Query 018524
Match_columns 354
No_of_seqs 346 out of 1760
Neff 8.4
Searched_HMMs 46136
Date Fri Mar 29 09:44:14 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/018524.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/018524hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG0564 RluA Pseudouridylate s 100.0 1.4E-57 2.9E-62 420.9 18.2 283 10-343 3-289 (289)
2 PRK11025 23S rRNA pseudouridyl 100.0 8.9E-57 1.9E-61 423.5 18.5 293 10-353 10-314 (317)
3 TIGR00005 rluA_subfam pseudour 100.0 1.9E-54 4.2E-59 405.9 17.6 288 16-352 2-298 (299)
4 PRK11180 rluD 23S rRNA pseudou 100.0 6.4E-54 1.4E-58 405.7 21.1 292 10-353 8-313 (325)
5 PRK11112 tRNA pseudouridine sy 100.0 6E-52 1.3E-56 379.5 18.4 230 84-353 2-235 (257)
6 cd02563 PseudoU_synth_TruC tRN 100.0 2.4E-50 5.3E-55 362.1 20.6 218 85-342 2-223 (223)
7 TIGR01621 RluA-like pseudourid 100.0 5.5E-50 1.2E-54 357.7 22.0 202 84-349 2-203 (217)
8 cd02558 PSRA_1 PSRA_1: Pseudou 100.0 9.1E-50 2E-54 362.8 22.4 206 83-342 38-245 (246)
9 PRK10158 23S rRNA/tRNA pseudou 100.0 3.5E-49 7.6E-54 353.2 18.9 206 83-342 13-218 (219)
10 cd02557 PseudoU_synth_ScRIB2 P 100.0 1.4E-48 2.9E-53 348.1 18.4 202 79-345 11-212 (213)
11 cd02869 PseudoU_synth_RluCD_li 100.0 2.1E-39 4.6E-44 283.2 17.2 185 93-326 1-185 (185)
12 KOG1919 RNA pseudouridylate sy 100.0 1.7E-38 3.6E-43 298.7 17.8 280 11-352 47-352 (371)
13 PRK10839 16S rRNA pseudouridyl 100.0 1.7E-36 3.6E-41 274.1 5.6 201 20-302 1-202 (232)
14 COG1187 RsuA 16S rRNA uridine- 100.0 1.8E-34 4E-39 257.8 8.1 209 18-300 1-210 (248)
15 cd02550 PseudoU_synth_Rsu_Rlu_ 100.0 1.5E-33 3.3E-38 239.1 12.9 147 93-298 1-147 (154)
16 PRK10700 23S rRNA pseudouridyl 100.0 4.3E-34 9.3E-39 264.8 8.3 201 19-299 2-209 (289)
17 cd02870 PseudoU_synth_RsuA_lik 100.0 8.5E-33 1.8E-37 232.4 9.0 140 93-299 1-140 (146)
18 cd02556 PseudoU_synth_RluB Pse 100.0 1.9E-32 4.1E-37 235.1 9.4 142 92-299 1-142 (167)
19 PRK10475 23S rRNA pseudouridin 100.0 1.5E-32 3.3E-37 253.7 6.9 194 19-299 6-202 (290)
20 cd02553 PseudoU_synth_RsuA Pse 100.0 3.2E-32 7E-37 233.6 7.9 144 93-305 2-145 (167)
21 PF00849 PseudoU_synth_2: RNA 100.0 3.7E-31 8E-36 226.7 12.6 164 92-292 1-164 (164)
22 cd02555 PSSA_1 PSSA_1: Pseudou 100.0 2.7E-30 5.9E-35 222.9 8.8 150 91-304 4-154 (177)
23 cd02566 PseudoU_synth_RluE Pse 100.0 5.2E-30 1.1E-34 220.2 9.3 156 93-303 1-158 (168)
24 PRK11394 23S rRNA pseudouridin 100.0 1E-28 2.2E-33 218.0 10.0 164 89-306 37-200 (217)
25 TIGR00093 pseudouridine syntha 99.9 2.9E-28 6.4E-33 200.0 7.3 110 141-305 1-110 (128)
26 cd02554 PseudoU_synth_RluF Pse 99.9 2.4E-26 5.2E-31 195.4 10.7 135 93-300 2-136 (164)
27 cd02868 PseudoU_synth_hTruB2_l 99.2 4.2E-11 9.2E-16 106.7 5.6 76 92-182 1-76 (226)
28 cd02572 PseudoU_synth_hDyskeri 97.7 6.8E-05 1.5E-09 65.0 5.9 70 91-182 2-71 (182)
29 PRK00989 truB tRNA pseudouridi 97.4 0.00019 4.1E-09 64.1 4.9 71 91-182 9-79 (230)
30 cd00506 PseudoU_synth_TruB_lik 97.4 0.00028 6E-09 62.5 5.6 72 92-185 1-73 (210)
31 cd00165 S4 S4/Hsp/ tRNA synthe 97.4 2.5E-05 5.5E-10 55.7 -1.3 65 20-97 1-70 (70)
32 PRK04099 truB tRNA pseudouridi 97.3 0.00039 8.3E-09 63.7 5.7 73 91-185 2-75 (273)
33 TIGR00431 TruB tRNA pseudourid 97.3 0.00046 1E-08 60.9 5.5 73 91-185 2-75 (209)
34 PRK00020 truB tRNA pseudouridi 97.3 0.00052 1.1E-08 61.8 5.8 70 91-182 10-79 (244)
35 PRK02484 truB tRNA pseudouridi 97.2 0.00065 1.4E-08 63.2 5.7 73 91-185 3-76 (294)
36 PRK14124 tRNA pseudouridine sy 97.1 0.00084 1.8E-08 62.7 6.0 70 91-182 3-72 (308)
37 PRK03287 truB tRNA pseudouridi 97.1 0.00072 1.6E-08 62.9 5.4 72 89-182 7-78 (298)
38 PRK00130 truB tRNA pseudouridi 97.1 0.00086 1.9E-08 62.3 5.9 70 91-182 2-71 (290)
39 PRK02193 truB tRNA pseudouridi 97.1 0.00084 1.8E-08 61.8 5.5 68 93-182 2-69 (279)
40 PRK05389 truB tRNA pseudouridi 97.1 0.0009 1.9E-08 62.5 5.7 73 91-185 13-86 (305)
41 PRK14123 tRNA pseudouridine sy 97.1 0.00093 2E-08 62.4 5.6 70 91-182 3-72 (305)
42 PRK02755 truB tRNA pseudouridi 97.0 0.001 2.2E-08 61.9 5.4 71 91-184 3-74 (295)
43 PRK04270 H/ACA RNA-protein com 97.0 0.0011 2.4E-08 62.1 5.6 73 88-182 19-91 (300)
44 PRK05033 truB tRNA pseudouridi 97.0 0.0013 2.8E-08 61.6 5.9 70 91-182 10-79 (312)
45 PRK01851 truB tRNA pseudouridi 97.0 0.0014 3E-08 61.1 6.0 70 91-182 16-85 (303)
46 PRK01550 truB tRNA pseudouridi 97.0 0.0014 3E-08 61.3 5.8 70 91-182 2-71 (304)
47 PRK14846 truB tRNA pseudouridi 97.0 0.0014 3E-08 61.5 5.8 70 91-182 3-72 (345)
48 cd02573 PseudoU_synth_EcTruB P 96.9 0.0015 3.2E-08 60.3 5.6 72 92-185 1-73 (277)
49 PRK01528 truB tRNA pseudouridi 96.9 0.0019 4.2E-08 59.9 5.9 73 91-185 3-76 (292)
50 cd01291 PseudoU_synth PseudoU_ 96.8 0.0051 1.1E-07 46.6 6.7 28 136-182 24-51 (87)
51 PRK14122 tRNA pseudouridine sy 96.7 0.003 6.4E-08 59.1 5.6 69 92-182 2-70 (312)
52 TIGR00425 CBF5 rRNA pseudourid 96.4 0.0051 1.1E-07 58.1 5.1 73 88-182 31-103 (322)
53 PRK04642 truB tRNA pseudouridi 96.3 0.0067 1.4E-07 56.5 5.4 70 91-182 10-79 (300)
54 COG0130 TruB Pseudouridine syn 96.1 0.0082 1.8E-07 55.2 5.1 69 92-182 16-84 (271)
55 cd02867 PseudoU_synth_TruB_4 P 96.0 0.012 2.7E-07 55.0 5.5 43 136-182 56-98 (312)
56 PF01479 S4: S4 domain; Inter 92.8 0.0032 6.9E-08 41.9 -4.9 43 20-74 1-44 (48)
57 KOG2559 Predicted pseudouridin 91.2 0.25 5.5E-06 44.0 3.8 23 136-158 89-111 (318)
58 PF01509 TruB_N: TruB family p 87.6 0.72 1.6E-05 38.6 3.8 43 136-182 7-49 (149)
59 TIGR02988 YaaA_near_RecF S4 do 81.6 0.093 2E-06 36.5 -3.5 45 17-74 6-52 (59)
60 COG1188 Ribosome-associated he 81.4 0.36 7.7E-06 37.2 -0.6 37 17-65 6-43 (100)
61 TIGR00478 tly hemolysin TlyA f 75.6 0.34 7.4E-06 43.6 -2.7 41 21-73 1-42 (228)
62 TIGR01017 rpsD_bact ribosomal 72.1 0.34 7.5E-06 42.7 -3.5 44 19-74 89-133 (200)
63 CHL00113 rps4 ribosomal protei 68.1 0.48 1E-05 41.7 -3.4 44 19-74 88-132 (201)
64 PRK10348 ribosome-associated h 61.5 1.2 2.6E-05 36.4 -2.0 43 19-74 8-51 (133)
65 TIGR03069 PS_II_S4 photosystem 57.1 1.2 2.7E-05 40.7 -2.9 49 14-74 178-226 (257)
66 PRK11507 ribosome-associated p 46.2 4.9 0.00011 28.9 -0.7 44 20-75 12-56 (70)
67 PF08068 DKCLD: DKCLD (NUC011) 43.2 11 0.00024 26.1 0.7 18 88-105 39-56 (59)
68 PF13021 DUF3885: Domain of un 39.2 41 0.00089 21.1 2.8 24 147-170 5-28 (38)
69 smart00363 S4 S4 RNA-binding d 39.2 2.9 6.2E-05 27.8 -2.8 35 20-66 1-36 (60)
70 PF13275 S4_2: S4 domain; PDB: 38.8 4.1 8.8E-05 29.0 -2.0 45 19-75 7-52 (65)
71 PRK05327 rpsD 30S ribosomal pr 37.9 3.1 6.8E-05 36.7 -3.4 43 20-74 93-136 (203)
72 PLN00051 RNA-binding S4 domain 36.3 4.6 0.0001 37.2 -2.7 49 14-74 186-234 (267)
73 COG1189 Predicted rRNA methyla 35.8 4.1 8.9E-05 36.7 -2.9 44 18-73 1-45 (245)
74 KOG2529 Pseudouridine synthase 32.3 35 0.00076 33.1 2.5 79 87-187 64-142 (395)
No 1
>COG0564 RluA Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.4e-57 Score=420.90 Aligned_cols=283 Identities=29% Similarity=0.384 Sum_probs=208.0
Q ss_pred ccccCCCCCCCcccccccccCCCCCCCCCCCCCCccccCCCCCCCCCCcccccc-eeEEeeccccccccccc-CCCccEE
Q 018524 10 TFTLTPKAVPRFRKTFFSLASMSNPTEPTSQNAPQTQQNYPTPLSPPLPAISKD-IELTRAMSASSKSSLYK-LSRSDVL 87 (354)
Q Consensus 10 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~-v~~~~~~~~~~~~~~~~-~~~~~Il 87 (354)
.|+++..+.++|+|+||+....-+|..+.+++.+|.+.-...++.+.+....|+ +.+.......+ ..... -.+++||
T Consensus 3 ~~~v~~~~~g~rld~~L~~l~~~sr~~~~~~i~~g~v~vNg~~v~~~~~l~~gd~i~~~~~~~~~~-~~~~~~~~~l~Il 81 (289)
T COG0564 3 EFEVPEEEAGQRLDKFLAKLLPISRSRIQKLIRKGRVRVNGKKVKPSYKLKPGDVVRIPLPEEPEE-EKLVPEDIPLDIL 81 (289)
T ss_pred eEEeChhhcCCCHHHHHHHccCcCHHHHHHHHHCCCEEECCEEccCCeeeCCCCEEEEeccccccc-ccccccCCCccEE
Confidence 467777889999999999832268999999999887743443344332222222 22222111110 00010 0136799
Q ss_pred EeCCcEEEEECCCCCccccccccccc-cccccccccccCCCccccccccccccccccCCCCCceEEEEEeCHHHHHHHHH
Q 018524 88 YEDEWLVAVNKPQGVYCESVLASVPC-LLAGDSAESKSGRLSEGTKLNLLELHLANRLDRDTSGVMVITKSHKVASKLVK 166 (354)
Q Consensus 88 yed~~~lvvnKP~Gl~~~~~~~~~~~-~~~~~~~~~~~~~l~~~~~~~~~~l~~vhRLDk~TSGllllAk~~~~a~~l~~ 166 (354)
|||+++||||||+|++||+....... ++..... ..... ...+++||||||+||||||+|||..++..|++
T Consensus 82 yED~~llVvnKP~Gl~vhp~~~~~~~tl~~~l~~-----~~~~~----~~~~~~vHRLDkdTSGlll~AK~~~a~~~l~~ 152 (289)
T COG0564 82 YEDEDLLVVNKPAGLVVHPGGGHHEGTLVNALLR-----HCQDG----VERPGIVHRLDKDTSGLLLVAKNREAARELSE 152 (289)
T ss_pred EecCCEEEEECCCCCcCcCCCCCccHhHHHHHHH-----hcccc----CCceeeeccCCCCCceEEEEECCHHHHHHHHH
Confidence 99999999999999999987433222 1111110 00000 15799999999999999999999999999999
Q ss_pred HhhcCccceEEEEEEeCCCCCCCceEEecCCCCCCCCceeEeeecCCccccCCCcccccceeeEEEeeecCCCCCCCCcc
Q 018524 167 AFTDHKVSKTYIALCIGPAPKWKRITIISGHGRSKFGAWRVYAASDVGRVLPGGSVVRDMVTSFEVLSVNGEGSFKEPSE 246 (354)
Q Consensus 167 ~f~~~~v~K~Y~A~v~G~~~~~~~~~i~~~i~~~~~~~~~~~~~~~~~~~~~~g~~~~~a~t~~~vl~~~~~~~~~~~~~ 246 (354)
+|+++.+.|+|+|+|.|.++. +.+.|+.++++.......... ...+. .+.|.|.|+++...
T Consensus 153 ~f~~r~v~K~Y~Alv~G~~~~-~~~~i~~pi~r~~~~~~~~~v-------~~~~~-gk~A~T~~~~l~~~---------- 213 (289)
T COG0564 153 QFKQRKVKKTYLALVRGHLPE-DEGTIDAPIGRDPKNRKKMAV-------VKEGS-GKPAITHYEVLERF---------- 213 (289)
T ss_pred HHhcCcCcEEEEEEEECcccC-CCCEEeeeeecCCcCCceEEE-------eccCC-CCceEEEEEehhcc----------
Confidence 999999999999999999876 457899999887765544332 11222 47899999998652
Q ss_pred hhcccccceeeeeehhhccCCCCc-eEEEEEEeCCCchhHHHHHHhhcCCceecCCCCCCccccCCCCCCCceeeeeeeE
Q 018524 247 LQEHEENNIVVEKKAVLDADAKKN-EILVRAFPRSGRTHQIRLHCQYLGISIRGDVKYEGVYEWNGKRYDGHELHAESLS 325 (354)
Q Consensus 247 ~~~~~~~~~~~~~~~~~~~~~~~~-~slv~~~~~TGR~HQIRvhla~lG~PIvGD~~Yg~~~~~~~~~~~~~~LHa~~L~ 325 (354)
.. .|+++|+|.||||||||+||+++||||+||.+||...........+++|||++|.
T Consensus 214 ----------------------~~~~tlv~~~~~TGRTHQIRVHl~~lghPI~GD~~Yg~~~~~~~~~~~r~~LHA~~l~ 271 (289)
T COG0564 214 ----------------------GDNYTLVELKPETGRTHQIRVHLAHLGHPIVGDPLYGGKDKSAGAGLKRQALHAYKLS 271 (289)
T ss_pred ----------------------CCceEEEEEEeCCCCHhHHHHHHHHCCCCeeCCcccCCchhhcccCcchhhhhhceeE
Confidence 23 6999999999999999999999999999999999853222334678999999999
Q ss_pred eeCCCCCCceEEEcCCCh
Q 018524 326 FDHPVTGCPVMVQAPLPL 343 (354)
Q Consensus 326 f~~P~~~~~~~~~aplP~ 343 (354)
|.||.+++.+.|++|+|.
T Consensus 272 f~hp~t~~~~~~~a~~p~ 289 (289)
T COG0564 272 FTHPLTGEELEFEAPLPE 289 (289)
T ss_pred ccCCCCCCEEEEecCCCC
Confidence 999999999999999984
No 2
>PRK11025 23S rRNA pseudouridylate synthase C; Provisional
Probab=100.00 E-value=8.9e-57 Score=423.55 Aligned_cols=293 Identities=24% Similarity=0.266 Sum_probs=210.7
Q ss_pred ccccCCCCCCCccccccccc-CCCCCCCCCCCCCCccccCCCCCCCCCCcc-cccceeEEeeccccccc-c---c---cc
Q 018524 10 TFTLTPKAVPRFRKTFFSLA-SMSNPTEPTSQNAPQTQQNYPTPLSPPLPA-ISKDIELTRAMSASSKS-S---L---YK 80 (354)
Q Consensus 10 ~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-v~~~v~~~~~~~~~~~~-~---~---~~ 80 (354)
+|++.+++.++|+++||+.. ...+|..++++++.|.+.-...++.+.+.. .++.|.+......++.. + . ..
T Consensus 10 ~~~v~~~~~g~RLd~~L~~~~~~~sr~~i~~li~~G~V~VNg~~v~~~~~v~~GD~I~i~~~~~~~~~~~p~~~~~~~~~ 89 (317)
T PRK11025 10 IVTISADEAGQRIDNFLRTQLKGVPKSMIYRILRKGEVRVNKKRIKPEYKLEAGDEVRIPPVRVAEREEEAVSPKLQKVA 89 (317)
T ss_pred EEEECcccCCchHHHHHHHhcccCCHHHHHHHHHcCCEEECCEEcCcccccCCCCEEEeCCCCccccccccccccccccc
Confidence 36888889999999999965 456999999999998773333333333222 23334432111111000 0 0 01
Q ss_pred CCCccEEEeCCcEEEEECCCCCccccccccccccccccccccccCCCccccccccccccccccCCCCCceEEEEEeCHHH
Q 018524 81 LSRSDVLYEDEWLVAVNKPQGVYCESVLASVPCLLAGDSAESKSGRLSEGTKLNLLELHLANRLDRDTSGVMVITKSHKV 160 (354)
Q Consensus 81 ~~~~~Ilyed~~~lvvnKP~Gl~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~l~~vhRLDk~TSGllllAk~~~~ 160 (354)
...+.|+|||++|+|||||+|++||+......+...... . +... ...+++|||||++||||||||||+++
T Consensus 90 ~~~~~Ilyed~~~lvvnKP~gl~~~~~~~~~~~~~~~~~-----~-~~~~----~~~~~~vhRLD~~TSGlll~Ak~~~a 159 (317)
T PRK11025 90 ALADVILYEDDHILVLNKPSGTAVHGGSGLSFGVIEGLR-----A-LRPE----ARFLELVHRLDRDTSGVLLVAKKRSA 159 (317)
T ss_pred cCcCCEEEECCCEEEEECCCCCcCcCCCCCCccHHHHHH-----H-hccC----CCcCceeCCCCCCCceEEEEEcCHHH
Confidence 124689999999999999999999975432222111110 0 0111 13478999999999999999999999
Q ss_pred HHHHHHHhhcCccceEEEEEEeCCCCCCCceEEecCCCCCCCCceeEeeecCCccccCCCcccccceeeEEEeeecCCCC
Q 018524 161 ASKLVKAFTDHKVSKTYIALCIGPAPKWKRITIISGHGRSKFGAWRVYAASDVGRVLPGGSVVRDMVTSFEVLSVNGEGS 240 (354)
Q Consensus 161 a~~l~~~f~~~~v~K~Y~A~v~G~~~~~~~~~i~~~i~~~~~~~~~~~~~~~~~~~~~~g~~~~~a~t~~~vl~~~~~~~ 240 (354)
++.|+.+|+++.|+|+|+|+|.|.++. ..+.++.++.+........... ..++ .+.+.|+|+++..
T Consensus 160 ~~~l~~~~~~~~v~K~Y~a~v~G~~~~-~~~~i~~~i~~~~~~~~~~~~~-----~~~~---gk~a~T~~~~l~~----- 225 (317)
T PRK11025 160 LRSLHEQLREKGMQKDYLALVRGQWQS-HVKVVQAPLLKNILQSGERIVR-----VSQE---GKPSETRFKVEER----- 225 (317)
T ss_pred HHHHHHHHHhCCccEEEEEEEeCcccC-CCceEecccccCcccCCceEEe-----cCCC---CccceEEEEEeEE-----
Confidence 999999999999999999999998865 3457888886653211110000 0112 3678999998864
Q ss_pred CCCCcchhcccccceeeeeehhhccCCCCceEEEEEEeCCCchhHHHHHHhhcCCceecCCCCCCccccC---CCCCCCc
Q 018524 241 FKEPSELQEHEENNIVVEKKAVLDADAKKNEILVRAFPRSGRTHQIRLHCQYLGISIRGDVKYEGVYEWN---GKRYDGH 317 (354)
Q Consensus 241 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~slv~~~~~TGR~HQIRvhla~lG~PIvGD~~Yg~~~~~~---~~~~~~~ 317 (354)
..++|||+|+|.||||||||+||+++||||+||.+||...... .....++
T Consensus 226 ---------------------------~~~~sLv~~~~~TGRtHQIRvhla~lG~PIlGD~~Yg~~~~~~~~~~~~~~r~ 278 (317)
T PRK11025 226 ---------------------------YAFATLVRASPVTGRTHQIRVHTQYAGHPIAFDDRYGDREFDQQLTGTGLNRL 278 (317)
T ss_pred ---------------------------cCCcEEEEEEeCCCCHHHHHHHHHHCCCCEECCcccCCcccchhhhccCCcch
Confidence 2457999999999999999999999999999999999642111 1124689
Q ss_pred eeeeeeeEeeCCCCCCceEEEcCCChhHHHHHHhcc
Q 018524 318 ELHAESLSFDHPVTGCPVMVQAPLPLWGTEALQSSS 353 (354)
Q Consensus 318 ~LHa~~L~f~~P~~~~~~~~~aplP~~f~~~l~~l~ 353 (354)
+|||++|+|.||.+++.+.|+||+|.+|..+++.|.
T Consensus 279 ~LHa~~l~f~~P~~~~~~~~~aplP~~~~~~l~~l~ 314 (317)
T PRK11025 279 FLHAAALKFTHPGTGEVMRIEAPLDEQLKRCLQKLR 314 (317)
T ss_pred hhhcCcceeeCCCCCCeEEEEcCCCHHHHHHHHHHh
Confidence 999999999999999999999999999999998765
No 3
>TIGR00005 rluA_subfam pseudouridine synthase, RluA family. modifies uracil-65 in transfer RNAs to pseudouridine.
Probab=100.00 E-value=1.9e-54 Score=405.86 Aligned_cols=288 Identities=26% Similarity=0.271 Sum_probs=204.3
Q ss_pred CCCCCcccccccccCC-CCCCCCCCCCCCccccCCC-CCCCCCC-cccccceeEEeecccccccccccCCCccEEEeCCc
Q 018524 16 KAVPRFRKTFFSLASM-SNPTEPTSQNAPQTQQNYP-TPLSPPL-PAISKDIELTRAMSASSKSSLYKLSRSDVLYEDEW 92 (354)
Q Consensus 16 ~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~-~~~~~~~-~~v~~~v~~~~~~~~~~~~~~~~~~~~~Ilyed~~ 92 (354)
++.+||+++||+.... .+|..+.+++..|.+.-.. ....+.. ...++.|.+......++... ..-..++|+|||++
T Consensus 2 ~~~g~rLd~~L~~~~~~~Sr~~~~kli~~G~V~VNg~~~~~~~~~v~~gd~I~i~~~~~~~~~~~-~~~~~~~i~~ed~~ 80 (299)
T TIGR00005 2 EQAGQRLDDFLASLLPDLSRSRIQKLIENGQVKVNGKVTANPKLKVKDGDRITVRVPEEEEHEVP-PQDIPLDILFEDED 80 (299)
T ss_pred CccchhHHHHHHHhcccCCHHHHHHHHHCCcEEECCEeccCcccCCCCCCEEEEecCCcccccCC-ccCCCccEEEeCCC
Confidence 5678999999998775 7999999999998772222 1222222 12233343322111111100 11114679999999
Q ss_pred EEEEECCCCCcccccccccc-ccccccccccccCCCccccccccccccccccCCCCCceEEEEEeCHHHHHHHHHHhhcC
Q 018524 93 LVAVNKPQGVYCESVLASVP-CLLAGDSAESKSGRLSEGTKLNLLELHLANRLDRDTSGVMVITKSHKVASKLVKAFTDH 171 (354)
Q Consensus 93 ~lvvnKP~Gl~~~~~~~~~~-~~~~~~~~~~~~~~l~~~~~~~~~~l~~vhRLDk~TSGllllAk~~~~a~~l~~~f~~~ 171 (354)
|+|||||+|++||+...... ++.+... ..+.... +...+++|||||++||||||||||+++++.|+++|+++
T Consensus 81 ~lvvnKP~g~~~~~~~~~~~~tl~~~l~-----~~~~~~~--~~~~~~~vhRLD~~TSGlll~ak~~~~~~~l~~~~~~~ 153 (299)
T TIGR00005 81 IIVINKPSGLVVHPGGGNPFGTVLNALL-----AHCPPIA--GVERVGIVHRLDRDTSGLMVVAKTPLALRELQRQLKNR 153 (299)
T ss_pred EEEEECCCCCeEeCCCCCCcccHHHHHH-----Hhccccc--CCCcCceECCCCCCCceEEEEEcCHHHHHHHHHHHHhC
Confidence 99999999999997543221 1111111 0010000 01458999999999999999999999999999999999
Q ss_pred ccceEEEEEEeCCCCCCCceEEecCCCCCCCCceeEeeecCCccccCCCcccccceeeEEEeeecCCCCCCCCcchhccc
Q 018524 172 KVSKTYIALCIGPAPKWKRITIISGHGRSKFGAWRVYAASDVGRVLPGGSVVRDMVTSFEVLSVNGEGSFKEPSELQEHE 251 (354)
Q Consensus 172 ~v~K~Y~A~v~G~~~~~~~~~i~~~i~~~~~~~~~~~~~~~~~~~~~~g~~~~~a~t~~~vl~~~~~~~~~~~~~~~~~~ 251 (354)
.|.|+|+|+|.|.++. +.+.++.++.+.......... ..+...+.+.|.|+++..
