Query 018538
Match_columns 354
No_of_seqs 267 out of 1610
Neff 5.8
Searched_HMMs 46136
Date Fri Mar 29 09:51:18 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/018538.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/018538hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG0564 RluA Pseudouridylate s 100.0 1.4E-35 3.1E-40 286.2 22.4 168 111-323 14-186 (289)
2 TIGR00005 rluA_subfam pseudour 100.0 3.7E-32 7.9E-37 262.1 21.6 169 111-322 7-181 (299)
3 PRK11180 rluD 23S rRNA pseudou 100.0 6.4E-32 1.4E-36 264.3 22.5 169 111-322 19-192 (325)
4 PRK11025 23S rRNA pseudouridyl 100.0 7.7E-32 1.7E-36 263.0 21.3 167 111-322 21-198 (317)
5 cd02558 PSRA_1 PSRA_1: Pseudou 99.9 6.4E-27 1.4E-31 221.0 16.6 128 188-319 12-142 (246)
6 cd02557 PseudoU_synth_ScRIB2 P 99.9 1.8E-24 3.8E-29 200.2 15.7 108 216-324 14-123 (213)
7 PRK10839 16S rRNA pseudouridyl 99.9 5.3E-25 1.1E-29 205.7 11.5 140 111-311 2-141 (232)
8 PRK10475 23S rRNA pseudouridin 99.9 1.9E-24 4.2E-29 208.9 14.2 140 111-312 8-147 (290)
9 PRK10700 23S rRNA pseudouridyl 99.9 1E-23 2.2E-28 203.9 15.8 143 111-311 4-149 (289)
10 TIGR01621 RluA-like pseudourid 99.9 9.8E-24 2.1E-28 195.9 14.7 104 218-324 2-107 (217)
11 PRK10158 23S rRNA/tRNA pseudou 99.9 1.3E-23 2.8E-28 195.3 14.6 103 217-322 13-118 (219)
12 PRK11112 tRNA pseudouridine sy 99.9 1.2E-23 2.5E-28 200.0 14.4 102 218-321 2-106 (257)
13 cd02563 PseudoU_synth_TruC tRN 99.9 1.7E-23 3.8E-28 194.6 14.1 104 218-323 1-107 (223)
14 KOG1919 RNA pseudouridylate sy 99.9 1.4E-21 3E-26 193.9 17.0 158 111-316 45-205 (371)
15 COG1187 RsuA 16S rRNA uridine- 99.8 1.1E-20 2.4E-25 178.6 13.5 142 111-311 4-147 (248)
16 PF00849 PseudoU_synth_2: RNA 99.8 3E-20 6.5E-25 162.9 10.1 96 226-321 1-101 (164)
17 cd02550 PseudoU_synth_Rsu_Rlu_ 99.8 3.4E-20 7.3E-25 163.0 10.1 91 227-321 1-92 (154)
18 cd02869 PseudoU_synth_RluCD_li 99.8 6.5E-19 1.4E-23 157.1 13.0 96 227-322 1-101 (185)
19 cd02556 PseudoU_synth_RluB Pse 99.8 2.2E-18 4.7E-23 153.9 9.3 82 226-311 1-82 (167)
20 cd02870 PseudoU_synth_RsuA_lik 99.7 1.6E-18 3.4E-23 151.2 5.5 80 227-311 1-80 (146)
21 cd02553 PseudoU_synth_RsuA Pse 99.7 6.8E-18 1.5E-22 150.9 9.2 81 227-311 2-82 (167)
22 cd02566 PseudoU_synth_RluE Pse 99.7 3.5E-17 7.5E-22 146.3 7.8 78 227-311 1-79 (168)
23 PRK11394 23S rRNA pseudouridin 99.6 8.7E-16 1.9E-20 143.1 8.6 80 225-311 39-118 (217)
24 cd02555 PSSA_1 PSSA_1: Pseudou 99.6 1.1E-15 2.5E-20 138.1 8.6 82 225-311 4-93 (177)
25 cd02554 PseudoU_synth_RluF Pse 99.6 4.5E-15 9.8E-20 132.8 8.8 78 227-311 2-79 (164)
26 cd02868 PseudoU_synth_hTruB2_l 99.2 6.4E-11 1.4E-15 111.2 7.8 75 227-307 2-76 (226)
27 TIGR00093 pseudouridine syntha 99.1 4.5E-11 9.7E-16 102.4 5.1 44 266-311 1-44 (128)
28 cd00165 S4 S4/Hsp/ tRNA synthe 98.8 2.2E-08 4.8E-13 73.8 7.7 68 111-231 2-70 (70)
29 TIGR02988 YaaA_near_RecF S4 do 98.4 7.9E-07 1.7E-11 66.3 5.7 54 105-202 3-59 (59)
30 PF01479 S4: S4 domain; Inter 98.2 3.8E-06 8.2E-11 59.7 6.2 46 111-199 2-48 (48)
31 cd02572 PseudoU_synth_hDyskeri 97.6 0.00021 4.5E-09 65.3 8.2 70 225-307 2-71 (182)
32 smart00363 S4 S4 RNA-binding d 97.5 0.00043 9.2E-09 49.2 6.4 50 111-203 2-52 (60)
33 COG1188 Ribosome-associated he 97.4 0.0003 6.5E-09 58.2 5.5 51 111-205 10-61 (100)
34 PLN00051 RNA-binding S4 domain 97.3 0.00054 1.2E-08 66.2 7.2 50 111-203 193-242 (267)
35 PRK00989 truB tRNA pseudouridi 97.3 0.0007 1.5E-08 64.0 7.5 71 225-307 9-79 (230)
36 cd00506 PseudoU_synth_TruB_lik 97.3 0.0009 1.9E-08 62.5 7.8 68 227-307 2-69 (210)
37 TIGR00431 TruB tRNA pseudourid 97.2 0.0012 2.6E-08 61.7 8.0 69 226-307 3-71 (209)
38 PRK04099 truB tRNA pseudouridi 97.2 0.0014 2.9E-08 63.6 8.1 70 225-307 2-71 (273)
39 PRK00020 truB tRNA pseudouridi 97.2 0.0015 3.3E-08 62.2 8.2 70 225-307 10-79 (244)
40 PRK02484 truB tRNA pseudouridi 97.0 0.0022 4.7E-08 62.8 8.2 70 225-307 3-72 (294)
41 PRK02193 truB tRNA pseudouridi 97.0 0.0021 4.5E-08 62.5 7.8 68 227-307 2-69 (279)
42 PRK14123 tRNA pseudouridine sy 97.0 0.0025 5.5E-08 62.7 8.2 70 225-307 3-72 (305)
43 TIGR03069 PS_II_S4 photosystem 97.0 0.0016 3.4E-08 62.6 6.4 50 111-203 185-234 (257)
44 cd02573 PseudoU_synth_EcTruB P 97.0 0.0028 6E-08 61.6 8.0 68 227-307 2-69 (277)
45 PRK14124 tRNA pseudouridine sy 97.0 0.0031 6.8E-08 62.1 8.4 70 225-307 3-72 (308)
46 PRK03287 truB tRNA pseudouridi 97.0 0.0028 6E-08 62.2 8.0 70 225-307 9-78 (298)
47 PRK00130 truB tRNA pseudouridi 96.9 0.0031 6.8E-08 61.6 8.3 70 225-307 2-71 (290)
48 PRK14846 truB tRNA pseudouridi 96.9 0.0031 6.6E-08 62.8 8.3 70 225-307 3-72 (345)
49 PRK02755 truB tRNA pseudouridi 96.9 0.0032 6.9E-08 61.7 8.0 69 225-307 3-71 (295)
50 PRK05389 truB tRNA pseudouridi 96.9 0.0033 7.1E-08 61.9 8.1 70 225-307 13-82 (305)
51 PRK04270 H/ACA RNA-protein com 96.9 0.0031 6.8E-08 61.8 7.8 70 225-307 22-91 (300)
52 PRK01528 truB tRNA pseudouridi 96.9 0.0038 8.3E-08 61.1 8.2 70 225-307 3-72 (292)
53 TIGR01017 rpsD_bact ribosomal 96.9 0.0022 4.7E-08 59.5 6.1 50 111-203 91-141 (200)
54 PRK01851 truB tRNA pseudouridi 96.8 0.0045 9.8E-08 60.8 8.3 70 225-307 16-85 (303)
55 PRK01550 truB tRNA pseudouridi 96.8 0.0044 9.6E-08 61.0 8.2 70 225-307 2-71 (304)
56 PRK05033 truB tRNA pseudouridi 96.8 0.005 1.1E-07 60.7 8.3 70 225-307 10-79 (312)
57 PRK14122 tRNA pseudouridine sy 96.7 0.0051 1.1E-07 60.7 7.9 69 226-307 2-70 (312)
58 CHL00113 rps4 ribosomal protei 96.7 0.003 6.4E-08 58.7 5.9 50 111-203 90-140 (201)
59 TIGR00478 tly hemolysin TlyA f 96.6 0.003 6.6E-08 59.6 5.3 50 111-203 1-51 (228)
60 PRK10348 ribosome-associated h 96.6 0.0064 1.4E-07 53.0 6.4 49 111-203 10-59 (133)
61 TIGR00425 CBF5 rRNA pseudourid 96.4 0.0092 2E-07 59.2 7.5 70 225-307 34-103 (322)
62 COG2302 Uncharacterized conser 96.4 0.0066 1.4E-07 57.9 6.2 57 104-203 174-231 (257)
63 PRK05327 rpsD 30S ribosomal pr 96.4 0.006 1.3E-07 56.6 5.8 50 111-203 94-144 (203)
64 PRK04642 truB tRNA pseudouridi 96.4 0.012 2.6E-07 57.8 8.0 70 225-307 10-79 (300)
65 cd02867 PseudoU_synth_TruB_4 P 95.9 0.027 5.9E-07 55.6 7.9 69 227-307 2-98 (312)
66 COG0130 TruB Pseudouridine syn 95.9 0.026 5.7E-07 54.7 7.6 69 226-307 16-84 (271)
67 COG0522 RpsD Ribosomal protein 95.4 0.031 6.8E-07 52.1 5.8 51 111-204 95-146 (205)
68 COG1189 Predicted rRNA methyla 94.6 0.077 1.7E-06 50.6 6.0 50 111-203 4-54 (245)
69 PRK11507 ribosome-associated p 93.8 0.21 4.5E-06 39.0 6.0 50 110-202 12-62 (70)
70 PRK04051 rps4p 30S ribosomal p 90.9 0.55 1.2E-05 42.9 5.8 50 111-203 104-154 (177)
71 COG2501 S4-like RNA binding pr 90.6 0.93 2E-05 35.7 6.1 52 108-202 10-62 (73)
72 PRK04313 30S ribosomal protein 89.8 1.3 2.9E-05 42.2 7.6 72 108-232 36-109 (237)
73 PF13275 S4_2: S4 domain; PDB: 88.5 0.12 2.6E-06 39.7 -0.3 49 111-202 9-58 (65)
74 PLN00036 40S ribosomal protein 88.3 1.9 4.1E-05 41.7 7.6 69 110-231 42-112 (261)
75 PTZ00223 40S ribosomal protein 88.0 2 4.3E-05 41.8 7.5 51 109-202 38-90 (273)
76 COG4332 Uncharacterized protei 87.7 0.85 1.8E-05 41.8 4.6 35 103-137 130-166 (203)
77 PTZ00118 40S ribosomal protein 87.5 2.3 5E-05 41.2 7.6 51 109-202 41-93 (262)
78 cd01291 PseudoU_synth PseudoU_ 87.3 1 2.2E-05 35.6 4.4 28 261-307 24-51 (87)
79 PF14451 Ub-Mut7C: Mut7-C ubiq 83.3 1.8 4E-05 34.5 4.0 22 172-203 54-75 (81)
80 PLN00189 40S ribosomal protein 82.8 1.2 2.6E-05 41.3 3.2 42 121-205 121-162 (194)
81 PRK01777 hypothetical protein; 82.7 1.9 4.2E-05 35.4 4.1 57 102-203 19-75 (95)
82 PF06353 DUF1062: Protein of u 82.4 2 4.3E-05 37.9 4.3 57 82-138 71-131 (142)
83 TIGR01018 rpsD_arch ribosomal 77.0 4.8 0.0001 36.3 5.0 49 111-202 105-154 (162)
84 PF01509 TruB_N: TruB family p 73.7 3.6 7.7E-05 36.5 3.3 43 261-307 7-49 (149)
85 PTZ00155 40S ribosomal protein 70.9 5.2 0.00011 36.7 3.8 50 111-203 108-158 (181)
86 COG1471 RPS4A Ribosomal protei 61.9 16 0.00035 34.9 5.2 27 111-137 42-70 (241)
87 PRK13354 tyrosyl-tRNA syntheta 60.6 15 0.00033 37.7 5.3 27 111-137 344-371 (410)
88 PRK05912 tyrosyl-tRNA syntheta 59.6 28 0.00061 35.7 7.0 28 110-137 343-371 (408)
89 PRK08364 sulfur carrier protei 56.9 23 0.0005 27.0 4.5 21 172-202 44-64 (70)
90 PRK05659 sulfur carrier protei 54.5 12 0.00026 27.8 2.5 25 172-202 36-60 (66)
91 cd00754 MoaD Ubiquitin domain 53.2 46 0.001 25.1 5.8 21 172-202 54-74 (80)
92 PRK06437 hypothetical protein; 51.2 29 0.00064 26.3 4.3 21 172-202 41-61 (67)
93 PRK06083 sulfur carrier protei 47.9 28 0.00061 27.9 3.9 25 172-202 54-78 (84)
94 PF02597 ThiS: ThiS family; I 47.7 54 0.0012 24.5 5.3 24 172-202 48-71 (77)
95 cd00565 ThiS ThiaminS ubiquiti 46.8 59 0.0013 24.1 5.3 25 172-202 35-59 (65)
96 KOG2559 Predicted pseudouridin 46.6 11 0.00023 36.5 1.4 22 262-283 90-111 (318)
97 PRK07440 hypothetical protein; 43.9 30 0.00065 26.6 3.3 25 172-202 40-64 (70)
98 cd01666 TGS_DRG_C TGS_DRG_C: 40.5 1.3E+02 0.0029 23.5 6.6 16 187-202 59-74 (75)
99 TIGR01683 thiS thiamine biosyn 40.1 49 0.0011 24.5 3.9 25 172-202 34-58 (64)
100 PF04225 OapA: Opacity-associa 38.9 38 0.00082 27.0 3.3 31 103-134 4-34 (85)
101 PLN02799 Molybdopterin synthas 35.3 1.4E+02 0.003 23.0 6.0 21 172-202 56-76 (82)
102 TIGR01764 excise DNA binding d 35.2 34 0.00074 22.9 2.2 22 116-137 7-28 (49)
103 PRK05863 sulfur carrier protei 33.2 33 0.00071 25.7 2.0 24 172-202 36-59 (65)
104 TIGR01687 moaD_arch MoaD famil 31.8 87 0.0019 24.4 4.4 23 172-202 60-82 (88)
105 PF03658 Ub-RnfH: RnfH family 30.9 34 0.00073 27.7 1.8 18 187-204 56-73 (84)
106 COG2104 ThiS Sulfur transfer p 30.8 1.3E+02 0.0027 23.2 4.9 25 172-202 38-62 (68)
107 cd01764 Urm1 Urm1-like ubuitin 30.2 64 0.0014 26.2 3.4 25 172-202 64-88 (94)
108 PRK11130 moaD molybdopterin sy 29.1 1.3E+02 0.0028 23.3 4.9 22 172-203 55-76 (81)
109 PF06633 DUF1155: Protein of u 28.5 26 0.00057 24.1 0.7 34 14-49 8-41 (42)
110 PF02824 TGS: TGS domain; Int 27.4 48 0.001 24.5 2.0 21 172-202 39-59 (60)
111 cd04762 HTH_MerR-trunc Helix-T 25.4 65 0.0014 21.2 2.3 22 116-137 6-27 (49)
112 PF12728 HTH_17: Helix-turn-he 25.3 62 0.0013 22.5 2.2 22 116-137 7-28 (51)
113 PRK08053 sulfur carrier protei 24.9 2.1E+02 0.0046 21.2 5.2 25 172-202 36-60 (66)
114 PF08068 DKCLD: DKCLD (NUC011) 24.4 27 0.00058 26.5 0.2 17 223-239 40-56 (59)
115 TIGR01682 moaD molybdopterin c 22.3 2.7E+02 0.0058 21.3 5.5 21 172-202 54-74 (80)
116 PRK11092 bifunctional (p)ppGpp 22.1 1.2E+02 0.0026 33.5 4.7 59 133-206 385-450 (702)
117 cd04480 RPA1_DBD_A_like RPA1_D 20.8 2.5E+02 0.0055 21.7 5.2 48 88-138 8-56 (86)
No 1
>COG0564 RluA Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.4e-35 Score=286.21 Aligned_cols=168 Identities=23% Similarity=0.300 Sum_probs=146.0
Q ss_pred cHHHHHHhhc-CCCHHHHHHHHHcCCEEEeeeCCCCCCCCchhhhhhhcccCCccccccccccCCeEEeecccccccccc
Q 018538 111 PVLEYICREL-NLPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTFRITHV 189 (354)
Q Consensus 111 ~L~~~L~~~~-~lSr~~~~~lI~~G~V~~~~~~~~~~~~~~~e~~r~~~~~~~~~v~~kr~~vnGk~vr~~~~~~~~~~~ 189 (354)
+|++||++ + .+||+.++++|++|.|. |||+.+ ++
T Consensus 14 rld~~L~~-l~~~sr~~~~~~i~~g~v~----------------------------------vNg~~v----------~~ 48 (289)
T COG0564 14 RLDKFLAK-LLPISRSRIQKLIRKGRVR----------------------------------VNGKKV----------KP 48 (289)
T ss_pred CHHHHHHH-ccCcCHHHHHHHHHCCCEE----------------------------------ECCEEc----------cC
Confidence 49999999 6 49999999999999999 899874 47
Q ss_pred ceeecCCcEEEEecCCCCCC-CCCCCCCCceeEeecCeEEEEECCCCccccCCCCCCcchHHHHHHHHhCC-CCCceecc
Q 018538 190 DQIVEAGTYLRVHVHPKRFP-RCYDIDWNSRIIAVTESHVVLDKPAGTSVGGTTDNIEESCATFASRALGL-TTPLRTTH 267 (354)
Q Consensus 190 ~~~V~~GD~I~V~~~~~~~~-~~~~~~~~l~IlYED~~llVVNKPaGl~vhp~~~~~~~TL~~~l~~~l~~-~~~~~~VH 267 (354)
+++|..||.|++...+.... ...+.+.+++|||||++++|||||+||+|||++++..+|+++.++.+... ...+++||
T Consensus 49 ~~~l~~gd~i~~~~~~~~~~~~~~~~~~~l~IlyED~~llVvnKP~Gl~vhp~~~~~~~tl~~~l~~~~~~~~~~~~~vH 128 (289)
T COG0564 49 SYKLKPGDVVRIPLPEEPEEEKLVPEDIPLDILYEDEDLLVVNKPAGLVVHPGGGHHEGTLVNALLRHCQDGVERPGIVH 128 (289)
T ss_pred CeeeCCCCEEEEecccccccccccccCCCccEEEecCCEEEEECCCCCcCcCCCCCccHhHHHHHHHhccccCCceeeec
Confidence 88999999999987653321 22235556899999999999999999999999998899999998887643 35799999
Q ss_pred CCCCCCceEEEeeCCHHHHHHHHHhHhcCccceEEEEEEeccCC--cceEEccccccC
Q 018538 268 QIDNCTEGCVVLARTQEYCSIFHRKIREKKVKKLYLALTTAPLP--VGIMTHYMRPIN 323 (354)
Q Consensus 268 RLDrdTSGLLL~AKn~~a~~~L~~~f~~~~V~K~YlAlV~G~l~--~G~I~~~L~pi~ 323 (354)
||||+||||||||||..++..|+++|+++.++|+|+|+|.|.++ +|+|+.++....
T Consensus 129 RLDkdTSGlll~AK~~~a~~~l~~~f~~r~v~K~Y~Alv~G~~~~~~~~i~~pi~r~~ 186 (289)
T COG0564 129 RLDKDTSGLLLVAKNREAARELSEQFKQRKVKKTYLALVRGHLPEDEGTIDAPIGRDP 186 (289)
T ss_pred cCCCCCceEEEEECCHHHHHHHHHHHhcCcCcEEEEEEEECcccCCCCEEeeeeecCC
Confidence 99999999999999999999999999999999999999999987 599996655543
No 2
>TIGR00005 rluA_subfam pseudouridine synthase, RluA family. modifies uracil-65 in transfer RNAs to pseudouridine.
Probab=100.00 E-value=3.7e-32 Score=262.13 Aligned_cols=169 Identities=21% Similarity=0.248 Sum_probs=142.1
Q ss_pred cHHHHHHhhcC-CCHHHHHHHHHcCCEEEeeeCCCCCCCCchhhhhhhcccCCccccccccccCCeEEeecccccccccc
Q 018538 111 PVLEYICRELN-LPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTFRITHV 189 (354)
Q Consensus 111 ~L~~~L~~~~~-lSr~~~~~lI~~G~V~~~~~~~~~~~~~~~e~~r~~~~~~~~~v~~kr~~vnGk~vr~~~~~~~~~~~ 189 (354)
+|++||++.+. +||+.++++|+.|.|+ |||+.+ +.+
T Consensus 7 rLd~~L~~~~~~~Sr~~~~kli~~G~V~----------------------------------VNg~~~---------~~~ 43 (299)
T TIGR00005 7 RLDDFLASLLPDLSRSRIQKLIENGQVK----------------------------------VNGKVT---------ANP 43 (299)
T ss_pred hHHHHHHHhcccCCHHHHHHHHHCCcEE----------------------------------ECCEec---------cCc
Confidence 59999999984 9999999999999999 889642 467
Q ss_pred ceeecCCcEEEEecCCCCCCCCCCCCCCceeEeecCeEEEEECCCCccccCCCCCCcchHHHHHHHHhCC---CCCceec
Q 018538 190 DQIVEAGTYLRVHVHPKRFPRCYDIDWNSRIIAVTESHVVLDKPAGTSVGGTTDNIEESCATFASRALGL---TTPLRTT 266 (354)
Q Consensus 190 ~~~V~~GD~I~V~~~~~~~~~~~~~~~~l~IlYED~~llVVNKPaGl~vhp~~~~~~~TL~~~l~~~l~~---~~~~~~V 266 (354)
++.|..||.|.++..+...+.......+++|+|||++|+|+|||+|++||+++.+..+|+.+.+..++.. ...+++|
T Consensus 44 ~~~v~~gd~I~i~~~~~~~~~~~~~~~~~~i~~ed~~~lvvnKP~g~~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~v 123 (299)
T TIGR00005 44 KLKVKDGDRITVRVPEEEEHEVPPQDIPLDILFEDEDIIVINKPSGLVVHPGGGNPFGTVLNALLAHCPPIAGVERVGIV 123 (299)
T ss_pred ccCCCCCCEEEEecCCcccccCCccCCCccEEEeCCCEEEEECCCCCeEeCCCCCCcccHHHHHHHhcccccCCCcCceE
Confidence 8899999999997653221111223346789999999999999999999998887777898888776542 1458999
Q ss_pred cCCCCCCceEEEeeCCHHHHHHHHHhHhcCccceEEEEEEeccCC--cceEEcccccc
Q 018538 267 HQIDNCTEGCVVLARTQEYCSIFHRKIREKKVKKLYLALTTAPLP--VGIMTHYMRPI 322 (354)
Q Consensus 267 HRLDrdTSGLLL~AKn~~a~~~L~~~f~~~~V~K~YlAlV~G~l~--~G~I~~~L~pi 322 (354)
||||++||||||||||+++++.|+++|+++.|.|+|+|+|.|.++ +|+|+.+|...
T Consensus 124 hRLD~~TSGlll~ak~~~~~~~l~~~~~~~~v~K~Y~a~v~g~~~~~~~~i~~~l~~~ 181 (299)
T TIGR00005 124 HRLDRDTSGLMVVAKTPLALRELQRQLKNRTVTKEYVALVHGQFDSGGGTVDAPLGRV 181 (299)
T ss_pred CCCCCCCceEEEEEcCHHHHHHHHHHHHhCCcceEEEEEEeccccCCCCEEeCceecC
Confidence 999999999999999999999999999999999999999999986 78899766553
No 3
>PRK11180 rluD 23S rRNA pseudouridine synthase D; Provisional
Probab=100.00 E-value=6.4e-32 Score=264.29 Aligned_cols=169 Identities=14% Similarity=0.167 Sum_probs=142.0
Q ss_pred cHHHHHHhhc-CCCHHHHHHHHHcCCEEEeeeCCCCCCCCchhhhhhhcccCCccccccccccCCeEEeecccccccccc
Q 018538 111 PVLEYICREL-NLPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTFRITHV 189 (354)
Q Consensus 111 ~L~~~L~~~~-~lSr~~~~~lI~~G~V~~~~~~~~~~~~~~~e~~r~~~~~~~~~v~~kr~~vnGk~vr~~~~~~~~~~~ 189 (354)
+|++||++.+ .+||+.++++|+.|.|+ |||+.+ ..+
T Consensus 19 RLd~~L~~~~~~~Sr~~~~~lI~~G~V~----------------------------------VNg~~v---------~~~ 55 (325)
T PRK11180 19 RLDQALAELFPDYSRSRIKEWILDQRVL----------------------------------VNGKVI---------NKP 55 (325)
T ss_pred cHHHHHHhhccccCHHHHHHHHHCCCEE----------------------------------ECCEEc---------cCC
Confidence 4999999987 68999999999999999 889863 356
Q ss_pred ceeecCCcEEEEecCCCCCCCCCCCCCCceeEeecCeEEEEECCCCccccCCCCCCcchHHHHHHHHhCC---CCCceec
Q 018538 190 DQIVEAGTYLRVHVHPKRFPRCYDIDWNSRIIAVTESHVVLDKPAGTSVGGTTDNIEESCATFASRALGL---TTPLRTT 266 (354)
Q Consensus 190 ~~~V~~GD~I~V~~~~~~~~~~~~~~~~l~IlYED~~llVVNKPaGl~vhp~~~~~~~TL~~~l~~~l~~---~~~~~~V 266 (354)
++.|..||.|.+...+.......+...+++|||||++|+|+|||+||+|||+..+...|+.+.+..++.. ...+++|
T Consensus 56 ~~~v~~gD~I~v~~~~~~~~~~~~~~~~~~iiyed~~~lvvnKP~gl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~v 135 (325)
T PRK11180 56 KEKVLGGEQVAIDAEIEEEARFEPQDIPLDIVYEDDDILVINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADVPRAGIV 135 (325)
T ss_pred CcCcCCCCEEEEeeccccccCCCCCCCCCcEEEECCCEEEEECCCCCeEeCCCCCCCCcHHHHHHHHhhhccCCccccee
Confidence 7889999999998643221111123456899999999999999999999998877677888888766532 2357899
Q ss_pred cCCCCCCceEEEeeCCHHHHHHHHHhHhcCccceEEEEEEeccCC-cceEEcccccc
Q 018538 267 HQIDNCTEGCVVLARTQEYCSIFHRKIREKKVKKLYLALTTAPLP-VGIMTHYMRPI 322 (354)
Q Consensus 267 HRLDrdTSGLLL~AKn~~a~~~L~~~f~~~~V~K~YlAlV~G~l~-~G~I~~~L~pi 322 (354)
||||++||||||||||..++..|+++|+++.|.|+|+|+|.|.++ +|+|+.+|...
