Query 023659
Match_columns 279
No_of_seqs 206 out of 1708
Neff 4.7
Searched_HMMs 46136
Date Fri Mar 29 05:41:25 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/023659.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/023659hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG0564 RluA Pseudouridylate s 99.9 2.1E-27 4.6E-32 221.6 14.2 123 110-277 13-138 (289)
2 TIGR00005 rluA_subfam pseudour 99.9 1.3E-23 2.8E-28 194.0 13.7 125 110-277 6-134 (299)
3 PRK11180 rluD 23S rRNA pseudou 99.9 2.7E-23 5.9E-28 195.4 15.3 124 111-277 19-146 (325)
4 PRK11025 23S rRNA pseudouridyl 99.9 3.7E-23 8E-28 194.0 15.8 136 97-277 5-151 (317)
5 cd02558 PSRA_1 PSRA_1: Pseudou 99.8 1E-19 2.2E-24 165.5 9.8 86 188-277 12-97 (246)
6 PRK10839 16S rRNA pseudouridyl 99.8 4.9E-19 1.1E-23 158.8 6.8 108 111-277 2-109 (232)
7 PRK10475 23S rRNA pseudouridin 99.7 3.5E-17 7.6E-22 153.3 10.0 108 110-277 7-114 (290)
8 KOG1919 RNA pseudouridylate sy 99.7 1.9E-16 4.1E-21 153.0 11.1 119 111-277 45-164 (371)
9 PRK10700 23S rRNA pseudouridyl 99.6 7E-16 1.5E-20 144.1 10.7 114 110-277 3-117 (289)
10 cd02557 PseudoU_synth_ScRIB2 P 99.6 4.3E-15 9.4E-20 132.4 7.5 60 217-277 15-74 (213)
11 TIGR01621 RluA-like pseudourid 99.6 4.9E-15 1.1E-19 132.6 6.3 57 218-277 2-58 (217)
12 cd02563 PseudoU_synth_TruC tRN 99.5 6.7E-15 1.5E-19 131.7 6.3 58 218-277 1-60 (223)
13 PRK10158 23S rRNA/tRNA pseudou 99.5 6.8E-15 1.5E-19 131.8 6.0 57 218-277 14-71 (219)
14 PRK11112 tRNA pseudouridine sy 99.5 9.4E-15 2E-19 133.9 6.2 58 218-277 2-61 (257)
15 cd00165 S4 S4/Hsp/ tRNA synthe 99.1 7.5E-10 1.6E-14 78.2 7.9 68 111-231 2-70 (70)
16 cd02870 PseudoU_synth_RsuA_lik 99.1 4.3E-11 9.4E-16 100.4 1.4 48 227-277 1-48 (146)
17 COG1187 RsuA 16S rRNA uridine- 99.0 1.1E-09 2.4E-14 101.2 7.7 111 110-277 3-115 (248)
18 PRK11394 23S rRNA pseudouridin 98.6 2.9E-08 6.4E-13 90.1 3.7 48 225-277 39-86 (217)
19 TIGR02988 YaaA_near_RecF S4 do 98.3 1.6E-06 3.4E-11 62.9 6.0 31 110-141 9-41 (59)
20 PF01479 S4: S4 domain; Inter 98.0 1.1E-05 2.4E-10 55.7 5.3 31 111-141 2-33 (48)
21 smart00363 S4 S4 RNA-binding d 97.5 0.00026 5.7E-09 48.2 5.9 31 111-141 2-33 (60)
22 COG1188 Ribosome-associated he 97.3 0.00066 1.4E-08 55.4 6.1 52 111-206 10-62 (100)
23 PLN00051 RNA-binding S4 domain 97.3 0.00055 1.2E-08 64.2 6.1 32 110-141 192-223 (267)
24 TIGR03069 PS_II_S4 photosystem 97.0 0.0013 2.7E-08 61.3 5.9 32 110-141 184-215 (257)
25 TIGR01017 rpsD_bact ribosomal 96.6 0.0037 8E-08 56.2 5.7 32 110-141 90-122 (200)
26 PRK05327 rpsD 30S ribosomal pr 96.3 0.0064 1.4E-07 54.8 5.4 32 110-141 93-125 (203)
27 COG2302 Uncharacterized conser 96.3 0.0055 1.2E-07 57.4 5.1 50 110-202 181-230 (257)
28 PF00849 PseudoU_synth_2: RNA 96.3 0.0018 3.9E-08 54.1 1.6 19 259-277 37-55 (164)
29 CHL00113 rps4 ribosomal protei 96.3 0.0082 1.8E-07 54.3 5.7 32 110-141 89-121 (201)
30 TIGR00478 tly hemolysin TlyA f 96.2 0.0074 1.6E-07 55.3 5.2 31 111-141 1-32 (228)
31 PRK10348 ribosome-associated h 96.2 0.013 2.7E-07 50.1 5.9 32 110-141 9-41 (133)
32 cd02550 PseudoU_synth_Rsu_Rlu_ 95.9 0.0057 1.2E-07 51.6 2.8 28 227-254 1-28 (154)
33 cd02555 PSSA_1 PSSA_1: Pseudou 95.7 0.0038 8.2E-08 54.8 0.7 15 263-277 47-61 (177)
34 COG0522 RpsD Ribosomal protein 94.8 0.051 1.1E-06 49.4 5.1 51 111-204 95-146 (205)
35 COG1189 Predicted rRNA methyla 93.5 0.12 2.7E-06 48.2 5.1 32 110-141 3-35 (245)
36 PF06353 DUF1062: Protein of u 91.9 0.48 1E-05 40.9 6.2 62 79-140 68-133 (142)
37 PRK04270 H/ACA RNA-protein com 91.6 0.2 4.3E-06 47.7 3.9 44 225-277 22-65 (300)
38 PRK11507 ribosome-associated p 90.2 0.66 1.4E-05 35.7 4.8 31 110-141 12-44 (70)
39 COG2501 S4-like RNA binding pr 90.1 0.91 2E-05 35.3 5.5 38 103-141 5-44 (73)
40 PRK01851 truB tRNA pseudouridi 89.4 0.44 9.5E-06 45.8 4.1 44 225-277 16-59 (303)
41 PRK04051 rps4p 30S ribosomal p 85.6 1.7 3.6E-05 38.9 5.2 32 110-141 103-135 (177)
42 PF13275 S4_2: S4 domain; PDB: 85.0 0.28 6.1E-06 37.1 0.1 31 110-141 8-40 (65)
43 PF14451 Ub-Mut7C: Mut7-C ubiq 84.9 2.8 6E-05 32.8 5.6 67 83-203 9-75 (81)
44 TIGR00425 CBF5 rRNA pseudourid 82.7 1.6 3.5E-05 42.2 4.2 44 225-277 34-77 (322)
45 PRK01777 hypothetical protein; 82.3 2.3 5.1E-05 34.2 4.3 58 102-204 19-76 (95)
46 PLN00189 40S ribosomal protein 79.1 3.7 8E-05 37.3 4.9 41 122-205 122-162 (194)
47 COG0130 TruB Pseudouridine syn 78.5 2.3 5.1E-05 40.3 3.7 43 226-277 16-58 (271)
48 COG4332 Uncharacterized protei 78.4 2.6 5.6E-05 38.2 3.7 64 77-140 102-169 (203)
49 PRK04313 30S ribosomal protein 65.3 19 0.0004 33.8 6.2 31 111-141 39-71 (237)
50 TIGR01018 rpsD_arch ribosomal 58.6 15 0.00033 32.4 4.3 20 122-141 117-136 (162)
51 PTZ00223 40S ribosomal protein 58.3 29 0.00062 33.2 6.3 31 111-141 40-72 (273)
52 PLN00036 40S ribosomal protein 58.2 30 0.00064 32.9 6.3 31 111-141 43-75 (261)
53 PTZ00118 40S ribosomal protein 54.7 35 0.00076 32.5 6.2 32 111-142 43-76 (262)
54 PF08068 DKCLD: DKCLD (NUC011) 50.1 7.8 0.00017 29.1 0.9 18 222-239 39-56 (59)
55 PTZ00155 40S ribosomal protein 49.6 17 0.00036 32.8 3.0 30 111-141 108-139 (181)
56 PRK04642 truB tRNA pseudouridi 47.7 10 0.00022 36.6 1.5 16 225-240 10-25 (300)
57 TIGR01764 excise DNA binding d 46.4 21 0.00045 23.2 2.5 22 116-137 7-28 (49)
58 PRK03287 truB tRNA pseudouridi 46.2 11 0.00025 36.2 1.5 16 225-240 9-24 (298)
59 PRK05033 truB tRNA pseudouridi 45.7 11 0.00025 36.4 1.5 16 225-240 10-25 (312)
60 PRK05389 truB tRNA pseudouridi 45.7 12 0.00025 36.2 1.5 16 225-240 13-28 (305)
61 PRK00020 truB tRNA pseudouridi 44.7 12 0.00027 35.1 1.5 16 225-240 10-25 (244)
62 PRK00989 truB tRNA pseudouridi 43.8 13 0.00028 34.6 1.5 15 226-240 10-24 (230)
63 PF11969 DcpS_C: Scavenger mRN 41.6 18 0.00039 29.4 1.9 15 217-231 13-27 (116)
64 PRK05912 tyrosyl-tRNA syntheta 41.6 64 0.0014 32.1 6.0 32 110-141 343-375 (408)
65 COG1471 RPS4A Ribosomal protei 40.2 69 0.0015 30.2 5.6 31 112-142 43-75 (241)
66 PRK08364 sulfur carrier protei 39.6 73 0.0016 23.6 4.8 14 189-202 51-64 (70)
67 cd00754 MoaD Ubiquitin domain 37.7 1.3E+02 0.0027 22.0 5.8 15 189-203 61-75 (80)
68 PRK13354 tyrosyl-tRNA syntheta 36.8 43 0.00094 33.4 4.0 31 111-141 344-375 (410)
69 cd04762 HTH_MerR-trunc Helix-T 35.0 41 0.00089 21.6 2.5 22 116-137 6-27 (49)
70 PF12728 HTH_17: Helix-turn-he 32.9 43 0.00094 22.7 2.4 21 116-136 7-27 (51)
71 PRK05659 sulfur carrier protei 29.9 65 0.0014 23.1 3.0 15 188-202 46-60 (66)
72 PF03658 Ub-RnfH: RnfH family 29.3 35 0.00076 27.1 1.6 17 188-204 57-73 (84)
73 PF14839 DOR: DOR family 29.1 33 0.00072 31.7 1.7 17 222-238 4-20 (216)
74 PF01230 HIT: HIT domain; Int 28.4 44 0.00096 25.7 2.1 21 217-237 5-26 (98)
75 PF06633 DUF1155: Protein of u 26.8 30 0.00064 24.0 0.7 34 14-49 8-41 (42)
76 PF04225 OapA: Opacity-associa 25.7 1.3E+02 0.0027 23.5 4.2 29 104-133 5-33 (85)
77 PRK06083 sulfur carrier protei 24.6 1E+02 0.0022 24.2 3.5 15 188-202 64-78 (84)
78 cd01291 PseudoU_synth PseudoU_ 23.7 59 0.0013 24.7 2.0 15 263-277 26-40 (87)
79 PF13348 Y_phosphatase3C: Tyro 22.8 1E+02 0.0022 22.3 3.0 23 110-132 43-65 (68)
80 PRK10687 purine nucleoside pho 22.6 75 0.0016 26.1 2.5 18 217-234 16-34 (119)
81 PF02597 ThiS: ThiS family; I 22.2 1.2E+02 0.0027 21.8 3.4 15 189-203 58-72 (77)
82 cd04761 HTH_MerR-SF Helix-Turn 22.1 93 0.002 20.4 2.5 22 116-137 6-27 (49)
83 cd00565 ThiS ThiaminS ubiquiti 22.1 1.3E+02 0.0028 21.7 3.4 14 190-203 47-60 (65)
84 TIGR02675 tape_meas_nterm tape 21.8 1.1E+02 0.0024 23.2 3.1 28 111-138 45-72 (75)
No 1
>COG0564 RluA Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]
Probab=99.95 E-value=2.1e-27 Score=221.55 Aligned_cols=123 Identities=19% Similarity=0.170 Sum_probs=102.3
Q ss_pred CcHHHHHHHhcC-CCHHHHHHHHHcCcEEEccccCCCCCCCCchhhhhccccCCcccccccccccCcceeeccccccccC
Q 023659 110 GPVLEYICRELN-LPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTFRITH 188 (279)
Q Consensus 110 grLd~~L~~~l~-lSr~~i~~LI~~G~V~vn~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~GK~v~~~q~~~rv~~ 188 (279)
.|||.||++ +. +||++++++++.|+|.+||+ .+ .
T Consensus 13 ~rld~~L~~-l~~~sr~~~~~~i~~g~v~vNg~----------------------------------~v----------~ 47 (289)
T COG0564 13 QRLDKFLAK-LLPISRSRIQKLIRKGRVRVNGK----------------------------------KV----------K 47 (289)
T ss_pred CCHHHHHHH-ccCcCHHHHHHHHHCCCEEECCE----------------------------------Ec----------c
Confidence 389999999 65 99999999999999999986 22 3
Q ss_pred CCceecCCCEEEEEcCCCCC-CCCCCCCCccceEEecCcEEEEeCCCCCcccCCCCCCcCcHHHHHHHHhCC-CCCcccc
Q 023659 189 VDQIVEAGTYLRVHVHPKRF-PRCYDIDWNSRIIAVTESHVVLDKPAGTSVGGTTDNIEESCATFASRALGL-TTPLRTT 266 (279)
Q Consensus 189 ~~~~Lk~GD~I~V~~~~~~~-~~~~~~~~~l~ILYEDedlLVVNKPaGl~VHPt~~~~~~TL~~~l~~~lg~-~~~l~~V 266 (279)
.+++|+.||.|++..+.... ....+.+++++|||||||+||||||+||+|||+.++..+|+++++....+. ...+.+|
T Consensus 48 ~~~~l~~gd~i~~~~~~~~~~~~~~~~~~~l~IlyED~~llVvnKP~Gl~vhp~~~~~~~tl~~~l~~~~~~~~~~~~~v 127 (289)
T COG0564 48 PSYKLKPGDVVRIPLPEEPEEEKLVPEDIPLDILYEDEDLLVVNKPAGLVVHPGGGHHEGTLVNALLRHCQDGVERPGIV 127 (289)
T ss_pred CCeeeCCCCEEEEecccccccccccccCCCccEEEecCCEEEEECCCCCcCcCCCCCccHhHHHHHHHhccccCCceeee
Confidence 57899999999999865332 334456667999999999999999999999999999999999988765432 2235679
Q ss_pred ccCCcCccccc
Q 023659 267 HQIDNCTEGWR 277 (279)
Q Consensus 267 HRLDrdTSGLL 277 (279)
|||||||||||
T Consensus 128 HRLDkdTSGll 138 (289)
T COG0564 128 HRLDKDTSGLL 138 (289)
T ss_pred ccCCCCCceEE
Confidence 99999999997
No 2
>TIGR00005 rluA_subfam pseudouridine synthase, RluA family. modifies uracil-65 in transfer RNAs to pseudouridine.
