Query gi|254780610|ref|YP_003065023.1| RNA-pseudouridylate synthase protein, ribosomal large subunit D [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 340
No_of_seqs 150 out of 5691
Neff 7.1
Searched_HMMs 39220
Date Sun May 29 21:40:44 2011
Command /home/congqian_1/programs/hhpred/hhsearch -i 254780610.hhm -d /home/congqian_1/database/cdd/Cdd.hhm
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK11180 rluD 23S rRNA pseudou 100.0 0 0 594.8 23.3 307 13-339 8-314 (325)
2 TIGR00005 rluA_subfam pseudour 100.0 0 0 599.6 19.0 309 18-338 1-337 (337)
3 PRK11025 23S rRNA pseudouridyl 100.0 0 0 570.9 22.5 304 7-339 4-315 (317)
4 COG0564 RluA Pseudouridylate s 100.0 0 0 544.6 21.3 288 11-328 1-289 (289)
5 cd02558 PSRA_1 PSRA_1: Pseudou 100.0 0 0 452.7 18.0 241 51-327 4-245 (246)
6 PRK11112 tRNA pseudouridine sy 100.0 0 0 449.6 16.2 230 90-340 2-237 (257)
7 PRK10158 23S rRNA/tRNA pseudou 100.0 0 0 415.1 14.6 210 84-327 8-218 (219)
8 cd02563 PseudoU_synth_TruC tRN 100.0 0 0 406.3 15.8 217 90-327 1-223 (223)
9 cd02557 PseudoU_synth_ScRIB2 P 100.0 0 0 392.4 12.1 198 87-328 13-210 (213)
10 KOG1919 consensus 100.0 0 0 324.0 18.3 301 15-339 36-354 (371)
11 cd02869 PseudoU_synth_RluCD_li 100.0 0 0 322.8 11.6 185 99-311 1-185 (185)
12 TIGR01621 RluA-like pseudourid 100.0 0 0 298.7 7.9 196 90-327 2-198 (222)
13 cd02550 PseudoU_synth_Rsu_Rlu_ 100.0 3E-40 7E-45 259.7 9.2 152 99-277 1-152 (154)
14 pfam00849 PseudoU_synth_2 RNA 100.0 1.2E-39 3.1E-44 256.0 9.8 151 99-266 1-151 (151)
15 cd02870 PseudoU_synth_RsuA_lik 100.0 4.6E-33 1.2E-37 216.8 8.8 143 99-276 1-143 (146)
16 COG1187 RsuA 16S rRNA uridine- 99.9 1.8E-25 4.6E-30 171.6 14.1 210 22-277 2-213 (248)
17 PRK10839 16S rRNA pseudouridyl 99.9 4.1E-25 1E-29 169.4 13.9 200 23-275 1-201 (231)
18 PRK10475 23S rRNA pseudouridin 99.9 5.8E-25 1.5E-29 168.5 13.3 202 19-275 3-204 (290)
19 PRK10700 23S rRNA pseudouridyl 99.9 7.6E-25 1.9E-29 167.8 11.7 209 22-276 2-212 (291)
20 cd02566 PseudoU_synth_RluE Pse 99.8 3.3E-19 8.3E-24 134.3 8.3 152 99-276 1-157 (168)
21 PRK11394 23S rRNA pseudouridin 99.7 4.8E-16 1.2E-20 115.4 8.6 146 98-275 30-185 (207)
22 cd02553 PseudoU_synth_RsuA Pse 99.6 6.2E-16 1.6E-20 114.7 7.7 140 99-275 2-141 (167)
23 cd02556 PseudoU_synth_RluB Pse 99.6 3.5E-15 8.9E-20 110.3 8.0 143 99-275 2-144 (167)
24 TIGR00093 TIGR00093 conserved 99.6 4.5E-15 1.1E-19 109.6 6.8 151 103-277 1-160 (185)
25 cd02555 PSSA_1 PSSA_1: Pseudou 99.5 3.2E-14 8.1E-19 104.5 7.6 145 99-274 6-150 (177)
26 cd02554 PseudoU_synth_RluF Pse 99.5 2E-13 5E-18 99.8 7.3 137 99-276 2-138 (164)
27 cd00165 S4 S4/Hsp/ tRNA synthe 99.1 2.1E-10 5.2E-15 81.8 6.9 70 23-103 1-70 (70)
28 smart00363 S4 S4 RNA-binding d 98.6 6.3E-08 1.6E-12 67.0 6.2 52 23-75 1-52 (60)
29 pfam01479 S4 S4 domain. The S4 98.5 9.4E-08 2.4E-12 66.0 4.7 48 23-71 1-48 (48)
30 TIGR03069 PS_II_S4 photosystem 98.3 1.7E-06 4.3E-11 58.5 6.7 53 20-74 181-233 (257)
31 COG1188 Ribosome-associated he 98.2 3.3E-06 8.5E-11 56.8 5.6 55 20-77 6-61 (100)
32 COG2302 Uncharacterized conser 98.1 5.6E-06 1.4E-10 55.4 5.8 54 19-74 177-230 (257)
33 TIGR01017 rpsD_bact ribosomal 98.1 2.3E-06 6E-11 57.7 3.4 61 21-83 98-158 (217)
34 CHL00113 rps4 ribosomal protei 98.0 6.8E-06 1.7E-10 54.9 4.8 54 21-75 87-140 (201)
35 PRK12565 30S ribosomal protein 98.0 9.3E-06 2.4E-10 54.1 4.9 53 21-74 86-138 (197)
36 PRK10348 ribosome-associated h 98.0 9.7E-06 2.5E-10 54.0 5.0 57 18-76 4-60 (133)
37 COG0522 RpsD Ribosomal protein 98.0 1.1E-05 2.8E-10 53.7 5.2 55 20-75 91-145 (205)
38 PRK05327 rpsD 30S ribosomal pr 97.8 2.3E-05 5.9E-10 51.7 3.4 53 21-74 90-142 (201)
39 COG1189 Predicted rRNA methyla 97.7 0.00011 2.8E-09 47.7 5.9 53 22-75 2-54 (245)
40 TIGR00478 tly hemolysin A; Int 97.6 0.00013 3.2E-09 47.3 5.0 53 24-77 1-53 (240)
41 cd00506 PseudoU_synth_TruB_lik 97.4 0.00035 9E-09 44.7 5.2 69 98-190 1-69 (210)
42 PRK00020 truB tRNA pseudouridi 97.3 0.00057 1.4E-08 43.4 5.2 70 97-190 10-79 (244)
43 PRK00989 truB tRNA pseudouridi 97.2 0.00051 1.3E-08 43.7 4.6 71 97-190 9-79 (235)
44 PRK00130 truB tRNA pseudouridi 97.1 0.00093 2.4E-08 42.2 5.0 70 97-190 2-71 (289)
45 PRK04099 truB tRNA pseudouridi 97.1 0.00069 1.8E-08 42.9 4.4 70 97-190 2-71 (272)
46 PRK02484 truB tRNA pseudouridi 97.1 0.00083 2.1E-08 42.5 4.6 70 97-190 3-72 (293)
47 PRK01851 truB tRNA pseudouridi 97.1 0.001 2.7E-08 41.9 5.0 71 96-190 16-86 (310)
48 cd02572 PseudoU_synth_hDyskeri 97.0 0.0015 3.8E-08 41.0 4.9 69 98-190 3-71 (182)
49 PRK01528 truB tRNA pseudouridi 96.9 0.0018 4.7E-08 40.4 5.2 70 97-190 3-72 (293)
50 cd02868 PseudoU_synth_hTruB2_l 96.9 0.0016 4.1E-08 40.7 4.6 76 98-190 1-76 (226)
51 PRK05389 truB tRNA pseudouridi 96.9 0.0023 5.8E-08 39.9 5.1 70 97-190 13-82 (305)
52 PRK04642 truB tRNA pseudouridi 96.9 0.0018 4.7E-08 40.4 4.6 70 97-190 10-79 (300)
53 PRK02193 truB tRNA pseudouridi 96.8 0.002 5.1E-08 40.2 4.6 68 99-190 2-69 (279)
54 PRK01550 truB tRNA pseudouridi 96.8 0.0018 4.5E-08 40.5 4.1 70 97-190 2-71 (307)
55 PRK03287 truB tRNA pseudouridi 96.7 0.0022 5.7E-08 39.9 4.4 70 97-190 9-78 (298)
56 PRK04270 H/ACA RNA-protein com 96.7 0.0025 6.5E-08 39.6 4.3 73 94-190 19-91 (300)
57 cd02867 PseudoU_synth_TruB_4 P 96.6 0.0025 6.5E-08 39.6 4.0 77 98-190 1-98 (312)
58 cd02573 PseudoU_synth_EcTruB P 96.6 0.0038 9.6E-08 38.5 4.8 69 98-190 1-69 (277)
59 COG0130 TruB Pseudouridine syn 96.6 0.0043 1.1E-07 38.2 4.9 69 98-190 16-84 (271)
60 PRK05033 truB tRNA pseudouridi 96.5 0.0037 9.3E-08 38.6 4.3 70 97-190 12-81 (314)
61 PRK02755 truB tRNA pseudouridi 96.0 0.0086 2.2E-07 36.4 4.0 69 97-190 2-70 (291)
62 TIGR02988 YaaA_near_RecF S4 do 95.7 0.023 5.9E-07 33.8 5.0 52 22-74 8-59 (60)
63 pfam06353 DUF1062 Protein of u 95.5 0.037 9.3E-07 32.7 5.6 49 4-54 84-132 (142)
64 PRK04051 rps4p 30S ribosomal p 95.3 0.039 1E-06 32.5 5.2 56 18-74 98-155 (177)
65 TIGR00431 TruB tRNA pseudourid 95.2 0.0079 2E-07 36.6 1.4 71 97-190 2-72 (236)
66 PRK04313 30S ribosomal protein 95.2 0.053 1.4E-06 31.7 5.5 55 20-74 35-89 (237)
67 TIGR01018 rpsD_arch ribosomal 95.0 0.011 2.8E-07 35.8 1.6 53 18-73 107-161 (170)
68 PTZ00223 40S ribosomal protein 95.0 0.069 1.8E-06 31.0 5.7 53 22-74 38-90 (273)
69 PTZ00118 40S ribosomal protein 95.0 0.068 1.7E-06 31.1 5.5 53 22-74 41-93 (262)
70 COG2501 S4-like RNA binding pr 94.9 0.12 3.2E-06 29.5 6.6 52 22-74 11-62 (73)
71 PRK11507 hypothetical protein; 94.6 0.072 1.8E-06 30.9 4.9 63 11-75 1-63 (70)
72 PTZ00155 40S ribosomal protein 93.6 0.1 2.5E-06 30.1 4.0 56 18-74 102-157 (188)
73 cd01291 PseudoU_synth PseudoU_ 93.1 0.096 2.5E-06 30.2 3.2 20 140-159 24-43 (87)
74 KOG2559 consensus 93.0 0.067 1.7E-06 31.1 2.3 23 142-164 91-113 (318)
75 COG1471 RPS4A Ribosomal protei 87.4 0.75 1.9E-05 24.9 3.6 58 38-105 56-113 (241)
76 TIGR00425 CBF5 rRNA pseudourid 86.0 1.3 3.2E-05 23.5 4.1 145 94-271 31-182 (326)
77 TIGR01687 moaD_arch MoaD famil 83.4 2.8 7.2E-05 21.4 5.0 66 9-77 13-90 (93)
78 pfam01509 TruB_N TruB family p 77.8 3.3 8.5E-05 21.0 3.8 43 140-190 7-49 (149)
79 COG0162 TyrS Tyrosyl-tRNA synt 76.4 3.2 8.1E-05 21.1 3.4 11 39-49 21-31 (401)
80 TIGR01344 malate_syn_A malate 66.7 3.6 9.1E-05 20.8 1.8 15 253-267 403-417 (522)
81 cd00754 MoaD MoaD family. Memb 65.4 11 0.00027 18.0 4.5 52 22-76 25-76 (80)
82 KOG2529 consensus 59.2 7.7 0.0002 18.8 2.4 78 94-195 65-142 (395)
83 PRK11092 bifunctional (p)ppGpp 58.0 14 0.00036 17.2 3.6 20 320-339 671-690 (702)
84 PRK10872 relA GDP/GTP pyrophos 55.4 16 0.0004 17.0 3.5 20 320-339 712-731 (743)
85 TIGR00670 asp_carb_tr aspartat 54.7 8.4 0.00021 18.6 2.0 49 264-336 172-224 (336)
86 cd01668 TGS_RelA_SpoT TGS_RelA 51.0 15 0.00039 17.1 2.8 24 50-74 36-59 (60)
87 pfam00498 FHA FHA domain. The 49.1 20 0.00051 16.4 3.3 24 50-73 43-66 (67)
88 TIGR00515 accD acetyl-CoA carb 47.5 6.2 0.00016 19.4 0.4 54 269-333 204-257 (292)
89 pfam02597 ThiS ThiS family. Th 46.3 22 0.00057 16.1 3.1 47 20-76 18-66 (70)
90 cd01616 TGS The TGS domain, na 45.7 18 0.00047 16.6 2.5 23 51-74 37-59 (60)
91 pfam02824 TGS TGS domain. The 45.6 19 0.0005 16.4 2.7 24 50-74 36-59 (60)
92 TIGR01764 excise DNA binding d 40.3 24 0.00061 15.9 2.4 26 24-52 3-28 (49)
93 PRK02268 hypothetical protein; 39.9 28 0.00071 15.5 3.2 42 36-78 8-49 (141)
94 TIGR00871 zwf glucose-6-phosph 39.2 27 0.00068 15.6 2.6 98 67-182 109-213 (498)
95 pfam03658 UPF0125 Uncharacteri 39.2 21 0.00054 16.2 2.0 31 47-78 45-75 (83)
96 PRK04439 S-adenosylmethionine 39.1 18 0.00046 16.6 1.7 23 30-52 34-57 (400)
97 PRK01777 hypothetical protein; 38.0 22 0.00056 16.1 2.0 31 48-79 49-79 (95)
98 PRK10687 purine nucleoside pho 36.7 13 0.00034 17.4 0.7 20 85-104 12-31 (119)
99 PRK00943 selenophosphate synth 35.7 33 0.00083 15.1 3.3 27 312-339 297-323 (347)
100 pfam01941 AdoMet_Synthase S-ad 33.8 20 0.0005 16.4 1.2 24 29-52 33-57 (396)
101 TIGR02040 PpsR-CrtJ transcript 33.7 19 0.00047 16.5 1.0 45 142-188 86-133 (453)
102 PRK05449 aspartate alpha-decar 32.8 32 0.00081 15.2 2.1 15 93-107 38-52 (126)
103 PRK11130 moaD molybdopterin sy 32.7 37 0.00093 14.8 3.3 59 12-76 17-77 (81)
104 pfam01230 HIT HIT domain. 32.6 18 0.00046 16.6 0.8 17 88-104 4-20 (98)
105 cd06919 Asp_decarbox Aspartate 31.9 25 0.00064 15.8 1.4 12 95-106 39-50 (111)
106 COG0317 SpoT Guanosine polypho 31.3 39 0.00098 14.7 3.7 27 51-78 425-451 (701)
107 pfam02261 Asp_decarbox Asparta 31.0 26 0.00066 15.7 1.4 10 96-105 41-50 (116)
108 TIGR02477 PFKA_PPi diphosphate 31.0 39 0.00098 14.7 2.3 43 146-204 167-211 (566)
109 cd01278 aprataxin_related apra 30.6 23 0.00059 16.0 1.1 14 91-104 17-30 (104)
110 TIGR01969 minD_arch cell divis 30.3 30 0.00076 15.3 1.6 27 82-108 93-121 (258)
111 cd01276 PKCI_related Protein K 30.2 21 0.00052 16.3 0.8 18 88-105 12-29 (104)
112 TIGR01393 lepA GTP-binding pro 29.6 25 0.00064 15.8 1.1 163 13-205 6-193 (598)
113 TIGR00691 spoT_relA RelA/SpoT 29.2 42 0.0011 14.4 3.6 31 50-80 417-447 (741)
114 cd01807 GDX_N GDX contains an 28.8 23 0.00058 16.0 0.8 70 1-75 1-71 (74)
115 TIGR02041 CysI sulfite reducta 28.4 30 0.00077 15.3 1.4 24 29-60 159-182 (550)
116 TIGR00223 panD aspartate 1-dec 27.8 37 0.00095 14.7 1.7 61 9-85 40-104 (127)
117 pfam11969 DcpS_C Scavenger mRN 27.2 25 0.00063 15.8 0.8 18 89-106 13-30 (113)
118 KOG0378 consensus 26.9 27 0.00069 15.6 0.9 47 28-74 47-93 (263)
119 cd06555 ASCH_PF0470_like ASC-1 26.3 46 0.0012 14.2 2.0 35 41-75 8-42 (109)
120 cd01277 HINT_subgroup HINT (hi 26.3 27 0.00068 15.6 0.8 17 88-104 12-28 (103)
121 PRK00416 dcd deoxycytidine tri 25.2 50 0.0013 14.0 4.1 39 37-75 2-43 (174)
122 KOG3275 consensus 24.7 29 0.00073 15.4 0.7 22 84-105 24-45 (127)
123 cd05126 Mth938 Mth938 domain. 24.7 51 0.0013 13.9 3.2 57 47-105 6-67 (117)
124 PRK06488 sulfur carrier protei 24.4 51 0.0013 13.9 3.2 27 50-76 32-61 (65)
125 TIGR01055 parE_Gneg DNA topois 23.7 53 0.0014 13.8 5.8 31 27-59 175-205 (647)
126 TIGR00844 c_cpa1 sodium/hydrog 23.4 32 0.00082 15.1 0.8 14 161-174 765-778 (923)
127 pfam04669 DUF579 Protein of un 22.6 56 0.0014 13.7 2.3 22 87-109 103-125 (187)
128 TIGR02013 rpoB DNA-directed RN 21.9 36 0.00091 14.9 0.7 22 316-338 1420-1441(1449)
129 COG4043 Preprotein translocase 21.1 60 0.0015 13.5 2.0 37 39-75 8-44 (111)
130 pfam02495 7kD_coat 7kD viral c 20.5 62 0.0016 13.4 2.1 24 315-338 31-55 (59)
131 cd01089 PA2G4-like Related to 20.4 62 0.0016 13.4 5.6 26 50-75 62-93 (228)
132 cd04687 Nudix_Hydrolase_28 Mem 20.2 63 0.0016 13.4 2.1 42 92-133 7-52 (128)
No 1
>PRK11180 rluD 23S rRNA pseudouridine synthase D; Provisional
Probab=100.00 E-value=0 Score=594.79 Aligned_cols=307 Identities=41% Similarity=0.641 Sum_probs=268.6
Q ss_pred EEEECHHHCCCCHHHHHHHHCCCCCCHHHHHHHHHCCCEEECCEEECCCCCEECCCCEEEEEECCCHHCCHHHHHHHHHH
Q ss_conf 99957113687578999987176889899999998599049989932867580489889997056011110233222221
Q gi|254780610|r 13 ISLLSDSTAEGRIDRWLATSLKEQFSRSYVKILILNGFISINGMVSKNPNRKVVPGDSFLITVPAAQKLNIAQENIPLDI 92 (340)
Q Consensus 13 ~~~V~~~~~g~RLD~~L~~~l~~~~sR~~i~kli~~G~V~vnG~~~~~~~~~l~~gd~I~i~~~~~~~~~~~~~~~~~~I 92 (340)
+++|+++++|+|||+||++.|+ ++||+.|+++|++|.|+|||+++++++++|..||.|.+..+.+.+....|++++++|
T Consensus 8 T~tV~~~~aG~RLD~fL~~~~~-~~srs~i~k~ir~g~I~VNgk~v~k~~~~v~~GD~I~i~~~~~~~~~~~p~~~~l~I 86 (325)
T PRK11180 8 TATVSESQLGQRLDQALAELFP-DYSRSRIKEWILDQRVLVNGKVINKPKEKVLGGEQVAIDAEIEEEARFEAQDIPLDI 86 (325)
T ss_pred EEEECCCCCCCHHHHHHHHHCC-CCCHHHHHHHHHCCCEEECCEECCCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCCE
T ss_conf 9999910079739999997578-889999999998698899999947821278899999981687763447722388518
Q ss_pred CCCCCEEEEEECCCHHHCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHHHHH
Q ss_conf 01440278996240111045678754210022222210244334444364324444332324057212035788889999
Q gi|254780610|r 93 LYEDDDIIVINKPAGLVVHPAPGNWTGTLVNALLYHCHNNLSSINGVKRPGIVHRLDKDTTGVMVVAKNDLAHQKLSEQF 172 (340)
Q Consensus 93 lyED~~llvinKPaGl~vhp~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~lVHRLDr~TSGlll~Ak~~~a~~~l~~~f 172 (340)
||||++|+|||||+||+|||++++..+|+++++.+++.+. ...+++++||||||+||||||||||..|++.|++||
T Consensus 87 lyED~~llVvnKP~Gl~vhp~~~~~~~tl~~~l~~~~~~~----~~~~r~~iVHRLDr~TSGlll~AK~~~a~~~l~~~f 162 (325)
T PRK11180 87 VYEDDDILVINKPRDLVVHPGAGNPDGTVLNALLHYYPPI----ADVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVEAL 162 (325)
T ss_pred EEECCCEEEEECCCCCEEECCCCCCCCCHHHHHHHHHHHC----CCCCCCCEEECCCCCCCEEEEECCCHHHHHHHHHHH
T ss_conf 9983889999889994476798988877999998753210----478767666427999741466417599999999999
Q ss_pred HHHCCCCCEEEEEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEECCCCCEEECCCCCCCCCEEEEEE
Q ss_conf 97211322133445432024332332110013434443322123444555553000012221011256677500123443
Q gi|254780610|r 173 VDHGKSTRLKRAYYAMVWGIPLPDSGIINAPLGRCKSNRLRRAVKGIDDKTADSAITHYQTIEIYNKNSNFAVSLLKCHL 252 (340)
Q Consensus 173 ~~~~~~~~v~K~Y~Aiv~G~~~~~~g~i~~~l~~~~~~~~~~~~~~~~~~~~k~a~T~~~~l~~~~~~~~~~~slv~~~~ 252 (340)
+ ++.|.|+|+|+|.|.++. .|+|+.||.+++..+.++.+ .+.|++|+|+|++++.+. .+|||+|+|
T Consensus 163 ~----~~~v~K~Y~Alv~G~~~~-~g~i~~pl~~~~~~~~~~~~----~~~gk~A~T~~~vl~~~~-----~~slv~~~l 228 (325)
T PRK11180 163 Q----KREITREYEAVAIGHMTA-GGTVDEPISRHPTKRTHMAV----HPMGKPAVTHYRIMEHFR-----VHTRLRLRL 228 (325)
T ss_pred H----HCCCCEEEEEEEEEEECC-CCEEECCCCCCCCCCEEEEE----CCCCEEECCHHHHHHHCC-----CCEEEEEEE
T ss_conf 7----388965999998104379-96585420137766628997----677702022101444358-----845799982
Q ss_pred CHHHHHHHHHHHHHHCCEEECCCCCCCCCCCCCCCCCCHHHHHHCCCCCHHHHHCEEEEECCCCCCEEEEECCCCHHHHH
Q ss_conf 11589999999987097860415447755444334570135544079804432100042468897689998499789999
Q gi|254780610|r 253 ETGRTHQIRVHMAHKGNPLIGDPLYGKGFKTKANIVNNNAKSAILSLARQALHAHSLSFSHPRNNQDMDFQVPIPEDMLT 332 (340)
Q Consensus 253 ~TGRtHQIRvhla~lG~PIvGD~~YG~~~~~~~~~~~~~~~~~~~~~~r~~LHA~~l~f~hP~t~~~~~f~aplP~~~~~ 332 (340)
+||||||||+||+++||||+||.+||+....... ..........+++||+|||++|+|.||.|++.++|+||||+||++
T Consensus 229 ~TGRtHQIRvHla~~G~PIvGD~~YG~~~~~~k~-~~~~~~~~~~~~~R~~LHA~~L~f~HP~t~~~~~~~aplP~d~~~ 307 (325)
T PRK11180 229 ETGRTHQIRVHMAHITHPLVGDQVYGGRPRPPKG-ASEEFISTLRKFDRQALHATMLRLYHPITGIEMEWHAPIPQDMVE 307 (325)
T ss_pred CCCCCHHHHHHHHHCCCCEECCCCCCCCCCCCCC-CCHHHHHHHHCCCCHHHHCCCCCCCCCCCCCEEEEECCCCHHHHH
T ss_conf 7588289999999879956375246886655544-347788876189766463184577578999879998069099999
Q ss_pred HHHHHHC
Q ss_conf 9998851
Q gi|254780610|r 333 VIRKLNE 339 (340)
Q Consensus 333 ~l~~L~~ 339 (340)
+|+.|+-
T Consensus 308 ~l~~Lr~ 314 (325)
T PRK11180 308 LIEALRA 314 (325)
T ss_pred HHHHHHH
T ss_conf 9999866
No 2
>TIGR00005 rluA_subfam pseudouridine synthase, RluA family; InterPro: IPR006225 This is the RluD subfamily of pseudouridine synthases. In Escherichia coli, RluD (SfhB) modifies uridine to pseudouridine at 23S RNA U1911, 1915, and 1917. RluC modifies 955, 2504 and 2580, and RluA modifies U746 and tRNA U32. An additional homologue from E. coli outside this family, TruC (Q46918 from SWISSPROT), modifies uracil-65 in transfer RNAs to pseudouridine. ; GO: 0003723 RNA binding, 0009982 pseudouridine synthase activity, 0001522 pseudouridine synthesis.
Probab=100.00 E-value=0 Score=599.63 Aligned_cols=309 Identities=46% Similarity=0.752 Sum_probs=277.6
Q ss_pred HHHCCCCHHHHHHHHCCCCCCHHHHHHHHHCCCEEECC-EEECCCCCEECCCCEEE-EEECCC-HHCCHHHHHHH----H
Q ss_conf 11368757899998717688989999999859904998-99328675804898899-970560-11110233222----2
Q gi|254780610|r 18 DSTAEGRIDRWLATSLKEQFSRSYVKILILNGFISING-MVSKNPNRKVVPGDSFL-ITVPAA-QKLNIAQENIP----L 90 (340)
Q Consensus 18 ~~~~g~RLD~~L~~~l~~~~sR~~i~kli~~G~V~vnG-~~~~~~~~~l~~gd~I~-i~~~~~-~~~~~~~~~~~----~ 90 (340)
++..|+|||+||++.|+ .+||+.++++|++|.|.||+ ++..+++++++.||.|. +..+.+ ....+.+++.| +
T Consensus 1 ~~~~g~Rld~~L~~~l~-~~sr~~~~~~i~~G~V~vN~~~~~~~~~~~~~~g~~~~~v~~~~~~~~~~~~~~~~p~~l~l 79 (337)
T TIGR00005 1 EEQAGQRLDDFLASLLP-DLSRSRIQKLIENGQVKVNKGKVTANPKLKIKDGDRITPVRVPEEQEELEVPVQDIPADLKL 79 (337)
T ss_pred CCCCCHHHHHHHHHHHC-CCCHHHHHHHHHCCCEEECCCCCCCCCCEEECCCCEEECEECCCCCCCCCCCCCCCCCCCCC
T ss_conf 97430269999999836-78888999998749689637642567430523874660100146433235766567342211
Q ss_pred HHCCCCCEEEEEECCCHHHCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHHH
Q ss_conf 21014402789962401110456787542100222222102443344443643244443323240572120357888899
Q gi|254780610|r 91 DILYEDDDIIVINKPAGLVVHPAPGNWTGTLVNALLYHCHNNLSSINGVKRPGIVHRLDKDTTGVMVVAKNDLAHQKLSE 170 (340)
Q Consensus 91 ~IlyED~~llvinKPaGl~vhp~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~lVHRLDr~TSGlll~Ak~~~a~~~l~~ 170 (340)
+||||||+|+|||||+||+|||++++..+|++++|++++......++...++++||||||+|||+|++||+..|+..|++
T Consensus 80 ~IlfEDe~i~vinKP~G~~vHP~~~~~~~Tv~~~L~~~~~~~~~gig~~~~~~~vHRLD~dTSGl~~vAK~~~A~~~L~~ 159 (337)
T TIGR00005 80 DILFEDEDILVINKPSGLVVHPGGGNSFGTVLNALLAHCPERLSGIGGVFRVGIVHRLDRDTSGLMVVAKTRLALRELQR 159 (337)
T ss_pred EEEEECCCEEEEECCCCEEECCCCCCCCHHHHHHHHHHCCCCCCCCCCCCCCCEEEECCCCCCEEEEEEECHHHHHHHHH
T ss_conf 37875083899978987564488888735489999986476643457612361355247787258999708689999999
Q ss_pred HHHHHCCCCCEEEEEEEEEECCCC-CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEECCCCCEEECCCCCCCCCEEE
Q ss_conf 999721132213344543202433-2332110013434443322123444555553000012221011256677500123
Q gi|254780610|r 171 QFVDHGKSTRLKRAYYAMVWGIPL-PDSGIINAPLGRCKSNRLRRAVKGIDDKTADSAITHYQTIEIYNKNSNFAVSLLK 249 (340)
Q Consensus 171 ~f~~~~~~~~v~K~Y~Aiv~G~~~-~~~g~i~~~l~~~~~~~~~~~~~~~~~~~~k~a~T~~~~l~~~~~~~~~~~slv~ 249 (340)
|| +++.+.|.|+|+|.|.+. ...|+|+.||+|+..++.+|.|...+.++||+|.|+|+++++. .....|||+
T Consensus 160 ql----~~~~~~k~Y~A~V~G~~~~~~~~~~~~P~~r~~~~~~~~~v~~~~~~~GK~A~T~f~~~~~~---A~~~~sl~~ 232 (337)
T TIGR00005 160 QL----KERTVTKEYVALVHGEFDLSKKGTVDAPLGRVPNNRGKMAVAPSSEKEGKPAVTHFKVLERI---ADGNASLVE 232 (337)
T ss_pred HH----HHCCCEEEEEEEEECCCCCCCCEEEECCCCCCCCCCEEEEEEECCCCCCCEEEEEEEEEHHH---CCCCCCEEE
T ss_conf 99----83861178999983176887644780653236886026899767888896123421210011---044521899
Q ss_pred EEECHHHHHHHHHHHHHHCCEEECCCCCCCCCCCCCCCCCCHHHHHHCCCCCHHHHHCEEEEECCCC---------CCEE
Q ss_conf 4431158999999998709786041544775544433457013554407980443210004246889---------7689
Q gi|254780610|r 250 CHLETGRTHQIRVHMAHKGNPLIGDPLYGKGFKTKANIVNNNAKSAILSLARQALHAHSLSFSHPRN---------NQDM 320 (340)
Q Consensus 250 ~~~~TGRtHQIRvhla~lG~PIvGD~~YG~~~~~~~~~~~~~~~~~~~~~~r~~LHA~~l~f~hP~t---------~~~~ 320 (340)
|+|+|||||||||||+++||||+||++||.......... ......+.||+|||++|.|.||.+ |+.+
T Consensus 233 ~~L~TGRTHQIRVHl~~~ghPl~gD~~YG~~~~~~~~~g----~~~~~~~~~q~LHA~~l~f~HP~~~~W~~~~~~ge~~ 308 (337)
T TIGR00005 233 CELETGRTHQIRVHLQYLGHPLAGDPLYGNKPKKGNNLG----LEGLLNFDRQALHAYELGFIHPATSSWYHNETKGELL 308 (337)
T ss_pred EEECCCCCHHHHHHHHHHCCCEECCCCCCCCCCCCCCCC----CCCCCCCCCEEEEHHHHHCCCCCCCCCCCCCCCCCEE
T ss_conf 985348973899999971685314325688887832145----1003675402311455310378886621447787143
Q ss_pred E-----------EECCCCHHHHHHHHHHH
Q ss_conf 9-----------98499789999999885
Q gi|254780610|r 321 D-----------FQVPIPEDMLTVIRKLN 338 (340)
Q Consensus 321 ~-----------f~aplP~~~~~~l~~L~ 338 (340)
+ |+||+|++|..+|+.|+
T Consensus 309 ~~~~C~~Ce~~~~~AP~p~~~~~~l~~L~ 337 (337)
T TIGR00005 309 EGKKCSECETELFEAPLPADLKELLEALR 337 (337)
T ss_pred CCCCCCCCCCCHHHCCCCHHHHHHHHHCC
T ss_conf 26505324762110588079999999609
No 3
>PRK11025 23S rRNA pseudouridylate synthase C; Provisional
Probab=100.00 E-value=0 Score=570.92 Aligned_cols=304 Identities=31% Similarity=0.447 Sum_probs=252.1
Q ss_pred HCCCEEEEEECHHHCCCCHHHHHHHHCCCCCCHHHHHHHHHCCCEEECCEEECCCCCEECCCCEEEEEECCCH---HCCH
Q ss_conf 0162499995711368757899998717688989999999859904998993286758048988999705601---1110
Q gi|254780610|r 7 NCSSIKISLLSDSTAEGRIDRWLATSLKEQFSRSYVKILILNGFISINGMVSKNPNRKVVPGDSFLITVPAAQ---KLNI 83 (340)
Q Consensus 7 ~~~~~~~~~V~~~~~g~RLD~~L~~~l~~~~sR~~i~kli~~G~V~vnG~~~~~~~~~l~~gd~I~i~~~~~~---~~~~ 83 (340)
-..+|++++|+++++|+|||+||++.|+ ++||++++++|++|.|+|||+++ +++++|..||.|.+...... ..+.
T Consensus 4 ~~~~v~~i~V~~~~~G~RLD~fL~~~l~-~~srs~i~klir~g~V~VNg~~v-k~~~~l~~GD~I~i~~~~~~~~~~~p~ 81 (317)
T PRK11025 4 ETPSVKIVAISADEAGQRIDNFLRTQLK-GVPKSMIYRILRKGEVRVNKKRI-KPEYKLEAGDEVRIPPVRVAEREEEAV 81 (317)
T ss_pred CCCCCEEEEECCCCCCCHHHHHHHHHCC-CCCHHHHHHHHHCCCEEECCEEC-CCCCCCCCCCEEEECCCCCCCCCCCCC
T ss_conf 8996279998930079759999997566-26999999999869989999995-710465799999988866564445778
Q ss_pred HH-----HHHHHHHCCCCCEEEEEECCCHHHCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCEEEE
Q ss_conf 23-----3222221014402789962401110456787542100222222102443344443643244443323240572
Q gi|254780610|r 84 AQ-----ENIPLDILYEDDDIIVINKPAGLVVHPAPGNWTGTLVNALLYHCHNNLSSINGVKRPGIVHRLDKDTTGVMVV 158 (340)
Q Consensus 84 ~~-----~~~~~~IlyED~~llvinKPaGl~vhp~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~lVHRLDr~TSGlll~ 158 (340)
.+ ..++++|||||++|+|||||+||+|||+++...+ +++.+..... ....+++||||||+|||||||
T Consensus 82 ~~~~~~~~~l~~~IlyED~~llvvnKPaGl~vhp~~~~~~~-~~~~l~~~~~-------~~~~~~iVHRLDr~TSGllv~ 153 (317)
T PRK11025 82 SPHLQKVAALADVILYEDDHILVLNKPSGTAVHGGSGLSFG-VIEGLRALRP-------EARFLELVHRLDRDTSGVLLV 153 (317)
T ss_pred CCCCCCCCCCCCEEEEECCCEEEEECCCCCEECCCCCCHHH-HHHHHHHHCC-------CCCCCCCEECCCCCCCEEEEE
T ss_conf 85511002455607994798899977435622688873168-9999997588-------887678131269987426887
Q ss_pred ECCHHHHHHHHHHHHHHCCCCCEEEEEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEECCCCCEEEC
Q ss_conf 12035788889999972113221334454320243323321100134344433221234445555530000122210112
Q gi|254780610|r 159 AKNDLAHQKLSEQFVDHGKSTRLKRAYYAMVWGIPLPDSGIINAPLGRCKSNRLRRAVKGIDDKTADSAITHYQTIEIYN 238 (340)
Q Consensus 159 Ak~~~a~~~l~~~f~~~~~~~~v~K~Y~Aiv~G~~~~~~g~i~~~l~~~~~~~~~~~~~~~~~~~~k~a~T~~~~l~~~~ 238 (340)
|||..|++.|++||+ ++.|.|+|+|+|.|.+....++|+.||.++.....++.+. ....|++|.|+|++++.+.
T Consensus 154 AK~~~a~~~l~~~f~----~r~v~K~Y~Alv~G~~~~~~~~i~~pl~~~~~~~~~~~~~--~~~~gk~a~T~~~v~~~~~ 227 (317)
T PRK11025 154 AKKRSALRSLHEQLR----EKGMQKDYLALVRGQWQSHVKVVQAPLLKNILQSGERIVR--VSQEGKPSETRFKVEERYA 227 (317)
T ss_pred ECCHHHHHHHHHHHH----HCCCCCEEEEEEECCCCCCCCEEEEEECCCCCCCCCEEEE--CCCCCCCCHHHHHHHHHCC
T ss_conf 168999999999997----3725755999982763677887961000466767645662--2777776410144676527
Q ss_pred CCCCCCCCEEEEEECHHHHHHHHHHHHHHCCEEECCCCCCCCCCCCCCCCCCHHHHHHCCCCCHHHHHCEEEEECCCCCC
Q ss_conf 56677500123443115899999999870978604154477554443345701355440798044321000424688976
Q gi|254780610|r 239 KNSNFAVSLLKCHLETGRTHQIRVHMAHKGNPLIGDPLYGKGFKTKANIVNNNAKSAILSLARQALHAHSLSFSHPRNNQ 318 (340)
Q Consensus 239 ~~~~~~~slv~~~~~TGRtHQIRvhla~lG~PIvGD~~YG~~~~~~~~~~~~~~~~~~~~~~r~~LHA~~l~f~hP~t~~ 318 (340)
.+|||+|+|+|||||||||||+++||||+||.+||+...... ....+++||+|||++|+|.||.||+
T Consensus 228 -----~~sLv~~~~~TGRtHQIRvHla~~G~PI~GD~~YG~~~~~~~--------~~~~~~~R~~LHA~~L~F~HP~t~~ 294 (317)
T PRK11025 228 -----FATLVRASPVTGRTHQIRVHTQYAGHPIAFDDRYGDREFDQQ--------LTGTGLNRLFLHAAALKFTHPGTGE 294 (317)
T ss_pred -----CCCCEEEECCCCCHHHHHHHHHHCCCCEECCCCCCCCCCCHH--------HHCCCCCCHHHHCCCCEEECCCCCC
T ss_conf -----864005755807589999999877996838520287421202--------3036885543521865718889998
Q ss_pred EEEEECCCCHHHHHHHHHHHC
Q ss_conf 899984997899999998851
Q gi|254780610|r 319 DMDFQVPIPEDMLTVIRKLNE 339 (340)
Q Consensus 319 ~~~f~aplP~~~~~~l~~L~~ 339 (340)
.++|+||+|+||+++|+.|+.
