Query 041166
Match_columns 133
No_of_seqs 179 out of 1080
Neff 7.5
Searched_HMMs 46136
Date Fri Mar 29 04:24:17 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/041166.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/041166hhsearch_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 3.4E-29 7.4E-34 196.7 12.3 105 19-130 53-161 (289)
2 cd02558 PSRA_1 PSRA_1: Pseudou 99.9 5.2E-27 1.1E-31 180.5 12.1 105 17-130 16-120 (246)
3 PRK11180 rluD 23S rRNA pseudou 99.9 1.7E-26 3.7E-31 183.7 13.1 125 1-130 18-169 (325)
4 TIGR00005 rluA_subfam pseudour 99.9 3.9E-26 8.5E-31 179.3 13.1 124 2-130 7-157 (299)
5 PRK11025 23S rRNA pseudouridyl 99.9 2.3E-25 4.9E-30 176.9 12.2 121 1-130 20-174 (317)
6 cd02557 PseudoU_synth_ScRIB2 P 99.9 2.8E-25 6.1E-30 167.6 10.2 91 31-130 6-97 (213)
7 PRK10158 23S rRNA/tRNA pseudou 99.9 1.6E-23 3.4E-28 158.7 10.4 81 39-130 13-94 (219)
8 TIGR01621 RluA-like pseudourid 99.9 1.2E-23 2.7E-28 159.1 9.4 80 40-130 2-81 (217)
9 PRK11112 tRNA pseudouridine sy 99.9 1.7E-23 3.8E-28 161.9 9.6 81 40-130 2-84 (257)
10 cd02563 PseudoU_synth_TruC tRN 99.9 2.1E-23 4.5E-28 158.2 9.5 81 40-130 1-83 (223)
11 KOG1919 RNA pseudouridylate sy 99.9 1.2E-22 2.6E-27 163.7 10.9 119 3-130 46-187 (371)
12 PF00849 PseudoU_synth_2: RNA 99.8 3.9E-20 8.5E-25 132.9 6.9 78 48-130 1-78 (164)
13 cd02550 PseudoU_synth_Rsu_Rlu_ 99.8 1.6E-19 3.4E-24 129.8 6.2 69 49-129 1-69 (154)
14 PRK10839 16S rRNA pseudouridyl 99.8 7.7E-20 1.7E-24 139.3 4.8 73 45-130 58-130 (232)
15 cd02869 PseudoU_synth_RluCD_li 99.8 2.2E-18 4.7E-23 125.9 8.4 77 49-130 1-77 (185)
16 cd02556 PseudoU_synth_RluB Pse 99.7 4.5E-18 9.8E-23 124.0 6.4 71 48-130 1-71 (167)
17 cd02870 PseudoU_synth_RsuA_lik 99.7 1.4E-18 3.1E-23 123.8 3.0 68 49-129 1-68 (146)
18 cd02553 PseudoU_synth_RsuA Pse 99.7 8.8E-18 1.9E-22 122.5 6.4 69 49-129 2-70 (167)
19 PRK10475 23S rRNA pseudouridin 99.7 2E-17 4.3E-22 130.2 7.7 65 44-121 64-128 (290)
20 PRK10700 23S rRNA pseudouridyl 99.7 8.2E-17 1.8E-21 126.6 9.1 73 45-129 65-137 (289)
21 cd02566 PseudoU_synth_RluE Pse 99.7 1.4E-16 3E-21 116.3 5.6 61 49-122 1-62 (168)
22 PRK11394 23S rRNA pseudouridin 99.6 4.4E-15 9.5E-20 112.6 6.2 68 47-129 39-106 (217)
23 cd02555 PSSA_1 PSSA_1: Pseudou 99.5 1.7E-14 3.7E-19 106.3 6.3 70 47-129 4-81 (177)
24 cd02554 PseudoU_synth_RluF Pse 99.5 7.9E-14 1.7E-18 101.7 6.7 63 49-124 2-64 (164)
25 cd02868 PseudoU_synth_hTruB2_l 99.3 2.5E-12 5.4E-17 98.1 5.6 66 48-127 1-66 (226)
26 COG1187 RsuA 16S rRNA uridine- 99.2 9.5E-12 2.1E-16 96.0 3.5 111 2-120 4-128 (248)
27 cd02572 PseudoU_synth_hDyskeri 97.8 5.1E-05 1.1E-09 56.3 6.0 59 47-124 2-60 (182)
28 PRK00989 truB tRNA pseudouridi 97.7 6.5E-05 1.4E-09 57.6 5.2 60 47-124 9-68 (230)
29 PRK04099 truB tRNA pseudouridi 97.6 0.00013 2.8E-09 57.3 5.9 60 47-125 2-61 (273)
30 cd00506 PseudoU_synth_TruB_lik 97.6 0.00015 3.3E-09 54.9 5.9 58 48-124 1-58 (210)
31 TIGR00431 TruB tRNA pseudourid 97.6 0.00019 4E-09 54.4 6.1 59 47-124 2-60 (209)
32 PRK00020 truB tRNA pseudouridi 97.5 0.00027 5.9E-09 54.6 5.8 59 47-124 10-68 (244)
33 PRK02484 truB tRNA pseudouridi 97.5 0.00031 6.7E-09 55.8 6.0 59 47-124 3-61 (294)
34 PRK03287 truB tRNA pseudouridi 97.4 0.00034 7.4E-09 55.6 6.0 60 46-124 8-67 (298)
35 PRK14123 tRNA pseudouridine sy 97.4 0.0004 8.7E-09 55.4 6.0 60 47-125 3-62 (305)
36 PRK14124 tRNA pseudouridine sy 97.4 0.00046 1E-08 55.1 6.3 59 47-124 3-61 (308)
37 PRK14846 truB tRNA pseudouridi 97.4 0.00047 1E-08 55.6 6.4 59 47-124 3-61 (345)
38 PRK00130 truB tRNA pseudouridi 97.4 0.00044 9.5E-09 54.8 6.1 60 47-125 2-61 (290)
39 PRK05389 truB tRNA pseudouridi 97.4 0.00048 1E-08 54.9 6.1 59 47-124 13-71 (305)
40 PRK02193 truB tRNA pseudouridi 97.3 0.00048 1E-08 54.3 5.7 57 49-124 2-58 (279)
41 PRK04270 H/ACA RNA-protein com 97.3 0.00057 1.2E-08 54.3 6.0 61 45-124 20-80 (300)
42 PRK05033 truB tRNA pseudouridi 97.3 0.00062 1.3E-08 54.4 6.2 60 47-125 10-69 (312)
43 cd02573 PseudoU_synth_EcTruB P 97.3 0.00064 1.4E-08 53.5 6.1 59 48-125 1-59 (277)
44 PRK01528 truB tRNA pseudouridi 97.3 0.00062 1.3E-08 54.0 6.1 51 46-113 2-52 (292)
45 PRK02755 truB tRNA pseudouridi 97.3 0.00061 1.3E-08 54.1 5.6 60 47-125 3-62 (295)
46 PRK01550 truB tRNA pseudouridi 97.2 0.00082 1.8E-08 53.6 5.9 60 47-125 2-61 (304)
47 PRK01851 truB tRNA pseudouridi 97.2 0.00095 2.1E-08 53.2 6.2 59 47-124 16-74 (303)
48 PRK14122 tRNA pseudouridine sy 97.0 0.002 4.4E-08 51.5 5.9 58 48-124 2-59 (312)
49 TIGR00425 CBF5 rRNA pseudourid 96.8 0.0026 5.7E-08 51.1 5.6 60 46-124 33-92 (322)
50 PRK04642 truB tRNA pseudouridi 96.8 0.003 6.5E-08 50.3 5.8 59 47-124 10-68 (300)
51 cd00165 S4 S4/Hsp/ tRNA synthe 96.7 0.0038 8.2E-08 37.2 4.2 27 20-53 44-70 (70)
52 COG0130 TruB Pseudouridine syn 96.6 0.0049 1.1E-07 48.4 5.7 62 48-127 16-77 (271)
53 cd02867 PseudoU_synth_TruB_4 P 96.4 0.0095 2.1E-07 47.7 6.1 67 48-123 1-87 (312)
54 KOG2559 Predicted pseudouridin 95.5 0.011 2.4E-07 45.9 2.6 22 92-113 90-111 (318)
55 cd01291 PseudoU_synth PseudoU_ 90.3 0.29 6.4E-06 31.4 2.6 21 90-110 23-43 (87)
56 PF08068 DKCLD: DKCLD (NUC011) 70.6 1.9 4.1E-05 26.3 0.6 18 44-61 39-56 (59)
57 PF13021 DUF3885: Domain of un 69.2 7.7 0.00017 21.5 2.8 24 102-125 5-28 (38)
58 PF11324 DUF3126: Protein of u 52.2 22 0.00048 21.9 3.0 40 1-47 3-46 (63)
59 PF11969 DcpS_C: Scavenger mRN 43.1 15 0.00033 24.8 1.4 19 39-57 13-33 (116)
60 cd01223 PH_Vav Vav pleckstrin 41.1 58 0.0013 22.5 4.0 80 39-124 21-108 (116)
61 PRK03427 cell division protein 40.3 55 0.0012 26.7 4.4 54 45-110 194-248 (333)
62 PF01509 TruB_N: TruB family p 35.8 26 0.00056 25.0 1.7 33 90-124 6-38 (149)
63 PRK14105 selenophosphate synth 32.1 63 0.0014 25.9 3.5 31 98-128 288-318 (345)
64 PF02863 Arg_repressor_C: Argi 29.6 52 0.0011 20.2 2.2 23 103-125 47-69 (70)
65 PF01230 HIT: HIT domain; Int 28.0 52 0.0011 21.0 2.0 15 39-53 5-19 (98)
66 PHA02096 hypothetical protein 26.7 31 0.00068 22.4 0.8 20 42-61 62-81 (103)
67 TIGR01293 Kv_beta voltage-depe 26.2 3E+02 0.0065 21.5 6.5 72 46-129 72-145 (317)
68 PF14839 DOR: DOR family 25.8 49 0.0011 25.3 1.8 17 44-60 4-20 (216)
69 COG0108 RibB 3,4-dihydroxy-2-b 25.6 44 0.00096 25.3 1.5 25 96-120 45-69 (203)
70 cd01276 PKCI_related Protein K 25.0 65 0.0014 20.6 2.1 13 40-52 14-26 (104)
71 COG3845 ABC-type uncharacteriz 24.9 25 0.00054 30.2 0.1 81 40-131 152-245 (501)
72 COG0667 Tas Predicted oxidored 24.0 3.2E+02 0.0068 21.7 6.2 72 47-129 76-151 (316)
73 PRK09912 L-glyceraldehyde 3-ph 22.6 1.1E+02 0.0025 24.3 3.4 74 46-130 89-164 (346)
74 PF11697 DUF3293: Protein of u 22.4 1E+02 0.0022 19.1 2.5 27 102-128 47-73 (73)
75 PF00248 Aldo_ket_red: Aldo/ke 21.8 97 0.0021 23.4 2.8 51 69-129 82-132 (283)
76 cd06660 Aldo_ket_red Aldo-keto 21.2 3.6E+02 0.0079 20.2 6.4 73 46-129 71-143 (285)
77 PRK06043 fumarate hydratase; P 21.1 1E+02 0.0023 23.1 2.7 23 104-127 26-48 (192)
78 cd01278 aprataxin_related apra 21.1 85 0.0019 20.1 2.1 15 39-53 15-29 (104)
79 PRK06842 fumarate hydratase; P 20.7 1.1E+02 0.0024 22.8 2.8 23 104-127 26-48 (185)
80 PRK01741 cell division protein 20.3 1.7E+02 0.0038 23.8 4.0 15 96-110 239-254 (332)
No 1
>COG0564 RluA Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]
Probab=99.96 E-value=3.4e-29 Score=196.69 Aligned_cols=105 Identities=31% Similarity=0.460 Sum_probs=88.2
Q ss_pred CCCcEEEEecCCCCC--C--CCCCCcceEEECCcEEEEECCCCceeecCCCCCcchHHHHHHHHHhhccCCCCCCCCccc
Q 041166 19 GAGSELVYHRLPWKE--P--DVPYLLEVFYEDDDLIALNKPSGLQVLPGGLFQQRTVLKQLQWRASKQSSSLSSQASHPV 94 (133)
Q Consensus 19 ~~g~~v~~~~~~~~~--~--~~~~~~~vlyed~~~lvvnKP~gl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~ 94 (133)
..||.+.+....... . +.+.++.|||||++++|||||+||+|||++.+...|+++++..++... ..+++
T Consensus 53 ~~gd~i~~~~~~~~~~~~~~~~~~~l~IlyED~~llVvnKP~Gl~vhp~~~~~~~tl~~~l~~~~~~~-------~~~~~ 125 (289)
T COG0564 53 KPGDVVRIPLPEEPEEEKLVPEDIPLDILYEDEDLLVVNKPAGLVVHPGGGHHEGTLVNALLRHCQDG-------VERPG 125 (289)
T ss_pred CCCCEEEEecccccccccccccCCCccEEEecCCEEEEECCCCCcCcCCCCCccHhHHHHHHHhcccc-------CCcee
Confidence 388999887644222 1 223347899999999999999999999998888899999998775432 46889
Q ss_pred ccccCCCCCceeeeeecChHHHHHHHHHHHcCCccc
Q 041166 95 PVHRLGRGTSGILLCAKTKLAKTCIAAYFADKTSVV 130 (133)
Q Consensus 95 ~vhRLDr~TSGlll~Ak~~~~~~~l~~~f~~~~v~~ 130 (133)
+||||||+|||+||||||..++..|+++|++|+|.+
T Consensus 126 ~vHRLDkdTSGlll~AK~~~a~~~l~~~f~~r~v~K 161 (289)
T COG0564 126 IVHRLDKDTSGLLLVAKNREAARELSEQFKQRKVKK 161 (289)
T ss_pred eeccCCCCCceEEEEECCHHHHHHHHHHHhcCcCcE
Confidence 999999999999999999999999999999998765
No 2
>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=5.2e-27 Score=180.50 Aligned_cols=105 Identities=27% Similarity=0.418 Sum_probs=88.4
Q ss_pred CCCCCcEEEEecCCCCCCCCCCCcceEEECCcEEEEECCCCceeecCCCCCcchHHHHHHHHHhhccCCCCCCCCccccc
Q 041166 17 LQGAGSELVYHRLPWKEPDVPYLLEVFYEDDDLIALNKPSGLQVLPGGLFQQRTVLKQLQWRASKQSSSLSSQASHPVPV 96 (133)
Q Consensus 17 ~~~~g~~v~~~~~~~~~~~~~~~~~vlyed~~~lvvnKP~gl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~v 96 (133)
....||.|.++....+++..+.+++|||||++|+|||||+|++|||+++....|+...+...+. ...+++|
T Consensus 16 ~l~~gd~i~~~~~~~~~~~~~~~~~Iiyed~~~lvvnKPaGl~~~~~~~~~~~t~~~~l~~~~~---------~~~~~~v 86 (246)
T cd02558 16 PYRPGTFVWYYRELPDEPPIPFEETILHQDEHLLVADKPHFLPVTPRGRYVTETLLVRLRRQTG---------NPDLTPA 86 (246)
T ss_pred eecCCCEEEEeCCCCCCCCCCCCcceEEecCCEEEEECCCCCccCCCCcchhhhHHHHHHHHhC---------CCccccc
Confidence 3569999998765444444455689999999999999999999999988777888888765432 3467799
Q ss_pred ccCCCCCceeeeeecChHHHHHHHHHHHcCCccc
Q 041166 97 HRLGRGTSGILLCAKTKLAKTCIAAYFADKTSVV 130 (133)
Q Consensus 97 hRLDr~TSGlll~Ak~~~~~~~l~~~f~~~~v~~ 130 (133)
||||++|||+||||||+++++.++++|++++|.+
T Consensus 87 hRLD~~TSGlll~Ak~~~~~~~l~~~~~~~~v~K 120 (246)
T cd02558 87 HRLDRLTAGLVLFSKRPETRGAYQTLFARREVSK 120 (246)
T ss_pred ccCCCCceeEEEEEcCHHHHHHHHHHHHcCCccE
Confidence 9999999999999999999999999999998875
No 3
>PRK11180 rluD 23S rRNA pseudouridine synthase D; Provisional
Probab=99.94 E-value=1.7e-26 Score=183.75 Aligned_cols=125 Identities=25% Similarity=0.299 Sum_probs=99.3
Q ss_pred ChHHHHHhhhCCCCCCCC------------------------CCCcEEEEecCCCCC---CCCCCCcceEEECCcEEEEE
Q 041166 1 LTLIEFYSTKHKNSAPLQ------------------------GAGSELVYHRLPWKE---PDVPYLLEVFYEDDDLIALN 53 (133)
Q Consensus 1 ~~l~~~~~~~~~~~~~~~------------------------~~g~~v~~~~~~~~~---~~~~~~~~vlyed~~~lvvn 53 (133)
.||++||.+.|...++.. .+||.|.+...+..+ .+...+++|||||++++|||
T Consensus 18 ~RLd~~L~~~~~~~Sr~~~~~lI~~G~V~VNg~~v~~~~~~v~~gD~I~v~~~~~~~~~~~~~~~~~~iiyed~~~lvvn 97 (325)
T PRK11180 18 QRLDQALAELFPDYSRSRIKEWILDQRVLVNGKVINKPKEKVLGGEQVAIDAEIEEEARFEPQDIPLDIVYEDDDILVIN 97 (325)
T ss_pred ccHHHHHHhhccccCHHHHHHHHHCCCEEECCEEccCCCcCcCCCCEEEEeeccccccCCCCCCCCCcEEEECCCEEEEE
Confidence 478999999887655551 278888887543221 12234689999999999999
Q ss_pred CCCCceeecCCCCCcchHHHHHHHHHhhccCCCCCCCCcccccccCCCCCceeeeeecChHHHHHHHHHHHcCCccc
Q 041166 54 KPSGLQVLPGGLFQQRTVLKQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTKLAKTCIAAYFADKTSVV 130 (133)
Q Consensus 54 KP~gl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~vhRLDr~TSGlll~Ak~~~~~~~l~~~f~~~~v~~ 130 (133)
||+||+|||+++....|+.+.+...+..... ..++++|||||++|||+||||||..++..|+++|++++|.+
T Consensus 98 KP~gl~~~~~~~~~~~tl~~~l~~~~~~~~~-----~~~~~~vhRLD~~TSGlll~Ak~~~~~~~l~~~~~~~~v~K 169 (325)
T PRK11180 98 KPRDLVVHPGAGNPDGTVLNALLHYYPPIAD-----VPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVEALQKREITR 169 (325)
T ss_pred CCCCCeEeCCCCCCCCcHHHHHHHHhhhccC-----CcccceeccCCCCCceeEEEECCHHHHHHHHHHHHhCCcce
Confidence 9999999998877677999888866543211 34678999999999999999999999999999999998865
No 4
>TIGR00005 rluA_subfam pseudouridine synthase, RluA family. modifies uracil-65 in transfer RNAs to pseudouridine.
