Query 023330
Match_columns 284
No_of_seqs 192 out of 1816
Neff 4.9
Searched_HMMs 46136
Date Fri Mar 29 03:12:05 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/023330.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/023330hhsearch_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 4.3E-29 9.4E-34 233.6 14.8 129 110-283 13-144 (289)
2 TIGR00005 rluA_subfam pseudour 99.9 2.2E-25 4.8E-30 206.6 14.5 131 110-283 6-140 (299)
3 PRK11025 23S rRNA pseudouridyl 99.9 1E-24 2.2E-29 205.4 16.5 129 110-283 20-157 (317)
4 PRK11180 rluD 23S rRNA pseudou 99.9 8.5E-25 1.8E-29 206.4 15.9 131 110-283 18-152 (325)
5 cd02558 PSRA_1 PSRA_1: Pseudou 99.9 7.5E-22 1.6E-26 180.2 10.3 92 188-283 12-103 (246)
6 PRK10839 16S rRNA pseudouridyl 99.8 7.7E-21 1.7E-25 171.1 7.5 114 111-283 2-115 (232)
7 PRK10475 23S rRNA pseudouridin 99.8 1.4E-18 3E-23 163.2 10.7 114 110-283 7-120 (290)
8 KOG1919 RNA pseudouridylate sy 99.8 1.7E-18 3.7E-23 167.5 11.6 154 83-284 12-171 (371)
9 PRK10700 23S rRNA pseudouridyl 99.7 1.9E-17 4.2E-22 155.1 11.3 120 110-283 3-123 (289)
10 cd02557 PseudoU_synth_ScRIB2 P 99.7 1.1E-17 2.4E-22 149.5 7.8 66 217-283 15-80 (213)
11 PRK10158 23S rRNA/tRNA pseudou 99.7 1.6E-17 3.4E-22 149.3 6.2 63 218-283 14-77 (219)
12 TIGR01621 RluA-like pseudourid 99.7 2.1E-17 4.6E-22 148.4 6.5 63 218-283 2-64 (217)
13 cd02563 PseudoU_synth_TruC tRN 99.7 3E-17 6.5E-22 147.4 7.2 64 218-283 1-66 (223)
14 PRK11112 tRNA pseudouridine sy 99.7 5.7E-17 1.2E-21 149.0 7.0 64 218-283 2-67 (257)
15 cd02550 PseudoU_synth_Rsu_Rlu_ 99.4 5.3E-14 1.1E-18 119.3 3.7 55 227-283 1-55 (154)
16 PF00849 PseudoU_synth_2: RNA 99.4 1.7E-13 3.7E-18 115.2 4.5 58 226-283 1-61 (164)
17 cd02553 PseudoU_synth_RsuA Pse 99.4 5E-13 1.1E-17 115.6 5.6 55 227-283 2-56 (167)
18 cd02556 PseudoU_synth_RluB Pse 99.4 3.9E-13 8.4E-18 116.2 4.5 55 227-283 2-56 (167)
19 cd02870 PseudoU_synth_RsuA_lik 99.4 1.2E-13 2.6E-18 116.3 1.3 54 227-283 1-54 (146)
20 COG1187 RsuA 16S rRNA uridine- 99.0 8E-10 1.7E-14 102.4 8.4 115 110-281 3-119 (248)
21 PRK11394 23S rRNA pseudouridin 99.0 2.5E-10 5.5E-15 103.7 4.3 53 226-283 40-92 (217)
22 cd00165 S4 S4/Hsp/ tRNA synthe 99.0 2.3E-09 4.9E-14 76.1 7.8 68 111-231 2-70 (70)
23 cd02555 PSSA_1 PSSA_1: Pseudou 98.9 1E-09 2.2E-14 96.4 4.5 55 226-283 5-67 (177)
24 TIGR02988 YaaA_near_RecF S4 do 98.2 4.7E-06 1E-10 60.6 6.0 31 110-141 9-41 (59)
25 PF01479 S4: S4 domain; Inter 97.9 2.8E-05 6E-10 53.8 5.4 31 111-141 2-33 (48)
26 cd02869 PseudoU_synth_RluCD_li 97.7 1.5E-05 3.2E-10 68.2 1.6 23 261-283 38-60 (185)
27 smart00363 S4 S4 RNA-binding d 97.4 0.00058 1.3E-08 46.7 6.0 31 111-141 2-33 (60)
28 COG1188 Ribosome-associated he 97.2 0.00079 1.7E-08 54.9 6.1 53 110-206 9-62 (100)
29 PLN00051 RNA-binding S4 domain 97.0 0.0014 3.1E-08 61.6 6.1 50 110-202 192-241 (267)
30 TIGR03069 PS_II_S4 photosystem 96.7 0.0034 7.4E-08 58.6 5.9 32 110-141 184-215 (257)
31 TIGR01017 rpsD_bact ribosomal 96.2 0.0091 2E-07 53.8 5.8 51 110-203 90-141 (200)
32 PRK10348 ribosome-associated h 96.0 0.018 3.8E-07 49.3 6.1 32 110-141 9-41 (133)
33 CHL00113 rps4 ribosomal protei 95.9 0.016 3.4E-07 52.6 5.6 51 110-203 89-140 (201)
34 PRK05327 rpsD 30S ribosomal pr 95.9 0.015 3.2E-07 52.6 5.4 32 110-141 93-125 (203)
35 TIGR00478 tly hemolysin TlyA f 95.8 0.017 3.6E-07 53.1 5.3 31 111-141 1-32 (228)
36 COG2302 Uncharacterized conser 95.6 0.017 3.8E-07 54.1 5.0 50 110-202 181-230 (257)
37 PRK00020 truB tRNA pseudouridi 95.6 0.017 3.8E-07 53.9 4.6 49 225-282 10-58 (244)
38 PRK05033 truB tRNA pseudouridi 95.1 0.029 6.3E-07 54.1 4.7 49 225-282 10-58 (312)
39 PRK05389 truB tRNA pseudouridi 95.1 0.028 6.1E-07 54.0 4.6 49 225-282 13-61 (305)
40 PRK04270 H/ACA RNA-protein com 94.8 0.034 7.3E-07 53.0 4.3 50 224-282 21-70 (300)
41 PRK01851 truB tRNA pseudouridi 94.3 0.058 1.3E-06 51.8 4.7 49 225-282 16-64 (303)
42 cd02566 PseudoU_synth_RluE Pse 94.1 0.036 7.8E-07 48.0 2.5 27 227-253 1-28 (168)
43 COG0522 RpsD Ribosomal protein 94.0 0.096 2.1E-06 47.7 5.2 51 111-204 95-146 (205)
44 PRK04642 truB tRNA pseudouridi 92.3 0.19 4E-06 48.4 4.5 49 225-282 10-58 (300)
45 TIGR00425 CBF5 rRNA pseudourid 92.3 0.19 4.2E-06 48.5 4.7 49 225-282 34-82 (322)
46 COG1189 Predicted rRNA methyla 92.3 0.24 5.2E-06 46.4 5.1 32 110-141 3-35 (245)
47 COG0130 TruB Pseudouridine syn 90.2 0.34 7.4E-06 45.9 4.0 48 226-282 16-63 (271)
48 PF14451 Ub-Mut7C: Mut7-C ubiq 89.0 1.2 2.6E-05 34.9 5.6 68 83-204 9-76 (81)
49 PRK11507 ribosome-associated p 88.4 1.2 2.7E-05 34.2 5.2 31 110-141 12-44 (70)
50 COG2501 S4-like RNA binding pr 87.4 1.7 3.7E-05 33.7 5.4 35 106-141 8-44 (73)
51 PF06353 DUF1062: Protein of u 86.9 1.9 4.1E-05 37.3 6.1 62 79-140 68-133 (142)
52 PRK04051 rps4p 30S ribosomal p 83.0 2.6 5.6E-05 37.7 5.3 31 111-141 104-135 (177)
53 cd02554 PseudoU_synth_RluF Pse 81.9 1.4 3E-05 38.6 3.1 27 227-254 2-28 (164)
54 PLN00189 40S ribosomal protein 78.2 4.8 0.0001 36.6 5.4 41 122-205 122-162 (194)
55 COG4332 Uncharacterized protei 78.0 5.6 0.00012 36.1 5.7 64 77-140 102-169 (203)
56 PF13275 S4_2: S4 domain; PDB: 76.3 0.75 1.6E-05 34.8 -0.2 31 110-141 8-40 (65)
57 PRK01777 hypothetical protein; 71.8 7 0.00015 31.5 4.3 57 102-203 19-75 (95)
58 PRK04313 30S ribosomal protein 62.3 21 0.00045 33.5 6.0 31 111-141 39-71 (237)
59 cd01291 PseudoU_synth PseudoU_ 58.0 6.7 0.00014 30.0 1.7 19 262-280 25-43 (87)
60 cd02572 PseudoU_synth_hDyskeri 55.6 6.4 0.00014 35.1 1.4 16 225-240 2-17 (182)
61 PLN00036 40S ribosomal protein 55.5 31 0.00068 32.8 6.0 31 111-141 43-75 (261)
62 PTZ00223 40S ribosomal protein 55.0 31 0.00068 33.0 5.9 31 111-141 40-72 (273)
63 TIGR01018 rpsD_arch ribosomal 51.1 26 0.00056 31.0 4.4 20 122-141 117-136 (162)
64 PRK04099 truB tRNA pseudouridi 50.7 8.3 0.00018 36.7 1.4 16 225-240 2-17 (273)
65 PTZ00118 40S ribosomal protein 50.7 40 0.00086 32.1 5.9 31 111-141 43-75 (262)
66 KOG2559 Predicted pseudouridin 49.6 7.6 0.00016 37.0 0.9 19 263-281 91-109 (318)
67 PRK02484 truB tRNA pseudouridi 49.5 8.9 0.00019 36.8 1.4 16 225-240 3-18 (294)
68 PRK01550 truB tRNA pseudouridi 48.2 9.6 0.00021 36.8 1.4 16 225-240 2-17 (304)
69 PRK00130 truB tRNA pseudouridi 46.7 11 0.00023 36.3 1.4 16 225-240 2-17 (290)
70 PRK01528 truB tRNA pseudouridi 46.4 11 0.00023 36.3 1.4 16 225-240 3-18 (292)
71 PRK02755 truB tRNA pseudouridi 45.6 11 0.00024 36.3 1.4 16 225-240 3-18 (295)
72 TIGR00431 TruB tRNA pseudourid 45.5 11 0.00025 34.4 1.4 15 226-240 3-17 (209)
73 PRK14123 tRNA pseudouridine sy 44.6 12 0.00026 36.2 1.4 16 225-240 3-18 (305)
74 PRK03287 truB tRNA pseudouridi 43.9 12 0.00027 36.0 1.4 16 225-240 9-24 (298)
75 PRK14124 tRNA pseudouridine sy 43.2 13 0.00028 36.0 1.4 16 225-240 3-18 (308)
76 PF08068 DKCLD: DKCLD (NUC011) 43.0 10 0.00023 28.3 0.6 18 222-239 39-56 (59)
77 PRK08364 sulfur carrier protei 41.9 71 0.0015 23.7 5.0 15 188-202 50-64 (70)
78 PTZ00155 40S ribosomal protein 41.9 27 0.00059 31.4 3.2 20 122-141 120-139 (181)
79 PRK00989 truB tRNA pseudouridi 40.9 15 0.00032 34.3 1.4 15 226-240 10-24 (230)
80 PRK14846 truB tRNA pseudouridi 40.2 15 0.00033 36.2 1.4 16 225-240 3-18 (345)
81 PRK05912 tyrosyl-tRNA syntheta 38.8 76 0.0017 31.6 6.1 32 110-141 343-375 (408)
82 PRK13354 tyrosyl-tRNA syntheta 38.4 40 0.00088 33.7 4.1 32 110-141 343-375 (410)
83 PRK14122 tRNA pseudouridine sy 38.4 16 0.00036 35.4 1.3 15 226-240 2-16 (312)
84 PRK06437 hypothetical protein; 38.0 77 0.0017 23.5 4.7 16 188-203 47-62 (67)
85 PF11969 DcpS_C: Scavenger mRN 37.8 23 0.0005 28.9 2.0 15 217-231 13-27 (116)
86 cd00754 MoaD Ubiquitin domain 37.7 1.2E+02 0.0026 22.1 5.7 15 189-203 61-75 (80)
87 TIGR01764 excise DNA binding d 35.0 39 0.00084 22.0 2.4 21 116-136 7-27 (49)
88 PF04225 OapA: Opacity-associa 33.1 73 0.0016 24.9 4.0 31 103-134 4-34 (85)
89 PF06633 DUF1155: Protein of u 27.0 29 0.00063 23.9 0.7 34 14-49 8-41 (42)
90 PF03658 Ub-RnfH: RnfH family 26.0 49 0.0011 26.3 1.9 18 187-204 56-73 (84)
91 cd04762 HTH_MerR-trunc Helix-T 25.2 73 0.0016 20.4 2.4 21 116-136 6-26 (49)
92 PF01230 HIT: HIT domain; Int 25.2 52 0.0011 25.3 1.9 20 217-236 5-25 (98)
93 PF12728 HTH_17: Helix-turn-he 23.2 79 0.0017 21.4 2.4 21 116-136 7-27 (51)
94 PF14839 DOR: DOR family 22.1 54 0.0012 30.4 1.7 18 222-239 4-21 (216)
95 PRK10687 purine nucleoside pho 21.9 78 0.0017 26.1 2.5 14 217-230 16-29 (119)
96 cd00565 ThiS ThiaminS ubiquiti 21.9 1.5E+02 0.0033 21.4 3.7 15 189-203 46-60 (65)
97 TIGR02675 tape_meas_nterm tape 20.6 1.1E+02 0.0025 23.1 3.0 29 111-139 45-73 (75)
98 PF13348 Y_phosphatase3C: Tyro 20.6 1.2E+02 0.0027 21.8 3.1 23 110-132 43-65 (68)
No 1
>COG0564 RluA Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]
Probab=99.96 E-value=4.3e-29 Score=233.63 Aligned_cols=129 Identities=17% Similarity=0.142 Sum_probs=107.9
Q ss_pred CcHHHHHHHhcC-CCHHHHHHHHHcCCEEEcCccCCCCCCCCchhhhhhcccCCcccccccccccCcchhhccccccccC
Q 023330 110 GPVLEYICRELN-LPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTFRITH 188 (284)
Q Consensus 110 g~L~~~L~~~l~-lSr~~i~~LI~~G~V~vng~~~~~p~~~~~~~~~~~~~~~~~~~~~kr~~~~Gk~vr~~~~~~r~~~ 188 (284)
.+++.||++ +. +|+++++++++.|.|.+||. . ..
T Consensus 13 ~rld~~L~~-l~~~sr~~~~~~i~~g~v~vNg~----------------------------------~----------v~ 47 (289)
T COG0564 13 QRLDKFLAK-LLPISRSRIQKLIRKGRVRVNGK----------------------------------K----------VK 47 (289)
T ss_pred CCHHHHHHH-ccCcCHHHHHHHHHCCCEEECCE----------------------------------E----------cc
Confidence 489999998 55 99999999999999999985 1 23
Q ss_pred cCceecCCCEEEEEcCCCCC-CCCCCCCCCcceEEeeCcEEEEECCCCCccCCCCCCccchHHHHHHHHhCC-CCCCccc
Q 023330 189 VDQIVEAGTYLRVHVHPKRF-PRCYDIDWNSRIIAVTESHVVLDKPAGTSVGGTTDNIEESCATFASRALGL-TTPLRTT 266 (284)
Q Consensus 189 ~~~~L~~GD~I~V~~~~~~~-~~~~~~~~~l~ILYEDedLLVVNKPaGl~VHPt~~~~~~TL~~~l~~~lg~-~~pl~~V 266 (284)
.++.|+.||.|++....... ....+.+.+++|||||||++|||||+||+|||+.++..+|+++++..+.+. ...+++|
T Consensus 48 ~~~~l~~gd~i~~~~~~~~~~~~~~~~~~~l~IlyED~~llVvnKP~Gl~vhp~~~~~~~tl~~~l~~~~~~~~~~~~~v 127 (289)
T COG0564 48 PSYKLKPGDVVRIPLPEEPEEEKLVPEDIPLDILYEDEDLLVVNKPAGLVVHPGGGHHEGTLVNALLRHCQDGVERPGIV 127 (289)
T ss_pred CCeeeCCCCEEEEecccccccccccccCCCccEEEecCCEEEEECCCCCcCcCCCCCccHhHHHHHHHhccccCCceeee
Confidence 67899999999998754332 223345566899999999999999999999999999999999988766543 3346789
Q ss_pred cCCCcccceeeeeeeeC
Q 023330 267 HQIDNCTEGWYCYFTTL 283 (284)
Q Consensus 267 HRLDRdTSGLLlfAKT~ 283 (284)
||||||||||||||||.
T Consensus 128 HRLDkdTSGlll~AK~~ 144 (289)
T COG0564 128 HRLDKDTSGLLLVAKNR 144 (289)
T ss_pred ccCCCCCceEEEEECCH
Confidence 99999999999999985
No 2
>TIGR00005 rluA_subfam pseudouridine synthase, RluA family. modifies uracil-65 in transfer RNAs to pseudouridine.
Probab=99.93 E-value=2.2e-25 Score=206.60 Aligned_cols=131 Identities=18% Similarity=0.131 Sum_probs=104.7
Q ss_pred CcHHHHHHHhcC-CCHHHHHHHHHcCCEEEcCccCCCCCCCCchhhhhhcccCCcccccccccccCcchhhccccccccC
Q 023330 110 GPVLEYICRELN-LPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTFRITH 188 (284)
Q Consensus 110 g~L~~~L~~~l~-lSr~~i~~LI~~G~V~vng~~~~~p~~~~~~~~~~~~~~~~~~~~~kr~~~~Gk~vr~~~~~~r~~~ 188 (284)
.+|++||++.+. +|++.++++|+.|.|++||.. ++.