T Consensus 295 ~~~f~aplP~d~~~~l~~Lr~ 315 (317)
T PRK11025 295 VMRIEAPLDNQLKRCLQKLRN 315 (317)
T ss_pred EEEEECCCHHHHHHHHHHHHC
T ss_conf 699982684999999999862
No 4
>COG0564 RluA Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=0 Score=544.57 Aligned_cols=288 Identities=50% Similarity=0.808 Sum_probs=255.6
Q ss_pred EEEEEECHHHCCCCHHHHHHHHCCCCCCHHHHHHHHHCCCEEECCEEECCCCCEECCCCEEEEEECCCH-HCCHHHHHHH
Q ss_conf 499995711368757899998717688989999999859904998993286758048988999705601-1110233222
Q gi|254780610|r 11 IKISLLSDSTAEGRIDRWLATSLKEQFSRSYVKILILNGFISINGMVSKNPNRKVVPGDSFLITVPAAQ-KLNIAQENIP 89 (340)
Q Consensus 11 ~~~~~V~~~~~g~RLD~~L~~~l~~~~sR~~i~kli~~G~V~vnG~~~~~~~~~l~~gd~I~i~~~~~~-~~~~~~~~~~ 89 (340)
+..+.|.++.+|+|||+||+. +.+ +||+++++++++|+|+|||++++ ++++|..||.|.+..+... .....+++++
T Consensus 1 ~~~~~i~~~~~g~rld~~L~~-l~~-~sr~~~~~~i~~g~v~vNg~~v~-~~~~l~~gd~i~~~~~~~~~~~~~~~~~~~ 77 (289)
T COG0564 1 MLEFEVPEEEAGQRLDKFLAK-LLP-ISRSRIQKLIRKGRVRVNGKKVK-PSYKLKPGDVVRIPLPEEPEEEKLVPEDIP 77 (289)
T ss_pred CCEEEECCHHCCCCHHHHHHH-HCC-CCHHHHHHHHHCCCEEECCEECC-CCEEECCCCEEEEECCCCCCCCCCCCCCCC
T ss_conf 944883611135479999987-257-47999999988898899999835-871608999999535655433345654778
Q ss_pred HHHCCCCCEEEEEECCCHHHCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHH
Q ss_conf 22101440278996240111045678754210022222210244334444364324444332324057212035788889
Q gi|254780610|r 90 LDILYEDDDIIVINKPAGLVVHPAPGNWTGTLVNALLYHCHNNLSSINGVKRPGIVHRLDKDTTGVMVVAKNDLAHQKLS 169 (340)
Q Consensus 90 ~~IlyED~~llvinKPaGl~vhp~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~lVHRLDr~TSGlll~Ak~~~a~~~l~ 169 (340)
++|||||++++|||||+||+|||++++..+|+++++++++... ..++++||||||+|||+||+|||..|++.|+
T Consensus 78 l~IlyED~~llVvnKP~Gl~vhp~~~~~~~tl~~~l~~~~~~~------~~~~~~vHRLDkdTSGlll~AK~~~a~~~l~ 151 (289)
T COG0564 78 LDILYEDEDLLVVNKPAGLVVHPGGGHHEGTLVNALLRHCQDG------VERPGIVHRLDKDTSGLLLVAKNREAARELS 151 (289)
T ss_pred CCEEEECCCEEEEECCCCCEECCCCCCCCHHHHHHHHHHCCCC------CCCEEEECCCCCCCCEEEEEECCHHHHHHHH
T ss_conf 7779976999999889997167798875267999998752334------7864351488999856999995999999999
Q ss_pred HHHHHHCCCCCEEEEEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEECCCCCEEECCCCCCCCCEEE
Q ss_conf 99997211322133445432024332332110013434443322123444555553000012221011256677500123
Q gi|254780610|r 170 EQFVDHGKSTRLKRAYYAMVWGIPLPDSGIINAPLGRCKSNRLRRAVKGIDDKTADSAITHYQTIEIYNKNSNFAVSLLK 249 (340)
Q Consensus 170 ~~f~~~~~~~~v~K~Y~Aiv~G~~~~~~g~i~~~l~~~~~~~~~~~~~~~~~~~~k~a~T~~~~l~~~~~~~~~~~slv~ 249 (340)
+||++ +.+.|+|+|+|.|.+++++|+|+.||+++..++.++.+..... |++|+|+|++++++... +||++
T Consensus 152 ~~f~~----r~v~K~Y~Alv~G~~~~~~~~i~~pi~r~~~~~~~~~v~~~~~--gk~A~T~~~~~~~~~~~----~tlv~ 221 (289)
T COG0564 152 EQFKQ----RKVKKTYLALVRGHLPEDEGTIDAPIGRDPKNRKKMAVVKEGS--GKPAITHYEVLERFGDN----YTLVE 221 (289)
T ss_pred HHHHC----CCCCEEEEEEEECCCCCCCCEEECCCCCCCCCCCCEEEECCCC--CCCEEEEEEEEEECCCC----CEEEE
T ss_conf 99851----8661799999968556668788354106767762169971688--98337999972063876----28999
Q ss_pred EEECHHHHHHHHHHHHHHCCEEECCCCCCCCCCCCCCCCCCHHHHHHCCCCCHHHHHCEEEEECCCCCCEEEEECCCCH
Q ss_conf 4431158999999998709786041544775544433457013554407980443210004246889768999849978
Q gi|254780610|r 250 CHLETGRTHQIRVHMAHKGNPLIGDPLYGKGFKTKANIVNNNAKSAILSLARQALHAHSLSFSHPRNNQDMDFQVPIPE 328 (340)
Q Consensus 250 ~~~~TGRtHQIRvhla~lG~PIvGD~~YG~~~~~~~~~~~~~~~~~~~~~~r~~LHA~~l~f~hP~t~~~~~f~aplP~ 328 (340)
|+|+|||||||||||+++||||+||++||+.. ........||+|||+.|.|.||.+++.++|+||+|.
T Consensus 222 ~~~~TGRTHQIRvHl~~lghPI~GD~~Yg~~~-----------~~~~~~~~r~~LHA~~l~f~hp~t~~~~~~~a~~p~ 289 (289)
T COG0564 222 LKPETGRTHQIRVHLAHLGHPIVGDPLYGGKD-----------KSAGAGLKRQALHAYKLSFTHPLTGEELEFEAPLPE 289 (289)
T ss_pred EEECCCCHHHHHHHHHHCCCCEECCCCCCCCC-----------CCCCCCCCHHHHHHHHHCCCCCCCCCEEEEECCCCC
T ss_conf 99688985199999998799743874678742-----------112356214788753517788999977999568899
No 5
>cd02558 PSRA_1 PSRA_1: Pseudouridine synthase, a subgroup of the RluA family. This group is comprised of bacterial proteins assigned to the RluA family of pseudouridine synthases. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. The RluA family is comprised of proteins related to Escherichia coli RluA.
Probab=100.00 E-value=0 Score=452.74 Aligned_cols=241 Identities=22% Similarity=0.260 Sum_probs=192.4
Q ss_pred EEECCEEECCCCCEECCCCEEEEEECCCHHCCHHHHHHHHHHCCCCCEEEEEECCCHHHCCCCCCCCCCCCHHHHHHHHC
Q ss_conf 04998993286758048988999705601111023322222101440278996240111045678754210022222210
Q gi|254780610|r 51 ISINGMVSKNPNRKVVPGDSFLITVPAAQKLNIAQENIPLDILYEDDDIIVINKPAGLVVHPAPGNWTGTLVNALLYHCH 130 (340)
Q Consensus 51 V~vnG~~~~~~~~~l~~gd~I~i~~~~~~~~~~~~~~~~~~IlyED~~llvinKPaGl~vhp~~~~~~~tl~~~l~~~~~ 130 (340)
|+|||++++ ++++|+.||.|.+..+++.++. .+++++||||||+|+|||||+||+|||++++..+|+++.+..++.
T Consensus 4 v~~~G~~v~-~~~~l~~Gd~v~~~~~~~~e~p---~p~~l~IlyEDd~llVVnKPaGl~vhP~~~~~~~tl~~~l~~~~~ 79 (246)
T cd02558 4 VDADGEPLD-PDSPYRPGTFVWYYRELPDEPP---IPFEETILHQDEHLLVADKPHFLPVTPRGRYVTETLLVRLRRQTG 79 (246)
T ss_pred ECCCCEECC-CCCEECCCCEEEEEECCCCCCC---CCCCCCEEEECCCEEEEECCCCCCEEECCCCCCCHHHHHHHHHCC
T ss_conf 880997979-9987279999999805899999---999899899789999999999985761899720179999988409
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHHHHHHHHCCCCCEEEEEEEEEECCCCCCCC-CCCCCCCCCCC
Q ss_conf 24433444436432444433232405721203578888999997211322133445432024332332-11001343444
Q gi|254780610|r 131 NNLSSINGVKRPGIVHRLDKDTTGVMVVAKNDLAHQKLSEQFVDHGKSTRLKRAYYAMVWGIPLPDSG-IINAPLGRCKS 209 (340)
Q Consensus 131 ~~~~~~~~~~~~~lVHRLDr~TSGlll~Ak~~~a~~~l~~~f~~~~~~~~v~K~Y~Aiv~G~~~~~~g-~i~~~l~~~~~ 209 (340)
. ..+++||||||+||||||||||+.+++.|++||+ ++.|.|+|+|+|.|.+..+.+ .+...+.+.
T Consensus 80 ~--------~~~~~VHRLDr~TSGllv~AK~~~a~~~l~~~f~----~r~v~K~Y~Alv~~~~~~~~~~~~~~~~~~~-- 145 (246)
T cd02558 80 N--------PDLTPAHRLDRLTAGLVLFSKRPETRGAYQTLFA----RREVSKTYEAVAPYVPALTFPLTVRSRIVKG-- 145 (246)
T ss_pred C--------CCCCEECCCCCCCCEEEEEECCHHHHHHHHHHHH----CCCCCEEEEEEEECCCCCCCCEEECCCCCCC--
T ss_conf 9--------8654734679987469999889999999999864----6845279999998337767863663655788--
Q ss_pred CCCCCCCCCCCCCCCCCCEECCCCCEEECCCCCCCCCEEEEEECHHHHHHHHHHHHHHCCEEECCCCCCCCCCCCCCCCC
Q ss_conf 33221234445555530000122210112566775001234431158999999998709786041544775544433457
Q gi|254780610|r 210 NRLRRAVKGIDDKTADSAITHYQTIEIYNKNSNFAVSLLKCHLETGRTHQIRVHMAHKGNPLIGDPLYGKGFKTKANIVN 289 (340)
Q Consensus 210 ~~~~~~~~~~~~~~~k~a~T~~~~l~~~~~~~~~~~slv~~~~~TGRtHQIRvhla~lG~PIvGD~~YG~~~~~~~~~~~ 289 (340)
+.... .....+++.|.|+|++++.. ..+||++|+|+||||||||+||+++||||+||.+||+........
T Consensus 146 -~~~~~--~~~~~g~~~A~T~~~~l~~~-----~~~slv~~~~~TGRtHQIRvHla~iGhPIvGD~~Yg~~~~~~~~~-- 215 (246)
T cd02558 146 -RGFFQ--AREVEGEPNAETRIELLARR-----GGWGLYRLSPHTGKTHQLRVHMAALGVPILNDPFYPVLLDKDPDD-- 215 (246)
T ss_pred -CCCEE--EECCCCCCCEEEEEEEEEEC-----CCEEEEEEEECCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCC--
T ss_conf -76448--98058998769999999983-----985899999687862999999998799350783777644344334--
Q ss_pred CHHHHHHCCCCCHHHHHCEEEEECCCCCCEEEEECCCC
Q ss_conf 01355440798044321000424688976899984997
Q gi|254780610|r 290 NNAKSAILSLARQALHAHSLSFSHPRNNQDMDFQVPIP 327 (340)
Q Consensus 290 ~~~~~~~~~~~r~~LHA~~l~f~hP~t~~~~~f~aplP 327 (340)
...+++|||++|+|.||.||+.++|+||.|
T Consensus 216 --------~~~~l~LHA~~L~F~HP~T~e~m~F~aP~~ 245 (246)
T cd02558 216 --------FSRPLQLLAKELEFTDPLTGRPRRFESGRS 245 (246)
T ss_pred --------CCCCCHHHHCEEEEECCCCCCEEEEECCCC
T ss_conf --------463302520784878929989889968998
No 6
>PRK11112 tRNA pseudouridine synthase C; Provisional
Probab=100.00 E-value=0 Score=449.63 Aligned_cols=230 Identities=27% Similarity=0.457 Sum_probs=182.5
Q ss_pred HHHCCCCCEEEEEECCCHHHCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHH
Q ss_conf 22101440278996240111045678754210022222210244334444364324444332324057212035788889
Q gi|254780610|r 90 LDILYEDDDIIVINKPAGLVVHPAPGNWTGTLVNALLYHCHNNLSSINGVKRPGIVHRLDKDTTGVMVVAKNDLAHQKLS 169 (340)
Q Consensus 90 ~~IlyED~~llvinKPaGl~vhp~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~lVHRLDr~TSGlll~Ak~~~a~~~l~ 169 (340)
++|||||++|||||||+||+|||+.....++.. +...+.... ...+++||||||+||||||||||+.+++.|+
T Consensus 2 L~IlyED~~llVVnKPaGl~vh~~~~~~~~~~~--~~~~l~~~~-----~~~~~~VHRLDr~TSGllv~AK~~~a~~~L~ 74 (257)
T PRK11112 2 LEILYQDEWLVAVNKPAGWLVHRSWLDRHETVF--VMQTVRDQI-----GQHVFTAHRLDRPTSGVLLMALSSEAARLLA 74 (257)
T ss_pred EEEEEECCCEEEEECCCCCCCCCCCCCCCCCHH--HHHHHHHHC-----CCCCCCCCCCCCCCCEEEEEECCHHHHHHHH
T ss_conf 579996698999999999864799888785199--999998752-----7765320577898751799968999999999
Q ss_pred HHHHHHCCCCCEEEEEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEECCCCCEEEC------CCCCC
Q ss_conf 999972113221334454320243323321100134344433221234445555530000122210112------56677
Q gi|254780610|r 170 EQFVDHGKSTRLKRAYYAMVWGIPLPDSGIINAPLGRCKSNRLRRAVKGIDDKTADSAITHYQTIEIYN------KNSNF 243 (340)
Q Consensus 170 ~~f~~~~~~~~v~K~Y~Aiv~G~~~~~~g~i~~~l~~~~~~~~~~~~~~~~~~~~k~a~T~~~~l~~~~------~~~~~ 243 (340)
+||+ +++|+|+|+|+|.|.+. +.++|+.|+.+........ .......+++|.|+|++++... .....
T Consensus 75 ~~f~----~~~v~K~Y~Alv~G~~~-~~~~i~~~l~~~~~~~~~~--~~~~~~~~k~a~T~~~~l~~~~~~~~~~~~~~~ 147 (257)
T PRK11112 75 QQFE----QHQIQKTYHAIVRGWLM-EEAVLDYPLKEELDKIADK--FAREDKEPQPAVTHYRGLATVEMPVATGRYPTT 147 (257)
T ss_pred HHHH----HCCCCEEEEEEEEEECC-CCCEEEEECCCCCCCCCCE--EECCCCCCEEEEEEEEEEEEEEEECCCCCCCCC
T ss_conf 9987----57686399999964538-9976852434466655631--302289863634541110268751012324678
Q ss_pred CCCEEEEEECHHHHHHHHHHHHHHCCEEECCCCCCCCCCCCCCCCCCHHHHHHCCCCCHHHHHCEEEEECCCCCCEEEEE
Q ss_conf 50012344311589999999987097860415447755444334570135544079804432100042468897689998
Q gi|254780610|r 244 AVSLLKCHLETGRTHQIRVHMAHKGNPLIGDPLYGKGFKTKANIVNNNAKSAILSLARQALHAHSLSFSHPRNNQDMDFQ 323 (340)
Q Consensus 244 ~~slv~~~~~TGRtHQIRvhla~lG~PIvGD~~YG~~~~~~~~~~~~~~~~~~~~~~r~~LHA~~l~f~hP~t~~~~~f~ 323 (340)
.+|||+|+|+|||||||||||+++||||+||.+||+...+ .......+++||||||++|+|+||.||+.++|+
T Consensus 148 ~~sLv~~~p~TGRtHQIRvHla~lGhPIvGD~~YG~~~~~-------~~~~~~~~~~R~~LHA~~L~F~HP~tge~~~~~ 220 (257)
T PRK11112 148 RYSLVELEPKTGRKHQLRRHMAHLRHPIIGDSKHGDLRQN-------RSFAEHFGCSRLMLHASELSLTHPFTGEPLTIT 220 (257)
T ss_pred CEEEEEEECCCCCHHHHHHHHHHCCCCEECCCCCCCCCCC-------CHHHHCCCCCCHHHCCCCCEEECCCCCCEEEEE
T ss_conf 5799999648685299999999879967577255875446-------014542399636550183475785999869998
Q ss_pred CCCCHHHHHHHHHHHCC
Q ss_conf 49978999999988519
Q gi|254780610|r 324 VPIPEDMLTVIRKLNEK 340 (340)
Q Consensus 324 aplP~~~~~~l~~L~~~ 340 (340)
||||+||+++|++|.-+
T Consensus 221 AplP~d~~~ll~~~g~~ 237 (257)
T PRK11112 221 AGLDETWQQLLSQFGWR 237 (257)
T ss_pred CCCHHHHHHHHHHCCCC
T ss_conf 16859999999976998
No 7
>PRK10158 23S rRNA/tRNA pseudouridine synthase A; Provisional
Probab=100.00 E-value=0 Score=415.08 Aligned_cols=210 Identities=34% Similarity=0.533 Sum_probs=171.3
Q ss_pred HHHHHHHHHCCCCCEEEEEECCCHHHCCCCCCCC-CCCCHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCH
Q ss_conf 2332222210144027899624011104567875-421002222221024433444436432444433232405721203
Q gi|254780610|r 84 AQENIPLDILYEDDDIIVINKPAGLVVHPAPGNW-TGTLVNALLYHCHNNLSSINGVKRPGIVHRLDKDTTGVMVVAKND 162 (340)
Q Consensus 84 ~~~~~~~~IlyED~~llvinKPaGl~vhp~~~~~-~~tl~~~l~~~~~~~~~~~~~~~~~~lVHRLDr~TSGlll~Ak~~ 162 (340)
.|++.+++|||||++|+|||||+||++||+.... ..++...+ ... ...+.+||||||+||||||||||+
T Consensus 8 pp~~~~l~IlyED~~llvvnKP~gl~~~pg~~~~~~~~~~~~~----~~~------~~~~~~vHRLDr~TSGlll~AK~~ 77 (219)
T PRK10158 8 PPQEPWLVILYQDDHIMVVNKPSGLLSVPGRLEEHKDSVMTRI----QRD------YPQAESVHRLDMATSGVIVVALTK 77 (219)
T ss_pred CCCCCCCCEEEECCCEEEEECCCCCCCCCCCCCCCCHHHHHHH----HHC------CCCCCCCCCCCCCCCCEEEEECCH
T ss_conf 8899995689979999999999998207997645620699987----740------786663477899975369997899
Q ss_pred HHHHHHHHHHHHHCCCCCEEEEEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEECCCCCEEECCCCC
Q ss_conf 57888899999721132213344543202433233211001343444332212344455555300001222101125667
Q gi|254780610|r 163 LAHQKLSEQFVDHGKSTRLKRAYYAMVWGIPLPDSGIINAPLGRCKSNRLRRAVKGIDDKTADSAITHYQTIEIYNKNSN 242 (340)
Q Consensus 163 ~a~~~l~~~f~~~~~~~~v~K~Y~Aiv~G~~~~~~g~i~~~l~~~~~~~~~~~~~~~~~~~~k~a~T~~~~l~~~~~~~~ 242 (340)
.+++.|+++|+ +++|.|+|+|+|.|.+.+.+|+|+.|+..+..++.++.+ ....|++|.|+|++++.. .
T Consensus 78 ~a~~~l~~~f~----~r~v~K~YlA~v~G~~~~~~g~i~~~l~~~~~~~~~~~~---~~~~gk~a~t~~~~l~~~----~ 146 (219)
T PRK10158 78 AAERELKRQFR----EREPKKQYVARVWGHPSPAEGLVDLPLICDWPNRPKQKV---CYETGKPAQTEYEVVEYA----A 146 (219)
T ss_pred HHHHHHHHHHH----HCCCCCEEEEEEECCCCCCCCCCCCCEEECCCCCCCEEE---ECCCCCCCCEEEEEEEEC----C
T ss_conf 99999988787----374673799998368664356112452504777761699---724674121589999973----8
Q ss_pred CCCCEEEEEECHHHHHHHHHHHHHHCCEEECCCCCCCCCCCCCCCCCCHHHHHHCCCCCHHHHHCEEEEECCCCCCEEEE
Q ss_conf 75001234431158999999998709786041544775544433457013554407980443210004246889768999
Q gi|254780610|r 243 FAVSLLKCHLETGRTHQIRVHMAHKGNPLIGDPLYGKGFKTKANIVNNNAKSAILSLARQALHAHSLSFSHPRNNQDMDF 322 (340)
Q Consensus 243 ~~~slv~~~~~TGRtHQIRvhla~lG~PIvGD~~YG~~~~~~~~~~~~~~~~~~~~~~r~~LHA~~l~f~hP~t~~~~~f 322 (340)
..+++|+|+|+||||||||+||+++|||||||.+||...... ..+|++|||++|+|.||.|++.++|
T Consensus 147 ~~~~lv~l~p~TGRtHQIRvhla~lG~PIvGD~~Yg~~~~~~-------------~~~rl~LHA~~L~f~HP~t~~~~~~ 213 (219)
T PRK10158 147 DNTARVVLKPITGRSHQLRVHMLALGHPILGDRFYASPEARA-------------MAPRLLLHAEMLTITHPAYGNSMTF 213 (219)
T ss_pred CCEEEEEEEECCCCHHHHHHHHHHCCCCEECCCCCCCCCCCC-------------CCCCHHHHCCEEEEECCCCCCEEEE
T ss_conf 985999998666851899999998799274787778843246-------------7758304108758588299998999
Q ss_pred ECCCC
Q ss_conf 84997
Q gi|254780610|r 323 QVPIP 327 (340)
Q Consensus 323 ~aplP 327 (340)
+||.|
T Consensus 214 ~aP~~ 218 (219)
T PRK10158 214 KAPAD 218 (219)
T ss_pred ECCCC
T ss_conf 67999
No 8
>cd02563 PseudoU_synth_TruC tRNA pseudouridine isomerase C: Pseudouridine synthases catalyze the isomerization of specific uridines in an tRNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. TruC makes psi65 in tRNAs. This psi residue is not universally conserved.
Probab=100.00 E-value=0 Score=406.27 Aligned_cols=217 Identities=33% Similarity=0.515 Sum_probs=167.4
Q ss_pred HHHCCCCCEEEEEECCCHHHCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHH
Q ss_conf 22101440278996240111045678754210022222210244334444364324444332324057212035788889
Q gi|254780610|r 90 LDILYEDDDIIVINKPAGLVVHPAPGNWTGTLVNALLYHCHNNLSSINGVKRPGIVHRLDKDTTGVMVVAKNDLAHQKLS 169 (340)
Q Consensus 90 ~~IlyED~~llvinKPaGl~vhp~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~lVHRLDr~TSGlll~Ak~~~a~~~l~ 169 (340)
++||||||+|+|||||+||+|||++....++.... ..+...+ ...+++||||||+||||||||||+.+++.|+
T Consensus 1 l~IvyED~~ilvvnKP~Gl~~hp~~~~~~~~~~~~--~~~~~~~-----~~~~~~vHRLDr~TSGllv~Ak~~~a~~~l~ 73 (223)
T cd02563 1 LEILYQDEHLVAINKPSGLLVHRSELDRHETRFAL--QTLRDQL-----GQHVYPVHRLDRPTSGVLLFALSSEVARKLG 73 (223)
T ss_pred CEEEEECCCEEEEECCCCCCCCCCCCCCCCHHHHH--HHHHHHC-----CCCCCEECCCCCCCCCEEEEECCHHHHHHHH
T ss_conf 97999679999999999982658999988369999--9988753-----7875340477898763599984589999999
Q ss_pred HHHHHHCCCCCEEEEEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEECCCCCEEEC------CCCCC
Q ss_conf 999972113221334454320243323321100134344433221234445555530000122210112------56677
Q gi|254780610|r 170 EQFVDHGKSTRLKRAYYAMVWGIPLPDSGIINAPLGRCKSNRLRRAVKGIDDKTADSAITHYQTIEIYN------KNSNF 243 (340)
Q Consensus 170 ~~f~~~~~~~~v~K~Y~Aiv~G~~~~~~g~i~~~l~~~~~~~~~~~~~~~~~~~~k~a~T~~~~l~~~~------~~~~~ 243 (340)
++|+ ++.|.|+|+|+|.|.++ ..+.++.++........++.+ .....++.+.|.|+++.... .....
T Consensus 74 ~~f~----~~~v~K~Y~Alv~G~~~-~~~~i~~~l~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 146 (223)
T cd02563 74 EQFT----EHRVHKTYLAVVRGYVP-ESGTIDYPLSEELDKLADKFA--SDDKAPQAATTHYRLLAVEELPVVVGKYPTS 146 (223)
T ss_pred HHHH----HCCCCCEEEEEEEEECC-CCCEEEEECCCCCCCCCCEEE--ECCCCCCCEEEEEEEEEEEECCEEECCCCCC
T ss_conf 9987----55112269999984079-998798654546775563687--4278876348898876553200010114777
Q ss_pred CCCEEEEEECHHHHHHHHHHHHHHCCEEECCCCCCCCCCCCCCCCCCHHHHHHCCCCCHHHHHCEEEEECCCCCCEEEEE
Q ss_conf 50012344311589999999987097860415447755444334570135544079804432100042468897689998
Q gi|254780610|r 244 AVSLLKCHLETGRTHQIRVHMAHKGNPLIGDPLYGKGFKTKANIVNNNAKSAILSLARQALHAHSLSFSHPRNNQDMDFQ 323 (340)
Q Consensus 244 ~~slv~~~~~TGRtHQIRvhla~lG~PIvGD~~YG~~~~~~~~~~~~~~~~~~~~~~r~~LHA~~l~f~hP~t~~~~~f~ 323 (340)
.+||++|+|+||||||||+||+++||||+||.+||+..... ......+++||+|||++|+|.||.||+.+.|+
T Consensus 147 ~~slv~~~~~TGRtHQIRvHla~lG~PIvGD~~YG~~~~~~-------~~~~~~~~~rl~LHA~~L~F~HP~tge~i~~e 219 (223)
T cd02563 147 RYSLVELTPHTGRKHQLRRHLAHIRHPIIGDTTHGDGRHNR-------FFREHFGCHRLLLAATRLEFTHPVTGERLLIE 219 (223)
T ss_pred CEEEEEEEECCCCHHHHHHHHHHCCCCEECCCCCCCCCCCH-------HHHHCCCCCCHHHHCCEEEEECCCCCCEEEEE
T ss_conf 47999999676870899999998799782772568754350-------23530499686474087483885999889998
Q ss_pred CCCC
Q ss_conf 4997
Q gi|254780610|r 324 VPIP 327 (340)
Q Consensus 324 aplP 327 (340)
|||.
T Consensus 220 aPl~ 223 (223)
T cd02563 220 APLD 223 (223)
T ss_pred CCCC
T ss_conf 3699
No 9
>cd02557 PseudoU_synth_ScRIB2 PseudoU_synth_ScRIB2_like: Pseudouridine synthase, Saccharomyces cerevisiae RIB2_like. This group is comprised of eukaryotic and bacterial proteins similar to Saccharomyces cerevisiae RIB2, S. cerevisiae Pus6p and human hRPUDSD2. S. cerevisiae RIB2 displays two distinct catalytic activities. The N-terminal domain of RIB2 is RNA:psi-synthase which makes psi32 on cytoplasmic tRNAs. Psi32 is highly phylogenetically conserved. The C-terminal domain of RIB2 has a DRAP deaminase activity which catalyses the formation of 5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione 5'-phosphate from 2,5-diamino-6-ribitylamino-4(3H)-pyrimidinone 5'-phosphate during riboflavin biosynthesis. S. cerevisiae Pus6p makes the psi31 of cytoplasmic and mitochondrial tRNAs.
Probab=100.00 E-value=0 Score=392.40 Aligned_cols=198 Identities=30% Similarity=0.507 Sum_probs=165.8
Q ss_pred HHHHHHCCCCCEEEEEECCCHHHCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHH
Q ss_conf 22222101440278996240111045678754210022222210244334444364324444332324057212035788
Q gi|254780610|r 87 NIPLDILYEDDDIIVINKPAGLVVHPAPGNWTGTLVNALLYHCHNNLSSINGVKRPGIVHRLDKDTTGVMVVAKNDLAHQ 166 (340)
Q Consensus 87 ~~~~~IlyED~~llvinKPaGl~vhp~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~lVHRLDr~TSGlll~Ak~~~a~~ 166 (340)
+.+++|||||++|||||||+||+|||+++...+++.+.+..... ...+++|||||++|||+||||||+.+++
T Consensus 13 ~~~l~IlyED~~iiVVnKP~Gl~~~p~~~~~~~~l~~~l~~~~~--------~~~~~~vHRLDr~TSGllv~Ak~~~a~~ 84 (213)
T cd02557 13 NDPIKIVHEDDDLLVVDKPSGIPVHPTGRYRYNTVTEILKSEYG--------LTELRPCHRLDRLTSGLLLFAKTSQTAS 84 (213)
T ss_pred CCCCEEEEECCCEEEEECCCCCCEECCCCCCCCHHHHHHHHHCC--------CCCCCEEECCCCCCCCEEEEECCHHHHH
T ss_conf 99988999689999999999986803899872479999997679--------9876264056888765289974578999
Q ss_pred HHHHHHHHHCCCCCEEEEEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEECCCCCEEECCCCCCCCC
Q ss_conf 88999997211322133445432024332332110013434443322123444555553000012221011256677500
Q gi|254780610|r 167 KLSEQFVDHGKSTRLKRAYYAMVWGIPLPDSGIINAPLGRCKSNRLRRAVKGIDDKTADSAITHYQTIEIYNKNSNFAVS 246 (340)
Q Consensus 167 ~l~~~f~~~~~~~~v~K~Y~Aiv~G~~~~~~g~i~~~l~~~~~~~~~~~~~~~~~~~~k~a~T~~~~l~~~~~~~~~~~s 246 (340)
.|+++|+ ++.|.|+|+|+|.|.++++++.++.|+....... .........|++|.|.|++++.. ....+|
T Consensus 85 ~l~~~f~----~~~v~K~Y~Alv~G~~~~~~~~i~~~i~~~~~~~---~~~~~~~~~~k~a~T~~~~l~~~---~~~~~s 154 (213)
T cd02557 85 RLQQQIR----SREVKKEYLARVKGEFPDGEVVVDQPIGLVSPKG---GLRNDVDEKGKDARTIFKRLSYN---GDLNTS 154 (213)
T ss_pred HHHHHHH----CCCCCEEEEEEEEEECCCCEEEEECCCCEECCCC---CEEEEECCCCCCCEEEEEEEEEC---CCCCEE
T ss_conf 9999972----4756359999997265888389953210007767---25885148886431699999983---889989
Q ss_pred EEEEEECHHHHHHHHHHHHHHCCEEECCCCCCCCCCCCCCCCCCHHHHHHCCCCCHHHHHCEEEEECCCCCCEEEEECCC
Q ss_conf 12344311589999999987097860415447755444334570135544079804432100042468897689998499
Q gi|254780610|r 247 LLKCHLETGRTHQIRVHMAHKGNPLIGDPLYGKGFKTKANIVNNNAKSAILSLARQALHAHSLSFSHPRNNQDMDFQVPI 326 (340)
Q Consensus 247 lv~~~~~TGRtHQIRvhla~lG~PIvGD~~YG~~~~~~~~~~~~~~~~~~~~~~r~~LHA~~l~f~hP~t~~~~~f~apl 326 (340)
|++|+|+||||||||+||+++||||+||.+||+ .++||||++|.| +.++|+|||
T Consensus 155 ll~~~~~TGRtHQIRvhla~lG~PIvGD~~YG~--------------------~~l~LHA~~~~~------~~~~f~~~~ 208 (213)
T cd02557 155 VVLCKPITGRTHQIRVHLQYLGHPIVNDPIYNN--------------------LGIYLHALRYEG------PDWSYETEL 208 (213)
T ss_pred EEEEEECCCCHHHHHHHHHHCCCCEECCCCCCC--------------------CCEEEEEEEECC------CCEEEECCC
T ss_conf 999995878889999999987995718513298--------------------566768635418------987997689
Q ss_pred CH
Q ss_conf 78
Q gi|254780610|r 327 PE 328 (340)
Q Consensus 327 P~ 328 (340)
|+
T Consensus 209 p~ 210 (213)
T cd02557 209 PD 210 (213)
T ss_pred CC
T ss_conf 97
No 10
>KOG1919 consensus
Probab=100.00 E-value=0 Score=324.04 Aligned_cols=301 Identities=28% Similarity=0.399 Sum_probs=219.7
Q ss_pred EECHHHCCCCHHHHHHHHCCCCCCHHHHHHHHHCCCEEECCEEECCCCCEECCCCEEEEEECCCHHCCHHHHHHHHHHCC
Q ss_conf 95711368757899998717688989999999859904998993286758048988999705601111023322222101
Q gi|254780610|r 15 LLSDSTAEGRIDRWLATSLKEQFSRSYVKILILNGFISINGMVSKNPNRKVVPGDSFLITVPAAQKLNIAQENIPLDILY 94 (340)
Q Consensus 15 ~V~~~~~g~RLD~~L~~~l~~~~sR~~i~kli~~G~V~vnG~~~~~~~~~l~~gd~I~i~~~~~~~~~~~~~~~~~~Ily 94 (340)
.+..-..+.-+..++...|. .-++..-+..|+.|.|++||+.+. .++.++.+|.+...+...+.+ ... .++.|+|
T Consensus 36 ~~~~rw~~k~~~~~~~~ef~-~~~~~~~~~~i~~g~v~~n~~~~~-v~~i~k~~d~l~~~vhrh~p~-~~~--~~~~Iv~ 110 (371)
T KOG1919 36 FVKGRWAGKKLVDVFVSEFR-LRERAYYESAIKLGRVTVNGEQVR-VSLIVKNGDVLCHTVHRHEPP-VAY--LPIRIVF 110 (371)
T ss_pred EEEEEECCCCHHHHHHHHHH-CCCHHHHHHHHHCCCEEECCEEEE-EEEEECCCCEEEEEECCCCCC-CCC--CCCCEEE
T ss_conf 88512446207799989875-371576665653686588858600-478712588887764047887-544--3441588
Q ss_pred CCCEEEEEECCCHHHCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHHHHHHH
Q ss_conf 44027899624011104567875421002222221024433444436432444433232405721203578888999997
Q gi|254780610|r 95 EDDDIIVINKPAGLVVHPAPGNWTGTLVNALLYHCHNNLSSINGVKRPGIVHRLDKDTTGVMVVAKNDLAHQKLSEQFVD 174 (340)
Q Consensus 95 ED~~llvinKPaGl~vhp~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~lVHRLDr~TSGlll~Ak~~~a~~~l~~~f~~ 174 (340)
||++++|||||+|++|||++....+|+...+... .....+..|||||+.|||+|+|||++.++..++++|+
T Consensus 111 ed~~~vVvnKP~gipVhp~g~~~~n~i~~~l~~~--------~~~~~~~~~hRLDr~tSGllvlAkt~~~~~~~~~~~r- 181 (371)
T KOG1919 111 EDKDYVVVNKPHGIPVHPTGRYRENTITKILAAL--------HKVEGLRPCHRLDRLTSGLLVLAKTKEAADKFHEVLR- 181 (371)
T ss_pred ECCCEEEEECCCCCCEECCCCCCCCCCHHHHHHH--------CCCCCCCCCCCCCCCCCCEEEEEECHHHHHHHHHHHH-
T ss_conf 5399899958998754016854436536888874--------1455662322467665644899856557689999974-
Q ss_pred HCCCCCEEEEE-EEEEECCCC-CCCCCCCCCCCCCCCCCCCCCCCCCCC---CCCCCCEECCCCCEEECCCCCCCCCEEE
Q ss_conf 21132213344-543202433-233211001343444332212344455---5553000012221011256677500123
Q gi|254780610|r 175 HGKSTRLKRAY-YAMVWGIPL-PDSGIINAPLGRCKSNRLRRAVKGIDD---KTADSAITHYQTIEIYNKNSNFAVSLLK 249 (340)
Q Consensus 175 ~~~~~~v~K~Y-~Aiv~G~~~-~~~g~i~~~l~~~~~~~~~~~~~~~~~---~~~k~a~T~~~~l~~~~~~~~~~~slv~ 249 (340)
.+.+.|.| +|-|.|.++ ...-+|..+++.... ..+|.+..... ..++.|.|.|+++... ...|+|+
T Consensus 182 ---~~~~~k~Y~v~~v~g~fp~~~~~~i~~~~~~~~~-~~~~~l~~~~~~~~~~~k~a~T~~~~~~~~-----~~ss~V~ 252 (371)
T KOG1919 182 ---KRTVKKEYVVARVEGPFPVVGEVEIKEPIGEEER-PLRMGLNAVGVRDEVAAKDAKTLFKVLSYD-----GGSSLVE 252 (371)
T ss_pred ---CCCCEEEEEEEEEECCCCCCCEEEECCCCCCCCC-CCCEEEEECCCCCCCCCCCCEEEEEECCCC-----CCEEEEE
T ss_conf ---3541037999997245787762771787553456-651576401224444565644688872348-----9669999
Q ss_pred EEECHHHHHHHHHHHHHHCCEEECCCCCCCCCCCCCCCCCCHHHH--------HHCCCCCHHHHHCEEEEECCCCC---C
Q ss_conf 443115899999999870978604154477554443345701355--------44079804432100042468897---6
Q gi|254780610|r 250 CHLETGRTHQIRVHMAHKGNPLIGDPLYGKGFKTKANIVNNNAKS--------AILSLARQALHAHSLSFSHPRNN---Q 318 (340)
Q Consensus 250 ~~~~TGRtHQIRvhla~lG~PIvGD~~YG~~~~~~~~~~~~~~~~--------~~~~~~r~~LHA~~l~f~hP~t~---~ 318 (340)
|.|+||||||||+||+++|+||+||.+|++..........+.... ........++++-... .||.++ +
T Consensus 253 ~~PlTGRtHQIRvHlq~lG~PI~gD~~Y~~~~~~~~~P~~g~~~~~~~~~~e~~~~~~~~~~~~~~~~~-~~~~~~~~~~ 331 (371)
T KOG1919 253 CRPLTGRTHQIRVHLQYLGHPIAGDPKYGNHIVWAGLPFTGREGTAKKKSLEEEIQRLIDVHLLENWLG-FHPRTGPLIE 331 (371)
T ss_pred EECCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHCCCCCCC-CCCCCCCCHH
T ss_conf 632679679999999971998578855666444455887898887666683100145542221343456-5666563145
Q ss_pred EEEEECCCC--HHHHHHHHHHHC
Q ss_conf 899984997--899999998851
Q gi|254780610|r 319 DMDFQVPIP--EDMLTVIRKLNE 339 (340)
Q Consensus 319 ~~~f~aplP--~~~~~~l~~L~~ 339 (340)
.+..+++.| .||..++-.|+-
T Consensus 332 ~~~~~C~~~~~~Dl~~~lha~~y 354 (371)
T KOG1919 332 ELCQECKVPIDNDLELFLHALKY 354 (371)
T ss_pred HHHHHCCCCCCCHHHHHHHHCCC
T ss_conf 55521799987327676421662
No 11
>cd02869 PseudoU_synth_RluCD_like PseudoU_synth_RsuA/RluD: Pseudouridine synthase, RsuA/RluD family. This group is comprised of eukaryotic, bacterial and archeal proteins similar to eight site specific Escherichia coli pseudouridine synthases: RsuA, RluA, RluB, RluC, RluD, RluE, RluF and TruA. Pseudouridine synthases catalyze the isomerization of specific uridines in a n RNA molecule to pseudouridines (5-ribosyluracil, psi) requiring no cofactors. E. coli RluC for example makes psi955, 2504 and 2580 in 23S RNA. Some psi sites such as psi1917 in 23S RNA made by RluD are universally conserved. Other psi sites occur in a more restricted fashion, for example psi2819 in 21S mitochondrial ribosomal RNA made by S. cerevisiae Pus5p is only found in mitochondrial large subunit rRNAs from some other species and in gram negative bacteria. The E. coli counterpart of this psi residue is psi2580 in 23S rRNA. psi2604in 23S RNA made by RluF has only been detected in E.coli.
