianl repeats. Spt4 binds to Spt5 NGN domain. Unlike Spt5, Spt4 is not essential for viability in yeast, however Spt4 is critical for normal function of the Spt4-Spt5 compl
Probab=44.97 E-value=82 Score=21.98 Aligned_cols=45 Identities=9% Similarity=0.212 Sum_probs=31.4
Q ss_pred CceeeeeeC-CHHHHHHhhcCCCCCCeEEEEEEecccChhhhhhhh
Q 031054 33 TTGLIIVTN-DGDFAQAVSHPSSKLQKEYIATIDGAVNKRHLIAIS 77 (166)
Q Consensus 33 TSGlll~ak-~~~~~~~l~~~~~~i~K~Y~a~v~g~~~~~~~~~~~ 77 (166)
=+|+|++.+ +.....+.+.-...+.=.|-+.|.|.++++....++
T Consensus 47 f~G~i~i~dP~~SwVAk~l~i~~~~pG~YAi~V~g~lp~~i~~~l~ 92 (98)
T cd07973 47 FEGIIALMDPEKSWVARWQRIDKFVPGIYAISVSGRLPEDIVEELE 92 (98)
T ss_pred cceEEEEECCchhHHHHHhCCCCCCCCeEEEEecCcCCHHHHHHHH
Confidence 379998863 334455555544557779999999999988765553
No 60
>smart00596 PRE_C2HC PRE_C2HC domain.
Probab=43.17 E-value=27 Score=22.90 Aligned_cols=25 Identities=12% Similarity=0.294 Sum_probs=21.6
Q ss_pred hhHHHHHHHHcCCceeeeeeeEEeC
Q 031054 115 NHEVRELVKNAGLKLYSLKRLRIGG 139 (166)
Q Consensus 115 ~HQIR~~l~~~G~pI~~l~R~~~g~ 139 (166)
++||..-|+..||++...++..-+.
T Consensus 1 ~~~I~~~L~~~G~~v~~i~~m~~~~ 25 (69)
T smart00596 1 TSQIEEALKDIGFPVLFIHNMLNRD 25 (69)
T ss_pred CHHHHHHHHHcCCceeEEEcccccC
Confidence 4799999999999999998876654
No 61
>PF00004 AAA: ATPase family associated with various cellular activities (AAA); InterPro: IPR003959 AAA ATPases (ATPases Associated with diverse cellular Activities) form a large protein family and play a number of roles in the cell including cell-cycle regulation, protein proteolysis and disaggregation, organelle biogenesis and intracellular transport. Some of them function as molecular chaperones, subunits of proteolytic complexes or independent proteases (FtsH, Lon). They also act as DNA helicases and transcription factors []. AAA ATPases belong to the AAA+ superfamily of ringshaped P-loop NTPases, which act via the energy-dependent unfolding of macromolecules [, ]. There are six major clades of AAA domains (proteasome subunits, metalloproteases, domains D1 and D2 of ATPases with two AAA domains, the MSP1/katanin/spastin group and BCS1 and it homologues), as well as a number of deeply branching minor clades []. They assemble into oligomeric assemblies (often hexamers) that form a ring-shaped structure with a central pore. These proteins produce a molecular motor that couples ATP binding and hydrolysis to changes in conformational states that act upon a target substrate, either translocating or remodelling it []. They are found in all living organisms and share the common feature of the presence of a highly conserved AAA domain called the AAA module. This domain is responsible for ATP binding and hydrolysis. It contains 200-250 residues, among them there are two classical motifs, Walker A (GX4GKT) and Walker B (HyDE) []. The functional variety seen between AAA ATPases is in part due to their extensive number of accessory domains and factors, and to their variable organisation within oligomeric assemblies, in addition to changes in key functional residues within the ATPase domain itself. More information about these proteins can be found at Protein of the Month: AAA ATPases [].; GO: 0005524 ATP binding; PDB: 3H4M_A 1NSF_A 1D2N_A 1HQY_E 1DO0_E 1DO2_C 1G4B_E 1HT1_F 1G4A_F 1HT2_G ....