Probab=99.94 E-value=3.9e-26 Score=179.31 Aligned_cols=124 Identities=31% Similarity=0.407 Sum_probs=97.8
Q ss_pred hHHHHHhhhCCCCCCCC------------------------CCCcEEEEecCCCCC---CCCCCCcceEEECCcEEEEEC
Q 041166 2 TLIEFYSTKHKNSAPLQ------------------------GAGSELVYHRLPWKE---PDVPYLLEVFYEDDDLIALNK 54 (133)
Q Consensus 2 ~l~~~~~~~~~~~~~~~------------------------~~g~~v~~~~~~~~~---~~~~~~~~vlyed~~~lvvnK 54 (133)
||++||...|...++.. .+||.|.+...+..+ +....+++|+|||++++||||
T Consensus 7 rLd~~L~~~~~~~Sr~~~~kli~~G~V~VNg~~~~~~~~~v~~gd~I~i~~~~~~~~~~~~~~~~~~i~~ed~~~lvvnK 86 (299)
T TIGR00005 7 RLDDFLASLLPDLSRSRIQKLIENGQVKVNGKVTANPKLKVKDGDRITVRVPEEEEHEVPPQDIPLDILFEDEDIIVINK 86 (299)
T ss_pred hHHHHHHHhcccCCHHHHHHHHHCCcEEECCEeccCcccCCCCCCEEEEecCCcccccCCccCCCccEEEeCCCEEEEEC
Confidence 78899998887555541 278888885433222 122235789999999999999
Q ss_pred CCCceeecCCCCCcchHHHHHHHHHhhccCCCCCCCCcccccccCCCCCceeeeeecChHHHHHHHHHHHcCCccc
Q 041166 55 PSGLQVLPGGLFQQRTVLKQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTKLAKTCIAAYFADKTSVV 130 (133)
Q Consensus 55 P~gl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~vhRLDr~TSGlll~Ak~~~~~~~l~~~f~~~~v~~ 130 (133)
|+|++||+.++....|+.+.+..++.... ....+++|||||++|||+||||||.++++.++++|++++|.+
T Consensus 87 P~g~~~~~~~~~~~~tl~~~l~~~~~~~~-----~~~~~~~vhRLD~~TSGlll~ak~~~~~~~l~~~~~~~~v~K 157 (299)
T TIGR00005 87 PSGLVVHPGGGNPFGTVLNALLAHCPPIA-----GVERVGIVHRLDRDTSGLMVVAKTPLALRELQRQLKNRTVTK 157 (299)
T ss_pred CCCCeEeCCCCCCcccHHHHHHHhccccc-----CCCcCceECCCCCCCceEEEEEcCHHHHHHHHHHHHhCCcce
Confidence 99999999887777889998876653211 135788999999999999999999999999999999998865
No 5
>PRK11025 23S rRNA pseudouridylate synthase C; Provisional
Probab=99.93 E-value=2.3e-25 Score=176.87 Aligned_cols=121 Identities=30% Similarity=0.339 Sum_probs=90.9
Q ss_pred ChHHHHHhhhCCCCCCCC-----------------------CCCcEEEEecCCCCC----CC-------CCCCcceEEEC
Q 041166 1 LTLIEFYSTKHKNSAPLQ-----------------------GAGSELVYHRLPWKE----PD-------VPYLLEVFYED 46 (133)
Q Consensus 1 ~~l~~~~~~~~~~~~~~~-----------------------~~g~~v~~~~~~~~~----~~-------~~~~~~vlyed 46 (133)
.||++||...+...++.. ..||.|.+......+ |. ...+++|||||
T Consensus 20 ~RLd~~L~~~~~~~sr~~i~~li~~G~V~VNg~~v~~~~~v~~GD~I~i~~~~~~~~~~~p~~~~~~~~~~~~~~Ilyed 99 (317)
T PRK11025 20 QRIDNFLRTQLKGVPKSMIYRILRKGEVRVNKKRIKPEYKLEAGDEVRIPPVRVAEREEEAVSPKLQKVAALADVILYED 99 (317)
T ss_pred chHHHHHHHhcccCCHHHHHHHHHcCCEEECCEEcCcccccCCCCEEEeCCCCccccccccccccccccccCcCCEEEEC
Confidence 378999998887655551 268888875322211 11 12356899999
Q ss_pred CcEEEEECCCCceeecCCCCCcchHHHHHHHHHhhccCCCCCCCCcccccccCCCCCceeeeeecChHHHHHHHHHHHcC
Q 041166 47 DDLIALNKPSGLQVLPGGLFQQRTVLKQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTKLAKTCIAAYFADK 126 (133)
Q Consensus 47 ~~~lvvnKP~gl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~vhRLDr~TSGlll~Ak~~~~~~~l~~~f~~~ 126 (133)
++++|||||+|++|||+.+.. .++.+.+...... ...+++|||||++|||+||||||..+++.|+++|+++
T Consensus 100 ~~~lvvnKP~gl~~~~~~~~~-~~~~~~~~~~~~~--------~~~~~~vhRLD~~TSGlll~Ak~~~a~~~l~~~~~~~ 170 (317)
T PRK11025 100 DHILVLNKPSGTAVHGGSGLS-FGVIEGLRALRPE--------ARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLREK 170 (317)
T ss_pred CCEEEEECCCCCcCcCCCCCC-ccHHHHHHHhccC--------CCcCceeCCCCCCCceEEEEEcCHHHHHHHHHHHHhC
Confidence 999999999999999987653 3556655543211 2346789999999999999999999999999999999
Q ss_pred Cccc
Q 041166 127 TSVV 130 (133)
Q Consensus 127 ~v~~ 130 (133)
+|.+
T Consensus 171 ~v~K 174 (317)
T PRK11025 171 GMQK 174 (317)
T ss_pred CccE
Confidence 8865
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=2.8e-25 Score=167.57 Aligned_cols=91 Identities=34% Similarity=0.485 Sum_probs=77.9
Q ss_pred CCCCCCC-CCcceEEECCcEEEEECCCCceeecCCCCCcchHHHHHHHHHhhccCCCCCCCCcccccccCCCCCceeeee
Q 041166 31 WKEPDVP-YLLEVFYEDDDLIALNKPSGLQVLPGGLFQQRTVLKQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLC 109 (133)
Q Consensus 31 ~~~~~~~-~~~~vlyed~~~lvvnKP~gl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~vhRLDr~TSGlll~ 109 (133)
.+||+.+ .+++|||||++++|||||+|++|++++.....|+.+.|...+. ...+++|||||++|||+|||
T Consensus 6 ~~~~~~~~~~~~iiyed~~~ivvnKP~Gl~~~~~~~~~~~sl~~~l~~~~~---------~~~~~~vhRLD~~TSGllll 76 (213)
T cd02557 6 RHEPPVTNDPIKIVHEDDDLLVVDKPSGIPVHPTGRYRYNTVTEILKSEYG---------LTELRPCHRLDRLTSGLLLF 76 (213)
T ss_pred ccCCCCCCCCCcEEEECCCEEEEECCCCCcCCCCCCCCcChHHHHHHHHcC---------CCCccCccCCCCCCceEEEE
Confidence 4555544 5899999999999999999999999877667788888875432 24678999999999999999
Q ss_pred ecChHHHHHHHHHHHcCCccc
Q 041166 110 AKTKLAKTCIAAYFADKTSVV 130 (133)
Q Consensus 110 Ak~~~~~~~l~~~f~~~~v~~ 130 (133)
|||+++++.|+++|++++|++
T Consensus 77 ak~~~~~~~l~~~f~~~~v~K 97 (213)
T cd02557 77 AKTSQTASRLQQQIRSREVKK 97 (213)
T ss_pred ECCHHHHHHHHHHHHcCCccE
Confidence 999999999999999998875
No 7
>PRK10158 23S rRNA/tRNA pseudouridine synthase A; Provisional
Probab=99.90 E-value=1.6e-23 Score=158.69 Aligned_cols=81 Identities=32% Similarity=0.554 Sum_probs=68.9
Q ss_pred CcceEEECCcEEEEECCCCceeecCCC-CCcchHHHHHHHHHhhccCCCCCCCCcccccccCCCCCceeeeeecChHHHH
Q 041166 39 LLEVFYEDDDLIALNKPSGLQVLPGGL-FQQRTVLKQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTKLAKT 117 (133)
Q Consensus 39 ~~~vlyed~~~lvvnKP~gl~v~~~~~-~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~vhRLDr~TSGlll~Ak~~~~~~ 117 (133)
.++|||||++|+|||||+|++||++.. ....++.+.+...+ ..+++|||||++||||||||||.++++
T Consensus 13 ~~~iiyed~~~lvvnKPaGl~~~~~~~~~~~~sl~~~l~~~~-----------~~~~~vhRLDr~TSGlll~Akt~~~~~ 81 (219)
T PRK10158 13 WLVILYQDEHIMVVNKPSGLLSVPGRLEEHKDSVMTRIQRDY-----------PQAESVHRLDMATSGVIVVALTKAAER 81 (219)
T ss_pred CCCEEEeCCCEEEEECCCCCcEeCCCCCccchhHHHHHHHhC-----------CCCCEECCCCCCCceEEEEECCHHHHH
Confidence 478999999999999999999998763 33457777665432 247799999999999999999999999
Q ss_pred HHHHHHHcCCccc
Q 041166 118 CIAAYFADKTSVV 130 (133)
Q Consensus 118 ~l~~~f~~~~v~~ 130 (133)
.|+++|++++|.+
T Consensus 82 ~l~~~f~~~~v~K 94 (219)
T PRK10158 82 ELKRQFREREPKK 94 (219)
T ss_pred HHHHHHHhCCccE
Confidence 9999999998865
No 8
>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=99.90 E-value=1.2e-23 Score=159.15 Aligned_cols=80 Identities=25% Similarity=0.357 Sum_probs=67.9
Q ss_pred cceEEECCcEEEEECCCCceeecCCCCCcchHHHHHHHHHhhccCCCCCCCCcccccccCCCCCceeeeeecChHHHHHH
Q 041166 40 LEVFYEDDDLIALNKPSGLQVLPGGLFQQRTVLKQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTKLAKTCI 119 (133)
Q Consensus 40 ~~vlyed~~~lvvnKP~gl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~vhRLDr~TSGlll~Ak~~~~~~~l 119 (133)
++|||||++++|||||+||+||++.. ..++...+..... ...+++|||||++|||+||||||+++++.|
T Consensus 2 ~~ilyed~~~lvvnKP~Gl~v~~~~~--~~~l~~~l~~~~~---------~~~~~~VhRLDr~TSGlll~Ak~~~~~~~L 70 (217)
T TIGR01621 2 FEILFTHPDFLLINKHPGISVHKDDG--ETGLLQEVATQLG---------VGQVWLVHRLDKMTSGILLLALNAESASEL 70 (217)
T ss_pred ceEEEeCCCEEEEECCCCCeECCCCC--cChHHHHHHHhcC---------CCCccEecCCCCCCceEEEEEcCHHHHHHH
Confidence 57999999999999999999998764 2466666653321 346889999999999999999999999999
Q ss_pred HHHHHcCCccc
Q 041166 120 AAYFADKTSVV 130 (133)
Q Consensus 120 ~~~f~~~~v~~ 130 (133)
+++|++++|.+
T Consensus 71 ~~~~~~~~v~K 81 (217)
T TIGR01621 71 SQGFAKRKIEK 81 (217)
T ss_pred HHHHhcCCccE
Confidence 99999999875
No 9
>PRK11112 tRNA pseudouridine synthase C; Provisional
Probab=99.90 E-value=1.7e-23 Score=161.88 Aligned_cols=81 Identities=33% Similarity=0.465 Sum_probs=65.8
Q ss_pred cceEEECCcEEEEECCCCceeecCCCCCcch--HHHHHHHHHhhccCCCCCCCCcccccccCCCCCceeeeeecChHHHH
Q 041166 40 LEVFYEDDDLIALNKPSGLQVLPGGLFQQRT--VLKQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTKLAKT 117 (133)
Q Consensus 40 ~~vlyed~~~lvvnKP~gl~v~~~~~~~~~t--l~~~l~~~~~~~~~~~~~~~~~~~~vhRLDr~TSGlll~Ak~~~~~~ 117 (133)
++|||||++|+|||||+||+||++......+ +...+...+ ...+++|||||++||||||||||.++++
T Consensus 2 l~IlyEd~~~lvvnKPaGl~~~~~~~~~~~~~~~~~~l~~~~----------~~~~~~VHRLDr~TSGlll~Ak~~~~~~ 71 (257)
T PRK11112 2 LEILYQDEWLVAVNKPAGWLVHRSWLDRHETVFVMQTVRDQI----------GQHVFTAHRLDRPTSGVLLMALSSEVAR 71 (257)
T ss_pred CcEEEecCCEEEEECCCCCeecCCCCCCCchHHHHHHHHHHh----------CCCceeeccCCCCCeeEEEEECCHHHHH
Confidence 5799999999999999999999875443333 223332221 2357799999999999999999999999
Q ss_pred HHHHHHHcCCccc
Q 041166 118 CIAAYFADKTSVV 130 (133)
Q Consensus 118 ~l~~~f~~~~v~~ 130 (133)
.|+++|++++|.+
T Consensus 72 ~L~~~f~~~~v~K 84 (257)
T PRK11112 72 LLAQQFEQHQIQK 84 (257)
T ss_pred HHHHHHHhCCcce
Confidence 9999999999875
No 10
>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=2.1e-23 Score=158.23 Aligned_cols=81 Identities=38% Similarity=0.566 Sum_probs=65.6
Q ss_pred cceEEECCcEEEEECCCCceeecCCCCCcch--HHHHHHHHHhhccCCCCCCCCcccccccCCCCCceeeeeecChHHHH
Q 041166 40 LEVFYEDDDLIALNKPSGLQVLPGGLFQQRT--VLKQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTKLAKT 117 (133)
Q Consensus 40 ~~vlyed~~~lvvnKP~gl~v~~~~~~~~~t--l~~~l~~~~~~~~~~~~~~~~~~~~vhRLDr~TSGlll~Ak~~~~~~ 117 (133)
++|||||++++|||||+|++|||+++....+ +...+...+ ...+++|||||++||||||||||+++++
T Consensus 1 ~~Ilyed~~~lvvnKP~G~~~~~~~~~~~~~~~~~~~l~~~~----------~~~~~~vhRLD~~TSGlll~Ak~~~~~~ 70 (223)
T cd02563 1 LEILYQDEHLVAINKPSGLLVHRSELDRHETRFALQTLRDQL----------GQHVYPVHRLDRPTSGVLLFALSSEVAR 70 (223)
T ss_pred CcEEEecCCEEEEECCCCCeEcCCCCCCCCcHHHHHHHHHHc----------CCCcccccCCCCCCeEEEEEEECHHHHH
Confidence 4699999999999999999999886443322 223332221 2467899999999999999999999999
Q ss_pred HHHHHHHcCCccc
Q 041166 118 CIAAYFADKTSVV 130 (133)
Q Consensus 118 ~l~~~f~~~~v~~ 130 (133)
.|+++|++++|.+
T Consensus 71 ~l~~~f~~~~v~K 83 (223)
T cd02563 71 KLGEQFTEHRVHK 83 (223)
T ss_pred HHHHHHhcCceeE
Confidence 9999999998865
No 11
>KOG1919 consensus RNA pseudouridylate synthases [RNA processing and modification]
Probab=99.88 E-value=1.2e-22 Score=163.73 Aligned_cols=119 Identities=27% Similarity=0.379 Sum_probs=98.7
Q ss_pred HHHHHhhhCCCCCCC-----------------------CCCCcEEEEecCCCCCCCCCCCcceEEECCcEEEEECCCCce
Q 041166 3 LIEFYSTKHKNSAPL-----------------------QGAGSELVYHRLPWKEPDVPYLLEVFYEDDDLIALNKPSGLQ 59 (133)
Q Consensus 3 l~~~~~~~~~~~~~~-----------------------~~~g~~v~~~~~~~~~~~~~~~~~vlyed~~~lvvnKP~gl~ 59 (133)
+.+++..+|....++ .+.||.+....+.++.+....++.|+|||++++|||||+|++
T Consensus 46 ~~~~~~~ef~~~~~~~~~~~i~~g~v~~n~~~~~v~~i~k~~d~l~~~vhrh~p~~~~~~~~Iv~ed~~~vVvnKP~gip 125 (371)
T KOG1919|consen 46 LVDVFVSEFRLRERAYYESAIKLGRVTVNGEQVRVSLIVKNGDVLCHTVHRHEPPVAYLPIRIVFEDKDYVVVNKPHGIP 125 (371)
T ss_pred hHHHHHHHHhcCchHhhhhhhhcCceEECcEeeeeEEEeccCCEEEEeeccCCCCccccccceEEecCCEEEEeCCCCCc
Confidence 567777777777655 247888876544444455556899999999999999999999