Probab=100.00 E-value=0 Score=322.84 Aligned_cols=185 Identities=52% Similarity=0.795 Sum_probs=153.6
Q ss_pred EEEEECCCHHHCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHHHHHHHHCCC
Q ss_conf 78996240111045678754210022222210244334444364324444332324057212035788889999972113
Q gi|254780610|r 99 IIVINKPAGLVVHPAPGNWTGTLVNALLYHCHNNLSSINGVKRPGIVHRLDKDTTGVMVVAKNDLAHQKLSEQFVDHGKS 178 (340)
Q Consensus 99 llvinKPaGl~vhp~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~lVHRLDr~TSGlll~Ak~~~a~~~l~~~f~~~~~~ 178 (340)
++|+|||+|++|||+++....++.+.+..+.... .....+++|||||++|||+|++|||+.+++.|+++| +.
T Consensus 1 ~lvvnKP~gl~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~vhRLD~~TSGl~l~Ak~~~~~~~l~~~~----~~ 72 (185)
T cd02869 1 LLVVNKPAGLPVHPGPGHLTGTLVNALLKLLLLL----GEEFRPGLVHRLDKDTSGLLLVAKNKKAAAKLSKQF----KE 72 (185)
T ss_pred CEEEECCCCCCEECCCCCCCCCHHHHHHHHHHHC----CCCCCCCEECCCCCCCCCCEEEECHHHHHHHHHHHH----CC
T ss_conf 9999999998364898998858999999999864----899865343478988756188866099999998744----65
Q ss_pred CCEEEEEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEECCCCCEEECCCCCCCCCEEEEEECHHHHH
Q ss_conf 22133445432024332332110013434443322123444555553000012221011256677500123443115899
Q gi|254780610|r 179 TRLKRAYYAMVWGIPLPDSGIINAPLGRCKSNRLRRAVKGIDDKTADSAITHYQTIEIYNKNSNFAVSLLKCHLETGRTH 258 (340)
Q Consensus 179 ~~v~K~Y~Aiv~G~~~~~~g~i~~~l~~~~~~~~~~~~~~~~~~~~k~a~T~~~~l~~~~~~~~~~~slv~~~~~TGRtH 258 (340)
+.+.|+|+|+|.|.++...+.++.++......... ......+++.|+|+|++++.. ..+||++|+|.|||||
T Consensus 73 ~~~~K~Y~a~~~g~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~k~a~t~~~~l~~~-----~~~slv~~~~~TGR~H 144 (185)
T cd02869 73 RKVKKTYLALVDGKPPEDEGTIDAPLGRKKRKKRA---RVVVSEDGKPAITHYKVLERF-----GNVTLVELQLETGRTH 144 (185)
T ss_pred CCEEEEEEEEECCCCCCCCCEEECCEEECCCCCCE---EEEECCCCCEEEEEHHHHHHC-----CCEEEEEEECCCCCHH
T ss_conf 64403999996676565765682214415666713---898569984762001345537-----9869999881658779
Q ss_pred HHHHHHHHHCCEEECCCCCCCCCCCCCCCCCCHHHHHHCCCCCHHHHHCEEEE
Q ss_conf 99999987097860415447755444334570135544079804432100042
Q gi|254780610|r 259 QIRVHMAHKGNPLIGDPLYGKGFKTKANIVNNNAKSAILSLARQALHAHSLSF 311 (340)
Q Consensus 259 QIRvhla~lG~PIvGD~~YG~~~~~~~~~~~~~~~~~~~~~~r~~LHA~~l~f 311 (340)
|||+||+++||||+||.+||+...... ...|++|||++|.|
T Consensus 145 QIR~hla~lg~PIvGD~~Yg~~~~~~~------------~~~r~~LHA~~l~f 185 (185)
T cd02869 145 QIRVHLASIGHPIVGDPKYGGKASDSP------------GLKRLALHAYRLSF 185 (185)
T ss_pred HHHHHHHHCCCCEECCCCCCCCCCCCC------------CCCCHHHCCCCCCC
T ss_conf 999999987996748635698533478------------99667334787879
No 12
>TIGR01621 RluA-like pseudouridine synthase Rlu family protein, TIGR01621; InterPro: IPR006508 These sequences represent a clade within the pseudouridine synthase superfamily. The superfamily includes E. coli proteins: RluA, RluB, RluC, RluD, and RsuA. The sequences in this family are most closely related to RluA ; only Neisseria does not appear to have an RluA homolog. It is presumed that these sequences function as pseudouridine synthases, although perhaps with different specificity..
Probab=100.00 E-value=0 Score=298.66 Aligned_cols=196 Identities=32% Similarity=0.538 Sum_probs=159.3
Q ss_pred HHHCCCCCEEEEEECCCHHHCCCCCCCCCCC-CHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHH
Q ss_conf 2210144027899624011104567875421-002222221024433444436432444433232405721203578888
Q gi|254780610|r 90 LDILYEDDDIIVINKPAGLVVHPAPGNWTGT-LVNALLYHCHNNLSSINGVKRPGIVHRLDKDTTGVMVVAKNDLAHQKL 168 (340)
Q Consensus 90 ~~IlyED~~llvinKPaGl~vhp~~~~~~~t-l~~~l~~~~~~~~~~~~~~~~~~lVHRLDr~TSGlll~Ak~~~a~~~l 168 (340)
++|||.-.|||+||||.|+.||-..+. | |...+.. + -+..+.+|||||||-|||+||||+|.++|++|
T Consensus 2 ~eilf~H~DF~~INK~~giSVHkD~ge---tgL~~~vA~----Q----lgv~~vwLvHRLDK~TSGiLllAlNaesAsel 70 (222)
T TIGR01621 2 LEILFRHSDFVLINKSEGISVHKDDGE---TGLLREVAK----Q----LGVEKVWLVHRLDKVTSGILLLALNAESASEL 70 (222)
T ss_pred CEEEEECCCEEEEECCCCEEEEECCCC---HHHHHHHHH----H----HCCCCEEEEEECCHHHHHHHHHHHCHHHHHHH
T ss_conf 057753686789867998327725711---138999999----8----18980899870003446899986047899999
Q ss_pred HHHHHHHCCCCCEEEEEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEECCCCCEEECCCCCCCCCEE
Q ss_conf 99999721132213344543202433233211001343444332212344455555300001222101125667750012
Q gi|254780610|r 169 SEQFVDHGKSTRLKRAYYAMVWGIPLPDSGIINAPLGRCKSNRLRRAVKGIDDKTADSAITHYQTIEIYNKNSNFAVSLL 248 (340)
Q Consensus 169 ~~~f~~~~~~~~v~K~Y~Aiv~G~~~~~~g~i~~~l~~~~~~~~~~~~~~~~~~~~k~a~T~~~~l~~~~~~~~~~~slv 248 (340)
+++|.. ++|+|+|+||-.-.|.+..|.|..-|.+...+..|.+- . .--+|+|+|.-+.. ....-|.
T Consensus 71 S~~Fa~----~ki~KtYLAls~~KPkKKQGlI~GdMeksR~g~WKL~~----~-~eNpAiTrF~S~s~-----a~~lRLF 136 (222)
T TIGR01621 71 SRLFAK----KKIKKTYLALSDKKPKKKQGLIIGDMEKSRRGAWKLVR----S-KENPAITRFESVSI-----AEKLRLF 136 (222)
T ss_pred HHHHHC----CEEEEEEEECCCCCCCCCCCEEECCHHHHHCCCCHHCC----C-CCCCEECCEEEEEE-----CCCCCEE
T ss_conf 876521----70666776313689874442025571242000100027----8-98960111245652-----3888637
Q ss_pred EEEECHHHHHHHHHHHHHHCCEEECCCCCCCCCCCCCCCCCCHHHHHHCCCCCHHHHHCEEEEECCCCCCEEEEECCCC
Q ss_conf 3443115899999999870978604154477554443345701355440798044321000424688976899984997
Q gi|254780610|r 249 KCHLETGRTHQIRVHMAHKGNPLIGDPLYGKGFKTKANIVNNNAKSAILSLARQALHAHSLSFSHPRNNQDMDFQVPIP 327 (340)
Q Consensus 249 ~~~~~TGRtHQIRvhla~lG~PIvGD~~YG~~~~~~~~~~~~~~~~~~~~~~r~~LHA~~l~f~hP~t~~~~~f~aplP 327 (340)
-|+|+||+||||||-|.+||-|||||.+||..... ..|++|||+.|.|.+ -++-+.+.|++-
T Consensus 137 ilkPhTGKTHQlRVAmKSlGSpIlGD~lYg~n~~e---------------sdr~yLhA~~l~FdY--~n~~i~~~c~p~ 198 (222)
T TIGR01621 137 ILKPHTGKTHQLRVAMKSLGSPILGDSLYGKNADE---------------SDRTYLHAFKLRFDY--QNEVIEVVCDPK 198 (222)
T ss_pred EECCCCCCHHHHHHHHHHCCCCCCCCCCCCCCCCH---------------HHHHHHHHHHHHHHC--CCCEEEEEECCC
T ss_conf 55689996378878887727630056767886421---------------332422222100100--475889986542
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=100.00 E-value=3e-40 Score=259.66 Aligned_cols=152 Identities=32% Similarity=0.412 Sum_probs=121.5
Q ss_pred EEEEECCCHHHCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHHHHHHHHCCC
Q ss_conf 78996240111045678754210022222210244334444364324444332324057212035788889999972113
Q gi|254780610|r 99 IIVINKPAGLVVHPAPGNWTGTLVNALLYHCHNNLSSINGVKRPGIVHRLDKDTTGVMVVAKNDLAHQKLSEQFVDHGKS 178 (340)
Q Consensus 99 llvinKPaGl~vhp~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~lVHRLDr~TSGlll~Ak~~~a~~~l~~~f~~~~~~ 178 (340)
|||+|||+|++|||++++..+|+.+.+..... .++++|||||++|||+||||||..+++.|+.+.
T Consensus 1 iivvnKP~G~~~~~~~~~~~~~~~~~l~~~~~---------~~l~~vhRLDr~TSGlll~ak~~~~~~~l~~~~------ 65 (154)
T cd02550 1 ILVLNKPSGLVCHPTDRDRDPTVVVRLDKLHG---------PRVHAAGRLDKDTSGLLLLTNDGRLQRRLTEPR------ 65 (154)
T ss_pred CEEEECCCCCEEECCCCCCCCCHHHHHHHHCC---------CCEEEECCCCCCCCCCEEECCCHHHHHHHHHHH------
T ss_conf 99999999971858999999709999875179---------861371268999978567737989999998500------
Q ss_pred CCEEEEEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEECCCCCEEECCCCCCCCCEEEEEECHHHHH
Q ss_conf 22133445432024332332110013434443322123444555553000012221011256677500123443115899
Q gi|254780610|r 179 TRLKRAYYAMVWGIPLPDSGIINAPLGRCKSNRLRRAVKGIDDKTADSAITHYQTIEIYNKNSNFAVSLLKCHLETGRTH 258 (340)
Q Consensus 179 ~~v~K~Y~Aiv~G~~~~~~g~i~~~l~~~~~~~~~~~~~~~~~~~~k~a~T~~~~l~~~~~~~~~~~slv~~~~~TGRtH 258 (340)
+.+.|+|+|+|.|.++++ +..+.+....... .....+++++|.|.|++++. ...+|+++|.|.|||||
T Consensus 66 ~~v~K~Y~a~v~g~~~~~-~~~~~~~~~~~~~------~~~~~~~~~~~~t~~~~~~~-----~~~~slv~~~l~TGR~H 133 (154)
T cd02550 66 REIEKEYLVTVRGELDEE-GIEDLATVRRGRL------SGLVDEGVPLAVTKVRVIGE-----HGGTGRLRLTLKTGRTH 133 (154)
T ss_pred CCCCEEEEEEEEEECCHH-HHEECCCCCCCCC------EEEECCCCEECCCEEEEECC-----CCCCEEEEEEECCCCCH
T ss_conf 565057999998727858-8244445642455------12665996204328899314-----79948999997988669
Q ss_pred HHHHHHHHHCCEEECCCCC
Q ss_conf 9999998709786041544
Q gi|254780610|r 259 QIRVHMAHKGNPLIGDPLY 277 (340)
Q Consensus 259 QIRvhla~lG~PIvGD~~Y 277 (340)
|||+||+++||||++|.+|
T Consensus 134 QIR~hl~~~G~PIl~l~R~ 152 (154)
T cd02550 134 QIRRHCAAVGFPVLRLHRV 152 (154)
T ss_pred HHHHHHHHCCCEEEEEEEE
T ss_conf 9999999869939568998
No 14
>pfam00849 PseudoU_synth_2 RNA pseudouridylate synthase. Members of this family are involved in modifying bases in RNA molecules. They carry out the conversion of uracil bases to pseudouridine. This family includes RluD, a pseudouridylate synthase that converts specific uracils to pseudouridine in 23S rRNA. RluA from E. coli converts bases in both rRNA and tRNA.
Probab=100.00 E-value=1.2e-39 Score=255.99 Aligned_cols=151 Identities=37% Similarity=0.506 Sum_probs=121.5
Q ss_pred EEEEECCCHHHCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHHHHHHHHCCC
Q ss_conf 78996240111045678754210022222210244334444364324444332324057212035788889999972113
Q gi|254780610|r 99 IIVINKPAGLVVHPAPGNWTGTLVNALLYHCHNNLSSINGVKRPGIVHRLDKDTTGVMVVAKNDLAHQKLSEQFVDHGKS 178 (340)
Q Consensus 99 llvinKPaGl~vhp~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~lVHRLDr~TSGlll~Ak~~~a~~~l~~~f~~~~~~ 178 (340)
|||||||+||+|||+++....++........ ....++++|||||++||||||||||..+++.|+++|. +
T Consensus 1 ~lvvnKP~Gl~~~~~~~~~~~~~~~~~~~~~-------~~~~~~~~vhRLD~~TSGlll~ak~~~~~~~l~~~f~----~ 69 (151)
T pfam00849 1 YIVVNKPAGVPVHPTDLSDLLSLTELLLVAE-------LGKFRLYPVHRLDRDTSGLLLLAKDGEAANKLNKLFP----E 69 (151)
T ss_pred CEEEECCCCCEEECCCCCCCCCHHHHHHHHC-------CCCCCEEEECCCCCCCCCEEEECCCHHHHHHHHHHHH----H
T ss_conf 9999999998582189987862888655551-------5997355851778888544786232688888999866----5
Q ss_pred CCEEEEEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEECCCCCEEECCCCCCCCCEEEEEECHHHHH
Q ss_conf 22133445432024332332110013434443322123444555553000012221011256677500123443115899
Q gi|254780610|r 179 TRLKRAYYAMVWGIPLPDSGIINAPLGRCKSNRLRRAVKGIDDKTADSAITHYQTIEIYNKNSNFAVSLLKCHLETGRTH 258 (340)
Q Consensus 179 ~~v~K~Y~Aiv~G~~~~~~g~i~~~l~~~~~~~~~~~~~~~~~~~~k~a~T~~~~l~~~~~~~~~~~slv~~~~~TGRtH 258 (340)
+.|+|+|+|+|.|.+ +++|.++.++.........+ .....+++.|.|.|++++... ....+|||+++|+|||||
T Consensus 70 ~~v~K~Y~a~v~g~~-~~~~~~~~~~~~~~~~~~~~---~~~~~~~k~a~t~~~~l~~~~--~~~~~slv~~~l~TGR~H 143 (151)
T pfam00849 70 RKVEKEYLALVDGPE-EEEGTIKAPIKKDKNKVPRR---KKEELDGKKAVTHLRVLRSGS--KIEDVSLVELELVTGRKH 143 (151)
T ss_pred CCCCEEEEEEEECCC-CCCCEEEEECCCCCCCCEEE---EEECCCCCCCCEEEEEEEECC--CCCCEEEEEEEECCCHHH
T ss_conf 355428999996777-87708981011367777279---875699842425999988725--689969999996728379
Q ss_pred HHHHHHHH
Q ss_conf 99999987
Q gi|254780610|r 259 QIRVHMAH 266 (340)
Q Consensus 259 QIRvhla~ 266 (340)
|||+|||+
T Consensus 144 QIRvhlas 151 (151)
T pfam00849 144 QIRAHLAA 151 (151)
T ss_pred HHHHHHCC
T ss_conf 99998669
No 15
>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=100.00 E-value=4.6e-33 Score=216.80 Aligned_cols=143 Identities=23% Similarity=0.339 Sum_probs=109.4
Q ss_pred EEEEECCCHHHCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHHHHHHHHCCC
Q ss_conf 78996240111045678754210022222210244334444364324444332324057212035788889999972113
Q gi|254780610|r 99 IIVINKPAGLVVHPAPGNWTGTLVNALLYHCHNNLSSINGVKRPGIVHRLDKDTTGVMVVAKNDLAHQKLSEQFVDHGKS 178 (340)
Q Consensus 99 llvinKPaGl~vhp~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~lVHRLDr~TSGlll~Ak~~~a~~~l~~~f~~~~~~ 178 (340)
++++|||+|++|+++......|+.+.+..+ ..+.++|||||++||||||||++.+++..|.. ..
T Consensus 1 yi~lnKP~G~~~~~~~~~~~~tv~~ll~~~----------~~~l~~V~RLD~~TsGLll~t~d~~~~~~l~~------~~ 64 (146)
T cd02870 1 YLLLNKPRGVVSTVRDPEGRPTVLDLLKDV----------GERLFPVGRLDYDTEGLLLLTNDGELANRLTH------PR 64 (146)
T ss_pred CEEEECCCCCEECCCCCCCCCCHHHHHHHC----------CCCEEECCCCCCCCCCEEEEECCHHHHHHHHC------CC
T ss_conf 989999998286166998998578954305----------78672266689778765999579899998754------03
Q ss_pred CCEEEEEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEECCCCCEEECCCCCCCCCEEEEEECHHHHH
Q ss_conf 22133445432024332332110013434443322123444555553000012221011256677500123443115899
Q gi|254780610|r 179 TRLKRAYYAMVWGIPLPDSGIINAPLGRCKSNRLRRAVKGIDDKTADSAITHYQTIEIYNKNSNFAVSLLKCHLETGRTH 258 (340)
Q Consensus 179 ~~v~K~Y~Aiv~G~~~~~~g~i~~~l~~~~~~~~~~~~~~~~~~~~k~a~T~~~~l~~~~~~~~~~~slv~~~~~TGRtH 258 (340)
.+++|+|+|+|.|.+.++... ..+.. ....+++.+.+++++++. ....|++++.|.|||+|
T Consensus 65 ~~i~K~Y~a~v~g~~~~~~~~-----------~~~~g---~~~~~~~~~~~~~~~~~~-----~~~~s~l~v~l~tGR~h 125 (146)
T cd02870 65 YGVEKTYLVKVRGVPSEEELR-----------RLRAG---VELDDGKTAPAKVKVLSR-----DPKNTLLEVTLHEGRNR 125 (146)
T ss_pred CCCCEEEEEEEECCCCHHHHH-----------HHHCC---EECCCCEEEEEEEEEECC-----CCCCEEEEEEECCCCHH
T ss_conf 542469999990269999999-----------98666---455898872148998237-----89959999997899439
Q ss_pred HHHHHHHHHCCEEECCCC
Q ss_conf 999999870978604154
Q gi|254780610|r 259 QIRVHMAHKGNPLIGDPL 276 (340)
Q Consensus 259 QIRvhla~lG~PIvGD~~ 276 (340)
|||+||+++||||+....
T Consensus 126 QIR~h~~~lg~pI~~L~R 143 (146)
T cd02870 126 QVRRMFEAVGHPVLRLKR 143 (146)
T ss_pred HHHHHHHHCCCEEEEEEE
T ss_conf 999999984997967999
No 16
>COG1187 RsuA 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]
Probab=99.94 E-value=1.8e-25 Score=171.56 Aligned_cols=210 Identities=25% Similarity=0.304 Sum_probs=140.9
Q ss_pred CCCHHHHHHHHCCCCCCHHHHHHHHHCCCEEECCEEECCCCCEECCCC-EEEEEECCCHHCCHHHHHHHHHHCC-CCCEE
Q ss_conf 875789999871768898999999985990499899328675804898-8999705601111023322222101-44027
Q gi|254780610|r 22 EGRIDRWLATSLKEQFSRSYVKILILNGFISINGMVSKNPNRKVVPGD-SFLITVPAAQKLNIAQENIPLDILY-EDDDI 99 (340)
Q Consensus 22 g~RLD~~L~~~l~~~~sR~~i~kli~~G~V~vnG~~~~~~~~~l~~gd-~I~i~~~~~~~~~~~~~~~~~~Ily-ED~~l 99 (340)
.+||++||++.- ..||+.++++|++|.|+|||++++.+...+.+++ .|.+.-.. +.+ +..-+
T Consensus 2 ~~RL~K~La~~G--~~SRr~ae~lI~~G~V~VnG~v~~~~~~~v~~~~~~i~v~g~~--------------~~~~~~~~y 65 (248)
T COG1187 2 SMRLNKFLAEAG--VGSRREAEKLIEEGRVTVNGKVATLGGVVVDPDDDVVEVDGKR--------------IELKEERVY 65 (248)
T ss_pred CCCHHHHHHHCC--CCCHHHHHHHHHCCCEEECCEEECCCCEEECCCCCEEEECCEE--------------EECCCCCEE
T ss_conf 520689998747--7788999999973987889999224776727987689989988--------------112666469
Q ss_pred EEEECCCHHHCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHHHHHHHHCCCC
Q ss_conf 89962401110456787542100222222102443344443643244443323240572120357888899999721132
Q gi|254780610|r 100 IVINKPAGLVVHPAPGNWTGTLVNALLYHCHNNLSSINGVKRPGIVHRLDKDTTGVMVVAKNDLAHQKLSEQFVDHGKST 179 (340)
Q Consensus 100 lvinKPaGl~vhp~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~lVHRLDr~TSGlll~Ak~~~a~~~l~~~f~~~~~~~ 179 (340)
+++|||.|+.|.-.......|+.+.+... .....+.+.|.|||++|||+||+.-+-..+.. +. ..+.
T Consensus 66 ~llnKP~G~v~s~~D~~gr~tv~D~lp~~-------~~~~~~~~pvGRLD~dTeGLLLLTnDG~la~r----L~--~P~~ 132 (248)
T COG1187 66 LLLNKPRGYVSSTEDDEGRPTVFDLLPER-------LPRKKRLFPVGRLDKDTEGLLLLTNDGELAHR----LM--HPSS 132 (248)
T ss_pred EEEECCCCEEECCCCCCCCCEEEEECCCC-------CCCCCCEEECCCCCCCCEEEEEEECCHHHHHH----HC--CCCC
T ss_conf 99989987692666889981600025543-------46666333426657777127999578789887----52--8888
Q ss_pred CEEEEEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEECCCCCEEECCCCCCCCCEEEEEECHHHHHH
Q ss_conf 21334454320243323321100134344433221234445555530000122210112566775001234431158999
Q gi|254780610|r 180 RLKRAYYAMVWGIPLPDSGIINAPLGRCKSNRLRRAVKGIDDKTADSAITHYQTIEIYNKNSNFAVSLLKCHLETGRTHQ 259 (340)
Q Consensus 180 ~v~K~Y~Aiv~G~~~~~~g~i~~~l~~~~~~~~~~~~~~~~~~~~k~a~T~~~~l~~~~~~~~~~~slv~~~~~TGRtHQ 259 (340)
.+.|+|+|-|.|.+.++. ++. .+..+.. ++...++|.-. .+.. ......|.+++.+.-||.||
T Consensus 133 ~~~K~Y~v~v~g~~~~~~--l~~---------l~~Gv~l-~d~~~~~~~~~--~l~~---~~~~~~s~~~itl~EGrnrQ 195 (248)
T COG1187 133 EVEKEYLVRVEGPVTEED--LEK---------LRKGVTL-DDGETKPAKPA--SLEK---EPGKNNSWLRITLTEGRNRQ 195 (248)
T ss_pred CCCEEEEEEEECCCCHHH--HHH---------HHCCCEE-CCCCCCCCEEE--EEEE---CCCCCCEEEEEEEECCCCHH
T ss_conf 997799999925899899--999---------8578386-67356601047--8983---17887469999995784789
Q ss_pred HHHHHHHHCCEEECCCCC
Q ss_conf 999998709786041544
Q gi|254780610|r 260 IRVHMAHKGNPLIGDPLY 277 (340)
Q Consensus 260 IRvhla~lG~PIvGD~~Y 277 (340)
||..+++.|+|++.=..+
T Consensus 196 VRRm~~a~G~~V~~L~R~ 213 (248)
T COG1187 196 VRRMFEAVGLEVLRLKRI 213 (248)
T ss_pred HHHHHHHCCCEEEEEEEE
T ss_conf 999999849967489999
No 17
>PRK10839 16S rRNA pseudouridylate synthase A; Provisional
Probab=99.93 E-value=4.1e-25 Score=169.45 Aligned_cols=200 Identities=20% Similarity=0.292 Sum_probs=134.9
Q ss_pred CCHHHHHHHHCCCCCCHHHHHHHHHCCCEEECCEEECCCCCEECCCCEEEEEECCCHHCCHHHHHHHHHHCCCCCEEEEE
Q ss_conf 75789999871768898999999985990499899328675804898899970560111102332222210144027899
Q gi|254780610|r 23 GRIDRWLATSLKEQFSRSYVKILILNGFISINGMVSKNPNRKVVPGDSFLITVPAAQKLNIAQENIPLDILYEDDDIIVI 102 (340)
Q Consensus 23 ~RLD~~L~~~l~~~~sR~~i~kli~~G~V~vnG~~~~~~~~~l~~gd~I~i~~~~~~~~~~~~~~~~~~IlyED~~llvi 102 (340)
+||++||++.- .+||+.++++|++|+|+|||+.++.+++.+.++|.|.+.-...... +..-++++
T Consensus 1 mRL~K~La~~g--~~SRR~ae~lI~~GrV~VNg~~v~~~~~~V~~~~~v~vdg~~i~~~-------------~~~~y~~l 65 (231)
T PRK10839 1 MRLDKFIAQQL--GVSRAIAGREIRGNRVTVDGEIVKNAAFKLLPEHDVAYDGNPLAQQ-------------HGPRYFML 65 (231)
T ss_pred CCHHHHHHHCC--CCCHHHHHHHHHCCEEEECCEEECCCCEECCCCCEEEECCCEECCC-------------CCCEEEEE
T ss_conf 93789998878--9569999999987979999999145880849998699919586146-------------68689999
Q ss_pred ECCCHHHCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHHHHHHHHCCCCCEE
Q ss_conf 62401110456787542100222222102443344443643244443323240572120357888899999721132213
Q gi|254780610|r 103 NKPAGLVVHPAPGNWTGTLVNALLYHCHNNLSSINGVKRPGIVHRLDKDTTGVMVVAKNDLAHQKLSEQFVDHGKSTRLK 182 (340)
Q Consensus 103 nKPaGl~vhp~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~lVHRLDr~TSGlll~Ak~~~a~~~l~~~f~~~~~~~~v~ 182 (340)
|||.|+.|...... ..++.+.+.. ....+.+.|.|||++|+|+|||.-+...+..|. .....+.
T Consensus 66 nKP~G~v~s~~d~~-~~~~~~~l~~---------~~~~~l~~vGRLD~ds~GLlllTnDg~l~~~l~------~P~~~i~ 129 (231)
T PRK10839 66 NKPQGYVCSTDDPD-HPTVLYFLDE---------PVAYKLHAAGRLDIDTTGLVLMTDDGQWSHRIT------SPRHHCE 129 (231)
T ss_pred ECCCCCCCCCCCCC-CCCEEEECCC---------CCCCCEEEEECCCCCCCCEEEECCCHHHHHHCC------CCCCCCC
T ss_conf 89987534788999-9726986376---------555635770046889877699768889995351------8768997
Q ss_pred EEEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC-CCCCCEECCCCCEEECCCCCCCCCEEEEEECHHHHHHHH
Q ss_conf 3445432024332332110013434443322123444555-553000012221011256677500123443115899999
Q gi|254780610|r 183 RAYYAMVWGIPLPDSGIINAPLGRCKSNRLRRAVKGIDDK-TADSAITHYQTIEIYNKNSNFAVSLLKCHLETGRTHQIR 261 (340)
Q Consensus 183 K~Y~Aiv~G~~~~~~g~i~~~l~~~~~~~~~~~~~~~~~~-~~k~a~T~~~~l~~~~~~~~~~~slv~~~~~TGRtHQIR 261 (340)
|+|++.|.|.+.++. +.. .+..+...+.. ..+++. ++.+ . -+.+++.+..|+.||||
T Consensus 130 k~Y~V~v~~~i~~~~--l~~---------l~~Gv~i~~~~~~~~~~~--v~~~---~------~~~~~i~l~eGk~rqIR 187 (231)
T PRK10839 130 KTYLVTLESPVADDT--AEQ---------FAKGVQLHNEKDLTKPAV--LEVI---T------PTQVRLTISEGRYHQVK 187 (231)
T ss_pred EEEEEEECCCCCHHH--HHH---------HHCCCEECCEECCEEEEE--EEEC---C------CCEEEEEEECCCCHHHH
T ss_conf 899999898799999--999---------967969878231160369--9984---8------96999999668767999
Q ss_pred HHHHHHCCEEECCC
Q ss_conf 99987097860415
Q gi|254780610|r 262 VHMAHKGNPLIGDP 275 (340)
Q Consensus 262 vhla~lG~PIvGD~ 275 (340)
..|+++|++++-=.
T Consensus 188 rmf~~~g~~V~~L~ 201 (231)
T PRK10839 188 RMFAAVGNRVVELH 201 (231)
T ss_pred HHHHHCCCEEEEEE
T ss_conf 99998599898999
No 18
>PRK10475 23S rRNA pseudouridine synthase F; Provisional
Probab=99.93 E-value=5.8e-25 Score=168.54 Aligned_cols=202 Identities=21% Similarity=0.244 Sum_probs=136.2
Q ss_pred HHCCCCHHHHHHHHCCCCCCHHHHHHHHHCCCEEECCEEECCCCCEECCCCEEEEEECCCHHCCHHHHHHHHHHCCCCCE
Q ss_conf 13687578999987176889899999998599049989932867580489889997056011110233222221014402
Q gi|254780610|r 19 STAEGRIDRWLATSLKEQFSRSYVKILILNGFISINGMVSKNPNRKVVPGDSFLITVPAAQKLNIAQENIPLDILYEDDD 98 (340)
Q Consensus 19 ~~~g~RLD~~L~~~l~~~~sR~~i~kli~~G~V~vnG~~~~~~~~~l~~gd~I~i~~~~~~~~~~~~~~~~~~IlyED~~ 98 (340)
++.+.||++||+.. ..+||+.+.+||.+|+|+|||++++ ....|.++|.|.++-....... .++--
T Consensus 3 ~~~~~RL~K~LA~~--G~~SRReAe~lI~~GrV~VNGk~v~-~g~~V~~~D~V~vdg~~i~~~~-----------~~~~~ 68 (290)
T PRK10475 3 PDSSTRLNKYISES--GICSRREADRYIEQGNVFINGKRAT-IGDQVKPGDVVKVNGQLIEPRE-----------AEDLV 68 (290)
T ss_pred CCCCCHHHHHHHHC--CCCHHHHHHHHHHCCCEEECCEECC-CCCCCCCCCEEEECCEECCCCC-----------CCCEE
T ss_conf 98861499999877--7835999999998597898999957-9888699998999998912336-----------67639
Q ss_pred EEEEECCCHHHCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHHHHHHHHCCC
Q ss_conf 78996240111045678754210022222210244334444364324444332324057212035788889999972113
Q gi|254780610|r 99 IIVINKPAGLVVHPAPGNWTGTLVNALLYHCHNNLSSINGVKRPGIVHRLDKDTTGVMVVAKNDLAHQKLSEQFVDHGKS 178 (340)
Q Consensus 99 llvinKPaGl~vhp~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~lVHRLDr~TSGlll~Ak~~~a~~~l~~~f~~~~~~ 178 (340)
++++|||.|+.|.... ....|+.+.+. ...+.+.|.|||++|+|||||.-+-..+..|. ...
T Consensus 69 yi~lnKP~G~v~t~~d-~~r~ti~d~l~-----------~~~rl~pVGRLD~dSeGLLlLTNDG~l~~~l~------hP~ 130 (290)
T PRK10475 69 LIALNKPVGIVSTTED-GERDNIVDFVN-----------HSKRVFPIGRLDKDSQGLIFLTNHGDLVNKIL------RAG 130 (290)
T ss_pred EEEEECCCCCCCCCCC-CCCCCEEECCC-----------CCCCEEECCCCCCCCCCEEEECCCHHHHHHHH------CCC
T ss_conf 9999589870677766-78986464147-----------75635050466877767599859879999873------576
Q ss_pred CCEEEEEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEECCCCCEEECCCCCCCCCEEEEEECHHHHH
Q ss_conf 22133445432024332332110013434443322123444555553000012221011256677500123443115899
Q gi|254780610|r 179 TRLKRAYYAMVWGIPLPDSGIINAPLGRCKSNRLRRAVKGIDDKTADSAITHYQTIEIYNKNSNFAVSLLKCHLETGRTH 258 (340)
Q Consensus 179 ~~v~K~Y~Aiv~G~~~~~~g~i~~~l~~~~~~~~~~~~~~~~~~~~k~a~T~~~~l~~~~~~~~~~~slv~~~~~TGRtH 258 (340)
..+.|+|++.|.|.+.++. +.. |. ..+.. +....+++. ++.+ . -+.+++.+..|+.|
T Consensus 131 ~~i~K~Y~V~v~g~i~~~~--l~~-l~--------~Gv~i-~g~~~~~~~--v~~~------~---~~~~~i~L~EGknR 187 (290)
T PRK10475 131 NDHEKEYLVTVDKPITDEF--IRG-MG--------AGVPI-LGTVTKKCK--VKKE------A---PFVFRITLVQGLNR 187 (290)
T ss_pred CCCCEEEEEEECCCCCHHH--HHH-HH--------CCCEE-CCEECCEEE--EEEC------C---CCEEEEEEECCCCH
T ss_conf 7895599999898589999--999-85--------89656-888601149--9964------8---97899999868049
Q ss_pred HHHHHHHHHCCEEECCC
Q ss_conf 99999987097860415
Q gi|254780610|r 259 QIRVHMAHKGNPLIGDP 275 (340)
Q Consensus 259 QIRvhla~lG~PIvGD~ 275 (340)
|||..|+++|++++-=.
T Consensus 188 qIRRm~~~~g~~V~~L~ 204 (290)
T PRK10475 188 QIRRMCEHFGYEVTKLE 204 (290)
T ss_pred HHHHHHHHCCCEEEEEE
T ss_conf 99999998599781789
No 19
>PRK10700 23S rRNA pseudouridylate synthase B; Provisional
Probab=99.92 E-value=7.6e-25 Score=167.83 Aligned_cols=209 Identities=20% Similarity=0.228 Sum_probs=133.8
Q ss_pred CCCHHHHHHHHCCCCCCHHHHHHHHHCCCEEECCEEECCCCCEEC--CCCEEEEEECCCHHCCHHHHHHHHHHCCCCCEE
Q ss_conf 875789999871768898999999985990499899328675804--898899970560111102332222210144027
Q gi|254780610|r 22 EGRIDRWLATSLKEQFSRSYVKILILNGFISINGMVSKNPNRKVV--PGDSFLITVPAAQKLNIAQENIPLDILYEDDDI 99 (340)
Q Consensus 22 g~RLD~~L~~~l~~~~sR~~i~kli~~G~V~vnG~~~~~~~~~l~--~gd~I~i~~~~~~~~~~~~~~~~~~IlyED~~l 99 (340)
.+||++||++.- ..||+.++++|++|.|+|||++++ ...++. .+|.|.+.-... ...+.. ..+ -.+
T Consensus 2 ~eRL~K~LA~~G--~~SRReae~lI~~GrV~VNG~v~~-lg~~v~~~~~~~V~vDG~~i---~~~~~~---~~~---~~~ 69 (291)
T PRK10700 2 SEKLQKVLARAG--HGSRREIESIIEAGRVSVDGKIAK-LGDRVEVTPGLKIRIDGHLI---SVKESA---EQI---CRV 69 (291)
T ss_pred HHHHHHHHHHCC--CCHHHHHHHHHHCCEEEECCEECC-CCCEECCCCCCEEEECCEEE---ECCCCC---CCC---EEE
T ss_conf 179999999878--943999999998694998999955-68826589998899999994---324554---430---146
Q ss_pred EEEECCCHHHCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHHHHHHHHCCCC
Q ss_conf 89962401110456787542100222222102443344443643244443323240572120357888899999721132
Q gi|254780610|r 100 IVINKPAGLVVHPAPGNWTGTLVNALLYHCHNNLSSINGVKRPGIVHRLDKDTTGVMVVAKNDLAHQKLSEQFVDHGKST 179 (340)
Q Consensus 100 lvinKPaGl~vhp~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~lVHRLDr~TSGlll~Ak~~~a~~~l~~~f~~~~~~~ 179 (340)
+++|||.|..|.........|+.+.+.... ..+.+.|.|||++|||||||.-+-+.+..|. ....
T Consensus 70 l~l~KP~G~v~T~~D~~~r~tV~dllp~~~---------~~rl~~VGRLD~dT~GLLLlTNDG~La~rL~------hP~~ 134 (291)
T PRK10700 70 LAYYKPEGELCTRNDPEGRPTVFDRLPKLR---------GARWIAVGRLDVNTCGLLLFTTDGELANRLM------HPSR 134 (291)
T ss_pred EEEECCCEEECCCCCCCCCCCHHHHCCCCC---------CCCEEEECCCCCCCCCCEEECCCHHHHHHHC------CCCC
T ss_conf 899878577546677557983778463223---------6645563057888877289838779998624------8867
Q ss_pred CEEEEEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEECCCCCEEECCCCCCCCCEEEEEECHHHHHH
Q ss_conf 21334454320243323321100134344433221234445555530000122210112566775001234431158999
Q gi|254780610|r 180 RLKRAYYAMVWGIPLPDSGIINAPLGRCKSNRLRRAVKGIDDKTADSAITHYQTIEIYNKNSNFAVSLLKCHLETGRTHQ 259 (340)
Q Consensus 180 ~v~K~Y~Aiv~G~~~~~~g~i~~~l~~~~~~~~~~~~~~~~~~~~k~a~T~~~~l~~~~~~~~~~~slv~~~~~TGRtHQ 259 (340)
.+.|+|.+.|.|.+.++. +.. ....+... ++ ++ .+..+..... ...-+.+++.+..||.||
T Consensus 135 ~v~K~Y~V~v~g~i~~~~--l~~---------l~~Gv~le---dg-~~--~~~~i~~~~~--~~~~~~~~i~L~EGrnrq 195 (291)
T PRK10700 135 EVEREYAVRVFGQVDDAK--LRD---------LSRGVQLE---DG-PA--AFKTIKFSGG--EGINQWYNVTLTEGRNRE 195 (291)
T ss_pred CCCEEEEEEECCCCCHHH--HHH---------HHCCCEEC---CC-EE--EEEEEEEECC--CCCCEEEEEEEEECCCHH
T ss_conf 987799999888799999--999---------97697767---80-14--6799988447--788579999999696889
Q ss_pred HHHHHHHHCCEEECCCC
Q ss_conf 99999870978604154
Q gi|254780610|r 260 IRVHMAHKGNPLIGDPL 276 (340)
Q Consensus 260 IRvhla~lG~PIvGD~~ 276 (340)
||..|+++|++++.=..