T Consensus 136 hRLD~~TSGlll~Ak~~~~~~~l~~~~~~~~v~K~Y~A~v~G~~~~~~~i~~~l~~~ 192 (325)
T PRK11180 136 HRLDKDTTGLMVVAKTVPAQTRLVEALQKREITREYEAVAIGHMTAGGTVDEPISRH 192 (325)
T ss_pred ccCCCCCceeEEEECCHHHHHHHHHHHHhCCcceEEEEEEecCCCCCCEEECceecC
Confidence 999999999999999999999999999999999999999999997 88999766543
No 4
>PRK11025 23S rRNA pseudouridylate synthase C; Provisional
Probab=100.00 E-value=7.7e-32 Score=263.00 Aligned_cols=167 Identities=20% Similarity=0.253 Sum_probs=135.0
Q ss_pred cHHHHHHhhc-CCCHHHHHHHHHcCCEEEeeeCCCCCCCCchhhhhhhcccCCccccccccccCCeEEeecccccccccc
Q 018538 111 PVLEYICREL-NLPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTFRITHV 189 (354)
Q Consensus 111 ~L~~~L~~~~-~lSr~~~~~lI~~G~V~~~~~~~~~~~~~~~e~~r~~~~~~~~~v~~kr~~vnGk~vr~~~~~~~~~~~ 189 (354)
+|++||++.+ .+||+.++++|+.|.|+ |||+.+ ++
T Consensus 21 RLd~~L~~~~~~~sr~~i~~li~~G~V~----------------------------------VNg~~v----------~~ 56 (317)
T PRK11025 21 RIDNFLRTQLKGVPKSMIYRILRKGEVR----------------------------------VNKKRI----------KP 56 (317)
T ss_pred hHHHHHHHhcccCCHHHHHHHHHcCCEE----------------------------------ECCEEc----------Cc
Confidence 5999999888 78999999999999999 889863 57
Q ss_pred ceeecCCcEEEEecCCCCCCCCC--------CCCCCceeEeecCeEEEEECCCCccccCCCCCCcchHHHHHHHHhCCCC
Q 018538 190 DQIVEAGTYLRVHVHPKRFPRCY--------DIDWNSRIIAVTESHVVLDKPAGTSVGGTTDNIEESCATFASRALGLTT 261 (354)
Q Consensus 190 ~~~V~~GD~I~V~~~~~~~~~~~--------~~~~~l~IlYED~~llVVNKPaGl~vhp~~~~~~~TL~~~l~~~l~~~~ 261 (354)
+++|..||.|.+........... ...++++|+|||++|+|||||+|++|||+.+.. .++.+.+..+.....
T Consensus 57 ~~~v~~GD~I~i~~~~~~~~~~~p~~~~~~~~~~~~~~Ilyed~~~lvvnKP~gl~~~~~~~~~-~~~~~~~~~~~~~~~ 135 (317)
T PRK11025 57 EYKLEAGDEVRIPPVRVAEREEEAVSPKLQKVAALADVILYEDDHILVLNKPSGTAVHGGSGLS-FGVIEGLRALRPEAR 135 (317)
T ss_pred ccccCCCCEEEeCCCCccccccccccccccccccCcCCEEEECCCEEEEECCCCCcCcCCCCCC-ccHHHHHHHhccCCC
Confidence 88999999999864221110000 012467999999999999999999999987654 345665554332223
Q ss_pred CceeccCCCCCCceEEEeeCCHHHHHHHHHhHhcCccceEEEEEEeccCC--cceEEcccccc
Q 018538 262 PLRTTHQIDNCTEGCVVLARTQEYCSIFHRKIREKKVKKLYLALTTAPLP--VGIMTHYMRPI 322 (354)
Q Consensus 262 ~~~~VHRLDrdTSGLLL~AKn~~a~~~L~~~f~~~~V~K~YlAlV~G~l~--~G~I~~~L~pi 322 (354)
.+++|||||++||||||||||..+++.|+++|+++.|+|+|+|+|.|.++ +|+|+.+|...
T Consensus 136 ~~~~vhRLD~~TSGlll~Ak~~~a~~~l~~~~~~~~v~K~Y~a~v~G~~~~~~~~i~~~i~~~ 198 (317)
T PRK11025 136 FLELVHRLDRDTSGVLLVAKKRSALRSLHEQLREKGMQKDYLALVRGQWQSHVKVVQAPLLKN 198 (317)
T ss_pred cCceeCCCCCCCceEEEEEcCHHHHHHHHHHHHhCCccEEEEEEEeCcccCCCceEecccccC
Confidence 47899999999999999999999999999999999999999999999986 78999777554
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=99.95 E-value=6.4e-27 Score=221.05 Aligned_cols=128 Identities=20% Similarity=0.219 Sum_probs=106.4
Q ss_pred ccceeecCCcEEEEecCCCCCCCCCCCCCCceeEeecCeEEEEECCCCccccCCCCCCcchHHHHHHHHhCCCCCceecc
Q 018538 188 HVDQIVEAGTYLRVHVHPKRFPRCYDIDWNSRIIAVTESHVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTH 267 (354)
Q Consensus 188 ~~~~~V~~GD~I~V~~~~~~~~~~~~~~~~l~IlYED~~llVVNKPaGl~vhp~~~~~~~TL~~~l~~~l~~~~~~~~VH 267 (354)
+++++|+.||.|.++...... .+.+.+++|||||++|+|||||+|++|||++++..+|+.+.+..+++. ..+++||
T Consensus 12 ~~~~~l~~gd~i~~~~~~~~~---~~~~~~~~Iiyed~~~lvvnKPaGl~~~~~~~~~~~t~~~~l~~~~~~-~~~~~vh 87 (246)
T cd02558 12 DPDSPYRPGTFVWYYRELPDE---PPIPFEETILHQDEHLLVADKPHFLPVTPRGRYVTETLLVRLRRQTGN-PDLTPAH 87 (246)
T ss_pred CCCceecCCCEEEEeCCCCCC---CCCCCCcceEEecCCEEEEECCCCCccCCCCcchhhhHHHHHHHHhCC-Ccccccc
Confidence 678899999999987532211 122346899999999999999999999999888778888887766542 3578999
Q ss_pred CCCCCCceEEEeeCCHHHHHHHHHhHhcCccceEEEEEEeccCC--cc-eEEccc
Q 018538 268 QIDNCTEGCVVLARTQEYCSIFHRKIREKKVKKLYLALTTAPLP--VG-IMTHYM 319 (354)
Q Consensus 268 RLDrdTSGLLL~AKn~~a~~~L~~~f~~~~V~K~YlAlV~G~l~--~G-~I~~~L 319 (354)
|||++||||||||||++++..|+.+|++++++|+|+|+|.|.++ .+ .++.++
T Consensus 88 RLD~~TSGlll~Ak~~~~~~~l~~~~~~~~v~K~YlA~v~G~~~~~~~~~~~~~i 142 (246)
T cd02558 88 RLDRLTAGLVLFSKRPETRGAYQTLFARREVSKTYEAVAPYVPALTFPLTVRSRI 142 (246)
T ss_pred cCCCCceeEEEEEcCHHHHHHHHHHHHcCCccEEEEEEEecCCCCCCCcceeccc
Confidence 99999999999999999999999999999999999999999886 33 466444
No 6
>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=99.92 E-value=1.8e-24 Score=200.22 Aligned_cols=108 Identities=27% Similarity=0.402 Sum_probs=95.1
Q ss_pred CCceeEeecCeEEEEECCCCccccCCCCCCcchHHHHHHHHhCCCCCceeccCCCCCCceEEEeeCCHHHHHHHHHhHhc
Q 018538 216 WNSRIIAVTESHVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQIDNCTEGCVVLARTQEYCSIFHRKIRE 295 (354)
Q Consensus 216 ~~l~IlYED~~llVVNKPaGl~vhp~~~~~~~TL~~~l~~~l~~~~~~~~VHRLDrdTSGLLL~AKn~~a~~~L~~~f~~ 295 (354)
.+++|||||++|+|+|||+|++|++++.....++.+.+..+++. ..+++|||||++||||||||||+++++.|+++|++
T Consensus 14 ~~~~iiyed~~~ivvnKP~Gl~~~~~~~~~~~sl~~~l~~~~~~-~~~~~vhRLD~~TSGllllak~~~~~~~l~~~f~~ 92 (213)
T cd02557 14 DPIKIVHEDDDLLVVDKPSGIPVHPTGRYRYNTVTEILKSEYGL-TELRPCHRLDRLTSGLLLFAKTSQTASRLQQQIRS 92 (213)
T ss_pred CCCcEEEECCCEEEEECCCCCcCCCCCCCCcChHHHHHHHHcCC-CCccCccCCCCCCceEEEEECCHHHHHHHHHHHHc
Confidence 36789999999999999999999998776677888888776542 35889999999999999999999999999999999
Q ss_pred CccceEEEEEEeccCC--cceEEccccccCC
Q 018538 296 KKVKKLYLALTTAPLP--VGIMTHYMRPINI 324 (354)
Q Consensus 296 ~~V~K~YlAlV~G~l~--~G~I~~~L~pi~r 324 (354)
++++|+|+|+|.|.++ ++.|+.+|.+...
T Consensus 93 ~~v~K~Y~a~v~G~~~~~~~~i~~~l~~~~~ 123 (213)
T cd02557 93 REVKKEYLARVKGEFPDGEVVVDQPIGLVSP 123 (213)
T ss_pred CCccEEEEEEEeCcCCCCCeEEecceeccCc
Confidence 9999999999999986 7899977765543
No 7
>PRK10839 16S rRNA pseudouridylate synthase A; Provisional
Probab=99.92 E-value=5.3e-25 Score=205.65 Aligned_cols=140 Identities=14% Similarity=0.220 Sum_probs=112.4
Q ss_pred cHHHHHHhhcCCCHHHHHHHHHcCCEEEeeeCCCCCCCCchhhhhhhcccCCccccccccccCCeEEeeccccccccccc
Q 018538 111 PVLEYICRELNLPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTFRITHVD 190 (354)
Q Consensus 111 ~L~~~L~~~~~lSr~~~~~lI~~G~V~~~~~~~~~~~~~~~e~~r~~~~~~~~~v~~kr~~vnGk~vr~~~~~~~~~~~~ 190 (354)
+|++||++.+.+||+.++++|+.|.|+ |||+.+ .+++
T Consensus 2 rld~~L~~~~~~Sr~~~~~li~~g~V~----------------------------------VNg~~~---------~~~~ 38 (232)
T PRK10839 2 RLDKFISQQLGVSRAIAGRELRANRVT----------------------------------VDGEIV---------KNGA 38 (232)
T ss_pred cHHHHHHHcCCCCHHHHHHHHHcCeEE----------------------------------ECCEEe---------ccCC
Confidence 499999988899999999999999999 899874 2467
Q ss_pred eeecCCcEEEEecCCCCCCCCCCCCCCceeEeecCeEEEEECCCCccccCCCCCCcchHHHHHHHHhCCCCCceeccCCC
Q 018538 191 QIVEAGTYLRVHVHPKRFPRCYDIDWNSRIIAVTESHVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQID 270 (354)
Q Consensus 191 ~~V~~GD~I~V~~~~~~~~~~~~~~~~l~IlYED~~llVVNKPaGl~vhp~~~~~~~TL~~~l~~~l~~~~~~~~VHRLD 270 (354)
++|.+||.|.+...+.. ..++++|+|+|||+||+||++... ..|+.+++.... ...+++|||||
T Consensus 39 ~~l~~gd~I~l~~~~~~-------------~~~~~~~lvvnKP~G~~~~~~~~~-~~tl~~~l~~~~--~~~~~~v~RLD 102 (232)
T PRK10839 39 FKLLPEHDVAYDGNPLA-------------QQHGPRYFMLNKPQGYVCSTDDPD-HPTVLYFLDEPV--AYKLHAAGRLD 102 (232)
T ss_pred cCcCCCCEEEECCEEcc-------------cCCCCEEEEEECCCCeEecccCCC-CCeEEEeccccc--ccCceecCCCC
Confidence 88999999988632110 113568999999999999987543 355544332211 23578999999
Q ss_pred CCCceEEEeeCCHHHHHHHHHhHhcCccceEEEEEEeccCC
Q 018538 271 NCTEGCVVLARTQEYCSIFHRKIREKKVKKLYLALTTAPLP 311 (354)
Q Consensus 271 rdTSGLLL~AKn~~a~~~L~~~f~~~~V~K~YlAlV~G~l~ 311 (354)
++||||||||||+.+++.|.. +++.++|+|+|++.+++.
T Consensus 103 ~~TSGlll~ak~~~~~~~l~~--~~~~i~K~Y~a~i~~~i~ 141 (232)
T PRK10839 103 IDTTGLVLMTDDGQWSHRITS--PRHHCEKTYLVTLESPVA 141 (232)
T ss_pred CCceeEEEEecCHHHHHHHhC--CCCCCCeEEEEEECCCCC
Confidence 999999999999999999986 678999999999999886
No 8
>PRK10475 23S rRNA pseudouridine synthase F; Provisional
Probab=99.92 E-value=1.9e-24 Score=208.90 Aligned_cols=140 Identities=19% Similarity=0.273 Sum_probs=115.9
Q ss_pred cHHHHHHhhcCCCHHHHHHHHHcCCEEEeeeCCCCCCCCchhhhhhhcccCCccccccccccCCeEEeeccccccccccc
Q 018538 111 PVLEYICRELNLPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTFRITHVD 190 (354)
Q Consensus 111 ~L~~~L~~~~~lSr~~~~~lI~~G~V~~~~~~~~~~~~~~~e~~r~~~~~~~~~v~~kr~~vnGk~vr~~~~~~~~~~~~ 190 (354)
+|++||++...+||+.++++|+.|.|+ |||+++ .++
T Consensus 8 RL~k~La~~g~~SRr~a~~lI~~G~V~----------------------------------VNGk~v----------~~~ 43 (290)
T PRK10475 8 RLNKYISESGICSRREADRYIEQGNVF----------------------------------INGKRA----------TIG 43 (290)
T ss_pred HHHHHHHhCCCCCHHHHHHHHHCCcEE----------------------------------ECCEEc----------cCC
Confidence 599999987678999999999999999 899863 567
Q ss_pred eeecCCcEEEEecCCCCCCCCCCCCCCceeEeecCeEEEEECCCCccccCCCCCCcchHHHHHHHHhCCCCCceeccCCC
Q 018538 191 QIVEAGTYLRVHVHPKRFPRCYDIDWNSRIIAVTESHVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQID 270 (354)
Q Consensus 191 ~~V~~GD~I~V~~~~~~~~~~~~~~~~l~IlYED~~llVVNKPaGl~vhp~~~~~~~TL~~~l~~~l~~~~~~~~VHRLD 270 (354)
++|.+||.|.|+..... + ..+||++|||+|||+|++||+... ...++.+++..+ ..+++|||||
T Consensus 44 ~~V~~gD~V~v~g~~i~-~----------~~~ed~~~lvlnKP~G~~~~~~~~-~~~tv~~~l~~~----~~l~~VgRLD 107 (290)
T PRK10475 44 DQVKAGDVVKVNGQLIE-P----------REAEDLVLIALNKPVGIVSTTEDG-ERDNIVDFVNHS----KRVFPIGRLD 107 (290)
T ss_pred CCcCCCCEEEECCEEcc-c----------cccCCCeEEEEECCCCCCcCCCCC-CCCcHHHHhhcc----ccccccccCC
Confidence 78999999988742110 0 014888999999999999997765 356888876532 3588999999
Q ss_pred CCCceEEEeeCCHHHHHHHHHhHhcCccceEEEEEEeccCCc
Q 018538 271 NCTEGCVVLARTQEYCSIFHRKIREKKVKKLYLALTTAPLPV 312 (354)
Q Consensus 271 rdTSGLLL~AKn~~a~~~L~~~f~~~~V~K~YlAlV~G~l~~ 312 (354)
+|||||||||+|+++++.|.+ ..+.+.|+|+|+|.|++++
T Consensus 108 rdTsGLLLlT~dg~~~~~L~~--p~~~i~K~Y~v~V~g~~~~ 147 (290)
T PRK10475 108 KDSQGLIFLTNHGDLVNKILR--AGNDHEKEYLVTVDKPITD 147 (290)
T ss_pred CCCcceEEEecCHHHHHHhhC--cCCCCCeEEEEEECCCCCH
Confidence 999999999999999999987 4558999999999999863
No 9
>PRK10700 23S rRNA pseudouridylate synthase B; Provisional
Probab=99.91 E-value=1e-23 Score=203.85 Aligned_cols=143 Identities=14% Similarity=0.134 Sum_probs=113.8
Q ss_pred cHHHHHHhhcCCCHHHHHHHHHcCCEEEeeeCCCCCCCCchhhhhhhcccCCccccccccccCCeEEeeccccccccccc
Q 018538 111 PVLEYICRELNLPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTFRITHVD 190 (354)
Q Consensus 111 ~L~~~L~~~~~lSr~~~~~lI~~G~V~~~~~~~~~~~~~~~e~~r~~~~~~~~~v~~kr~~vnGk~vr~~~~~~~~~~~~ 190 (354)
+|++||++...+||+.++++|+.|.|+ |||+.+ .+.
T Consensus 4 RL~k~La~~g~~SRr~a~~lI~~G~V~----------------------------------VNG~~~----------~~g 39 (289)
T PRK10700 4 KLQKVLARAGHGSRREIESIIEAGRVS----------------------------------VDGKIA----------TLG 39 (289)
T ss_pred hHHHHHHHCCCCCHHHHHHHHHcCCEE----------------------------------ECCEec----------cCC
Confidence 499999986569999999999999999 899863 567
Q ss_pred eeecCCc--EEEEecCCCCCCCCCCCCCCceeEe-ecCeEEEEECCCCccccCCCCCCcchHHHHHHHHhCCCCCceecc
Q 018538 191 QIVEAGT--YLRVHVHPKRFPRCYDIDWNSRIIA-VTESHVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTH 267 (354)
Q Consensus 191 ~~V~~GD--~I~V~~~~~~~~~~~~~~~~l~IlY-ED~~llVVNKPaGl~vhp~~~~~~~TL~~~l~~~l~~~~~~~~VH 267 (354)
++|..+| .|.++...... ...+ ||++|+++|||+|++|++.+.....|+++++.... ...+++||
T Consensus 40 ~~V~~~~~d~I~v~g~~~~~----------~~~~~e~~~ylvlnKP~G~~~s~~d~~~~~tv~d~l~~~~--~~~~~~Vg 107 (289)
T PRK10700 40 DRVEVTPGLKIRIDGHLISV----------KESAEQICRVLAYYKPEGELCTRNDPEGRPTVFDRLPKLR--GARWIAVG 107 (289)
T ss_pred CEeCCCCCeEEEECCEEeec----------ccccccCCeEEEEECCCCCEeecCCCCCCccHHHHhhhhc--CCceeEcc
Confidence 7787774 45554211100 0111 56789999999999999887655678888775421 23578999
Q ss_pred CCCCCCceEEEeeCCHHHHHHHHHhHhcCccceEEEEEEeccCC
Q 018538 268 QIDNCTEGCVVLARTQEYCSIFHRKIREKKVKKLYLALTTAPLP 311 (354)
Q Consensus 268 RLDrdTSGLLL~AKn~~a~~~L~~~f~~~~V~K~YlAlV~G~l~ 311 (354)
|||++||||||||+|+++++.|.. ++++|.|+|+|+|.|.++
T Consensus 108 RLD~dTsGLLLlTndg~~~~~L~~--p~~~i~K~Y~v~V~G~~~ 149 (289)
T PRK10700 108 RLDVNTCGLLLFTTDGELANRLMH--PSREVEREYAVRVFGQVD 149 (289)
T ss_pred CCCCCCceEEEEEcCHHHHHHHhC--ccCCCCeEEEEEEccCCC
Confidence 999999999999999999999987 688999999999999986
No 10
>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=99.91 E-value=9.8e-24 Score=195.95 Aligned_cols=104 Identities=22% Similarity=0.314 Sum_probs=89.7
Q ss_pred ceeEeecCeEEEEECCCCccccCCCCCCcchHHHHHHHHhCCCCCceeccCCCCCCceEEEeeCCHHHHHHHHHhHhcCc
Q 018538 218 SRIIAVTESHVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQIDNCTEGCVVLARTQEYCSIFHRKIREKK 297 (354)
Q Consensus 218 l~IlYED~~llVVNKPaGl~vhp~~~~~~~TL~~~l~~~l~~~~~~~~VHRLDrdTSGLLL~AKn~~a~~~L~~~f~~~~ 297 (354)
++|||||++|+|||||+|++||++... .++.+.+..++. ...+++|||||++||||||||||+++++.|+++|++++
T Consensus 2 ~~ilyed~~~lvvnKP~Gl~v~~~~~~--~~l~~~l~~~~~-~~~~~~VhRLDr~TSGlll~Ak~~~~~~~L~~~~~~~~ 78 (217)
T TIGR01621 2 FEILFTHPDFLLINKHPGISVHKDDGE--TGLLQEVATQLG-VGQVWLVHRLDKMTSGILLLALNAESASELSQGFAKRK 78 (217)
T ss_pred ceEEEeCCCEEEEECCCCCeECCCCCc--ChHHHHHHHhcC-CCCccEecCCCCCCceEEEEEcCHHHHHHHHHHHhcCC
Confidence 579999999999999999999987642 466666655543 24689999999999999999999999999999999999
Q ss_pred cceEEEEEEeccCC--cceEEccccccCC
Q 018538 298 VKKLYLALTTAPLP--VGIMTHYMRPINI 324 (354)
Q Consensus 298 V~K~YlAlV~G~l~--~G~I~~~L~pi~r 324 (354)
|+|+|+|+|.|.++ +|+|+.+|.+...
T Consensus 79 v~K~YlAlV~g~~~~~~~~i~~~~~~~~~ 107 (217)
T TIGR01621 79 IEKTYLALSSKKPKKKQGLICGDMEKSRR 107 (217)
T ss_pred ccEEEEEEEeccccCCCCEEeCCcccCCC
Confidence 99999999999986 7899987765443
No 11
>PRK10158 23S rRNA/tRNA pseudouridine synthase A; Provisional
Probab=99.91 E-value=1.3e-23 Score=195.31 Aligned_cols=103 Identities=23% Similarity=0.231 Sum_probs=89.4
Q ss_pred CceeEeecCeEEEEECCCCccccCCCC-CCcchHHHHHHHHhCCCCCceeccCCCCCCceEEEeeCCHHHHHHHHHhHhc
Q 018538 217 NSRIIAVTESHVVLDKPAGTSVGGTTD-NIEESCATFASRALGLTTPLRTTHQIDNCTEGCVVLARTQEYCSIFHRKIRE 295 (354)
Q Consensus 217 ~l~IlYED~~llVVNKPaGl~vhp~~~-~~~~TL~~~l~~~l~~~~~~~~VHRLDrdTSGLLL~AKn~~a~~~L~~~f~~ 295 (354)
.++|||||++|+|+|||+|++||++.. ....++.+.+..++ ..+++|||||++||||||||||.+++..|.++|++
T Consensus 13 ~~~iiyed~~~lvvnKPaGl~~~~~~~~~~~~sl~~~l~~~~---~~~~~vhRLDr~TSGlll~Akt~~~~~~l~~~f~~ 89 (219)
T PRK10158 13 WLVILYQDEHIMVVNKPSGLLSVPGRLEEHKDSVMTRIQRDY---PQAESVHRLDMATSGVIVVALTKAAERELKRQFRE 89 (219)
T ss_pred CCCEEEeCCCEEEEECCCCCcEeCCCCCccchhHHHHHHHhC---CCCCEECCCCCCCceEEEEECCHHHHHHHHHHHHh
Confidence 468999999999999999999998763 34557777766554 24789999999999999999999999999999999
Q ss_pred CccceEEEEEEeccCC--cceEEcccccc
Q 018538 296 KKVKKLYLALTTAPLP--VGIMTHYMRPI 322 (354)
Q Consensus 296 ~~V~K~YlAlV~G~l~--~G~I~~~L~pi 322 (354)
++|.|+|+|+|.|.++ +++|+.+|...
T Consensus 90 ~~v~K~Yla~v~G~~~~~~~~i~~~i~~~ 118 (219)
T PRK10158 90 REPKKQYVARVWGHPSPAEGLVDLPLICD 118 (219)
T ss_pred CCccEEEEEEEecccCCCCcEEecceecC
Confidence 9999999999999986 78999777554
No 12
>PRK11112 tRNA pseudouridine synthase C; Provisional
Probab=99.91 E-value=1.2e-23 Score=200.02 Aligned_cols=102 Identities=21% Similarity=0.301 Sum_probs=85.2
Q ss_pred ceeEeecCeEEEEECCCCccccCCCCCCcch--HHHHHHHHhCCCCCceeccCCCCCCceEEEeeCCHHHHHHHHHhHhc
Q 018538 218 SRIIAVTESHVVLDKPAGTSVGGTTDNIEES--CATFASRALGLTTPLRTTHQIDNCTEGCVVLARTQEYCSIFHRKIRE 295 (354)
Q Consensus 218 l~IlYED~~llVVNKPaGl~vhp~~~~~~~T--L~~~l~~~l~~~~~~~~VHRLDrdTSGLLL~AKn~~a~~~L~~~f~~ 295 (354)
++|||||++|+|||||+||+||++.....++ +...+..+++ ..+++|||||++||||||||||+++++.|+++|++
T Consensus 2 l~IlyEd~~~lvvnKPaGl~~~~~~~~~~~~~~~~~~l~~~~~--~~~~~VHRLDr~TSGlll~Ak~~~~~~~L~~~f~~ 79 (257)
T PRK11112 2 LEILYQDEWLVAVNKPAGWLVHRSWLDRHETVFVMQTVRDQIG--QHVFTAHRLDRPTSGVLLMALSSEVARLLAQQFEQ 79 (257)
T ss_pred CcEEEecCCEEEEECCCCCeecCCCCCCCchHHHHHHHHHHhC--CCceeeccCCCCCeeEEEEECCHHHHHHHHHHHHh
Confidence 5799999999999999999999875433333 3333333332 35789999999999999999999999999999999
Q ss_pred CccceEEEEEEeccCC-cceEEccccc
Q 018538 296 KKVKKLYLALTTAPLP-VGIMTHYMRP 321 (354)
Q Consensus 296 ~~V~K~YlAlV~G~l~-~G~I~~~L~p 321 (354)
+.|+|+|+|+|.|.++ +|+|+.+|..
T Consensus 80 ~~v~K~Y~Alv~G~~~~~~~i~~~l~~ 106 (257)
T PRK11112 80 HQIQKTYHAIVRGWLMEEAVLDYPLKE 106 (257)
T ss_pred CCcceEEEEEEEeEeCCCCeEeeeeee
Confidence 9999999999999987 8899966654
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=99.90 E-value=1.7e-23 Score=194.59 Aligned_cols=104 Identities=23% Similarity=0.315 Sum_probs=86.1
Q ss_pred ceeEeecCeEEEEECCCCccccCCCCCCcc--hHHHHHHHHhCCCCCceeccCCCCCCceEEEeeCCHHHHHHHHHhHhc
Q 018538 218 SRIIAVTESHVVLDKPAGTSVGGTTDNIEE--SCATFASRALGLTTPLRTTHQIDNCTEGCVVLARTQEYCSIFHRKIRE 295 (354)
Q Consensus 218 l~IlYED~~llVVNKPaGl~vhp~~~~~~~--TL~~~l~~~l~~~~~~~~VHRLDrdTSGLLL~AKn~~a~~~L~~~f~~ 295 (354)
++|||||++|+|+|||+|++||++...... ++...+..+++ ..+++|||||++||||||||||++++..|+++|++
T Consensus 1 ~~Ilyed~~~lvvnKP~G~~~~~~~~~~~~~~~~~~~l~~~~~--~~~~~vhRLD~~TSGlll~Ak~~~~~~~l~~~f~~ 78 (223)
T cd02563 1 LEILYQDEHLVAINKPSGLLVHRSELDRHETRFALQTLRDQLG--QHVYPVHRLDRPTSGVLLFALSSEVARKLGEQFTE 78 (223)
T ss_pred CcEEEecCCEEEEECCCCCeEcCCCCCCCCcHHHHHHHHHHcC--CCcccccCCCCCCeEEEEEEECHHHHHHHHHHHhc
Confidence 369999999999999999999987643222 23333333332 35889999999999999999999999999999999
Q ss_pred CccceEEEEEEeccCC-cceEEccccccC
Q 018538 296 KKVKKLYLALTTAPLP-VGIMTHYMRPIN 323 (354)
Q Consensus 296 ~~V~K~YlAlV~G~l~-~G~I~~~L~pi~ 323 (354)
+.|+|+|+|+|.|.++ +|+|+.+|....