Probab=99.90 E-value=1.3e-23 Score=193.99 Aligned_cols=125 Identities=18% Similarity=0.142 Sum_probs=99.3
Q ss_pred CcHHHHHHHhcC-CCHHHHHHHHHcCcEEEccccCCCCCCCCchhhhhccccCCcccccccccccCcceeeccccccccC
Q 023659 110 GPVLEYICRELN-LPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTFRITH 188 (279)
Q Consensus 110 grLd~~L~~~l~-lSr~~i~~LI~~G~V~vn~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~GK~v~~~q~~~rv~~ 188 (279)
.+|++||++.+. +||+.++++|+.|.|+|||.. +..
T Consensus 6 ~rLd~~L~~~~~~~Sr~~~~kli~~G~V~VNg~~-------------------------------------------~~~ 42 (299)
T TIGR00005 6 QRLDDFLASLLPDLSRSRIQKLIENGQVKVNGKV-------------------------------------------TAN 42 (299)
T ss_pred hhHHHHHHHhcccCCHHHHHHHHHCCcEEECCEe-------------------------------------------ccC
Confidence 389999999996 999999999999999999841 114
Q ss_pred CCceecCCCEEEEEcCCCCCCCCCCCCCccceEEecCcEEEEeCCCCCcccCCCCCCcCcHHHHHHHHhCC---CCCccc
Q 023659 189 VDQIVEAGTYLRVHVHPKRFPRCYDIDWNSRIIAVTESHVVLDKPAGTSVGGTTDNIEESCATFASRALGL---TTPLRT 265 (279)
Q Consensus 189 ~~~~Lk~GD~I~V~~~~~~~~~~~~~~~~l~ILYEDedlLVVNKPaGl~VHPt~~~~~~TL~~~l~~~lg~---~~~l~~ 265 (279)
.++.|+.||.|.+...+...+...+.+.+++|+|||++++|||||+||+|||+.++..+|+.+.+..+++. ...+++
T Consensus 43 ~~~~v~~gd~I~i~~~~~~~~~~~~~~~~~~i~~ed~~~lvvnKP~g~~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~ 122 (299)
T TIGR00005 43 PKLKVKDGDRITVRVPEEEEHEVPPQDIPLDILFEDEDIIVINKPSGLVVHPGGGNPFGTVLNALLAHCPPIAGVERVGI 122 (299)
T ss_pred cccCCCCCCEEEEecCCcccccCCccCCCccEEEeCCCEEEEECCCCCeEeCCCCCCcccHHHHHHHhcccccCCCcCce
Confidence 46789999999997643222222334456889999999999999999999999887778888887655431 133678
Q ss_pred cccCCcCccccc
Q 023659 266 THQIDNCTEGWR 277 (279)
Q Consensus 266 VHRLDrdTSGLL 277 (279)
|||||++|||||
T Consensus 123 vhRLD~~TSGll 134 (299)
T TIGR00005 123 VHRLDRDTSGLM 134 (299)
T ss_pred ECCCCCCCceEE
Confidence 999999999997
No 3
>PRK11180 rluD 23S rRNA pseudouridine synthase D; Provisional
Probab=99.90 E-value=2.7e-23 Score=195.38 Aligned_cols=124 Identities=14% Similarity=0.086 Sum_probs=98.0
Q ss_pred cHHHHHHHhc-CCCHHHHHHHHHcCcEEEccccCCCCCCCCchhhhhccccCCcccccccccccCcceeeccccccccCC
Q 023659 111 PVLEYICREL-NLPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTFRITHV 189 (279)
Q Consensus 111 rLd~~L~~~l-~lSr~~i~~LI~~G~V~vn~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~GK~v~~~q~~~rv~~~ 189 (279)
|||+||++.+ .+||+.++++|+.|.|++||+. +..+
T Consensus 19 RLd~~L~~~~~~~Sr~~~~~lI~~G~V~VNg~~-------------------------------------------v~~~ 55 (325)
T PRK11180 19 RLDQALAELFPDYSRSRIKEWILDQRVLVNGKV-------------------------------------------INKP 55 (325)
T ss_pred cHHHHHHhhccccCHHHHHHHHHCCCEEECCEE-------------------------------------------ccCC
Confidence 8999999987 4899999999999999999861 1134
Q ss_pred CceecCCCEEEEEcCCCCCCCCCCCCCccceEEecCcEEEEeCCCCCcccCCCCCCcCcHHHHHHHHhCC---CCCcccc
Q 023659 190 DQIVEAGTYLRVHVHPKRFPRCYDIDWNSRIIAVTESHVVLDKPAGTSVGGTTDNIEESCATFASRALGL---TTPLRTT 266 (279)
Q Consensus 190 ~~~Lk~GD~I~V~~~~~~~~~~~~~~~~l~ILYEDedlLVVNKPaGl~VHPt~~~~~~TL~~~l~~~lg~---~~~l~~V 266 (279)
++.|+.||.|.+...+.......+.+.+++|||||+++||||||+||+|||+.++..+|+.+.+..++.. ...+++|
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 6788999999998643222222344567899999999999999999999999887778888877654321 1224579
Q ss_pred ccCCcCccccc
Q 023659 267 HQIDNCTEGWR 277 (279)
Q Consensus 267 HRLDrdTSGLL 277 (279)
||||++|||||
T Consensus 136 hRLD~~TSGll 146 (325)
T PRK11180 136 HRLDKDTTGLM 146 (325)
T ss_pred ccCCCCCceeE
Confidence 99999999997
No 4
>PRK11025 23S rRNA pseudouridylate synthase C; Provisional
Probab=99.90 E-value=3.7e-23 Score=194.05 Aligned_cols=136 Identities=18% Similarity=0.179 Sum_probs=96.6
Q ss_pred CCCceEEEeeCC-CC-cHHHHHHHhc-CCCHHHHHHHHHcCcEEEccccCCCCCCCCchhhhhccccCCccccccccccc
Q 023659 97 CPPRVEHLVVSE-GG-PVLEYICREL-NLPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIK 173 (279)
Q Consensus 97 ~~~rv~~~v~~~-~g-rLd~~L~~~l-~lSr~~i~~LI~~G~V~vn~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~ 173 (279)
.|++..+.+... +| ||++||++.+ .+||+.++++|+.|.|++||..
T Consensus 5 ~~~~~~~~v~~~~~g~RLd~~L~~~~~~~sr~~i~~li~~G~V~VNg~~------------------------------- 53 (317)
T PRK11025 5 TPSVKIVTISADEAGQRIDNFLRTQLKGVPKSMIYRILRKGEVRVNKKR------------------------------- 53 (317)
T ss_pred CCccEEEEECcccCCchHHHHHHHhcccCCHHHHHHHHHcCCEEECCEE-------------------------------
Confidence 344434444333 34 9999999888 5899999999999999999851
Q ss_pred CcceeeccccccccCCCceecCCCEEEEEcCCCCC---CCCC-----CCCCccceEEecCcEEEEeCCCCCcccCCCCCC
Q 023659 174 GKTVREAQKTFRITHVDQIVEAGTYLRVHVHPKRF---PRCY-----DIDWNSRIIAVTESHVVLDKPAGTSVGGTTDNI 245 (279)
Q Consensus 174 GK~v~~~q~~~rv~~~~~~Lk~GD~I~V~~~~~~~---~~~~-----~~~~~l~ILYEDedlLVVNKPaGl~VHPt~~~~ 245 (279)
+ ..+++|+.||.|++....... .+.. ...++++|||||+++||||||+||+|||+.+..
T Consensus 54 ---v----------~~~~~v~~GD~I~i~~~~~~~~~~~p~~~~~~~~~~~~~~Ilyed~~~lvvnKP~gl~~~~~~~~~ 120 (317)
T PRK11025 54 ---I----------KPEYKLEAGDEVRIPPVRVAEREEEAVSPKLQKVAALADVILYEDDHILVLNKPSGTAVHGGSGLS 120 (317)
T ss_pred ---c----------CcccccCCCCEEEeCCCCccccccccccccccccccCcCCEEEECCCEEEEECCCCCcCcCCCCCC
Confidence 1 346789999999986422111 1010 123567999999999999999999999987653
Q ss_pred cCcHHHHHHHHhCCCCCccccccCCcCccccc
Q 023659 246 EESCATFASRALGLTTPLRTTHQIDNCTEGWR 277 (279)
Q Consensus 246 ~~TL~~~l~~~lg~~~~l~~VHRLDrdTSGLL 277 (279)
. ++.+.+.........+++||||||+|||||
T Consensus 121 ~-~~~~~~~~~~~~~~~~~~vhRLD~~TSGll 151 (317)
T PRK11025 121 F-GVIEGLRALRPEARFLELVHRLDRDTSGVL 151 (317)
T ss_pred c-cHHHHHHHhccCCCcCceeCCCCCCCceEE
Confidence 3 455555433222223467999999999997
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=99.80 E-value=1e-19 Score=165.54 Aligned_cols=86 Identities=22% Similarity=0.215 Sum_probs=68.9
Q ss_pred CCCceecCCCEEEEEcCCCCCCCCCCCCCccceEEecCcEEEEeCCCCCcccCCCCCCcCcHHHHHHHHhCCCCCccccc
Q 023659 188 HVDQIVEAGTYLRVHVHPKRFPRCYDIDWNSRIIAVTESHVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTH 267 (279)
Q Consensus 188 ~~~~~Lk~GD~I~V~~~~~~~~~~~~~~~~l~ILYEDedlLVVNKPaGl~VHPt~~~~~~TL~~~l~~~lg~~~~l~~VH 267 (279)
..+++|+.||.|.++....+. .+.+.+++|||||++++|||||+||+|||+.++..+|+.+.+....+.. .+.+||
T Consensus 12 ~~~~~l~~gd~i~~~~~~~~~---~~~~~~~~Iiyed~~~lvvnKPaGl~~~~~~~~~~~t~~~~l~~~~~~~-~~~~vh 87 (246)
T cd02558 12 DPDSPYRPGTFVWYYRELPDE---PPIPFEETILHQDEHLLVADKPHFLPVTPRGRYVTETLLVRLRRQTGNP-DLTPAH 87 (246)
T ss_pred CCCceecCCCEEEEeCCCCCC---CCCCCCcceEEecCCEEEEECCCCCccCCCCcchhhhHHHHHHHHhCCC-cccccc
Confidence 568899999999998532211 1334568999999999999999999999998888888888776555543 356799
Q ss_pred cCCcCccccc
Q 023659 268 QIDNCTEGWR 277 (279)
Q Consensus 268 RLDrdTSGLL 277 (279)
|||++|||||
T Consensus 88 RLD~~TSGll 97 (246)
T cd02558 88 RLDRLTAGLV 97 (246)
T ss_pred cCCCCceeEE
Confidence 9999999997
No 6
>PRK10839 16S rRNA pseudouridylate synthase A; Provisional
Probab=99.77 E-value=4.9e-19 Score=158.78 Aligned_cols=108 Identities=13% Similarity=0.089 Sum_probs=80.2
Q ss_pred cHHHHHHHhcCCCHHHHHHHHHcCcEEEccccCCCCCCCCchhhhhccccCCcccccccccccCcceeeccccccccCCC
Q 023659 111 PVLEYICRELNLPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTFRITHVD 190 (279)
Q Consensus 111 rLd~~L~~~l~lSr~~i~~LI~~G~V~vn~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~GK~v~~~q~~~rv~~~~ 190 (279)
+|++||++.+.+||+.++++|+.|.|++||+. + ...+
T Consensus 2 rld~~L~~~~~~Sr~~~~~li~~g~V~VNg~~----------------------------------~---------~~~~ 38 (232)
T PRK10839 2 RLDKFISQQLGVSRAIAGRELRANRVTVDGEI----------------------------------V---------KNGA 38 (232)
T ss_pred cHHHHHHHcCCCCHHHHHHHHHcCeEEECCEE----------------------------------e---------ccCC
Confidence 68999998888999999999999999999851 1 1356
Q ss_pred ceecCCCEEEEEcCCCCCCCCCCCCCccceEEecCcEEEEeCCCCCcccCCCCCCcCcHHHHHHHHhCCCCCccccccCC
Q 023659 191 QIVEAGTYLRVHVHPKRFPRCYDIDWNSRIIAVTESHVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQID 270 (279)
Q Consensus 191 ~~Lk~GD~I~V~~~~~~~~~~~~~~~~l~ILYEDedlLVVNKPaGl~VHPt~~~~~~TL~~~l~~~lg~~~~l~~VHRLD 270 (279)
++|+.||.|.+...+.. ..+|+++||||||+||+|||+.. ...|+..++.. +....+++|||||
T Consensus 39 ~~l~~gd~I~l~~~~~~-------------~~~~~~~lvvnKP~G~~~~~~~~-~~~tl~~~l~~--~~~~~~~~v~RLD 102 (232)
T PRK10839 39 FKLLPEHDVAYDGNPLA-------------QQHGPRYFMLNKPQGYVCSTDDP-DHPTVLYFLDE--PVAYKLHAAGRLD 102 (232)
T ss_pred cCcCCCCEEEECCEEcc-------------cCCCCEEEEEECCCCeEecccCC-CCCeEEEeccc--ccccCceecCCCC
Confidence 78999999988632100 11467999999999999999844 23555443321 1112356899999
Q ss_pred cCccccc
Q 023659 271 NCTEGWR 277 (279)
Q Consensus 271 rdTSGLL 277 (279)
+||||||
T Consensus 103 ~~TSGll 109 (232)
T PRK10839 103 IDTTGLV 109 (232)
T ss_pred CCceeEE
Confidence 9999997
No 7
>PRK10475 23S rRNA pseudouridine synthase F; Provisional
Probab=99.71 E-value=3.5e-17 Score=153.26 Aligned_cols=108 Identities=16% Similarity=0.149 Sum_probs=83.0
Q ss_pred CcHHHHHHHhcCCCHHHHHHHHHcCcEEEccccCCCCCCCCchhhhhccccCCcccccccccccCcceeeccccccccCC
Q 023659 110 GPVLEYICRELNLPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTFRITHV 189 (279)
Q Consensus 110 grLd~~L~~~l~lSr~~i~~LI~~G~V~vn~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~GK~v~~~q~~~rv~~~ 189 (279)
.+|++||++....||..+.+||+.|.|+|||+. + ..