T Consensus 196 IRRMf~~~G~~V~~LkR 212 (291)
T PRK10700 196 VRRLWEAVGVQVSRLIR 212 (291)
T ss_pred HHHHHHHCCCEEEEEEE
T ss_conf 99999985997918899
No 20
>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=99.79 E-value=3.3e-19 Score=134.27 Aligned_cols=152 Identities=21% Similarity=0.296 Sum_probs=91.9
Q ss_pred EEEEECCCHHHCCCCCC-CCCCCCHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHHHHHHHHCC
Q ss_conf 78996240111045678-75421002222221024433444436432444433232405721203578888999997211
Q gi|254780610|r 99 IIVINKPAGLVVHPAPG-NWTGTLVNALLYHCHNNLSSINGVKRPGIVHRLDKDTTGVMVVAKNDLAHQKLSEQFVDHGK 177 (340)
Q Consensus 99 llvinKPaGl~vhp~~~-~~~~tl~~~l~~~~~~~~~~~~~~~~~~lVHRLDr~TSGlll~Ak~~~a~~~l~~~f~~~~~ 177 (340)
++++|||.|+.|..... ....|+.+.+. .++.+.|+|||++|||+|||+.+...++.|.. .
T Consensus 1 ~i~lnKP~G~v~t~~d~~~~~~~v~d~~~------------~~~l~~VGRLD~ds~GLLLlTnDG~l~~~L~h------P 62 (168)
T cd02566 1 LILFNKPYGVLSQFTDESEKHKTLKDYID------------DPGVYAAGRLDRDSEGLLLLTDDGRLQHRITD------P 62 (168)
T ss_pred CEEEECCCCEEECCCCCCCCCCEEHHHCC------------CCCEEECCCCCCCCCCEEEEECCHHHHHHHHC------C
T ss_conf 98998999979796688899978244078------------88817842667898875998296999998737------7
Q ss_pred CCCEEEEEEEEEECCCCCCCCCCCCCCCCC--CCCCCCC--CCCCCCCCCCCCCEECCCCCEEECCCCCCCCCEEEEEEC
Q ss_conf 322133445432024332332110013434--4433221--234445555530000122210112566775001234431
Q gi|254780610|r 178 STRLKRAYYAMVWGIPLPDSGIINAPLGRC--KSNRLRR--AVKGIDDKTADSAITHYQTIEIYNKNSNFAVSLLKCHLE 253 (340)
Q Consensus 178 ~~~v~K~Y~Aiv~G~~~~~~g~i~~~l~~~--~~~~~~~--~~~~~~~~~~k~a~T~~~~l~~~~~~~~~~~slv~~~~~ 253 (340)
...+.|+|+|.|.|.+.++. +.. |.+. -.+.... .+...+......... .. + ....+...|.+++.+.
T Consensus 63 ~~~i~K~Y~v~v~g~~~~~~--l~~-l~~Gv~i~~~~~~~~~~~~i~~~~~~~~~~-~~-~---~~~~~~~~s~~~i~l~ 134 (168)
T cd02566 63 SFKHPKTYYVQVEGVPTEDA--LEQ-LRNGVELGDGLTLPAKVEKVDEPPWLWERE-PP-I---RFRKNIPTSWIEITIC 134 (168)
T ss_pred CCCCCEEEEEEECCCCCHHH--HHH-HHCCCEECCEEEEEEEEEEECCCCCCCCCC-CC-C---EEECCCCCEEEEEEEE
T ss_conf 67997799999866799999--999-877969798786445999942654432125-66-1---3201478348999996
Q ss_pred HHHHHHHHHHHHHHCCEEECCCC
Q ss_conf 15899999999870978604154
Q gi|254780610|r 254 TGRTHQIRVHMAHKGNPLIGDPL 276 (340)
Q Consensus 254 TGRtHQIRvhla~lG~PIvGD~~ 276 (340)
+||.||||.+|+++||||..=..
T Consensus 135 eGknrqIRrm~~~~g~~V~~L~R 157 (168)
T cd02566 135 EGKNRQVRRMTAAVGFPTLRLIR 157 (168)
T ss_pred ECCHHHHHHHHHHCCCEEEEEEE
T ss_conf 17219999999985996958999
No 21
>PRK11394 23S rRNA pseudouridine synthase E; Provisional
Probab=99.65 E-value=4.8e-16 Score=115.39 Aligned_cols=146 Identities=27% Similarity=0.361 Sum_probs=92.9
Q ss_pred EEEEEECCCHHHCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHHHHHHHHCC
Q ss_conf 27899624011104567875421002222221024433444436432444433232405721203578888999997211
Q gi|254780610|r 98 DIIVINKPAGLVVHPAPGNWTGTLVNALLYHCHNNLSSINGVKRPGIVHRLDKDTTGVMVVAKNDLAHQKLSEQFVDHGK 177 (340)
Q Consensus 98 ~llvinKPaGl~vhp~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~lVHRLDr~TSGlll~Ak~~~a~~~l~~~f~~~~~ 177 (340)
-++++|||.|+.|..+......|+.+.+. ..+.+.|.|||++|+|+|||.-+-..+..|. ..
T Consensus 30 r~illnKP~G~i~T~~D~~gR~tV~dllp------------~~~l~pVGRLD~dSeGLLLlTNDG~la~~L~------hP 91 (207)
T PRK11394 30 RVILFNKPYDVLPQFTDEAGRKTLKEFIP------------VQGVYAAGRLDRDSEGLLVLTNNGALQARLT------QP 91 (207)
T ss_pred EEEEEECCCCEEECCCCCCCCCCHHHHCC------------CCCCEECCCCCCCCCCEEEECCCHHHHHHHH------CC
T ss_conf 89999899985868889999976789688------------5674577776789877299808789998752------56
Q ss_pred CCCEEEEEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEECCCCCE----------EECCCCCCCCCE
Q ss_conf 3221334454320243323321100134344433221234445555530000122210----------112566775001
Q gi|254780610|r 178 STRLKRAYYAMVWGIPLPDSGIINAPLGRCKSNRLRRAVKGIDDKTADSAITHYQTIE----------IYNKNSNFAVSL 247 (340)
Q Consensus 178 ~~~v~K~Y~Aiv~G~~~~~~g~i~~~l~~~~~~~~~~~~~~~~~~~~k~a~T~~~~l~----------~~~~~~~~~~sl 247 (340)
+..+.|+|.+.|.|.+.++. ++. |. ..+...+. ...+|.- +++. ..........|.
T Consensus 92 ~~~i~K~Y~V~v~g~~~~~~--l~~-l~--------~Gv~i~dg-~~~p~~~--~~v~~~~~~~~~~~~~~~~~~~~~s~ 157 (207)
T PRK11394 92 GKRTGKIYYVQVEGIPTQDA--LEA-LR--------NGVTLNDG-PTLPAGA--ELVDEPAWLWPRNPPIRERKSIPTSW 157 (207)
T ss_pred CCCCCEEEEEEECCCCCHHH--HHH-HH--------CCCEECCE-EEEEEEE--EEECCCCCCCCCCCCHHHCCCCCCCE
T ss_conf 57977899999916899999--999-97--------79785984-7645489--99447421234576411102578657
Q ss_pred EEEEECHHHHHHHHHHHHHHCCEEECCC
Q ss_conf 2344311589999999987097860415
Q gi|254780610|r 248 LKCHLETGRTHQIRVHMAHKGNPLIGDP 275 (340)
Q Consensus 248 v~~~~~TGRtHQIRvhla~lG~PIvGD~ 275 (340)
+++.+..||.||||..|+++|++++-=.
T Consensus 158 l~i~L~EGKnRqIRRmf~~~G~~V~~L~ 185 (207)
T PRK11394 158 LKITLYEGRNRQVRRMTAHVGFPTLRLI 185 (207)
T ss_pred EEEEEEECCCHHHHHHHHHCCCEEEEEE
T ss_conf 9999974635999999998699793899
No 22
>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=99.64 E-value=6.2e-16 Score=114.74 Aligned_cols=140 Identities=22% Similarity=0.318 Sum_probs=89.5
Q ss_pred EEEEECCCHHHCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHHHHHHHHCCC
Q ss_conf 78996240111045678754210022222210244334444364324444332324057212035788889999972113
Q gi|254780610|r 99 IIVINKPAGLVVHPAPGNWTGTLVNALLYHCHNNLSSINGVKRPGIVHRLDKDTTGVMVVAKNDLAHQKLSEQFVDHGKS 178 (340)
Q Consensus 99 llvinKPaGl~vhp~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~lVHRLDr~TSGlll~Ak~~~a~~~l~~~f~~~~~~ 178 (340)
++++|||.|..|....... .|+.+.+.... ...+.+.|.|||++|||+|||.-+...++.|.. .+
T Consensus 2 YillnKP~G~v~t~~d~~~-ktv~dll~~~~--------~~~~l~~vGRLD~~s~GLLLlTNDG~l~~~l~h------P~ 66 (167)
T cd02553 2 YLMLNKPAGVVCATKDPHH-PTVIDLLPEPD--------RRRDLFPVGRLDKDTTGLLLLTNDGQLAHRLTS------PK 66 (167)
T ss_pred EEEEECCCCEEECCCCCCC-CCHHHHCCCCC--------CCCCEEECCCCCCCCCCEEEECCCHHHHHHHHC------CC
T ss_conf 9999889997969889999-97744335500--------367556744568997622999188889976414------44
Q ss_pred CCEEEEEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEECCCCCEEECCCCCCCCCEEEEEECHHHHH
Q ss_conf 22133445432024332332110013434443322123444555553000012221011256677500123443115899
Q gi|254780610|r 179 TRLKRAYYAMVWGIPLPDSGIINAPLGRCKSNRLRRAVKGIDDKTADSAITHYQTIEIYNKNSNFAVSLLKCHLETGRTH 258 (340)
Q Consensus 179 ~~v~K~Y~Aiv~G~~~~~~g~i~~~l~~~~~~~~~~~~~~~~~~~~k~a~T~~~~l~~~~~~~~~~~slv~~~~~TGRtH 258 (340)
..+.|+|++.|.|.+.++. ++ ..+..+...+....++|. .+.+ . -+.+++.+..||.|
T Consensus 67 ~~i~K~Y~V~v~~~i~~~~--l~---------~l~~Gv~i~dg~~~~~~~--v~~~---~------~~~~~i~l~eGknr 124 (167)
T cd02553 67 KHVPKTYEVTLAGPLTEDD--IE---------AFAEGVLLHDGYPTKPAK--LEIL---S------PTTVRLTITEGKYH 124 (167)
T ss_pred CCCCEEEEEEECCCCCHHH--HH---------HHHCCCEECCCCEEEEEE--EEEE---C------CCEEEEEEECCCCH
T ss_conf 7888899998767899999--99---------997698964985975179--9992---5------86899999888462
Q ss_pred HHHHHHHHHCCEEECCC
Q ss_conf 99999987097860415
Q gi|254780610|r 259 QIRVHMAHKGNPLIGDP 275 (340)
Q Consensus 259 QIRvhla~lG~PIvGD~ 275 (340)
|||..|+++|++|..=.
T Consensus 125 qIRrm~~~~g~~V~~L~ 141 (167)
T cd02553 125 QVKRMFAAVGNKVVALH 141 (167)
T ss_pred HHHHHHHHCCCEEEEEE
T ss_conf 99999998698885899
No 23
>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=99.60 E-value=3.5e-15 Score=110.26 Aligned_cols=143 Identities=22% Similarity=0.273 Sum_probs=92.2
Q ss_pred EEEEECCCHHHCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHHHHHHHHCCC
Q ss_conf 78996240111045678754210022222210244334444364324444332324057212035788889999972113
Q gi|254780610|r 99 IIVINKPAGLVVHPAPGNWTGTLVNALLYHCHNNLSSINGVKRPGIVHRLDKDTTGVMVVAKNDLAHQKLSEQFVDHGKS 178 (340)
Q Consensus 99 llvinKPaGl~vhp~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~lVHRLDr~TSGlll~Ak~~~a~~~l~~~f~~~~~~ 178 (340)
++++|||.|..|.-.......|+.+.+... ...+.+.|.|||++|||+||+.-+...+..|. ..+
T Consensus 2 ~illnKP~G~v~s~~d~~~r~tv~dll~~~---------~~~rl~~vGRLD~ds~GLLLlTnDG~l~~~l~------hP~ 66 (167)
T cd02556 2 VLIYHKPEGLICTRKDPKGRPTVFDLLPKL---------GIPRWISVGRLDLNTEGLLLFTNDGELANRLM------HPS 66 (167)
T ss_pred EEEEECCCCEEECCCCCCCCCCHHHHCCCC---------CCCCCCCCCCCCCCCCCEEEEECCHHHHHHHC------CCC
T ss_conf 899989999897862998897578965533---------55572364138957678599927836757640------987
Q ss_pred CCEEEEEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEECCCCCEEECCCCCCCCCEEEEEECHHHHH
Q ss_conf 22133445432024332332110013434443322123444555553000012221011256677500123443115899
Q gi|254780610|r 179 TRLKRAYYAMVWGIPLPDSGIINAPLGRCKSNRLRRAVKGIDDKTADSAITHYQTIEIYNKNSNFAVSLLKCHLETGRTH 258 (340)
Q Consensus 179 ~~v~K~Y~Aiv~G~~~~~~g~i~~~l~~~~~~~~~~~~~~~~~~~~k~a~T~~~~l~~~~~~~~~~~slv~~~~~TGRtH 258 (340)
..+.|+|++.+.|.+.++. ++. + +..+.. +....+++. .+.+ ......+.+++.+..||.|
T Consensus 67 ~~i~k~Y~V~v~~~~~~~~--l~~-l--------~~Gv~i-~~~~~~~~~--v~~~-----~~~~~~~~~~i~l~eGk~r 127 (167)
T cd02556 67 NEIEREYAVRVFGQVTDEQ--LKS-L--------KKGVEL-EDGFAGFKS--IQLE-----GGEGKNSWYRVTLREGRNR 127 (167)
T ss_pred CCCCEEEEEEECCCCCHHH--HHH-H--------HCCCEE-CCEEEEEEE--EEEE-----CCCCCCEEEEEEEECCCHH
T ss_conf 7885799999758999999--999-8--------779787-998840069--9996-----2679967999999769468
Q ss_pred HHHHHHHHHCCEEECCC
Q ss_conf 99999987097860415
Q gi|254780610|r 259 QIRVHMAHKGNPLIGDP 275 (340)
Q Consensus 259 QIRvhla~lG~PIvGD~ 275 (340)
|||..|+++|++|+.=.
T Consensus 128 qIRrmf~~~g~~V~~L~ 144 (167)
T cd02556 128 EVRRLWEAFGLQVSRLI 144 (167)
T ss_pred HHHHHHHHCCCEEEEEE
T ss_conf 99999998699895899
No 24
>TIGR00093 TIGR00093 conserved hypothetical protein; InterPro: IPR000748 Pseudouridine synthases are responsible for the synthesis of pseudouridine from uracil in ribosomal RNA. Several bacterial proteins from the Rsu family of pseudouridine synthases have been shown to share regions of similarities, including Escherichia coli and Haemophilus influenzae 16S pseudouridylate 516 synthase (gene rsuA); E. coli hypothetical proteins yciL and ymfC and the corresponding H. influenzae proteins HI1199 and HI0694 respectively; Aquifex aeolicus hypothetical proteins AQ_554 and AQ_1464; Bacillus subtilis hypothetical proteins ypuL and ytzF; Borrelia burgdorferi hypothetical protein BB0129; Helicobacter pylori hypothetical protein HP1459; and Synechocystis sp. (strain PCC 6803) hypothetical proteins slr0361 and slr0612. These are proteins of from 25 to 40 kD which contain a number of conserved regions in their central section.; GO: 0003723 RNA binding, 0004730 pseudouridylate synthase activity, 0001522 pseudouridine synthesis.
Probab=99.57 E-value=4.5e-15 Score=109.61 Aligned_cols=151 Identities=23% Similarity=0.302 Sum_probs=95.5
Q ss_pred ECCCHHHCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHHHHHHHHCCCCCEE
Q ss_conf 62401110456787542100222222102443344443643244443323240572120357888899999721132213
Q gi|254780610|r 103 NKPAGLVVHPAPGNWTGTLVNALLYHCHNNLSSINGVKRPGIVHRLDKDTTGVMVVAKNDLAHQKLSEQFVDHGKSTRLK 182 (340)
Q Consensus 103 nKPaGl~vhp~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~lVHRLDr~TSGlll~Ak~~~a~~~l~~~f~~~~~~~~v~ 182 (340)
|||.|++|+-..+....|+.+.+-..+ ....+.+.|.|||++|+|+||+.-+-+....|.. ....++
T Consensus 1 nKP~g~l~~~~Dp~~r~~~~~~l~~~~-------~~~~~~~a~GRLD~ds~GLlLLT~~G~L~~RL~~------p~~~~e 67 (185)
T TIGR00093 1 NKPQGVLCTTDDPEGRKTVKDLLPKKL-------IRGKRLHAVGRLDRDSEGLLLLTNDGELQHRLTH------PKFHHE 67 (185)
T ss_pred CCCCCEEECCCCCCCCCEEEECCCHHH-------HCCCCEEEEECCCCCCCCEEEECCCHHHHHHHHC------CCCCCC
T ss_conf 998504435849887723500452023-------1057467740267456203899069799998717------643589
Q ss_pred EEEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC-CCCEECC----CC-CEEE---CCCCCCCCCEEEEEEC
Q ss_conf 344543202433233211001343444332212344455555-3000012----22-1011---2566775001234431
Q gi|254780610|r 183 RAYYAMVWGIPLPDSGIINAPLGRCKSNRLRRAVKGIDDKTA-DSAITHY----QT-IEIY---NKNSNFAVSLLKCHLE 253 (340)
Q Consensus 183 K~Y~Aiv~G~~~~~~g~i~~~l~~~~~~~~~~~~~~~~~~~~-k~a~T~~----~~-l~~~---~~~~~~~~slv~~~~~ 253 (340)
|+|++-|+|.|.++. +. ..+..+...+.... |+|.-.+ .. -.+. ...+.-.+|-+.+.|.
T Consensus 68 K~Y~V~v~g~v~~~~--~~---------~~~~Gv~L~~~~~~tk~a~~~~~~~~~~~~pr~ppir~r~~i~~S~l~~tl~ 136 (185)
T TIGR00093 68 KTYLVTVEGPVTDED--LE---------ALRKGVQLEDGKTLTKPAKLKVISEPEDLWPRNPPIRERKSIPTSWLRVTLT 136 (185)
T ss_pred CEEEEEECCCCCHHH--HH---------HHHCCCEECCCCCCCCCEEEEEECCCCCCCCCCCCEEECCCCCCCEEEEEEE
T ss_conf 669999559858889--98---------9871760058735644237787067131356787312003688225899996
Q ss_pred HHHHHHHHHHHHHHCCEEECCCCC
Q ss_conf 158999999998709786041544
Q gi|254780610|r 254 TGRTHQIRVHMAHKGNPLIGDPLY 277 (340)
Q Consensus 254 TGRtHQIRvhla~lG~PIvGD~~Y 277 (340)
-||.||||..+|++|++++.=..+
T Consensus 137 EGRNRqvRRm~a~~G~~V~~L~R~ 160 (185)
T TIGR00093 137 EGRNRQVRRMFAAVGFPVLRLHRV 160 (185)
T ss_pred ECCCHHHHHHHHHHCCEEEEEEEE
T ss_conf 087068878889838903478988
No 25
>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=99.52 E-value=3.2e-14 Score=104.54 Aligned_cols=145 Identities=21% Similarity=0.269 Sum_probs=84.3
Q ss_pred EEEEECCCHHHCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHHHHHHHHCCC
Q ss_conf 78996240111045678754210022222210244334444364324444332324057212035788889999972113
Q gi|254780610|r 99 IIVINKPAGLVVHPAPGNWTGTLVNALLYHCHNNLSSINGVKRPGIVHRLDKDTTGVMVVAKNDLAHQKLSEQFVDHGKS 178 (340)
Q Consensus 99 llvinKPaGl~vhp~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~lVHRLDr~TSGlll~Ak~~~a~~~l~~~f~~~~~~ 178 (340)
++++|||+|..|.-+......+..... ... ..........+.+.|.|||++|||+||+.-+...+..|. | ..
T Consensus 6 yllLnKP~G~v~t~~d~~~~~~~~~~~-~~~-~~~~l~~~~~rl~pVGRLD~~s~GLLllTNDG~l~~~l~-----~-P~ 77 (177)
T cd02555 6 TLLLHKPAGMVSEQALALLGPGQRSAA-DRS-GRRPLKGHFARLAPIGPLDKDASGLLVFSQDGRVLRKLI-----G-DA 77 (177)
T ss_pred EEEEECCCCEECCCCCCCCCCCCCCCC-CCC-CCCCCCCCCCCEEEECCCCCCCCEEEEEECCHHHHHHHC-----C-CC
T ss_conf 999989984870775766787501333-454-100010223662160478999811899918889998754-----9-86
Q ss_pred CCEEEEEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEECCCCCEEECCCCCCCCCEEEEEECHHHHH
Q ss_conf 22133445432024332332110013434443322123444555553000012221011256677500123443115899
Q gi|254780610|r 179 TRLKRAYYAMVWGIPLPDSGIINAPLGRCKSNRLRRAVKGIDDKTADSAITHYQTIEIYNKNSNFAVSLLKCHLETGRTH 258 (340)
Q Consensus 179 ~~v~K~Y~Aiv~G~~~~~~g~i~~~l~~~~~~~~~~~~~~~~~~~~k~a~T~~~~l~~~~~~~~~~~slv~~~~~TGRtH 258 (340)
..+.|+|++.|.|.+.++. ++. +. ..+.. ++..-+++.-.+ . + . +-+++.+..||.|
T Consensus 78 ~~i~k~Y~V~v~~~~~~~~--l~~-l~--------~Gv~l-~g~~~~~~~v~~--~-----~-~---~~~~i~l~eGknr 134 (177)
T cd02555 78 SRLEQEYLVEVRGELTAGG--LER-LN--------HGLTY-DGRELPPAKVSW--Q-----N-E---QRLRFALKEPQPG 134 (177)
T ss_pred CCCCEEEEEEECCCCCHHH--HHH-HH--------CCEEE-CCEEECCEEEEE--E-----C-C---CEEEEEEECCCCH
T ss_conf 6897899999898799999--987-52--------87678-998967869999--5-----7-9---9599999918416
Q ss_pred HHHHHHHHHCCEEECC
Q ss_conf 9999998709786041
Q gi|254780610|r 259 QIRVHMAHKGNPLIGD 274 (340)
Q Consensus 259 QIRvhla~lG~PIvGD 274 (340)
|||..|+++|++|..=
T Consensus 135 qIRrm~~~~g~~V~~L 150 (177)
T cd02555 135 QIRRMCESVGLEVVAL 150 (177)
T ss_pred HHHHHHHHCCCEEEEE
T ss_conf 9999999879979899
No 26
>cd02554 PseudoU_synth_RluF PseudoU_synth_RluF_like: Pseudouridine synthase, Escherichia coli RluF like. This group is comprised of bacterial proteins similar to Escherichia coli RluF. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. E.coli RluF makes psi2604 in 23S RNA. psi2604 has only been detected in E. coli. It is absent from other eubacteria despite a precursor U at that site and from eukarya and archea which lack a precursor U at that site.
Probab=99.46 E-value=2e-13 Score=99.82 Aligned_cols=137 Identities=18% Similarity=0.198 Sum_probs=86.4
Q ss_pred EEEEECCCHHHCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHHHHHHHHCCC
Q ss_conf 78996240111045678754210022222210244334444364324444332324057212035788889999972113
Q gi|254780610|r 99 IIVINKPAGLVVHPAPGNWTGTLVNALLYHCHNNLSSINGVKRPGIVHRLDKDTTGVMVVAKNDLAHQKLSEQFVDHGKS 178 (340)
Q Consensus 99 llvinKPaGl~vhp~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~lVHRLDr~TSGlll~Ak~~~a~~~l~~~f~~~~~~ 178 (340)
++++|||.|+.|.....+ ..++.+.+. ...+.+.|.|||++|+|+||+.-+...++.|. ..+
T Consensus 2 YillnKP~G~v~s~~~~~-~~~~~~~l~-----------~~~rl~~vGRLD~~s~GLLLlTNDg~l~~~L~------hP~ 63 (164)
T cd02554 2 YIAYNKPVGIDCTLERAD-EDNIIDFVN-----------PPPRIFPIGRLDKDSEGLILLTNDGDLVNKIL------HAD 63 (164)
T ss_pred EEEEECCCCEEECCCCCC-CCCEEEECC-----------CCCCEEECCCCCCCCCCEEEEECCHHHHHHHC------CCC
T ss_conf 999989998283878999-996699748-----------86777888678999856599957889997621------998
Q ss_pred CCEEEEEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEECCCCCEEECCCCCCCCCEEEEEECHHHHH
Q ss_conf 22133445432024332332110013434443322123444555553000012221011256677500123443115899
Q gi|254780610|r 179 TRLKRAYYAMVWGIPLPDSGIINAPLGRCKSNRLRRAVKGIDDKTADSAITHYQTIEIYNKNSNFAVSLLKCHLETGRTH 258 (340)
Q Consensus 179 ~~v~K~Y~Aiv~G~~~~~~g~i~~~l~~~~~~~~~~~~~~~~~~~~k~a~T~~~~l~~~~~~~~~~~slv~~~~~TGRtH 258 (340)
..+.|+|++.+.|.+.++. ++. | +..+.. +....+++.. +.+ .. +-+++.+..|+.|
T Consensus 64 ~~i~k~Y~V~~~~~i~~~~--l~~-l--------~~Gi~i-~~~~~~~~~v--~~~---~~------~~~~i~l~eGknr 120 (164)
T cd02554 64 NNHEKEYLVTVNKPITDEF--IEG-M--------SNGVVI-LGTVTKPCKV--ERL---AK------DKFRIVLTQGLNR 120 (164)
T ss_pred CCCCCEEEEEECCCCCHHH--HHH-H--------HCCEEE-CCEEEECEEE--EEE---CC------CEEEEEEEECCCH
T ss_conf 8896299999956699999--998-7--------478598-9889802199--994---79------8499999926748
Q ss_pred HHHHHHHHHCCEEECCCC
Q ss_conf 999999870978604154
Q gi|254780610|r 259 QIRVHMAHKGNPLIGDPL 276 (340)
Q Consensus 259 QIRvhla~lG~PIvGD~~ 276 (340)
|||..|+++|+++.-=..
T Consensus 121 qIRrmf~~~g~~V~~L~R 138 (164)
T cd02554 121 QIRRMCEALGYRVTDLKR 138 (164)
T ss_pred HHHHHHHHCCCEEEEEEE
T ss_conf 999999986998848999
No 27
>cd00165 S4 S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, charged residues that define a likely RNA-binding site; Found in stress proteins, ribosomal proteins and tRNA synthetases; This may imply a hitherto unrecognized functional similarity between these three protein classes.
Probab=99.11 E-value=2.1e-10 Score=81.84 Aligned_cols=70 Identities=37% Similarity=0.544 Sum_probs=60.6
Q ss_pred CCHHHHHHHHCCCCCCHHHHHHHHHCCCEEECCEEECCCCCEECCCCEEEEEECCCHHCCHHHHHHHHHHCCCCCEEEEE
Q ss_conf 75789999871768898999999985990499899328675804898899970560111102332222210144027899
Q gi|254780610|r 23 GRIDRWLATSLKEQFSRSYVKILILNGFISINGMVSKNPNRKVVPGDSFLITVPAAQKLNIAQENIPLDILYEDDDIIVI 102 (340)
Q Consensus 23 ~RLD~~L~~~l~~~~sR~~i~kli~~G~V~vnG~~~~~~~~~l~~gd~I~i~~~~~~~~~~~~~~~~~~IlyED~~llvi 102 (340)
+|||+||.+..+ ..||++++++|+.|.|+|||+++++++++|..||.|.+..+.... +++|||++++++
T Consensus 1 ~RLd~~l~~~~~-~~Sr~~a~~~I~~g~V~VNg~~v~~~~~~v~~gd~i~i~~~~~~~----------~i~~~~~~~~~i 69 (70)
T cd00165 1 MRLDKILARLGL-APSRSEARQLIKHGHVLVNGKVVTKPSYKVKPGDVIEVDGKSIEE----------DIVYEDKKLLVV 69 (70)
T ss_pred CCHHHHHHHCCC-CCCHHHHHHHHHCCEEEECCEEECCCCCCCCCCCEEEECCCCCCC----------CEEEECCCEEEE
T ss_conf 948899987487-158999999998193898999958888898999999987877886----------732326989996
Q ss_pred E
Q ss_conf 6
Q gi|254780610|r 103 N 103 (340)
Q Consensus 103 n 103 (340)
|
T Consensus 70 ~ 70 (70)
T cd00165 70 N 70 (70)
T ss_pred C
T ss_conf 9
No 28
>smart00363 S4 S4 RNA-binding domain.
Probab=98.65 E-value=6.3e-08 Score=67.01 Aligned_cols=52 Identities=33% Similarity=0.416 Sum_probs=47.7
Q ss_pred CCHHHHHHHHCCCCCCHHHHHHHHHCCCEEECCEEECCCCCEECCCCEEEEEE
Q ss_conf 75789999871768898999999985990499899328675804898899970
Q gi|254780610|r 23 GRIDRWLATSLKEQFSRSYVKILILNGFISINGMVSKNPNRKVVPGDSFLITV 75 (340)
Q Consensus 23 ~RLD~~L~~~l~~~~sR~~i~kli~~G~V~vnG~~~~~~~~~l~~gd~I~i~~ 75 (340)
+|||+||.+... ..||++++++|+.|.|+|||++++.+++.|..||.|.+..
T Consensus 1 ~RLD~~l~~~~~-~~Sr~~a~~~I~~g~V~VNg~~v~~~~~~v~~~d~I~~~~ 52 (60)
T smart00363 1 RRLDKFLARLGL-APSRSQARKLIEQGRVKVNGKKVTKPSYIVKPGDVISVRG 52 (60)
T ss_pred CCHHHHHHHCCC-CCCHHHHHHHHHCCCEEECCEEECCCCCCCCCCCEEEECC
T ss_conf 978899998387-0479999999984917989999478988989999999988
No 29
>pfam01479 S4 S4 domain. The S4 domain is a small domain consisting of 60-65 amino acid residues that was detected in the bacterial ribosomal protein S4, eukaryotic ribosomal S9, two families of pseudouridine synthases, a novel family of predicted RNA methylases, a yeast protein containing a pseudouridine synthetase and a deaminase domain, bacterial tyrosyl-tRNA synthetases, and a number of uncharacterized, small proteins that may be involved in translation regulation. The S4 domain probably mediates binding to RNA.
Probab=98.55 E-value=9.4e-08 Score=65.99 Aligned_cols=48 Identities=40% Similarity=0.535 Sum_probs=43.6
Q ss_pred CCHHHHHHHHCCCCCCHHHHHHHHHCCCEEECCEEECCCCCEECCCCEE
Q ss_conf 7578999987176889899999998599049989932867580489889
Q gi|254780610|r 23 GRIDRWLATSLKEQFSRSYVKILILNGFISINGMVSKNPNRKVVPGDSF 71 (340)
Q Consensus 23 ~RLD~~L~~~l~~~~sR~~i~kli~~G~V~vnG~~~~~~~~~l~~gd~I 71 (340)
+|||+||.+... ..||++++++|+.|.|+|||++++++++.|.+||.|
T Consensus 1 ~RLd~~l~~~~~-~~Sr~~a~~~I~~G~V~VNg~~v~~~~~~v~~gD~i 48 (48)
T pfam01479 1 MRLDKVLARLGL-ASSRSEARQLIRHGHVRVNGKVVKDPSYRVKPGDVI 48 (48)
T ss_pred CCHHHHHHHCCC-CCCHHHHHHHHHCCCEEECCEEECCCCCCCCCCCCC
T ss_conf 966799998676-148999999998897798999957898688992999
No 30
>TIGR03069 PS_II_S4 photosystem II S4 domain protein. Members of this protein family are about 265 residues long and each contains an S4 RNA-binding domain of about 48 residues. The member from the Cyanobacterium, Synechocystis sp. PCC 6803, was detected as a novel polypeptide in a highly purified preparation of active photosystem II (Kashino, et al., 2002). The phylogenetic distribution, including Cyanobacteria and Arabidopsis, supports a role in photosystem II, although the high bit score cutoffs for this model reflect similar sequences in non-photosynthetic organisms such as Carboxydothermus hydrogenoformans, a Gram-positive bacterium.
Probab=98.33 E-value=1.7e-06 Score=58.53 Aligned_cols=53 Identities=26% Similarity=0.325 Sum_probs=44.5
Q ss_pred HCCCCHHHHHHHHCCCCCCHHHHHHHHHCCCEEECCEEECCCCCEECCCCEEEEE
Q ss_conf 3687578999987176889899999998599049989932867580489889997
Q gi|254780610|r 20 TAEGRIDRWLATSLKEQFSRSYVKILILNGFISINGMVSKNPNRKVVPGDSFLIT 74 (340)
Q Consensus 20 ~~g~RLD~~L~~~l~~~~sR~~i~kli~~G~V~vnG~~~~~~~~~l~~gd~I~i~ 74 (340)
.+..|||..++.-+ ++||+.+..+|++|.|.||++.+.++++.|..||.|++-
T Consensus 181 vsSlRLDavvs~~~--~~SRska~~lI~~g~V~vN~~~v~~~s~~v~~gDiiSvR 233 (257)
T TIGR03069 181 EASLRIDAIASAGF--GLSRSKIVDQIKAGRLRLNWKTVTQPSRELKVGDRLQLR 233 (257)
T ss_pred ECCCCHHHHHHHHH--CCCHHHHHHHHHCCEEEECCEEECCCCCCCCCCCEEEEE
T ss_conf 21213899999886--657999999988496898999905787566899999990
No 31
>COG1188 Ribosome-associated heat shock protein implicated in the recycling of the 50S subunit (S4 paralog) [Translation, ribosomal structure and biogenesis]
Probab=98.19 E-value=3.3e-06 Score=56.76 Aligned_cols=55 Identities=29% Similarity=0.487 Sum_probs=46.9
Q ss_pred HCCCCHHHHHHHH-CCCCCCHHHHHHHHHCCCEEECCEEECCCCCEECCCCEEEEEECC
Q ss_conf 3687578999987-176889899999998599049989932867580489889997056
Q gi|254780610|r 20 TAEGRIDRWLATS-LKEQFSRSYVKILILNGFISINGMVSKNPNRKVVPGDSFLITVPA 77 (340)
Q Consensus 20 ~~g~RLD~~L~~~-l~~~~sR~~i~kli~~G~V~vnG~~~~~~~~~l~~gd~I~i~~~~ 77 (340)
..-+|||+||--. |- =+|+.++++++.|+|.+||.++ +|++.|+.||+|.+....
T Consensus 6 ~~~mRLDKwL~~aR~~--KrRslAk~~~~~GrV~vNG~~a-KpS~~VK~GD~l~i~~~~ 61 (100)
T COG1188 6 ADRMRLDKWLWAARFI--KRRSLAKEMIEGGRVKVNGQRA-KPSKEVKVGDILTIRFGN 61 (100)
T ss_pred CCCEEHHHHHHHHHHH--HHHHHHHHHHHCCEEEECCEEC-CCCCCCCCCCEEEEEECC
T ss_conf 6516567888788774--2289999998779698999675-655614779899999578
No 32
>COG2302 Uncharacterized conserved protein, contains S4-like domain [Function unknown]
Probab=98.13 E-value=5.6e-06 Score=55.42 Aligned_cols=54 Identities=24% Similarity=0.313 Sum_probs=47.7
Q ss_pred HHCCCCHHHHHHHHCCCCCCHHHHHHHHHCCCEEECCEEECCCCCEECCCCEEEEE
Q ss_conf 13687578999987176889899999998599049989932867580489889997
Q gi|254780610|r 19 STAEGRIDRWLATSLKEQFSRSYVKILILNGFISINGMVSKNPNRKVVPGDSFLIT 74 (340)
Q Consensus 19 ~~~g~RLD~~L~~~l~~~~sR~~i~kli~~G~V~vnG~~~~~~~~~l~~gd~I~i~ 74 (340)
..+..|||..++..+ ++||+.+.++|.+|.|.||.+.++++++.++.||.|++-
T Consensus 177 ~vsSlRLD~vis~~~--~~SR~~a~~lIe~g~VkVN~k~v~~~s~~v~~GDliSir 230 (257)
T COG2302 177 TVSSLRLDVVISEGF--GLSRAKAQQLIEKGKVKVNWKVVDKASYEVQEGDLISIR 230 (257)
T ss_pred EEEHHHHHHHHHHHH--HHHHHHHHHHHHCCCEEEEEEEECCCCCEECCCCEEEEE
T ss_conf 421240799999887--655999999877373277129912666332249899984
No 33
>TIGR01017 rpsD_bact ribosomal protein S4; InterPro: IPR005709 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites , . About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many of ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome , . The S4 domain is a small domain consisting of 60-65 amino acid residues that probably mediates binding to RNA. This family consists of organelle (chloroplast and mitochondrial) ribosomal protein S4 as well as bacterial ribosomal protein S4.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0015935 small ribosomal subunit.
Probab=98.10 E-value=2.3e-06 Score=57.65 Aligned_cols=61 Identities=28% Similarity=0.399 Sum_probs=49.2
Q ss_pred CCCCHHHHHHHHCCCCCCHHHHHHHHHCCCEEECCEEECCCCCEECCCCEEEEEECCCHHCCH
Q ss_conf 687578999987176889899999998599049989932867580489889997056011110
Q gi|254780610|r 21 AEGRIDRWLATSLKEQFSRSYVKILILNGFISINGMVSKNPNRKVVPGDSFLITVPAAQKLNI 83 (340)
Q Consensus 21 ~g~RLD~~L~~~l~~~~sR~~i~kli~~G~V~vnG~~~~~~~~~l~~gd~I~i~~~~~~~~~~ 83 (340)
-++|||+.+= ++.=+-+|.+|++|+-.|.|.|||+++.-||+.|++||.|.|- +.......
T Consensus 98 LE~RLDNvVY-RlGfA~Tr~~ARQLVsHGhi~vNGk~VdIPSy~v~~Gd~i~ik-Ek~~~~~~ 158 (217)
T TIGR01017 98 LESRLDNVVY-RLGFAPTRRAARQLVSHGHILVNGKKVDIPSYQVRPGDIISIK-EKSKKIPL 158 (217)
T ss_pred HHCCCCCEEE-CCCCHHHHHHHHHHHHCCEEEECCEEECCCEEEECCCCEEEEE-ECCCCCCH
T ss_conf 6110010102-1271200787635640880787981852240670799889981-03203535
No 34
>CHL00113 rps4 ribosomal protein S4; Reviewed
Probab=98.04 E-value=6.8e-06 Score=54.90 Aligned_cols=54 Identities=26% Similarity=0.308 Sum_probs=46.8
Q ss_pred CCCCHHHHHHHHCCCCCCHHHHHHHHHCCCEEECCEEECCCCCEECCCCEEEEEE
Q ss_conf 6875789999871768898999999985990499899328675804898899970
Q gi|254780610|r 21 AEGRIDRWLATSLKEQFSRSYVKILILNGFISINGMVSKNPNRKVVPGDSFLITV 75 (340)
Q Consensus 21 ~g~RLD~~L~~~l~~~~sR~~i~kli~~G~V~vnG~~~~~~~~~l~~gd~I~i~~ 75 (340)
-++|||+.+- ++.-.-|+.++++++..|.|.|||+++.-|++.+++||.|.+.-
T Consensus 87 LE~RLDnvVy-RlGfA~Tr~~ARQlV~HgHi~VNgkkVnIPSy~vk~GDvI~v~~ 140 (201)
T CHL00113 87 LEMRLDNILF-RLGMAPTIPAARQLVNHGHILVNGRIVDIPSYRCKPRDIITIKD 140 (201)
T ss_pred HHHHHHHHHH-HCCCCCCHHHHHHEEECCEEEECCEEECCCCEEEECCCEEEECC
T ss_conf 9999999998-70540588876105846629989989337875842799899753
No 35
>PRK12565 30S ribosomal protein S4; Provisional
Probab=98.00 E-value=9.3e-06 Score=54.10 Aligned_cols=53 Identities=23% Similarity=0.283 Sum_probs=46.4
Q ss_pred CCCCHHHHHHHHCCCCCCHHHHHHHHHCCCEEECCEEECCCCCEECCCCEEEEE
Q ss_conf 687578999987176889899999998599049989932867580489889997
Q gi|254780610|r 21 AEGRIDRWLATSLKEQFSRSYVKILILNGFISINGMVSKNPNRKVVPGDSFLIT 74 (340)
Q Consensus 21 ~g~RLD~~L~~~l~~~~sR~~i~kli~~G~V~vnG~~~~~~~~~l~~gd~I~i~ 74 (340)
-+.|||+.+-+ +.-.-|+.++++++..|.|.|||+++.-|++.+++||.|.+.