Q ss_pred eecCCCCCcchHHHHHHHHHhhccCCCCCCCCcccccccCCCCCceeeeeecChHHHHHHHHHHHcCCccc
Q 041166 60 VLPGGLFQQRTVLKQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTKLAKTCIAAYFADKTSVV 130 (133)
Q Consensus 60 v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~vhRLDr~TSGlll~Ak~~~~~~~l~~~f~~~~v~~ 130 (133)
|||++.+..+++...+..... ...+++|||||+.|||+|+|||+++++..++++|+++++.+
T Consensus 126 Vhp~g~~~~n~i~~~l~~~~~---------~~~~~~~hRLDr~tSGllvlAkt~~~~~~~~~~~r~~~~~k 187 (371)
T KOG1919|consen 126 VHPTGRYRENTITKILAALHK---------VEGLRPCHRLDRLTSGLLVLAKTKEAADKFHEVLRKRTVKK 187 (371)
T ss_pred eeccCccccccchHHHHHhcc---------ccccccccccCccccceEEEEechhHhHHHHHHHhccccee
Confidence 999999999999888876521 56788999999999999999999999999999999997764
No 12
>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=99.81 E-value=3.9e-20 Score=132.91 Aligned_cols=78 Identities=32% Similarity=0.456 Sum_probs=57.7
Q ss_pred cEEEEECCCCceeecCCCCCcchHHHHHHHHHhhccCCCCCCCCcccccccCCCCCceeeeeecChHHHHHHHHHHHcCC
Q 041166 48 DLIALNKPSGLQVLPGGLFQQRTVLKQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTKLAKTCIAAYFADKT 127 (133)
Q Consensus 48 ~~lvvnKP~gl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~vhRLDr~TSGlll~Ak~~~~~~~l~~~f~~~~ 127 (133)
+|+|||||+||+|++.+.................... ..++++|||||++||||||||+|.++++.|+++|++++
T Consensus 1 ~~ivvnKP~G~~~~~~~~~~~~~~~~~~~~~~~~~~~-----~~~~~~v~RLD~~TsGlll~a~~~~~~~~l~~~f~~~~ 75 (164)
T PF00849_consen 1 NLIVVNKPAGVPVHPSDGNESKSVKELPALSLKRGDD-----PPELYPVHRLDRDTSGLLLFAKDKEAAAKLSKQFPKRK 75 (164)
T ss_dssp SEEEEEE-TTSBSSSSSTBSSSSHHCHHHHHHHHCTT-----SGGGEESS---TT-EEEEEEESSHHHHHHHHHHHHTTC
T ss_pred CEEEEECCCCCeEecCCCCCcccccchhhhhhhhccC-----CCceEECCCCCccccCCeeccCCcccccccccccccCC
Confidence 6899999999999998854444444444433333222 67899999999999999999999999999999999998
Q ss_pred ccc
Q 041166 128 SVV 130 (133)
Q Consensus 128 v~~ 130 (133)
+.+
T Consensus 76 ~~K 78 (164)
T PF00849_consen 76 VEK 78 (164)
T ss_dssp SEE
T ss_pred CcE
Confidence 765
No 13
>cd02550 PseudoU_synth_Rsu_Rlu_like PseudoU_synth_Rsu_Rlu: Pseudouridine synthase, Rsu/Rlu family. This group is comprised of eukaryotic, bacterial and archeal proteins similar to eight site specific Escherichia coli pseudouridine synthases: RsuA, RluA, RluB, RluC, RluD, RluE, RluF and TruA. Pseudouridine synthases catalyze the isomerization of specific uridines in a n RNA molecule to pseudouridines (5-ribosyluracil, psi) requiring no cofactors. E. coli RluC for example makes psi955, 2504 and 2580 in 23S RNA. Some psi sites such as psi1917 in 23S RNA made by RluD are universally conserved. Other psi sites occur in a more restricted fashion, for example psi2819 in 21S mitochondrial ribosomal RNA made by S. cerevisiae Pus5p is only found in mitochondrial large subunit rRNAs from some other species and in gram negative bacteria. The E. coli counterpart of this psi residue is psi2580 in 23S rRNA. psi2604in 23S RNA made by RluF has only been detected in E.coli.
Probab=99.79 E-value=1.6e-19 Score=129.79 Aligned_cols=69 Identities=26% Similarity=0.315 Sum_probs=57.4
Q ss_pred EEEEECCCCceeecCCCCCcchHHHHHHHHHhhccCCCCCCCCcccccccCCCCCceeeeeecChHHHHHHHHHHHcCCc
Q 041166 49 LIALNKPSGLQVLPGGLFQQRTVLKQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTKLAKTCIAAYFADKTS 128 (133)
Q Consensus 49 ~lvvnKP~gl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~vhRLDr~TSGlll~Ak~~~~~~~l~~~f~~~~v 128 (133)
++|+|||+|++||++.+....++...+.... ..++++|||||++|||+||||+|+++++.|+++ ++++
T Consensus 1 ~ivvnKP~G~~~~~~~~~~~~~~~~~l~~~~----------~~~~~~vhRLD~~TSGlll~ak~~~~~~~l~~~--~~~v 68 (154)
T cd02550 1 ILVLNKPSGLVCHPTDRDRDPTVVVRLDKLH----------GPRVHAAGRLDKDTSGLLLLTNDGRLQRRLTEP--RREI 68 (154)
T ss_pred CEEEECCCCCEEecCCCCCCCcHHHhhhccc----------CCceeEeccCCCCCeeEEEEEcCHHHHHHHhhh--hccC
Confidence 5899999999999988776678777654221 356889999999999999999999999999998 5555
Q ss_pred c
Q 041166 129 V 129 (133)
Q Consensus 129 ~ 129 (133)
.
T Consensus 69 ~ 69 (154)
T cd02550 69 E 69 (154)
T ss_pred c
Confidence 4
No 14
>PRK10839 16S rRNA pseudouridylate synthase A; Provisional
Probab=99.79 E-value=7.7e-20 Score=139.29 Aligned_cols=73 Identities=22% Similarity=0.159 Sum_probs=55.0
Q ss_pred ECCcEEEEECCCCceeecCCCCCcchHHHHHHHHHhhccCCCCCCCCcccccccCCCCCceeeeeecChHHHHHHHHHHH
Q 041166 45 EDDDLIALNKPSGLQVLPGGLFQQRTVLKQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTKLAKTCIAAYFA 124 (133)
Q Consensus 45 ed~~~lvvnKP~gl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~vhRLDr~TSGlll~Ak~~~~~~~l~~~f~ 124 (133)
++++++|||||+||+|||+... ..|+...+... ...++++|||||++||||||||||..+++.|.. .
T Consensus 58 ~~~~~lvvnKP~G~~~~~~~~~-~~tl~~~l~~~----------~~~~~~~v~RLD~~TSGlll~ak~~~~~~~l~~--~ 124 (232)
T PRK10839 58 HGPRYFMLNKPQGYVCSTDDPD-HPTVLYFLDEP----------VAYKLHAAGRLDIDTTGLVLMTDDGQWSHRITS--P 124 (232)
T ss_pred CCCEEEEEECCCCeEecccCCC-CCeEEEecccc----------cccCceecCCCCCCceeEEEEecCHHHHHHHhC--C
Confidence 3568999999999999987543 35655443211 034678999999999999999999999988885 4
Q ss_pred cCCccc
Q 041166 125 DKTSVV 130 (133)
Q Consensus 125 ~~~v~~ 130 (133)
++.|.+
T Consensus 125 ~~~i~K 130 (232)
T PRK10839 125 RHHCEK 130 (232)
T ss_pred CCCCCe
Confidence 555543
No 15
>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=99.76 E-value=2.2e-18 Score=125.92 Aligned_cols=77 Identities=34% Similarity=0.433 Sum_probs=63.4
Q ss_pred EEEEECCCCceeecCCCCCcchHHHHHHHHHhhccCCCCCCCCcccccccCCCCCceeeeeecChHHHHHHHHHHHcCCc
Q 041166 49 LIALNKPSGLQVLPGGLFQQRTVLKQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTKLAKTCIAAYFADKTS 128 (133)
Q Consensus 49 ~lvvnKP~gl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~vhRLDr~TSGlll~Ak~~~~~~~l~~~f~~~~v 128 (133)
++|+|||+|++|++.......++...+........ ....+++|||||++|||+||||+++++++.|.++|+++.+
T Consensus 1 ~lvvnKP~g~~~~~~~~~~~~~~~~~~~~~~~~~~-----~~~~~~~v~RLD~~tsGlll~ak~~~~~~~l~~~~~~~~~ 75 (185)
T cd02869 1 LLVVNKPAGLPVHPGPGHLTGTLVNALLKLLLLLG-----EEFRPGLVHRLDKDTSGLLLVAKNKKAAAKLSKQFKERKV 75 (185)
T ss_pred CEEEECCCCCeeecCCCCCCCCHHHHHHHHHhhcC-----CCCcCceecccCCCCceEEEEEcCHHHHHHHHHHHhcCce
Confidence 58999999999999888777788777632222211 1467889999999999999999999999999999999887
Q ss_pred cc
Q 041166 129 VV 130 (133)
Q Consensus 129 ~~ 130 (133)
.+
T Consensus 76 ~K 77 (185)
T cd02869 76 KK 77 (185)
T ss_pred eE
Confidence 64
No 16
>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=99.73 E-value=4.5e-18 Score=123.98 Aligned_cols=71 Identities=20% Similarity=0.185 Sum_probs=57.6
Q ss_pred cEEEEECCCCceeecCCCCCcchHHHHHHHHHhhccCCCCCCCCcccccccCCCCCceeeeeecChHHHHHHHHHHHcCC
Q 041166 48 DLIALNKPSGLQVLPGGLFQQRTVLKQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTKLAKTCIAAYFADKT 127 (133)
Q Consensus 48 ~~lvvnKP~gl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~vhRLDr~TSGlll~Ak~~~~~~~l~~~f~~~~ 127 (133)
.++|+|||+|++||+.......|+.+.+..+. ..++++|||||++|||+||||+|.++++.|.. .+++
T Consensus 1 ~~lvvnKP~G~~~~~~~~~~~~tl~~~l~~~~----------~~~~~~V~RLD~~TsGLll~ak~~~~~~~L~~--~~~~ 68 (167)
T cd02556 1 RVLIYHKPEGLICTRKDPKGRPTVFDLLPKLG----------IPRWISVGRLDLNTEGLLLFTNDGELANRLMH--PSNE 68 (167)
T ss_pred CEEEEECCCCcEECccCCCCCccHHHhhhhhc----------cCceEEcCcCCCCCeeEEEEECCHHHHHHHhC--CcCC
Confidence 37899999999999866555678888776431 34678999999999999999999999999974 5666
Q ss_pred ccc
Q 041166 128 SVV 130 (133)
Q Consensus 128 v~~ 130 (133)
|.+
T Consensus 69 i~K 71 (167)
T cd02556 69 IER 71 (167)
T ss_pred CCe
Confidence 653
No 17
>cd02870 PseudoU_synth_RsuA_like Pseudouridine synthases are responsible for the synthesis of pseudouridine from uracil in ribosomal RNA. The RsuA subfamily includes Pseudouridine Synthase similar to Ribosomal small subunit pseudouridine 516 synthase. Most of the proteins in this family are bacterial proteins.
Probab=99.73 E-value=1.4e-18 Score=123.83 Aligned_cols=68 Identities=25% Similarity=0.235 Sum_probs=54.0
Q ss_pred EEEEECCCCceeecCCCCCcchHHHHHHHHHhhccCCCCCCCCcccccccCCCCCceeeeeecChHHHHHHHHHHHcCCc
Q 041166 49 LIALNKPSGLQVLPGGLFQQRTVLKQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTKLAKTCIAAYFADKTS 128 (133)
Q Consensus 49 ~lvvnKP~gl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~vhRLDr~TSGlll~Ak~~~~~~~l~~~f~~~~v 128 (133)
|+|+|||+|++|++.......++.+.+... ..++++|||||++|||+||||+|.++++.|.. +++.|
T Consensus 1 ~ivvnKP~G~~~~~~~~~~~~~l~~~l~~~-----------~~~~~~vhRLD~~TsGlll~ak~~~~~~~l~~--~~~~i 67 (146)
T cd02870 1 YLLLNKPRGVVSTVRDPEGRPTVLDLLKDV-----------GERLFPVGRLDYDTEGLLLLTNDGELANRLTH--PRYGV 67 (146)
T ss_pred CEEEECCCCcEecccCCCCCCEEeeecccc-----------CCCEEECCCCCCCCeeEEEEeCCHHHHHHhhC--ccCCC
Confidence 589999999999987765556776554311 35688999999999999999999999999976 34444
Q ss_pred c
Q 041166 129 V 129 (133)
Q Consensus 129 ~ 129 (133)
.
T Consensus 68 ~ 68 (146)
T cd02870 68 E 68 (146)
T ss_pred C
Confidence 4
No 18
>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=99.72 E-value=8.8e-18 Score=122.51 Aligned_cols=69 Identities=25% Similarity=0.332 Sum_probs=55.1
Q ss_pred EEEEECCCCceeecCCCCCcchHHHHHHHHHhhccCCCCCCCCcccccccCCCCCceeeeeecChHHHHHHHHHHHcCCc
Q 041166 49 LIALNKPSGLQVLPGGLFQQRTVLKQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTKLAKTCIAAYFADKTS 128 (133)
Q Consensus 49 ~lvvnKP~gl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~vhRLDr~TSGlll~Ak~~~~~~~l~~~f~~~~v 128 (133)
|+|+|||+|++||++. ....|+.+.+..++. ..++++|||||++|||+||||||.++++.+.. ++++|
T Consensus 2 ~ivvnKP~G~~~~~~~-~~~~tl~~~l~~~~~---------~~~~~~vhRLD~~TSGlll~ak~~~~~~~l~~--~~~~i 69 (167)
T cd02553 2 YLMLNKPAGVVCATKD-PHHPTVIDLLPEPDR---------RRDLFPVGRLDKDTTGLLLLTNDGQLAHRLTS--PKKHV 69 (167)
T ss_pred EEEEECCCCCEeCCCC-CCCCcHHHHhhhhcc---------cCCeEEcccCCCCCEEEEEEEeCHHHHHHhhC--CcCCC
Confidence 7999999999999654 446788888875532 35688999999999999999999998887765 34555
Q ss_pred c
Q 041166 129 V 129 (133)
Q Consensus 129 ~ 129 (133)
.
T Consensus 70 ~ 70 (167)
T cd02553 70 P 70 (167)
T ss_pred c
Confidence 4
No 19
>PRK10475 23S rRNA pseudouridine synthase F; Provisional
Probab=99.71 E-value=2e-17 Score=130.19 Aligned_cols=65 Identities=23% Similarity=0.302 Sum_probs=54.9
Q ss_pred EECCcEEEEECCCCceeecCCCCCcchHHHHHHHHHhhccCCCCCCCCcccccccCCCCCceeeeeecChHHHHHHHH
Q 041166 44 YEDDDLIALNKPSGLQVLPGGLFQQRTVLKQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTKLAKTCIAA 121 (133)
Q Consensus 44 yed~~~lvvnKP~gl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~vhRLDr~TSGlll~Ak~~~~~~~l~~ 121 (133)
+||++++|+|||+|++||++... ..|+.+.+.. ..++++|||||++||||||||+|.++++.|..