T Consensus 7 ~RL~k~La~~g~~SRr~a~~lI~~G~V~VNGk~----------------------------------v----------~~ 42 (290)
T PRK10475 7 TRLNKYISESGICSRREADRYIEQGNVFINGKR----------------------------------A----------TI 42 (290)
T ss_pred HHHHHHHHhCCCCCHHHHHHHHHCCcEEECCEE----------------------------------c----------cC
Confidence 389999997655799999999999999999861 1 34
Q ss_pred CceecCCCEEEEEcCCCCCCCCCCCCCccceEEecCcEEEEeCCCCCcccCCCCCCcCcHHHHHHHHhCCCCCccccccC
Q 023659 190 DQIVEAGTYLRVHVHPKRFPRCYDIDWNSRIIAVTESHVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQI 269 (279)
Q Consensus 190 ~~~Lk~GD~I~V~~~~~~~~~~~~~~~~l~ILYEDedlLVVNKPaGl~VHPt~~~~~~TL~~~l~~~lg~~~~l~~VHRL 269 (279)
+++|.+||.|.|.... ..+. .+||+++||+|||+|+++|+... ...|+.+++... ..+++||||
T Consensus 43 ~~~V~~gD~V~v~g~~-----i~~~------~~ed~~~lvlnKP~G~~~~~~~~-~~~tv~~~l~~~----~~l~~VgRL 106 (290)
T PRK10475 43 GDQVKAGDVVKVNGQL-----IEPR------EAEDLVLIALNKPVGIVSTTEDG-ERDNIVDFVNHS----KRVFPIGRL 106 (290)
T ss_pred CCCcCCCCEEEECCEE-----cccc------ccCCCeEEEEECCCCCCcCCCCC-CCCcHHHHhhcc----ccccccccC
Confidence 5678999999886311 1010 14899999999999999998764 457777766431 235689999
Q ss_pred CcCccccc
Q 023659 270 DNCTEGWR 277 (279)
Q Consensus 270 DrdTSGLL 277 (279)
|+||||||
T Consensus 107 DrdTsGLL 114 (290)
T PRK10475 107 DKDSQGLI 114 (290)
T ss_pred CCCCcceE
Confidence 99999997
No 8
>KOG1919 consensus RNA pseudouridylate synthases [RNA processing and modification]
Probab=99.68 E-value=1.9e-16 Score=152.99 Aligned_cols=119 Identities=24% Similarity=0.277 Sum_probs=91.1
Q ss_pred cHHHHHHHhc-CCCHHHHHHHHHcCcEEEccccCCCCCCCCchhhhhccccCCcccccccccccCcceeeccccccccCC
Q 023659 111 PVLEYICREL-NLPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTFRITHV 189 (279)
Q Consensus 111 rLd~~L~~~l-~lSr~~i~~LI~~G~V~vn~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~GK~v~~~q~~~rv~~~ 189 (279)
.+.+++..+| ..++.+.+..|+.|.|++||+ .+ ..
T Consensus 45 ~~~~~~~~ef~~~~~~~~~~~i~~g~v~~n~~----------------------------------~~----------~v 80 (371)
T KOG1919|consen 45 KLVDVFVSEFRLRERAYYESAIKLGRVTVNGE----------------------------------QV----------RV 80 (371)
T ss_pred chHHHHHHHHhcCchHhhhhhhhcCceEECcE----------------------------------ee----------ee
Confidence 4667776666 689999999999999999986 11 24
Q ss_pred CceecCCCEEEEEcCCCCCCCCCCCCCccceEEecCcEEEEeCCCCCcccCCCCCCcCcHHHHHHHHhCCCCCccccccC
Q 023659 190 DQIVEAGTYLRVHVHPKRFPRCYDIDWNSRIIAVTESHVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQI 269 (279)
Q Consensus 190 ~~~Lk~GD~I~V~~~~~~~~~~~~~~~~l~ILYEDedlLVVNKPaGl~VHPt~~~~~~TL~~~l~~~lg~~~~l~~VHRL 269 (279)
+..++.||.|...++..+.+ ...+++.|+|||+++||||||+|++|||++....+++...+....... .+++||||
T Consensus 81 ~~i~k~~d~l~~~vhrh~p~---~~~~~~~Iv~ed~~~vVvnKP~gipVhp~g~~~~n~i~~~l~~~~~~~-~~~~~hRL 156 (371)
T KOG1919|consen 81 SLIVKNGDVLCHTVHRHEPP---VAYLPIRIVFEDKDYVVVNKPHGIPVHPTGRYRENTITKILAALHKVE-GLRPCHRL 156 (371)
T ss_pred EEEeccCCEEEEeeccCCCC---ccccccceEEecCCEEEEeCCCCCceeccCccccccchHHHHHhcccc-cccccccc
Confidence 67899999998877643222 123578999999999999999999999988766666655554432222 36789999
Q ss_pred CcCccccc
Q 023659 270 DNCTEGWR 277 (279)
Q Consensus 270 DrdTSGLL 277 (279)
|+.|||||
T Consensus 157 Dr~tSGll 164 (371)
T KOG1919|consen 157 DRLTSGLL 164 (371)
T ss_pred CccccceE
Confidence 99999998
No 9
>PRK10700 23S rRNA pseudouridylate synthase B; Provisional
Probab=99.65 E-value=7e-16 Score=144.14 Aligned_cols=114 Identities=11% Similarity=0.027 Sum_probs=79.6
Q ss_pred CcHHHHHHHhcC-CCHHHHHHHHHcCcEEEccccCCCCCCCCchhhhhccccCCcccccccccccCcceeeccccccccC
Q 023659 110 GPVLEYICRELN-LPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTFRITH 188 (279)
Q Consensus 110 grLd~~L~~~l~-lSr~~i~~LI~~G~V~vn~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~GK~v~~~q~~~rv~~ 188 (279)
.||++||++ ++ .||+.+.+||+.|.|+|||+. + .
T Consensus 3 ~RL~k~La~-~g~~SRr~a~~lI~~G~V~VNG~~----------------------------------~----------~ 37 (289)
T PRK10700 3 EKLQKVLAR-AGHGSRREIESIIEAGRVSVDGKI----------------------------------A----------T 37 (289)
T ss_pred hhHHHHHHH-CCCCCHHHHHHHHHcCCEEECCEe----------------------------------c----------c
Confidence 479999997 45 899999999999999999862 1 2
Q ss_pred CCceecCCCEEEEEcCCCCCCCCCCCCCccceEEecCcEEEEeCCCCCcccCCCCCCcCcHHHHHHHHhCCCCCcccccc
Q 023659 189 VDQIVEAGTYLRVHVHPKRFPRCYDIDWNSRIIAVTESHVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQ 268 (279)
Q Consensus 189 ~~~~Lk~GD~I~V~~~~~~~~~~~~~~~~l~ILYEDedlLVVNKPaGl~VHPt~~~~~~TL~~~l~~~lg~~~~l~~VHR 268 (279)
..+.|..+|...|.+..+.... .. ..-||++++++|||+|+++|++......|+.+++.... ...+.+|||
T Consensus 38 ~g~~V~~~~~d~I~v~g~~~~~--~~-----~~~e~~~ylvlnKP~G~~~s~~d~~~~~tv~d~l~~~~--~~~~~~VgR 108 (289)
T PRK10700 38 LGDRVEVTPGLKIRIDGHLISV--KE-----SAEQICRVLAYYKPEGELCTRNDPEGRPTVFDRLPKLR--GARWIAVGR 108 (289)
T ss_pred CCCEeCCCCCeEEEECCEEeec--cc-----ccccCCeEEEEECCCCCEeecCCCCCCccHHHHhhhhc--CCceeEccC
Confidence 3456766643333332211000 00 00167789999999999999987666678888775321 123568999
Q ss_pred CCcCccccc
Q 023659 269 IDNCTEGWR 277 (279)
Q Consensus 269 LDrdTSGLL 277 (279)
||+||||||
T Consensus 109 LD~dTsGLL 117 (289)
T PRK10700 109 LDVNTCGLL 117 (289)
T ss_pred CCCCCceEE
Confidence 999999997
No 10
>cd02557 PseudoU_synth_ScRIB2 PseudoU_synth_ScRIB2_like: Pseudouridine synthase, Saccharomyces cerevisiae RIB2_like. This group is comprised of eukaryotic and bacterial proteins similar to Saccharomyces cerevisiae RIB2, S. cerevisiae Pus6p and human hRPUDSD2. S. cerevisiae RIB2 displays two distinct catalytic activities. The N-terminal domain of RIB2 is RNA:psi-synthase which makes psi32 on cytoplasmic tRNAs. Psi32 is highly phylogenetically conserved. The C-terminal domain of RIB2 has a DRAP deaminase activity which catalyses the formation of 5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione 5'-phosphate from 2,5-diamino-6-ribitylamino-4(3H)-pyrimidinone 5'-phosphate during riboflavin biosynthesis. S. cerevisiae Pus6p makes the psi31 of cytoplasmic and mitochondrial tRNAs.
Probab=99.57 E-value=4.3e-15 Score=132.38 Aligned_cols=60 Identities=28% Similarity=0.415 Sum_probs=50.4
Q ss_pred ccceEEecCcEEEEeCCCCCcccCCCCCCcCcHHHHHHHHhCCCCCccccccCCcCccccc
Q 023659 217 NSRIIAVTESHVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQIDNCTEGWR 277 (279)
Q Consensus 217 ~l~ILYEDedlLVVNKPaGl~VHPt~~~~~~TL~~~l~~~lg~~~~l~~VHRLDrdTSGLL 277 (279)
.++|||||++++|||||+||+|||+......++...+....+.. .+.+|||||++|||||
T Consensus 15 ~~~iiyed~~~ivvnKP~Gl~~~~~~~~~~~sl~~~l~~~~~~~-~~~~vhRLD~~TSGll 74 (213)
T cd02557 15 PIKIVHEDDDLLVVDKPSGIPVHPTGRYRYNTVTEILKSEYGLT-ELRPCHRLDRLTSGLL 74 (213)
T ss_pred CCcEEEECCCEEEEECCCCCcCCCCCCCCcChHHHHHHHHcCCC-CccCccCCCCCCceEE
Confidence 57899999999999999999999987666778888776655432 3567999999999997
No 11
>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=99.55 E-value=4.9e-15 Score=132.64 Aligned_cols=57 Identities=21% Similarity=0.295 Sum_probs=45.2
Q ss_pred cceEEecCcEEEEeCCCCCcccCCCCCCcCcHHHHHHHHhCCCCCccccccCCcCccccc
Q 023659 218 SRIIAVTESHVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQIDNCTEGWR 277 (279)
Q Consensus 218 l~ILYEDedlLVVNKPaGl~VHPt~~~~~~TL~~~l~~~lg~~~~l~~VHRLDrdTSGLL 277 (279)
++|||||++++|||||+||+|||+.+ ..++...+....+.. .+++|||||++|||||
T Consensus 2 ~~ilyed~~~lvvnKP~Gl~v~~~~~--~~~l~~~l~~~~~~~-~~~~VhRLDr~TSGll 58 (217)
T TIGR01621 2 FEILFTHPDFLLINKHPGISVHKDDG--ETGLLQEVATQLGVG-QVWLVHRLDKMTSGIL 58 (217)
T ss_pred ceEEEeCCCEEEEECCCCCeECCCCC--cChHHHHHHHhcCCC-CccEecCCCCCCceEE
Confidence 57999999999999999999999764 345665554443322 3678999999999997
No 12
>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=99.54 E-value=6.7e-15 Score=131.69 Aligned_cols=58 Identities=24% Similarity=0.283 Sum_probs=43.1
Q ss_pred cceEEecCcEEEEeCCCCCcccCCCCCCcCcH--HHHHHHHhCCCCCccccccCCcCccccc
Q 023659 218 SRIIAVTESHVVLDKPAGTSVGGTTDNIEESC--ATFASRALGLTTPLRTTHQIDNCTEGWR 277 (279)
Q Consensus 218 l~ILYEDedlLVVNKPaGl~VHPt~~~~~~TL--~~~l~~~lg~~~~l~~VHRLDrdTSGLL 277 (279)
++|||||++|||||||+||+|||+..+...+. ...+....+ ..+++|||||++|||||
T Consensus 1 ~~Ilyed~~~lvvnKP~G~~~~~~~~~~~~~~~~~~~l~~~~~--~~~~~vhRLD~~TSGll 60 (223)
T cd02563 1 LEILYQDEHLVAINKPSGLLVHRSELDRHETRFALQTLRDQLG--QHVYPVHRLDRPTSGVL 60 (223)
T ss_pred CcEEEecCCEEEEECCCCCeEcCCCCCCCCcHHHHHHHHHHcC--CCcccccCCCCCCeEEE
Confidence 36999999999999999999999865433332 222322223 23568999999999997
No 13
>PRK10158 23S rRNA/tRNA pseudouridine synthase A; Provisional
Probab=99.54 E-value=6.8e-15 Score=131.78 Aligned_cols=57 Identities=23% Similarity=0.227 Sum_probs=45.2
Q ss_pred cceEEecCcEEEEeCCCCCcccCCCC-CCcCcHHHHHHHHhCCCCCccccccCCcCccccc
Q 023659 218 SRIIAVTESHVVLDKPAGTSVGGTTD-NIEESCATFASRALGLTTPLRTTHQIDNCTEGWR 277 (279)
Q Consensus 218 l~ILYEDedlLVVNKPaGl~VHPt~~-~~~~TL~~~l~~~lg~~~~l~~VHRLDrdTSGLL 277 (279)
++|||||++++|||||+|++|||+.. ....++.+.+...+ . .+.+|||||++|||||
T Consensus 14 ~~iiyed~~~lvvnKPaGl~~~~~~~~~~~~sl~~~l~~~~--~-~~~~vhRLDr~TSGll 71 (219)
T PRK10158 14 LVILYQDEHIMVVNKPSGLLSVPGRLEEHKDSVMTRIQRDY--P-QAESVHRLDMATSGVI 71 (219)
T ss_pred CCEEEeCCCEEEEECCCCCcEeCCCCCccchhHHHHHHHhC--C-CCCEECCCCCCCceEE
Confidence 68999999999999999999999764 33456666554332 2 2567999999999997
No 14
>PRK11112 tRNA pseudouridine synthase C; Provisional
Probab=99.53 E-value=9.4e-15 Score=133.86 Aligned_cols=58 Identities=26% Similarity=0.260 Sum_probs=43.3
