Query psy230
Match_columns 222
No_of_seqs 142 out of 649
Neff 6.8
Searched_HMMs 46136
Date Fri Aug 16 21:11:37 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy230.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/230hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1004|consensus 100.0 6E-59 1.3E-63 385.9 23.3 219 1-221 5-228 (230)
2 COG1097 RRP4 RNA-binding prote 100.0 3.6E-58 7.9E-63 390.4 24.2 209 1-221 12-225 (239)
3 PRK04163 exosome complex RNA-b 100.0 2E-51 4.3E-56 354.2 23.8 208 1-221 12-224 (235)
4 KOG3013|consensus 100.0 1.2E-39 2.6E-44 277.6 11.6 169 1-185 33-212 (301)
5 cd05790 S1_Rrp40 S1_Rrp40: Rrp 100.0 1.8E-31 4E-36 196.3 10.3 86 51-136 1-86 (86)
6 PRK09521 exosome complex RNA-b 99.9 6.6E-25 1.4E-29 183.5 16.0 139 1-148 9-166 (189)
7 COG1096 Predicted RNA-binding 99.9 7.2E-24 1.6E-28 174.4 14.0 127 1-136 9-148 (188)
8 KOG3409|consensus 99.8 1.7E-20 3.6E-25 152.2 11.4 144 1-151 9-175 (193)
9 cd05791 S1_CSL4 S1_CSL4: CSL4, 99.8 5.8E-19 1.3E-23 131.7 8.6 80 52-136 2-92 (92)
10 cd04454 S1_Rrp4_like S1_Rrp4_l 99.8 2.2E-18 4.7E-23 125.2 9.1 81 51-136 1-82 (82)
11 cd05789 S1_Rrp4 S1_Rrp4: Rrp4 99.6 7.6E-15 1.6E-19 107.3 8.2 81 51-136 1-86 (86)
12 PF10447 EXOSC1: Exosome compo 99.3 4.6E-12 9.9E-17 92.5 5.9 60 53-113 1-82 (82)
13 PF14382 ECR1_N: Exosome compl 99.0 6.2E-10 1.3E-14 70.2 3.6 36 1-38 3-38 (39)
14 cd05687 S1_RPS1_repeat_ec1_hs1 98.7 8.6E-08 1.9E-12 66.9 8.2 67 57-123 1-69 (70)
15 cd05704 S1_Rrp5_repeat_hs13 S1 98.7 1.1E-07 2.5E-12 67.3 7.7 68 55-123 2-71 (72)
16 smart00316 S1 Ribosomal protei 98.6 1.8E-07 3.9E-12 64.0 7.7 69 55-123 1-71 (72)
17 cd05691 S1_RPS1_repeat_ec6 S1_ 98.6 3.3E-07 7.1E-12 64.1 8.4 69 57-125 1-71 (73)
18 cd04452 S1_IF2_alpha S1_IF2_al 98.6 3.7E-07 7.9E-12 64.5 8.2 71 54-124 1-75 (76)
19 cd05692 S1_RPS1_repeat_hs4 S1_ 98.6 4.8E-07 1E-11 62.0 8.1 67 57-123 1-68 (69)
20 PF00575 S1: S1 RNA binding do 98.5 9.6E-07 2.1E-11 62.1 7.9 70 54-123 2-73 (74)
21 cd05706 S1_Rrp5_repeat_sc10 S1 98.5 1.8E-06 4E-11 60.6 9.2 69 55-123 2-72 (73)
22 cd05702 S1_Rrp5_repeat_hs11_sc 98.4 1E-06 2.2E-11 61.8 7.1 61 57-117 1-64 (70)
23 cd05708 S1_Rrp5_repeat_sc12 S1 98.4 3.1E-06 6.7E-11 59.6 8.3 71 55-125 1-74 (77)
24 PRK08582 hypothetical protein; 98.3 4.6E-06 1E-10 66.7 9.9 72 54-125 3-75 (139)
25 PRK07252 hypothetical protein; 98.3 4.1E-06 8.9E-11 65.4 9.3 71 55-125 2-74 (120)
26 cd05707 S1_Rrp5_repeat_sc11 S1 98.3 2.6E-06 5.6E-11 59.2 7.3 65 57-121 1-67 (68)
27 PRK08563 DNA-directed RNA poly 98.3 3.7E-06 8E-11 70.1 8.5 80 51-136 76-173 (187)
28 cd05705 S1_Rrp5_repeat_hs14 S1 98.3 4.6E-06 1E-10 59.5 7.8 67 55-121 2-73 (74)
29 PRK08059 general stress protei 98.3 5.3E-06 1.1E-10 64.8 8.8 72 54-125 5-78 (123)
30 cd05693 S1_Rrp5_repeat_hs1_sc1 98.2 3.8E-06 8.2E-11 63.5 6.7 70 55-124 2-95 (100)
31 cd05698 S1_Rrp5_repeat_hs6_sc5 98.2 1.3E-05 2.9E-10 55.6 8.0 67 57-123 1-69 (70)
32 PRK03987 translation initiatio 98.2 9.9E-06 2.2E-10 71.2 9.0 74 52-125 4-81 (262)
33 cd05686 S1_pNO40 S1_pNO40: pNO 98.2 1.6E-05 3.4E-10 56.3 8.4 70 54-123 1-72 (73)
34 cd05703 S1_Rrp5_repeat_hs12_sc 98.1 1.5E-05 3.2E-10 56.6 8.0 68 57-124 1-72 (73)
35 cd04461 S1_Rrp5_repeat_hs8_sc7 98.1 1.3E-05 2.9E-10 57.9 7.8 72 52-123 10-83 (83)
36 TIGR00448 rpoE DNA-directed RN 98.1 1.8E-05 3.8E-10 65.7 8.8 81 51-137 76-174 (179)
37 COG1098 VacB Predicted RNA bin 98.1 5.1E-06 1.1E-10 64.7 5.1 73 53-125 2-75 (129)
38 PRK05807 hypothetical protein; 98.1 2.9E-05 6.2E-10 61.9 9.3 70 55-125 4-74 (136)
39 cd05688 S1_RPS1_repeat_ec3 S1_ 98.1 1.4E-05 3.1E-10 54.6 6.6 60 56-116 1-61 (68)
40 cd04472 S1_PNPase S1_PNPase: P 98.1 2.8E-05 6.1E-10 53.2 8.0 66 57-122 1-67 (68)
41 cd05685 S1_Tex S1_Tex: The C-t 98.0 1.8E-05 3.9E-10 54.0 6.5 65 57-121 1-67 (68)
42 PHA02945 interferon resistance 98.0 4.5E-05 9.7E-10 56.1 8.3 70 53-125 8-83 (88)
43 cd05697 S1_Rrp5_repeat_hs5 S1_ 98.0 3.8E-05 8.2E-10 53.4 7.7 66 57-122 1-68 (69)
44 cd05694 S1_Rrp5_repeat_hs2_sc2 98.0 7.3E-05 1.6E-09 53.3 9.1 66 55-125 3-70 (74)
45 cd00164 S1_like S1_like: Ribos 98.0 2.7E-05 5.8E-10 52.0 6.1 56 60-115 1-57 (65)
46 cd04453 S1_RNase_E S1_RNase_E: 98.0 5.3E-05 1.2E-09 55.9 8.2 71 54-124 5-82 (88)
47 cd02393 PNPase_KH Polynucleoti 98.0 1.4E-05 2.9E-10 55.0 4.7 47 141-189 5-51 (61)
48 cd05695 S1_Rrp5_repeat_hs3 S1_ 97.9 6.8E-05 1.5E-09 52.1 7.8 59 57-116 1-59 (66)
49 cd04455 S1_NusA S1_NusA: N-uti 97.9 8.8E-05 1.9E-09 51.6 8.3 56 55-116 2-57 (67)
50 PTZ00248 eukaryotic translatio 97.9 5.1E-05 1.1E-09 68.4 8.3 94 52-145 13-117 (319)
51 cd05684 S1_DHX8_helicase S1_DH 97.8 0.00024 5.1E-09 50.7 8.5 68 57-125 1-73 (79)
52 COG1095 RPB7 DNA-directed RNA 97.7 0.00015 3.3E-09 60.3 7.4 81 51-137 76-174 (183)
53 cd05690 S1_RPS1_repeat_ec5 S1_ 97.7 0.0002 4.4E-09 49.3 6.7 60 57-116 1-62 (69)
54 COG1093 SUI2 Translation initi 97.6 7.6E-05 1.6E-09 65.1 5.1 149 50-207 5-209 (269)
55 cd04473 S1_RecJ_like S1_RecJ_l 97.6 0.0011 2.3E-08 47.3 9.9 64 53-123 13-76 (77)
56 cd04460 S1_RpoE S1_RpoE: RpoE, 97.6 0.00034 7.5E-09 52.2 7.5 73 58-136 1-91 (99)
57 cd05696 S1_Rrp5_repeat_hs4 S1_ 97.6 0.0006 1.3E-08 47.9 8.0 67 57-123 1-71 (71)
58 cd04465 S1_RPS1_repeat_ec2_hs2 97.5 0.00052 1.1E-08 47.4 7.4 65 57-123 1-66 (67)
59 PRK07400 30S ribosomal protein 97.5 0.00031 6.8E-09 63.4 7.9 74 52-125 27-102 (318)
60 PRK11824 polynucleotide phosph 97.5 0.00064 1.4E-08 67.4 9.6 98 23-124 591-690 (693)
61 cd05689 S1_RPS1_repeat_ec4 S1_ 97.4 0.0011 2.4E-08 46.2 7.7 62 55-116 2-65 (72)
62 PTZ00162 DNA-directed RNA poly 97.4 0.00098 2.1E-08 55.4 8.2 81 51-137 76-172 (176)
63 TIGR02696 pppGpp_PNP guanosine 97.4 0.00063 1.4E-08 67.2 8.2 70 53-122 644-718 (719)
64 COG0539 RpsA Ribosomal protein 97.4 0.00051 1.1E-08 65.9 7.2 72 53-125 189-262 (541)
65 PRK07400 30S ribosomal protein 97.3 0.0015 3.3E-08 59.0 8.7 73 52-125 192-266 (318)
66 TIGR03591 polynuc_phos polyrib 97.2 0.00089 1.9E-08 66.3 7.5 65 53-117 615-680 (684)
67 PRK06299 rpsA 30S ribosomal pr 97.1 0.003 6.6E-08 60.9 9.6 71 55-125 372-445 (565)
68 PRK13806 rpsA 30S ribosomal pr 97.1 0.003 6.6E-08 60.2 9.2 73 53-125 199-277 (491)
69 cd04471 S1_RNase_R S1_RNase_R: 97.0 0.0063 1.4E-07 43.1 8.4 67 56-122 1-81 (83)
70 TIGR00717 rpsA ribosomal prote 97.0 0.0027 5.8E-08 60.5 8.3 68 54-125 16-84 (516)
71 PRK06676 rpsA 30S ribosomal pr 97.0 0.0037 8E-08 57.6 8.8 73 53-125 14-89 (390)
72 PRK07899 rpsA 30S ribosomal pr 96.9 0.0036 7.9E-08 59.6 8.5 72 54-125 33-106 (486)
73 PRK06676 rpsA 30S ribosomal pr 96.9 0.0037 7.9E-08 57.6 8.2 72 53-125 189-262 (390)
74 PRK07899 rpsA 30S ribosomal pr 96.9 0.0049 1.1E-07 58.8 8.9 71 54-125 206-278 (486)
75 PRK06299 rpsA 30S ribosomal pr 96.9 0.0048 1E-07 59.5 8.7 71 55-125 459-531 (565)
76 PRK13806 rpsA 30S ribosomal pr 96.8 0.0088 1.9E-07 57.0 10.1 72 54-125 290-364 (491)
77 PRK12327 nusA transcription el 96.8 0.0037 7.9E-08 57.5 7.1 69 51-125 129-200 (362)
78 COG0539 RpsA Ribosomal protein 96.7 0.0064 1.4E-07 58.5 8.4 95 50-146 15-127 (541)
79 PRK00087 4-hydroxy-3-methylbut 96.7 0.0071 1.5E-07 59.5 8.9 71 54-125 475-547 (647)
80 PRK00087 4-hydroxy-3-methylbut 96.7 0.0096 2.1E-07 58.6 9.7 75 51-125 297-373 (647)
81 TIGR00717 rpsA ribosomal prote 96.7 0.027 5.9E-07 53.6 12.4 72 54-125 270-344 (516)
82 cd02394 vigilin_like_KH K homo 96.7 0.0031 6.7E-08 42.8 4.2 44 141-186 3-50 (62)
83 PLN00207 polyribonucleotide nu 96.4 0.01 2.3E-07 60.1 8.1 73 53-125 750-824 (891)
84 PRK12269 bifunctional cytidyla 96.4 0.015 3.3E-07 59.0 8.8 63 54-124 319-381 (863)
85 TIGR00757 RNaseEG ribonuclease 96.1 0.052 1.1E-06 50.8 10.4 71 53-123 22-108 (414)
86 PRK09202 nusA transcription el 96.1 0.017 3.7E-07 54.9 7.1 69 51-125 129-200 (470)
87 TIGR01953 NusA transcription t 96.1 0.02 4.3E-07 52.3 7.1 70 50-125 125-198 (341)
88 COG2183 Tex Transcriptional ac 96.0 0.02 4.3E-07 56.9 7.3 73 54-126 656-730 (780)
89 cd04462 S1_RNAPII_Rpb7 S1_RNAP 96.0 0.034 7.5E-07 40.9 6.9 59 56-114 1-70 (88)
90 PRK12269 bifunctional cytidyla 95.8 0.031 6.7E-07 56.8 7.8 72 54-125 576-650 (863)
91 cd00105 KH-I K homology RNA-bi 95.5 0.038 8.3E-07 37.1 5.0 44 141-186 3-52 (64)
92 PRK12328 nusA transcription el 95.4 0.059 1.3E-06 49.8 7.4 60 51-116 133-193 (374)
93 PF00013 KH_1: KH domain syndr 95.1 0.042 9.1E-07 36.8 4.3 51 141-194 3-56 (60)
94 PRK12329 nusA transcription el 94.5 0.15 3.2E-06 48.1 7.6 61 51-116 147-212 (449)
95 KOG1070|consensus 93.5 0.47 1E-05 50.2 9.5 71 55-125 1161-1233(1710)
96 smart00322 KH K homology RNA-b 93.3 0.3 6.5E-06 32.2 5.5 58 140-200 5-66 (69)
97 TIGR03591 polynuc_phos polyrib 92.6 0.28 6E-06 48.9 6.3 58 140-199 553-610 (684)
98 KOG1856|consensus 92.4 0.18 3.9E-06 52.2 4.7 72 55-126 984-1060(1299)
99 PRK11642 exoribonuclease R; Pr 92.2 0.94 2E-05 46.0 9.6 83 54-136 641-737 (813)
100 TIGR02063 RNase_R ribonuclease 91.7 0.81 1.8E-05 45.7 8.5 70 53-122 624-707 (709)
101 COG1185 Pnp Polyribonucleotide 91.3 0.6 1.3E-05 46.1 6.8 74 52-125 615-689 (692)
102 PRK13763 putative RNA-processi 90.6 0.86 1.9E-05 37.8 6.3 61 140-202 5-69 (180)
103 PRK11712 ribonuclease G; Provi 90.4 2.6 5.7E-05 40.4 10.2 72 52-123 34-121 (489)
104 TIGR03665 arCOG04150 arCOG0415 90.2 0.68 1.5E-05 38.1 5.3 59 142-202 2-63 (172)
105 PRK10811 rne ribonuclease E; R 90.1 2.7 5.9E-05 43.4 10.3 70 54-123 36-118 (1068)
106 TIGR02696 pppGpp_PNP guanosine 89.5 0.89 1.9E-05 45.5 6.4 60 140-201 580-639 (719)
107 PHA02858 EIF2a-like PKR inhibi 88.9 1.7 3.7E-05 31.9 5.9 63 53-117 13-78 (86)
108 cd05699 S1_Rrp5_repeat_hs7 S1_ 87.7 2.7 5.8E-05 29.9 6.2 66 57-123 1-71 (72)
109 cd02395 SF1_like-KH Splicing f 87.0 1.4 3.1E-05 34.3 4.9 52 147-200 15-91 (120)
110 PF13509 S1_2: S1 domain; PDB: 86.2 4.4 9.4E-05 27.4 6.5 60 56-123 1-60 (61)
111 cd02396 PCBP_like_KH K homolog 85.7 2.1 4.6E-05 29.1 4.8 37 142-180 4-40 (65)
112 TIGR00358 3_prime_RNase VacB a 85.2 3 6.5E-05 41.4 7.3 70 53-122 569-652 (654)
113 KOG1070|consensus 84.7 1.7 3.7E-05 46.3 5.4 69 49-118 878-950 (1710)
114 cd03524 RPA2_OBF_family RPA2_O 84.5 5.5 0.00012 26.0 6.4 64 60-123 2-70 (75)
115 KOG3298|consensus 82.5 11 0.00024 31.0 8.3 65 50-114 75-150 (170)
116 PRK04012 translation initiatio 82.0 8.2 0.00018 29.1 6.9 57 53-114 17-74 (100)
117 PF08292 RNA_pol_Rbc25: RNA po 81.2 4.6 0.0001 31.5 5.5 61 54-114 1-75 (122)
118 PF10246 MRP-S35: Mitochondria 81.0 7.2 0.00016 29.7 6.2 53 54-112 21-73 (104)
119 PF01336 tRNA_anti-codon: OB-f 80.9 4.4 9.5E-05 27.4 4.9 62 60-123 3-69 (75)
120 KOG3297|consensus 80.1 8.3 0.00018 32.4 6.9 62 52-113 77-156 (202)
121 smart00652 eIF1a eukaryotic tr 78.9 12 0.00025 27.2 6.7 55 54-113 2-57 (83)
122 cd04456 S1_IF1A_like S1_IF1A_l 77.1 22 0.00048 25.5 7.6 50 60-113 2-52 (78)
123 PF01176 eIF-1a: Translation i 77.1 6 0.00013 27.2 4.5 52 57-114 2-56 (65)
124 PF01959 DHQS: 3-dehydroquinat 76.5 30 0.00065 31.9 10.1 92 2-116 249-342 (354)
125 KOG3038|consensus 75.6 11 0.00024 33.2 6.7 74 42-149 116-189 (264)
126 COG2996 Predicted RNA-bindinin 74.1 13 0.00028 33.1 6.8 31 95-125 187-217 (287)
127 cd05793 S1_IF1A S1_IF1A: Trans 73.9 15 0.00032 26.3 6.0 50 60-113 2-52 (77)
128 PLN00208 translation initiatio 73.8 14 0.00031 29.8 6.5 57 53-114 28-85 (145)
129 PF07494 Reg_prop: Two compone 72.9 4.5 9.8E-05 22.2 2.5 18 169-186 6-23 (24)
130 PRK13763 putative RNA-processi 71.9 21 0.00045 29.5 7.3 69 148-220 105-174 (180)
131 TIGR03665 arCOG04150 arCOG0415 71.7 27 0.00058 28.6 7.9 70 147-220 98-168 (172)
132 TIGR00008 infA translation ini 70.4 24 0.00053 24.8 6.3 52 60-114 7-59 (68)
133 PRK02290 3-dehydroquinate synt 70.3 59 0.0013 29.9 10.4 92 2-116 239-332 (344)
134 PF15057 DUF4537: Domain of un 68.7 53 0.0011 25.5 9.4 48 62-110 17-66 (124)
135 COG2932 Predicted transcriptio 66.0 51 0.0011 27.6 8.7 65 2-69 139-211 (214)
136 COG1094 Predicted RNA-binding 65.3 36 0.00077 28.8 7.4 71 141-213 11-87 (194)
137 COG0361 InfA Translation initi 65.3 30 0.00066 24.8 6.0 55 57-114 6-61 (75)
138 COG1096 Predicted RNA-binding 65.3 32 0.0007 28.9 7.1 30 95-125 57-86 (188)
139 cd05791 S1_CSL4 S1_CSL4: CSL4, 65.0 9.1 0.0002 28.1 3.4 28 55-82 62-90 (92)
140 PLN00207 polyribonucleotide nu 63.6 9.2 0.0002 39.4 4.2 61 139-201 686-747 (891)
141 PF10447 EXOSC1: Exosome compo 63.4 14 0.0003 26.8 4.1 25 101-125 3-28 (82)
142 TIGR00523 eIF-1A eukaryotic/ar 62.8 63 0.0014 24.3 8.0 53 51-109 11-67 (99)
143 PRK12442 translation initiatio 62.2 36 0.00079 25.1 6.0 53 60-115 9-62 (87)
144 cd05841 BS69_related The PWWP 61.7 5.7 0.00012 29.0 1.8 18 97-114 4-21 (83)
145 PF03625 DUF302: Domain of unk 59.3 26 0.00056 23.6 4.7 42 140-187 21-64 (65)
146 KOG4134|consensus 59.1 13 0.00029 32.2 3.8 69 43-115 94-162 (253)
147 COG1185 Pnp Polyribonucleotide 57.5 24 0.00052 35.2 5.8 63 138-202 552-614 (692)
148 cd04489 ExoVII_LU_OBF ExoVII_L 56.7 60 0.0013 22.1 7.4 63 60-123 4-71 (78)
149 PF01436 NHL: NHL repeat; Int 56.2 15 0.00033 20.7 2.6 19 168-186 2-20 (28)
150 PTZ00329 eukaryotic translatio 55.1 53 0.0012 26.8 6.5 53 53-110 28-81 (155)
151 PF01835 A2M_N: MG2 domain; I 53.8 15 0.00033 26.5 3.0 35 95-129 6-48 (99)
152 COG1315 Uncharacterized conser 53.5 20 0.00043 34.6 4.3 100 13-113 220-337 (543)
153 PRK00276 infA translation init 53.4 74 0.0016 22.1 6.9 52 60-114 9-61 (72)
154 PRK05435 rpmA 50S ribosomal pr 53.0 40 0.00086 24.6 4.9 37 2-38 33-70 (82)
155 CHL00121 rpl27 ribosomal prote 52.8 32 0.0007 25.3 4.4 46 2-47 33-83 (86)
156 CHL00010 infA translation init 51.4 86 0.0019 22.3 6.6 52 60-114 9-61 (78)
157 cd04482 RPA2_OBF_like RPA2_OBF 51.2 51 0.0011 24.0 5.4 49 60-109 3-57 (91)
158 smart00293 PWWP domain with co 50.0 11 0.00024 25.5 1.6 15 100-114 1-15 (63)
159 PF12508 DUF3714: Protein of u 49.1 99 0.0021 26.2 7.5 54 23-78 51-109 (200)
160 PF13014 KH_3: KH domain 49.1 11 0.00023 23.3 1.3 27 149-177 2-28 (43)
161 COG1530 CafA Ribonucleases G a 48.3 36 0.00079 32.7 5.3 71 55-125 36-114 (487)
162 PRK11824 polynucleotide phosph 48.3 22 0.00047 35.7 3.9 59 140-203 556-614 (693)
163 PF03961 DUF342: Protein of un 47.2 46 0.001 31.3 5.8 34 13-47 144-180 (451)
164 cd05834 HDGF_related The PWWP 46.4 13 0.00029 26.8 1.6 16 99-114 2-17 (83)
165 cd04491 SoSSB_OBF SoSSB_OBF: A 45.5 1E+02 0.0022 21.4 7.8 25 97-123 46-73 (82)
166 cd04466 S1_YloQ_GTPase S1_YloQ 45.1 74 0.0016 21.1 5.2 44 62-110 3-48 (68)
167 PLN02800 imidazoleglycerol-pho 43.7 76 0.0016 28.1 6.1 44 157-202 100-145 (261)
168 cd05836 N_Pac_NP60 The PWWP do 43.5 15 0.00032 26.7 1.5 15 100-114 1-15 (86)
169 cd05840 SPBC215_ISWI_like The 42.8 15 0.00033 27.1 1.5 15 100-114 1-15 (93)
170 PF01016 Ribosomal_L27: Riboso 42.7 43 0.00094 24.3 3.8 38 1-38 31-69 (81)
171 PF13742 tRNA_anti_2: OB-fold 42.2 1.4E+02 0.003 22.0 7.6 65 59-124 25-95 (99)
172 COG0557 VacB Exoribonuclease R 42.1 1.3E+02 0.0029 30.2 8.4 69 55-123 621-703 (706)
173 cd07914 IGPD Imidazoleglycerol 41.3 66 0.0014 27.1 5.2 44 157-202 34-79 (190)
174 PF14398 ATPgrasp_YheCD: YheC/ 41.3 16 0.00034 32.0 1.5 16 168-183 211-226 (262)
175 PRK00951 hisB imidazoleglycero 40.5 96 0.0021 26.3 6.1 44 157-202 38-83 (195)
176 PRK06763 F0F1 ATP synthase sub 40.1 1.5E+02 0.0032 25.3 7.1 21 57-77 39-59 (213)
177 COG2810 Predicted type IV rest 39.8 45 0.00097 29.4 4.0 54 131-185 59-112 (284)
178 PF07208 DUF1414: Protein of u 39.5 62 0.0013 20.8 3.7 31 192-222 10-42 (44)
179 PF14069 SpoVIF: Stage VI spor 39.4 48 0.001 24.0 3.6 34 187-220 11-44 (79)
180 KOG1067|consensus 39.0 70 0.0015 31.6 5.6 72 52-123 659-736 (760)
181 COG0131 HisB Imidazoleglycerol 38.2 1.4E+02 0.003 25.3 6.5 76 107-202 5-84 (195)
182 PF04319 NifZ: NifZ domain; I 38.2 67 0.0015 23.0 4.1 21 96-116 1-21 (75)
183 PF07116 DUF1372: Protein of u 38.1 72 0.0016 24.2 4.4 44 55-106 53-98 (104)
184 PRK10553 assembly protein for 37.5 1.6E+02 0.0035 21.5 6.8 56 138-203 8-65 (87)
185 PF10844 DUF2577: Protein of u 36.8 85 0.0018 23.3 4.8 22 55-78 15-36 (100)
186 cd05835 Dnmt3b_related The PWW 36.5 23 0.00049 25.7 1.5 15 100-114 1-15 (87)
187 TIGR00638 Mop molybdenum-pteri 36.2 1.1E+02 0.0024 20.2 4.9 50 57-112 6-61 (69)
188 cd04454 S1_Rrp4_like S1_Rrp4_l 36.1 76 0.0017 22.0 4.3 31 52-82 49-80 (82)
189 PRK05054 exoribonuclease II; P 35.9 1.1E+02 0.0025 30.3 6.8 63 54-116 557-635 (644)
190 PF05257 CHAP: CHAP domain; I 35.8 42 0.00092 25.3 3.1 27 50-76 59-97 (124)
191 PF01938 TRAM: TRAM domain; I 34.3 1.4E+02 0.0029 19.6 5.1 23 53-75 37-59 (61)
192 PHA00691 hypothetical protein 34.3 21 0.00047 24.3 1.0 9 177-185 11-19 (68)
193 PF07497 Rho_RNA_bind: Rho ter 34.2 58 0.0013 23.4 3.3 36 33-68 15-57 (78)
194 PF08460 SH3_5: Bacterial SH3 33.5 41 0.00088 23.2 2.3 20 168-187 36-55 (65)
195 PRK00215 LexA repressor; Valid 33.4 1.7E+02 0.0037 24.0 6.6 30 40-69 170-203 (205)
196 KOG4078|consensus 32.4 85 0.0018 25.4 4.2 80 52-150 78-157 (173)
197 cd05790 S1_Rrp40 S1_Rrp40: Rrp 31.6 49 0.0011 24.1 2.7 20 51-70 47-66 (86)
198 cd04497 hPOT1_OB1_like hPOT1_O 31.6 1.5E+02 0.0034 23.0 5.7 61 60-123 19-93 (138)
199 PRK13598 hisB imidazoleglycero 31.4 1.6E+02 0.0034 25.0 5.9 44 157-202 38-83 (193)
200 PF13953 PapC_C: PapC C-termin 31.3 23 0.00051 24.2 0.9 21 169-189 22-42 (68)
201 COG3439 Uncharacterized conser 31.1 2.7E+02 0.0057 22.1 7.0 72 140-220 62-135 (137)
202 cd05693 S1_Rrp5_repeat_hs1_sc1 31.1 53 0.0011 24.4 2.8 23 100-123 1-23 (100)
203 cd05162 PWWP The PWWP domain, 31.1 31 0.00068 24.5 1.5 15 100-114 1-15 (87)
204 cd06080 MUM1_like Mutated mela 30.9 29 0.00063 25.1 1.3 15 100-114 1-15 (80)
205 TIGR00062 L27 ribosomal protei 30.8 74 0.0016 23.3 3.4 37 2-38 33-70 (83)
206 PF03927 NapD: NapD protein; 30.6 2E+02 0.0043 20.4 6.3 55 139-203 7-62 (79)
207 PF04085 MreC: rod shape-deter 30.6 2.1E+02 0.0045 22.7 6.4 30 57-86 33-62 (152)
208 PF02216 B: B domain; InterPr 30.4 55 0.0012 21.9 2.4 21 198-218 16-36 (54)
209 KOG0147|consensus 30.2 89 0.0019 30.4 4.7 40 158-199 469-511 (549)
210 cd04485 DnaE_OBF DnaE_OBF: A s 29.8 1.4E+02 0.003 19.8 4.7 63 60-123 2-71 (84)
211 TIGR03319 YmdA_YtgF conserved 29.8 1.8E+02 0.0039 28.2 6.9 71 148-220 215-289 (514)
212 PF14444 S1-like: S1-like 29.8 54 0.0012 22.4 2.4 18 50-67 30-47 (58)
213 TIGR00074 hypC_hupF hydrogenas 29.6 1E+02 0.0022 22.0 4.0 39 62-110 7-46 (76)
214 KOG0207|consensus 29.5 49 0.0011 34.3 3.0 53 168-220 439-496 (951)
215 PF15533 Toxin_54: Putative to 29.1 63 0.0014 22.5 2.6 29 158-186 24-52 (66)
216 cd04478 RPA2_DBD_D RPA2_DBD_D: 29.0 2.1E+02 0.0046 20.2 8.0 61 60-123 4-71 (95)
217 TIGR00182 plsX fatty acid/phos 28.7 1.2E+02 0.0027 27.4 5.3 57 158-220 257-318 (322)
218 cd04474 RPA1_DBD_A RPA1_DBD_A: 28.6 79 0.0017 23.4 3.4 35 73-107 38-72 (104)
219 COG3822 ABC-type sugar transpo 28.1 1.2E+02 0.0026 25.8 4.7 43 29-71 149-192 (225)
220 TIGR00617 rpa1 replication fac 27.9 1.4E+02 0.0031 29.4 6.0 64 59-123 194-276 (608)
221 COG3602 Uncharacterized protei 27.6 47 0.001 25.9 2.0 18 94-111 12-29 (134)
222 PF00855 PWWP: PWWP domain; I 27.1 39 0.00085 23.6 1.5 13 100-112 1-13 (86)
223 PRK09521 exosome complex RNA-b 26.4 1.1E+02 0.0023 25.3 4.2 32 54-86 119-150 (189)
224 PF07385 DUF1498: Protein of u 26.4 1E+02 0.0022 26.7 4.1 51 20-70 140-192 (225)
225 cd04451 S1_IF1 S1_IF1: Transla 25.9 2.1E+02 0.0045 19.1 7.3 51 60-113 3-54 (64)
226 COG1107 Archaea-specific RecJ- 25.8 2.2E+02 0.0047 28.4 6.5 44 79-124 238-283 (715)
227 KOG2916|consensus 25.7 60 0.0013 29.0 2.5 73 53-125 13-89 (304)
228 PRK12704 phosphodiesterase; Pr 25.3 1.5E+02 0.0032 28.8 5.5 71 148-220 221-295 (520)
229 PRK15491 replication factor A; 25.2 3.3E+02 0.0072 25.2 7.6 63 60-123 181-257 (374)
230 PF09953 DUF2187: Uncharacteri 24.9 1.5E+02 0.0033 20.1 3.9 19 60-78 16-34 (57)
231 PRK05331 putative phosphate ac 24.4 2.2E+02 0.0047 25.9 6.1 57 158-220 270-331 (334)
232 PF11763 DIPSY: Cell-wall adhe 24.3 84 0.0018 24.5 2.8 19 168-186 82-100 (123)
233 TIGR03779 Bac_Flav_CT_M Bacter 24.1 3E+02 0.0065 26.0 7.0 55 22-78 253-312 (410)
234 PF02541 Ppx-GppA: Ppx/GppA ph 24.0 1.8E+02 0.0039 25.2 5.3 54 168-221 121-174 (285)
235 COG1792 MreC Cell shape-determ 23.9 2E+02 0.0044 25.5 5.7 27 60-86 156-182 (284)
236 PRK05585 yajC preprotein trans 23.9 1.7E+02 0.0036 22.2 4.4 26 53-78 52-83 (106)
237 PRK06531 yajC preprotein trans 23.7 1.8E+02 0.0039 22.4 4.6 47 94-154 31-84 (113)
238 cd04487 RecJ_OBF2_like RecJ_OB 23.6 2.6E+02 0.0056 19.4 5.7 49 72-123 17-67 (73)
239 PF08869 XisI: XisI protein; 23.5 83 0.0018 24.2 2.7 18 169-189 59-76 (111)
240 PF05402 PqqD: Coenzyme PQQ sy 23.4 42 0.00091 22.4 1.0 42 180-221 21-62 (68)
241 TIGR00739 yajC preprotein tran 23.4 1.9E+02 0.004 20.9 4.4 26 53-78 37-68 (84)
242 PRK04163 exosome complex RNA-b 23.1 1.4E+02 0.003 25.7 4.3 32 54-85 112-144 (235)
243 COG0093 RplN Ribosomal protein 23.0 3.7E+02 0.0081 21.0 6.2 45 43-114 22-66 (122)
244 TIGR02554 PrgH type III secret 22.8 1.3E+02 0.0028 28.2 4.3 35 168-202 178-212 (389)
245 PRK00106 hypothetical protein; 22.5 3E+02 0.0065 26.9 6.9 71 148-220 236-310 (535)
246 PRK05446 imidazole glycerol-ph 22.4 2.4E+02 0.0052 26.0 6.0 44 157-202 201-246 (354)
247 cd04459 Rho_CSD Rho_CSD: Rho p 22.3 72 0.0016 22.3 2.0 25 42-66 28-53 (68)
248 PF00475 IGPD: Imidazoleglycer 22.1 27 0.00059 28.2 -0.2 43 157-201 7-51 (145)
249 COG2996 Predicted RNA-bindinin 21.7 3E+02 0.0065 24.7 6.1 56 52-111 69-126 (287)
250 KOG3409|consensus 21.5 1.3E+02 0.0028 25.2 3.6 25 101-125 67-92 (193)
251 PF14842 FliG_N: FliG N-termin 21.3 1.5E+02 0.0033 22.1 3.8 33 187-219 31-63 (108)
252 PF02765 POT1: Telomeric singl 20.4 3.5E+02 0.0075 21.2 5.9 39 83-123 57-98 (146)
253 PRK13689 hypothetical protein; 20.3 1.9E+02 0.0041 20.7 3.8 32 191-222 34-67 (75)
254 PTZ00329 eukaryotic translatio 20.1 2.5E+02 0.0054 22.9 5.0 36 16-64 42-81 (155)
255 cd05837 MSH6_like The PWWP dom 20.1 65 0.0014 24.4 1.5 15 99-113 2-16 (110)
No 1
>KOG1004|consensus
Probab=100.00 E-value=6e-59 Score=385.92 Aligned_cols=219 Identities=44% Similarity=0.864 Sum_probs=207.1
Q ss_pred CCCCeecCCCCCCeeeCCCeEEeCCEEEEEEeeEEEEec-Cc----EEEEEccccccCCCCCCEEEEEEEEEecceEEEE
Q psy230 1 MAGDTLSLNAEPRLILGPGLRRESSAILVSQSGILRHAK-PF----TYYVDYIQRRYVPTRGDLVIGVVTSRVGDNYRVD 75 (222)
Q Consensus 1 ~PGd~l~~~~~~~~~~G~G~y~~~~~i~as~~G~l~~~~-~~----~v~V~~~~~~Y~P~vGDiVIG~V~~v~~~~~~Vd 75 (222)
+|||.+......+..+|+|++..++.+.++.+|.++... ++ .+||...++||+|.+||.|||+|++..+|.|+||
T Consensus 5 ~pg~~~~~~~~~sv~~G~g~~~~g~~~~~~~~G~~~~~~~gk~~~~v~~vds~~kRYiP~~~D~VIGiV~~~~gd~ykVD 84 (230)
T KOG1004|consen 5 FPGDSIPRPRLCSVVLGPGLRRRGQERLVTKCGRLRHKEPGKGGGGVYWVDSQQKRYIPVKGDHVIGIVTSKSGDIYKVD 84 (230)
T ss_pred cCCcccccCccCceeecCCccccCceEEeccccceeeccCCcccceeEEEecccceecCCCCCEEEEEEEeccCceEEEe
Confidence 699999854434588999999999999999999877653 22 7899999999999999999999999999999999
Q ss_pred ECCCCCeeeeccccccccccCCcCCCCCCEEEEEEEecCCCCeeEEEEecCCCccccCcccCCceEEEechhhhhhccCC
Q psy230 76 IGSHDPAVLSYLAFEGATKKNPPKVETGDVVAGKLLTANKDMESEMVCVDSRGKEFIMGILNDGYLLHTSISLCRKLLNP 155 (222)
Q Consensus 76 I~~~~~a~L~~~~f~gatk~~r~~l~~GDlV~ArV~~~~~~~~~~Ls~~~~~~~~~~~G~L~~G~l~~v~~~~~~rl~~~ 155 (222)
|++++.|.||+++||||||||||+|+.||+|||||..+++++|++|+|+|++||+.+||+|++|+||++|++++|+|+.+
T Consensus 85 igg~~~a~L~~laFe~AtkrNrPnl~vGdliyakv~~a~~~~Epel~Cids~graaGfG~LkdG~if~vs~~~~R~Ll~p 164 (230)
T KOG1004|consen 85 IGGSEPASLSYLAFEGATKRNRPNLQVGDLIYAKVVDANKDMEPELTCIDSTGRAAGFGVLKDGMIFKVSLGLCRKLLLP 164 (230)
T ss_pred cCCCCeeeeeeccccCccccCCCccccccEEEEEEEecCCCcCcceEEEcccCcccCcccccCceEEEecHHHHHHHHcC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ChhHHHHhhhcCCCcEEEEEEeCCeEEEeeCCchhHHHHHHHHHHhhcCCHHHHHHHHHHHHHHhc
Q psy230 156 KCPLLKQLAKRSRQKMELSIGMNGKIWIRCESFSDTVRVGNLIMSCELLSYEEILNLCESIHIRFL 221 (222)
Q Consensus 156 ~~~~l~~l~~~~~~~~ei~vG~NG~iWi~~~~~~~~~~i~~~i~~~e~~~~~~~~~~~~~~~~~l~ 221 (222)
.|.+|+.+++ +++|||++|+||||||++++..++++++++|.+||.|+.+|...|++++.+.+.