T Consensus 154 ~v~K~Y~a~v~g~~~~-~~~~i~~~l~~~~~~~~~~~~--------~~~~~~k~a~t~~~~l~~---------------- 208 (299)
T TIGR00005 154 TVTKEYVALVHGQFDS-GGGTVDAPLGRVPNNRGLMAV--------HPSSEGKPAVTHFRVLER---------------- 208 (299)
T ss_pred CcceEEEEEEeccccC-CCCEEeCceecCCCCCceEEE--------ecCCCCCeeeEEEEEeEE----------------
Confidence 9999999999999875 445677777654322211111 011123678888988754
Q ss_pred ccceeeeeehhhccCCCCceEEEEEEeCCCchhHHHHHHhhcCCceecCCCCCCcccc-----CCCCCCCceeeeeeeEe
Q 018524 252 ENNIVVEKKAVLDADAKKNEILVRAFPRSGRTHQIRLHCQYLGISIRGDVKYEGVYEW-----NGKRYDGHELHAESLSF 326 (354)
Q Consensus 252 ~~~~~~~~~~~~~~~~~~~~slv~~~~~TGR~HQIRvhla~lG~PIvGD~~Yg~~~~~-----~~~~~~~~~LHa~~L~f 326 (354)
..++|+++|+|.|||+||||+||+++||||+||.+||+...+ ......+++|||++|+|
T Consensus 209 ----------------~~~~slv~~~l~tGR~HQIR~hla~lG~pI~gD~~Yg~~~~~~~~~~~~~~~~r~~Lha~~l~f 272 (299)
T TIGR00005 209 ----------------FGNASLVECELETGRTHQIRVHLQYLGHPLAGDPLYGNKPVPGNNLNGLLNFDRQALHAYELGF 272 (299)
T ss_pred ----------------cCCeEEEEEEeCCCChHHHHHHHHHCCCcEeCccccCCccccccccccccCCcchhhccCeeec
Confidence 245789999999999999999999999999999999975321 01234689999999999
Q ss_pred eCCCCCCceEEEcCCChhHHHHHHhc
Q 018524 327 DHPVTGCPVMVQAPLPLWGTEALQSS 352 (354)
Q Consensus 327 ~~P~~~~~~~~~aplP~~f~~~l~~l 352 (354)
.||.+++.+.|.||+|.+|..+++.|
T Consensus 273 ~~p~~~~~~~~~a~~p~~~~~~~~~~ 298 (299)
T TIGR00005 273 IHPATGEILEFEAPLPADLVLLLEAL 298 (299)
T ss_pred cCCCCCCEEEEEcCChHHHHHHHHhh
Confidence 99999999999999999999998876
No 4
>PRK11180 rluD 23S rRNA pseudouridine synthase D; Provisional
Probab=100.00 E-value=6.4e-54 Score=405.69 Aligned_cols=292 Identities=21% Similarity=0.258 Sum_probs=210.6
Q ss_pred ccccCCCCCCCccccccccc-CCCCCCCCCCCCCCccccCCCCCCC-CCC-cccccceeEEeecccccccccccCCCccE
Q 018524 10 TFTLTPKAVPRFRKTFFSLA-SMSNPTEPTSQNAPQTQQNYPTPLS-PPL-PAISKDIELTRAMSASSKSSLYKLSRSDV 86 (354)
Q Consensus 10 ~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~-~~~-~~v~~~v~~~~~~~~~~~~~~~~~~~~~I 86 (354)
++.+..++.++|+|+|++.. ...||..+.+++..|.|.-...++. +.. ...++.|.+........... ..-.++.|
T Consensus 8 ~~~v~~~~~g~RLd~~L~~~~~~~Sr~~~~~lI~~G~V~VNg~~v~~~~~~v~~gD~I~v~~~~~~~~~~~-~~~~~~~i 86 (325)
T PRK11180 8 TATVSESQLGQRLDQALAELFPDYSRSRIKEWILDQRVLVNGKVINKPKEKVLGGEQVAIDAEIEEEARFE-PQDIPLDI 86 (325)
T ss_pred EEEECcccCCccHHHHHHhhccccCHHHHHHHHHCCCEEECCEEccCCCcCcCCCCEEEEeeccccccCCC-CCCCCCcE
Confidence 46677788899999999987 4679999999999997733333332 221 22344444433211110000 01125689
Q ss_pred EEeCCcEEEEECCCCCccccccccc-cccccccccccccCCCccccccccccccccccCCCCCceEEEEEeCHHHHHHHH
Q 018524 87 LYEDEWLVAVNKPQGVYCESVLASV-PCLLAGDSAESKSGRLSEGTKLNLLELHLANRLDRDTSGVMVITKSHKVASKLV 165 (354)
Q Consensus 87 lyed~~~lvvnKP~Gl~~~~~~~~~-~~~~~~~~~~~~~~~l~~~~~~~~~~l~~vhRLDk~TSGllllAk~~~~a~~l~ 165 (354)
||||++|||||||+|++||+..... .++.+... ..+.... +...+++|||||++||||||||||.++++.|+
T Consensus 87 iyed~~~lvvnKP~gl~~~~~~~~~~~tl~~~l~-----~~~~~~~--~~~~~~~vhRLD~~TSGlll~Ak~~~~~~~l~ 159 (325)
T PRK11180 87 VYEDDDILVINKPRDLVVHPGAGNPDGTVLNALL-----HYYPPIA--DVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLV 159 (325)
T ss_pred EEECCCEEEEECCCCCeEeCCCCCCCCcHHHHHH-----HHhhhcc--CCcccceeccCCCCCceeEEEECCHHHHHHHH
Confidence 9999999999999999999754321 11111111 0111100 11357899999999999999999999999999
Q ss_pred HHhhcCccceEEEEEEeCCCCCCCceEEecCCCCCCCCceeEeeecCCccccCCCcccccceeeEEEeeecCCCCCCCCc
Q 018524 166 KAFTDHKVSKTYIALCIGPAPKWKRITIISGHGRSKFGAWRVYAASDVGRVLPGGSVVRDMVTSFEVLSVNGEGSFKEPS 245 (354)
Q Consensus 166 ~~f~~~~v~K~Y~A~v~G~~~~~~~~~i~~~i~~~~~~~~~~~~~~~~~~~~~~g~~~~~a~t~~~vl~~~~~~~~~~~~ 245 (354)
++|+++.|.|+|+|+|.|.++. .+.++.++.+.......+.. .+. .+.+.|.|+++..
T Consensus 160 ~~~~~~~v~K~Y~A~v~G~~~~--~~~i~~~l~~~~~~~~~~~~-------~~~---gk~a~T~~~~l~~---------- 217 (325)
T PRK11180 160 EALQKREITREYEAVAIGHMTA--GGTVDEPISRHPTKRTHMAV-------HPM---GKPAVTHYRIMEH---------- 217 (325)
T ss_pred HHHHhCCcceEEEEEEecCCCC--CCEEECceecCCCcCcEEEe-------CCC---CcEEeEEEEEeEE----------
Confidence 9999999999999999999874 35677777654322211110 112 2678899998864
Q ss_pred chhcccccceeeeeehhhccCCCCceEEEEEEeCCCchhHHHHHHhhcCCceecCCCCCCccccC----------CCCCC
Q 018524 246 ELQEHEENNIVVEKKAVLDADAKKNEILVRAFPRSGRTHQIRLHCQYLGISIRGDVKYEGVYEWN----------GKRYD 315 (354)
Q Consensus 246 ~~~~~~~~~~~~~~~~~~~~~~~~~~slv~~~~~TGR~HQIRvhla~lG~PIvGD~~Yg~~~~~~----------~~~~~ 315 (354)
..++++++|+|+||||||||+||+++||||+||.+||+..... .....
T Consensus 218 ----------------------~~~~slv~~~~~TGRtHQIRvhla~lG~PI~GD~~Yg~~~~~~~~~~~~~~~~~~~~~ 275 (325)
T PRK11180 218 ----------------------FRVHTRLRLRLETGRTHQIRVHMAHITHPLVGDQVYGGRPRPPKGASEEFISTLRKFD 275 (325)
T ss_pred ----------------------cCCeEEEEEEeCCCCHHHHHHHHHhCCCCEeCccccCCCcccccccchhhhhhccccc
Confidence 2457999999999999999999999999999999999753210 00246
Q ss_pred CceeeeeeeEeeCCCCCCceEEEcCCChhHHHHHHhcc
Q 018524 316 GHELHAESLSFDHPVTGCPVMVQAPLPLWGTEALQSSS 353 (354)
Q Consensus 316 ~~~LHa~~L~f~~P~~~~~~~~~aplP~~f~~~l~~l~ 353 (354)
+++|||++|+|.||.+++.+.|.||+|++|.++++.|.
T Consensus 276 r~~Lha~~l~f~hP~~~~~~~~~a~~p~~~~~~~~~l~ 313 (325)
T PRK11180 276 RQALHATMLRLYHPITGIEMEWHAPLPQDMVELIEALR 313 (325)
T ss_pred hhhhhcceeEeeCCCCCCeEEEECCChHHHHHHHHHhh
Confidence 89999999999999999999999999999999998774
No 5
>PRK11112 tRNA pseudouridine synthase C; Provisional
Probab=100.00 E-value=6e-52 Score=379.48 Aligned_cols=230 Identities=27% Similarity=0.303 Sum_probs=168.0
Q ss_pred ccEEEeCCcEEEEECCCCCccccccccccccccccccccccCCCccccccccccccccccCCCCCceEEEEEeCHHHHHH
Q 018524 84 SDVLYEDEWLVAVNKPQGVYCESVLASVPCLLAGDSAESKSGRLSEGTKLNLLELHLANRLDRDTSGVMVITKSHKVASK 163 (354)
Q Consensus 84 ~~Ilyed~~~lvvnKP~Gl~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~l~~vhRLDk~TSGllllAk~~~~a~~ 163 (354)
++|||||++|||||||+|++||+......... .+...+..... ..+++|||||++||||||||||+++++.
T Consensus 2 l~IlyEd~~~lvvnKPaGl~~~~~~~~~~~~~------~~~~~l~~~~~---~~~~~VHRLDr~TSGlll~Ak~~~~~~~ 72 (257)
T PRK11112 2 LEILYQDEWLVAVNKPAGWLVHRSWLDRHETV------FVMQTVRDQIG---QHVFTAHRLDRPTSGVLLMALSSEVARL 72 (257)
T ss_pred CcEEEecCCEEEEECCCCCeecCCCCCCCchH------HHHHHHHHHhC---CCceeeccCCCCCeeEEEEECCHHHHHH
Confidence 47999999999999999999987521111100 01111111111 3478999999999999999999999999
Q ss_pred HHHHhhcCccceEEEEEEeCCCCCCCceEEecCCCCCCCCceeEeeecCCccccCCCcccccceeeEEEeeecCCCCCCC
Q 018524 164 LVKAFTDHKVSKTYIALCIGPAPKWKRITIISGHGRSKFGAWRVYAASDVGRVLPGGSVVRDMVTSFEVLSVNGEGSFKE 243 (354)
Q Consensus 164 l~~~f~~~~v~K~Y~A~v~G~~~~~~~~~i~~~i~~~~~~~~~~~~~~~~~~~~~~g~~~~~a~t~~~vl~~~~~~~~~~ 243 (354)
|+++|+++.|.|+|+|+|.|.++.+ ..++.++........... .......+++.|.|+++.......
T Consensus 73 L~~~f~~~~v~K~Y~Alv~G~~~~~--~~i~~~l~~~~~~~~~~~--------~~~~~~~k~a~T~~~~l~~~~~~~--- 139 (257)
T PRK11112 73 LAQQFEQHQIQKTYHAIVRGWLMEE--AVLDYPLKEELDKIADKF--------AREDKAPQPAVTHYRGLATVEMPV--- 139 (257)
T ss_pred HHHHHHhCCcceEEEEEEEeEeCCC--CeEeeeeeecccccceee--------cccCCCCeEeEEEEEEEEEecccc---
Confidence 9999999999999999999988643 456666654321110000 001122467899999886421100
Q ss_pred CcchhcccccceeeeeehhhccCCCCceEEEEEEeCCCchhHHHHHHhhcCCceecCCCCCCccccC----CCCCCCcee
Q 018524 244 PSELQEHEENNIVVEKKAVLDADAKKNEILVRAFPRSGRTHQIRLHCQYLGISIRGDVKYEGVYEWN----GKRYDGHEL 319 (354)
Q Consensus 244 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~slv~~~~~TGR~HQIRvhla~lG~PIvGD~~Yg~~~~~~----~~~~~~~~L 319 (354)
.. ......++++++|+|.|||+||||+||+++||||+||.+||...... .....+++|
T Consensus 140 --~~----------------~~~~~~~~slv~i~~~TGRtHQIRvhla~lG~PIvGD~~Yg~~~~~~~~~~~~~~~rl~L 201 (257)
T PRK11112 140 --AT----------------GRYPTTRYSLVELEPKTGRKHQLRRHMAHLRHPIIGDTKHGDLRQNRSLAEHFGCSRLML 201 (257)
T ss_pred --cc----------------cccCCCCeEEEEEEcCCCChHHHHHHHHHcCCCEeCCcccCCcccchhhhhccCCcchhH
Confidence 00 00012457999999999999999999999999999999999742211 113468999
Q ss_pred eeeeeEeeCCCCCCceEEEcCCChhHHHHHHhcc
Q 018524 320 HAESLSFDHPVTGCPVMVQAPLPLWGTEALQSSS 353 (354)
Q Consensus 320 Ha~~L~f~~P~~~~~~~~~aplP~~f~~~l~~l~ 353 (354)
||++|+|.||.+++.+.|+||+|.+|+.+++.|+
T Consensus 202 HA~~L~F~hP~t~e~~~~~a~~p~~~~~~~~~~~ 235 (257)
T PRK11112 202 HASELSLTHPFTGEPLTITAGLDETWQQLLSQFG 235 (257)
T ss_pred hhCccCccCCCCCCEEEEEcCCCHHHHHHHHHcC
Confidence 9999999999999999999999999999998875
No 6
>cd02563 PseudoU_synth_TruC tRNA pseudouridine isomerase C: Pseudouridine synthases catalyze the isomerization of specific uridines in an tRNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. TruC makes psi65 in tRNAs. This psi residue is not universally conserved.
Probab=100.00 E-value=2.4e-50 Score=362.10 Aligned_cols=218 Identities=30% Similarity=0.367 Sum_probs=158.0
Q ss_pred cEEEeCCcEEEEECCCCCccccccccccccccccccccccCCCccccccccccccccccCCCCCceEEEEEeCHHHHHHH
Q 018524 85 DVLYEDEWLVAVNKPQGVYCESVLASVPCLLAGDSAESKSGRLSEGTKLNLLELHLANRLDRDTSGVMVITKSHKVASKL 164 (354)
Q Consensus 85 ~Ilyed~~~lvvnKP~Gl~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~l~~vhRLDk~TSGllllAk~~~~a~~l 164 (354)
+|||||++|+|||||+|++|++......... .....+..... ..+++|||||++||||||||||+++++.|
T Consensus 2 ~Ilyed~~~lvvnKP~G~~~~~~~~~~~~~~------~~~~~l~~~~~---~~~~~vhRLD~~TSGlll~Ak~~~~~~~l 72 (223)
T cd02563 2 EILYQDEHLVAINKPSGLLVHRSELDRHETR------FALQTLRDQLG---QHVYPVHRLDRPTSGVLLFALSSEVARKL 72 (223)
T ss_pred cEEEecCCEEEEECCCCCeEcCCCCCCCCcH------HHHHHHHHHcC---CCcccccCCCCCCeEEEEEEECHHHHHHH
Confidence 6999999999999999999986532111100 00011111111 35889999999999999999999999999
Q ss_pred HHHhhcCccceEEEEEEeCCCCCCCceEEecCCCCCCCCceeEeeecCCccccCCCcccccceeeEEEeeecCCCCCCCC
Q 018524 165 VKAFTDHKVSKTYIALCIGPAPKWKRITIISGHGRSKFGAWRVYAASDVGRVLPGGSVVRDMVTSFEVLSVNGEGSFKEP 244 (354)
Q Consensus 165 ~~~f~~~~v~K~Y~A~v~G~~~~~~~~~i~~~i~~~~~~~~~~~~~~~~~~~~~~g~~~~~a~t~~~vl~~~~~~~~~~~ 244 (354)
+++|+++.++|+|+|+|.|.++. ...++.++.+.......... ......+.+.|.|+++.......
T Consensus 73 ~~~f~~~~v~K~Y~alv~G~~~~--~~~i~~~l~~~~~~~~~~~~--------~~~~~~~~a~t~~~~l~~~~~~~---- 138 (223)
T cd02563 73 GEQFTEHRVHKTYLAVVRGYVPE--SGTIDYPLSEELDKLADKFA--------SDDKAPQAATTHYRLLAVEELPV---- 138 (223)
T ss_pred HHHHhcCceeEEEEEEEECccCC--CCeEEEeeeeCCCccceEEe--------ecCCCCceeEEEEEEeeeccccc----
Confidence 99999999999999999999865 34666666544322111100 01112367889999886421100
Q ss_pred cchhcccccceeeeeehhhccCCCCceEEEEEEeCCCchhHHHHHHhhcCCceecCCCCCCcccc----CCCCCCCceee
Q 018524 245 SELQEHEENNIVVEKKAVLDADAKKNEILVRAFPRSGRTHQIRLHCQYLGISIRGDVKYEGVYEW----NGKRYDGHELH 320 (354)
Q Consensus 245 ~~~~~~~~~~~~~~~~~~~~~~~~~~~slv~~~~~TGR~HQIRvhla~lG~PIvGD~~Yg~~~~~----~~~~~~~~~LH 320 (354)
........++++++|+|.|||+||||+||+++||||+||.+||+.... ......+++||
T Consensus 139 -----------------~~~~~~~~~~slv~~~~~TGR~HQIRvhla~lG~PIvGD~~Yg~~~~~~~~~~~~~~~rl~Lh 201 (223)
T cd02563 139 -----------------VVGKYPTSRYSLVELTPHTGRKHQLRRHLAHIRHPIIGDTTHGDGRHNRFFREHFGCHRLLLA 201 (223)
T ss_pred -----------------ccccCCCCCeEEEEEEeCCCCHHHHHHHHHHcCCCeeCCcccCCcccChhHHhhcCCccceee
Confidence 000001235899999999999999999999999999999999975311 11234689999
Q ss_pred eeeeEeeCCCCCCceEEEcCCC
Q 018524 321 AESLSFDHPVTGCPVMVQAPLP 342 (354)
Q Consensus 321 a~~L~f~~P~~~~~~~~~aplP 342 (354)
|++|.|.||.+|+.+.|+||+|
T Consensus 202 a~~L~F~hP~t~~~~~~~a~~~ 223 (223)
T cd02563 202 ATRLEFTHPVTGERLLIEAPLD 223 (223)
T ss_pred cCeeEeeCCCCCCeEEEEccCC
Confidence 9999999999999999999987
No 7
>TIGR01621 RluA-like pseudouridine synthase Rlu family protein, TIGR01621. This model represents a clade of sequences within the pseudouridine synthase superfamily (pfam00849). The superfamily includes E. coli proteins: RluA, RluB, RluC, RluD, and RsuA. The sequences modeled here are most closely related to RluA. Neisseria, among those species hitting this model, does not appear to have an RluA homolog. It is presumed that these sequences function as pseudouridine synthases, although perhaps with different specificity.
Probab=100.00 E-value=5.5e-50 Score=357.67 Aligned_cols=202 Identities=26% Similarity=0.342 Sum_probs=158.0
Q ss_pred ccEEEeCCcEEEEECCCCCccccccccccccccccccccccCCCccccccccccccccccCCCCCceEEEEEeCHHHHHH
Q 018524 84 SDVLYEDEWLVAVNKPQGVYCESVLASVPCLLAGDSAESKSGRLSEGTKLNLLELHLANRLDRDTSGVMVITKSHKVASK 163 (354)
Q Consensus 84 ~~Ilyed~~~lvvnKP~Gl~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~l~~vhRLDk~TSGllllAk~~~~a~~ 163 (354)
++|||||++|+|||||+|++||+.... ..+... +.... +...+++|||||++||||||||||+++++.
T Consensus 2 ~~ilyed~~~lvvnKP~Gl~v~~~~~~-~~l~~~---------l~~~~--~~~~~~~VhRLDr~TSGlll~Ak~~~~~~~ 69 (217)
T TIGR01621 2 FEILFTHPDFLLINKHPGISVHKDDGE-TGLLQE---------VATQL--GVGQVWLVHRLDKMTSGILLLALNAESASE 69 (217)
T ss_pred ceEEEeCCCEEEEECCCCCeECCCCCc-ChHHHH---------HHHhc--CCCCccEecCCCCCCceEEEEEcCHHHHHH
Confidence 479999999999999999999865321 111111 10110 114689999999999999999999999999
Q ss_pred HHHHhhcCccceEEEEEEeCCCCCCCceEEecCCCCCCCCceeEeeecCCccccCCCcccccceeeEEEeeecCCCCCCC
Q 018524 164 LVKAFTDHKVSKTYIALCIGPAPKWKRITIISGHGRSKFGAWRVYAASDVGRVLPGGSVVRDMVTSFEVLSVNGEGSFKE 243 (354)
Q Consensus 164 l~~~f~~~~v~K~Y~A~v~G~~~~~~~~~i~~~i~~~~~~~~~~~~~~~~~~~~~~g~~~~~a~t~~~vl~~~~~~~~~~ 243 (354)
|+++|+++.++|+|+|+|.|.++. +.+.++.++.....+.+.+.. .+ .+.+.|+|+++..
T Consensus 70 L~~~~~~~~v~K~YlAlV~g~~~~-~~~~i~~~~~~~~~~~~~~~~--------~~---~k~a~t~~~~~~~-------- 129 (217)
T TIGR01621 70 LSQGFAKRKIEKTYLALSSKKPKK-KQGLICGDMEKSRRGSWKLVN--------SQ---ENPAITRFFSASA-------- 129 (217)
T ss_pred HHHHHhcCCccEEEEEEEeccccC-CCCEEeCCcccCCCCCEEEeC--------CC---CCceeEEEEEEEE--------
Confidence 999999999999999999999875 445677777655544332210 11 2567888888754
Q ss_pred CcchhcccccceeeeeehhhccCCCCceEEEEEEeCCCchhHHHHHHhhcCCceecCCCCCCccccCCCCCCCceeeeee
Q 018524 244 PSELQEHEENNIVVEKKAVLDADAKKNEILVRAFPRSGRTHQIRLHCQYLGISIRGDVKYEGVYEWNGKRYDGHELHAES 323 (354)
Q Consensus 244 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~slv~~~~~TGR~HQIRvhla~lG~PIvGD~~Yg~~~~~~~~~~~~~~LHa~~ 323 (354)
..+.++++|+|.|||+||||+||+++||||+||.+||+.. ...+++|||++
T Consensus 130 ------------------------~~~~slv~~~~~TGR~HQIRvhla~lG~PIlGD~~Yg~~~-----~~~~~~Lha~~ 180 (217)
T TIGR01621 130 ------------------------ATGLRLFILKPHTGKTHQLRVAMKSLGSPILGDPLYGTTD-----ESDRGYLHAFA 180 (217)
T ss_pred ------------------------cCCeEEEEEEeCCCCHHHHHHHHHHCCCceeCCcccCCCC-----CccCceeeeeE
Confidence 2457999999999999999999999999999999999742 24679999999
Q ss_pred eEeeCCCCCCceEEEcCCChhHHHHH
Q 018524 324 LSFDHPVTGCPVMVQAPLPLWGTEAL 349 (354)
Q Consensus 324 L~f~~P~~~~~~~~~aplP~~f~~~l 349 (354)
|.|+| +++.+.|+|| |++|..++
T Consensus 181 l~f~~--~~~~~~~~~~-~~~~~~~~ 203 (217)
T TIGR01621 181 LRFDY--QNEVIQWLCD-PRQFQKWH 203 (217)
T ss_pred eEEEE--CCeEEEEEEC-cHHHHHHH
Confidence 99998 5899999999 66665443
No 8
>cd02558 PSRA_1 PSRA_1: Pseudouridine synthase, a subgroup of the RluA family. This group is comprised of bacterial proteins assigned to the RluA family of pseudouridine synthases. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. The RluA family is comprised of proteins related to Escherichia coli RluA.
Probab=100.00 E-value=9.1e-50 Score=362.80 Aligned_cols=206 Identities=27% Similarity=0.300 Sum_probs=154.7
Q ss_pred CccEEEeCCcEEEEECCCCCccccccccccc-cccccccccccCCCccccccccccccccccCCCCCceEEEEEeCHHHH
Q 018524 83 RSDVLYEDEWLVAVNKPQGVYCESVLASVPC-LLAGDSAESKSGRLSEGTKLNLLELHLANRLDRDTSGVMVITKSHKVA 161 (354)
Q Consensus 83 ~~~Ilyed~~~lvvnKP~Gl~~~~~~~~~~~-~~~~~~~~~~~~~l~~~~~~~~~~l~~vhRLDk~TSGllllAk~~~~a 161 (354)
+++|||||++|+|||||+|++||+....... ++.. +.... +...+++|||||++||||||||||++++
T Consensus 38 ~~~Iiyed~~~lvvnKPaGl~~~~~~~~~~~t~~~~---------l~~~~--~~~~~~~vhRLD~~TSGlll~Ak~~~~~ 106 (246)
T cd02558 38 EETILHQDEHLLVADKPHFLPVTPRGRYVTETLLVR---------LRRQT--GNPDLTPAHRLDRLTAGLVLFSKRPETR 106 (246)
T ss_pred CcceEEecCCEEEEECCCCCccCCCCcchhhhHHHH---------HHHHh--CCCcccccccCCCCceeEEEEEcCHHHH
Confidence 5789999999999999999999975432221 1111 11110 1145789999999999999999999999
Q ss_pred HHHHHHhhcCccceEEEEEEeCCCCCCCceEEecCCCCCCCCceeEeeecCCccccCCCcccccceeeEEEeeecCCCCC
Q 018524 162 SKLVKAFTDHKVSKTYIALCIGPAPKWKRITIISGHGRSKFGAWRVYAASDVGRVLPGGSVVRDMVTSFEVLSVNGEGSF 241 (354)
Q Consensus 162 ~~l~~~f~~~~v~K~Y~A~v~G~~~~~~~~~i~~~i~~~~~~~~~~~~~~~~~~~~~~g~~~~~a~t~~~vl~~~~~~~~ 241 (354)
+.++.+|+++.++|+|+|+|.|.++.+....+...+.+.... ... ...+| .+.+.|+|+++..