T Consensus 64 ~ed~~~lvlnKP~G~~~~~~~~~-~~tv~~~l~~------------~~~l~~VgRLDrdTsGLLLlT~dg~~~~~L~~ 128 (290)
T PRK10475 64 AEDLVLIALNKPVGIVSTTEDGE-RDNIVDFVNH------------SKRVFPIGRLDKDSQGLIFLTNHGDLVNKILR 128 (290)
T ss_pred cCCCeEEEEECCCCCCcCCCCCC-CCcHHHHhhc------------cccccccccCCCCCcceEEEecCHHHHHHhhC
Confidence 47889999999999999977653 5688777742 13578999999999999999999999999866
No 20
>PRK10700 23S rRNA pseudouridylate synthase B; Provisional
Probab=99.69 E-value=8.2e-17 Score=126.64 Aligned_cols=73 Identities=19% Similarity=0.169 Sum_probs=59.0
Q ss_pred ECCcEEEEECCCCceeecCCCCCcchHHHHHHHHHhhccCCCCCCCCcccccccCCCCCceeeeeecChHHHHHHHHHHH
Q 041166 45 EDDDLIALNKPSGLQVLPGGLFQQRTVLKQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTKLAKTCIAAYFA 124 (133)
Q Consensus 45 ed~~~lvvnKP~gl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~vhRLDr~TSGlll~Ak~~~~~~~l~~~f~ 124 (133)
||+.|+++|||+|++|++.......|+.+.+.... ..++++|||||++||||||||++.++++.|.. .
T Consensus 65 e~~~ylvlnKP~G~~~s~~d~~~~~tv~d~l~~~~----------~~~~~~VgRLD~dTsGLLLlTndg~~~~~L~~--p 132 (289)
T PRK10700 65 QICRVLAYYKPEGELCTRNDPEGRPTVFDRLPKLR----------GARWIAVGRLDVNTCGLLLFTTDGELANRLMH--P 132 (289)
T ss_pred cCCeEEEEECCCCCEeecCCCCCCccHHHHhhhhc----------CCceeEccCCCCCCceEEEEEcCHHHHHHHhC--c
Confidence 44679999999999999886555679988886421 34678999999999999999999999999975 4
Q ss_pred cCCcc
Q 041166 125 DKTSV 129 (133)
Q Consensus 125 ~~~v~ 129 (133)
++.|.
T Consensus 133 ~~~i~ 137 (289)
T PRK10700 133 SREVE 137 (289)
T ss_pred cCCCC
Confidence 55544
No 21
>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=99.66 E-value=1.4e-16 Score=116.29 Aligned_cols=61 Identities=23% Similarity=0.259 Sum_probs=48.8
Q ss_pred EEEEECCCCceeecCCC-CCcchHHHHHHHHHhhccCCCCCCCCcccccccCCCCCceeeeeecChHHHHHHHHH
Q 041166 49 LIALNKPSGLQVLPGGL-FQQRTVLKQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTKLAKTCIAAY 122 (133)
Q Consensus 49 ~lvvnKP~gl~v~~~~~-~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~vhRLDr~TSGlll~Ak~~~~~~~l~~~ 122 (133)
++|+|||+|++||++.. ....|+.+.+. ..++++|||||++|||+||||+|+++++.|...
T Consensus 1 ~lv~nKP~G~~~~~~~~~~~~~~l~~~l~-------------~~~~~~v~RLD~~TsGlll~a~d~~~~~~l~~~ 62 (168)
T cd02566 1 LILFNKPYGVLSQFTDESEKHKTLKDYID-------------DPGVYAAGRLDRDSEGLLLLTDDGRLQHRITDP 62 (168)
T ss_pred CEEEECCCCCEEecCCCcCCCccHHHHcC-------------cCCeEEccCCCCCCeEEEEEEeCHHHHHHHHCC
Confidence 58999999999998764 34467766552 135679999999999999999999887777664
No 22
>PRK11394 23S rRNA pseudouridine synthase E; Provisional
Probab=99.57 E-value=4.4e-15 Score=112.58 Aligned_cols=68 Identities=16% Similarity=0.180 Sum_probs=54.8
Q ss_pred CcEEEEECCCCceeecCCCCCcchHHHHHHHHHhhccCCCCCCCCcccccccCCCCCceeeeeecChHHHHHHHHHHHcC
Q 041166 47 DDLIALNKPSGLQVLPGGLFQQRTVLKQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTKLAKTCIAAYFADK 126 (133)
Q Consensus 47 ~~~lvvnKP~gl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~vhRLDr~TSGlll~Ak~~~~~~~l~~~f~~~ 126 (133)
..|+++|||+|++|+........++.+.+. ..++++|||||++|||+||||+|.++++.|... ++
T Consensus 39 ~~ylllnKP~G~l~~~~d~~~~~tl~d~l~-------------~~~~~~vgRLD~~TsGllLlt~d~~~~~~L~~~--~~ 103 (217)
T PRK11394 39 TRVILFNKPYDVLPQFTDEAGRKTLKEFIP-------------VQGVYAAGRLDRDSEGLLVLTNNGALQARLTQP--GK 103 (217)
T ss_pred CEEEEEECCCCCEEeeCCccCCcchHHhcc-------------cCCeEEecCCCCCCeeEEEEECCHHHHHHHhCc--cc
Confidence 458999999999999655544567777653 236789999999999999999999999999985 44
Q ss_pred Ccc
Q 041166 127 TSV 129 (133)
Q Consensus 127 ~v~ 129 (133)
.|.
T Consensus 104 ~i~ 106 (217)
T PRK11394 104 RTG 106 (217)
T ss_pred CCC
Confidence 443
No 23
>cd02555 PSSA_1 PSSA_1: Pseudouridine synthase, a subgroup of the RsuA family. This group is comprised of bacterial proteins assigned to the RsuA family of pseudouridine synthases. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. The TruA family is comprised of proteins related to Escherichia coli RsuA.
Probab=99.53 E-value=1.7e-14 Score=106.29 Aligned_cols=70 Identities=16% Similarity=0.158 Sum_probs=50.1
Q ss_pred CcEEEEECCCCceeecCC--------CCCcchHHHHHHHHHhhccCCCCCCCCcccccccCCCCCceeeeeecChHHHHH
Q 041166 47 DDLIALNKPSGLQVLPGG--------LFQQRTVLKQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTKLAKTC 118 (133)
Q Consensus 47 ~~~lvvnKP~gl~v~~~~--------~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~vhRLDr~TSGlll~Ak~~~~~~~ 118 (133)
.-++++|||+|++|.... .....++...+... ..++++|||||++||||||||+|+++++.
T Consensus 4 ~~y~llnKP~G~l~s~~d~~~~~g~~~~~~~~~~~~l~~~-----------~~~l~~VgRLD~dTsGLLl~t~d~~~~~~ 72 (177)
T cd02555 4 PVTLLLHKPAGMVSEQALALLGPGQRSAADRSGRRPLKGH-----------FARLAPIGPLDKDASGLLVFSQDGRVLRK 72 (177)
T ss_pred cEEEEEECCCceEecCCCcccccccccccccchhhhhhhc-----------CCceeEecCCCCCCeeEEEEECCHHHHHH
Confidence 347899999999986433 11112333333322 23688999999999999999999999999
Q ss_pred HHHHHHcCCcc
Q 041166 119 IAAYFADKTSV 129 (133)
Q Consensus 119 l~~~f~~~~v~ 129 (133)
|.... +.|.
T Consensus 73 L~~~~--~~i~ 81 (177)
T cd02555 73 LIGDA--SRLE 81 (177)
T ss_pred HhChh--cCCC
Confidence 99853 4444
No 24
>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=99.48 E-value=7.9e-14 Score=101.68 Aligned_cols=63 Identities=19% Similarity=0.266 Sum_probs=51.7
Q ss_pred EEEEECCCCceeecCCCCCcchHHHHHHHHHhhccCCCCCCCCcccccccCCCCCceeeeeecChHHHHHHHHHHH
Q 041166 49 LIALNKPSGLQVLPGGLFQQRTVLKQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTKLAKTCIAAYFA 124 (133)
Q Consensus 49 ~lvvnKP~gl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~vhRLDr~TSGlll~Ak~~~~~~~l~~~f~ 124 (133)
|+++|||+|++|+++.. ...|+.+.+.. ..++++|||||++|||+||||+|.++++.|.....
T Consensus 2 y~~lnKP~G~l~s~~~~-~~~tv~~~l~~------------~~~~~~vgRLD~~tsGlll~t~dg~~~~~L~~p~~ 64 (164)
T cd02554 2 YIAYNKPVGIDCTLERA-DEDNIIDFVNP------------PPRIFPIGRLDKDSEGLILLTNDGDLVNKILHADN 64 (164)
T ss_pred EEEEECCCCcEeecCCC-CCCcHHHHhcC------------cCCEEEccCCCCCCeeEEEEEcCHHHHHHHhhhhc
Confidence 68999999999998754 34677766531 24688999999999999999999999999976443
No 25
>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=99.32 E-value=2.5e-12 Score=98.10 Aligned_cols=66 Identities=23% Similarity=0.201 Sum_probs=48.5
Q ss_pred cEEEEECCCCceeecCCCCCcchHHHHHHHHHhhccCCCCCCCCcccccccCCCCCceeeeeecChHHHHHHHHHHHcCC
Q 041166 48 DLIALNKPSGLQVLPGGLFQQRTVLKQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTKLAKTCIAAYFADKT 127 (133)
Q Consensus 48 ~~lvvnKP~gl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~vhRLDr~TSGlll~Ak~~~~~~~l~~~f~~~~ 127 (133)
.++|||||+||.+++.. +++...+...++. ....++|||||+.|||+|+||++..+ ++.++|.++.
T Consensus 1 GilvvnKP~Gi~s~~~~----~~~~~~l~~~~~~--------~k~~~~vhrLD~~aSGvl~~a~~~~t--kl~~~~~~~~ 66 (226)
T cd02868 1 GLFAVYKPPGVHWKHVR----DTIESNLLKYFPE--------DKVLVGVHRLDAFSSGVLVLGVNHGN--KLLSHLYSNH 66 (226)
T ss_pred CEEEEEcCCCCChhHHH----HHHHHHHHHHccc--------cceeeEccccCCCCceEEEEEeChhH--hHHHHHHhcC
Confidence 47999999999876432 3444434333321 22366789999999999999999987 6999998864
No 26
>COG1187 RsuA 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]
Probab=99.20 E-value=9.5e-12 Score=95.97 Aligned_cols=111 Identities=20% Similarity=0.136 Sum_probs=72.3
Q ss_pred hHHHHHhhhCCCCCCCCC---CCcEEEEecCCCCCC------CC----CCCcceEE-ECCcEEEEECCCCceeecCCCCC
Q 041166 2 TLIEFYSTKHKNSAPLQG---AGSELVYHRLPWKEP------DV----PYLLEVFY-EDDDLIALNKPSGLQVLPGGLFQ 67 (133)
Q Consensus 2 ~l~~~~~~~~~~~~~~~~---~g~~v~~~~~~~~~~------~~----~~~~~vly-ed~~~lvvnKP~gl~v~~~~~~~ 67 (133)
||.+||+..--.|.+... .+..|.++......+ .. ...-.+.+ +..-|+++|||.|+.|.......
T Consensus 4 RL~K~La~~G~~SRr~ae~lI~~G~V~VnG~v~~~~~~~v~~~~~~i~v~g~~~~~~~~~~y~llnKP~G~v~s~~D~~g 83 (248)
T COG1187 4 RLNKFLAEAGVGSRREAEKLIEEGRVTVNGKVATLGGVVVDPDDDVVEVDGKRIELKEERVYLLLNKPRGYVSSTEDDEG 83 (248)
T ss_pred chHHHHHHcCCCCHHHHHHHHHcCCEEECCEEeccCCeEeCCCCcEEEECCEEeeccccceEEEEECCCCeEecccCCCC
Confidence 788999887766666632 222222222111111 10 01122444 34449999999999998664445
Q ss_pred cchHHHHHHHHHhhccCCCCCCCCcccccccCCCCCceeeeeecChHHHHHHH
Q 041166 68 QRTVLKQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTKLAKTCIA 120 (133)
Q Consensus 68 ~~tl~~~l~~~~~~~~~~~~~~~~~~~~vhRLDr~TSGlll~Ak~~~~~~~l~ 120 (133)
..|+.+.+....+ ...++++|.|||++|+|+||++.+++.++.|.
T Consensus 84 r~tv~D~lp~~~~--------~~~~~~pvGRLD~dTeGLLLLTnDG~la~rL~ 128 (248)
T COG1187 84 RPTVFDLLPERLP--------RKKRLFPVGRLDKDTEGLLLLTNDGELAHRLM 128 (248)
T ss_pred Cceeeeecccccc--------cccceeeccccCCCCeeEEEEeCCHHHHHHhc
Confidence 6788877763311 15679999999999999999999999888763
No 27
>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=97.83 E-value=5.1e-05 Score=56.29 Aligned_cols=59 Identities=20% Similarity=0.180 Sum_probs=45.2
Q ss_pred CcEEEEECCCCceeecCCCCCcchHHHHHHHHHhhccCCCCCCCCcccccccCCCCCceeeeeecChHHHHHHHHHHH
Q 041166 47 DDLIALNKPSGLQVLPGGLFQQRTVLKQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTKLAKTCIAAYFA 124 (133)
Q Consensus 47 ~~~lvvnKP~gl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~vhRLDr~TSGlll~Ak~~~~~~~l~~~f~ 124 (133)
+.+++||||.||.+| .+++.+++.+. ..+++-++.||-..||+|+++-+. + .++.+.|.
T Consensus 2 ~g~l~i~Kp~g~tS~--------~~v~~~k~~~~---------~kkvGH~GTLDp~A~GvLiv~~g~-~-Tk~~~~~~ 60 (182)
T cd02572 2 YGVINLDKPSGPSSH--------EVVAWIKRILG---------VEKTGHSGTLDPKVTGCLPVCIDR-A-TRLVKSQQ 60 (182)
T ss_pred CeEEEEecCCCCCHH--------HHHHHHHHHhC---------CCccCcCCCCCCcCeeEEEEEECH-H-hhhhHHHh
Confidence 469999999999775 56777877664 346777999999999999999887 3 34444443
No 28
>PRK00989 truB tRNA pseudouridine synthase B; Provisional
Probab=97.72 E-value=6.5e-05 Score=57.61 Aligned_cols=60 Identities=12% Similarity=0.218 Sum_probs=46.7
Q ss_pred CcEEEEECCCCceeecCCCCCcchHHHHHHHHHhhccCCCCCCCCcccccccCCCCCceeeeeecChHHHHHHHHHHH
Q 041166 47 DDLIALNKPSGLQVLPGGLFQQRTVLKQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTKLAKTCIAAYFA 124 (133)
Q Consensus 47 ~~~lvvnKP~gl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~vhRLDr~TSGlll~Ak~~~~~~~l~~~f~ 124 (133)
+.+++||||.|+.+| .+++.+++.+. ..+++-.+.||-..||+|+++-.. ++.+|.+.|.
T Consensus 9 ~G~l~i~KP~g~TS~--------dvv~~ikk~~~---------~kKvGH~GTLDP~AtGvLiv~vG~-~aTkl~~~~~ 68 (230)
T PRK00989 9 EGILLVDKPQGRTSF--------SLIRSLTKLIG---------VKKIGHAGTLDPFATGVMVMLIGR-KFTRLSDILL 68 (230)
T ss_pred CEEEEEeCCCCCCHH--------HHHHHHHHHhC---------CCcCCcCccCCCCCeeEEEEEECC-chhhhHHHhc
Confidence 479999999999776 56788887764 457778999999999999999776 3344555543
No 29
>PRK04099 truB tRNA pseudouridine synthase B; Provisional
Probab=97.64 E-value=0.00013 Score=57.26 Aligned_cols=60 Identities=20% Similarity=0.285 Sum_probs=47.0
Q ss_pred CcEEEEECCCCceeecCCCCCcchHHHHHHHHHhhccCCCCCCCCcccccccCCCCCceeeeeecChHHHHHHHHHHHc
Q 041166 47 DDLIALNKPSGLQVLPGGLFQQRTVLKQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTKLAKTCIAAYFAD 125 (133)
Q Consensus 47 ~~~lvvnKP~gl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~vhRLDr~TSGlll~Ak~~~~~~~l~~~f~~ 125 (133)
+.++++|||+||.+| .+++.+++.+. ..+++-.+.||-..||+|+++-... .++.+.+.+
T Consensus 2 ngil~vdKP~g~tS~--------~vv~~ikk~~~---------~kKvGH~GTLDP~AtGvLiv~iG~a--TKl~~~l~~ 61 (273)
T PRK04099 2 NRLFVANKPAGMSSN--------AFLSRLKRKYG---------VKKAGFSGTLDPFAKGVLIVAFGQY--TKLFRFLKK 61 (273)
T ss_pred CeEEEEeCCCCCCHH--------HHHHHHHHHhC---------CCccccCccCCCCCeeEEEEEEChH--hhhHHHhcc
Confidence 468999999999776 67888887774 4567789999999999999998874 335554443
No 30
>cd00506 PseudoU_synth_TruB_like PseudoU_synth_TruB: Pseudouridine synthase, TruB family. This group consists of eukaryotic, bacterial and archeal pseudouridine synthases similar to Escherichia coli TruB, Saccharomyces cerevisiae Pus4, M. tuberculosis TruB, S. cerevisiae Cbf5 and human dyskerin. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. E. coli TruB, M. tuberculosis TruB and S. cerevisiae Pus4, make psi55 in the T loop of tRNAs. Pus4 catalyses the formation of psi55 in both cytoplasmic and mitochondrial tRNAs. Psi55 is almost universally conserved. S. cerevisiae Cbf5 and human dyskerin are nucleolar proteins that, with the help of guide RNAs, make the hundreds of psueudouridnes present in rRNA and small nuclear RNAs (snRNAs). Cbf5/Dyskerin is the catalytic subunit of eukaryotic box H/ACA small nucleolar ribonucleoprotein (snoRNP) particles. Mutations in human dysker
Probab=97.62 E-value=0.00015 Score=54.87 Aligned_cols=58 Identities=21% Similarity=0.187 Sum_probs=44.5
Q ss_pred cEEEEECCCCceeecCCCCCcchHHHHHHHHHhhccCCCCCCCCcccccccCCCCCceeeeeecChHHHHHHHHHHH
Q 041166 48 DLIALNKPSGLQVLPGGLFQQRTVLKQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTKLAKTCIAAYFA 124 (133)
Q Consensus 48 ~~lvvnKP~gl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~vhRLDr~TSGlll~Ak~~~~~~~l~~~f~ 124 (133)
.+++||||.||-+| .+++.+++.+. ..+++-.+.||-..||+|+++-+.. .++...|.