T Consensus 165 ~~~iLq~vGk--~~~FEia~GlNGriWV~ae~~~~t~~i~~~l~~~e~~td~~q~~~~k~~~~~~~ 228 (230)
T KOG1004|consen 165 DCPILQTVGK--KYPFEIAFGLNGRIWVKAETLSDTLIIANILMNCEFMTDTQQRIMVKQLFKRLA 228 (230)
T ss_pred CCcHHHHhhc--ccceEEEEecCceEEEeccCcchHHHHHHHHHHhhccCcHHHHHHHHHHHHHHh
Confidence 9999999999 999999999999999999999999999999999999999998899999888764
No 2
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=3.6e-58 Score=390.45 Aligned_cols=209 Identities=29% Similarity=0.383 Sum_probs=199.2
Q ss_pred CCCCeecCCCCCCeeeCCCeEEeCCEEEEEEeeEEEEecCcEEEEEccccccCCCCCCEEEEEEEEEecceEEEEECCCC
Q psy230 1 MAGDTLSLNAEPRLILGPGLRRESSAILVSQSGILRHAKPFTYYVDYIQRRYVPTRGDLVIGVVTSRVGDNYRVDIGSHD 80 (222)
Q Consensus 1 ~PGd~l~~~~~~~~~~G~G~y~~~~~i~as~~G~l~~~~~~~v~V~~~~~~Y~P~vGDiVIG~V~~v~~~~~~VdI~~~~ 80 (222)
+|||.+... .++..|||||.+++++||+++|.++.++ +.+.|.|++++|+|++||+|||+|+++.++.|+|||++++
T Consensus 12 ~PGd~vl~~--~~~~~G~Gty~~~~~iyssv~G~~~~~~-~~v~VIpl~g~YiP~~gD~VIG~I~~v~~~~W~VDI~sp~ 88 (239)
T COG1097 12 LPGDLVLAE--GSYKLGHGTYFEGGKIYSSVVGLLDVKG-KLVRVIPLEGRYIPEVGDVVIGKIIEVGPSGWKVDIGSPY 88 (239)
T ss_pred cCCCccCCC--CCEecCCCcEecCCEEEEEEEeEEEEeC-CEEEEEeCCCcccCCCCCEEEEEEEEEcccceEEEcCCcc
Confidence 699976655 4699999999999999999999999995 7789999999999999999999999999999999999999
Q ss_pred Ceeeecccc-----ccccccCCcCCCCCCEEEEEEEecCCCCeeEEEEecCCCccccCcccCCceEEEechhhhhhccCC
Q psy230 81 PAVLSYLAF-----EGATKKNPPKVETGDVVAGKLLTANKDMESEMVCVDSRGKEFIMGILNDGYLLHTSISLCRKLLNP 155 (222)
Q Consensus 81 ~a~L~~~~f-----~gatk~~r~~l~~GDlV~ArV~~~~~~~~~~Ls~~~~~~~~~~~G~L~~G~l~~v~~~~~~rl~~~ 155 (222)
.|.||+++| +.++++||++|++||+|+|||+.++++++++|+|++ .+||+|++|++++|+|++++|++++
T Consensus 89 ~A~L~ls~~~~r~~~~~~~~~r~~l~vGD~v~AkV~~vd~~~~~~L~~k~-----~~~GkL~~G~iv~i~p~kVpRvig~ 163 (239)
T COG1097 89 PALLSLSDFLRRKFENAEKDLRPFLNVGDLVYAKVVDVDRDGEVELTLKD-----EGLGKLKNGQIVKIPPSKVPRVIGK 163 (239)
T ss_pred ceEeehhhhhcccccccccccccccccCCEEEEEEEEccCCCceEEEeec-----CCCccccCCEEEEEchhhcceEecC
Confidence 999999887 567899999999999999999999999999999966 9999999999999999999999999
Q ss_pred ChhHHHHhhhcCCCcEEEEEEeCCeEEEeeCCchhHHHHHHHHHHhhcCCHHHHHHHHHHHHHHhc
Q psy230 156 KCPLLKQLAKRSRQKMELSIGMNGKIWIRCESFSDTVRVGNLIMSCELLSYEEILNLCESIHIRFL 221 (222)
Q Consensus 156 ~~~~l~~l~~~~~~~~ei~vG~NG~iWi~~~~~~~~~~i~~~i~~~e~~~~~~~~~~~~~~~~~l~ 221 (222)
+.+|+++|++ +++|||+||+||||||++++...+.++..||.+||. ++|+.+++++++++|.
T Consensus 164 ~~sm~~~l~~--~~~~~I~VG~NG~IWV~~~~~~~e~~~~~aI~~ie~--ea~~~gltdr~~~~i~ 225 (239)
T COG1097 164 KGSMLNMLKE--KTGCEIIVGQNGRIWVDGENESLEELAIEAIRKIER--EAHTSGLTDRIKEFLK 225 (239)
T ss_pred CCcHHHHhhh--hcCeEEEEecCCEEEecCCCcchHHHHHHHHHHHhh--hhhhhhHHHHHHHHHH
Confidence 9999999999 999999999999999999999889999999999999 9999999999998874
No 3
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=100.00 E-value=2e-51 Score=354.21 Aligned_cols=208 Identities=21% Similarity=0.291 Sum_probs=197.9
Q ss_pred CCCCeecCCCCCCeeeCCCeEEeCCEEEEEEeeEEEEecCcEEEEEccccccCCCCCCEEEEEEEEEecceEEEEECCCC
Q psy230 1 MAGDTLSLNAEPRLILGPGLRRESSAILVSQSGILRHAKPFTYYVDYIQRRYVPTRGDLVIGVVTSRVGDNYRVDIGSHD 80 (222)
Q Consensus 1 ~PGd~l~~~~~~~~~~G~G~y~~~~~i~as~~G~l~~~~~~~v~V~~~~~~Y~P~vGDiVIG~V~~v~~~~~~VdI~~~~ 80 (222)
+|||.|+. ++|.+|+|||.++|.|+||++|.++.++ +.++|.|.+++|+|++||+|+|+|++++++.|+|||++++
T Consensus 12 ~PGd~l~~---~~~~~G~Gty~~~g~i~As~~G~~~~~~-~~i~V~p~~~~y~P~vGDiViG~V~~i~~~~~~vdI~~~~ 87 (235)
T PRK04163 12 VPGDLLAE---GEFKAGRGTYKENGKIYSTVVGLVDIKD-DKVRVIPLEGKYIPKVGDLVIGKVTDVTFSGWEVDINSPY 87 (235)
T ss_pred CCCCCcCc---CCeecCCceEEeCCEEEEEEeEEEEEEC-CEEEEEECCCcccCCCCCEEEEEEEEEeCceEEEEeCCCc
Confidence 69999973 4799999999999999999999999885 7999999999999999999999999999999999999999
Q ss_pred Ceeeeccccccc-----cccCCcCCCCCCEEEEEEEecCCCCeeEEEEecCCCccccCcccCCceEEEechhhhhhccCC
Q psy230 81 PAVLSYLAFEGA-----TKKNPPKVETGDVVAGKLLTANKDMESEMVCVDSRGKEFIMGILNDGYLLHTSISLCRKLLNP 155 (222)
Q Consensus 81 ~a~L~~~~f~ga-----tk~~r~~l~~GDlV~ArV~~~~~~~~~~Ls~~~~~~~~~~~G~L~~G~l~~v~~~~~~rl~~~ 155 (222)
.|+||.++|.++ +++|+++|++||+|+|||+++++++.++|||++ ++||+|.+|++++|++.++++|+++
T Consensus 88 ~g~L~~s~i~~~~~~~d~~~~~~~~~~GDlV~akV~~i~~~~~~~LS~k~-----~~lG~L~~G~~~~V~~~~i~~lig~ 162 (235)
T PRK04163 88 KAYLPVSEVLGRPVNVEGTDLRKYLDIGDYIIAKVKDVDRTRDVVLTLKG-----KGLGKIEGGTIVEIKPVKVPRVIGK 162 (235)
T ss_pred eeEEEHHHcCCCccccchhhhHhhCCCCCEEEEEEEEECCCCcEEEEEcC-----CCCCccCCCEEEEECHHHHHhhcCC
Confidence 999999988764 489999999999999999999988889999965 8999999999999999999999999
Q ss_pred ChhHHHHhhhcCCCcEEEEEEeCCeEEEeeCCchhHHHHHHHHHHhhcCCHHHHHHHHHHHHHHhc
Q psy230 156 KCPLLKQLAKRSRQKMELSIGMNGKIWIRCESFSDTVRVGNLIMSCELLSYEEILNLCESIHIRFL 221 (222)
Q Consensus 156 ~~~~l~~l~~~~~~~~ei~vG~NG~iWi~~~~~~~~~~i~~~i~~~e~~~~~~~~~~~~~~~~~l~ 221 (222)
++++++.|.+ .++|+|++|.||+|||.+++.+.+..+.++|+++|+ ++|..+|+++++++|.
T Consensus 163 ~g~~i~~l~~--~~~~~I~ig~NG~VwI~~~~~~~~~~a~~~I~~~e~--~~~~~~l~~~v~~~~~ 224 (235)
T PRK04163 163 KGSMINMLKE--ETGCDIIVGQNGRIWIKGPDEEDEEIAIEAIKKIER--EAHTSGLTDRIKEFLE 224 (235)
T ss_pred CChhHhhhhh--hhCcEEEEcCCcEEEEeeCCHHHHHHHHHHHHHHHh--hhhccChHHHHHHHHH
Confidence 9999999999 999999999999999999999999999999999999 9999999999999984
No 4
>KOG3013|consensus
Probab=100.00 E-value=1.2e-39 Score=277.63 Aligned_cols=169 Identities=22% Similarity=0.387 Sum_probs=153.4
Q ss_pred CCCCeecCCCCCCeeeCCCeEEeCCEEEEEEeeEEEEecCcEEEEEccccccCCCCCCEEEEEEEEEecceEEEEECCCC
Q psy230 1 MAGDTLSLNAEPRLILGPGLRRESSAILVSQSGILRHAKPFTYYVDYIQRRYVPTRGDLVIGVVTSRVGDNYRVDIGSHD 80 (222)
Q Consensus 1 ~PGd~l~~~~~~~~~~G~G~y~~~~~i~as~~G~l~~~~~~~v~V~~~~~~Y~P~vGDiVIG~V~~v~~~~~~VdI~~~~ 80 (222)
+||+.+... ..|..|||||..++.|+||++|.++.. |++++|+|++.||.|++||+|+|+|+++.+++|+||+|+..
T Consensus 33 tPG~~V~~d--~~fmRGHGTy~~d~~i~ssvaG~v~rv-NkLi~V~plk~rY~pEvGDvVVgRV~eVq~KRWkvd~nsk~ 109 (301)
T KOG3013|consen 33 TPGELVTDD--PGFMRGHGTYVRDGEIYSSVAGVVQRV-NKLISVKPLKSRYAPEVGDVVVGRVIEVQQKRWKVDLNSKQ 109 (301)
T ss_pred cCCccccCc--hhhhhcccceecCCeEEEeecchhhhh-cceEEEeehhhhcCCccCCEEEEEeeeeecceeEEeccccc
Confidence 599999876 469999999999999999999999988 59999999999999999999999999999999999999999
Q ss_pred Ceeeeccc--ccccc---------ccCCcCCCCCCEEEEEEEecCCCCeeEEEEecCCCccccCcccCCceEEEechhhh
Q psy230 81 PAVLSYLA--FEGAT---------KKNPPKVETGDVVAGKLLTANKDMESEMVCVDSRGKEFIMGILNDGYLLHTSISLC 149 (222)
Q Consensus 81 ~a~L~~~~--f~gat---------k~~r~~l~~GDlV~ArV~~~~~~~~~~Ls~~~~~~~~~~~G~L~~G~l~~v~~~~~ 149 (222)
+|+|.+++ +||.. ..||.+|+.||+|.|+|+.+..++...|+|+ +..||||..|++++|+|.++
T Consensus 110 d~vL~LsSvNLPGg~~RRk~~~DEl~MR~fl~egDLi~AEVQ~v~~dGs~sLhTR-----S~KYGKL~~G~lvkVpp~Lv 184 (301)
T KOG3013|consen 110 DAVLMLSSVNLPGGIQRRKSEEDELQMRSFLKEGDLIVAEVQNVFHDGSLSLHTR-----SLKYGKLGQGILVKVPPALV 184 (301)
T ss_pred ceEEEeecccCCchhhhccchhhHHHHHHHhhccCeehHHHHHhccCCeEEEEec-----chhcccccCceEEEeCHHHh
Confidence 99999865 67743 2699999999999999999999999999995 49999999999999999999
Q ss_pred hhccCCChhHHHHhhhcCCCcEEEEEEeCCeEEEee
Q psy230 150 RKLLNPKCPLLKQLAKRSRQKMELSIGMNGKIWIRC 185 (222)
Q Consensus 150 ~rl~~~~~~~l~~l~~~~~~~~ei~vG~NG~iWi~~ 185 (222)
+|... +++ .+ .++.++|+|+||+|||..
T Consensus 185 kr~K~---hfh-~l----p~g~~vIlG~NGyIWv~~ 212 (301)
T KOG3013|consen 185 KRSKT---HFH-NL----PGGVDVILGCNGYIWVGP 212 (301)
T ss_pred hhhhh---hhc-cC----CCCeEEEEecCceEEecC
Confidence 98764 333 23 689999999999999986
No 5
>cd05790 S1_Rrp40 S1_Rrp40: Rrp40 S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In Saccharomyces cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".
Probab=99.97 E-value=1.8e-31 Score=196.27 Aligned_cols=86 Identities=56% Similarity=0.969 Sum_probs=84.3
Q ss_pred ccCCCCCCEEEEEEEEEecceEEEEECCCCCeeeeccccccccccCCcCCCCCCEEEEEEEecCCCCeeEEEEecCCCcc
Q psy230 51 RYVPTRGDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFEGATKKNPPKVETGDVVAGKLLTANKDMESEMVCVDSRGKE 130 (222)
Q Consensus 51 ~Y~P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~gatk~~r~~l~~GDlV~ArV~~~~~~~~~~Ls~~~~~~~~ 130 (222)
||+|++||+|||+|+++.+++|+|||++++.|+||.++|+|++|+|||+|++||+|||||.+++++++++|||++++||+
T Consensus 1 rY~P~~gD~VIG~V~~~~~~~~~VdI~s~~~a~L~~~~f~gatk~~rp~L~~GDlV~ArV~~~~~~~~~eLtc~~~~~k~ 80 (86)
T cd05790 1 RYVPAKGDHVIGIVVAKAGDFFKVDIGGSEPASLSYLAFEGATKRNRPNLNVGDLVYARVVKANRDMEPELSCVDSSGKA 80 (86)
T ss_pred CCcCCCCCEEEEEEEEEcCCeEEEEcCCCcceEechHHcccccccccccCCCCCEEEEEEEecCCCCCeEEEEeCCCCcc
Confidence 69999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccCccc
Q psy230 131 FIMGIL 136 (222)
Q Consensus 131 ~~~G~L 136 (222)
.+||.|
T Consensus 81 ~g~G~L 86 (86)
T cd05790 81 DGFGPL 86 (86)
T ss_pred cccccC
Confidence 999986
No 6
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=99.93 E-value=6.6e-25 Score=183.49 Aligned_cols=139 Identities=17% Similarity=0.192 Sum_probs=118.8
Q ss_pred CCCCeecCCCCCCeeeCCCeEEeCCEEEEEEeeEEEEec-CcEEEEEcccc-ccCCCCCCEEEEEEEEEecceEEEEECC
Q psy230 1 MAGDTLSLNAEPRLILGPGLRRESSAILVSQSGILRHAK-PFTYYVDYIQR-RYVPTRGDLVIGVVTSRVGDNYRVDIGS 78 (222)
Q Consensus 1 ~PGd~l~~~~~~~~~~G~G~y~~~~~i~as~~G~l~~~~-~~~v~V~~~~~-~Y~P~vGDiVIG~V~~v~~~~~~VdI~~ 78 (222)
+|||.|+.. ++|.+|+|||.+++.|+||++|.++.+. ++.++|.|.+. .|.|++||+|+|+|+++..+.|.|||++
T Consensus 9 ~PGe~l~~~--~e~~~G~Gty~~~~~i~as~~G~~~id~~~~~Isv~P~~~~~~~~~~GdiV~GkV~~i~~~g~~V~I~~ 86 (189)
T PRK09521 9 LPGDYLAVI--EEYLPGEGTYEDNGEVYASVVGKVFIDDINRKISVIPFKKTPPLLKKGDIVYGRVVDVKEQRALVRIVS 86 (189)
T ss_pred CCCCccccc--cceEcCCCEEeeCCEEEEEeeEEEEEcCCCCEEEEecCcCCCCCCCCCCEEEEEEEEEcCCeEEEEEEE
Confidence 699999875 4799999999999999999999999864 56899999876 8999999999999999999999999963
Q ss_pred ----------CCCeeeeccccc-cccccCCcCCCCCCEEEEEEEecCCCCeeEEEEecCCCccccCcccC------CceE
Q psy230 79 ----------HDPAVLSYLAFE-GATKKNPPKVETGDVVAGKLLTANKDMESEMVCVDSRGKEFIMGILN------DGYL 141 (222)
Q Consensus 79 ----------~~~a~L~~~~f~-gatk~~r~~l~~GDlV~ArV~~~~~~~~~~Ls~~~~~~~~~~~G~L~------~G~l 141 (222)
+..|+||.+.+. ...+++++.|++||+|+|||++++ ..++|||++ +.||+|. ++.|
T Consensus 87 ~~~~~~~l~~~~~G~l~~s~i~~~~~~~~~~~~~~GD~V~akV~~i~--~~i~LS~k~-----~~lGvv~a~~~~~g~~~ 159 (189)
T PRK09521 87 IEGSERELATSKLAYIHISQVSDGYVESLTDAFKIGDIVRAKVISYT--DPLQLSTKG-----KDLGVIYAMCSRCRTPL 159 (189)
T ss_pred ecccccccCCCceeeEEhhHcChhhhhhHHhccCCCCEEEEEEEecC--CcEEEEEec-----CCceEEEEEccccCCce
Confidence 567888877653 345678999999999999999998 689999965 8999993 4556
Q ss_pred EEechhh
Q psy230 142 LHTSISL 148 (222)
Q Consensus 142 ~~v~~~~ 148 (222)
+++++..
T Consensus 160 ~~~~~~~ 166 (189)
T PRK09521 160 VKKGENE 166 (189)
T ss_pred EECCCCE
Confidence 6666544
No 7
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=99.91 E-value=7.2e-24 Score=174.40 Aligned_cols=127 Identities=20% Similarity=0.310 Sum_probs=114.6
Q ss_pred CCCCeecCCCCCCeeeCCCeEEeCCEEEEEEeeEEEEec-CcEEEEEcccc-ccCCCCCCEEEEEEEEEecceEEEEECC
Q psy230 1 MAGDTLSLNAEPRLILGPGLRRESSAILVSQSGILRHAK-PFTYYVDYIQR-RYVPTRGDLVIGVVTSRVGDNYRVDIGS 78 (222)
Q Consensus 1 ~PGd~l~~~~~~~~~~G~G~y~~~~~i~as~~G~l~~~~-~~~v~V~~~~~-~Y~P~vGDiVIG~V~~v~~~~~~VdI~~ 78 (222)
+|||.|+.. +||++|.|||+++|.|+|+.+|.+..++ +.+++|+|.++ ..+|+.||+|+|+|+++..+.+.|.|-+
T Consensus 9 ~PGd~~a~~--EE~~~G~gt~~~~g~i~Aa~~G~~~~d~~n~~~~V~p~~~~~~~~K~GdiV~grV~~v~~~~a~V~i~~ 86 (188)
T COG1096 9 LPGDVLAVI--EEFLPGEGTYEEGGEIRAAATGVVRRDDKNRVISVKPGKKTPPLPKGGDIVYGRVTDVREQRALVRIVG 86 (188)
T ss_pred cCcceeeee--eeeecCCCeEeECCEEEEeecccEEEcccceEEEeccCCCCCCCCCCCCEEEEEEeeccceEEEEEEEE
Confidence 799999987 6899999999999999999999998874 57799999888 7999999999999999999999999843
Q ss_pred ----------CCCeeeecccc-ccccccCCcCCCCCCEEEEEEEecCCCCeeEEEEecCCCccccCccc
Q psy230 79 ----------HDPAVLSYLAF-EGATKKNPPKVETGDVVAGKLLTANKDMESEMVCVDSRGKEFIMGIL 136 (222)
Q Consensus 79 ----------~~~a~L~~~~f-~gatk~~r~~l~~GDlV~ArV~~~~~~~~~~Ls~~~~~~~~~~~G~L 136 (222)
+..|.+|+++. .+..++.+++|++||+|+|||+|.. ..++|||.+ +.||++
T Consensus 87 ve~~~r~~~~~~~~~ihvs~~~~~~~~~~~d~f~~GDivrA~Vis~~--~~~~Lst~~-----~dlGVI 148 (188)
T COG1096 87 VEGKERELATSGAADIHVSQVRDGYVEKLSDAFRIGDIVRARVISTG--DPIQLSTKG-----NDLGVI 148 (188)
T ss_pred EecccccCCCCceeeEEEEecccccccccccccccccEEEEEEEecC--CCeEEEecC-----CcceEE
Confidence 56789998764 5677899999999999999999998 579999976 999999
No 8
>KOG3409|consensus
Probab=99.84 E-value=1.7e-20 Score=152.18 Aligned_cols=144 Identities=16% Similarity=0.175 Sum_probs=113.3
Q ss_pred CCCCeecCCCCCCeeeCCCeEEeCCEEEEEEeeEEEEec-CcEEEEE----ccccccCCCCCCEEEEEEEEEecceEEEE
Q psy230 1 MAGDTLSLNAEPRLILGPGLRRESSAILVSQSGILRHAK-PFTYYVD----YIQRRYVPTRGDLVIGVVTSRVGDNYRVD 75 (222)
Q Consensus 1 ~PGd~l~~~~~~~~~~G~G~y~~~~~i~as~~G~l~~~~-~~~v~V~----~~~~~Y~P~vGDiVIG~V~~v~~~~~~Vd 75 (222)
+|||+++... +++..|.|||+.++.|+||.+|....++ .....|. +....-+|.+||+|.++|+.++..+++||
T Consensus 9 lpG~~~c~~e-~~~~~g~Gtye~~~yI~aS~ag~~~~~~~~~~~~v~~~~~~~~~~~LP~~G~IVtarV~~i~~rfAkv~ 87 (193)
T KOG3409|consen 9 LPGEVVCRAE-GEYRMGEGTYERNGYIFASVAGVNFRDNLVQKIEVVSVEKQLFNELLPFVGAIVTARVSRINLRFAKVD 87 (193)
T ss_pred cccceeeecc-cccccccceeecCCeEEeccccceeecCCccceeeeeecccchhhcCCccCcEEEEEEEeeccceeeEE
Confidence 6999999754 4689999999999999999999654442 1222333 23346899999999999999999999999
Q ss_pred ECC--------CCCeeeeccccccccc----cCCcCCCCCCEEEEEEEecCCCCeeEEEEecCCCccccCccc------C
Q psy230 76 IGS--------HDPAVLSYLAFEGATK----KNPPKVETGDVVAGKLLTANKDMESEMVCVDSRGKEFIMGIL------N 137 (222)
Q Consensus 76 I~~--------~~~a~L~~~~f~gatk----~~r~~l~~GDlV~ArV~~~~~~~~~~Ls~~~~~~~~~~~G~L------~ 137 (222)
|.+ ++.|+|+..... +|+ +...+|+|||+|.|+|+|.+...++.||+.+ +.||++ .
T Consensus 88 I~~V~d~~lk~~FrglirkqdvR-~tEkdrv~v~ksFrPgDiVlAkVis~~~~~~y~LTtAe-----neLGVV~a~as~~ 161 (193)
T KOG3409|consen 88 ILSVGDKPLKKSFRGLIRKQDVR-ATEKDRVKVYKSFRPGDIVLAKVISLGDGSNYLLTTAE-----NELGVVFARASET 161 (193)
T ss_pred EEEEcCEEhhhhhcceeehhhcc-ccccchhhhhhccCCCcEEEEEEeecCCCCcEEEEEec-----ccceEEEEecccc
Confidence 976 344555432221 232 4568999999999999998888899999987 999998 5
Q ss_pred CceEEEechhhhhh
Q psy230 138 DGYLLHTSISLCRK 151 (222)
Q Consensus 138 ~G~l~~v~~~~~~r 151 (222)
++.|++|+++.+..
T Consensus 162 g~~M~pvdw~~mqs 175 (193)
T KOG3409|consen 162 GEPMVPVDWQEMQS 175 (193)
T ss_pred CCceeeccceeEEc
Confidence 78999999988764
No 9
>cd05791 S1_CSL4 S1_CSL4: CSL4, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. ScCSL4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In S. cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".
Probab=99.78 E-value=5.8e-19 Score=131.70 Aligned_cols=80 Identities=19% Similarity=0.222 Sum_probs=71.4
Q ss_pred cCCCCCCEEEEEEEEEecceEEEEE--------CCCCCeeeeccccc-cccc--cCCcCCCCCCEEEEEEEecCCCCeeE
Q psy230 52 YVPTRGDLVIGVVTSRVGDNYRVDI--------GSHDPAVLSYLAFE-GATK--KNPPKVETGDVVAGKLLTANKDMESE 120 (222)
Q Consensus 52 Y~P~vGDiVIG~V~~v~~~~~~VdI--------~~~~~a~L~~~~f~-gatk--~~r~~l~~GDlV~ArV~~~~~~~~~~ 120 (222)
|.|++||+|+|+|++++.++|.||| ++++.|+|+.+.+. ...+ +|+.+|++||+|+|||++.++.++++
T Consensus 2 ~~P~~GDiVig~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~~dv~~~~~d~~~~~~~f~~GDiV~AkVis~~~~~~~~ 81 (92)
T cd05791 2 VLPKVGSIVIARVTRINPRFAKVDILCVGGRPLKESFRGVIRKEDIRATEKDKVEMYKCFRPGDIVRAKVISLGDASSYY 81 (92)
T ss_pred CCCCCCCEEEEEEEEEcCCEEEEEEEEecCeecCCCcccEEEHHHccccccchHHHHhhcCCCCEEEEEEEEcCCCCCcE
Confidence 8999999999999999999999999 78999999987653 3333 79999999999999999999888999
Q ss_pred EEEecCCCccccCccc
Q psy230 121 MVCVDSRGKEFIMGIL 136 (222)
Q Consensus 121 Ls~~~~~~~~~~~G~L 136 (222)
||+.+ ++||++
T Consensus 82 Lst~~-----~~lGVv 92 (92)
T cd05791 82 LSTAE-----NELGVV 92 (92)
T ss_pred EEecC-----CCCccC
Confidence 99976 889975
No 10
>cd04454 S1_Rrp4_like S1_Rrp4_like: Rrp4-like, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein, and Rrp40 and Csl4 proteins, also represented in this group, are subunits of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In Saccharomyces cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".
Probab=99.77 E-value=2.2e-18 Score=125.23 Aligned_cols=81 Identities=30% Similarity=0.478 Sum_probs=75.2
Q ss_pred ccCCCCCCEEEEEEEEEecceEEEEECCCCCeeeecccccc-ccccCCcCCCCCCEEEEEEEecCCCCeeEEEEecCCCc
Q psy230 51 RYVPTRGDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFEG-ATKKNPPKVETGDVVAGKLLTANKDMESEMVCVDSRGK 129 (222)
Q Consensus 51 ~Y~P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~g-atk~~r~~l~~GDlV~ArV~~~~~~~~~~Ls~~~~~~~ 129 (222)
+|+|++||+|+|+|+++..+.|.|||++...|+||.++|.. ..+++++.|++||+|.|+|+++++.+.+.|||.+
T Consensus 1 ~y~p~~GdiV~G~V~~v~~~~~~V~i~~~~~g~l~~~~~~~~~~~~~~~~~~~GD~i~~~V~~~~~~~~i~LS~~~---- 76 (82)
T cd04454 1 RYLPDVGDIVIGIVTEVNSRFWKVDILSRGTARLEDSSATEKDKKEIRKSLQPGDLILAKVISLGDDMNVLLTTAD---- 76 (82)
T ss_pred CCCCCCCCEEEEEEEEEcCCEEEEEeCCCceEEeechhccCcchHHHHhcCCCCCEEEEEEEEeCCCCCEEEEECC----
Confidence 69999999999999999999999999999999999999875 4788999999999999999999887889999966
Q ss_pred cccCccc
Q psy230 130 EFIMGIL 136 (222)
Q Consensus 130 ~~~~G~L 136 (222)
++||+|
T Consensus 77 -~~~Gvi 82 (82)
T cd04454 77 -NELGVI 82 (82)
T ss_pred -CCCccC
Confidence 889985
No 11
>cd05789 S1_Rrp4 S1_Rrp4: Rrp4 S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In Saccharomyces cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".
Probab=99.58 E-value=7.6e-15 Score=107.25 Aligned_cols=81 Identities=27% Similarity=0.379 Sum_probs=72.8
Q ss_pred ccCCCCCCEEEEEEEEEecceEEEEECCCCCeeeecccccc-----ccccCCcCCCCCCEEEEEEEecCCCCeeEEEEec
Q psy230 51 RYVPTRGDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFEG-----ATKKNPPKVETGDVVAGKLLTANKDMESEMVCVD 125 (222)
Q Consensus 51 ~Y~P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~g-----atk~~r~~l~~GDlV~ArV~~~~~~~~~~Ls~~~ 125 (222)
+|.|++||+|.|+|+++.++.|.|+|++...|+||.+.+.. ..+++.+.|++||.|.|+|+++++++.+.||+..
T Consensus 1 ~y~p~~GdiV~g~V~~i~~~g~~v~i~~~~~G~l~~se~~~~~~~~~~~~~~~~l~vGd~i~~~V~~~~~~~~i~LS~~~ 80 (86)
T cd05789 1 RYIPEVGDVVIGRVTEVGFKRWKVDINSPYDAVLPLSEVNLPRTDEDELNMRSYLDEGDLIVAEVQSVDSDGSVSLHTRS 80 (86)
T ss_pred CCcCCCCCEEEEEEEEECCCEEEEECCCCeEEEEEHHHccCCCCccchHHHHhhCCCCCEEEEEEEEECCCCCEEEEeCc
Confidence 69999999999999999999999999999999999988752 3456778899999999999999887889999965
Q ss_pred CCCccccCccc
Q psy230 126 SRGKEFIMGIL 136 (222)
Q Consensus 126 ~~~~~~~~G~L 136 (222)
.+||+|
T Consensus 81 -----~~~g~~ 86 (86)
T cd05789 81 -----LKYGKL 86 (86)
T ss_pred -----ccccCC
Confidence 888876
No 12
>PF10447 EXOSC1: Exosome component EXOSC1/CSL4; InterPro: IPR019495 The exosome mediates degradation of unstable mRNAs that contain AU-rich elements (AREs) within their 3' untranslated regions []. The proteins in this entry are components of the exosome 3'->5' exoribonuclease complex. They do not have exonuclease activity, but are required for the 3'-processing of the 7S pre-RNA to the mature 5.8S rRNA and for mRNA decay [, ].; PDB: 2NN6_I.
Probab=99.30 E-value=4.6e-12 Score=92.50 Aligned_cols=60 Identities=28% Similarity=0.386 Sum_probs=38.0
Q ss_pred CCCCCCEEEEEEEEEecceEEEEECCC----------CCeeeeccccccc--------cc----cCCcCCCCCCEEEEEE
Q psy230 53 VPTRGDLVIGVVTSRVGDNYRVDIGSH----------DPAVLSYLAFEGA--------TK----KNPPKVETGDVVAGKL 110 (222)
Q Consensus 53 ~P~vGDiVIG~V~~v~~~~~~VdI~~~----------~~a~L~~~~f~ga--------tk----~~r~~l~~GDlV~ArV 110 (222)
+|++||+|+|+|+++++.++.|+|.+- ....|. ..|.|. |+ +|..+|+|||+|+|||
T Consensus 1 lP~vGdiV~~rVtrv~~~~a~v~Il~v~~~~~~~~~~~~~~l~-~~f~GiIR~~DVR~te~Dkv~~~~~FrpGDIVrA~V 79 (82)
T PF10447_consen 1 LPKVGDIVIARVTRVNPRQAKVEILCVEGKGNDSINAGDRPLK-EPFQGIIRKQDVRATEKDKVKMYDCFRPGDIVRARV 79 (82)
T ss_dssp ---TT-EEEEEEEEE-SSEEEEEEEES----------SSS-----SS-S-EEEEGGGT-SS----GGGT--SSSEEEEEE
T ss_pred CCCCCCEEEEEEEEEeccEEEEEEEEEEeccccccccCCcccc-cccEEEEEeeeecccccchhhHHhccCCCCEEEEEE
Confidence 599999999999999999999999765 222222 245542 21 5899999999999999
Q ss_pred Eec
Q psy230 111 LTA 113 (222)
Q Consensus 111 ~~~ 113 (222)
+|.
T Consensus 80 iSl 82 (82)
T PF10447_consen 80 ISL 82 (82)
T ss_dssp EEE
T ss_pred eeC
Confidence 984
No 13
>PF14382 ECR1_N: Exosome complex exonuclease RRP4 N-terminal region; PDB: 2NN6_I 3M7N_C 2BA1_A 3M85_C.
Probab=98.96 E-value=6.2e-10 Score=70.17 Aligned_cols=36 Identities=22% Similarity=0.355 Sum_probs=31.6
Q ss_pred CCCCeecCCCCCCeeeCCCeEEeCCEEEEEEeeEEEEe
Q psy230 1 MAGDTLSLNAEPRLILGPGLRRESSAILVSQSGILRHA 38 (222)
Q Consensus 1 ~PGd~l~~~~~~~~~~G~G~y~~~~~i~as~~G~l~~~ 38 (222)
+|||.|+.. ++|.+|+|||+++++|+||++|.++.+
T Consensus 3 ~PG~~l~~~--~e~~~G~GTY~~~g~I~asv~G~v~~~ 38 (39)
T PF14382_consen 3 VPGDRLGSS--EEYMPGHGTYVRDGNIYASVAGTVKID 38 (39)
T ss_dssp -TT-EEEET--TTSEESTTEEEETTEEEESSSEEEEEE
T ss_pred CCCCEeecC--CCEecCCCEEEeCCEEEEEeeEEEEEc
Confidence 699999986 579999999999999999999999875
No 14
>cd05687 S1_RPS1_repeat_ec1_hs1 S1_RPS1_repeat_ec1_hs1: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 1 of the Escherichia coli and Homo sapiens RPS1 (ec1 and hs1, respectively). Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=98.72 E-value=8.6e-08 Score=66.93 Aligned_cols=67 Identities=25% Similarity=0.356 Sum_probs=56.7
Q ss_pred CCEEEEEEEEEecceEEEEECCCCCeeeeccccc-cccccCCcCCCCCCEEEEEEEecCC-CCeeEEEE
Q psy230 57 GDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFE-GATKKNPPKVETGDVVAGKLLTANK-DMESEMVC 123 (222)
Q Consensus 57 GDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~-gatk~~r~~l~~GDlV~ArV~~~~~-~~~~~Ls~ 123 (222)
||+|.|+|+++.++.+.||+++...|.||.+.+. ...++....|++||.+.|+|.++++ ...+.||.