T Consensus 107 ~~l~~~~~~~~v~K~YlA~v~G~~~~~~~~~~~~~i~~~~~~-~~~--------~~~~~--~~~a~T~~~~l~~------ 169 (246)
T cd02558 107 GAYQTLFARREVSKTYEAVAPYVPALTFPLTVRSRIVKGRGF-FQA--------REVEG--EPNAETRIELLAR------ 169 (246)
T ss_pred HHHHHHHHcCCccEEEEEEEecCCCCCCCcceeccccccCCc-cee--------eccCC--CCCceEEEEEEEe------
Confidence 999999999999999999999987643322344444332211 000 01112 2467888888754
Q ss_pred CCCcchhcccccceeeeeehhhccCCCCceEEEEEEeCCCchhHHHHHHhhcCCceecCCCCCCccccCCCC-CCCceee
Q 018524 242 KEPSELQEHEENNIVVEKKAVLDADAKKNEILVRAFPRSGRTHQIRLHCQYLGISIRGDVKYEGVYEWNGKR-YDGHELH 320 (354)
Q Consensus 242 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~slv~~~~~TGR~HQIRvhla~lG~PIvGD~~Yg~~~~~~~~~-~~~~~LH 320 (354)
..++|+++|+|.|||+||||+||+++||||+||.+||......... ..+++||
T Consensus 170 --------------------------~~~~slv~~~l~TGRtHQIRvhla~lG~PIvGD~~Yg~~~~~~~~~~~~~~~Lh 223 (246)
T cd02558 170 --------------------------RGGWGLYRLSPHTGKTHQLRVHMAALGVPILNDPFYPVLLDKDPDDFSRPLQLL 223 (246)
T ss_pred --------------------------cCCeEEEEEEeCCCCHHHHHHHHHHCCCcccCCccCCCCCcccccccccCchhh
Confidence 2467899999999999999999999999999999999742111111 2358999
Q ss_pred eeeeEeeCCCCCCceEEEcCCC
Q 018524 321 AESLSFDHPVTGCPVMVQAPLP 342 (354)
Q Consensus 321 a~~L~f~~P~~~~~~~~~aplP 342 (354)
|++|.|.||.+++.+.|+||+|
T Consensus 224 a~~l~f~hP~t~~~~~~~~~~~ 245 (246)
T cd02558 224 AKELEFTDPLTGRPRRFESGRS 245 (246)
T ss_pred hcccCccCCCCCCEEEEecCCC
Confidence 9999999999999999999998
No 9
>PRK10158 23S rRNA/tRNA pseudouridine synthase A; Provisional
Probab=100.00 E-value=3.5e-49 Score=353.15 Aligned_cols=206 Identities=26% Similarity=0.310 Sum_probs=156.3
Q ss_pred CccEEEeCCcEEEEECCCCCccccccccccccccccccccccCCCccccccccccccccccCCCCCceEEEEEeCHHHHH
Q 018524 83 RSDVLYEDEWLVAVNKPQGVYCESVLASVPCLLAGDSAESKSGRLSEGTKLNLLELHLANRLDRDTSGVMVITKSHKVAS 162 (354)
Q Consensus 83 ~~~Ilyed~~~lvvnKP~Gl~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~l~~vhRLDk~TSGllllAk~~~~a~ 162 (354)
.+.|||||++|+|||||+|++|++....... .++...+.... ..+++|||||++||||||+|||.++++
T Consensus 13 ~~~iiyed~~~lvvnKPaGl~~~~~~~~~~~-------~sl~~~l~~~~----~~~~~vhRLDr~TSGlll~Akt~~~~~ 81 (219)
T PRK10158 13 WLVILYQDEHIMVVNKPSGLLSVPGRLEEHK-------DSVMTRIQRDY----PQAESVHRLDMATSGVIVVALTKAAER 81 (219)
T ss_pred CCCEEEeCCCEEEEECCCCCcEeCCCCCccc-------hhHHHHHHHhC----CCCCEECCCCCCCceEEEEECCHHHHH
Confidence 3579999999999999999999864311000 01111111111 357899999999999999999999999
Q ss_pred HHHHHhhcCccceEEEEEEeCCCCCCCceEEecCCCCCCCCceeEeeecCCccccCCCcccccceeeEEEeeecCCCCCC
Q 018524 163 KLVKAFTDHKVSKTYIALCIGPAPKWKRITIISGHGRSKFGAWRVYAASDVGRVLPGGSVVRDMVTSFEVLSVNGEGSFK 242 (354)
Q Consensus 163 ~l~~~f~~~~v~K~Y~A~v~G~~~~~~~~~i~~~i~~~~~~~~~~~~~~~~~~~~~~g~~~~~a~t~~~vl~~~~~~~~~ 242 (354)
.|+++|.++.|.|+|+|+|.|.++. ....++.++............ ...+| +.+.|.|+++...
T Consensus 82 ~l~~~f~~~~v~K~Yla~v~G~~~~-~~~~i~~~i~~~~~~~~~~~~------~~~~g---k~a~t~~~~l~~~------ 145 (219)
T PRK10158 82 ELKRQFREREPKKQYVARVWGHPSP-AEGLVDLPLICDWPNRPKQKV------CYETG---KPAQTEYEVVEYA------ 145 (219)
T ss_pred HHHHHHHhCCccEEEEEEEecccCC-CCcEEecceecCCCCCceEEe------cCCCC---ceeeEEEEEEEEc------
Confidence 9999999999999999999999865 445677776543222111111 01222 5788888887641
Q ss_pred CCcchhcccccceeeeeehhhccCCCCceEEEEEEeCCCchhHHHHHHhhcCCceecCCCCCCccccCCCCCCCceeeee
Q 018524 243 EPSELQEHEENNIVVEKKAVLDADAKKNEILVRAFPRSGRTHQIRLHCQYLGISIRGDVKYEGVYEWNGKRYDGHELHAE 322 (354)
Q Consensus 243 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~slv~~~~~TGR~HQIRvhla~lG~PIvGD~~Yg~~~~~~~~~~~~~~LHa~ 322 (354)
....++++|+|+|||+||||+||+++||||+||.+||..... ....+++|||+
T Consensus 146 -------------------------~~~~sll~~~~~TGRtHQIR~hla~lG~PIvGD~~Yg~~~~~--~~~~r~~Lha~ 198 (219)
T PRK10158 146 -------------------------ADNTARVVLKPITGRSHQLRVHMLALGHPILGDRFYASPEAR--AMAPRLLLHAE 198 (219)
T ss_pred -------------------------CCCCEEEEEEeCCCCHHHHHHHHHHCCCcEECCcccCCcccc--ccccchhhhhC
Confidence 123479999999999999999999999999999999974321 12467999999
Q ss_pred eeEeeCCCCCCceEEEcCCC
Q 018524 323 SLSFDHPVTGCPVMVQAPLP 342 (354)
Q Consensus 323 ~L~f~~P~~~~~~~~~aplP 342 (354)
+|.|.||.+++.+.|.||.|
T Consensus 199 ~l~f~~P~~~~~~~~~a~~~ 218 (219)
T PRK10158 199 MLTITHPAYGNSMTFKAPAD 218 (219)
T ss_pred ccCccCCCCCCeEEEEeCCC
Confidence 99999999999999999986
No 10
>cd02557 PseudoU_synth_ScRIB2 PseudoU_synth_ScRIB2_like: Pseudouridine synthase, Saccharomyces cerevisiae RIB2_like. This group is comprised of eukaryotic and bacterial proteins similar to Saccharomyces cerevisiae RIB2, S. cerevisiae Pus6p and human hRPUDSD2. S. cerevisiae RIB2 displays two distinct catalytic activities. The N-terminal domain of RIB2 is RNA:psi-synthase which makes psi32 on cytoplasmic tRNAs. Psi32 is highly phylogenetically conserved. The C-terminal domain of RIB2 has a DRAP deaminase activity which catalyses the formation of 5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione 5'-phosphate from 2,5-diamino-6-ribitylamino-4(3H)-pyrimidinone 5'-phosphate during riboflavin biosynthesis. S. cerevisiae Pus6p makes the psi31 of cytoplasmic and mitochondrial tRNAs.
Probab=100.00 E-value=1.4e-48 Score=348.08 Aligned_cols=202 Identities=30% Similarity=0.346 Sum_probs=154.3
Q ss_pred ccCCCccEEEeCCcEEEEECCCCCccccccccccccccccccccccCCCccccccccccccccccCCCCCceEEEEEeCH
Q 018524 79 YKLSRSDVLYEDEWLVAVNKPQGVYCESVLASVPCLLAGDSAESKSGRLSEGTKLNLLELHLANRLDRDTSGVMVITKSH 158 (354)
Q Consensus 79 ~~~~~~~Ilyed~~~lvvnKP~Gl~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~l~~vhRLDk~TSGllllAk~~ 158 (354)
+...+++|||||++|+|+|||+|++|++....... ++.+.+..... ...+++|||||++||||||||||+
T Consensus 11 ~~~~~~~iiyed~~~ivvnKP~Gl~~~~~~~~~~~--------sl~~~l~~~~~--~~~~~~vhRLD~~TSGllllak~~ 80 (213)
T cd02557 11 VTNDPIKIVHEDDDLLVVDKPSGIPVHPTGRYRYN--------TVTEILKSEYG--LTELRPCHRLDRLTSGLLLFAKTS 80 (213)
T ss_pred CCCCCCcEEEECCCEEEEECCCCCcCCCCCCCCcC--------hHHHHHHHHcC--CCCccCccCCCCCCceEEEEECCH
Confidence 33447899999999999999999999864332111 11112211111 135889999999999999999999
Q ss_pred HHHHHHHHHhhcCccceEEEEEEeCCCCCCCceEEecCCCCCCCCceeEeeecCCccccCCCcccccceeeEEEeeecCC
Q 018524 159 KVASKLVKAFTDHKVSKTYIALCIGPAPKWKRITIISGHGRSKFGAWRVYAASDVGRVLPGGSVVRDMVTSFEVLSVNGE 238 (354)
Q Consensus 159 ~~a~~l~~~f~~~~v~K~Y~A~v~G~~~~~~~~~i~~~i~~~~~~~~~~~~~~~~~~~~~~g~~~~~a~t~~~vl~~~~~ 238 (354)
+++++|+++|+++.++|+|+|+|.|.++. +...++.++.......... .......+.+.|.|+++....
T Consensus 81 ~~~~~l~~~f~~~~v~K~Y~a~v~G~~~~-~~~~i~~~l~~~~~~~~~~---------~~~~~~~~~a~t~~~~~~~~~- 149 (213)
T cd02557 81 QTASRLQQQIRSREVKKEYLARVKGEFPD-GEVVVDQPIGLVSPKGGLR---------NDVDEKGKDARTIFKRLSYNG- 149 (213)
T ss_pred HHHHHHHHHHHcCCccEEEEEEEeCcCCC-CCeEEecceeccCcCCcee---------eccCCCCceeeEEEEEEEEcC-
Confidence 99999999999999999999999999875 4566777765432211100 011122366788888876421
Q ss_pred CCCCCCcchhcccccceeeeeehhhccCCCCceEEEEEEeCCCchhHHHHHHhhcCCceecCCCCCCccccCCCCCCCce
Q 018524 239 GSFKEPSELQEHEENNIVVEKKAVLDADAKKNEILVRAFPRSGRTHQIRLHCQYLGISIRGDVKYEGVYEWNGKRYDGHE 318 (354)
Q Consensus 239 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~slv~~~~~TGR~HQIRvhla~lG~PIvGD~~Yg~~~~~~~~~~~~~~ 318 (354)
..++++++|+|.|||+||||+||+++||||+||.+||+ .+++
T Consensus 150 -----------------------------~~~~slv~v~~~TGR~HQIR~hla~lG~PIlGD~~Yg~---------~~l~ 191 (213)
T cd02557 150 -----------------------------DLNTSVVLCKPITGRTHQIRVHLQYLGHPIVNDPIYNN---------LGIY 191 (213)
T ss_pred -----------------------------CCCeEEEEEEeCCCCHHHHHHHHHHCCCCCcCccccCC---------cChh
Confidence 12578999999999999999999999999999999997 3599
Q ss_pred eeeeeeEeeCCCCCCceEEEcCCChhH
Q 018524 319 LHAESLSFDHPVTGCPVMVQAPLPLWG 345 (354)
Q Consensus 319 LHa~~L~f~~P~~~~~~~~~aplP~~f 345 (354)
|||++|.|+ .++|.||+|.||
T Consensus 192 Lha~~l~f~------~~~~~~~~p~~~ 212 (213)
T cd02557 192 LHALRYEGP------DWSYETELPDWA 212 (213)
T ss_pred hhhccCcCc------cEEEEeCCCccc
Confidence 999999995 799999999887
No 11
>cd02869 PseudoU_synth_RluCD_like PseudoU_synth_RsuA/RluD: Pseudouridine synthase, RsuA/RluD family. This group is comprised of eukaryotic, bacterial and archeal proteins similar to eight site specific Escherichia coli pseudouridine synthases: RsuA, RluA, RluB, RluC, RluD, RluE, RluF and TruA. Pseudouridine synthases catalyze the isomerization of specific uridines in a n RNA molecule to pseudouridines (5-ribosyluracil, psi) requiring no cofactors. E. coli RluC for example makes psi955, 2504 and 2580 in 23S RNA. Some psi sites such as psi1917 in 23S RNA made by RluD are universally conserved. Other psi sites occur in a more restricted fashion, for example psi2819 in 21S mitochondrial ribosomal RNA made by S. cerevisiae Pus5p is only found in mitochondrial large subunit rRNAs from some other species and in gram negative bacteria. The E. coli counterpart of this psi residue is psi2580 in 23S rRNA. psi2604in 23S RNA made by RluF has only been detected in E.coli.
Probab=100.00 E-value=2.1e-39 Score=283.25 Aligned_cols=185 Identities=35% Similarity=0.421 Sum_probs=130.9
Q ss_pred EEEEECCCCCccccccccccccccccccccccCCCccccccccccccccccCCCCCceEEEEEeCHHHHHHHHHHhhcCc
Q 018524 93 LVAVNKPQGVYCESVLASVPCLLAGDSAESKSGRLSEGTKLNLLELHLANRLDRDTSGVMVITKSHKVASKLVKAFTDHK 172 (354)
Q Consensus 93 ~lvvnKP~Gl~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~l~~vhRLDk~TSGllllAk~~~~a~~l~~~f~~~~ 172 (354)
|+|+|||+|++|++........+...... ....... ...+++|||||++||||||||+|+++++.|.++|+++.
T Consensus 1 ~lvvnKP~g~~~~~~~~~~~~~~~~~~~~---~~~~~~~---~~~~~~v~RLD~~tsGlll~ak~~~~~~~l~~~~~~~~ 74 (185)
T cd02869 1 LLVVNKPAGLPVHPGPGHLTGTLVNALLK---LLLLLGE---EFRPGLVHRLDKDTSGLLLVAKNKKAAAKLSKQFKERK 74 (185)
T ss_pred CEEEECCCCCeeecCCCCCCCCHHHHHHH---HHhhcCC---CCcCceecccCCCCceEEEEEcCHHHHHHHHHHHhcCc
Confidence 68999999999987543222111110000 0000111 15689999999999999999999999999999999999
Q ss_pred cceEEEEEEeCCCCCCCceEEecCCCCCCCCceeEeeecCCccccCCCcccccceeeEEEeeecCCCCCCCCcchhcccc
Q 018524 173 VSKTYIALCIGPAPKWKRITIISGHGRSKFGAWRVYAASDVGRVLPGGSVVRDMVTSFEVLSVNGEGSFKEPSELQEHEE 252 (354)
Q Consensus 173 v~K~Y~A~v~G~~~~~~~~~i~~~i~~~~~~~~~~~~~~~~~~~~~~g~~~~~a~t~~~vl~~~~~~~~~~~~~~~~~~~ 252 (354)
+.|+|+|+|.|.++. ....+..++.......... .......+.+.|.|+++..
T Consensus 75 ~~K~Y~a~v~g~~~~-~~~~~~~~~~~~~~~~~~~---------~~~~~~~~~~~t~~~~l~~----------------- 127 (185)
T cd02869 75 VKKTYLALVDGKPPE-DEGTIDAPLGRKKRKKRAR---------VVVSEDGKPAITHYKVLER----------------- 127 (185)
T ss_pred eeEEEEEEEeCCCCC-CccEEecccccCCccCceE---------EEECCCCeEEEEEEEEEEE-----------------
Confidence 999999999999875 3344554443221000000 0001112567788888754
Q ss_pred cceeeeeehhhccCCCCceEEEEEEeCCCchhHHHHHHhhcCCceecCCCCCCccccCCCCCCCceeeeeeeEe
Q 018524 253 NNIVVEKKAVLDADAKKNEILVRAFPRSGRTHQIRLHCQYLGISIRGDVKYEGVYEWNGKRYDGHELHAESLSF 326 (354)
Q Consensus 253 ~~~~~~~~~~~~~~~~~~~slv~~~~~TGR~HQIRvhla~lG~PIvGD~~Yg~~~~~~~~~~~~~~LHa~~L~f 326 (354)
..++++++|+|.|||+||||+||+++||||+||.+||....... ...+++|||++|.|
T Consensus 128 ---------------~~~~s~~~~~l~tGR~HQIR~hl~~~G~pIvGD~~Yg~~~~~~~-~~~~~~Lha~~l~~ 185 (185)
T cd02869 128 ---------------FGNVTLVELQLETGRTHQIRVHLASIGHPIVGDPKYGGKASDSP-GLKRLALHAYRLSF 185 (185)
T ss_pred ---------------cCCcEEEEEEeCcCCccHHHHHHHHCCCCEeCccccCCcccccc-CCcchhhcccEeEC
Confidence 23678999999999999999999999999999999997643211 24689999999987
No 12
>KOG1919 consensus RNA pseudouridylate synthases [RNA processing and modification]
Probab=100.00 E-value=1.7e-38 Score=298.69 Aligned_cols=280 Identities=26% Similarity=0.304 Sum_probs=195.8
Q ss_pred cccCCCCCCCcccccccccCCCCCCCCCCCCCCccccCCCCCCCCCCcccccceeEEeecccccccccccCCCccEEEeC
Q 018524 11 FTLTPKAVPRFRKTFFSLASMSNPTEPTSQNAPQTQQNYPTPLSPPLPAISKDIELTRAMSASSKSSLYKLSRSDVLYED 90 (354)
Q Consensus 11 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~v~~~~~~~~~~~~~~~~~~~~~Ilyed 90 (354)
...+..||..+-..|+..+...++..+++....-.. ..-++++..+..++++|+... ..+.|+|||
T Consensus 47 ~~~~~~ef~~~~~~~~~~~i~~g~v~~n~~~~~v~~-----------i~k~~d~l~~~vhrh~p~~~~---~~~~Iv~ed 112 (371)
T KOG1919|consen 47 VDVFVSEFRLRERAYYESAIKLGRVTVNGEQVRVSL-----------IVKNGDVLCHTVHRHEPPVAY---LPIRIVFED 112 (371)
T ss_pred HHHHHHHHhcCchHhhhhhhhcCceEECcEeeeeEE-----------EeccCCEEEEeeccCCCCccc---cccceEEec
Confidence 445556666666677777777777777665444111 124566666778888887543 478999999
Q ss_pred CcEEEEECCCCCccccccccccccccccccccccCCCccccccccccccccccCCCCCceEEEEEeCHHHHHHHHHHhhc
Q 018524 91 EWLVAVNKPQGVYCESVLASVPCLLAGDSAESKSGRLSEGTKLNLLELHLANRLDRDTSGVMVITKSHKVASKLVKAFTD 170 (354)
Q Consensus 91 ~~~lvvnKP~Gl~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~l~~vhRLDk~TSGllllAk~~~~a~~l~~~f~~ 170 (354)
++|+|||||+|++||+......+.+..... ... ....+++|||||+.|||||+||++.+++..++++|++
T Consensus 113 ~~~vVvnKP~gipVhp~g~~~~n~i~~~l~--------~~~--~~~~~~~~hRLDr~tSGllvlAkt~~~~~~~~~~~r~ 182 (371)
T KOG1919|consen 113 KDYVVVNKPHGIPVHPTGRYRENTITKILA--------ALH--KVEGLRPCHRLDRLTSGLLVLAKTKEAADKFHEVLRK 182 (371)
T ss_pred CCEEEEeCCCCCceeccCccccccchHHHH--------Hhc--cccccccccccCccccceEEEEechhHhHHHHHHHhc
Confidence 999999999999999765544442222111 100 1156999999999999999999999999999999999
Q ss_pred CccceEE-EEEEeCCCCCCCceEEecCCCCCCC-CceeEeeecCCccccCCCcccccceeeEEEeeecCCCCCCCCcchh
Q 018524 171 HKVSKTY-IALCIGPAPKWKRITIISGHGRSKF-GAWRVYAASDVGRVLPGGSVVRDMVTSFEVLSVNGEGSFKEPSELQ 248 (354)
Q Consensus 171 ~~v~K~Y-~A~v~G~~~~~~~~~i~~~i~~~~~-~~~~~~~~~~~~~~~~~g~~~~~a~t~~~vl~~~~~~~~~~~~~~~ 248 (354)
+.+.|.| +|-|.|.+|..+...+..+++.... ..+.+.. .+ ..++...+.+.|.|+++..
T Consensus 183 ~~~~k~Y~v~~v~g~fp~~~~~~i~~~~~~~~~~~~~~l~~---~~--~~~~~~~k~a~T~~~~~~~------------- 244 (371)
T KOG1919|consen 183 RTVKKEYVVARVEGPFPVVGEVEIKEPIGEEERPLRMGLNA---VG--VRDEVAAKDAKTLFKVLSY------------- 244 (371)
T ss_pred ccceeEEEEEEEeccCCCCceEEeCCCccccccccceEeee---cc--cccccccccceeEEEEccc-------------
Confidence 9999999 7999999997677777777755432 1111110 00 0111235788889988765
Q ss_pred cccccceeeeeehhhccCCCCceEEEEEEeCCCchhHHHHHHhhcCCceecCCCCCCccccCCC----------------
Q 018524 249 EHEENNIVVEKKAVLDADAKKNEILVRAFPRSGRTHQIRLHCQYLGISIRGDVKYEGVYEWNGK---------------- 312 (354)
Q Consensus 249 ~~~~~~~~~~~~~~~~~~~~~~~slv~~~~~TGR~HQIRvhla~lG~PIvGD~~Yg~~~~~~~~---------------- 312 (354)
+..+++|+|.|+||||||||+||+++|+||+||.+|++...+...
T Consensus 245 -------------------~~~ss~V~~~PlTGRtHQIRvHlq~lG~PI~gD~~Y~~~~~~~~~P~~g~~~~~~~~~~e~ 305 (371)
T KOG1919|consen 245 -------------------DGGSSLVECRPLTGRTHQIRVHLQYLGHPIAGDPKYGNHIVWAGLPFTGREGTAKKKSLEE 305 (371)
T ss_pred -------------------CCceEEEEeeccCCcHHHHHHHHHHhCCCcCCCcccccccccccCCCCCCCCCccccCccc
Confidence 356799999999999999999999999999999999765443311
Q ss_pred ---CCCCceeeeeeeEeeCCCCC---CceEEEcCCC--hhHHHHHHhc
Q 018524 313 ---RYDGHELHAESLSFDHPVTG---CPVMVQAPLP--LWGTEALQSS 352 (354)
Q Consensus 313 ---~~~~~~LHa~~L~f~~P~~~---~~~~~~aplP--~~f~~~l~~l 352 (354)
.....++++-... .||.++ +.+..+|+.| .++..+|-.|
T Consensus 306 ~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~C~~~~~~Dl~~~lha~ 352 (371)
T KOG1919|consen 306 EIQRLIDVHLLENWLG-FHPRTGPLIEELCQECKVPIDNDLELFLHAL 352 (371)
T ss_pred cccccchhhccccccc-cccccccchhhhhhhCCCCCCchHhHhhhhc
Confidence 1112334443333 467777 5667778887 6666665544
No 13
>PRK10839 16S rRNA pseudouridylate synthase A; Provisional
Probab=100.00 E-value=1.7e-36 Score=274.14 Aligned_cols=201 Identities=20% Similarity=0.212 Sum_probs=140.7
Q ss_pred CcccccccccCCCCCCCCCCCCCCccccCCCCCCCCCCcccccceeEEeecccccccccccCCCccE-EEeCCcEEEEEC
Q 018524 20 RFRKTFFSLASMSNPTEPTSQNAPQTQQNYPTPLSPPLPAISKDIELTRAMSASSKSSLYKLSRSDV-LYEDEWLVAVNK 98 (354)
Q Consensus 20 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~v~~~~~~~~~~~~~~~~~~~~~I-lyed~~~lvvnK 98 (354)
||+|+|++.....||..+.++++.|.+ .||+.+.......+.+. +.+.+....+ ..++++|+|+||
T Consensus 1 ~rld~~L~~~~~~Sr~~~~~li~~g~V------------~VNg~~~~~~~~~l~~g-d~I~l~~~~~~~~~~~~~lvvnK 67 (232)
T PRK10839 1 MRLDKFISQQLGVSRAIAGRELRANRV------------TVDGEIVKNGAFKLLPE-HDVAYDGNPLAQQHGPRYFMLNK 67 (232)
T ss_pred CcHHHHHHHcCCCCHHHHHHHHHcCeE------------EECCEEeccCCcCcCCC-CEEEECCEEcccCCCCEEEEEEC
Confidence 589999998877899999999999988 67776554334444332 3344432222 124678999999
Q ss_pred CCCCccccccccccccccccccccccCCCccccccccccccccccCCCCCceEEEEEeCHHHHHHHHHHhhcCccceEEE
Q 018524 99 PQGVYCESVLASVPCLLAGDSAESKSGRLSEGTKLNLLELHLANRLDRDTSGVMVITKSHKVASKLVKAFTDHKVSKTYI 178 (354)
Q Consensus 99 P~Gl~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~l~~vhRLDk~TSGllllAk~~~~a~~l~~~f~~~~v~K~Y~ 178 (354)
|+|++||+......++. ..+..... ..+++|||||++||||||||||+++++.|.. +++.+.|+|+
T Consensus 68 P~G~~~~~~~~~~~tl~---------~~l~~~~~---~~~~~v~RLD~~TSGlll~ak~~~~~~~l~~--~~~~i~K~Y~ 133 (232)
T PRK10839 68 PQGYVCSTDDPDHPTVL---------YFLDEPVA---YKLHAAGRLDIDTTGLVLMTDDGQWSHRITS--PRHHCEKTYL 133 (232)
T ss_pred CCCeEecccCCCCCeEE---------Eecccccc---cCceecCCCCCCceeEEEEecCHHHHHHHhC--CCCCCCeEEE
Confidence 99999997543222211 11211111 3578999999999999999999999999997 7889999999
Q ss_pred EEEeCCCCCCCceEEecCCCCCCCCceeEeeecCCccccCCCcccccceeeEEEeeecCCCCCCCCcchhcccccceeee
Q 018524 179 ALCIGPAPKWKRITIISGHGRSKFGAWRVYAASDVGRVLPGGSVVRDMVTSFEVLSVNGEGSFKEPSELQEHEENNIVVE 258 (354)
Q Consensus 179 A~v~G~~~~~~~~~i~~~i~~~~~~~~~~~~~~~~~~~~~~g~~~~~a~t~~~vl~~~~~~~~~~~~~~~~~~~~~~~~~ 258 (354)
|.+.+.+..+....+..++ ..+| +.+.|++.++...