Q ss_pred cceEEecCcEEEEeCCCCCcccCCCCCCcCcH--HHHHHHHhCCCCCccccccCCcCccccc
Q 023659 218 SRIIAVTESHVVLDKPAGTSVGGTTDNIEESC--ATFASRALGLTTPLRTTHQIDNCTEGWR 277 (279)
Q Consensus 218 l~ILYEDedlLVVNKPaGl~VHPt~~~~~~TL--~~~l~~~lg~~~~l~~VHRLDrdTSGLL 277 (279)
++|||||+++||||||+||+|||+..+..++. ...+....+ ..+++|||||++|||||
T Consensus 2 l~IlyEd~~~lvvnKPaGl~~~~~~~~~~~~~~~~~~l~~~~~--~~~~~VHRLDr~TSGll 61 (257)
T PRK11112 2 LEILYQDEWLVAVNKPAGWLVHRSWLDRHETVFVMQTVRDQIG--QHVFTAHRLDRPTSGVL 61 (257)
T ss_pred CcEEEecCCEEEEECCCCCeecCCCCCCCchHHHHHHHHHHhC--CCceeeccCCCCCeeEE
Confidence 57999999999999999999999864444432 222322222 23568999999999997
No 15
>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=99.06 E-value=7.5e-10 Score=78.16 Aligned_cols=68 Identities=16% Similarity=0.128 Sum_probs=54.4
Q ss_pred cHHHHHHHhc-CCCHHHHHHHHHcCcEEEccccCCCCCCCCchhhhhccccCCcccccccccccCcceeeccccccccCC
Q 023659 111 PVLEYICREL-NLPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTFRITHV 189 (279)
Q Consensus 111 rLd~~L~~~l-~lSr~~i~~LI~~G~V~vn~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~GK~v~~~q~~~rv~~~ 189 (279)
+|+.||.+.+ ..|++.++++|+.|.|++||+. ++.+
T Consensus 2 rl~~~l~~~~~~~sr~~~~~~i~~g~V~vn~~~-------------------------------------------~~~~ 38 (70)
T cd00165 2 RLDKILARLGLAPSRSEARQLIKHGHVLVNGKV-------------------------------------------VTKP 38 (70)
T ss_pred cHHHHHHHhccccCHHHHHHHHHcCCEEECCEE-------------------------------------------ccCC
Confidence 6899999874 6899999999999999999861 1244
Q ss_pred CceecCCCEEEEEcCCCCCCCCCCCCCccceEEecCcEEEEe
Q 023659 190 DQIVEAGTYLRVHVHPKRFPRCYDIDWNSRIIAVTESHVVLD 231 (279)
Q Consensus 190 ~~~Lk~GD~I~V~~~~~~~~~~~~~~~~l~ILYEDedlLVVN 231 (279)
++.+..||.|.+...+ . +.+|+|||+++||||
T Consensus 39 ~~~v~~~d~i~i~~~~---~-------~~~i~~ed~~~lvv~ 70 (70)
T cd00165 39 SYKVKPGDVIEVDGKS---I-------EEDIVYEDKKLLVVN 70 (70)
T ss_pred ccCcCCCCEEEEcCCC---c-------ccceeeccCCEEEeC
Confidence 6788999998886421 1 128999999999997
No 16
>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=99.05 E-value=4.3e-11 Score=100.43 Aligned_cols=48 Identities=19% Similarity=0.194 Sum_probs=36.4
Q ss_pred EEEEeCCCCCcccCCCCCCcCcHHHHHHHHhCCCCCccccccCCcCccccc
Q 023659 227 HVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQIDNCTEGWR 277 (279)
Q Consensus 227 lLVVNKPaGl~VHPt~~~~~~TL~~~l~~~lg~~~~l~~VHRLDrdTSGLL 277 (279)
++|+|||+||++||+......++.+.+.. ....+.+|||||++|||||
T Consensus 1 ~ivvnKP~G~~~~~~~~~~~~~l~~~l~~---~~~~~~~vhRLD~~TsGll 48 (146)
T cd02870 1 YLLLNKPRGVVSTVRDPEGRPTVLDLLKD---VGERLFPVGRLDYDTEGLL 48 (146)
T ss_pred CEEEECCCCcEecccCCCCCCEEeeeccc---cCCCEEECCCCCCCCeeEE
Confidence 58999999999999876656666554432 1223678999999999997
No 17
>COG1187 RsuA 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]
Probab=98.98 E-value=1.1e-09 Score=101.24 Aligned_cols=111 Identities=19% Similarity=0.125 Sum_probs=74.1
Q ss_pred CcHHHHHHHhcCCCHHHHHHHHHcCcEEEccccCCCCCCCCchhhhhccccCCcccccccccccCcceeeccccccccCC
Q 023659 110 GPVLEYICRELNLPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTFRITHV 189 (279)
Q Consensus 110 grLd~~L~~~l~lSr~~i~~LI~~G~V~vn~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~GK~v~~~q~~~rv~~~ 189 (279)
.||++||++.--.||..+.+||..|.|.|||++ + +..
T Consensus 3 ~RL~K~La~~G~~SRr~ae~lI~~G~V~VnG~v----------------------------------~---------~~~ 39 (248)
T COG1187 3 MRLNKFLAEAGVGSRREAEKLIEEGRVTVNGKV----------------------------------A---------TLG 39 (248)
T ss_pred cchHHHHHHcCCCCHHHHHHHHHcCCEEECCEE----------------------------------e---------ccC
Confidence 379999998555899999999999999999862 0 012
Q ss_pred CceecCCC-EEEEEcCCCCCCCCCCCCCccceEE-ecCcEEEEeCCCCCcccCCCCCCcCcHHHHHHHHhCCCCCccccc
Q 023659 190 DQIVEAGT-YLRVHVHPKRFPRCYDIDWNSRIIA-VTESHVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTH 267 (279)
Q Consensus 190 ~~~Lk~GD-~I~V~~~~~~~~~~~~~~~~l~ILY-EDedlLVVNKPaGl~VHPt~~~~~~TL~~~l~~~lg~~~~l~~VH 267 (279)
...+.+++ .|.+.- . .+.+ +..-+++.|||.|+++.-..+....|+..++.........+++|-
T Consensus 40 ~~~v~~~~~~i~v~g--~------------~~~~~~~~~y~llnKP~G~v~s~~D~~gr~tv~D~lp~~~~~~~~~~pvG 105 (248)
T COG1187 40 GVVVDPDDDVVEVDG--K------------RIELKEERVYLLLNKPRGYVSSTEDDEGRPTVFDLLPERLPRKKRLFPVG 105 (248)
T ss_pred CeEeCCCCcEEEECC--E------------EeeccccceEEEEECCCCeEecccCCCCCceeeeecccccccccceeecc
Confidence 23445553 444431 0 1233 223399999999999986644455666555432111122367899
Q ss_pred cCCcCccccc
Q 023659 268 QIDNCTEGWR 277 (279)
Q Consensus 268 RLDrdTSGLL 277 (279)
|||+||+|||
T Consensus 106 RLD~dTeGLL 115 (248)
T COG1187 106 RLDKDTEGLL 115 (248)
T ss_pred ccCCCCeeEE
Confidence 9999999997
No 18
>PRK11394 23S rRNA pseudouridine synthase E; Provisional
Probab=98.60 E-value=2.9e-08 Score=90.12 Aligned_cols=48 Identities=15% Similarity=0.199 Sum_probs=36.2
Q ss_pred CcEEEEeCCCCCcccCCCCCCcCcHHHHHHHHhCCCCCccccccCCcCccccc
Q 023659 225 ESHVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQIDNCTEGWR 277 (279)
Q Consensus 225 edlLVVNKPaGl~VHPt~~~~~~TL~~~l~~~lg~~~~l~~VHRLDrdTSGLL 277 (279)
-.++++|||+|+++|+.......++...+. .. .+++|||||+||||||
T Consensus 39 ~~ylllnKP~G~l~~~~d~~~~~tl~d~l~----~~-~~~~vgRLD~~TsGll 86 (217)
T PRK11394 39 TRVILFNKPYDVLPQFTDEAGRKTLKEFIP----VQ-GVYAAGRLDRDSEGLL 86 (217)
T ss_pred CEEEEEECCCCCEEeeCCccCCcchHHhcc----cC-CeEEecCCCCCCeeEE
Confidence 358999999999999654444566666542 12 3568999999999997
No 19
>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=98.32 E-value=1.6e-06 Score=62.94 Aligned_cols=31 Identities=3% Similarity=-0.212 Sum_probs=28.7
Q ss_pred CcHHHHHHHhcCC--CHHHHHHHHHcCcEEEccc
Q 023659 110 GPVLEYICRELNL--PPLFVADLIHFGAVYYALV 141 (279)
Q Consensus 110 grLd~~L~~~l~l--Sr~~i~~LI~~G~V~vn~~ 141 (279)
.|||.||++. ++ ||+.+++||+.|.|+|||.
T Consensus 9 ~rLd~~L~~~-~~~~SR~~~k~li~~G~V~VNg~ 41 (59)
T TIGR02988 9 ITLGQLLKEL-GIIDSGGQAKWFLQENEVLVNGE 41 (59)
T ss_pred HHHHHHHHHc-CCccCHHHHHHHHHcCCEEECCE
Confidence 4899999987 77 9999999999999999986
No 20
>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=98.03 E-value=1.1e-05 Score=55.71 Aligned_cols=31 Identities=16% Similarity=-0.001 Sum_probs=27.4
Q ss_pred cHHHHHHHhc-CCCHHHHHHHHHcCcEEEccc
Q 023659 111 PVLEYICREL-NLPPLFVADLIHFGAVYYALV 141 (279)
Q Consensus 111 rLd~~L~~~l-~lSr~~i~~LI~~G~V~vn~~ 141 (279)
|||.||.+.. ..||+++++||+.|.|+|||+
T Consensus 2 RLd~~L~~~~~~~sr~~a~~~I~~g~V~VNg~ 33 (48)
T PF01479_consen 2 RLDKFLSRLGLASSRSEARRLIKQGRVKVNGK 33 (48)
T ss_dssp BHHHHHHHTTSSSSHHHHHHHHHTTTEEETTE
T ss_pred CHHHHHHHcCCcCCHHHHHHhcCCCEEEECCE
Confidence 7999998544 578999999999999999986
No 21
>smart00363 S4 S4 RNA-binding domain.
Probab=97.55 E-value=0.00026 Score=48.22 Aligned_cols=31 Identities=19% Similarity=0.112 Sum_probs=27.7
Q ss_pred cHHHHHHHh-cCCCHHHHHHHHHcCcEEEccc
Q 023659 111 PVLEYICRE-LNLPPLFVADLIHFGAVYYALV 141 (279)
Q Consensus 111 rLd~~L~~~-l~lSr~~i~~LI~~G~V~vn~~ 141 (279)
+|+.||.+. +..|+..+++++..|.|++||+
T Consensus 2 rl~~~l~~~~~~~s~~~~~~~i~~g~i~vng~ 33 (60)
T smart00363 2 RLDKFLARLGLAPSRSQARKLIEQGRVKVNGK 33 (60)
T ss_pred cHHHHHHHcCcccCHHHHHHHHHcCCEEECCE
Confidence 689999876 3689999999999999999986
No 22
>COG1188 Ribosome-associated heat shock protein implicated in the recycling of the 50S subunit (S4 paralog) [Translation, ribosomal structure and biogenesis]
Probab=97.29 E-value=0.00066 Score=55.41 Aligned_cols=52 Identities=13% Similarity=0.124 Sum_probs=43.0
Q ss_pred cHHHHHHH-hcCCCHHHHHHHHHcCcEEEccccCCCCCCCCchhhhhccccCCcccccccccccCcceeeccccccccCC
Q 023659 111 PVLEYICR-ELNLPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTFRITHV 189 (279)
Q Consensus 111 rLd~~L~~-~l~lSr~~i~~LI~~G~V~vn~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~GK~v~~~q~~~rv~~~ 189 (279)
|||.||.- +|==+|+.++++++.|.|.|||.. .++
T Consensus 10 RLDKwL~~aR~~KrRslAk~~~~~GrV~vNG~~--------------------------------------------aKp 45 (100)
T COG1188 10 RLDKWLWAARFIKRRSLAKEMIEGGRVKVNGQR--------------------------------------------AKP 45 (100)
T ss_pred ehHHHHHHHHHhhhHHHHHHHHHCCeEEECCEE--------------------------------------------ccc
Confidence 89999954 455689999999999999999862 156
Q ss_pred CceecCCCEEEEEcCCC
Q 023659 190 DQIVEAGTYLRVHVHPK 206 (279)
Q Consensus 190 ~~~Lk~GD~I~V~~~~~ 206 (279)
++.|+.||+|+|++...
T Consensus 46 S~~VK~GD~l~i~~~~~ 62 (100)
T COG1188 46 SKEVKVGDILTIRFGNK 62 (100)
T ss_pred ccccCCCCEEEEEeCCc
Confidence 78899999999997643
No 23
>PLN00051 RNA-binding S4 domain-containing protein; Provisional
Probab=97.26 E-value=0.00055 Score=64.22 Aligned_cols=32 Identities=16% Similarity=0.054 Sum_probs=30.6
Q ss_pred CcHHHHHHHhcCCCHHHHHHHHHcCcEEEccc
Q 023659 110 GPVLEYICRELNLPPLFVADLIHFGAVYYALV 141 (279)
Q Consensus 110 grLd~~L~~~l~lSr~~i~~LI~~G~V~vn~~ 141 (279)
.|||.+++..+++||+.+++||+.|.|.+|+.
T Consensus 192 ~RLD~vla~~~~~SRsk~~~lI~~g~V~vN~~ 223 (267)
T PLN00051 192 LRLDALASAGFRMSRSKLVDLISSGDVRVNWR 223 (267)
T ss_pred ccHHHHHHHHhccCHHHHHHHHHcCcEEECCE
Confidence 49999999999999999999999999999986
No 24
>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=97.01 E-value=0.0013 Score=61.31 Aligned_cols=32 Identities=13% Similarity=0.038 Sum_probs=30.2
Q ss_pred CcHHHHHHHhcCCCHHHHHHHHHcCcEEEccc
Q 023659 110 GPVLEYICRELNLPPLFVADLIHFGAVYYALV 141 (279)
Q Consensus 110 grLd~~L~~~l~lSr~~i~~LI~~G~V~vn~~ 141 (279)
.|||.+++..+++||+.+++||+.|.|.|||.