T Consensus 1 G~iv~g~V~~i~~~~~~v~l~~~~~g~l~~~e~~~~~~~~~~~~~~~Gd~i~~~i~~~~~~~~~i~lS~ 69 (70)
T cd05687 1 GDIVKGTVVSVDDDEVLVDIGYKSEGIIPISEFSDDPIENGEDEVKVGDEVEVYVLRVEDEEGNVVLSK 69 (70)
T ss_pred CCEEEEEEEEEeCCEEEEEeCCCceEEEEHHHhCccccCCHhHcCCCCCEEEEEEEEEECCCCeEEEEe
Confidence 8999999999999999999998899999987764 3445667789999999999999974 34566664
No 15
>cd05704 S1_Rrp5_repeat_hs13 S1_Rrp5_repeat_hs13: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 13 (hs13). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=98.67 E-value=1.1e-07 Score=67.32 Aligned_cols=68 Identities=15% Similarity=0.252 Sum_probs=58.8
Q ss_pred CCCCEEEEEEEEEec-ceEEEEECCCCCeeeeccccc-cccccCCcCCCCCCEEEEEEEecCCCCeeEEEE
Q psy230 55 TRGDLVIGVVTSRVG-DNYRVDIGSHDPAVLSYLAFE-GATKKNPPKVETGDVVAGKLLTANKDMESEMVC 123 (222)
Q Consensus 55 ~vGDiVIG~V~~v~~-~~~~VdI~~~~~a~L~~~~f~-gatk~~r~~l~~GDlV~ArV~~~~~~~~~~Ls~ 123 (222)
++||+|.|+|+++.+ ..+.|++.....|.+|.+.+. ...++..+.|++||.|.|+|.++++ ..+.||+
T Consensus 2 ~~G~iv~G~V~~i~~~~g~~v~l~~~~~Glvhis~~s~~~~~~~~~~~~~Gd~v~~kV~~~~~-~~i~LSl 71 (72)
T cd05704 2 EEGAVTLGMVTKVIPHSGLTVQLPFGKTGLVSIFHLSDSYTENPLEGFKPGKIVRCCILSKKD-GKYQLSL 71 (72)
T ss_pred CCCCEEEEEEEEeeCCcEEEEECCCCCEEEEEHHHhcCcccCCHHHhCCCCCEEEEEEEEecC-CEEEEEe
Confidence 589999999999986 589999999999999998774 3455556789999999999999976 6788886
No 16
>smart00316 S1 Ribosomal protein S1-like RNA-binding domain.
Probab=98.63 E-value=1.8e-07 Score=64.01 Aligned_cols=69 Identities=22% Similarity=0.247 Sum_probs=59.0
Q ss_pred CCCCEEEEEEEEEecceEEEEECCCCCeeeeccccccc-cccCCcCCCCCCEEEEEEEecCCC-CeeEEEE
Q psy230 55 TRGDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFEGA-TKKNPPKVETGDVVAGKLLTANKD-MESEMVC 123 (222)
Q Consensus 55 ~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~ga-tk~~r~~l~~GDlV~ArV~~~~~~-~~~~Ls~ 123 (222)
++||+|.|+|+++....|.|++++...|.+|.+.+... .+++...|++||.|.|+|.+++.+ ..+.||+
T Consensus 1 ~~G~~v~g~V~~v~~~g~~v~i~~~~~g~l~~~~~~~~~~~~~~~~~~~G~~v~~~V~~~~~~~~~i~ls~ 71 (72)
T smart00316 1 EVGDVVEGTVTEITPFGAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILSL 71 (72)
T ss_pred CCCCEEEEEEEEEEccEEEEEeCCCCEEEEEHHHCCccccCCHHHeecCCCEEEEEEEEEeCCCCEEEEEe
Confidence 46999999999999999999999889999998766533 455567799999999999999876 6788876
No 17
>cd05691 S1_RPS1_repeat_ec6 S1_RPS1_repeat_ec6: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 6 (ec6) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=98.60 E-value=3.3e-07 Score=64.09 Aligned_cols=69 Identities=17% Similarity=0.263 Sum_probs=59.9
Q ss_pred CCEEEEEEEEEecceEEEEECCCCCeeeecccccc-ccccCCcCCCCCCEEEEEEEecCCC-CeeEEEEec
Q psy230 57 GDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFEG-ATKKNPPKVETGDVVAGKLLTANKD-MESEMVCVD 125 (222)
Q Consensus 57 GDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~g-atk~~r~~l~~GDlV~ArV~~~~~~-~~~~Ls~~~ 125 (222)
||+|.|+|+++.+..+.|++.+...|.+|.+.+.. ..++....|++||.|.|+|.+++.. ..+.||++.
T Consensus 1 G~~v~g~V~~v~~~g~~v~l~~~~~g~i~~~~~~~~~~~~~~~~~~~Gd~v~~~v~~~d~~~~~i~ls~k~ 71 (73)
T cd05691 1 GSIVTGKVTEVDAKGATVKLGDGVEGFLRAAELSRDRVEDATERFKVGDEVEAKITNVDRKNRKISLSIKA 71 (73)
T ss_pred CCEEEEEEEEEECCeEEEEeCCCCEEEEEHHHCCCccccCHHHccCCCCEEEEEEEEEeCCCCEEEEEEEE
Confidence 79999999999999999999998999999887643 3456678899999999999999876 568999854
No 18
>cd04452 S1_IF2_alpha S1_IF2_alpha: The alpha subunit of translation Initiation Factor 2, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Eukaryotic and archaeal Initiation Factor 2 (e- and aIF2, respectively) are heterotrimeric proteins with three subunits (alpha, beta, and gamma). IF2 plays a crucial role in the process of translation initiation. The IF2 gamma subunit contains a GTP-binding site. The IF2 beta and gamma subunits together are thought to be responsible for binding methionyl-initiator tRNA. The ternary complex consisting of IF2, GTP, and the methionyl-initiator tRNA binds to the small subunit of the ribosome, as part of a pre-initiation complex that scans the mRNA to find the AUG start codon. The IF2-bound GTP is hydrolyzed to GDP when the methionyl-initiator tRNA binds the AUG start codon, at which time the IF2 is released with its bound GDP. The large ribosomal subunit then joins with the small subunit to c
Probab=98.58 E-value=3.7e-07 Score=64.49 Aligned_cols=71 Identities=15% Similarity=0.142 Sum_probs=60.0
Q ss_pred CCCCCEEEEEEEEEecceEEEEECC--CCCeeeecccccc-ccccCCcCCCCCCEEEEEEEecCCC-CeeEEEEe
Q psy230 54 PTRGDLVIGVVTSRVGDNYRVDIGS--HDPAVLSYLAFEG-ATKKNPPKVETGDVVAGKLLTANKD-MESEMVCV 124 (222)
Q Consensus 54 P~vGDiVIG~V~~v~~~~~~VdI~~--~~~a~L~~~~f~g-atk~~r~~l~~GDlV~ArV~~~~~~-~~~~Ls~~ 124 (222)
|++|++|.|+|+++....+.|++.. ...|.+|.+.+.. ..++....|++||.|.|+|.+++.. ..+.||++
T Consensus 1 ~~~G~~~~g~V~~v~~~g~~v~l~~~~~~~gll~~s~l~~~~~~~~~~~~~~Gd~v~vkv~~~d~~~~~i~ls~k 75 (76)
T cd04452 1 PEEGELVVVTVKSIADMGAYVSLLEYGNIEGMILLSELSRRRIRSIRKLVKVGRKEVVKVIRVDKEKGYIDLSKK 75 (76)
T ss_pred CCCCCEEEEEEEEEEccEEEEEEcCCCCeEEEEEhHHcCCcccCCHHHeeCCCCEEEEEEEEEECCCCEEEEEEc
Confidence 7899999999999999999999975 3789999887753 3456677899999999999999864 56888874
No 19
>cd05692 S1_RPS1_repeat_hs4 S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 4 (hs4) of the H. sapiens RPS1 homolog. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=98.56 E-value=4.8e-07 Score=61.96 Aligned_cols=67 Identities=19% Similarity=0.181 Sum_probs=57.3
Q ss_pred CCEEEEEEEEEecceEEEEECCCCCeeeeccccccc-cccCCcCCCCCCEEEEEEEecCCCCeeEEEE
Q psy230 57 GDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFEGA-TKKNPPKVETGDVVAGKLLTANKDMESEMVC 123 (222)
Q Consensus 57 GDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~ga-tk~~r~~l~~GDlV~ArV~~~~~~~~~~Ls~ 123 (222)
||+|.|+|+++....|.|+|.....|.||.+.+... .+.....|++||.|.++|.+++..+.+.||+
T Consensus 1 G~~~~g~V~~i~~~g~~v~i~~~~~g~l~~~~l~~~~~~~~~~~~~~Gd~v~v~v~~~~~~~~i~ls~ 68 (69)
T cd05692 1 GSVVEGTVTRLKPFGAFVELGGGISGLVHISQIAHKRVKDVKDVLKEGDKVKVKVLSIDARGRISLSI 68 (69)
T ss_pred CCEEEEEEEEEEeeeEEEEECCCCEEEEEhHHcCCcccCCHHHccCCCCEEEEEEEEECCCCcEEEEE
Confidence 799999999999999999999999999998776532 3344467999999999999998766788887
No 20
>PF00575 S1: S1 RNA binding domain; InterPro: IPR003029 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. The S1 domain was originally identified in ribosomal protein S1 but is found in a large number of RNA-associated proteins. The structure of the S1 RNA-binding domain from the Escherichia coli polynucleotide phosphorylase has been determined using NMR methods and consists of a five-stranded antiparallel beta barrel. Conserved residues on one face of the barrel and adjacent loops form the putative RNA-binding site []. The structure of the S1 domain is very similar to that of cold shock proteins. This suggests that they may both be derived from an ancient nucleic acid-binding protein []. More information about these proteins can be found at Protein of the Month: RNA Exosomes []. This entry does not include translation initiation factor IF-1 S1 domains.; GO: 0003723 RNA binding; PDB: 3L7Z_F 2JE6_I 2JEA_I 2JEB_I 1E3P_A 2Y0S_E 1WI5_A 2BH8_A 2CQO_A 2EQS_A ....
Probab=98.47 E-value=9.6e-07 Score=62.08 Aligned_cols=70 Identities=20% Similarity=0.228 Sum_probs=61.5
Q ss_pred CCCCCEEEEEEEEEecceEEEEECCCCCeeeecccccc-ccccCCcCCCCCCEEEEEEEecCCCC-eeEEEE
Q psy230 54 PTRGDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFEG-ATKKNPPKVETGDVVAGKLLTANKDM-ESEMVC 123 (222)
Q Consensus 54 P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~g-atk~~r~~l~~GDlV~ArV~~~~~~~-~~~Ls~ 123 (222)
|++||+|-|+|+++....+.||++....|.+|...+.. ........+++||-|.|+|.+++.+. .+.||+
T Consensus 2 ~~~G~iv~g~V~~v~~~g~~V~l~~~~~g~ip~~~l~~~~~~~~~~~~~~G~~v~v~v~~vd~~~~~i~lS~ 73 (74)
T PF00575_consen 2 LKEGDIVEGKVTSVEDFGVFVDLGNGIEGFIPISELSDDRIDDPSEVYKIGQTVRVKVIKVDKEKGRIRLSL 73 (74)
T ss_dssp SSTTSEEEEEEEEEETTEEEEEESTSSEEEEEGGGSSSSEESSSHGTCETTCEEEEEEEEEETTTTEEEEES
T ss_pred CCCCCEEEEEEEEEECCEEEEEECCcEEEEEEeehhcCccccccccccCCCCEEEEEEEEEECCCCeEEEEE
Confidence 78999999999999999999999999999999988764 34567789999999999999998764 477775
No 21
>cd05706 S1_Rrp5_repeat_sc10 S1_Rrp5_repeat_sc10: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 10 (sc10). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=98.46 E-value=1.8e-06 Score=60.62 Aligned_cols=69 Identities=17% Similarity=0.158 Sum_probs=59.3
Q ss_pred CCCCEEEEEEEEEecceEEEEECCCCCeeeecccccc-ccccCCcCCCCCCEEEEEEEecCCC-CeeEEEE
Q psy230 55 TRGDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFEG-ATKKNPPKVETGDVVAGKLLTANKD-MESEMVC 123 (222)
Q Consensus 55 ~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~g-atk~~r~~l~~GDlV~ArV~~~~~~-~~~~Ls~ 123 (222)
++||+|-|+|+++.+..+.|++.....|.+|.+.+.. ..++....|++||.|.|+|.+++.+ ..+.||+
T Consensus 2 ~~G~iv~g~V~~v~~~gi~v~l~~~~~g~v~~s~l~~~~~~~~~~~~~~Gd~v~~~V~~~d~~~~~i~ls~ 72 (73)
T cd05706 2 KVGDILPGRVTKVNDRYVLVQLGNKVTGPSFITDALDDYSEALPYKFKKNDIVRACVLSVDVPNKKIALSL 72 (73)
T ss_pred CCCCEEEEEEEEEeCCeEEEEeCCCcEEEEEhhhccCccccccccccCCCCEEEEEEEEEeCCCCEEEEEE
Confidence 5799999999999999999999999999999887653 3345677899999999999999864 5788886
No 22
>cd05702 S1_Rrp5_repeat_hs11_sc8 S1_Rrp5_repeat_hs11_sc8: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 11 (hs11) and S. cerevisiae S1 repeat 8 (sc8). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=98.43 E-value=1e-06 Score=61.82 Aligned_cols=61 Identities=16% Similarity=0.197 Sum_probs=53.4
Q ss_pred CCEEEEEEEEEecceEEEEECCCCCeeeecccccc---ccccCCcCCCCCCEEEEEEEecCCCC
Q psy230 57 GDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFEG---ATKKNPPKVETGDVVAGKLLTANKDM 117 (222)
Q Consensus 57 GDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~g---atk~~r~~l~~GDlV~ArV~~~~~~~ 117 (222)
||+|.|+|+++....+.|++.+...|.+|...+.. ..+++...|++||.|.|+|++++...
T Consensus 1 G~iV~g~V~~i~~~gi~v~l~~~i~g~i~~~~i~~~~~~~~~~~~~~~~Gd~i~~kVl~~d~~~ 64 (70)
T cd05702 1 GDLVKAKVKSVKPTQLNVQLADNVHGRIHVSEVFDEWPDGKNPLSKFKIGQKIKARVIGGHDAK 64 (70)
T ss_pred CCEEEEEEEEEECCcEEEEeCCCcEEEEEHHHhccccccccChhHhCCCCCEEEEEEEEEeCcc
Confidence 89999999999999999999999999999877642 25567788999999999999997654
No 23
>cd05708 S1_Rrp5_repeat_sc12 S1_Rrp5_repeat_sc12: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 12 (sc12). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=98.36 E-value=3.1e-06 Score=59.60 Aligned_cols=71 Identities=14% Similarity=0.119 Sum_probs=59.3
Q ss_pred CCCCEEEEEEEEEecceEEEEECC-CCCeeeecccccc-ccccCCcCCCCCCEEEEEEEecCC-CCeeEEEEec
Q psy230 55 TRGDLVIGVVTSRVGDNYRVDIGS-HDPAVLSYLAFEG-ATKKNPPKVETGDVVAGKLLTANK-DMESEMVCVD 125 (222)
Q Consensus 55 ~vGDiVIG~V~~v~~~~~~VdI~~-~~~a~L~~~~f~g-atk~~r~~l~~GDlV~ArV~~~~~-~~~~~Ls~~~ 125 (222)
++|++|.|+|+++....+.|++.. ...|.+|.+.+.. ...+....|++||.|.|+|.+++. ...+.|+++.
T Consensus 1 ~~g~~v~g~V~~i~~~g~~v~l~~~~~~g~i~~~~l~~~~~~~~~~~~~~Gd~v~v~i~~vd~~~~~i~ls~k~ 74 (77)
T cd05708 1 KVGQKIDGTVRRVEDYGVFIDIDGTNVSGLCHKSEISDNRVADASKLFRVGDKVRAKVLKIDAEKKRISLGLKA 74 (77)
T ss_pred CCCCEEEEEEEEEEcceEEEEECCCCeEEEEEHHHCCCCccCCHhHeecCCCEEEEEEEEEeCCCCEEEEEEEe
Confidence 469999999999999999999985 7899999877643 334556789999999999999986 4678888864
No 24
>PRK08582 hypothetical protein; Provisional
Probab=98.34 E-value=4.6e-06 Score=66.69 Aligned_cols=72 Identities=17% Similarity=0.135 Sum_probs=63.9
Q ss_pred CCCCCEEEEEEEEEecceEEEEECCCCCeeeeccccc-cccccCCcCCCCCCEEEEEEEecCCCCeeEEEEec
Q psy230 54 PTRGDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFE-GATKKNPPKVETGDVVAGKLLTANKDMESEMVCVD 125 (222)
Q Consensus 54 P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~-gatk~~r~~l~~GDlV~ArV~~~~~~~~~~Ls~~~ 125 (222)
.++|++|.|+|++++...+.|+|.....|++|++.+. ...++....|++||.|.|+|++++.+..+.||+..
T Consensus 3 ~kvG~iv~G~V~~I~~fG~fV~L~~~~~GlVhiSels~~~v~~~~~~l~vGD~VkvkV~~id~~gkI~LSlk~ 75 (139)
T PRK08582 3 IEVGSKLQGKVTGITNFGAFVELPEGKTGLVHISEVADNYVKDINDHLKVGDEVEVKVLNVEDDGKIGLSIKK 75 (139)
T ss_pred CcCCCEEEEEEEEEECCeEEEEECCCCEEEEEeeccCcccccccccccCCCCEEEEEEEEECCCCcEEEEEEe
Confidence 4689999999999999999999999999999998774 34566678899999999999999877889999875
No 25
>PRK07252 hypothetical protein; Provisional
Probab=98.34 E-value=4.1e-06 Score=65.40 Aligned_cols=71 Identities=10% Similarity=0.090 Sum_probs=61.3
Q ss_pred CCCCEEEEEEEEEecceEEEEECCCCCeeeecccccc-ccccCCcCCCCCCEEEEEEEecCC-CCeeEEEEec
Q psy230 55 TRGDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFEG-ATKKNPPKVETGDVVAGKLLTANK-DMESEMVCVD 125 (222)
Q Consensus 55 ~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~g-atk~~r~~l~~GDlV~ArV~~~~~-~~~~~Ls~~~ 125 (222)
++||+|.|+|+++....+.|+|.....|.+|.+.+.. ..+.....|++||.|.++|.+++. ...+.|+++.
T Consensus 2 kvG~iv~G~V~~V~~~G~fVei~~~~~GllhiseLs~~~~~~~~~~~~vGD~V~VkI~~iD~~~~ri~lSlk~ 74 (120)
T PRK07252 2 KIGDKLKGTITGIKPYGAFVALENGTTGLIHISEIKTGFIDNIHQLLKVGEEVLVQVVDFDEYTGKASLSLRT 74 (120)
T ss_pred CCCCEEEEEEEEEeCcEEEEEECCCCEEEEEHHHcCCccccChhhccCCCCEEEEEEEEEeCCCCEEEEEEee
Confidence 4799999999999999999999988999999887643 334556789999999999999986 5678999986
No 26
>cd05707 S1_Rrp5_repeat_sc11 S1_Rrp5_repeat_sc11: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 11 (sc11). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=98.33 E-value=2.6e-06 Score=59.19 Aligned_cols=65 Identities=25% Similarity=0.342 Sum_probs=55.3
Q ss_pred CCEEEEEEEEEecceEEEEECCCCCeeeecccccc-ccccCCcCCCCCCEEEEEEEecCCC-CeeEE
Q psy230 57 GDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFEG-ATKKNPPKVETGDVVAGKLLTANKD-MESEM 121 (222)
Q Consensus 57 GDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~g-atk~~r~~l~~GDlV~ArV~~~~~~-~~~~L 121 (222)
||+|.|+|+++.+..+.|++.....|.+|.+.+.. ..++....|++||.|.|+|.++++. ..+.|
T Consensus 1 G~~v~g~V~~v~~~Gv~V~l~~~~~G~v~~s~l~~~~~~~~~~~~~~Gd~v~~~v~~~d~~~~~i~l 67 (68)
T cd05707 1 GDVVRGFVKNIANNGVFVTLGRGVDARVRVSELSDSYLKDWKKRFKVGQLVKGKIVSIDPDNGRIEM 67 (68)
T ss_pred CCEEEEEEEEEECccEEEEeCCCCEEEEEHHHCCchhhcCHhhccCCCCEEEEEEEEEeCCCCEEec
Confidence 79999999999999999999988999999987753 4556678899999999999999863 34444
No 27
>PRK08563 DNA-directed RNA polymerase subunit E'; Provisional
Probab=98.29 E-value=3.7e-06 Score=70.06 Aligned_cols=80 Identities=20% Similarity=0.216 Sum_probs=64.6
Q ss_pred ccCCCCCCEEEEEEEEEecceEEEEECCCCCeeeeccccccc------------cccCCcCCCCCCEEEEEEEecCCC--
Q psy230 51 RYVPTRGDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFEGA------------TKKNPPKVETGDVVAGKLLTANKD-- 116 (222)
Q Consensus 51 ~Y~P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~ga------------tk~~r~~l~~GDlV~ArV~~~~~~-- 116 (222)
.|.|.+|++|.|+|++++...+.|+++ +..++++..+.+.. .++....++.||.|++||.+++.+
T Consensus 76 vf~P~~GEVv~g~V~~v~~~Gi~V~lg-~~~g~v~~~~l~~~~~~~d~~~~~~~~~~~~~~i~~Gd~VrvrV~~v~~~~~ 154 (187)
T PRK08563 76 VFKPELQEVVEGEVVEVVEFGAFVRIG-PVDGLLHISQIMDDYISYDPKNGRLIGKESKRVLKVGDVVRARIVAVSLKER 154 (187)
T ss_pred EEeccCCCEEEEEEEEEEccEEEEEEe-CceEEEEcHHcCCCceEEccccceEEEccCCeEEcCCCEEEEEEEEEEcccC
Confidence 367999999999999999999999998 58888887654321 134567899999999999998743
Q ss_pred ----CeeEEEEecCCCccccCccc
Q psy230 117 ----MESEMVCVDSRGKEFIMGIL 136 (222)
Q Consensus 117 ----~~~~Ls~~~~~~~~~~~G~L 136 (222)
..+.||+.+ ++||++
T Consensus 155 ~~~~~~I~ls~~~-----~~LG~~ 173 (187)
T PRK08563 155 RPRGSKIGLTMRQ-----PGLGKL 173 (187)
T ss_pred CCCCCEEEEEecC-----CCCCcH
Confidence 357888865 899987
No 28
>cd05705 S1_Rrp5_repeat_hs14 S1_Rrp5_repeat_hs14: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 14 (hs14). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=98.28 E-value=4.6e-06 Score=59.49 Aligned_cols=67 Identities=16% Similarity=0.189 Sum_probs=54.6
Q ss_pred CCCCEEEEEEEEEecceEEEEECCCCCeeeecccccccc-c---cCCcCCCCCCEEEEEEEecCCCC-eeEE
Q psy230 55 TRGDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFEGAT-K---KNPPKVETGDVVAGKLLTANKDM-ESEM 121 (222)
Q Consensus 55 ~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~gat-k---~~r~~l~~GDlV~ArV~~~~~~~-~~~L 121 (222)
++||+|.|+|+++++..+.|+++..-.|.+|++...... + .....|++||.|.|+|++++++. .+.|
T Consensus 2 k~G~~V~g~V~~i~~~G~fV~l~~~v~G~v~~~~ls~~~~~~~~~~~~~~~~G~~v~~kVl~id~~~~~i~L 73 (74)
T cd05705 2 KEGQLLRGYVSSVTKQGVFFRLSSSIVGRVLFQNVTKYFVSDPSLYNKYLPEGKLLTAKVLSVNSEKNLVEL 73 (74)
T ss_pred CCCCEEEEEEEEEeCCcEEEEeCCCCEEEEEHHHccCccccChhhHhcccCCCCEEEEEEEEEECCCCEEec
Confidence 589999999999999999999998899999987654321 2 24578999999999999998653 3444
No 29
>PRK08059 general stress protein 13; Validated
Probab=98.28 E-value=5.3e-06 Score=64.84 Aligned_cols=72 Identities=17% Similarity=0.118 Sum_probs=61.6
Q ss_pred CCCCCEEEEEEEEEecceEEEEECCCCCeeeecccccc-ccccCCcCCCCCCEEEEEEEecCC-CCeeEEEEec
Q psy230 54 PTRGDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFEG-ATKKNPPKVETGDVVAGKLLTANK-DMESEMVCVD 125 (222)
Q Consensus 54 P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~g-atk~~r~~l~~GDlV~ArV~~~~~-~~~~~Ls~~~ 125 (222)
.++||+|.|+|+++....+.|+|.....|.+|.+.++. ..++....|++||.|.|+|.+++. ...+.||++.
T Consensus 5 ~k~G~iv~G~V~~i~~~G~fV~i~~~~~Gli~~sel~~~~~~~~~~~~~vGD~I~vkI~~id~~~~~i~lslk~ 78 (123)
T PRK08059 5 YEVGSVVTGKVTGIQPYGAFVALDEETQGLVHISEITHGFVKDIHDFLSVGDEVKVKVLSVDEEKGKISLSIRA 78 (123)
T ss_pred CCCCCEEEEEEEEEecceEEEEECCCCEEEEEHHHCCcccccCHHHcCCCCCEEEEEEEEEECCCCeEEEEEEE
Confidence 46799999999999999999999999999999887653 333446679999999999999964 5689999976
No 30
>cd05693 S1_Rrp5_repeat_hs1_sc1 S1_Rrp5_repeat_hs1_sc1: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 1 (hs1) and S. cerevisiae S1 repeat 1 (sc1). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=98.23 E-value=3.8e-06 Score=63.49 Aligned_cols=70 Identities=16% Similarity=0.167 Sum_probs=58.1
Q ss_pred CCCCEEEEEEEEEecceEEEEECCCCCeeeecccccc-cc-------------------ccCCcCCCCCCEEEEEEEecC
Q psy230 55 TRGDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFEG-AT-------------------KKNPPKVETGDVVAGKLLTAN 114 (222)
Q Consensus 55 ~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~g-at-------------------k~~r~~l~~GDlV~ArV~~~~ 114 (222)
++||+|.|+|+++......|++.....|++|++.+.. .+ .+....|++||+|.|+|++++
T Consensus 2 ~~G~vV~G~V~~v~~~gl~v~L~~g~~G~v~~seis~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~vGd~V~~kVi~~d 81 (100)
T cd05693 2 SEGMLVLGQVKEITKLDLVISLPNGLTGYVPITNISDAYTERLEELDEESEEEDDEEELPDLEDLFSVGQLVRCKVVSLD 81 (100)
T ss_pred CCCCEEEEEEEEEcCCCEEEECCCCcEEEEEHHHhhHHHHHHHHHhhhhccccccccccCCHHHhccCCCEEEEEEEEcc
Confidence 5899999999999999999999888899999865531 11 235688999999999999999
Q ss_pred CC----CeeEEEEe
Q psy230 115 KD----MESEMVCV 124 (222)
Q Consensus 115 ~~----~~~~Ls~~ 124 (222)
+. ..+.||.+
T Consensus 82 ~~~~~~~~i~LSlr 95 (100)
T cd05693 82 KSKSGKKRIELSLE 95 (100)
T ss_pred CCcCCCcEEEEEec
Confidence 75 46788875
No 31
>cd05698 S1_Rrp5_repeat_hs6_sc5 S1_Rrp5_repeat_hs6_sc5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 6 (hs6) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=98.17 E-value=1.3e-05 Score=55.64 Aligned_cols=67 Identities=16% Similarity=0.190 Sum_probs=56.7
Q ss_pred CCEEEEEEEEEecceEEEEECCCCCeeeecccccc-ccccCCcCCCCCCEEEEEEEecCCC-CeeEEEE
Q psy230 57 GDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFEG-ATKKNPPKVETGDVVAGKLLTANKD-MESEMVC 123 (222)
Q Consensus 57 GDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~g-atk~~r~~l~~GDlV~ArV~~~~~~-~~~~Ls~ 123 (222)
||++.|+|+++.+..+.|++...-.|.+|.+.+.. ...+....|++||.|.++|.++++. ..+.||+
T Consensus 1 g~~~~g~V~~v~~~G~~V~l~~~~~gli~~s~l~~~~~~~~~~~~~~G~~i~v~v~~~d~~~~~i~ls~ 69 (70)
T cd05698 1 GLKTHGTIVKVKPNGCIVSFYNNVKGFLPKSELSEAFIKDPEEHFRVGQVVKVKVLSCDPEQQRLLLSC 69 (70)
T ss_pred CCEEEEEEEEEecCcEEEEECCCCEEEEEHHHcChhhcCCHHHcccCCCEEEEEEEEEcCCCCEEEEEe
Confidence 89999999999999999999877899999887642 3334456799999999999999874 5788886
No 32
>PRK03987 translation initiation factor IF-2 subunit alpha; Validated
Probab=98.17 E-value=9.9e-06 Score=71.24 Aligned_cols=74 Identities=18% Similarity=0.206 Sum_probs=63.9
Q ss_pred cCCCCCCEEEEEEEEEecceEEEEECC--CCCeeeeccccc-cccccCCcCCCCCCEEEEEEEecCCC-CeeEEEEec
Q psy230 52 YVPTRGDLVIGVVTSRVGDNYRVDIGS--HDPAVLSYLAFE-GATKKNPPKVETGDVVAGKLLTANKD-MESEMVCVD 125 (222)
Q Consensus 52 Y~P~vGDiVIG~V~~v~~~~~~VdI~~--~~~a~L~~~~f~-gatk~~r~~l~~GDlV~ArV~~~~~~-~~~~Ls~~~ 125 (222)
-.|++||+|.|+|+++....|.|++.. ...|.+|.+.+. +..+.++..|++||.|.|+|.+++.. ..+.||.+.
T Consensus 4 ~~P~~GdiV~G~V~~I~~~G~fV~L~e~~gieGlI~iSEls~~~i~~i~~~~kvGd~V~vkVi~VD~~k~~I~LSlK~ 81 (262)
T PRK03987 4 EWPEEGELVVGTVKEVKDFGAFVTLDEYPGKEGFIHISEVASGWVKNIRDHVKEGQKVVCKVIRVDPRKGHIDLSLKR 81 (262)
T ss_pred CCCCCCCEEEEEEEEEECCEEEEEECCCCCcEEEEEHHHcCcccccCHHHhCCCCCEEEEEEEEEecccCeEEEEEEe
Confidence 469999999999999999999999976 478999988764 45567788999999999999999875 468999975
No 33
>cd05686 S1_pNO40 S1_pNO40: pNO40 , S1-like RNA-binding domain. pNO40 is a nucleolar protein of unknown function with an N-terminal S1 RNA binding domain, a CCHC type zinc finger, and clusters of basic amino acids representing a potential nucleolar targeting signal. pNO40 was identified through a yeast two-hybrid interaction screen of a human kidney cDNA library using the pinin (pnn) protein as bait. pNO40 is thought to play a role in ribosome maturation and/or biogenesis.
Probab=98.17 E-value=1.6e-05 Score=56.27 Aligned_cols=70 Identities=14% Similarity=0.121 Sum_probs=57.8
Q ss_pred CCCCCEEEEEEEEEecceEEEEECC-CCCeeeecccccc-ccccCCcCCCCCCEEEEEEEecCCCCeeEEEE
Q psy230 54 PTRGDLVIGVVTSRVGDNYRVDIGS-HDPAVLSYLAFEG-ATKKNPPKVETGDVVAGKLLTANKDMESEMVC 123 (222)
Q Consensus 54 P~vGDiVIG~V~~v~~~~~~VdI~~-~~~a~L~~~~f~g-atk~~r~~l~~GDlV~ArV~~~~~~~~~~Ls~ 123 (222)
|+.|+++-|+|+++.+..+.|++.. ...|.+|.+.+.. ..++.+..|++||-|.++|.+++....+.||.
T Consensus 1 ~~~g~~~~g~V~~i~~fG~fv~l~~~~~eGlvh~sel~~~~~~~~~~~~~~Gd~v~vkv~~vd~~~ki~ls~ 72 (73)
T cd05686 1 PALYQIFKGEVASVTEYGAFVKIPGCRKQGLVHKSHMSSCRVDDPSEVVDVGEKVWVKVIGREMKDKMKLSL 72 (73)
T ss_pred CcCCCEEEEEEEEEEeeeEEEEECCCCeEEEEEchhhCCCcccCHhhEECCCCEEEEEEEEECCCCcEEEEe
Confidence 6899999999999999999999954 3589999887643 33456677999999999999998765666664
No 34
>cd05703 S1_Rrp5_repeat_hs12_sc9 S1_Rrp5_repeat_hs12_sc9: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 12 (hs12) and S. cerevisiae S1 repeat 9 (sc9). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=98.15 E-value=1.5e-05 Score=56.59 Aligned_cols=68 Identities=15% Similarity=0.204 Sum_probs=57.5
Q ss_pred CCEEEEEEEEEecceEEEEECCCCCeeeeccccccc---cccCCcCCCCCCEEEEEEEecCCC-CeeEEEEe
Q psy230 57 GDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFEGA---TKKNPPKVETGDVVAGKLLTANKD-MESEMVCV 124 (222)
Q Consensus 57 GDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~ga---tk~~r~~l~~GDlV~ArV~~~~~~-~~~~Ls~~ 124 (222)
||+|-|+|+++.+..+.|++...-.|.+|.+.+... .++....|++||.|.|+|+++++. ..+.||.+
T Consensus 1 G~~V~g~V~~i~~~g~~V~l~~~i~G~i~~~~ls~~~~~~~~~~~~~~vG~~v~~kV~~id~~~~~i~Ls~k 72 (73)
T cd05703 1 GQEVTGFVNNVSKEFVWLTISPDVKGRIPLLDLSDDVSVLEHPEKKFPIGQALKAKVVGVDKEHKLLRLSAR 72 (73)
T ss_pred CCEEEEEEEEEeCCEEEEEeCCCcEEEEEHHHcCCccccccCHHHhCCCCCEEEEEEEEEeCCCCEEEEEec
Confidence 899999999999999999998889999998876422 445667899999999999999865 46788763
No 35
>cd04461 S1_Rrp5_repeat_hs8_sc7 S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 repeat 7 (sc7)-like domains. Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in S. cerevisiae Rrp5 and 14 S1 repeats in H. sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 8 and S. cerevisiae S1 repeat 7. Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=98.15 E-value=1.3e-05 Score=57.86 Aligned_cols=72 Identities=11% Similarity=0.015 Sum_probs=61.0
Q ss_pred cCCCCCCEEEEEEEEEecceEEEEECCCCCeeeecccccc-ccccCCcCCCCCCEEEEEEEecCCC-CeeEEEE
Q psy230 52 YVPTRGDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFEG-ATKKNPPKVETGDVVAGKLLTANKD-MESEMVC 123 (222)
Q Consensus 52 Y~P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~g-atk~~r~~l~~GDlV~ArV~~~~~~-~~~~Ls~ 123 (222)
..+++|+++-|+|+++......|++...-.|.+|.+.+.. ...+....|++||.|.++|.+++.. ..+.||+
T Consensus 10 ~~~~~G~i~~g~V~~v~~~G~fv~l~~~~~g~v~~~el~~~~~~~~~~~~~~Gd~v~vkV~~id~~~~~i~lsl 83 (83)
T cd04461 10 SDLKPGMVVHGYVRNITPYGVFVEFLGGLTGLAPKSYISDEFVTDPSFGFKKGQSVTAKVTSVDEEKQRFLLSL 83 (83)
T ss_pred HhCCCCCEEEEEEEEEeeceEEEEcCCCCEEEEEHHHCCcccccCHHHhcCCCCEEEEEEEEEcCCCCEEEEeC
Confidence 4578999999999999999999999988999999877643 3456778899999999999999864 5677764
No 36
>TIGR00448 rpoE DNA-directed RNA polymerase (rpoE), archaeal and eukaryotic form. This family seems to be confined to the archea and eukaryotic taxa and are quite dissimilar to E.coli rpoE.