T Consensus 6 ~rLd~~L~~~~~~~Sr~~~~kli~~G~V~VNg~~-------------------------------------------~~~ 42 (299)
T TIGR00005 6 QRLDDFLASLLPDLSRSRIQKLIENGQVKVNGKV-------------------------------------------TAN 42 (299)
T ss_pred hhHHHHHHHhcccCCHHHHHHHHHCCcEEECCEe-------------------------------------------ccC
Confidence 489999999886 999999999999999999831 135
Q ss_pred cCceecCCCEEEEEcCCCCCCCCCCCCCCcceEEeeCcEEEEECCCCCccCCCCCCccchHHHHHHHHhCC---CCCCcc
Q 023330 189 VDQIVEAGTYLRVHVHPKRFPRCYDIDWNSRIIAVTESHVVLDKPAGTSVGGTTDNIEESCATFASRALGL---TTPLRT 265 (284)
Q Consensus 189 ~~~~L~~GD~I~V~~~~~~~~~~~~~~~~l~ILYEDedLLVVNKPaGl~VHPt~~~~~~TL~~~l~~~lg~---~~pl~~ 265 (284)
.++.|+.||.|.|...+...+.....+.+++|+|||++++|||||+||+|||+.++..+|+.+.+..++.. ...+++
T Consensus 43 ~~~~v~~gd~I~i~~~~~~~~~~~~~~~~~~i~~ed~~~lvvnKP~g~~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~ 122 (299)
T TIGR00005 43 PKLKVKDGDRITVRVPEEEEHEVPPQDIPLDILFEDEDIIVINKPSGLVVHPGGGNPFGTVLNALLAHCPPIAGVERVGI 122 (299)
T ss_pred cccCCCCCCEEEEecCCcccccCCccCCCccEEEeCCCEEEEECCCCCeEeCCCCCCcccHHHHHHHhcccccCCCcCce
Confidence 57799999999997543221222223446789999999999999999999999887778888877655432 134678
Q ss_pred ccCCCcccceeeeeeeeC
Q 023330 266 THQIDNCTEGWYCYFTTL 283 (284)
Q Consensus 266 VHRLDRdTSGLLlfAKT~ 283 (284)
|||||++||||||||||.
T Consensus 123 vhRLD~~TSGlll~ak~~ 140 (299)
T TIGR00005 123 VHRLDRDTSGLMVVAKTP 140 (299)
T ss_pred ECCCCCCCceEEEEEcCH
Confidence 999999999999999984
No 3
>PRK11025 23S rRNA pseudouridylate synthase C; Provisional
Probab=99.92 E-value=1e-24 Score=205.39 Aligned_cols=129 Identities=17% Similarity=0.129 Sum_probs=96.4
Q ss_pred CcHHHHHHHhc-CCCHHHHHHHHHcCCEEEcCccCCCCCCCCchhhhhhcccCCcccccccccccCcchhhccccccccC
Q 023330 110 GPVLEYICREL-NLPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTFRITH 188 (284)
Q Consensus 110 g~L~~~L~~~l-~lSr~~i~~LI~~G~V~vng~~~~~p~~~~~~~~~~~~~~~~~~~~~kr~~~~Gk~vr~~~~~~r~~~ 188 (284)
.+|++||++.+ .+|++.++++|+.|.|++||.. ..
T Consensus 20 ~RLd~~L~~~~~~~sr~~i~~li~~G~V~VNg~~--------------------------------------------v~ 55 (317)
T PRK11025 20 QRIDNFLRTQLKGVPKSMIYRILRKGEVRVNKKR--------------------------------------------IK 55 (317)
T ss_pred chHHHHHHHhcccCCHHHHHHHHHcCCEEECCEE--------------------------------------------cC
Confidence 48999999877 5899999999999999999851 24
Q ss_pred cCceecCCCEEEEEcCCCCCCCCC--------CCCCCcceEEeeCcEEEEECCCCCccCCCCCCccchHHHHHHHHhCCC
Q 023330 189 VDQIVEAGTYLRVHVHPKRFPRCY--------DIDWNSRIIAVTESHVVLDKPAGTSVGGTTDNIEESCATFASRALGLT 260 (284)
Q Consensus 189 ~~~~L~~GD~I~V~~~~~~~~~~~--------~~~~~l~ILYEDedLLVVNKPaGl~VHPt~~~~~~TL~~~l~~~lg~~ 260 (284)
+++.|+.||.|++........... ...++++|||||++++|||||+||+|||+.+... ++.+.+.......
T Consensus 56 ~~~~v~~GD~I~i~~~~~~~~~~~p~~~~~~~~~~~~~~Ilyed~~~lvvnKP~gl~~~~~~~~~~-~~~~~~~~~~~~~ 134 (317)
T PRK11025 56 PEYKLEAGDEVRIPPVRVAEREEEAVSPKLQKVAALADVILYEDDHILVLNKPSGTAVHGGSGLSF-GVIEGLRALRPEA 134 (317)
T ss_pred cccccCCCCEEEeCCCCccccccccccccccccccCcCCEEEECCCEEEEECCCCCcCcCCCCCCc-cHHHHHHHhccCC
Confidence 567999999999863211100000 0124679999999999999999999999876533 4555444332222
Q ss_pred CCCccccCCCcccceeeeeeeeC
Q 023330 261 TPLRTTHQIDNCTEGWYCYFTTL 283 (284)
Q Consensus 261 ~pl~~VHRLDRdTSGLLlfAKT~ 283 (284)
..+++||||||+||||||||||.
T Consensus 135 ~~~~~vhRLD~~TSGlll~Ak~~ 157 (317)
T PRK11025 135 RFLELVHRLDRDTSGVLLVAKKR 157 (317)
T ss_pred CcCceeCCCCCCCceEEEEEcCH
Confidence 33568999999999999999985
No 4
>PRK11180 rluD 23S rRNA pseudouridine synthase D; Provisional
Probab=99.92 E-value=8.5e-25 Score=206.37 Aligned_cols=131 Identities=14% Similarity=0.085 Sum_probs=103.5
Q ss_pred CcHHHHHHHhc-CCCHHHHHHHHHcCCEEEcCccCCCCCCCCchhhhhhcccCCcccccccccccCcchhhccccccccC
Q 023330 110 GPVLEYICREL-NLPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTFRITH 188 (284)
Q Consensus 110 g~L~~~L~~~l-~lSr~~i~~LI~~G~V~vng~~~~~p~~~~~~~~~~~~~~~~~~~~~kr~~~~Gk~vr~~~~~~r~~~ 188 (284)
.+|++||++.+ .+|++.++++|+.|.|++||+. +..
T Consensus 18 ~RLd~~L~~~~~~~Sr~~~~~lI~~G~V~VNg~~-------------------------------------------v~~ 54 (325)
T PRK11180 18 QRLDQALAELFPDYSRSRIKEWILDQRVLVNGKV-------------------------------------------INK 54 (325)
T ss_pred ccHHHHHHhhccccCHHHHHHHHHCCCEEECCEE-------------------------------------------ccC
Confidence 48999999887 4899999999999999999851 124
Q ss_pred cCceecCCCEEEEEcCCCCCCCCCCCCCCcceEEeeCcEEEEECCCCCccCCCCCCccchHHHHHHHHhCC---CCCCcc
Q 023330 189 VDQIVEAGTYLRVHVHPKRFPRCYDIDWNSRIIAVTESHVVLDKPAGTSVGGTTDNIEESCATFASRALGL---TTPLRT 265 (284)
Q Consensus 189 ~~~~L~~GD~I~V~~~~~~~~~~~~~~~~l~ILYEDedLLVVNKPaGl~VHPt~~~~~~TL~~~l~~~lg~---~~pl~~ 265 (284)
+++.|+.||.|++...+.......+.+.+++|||||++++|||||+||+|||+.++..+|+.+.+..++.. ...+++
T Consensus 55 ~~~~v~~gD~I~v~~~~~~~~~~~~~~~~~~iiyed~~~lvvnKP~gl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~ 134 (325)
T PRK11180 55 PKEKVLGGEQVAIDAEIEEEARFEPQDIPLDIVYEDDDILVINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADVPRAGI 134 (325)
T ss_pred CCcCcCCCCEEEEeeccccccCCCCCCCCCcEEEECCCEEEEECCCCCeEeCCCCCCCCcHHHHHHHHhhhccCCcccce
Confidence 56788999999998643221112233456899999999999999999999999887778888877655421 123568
Q ss_pred ccCCCcccceeeeeeeeC
Q 023330 266 THQIDNCTEGWYCYFTTL 283 (284)
Q Consensus 266 VHRLDRdTSGLLlfAKT~ 283 (284)
|||||++||||||||||.
T Consensus 135 vhRLD~~TSGlll~Ak~~ 152 (325)
T PRK11180 135 VHRLDKDTTGLMVVAKTV 152 (325)
T ss_pred eccCCCCCceeEEEECCH
Confidence 999999999999999984
No 5
>cd02558 PSRA_1 PSRA_1: Pseudouridine synthase, a subgroup of the RluA family. This group is comprised of bacterial proteins assigned to the RluA family of pseudouridine synthases. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. The RluA family is comprised of proteins related to Escherichia coli RluA.
Probab=99.86 E-value=7.5e-22 Score=180.18 Aligned_cols=92 Identities=21% Similarity=0.198 Sum_probs=74.7
Q ss_pred CcCceecCCCEEEEEcCCCCCCCCCCCCCCcceEEeeCcEEEEECCCCCccCCCCCCccchHHHHHHHHhCCCCCCcccc
Q 023330 188 HVDQIVEAGTYLRVHVHPKRFPRCYDIDWNSRIIAVTESHVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTH 267 (284)
Q Consensus 188 ~~~~~L~~GD~I~V~~~~~~~~~~~~~~~~l~ILYEDedLLVVNKPaGl~VHPt~~~~~~TL~~~l~~~lg~~~pl~~VH 267 (284)
.+++.|+.||.|.++...... .+.+++++|||||++++|||||+||+|||+.++..+|+.+.+....+.. .+++||
T Consensus 12 ~~~~~l~~gd~i~~~~~~~~~---~~~~~~~~Iiyed~~~lvvnKPaGl~~~~~~~~~~~t~~~~l~~~~~~~-~~~~vh 87 (246)
T cd02558 12 DPDSPYRPGTFVWYYRELPDE---PPIPFEETILHQDEHLLVADKPHFLPVTPRGRYVTETLLVRLRRQTGNP-DLTPAH 87 (246)
T ss_pred CCCceecCCCEEEEeCCCCCC---CCCCCCcceEEecCCEEEEECCCCCccCCCCcchhhhHHHHHHHHhCCC-cccccc
Confidence 567899999999998532211 1234568999999999999999999999998888888888776655533 456899
Q ss_pred CCCcccceeeeeeeeC
Q 023330 268 QIDNCTEGWYCYFTTL 283 (284)
Q Consensus 268 RLDRdTSGLLlfAKT~ 283 (284)
|||++||||||||||.
T Consensus 88 RLD~~TSGlll~Ak~~ 103 (246)
T cd02558 88 RLDRLTAGLVLFSKRP 103 (246)
T ss_pred cCCCCceeEEEEEcCH
Confidence 9999999999999985
No 6
>PRK10839 16S rRNA pseudouridylate synthase A; Provisional
Probab=99.83 E-value=7.7e-21 Score=171.10 Aligned_cols=114 Identities=11% Similarity=0.068 Sum_probs=85.2
Q ss_pred cHHHHHHHhcCCCHHHHHHHHHcCCEEEcCccCCCCCCCCchhhhhhcccCCcccccccccccCcchhhccccccccCcC
Q 023330 111 PVLEYICRELNLPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTFRITHVD 190 (284)
Q Consensus 111 ~L~~~L~~~l~lSr~~i~~LI~~G~V~vng~~~~~p~~~~~~~~~~~~~~~~~~~~~kr~~~~Gk~vr~~~~~~r~~~~~ 190 (284)
+|+.||++.+.+|++.++++|+.|.|++||.. +..++
T Consensus 2 rld~~L~~~~~~Sr~~~~~li~~g~V~VNg~~-------------------------------------------~~~~~ 38 (232)
T PRK10839 2 RLDKFISQQLGVSRAIAGRELRANRVTVDGEI-------------------------------------------VKNGA 38 (232)
T ss_pred cHHHHHHHcCCCCHHHHHHHHHcCeEEECCEE-------------------------------------------eccCC
Confidence 68999998888999999999999999999851 12456
Q ss_pred ceecCCCEEEEEcCCCCCCCCCCCCCCcceEEeeCcEEEEECCCCCccCCCCCCccchHHHHHHHHhCCCCCCccccCCC
Q 023330 191 QIVEAGTYLRVHVHPKRFPRCYDIDWNSRIIAVTESHVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQID 270 (284)
Q Consensus 191 ~~L~~GD~I~V~~~~~~~~~~~~~~~~l~ILYEDedLLVVNKPaGl~VHPt~~~~~~TL~~~l~~~lg~~~pl~~VHRLD 270 (284)
+.|++||.|.+...+.. ..+|++++|||||+||+|||+.. ...|+..++... ....+++|||||
T Consensus 39 ~~l~~gd~I~l~~~~~~-------------~~~~~~~lvvnKP~G~~~~~~~~-~~~tl~~~l~~~--~~~~~~~v~RLD 102 (232)
T PRK10839 39 FKLLPEHDVAYDGNPLA-------------QQHGPRYFMLNKPQGYVCSTDDP-DHPTVLYFLDEP--VAYKLHAAGRLD 102 (232)
T ss_pred cCcCCCCEEEECCEEcc-------------cCCCCEEEEEECCCCeEecccCC-CCCeEEEecccc--cccCceecCCCC
Confidence 79999999987531100 11457999999999999999843 234554332211 122356899999
Q ss_pred cccceeeeeeeeC
Q 023330 271 NCTEGWYCYFTTL 283 (284)
Q Consensus 271 RdTSGLLlfAKT~ 283 (284)
+|||||||||||.
T Consensus 103 ~~TSGlll~ak~~ 115 (232)
T PRK10839 103 IDTTGLVLMTDDG 115 (232)
T ss_pred CCceeEEEEecCH
Confidence 9999999999985
No 7
>PRK10475 23S rRNA pseudouridine synthase F; Provisional
Probab=99.77 E-value=1.4e-18 Score=163.20 Aligned_cols=114 Identities=15% Similarity=0.127 Sum_probs=88.1
Q ss_pred CcHHHHHHHhcCCCHHHHHHHHHcCCEEEcCccCCCCCCCCchhhhhhcccCCcccccccccccCcchhhccccccccCc
Q 023330 110 GPVLEYICRELNLPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTFRITHV 189 (284)
Q Consensus 110 g~L~~~L~~~l~lSr~~i~~LI~~G~V~vng~~~~~p~~~~~~~~~~~~~~~~~~~~~kr~~~~Gk~vr~~~~~~r~~~~ 189 (284)
.+|++||++....||..+.++|..|.|+|||+. +..
T Consensus 7 ~RL~k~La~~g~~SRr~a~~lI~~G~V~VNGk~--------------------------------------------v~~ 42 (290)
T PRK10475 7 TRLNKYISESGICSRREADRYIEQGNVFINGKR--------------------------------------------ATI 42 (290)
T ss_pred HHHHHHHHhCCCCCHHHHHHHHHCCcEEECCEE--------------------------------------------ccC
Confidence 489999987645799999999999999999851 234
Q ss_pred CceecCCCEEEEEcCCCCCCCCCCCCCCcceEEeeCcEEEEECCCCCccCCCCCCccchHHHHHHHHhCCCCCCccccCC
Q 023330 190 DQIVEAGTYLRVHVHPKRFPRCYDIDWNSRIIAVTESHVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQI 269 (284)
Q Consensus 190 ~~~L~~GD~I~V~~~~~~~~~~~~~~~~l~ILYEDedLLVVNKPaGl~VHPt~~~~~~TL~~~l~~~lg~~~pl~~VHRL 269 (284)
++.|.+||.|.|.... ..+ ..+||+++||+|||+|++||+... ...|+.+++... ..+++||||
T Consensus 43 ~~~V~~gD~V~v~g~~-----i~~------~~~ed~~~lvlnKP~G~~~~~~~~-~~~tv~~~l~~~----~~l~~VgRL 106 (290)
T PRK10475 43 GDQVKAGDVVKVNGQL-----IEP------REAEDLVLIALNKPVGIVSTTEDG-ERDNIVDFVNHS----KRVFPIGRL 106 (290)
T ss_pred CCCcCCCCEEEECCEE-----ccc------cccCCCeEEEEECCCCCCcCCCCC-CCCcHHHHhhcc----ccccccccC
Confidence 5678999999886311 000 114899999999999999998765 457777766431 236789999
Q ss_pred CcccceeeeeeeeC
Q 023330 270 DNCTEGWYCYFTTL 283 (284)
Q Consensus 270 DRdTSGLLlfAKT~ 283 (284)
|+|||||||||++-
T Consensus 107 DrdTsGLLLlT~dg 120 (290)
T PRK10475 107 DKDSQGLIFLTNHG 120 (290)
T ss_pred CCCCcceEEEecCH
Confidence 99999999999974
No 8
>KOG1919 consensus RNA pseudouridylate synthases [RNA processing and modification]
Probab=99.77 E-value=1.7e-18 Score=167.46 Aligned_cols=154 Identities=21% Similarity=0.219 Sum_probs=108.7
Q ss_pred CCCccccccCCCCCCCCceE---EEeeCC-CC-cHHHHHHHhc-CCCHHHHHHHHHcCCEEEcCccCCCCCCCCchhhhh
Q 023330 83 YPEYHRLLPCPSQNCPPRVE---HLVVSE-GG-PVLEYICREL-NLPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRV 156 (284)
Q Consensus 83 ~~~~~~~~~~~~~~~~~rv~---~~vv~~-~g-~L~~~L~~~l-~lSr~~i~~LI~~G~V~vng~~~~~p~~~~~~~~~~ 156 (284)
+.+|.-.+..+.....+.+. .++... .+ .+.+++..++ ..++.+-...|+.|.|.+||..