T Consensus 1 Gil~i~KP~g~tS~--------~vv~~ik~~~~---------~kKvGH~GTLDP~AsGvLiv~vG~a--Tkl~~~~~ 58 (210)
T cd00506 1 GLFAVDKPQGPSSH--------DVVDTIRRIFL---------AEKVGHGGTLDPFATGVLVVGIGKA--TKLLKHLL 58 (210)
T ss_pred CEEEEEcCCCCCHH--------HHHHHHHHHhC---------ccccCCCCcCCCcCeeEEEEEECHH--HhhhHHHh
Confidence 37999999999776 56777887764 3577779999999999999998873 33444443
No 31
>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=97.60 E-value=0.00019 Score=54.39 Aligned_cols=59 Identities=17% Similarity=0.293 Sum_probs=46.7
Q ss_pred CcEEEEECCCCceeecCCCCCcchHHHHHHHHHhhccCCCCCCCCcccccccCCCCCceeeeeecChHHHHHHHHHHH
Q 041166 47 DDLIALNKPSGLQVLPGGLFQQRTVLKQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTKLAKTCIAAYFA 124 (133)
Q Consensus 47 ~~~lvvnKP~gl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~vhRLDr~TSGlll~Ak~~~~~~~l~~~f~ 124 (133)
+.+++||||.||.+| .+++.+++.+. ..+++-.+.||-..||+|+++-+..+ ++...|.
T Consensus 2 ~G~l~v~KP~g~tS~--------~vv~~vkk~~~---------~kKvGH~GTLDP~AsGvLiv~vG~~T--kl~~~~~ 60 (209)
T TIGR00431 2 NGVLLLDKPQGMTSF--------DALAKVRRLLN---------VKKVGHTGTLDPFATGVLPILVGKAT--KLSPYLT 60 (209)
T ss_pred CeEEEEECCCCCCHH--------HHHHHHHHHhC---------CCcCCCCCCCCCcCceEEEEEEChHh--hhhHHHc
Confidence 368999999999765 57788887774 45677799999999999999998853 4555554
No 32
>PRK00020 truB tRNA pseudouridine synthase B; Provisional
Probab=97.48 E-value=0.00027 Score=54.63 Aligned_cols=59 Identities=25% Similarity=0.392 Sum_probs=45.7
Q ss_pred CcEEEEECCCCceeecCCCCCcchHHHHHHHHHhhccCCCCCCCCcccccccCCCCCceeeeeecChHHHHHHHHHHH
Q 041166 47 DDLIALNKPSGLQVLPGGLFQQRTVLKQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTKLAKTCIAAYFA 124 (133)
Q Consensus 47 ~~~lvvnKP~gl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~vhRLDr~TSGlll~Ak~~~~~~~l~~~f~ 124 (133)
+.+++||||.|+.+| .++..+++.+. ..+++-.+-||-..||+|+++-.. + .++...|.
T Consensus 10 ~Gil~vdKP~G~TS~--------dvv~~vkr~~~---------~kKvGH~GTLDP~AtGvLiv~iG~-a-TKl~~~l~ 68 (244)
T PRK00020 10 DGVLLLDKPVGLSSN--------HALQRAKRTVD---------AAKAGHTGTLDPFATGLLVCCMGR-A-TKISGRML 68 (244)
T ss_pred CeEEEEecCCCCCHH--------HHHHHHHHHhC---------CCCCCcCCcCCCcCeeEEEEEECH-H-hhhhHHhc
Confidence 479999999999776 56788887664 457777999999999999999887 3 34444443
No 33
>PRK02484 truB tRNA pseudouridine synthase B; Provisional
Probab=97.47 E-value=0.00031 Score=55.76 Aligned_cols=59 Identities=20% Similarity=0.219 Sum_probs=46.1
Q ss_pred CcEEEEECCCCceeecCCCCCcchHHHHHHHHHhhccCCCCCCCCcccccccCCCCCceeeeeecChHHHHHHHHHHH
Q 041166 47 DDLIALNKPSGLQVLPGGLFQQRTVLKQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTKLAKTCIAAYFA 124 (133)
Q Consensus 47 ~~~lvvnKP~gl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~vhRLDr~TSGlll~Ak~~~~~~~l~~~f~ 124 (133)
+.+++||||+||.+| .+++.+++.+. ..+++-.+.||-..||+|+++-... .++.+.+.
T Consensus 3 ~Gil~i~KP~G~TS~--------dvv~~vrr~l~---------~kKvGH~GTLDP~AtGvL~i~vG~a--Tkl~~~l~ 61 (294)
T PRK02484 3 NGIINLKKEAGMTSH--------DAVFKLRKILQ---------TKKIGHGGTLDPDVVGVLPIAVGKA--TRLIEYMT 61 (294)
T ss_pred ceEEEEeCCCCCCHH--------HHHHHHHHHhC---------CCccccCCCCCCCCeeEEEEEEChh--hhhhHHhc
Confidence 469999999999776 57788887764 4577789999999999999998873 33444444
No 34
>PRK03287 truB tRNA pseudouridine synthase B; Provisional
Probab=97.45 E-value=0.00034 Score=55.59 Aligned_cols=60 Identities=17% Similarity=0.257 Sum_probs=46.5
Q ss_pred CCcEEEEECCCCceeecCCCCCcchHHHHHHHHHhhccCCCCCCCCcccccccCCCCCceeeeeecChHHHHHHHHHHH
Q 041166 46 DDDLIALNKPSGLQVLPGGLFQQRTVLKQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTKLAKTCIAAYFA 124 (133)
Q Consensus 46 d~~~lvvnKP~gl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~vhRLDr~TSGlll~Ak~~~~~~~l~~~f~ 124 (133)
-+.+++||||.|+.+| .+++.+++.+. ..+++-.+-||-..||+|+++-.. + .++.+.+.
T Consensus 8 ~~Gil~i~KP~G~TS~--------dvv~~vrr~~~---------~kKvGH~GTLDP~AtGvL~i~vG~-a-TKl~~~l~ 67 (298)
T PRK03287 8 GSGLVVVDKPAGMTSH--------DVVARCRRLFG---------TRKVGHAGTLDPMATGVLVLGVER-A-TKLLGHLT 67 (298)
T ss_pred cCeEEEEeCCCCCCHH--------HHHHHHHHHhC---------CCCCCcCccCCCcceeEEEEEeCh-h-hhhhHHHh
Confidence 3579999999999776 57788887775 346777999999999999999886 3 34444444
No 35
>PRK14123 tRNA pseudouridine synthase B; Provisional
Probab=97.41 E-value=0.0004 Score=55.37 Aligned_cols=60 Identities=17% Similarity=0.221 Sum_probs=47.0
Q ss_pred CcEEEEECCCCceeecCCCCCcchHHHHHHHHHhhccCCCCCCCCcccccccCCCCCceeeeeecChHHHHHHHHHHHc
Q 041166 47 DDLIALNKPSGLQVLPGGLFQQRTVLKQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTKLAKTCIAAYFAD 125 (133)
Q Consensus 47 ~~~lvvnKP~gl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~vhRLDr~TSGlll~Ak~~~~~~~l~~~f~~ 125 (133)
+.+++||||.||.+| .++..+++.+. ..+++-.+.||-..||+|+++-...+ ++.+.+.+
T Consensus 3 ~Gil~i~KP~G~TS~--------dvv~~vrr~~~---------~kKvGH~GTLDP~AtGvL~v~vG~aT--kl~~~l~~ 62 (305)
T PRK14123 3 NGILPVYKERGLTSH--------DVVFKLRKILK---------TKKIGHTGTLDPEVAGVLPVCIGNAT--RVSDYVMD 62 (305)
T ss_pred ceEEEEeCCCCCCHH--------HHHHHHHHHhC---------CCccccCcCCCCcCeeEEEEEEChhh--hhHHHhcC
Confidence 479999999999776 57788887764 45677899999999999999988743 45555543
No 36
>PRK14124 tRNA pseudouridine synthase B; Provisional
Probab=97.40 E-value=0.00046 Score=55.08 Aligned_cols=59 Identities=17% Similarity=0.264 Sum_probs=46.0
Q ss_pred CcEEEEECCCCceeecCCCCCcchHHHHHHHHHhhccCCCCCCCCcccccccCCCCCceeeeeecChHHHHHHHHHHH
Q 041166 47 DDLIALNKPSGLQVLPGGLFQQRTVLKQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTKLAKTCIAAYFA 124 (133)
Q Consensus 47 ~~~lvvnKP~gl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~vhRLDr~TSGlll~Ak~~~~~~~l~~~f~ 124 (133)
+.+++||||+|+.+| .+++.+++.+. ..+++-.+-||-..||+|+++-+.. .++.+.|.
T Consensus 3 ~Gil~i~KP~G~TS~--------dvv~~vrr~l~---------~kKvGH~GTLDP~AtGvL~v~vG~a--Tkl~~~l~ 61 (308)
T PRK14124 3 HGFLVAYKPKGPTSH--------DVVDEVRKKLK---------TRKVGHAGTLDPFATGVLIVGVNKA--TRLLEYLK 61 (308)
T ss_pred ceEEEEECCCCCCHH--------HHHHHHHHHcC---------CCccCcCcCCCCCCcEEEEEEEChH--HhhhHHHh
Confidence 468999999999776 57788887764 3467779999999999999998874 33444444
No 37
>PRK14846 truB tRNA pseudouridine synthase B; Provisional
Probab=97.40 E-value=0.00047 Score=55.63 Aligned_cols=59 Identities=15% Similarity=0.157 Sum_probs=45.8
Q ss_pred CcEEEEECCCCceeecCCCCCcchHHHHHHHHHhhccCCCCCCCCcccccccCCCCCceeeeeecChHHHHHHHHHHH
Q 041166 47 DDLIALNKPSGLQVLPGGLFQQRTVLKQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTKLAKTCIAAYFA 124 (133)
Q Consensus 47 ~~~lvvnKP~gl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~vhRLDr~TSGlll~Ak~~~~~~~l~~~f~ 124 (133)
+.+++||||.||.+| .+++.+++.+. ..+++-.+.||-..||+|+++-... .++.+.+.
T Consensus 3 nGiL~idKP~G~TS~--------dvv~~vrk~l~---------~kKVGH~GTLDP~AtGVL~i~vG~a--TKl~~~l~ 61 (345)
T PRK14846 3 NYWLNIYKPRGISSA--------QLVSIVKKILG---------KTKIGHAGTLDVEAEGILPFAVGEA--TKLIHLLI 61 (345)
T ss_pred CeEEEEeCCCCCCHH--------HHHHHHHHHhC---------CCcCCcCccCCCcCceEEEEEEChh--hhhhHHHh
Confidence 579999999999776 57788887764 4577789999999999999998873 34444443
No 38
>PRK00130 truB tRNA pseudouridine synthase B; Provisional
Probab=97.40 E-value=0.00044 Score=54.79 Aligned_cols=60 Identities=23% Similarity=0.343 Sum_probs=46.7
Q ss_pred CcEEEEECCCCceeecCCCCCcchHHHHHHHHHhhccCCCCCCCCcccccccCCCCCceeeeeecChHHHHHHHHHHHc
Q 041166 47 DDLIALNKPSGLQVLPGGLFQQRTVLKQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTKLAKTCIAAYFAD 125 (133)
Q Consensus 47 ~~~lvvnKP~gl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~vhRLDr~TSGlll~Ak~~~~~~~l~~~f~~ 125 (133)
+.+++||||.|+.+| .++..+++.+. ..+++-.+-||-..||+|+++-... .++.+.|.+
T Consensus 2 ~Gil~i~KP~G~tS~--------dvv~~vrr~~~---------~kKvGH~GTLDP~AtGvL~v~vG~a--Tkl~~~l~~ 61 (290)
T PRK00130 2 DGILNILKPPGMTSF--------DVVRKIRKIAK---------IKKVGHTGTLDPLASGVLPVCLGKA--TKIVDYLME 61 (290)
T ss_pred CeEEEEeCCCCCCHH--------HHHHHHHHHhC---------CCccCcCCCCCCCCeeEEEEEEChh--hhhHHHhcc
Confidence 478999999999776 57788887764 3467779999999999999998873 345555543
No 39
>PRK05389 truB tRNA pseudouridine synthase B; Provisional
Probab=97.37 E-value=0.00048 Score=54.91 Aligned_cols=59 Identities=22% Similarity=0.342 Sum_probs=46.1
Q ss_pred CcEEEEECCCCceeecCCCCCcchHHHHHHHHHhhccCCCCCCCCcccccccCCCCCceeeeeecChHHHHHHHHHHH
Q 041166 47 DDLIALNKPSGLQVLPGGLFQQRTVLKQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTKLAKTCIAAYFA 124 (133)
Q Consensus 47 ~~~lvvnKP~gl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~vhRLDr~TSGlll~Ak~~~~~~~l~~~f~ 124 (133)
+.+++||||.|+.+| .+++.+++.+. ..+++-.+-||-..||+|+++-.. +.++.+.|.
T Consensus 13 ~Gil~i~KP~G~TS~--------dvv~~vrk~~~---------~kKvGH~GTLDP~AtGvL~v~vG~--aTkl~~~l~ 71 (305)
T PRK05389 13 SGWLILDKPAGMTST--------EAVSKVKWLFD---------AQKAGHAGTLDPLASGVLPIALGE--ATKTVPYVM 71 (305)
T ss_pred CeEEEEeCCCCCCHH--------HHHHHHHHHhc---------ccccCCcccCCCCCceEEEEEECh--hhhhhHHhc
Confidence 579999999999776 57788887765 346777899999999999999887 244444444
No 40
>PRK02193 truB tRNA pseudouridine synthase B; Provisional
Probab=97.34 E-value=0.00048 Score=54.28 Aligned_cols=57 Identities=23% Similarity=0.295 Sum_probs=44.0
Q ss_pred EEEEECCCCceeecCCCCCcchHHHHHHHHHhhccCCCCCCCCcccccccCCCCCceeeeeecChHHHHHHHHHHH
Q 041166 49 LIALNKPSGLQVLPGGLFQQRTVLKQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTKLAKTCIAAYFA 124 (133)
Q Consensus 49 ~lvvnKP~gl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~vhRLDr~TSGlll~Ak~~~~~~~l~~~f~ 124 (133)
++++|||.||.+| .+++.+++.+. ..+++-.+.||-..||+|+++-... .++.+.+.
T Consensus 2 il~i~KP~G~tS~--------dvv~~vrr~~~---------~kKvGH~GTLDP~AtGvL~v~vG~a--Tkl~~~l~ 58 (279)
T PRK02193 2 IKLLYKPKGISSF--------KFIKNFAKTNN---------IKKIGHTGTLDPLASGLLLVATDED--TKLIDYLD 58 (279)
T ss_pred EEEEECCCCCCHH--------HHHHHHHHHcC---------CCccccCccCCCcCeeEEEEEEChh--hhhhHHhc
Confidence 7899999999776 56777777664 4577789999999999999998873 34444443
No 41
>PRK04270 H/ACA RNA-protein complex component Cbf5p; Reviewed
Probab=97.32 E-value=0.00057 Score=54.34 Aligned_cols=61 Identities=18% Similarity=0.112 Sum_probs=46.8
Q ss_pred ECCcEEEEECCCCceeecCCCCCcchHHHHHHHHHhhccCCCCCCCCcccccccCCCCCceeeeeecChHHHHHHHHHHH
Q 041166 45 EDDDLIALNKPSGLQVLPGGLFQQRTVLKQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTKLAKTCIAAYFA 124 (133)
Q Consensus 45 ed~~~lvvnKP~gl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~vhRLDr~TSGlll~Ak~~~~~~~l~~~f~ 124 (133)
-.+.++++|||.|+.+| .+++.+++.+. ..+++-.+-||-..||+|+++-+.. .++.+.+.