Probab=98.11 E-value=1.8e-05 Score=65.69 Aligned_cols=81 Identities=17% Similarity=0.255 Sum_probs=64.6
Q ss_pred ccCCCCCCEEEEEEEEEecceEEEEECCCCCeeeecccccc-------c-----cccCCcCCCCCCEEEEEEEecC----
Q psy230 51 RYVPTRGDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFEG-------A-----TKKNPPKVETGDVVAGKLLTAN---- 114 (222)
Q Consensus 51 ~Y~P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~g-------a-----tk~~r~~l~~GDlV~ArV~~~~---- 114 (222)
.|.|.+|+++-|+|++++...+.|+++ +..++++..++.. . -++....++.||.|++||.+++
T Consensus 76 ~f~p~~gEvv~G~V~~v~~~GifV~lg-~~~gi~~~~~l~~~~~~~d~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~~ 154 (179)
T TIGR00448 76 VFKPELGEIVEGEVIEIVEFGAFVSLG-PFDGLFHVSQVTDDYCYYDPKESALIGKETKKVLDEGDKVRARIVALSLKDR 154 (179)
T ss_pred EEeccCCCEEEEEEEEEEeeEEEEEeC-CceEEEEcHHhCCCceEEccccceEEEccCCeEEcCCCEEEEEEEEEEccCC
Confidence 378999999999999999999999995 6888888654321 1 1245578999999999999986
Q ss_pred --CCCeeEEEEecCCCccccCcccC
Q psy230 115 --KDMESEMVCVDSRGKEFIMGILN 137 (222)
Q Consensus 115 --~~~~~~Ls~~~~~~~~~~~G~L~ 137 (222)
+...+.||+++ +++|+++
T Consensus 155 ~~~~~~I~lt~k~-----~~LG~~~ 174 (179)
T TIGR00448 155 RPEGSKIGLTMRQ-----PLLGKLE 174 (179)
T ss_pred CCCcceEEEEecc-----CcCCccc
Confidence 23468889865 8999984
No 37
>COG1098 VacB Predicted RNA binding protein (contains ribosomal protein S1 domain) [Translation, ribosomal structure and biogenesis]
Probab=98.10 E-value=5.1e-06 Score=64.73 Aligned_cols=73 Identities=14% Similarity=0.150 Sum_probs=68.4
Q ss_pred CCCCCCEEEEEEEEEecceEEEEECCCCCeeeecccc-ccccccCCcCCCCCCEEEEEEEecCCCCeeEEEEec
Q psy230 53 VPTRGDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAF-EGATKKNPPKVETGDVVAGKLLTANKDMESEMVCVD 125 (222)
Q Consensus 53 ~P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f-~gatk~~r~~l~~GDlV~ArV~~~~~~~~~~Ls~~~ 125 (222)
.+++||+|-|+||.+++-.++|++.....++.|++.. .|..+++.+.|.+||-|.++|+++++++.+.||++.
T Consensus 2 ~~kvG~~l~GkItgI~~yGAFV~l~~g~tGLVHISEIa~~fVkdI~d~L~vG~eV~vKVl~ide~GKisLSIr~ 75 (129)
T COG1098 2 SMKVGSKLKGKITGITPYGAFVELEGGKTGLVHISEIADGFVKDIHDHLKVGQEVKVKVLDIDENGKISLSIRK 75 (129)
T ss_pred CccccceEEEEEEeeEecceEEEecCCCcceEEehHhhhhhHHhHHHHhcCCCEEEEEEEeeccCCCcceehHH
Confidence 3689999999999999999999999999999999876 578899999999999999999999999999999976
No 38
>PRK05807 hypothetical protein; Provisional
Probab=98.09 E-value=2.9e-05 Score=61.88 Aligned_cols=70 Identities=11% Similarity=0.133 Sum_probs=61.0
Q ss_pred CCCCEEEEEEEEEecceEEEEECCCCCeeeeccccc-cccccCCcCCCCCCEEEEEEEecCCCCeeEEEEec
Q psy230 55 TRGDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFE-GATKKNPPKVETGDVVAGKLLTANKDMESEMVCVD 125 (222)
Q Consensus 55 ~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~-gatk~~r~~l~~GDlV~ArV~~~~~~~~~~Ls~~~ 125 (222)
++||+|.|+|+++.+..+.|++. ...|++|.+.+. +..++....|++||.|.++|.+++.++.+.||+..
T Consensus 4 ~vG~vv~G~Vt~i~~~GafV~L~-~~~Glvhiseis~~~v~~~~~~~kvGd~V~VkV~~id~~gkI~LSlk~ 74 (136)
T PRK05807 4 KAGSILEGTVVNITNFGAFVEVE-GKTGLVHISEVADTYVKDIREHLKEQDKVKVKVISIDDNGKISLSIKQ 74 (136)
T ss_pred cCCCEEEEEEEEEECCeEEEEEC-CEEEEEEhhhcccccccCccccCCCCCEEEEEEEEECCCCcEEEEEEe
Confidence 57999999999999999999994 468999988764 45566678899999999999999877789999865
No 39
>cd05688 S1_RPS1_repeat_ec3 S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 3 (ec3) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=98.08 E-value=1.4e-05 Score=54.60 Aligned_cols=60 Identities=32% Similarity=0.386 Sum_probs=49.9
Q ss_pred CCCEEEEEEEEEecceEEEEECCCCCeeeeccccc-cccccCCcCCCCCCEEEEEEEecCCC
Q psy230 56 RGDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFE-GATKKNPPKVETGDVVAGKLLTANKD 116 (222)
Q Consensus 56 vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~-gatk~~r~~l~~GDlV~ArV~~~~~~ 116 (222)
+|++|.|+|+++....|.|+++ ...|.||...+. ...+..+..|++||.|.|+|.+++.+
T Consensus 1 ~g~~~~g~V~~v~~~g~~v~l~-~~~g~l~~~e~~~~~~~~~~~~~~~Gd~v~v~i~~vd~~ 61 (68)
T cd05688 1 EGDVVEGTVKSITDFGAFVDLG-GVDGLLHISDMSWGRVKHPSEVVNVGDEVEVKVLKIDKE 61 (68)
T ss_pred CCCEEEEEEEEEEeeeEEEEEC-CeEEEEEhHHCCCccccCHhHEECCCCEEEEEEEEEECC
Confidence 4899999999999999999998 588999986653 23344556799999999999999764
No 40
>cd04472 S1_PNPase S1_PNPase: Polynucleotide phosphorylase (PNPase), ), S1-like RNA-binding domain. PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA. It is a trimeric multidomain protein. The C-terminus contains the S1 domain which binds ssRNA. This family is classified based on the S1 domain. PNPase nonspecifically removes the 3' nucleotides from mRNA, but is stalled by double-stranded RNA structures such as a stem-loop. Evidence shows that a minimum of 7-10 unpaired nucleotides at the 3' end, is required for PNPase degradation. It is suggested that PNPase also dephosphorylates the RNA 5' end. This additional activity may regulate the 5'-dependent activity of RNaseE in vivo.
Probab=98.07 E-value=2.8e-05 Score=53.20 Aligned_cols=66 Identities=15% Similarity=0.141 Sum_probs=54.5
Q ss_pred CCEEEEEEEEEecceEEEEECCCCCeeeeccccccc-cccCCcCCCCCCEEEEEEEecCCCCeeEEE
Q psy230 57 GDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFEGA-TKKNPPKVETGDVVAGKLLTANKDMESEMV 122 (222)
Q Consensus 57 GDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~ga-tk~~r~~l~~GDlV~ArV~~~~~~~~~~Ls 122 (222)
|+++.|+|+++....+.|+|.....|.||...++.. .......|++||.|.++|.+++....+.||
T Consensus 1 g~~~~g~V~~v~~~G~~v~l~~~~~g~l~~~~l~~~~~~~~~~~~~~Gd~v~v~v~~~d~~~~i~ls 67 (68)
T cd04472 1 GKIYEGKVVKIKDFGAFVEILPGKDGLVHISELSDERVEKVEDVLKVGDEVKVKVIEVDDRGRISLS 67 (68)
T ss_pred CCEEEEEEEEEEEeEEEEEeCCCCEEEEEhHHcCCccccCHHHccCCCCEEEEEEEEECCCCcEEee
Confidence 789999999999999999999889999998877543 223345799999999999999875566665
No 41
>cd05685 S1_Tex S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has been characterized in Bordetella pertussis and Pseudomonas aeruginosa. The tex gene is essential in Bortella pertusis and is named for its role in toxin expression. Tex has two functional domains, an N-terminal domain homologous to the Escherichia coli maltose repression protein, which is a poorly defined transcriptional factor, and a C-terminal S1 RNA-binding domain. Tex is found in prokaryotes, eukaryotes, and archaea.
Probab=98.04 E-value=1.8e-05 Score=53.95 Aligned_cols=65 Identities=22% Similarity=0.300 Sum_probs=52.8
Q ss_pred CCEEEEEEEEEecceEEEEECCCCCeeeecccccc-ccccCCcCCCCCCEEEEEEEecCCC-CeeEE
Q psy230 57 GDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFEG-ATKKNPPKVETGDVVAGKLLTANKD-MESEM 121 (222)
Q Consensus 57 GDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~g-atk~~r~~l~~GDlV~ArV~~~~~~-~~~~L 121 (222)
|+++.|+|+++.+..+.|+++....|.+|...+.. ...+....|++||.|.|+|.+++.. ..+.|
T Consensus 1 g~~~~g~V~~i~~~G~fv~l~~~~~g~~~~~~l~~~~~~~~~~~~~~Gd~v~v~i~~vd~~~~~i~l 67 (68)
T cd05685 1 GMVLEGVVTNVTDFGAFVDIGVKQDGLIHISKMADRFVSHPSDVVSVGDIVEVKVISIDEERGRISL 67 (68)
T ss_pred CCEEEEEEEEEecccEEEEcCCCCEEEEEHHHCCCccccCHHHhcCCCCEEEEEEEEEECCCCEEec
Confidence 78999999999999999999988899999876543 2334556799999999999999863 34444
No 42
>PHA02945 interferon resistance protein; Provisional
Probab=98.01 E-value=4.5e-05 Score=56.09 Aligned_cols=70 Identities=21% Similarity=0.241 Sum_probs=59.0
Q ss_pred CCCCCCEEEEEEEEEecceEEEEECC--CCCeeeecccc---ccccccCCcCCCCCCEEEEEEEecCCCC-eeEEEEec
Q psy230 53 VPTRGDLVIGVVTSRVGDNYRVDIGS--HDPAVLSYLAF---EGATKKNPPKVETGDVVAGKLLTANKDM-ESEMVCVD 125 (222)
Q Consensus 53 ~P~vGDiVIG~V~~v~~~~~~VdI~~--~~~a~L~~~~f---~gatk~~r~~l~~GDlV~ArV~~~~~~~-~~~Ls~~~ 125 (222)
.|.+||+|+|+|+. .+..+.|++.- .-.|.+|.+.. +|..|. |+.+ .|..|.|+|+.+++.. -+.||.+.
T Consensus 8 ~P~~GelvigtV~~-~d~ga~v~L~EY~g~eg~i~~seveva~~wvK~-rd~l-~GqkvV~KVirVd~~kg~IDlSlK~ 83 (88)
T PHA02945 8 LPNVGDVLKGKVYE-NGYALYIDLFDYPHSEAILAESVQMHMNRYFKY-RDKL-VGKTVKVKVIRVDYTKGYIDVNYKR 83 (88)
T ss_pred CCCCCcEEEEEEEe-cCceEEEEecccCCcEEEEEeehhhhccceEee-eeEe-cCCEEEEEEEEECCCCCEEEeEeeE
Confidence 69999999999999 99999999975 45799998744 355566 9999 9999999999999763 57888765
No 43
>cd05697 S1_Rrp5_repeat_hs5 S1_Rrp5_repeat_hs5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 5 (hs5) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=98.01 E-value=3.8e-05 Score=53.38 Aligned_cols=66 Identities=15% Similarity=0.221 Sum_probs=55.0
Q ss_pred CCEEEEEEEEEecceEEEEECCCCCeeeecccccc-ccccCCcCCCCCCEEEEEEEecCCC-CeeEEE
Q psy230 57 GDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFEG-ATKKNPPKVETGDVVAGKLLTANKD-MESEMV 122 (222)
Q Consensus 57 GDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~g-atk~~r~~l~~GDlV~ArV~~~~~~-~~~~Ls 122 (222)
|++|-|+|+++....+.|++...-.|.+|.+.+.. ..++....|++||.+.++|.+++.+ ..+.||
T Consensus 1 G~~v~g~V~~v~~~Gv~V~l~~~v~g~i~~~~l~~~~~~~~~~~~~~Gd~i~~~V~~id~~~~~i~ls 68 (69)
T cd05697 1 GQVVKGTIRKLRPSGIFVKLSDHIKGLVPPMHLADVRLKHPEKKFKPGLKVKCRVLSVEPERKRLVLT 68 (69)
T ss_pred CCEEEEEEEEEeccEEEEEecCCcEEEEEHHHCCCccccCHHHcCCCCCEEEEEEEEEECCCCEEEEE
Confidence 78999999999999999999877899999877653 2344556799999999999999864 566665
No 44
>cd05694 S1_Rrp5_repeat_hs2_sc2 S1_Rrp5_repeat_hs2_sc2: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 2 (hs2) and S. cerevisiae S1 repeat 2 (sc2). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=97.99 E-value=7.3e-05 Score=53.33 Aligned_cols=66 Identities=18% Similarity=0.234 Sum_probs=54.8
Q ss_pred CCCCEEEEEEEEEecceEEEEEC-CCCCeeeeccccccccccCCcCCCCCCEEEEEEEecCCC-CeeEEEEec
Q psy230 55 TRGDLVIGVVTSRVGDNYRVDIG-SHDPAVLSYLAFEGATKKNPPKVETGDVVAGKLLTANKD-MESEMVCVD 125 (222)
Q Consensus 55 ~vGDiVIG~V~~v~~~~~~VdI~-~~~~a~L~~~~f~gatk~~r~~l~~GDlV~ArV~~~~~~-~~~~Ls~~~ 125 (222)
+.|++|-|.|.++.+..|.||++ ....|+||....... ..|++||.+.|+|.++++. ..+.||+..
T Consensus 3 ~~G~~v~g~V~si~d~G~~v~~g~~gv~Gfl~~~~~~~~-----~~~~~Gq~v~~~V~~vd~~~~~v~ls~k~ 70 (74)
T cd05694 3 VEGMVLSGCVSSVEDHGYILDIGIPGTTGFLPKKDAGNF-----SKLKVGQLLLCVVEKVKDDGRVVSLSADP 70 (74)
T ss_pred CCCCEEEEEEEEEeCCEEEEEeCCCCcEEEEEHHHCCcc-----cccCCCCEEEEEEEEEECCCCEEEEEEee
Confidence 57999999999999999999997 456899997554311 7899999999999999865 457888864
No 45
>cd00164 S1_like S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains are members of the Oligonucleotide/oligosaccharide Binding (OB) fold.
Probab=97.97 E-value=2.7e-05 Score=52.01 Aligned_cols=56 Identities=20% Similarity=0.173 Sum_probs=47.8
Q ss_pred EEEEEEEEecceEEEEECCCCCeeeecccccc-ccccCCcCCCCCCEEEEEEEecCC
Q psy230 60 VIGVVTSRVGDNYRVDIGSHDPAVLSYLAFEG-ATKKNPPKVETGDVVAGKLLTANK 115 (222)
Q Consensus 60 VIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~g-atk~~r~~l~~GDlV~ArV~~~~~ 115 (222)
|.|+|+++....+.|++.....|.+|.+.+.. ..++++..|++||.|.|+|.+++.
T Consensus 1 v~g~V~~v~~~g~~v~l~~~~~g~~~~~~~~~~~~~~~~~~~~~G~~v~~~v~~~d~ 57 (65)
T cd00164 1 VTGKVVSITKFGVFVELEDGVEGLVHISELSDKFVKDPSEVFKVGDEVEVKVLEVDP 57 (65)
T ss_pred CEEEEEEEEeeeEEEEecCCCEEEEEHHHCCCccccCHhhEeCCCCEEEEEEEEEcC
Confidence 47999999999999999988999999877653 234567789999999999999875
No 46
>cd04453 S1_RNase_E S1_RNase_E: RNase E and RNase G, S1-like RNA-binding domain. RNase E is an essential endoribonuclease in the processing and degradation of RNA. In addition to its role in mRNA degradation, RNase E has also been implicated in the processing of rRNA, and the maturation of tRNA, 10Sa RNA and the M1 precursor of RNase P. RNase E associates with PNPase (3' to 5' exonuclease), Rhl B (DEAD-box RNA helicase) and enolase (glycolytic enzyme) to form the RNA degradosome. RNase E tends to cut mRNA within single-stranded regions that are rich in A/U nucleotides. The N-terminal region of RNase E contains the catalytic site. Within the conserved N-terminal domain of RNAse E and RNase G, there is an S1-like subdomain, which is an ancient single-stranded RNA-binding domain. S1 domain is an RNA-binding module originally identified in the ribosomal protein S1. The S1 domain is required for RNA cleavage by RNase E. RNase G is paralogous to RNase E with an N-terminal catalytic domain th
Probab=97.96 E-value=5.3e-05 Score=55.85 Aligned_cols=71 Identities=18% Similarity=0.200 Sum_probs=56.6
Q ss_pred CCCCCEEEEEEEEEecc--eEEEEECCCCCeeeecccccc----ccccCCcCCCCCCEEEEEEEecCCC-CeeEEEEe
Q psy230 54 PTRGDLVIGVVTSRVGD--NYRVDIGSHDPAVLSYLAFEG----ATKKNPPKVETGDVVAGKLLTANKD-MESEMVCV 124 (222)
Q Consensus 54 P~vGDiVIG~V~~v~~~--~~~VdI~~~~~a~L~~~~f~g----atk~~r~~l~~GDlV~ArV~~~~~~-~~~~Ls~~ 124 (222)
|++||++.|+|+++.+. .+.|||+....|+||.+.... ..++....|++||.|.++|...... ..+.||+.
T Consensus 5 ~~~G~iy~g~V~~i~~~~~GaFV~l~~g~~Gllh~seis~~~~~~v~~~~~~~~~Gd~v~VqV~~~~~~~K~~~lt~~ 82 (88)
T cd04453 5 PIVGNIYLGRVKKIVPGLQAAFVDIGLGKNGFLHLSDILPAYFKKHKKIAKLLKEGQEILVQVVKEPIGTKGPRLTTN 82 (88)
T ss_pred CCCCCEEEEEEEEeccCCcEEEEEeCCCCEEEEEhHHcCchhccccCCHHHcCCCCCEEEEEEEEecCCCCCceEEEE
Confidence 57999999999999985 999999988899999877632 2234466899999999999986533 34666653
No 47
>cd02393 PNPase_KH Polynucleotide phosphorylase (PNPase) K homology RNA-binding domain (KH). PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA in prokaryotes and plant chloroplasts. The C-terminal region of PNPase contains domains homologous to those in other RNA binding proteins: a KH domain and an S1 domain. KH domains bind single-stranded RNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=97.96 E-value=1.4e-05 Score=55.02 Aligned_cols=47 Identities=13% Similarity=0.309 Sum_probs=44.2
Q ss_pred EEEechhhhhhccCCChhHHHHhhhcCCCcEEEEEEeCCeEEEeeCCch
Q psy230 141 LLHTSISLCRKLLNPKCPLLKQLAKRSRQKMELSIGMNGKIWIRCESFS 189 (222)
Q Consensus 141 l~~v~~~~~~rl~~~~~~~l~~l~~~~~~~~ei~vG~NG~iWi~~~~~~ 189 (222)
.+.|++.++.+++|++++.++.|.+ .+++.|-+..||.|||.+.+..
T Consensus 5 ~i~Ip~~~ig~iIGkgG~~ik~I~~--~tg~~I~i~~~g~v~I~G~~~~ 51 (61)
T cd02393 5 TMKIPPDKIRDVIGPGGKTIKKIIE--ETGVKIDIEDDGTVYIAASDKE 51 (61)
T ss_pred EEEeChhheeeeECCCchHHHHHHH--HHCCEEEeCCCCEEEEEeCCHH
Confidence 5889999999999999999999999 9999999999999999998765
No 48
>cd05695 S1_Rrp5_repeat_hs3 S1_Rrp5_repeat_hs3: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 3 (hs3). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=97.93 E-value=6.8e-05 Score=52.10 Aligned_cols=59 Identities=17% Similarity=0.254 Sum_probs=50.2
Q ss_pred CCEEEEEEEEEecceEEEEECCCCCeeeeccccccccccCCcCCCCCCEEEEEEEecCCC
Q psy230 57 GDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFEGATKKNPPKVETGDVVAGKLLTANKD 116 (222)
Q Consensus 57 GDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~gatk~~r~~l~~GDlV~ArV~~~~~~ 116 (222)
||+|-|+|+++.+....|++.....|.+|.+.+...... ...|++||-|.|||+.+++.
T Consensus 1 G~~V~g~V~~i~~~G~~v~l~~~v~g~v~~~~l~~~~~~-~~~~~~G~~i~~kVi~id~~ 59 (66)
T cd05695 1 GMLVNARVKKVLSNGLILDFLSSFTGTVDFLHLDPEKSS-KSTYKEGQKVRARILYVDPS 59 (66)
T ss_pred CCEEEEEEEEEeCCcEEEEEcCCceEEEEHHHcCCccCc-ccCcCCCCEEEEEEEEEeCC
Confidence 899999999999999999997778999998776422222 67799999999999999864
No 49
>cd04455 S1_NusA S1_NusA: N-utilizing substance A protein (NusA), S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. NusA is a transcription elongation factor containing an N-terminal catalytic domain and three RNA binding domains (RBD's). The RBD's include one S1 domain and two KH domains that form an RNA binding surface. DNA transcription by RNA polymerase (RNAP) includes three phases - initiation, elongation, and termination. During initiation, sigma factors bind RNAP and target RNAP to specific promoters. During elongation, N-utilization substances (NusA, B, E, and G) replace sigma factors and regulate pausing, termination, and antitermination. NusA is cold-shock-inducible.
Probab=97.92 E-value=8.8e-05 Score=51.60 Aligned_cols=56 Identities=25% Similarity=0.319 Sum_probs=48.5
Q ss_pred CCCCEEEEEEEEEecceEEEEECCCCCeeeeccccccccccCCcCCCCCCEEEEEEEecCCC
Q psy230 55 TRGDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFEGATKKNPPKVETGDVVAGKLLTANKD 116 (222)
Q Consensus 55 ~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~gatk~~r~~l~~GDlV~ArV~~~~~~ 116 (222)
..|++|-|+|.++..+.+.|||+. ..|+||...+. .++.|++||-|.+.|.+++++
T Consensus 2 ~~g~iV~G~V~~~~~~~~~vdig~-~eg~lp~~e~~-----~~~~~~~Gd~v~v~v~~v~~~ 57 (67)
T cd04455 2 REGEIVTGIVKRVDRGNVIVDLGK-VEAILPKKEQI-----PGESYRPGDRIKAYVLEVRKT 57 (67)
T ss_pred CCCCEEEEEEEEEcCCCEEEEcCC-eEEEeeHHHCC-----CCCcCCCCCEEEEEEEEEecC
Confidence 579999999999999999999987 89999977663 234689999999999998754
No 50
>PTZ00248 eukaryotic translation initiation factor 2 subunit 1; Provisional
Probab=97.89 E-value=5.1e-05 Score=68.37 Aligned_cols=94 Identities=12% Similarity=0.028 Sum_probs=73.4
Q ss_pred cCCCCCCEEEEEEEEEecceEEEEEC--CCCCeeeeccccc-cccccCCcCCCCCCEEEEEEEecCCC-CeeEEEEecCC
Q psy230 52 YVPTRGDLVIGVVTSRVGDNYRVDIG--SHDPAVLSYLAFE-GATKKNPPKVETGDVVAGKLLTANKD-MESEMVCVDSR 127 (222)
Q Consensus 52 Y~P~vGDiVIG~V~~v~~~~~~VdI~--~~~~a~L~~~~f~-gatk~~r~~l~~GDlV~ArV~~~~~~-~~~~Ls~~~~~ 127 (222)
-.|.+||+|.|+|+++....+.|+|. ....|++|.+.+. +..++.+..+++||-|.++|+++++. +.+.||.+..+
T Consensus 13 ~~P~~GdvV~g~V~~I~d~GafV~L~EY~gvEGlIhiSElS~~ri~~i~d~vkvGd~v~vkVl~VD~ekg~IdLS~K~v~ 92 (319)
T PTZ00248 13 KFPEEDDLVMVKVVRITEMGAYVSLLEYDDIEGMILMSELSKRRIRSINKLIRVGRHEVVVVLRVDKEKGYIDLSKKRVS 92 (319)
T ss_pred hCCCCCCEEEEEEEEEeCCeEEEEecCCCCcEEEEEHHHhcccccCCHHHhcCCCCEEEEEEEEEeCCCCEEEEEeeecc
Confidence 36899999999999999999999996 3579999998764 46678889999999999999999754 45899988632
Q ss_pred Cc-----ccc--CcccCCceEEEec
Q psy230 128 GK-----EFI--MGILNDGYLLHTS 145 (222)
Q Consensus 128 ~~-----~~~--~G~L~~G~l~~v~ 145 (222)
.. ... -|..-.|.+..+.
T Consensus 93 ~~pw~~~~e~~~~g~~v~~~V~~ia 117 (319)
T PTZ00248 93 PEDIEACEEKFSKSKKVHSIMRHIA 117 (319)
T ss_pred cchHHHHHHhCcCCCEEEEEEEEch
Confidence 11 111 2666666666663
No 51
>cd05684 S1_DHX8_helicase S1_DHX8_helicase: The N-terminal S1 domain of human ATP-dependent RNA helicase DHX8, a DEAH (Asp-Glu-Ala-His) box polypeptide. The DEAH-box RNA helicases are thought to play key roles in pre-mRNA splicing and DHX8 facilitates nuclear export of spliced mRNA by releasing the RNA from the spliceosome. DHX8 is also known as HRH1 (human RNA helicase 1) in Homo sapiens and PRP22 in Saccharomyces cerevisiae.
Probab=97.76 E-value=0.00024 Score=50.70 Aligned_cols=68 Identities=16% Similarity=0.174 Sum_probs=58.5
Q ss_pred CCEEEEEEEEEecceEEEEEC---CCCCeeeeccccccc-c-ccCCcCCCCCCEEEEEEEecCCCCeeEEEEec
Q psy230 57 GDLVIGVVTSRVGDNYRVDIG---SHDPAVLSYLAFEGA-T-KKNPPKVETGDVVAGKLLTANKDMESEMVCVD 125 (222)
Q Consensus 57 GDiVIG~V~~v~~~~~~VdI~---~~~~a~L~~~~f~ga-t-k~~r~~l~~GDlV~ArV~~~~~~~~~~Ls~~~ 125 (222)
|+++-|+|+++.+..+.|+|. ....|.+|.+.++.. . ++.+..|++||.|.++|.+++ ...+.|+++.
T Consensus 1 G~~~~g~V~~v~~~G~fv~l~~~~~~~~gll~~s~l~~~~~~~~~~~~~~~Gd~v~v~v~~vd-~~~i~~s~k~ 73 (79)
T cd05684 1 GKIYKGKVTSIMDFGCFVQLEGLKGRKEGLVHISQLSFEGRVANPSDVVKRGQKVKVKVISIQ-NGKISLSMKD 73 (79)
T ss_pred CCEEEEEEEEEEeeeEEEEEeCCCCCcEEEEEhHhccCCCCcCChhheeCCCCEEEEEEEEEe-CCEEEEEEEe
Confidence 688999999999999999998 357899999887543 2 566778999999999999998 7789999865
No 52
>COG1095 RPB7 DNA-directed RNA polymerase, subunit E' [Transcription]
Probab=97.69 E-value=0.00015 Score=60.27 Aligned_cols=81 Identities=19% Similarity=0.238 Sum_probs=64.0
Q ss_pred ccCCCCCCEEEEEEEEEecceEEEEECCCCCeeeeccccccc------------cccCCcCCCCCCEEEEEEEecCCCC-
Q psy230 51 RYVPTRGDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFEGA------------TKKNPPKVETGDVVAGKLLTANKDM- 117 (222)
Q Consensus 51 ~Y~P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~ga------------tk~~r~~l~~GDlV~ArV~~~~~~~- 117 (222)
.|.|..|.+|-|.|+++....++|.|+ |.++.+|.++.... .+..+..|+.||.|+|||.+.+...
T Consensus 76 ~fkP~~gEVV~GeVv~~~~~G~fV~ig-p~dglvh~sqi~dd~~~~d~~~~~~~g~~tk~~i~~gd~VR~RIv~~s~~~~ 154 (183)
T COG1095 76 VFKPFRGEVVEGEVVEVVEFGAFVRIG-PLDGLVHVSQIMDDYIDYDEKNKVLIGEETKRVLKVGDKVRARIVGVSLKSR 154 (183)
T ss_pred EEEeccccEEEEEEEEEeecceEEEec-cccccccHhhccCcccccCcccceeeecccceEEecCCEEEEEEEEEecccC
Confidence 489999999999999999999999999 78999998764311 1345568999999999999876432
Q ss_pred -----eeEEEEecCCCccccCcccC
Q psy230 118 -----ESEMVCVDSRGKEFIMGILN 137 (222)
Q Consensus 118 -----~~~Ls~~~~~~~~~~~G~L~ 137 (222)
.+.||. |.+++|+++
T Consensus 155 ~~~~~~I~lTm-----rq~~LGkle 174 (183)
T COG1095 155 RPRESKIGLTM-----RQPGLGKLE 174 (183)
T ss_pred ccccceEEEEe-----ccccCCcch
Confidence 244554 559999984
No 53
>cd05690 S1_RPS1_repeat_ec5 S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 5 (ec5) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=97.66 E-value=0.0002 Score=49.30 Aligned_cols=60 Identities=13% Similarity=0.142 Sum_probs=51.7
Q ss_pred CCEEEEEEEEEecceEEEEECCCCCeeeecccccc--ccccCCcCCCCCCEEEEEEEecCCC
Q psy230 57 GDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFEG--ATKKNPPKVETGDVVAGKLLTANKD 116 (222)
Q Consensus 57 GDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~g--atk~~r~~l~~GDlV~ArV~~~~~~ 116 (222)
|+++-|+|+++.+..+.|++.....|.+|.+.++. ..++.+..|++||.|.|+|.+++..
T Consensus 1 G~~~~g~V~~i~~~G~fv~l~~~~~Glv~~~~l~~~~~~~~~~~~~~~G~~v~v~v~~id~~ 62 (69)
T cd05690 1 GTVVSGKIKSITDFGIFVGLDGGIDGLVHISDISWTQRVRHPSEIYKKGQEVEAVVLNIDVE 62 (69)
T ss_pred CCEEEEEEEEEEeeeEEEEeCCCCEEEEEHHHCCCccccCChhhEECCCCEEEEEEEEEECC
Confidence 78999999999999999999988899999887753 3345567899999999999998754
No 54
>COG1093 SUI2 Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis]
Probab=97.64 E-value=7.6e-05 Score=65.08 Aligned_cols=149 Identities=17% Similarity=0.211 Sum_probs=104.1
Q ss_pred cccCCCCCCEEEEEEEEEecceEEEEECC--CCCeeeecccc-ccccccCCcCCCCCCEEEEEEEecCCCC-eeEEEEec
Q psy230 50 RRYVPTRGDLVIGVVTSRVGDNYRVDIGS--HDPAVLSYLAF-EGATKKNPPKVETGDVVAGKLLTANKDM-ESEMVCVD 125 (222)
Q Consensus 50 ~~Y~P~vGDiVIG~V~~v~~~~~~VdI~~--~~~a~L~~~~f-~gatk~~r~~l~~GDlV~ArV~~~~~~~-~~~Ls~~~ 125 (222)
.+-.|..||+|||+|.++.+-.+.|.+.- .-.|.+|++.. .|..|..|+.+++|.-+.|+|+.+++.+ -+.||.+.
T Consensus 5 ~~~~PeeGEiVv~tV~~V~~~GAyv~L~EY~g~Eg~ihiSEvas~wVknIrd~vkegqkvV~kVlrVd~~rg~IDLSlkr 84 (269)
T COG1093 5 RREYPEEGEIVVGTVKQVADYGAYVELDEYPGKEGFIHISEVASGWVKNIRDYVKEGQKVVAKVLRVDPKRGHIDLSLKR 84 (269)
T ss_pred ccCCCCCCcEEEEEEEEeeccccEEEeeccCCeeeeEEHHHHHHHHHHHHHHHhhcCCeEEEEEEEEcCCCCeEeeehhh
Confidence 44579999999999999999999999975 35799998875 5788999999999999999999999764 58999987
Q ss_pred CCC--c---------------------------------------cccCcccCCceEEEechhhhh----hcc--CCC--
Q psy230 126 SRG--K---------------------------------------EFIMGILNDGYLLHTSISLCR----KLL--NPK-- 156 (222)
Q Consensus 126 ~~~--~---------------------------------------~~~~G~L~~G~l~~v~~~~~~----rl~--~~~-- 156 (222)
.+. + ...||.+-.+|= ..+. -|. +..
T Consensus 85 V~~~q~~~k~~~wk~~qka~klle~aaekl~~~~ee~~~~vg~~L~e~fG~~y~aFE-----~aa~~g~~~l~~~~~~~~ 159 (269)
T COG1093 85 VTEHQRRKKIQEWKKEQKADKLLELAAEKLGKDLEEAYEEVGWKLEEEFGSLYDAFE-----AAAKEGGEVLDDEGVPEE 159 (269)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCHHHHHHHHhHHHHHHhCCHHHHHH-----HHHhcCCcccccCCCCHH
Confidence 431 0 122555522211 0000 000 011
Q ss_pred --hhHHHHhhhcCCCcEEE-EEEeCCeEEEeeCCchhHHHHHHHHHHhhcCCHH
Q psy230 157 --CPLLKQLAKRSRQKMEL-SIGMNGKIWIRCESFSDTVRVGNLIMSCELLSYE 207 (222)
Q Consensus 157 --~~~l~~l~~~~~~~~ei-~vG~NG~iWi~~~~~~~~~~i~~~i~~~e~~~~~ 207 (222)
..+++..++ .++. .|-.-|+|=+.|..+.-+..|-.||...+...+.
T Consensus 160 ~~~~l~e~a~e----~i~~~~VkI~g~vev~s~~~dGVe~IK~aL~~A~~~~~~ 209 (269)
T COG1093 160 WKEVLKEIARE----NIEPPTVKIRGYVEVTSPAPDGVEKIKKALKAAEDNGEE 209 (269)
T ss_pred HHHHHHHHHHh----cCCCCceEEEEEEEEEecCCCcHHHHHHHHHHHHhcCcc
Confidence 134444443 2222 4556789999999999899999999988765433
No 55
>cd04473 S1_RecJ_like S1_RecJ_like: The S1 domain of the archaea-specific RecJ-like exonuclease. The function of this family is not fully understood. In Escherichia coli, RecJ degrades single-stranded DNA in the 5'-3' direction and participates in homologous recombination and mismatch repair.
Probab=97.60 E-value=0.0011 Score=47.34 Aligned_cols=64 Identities=17% Similarity=0.159 Sum_probs=54.6
Q ss_pred CCCCCCEEEEEEEEEecceEEEEECCCCCeeeeccccccccccCCcCCCCCCEEEEEEEecCCCCeeEEEE
Q psy230 53 VPTRGDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFEGATKKNPPKVETGDVVAGKLLTANKDMESEMVC 123 (222)
Q Consensus 53 ~P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~gatk~~r~~l~~GDlV~ArV~~~~~~~~~~Ls~ 123 (222)
-.++|+.+.|+|+++++..+.|++.....|.+|.+.+ ...++.||.+.++|.++..++.+.|+.
T Consensus 13 ~~~~G~~~~g~V~~i~~~G~fV~l~~~~~Glv~~se~-------~~~~~iGd~v~v~I~~i~e~~~i~l~~ 76 (77)
T cd04473 13 DLEVGKLYKGKVNGVAKYGVFVDLNDHVRGLIHRSNL-------LRDYEVGDEVIVQVTDIPENGNIDLIP 76 (77)
T ss_pred hCCCCCEEEEEEEeEecceEEEEECCCcEEEEEchhc-------cCcCCCCCEEEEEEEEECCCCcEEEEE
Confidence 4789999999999999999999999889999997654 356999999999999995556677664
No 56
>cd04460 S1_RpoE S1_RpoE: RpoE, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. RpoE is subunit E of archaeal RNA polymerase. Archaeal cells contain a single RNA polymerase made up of 12 subunits, which are homologous to the 12 subunits (RPB1-12) of eukaryotic RNA polymerase II. RpoE is homologous to Rpa43 of eukaryotic RNA polymerase I, RPB7 of eukaryotic RNA polymerase II, and Rpc25 of eukaryotic RNA polymerase III. RpoE is composed of two domains, the N-terminal RNP (ribonucleoprotein) domain and the C-terminal S1 domain. This S1 domain binds ssRNA and ssDNA. This family is classified based on the C-terminal S1 domain. The function of RpoE is not fully understood. In eukaryotes, RPB7 and RPB4 form a heterodimer that reversibly associates with the RNA polymerase II core.