T Consensus 12 ~~~~~~~~~~~~~~v~pyy~~~~~~~~~rw~~k~~~~~~~~ef~~~~~~~~~~~i~~g~v~~n~~~-------------- 77 (371)
T KOG1919|consen 12 SDEISVYIDGGLRKVAPYYFTYRTFVKGRWAGKKLVDVFVSEFRLRERAYYESAIKLGRVTVNGEQ-------------- 77 (371)
T ss_pred ccccceeecCCcceeeeEEEeeeEEEeeeecccchHHHHHHHHhcCchHhhhhhhhcCceEECcEe--------------
Confidence 34444455555555555422 111111 12 4677776666 6899999999999999999851
Q ss_pred hcccCCcccccccccccCcchhhccccccccCcCceecCCCEEEEEcCCCCCCCCCCCCCCcceEEeeCcEEEEECCCCC
Q 023330 157 FKEVTDPSVLSKRSSIKGKTVREAQKTFRITHVDQIVEAGTYLRVHVHPKRFPRCYDIDWNSRIIAVTESHVVLDKPAGT 236 (284)
Q Consensus 157 ~~~~~~~~~~~kr~~~~Gk~vr~~~~~~r~~~~~~~L~~GD~I~V~~~~~~~~~~~~~~~~l~ILYEDedLLVVNKPaGl 236 (284)
...++.++.||.|...++....+ ...++++|+|||++++|||||+||
T Consensus 78 ------------------------------~~v~~i~k~~d~l~~~vhrh~p~---~~~~~~~Iv~ed~~~vVvnKP~gi 124 (371)
T KOG1919|consen 78 ------------------------------VRVSLIVKNGDVLCHTVHRHEPP---VAYLPIRIVFEDKDYVVVNKPHGI 124 (371)
T ss_pred ------------------------------eeeEEEeccCCEEEEeeccCCCC---ccccccceEEecCCEEEEeCCCCC
Confidence 13457889999998776543322 123678999999999999999999
Q ss_pred ccCCCCCCccchHHHHHHHHhCCCCCCccccCCCcccceeeeeeeeCC
Q 023330 237 SVGGTTDNIEESCATFASRALGLTTPLRTTHQIDNCTEGWYCYFTTLA 284 (284)
Q Consensus 237 ~VHPt~~~~~~TL~~~l~~~lg~~~pl~~VHRLDRdTSGLLlfAKT~~ 284 (284)
+|||++....+++...+..... ...+++||||||.|||+|+||||.+
T Consensus 125 pVhp~g~~~~n~i~~~l~~~~~-~~~~~~~hRLDr~tSGllvlAkt~~ 171 (371)
T KOG1919|consen 125 PVHPTGRYRENTITKILAALHK-VEGLRPCHRLDRLTSGLLVLAKTKE 171 (371)
T ss_pred ceeccCccccccchHHHHHhcc-ccccccccccCccccceEEEEechh
Confidence 9999888777777665543322 2346789999999999999999963
No 9
>PRK10700 23S rRNA pseudouridylate synthase B; Provisional
Probab=99.73 E-value=1.9e-17 Score=155.07 Aligned_cols=120 Identities=13% Similarity=0.040 Sum_probs=84.9
Q ss_pred CcHHHHHHHhcCCCHHHHHHHHHcCCEEEcCccCCCCCCCCchhhhhhcccCCcccccccccccCcchhhccccccccCc
Q 023330 110 GPVLEYICRELNLPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTFRITHV 189 (284)
Q Consensus 110 g~L~~~L~~~l~lSr~~i~~LI~~G~V~vng~~~~~p~~~~~~~~~~~~~~~~~~~~~kr~~~~Gk~vr~~~~~~r~~~~ 189 (284)
.+|++||++.-..||..++++|+.|.|+|||+. +.+
T Consensus 3 ~RL~k~La~~g~~SRr~a~~lI~~G~V~VNG~~--------------------------------------------~~~ 38 (289)
T PRK10700 3 EKLQKVLARAGHGSRREIESIIEAGRVSVDGKI--------------------------------------------ATL 38 (289)
T ss_pred hhHHHHHHHCCCCCHHHHHHHHHcCCEEECCEe--------------------------------------------ccC
Confidence 478999997423899999999999999999851 134
Q ss_pred CceecCCCEEEEEcCCCCCCCCCCCCCCcceEE-eeCcEEEEECCCCCccCCCCCCccchHHHHHHHHhCCCCCCccccC
Q 023330 190 DQIVEAGTYLRVHVHPKRFPRCYDIDWNSRIIA-VTESHVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQ 268 (284)
Q Consensus 190 ~~~L~~GD~I~V~~~~~~~~~~~~~~~~l~ILY-EDedLLVVNKPaGl~VHPt~~~~~~TL~~~l~~~lg~~~pl~~VHR 268 (284)
.+.|..+|...|.++.+.... ...+ ||++++++|||+|++||++......|+.+++... ....+++|||
T Consensus 39 g~~V~~~~~d~I~v~g~~~~~--------~~~~~e~~~ylvlnKP~G~~~s~~d~~~~~tv~d~l~~~--~~~~~~~VgR 108 (289)
T PRK10700 39 GDRVEVTPGLKIRIDGHLISV--------KESAEQICRVLAYYKPEGELCTRNDPEGRPTVFDRLPKL--RGARWIAVGR 108 (289)
T ss_pred CCEeCCCCCeEEEECCEEeec--------ccccccCCeEEEEECCCCCEeecCCCCCCccHHHHhhhh--cCCceeEccC
Confidence 456776644333332211100 0111 6678999999999999998765567888766432 1123568999
Q ss_pred CCcccceeeeeeeeC
Q 023330 269 IDNCTEGWYCYFTTL 283 (284)
Q Consensus 269 LDRdTSGLLlfAKT~ 283 (284)
||+|||||||||++-
T Consensus 109 LD~dTsGLLLlTndg 123 (289)
T PRK10700 109 LDVNTCGLLLFTTDG 123 (289)
T ss_pred CCCCCceEEEEEcCH
Confidence 999999999999873
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=99.72 E-value=1.1e-17 Score=149.53 Aligned_cols=66 Identities=27% Similarity=0.397 Sum_probs=56.4
Q ss_pred CcceEEeeCcEEEEECCCCCccCCCCCCccchHHHHHHHHhCCCCCCccccCCCcccceeeeeeeeC
Q 023330 217 NSRIIAVTESHVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQIDNCTEGWYCYFTTL 283 (284)
Q Consensus 217 ~l~ILYEDedLLVVNKPaGl~VHPt~~~~~~TL~~~l~~~lg~~~pl~~VHRLDRdTSGLLlfAKT~ 283 (284)
+++|||||++++|||||+||+||++......++.+.+....+. ..+++|||||++||||||||||.
T Consensus 15 ~~~iiyed~~~ivvnKP~Gl~~~~~~~~~~~sl~~~l~~~~~~-~~~~~vhRLD~~TSGllllak~~ 80 (213)
T cd02557 15 PIKIVHEDDDLLVVDKPSGIPVHPTGRYRYNTVTEILKSEYGL-TELRPCHRLDRLTSGLLLFAKTS 80 (213)
T ss_pred CCcEEEECCCEEEEECCCCCcCCCCCCCCcChHHHHHHHHcCC-CCccCccCCCCCCceEEEEECCH
Confidence 5789999999999999999999998776677888877665543 24668999999999999999985
No 11
>PRK10158 23S rRNA/tRNA pseudouridine synthase A; Provisional
Probab=99.70 E-value=1.6e-17 Score=149.30 Aligned_cols=63 Identities=22% Similarity=0.192 Sum_probs=51.3
Q ss_pred cceEEeeCcEEEEECCCCCccCCCCC-CccchHHHHHHHHhCCCCCCccccCCCcccceeeeeeeeC
Q 023330 218 SRIIAVTESHVVLDKPAGTSVGGTTD-NIEESCATFASRALGLTTPLRTTHQIDNCTEGWYCYFTTL 283 (284)
Q Consensus 218 l~ILYEDedLLVVNKPaGl~VHPt~~-~~~~TL~~~l~~~lg~~~pl~~VHRLDRdTSGLLlfAKT~ 283 (284)
++|||||++++|||||+|++|||+.+ ....++.+.+...+ . .+++||||||+||||||||||.
T Consensus 14 ~~iiyed~~~lvvnKPaGl~~~~~~~~~~~~sl~~~l~~~~--~-~~~~vhRLDr~TSGlll~Akt~ 77 (219)
T PRK10158 14 LVILYQDEHIMVVNKPSGLLSVPGRLEEHKDSVMTRIQRDY--P-QAESVHRLDMATSGVIVVALTK 77 (219)
T ss_pred CCEEEeCCCEEEEECCCCCcEeCCCCCccchhHHHHHHHhC--C-CCCEECCCCCCCceEEEEECCH
Confidence 68999999999999999999999763 34456666554432 2 3568999999999999999985
No 12
>TIGR01621 RluA-like pseudouridine synthase Rlu family protein, TIGR01621. This model represents a clade of sequences within the pseudouridine synthase superfamily (pfam00849). The superfamily includes E. coli proteins: RluA, RluB, RluC, RluD, and RsuA. The sequences modeled here are most closely related to RluA. Neisseria, among those species hitting this model, does not appear to have an RluA homolog. It is presumed that these sequences function as pseudouridine synthases, although perhaps with different specificity.
Probab=99.69 E-value=2.1e-17 Score=148.39 Aligned_cols=63 Identities=19% Similarity=0.248 Sum_probs=51.2
Q ss_pred cceEEeeCcEEEEECCCCCccCCCCCCccchHHHHHHHHhCCCCCCccccCCCcccceeeeeeeeC
Q 023330 218 SRIIAVTESHVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQIDNCTEGWYCYFTTL 283 (284)
Q Consensus 218 l~ILYEDedLLVVNKPaGl~VHPt~~~~~~TL~~~l~~~lg~~~pl~~VHRLDRdTSGLLlfAKT~ 283 (284)
++|||||++++|||||+||+||++.+ ..++.+.+....+. ..+++||||||+||||||||||.
T Consensus 2 ~~ilyed~~~lvvnKP~Gl~v~~~~~--~~~l~~~l~~~~~~-~~~~~VhRLDr~TSGlll~Ak~~ 64 (217)
T TIGR01621 2 FEILFTHPDFLLINKHPGISVHKDDG--ETGLLQEVATQLGV-GQVWLVHRLDKMTSGILLLALNA 64 (217)
T ss_pred ceEEEeCCCEEEEECCCCCeECCCCC--cChHHHHHHHhcCC-CCccEecCCCCCCceEEEEEcCH
Confidence 47999999999999999999999764 34566655544332 34678999999999999999985
No 13
>cd02563 PseudoU_synth_TruC tRNA pseudouridine isomerase C: Pseudouridine synthases catalyze the isomerization of specific uridines in an tRNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. TruC makes psi65 in tRNAs. This psi residue is not universally conserved.
Probab=99.69 E-value=3e-17 Score=147.39 Aligned_cols=64 Identities=22% Similarity=0.279 Sum_probs=48.8
Q ss_pred cceEEeeCcEEEEECCCCCccCCCCCCccch--HHHHHHHHhCCCCCCccccCCCcccceeeeeeeeC
Q 023330 218 SRIIAVTESHVVLDKPAGTSVGGTTDNIEES--CATFASRALGLTTPLRTTHQIDNCTEGWYCYFTTL 283 (284)
Q Consensus 218 l~ILYEDedLLVVNKPaGl~VHPt~~~~~~T--L~~~l~~~lg~~~pl~~VHRLDRdTSGLLlfAKT~ 283 (284)
++|||||++++|||||+||+|||+.+....+ +...+....+ ..+++|||||++||||||||||.
T Consensus 1 ~~Ilyed~~~lvvnKP~G~~~~~~~~~~~~~~~~~~~l~~~~~--~~~~~vhRLD~~TSGlll~Ak~~ 66 (223)
T cd02563 1 LEILYQDEHLVAINKPSGLLVHRSELDRHETRFALQTLRDQLG--QHVYPVHRLDRPTSGVLLFALSS 66 (223)
T ss_pred CcEEEecCCEEEEECCCCCeEcCCCCCCCCcHHHHHHHHHHcC--CCcccccCCCCCCeEEEEEEECH
Confidence 3699999999999999999999986433332 2222333322 34678999999999999999985
No 14
>PRK11112 tRNA pseudouridine synthase C; Provisional
Probab=99.68 E-value=5.7e-17 Score=148.99 Aligned_cols=64 Identities=23% Similarity=0.217 Sum_probs=49.0
Q ss_pred cceEEeeCcEEEEECCCCCccCCCCCCccchH--HHHHHHHhCCCCCCccccCCCcccceeeeeeeeC
Q 023330 218 SRIIAVTESHVVLDKPAGTSVGGTTDNIEESC--ATFASRALGLTTPLRTTHQIDNCTEGWYCYFTTL 283 (284)
Q Consensus 218 l~ILYEDedLLVVNKPaGl~VHPt~~~~~~TL--~~~l~~~lg~~~pl~~VHRLDRdTSGLLlfAKT~ 283 (284)
++|||||++++|||||+||+|||+..+..++. ...+....+ ..+++||||||+||||||||||.
T Consensus 2 l~IlyEd~~~lvvnKPaGl~~~~~~~~~~~~~~~~~~l~~~~~--~~~~~VHRLDr~TSGlll~Ak~~ 67 (257)
T PRK11112 2 LEILYQDEWLVAVNKPAGWLVHRSWLDRHETVFVMQTVRDQIG--QHVFTAHRLDRPTSGVLLMALSS 67 (257)
T ss_pred CcEEEecCCEEEEECCCCCeecCCCCCCCchHHHHHHHHHHhC--CCceeeccCCCCCeeEEEEECCH
Confidence 47999999999999999999999854444432 233322222 24568999999999999999985
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=99.44 E-value=5.3e-14 Score=119.32 Aligned_cols=55 Identities=16% Similarity=0.195 Sum_probs=43.8
Q ss_pred EEEEECCCCCccCCCCCCccchHHHHHHHHhCCCCCCccccCCCcccceeeeeeeeC
Q 023330 227 HVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQIDNCTEGWYCYFTTL 283 (284)
Q Consensus 227 LLVVNKPaGl~VHPt~~~~~~TL~~~l~~~lg~~~pl~~VHRLDRdTSGLLlfAKT~ 283 (284)
++|||||+|++||++.+....++...+.... ...+++|||||++||||||||||.
T Consensus 1 ~ivvnKP~G~~~~~~~~~~~~~~~~~l~~~~--~~~~~~vhRLD~~TSGlll~ak~~ 55 (154)
T cd02550 1 ILVLNKPSGLVCHPTDRDRDPTVVVRLDKLH--GPRVHAAGRLDKDTSGLLLLTNDG 55 (154)
T ss_pred CEEEECCCCCEEecCCCCCCCcHHHhhhccc--CCceeEeccCCCCCeeEEEEEcCH
Confidence 5899999999999988766677766543221 234678999999999999999985
No 16
>PF00849 PseudoU_synth_2: RNA pseudouridylate synthase This Prosite family is a subset of the Pfam family. This Prosite family is a subset of the Pfam family.; InterPro: IPR006145 Pseudouridine synthases catalyse the isomerisation of uridine to pseudouridine (Psi) in a variety of RNA molecules, and may function as RNA chaperones. Pseudouridine is the most abundant modified nucleotide found in all cellular RNAs. There are four distinct families of pseudouridine synthases that share no global sequence similarity, but which do share the same fold of their catalytic domain(s) and uracil-binding site and are descended from a common molecular ancestor. The catalytic domain consists of two subdomains, each of which has an alpha+beta structure that has some similarity to the ferredoxin-like fold (note: some pseudouridine synthases contain additional domains). The active site is the most conserved structural region of the superfamily and is located between the two homologous domains. These families are []: Pseudouridine synthase I, TruA. Pseudouridine synthase II, TruB, which contains and additional C-terminal PUA domain. Pseudouridine synthase RsuA (ribosomal small subunit) and RluC/RluD (ribosomal large subunits), both of which contain an additional N-terminal alpha-L RNA-binding motif. Pseudouridine synthase TruD, which has a natural circular permutation in the catalytic domain, as well as an insertion of a family-specific alpha+beta subdomain. This entry represents several different pseudouridine synthases from family 3, including: RsuA (acts on small ribosomal subunit), RluA, RluB, RluC, RluD, RluE and RluF (act on large ribosomal subunit). RsuA from Escherichia coli catalyses formation of pseudouridine at position 516 in 16S rRNA during assembly of the 30S ribosomal subunit [, ]. RsuA consists of an N-terminal domain connected by an extended linker to the central and C-terminal domains. Uracil and UMP bind in a cleft between the central and C-terminal domains near the catalytic residue Asp 102. The N-terminal domain shows structural similarity to the ribosomal protein S4. Despite only 15% amino acid identity, the other two domains are structurally similar to those of the tRNA-specific psi-synthase TruA, including the position of the catalytic Asp. Our results suggest that all four families of pseudouridine synthases share the same fold of their catalytic domain(s) and uracil-binding site. RluB, RluC, RluD, RluE and RluF are homologous enzymes which each convert specific uridine bases in E. coli ribosomal 23S RNA to pseudouridine: RluB modifies uracil-2605. RluC modifies uracil-955, U-2504, and U-2580. RluD modifies uracil-1911, U-1915, and U-1917. RluE modifies uracil-3457. RluF modifies uracil-2604, and to a lesser extent U-2605. RluD also possesses a second function related to proper assembly of the 50S ribosomal subunit that is independent of Psi-synthesis [, ]. Both RluC and RluD have an N-terminal S4 RNA binding domain. Despite the conserved topology shared by RluC and RluD, the surface shape and charge distribution are very different. ; GO: 0003723 RNA binding, 0009982 pseudouridine synthase activity, 0001522 pseudouridine synthesis, 0009451 RNA modification; PDB: 2GML_A 3DH3_B 1VIO_A 2I82_B 1XPI_B 1V9K_B 1PRZ_A 1V9F_A 2IST_A 1QYU_A ....
Probab=99.40 E-value=1.7e-13 Score=115.22 Aligned_cols=58 Identities=22% Similarity=0.318 Sum_probs=37.8
Q ss_pred cEEEEECCCCCccCCCCCCccchHHHHHH---HHhCCCCCCccccCCCcccceeeeeeeeC
Q 023330 226 SHVVLDKPAGTSVGGTTDNIEESCATFAS---RALGLTTPLRTTHQIDNCTEGWYCYFTTL 283 (284)
Q Consensus 226 dLLVVNKPaGl~VHPt~~~~~~TL~~~l~---~~lg~~~pl~~VHRLDRdTSGLLlfAKT~ 283 (284)
|++|||||+||++|+........+..... ........+++|||||++||||||||+|.