T Consensus 134 a~i~~~i~~~~~~~~~~~~-------------------~~~g---~~a~t~~~~~~~~---------------------- 169 (232)
T PRK10839 134 VTLESPVADDTAEQFAKGV-------------------QLHN---EKDLTKPAVLEVI---------------------- 169 (232)
T ss_pred EEECCCCCHHHHHHHHCCe-------------------EECC---CcccccccEEEEe----------------------
Confidence 9999987542111111000 0112 3456777666431
Q ss_pred eehhhccCCCCceEEEEEEeCCCchhHHHHHHhhcCCceecCCC
Q 018524 259 KKAVLDADAKKNEILVRAFPRSGRTHQIRLHCQYLGISIRGDVK 302 (354)
Q Consensus 259 ~~~~~~~~~~~~~slv~~~~~TGR~HQIRvhla~lG~PIvGD~~ 302 (354)
+.++++|+|.|||+||||+||+++||||+|=..
T Consensus 170 -----------~~sll~~~l~tGRtHQIR~h~~~~G~pi~gl~R 202 (232)
T PRK10839 170 -----------TPTQVRLTISEGRYHQVKRMFAAVGNHVVELHR 202 (232)
T ss_pred -----------cCCEEEEEEEcCcCHHHHHHHHHcCCeEeeEEE
Confidence 127999999999999999999999999998644
No 14
>COG1187 RsuA 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.8e-34 Score=257.79 Aligned_cols=209 Identities=18% Similarity=0.238 Sum_probs=160.6
Q ss_pred CCCcccccccccCCCCCCCCCCCCCCccccCCCCCCCCCCcccccceeEEeecccccccccccCCCccEEE-eCCcEEEE
Q 018524 18 VPRFRKTFFSLASMSNPTEPTSQNAPQTQQNYPTPLSPPLPAISKDIELTRAMSASSKSSLYKLSRSDVLY-EDEWLVAV 96 (354)
Q Consensus 18 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~v~~~~~~~~~~~~~~~~~~~~~Ily-ed~~~lvv 96 (354)
++||++||+|+++.+||++++.+|+.|.| .|||.+.......+++..+.+.+++..+.+ +...|+++
T Consensus 1 ~~~RL~K~La~~G~~SRr~ae~lI~~G~V------------~VnG~v~~~~~~~v~~~~~~i~v~g~~~~~~~~~~y~ll 68 (248)
T COG1187 1 DSMRLNKFLAEAGVGSRREAEKLIEEGRV------------TVNGKVATLGGVVVDPDDDVVEVDGKRIELKEERVYLLL 68 (248)
T ss_pred CccchHHHHHHcCCCCHHHHHHHHHcCCE------------EECCEEeccCCeEeCCCCcEEEECCEEeeccccceEEEE
Confidence 46999999999999999999999999999 999999999999999987778888888887 45559999
Q ss_pred ECCCCCccccccccccccccccccccccCCCccccccccccccccccCCCCCceEEEEEeCHHHHHHHHHHhhcCccceE
Q 018524 97 NKPQGVYCESVLASVPCLLAGDSAESKSGRLSEGTKLNLLELHLANRLDRDTSGVMVITKSHKVASKLVKAFTDHKVSKT 176 (354)
Q Consensus 97 nKP~Gl~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~l~~vhRLDk~TSGllllAk~~~~a~~l~~~f~~~~v~K~ 176 (354)
|||.|++|+..++. +..++.+.++.. ......+++|+|||+||+|||||++|++++++|.+ ++.++.|+
T Consensus 69 nKP~G~v~s~~D~~--------gr~tv~D~lp~~-~~~~~~~~pvGRLD~dTeGLLLLTnDG~la~rL~~--P~~~~~K~ 137 (248)
T COG1187 69 NKPRGYVSSTEDDE--------GRPTVFDLLPER-LPRKKRLFPVGRLDKDTEGLLLLTNDGELAHRLMH--PSSEVEKE 137 (248)
T ss_pred ECCCCeEecccCCC--------CCceeeeecccc-cccccceeeccccCCCCeeEEEEeCCHHHHHHhcC--CCCCCCEE
Confidence 99999988754322 333455555532 00115699999999999999999999999999999 99999999
Q ss_pred EEEEEeCCCCCCCceEEecCCCCCCCCceeEeeecCCccccCCCcccccceeeEEEeeecCCCCCCCCcchhccccccee
Q 018524 177 YIALCIGPAPKWKRITIISGHGRSKFGAWRVYAASDVGRVLPGGSVVRDMVTSFEVLSVNGEGSFKEPSELQEHEENNIV 256 (354)
Q Consensus 177 Y~A~v~G~~~~~~~~~i~~~i~~~~~~~~~~~~~~~~~~~~~~g~~~~~a~t~~~vl~~~~~~~~~~~~~~~~~~~~~~~ 256 (354)
|+|.|.|.++++....+..|+. +.+| ..+++ ....+...
T Consensus 138 Y~v~v~g~~~~~~l~~l~~Gv~------------------l~d~-~~~~~--~~~~l~~~-------------------- 176 (248)
T COG1187 138 YLVRVEGPVTEEDLEKLRKGVT------------------LDDG-ETKPA--KPASLEKE-------------------- 176 (248)
T ss_pred EEEEEecCCCHHHHHHHhCCcE------------------ecCc-ccccc--eeEEEEec--------------------
Confidence 9999999887644434443331 1121 11111 11111110
Q ss_pred eeeehhhccCCCCceEEEEEEeCCCchhHHHHHHhhcCCceecC
Q 018524 257 VEKKAVLDADAKKNEILVRAFPRSGRTHQIRLHCQYLGISIRGD 300 (354)
Q Consensus 257 ~~~~~~~~~~~~~~~slv~~~~~TGR~HQIRvhla~lG~PIvGD 300 (354)
.....++++++|.+||+||||+||+++|+|++.=
T Consensus 177 ----------~~~~~s~~~itl~EGrnrQVRRm~~a~G~~V~~L 210 (248)
T COG1187 177 ----------PGKNNSWLRITLTEGRNRQVRRMFEAVGLEVLRL 210 (248)
T ss_pred ----------CCCCceEEEEEEeCCcCHHHHHHHHHcCCEEeEE
Confidence 0114689999999999999999999999999754
No 15
>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=1.5e-33 Score=239.06 Aligned_cols=147 Identities=28% Similarity=0.399 Sum_probs=105.0
Q ss_pred EEEEECCCCCccccccccccccccccccccccCCCccccccccccccccccCCCCCceEEEEEeCHHHHHHHHHHhhcCc
Q 018524 93 LVAVNKPQGVYCESVLASVPCLLAGDSAESKSGRLSEGTKLNLLELHLANRLDRDTSGVMVITKSHKVASKLVKAFTDHK 172 (354)
Q Consensus 93 ~lvvnKP~Gl~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~l~~vhRLDk~TSGllllAk~~~~a~~l~~~f~~~~ 172 (354)
|+|+|||+|++|++....... ++...+..... ..+++|||||++||||||||||+++++.|+++ ++.
T Consensus 1 ~ivvnKP~G~~~~~~~~~~~~--------~~~~~l~~~~~---~~~~~vhRLD~~TSGlll~ak~~~~~~~l~~~--~~~ 67 (154)
T cd02550 1 ILVLNKPSGLVCHPTDRDRDP--------TVVVRLDKLHG---PRVHAAGRLDKDTSGLLLLTNDGRLQRRLTEP--RRE 67 (154)
T ss_pred CEEEECCCCCEEecCCCCCCC--------cHHHhhhcccC---CceeEeccCCCCCeeEEEEEcCHHHHHHHhhh--hcc
Confidence 689999999999975432111 11112212111 56899999999999999999999999999996 889
Q ss_pred cceEEEEEEeCCCCCCCceEEecCCCCCCCCceeEeeecCCccccCCCcccccceeeEEEeeecCCCCCCCCcchhcccc
Q 018524 173 VSKTYIALCIGPAPKWKRITIISGHGRSKFGAWRVYAASDVGRVLPGGSVVRDMVTSFEVLSVNGEGSFKEPSELQEHEE 252 (354)
Q Consensus 173 v~K~Y~A~v~G~~~~~~~~~i~~~i~~~~~~~~~~~~~~~~~~~~~~g~~~~~a~t~~~vl~~~~~~~~~~~~~~~~~~~ 252 (354)
+.|+|+|+|.|.++++. .+...+.. .+... +....+ .+.+.|+|+++..
T Consensus 68 v~K~Y~a~v~g~~~~~~--~~~~~~~~--~~~~~-------~~~~~~---~~~~~t~~~~l~~----------------- 116 (154)
T cd02550 68 IEKEYLVTVRGELDEEG--IEDLATVR--RGRLS-------GLVDEG---VPLAVTKVRVIGE----------------- 116 (154)
T ss_pred CcEEEEEEEEeecCcch--heeccccc--cCcce-------eEEcCC---CcccceEEEEEEe-----------------
Confidence 99999999999987532 23333322 11000 001112 2456788888753
Q ss_pred cceeeeeehhhccCCCCceEEEEEEeCCCchhHHHHHHhhcCCcee
Q 018524 253 NNIVVEKKAVLDADAKKNEILVRAFPRSGRTHQIRLHCQYLGISIR 298 (354)
Q Consensus 253 ~~~~~~~~~~~~~~~~~~~slv~~~~~TGR~HQIRvhla~lG~PIv 298 (354)
..++++++|+|.|||+||||+||+++||||.
T Consensus 117 ---------------~~~~sll~~~l~tGR~HQIR~hla~~G~pI~ 147 (154)
T cd02550 117 ---------------HGGTGRLRLTLKTGRTHQIRRHCAAVGFPVL 147 (154)
T ss_pred ---------------cCCcEEEEEEEcCCCcHHHHHHHHHcCCcEE
Confidence 2356899999999999999999999999996
No 16
>PRK10700 23S rRNA pseudouridylate synthase B; Provisional
Probab=100.00 E-value=4.3e-34 Score=264.84 Aligned_cols=201 Identities=17% Similarity=0.237 Sum_probs=143.2
Q ss_pred CCcccccccccCCCCCCCCCCCCCCccccCCCCCCCCCCcccccceeEEeecccccc-cccccCCCccEEE-----eCCc
Q 018524 19 PRFRKTFFSLASMSNPTEPTSQNAPQTQQNYPTPLSPPLPAISKDIELTRAMSASSK-SSLYKLSRSDVLY-----EDEW 92 (354)
Q Consensus 19 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~v~~~~~~~~~~~-~~~~~~~~~~Ily-----ed~~ 92 (354)
+||+++||+.++.+||.++..+|..|.| .|||.+. .....+.+. .+.+.+++..+-+ ||++
T Consensus 2 ~~RL~k~La~~g~~SRr~a~~lI~~G~V------------~VNG~~~-~~g~~V~~~~~d~I~v~g~~~~~~~~~~e~~~ 68 (289)
T PRK10700 2 SEKLQKVLARAGHGSRREIESIIEAGRV------------SVDGKIA-TLGDRVEVTPGLKIRIDGHLISVKESAEQICR 68 (289)
T ss_pred chhHHHHHHHCCCCCHHHHHHHHHcCCE------------EECCEec-cCCCEeCCCCCeEEEECCEEeecccccccCCe
Confidence 4899999999999999999999999999 8999865 566666543 2445555433322 4467
Q ss_pred EEEEECCCCCcccccccc-ccccccccccccccCCCccccccccccccccccCCCCCceEEEEEeCHHHHHHHHHHhhcC
Q 018524 93 LVAVNKPQGVYCESVLAS-VPCLLAGDSAESKSGRLSEGTKLNLLELHLANRLDRDTSGVMVITKSHKVASKLVKAFTDH 171 (354)
Q Consensus 93 ~lvvnKP~Gl~~~~~~~~-~~~~~~~~~~~~~~~~l~~~~~~~~~~l~~vhRLDk~TSGllllAk~~~~a~~l~~~f~~~ 171 (354)
|+|+|||+|++|++.+.. ..+++ +.+..... ..+++|||||++||||||||+|+++++.|.+ +++
T Consensus 69 ylvlnKP~G~~~s~~d~~~~~tv~---------d~l~~~~~---~~~~~VgRLD~dTsGLLLlTndg~~~~~L~~--p~~ 134 (289)
T PRK10700 69 VLAYYKPEGELCTRNDPEGRPTVF---------DRLPKLRG---ARWIAVGRLDVNTCGLLLFTTDGELANRLMH--PSR 134 (289)
T ss_pred EEEEECCCCCEeecCCCCCCccHH---------HHhhhhcC---CceeEccCCCCCCceEEEEEcCHHHHHHHhC--ccC
Confidence 999999999999865432 12222 22221111 3578999999999999999999999999988 899
Q ss_pred ccceEEEEEEeCCCCCCCceEEecCCCCCCCCceeEeeecCCccccCCCcccccceeeEEEeeecCCCCCCCCcchhccc
Q 018524 172 KVSKTYIALCIGPAPKWKRITIISGHGRSKFGAWRVYAASDVGRVLPGGSVVRDMVTSFEVLSVNGEGSFKEPSELQEHE 251 (354)
Q Consensus 172 ~v~K~Y~A~v~G~~~~~~~~~i~~~i~~~~~~~~~~~~~~~~~~~~~~g~~~~~a~t~~~vl~~~~~~~~~~~~~~~~~~ 251 (354)
++.|+|+|+|.|.++++....+..|+ .+.++ .+.+..+....
T Consensus 135 ~i~K~Y~v~V~G~~~~~~l~~l~~Gv------------------~l~~~------~~~~~~v~~~~-------------- 176 (289)
T PRK10700 135 EVEREYAVRVFGQVDDAKLRQLSRGV------------------QLEDG------PAAFKTIKFSG-------------- 176 (289)
T ss_pred CCCeEEEEEEccCCCHHHHHHHHcCC------------------EeCCc------eeeeEEEEecc--------------
Confidence 99999999999998753322222222 11111 12222222100
Q ss_pred ccceeeeeehhhccCCCCceEEEEEEeCCCchhHHHHHHhhcCCceec
Q 018524 252 ENNIVVEKKAVLDADAKKNEILVRAFPRSGRTHQIRLHCQYLGISIRG 299 (354)
Q Consensus 252 ~~~~~~~~~~~~~~~~~~~~slv~~~~~TGR~HQIRvhla~lG~PIvG 299 (354)
.....++++|+|.|||+||||+||+++|+||+.
T Consensus 177 ---------------~~~~~s~l~v~L~EGk~hQIRrm~~~lG~~V~~ 209 (289)
T PRK10700 177 ---------------GEGINQWYNVTLTEGRNREVRRLWEAVGVQVSR 209 (289)
T ss_pred ---------------CCCCceEEEEEEeCCccHHHHHHHHHcCCEEeE
Confidence 012347899999999999999999999999974
No 17
>cd02870 PseudoU_synth_RsuA_like Pseudouridine synthases are responsible for the synthesis of pseudouridine from uracil in ribosomal RNA. The RsuA subfamily includes Pseudouridine Synthase similar to Ribosomal small subunit pseudouridine 516 synthase. Most of the proteins in this family are bacterial proteins.
Probab=99.98 E-value=8.5e-33 Score=232.36 Aligned_cols=140 Identities=24% Similarity=0.296 Sum_probs=101.5
Q ss_pred EEEEECCCCCccccccccccccccccccccccCCCccccccccccccccccCCCCCceEEEEEeCHHHHHHHHHHhhcCc
Q 018524 93 LVAVNKPQGVYCESVLASVPCLLAGDSAESKSGRLSEGTKLNLLELHLANRLDRDTSGVMVITKSHKVASKLVKAFTDHK 172 (354)
Q Consensus 93 ~lvvnKP~Gl~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~l~~vhRLDk~TSGllllAk~~~~a~~l~~~f~~~~ 172 (354)
|+|+|||+|++|++....... ++.+.+.... ..+++|||||++||||||||||+++++.|.. +++.
T Consensus 1 ~ivvnKP~G~~~~~~~~~~~~--------~l~~~l~~~~----~~~~~vhRLD~~TsGlll~ak~~~~~~~l~~--~~~~ 66 (146)
T cd02870 1 YLLLNKPRGVVSTVRDPEGRP--------TVLDLLKDVG----ERLFPVGRLDYDTEGLLLLTNDGELANRLTH--PRYG 66 (146)
T ss_pred CEEEECCCCcEecccCCCCCC--------EEeeeccccC----CCEEECCCCCCCCeeEEEEeCCHHHHHHhhC--ccCC
Confidence 689999999999865422111 1111222211 4689999999999999999999999999987 7888
Q ss_pred cceEEEEEEeCCCCCCCceEEecCCCCCCCCceeEeeecCCccccCCCcccccceeeEEEeeecCCCCCCCCcchhcccc
Q 018524 173 VSKTYIALCIGPAPKWKRITIISGHGRSKFGAWRVYAASDVGRVLPGGSVVRDMVTSFEVLSVNGEGSFKEPSELQEHEE 252 (354)
Q Consensus 173 v~K~Y~A~v~G~~~~~~~~~i~~~i~~~~~~~~~~~~~~~~~~~~~~g~~~~~a~t~~~vl~~~~~~~~~~~~~~~~~~~ 252 (354)
+.|+|+|+|.|.++.+....+. .|. ...+| +.+.|.++++..
T Consensus 67 i~K~Y~a~v~g~~~~~~~~~~~-------~~~-----------~~~~~---~~~~t~~~~l~~----------------- 108 (146)
T cd02870 67 VEKTYLVKVRGVPSEEELRRLR-------AGV-----------ELDDG---KTAPAKVKVLSR----------------- 108 (146)
T ss_pred CCeEEEEEECCCCCHHHHHHHH-------CCe-----------EeCCc---eEcceEEEEecc-----------------
Confidence 9999999999998643211110 000 11112 456678887643
Q ss_pred cceeeeeehhhccCCCCceEEEEEEeCCCchhHHHHHHhhcCCceec
Q 018524 253 NNIVVEKKAVLDADAKKNEILVRAFPRSGRTHQIRLHCQYLGISIRG 299 (354)
Q Consensus 253 ~~~~~~~~~~~~~~~~~~~slv~~~~~TGR~HQIRvhla~lG~PIvG 299 (354)
..+.++++|+|.|||+||||+||+++|+||+.
T Consensus 109 ---------------~~~~sll~~~l~tGR~HQIR~hla~~G~pI~~ 140 (146)
T cd02870 109 ---------------DPKNTLLEVTLHEGRNRQVRRMFEAVGHPVLR 140 (146)
T ss_pred ---------------CCCCcEEEEEEEeCCcHHHHHHHHHcCCcCCe
Confidence 23468999999999999999999999999973
No 18
>cd02556 PseudoU_synth_RluB PseudoU_synth_RluB: Pseudouridine synthase, Escherichia coli RluB like. This group is comprised of bacterial and eukaryotic proteins similar to E. coli RluB. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. E.coli RluB makes psi2605 in 23S RNA. psi2605 has been detected in eubacteria but, not in eukarya and archea despite the presence of a precursor U at that site.
Probab=99.97 E-value=1.9e-32 Score=235.12 Aligned_cols=142 Identities=18% Similarity=0.261 Sum_probs=101.3
Q ss_pred cEEEEECCCCCccccccccccccccccccccccCCCccccccccccccccccCCCCCceEEEEEeCHHHHHHHHHHhhcC
Q 018524 92 WLVAVNKPQGVYCESVLASVPCLLAGDSAESKSGRLSEGTKLNLLELHLANRLDRDTSGVMVITKSHKVASKLVKAFTDH 171 (354)
Q Consensus 92 ~~lvvnKP~Gl~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~l~~vhRLDk~TSGllllAk~~~~a~~l~~~f~~~ 171 (354)
.|+|+|||+|++|++....... ++.+.+..... ..+++|||||++||||||||||+++++.|+. +++
T Consensus 1 ~~lvvnKP~G~~~~~~~~~~~~--------tl~~~l~~~~~---~~~~~V~RLD~~TsGLll~ak~~~~~~~L~~--~~~ 67 (167)
T cd02556 1 RVLIYHKPEGLICTRKDPKGRP--------TVFDLLPKLGI---PRWISVGRLDLNTEGLLLFTNDGELANRLMH--PSN 67 (167)
T ss_pred CEEEEECCCCcEECccCCCCCc--------cHHHhhhhhcc---CceEEcCcCCCCCeeEEEEECCHHHHHHHhC--CcC
Confidence 3799999999999864321111 12222221111 4578999999999999999999999999986 899
Q ss_pred ccceEEEEEEeCCCCCCCceEEecCCCCCCCCceeEeeecCCccccCCCcccccceeeEEEeeecCCCCCCCCcchhccc
Q 018524 172 KVSKTYIALCIGPAPKWKRITIISGHGRSKFGAWRVYAASDVGRVLPGGSVVRDMVTSFEVLSVNGEGSFKEPSELQEHE 251 (354)
Q Consensus 172 ~v~K~Y~A~v~G~~~~~~~~~i~~~i~~~~~~~~~~~~~~~~~~~~~~g~~~~~a~t~~~vl~~~~~~~~~~~~~~~~~~ 251 (354)
.+.|+|+|+|.|.++.+....+. .|. ...+| +.+.|.++++..
T Consensus 68 ~i~K~Y~a~V~g~~~~~~~~~~~-------~gv-----------~~~~~---~~~~~~~~~~~~---------------- 110 (167)
T cd02556 68 EIEREYAVRVFGQVTDEQLKSLK-------KGV-----------ELEDG---FAGFKSIQLEGG---------------- 110 (167)
T ss_pred CCCeEEEEEECccCCHHHHHHHH-------cCC-----------EECCC---cCcceEEEEEec----------------
Confidence 99999999999998653211000 010 11122 345667777642
Q ss_pred ccceeeeeehhhccCCCCceEEEEEEeCCCchhHHHHHHhhcCCceec
Q 018524 252 ENNIVVEKKAVLDADAKKNEILVRAFPRSGRTHQIRLHCQYLGISIRG 299 (354)
Q Consensus 252 ~~~~~~~~~~~~~~~~~~~~slv~~~~~TGR~HQIRvhla~lG~PIvG 299 (354)
..++++++|+|.|||+||||+||+++||||+-
T Consensus 111 ----------------~~~~sll~v~l~tGR~HQIR~~~a~~G~pV~~ 142 (167)
T cd02556 111 ----------------EGKNSWYRVTLREGRNREVRRLWEAFGLQVSR 142 (167)
T ss_pred ----------------CCCcEEEEEEEEeCCCHHHHHHHHHcCCeEeE
Confidence 23458999999999999999999999999964
No 19
>PRK10475 23S rRNA pseudouridine synthase F; Provisional
Probab=99.97 E-value=1.5e-32 Score=253.72 Aligned_cols=194 Identities=17% Similarity=0.217 Sum_probs=140.8
Q ss_pred CCcccccccccCCCCCCCCCCCCCCccccCCCCCCCCCCcccccceeEEeecccccccccccCCCccEE---EeCCcEEE
Q 018524 19 PRFRKTFFSLASMSNPTEPTSQNAPQTQQNYPTPLSPPLPAISKDIELTRAMSASSKSSLYKLSRSDVL---YEDEWLVA 95 (354)
Q Consensus 19 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~v~~~~~~~~~~~~~~~~~~~~~Il---yed~~~lv 95 (354)
+||+++||+.++.+||.++..+|..|.| .|||.++ .....+.+. +.+.+++..|. +||++|||
T Consensus 6 ~~RL~k~La~~g~~SRr~a~~lI~~G~V------------~VNGk~v-~~~~~V~~g-D~V~v~g~~i~~~~~ed~~~lv 71 (290)
T PRK10475 6 STRLNKYISESGICSRREADRYIEQGNV------------FINGKRA-TIGDQVKAG-DVVKVNGQLIEPREAEDLVLIA 71 (290)
T ss_pred HHHHHHHHHhCCCCCHHHHHHHHHCCcE------------EECCEEc-cCCCCcCCC-CEEEECCEEccccccCCCeEEE
Confidence 4899999999999999999999999999 8888765 455555543 55666654332 47889999
Q ss_pred EECCCCCccccccccccccccccccccccCCCccccccccccccccccCCCCCceEEEEEeCHHHHHHHHHHhhcCccce
Q 018524 96 VNKPQGVYCESVLASVPCLLAGDSAESKSGRLSEGTKLNLLELHLANRLDRDTSGVMVITKSHKVASKLVKAFTDHKVSK 175 (354)
Q Consensus 96 vnKP~Gl~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~l~~vhRLDk~TSGllllAk~~~~a~~l~~~f~~~~v~K 175 (354)
+|||+|++|++......+ +.+.+... ..+++|||||++||||||||+|+++++.|.+ +.+.+.|
T Consensus 72 lnKP~G~~~~~~~~~~~t---------v~~~l~~~-----~~l~~VgRLDrdTsGLLLlT~dg~~~~~L~~--p~~~i~K 135 (290)
T PRK10475 72 LNKPVGIVSTTEDGERDN---------IVDFVNHS-----KRVFPIGRLDKDSQGLIFLTNHGDLVNKILR--AGNDHEK 135 (290)
T ss_pred EECCCCCCcCCCCCCCCc---------HHHHhhcc-----ccccccccCCCCCcceEEEecCHHHHHHhhC--cCCCCCe
Confidence 999999999864332222 22222211 3588999999999999999999999999988 7888999
Q ss_pred EEEEEEeCCCCCCCceEEecCCCCCCCCceeEeeecCCccccCCCcccccceeeEEEeeecCCCCCCCCcchhcccccce
Q 018524 176 TYIALCIGPAPKWKRITIISGHGRSKFGAWRVYAASDVGRVLPGGSVVRDMVTSFEVLSVNGEGSFKEPSELQEHEENNI 255 (354)
Q Consensus 176 ~Y~A~v~G~~~~~~~~~i~~~i~~~~~~~~~~~~~~~~~~~~~~g~~~~~a~t~~~vl~~~~~~~~~~~~~~~~~~~~~~ 255 (354)
+|+|+|.|.++++....+..|+. + +|...+++ .++.
T Consensus 136 ~Y~v~V~g~~~~~~l~~l~~Gv~------------------l-~~~~~~~~--~v~~----------------------- 171 (290)
T PRK10475 136 EYLVTVDKPITDEFIRGMGAGVP------------------I-LGTVTKKC--KVKK----------------------- 171 (290)
T ss_pred EEEEEECCCCCHHHHHHHhCCcE------------------E-CCEEecce--EEEe-----------------------
Confidence 99999999987633222222221 1 11111111 1111
Q ss_pred eeeeehhhccCCCCceEEEEEEeCCCchhHHHHHHhhcCCceec
Q 018524 256 VVEKKAVLDADAKKNEILVRAFPRSGRTHQIRLHCQYLGISIRG 299 (354)
Q Consensus 256 ~~~~~~~~~~~~~~~~slv~~~~~TGR~HQIRvhla~lG~PIvG 299 (354)
.+.+.++|++.+||+||||+||+++|++|+-
T Consensus 172 -------------~~~~~~~i~l~eGk~rqIRrm~~~~G~~V~~ 202 (290)
T PRK10475 172 -------------EAPFVFRITLVQGLNRQIRRMCEHFGYEVTK 202 (290)
T ss_pred -------------cCCcEEEEEEECCcCHHHHHHHHHcCCEEeE
Confidence 0124689999999999999999999999974
No 20
>cd02553 PseudoU_synth_RsuA PseudoU_synth_RsuA: Pseudouridine synthase, Escherichia coli RsuA like. This group is comprised of eukaryotic and bacterial proteins similar to Escherichia coli RsuA. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. E.coli RsuA makes psi516 in 16S RNA. Psi at this position is not generally conserved in other organisms.