Probab=97.59 E-value=0.00034 Score=52.22 Aligned_cols=73 Identities=19% Similarity=0.206 Sum_probs=57.6
Q ss_pred CEEEEEEEEEecceEEEEECCCCCeeeeccccccc-c-----------ccCCcCCCCCCEEEEEEEecCCC------Cee
Q psy230 58 DLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFEGA-T-----------KKNPPKVETGDVVAGKLLTANKD------MES 119 (222)
Q Consensus 58 DiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~ga-t-----------k~~r~~l~~GDlV~ArV~~~~~~------~~~ 119 (222)
++|.|+|+++....+.|++. +..|.+|...+... . ++....|++||.|.++|.+++.. ..+
T Consensus 1 ~vv~g~V~~i~~~GifV~l~-~v~G~v~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~Gd~v~vkI~~vd~~~~~~~~~~i 79 (99)
T cd04460 1 EVVEGEVVEVVDFGAFVRIG-PVDGLLHISQIMDDYISYDPKNKRLIGEETKRVLKVGDVVRARIVAVSLKERRPRESKI 79 (99)
T ss_pred CEEEEEEEEEEeccEEEEEc-CeEEEEEEEEccCCceEechhheeecccCcCCEECCCCEEEEEEEEEeHHHCcCCCceE
Confidence 47899999999999999998 47888887665321 1 12346789999999999999854 468
Q ss_pred EEEEecCCCccccCccc
Q psy230 120 EMVCVDSRGKEFIMGIL 136 (222)
Q Consensus 120 ~Ls~~~~~~~~~~~G~L 136 (222)
.||..+ +.+|.+
T Consensus 80 ~ls~k~-----~~~g~~ 91 (99)
T cd04460 80 GLTMRQ-----PGLGKL 91 (99)
T ss_pred EEEEec-----CCCCcH
Confidence 899865 888887
No 57
>cd05696 S1_Rrp5_repeat_hs4 S1_Rrp5_repeat_hs4: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 4 (hs4). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=97.55 E-value=0.0006 Score=47.92 Aligned_cols=67 Identities=7% Similarity=-0.012 Sum_probs=54.3
Q ss_pred CCEEE-EEEEEE-ecceEEEEECCCCCeeeeccccc-cccccCCcCCCCCCEEEEEEEecCCC-CeeEEEE
Q psy230 57 GDLVI-GVVTSR-VGDNYRVDIGSHDPAVLSYLAFE-GATKKNPPKVETGDVVAGKLLTANKD-MESEMVC 123 (222)
Q Consensus 57 GDiVI-G~V~~v-~~~~~~VdI~~~~~a~L~~~~f~-gatk~~r~~l~~GDlV~ArV~~~~~~-~~~~Ls~ 123 (222)
|+++= |+|+++ ....+.|++.....|.+|.+.+. ...++....|++||.+.|+|+++++. ..+.||+
T Consensus 1 G~v~~~g~V~~v~~~~G~~V~l~~gv~G~i~~s~l~~~~~~~~~~~~~vG~~v~~kV~~id~~~~~i~lS~ 71 (71)
T cd05696 1 GAVVDSVKVTKVEPDLGAVFELKDGLLGFVHISHLSDDKVPSDTGPFKAGTTHKARIIGYSPMDGLLQLSL 71 (71)
T ss_pred CcEeeeeEEEEEccCceEEEEeCCCCEEEEEHHHCCcchhcCcccccCCCCEEEEEEEEEeCCCCEEEEeC
Confidence 66777 899998 68889999987789999998775 34455667799999999999999854 4567764
No 58
>cd04465 S1_RPS1_repeat_ec2_hs2 S1_RPS1_repeat_ec2_hs2: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain.While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 2 of the Escherichia coli and Homo sapiens RPS1 (ec2 and hs2, respectively). Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=97.55 E-value=0.00052 Score=47.36 Aligned_cols=65 Identities=20% Similarity=0.197 Sum_probs=49.9
Q ss_pred CCEEEEEEEEEecceEEEEECCCCCeeeeccccccccccCCcCCCCCCEEEEEEEecCC-CCeeEEEE
Q psy230 57 GDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFEGATKKNPPKVETGDVVAGKLLTANK-DMESEMVC 123 (222)
Q Consensus 57 GDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~gatk~~r~~l~~GDlV~ArV~~~~~-~~~~~Ls~ 123 (222)
|++|-|+|+++....+.|++ ....|.+|.+.......+. +.-.+||.+.|+|.++++ ...+.||.
T Consensus 1 G~iv~g~V~~v~~~G~~v~l-~g~~gfip~s~~~~~~~~~-~~~~vG~~i~~~i~~vd~~~~~i~lS~ 66 (67)
T cd04465 1 GEIVEGKVTEKVKGGLIVDI-EGVRAFLPASQVDLRPVED-LDEYVGKELKFKIIEIDRERNNIVLSR 66 (67)
T ss_pred CCEEEEEEEEEECCeEEEEE-CCEEEEEEHHHCCCcccCC-hHHhCCCEEEEEEEEEeCCCCEEEEEc
Confidence 78999999999999999999 4589999987654221111 112489999999999986 45677774
No 59
>PRK07400 30S ribosomal protein S1; Reviewed
Probab=97.54 E-value=0.00031 Score=63.40 Aligned_cols=74 Identities=16% Similarity=0.186 Sum_probs=63.6
Q ss_pred cCCCCCCEEEEEEEEEecceEEEEECCCCCeeeeccccc-cccccCCcCCCCCCEEEEEEEecCCC-CeeEEEEec
Q psy230 52 YVPTRGDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFE-GATKKNPPKVETGDVVAGKLLTANKD-MESEMVCVD 125 (222)
Q Consensus 52 Y~P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~-gatk~~r~~l~~GDlV~ArV~~~~~~-~~~~Ls~~~ 125 (222)
|..++||+|-|+|+++..+...|||+....|.||.+.+. ...++....|++||.|.+.|++.++. ..+.|||+.
T Consensus 27 ~~~~~G~iv~G~V~~i~~~g~~Vdig~k~~g~lp~sEis~~~~~~~~~~~~~G~~v~~~Vi~~~~~~~~i~lS~k~ 102 (318)
T PRK07400 27 YHFKPGDIVNGTVFSLEPRGALIDIGAKTAAFMPIQEMSINRVEGPEEVLQPNETREFFILSDENEDGQLTLSIRR 102 (318)
T ss_pred hhcCCCCEEEEEEEEEECCEEEEEECCCeEEEEEHHHhccccccCHHHccCCCCEEEEEEEEEeCCCCeEEEehhh
Confidence 557999999999999999999999998889999988764 34456677899999999999998653 578999975
No 60
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=97.46 E-value=0.00064 Score=67.39 Aligned_cols=98 Identities=14% Similarity=0.061 Sum_probs=76.1
Q ss_pred eCCEEEEEEeeEEEEec-CcEEEEEccccccCCCCCCEEEEEEEEEecceEEEEECCCCCeeeeccccc-cccccCCcCC
Q psy230 23 ESSAILVSQSGILRHAK-PFTYYVDYIQRRYVPTRGDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFE-GATKKNPPKV 100 (222)
Q Consensus 23 ~~~~i~as~~G~l~~~~-~~~v~V~~~~~~Y~P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~-gatk~~r~~l 100 (222)
++|.++++..+....+. +..+...+ ..|++|+++.|+|+++....++|+|.....|.+|++.+. ...++....|
T Consensus 591 d~G~v~i~~~~~~~~~~a~~~I~~~~----~~~~vG~v~~G~V~~I~~fGafVei~~~~~GllhiSels~~~v~~~~~v~ 666 (693)
T PRK11824 591 DDGTVKIAATDGEAAEAAKERIEGIT----AEPEVGEIYEGKVVRIVDFGAFVEILPGKDGLVHISEIADERVEKVEDVL 666 (693)
T ss_pred CCceEEEEcccHHHHHHHHHHHHHhc----ccCcCCeEEEEEEEEEECCeEEEEECCCCEEEEEeeeccCccccCcccee
Confidence 46777777777655432 11222222 247899999999999999999999998899999998875 3456677889
Q ss_pred CCCCEEEEEEEecCCCCeeEEEEe
Q psy230 101 ETGDVVAGKLLTANKDMESEMVCV 124 (222)
Q Consensus 101 ~~GDlV~ArV~~~~~~~~~~Ls~~ 124 (222)
++||.|.++|.+++....+.||++
T Consensus 667 kvGD~V~VkV~~iD~~grI~LS~k 690 (693)
T PRK11824 667 KEGDEVKVKVLEIDKRGRIRLSRK 690 (693)
T ss_pred CCCCEEEEEEEEECCCCcEEEEEE
Confidence 999999999999987678999985
No 61
>cd05689 S1_RPS1_repeat_ec4 S1_RPS1_repeat_ec4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 4 (ec4) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=97.40 E-value=0.0011 Score=46.17 Aligned_cols=62 Identities=16% Similarity=0.179 Sum_probs=52.3
Q ss_pred CCCCEEEEEEEEEecceEEEEECCCCCeeeecccccc--ccccCCcCCCCCCEEEEEEEecCCC
Q psy230 55 TRGDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFEG--ATKKNPPKVETGDVVAGKLLTANKD 116 (222)
Q Consensus 55 ~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~g--atk~~r~~l~~GDlV~ArV~~~~~~ 116 (222)
.+|+.+-|+|+++....+.|++.....|.+|.+.++. ...+....|++||.|.++|.+++.+
T Consensus 2 ~~g~~~~g~V~~i~~~G~fv~l~~~~~Gl~~~~~l~~~~~~~~~~~~~~~Gd~v~v~v~~id~~ 65 (72)
T cd05689 2 PEGTRLFGKVTNLTDYGCFVELEEGVEGLVHVSEMDWTNKNIHPSKVVSLGDEVEVMVLDIDEE 65 (72)
T ss_pred cCCCEEEEEEEEEEeeEEEEEcCCCCEEEEEEEeccCcccccCcccEeCCCCEEEEEEEEeeCC
Confidence 3699999999999999999999887899999887752 2234456799999999999998754
No 62
>PTZ00162 DNA-directed RNA polymerase II subunit 7; Provisional
Probab=97.37 E-value=0.00098 Score=55.35 Aligned_cols=81 Identities=12% Similarity=0.134 Sum_probs=61.0
Q ss_pred ccCCCCCCEEEEEEEEEecceEEEEECCCCCeeeeccccc------cc-------cccCCcCCCCCCEEEEEEEecCC--
Q psy230 51 RYVPTRGDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFE------GA-------TKKNPPKVETGDVVAGKLLTANK-- 115 (222)
Q Consensus 51 ~Y~P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~------ga-------tk~~r~~l~~GDlV~ArV~~~~~-- 115 (222)
.|.|-+|.+|.|+|++++...+.|+++. ..+.+|.++.+ .. .++.+..++.||.|++||..+.-
T Consensus 76 vFrPf~gEVv~g~V~~v~~~G~~v~~Gp-~~ifI~~~~l~~~~~fd~~~~~~~~~~~~~~~~i~~g~~VR~rV~~v~~~~ 154 (176)
T PTZ00162 76 VFKPFKDEVLDAIVTDVNKLGFFAQAGP-LKAFVSRSAIPPDFVYDSDSAYPCYISSDGQIQIKPNTEVRLRLQGVRYDA 154 (176)
T ss_pred EEecCCCCEEEEEEEEEecceEEEEeeC-eEEEEcHHHCCCccEECCCCCcceEecCCCcEEECCCCEEEEEEEEEEecC
Confidence 5899999999999999999999999975 44888765433 21 12335689999999999987742
Q ss_pred -CCeeEEEEecCCCccccCcccC
Q psy230 116 -DMESEMVCVDSRGKEFIMGILN 137 (222)
Q Consensus 116 -~~~~~Ls~~~~~~~~~~~G~L~ 137 (222)
+.....|+ |.++||++.
T Consensus 155 ~~~~~i~T~-----~~~~LG~~~ 172 (176)
T PTZ00162 155 SNLFAIATI-----NSDYLGPIE 172 (176)
T ss_pred CCcEEEEEe-----cCCCcCccc
Confidence 22345555 459999983
No 63
>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase. Sohlberg, et al. present characterization of two proteins from Streptomyces coelicolor. The protein in this family was shown to have poly(A) polymerase activity and may be responsible for polyadenylating RNA in this species. Reference 2 showed that a nearly identical plasmid-encoded protein from Streptomyces antibioticus is a bifunctional enzyme that acts also as a guanosine pentaphosphate synthetase.
Probab=97.37 E-value=0.00063 Score=67.23 Aligned_cols=70 Identities=11% Similarity=0.157 Sum_probs=60.4
Q ss_pred CCCCCCEEEEEEEEEecceEEEEECCCCCeeeeccccc-----cccccCCcCCCCCCEEEEEEEecCCCCeeEEE
Q psy230 53 VPTRGDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFE-----GATKKNPPKVETGDVVAGKLLTANKDMESEMV 122 (222)
Q Consensus 53 ~P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~-----gatk~~r~~l~~GDlV~ArV~~~~~~~~~~Ls 122 (222)
.|++|++|.|+|+++.+-.++|+|.....|++|++.+. ...++.++.|++||.|.++|+++++...+.|+
T Consensus 644 ~~~vG~i~~GkV~~I~dfGaFVel~~G~eGLvHISeisdls~~~rv~~~~dv~kvGd~V~VKVl~ID~~gKI~L~ 718 (719)
T TIGR02696 644 MPEVGERFLGTVVKTTAFGAFVSLLPGKDGLLHISQIRKLAGGKRVENVEDVLSVGQKIQVEIADIDDRGKLSLV 718 (719)
T ss_pred cCCCCCEEEEEEEEEECceEEEEecCCceEEEEhhhccccccccCcCCHHHcCCCCCEEEEEEEEECCCCCeeec
Confidence 58999999999999999999999987789999998763 35567788999999999999999865555554
No 64
>COG0539 RpsA Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]
Probab=97.36 E-value=0.00051 Score=65.87 Aligned_cols=72 Identities=21% Similarity=0.234 Sum_probs=63.9
Q ss_pred CCCCCCEEEEEEEEEecceEEEEECCCCCeeeeccccc-cccccCCcCCCCCCEEEEEEEecCCC-CeeEEEEec
Q psy230 53 VPTRGDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFE-GATKKNPPKVETGDVVAGKLLTANKD-MESEMVCVD 125 (222)
Q Consensus 53 ~P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~-gatk~~r~~l~~GDlV~ArV~~~~~~-~~~~Ls~~~ 125 (222)
.-++||+|-|+|+++++-.++|||++ -.|.||.+... ++.+.-...|++||-|.++|++++.+ .-+.||++.
T Consensus 189 ~l~~G~vV~G~V~~It~~GafVdigG-vdGLlHiseiS~~rv~~P~~vvkvGd~VkvkVi~~D~e~~RVsLSlK~ 262 (541)
T COG0539 189 KLEVGEVVEGVVKNITDYGAFVDIGG-VDGLLHISEISWKRVDHPSEVVKVGDEVKVKVISLDEERGRVSLSLKQ 262 (541)
T ss_pred cCCCCceEEEEEEEeecCcEEEEecC-eeeEEehhhccccccCCHHHhcccCCEEEEEEEEEccCCCeEEEEehh
Confidence 45899999999999999999999999 99999998765 46677888999999999999999965 458999975
No 65
>PRK07400 30S ribosomal protein S1; Reviewed
Probab=97.25 E-value=0.0015 Score=58.96 Aligned_cols=73 Identities=12% Similarity=0.116 Sum_probs=61.0
Q ss_pred cCCCCCCEEEEEEEEEecceEEEEECCCCCeeeecccccc-ccccCCcCCCCCCEEEEEEEecCC-CCeeEEEEec
Q psy230 52 YVPTRGDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFEG-ATKKNPPKVETGDVVAGKLLTANK-DMESEMVCVD 125 (222)
Q Consensus 52 Y~P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~g-atk~~r~~l~~GDlV~ArV~~~~~-~~~~~Ls~~~ 125 (222)
...++||+|.|+|+++....+.|++++ ..|++|.+.+.. ...+....|++||.|.|+|.+++. ...+.||++.
T Consensus 192 ~~~k~G~vv~G~V~~I~~~G~fV~i~g-v~Gllhisels~~~~~~~~~~~~vGd~VkvkVl~iD~e~~rI~LS~K~ 266 (318)
T PRK07400 192 NRLEVGEVVVGTVRGIKPYGAFIDIGG-VSGLLHISEISHEHIETPHSVFNVNDEMKVMIIDLDAERGRISLSTKQ 266 (318)
T ss_pred ccCCCCCEEEEEEEEEECCeEEEEECC-EEEEEEHHHcccccccChhhccCCCCEEEEEEEEEeCCCCEEEEEEec
Confidence 346889999999999999999999964 679999877653 345667889999999999999975 4678999864
No 66
>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase. Members of this protein family are polyribonucleotide nucleotidyltransferase, also called polynucleotide phosphorylase. Some members have been shown also to have additional functions as guanosine pentaphosphate synthetase and as poly(A) polymerase (see model TIGR02696 for an exception clade, within this family).
Probab=97.23 E-value=0.00089 Score=66.28 Aligned_cols=65 Identities=20% Similarity=0.181 Sum_probs=57.6
Q ss_pred CCCCCCEEEEEEEEEecceEEEEECCCCCeeeeccccc-cccccCCcCCCCCCEEEEEEEecCCCC
Q psy230 53 VPTRGDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFE-GATKKNPPKVETGDVVAGKLLTANKDM 117 (222)
Q Consensus 53 ~P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~-gatk~~r~~l~~GDlV~ArV~~~~~~~ 117 (222)
.|++|+++.|+|+++....+.|+|.....|.||.+... ...++....|++||.|.++|.+++..+
T Consensus 615 ~~~~G~i~~G~V~~I~~~GafVei~~g~~GllHiSei~~~~v~~~~~~~kvGD~V~VkVi~id~~g 680 (684)
T TIGR03591 615 EPEVGKIYEGKVVRIMDFGAFVEILPGKDGLVHISEIANERVEKVEDVLKEGDEVKVKVLEIDKQG 680 (684)
T ss_pred ccccCcEEEEEEEEEeCCEEEEEECCCcEEEEEHHHcCCCcccChhhccCCCCEEEEEEEEECCCC
Confidence 58999999999999999999999998899999998874 346677888999999999999998643
No 67
>PRK06299 rpsA 30S ribosomal protein S1; Reviewed
Probab=97.10 E-value=0.003 Score=60.89 Aligned_cols=71 Identities=14% Similarity=0.090 Sum_probs=61.1
Q ss_pred CCCCEEEEEEEEEecceEEEEECCCCCeeeecccccc-cc-ccCCcCCCCCCEEEEEEEecCC-CCeeEEEEec
Q psy230 55 TRGDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFEG-AT-KKNPPKVETGDVVAGKLLTANK-DMESEMVCVD 125 (222)
Q Consensus 55 ~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~g-at-k~~r~~l~~GDlV~ArV~~~~~-~~~~~Ls~~~ 125 (222)
.+||+|-|+|++++...+.|+|+....|.+|.+.+.. .. ++....|++||.|.|+|.+++. ...+.||++.
T Consensus 372 ~~G~~v~g~V~~v~~~G~fV~l~~~v~g~i~~s~l~~~~~~~~~~~~~~~Gd~v~v~Il~vd~~~~~i~ls~k~ 445 (565)
T PRK06299 372 PVGDVVEGKVKNITDFGAFVGLEGGIDGLVHLSDISWDKKGEEAVELYKKGDEVEAVVLKVDVEKERISLGIKQ 445 (565)
T ss_pred CCCCEEEEEEEEEecceEEEECCCCCEEEEEHHHcCccccccChHhhCCCCCEEEEEEEEEeCCCCEEEEEEeh
Confidence 5799999999999999999999988999999877653 33 5666889999999999999985 4679999876
No 68
>PRK13806 rpsA 30S ribosomal protein S1; Provisional
Probab=97.07 E-value=0.003 Score=60.18 Aligned_cols=73 Identities=19% Similarity=0.185 Sum_probs=61.6
Q ss_pred CCCCCCEEEEEEEEEecceEEEEECCCCCeeeecccccc-ccccCCcCCCCCCEEEEEEEecCCCC-----eeEEEEec
Q psy230 53 VPTRGDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFEG-ATKKNPPKVETGDVVAGKLLTANKDM-----ESEMVCVD 125 (222)
Q Consensus 53 ~P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~g-atk~~r~~l~~GDlV~ArV~~~~~~~-----~~~Ls~~~ 125 (222)
..++||+|-|+|+++....+.|||+....|.+|.+.+.. ...+....|++||.|.|+|.+++.+. .+.||++.
T Consensus 199 ~l~~G~iv~G~V~~v~~~G~fV~l~~gv~g~v~~sels~~~~~~~~~~~~vGd~i~vkVl~id~~~~~~~~ri~lS~K~ 277 (491)
T PRK13806 199 TVKEGDVVEGTVTRLAPFGAFVELAPGVEGMVHISELSWSRVQKADEAVSVGDTVRVKVLGIERAKKGKGLRISLSIKQ 277 (491)
T ss_pred hCCCCCEEEEEEEEEeCCeEEEEcCCCcEEEEEHHHCCCccccChhHhcCCCCEEEEEEEEEecccCCcceEEEEEehh
Confidence 468999999999999999999999877899999887653 44566778999999999999998753 47788765
No 69
>cd04471 S1_RNase_R S1_RNase_R: RNase R C-terminal S1 domain. RNase R is a processive 3' to 5' exoribonuclease, which is a homolog of RNase II. RNase R degrades RNA with secondary structure having a 3' overhang of at least 7 nucleotides. RNase R and PNPase play an important role in the degradation of RNA with extensive secondary structure, such as rRNA, tRNA, and certain mRNA which contains repetitive extragenic palindromic sequences. The C-terminal S1 domain binds ssRNA.
Probab=97.01 E-value=0.0063 Score=43.12 Aligned_cols=67 Identities=12% Similarity=0.169 Sum_probs=52.7
Q ss_pred CCCEEEEEEEEEecceEEEEECC-CCCeeeecccccccc------------ccCCcCCCCCCEEEEEEEecCCC-CeeEE
Q psy230 56 RGDLVIGVVTSRVGDNYRVDIGS-HDPAVLSYLAFEGAT------------KKNPPKVETGDVVAGKLLTANKD-MESEM 121 (222)
Q Consensus 56 vGDiVIG~V~~v~~~~~~VdI~~-~~~a~L~~~~f~gat------------k~~r~~l~~GDlV~ArV~~~~~~-~~~~L 121 (222)
+|+++-|.|++++...+.|++.. .-.|.+|.+.++... ++....|++||.|.++|.+++.. ..+.+
T Consensus 1 ~g~~~~g~V~~v~~~G~fv~l~~~~~~G~v~~~~l~~~~~~~d~~~~~~~~~~~~~~~~~gd~v~v~v~~vd~~~~~i~~ 80 (83)
T cd04471 1 VGEEFDGVISGVTSFGLFVELDNLTVEGLVHVSTLGDDYYEFDEENHALVGERTGKVFRLGDKVKVRVVRVDLDRRKIDF 80 (83)
T ss_pred CCCEEEEEEEeEEeeeEEEEecCCCEEEEEEEEecCCCcEEEcccceEEEeccCCCEEcCCCEEEEEEEEeccccCEEEE
Confidence 48899999999999999999987 478899987765311 13457899999999999999863 44555
Q ss_pred E
Q psy230 122 V 122 (222)
Q Consensus 122 s 122 (222)
+
T Consensus 81 ~ 81 (83)
T cd04471 81 E 81 (83)
T ss_pred E
Confidence 4
No 70
>TIGR00717 rpsA ribosomal protein S1. This model provides trusted hits to most long form (6 repeat) examples of RpsA. Among homologs with only four repeats are some to which other (perhaps secondary) functions have been assigned.
Probab=97.01 E-value=0.0027 Score=60.49 Aligned_cols=68 Identities=22% Similarity=0.232 Sum_probs=59.1
Q ss_pred CCCCCEEEEEEEEEecceEEEEECCCCCeeeeccccccccccCCcCCCCCCEEEEEEEecCC-CCeeEEEEec
Q psy230 54 PTRGDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFEGATKKNPPKVETGDVVAGKLLTANK-DMESEMVCVD 125 (222)
Q Consensus 54 P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~gatk~~r~~l~~GDlV~ArV~~~~~-~~~~~Ls~~~ 125 (222)
.++|++|-|+|+++..+.+.||++....|.+|...+.. ..+.|++||.|.++|.+.++ .+.+.||+..
T Consensus 16 ~~~G~~v~g~V~~i~~~~~~v~~g~k~~g~i~~~E~~~----~~~~~~vGd~i~~~V~~~~~~~g~i~lS~~~ 84 (516)
T TIGR00717 16 TRPGSIVKGTVVAINKDTVFVDVGLKSEGRIPKEEFLD----APLEIQVGDEVEVYLDRVEDRFGETVLSREK 84 (516)
T ss_pred CCCCCEEEEEEEEEECCEEEEEcCCCcEEEEEHHHhcC----CccCCCCCCEEEEEEEEEeCCCCcEEEEHHH
Confidence 58899999999999999999999999999999877753 23679999999999998865 4678999863
No 71
>PRK06676 rpsA 30S ribosomal protein S1; Reviewed
Probab=97.00 E-value=0.0037 Score=57.55 Aligned_cols=73 Identities=18% Similarity=0.145 Sum_probs=59.9
Q ss_pred CCCCCCEEEEEEEEEecceEEEEE-CCCCCeeeecccccc-ccccCCcCCCCCCEEEEEEEecCCCC-eeEEEEec
Q psy230 53 VPTRGDLVIGVVTSRVGDNYRVDI-GSHDPAVLSYLAFEG-ATKKNPPKVETGDVVAGKLLTANKDM-ESEMVCVD 125 (222)
Q Consensus 53 ~P~vGDiVIG~V~~v~~~~~~VdI-~~~~~a~L~~~~f~g-atk~~r~~l~~GDlV~ArV~~~~~~~-~~~Ls~~~ 125 (222)
..++||+|.|+|+++..+.+.||| +....|.||...+.. ..+.....|++||-|.|+|.+++++. .+.||.+.
T Consensus 14 ~~~~G~iv~G~V~~i~~~g~~V~i~~~~~~g~lp~~e~~~~~~~~~~~~~~vGd~v~~~V~~v~~~~~~i~lS~k~ 89 (390)
T PRK06676 14 EVEVGDVVTGEVLKVEDKQVFVNIEGYKVEGVIPISELSNDHIEDINDVVKVGDELEVYVLKVEDGEGNLLLSKRR 89 (390)
T ss_pred cccCCCEEEEEEEEEECCeEEEEEecCCcEEEEEHHHhccccccCcccccCCCCEEEEEEEEEECCCCCEEEEHHH
Confidence 468899999999999999999999 777899999876643 33445567999999999999997653 47888764
No 72
>PRK07899 rpsA 30S ribosomal protein S1; Reviewed
Probab=96.95 E-value=0.0036 Score=59.64 Aligned_cols=72 Identities=22% Similarity=0.198 Sum_probs=59.3
Q ss_pred CCCCCEEEEEEEEEecceEEEEECCCCCeeeecccccc-ccccCCcCCCCCCEEEEEEEecCCC-CeeEEEEec
Q psy230 54 PTRGDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFEG-ATKKNPPKVETGDVVAGKLLTANKD-MESEMVCVD 125 (222)
Q Consensus 54 P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~g-atk~~r~~l~~GDlV~ArV~~~~~~-~~~~Ls~~~ 125 (222)
.+.||+|-|+|+++..+...|||+....|.||...+.. ...+....|++||-|.|.|++.++. +.+.||.+.
T Consensus 33 ~~~GdiV~G~V~~v~~~gv~VdIg~k~eG~Ip~~Els~~~~~~~~~~~~vGd~Ie~~V~~~~~~~g~liLS~k~ 106 (486)
T PRK07899 33 FNDGDIVEGTVVKVDRDEVLLDIGYKTEGVIPSRELSIKHDVDPNEVVEVGDEVEALVLQKEDKEGRLILSKKR 106 (486)
T ss_pred CCCCCEEEEEEEEEECCcEEEEECCCcEEEEEHHHhcccccCChhhcCCCCCEEEEEEEEEECCCCeEEEEehh
Confidence 68999999999999999999999988899999876643 2233455699999999999998643 568888864
No 73
>PRK06676 rpsA 30S ribosomal protein S1; Reviewed
Probab=96.93 E-value=0.0037 Score=57.56 Aligned_cols=72 Identities=22% Similarity=0.215 Sum_probs=60.1
Q ss_pred CCCCCCEEEEEEEEEecceEEEEECCCCCeeeecccccc-ccccCCcCCCCCCEEEEEEEecCC-CCeeEEEEec
Q psy230 53 VPTRGDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFEG-ATKKNPPKVETGDVVAGKLLTANK-DMESEMVCVD 125 (222)
Q Consensus 53 ~P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~g-atk~~r~~l~~GDlV~ArV~~~~~-~~~~~Ls~~~ 125 (222)
..++||+|-|+|+++.+..+.|+++. ..|.+|.+.+.. ..++....|++||.|.|+|.++++ ...+.||++.
T Consensus 189 ~~~~G~~v~g~V~~v~~~G~fV~l~~-v~g~v~~sels~~~~~~~~~~~~vGd~i~~~Vl~vd~~~~~i~lS~k~ 262 (390)
T PRK06676 189 SLKEGDVVEGTVARLTDFGAFVDIGG-VDGLVHISELSHERVEKPSEVVSVGQEVEVKVLSIDWETERISLSLKD 262 (390)
T ss_pred hCCCCCEEEEEEEEEecceEEEEeCC-eEEEEEHHHcCccccCCHHHhcCCCCEEEEEEEEEeCCCCEEEEEEee
Confidence 35899999999999999999999975 789999877643 344556779999999999999975 4678999875
No 74
>PRK07899 rpsA 30S ribosomal protein S1; Reviewed
Probab=96.89 E-value=0.0049 Score=58.76 Aligned_cols=71 Identities=21% Similarity=0.221 Sum_probs=59.7
Q ss_pred CCCCCEEEEEEEEEecceEEEEECCCCCeeeecccccc-ccccCCcCCCCCCEEEEEEEecCCC-CeeEEEEec
Q psy230 54 PTRGDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFEG-ATKKNPPKVETGDVVAGKLLTANKD-MESEMVCVD 125 (222)
Q Consensus 54 P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~g-atk~~r~~l~~GDlV~ArV~~~~~~-~~~~Ls~~~ 125 (222)
-++||+|-|+|+++.+....|||+. -.|.+|.+.+.. ..++....|++||.|.++|..++.. ..+.||++.
T Consensus 206 lk~G~iv~G~V~~i~~~G~FVdlgg-v~Glv~~Sels~~~v~~~~~~~kvGd~V~vkVl~iD~e~~rI~LSlK~ 278 (486)
T PRK07899 206 LQKGQVRKGVVSSIVNFGAFVDLGG-VDGLVHVSELSWKHIDHPSEVVEVGQEVTVEVLDVDMDRERVSLSLKA 278 (486)
T ss_pred ccCCCEEEEEEEEEECCeEEEEECC-EEEEEEHHHCCCcccCCHHHhcCCCCEEEEEEEEEECCCCEEEEEEee
Confidence 3589999999999999999999975 789999887653 3345556899999999999999864 678899875
No 75
>PRK06299 rpsA 30S ribosomal protein S1; Reviewed
Probab=96.86 E-value=0.0048 Score=59.55 Aligned_cols=71 Identities=14% Similarity=0.239 Sum_probs=61.6
Q ss_pred CCCCEEEEEEEEEecceEEEEECCCCCeeeeccccc-cccccCCcCCCCCCEEEEEEEecCCC-CeeEEEEec
Q psy230 55 TRGDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFE-GATKKNPPKVETGDVVAGKLLTANKD-MESEMVCVD 125 (222)
Q Consensus 55 ~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~-gatk~~r~~l~~GDlV~ArV~~~~~~-~~~~Ls~~~ 125 (222)
++||+|.|+|+++......|.+.....|++|.+... ...++....|++||.|.|+|++++.+ ..+.||+..
T Consensus 459 ~~G~vV~G~V~~v~~~G~fV~l~~gi~g~i~~se~s~~~~~~~~~~~~~Gd~v~~~V~~vd~~~~~i~LS~k~ 531 (565)
T PRK06299 459 KKGSIVTGTVTEVKDKGAFVELEDGVEGLIRASELSRDRVEDATEVLKVGDEVEAKVINIDRKNRRISLSIKA 531 (565)
T ss_pred CCCCEEEEEEEEEecCceEEecCCCcEEEEEHHHhcchhccCccccCCCCCEEEEEEEEEccccCEEEEEeee
Confidence 689999999999999999999987789999987653 34567788999999999999999864 678999975
No 76
>PRK13806 rpsA 30S ribosomal protein S1; Provisional
Probab=96.83 E-value=0.0088 Score=57.04 Aligned_cols=72 Identities=21% Similarity=0.116 Sum_probs=61.3
Q ss_pred CCCCCEEEEEEEEEecceEEEEECCCCCeeeecccccc--ccccCCcCCCCCCEEEEEEEecCCC-CeeEEEEec
Q psy230 54 PTRGDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFEG--ATKKNPPKVETGDVVAGKLLTANKD-MESEMVCVD 125 (222)
Q Consensus 54 P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~g--atk~~r~~l~~GDlV~ArV~~~~~~-~~~~Ls~~~ 125 (222)
-.+|++|-|+|+++.+..+.|++...-.|.+|.+.+.. ...+....|++||.|.++|.+++.. ..+.||++.
T Consensus 290 ~~~G~~v~G~V~~v~~~G~fV~l~~gv~Glvh~sels~~~~~~~~~~~~~~Gd~v~vkVl~iD~e~~ri~Ls~K~ 364 (491)
T PRK13806 290 LKAGDKVTGKVVRLAPFGAFVEILPGIEGLVHVSEMSWTRRVNKPEDVVAPGDAVAVKIKDIDPAKRRISLSLRD 364 (491)
T ss_pred CCCCCEEEEEEEEEeCceEEEEeCCCcEEEEEHHHcCcccccCCHHHcCCCCCEEEEEEEEEEccCCEEEEEEee
Confidence 36899999999999999999999877899999887653 3345567899999999999999764 578999986
No 77
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=96.82 E-value=0.0037 Score=57.52 Aligned_cols=69 Identities=22% Similarity=0.233 Sum_probs=56.2
Q ss_pred ccCCCCCCEEEEEEEEEecceEEEEECCCCCeeeeccccccccccCCcCCCCCCEEEEEEEecCCCC---eeEEEEec
Q psy230 51 RYVPTRGDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFEGATKKNPPKVETGDVVAGKLLTANKDM---ESEMVCVD 125 (222)
Q Consensus 51 ~Y~P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~gatk~~r~~l~~GDlV~ArV~~~~~~~---~~~Ls~~~ 125 (222)
.|.++.|++|.|+|.++....|.|||+. ..|+||.... --+..|++||-|.|-|..+..+. .+.||-.+
T Consensus 129 ef~~k~GeiV~G~V~~~~~~~~~Vdlg~-vEa~LP~~E~-----ip~e~~~~Gd~Ika~V~~V~~~~kgp~IivSRt~ 200 (362)
T PRK12327 129 EFSEREGDIVTGVVQRRDNRFVYVNLGK-IEAVLPPAEQ-----IPGETYKHGDRIKVYVVKVEKTTKGPQIFVSRTH 200 (362)
T ss_pred HHHHhcCCEEEEEEEEEeCCcEEEEeCC-eEEEecHHHc-----CCCCCCCCCCEEEEEEEEEecCCCCCeEEEEeCC
Confidence 5899999999999999999999999987 7999996432 12566999999999999998443 46666543
No 78
>COG0539 RpsA Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]
Probab=96.74 E-value=0.0064 Score=58.46 Aligned_cols=95 Identities=24% Similarity=0.277 Sum_probs=74.8
Q ss_pred cccCCCCCCEEEEEEEEEecceEEEEECCCCCeeeeccccccccccCCcCCCCCCEEEEEEEecCCCC-eeEEEEecCC-
Q psy230 50 RRYVPTRGDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFEGATKKNPPKVETGDVVAGKLLTANKDM-ESEMVCVDSR- 127 (222)
Q Consensus 50 ~~Y~P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~gatk~~r~~l~~GDlV~ArV~~~~~~~-~~~Ls~~~~~- 127 (222)
..+.+++||+|-|.|+++..++..|||+.-..+.+|...|.+.-... .|++||.|-+.|....+.. .+.||-....