T Consensus 86 LE~RLDnvv~R-~gfa~t~~~ARQlV~Hghi~vng~kVdIPSy~vk~GDvI~vk 138 (197)
T PRK12565 86 LECRLDNVVYR-IGFASSIRQARQMVNHGHILVNGKKVNIPSYEVKVGDEITLR 138 (197)
T ss_pred HHHHHHHHHHH-CCCCCCHHHHHHHHHCCCEEECCEEECCCCEEECCCCEEEEC
T ss_conf 99866677113-441057999866740788897998955887670699999973
No 36
>PRK10348 ribosome-associated heat shock protein Hsp15; Provisional
Probab=98.00 E-value=9.7e-06 Score=53.98 Aligned_cols=57 Identities=23% Similarity=0.349 Sum_probs=46.2
Q ss_pred HHHCCCCHHHHHHHHCCCCCCHHHHHHHHHCCCEEECCEEECCCCCEECCCCEEEEEEC
Q ss_conf 11368757899998717688989999999859904998993286758048988999705
Q gi|254780610|r 18 DSTAEGRIDRWLATSLKEQFSRSYVKILILNGFISINGMVSKNPNRKVVPGDSFLITVP 76 (340)
Q Consensus 18 ~~~~g~RLD~~L~~~l~~~~sR~~i~kli~~G~V~vnG~~~~~~~~~l~~gd~I~i~~~ 76 (340)
+....+|||+||=..-.- =||+.+.++|+.|+|.|||.++ +|+..|..||.|.+...
T Consensus 4 ~p~~k~RiDkwLW~aRff-KTRslA~~a~~~G~V~vnG~~~-Kps~~V~~GD~l~i~~~ 60 (133)
T PRK10348 4 KPAVEVRLDKWLWAARFY-KTRALAREMIEGGKVHYNGQRS-KPSKIVELNATLTLRQG 60 (133)
T ss_pred CCCCCEEEHHHHHHHEEH-HHHHHHHHHHHCCCEEECCEEC-CCCCCCCCCCEEEEEEC
T ss_conf 875505402003152010-0099999999879889899886-88887689999999869
No 37
>COG0522 RpsD Ribosomal protein S4 and related proteins [Translation, ribosomal structure and biogenesis]
Probab=98.00 E-value=1.1e-05 Score=53.67 Aligned_cols=55 Identities=25% Similarity=0.315 Sum_probs=46.9
Q ss_pred HCCCCHHHHHHHHCCCCCCHHHHHHHHHCCCEEECCEEECCCCCEECCCCEEEEEE
Q ss_conf 36875789999871768898999999985990499899328675804898899970
Q gi|254780610|r 20 TAEGRIDRWLATSLKEQFSRSYVKILILNGFISINGMVSKNPNRKVVPGDSFLITV 75 (340)
Q Consensus 20 ~~g~RLD~~L~~~l~~~~sR~~i~kli~~G~V~vnG~~~~~~~~~l~~gd~I~i~~ 75 (340)
--++|||+.+-+. .-.-|+.+++++|..|+|.|||+++..|++.|.+||++.+..
T Consensus 91 ~LErRLd~vVyR~-GfA~T~~qARQlV~HGHI~VnGk~V~iPSy~V~~gdei~V~~ 145 (205)
T COG0522 91 LLERRLDNVVYRL-GFAKTRRQARQLVSHGHILVNGKRVNIPSYLVSPGDEISVRE 145 (205)
T ss_pred HHHHHHHHHHHHH-CCCCCHHHHHHHHHCCEEEECCEEECCCCEEECCCCEEEEEC
T ss_conf 9998878999984-041359999988406628999999526737963777887520
No 38
>PRK05327 rpsD 30S ribosomal protein S4; Validated
Probab=97.76 E-value=2.3e-05 Score=51.73 Aligned_cols=53 Identities=26% Similarity=0.360 Sum_probs=46.1
Q ss_pred CCCCHHHHHHHHCCCCCCHHHHHHHHHCCCEEECCEEECCCCCEECCCCEEEEE
Q ss_conf 687578999987176889899999998599049989932867580489889997
Q gi|254780610|r 21 AEGRIDRWLATSLKEQFSRSYVKILILNGFISINGMVSKNPNRKVVPGDSFLIT 74 (340)
Q Consensus 21 ~g~RLD~~L~~~l~~~~sR~~i~kli~~G~V~vnG~~~~~~~~~l~~gd~I~i~ 74 (340)
-+.|||..+-+. .-.-|+.+++++|..|.|.|||+++.-|++.+++||.|.+-
T Consensus 90 LE~RLD~vv~r~-g~a~t~~~ARQ~v~Hghi~vNg~~v~ips~~~k~gd~i~vk 142 (201)
T PRK05327 90 LERRLDNVVYRL-GFAPTRAQARQLVSHGHILVNGKKVNIPSYQVKPGDVIEVR 142 (201)
T ss_pred HHHHHHHHHHHH-CCCCCHHHHHHEEEEEEEEECCEEECCCCEECCCCCEEEEC
T ss_conf 999988999871-41058888620064405998999835787473899999977
No 39
>COG1189 Predicted rRNA methylase [Translation, ribosomal structure and biogenesis]
Probab=97.68 E-value=0.00011 Score=47.73 Aligned_cols=53 Identities=28% Similarity=0.252 Sum_probs=47.8
Q ss_pred CCCHHHHHHHHCCCCCCHHHHHHHHHCCCEEECCEEECCCCCEECCCCEEEEEE
Q ss_conf 875789999871768898999999985990499899328675804898899970
Q gi|254780610|r 22 EGRIDRWLATSLKEQFSRSYVKILILNGFISINGMVSKNPNRKVVPGDSFLITV 75 (340)
Q Consensus 22 g~RLD~~L~~~l~~~~sR~~i~kli~~G~V~vnG~~~~~~~~~l~~gd~I~i~~ 75 (340)
.+|||.+|.++-. .-||+.++.+|.+|.|.|||.++.+|++.|..++.|.+..
T Consensus 2 k~RLD~~Lv~rgl-~~sR~~A~~~I~~G~V~Vng~~v~KP~~~V~~~~~i~v~~ 54 (245)
T COG1189 2 KMRLDALLVERGL-FESREKAKELILAGNVLVNGEKVTKPSQLVDIDDEIEVKG 54 (245)
T ss_pred CCHHHHHHHHCCC-HHHHHHHHHHHHCCEEEECCEEECCCCEECCCCCEEEECC
T ss_conf 3238999997353-3209999999876857889999427652458986378756
No 40
>TIGR00478 tly hemolysin A; InterPro: IPR004538 Hemolysins are exotoxins that attack blood cell membranes and cause cell rupture. The mechanism of action is not well defined. Hemolysin A is induced by sodium ribonucleate, and is produced by pathogenic bacterial strains. Hemolysin A from Treponema hyodysenteriae causes swine dysentry.; GO: 0003723 RNA binding, 0019836 hemolysis by symbiont of host red blood cells.
Probab=97.58 E-value=0.00013 Score=47.33 Aligned_cols=53 Identities=25% Similarity=0.195 Sum_probs=47.7
Q ss_pred CHHHHHHHHCCCCCCHHHHHHHHHCCCEEECCEEECCCCCEECCCCEEEEEECC
Q ss_conf 578999987176889899999998599049989932867580489889997056
Q gi|254780610|r 24 RIDRWLATSLKEQFSRSYVKILILNGFISINGMVSKNPNRKVVPGDSFLITVPA 77 (340)
Q Consensus 24 RLD~~L~~~l~~~~sR~~i~kli~~G~V~vnG~~~~~~~~~l~~gd~I~i~~~~ 77 (340)
|||..|.++.+. =||+.++.+|.+|.|.||+.++++|+..|...+.|.+.-++
T Consensus 1 RLD~lLv~rgl~-~sR~~Ak~lI~kG~V~VN~~~v~KP~~~v~~~~~i~l~~~~ 53 (240)
T TIGR00478 1 RLDILLVKRGLV-ESREKAKRLILKGEVLVNKKKVDKPSALVDKDAKIELVQNP 53 (240)
T ss_pred CCHHHHHHHCHH-HHHHHHHHHHHCCCEEECCEEECCCCCEECCCCCEEEECCC
T ss_conf 903677650114-57899999987394555576520886044167603441477
No 41
>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=97.38 E-value=0.00035 Score=44.69 Aligned_cols=69 Identities=25% Similarity=0.361 Sum_probs=48.8
Q ss_pred EEEEEECCCHHHCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHHHHHHHHCC
Q ss_conf 27899624011104567875421002222221024433444436432444433232405721203578888999997211
Q gi|254780610|r 98 DIIVINKPAGLVVHPAPGNWTGTLVNALLYHCHNNLSSINGVKRPGIVHRLDKDTTGVMVVAKNDLAHQKLSEQFVDHGK 177 (340)
Q Consensus 98 ~llvinKPaGl~vhp~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~lVHRLDr~TSGlll~Ak~~~a~~~l~~~f~~~~~ 177 (340)
.++++|||.|+.+| .+++.+...+. ..+.|-...||-..||||+++-+.. ..+...|..
T Consensus 1 Gil~i~KP~G~TS~--------~vv~~vk~~~~--------~kKvGH~GTLDP~AtGvL~i~vG~a--TK~~~~~~~--- 59 (210)
T cd00506 1 GLFAVDKPQGPSSH--------DVVDTIRRIFL--------AEKVGHGGTLDPFATGVLVVGIGKA--TKLLKHLLA--- 59 (210)
T ss_pred CEEEEECCCCCCHH--------HHHHHHHHHHC--------CCCCCCCCCCCCCCCCEEEEEECHH--HHHHHHHCC---
T ss_conf 98999679999989--------99999999858--------7735768666974524289997788--879998755---
Q ss_pred CCCEEEEEEEEEE
Q ss_conf 3221334454320
Q gi|254780610|r 178 STRLKRAYYAMVW 190 (340)
Q Consensus 178 ~~~v~K~Y~Aiv~ 190 (340)
-.|+|.|.+.
T Consensus 60 ---~~K~Y~~~~~ 69 (210)
T cd00506 60 ---ATKDYTAIGR 69 (210)
T ss_pred ---CCCEEEEEEE
T ss_conf ---9977879999
No 42
>PRK00020 truB tRNA pseudouridine synthase B; Provisional
Probab=97.26 E-value=0.00057 Score=43.45 Aligned_cols=70 Identities=21% Similarity=0.384 Sum_probs=49.6
Q ss_pred CEEEEEECCCHHHCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHHHHHHHHC
Q ss_conf 02789962401110456787542100222222102443344443643244443323240572120357888899999721
Q gi|254780610|r 97 DDIIVINKPAGLVVHPAPGNWTGTLVNALLYHCHNNLSSINGVKRPGIVHRLDKDTTGVMVVAKNDLAHQKLSEQFVDHG 176 (340)
Q Consensus 97 ~~llvinKPaGl~vhp~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~lVHRLDr~TSGlll~Ak~~~a~~~l~~~f~~~~ 176 (340)
+.++++|||.|+.+| .+++.+...+.. .+.|-..-||-..||+|+++-+.. ..+...|.
T Consensus 10 ~G~l~idKP~G~TS~--------~vv~~vkk~l~~--------kKvGH~GTLDP~AtGvLiv~vG~a--TKl~~~~~--- 68 (244)
T PRK00020 10 DGVLLLDKPVGLSSN--------HALQRAKRTVDA--------AKAGHTGTLDPFATGLLVCCMGRA--TKISGRML--- 68 (244)
T ss_pred CEEEEEECCCCCCHH--------HHHHHHHHHHCC--------CCCCCCCCCCCCCCCEEEEEECHH--HHHHHHHC---
T ss_conf 779997169989989--------999999998298--------715778667975514189996737--67659766---
Q ss_pred CCCCEEEEEEEEEE
Q ss_conf 13221334454320
Q gi|254780610|r 177 KSTRLKRAYYAMVW 190 (340)
Q Consensus 177 ~~~~v~K~Y~Aiv~ 190 (340)
.-.|+|.|.+.
T Consensus 69 ---~~~K~Y~a~i~ 79 (244)
T PRK00020 69 ---EADKTYQATLQ 79 (244)
T ss_pred ---CCCCEEEEEEE
T ss_conf ---89927999999
No 43
>PRK00989 truB tRNA pseudouridine synthase B; Provisional
Probab=97.22 E-value=0.00051 Score=43.73 Aligned_cols=71 Identities=28% Similarity=0.382 Sum_probs=49.5
Q ss_pred CEEEEEECCCHHHCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHHHHHHHHC
Q ss_conf 02789962401110456787542100222222102443344443643244443323240572120357888899999721
Q gi|254780610|r 97 DDIIVINKPAGLVVHPAPGNWTGTLVNALLYHCHNNLSSINGVKRPGIVHRLDKDTTGVMVVAKNDLAHQKLSEQFVDHG 176 (340)
Q Consensus 97 ~~llvinKPaGl~vhp~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~lVHRLDr~TSGlll~Ak~~~a~~~l~~~f~~~~ 176 (340)
+.++++|||.|+.+| .+++.+...+.. .+.|-..=||-..||||++|-+..+ ..|.+.|.
T Consensus 9 ~GillidKP~G~TS~--------~vv~~vkk~l~~--------kKvGH~GTLDP~AtGvLiv~iG~~~-Tkl~~~~~--- 68 (235)
T PRK00989 9 EGILLVDKPQGRTSF--------SLIRALTKLIGV--------KKIGHAGTLDPFATGVMVMLIGRKF-TRLSDILL--- 68 (235)
T ss_pred CCEEEEECCCCCCHH--------HHHHHHHHHHCC--------CCCCCCCCCCCCCCCEEEEECCCCC-CCHHHHHC---
T ss_conf 819999789999989--------999999998587--------7468786779744352888407451-12789867---
Q ss_pred CCCCEEEEEEEEEE
Q ss_conf 13221334454320
Q gi|254780610|r 177 KSTRLKRAYYAMVW 190 (340)
Q Consensus 177 ~~~~v~K~Y~Aiv~ 190 (340)
.-.|+|.|.+.
T Consensus 69 ---~~~K~Y~a~i~ 79 (235)
T PRK00989 69 ---FEDKEYAAIAH 79 (235)
T ss_pred ---CCCCEEEEEEE
T ss_conf ---57846999999
No 44
>PRK00130 truB tRNA pseudouridine synthase B; Provisional
Probab=97.11 E-value=0.00093 Score=42.17 Aligned_cols=70 Identities=21% Similarity=0.315 Sum_probs=49.2
Q ss_pred CEEEEEECCCHHHCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHHHHHHHHC
Q ss_conf 02789962401110456787542100222222102443344443643244443323240572120357888899999721
Q gi|254780610|r 97 DDIIVINKPAGLVVHPAPGNWTGTLVNALLYHCHNNLSSINGVKRPGIVHRLDKDTTGVMVVAKNDLAHQKLSEQFVDHG 176 (340)
Q Consensus 97 ~~llvinKPaGl~vhp~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~lVHRLDr~TSGlll~Ak~~~a~~~l~~~f~~~~ 176 (340)
+.++.+|||.|+.+| .+++.+...+.. .+.|-..-||-..||+|++|-+.. ..+...|.
T Consensus 2 ~G~l~i~KP~g~TS~--------~vv~~vkk~l~~--------kKvGH~GTLDP~AtGvL~v~~G~a--TK~~~~~~--- 60 (289)
T PRK00130 2 NGVINVYKPKGMTSF--------DVVRKIRKIAKI--------KKVGHTGTLDPLASGVLPVCLGKA--TKIVDYIM--- 60 (289)
T ss_pred CEEEEEECCCCCCHH--------HHHHHHHHHHCC--------CCCCCCCCCCCCCCCEEEEEECHH--HHHHHHHC---
T ss_conf 779996089999989--------999999998488--------855778467985604289997877--61436767---
Q ss_pred CCCCEEEEEEEEEE
Q ss_conf 13221334454320
Q gi|254780610|r 177 KSTRLKRAYYAMVW 190 (340)
Q Consensus 177 ~~~~v~K~Y~Aiv~ 190 (340)
.-.|+|.|.+.
T Consensus 61 ---~~~K~Y~a~~~ 71 (289)
T PRK00130 61 ---EGKKVYRVELK 71 (289)
T ss_pred ---CCCEEEEEEEE
T ss_conf ---99907999999
No 45
>PRK04099 truB tRNA pseudouridine synthase B; Provisional
Probab=97.11 E-value=0.00069 Score=42.94 Aligned_cols=70 Identities=29% Similarity=0.469 Sum_probs=49.0
Q ss_pred CEEEEEECCCHHHCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHHHHHHHHC
Q ss_conf 02789962401110456787542100222222102443344443643244443323240572120357888899999721
Q gi|254780610|r 97 DDIIVINKPAGLVVHPAPGNWTGTLVNALLYHCHNNLSSINGVKRPGIVHRLDKDTTGVMVVAKNDLAHQKLSEQFVDHG 176 (340)
Q Consensus 97 ~~llvinKPaGl~vhp~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~lVHRLDr~TSGlll~Ak~~~a~~~l~~~f~~~~ 176 (340)
+.++++|||.|+.+| .+++.+...+.. .+.|-..=||-..||||++|-+.. ..+.+.|.
T Consensus 2 ngil~i~KP~G~TS~--------~vv~~vkk~l~~--------kKvGH~GTLDP~AtGvLiv~~G~a--TKl~~~l~--- 60 (272)
T PRK04099 2 NRLFVANKPPGLSSN--------AFLSRLKRKYGV--------KKAGFSGTLDPFAKGVLIVAFGQY--TKLFRFLD--- 60 (272)
T ss_pred CEEEEEECCCCCCHH--------HHHHHHHHHHCC--------CCCCCCCCCCCCCCCEEEEEECHH--HHHHHHHC---
T ss_conf 739996189989989--------999999998499--------844637056986604599998877--63117667---
Q ss_pred CCCCEEEEEEEEEE
Q ss_conf 13221334454320
Q gi|254780610|r 177 KSTRLKRAYYAMVW 190 (340)
Q Consensus 177 ~~~~v~K~Y~Aiv~ 190 (340)
...|+|.|.+.
T Consensus 61 ---~~~K~Y~a~i~ 71 (272)
T PRK04099 61 ---KTPKTYKATLW 71 (272)
T ss_pred ---CCCCEEEEEEE
T ss_conf ---78827999999
No 46
>PRK02484 truB tRNA pseudouridine synthase B; Provisional
Probab=97.09 E-value=0.00083 Score=42.48 Aligned_cols=70 Identities=27% Similarity=0.338 Sum_probs=48.9
Q ss_pred CEEEEEECCCHHHCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHHHHHHHHC
Q ss_conf 02789962401110456787542100222222102443344443643244443323240572120357888899999721
Q gi|254780610|r 97 DDIIVINKPAGLVVHPAPGNWTGTLVNALLYHCHNNLSSINGVKRPGIVHRLDKDTTGVMVVAKNDLAHQKLSEQFVDHG 176 (340)
Q Consensus 97 ~~llvinKPaGl~vhp~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~lVHRLDr~TSGlll~Ak~~~a~~~l~~~f~~~~ 176 (340)
+.++++|||.|+.+| .+++.+...+.. .+.|-..=||-..||+|++|-+.. ..+.+.|..
T Consensus 3 ~G~l~vdKP~G~TS~--------~vv~~ikk~~~~--------kKvGH~GTLDP~AtGvL~v~~G~a--Tkl~~~~~~-- 62 (293)
T PRK02484 3 NGIINLKKEAGMTSH--------DAVFKLRKILQT--------KKIGHGGTLDPDVVGVLPIAVGKA--TRVIEYMTE-- 62 (293)
T ss_pred CEEEEEECCCCCCHH--------HHHHHHHHHHCC--------CCCCCCCCCCCCCEEEEEEEECHH--HHHHHHHCC--
T ss_conf 669997269999989--------999999998489--------855658367986612689997887--715187664--
Q ss_pred CCCCEEEEEEEEEE
Q ss_conf 13221334454320
Q gi|254780610|r 177 KSTRLKRAYYAMVW 190 (340)
Q Consensus 177 ~~~~v~K~Y~Aiv~ 190 (340)
-.|+|.|.+.
T Consensus 63 ----~~K~Y~~~~~ 72 (293)
T PRK02484 63 ----AGKVYEGEVT 72 (293)
T ss_pred ----CCCEEEEEEE
T ss_conf ----8938999999
No 47
>PRK01851 truB tRNA pseudouridine synthase B; Provisional
Probab=97.07 E-value=0.001 Score=41.86 Aligned_cols=71 Identities=20% Similarity=0.340 Sum_probs=49.8
Q ss_pred CCEEEEEECCCHHHCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHHHHHHHH
Q ss_conf 40278996240111045678754210022222210244334444364324444332324057212035788889999972
Q gi|254780610|r 96 DDDIIVINKPAGLVVHPAPGNWTGTLVNALLYHCHNNLSSINGVKRPGIVHRLDKDTTGVMVVAKNDLAHQKLSEQFVDH 175 (340)
Q Consensus 96 D~~llvinKPaGl~vhp~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~lVHRLDr~TSGlll~Ak~~~a~~~l~~~f~~~ 175 (340)
=+.+|++|||.|+.+| .++..+.+.+.. .+.|-..=||-..||||++|-+.. ..+...|..
T Consensus 16 m~G~l~idKP~G~TS~--------~vv~~vk~~~~~--------kKvGH~GTLDP~AtGvL~v~~G~a--TK~~~~~~~- 76 (310)
T PRK01851 16 LDGVLLLDKPVGLSSN--------DALIRAKRLLLA--------KKAGHTGTLDPLASGLLPLCFGEA--TKFSQDLLE- 76 (310)
T ss_pred CCEEEEEECCCCCCHH--------HHHHHHHHHHCC--------CCCCCCCCCCCCCCCEEEEEECHH--HHHHHHHCC-
T ss_conf 6789997059989989--------999999998588--------845778677973404068997887--733177576-
Q ss_pred CCCCCEEEEEEEEEE
Q ss_conf 113221334454320
Q gi|254780610|r 176 GKSTRLKRAYYAMVW 190 (340)
Q Consensus 176 ~~~~~v~K~Y~Aiv~ 190 (340)
-.|+|.|.+.
T Consensus 77 -----~~K~Y~~~~~ 86 (310)
T PRK01851 77 -----ADKTYEATMR 86 (310)
T ss_pred -----CCCEEEEEEE
T ss_conf -----9808999999
No 48
>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=96.95 E-value=0.0015 Score=40.97 Aligned_cols=69 Identities=20% Similarity=0.304 Sum_probs=49.2
Q ss_pred EEEEEECCCHHHCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHHHHHHHHCC
Q ss_conf 27899624011104567875421002222221024433444436432444433232405721203578888999997211
Q gi|254780610|r 98 DIIVINKPAGLVVHPAPGNWTGTLVNALLYHCHNNLSSINGVKRPGIVHRLDKDTTGVMVVAKNDLAHQKLSEQFVDHGK 177 (340)
Q Consensus 98 ~llvinKPaGl~vhp~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~lVHRLDr~TSGlll~Ak~~~a~~~l~~~f~~~~~ 177 (340)
.++++|||.|+.+| .+++.+...+.. .+.|-..=||-..||||+++-+.. ..+.+.|.
T Consensus 3 Gil~idKP~G~TS~--------~vv~~ikk~l~~--------kKvGH~GTLDP~AtGvL~v~iG~a--TKl~~~~~---- 60 (182)
T cd02572 3 GVINLDKPSGPSSH--------EVVAWIKRILGV--------EKTGHSGTLDPKVTGCLPVCIDRA--TRLVKSQQ---- 60 (182)
T ss_pred EEEEEECCCCCCHH--------HHHHHHHHHHCC--------CCCCCCCCCCCCCCCEEEEECCHH--HHHHHHHC----
T ss_conf 89999579999989--------999999998576--------646889777975543477632678--89999867----
Q ss_pred CCCEEEEEEEEEE
Q ss_conf 3221334454320
Q gi|254780610|r 178 STRLKRAYYAMVW 190 (340)
Q Consensus 178 ~~~v~K~Y~Aiv~ 190 (340)
.-.|+|.|.+.
T Consensus 61 --~~~K~Y~~~~~ 71 (182)
T cd02572 61 --EAGKEYVCVMR 71 (182)
T ss_pred --CCCEEEEEEEE
T ss_conf --79808998167
No 49
>PRK01528 truB tRNA pseudouridine synthase B; Provisional
Probab=96.93 E-value=0.0018 Score=40.42 Aligned_cols=70 Identities=23% Similarity=0.310 Sum_probs=49.1
Q ss_pred CEEEEEECCCHHHCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHHHHHHHHC
Q ss_conf 02789962401110456787542100222222102443344443643244443323240572120357888899999721
Q gi|254780610|r 97 DDIIVINKPAGLVVHPAPGNWTGTLVNALLYHCHNNLSSINGVKRPGIVHRLDKDTTGVMVVAKNDLAHQKLSEQFVDHG 176 (340)
Q Consensus 97 ~~llvinKPaGl~vhp~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~lVHRLDr~TSGlll~Ak~~~a~~~l~~~f~~~~ 176 (340)
+.+|+||||.|+.+| .++..+...+.. .+.|-..=||-..||||++|-+.. ..+...|.
T Consensus 3 ng~l~i~KP~g~TS~--------~vv~~vkk~~~~--------~KvGH~GTLDP~AtGvL~i~~g~a--TK~~~~~~--- 61 (293)
T PRK01528 3 NYWLNIYKPRGISSA--------KLVSIVKKILGK--------VKIGHAGTLDVEAEGILPLAVGEA--TKLIQLLI--- 61 (293)
T ss_pred CEEEEEECCCCCCHH--------HHHHHHHHHHCC--------CCCCCCCCCCCCCCCEEEEEECHH--HHHHHHHC---
T ss_conf 758998779999989--------999999998489--------805768678875701589997866--50337865---
Q ss_pred CCCCEEEEEEEEEE
Q ss_conf 13221334454320
Q gi|254780610|r 177 KSTRLKRAYYAMVW 190 (340)
Q Consensus 177 ~~~~v~K~Y~Aiv~ 190 (340)
.-.|+|.|.+.
T Consensus 62 ---~~~K~Y~~~~~ 72 (293)
T PRK01528 62 ---DAKKTYIFTVK 72 (293)
T ss_pred ---CCCEEEEEEEE
T ss_conf ---79806999999
No 50
>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=96.88 E-value=0.0016 Score=40.74 Aligned_cols=76 Identities=22% Similarity=0.255 Sum_probs=45.3
Q ss_pred EEEEEECCCHHHCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHHHHHHHHCC
Q ss_conf 27899624011104567875421002222221024433444436432444433232405721203578888999997211
Q gi|254780610|r 98 DIIVINKPAGLVVHPAPGNWTGTLVNALLYHCHNNLSSINGVKRPGIVHRLDKDTTGVMVVAKNDLAHQKLSEQFVDHGK 177 (340)
Q Consensus 98 ~llvinKPaGl~vhp~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~lVHRLDr~TSGlll~Ak~~~a~~~l~~~f~~~~~ 177 (340)
.+++||||+|+.+| .+++.+.+.+...... ....+-+.-||-..||||++|-+... .+...|..
T Consensus 1 Gil~v~KP~G~TS~--------~vv~~v~~~l~k~~~~---~kk~g~~GTLDP~AtGvLvi~vG~aT--Kl~~~l~~--- 64 (226)
T cd02868 1 GLFAVYKPPGVHWK--------HVRDTIESNLLKYFPE---DKVLVGVHRLDAFSSGVLVLGVNHGN--KLLSHLYS--- 64 (226)
T ss_pred CEEEEECCCCCCHH--------HHHHHHHHHHHHHHCC---CEEEECCCCCCCCCCCCEEEEECHHH--HHHHHHHC---
T ss_conf 98999759999899--------9999999999766417---74696088889756033899988777--25699866---
Q ss_pred CCCEEEEEEEEEE
Q ss_conf 3221334454320
Q gi|254780610|r 178 STRLKRAYYAMVW 190 (340)
Q Consensus 178 ~~~v~K~Y~Aiv~ 190 (340)
....|+|.|.+.
T Consensus 65 -~~~~K~Y~~~~~ 76 (226)
T cd02868 65 -NHPTRVYTIRGL 76 (226)
T ss_pred -CCCCEEEEEEEE
T ss_conf -899769999999
No 51
>PRK05389 truB tRNA pseudouridine synthase B; Provisional
Probab=96.86 E-value=0.0023 Score=39.88 Aligned_cols=70 Identities=21% Similarity=0.337 Sum_probs=48.4
Q ss_pred CEEEEEECCCHHHCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHHHHHHHHC
Q ss_conf 02789962401110456787542100222222102443344443643244443323240572120357888899999721
Q gi|254780610|r 97 DDIIVINKPAGLVVHPAPGNWTGTLVNALLYHCHNNLSSINGVKRPGIVHRLDKDTTGVMVVAKNDLAHQKLSEQFVDHG 176 (340)
Q Consensus 97 ~~llvinKPaGl~vhp~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~lVHRLDr~TSGlll~Ak~~~a~~~l~~~f~~~~ 176 (340)
+.+|++|||.|+.+| .++..+...+.. .+.|-..=||-..||||++|-+.. ..+...|.+
T Consensus 13 ~G~l~idKP~G~TS~--------~vv~~vkk~~~~--------kKvGH~GTLDP~AtGvL~i~~G~a--Tk~~~~~~~-- 72 (305)
T PRK05389 13 SGWLILDKPAGMTST--------EAVSKVKWLFDA--------QKAGHAGTLDPLASGVLPIALGEA--TKTVPYVMD-- 72 (305)
T ss_pred CEEEEEECCCCCCHH--------HHHHHHHHHHCC--------CCCCCCCCCCCCCCCEEEEEECHH--HHHHHHHCC--
T ss_conf 779998249999989--------999999998588--------856778677986602388998877--623367656--
Q ss_pred CCCCEEEEEEEEEE
Q ss_conf 13221334454320
Q gi|254780610|r 177 KSTRLKRAYYAMVW 190 (340)
Q Consensus 177 ~~~~v~K~Y~Aiv~ 190 (340)
-.|+|.|.+.
T Consensus 73 ----~~K~Y~~~~~ 82 (305)
T PRK05389 73 ----GTKRYRFTVA 82 (305)
T ss_pred ----CCEEEEEEEE
T ss_conf ----8807999999
No 52
>PRK04642 truB tRNA pseudouridine synthase B; Provisional
Probab=96.85 E-value=0.0018 Score=40.42 Aligned_cols=70 Identities=23% Similarity=0.348 Sum_probs=48.7
Q ss_pred CEEEEEECCCHHHCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHHHHHHHHC
Q ss_conf 02789962401110456787542100222222102443344443643244443323240572120357888899999721
Q gi|254780610|r 97 DDIIVINKPAGLVVHPAPGNWTGTLVNALLYHCHNNLSSINGVKRPGIVHRLDKDTTGVMVVAKNDLAHQKLSEQFVDHG 176 (340)
Q Consensus 97 ~~llvinKPaGl~vhp~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~lVHRLDr~TSGlll~Ak~~~a~~~l~~~f~~~~ 176 (340)
+.++++|||.|+.+| .++..+.+.+.. .+.|-..=||-..||||++|-+.. ..+...|.+
T Consensus 10 ~Gil~idKP~g~TS~--------~vv~~vrr~l~~--------~KvGH~GTLDP~AtGvL~i~~g~a--TK~~~~~~~-- 69 (300)
T PRK04642 10 HGILLLDKPAGLSSN--------NALQAARRLLRA--------EKGGHTGSLDPLATGLLPLCFGEA--TKIAGLLLG-- 69 (300)
T ss_pred CEEEEEECCCCCCHH--------HHHHHHHHHHCC--------CCCCCCCCCCCCCCCEEEEEECHH--HHHCHHHCC--
T ss_conf 779997079989989--------999999998689--------845768577985604378997876--513666561--
Q ss_pred CCCCEEEEEEEEEE
Q ss_conf 13221334454320
Q gi|254780610|r 177 KSTRLKRAYYAMVW 190 (340)
Q Consensus 177 ~~~~v~K~Y~Aiv~ 190 (340)
-.|+|.|.+.
T Consensus 70 ----~~K~Y~~~~~ 79 (300)
T PRK04642 70 ----SAKAYDAEIV 79 (300)
T ss_pred ----CCCEEEEEEE
T ss_conf ----3664379999
No 53
>PRK02193 truB tRNA pseudouridine synthase B; Provisional
Probab=96.81 E-value=0.002 Score=40.17 Aligned_cols=68 Identities=22% Similarity=0.341 Sum_probs=46.4
Q ss_pred EEEEECCCHHHCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHHHHHHHHCCC
Q ss_conf 78996240111045678754210022222210244334444364324444332324057212035788889999972113
Q gi|254780610|r 99 IIVINKPAGLVVHPAPGNWTGTLVNALLYHCHNNLSSINGVKRPGIVHRLDKDTTGVMVVAKNDLAHQKLSEQFVDHGKS 178 (340)
Q Consensus 99 llvinKPaGl~vhp~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~lVHRLDr~TSGlll~Ak~~~a~~~l~~~f~~~~~~ 178 (340)
|+++|||.|+.+| .++..+...+. ..+.|-..-||-..||+|++|-+..+ .+...|..
T Consensus 2 illi~KP~G~TS~--------~vv~~vkk~~~--------~kKvGH~GTLDP~AtGvL~v~~G~aT--K~~~~~~~---- 59 (279)
T PRK02193 2 ITLLYKPKKISSF--------KFIRQFSKTNL--------IKKIGHAGTLDPLATGLLLVATDEDT--KLLDYLDQ---- 59 (279)
T ss_pred EEEEECCCCCCHH--------HHHHHHHHHHC--------CCCCCCCCCCCCCCEEEEEEEECHHH--HHCHHHCC----
T ss_conf 8999899989989--------99999999839--------99536174679867447999978665--12645545----
Q ss_pred CCEEEEEEEEEE
Q ss_conf 221334454320
Q gi|254780610|r 179 TRLKRAYYAMVW 190 (340)
Q Consensus 179 ~~v~K~Y~Aiv~ 190 (340)
-.|+|.|.+.
T Consensus 60 --~~K~Y~~~~~ 69 (279)
T PRK02193 60 --KTKTYLAKIQ 69 (279)
T ss_pred --CCCEEEEEEE
T ss_conf --7826999999
No 54
>PRK01550 truB tRNA pseudouridine synthase B; Provisional
Probab=96.77 E-value=0.0018 Score=40.52 Aligned_cols=70 Identities=26% Similarity=0.399 Sum_probs=48.7
Q ss_pred CEEEEEECCCHHHCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHHHHHHHHC
Q ss_conf 02789962401110456787542100222222102443344443643244443323240572120357888899999721
Q gi|254780610|r 97 DDIIVINKPAGLVVHPAPGNWTGTLVNALLYHCHNNLSSINGVKRPGIVHRLDKDTTGVMVVAKNDLAHQKLSEQFVDHG 176 (340)
Q Consensus 97 ~~llvinKPaGl~vhp~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~lVHRLDr~TSGlll~Ak~~~a~~~l~~~f~~~~ 176 (340)
+.++++|||.|+.+| .++..+...+.. .+.|-..=||-..||||++|-+.. ..+...+.+
T Consensus 2 ~Gil~idKP~G~TS~--------~vv~~vr~~l~~--------kKvGH~GTLDP~AtGvL~i~iG~a--TKl~~~l~~-- 61 (307)
T PRK01550 2 EGVVLLHKPKGMTSH--------DCVFKLRKILRE--------KRIGHTGTLDPDVTGVLPICVGRA--TKIAQFLTS-- 61 (307)
T ss_pred CEEEEECCCCCCCHH--------HHHHHHHHHHCC--------CCCCCCCCCCCCCEEEEEEEECCC--HHHCHHHCC--
T ss_conf 779997069989989--------999999998489--------834647467986621699997800--001344466--
Q ss_pred CCCCEEEEEEEEEE
Q ss_conf 13221334454320
Q gi|254780610|r 177 KSTRLKRAYYAMVW 190 (340)
Q Consensus 177 ~~~~v~K~Y~Aiv~ 190 (340)
-.|+|.|.+.
T Consensus 62 ----~~K~Y~a~~~ 71 (307)
T PRK01550 62 ----ETKTYEGEVT 71 (307)
T ss_pred ----CCCEEEEEEE
T ss_conf ----7834899999
No 55
>PRK03287 truB tRNA pseudouridine synthase B; Provisional
Probab=96.74 E-value=0.0022 Score=39.92 Aligned_cols=70 Identities=27% Similarity=0.436 Sum_probs=48.3
Q ss_pred CEEEEEECCCHHHCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHHHHHHHHC
Q ss_conf 02789962401110456787542100222222102443344443643244443323240572120357888899999721
Q gi|254780610|r 97 DDIIVINKPAGLVVHPAPGNWTGTLVNALLYHCHNNLSSINGVKRPGIVHRLDKDTTGVMVVAKNDLAHQKLSEQFVDHG 176 (340)
Q Consensus 97 ~~llvinKPaGl~vhp~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~lVHRLDr~TSGlll~Ak~~~a~~~l~~~f~~~~ 176 (340)
..+++||||.|+.+| .++..+...+.. .+.|-..=||-..||||+++-+.. ..+...|.+
T Consensus 9 sGil~idKP~G~TS~--------~vv~~vk~~~~~--------kKvGH~GTLDP~AtGvL~v~~G~a--TKl~~~~~~-- 68 (298)
T PRK03287 9 SGLVVVDKPAGMTSH--------DVVARCRRIFGT--------RKVGHAGTLDPMATGVLVLGVERA--TKLLGHLVA-- 68 (298)
T ss_pred CEEEEEECCCCCCHH--------HHHHHHHHHHCC--------CCCCCCCCCCCCCCCEEEEEECHH--HCCCHHHCC--
T ss_conf 789999479999989--------999999998489--------833668577974604389997877--621874655--
Q ss_pred CCCCEEEEEEEEEE
Q ss_conf 13221334454320
Q gi|254780610|r 177 KSTRLKRAYYAMVW 190 (340)
Q Consensus 177 ~~~~v~K~Y~Aiv~ 190 (340)
-.|+|.|.+.