Probab=99.97 E-value=3.2e-32 Score=233.56 Aligned_cols=144 Identities=25% Similarity=0.365 Sum_probs=99.1
Q ss_pred EEEEECCCCCccccccccccccccccccccccCCCccccccccccccccccCCCCCceEEEEEeCHHHHHHHHHHhhcCc
Q 018524 93 LVAVNKPQGVYCESVLASVPCLLAGDSAESKSGRLSEGTKLNLLELHLANRLDRDTSGVMVITKSHKVASKLVKAFTDHK 172 (354)
Q Consensus 93 ~lvvnKP~Gl~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~l~~vhRLDk~TSGllllAk~~~~a~~l~~~f~~~~ 172 (354)
|+|+|||+|++|++......++ ...+..... ...+++|||||++||||||||||.++++.+.+ +++.
T Consensus 2 ~ivvnKP~G~~~~~~~~~~~tl---------~~~l~~~~~--~~~~~~vhRLD~~TSGlll~ak~~~~~~~l~~--~~~~ 68 (167)
T cd02553 2 YLMLNKPAGVVCATKDPHHPTV---------IDLLPEPDR--RRDLFPVGRLDKDTTGLLLLTNDGQLAHRLTS--PKKH 68 (167)
T ss_pred EEEEECCCCCEeCCCCCCCCcH---------HHHhhhhcc--cCCeEEcccCCCCCEEEEEEEeCHHHHHHhhC--CcCC
Confidence 7999999999998532221111 111211110 14689999999999999999999999999887 6889
Q ss_pred cceEEEEEEeCCCCCCCceEEecCCCCCCCCceeEeeecCCccccCCCcccccceeeEEEeeecCCCCCCCCcchhcccc
Q 018524 173 VSKTYIALCIGPAPKWKRITIISGHGRSKFGAWRVYAASDVGRVLPGGSVVRDMVTSFEVLSVNGEGSFKEPSELQEHEE 252 (354)
Q Consensus 173 v~K~Y~A~v~G~~~~~~~~~i~~~i~~~~~~~~~~~~~~~~~~~~~~g~~~~~a~t~~~vl~~~~~~~~~~~~~~~~~~~ 252 (354)
++|+|+|+|.|.++.+....+..++ ...++... ..+.++++
T Consensus 69 i~K~Y~a~V~G~~~~~~~~~~~~~~------------------~~~~~~~~--~~~~~~~~------------------- 109 (167)
T cd02553 69 VPKTYEVTLAGPLTEDDIEAFAEGV------------------LLHDGYPT--KPAKLEIL------------------- 109 (167)
T ss_pred CceEEEEEEccCCCHHHHHHHHCCe------------------EEcCCCEe--eeeEEEEe-------------------
Confidence 9999999999998653211110000 01111111 11223322
Q ss_pred cceeeeeehhhccCCCCceEEEEEEeCCCchhHHHHHHhhcCCceecCCCCCC
Q 018524 253 NNIVVEKKAVLDADAKKNEILVRAFPRSGRTHQIRLHCQYLGISIRGDVKYEG 305 (354)
Q Consensus 253 ~~~~~~~~~~~~~~~~~~~slv~~~~~TGR~HQIRvhla~lG~PIvGD~~Yg~ 305 (354)
+.++++|+|.|||+||||+||+++||||++|..++-
T Consensus 110 -----------------~~sll~v~l~tGR~HQIR~hla~lG~pI~~~~R~~~ 145 (167)
T cd02553 110 -----------------SPTTVRLTITEGKYHQVKRMFAAVGNKVVALHRIRI 145 (167)
T ss_pred -----------------CCcEEEEEEEeCCCHHHHHHHHHcCCeEEEEEEEEE
Confidence 127899999999999999999999999999977764
No 21
>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=99.97 E-value=3.7e-31 Score=226.74 Aligned_cols=164 Identities=31% Similarity=0.339 Sum_probs=104.2
Q ss_pred cEEEEECCCCCccccccccccccccccccccccCCCccccccccccccccccCCCCCceEEEEEeCHHHHHHHHHHhhcC
Q 018524 92 WLVAVNKPQGVYCESVLASVPCLLAGDSAESKSGRLSEGTKLNLLELHLANRLDRDTSGVMVITKSHKVASKLVKAFTDH 171 (354)
Q Consensus 92 ~~lvvnKP~Gl~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~l~~vhRLDk~TSGllllAk~~~~a~~l~~~f~~~ 171 (354)
||||||||+|++|++.............. ....... ....+++|||||++||||||||+|++++++|+++|+++
T Consensus 1 ~~ivvnKP~G~~~~~~~~~~~~~~~~~~~---~~~~~~~---~~~~~~~v~RLD~~TsGlll~a~~~~~~~~l~~~f~~~ 74 (164)
T PF00849_consen 1 NLIVVNKPAGVPVHPSDGNESKSVKELPA---LSLKRGD---DPPELYPVHRLDRDTSGLLLFAKDKEAAAKLSKQFPKR 74 (164)
T ss_dssp SEEEEEE-TTSBSSSSSTBSSSSHHCHHH---HHHHHCT---TSGGGEESS---TT-EEEEEEESSHHHHHHHHHHHHTT
T ss_pred CEEEEECCCCCeEecCCCCCcccccchhh---hhhhhcc---CCCceEECCCCCccccCCeeccCCcccccccccccccC
Confidence 69999999999999766311111111000 0000011 12679999999999999999999999999999999999
Q ss_pred ccceEEEEEEeCCCCCCCceEEecCCCCCCCCceeEeeecCCccccCCCcccccceeeEEEeeecCCCCCCCCcchhccc
Q 018524 172 KVSKTYIALCIGPAPKWKRITIISGHGRSKFGAWRVYAASDVGRVLPGGSVVRDMVTSFEVLSVNGEGSFKEPSELQEHE 251 (354)
Q Consensus 172 ~v~K~Y~A~v~G~~~~~~~~~i~~~i~~~~~~~~~~~~~~~~~~~~~~g~~~~~a~t~~~vl~~~~~~~~~~~~~~~~~~ 251 (354)
.++|+|+|+|.|.+.. +...++.++....... ......+.+...+.+.|.++++......
T Consensus 75 ~~~K~Y~a~v~~~~~~-~~~~~~~~~~~~~~~~-------~~~~~~~~~~~~~~~~t~~~~l~~~~~~------------ 134 (164)
T PF00849_consen 75 KVEKTYLALVEGGPVE-EEGKINSPLGKDVGKN-------KSSNKDPPGRDGKPAITRYRVLRSGSRT------------ 134 (164)
T ss_dssp CSEEEEEEEECSSSST-TCEEEESHEEE-EECS-------SCTCCEEETTTSBTSEEEEEEEEEETT-------------
T ss_pred CCcEEEEEeEcccccc-cceeeecccccccccc-------ccceeeeecccccccceeeeeecccccc------------
Confidence 9999999999965544 4556666654410000 0000111222346788999998763111
Q ss_pred ccceeeeeehhhccCCCCceEEEEEEeCCCchhHHHHHHhh
Q 018524 252 ENNIVVEKKAVLDADAKKNEILVRAFPRSGRTHQIRLHCQY 292 (354)
Q Consensus 252 ~~~~~~~~~~~~~~~~~~~~slv~~~~~TGR~HQIRvhla~ 292 (354)
........+++++|+|.|||+||||+|||+
T Consensus 135 -----------~~~~~~~~~s~v~~~l~tGr~HQIR~hla~ 164 (164)
T PF00849_consen 135 -----------PSKDENAGCSLVECELITGRTHQIRVHLAH 164 (164)
T ss_dssp -------------EECCSSEEEEEEEESS-STTHHHHHHHH
T ss_pred -----------ccccccCCCEEEEEEECcCCCHHHHHHhcC
Confidence 001124678999999999999999999986
No 22
>cd02555 PSSA_1 PSSA_1: Pseudouridine synthase, a subgroup of the RsuA family. This group is comprised of bacterial proteins assigned to the RsuA family of pseudouridine synthases. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. The TruA family is comprised of proteins related to Escherichia coli RsuA.
Probab=99.96 E-value=2.7e-30 Score=222.93 Aligned_cols=150 Identities=21% Similarity=0.278 Sum_probs=99.7
Q ss_pred CcEEEEECCCCCccccccccc-cccccccccccccCCCccccccccccccccccCCCCCceEEEEEeCHHHHHHHHHHhh
Q 018524 91 EWLVAVNKPQGVYCESVLASV-PCLLAGDSAESKSGRLSEGTKLNLLELHLANRLDRDTSGVMVITKSHKVASKLVKAFT 169 (354)
Q Consensus 91 ~~~lvvnKP~Gl~~~~~~~~~-~~~~~~~~~~~~~~~l~~~~~~~~~~l~~vhRLDk~TSGllllAk~~~~a~~l~~~f~ 169 (354)
..|+++|||+|++|+..+... +.. ....+.+....+.... ..+++|||||++||||||||+|+++++.|++ +
T Consensus 4 ~~y~llnKP~G~l~s~~d~~~~~g~-~~~~~~~~~~~l~~~~----~~l~~VgRLD~dTsGLLl~t~d~~~~~~L~~--~ 76 (177)
T cd02555 4 PVTLLLHKPAGMVSEQALALLGPGQ-RSAADRSGRRPLKGHF----ARLAPIGPLDKDASGLLVFSQDGRVLRKLIG--D 76 (177)
T ss_pred cEEEEEECCCceEecCCCccccccc-ccccccchhhhhhhcC----CceeEecCCCCCCeeEEEEECCHHHHHHHhC--h
Confidence 457999999999886543110 000 0000011112222211 4688999999999999999999999999999 6
Q ss_pred cCccceEEEEEEeCCCCCCCceEEecCCCCCCCCceeEeeecCCccccCCCcccccceeeEEEeeecCCCCCCCCcchhc
Q 018524 170 DHKVSKTYIALCIGPAPKWKRITIISGHGRSKFGAWRVYAASDVGRVLPGGSVVRDMVTSFEVLSVNGEGSFKEPSELQE 249 (354)
Q Consensus 170 ~~~v~K~Y~A~v~G~~~~~~~~~i~~~i~~~~~~~~~~~~~~~~~~~~~~g~~~~~a~t~~~vl~~~~~~~~~~~~~~~~ 249 (354)
.+.+.|+|+|+|.|.++++....+..++. + +|..... +++.
T Consensus 77 ~~~i~K~Y~v~v~g~~~~~~l~~l~~g~~------------------~-~~~~~~~----~~~~---------------- 117 (177)
T cd02555 77 ASRLEQEYLVEVRGELTAGGLERLNHGLT------------------Y-DGRELPP----AKVS---------------- 117 (177)
T ss_pred hcCCCEEEEEEEcccCCHHHHHHHhcCcc------------------c-CCeecce----EEEE----------------
Confidence 78899999999999987532111222210 0 1111111 1110
Q ss_pred ccccceeeeeehhhccCCCCceEEEEEEeCCCchhHHHHHHhhcCCceecCCCCC
Q 018524 250 HEENNIVVEKKAVLDADAKKNEILVRAFPRSGRTHQIRLHCQYLGISIRGDVKYE 304 (354)
Q Consensus 250 ~~~~~~~~~~~~~~~~~~~~~~slv~~~~~TGR~HQIRvhla~lG~PIvGD~~Yg 304 (354)
..+.++++++|.|||+||||+||+++||||+|+....
T Consensus 118 ------------------~~~~~~l~i~l~tGr~hQIR~~~~~~G~pV~~L~R~~ 154 (177)
T cd02555 118 ------------------WQNEQRLRFALKEPQPGQIRRMCESVGLEVVALRRIR 154 (177)
T ss_pred ------------------EcCCCEEEEEEECCcChHHHHHHHHcCCeEEEEEEEE
Confidence 0123689999999999999999999999999997764
No 23
>cd02566 PseudoU_synth_RluE PseudoU_synth_RluE: Pseudouridine synthase, Escherichia coli RluE. This group is comprised of bacterial proteins similar to E. coli RluE. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. Escherichia coli RluE makes psi2457 in 23S RNA. psi2457 is not universally conserved.
Probab=99.96 E-value=5.2e-30 Score=220.19 Aligned_cols=156 Identities=17% Similarity=0.194 Sum_probs=97.5
Q ss_pred EEEEECCCCCccccccc--cccccccccccccccCCCccccccccccccccccCCCCCceEEEEEeCHHHHHHHHHHhhc
Q 018524 93 LVAVNKPQGVYCESVLA--SVPCLLAGDSAESKSGRLSEGTKLNLLELHLANRLDRDTSGVMVITKSHKVASKLVKAFTD 170 (354)
Q Consensus 93 ~lvvnKP~Gl~~~~~~~--~~~~~~~~~~~~~~~~~l~~~~~~~~~~l~~vhRLDk~TSGllllAk~~~~a~~l~~~f~~ 170 (354)
|+|+|||+|++|++... ...+ +.+.+.. ..+++|||||++||||||||+|+++++.|.+ ++
T Consensus 1 ~lv~nKP~G~~~~~~~~~~~~~~---------l~~~l~~------~~~~~v~RLD~~TsGlll~a~d~~~~~~l~~--~~ 63 (168)
T cd02566 1 LILFNKPYGVLSQFTDESEKHKT---------LKDYIDD------PGVYAAGRLDRDSEGLLLLTDDGRLQHRITD--PS 63 (168)
T ss_pred CEEEECCCCCEEecCCCcCCCcc---------HHHHcCc------CCeEEccCCCCCCeEEEEEEeCHHHHHHHHC--CC
Confidence 68999999999986533 1122 2222211 3578999999999999999999999999988 67
Q ss_pred CccceEEEEEEeCCCCCCCceEEecCCCCCCCCceeEeeecCCccccCCCcccccceeeEEEeeecCCCCCCCCcchhcc
Q 018524 171 HKVSKTYIALCIGPAPKWKRITIISGHGRSKFGAWRVYAASDVGRVLPGGSVVRDMVTSFEVLSVNGEGSFKEPSELQEH 250 (354)
Q Consensus 171 ~~v~K~Y~A~v~G~~~~~~~~~i~~~i~~~~~~~~~~~~~~~~~~~~~~g~~~~~a~t~~~vl~~~~~~~~~~~~~~~~~ 250 (354)
+.++|+|+|+|.|.++.+....+..|+.. .++ ...+ +.+...+. .
T Consensus 64 ~~v~K~Y~a~v~g~~~~~~~~~l~~g~~~------------------~~~-~~~~--~~v~~~~~---~----------- 108 (168)
T cd02566 64 FKHPKTYYVQVEGVPTEDALEQLRNGVEL------------------GDG-LTLP--AKVEKVDE---P----------- 108 (168)
T ss_pred CCCCEEEEEEECCcCCHHHHHHHhCCcEE------------------CCe-Eecc--eEEEEecc---c-----------
Confidence 78999999999999865321111122210 000 0000 11111100 0
Q ss_pred cccceeeeeehhhccCCCCceEEEEEEeCCCchhHHHHHHhhcCCceecCCCC
Q 018524 251 EENNIVVEKKAVLDADAKKNEILVRAFPRSGRTHQIRLHCQYLGISIRGDVKY 303 (354)
Q Consensus 251 ~~~~~~~~~~~~~~~~~~~~~slv~~~~~TGR~HQIRvhla~lG~PIvGD~~Y 303 (354)
.+.++.. .........+.++++|+|.|||+||||+||+++||||+.....
T Consensus 109 -~~~~~~~--~~~~~~~~~~~sll~v~l~tGR~HQIR~~la~lG~pV~~L~R~ 158 (168)
T cd02566 109 -PWLWERE--PPIRFRKNIPTSWIEITICEGKNRQVRRMTAAVGFPTLRLIRV 158 (168)
T ss_pred -ccccccc--cccccccCCCccEEEEEEecCccHHHHHHHHHcCCeEeEEEEE
Confidence 0000000 0000001234579999999999999999999999999876543
No 24
>PRK11394 23S rRNA pseudouridine synthase E; Provisional
Probab=99.95 E-value=1e-28 Score=218.00 Aligned_cols=164 Identities=16% Similarity=0.200 Sum_probs=105.5
Q ss_pred eCCcEEEEECCCCCccccccccccccccccccccccCCCccccccccccccccccCCCCCceEEEEEeCHHHHHHHHHHh
Q 018524 89 EDEWLVAVNKPQGVYCESVLASVPCLLAGDSAESKSGRLSEGTKLNLLELHLANRLDRDTSGVMVITKSHKVASKLVKAF 168 (354)
Q Consensus 89 ed~~~lvvnKP~Gl~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~l~~vhRLDk~TSGllllAk~~~~a~~l~~~f 168 (354)
+...|+++|||.|++|+..+... ..++.+.+.. ..+++|||||++||||||||+|+++++.|.+
T Consensus 37 ~~~~ylllnKP~G~l~~~~d~~~--------~~tl~d~l~~------~~~~~vgRLD~~TsGllLlt~d~~~~~~L~~-- 100 (217)
T PRK11394 37 QPTRVILFNKPYDVLPQFTDEAG--------RKTLKEFIPV------QGVYAAGRLDRDSEGLLVLTNNGALQARLTQ-- 100 (217)
T ss_pred CCCEEEEEECCCCCEEeeCCccC--------CcchHHhccc------CCeEEecCCCCCCeeEEEEECCHHHHHHHhC--
Confidence 34569999999999998533211 1122222221 4589999999999999999999999999999
Q ss_pred hcCccceEEEEEEeCCCCCCCceEEecCCCCCCCCceeEeeecCCccccCCCcccccceeeEEEeeecCCCCCCCCcchh
Q 018524 169 TDHKVSKTYIALCIGPAPKWKRITIISGHGRSKFGAWRVYAASDVGRVLPGGSVVRDMVTSFEVLSVNGEGSFKEPSELQ 248 (354)
Q Consensus 169 ~~~~v~K~Y~A~v~G~~~~~~~~~i~~~i~~~~~~~~~~~~~~~~~~~~~~g~~~~~a~t~~~vl~~~~~~~~~~~~~~~ 248 (354)
+++.+.|+|+|+|.|.++.+....+..|+. +.++ ...++ .++++.... +. +.
T Consensus 101 ~~~~i~K~Y~~~v~g~~~~~~l~~l~~Gv~------------------i~~~-~~~p~--~~~~i~~~~---~~--~~-- 152 (217)
T PRK11394 101 PGKRTGKIYYVQVEGIPTQDALEALRNGVT------------------LNDG-PTLPA--GAELVDEPA---WL--WP-- 152 (217)
T ss_pred cccCCCEEEEEEECCCCCHHHHHHHhCCeE------------------ECCc-ccccc--EEEEecccc---cc--cc--
Confidence 688999999999999986532211122210 1111 11111 222221100 00 00
Q ss_pred cccccceeeeeehhhccCCCCceEEEEEEeCCCchhHHHHHHhhcCCceecCCCCCCc
Q 018524 249 EHEENNIVVEKKAVLDADAKKNEILVRAFPRSGRTHQIRLHCQYLGISIRGDVKYEGV 306 (354)
Q Consensus 249 ~~~~~~~~~~~~~~~~~~~~~~~slv~~~~~TGR~HQIRvhla~lG~PIvGD~~Yg~~ 306 (354)
. ...... ......++++|+|.|||+||||+||+++||||+||.+|+-.
T Consensus 153 --~-------~~~~~~-~~~~~~s~l~I~L~eGR~hQIRrm~a~lG~pVl~L~Ry~iG 200 (217)
T PRK11394 153 --R-------NPPIRE-RKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMG 200 (217)
T ss_pred --c-------cccccc-ccCCCceEEEEEEeCCCCHHHHHHHHHcCCeEeeeEEEEEC
Confidence 0 000000 00124688999999999999999999999999999999853
No 25
>TIGR00093 pseudouridine synthase. This model identifies panels of pseudouridine synthase enzymes that RNA modifications involved in maturing the protein translation apparatus. Counts per genome vary: two in Staphylococcus aureus, three in Pseudomonas putida, four in E. coli, etc.
Probab=99.95 E-value=2.9e-28 Score=199.97 Aligned_cols=110 Identities=24% Similarity=0.348 Sum_probs=84.0
Q ss_pred cccCCCCCceEEEEEeCHHHHHHHHHHhhcCccceEEEEEEeCCCCCCCceEEecCCCCCCCCceeEeeecCCccccCCC
Q 018524 141 ANRLDRDTSGVMVITKSHKVASKLVKAFTDHKVSKTYIALCIGPAPKWKRITIISGHGRSKFGAWRVYAASDVGRVLPGG 220 (354)
Q Consensus 141 vhRLDk~TSGllllAk~~~~a~~l~~~f~~~~v~K~Y~A~v~G~~~~~~~~~i~~~i~~~~~~~~~~~~~~~~~~~~~~g 220 (354)
|||||++||||||||+|+++++.|.. +++.+.|+|+|+|.|.++.+....+. .|. ...++
T Consensus 1 v~RLD~~TSGlll~akd~~~~~~L~~--~~~~i~K~Y~a~v~g~~~~~~~~~~~-------~g~-----------~~~~~ 60 (128)
T TIGR00093 1 AGRLDRDSEGLLLLTNDGELVHRLTH--PGHHCEKTYLVTVEGPVTDEDLEALR-------KGV-----------QLEDG 60 (128)
T ss_pred CCCCCCCCEEEEEEEeCHHHHHHHhC--CCCCCCeEEEEEECCCCCHHHHHHHh-------CCe-----------EECCc
Confidence 79999999999999999999999998 88999999999999998653211000 000 01111
Q ss_pred cccccceeeEEEeeecCCCCCCCCcchhcccccceeeeeehhhccCCCCceEEEEEEeCCCchhHHHHHHhhcCCceecC
Q 018524 221 SVVRDMVTSFEVLSVNGEGSFKEPSELQEHEENNIVVEKKAVLDADAKKNEILVRAFPRSGRTHQIRLHCQYLGISIRGD 300 (354)
Q Consensus 221 ~~~~~a~t~~~vl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~slv~~~~~TGR~HQIRvhla~lG~PIvGD 300 (354)
+.+.+.++++.. ....++++|+|.|||+||||+||+++||||+||
T Consensus 61 ---~~~~~~~~~l~~--------------------------------~~~~~~l~~~l~tGR~HQIR~~~~~lG~pI~g~ 105 (128)
T TIGR00093 61 ---PTKPAKLEVITE--------------------------------PGFPTWLRITLSEGRNRQVRRMFAAVGFPVLRL 105 (128)
T ss_pred ---EEeeeEEEEEcc--------------------------------CCCceEEEEEEeCCCCHHHHHHHHHcCCeEeEE
Confidence 224456666532 233579999999999999999999999999999
Q ss_pred CCCCC
Q 018524 301 VKYEG 305 (354)
Q Consensus 301 ~~Yg~ 305 (354)
..|.-
T Consensus 106 ~R~~~ 110 (128)
T TIGR00093 106 HRVRI 110 (128)
T ss_pred EEEEE
Confidence 88763
No 26
>cd02554 PseudoU_synth_RluF PseudoU_synth_RluF_like: Pseudouridine synthase, Escherichia coli RluF like. This group is comprised of bacterial proteins similar to Escherichia coli RluF. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. E.coli RluF makes psi2604 in 23S RNA. psi2604 has only been detected in E. coli. It is absent from other eubacteria despite a precursor U at that site and from eukarya and archea which lack a precursor U at that site.
Probab=99.93 E-value=2.4e-26 Score=195.37 Aligned_cols=135 Identities=22% Similarity=0.293 Sum_probs=95.8
Q ss_pred EEEEECCCCCccccccccccccccccccccccCCCccccccccccccccccCCCCCceEEEEEeCHHHHHHHHHHhhcCc
Q 018524 93 LVAVNKPQGVYCESVLASVPCLLAGDSAESKSGRLSEGTKLNLLELHLANRLDRDTSGVMVITKSHKVASKLVKAFTDHK 172 (354)
Q Consensus 93 ~lvvnKP~Gl~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~l~~vhRLDk~TSGllllAk~~~~a~~l~~~f~~~~ 172 (354)
|+++|||+|++|++.....+ ++.+.+... ..+++|||||++||||||||+|++++++|+. +.+.
T Consensus 2 y~~lnKP~G~l~s~~~~~~~---------tv~~~l~~~-----~~~~~vgRLD~~tsGlll~t~dg~~~~~L~~--p~~~ 65 (164)
T cd02554 2 YIAYNKPVGIDCTLERADED---------NIIDFVNPP-----PRIFPIGRLDKDSEGLILLTNDGDLVNKILH--ADNN 65 (164)
T ss_pred EEEEECCCCcEeecCCCCCC---------cHHHHhcCc-----CCEEEccCCCCCCeeEEEEEcCHHHHHHHhh--hhcC
Confidence 79999999999986532222 233333221 4699999999999999999999999999987 8889
Q ss_pred cceEEEEEEeCCCCCCCceEEecCCCCCCCCceeEeeecCCccccCCCcccccceeeEEEeeecCCCCCCCCcchhcccc
Q 018524 173 VSKTYIALCIGPAPKWKRITIISGHGRSKFGAWRVYAASDVGRVLPGGSVVRDMVTSFEVLSVNGEGSFKEPSELQEHEE 252 (354)
Q Consensus 173 v~K~Y~A~v~G~~~~~~~~~i~~~i~~~~~~~~~~~~~~~~~~~~~~g~~~~~a~t~~~vl~~~~~~~~~~~~~~~~~~~ 252 (354)
+.|+|+|.|.|.+.++....+..| ....+..|....+..