Probab=32.75 E-value=47 Score=22.68 Aligned_cols=26 Identities=15% Similarity=0.270 Sum_probs=21.8
Q ss_pred ecCCchhHHHHHHHHcCCceeeeeee
Q 031054 110 VHEGRNHEVRELVKNAGLKLYSLKRL 135 (166)
Q Consensus 110 l~tGR~HQIR~~l~~~G~pI~~l~R~ 135 (166)
+-+||+.-+|..+..+|.|++.+...
T Consensus 7 ~G~GKT~l~~~la~~l~~~~~~i~~~ 32 (132)
T PF00004_consen 7 PGTGKTTLARALAQYLGFPFIEIDGS 32 (132)
T ss_dssp TTSSHHHHHHHHHHHTTSEEEEEETT
T ss_pred CCCCeeHHHHHHHhhccccccccccc
Confidence 34899999999999999998766553
No 62
>PF14401 RLAN: RimK-like ATPgrasp N-terminal domain
Probab=26.67 E-value=80 Score=23.71 Aligned_cols=46 Identities=20% Similarity=0.265 Sum_probs=39.3
Q ss_pred hHHHHHHHHcCCceeeeeeeEEeC-eecCCCCCCCcEEEcCHHHHhhc
Q 031054 116 HEVRELVKNAGLKLYSLKRLRIGG-FRLPSDLGIGMHVELKQSDLKLM 162 (166)
Q Consensus 116 HQIR~~l~~~G~pI~~l~R~~~g~-~~l~~~l~~G~~r~l~~~e~~~l 162 (166)
.--|..|...-.|++.+.=.+-++ +.+ ..+.+.....|+++|-..+
T Consensus 102 ~lAr~lFe~F~~PlL~v~~~~~~~~w~i-~~i~~~~~~~l~~~e~~~f 148 (153)
T PF14401_consen 102 RLARQLFERFPCPLLEVEFVRDDGKWRI-SSIKPLSLSELSEEEQDFF 148 (153)
T ss_pred HHHHHHHHhCCCceEEEEEEecCCcEEE-eeEeecChhhCCHHHHHHH
Confidence 345788999999999998888888 999 5999999999999987654
No 63
>KOG3490 consensus Transcription elongation factor SPT4 [Transcription]
Probab=22.05 E-value=2.3e+02 Score=20.19 Aligned_cols=44 Identities=9% Similarity=0.207 Sum_probs=35.7
Q ss_pred ceeeee-eCCHHHHHHhhcCCCCCCeEEEEEEecccChhhhhhhh
Q 031054 34 TGLIIV-TNDGDFAQAVSHPSSKLQKEYIATIDGAVNKRHLIAIS 77 (166)
Q Consensus 34 SGlll~-ak~~~~~~~l~~~~~~i~K~Y~a~v~g~~~~~~~~~~~ 77 (166)
.|+|-+ +++...+.+-+.-.+...=-|-+.|+|.++++.+..++
T Consensus 52 ~GiIa~m~Pt~SWVakWqri~~f~~G~YAi~VsG~Lpe~~v~~l~ 96 (111)
T KOG3490|consen 52 DGIIAMMSPTESWVAKWQRIGRFTPGMYAISVSGVLPEEVVESLK 96 (111)
T ss_pred cceeeeeCccHHHHHHHHhhccccCceEEEEecccCCHHHHHHHH
Confidence 477754 66777788888877788889999999999998887665
No 64
>KOG2553 consensus Pseudouridylate synthase [Translation, ribosomal structure and biogenesis]
Probab=20.43 E-value=53 Score=28.83 Aligned_cols=23 Identities=26% Similarity=0.444 Sum_probs=17.1
Q ss_pred CceEEEEEecCCc---hhHHHHHHHHc
Q 031054 102 PRPRIRIVVHEGR---NHEVRELVKNA 125 (166)
Q Consensus 102 ~~~ll~~~l~tGR---~HQIR~~l~~~ 125 (166)
+.-|+.|.+ .|. .||||+|.+.+
T Consensus 263 ~~e~V~i~i-~GQSFMLHQIRKMVgla 288 (416)
T KOG2553|consen 263 GVEFVKIKI-HGQSFMLHQIRKMVGLA 288 (416)
T ss_pred CceEEEEEE-EcchhHHHHHHHHHHHH
Confidence 456888887 455 49999998754
Done!