T Consensus 69 ----~~K~Y~a~~~ 78 (298)
T PRK03287 69 ----TDKSYTATIR 78 (298)
T ss_pred ----CCCEEEEEEE
T ss_conf ----7817999999
No 56
>PRK04270 H/ACA RNA-protein complex component Cbf5p; Reviewed
Probab=96.67 E-value=0.0025 Score=39.57 Aligned_cols=73 Identities=21% Similarity=0.331 Sum_probs=50.4
Q ss_pred CCCCEEEEEECCCHHHCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHHHHHH
Q ss_conf 14402789962401110456787542100222222102443344443643244443323240572120357888899999
Q gi|254780610|r 94 YEDDDIIVINKPAGLVVHPAPGNWTGTLVNALLYHCHNNLSSINGVKRPGIVHRLDKDTTGVMVVAKNDLAHQKLSEQFV 173 (340)
Q Consensus 94 yED~~llvinKPaGl~vhp~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~lVHRLDr~TSGlll~Ak~~~a~~~l~~~f~ 173 (340)
|-+..+|.+|||.|+.+| .++..+...+.. .+.|-..-||-..||||+++-... ..+...|.
T Consensus 19 ~~~~Gil~idKP~G~TS~--------~vv~~vrk~l~~--------kKvGH~GTLDP~AtGvL~i~~G~a--TK~~~~l~ 80 (300)
T PRK04270 19 YINYGVVNLDKPPGPTSH--------EVAAWVRDILGV--------EKAGHGGTLDPKVTGVLPVALGKA--TKVVQALL 80 (300)
T ss_pred HHHCCEEEEECCCCCCHH--------HHHHHHHHHHCC--------CCCCCCCCCCCCCCCEEEEEECHH--HHHHHHHC
T ss_conf 972999999689899989--------999999998588--------846878678974623378886798--88869867
Q ss_pred HHCCCCCEEEEEEEEEE
Q ss_conf 72113221334454320
Q gi|254780610|r 174 DHGKSTRLKRAYYAMVW 190 (340)
Q Consensus 174 ~~~~~~~v~K~Y~Aiv~ 190 (340)
+ -.|+|.|.+.
T Consensus 81 ~------~~K~Y~~~~~ 91 (300)
T PRK04270 81 E------SPKEYVCVMH 91 (300)
T ss_pred C------CCCEEEEEEE
T ss_conf 5------8945877101
No 57
>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=96.63 E-value=0.0025 Score=39.57 Aligned_cols=77 Identities=25% Similarity=0.275 Sum_probs=46.8
Q ss_pred EEEEEECCCHHHCCCCCCCCCCCCHHHHHHHHCCCCC---------------------CCCCCCCCCCCCCCCCCCCCEE
Q ss_conf 2789962401110456787542100222222102443---------------------3444436432444433232405
Q gi|254780610|r 98 DIIVINKPAGLVVHPAPGNWTGTLVNALLYHCHNNLS---------------------SINGVKRPGIVHRLDKDTTGVM 156 (340)
Q Consensus 98 ~llvinKPaGl~vhp~~~~~~~tl~~~l~~~~~~~~~---------------------~~~~~~~~~lVHRLDr~TSGll 156 (340)
.+++||||+|+.+|- +++.+.+.+..... ......+.|-..-||=..||||
T Consensus 1 Gi~~vdKP~GiTS~~--------vv~~lk~~f~~s~~f~~~~~~~~~~~~~~~~r~k~~~~~~~KvGH~GTLDP~AtGvL 72 (312)
T cd02867 1 GVFAINKPSGITSAQ--------VLNDLKPLFLNSALFKDKIQRAVAKRGKKARRRKGRKRSKLKIGHGGTLDPLATGVL 72 (312)
T ss_pred CEEEEECCCCCCHHH--------HHHHHHHHHCCCCCCCCHHHHHHHHCCCCCCHHCCCCCCCCEEEECCCCCCCCCCEE
T ss_conf 968874799999899--------999999983411102310222222101100000012457744402656787460338
Q ss_pred EEECCHHHHHHHHHHHHHHCCCCCEEEEEEEEEE
Q ss_conf 7212035788889999972113221334454320
Q gi|254780610|r 157 VVAKNDLAHQKLSEQFVDHGKSTRLKRAYYAMVW 190 (340)
Q Consensus 157 l~Ak~~~a~~~l~~~f~~~~~~~~v~K~Y~Aiv~ 190 (340)
+++-... ..+...|. .-.|+|.|.+.
T Consensus 73 ~i~~G~a--TK~~~~~~------~~~K~Y~a~~~ 98 (312)
T cd02867 73 VVGVGAG--TKQLQDYL------SCSKTYEATGL 98 (312)
T ss_pred EEEECHH--HEECHHHC------CCCCEEEEEEE
T ss_conf 8998754--40458666------79917999999
No 58
>cd02573 PseudoU_synth_EcTruB PseudoU_synth_EcTruB: Pseudouridine synthase, Escherichia coli TruB like. This group consists of bacterial pseudouridine synthases similar to E. coli TruB and Mycobacterium tuberculosis TruB. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). E. coli TruB and M. tuberculosis TruB make psi55 in the T loop of tRNAs. Psi55 is nearly universally conserved. E. coli TruB is not inhibited by RNA containing 5-fluorouridine.
Probab=96.61 E-value=0.0038 Score=38.54 Aligned_cols=69 Identities=32% Similarity=0.470 Sum_probs=47.8
Q ss_pred EEEEEECCCHHHCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHHHHHHHHCC
Q ss_conf 27899624011104567875421002222221024433444436432444433232405721203578888999997211
Q gi|254780610|r 98 DIIVINKPAGLVVHPAPGNWTGTLVNALLYHCHNNLSSINGVKRPGIVHRLDKDTTGVMVVAKNDLAHQKLSEQFVDHGK 177 (340)
Q Consensus 98 ~llvinKPaGl~vhp~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~lVHRLDr~TSGlll~Ak~~~a~~~l~~~f~~~~~ 177 (340)
.++++|||.|+.+| .+++.+...+.. .+.|-..=||-..||||++|-+.. ..+...|.
T Consensus 1 G~l~i~Kp~g~tS~--------~~v~~~k~~~~~--------kKvGH~GTLDP~AtGvL~i~~g~a--TKl~~~~~---- 58 (277)
T cd02573 1 GILLLDKPAGLTSH--------DVVQKVRRLLGT--------KKVGHTGTLDPLATGVLPIALGEA--TKLSQYLL---- 58 (277)
T ss_pred CEEEEECCCCCCHH--------HHHHHHHHHHCC--------CCCCCCCCCCCCCCCEEEEEECHH--HHHHHHHC----
T ss_conf 98999679999989--------999999998588--------855637577976603378998888--70527867----
Q ss_pred CCCEEEEEEEEEE
Q ss_conf 3221334454320
Q gi|254780610|r 178 STRLKRAYYAMVW 190 (340)
Q Consensus 178 ~~~v~K~Y~Aiv~ 190 (340)
.-.|+|.|.+.
T Consensus 59 --~~~K~Y~~~~~ 69 (277)
T cd02573 59 --DADKTYRATVR 69 (277)
T ss_pred --CCCCEEEEEEE
T ss_conf --89917999999
No 59
>COG0130 TruB Pseudouridine synthase [Translation, ribosomal structure and biogenesis]
Probab=96.57 E-value=0.0043 Score=38.23 Aligned_cols=69 Identities=29% Similarity=0.377 Sum_probs=47.6
Q ss_pred EEEEEECCCHHHCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHHHHHHHHCC
Q ss_conf 27899624011104567875421002222221024433444436432444433232405721203578888999997211
Q gi|254780610|r 98 DIIVINKPAGLVVHPAPGNWTGTLVNALLYHCHNNLSSINGVKRPGIVHRLDKDTTGVMVVAKNDLAHQKLSEQFVDHGK 177 (340)
Q Consensus 98 ~llvinKPaGl~vhp~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~lVHRLDr~TSGlll~Ak~~~a~~~l~~~f~~~~~ 177 (340)
.++++|||.|+.+|. .+..+...++ ..+.|-..-||-..||+|.+|-. +| ..+...+.+
T Consensus 16 Gil~ldKP~G~tS~~--------~v~~vkkil~--------~~K~GH~GTLDP~atGvLpi~ig-~a-TKl~~~l~~--- 74 (271)
T COG0130 16 GVINLDKPPGPTSHE--------VVAWVKRILG--------VEKAGHGGTLDPLATGVLPICLG-EA-TKLVQYLLD--- 74 (271)
T ss_pred CEEEEECCCCCCHHH--------HHHHHHHHHC--------CCCCCCCCCCCCCCCCEEEEEEC-HH-HHHHHHHHH---
T ss_conf 469840799997799--------9999999858--------64056463448743441888834-14-748988720---
Q ss_pred CCCEEEEEEEEEE
Q ss_conf 3221334454320
Q gi|254780610|r 178 STRLKRAYYAMVW 190 (340)
Q Consensus 178 ~~~v~K~Y~Aiv~ 190 (340)
-.|.|.|.+.
T Consensus 75 ---~~K~Y~a~~~ 84 (271)
T COG0130 75 ---ADKEYVATVR 84 (271)
T ss_pred ---CCCEEEEEEE
T ss_conf ---8947999999
No 60
>PRK05033 truB tRNA pseudouridine synthase B; Provisional
Probab=96.52 E-value=0.0037 Score=38.63 Aligned_cols=70 Identities=17% Similarity=0.372 Sum_probs=47.8
Q ss_pred CEEEEEECCCHHHCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHHHHHHHHC
Q ss_conf 02789962401110456787542100222222102443344443643244443323240572120357888899999721
Q gi|254780610|r 97 DDIIVINKPAGLVVHPAPGNWTGTLVNALLYHCHNNLSSINGVKRPGIVHRLDKDTTGVMVVAKNDLAHQKLSEQFVDHG 176 (340)
Q Consensus 97 ~~llvinKPaGl~vhp~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~lVHRLDr~TSGlll~Ak~~~a~~~l~~~f~~~~ 176 (340)
+.+|++|||.|+.+| -++..+...+.. .+.|-..=||-..||+|++|-+.. ..+...|.+
T Consensus 12 ~Gil~idKP~g~TS~--------~~v~~~kk~~~~--------kKvGH~GTLDP~AtGvL~i~~G~a--TK~~~~~~~-- 71 (314)
T PRK05033 12 NGVLLLDKPQGMSSN--------DALQKVKRIYNA--------NKAGHTGALDPLATGMLPICLGEA--TKFSQFLLD-- 71 (314)
T ss_pred CEEEEEECCCCCCHH--------HHHHHHHHHHCC--------CCCCCCCCCCCCCCCEEEEEECHH--HHHHHHHCC--
T ss_conf 679998159999989--------999999998588--------856878577975602189998888--704088668--
Q ss_pred CCCCEEEEEEEEEE
Q ss_conf 13221334454320
Q gi|254780610|r 177 KSTRLKRAYYAMVW 190 (340)
Q Consensus 177 ~~~~v~K~Y~Aiv~ 190 (340)
-.|+|.|.+.
T Consensus 72 ----~~K~Y~~~~~ 81 (314)
T PRK05033 72 ----SDKRYRVIAK 81 (314)
T ss_pred ----CCCEEEEEEE
T ss_conf ----9917999999
No 61
>PRK02755 truB tRNA pseudouridine synthase B; Provisional
Probab=96.02 E-value=0.0086 Score=36.41 Aligned_cols=69 Identities=32% Similarity=0.374 Sum_probs=46.6
Q ss_pred CEEEEEECCCHHHCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHHHHHHHHC
Q ss_conf 02789962401110456787542100222222102443344443643244443323240572120357888899999721
Q gi|254780610|r 97 DDIIVINKPAGLVVHPAPGNWTGTLVNALLYHCHNNLSSINGVKRPGIVHRLDKDTTGVMVVAKNDLAHQKLSEQFVDHG 176 (340)
Q Consensus 97 ~~llvinKPaGl~vhp~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~lVHRLDr~TSGlll~Ak~~~a~~~l~~~f~~~~ 176 (340)
+.++.+|||.|+.+| -++..+...+.. .+.|-..=||-..||+|++|-+..+ .+.+.+
T Consensus 2 ~G~l~i~Kp~G~tS~--------~vv~~~k~~~~~--------kKvGH~GTLDP~AtGvL~i~~G~aT--k~~~~l---- 59 (291)
T PRK02755 2 QGFLNLNKPAGWTSH--------DCVAKLRRLLRL--------KRVGHGGTLDPAATGVLPIAVGKAT--RLLPYL---- 59 (291)
T ss_pred CEEEEEECCCCCCHH--------HHHHHHHHHHCC--------CCCCCCCCCCCCCCCEEEEEECHHH--EECCCC----
T ss_conf 769998359989989--------999999998588--------8367785779755052899976576--643004----
Q ss_pred CCCCEEEEEEEEEE
Q ss_conf 13221334454320
Q gi|254780610|r 177 KSTRLKRAYYAMVW 190 (340)
Q Consensus 177 ~~~~v~K~Y~Aiv~ 190 (340)
. . .|+|.|.+.
T Consensus 60 ~--~-~K~Y~~~~~ 70 (291)
T PRK02755 60 P--S-GKAYKATVR 70 (291)
T ss_pred C--C-CCEEEEEEE
T ss_conf 8--9-958999999
No 62
>TIGR02988 YaaA_near_RecF S4 domain protein YaaA; InterPro: IPR014330 This small protein has a single S4 domain (IPR002942 from INTERPRO); it is also found in bacterial S4 ribosomal proteins, some pseudouridine synthases and tyrosyl-tRNA synthetases. The S4 domain may bind RNA. Members of this protein are found almost exclusively in the Firmicutes, and almost invariably just a few nucleotides upstream of the gene for the DNA replication and repair protein RecF. The few members that are not near recF are found instead near dnaA and/or dnaN, the usual neighbours of recF, near the origin of replication. The conserved location suggests a possible role in replication in the Firmicutes lineage..
Probab=95.67 E-value=0.023 Score=33.84 Aligned_cols=52 Identities=19% Similarity=0.203 Sum_probs=40.6
Q ss_pred CCCHHHHHHHHCCCCCCHHHHHHHHHCCCEEECCEEECCCCCEECCCCEEEEE
Q ss_conf 87578999987176889899999998599049989932867580489889997
Q gi|254780610|r 22 EGRIDRWLATSLKEQFSRSYVKILILNGFISINGMVSKNPNRKVVPGDSFLIT 74 (340)
Q Consensus 22 g~RLD~~L~~~l~~~~sR~~i~kli~~G~V~vnG~~~~~~~~~l~~gd~I~i~ 74 (340)
-.+|+.||... .=--|=.+|+..|..+.|.|||++..+=+++|+.||.|.+.
T Consensus 8 yITLgQlLK~~-~~i~sGG~AK~fL~e~~V~vNGe~e~RRGkKL~~gD~i~i~ 59 (60)
T TIGR02988 8 YITLGQLLKEL-GIIDSGGQAKWFLQENEVLVNGELENRRGKKLYPGDVIEIP 59 (60)
T ss_pred EECHHHHHHHH-HHHCCHHHHHHHHHCCCEEECCEEECCCCCEECCCCEEEEC
T ss_conf 16276786688-56228257889870695554784404588700489668826
No 63
>pfam06353 DUF1062 Protein of unknown function (DUF1062). This family consists of several hypothetical bacterial proteins of unknown function.
Probab=95.53 E-value=0.037 Score=32.67 Aligned_cols=49 Identities=33% Similarity=0.325 Sum_probs=41.6
Q ss_pred CCHHCCCEEEEEECHHHCCCCHHHHHHHHCCCCCCHHHHHHHHHCCCEEEC
Q ss_conf 511016249999571136875789999871768898999999985990499
Q gi|254780610|r 4 TLDNCSSIKISLLSDSTAEGRIDRWLATSLKEQFSRSYVKILILNGFISIN 54 (340)
Q Consensus 4 ~~~~~~~~~~~~V~~~~~g~RLD~~L~~~l~~~~sR~~i~kli~~G~V~vn 54 (340)
....+..+++.+.-+.....|+|+.|+..| ++||+.+++++.+|.|+-+
T Consensus 84 ~~~~~~~i~I~i~~~~~~~~Rl~~Lla~~L--~lSrs~l~~l~~~G~i~~~ 132 (142)
T pfam06353 84 GIASHAAIEIQLRLEFPFSLRLDRLLAEEL--GLSRSRLQRLIDQGQIRGV 132 (142)
T ss_pred CCCCCCCEEEEEECCCCCCCCHHHHHHHHH--CCCHHHHHHHHHCCCEECC
T ss_conf 777777669999627877642999999881--8689999999988987705
No 64
>PRK04051 rps4p 30S ribosomal protein S4; Validated
Probab=95.34 E-value=0.039 Score=32.49 Aligned_cols=56 Identities=20% Similarity=0.233 Sum_probs=42.9
Q ss_pred HHHCCCCHHHHHHHHCCCCCCHHHHHHHHHCCCEEECCEEECCCCCEECCC--CEEEEE
Q ss_conf 113687578999987176889899999998599049989932867580489--889997
Q gi|254780610|r 18 DSTAEGRIDRWLATSLKEQFSRSYVKILILNGFISINGMVSKNPNRKVVPG--DSFLIT 74 (340)
Q Consensus 18 ~~~~g~RLD~~L~~~l~~~~sR~~i~kli~~G~V~vnG~~~~~~~~~l~~g--d~I~i~ 74 (340)
++-...||+..+.+. .-.-|-.+++++|..|.|+|||++++.|++.|..+ |.|.+.
T Consensus 98 ~~~l~RRL~~vv~r~-~~a~si~~Ar~lI~hgHi~V~~~~v~~Ps~~V~r~~Ed~I~~~ 155 (177)
T PRK04051 98 EDILERRLQTIVYRK-GLARTPKQARQLIVHGHIAVNGRRVTSPGYLVSREEEDKIDYY 155 (177)
T ss_pred HHHHHHHHHHHHHHC-CCCCCHHHHHHHHHCCEEEECCEEECCCCEEEEECCCCCEEEC
T ss_conf 899996888999880-5668899999997478289999995368658865566854631
No 65
>TIGR00431 TruB tRNA pseudouridine synthase B; InterPro: IPR014780 TruB, the tRNA pseudouridine 55 synthase, converts uracil to pseudouridine in the T loop 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 functions.; GO: 0003723 RNA binding, 0016439 tRNA-pseudouridine synthase activity, 0031119 tRNA pseudouridine synthesis.
Probab=95.25 E-value=0.0079 Score=36.62 Aligned_cols=71 Identities=25% Similarity=0.364 Sum_probs=49.0
Q ss_pred CEEEEEECCCHHHCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHHHHHHHHC
Q ss_conf 02789962401110456787542100222222102443344443643244443323240572120357888899999721
Q gi|254780610|r 97 DDIIVINKPAGLVVHPAPGNWTGTLVNALLYHCHNNLSSINGVKRPGIVHRLDKDTTGVMVVAKNDLAHQKLSEQFVDHG 176 (340)
Q Consensus 97 ~~llvinKPaGl~vhp~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~lVHRLDr~TSGlll~Ak~~~a~~~l~~~f~~~~ 176 (340)
+.+|.+|||.||.+|. .+.-+.+.+.. .+.|-..=||+..||+|+++--.++ .+|+..|-+
T Consensus 2 ~GvLll~Kp~G~TSfd--------~~~~v~rLl~~--------kkvGHtGTLDp~A~G~L~~~vGr~a-Tkl~~yl~~-- 62 (236)
T TIGR00431 2 NGVLLLDKPQGMTSFD--------ALAKVRRLLGV--------KKVGHTGTLDPFATGVLPILVGRKA-TKLSPYLTD-- 62 (236)
T ss_pred CCCCCCCCCCCCCHHH--------HHHHHHHHHCC--------CCCCCCCCCCHHHHHHHHHHHHHHH-HHHHHHHCC--
T ss_conf 7204155788878899--------99999998707--------8522066653024103542230013-434333126--
Q ss_pred CCCCEEEEEEEEEE
Q ss_conf 13221334454320
Q gi|254780610|r 177 KSTRLKRAYYAMVW 190 (340)
Q Consensus 177 ~~~~v~K~Y~Aiv~ 190 (340)
-.|.|.|...
T Consensus 63 ----~dK~Y~A~~~ 72 (236)
T TIGR00431 63 ----LDKEYEAEIR 72 (236)
T ss_pred ----CCCEEEEEEE
T ss_conf ----4761799998
No 66
>PRK04313 30S ribosomal protein S4e; Validated
Probab=95.21 E-value=0.053 Score=31.70 Aligned_cols=55 Identities=18% Similarity=0.062 Sum_probs=46.7
Q ss_pred HCCCCHHHHHHHHCCCCCCHHHHHHHHHCCCEEECCEEECCCCCEECCCCEEEEE
Q ss_conf 3687578999987176889899999998599049989932867580489889997
Q gi|254780610|r 20 TAEGRIDRWLATSLKEQFSRSYVKILILNGFISINGMVSKNPNRKVVPGDSFLIT 74 (340)
Q Consensus 20 ~~g~RLD~~L~~~l~~~~sR~~i~kli~~G~V~vnG~~~~~~~~~l~~gd~I~i~ 74 (340)
+.+.-|--+|...|.-..+.+.+++.+.+|.|.|||++.++..+.+-.-|.|++.
T Consensus 35 ~~siPL~v~LRd~L~~a~t~rEak~Il~~~~V~VDG~vr~d~~~pvGlmDVisi~ 89 (237)
T PRK04313 35 ESSLPLLIVLRDVLGYADTAREARKIISEGKVLVDGRVRKDYKFPVGLMDVISIP 89 (237)
T ss_pred CCCCCCHHHHHHHHHHHCCHHHHHHHHHCCEEEECCEEEECCCCCCCEEEEEEEC
T ss_conf 5542338999877725044889999864885998999960378875416799864
No 67
>TIGR01018 rpsD_arch ribosomal protein S4; InterPro: IPR005710 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites , . About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many of ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome , . The S4 domain is a small domain consisting of 60-65 amino acid residues that probably mediates binding to RNA. This model finds eukaryotic ribosomal protein S9 as well as eukaryotic and archaeal ribosomal protein S4.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0015935 small ribosomal subunit.
Probab=95.05 E-value=0.011 Score=35.82 Aligned_cols=53 Identities=21% Similarity=0.346 Sum_probs=38.2
Q ss_pred HHHCCCCHHHHHHHHCCCCCCHH--HHHHHHHCCCEEECCEEECCCCCEECCCCEEEE
Q ss_conf 11368757899998717688989--999999859904998993286758048988999
Q gi|254780610|r 18 DSTAEGRIDRWLATSLKEQFSRS--YVKILILNGFISINGMVSKNPNRKVVPGDSFLI 73 (340)
Q Consensus 18 ~~~~g~RLD~~L~~~l~~~~sR~--~i~kli~~G~V~vnG~~~~~~~~~l~~gd~I~i 73 (340)
||=-..||.+..-++ ++-|+ +++++|..|+|.|||++++.|+|.|..+.+=.|
T Consensus 107 ED~LERRLQT~Vyk~---GLArTi~~ARqLi~hGHI~v~Gr~v~~Psy~V~~e~e~kI 161 (170)
T TIGR01018 107 EDVLERRLQTLVYKK---GLARTIKQARQLIVHGHIAVDGRRVTSPSYIVRREEEDKI 161 (170)
T ss_pred HHHHHHHHHHHHHHH---HHCCCHHHCCEEEEECEEEECCEEEECCCEEEECCCCCCC
T ss_conf 145534567899986---3022632343023203388768477358616746554421
No 68
>PTZ00223 40S ribosomal protein S4; Provisional
Probab=95.02 E-value=0.069 Score=31.04 Aligned_cols=53 Identities=13% Similarity=0.114 Sum_probs=46.0
Q ss_pred CCCHHHHHHHHCCCCCCHHHHHHHHHCCCEEECCEEECCCCCEECCCCEEEEE
Q ss_conf 87578999987176889899999998599049989932867580489889997
Q gi|254780610|r 22 EGRIDRWLATSLKEQFSRSYVKILILNGFISINGMVSKNPNRKVVPGDSFLIT 74 (340)
Q Consensus 22 g~RLD~~L~~~l~~~~sR~~i~kli~~G~V~vnG~~~~~~~~~l~~gd~I~i~ 74 (340)
..-|--||...|.-..+...+++.+.+|.|.|||++.++..+.+-.-|.|++.
T Consensus 38 slPL~iiLRd~LkyA~t~rEak~Il~~~~V~VDGkvr~D~~~PvG~MDVIsI~ 90 (273)
T PTZ00223 38 CLPLLIIIRNRLKYALNAREAQMILRQGLVCVDGKPRKDGKYPAGFMDVVEIP 90 (273)
T ss_pred CCCCHHHHHHHHCCCCCHHHHHHHHHCCCEEECCEEECCCCCCCCEEEEEEEC
T ss_conf 44425787656452165799999987793797799965589988578999985
No 69
>PTZ00118 40S ribosomal protein S4; Provisional
Probab=94.96 E-value=0.068 Score=31.05 Aligned_cols=53 Identities=19% Similarity=0.182 Sum_probs=46.0
Q ss_pred CCCHHHHHHHHCCCCCCHHHHHHHHHCCCEEECCEEECCCCCEECCCCEEEEE
Q ss_conf 87578999987176889899999998599049989932867580489889997
Q gi|254780610|r 22 EGRIDRWLATSLKEQFSRSYVKILILNGFISINGMVSKNPNRKVVPGDSFLIT 74 (340)
Q Consensus 22 g~RLD~~L~~~l~~~~sR~~i~kli~~G~V~vnG~~~~~~~~~l~~gd~I~i~ 74 (340)
..-|--||...|.-..+.+.+++.+.+|.|.|||++.++..+.+-.-|.|++.
T Consensus 41 slPL~iiLRd~LkyA~t~rEak~Il~~~~V~VDGkvr~D~~~PvG~MDVIsI~ 93 (262)
T PTZ00118 41 CLPLVILLRNRLKYALTYDEVKLIVIQKIVKVDGKVRTDCTYPVGFMDVVSLT 93 (262)
T ss_pred CCCCHHHHHHHHCCCCCHHHHHHHHHCCEEEECCEEECCCCCCCCEEEEEEEC
T ss_conf 55433564346452265899999986790888999953489987467899985
No 70
>COG2501 S4-like RNA binding protein [Replication, recombination, and repair]
Probab=94.86 E-value=0.12 Score=29.49 Aligned_cols=52 Identities=23% Similarity=0.223 Sum_probs=41.3
Q ss_pred CCCHHHHHHHHCCCCCCHHHHHHHHHCCCEEECCEEECCCCCEECCCCEEEEE
Q ss_conf 87578999987176889899999998599049989932867580489889997
Q gi|254780610|r 22 EGRIDRWLATSLKEQFSRSYVKILILNGFISINGMVSKNPNRKVVPGDSFLIT 74 (340)
Q Consensus 22 g~RLD~~L~~~l~~~~sR~~i~kli~~G~V~vnG~~~~~~~~~l~~gd~I~i~ 74 (340)
-..|+.||.-. .-.=|=.+++.+|..|.|.|||+..+.-..+++.||.|.+.
T Consensus 11 ~I~L~qlLK~~-g~i~sGG~AK~~i~eg~V~vNGe~EtRRgkKlr~gd~V~i~ 62 (73)
T COG2501 11 FITLGQLLKLA-GLIESGGQAKAFIAEGEVKVNGEVETRRGKKLRDGDVVEIP 62 (73)
T ss_pred EEEHHHHHHHH-CCCCCCHHHHHHHHCCEEEECCEEECCCCCEEECCCEEEEC
T ss_conf 18799999874-95057478889987791898886630167760169899989
No 71
>PRK11507 hypothetical protein; Provisional
Probab=94.60 E-value=0.072 Score=30.92 Aligned_cols=63 Identities=19% Similarity=0.180 Sum_probs=44.2
Q ss_pred EEEEEECHHHCCCCHHHHHHHHCCCCCCHHHHHHHHHCCCEEECCEEECCCCCEECCCCEEEEEE
Q ss_conf 49999571136875789999871768898999999985990499899328675804898899970
Q gi|254780610|r 11 IKISLLSDSTAEGRIDRWLATSLKEQFSRSYVKILILNGFISINGMVSKNPNRKVVPGDSFLITV 75 (340)
Q Consensus 11 ~~~~~V~~~~~g~RLD~~L~~~l~~~~sR~~i~kli~~G~V~vnG~~~~~~~~~l~~gd~I~i~~ 75 (340)
|+++-.. ...-..|+++|.-.=. .-|=..++.+|..|.|+|||++.++-..++..||.|.+.-
T Consensus 1 M~~f~L~-~~~yIeL~~lLK~~gl-v~sGg~AK~~Ia~G~V~VnGevEtRKr~Ki~~GdvV~f~g 63 (70)
T PRK11507 1 MATFSLG-KHPHVELCDLLKLEGW-SESGAQAKIAIAEGQVKVDGAVETRKRCKIVAGQTVSFAG 63 (70)
T ss_pred CCEEECC-CCCCEEHHHHHHHCCC-CCCCHHHHHHEECCEEEECCEEEEEEEEEEECCCEEEECC
T ss_conf 9428638-9871008888847172-0465877865418768999999633102510899999999
No 72
>PTZ00155 40S ribosomal protein S9; Provisional
Probab=93.60 E-value=0.1 Score=30.07 Aligned_cols=56 Identities=16% Similarity=0.077 Sum_probs=39.5
Q ss_pred HHHCCCCHHHHHHHHCCCCCCHHHHHHHHHCCCEEECCEEECCCCCEECCCCEEEEE
Q ss_conf 113687578999987176889899999998599049989932867580489889997
Q gi|254780610|r 18 DSTAEGRIDRWLATSLKEQFSRSYVKILILNGFISINGMVSKNPNRKVVPGDSFLIT 74 (340)
Q Consensus 18 ~~~~g~RLD~~L~~~l~~~~sR~~i~kli~~G~V~vnG~~~~~~~~~l~~gd~I~i~ 74 (340)
++-...||..++.+. .-.-|-.+++.+|..|.|.|+|++++.|++.|..+++=.+.
T Consensus 102 e~~l~RRLqt~v~~~-glA~si~~Ar~lI~hgHI~V~~~~V~~Ps~lV~r~~Ed~I~ 157 (188)
T PTZ00155 102 PDILERRLQTKVFKL-GLAKSVHHARVLIRQRHIRVGKQIVDIPSFLVRVDSEKHIA 157 (188)
T ss_pred HHHHHHHHHHHHHHH-CCCCCHHHHHHHEECCEEEECCEEECCCCEEEEECCCCCEE
T ss_conf 889987676899986-01158898888834462889998953774588605446445
No 73
>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=93.09 E-value=0.096 Score=30.17 Aligned_cols=20 Identities=35% Similarity=0.429 Sum_probs=16.9
Q ss_pred CCCCCCCCCCCCCCCEEEEE
Q ss_conf 36432444433232405721
Q gi|254780610|r 140 KRPGIVHRLDKDTTGVMVVA 159 (340)
Q Consensus 140 ~~~~lVHRLDr~TSGlll~A 159 (340)
.+.+.++|+||.++|+.+++
T Consensus 24 ~~v~~aG~kDk~a~t~Q~~s 43 (87)
T cd01291 24 KRVGYAGRKDKRAVTTQLVS 43 (87)
T ss_pred HHEEECCCCCCCEEEEEEEE
T ss_conf 77517446666554788764
No 74
>KOG2559 consensus
Probab=93.01 E-value=0.067 Score=31.11 Aligned_cols=23 Identities=26% Similarity=0.335 Sum_probs=19.3
Q ss_pred CCCCCCCCCCCCCEEEEECCHHH
Q ss_conf 43244443323240572120357
Q gi|254780610|r 142 PGIVHRLDKDTTGVMVVAKNDLA 164 (340)
Q Consensus 142 ~~lVHRLDr~TSGlll~Ak~~~a 164 (340)
.+++||||-.|||+++|+-+..+
T Consensus 91 V~v~h~l~~~~sgvl~~gVghgc 113 (318)
T KOG2559 91 VQVVHVLPLATSGVLLFGVGHGC 113 (318)
T ss_pred EEEEEEECCCCCCEEEEECCCCH
T ss_conf 13677504422542887317531
No 75
>COG1471 RPS4A Ribosomal protein S4E [Translation, ribosomal structure and biogenesis]
Probab=87.42 E-value=0.75 Score=24.86 Aligned_cols=58 Identities=16% Similarity=0.175 Sum_probs=38.3
Q ss_pred CHHHHHHHHHCCCEEECCEEECCCCCEECCCCEEEEEECCCHHCCHHHHHHHHHHCCCCCEEEEEECC
Q ss_conf 98999999985990499899328675804898899970560111102332222210144027899624
Q gi|254780610|r 38 SRSYVKILILNGFISINGMVSKNPNRKVVPGDSFLITVPAAQKLNIAQENIPLDILYEDDDIIVINKP 105 (340)
Q Consensus 38 sR~~i~kli~~G~V~vnG~~~~~~~~~l~~gd~I~i~~~~~~~~~~~~~~~~~~IlyED~~llvinKP 105 (340)
.-+.++++|..|.|.|||++.++....+-.=|.|++..-. -.++|||.....+++.+=
T Consensus 56 ~~REa~~Ii~~g~v~VDG~vRkd~kfPVGlmDVisip~tg----------E~yRvl~d~~grl~l~~i 113 (241)
T COG1471 56 NAREARKILSEGKVLVDGKVRKDYKFPVGLMDVISIPKTG----------EHYRVLPDEKGRLVLHPI 113 (241)
T ss_pred CHHHHHHHHHCCCEEECCEEECCCCCCCCEEEEEEECCCC----------CEEEEEECCCCCEEEEEC
T ss_conf 3488999876695798889801355784068999976889----------658988667850788754
No 76
>TIGR00425 CBF5 rRNA pseudouridine synthase, putative; InterPro: IPR004802 This family contains 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 the archaeal proteins in this family modify tRNA, rRNA, or both. .
Probab=86.00 E-value=1.3 Score=23.52 Aligned_cols=145 Identities=21% Similarity=0.281 Sum_probs=76.4
Q ss_pred CCCCEEEEEECCCHHHCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHHHHHH
Q ss_conf 14402789962401110456787542100222222102443344443643244443323240572120357888899999
Q gi|254780610|r 94 YEDDDIIVINKPAGLVVHPAPGNWTGTLVNALLYHCHNNLSSINGVKRPGIVHRLDKDTTGVMVVAKNDLAHQKLSEQFV 173 (340)
Q Consensus 94 yED~~llvinKPaGl~vhp~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~lVHRLDr~TSGlll~Ak~~~a~~~l~~~f~ 173 (340)
|=-..++.+|||+|=.+|. ++.++..-+.-+ +.|--.=||==.||||+++-.+.+ .+-+.++
T Consensus 31 yI~~Gvv~lDKP~gPsSHe--------V~~Wvr~iL~ve--------KtGH~GTLDPKVTGvLpv~ierAT--r~v~~~~ 92 (326)
T TIGR00425 31 YIRKGVVNLDKPSGPSSHE--------VVAWVRRILRVE--------KTGHGGTLDPKVTGVLPVCIERAT--RLVKSLQ 92 (326)
T ss_pred HHHCCEEEEECCCCCCCCE--------EHHHHHHHHCCC--------CCCCCCCCCCCEEEEEEEEEHHHH--HHHHHHH
T ss_conf 6206507876484188640--------102212101011--------246587578831246212100023--5644531
Q ss_pred HHCCCCCEEEEEEEEEE--CCCCCCCCCCCCCCCC-----CCCCCCCCCCCCCCCCCCCCCEECCCCCEEECCCCCCCCC
Q ss_conf 72113221334454320--2433233211001343-----4443322123444555553000012221011256677500
Q gi|254780610|r 174 DHGKSTRLKRAYYAMVW--GIPLPDSGIINAPLGR-----CKSNRLRRAVKGIDDKTADSAITHYQTIEIYNKNSNFAVS 246 (340)
Q Consensus 174 ~~~~~~~v~K~Y~Aiv~--G~~~~~~g~i~~~l~~-----~~~~~~~~~~~~~~~~~~k~a~T~~~~l~~~~~~~~~~~s 246 (340)
.-.|.|++++. +...++ -.|.--|.. .+..+.+-+| +..-.-.|-|+. +.+.......+-
T Consensus 93 ------~a~KEYVClmRLH~~~~~e-~~~~rvl~~f~G~ifQrPPLksAV-----Kr~LRvR~IYe~-~llE~Dg~d~Lv 159 (326)
T TIGR00425 93 ------EAPKEYVCLMRLHRDAKEE-KDIERVLKEFTGRIFQRPPLKSAV-----KRQLRVRTIYES-ELLEVDGKDRLV 159 (326)
T ss_pred ------CCCCCEEEEEEECHHHHHH-HHHHHHHHHCCCEEECCCCCHHHH-----CCCCCEEEEEEE-EEEEECCCCCEE
T ss_conf ------6997459977612012125-789999885183033388625652-----233650168998-877207996268
Q ss_pred EEEEEECHHHHHHHHHHHHHHCCEE
Q ss_conf 1234431158999999998709786
Q gi|254780610|r 247 LLKCHLETGRTHQIRVHMAHKGNPL 271 (340)
Q Consensus 247 lv~~~~~TGRtHQIRvhla~lG~PI 271 (340)
|.++.-+.|= =||--|.++|-=+
T Consensus 160 lFrv~CeaGT--YiRkLC~d~G~~L 182 (326)
T TIGR00425 160 LFRVSCEAGT--YIRKLCVDIGELL 182 (326)
T ss_pred EEEEEECCCC--CHHHHHHHHHHHH
T ss_conf 9999875786--1568788886761
No 77
>TIGR01687 moaD_arch MoaD family protein; InterPro: IPR010038 Members of this family appear to be archaeal and bacterial (proteobacteria and Thermus) versions of MoaD, subunit 1 of molybdopterin converting factor..
Probab=83.39 E-value=2.8 Score=21.41 Aligned_cols=66 Identities=18% Similarity=0.291 Sum_probs=40.7
Q ss_pred CCEEEEEECHHHCCCCHHHHHHHHCCCCCCHHHHHHHHHC-C-------CEEECCE-EECC---CCCEECCCCEEEEEEC
Q ss_conf 6249999571136875789999871768898999999985-9-------9049989-9328---6758048988999705
Q gi|254780610|r 9 SSIKISLLSDSTAEGRIDRWLATSLKEQFSRSYVKILILN-G-------FISINGM-VSKN---PNRKVVPGDSFLITVP 76 (340)
Q Consensus 9 ~~~~~~~V~~~~~g~RLD~~L~~~l~~~~sR~~i~kli~~-G-------~V~vnG~-~~~~---~~~~l~~gd~I~i~~~ 76 (340)
...+...| +-+.|.+++..| +.|...+++.. ++++.. | .|.|||+ -+.. -++.|+.||.|.+..|
T Consensus 13 ~Gk~~eei-E~~~g~tv~dll-~~l~~~Yp~~~-~e~~~et~~~~~~~v~ilvNGran~~~l~GL~~~LkdGD~vai~PP 89 (93)
T TIGR01687 13 TGKKSEEI-ELEDGKTVGDLL-EELSSRYPKEF-SELFKETGLGLVPNVIILVNGRANVDWLEGLETELKDGDVVAIFPP 89 (93)
T ss_pred CCCEEEEE-ECCCCCCHHHHH-HHHHHHCCHHH-HHHHCCCCCCCCCEEEEEECCCCCCCCCCCCCCCCCCCCEEEEECC
T ss_conf 08847898-779998079989-99886156556-6651477887646578985164143220365752327875675069
Q ss_pred C
Q ss_conf 6
Q gi|254780610|r 77 A 77 (340)
Q Consensus 77 ~ 77 (340)
.
T Consensus 90 V 90 (93)
T TIGR01687 90 V 90 (93)
T ss_pred C
T ss_conf 9
No 78
>pfam01509 TruB_N TruB family pseudouridylate synthase (N terminal domain). Members of this family are involved in modifying bases in RNA molecules. They carry out the conversion of uracil bases to pseudouridine. This family includes TruB, a pseudouridylate synthase that specifically converts uracil 55 to pseudouridine in most tRNAs. This family also includes Cbf5p that modifies rRNA.