T Consensus 66 ~~K~Y~V~v~~~l~~~~l~~l~~G------------------------~~~~~~~~~~~~v~~----------------- 104 (164)
T cd02554 66 HEKEYLVTVNKPITDEFIEGMSNG------------------------VVILGTVTKPCKVER----------------- 104 (164)
T ss_pred CCeEEEEEECCCCCHHHHHHHhCC------------------------CEECCeEEcceEEEE-----------------
Confidence 999999999999875322222222 111222222222211
Q ss_pred cceeeeeehhhccCCCCceEEEEEEeCCCchhHHHHHHhhcCCceecC
Q 018524 253 NNIVVEKKAVLDADAKKNEILVRAFPRSGRTHQIRLHCQYLGISIRGD 300 (354)
Q Consensus 253 ~~~~~~~~~~~~~~~~~~~slv~~~~~TGR~HQIRvhla~lG~PIvGD 300 (354)
... +.++|++.|||+||||+||+++|+||+-=
T Consensus 105 ---------------~~~-~~l~i~l~eGr~~qIRrm~~~~G~~V~~L 136 (164)
T cd02554 105 ---------------LAK-DKFRIVLTQGLNRQIRRMCEALGYRVTDL 136 (164)
T ss_pred ---------------CCC-CEEEEEEECCcCHHHHHHHHHcCCEEEEE
Confidence 011 24899999999999999999999999753
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=99.15 E-value=4.2e-11 Score=106.75 Aligned_cols=76 Identities=29% Similarity=0.333 Sum_probs=54.7
Q ss_pred cEEEEECCCCCccccccccccccccccccccccCCCccccccccccccccccCCCCCceEEEEEeCHHHHHHHHHHhhcC
Q 018524 92 WLVAVNKPQGVYCESVLASVPCLLAGDSAESKSGRLSEGTKLNLLELHLANRLDRDTSGVMVITKSHKVASKLVKAFTDH 171 (354)
Q Consensus 92 ~~lvvnKP~Gl~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~l~~vhRLDk~TSGllllAk~~~~a~~l~~~f~~~ 171 (354)
.+||||||+|+.++...+.+...+. ..+.. . ...++|||||++|||||+||++..+ ++..+|.++
T Consensus 1 GilvvnKP~Gi~s~~~~~~~~~~l~--------~~~~~-~----k~~~~vhrLD~~aSGvl~~a~~~~t--kl~~~~~~~ 65 (226)
T cd02868 1 GLFAVYKPPGVHWKHVRDTIESNLL--------KYFPE-D----KVLVGVHRLDAFSSGVLVLGVNHGN--KLLSHLYSN 65 (226)
T ss_pred CEEEEEcCCCCChhHHHHHHHHHHH--------HHccc-c----ceeeEccccCCCCceEEEEEeChhH--hHHHHHHhc
Confidence 3799999999987654322111100 00101 0 2367889999999999999999986 699999999
Q ss_pred ccceEEEEEEe
Q 018524 172 KVSKTYIALCI 182 (354)
Q Consensus 172 ~v~K~Y~A~v~ 182 (354)
.+.|+|+|...
T Consensus 66 ~~~K~Y~~~~~ 76 (226)
T cd02868 66 HPTRVYTIRGL 76 (226)
T ss_pred CCCeEEEEEEE
Confidence 99999996654
No 28
>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=97.71 E-value=6.8e-05 Score=64.99 Aligned_cols=70 Identities=21% Similarity=0.359 Sum_probs=49.2
Q ss_pred CcEEEEECCCCCccccccccccccccccccccccCCCccccccccccccccccCCCCCceEEEEEeCHHHHHHHHHHhhc
Q 018524 91 EWLVAVNKPQGVYCESVLASVPCLLAGDSAESKSGRLSEGTKLNLLELHLANRLDRDTSGVMVITKSHKVASKLVKAFTD 170 (354)
Q Consensus 91 ~~~lvvnKP~Gl~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~l~~vhRLDk~TSGllllAk~~~~a~~l~~~f~~ 170 (354)
+.+|+||||.|+.++.....+... .+...+.-.|-||...||||+++-+. +-++.+.|.+
T Consensus 2 ~g~l~i~Kp~g~tS~~~v~~~k~~------------------~~~kkvGH~GTLDp~A~GvLiv~~g~--~Tk~~~~~~~ 61 (182)
T cd02572 2 YGVINLDKPSGPSSHEVVAWIKRI------------------LGVEKTGHSGTLDPKVTGCLPVCIDR--ATRLVKSQQE 61 (182)
T ss_pred CeEEEEecCCCCCHHHHHHHHHHH------------------hCCCccCcCCCCCCcCeeEEEEEECH--HhhhhHHHhC
Confidence 469999999999876432221110 11146788999999999999999987 3445554544
Q ss_pred CccceEEEEEEe
Q 018524 171 HKVSKTYIALCI 182 (354)
Q Consensus 171 ~~v~K~Y~A~v~ 182 (354)
. .|+|.|.+.
T Consensus 62 ~--~K~Y~a~v~ 71 (182)
T cd02572 62 A--GKEYVCVMR 71 (182)
T ss_pred C--CCEEEEEEE
Confidence 3 499999876
No 29
>PRK00989 truB tRNA pseudouridine synthase B; Provisional
Probab=97.43 E-value=0.00019 Score=64.06 Aligned_cols=71 Identities=28% Similarity=0.340 Sum_probs=50.6
Q ss_pred CcEEEEECCCCCccccccccccccccccccccccCCCccccccccccccccccCCCCCceEEEEEeCHHHHHHHHHHhhc
Q 018524 91 EWLVAVNKPQGVYCESVLASVPCLLAGDSAESKSGRLSEGTKLNLLELHLANRLDRDTSGVMVITKSHKVASKLVKAFTD 170 (354)
Q Consensus 91 ~~~lvvnKP~Gl~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~l~~vhRLDk~TSGllllAk~~~~a~~l~~~f~~ 170 (354)
+.+|.||||.|+.++.....+... ++...+.-.|.||...||||+++-.. .+.+|.+.+.+
T Consensus 9 ~G~l~i~KP~g~TS~dvv~~ikk~------------------~~~kKvGH~GTLDP~AtGvLiv~vG~-~aTkl~~~~~~ 69 (230)
T PRK00989 9 EGILLVDKPQGRTSFSLIRSLTKL------------------IGVKKIGHAGTLDPFATGVMVMLIGR-KFTRLSDILLF 69 (230)
T ss_pred CEEEEEeCCCCCCHHHHHHHHHHH------------------hCCCcCCcCccCCCCCeeEEEEEECC-chhhhHHHhcC
Confidence 479999999999876433222211 11146888999999999999999775 34455555444
Q ss_pred CccceEEEEEEe
Q 018524 171 HKVSKTYIALCI 182 (354)
Q Consensus 171 ~~v~K~Y~A~v~ 182 (354)
..|+|+|.+.
T Consensus 70 --~~K~Y~~~~~ 79 (230)
T PRK00989 70 --EDKEYAAVAH 79 (230)
T ss_pred --CCcEEEEEEE
Confidence 6899999886
No 30
>cd00506 PseudoU_synth_TruB_like PseudoU_synth_TruB: Pseudouridine synthase, TruB family. This group consists of eukaryotic, bacterial and archeal pseudouridine synthases similar to Escherichia coli TruB, Saccharomyces cerevisiae Pus4, M. tuberculosis TruB, S. cerevisiae Cbf5 and human dyskerin. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. E. coli TruB, M. tuberculosis TruB and S. cerevisiae Pus4, make psi55 in the T loop of tRNAs. Pus4 catalyses the formation of psi55 in both cytoplasmic and mitochondrial tRNAs. Psi55 is almost universally conserved. S. cerevisiae Cbf5 and human dyskerin are nucleolar proteins that, with the help of guide RNAs, make the hundreds of psueudouridnes present in rRNA and small nuclear RNAs (snRNAs). Cbf5/Dyskerin is the catalytic subunit of eukaryotic box H/ACA small nucleolar ribonucleoprotein (snoRNP) particles. Mutations in human dysker
Probab=97.40 E-value=0.00028 Score=62.47 Aligned_cols=72 Identities=29% Similarity=0.404 Sum_probs=50.7
Q ss_pred cEEEEECCCCCccccccccccccccccccccccCCCccccccccccccccccCCCCCceEEEEEeCHHHHHHHHHHhhcC
Q 018524 92 WLVAVNKPQGVYCESVLASVPCLLAGDSAESKSGRLSEGTKLNLLELHLANRLDRDTSGVMVITKSHKVASKLVKAFTDH 171 (354)
Q Consensus 92 ~~lvvnKP~Gl~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~l~~vhRLDk~TSGllllAk~~~~a~~l~~~f~~~ 171 (354)
.++.||||.|+.|+.....+... ++...+.-.|-||...||||+++-+.. .++...|.+
T Consensus 1 Gil~i~KP~g~tS~~vv~~ik~~------------------~~~kKvGH~GTLDP~AsGvLiv~vG~a--Tkl~~~~~~- 59 (210)
T cd00506 1 GLFAVDKPQGPSSHDVVDTIRRI------------------FLAEKVGHGGTLDPFATGVLVVGIGKA--TKLLKHLLA- 59 (210)
T ss_pred CEEEEEcCCCCCHHHHHHHHHHH------------------hCccccCCCCcCCCcCeeEEEEEECHH--HhhhHHHhc-
Confidence 37999999999876433222210 111468889999999999999999863 455554544
Q ss_pred ccceEEEEEEe-CCC
Q 018524 172 KVSKTYIALCI-GPA 185 (354)
Q Consensus 172 ~v~K~Y~A~v~-G~~ 185 (354)
..|+|.|.+. |.-
T Consensus 60 -~~K~Y~~~~~lG~~ 73 (210)
T cd00506 60 -ATKDYTAIGRLGQA 73 (210)
T ss_pred -CCceEEEEEEECCc
Confidence 7999999875 443
No 31
>cd00165 S4 S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, charged residues that define a likely RNA-binding site; Found in stress proteins, ribosomal proteins and tRNA synthetases; This may imply a hitherto unrecognized functional similarity between these three protein classes.
Probab=97.35 E-value=2.5e-05 Score=55.71 Aligned_cols=65 Identities=12% Similarity=0.169 Sum_probs=43.5
Q ss_pred Cccccccccc-CCCCCCCCCCCCCCccccCCCCCCCCCCcccccceeEEeecccccccccccCC----CccEEEeCCcEE
Q 018524 20 RFRKTFFSLA-SMSNPTEPTSQNAPQTQQNYPTPLSPPLPAISKDIELTRAMSASSKSSLYKLS----RSDVLYEDEWLV 94 (354)
Q Consensus 20 ~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~v~~~~~~~~~~~~~~~~~~----~~~Ilyed~~~l 94 (354)
||+++|+... ...++.++..++..|.+ .+|+...........+. +.+.+. ...|+|||++++
T Consensus 1 ~rl~~~l~~~~~~~sr~~~~~~i~~g~V------------~vn~~~~~~~~~~v~~~-d~i~i~~~~~~~~i~~ed~~~l 67 (70)
T cd00165 1 MRLDKILARLGLAPSRSEARQLIKHGHV------------LVNGKVVTKPSYKVKPG-DVIEVDGKSIEEDIVYEDKKLL 67 (70)
T ss_pred CcHHHHHHHhccccCHHHHHHHHHcCCE------------EECCEEccCCccCcCCC-CEEEEcCCCcccceeeccCCEE
Confidence 5888999877 56799999999999888 45555443333333221 112221 127999999999
Q ss_pred EEE
Q 018524 95 AVN 97 (354)
Q Consensus 95 vvn 97 (354)
|+|
T Consensus 68 vv~ 70 (70)
T cd00165 68 VVN 70 (70)
T ss_pred EeC
Confidence 997
No 32
>PRK04099 truB tRNA pseudouridine synthase B; Provisional
Probab=97.32 E-value=0.00039 Score=63.74 Aligned_cols=73 Identities=23% Similarity=0.363 Sum_probs=51.2
Q ss_pred CcEEEEECCCCCccccccccccccccccccccccCCCccccccccccccccccCCCCCceEEEEEeCHHHHHHHHHHhhc
Q 018524 91 EWLVAVNKPQGVYCESVLASVPCLLAGDSAESKSGRLSEGTKLNLLELHLANRLDRDTSGVMVITKSHKVASKLVKAFTD 170 (354)
Q Consensus 91 ~~~lvvnKP~Gl~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~l~~vhRLDk~TSGllllAk~~~~a~~l~~~f~~ 170 (354)
+.++++|||+|+.||.....+... + +...+.-.+-||-..||||+++-... -++...+.+
T Consensus 2 ngil~vdKP~g~tS~~vv~~ikk~------------~------~~kKvGH~GTLDP~AtGvLiv~iG~a--TKl~~~l~~ 61 (273)
T PRK04099 2 NRLFVANKPAGMSSNAFLSRLKRK------------Y------GVKKAGFSGTLDPFAKGVLIVAFGQY--TKLFRFLKK 61 (273)
T ss_pred CeEEEEeCCCCCCHHHHHHHHHHH------------h------CCCccccCccCCCCCeeEEEEEEChH--hhhHHHhcc
Confidence 368999999999887433222211 0 11457889999999999999999874 345554444
Q ss_pred CccceEEEEEEe-CCC
Q 018524 171 HKVSKTYIALCI-GPA 185 (354)
Q Consensus 171 ~~v~K~Y~A~v~-G~~ 185 (354)
..|+|.|.+. |.-
T Consensus 62 --~~K~Y~a~~~lG~~ 75 (273)
T PRK04099 62 --TPKTYRATLWLGAS 75 (273)
T ss_pred --CCceEEEEEEECCc
Confidence 3899999875 443
No 33
>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=97.28 E-value=0.00046 Score=60.90 Aligned_cols=73 Identities=30% Similarity=0.349 Sum_probs=51.6
Q ss_pred CcEEEEECCCCCccccccccccccccccccccccCCCccccccccccccccccCCCCCceEEEEEeCHHHHHHHHHHhhc
Q 018524 91 EWLVAVNKPQGVYCESVLASVPCLLAGDSAESKSGRLSEGTKLNLLELHLANRLDRDTSGVMVITKSHKVASKLVKAFTD 170 (354)
Q Consensus 91 ~~~lvvnKP~Gl~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~l~~vhRLDk~TSGllllAk~~~~a~~l~~~f~~ 170 (354)
+.+++||||.|+.++.....+... + +...+.-.|-||-..||||+++-+... ++...|.
T Consensus 2 ~G~l~v~KP~g~tS~~vv~~vkk~------------~------~~kKvGH~GTLDP~AsGvLiv~vG~~T--kl~~~~~- 60 (209)
T TIGR00431 2 NGVLLLDKPQGMTSFDALAKVRRL------------L------NVKKVGHTGTLDPFATGVLPILVGKAT--KLSPYLT- 60 (209)
T ss_pred CeEEEEECCCCCCHHHHHHHHHHH------------h------CCCcCCCCCCCCCcCceEEEEEEChHh--hhhHHHc-
Confidence 368999999999776433222211 0 114577899999999999999998753 5666554
Q ss_pred CccceEEEEEEe-CCC
Q 018524 171 HKVSKTYIALCI-GPA 185 (354)
Q Consensus 171 ~~v~K~Y~A~v~-G~~ 185 (354)
.-.|+|.|.+. |.-
T Consensus 61 -~~~K~Y~~~~~~G~~ 75 (209)
T TIGR00431 61 -DLDKEYRAEIRLGVR 75 (209)
T ss_pred -CCCCeEEEEEEECCc
Confidence 57899999875 443
No 34
>PRK00020 truB tRNA pseudouridine synthase B; Provisional
Probab=97.26 E-value=0.00052 Score=61.77 Aligned_cols=70 Identities=20% Similarity=0.281 Sum_probs=49.4
Q ss_pred CcEEEEECCCCCccccccccccccccccccccccCCCccccccccccccccccCCCCCceEEEEEeCHHHHHHHHHHhhc
Q 018524 91 EWLVAVNKPQGVYCESVLASVPCLLAGDSAESKSGRLSEGTKLNLLELHLANRLDRDTSGVMVITKSHKVASKLVKAFTD 170 (354)
Q Consensus 91 ~~~lvvnKP~Gl~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~l~~vhRLDk~TSGllllAk~~~~a~~l~~~f~~ 170 (354)
+.+|+||||.|+.|+.....+... ++...+.-.+-||...||||+++-.. +-++...|.+
T Consensus 10 ~Gil~vdKP~G~TS~dvv~~vkr~------------------~~~kKvGH~GTLDP~AtGvLiv~iG~--aTKl~~~l~~ 69 (244)
T PRK00020 10 DGVLLLDKPVGLSSNHALQRAKRT------------------VDAAKAGHTGTLDPFATGLLVCCMGR--ATKISGRMLE 69 (244)
T ss_pred CeEEEEecCCCCCHHHHHHHHHHH------------------hCCCCCCcCCcCCCcCeeEEEEEECH--HhhhhHHhcc
Confidence 469999999999877433222210 11146778999999999999999987 3445554443
Q ss_pred CccceEEEEEEe
Q 018524 171 HKVSKTYIALCI 182 (354)
Q Consensus 171 ~~v~K~Y~A~v~ 182 (354)
..|+|+|.+.
T Consensus 70 --~~K~Y~a~~~ 79 (244)
T PRK00020 70 --ADKTYQATLQ 79 (244)
T ss_pred --CCcEEEEEEE
Confidence 3599999875
No 35
>PRK02484 truB tRNA pseudouridine synthase B; Provisional
Probab=97.18 E-value=0.00065 Score=63.15 Aligned_cols=73 Identities=19% Similarity=0.324 Sum_probs=50.7
Q ss_pred CcEEEEECCCCCccccccccccccccccccccccCCCccccccccccccccccCCCCCceEEEEEeCHHHHHHHHHHhhc
Q 018524 91 EWLVAVNKPQGVYCESVLASVPCLLAGDSAESKSGRLSEGTKLNLLELHLANRLDRDTSGVMVITKSHKVASKLVKAFTD 170 (354)
Q Consensus 91 ~~~lvvnKP~Gl~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~l~~vhRLDk~TSGllllAk~~~~a~~l~~~f~~ 170 (354)
+.+|++|||.|+.||.....+... ++...+.-.|-||-..||||+++-... -++.+.+.+
T Consensus 3 ~Gil~i~KP~G~TS~dvv~~vrr~------------------l~~kKvGH~GTLDP~AtGvL~i~vG~a--Tkl~~~l~~ 62 (294)
T PRK02484 3 NGIINLKKEAGMTSHDAVFKLRKI------------------LQTKKIGHGGTLDPDVVGVLPIAVGKA--TRLIEYMTE 62 (294)
T ss_pred ceEEEEeCCCCCCHHHHHHHHHHH------------------hCCCccccCCCCCCCCeeEEEEEEChh--hhhhHHhcc
Confidence 368999999999877433222211 011467889999999999999998863 345554443
Q ss_pred CccceEEEEEEe-CCC
Q 018524 171 HKVSKTYIALCI-GPA 185 (354)
Q Consensus 171 ~~v~K~Y~A~v~-G~~ 185 (354)
-.|+|.|.+. |.-
T Consensus 63 --~~K~Y~a~~~lG~~ 76 (294)
T PRK02484 63 --AGKVYEGEITLGYS 76 (294)
T ss_pred --CCcEEEEEEEECCc
Confidence 3599999876 443
No 36
>PRK14124 tRNA pseudouridine synthase B; Provisional
Probab=97.14 E-value=0.00084 Score=62.71 Aligned_cols=70 Identities=20% Similarity=0.301 Sum_probs=49.8
Q ss_pred CcEEEEECCCCCccccccccccccccccccccccCCCccccccccccccccccCCCCCceEEEEEeCHHHHHHHHHHhhc
Q 018524 91 EWLVAVNKPQGVYCESVLASVPCLLAGDSAESKSGRLSEGTKLNLLELHLANRLDRDTSGVMVITKSHKVASKLVKAFTD 170 (354)
Q Consensus 91 ~~~lvvnKP~Gl~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~l~~vhRLDk~TSGllllAk~~~~a~~l~~~f~~ 170 (354)
+.+++||||.|+.||.....+... + +...+.-.+-||...||||+++-+.. .++.+.+..
T Consensus 3 ~Gil~i~KP~G~TS~dvv~~vrr~------------l------~~kKvGH~GTLDP~AtGvL~v~vG~a--Tkl~~~l~~ 62 (308)
T PRK14124 3 HGFLVAYKPKGPTSHDVVDEVRKK------------L------KTRKVGHAGTLDPFATGVLIVGVNKA--TRLLEYLKN 62 (308)
T ss_pred ceEEEEECCCCCCHHHHHHHHHHH------------c------CCCccCcCcCCCCCCcEEEEEEEChH--HhhhHHHhc
Confidence 368999999999877433222211 0 11457889999999999999999864 345555544
Q ss_pred CccceEEEEEEe
Q 018524 171 HKVSKTYIALCI 182 (354)
Q Consensus 171 ~~v~K~Y~A~v~ 182 (354)
. .|+|.|.+.
T Consensus 63 ~--~K~Y~a~~~ 72 (308)
T PRK14124 63 E--KKVYYVKMR 72 (308)
T ss_pred C--CceEEEEEE
Confidence 3 899999885
No 37
>PRK03287 truB tRNA pseudouridine synthase B; Provisional
Probab=97.13 E-value=0.00072 Score=62.87 Aligned_cols=72 Identities=31% Similarity=0.381 Sum_probs=50.4
Q ss_pred eCCcEEEEECCCCCccccccccccccccccccccccCCCccccccccccccccccCCCCCceEEEEEeCHHHHHHHHHHh
Q 018524 89 EDEWLVAVNKPQGVYCESVLASVPCLLAGDSAESKSGRLSEGTKLNLLELHLANRLDRDTSGVMVITKSHKVASKLVKAF 168 (354)
Q Consensus 89 ed~~~lvvnKP~Gl~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~l~~vhRLDk~TSGllllAk~~~~a~~l~~~f 168 (354)
+-+.+|+||||.|+.||.....+...+ +...+.-.+-||-..||||+++-.. +-++.+.+
T Consensus 7 ~~~Gil~i~KP~G~TS~dvv~~vrr~~------------------~~kKvGH~GTLDP~AtGvL~i~vG~--aTKl~~~l 66 (298)
T PRK03287 7 TGSGLVVVDKPAGMTSHDVVARCRRLF------------------GTRKVGHAGTLDPMATGVLVLGVER--ATKLLGHL 66 (298)
T ss_pred CcCeEEEEeCCCCCCHHHHHHHHHHHh------------------CCCCCCcCccCCCcceeEEEEEeCh--hhhhhHHH
Confidence 345799999999998764332222210 1145778999999999999999985 33444444
Q ss_pred hcCccceEEEEEEe
Q 018524 169 TDHKVSKTYIALCI 182 (354)
Q Consensus 169 ~~~~v~K~Y~A~v~ 182 (354)
.+ -.|+|.|.+.
T Consensus 67 ~~--~~K~Y~a~~~ 78 (298)
T PRK03287 67 TL--TDKSYTATIR 78 (298)
T ss_pred hc--CCcEEEEEEE
Confidence 44 3899999875
No 38
>PRK00130 truB tRNA pseudouridine synthase B; Provisional
Probab=97.12 E-value=0.00086 Score=62.27 Aligned_cols=70 Identities=21% Similarity=0.291 Sum_probs=49.9
Q ss_pred CcEEEEECCCCCccccccccccccccccccccccCCCccccccccccccccccCCCCCceEEEEEeCHHHHHHHHHHhhc
Q 018524 91 EWLVAVNKPQGVYCESVLASVPCLLAGDSAESKSGRLSEGTKLNLLELHLANRLDRDTSGVMVITKSHKVASKLVKAFTD 170 (354)
Q Consensus 91 ~~~lvvnKP~Gl~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~l~~vhRLDk~TSGllllAk~~~~a~~l~~~f~~ 170 (354)
+.+|+||||.|+.||.....+... ++...+.-.+-||-..||||+++-... -++.+.+..
T Consensus 2 ~Gil~i~KP~G~tS~dvv~~vrr~------------------~~~kKvGH~GTLDP~AtGvL~v~vG~a--Tkl~~~l~~ 61 (290)
T PRK00130 2 DGILNILKPPGMTSFDVVRKIRKI------------------AKIKKVGHTGTLDPLASGVLPVCLGKA--TKIVDYLME 61 (290)
T ss_pred CeEEEEeCCCCCCHHHHHHHHHHH------------------hCCCccCcCCCCCCCCeeEEEEEEChh--hhhHHHhcc
Confidence 368999999999877433222211 011457889999999999999999873 345555544
Q ss_pred CccceEEEEEEe
Q 018524 171 HKVSKTYIALCI 182 (354)
Q Consensus 171 ~~v~K~Y~A~v~ 182 (354)
-.|+|.|.+.
T Consensus 62 --~~K~Y~a~~~ 71 (290)
T PRK00130 62 --GKKTYRAEIK 71 (290)
T ss_pred --CCcEEEEEEE
Confidence 3899999876
No 39
>PRK02193 truB tRNA pseudouridine synthase B; Provisional
Probab=97.10 E-value=0.00084 Score=61.83 Aligned_cols=68 Identities=22% Similarity=0.352 Sum_probs=48.6
Q ss_pred EEEEECCCCCccccccccccccccccccccccCCCccccccccccccccccCCCCCceEEEEEeCHHHHHHHHHHhhcCc
Q 018524 93 LVAVNKPQGVYCESVLASVPCLLAGDSAESKSGRLSEGTKLNLLELHLANRLDRDTSGVMVITKSHKVASKLVKAFTDHK 172 (354)
Q Consensus 93 ~lvvnKP~Gl~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~l~~vhRLDk~TSGllllAk~~~~a~~l~~~f~~~~ 172 (354)
++++|||.|+.||.....+... ++...+.-.|-||-..||||+++-... .++.+.+ ..
T Consensus 2 il~i~KP~G~tS~dvv~~vrr~------------------~~~kKvGH~GTLDP~AtGvL~v~vG~a--Tkl~~~l--~~ 59 (279)
T PRK02193 2 IKLLYKPKGISSFKFIKNFAKT------------------NNIKKIGHTGTLDPLASGLLLVATDED--TKLIDYL--DQ 59 (279)
T ss_pred EEEEECCCCCCHHHHHHHHHHH------------------cCCCccccCccCCCcCeeEEEEEEChh--hhhhHHh--cc
Confidence 7899999999877433222210 011467889999999999999998863 4455544 34
Q ss_pred cceEEEEEEe
Q 018524 173 VSKTYIALCI 182 (354)
Q Consensus 173 v~K~Y~A~v~ 182 (354)
..|+|.|.+.
T Consensus 60 ~~K~Y~a~~~ 69 (279)
T PRK02193 60 KDKTYIAKIK 69 (279)
T ss_pred CCcEEEEEEE
Confidence 6899999875
No 40
>PRK05389 truB tRNA pseudouridine synthase B; Provisional
Probab=97.09 E-value=0.0009 Score=62.50 Aligned_cols=73 Identities=26% Similarity=0.307 Sum_probs=51.1
Q ss_pred CcEEEEECCCCCccccccccccccccccccccccCCCccccccccccccccccCCCCCceEEEEEeCHHHHHHHHHHhhc
Q 018524 91 EWLVAVNKPQGVYCESVLASVPCLLAGDSAESKSGRLSEGTKLNLLELHLANRLDRDTSGVMVITKSHKVASKLVKAFTD 170 (354)
Q Consensus 91 ~~~lvvnKP~Gl~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~l~~vhRLDk~TSGllllAk~~~~a~~l~~~f~~ 170 (354)
+.+|+||||.|+.||.....+... + +...+.-.+-||...||||+++-.. +-++.+.+..