T Consensus 20 ~~~g~l~i~Kp~g~tS~--------~~v~~~r~~~~---------~kkvGH~GTLDp~A~GvL~v~~g~a--tk~~~~~~ 80 (300)
T PRK04270 20 IKFGVVNLDKPPGPTSH--------EVAAWVRDILG---------VEKAGHGGTLDPKVTGVLPVALGKA--TKVVQALL 80 (300)
T ss_pred cCCCEEEEECCCCCCHH--------HHHHHHHHHhc---------cccccCCCCCCCcCeEEEEEEEChH--hhhhHHhc
Confidence 34589999999999776 56788887664 3467778999999999999998873 44444444
No 42
>PRK05033 truB tRNA pseudouridine synthase B; Provisional
Probab=97.32 E-value=0.00062 Score=54.42 Aligned_cols=60 Identities=20% Similarity=0.303 Sum_probs=46.8
Q ss_pred CcEEEEECCCCceeecCCCCCcchHHHHHHHHHhhccCCCCCCCCcccccccCCCCCceeeeeecChHHHHHHHHHHHc
Q 041166 47 DDLIALNKPSGLQVLPGGLFQQRTVLKQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTKLAKTCIAAYFAD 125 (133)
Q Consensus 47 ~~~lvvnKP~gl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~vhRLDr~TSGlll~Ak~~~~~~~l~~~f~~ 125 (133)
+.+++||||.||.+| .++..+++.+. ..+++-...||-..||+|+++-... .++.+.+.+
T Consensus 10 ~Gil~i~KP~G~TS~--------dvv~~vrr~l~---------~kKvGH~GTLDP~AtGvL~v~vG~a--Tkl~~~~~~ 69 (312)
T PRK05033 10 NGVLLLDKPQGMSSN--------DALQKVKRLFN---------ANKAGHTGALDPLATGMLPICLGEA--TKFSQYLLD 69 (312)
T ss_pred CeEEEEeCCCCCCHH--------HHHHHHHHHhC---------CCCCCCCCcCCCcCeeEEEEEECHH--hhhhHHhcC
Confidence 579999999999776 56788887764 3567778999999999999998874 335555543
No 43
>cd02573 PseudoU_synth_EcTruB PseudoU_synth_EcTruB: Pseudouridine synthase, Escherichia coli TruB like. This group consists of bacterial pseudouridine synthases similar to E. coli TruB and Mycobacterium tuberculosis TruB. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). E. coli TruB and M. tuberculosis TruB make psi55 in the T loop of tRNAs. Psi55 is nearly universally conserved. E. coli TruB is not inhibited by RNA containing 5-fluorouridine.
Probab=97.32 E-value=0.00064 Score=53.55 Aligned_cols=59 Identities=22% Similarity=0.328 Sum_probs=45.7
Q ss_pred cEEEEECCCCceeecCCCCCcchHHHHHHHHHhhccCCCCCCCCcccccccCCCCCceeeeeecChHHHHHHHHHHHc
Q 041166 48 DLIALNKPSGLQVLPGGLFQQRTVLKQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTKLAKTCIAAYFAD 125 (133)
Q Consensus 48 ~~lvvnKP~gl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~vhRLDr~TSGlll~Ak~~~~~~~l~~~f~~ 125 (133)
.+++||||.||.+| .+++.+++.+. ..+++-.+-||-..||+|+++-+.. .+|.+.+.+
T Consensus 1 Gil~i~KP~G~tS~--------~vv~~vr~~~~---------~kKvGH~GTLDP~AtGvL~v~vG~a--Tkl~~~l~~ 59 (277)
T cd02573 1 GILLLDKPAGLTSH--------DVVQKVRRLLG---------TKKVGHTGTLDPLATGVLPIALGEA--TKLSQYLLD 59 (277)
T ss_pred CEEEEECCCCCCHH--------HHHHHHHHHhC---------cCccCCCCCCCCcCeEEEEEEEChH--HhhHHHhcC
Confidence 47899999999776 56788887765 3467778999999999999998874 345555543
No 44
>PRK01528 truB tRNA pseudouridine synthase B; Provisional
Probab=97.32 E-value=0.00062 Score=53.98 Aligned_cols=51 Identities=14% Similarity=0.153 Sum_probs=42.4
Q ss_pred CCcEEEEECCCCceeecCCCCCcchHHHHHHHHHhhccCCCCCCCCcccccccCCCCCceeeeeecCh
Q 041166 46 DDDLIALNKPSGLQVLPGGLFQQRTVLKQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTK 113 (133)
Q Consensus 46 d~~~lvvnKP~gl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~vhRLDr~TSGlll~Ak~~ 113 (133)
.+.+++||||.||.+| .+++.+++.+. ..+++-.+-||-..||+|+++-..
T Consensus 2 ~~GiL~i~KP~G~TS~--------dvv~~vrk~~~---------~kKvGH~GTLDP~AtGvL~v~vG~ 52 (292)
T PRK01528 2 SNYWLNIYKPRGISSA--------KLVSIVKKILG---------KVKIGHAGTLDVEAEGVLPLAVGE 52 (292)
T ss_pred CCEEEEEeCCCCCCHH--------HHHHHHHHHcC---------CCccCcCccCCCcCceEEEEEECh
Confidence 3579999999999776 56788887764 346777999999999999999887
No 45
>PRK02755 truB tRNA pseudouridine synthase B; Provisional
Probab=97.27 E-value=0.00061 Score=54.08 Aligned_cols=60 Identities=20% Similarity=0.253 Sum_probs=47.2
Q ss_pred CcEEEEECCCCceeecCCCCCcchHHHHHHHHHhhccCCCCCCCCcccccccCCCCCceeeeeecChHHHHHHHHHHHc
Q 041166 47 DDLIALNKPSGLQVLPGGLFQQRTVLKQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTKLAKTCIAAYFAD 125 (133)
Q Consensus 47 ~~~lvvnKP~gl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~vhRLDr~TSGlll~Ak~~~~~~~l~~~f~~ 125 (133)
+.+++||||.||.+| .+++.+++.+. ..+++-.+-||-..||+|+++-.+.+ ++.+.+.+
T Consensus 3 ~Gil~i~KP~G~TS~--------dvv~~vrr~~~---------~kKvGH~GTLDP~AtGvL~i~vG~aT--kl~~~l~~ 62 (295)
T PRK02755 3 FGFLNLDKPAGLTSH--------DCVARLRRLLR---------LKRVGHGGTLDPAATGVLPIALGKAT--RLLPYLPG 62 (295)
T ss_pred ceEEEEeCCCCCCHH--------HHHHHHHHHhC---------CCccccCCCCCCcCeeEEEEEEChhh--hhHHHhCC
Confidence 479999999999776 67888887765 35677799999999999999988743 45555543
No 46
>PRK01550 truB tRNA pseudouridine synthase B; Provisional
Probab=97.23 E-value=0.00082 Score=53.57 Aligned_cols=60 Identities=23% Similarity=0.307 Sum_probs=46.1
Q ss_pred CcEEEEECCCCceeecCCCCCcchHHHHHHHHHhhccCCCCCCCCcccccccCCCCCceeeeeecChHHHHHHHHHHHc
Q 041166 47 DDLIALNKPSGLQVLPGGLFQQRTVLKQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTKLAKTCIAAYFAD 125 (133)
Q Consensus 47 ~~~lvvnKP~gl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~vhRLDr~TSGlll~Ak~~~~~~~l~~~f~~ 125 (133)
+.+++||||+||.+| .+++.+++.+. ..+++-..-||-..||+|+++-... .++.+.+.+
T Consensus 2 ~Gil~i~KP~G~TS~--------dvv~~vrr~~~---------~kKvGH~GTLDP~AtGvL~i~vG~a--Tkl~~~l~~ 61 (304)
T PRK01550 2 NGVLLLHKPRGMTSH--------DCVFKLRKILR---------TKKVGHTGTLDPEVSGVLPICVGRA--TKIAEYLTD 61 (304)
T ss_pred CeEEEEECCCCCCHH--------HHHHHHHHHcC---------CCCcccCCCCCCcCeeEEEEEEChh--hhhhHHhcC
Confidence 469999999999776 56788887764 3466778999999999999998873 335555543
No 47
>PRK01851 truB tRNA pseudouridine synthase B; Provisional
Probab=97.22 E-value=0.00095 Score=53.17 Aligned_cols=59 Identities=20% Similarity=0.204 Sum_probs=46.1
Q ss_pred CcEEEEECCCCceeecCCCCCcchHHHHHHHHHhhccCCCCCCCCcccccccCCCCCceeeeeecChHHHHHHHHHHH
Q 041166 47 DDLIALNKPSGLQVLPGGLFQQRTVLKQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTKLAKTCIAAYFA 124 (133)
Q Consensus 47 ~~~lvvnKP~gl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~vhRLDr~TSGlll~Ak~~~~~~~l~~~f~ 124 (133)
+.+++||||.||.+| .+++.+++.+. ..+++-...||-..||+|+++-... .++.+.+.
T Consensus 16 ~Gil~i~KP~G~TS~--------dvv~~vrr~l~---------~kKvGH~GTLDP~AtGvL~v~vG~a--Tkl~~~l~ 74 (303)
T PRK01851 16 DGVLLLDKPLGLSSN--------DALQRAKRLLR---------AKKAGHTGTLDPLATGLLPLCFGEA--TKFSQDLL 74 (303)
T ss_pred CeEEEEeCCCCCCHH--------HHHHHHHHHhC---------cccCCCCCCCCCCCceEEEEEECHH--HhhhHHhc
Confidence 589999999999776 57888887775 3466678999999999999998874 33444444
No 48
>PRK14122 tRNA pseudouridine synthase B; Provisional
Probab=96.97 E-value=0.002 Score=51.52 Aligned_cols=58 Identities=17% Similarity=0.267 Sum_probs=44.8
Q ss_pred cEEEEECCCCceeecCCCCCcchHHHHHHHHHhhccCCCCCCCCcccccccCCCCCceeeeeecChHHHHHHHHHHH
Q 041166 48 DLIALNKPSGLQVLPGGLFQQRTVLKQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTKLAKTCIAAYFA 124 (133)
Q Consensus 48 ~~lvvnKP~gl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~vhRLDr~TSGlll~Ak~~~~~~~l~~~f~ 124 (133)
.+++||||.||.+| .+++.+++.+. ..+++-..-||-..||+|+++-... .+|.+.+.
T Consensus 2 ~il~idKP~G~TS~--------dvv~~vrr~l~---------~kKvGH~GTLDP~AtGvL~i~iG~a--TKl~~~l~ 59 (312)
T PRK14122 2 PVYAVDKPLGLTSH--------DVVNRARRALG---------TRRVGHTGTLDPLATGVLVLCTDDS--TKLVPFLS 59 (312)
T ss_pred cEEEEECCCCCCHH--------HHHHHHHHHhC---------CCCCCCCCCCCCcCeeeEEEEEChh--hhhhHHhc
Confidence 37899999999776 57788887764 3466778999999999999998874 33555553
No 49
>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=96.84 E-value=0.0026 Score=51.09 Aligned_cols=60 Identities=17% Similarity=0.187 Sum_probs=46.0
Q ss_pred CCcEEEEECCCCceeecCCCCCcchHHHHHHHHHhhccCCCCCCCCcccccccCCCCCceeeeeecChHHHHHHHHHHH
Q 041166 46 DDDLIALNKPSGLQVLPGGLFQQRTVLKQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTKLAKTCIAAYFA 124 (133)
Q Consensus 46 d~~~lvvnKP~gl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~vhRLDr~TSGlll~Ak~~~~~~~l~~~f~ 124 (133)
.+.+++||||.||.+| .+++.+++.+. ..+++-..-||-..||+|+++-... .++.+.+.
T Consensus 33 ~~G~l~i~KP~g~tS~--------~~v~~vr~~~~---------~kkvGH~GTLDP~A~GvL~v~~G~a--Tkl~~~~~ 92 (322)
T TIGR00425 33 SYGVVNLDKPSGPSSH--------EVVAWVRRILN---------VEKTGHGGTLDPKVTGVLPVCIERA--TRLVKSLQ 92 (322)
T ss_pred CCCEEEEeCCCCCCHH--------HHHHHHHHHhc---------ccccCCCCCCCCCCceEEEEEEChH--hhccHHhc
Confidence 3479999999999776 56788887764 3466678999999999999998873 44444444
No 50
>PRK04642 truB tRNA pseudouridine synthase B; Provisional
Probab=96.83 E-value=0.003 Score=50.30 Aligned_cols=59 Identities=24% Similarity=0.254 Sum_probs=45.8
Q ss_pred CcEEEEECCCCceeecCCCCCcchHHHHHHHHHhhccCCCCCCCCcccccccCCCCCceeeeeecChHHHHHHHHHHH
Q 041166 47 DDLIALNKPSGLQVLPGGLFQQRTVLKQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTKLAKTCIAAYFA 124 (133)
Q Consensus 47 ~~~lvvnKP~gl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~vhRLDr~TSGlll~Ak~~~~~~~l~~~f~ 124 (133)
+.+++||||.||.+| .+++.+++.+. ..+++-..-||-..||+|+++-... .++.+.+.
T Consensus 10 ~Gil~i~KP~G~TS~--------dvv~~vrr~~~---------~kKvGH~GTLDP~AtGvL~v~~G~a--Tkl~~~l~ 68 (300)
T PRK04642 10 DGILLLDKPAGLSSN--------NALQAARRLLR---------AEKGGHTGSLDPLATGLLPLCFGEA--TKIAGLLL 68 (300)
T ss_pred CeEEEEecCCCCCHH--------HHHHHHHHHhC---------CCcccCCCccCCcCeeeEEEEEChh--hhhhHHhc
Confidence 579999999999776 57888887765 3466678899999999999998763 44444444
No 51
>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=96.66 E-value=0.0038 Score=37.24 Aligned_cols=27 Identities=22% Similarity=0.399 Sum_probs=18.6
Q ss_pred CCcEEEEecCCCCCCCCCCCcceEEECCcEEEEE
Q 041166 20 AGSELVYHRLPWKEPDVPYLLEVFYEDDDLIALN 53 (133)
Q Consensus 20 ~g~~v~~~~~~~~~~~~~~~~~vlyed~~~lvvn 53 (133)
+|+.+.+...+ .+..|+|||++++|+|
T Consensus 44 ~~d~i~i~~~~-------~~~~i~~ed~~~lvv~ 70 (70)
T cd00165 44 PGDVIEVDGKS-------IEEDIVYEDKKLLVVN 70 (70)
T ss_pred CCCEEEEcCCC-------cccceeeccCCEEEeC
Confidence 56666655321 1238999999999986
No 52
>COG0130 TruB Pseudouridine synthase [Translation, ribosomal structure and biogenesis]
Probab=96.65 E-value=0.0049 Score=48.44 Aligned_cols=62 Identities=16% Similarity=0.144 Sum_probs=47.8
Q ss_pred cEEEEECCCCceeecCCCCCcchHHHHHHHHHhhccCCCCCCCCcccccccCCCCCceeeeeecChHHHHHHHHHHHcCC
Q 041166 48 DLIALNKPSGLQVLPGGLFQQRTVLKQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTKLAKTCIAAYFADKT 127 (133)
Q Consensus 48 ~~lvvnKP~gl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~vhRLDr~TSGlll~Ak~~~~~~~l~~~f~~~~ 127 (133)
.++++|||.|+.+| .++.++++.+. ..+.+-..-||-..||+|++|-. ++.+.++-+....+
T Consensus 16 Gil~ldKP~G~tS~--------~~v~~vkkil~---------~~K~GH~GTLDP~atGvLpi~ig-~aTKl~~~l~~~~K 77 (271)
T COG0130 16 GVINLDKPPGPTSH--------EVVAWVKRILG---------VEKAGHGGTLDPLATGVLPICLG-EATKLVQYLLDADK 77 (271)
T ss_pred ceEEeeCCCCCCHH--------HHHHHHHHHhC---------ccccccccccCCcccceEEEEec-hhHhHHHHHhhCCc
Confidence 89999999999776 67788888876 45666678999999999999988 55555554444433
No 53
>cd02867 PseudoU_synth_TruB_4 PseudoU_synth_TruB_4: Pseudouridine synthase homolog 4. This group consists of Eukaryotic TruB proteins similar to Saccharomyces cerevisiae Pus4. S. cerevisiae Pus4, makes psi55 in the T loop of both cytoplasmic and mitochondrial tRNAs. Psi55 is almost universally conserved. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi).
Probab=96.41 E-value=0.0095 Score=47.70 Aligned_cols=67 Identities=19% Similarity=0.195 Sum_probs=44.6
Q ss_pred cEEEEECCCCceeecCCCCCcchHHHHHHHHHhhccC--------------------CCCCCCCcccccccCCCCCceee
Q 041166 48 DLIALNKPSGLQVLPGGLFQQRTVLKQLQWRASKQSS--------------------SLSSQASHPVPVHRLGRGTSGIL 107 (133)
Q Consensus 48 ~~lvvnKP~gl~v~~~~~~~~~tl~~~l~~~~~~~~~--------------------~~~~~~~~~~~vhRLDr~TSGll 107 (133)
.+++||||.||.+| .+++.+++.+..... .......+++-.+-||=..||+|
T Consensus 1 Gil~i~KP~G~TS~--------~vv~~lk~~l~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~KiGH~GTLDPlAsGVL 72 (312)
T cd02867 1 GVFAINKPSGITSA--------QVLNDLKPLFLNSALFKDKIQRAVAKRGKKARRRKGRKRSKLKIGHGGTLDPLATGVL 72 (312)
T ss_pred CeEEEeCCCCCCHH--------HHHHHHHHHhcccccccchhhhhhhhhhhhhhhhccccccccccccccccCCccceeE
Confidence 37999999999775 567777766543100 00011246777899999999999
Q ss_pred eeecChHHHHHHHHHH
Q 041166 108 LCAKTKLAKTCIAAYF 123 (133)
Q Consensus 108 l~Ak~~~~~~~l~~~f 123 (133)
+++-..- .+.++..+
T Consensus 73 vvgvG~a-TK~l~~~l 87 (312)
T cd02867 73 VVGVGAG-TKQLQDYL 87 (312)
T ss_pred EEEECcH-HHHHHHHh
Confidence 9998763 44444444
No 54
>KOG2559 consensus Predicted pseudouridine synthase [Translation, ribosomal structure and biogenesis]
Probab=95.48 E-value=0.011 Score=45.90 Aligned_cols=22 Identities=36% Similarity=0.354 Sum_probs=19.0
Q ss_pred cccccccCCCCCceeeeeecCh
Q 041166 92 HPVPVHRLGRGTSGILLCAKTK 113 (133)
Q Consensus 92 ~~~~vhRLDr~TSGlll~Ak~~ 113 (133)
.+.++||||-.|||+++|.-+.