T Consensus 79 ~~v~K~Y~alv~G~~~~~~~i~~~l~~~~ 107 (223)
T cd02563 79 HRVHKTYLAVVRGYVPESGTIDYPLSEEL 107 (223)
T ss_pred CceeEEEEEEEECccCCCCeEEEeeeeCC
Confidence 9999999999999987 899997775543
No 14
>KOG1919 consensus RNA pseudouridylate synthases [RNA processing and modification]
Probab=99.87 E-value=1.4e-21 Score=193.93 Aligned_cols=158 Identities=30% Similarity=0.430 Sum_probs=132.0
Q ss_pred cHHHHHHhhc-CCCHHHHHHHHHcCCEEEeeeCCCCCCCCchhhhhhhcccCCccccccccccCCeEEeecccccccccc
Q 018538 111 PVLEYICREL-NLPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTFRITHV 189 (354)
Q Consensus 111 ~L~~~L~~~~-~lSr~~~~~lI~~G~V~~~~~~~~~~~~~~~e~~r~~~~~~~~~v~~kr~~vnGk~vr~~~~~~~~~~~ 189 (354)
.+.+++.+.| ..++.+.+..|+.|.|+ +||+.+ ..
T Consensus 45 ~~~~~~~~ef~~~~~~~~~~~i~~g~v~----------------------------------~n~~~~----------~v 80 (371)
T KOG1919|consen 45 KLVDVFVSEFRLRERAYYESAIKLGRVT----------------------------------VNGEQV----------RV 80 (371)
T ss_pred chHHHHHHHHhcCchHhhhhhhhcCceE----------------------------------ECcEee----------ee
Confidence 4677777777 88999999999999999 888874 46
Q ss_pred ceeecCCcEEEEecCCCCCCCCCCCCCCceeEeecCeEEEEECCCCccccCCCCCCcchHHHHHHHHhCCCCCceeccCC
Q 018538 190 DQIVEAGTYLRVHVHPKRFPRCYDIDWNSRIIAVTESHVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQI 269 (354)
Q Consensus 190 ~~~V~~GD~I~V~~~~~~~~~~~~~~~~l~IlYED~~llVVNKPaGl~vhp~~~~~~~TL~~~l~~~l~~~~~~~~VHRL 269 (354)
++.++.||.|...++....+. ..+.+.|+|||++|+|||||+|++|||++.+..+++...+..... ...+++||||
T Consensus 81 ~~i~k~~d~l~~~vhrh~p~~---~~~~~~Iv~ed~~~vVvnKP~gipVhp~g~~~~n~i~~~l~~~~~-~~~~~~~hRL 156 (371)
T KOG1919|consen 81 SLIVKNGDVLCHTVHRHEPPV---AYLPIRIVFEDKDYVVVNKPHGIPVHPTGRYRENTITKILAALHK-VEGLRPCHRL 156 (371)
T ss_pred EEEeccCCEEEEeeccCCCCc---cccccceEEecCCEEEEeCCCCCceeccCccccccchHHHHHhcc-cccccccccc
Confidence 778999999987665432221 235789999999999999999999999998888887766554322 2458999999
Q ss_pred CCCCceEEEeeCCHHHHHHHHHhHhcCccceEE-EEEEeccCC-cceEE
Q 018538 270 DNCTEGCVVLARTQEYCSIFHRKIREKKVKKLY-LALTTAPLP-VGIMT 316 (354)
Q Consensus 270 DrdTSGLLL~AKn~~a~~~L~~~f~~~~V~K~Y-lAlV~G~l~-~G~I~ 316 (354)
|+.|||||+|||+.+.+..|.+.|+++++.|.| .|-|.|.+| .+.+.
T Consensus 157 Dr~tSGllvlAkt~~~~~~~~~~~r~~~~~k~Y~v~~v~g~fp~~~~~~ 205 (371)
T KOG1919|consen 157 DRLTSGLLVLAKTKEAADKFHEVLRKRTVKKEYVVARVEGPFPVVGEVE 205 (371)
T ss_pred CccccceEEEEechhHhHHHHHHHhcccceeEEEEEEEeccCCCCceEE
Confidence 999999999999999999999999999999999 799999998 55443
No 15
>COG1187 RsuA 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]
Probab=99.85 E-value=1.1e-20 Score=178.57 Aligned_cols=142 Identities=20% Similarity=0.229 Sum_probs=114.0
Q ss_pred cHHHHHHhhcCCCHHHHHHHHHcCCEEEeeeCCCCCCCCchhhhhhhcccCCccccccccccCCeEEeeccccccccccc
Q 018538 111 PVLEYICRELNLPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTFRITHVD 190 (354)
Q Consensus 111 ~L~~~L~~~~~lSr~~~~~lI~~G~V~~~~~~~~~~~~~~~e~~r~~~~~~~~~v~~kr~~vnGk~vr~~~~~~~~~~~~ 190 (354)
+|++||++...+||+.+++||..|+|. |||++++ ...
T Consensus 4 RL~K~La~~G~~SRr~ae~lI~~G~V~----------------------------------VnG~v~~---------~~~ 40 (248)
T COG1187 4 RLNKFLAEAGVGSRREAEKLIEEGRVT----------------------------------VNGKVAT---------LGG 40 (248)
T ss_pred chHHHHHHcCCCCHHHHHHHHHcCCEE----------------------------------ECCEEec---------cCC
Confidence 399999998889999999999999999 9999853 455
Q ss_pred eeecCCc-EEEEecCCCCCCCCCCCCCCceeEe-ecCeEEEEECCCCccccCCCCCCcchHHHHHHHHhCCCCCceeccC
Q 018538 191 QIVEAGT-YLRVHVHPKRFPRCYDIDWNSRIIA-VTESHVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQ 268 (354)
Q Consensus 191 ~~V~~GD-~I~V~~~~~~~~~~~~~~~~l~IlY-ED~~llVVNKPaGl~vhp~~~~~~~TL~~~l~~~l~~~~~~~~VHR 268 (354)
..+.+++ .|.+.. ..+.+ +...|+++|||.|++|.-.+.....|+.+++...+....++++|+|
T Consensus 41 ~~v~~~~~~i~v~g--------------~~~~~~~~~~y~llnKP~G~v~s~~D~~gr~tv~D~lp~~~~~~~~~~pvGR 106 (248)
T COG1187 41 VVVDPDDDVVEVDG--------------KRIELKEERVYLLLNKPRGYVSSTEDDEGRPTVFDLLPERLPRKKRLFPVGR 106 (248)
T ss_pred eEeCCCCcEEEECC--------------EEeeccccceEEEEECCCCeEecccCCCCCceeeeecccccccccceeeccc
Confidence 6677774 566552 12333 3344999999999998877555667887776532222346999999
Q ss_pred CCCCCceEEEeeCCHHHHHHHHHhHhcCccceEEEEEEeccCC
Q 018538 269 IDNCTEGCVVLARTQEYCSIFHRKIREKKVKKLYLALTTAPLP 311 (354)
Q Consensus 269 LDrdTSGLLL~AKn~~a~~~L~~~f~~~~V~K~YlAlV~G~l~ 311 (354)
||+||+|||||++|+++++.|.. ++.++.|+|+|.|.|.+.
T Consensus 107 LD~dTeGLLLLTnDG~la~rL~~--P~~~~~K~Y~v~v~g~~~ 147 (248)
T COG1187 107 LDKDTEGLLLLTNDGELAHRLMH--PSSEVEKEYLVRVEGPVT 147 (248)
T ss_pred cCCCCeeEEEEeCCHHHHHHhcC--CCCCCCEEEEEEEecCCC
Confidence 99999999999999999999987 778999999999999886
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=99.82 E-value=3e-20 Score=162.88 Aligned_cols=96 Identities=25% Similarity=0.414 Sum_probs=72.9
Q ss_pred eEEEEECCCCccccCCCCCCcchHHHHHH---HHhCCCCCceeccCCCCCCceEEEeeCCHHHHHHHHHhHhcCccceEE
Q 018538 226 SHVVLDKPAGTSVGGTTDNIEESCATFAS---RALGLTTPLRTTHQIDNCTEGCVVLARTQEYCSIFHRKIREKKVKKLY 302 (354)
Q Consensus 226 ~llVVNKPaGl~vhp~~~~~~~TL~~~l~---~~l~~~~~~~~VHRLDrdTSGLLL~AKn~~a~~~L~~~f~~~~V~K~Y 302 (354)
||||||||+||+||+.+......+..... ........+++|||||++||||||||+|+++++.|.++|++++++|+|
T Consensus 1 ~~ivvnKP~G~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~RLD~~TsGlll~a~~~~~~~~l~~~f~~~~~~K~Y 80 (164)
T PF00849_consen 1 NLIVVNKPAGVPVHPSDGNESKSVKELPALSLKRGDDPPELYPVHRLDRDTSGLLLFAKDKEAAAKLSKQFPKRKVEKTY 80 (164)
T ss_dssp SEEEEEE-TTSBSSSSSTBSSSSHHCHHHHHHHHCTTSGGGEESS---TT-EEEEEEESSHHHHHHHHHHHHTTCSEEEE
T ss_pred CEEEEECCCCCeEecCCCCCcccccchhhhhhhhccCCCceEECCCCCccccCCeeccCCcccccccccccccCCCcEEE
Confidence 68999999999999988433333322222 222334569999999999999999999999999999999999999999
Q ss_pred EEEEec-cCC-cceEEccccc
Q 018538 303 LALTTA-PLP-VGIMTHYMRP 321 (354)
Q Consensus 303 lAlV~G-~l~-~G~I~~~L~p 321 (354)
+|+|.| ..+ +|.++.++.+
T Consensus 81 ~a~v~~~~~~~~~~~~~~~~~ 101 (164)
T PF00849_consen 81 LALVEGGPVEEEGKINSPLGK 101 (164)
T ss_dssp EEEECSSSSTTCEEEESHEEE
T ss_pred EEeEcccccccceeeeccccc
Confidence 999994 555 8999988866
No 17
>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=99.82 E-value=3.4e-20 Score=162.96 Aligned_cols=91 Identities=18% Similarity=0.239 Sum_probs=75.9
Q ss_pred EEEEECCCCccccCCCCCCcchHHHHHHHHhCCCCCceeccCCCCCCceEEEeeCCHHHHHHHHHhHhcCccceEEEEEE
Q 018538 227 HVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQIDNCTEGCVVLARTQEYCSIFHRKIREKKVKKLYLALT 306 (354)
Q Consensus 227 llVVNKPaGl~vhp~~~~~~~TL~~~l~~~l~~~~~~~~VHRLDrdTSGLLL~AKn~~a~~~L~~~f~~~~V~K~YlAlV 306 (354)
|+|+|||+|++||+++.....++.+.+.... ...+++|||||++||||||||||+++++.|+++ +++++|+|+|+|
T Consensus 1 ~ivvnKP~G~~~~~~~~~~~~~~~~~l~~~~--~~~~~~vhRLD~~TSGlll~ak~~~~~~~l~~~--~~~v~K~Y~a~v 76 (154)
T cd02550 1 ILVLNKPSGLVCHPTDRDRDPTVVVRLDKLH--GPRVHAAGRLDKDTSGLLLLTNDGRLQRRLTEP--RREIEKEYLVTV 76 (154)
T ss_pred CEEEECCCCCEEecCCCCCCCcHHHhhhccc--CCceeEeccCCCCCeeEEEEEcCHHHHHHHhhh--hccCcEEEEEEE
Confidence 6899999999999988766677776554322 246889999999999999999999999999998 778999999999
Q ss_pred eccCC-cceEEccccc
Q 018538 307 TAPLP-VGIMTHYMRP 321 (354)
Q Consensus 307 ~G~l~-~G~I~~~L~p 321 (354)
.|.++ ++.++.++..
T Consensus 77 ~g~~~~~~~~~~~~~~ 92 (154)
T cd02550 77 RGELDEEGIEDLATVR 92 (154)
T ss_pred EeecCcchheeccccc
Confidence 99987 6666644433
No 18
>cd02869 PseudoU_synth_RluCD_like PseudoU_synth_RsuA/RluD: Pseudouridine synthase, RsuA/RluD family. This group is comprised of eukaryotic, bacterial and archeal proteins similar to eight site specific Escherichia coli pseudouridine synthases: RsuA, RluA, RluB, RluC, RluD, RluE, RluF and TruA. Pseudouridine synthases catalyze the isomerization of specific uridines in a n RNA molecule to pseudouridines (5-ribosyluracil, psi) requiring no cofactors. E. coli RluC for example makes psi955, 2504 and 2580 in 23S RNA. Some psi sites such as psi1917 in 23S RNA made by RluD are universally conserved. Other psi sites occur in a more restricted fashion, for example psi2819 in 21S mitochondrial ribosomal RNA made by S. cerevisiae Pus5p is only found in mitochondrial large subunit rRNAs from some other species and in gram negative bacteria. The E. coli counterpart of this psi residue is psi2580 in 23S rRNA. psi2604in 23S RNA made by RluF has only been detected in E.coli.
Probab=99.80 E-value=6.5e-19 Score=157.11 Aligned_cols=96 Identities=25% Similarity=0.381 Sum_probs=80.7
Q ss_pred EEEEECCCCccccCCCCCCcchHHHHHHHHh---CCCCCceeccCCCCCCceEEEeeCCHHHHHHHHHhHhcCccceEEE
Q 018538 227 HVVLDKPAGTSVGGTTDNIEESCATFASRAL---GLTTPLRTTHQIDNCTEGCVVLARTQEYCSIFHRKIREKKVKKLYL 303 (354)
Q Consensus 227 llVVNKPaGl~vhp~~~~~~~TL~~~l~~~l---~~~~~~~~VHRLDrdTSGLLL~AKn~~a~~~L~~~f~~~~V~K~Yl 303 (354)
|+|+|||+|++++++......++.+.+.... .....+++|||||++||||||||||+++++.|.++|+++.+.|+|+
T Consensus 1 ~lvvnKP~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~RLD~~tsGlll~ak~~~~~~~l~~~~~~~~~~K~Y~ 80 (185)
T cd02869 1 LLVVNKPAGLPVHPGPGHLTGTLVNALLKLLLLLGEEFRPGLVHRLDKDTSGLLLVAKNKKAAAKLSKQFKERKVKKTYL 80 (185)
T ss_pred CEEEECCCCCeeecCCCCCCCCHHHHHHHHHhhcCCCCcCceecccCCCCceEEEEEcCHHHHHHHHHHHhcCceeEEEE
Confidence 5899999999999988776777776642222 2234689999999999999999999999999999999999999999
Q ss_pred EEEeccCC--cceEEcccccc
Q 018538 304 ALTTAPLP--VGIMTHYMRPI 322 (354)
Q Consensus 304 AlV~G~l~--~G~I~~~L~pi 322 (354)
|+|.|.++ .+.++.++.+.
T Consensus 81 a~v~g~~~~~~~~~~~~~~~~ 101 (185)
T cd02869 81 ALVDGKPPEDEGTIDAPLGRK 101 (185)
T ss_pred EEEeCCCCCCccEEecccccC
Confidence 99999987 67888666543
No 19
>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=99.76 E-value=2.2e-18 Score=153.93 Aligned_cols=82 Identities=11% Similarity=0.160 Sum_probs=70.7
Q ss_pred eEEEEECCCCccccCCCCCCcchHHHHHHHHhCCCCCceeccCCCCCCceEEEeeCCHHHHHHHHHhHhcCccceEEEEE
Q 018538 226 SHVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQIDNCTEGCVVLARTQEYCSIFHRKIREKKVKKLYLAL 305 (354)
Q Consensus 226 ~llVVNKPaGl~vhp~~~~~~~TL~~~l~~~l~~~~~~~~VHRLDrdTSGLLL~AKn~~a~~~L~~~f~~~~V~K~YlAl 305 (354)
.|+|+|||+|++||+.+.....++.+.+..+. ...+++|||||++||||||||||+++++.|+. +++.+.|+|+|+
T Consensus 1 ~~lvvnKP~G~~~~~~~~~~~~tl~~~l~~~~--~~~~~~V~RLD~~TsGLll~ak~~~~~~~L~~--~~~~i~K~Y~a~ 76 (167)
T cd02556 1 RVLIYHKPEGLICTRKDPKGRPTVFDLLPKLG--IPRWISVGRLDLNTEGLLLFTNDGELANRLMH--PSNEIEREYAVR 76 (167)
T ss_pred CEEEEECCCCcEECccCCCCCccHHHhhhhhc--cCceEEcCcCCCCCeeEEEEECCHHHHHHHhC--CcCCCCeEEEEE
Confidence 37899999999999866555678888776542 23578999999999999999999999999976 788999999999
Q ss_pred EeccCC
Q 018538 306 TTAPLP 311 (354)
Q Consensus 306 V~G~l~ 311 (354)
|.|.++
T Consensus 77 V~g~~~ 82 (167)
T cd02556 77 VFGQVT 82 (167)
T ss_pred ECccCC
Confidence 999987
No 20
>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=99.74 E-value=1.6e-18 Score=151.25 Aligned_cols=80 Identities=19% Similarity=0.206 Sum_probs=67.7
Q ss_pred EEEEECCCCccccCCCCCCcchHHHHHHHHhCCCCCceeccCCCCCCceEEEeeCCHHHHHHHHHhHhcCccceEEEEEE
Q 018538 227 HVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQIDNCTEGCVVLARTQEYCSIFHRKIREKKVKKLYLALT 306 (354)
Q Consensus 227 llVVNKPaGl~vhp~~~~~~~TL~~~l~~~l~~~~~~~~VHRLDrdTSGLLL~AKn~~a~~~L~~~f~~~~V~K~YlAlV 306 (354)
|+|+|||+|++||+++.....++.+.+... ...+++|||||++||||||||||+++++.|.. +++.++|+|+|+|
T Consensus 1 ~ivvnKP~G~~~~~~~~~~~~~l~~~l~~~---~~~~~~vhRLD~~TsGlll~ak~~~~~~~l~~--~~~~i~K~Y~a~v 75 (146)
T cd02870 1 YLLLNKPRGVVSTVRDPEGRPTVLDLLKDV---GERLFPVGRLDYDTEGLLLLTNDGELANRLTH--PRYGVEKTYLVKV 75 (146)
T ss_pred CEEEECCCCcEecccCCCCCCEEeeecccc---CCCEEECCCCCCCCeeEEEEeCCHHHHHHhhC--ccCCCCeEEEEEE
Confidence 689999999999988765556766544321 24689999999999999999999999999986 5678999999999
Q ss_pred eccCC
Q 018538 307 TAPLP 311 (354)
Q Consensus 307 ~G~l~ 311 (354)
.|.++
T Consensus 76 ~g~~~ 80 (146)
T cd02870 76 RGVPS 80 (146)
T ss_pred CCCCC
Confidence 99987
No 21
>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=99.74 E-value=6.8e-18 Score=150.86 Aligned_cols=81 Identities=20% Similarity=0.271 Sum_probs=69.3
Q ss_pred EEEEECCCCccccCCCCCCcchHHHHHHHHhCCCCCceeccCCCCCCceEEEeeCCHHHHHHHHHhHhcCccceEEEEEE
Q 018538 227 HVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQIDNCTEGCVVLARTQEYCSIFHRKIREKKVKKLYLALT 306 (354)
Q Consensus 227 llVVNKPaGl~vhp~~~~~~~TL~~~l~~~l~~~~~~~~VHRLDrdTSGLLL~AKn~~a~~~L~~~f~~~~V~K~YlAlV 306 (354)
|+|+|||+|++||++.. ...++.+.+..++. ...+++|||||++||||||||||.++++.|.. +.++++|+|+|+|
T Consensus 2 ~ivvnKP~G~~~~~~~~-~~~tl~~~l~~~~~-~~~~~~vhRLD~~TSGlll~ak~~~~~~~l~~--~~~~i~K~Y~a~V 77 (167)
T cd02553 2 YLMLNKPAGVVCATKDP-HHPTVIDLLPEPDR-RRDLFPVGRLDKDTTGLLLLTNDGQLAHRLTS--PKKHVPKTYEVTL 77 (167)
T ss_pred EEEEECCCCCEeCCCCC-CCCcHHHHhhhhcc-cCCeEEcccCCCCCEEEEEEEeCHHHHHHhhC--CcCCCceEEEEEE
Confidence 79999999999996544 46788887776543 24589999999999999999999998888876 5778999999999
Q ss_pred eccCC
Q 018538 307 TAPLP 311 (354)
Q Consensus 307 ~G~l~ 311 (354)
.|.++
T Consensus 78 ~G~~~ 82 (167)
T cd02553 78 AGPLT 82 (167)
T ss_pred ccCCC
Confidence 99987
No 22
>cd02566 PseudoU_synth_RluE PseudoU_synth_RluE: Pseudouridine synthase, Escherichia coli RluE. This group is comprised of bacterial proteins similar to E. coli RluE. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. Escherichia coli RluE makes psi2457 in 23S RNA. psi2457 is not universally conserved.
Probab=99.69 E-value=3.5e-17 Score=146.34 Aligned_cols=78 Identities=14% Similarity=0.181 Sum_probs=65.7
Q ss_pred EEEEECCCCccccCCCC-CCcchHHHHHHHHhCCCCCceeccCCCCCCceEEEeeCCHHHHHHHHHhHhcCccceEEEEE
Q 018538 227 HVVLDKPAGTSVGGTTD-NIEESCATFASRALGLTTPLRTTHQIDNCTEGCVVLARTQEYCSIFHRKIREKKVKKLYLAL 305 (354)
Q Consensus 227 llVVNKPaGl~vhp~~~-~~~~TL~~~l~~~l~~~~~~~~VHRLDrdTSGLLL~AKn~~a~~~L~~~f~~~~V~K~YlAl 305 (354)
|+|+|||+|++||+++. ....++.+.+. ...+++|||||++||||||||+|+++++.|.+. ++.++|+|+|+
T Consensus 1 ~lv~nKP~G~~~~~~~~~~~~~~l~~~l~-----~~~~~~v~RLD~~TsGlll~a~d~~~~~~l~~~--~~~v~K~Y~a~ 73 (168)
T cd02566 1 LILFNKPYGVLSQFTDESEKHKTLKDYID-----DPGVYAAGRLDRDSEGLLLLTDDGRLQHRITDP--SFKHPKTYYVQ 73 (168)
T ss_pred CEEEECCCCCEEecCCCcCCCccHHHHcC-----cCCeEEccCCCCCCeEEEEEEeCHHHHHHHHCC--CCCCCEEEEEE
Confidence 58999999999998765 44567766542 135789999999999999999999999999874 55799999999
Q ss_pred EeccCC
Q 018538 306 TTAPLP 311 (354)
Q Consensus 306 V~G~l~ 311 (354)
|.|.++
T Consensus 74 v~g~~~ 79 (168)
T cd02566 74 VEGVPT 79 (168)
T ss_pred ECCcCC
Confidence 999986
No 23
>PRK11394 23S rRNA pseudouridine synthase E; Provisional
Probab=99.62 E-value=8.7e-16 Score=143.08 Aligned_cols=80 Identities=15% Similarity=0.203 Sum_probs=69.3
Q ss_pred CeEEEEECCCCccccCCCCCCcchHHHHHHHHhCCCCCceeccCCCCCCceEEEeeCCHHHHHHHHHhHhcCccceEEEE
Q 018538 225 ESHVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQIDNCTEGCVVLARTQEYCSIFHRKIREKKVKKLYLA 304 (354)
Q Consensus 225 ~~llVVNKPaGl~vhp~~~~~~~TL~~~l~~~l~~~~~~~~VHRLDrdTSGLLL~AKn~~a~~~L~~~f~~~~V~K~YlA 304 (354)
..|+++|||+|++|+..+.....++.+.+. ..++++|||||++||||||||+|+++++.|.++ ++.+.|+|+|
T Consensus 39 ~~ylllnKP~G~l~~~~d~~~~~tl~d~l~-----~~~~~~vgRLD~~TsGllLlt~d~~~~~~L~~~--~~~i~K~Y~~ 111 (217)
T PRK11394 39 TRVILFNKPYDVLPQFTDEAGRKTLKEFIP-----VQGVYAAGRLDRDSEGLLVLTNNGALQARLTQP--GKRTGKIYYV 111 (217)
T ss_pred CEEEEEECCCCCEEeeCCccCCcchHHhcc-----cCCeEEecCCCCCCeeEEEEECCHHHHHHHhCc--ccCCCEEEEE
Confidence 479999999999999765555567777653 236899999999999999999999999999995 7789999999
Q ss_pred EEeccCC
Q 018538 305 LTTAPLP 311 (354)
Q Consensus 305 lV~G~l~ 311 (354)
+|.|.++
T Consensus 112 ~v~g~~~ 118 (217)
T PRK11394 112 QVEGIPT 118 (217)
T ss_pred EECCCCC
Confidence 9999986
No 24
>cd02555 PSSA_1 PSSA_1: Pseudouridine synthase, a subgroup of the RsuA family. This group is comprised of bacterial proteins assigned to the RsuA family of pseudouridine synthases. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. The TruA family is comprised of proteins related to Escherichia coli RsuA.
Probab=99.62 E-value=1.1e-15 Score=138.11 Aligned_cols=82 Identities=16% Similarity=0.210 Sum_probs=64.9
Q ss_pred CeEEEEECCCCccccCCC--------CCCcchHHHHHHHHhCCCCCceeccCCCCCCceEEEeeCCHHHHHHHHHhHhcC
Q 018538 225 ESHVVLDKPAGTSVGGTT--------DNIEESCATFASRALGLTTPLRTTHQIDNCTEGCVVLARTQEYCSIFHRKIREK 296 (354)
Q Consensus 225 ~~llVVNKPaGl~vhp~~--------~~~~~TL~~~l~~~l~~~~~~~~VHRLDrdTSGLLL~AKn~~a~~~L~~~f~~~ 296 (354)
..|+++|||+|++|...+ .....++.+.+..++ .++++|||||++||||||||+|+++++.|.++ .+
T Consensus 4 ~~y~llnKP~G~l~s~~d~~~~~g~~~~~~~~~~~~l~~~~---~~l~~VgRLD~dTsGLLl~t~d~~~~~~L~~~--~~ 78 (177)
T cd02555 4 PVTLLLHKPAGMVSEQALALLGPGQRSAADRSGRRPLKGHF---ARLAPIGPLDKDASGLLVFSQDGRVLRKLIGD--AS 78 (177)
T ss_pred cEEEEEECCCceEecCCCcccccccccccccchhhhhhhcC---CceeEecCCCCCCeeEEEEECCHHHHHHHhCh--hc
Confidence 357999999999886443 112234444444333 36889999999999999999999999999995 46
Q ss_pred ccceEEEEEEeccCC
Q 018538 297 KVKKLYLALTTAPLP 311 (354)
Q Consensus 297 ~V~K~YlAlV~G~l~ 311 (354)
.|.|+|+|+|.|.++
T Consensus 79 ~i~K~Y~v~v~g~~~ 93 (177)
T cd02555 79 RLEQEYLVEVRGELT 93 (177)
T ss_pred CCCEEEEEEEcccCC
Confidence 899999999999987
No 25
>cd02554 PseudoU_synth_RluF PseudoU_synth_RluF_like: Pseudouridine synthase, Escherichia coli RluF like. This group is comprised of bacterial proteins similar to Escherichia coli RluF. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. E.coli RluF makes psi2604 in 23S RNA. psi2604 has only been detected in E. coli. It is absent from other eubacteria despite a precursor U at that site and from eukarya and archea which lack a precursor U at that site.
Probab=99.58 E-value=4.5e-15 Score=132.82 Aligned_cols=78 Identities=17% Similarity=0.333 Sum_probs=66.6
Q ss_pred EEEEECCCCccccCCCCCCcchHHHHHHHHhCCCCCceeccCCCCCCceEEEeeCCHHHHHHHHHhHhcCccceEEEEEE
Q 018538 227 HVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQIDNCTEGCVVLARTQEYCSIFHRKIREKKVKKLYLALT 306 (354)
Q Consensus 227 llVVNKPaGl~vhp~~~~~~~TL~~~l~~~l~~~~~~~~VHRLDrdTSGLLL~AKn~~a~~~L~~~f~~~~V~K~YlAlV 306 (354)
|+++|||+|++|++++.. ..++.+++.. ..++++|||||++||||||||+|+++++.|+.. .+.+.|+|+|.|
T Consensus 2 y~~lnKP~G~l~s~~~~~-~~tv~~~l~~----~~~~~~vgRLD~~tsGlll~t~dg~~~~~L~~p--~~~~~K~Y~V~v 74 (164)
T cd02554 2 YIAYNKPVGIDCTLERAD-EDNIIDFVNP----PPRIFPIGRLDKDSEGLILLTNDGDLVNKILHA--DNNHEKEYLVTV 74 (164)
T ss_pred EEEEECCCCcEeecCCCC-CCcHHHHhcC----cCCEEEccCCCCCCeeEEEEEcCHHHHHHHhhh--hcCCCeEEEEEE
Confidence 789999999999987653 4677776532 246999999999999999999999999999774 448899999999
Q ss_pred eccCC
Q 018538 307 TAPLP 311 (354)
Q Consensus 307 ~G~l~ 311 (354)
.|.+.