T Consensus 15 ~~~~~~~G~vV~G~Vv~i~~~~v~Vdig~Kseg~ip~~E~~~~~~~~--~~~~gd~v~v~v~~~e~~~g~~~lS~~k~~~ 92 (541)
T COG0539 15 SDEEFEPGDVVKGTVVSIEKDGVLVDIGGKSEGVIPISEFSNEPVED--VVQVGDEVEVLVLRVEDGEGELVLSRRKAER 92 (541)
T ss_pred chhccCCCCEEEEEEEEEeCCeEEEEecCccccEeEHHHhccccccc--eecCCCEEEEEEEEEecCCceEEeeHHHHHH
Confidence 45789999999999999999999999999999999998887543322 7999999999999886553 5777754310
Q ss_pred -------------C---ccccCcccCCceEEEech
Q psy230 128 -------------G---KEFIMGILNDGYLLHTSI 146 (222)
Q Consensus 128 -------------~---~~~~~G~L~~G~l~~v~~ 146 (222)
+ ++.-.|++.+|+++.+..
T Consensus 93 ~~~w~~l~~~~e~~~~V~~~v~~~vKGG~~Vdi~g 127 (541)
T COG0539 93 ERAWEKLEEAFENGEIVEGKITGKVKGGLTVDIEG 127 (541)
T ss_pred HHhHHHHHHHHhcCCeEEEEEEEEecCcEEEEECC
Confidence 0 122367889999999853
No 79
>PRK00087 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed
Probab=96.73 E-value=0.0071 Score=59.53 Aligned_cols=71 Identities=21% Similarity=0.225 Sum_probs=59.2
Q ss_pred CCCCCEEEEEEEEEecceEEEEECCCCCeeeeccccc-cccccCCcCCCCCCEEEEEEEecCC-CCeeEEEEec
Q psy230 54 PTRGDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFE-GATKKNPPKVETGDVVAGKLLTANK-DMESEMVCVD 125 (222)
Q Consensus 54 P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~-gatk~~r~~l~~GDlV~ArV~~~~~-~~~~~Ls~~~ 125 (222)
.++||+|-|+|+++....+.|++ ....|.+|.+.+. ...++....|++||.|.|+|.++++ ...+.||++.
T Consensus 475 l~~G~iV~g~V~~v~~~G~fV~l-~gv~Gll~~sels~~~~~~~~~~~~vGd~V~vkV~~id~~~~~I~lS~K~ 547 (647)
T PRK00087 475 LEEGDVVEGEVKRLTDFGAFVDI-GGVDGLLHVSEISWGRVEKPSDVLKVGDEIKVYILDIDKENKKLSLSLKK 547 (647)
T ss_pred CCCCCEEEEEEEEEeCCcEEEEE-CCEEEEEEHHHcCccccCCHHHhcCCCCEEEEEEEEEECCCCEEEEEeec
Confidence 46899999999999999999999 5678999987654 3345566789999999999999975 4678999875
No 80
>PRK00087 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed
Probab=96.71 E-value=0.0096 Score=58.63 Aligned_cols=75 Identities=23% Similarity=0.239 Sum_probs=62.3
Q ss_pred ccCCCCCCEEEEEEEEEecceEEEEECCCCCeeeecccccc-ccccCCcCCCCCCEEEEEEEecCC-CCeeEEEEec
Q psy230 51 RYVPTRGDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFEG-ATKKNPPKVETGDVVAGKLLTANK-DMESEMVCVD 125 (222)
Q Consensus 51 ~Y~P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~g-atk~~r~~l~~GDlV~ArV~~~~~-~~~~~Ls~~~ 125 (222)
.+..++|++|-|+|+++..+.+.||++....|.||...+.. ..+.....|++||.|.++|.++++ ++.+.||...
T Consensus 297 ~~~l~~G~iV~G~V~~v~~~gv~Vdig~~~~G~lp~~els~~~~~~~~~~~~vGd~V~v~V~~vd~~~g~i~LS~k~ 373 (647)
T PRK00087 297 EKQIRRGDIVKGTVVSVNENEVFVDVGYKSEGVIPLRELTLDEISSLKESVKVGDEIEVKVLKLEDEDGYVVLSKKE 373 (647)
T ss_pred HhhccCCCEEEEEEEEEECCEEEEEECCCeEEEEEHHHhcccccCChhhccCCCCEEEEEEEEEECCCCcEEEEeeh
Confidence 35689999999999999999999999988899999876542 334556679999999999999863 4568888875
No 81
>TIGR00717 rpsA ribosomal protein S1. This model provides trusted hits to most long form (6 repeat) examples of RpsA. Among homologs with only four repeats are some to which other (perhaps secondary) functions have been assigned.
Probab=96.69 E-value=0.027 Score=53.62 Aligned_cols=72 Identities=17% Similarity=0.125 Sum_probs=58.3
Q ss_pred CCCCCEEEEEEEEEecceEEEEECCCCCeeeeccccccc--cccCCcCCCCCCEEEEEEEecCCC-CeeEEEEec
Q psy230 54 PTRGDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFEGA--TKKNPPKVETGDVVAGKLLTANKD-MESEMVCVD 125 (222)
Q Consensus 54 P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~ga--tk~~r~~l~~GDlV~ArV~~~~~~-~~~~Ls~~~ 125 (222)
-++||++-|+|+++....+.|+++....|.+|.+.+... ..+....|++||.|.|+|.+++.+ ..+.||++.
T Consensus 270 ~~~G~i~~g~V~~v~~~G~fV~l~~~v~g~v~~sels~~~~~~~~~~~~~vG~~v~v~V~~id~~~~~i~lS~k~ 344 (516)
T TIGR00717 270 FPVGDKITGRVTNLTDYGVFVEIEEGIEGLVHVSEMSWVKKNSHPSKVVKKGDEVEVMILDIDPERRRLSLGLKQ 344 (516)
T ss_pred ccCCCEEEEEEEEeeCCcEEEEeCCCCEEEEEHHHcCCccccCCHHHhccCCCEEEEEEEEEcCCCCEEEEEehh
Confidence 357999999999999999999999888999998766422 222234599999999999999864 568888764
No 82
>cd02394 vigilin_like_KH K homology RNA-binding domain_vigilin_like. The vigilin family is a large and extended family of multiple KH-domain proteins, including vigilin, also called high density lipoprotein binding protien (HBP), fungal Scp160 and bicaudal-C. Yeast Scp160p has been shown to bind RNA and to associate with both soluble and membrane-bound polyribosomes as a mRNP component. Bicaudal-C is a RNA-binding molecule believed to function in embryonic development at the post-transcriptional level. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=96.67 E-value=0.0031 Score=42.78 Aligned_cols=44 Identities=11% Similarity=0.151 Sum_probs=41.4
Q ss_pred EEEechhhhhhccCCChhHHHHhhhcCCCcEEEEEEe----CCeEEEeeC
Q psy230 141 LLHTSISLCRKLLNPKCPLLKQLAKRSRQKMELSIGM----NGKIWIRCE 186 (222)
Q Consensus 141 l~~v~~~~~~rl~~~~~~~l~~l~~~~~~~~ei~vG~----NG~iWi~~~ 186 (222)
-+.|+..++++++|+++..++.|.+ .+++.|.+.. ++.|||.++
T Consensus 3 ~i~Vp~~~~~~iIG~~G~~i~~i~~--~~g~~I~i~~~~~~~~~v~I~G~ 50 (62)
T cd02394 3 EVEIPKKLHRFIIGKKGSNIRKIME--ETGVKIRFPDPGSKSDTITITGP 50 (62)
T ss_pred EEEeCHHHhhhccCCCCCcHHHHHH--HhCCEEEcCCCCCCCCEEEEEcC
Confidence 4789999999999999999999999 9999999999 899999998
No 83
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=96.45 E-value=0.01 Score=60.09 Aligned_cols=73 Identities=19% Similarity=0.163 Sum_probs=63.4
Q ss_pred CCCCCCEEE-EEEEEEecceEEEEECCCCCeeeecccccc-ccccCCcCCCCCCEEEEEEEecCCCCeeEEEEec
Q psy230 53 VPTRGDLVI-GVVTSRVGDNYRVDIGSHDPAVLSYLAFEG-ATKKNPPKVETGDVVAGKLLTANKDMESEMVCVD 125 (222)
Q Consensus 53 ~P~vGDiVI-G~V~~v~~~~~~VdI~~~~~a~L~~~~f~g-atk~~r~~l~~GDlV~ArV~~~~~~~~~~Ls~~~ 125 (222)
.|++|+++- |+|+++.+-.++|+|.....+.+|++.+.. ..++....|++||.|..+|.+++..+.+.|+.+.
T Consensus 750 ~~~vG~iy~~g~V~~I~~FGaFVeL~~g~EGLVHISeLs~~rv~~~~dv~kvGD~V~VkVi~ID~~grI~LSlK~ 824 (891)
T PLN00207 750 VPTVGDIYRNCEIKSIAPYGAFVEIAPGREGLCHISELSSNWLAKPEDAFKVGDRIDVKLIEVNDKGQLRLSRRA 824 (891)
T ss_pred CcCCCcEEECcEEEEEeccEEEEEeCCCCEEEEEhhhcCCccccCHHHhcCCCCEEEEEEEEECCCCcEEEEEec
Confidence 489999995 699999999999999877899999988753 4566678899999999999999976788999864
No 84
>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional
Probab=96.38 E-value=0.015 Score=59.01 Aligned_cols=63 Identities=22% Similarity=0.249 Sum_probs=55.4
Q ss_pred CCCCCEEEEEEEEEecceEEEEECCCCCeeeeccccccccccCCcCCCCCCEEEEEEEecCCCCeeEEEEe
Q psy230 54 PTRGDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFEGATKKNPPKVETGDVVAGKLLTANKDMESEMVCV 124 (222)
Q Consensus 54 P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~gatk~~r~~l~~GDlV~ArV~~~~~~~~~~Ls~~ 124 (222)
+++||+|-|+|+++..+...|||+.-..|++|...|.. .+++||-|.|.|.+.+.+. +.||-.
T Consensus 319 ~~~G~iV~G~Vv~i~~~~v~VdiG~K~eGiI~~~E~~~-------~~kvGd~i~~~V~~~~~~~-~~LS~~ 381 (863)
T PRK12269 319 PEPGSVRMGTVVQVNAGTVFVDIGGKSEGRVPVEEFEA-------PPKAGDGVRVYVERVTPYG-PELSKT 381 (863)
T ss_pred CCCCCEEEEEEEEEECCEEEEEeCCCceEEeEHHHhcc-------CCCCCCEEEEEEEEEcCCc-eEEEeh
Confidence 89999999999999999999999999999999877731 2589999999999987654 788865
No 85
>TIGR00757 RNaseEG ribonuclease, Rne/Rng family. The C-terminal half of RNase E (excluded from the seed alignment for this model) lacks ribonuclease activity but participates in mRNA degradation by organizing the degradosome.
Probab=96.13 E-value=0.052 Score=50.83 Aligned_cols=71 Identities=17% Similarity=0.171 Sum_probs=54.1
Q ss_pred CCCCCCEEEEEEEEEecc--eEEEEECCCCCeeeecccccc-------------ccccCCcCCCCCCEEEEEEEecC-CC
Q psy230 53 VPTRGDLVIGVVTSRVGD--NYRVDIGSHDPAVLSYLAFEG-------------ATKKNPPKVETGDVVAGKLLTAN-KD 116 (222)
Q Consensus 53 ~P~vGDiVIG~V~~v~~~--~~~VdI~~~~~a~L~~~~f~g-------------atk~~r~~l~~GDlV~ArV~~~~-~~ 116 (222)
.+.+||+..|+|+++.+. .++|||+....|+||+..... ..++....+++||-|..+|..-. ..
T Consensus 22 ~~~vGnIY~GrV~~i~p~l~aAFVdiG~~k~gfL~~~d~~~~~~~~~~~~~~~~~~~~i~~~l~~G~~IlVQV~Ke~~~~ 101 (414)
T TIGR00757 22 RQLKGNIYKGRVTRILPSLQAAFVDIGLEKNGFLHASDIGPNYECLAPAEAKREAGPSISELLRPGQSVLVQVVKEPRGN 101 (414)
T ss_pred cCCCCCEEEEEEeeecCCCceEEEEcCCCceEEEEHHHcCchhhccccccccccccCCHHHhCcCCCEEEEEEeeCCcCC
Confidence 456899999999999887 999999999999999876421 11223446999999999998732 23
Q ss_pred CeeEEEE
Q psy230 117 MESEMVC 123 (222)
Q Consensus 117 ~~~~Ls~ 123 (222)
..+.||+
T Consensus 102 Kgp~lT~ 108 (414)
T TIGR00757 102 KGARLTT 108 (414)
T ss_pred CCCeEEE
Confidence 3466666
No 86
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=96.11 E-value=0.017 Score=54.91 Aligned_cols=69 Identities=22% Similarity=0.280 Sum_probs=56.4
Q ss_pred ccCCCCCCEEEEEEEEEecceEEEEECCCCCeeeeccccccccccCCcCCCCCCEEEEEEEecCCC---CeeEEEEec
Q psy230 51 RYVPTRGDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFEGATKKNPPKVETGDVVAGKLLTANKD---MESEMVCVD 125 (222)
Q Consensus 51 ~Y~P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~gatk~~r~~l~~GDlV~ArV~~~~~~---~~~~Ls~~~ 125 (222)
.|..+.|++|.|+|.++....+.||++. ..|+||.+.. --+..|++||-|.|.|..+.+. ..+.||-..
T Consensus 129 eyk~~~GeIV~G~V~ri~~~giiVDLgg-vea~LP~sE~-----ip~E~~~~GdrIka~I~~Vd~~~kg~qIilSRt~ 200 (470)
T PRK09202 129 EYKDRVGEIITGVVKRVERGNIIVDLGR-AEAILPRKEQ-----IPRENFRPGDRVRAYVYEVRKEARGPQIILSRTH 200 (470)
T ss_pred HHHhhcCCEEEEEEEEEecCCEEEEECC-eEEEecHHHc-----CCCccCCCCCEEEEEEEEEecCCCCCeEEEEeCc
Confidence 5888999999999999999999999964 6999996542 2456799999999999999764 246666543
No 87
>TIGR01953 NusA transcription termination factor NusA. This model describes NusA, or N utilization substance protein A, a bacterial transcription termination factor. It binds to RNA polymerase alpha subunit and promotes termination at certain RNA hairpin structures. It is named for the interaction in E. coli of phage lambda antitermination protein N with the N-utilization substance, consisting of NusA, NusB, NusE (ribosomal protein S10), and nusG. This model represents a region of NusA shared in all bacterial forms, and including an S1 (pfam00575) and a KH (pfam00013) RNA binding domains. Proteobacterial forms have an additional C-terminal region, not included in this model, with two repeats of 50-residue domain rich in acidic amino acids.
Probab=96.06 E-value=0.02 Score=52.33 Aligned_cols=70 Identities=14% Similarity=0.222 Sum_probs=54.8
Q ss_pred cccCCCCCCEEEEEEEEEecce-EEEEECCCCCeeeeccccccccccCCcCCCCCCEEEEEEEecCCC---CeeEEEEec
Q psy230 50 RRYVPTRGDLVIGVVTSRVGDN-YRVDIGSHDPAVLSYLAFEGATKKNPPKVETGDVVAGKLLTANKD---MESEMVCVD 125 (222)
Q Consensus 50 ~~Y~P~vGDiVIG~V~~v~~~~-~~VdI~~~~~a~L~~~~f~gatk~~r~~l~~GDlV~ArV~~~~~~---~~~~Ls~~~ 125 (222)
..|..+.|++|-|+|.++..+. |.|||+ ...|+||..... .+..|++||-|.|-|.++.++ ..+.||-..
T Consensus 125 ~ey~~k~GeiV~G~V~~v~~~g~v~VdiG-~~ea~LP~~E~i-----p~E~~~~Gd~ik~~V~~V~~~~kg~qIivSRt~ 198 (341)
T TIGR01953 125 DEFSSKEGEIISGTVKRVNRRGNLYVELG-KTEGILPKKEQI-----PGEKFRIGDRIKAYVYEVRKTAKGPQIILSRTH 198 (341)
T ss_pred HHHHhhcCCEEEEEEEEEecCCcEEEEEC-CeEEEecHHHcC-----CCcCCCCCCEEEEEEEEEEcCCCCCeEEEEeCc
Confidence 3588899999999999998855 799996 578999965432 233499999999999999754 346777543
No 88
>COG2183 Tex Transcriptional accessory protein [Transcription]
Probab=96.01 E-value=0.02 Score=56.95 Aligned_cols=73 Identities=21% Similarity=0.242 Sum_probs=63.3
Q ss_pred CCCCCEEEEEEEEEecceEEEEECCCCCeeeeccccccc-cccCCcCCCCCCEEEEEEEecCCC-CeeEEEEecC
Q psy230 54 PTRGDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFEGA-TKKNPPKVETGDVVAGKLLTANKD-MESEMVCVDS 126 (222)
Q Consensus 54 P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~ga-tk~~r~~l~~GDlV~ArV~~~~~~-~~~~Ls~~~~ 126 (222)
-++|-++.|.|.++..-...|||+...++.+|++..... .+.-...+++||+|.++|.+++-. ..+.||++..
T Consensus 656 Lk~Gm~leg~Vrnv~~fgafVdIgv~qDglvHis~ls~~fv~~P~~vv~vGdiV~v~V~~vD~~r~rI~Lsmr~~ 730 (780)
T COG2183 656 LKPGMILEGTVRNVVDFGAFVDIGVHQDGLVHISQLSDKFVKDPNEVVKVGDIVKVKVIEVDTARKRIALSMRLD 730 (780)
T ss_pred ccCCCEEEEEEEEeeeccceEEeccccceeeeHHHhhhhhcCChHHhcccCCEEEEEEEEEecccCeeeeEeecc
Confidence 388999999999999999999999999999999876543 455578999999999999999754 4689999863
No 89
>cd04462 S1_RNAPII_Rpb7 S1_RNAPII_Rpb7: Eukaryotic RNA polymerase II (RNAPII) Rpb7 subunit C-terminal S1 domain. RNAPII is composed of 12 subunits (Rpb1-12). Rpb4 and Rpb7 form a heterodimer that associate with the RNAPII core. Rpb7 is a homolog of the Rpc25 of RNA polymerase III, RpoE of the archaeal RNA polymerase, and Rpa43 of eukaryotic RNA polymerase I. Rpb7 has two domains, an N-terminal ribonucleoprotein (RNP) domain and a C-terminal S1 domain, both of which bind single-stranded RNA. It is possible that the S1 domain interacts with the nascent RNA transcript, assisted by the RNP domain. In yeast, Rpb4/Rpb7 is necessary for promoter-directed transcription initiation. They also play a role in regulating transcription-coupled repair in the Rad26-dependent pathway, in efficient mRNA export, and in transcription termination.
Probab=95.99 E-value=0.034 Score=40.88 Aligned_cols=59 Identities=17% Similarity=0.308 Sum_probs=41.4
Q ss_pred CCCEEEEEEEEEecceEEEEECC----CCCeeeec-cccccc------cccCCcCCCCCCEEEEEEEecC
Q psy230 56 RGDLVIGVVTSRVGDNYRVDIGS----HDPAVLSY-LAFEGA------TKKNPPKVETGDVVAGKLLTAN 114 (222)
Q Consensus 56 vGDiVIG~V~~v~~~~~~VdI~~----~~~a~L~~-~~f~ga------tk~~r~~l~~GDlV~ArV~~~~ 114 (222)
+|.+|.|+|++++...+.|+++. -....+|. ..|++. ..+.+..++.||.|++||.++.
T Consensus 1 kgEVi~g~V~~v~~~G~~v~~Gpl~~f~~~~~ip~~~~~~~~~~~~~~~~~~~~~i~~g~~VR~rV~~v~ 70 (88)
T cd04462 1 KGEVVDAIVTSVNKTGFFAEVGPLSIFISRHLIPSDMEFDPNASPPCFTSNEDIVIKKDTEVRLKIIGTR 70 (88)
T ss_pred CCcEEEEEEEEEeccEEEEEEcCceEEEEeeecCccceECCcCCCCeEeCCCcEEECCCCEEEEEEEEEE
Confidence 48899999999999999999984 22222221 112221 1124677999999999998875
No 90
>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional
Probab=95.79 E-value=0.031 Score=56.84 Aligned_cols=72 Identities=18% Similarity=0.091 Sum_probs=60.4
Q ss_pred CCCCCEEEEEEEEEecceEEEEECCCCCeeeecccccc--ccccCCcCCCCCCEEEEEEEecCCC-CeeEEEEec
Q psy230 54 PTRGDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFEG--ATKKNPPKVETGDVVAGKLLTANKD-MESEMVCVD 125 (222)
Q Consensus 54 P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~g--atk~~r~~l~~GDlV~ArV~~~~~~-~~~~Ls~~~ 125 (222)
..+||+|-|+|+++.+..+.|++.....|.+|.+.+.. ...+....|++||-|.|+|++++.. ..+.||.+.
T Consensus 576 ~~vG~iV~G~V~~I~~fG~fVeL~~gveGLvhiSEls~~~~~~~p~~~~kvGd~V~vkVl~iD~e~~rIsLS~K~ 650 (863)
T PRK12269 576 FGVNDVVKGRVTKIADFGAFIELAEGIEGLAHISEFSWVKKTSKPSDMVKIGDEVECMILGYDIQAGRVSLGLKQ 650 (863)
T ss_pred CCCCCEEEEEEEEEeCCeEEEEecCCceeeeEHHHhcCccccCCHHHcCCCCCEEEEEEEEEecccCceEEEehh
Confidence 46899999999999999999999988899999987753 2345566799999999999999754 467888875
No 91
>cd00105 KH-I K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include N-terminal extension and type I KH domains (e.g. hnRNP K) contain C-terminal extension.
Probab=95.47 E-value=0.038 Score=37.08 Aligned_cols=44 Identities=11% Similarity=0.138 Sum_probs=39.2
Q ss_pred EEEechhhhhhccCCChhHHHHhhhcCCCcEEEEEEe------CCeEEEeeC
Q psy230 141 LLHTSISLCRKLLNPKCPLLKQLAKRSRQKMELSIGM------NGKIWIRCE 186 (222)
Q Consensus 141 l~~v~~~~~~rl~~~~~~~l~~l~~~~~~~~ei~vG~------NG~iWi~~~ 186 (222)
-+.|+..++++++|+++..++.|.+ .+++.|.+.. +..|||.+.
T Consensus 3 ~i~ip~~~~~~vIG~~G~~i~~I~~--~s~~~I~i~~~~~~~~~~~v~i~G~ 52 (64)
T cd00105 3 RVLVPSSLVGRIIGKGGSTIKEIRE--ETGAKIKIPDSGSGSEERIVTITGT 52 (64)
T ss_pred EEEEchhhcceeECCCCHHHHHHHH--HHCCEEEEcCCCCCCCceEEEEEcC
Confidence 4789999999999999999999999 8888898877 467999987
No 92
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=95.38 E-value=0.059 Score=49.75 Aligned_cols=60 Identities=28% Similarity=0.367 Sum_probs=48.8
Q ss_pred ccCCCCCCEEEEEEEEEec-ceEEEEECCCCCeeeeccccccccccCCcCCCCCCEEEEEEEecCCC
Q psy230 51 RYVPTRGDLVIGVVTSRVG-DNYRVDIGSHDPAVLSYLAFEGATKKNPPKVETGDVVAGKLLTANKD 116 (222)
Q Consensus 51 ~Y~P~vGDiVIG~V~~v~~-~~~~VdI~~~~~a~L~~~~f~gatk~~r~~l~~GDlV~ArV~~~~~~ 116 (222)
.|.+++|++|.|+|.++.. ..+.||++. ..|+||... .--+..|++||-|.|-|..+..+
T Consensus 133 ey~~~~Geiv~g~V~r~~~~~~i~vdlg~-~ea~LP~~e-----qip~E~~~~Gdrik~~i~~V~~~ 193 (374)
T PRK12328 133 KYKKKVGKIVFGTVVRVDNEENTFIEIDE-IRAVLPMKN-----RIKGEKFKVGDVVKAVLKRVKID 193 (374)
T ss_pred HHHHhcCcEEEEEEEEEecCCCEEEEcCC-eEEEeCHHH-----cCCCCcCCCCCEEEEEEEEEecC
Confidence 5999999999999999986 568899984 799999532 12345699999999999988654
No 93
>PF00013 KH_1: KH domain syndrome, contains KH motifs.; InterPro: IPR018111 The K homology (KH) domain was first identified in the human heterogeneous nuclear ribonucleoprotein (hnRNP) K. It is a domain of around 70 amino acids that is present in a wide variety of quite diverse nucleic acid-binding proteins []. It has been shown to bind RNA [, ]. Like many other RNA-binding motifs, KH motifs are found in one or multiple copies (14 copies in chicken vigilin) and, at least for hnRNP K (three copies) and FMR-1 (two copies), each motif is necessary for in vitro RNA binding activity, suggesting that they may function cooperatively or, in the case of single KH motif proteins (for example, Mer1p), independently []. According to structural [, , ] analysis the KH domain can be separated in two groups. The first group or type-1 contain a beta-alpha-alpha-beta-beta-alpha structure, whereas in the type-2 the two last beta-sheet are located in the N-terminal part of the domain (alpha-beta-beta-alpha-alpha-beta). Sequence similarity between these two folds are limited to a short region (VIGXXGXXI) in the RNA binding motif. This motif is located between helice 1 and 2 in type-1 and between helice 2 and 3 in type-2. Proteins known to contain a type-1 KH domain include bacterial polyribonucleotide nucleotidyltransferases (2.7.7.8 from EC); vertebrate fragile X mental retardation protein 1 (FMR1); eukaryotic heterogeneous nuclear ribonucleoprotein K (hnRNP K), one of at least 20 major proteins that are part of hnRNP particles in mammalian cells; mammalian poly(rC) binding proteins; Artemia salina glycine-rich protein GRP33; yeast PAB1-binding protein 2 (PBP2); vertebrate vigilin; and human high-density lipoprotein binding protein (HDL-binding protein). More information about these proteins can be found at Protein of the Month: RNA Exosomes [].; GO: 0003723 RNA binding; PDB: 1TUA_A 2Z0S_A 1WE8_A 4AM3_B 4AIM_A 4AID_A 2HH3_A 2JVZ_A 1J4W_A 2HH2_A ....
Probab=95.12 E-value=0.042 Score=36.84 Aligned_cols=51 Identities=14% Similarity=0.196 Sum_probs=42.8
Q ss_pred EEEechhhhhhccCCChhHHHHhhhcCCCcEEEEEEeC---CeEEEeeCCchhHHHH
Q psy230 141 LLHTSISLCRKLLNPKCPLLKQLAKRSRQKMELSIGMN---GKIWIRCESFSDTVRV 194 (222)
Q Consensus 141 l~~v~~~~~~rl~~~~~~~l~~l~~~~~~~~ei~vG~N---G~iWi~~~~~~~~~~i 194 (222)
-+.|+..++.+++|+++..++.|.+ .+++.|-+-.+ ..|.|.+ +++....+
T Consensus 3 ~i~vp~~~~~~iIG~~G~~i~~I~~--~t~~~I~i~~~~~~~~v~I~G-~~~~v~~A 56 (60)
T PF00013_consen 3 RIEVPSSLVGRIIGKKGSNIKEIEE--ETGVKIQIPDDDERDIVTISG-SPEQVEKA 56 (60)
T ss_dssp EEEEEHHHHHHHHTGGGHHHHHHHH--HHTSEEEEESTTEEEEEEEEE-SHHHHHHH
T ss_pred EEEECHHHcCEEECCCCCcHHHhhh--hcCeEEEEcCCCCcEEEEEEe-CHHHHHHH
Confidence 4789999999999999999999999 89999999875 6899999 55533333
No 94
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=94.51 E-value=0.15 Score=48.06 Aligned_cols=61 Identities=8% Similarity=-0.011 Sum_probs=49.7
Q ss_pred ccCCCCCCEEEEEEEEEecceEEEEECC-----CCCeeeeccccccccccCCcCCCCCCEEEEEEEecCCC
Q psy230 51 RYVPTRGDLVIGVVTSRVGDNYRVDIGS-----HDPAVLSYLAFEGATKKNPPKVETGDVVAGKLLTANKD 116 (222)
Q Consensus 51 ~Y~P~vGDiVIG~V~~v~~~~~~VdI~~-----~~~a~L~~~~f~gatk~~r~~l~~GDlV~ArV~~~~~~ 116 (222)
.|.+++|++|.|+|.++..+.+.||+++ ...|+||... .--+..|++||-|.|-|..+...
T Consensus 147 ef~~~~GeIV~G~V~r~e~~~viv~l~~~~g~~~~EaiLP~~E-----qip~E~y~~Gdrika~i~~V~~~ 212 (449)
T PRK12329 147 EFQDLEDTVLTARVLRFERQSVIMAVSSGFGQPEVEAELPKRE-----QLPNDNYRANATFKVFLKEVSEG 212 (449)
T ss_pred HHHHhcCcEEEEEEEEEcCCCEEEEecccCCCcceEEEecHHH-----cCCCCcCCCCCEEEEEEEEeecC
Confidence 5999999999999999999999999953 2678999532 12345699999999999999654
No 95
>KOG1070|consensus
Probab=93.49 E-value=0.47 Score=50.23 Aligned_cols=71 Identities=18% Similarity=0.303 Sum_probs=63.4
Q ss_pred CCCCEEEEEEEEEecceEEEEECCCCCeeeecccc-ccccccCCcCCCCCCEEEEEEEecCCCC-eeEEEEec
Q psy230 55 TRGDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAF-EGATKKNPPKVETGDVVAGKLLTANKDM-ESEMVCVD 125 (222)
Q Consensus 55 ~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f-~gatk~~r~~l~~GDlV~ArV~~~~~~~-~~~Ls~~~ 125 (222)
+.||+|-|.|..+.....++-++....|.++++.+ +-..+.-++.|.+|++|-+||.+++.+. .++|+...
T Consensus 1161 k~g~iv~G~V~nv~~~glfi~ls~~v~a~v~is~~~ds~~k~w~k~~~~gklv~~rv~~ve~~s~riel~Lk~ 1233 (1710)
T KOG1070|consen 1161 KIGDIVRGFVKNVETKGLFIALSRKVEAFVPISGLSDSFEKEWEKHLPVGKLVTGRVLSVEEDSKRIELSLKN 1233 (1710)
T ss_pred ccCceeEEEEEEecCCcEEEEEccceEEEEEccccccchhhhhhccCCccceeeeEEEEeeccCceEEEEEec
Confidence 78999999999999999999999999999998775 4455788899999999999999998664 78999986
No 96
>smart00322 KH K homology RNA-binding domain.
Probab=93.26 E-value=0.3 Score=32.19 Aligned_cols=58 Identities=9% Similarity=0.122 Sum_probs=46.1
Q ss_pred eEEEechhhhhhccCCChhHHHHhhhcCCCcEEEEEEeC----CeEEEeeCCchhHHHHHHHHHH
Q psy230 140 YLLHTSISLCRKLLNPKCPLLKQLAKRSRQKMELSIGMN----GKIWIRCESFSDTVRVGNLIMS 200 (222)
Q Consensus 140 ~l~~v~~~~~~rl~~~~~~~l~~l~~~~~~~~ei~vG~N----G~iWi~~~~~~~~~~i~~~i~~ 200 (222)
.-+.|+..+..+++|+++..++.|.+ .+++.|.+..+ ..++|.++ ..+...+..+|..
T Consensus 5 ~~i~i~~~~~~~liG~~G~~i~~i~~--~~~~~i~~~~~~~~~~~v~i~g~-~~~v~~a~~~i~~ 66 (69)
T smart00322 5 IEVLIPADKVGLIIGKGGSTIKKIEE--ETGVKIDIPEDGSEERVVEITGP-PENVEKAAELILE 66 (69)
T ss_pred EEEEEcchhcceeECCCchHHHHHHH--HHCCEEEECCCCCCccEEEEEcC-HHHHHHHHHHHHH
Confidence 45788999999999999999999999 88888888774 78999987 4445555555543
No 97
>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase. Members of this protein family are polyribonucleotide nucleotidyltransferase, also called polynucleotide phosphorylase. Some members have been shown also to have additional functions as guanosine pentaphosphate synthetase and as poly(A) polymerase (see model TIGR02696 for an exception clade, within this family).
Probab=92.59 E-value=0.28 Score=48.87 Aligned_cols=58 Identities=10% Similarity=0.189 Sum_probs=49.3
Q ss_pred eEEEechhhhhhccCCChhHHHHhhhcCCCcEEEEEEeCCeEEEeeCCchhHHHHHHHHH
Q psy230 140 YLLHTSISLCRKLLNPKCPLLKQLAKRSRQKMELSIGMNGKIWIRCESFSDTVRVGNLIM 199 (222)
Q Consensus 140 ~l~~v~~~~~~rl~~~~~~~l~~l~~~~~~~~ei~vG~NG~iWi~~~~~~~~~~i~~~i~ 199 (222)
..++|+|.+++.++|+++.+++.|.+ .+++.|-|-.+|.|+|.+.+......+.+.|+
T Consensus 553 ~~~~I~~~kI~~vIG~gGk~Ik~I~~--~tg~~I~i~ddG~V~i~~~~~~~~~~a~~~I~ 610 (684)
T TIGR03591 553 ETIKINPDKIRDVIGPGGKVIREITE--ETGAKIDIEDDGTVKIAASDGEAAEAAIKMIE 610 (684)
T ss_pred EEEecCHHHHHhhcCCCcHHHHHHHH--HHCCEEEEecCeEEEEEECcHHHHHHHHHHHH
Confidence 56899999999999999999999999 99999999999999999988764444333333
No 98
>KOG1856|consensus
Probab=92.42 E-value=0.18 Score=52.18 Aligned_cols=72 Identities=19% Similarity=0.274 Sum_probs=59.3
Q ss_pred CCCCEEEEEEEEEecce---EEEEECCCCCeeeecccccc-ccccCCcCCCCCCEEEEEEEecCCCC-eeEEEEecC
Q psy230 55 TRGDLVIGVVTSRVGDN---YRVDIGSHDPAVLSYLAFEG-ATKKNPPKVETGDVVAGKLLTANKDM-ESEMVCVDS 126 (222)
Q Consensus 55 ~vGDiVIG~V~~v~~~~---~~VdI~~~~~a~L~~~~f~g-atk~~r~~l~~GDlV~ArV~~~~~~~-~~~Ls~~~~ 126 (222)
.+|-+|.+.|++++... .+|-..|.-+++++.....+ ..++.-..+++|+.|+|||+++.... .++|||+++
T Consensus 984 ~~g~iV~~~V~~vt~rr~~Cv~v~ld~G~~g~i~~~~~Sd~~v~~p~~~v~vgq~v~~kvi~id~e~f~v~Ls~r~s 1060 (1299)
T KOG1856|consen 984 YEGAIVPVTVTKVTHRRGICVRVRLDCGVTGFILAKNLSDRDVRRPENRVKVGQTVYCKVIKIDKERFSVELSCRTS 1060 (1299)
T ss_pred ccCceEEEeeeEEEecccceeEEEecCCCceeeeccccChhhccCHHHhhccCceEEEEeeeeeHhhhhhhhhhhhH
Confidence 57999999999999999 55588999999999766554 44566667889999999999998664 589999873
No 99
>PRK11642 exoribonuclease R; Provisional
Probab=92.20 E-value=0.94 Score=46.03 Aligned_cols=83 Identities=16% Similarity=0.205 Sum_probs=63.1
Q ss_pred CCCCCEEEEEEEEEecceEEEEECCC-CCeeeeccccccc------------cccCCcCCCCCCEEEEEEEecCCC-Cee
Q psy230 54 PTRGDLVIGVVTSRVGDNYRVDIGSH-DPAVLSYLAFEGA------------TKKNPPKVETGDVVAGKLLTANKD-MES 119 (222)
Q Consensus 54 P~vGDiVIG~V~~v~~~~~~VdI~~~-~~a~L~~~~f~ga------------tk~~r~~l~~GDlV~ArV~~~~~~-~~~ 119 (222)
..+|+.+-|+|++++...+.|.+... -.|.+|++.+... -++....|++||-|..+|.+++.. ..+
T Consensus 641 ~~iGe~f~G~Is~V~~fGifVeL~~~~vEGlV~vs~L~~d~y~~d~~~~~L~g~~~~~~~~lGD~V~VkV~~vD~~~rkI 720 (813)
T PRK11642 641 DQVGNVFKGVISSVTGFGFFVRLDDLFIDGLVHVSSLDNDYYRFDQVGQRLIGESSGQTYRLGDRVEVRVEAVNMDERKI 720 (813)
T ss_pred ccCCcEEEEEEEEeecCceEEEECCCCeeeeEEEeecCCcceEecchheEEecccCCcEECCCCEEEEEEEEeecCCCeE
Confidence 47899999999999999999999764 7899998765421 024457899999999999998753 568
Q ss_pred EEEEecCCCccccCccc
Q psy230 120 EMVCVDSRGKEFIMGIL 136 (222)
Q Consensus 120 ~Ls~~~~~~~~~~~G~L 136 (222)
.++....+.+..+.|+-
T Consensus 721 ~f~l~~~~~~~~~~~~~ 737 (813)
T PRK11642 721 DFSLISSERAPRNVGKT 737 (813)
T ss_pred EEEEecccccCCCCCcc
Confidence 88877644444455543
No 100
>TIGR02063 RNase_R ribonuclease R. This family consists of an exoribonuclease, ribonuclease R, also called VacB. It is one of the eight exoribonucleases reported in E. coli and is broadly distributed throughout the bacteria. In E. coli, double mutants of this protein and polynucleotide phosphorylase are not viable. Scoring between trusted and noise cutoffs to the model are shorter, divergent forms from the Chlamydiae, and divergent forms from the Campylobacterales (including Helicobacter pylori) and Leptospira interrogans.