T Consensus 1 ~~ivvnKP~G~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~RLD~~TsGlll~a~~~ 61 (164)
T PF00849_consen 1 NLIVVNKPAGVPVHPSDGNESKSVKELPALSLKRGDDPPELYPVHRLDRDTSGLLLFAKDK 61 (164)
T ss_dssp SEEEEEE-TTSBSSSSSTBSSSSHHCHHHHHHHHCTTSGGGEESS---TT-EEEEEEESSH
T ss_pred CEEEEECCCCCeEecCCCCCcccccchhhhhhhhccCCCceEECCCCCccccCCeeccCCc
Confidence 68999999999999988433333322222 22233456789999999999999999974
No 17
>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=99.38 E-value=5e-13 Score=115.60 Aligned_cols=55 Identities=16% Similarity=0.146 Sum_probs=44.3
Q ss_pred EEEEECCCCCccCCCCCCccchHHHHHHHHhCCCCCCccccCCCcccceeeeeeeeC
Q 023330 227 HVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQIDNCTEGWYCYFTTL 283 (284)
Q Consensus 227 LLVVNKPaGl~VHPt~~~~~~TL~~~l~~~lg~~~pl~~VHRLDRdTSGLLlfAKT~ 283 (284)
++|||||+||+||++. +...++.+.+..+... ..+++|||||++||||||||||.
T Consensus 2 ~ivvnKP~G~~~~~~~-~~~~tl~~~l~~~~~~-~~~~~vhRLD~~TSGlll~ak~~ 56 (167)
T cd02553 2 YLMLNKPAGVVCATKD-PHHPTVIDLLPEPDRR-RDLFPVGRLDKDTTGLLLLTNDG 56 (167)
T ss_pred EEEEECCCCCEeCCCC-CCCCcHHHHhhhhccc-CCeEEcccCCCCCEEEEEEEeCH
Confidence 6899999999999764 4568888877655432 24678999999999999999985
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=99.37 E-value=3.9e-13 Score=116.16 Aligned_cols=55 Identities=13% Similarity=0.111 Sum_probs=43.5
Q ss_pred EEEEECCCCCccCCCCCCccchHHHHHHHHhCCCCCCccccCCCcccceeeeeeeeC
Q 023330 227 HVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQIDNCTEGWYCYFTTL 283 (284)
Q Consensus 227 LLVVNKPaGl~VHPt~~~~~~TL~~~l~~~lg~~~pl~~VHRLDRdTSGLLlfAKT~ 283 (284)
++|+|||+|++||++......|+.+.+..+. ...+++|||||+||||||||||+.
T Consensus 2 ~lvvnKP~G~~~~~~~~~~~~tl~~~l~~~~--~~~~~~V~RLD~~TsGLll~ak~~ 56 (167)
T cd02556 2 VLIYHKPEGLICTRKDPKGRPTVFDLLPKLG--IPRWISVGRLDLNTEGLLLFTNDG 56 (167)
T ss_pred EEEEECCCCcEECccCCCCCccHHHhhhhhc--cCceEEcCcCCCCCeeEEEEECCH
Confidence 7899999999999966555677777664431 223568999999999999999985
No 19
>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=99.37 E-value=1.2e-13 Score=116.33 Aligned_cols=54 Identities=17% Similarity=0.140 Sum_probs=41.9
Q ss_pred EEEEECCCCCccCCCCCCccchHHHHHHHHhCCCCCCccccCCCcccceeeeeeeeC
Q 023330 227 HVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQIDNCTEGWYCYFTTL 283 (284)
Q Consensus 227 LLVVNKPaGl~VHPt~~~~~~TL~~~l~~~lg~~~pl~~VHRLDRdTSGLLlfAKT~ 283 (284)
++|||||+||++|++......++.+.+.. ....+.+|||||++|||||||||+.
T Consensus 1 ~ivvnKP~G~~~~~~~~~~~~~l~~~l~~---~~~~~~~vhRLD~~TsGlll~ak~~ 54 (146)
T cd02870 1 YLLLNKPRGVVSTVRDPEGRPTVLDLLKD---VGERLFPVGRLDYDTEGLLLLTNDG 54 (146)
T ss_pred CEEEECCCCcEecccCCCCCCEEeeeccc---cCCCEEECCCCCCCCeeEEEEeCCH
Confidence 58999999999999875555666554332 1234678999999999999999985
No 20
>COG1187 RsuA 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]
Probab=99.02 E-value=8e-10 Score=102.40 Aligned_cols=115 Identities=18% Similarity=0.120 Sum_probs=77.0
Q ss_pred CcHHHHHHHhcCCCHHHHHHHHHcCCEEEcCccCCCCCCCCchhhhhhcccCCcccccccccccCcchhhccccccccCc
Q 023330 110 GPVLEYICRELNLPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTFRITHV 189 (284)
Q Consensus 110 g~L~~~L~~~l~lSr~~i~~LI~~G~V~vng~~~~~p~~~~~~~~~~~~~~~~~~~~~kr~~~~Gk~vr~~~~~~r~~~~ 189 (284)
.+|++||++.---||..+++||..|.|.|||++ +...
T Consensus 3 ~RL~K~La~~G~~SRr~ae~lI~~G~V~VnG~v-------------------------------------------~~~~ 39 (248)
T COG1187 3 MRLNKFLAEAGVGSRREAEKLIEEGRVTVNGKV-------------------------------------------ATLG 39 (248)
T ss_pred cchHHHHHHcCCCCHHHHHHHHHcCCEEECCEE-------------------------------------------eccC
Confidence 478999987555899999999999999999962 0122
Q ss_pred CceecCCC-EEEEEcCCCCCCCCCCCCCCcceEE-eeCcEEEEECCCCCccCCCCCCccchHHHHHHHHhCCCCCCcccc
Q 023330 190 DQIVEAGT-YLRVHVHPKRFPRCYDIDWNSRIIA-VTESHVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTH 267 (284)
Q Consensus 190 ~~~L~~GD-~I~V~~~~~~~~~~~~~~~~l~ILY-EDedLLVVNKPaGl~VHPt~~~~~~TL~~~l~~~lg~~~pl~~VH 267 (284)
...+.+++ .|.+. .. .+.+ +..-++..|||.|+++.-.......|+..++-........+++|=
T Consensus 40 ~~~v~~~~~~i~v~--g~------------~~~~~~~~~y~llnKP~G~v~s~~D~~gr~tv~D~lp~~~~~~~~~~pvG 105 (248)
T COG1187 40 GVVVDPDDDVVEVD--GK------------RIELKEERVYLLLNKPRGYVSSTEDDEGRPTVFDLLPERLPRKKRLFPVG 105 (248)
T ss_pred CeEeCCCCcEEEEC--CE------------EeeccccceEEEEECCCCeEecccCCCCCceeeeecccccccccceeecc
Confidence 33555553 44442 11 1333 233399999999999987644445555554321111222378899
Q ss_pred CCCcccceeeeeee
Q 023330 268 QIDNCTEGWYCYFT 281 (284)
Q Consensus 268 RLDRdTSGLLlfAK 281 (284)
|||+||+||||+.-
T Consensus 106 RLD~dTeGLLLLTn 119 (248)
T COG1187 106 RLDKDTEGLLLLTN 119 (248)
T ss_pred ccCCCCeeEEEEeC
Confidence 99999999999863
No 21
>PRK11394 23S rRNA pseudouridine synthase E; Provisional
Probab=99.00 E-value=2.5e-10 Score=103.73 Aligned_cols=53 Identities=13% Similarity=0.149 Sum_probs=41.7
Q ss_pred cEEEEECCCCCccCCCCCCccchHHHHHHHHhCCCCCCccccCCCcccceeeeeeeeC
Q 023330 226 SHVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQIDNCTEGWYCYFTTL 283 (284)
Q Consensus 226 dLLVVNKPaGl~VHPt~~~~~~TL~~~l~~~lg~~~pl~~VHRLDRdTSGLLlfAKT~ 283 (284)
.++++|||+|+++|+.......++.+.+. ...+++|||||+|||||||||++.
T Consensus 40 ~ylllnKP~G~l~~~~d~~~~~tl~d~l~-----~~~~~~vgRLD~~TsGllLlt~d~ 92 (217)
T PRK11394 40 RVILFNKPYDVLPQFTDEAGRKTLKEFIP-----VQGVYAAGRLDRDSEGLLVLTNNG 92 (217)
T ss_pred EEEEEECCCCCEEeeCCccCCcchHHhcc-----cCCeEEecCCCCCCeeEEEEECCH
Confidence 58999999999999755444566666542 124678999999999999999974
No 22
>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=98.99 E-value=2.3e-09 Score=76.05 Aligned_cols=68 Identities=16% Similarity=0.132 Sum_probs=54.1
Q ss_pred cHHHHHHHhc-CCCHHHHHHHHHcCCEEEcCccCCCCCCCCchhhhhhcccCCcccccccccccCcchhhccccccccCc
Q 023330 111 PVLEYICREL-NLPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTFRITHV 189 (284)
Q Consensus 111 ~L~~~L~~~l-~lSr~~i~~LI~~G~V~vng~~~~~p~~~~~~~~~~~~~~~~~~~~~kr~~~~Gk~vr~~~~~~r~~~~ 189 (284)
+|++||.+.+ ..|++.++++|..|+|++||.. ++.+
T Consensus 2 rl~~~l~~~~~~~sr~~~~~~i~~g~V~vn~~~-------------------------------------------~~~~ 38 (70)
T cd00165 2 RLDKILARLGLAPSRSEARQLIKHGHVLVNGKV-------------------------------------------VTKP 38 (70)
T ss_pred cHHHHHHHhccccCHHHHHHHHHcCCEEECCEE-------------------------------------------ccCC
Confidence 5789998774 5899999999999999999851 1355
Q ss_pred CceecCCCEEEEEcCCCCCCCCCCCCCCcceEEeeCcEEEEE
Q 023330 190 DQIVEAGTYLRVHVHPKRFPRCYDIDWNSRIIAVTESHVVLD 231 (284)
Q Consensus 190 ~~~L~~GD~I~V~~~~~~~~~~~~~~~~l~ILYEDedLLVVN 231 (284)
++.+..||.|.+...+ ++.+|+|||++++|||
T Consensus 39 ~~~v~~~d~i~i~~~~----------~~~~i~~ed~~~lvv~ 70 (70)
T cd00165 39 SYKVKPGDVIEVDGKS----------IEEDIVYEDKKLLVVN 70 (70)
T ss_pred ccCcCCCCEEEEcCCC----------cccceeeccCCEEEeC
Confidence 6788999998886421 1128999999999997
No 23
>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=98.91 E-value=1e-09 Score=96.41 Aligned_cols=55 Identities=16% Similarity=0.180 Sum_probs=37.1
Q ss_pred cEEEEECCCCCccCCCC--------CCccchHHHHHHHHhCCCCCCccccCCCcccceeeeeeeeC
Q 023330 226 SHVVLDKPAGTSVGGTT--------DNIEESCATFASRALGLTTPLRTTHQIDNCTEGWYCYFTTL 283 (284)
Q Consensus 226 dLLVVNKPaGl~VHPt~--------~~~~~TL~~~l~~~lg~~~pl~~VHRLDRdTSGLLlfAKT~ 283 (284)
-++++|||+|+++.... .....+....+.... ..+++|||||+|||||||||++.
T Consensus 5 ~y~llnKP~G~l~s~~d~~~~~g~~~~~~~~~~~~l~~~~---~~l~~VgRLD~dTsGLLl~t~d~ 67 (177)
T cd02555 5 VTLLLHKPAGMVSEQALALLGPGQRSAADRSGRRPLKGHF---ARLAPIGPLDKDASGLLVFSQDG 67 (177)
T ss_pred EEEEEECCCceEecCCCcccccccccccccchhhhhhhcC---CceeEecCCCCCCeeEEEEECCH
Confidence 36899999999885432 112233333332222 24678999999999999999974
No 24
>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=98.18 E-value=4.7e-06 Score=60.58 Aligned_cols=31 Identities=3% Similarity=-0.212 Sum_probs=28.4
Q ss_pred CcHHHHHHHhcCC--CHHHHHHHHHcCCEEEcCc
Q 023330 110 GPVLEYICRELNL--PPLFVADLIHFGAVYYALV 141 (284)
Q Consensus 110 g~L~~~L~~~l~l--Sr~~i~~LI~~G~V~vng~ 141 (284)
.+|+.||++. ++ ||+.++.+|+.|.|++||.
T Consensus 9 ~rLd~~L~~~-~~~~SR~~~k~li~~G~V~VNg~ 41 (59)
T TIGR02988 9 ITLGQLLKEL-GIIDSGGQAKWFLQENEVLVNGE 41 (59)
T ss_pred HHHHHHHHHc-CCccCHHHHHHHHHcCCEEECCE
Confidence 5899999987 77 9999999999999999985
No 25
>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=97.91 E-value=2.8e-05 Score=53.80 Aligned_cols=31 Identities=19% Similarity=0.089 Sum_probs=27.2
Q ss_pred cHHHHHHHh-cCCCHHHHHHHHHcCCEEEcCc
Q 023330 111 PVLEYICRE-LNLPPLFVADLIHFGAVYYALV 141 (284)
Q Consensus 111 ~L~~~L~~~-l~lSr~~i~~LI~~G~V~vng~ 141 (284)
+|+.||.+. +..|+++++++|+.|.|+|||+
T Consensus 2 RLd~~L~~~~~~~sr~~a~~~I~~g~V~VNg~ 33 (48)
T PF01479_consen 2 RLDKFLSRLGLASSRSEARRLIKQGRVKVNGK 33 (48)
T ss_dssp BHHHHHHHTTSSSSHHHHHHHHHTTTEEETTE
T ss_pred CHHHHHHHcCCcCCHHHHHHhcCCCEEEECCE
Confidence 689999854 4578999999999999999985
No 26
>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=97.70 E-value=1.5e-05 Score=68.16 Aligned_cols=23 Identities=17% Similarity=0.105 Sum_probs=20.3
Q ss_pred CCCccccCCCcccceeeeeeeeC
Q 023330 261 TPLRTTHQIDNCTEGWYCYFTTL 283 (284)
Q Consensus 261 ~pl~~VHRLDRdTSGLLlfAKT~ 283 (284)
..+.+|||||++|||||||||+.
T Consensus 38 ~~~~~v~RLD~~tsGlll~ak~~ 60 (185)
T cd02869 38 FRPGLVHRLDKDTSGLLLVAKNK 60 (185)
T ss_pred CcCceecccCCCCceEEEEEcCH
Confidence 34678999999999999999974
No 27
>smart00363 S4 S4 RNA-binding domain.
Probab=97.38 E-value=0.00058 Score=46.66 Aligned_cols=31 Identities=19% Similarity=0.112 Sum_probs=27.0
Q ss_pred cHHHHHHHh-cCCCHHHHHHHHHcCCEEEcCc
Q 023330 111 PVLEYICRE-LNLPPLFVADLIHFGAVYYALV 141 (284)
Q Consensus 111 ~L~~~L~~~-l~lSr~~i~~LI~~G~V~vng~ 141 (284)
+++.||.+. +..|+..+++++..|.|++||.
T Consensus 2 rl~~~l~~~~~~~s~~~~~~~i~~g~i~vng~ 33 (60)
T smart00363 2 RLDKFLARLGLAPSRSQARKLIEQGRVKVNGK 33 (60)
T ss_pred cHHHHHHHcCcccCHHHHHHHHHcCCEEECCE
Confidence 578888876 3689999999999999999985
No 28
>COG1188 Ribosome-associated heat shock protein implicated in the recycling of the 50S subunit (S4 paralog) [Translation, ribosomal structure and biogenesis]
Probab=97.24 E-value=0.00079 Score=54.94 Aligned_cols=53 Identities=13% Similarity=0.100 Sum_probs=43.4
Q ss_pred CcHHHHHHH-hcCCCHHHHHHHHHcCCEEEcCccCCCCCCCCchhhhhhcccCCcccccccccccCcchhhccccccccC
Q 023330 110 GPVLEYICR-ELNLPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTFRITH 188 (284)
Q Consensus 110 g~L~~~L~~-~l~lSr~~i~~LI~~G~V~vng~~~~~p~~~~~~~~~~~~~~~~~~~~~kr~~~~Gk~vr~~~~~~r~~~ 188 (284)
.+||.||.- ++=-+|+.++++++.|.|++||.+ ++
T Consensus 9 mRLDKwL~~aR~~KrRslAk~~~~~GrV~vNG~~--------------------------------------------aK 44 (100)
T COG1188 9 MRLDKWLWAARFIKRRSLAKEMIEGGRVKVNGQR--------------------------------------------AK 44 (100)
T ss_pred eehHHHHHHHHHhhhHHHHHHHHHCCeEEECCEE--------------------------------------------cc
Confidence 589999953 344589999999999999999851 46
Q ss_pred cCceecCCCEEEEEcCCC
Q 023330 189 VDQIVEAGTYLRVHVHPK 206 (284)
Q Consensus 189 ~~~~L~~GD~I~V~~~~~ 206 (284)
+++.|+.||.|+|++...