T Consensus 75 ~~~l~ 79 (164)
T cd02554 75 NKPIT 79 (164)
T ss_pred CCCCC
Confidence 99986
No 26
>cd02868 PseudoU_synth_hTruB2_like PseudoU_synth_ hTRUB2_Like: Pseudouridine synthase, humanTRUB2_like. This group consists of eukaryotic pseudouridine synthases similar to human TruB pseudouridine synthase homolog 2 (TRUB2). Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi).
Probab=99.16 E-value=6.4e-11 Score=111.20 Aligned_cols=75 Identities=13% Similarity=0.177 Sum_probs=58.0
Q ss_pred EEEEECCCCccccCCCCCCcchHHHHHHHHhCCCCCceeccCCCCCCceEEEeeCCHHHHHHHHHhHhcCccceEEEEEE
Q 018538 227 HVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQIDNCTEGCVVLARTQEYCSIFHRKIREKKVKKLYLALT 306 (354)
Q Consensus 227 llVVNKPaGl~vhp~~~~~~~TL~~~l~~~l~~~~~~~~VHRLDrdTSGLLL~AKn~~a~~~L~~~f~~~~V~K~YlAlV 306 (354)
++|||||+||.++... +.+...+...++.....+.|||||++|||||+||++... +|.+.|.++.+.|+|++..
T Consensus 2 ilvvnKP~Gi~s~~~~----~~~~~~l~~~~~~~k~~~~vhrLD~~aSGvl~~a~~~~t--kl~~~~~~~~~~K~Y~~~~ 75 (226)
T cd02868 2 LFAVYKPPGVHWKHVR----DTIESNLLKYFPEDKVLVGVHRLDAFSSGVLVLGVNHGN--KLLSHLYSNHPTRVYTIRG 75 (226)
T ss_pred EEEEEcCCCCChhHHH----HHHHHHHHHHccccceeeEccccCCCCceEEEEEeChhH--hHHHHHHhcCCCeEEEEEE
Confidence 7899999999776532 344444444444333367889999999999999999986 6999999888999999665
Q ss_pred e
Q 018538 307 T 307 (354)
Q Consensus 307 ~ 307 (354)
.
T Consensus 76 ~ 76 (226)
T cd02868 76 L 76 (226)
T ss_pred E
Confidence 3
No 27
>TIGR00093 pseudouridine synthase. This model identifies panels of pseudouridine synthase enzymes that RNA modifications involved in maturing the protein translation apparatus. Counts per genome vary: two in Staphylococcus aureus, three in Pseudomonas putida, four in E. coli, etc.
Probab=99.14 E-value=4.5e-11 Score=102.40 Aligned_cols=44 Identities=20% Similarity=0.375 Sum_probs=41.9
Q ss_pred ccCCCCCCceEEEeeCCHHHHHHHHHhHhcCccceEEEEEEeccCC
Q 018538 266 THQIDNCTEGCVVLARTQEYCSIFHRKIREKKVKKLYLALTTAPLP 311 (354)
Q Consensus 266 VHRLDrdTSGLLL~AKn~~a~~~L~~~f~~~~V~K~YlAlV~G~l~ 311 (354)
|||||++||||||||||+++++.|.+ ++++|.|+|+|+|.|.++
T Consensus 1 v~RLD~~TSGlll~akd~~~~~~L~~--~~~~i~K~Y~a~v~g~~~ 44 (128)
T TIGR00093 1 AGRLDRDSEGLLLLTNDGELVHRLTH--PGHHCEKTYLVTVEGPVT 44 (128)
T ss_pred CCCCCCCCEEEEEEEeCHHHHHHHhC--CCCCCCeEEEEEECCCCC
Confidence 79999999999999999999999988 678999999999999987
No 28
>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=98.80 E-value=2.2e-08 Score=73.83 Aligned_cols=68 Identities=21% Similarity=0.237 Sum_probs=56.7
Q ss_pred cHHHHHHhhc-CCCHHHHHHHHHcCCEEEeeeCCCCCCCCchhhhhhhcccCCccccccccccCCeEEeecccccccccc
Q 018538 111 PVLEYICREL-NLPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTFRITHV 189 (354)
Q Consensus 111 ~L~~~L~~~~-~lSr~~~~~lI~~G~V~~~~~~~~~~~~~~~e~~r~~~~~~~~~v~~kr~~vnGk~vr~~~~~~~~~~~ 189 (354)
+|++||.+.+ ..|++.++++|+.|.|+ +||+.+ +.+
T Consensus 2 rl~~~l~~~~~~~sr~~~~~~i~~g~V~----------------------------------vn~~~~---------~~~ 38 (70)
T cd00165 2 RLDKILARLGLAPSRSEARQLIKHGHVL----------------------------------VNGKVV---------TKP 38 (70)
T ss_pred cHHHHHHHhccccCHHHHHHHHHcCCEE----------------------------------ECCEEc---------cCC
Confidence 4999999885 78999999999999999 899873 367
Q ss_pred ceeecCCcEEEEecCCCCCCCCCCCCCCceeEeecCeEEEEE
Q 018538 190 DQIVEAGTYLRVHVHPKRFPRCYDIDWNSRIIAVTESHVVLD 231 (354)
Q Consensus 190 ~~~V~~GD~I~V~~~~~~~~~~~~~~~~l~IlYED~~llVVN 231 (354)
++.+..||.|.+...+ ....|+|||++++|+|
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 8889999999887421 1238999999999987
No 29
>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=98.37 E-value=7.9e-07 Score=66.29 Aligned_cols=54 Identities=6% Similarity=0.019 Sum_probs=45.4
Q ss_pred eeCCC-CcHHHHHHhhcCC--CHHHHHHHHHcCCEEEeeeCCCCCCCCchhhhhhhcccCCccccccccccCCeEEeecc
Q 018538 105 VVSEG-GPVLEYICRELNL--PPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQ 181 (354)
Q Consensus 105 ~v~~~-~~L~~~L~~~~~l--Sr~~~~~lI~~G~V~~~~~~~~~~~~~~~e~~r~~~~~~~~~v~~kr~~vnGk~vr~~~ 181 (354)
.+.++ .+|++||++. ++ ||+.++++|+.|.|+ |||+++
T Consensus 3 ~~~~~~~rLd~~L~~~-~~~~SR~~~k~li~~G~V~----------------------------------VNg~~~---- 43 (59)
T TIGR02988 3 KIFTEYITLGQLLKEL-GIIDSGGQAKWFLQENEVL----------------------------------VNGELE---- 43 (59)
T ss_pred eecchHHHHHHHHHHc-CCccCHHHHHHHHHcCCEE----------------------------------ECCEEc----
Confidence 34445 4799999998 66 999999999999999 999973
Q ss_pred ccccccccceeecCCcEEEEe
Q 018538 182 KTFRITHVDQIVEAGTYLRVH 202 (354)
Q Consensus 182 ~~~~~~~~~~~V~~GD~I~V~ 202 (354)
..++++|.+||.|.|+
T Consensus 44 -----~~~~~~l~~Gd~v~i~ 59 (59)
T TIGR02988 44 -----NRRGKKLYPGDVIEIP 59 (59)
T ss_pred -----cCCCCCCCCCCEEEeC
Confidence 3678999999999863
No 30
>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=98.22 E-value=3.8e-06 Score=59.68 Aligned_cols=46 Identities=24% Similarity=0.284 Sum_probs=40.9
Q ss_pred cHHHHHHhhc-CCCHHHHHHHHHcCCEEEeeeCCCCCCCCchhhhhhhcccCCccccccccccCCeEEeecccccccccc
Q 018538 111 PVLEYICREL-NLPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTFRITHV 189 (354)
Q Consensus 111 ~L~~~L~~~~-~lSr~~~~~lI~~G~V~~~~~~~~~~~~~~~e~~r~~~~~~~~~v~~kr~~vnGk~vr~~~~~~~~~~~ 189 (354)
|||+||.+.. ..||++++++|+.|.|+ |||+.+ .++
T Consensus 2 RLd~~L~~~~~~~sr~~a~~~I~~g~V~----------------------------------VNg~~v---------~~~ 38 (48)
T PF01479_consen 2 RLDKFLSRLGLASSRSEARRLIKQGRVK----------------------------------VNGKVV---------KDP 38 (48)
T ss_dssp BHHHHHHHTTSSSSHHHHHHHHHTTTEE----------------------------------ETTEEE---------SST
T ss_pred CHHHHHHHcCCcCCHHHHHHhcCCCEEE----------------------------------ECCEEE---------cCC
Confidence 4999998766 67899999999999999 999985 468
Q ss_pred ceeecCCcEE
Q 018538 190 DQIVEAGTYL 199 (354)
Q Consensus 190 ~~~V~~GD~I 199 (354)
++.|.+||.|
T Consensus 39 ~~~v~~~d~I 48 (48)
T PF01479_consen 39 SYIVKPGDVI 48 (48)
T ss_dssp TSBESTTEEE
T ss_pred CCCCCCcCCC
Confidence 9999999986
No 31
>cd02572 PseudoU_synth_hDyskerin PseudoU_synth_hDyskerin_Like: Pseudouridine synthase, human dyskerin like. This group consists of eukaryotic and archeal pseudouridine synthases similar to human dyskerin, Saccharomyces cerevisiae Cbf5, and Drosophila melanogaster Mfl (minifly protein). Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactor is required. S. cerevisiae Cbf5 and human dyskerin are nucleolar proteins that, with the help of guide RNAs, make the hundreds of psueudouridnes present in rRNA and small nuclear RNAs (snRNAs). Cbf5/Dyskerin is the catalytic subunit of eukaryotic box H/ACA small nucleolar ribonucleoprotein (snoRNP) particles. D. melanogaster mfl hosts in its fourth intron, a box H/AC snoRNA gene. In addition dyskerin is likely to have a structural role in the telomerase complex. Mutations in human dyskerin cause X-linked dyskeratosis congenitas. Mutations in Drosophila Mfl r
Probab=97.63 E-value=0.00021 Score=65.28 Aligned_cols=70 Identities=20% Similarity=0.368 Sum_probs=54.5
Q ss_pred CeEEEEECCCCccccCCCCCCcchHHHHHHHHhCCCCCceeccCCCCCCceEEEeeCCHHHHHHHHHhHhcCccceEEEE
Q 018538 225 ESHVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQIDNCTEGCVVLARTQEYCSIFHRKIREKKVKKLYLA 304 (354)
Q Consensus 225 ~~llVVNKPaGl~vhp~~~~~~~TL~~~l~~~l~~~~~~~~VHRLDrdTSGLLL~AKn~~a~~~L~~~f~~~~V~K~YlA 304 (354)
+.++++|||.|+.+| .+++.+.+.++. .+++..+-||-..||||+++-+.. .++.+.+. .-.|+|.|
T Consensus 2 ~g~l~i~Kp~g~tS~--------~~v~~~k~~~~~-kkvGH~GTLDp~A~GvLiv~~g~~--Tk~~~~~~--~~~K~Y~a 68 (182)
T cd02572 2 YGVINLDKPSGPSSH--------EVVAWIKRILGV-EKTGHSGTLDPKVTGCLPVCIDRA--TRLVKSQQ--EAGKEYVC 68 (182)
T ss_pred CeEEEEecCCCCCHH--------HHHHHHHHHhCC-CccCcCCCCCCcCeeEEEEEECHH--hhhhHHHh--CCCCEEEE
Confidence 368999999999775 456667766664 468899999999999999999873 44555555 34599999
Q ss_pred EEe
Q 018538 305 LTT 307 (354)
Q Consensus 305 lV~ 307 (354)
.+.
T Consensus 69 ~v~ 71 (182)
T cd02572 69 VMR 71 (182)
T ss_pred EEE
Confidence 875
No 32
>smart00363 S4 S4 RNA-binding domain.
Probab=97.47 E-value=0.00043 Score=49.18 Aligned_cols=50 Identities=26% Similarity=0.297 Sum_probs=43.1
Q ss_pred cHHHHHHhhc-CCCHHHHHHHHHcCCEEEeeeCCCCCCCCchhhhhhhcccCCccccccccccCCeEEeecccccccccc
Q 018538 111 PVLEYICREL-NLPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTFRITHV 189 (354)
Q Consensus 111 ~L~~~L~~~~-~lSr~~~~~lI~~G~V~~~~~~~~~~~~~~~e~~r~~~~~~~~~v~~kr~~vnGk~vr~~~~~~~~~~~ 189 (354)
+|+.||.+.+ ..|++.++++++.|.|+ |||+.+ ..+
T Consensus 2 rl~~~l~~~~~~~s~~~~~~~i~~g~i~----------------------------------vng~~~---------~~~ 38 (60)
T smart00363 2 RLDKFLARLGLAPSRSQARKLIEQGRVK----------------------------------VNGKKV---------TKP 38 (60)
T ss_pred cHHHHHHHcCcccCHHHHHHHHHcCCEE----------------------------------ECCEEe---------cCC
Confidence 4899998874 78999999999999999 899874 367
Q ss_pred ceeecCCcEEEEec
Q 018538 190 DQIVEAGTYLRVHV 203 (354)
Q Consensus 190 ~~~V~~GD~I~V~~ 203 (354)
++.+..||.|.+..
T Consensus 39 ~~~l~~gd~i~~~~ 52 (60)
T smart00363 39 SYIVKPGDVISVRG 52 (60)
T ss_pred CeEeCCCCEEEEcc
Confidence 88899999998875
No 33
>COG1188 Ribosome-associated heat shock protein implicated in the recycling of the 50S subunit (S4 paralog) [Translation, ribosomal structure and biogenesis]
Probab=97.41 E-value=0.0003 Score=58.21 Aligned_cols=51 Identities=14% Similarity=0.242 Sum_probs=44.4
Q ss_pred cHHHHHHhh-cCCCHHHHHHHHHcCCEEEeeeCCCCCCCCchhhhhhhcccCCccccccccccCCeEEeecccccccccc
Q 018538 111 PVLEYICRE-LNLPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTFRITHV 189 (354)
Q Consensus 111 ~L~~~L~~~-~~lSr~~~~~lI~~G~V~~~~~~~~~~~~~~~e~~r~~~~~~~~~v~~kr~~vnGk~vr~~~~~~~~~~~ 189 (354)
|||+||--. +--+|+.++++++.|+|+ +||+. +++
T Consensus 10 RLDKwL~~aR~~KrRslAk~~~~~GrV~----------------------------------vNG~~----------aKp 45 (100)
T COG1188 10 RLDKWLWAARFIKRRSLAKEMIEGGRVK----------------------------------VNGQR----------AKP 45 (100)
T ss_pred ehHHHHHHHHHhhhHHHHHHHHHCCeEE----------------------------------ECCEE----------ccc
Confidence 399999554 577999999999999999 89987 488
Q ss_pred ceeecCCcEEEEecCC
Q 018538 190 DQIVEAGTYLRVHVHP 205 (354)
Q Consensus 190 ~~~V~~GD~I~V~~~~ 205 (354)
++.|+.||.|+|.+..
T Consensus 46 S~~VK~GD~l~i~~~~ 61 (100)
T COG1188 46 SKEVKVGDILTIRFGN 61 (100)
T ss_pred ccccCCCCEEEEEeCC
Confidence 9999999999998754
No 34
>PLN00051 RNA-binding S4 domain-containing protein; Provisional
Probab=97.33 E-value=0.00054 Score=66.16 Aligned_cols=50 Identities=18% Similarity=0.204 Sum_probs=45.8
Q ss_pred cHHHHHHhhcCCCHHHHHHHHHcCCEEEeeeCCCCCCCCchhhhhhhcccCCccccccccccCCeEEeeccccccccccc
Q 018538 111 PVLEYICRELNLPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTFRITHVD 190 (354)
Q Consensus 111 ~L~~~L~~~~~lSr~~~~~lI~~G~V~~~~~~~~~~~~~~~e~~r~~~~~~~~~v~~kr~~vnGk~vr~~~~~~~~~~~~ 190 (354)
|||.+|+..+++||+.++++|+.|.|. |||+.+ .+++
T Consensus 193 RLD~vla~~~~~SRsk~~~lI~~g~V~----------------------------------vN~~~v---------~~~s 229 (267)
T PLN00051 193 RLDALASAGFRMSRSKLVDLISSGDVR----------------------------------VNWREV---------TKNG 229 (267)
T ss_pred cHHHHHHHHhccCHHHHHHHHHcCcEE----------------------------------ECCEEc---------CCCC
Confidence 699999999999999999999999999 899874 4788
Q ss_pred eeecCCcEEEEec
Q 018538 191 QIVEAGTYLRVHV 203 (354)
Q Consensus 191 ~~V~~GD~I~V~~ 203 (354)
+.|++||.|.|..
T Consensus 230 ~~v~~gD~isiRG 242 (267)
T PLN00051 230 TTLKTGDVVSVSG 242 (267)
T ss_pred CCCCCCCEEEEee
Confidence 9999999999974
No 35
>PRK00989 truB tRNA pseudouridine synthase B; Provisional
Probab=97.31 E-value=0.0007 Score=64.02 Aligned_cols=71 Identities=18% Similarity=0.274 Sum_probs=55.8
Q ss_pred CeEEEEECCCCccccCCCCCCcchHHHHHHHHhCCCCCceeccCCCCCCceEEEeeCCHHHHHHHHHhHhcCccceEEEE
Q 018538 225 ESHVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQIDNCTEGCVVLARTQEYCSIFHRKIREKKVKKLYLA 304 (354)
Q Consensus 225 ~~llVVNKPaGl~vhp~~~~~~~TL~~~l~~~l~~~~~~~~VHRLDrdTSGLLL~AKn~~a~~~L~~~f~~~~V~K~YlA 304 (354)
+.++.+|||.|+.+| .+++.+.+.++. .+++..|.||-..||||+++-... +.+|.+.+. ...|+|+|
T Consensus 9 ~G~l~i~KP~g~TS~--------dvv~~ikk~~~~-kKvGH~GTLDP~AtGvLiv~vG~~-aTkl~~~~~--~~~K~Y~~ 76 (230)
T PRK00989 9 EGILLVDKPQGRTSF--------SLIRSLTKLIGV-KKIGHAGTLDPFATGVMVMLIGRK-FTRLSDILL--FEDKEYAA 76 (230)
T ss_pred CEEEEEeCCCCCCHH--------HHHHHHHHHhCC-CcCCcCccCCCCCeeEEEEEECCc-hhhhHHHhc--CCCcEEEE
Confidence 479999999999776 456667777764 468899999999999999998763 355555555 37899999
Q ss_pred EEe
Q 018538 305 LTT 307 (354)
Q Consensus 305 lV~ 307 (354)
.+.
T Consensus 77 ~~~ 79 (230)
T PRK00989 77 VAH 79 (230)
T ss_pred EEE
Confidence 986
No 36
>cd00506 PseudoU_synth_TruB_like PseudoU_synth_TruB: Pseudouridine synthase, TruB family. This group consists of eukaryotic, bacterial and archeal pseudouridine synthases similar to Escherichia coli TruB, Saccharomyces cerevisiae Pus4, M. tuberculosis TruB, S. cerevisiae Cbf5 and human dyskerin. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. E. coli TruB, M. tuberculosis TruB and S. cerevisiae Pus4, make psi55 in the T loop of tRNAs. Pus4 catalyses the formation of psi55 in both cytoplasmic and mitochondrial tRNAs. Psi55 is almost universally conserved. S. cerevisiae Cbf5 and human dyskerin are nucleolar proteins that, with the help of guide RNAs, make the hundreds of psueudouridnes present in rRNA and small nuclear RNAs (snRNAs). Cbf5/Dyskerin is the catalytic subunit of eukaryotic box H/ACA small nucleolar ribonucleoprotein (snoRNP) particles. Mutations in human dysker
Probab=97.28 E-value=0.0009 Score=62.51 Aligned_cols=68 Identities=18% Similarity=0.237 Sum_probs=54.0
Q ss_pred EEEEECCCCccccCCCCCCcchHHHHHHHHhCCCCCceeccCCCCCCceEEEeeCCHHHHHHHHHhHhcCccceEEEEEE
Q 018538 227 HVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQIDNCTEGCVVLARTQEYCSIFHRKIREKKVKKLYLALT 306 (354)
Q Consensus 227 llVVNKPaGl~vhp~~~~~~~TL~~~l~~~l~~~~~~~~VHRLDrdTSGLLL~AKn~~a~~~L~~~f~~~~V~K~YlAlV 306 (354)
++.+|||.|+.+| .+++.+.+.++. .+++..+-||-..||||+++-+.. .++...|. ...|+|.|.+
T Consensus 2 il~i~KP~g~tS~--------~vv~~ik~~~~~-kKvGH~GTLDP~AsGvLiv~vG~a--Tkl~~~~~--~~~K~Y~~~~ 68 (210)
T cd00506 2 LFAVDKPQGPSSH--------DVVDTIRRIFLA-EKVGHGGTLDPFATGVLVVGIGKA--TKLLKHLL--AATKDYTAIG 68 (210)
T ss_pred EEEEEcCCCCCHH--------HHHHHHHHHhCc-cccCCCCcCCCcCeeEEEEEECHH--HhhhHHHh--cCCceEEEEE
Confidence 7899999999775 456667776654 468889999999999999999874 44555555 3889999997
Q ss_pred e
Q 018538 307 T 307 (354)
Q Consensus 307 ~ 307 (354)
.
T Consensus 69 ~ 69 (210)
T cd00506 69 R 69 (210)
T ss_pred E
Confidence 5
No 37
>TIGR00431 TruB tRNA pseudouridine 55 synthase. TruB, the tRNA pseudouridine 55 synthase, converts uracil to pseudouridine in the T loop (not the anticodon loop - beware mis-annotation in Swiss-Prot) of most tRNAs of all three domains of life. This model is built on a seed alignment of bacterial proteins only. Saccharomyces cerevisiae protein YNL292w (Pus4) has been shown to be the pseudouridine 55 synthase of both cytosolic and mitochondrial compartments, active at no other position on tRNA and the only enzyme active at that position in the species. A distinct yeast protein YLR175w, (centromere/microtubule-binding protein CBF5) is an rRNA pseudouridine synthase, and the archaeal set is much more similar to CBF5 than to Pus4. It is unclear whether the archaeal proteins found by this model are tRNA pseudouridine 55 synthases like TruB, rRNA pseudouridine synthases like CBF5, or (as suggested by the absence of paralogs in the Archaea) both. CBF5 likely has additional, eukaryotic-specific
Probab=97.23 E-value=0.0012 Score=61.68 Aligned_cols=69 Identities=19% Similarity=0.251 Sum_probs=55.6
Q ss_pred eEEEEECCCCccccCCCCCCcchHHHHHHHHhCCCCCceeccCCCCCCceEEEeeCCHHHHHHHHHhHhcCccceEEEEE
Q 018538 226 SHVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQIDNCTEGCVVLARTQEYCSIFHRKIREKKVKKLYLAL 305 (354)
Q Consensus 226 ~llVVNKPaGl~vhp~~~~~~~TL~~~l~~~l~~~~~~~~VHRLDrdTSGLLL~AKn~~a~~~L~~~f~~~~V~K~YlAl 305 (354)
.++++|||.|+.+| .+++.+.+.++. .+++..+-||-..||||+++-+.. .+|...+. .-.|+|.|.
T Consensus 3 G~l~v~KP~g~tS~--------~vv~~vkk~~~~-kKvGH~GTLDP~AsGvLiv~vG~~--Tkl~~~~~--~~~K~Y~~~ 69 (209)
T TIGR00431 3 GVLLLDKPQGMTSF--------DALAKVRRLLNV-KKVGHTGTLDPFATGVLPILVGKA--TKLSPYLT--DLDKEYRAE 69 (209)
T ss_pred eEEEEECCCCCCHH--------HHHHHHHHHhCC-CcCCCCCCCCCcCceEEEEEEChH--hhhhHHHc--CCCCeEEEE
Confidence 68999999999764 466777777764 468889999999999999999975 35666665 678999999
Q ss_pred Ee
Q 018538 306 TT 307 (354)
Q Consensus 306 V~ 307 (354)
+.
T Consensus 70 ~~ 71 (209)
T TIGR00431 70 IR 71 (209)
T ss_pred EE
Confidence 75
No 38
>PRK04099 truB tRNA pseudouridine synthase B; Provisional
Probab=97.18 E-value=0.0014 Score=63.58 Aligned_cols=70 Identities=24% Similarity=0.296 Sum_probs=55.6
Q ss_pred CeEEEEECCCCccccCCCCCCcchHHHHHHHHhCCCCCceeccCCCCCCceEEEeeCCHHHHHHHHHhHhcCccceEEEE
Q 018538 225 ESHVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQIDNCTEGCVVLARTQEYCSIFHRKIREKKVKKLYLA 304 (354)
Q Consensus 225 ~~llVVNKPaGl~vhp~~~~~~~TL~~~l~~~l~~~~~~~~VHRLDrdTSGLLL~AKn~~a~~~L~~~f~~~~V~K~YlA 304 (354)
+.++++|||+|+.+| .+++.+.+.++. .+++..+-||-..||||+++-... .+|.+.+. .-.|+|.|
T Consensus 2 ngil~vdKP~g~tS~--------~vv~~ikk~~~~-kKvGH~GTLDP~AtGvLiv~iG~a--TKl~~~l~--~~~K~Y~a 68 (273)
T PRK04099 2 NRLFVANKPAGMSSN--------AFLSRLKRKYGV-KKAGFSGTLDPFAKGVLIVAFGQY--TKLFRFLK--KTPKTYRA 68 (273)
T ss_pred CeEEEEeCCCCCCHH--------HHHHHHHHHhCC-CccccCccCCCCCeeEEEEEEChH--hhhHHHhc--cCCceEEE
Confidence 368999999999776 466777777753 468899999999999999999875 44555555 34899999
Q ss_pred EEe
Q 018538 305 LTT 307 (354)
Q Consensus 305 lV~ 307 (354)
.+.
T Consensus 69 ~~~ 71 (273)
T PRK04099 69 TLW 71 (273)
T ss_pred EEE
Confidence 975
No 39
>PRK00020 truB tRNA pseudouridine synthase B; Provisional
Probab=97.17 E-value=0.0015 Score=62.24 Aligned_cols=70 Identities=21% Similarity=0.289 Sum_probs=55.1
Q ss_pred CeEEEEECCCCccccCCCCCCcchHHHHHHHHhCCCCCceeccCCCCCCceEEEeeCCHHHHHHHHHhHhcCccceEEEE
Q 018538 225 ESHVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQIDNCTEGCVVLARTQEYCSIFHRKIREKKVKKLYLA 304 (354)
Q Consensus 225 ~~llVVNKPaGl~vhp~~~~~~~TL~~~l~~~l~~~~~~~~VHRLDrdTSGLLL~AKn~~a~~~L~~~f~~~~V~K~YlA 304 (354)
+.++++|||.|+.+| .+++.+.+.++. .+++..+-||-..||||+++-... .+|...+. .-.|+|.|
T Consensus 10 ~Gil~vdKP~G~TS~--------dvv~~vkr~~~~-kKvGH~GTLDP~AtGvLiv~iG~a--TKl~~~l~--~~~K~Y~a 76 (244)
T PRK00020 10 DGVLLLDKPVGLSSN--------HALQRAKRTVDA-AKAGHTGTLDPFATGLLVCCMGRA--TKISGRML--EADKTYQA 76 (244)
T ss_pred CeEEEEecCCCCCHH--------HHHHHHHHHhCC-CCCCcCCcCCCcCeeEEEEEECHH--hhhhHHhc--cCCcEEEE
Confidence 479999999999776 456667776764 478899999999999999999873 44555555 35699999
Q ss_pred EEe
Q 018538 305 LTT 307 (354)
Q Consensus 305 lV~ 307 (354)
.+.