T Consensus 13 ~Gil~i~KP~G~TS~dvv~~vrk~------------~------~~kKvGH~GTLDP~AtGvL~v~vG~--aTkl~~~l~~ 72 (305)
T PRK05389 13 SGWLILDKPAGMTSTEAVSKVKWL------------F------DAQKAGHAGTLDPLASGVLPIALGE--ATKTVPYVMD 72 (305)
T ss_pred CeEEEEeCCCCCCHHHHHHHHHHH------------h------cccccCCcccCCCCCceEEEEEECh--hhhhhHHhcc
Confidence 479999999999877433222211 0 1145778999999999999999886 3445555543
Q ss_pred CccceEEEEEEe-CCC
Q 018524 171 HKVSKTYIALCI-GPA 185 (354)
Q Consensus 171 ~~v~K~Y~A~v~-G~~ 185 (354)
-.|+|.|.+. |.-
T Consensus 73 --~~K~Y~a~~~lG~~ 86 (305)
T PRK05389 73 --GTKRYRFTVAWGEE 86 (305)
T ss_pred --CCcEEEEEEEECCc
Confidence 3899999875 443
No 41
>PRK14123 tRNA pseudouridine synthase B; Provisional
Probab=97.07 E-value=0.00093 Score=62.44 Aligned_cols=70 Identities=19% Similarity=0.301 Sum_probs=50.3
Q ss_pred CcEEEEECCCCCccccccccccccccccccccccCCCccccccccccccccccCCCCCceEEEEEeCHHHHHHHHHHhhc
Q 018524 91 EWLVAVNKPQGVYCESVLASVPCLLAGDSAESKSGRLSEGTKLNLLELHLANRLDRDTSGVMVITKSHKVASKLVKAFTD 170 (354)
Q Consensus 91 ~~~lvvnKP~Gl~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~l~~vhRLDk~TSGllllAk~~~~a~~l~~~f~~ 170 (354)
+.+|+||||.|+.||.....+... + +...+.-.|-||-..||||+++-...+ ++.+.+..
T Consensus 3 ~Gil~i~KP~G~TS~dvv~~vrr~------------~------~~kKvGH~GTLDP~AtGvL~v~vG~aT--kl~~~l~~ 62 (305)
T PRK14123 3 NGILPVYKERGLTSHDVVFKLRKI------------L------KTKKIGHTGTLDPEVAGVLPVCIGNAT--RVSDYVMD 62 (305)
T ss_pred ceEEEEeCCCCCCHHHHHHHHHHH------------h------CCCccccCcCCCCcCeeEEEEEEChhh--hhHHHhcC
Confidence 369999999999877433222211 0 114678899999999999999998743 45554443
Q ss_pred CccceEEEEEEe
Q 018524 171 HKVSKTYIALCI 182 (354)
Q Consensus 171 ~~v~K~Y~A~v~ 182 (354)
..|+|.|.+.
T Consensus 63 --~~K~Y~~~~~ 72 (305)
T PRK14123 63 --MGKAYEATVS 72 (305)
T ss_pred --CCcEEEEEEE
Confidence 6899999875
No 42
>PRK02755 truB tRNA pseudouridine synthase B; Provisional
Probab=97.03 E-value=0.001 Score=61.89 Aligned_cols=71 Identities=24% Similarity=0.341 Sum_probs=50.8
Q ss_pred CcEEEEECCCCCccccccccccccccccccccccCCCccccccccccccccccCCCCCceEEEEEeCHHHHHHHHHHhhc
Q 018524 91 EWLVAVNKPQGVYCESVLASVPCLLAGDSAESKSGRLSEGTKLNLLELHLANRLDRDTSGVMVITKSHKVASKLVKAFTD 170 (354)
Q Consensus 91 ~~~lvvnKP~Gl~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~l~~vhRLDk~TSGllllAk~~~~a~~l~~~f~~ 170 (354)
+.+|+||||.|+.||.....+... ++...+.-.+-||-..||||+++-...+ ++...+.
T Consensus 3 ~Gil~i~KP~G~TS~dvv~~vrr~------------------~~~kKvGH~GTLDP~AtGvL~i~vG~aT--kl~~~l~- 61 (295)
T PRK02755 3 FGFLNLDKPAGLTSHDCVARLRRL------------------LRLKRVGHGGTLDPAATGVLPIALGKAT--RLLPYLP- 61 (295)
T ss_pred ceEEEEeCCCCCCHHHHHHHHHHH------------------hCCCccccCCCCCCcCeeEEEEEEChhh--hhHHHhC-
Confidence 369999999999877433222211 1114578899999999999999998743 5666554
Q ss_pred CccceEEEEEEe-CC
Q 018524 171 HKVSKTYIALCI-GP 184 (354)
Q Consensus 171 ~~v~K~Y~A~v~-G~ 184 (354)
. .|+|.|.+. |.
T Consensus 62 -~-~K~Y~a~~~lG~ 74 (295)
T PRK02755 62 -G-EKTYRGTIRFGV 74 (295)
T ss_pred -C-CcEEEEEEEECC
Confidence 3 799999875 44
No 43
>PRK04270 H/ACA RNA-protein complex component Cbf5p; Reviewed
Probab=97.01 E-value=0.0011 Score=62.08 Aligned_cols=73 Identities=23% Similarity=0.321 Sum_probs=51.0
Q ss_pred EeCCcEEEEECCCCCccccccccccccccccccccccCCCccccccccccccccccCCCCCceEEEEEeCHHHHHHHHHH
Q 018524 88 YEDEWLVAVNKPQGVYCESVLASVPCLLAGDSAESKSGRLSEGTKLNLLELHLANRLDRDTSGVMVITKSHKVASKLVKA 167 (354)
Q Consensus 88 yed~~~lvvnKP~Gl~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~l~~vhRLDk~TSGllllAk~~~~a~~l~~~ 167 (354)
|..+.+|++|||.|+.+|.....+... + +...+.-.+-||...||||+++-+.. -++.+.
T Consensus 19 ~~~~g~l~i~Kp~g~tS~~~v~~~r~~------------~------~~kkvGH~GTLDp~A~GvL~v~~g~a--tk~~~~ 78 (300)
T PRK04270 19 LIKFGVVNLDKPPGPTSHEVAAWVRDI------------L------GVEKAGHGGTLDPKVTGVLPVALGKA--TKVVQA 78 (300)
T ss_pred hcCCCEEEEECCCCCCHHHHHHHHHHH------------h------ccccccCCCCCCCcCeEEEEEEEChH--hhhhHH
Confidence 445689999999999876432222210 0 11457789999999999999998863 455554
Q ss_pred hhcCccceEEEEEEe
Q 018524 168 FTDHKVSKTYIALCI 182 (354)
Q Consensus 168 f~~~~v~K~Y~A~v~ 182 (354)
+.+ -.|+|.|.+.
T Consensus 79 ~~~--~~K~Y~~~~~ 91 (300)
T PRK04270 79 LLE--SGKEYVCVMH 91 (300)
T ss_pred hcc--CCcEEEEEEE
Confidence 443 3599999875
No 44
>PRK05033 truB tRNA pseudouridine synthase B; Provisional
Probab=97.00 E-value=0.0013 Score=61.55 Aligned_cols=70 Identities=23% Similarity=0.306 Sum_probs=50.1
Q ss_pred CcEEEEECCCCCccccccccccccccccccccccCCCccccccccccccccccCCCCCceEEEEEeCHHHHHHHHHHhhc
Q 018524 91 EWLVAVNKPQGVYCESVLASVPCLLAGDSAESKSGRLSEGTKLNLLELHLANRLDRDTSGVMVITKSHKVASKLVKAFTD 170 (354)
Q Consensus 91 ~~~lvvnKP~Gl~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~l~~vhRLDk~TSGllllAk~~~~a~~l~~~f~~ 170 (354)
+.+|+||||.|+.||.....+... + +...+.-.+-||-..||||+++-... -++.+.+.+
T Consensus 10 ~Gil~i~KP~G~TS~dvv~~vrr~------------l------~~kKvGH~GTLDP~AtGvL~v~vG~a--Tkl~~~~~~ 69 (312)
T PRK05033 10 NGVLLLDKPQGMSSNDALQKVKRL------------F------NANKAGHTGALDPLATGMLPICLGEA--TKFSQYLLD 69 (312)
T ss_pred CeEEEEeCCCCCCHHHHHHHHHHH------------h------CCCCCCCCCcCCCcCeeEEEEEECHH--hhhhHHhcC
Confidence 479999999999887433222221 0 11457788999999999999998864 335555544
Q ss_pred CccceEEEEEEe
Q 018524 171 HKVSKTYIALCI 182 (354)
Q Consensus 171 ~~v~K~Y~A~v~ 182 (354)
-.|+|.|.+.
T Consensus 70 --~~K~Y~a~~~ 79 (312)
T PRK05033 70 --SDKRYRVTAR 79 (312)
T ss_pred --CCcEEEEEEE
Confidence 4899999876
No 45
>PRK01851 truB tRNA pseudouridine synthase B; Provisional
Probab=96.99 E-value=0.0014 Score=61.11 Aligned_cols=70 Identities=21% Similarity=0.294 Sum_probs=49.4
Q ss_pred CcEEEEECCCCCccccccccccccccccccccccCCCccccccccccccccccCCCCCceEEEEEeCHHHHHHHHHHhhc
Q 018524 91 EWLVAVNKPQGVYCESVLASVPCLLAGDSAESKSGRLSEGTKLNLLELHLANRLDRDTSGVMVITKSHKVASKLVKAFTD 170 (354)
Q Consensus 91 ~~~lvvnKP~Gl~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~l~~vhRLDk~TSGllllAk~~~~a~~l~~~f~~ 170 (354)
+.+|+||||.|+.||.....+... + +...+.-.+-||-..||||+++-... -++.+.+..
T Consensus 16 ~Gil~i~KP~G~TS~dvv~~vrr~------------l------~~kKvGH~GTLDP~AtGvL~v~vG~a--Tkl~~~l~~ 75 (303)
T PRK01851 16 DGVLLLDKPLGLSSNDALQRAKRL------------L------RAKKAGHTGTLDPLATGLLPLCFGEA--TKFSQDLLD 75 (303)
T ss_pred CeEEEEeCCCCCCHHHHHHHHHHH------------h------CcccCCCCCCCCCCCceEEEEEECHH--HhhhHHhcc
Confidence 479999999999877433222221 0 11457778999999999999999864 345554444
Q ss_pred CccceEEEEEEe
Q 018524 171 HKVSKTYIALCI 182 (354)
Q Consensus 171 ~~v~K~Y~A~v~ 182 (354)
-.|+|.|.+.
T Consensus 76 --~~K~Y~~~~~ 85 (303)
T PRK01851 76 --ADKTYEATLR 85 (303)
T ss_pred --cCeEEEEEEE
Confidence 3599999875
No 46
>PRK01550 truB tRNA pseudouridine synthase B; Provisional
Probab=96.97 E-value=0.0014 Score=61.25 Aligned_cols=70 Identities=23% Similarity=0.345 Sum_probs=49.4
Q ss_pred CcEEEEECCCCCccccccccccccccccccccccCCCccccccccccccccccCCCCCceEEEEEeCHHHHHHHHHHhhc
Q 018524 91 EWLVAVNKPQGVYCESVLASVPCLLAGDSAESKSGRLSEGTKLNLLELHLANRLDRDTSGVMVITKSHKVASKLVKAFTD 170 (354)
Q Consensus 91 ~~~lvvnKP~Gl~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~l~~vhRLDk~TSGllllAk~~~~a~~l~~~f~~ 170 (354)
+.+|+||||.|+.||.....+... + +...+.-.+-||-..||||+++-... -++.+.+..
T Consensus 2 ~Gil~i~KP~G~TS~dvv~~vrr~------------~------~~kKvGH~GTLDP~AtGvL~i~vG~a--Tkl~~~l~~ 61 (304)
T PRK01550 2 NGVLLLHKPRGMTSHDCVFKLRKI------------L------RTKKVGHTGTLDPEVSGVLPICVGRA--TKIAEYLTD 61 (304)
T ss_pred CeEEEEECCCCCCHHHHHHHHHHH------------c------CCCCcccCCCCCCcCeeEEEEEEChh--hhhhHHhcC
Confidence 368999999999877433222211 0 11457778999999999999998863 345555543
Q ss_pred CccceEEEEEEe
Q 018524 171 HKVSKTYIALCI 182 (354)
Q Consensus 171 ~~v~K~Y~A~v~ 182 (354)
-.|+|.|.+.
T Consensus 62 --~~K~Y~a~~~ 71 (304)
T PRK01550 62 --EGKTYEGEVT 71 (304)
T ss_pred --CCcEEEEEEE
Confidence 3899999875
No 47
>PRK14846 truB tRNA pseudouridine synthase B; Provisional
Probab=96.97 E-value=0.0014 Score=61.54 Aligned_cols=70 Identities=21% Similarity=0.401 Sum_probs=49.2
Q ss_pred CcEEEEECCCCCccccccccccccccccccccccCCCccccccccccccccccCCCCCceEEEEEeCHHHHHHHHHHhhc
Q 018524 91 EWLVAVNKPQGVYCESVLASVPCLLAGDSAESKSGRLSEGTKLNLLELHLANRLDRDTSGVMVITKSHKVASKLVKAFTD 170 (354)
Q Consensus 91 ~~~lvvnKP~Gl~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~l~~vhRLDk~TSGllllAk~~~~a~~l~~~f~~ 170 (354)
+.+|+||||.|+.++.....+... + +...+.-.|-||...||||+++-... -++...+.
T Consensus 3 nGiL~idKP~G~TS~dvv~~vrk~------------l------~~kKVGH~GTLDP~AtGVL~i~vG~a--TKl~~~l~- 61 (345)
T PRK14846 3 NYWLNIYKPRGISSAQLVSIVKKI------------L------GKTKIGHAGTLDVEAEGILPFAVGEA--TKLIHLLI- 61 (345)
T ss_pred CeEEEEeCCCCCCHHHHHHHHHHH------------h------CCCcCCcCccCCCcCceEEEEEEChh--hhhhHHHh-
Confidence 479999999999876433222211 0 11468889999999999999998763 34444333
Q ss_pred CccceEEEEEEe
Q 018524 171 HKVSKTYIALCI 182 (354)
Q Consensus 171 ~~v~K~Y~A~v~ 182 (354)
...|+|.|.+.
T Consensus 62 -~~~K~Y~a~~~ 72 (345)
T PRK14846 62 -DARKTYIFTVK 72 (345)
T ss_pred -cCCceEEEEEE
Confidence 35799999875
No 48
>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=96.93 E-value=0.0015 Score=60.32 Aligned_cols=72 Identities=29% Similarity=0.388 Sum_probs=50.4
Q ss_pred cEEEEECCCCCccccccccccccccccccccccCCCccccccccccccccccCCCCCceEEEEEeCHHHHHHHHHHhhcC
Q 018524 92 WLVAVNKPQGVYCESVLASVPCLLAGDSAESKSGRLSEGTKLNLLELHLANRLDRDTSGVMVITKSHKVASKLVKAFTDH 171 (354)
Q Consensus 92 ~~lvvnKP~Gl~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~l~~vhRLDk~TSGllllAk~~~~a~~l~~~f~~~ 171 (354)
.+|++|||.|+.||.....+... ++...+.-.+-||-..||||+++-+.. -+|...+.+
T Consensus 1 Gil~i~KP~G~tS~~vv~~vr~~------------------~~~kKvGH~GTLDP~AtGvL~v~vG~a--Tkl~~~l~~- 59 (277)
T cd02573 1 GILLLDKPAGLTSHDVVQKVRRL------------------LGTKKVGHTGTLDPLATGVLPIALGEA--TKLSQYLLD- 59 (277)
T ss_pred CEEEEECCCCCCHHHHHHHHHHH------------------hCcCccCCCCCCCCcCeEEEEEEEChH--HhhHHHhcC-
Confidence 37999999999876433222211 011457789999999999999999864 345555544
Q ss_pred ccceEEEEEEe-CCC
Q 018524 172 KVSKTYIALCI-GPA 185 (354)
Q Consensus 172 ~v~K~Y~A~v~-G~~ 185 (354)
..|+|.|.+. |.-
T Consensus 60 -~~K~Y~~~~~~G~~ 73 (277)
T cd02573 60 -ADKTYRATVRLGEA 73 (277)
T ss_pred -CCcEEEEEEEECCc
Confidence 5899999876 443
No 49
>PRK01528 truB tRNA pseudouridine synthase B; Provisional
Probab=96.88 E-value=0.0019 Score=59.87 Aligned_cols=73 Identities=26% Similarity=0.460 Sum_probs=50.2
Q ss_pred CcEEEEECCCCCccccccccccccccccccccccCCCccccccccccccccccCCCCCceEEEEEeCHHHHHHHHHHhhc
Q 018524 91 EWLVAVNKPQGVYCESVLASVPCLLAGDSAESKSGRLSEGTKLNLLELHLANRLDRDTSGVMVITKSHKVASKLVKAFTD 170 (354)
Q Consensus 91 ~~~lvvnKP~Gl~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~l~~vhRLDk~TSGllllAk~~~~a~~l~~~f~~ 170 (354)
+.+|+||||.|+.||.....+... + +...+.-.+-||...||||+++-... -++.+.+.+
T Consensus 3 ~GiL~i~KP~G~TS~dvv~~vrk~------------~------~~kKvGH~GTLDP~AtGvL~v~vG~a--TKl~~~l~~ 62 (292)
T PRK01528 3 NYWLNIYKPRGISSAKLVSIVKKI------------L------GKVKIGHAGTLDVEAEGVLPLAVGEA--TKLVQLLID 62 (292)
T ss_pred CEEEEEeCCCCCCHHHHHHHHHHH------------c------CCCccCcCccCCCcCceEEEEEEChH--hhhhHHHhc
Confidence 479999999999877433222221 1 11457889999999999999998863 344444433
Q ss_pred CccceEEEEEEe-CCC
Q 018524 171 HKVSKTYIALCI-GPA 185 (354)
Q Consensus 171 ~~v~K~Y~A~v~-G~~ 185 (354)
..|+|.|.+. |.-
T Consensus 63 --~~K~Y~~~~~lG~~ 76 (292)
T PRK01528 63 --AKKTYIFTVKFGKQ 76 (292)
T ss_pred --CCceEEEEEEECCc
Confidence 4699999875 443
No 50
>cd01291 PseudoU_synth PseudoU_synth: Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). Pseudouridine synthases contains the RsuA/RluD, TruA, TruB and TruD families. This group consists of eukaryotic, bacterial and archeal pseudouridine synthases. Some psi sites such as psi55,13,38 and 39 in tRNA are highly conserved, being in the same position in eubacteria, archeabacteria and eukaryotes. Other psi sites occur in a more restricted fashion, for example psi2604in 23S RNA made by E.coli RluF has only been detected in E.coli. Human dyskerin with the help of guide RNAs makes the hundreds of psueudouridnes present in rRNA and small nuclear RNAs (snRNAs). Mutations in human dyskerin cause X-linked dyskeratosis congenitas. Missense mutation in human PUS1 causes mitochondrial myopathy and sideroblastic anemia (MLASA).
Probab=96.80 E-value=0.0051 Score=46.56 Aligned_cols=28 Identities=11% Similarity=0.171 Sum_probs=25.7
Q ss_pred ccccccccCCCCCceEEEEEeCHHHHHHHHHHhhcCccceEEEEEEe
Q 018524 136 LELHLANRLDRDTSGVMVITKSHKVASKLVKAFTDHKVSKTYIALCI 182 (354)
Q Consensus 136 ~~l~~vhRLDk~TSGllllAk~~~~a~~l~~~f~~~~v~K~Y~A~v~ 182 (354)
..+..+|++|+.++|+++++ ++|...+.
T Consensus 24 ~~i~~aG~kDk~a~t~q~v~-------------------n~f~i~~r 51 (87)
T cd01291 24 KRVGYAGRKDKRAVTTQLVS-------------------NRFTITLR 51 (87)
T ss_pred heEEECccCCCCeeEEEEEc-------------------ccEEEEEE
Confidence 56889999999999999999 88988887
No 51
>PRK14122 tRNA pseudouridine synthase B; Provisional
Probab=96.69 E-value=0.003 Score=59.09 Aligned_cols=69 Identities=26% Similarity=0.331 Sum_probs=49.0
Q ss_pred cEEEEECCCCCccccccccccccccccccccccCCCccccccccccccccccCCCCCceEEEEEeCHHHHHHHHHHhhcC
Q 018524 92 WLVAVNKPQGVYCESVLASVPCLLAGDSAESKSGRLSEGTKLNLLELHLANRLDRDTSGVMVITKSHKVASKLVKAFTDH 171 (354)
Q Consensus 92 ~~lvvnKP~Gl~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~l~~vhRLDk~TSGllllAk~~~~a~~l~~~f~~~ 171 (354)
.+|+||||.|+.||.....+... .+...+.-.+-||-..||||+++-...+ +|...+ .
T Consensus 2 ~il~idKP~G~TS~dvv~~vrr~------------------l~~kKvGH~GTLDP~AtGvL~i~iG~aT--Kl~~~l--~ 59 (312)
T PRK14122 2 PVYAVDKPLGLTSHDVVNRARRA------------------LGTRRVGHTGTLDPLATGVLVLCTDDST--KLVPFL--S 59 (312)
T ss_pred cEEEEECCCCCCHHHHHHHHHHH------------------hCCCCCCCCCCCCCcCeeeEEEEEChhh--hhhHHh--c
Confidence 47999999999877433322221 0114577789999999999999998743 355544 3
Q ss_pred ccceEEEEEEe
Q 018524 172 KVSKTYIALCI 182 (354)
Q Consensus 172 ~v~K~Y~A~v~ 182 (354)
...|+|.|.+.
T Consensus 60 ~~~K~Y~a~~~ 70 (312)
T PRK14122 60 AEDKEYLAWVS 70 (312)
T ss_pred CCCceEEEEEE
Confidence 46899999875
No 52
>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=96.36 E-value=0.0051 Score=58.14 Aligned_cols=73 Identities=27% Similarity=0.414 Sum_probs=50.6
Q ss_pred EeCCcEEEEECCCCCccccccccccccccccccccccCCCccccccccccccccccCCCCCceEEEEEeCHHHHHHHHHH
Q 018524 88 YEDEWLVAVNKPQGVYCESVLASVPCLLAGDSAESKSGRLSEGTKLNLLELHLANRLDRDTSGVMVITKSHKVASKLVKA 167 (354)
Q Consensus 88 yed~~~lvvnKP~Gl~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~l~~vhRLDk~TSGllllAk~~~~a~~l~~~ 167 (354)
+-.+.+|+||||.|+.||.....+... + +...+.-.+=||-..||||+++-... -++.+.
T Consensus 31 ~~~~G~l~i~KP~g~tS~~~v~~vr~~------------~------~~kkvGH~GTLDP~A~GvL~v~~G~a--Tkl~~~ 90 (322)
T TIGR00425 31 YISYGVVNLDKPSGPSSHEVVAWVRRI------------L------NVEKTGHGGTLDPKVTGVLPVCIERA--TRLVKS 90 (322)
T ss_pred hcCCCEEEEeCCCCCCHHHHHHHHHHH------------h------cccccCCCCCCCCCCceEEEEEEChH--hhccHH
Confidence 335589999999999877433222221 0 11457778899999999999998763 345454
Q ss_pred hhcCccceEEEEEEe
Q 018524 168 FTDHKVSKTYIALCI 182 (354)
Q Consensus 168 f~~~~v~K~Y~A~v~ 182 (354)
+. .-.|+|.|.+.
T Consensus 91 ~~--~~~K~Y~~~v~ 103 (322)
T TIGR00425 91 LQ--EAPKEYVCLMR 103 (322)
T ss_pred hc--cCCCEEEEEEE
Confidence 43 35899998875
No 53
>PRK04642 truB tRNA pseudouridine synthase B; Provisional
Probab=96.30 E-value=0.0067 Score=56.46 Aligned_cols=70 Identities=19% Similarity=0.263 Sum_probs=49.1
Q ss_pred CcEEEEECCCCCccccccccccccccccccccccCCCccccccccccccccccCCCCCceEEEEEeCHHHHHHHHHHhhc
Q 018524 91 EWLVAVNKPQGVYCESVLASVPCLLAGDSAESKSGRLSEGTKLNLLELHLANRLDRDTSGVMVITKSHKVASKLVKAFTD 170 (354)
Q Consensus 91 ~~~lvvnKP~Gl~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~l~~vhRLDk~TSGllllAk~~~~a~~l~~~f~~ 170 (354)
+.+|+||||.|+.||.....+... + +...+.-.+=||-..||||+++-... -++.+.+.
T Consensus 10 ~Gil~i~KP~G~TS~dvv~~vrr~------------~------~~kKvGH~GTLDP~AtGvL~v~~G~a--Tkl~~~l~- 68 (300)
T PRK04642 10 DGILLLDKPAGLSSNNALQAARRL------------L------RAEKGGHTGSLDPLATGLLPLCFGEA--TKIAGLLL- 68 (300)
T ss_pred CeEEEEecCCCCCHHHHHHHHHHH------------h------CCCcccCCCccCCcCeeeEEEEEChh--hhhhHHhc-
Confidence 479999999999887433222221 0 11457778899999999999998763 44555443
Q ss_pred CccceEEEEEEe
Q 018524 171 HKVSKTYIALCI 182 (354)
Q Consensus 171 ~~v~K~Y~A~v~ 182 (354)
.-.|+|.|.+.
T Consensus 69 -~~~K~Y~a~~~ 79 (300)
T PRK04642 69 -GSAKAYDAEIV 79 (300)
T ss_pred -CCCcEEEEEEE
Confidence 35799999884
No 54
>COG0130 TruB Pseudouridine synthase [Translation, ribosomal structure and biogenesis]
Probab=96.15 E-value=0.0082 Score=55.16 Aligned_cols=69 Identities=22% Similarity=0.285 Sum_probs=48.2
Q ss_pred cEEEEECCCCCccccccccccccccccccccccCCCccccccccccccccccCCCCCceEEEEEeCHHHHHHHHHHhhcC
Q 018524 92 WLVAVNKPQGVYCESVLASVPCLLAGDSAESKSGRLSEGTKLNLLELHLANRLDRDTSGVMVITKSHKVASKLVKAFTDH 171 (354)
Q Consensus 92 ~~lvvnKP~Gl~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~l~~vhRLDk~TSGllllAk~~~~a~~l~~~f~~~ 171 (354)
.++++|||.|+.||.....+... + +.....-.+-||-..||+|+++-. ++.+.+.- +.
T Consensus 16 Gil~ldKP~G~tS~~~v~~vkki------------l------~~~K~GH~GTLDP~atGvLpi~ig-~aTKl~~~-l~-- 73 (271)
T COG0130 16 GVINLDKPPGPTSHEVVAWVKRI------------L------GVEKAGHGGTLDPLATGVLPICLG-EATKLVQY-LL-- 73 (271)
T ss_pred ceEEeeCCCCCCHHHHHHHHHHH------------h------CccccccccccCCcccceEEEEec-hhHhHHHH-Hh--
Confidence 89999999999877433222211 1 114567788999999999999998 44444433 22
Q ss_pred ccceEEEEEEe
Q 018524 172 KVSKTYIALCI 182 (354)
Q Consensus 172 ~v~K~Y~A~v~ 182 (354)
.-.|+|.|.+.
T Consensus 74 ~~~K~Y~a~~~ 84 (271)
T COG0130 74 DADKEYVATVR 84 (271)
T ss_pred hCCcEEEEEEE
Confidence 35799999986
No 55
>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=95.98 E-value=0.012 Score=54.98 Aligned_cols=43 Identities=28% Similarity=0.411 Sum_probs=32.7
Q ss_pred ccccccccCCCCCceEEEEEeCHHHHHHHHHHhhcCccceEEEEEEe
Q 018524 136 LELHLANRLDRDTSGVMVITKSHKVASKLVKAFTDHKVSKTYIALCI 182 (354)
Q Consensus 136 ~~l~~vhRLDk~TSGllllAk~~~~a~~l~~~f~~~~v~K~Y~A~v~ 182 (354)
..+.-.+-||-..||||+++-... .+.+ +.|.. ..|+|.|...