T Consensus 184 ~RLD~lls~~~~~SRs~a~~lI~~G~V~VNg~ 215 (257)
T TIGR03069 184 LRIDAIASAGFGLSRSKIVDQIKAGRLRLNWK 215 (257)
T ss_pred ccHHHHHHhhhhhhHHHHHHHHHCCeEEECCE
Confidence 49999999999999999999999999999986
No 25
>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=96.64 E-value=0.0037 Score=56.20 Aligned_cols=32 Identities=9% Similarity=0.091 Sum_probs=27.9
Q ss_pred CcHHHHHHHh-cCCCHHHHHHHHHcCcEEEccc
Q 023659 110 GPVLEYICRE-LNLPPLFVADLIHFGAVYYALV 141 (279)
Q Consensus 110 grLd~~L~~~-l~lSr~~i~~LI~~G~V~vn~~ 141 (279)
.|||.+|... +..||..++.||..|.|.|||+
T Consensus 90 ~RLD~~L~~~g~~~SR~~ArqlI~~G~V~VNgk 122 (200)
T TIGR01017 90 SRLDNVVYRLGFAPTRFAARQLVSHGHILVNGK 122 (200)
T ss_pred HHHHHHHHHcCCCCCHHHHHHHHHCCCEEECCE
Confidence 4899999654 3689999999999999999986
No 26
>PRK05327 rpsD 30S ribosomal protein S4; Validated
Probab=96.35 E-value=0.0064 Score=54.77 Aligned_cols=32 Identities=9% Similarity=0.065 Sum_probs=27.7
Q ss_pred CcHHHHHHH-hcCCCHHHHHHHHHcCcEEEccc
Q 023659 110 GPVLEYICR-ELNLPPLFVADLIHFGAVYYALV 141 (279)
Q Consensus 110 grLd~~L~~-~l~lSr~~i~~LI~~G~V~vn~~ 141 (279)
.|||.+|.+ .+..||..+++||..|.|+|||+
T Consensus 93 ~RLD~iL~~~g~~~SR~~arqlI~~G~V~VNgk 125 (203)
T PRK05327 93 SRLDNVVYRLGFAPTRRQARQLVSHGHILVNGK 125 (203)
T ss_pred HHHHHHHHHcCccCCHHHHHHHHHCCcEEECCE
Confidence 489999964 34689999999999999999985
No 27
>COG2302 Uncharacterized conserved protein, contains S4-like domain [Function unknown]
Probab=96.35 E-value=0.0055 Score=57.35 Aligned_cols=50 Identities=16% Similarity=0.149 Sum_probs=44.4
Q ss_pred CcHHHHHHHhcCCCHHHHHHHHHcCcEEEccccCCCCCCCCchhhhhccccCCcccccccccccCcceeeccccccccCC
Q 023659 110 GPVLEYICRELNLPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTFRITHV 189 (279)
Q Consensus 110 grLd~~L~~~l~lSr~~i~~LI~~G~V~vn~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~GK~v~~~q~~~rv~~~ 189 (279)
=|||..+++.+++||+..++||+.|.|.||++. +.++
T Consensus 181 lRLD~vis~~~~~SR~~a~~lIe~g~VkVN~k~-------------------------------------------v~~~ 217 (257)
T COG2302 181 LRLDVVISEGFGLSRAKAQQLIEKGKVKVNWKV-------------------------------------------VDKA 217 (257)
T ss_pred hhHHHHHHHHHhhhHHHHHHHHHcCceEEeeEE-------------------------------------------eccc
Confidence 489999999999999999999999999999751 2356
Q ss_pred CceecCCCEEEEE
Q 023659 190 DQIVEAGTYLRVH 202 (279)
Q Consensus 190 ~~~Lk~GD~I~V~ 202 (279)
++.|+.||.|.+.
T Consensus 218 s~~v~~GDliSir 230 (257)
T COG2302 218 SYEVQEGDLISIR 230 (257)
T ss_pred cceeccCCEEEEe
Confidence 8999999999986
No 28
>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=96.32 E-value=0.0018 Score=54.07 Aligned_cols=19 Identities=26% Similarity=0.291 Sum_probs=11.8
Q ss_pred CCCCccccccCCcCccccc
Q 023659 259 LTTPLRTTHQIDNCTEGWR 277 (279)
Q Consensus 259 ~~~~l~~VHRLDrdTSGLL 277 (279)
....+++|||||++|||||
T Consensus 37 ~~~~~~~v~RLD~~TsGll 55 (164)
T PF00849_consen 37 DPPELYPVHRLDRDTSGLL 55 (164)
T ss_dssp TSGGGEESS---TT-EEEE
T ss_pred CCCceEECCCCCccccCCe
Confidence 3345778999999999997
No 29
>CHL00113 rps4 ribosomal protein S4; Reviewed
Probab=96.27 E-value=0.0082 Score=54.28 Aligned_cols=32 Identities=9% Similarity=-0.069 Sum_probs=28.0
Q ss_pred CcHHHHHHHhc-CCCHHHHHHHHHcCcEEEccc
Q 023659 110 GPVLEYICREL-NLPPLFVADLIHFGAVYYALV 141 (279)
Q Consensus 110 grLd~~L~~~l-~lSr~~i~~LI~~G~V~vn~~ 141 (279)
.|||.+|.+.. ..||..+++||..|.|.|||.
T Consensus 89 ~RLD~~L~r~g~~~SR~~ArqlI~~G~V~VNGk 121 (201)
T CHL00113 89 MRLDNILFRLGMAPTIPAARQLVNHGHILVNGR 121 (201)
T ss_pred HHHHHHHHHcCCCCCHHHHHHHHHCCcEEECCE
Confidence 37999997654 579999999999999999986
No 30
>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=96.22 E-value=0.0074 Score=55.27 Aligned_cols=31 Identities=16% Similarity=-0.130 Sum_probs=27.8
Q ss_pred cHHHHHHHhc-CCCHHHHHHHHHcCcEEEccc
Q 023659 111 PVLEYICREL-NLPPLFVADLIHFGAVYYALV 141 (279)
Q Consensus 111 rLd~~L~~~l-~lSr~~i~~LI~~G~V~vn~~ 141 (279)
|||.||.+.. ..||+.+++||+.|.|++||+
T Consensus 1 RLD~~L~~~g~~~SR~~a~~lI~~G~V~Vng~ 32 (228)
T TIGR00478 1 RLDILLVRRGLFESREKAKRLILKGFVLVNGK 32 (228)
T ss_pred CHHHHHHHcCCccHHHHHHHHHHCCcEEECCE
Confidence 6899998765 578999999999999999986
No 31
>PRK10348 ribosome-associated heat shock protein Hsp15; Provisional
Probab=96.16 E-value=0.013 Score=50.15 Aligned_cols=32 Identities=13% Similarity=0.129 Sum_probs=27.8
Q ss_pred CcHHHHHHH-hcCCCHHHHHHHHHcCcEEEccc
Q 023659 110 GPVLEYICR-ELNLPPLFVADLIHFGAVYYALV 141 (279)
Q Consensus 110 grLd~~L~~-~l~lSr~~i~~LI~~G~V~vn~~ 141 (279)
.|||.||.. .|--+|+.+++||..|.|.+||.
T Consensus 9 ~RlDk~L~~~rl~ktRs~A~~lI~~G~V~vnG~ 41 (133)
T PRK10348 9 VRLDKWLWAARFYKTRALAREMIEGGKVHYNGQ 41 (133)
T ss_pred ccHHHHHHHcCccccHHHHHHHHHCCCEEECCE
Confidence 389999964 44579999999999999999986
No 32
>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=95.92 E-value=0.0057 Score=51.64 Aligned_cols=28 Identities=21% Similarity=0.291 Sum_probs=22.8
Q ss_pred EEEEeCCCCCcccCCCCCCcCcHHHHHH
Q 023659 227 HVVLDKPAGTSVGGTTDNIEESCATFAS 254 (279)
Q Consensus 227 lLVVNKPaGl~VHPt~~~~~~TL~~~l~ 254 (279)
++|+|||+|+++|++.....+++...+.
T Consensus 1 ~ivvnKP~G~~~~~~~~~~~~~~~~~l~ 28 (154)
T cd02550 1 ILVLNKPSGLVCHPTDRDRDPTVVVRLD 28 (154)
T ss_pred CEEEECCCCCEEecCCCCCCCcHHHhhh
Confidence 5899999999999988766677766553
No 33
>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=95.66 E-value=0.0038 Score=54.84 Aligned_cols=15 Identities=20% Similarity=0.244 Sum_probs=13.7
Q ss_pred ccccccCCcCccccc
Q 023659 263 LRTTHQIDNCTEGWR 277 (279)
Q Consensus 263 l~~VHRLDrdTSGLL 277 (279)
+.+|||||+||||||
T Consensus 47 l~~VgRLD~dTsGLL 61 (177)
T cd02555 47 LAPIGPLDKDASGLL 61 (177)
T ss_pred eeEecCCCCCCeeEE
Confidence 568999999999997
No 34
>COG0522 RpsD Ribosomal protein S4 and related proteins [Translation, ribosomal structure and biogenesis]
Probab=94.76 E-value=0.051 Score=49.41 Aligned_cols=51 Identities=12% Similarity=0.132 Sum_probs=40.4
Q ss_pred cHHHHHHH-hcCCCHHHHHHHHHcCcEEEccccCCCCCCCCchhhhhccccCCcccccccccccCcceeeccccccccCC
Q 023659 111 PVLEYICR-ELNLPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTFRITHV 189 (279)
Q Consensus 111 rLd~~L~~-~l~lSr~~i~~LI~~G~V~vn~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~GK~v~~~q~~~rv~~~ 189 (279)
|||..+.. .|.-|+.++++||..|+|.|||+ . ++.+
T Consensus 95 RLd~vVyR~GfA~T~~qARQlV~HGHI~VnGk----------------------------------~---------V~iP 131 (205)
T COG0522 95 RLDNVVYRLGFAKTRRQARQLVSHGHILVNGK----------------------------------R---------VNIP 131 (205)
T ss_pred HHHHHHHHhcccccHHHHHHHhhcceEEECCE----------------------------------E---------eccC
Confidence 66666643 23468999999999999999986 2 4577
Q ss_pred CceecCCCEEEEEcC
Q 023659 190 DQIVEAGTYLRVHVH 204 (279)
Q Consensus 190 ~~~Lk~GD~I~V~~~ 204 (279)
++.|++||++.|..-
T Consensus 132 Sy~V~~gdei~V~~k 146 (205)
T COG0522 132 SYLVSPGDEISVREK 146 (205)
T ss_pred cEEecCCCEEEeeec
Confidence 999999999999753
No 35
>COG1189 Predicted rRNA methylase [Translation, ribosomal structure and biogenesis]
Probab=93.50 E-value=0.12 Score=48.22 Aligned_cols=32 Identities=16% Similarity=-0.032 Sum_probs=28.5
Q ss_pred CcHHHHHHHh-cCCCHHHHHHHHHcCcEEEccc
Q 023659 110 GPVLEYICRE-LNLPPLFVADLIHFGAVYYALV 141 (279)
Q Consensus 110 grLd~~L~~~-l~lSr~~i~~LI~~G~V~vn~~ 141 (279)
.|||.+|.++ +--||+.++++|..|.|++||.
T Consensus 3 ~RLD~~Lv~rgl~~sR~~A~~~I~~G~V~Vng~ 35 (245)
T COG1189 3 MRLDALLVERGLFESREKAKELILAGNVLVNGE 35 (245)
T ss_pred chHHHHHHHccchhhHHHHHHHHHcCeEEECCE
Confidence 3799999886 4579999999999999999986
No 36
>PF06353 DUF1062: Protein of unknown function (DUF1062); InterPro: IPR009412 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=91.93 E-value=0.48 Score=40.90 Aligned_cols=62 Identities=16% Similarity=0.138 Sum_probs=43.1
Q ss_pred CCCCCccccccccCCCCCCC-CceEE-EeeCC--CCcHHHHHHHhcCCCHHHHHHHHHcCcEEEcc
Q 023659 79 SSYGYPEYHRLLPCPSQNCP-PRVEH-LVVSE--GGPVLEYICRELNLPPLFVADLIHFGAVYYAL 140 (279)
Q Consensus 79 ~~~~~~~~~~~~~~~~~~~~-~rv~~-~v~~~--~grLd~~L~~~l~lSr~~i~~LI~~G~V~vn~ 140 (279)
...++|+|.=....+..... +.++. +..+. .-+|+.+|++.|++||+.+++|+..|.|....
T Consensus 68 ~~~~~~~~~v~~~~~~~~~~~~~~~v~i~~~~~~~~Rld~lLa~~L~lSrs~l~~l~~~G~I~~~~ 133 (142)
T PF06353_consen 68 ELDEFPEYDVEKRLDTEDDDWADIEVEIRFPFPFPLRLDRLLARQLGLSRSRLKRLIEQGLIRSDP 133 (142)
T ss_pred eeCCCCceEEEEEeccCCccccceEEEEEeCCCCCccHHHHHHHHhCcCHHHHHHHHHCCCEEecC
Confidence 34478888766544333322 22442 22222 24899999999999999999999999999873
No 37
>PRK04270 H/ACA RNA-protein complex component Cbf5p; Reviewed
Probab=91.65 E-value=0.2 Score=47.69 Aligned_cols=44 Identities=25% Similarity=0.288 Sum_probs=35.4
Q ss_pred CcEEEEeCCCCCcccCCCCCCcCcHHHHHHHHhCCCCCccccccCCcCccccc
Q 023659 225 ESHVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQIDNCTEGWR 277 (279)
Q Consensus 225 edlLVVNKPaGl~VHPt~~~~~~TL~~~l~~~lg~~~~l~~VHRLDrdTSGLL 277 (279)
+.||+||||.|+.+|. +++.+.+.++.....| ..-||-..||+|
T Consensus 22 ~g~l~i~Kp~g~tS~~--------~v~~~r~~~~~kkvGH-~GTLDp~A~GvL 65 (300)
T PRK04270 22 FGVVNLDKPPGPTSHE--------VAAWVRDILGVEKAGH-GGTLDPKVTGVL 65 (300)
T ss_pred CCEEEEECCCCCCHHH--------HHHHHHHHhccccccC-CCCCCCcCeEEE
Confidence 5799999999998873 4566777777665454 999999999997
No 38
>PRK11507 ribosome-associated protein; Provisional
Probab=90.16 E-value=0.66 Score=35.72 Aligned_cols=31 Identities=10% Similarity=-0.182 Sum_probs=25.7
Q ss_pred CcHHHHHHHhcC--CCHHHHHHHHHcCcEEEccc
Q 023659 110 GPVLEYICRELN--LPPLFVADLIHFGAVYYALV 141 (279)
Q Consensus 110 grLd~~L~~~l~--lSr~~i~~LI~~G~V~vn~~ 141 (279)
-+|+.||+- .+ -|=..++.+|..|.|.|||+
T Consensus 12 I~L~QlLK~-~~~v~SGG~AK~~I~eg~V~VNGe 44 (70)
T PRK11507 12 VELCDLLKL-EGWSESGAQAKIAIAEGQVKVDGA 44 (70)
T ss_pred EEHHHHHhh-hCcccChHHHHHHHHcCceEECCE
Confidence 379999974 45 35569999999999999997
No 39
>COG2501 S4-like RNA binding protein [Replication, recombination, and repair]
Probab=90.08 E-value=0.91 Score=35.29 Aligned_cols=38 Identities=16% Similarity=-0.070 Sum_probs=28.9
Q ss_pred EEeeCCCCcHHHHHHHhcCC--CHHHHHHHHHcCcEEEccc
Q 023659 103 HLVVSEGGPVLEYICRELNL--PPLFVADLIHFGAVYYALV 141 (279)
Q Consensus 103 ~~v~~~~grLd~~L~~~l~l--Sr~~i~~LI~~G~V~vn~~ 141 (279)
+.+..+.-.|.+||+. .|+ |=.+++..|..|.|+|||+
T Consensus 5 ~~i~~e~I~L~qlLK~-~g~i~sGG~AK~~i~eg~V~vNGe 44 (73)
T COG2501 5 VLIKTEFITLGQLLKL-AGLIESGGQAKAFIAEGEVKVNGE 44 (73)
T ss_pred EEeccceEEHHHHHHH-hCcccCcHHHHHHHHCCeEEECCe
Confidence 3344444589999975 564 4559999999999999997
No 40
>PRK01851 truB tRNA pseudouridine synthase B; Provisional
Probab=89.45 E-value=0.44 Score=45.82 Aligned_cols=44 Identities=27% Similarity=0.312 Sum_probs=35.2
Q ss_pred CcEEEEeCCCCCcccCCCCCCcCcHHHHHHHHhCCCCCccccccCCcCccccc
Q 023659 225 ESHVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQIDNCTEGWR 277 (279)
Q Consensus 225 edlLVVNKPaGl~VHPt~~~~~~TL~~~l~~~lg~~~~l~~VHRLDrdTSGLL 277 (279)
+-||+||||.||.+|. +++.+.+.++....+| .--||-..||+|
T Consensus 16 ~Gil~i~KP~G~TS~d--------vv~~vrr~l~~kKvGH-~GTLDP~AtGvL 59 (303)
T PRK01851 16 DGVLLLDKPLGLSSND--------ALQRAKRLLRAKKAGH-TGTLDPLATGLL 59 (303)
T ss_pred CeEEEEeCCCCCCHHH--------HHHHHHHHhCcccCCC-CCCCCCCCceEE
Confidence 4799999999998873 4566777777665444 889999999997
No 41
>PRK04051 rps4p 30S ribosomal protein S4P; Validated
Probab=85.57 E-value=1.7 Score=38.88 Aligned_cols=32 Identities=16% Similarity=0.124 Sum_probs=25.6
Q ss_pred CcHHHHHHH-hcCCCHHHHHHHHHcCcEEEccc
Q 023659 110 GPVLEYICR-ELNLPPLFVADLIHFGAVYYALV 141 (279)
Q Consensus 110 grLd~~L~~-~l~lSr~~i~~LI~~G~V~vn~~ 141 (279)
.|||.+|.+ .|--|+.+++.||..|.|.|||.