T Consensus 77 ~~~ 79 (244)
T PRK00020 77 TLQ 79 (244)
T ss_pred EEE
Confidence 975
No 40
>PRK02484 truB tRNA pseudouridine synthase B; Provisional
Probab=97.04 E-value=0.0022 Score=62.82 Aligned_cols=70 Identities=16% Similarity=0.154 Sum_probs=55.2
Q ss_pred CeEEEEECCCCccccCCCCCCcchHHHHHHHHhCCCCCceeccCCCCCCceEEEeeCCHHHHHHHHHhHhcCccceEEEE
Q 018538 225 ESHVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQIDNCTEGCVVLARTQEYCSIFHRKIREKKVKKLYLA 304 (354)
Q Consensus 225 ~~llVVNKPaGl~vhp~~~~~~~TL~~~l~~~l~~~~~~~~VHRLDrdTSGLLL~AKn~~a~~~L~~~f~~~~V~K~YlA 304 (354)
+.++++|||.|+.+| .+++.+.+.++. .+++..+-||-..||||+++-... .++.+.+. .-.|+|.|
T Consensus 3 ~Gil~i~KP~G~TS~--------dvv~~vrr~l~~-kKvGH~GTLDP~AtGvL~i~vG~a--Tkl~~~l~--~~~K~Y~a 69 (294)
T PRK02484 3 NGIINLKKEAGMTSH--------DAVFKLRKILQT-KKIGHGGTLDPDVVGVLPIAVGKA--TRLIEYMT--EAGKVYEG 69 (294)
T ss_pred ceEEEEeCCCCCCHH--------HHHHHHHHHhCC-CccccCCCCCCCCeeEEEEEEChh--hhhhHHhc--cCCcEEEE
Confidence 368999999999776 456667776664 468899999999999999999874 44555555 34599999
Q ss_pred EEe
Q 018538 305 LTT 307 (354)
Q Consensus 305 lV~ 307 (354)
.+.
T Consensus 70 ~~~ 72 (294)
T PRK02484 70 EIT 72 (294)
T ss_pred EEE
Confidence 985
No 41
>PRK02193 truB tRNA pseudouridine synthase B; Provisional
Probab=97.02 E-value=0.0021 Score=62.49 Aligned_cols=68 Identities=18% Similarity=0.229 Sum_probs=53.8
Q ss_pred EEEEECCCCccccCCCCCCcchHHHHHHHHhCCCCCceeccCCCCCCceEEEeeCCHHHHHHHHHhHhcCccceEEEEEE
Q 018538 227 HVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQIDNCTEGCVVLARTQEYCSIFHRKIREKKVKKLYLALT 306 (354)
Q Consensus 227 llVVNKPaGl~vhp~~~~~~~TL~~~l~~~l~~~~~~~~VHRLDrdTSGLLL~AKn~~a~~~L~~~f~~~~V~K~YlAlV 306 (354)
++++|||.|+.+| .+++.+.+.++. .+++..|-||-..||||+++-... .++.+.+. ...|+|.|.+
T Consensus 2 il~i~KP~G~tS~--------dvv~~vrr~~~~-kKvGH~GTLDP~AtGvL~v~vG~a--Tkl~~~l~--~~~K~Y~a~~ 68 (279)
T PRK02193 2 IKLLYKPKGISSF--------KFIKNFAKTNNI-KKIGHTGTLDPLASGLLLVATDED--TKLIDYLD--QKDKTYIAKI 68 (279)
T ss_pred EEEEECCCCCCHH--------HHHHHHHHHcCC-CccccCccCCCcCeeEEEEEEChh--hhhhHHhc--cCCcEEEEEE
Confidence 6899999999776 456667776654 468899999999999999999874 44555554 5789999997
Q ss_pred e
Q 018538 307 T 307 (354)
Q Consensus 307 ~ 307 (354)
.
T Consensus 69 ~ 69 (279)
T PRK02193 69 K 69 (279)
T ss_pred E
Confidence 5
No 42
>PRK14123 tRNA pseudouridine synthase B; Provisional
Probab=97.00 E-value=0.0025 Score=62.68 Aligned_cols=70 Identities=13% Similarity=0.108 Sum_probs=55.7
Q ss_pred CeEEEEECCCCccccCCCCCCcchHHHHHHHHhCCCCCceeccCCCCCCceEEEeeCCHHHHHHHHHhHhcCccceEEEE
Q 018538 225 ESHVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQIDNCTEGCVVLARTQEYCSIFHRKIREKKVKKLYLA 304 (354)
Q Consensus 225 ~~llVVNKPaGl~vhp~~~~~~~TL~~~l~~~l~~~~~~~~VHRLDrdTSGLLL~AKn~~a~~~L~~~f~~~~V~K~YlA 304 (354)
+.++++|||.|+.+| .+++.+.+.++. .+++..+-||-..||||+++-... .++.+.+. ...|+|.|
T Consensus 3 ~Gil~i~KP~G~TS~--------dvv~~vrr~~~~-kKvGH~GTLDP~AtGvL~v~vG~a--Tkl~~~l~--~~~K~Y~~ 69 (305)
T PRK14123 3 NGILPVYKERGLTSH--------DVVFKLRKILKT-KKIGHTGTLDPEVAGVLPVCIGNA--TRVSDYVM--DMGKAYEA 69 (305)
T ss_pred ceEEEEeCCCCCCHH--------HHHHHHHHHhCC-CccccCcCCCCcCeeEEEEEEChh--hhhHHHhc--CCCcEEEE
Confidence 368999999999776 456667776654 468899999999999999999875 34555555 37899999
Q ss_pred EEe
Q 018538 305 LTT 307 (354)
Q Consensus 305 lV~ 307 (354)
.+.
T Consensus 70 ~~~ 72 (305)
T PRK14123 70 TVS 72 (305)
T ss_pred EEE
Confidence 975
No 43
>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=96.98 E-value=0.0016 Score=62.61 Aligned_cols=50 Identities=20% Similarity=0.221 Sum_probs=45.0
Q ss_pred cHHHHHHhhcCCCHHHHHHHHHcCCEEEeeeCCCCCCCCchhhhhhhcccCCccccccccccCCeEEeeccccccccccc
Q 018538 111 PVLEYICRELNLPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTFRITHVD 190 (354)
Q Consensus 111 ~L~~~L~~~~~lSr~~~~~lI~~G~V~~~~~~~~~~~~~~~e~~r~~~~~~~~~v~~kr~~vnGk~vr~~~~~~~~~~~~ 190 (354)
|||.+++..+++||+.++++|+.|.|. |||+.+ .+++
T Consensus 185 RLD~lls~~~~~SRs~a~~lI~~G~V~----------------------------------VNg~~v---------~~~s 221 (257)
T TIGR03069 185 RIDAIASAGFGLSRSKIVDQIKAGRLR----------------------------------LNWKTV---------TQPS 221 (257)
T ss_pred cHHHHHHhhhhhhHHHHHHHHHCCeEE----------------------------------ECCEEc---------CCCC
Confidence 699999888899999999999999999 999874 4788
Q ss_pred eeecCCcEEEEec
Q 018538 191 QIVEAGTYLRVHV 203 (354)
Q Consensus 191 ~~V~~GD~I~V~~ 203 (354)
+.|.+||.|.|..
T Consensus 222 ~~v~~gD~IsvrG 234 (257)
T TIGR03069 222 RELKVGDRLQLRG 234 (257)
T ss_pred CcCCCCCEEEEcC
Confidence 8999999999874
No 44
>cd02573 PseudoU_synth_EcTruB PseudoU_synth_EcTruB: Pseudouridine synthase, Escherichia coli TruB like. This group consists of bacterial pseudouridine synthases similar to E. coli TruB and Mycobacterium tuberculosis TruB. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). E. coli TruB and M. tuberculosis TruB make psi55 in the T loop of tRNAs. Psi55 is nearly universally conserved. E. coli TruB is not inhibited by RNA containing 5-fluorouridine.
Probab=96.96 E-value=0.0028 Score=61.61 Aligned_cols=68 Identities=24% Similarity=0.322 Sum_probs=54.6
Q ss_pred EEEEECCCCccccCCCCCCcchHHHHHHHHhCCCCCceeccCCCCCCceEEEeeCCHHHHHHHHHhHhcCccceEEEEEE
Q 018538 227 HVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQIDNCTEGCVVLARTQEYCSIFHRKIREKKVKKLYLALT 306 (354)
Q Consensus 227 llVVNKPaGl~vhp~~~~~~~TL~~~l~~~l~~~~~~~~VHRLDrdTSGLLL~AKn~~a~~~L~~~f~~~~V~K~YlAlV 306 (354)
++.+|||.|+.+| .+++.+.+.++. .+++..+-||-..||||+++-+.. .+|.+.+. .-.|+|.|.+
T Consensus 2 il~i~KP~G~tS~--------~vv~~vr~~~~~-kKvGH~GTLDP~AtGvL~v~vG~a--Tkl~~~l~--~~~K~Y~~~~ 68 (277)
T cd02573 2 ILLLDKPAGLTSH--------DVVQKVRRLLGT-KKVGHTGTLDPLATGVLPIALGEA--TKLSQYLL--DADKTYRATV 68 (277)
T ss_pred EEEEECCCCCCHH--------HHHHHHHHHhCc-CccCCCCCCCCcCeEEEEEEEChH--HhhHHHhc--CCCcEEEEEE
Confidence 7899999999776 456667776664 468889999999999999999874 44666665 3689999998
Q ss_pred e
Q 018538 307 T 307 (354)
Q Consensus 307 ~ 307 (354)
.
T Consensus 69 ~ 69 (277)
T cd02573 69 R 69 (277)
T ss_pred E
Confidence 5
No 45
>PRK14124 tRNA pseudouridine synthase B; Provisional
Probab=96.96 E-value=0.0031 Score=62.09 Aligned_cols=70 Identities=14% Similarity=0.253 Sum_probs=55.1
Q ss_pred CeEEEEECCCCccccCCCCCCcchHHHHHHHHhCCCCCceeccCCCCCCceEEEeeCCHHHHHHHHHhHhcCccceEEEE
Q 018538 225 ESHVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQIDNCTEGCVVLARTQEYCSIFHRKIREKKVKKLYLA 304 (354)
Q Consensus 225 ~~llVVNKPaGl~vhp~~~~~~~TL~~~l~~~l~~~~~~~~VHRLDrdTSGLLL~AKn~~a~~~L~~~f~~~~V~K~YlA 304 (354)
+.++++|||.|+.+| .+++.+.+.++. .+++..+-||-..||||+++-+.. .+|.+.+.. -.|+|.|
T Consensus 3 ~Gil~i~KP~G~TS~--------dvv~~vrr~l~~-kKvGH~GTLDP~AtGvL~v~vG~a--Tkl~~~l~~--~~K~Y~a 69 (308)
T PRK14124 3 HGFLVAYKPKGPTSH--------DVVDEVRKKLKT-RKVGHAGTLDPFATGVLIVGVNKA--TRLLEYLKN--EKKVYYV 69 (308)
T ss_pred ceEEEEECCCCCCHH--------HHHHHHHHHcCC-CccCcCcCCCCCCcEEEEEEEChH--HhhhHHHhc--CCceEEE
Confidence 368999999999776 456667776654 468899999999999999999874 445555553 3899999
Q ss_pred EEe
Q 018538 305 LTT 307 (354)
Q Consensus 305 lV~ 307 (354)
.+.
T Consensus 70 ~~~ 72 (308)
T PRK14124 70 KMR 72 (308)
T ss_pred EEE
Confidence 985
No 46
>PRK03287 truB tRNA pseudouridine synthase B; Provisional
Probab=96.95 E-value=0.0028 Score=62.18 Aligned_cols=70 Identities=23% Similarity=0.326 Sum_probs=55.1
Q ss_pred CeEEEEECCCCccccCCCCCCcchHHHHHHHHhCCCCCceeccCCCCCCceEEEeeCCHHHHHHHHHhHhcCccceEEEE
Q 018538 225 ESHVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQIDNCTEGCVVLARTQEYCSIFHRKIREKKVKKLYLA 304 (354)
Q Consensus 225 ~~llVVNKPaGl~vhp~~~~~~~TL~~~l~~~l~~~~~~~~VHRLDrdTSGLLL~AKn~~a~~~L~~~f~~~~V~K~YlA 304 (354)
+.++++|||.|+.+| .+++.+.+.++. .+++..+-||-..||||+++-... .++.+.+. .-.|+|.|
T Consensus 9 ~Gil~i~KP~G~TS~--------dvv~~vrr~~~~-kKvGH~GTLDP~AtGvL~i~vG~a--TKl~~~l~--~~~K~Y~a 75 (298)
T PRK03287 9 SGLVVVDKPAGMTSH--------DVVARCRRLFGT-RKVGHAGTLDPMATGVLVLGVERA--TKLLGHLT--LTDKSYTA 75 (298)
T ss_pred CeEEEEeCCCCCCHH--------HHHHHHHHHhCC-CCCCcCccCCCcceeEEEEEeChh--hhhhHHHh--cCCcEEEE
Confidence 579999999999776 456667776664 468899999999999999999863 44445555 34899999
Q ss_pred EEe
Q 018538 305 LTT 307 (354)
Q Consensus 305 lV~ 307 (354)
.+.
T Consensus 76 ~~~ 78 (298)
T PRK03287 76 TIR 78 (298)
T ss_pred EEE
Confidence 975
No 47
>PRK00130 truB tRNA pseudouridine synthase B; Provisional
Probab=96.95 E-value=0.0031 Score=61.62 Aligned_cols=70 Identities=14% Similarity=0.141 Sum_probs=55.6
Q ss_pred CeEEEEECCCCccccCCCCCCcchHHHHHHHHhCCCCCceeccCCCCCCceEEEeeCCHHHHHHHHHhHhcCccceEEEE
Q 018538 225 ESHVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQIDNCTEGCVVLARTQEYCSIFHRKIREKKVKKLYLA 304 (354)
Q Consensus 225 ~~llVVNKPaGl~vhp~~~~~~~TL~~~l~~~l~~~~~~~~VHRLDrdTSGLLL~AKn~~a~~~L~~~f~~~~V~K~YlA 304 (354)
+.++++|||.|+.+| .+++.+.+.++. .+++..+-||-..||||+++-... .++.+.+. .-.|+|.|
T Consensus 2 ~Gil~i~KP~G~tS~--------dvv~~vrr~~~~-kKvGH~GTLDP~AtGvL~v~vG~a--Tkl~~~l~--~~~K~Y~a 68 (290)
T PRK00130 2 DGILNILKPPGMTSF--------DVVRKIRKIAKI-KKVGHTGTLDPLASGVLPVCLGKA--TKIVDYLM--EGKKTYRA 68 (290)
T ss_pred CeEEEEeCCCCCCHH--------HHHHHHHHHhCC-CccCcCCCCCCCCeeEEEEEEChh--hhhHHHhc--cCCcEEEE
Confidence 368999999999776 456667776764 468899999999999999999874 44556565 34899999
Q ss_pred EEe
Q 018538 305 LTT 307 (354)
Q Consensus 305 lV~ 307 (354)
.+.
T Consensus 69 ~~~ 71 (290)
T PRK00130 69 EIK 71 (290)
T ss_pred EEE
Confidence 975
No 48
>PRK14846 truB tRNA pseudouridine synthase B; Provisional
Probab=96.95 E-value=0.0031 Score=62.77 Aligned_cols=70 Identities=19% Similarity=0.266 Sum_probs=55.1
Q ss_pred CeEEEEECCCCccccCCCCCCcchHHHHHHHHhCCCCCceeccCCCCCCceEEEeeCCHHHHHHHHHhHhcCccceEEEE
Q 018538 225 ESHVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQIDNCTEGCVVLARTQEYCSIFHRKIREKKVKKLYLA 304 (354)
Q Consensus 225 ~~llVVNKPaGl~vhp~~~~~~~TL~~~l~~~l~~~~~~~~VHRLDrdTSGLLL~AKn~~a~~~L~~~f~~~~V~K~YlA 304 (354)
+.++++|||.|+.+| .+++.+.+.++. .+++..|-||-..||||+++-... .++.+.+. .-.|+|.|
T Consensus 3 nGiL~idKP~G~TS~--------dvv~~vrk~l~~-kKVGH~GTLDP~AtGVL~i~vG~a--TKl~~~l~--~~~K~Y~a 69 (345)
T PRK14846 3 NYWLNIYKPRGISSA--------QLVSIVKKILGK-TKIGHAGTLDVEAEGILPFAVGEA--TKLIHLLI--DARKTYIF 69 (345)
T ss_pred CeEEEEeCCCCCCHH--------HHHHHHHHHhCC-CcCCcCccCCCcCceEEEEEEChh--hhhhHHHh--cCCceEEE
Confidence 469999999999775 456667776654 478999999999999999999874 44555554 46799999
Q ss_pred EEe
Q 018538 305 LTT 307 (354)
Q Consensus 305 lV~ 307 (354)
.+.
T Consensus 70 ~~~ 72 (345)
T PRK14846 70 TVK 72 (345)
T ss_pred EEE
Confidence 975
No 49
>PRK02755 truB tRNA pseudouridine synthase B; Provisional
Probab=96.91 E-value=0.0032 Score=61.69 Aligned_cols=69 Identities=22% Similarity=0.274 Sum_probs=55.2
Q ss_pred CeEEEEECCCCccccCCCCCCcchHHHHHHHHhCCCCCceeccCCCCCCceEEEeeCCHHHHHHHHHhHhcCccceEEEE
Q 018538 225 ESHVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQIDNCTEGCVVLARTQEYCSIFHRKIREKKVKKLYLA 304 (354)
Q Consensus 225 ~~llVVNKPaGl~vhp~~~~~~~TL~~~l~~~l~~~~~~~~VHRLDrdTSGLLL~AKn~~a~~~L~~~f~~~~V~K~YlA 304 (354)
+.++++|||.|+.+| .+++.+.+.++. .+++..+-||-..||||+++-.... +|.+.+. . .|+|.|
T Consensus 3 ~Gil~i~KP~G~TS~--------dvv~~vrr~~~~-kKvGH~GTLDP~AtGvL~i~vG~aT--kl~~~l~--~-~K~Y~a 68 (295)
T PRK02755 3 FGFLNLDKPAGLTSH--------DCVARLRRLLRL-KRVGHGGTLDPAATGVLPIALGKAT--RLLPYLP--G-EKTYRG 68 (295)
T ss_pred ceEEEEeCCCCCCHH--------HHHHHHHHHhCC-CccccCCCCCCcCeeEEEEEEChhh--hhHHHhC--C-CcEEEE
Confidence 368999999999776 456777777764 4688999999999999999998753 4556665 3 799999
Q ss_pred EEe
Q 018538 305 LTT 307 (354)
Q Consensus 305 lV~ 307 (354)
.+.
T Consensus 69 ~~~ 71 (295)
T PRK02755 69 TIR 71 (295)
T ss_pred EEE
Confidence 975
No 50
>PRK05389 truB tRNA pseudouridine synthase B; Provisional
Probab=96.91 E-value=0.0033 Score=61.89 Aligned_cols=70 Identities=16% Similarity=0.173 Sum_probs=55.1
Q ss_pred CeEEEEECCCCccccCCCCCCcchHHHHHHHHhCCCCCceeccCCCCCCceEEEeeCCHHHHHHHHHhHhcCccceEEEE
Q 018538 225 ESHVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQIDNCTEGCVVLARTQEYCSIFHRKIREKKVKKLYLA 304 (354)
Q Consensus 225 ~~llVVNKPaGl~vhp~~~~~~~TL~~~l~~~l~~~~~~~~VHRLDrdTSGLLL~AKn~~a~~~L~~~f~~~~V~K~YlA 304 (354)
+.++++|||.|+.+| .+++.+.+.++. .+++..+-||-..||||+++-... .++.+.+. .-.|+|.|
T Consensus 13 ~Gil~i~KP~G~TS~--------dvv~~vrk~~~~-kKvGH~GTLDP~AtGvL~v~vG~a--Tkl~~~l~--~~~K~Y~a 79 (305)
T PRK05389 13 SGWLILDKPAGMTST--------EAVSKVKWLFDA-QKAGHAGTLDPLASGVLPIALGEA--TKTVPYVM--DGTKRYRF 79 (305)
T ss_pred CeEEEEeCCCCCCHH--------HHHHHHHHHhcc-cccCCcccCCCCCceEEEEEEChh--hhhhHHhc--cCCcEEEE
Confidence 479999999999776 456667766654 468889999999999999999873 45555555 34899999
Q ss_pred EEe
Q 018538 305 LTT 307 (354)
Q Consensus 305 lV~ 307 (354)
.+.
T Consensus 80 ~~~ 82 (305)
T PRK05389 80 TVA 82 (305)
T ss_pred EEE
Confidence 975
No 51
>PRK04270 H/ACA RNA-protein complex component Cbf5p; Reviewed
Probab=96.89 E-value=0.0031 Score=61.81 Aligned_cols=70 Identities=20% Similarity=0.268 Sum_probs=55.0
Q ss_pred CeEEEEECCCCccccCCCCCCcchHHHHHHHHhCCCCCceeccCCCCCCceEEEeeCCHHHHHHHHHhHhcCccceEEEE
Q 018538 225 ESHVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQIDNCTEGCVVLARTQEYCSIFHRKIREKKVKKLYLA 304 (354)
Q Consensus 225 ~~llVVNKPaGl~vhp~~~~~~~TL~~~l~~~l~~~~~~~~VHRLDrdTSGLLL~AKn~~a~~~L~~~f~~~~V~K~YlA 304 (354)
+.++++|||.|+.+| .+++.+.+.++. .+++..+-||-..||||+++-+.. .+|.+.+. .-.|+|.|
T Consensus 22 ~g~l~i~Kp~g~tS~--------~~v~~~r~~~~~-kkvGH~GTLDp~A~GvL~v~~g~a--tk~~~~~~--~~~K~Y~~ 88 (300)
T PRK04270 22 FGVVNLDKPPGPTSH--------EVAAWVRDILGV-EKAGHGGTLDPKVTGVLPVALGKA--TKVVQALL--ESGKEYVC 88 (300)
T ss_pred CCEEEEECCCCCCHH--------HHHHHHHHHhcc-ccccCCCCCCCcCeEEEEEEEChH--hhhhHHhc--cCCcEEEE
Confidence 579999999999776 456667666653 468889999999999999999874 55555555 35699999
Q ss_pred EEe
Q 018538 305 LTT 307 (354)
Q Consensus 305 lV~ 307 (354)
.+.
T Consensus 89 ~~~ 91 (300)
T PRK04270 89 VMH 91 (300)
T ss_pred EEE
Confidence 874
No 52
>PRK01528 truB tRNA pseudouridine synthase B; Provisional
Probab=96.87 E-value=0.0038 Score=61.07 Aligned_cols=70 Identities=20% Similarity=0.276 Sum_probs=54.9
Q ss_pred CeEEEEECCCCccccCCCCCCcchHHHHHHHHhCCCCCceeccCCCCCCceEEEeeCCHHHHHHHHHhHhcCccceEEEE
Q 018538 225 ESHVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQIDNCTEGCVVLARTQEYCSIFHRKIREKKVKKLYLA 304 (354)
Q Consensus 225 ~~llVVNKPaGl~vhp~~~~~~~TL~~~l~~~l~~~~~~~~VHRLDrdTSGLLL~AKn~~a~~~L~~~f~~~~V~K~YlA 304 (354)
+.++++|||.|+.+| .+++.+.+.++. .+++..+-||-..||||+++-... .++.+.+. .-.|+|.|
T Consensus 3 ~GiL~i~KP~G~TS~--------dvv~~vrk~~~~-kKvGH~GTLDP~AtGvL~v~vG~a--TKl~~~l~--~~~K~Y~~ 69 (292)
T PRK01528 3 NYWLNIYKPRGISSA--------KLVSIVKKILGK-VKIGHAGTLDVEAEGVLPLAVGEA--TKLVQLLI--DAKKTYIF 69 (292)
T ss_pred CEEEEEeCCCCCCHH--------HHHHHHHHHcCC-CccCcCccCCCcCceEEEEEEChH--hhhhHHHh--cCCceEEE
Confidence 479999999999776 456667776653 468899999999999999999874 44445454 45699999
Q ss_pred EEe
Q 018538 305 LTT 307 (354)
Q Consensus 305 lV~ 307 (354)
.+.
T Consensus 70 ~~~ 72 (292)
T PRK01528 70 TVK 72 (292)
T ss_pred EEE
Confidence 975
No 53
>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=96.86 E-value=0.0022 Score=59.45 Aligned_cols=50 Identities=16% Similarity=0.226 Sum_probs=44.1
Q ss_pred cHHHHHHhhc-CCCHHHHHHHHHcCCEEEeeeCCCCCCCCchhhhhhhcccCCccccccccccCCeEEeecccccccccc
Q 018538 111 PVLEYICREL-NLPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTFRITHV 189 (354)
Q Consensus 111 ~L~~~L~~~~-~lSr~~~~~lI~~G~V~~~~~~~~~~~~~~~e~~r~~~~~~~~~v~~kr~~vnGk~vr~~~~~~~~~~~ 189 (354)
+||.+|.+.. ..||+.++++|..|.|. |||+.+ ..+
T Consensus 91 RLD~~L~~~g~~~SR~~ArqlI~~G~V~----------------------------------VNgk~v---------~~p 127 (200)
T TIGR01017 91 RLDNVVYRLGFAPTRFAARQLVSHGHIL----------------------------------VNGKKV---------DIP 127 (200)
T ss_pred HHHHHHHHcCCCCCHHHHHHHHHCCCEE----------------------------------ECCEEe---------CCC
Confidence 4999997766 78999999999999999 999874 478
Q ss_pred ceeecCCcEEEEec
Q 018538 190 DQIVEAGTYLRVHV 203 (354)
Q Consensus 190 ~~~V~~GD~I~V~~ 203 (354)
++.|.+||.|.|..
T Consensus 128 s~~V~~GD~I~V~~ 141 (200)
T TIGR01017 128 SYQVRPGDIISIKE 141 (200)
T ss_pred CCCCCCCCEEEEee
Confidence 89999999999874
No 54
>PRK01851 truB tRNA pseudouridine synthase B; Provisional
Probab=96.82 E-value=0.0045 Score=60.82 Aligned_cols=70 Identities=24% Similarity=0.294 Sum_probs=55.5
Q ss_pred CeEEEEECCCCccccCCCCCCcchHHHHHHHHhCCCCCceeccCCCCCCceEEEeeCCHHHHHHHHHhHhcCccceEEEE
Q 018538 225 ESHVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQIDNCTEGCVVLARTQEYCSIFHRKIREKKVKKLYLA 304 (354)
Q Consensus 225 ~~llVVNKPaGl~vhp~~~~~~~TL~~~l~~~l~~~~~~~~VHRLDrdTSGLLL~AKn~~a~~~L~~~f~~~~V~K~YlA 304 (354)
+.++++|||.|+.+| .+++.+.+.++. .+++..+-||-..||||+++-... .+|.+.+. .-.|+|.|
T Consensus 16 ~Gil~i~KP~G~TS~--------dvv~~vrr~l~~-kKvGH~GTLDP~AtGvL~v~vG~a--Tkl~~~l~--~~~K~Y~~ 82 (303)
T PRK01851 16 DGVLLLDKPLGLSSN--------DALQRAKRLLRA-KKAGHTGTLDPLATGLLPLCFGEA--TKFSQDLL--DADKTYEA 82 (303)
T ss_pred CeEEEEeCCCCCCHH--------HHHHHHHHHhCc-ccCCCCCCCCCCCceEEEEEECHH--HhhhHHhc--ccCeEEEE
Confidence 479999999999776 456667776654 468889999999999999999874 44555565 34599999
Q ss_pred EEe
Q 018538 305 LTT 307 (354)
Q Consensus 305 lV~ 307 (354)
.+.
T Consensus 83 ~~~ 85 (303)
T PRK01851 83 TLR 85 (303)
T ss_pred EEE
Confidence 975
No 55
>PRK01550 truB tRNA pseudouridine synthase B; Provisional
Probab=96.82 E-value=0.0044 Score=60.95 Aligned_cols=70 Identities=17% Similarity=0.238 Sum_probs=55.5
Q ss_pred CeEEEEECCCCccccCCCCCCcchHHHHHHHHhCCCCCceeccCCCCCCceEEEeeCCHHHHHHHHHhHhcCccceEEEE
Q 018538 225 ESHVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQIDNCTEGCVVLARTQEYCSIFHRKIREKKVKKLYLA 304 (354)
Q Consensus 225 ~~llVVNKPaGl~vhp~~~~~~~TL~~~l~~~l~~~~~~~~VHRLDrdTSGLLL~AKn~~a~~~L~~~f~~~~V~K~YlA 304 (354)
+.++++|||.|+.+| .+++.+.+.++. .+++..+-||-..||||+++-... .+|.+.+. .-.|+|.|
T Consensus 2 ~Gil~i~KP~G~TS~--------dvv~~vrr~~~~-kKvGH~GTLDP~AtGvL~i~vG~a--Tkl~~~l~--~~~K~Y~a 68 (304)
T PRK01550 2 NGVLLLHKPRGMTSH--------DCVFKLRKILRT-KKVGHTGTLDPEVSGVLPICVGRA--TKIAEYLT--DEGKTYEG 68 (304)
T ss_pred CeEEEEECCCCCCHH--------HHHHHHHHHcCC-CCcccCCCCCCcCeeEEEEEEChh--hhhhHHhc--CCCcEEEE
Confidence 368999999999776 456667777764 468889999999999999999874 44656665 34899999
Q ss_pred EEe
Q 018538 305 LTT 307 (354)
Q Consensus 305 lV~ 307 (354)
.+.