T Consensus 45 pS~~VK~GD~l~i~~~~~ 62 (100)
T COG1188 45 PSKEVKVGDILTIRFGNK 62 (100)
T ss_pred cccccCCCCEEEEEeCCc
Confidence 778999999999997653
No 29
>PLN00051 RNA-binding S4 domain-containing protein; Provisional
Probab=96.99 E-value=0.0014 Score=61.57 Aligned_cols=50 Identities=16% Similarity=0.131 Sum_probs=44.3
Q ss_pred CcHHHHHHHhcCCCHHHHHHHHHcCCEEEcCccCCCCCCCCchhhhhhcccCCcccccccccccCcchhhccccccccCc
Q 023330 110 GPVLEYICRELNLPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTFRITHV 189 (284)
Q Consensus 110 g~L~~~L~~~l~lSr~~i~~LI~~G~V~vng~~~~~p~~~~~~~~~~~~~~~~~~~~~kr~~~~Gk~vr~~~~~~r~~~~ 189 (284)
.|||.+++..+++||++++++|+.|.|.+|+.. +.++
T Consensus 192 ~RLD~vla~~~~~SRsk~~~lI~~g~V~vN~~~-------------------------------------------v~~~ 228 (267)
T PLN00051 192 LRLDALASAGFRMSRSKLVDLISSGDVRVNWRE-------------------------------------------VTKN 228 (267)
T ss_pred ccHHHHHHHHhccCHHHHHHHHHcCcEEECCEE-------------------------------------------cCCC
Confidence 589999999999999999999999999999851 2467
Q ss_pred CceecCCCEEEEE
Q 023330 190 DQIVEAGTYLRVH 202 (284)
Q Consensus 190 ~~~L~~GD~I~V~ 202 (284)
++.|++||.|.|.
T Consensus 229 s~~v~~gD~isiR 241 (267)
T PLN00051 229 GTTLKTGDVVSVS 241 (267)
T ss_pred CCCCCCCCEEEEe
Confidence 7899999999886
No 30
>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=96.66 E-value=0.0034 Score=58.55 Aligned_cols=32 Identities=13% Similarity=0.038 Sum_probs=29.8
Q ss_pred CcHHHHHHHhcCCCHHHHHHHHHcCCEEEcCc
Q 023330 110 GPVLEYICRELNLPPLFVADLIHFGAVYYALV 141 (284)
Q Consensus 110 g~L~~~L~~~l~lSr~~i~~LI~~G~V~vng~ 141 (284)
.+||.+++..+++||+.+++||+.|.|.+||.
T Consensus 184 ~RLD~lls~~~~~SRs~a~~lI~~G~V~VNg~ 215 (257)
T TIGR03069 184 LRIDAIASAGFGLSRSKIVDQIKAGRLRLNWK 215 (257)
T ss_pred ccHHHHHHhhhhhhHHHHHHHHHCCeEEECCE
Confidence 58999998888999999999999999999985
No 31
>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=96.23 E-value=0.0091 Score=53.79 Aligned_cols=51 Identities=10% Similarity=0.085 Sum_probs=42.1
Q ss_pred CcHHHHHHHhc-CCCHHHHHHHHHcCCEEEcCccCCCCCCCCchhhhhhcccCCcccccccccccCcchhhccccccccC
Q 023330 110 GPVLEYICREL-NLPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTFRITH 188 (284)
Q Consensus 110 g~L~~~L~~~l-~lSr~~i~~LI~~G~V~vng~~~~~p~~~~~~~~~~~~~~~~~~~~~kr~~~~Gk~vr~~~~~~r~~~ 188 (284)
.+||.+|.+.. ..|+..++++|..|.|.|||. . +..
T Consensus 90 ~RLD~~L~~~g~~~SR~~ArqlI~~G~V~VNgk----------------------------------~---------v~~ 126 (200)
T TIGR01017 90 SRLDNVVYRLGFAPTRFAARQLVSHGHILVNGK----------------------------------K---------VDI 126 (200)
T ss_pred HHHHHHHHHcCCCCCHHHHHHHHHCCCEEECCE----------------------------------E---------eCC
Confidence 57899996543 679999999999999999985 1 246
Q ss_pred cCceecCCCEEEEEc
Q 023330 189 VDQIVEAGTYLRVHV 203 (284)
Q Consensus 189 ~~~~L~~GD~I~V~~ 203 (284)
+++.|++||.|+|.-
T Consensus 127 ps~~V~~GD~I~V~~ 141 (200)
T TIGR01017 127 PSYQVRPGDIISIKE 141 (200)
T ss_pred CCCCCCCCCEEEEee
Confidence 788999999999863
No 32
>PRK10348 ribosome-associated heat shock protein Hsp15; Provisional
Probab=96.00 E-value=0.018 Score=49.30 Aligned_cols=32 Identities=13% Similarity=0.129 Sum_probs=27.5
Q ss_pred CcHHHHHH-HhcCCCHHHHHHHHHcCCEEEcCc
Q 023330 110 GPVLEYIC-RELNLPPLFVADLIHFGAVYYALV 141 (284)
Q Consensus 110 g~L~~~L~-~~l~lSr~~i~~LI~~G~V~vng~ 141 (284)
.+||.||. ..|--+|+.++++|..|.|++||.
T Consensus 9 ~RlDk~L~~~rl~ktRs~A~~lI~~G~V~vnG~ 41 (133)
T PRK10348 9 VRLDKWLWAARFYKTRALAREMIEGGKVHYNGQ 41 (133)
T ss_pred ccHHHHHHHcCccccHHHHHHHHHCCCEEECCE
Confidence 48999985 345579999999999999999985
No 33
>CHL00113 rps4 ribosomal protein S4; Reviewed
Probab=95.89 E-value=0.016 Score=52.59 Aligned_cols=51 Identities=8% Similarity=-0.057 Sum_probs=41.9
Q ss_pred CcHHHHHHHhc-CCCHHHHHHHHHcCCEEEcCccCCCCCCCCchhhhhhcccCCcccccccccccCcchhhccccccccC
Q 023330 110 GPVLEYICREL-NLPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTFRITH 188 (284)
Q Consensus 110 g~L~~~L~~~l-~lSr~~i~~LI~~G~V~vng~~~~~p~~~~~~~~~~~~~~~~~~~~~kr~~~~Gk~vr~~~~~~r~~~ 188 (284)
.+||.+|.+.. ..|+..++++|..|.|+|||.. +..
T Consensus 89 ~RLD~~L~r~g~~~SR~~ArqlI~~G~V~VNGk~-------------------------------------------v~~ 125 (201)
T CHL00113 89 MRLDNILFRLGMAPTIPAARQLVNHGHILVNGRI-------------------------------------------VDI 125 (201)
T ss_pred HHHHHHHHHcCCCCCHHHHHHHHHCCcEEECCEE-------------------------------------------ecC
Confidence 47899997654 5799999999999999999851 246
Q ss_pred cCceecCCCEEEEEc
Q 023330 189 VDQIVEAGTYLRVHV 203 (284)
Q Consensus 189 ~~~~L~~GD~I~V~~ 203 (284)
+++.|++||.|+|.-
T Consensus 126 ps~~Vk~GD~I~V~~ 140 (201)
T CHL00113 126 PSYRCKPKDIITVKD 140 (201)
T ss_pred ccccCCCCCEEEEcc
Confidence 788999999999863
No 34
>PRK05327 rpsD 30S ribosomal protein S4; Validated
Probab=95.89 E-value=0.015 Score=52.57 Aligned_cols=32 Identities=9% Similarity=0.044 Sum_probs=27.1
Q ss_pred CcHHHHHHHh-cCCCHHHHHHHHHcCCEEEcCc
Q 023330 110 GPVLEYICRE-LNLPPLFVADLIHFGAVYYALV 141 (284)
Q Consensus 110 g~L~~~L~~~-l~lSr~~i~~LI~~G~V~vng~ 141 (284)
.+||.+|.+. +..|+..++++|..|.|+|||.
T Consensus 93 ~RLD~iL~~~g~~~SR~~arqlI~~G~V~VNgk 125 (203)
T PRK05327 93 SRLDNVVYRLGFAPTRRQARQLVSHGHILVNGK 125 (203)
T ss_pred HHHHHHHHHcCccCCHHHHHHHHHCCcEEECCE
Confidence 5788888643 4689999999999999999985
No 35
>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=95.75 E-value=0.017 Score=53.09 Aligned_cols=31 Identities=16% Similarity=-0.130 Sum_probs=27.2
Q ss_pred cHHHHHHHhc-CCCHHHHHHHHHcCCEEEcCc
Q 023330 111 PVLEYICREL-NLPPLFVADLIHFGAVYYALV 141 (284)
Q Consensus 111 ~L~~~L~~~l-~lSr~~i~~LI~~G~V~vng~ 141 (284)
+||.||.+.. ..||++++++|..|.|++||+
T Consensus 1 RLD~~L~~~g~~~SR~~a~~lI~~G~V~Vng~ 32 (228)
T TIGR00478 1 RLDILLVRRGLFESREKAKRLILKGFVLVNGK 32 (228)
T ss_pred CHHHHHHHcCCccHHHHHHHHHHCCcEEECCE
Confidence 5889988765 578999999999999999985
No 36
>COG2302 Uncharacterized conserved protein, contains S4-like domain [Function unknown]
Probab=95.64 E-value=0.017 Score=54.10 Aligned_cols=50 Identities=16% Similarity=0.149 Sum_probs=44.4
Q ss_pred CcHHHHHHHhcCCCHHHHHHHHHcCCEEEcCccCCCCCCCCchhhhhhcccCCcccccccccccCcchhhccccccccCc
Q 023330 110 GPVLEYICRELNLPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTFRITHV 189 (284)
Q Consensus 110 g~L~~~L~~~l~lSr~~i~~LI~~G~V~vng~~~~~p~~~~~~~~~~~~~~~~~~~~~kr~~~~Gk~vr~~~~~~r~~~~ 189 (284)
-|||..+++.+++||++++++|+.|.|.||+. . +.++
T Consensus 181 lRLD~vis~~~~~SR~~a~~lIe~g~VkVN~k----------------------------------~---------v~~~ 217 (257)
T COG2302 181 LRLDVVISEGFGLSRAKAQQLIEKGKVKVNWK----------------------------------V---------VDKA 217 (257)
T ss_pred hhHHHHHHHHHhhhHHHHHHHHHcCceEEeeE----------------------------------E---------eccc
Confidence 58999999999999999999999999999974 1 2467
Q ss_pred CceecCCCEEEEE
Q 023330 190 DQIVEAGTYLRVH 202 (284)
Q Consensus 190 ~~~L~~GD~I~V~ 202 (284)
++.|+.||.|.+.
T Consensus 218 s~~v~~GDliSir 230 (257)
T COG2302 218 SYEVQEGDLISIR 230 (257)
T ss_pred cceeccCCEEEEe
Confidence 8999999999886
No 37
>PRK00020 truB tRNA pseudouridine synthase B; Provisional
Probab=95.55 E-value=0.017 Score=53.86 Aligned_cols=49 Identities=22% Similarity=0.304 Sum_probs=39.9
Q ss_pred CcEEEEECCCCCccCCCCCCccchHHHHHHHHhCCCCCCccccCCCcccceeeeeeee
Q 023330 225 ESHVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQIDNCTEGWYCYFTT 282 (284)
Q Consensus 225 edLLVVNKPaGl~VHPt~~~~~~TL~~~l~~~lg~~~pl~~VHRLDRdTSGLLlfAKT 282 (284)
+.+++||||.||.+|- +++.+.+.++...- ....-||-..||||+++-.
T Consensus 10 ~Gil~vdKP~G~TS~d--------vv~~vkr~~~~kKv-GH~GTLDP~AtGvLiv~iG 58 (244)
T PRK00020 10 DGVLLLDKPVGLSSNH--------ALQRAKRTVDAAKA-GHTGTLDPFATGLLVCCMG 58 (244)
T ss_pred CeEEEEecCCCCCHHH--------HHHHHHHHhCCCCC-CcCCcCCCcCeeEEEEEEC
Confidence 3699999999999874 56667777776654 4489999999999999864
No 38
>PRK05033 truB tRNA pseudouridine synthase B; Provisional
Probab=95.11 E-value=0.029 Score=54.07 Aligned_cols=49 Identities=20% Similarity=0.233 Sum_probs=39.4
Q ss_pred CcEEEEECCCCCccCCCCCCccchHHHHHHHHhCCCCCCccccCCCcccceeeeeeee
Q 023330 225 ESHVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQIDNCTEGWYCYFTT 282 (284)
Q Consensus 225 edLLVVNKPaGl~VHPt~~~~~~TL~~~l~~~lg~~~pl~~VHRLDRdTSGLLlfAKT 282 (284)
+.+++||||.||.+|- +++.+.+.++... +....-||-..||||+++-.
T Consensus 10 ~Gil~i~KP~G~TS~d--------vv~~vrr~l~~kK-vGH~GTLDP~AtGvL~v~vG 58 (312)
T PRK05033 10 NGVLLLDKPQGMSSND--------ALQKVKRLFNANK-AGHTGALDPLATGMLPICLG 58 (312)
T ss_pred CeEEEEeCCCCCCHHH--------HHHHHHHHhCCCC-CCCCCcCCCcCeeEEEEEEC
Confidence 4799999999999884 5566777777654 34489999999999999854
No 39
>PRK05389 truB tRNA pseudouridine synthase B; Provisional
Probab=95.08 E-value=0.028 Score=53.98 Aligned_cols=49 Identities=16% Similarity=0.182 Sum_probs=39.6
Q ss_pred CcEEEEECCCCCccCCCCCCccchHHHHHHHHhCCCCCCccccCCCcccceeeeeeee
Q 023330 225 ESHVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQIDNCTEGWYCYFTT 282 (284)
Q Consensus 225 edLLVVNKPaGl~VHPt~~~~~~TL~~~l~~~lg~~~pl~~VHRLDRdTSGLLlfAKT 282 (284)
+.+|+||||.||.+|- +++.+.+.++... +....-||-..||||+++-.
T Consensus 13 ~Gil~i~KP~G~TS~d--------vv~~vrk~~~~kK-vGH~GTLDP~AtGvL~v~vG 61 (305)
T PRK05389 13 SGWLILDKPAGMTSTE--------AVSKVKWLFDAQK-AGHAGTLDPLASGVLPIALG 61 (305)
T ss_pred CeEEEEeCCCCCCHHH--------HHHHHHHHhcccc-cCCcccCCCCCceEEEEEEC
Confidence 4799999999999874 5666777777654 34489999999999999854
No 40
>PRK04270 H/ACA RNA-protein complex component Cbf5p; Reviewed
Probab=94.82 E-value=0.034 Score=53.01 Aligned_cols=50 Identities=22% Similarity=0.216 Sum_probs=39.8
Q ss_pred eCcEEEEECCCCCccCCCCCCccchHHHHHHHHhCCCCCCccccCCCcccceeeeeeee
Q 023330 224 TESHVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQIDNCTEGWYCYFTT 282 (284)
Q Consensus 224 DedLLVVNKPaGl~VHPt~~~~~~TL~~~l~~~lg~~~pl~~VHRLDRdTSGLLlfAKT 282 (284)
-+.+|+||||.||.+|- +++.+.+.++... +....-||-..||+|+++-.
T Consensus 21 ~~g~l~i~Kp~g~tS~~--------~v~~~r~~~~~kk-vGH~GTLDp~A~GvL~v~~g 70 (300)
T PRK04270 21 KFGVVNLDKPPGPTSHE--------VAAWVRDILGVEK-AGHGGTLDPKVTGVLPVALG 70 (300)
T ss_pred CCCEEEEECCCCCCHHH--------HHHHHHHHhcccc-ccCCCCCCCcCeEEEEEEEC
Confidence 35799999999999874 5566777776554 44599999999999999864
No 41
>PRK01851 truB tRNA pseudouridine synthase B; Provisional
Probab=94.33 E-value=0.058 Score=51.84 Aligned_cols=49 Identities=24% Similarity=0.253 Sum_probs=39.2
Q ss_pred CcEEEEECCCCCccCCCCCCccchHHHHHHHHhCCCCCCccccCCCcccceeeeeeee
Q 023330 225 ESHVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQIDNCTEGWYCYFTT 282 (284)
Q Consensus 225 edLLVVNKPaGl~VHPt~~~~~~TL~~~l~~~lg~~~pl~~VHRLDRdTSGLLlfAKT 282 (284)
+.+++||||.||.+|- +++.+.+.++... +...--||-..||||+++-.
T Consensus 16 ~Gil~i~KP~G~TS~d--------vv~~vrr~l~~kK-vGH~GTLDP~AtGvL~v~vG 64 (303)
T PRK01851 16 DGVLLLDKPLGLSSND--------ALQRAKRLLRAKK-AGHTGTLDPLATGLLPLCFG 64 (303)
T ss_pred CeEEEEeCCCCCCHHH--------HHHHHHHHhCccc-CCCCCCCCCCCceEEEEEEC
Confidence 4799999999999874 5666777777654 33478999999999999854
No 42
>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=94.07 E-value=0.036 Score=47.99 Aligned_cols=27 Identities=15% Similarity=0.281 Sum_probs=20.8
Q ss_pred EEEEECCCCCccCCCCC-CccchHHHHH
Q 023330 227 HVVLDKPAGTSVGGTTD-NIEESCATFA 253 (284)
Q Consensus 227 LLVVNKPaGl~VHPt~~-~~~~TL~~~l 253 (284)
++|+|||+|++||++.. ....++.+.+
T Consensus 1 ~lv~nKP~G~~~~~~~~~~~~~~l~~~l 28 (168)
T cd02566 1 LILFNKPYGVLSQFTDESEKHKTLKDYI 28 (168)
T ss_pred CEEEECCCCCEEecCCCcCCCccHHHHc
Confidence 58999999999998764 4456776655
No 43
>COG0522 RpsD Ribosomal protein S4 and related proteins [Translation, ribosomal structure and biogenesis]
Probab=94.00 E-value=0.096 Score=47.73 Aligned_cols=51 Identities=14% Similarity=0.151 Sum_probs=39.8
Q ss_pred cHHHHHHHh-cCCCHHHHHHHHHcCCEEEcCccCCCCCCCCchhhhhhcccCCcccccccccccCcchhhccccccccCc
Q 023330 111 PVLEYICRE-LNLPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTFRITHV 189 (284)
Q Consensus 111 ~L~~~L~~~-l~lSr~~i~~LI~~G~V~vng~~~~~p~~~~~~~~~~~~~~~~~~~~~kr~~~~Gk~vr~~~~~~r~~~~ 189 (284)
+|+..+.+. |.-|+.++.+||..|.|.|||+ +|..+
T Consensus 95 RLd~vVyR~GfA~T~~qARQlV~HGHI~VnGk-------------------------------------------~V~iP 131 (205)
T COG0522 95 RLDNVVYRLGFAKTRRQARQLVSHGHILVNGK-------------------------------------------RVNIP 131 (205)
T ss_pred HHHHHHHHhcccccHHHHHHHhhcceEEECCE-------------------------------------------EeccC
Confidence 455555432 3468889999999999999985 24688
Q ss_pred CceecCCCEEEEEcC
Q 023330 190 DQIVEAGTYLRVHVH 204 (284)
Q Consensus 190 ~~~L~~GD~I~V~~~ 204 (284)
++.|++||++.|..-
T Consensus 132 Sy~V~~gdei~V~~k 146 (205)
T COG0522 132 SYLVSPGDEISVREK 146 (205)
T ss_pred cEEecCCCEEEeeec
Confidence 999999999999854
No 44
>PRK04642 truB tRNA pseudouridine synthase B; Provisional
Probab=92.30 E-value=0.19 Score=48.38 Aligned_cols=49 Identities=27% Similarity=0.280 Sum_probs=39.1
Q ss_pred CcEEEEECCCCCccCCCCCCccchHHHHHHHHhCCCCCCccccCCCcccceeeeeeee
Q 023330 225 ESHVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQIDNCTEGWYCYFTT 282 (284)
Q Consensus 225 edLLVVNKPaGl~VHPt~~~~~~TL~~~l~~~lg~~~pl~~VHRLDRdTSGLLlfAKT 282 (284)
+.+++||||.||.+|- +++.+.+.++...- ...-=||-..||+|+++-.