T Consensus 103 rRLd~il~r~gla~S~~~Ar~lI~hGhV~V~g~ 135 (177)
T PRK04051 103 RRLQTIVYRKGLARTPKQARQFIVHGHIAVNGR 135 (177)
T ss_pred hHHHHHHHHccCcCCHHHHHHHHHcCCEEECCE
Confidence 367777754 23469999999999999999976
No 42
>PF13275 S4_2: S4 domain; PDB: 1P9K_A.
Probab=84.99 E-value=0.28 Score=37.11 Aligned_cols=31 Identities=16% Similarity=-0.093 Sum_probs=23.7
Q ss_pred CcHHHHHHHhcCC--CHHHHHHHHHcCcEEEccc
Q 023659 110 GPVLEYICRELNL--PPLFVADLIHFGAVYYALV 141 (279)
Q Consensus 110 grLd~~L~~~l~l--Sr~~i~~LI~~G~V~vn~~ 141 (279)
-+|+.||+. .++ |=..++.+|..|.|++||+
T Consensus 8 I~L~qlLK~-~glv~sGGeAK~~I~~g~V~VNGe 40 (65)
T PF13275_consen 8 ITLGQLLKL-AGLVSSGGEAKALIQEGEVKVNGE 40 (65)
T ss_dssp --HHHHHHH-HTS-SSSSTTSHHHHHHHHEETTB
T ss_pred EEHHHHHhH-cCCcccHHHHHHHHHcCceEECCE
Confidence 479999975 453 4448999999999999997
No 43
>PF14451 Ub-Mut7C: Mut7-C ubiquitin
Probab=84.86 E-value=2.8 Score=32.81 Aligned_cols=67 Identities=22% Similarity=0.307 Sum_probs=43.8
Q ss_pred CccccccccCCCCCCCCceEEEeeCCCCcHHHHHHHhcCCCHHHHHHHHHcCcEEEccccCCCCCCCCchhhhhccccCC
Q 023659 83 YPEYHRLLPCPSQNCPPRVEHLVVSEGGPVLEYICRELNLPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTD 162 (279)
Q Consensus 83 ~~~~~~~~~~~~~~~~~rv~~~v~~~~grLd~~L~~~l~lSr~~i~~LI~~G~V~vn~~~~~~~~~~~~~~~~~~~~~~~ 162 (279)
|++++..+|-.....+ + ..-..+..++.+.+ +.||+|... -|.|.+||+
T Consensus 9 ~~~L~~flp~~~r~~~--~-~~~~~~~~tvkd~I-EsLGVP~tE------V~~i~vNG~--------------------- 57 (81)
T PF14451_consen 9 YAELNDFLPPERRGGP--F-THPFDGGATVKDVI-ESLGVPHTE------VGLILVNGR--------------------- 57 (81)
T ss_pred chHHhhhcChhhcCCc--e-EEecCCCCcHHHHH-HHcCCChHH------eEEEEECCE---------------------
Confidence 6667777774222111 1 11223334788877 569999854 578999986
Q ss_pred cccccccccccCcceeeccccccccCCCceecCCCEEEEEc
Q 023659 163 PSVLSKRSSIKGKTVREAQKTFRITHVDQIVEAGTYLRVHV 203 (279)
Q Consensus 163 ~~~~~~r~~~~GK~v~~~q~~~rv~~~~~~Lk~GD~I~V~~ 203 (279)
.+ ..++.++.||.|.|+.
T Consensus 58 -------------~v----------~~~~~~~~Gd~v~V~P 75 (81)
T PF14451_consen 58 -------------PV----------DFDYRLKDGDRVAVYP 75 (81)
T ss_pred -------------EC----------CCcccCCCCCEEEEEe
Confidence 22 5578999999999984
No 44
>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=82.73 E-value=1.6 Score=42.17 Aligned_cols=44 Identities=25% Similarity=0.280 Sum_probs=34.1
Q ss_pred CcEEEEeCCCCCcccCCCCCCcCcHHHHHHHHhCCCCCccccccCCcCccccc
Q 023659 225 ESHVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQIDNCTEGWR 277 (279)
Q Consensus 225 edlLVVNKPaGl~VHPt~~~~~~TL~~~l~~~lg~~~~l~~VHRLDrdTSGLL 277 (279)
+.+|+||||.||.+|. +++.+.+.++....+| .-=||-.-+|+|
T Consensus 34 ~G~l~i~KP~g~tS~~--------~v~~vr~~~~~kkvGH-~GTLDP~A~GvL 77 (322)
T TIGR00425 34 YGVVNLDKPSGPSSHE--------VVAWVRRILNVEKTGH-GGTLDPKVTGVL 77 (322)
T ss_pred CCEEEEeCCCCCCHHH--------HHHHHHHHhcccccCC-CCCCCCCCceEE
Confidence 4799999999998873 4566777777655444 788999999987
No 45
>PRK01777 hypothetical protein; Validated
Probab=82.30 E-value=2.3 Score=34.20 Aligned_cols=58 Identities=17% Similarity=0.111 Sum_probs=39.7
Q ss_pred EEEeeCCCCcHHHHHHHhcCCCHHHHHHHHHcCcEEEccccCCCCCCCCchhhhhccccCCcccccccccccCcceeecc
Q 023659 102 EHLVVSEGGPVLEYICRELNLPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQ 181 (279)
Q Consensus 102 ~~~v~~~~grLd~~L~~~l~lSr~~i~~LI~~G~V~vn~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~GK~v~~~q 181 (279)
..+-++++.++.+.|.. +|+...+-.--+..+.|-|||+ .+
T Consensus 19 ~~l~vp~GtTv~dal~~-sgi~~~~pei~~~~~~vgI~Gk----------------------------------~v---- 59 (95)
T PRK01777 19 QRLTLQEGATVEEAIRA-SGLLELRTDIDLAKNKVGIYSR----------------------------------PA---- 59 (95)
T ss_pred EEEEcCCCCcHHHHHHH-cCCCccCcccccccceEEEeCe----------------------------------EC----
Confidence 34445556689998864 7877763222235678888875 22
Q ss_pred ccccccCCCceecCCCEEEEEcC
Q 023659 182 KTFRITHVDQIVEAGTYLRVHVH 204 (279)
Q Consensus 182 ~~~rv~~~~~~Lk~GD~I~V~~~ 204 (279)
..++.|+.||.|+|+.+
T Consensus 60 ------~~d~~L~dGDRVeIyrP 76 (95)
T PRK01777 60 ------KLTDVLRDGDRVEIYRP 76 (95)
T ss_pred ------CCCCcCCCCCEEEEecC
Confidence 45789999999999854
No 46
>PLN00189 40S ribosomal protein S9; Provisional
Probab=79.14 E-value=3.7 Score=37.34 Aligned_cols=41 Identities=7% Similarity=-0.041 Sum_probs=33.8
Q ss_pred CCHHHHHHHHHcCcEEEccccCCCCCCCCchhhhhccccCCcccccccccccCcceeeccccccccCCCceecCCCEEEE
Q 023659 122 LPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTFRITHVDQIVEAGTYLRV 201 (279)
Q Consensus 122 lSr~~i~~LI~~G~V~vn~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~GK~v~~~q~~~rv~~~~~~Lk~GD~I~V 201 (279)
-|..+++.||..|.|.|||+ . ++.+++.|..|+++.|
T Consensus 122 ~si~~ARqlI~hgHI~V~~~----------------------------------~---------V~~Ps~~V~~~~e~~I 158 (194)
T PLN00189 122 KSIHHARVLIRQRHIRVGKQ----------------------------------I---------VNVPSFMVRVDSQKHI 158 (194)
T ss_pred CCHHHHHHheeCCCEeECCE----------------------------------E---------EecCcEEEecCCEEEE
Confidence 47779999999999999975 1 3467899999999988
Q ss_pred EcCC
Q 023659 202 HVHP 205 (279)
Q Consensus 202 ~~~~ 205 (279)
.+.+
T Consensus 159 tw~~ 162 (194)
T PLN00189 159 DFSL 162 (194)
T ss_pred EEec
Confidence 8743
No 47
>COG0130 TruB Pseudouridine synthase [Translation, ribosomal structure and biogenesis]
Probab=78.52 E-value=2.3 Score=40.28 Aligned_cols=43 Identities=23% Similarity=0.360 Sum_probs=34.0
Q ss_pred cEEEEeCCCCCcccCCCCCCcCcHHHHHHHHhCCCCCccccccCCcCccccc
Q 023659 226 SHVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQIDNCTEGWR 277 (279)
Q Consensus 226 dlLVVNKPaGl~VHPt~~~~~~TL~~~l~~~lg~~~~l~~VHRLDrdTSGLL 277 (279)
-++++|||.|+.+|. ++..+.+.++....+| .--||-.-||+|
T Consensus 16 Gil~ldKP~G~tS~~--------~v~~vkkil~~~K~GH-~GTLDP~atGvL 58 (271)
T COG0130 16 GVINLDKPPGPTSHE--------VVAWVKRILGVEKAGH-GGTLDPLATGVL 58 (271)
T ss_pred ceEEeeCCCCCCHHH--------HHHHHHHHhCcccccc-ccccCCcccceE
Confidence 899999999998873 4556667777665555 788999999987
No 48
>COG4332 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=78.37 E-value=2.6 Score=38.25 Aligned_cols=64 Identities=20% Similarity=0.219 Sum_probs=43.0
Q ss_pred CCCCCCCccccccccCCCCCCCCc-eE-EEeeCCC--CcHHHHHHHhcCCCHHHHHHHHHcCcEEEcc
Q 023659 77 TPSSYGYPEYHRLLPCPSQNCPPR-VE-HLVVSEG--GPVLEYICRELNLPPLFVADLIHFGAVYYAL 140 (279)
Q Consensus 77 ~~~~~~~~~~~~~~~~~~~~~~~r-v~-~~v~~~~--grLd~~L~~~l~lSr~~i~~LI~~G~V~vn~ 140 (279)
..-.+++|.++--...-.....-+ +| ++.++.. -+|+..|++.|++||+.++.||+.|.|....