Probab=91.75 E-value=0.81 Score=45.66 Aligned_cols=70 Identities=13% Similarity=0.168 Sum_probs=55.7
Q ss_pred CCCCCCEEEEEEEEEecceEEEEECC-CCCeeeeccccccc------------cccCCcCCCCCCEEEEEEEecCCC-Ce
Q psy230 53 VPTRGDLVIGVVTSRVGDNYRVDIGS-HDPAVLSYLAFEGA------------TKKNPPKVETGDVVAGKLLTANKD-ME 118 (222)
Q Consensus 53 ~P~vGDiVIG~V~~v~~~~~~VdI~~-~~~a~L~~~~f~ga------------tk~~r~~l~~GDlV~ArV~~~~~~-~~ 118 (222)
.+.+|..+-|+|+++..-.+.|++.. ...|.+|++.+.+. .++....|++||-|..+|.+++.. ..
T Consensus 624 ~~~iG~~~~g~V~~v~~fGifV~L~~~~~eGlvhis~l~~d~~~~d~~~~~l~g~~~~~~~~lGd~V~Vkv~~vd~~~~~ 703 (709)
T TIGR02063 624 SEKIGEEFEGVISGVTSFGLFVELENNTIEGLVHISTLKDDYYVFDEKGLALVGERTGKVFRLGDRVKVRVVKADLDTGK 703 (709)
T ss_pred hccCCcEEEEEEEEEEeCCEEEEecCCceEEEEEeeecCCCcEEEcccceEEEeccCCcEECCCCEEEEEEEEEecccCe
Confidence 46789999999999999999999986 57899998776521 023356799999999999999853 45
Q ss_pred eEEE
Q psy230 119 SEMV 122 (222)
Q Consensus 119 ~~Ls 122 (222)
+.++
T Consensus 704 I~~~ 707 (709)
T TIGR02063 704 IDFE 707 (709)
T ss_pred EEEE
Confidence 5554
No 101
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=91.30 E-value=0.6 Score=46.12 Aligned_cols=74 Identities=15% Similarity=0.113 Sum_probs=65.3
Q ss_pred cCCCCCCEEEEEEEEEecceEEEEECCCCCeeeeccccc-cccccCCcCCCCCCEEEEEEEecCCCCeeEEEEec
Q psy230 52 YVPTRGDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFE-GATKKNPPKVETGDVVAGKLLTANKDMESEMVCVD 125 (222)
Q Consensus 52 Y~P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~-gatk~~r~~l~~GDlV~ArV~~~~~~~~~~Ls~~~ 125 (222)
--|++|.+=.|+|+++..-.++|.+.....+.+|.+... ....+-.+.+++||.|+.||..+++.+.+.|+.+.
T Consensus 615 ~e~evg~iy~G~V~ri~~fGaFv~l~~gkdgl~hiS~~~~~rv~kv~dvlk~Gd~v~Vkv~~iD~~Gri~ls~~~ 689 (692)
T COG1185 615 REVEVGEVYEGTVVRIVDFGAFVELLPGKDGLVHISQLAKERVEKVEDVLKEGDEVKVKVIEIDKQGRIRLSIKA 689 (692)
T ss_pred hhcccccEEEEEEEEEeecceEEEecCCcceeEEehhhhhhhhhcccceeecCceEEEEEeeecccCCccceehh
Confidence 358999999999999999999999999999999988753 34567778999999999999999998888888753
No 102
>PRK13763 putative RNA-processing protein; Provisional
Probab=90.56 E-value=0.86 Score=37.81 Aligned_cols=61 Identities=15% Similarity=0.208 Sum_probs=50.2
Q ss_pred eEEEechhhhhhccCCChhHHHHhhhcCCCcEEEEEEeC-CeEEEe---eCCchhHHHHHHHHHHhh
Q psy230 140 YLLHTSISLCRKLLNPKCPLLKQLAKRSRQKMELSIGMN-GKIWIR---CESFSDTVRVGNLIMSCE 202 (222)
Q Consensus 140 ~l~~v~~~~~~rl~~~~~~~l~~l~~~~~~~~ei~vG~N-G~iWi~---~~~~~~~~~i~~~i~~~e 202 (222)
..+.||+.++..++|+++..++.|.+ .+++.|-+-.+ |.|-|. +.++.....+...|+.+-
T Consensus 5 ~~i~IP~~kig~iIG~gGk~Ik~I~e--~tg~~I~i~~~~g~V~I~~~~~~d~~~i~kA~~~I~ai~ 69 (180)
T PRK13763 5 EYVKIPKDRIGVLIGKKGETKKEIEE--RTGVKLEIDSETGEVIIEPTDGEDPLAVLKARDIVKAIG 69 (180)
T ss_pred EEEEcCHHHhhhHhccchhHHHHHHH--HHCcEEEEECCCCeEEEEeCCCCCHHHHHHHHHHHHHHh
Confidence 35789999999999999999999999 88888888888 999999 667765555555555443
No 103
>PRK11712 ribonuclease G; Provisional
Probab=90.38 E-value=2.6 Score=40.41 Aligned_cols=72 Identities=15% Similarity=0.148 Sum_probs=52.4
Q ss_pred cCCCCCCEEEEEEEEEec--ceEEEEECCCCCeeeecccc-cc------c------cccCCcCCCCCCEEEEEEEecC-C
Q psy230 52 YVPTRGDLVIGVVTSRVG--DNYRVDIGSHDPAVLSYLAF-EG------A------TKKNPPKVETGDVVAGKLLTAN-K 115 (222)
Q Consensus 52 Y~P~vGDiVIG~V~~v~~--~~~~VdI~~~~~a~L~~~~f-~g------a------tk~~r~~l~~GDlV~ArV~~~~-~ 115 (222)
....+|++-.|+|.++.+ +.++|||+..-.|+||+... +. . .......+++||-|...|..-. .
T Consensus 34 ~~~~vGnIY~G~V~~v~pg~~AAFVdIG~~k~gFL~~~d~~~~~~~~~~~~~~~~~~~~i~~~l~~Gq~iLVQV~Ke~~~ 113 (489)
T PRK11712 34 KRGIVGNIYKGRVSRVLPGMQAAFVDIGLDKAAFLHASDIVPHTECVAGEEQKQFVVRDISELVRQGQDIMVQVVKDPLG 113 (489)
T ss_pred cccccccEEEEEEeecCCCCceeEEeeCCCccEEEEhhhccchhhhcccccccccccccHHHhccCCCEEEEEEEeCCcC
Confidence 445689999999999965 78999999999999998653 11 0 0112344999999999998642 2
Q ss_pred CCeeEEEE
Q psy230 116 DMESEMVC 123 (222)
Q Consensus 116 ~~~~~Ls~ 123 (222)
...+.||+
T Consensus 114 ~KG~~lT~ 121 (489)
T PRK11712 114 TKGARLTT 121 (489)
T ss_pred CCCCeEEE
Confidence 33466665
No 104
>TIGR03665 arCOG04150 arCOG04150 universal archaeal KH domain protein. This family of proteins is universal among the 41 archaeal genomes analyzed in and is not observed outside of the archaea. The proteins contain a single KH domain (pfam00013) which is likely to confer the ability to bind RNA.
Probab=90.19 E-value=0.68 Score=38.13 Aligned_cols=59 Identities=14% Similarity=0.178 Sum_probs=49.0
Q ss_pred EEechhhhhhccCCChhHHHHhhhcCCCcEEEEEEeC-CeEEE--eeCCchhHHHHHHHHHHhh
Q psy230 142 LHTSISLCRKLLNPKCPLLKQLAKRSRQKMELSIGMN-GKIWI--RCESFSDTVRVGNLIMSCE 202 (222)
Q Consensus 142 ~~v~~~~~~rl~~~~~~~l~~l~~~~~~~~ei~vG~N-G~iWi--~~~~~~~~~~i~~~i~~~e 202 (222)
+.||+.++..++|+++..++.|.+ .+++.|-+-.+ |.|-| .+.++.....+...|+.+-
T Consensus 2 i~Ip~~kig~vIG~gG~~Ik~I~~--~tgv~I~Id~~~g~V~I~~~t~d~~~i~kA~~~I~~i~ 63 (172)
T TIGR03665 2 VKIPKDRIGVLIGKGGETKKEIEE--RTGVKLDIDSETGEVKIEEEDEDPLAVMKAREVVKAIG 63 (172)
T ss_pred ccCCHHHhhhHhCCchhHHHHHHH--HhCcEEEEEcCCceEEEecCCCCHHHHHHHHHHHHHHH
Confidence 679999999999999999999999 89999988888 99999 6777765566655555543
No 105
>PRK10811 rne ribonuclease E; Reviewed
Probab=90.07 E-value=2.7 Score=43.39 Aligned_cols=70 Identities=11% Similarity=0.126 Sum_probs=50.7
Q ss_pred CCCCCEEEEEEEEEe--cceEEEEECCCCCeeeecccc-----ccc-----cccCCcCCCCCCEEEEEEEecC-CCCeeE
Q psy230 54 PTRGDLVIGVVTSRV--GDNYRVDIGSHDPAVLSYLAF-----EGA-----TKKNPPKVETGDVVAGKLLTAN-KDMESE 120 (222)
Q Consensus 54 P~vGDiVIG~V~~v~--~~~~~VdI~~~~~a~L~~~~f-----~ga-----tk~~r~~l~~GDlV~ArV~~~~-~~~~~~ 120 (222)
+.+|+|-+|+|.++- -+.++|||+....|+|++... ... ..+....|++||-|.-.|..-. +..-+.
T Consensus 36 ~~vGnIYkGkVenIvPGInAAFVDIG~gknGFL~L~Di~~~~f~~~~~~~~~~~i~~~Lk~GqeILVQV~KEa~gtKGp~ 115 (1068)
T PRK10811 36 QKKANIYKGKITRIEPSLEAAFVDYGAERHGFLPLKEIAREYFPANYSAHGRPNIKDVLREGQEVIVQIDKEERGNKGAA 115 (1068)
T ss_pred cCccceEEEEEecccCCcceeEEEecCCcceEEEhhhccccccccccccccccccccccCCCCEEEEEEeecccCCCCCc
Confidence 468999999999994 478999999999999997543 111 0123456999999999998632 333355
Q ss_pred EEE
Q psy230 121 MVC 123 (222)
Q Consensus 121 Ls~ 123 (222)
||+
T Consensus 116 LTt 118 (1068)
T PRK10811 116 LTT 118 (1068)
T ss_pred eee
Confidence 554
No 106
>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase. Sohlberg, et al. present characterization of two proteins from Streptomyces coelicolor. The protein in this family was shown to have poly(A) polymerase activity and may be responsible for polyadenylating RNA in this species. Reference 2 showed that a nearly identical plasmid-encoded protein from Streptomyces antibioticus is a bifunctional enzyme that acts also as a guanosine pentaphosphate synthetase.
Probab=89.50 E-value=0.89 Score=45.48 Aligned_cols=60 Identities=15% Similarity=0.284 Sum_probs=51.1
Q ss_pred eEEEechhhhhhccCCChhHHHHhhhcCCCcEEEEEEeCCeEEEeeCCchhHHHHHHHHHHh
Q psy230 140 YLLHTSISLCRKLLNPKCPLLKQLAKRSRQKMELSIGMNGKIWIRCESFSDTVRVGNLIMSC 201 (222)
Q Consensus 140 ~l~~v~~~~~~rl~~~~~~~l~~l~~~~~~~~ei~vG~NG~iWi~~~~~~~~~~i~~~i~~~ 201 (222)
..++|+|.+++.++|+++.+++.|.+ .++++|=+-.+|.|.|.+.+......+...|+.+
T Consensus 580 ~~~~I~~~ki~~vIG~gGk~I~~i~~--~tg~~Idi~d~G~V~I~a~d~~~~~~A~~~I~~i 639 (719)
T TIGR02696 580 ITVKIPVDKIGEVIGPKGKMINQIQD--ETGAEISIEDDGTVYIGAADGPSAEAARAMINAI 639 (719)
T ss_pred EEEEeChHHhhheeCCCcHhHHHHHH--HHCCEEEEecCcEEEEEeCCHHHHHHHHHHHHHh
Confidence 67899999999999999999999999 9999999999999999998876554444444443
No 107
>PHA02858 EIF2a-like PKR inhibitor; Provisional
Probab=88.88 E-value=1.7 Score=31.86 Aligned_cols=63 Identities=13% Similarity=0.203 Sum_probs=47.1
Q ss_pred CCCCCCEEEEEEEEEecceEEEEECCC-CCe-eeecccccc-ccccCCcCCCCCCEEEEEEEecCCCC
Q psy230 53 VPTRGDLVIGVVTSRVGDNYRVDIGSH-DPA-VLSYLAFEG-ATKKNPPKVETGDVVAGKLLTANKDM 117 (222)
Q Consensus 53 ~P~vGDiVIG~V~~v~~~~~~VdI~~~-~~a-~L~~~~f~g-atk~~r~~l~~GDlV~ArV~~~~~~~ 117 (222)
.|++||+|. .|..+....+.|.+--. ..| +|+++...- ..++++..+ +|-.+.++|+.+++..
T Consensus 13 ~P~v~dvv~-~Vv~i~d~~~YV~LleY~iegmIl~~selsr~rirsi~kll-VGk~e~v~ViRVDk~K 78 (86)
T PHA02858 13 FPNINEVTK-GIVFVKDNIFYVKLIDYGLEALIVNYVNVNADRAEKLKKKL-VGKTINVQVIRTDKLK 78 (86)
T ss_pred cCCCCeEEE-EEEEEeccEEEEEEecCccceEEecHHHHhHHHHHhhhhhh-cCCeeEEEEEEECCCC
Confidence 699999999 78888998899988542 334 343555432 345667778 9999999999998763
No 108
>cd05699 S1_Rrp5_repeat_hs7 S1_Rrp5_repeat_hs7: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 7 (hs7). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=87.71 E-value=2.7 Score=29.93 Aligned_cols=66 Identities=17% Similarity=0.064 Sum_probs=46.4
Q ss_pred CCEEEEEEEEEecceEEEEECC-CCCeeeeccccccccc---cCCcCCCCCCEE-EEEEEecCCCCeeEEEE
Q psy230 57 GDLVIGVVTSRVGDNYRVDIGS-HDPAVLSYLAFEGATK---KNPPKVETGDVV-AGKLLTANKDMESEMVC 123 (222)
Q Consensus 57 GDiVIG~V~~v~~~~~~VdI~~-~~~a~L~~~~f~gatk---~~r~~l~~GDlV-~ArV~~~~~~~~~~Ls~ 123 (222)
|++|=|+|.+++.|...|++.. .-.|.||......... .....+++||-+ -+-|.+. ....+.||+
T Consensus 1 G~lV~~~V~EKt~D~l~v~l~~~~l~a~l~~~HLsD~~~k~~~~~~klrvG~~L~~~lvL~~-~~r~i~lt~ 71 (72)
T cd05699 1 GKLVDARVLKKTLNGLEVAILPEEIRAFLPTMHLSDHVSNCPLLWHCLQEGDTIPNLMCLSN-YKGRIILTK 71 (72)
T ss_pred CceEEEEEEEEcCCcEEEEecCCCcEEEEEccccCCchhhCHHHHhhhhcCCCccceEEEec-cccEEEEec
Confidence 7899999999999999999987 6689998754432222 345678899988 6666622 223444543
No 109
>cd02395 SF1_like-KH Splicing factor 1 (SF1) K homology RNA-binding domain (KH). Splicing factor 1 (SF1) specifically recognizes the intron branch point sequence (BPS) UACUAAC in the pre-mRNA transcripts during spliceosome assembly. We show that the KH-QUA2 region of SF1 defines an enlarged KH (hnRNP K) fold which is necessary and sufficient for BPS binding. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=86.98 E-value=1.4 Score=34.28 Aligned_cols=52 Identities=23% Similarity=0.255 Sum_probs=40.1
Q ss_pred hhhhhccCCChhHHHHhhhcCCCcEEEEEEeC-----------------------CeEEEeeCC--chhHHHHHHHHHH
Q psy230 147 SLCRKLLNPKCPLLKQLAKRSRQKMELSIGMN-----------------------GKIWIRCES--FSDTVRVGNLIMS 200 (222)
Q Consensus 147 ~~~~rl~~~~~~~l~~l~~~~~~~~ei~vG~N-----------------------G~iWi~~~~--~~~~~~i~~~i~~ 200 (222)
+++.+++|+++..++.|.+ .++|.|.|--. |.|.|.+.+ ......+...|+.
T Consensus 15 N~IG~IIGPgG~tiK~i~~--eTg~kI~Irg~gs~~~~~~~~~~~~~~~~~~~eplhV~I~a~~~~~e~~~~A~~~I~~ 91 (120)
T cd02395 15 NFVGLILGPRGNTLKQLEK--ETGAKISIRGKGSMKDGKKEEELRGPKYAHLNEPLHVLITAETPPEEALAKAVEAIEE 91 (120)
T ss_pred CeeEEEECCCChHHHHHHH--HHCCEEEEecCcccccccccccccCcccccCCCCcEEEEEeCCcHHHHHHHHHHHHHH
Confidence 6778889999999999999 99999977655 899999988 4434444444443
No 110
>PF13509 S1_2: S1 domain; PDB: 3GO5_A.
Probab=86.19 E-value=4.4 Score=27.45 Aligned_cols=60 Identities=18% Similarity=0.165 Sum_probs=32.6
Q ss_pred CCCEEEEEEEEEecceEEEEECCCCCeeeeccccccccccCCcCCCCCCEEEEEEEecCCCCeeEEEE
Q psy230 56 RGDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFEGATKKNPPKVETGDVVAGKLLTANKDMESEMVC 123 (222)
Q Consensus 56 vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~gatk~~r~~l~~GDlV~ArV~~~~~~~~~~Ls~ 123 (222)
+|+++-.+|++++...|.+|-+......||.... ...+++||-|..-|=. +++.....||
T Consensus 1 iG~~~~L~V~~~~~~g~fL~~~~~~~vlLp~~e~-------~~~~~~Gd~v~VFvY~-D~~~rl~AT~ 60 (61)
T PF13509_consen 1 IGQINTLKVVDKNEFGYFLDDGEGKEVLLPKSEV-------PEPLKVGDEVEVFVYL-DKEGRLVATT 60 (61)
T ss_dssp --------EEEE-SSEEEEEETT-EEEEEEGGG-------------TTSEEEEEEEE--TTS-EEEE-
T ss_pred CCCCcceEEEEEeCCEEEEECCCCCEEEechHHc-------CCCCCCCCEEEEEEEE-CCCCCEEEec
Confidence 5889999999999999999998889999996433 3458899999888743 3333444444
No 111
>cd02396 PCBP_like_KH K homology RNA-binding domain, PCBP_like. Members of this group possess KH domains in a tandem arrangement. Most members, similar to the poly(C) binding proteins (PCBPs) and Nova, containing three KH domains, with the first and second domains, which are represented here, in tandem arrangement, followed by a large spacer region, with the third domain near the C-terminal end of the protein. The poly(C) binding proteins (PCBPs) can be divided into two groups, hnRNPs K/J and the alphaCPs, which share a triple KH domain configuration and poly(C) binding specificity. They play roles in mRNA stabilization, translational activation, and translational silencing. Nova-1 and Nova-2 are nuclear RNA-binding proteins that regulate splicing. This group also contains plant proteins that seem to have two tandem repeat arrrangements, like Hen4, a protein that plays a role in AGAMOUS (AG) pre-mRNA processing and important step in plant development. In general, KH binds single-stran
Probab=85.72 E-value=2.1 Score=29.08 Aligned_cols=37 Identities=8% Similarity=0.123 Sum_probs=34.0
Q ss_pred EEechhhhhhccCCChhHHHHhhhcCCCcEEEEEEeCCe
Q psy230 142 LHTSISLCRKLLNPKCPLLKQLAKRSRQKMELSIGMNGK 180 (222)
Q Consensus 142 ~~v~~~~~~rl~~~~~~~l~~l~~~~~~~~ei~vG~NG~ 180 (222)
+.||..++.+++|+++..++.|.+ .+++.|-+..|..
T Consensus 4 ~~ip~~~vg~iIG~~G~~i~~i~~--~tga~I~i~~~~~ 40 (65)
T cd02396 4 LLVPSSQAGSIIGKGGSTIKEIRE--ETGAKIRVSKSVL 40 (65)
T ss_pred EEECHHHcCeeECCCcHHHHHHHH--HHCCEEEEcCCCC
Confidence 678999999999999999999999 8999999988873
No 112
>TIGR00358 3_prime_RNase VacB and RNase II family 3'-5' exoribonucleases. This model is defined to identify a pair of paralogous 3-prime exoribonucleases in E. coli, plus the set of proteins apparently orthologous to one or the other in other eubacteria. VacB was characterized originally as required for the expression of virulence genes, but is now recognized as the exoribonuclease RNase R (Rnr). Its paralog in E. coli and H. influenzae is designated exoribonuclease II (Rnb). Both are involved in the degradation of mRNA, and consequently have strong pleiotropic effects that may be difficult to disentangle. Both these proteins share domain-level similarity (RNB, S1) with a considerable number of other proteins, and full-length similarity scoring below the trusted cutoff to proteins associated with various phenotypes but uncertain biochemistry; it may be that these latter proteins are also 3-prime exoribonucleases.
Probab=85.21 E-value=3 Score=41.36 Aligned_cols=70 Identities=16% Similarity=0.091 Sum_probs=54.4
Q ss_pred CCCCCCEEEEEEEEEecceEEEEEC-CCCCeeeecccccccc------------ccCCcCCCCCCEEEEEEEecCCC-Ce
Q psy230 53 VPTRGDLVIGVVTSRVGDNYRVDIG-SHDPAVLSYLAFEGAT------------KKNPPKVETGDVVAGKLLTANKD-ME 118 (222)
Q Consensus 53 ~P~vGDiVIG~V~~v~~~~~~VdI~-~~~~a~L~~~~f~gat------------k~~r~~l~~GDlV~ArV~~~~~~-~~ 118 (222)
...+|..+-|+|++++...+.|+|. ....|.+|++.+++.. ++....|++||.|..+|.+++.. ..
T Consensus 569 ~~~iG~~~~g~I~~v~~~GifV~L~~~~veGlV~~s~l~~d~y~~d~~~~~l~g~~~~~~~~lGD~V~Vki~~vd~~~~~ 648 (654)
T TIGR00358 569 LDKVGTEFSGEISSVTRFGMFVRLDDNGIDGLIHISTLHNDYYVFDQEKMALIGKGTGKVYRIGDRVTVKLTEVNMETRS 648 (654)
T ss_pred hhCCCcEEEEEEEeEEcCcEEEEecCCceEEEEEeEeCCCcceEEeccccEEEeccCCcEECCCCEEEEEEEEEecccCe
Confidence 3467999999999999999999997 4588999987765321 23457899999999999999753 34
Q ss_pred eEEE
Q psy230 119 SEMV 122 (222)
Q Consensus 119 ~~Ls 122 (222)
+.++
T Consensus 649 I~f~ 652 (654)
T TIGR00358 649 IIFE 652 (654)
T ss_pred EEEE
Confidence 4443
No 113
>KOG1070|consensus
Probab=84.70 E-value=1.7 Score=46.31 Aligned_cols=69 Identities=14% Similarity=0.148 Sum_probs=56.9
Q ss_pred ccccCCCCCCEEEEEEEEEecceEEEEECCCCCeeeeccc-cc---cccccCCcCCCCCCEEEEEEEecCCCCe
Q psy230 49 QRRYVPTRGDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLA-FE---GATKKNPPKVETGDVVAGKLLTANKDME 118 (222)
Q Consensus 49 ~~~Y~P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~-f~---gatk~~r~~l~~GDlV~ArV~~~~~~~~ 118 (222)
+..|.-++|++|-|.|+++.++.-.|+..+...+-+|++. |. ..+. .-..|++||-|.|||+.-++..+
T Consensus 878 k~~~~~~igsiv~a~v~svKp~~L~v~l~~~~~gri~isev~d~~~eitD-p~~k~~vG~~I~vrviG~~D~k~ 950 (1710)
T KOG1070|consen 878 KSTEDLSIGSIVRAYVKSVKPDQLNVLLAANHHGRIHISEVLDNLHEITD-PLDKFKVGDGIFVRVIGGHDVKD 950 (1710)
T ss_pred ccccceeeeeEEEEEEeeecccceEEeccccccCceehHHhhccccccCC-hhhhcccCCeEEEEEEcCCcccc
Confidence 4578889999999999999999999999999999999864 33 2333 56679999999999997654433
No 114
>cd03524 RPA2_OBF_family RPA2_OBF_family: A family of oligonucleotide binding (OB) folds with similarity to the OB fold of the single strand (ss) DNA-binding domain (DBD)-D of human RPA2 (also called RPA32). RPA2 is a subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). RPA contains six OB folds, which are involved in ssDNA binding and in trimerization. The ssDNA binding mechanism is believed to be multistep and to involve conformational change. This family also includes OB folds similar to those found in Escherichia coli SSB, the wedge domain of E. coli RecG (a branched-DNA-specific helicase), E. coli ssDNA specific exodeoxyribonuclease VII large subunit, Pyroco
Probab=84.52 E-value=5.5 Score=25.98 Aligned_cols=64 Identities=11% Similarity=0.093 Sum_probs=41.8
Q ss_pred EEEEEEEEec-----ceEEEEECCCCCeeeeccccccccccCCcCCCCCCEEEEEEEecCCCCeeEEEE
Q psy230 60 VIGVVTSRVG-----DNYRVDIGSHDPAVLSYLAFEGATKKNPPKVETGDVVAGKLLTANKDMESEMVC 123 (222)
Q Consensus 60 VIG~V~~v~~-----~~~~VdI~~~~~a~L~~~~f~gatk~~r~~l~~GDlV~ArV~~~~~~~~~~Ls~ 123 (222)
|.|+|.++.. .++.+.|.....+.+++..|+....+....+.+|+.++.+..--.....+.|.+
T Consensus 2 v~g~v~~~~~~~~~~~~~~~~l~D~~~~~i~~~~~~~~~~~~~~~~~~g~~v~v~g~v~~~~~~~~l~~ 70 (75)
T cd03524 2 IVGIVVAVEEIRTEGKVLIFTLTDGTGGTIRVTLFGELAEELENLLKEGQVVYIKGKVKKFRGRLQLIV 70 (75)
T ss_pred eEEEEEeecccccCCeEEEEEEEcCCCCEEEEEEEchHHHHHHhhccCCCEEEEEEEEEecCCeEEEEe
Confidence 5677777764 457777776554777777776554556678999999887743222233456655
No 115
>KOG3298|consensus
Probab=82.50 E-value=11 Score=30.96 Aligned_cols=65 Identities=23% Similarity=0.285 Sum_probs=46.6
Q ss_pred cccCCCCCCEEEEEEEEEecceEEEEECCCCCeeeecc-----cc-cccc-----ccCCcCCCCCCEEEEEEEecC
Q psy230 50 RRYVPTRGDLVIGVVTSRVGDNYRVDIGSHDPAVLSYL-----AF-EGAT-----KKNPPKVETGDVVAGKLLTAN 114 (222)
Q Consensus 50 ~~Y~P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~-----~f-~gat-----k~~r~~l~~GDlV~ArV~~~~ 114 (222)
-.+.|-.|++|=|.|+.++...+.++++.-...+++.+ .| +|.. ...-..++.|+-|+-+|+...
T Consensus 75 v~FkpfKGEVvdgvV~~Vnk~G~F~~~GPl~~f~sshl~ppd~~f~p~~n~P~f~~~d~s~I~~~~~VR~kiigtr 150 (170)
T KOG3298|consen 75 VTFKPFKGEVVDGVVTKVNKMGVFARSGPLEVFYSSHLKPPDYEFDPGENPPNFQTEDESVIQKGVEVRLKIIGTR 150 (170)
T ss_pred EEEeecCCcEEEEEEEEEeeeeEEEeccceEeeeecccCCCCcccCCCCCCCcccccccceeeeCcEEEEEEEEEE
Confidence 35889999999999999999999999998665555532 23 2211 111225778888888888653
No 116
>PRK04012 translation initiation factor IF-1A; Provisional
Probab=81.98 E-value=8.2 Score=29.14 Aligned_cols=57 Identities=25% Similarity=0.227 Sum_probs=39.1
Q ss_pred CCCCCCEEEEEEEEE-ecceEEEEECCCCCeeeeccccccccccCCcCCCCCCEEEEEEEecC
Q psy230 53 VPTRGDLVIGVVTSR-VGDNYRVDIGSHDPAVLSYLAFEGATKKNPPKVETGDVVAGKLLTAN 114 (222)
Q Consensus 53 ~P~vGDiVIG~V~~v-~~~~~~VdI~~~~~a~L~~~~f~gatk~~r~~l~~GDlV~ArV~~~~ 114 (222)
.| ..+-++|+|+.. .++.|.|....-.. .|- .++|..++ +-.+++||.|..+....+
T Consensus 17 ~p-~e~e~~g~V~~~lG~~~~~V~~~dG~~-~la--~i~GK~Rk-~IwI~~GD~VlVe~~~~~ 74 (100)
T PRK04012 17 MP-EEGEVFGVVEQMLGANRVRVRCMDGVE-RMG--RIPGKMKK-RMWIREGDVVIVAPWDFQ 74 (100)
T ss_pred CC-CCCEEEEEEEEEcCCCEEEEEeCCCCE-EEE--EEchhhcc-cEEecCCCEEEEEecccC
Confidence 44 456699999998 45788888864322 111 23454455 778999999999986665
No 117
>PF08292 RNA_pol_Rbc25: RNA polymerase III subunit Rpc25; InterPro: IPR013238 Rpc25 is a strongly conserved subunit of RNA polymerase III and has homology to Rpa43 in RNA polymerase I, Rpb7 in RNA polymerase II and the archaeal RpoE subunit. Rpc25 is required for transcription initiation and is not essential for the elongating properties of RNA polymerase III [].; PDB: 2CKZ_D 3AYH_B.
Probab=81.19 E-value=4.6 Score=31.52 Aligned_cols=61 Identities=16% Similarity=0.316 Sum_probs=41.8
Q ss_pred CCCCCEEEEEEEEEecceEEEEECCCCCeeeecc------cccccc--------ccCCcCCCCCCEEEEEEEecC
Q psy230 54 PTRGDLVIGVVTSRVGDNYRVDIGSHDPAVLSYL------AFEGAT--------KKNPPKVETGDVVAGKLLTAN 114 (222)
Q Consensus 54 P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~------~f~gat--------k~~r~~l~~GDlV~ArV~~~~ 114 (222)
|-+|.++.|+|.+.+.+..+|.++--.+-.+|.. .|.... ...+-+++.|+-|+=||.+..
T Consensus 1 PF~gEvl~g~I~~~~~~Gi~vslgFFddI~IP~~~L~~ps~fd~~~~~W~W~~~~~~~l~~d~ge~IRFRV~~~~ 75 (122)
T PF08292_consen 1 PFVGEVLTGKIKSSTAEGIRVSLGFFDDIFIPPSLLPEPSRFDEEEQAWVWEYDEEQELFFDIGEEIRFRVESEI 75 (122)
T ss_dssp --TT-EEEEEEEEEETTEEEEEECCEEEEEEECCCC-TTEEEECCCTEEEEEESSSEEEEE-TT-EEEEEEEEEE
T ss_pred CCCCCEEEEEEEecCCCcEEEEecccccEEECHHHCCCCCccCccCCEEEEECCCCceeEccCCCEEEEEEeEEE
Confidence 6789999999999999999999976444444433 333211 455667899999999998764
No 118
>PF10246 MRP-S35: Mitochondrial ribosomal protein MRP-S35; InterPro: IPR019375 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This is a family of short mitochondrial ribosomal proteins, less than 200 amino acids long. MRP-S35 was proposed as a more appropriate name to this group of proteins [].
Probab=80.96 E-value=7.2 Score=29.66 Aligned_cols=53 Identities=28% Similarity=0.310 Sum_probs=42.6
Q ss_pred CCCCCEEEEEEEEEecceEEEEECCCCCeeeeccccccccccCCcCCCCCCEEEEEEEe
Q psy230 54 PTRGDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFEGATKKNPPKVETGDVVAGKLLT 112 (222)
Q Consensus 54 P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~gatk~~r~~l~~GDlV~ArV~~ 112 (222)
|..|-+|+|+|..+..+---+|.|.-+.++.+--+ .+...|..|+-|.-|+..
T Consensus 21 ~~~gk~V~G~I~hvv~ddLYIDfG~KFhcVc~rp~------~~~~~y~~G~rV~lrLkd 73 (104)
T PF10246_consen 21 DPEGKIVIGKIFHVVDDDLYIDFGGKFHCVCKRPA------VNGEKYVRGSRVRLRLKD 73 (104)
T ss_pred CccCCEEEEEEEEEecCceEEEeCCceeEEEeccc------ccccccccCCEEEEEECC
Confidence 45799999999999999999999998888887322 334568899999999753
No 119
>PF01336 tRNA_anti-codon: OB-fold nucleic acid binding domain; InterPro: IPR004365 The OB-fold (oligonucleotide/oligosaccharide-binding fold) is found in all three kingdoms and its common architecture presents a binding face that has adapted to bind different ligands. The OB-fold is a five/six-stranded closed beta-barrel formed by 70-80 amino acid residues. The strands are connected by loops of varying length which form the functional appendages of the protein. The majority of OB-fold proteins use the same face for ligand binding or as an active site. Different OB-fold proteins use this 'fold-related binding face' to, variously, bind oligosaccharides, oligonucleotides, proteins, metal ions and catalytic substrates. This entry contains OB-fold domains that bind to nucleic acids []. It includes the anti-codon binding domain of lysyl, aspartyl, and asparaginyl-tRNA synthetases (See IPR004364 from INTERPRO). Aminoacyl-tRNA synthetases catalyse the addition of an amino acid to the appropriate tRNA molecule 6.1.1 from EC. This domain is found in RecG helicase involved in DNA repair. Replication factor A is a heterotrimeric complex, that contains a subunit in this family [, ]. This domain is also found at the C terminus of bacterial DNA polymerase III alpha chain.; GO: 0003676 nucleic acid binding; PDB: 1BBU_A 1KRS_A 1BBW_A 1KRT_A 1EQR_B 1IL2_B 1C0A_A 3KFU_A 1EOV_A 1ASY_A ....
Probab=80.93 E-value=4.4 Score=27.37 Aligned_cols=62 Identities=23% Similarity=0.248 Sum_probs=42.4
Q ss_pred EEEEEEEE---ecceEEEEECCCCCeeeeccccccccccCCcCCCCCCEEEEE--EEecCCCCeeEEEE
Q psy230 60 VIGVVTSR---VGDNYRVDIGSHDPAVLSYLAFEGATKKNPPKVETGDVVAGK--LLTANKDMESEMVC 123 (222)
Q Consensus 60 VIG~V~~v---~~~~~~VdI~~~~~a~L~~~~f~gatk~~r~~l~~GDlV~Ar--V~~~~~~~~~~Ls~ 123 (222)
|.|+|+++ ......++|.... +.+.+..|.....+..+.+++||.|..+ |.... ..+++|++
T Consensus 3 v~G~V~~~~~~~~~~~~~~l~D~t-g~i~~~~~~~~~~~~~~~l~~g~~v~v~G~v~~~~-~~~~~l~~ 69 (75)
T PF01336_consen 3 VEGRVTSIRRSGGKIVFFTLEDGT-GSIQVVFFNEEYERFREKLKEGDIVRVRGKVKRYN-GGELELIV 69 (75)
T ss_dssp EEEEEEEEEEEETTEEEEEEEETT-EEEEEEEETHHHHHHHHTS-TTSEEEEEEEEEEET-TSSEEEEE
T ss_pred EEEEEEEEEcCCCCEEEEEEEECC-ccEEEEEccHHhhHHhhcCCCCeEEEEEEEEEEEC-CccEEEEE
Confidence 67888877 5677888887654 7777767765556777789999998655 55443 23477766
No 120
>KOG3297|consensus
Probab=80.09 E-value=8.3 Score=32.40 Aligned_cols=62 Identities=16% Similarity=0.296 Sum_probs=45.4
Q ss_pred cCCCCCCEEEEEEEEEecceEEEEECCCCCeeeeccc------cccc---------c---ccCCcCCCCCCEEEEEEEec
Q psy230 52 YVPTRGDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLA------FEGA---------T---KKNPPKVETGDVVAGKLLTA 113 (222)
Q Consensus 52 Y~P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~------f~ga---------t---k~~r~~l~~GDlV~ArV~~~ 113 (222)
+.|-+|.++.|+|.+-..+..+|.|+--.+=..|... |+-+ . ...+-+|++|.-|+=||.+.