T Consensus 10 ~Gil~i~KP~G~TS~d--------vv~~vrr~~~~kKv-GH~GTLDP~AtGvL~v~~G 58 (300)
T PRK04642 10 DGILLLDKPAGLSSNN--------ALQAARRLLRAEKG-GHTGSLDPLATGLLPLCFG 58 (300)
T ss_pred CeEEEEecCCCCCHHH--------HHHHHHHHhCCCcc-cCCCccCCcCeeeEEEEEC
Confidence 4799999999999874 56777777776543 3377899999999999854
No 45
>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=92.28 E-value=0.19 Score=48.53 Aligned_cols=49 Identities=22% Similarity=0.236 Sum_probs=38.4
Q ss_pred CcEEEEECCCCCccCCCCCCccchHHHHHHHHhCCCCCCccccCCCcccceeeeeeee
Q 023330 225 ESHVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQIDNCTEGWYCYFTT 282 (284)
Q Consensus 225 edLLVVNKPaGl~VHPt~~~~~~TL~~~l~~~lg~~~pl~~VHRLDRdTSGLLlfAKT 282 (284)
+.+|+||||.||.+|- +++.+.+.++... +...-=||-..+|||+++-.
T Consensus 34 ~G~l~i~KP~g~tS~~--------~v~~vr~~~~~kk-vGH~GTLDP~A~GvL~v~~G 82 (322)
T TIGR00425 34 YGVVNLDKPSGPSSHE--------VVAWVRRILNVEK-TGHGGTLDPKVTGVLPVCIE 82 (322)
T ss_pred CCEEEEeCCCCCCHHH--------HHHHHHHHhcccc-cCCCCCCCCCCceEEEEEEC
Confidence 4799999999999874 5566777776554 33477899999999999854
No 46
>COG1189 Predicted rRNA methylase [Translation, ribosomal structure and biogenesis]
Probab=92.26 E-value=0.24 Score=46.39 Aligned_cols=32 Identities=16% Similarity=-0.032 Sum_probs=28.1
Q ss_pred CcHHHHHHHh-cCCCHHHHHHHHHcCCEEEcCc
Q 023330 110 GPVLEYICRE-LNLPPLFVADLIHFGAVYYALV 141 (284)
Q Consensus 110 g~L~~~L~~~-l~lSr~~i~~LI~~G~V~vng~ 141 (284)
.|||.+|.++ +--||++++++|..|.|++||.
T Consensus 3 ~RLD~~Lv~rgl~~sR~~A~~~I~~G~V~Vng~ 35 (245)
T COG1189 3 MRLDALLVERGLFESREKAKELILAGNVLVNGE 35 (245)
T ss_pred chHHHHHHHccchhhHHHHHHHHHcCeEEECCE
Confidence 4789999876 4579999999999999999985
No 47
>COG0130 TruB Pseudouridine synthase [Translation, ribosomal structure and biogenesis]
Probab=90.18 E-value=0.34 Score=45.93 Aligned_cols=48 Identities=21% Similarity=0.290 Sum_probs=39.1
Q ss_pred cEEEEECCCCCccCCCCCCccchHHHHHHHHhCCCCCCccccCCCcccceeeeeeee
Q 023330 226 SHVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQIDNCTEGWYCYFTT 282 (284)
Q Consensus 226 dLLVVNKPaGl~VHPt~~~~~~TL~~~l~~~lg~~~pl~~VHRLDRdTSGLLlfAKT 282 (284)
.++++|||.|+.+|- ++..+.+.++...-.+ .--||-..||+|++|-.
T Consensus 16 Gil~ldKP~G~tS~~--------~v~~vkkil~~~K~GH-~GTLDP~atGvLpi~ig 63 (271)
T COG0130 16 GVINLDKPPGPTSHE--------VVAWVKRILGVEKAGH-GGTLDPLATGVLPICLG 63 (271)
T ss_pred ceEEeeCCCCCCHHH--------HHHHHHHHhCcccccc-ccccCCcccceEEEEec
Confidence 899999999999874 5667778887665444 77899999999999853
No 48
>PF14451 Ub-Mut7C: Mut7-C ubiquitin
Probab=88.96 E-value=1.2 Score=34.87 Aligned_cols=68 Identities=21% Similarity=0.254 Sum_probs=43.8
Q ss_pred CCCccccccCCCCCCCCceEEEeeCCCCcHHHHHHHhcCCCHHHHHHHHHcCCEEEcCccCCCCCCCCchhhhhhcccCC
Q 023330 83 YPEYHRLLPCPSQNCPPRVEHLVVSEGGPVLEYICRELNLPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTD 162 (284)
Q Consensus 83 ~~~~~~~~~~~~~~~~~rv~~~vv~~~g~L~~~L~~~l~lSr~~i~~LI~~G~V~vng~~~~~p~~~~~~~~~~~~~~~~ 162 (284)
|++.+..+|-.... ..+. ....+..++.+.+ +.+|+|...+ |.|.+||+
T Consensus 9 ~~~L~~flp~~~r~--~~~~-~~~~~~~tvkd~I-EsLGVP~tEV------~~i~vNG~--------------------- 57 (81)
T PF14451_consen 9 YAELNDFLPPERRG--GPFT-HPFDGGATVKDVI-ESLGVPHTEV------GLILVNGR--------------------- 57 (81)
T ss_pred chHHhhhcChhhcC--CceE-EecCCCCcHHHHH-HHcCCChHHe------EEEEECCE---------------------
Confidence 45555566643322 1122 2233345777755 6799998654 78999985
Q ss_pred cccccccccccCcchhhccccccccCcCceecCCCEEEEEcC
Q 023330 163 PSVLSKRSSIKGKTVREAQKTFRITHVDQIVEAGTYLRVHVH 204 (284)
Q Consensus 163 ~~~~~kr~~~~Gk~vr~~~~~~r~~~~~~~L~~GD~I~V~~~ 204 (284)
. ...++.++.||.|.|+..
T Consensus 58 -------------~----------v~~~~~~~~Gd~v~V~P~ 76 (81)
T PF14451_consen 58 -------------P----------VDFDYRLKDGDRVAVYPV 76 (81)
T ss_pred -------------E----------CCCcccCCCCCEEEEEec
Confidence 1 366889999999999853
No 49
>PRK11507 ribosome-associated protein; Provisional
Probab=88.43 E-value=1.2 Score=34.21 Aligned_cols=31 Identities=10% Similarity=-0.182 Sum_probs=24.9
Q ss_pred CcHHHHHHHhcC--CCHHHHHHHHHcCCEEEcCc
Q 023330 110 GPVLEYICRELN--LPPLFVADLIHFGAVYYALV 141 (284)
Q Consensus 110 g~L~~~L~~~l~--lSr~~i~~LI~~G~V~vng~ 141 (284)
-.|+.||+- .+ -|=..++.+|..|.|.+||+
T Consensus 12 I~L~QlLK~-~~~v~SGG~AK~~I~eg~V~VNGe 44 (70)
T PRK11507 12 VELCDLLKL-EGWSESGAQAKIAIAEGQVKVDGA 44 (70)
T ss_pred EEHHHHHhh-hCcccChHHHHHHHHcCceEECCE
Confidence 478888863 34 36669999999999999996
No 50
>COG2501 S4-like RNA binding protein [Replication, recombination, and repair]
Probab=87.35 E-value=1.7 Score=33.75 Aligned_cols=35 Identities=14% Similarity=-0.130 Sum_probs=26.4
Q ss_pred eCCCCcHHHHHHHhcCC--CHHHHHHHHHcCCEEEcCc
Q 023330 106 VSEGGPVLEYICRELNL--PPLFVADLIHFGAVYYALV 141 (284)
Q Consensus 106 v~~~g~L~~~L~~~l~l--Sr~~i~~LI~~G~V~vng~ 141 (284)
..+.-.|.+||+ ..++ |=.+++..|..|.|++||+
T Consensus 8 ~~e~I~L~qlLK-~~g~i~sGG~AK~~i~eg~V~vNGe 44 (73)
T COG2501 8 KTEFITLGQLLK-LAGLIESGGQAKAFIAEGEVKVNGE 44 (73)
T ss_pred ccceEEHHHHHH-HhCcccCcHHHHHHHHCCeEEECCe
Confidence 333357888886 3553 5559999999999999996
No 51
>PF06353 DUF1062: Protein of unknown function (DUF1062); InterPro: IPR009412 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=86.91 E-value=1.9 Score=37.32 Aligned_cols=62 Identities=16% Similarity=0.151 Sum_probs=44.4
Q ss_pred CCCCCCCccccccCCCCCCC-CceE-EEeeCCC--CcHHHHHHHhcCCCHHHHHHHHHcCCEEEcC
Q 023330 79 SSYGYPEYHRLLPCPSQNCP-PRVE-HLVVSEG--GPVLEYICRELNLPPLFVADLIHFGAVYYAL 140 (284)
Q Consensus 79 ~~~~~~~~~~~~~~~~~~~~-~rv~-~~vv~~~--g~L~~~L~~~l~lSr~~i~~LI~~G~V~vng 140 (284)
...++|+|.=....+..... ..++ ++..+.. -+++..|++.|++|++.+++|+..|.|..+.
T Consensus 68 ~~~~~~~~~v~~~~~~~~~~~~~~~v~i~~~~~~~~Rld~lLa~~L~lSrs~l~~l~~~G~I~~~~ 133 (142)
T PF06353_consen 68 ELDEFPEYDVEKRLDTEDDDWADIEVEIRFPFPFPLRLDRLLARQLGLSRSRLKRLIEQGLIRSDP 133 (142)
T ss_pred eeCCCCceEEEEEeccCCccccceEEEEEeCCCCCccHHHHHHHHhCcCHHHHHHHHHCCCEEecC
Confidence 34478888766554443322 2244 3333333 4899999999999999999999999999884
No 52
>PRK04051 rps4p 30S ribosomal protein S4P; Validated
Probab=83.00 E-value=2.6 Score=37.74 Aligned_cols=31 Identities=16% Similarity=0.139 Sum_probs=24.1
Q ss_pred cHHHHHHH-hcCCCHHHHHHHHHcCCEEEcCc
Q 023330 111 PVLEYICR-ELNLPPLFVADLIHFGAVYYALV 141 (284)
Q Consensus 111 ~L~~~L~~-~l~lSr~~i~~LI~~G~V~vng~ 141 (284)
+|+.+|.+ .|--|+.++++||..|.|.|||.
T Consensus 104 RLd~il~r~gla~S~~~Ar~lI~hGhV~V~g~ 135 (177)
T PRK04051 104 RLQTIVYRKGLARTPKQARQFIVHGHIAVNGR 135 (177)
T ss_pred HHHHHHHHccCcCCHHHHHHHHHcCCEEECCE
Confidence 56665543 23478999999999999999985
No 53
>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=81.93 E-value=1.4 Score=38.59 Aligned_cols=27 Identities=19% Similarity=0.298 Sum_probs=20.6
Q ss_pred EEEEECCCCCccCCCCCCccchHHHHHH
Q 023330 227 HVVLDKPAGTSVGGTTDNIEESCATFAS 254 (284)
Q Consensus 227 LLVVNKPaGl~VHPt~~~~~~TL~~~l~ 254 (284)
++++|||+|++++++.. ...++.+++.
T Consensus 2 y~~lnKP~G~l~s~~~~-~~~tv~~~l~ 28 (164)
T cd02554 2 YIAYNKPVGIDCTLERA-DEDNIIDFVN 28 (164)
T ss_pred EEEEECCCCcEeecCCC-CCCcHHHHhc
Confidence 68999999999998754 3467766553
No 54
>PLN00189 40S ribosomal protein S9; Provisional
Probab=78.21 E-value=4.8 Score=36.65 Aligned_cols=41 Identities=7% Similarity=-0.056 Sum_probs=34.5
Q ss_pred CCHHHHHHHHHcCCEEEcCccCCCCCCCCchhhhhhcccCCcccccccccccCcchhhccccccccCcCceecCCCEEEE
Q 023330 122 LPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTFRITHVDQIVEAGTYLRV 201 (284)
Q Consensus 122 lSr~~i~~LI~~G~V~vng~~~~~p~~~~~~~~~~~~~~~~~~~~~kr~~~~Gk~vr~~~~~~r~~~~~~~L~~GD~I~V 201 (284)
-|...+.++|..|.|.|||. +|+.+++.|..||++.|
T Consensus 122 ~si~~ARqlI~hgHI~V~~~-------------------------------------------~V~~Ps~~V~~~~e~~I 158 (194)
T PLN00189 122 KSIHHARVLIRQRHIRVGKQ-------------------------------------------IVNVPSFMVRVDSQKHI 158 (194)
T ss_pred CCHHHHHHheeCCCEeECCE-------------------------------------------EEecCcEEEecCCEEEE
Confidence 47778999999999999985 24688899999999999
Q ss_pred EcCC
Q 023330 202 HVHP 205 (284)
Q Consensus 202 ~~~~ 205 (284)
.+.+
T Consensus 159 tw~~ 162 (194)
T PLN00189 159 DFSL 162 (194)
T ss_pred EEec
Confidence 8754
No 55
>COG4332 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=78.02 E-value=5.6 Score=36.13 Aligned_cols=64 Identities=20% Similarity=0.219 Sum_probs=43.1
Q ss_pred CCCCCCCCCccccccCCCCCCCCc-eE-EEeeCCC--CcHHHHHHHhcCCCHHHHHHHHHcCCEEEcC
Q 023330 77 TPSSYGYPEYHRLLPCPSQNCPPR-VE-HLVVSEG--GPVLEYICRELNLPPLFVADLIHFGAVYYAL 140 (284)
Q Consensus 77 ~~~~~~~~~~~~~~~~~~~~~~~r-v~-~~vv~~~--g~L~~~L~~~l~lSr~~i~~LI~~G~V~vng 140 (284)
..-.+++|.++--...-.+...-+ +| ++.++.. -+|+..|+++|++|++.++.|+..|.|..+.
T Consensus 102 ~~r~~g~pd~~i~krilge~~~~~~vel~l~~~~p~qlrl~~Ll~seL~LSrS~lq~lie~g~Irgdt 169 (203)
T COG4332 102 NARLSGFPDFHIQKRILGEIASHAAVELSLRISRPFQLRLDRLLASELGLSRSELQRLIETGQIRGDT 169 (203)
T ss_pred cccccCCCchhhhhheecCcccceeEEEEEcccCcchhHHHHHHHHHhCcCHHHHHHHHHcCceeecc
Confidence 344578887654433212221212 44 4445444 3799999999999999999999999998773
No 56
>PF13275 S4_2: S4 domain; PDB: 1P9K_A.
Probab=76.33 E-value=0.75 Score=34.83 Aligned_cols=31 Identities=16% Similarity=-0.093 Sum_probs=22.6
Q ss_pred CcHHHHHHHhcCC--CHHHHHHHHHcCCEEEcCc
Q 023330 110 GPVLEYICRELNL--PPLFVADLIHFGAVYYALV 141 (284)
Q Consensus 110 g~L~~~L~~~l~l--Sr~~i~~LI~~G~V~vng~ 141 (284)
-.|..||+. .++ |=..++.+|..|.|.+||+
T Consensus 8 I~L~qlLK~-~glv~sGGeAK~~I~~g~V~VNGe 40 (65)
T PF13275_consen 8 ITLGQLLKL-AGLVSSGGEAKALIQEGEVKVNGE 40 (65)
T ss_dssp --HHHHHHH-HTS-SSSSTTSHHHHHHHHEETTB
T ss_pred EEHHHHHhH-cCCcccHHHHHHHHHcCceEECCE
Confidence 468888863 342 4448889999999999996
No 57
>PRK01777 hypothetical protein; Validated
Probab=71.85 E-value=7 Score=31.48 Aligned_cols=57 Identities=18% Similarity=0.125 Sum_probs=38.3
Q ss_pred EEEeeCCCCcHHHHHHHhcCCCHHHHHHHHHcCCEEEcCccCCCCCCCCchhhhhhcccCCcccccccccccCcchhhcc
Q 023330 102 EHLVVSEGGPVLEYICRELNLPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQ 181 (284)
Q Consensus 102 ~~~vv~~~g~L~~~L~~~l~lSr~~i~~LI~~G~V~vng~~~~~p~~~~~~~~~~~~~~~~~~~~~kr~~~~Gk~vr~~~ 181 (284)
..+.++++.++.+.|. .+|+...+-.--+..+.|-|||+ .
T Consensus 19 ~~l~vp~GtTv~dal~-~sgi~~~~pei~~~~~~vgI~Gk----------------------------------~----- 58 (95)
T PRK01777 19 QRLTLQEGATVEEAIR-ASGLLELRTDIDLAKNKVGIYSR----------------------------------P----- 58 (95)
T ss_pred EEEEcCCCCcHHHHHH-HcCCCccCcccccccceEEEeCe----------------------------------E-----
Confidence 3445566668888775 47876662221234577888874 1
Q ss_pred ccccccCcCceecCCCEEEEEc
Q 023330 182 KTFRITHVDQIVEAGTYLRVHV 203 (284)
Q Consensus 182 ~~~r~~~~~~~L~~GD~I~V~~ 203 (284)
...++.|+.||.|+|+.