T Consensus 102 ~~r~~g~pd~~i~krilge~~~~~~vel~l~~~~p~qlrl~~Ll~seL~LSrS~lq~lie~g~Irgdt 169 (203)
T COG4332 102 NARLSGFPDFHIQKRILGEIASHAAVELSLRISRPFQLRLDRLLASELGLSRSELQRLIETGQIRGDT 169 (203)
T ss_pred cccccCCCchhhhhheecCcccceeEEEEEcccCcchhHHHHHHHHHhCcCHHHHHHHHHcCceeecc
Confidence 344578887764433222222222 33 3333332 3899999999999999999999999999873
No 49
>PRK04313 30S ribosomal protein S4e; Validated
Probab=65.30 E-value=19 Score=33.79 Aligned_cols=31 Identities=19% Similarity=0.105 Sum_probs=28.0
Q ss_pred cHHHHHHHhcC--CCHHHHHHHHHcCcEEEccc
Q 023659 111 PVLEYICRELN--LPPLFVADLIHFGAVYYALV 141 (279)
Q Consensus 111 rLd~~L~~~l~--lSr~~i~~LI~~G~V~vn~~ 141 (279)
+|.-+|.+.|+ .+...++..+..|.|+|||+
T Consensus 39 PL~iiLRd~L~yA~t~rEak~Il~~~~V~VDGk 71 (237)
T PRK04313 39 PLLVVLRDVLGYADTAREAKKIINEGKVLVDGR 71 (237)
T ss_pred ccHHHHHhHhhhhccHHHHHHHHhCCcEEECCE
Confidence 68889999887 68889999999999999997
No 50
>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=58.62 E-value=15 Score=32.40 Aligned_cols=20 Identities=15% Similarity=-0.064 Sum_probs=18.0
Q ss_pred CCHHHHHHHHHcCcEEEccc
Q 023659 122 LPPLFVADLIHFGAVYYALV 141 (279)
Q Consensus 122 lSr~~i~~LI~~G~V~vn~~ 141 (279)
-|..+++.||..|.|.||++
T Consensus 117 ~s~~~ArqlI~hgHI~V~~~ 136 (162)
T TIGR01018 117 RTIHQARQLIVHGHIAVDGR 136 (162)
T ss_pred CCHHHHHHHhhCCCeeECCE
Confidence 57789999999999999976
No 51
>PTZ00223 40S ribosomal protein S4; Provisional
Probab=58.34 E-value=29 Score=33.24 Aligned_cols=31 Identities=23% Similarity=0.173 Sum_probs=27.7
Q ss_pred cHHHHHHHhcC--CCHHHHHHHHHcCcEEEccc
Q 023659 111 PVLEYICRELN--LPPLFVADLIHFGAVYYALV 141 (279)
Q Consensus 111 rLd~~L~~~l~--lSr~~i~~LI~~G~V~vn~~ 141 (279)
+|.-+|.+.|+ .+...++..+..|.|.|||+
T Consensus 40 PL~iiLRd~LkyA~t~rEak~Il~~~~V~VDGk 72 (273)
T PTZ00223 40 PLLIIIRNRLKYALNAREAQMILRQGLVCVDGK 72 (273)
T ss_pred ccHHHHHHHhhhhccHHHHHHHHhCCeEEECCE
Confidence 68889999887 57779999999999999997
No 52
>PLN00036 40S ribosomal protein S4; Provisional
Probab=58.20 E-value=30 Score=32.92 Aligned_cols=31 Identities=19% Similarity=0.083 Sum_probs=27.6
Q ss_pred cHHHHHHHhcC--CCHHHHHHHHHcCcEEEccc
Q 023659 111 PVLEYICRELN--LPPLFVADLIHFGAVYYALV 141 (279)
Q Consensus 111 rLd~~L~~~l~--lSr~~i~~LI~~G~V~vn~~ 141 (279)
+|.-+|.+.|+ .+...++..+..|.|.|||+
T Consensus 43 PL~i~LRd~LkyA~t~rEak~Il~~~~V~VDGk 75 (261)
T PLN00036 43 PLLLILRNRLKYALTYREVQAILMQRHVKVDGK 75 (261)
T ss_pred ccHHHHHhHhhhhccHHHHHHHHhCCeEEECCE
Confidence 68889999887 57779999999999999997
No 53
>PTZ00118 40S ribosomal protein S4; Provisional
Probab=54.72 E-value=35 Score=32.46 Aligned_cols=32 Identities=16% Similarity=-0.001 Sum_probs=28.0
Q ss_pred cHHHHHHHhcC--CCHHHHHHHHHcCcEEEcccc
Q 023659 111 PVLEYICRELN--LPPLFVADLIHFGAVYYALVC 142 (279)
Q Consensus 111 rLd~~L~~~l~--lSr~~i~~LI~~G~V~vn~~~ 142 (279)
+|.-+|.+.|+ .+...++..+..|.|.|||++
T Consensus 43 PL~i~LRd~LkyA~t~rEak~Il~~~~V~VDGkv 76 (262)
T PTZ00118 43 PLVILLRNRLKYALTYDEVKLIVIQKIVKVDGKV 76 (262)
T ss_pred ccHHHHHhhhhhhccHHHHHHHHHCCcEEECCEE
Confidence 68889999887 577799999999999999973
No 54
>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=50.09 E-value=7.8 Score=29.06 Aligned_cols=18 Identities=28% Similarity=0.445 Sum_probs=13.1
Q ss_pred EecCcEEEEeCCCCCccc
Q 023659 222 AVTESHVVLDKPAGTSVG 239 (279)
Q Consensus 222 YEDedlLVVNKPaGl~VH 239 (279)
|-...+|++|||+|-.+|
T Consensus 39 ~i~~GvinlDKP~gPtSH 56 (59)
T PF08068_consen 39 YIKYGVINLDKPSGPTSH 56 (59)
T ss_dssp HHHTEEEEEEE-SSS-HH
T ss_pred HHhCCcEEeeCCCCCCcc
Confidence 345789999999998877
No 55
>PTZ00155 40S ribosomal protein S9; Provisional
Probab=49.61 E-value=17 Score=32.76 Aligned_cols=30 Identities=10% Similarity=-0.018 Sum_probs=22.1
Q ss_pred cHHHHHHHhcC--CCHHHHHHHHHcCcEEEccc
Q 023659 111 PVLEYICRELN--LPPLFVADLIHFGAVYYALV 141 (279)
Q Consensus 111 rLd~~L~~~l~--lSr~~i~~LI~~G~V~vn~~ 141 (279)
||+..+.+ +| -+...++.||..|.|.|||+
T Consensus 108 RL~~iv~r-~g~A~ti~~ARqlI~HGHI~V~~~ 139 (181)
T PTZ00155 108 RLQTKVFK-LGLAKSIHHARVLIRQRHIRVGKQ 139 (181)
T ss_pred hhhhHHHh-ccCcCCHHHhhhheeCCCEEECCE
Confidence 45544432 34 46779999999999999976
No 56
>PRK04642 truB tRNA pseudouridine synthase B; Provisional
Probab=47.65 E-value=10 Score=36.57 Aligned_cols=16 Identities=44% Similarity=0.702 Sum_probs=14.5
Q ss_pred CcEEEEeCCCCCcccC
Q 023659 225 ESHVVLDKPAGTSVGG 240 (279)
Q Consensus 225 edlLVVNKPaGl~VHP 240 (279)
+.||+||||.||.+|.
T Consensus 10 ~Gil~i~KP~G~TS~d 25 (300)
T PRK04642 10 DGILLLDKPAGLSSNN 25 (300)
T ss_pred CeEEEEecCCCCCHHH
Confidence 4799999999999996
No 57
>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=46.38 E-value=21 Score=23.25 Aligned_cols=22 Identities=27% Similarity=0.206 Sum_probs=18.6
Q ss_pred HHHhcCCCHHHHHHHHHcCcEE
Q 023659 116 ICRELNLPPLFVADLIHFGAVY 137 (279)
Q Consensus 116 L~~~l~lSr~~i~~LI~~G~V~ 137 (279)
+++.+|+|+..+.+|++.|.+-
T Consensus 7 ~a~~lgis~~ti~~~~~~g~i~ 28 (49)
T TIGR01764 7 AAEYLGVSKDTVYRLIHEGELP 28 (49)
T ss_pred HHHHHCCCHHHHHHHHHcCCCC
Confidence 4577899999999999998643
No 58
>PRK03287 truB tRNA pseudouridine synthase B; Provisional
Probab=46.18 E-value=11 Score=36.18 Aligned_cols=16 Identities=44% Similarity=0.634 Sum_probs=14.5
Q ss_pred CcEEEEeCCCCCcccC
Q 023659 225 ESHVVLDKPAGTSVGG 240 (279)
Q Consensus 225 edlLVVNKPaGl~VHP 240 (279)
+-||+||||.||.+|.
T Consensus 9 ~Gil~i~KP~G~TS~d 24 (298)
T PRK03287 9 SGLVVVDKPAGMTSHD 24 (298)
T ss_pred CeEEEEeCCCCCCHHH
Confidence 4799999999999996
No 59
>PRK05033 truB tRNA pseudouridine synthase B; Provisional
Probab=45.69 E-value=11 Score=36.39 Aligned_cols=16 Identities=38% Similarity=0.623 Sum_probs=14.5
Q ss_pred CcEEEEeCCCCCcccC
Q 023659 225 ESHVVLDKPAGTSVGG 240 (279)
Q Consensus 225 edlLVVNKPaGl~VHP 240 (279)
+-||+||||.||.+|.
T Consensus 10 ~Gil~i~KP~G~TS~d 25 (312)
T PRK05033 10 NGVLLLDKPQGMSSND 25 (312)
T ss_pred CeEEEEeCCCCCCHHH
Confidence 4799999999999996
No 60
>PRK05389 truB tRNA pseudouridine synthase B; Provisional
Probab=45.66 E-value=12 Score=36.22 Aligned_cols=16 Identities=38% Similarity=0.650 Sum_probs=14.5
Q ss_pred CcEEEEeCCCCCcccC
Q 023659 225 ESHVVLDKPAGTSVGG 240 (279)
Q Consensus 225 edlLVVNKPaGl~VHP 240 (279)
+.||+||||.|+.+|.
T Consensus 13 ~Gil~i~KP~G~TS~d 28 (305)
T PRK05389 13 SGWLILDKPAGMTSTE 28 (305)
T ss_pred CeEEEEeCCCCCCHHH
Confidence 4799999999999996
No 61
>PRK00020 truB tRNA pseudouridine synthase B; Provisional
Probab=44.68 E-value=12 Score=35.06 Aligned_cols=16 Identities=38% Similarity=0.621 Sum_probs=14.4
Q ss_pred CcEEEEeCCCCCcccC
Q 023659 225 ESHVVLDKPAGTSVGG 240 (279)
Q Consensus 225 edlLVVNKPaGl~VHP 240 (279)
+.||+||||.|+.+|.
T Consensus 10 ~Gil~vdKP~G~TS~d 25 (244)
T PRK00020 10 DGVLLLDKPVGLSSNH 25 (244)
T ss_pred CeEEEEecCCCCCHHH
Confidence 3699999999999996
No 62
>PRK00989 truB tRNA pseudouridine synthase B; Provisional
Probab=43.76 E-value=13 Score=34.59 Aligned_cols=15 Identities=27% Similarity=0.468 Sum_probs=13.9
Q ss_pred cEEEEeCCCCCcccC
Q 023659 226 SHVVLDKPAGTSVGG 240 (279)
Q Consensus 226 dlLVVNKPaGl~VHP 240 (279)
.||+||||.|+.+|.
T Consensus 10 G~l~i~KP~g~TS~d 24 (230)
T PRK00989 10 GILLVDKPQGRTSFS 24 (230)
T ss_pred EEEEEeCCCCCCHHH
Confidence 699999999999996
No 63
>PF11969 DcpS_C: Scavenger mRNA decapping enzyme C-term binding; PDB: 1VLR_B 1XMM_D 1XML_B 1ST0_A 3BLA_B 3BL9_B 3BL7_B 1ST4_B 1XQU_B.
Probab=41.60 E-value=18 Score=29.43 Aligned_cols=15 Identities=20% Similarity=0.406 Sum_probs=13.1
Q ss_pred ccceEEecCcEEEEe
Q 023659 217 NSRIIAVTESHVVLD 231 (279)
Q Consensus 217 ~l~ILYEDedlLVVN 231 (279)
+.+|||||++++|+.
T Consensus 13 ~~~vly~d~~~v~~~ 27 (116)
T PF11969_consen 13 PERVLYEDDDFVVFK 27 (116)
T ss_dssp GGGESEEETSEEEEE
T ss_pred CCcEEEEeCCEEEee
Confidence 458999999999986
No 64
>PRK05912 tyrosyl-tRNA synthetase; Validated
Probab=41.55 E-value=64 Score=32.12 Aligned_cols=32 Identities=19% Similarity=0.038 Sum_probs=25.7
Q ss_pred CcHHHHHHHh-cCCCHHHHHHHHHcCcEEEccc
Q 023659 110 GPVLEYICRE-LNLPPLFVADLIHFGAVYYALV 141 (279)
Q Consensus 110 grLd~~L~~~-l~lSr~~i~~LI~~G~V~vn~~ 141 (279)
..+.++|.+. +--|++.+++||+.|+|+||++
T Consensus 343 ~~~~~~l~~~~~~~S~~earr~i~~g~v~in~~ 375 (408)
T PRK05912 343 IDLLALLVEAGLVPSKSEARRLIKQGGVKINGE 375 (408)
T ss_pred CcHHHHHHHhCCCCCHHHHHHHHHcCCEEECCE
Confidence 3677777642 3469999999999999999986
No 65
>COG1471 RPS4A Ribosomal protein S4E [Translation, ribosomal structure and biogenesis]
Probab=40.21 E-value=69 Score=30.18 Aligned_cols=31 Identities=16% Similarity=-0.001 Sum_probs=21.4
Q ss_pred HHHHHHHhcC--CCHHHHHHHHHcCcEEEcccc
Q 023659 112 VLEYICRELN--LPPLFVADLIHFGAVYYALVC 142 (279)
Q Consensus 112 Ld~~L~~~l~--lSr~~i~~LI~~G~V~vn~~~ 142 (279)
|.-++.+.|+ -.-..++..|..|.|+|||++
T Consensus 43 L~~iiRd~LkyAd~~REa~~Ii~~g~v~VDG~v 75 (241)
T COG1471 43 LLVIIRDYLKYADNAREARKILSEGKVLVDGKV 75 (241)
T ss_pred EEeeehhHHHhccchHHHHHHHhcCcEEECCEE
Confidence 3344444443 344579999999999999973
No 66
>PRK08364 sulfur carrier protein ThiS; Provisional
Probab=39.60 E-value=73 Score=23.61 Aligned_cols=14 Identities=36% Similarity=0.553 Sum_probs=11.8
Q ss_pred CCceecCCCEEEEE
Q 023659 189 VDQIVEAGTYLRVH 202 (279)
Q Consensus 189 ~~~~Lk~GD~I~V~ 202 (279)
.++.|+.||.|++.
T Consensus 51 ~~~~l~~gD~Veii 64 (70)
T PRK08364 51 EDDPVKDGDYVEVI 64 (70)
T ss_pred CCcCcCCCCEEEEE
Confidence 46789999999986
No 67
>cd00754 MoaD Ubiquitin domain of MoaD-like proteins. MoaD family. Members of this family are involved in biosynthesis of the molybdenum cofactor (Moco), an essential cofactor of a diverse group of redox enzymes. Moco biosynthesis is an evolutionarily conserved pathway present in eubacteria, archaea and eukaryotes. Moco contains a tricyclic pyranopterin, termed molybdopterin (MPT), that contains the cis-dithiolene group responsible for molybdenum ligation. This dithiolene group is generated by MPT synthase, the second major step in Moco biosynthesis. MPT synthase consists of a large (MoeE) and small (MoaD) subunit. The small subunit is inserted into the lare subunit to form the active site. The small subunit, which is structurally similar to ubiquitin, contains a C-terminal thiocarboxylated glycine residue that serves as a sulfur donor for the synthesis of the MPT dithiolene group.
Probab=37.65 E-value=1.3e+02 Score=21.97 Aligned_cols=15 Identities=13% Similarity=0.242 Sum_probs=12.1
Q ss_pred CCceecCCCEEEEEc
Q 023659 189 VDQIVEAGTYLRVHV 203 (279)
Q Consensus 189 ~~~~Lk~GD~I~V~~ 203 (279)
.+..|+.||.|.+..