T Consensus 69 ~~~ 71 (304)
T PRK01550 69 EVT 71 (304)
T ss_pred EEE
Confidence 975
No 56
>PRK05033 truB tRNA pseudouridine synthase B; Provisional
Probab=96.78 E-value=0.005 Score=60.75 Aligned_cols=70 Identities=19% Similarity=0.261 Sum_probs=55.5
Q ss_pred CeEEEEECCCCccccCCCCCCcchHHHHHHHHhCCCCCceeccCCCCCCceEEEeeCCHHHHHHHHHhHhcCccceEEEE
Q 018538 225 ESHVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQIDNCTEGCVVLARTQEYCSIFHRKIREKKVKKLYLA 304 (354)
Q Consensus 225 ~~llVVNKPaGl~vhp~~~~~~~TL~~~l~~~l~~~~~~~~VHRLDrdTSGLLL~AKn~~a~~~L~~~f~~~~V~K~YlA 304 (354)
+.+++||||.|+.+| .+++.+.+.++. .+++..+-||-..||||+++-... .+|.+.+. .-.|+|.|
T Consensus 10 ~Gil~i~KP~G~TS~--------dvv~~vrr~l~~-kKvGH~GTLDP~AtGvL~v~vG~a--Tkl~~~~~--~~~K~Y~a 76 (312)
T PRK05033 10 NGVLLLDKPQGMSSN--------DALQKVKRLFNA-NKAGHTGALDPLATGMLPICLGEA--TKFSQYLL--DSDKRYRV 76 (312)
T ss_pred CeEEEEeCCCCCCHH--------HHHHHHHHHhCC-CCCCCCCcCCCcCeeEEEEEECHH--hhhhHHhc--CCCcEEEE
Confidence 479999999999776 356667766653 468889999999999999999874 44666665 35899999
Q ss_pred EEe
Q 018538 305 LTT 307 (354)
Q Consensus 305 lV~ 307 (354)
.+.
T Consensus 77 ~~~ 79 (312)
T PRK05033 77 TAR 79 (312)
T ss_pred EEE
Confidence 975
No 57
>PRK14122 tRNA pseudouridine synthase B; Provisional
Probab=96.72 E-value=0.0051 Score=60.66 Aligned_cols=69 Identities=26% Similarity=0.335 Sum_probs=54.8
Q ss_pred eEEEEECCCCccccCCCCCCcchHHHHHHHHhCCCCCceeccCCCCCCceEEEeeCCHHHHHHHHHhHhcCccceEEEEE
Q 018538 226 SHVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQIDNCTEGCVVLARTQEYCSIFHRKIREKKVKKLYLAL 305 (354)
Q Consensus 226 ~llVVNKPaGl~vhp~~~~~~~TL~~~l~~~l~~~~~~~~VHRLDrdTSGLLL~AKn~~a~~~L~~~f~~~~V~K~YlAl 305 (354)
.++++|||.|+.+| .+++.+.+.++. .+++..+-||-..||||+++-... .+|.+.+. .-.|+|.|.
T Consensus 2 ~il~idKP~G~TS~--------dvv~~vrr~l~~-kKvGH~GTLDP~AtGvL~i~iG~a--TKl~~~l~--~~~K~Y~a~ 68 (312)
T PRK14122 2 PVYAVDKPLGLTSH--------DVVNRARRALGT-RRVGHTGTLDPLATGVLVLCTDDS--TKLVPFLS--AEDKEYLAW 68 (312)
T ss_pred cEEEEECCCCCCHH--------HHHHHHHHHhCC-CCCCCCCCCCCcCeeeEEEEEChh--hhhhHHhc--CCCceEEEE
Confidence 47899999999776 456777776664 468889999999999999999874 33666564 578999999
Q ss_pred Ee
Q 018538 306 TT 307 (354)
Q Consensus 306 V~ 307 (354)
+.
T Consensus 69 ~~ 70 (312)
T PRK14122 69 VS 70 (312)
T ss_pred EE
Confidence 74
No 58
>CHL00113 rps4 ribosomal protein S4; Reviewed
Probab=96.72 E-value=0.003 Score=58.69 Aligned_cols=50 Identities=12% Similarity=0.110 Sum_probs=44.3
Q ss_pred cHHHHHHhhc-CCCHHHHHHHHHcCCEEEeeeCCCCCCCCchhhhhhhcccCCccccccccccCCeEEeecccccccccc
Q 018538 111 PVLEYICREL-NLPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTFRITHV 189 (354)
Q Consensus 111 ~L~~~L~~~~-~lSr~~~~~lI~~G~V~~~~~~~~~~~~~~~e~~r~~~~~~~~~v~~kr~~vnGk~vr~~~~~~~~~~~ 189 (354)
+||.||.+.. ..||..++++|..|.|+ |||+.+ ..+
T Consensus 90 RLD~~L~r~g~~~SR~~ArqlI~~G~V~----------------------------------VNGk~v---------~~p 126 (201)
T CHL00113 90 RLDNILFRLGMAPTIPAARQLVNHGHIL----------------------------------VNGRIV---------DIP 126 (201)
T ss_pred HHHHHHHHcCCCCCHHHHHHHHHCCcEE----------------------------------ECCEEe---------cCc
Confidence 4999998877 67999999999999999 999984 478
Q ss_pred ceeecCCcEEEEec
Q 018538 190 DQIVEAGTYLRVHV 203 (354)
Q Consensus 190 ~~~V~~GD~I~V~~ 203 (354)
++.|.+||.|.|.-
T Consensus 127 s~~Vk~GD~I~V~~ 140 (201)
T CHL00113 127 SYRCKPKDIITVKD 140 (201)
T ss_pred cccCCCCCEEEEcc
Confidence 89999999999874
No 59
>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=96.62 E-value=0.003 Score=59.61 Aligned_cols=50 Identities=18% Similarity=0.123 Sum_probs=43.9
Q ss_pred cHHHHHHhhc-CCCHHHHHHHHHcCCEEEeeeCCCCCCCCchhhhhhhcccCCccccccccccCCeEEeecccccccccc
Q 018538 111 PVLEYICREL-NLPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTFRITHV 189 (354)
Q Consensus 111 ~L~~~L~~~~-~lSr~~~~~lI~~G~V~~~~~~~~~~~~~~~e~~r~~~~~~~~~v~~kr~~vnGk~vr~~~~~~~~~~~ 189 (354)
|||+||.+.. ..||+.++++|+.|.|+ |||+++ +++
T Consensus 1 RLD~~L~~~g~~~SR~~a~~lI~~G~V~----------------------------------Vng~~v---------~k~ 37 (228)
T TIGR00478 1 RLDILLVRRGLFESREKAKRLILKGFVL----------------------------------VNGKKV---------DKP 37 (228)
T ss_pred CHHHHHHHcCCccHHHHHHHHHHCCcEE----------------------------------ECCEEe---------CCC
Confidence 4999999887 67999999999999999 899874 478
Q ss_pred ceeecCCcEEEEec
Q 018538 190 DQIVEAGTYLRVHV 203 (354)
Q Consensus 190 ~~~V~~GD~I~V~~ 203 (354)
++.|..||.|++..
T Consensus 38 s~~V~~~d~I~v~~ 51 (228)
T TIGR00478 38 SALVDFDAKIELLQ 51 (228)
T ss_pred CCCCCCCCEEeccC
Confidence 88999999998874
No 60
>PRK10348 ribosome-associated heat shock protein Hsp15; Provisional
Probab=96.56 E-value=0.0064 Score=53.02 Aligned_cols=49 Identities=16% Similarity=0.228 Sum_probs=43.2
Q ss_pred cHHHHHHhhc-CCCHHHHHHHHHcCCEEEeeeCCCCCCCCchhhhhhhcccCCccccccccccCCeEEeecccccccccc
Q 018538 111 PVLEYICREL-NLPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTFRITHV 189 (354)
Q Consensus 111 ~L~~~L~~~~-~lSr~~~~~lI~~G~V~~~~~~~~~~~~~~~e~~r~~~~~~~~~v~~kr~~vnGk~vr~~~~~~~~~~~ 189 (354)
+||+||-... --||+.++++|..|.|. +||++ +++
T Consensus 10 RlDk~L~~~rl~ktRs~A~~lI~~G~V~----------------------------------vnG~~----------~Kp 45 (133)
T PRK10348 10 RLDKWLWAARFYKTRALAREMIEGGKVH----------------------------------YNGQR----------SKP 45 (133)
T ss_pred cHHHHHHHcCccccHHHHHHHHHCCCEE----------------------------------ECCEE----------CCC
Confidence 4999997755 77999999999999999 89986 478
Q ss_pred ceeecCCcEEEEec
Q 018538 190 DQIVEAGTYLRVHV 203 (354)
Q Consensus 190 ~~~V~~GD~I~V~~ 203 (354)
+..|..||.|.|..
T Consensus 46 s~~V~~gd~l~v~~ 59 (133)
T PRK10348 46 SKIVELNATLTLRQ 59 (133)
T ss_pred CCccCCCCEEEEEE
Confidence 88999999999875
No 61
>TIGR00425 CBF5 rRNA pseudouridine synthase, putative. This family, found in archaea and eukaryotes, includes the only archaeal proteins markedly similar to bacterial TruB, the tRNA pseudouridine 55 synthase. However, among two related yeast proteins, the archaeal set matches yeast YLR175w far better than YNL292w. The first, termed centromere/microtubule binding protein 5 (CBF5), is an apparent rRNA pseudouridine synthase, while the second is the exclusive tRNA pseudouridine 55 synthase for both cytosolic and mitochondrial compartments. It is unclear whether archaeal proteins found by this model modify tRNA, rRNA, or both.
Probab=96.43 E-value=0.0092 Score=59.18 Aligned_cols=70 Identities=20% Similarity=0.311 Sum_probs=55.5
Q ss_pred CeEEEEECCCCccccCCCCCCcchHHHHHHHHhCCCCCceeccCCCCCCceEEEeeCCHHHHHHHHHhHhcCccceEEEE
Q 018538 225 ESHVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQIDNCTEGCVVLARTQEYCSIFHRKIREKKVKKLYLA 304 (354)
Q Consensus 225 ~~llVVNKPaGl~vhp~~~~~~~TL~~~l~~~l~~~~~~~~VHRLDrdTSGLLL~AKn~~a~~~L~~~f~~~~V~K~YlA 304 (354)
+.++++|||.|+.+| .+++.+.+.++. .+++..+=||-..+|||+++-... .+|.+.+. .-.|+|.|
T Consensus 34 ~G~l~i~KP~g~tS~--------~~v~~vr~~~~~-kkvGH~GTLDP~A~GvL~v~~G~a--Tkl~~~~~--~~~K~Y~~ 100 (322)
T TIGR00425 34 YGVVNLDKPSGPSSH--------EVVAWVRRILNV-EKTGHGGTLDPKVTGVLPVCIERA--TRLVKSLQ--EAPKEYVC 100 (322)
T ss_pred CCEEEEeCCCCCCHH--------HHHHHHHHHhcc-cccCCCCCCCCCCceEEEEEEChH--hhccHHhc--cCCCEEEE
Confidence 479999999999776 456667776654 468889999999999999999874 55555555 56899999
Q ss_pred EEe
Q 018538 305 LTT 307 (354)
Q Consensus 305 lV~ 307 (354)
.+.
T Consensus 101 ~v~ 103 (322)
T TIGR00425 101 LMR 103 (322)
T ss_pred EEE
Confidence 874
No 62
>COG2302 Uncharacterized conserved protein, contains S4-like domain [Function unknown]
Probab=96.42 E-value=0.0066 Score=57.90 Aligned_cols=57 Identities=21% Similarity=0.208 Sum_probs=48.9
Q ss_pred EeeCCCC-cHHHHHHhhcCCCHHHHHHHHHcCCEEEeeeCCCCCCCCchhhhhhhcccCCccccccccccCCeEEeeccc
Q 018538 104 LVVSEGG-PVLEYICRELNLPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQK 182 (354)
Q Consensus 104 ~~v~~~~-~L~~~L~~~~~lSr~~~~~lI~~G~V~~~~~~~~~~~~~~~e~~r~~~~~~~~~v~~kr~~vnGk~vr~~~~ 182 (354)
..+..+. |||..+++.+++||+.++.+|..|.|. ||.+.+
T Consensus 174 ~~~~vsSlRLD~vis~~~~~SR~~a~~lIe~g~Vk----------------------------------VN~k~v----- 214 (257)
T COG2302 174 LDVTVSSLRLDVVISEGFGLSRAKAQQLIEKGKVK----------------------------------VNWKVV----- 214 (257)
T ss_pred EeeeeehhhHHHHHHHHHhhhHHHHHHHHHcCceE----------------------------------EeeEEe-----
Confidence 3444444 899999999999999999999999999 899985
Q ss_pred cccccccceeecCCcEEEEec
Q 018538 183 TFRITHVDQIVEAGTYLRVHV 203 (354)
Q Consensus 183 ~~~~~~~~~~V~~GD~I~V~~ 203 (354)
.++++.|+.||.|.+..
T Consensus 215 ----~~~s~~v~~GDliSirG 231 (257)
T COG2302 215 ----DKASYEVQEGDLISIRG 231 (257)
T ss_pred ----ccccceeccCCEEEEec
Confidence 36789999999999874
No 63
>PRK05327 rpsD 30S ribosomal protein S4; Validated
Probab=96.41 E-value=0.006 Score=56.63 Aligned_cols=50 Identities=18% Similarity=0.205 Sum_probs=43.4
Q ss_pred cHHHHHHhhc-CCCHHHHHHHHHcCCEEEeeeCCCCCCCCchhhhhhhcccCCccccccccccCCeEEeecccccccccc
Q 018538 111 PVLEYICREL-NLPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTFRITHV 189 (354)
Q Consensus 111 ~L~~~L~~~~-~lSr~~~~~lI~~G~V~~~~~~~~~~~~~~~e~~r~~~~~~~~~v~~kr~~vnGk~vr~~~~~~~~~~~ 189 (354)
+||.+|.+.. ..||..++++|..|.|+ |||+.+ ..+
T Consensus 94 RLD~iL~~~g~~~SR~~arqlI~~G~V~----------------------------------VNgk~v---------~~p 130 (203)
T PRK05327 94 RLDNVVYRLGFAPTRRQARQLVSHGHIL----------------------------------VNGKKV---------NIP 130 (203)
T ss_pred HHHHHHHHcCccCCHHHHHHHHHCCcEE----------------------------------ECCEEE---------CCC
Confidence 5999997655 78999999999999999 899874 468
Q ss_pred ceeecCCcEEEEec
Q 018538 190 DQIVEAGTYLRVHV 203 (354)
Q Consensus 190 ~~~V~~GD~I~V~~ 203 (354)
++.|.+||.|+|..
T Consensus 131 s~~v~~GD~I~v~~ 144 (203)
T PRK05327 131 SYRVKPGDVIEVRE 144 (203)
T ss_pred CcCCCCCCEEEECC
Confidence 89999999998873
No 64
>PRK04642 truB tRNA pseudouridine synthase B; Provisional
Probab=96.39 E-value=0.012 Score=57.82 Aligned_cols=70 Identities=24% Similarity=0.219 Sum_probs=55.8
Q ss_pred CeEEEEECCCCccccCCCCCCcchHHHHHHHHhCCCCCceeccCCCCCCceEEEeeCCHHHHHHHHHhHhcCccceEEEE
Q 018538 225 ESHVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQIDNCTEGCVVLARTQEYCSIFHRKIREKKVKKLYLA 304 (354)
Q Consensus 225 ~~llVVNKPaGl~vhp~~~~~~~TL~~~l~~~l~~~~~~~~VHRLDrdTSGLLL~AKn~~a~~~L~~~f~~~~V~K~YlA 304 (354)
+.++++|||.|+.+| .+++.+.+.++. .+++..+=||-..||||+++-... .+|.+.+. .-.|+|.|
T Consensus 10 ~Gil~i~KP~G~TS~--------dvv~~vrr~~~~-kKvGH~GTLDP~AtGvL~v~~G~a--Tkl~~~l~--~~~K~Y~a 76 (300)
T PRK04642 10 DGILLLDKPAGLSSN--------NALQAARRLLRA-EKGGHTGSLDPLATGLLPLCFGEA--TKIAGLLL--GSAKAYDA 76 (300)
T ss_pred CeEEEEecCCCCCHH--------HHHHHHHHHhCC-CcccCCCccCCcCeeeEEEEEChh--hhhhHHhc--CCCcEEEE
Confidence 479999999999776 456777777764 468889999999999999998874 55555555 46799999
Q ss_pred EEe
Q 018538 305 LTT 307 (354)
Q Consensus 305 lV~ 307 (354)
.+.
T Consensus 77 ~~~ 79 (300)
T PRK04642 77 EIV 79 (300)
T ss_pred EEE
Confidence 984
No 65
>cd02867 PseudoU_synth_TruB_4 PseudoU_synth_TruB_4: Pseudouridine synthase homolog 4. This group consists of Eukaryotic TruB proteins similar to Saccharomyces cerevisiae Pus4. S. cerevisiae Pus4, makes psi55 in the T loop of both cytoplasmic and mitochondrial tRNAs. Psi55 is almost universally conserved. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi).
Probab=95.92 E-value=0.027 Score=55.63 Aligned_cols=69 Identities=13% Similarity=0.138 Sum_probs=50.4
Q ss_pred EEEEECCCCccccCCCCCCcchHHHHHHHHhCC----------------------------CCCceeccCCCCCCceEEE
Q 018538 227 HVVLDKPAGTSVGGTTDNIEESCATFASRALGL----------------------------TTPLRTTHQIDNCTEGCVV 278 (354)
Q Consensus 227 llVVNKPaGl~vhp~~~~~~~TL~~~l~~~l~~----------------------------~~~~~~VHRLDrdTSGLLL 278 (354)
+++||||.|+.+| .+++.+.+.++. ..+++..+-||=..||||+
T Consensus 2 il~i~KP~G~TS~--------~vv~~lk~~l~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~KiGH~GTLDPlAsGVLv 73 (312)
T cd02867 2 VFAINKPSGITSA--------QVLNDLKPLFLNSALFKDKIQRAVAKRGKKARRRKGRKRSKLKIGHGGTLDPLATGVLV 73 (312)
T ss_pred eEEEeCCCCCCHH--------HHHHHHHHHhcccccccchhhhhhhhhhhhhhhhccccccccccccccccCCccceeEE
Confidence 7899999999776 344444444431 1368889999999999999
Q ss_pred eeCCHHHHHHHHHhHhcCccceEEEEEEe
Q 018538 279 LARTQEYCSIFHRKIREKKVKKLYLALTT 307 (354)
Q Consensus 279 ~AKn~~a~~~L~~~f~~~~V~K~YlAlV~ 307 (354)
++-... .+.++..+. ..|+|.+.+.
T Consensus 74 vgvG~a-TK~l~~~l~---~~K~Y~~~~~ 98 (312)
T cd02867 74 VGVGAG-TKQLQDYLS---CSKTYEATGL 98 (312)
T ss_pred EEECcH-HHHHHHHhc---CCceEEEEEE
Confidence 999864 444544332 7899999875
No 66
>COG0130 TruB Pseudouridine synthase [Translation, ribosomal structure and biogenesis]
Probab=95.90 E-value=0.026 Score=54.70 Aligned_cols=69 Identities=20% Similarity=0.330 Sum_probs=53.9
Q ss_pred eEEEEECCCCccccCCCCCCcchHHHHHHHHhCCCCCceeccCCCCCCceEEEeeCCHHHHHHHHHhHhcCccceEEEEE
Q 018538 226 SHVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQIDNCTEGCVVLARTQEYCSIFHRKIREKKVKKLYLAL 305 (354)
Q Consensus 226 ~llVVNKPaGl~vhp~~~~~~~TL~~~l~~~l~~~~~~~~VHRLDrdTSGLLL~AKn~~a~~~L~~~f~~~~V~K~YlAl 305 (354)
.++++|||.|+.+| .++..+.+.++. .+.+..+-||-..||+|+++-. ++.+.+. .+. .-.|+|.|.
T Consensus 16 Gil~ldKP~G~tS~--------~~v~~vkkil~~-~K~GH~GTLDP~atGvLpi~ig-~aTKl~~-~l~--~~~K~Y~a~ 82 (271)
T COG0130 16 GVINLDKPPGPTSH--------EVVAWVKRILGV-EKAGHGGTLDPLATGVLPICLG-EATKLVQ-YLL--DADKEYVAT 82 (271)
T ss_pred ceEEeeCCCCCCHH--------HHHHHHHHHhCc-cccccccccCCcccceEEEEec-hhHhHHH-HHh--hCCcEEEEE
Confidence 79999999999776 456667777764 4688899999999999999998 4444444 333 467999999
Q ss_pred Ee
Q 018538 306 TT 307 (354)
Q Consensus 306 V~ 307 (354)
+.
T Consensus 83 ~~ 84 (271)
T COG0130 83 VR 84 (271)
T ss_pred EE
Confidence 85
No 67
>COG0522 RpsD Ribosomal protein S4 and related proteins [Translation, ribosomal structure and biogenesis]
Probab=95.41 E-value=0.031 Score=52.10 Aligned_cols=51 Identities=18% Similarity=0.217 Sum_probs=44.0
Q ss_pred cHHHHHHhhc-CCCHHHHHHHHHcCCEEEeeeCCCCCCCCchhhhhhhcccCCccccccccccCCeEEeecccccccccc
Q 018538 111 PVLEYICREL-NLPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTFRITHV 189 (354)
Q Consensus 111 ~L~~~L~~~~-~lSr~~~~~lI~~G~V~~~~~~~~~~~~~~~e~~r~~~~~~~~~v~~kr~~vnGk~vr~~~~~~~~~~~ 189 (354)
|||..+.+.. .-|+.++++||..|.|. |||++| ..|
T Consensus 95 RLd~vVyR~GfA~T~~qARQlV~HGHI~----------------------------------VnGk~V---------~iP 131 (205)
T COG0522 95 RLDNVVYRLGFAKTRRQARQLVSHGHIL----------------------------------VNGKRV---------NIP 131 (205)
T ss_pred HHHHHHHHhcccccHHHHHHHhhcceEE----------------------------------ECCEEe---------ccC
Confidence 5777776655 68999999999999999 999985 579
Q ss_pred ceeecCCcEEEEecC
Q 018538 190 DQIVEAGTYLRVHVH 204 (354)
Q Consensus 190 ~~~V~~GD~I~V~~~ 204 (354)
++.|.+||.+.|...
T Consensus 132 Sy~V~~gdei~V~~k 146 (205)
T COG0522 132 SYLVSPGDEISVREK 146 (205)
T ss_pred cEEecCCCEEEeeec
Confidence 999999999999854
No 68
>COG1189 Predicted rRNA methylase [Translation, ribosomal structure and biogenesis]
Probab=94.58 E-value=0.077 Score=50.60 Aligned_cols=50 Identities=20% Similarity=0.193 Sum_probs=45.1
Q ss_pred cHHHHHHhhc-CCCHHHHHHHHHcCCEEEeeeCCCCCCCCchhhhhhhcccCCccccccccccCCeEEeecccccccccc
Q 018538 111 PVLEYICREL-NLPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTFRITHV 189 (354)
Q Consensus 111 ~L~~~L~~~~-~lSr~~~~~lI~~G~V~~~~~~~~~~~~~~~e~~r~~~~~~~~~v~~kr~~vnGk~vr~~~~~~~~~~~ 189 (354)
|||.||.++. .-||+.++++|..|.|+ +||.++ ++|
T Consensus 4 RLD~~Lv~rgl~~sR~~A~~~I~~G~V~----------------------------------Vng~~v---------~KP 40 (245)
T COG1189 4 RLDALLVERGLFESREKAKELILAGNVL----------------------------------VNGEKV---------TKP 40 (245)
T ss_pred hHHHHHHHccchhhHHHHHHHHHcCeEE----------------------------------ECCEEe---------cCc
Confidence 4999999986 67999999999999999 899884 689
Q ss_pred ceeecCCcEEEEec
Q 018538 190 DQIVEAGTYLRVHV 203 (354)
Q Consensus 190 ~~~V~~GD~I~V~~ 203 (354)
++.|..++.|+|..
T Consensus 41 ~~~V~~~~~i~v~~ 54 (245)
T COG1189 41 SQLVDIDDEIEVKG 54 (245)
T ss_pred ceecCCCceEEEcc
Confidence 99999999999874
No 69
>PRK11507 ribosome-associated protein; Provisional
Probab=93.85 E-value=0.21 Score=39.02 Aligned_cols=50 Identities=16% Similarity=0.034 Sum_probs=39.9
Q ss_pred CcHHHHHHhhc-CCCHHHHHHHHHcCCEEEeeeCCCCCCCCchhhhhhhcccCCccccccccccCCeEEeeccccccccc
Q 018538 110 GPVLEYICREL-NLPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTFRITH 188 (354)
Q Consensus 110 ~~L~~~L~~~~-~lSr~~~~~lI~~G~V~~~~~~~~~~~~~~~e~~r~~~~~~~~~v~~kr~~vnGk~vr~~~~~~~~~~ 188 (354)
-+|++||.-.. --|=..++.+|..|.|. |||... +.
T Consensus 12 I~L~QlLK~~~~v~SGG~AK~~I~eg~V~----------------------------------VNGeve---------~r 48 (70)
T PRK11507 12 VELCDLLKLEGWSESGAQAKIAIAEGQVK----------------------------------VDGAVE---------TR 48 (70)
T ss_pred EEHHHHHhhhCcccChHHHHHHHHcCceE----------------------------------ECCEEe---------cc
Confidence 37999996554 34778899999999999 899874 23
Q ss_pred cceeecCCcEEEEe
Q 018538 189 VDQIVEAGTYLRVH 202 (354)
Q Consensus 189 ~~~~V~~GD~I~V~ 202 (354)
...++.+||.|++.
T Consensus 49 RgkKl~~GD~V~~~ 62 (70)
T PRK11507 49 KRCKIVAGQTVSFA 62 (70)
T ss_pred cCCCCCCCCEEEEC
Confidence 45678999999886
No 70
>PRK04051 rps4p 30S ribosomal protein S4P; Validated
Probab=90.85 E-value=0.55 Score=42.93 Aligned_cols=50 Identities=16% Similarity=0.195 Sum_probs=40.6
Q ss_pred cHHHHHHhhc-CCCHHHHHHHHHcCCEEEeeeCCCCCCCCchhhhhhhcccCCccccccccccCCeEEeecccccccccc
Q 018538 111 PVLEYICREL-NLPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTFRITHV 189 (354)
Q Consensus 111 ~L~~~L~~~~-~lSr~~~~~lI~~G~V~~~~~~~~~~~~~~~e~~r~~~~~~~~~v~~kr~~vnGk~vr~~~~~~~~~~~ 189 (354)
||+.+|.+.. --|+..++.+|..|.|. |||++| ++|
T Consensus 104 RLd~il~r~gla~S~~~Ar~lI~hGhV~----------------------------------V~g~~V---------~~P 140 (177)
T PRK04051 104 RLQTIVYRKGLARTPKQARQFIVHGHIA----------------------------------VNGRRV---------TSP 140 (177)
T ss_pred HHHHHHHHccCcCCHHHHHHHHHcCCEE----------------------------------ECCEEe---------CCC
Confidence 5888887765 67999999999999999 899985 688
Q ss_pred ceeecCCcEEEEec
Q 018538 190 DQIVEAGTYLRVHV 203 (354)
Q Consensus 190 ~~~V~~GD~I~V~~ 203 (354)
++.|..|+.-.|.+
T Consensus 141 s~~V~~~~ed~I~~ 154 (177)
T PRK04051 141 SYLVSVEEEDLIDY 154 (177)
T ss_pred CeECCCCCcceEEE
Confidence 99999886444433
No 71
>COG2501 S4-like RNA binding protein [Replication, recombination, and repair]
Probab=90.60 E-value=0.93 Score=35.66 Aligned_cols=52 Identities=13% Similarity=0.024 Sum_probs=40.2
Q ss_pred CCCcHHHHHHhhc-CCCHHHHHHHHHcCCEEEeeeCCCCCCCCchhhhhhhcccCCccccccccccCCeEEeeccccccc
Q 018538 108 EGGPVLEYICREL-NLPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTFRI 186 (354)
Q Consensus 108 ~~~~L~~~L~~~~-~lSr~~~~~lI~~G~V~~~~~~~~~~~~~~~e~~r~~~~~~~~~v~~kr~~vnGk~vr~~~~~~~~ 186 (354)
|.-.|.+||.... -=|=.+++..|..|.|+ |||+.-
T Consensus 10 e~I~L~qlLK~~g~i~sGG~AK~~i~eg~V~----------------------------------vNGe~E--------- 46 (73)
T COG2501 10 EFITLGQLLKLAGLIESGGQAKAFIAEGEVK----------------------------------VNGEVE--------- 46 (73)
T ss_pred ceEEHHHHHHHhCcccCcHHHHHHHHCCeEE----------------------------------ECCeee---------
Confidence 3347999996654 34668899999999999 889874
Q ss_pred cccceeecCCcEEEEe
Q 018538 187 THVDQIVEAGTYLRVH 202 (354)
Q Consensus 187 ~~~~~~V~~GD~I~V~ 202 (354)
+....++..||.|.+.