T Consensus 59 -----v~~d~~L~dGDRVeIyr 75 (95)
T PRK01777 59 -----AKLTDVLRDGDRVEIYR 75 (95)
T ss_pred -----CCCCCcCCCCCEEEEec
Confidence 35678999999999985
No 58
>PRK04313 30S ribosomal protein S4e; Validated
Probab=62.27 E-value=21 Score=33.52 Aligned_cols=31 Identities=19% Similarity=0.105 Sum_probs=27.0
Q ss_pred cHHHHHHHhcC--CCHHHHHHHHHcCCEEEcCc
Q 023330 111 PVLEYICRELN--LPPLFVADLIHFGAVYYALV 141 (284)
Q Consensus 111 ~L~~~L~~~l~--lSr~~i~~LI~~G~V~vng~ 141 (284)
+|.-+|.+.|+ .+...++..+.+|.|.|||+
T Consensus 39 PL~iiLRd~L~yA~t~rEak~Il~~~~V~VDGk 71 (237)
T PRK04313 39 PLLVVLRDVLGYADTAREAKKIINEGKVLVDGR 71 (237)
T ss_pred ccHHHHHhHhhhhccHHHHHHHHhCCcEEECCE
Confidence 67778888776 68889999999999999996
No 59
>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=58.05 E-value=6.7 Score=30.05 Aligned_cols=19 Identities=5% Similarity=-0.226 Sum_probs=16.5
Q ss_pred CCccccCCCcccceeeeee
Q 023330 262 PLRTTHQIDNCTEGWYCYF 280 (284)
Q Consensus 262 pl~~VHRLDRdTSGLLlfA 280 (284)
.+....++|+.++|+++++
T Consensus 25 ~i~~aG~kDk~a~t~q~v~ 43 (87)
T cd01291 25 RVGYAGRKDKRAVTTQLVS 43 (87)
T ss_pred eEEECccCCCCeeEEEEEc
Confidence 3556999999999999987
No 60
>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=55.62 E-value=6.4 Score=35.07 Aligned_cols=16 Identities=38% Similarity=0.478 Sum_probs=14.2
Q ss_pred CcEEEEECCCCCccCC
Q 023330 225 ESHVVLDKPAGTSVGG 240 (284)
Q Consensus 225 edLLVVNKPaGl~VHP 240 (284)
+.+++||||.||.+|-
T Consensus 2 ~g~l~i~Kp~g~tS~~ 17 (182)
T cd02572 2 YGVINLDKPSGPSSHE 17 (182)
T ss_pred CeEEEEecCCCCCHHH
Confidence 3699999999999985
No 61
>PLN00036 40S ribosomal protein S4; Provisional
Probab=55.54 E-value=31 Score=32.80 Aligned_cols=31 Identities=19% Similarity=0.083 Sum_probs=26.7
Q ss_pred cHHHHHHHhcC--CCHHHHHHHHHcCCEEEcCc
Q 023330 111 PVLEYICRELN--LPPLFVADLIHFGAVYYALV 141 (284)
Q Consensus 111 ~L~~~L~~~l~--lSr~~i~~LI~~G~V~vng~ 141 (284)
+|.-+|.+.|+ .+...++..+.+|.|.|||+
T Consensus 43 PL~i~LRd~LkyA~t~rEak~Il~~~~V~VDGk 75 (261)
T PLN00036 43 PLLLILRNRLKYALTYREVQAILMQRHVKVDGK 75 (261)
T ss_pred ccHHHHHhHhhhhccHHHHHHHHhCCeEEECCE
Confidence 57788888887 56779999999999999996
No 62
>PTZ00223 40S ribosomal protein S4; Provisional
Probab=55.04 E-value=31 Score=33.02 Aligned_cols=31 Identities=23% Similarity=0.173 Sum_probs=26.7
Q ss_pred cHHHHHHHhcC--CCHHHHHHHHHcCCEEEcCc
Q 023330 111 PVLEYICRELN--LPPLFVADLIHFGAVYYALV 141 (284)
Q Consensus 111 ~L~~~L~~~l~--lSr~~i~~LI~~G~V~vng~ 141 (284)
+|.-+|.+.|+ .+...++..+..|.|.|||+
T Consensus 40 PL~iiLRd~LkyA~t~rEak~Il~~~~V~VDGk 72 (273)
T PTZ00223 40 PLLIIIRNRLKYALNAREAQMILRQGLVCVDGK 72 (273)
T ss_pred ccHHHHHHHhhhhccHHHHHHHHhCCeEEECCE
Confidence 67788888887 56779999999999999996
No 63
>TIGR01018 rpsD_arch ribosomal protein S4(archaeal type)/S9(eukaryote cytosolic type). This model finds eukaryotic ribosomal protein S9 as well as archaeal ribosomal protein S4.
Probab=51.13 E-value=26 Score=31.04 Aligned_cols=20 Identities=15% Similarity=-0.064 Sum_probs=17.9
Q ss_pred CCHHHHHHHHHcCCEEEcCc
Q 023330 122 LPPLFVADLIHFGAVYYALV 141 (284)
Q Consensus 122 lSr~~i~~LI~~G~V~vng~ 141 (284)
-|..++.++|..|.|.||++
T Consensus 117 ~s~~~ArqlI~hgHI~V~~~ 136 (162)
T TIGR01018 117 RTIHQARQLIVHGHIAVDGR 136 (162)
T ss_pred CCHHHHHHHhhCCCeeECCE
Confidence 57789999999999999985
No 64
>PRK04099 truB tRNA pseudouridine synthase B; Provisional
Probab=50.68 E-value=8.3 Score=36.74 Aligned_cols=16 Identities=38% Similarity=0.513 Sum_probs=14.2
Q ss_pred CcEEEEECCCCCccCC
Q 023330 225 ESHVVLDKPAGTSVGG 240 (284)
Q Consensus 225 edLLVVNKPaGl~VHP 240 (284)
+.+++||||+||.+|-
T Consensus 2 ngil~vdKP~g~tS~~ 17 (273)
T PRK04099 2 NRLFVANKPAGMSSNA 17 (273)
T ss_pred CeEEEEeCCCCCCHHH
Confidence 3689999999999995
No 65
>PTZ00118 40S ribosomal protein S4; Provisional
Probab=50.68 E-value=40 Score=32.13 Aligned_cols=31 Identities=16% Similarity=-0.001 Sum_probs=26.6
Q ss_pred cHHHHHHHhcC--CCHHHHHHHHHcCCEEEcCc
Q 023330 111 PVLEYICRELN--LPPLFVADLIHFGAVYYALV 141 (284)
Q Consensus 111 ~L~~~L~~~l~--lSr~~i~~LI~~G~V~vng~ 141 (284)
+|.-+|.+.|+ .+...++..+.+|.|.|||+
T Consensus 43 PL~i~LRd~LkyA~t~rEak~Il~~~~V~VDGk 75 (262)
T PTZ00118 43 PLVILLRNRLKYALTYDEVKLIVIQKIVKVDGK 75 (262)
T ss_pred ccHHHHHhhhhhhccHHHHHHHHHCCcEEECCE
Confidence 57778888886 67779999999999999996
No 66
>KOG2559 consensus Predicted pseudouridine synthase [Translation, ribosomal structure and biogenesis]
Probab=49.63 E-value=7.6 Score=37.03 Aligned_cols=19 Identities=16% Similarity=0.221 Sum_probs=16.8
Q ss_pred CccccCCCcccceeeeeee
Q 023330 263 LRTTHQIDNCTEGWYCYFT 281 (284)
Q Consensus 263 l~~VHRLDRdTSGLLlfAK 281 (284)
+.++||||-.|||+++|+-
T Consensus 91 V~v~h~l~~~~sgvl~~gV 109 (318)
T KOG2559|consen 91 VQVVHVLPLATSGVLLFGV 109 (318)
T ss_pred eeeEEeecccccceEEEec
Confidence 5579999999999999874
No 67
>PRK02484 truB tRNA pseudouridine synthase B; Provisional
Probab=49.46 E-value=8.9 Score=36.82 Aligned_cols=16 Identities=25% Similarity=0.310 Sum_probs=14.2
Q ss_pred CcEEEEECCCCCccCC
Q 023330 225 ESHVVLDKPAGTSVGG 240 (284)
Q Consensus 225 edLLVVNKPaGl~VHP 240 (284)
+.+++||||.||.+|-
T Consensus 3 ~Gil~i~KP~G~TS~d 18 (294)
T PRK02484 3 NGIINLKKEAGMTSHD 18 (294)
T ss_pred ceEEEEeCCCCCCHHH
Confidence 3689999999999985
No 68
>PRK01550 truB tRNA pseudouridine synthase B; Provisional
Probab=48.25 E-value=9.6 Score=36.77 Aligned_cols=16 Identities=25% Similarity=0.474 Sum_probs=14.1
Q ss_pred CcEEEEECCCCCccCC
Q 023330 225 ESHVVLDKPAGTSVGG 240 (284)
Q Consensus 225 edLLVVNKPaGl~VHP 240 (284)
+.+++||||.||.+|-
T Consensus 2 ~Gil~i~KP~G~TS~d 17 (304)
T PRK01550 2 NGVLLLHKPRGMTSHD 17 (304)
T ss_pred CeEEEEECCCCCCHHH
Confidence 3689999999999985
No 69
>PRK00130 truB tRNA pseudouridine synthase B; Provisional
Probab=46.68 E-value=11 Score=36.26 Aligned_cols=16 Identities=19% Similarity=0.248 Sum_probs=14.1
Q ss_pred CcEEEEECCCCCccCC
Q 023330 225 ESHVVLDKPAGTSVGG 240 (284)
Q Consensus 225 edLLVVNKPaGl~VHP 240 (284)
+.+|+||||.||.+|-
T Consensus 2 ~Gil~i~KP~G~tS~d 17 (290)
T PRK00130 2 DGILNILKPPGMTSFD 17 (290)
T ss_pred CeEEEEeCCCCCCHHH
Confidence 3689999999999985
No 70
>PRK01528 truB tRNA pseudouridine synthase B; Provisional
Probab=46.38 E-value=11 Score=36.32 Aligned_cols=16 Identities=25% Similarity=0.306 Sum_probs=14.3
Q ss_pred CcEEEEECCCCCccCC
Q 023330 225 ESHVVLDKPAGTSVGG 240 (284)
Q Consensus 225 edLLVVNKPaGl~VHP 240 (284)
+.+|+||||.||.+|-
T Consensus 3 ~GiL~i~KP~G~TS~d 18 (292)
T PRK01528 3 NYWLNIYKPRGISSAK 18 (292)
T ss_pred CEEEEEeCCCCCCHHH
Confidence 4799999999999985
No 71
>PRK02755 truB tRNA pseudouridine synthase B; Provisional
Probab=45.56 E-value=11 Score=36.25 Aligned_cols=16 Identities=38% Similarity=0.468 Sum_probs=14.2
Q ss_pred CcEEEEECCCCCccCC
Q 023330 225 ESHVVLDKPAGTSVGG 240 (284)
Q Consensus 225 edLLVVNKPaGl~VHP 240 (284)
+.+++||||.||.+|-
T Consensus 3 ~Gil~i~KP~G~TS~d 18 (295)
T PRK02755 3 FGFLNLDKPAGLTSHD 18 (295)
T ss_pred ceEEEEeCCCCCCHHH
Confidence 3689999999999995
No 72
>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=45.54 E-value=11 Score=34.41 Aligned_cols=15 Identities=33% Similarity=0.505 Sum_probs=13.6
Q ss_pred cEEEEECCCCCccCC
Q 023330 226 SHVVLDKPAGTSVGG 240 (284)
Q Consensus 226 dLLVVNKPaGl~VHP 240 (284)
.+++||||.||.+|-
T Consensus 3 G~l~v~KP~g~tS~~ 17 (209)
T TIGR00431 3 GVLLLDKPQGMTSFD 17 (209)
T ss_pred eEEEEECCCCCCHHH
Confidence 689999999999885
No 73
>PRK14123 tRNA pseudouridine synthase B; Provisional
Probab=44.57 E-value=12 Score=36.18 Aligned_cols=16 Identities=13% Similarity=0.100 Sum_probs=14.2
Q ss_pred CcEEEEECCCCCccCC
Q 023330 225 ESHVVLDKPAGTSVGG 240 (284)
Q Consensus 225 edLLVVNKPaGl~VHP 240 (284)
+.+|+||||.||.+|-
T Consensus 3 ~Gil~i~KP~G~TS~d 18 (305)
T PRK14123 3 NGILPVYKERGLTSHD 18 (305)
T ss_pred ceEEEEeCCCCCCHHH
Confidence 3689999999999985
No 74
>PRK03287 truB tRNA pseudouridine synthase B; Provisional
Probab=43.94 E-value=12 Score=35.98 Aligned_cols=16 Identities=44% Similarity=0.634 Sum_probs=14.3
Q ss_pred CcEEEEECCCCCccCC
Q 023330 225 ESHVVLDKPAGTSVGG 240 (284)
Q Consensus 225 edLLVVNKPaGl~VHP 240 (284)
+.+++||||.||.+|-
T Consensus 9 ~Gil~i~KP~G~TS~d 24 (298)
T PRK03287 9 SGLVVVDKPAGMTSHD 24 (298)
T ss_pred CeEEEEeCCCCCCHHH
Confidence 4799999999999985
No 75
>PRK14124 tRNA pseudouridine synthase B; Provisional
Probab=43.25 E-value=13 Score=36.04 Aligned_cols=16 Identities=25% Similarity=0.380 Sum_probs=14.1
Q ss_pred CcEEEEECCCCCccCC
Q 023330 225 ESHVVLDKPAGTSVGG 240 (284)
Q Consensus 225 edLLVVNKPaGl~VHP 240 (284)
+.+++||||.||.+|-
T Consensus 3 ~Gil~i~KP~G~TS~d 18 (308)
T PRK14124 3 HGFLVAYKPKGPTSHD 18 (308)
T ss_pred ceEEEEECCCCCCHHH
Confidence 3689999999999985
No 76
>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=42.97 E-value=10 Score=28.35 Aligned_cols=18 Identities=28% Similarity=0.445 Sum_probs=13.1
Q ss_pred EeeCcEEEEECCCCCccC
Q 023330 222 AVTESHVVLDKPAGTSVG 239 (284)
Q Consensus 222 YEDedLLVVNKPaGl~VH 239 (284)
|-...+|++|||+|-.+|
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 345789999999998776
No 77
>PRK08364 sulfur carrier protein ThiS; Provisional
Probab=41.94 E-value=71 Score=23.71 Aligned_cols=15 Identities=33% Similarity=0.474 Sum_probs=12.4
Q ss_pred CcCceecCCCEEEEE
Q 023330 188 HVDQIVEAGTYLRVH 202 (284)
Q Consensus 188 ~~~~~L~~GD~I~V~ 202 (284)
..++.|+.||.|++.
T Consensus 50 ~~~~~l~~gD~Veii 64 (70)
T PRK08364 50 LEDDPVKDGDYVEVI 64 (70)
T ss_pred CCCcCcCCCCEEEEE
Confidence 446789999999986
No 78
>PTZ00155 40S ribosomal protein S9; Provisional
Probab=41.91 E-value=27 Score=31.43 Aligned_cols=20 Identities=10% Similarity=-0.137 Sum_probs=17.5
Q ss_pred CCHHHHHHHHHcCCEEEcCc
Q 023330 122 LPPLFVADLIHFGAVYYALV 141 (284)
Q Consensus 122 lSr~~i~~LI~~G~V~vng~ 141 (284)
-+...+.++|..|.|.|||.
T Consensus 120 ~ti~~ARqlI~HGHI~V~~~ 139 (181)
T PTZ00155 120 KSIHHARVLIRQRHIRVGKQ 139 (181)
T ss_pred CCHHHhhhheeCCCEEECCE
Confidence 46778899999999999985
No 79
>PRK00989 truB tRNA pseudouridine synthase B; Provisional
Probab=40.90 E-value=15 Score=34.27 Aligned_cols=15 Identities=27% Similarity=0.468 Sum_probs=13.7
Q ss_pred cEEEEECCCCCccCC
Q 023330 226 SHVVLDKPAGTSVGG 240 (284)
Q Consensus 226 dLLVVNKPaGl~VHP 240 (284)
.+++||||.||.+|-
T Consensus 10 G~l~i~KP~g~TS~d 24 (230)
T PRK00989 10 GILLVDKPQGRTSFS 24 (230)
T ss_pred EEEEEeCCCCCCHHH
Confidence 699999999999985
No 80
>PRK14846 truB tRNA pseudouridine synthase B; Provisional
Probab=40.21 E-value=15 Score=36.22 Aligned_cols=16 Identities=25% Similarity=0.308 Sum_probs=14.3
Q ss_pred CcEEEEECCCCCccCC
Q 023330 225 ESHVVLDKPAGTSVGG 240 (284)
Q Consensus 225 edLLVVNKPaGl~VHP 240 (284)
+.+|+||||.||.+|-
T Consensus 3 nGiL~idKP~G~TS~d 18 (345)
T PRK14846 3 NYWLNIYKPRGISSAQ 18 (345)
T ss_pred CeEEEEeCCCCCCHHH
Confidence 4799999999999985
No 81
>PRK05912 tyrosyl-tRNA synthetase; Validated
Probab=38.84 E-value=76 Score=31.64 Aligned_cols=32 Identities=19% Similarity=0.038 Sum_probs=26.0
Q ss_pred CcHHHHHHHh-cCCCHHHHHHHHHcCCEEEcCc
Q 023330 110 GPVLEYICRE-LNLPPLFVADLIHFGAVYYALV 141 (284)
Q Consensus 110 g~L~~~L~~~-l~lSr~~i~~LI~~G~V~vng~ 141 (284)
..+.+.|.+. +--|++.++++|+.|+|++||+
T Consensus 343 ~~~~~~l~~~~~~~S~~earr~i~~g~v~in~~ 375 (408)
T PRK05912 343 IDLLALLVEAGLVPSKSEARRLIKQGGVKINGE 375 (408)
T ss_pred CcHHHHHHHhCCCCCHHHHHHHHHcCCEEECCE
Confidence 4677777543 3479999999999999999986
No 82
>PRK13354 tyrosyl-tRNA synthetase; Provisional
Probab=38.40 E-value=40 Score=33.67 Aligned_cols=32 Identities=16% Similarity=0.089 Sum_probs=25.8
Q ss_pred CcHHHHHHHh-cCCCHHHHHHHHHcCCEEEcCc
Q 023330 110 GPVLEYICRE-LNLPPLFVADLIHFGAVYYALV 141 (284)
Q Consensus 110 g~L~~~L~~~-l~lSr~~i~~LI~~G~V~vng~ 141 (284)
..+.+.|.+. +--|++.+++||..|+|++||+
T Consensus 343 ~~~~~~l~~~~~~~S~~earrli~~ggv~in~~ 375 (410)
T PRK13354 343 KNLVDLLVDLGLEPSKREARRLIQNGAIKINGE 375 (410)
T ss_pred CCHHHHHHHhCCCCCHHHHHHHHHcCCEEECCE
Confidence 4677776542 3479999999999999999986
No 83
>PRK14122 tRNA pseudouridine synthase B; Provisional
Probab=38.38 E-value=16 Score=35.40 Aligned_cols=15 Identities=27% Similarity=0.401 Sum_probs=13.4
Q ss_pred cEEEEECCCCCccCC
Q 023330 226 SHVVLDKPAGTSVGG 240 (284)
Q Consensus 226 dLLVVNKPaGl~VHP 240 (284)
-+++||||.||.+|-
T Consensus 2 ~il~idKP~G~TS~d 16 (312)
T PRK14122 2 PVYAVDKPLGLTSHD 16 (312)
T ss_pred cEEEEECCCCCCHHH
Confidence 379999999999985
No 84
>PRK06437 hypothetical protein; Provisional
Probab=37.99 E-value=77 Score=23.49 Aligned_cols=16 Identities=13% Similarity=-0.022 Sum_probs=12.8
Q ss_pred CcCceecCCCEEEEEc
Q 023330 188 HVDQIVEAGTYLRVHV 203 (284)
Q Consensus 188 ~~~~~L~~GD~I~V~~ 203 (284)
..++.|+.||.|+|..