T Consensus 61 ~~~~l~~gD~v~i~p 75 (80)
T cd00754 61 LDTPLKDGDEVAIIP 75 (80)
T ss_pred CCcccCCCCEEEEeC
Confidence 356899999998863
No 68
>PRK13354 tyrosyl-tRNA synthetase; Provisional
Probab=36.82 E-value=43 Score=33.40 Aligned_cols=31 Identities=16% Similarity=0.125 Sum_probs=25.2
Q ss_pred cHHHHHHH-hcCCCHHHHHHHHHcCcEEEccc
Q 023659 111 PVLEYICR-ELNLPPLFVADLIHFGAVYYALV 141 (279)
Q Consensus 111 rLd~~L~~-~l~lSr~~i~~LI~~G~V~vn~~ 141 (279)
+|.++|.+ .+--|++.+++||..|+|+|||+
T Consensus 344 ~~~~~l~~~~~~~S~~earrli~~ggv~in~~ 375 (410)
T PRK13354 344 NLVDLLVDLGLEPSKREARRLIQNGAIKINGE 375 (410)
T ss_pred CHHHHHHHhCCCCCHHHHHHHHHcCCEEECCE
Confidence 67777764 23469999999999999999986
No 69
>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=34.98 E-value=41 Score=21.58 Aligned_cols=22 Identities=14% Similarity=0.200 Sum_probs=19.0
Q ss_pred HHHhcCCCHHHHHHHHHcCcEE
Q 023659 116 ICRELNLPPLFVADLIHFGAVY 137 (279)
Q Consensus 116 L~~~l~lSr~~i~~LI~~G~V~ 137 (279)
+++.+++|+..+.++++.|.+-
T Consensus 6 ~a~~lgvs~~tl~~~~~~g~~~ 27 (49)
T cd04762 6 AAELLGVSPSTLRRWVKEGKLK 27 (49)
T ss_pred HHHHHCcCHHHHHHHHHcCCCC
Confidence 5677899999999999998763
No 70
>PF12728 HTH_17: Helix-turn-helix domain
Probab=32.86 E-value=43 Score=22.72 Aligned_cols=21 Identities=19% Similarity=0.180 Sum_probs=18.2
Q ss_pred HHHhcCCCHHHHHHHHHcCcE
Q 023659 116 ICRELNLPPLFVADLIHFGAV 136 (279)
Q Consensus 116 L~~~l~lSr~~i~~LI~~G~V 136 (279)
+++.|++|++.+.+|++.|.+
T Consensus 7 ~a~~l~is~~tv~~~~~~g~i 27 (51)
T PF12728_consen 7 AAELLGISRSTVYRWIRQGKI 27 (51)
T ss_pred HHHHHCcCHHHHHHHHHcCCC
Confidence 456789999999999999866
No 71
>PRK05659 sulfur carrier protein ThiS; Validated
Probab=29.86 E-value=65 Score=23.13 Aligned_cols=15 Identities=13% Similarity=0.375 Sum_probs=12.6
Q ss_pred CCCceecCCCEEEEE
Q 023659 188 HVDQIVEAGTYLRVH 202 (279)
Q Consensus 188 ~~~~~Lk~GD~I~V~ 202 (279)
..++.|+.||.|+|.
T Consensus 46 ~~~~~l~~gD~vei~ 60 (66)
T PRK05659 46 HASTALREGDVVEIV 60 (66)
T ss_pred cCcccCCCCCEEEEE
Confidence 456789999999986
No 72
>PF03658 Ub-RnfH: RnfH family Ubiquitin; InterPro: IPR005346 This is a small family of proteins of unknown function.; PDB: 2HJ1_B.
Probab=29.32 E-value=35 Score=27.11 Aligned_cols=17 Identities=12% Similarity=0.333 Sum_probs=9.8
Q ss_pred CCCceecCCCEEEEEcC
Q 023659 188 HVDQIVEAGTYLRVHVH 204 (279)
Q Consensus 188 ~~~~~Lk~GD~I~V~~~ 204 (279)
+.++.|+.||.|+|+.+
T Consensus 57 ~~d~~L~~GDRVEIYRP 73 (84)
T PF03658_consen 57 KLDTVLRDGDRVEIYRP 73 (84)
T ss_dssp -TT-B--TT-EEEEE-S
T ss_pred CCCCcCCCCCEEEEecc
Confidence 56789999999999975
No 73
>PF14839 DOR: DOR family
Probab=29.14 E-value=33 Score=31.74 Aligned_cols=17 Identities=12% Similarity=0.181 Sum_probs=13.8
Q ss_pred EecCcEEEEeCCCCCcc
Q 023659 222 AVTESHVVLDKPAGTSV 238 (279)
Q Consensus 222 YEDedlLVVNKPaGl~V 238 (279)
.|||+||+||++.|+..
T Consensus 4 ~edD~WilVD~~~~~~~ 20 (216)
T PF14839_consen 4 EEDDEWILVDFIDGLPR 20 (216)
T ss_pred cccCCeEEEEecCCCcc
Confidence 48999999999996433
No 74
>PF01230 HIT: HIT domain; InterPro: IPR001310 The Histidine Triad (HIT) motif, His-x-His-x-His-x-x (x, a hydrophobic amino acid) was identified as being highly conserved in a variety of organisms []. Crystal structure of rabbit Hint, purified as an adenosine and AMP-binding protein, showed that proteins in the HIT superfamily are conserved as nucleotide-binding proteins and that Hint homologues, which are found in all forms of life, are structurally related to Fhit homologues and GalT-related enzymes, which have more restricted phylogenetic profiles []. Hint homologues including rabbit Hint and yeast Hnt1 hydrolyse adenosine 5' monophosphoramide substrates such as AMP-NH2 and AMP-lysine to AMP plus the amine product and function as positive regulators of Cdk7/Kin28 in vivo []. Fhit homologues are diadenosine polyphosphate hydrolases [] and function as tumour suppressors in human and mouse [] though the tumour suppressing function of Fhit does not depend on ApppA hydrolysis []. The third branch of the HIT superfamily, which includes GalT homologues, contains a related His-X-His-X-Gln motif and transfers nucleoside monophosphate moieties to phosphorylated second substrates rather than hydrolysing them [].; PDB: 3LB5_B 1EMS_A 1Y23_A 3ANO_B 1KPE_B 1KPC_A 4EQE_B 1KPA_A 1KPB_B 4EQG_B ....
Probab=28.45 E-value=44 Score=25.66 Aligned_cols=21 Identities=19% Similarity=0.214 Sum_probs=13.4
Q ss_pred ccceEEecCcEEE-EeCCCCCc
Q 023659 217 NSRIIAVTESHVV-LDKPAGTS 237 (279)
Q Consensus 217 ~l~ILYEDedlLV-VNKPaGl~ 237 (279)
+-.||||||+++| .|+-+-.+
T Consensus 5 ~~~vv~e~~~~~~~~~~~p~~~ 26 (98)
T PF01230_consen 5 PARVVYEDDHFVAFLDIFPISP 26 (98)
T ss_dssp HCEEEEE-SSEEEEEESSTSST
T ss_pred CeeEEEECCCEEEEEcCCCCCC
Confidence 4589999998775 45544443
No 75
>PF06633 DUF1155: Protein of unknown function (DUF1155); InterPro: IPR009536 This family consists of several Cucumber mosaic virus ORF IIB proteins. The function of this family is unknown.
Probab=26.76 E-value=30 Score=23.96 Aligned_cols=34 Identities=24% Similarity=0.178 Sum_probs=27.3
Q ss_pred CcccCcchhHHHhhhccccccccccccccceeeecc
Q 023659 14 GRSLGAPVSLLRTLASTHASCHRNIYKSNVVLSFSS 49 (279)
Q Consensus 14 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 49 (279)
-++|-+|.+|++-...--+..-.++.||. ++|.+
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 58999999999887777777777777888 77754
No 76
>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=25.70 E-value=1.3e+02 Score=23.51 Aligned_cols=29 Identities=10% Similarity=0.093 Sum_probs=17.3
Q ss_pred EeeCCCCcHHHHHHHhcCCCHHHHHHHHHc
Q 023659 104 LVVSEGGPVLEYICRELNLPPLFVADLIHF 133 (279)
Q Consensus 104 ~v~~~~grLd~~L~~~l~lSr~~i~~LI~~ 133 (279)
.+|..+.+|..++. .+|+|.+.+.+++..
T Consensus 5 ~~V~~GDtLs~iF~-~~gls~~dl~~v~~~ 33 (85)
T PF04225_consen 5 YTVKSGDTLSTIFR-RAGLSASDLYAVLEA 33 (85)
T ss_dssp EE--TT--HHHHHH-HTT--HHHHHHHHHH
T ss_pred EEECCCCcHHHHHH-HcCCCHHHHHHHHhc
Confidence 34444557877665 479999999999875
No 77
>PRK06083 sulfur carrier protein ThiS; Provisional
Probab=24.57 E-value=1e+02 Score=24.17 Aligned_cols=15 Identities=7% Similarity=0.293 Sum_probs=12.3
Q ss_pred CCCceecCCCEEEEE
Q 023659 188 HVDQIVEAGTYLRVH 202 (279)
Q Consensus 188 ~~~~~Lk~GD~I~V~ 202 (279)
..+..|+.||.|+|.
T Consensus 64 w~~t~L~egD~IEIv 78 (84)
T PRK06083 64 WQSTVLSSGDAISLF 78 (84)
T ss_pred cCcccCCCCCEEEEE
Confidence 446789999999985
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=23.67 E-value=59 Score=24.67 Aligned_cols=15 Identities=7% Similarity=-0.077 Sum_probs=13.0
Q ss_pred ccccccCCcCccccc
Q 023659 263 LRTTHQIDNCTEGWR 277 (279)
Q Consensus 263 l~~VHRLDrdTSGLL 277 (279)
+..++++|+..+|++
T Consensus 26 i~~aG~kDk~a~t~q 40 (87)
T cd01291 26 VGYAGRKDKRAVTTQ 40 (87)
T ss_pred EEECccCCCCeeEEE
Confidence 556999999999985
No 79
>PF13348 Y_phosphatase3C: Tyrosine phosphatase family C-terminal region; PDB: 1YWF_A 2OZ5_B.
Probab=22.83 E-value=1e+02 Score=22.26 Aligned_cols=23 Identities=30% Similarity=0.388 Sum_probs=17.8
Q ss_pred CcHHHHHHHhcCCCHHHHHHHHH
Q 023659 110 GPVLEYICRELNLPPLFVADLIH 132 (279)
Q Consensus 110 grLd~~L~~~l~lSr~~i~~LI~ 132 (279)
|.++.||.+.+|++...+.+|.+
T Consensus 43 Gs~e~Yl~~~lgl~~~~i~~Lr~ 65 (68)
T PF13348_consen 43 GSVENYLREELGLSEEDIERLRE 65 (68)
T ss_dssp SSHHHHHHHT-T--HHHHHHHHH
T ss_pred CCHHHHHHHcCCCCHHHHHHHHH
Confidence 78999999999999999998864
No 80
>PRK10687 purine nucleoside phosphoramidase; Provisional
Probab=22.61 E-value=75 Score=26.13 Aligned_cols=18 Identities=22% Similarity=0.174 Sum_probs=12.8
Q ss_pred ccceEEecCcEEEE-eCCC
Q 023659 217 NSRIIAVTESHVVL-DKPA 234 (279)
Q Consensus 217 ~l~ILYEDedlLVV-NKPa 234 (279)
+..+|||||+++++ |.-+
T Consensus 16 p~~~v~edd~~~aflD~~P 34 (119)
T PRK10687 16 PSDIVYQDELVTAFRDISP 34 (119)
T ss_pred CCCEEEECCCEEEEEcCCC
Confidence 45799999998665 4433
No 81
>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=22.23 E-value=1.2e+02 Score=21.82 Aligned_cols=15 Identities=13% Similarity=0.248 Sum_probs=12.2
Q ss_pred CCceecCCCEEEEEc
Q 023659 189 VDQIVEAGTYLRVHV 203 (279)
Q Consensus 189 ~~~~Lk~GD~I~V~~ 203 (279)
.+..|+.||.|.+..
T Consensus 58 ~~~~l~~gD~V~i~p 72 (77)
T PF02597_consen 58 LDTPLKDGDEVAILP 72 (77)
T ss_dssp TTSBEETTEEEEEEE
T ss_pred CCcCcCCCCEEEEEC
Confidence 367899999999863
No 82
>cd04761 HTH_MerR-SF Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily. Helix-turn-helix (HTH) transcription regulator MerR superfamily, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=22.13 E-value=93 Score=20.43 Aligned_cols=22 Identities=9% Similarity=0.159 Sum_probs=19.2
Q ss_pred HHHhcCCCHHHHHHHHHcCcEE
Q 023659 116 ICRELNLPPLFVADLIHFGAVY 137 (279)
Q Consensus 116 L~~~l~lSr~~i~~LI~~G~V~ 137 (279)
+++.+|++...++.+++.|.+-
T Consensus 6 ~a~~~gv~~~tlr~~~~~g~l~ 27 (49)
T cd04761 6 LAKLTGVSPSTLRYYERIGLLS 27 (49)
T ss_pred HHHHHCcCHHHHHHHHHCCCCC
Confidence 5667899999999999999865
No 83
>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=22.07 E-value=1.3e+02 Score=21.70 Aligned_cols=14 Identities=7% Similarity=0.245 Sum_probs=11.5
Q ss_pred CceecCCCEEEEEc
Q 023659 190 DQIVEAGTYLRVHV 203 (279)
Q Consensus 190 ~~~Lk~GD~I~V~~ 203 (279)
++.|+.||.|.+..
T Consensus 47 ~~~L~~gD~V~ii~ 60 (65)
T cd00565 47 STPLQDGDRIEIVT 60 (65)
T ss_pred ceecCCCCEEEEEE
Confidence 47899999998863
No 84
>TIGR02675 tape_meas_nterm tape measure domain. Proteins containing this domain are strictly bacterial, including bacteriophage and prophage regions of bacterial genomes. Most members are 800 to 1800 amino acids long, making them among the longest predicted proteins of their respective phage genomes, where they are encoded in tail protein regions. This roughly 80-residue domain described here usually begins between residue 100 and 250. Many members are known or predicted to act as phage tail tape measure proteins, a minor tail component that regulates tail length.
Probab=21.81 E-value=1.1e+02 Score=23.19 Aligned_cols=28 Identities=7% Similarity=0.126 Sum_probs=25.5
Q ss_pred cHHHHHHHhcCCCHHHHHHHHHcCcEEE
Q 023659 111 PVLEYICRELNLPPLFVADLIHFGAVYY 138 (279)
Q Consensus 111 rLd~~L~~~l~lSr~~i~~LI~~G~V~v 138 (279)
++.+.|++.+|++...++++...|.|..
T Consensus 45 ~~~~~lAk~~G~t~~~l~~~~~~Gkit~ 72 (75)
T TIGR02675 45 GALQALAKAMGVTRGELRKMLSDGKLTA 72 (75)
T ss_pred HHHHHHHHHhCCCHHHHHHHHHCCCCcc
Confidence 4889999999999999999999999864
Done!