T Consensus 47 tRRgkKlr~gd~V~i~ 62 (73)
T COG2501 47 TRRGKKLRDGDVVEIP 62 (73)
T ss_pred eccCCEeecCCEEEEC
Confidence 2345678999999886
No 72
>PRK04313 30S ribosomal protein S4e; Validated
Probab=89.79 E-value=1.3 Score=42.22 Aligned_cols=72 Identities=17% Similarity=0.126 Sum_probs=51.9
Q ss_pred CCCcHHHHHHhhc--CCCHHHHHHHHHcCCEEEeeeCCCCCCCCchhhhhhhcccCCccccccccccCCeEEeecccccc
Q 018538 108 EGGPVLEYICREL--NLPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTFR 185 (354)
Q Consensus 108 ~~~~L~~~L~~~~--~lSr~~~~~lI~~G~V~~~~~~~~~~~~~~~e~~r~~~~~~~~~v~~kr~~vnGk~vr~~~~~~~ 185 (354)
+.-+|.-+|+..| -.+.+++++++.+|.|. |||++.
T Consensus 36 ~siPL~iiLRd~L~yA~t~rEak~Il~~~~V~----------------------------------VDGkvr-------- 73 (237)
T PRK04313 36 ESIPLLVVLRDVLGYADTAREAKKIINEGKVL----------------------------------VDGRVR-------- 73 (237)
T ss_pred cccccHHHHHhHhhhhccHHHHHHHHhCCcEE----------------------------------ECCEEE--------
Confidence 3336888898888 47899999999999999 999984
Q ss_pred ccccceeecCCcEEEEecCCCCCCCCCCCCCCceeEeecCeEEEEEC
Q 018538 186 ITHVDQIVEAGTYLRVHVHPKRFPRCYDIDWNSRIIAVTESHVVLDK 232 (354)
Q Consensus 186 ~~~~~~~V~~GD~I~V~~~~~~~~~~~~~~~~l~IlYED~~llVVNK 232 (354)
++..+.+---|+|+|.-.. ...+++|.....+++.+
T Consensus 74 -~D~~~PvGlmDVIsI~~~~----------e~yRvl~d~kgr~~l~~ 109 (237)
T PRK04313 74 -KDYKFPVGLMDVISIPETG----------EYYRVLPDEKGRLVLIP 109 (237)
T ss_pred -cccccCcCceeEEEEccCC----------CeEEEEECCCCcEEEEE
Confidence 4666777777999886322 13566666655555443
No 73
>PF13275 S4_2: S4 domain; PDB: 1P9K_A.
Probab=88.48 E-value=0.12 Score=39.73 Aligned_cols=49 Identities=14% Similarity=0.108 Sum_probs=32.5
Q ss_pred cHHHHHHhhc-CCCHHHHHHHHHcCCEEEeeeCCCCCCCCchhhhhhhcccCCccccccccccCCeEEeecccccccccc
Q 018538 111 PVLEYICREL-NLPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTFRITHV 189 (354)
Q Consensus 111 ~L~~~L~~~~-~lSr~~~~~lI~~G~V~~~~~~~~~~~~~~~e~~r~~~~~~~~~v~~kr~~vnGk~vr~~~~~~~~~~~ 189 (354)
+|++||.... --|=.+++.+|..|.|+ |||... +..
T Consensus 9 ~L~qlLK~~glv~sGGeAK~~I~~g~V~----------------------------------VNGe~e---------~rr 45 (65)
T PF13275_consen 9 TLGQLLKLAGLVSSGGEAKALIQEGEVK----------------------------------VNGEVE---------TRR 45 (65)
T ss_dssp -HHHHHHHHTS-SSSSTTSHHHHHHHHE----------------------------------ETTB-------------S
T ss_pred EHHHHHhHcCCcccHHHHHHHHHcCceE----------------------------------ECCEEc---------ccc
Confidence 6999996654 23666899999999999 899874 345
Q ss_pred ceeecCCcEEEEe
Q 018538 190 DQIVEAGTYLRVH 202 (354)
Q Consensus 190 ~~~V~~GD~I~V~ 202 (354)
..++.+||.|.+.
T Consensus 46 g~Kl~~GD~V~~~ 58 (65)
T PF13275_consen 46 GKKLRPGDVVEID 58 (65)
T ss_dssp S----SSEEEEET
T ss_pred CCcCCCCCEEEEC
Confidence 6689999999885
No 74
>PLN00036 40S ribosomal protein S4; Provisional
Probab=88.33 E-value=1.9 Score=41.73 Aligned_cols=69 Identities=19% Similarity=0.130 Sum_probs=48.8
Q ss_pred CcHHHHHHhhc--CCCHHHHHHHHHcCCEEEeeeCCCCCCCCchhhhhhhcccCCccccccccccCCeEEeecccccccc
Q 018538 110 GPVLEYICREL--NLPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTFRIT 187 (354)
Q Consensus 110 ~~L~~~L~~~~--~lSr~~~~~lI~~G~V~~~~~~~~~~~~~~~e~~r~~~~~~~~~v~~kr~~vnGk~vr~~~~~~~~~ 187 (354)
-+|.-+|...| -.+.+++++++.+|.|. |||++. +
T Consensus 42 lPL~i~LRd~LkyA~t~rEak~Il~~~~V~----------------------------------VDGkvr---------~ 78 (261)
T PLN00036 42 LPLLLILRNRLKYALTYREVQAILMQRHVK----------------------------------VDGKVR---------T 78 (261)
T ss_pred cccHHHHHhHhhhhccHHHHHHHHhCCeEE----------------------------------ECCEEe---------c
Confidence 36888998887 46888999999999999 999984 4
Q ss_pred ccceeecCCcEEEEecCCCCCCCCCCCCCCceeEeecCeEEEEE
Q 018538 188 HVDQIVEAGTYLRVHVHPKRFPRCYDIDWNSRIIAVTESHVVLD 231 (354)
Q Consensus 188 ~~~~~V~~GD~I~V~~~~~~~~~~~~~~~~l~IlYED~~llVVN 231 (354)
+..+.+---|+|+|.-..+ ..+++|.....+++.
T Consensus 79 D~~fPvG~mDVIsI~kt~e----------~yRvl~D~kGrf~l~ 112 (261)
T PLN00036 79 DKTYPAGFMDVISIPKTNE----------NFRLLYDTKGRFRLH 112 (261)
T ss_pred cCCCCCceeEEEEEcCCCC----------eEEEEECCCceEEEE
Confidence 5666666668888763221 345666555544443
No 75
>PTZ00223 40S ribosomal protein S4; Provisional
Probab=87.98 E-value=2 Score=41.85 Aligned_cols=51 Identities=18% Similarity=0.123 Sum_probs=40.6
Q ss_pred CCcHHHHHHhhcC--CCHHHHHHHHHcCCEEEeeeCCCCCCCCchhhhhhhcccCCccccccccccCCeEEeeccccccc
Q 018538 109 GGPVLEYICRELN--LPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTFRI 186 (354)
Q Consensus 109 ~~~L~~~L~~~~~--lSr~~~~~lI~~G~V~~~~~~~~~~~~~~~e~~r~~~~~~~~~v~~kr~~vnGk~vr~~~~~~~~ 186 (354)
.-+|.-+|...|+ .+.+++++++.+|.|. |||++.
T Consensus 38 siPL~iiLRd~LkyA~t~rEak~Il~~~~V~----------------------------------VDGkvr--------- 74 (273)
T PTZ00223 38 CLPLLIIIRNRLKYALNAREAQMILRQGLVC----------------------------------VDGKPR--------- 74 (273)
T ss_pred ccccHHHHHHHhhhhccHHHHHHHHhCCeEE----------------------------------ECCEEE---------
Confidence 3368889988884 6888999999999999 999974
Q ss_pred cccceeecCCcEEEEe
Q 018538 187 THVDQIVEAGTYLRVH 202 (354)
Q Consensus 187 ~~~~~~V~~GD~I~V~ 202 (354)
++..+.+---|+|+|.
T Consensus 75 ~D~~~PvGlMDVIsI~ 90 (273)
T PTZ00223 75 KDGKYPAGFMDVVEIP 90 (273)
T ss_pred ccCCCCCceeEEEEEc
Confidence 4556666666888875
No 76
>COG4332 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=87.73 E-value=0.85 Score=41.81 Aligned_cols=35 Identities=23% Similarity=0.209 Sum_probs=30.5
Q ss_pred EEeeCCCC--cHHHHHHhhcCCCHHHHHHHHHcCCEE
Q 018538 103 HLVVSEGG--PVLEYICRELNLPPLFVADLIHFGAVY 137 (354)
Q Consensus 103 ~~~v~~~~--~L~~~L~~~~~lSr~~~~~lI~~G~V~ 137 (354)
|+.++.+. +|+.+|++++++|++.++++|..|.|.
T Consensus 130 ~l~~~~p~qlrl~~Ll~seL~LSrS~lq~lie~g~Ir 166 (203)
T COG4332 130 SLRISRPFQLRLDRLLASELGLSRSELQRLIETGQIR 166 (203)
T ss_pred EEcccCcchhHHHHHHHHHhCcCHHHHHHHHHcCcee
Confidence 45555554 799999999999999999999999999
No 77
>PTZ00118 40S ribosomal protein S4; Provisional
Probab=87.45 E-value=2.3 Score=41.19 Aligned_cols=51 Identities=18% Similarity=0.058 Sum_probs=40.7
Q ss_pred CCcHHHHHHhhc--CCCHHHHHHHHHcCCEEEeeeCCCCCCCCchhhhhhhcccCCccccccccccCCeEEeeccccccc
Q 018538 109 GGPVLEYICREL--NLPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTFRI 186 (354)
Q Consensus 109 ~~~L~~~L~~~~--~lSr~~~~~lI~~G~V~~~~~~~~~~~~~~~e~~r~~~~~~~~~v~~kr~~vnGk~vr~~~~~~~~ 186 (354)
.-+|.-+|...| -.+.+++++++.+|.|. |||++.
T Consensus 41 slPL~i~LRd~LkyA~t~rEak~Il~~~~V~----------------------------------VDGkvr--------- 77 (262)
T PTZ00118 41 CLPLVILLRNRLKYALTYDEVKLIVIQKIVK----------------------------------VDGKVR--------- 77 (262)
T ss_pred ccccHHHHHhhhhhhccHHHHHHHHHCCcEE----------------------------------ECCEEE---------
Confidence 336888998888 46888999999999999 999974
Q ss_pred cccceeecCCcEEEEe
Q 018538 187 THVDQIVEAGTYLRVH 202 (354)
Q Consensus 187 ~~~~~~V~~GD~I~V~ 202 (354)
++..+.+---|+|+|.
T Consensus 78 ~D~~fPvG~mDVIsI~ 93 (262)
T PTZ00118 78 TDCTYPVGFMDVVSLT 93 (262)
T ss_pred ccCCCCCceeEEEEEc
Confidence 4566666666888876
No 78
>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=87.27 E-value=1 Score=35.60 Aligned_cols=28 Identities=4% Similarity=-0.008 Sum_probs=25.3
Q ss_pred CCceeccCCCCCCceEEEeeCCHHHHHHHHHhHhcCccceEEEEEEe
Q 018538 261 TPLRTTHQIDNCTEGCVVLARTQEYCSIFHRKIREKKVKKLYLALTT 307 (354)
Q Consensus 261 ~~~~~VHRLDrdTSGLLL~AKn~~a~~~L~~~f~~~~V~K~YlAlV~ 307 (354)
..++..+++|+.++|+++++ ++|..++.
T Consensus 24 ~~i~~aG~kDk~a~t~q~v~-------------------n~f~i~~r 51 (87)
T cd01291 24 KRVGYAGRKDKRAVTTQLVS-------------------NRFTITLR 51 (87)
T ss_pred heEEECccCCCCeeEEEEEc-------------------ccEEEEEE
Confidence 46899999999999999999 78888887
No 79
>PF14451 Ub-Mut7C: Mut7-C ubiquitin
Probab=83.26 E-value=1.8 Score=34.53 Aligned_cols=22 Identities=18% Similarity=0.342 Sum_probs=19.5
Q ss_pred cCCeEEeeccccccccccceeecCCcEEEEec
Q 018538 172 IKGKTVREAQKTFRITHVDQIVEAGTYLRVHV 203 (354)
Q Consensus 172 vnGk~vr~~~~~~~~~~~~~~V~~GD~I~V~~ 203 (354)
+||+. +.+++.++.||.|.|+.
T Consensus 54 vNG~~----------v~~~~~~~~Gd~v~V~P 75 (81)
T PF14451_consen 54 VNGRP----------VDFDYRLKDGDRVAVYP 75 (81)
T ss_pred ECCEE----------CCCcccCCCCCEEEEEe
Confidence 89987 48899999999999984
No 80
>PLN00189 40S ribosomal protein S9; Provisional
Probab=82.84 E-value=1.2 Score=41.34 Aligned_cols=42 Identities=10% Similarity=0.012 Sum_probs=36.2
Q ss_pred CCCHHHHHHHHHcCCEEEeeeCCCCCCCCchhhhhhhcccCCccccccccccCCeEEeeccccccccccceeecCCcEEE
Q 018538 121 NLPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTFRITHVDQIVEAGTYLR 200 (354)
Q Consensus 121 ~lSr~~~~~lI~~G~V~~~~~~~~~~~~~~~e~~r~~~~~~~~~v~~kr~~vnGk~vr~~~~~~~~~~~~~~V~~GD~I~ 200 (354)
.-|...+..+|..|.|. |||++| +.|++.|..|+.+.
T Consensus 121 a~si~~ARqlI~hgHI~----------------------------------V~~~~V---------~~Ps~~V~~~~e~~ 157 (194)
T PLN00189 121 AKSIHHARVLIRQRHIR----------------------------------VGKQIV---------NVPSFMVRVDSQKH 157 (194)
T ss_pred cCCHHHHHHheeCCCEe----------------------------------ECCEEE---------ecCcEEEecCCEEE
Confidence 45788899999999999 999985 58999999999998
Q ss_pred EecCC
Q 018538 201 VHVHP 205 (354)
Q Consensus 201 V~~~~ 205 (354)
|.+.+
T Consensus 158 Itw~~ 162 (194)
T PLN00189 158 IDFSL 162 (194)
T ss_pred EEEec
Confidence 87643
No 81
>PRK01777 hypothetical protein; Validated
Probab=82.75 E-value=1.9 Score=35.43 Aligned_cols=57 Identities=19% Similarity=0.192 Sum_probs=38.3
Q ss_pred EEEeeCCCCcHHHHHHhhcCCCHHHHHHHHHcCCEEEeeeCCCCCCCCchhhhhhhcccCCccccccccccCCeEEeecc
Q 018538 102 EHLVVSEGGPVLEYICRELNLPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQ 181 (354)
Q Consensus 102 ~~~~v~~~~~L~~~L~~~~~lSr~~~~~lI~~G~V~~~~~~~~~~~~~~~e~~r~~~~~~~~~v~~kr~~vnGk~vr~~~ 181 (354)
..+.+++..++.+.|.. +|+...+-.--+..+.|- |||+.
T Consensus 19 ~~l~vp~GtTv~dal~~-sgi~~~~pei~~~~~~vg----------------------------------I~Gk~----- 58 (95)
T PRK01777 19 QRLTLQEGATVEEAIRA-SGLLELRTDIDLAKNKVG----------------------------------IYSRP----- 58 (95)
T ss_pred EEEEcCCCCcHHHHHHH-cCCCccCcccccccceEE----------------------------------EeCeE-----
Confidence 56777777788888854 465444211112234444 89987
Q ss_pred ccccccccceeecCCcEEEEec
Q 018538 182 KTFRITHVDQIVEAGTYLRVHV 203 (354)
Q Consensus 182 ~~~~~~~~~~~V~~GD~I~V~~ 203 (354)
...++.|+.||+|+|+.
T Consensus 59 -----v~~d~~L~dGDRVeIyr 75 (95)
T PRK01777 59 -----AKLTDVLRDGDRVEIYR 75 (95)
T ss_pred -----CCCCCcCCCCCEEEEec
Confidence 47889999999999985
No 82
>PF06353 DUF1062: Protein of unknown function (DUF1062); InterPro: IPR009412 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=82.40 E-value=2 Score=37.94 Aligned_cols=57 Identities=18% Similarity=0.181 Sum_probs=38.1
Q ss_pred CCCCCceeecCCCCCC-CCceE-EEeeCCC--CcHHHHHHhhcCCCHHHHHHHHHcCCEEE
Q 018538 82 GYPEYHRLLPCPSQNC-PPRVE-HLVVSEG--GPVLEYICRELNLPPLFVADLIHFGAVYY 138 (354)
Q Consensus 82 ~~~~~~~~~~~p~~~~-~~R~~-~~~v~~~--~~L~~~L~~~~~lSr~~~~~lI~~G~V~~ 138 (354)
..|+|.-..-.+.... ...++ ++..+.. -+|+.+|++.+++||+.+++|+..|.|..
T Consensus 71 ~~~~~~v~~~~~~~~~~~~~~~v~i~~~~~~~~Rld~lLa~~L~lSrs~l~~l~~~G~I~~ 131 (142)
T PF06353_consen 71 EFPEYDVEKRLDTEDDDWADIEVEIRFPFPFPLRLDRLLARQLGLSRSRLKRLIEQGLIRS 131 (142)
T ss_pred CCCceEEEEEeccCCccccceEEEEEeCCCCCccHHHHHHHHhCcCHHHHHHHHHCCCEEe
Confidence 4666654443333321 12232 2333333 28999999999999999999999999993
No 83
>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=76.96 E-value=4.8 Score=36.34 Aligned_cols=49 Identities=16% Similarity=0.178 Sum_probs=37.1
Q ss_pred cHHHHHHhhc-CCCHHHHHHHHHcCCEEEeeeCCCCCCCCchhhhhhhcccCCccccccccccCCeEEeecccccccccc
Q 018538 111 PVLEYICREL-NLPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTFRITHV 189 (354)
Q Consensus 111 ~L~~~L~~~~-~lSr~~~~~lI~~G~V~~~~~~~~~~~~~~~e~~r~~~~~~~~~v~~kr~~vnGk~vr~~~~~~~~~~~ 189 (354)
||+-.+.+.. .-|...+..+|..|.|. |||+.| +.|
T Consensus 105 RL~~vv~r~g~a~s~~~ArqlI~hgHI~----------------------------------V~~~~V---------~~P 141 (162)
T TIGR01018 105 RLQTQVFKKGLARTIHQARQLIVHGHIA----------------------------------VDGRRV---------TSP 141 (162)
T ss_pred hHhhHhhhccCcCCHHHHHHHhhCCCee----------------------------------ECCEEe---------ccC
Confidence 4555555543 56889999999999999 999985 588
Q ss_pred ceeecCCcEEEEe
Q 018538 190 DQIVEAGTYLRVH 202 (354)
Q Consensus 190 ~~~V~~GD~I~V~ 202 (354)
++.|..|+.=.|.
T Consensus 142 s~~V~~~~Ed~I~ 154 (162)
T TIGR01018 142 SYIVRREEEKKID 154 (162)
T ss_pred ceEecCCCCCeee
Confidence 9999998544343
No 84
>PF01509 TruB_N: TruB family pseudouridylate synthase (N terminal domain); InterPro: IPR002501 Pseudouridine synthases catalyse the isomerisation of uridine to pseudouridine (Psi) in a variety of RNA molecules, and may function as RNA chaperones. Pseudouridine is the most abundant modified nucleotide found in all cellular RNAs. There are four distinct families of pseudouridine synthases that share no global sequence similarity, but which do share the same fold of their catalytic domain(s) and uracil-binding site and are descended from a common molecular ancestor. The catalytic domain consists of two subdomains, each of which has an alpha+beta structure that has some similarity to the ferredoxin-like fold (note: some pseudouridine synthases contain additional domains). The active site is the most conserved structural region of the superfamily and is located between the two homologous domains. These families are []: Pseudouridine synthase I, TruA. Pseudouridine synthase II, TruB, which contains and additional C-terminal PUA domain. Pseudouridine synthase RsuA (ribosomal small subunit) and RluC/RluD (ribosomal large subunits), both of which contain an additional N-terminal alpha-L RNA-binding motif. Pseudouridine synthase TruD, which has a natural circular permutation in the catalytic domain, as well as an insertion of a family-specific alpha+beta subdomain. TruB is responsible for the pseudouridine residue present in the T loops of virtually all tRNAs. TruB recognises the preformed 3-D structure of the T loop primarily through shape complementarity. It accesses its substrate uridyl residue by flipping out the nucleotide and disrupts the tertiary structure of tRNA []. This entry represents pseudouridine synthase TruB, as well as Cbf5p that modifies rRNA [].; GO: 0006396 RNA processing; PDB: 1SGV_B 2AUS_C 3UAI_A 3U28_A 2RFK_A 3LWV_A 3HJY_A 3HAX_A 3LWO_A 3HAY_A ....
Probab=73.72 E-value=3.6 Score=36.48 Aligned_cols=43 Identities=14% Similarity=0.224 Sum_probs=32.1
Q ss_pred CCceeccCCCCCCceEEEeeCCHHHHHHHHHhHhcCccceEEEEEEe
Q 018538 261 TPLRTTHQIDNCTEGCVVLARTQEYCSIFHRKIREKKVKKLYLALTT 307 (354)
Q Consensus 261 ~~~~~VHRLDrdTSGLLL~AKn~~a~~~L~~~f~~~~V~K~YlAlV~ 307 (354)
.+++..+.||-..||||+++-+.. .+|.+.+. ...|+|.|...
T Consensus 7 ~KvGH~GTLDP~AsGvL~v~vg~~--Tkl~~~l~--~~~K~Y~~~~~ 49 (149)
T PF01509_consen 7 KKVGHGGTLDPFASGVLVVGVGKA--TKLLSYLQ--NSDKEYVATIR 49 (149)
T ss_dssp SSEEESS-SSTT-EEEEEEEEGGG--GGGHHHHT--TSEEEEEEEEE
T ss_pred ceeccccccCCcceEEEEEEECCc--chHHHHhh--ccCCEEEEEEE
Confidence 468889999999999999999873 34555665 45599999874
No 85
>PTZ00155 40S ribosomal protein S9; Provisional
Probab=70.95 E-value=5.2 Score=36.73 Aligned_cols=50 Identities=8% Similarity=-0.016 Sum_probs=39.2
Q ss_pred cHHHHHHhhc-CCCHHHHHHHHHcCCEEEeeeCCCCCCCCchhhhhhhcccCCccccccccccCCeEEeecccccccccc
Q 018538 111 PVLEYICREL-NLPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTFRITHV 189 (354)
Q Consensus 111 ~L~~~L~~~~-~lSr~~~~~lI~~G~V~~~~~~~~~~~~~~~e~~r~~~~~~~~~v~~kr~~vnGk~vr~~~~~~~~~~~ 189 (354)
||+-.+.+.. .-|...+..+|..|.|. |||++| +.|
T Consensus 108 RL~~iv~r~g~A~ti~~ARqlI~HGHI~----------------------------------V~~~~V---------~~P 144 (181)
T PTZ00155 108 RLQTKVFKLGLAKSIHHARVLIRQRHIR----------------------------------VGKQIV---------DIP 144 (181)
T ss_pred hhhhHHHhccCcCCHHHhhhheeCCCEE----------------------------------ECCEEe---------ccC
Confidence 4666665544 46888899999999999 999985 588
Q ss_pred ceeecCCcEEEEec
Q 018538 190 DQIVEAGTYLRVHV 203 (354)
Q Consensus 190 ~~~V~~GD~I~V~~ 203 (354)
++.|..|+.=.|.+
T Consensus 145 s~~V~~~~Ed~I~~ 158 (181)
T PTZ00155 145 SFLVRVDSEKHIDF 158 (181)
T ss_pred ceEeccCccCceee
Confidence 99999998765554
No 86
>COG1471 RPS4A Ribosomal protein S4E [Translation, ribosomal structure and biogenesis]
Probab=61.87 E-value=16 Score=34.87 Aligned_cols=27 Identities=22% Similarity=0.171 Sum_probs=19.1
Q ss_pred cHHHHHHhhc--CCCHHHHHHHHHcCCEE
Q 018538 111 PVLEYICREL--NLPPLFVADLIHFGAVY 137 (354)
Q Consensus 111 ~L~~~L~~~~--~lSr~~~~~lI~~G~V~ 137 (354)
+|.-+|+..| --.-++++++|..|.|+
T Consensus 42 PL~~iiRd~LkyAd~~REa~~Ii~~g~v~ 70 (241)
T COG1471 42 PLLVIIRDYLKYADNAREARKILSEGKVL 70 (241)
T ss_pred cEEeeehhHHHhccchHHHHHHHhcCcEE
Confidence 4444455544 34557899999999999
No 87
>PRK13354 tyrosyl-tRNA synthetase; Provisional
Probab=60.55 E-value=15 Score=37.73 Aligned_cols=27 Identities=15% Similarity=0.105 Sum_probs=23.5
Q ss_pred cHHHHHHhhc-CCCHHHHHHHHHcCCEE
Q 018538 111 PVLEYICREL-NLPPLFVADLIHFGAVY 137 (354)
Q Consensus 111 ~L~~~L~~~~-~lSr~~~~~lI~~G~V~ 137 (354)
+|.++|.+.. --|+++++++|++|.|+
T Consensus 344 ~~~~~l~~~~~~~S~~earrli~~ggv~ 371 (410)
T PRK13354 344 NLVDLLVDLGLEPSKREARRLIQNGAIK 371 (410)
T ss_pred CHHHHHHHhCCCCCHHHHHHHHHcCCEE
Confidence 5888887654 67999999999999999
No 88
>PRK05912 tyrosyl-tRNA synthetase; Validated
Probab=59.61 E-value=28 Score=35.70 Aligned_cols=28 Identities=18% Similarity=0.030 Sum_probs=23.8
Q ss_pred CcHHHHHHhhc-CCCHHHHHHHHHcCCEE
Q 018538 110 GPVLEYICREL-NLPPLFVADLIHFGAVY 137 (354)
Q Consensus 110 ~~L~~~L~~~~-~lSr~~~~~lI~~G~V~ 137 (354)
..+.++|.+.. --|+++++++|+.|.|+
T Consensus 343 ~~~~~~l~~~~~~~S~~earr~i~~g~v~ 371 (408)
T PRK05912 343 IDLLALLVEAGLVPSKSEARRLIKQGGVK 371 (408)
T ss_pred CcHHHHHHHhCCCCCHHHHHHHHHcCCEE
Confidence 36888887654 67999999999999999
No 89
>PRK08364 sulfur carrier protein ThiS; Provisional
Probab=56.87 E-value=23 Score=26.98 Aligned_cols=21 Identities=33% Similarity=0.558 Sum_probs=17.5
Q ss_pred cCCeEEeeccccccccccceeecCCcEEEEe
Q 018538 172 IKGKTVREAQKTFRITHVDQIVEAGTYLRVH 202 (354)
Q Consensus 172 vnGk~vr~~~~~~~~~~~~~~V~~GD~I~V~ 202 (354)
+||+.+ ..++.++.||.|.+.