Probab=77.79 E-value=3.3 Score=20.99 Aligned_cols=43 Identities=33% Similarity=0.431 Sum_probs=30.9
Q ss_pred CCCCCCCCCCCCCCCEEEEECCHHHHHHHHHHHHHHCCCCCEEEEEEEEEE
Q ss_conf 364324444332324057212035788889999972113221334454320
Q gi|254780610|r 140 KRPGIVHRLDKDTTGVMVVAKNDLAHQKLSEQFVDHGKSTRLKRAYYAMVW 190 (340)
Q Consensus 140 ~~~~lVHRLDr~TSGlll~Ak~~~a~~~l~~~f~~~~~~~~v~K~Y~Aiv~ 190 (340)
.+.|-...||--.||+|++|-+. + ..+...|.. -.|+|.|.+.
T Consensus 7 kKvGH~GTLDP~AsGlL~i~ig~-~-TK~~~~~~~------~~K~Y~~~~~ 49 (149)
T pfam01509 7 KKVGHTGTLDPLATGVLPVCVGK-A-TKLLQYLLD------ADKEYRATIR 49 (149)
T ss_pred CCCCCCCCCCCCCEEEEEEEECH-H-HHHHHHHCC------CCCEEEEEEE
T ss_conf 60242744698665689999987-8-712188758------9817999998
No 79
>COG0162 TyrS Tyrosyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=76.41 E-value=3.2 Score=21.12 Aligned_cols=11 Identities=18% Similarity=0.359 Sum_probs=4.5
Q ss_pred HHHHHHHHHCC
Q ss_conf 89999999859
Q gi|254780610|r 39 RSYVKILILNG 49 (340)
Q Consensus 39 R~~i~kli~~G 49 (340)
...++++++.+
T Consensus 21 ee~l~~ll~~~ 31 (401)
T COG0162 21 EEELRKLLEEG 31 (401)
T ss_pred HHHHHHHHHCC
T ss_conf 99999997458
No 80
>TIGR01344 malate_syn_A malate synthase A; InterPro: IPR006252 These sequences represent plant malate synthase and one of two bacterial forms, designated malate synthase A. This enzyme and isocitrate lyase are the two characteristic enzymes of the glyoxylate shunt. The shunt enables the cell to use acetyl-CoA to generate increased levels of TCA cycle intermediates for biosynthetic pathways such as gluconeogenesis.; GO: 0004474 malate synthase activity, 0006097 glyoxylate cycle.
Probab=66.66 E-value=3.6 Score=20.81 Aligned_cols=15 Identities=40% Similarity=0.521 Sum_probs=10.7
Q ss_pred CHHHHHHHHHHHHHH
Q ss_conf 115899999999870
Q gi|254780610|r 253 ETGRTHQIRVHMAHK 267 (340)
Q Consensus 253 ~TGRtHQIRvhla~l 267 (340)
.-|=+|-|||=+.++
T Consensus 403 e~G~R~NiRVG~qY~ 417 (522)
T TIGR01344 403 EEGLRHNIRVGLQYI 417 (522)
T ss_pred HHHHHHHHHHHHHHH
T ss_conf 655688889999999
No 81
>cd00754 MoaD MoaD family. Members of this family are involved in biosynthesis of the molybdenum cofactor (Moco), an essential cofactor of a diverse group of redox enzymes. Moco biosynthesis is an evolutionarily conserved pathway present in eubacteria, archaea and eukaryotes. Moco contains a tricyclic pyranopterin, termed molybdopterin (MPT), that contains the cis-dithiolene group responsible for molybdenum ligation. This dithiolene group is generated by MPT synthase, the second major step in Moco biosynthesis. MPT synthase consists of a large (MoeE) and small (MoaD) subunit. The small subunit is inserted into the lare subunit to form the active site. The small subunit, which is structurally similar to ubiquitin, contains a C-terminal thiocarboxylated glycine residue that serves as a sulfur donor for the synthesis of the MPT dithiolene group.
Probab=65.41 E-value=11 Score=18.01 Aligned_cols=52 Identities=19% Similarity=0.332 Sum_probs=31.7
Q ss_pred CCCHHHHHHHHCCCCCCHHHHHHHHHCCCEEECCEEECCCCCEECCCCEEEEEEC
Q ss_conf 8757899998717688989999999859904998993286758048988999705
Q gi|254780610|r 22 EGRIDRWLATSLKEQFSRSYVKILILNGFISINGMVSKNPNRKVVPGDSFLITVP 76 (340)
Q Consensus 22 g~RLD~~L~~~l~~~~sR~~i~kli~~G~V~vnG~~~~~~~~~l~~gd~I~i~~~ 76 (340)
+.++...+ +.|...++.. ...+...-.|.||++-+. .++.|..||+|.+..|
T Consensus 25 ~~Tv~~L~-~~L~~~~~~~-~~~~~~~~~iavN~~~~~-~~~~l~~gdEva~~PP 76 (80)
T cd00754 25 GATVGELL-DALEARYPGL-LEELLARVRIAVNGEYVR-LDTPLKDGDEVAIIPP 76 (80)
T ss_pred CCCHHHHH-HHHHHHCCHH-HHHHHHCEEEEECCEECC-CCCCCCCCCEEEEECC
T ss_conf 98899999-9999878176-764310409988879836-7715699999999799
No 82
>KOG2529 consensus
Probab=59.21 E-value=7.7 Score=18.84 Aligned_cols=78 Identities=23% Similarity=0.340 Sum_probs=45.7
Q ss_pred CCCCEEEEEECCCHHHCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHHHHHH
Q ss_conf 14402789962401110456787542100222222102443344443643244443323240572120357888899999
Q gi|254780610|r 94 YEDDDIIVINKPAGLVVHPAPGNWTGTLVNALLYHCHNNLSSINGVKRPGIVHRLDKDTTGVMVVAKNDLAHQKLSEQFV 173 (340)
Q Consensus 94 yED~~llvinKPaGl~vhp~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~lVHRLDr~TSGlll~Ak~~~a~~~l~~~f~ 173 (340)
|--..+++++||++ |++.+ .+.++...+.. ...|-..-||=+.||+++..-+... +.+..|
T Consensus 65 ~~~sgv~~i~kpa~----pss~e----~~swvk~iL~~--------ek~Gh~gTlDP~vtg~l~v~~~~~t-r~~~s~-- 125 (395)
T KOG2529 65 YSRSGVINIDKPAN----PSSHE----VVSWVKNILRV--------EKTGHSGTLDPEVTGCLIVCIDRAT-RLLKSQ-- 125 (395)
T ss_pred HHHCCCEECCCCCC----CCHHH----HHHHHHHHHHH--------HHHCCCCCCCCCCCCEEEEEEECCC-CCCCCH--
T ss_conf 76447463368979----86078----88888887668--------8707998889652322799960000-242120--
Q ss_pred HHCCCCCEEEEEEEEEECCCCC
Q ss_conf 7211322133445432024332
Q gi|254780610|r 174 DHGKSTRLKRAYYAMVWGIPLP 195 (340)
Q Consensus 174 ~~~~~~~v~K~Y~Aiv~G~~~~ 195 (340)
....|+|.+++++.+.-
T Consensus 126 -----~s~gk~yvg~~~lt~~v 142 (395)
T KOG2529 126 -----QSAGKEYVGIGKLTPEV 142 (395)
T ss_pred -----HCCCCEEEEEEECCCCH
T ss_conf -----10586799998547523
No 83
>PRK11092 bifunctional (p)ppGpp synthetase II/ guanosine-3',5'-bis pyrophosphate 3'-pyrophosphohydrolase; Provisional
Probab=58.03 E-value=14 Score=17.24 Aligned_cols=20 Identities=10% Similarity=0.235 Sum_probs=13.1
Q ss_pred EEEECCCCHHHHHHHHHHHC
Q ss_conf 99984997899999998851
Q gi|254780610|r 320 MDFQVPIPEDMLTVIRKLNE 339 (340)
Q Consensus 320 ~~f~aplP~~~~~~l~~L~~ 339 (340)
+.++-.=..+|..++++|+.
T Consensus 671 i~ieV~d~~hL~~ii~~Lr~ 690 (702)
T PRK11092 671 IRLTARDRVHLANIMRKIRV 690 (702)
T ss_pred EEEEECCHHHHHHHHHHHHC
T ss_conf 99998989999999999867
No 84
>PRK10872 relA GDP/GTP pyrophosphokinase; Provisional
Probab=55.42 E-value=16 Score=16.96 Aligned_cols=20 Identities=25% Similarity=0.282 Sum_probs=13.5
Q ss_pred EEEECCCCHHHHHHHHHHHC
Q ss_conf 99984997899999998851
Q gi|254780610|r 320 MDFQVPIPEDMLTVIRKLNE 339 (340)
Q Consensus 320 ~~f~aplP~~~~~~l~~L~~ 339 (340)
++++-.=-++|..++++|+.
T Consensus 712 ~~ieV~d~~~L~~li~~Lr~ 731 (743)
T PRK10872 712 MTIEIYNLQVLGRVLGKLNQ 731 (743)
T ss_pred EEEEECCHHHHHHHHHHHHC
T ss_conf 99997889999999999758
No 85
>TIGR00670 asp_carb_tr aspartate carbamoyltransferase; InterPro: IPR002082 Aspartate carbamoyltransferase (ATCase) catalyses the formation of carbamoyl-aspartate in the pyrimidine biosynthesis pathway, by the association of aspartate and carbamoyl-phosphate. This is the commitment step in the Escherichia coli pathway and is regulated by feedback inhibition by CTP, the final product of the pathway. The structural organisation of the ATCase protein varies considerably between different organisms. In bacteria such as E. coli, Salmonella typhimurium and Serratia marcescens, the ATCase is a dodecamer of 2 catalytic (c) trimers and 3 regulatory (r) dimers. The catalytic domains are coded for by the pyrB gene, and the regulatory domains by pyrI. In Gram-positive bacteria such as Bacillus subtilis, ATCase exists as a trimer of catalytic subunits, but unlike in E. coli, it neither contains nor binds to regulatory subunits. In eukaryotes, ATCase is found as a single domain in a multifunctional enzyme that contains activity for glutamine amidotransferase, carbamoylphosphate synthetase, dihydroorotase, and aspartate carbamoyltransferase. ; GO: 0004070 aspartate carbamoyltransferase activity, 0006207 'de novo' pyrimidine base biosynthetic process.
Probab=54.72 E-value=8.4 Score=18.59 Aligned_cols=49 Identities=22% Similarity=0.450 Sum_probs=28.2
Q ss_pred HHHHCCEEECCCCCCCCCCCCCCCCCCHHHHHHCCCCCHHHHHCEEEEECCCCCCEEEEECCC----CHHHHHHHHH
Q ss_conf 987097860415447755444334570135544079804432100042468897689998499----7899999998
Q gi|254780610|r 264 MAHKGNPLIGDPLYGKGFKTKANIVNNNAKSAILSLARQALHAHSLSFSHPRNNQDMDFQVPI----PEDMLTVIRK 336 (340)
Q Consensus 264 la~lG~PIvGD~~YG~~~~~~~~~~~~~~~~~~~~~~r~~LHA~~l~f~hP~t~~~~~f~apl----P~~~~~~l~~ 336 (340)
+..+---++||-+||..-.- | ++.|.+ +.+-.+.|.||- |+++.+-+++
T Consensus 172 ~~Gl~iA~vGDlkygRtvhS--------------------~-~~~L~~---f~~~~v~l~sP~~LrmP~~~~e~~~~ 224 (336)
T TIGR00670 172 LDGLKIALVGDLKYGRTVHS--------------------L-IKALAL---FGNAEVYLISPEELRMPKEILEDLKA 224 (336)
T ss_pred CCCCEEEEEEECCCCHHHHH--------------------H-HHHHHH---HCCCEEEEECCHHHHCHHHHHHHHHH
T ss_conf 28857999843120247667--------------------8-899865---18956998677243061788999852
No 86
>cd01668 TGS_RelA_SpoT TGS_RelA_SpoT: The RelA (SpoT) protein, also referred to as ppGpp hydrolase/synthetase, is a ribosome-associated protein that is activated during amino acid starvation and thought to mediate the stringent response. RelA contains a TGS domain, named after the Threonyl-tRNA Synthetase, GTPase, and SpoT proteins where it occurs. The function of the TGS domain is unknown.
Probab=50.99 E-value=15 Score=17.07 Aligned_cols=24 Identities=21% Similarity=0.174 Sum_probs=19.7
Q ss_pred CEEECCEEECCCCCEECCCCEEEEE
Q ss_conf 9049989932867580489889997
Q gi|254780610|r 50 FISINGMVSKNPNRKVVPGDSFLIT 74 (340)
Q Consensus 50 ~V~vnG~~~~~~~~~l~~gd~I~i~ 74 (340)
..+|||+.+ ..++.|+.||.|++.
T Consensus 36 ~a~vNg~~~-~l~~~L~~GD~VeIi 59 (60)
T cd01668 36 GAKVNGKLV-PLSTVLKDGDIVEII 59 (60)
T ss_pred EEEECCEEC-CCCCCCCCCCEEEEE
T ss_conf 999999998-987682899999987
No 87
>pfam00498 FHA FHA domain. The FHA (Forkhead-associated) domain is a phosphopeptide binding motif.
Probab=49.14 E-value=20 Score=16.35 Aligned_cols=24 Identities=17% Similarity=0.119 Sum_probs=13.2
Q ss_pred CEEECCEEECCCCCEECCCCEEEE
Q ss_conf 904998993286758048988999
Q gi|254780610|r 50 FISINGMVSKNPNRKVVPGDSFLI 73 (340)
Q Consensus 50 ~V~vnG~~~~~~~~~l~~gd~I~i 73 (340)
...|||+++....++|+.||+|.+
T Consensus 43 Gt~vNg~~i~~~~~~L~~GD~i~i 66 (67)
T pfam00498 43 GTFVNGQRLGPEPVRLKDGDVIRL 66 (67)
T ss_pred CEEECCEECCCCCEECCCCCEEEE
T ss_conf 859999996788769999999984
No 88
>TIGR00515 accD acetyl-CoA carboxylase, carboxyl transferase, beta subunit; InterPro: IPR000438 Fatty acid synthesis involves a set of reactions, commencing with carboxylation of acetyl-CoA to malonyl-CoA. This is an irreversible reaction, catalysed by the acetyl-CoA carboxylase complex (6.4.1.2 from EC); a heterohexamer of biotin carboxyl carrier protein, biotin carboxylase and two non-identical carboxyl transferase subunits (alpha and beta) in a 2:2 association . The reaction involves two steps: Biotin carrier protein + ATP + HCO_3^- = Carboxybiotin carrier protein + ADP + P_i Carboxybiotin carrier protein + Acetyl-CoA = Malonyl-CoA + Biotin carrier protein In the first step, biotin carboxylase catalyses the carboxylation of the carrier protein to form an intermediate. Next, the transcarboxylase complex transfers the carboxyl group from the intermediate to acetyl-CoA forming malonyl-CoA.; GO: 0003989 acetyl-CoA carboxylase activity, 0006633 fatty acid biosynthetic process, 0009317 acetyl-CoA carboxylase complex.
Probab=47.47 E-value=6.2 Score=19.38 Aligned_cols=54 Identities=22% Similarity=0.289 Sum_probs=35.4
Q ss_pred CEEECCCCCCCCCCCCCCCCCCHHHHHHCCCCCHHHHHCEEEEECCCCCCEEEEECCCCHHHHHH
Q ss_conf 78604154477554443345701355440798044321000424688976899984997899999
Q gi|254780610|r 269 NPLIGDPLYGKGFKTKANIVNNNAKSAILSLARQALHAHSLSFSHPRNNQDMDFQVPIPEDMLTV 333 (340)
Q Consensus 269 ~PIvGD~~YG~~~~~~~~~~~~~~~~~~~~~~r~~LHA~~l~f~hP~t~~~~~f~aplP~~~~~~ 333 (340)
-|++-|+.|||...-++-..+-...++ -+ -|.|--|.= =..++-..||++|+..
T Consensus 204 ISvLTdPT~GGVSASFA~LGDL~iAEP------kA----lIGFAGpRV-IeQT~rekLPegFQts 257 (292)
T TIGR00515 204 ISVLTDPTTGGVSASFAMLGDLNIAEP------KA----LIGFAGPRV-IEQTIREKLPEGFQTS 257 (292)
T ss_pred EEECCCCCCCHHHHHHHHHHHHHHHCC------CC----CCCCCCCEE-EEECCCCCCCCCHHHH
T ss_conf 441368897226789876402544156------42----312787502-3232656586700358
No 89
>pfam02597 ThiS ThiS family. ThiS (thiaminS) is a 66 aa protein involved in sulphur transfer. ThiS is coded in the thiCEFSGH operon in E. coli. This family of proteins have two conserved Glycines at the COOH terminus. Thiocarboxylate is formed at the last G in the activation process. Sulphur is transferred from ThiI to ThiS in a reaction catalysed by IscS. MoaD, a protein involved sulphur transfer in molybdopterin synthesis, is about the same length and shows limited sequence similarity to ThiS. Both have the conserved GG at the COOH end.
Probab=46.32 E-value=22 Score=16.09 Aligned_cols=47 Identities=17% Similarity=0.289 Sum_probs=30.3
Q ss_pred HCCCCHHHHHHHHCCCCCCHHHHHHHHHCCCEEECCEEECC--CCCEECCCCEEEEEEC
Q ss_conf 36875789999871768898999999985990499899328--6758048988999705
Q gi|254780610|r 20 TAEGRIDRWLATSLKEQFSRSYVKILILNGFISINGMVSKN--PNRKVVPGDSFLITVP 76 (340)
Q Consensus 20 ~~g~RLD~~L~~~l~~~~sR~~i~kli~~G~V~vnG~~~~~--~~~~l~~gd~I~i~~~ 76 (340)
..+.++..+|. .|. ++ .+.=.|-+||+.+.. .++.|+.||+|.+..+
T Consensus 18 ~~~~tv~~ll~-~l~--~~-------~~~v~v~vN~~~v~~~~~~~~L~~gD~v~ivpp 66 (70)
T pfam02597 18 PEGATVAELLE-ALG--LN-------PERVAVAVNGEIVPRSQADTPLKDGDEVAIIPP 66 (70)
T ss_pred CCCCCHHHHHH-HHC--CC-------CCCEEEEECCEECCCCCCCCCCCCCCEEEEECC
T ss_conf 99996999999-838--88-------888899999998678567767799999999788
No 90
>cd01616 TGS The TGS domain, named after the ThrRS, GTPase, and SpoT/RelA proteins where it occurs, is structurally similar to ubiquitin. TGS is a small domain of about 50 amino acid residues with a predominantly beta-sheet structure. There is no direct information on the function of the TGS domain, but its presence in two types of regulatory proteins (the GTPases and guanosine polyphosphate phosphohydrolases/synthetases) suggests a ligand (most likely nucleotide)-binding, regulatory role.
Probab=45.67 E-value=18 Score=16.57 Aligned_cols=23 Identities=22% Similarity=0.348 Sum_probs=19.3
Q ss_pred EEECCEEECCCCCEECCCCEEEEE
Q ss_conf 049989932867580489889997
Q gi|254780610|r 51 ISINGMVSKNPNRKVVPGDSFLIT 74 (340)
Q Consensus 51 V~vnG~~~~~~~~~l~~gd~I~i~ 74 (340)
..|||+.+ ..++.|+.||.|++.
T Consensus 37 a~Vng~~~-~l~~~L~~gd~V~Ii 59 (60)
T cd01616 37 ALVNGQLV-DLSYTLQDGDTVSIV 59 (60)
T ss_pred EEECCEEC-CCCCCCCCCCEEEEE
T ss_conf 99999996-516699999999997
No 91
>pfam02824 TGS TGS domain. The TGS domain is named after ThrRS, GTPase, and SpoT. Interestingly, TGS domain was detected also at the amino terminus of the uridine kinase from the spirochaete Treponema pallidum (but not any other organism, including the related spirochaete Borrelia burgdorferi). TGS is a small domain that consists of ~50 amino acid residues and is predicted to possess a predominantly beta-sheet structure. There is no direct information on the functions of the TGS domain, but its presence in two types of regulatory proteins (the GTPases and guanosine polyphosphate phosphohydrolases/synthetases) suggests a ligand (most likely nucleotide)-binding, regulatory role.
Probab=45.59 E-value=19 Score=16.43 Aligned_cols=24 Identities=21% Similarity=0.191 Sum_probs=19.7
Q ss_pred CEEECCEEECCCCCEECCCCEEEEE
Q ss_conf 9049989932867580489889997
Q gi|254780610|r 50 FISINGMVSKNPNRKVVPGDSFLIT 74 (340)
Q Consensus 50 ~V~vnG~~~~~~~~~l~~gd~I~i~ 74 (340)
...|||+.+ ..++.|+.||.|++.
T Consensus 36 ~A~VnG~~v-~l~~~L~~gd~V~Ii 59 (60)
T pfam02824 36 GAKVNGQRV-GLDHVLEDGDVVEIV 59 (60)
T ss_pred EEEECCEEC-CCCCCCCCCCEEEEE
T ss_conf 789998887-621124899999987
No 92
>TIGR01764 excise DNA binding domain, excisionase family; InterPro: IPR010093 An excisionase, or Xis protein, is a small protein that binds and promotes excisive recombination; it is not enzymatically active. This entry represents a number of putative excisionases and related proteins from temperate phage, plasmids, and transposons, as well as DNA binding domains of other proteins, such as a DNA modification methylase. This entry identifies mostly small proteins and N-terminal regions of large proteins, but some proteins appear to have two copies. This domain appears similar, in both sequence and predicted secondary structure (PSIPRED) to the MerR family of transcriptional regulators (IPR000551 from INTERPRO).; GO: 0003677 DNA binding.
Probab=40.29 E-value=24 Score=15.89 Aligned_cols=26 Identities=31% Similarity=0.314 Sum_probs=20.8
Q ss_pred CHHHHHHHHCCCCCCHHHHHHHHHCCCEE
Q ss_conf 57899998717688989999999859904
Q gi|254780610|r 24 RIDRWLATSLKEQFSRSYVKILILNGFIS 52 (340)
Q Consensus 24 RLD~~L~~~l~~~~sR~~i~kli~~G~V~ 52 (340)
+++. .++.| ++|+..+++||++|.+.
T Consensus 3 Tv~E-aA~yL--gv~~~t~~~l~~~g~l~ 28 (49)
T TIGR01764 3 TVEE-AAEYL--GVSKSTVYRLIEEGELP 28 (49)
T ss_pred CHHH-HHHHC--CCCHHHHHHHHHCCCCC
T ss_conf 7788-99771--99905789999718985
No 93
>PRK02268 hypothetical protein; Provisional
Probab=39.90 E-value=28 Score=15.49 Aligned_cols=42 Identities=24% Similarity=0.362 Sum_probs=33.3
Q ss_pred CCCHHHHHHHHHCCCEEECCEEECCCCCEECCCCEEEEEECCC
Q ss_conf 8898999999985990499899328675804898899970560
Q gi|254780610|r 36 QFSRSYVKILILNGFISINGMVSKNPNRKVVPGDSFLITVPAA 78 (340)
Q Consensus 36 ~~sR~~i~kli~~G~V~vnG~~~~~~~~~l~~gd~I~i~~~~~ 78 (340)
-.|+..+++-...|-..++.-+. .|-.++++||.|.++.|..
T Consensus 8 VaS~~HV~~g~~~GF~QvcHGK~-apL~Rm~~GD~ivYYSPk~ 49 (141)
T PRK02268 8 VVSAEHVRRGVEGGFMQVCHGKA-APLRRMKPGDWIIYYSPKT 49 (141)
T ss_pred EEEHHHHHHHHHCCEEEECCCCC-CHHHCCCCCCEEEEECCEE
T ss_conf 54099999887487534137840-1553289999899957841
No 94
>TIGR00871 zwf glucose-6-phosphate 1-dehydrogenase; InterPro: IPR001282 Glucose-6-phosphate dehydrogenase (1.1.1.49 from EC) (G6PDH) is a ubiquitous protein, present in bacteria and all eukaryotic cell types . The enzyme catalyses the the first step in the pentose pathway, i.e. the conversion of glucose-6-phosphate to gluconolactone 6-phosphate in the presence of NADP, producing NADPH. The ubiquitous expression of the enzyme gives it a major role in the production of NADPH for the many NADPH-mediated reductive processes in all cells . Deficiency of G6PDH is a common genetic abnormality affecting millions of people worldwide. Many sequence variants, most caused by single point mutations, are known, exhibiting a wide variety of phenotypes .; GO: 0004345 glucose-6-phosphate dehydrogenase activity, 0006006 glucose metabolic process.
Probab=39.23 E-value=27 Score=15.59 Aligned_cols=98 Identities=19% Similarity=0.189 Sum_probs=43.1
Q ss_pred CCCEEEEEECCCHHCCHHHHHHHHHHCCC----CC---EEEEEECCCHHHCCCCCCCCCCCCHHHHHHHHCCCCCCCCCC
Q ss_conf 89889997056011110233222221014----40---278996240111045678754210022222210244334444
Q gi|254780610|r 67 PGDSFLITVPAAQKLNIAQENIPLDILYE----DD---DIIVINKPAGLVVHPAPGNWTGTLVNALLYHCHNNLSSINGV 139 (340)
Q Consensus 67 ~gd~I~i~~~~~~~~~~~~~~~~~~IlyE----D~---~llvinKPaGl~vhp~~~~~~~tl~~~l~~~~~~~~~~~~~~ 139 (340)
.|-.|.+.--++......++.+.-..+.+ .. .=|||.||.| |-- .+...|-..+...|.+.. .
T Consensus 109 ~gNr~fYLa~PP~~F~~i~~~L~~~~l~~~nq~~~~~w~Rvv~EKPFG---~DL--~SA~~Ln~~~~~~F~E~q-----i 178 (498)
T TIGR00871 109 EGNRLFYLATPPSLFGTIIKQLKKHGLNERNQEQGKTWSRVVIEKPFG---HDL--ASAQELNKQLRAVFKEDQ-----I 178 (498)
T ss_pred CCCEEEECCCCCCCCHHHHHHHHHHHCCCCCCCCCCCEEEEEEECCCC---CCH--HHHHHHHHHHHHHCCCCC-----E
T ss_conf 897456504784410267887765310001355788447999878899---987--899999999886548464-----4
Q ss_pred CCCCCCCCCCCCCCCEEEEECCHHHHHHHHHHHHHHCCCCCEE
Q ss_conf 3643244443323240572120357888899999721132213
Q gi|254780610|r 140 KRPGIVHRLDKDTTGVMVVAKNDLAHQKLSEQFVDHGKSTRLK 182 (340)
Q Consensus 140 ~~~~lVHRLDr~TSGlll~Ak~~~a~~~l~~~f~~~~~~~~v~ 182 (340)
.+|=|=|.|+|== |-.+.+--++.|...|.++.|.
T Consensus 179 --YRIDHYLGKEtVq------NllvlRFAN~~Fep~WNr~~Id 213 (498)
T TIGR00871 179 --YRIDHYLGKETVQ------NLLVLRFANQIFEPLWNRRYID 213 (498)
T ss_pred --EEEECCCCCHHHH------HHHHHHHHHHHHHHHCCCCCCC
T ss_conf --6741012645788------9999964788753211577644
No 95
>pfam03658 UPF0125 Uncharacterized protein family (UPF0125).
Probab=39.16 E-value=21 Score=16.22 Aligned_cols=31 Identities=23% Similarity=0.204 Sum_probs=23.7
Q ss_pred HCCCEEECCEEECCCCCEECCCCEEEEEECCC
Q ss_conf 85990499899328675804898899970560
Q gi|254780610|r 47 LNGFISINGMVSKNPNRKVVPGDSFLITVPAA 78 (340)
Q Consensus 47 ~~G~V~vnG~~~~~~~~~l~~gd~I~i~~~~~ 78 (340)
....+-|=|+.+. .++.|+.||+|.++.|-.
T Consensus 45 ~~~~vGIfgk~v~-l~~~L~~GDRVEIYRPL~ 75 (83)
T pfam03658 45 SKNKVGIFGKPVK-LDDPLKDGDRIEIYRPLL 75 (83)
T ss_pred CCCCEEEECCCCC-CCCCCCCCCEEEEECCCC
T ss_conf 6463646884738-877079999999953665
No 96
>PRK04439 S-adenosylmethionine synthetase; Provisional
Probab=39.13 E-value=18 Score=16.63 Aligned_cols=23 Identities=22% Similarity=0.276 Sum_probs=9.3
Q ss_pred HHHCCCCCCHHHHHHHHH-CCCEE
Q ss_conf 987176889899999998-59904
Q gi|254780610|r 30 ATSLKEQFSRSYVKILIL-NGFIS 52 (340)
Q Consensus 30 ~~~l~~~~sR~~i~kli~-~G~V~ 52 (340)
+..+-..+||...+-.++ =|.|.
T Consensus 34 cDgiaE~vS~~Lsr~Yl~~fG~Il 57 (400)
T PRK04439 34 CDGIAEAVSRALSRYYLERFGAIL 57 (400)
T ss_pred HHHHHHHHHHHHHHHHHHHHCCEE
T ss_conf 799999999999999999729760
No 97
>PRK01777 hypothetical protein; Validated
Probab=37.98 E-value=22 Score=16.10 Aligned_cols=31 Identities=19% Similarity=0.112 Sum_probs=22.8
Q ss_pred CCCEEECCEEECCCCCEECCCCEEEEEECCCH
Q ss_conf 59904998993286758048988999705601
Q gi|254780610|r 48 NGFISINGMVSKNPNRKVVPGDSFLITVPAAQ 79 (340)
Q Consensus 48 ~G~V~vnG~~~~~~~~~l~~gd~I~i~~~~~~ 79 (340)
...+-|=|+.++ .++.|+.||+|.++.|-.-
T Consensus 49 ~~~vGIfgk~~~-ld~~L~~GDRVEIYRPL~~ 79 (95)
T PRK01777 49 KNKVGIFSRPVK-LTDVLRDGDRVEIYRPLLA 79 (95)
T ss_pred CCCEEEECCCCC-CCCCCCCCCEEEEECCCCC
T ss_conf 474507884838-8772899999998536554
No 98
>PRK10687 purine nucleoside phosphoramidase; Provisional
Probab=36.74 E-value=13 Score=17.38 Aligned_cols=20 Identities=30% Similarity=0.669 Sum_probs=14.6
Q ss_pred HHHHHHHHCCCCCEEEEEEC
Q ss_conf 33222221014402789962
Q gi|254780610|r 85 QENIPLDILYEDDDIIVINK 104 (340)
Q Consensus 85 ~~~~~~~IlyED~~llvinK 104 (340)
...+|-.+|||||+++++-=
T Consensus 12 ~geipa~~VyEdd~~~AFlD 31 (119)
T PRK10687 12 RREIPSDIVYQDELVTAFRD 31 (119)
T ss_pred CCCCCCCEEEECCCEEEEEC
T ss_conf 48877657974798899867
No 99
>PRK00943 selenophosphate synthetase; Provisional
Probab=35.70 E-value=33 Score=15.09 Aligned_cols=27 Identities=22% Similarity=0.337 Sum_probs=15.3
Q ss_pred ECCCCCCEEEEECCCCHHHHHHHHHHHC
Q ss_conf 4688976899984997899999998851
Q gi|254780610|r 312 SHPRNNQDMDFQVPIPEDMLTVIRKLNE 339 (340)
Q Consensus 312 ~hP~t~~~~~f~aplP~~~~~~l~~L~~ 339 (340)
.+|.|...+-+.. .|++-.++++.|++
T Consensus 297 ~DPQTSGGLLiaV-~~e~a~~~l~~L~~ 323 (347)
T PRK00943 297 CDPQTSGGLLVAV-APEAEDEVLATFAE 323 (347)
T ss_pred CCCCCCCCEEEEE-CHHHHHHHHHHHHH
T ss_conf 3855777679998-59999999999996
No 100
>pfam01941 AdoMet_Synthase S-adenosylmethionine synthetase (AdoMet synthetase). This family consists of several archaebacterial S-adenosylmethionine synthetase C(AdoMet synthetase or MAT) (EC 2.5.1.6). S-Adenosylmethionine (AdoMet) occupies a central role in the metabolism of all cells. The biological roles of AdoMet include acting as the primary methyl group donor, as a precursor to the polyamines, and as a progenitor of a 5'-deoxyadenosyl radical. S-Adenosylmethionine synthetase catalyses the only known route of AdoMet biosynthesis. The synthetic process occurs in a unique reaction in which the complete triphosphate chain is displaced from ATP and a sulfonium ion formed. MATs from various organisms contain ~400-amino acid polypeptide chains.
Probab=33.78 E-value=20 Score=16.39 Aligned_cols=24 Identities=21% Similarity=0.289 Sum_probs=10.1
Q ss_pred HHHHCCCCCCHHHHHHHHH-CCCEE
Q ss_conf 9987176889899999998-59904
Q gi|254780610|r 29 LATSLKEQFSRSYVKILIL-NGFIS 52 (340)
Q Consensus 29 L~~~l~~~~sR~~i~kli~-~G~V~ 52 (340)
++..+-..+||...+-.++ =|.|.
T Consensus 33 icD~iaE~vS~aLs~~Yl~~fG~Il 57 (396)
T pfam01941 33 ICDGIAEAVSRALCREYLERFGAIL 57 (396)
T ss_pred HHHHHHHHHHHHHHHHHHHHHCCEE
T ss_conf 8799999999999999999739660
No 101
>TIGR02040 PpsR-CrtJ transcriptional regulator PpsR; InterPro: IPR011785 This entry represents the transcriptional regulator PpsR which is strictly associated with photosynthetic proteobacteria and found in photosynthetic operons. PpsR has been reported to be a repressor . These proteins contain a Helix-Turn-Helix motif of the "fis" type..
Probab=33.74 E-value=19 Score=16.54 Aligned_cols=45 Identities=20% Similarity=0.433 Sum_probs=32.2
Q ss_pred CCCCCCCCC---CCCCEEEEECCHHHHHHHHHHHHHHCCCCCEEEEEEEE
Q ss_conf 432444433---23240572120357888899999721132213344543
Q gi|254780610|r 142 PGIVHRLDK---DTTGVMVVAKNDLAHQKLSEQFVDHGKSTRLKRAYYAM 188 (340)
Q Consensus 142 ~~lVHRLDr---~TSGlll~Ak~~~a~~~l~~~f~~~~~~~~v~K~Y~Ai 188 (340)
-|..|||-- --.|+|.|+|+-.+-.+|++|+-.. +..+++-||.+
T Consensus 86 ~F~~~~L~~sdGk~~~vLa~GrdLr~vA~lqq~lv~A--Q~AmErDYW~l 133 (453)
T TIGR02040 86 EFVLVRLGASDGKDEGVLALGRDLRAVAELQQRLVEA--QQAMERDYWKL 133 (453)
T ss_pred EEEEECCCCCCCCCCCEEEECCCCHHHHHHHHHHHHH--HHHHHHHHHHH
T ss_conf 3467616787888873588846524789999999999--87888879998
No 102
>PRK05449 aspartate alpha-decarboxylase; Provisional
Probab=32.78 E-value=32 Score=15.16 Aligned_cols=15 Identities=20% Similarity=0.552 Sum_probs=6.7
Q ss_pred CCCCCEEEEEECCCH
Q ss_conf 014402789962401
Q gi|254780610|r 93 LYEDDDIIVINKPAG 107 (340)
Q Consensus 93 lyED~~llvinKPaG 107 (340)
+.+.+.+.|+|.-.|
T Consensus 38 i~~~E~V~V~Nv~NG 52 (126)
T PRK05449 38 ILENEKVDIVNVNNG 52 (126)
T ss_pred CCCCCEEEEEECCCC
T ss_conf 998988999989899
No 103
>PRK11130 moaD molybdopterin synthase small subunit; Provisional
Probab=32.71 E-value=37 Score=14.79 Aligned_cols=59 Identities=15% Similarity=0.168 Sum_probs=34.5
Q ss_pred EEEEECHHHCCCCHHHHHHHHCCCCCCHHHHHHHHHCCC--EEECCEEECCCCCEECCCCEEEEEEC
Q ss_conf 999957113687578999987176889899999998599--04998993286758048988999705
Q gi|254780610|r 12 KISLLSDSTAEGRIDRWLATSLKEQFSRSYVKILILNGF--ISINGMVSKNPNRKVVPGDSFLITVP 76 (340)
Q Consensus 12 ~~~~V~~~~~g~RLD~~L~~~l~~~~sR~~i~kli~~G~--V~vnG~~~~~~~~~l~~gd~I~i~~~ 76 (340)
..+.++.+ +..++. |...|....+ .+...+..+. +.||.+-+. .+..|+.||+|.+..|
T Consensus 17 ~~~~l~~~--~~tv~~-l~~~L~~~~~--~~~~~l~~~~~~~AVNq~~~~-~d~~l~~gDEVAffPP 77 (81)
T PRK11130 17 DALELAAD--FPTVEA-LRQHLAQQGD--RWALALEDGKLLAAVNQTLVS-FDHPLTDGDEVAFFPP 77 (81)
T ss_pred CEEECCCC--CCCHHH-HHHHHHHHCC--HHHHHHCCCCEEEEECCEECC-CCCCCCCCCEEEECCC
T ss_conf 64787899--988999-9999998583--588862468567733137768-9976699999998089
No 104
>pfam01230 HIT HIT domain.
Probab=32.56 E-value=18 Score=16.60 Aligned_cols=17 Identities=35% Similarity=0.700 Sum_probs=13.4
Q ss_pred HHHHHCCCCCEEEEEEC
Q ss_conf 22221014402789962
Q gi|254780610|r 88 IPLDILYEDDDIIVINK 104 (340)
Q Consensus 88 ~~~~IlyED~~llvinK 104 (340)
+|-.|||||++++++-=
T Consensus 4 ~p~~ivyed~~~~aflD 20 (98)
T pfam01230 4 IPSTVVYEDDLVLAFLD 20 (98)
T ss_pred CCCCEEEECCCEEEEEC
T ss_conf 67618997897999987
No 105
>cd06919 Asp_decarbox Aspartate alpha-decarboxylase or L-aspartate 1-decarboxylase, a pyruvoyl group-dependent decarboxylase in beta-alanine production. Decarboxylation of aspartate is the major route of beta-alanine production in bacteria, and is catalyzed by the enzyme L-aspartate decarboxylase (ADC), EC:4.1.1.11 which requires a pyruvoyl group for its activity. The pyruvoyl cofactor is covalently bound to the enzyme. The protein is synthesized as a proenzyme and cleaved via self-processing at Gly23-Ser24 to yield an alpha chain (C-terminal fragment) and beta chain (N-terminal fragment), and the pyruvoyl group. Beta-alanine is required for the biosynthesis of pantothenate, in which the enzyme plays a critical regulatory role. The active site of the tetrameric enzyme is located at the interface of two subunits, with a Lysine and a Histidine from the beta chain of one subunit forming the active site with residues from the alpha chain of the adjacent subunit. This alignment
Probab=31.90 E-value=25 Score=15.78 Aligned_cols=12 Identities=17% Similarity=0.368 Sum_probs=4.2
Q ss_pred CCCEEEEEECCC
Q ss_conf 440278996240
Q gi|254780610|r 95 EDDDIIVINKPA 106 (340)
Q Consensus 95 ED~~llvinKPa 106 (340)
+.+.+.|+|.-.