T Consensus 90 ~V~v~h~l~~~~sgvl~~gVgh 111 (318)
T KOG2559|consen 90 DVQVVHVLPLATSGVLLFGVGH 111 (318)
T ss_pred ceeeEEeecccccceEEEecCc
Confidence 3678999999999999998654
No 55
>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=90.33 E-value=0.29 Score=31.39 Aligned_cols=21 Identities=10% Similarity=-0.040 Sum_probs=19.2
Q ss_pred CCcccccccCCCCCceeeeee
Q 041166 90 ASHPVPVHRLGRGTSGILLCA 110 (133)
Q Consensus 90 ~~~~~~vhRLDr~TSGlll~A 110 (133)
..+++.++++|+.++|+++++
T Consensus 23 ~~~i~~aG~kDk~a~t~q~v~ 43 (87)
T cd01291 23 PKRVGYAGRKDKRAVTTQLVS 43 (87)
T ss_pred hheEEECccCCCCeeEEEEEc
Confidence 567889999999999999998
No 56
>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=70.63 E-value=1.9 Score=26.25 Aligned_cols=18 Identities=39% Similarity=0.538 Sum_probs=12.8
Q ss_pred EECCcEEEEECCCCceee
Q 041166 44 YEDDDLIALNKPSGLQVL 61 (133)
Q Consensus 44 yed~~~lvvnKP~gl~v~ 61 (133)
|-...+|.+|||+|-.+|
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 335789999999998766
No 57
>PF13021 DUF3885: Domain of unknown function (DUF3885)
Probab=69.21 E-value=7.7 Score=21.46 Aligned_cols=24 Identities=17% Similarity=0.116 Sum_probs=20.9
Q ss_pred CCceeeeeecChHHHHHHHHHHHc
Q 041166 102 GTSGILLCAKTKLAKTCIAAYFAD 125 (133)
Q Consensus 102 ~TSGlll~Ak~~~~~~~l~~~f~~ 125 (133)
+..||-|+|.+++..+.|-..|.+
T Consensus 5 DDRGcdvia~~~~~i~~ly~~y~~ 28 (38)
T PF13021_consen 5 DDRGCDVIANNKERIRPLYEKYND 28 (38)
T ss_pred cCCCcEEeeCCHHHHHHHHHHHHH
Confidence 567999999999999999888764
No 58
>PF11324 DUF3126: Protein of unknown function (DUF3126); InterPro: IPR021473 This family of proteins with unknown function appear to be restricted to Alphaproteobacteria.
Probab=52.21 E-value=22 Score=21.87 Aligned_cols=40 Identities=13% Similarity=0.083 Sum_probs=23.6
Q ss_pred ChHHHHHhhhCCCCCCCC----CCCcEEEEecCCCCCCCCCCCcceEEECC
Q 041166 1 LTLIEFYSTKHKNSAPLQ----GAGSELVYHRLPWKEPDVPYLLEVFYEDD 47 (133)
Q Consensus 1 ~~l~~~~~~~~~~~~~~~----~~g~~v~~~~~~~~~~~~~~~~~vlyed~ 47 (133)
++|..||.+.|.+..... +++|.++++.-. .-+-+||.|+
T Consensus 3 ~klq~yLr~~f~n~~i~v~~rpk~~dsaEV~~g~-------EfiGvi~~De 46 (63)
T PF11324_consen 3 KKLQAYLRRTFGNPGITVKARPKKDDSAEVYIGD-------EFIGVIYRDE 46 (63)
T ss_pred HHHHHHHHHHhCCCceEEEcCCCCCCceEEEeCC-------EEEEEEEeec
Confidence 368899999997665442 355555555211 2245666654
No 59
>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=43.07 E-value=15 Score=24.81 Aligned_cols=19 Identities=37% Similarity=0.707 Sum_probs=15.0
Q ss_pred CcceEEECCcEEEEE--CCCC
Q 041166 39 LLEVFYEDDDLIALN--KPSG 57 (133)
Q Consensus 39 ~~~vlyed~~~lvvn--KP~g 57 (133)
+-+|+|||++++++. +|..
T Consensus 13 ~~~vly~d~~~v~~~D~~P~a 33 (116)
T PF11969_consen 13 PERVLYEDDDFVVFKDIYPKA 33 (116)
T ss_dssp GGGESEEETSEEEEE-TT-SC
T ss_pred CCcEEEEeCCEEEeeCCCCCc
Confidence 457999999999998 6664
No 60
>cd01223 PH_Vav Vav pleckstrin homology (PH) domain. Vav pleckstrin homology (PH) domain. Vav acts as a guanosine nucleotide exchange factor(GEF) for Rho/Rac proteins. Mammalian Vav proteins consist of a calponin homology (CH) domain, an acidic region, a rho-GEF (DH)domain, a PH domain, a Zinc finger region and an SH2 domain, flanked by two SH3 domains. In invertebrates such as Drosophila and C.elegans, Vav is missing the N-terminal SH3 domain . PH domains share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains.
Probab=41.11 E-value=58 Score=22.47 Aligned_cols=80 Identities=15% Similarity=0.049 Sum_probs=45.6
Q ss_pred CcceEEECCcEEEEECCCCceeecCCCCCcchHHHHHHH-H--HhhccCCCC-----CCCCcccccccCCCCCceeeeee
Q 041166 39 LLEVFYEDDDLIALNKPSGLQVLPGGLFQQRTVLKQLQW-R--ASKQSSSLS-----SQASHPVPVHRLGRGTSGILLCA 110 (133)
Q Consensus 39 ~~~vlyed~~~lvvnKP~gl~v~~~~~~~~~tl~~~l~~-~--~~~~~~~~~-----~~~~~~~~vhRLDr~TSGlll~A 110 (133)
.-+=+|-=+..+|+.|+.|-... +. +-++-+.+.- . ......... .-...+.++|+ ...+|+.+++
T Consensus 21 k~RyiFLFDk~lI~CK~~~~~~~-~~---~Y~~Ke~~~l~~~~I~~~~~~d~~~~~~~~~~~f~L~~~--~~~~~~~f~~ 94 (116)
T cd01223 21 KLRYIFLFDKAVIVCKALGDNTG-DM---QYTYKDIHDLADYKIENNPSRDTEGRDTRWKYGFYLAHK--QGKTGFTFYF 94 (116)
T ss_pred ceeEEEEecceEEEEEecCCCCC-Cc---cEEhHHhhhhheeeeEecCccCcccCCcceEEEEEEEec--CCCccEEEEe
Confidence 35667777889999998876432 11 2233333321 1 111100000 01123457776 4468899999
Q ss_pred cChHHHHHHHHHHH
Q 041166 111 KTKLAKTCIAAYFA 124 (133)
Q Consensus 111 k~~~~~~~l~~~f~ 124 (133)
||.+.-....++|.
T Consensus 95 Ktee~K~kWm~al~ 108 (116)
T cd01223 95 KTEHLRKKWLKALE 108 (116)
T ss_pred CCHHHHHHHHHHHH
Confidence 99999998777775
No 61
>PRK03427 cell division protein ZipA; Provisional
Probab=40.31 E-value=55 Score=26.67 Aligned_cols=54 Identities=19% Similarity=0.249 Sum_probs=26.6
Q ss_pred ECCcEEEEECCCCceeecCCCCCcchHHHHHHHHHhhccCCCCCCCCcccccccC-CCCCceeeeee
Q 041166 45 EDDDLIALNKPSGLQVLPGGLFQQRTVLKQLQWRASKQSSSLSSQASHPVPVHRL-GRGTSGILLCA 110 (133)
Q Consensus 45 ed~~~lvvnKP~gl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~vhRL-Dr~TSGlll~A 110 (133)
+.+.+|++| +..+.+.......|...+...--. -..-.+-||. |.+.+|-++|+
T Consensus 194 ~~e~vIvin----VvA~~g~~f~G~~Ll~~le~~Gf~--------fGem~IFHRh~~~~g~G~vLFS 248 (333)
T PRK03427 194 RKEAVIVMN----VAAHHGSELNGEVLLNSIQQAGFQ--------FGDMNIFHRHLSPDGSGPVLFS 248 (333)
T ss_pred CCCcEEEEE----EeeCCCCcccHHHHHHHHHHcCCc--------ccCCcceeecccCCCCCceEEE
Confidence 344677776 333333334445666665533110 0112234774 66667777776
No 62
>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=35.78 E-value=26 Score=25.04 Aligned_cols=33 Identities=21% Similarity=0.172 Sum_probs=22.5
Q ss_pred CCcccccccCCCCCceeeeeecChHHHHHHHHHHH
Q 041166 90 ASHPVPVHRLGRGTSGILLCAKTKLAKTCIAAYFA 124 (133)
Q Consensus 90 ~~~~~~vhRLDr~TSGlll~Ak~~~~~~~l~~~f~ 124 (133)
..+++-.+.||-..||+|+++-+.. .++.+.|.
T Consensus 6 ~~KvGH~GTLDP~AsGvL~v~vg~~--Tkl~~~l~ 38 (149)
T PF01509_consen 6 IKKVGHGGTLDPFASGVLVVGVGKA--TKLLSYLQ 38 (149)
T ss_dssp BSSEEESS-SSTT-EEEEEEEEGGG--GGGHHHHT
T ss_pred cceeccccccCCcceEEEEEEECCc--chHHHHhh
Confidence 3467778999999999999998762 33444444
No 63
>PRK14105 selenophosphate synthetase; Provisional
Probab=32.09 E-value=63 Score=25.89 Aligned_cols=31 Identities=19% Similarity=0.147 Sum_probs=26.2
Q ss_pred cCCCCCceeeeeecChHHHHHHHHHHHcCCc
Q 041166 98 RLGRGTSGILLCAKTKLAKTCIAAYFADKTS 128 (133)
Q Consensus 98 RLDr~TSGlll~Ak~~~~~~~l~~~f~~~~v 128 (133)
-.|..|||-+||+-+++.+..+.+.+++..+
T Consensus 288 g~~~~ssGgLl~tv~~e~~~~~~~~l~~~g~ 318 (345)
T PRK14105 288 GYGAETAGGLLISVKPEYKDKLIDKLEKNNV 318 (345)
T ss_pred CCCCcccCeEEEEecHHHHHHHHHHHHhCCC
Confidence 4588899999999999999999998886544
No 64
>PF02863 Arg_repressor_C: Arginine repressor, C-terminal domain; InterPro: IPR020899 The arginine dihydrolase (AD) pathway is found in many prokaryotes and some primitive eukaryotes, an example of the latter being Giardia lamblia (Giardia intestinalis) []. The three-enzyme anaerobic pathway breaks down L-arginine to form 1 mol of ATP, carbon dioxide and ammonia. In simpler bacteria, the first enzyme, arginine deiminase, can account for up to 10% of total cell protein []. Most prokaryotic arginine deiminase pathways are under the control of a repressor gene, termed ArgR []. This is a negative regulator, and will only release the arginine deiminase operon for expression in the presence of arginine []. The crystal structure of apo-ArgR from Bacillus stearothermophilus has been determined to 2.5A by means of X-ray crystallography []. The protein exists as a hexamer of identical subunits, and is shown to have six DNA-binding domains, clustered around a central oligomeric core when bound to arginine. It predominantly interacts with A.T residues in ARG boxes. This hexameric protein binds DNA at its N terminus to repress arginine biosyntheis or activate arginine catabolism. Some species have several ArgR paralogs. In a neighbour-joining tree, some of these paralogous sequences show long branches and differ significantly from the well-conserved C-terminal region. ; GO: 0006355 regulation of transcription, DNA-dependent; PDB: 1B4B_B 1B4A_A 3V4G_A 1F9N_F 2P5M_A 1XXA_E 1XXC_C 1XXB_F 3LAJ_D 3BUE_D ....
Probab=29.56 E-value=52 Score=20.16 Aligned_cols=23 Identities=9% Similarity=0.182 Sum_probs=19.7
Q ss_pred CceeeeeecChHHHHHHHHHHHc
Q 041166 103 TSGILLCAKTKLAKTCIAAYFAD 125 (133)
Q Consensus 103 TSGlll~Ak~~~~~~~l~~~f~~ 125 (133)
..-+++++++.+.+..+.+.|++
T Consensus 47 dDTilvi~~~~~~a~~l~~~l~~ 69 (70)
T PF02863_consen 47 DDTILVICRSEEDAEELEEKLKE 69 (70)
T ss_dssp SSEEEEEESTTSHHHHHHHHHHT
T ss_pred CCEEEEEeCCHHHHHHHHHHHHh
Confidence 35689999999999999988864
No 65
>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=28.02 E-value=52 Score=20.99 Aligned_cols=15 Identities=40% Similarity=0.625 Sum_probs=10.3
Q ss_pred CcceEEECCcEEEEE
Q 041166 39 LLEVFYEDDDLIALN 53 (133)
Q Consensus 39 ~~~vlyed~~~lvvn 53 (133)
+-.+||||+.++|+-
T Consensus 5 ~~~vv~e~~~~~~~~ 19 (98)
T PF01230_consen 5 PARVVYEDDHFVAFL 19 (98)
T ss_dssp HCEEEEE-SSEEEEE
T ss_pred CeeEEEECCCEEEEE
Confidence 446999999876553
No 66
>PHA02096 hypothetical protein
Probab=26.73 E-value=31 Score=22.43 Aligned_cols=20 Identities=25% Similarity=0.479 Sum_probs=15.4
Q ss_pred eEEECCcEEEEECCCCceee
Q 041166 42 VFYEDDDLIALNKPSGLQVL 61 (133)
Q Consensus 42 vlyed~~~lvvnKP~gl~v~ 61 (133)
-+|--+.++.||||+|.+..
T Consensus 62 rlfg~ptiv~inkps~~lan 81 (103)
T PHA02096 62 RLFGPPTIVSVNKPSGHLAN 81 (103)
T ss_pred hhcCCCeEEEecCchHHHHH
Confidence 45666788999999997643
No 67
>TIGR01293 Kv_beta voltage-dependent potassium channel beta subunit, animal. Plant beta subunits and their closely related bacterial homologs (in Deinococcus radiudurans, Xylella fastidiosa, etc.) appear more closely related to each other than to animal forms. However, the bacterial species lack convincing counterparts the Kv alpha subunit and the Kv beta homolog may serve as an enzyme. Cutoffs are set for this model such that yeast and plant forms and bacterial close homologs score between trusted and noise cutoffs.
Probab=26.19 E-value=3e+02 Score=21.48 Aligned_cols=72 Identities=8% Similarity=0.045 Sum_probs=43.6
Q ss_pred CCcEEEEEC--CCCceeecCCCCCcchHHHHHHHHHhhccCCCCCCCCcccccccCCCCCceeeeeecChHHHHHHHHHH
Q 041166 46 DDDLIALNK--PSGLQVLPGGLFQQRTVLKQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTKLAKTCIAAYF 123 (133)
Q Consensus 46 d~~~lvvnK--P~gl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~vhRLDr~TSGlll~Ak~~~~~~~l~~~f 123 (133)
.+.++|..| +.+... .........+...+...+...+.. ...++.+|+.|..+. -.++...|.++.
T Consensus 72 R~~~~iaTK~~~~~~~~-~~~~~~~~~i~~~~~~SL~rL~td----~iDl~~lH~~~~~~~-------~~e~~~aL~~l~ 139 (317)
T TIGR01293 72 RSSYVITTKIFWGGKAE-TERGLSRKHIIEGLKASLERLQLE----YVDIVFANRPDPNTP-------MEETVRAMTYVI 139 (317)
T ss_pred cccEEEEeeeccCCCCC-CCCCCCHHHHHHHHHHHHHHhCCC----cEeEEEeccCCCCCC-------HHHHHHHHHHHH
Confidence 356888888 221111 011122345666666665554321 457889999987542 246788899999
Q ss_pred HcCCcc
Q 041166 124 ADKTSV 129 (133)
Q Consensus 124 ~~~~v~ 129 (133)
++|+|.
T Consensus 140 ~~G~ir 145 (317)
T TIGR01293 140 NQGMAM 145 (317)
T ss_pred HcCCee
Confidence 999875
No 68
>PF14839 DOR: DOR family
Probab=25.85 E-value=49 Score=25.28 Aligned_cols=17 Identities=35% Similarity=0.435 Sum_probs=13.8
Q ss_pred EECCcEEEEECCCCcee
Q 041166 44 YEDDDLIALNKPSGLQV 60 (133)
Q Consensus 44 yed~~~lvvnKP~gl~v 60 (133)
.||+++|+||++.|+..