T Consensus 56 ~KiGH~GTLDPlAsGVLvvgvG~a-TK~l-~~~l~--~~K~Y~~~~~ 98 (312)
T cd02867 56 LKIGHGGTLDPLATGVLVVGVGAG-TKQL-QDYLS--CSKTYEATGL 98 (312)
T ss_pred cccccccccCCccceeEEEEECcH-HHHH-HHHhc--CCceEEEEEE
Confidence 357778999999999999998763 3334 33333 7999999875
No 56
>PF01479 S4: S4 domain; InterPro: IPR002942 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. The S4 domain is a small domain consisting of 60-65 amino acid residues that was detected in the bacterial ribosomal protein S4, eukaryotic ribosomal S9, two families of pseudouridine synthases, a novel family of predicted RNA methylases, a yeast protein containing a pseudouridine synthetase and a deaminase domain, bacterial tyrosyl-tRNA synthetases, and a number of uncharacterised, small proteins that may be involved in translation regulation []. The S4 domain probably mediates binding to RNA.; GO: 0003723 RNA binding; PDB: 3BBU_A 1DM9_B 2K6P_A 3U5G_E 3U5C_E 3IZB_D 2XZM_D 2XZN_D 3O30_E 3O2Z_E ....
Probab=92.81 E-value=0.0032 Score=41.88 Aligned_cols=43 Identities=7% Similarity=0.032 Sum_probs=36.6
Q ss_pred CcccccccccCCC-CCCCCCCCCCCccccCCCCCCCCCCcccccceeEEeeccccc
Q 018524 20 RFRKTFFSLASMS-NPTEPTSQNAPQTQQNYPTPLSPPLPAISKDIELTRAMSASS 74 (354)
Q Consensus 20 ~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~v~~~~~~~~~~ 74 (354)
||+|+|++.++.+ ||.++..+|..|.+ .|||.++.++...+.+
T Consensus 1 ~RLd~~L~~~~~~~sr~~a~~~I~~g~V------------~VNg~~v~~~~~~v~~ 44 (48)
T PF01479_consen 1 MRLDKFLSRLGLASSRSEARRLIKQGRV------------KVNGKVVKDPSYIVKP 44 (48)
T ss_dssp EBHHHHHHHTTSSSSHHHHHHHHHTTTE------------EETTEEESSTTSBEST
T ss_pred CCHHHHHHHcCCcCCHHHHHHhcCCCEE------------EECCEEEcCCCCCCCC
Confidence 7999999977776 59999999999999 9999988877666654
No 57
>KOG2559 consensus Predicted pseudouridine synthase [Translation, ribosomal structure and biogenesis]
Probab=91.21 E-value=0.25 Score=44.03 Aligned_cols=23 Identities=26% Similarity=0.417 Sum_probs=19.8
Q ss_pred ccccccccCCCCCceEEEEEeCH
Q 018524 136 LELHLANRLDRDTSGVMVITKSH 158 (354)
Q Consensus 136 ~~l~~vhRLDk~TSGllllAk~~ 158 (354)
..+.++||||-.|||++||.-+-
T Consensus 89 ~~V~v~h~l~~~~sgvl~~gVgh 111 (318)
T KOG2559|consen 89 EDVQVVHVLPLATSGVLLFGVGH 111 (318)
T ss_pred cceeeEEeecccccceEEEecCc
Confidence 35789999999999999998653
No 58
>PF01509 TruB_N: TruB family pseudouridylate synthase (N terminal domain); InterPro: IPR002501 Pseudouridine synthases catalyse the isomerisation of uridine to pseudouridine (Psi) in a variety of RNA molecules, and may function as RNA chaperones. Pseudouridine is the most abundant modified nucleotide found in all cellular RNAs. There are four distinct families of pseudouridine synthases that share no global sequence similarity, but which do share the same fold of their catalytic domain(s) and uracil-binding site and are descended from a common molecular ancestor. The catalytic domain consists of two subdomains, each of which has an alpha+beta structure that has some similarity to the ferredoxin-like fold (note: some pseudouridine synthases contain additional domains). The active site is the most conserved structural region of the superfamily and is located between the two homologous domains. These families are []: Pseudouridine synthase I, TruA. Pseudouridine synthase II, TruB, which contains and additional C-terminal PUA domain. Pseudouridine synthase RsuA (ribosomal small subunit) and RluC/RluD (ribosomal large subunits), both of which contain an additional N-terminal alpha-L RNA-binding motif. Pseudouridine synthase TruD, which has a natural circular permutation in the catalytic domain, as well as an insertion of a family-specific alpha+beta subdomain. TruB is responsible for the pseudouridine residue present in the T loops of virtually all tRNAs. TruB recognises the preformed 3-D structure of the T loop primarily through shape complementarity. It accesses its substrate uridyl residue by flipping out the nucleotide and disrupts the tertiary structure of tRNA []. This entry represents pseudouridine synthase TruB, as well as Cbf5p that modifies rRNA [].; GO: 0006396 RNA processing; PDB: 1SGV_B 2AUS_C 3UAI_A 3U28_A 2RFK_A 3LWV_A 3HJY_A 3HAX_A 3LWO_A 3HAY_A ....
Probab=87.58 E-value=0.72 Score=38.61 Aligned_cols=43 Identities=26% Similarity=0.352 Sum_probs=31.2
Q ss_pred ccccccccCCCCCceEEEEEeCHHHHHHHHHHhhcCccceEEEEEEe
Q 018524 136 LELHLANRLDRDTSGVMVITKSHKVASKLVKAFTDHKVSKTYIALCI 182 (354)
Q Consensus 136 ~~l~~vhRLDk~TSGllllAk~~~~a~~l~~~f~~~~v~K~Y~A~v~ 182 (354)
..+.-.+.||...||||+++-+.. -++.+.|.+ ..|+|.|...
T Consensus 7 ~KvGH~GTLDP~AsGvL~v~vg~~--Tkl~~~l~~--~~K~Y~~~~~ 49 (149)
T PF01509_consen 7 KKVGHGGTLDPFASGVLVVGVGKA--TKLLSYLQN--SDKEYVATIR 49 (149)
T ss_dssp SSEEESS-SSTT-EEEEEEEEGGG--GGGHHHHTT--SEEEEEEEEE
T ss_pred ceeccccccCCcceEEEEEEECCc--chHHHHhhc--cCCEEEEEEE
Confidence 467778999999999999999763 335555554 4599999875
No 59
>TIGR02988 YaaA_near_RecF S4 domain protein YaaA. This small protein has a single S4 domain (pfam01479), as do bacterial ribosomal protein S4, some pseudouridine synthases, tyrosyl-tRNA synthetases. The S4 domain may bind RNA. Members of this protein family are found almost exclusively in the Firmicutes, and almost invariably just a few nucleotides upstream of the gene for the DNA replication and repair protein RecF. The few members of this family that are not near recF are found instead near dnaA and/or dnaN, the usual neighbors of recF, near the origin of replication. The conserved location suggests a possible role in replication in the Firmicutes lineage.
Probab=81.59 E-value=0.093 Score=36.48 Aligned_cols=45 Identities=4% Similarity=-0.137 Sum_probs=34.7
Q ss_pred CCCCcccccccccCCC--CCCCCCCCCCCccccCCCCCCCCCCcccccceeEEeeccccc
Q 018524 17 AVPRFRKTFFSLASMS--NPTEPTSQNAPQTQQNYPTPLSPPLPAISKDIELTRAMSASS 74 (354)
Q Consensus 17 ~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~v~~~~~~~~~~ 74 (354)
+-++|+|+||+.. .. ||..++.++..|.| .|||.++..+..+..+
T Consensus 6 ~~~~rLd~~L~~~-~~~~SR~~~k~li~~G~V------------~VNg~~~~~~~~~l~~ 52 (59)
T TIGR02988 6 TEYITLGQLLKEL-GIIDSGGQAKWFLQENEV------------LVNGELENRRGKKLYP 52 (59)
T ss_pred chHHHHHHHHHHc-CCccCHHHHHHHHHcCCE------------EECCEEccCCCCCCCC
Confidence 3458999999998 44 89999999999999 8888876544444443
No 60
>COG1188 Ribosome-associated heat shock protein implicated in the recycling of the 50S subunit (S4 paralog) [Translation, ribosomal structure and biogenesis]
Probab=81.42 E-value=0.36 Score=37.23 Aligned_cols=37 Identities=5% Similarity=-0.114 Sum_probs=32.2
Q ss_pred CCCCccccccccc-CCCCCCCCCCCCCCccccCCCCCCCCCCccccccee
Q 018524 17 AVPRFRKTFFSLA-SMSNPTEPTSQNAPQTQQNYPTPLSPPLPAISKDIE 65 (354)
Q Consensus 17 ~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~v~ 65 (354)
...||+|+||-.+ ...+|..++..+..|+| .+||...
T Consensus 6 ~~~mRLDKwL~~aR~~KrRslAk~~~~~GrV------------~vNG~~a 43 (100)
T COG1188 6 ADRMRLDKWLWAARFIKRRSLAKEMIEGGRV------------KVNGQRA 43 (100)
T ss_pred ccceehHHHHHHHHHhhhHHHHHHHHHCCeE------------EECCEEc
Confidence 5679999999888 77889999999999999 8888765
No 61
>TIGR00478 tly hemolysin TlyA family protein. Hemolysins are exotoxins that attack blood cell membranes and cause cell rupture, often by forming a pore in the membrane. At least two members of this protein family have been characterized indirectly as pore-forming hemolysins, one from the spirochete Serpula (Treponema) hyodysenteriae and one from Mycobacterium tuberculosis. However, homology domains in this protein suggest methyltransferase activity (pfam01728) and RNA-binding activity (pfam01479).
Probab=75.60 E-value=0.34 Score=43.60 Aligned_cols=41 Identities=0% Similarity=-0.177 Sum_probs=33.6
Q ss_pred cccccccccCCC-CCCCCCCCCCCccccCCCCCCCCCCcccccceeEEeecccc
Q 018524 21 FRKTFFSLASMS-NPTEPTSQNAPQTQQNYPTPLSPPLPAISKDIELTRAMSAS 73 (354)
Q Consensus 21 ~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~v~~~~~~~~~ 73 (354)
|+|+|++..+.+ ||.++..+|+.|.| .+|+.+....+..+.
T Consensus 1 RLD~~L~~~g~~~SR~~a~~lI~~G~V------------~Vng~~v~k~s~~V~ 42 (228)
T TIGR00478 1 RLDILLVRRGLFESREKAKRLILKGFV------------LVNGKKVDKPSALVD 42 (228)
T ss_pred CHHHHHHHcCCccHHHHHHHHHHCCcE------------EECCEEeCCCCCCCC
Confidence 789999998865 79999999999999 899987765554443
No 62
>TIGR01017 rpsD_bact ribosomal protein S4, bacterial/organelle type. This model finds organelle (chloroplast and mitochondrial) ribosomal protein S4 as well as bacterial ribosomal protein S4.
Probab=72.11 E-value=0.34 Score=42.66 Aligned_cols=44 Identities=0% Similarity=-0.166 Sum_probs=35.3
Q ss_pred CCcccccccccCCC-CCCCCCCCCCCccccCCCCCCCCCCcccccceeEEeeccccc
Q 018524 19 PRFRKTFFSLASMS-NPTEPTSQNAPQTQQNYPTPLSPPLPAISKDIELTRAMSASS 74 (354)
Q Consensus 19 ~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~v~~~~~~~~~~ 74 (354)
.||+|.++..++.+ ||.++..+|..|.| .||+.++..++..+.+
T Consensus 89 e~RLD~~L~~~g~~~SR~~ArqlI~~G~V------------~VNgk~v~~ps~~V~~ 133 (200)
T TIGR01017 89 ESRLDNVVYRLGFAPTRFAARQLVSHGHI------------LVNGKKVDIPSYQVRP 133 (200)
T ss_pred HHHHHHHHHHcCCCCCHHHHHHHHHCCCE------------EECCEEeCCCCCCCCC
Confidence 38999999877755 89999999999999 8888876655555544
No 63
>CHL00113 rps4 ribosomal protein S4; Reviewed
Probab=68.12 E-value=0.48 Score=41.71 Aligned_cols=44 Identities=5% Similarity=-0.106 Sum_probs=35.6
Q ss_pred CCcccccccccCCC-CCCCCCCCCCCccccCCCCCCCCCCcccccceeEEeeccccc
Q 018524 19 PRFRKTFFSLASMS-NPTEPTSQNAPQTQQNYPTPLSPPLPAISKDIELTRAMSASS 74 (354)
Q Consensus 19 ~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~v~~~~~~~~~~ 74 (354)
.||+|+|+..++.+ +|.++..+|..|.| .|||.++..++..+.+
T Consensus 88 E~RLD~~L~r~g~~~SR~~ArqlI~~G~V------------~VNGk~v~~ps~~Vk~ 132 (201)
T CHL00113 88 EMRLDNILFRLGMAPTIPAARQLVNHGHI------------LVNGRIVDIPSYRCKP 132 (201)
T ss_pred HHHHHHHHHHcCCCCCHHHHHHHHHCCcE------------EECCEEecCccccCCC
Confidence 48999999988855 77999999999999 8898877665555544
No 64
>PRK10348 ribosome-associated heat shock protein Hsp15; Provisional
Probab=61.49 E-value=1.2 Score=36.41 Aligned_cols=43 Identities=2% Similarity=-0.184 Sum_probs=33.6
Q ss_pred CCcccccccccC-CCCCCCCCCCCCCccccCCCCCCCCCCcccccceeEEeeccccc
Q 018524 19 PRFRKTFFSLAS-MSNPTEPTSQNAPQTQQNYPTPLSPPLPAISKDIELTRAMSASS 74 (354)
Q Consensus 19 ~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~v~~~~~~~~~~ 74 (354)
.||+|+||-.+. +.+|..+..+|..|.| .+||.. ..++..+.+
T Consensus 8 ~~RlDk~L~~~rl~ktRs~A~~lI~~G~V------------~vnG~~-~Kps~~V~~ 51 (133)
T PRK10348 8 EVRLDKWLWAARFYKTRALAREMIEGGKV------------HYNGQR-SKPSKIVEL 51 (133)
T ss_pred cccHHHHHHHcCccccHHHHHHHHHCCCE------------EECCEE-CCCCCccCC
Confidence 489999999775 5678888999999999 888887 555555543
No 65
>TIGR03069 PS_II_S4 photosystem II S4 domain protein. Members of this protein family are about 265 residues long and each contains an S4 RNA-binding domain of about 48 residues. The member from the Cyanobacterium, Synechocystis sp. PCC 6803, was detected as a novel polypeptide in a highly purified preparation of active photosystem II (Kashino, et al., 2002). The phylogenetic distribution, including Cyanobacteria and Arabidopsis, supports a role in photosystem II, although the high bit score cutoffs for this model reflect similar sequences in non-photosynthetic organisms such as Carboxydothermus hydrogenoformans, a Gram-positive bacterium.
Probab=57.12 E-value=1.2 Score=40.75 Aligned_cols=49 Identities=6% Similarity=-0.153 Sum_probs=37.7
Q ss_pred CCCCCCCcccccccccCCCCCCCCCCCCCCccccCCCCCCCCCCcccccceeEEeeccccc
Q 018524 14 TPKAVPRFRKTFFSLASMSNPTEPTSQNAPQTQQNYPTPLSPPLPAISKDIELTRAMSASS 74 (354)
Q Consensus 14 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~v~~~~~~~~~~ 74 (354)
.....+||+|.+++....-||..+..+|..|.| .||+.++......+.+
T Consensus 178 ~~~v~s~RLD~lls~~~~~SRs~a~~lI~~G~V------------~VNg~~v~~~s~~v~~ 226 (257)
T TIGR03069 178 TTVEASLRIDAIASAGFGLSRSKIVDQIKAGRL------------RLNWKTVTQPSRELKV 226 (257)
T ss_pred cCCCccccHHHHHHhhhhhhHHHHHHHHHCCeE------------EECCEEcCCCCCcCCC
Confidence 344467999987776665599999999999999 8998776655555544
No 66
>PRK11507 ribosome-associated protein; Provisional
Probab=46.24 E-value=4.9 Score=28.94 Aligned_cols=44 Identities=7% Similarity=-0.029 Sum_probs=34.8
Q ss_pred Cccccccccc-CCCCCCCCCCCCCCccccCCCCCCCCCCcccccceeEEeecccccc
Q 018524 20 RFRKTFFSLA-SMSNPTEPTSQNAPQTQQNYPTPLSPPLPAISKDIELTRAMSASSK 75 (354)
Q Consensus 20 ~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~v~~~~~~~~~~~ 75 (354)
..|+.+|-.+ ..+|--+++..|..|.| .|||.++..+....-+.
T Consensus 12 I~L~QlLK~~~~v~SGG~AK~~I~eg~V------------~VNGeve~rRgkKl~~G 56 (70)
T PRK11507 12 VELCDLLKLEGWSESGAQAKIAIAEGQV------------KVDGAVETRKRCKIVAG 56 (70)
T ss_pred EEHHHHHhhhCcccChHHHHHHHHcCce------------EECCEEecccCCCCCCC
Confidence 4677777755 45567889999999999 99999999888776653
No 67
>PF08068 DKCLD: DKCLD (NUC011) domain; InterPro: IPR012960 This is an N-terminal domain of dyskerin-like proteins, which is often associated with the TruB N-terminal(IPR002501 from INTERPRO) and PUA(IPR002478 from INTERPRO) domains [].; PDB: 3ZV0_D 3UAI_A 3U28_A 2AUS_C 2RFK_A 3LWV_A 3HJY_A 3HAX_A 3LWO_A 3HAY_A ....
Probab=43.21 E-value=11 Score=26.12 Aligned_cols=18 Identities=22% Similarity=0.407 Sum_probs=13.0
Q ss_pred EeCCcEEEEECCCCCccc
Q 018524 88 YEDEWLVAVNKPQGVYCE 105 (354)
Q Consensus 88 yed~~~lvvnKP~Gl~~~ 105 (354)
|-...+|.+|||+|-.+|
T Consensus 39 ~i~~GvinlDKP~gPtSH 56 (59)
T PF08068_consen 39 YIKYGVINLDKPSGPTSH 56 (59)
T ss_dssp HHHTEEEEEEE-SSS-HH
T ss_pred HHhCCcEEeeCCCCCCcc
Confidence 456789999999997655
No 68
>PF13021 DUF3885: Domain of unknown function (DUF3885)
Probab=39.22 E-value=41 Score=21.12 Aligned_cols=24 Identities=25% Similarity=0.418 Sum_probs=20.5
Q ss_pred CCceEEEEEeCHHHHHHHHHHhhc
Q 018524 147 DTSGVMVITKSHKVASKLVKAFTD 170 (354)
Q Consensus 147 ~TSGllllAk~~~~a~~l~~~f~~ 170 (354)
|-.||-|+|+|.+..+.|-..|.+
T Consensus 5 DDRGcdvia~~~~~i~~ly~~y~~ 28 (38)
T PF13021_consen 5 DDRGCDVIANNKERIRPLYEKYND 28 (38)
T ss_pred cCCCcEEeeCCHHHHHHHHHHHHH
Confidence 456999999999999999887764
No 69
>smart00363 S4 S4 RNA-binding domain.
Probab=39.17 E-value=2.9 Score=27.82 Aligned_cols=35 Identities=6% Similarity=-0.016 Sum_probs=27.5
Q ss_pred Cccccccccc-CCCCCCCCCCCCCCccccCCCCCCCCCCcccccceeE
Q 018524 20 RFRKTFFSLA-SMSNPTEPTSQNAPQTQQNYPTPLSPPLPAISKDIEL 66 (354)
Q Consensus 20 ~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~v~~ 66 (354)
|+++.|+... ...++.++..++..|.+ .+|+....
T Consensus 1 ~rl~~~l~~~~~~~s~~~~~~~i~~g~i------------~vng~~~~ 36 (60)
T smart00363 1 RRLDKFLARLGLAPSRSQARKLIEQGRV------------KVNGKKVT 36 (60)
T ss_pred CcHHHHHHHcCcccCHHHHHHHHHcCCE------------EECCEEec
Confidence 5788898876 35789999999998888 78887553
No 70
>PF13275 S4_2: S4 domain; PDB: 1P9K_A.
Probab=38.84 E-value=4.1 Score=28.96 Aligned_cols=45 Identities=13% Similarity=0.087 Sum_probs=27.2
Q ss_pred CCcccccccccC-CCCCCCCCCCCCCccccCCCCCCCCCCcccccceeEEeecccccc
Q 018524 19 PRFRKTFFSLAS-MSNPTEPTSQNAPQTQQNYPTPLSPPLPAISKDIELTRAMSASSK 75 (354)
Q Consensus 19 ~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~v~~~~~~~~~~~ 75 (354)
...++.+|-.++ .+|-.+++.+|..|.| .|||.++..+.....+.
T Consensus 7 ~I~L~qlLK~~glv~sGGeAK~~I~~g~V------------~VNGe~e~rrg~Kl~~G 52 (65)
T PF13275_consen 7 YITLGQLLKLAGLVSSGGEAKALIQEGEV------------KVNGEVETRRGKKLRPG 52 (65)
T ss_dssp ---HHHHHHHHTS-SSSSTTSHHHHHHHH------------EETTB----SS----SS
T ss_pred cEEHHHHHhHcCCcccHHHHHHHHHcCce------------EECCEEccccCCcCCCC
Confidence 456777887664 4577899999999999 99999999888776653
No 71
>PRK05327 rpsD 30S ribosomal protein S4; Validated
Probab=37.88 E-value=3.1 Score=36.71 Aligned_cols=43 Identities=0% Similarity=-0.154 Sum_probs=33.0
Q ss_pred CcccccccccC-CCCCCCCCCCCCCccccCCCCCCCCCCcccccceeEEeeccccc
Q 018524 20 RFRKTFFSLAS-MSNPTEPTSQNAPQTQQNYPTPLSPPLPAISKDIELTRAMSASS 74 (354)
Q Consensus 20 ~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~v~~~~~~~~~~ 74 (354)
+|+|.++...+ ..||.++..++..|.| .||+.++..++..+.+
T Consensus 93 ~RLD~iL~~~g~~~SR~~arqlI~~G~V------------~VNgk~v~~ps~~v~~ 136 (203)
T PRK05327 93 SRLDNVVYRLGFAPTRRQARQLVSHGHI------------LVNGKKVNIPSYRVKP 136 (203)
T ss_pred HHHHHHHHHcCccCCHHHHHHHHHCCcE------------EECCEEECCCCcCCCC
Confidence 79999997665 4589999999999998 7888766545544443
No 72
>PLN00051 RNA-binding S4 domain-containing protein; Provisional
Probab=36.26 E-value=4.6 Score=37.21 Aligned_cols=49 Identities=2% Similarity=-0.136 Sum_probs=38.4
Q ss_pred CCCCCCCcccccccccCCCCCCCCCCCCCCccccCCCCCCCCCCcccccceeEEeeccccc
Q 018524 14 TPKAVPRFRKTFFSLASMSNPTEPTSQNAPQTQQNYPTPLSPPLPAISKDIELTRAMSASS 74 (354)
Q Consensus 14 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~v~~~~~~~~~~ 74 (354)
......+|+|.+++....-||..+..+|..|.| .+|+..+...+..+.+
T Consensus 186 ~~~vas~RLD~vla~~~~~SRsk~~~lI~~g~V------------~vN~~~v~~~s~~v~~ 234 (267)
T PLN00051 186 KSVEASLRLDALASAGFRMSRSKLVDLISSGDV------------RVNWREVTKNGTTLKT 234 (267)
T ss_pred cCCcCcccHHHHHHHHhccCHHHHHHHHHcCcE------------EECCEEcCCCCCCCCC
Confidence 334456999999999999999999999999999 7777666555544444
No 73
>COG1189 Predicted rRNA methylase [Translation, ribosomal structure and biogenesis]
Probab=35.85 E-value=4.1 Score=36.69 Aligned_cols=44 Identities=0% Similarity=-0.135 Sum_probs=35.4
Q ss_pred CCCccccccccc-CCCCCCCCCCCCCCccccCCCCCCCCCCcccccceeEEeecccc
Q 018524 18 VPRFRKTFFSLA-SMSNPTEPTSQNAPQTQQNYPTPLSPPLPAISKDIELTRAMSAS 73 (354)
Q Consensus 18 ~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~v~~~~~~~~~ 73 (354)
..||+|.||... ...||..++.+|..|.| .||+..+..++..++
T Consensus 1 ~k~RLD~~Lv~rgl~~sR~~A~~~I~~G~V------------~Vng~~v~KP~~~V~ 45 (245)
T COG1189 1 NKMRLDALLVERGLFESREKAKELILAGNV------------LVNGEKVTKPSQLVD 45 (245)
T ss_pred CcchHHHHHHHccchhhHHHHHHHHHcCeE------------EECCEEecCcceecC
Confidence 369999999987 56789999999999999 888887776554443
No 74
>KOG2529 consensus Pseudouridine synthase [Translation, ribosomal structure and biogenesis]
Probab=32.31 E-value=35 Score=33.09 Aligned_cols=79 Identities=11% Similarity=0.170 Sum_probs=51.4
Q ss_pred EEeCCcEEEEECCCCCccccccccccccccccccccccCCCccccccccccccccccCCCCCceEEEEEeCHHHHHHHHH
Q 018524 87 LYEDEWLVAVNKPQGVYCESVLASVPCLLAGDSAESKSGRLSEGTKLNLLELHLANRLDRDTSGVMVITKSHKVASKLVK 166 (354)
Q Consensus 87 lyed~~~lvvnKP~Gl~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~l~~vhRLDk~TSGllllAk~~~~a~~l~~ 166 (354)
.|--..+++++||++=.+| +.+.+.. ..|. ....+-.+-||-+.||+++...+.....-..
T Consensus 64 ~~~~sgv~~i~kpa~pss~-------e~~swvk-----~iL~------~ek~Gh~gTlDP~vtg~l~v~~~~~tr~~~s- 124 (395)
T KOG2529|consen 64 EYSRSGVINIDKPANPSSH-------EVVSWVK-----NILR------VEKTGHSGTLDPEVTGCLIVCIDRATRLLKS- 124 (395)
T ss_pred hHhhcCceeccCCCCCchH-------HHHHHHH-----HHhh------HHHhCCCCCCCccccceEEEEeecccccccc-
Confidence 4666789999999954332 2111111 0111 1346668899999999999998866433332
Q ss_pred HhhcCccceEEEEEEeCCCCC
Q 018524 167 AFTDHKVSKTYIALCIGPAPK 187 (354)
Q Consensus 167 ~f~~~~v~K~Y~A~v~G~~~~ 187 (354)
.....|+|.+++....+-
T Consensus 125 ---~~s~gk~yvg~~~lt~~v 142 (395)
T KOG2529|consen 125 ---QQSAGKEYVGIGKLTPEV 142 (395)
T ss_pred ---hhccCcEEEEEEecCcch
Confidence 345789999999877653
Done!