T Consensus 39 ~~E~V~V~N~~N 50 (111)
T cd06919 39 PYEKVLVVNVNN 50 (111)
T ss_pred CCCEEEEEECCC
T ss_conf 898899998989
No 106
>COG0317 SpoT Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]
Probab=31.35 E-value=39 Score=14.66 Aligned_cols=27 Identities=22% Similarity=0.314 Sum_probs=18.9
Q ss_pred EEECCEEECCCCCEECCCCEEEEEECCC
Q ss_conf 0499899328675804898899970560
Q gi|254780610|r 51 ISINGMVSKNPNRKVVPGDSFLITVPAA 78 (340)
Q Consensus 51 V~vnG~~~~~~~~~l~~gd~I~i~~~~~ 78 (340)
.+|||+.+ .-++.|+.||+|.+...+.
T Consensus 425 AkVnG~iv-pl~~~Lk~Gd~VEIit~k~ 451 (701)
T COG0317 425 AKVNGRIV-PLTTKLQTGDQVEIITSKH 451 (701)
T ss_pred EEECCEEE-CCCEECCCCCEEEEEECCC
T ss_conf 78899981-4650347899899994899
No 107
>pfam02261 Asp_decarbox Aspartate decarboxylase. Decarboxylation of aspartate is the major route of beta-alanine production in bacteria, and is catalysed by the enzyme aspartate decarboxylase EC:4.1.1.11 which requires a pyruvoyl group for its activity. It is synthesized initially as a proenzyme which is then proteolytically cleaved to an alpha (C-terminal) and beta (N-terminal) subunit and a pyruvoyl group. This family contains both chains of aspartate decarboxylase.
Probab=31.02 E-value=26 Score=15.69 Aligned_cols=10 Identities=10% Similarity=0.302 Sum_probs=3.5
Q ss_pred CCEEEEEECC
Q ss_conf 4027899624
Q gi|254780610|r 96 DDDIIVINKP 105 (340)
Q Consensus 96 D~~llvinKP 105 (340)
.+.+.|+|.-
T Consensus 41 ~E~V~V~Nv~ 50 (116)
T pfam02261 41 YEKVQIVNVN 50 (116)
T ss_pred CCEEEEEECC
T ss_conf 9889999898
No 108
>TIGR02477 PFKA_PPi diphosphate--fructose-6-phosphate 1-phosphotransferase; InterPro: IPR011183 Diphosphate--fructose-6-phosphate 1-phosphotransferase catalyses the addition of phosphate from diphosphate (PPi) to fructose 6-phosphate to give fructose 1,6-bisphosphate (2.7.1.90 from EC). The enzyme is also known as pyrophosphate-dependent phosphofructokinase. The usage of PPi-dependent enzymes in glycolysis presumably frees up ATP for other processes . IPR012828 from INTERPRO represents the ATP-dependent 6-phosphofructokinase enzyme contained within Phosphofructokinase. This entry contains primarily bacterial, plant alpha, and plant beta sequences. These may be dimeric nonallosteric enzymes (bacteria) or allosteric heterotetramers (plants) . For additional information please see , , , .; GO: 0005524 ATP binding, 0047334 diphosphate-fructose-6-phosphate 1-phosphotransferase activity, 0006096 glycolysis, 0005945 6-phosphofructokinase complex.
Probab=30.97 E-value=39 Score=14.65 Aligned_cols=43 Identities=26% Similarity=0.517 Sum_probs=30.1
Q ss_pred CCCCCCCCCEEEEE--CCHHHHHHHHHHHHHHCCCCCEEEEEEEEEECCCCCCCCCCCCCC
Q ss_conf 44433232405721--203578888999997211322133445432024332332110013
Q gi|254780610|r 146 HRLDKDTTGVMVVA--KNDLAHQKLSEQFVDHGKSTRLKRAYYAMVWGIPLPDSGIINAPL 204 (340)
Q Consensus 146 HRLDr~TSGlll~A--k~~~a~~~l~~~f~~~~~~~~v~K~Y~Aiv~G~~~~~~g~i~~~l 204 (340)
+-|| |+||++ -+...|..|++.|.. |.+-..|-|+|. |||.-|
T Consensus 167 l~Ld----gLVIIGGDdSNTnAA~LAEyF~~--------~~~~t~viGVPK----TIDGDL 211 (566)
T TIGR02477 167 LKLD----GLVIIGGDDSNTNAALLAEYFAK--------KGLKTQVIGVPK----TIDGDL 211 (566)
T ss_pred HCCC----EEEEECCCCCHHHHHHHHHHHHH--------CCCCCEEEEEEC----CCCHHH
T ss_conf 0896----48997479867999999999997--------389922786402----547211
No 109
>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=30.55 E-value=23 Score=15.99 Aligned_cols=14 Identities=43% Similarity=0.881 Sum_probs=11.5
Q ss_pred HHCCCCCEEEEEEC
Q ss_conf 21014402789962
Q gi|254780610|r 91 DILYEDDDIIVINK 104 (340)
Q Consensus 91 ~IlyED~~llvinK 104 (340)
.++||||+++++.=
T Consensus 17 ~ivyEdd~~~af~D 30 (104)
T cd01278 17 DQVYEDDRVVVFKD 30 (104)
T ss_pred CEEEECCCEEEEEC
T ss_conf 67975797999967
No 110
>TIGR01969 minD_arch cell division ATPase MinD; InterPro: IPR010224 Proper placement of the bacterial cell division site requires the site-specific inactivation of other potential division sites. In Escherichia coli, selection of the correct mid-cell site is mediated by the MinC, MinD and MinE proteins. Several members of this family are found in archaeal genomes but their function is uncharacterised. More distantly related proteins include flagellar biosynthesis proteins and ParA chromosome partitioning proteins. This entry represents the archaeal MinD family. The exact roles of the various archaeal MinD homologs are unknown. .
Probab=30.27 E-value=30 Score=15.33 Aligned_cols=27 Identities=30% Similarity=0.658 Sum_probs=20.6
Q ss_pred CHHHHHHH--HHHCCCCCEEEEEECCCHH
Q ss_conf 10233222--2210144027899624011
Q gi|254780610|r 82 NIAQENIP--LDILYEDDDIIVINKPAGL 108 (340)
Q Consensus 82 ~~~~~~~~--~~IlyED~~llvinKPaGl 108 (340)
...|++++ ++=|.+|-|||+||=||||
T Consensus 93 KA~~~~L~dV~~~i~~~~D~lLIDAPAGL 121 (258)
T TIGR01969 93 KADPDKLEDVLKEIIDDTDFLLIDAPAGL 121 (258)
T ss_pred CCCHHHHHHHHHHHHCCCCEEEEECCCCC
T ss_conf 26833328999987204377887478983
No 111
>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=30.15 E-value=21 Score=16.29 Aligned_cols=18 Identities=33% Similarity=0.744 Sum_probs=13.4
Q ss_pred HHHHHCCCCCEEEEEECC
Q ss_conf 222210144027899624
Q gi|254780610|r 88 IPLDILYEDDDIIVINKP 105 (340)
Q Consensus 88 ~~~~IlyED~~llvinKP 105 (340)
.|-.++||||+++++.=-
T Consensus 12 ~p~~ivyede~~~aflD~ 29 (104)
T cd01276 12 IPAKKVYEDDEVLAFHDI 29 (104)
T ss_pred CCCCEEEECCCEEEEECC
T ss_conf 787889979979999888
No 112
>TIGR01393 lepA GTP-binding protein LepA; InterPro: IPR006297 LepA (GUF1 in Saccaromyces) is a GTP-binding membrane protein related to EF-G and EF-Tu. Two types of phylogenetic tree, rooted by other GTP-binding proteins, suggest that eukaryotic homologs (including GUF1 of yeast) originated within the bacterial LepA family. The function of the proteins in this family are unknown. ; GO: 0005525 GTP binding.
Probab=29.57 E-value=25 Score=15.75 Aligned_cols=163 Identities=18% Similarity=0.303 Sum_probs=76.0
Q ss_pred EEEECHHHCCC-CH-HHHHHHHCCCCCCHHHH-HHHH------HCCCEEECCEEECCCCCE-ECCCCEEEEEECCCHH-C
Q ss_conf 99957113687-57-89999871768898999-9999------859904998993286758-0489889997056011-1
Q gi|254780610|r 13 ISLLSDSTAEG-RI-DRWLATSLKEQFSRSYV-KILI------LNGFISINGMVSKNPNRK-VVPGDSFLITVPAAQK-L 81 (340)
Q Consensus 13 ~~~V~~~~~g~-RL-D~~L~~~l~~~~sR~~i-~kli------~~G~V~vnG~~~~~~~~~-l~~gd~I~i~~~~~~~-~ 81 (340)
.|||..=|-|- +| ||+|... ..+|.+.. .+++ |...||+--..++ -+|. -..|+.-.+++=..+. .
T Consensus 6 FsIIAHIDHGKSTLADRlle~T--~~~s~R~m~~Q~LD~MDlERERGITIK~qaV~-l~Yk~~~DGe~Y~LNLIDTPGHV 82 (598)
T TIGR01393 6 FSIIAHIDHGKSTLADRLLEKT--GAVSEREMREQVLDSMDLERERGITIKAQAVR-LKYKVAKDGETYVLNLIDTPGHV 82 (598)
T ss_pred EEEEEEECCCCCHHHHHHHHHC--CCCCCHHHHHCCCCCCCEEECCCCEEECCCEE-EEEEEECCCCEEEEEEECCCCCC
T ss_conf 6788462489324889999861--74562025430577510000058201156347-53375338878899645288972
Q ss_pred CHHHHHHHHHHCCCCCEEEEEECCCHHHCCCCCCCCCCCCHHHHHHHHCC----------CCCCCCCCCC--CCCCCCCC
Q ss_conf 10233222221014402789962401110456787542100222222102----------4433444436--43244443
Q gi|254780610|r 82 NIAQENIPLDILYEDDDIIVINKPAGLVVHPAPGNWTGTLVNALLYHCHN----------NLSSINGVKR--PGIVHRLD 149 (340)
Q Consensus 82 ~~~~~~~~~~IlyED~~llvinKPaGl~vhp~~~~~~~tl~~~l~~~~~~----------~~~~~~~~~~--~~lVHRLD 149 (340)
++..|--. ++=-=-..||+||==-|+=. .|++|.-+.--.+ .|+... .++ -.+-|=|.
T Consensus 83 DFsYEVSR-SLAACEGALL~VDA~QGvEA--------QT~aN~YlAlE~dLeIIPViNKIDLP~Ad-pe~v~~eIe~~iG 152 (598)
T TIGR01393 83 DFSYEVSR-SLAACEGALLLVDAAQGVEA--------QTLANVYLALENDLEIIPVINKIDLPSAD-PERVKKEIEEVIG 152 (598)
T ss_pred CCCHHHHH-HHHHHCCEEEEEECCCCHHH--------HHHHHHHHHHHCCCEEEEEECCCCCCCCC-HHHHHHHHHHHCC
T ss_conf 12737888-88871640356141032358--------88999988756187584778253688888-5899998765418
Q ss_pred CCCCCEEEE-ECCHHHHHHHHHHHHHHCCCCCEEEEEEEEEECCCCCCCCCCC-CCCC
Q ss_conf 323240572-1203578888999997211322133445432024332332110-0134
Q gi|254780610|r 150 KDTTGVMVV-AKNDLAHQKLSEQFVDHGKSTRLKRAYYAMVWGIPLPDSGIIN-APLG 205 (340)
Q Consensus 150 r~TSGlll~-Ak~~~a~~~l~~~f~~~~~~~~v~K~Y~Aiv~G~~~~~~g~i~-~~l~ 205 (340)
-+++=++++ ||+-..-.++= -|||+=+|+| .|..+ .||.
T Consensus 153 ld~~~ai~~SAKtG~Gi~e~L----------------EaIv~~vPpP-~Gd~~DapLk 193 (598)
T TIGR01393 153 LDASEAILASAKTGIGIEEIL----------------EAIVKRVPPP-KGDPDDAPLK 193 (598)
T ss_pred CCCCCCEEEEECCCCCHHHHH----------------HHHHHCCCCC-CCCCCCCCCE
T ss_conf 896430387503678889998----------------8971018100-1138886632
No 113
>TIGR00691 spoT_relA RelA/SpoT family protein; InterPro: IPR004811 The functions of Escherichia coli RelA and SpoT differ somewhat. RelA (2.7.6.5 from EC) produces pppGpp (or ppGpp) from ATP and GTP (or GDP). SpoT (3.1.7.2 from EC) degrades ppGpp, but may also act as a secondary ppGpp synthetase. The two proteins are strongly similar. In many species, a single homolog to SpoT and RelA appears responsible for both ppGpp synthesis and ppGpp degradation. (p)ppGpp is a regulatory metabolite of the stringent response, but appears also to be involved in antibiotic biosynthesis in some species. ; GO: 0015969 guanosine tetraphosphate metabolic process.
Probab=29.20 E-value=42 Score=14.43 Aligned_cols=31 Identities=16% Similarity=0.229 Sum_probs=24.9
Q ss_pred CEEECCEEECCCCCEECCCCEEEEEECCCHH
Q ss_conf 9049989932867580489889997056011
Q gi|254780610|r 50 FISINGMVSKNPNRKVVPGDSFLITVPAAQK 80 (340)
Q Consensus 50 ~V~vnG~~~~~~~~~l~~gd~I~i~~~~~~~ 80 (340)
.++|||+.+.+-++.|..||.|.+...+...
T Consensus 417 ga~~ng~~~~Sl~~~L~nG~vVEi~t~k~~~ 447 (741)
T TIGR00691 417 GAKVNGKIVPSLDKELENGDVVEIITGKNSN 447 (741)
T ss_pred EEEECCEEECCCCEEECCCCEEEEEECCCCC
T ss_conf 4689788803445010378689998578877
No 114
>cd01807 GDX_N GDX contains an N-terminal ubiquitin-like domain as well as an uncharacterized c-terminal domain. The function of GDX is unknown.
Probab=28.78 E-value=23 Score=16.03 Aligned_cols=70 Identities=11% Similarity=0.149 Sum_probs=42.9
Q ss_pred CCCCCHHCCCEE-EEEECHHHCCCCHHHHHHHHCCCCCCHHHHHHHHHCCCEEECCEEECCCCCEECCCCEEEEEE
Q ss_conf 976511016249-999571136875789999871768898999999985990499899328675804898899970
Q gi|254780610|r 1 MQQTLDNCSSIK-ISLLSDSTAEGRIDRWLATSLKEQFSRSYVKILILNGFISINGMVSKNPNRKVVPGDSFLITV 75 (340)
Q Consensus 1 ~~~~~~~~~~~~-~~~V~~~~~g~RLD~~L~~~l~~~~sR~~i~kli~~G~V~vnG~~~~~~~~~l~~gd~I~i~~ 75 (340)
||-.+..-++-. .+-|+.++.=.-+..-+..+. ++|-++ +++|-+|++.-|++... +|-+..|+.|.+-+
T Consensus 1 M~I~VKtL~Gk~~~~~v~~~~tV~~lK~~I~ek~--gIP~~q-QRLIf~Gk~L~D~~tL~--dY~I~~~stihLVl 71 (74)
T cd01807 1 MFLTVKLLQGRECSLQVSEKESVSTLKKLVSEHL--NVPEEQ-QRLLFKGKALADDKRLS--DYSIGPNAKLNLVV 71 (74)
T ss_pred CEEEEEECCCCEEEEEECCCCHHHHHHHHHHHHH--CCCHHH-EEEEECCCCCCCCCCHH--HCCCCCCCEEEEEE
T ss_conf 9799990799789999799692999999999887--979689-48886782457888988--80999999999986
No 115
>TIGR02041 CysI sulfite reductase (NADPH) hemoprotein, beta-component; InterPro: IPR011786 Sulphite reductase (NADPH) catalyzes a six electron reduction of sulphite to sulphide in prokaryotic organisms. It is a complex oligomeric enzyme composed of two different peptides with a subunit composition of alpha(8)-beta(4). The alpha component, encoded by cysJ, is a flavoprotein containing both FMN and FAD, while the beta component, encoded by cysI, is a siroheme, iron-sulphur protein.; GO: 0004783 sulfite reductase (NADPH) activity, 0050661 NADP binding, 0051539 4 iron 4 sulfur cluster binding, 0008652 amino acid biosynthetic process, 0009337 sulfite reductase complex (NADPH).
Probab=28.42 E-value=30 Score=15.28 Aligned_cols=24 Identities=13% Similarity=0.092 Sum_probs=17.4
Q ss_pred HHHHCCCCCCHHHHHHHHHCCCEEECCEEECC
Q ss_conf 99871768898999999985990499899328
Q gi|254780610|r 29 LATSLKEQFSRSYVKILILNGFISINGMVSKN 60 (340)
Q Consensus 29 L~~~l~~~~sR~~i~kli~~G~V~vnG~~~~~ 60 (340)
|+..| +||++++. .||+|++++..
T Consensus 159 iSehL---LPrTRAY~-----EIWLD~~KV~g 182 (550)
T TIGR02041 159 ISEHL---LPRTRAYH-----EIWLDEEKVAG 182 (550)
T ss_pred HHHHH---CCCCCCCE-----EEEECCCEECC
T ss_conf 76651---77654441-----46533442147
No 116
>TIGR00223 panD aspartate 1-decarboxylase; InterPro: IPR003190 Decarboxylation of aspartate is the major route of alanine production in bacteria, and is catalysed by the enzyme aspartate decarboxylase. The enzyme is translated as an inactive proenzyme of two chains, A and B. This family contains both chains of aspartate decarboxylase.; GO: 0004068 aspartate 1-decarboxylase activity, 0006523 alanine biosynthetic process.
Probab=27.75 E-value=37 Score=14.74 Aligned_cols=61 Identities=18% Similarity=0.312 Sum_probs=34.5
Q ss_pred CCEEEEEECHHHCCCCHHHHHHHHCCCCCCHHHHHHHHHCCCEEECCEEECCCCCEECCCCEEEEE----ECCCHHCCHH
Q ss_conf 624999957113687578999987176889899999998599049989932867580489889997----0560111102
Q gi|254780610|r 9 SSIKISLLSDSTAEGRIDRWLATSLKEQFSRSYVKILILNGFISINGMVSKNPNRKVVPGDSFLIT----VPAAQKLNIA 84 (340)
Q Consensus 9 ~~~~~~~V~~~~~g~RLD~~L~~~l~~~~sR~~i~kli~~G~V~vnG~~~~~~~~~l~~gd~I~i~----~~~~~~~~~~ 84 (340)
-.+++-+| ....|.|+.+|..- +=.|. +|-|+|||.-+ +.+..||.|.+. ++..+-..+.
T Consensus 40 enekv~Iv-nvnNG~RfsTY~I~----gkkRG-------s~~IcvNGAAA----r~v~~GD~VII~sy~~M~d~Ea~~h~ 103 (127)
T TIGR00223 40 ENEKVDIV-NVNNGKRFSTYVIA----GKKRG-------SRVICVNGAAA----RLVSVGDVVIILSYVTMSDEEARAHK 103 (127)
T ss_pred CCCEEEEE-ECCCCCCEEEEEEC----CCCCC-------CEEEEECHHHH----CEECCCCEEEEEEECCCCHHHHHHCC
T ss_conf 99848998-66899712346651----42358-------72377050451----10023889998851578858875249
Q ss_pred H
Q ss_conf 3
Q gi|254780610|r 85 Q 85 (340)
Q Consensus 85 ~ 85 (340)
|
T Consensus 104 P 104 (127)
T TIGR00223 104 P 104 (127)
T ss_pred C
T ss_conf 8
No 117
>pfam11969 DcpS_C Scavenger mRNA decapping enzyme C-term binding. This family consists of several scavenger mRNA decapping enzymes (DcpS) and is the C-terminal region. DcpS is a scavenger pyrophosphatase that hydrolyses the residual cap structure following 3' to 5' decay of an mRNA. The association of DcpS with 3' to 5' exonuclease exosome components suggests that these two activities are linked and there is a coupled exonucleolytic decay-dependent decapping pathway. The C-terminal domain contains a histidine triad (HIT) sequence with three histidines separated by hydrophobic residues. The central histidine within the DcpS HIT motif is critical for decapping activity and defines the HIT motif as a new mRNA decapping domain, making DcpS the first member of the HIT family of proteins with a defined biological function.
Probab=27.24 E-value=25 Score=15.81 Aligned_cols=18 Identities=33% Similarity=0.643 Sum_probs=13.4
Q ss_pred HHHHCCCCCEEEEEECCC
Q ss_conf 222101440278996240
Q gi|254780610|r 89 PLDILYEDDDIIVINKPA 106 (340)
Q Consensus 89 ~~~IlyED~~llvinKPa 106 (340)
|-++|||||+++++.=-.
T Consensus 13 p~~ivyedd~~vaf~D~~ 30 (113)
T pfam11969 13 PERIVYEDDGFVAFKDIK 30 (113)
T ss_pred CCCEEEECCCEEEEECCC
T ss_conf 778899799999986899
No 118
>KOG0378 consensus
Probab=26.87 E-value=27 Score=15.56 Aligned_cols=47 Identities=21% Similarity=0.244 Sum_probs=30.1
Q ss_pred HHHHHCCCCCCHHHHHHHHHCCCEEECCEEECCCCCEECCCCEEEEE
Q ss_conf 99987176889899999998599049989932867580489889997
Q gi|254780610|r 28 WLATSLKEQFSRSYVKILILNGFISINGMVSKNPNRKVVPGDSFLIT 74 (340)
Q Consensus 28 ~L~~~l~~~~sR~~i~kli~~G~V~vnG~~~~~~~~~l~~gd~I~i~ 74 (340)
||..+|..++.-..+.+.+-+..|.|||+..++..|..-.=|.|.+.
T Consensus 47 ~~~~~Lkya~~~~e~~~I~~qr~i~v~gkvrt~~~yp~g~mDvisie 93 (263)
T KOG0378 47 FLRNRLKYALNGKEVKKILMQREIKVDGKVRTDSTYPAGFMDVISIE 93 (263)
T ss_pred EEEHHHHHHHCCHHHHHHHHHHHHHCCCEEECCCCCCCCEEEEEEEC
T ss_conf 95235555304108889887766530545641666765203688720
No 119
>cd06555 ASCH_PF0470_like ASC-1 homology domain, subfamily similar to Pyrococcus furiosus Pf0470. The ASCH domain, a small beta-barrel domain found in all three kingdoms of life, resembles the RNA-binding PUA domain and may also interact with RNA. ASCH has been proposed to function as an RNA-binding domain during coactivation, RNA-processing and the regulation of prokaryotic translation.
Probab=26.32 E-value=46 Score=14.20 Aligned_cols=35 Identities=20% Similarity=0.184 Sum_probs=27.1
Q ss_pred HHHHHHHCCCEEECCEEECCCCCEECCCCEEEEEE
Q ss_conf 99999985990499899328675804898899970
Q gi|254780610|r 41 YVKILILNGFISINGMVSKNPNRKVVPGDSFLITV 75 (340)
Q Consensus 41 ~i~kli~~G~V~vnG~~~~~~~~~l~~gd~I~i~~ 75 (340)
.+-.+|++|.=+|-++.....-..++.||.|.+.-
T Consensus 8 ~~F~~Ik~G~KtIE~Rl~d~kr~~ik~GD~I~F~~ 42 (109)
T cd06555 8 EPFELIKSGKKTIEIRLNDEKRQQIKVGDKILFND 42 (109)
T ss_pred CHHHHHHCCCCEEEEECCCHHHHHCCCCCEEEEEE
T ss_conf 55899876997799982706787189999999998
No 120
>cd01277 HINT_subgroup HINT (histidine triad nucleotide-binding protein) subgroup: Members of this CD belong to the superfamily of histidine triad hydrolases that act on alpha-phosphate of ribonucleotides. This subgroup includes members from all three forms of cellular life. Although the biochemical function has not been characterised for many of the members of this subgroup, the proteins from Yeast have been shown to be involved in secretion, peroxisome formation and gene expression.
Probab=26.26 E-value=27 Score=15.61 Aligned_cols=17 Identities=35% Similarity=0.630 Sum_probs=12.8
Q ss_pred HHHHHCCCCCEEEEEEC
Q ss_conf 22221014402789962
Q gi|254780610|r 88 IPLDILYEDDDIIVINK 104 (340)
Q Consensus 88 ~~~~IlyED~~llvinK 104 (340)
.|-.|||||++++++.=
T Consensus 12 ~~~~iv~E~e~~~af~d 28 (103)
T cd01277 12 IPSYKVYEDDHVLAFLD 28 (103)
T ss_pred CCCCEEEECCCEEEEEC
T ss_conf 87677997997999977
No 121
>PRK00416 dcd deoxycytidine triphosphate deaminase; Reviewed
Probab=25.23 E-value=50 Score=14.00 Aligned_cols=39 Identities=13% Similarity=0.142 Sum_probs=31.1
Q ss_pred CCHHHHHHHHHCCCEEEC---CEEECCCCCEECCCCEEEEEE
Q ss_conf 898999999985990499---899328675804898899970
Q gi|254780610|r 37 FSRSYVKILILNGFISIN---GMVSKNPNRKVVPGDSFLITV 75 (340)
Q Consensus 37 ~sR~~i~kli~~G~V~vn---G~~~~~~~~~l~~gd~I~i~~ 75 (340)
+|-..|++++++|.+.++ -+.+...++-++-|+.+.++.
T Consensus 2 Lsd~~I~~~~~~g~i~I~Pf~~~~i~p~syDlrLg~~~~v~~ 43 (174)
T PRK00416 2 LSDDDIIRRLAEGRLMIEPFDPEQVRPNGYDLRLGNEFKVFT 43 (174)
T ss_pred CCHHHHHHHHHCCCEEECCCCHHHCCCCEEEEEECCEEEEEE
T ss_conf 887999999974982786999788387437378567889985
No 122
>KOG3275 consensus
Probab=24.74 E-value=29 Score=15.43 Aligned_cols=22 Identities=27% Similarity=0.610 Sum_probs=15.2
Q ss_pred HHHHHHHHHCCCCCEEEEEECC
Q ss_conf 2332222210144027899624
Q gi|254780610|r 84 AQENIPLDILYEDDDIIVINKP 105 (340)
Q Consensus 84 ~~~~~~~~IlyED~~llvinKP 105 (340)
....+|-.||||||..+++.--
T Consensus 24 i~keIPa~ii~Edd~~lAF~Di 45 (127)
T KOG3275 24 IRKEIPAKIIFEDDRCLAFHDI 45 (127)
T ss_pred ECCCCCCCEEEECCCEEEEEEC
T ss_conf 1046773068623546898723
No 123
>cd05126 Mth938 Mth938 domain. Mth938 is a hypothetical protein encoded by the Methanobacterium thermoautotrophicum (Mth) genome. This protein crystallizes as a dimer, although it is monomeric in solution, with one disulfide bond in each monomer. The function of the protein has not been determined.
Probab=24.72 E-value=51 Score=13.95 Aligned_cols=57 Identities=21% Similarity=0.241 Sum_probs=38.1
Q ss_pred HCCCEEECCEEECCCCCEECCCCEEEEEECCC-----HHCCHHHHHHHHHHCCCCCEEEEEECC
Q ss_conf 85990499899328675804898899970560-----111102332222210144027899624
Q gi|254780610|r 47 LNGFISINGMVSKNPNRKVVPGDSFLITVPAA-----QKLNIAQENIPLDILYEDDDIIVINKP 105 (340)
Q Consensus 47 ~~G~V~vnG~~~~~~~~~l~~gd~I~i~~~~~-----~~~~~~~~~~~~~IlyED~~llvinKP 105 (340)
.-|.|.|||+.-+ .+-.|.++..+....... ....+.|+++. .++-++-++|++-.=
T Consensus 6 sfG~i~v~g~~y~-~Dvvv~p~g~~~~~~~~~~k~~~~~h~l~~~dl~-~ll~~~~evlviGTG 67 (117)
T cd05126 6 SFGSITVGGETYE-HDIVVYPDGSRARRWKELSKKTGTSHGLQPEELE-ELLEEGVEVIVIGTG 67 (117)
T ss_pred CCEEEEECCEEEC-CCEEECCCCCEEHHHHHHCCCCCCCCCCCHHHHH-HHHHCCCCEEEECCC
T ss_conf 5328999989832-6789937984432444413534778988999999-999719999998589
No 124
>PRK06488 sulfur carrier protein ThiS; Validated
Probab=24.40 E-value=51 Score=13.91 Aligned_cols=27 Identities=22% Similarity=0.315 Sum_probs=20.6
Q ss_pred CEEECCEEEC---CCCCEECCCCEEEEEEC
Q ss_conf 9049989932---86758048988999705
Q gi|254780610|r 50 FISINGMVSK---NPNRKVVPGDSFLITVP 76 (340)
Q Consensus 50 ~V~vnG~~~~---~~~~~l~~gd~I~i~~~ 76 (340)
.+-|||..+. ..++.|+.||+|.+..+
T Consensus 32 AvAvN~~~Vpr~~~~~~~L~eGDriEIv~p 61 (65)
T PRK06488 32 ATAVNGELVHSEARAQFVLHEGDRIEILSP 61 (65)
T ss_pred EEEECCEEECHHHHCCCCCCCCCEEEEECC
T ss_conf 999899987424505451799999999646
No 125
>TIGR01055 parE_Gneg DNA topoisomerase IV, B subunit; InterPro: IPR005737 DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis , . DNA topoisomerases are divided into two classes: type I enzymes (5.99.1.2 from EC; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (5.99.1.3 from EC; topoisomerases II, IV and VI) break double-strand DNA . Type II topoisomerases are ATP-dependent enzymes, and can be subdivided according to their structure and reaction mechanisms: type IIA (topoisomerase II or gyrase, and topoisomerase IV) and type IIB (topoisomerase VI). These enzymes are responsible for relaxing supercoiled DNA as well as for introducing both negative and positive supercoils . This entry represents subunit B (parE) of topoisomerase IV from Gram negative bacteria. Topoisomerase IV primarily decatenates DNA and relaxes positive supercoils, which is important in bacteria, where the circular chromosome becomes catenated, or linked, during replication . Topoisomerase IV consists of two polypeptide subunits, parC (subunit A), which is homologous to gyrA of topoisomerase II, and parE (subunit B), which is homologous to gyrB of topoisomerase II. More information about this protein can be found at Protein of the Month: DNA Topoisomerase .; GO: 0003677 DNA binding, 0003918 DNA topoisomerase (ATP-hydrolyzing) activity, 0005524 ATP binding, 0006265 DNA topological change, 0005694 chromosome.
Probab=23.70 E-value=53 Score=13.83 Aligned_cols=31 Identities=16% Similarity=0.196 Sum_probs=20.5
Q ss_pred HHHHHHCCCCCCHHHHHHHHHCCCEEECCEEEC
Q ss_conf 999987176889899999998599049989932
Q gi|254780610|r 27 RWLATSLKEQFSRSYVKILILNGFISINGMVSK 59 (340)
Q Consensus 27 ~~L~~~l~~~~sR~~i~kli~~G~V~vnG~~~~ 59 (340)
+|...+. .+|-++++.+++.+.+...|--++
T Consensus 175 ~~F~~k~--~F~~~~l~~~~raKA~L~~Gv~I~ 205 (647)
T TIGR01055 175 EIFDSKL--KFSVSRLYHILRAKAVLCRGVEIE 205 (647)
T ss_pred CHHCCCC--CCCHHHHHHHHHHHHHCCCCCEEE
T ss_conf 0103122--557899999986324202672078
No 126
>TIGR00844 c_cpa1 sodium/hydrogen antiporter; InterPro: IPR004712 Na^+/H^+ exchange proteins eject protons from cells, effectively eliminating excess acid from actively metabolising cells. Na^+/H^+ exchange activity is also crucial for the regulation of cell volume, and for the reabsorption of NaCl across renal, intestinal, and other epithelia. These antiports exchange Na^+ for H^+ in an electroneutral manner, and this activity is carried out by a family of Na^+/H^+ exchangers, or NHEs, which are known to be present in both prokaryotic and eukaryotic cells. In mammalian cells, Na^+/H^+ exchange activity is found in both the plasma membrane and inner mitochondrial membrane. To date, six mammalian isoforms have been identified (designated NHE1-NHE6) , . These exchangers are highly-regulated (glyco)phosphoproteins, which, based on their primary structure, appear to contain 10-12 membrane-spanning regions (M) at the N-terminus and a large cytoplasmic region at the C-terminus. The transmembrane regions M3-M12 share identity with other members of the family. The M6 and M7 regions are highly conserved. Thus, this is thought to be the region that is involved in the transport of sodium and hydrogen ions. The cytoplasmic region has little similarity throughout the family. There is some evidence that the exchangers may exist in the cell membrane as homodimers, but little is currently known about the mechanism of their antiport . This group is specific for the fungal members of this family. ; GO: 0015385 sodium:hydrogen antiporter activity, 0006814 sodium ion transport, 0016021 integral to membrane.
Probab=23.42 E-value=32 Score=15.11 Aligned_cols=14 Identities=14% Similarity=0.095 Sum_probs=5.4
Q ss_pred CHHHHHHHHHHHHH
Q ss_conf 03578888999997
Q gi|254780610|r 161 NDLAHQKLSEQFVD 174 (340)
Q Consensus 161 ~~~a~~~l~~~f~~ 174 (340)
+|.+...|++....
T Consensus 765 ~P~sL~kl~~~~~~ 778 (923)
T TIGR00844 765 SPPSLEKLHQITNE 778 (923)
T ss_pred CCCCHHHHHHHHHH
T ss_conf 78415789999987
No 127
>pfam04669 DUF579 Protein of unknown function (DUF579). This is a eukaryotic family of uncharacterized proteins.
Probab=22.59 E-value=56 Score=13.70 Aligned_cols=22 Identities=27% Similarity=0.684 Sum_probs=16.6
Q ss_pred HHHHHHCCCCCE-EEEEECCCHHH
Q ss_conf 222221014402-78996240111
Q gi|254780610|r 87 NIPLDILYEDDD-IIVINKPAGLV 109 (340)
Q Consensus 87 ~~~~~IlyED~~-llvinKPaGl~ 109 (340)
++| ..+|+-++ +++||.|.|..
T Consensus 103 ~lP-~~vy~~~WDvi~VD~P~G~~ 125 (187)
T pfam04669 103 DLP-NEVYKEKWDRIFVDAPEGYV 125 (187)
T ss_pred CCC-HHHHCCCCCEEEEECCCCCC
T ss_conf 598-89955706689980899989
No 128
>TIGR02013 rpoB DNA-directed RNA polymerase, beta subunit; InterPro: IPR010243 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length . The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kD, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. This entry describes orthologues of the beta subunit of bacterial RNA polymerase. The core enzyme consists of two alpha chains, one beta chain, and one beta' subunit.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006350 transcription.
Probab=21.91 E-value=36 Score=14.86 Aligned_cols=22 Identities=23% Similarity=0.369 Sum_probs=16.3
Q ss_pred CCCEEEEECCCCHHHHHHHHHHH
Q ss_conf 97689998499789999999885
Q gi|254780610|r 316 NNQDMDFQVPIPEDMLTVIRKLN 338 (340)
Q Consensus 316 t~~~~~f~aplP~~~~~~l~~L~ 338 (340)
.|+. ..++-+|+-|+=++|+|+
T Consensus 1420 KGe~-~~epGiPESFnVL~kElq 1441 (1449)
T TIGR02013 1420 KGEN-LPEPGIPESFNVLIKELQ 1441 (1449)
T ss_pred CCCC-CCCCCCCCCHHHHHHHHH
T ss_conf 4688-765446841579999997
No 129
>COG4043 Preprotein translocase subunit Sec61beta [Intracellular trafficking, secretion, and vesicular transport]
Probab=21.07 E-value=60 Score=13.51 Aligned_cols=37 Identities=24% Similarity=0.307 Sum_probs=26.4
Q ss_pred HHHHHHHHHCCCEEECCEEECCCCCEECCCCEEEEEE
Q ss_conf 8999999985990499899328675804898899970
Q gi|254780610|r 39 RSYVKILILNGFISINGMVSKNPNRKVVPGDSFLITV 75 (340)
Q Consensus 39 R~~i~kli~~G~V~vnG~~~~~~~~~l~~gd~I~i~~ 75 (340)
+.---.+|.+|+-+|.++..-..-+.+++||.|.++.
T Consensus 8 ~eeylE~IK~GkK~iEvRl~d~krr~ik~GD~IiF~~ 44 (111)
T COG4043 8 REEYLELIKAGKKKIEVRLADPKRRQIKPGDKIIFNG 44 (111)
T ss_pred HHHHHHHHHCCCCEEEEEECCHHHCCCCCCCEEEECC
T ss_conf 7889999870443689995577662789899899838
No 130
>pfam02495 7kD_coat 7kD viral coat protein. This family consists of a 7kD coat protein from carlavirus and potexvirus.
Probab=20.50 E-value=62 Score=13.44 Aligned_cols=24 Identities=4% Similarity=0.275 Sum_probs=20.0
Q ss_pred CCCCEEEEE-CCCCHHHHHHHHHHH
Q ss_conf 897689998-499789999999885
Q gi|254780610|r 315 RNNQDMDFQ-VPIPEDMLTVIRKLN 338 (340)
Q Consensus 315 ~t~~~~~f~-aplP~~~~~~l~~L~ 338 (340)
+|||-.+|. ++.+++|-+.++.|+
T Consensus 31 ITGeSv~i~gC~~~~~~ie~~~~Lk 55 (59)
T pfam02495 31 ITGESVTITGCEFTPEFIEALKGLK 55 (59)
T ss_pred EECCEEEEECCEECHHHHHHHHHCC
T ss_conf 9776899985160899999996266
No 131
>cd01089 PA2G4-like Related to aminopepdidase M, this family contains proliferation-associated protein 2G4. Family members have been implicated in cell cycle control.
Probab=20.37 E-value=62 Score=13.42 Aligned_cols=26 Identities=27% Similarity=0.327 Sum_probs=18.4
Q ss_pred CEEECCEEECC------CCCEECCCCEEEEEE
Q ss_conf 90499899328------675804898899970
Q gi|254780610|r 50 FISINGMVSKN------PNRKVVPGDSFLITV 75 (340)
Q Consensus 50 ~V~vnG~~~~~------~~~~l~~gd~I~i~~ 75 (340)
+++||...+.- .++.|+.||.|.++.
T Consensus 62 CiSvNe~v~HGiP~~~~~~~~L~~GDiV~iD~ 93 (228)
T cd01089 62 CISVNNCVCHFSPLKSDATYTLKDGDVVKIDL 93 (228)
T ss_pred EECCCCEEECCCCCCCCCCCCCCCCCEEEEEE
T ss_conf 75025444568999888873546899899977
No 132
>cd04687 Nudix_Hydrolase_28 Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, where U = I, L or V), which functions as a metal binding and catalytic site. Substrates of nudix hydrolases include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the nudix hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance & "house-cleaning" enzymes. Substrate specificity is used to define families within the superfamily. Differences in substrate
Probab=20.23 E-value=63 Score=13.40 Aligned_cols=42 Identities=26% Similarity=0.573 Sum_probs=28.3
Q ss_pred HCCCCCEEEEEE--CCCHHH-CCCCCCCCCC-CCHHHHHHHHCCCC
Q ss_conf 101440278996--240111-0456787542-10022222210244
Q gi|254780610|r 92 ILYEDDDIIVIN--KPAGLV-VHPAPGNWTG-TLVNALLYHCHNNL 133 (340)
Q Consensus 92 IlyED~~llvin--KPaGl~-vhp~~~~~~~-tl~~~l~~~~~~~~ 133 (340)
||.+|+.+|++- .+.+.- +-|+++...| |+.+++.+.+.++.
T Consensus 7 vI~~~~~vLL~r~~~~~~~~w~lPGG~ve~GEt~~~Al~RE~~EEt 52 (128)
T cd04687 7 VIIKNDKILLIKHHDDGGVWYILPGGGQEPGETLEDAAHRECKEEI 52 (128)
T ss_pred EEEECCEEEEEEECCCCCCEEECCCCCCCCCCCHHHHHHHHHHHHH
T ss_conf 9998999999998369981698988667699799999999887863
Done!