T Consensus 4 ~edD~WilVD~~~~~~~ 20 (216)
T PF14839_consen 4 EEDDEWILVDFIDGLPR 20 (216)
T ss_pred cccCCeEEEEecCCCcc
Confidence 37899999999996544
No 69
>COG0108 RibB 3,4-dihydroxy-2-butanone 4-phosphate synthase [Coenzyme metabolism]
Probab=25.59 E-value=44 Score=25.31 Aligned_cols=25 Identities=20% Similarity=0.256 Sum_probs=20.4
Q ss_pred cccCCCCCceeeeeecChHHHHHHH
Q 041166 96 VHRLGRGTSGILLCAKTKLAKTCIA 120 (133)
Q Consensus 96 vhRLDr~TSGlll~Ak~~~~~~~l~ 120 (133)
+.-+=+.+||+++++-+.+.+.+|.
T Consensus 45 i~fm~~~a~GliC~~lt~e~~~~L~ 69 (203)
T COG0108 45 IAFMRRHASGLICVALTEERAKRLG 69 (203)
T ss_pred HHHHHHhCCeeEEEeCCHHHHHhCC
Confidence 4555578999999999999888764
No 70
>cd01276 PKCI_related Protein Kinase C Interacting protein related (PKCI): PKCI and related proteins belong to the ubiquitous HIT family of hydrolases that act on alpha-phosphates of ribonucleotides. The members of this subgroup have a conserved HxHxHxx motif (x is a hydrophobic residue) that is a signature for this family. No enzymatic activity has been reported however, for PKCI and its related members.
Probab=24.98 E-value=65 Score=20.64 Aligned_cols=13 Identities=38% Similarity=0.792 Sum_probs=11.1
Q ss_pred cceEEECCcEEEE
Q 041166 40 LEVFYEDDDLIAL 52 (133)
Q Consensus 40 ~~vlyed~~~lvv 52 (133)
-.+||||+.++++
T Consensus 14 ~~iv~e~~~~~a~ 26 (104)
T cd01276 14 AKKVYEDDEVLAF 26 (104)
T ss_pred cCEEEECCCEEEE
Confidence 5699999998777
No 71
>COG3845 ABC-type uncharacterized transport systems, ATPase components [General function prediction only]
Probab=24.86 E-value=25 Score=30.15 Aligned_cols=81 Identities=17% Similarity=0.287 Sum_probs=50.5
Q ss_pred cceEEECCcEEEEECCCCceeecCCCCCcchHHHHHHHHHhhccCCCCCCCCcccccccCC-------CCC---ceeeee
Q 041166 40 LEVFYEDDDLIALNKPSGLQVLPGGLFQQRTVLKQLQWRASKQSSSLSSQASHPVPVHRLG-------RGT---SGILLC 109 (133)
Q Consensus 40 ~~vlyed~~~lvvnKP~gl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~vhRLD-------r~T---SGlll~ 109 (133)
++.+|.+.+++++|-|..+++-.. -+.+...++..- ..+ ..-+++-|+|+ +-| .|=++-
T Consensus 152 lKaLyr~a~iLILDEPTaVLTP~E----~~~lf~~l~~l~-~~G------~tIi~ITHKL~Ev~~iaDrvTVLR~Gkvvg 220 (501)
T COG3845 152 LKALYRGARLLILDEPTAVLTPQE----ADELFEILRRLA-AEG------KTIIFITHKLKEVMAIADRVTVLRRGKVVG 220 (501)
T ss_pred HHHHhcCCCEEEEcCCcccCCHHH----HHHHHHHHHHHH-HCC------CEEEEEeccHHHHHHhhCeeEEEeCCeEEe
Confidence 578999999999999999877422 245566555333 221 34566677764 222 243333
Q ss_pred ecC---hHHHHHHHHHHHcCCcccc
Q 041166 110 AKT---KLAKTCIAAYFADKTSVVD 131 (133)
Q Consensus 110 Ak~---~~~~~~l~~~f~~~~v~~~ 131 (133)
.-+ ......+.+++-.++|...
T Consensus 221 t~~~~~~~t~~ela~lMvG~~v~~~ 245 (501)
T COG3845 221 TVDPVAETTEEELAELMVGREVVLR 245 (501)
T ss_pred eecCCCCCCHHHHHHHhcCCccccc
Confidence 333 2367788888887777643
No 72
>COG0667 Tas Predicted oxidoreductases (related to aryl-alcohol dehydrogenases) [Energy production and conversion]
Probab=23.99 E-value=3.2e+02 Score=21.70 Aligned_cols=72 Identities=10% Similarity=0.064 Sum_probs=44.4
Q ss_pred CcEEEEECCCCceeecCC----CCCcchHHHHHHHHHhhccCCCCCCCCcccccccCCCCCceeeeeecChHHHHHHHHH
Q 041166 47 DDLIALNKPSGLQVLPGG----LFQQRTVLKQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTKLAKTCIAAY 122 (133)
Q Consensus 47 ~~~lvvnKP~gl~v~~~~----~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~vhRLDr~TSGlll~Ak~~~~~~~l~~~ 122 (133)
++++|.-|=......+.. ......+...+...+...+.. ...++.+||-|.+| -..+....|.++
T Consensus 76 d~vvIaTK~g~~~~~~~~~~~~~~s~~~i~~~v~~SL~RLgtd----~IDl~~iH~~d~~~-------p~~e~~~aL~~l 144 (316)
T COG0667 76 DKVVIATKVGYRPGDPGPNGVFGLSRDHIRRAVEASLKRLGTD----YIDLYQLHRPDPET-------PIEETLEALDEL 144 (316)
T ss_pred CeEEEEEeeccCCCCCCCCccCCCCHHHHHHHHHHHHHHhCCC----ceeEEEeCCCCCCC-------CHHHHHHHHHHH
Confidence 557777775555432211 122345666666665554421 45788899999933 345567888888
Q ss_pred HHcCCcc
Q 041166 123 FADKTSV 129 (133)
Q Consensus 123 f~~~~v~ 129 (133)
.++|+|.
T Consensus 145 ~~~G~ir 151 (316)
T COG0667 145 VREGKIR 151 (316)
T ss_pred HHcCCee
Confidence 8888875
No 73
>PRK09912 L-glyceraldehyde 3-phosphate reductase; Provisional
Probab=22.55 E-value=1.1e+02 Score=24.35 Aligned_cols=74 Identities=16% Similarity=0.142 Sum_probs=42.6
Q ss_pred CCcEEEEECCCC-ceeec-CCCCCcchHHHHHHHHHhhccCCCCCCCCcccccccCCCCCceeeeeecChHHHHHHHHHH
Q 041166 46 DDDLIALNKPSG-LQVLP-GGLFQQRTVLKQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTKLAKTCIAAYF 123 (133)
Q Consensus 46 d~~~lvvnKP~g-l~v~~-~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~vhRLDr~TSGlll~Ak~~~~~~~l~~~f 123 (133)
-++++|..|=.. ....+ ........+...+...+...+.. ...++.+|+-|..+. -.++...|.++.
T Consensus 89 Rd~~~I~TK~g~~~~~~~~~~~~s~~~i~~~~e~SL~rLg~d----~iDl~~lH~~~~~~~-------~~e~~~al~~l~ 157 (346)
T PRK09912 89 RDELIISTKAGYDMWPGPYGSGGSRKYLLASLDQSLKRMGLE----YVDIFYSHRVDENTP-------MEETASALAHAV 157 (346)
T ss_pred CCeEEEEEEecccCCCCcCCCCCCHHHHHHHHHHHHHHHCCC----cEEEEEeCCCCCCCC-------HHHHHHHHHHHH
Confidence 356888888210 00000 01112334555665555544321 457889999986543 246788999999
Q ss_pred HcCCccc
Q 041166 124 ADKTSVV 130 (133)
Q Consensus 124 ~~~~v~~ 130 (133)
++|+|..
T Consensus 158 ~~GkIr~ 164 (346)
T PRK09912 158 QSGKALY 164 (346)
T ss_pred HcCCeeE
Confidence 9998753
No 74
>PF11697 DUF3293: Protein of unknown function (DUF3293); InterPro: IPR021710 This bacterial family of proteins has no known function.
Probab=22.44 E-value=1e+02 Score=19.10 Aligned_cols=27 Identities=4% Similarity=0.038 Sum_probs=23.3
Q ss_pred CCceeeeeecChHHHHHHHHHHHcCCc
Q 041166 102 GTSGILLCAKTKLAKTCIAAYFADKTS 128 (133)
Q Consensus 102 ~TSGlll~Ak~~~~~~~l~~~f~~~~v 128 (133)
.-.|.+|+.-+.+.+..|.+.|.+.-|
T Consensus 47 ~E~s~~V~~i~~~~A~~Lg~~f~QnAI 73 (73)
T PF11697_consen 47 REPSFAVLGISLEEAIALGRKFGQNAI 73 (73)
T ss_pred cCCEeEEcCCCHHHHHHHHHHhCcCcC
Confidence 345899999999999999999988754
No 75
>PF00248 Aldo_ket_red: Aldo/keto reductase family; InterPro: IPR023210 The aldo-keto reductase family includes a number of related monomeric NADPH-dependent oxidoreductases, such as aldehyde reductase, aldose reductase, prostaglandin F synthase, xylose reductase, rho crystallin, and many others []. All possess a similar structure, with a beta-alpha-beta fold characteristic of nucleotide binding proteins []. The fold comprises a parallel beta-8/alpha-8-barrel, which contains a novel NADP-binding motif. The binding site is located in a large, deep, elliptical pocket in the C-terminal end of the beta sheet, the substrate being bound in an extended conformation. The hydrophobic nature of the pocket favours aromatic and apolar substrates over highly polar ones []. Binding of the NADPH coenzyme causes a massive conformational change, reorienting a loop, effectively locking the coenzyme in place. This binding is more similar to FAD- than to NAD(P)-binding oxidoreductases []. Some proteins of this entry contain a K+ ion channel beta chain regulatory domain; these are reported to have oxidoreductase activity []. This entry represents the NADP-dependent oxidoreductase domain found in these proteins.; PDB: 1C9W_A 4F40_B 1VBJ_A 1XGD_A 1X97_A 2ACS_A 1EF3_A 2ACU_A 1PWM_A 2NVD_A ....
Probab=21.82 E-value=97 Score=23.42 Aligned_cols=51 Identities=4% Similarity=-0.010 Sum_probs=38.5
Q ss_pred chHHHHHHHHHhhccCCCCCCCCcccccccCCCCCceeeeeecChHHHHHHHHHHHcCCcc
Q 041166 69 RTVLKQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTKLAKTCIAAYFADKTSV 129 (133)
Q Consensus 69 ~tl~~~l~~~~~~~~~~~~~~~~~~~~vhRLDr~TSGlll~Ak~~~~~~~l~~~f~~~~v~ 129 (133)
..+...+...+...+.. ...++.+|..|.... ...++...|.++-++|.|.
T Consensus 82 ~~i~~~~~~sL~~L~~d----~iDl~~lH~~~~~~~------~~~~~~~~l~~l~~~G~ir 132 (283)
T PF00248_consen 82 DSIRESLERSLERLGTD----YIDLLLLHWPDPSED------ALEEVWEALEELKKEGKIR 132 (283)
T ss_dssp HHHHHHHHHHHHHHTSS----SEEEEEESSSSTTSS------HHHHHHHHHHHHHHTTSEE
T ss_pred ccccccccccccccccc----chhcccccccccccc------ccchhhhhhhhcccccccc
Confidence 45666666666554431 457788999999888 7888899999999999875
No 76
>cd06660 Aldo_ket_red Aldo-keto reductases (AKRs) are a superfamily of soluble NAD(P)(H) oxidoreductases whose chief purpose is to reduce aldehydes and ketones to primary and secondary alcohols. AKRs are present in all phyla and are of importance to both health and industrial applications. Members have very distinct functions and include the prokaryotic 2,5-diketo-D-gluconic acid reductases and beta-keto ester reductases, the eukaryotic aldose reductases, aldehyde reductases, hydroxysteroid dehydrogenases, steroid 5beta-reductases, potassium channel beta-subunits and aflatoxin aldehyde reductases, among others.
Probab=21.22 E-value=3.6e+02 Score=20.23 Aligned_cols=73 Identities=4% Similarity=-0.034 Sum_probs=46.2
Q ss_pred CCcEEEEECCCCceeecCCCCCcchHHHHHHHHHhhccCCCCCCCCcccccccCCCCCceeeeeecChHHHHHHHHHHHc
Q 041166 46 DDDLIALNKPSGLQVLPGGLFQQRTVLKQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTKLAKTCIAAYFAD 125 (133)
Q Consensus 46 d~~~lvvnKP~gl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~vhRLDr~TSGlll~Ak~~~~~~~l~~~f~~ 125 (133)
-++++|.-|=..-.... .......+...+...+...+. ....+..+|+.|.... ...++...|.++-++
T Consensus 71 R~~~~i~tK~~~~~~~~-~~~~~~~~~~~l~~sL~~L~~----~~iDl~~lh~~~~~~~------~~~~~~~~l~~l~~~ 139 (285)
T cd06660 71 REEVFIATKVGPRPGDG-RDLSPEHIRRAVEESLKRLGT----DYIDLYLLHWPDPDTP------DIEETLRALEELVKE 139 (285)
T ss_pred cCcEEEEeeecCCCCCC-CCCCHHHHHHHHHHHHHHhCC----CceeEEEecCCCCCCC------CHHHHHHHHHHHHHc
Confidence 45677777743221110 112234566666655555432 1467888999988765 678889999999999
Q ss_pred CCcc
Q 041166 126 KTSV 129 (133)
Q Consensus 126 ~~v~ 129 (133)
|.|.
T Consensus 140 G~ir 143 (285)
T cd06660 140 GKIR 143 (285)
T ss_pred CCcc
Confidence 8875
No 77
>PRK06043 fumarate hydratase; Provisional
Probab=21.09 E-value=1e+02 Score=23.10 Aligned_cols=23 Identities=26% Similarity=0.218 Sum_probs=20.3
Q ss_pred ceeeeeecChHHHHHHHHHHHcCC
Q 041166 104 SGILLCAKTKLAKTCIAAYFADKT 127 (133)
Q Consensus 104 SGlll~Ak~~~~~~~l~~~f~~~~ 127 (133)
||.|+.|++ .+++++.+++.+|+
T Consensus 26 sG~IytaRD-aaH~rl~e~~~~G~ 48 (192)
T PRK06043 26 SGEILTARD-EAHARILEMKEKGK 48 (192)
T ss_pred EEEEEEEeH-HHHHHHHHHHhcCC
Confidence 899999999 78899999888875
No 78
>cd01278 aprataxin_related aprataxin related: Aprataxin, a HINT family hydrolase is mutated in ataxia oculomotor apraxia syndrome. All the members of this subgroup have the conserved HxHxHxx (where x is a hydrophobic residue) signature motif. Members of this subgroup are predominantly eukaryotic in origin.
Probab=21.05 E-value=85 Score=20.14 Aligned_cols=15 Identities=27% Similarity=0.545 Sum_probs=12.4
Q ss_pred CcceEEECCcEEEEE
Q 041166 39 LLEVFYEDDDLIALN 53 (133)
Q Consensus 39 ~~~vlyed~~~lvvn 53 (133)
+-++|||+++++++.
T Consensus 15 ~~~iv~~~~~~~a~~ 29 (104)
T cd01278 15 PEDQVYEDDRVVVFK 29 (104)
T ss_pred CccEEEeCCCEEEEE
Confidence 457999999988874
No 79
>PRK06842 fumarate hydratase; Provisional
Probab=20.73 E-value=1.1e+02 Score=22.79 Aligned_cols=23 Identities=17% Similarity=0.265 Sum_probs=20.2
Q ss_pred ceeeeeecChHHHHHHHHHHHcCC
Q 041166 104 SGILLCAKTKLAKTCIAAYFADKT 127 (133)
Q Consensus 104 SGlll~Ak~~~~~~~l~~~f~~~~ 127 (133)
||.|+.|++ .+++++.+.+.+|+
T Consensus 26 sG~i~taRD-aAHkrl~e~l~~G~ 48 (185)
T PRK06842 26 SGYIYTARD-AAHKRLIELLDKGE 48 (185)
T ss_pred eEEEEEEeH-HHHHHHHHHHhcCC
Confidence 899999999 78888988888875
No 80
>PRK01741 cell division protein ZipA; Provisional
Probab=20.26 E-value=1.7e+02 Score=23.82 Aligned_cols=15 Identities=27% Similarity=0.377 Sum_probs=10.1
Q ss_pred ccc-CCCCCceeeeee
Q 041166 96 VHR-LGRGTSGILLCA 110 (133)
Q Consensus 96 vhR-LDr~TSGlll~A 110 (133)
-|| +|.+.+|-++|+
T Consensus 239 FHRh~d~~g~g~VLFS 254 (332)
T PRK01741 239 YHRHLDLSVASPVLFS 254 (332)
T ss_pred eeeccccCCCCceEEE
Confidence 377 466666777776
Done!