T Consensus 47 ~~~~~L~dgD~Veiv~ 62 (67)
T PRK06437 47 LEDHNVKKEDDVLILE 62 (67)
T ss_pred CCceEcCCCCEEEEEe
Confidence 3567999999999863
No 85
>PF11969 DcpS_C: Scavenger mRNA decapping enzyme C-term binding; PDB: 1VLR_B 1XMM_D 1XML_B 1ST0_A 3BLA_B 3BL9_B 3BL7_B 1ST4_B 1XQU_B.
Probab=37.82 E-value=23 Score=28.87 Aligned_cols=15 Identities=20% Similarity=0.406 Sum_probs=13.0
Q ss_pred CcceEEeeCcEEEEE
Q 023330 217 NSRIIAVTESHVVLD 231 (284)
Q Consensus 217 ~l~ILYEDedLLVVN 231 (284)
+.+|||||++++|+.
T Consensus 13 ~~~vly~d~~~v~~~ 27 (116)
T PF11969_consen 13 PERVLYEDDDFVVFK 27 (116)
T ss_dssp GGGESEEETSEEEEE
T ss_pred CCcEEEEeCCEEEee
Confidence 458999999999986
No 86
>cd00754 MoaD Ubiquitin domain of MoaD-like proteins. MoaD family. Members of this family are involved in biosynthesis of the molybdenum cofactor (Moco), an essential cofactor of a diverse group of redox enzymes. Moco biosynthesis is an evolutionarily conserved pathway present in eubacteria, archaea and eukaryotes. Moco contains a tricyclic pyranopterin, termed molybdopterin (MPT), that contains the cis-dithiolene group responsible for molybdenum ligation. This dithiolene group is generated by MPT synthase, the second major step in Moco biosynthesis. MPT synthase consists of a large (MoeE) and small (MoaD) subunit. The small subunit is inserted into the lare subunit to form the active site. The small subunit, which is structurally similar to ubiquitin, contains a C-terminal thiocarboxylated glycine residue that serves as a sulfur donor for the synthesis of the MPT dithiolene group.
Probab=37.71 E-value=1.2e+02 Score=22.14 Aligned_cols=15 Identities=13% Similarity=0.242 Sum_probs=12.1
Q ss_pred cCceecCCCEEEEEc
Q 023330 189 VDQIVEAGTYLRVHV 203 (284)
Q Consensus 189 ~~~~L~~GD~I~V~~ 203 (284)
.+..|+.||.|.|..
T Consensus 61 ~~~~l~~gD~v~i~p 75 (80)
T cd00754 61 LDTPLKDGDEVAIIP 75 (80)
T ss_pred CCcccCCCCEEEEeC
Confidence 456899999998863
No 87
>TIGR01764 excise DNA binding domain, excisionase family. An excisionase, or Xis protein, is a small protein that binds and promotes excisive recombination; it is not enzymatically active. This model represents a number of putative excisionases and related proteins from temperate phage, plasmids, and transposons, as well as DNA binding domains of other proteins, such as a DNA modification methylase. This model identifies mostly small proteins and N-terminal regions of large proteins, but some proteins appear to have two copies. This domain appears similar, in both sequence and predicted secondary structure (PSIPRED) to the MerR family of transcriptional regulators (pfam00376).
Probab=34.98 E-value=39 Score=21.96 Aligned_cols=21 Identities=29% Similarity=0.265 Sum_probs=18.2
Q ss_pred HHHhcCCCHHHHHHHHHcCCE
Q 023330 116 ICRELNLPPLFVADLIHFGAV 136 (284)
Q Consensus 116 L~~~l~lSr~~i~~LI~~G~V 136 (284)
+++.+|+|+..+.++++.|.+
T Consensus 7 ~a~~lgis~~ti~~~~~~g~i 27 (49)
T TIGR01764 7 AAEYLGVSKDTVYRLIHEGEL 27 (49)
T ss_pred HHHHHCCCHHHHHHHHHcCCC
Confidence 567889999999999998863
No 88
>PF04225 OapA: Opacity-associated protein A LysM-like domain; InterPro: IPR007340 This entry includes the Haemophilus influenzae opacity-associated protein. This protein is required for efficient nasopharyngeal mucosal colonization, and its expression is associated with a distinctive transparent colony phenotype. OapA is thought to be a secreted protein, and its expression exhibits high-frequency phase variation [].; PDB: 2GU1_A.
Probab=33.11 E-value=73 Score=24.88 Aligned_cols=31 Identities=10% Similarity=0.093 Sum_probs=18.0
Q ss_pred EEeeCCCCcHHHHHHHhcCCCHHHHHHHHHcC
Q 023330 103 HLVVSEGGPVLEYICRELNLPPLFVADLIHFG 134 (284)
Q Consensus 103 ~~vv~~~g~L~~~L~~~l~lSr~~i~~LI~~G 134 (284)
.++|..+.+|...+. .+|+|.+.+.+++...
T Consensus 4 ~~~V~~GDtLs~iF~-~~gls~~dl~~v~~~~ 34 (85)
T PF04225_consen 4 EYTVKSGDTLSTIFR-RAGLSASDLYAVLEAD 34 (85)
T ss_dssp EEE--TT--HHHHHH-HTT--HHHHHHHHHHG
T ss_pred EEEECCCCcHHHHHH-HcCCCHHHHHHHHhcc
Confidence 455555567766554 5799999999999843
No 89
>PF06633 DUF1155: Protein of unknown function (DUF1155); InterPro: IPR009536 This family consists of several Cucumber mosaic virus ORF IIB proteins. The function of this family is unknown.
Probab=26.97 E-value=29 Score=23.94 Aligned_cols=34 Identities=24% Similarity=0.178 Sum_probs=27.3
Q ss_pred CcccCcchhHHHhhhccccccccccccccceeeecc
Q 023330 14 GRSLGAPVSLLRTLASTHASCHRNIYKSNVVLSFSS 49 (284)
Q Consensus 14 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 49 (284)
-++|-+|.+|++-...--+..-.++.||. ++|.+
T Consensus 8 ~~sfepplslla~pg~wfa~t~df~k~~~--~~~~~ 41 (42)
T PF06633_consen 8 TLSFEPPLSLLAEPGTWFADTMDFRKKHS--VRWYS 41 (42)
T ss_pred eeccCCchHHHcCCCchhhhhhhhhhhhh--ccccc
Confidence 58999999999887776677777777888 77754
No 90
>PF03658 Ub-RnfH: RnfH family Ubiquitin; InterPro: IPR005346 This is a small family of proteins of unknown function.; PDB: 2HJ1_B.
Probab=26.03 E-value=49 Score=26.30 Aligned_cols=18 Identities=11% Similarity=0.314 Sum_probs=9.8
Q ss_pred cCcCceecCCCEEEEEcC
Q 023330 187 THVDQIVEAGTYLRVHVH 204 (284)
Q Consensus 187 ~~~~~~L~~GD~I~V~~~ 204 (284)
.+.++.|+.||.|+|+.+
T Consensus 56 ~~~d~~L~~GDRVEIYRP 73 (84)
T PF03658_consen 56 VKLDTVLRDGDRVEIYRP 73 (84)
T ss_dssp --TT-B--TT-EEEEE-S
T ss_pred cCCCCcCCCCCEEEEecc
Confidence 467889999999999953
No 91
>cd04762 HTH_MerR-trunc Helix-Turn-Helix DNA binding domain of truncated MerR-like proteins. Proteins in this family mostly have a truncated helix-turn-helix (HTH) MerR-like domain. They lack a portion of the C-terminal region, called Wing 2 and the long dimerization helix that is typically present in MerR-like proteins. These truncated domains are found in response regulator receiver (REC) domain proteins (i.e., CheY), cytosine-C5 specific DNA methylases, IS607 transposase-like proteins, and RacA, a bacterial protein that anchors chromosomes to cell poles.
Probab=25.17 E-value=73 Score=20.38 Aligned_cols=21 Identities=14% Similarity=0.243 Sum_probs=18.6
Q ss_pred HHHhcCCCHHHHHHHHHcCCE
Q 023330 116 ICRELNLPPLFVADLIHFGAV 136 (284)
Q Consensus 116 L~~~l~lSr~~i~~LI~~G~V 136 (284)
+++.+++|+..+..+++.|.+
T Consensus 6 ~a~~lgvs~~tl~~~~~~g~~ 26 (49)
T cd04762 6 AAELLGVSPSTLRRWVKEGKL 26 (49)
T ss_pred HHHHHCcCHHHHHHHHHcCCC
Confidence 567889999999999999875
No 92
>PF01230 HIT: HIT domain; InterPro: IPR001310 The Histidine Triad (HIT) motif, His-x-His-x-His-x-x (x, a hydrophobic amino acid) was identified as being highly conserved in a variety of organisms []. Crystal structure of rabbit Hint, purified as an adenosine and AMP-binding protein, showed that proteins in the HIT superfamily are conserved as nucleotide-binding proteins and that Hint homologues, which are found in all forms of life, are structurally related to Fhit homologues and GalT-related enzymes, which have more restricted phylogenetic profiles []. Hint homologues including rabbit Hint and yeast Hnt1 hydrolyse adenosine 5' monophosphoramide substrates such as AMP-NH2 and AMP-lysine to AMP plus the amine product and function as positive regulators of Cdk7/Kin28 in vivo []. Fhit homologues are diadenosine polyphosphate hydrolases [] and function as tumour suppressors in human and mouse [] though the tumour suppressing function of Fhit does not depend on ApppA hydrolysis []. The third branch of the HIT superfamily, which includes GalT homologues, contains a related His-X-His-X-Gln motif and transfers nucleoside monophosphate moieties to phosphorylated second substrates rather than hydrolysing them [].; PDB: 3LB5_B 1EMS_A 1Y23_A 3ANO_B 1KPE_B 1KPC_A 4EQE_B 1KPA_A 1KPB_B 4EQG_B ....
Probab=25.16 E-value=52 Score=25.30 Aligned_cols=20 Identities=15% Similarity=0.185 Sum_probs=12.7
Q ss_pred CcceEEeeCcEEEE-ECCCCC
Q 023330 217 NSRIIAVTESHVVL-DKPAGT 236 (284)
Q Consensus 217 ~l~ILYEDedLLVV-NKPaGl 236 (284)
+-+||||||+++|+ |+-+-.
T Consensus 5 ~~~vv~e~~~~~~~~~~~p~~ 25 (98)
T PF01230_consen 5 PARVVYEDDHFVAFLDIFPIS 25 (98)
T ss_dssp HCEEEEE-SSEEEEEESSTSS
T ss_pred CeeEEEECCCEEEEEcCCCCC
Confidence 45899999987754 554433
No 93
>PF12728 HTH_17: Helix-turn-helix domain
Probab=23.22 E-value=79 Score=21.43 Aligned_cols=21 Identities=19% Similarity=0.180 Sum_probs=18.4
Q ss_pred HHHhcCCCHHHHHHHHHcCCE
Q 023330 116 ICRELNLPPLFVADLIHFGAV 136 (284)
Q Consensus 116 L~~~l~lSr~~i~~LI~~G~V 136 (284)
+++.+++|+..+.++++.|.+
T Consensus 7 ~a~~l~is~~tv~~~~~~g~i 27 (51)
T PF12728_consen 7 AAELLGISRSTVYRWIRQGKI 27 (51)
T ss_pred HHHHHCcCHHHHHHHHHcCCC
Confidence 567789999999999998865
No 94
>PF14839 DOR: DOR family
Probab=22.11 E-value=54 Score=30.40 Aligned_cols=18 Identities=11% Similarity=0.178 Sum_probs=14.4
Q ss_pred EeeCcEEEEECCCCCccC
Q 023330 222 AVTESHVVLDKPAGTSVG 239 (284)
Q Consensus 222 YEDedLLVVNKPaGl~VH 239 (284)
.|||+||+||++.|+...
T Consensus 4 ~edD~WilVD~~~~~~~~ 21 (216)
T PF14839_consen 4 EEDDEWILVDFIDGLPRS 21 (216)
T ss_pred cccCCeEEEEecCCCccc
Confidence 379999999999965443
No 95
>PRK10687 purine nucleoside phosphoramidase; Provisional
Probab=21.91 E-value=78 Score=26.05 Aligned_cols=14 Identities=21% Similarity=0.145 Sum_probs=11.2
Q ss_pred CcceEEeeCcEEEE
Q 023330 217 NSRIIAVTESHVVL 230 (284)
Q Consensus 217 ~l~ILYEDedLLVV 230 (284)
+..+|||||+++++
T Consensus 16 p~~~v~edd~~~af 29 (119)
T PRK10687 16 PSDIVYQDELVTAF 29 (119)
T ss_pred CCCEEEECCCEEEE
Confidence 45799999988665
No 96
>cd00565 ThiS ThiaminS ubiquitin-like sulfur carrier protein. ThiS (ThiaminS) is a sulfur carrier protein involved in thiamin biosynthesis in bacteria. The ThiS fold, like those of two closely related proteins MoaD and Urm1, is similar to that of ubiquitin although there is little or no sequence similarity.
Probab=21.86 E-value=1.5e+02 Score=21.36 Aligned_cols=15 Identities=7% Similarity=0.231 Sum_probs=11.9
Q ss_pred cCceecCCCEEEEEc
Q 023330 189 VDQIVEAGTYLRVHV 203 (284)
Q Consensus 189 ~~~~L~~GD~I~V~~ 203 (284)
.++.|+.||.|.+..
T Consensus 46 ~~~~L~~gD~V~ii~ 60 (65)
T cd00565 46 ASTPLQDGDRIEIVT 60 (65)
T ss_pred CceecCCCCEEEEEE
Confidence 346899999999863
No 97
>TIGR02675 tape_meas_nterm tape measure domain. Proteins containing this domain are strictly bacterial, including bacteriophage and prophage regions of bacterial genomes. Most members are 800 to 1800 amino acids long, making them among the longest predicted proteins of their respective phage genomes, where they are encoded in tail protein regions. This roughly 80-residue domain described here usually begins between residue 100 and 250. Many members are known or predicted to act as phage tail tape measure proteins, a minor tail component that regulates tail length.
Probab=20.62 E-value=1.1e+02 Score=23.15 Aligned_cols=29 Identities=7% Similarity=0.118 Sum_probs=25.3
Q ss_pred cHHHHHHHhcCCCHHHHHHHHHcCCEEEc
Q 023330 111 PVLEYICRELNLPPLFVADLIHFGAVYYA 139 (284)
Q Consensus 111 ~L~~~L~~~l~lSr~~i~~LI~~G~V~vn 139 (284)
.+.+.|++.+|++...+++++..|.|..+
T Consensus 45 ~~~~~lAk~~G~t~~~l~~~~~~Gkit~~ 73 (75)
T TIGR02675 45 GALQALAKAMGVTRGELRKMLSDGKLTAD 73 (75)
T ss_pred HHHHHHHHHhCCCHHHHHHHHHCCCCccc
Confidence 36788999999999999999999998643
No 98
>PF13348 Y_phosphatase3C: Tyrosine phosphatase family C-terminal region; PDB: 1YWF_A 2OZ5_B.
Probab=20.58 E-value=1.2e+02 Score=21.83 Aligned_cols=23 Identities=30% Similarity=0.388 Sum_probs=17.5
Q ss_pred CcHHHHHHHhcCCCHHHHHHHHH
Q 023330 110 GPVLEYICRELNLPPLFVADLIH 132 (284)
Q Consensus 110 g~L~~~L~~~l~lSr~~i~~LI~ 132 (284)
|.+..||.+.+|++...+.+|.+
T Consensus 43 Gs~e~Yl~~~lgl~~~~i~~Lr~ 65 (68)
T PF13348_consen 43 GSVENYLREELGLSEEDIERLRE 65 (68)
T ss_dssp SSHHHHHHHT-T--HHHHHHHHH
T ss_pred CCHHHHHHHcCCCCHHHHHHHHH
Confidence 78999999999999999998764
Done!