T Consensus 44 vNg~iv----------~~~~~l~~gD~Veii 64 (70)
T PRK08364 44 VNGKVA----------LEDDPVKDGDYVEVI 64 (70)
T ss_pred ECCEEC----------CCCcCcCCCCEEEEE
Confidence 899874 567889999999886
No 90
>PRK05659 sulfur carrier protein ThiS; Validated
Probab=54.47 E-value=12 Score=27.82 Aligned_cols=25 Identities=16% Similarity=0.426 Sum_probs=18.5
Q ss_pred cCCeEEeeccccccccccceeecCCcEEEEe
Q 018538 172 IKGKTVREAQKTFRITHVDQIVEAGTYLRVH 202 (354)
Q Consensus 172 vnGk~vr~~~~~~~~~~~~~~V~~GD~I~V~ 202 (354)
+||+.+... ...++.|+.||+|+|.
T Consensus 36 vNg~iv~r~------~~~~~~l~~gD~vei~ 60 (66)
T PRK05659 36 VNGEIVPRS------QHASTALREGDVVEIV 60 (66)
T ss_pred ECCeEeCHH------HcCcccCCCCCEEEEE
Confidence 788776332 2467889999999986
No 91
>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=53.24 E-value=46 Score=25.15 Aligned_cols=21 Identities=19% Similarity=0.420 Sum_probs=17.3
Q ss_pred cCCeEEeeccccccccccceeecCCcEEEEe
Q 018538 172 IKGKTVREAQKTFRITHVDQIVEAGTYLRVH 202 (354)
Q Consensus 172 vnGk~vr~~~~~~~~~~~~~~V~~GD~I~V~ 202 (354)
+||+.+ ..++.|+.||.|.|.
T Consensus 54 vNg~~v----------~~~~~l~~gD~v~i~ 74 (80)
T cd00754 54 VNGEYV----------RLDTPLKDGDEVAII 74 (80)
T ss_pred ECCeEc----------CCCcccCCCCEEEEe
Confidence 899874 467789999999886
No 92
>PRK06437 hypothetical protein; Provisional
Probab=51.20 E-value=29 Score=26.32 Aligned_cols=21 Identities=19% Similarity=0.237 Sum_probs=17.6
Q ss_pred cCCeEEeeccccccccccceeecCCcEEEEe
Q 018538 172 IKGKTVREAQKTFRITHVDQIVEAGTYLRVH 202 (354)
Q Consensus 172 vnGk~vr~~~~~~~~~~~~~~V~~GD~I~V~ 202 (354)
+||+.+ ..++.|+.||.|++.
T Consensus 41 vNg~iv----------~~~~~L~dgD~Veiv 61 (67)
T PRK06437 41 VNGSPV----------LEDHNVKKEDDVLIL 61 (67)
T ss_pred ECCEEC----------CCceEcCCCCEEEEE
Confidence 889874 578899999999886
No 93
>PRK06083 sulfur carrier protein ThiS; Provisional
Probab=47.90 E-value=28 Score=27.88 Aligned_cols=25 Identities=12% Similarity=0.341 Sum_probs=19.2
Q ss_pred cCCeEEeeccccccccccceeecCCcEEEEe
Q 018538 172 IKGKTVREAQKTFRITHVDQIVEAGTYLRVH 202 (354)
Q Consensus 172 vnGk~vr~~~~~~~~~~~~~~V~~GD~I~V~ 202 (354)
+||..|...+ -.++.|+.||.|+|-
T Consensus 54 vNg~iVpr~~------w~~t~L~egD~IEIv 78 (84)
T PRK06083 54 INNQVVPRSE------WQSTVLSSGDAISLF 78 (84)
T ss_pred ECCEEeCHHH------cCcccCCCCCEEEEE
Confidence 8999875432 456789999999875
No 94
>PF02597 ThiS: ThiS family; InterPro: IPR003749 ThiS (thiaminS) is a 66 aa protein involved in sulphur transfer. ThiS is coded in the thiCEFSGH operon in Escherichia coli. This family of proteins have two conserved Glycines at the COOH terminus. Thiocarboxylate is formed at the last G in the activation process. Sulphur is transferred from ThiI to ThiS in a reaction catalysed by IscS []. MoaD, a protein involved in sulphur transfer during molybdopterin synthesis, is about the same length and shows limited sequence similarity to ThiS. Both have the conserved GG at the COOH end.; PDB: 1JW9_D 1JWB_D 1JWA_D 3BII_D 1NVI_D 1FMA_D 1FM0_D 2QIE_G 2Q5W_D 2K5P_A ....
Probab=47.70 E-value=54 Score=24.53 Aligned_cols=24 Identities=17% Similarity=0.400 Sum_probs=18.1
Q ss_pred cCCeEEeeccccccccccceeecCCcEEEEe
Q 018538 172 IKGKTVREAQKTFRITHVDQIVEAGTYLRVH 202 (354)
Q Consensus 172 vnGk~vr~~~~~~~~~~~~~~V~~GD~I~V~ 202 (354)
+||+.++. + ..++.|+.||.|.+.
T Consensus 48 vN~~~v~~-~------~~~~~l~~gD~V~i~ 71 (77)
T PF02597_consen 48 VNGEIVPD-D------GLDTPLKDGDEVAIL 71 (77)
T ss_dssp ETTEEEGG-G------TTTSBEETTEEEEEE
T ss_pred ECCEEcCC-c------cCCcCcCCCCEEEEE
Confidence 89998632 1 237889999999886
No 95
>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=46.80 E-value=59 Score=24.11 Aligned_cols=25 Identities=12% Similarity=0.348 Sum_probs=17.1
Q ss_pred cCCeEEeeccccccccccceeecCCcEEEEe
Q 018538 172 IKGKTVREAQKTFRITHVDQIVEAGTYLRVH 202 (354)
Q Consensus 172 vnGk~vr~~~~~~~~~~~~~~V~~GD~I~V~ 202 (354)
+||+.+...+ -.++.|+.||.|.+.
T Consensus 35 vNg~~v~~~~------~~~~~L~~gD~V~ii 59 (65)
T cd00565 35 LNGEIVPRSE------WASTPLQDGDRIEIV 59 (65)
T ss_pred ECCEEcCHHH------cCceecCCCCEEEEE
Confidence 8998752211 123789999999886
No 96
>KOG2559 consensus Predicted pseudouridine synthase [Translation, ribosomal structure and biogenesis]
Probab=46.56 E-value=11 Score=36.52 Aligned_cols=22 Identities=14% Similarity=0.308 Sum_probs=19.9
Q ss_pred CceeccCCCCCCceEEEeeCCH
Q 018538 262 PLRTTHQIDNCTEGCVVLARTQ 283 (354)
Q Consensus 262 ~~~~VHRLDrdTSGLLL~AKn~ 283 (354)
++.++||||-.|||+++|+-+.
T Consensus 90 ~V~v~h~l~~~~sgvl~~gVgh 111 (318)
T KOG2559|consen 90 DVQVVHVLPLATSGVLLFGVGH 111 (318)
T ss_pred ceeeEEeecccccceEEEecCc
Confidence 5889999999999999998764
No 97
>PRK07440 hypothetical protein; Provisional
Probab=43.91 E-value=30 Score=26.55 Aligned_cols=25 Identities=16% Similarity=0.264 Sum_probs=18.9
Q ss_pred cCCeEEeeccccccccccceeecCCcEEEEe
Q 018538 172 IKGKTVREAQKTFRITHVDQIVEAGTYLRVH 202 (354)
Q Consensus 172 vnGk~vr~~~~~~~~~~~~~~V~~GD~I~V~ 202 (354)
+||+.+... .-.++.|+.||.|+|-
T Consensus 40 ~N~~iv~r~------~w~~~~L~~gD~IEIv 64 (70)
T PRK07440 40 YNGEILHRQ------FWEQTQVQPGDRLEIV 64 (70)
T ss_pred ECCEEeCHH------HcCceecCCCCEEEEE
Confidence 899987433 2467789999999875
No 98
>cd01666 TGS_DRG_C TGS_DRG_C: DRG (developmentally regulated GTP-binding protein) represents a family of GTP-binding proteins that includes two members, DRG1 and DRG2. DRG1 and DRG2 have a C-terminal TGS domain (named after the ThrRS, GTPase, and SpoT proteins where it occurs) with a predominantly beta-sheet structure. The function of TGS is unknown but its presence in two types of regulatory proteins (the DRG GTPases and guanosine polyphosphate phosphohydrolases/synthetases) suggests a ligand (most likely nucleotide)-binding, regulatory role.
Probab=40.50 E-value=1.3e+02 Score=23.47 Aligned_cols=16 Identities=13% Similarity=0.355 Sum_probs=13.9
Q ss_pred cccceeecCCcEEEEe
Q 018538 187 THVDQIVEAGTYLRVH 202 (354)
Q Consensus 187 ~~~~~~V~~GD~I~V~ 202 (354)
+..++.|+.||+|+|.
T Consensus 59 Vgl~~~L~d~DvVeI~ 74 (75)
T cd01666 59 VGLDHVLEDEDVVQIV 74 (75)
T ss_pred CCCCCEecCCCEEEEe
Confidence 4788999999999985
No 99
>TIGR01683 thiS thiamine biosynthesis protein ThiS. This model represents ThiS, a small thiamine-biosynthesis protein related to MoaD, a molybdenum cofactor biosynthesis protein. Both proteins are involved in sulfur transfer. ThiS has a conserved Gly-Gly C-terminus that is modified, in reactions requiring ThiI, ThiF, IscS, and a sulfur atom from Cys, into the thiocarboxylate that provides the sulfur for thiazole biosynthesis.
Probab=40.12 E-value=49 Score=24.51 Aligned_cols=25 Identities=20% Similarity=0.453 Sum_probs=17.7
Q ss_pred cCCeEEeeccccccccccceeecCCcEEEEe
Q 018538 172 IKGKTVREAQKTFRITHVDQIVEAGTYLRVH 202 (354)
Q Consensus 172 vnGk~vr~~~~~~~~~~~~~~V~~GD~I~V~ 202 (354)
+||+.+...+ ..++.|+.||.|.|.
T Consensus 34 vN~~iv~~~~------~~~~~L~~gD~veii 58 (64)
T TIGR01683 34 VNGEIVPRSE------WDDTILKEGDRIEIV 58 (64)
T ss_pred ECCEEcCHHH------cCceecCCCCEEEEE
Confidence 8998763221 344689999999886
No 100
>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=38.89 E-value=38 Score=27.05 Aligned_cols=31 Identities=13% Similarity=0.139 Sum_probs=19.8
Q ss_pred EEeeCCCCcHHHHHHhhcCCCHHHHHHHHHcC
Q 018538 103 HLVVSEGGPVLEYICRELNLPPLFVADLIHFG 134 (354)
Q Consensus 103 ~~~v~~~~~L~~~L~~~~~lSr~~~~~lI~~G 134 (354)
+++|....+|...+.+ +|+|.+.+.+++...
T Consensus 4 ~~~V~~GDtLs~iF~~-~gls~~dl~~v~~~~ 34 (85)
T PF04225_consen 4 EYTVKSGDTLSTIFRR-AGLSASDLYAVLEAD 34 (85)
T ss_dssp EEE--TT--HHHHHHH-TT--HHHHHHHHHHG
T ss_pred EEEECCCCcHHHHHHH-cCCCHHHHHHHHhcc
Confidence 5677777788887755 599999999999864
No 101
>PLN02799 Molybdopterin synthase sulfur carrier subunit
Probab=35.35 E-value=1.4e+02 Score=23.00 Aligned_cols=21 Identities=10% Similarity=0.166 Sum_probs=17.0
Q ss_pred cCCeEEeeccccccccccceeecCCcEEEEe
Q 018538 172 IKGKTVREAQKTFRITHVDQIVEAGTYLRVH 202 (354)
Q Consensus 172 vnGk~vr~~~~~~~~~~~~~~V~~GD~I~V~ 202 (354)
+||+.+ ..++.|+.||.|.|.
T Consensus 56 vN~~~v----------~~~~~l~dgDeVai~ 76 (82)
T PLN02799 56 LNEEYT----------TESAALKDGDELAII 76 (82)
T ss_pred ECCEEc----------CCCcCcCCCCEEEEe
Confidence 788863 567789999999886
No 102
>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=35.23 E-value=34 Score=22.88 Aligned_cols=22 Identities=27% Similarity=0.206 Sum_probs=19.4
Q ss_pred HHhhcCCCHHHHHHHHHcCCEE
Q 018538 116 ICRELNLPPLFVADLIHFGAVY 137 (354)
Q Consensus 116 L~~~~~lSr~~~~~lI~~G~V~ 137 (354)
+++.+++|++.+.++++.|.+-
T Consensus 7 ~a~~lgis~~ti~~~~~~g~i~ 28 (49)
T TIGR01764 7 AAEYLGVSKDTVYRLIHEGELP 28 (49)
T ss_pred HHHHHCCCHHHHHHHHHcCCCC
Confidence 5567799999999999999876
No 103
>PRK05863 sulfur carrier protein ThiS; Provisional
Probab=33.17 E-value=33 Score=25.72 Aligned_cols=24 Identities=13% Similarity=0.149 Sum_probs=17.0
Q ss_pred cCCeEEeeccccccccccceeecCCcEEEEe
Q 018538 172 IKGKTVREAQKTFRITHVDQIVEAGTYLRVH 202 (354)
Q Consensus 172 vnGk~vr~~~~~~~~~~~~~~V~~GD~I~V~ 202 (354)
+||..++.. .+++.|+.||.|+|.
T Consensus 36 ~N~~iv~r~-------~~~~~L~~gD~ieIv 59 (65)
T PRK05863 36 VDWSVLPRS-------DWATKLRDGARLEVV 59 (65)
T ss_pred ECCcCcChh-------HhhhhcCCCCEEEEE
Confidence 788866443 334459999999885
No 104
>TIGR01687 moaD_arch MoaD family protein, archaeal. Members of this family appear to be archaeal versions of MoaD, subunit 1 of molybdopterin converting factor. This model has been split from the bacterial/eukaryotic equivalog model TIGR01682 because the presence of two members of this family in a substantial number of archaeal species suggests that roles might not be interchangeable.
Probab=31.78 E-value=87 Score=24.38 Aligned_cols=23 Identities=13% Similarity=0.331 Sum_probs=15.9
Q ss_pred cCCeEEeeccccccccccceeecCCcEEEEe
Q 018538 172 IKGKTVREAQKTFRITHVDQIVEAGTYLRVH 202 (354)
Q Consensus 172 vnGk~vr~~~~~~~~~~~~~~V~~GD~I~V~ 202 (354)
+||+.++. ...+.|+.||.|.+.
T Consensus 60 vN~~~v~~--------~~~~~l~dgdev~i~ 82 (88)
T TIGR01687 60 VNGRNVDW--------GLGTELKDGDVVAIF 82 (88)
T ss_pred ECCEecCc--------cCCCCCCCCCEEEEe
Confidence 88887521 111479999999886
No 105
>PF03658 Ub-RnfH: RnfH family Ubiquitin; InterPro: IPR005346 This is a small family of proteins of unknown function.; PDB: 2HJ1_B.
Probab=30.92 E-value=34 Score=27.66 Aligned_cols=18 Identities=11% Similarity=0.314 Sum_probs=9.8
Q ss_pred cccceeecCCcEEEEecC
Q 018538 187 THVDQIVEAGTYLRVHVH 204 (354)
Q Consensus 187 ~~~~~~V~~GD~I~V~~~ 204 (354)
++.++.|+.||+|+|+.+
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 478889999999999953
No 106
>COG2104 ThiS Sulfur transfer protein involved in thiamine biosynthesis [Coenzyme metabolism]
Probab=30.85 E-value=1.3e+02 Score=23.24 Aligned_cols=25 Identities=28% Similarity=0.510 Sum_probs=18.4
Q ss_pred cCCeEEeeccccccccccceeecCCcEEEEe
Q 018538 172 IKGKTVREAQKTFRITHVDQIVEAGTYLRVH 202 (354)
Q Consensus 172 vnGk~vr~~~~~~~~~~~~~~V~~GD~I~V~ 202 (354)
+||..+-..+ ..++.++.||.|+|-
T Consensus 38 vNg~iVpr~~------~~~~~l~~gD~ievv 62 (68)
T COG2104 38 VNGEIVPRSQ------WADTILKEGDRIEVV 62 (68)
T ss_pred ECCEEccchh------hhhccccCCCEEEEE
Confidence 8999863221 367889999999875
No 107
>cd01764 Urm1 Urm1-like ubuitin domain. Urm1 (Ubiquitin-Related Modifier1) The Urm1 fold, like those of two closely related proteins MoaD (molybdopterin synthase) and ThiS (sulfur carrier protein), is similar to that of ubiquitin although there is little or no sequence similarity. The C-terminal glycines of Urm1 are conjugated to an E1-like protein Uba4 as part of a novel conjugation system in yeast. The Urm1 fold is found only in eukaryotes.
Probab=30.25 E-value=64 Score=26.19 Aligned_cols=25 Identities=20% Similarity=0.142 Sum_probs=18.4
Q ss_pred cCCeEEeeccccccccccceeecCCcEEEEe
Q 018538 172 IKGKTVREAQKTFRITHVDQIVEAGTYLRVH 202 (354)
Q Consensus 172 vnGk~vr~~~~~~~~~~~~~~V~~GD~I~V~ 202 (354)
|||.-++-.+ ..++.|+.||.|.+.
T Consensus 64 vN~~di~~l~------g~~t~L~dgD~v~i~ 88 (94)
T cd01764 64 INDTDWELLG------EEDYILEDGDHVVFI 88 (94)
T ss_pred ECCccccccC------CcccCCCCcCEEEEE
Confidence 7887654221 467889999999887
No 108
>PRK11130 moaD molybdopterin synthase small subunit; Provisional
Probab=29.11 E-value=1.3e+02 Score=23.29 Aligned_cols=22 Identities=9% Similarity=0.148 Sum_probs=17.1
Q ss_pred cCCeEEeeccccccccccceeecCCcEEEEec
Q 018538 172 IKGKTVREAQKTFRITHVDQIVEAGTYLRVHV 203 (354)
Q Consensus 172 vnGk~vr~~~~~~~~~~~~~~V~~GD~I~V~~ 203 (354)
||+.. ...++.|+.||.|.+..
T Consensus 55 VN~~~----------~~~~~~l~dgDeVai~P 76 (81)
T PRK11130 55 VNQTL----------VSFDHPLTDGDEVAFFP 76 (81)
T ss_pred ECCEE----------cCCCCCCCCCCEEEEeC
Confidence 78865 35677899999999873
No 109
>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=28.48 E-value=26 Score=24.15 Aligned_cols=34 Identities=24% Similarity=0.178 Sum_probs=27.2
Q ss_pred CcccCcchhHHHhhhccccccccccccccceeeecc
Q 018538 14 GRSLGAPVSLLRTLASTHASCHRNIYKSNVVLSFSS 49 (354)
Q Consensus 14 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 49 (354)
-++|-+|.+|++-...--+..-.++.||. ++|.+
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 58999999999888777777777777888 77754
No 110
>PF02824 TGS: TGS domain; InterPro: IPR004095 The TGS domain is present in a number of enzymes, for example, in threonyl-tRNA synthetase (ThrRS), GTPase, and guanosine-3',5'-bis(diphosphate) 3'-pyrophosphohydrolase (SpoT) []. The TGS domain is also present at the amino terminus of the uridine kinase from the spirochaete Treponema pallidum (but not any other organism, including the related spirochaete Borrelia burgdorferi). TGS is a small domain that consists of ~50 amino acid residues and is predicted to possess a predominantly beta-sheet structure. There is no direct information on the functions of the TGS domain, but its presence in two types of regulatory proteins (the GTPases and guanosine polyphosphate phosphohydrolases/synthetases) suggests a ligand (most likely nucleotide)-binding, regulatory role []. ; PDB: 1WXQ_A 1NYR_B 1NYQ_B 2KMM_A 1WWT_A 1TKE_A 1TKG_A 1TJE_A 1QF6_A 1TKY_A ....
Probab=27.39 E-value=48 Score=24.48 Aligned_cols=21 Identities=19% Similarity=0.476 Sum_probs=17.0
Q ss_pred cCCeEEeeccccccccccceeecCCcEEEEe
Q 018538 172 IKGKTVREAQKTFRITHVDQIVEAGTYLRVH 202 (354)
Q Consensus 172 vnGk~vr~~~~~~~~~~~~~~V~~GD~I~V~ 202 (354)
|||+. +..++.|+.||.|+|.
T Consensus 39 Vng~~----------vdl~~~L~~~d~v~ii 59 (60)
T PF02824_consen 39 VNGQL----------VDLDHPLEDGDVVEII 59 (60)
T ss_dssp ETTEE----------EETTSBB-SSEEEEEE
T ss_pred EcCEE----------CCCCCCcCCCCEEEEE
Confidence 89987 4788999999999874
No 111
>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=25.36 E-value=65 Score=21.24 Aligned_cols=22 Identities=14% Similarity=0.200 Sum_probs=19.4
Q ss_pred HHhhcCCCHHHHHHHHHcCCEE
Q 018538 116 ICRELNLPPLFVADLIHFGAVY 137 (354)
Q Consensus 116 L~~~~~lSr~~~~~lI~~G~V~ 137 (354)
+++.+++|++.+.++++.|.+.
T Consensus 6 ~a~~lgvs~~tl~~~~~~g~~~ 27 (49)
T cd04762 6 AAELLGVSPSTLRRWVKEGKLK 27 (49)
T ss_pred HHHHHCcCHHHHHHHHHcCCCC
Confidence 5667899999999999999875
No 112
>PF12728 HTH_17: Helix-turn-helix domain
Probab=25.27 E-value=62 Score=22.50 Aligned_cols=22 Identities=18% Similarity=0.125 Sum_probs=19.3
Q ss_pred HHhhcCCCHHHHHHHHHcCCEE
Q 018538 116 ICRELNLPPLFVADLIHFGAVY 137 (354)
Q Consensus 116 L~~~~~lSr~~~~~lI~~G~V~ 137 (354)
+++.+++|++.+.++++.|.+.
T Consensus 7 ~a~~l~is~~tv~~~~~~g~i~ 28 (51)
T PF12728_consen 7 AAELLGISRSTVYRWIRQGKIP 28 (51)
T ss_pred HHHHHCcCHHHHHHHHHcCCCC
Confidence 4566799999999999999886
No 113
>PRK08053 sulfur carrier protein ThiS; Provisional
Probab=24.91 E-value=2.1e+02 Score=21.22 Aligned_cols=25 Identities=20% Similarity=0.367 Sum_probs=17.9
Q ss_pred cCCeEEeeccccccccccceeecCCcEEEEe
Q 018538 172 IKGKTVREAQKTFRITHVDQIVEAGTYLRVH 202 (354)
Q Consensus 172 vnGk~vr~~~~~~~~~~~~~~V~~GD~I~V~ 202 (354)
+|++.|.+.+ -.++.|++||.|+|-
T Consensus 36 vN~~iv~r~~------w~~~~L~~gD~Ieii 60 (66)
T PRK08053 36 INQQIIPREQ------WAQHIVQDGDQILLF 60 (66)
T ss_pred ECCEEeChHH------cCccccCCCCEEEEE
Confidence 8999874321 244579999999875
No 114
>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=24.44 E-value=27 Score=26.46 Aligned_cols=17 Identities=29% Similarity=0.514 Sum_probs=12.5
Q ss_pred ecCeEEEEECCCCcccc
Q 018538 223 VTESHVVLDKPAGTSVG 239 (354)
Q Consensus 223 ED~~llVVNKPaGl~vh 239 (354)
-...+|.+|||+|-.+|
T Consensus 40 i~~GvinlDKP~gPtSH 56 (59)
T PF08068_consen 40 IKYGVINLDKPSGPTSH 56 (59)
T ss_dssp HHTEEEEEEE-SSS-HH
T ss_pred HhCCcEEeeCCCCCCcc
Confidence 34689999999998776
No 115
>TIGR01682 moaD molybdopterin converting factor, subunit 1, non-archaeal. The C-terminal Gly-Gly of this model is critical to function.
Probab=22.32 E-value=2.7e+02 Score=21.29 Aligned_cols=21 Identities=14% Similarity=0.249 Sum_probs=17.0
Q ss_pred cCCeEEeeccccccccccceeecCCcEEEEe
Q 018538 172 IKGKTVREAQKTFRITHVDQIVEAGTYLRVH 202 (354)
Q Consensus 172 vnGk~vr~~~~~~~~~~~~~~V~~GD~I~V~ 202 (354)
+||+.+ ..+..|+.||.|.+.
T Consensus 54 vn~~~v----------~~~~~l~dgDevai~ 74 (80)
T TIGR01682 54 VNEEYV----------TDDALLNEGDEVAFI 74 (80)
T ss_pred ECCEEc----------CCCcCcCCCCEEEEe
Confidence 888864 456789999999887
No 116
>PRK11092 bifunctional (p)ppGpp synthetase II/ guanosine-3',5'-bis pyrophosphate 3'-pyrophosphohydrolase; Provisional
Probab=22.13 E-value=1.2e+02 Score=33.51 Aligned_cols=59 Identities=19% Similarity=0.320 Sum_probs=39.2
Q ss_pred cCCEEEeeeCCC-----CCCCCchhhhh--hhcccCCccccccccccCCeEEeeccccccccccceeecCCcEEEEecCC
Q 018538 133 FGAVYYALVCPK-----PPLTATPEQMR--VFKEVTDPSVLSKRSSIKGKTVREAQKTFRITHVDQIVEAGTYLRVHVHP 205 (354)
Q Consensus 133 ~G~V~~~~~~~~-----~~~~~~~e~~r--~~~~~~~~~v~~kr~~vnGk~vr~~~~~~~~~~~~~~V~~GD~I~V~~~~ 205 (354)
...|++- .|+ .|.++||=+.. |-.+++...+.- .|||+. +..++.|+.||+|+|-..+
T Consensus 385 ~d~v~Vf--TP~G~v~~LP~GaT~lDFAY~iHt~iG~~c~gA---kVNg~~----------vpL~~~L~~Gd~VeIiT~~ 449 (702)
T PRK11092 385 PDEIYVF--TPEGRIVELPAGATPVDFAYAVHTDIGHACVGA---RVDRQP----------YPLSQPLTSGQTVEIITAP 449 (702)
T ss_pred cceEEEE--CCCCCEEeCCCCCchhhhhHhhCchhhceeEEE---EECCEE----------CCCCccCCCCCEEEEEeCC
Confidence 3556643 454 57777776654 455555443332 289986 4889999999999997654
Q ss_pred C
Q 018538 206 K 206 (354)
Q Consensus 206 ~ 206 (354)
.
T Consensus 450 ~ 450 (702)
T PRK11092 450 G 450 (702)
T ss_pred C
Confidence 3
No 117
>cd04480 RPA1_DBD_A_like RPA1_DBD_A_like: A subgroup of uncharacterized plant OB folds with similarity to the second OB fold, the ssDNA-binding domain (DBD)-A, of human RPA1 (also called RPA70). RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-A, RPA1 contains three other OB folds: DBD-B, DBD-C, and RPA1N. The major DNA binding activity of RPA is associated with DBD-A and DBD-B of RPA1. RPA1 DBD-C is involved in trimerization. The ssDNA-binding mechanism is believed to be multistep and to involve conformational change.
Probab=20.83 E-value=2.5e+02 Score=21.67 Aligned_cols=48 Identities=23% Similarity=0.265 Sum_probs=30.6
Q ss_pred eeecCCCCCCCCceEEEeeCCCC-cHHHHHHhhcCCCHHHHHHHHHcCCEEE
Q 018538 88 RLLPCPSQNCPPRVEHLVVSEGG-PVLEYICRELNLPPLFVADLIHFGAVYY 138 (354)
Q Consensus 88 ~~~~~p~~~~~~R~~~~~v~~~~-~L~~~L~~~~~lSr~~~~~lI~~G~V~~ 138 (354)
|.|..+....+.-++.+.+++.| .+.-.+-+.+ -.....+|+.|.|+.
T Consensus 8 r~W~~~~~~~~~~~~miL~De~G~~I~a~i~~~~---~~~f~~~L~eg~vy~ 56 (86)
T cd04480 8 RLWDVYNNASGESLEMVLVDEKGNRIHATIPKRL---AAKFRPLLKEGKWYT 56 (86)
T ss_pred EEEcCcCCCCCcEEEEEEEcCCCCEEEEEECHHH---HHhhhhhceeCCEEE
Confidence 45666666677778888999988 3332222211 123567899999994
Done!