T Consensus 77 FrPF~gEVi~gki~~cs~eG~rvtl~FFdDI~IP~~~L~~p~~f~~~e~vWVWey~~Edg~~~~Ly~D~~e~IRFRV~~e 156 (202)
T KOG3297|consen 77 FRPFVGEVITGKIKECSEEGLRVTLGFFDDIFIPKEMLPEPCVFEPDEQVWVWEYEQEDGPGTKLYFDVGEEIRFRVEDE 156 (202)
T ss_pred EecccceEEEEEeecCCccceEEEEEeeeceeechhhCCCCcccccccEEEEEEecccCCCCceeEecCCCeEEEEEeee
Confidence 6799999999999999999999998753333333322 2211 1 14566899999999999875
No 121
>smart00652 eIF1a eukaryotic translation initiation factor 1A.
Probab=78.91 E-value=12 Score=27.24 Aligned_cols=55 Identities=15% Similarity=0.093 Sum_probs=36.6
Q ss_pred CCCCCEEEEEEEEE-ecceEEEEECCCCCeeeeccccccccccCCcCCCCCCEEEEEEEec
Q psy230 54 PTRGDLVIGVVTSR-VGDNYRVDIGSHDPAVLSYLAFEGATKKNPPKVETGDVVAGKLLTA 113 (222)
Q Consensus 54 P~vGDiVIG~V~~v-~~~~~~VdI~~~~~a~L~~~~f~gatk~~r~~l~~GDlV~ArV~~~ 113 (222)
|. .+-++|+|+.. .++.|.|....-..-.- .++|..++ +-.++.||.|..+....
T Consensus 2 p~-e~q~~g~V~~~lG~~~~~V~~~dG~~~la---~ipgK~Rk-~iwI~~GD~VlVe~~~~ 57 (83)
T smart00652 2 KE-DGQEIAQVVKMLGNGRLEVMCADGKERLA---RIPGKMRK-KVWIRRGDIVLVDPWDF 57 (83)
T ss_pred CC-CCcEEEEEEEEcCCCEEEEEECCCCEEEE---EEchhhcc-cEEEcCCCEEEEEecCC
Confidence 54 45689999998 56788888865322211 23344444 67799999999987544
No 122
>cd04456 S1_IF1A_like S1_IF1A_like: Translation initiation factor IF1A-like, S1-like RNA-binding domain. IF1A is also referred to as eIF1A in eukaryotes and aIF1A in archaea. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. IF1A is essential for translation initiation. eIF1A acts synergistically with eIF1 to mediate assembly of ribosomal initiation complexes at the initiation codon and maintain the accuracy of this process by recognizing and destabilizing aberrant preinitiation complexes from the mRNA. Without eIF1A and eIF1, 43S ribosomal preinitiation complexes can bind to the cap-proximal region, but are unable to reach the initiation codon. eIF1a also enhances the formation of 5'-terminal complexes in the presence of other translation initiation factors. This protein family is only found in eukaryotes and archaea.
Probab=77.10 E-value=22 Score=25.45 Aligned_cols=50 Identities=16% Similarity=0.182 Sum_probs=33.4
Q ss_pred EEEEEEEE-ecceEEEEECCCCCeeeeccccccccccCCcCCCCCCEEEEEEEec
Q psy230 60 VIGVVTSR-VGDNYRVDIGSHDPAVLSYLAFEGATKKNPPKVETGDVVAGKLLTA 113 (222)
Q Consensus 60 VIG~V~~v-~~~~~~VdI~~~~~a~L~~~~f~gatk~~r~~l~~GDlV~ArV~~~ 113 (222)
+||+|++. .++.|.|.......-.- .++|..++. -.+++||.|.++....
T Consensus 2 ~i~~V~~~lG~~~~~V~~~dg~~~l~---~i~gK~Rk~-iwI~~GD~VlV~~~~~ 52 (78)
T cd04456 2 QIVRVLRMLGNNRHEVECADGQRRLV---SIPGKLRKN-IWIKRGDFLIVDPIEE 52 (78)
T ss_pred eEEEEEEECCCCEEEEEECCCCEEEE---EEchhhccC-EEEcCCCEEEEEeccc
Confidence 68999998 45788888864322221 223433433 6799999999987665
No 123
>PF01176 eIF-1a: Translation initiation factor 1A / IF-1; InterPro: IPR006196 The S1 domain of around 70 amino acids, originally identified in ribosomal protein S1, is found in a large number of RNA-associated proteins. It has been shown that S1 proteins bind RNA through their S1 domains with some degree of sequence specificity. This type of S1 domain is found in translation initiation factor 1. The solution structure of one S1 RNA-binding domain from Escherichia coli polynucleotide phosphorylase has been determined []. It displays some similarity with the cold shock domain (CSD) (IPR002059 from INTERPRO). Both the S1 and the CSD domain consist of an antiparallel beta barrel of the same topology with 5 beta strands. This fold is also shared by many other proteins of unrelated function and is known as the OB fold. However, the S1 and CSD fold can be distinguished from the other OB folds by the presence of a short 3(10) helix at the end of strand 3. This unique feature is likely to form a part of the DNA/RNA-binding site. This entry is specific for bacterial, chloroplastic and eukaryotic IF-1 type S1 domains.; GO: 0003723 RNA binding, 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 1JT8_A 3I4O_A 1AH9_A 1ZO1_W 1D7Q_A 2OQK_A 2DGY_A 1HR0_W.
Probab=77.07 E-value=6 Score=27.19 Aligned_cols=52 Identities=21% Similarity=0.244 Sum_probs=34.1
Q ss_pred CCEEEEEEEEEe-cceEEEEECCCC--CeeeeccccccccccCCcCCCCCCEEEEEEEecC
Q psy230 57 GDLVIGVVTSRV-GDNYRVDIGSHD--PAVLSYLAFEGATKKNPPKVETGDVVAGKLLTAN 114 (222)
Q Consensus 57 GDiVIG~V~~v~-~~~~~VdI~~~~--~a~L~~~~f~gatk~~r~~l~~GDlV~ArV~~~~ 114 (222)
.+-++|+|++.. ++.|.|...... .|.+| |. .+.+-.+++||.|...+...+
T Consensus 2 e~e~~~~V~~~lG~~~~~V~~~dg~~~l~~i~-----gK-~r~~iwI~~GD~V~V~~~~~d 56 (65)
T PF01176_consen 2 EGEVIGRVTEMLGNNLFEVECEDGEERLARIP-----GK-FRKRIWIKRGDFVLVEPSPYD 56 (65)
T ss_dssp TTEEEEEEEEEESSSEEEEEETTSEEEEEEE------HH-HHTCC---TTEEEEEEESTTC
T ss_pred CcEEEEEEEEECCCCEEEEEeCCCCEEEEEec-----cc-eeeeEecCCCCEEEEEecccC
Confidence 356899999984 588999886522 33333 44 577778999999999885443
No 124
>PF01959 DHQS: 3-dehydroquinate synthase (EC 4.6.1.3); InterPro: IPR002812 3-Dehydroquinate synthase (4.2.3.4 from EC) is an enzyme in the common pathway of aromatic amino acid biosynthesis that catalyses the conversion of 3-deoxy-D-arabino-heptulosonic acid 7-phosphate (DAHP) into 3-dehydroquinic acid []. This synthesis of aromatic amino acids is an essential metabolic function for most prokaryotic as well as lower eukaryotic cells, including plants. The pathway is absent in humans; therefore, DHQS represents a potential target for the development of novel and selective antimicrobial agents. Owing to the threat posed by the spread of pathogenic bacteria resistant to many currently used antimicrobial drugs, there is clearly a need to develop new anti-infective drugs acting at novel targets. A further potential use for DHQS inhibitors is as herbicides [].; GO: 0016491 oxidoreductase activity, 0055114 oxidation-reduction process
Probab=76.52 E-value=30 Score=31.91 Aligned_cols=92 Identities=12% Similarity=0.090 Sum_probs=62.9
Q ss_pred CCCeecCCCCCCeeeCCCeEE--eCCEEEEEEeeEEEEecCcEEEEEccccccCCCCCCEEEEEEEEEecceEEEEECCC
Q psy230 2 AGDTLSLNAEPRLILGPGLRR--ESSAILVSQSGILRHAKPFTYYVDYIQRRYVPTRGDLVIGVVTSRVGDNYRVDIGSH 79 (222)
Q Consensus 2 PGd~l~~~~~~~~~~G~G~y~--~~~~i~as~~G~l~~~~~~~v~V~~~~~~Y~P~vGDiVIG~V~~v~~~~~~VdI~~~ 79 (222)
||+.-... .++..|.-+.. .+|+-+....|.+++....++-|+... ++ -++.-+-++-|.|.+-.+
T Consensus 249 pg~kT~YL--SEL~sG~~VlvVd~~G~tR~~~VGRvKIE~RPLllIeA~~-------~g---~~~svilQnaetIRlv~p 316 (354)
T PF01959_consen 249 PGGKTRYL--SELRSGDEVLVVDADGRTRTAIVGRVKIERRPLLLIEAEA-------DG---KRISVILQNAETIRLVGP 316 (354)
T ss_pred CCCceeeh--hhhcCCCEEEEEeCCCCEEEEEeeEEEEeecceEEEEEEe-------CC---eEEEEEEecCcEEEEECC
Confidence 45444333 24555655443 368899999999998765677777532 33 334445678899999888
Q ss_pred CCeeeeccccccccccCCcCCCCCCEEEEEEEecCCC
Q psy230 80 DPAVLSYLAFEGATKKNPPKVETGDVVAGKLLTANKD 116 (222)
Q Consensus 80 ~~a~L~~~~f~gatk~~r~~l~~GDlV~ArV~~~~~~ 116 (222)
....+++.. |++||-|.+++....++
T Consensus 317 ~G~~vsVt~-----------Lk~GD~vL~~~~~~~RH 342 (354)
T PF01959_consen 317 DGEPVSVTE-----------LKPGDEVLVYLEEAGRH 342 (354)
T ss_pred CCCEeeeee-----------cCCCCEEEEEecCCCcc
Confidence 776677544 78999999999887665
No 125
>KOG3038|consensus
Probab=75.63 E-value=11 Score=33.16 Aligned_cols=74 Identities=23% Similarity=0.192 Sum_probs=52.5
Q ss_pred EEEEEccccccCCCCCCEEEEEEEEEecceEEEEECCCCCeeeeccccccccccCCcCCCCCCEEEEEEEecCCCCeeEE
Q psy230 42 TYYVDYIQRRYVPTRGDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFEGATKKNPPKVETGDVVAGKLLTANKDMESEM 121 (222)
Q Consensus 42 ~v~V~~~~~~Y~P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~gatk~~r~~l~~GDlV~ArV~~~~~~~~~~L 121 (222)
...-.|.++-|.+..||-|-++|+....+ ||.|.|+|+++..+..++.
T Consensus 116 ~~gaip~~~~~~~~~gd~VAa~v~~~~~d--------------------------------g~WIlaeVv~~~~~~~ye~ 163 (264)
T KOG3038|consen 116 LCGAIPAQGDYVLLKGDEVAARVKAVSED--------------------------------GDWILAEVVKVSSETRYEF 163 (264)
T ss_pred ccccccccCCccccCCceeeeeeeeccCC--------------------------------CCEEEEEEEEEecCCceEe
Confidence 34455667778888888888888876554 7899999999987766887
Q ss_pred EEecCCCccccCcccCCceEEEechhhh
Q psy230 122 VCVDSRGKEFIMGILNDGYLLHTSISLC 149 (222)
Q Consensus 122 s~~~~~~~~~~~G~L~~G~l~~v~~~~~ 149 (222)
..+|+..+.. =..+.|.+++.+-+.+
T Consensus 164 ev~D~Epk~d--~~g~r~~~yklp~~~~ 189 (264)
T KOG3038|consen 164 EVVDPEPKKD--EVGNRGQLYKLPRWKL 189 (264)
T ss_pred EecCCCcccc--ccccccceecccHhhc
Confidence 7777332222 2336778888777665
No 126
>COG2996 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only]
Probab=74.06 E-value=13 Score=33.14 Aligned_cols=31 Identities=6% Similarity=0.145 Sum_probs=27.0
Q ss_pred cCCcCCCCCCEEEEEEEecCCCCeeEEEEec
Q psy230 95 KNPPKVETGDVVAGKLLTANKDMESEMVCVD 125 (222)
Q Consensus 95 ~~r~~l~~GDlV~ArV~~~~~~~~~~Ls~~~ 125 (222)
......+.|+.+-|||+.+..++++.||+.-
T Consensus 187 Er~~~prlG~~l~~rVi~~reDg~lnLSl~p 217 (287)
T COG2996 187 ERFAEPRLGERLTARVIGVREDGKLNLSLRP 217 (287)
T ss_pred hhcccccCCceEEEEEEEEccCCeeeccccc
Confidence 3456688999999999999999999999965
No 127
>cd05793 S1_IF1A S1_IF1A: Translation initiation factor IF1A, also referred to as eIF1A in eukaryotes and aIF1A in archaea, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. IF1A is essential for translation initiation. eIF1A acts synergistically with eIF1 to mediate assembly of ribosomal initiation complexes at the initiation codon and maintain the accuracy of this process by recognizing and destabilizing aberrant preinitiation complexes from the mRNA. Without eIF1A and eIF1, 43S ribosomal preinitiation complexes can bind to the cap-proximal region, but are unable to reach the initiation codon. eIF1a also enhances the formation of 5'-terminal complexes in the presence of other translation initiation factors. This protein family is only found in eukaryotes and archaea.
Probab=73.86 E-value=15 Score=26.33 Aligned_cols=50 Identities=16% Similarity=0.104 Sum_probs=34.4
Q ss_pred EEEEEEEE-ecceEEEEECCCCCeeeeccccccccccCCcCCCCCCEEEEEEEec
Q psy230 60 VIGVVTSR-VGDNYRVDIGSHDPAVLSYLAFEGATKKNPPKVETGDVVAGKLLTA 113 (222)
Q Consensus 60 VIG~V~~v-~~~~~~VdI~~~~~a~L~~~~f~gatk~~r~~l~~GDlV~ArV~~~ 113 (222)
++|+|++. .++.|.|.......-.- .++|..++ +-.+++||.|..+....
T Consensus 2 ~~g~V~~~~g~~~~~V~~~~g~~~la---~i~gK~rk-~iwI~~GD~V~Ve~~~~ 52 (77)
T cd05793 2 EYGQVEKMLGNGRLEVRCFDGKKRLC---RIRGKMRK-RVWINEGDIVLVAPWDF 52 (77)
T ss_pred EEEEEEEEcCCCEEEEEECCCCEEEE---EEchhhcc-cEEEcCCCEEEEEeccc
Confidence 68999998 45788888865322111 23454454 67899999999996554
No 128
>PLN00208 translation initiation factor (eIF); Provisional
Probab=73.80 E-value=14 Score=29.78 Aligned_cols=57 Identities=12% Similarity=0.069 Sum_probs=37.3
Q ss_pred CCCCCCEEEEEEEEE-ecceEEEEECCCCCeeeeccccccccccCCcCCCCCCEEEEEEEecC
Q psy230 53 VPTRGDLVIGVVTSR-VGDNYRVDIGSHDPAVLSYLAFEGATKKNPPKVETGDVVAGKLLTAN 114 (222)
Q Consensus 53 ~P~vGDiVIG~V~~v-~~~~~~VdI~~~~~a~L~~~~f~gatk~~r~~l~~GDlV~ArV~~~~ 114 (222)
.|..|. ++|+|+.. .+..+.|.......-.- .++|..++ +-.+++||+|..+.....
T Consensus 28 ~p~egq-~~g~V~~~lGn~~~~V~c~dG~~rLa---~IpGKmRK-rIWI~~GD~VlVel~~~d 85 (145)
T PLN00208 28 FKEDGQ-EYAQVLRMLGNGRCEALCIDGTKRLC---HIRGKMRK-KVWIAAGDIILVGLRDYQ 85 (145)
T ss_pred cCCCCc-EEEEEEEEcCCCEEEEEECCCCEEEE---EEecccee-eEEecCCCEEEEEccCCC
Confidence 466554 89999988 45788888764322221 23344444 677999999999954443
No 129
>PF07494 Reg_prop: Two component regulator propeller; InterPro: IPR011110 A large group of two component regulator proteins appear to have the same N-terminal structure of 14 tandem repeats. These repeats show homology to members of IPR002372 from INTERPRO and IPR001680 from INTERPRO indicating that they are likely to form a beta-propeller. This family has been built with artificially high cut-offs in order to avoid overlaps with other beta-propeller families. The fourteen repeats are likely to form two propellers; it is not clear if these structures are likely to recruit other proteins or interact with DNA.; PDB: 3V9F_D 3VA6_B 3OTT_B 4A2M_D 4A2L_B.
Probab=72.90 E-value=4.5 Score=22.18 Aligned_cols=18 Identities=17% Similarity=0.407 Sum_probs=13.5
Q ss_pred CcEEEEEEeCCeEEEeeC
Q psy230 169 QKMELSIGMNGKIWIRCE 186 (222)
Q Consensus 169 ~~~ei~vG~NG~iWi~~~ 186 (222)
.=..|....||++||.+.
T Consensus 6 ~I~~i~~D~~G~lWigT~ 23 (24)
T PF07494_consen 6 NIYSIYEDSDGNLWIGTY 23 (24)
T ss_dssp CEEEEEE-TTSCEEEEET
T ss_pred eEEEEEEcCCcCEEEEeC
Confidence 345688899999999875
No 130
>PRK13763 putative RNA-processing protein; Provisional
Probab=71.87 E-value=21 Score=29.51 Aligned_cols=69 Identities=6% Similarity=-0.023 Sum_probs=51.0
Q ss_pred hhhhccCCChhHHHHhhhcCCCcEEEEEEeCCeEEEeeCCchhHHHHHHHHHHhhc-CCHHHHHHHHHHHHHHh
Q psy230 148 LCRKLLNPKCPLLKQLAKRSRQKMELSIGMNGKIWIRCESFSDTVRVGNLIMSCEL-LSYEEILNLCESIHIRF 220 (222)
Q Consensus 148 ~~~rl~~~~~~~l~~l~~~~~~~~ei~vG~NG~iWi~~~~~~~~~~i~~~i~~~e~-~~~~~~~~~~~~~~~~l 220 (222)
...|++|+++..++.|.+ .+++.|.|.-+ .|-|.+ ++.....+.++|..+-. -..+-+-.+++..+..|
T Consensus 105 ~~griIG~~G~~~k~ie~--~t~~~i~i~~~-~v~i~G-~~~~~~~A~~~I~~li~g~~~~~~~~~l~~~~~~~ 174 (180)
T PRK13763 105 IKGRIIGEGGKTRRIIEE--LTGVDISVYGK-TVAIIG-DPEQVEIAREAIEMLIEGAPHGTVYKFLERKKREL 174 (180)
T ss_pred HhhheeCCCcHHHHHHHH--HHCcEEEEcCC-EEEEEe-CHHHHHHHHHHHHHHHcCCCcHHHHHHHHHHHHHH
Confidence 567789999999999999 99999988754 477776 66667777777776653 34556666666666554
No 131
>TIGR03665 arCOG04150 arCOG04150 universal archaeal KH domain protein. This family of proteins is universal among the 41 archaeal genomes analyzed in and is not observed outside of the archaea. The proteins contain a single KH domain (pfam00013) which is likely to confer the ability to bind RNA.
Probab=71.70 E-value=27 Score=28.63 Aligned_cols=70 Identities=6% Similarity=-0.044 Sum_probs=49.6
Q ss_pred hhhhhccCCChhHHHHhhhcCCCcEEEEEEeCCeEEEeeCCchhHHHHHHHHHHhhc-CCHHHHHHHHHHHHHHh
Q psy230 147 SLCRKLLNPKCPLLKQLAKRSRQKMELSIGMNGKIWIRCESFSDTVRVGNLIMSCEL-LSYEEILNLCESIHIRF 220 (222)
Q Consensus 147 ~~~~rl~~~~~~~l~~l~~~~~~~~ei~vG~NG~iWi~~~~~~~~~~i~~~i~~~e~-~~~~~~~~~~~~~~~~l 220 (222)
....|++|+++..++.|.. .+++.|.|.- ..|-|.+ ++.....+.++|..+-. -...-+-+.+++-...+
T Consensus 98 ~~~griIG~~G~t~~~ie~--~t~~~i~i~~-~~v~i~G-~~~~~~~A~~~i~~li~~~~~~~vy~~l~~~~~~~ 168 (172)
T TIGR03665 98 RIKGRIIGEGGKTRRIIEE--LTGVSISVYG-KTVGIIG-DPEQVQIAREAIEMLIEGAPHGTVYKFLERKRREL 168 (172)
T ss_pred HHHhhhcCCCcHHHHHHHH--HHCCeEEEcC-CEEEEEC-CHHHHHHHHHHHHHHHcCCCChhHHHHHHHHHHHH
Confidence 3678899999999999999 9999998874 6788888 66667777777766553 22334444554444433
No 132
>TIGR00008 infA translation initiation factor IF-1. This family consists of translation initiation factor IF-1 as found in bacteria and chloroplasts. This protein, about 70 residues in length, consists largely of an S1 RNA binding domain (pfam00575).
Probab=70.43 E-value=24 Score=24.75 Aligned_cols=52 Identities=19% Similarity=0.272 Sum_probs=36.3
Q ss_pred EEEEEEEE-ecceEEEEECCCCCeeeeccccccccccCCcCCCCCCEEEEEEEecC
Q psy230 60 VIGVVTSR-VGDNYRVDIGSHDPAVLSYLAFEGATKKNPPKVETGDVVAGKLLTAN 114 (222)
Q Consensus 60 VIG~V~~v-~~~~~~VdI~~~~~a~L~~~~f~gatk~~r~~l~~GDlV~ArV~~~~ 114 (222)
+.|+|++. .+..|+|.+.....-.- -.+|..++++-.+.+||.|..+....+
T Consensus 7 ~~G~V~e~L~~~~f~V~l~ng~~vla---~i~GKmr~~rI~I~~GD~V~Ve~spyd 59 (68)
T TIGR00008 7 MEGKVTESLPNAMFRVELENGHEVLA---HISGKIRMHYIRILPGDKVKVELSPYD 59 (68)
T ss_pred EEEEEEEECCCCEEEEEECCCCEEEE---EecCcchhccEEECCCCEEEEEECccc
Confidence 67899988 45778888864322111 134666777888999999998876554
No 133
>PRK02290 3-dehydroquinate synthase; Provisional
Probab=70.26 E-value=59 Score=29.91 Aligned_cols=92 Identities=17% Similarity=0.209 Sum_probs=60.8
Q ss_pred CCCeecCCCCCCeeeCCCeE--EeCCEEEEEEeeEEEEecCcEEEEEccccccCCCCCCEEEEEEEEEecceEEEEECCC
Q psy230 2 AGDTLSLNAEPRLILGPGLR--RESSAILVSQSGILRHAKPFTYYVDYIQRRYVPTRGDLVIGVVTSRVGDNYRVDIGSH 79 (222)
Q Consensus 2 PGd~l~~~~~~~~~~G~G~y--~~~~~i~as~~G~l~~~~~~~v~V~~~~~~Y~P~vGDiVIG~V~~v~~~~~~VdI~~~ 79 (222)
||+.-... .++..|.-+. ..+|+-+....|.+++....++-|+.. | ++ -++.-+-++-|.+.+-.+
T Consensus 239 pgg~T~YL--sEL~sG~eVlvVd~~G~tR~~~VGRvKIE~RPL~lIeAe---~----~g---~~~~viLQnaetIrlv~~ 306 (344)
T PRK02290 239 PGDKTRYL--SELRSGDEVLVVDADGNTREAIVGRVKIEKRPLLLIEAE---Y----GG---KRIRTILQNAETIRLVTP 306 (344)
T ss_pred CCCcchhh--HhhcCCCEEEEEeCCCCEEEEEeeEEEEeeccEEEEEEE---e----CC---eEEEEEEecCcEEEEECC
Confidence 55544433 2455565543 347899999999999876556667653 1 22 233334578899998887
Q ss_pred CCeeeeccccccccccCCcCCCCCCEEEEEEEecCCC
Q psy230 80 DPAVLSYLAFEGATKKNPPKVETGDVVAGKLLTANKD 116 (222)
Q Consensus 80 ~~a~L~~~~f~gatk~~r~~l~~GDlV~ArV~~~~~~ 116 (222)
....+++.. |++||-|.+++....++
T Consensus 307 dG~~vsVt~-----------Lk~GD~VL~~~~~~~RH 332 (344)
T PRK02290 307 DGKPVSVVD-----------LKPGDEVLGYLEEAARH 332 (344)
T ss_pred CCCEeeeee-----------cCCCCEEEEEecCCccc
Confidence 655555433 88999999999876654
No 134
>PF15057 DUF4537: Domain of unknown function (DUF4537)
Probab=68.68 E-value=53 Score=25.48 Aligned_cols=48 Identities=15% Similarity=0.195 Sum_probs=28.6
Q ss_pred EEEEEE-ecceEEEEECCCCCeeeeccc-cccccccCCcCCCCCCEEEEEE
Q psy230 62 GVVTSR-VGDNYRVDIGSHDPAVLSYLA-FEGATKKNPPKVETGDVVAGKL 110 (222)
Q Consensus 62 G~V~~v-~~~~~~VdI~~~~~a~L~~~~-f~gatk~~r~~l~~GDlV~ArV 110 (222)
|+|.+. ....+.|+-.+...-..+... .+. ...+++.|++||-|.|+.
T Consensus 17 GtV~~~~~~~~~lV~f~~~~~~~v~~~~iI~~-~~~~~~~L~~GD~VLA~~ 66 (124)
T PF15057_consen 17 GTVKKCVSSGQFLVEFDDGDTQEVPISDIIAL-SDAMRHSLQVGDKVLAPW 66 (124)
T ss_pred EEEEEccCCCEEEEEECCCCEEEeChHHeEEc-cCcccCcCCCCCEEEEec
Confidence 455554 667788877443333333221 111 123488999999999984
No 135
>COG2932 Predicted transcriptional regulator [Transcription]
Probab=66.03 E-value=51 Score=27.57 Aligned_cols=65 Identities=18% Similarity=0.173 Sum_probs=35.5
Q ss_pred CCCeecCCCCCCeeeCCCeEEe--CCEEEEEEeeEEEEecCcEEEEEcccccc----CCCCCC-E-EEEEEEEEec
Q psy230 2 AGDTLSLNAEPRLILGPGLRRE--SSAILVSQSGILRHAKPFTYYVDYIQRRY----VPTRGD-L-VIGVVTSRVG 69 (222)
Q Consensus 2 PGd~l~~~~~~~~~~G~G~y~~--~~~i~as~~G~l~~~~~~~v~V~~~~~~Y----~P~vGD-i-VIG~V~~v~~ 69 (222)
|||.+....+.....|.++|.. ++..+..+... .+++.+.+.+..+.| .+...| + +||+|.....
T Consensus 139 ~Gd~ilVd~~~~~~~gd~v~v~~~g~~~~VK~l~~---~~~~~~~l~S~N~~~~~~~~~~~~~~v~iIgrVv~~~~ 211 (214)
T COG2932 139 DGDTLLVDPGVNTRRGDRVYVETDGGELYVKKLQR---EPGGLLRLVSLNPDYYPDEIFSEDDDVEIIGRVVWVSR 211 (214)
T ss_pred CCCEEEECCCCceeeCCEEEEEEeCCeEEEEEEEE---ecCCeEEEEeCCCCCCcccccCccceEEEEEEEEEEee
Confidence 6787665443444455555542 33444433332 234555566654443 556666 5 8999987653
No 136
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=65.34 E-value=36 Score=28.81 Aligned_cols=71 Identities=14% Similarity=0.174 Sum_probs=54.6
Q ss_pred EEEechhhhhhccCCChhHHHHhhhcCCCcEEEEEEeC-CeEEEeeC----CchhHHHHHHHHHHhhc-CCHHHHHHHH
Q psy230 141 LLHTSISLCRKLLNPKCPLLKQLAKRSRQKMELSIGMN-GKIWIRCE----SFSDTVRVGNLIMSCEL-LSYEEILNLC 213 (222)
Q Consensus 141 l~~v~~~~~~rl~~~~~~~l~~l~~~~~~~~ei~vG~N-G~iWi~~~----~~~~~~~i~~~i~~~e~-~~~~~~~~~~ 213 (222)
.+.||+....-|+++.+.+.+.|.+ ++.+.+.+... |.|||.+. |+-....+.+.++.+-. .+.++--.|+
T Consensus 11 ~v~iPk~R~~~lig~~g~v~k~ie~--~~~~~~~iD~~~~~V~i~~~~~t~Dp~~~~ka~d~VkAIgrGF~pe~A~~LL 87 (194)
T COG1094 11 AVKIPKDRIGVLIGKWGEVKKAIEE--KTGVKLRIDSKTGSVTIRTTRKTEDPLALLKARDVVKAIGRGFPPEKALKLL 87 (194)
T ss_pred eeecCchhheeeecccccchHHHHh--hcCeEEEEECCCCeEEEEecCCCCChHHHHHHHHHHHHHhcCCCHHHHHHHh
Confidence 3778888888899999999999998 88899988766 99999988 67667777777776653 4455444433
No 137
>COG0361 InfA Translation initiation factor 1 (IF-1) [Translation, ribosomal structure and biogenesis]
Probab=65.33 E-value=30 Score=24.78 Aligned_cols=55 Identities=22% Similarity=0.295 Sum_probs=38.8
Q ss_pred CCEEEEEEEEE-ecceEEEEECCCCCeeeeccccccccccCCcCCCCCCEEEEEEEecC
Q psy230 57 GDLVIGVVTSR-VGDNYRVDIGSHDPAVLSYLAFEGATKKNPPKVETGDVVAGKLLTAN 114 (222)
Q Consensus 57 GDiVIG~V~~v-~~~~~~VdI~~~~~a~L~~~~f~gatk~~r~~l~~GDlV~ArV~~~~ 114 (222)
..-+.|+|++. .+..|+|.......-.=+ .+|.-++++-.+.+||+|..+.....
T Consensus 6 ~~e~~g~V~e~L~~~~f~v~~edg~~~~ah---I~GKmr~~~i~I~~GD~V~Ve~~~~d 61 (75)
T COG0361 6 EIEMEGTVIEMLPNGRFRVELENGHERLAH---ISGKMRKNRIRILPGDVVLVELSPYD 61 (75)
T ss_pred ccEEEEEEEEecCCCEEEEEecCCcEEEEE---ccCcchheeEEeCCCCEEEEEecccc
Confidence 45688999998 567888887653322212 33555677888999999999876554
No 138
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=65.26 E-value=32 Score=28.90 Aligned_cols=30 Identities=27% Similarity=0.487 Sum_probs=23.1
Q ss_pred cCCcCCCCCCEEEEEEEecCCCCeeEEEEec
Q psy230 95 KNPPKVETGDVVAGKLLTANKDMESEMVCVD 125 (222)
Q Consensus 95 ~~r~~l~~GDlV~ArV~~~~~~~~~~Ls~~~ 125 (222)
+..+..+.||+|||||+++..+ -+.+.+..
T Consensus 57 ~~~~~~K~GdiV~grV~~v~~~-~a~V~i~~ 86 (188)
T COG1096 57 KTPPLPKGGDIVYGRVTDVREQ-RALVRIVG 86 (188)
T ss_pred CCCCCCCCCCEEEEEEeeccce-EEEEEEEE
Confidence 3466788999999999999764 46666654
No 139
>cd05791 S1_CSL4 S1_CSL4: CSL4, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. ScCSL4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In S. cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".
Probab=65.00 E-value=9.1 Score=28.08 Aligned_cols=28 Identities=21% Similarity=0.291 Sum_probs=22.5
Q ss_pred CCCCEEEEEEEEEec-ceEEEEECCCCCe
Q psy230 55 TRGDLVIGVVTSRVG-DNYRVDIGSHDPA 82 (222)
Q Consensus 55 ~vGDiVIG~V~~v~~-~~~~VdI~~~~~a 82 (222)
++||+|.++|.+... ..|.+.+.....+
T Consensus 62 ~~GDiV~AkVis~~~~~~~~Lst~~~~lG 90 (92)
T cd05791 62 RPGDIVRAKVISLGDASSYYLSTAENELG 90 (92)
T ss_pred CCCCEEEEEEEEcCCCCCcEEEecCCCCc
Confidence 899999999999975 6677777665544
No 140
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=63.61 E-value=9.2 Score=39.37 Aligned_cols=61 Identities=11% Similarity=0.158 Sum_probs=50.5
Q ss_pred ceEEEechhhhhhccCCChhHHHHhhhcCCCcEE-EEEEeCCeEEEeeCCchhHHHHHHHHHHh
Q psy230 139 GYLLHTSISLCRKLLNPKCPLLKQLAKRSRQKME-LSIGMNGKIWIRCESFSDTVRVGNLIMSC 201 (222)
Q Consensus 139 G~l~~v~~~~~~rl~~~~~~~l~~l~~~~~~~~e-i~vG~NG~iWi~~~~~~~~~~i~~~i~~~ 201 (222)
=..++|+|.+++.++|+++..++.|-+ .++.. |=+.-.|.|-|-+.+......+...|+.+
T Consensus 686 i~~~~i~~~ki~~vIG~GGktIk~I~e--etg~~~Idi~ddg~V~I~a~d~~~i~~A~~~I~~l 747 (891)
T PLN00207 686 IHIMKVKPEKVNMIIGSGGKKVKSIIE--ETGVEAIDTQDDGTVKITAKDLSSLEKSKAIISSL 747 (891)
T ss_pred eEEEEcCHHHHHHHhcCCchhHHHHHH--HHCCCccCcCCCeeEEEEeCCHHHHHHHHHHHHHH
Confidence 367899999999999999999999999 89998 89999999999999876444444444433
No 141
>PF10447 EXOSC1: Exosome component EXOSC1/CSL4; InterPro: IPR019495 The exosome mediates degradation of unstable mRNAs that contain AU-rich elements (AREs) within their 3' untranslated regions []. The proteins in this entry are components of the exosome 3'->5' exoribonuclease complex. They do not have exonuclease activity, but are required for the 3'-processing of the 7S pre-RNA to the mature 5.8S rRNA and for mRNA decay [, ].; PDB: 2NN6_I.
Probab=63.39 E-value=14 Score=26.84 Aligned_cols=25 Identities=28% Similarity=0.659 Sum_probs=17.0
Q ss_pred CCCCEEEEEEEecCCCC-eeEEEEec
Q psy230 101 ETGDVVAGKLLTANKDM-ESEMVCVD 125 (222)
Q Consensus 101 ~~GDlV~ArV~~~~~~~-~~~Ls~~~ 125 (222)
++||+|.|||.+++... ..++.|++
T Consensus 3 ~vGdiV~~rVtrv~~~~a~v~Il~v~ 28 (82)
T PF10447_consen 3 KVGDIVIARVTRVNPRQAKVEILCVE 28 (82)
T ss_dssp -TT-EEEEEEEEE-SSEEEEEEEES-
T ss_pred CCCCEEEEEEEEEeccEEEEEEEEEE
Confidence 48999999999998654 35777773
No 142
>TIGR00523 eIF-1A eukaryotic/archaeal initiation factor 1A. Recommended nomenclature: eIF-1A for eukaryotes, aIF-1A for Archaea. Also called eIF-4C
Probab=62.82 E-value=63 Score=24.26 Aligned_cols=53 Identities=23% Similarity=0.248 Sum_probs=36.4
Q ss_pred ccCCCC-CCEEEEEEEEE-ecceEEEEECCC--CCeeeeccccccccccCCcCCCCCCEEEEE
Q psy230 51 RYVPTR-GDLVIGVVTSR-VGDNYRVDIGSH--DPAVLSYLAFEGATKKNPPKVETGDVVAGK 109 (222)
Q Consensus 51 ~Y~P~v-GDiVIG~V~~v-~~~~~~VdI~~~--~~a~L~~~~f~gatk~~r~~l~~GDlV~Ar 109 (222)
+-+|.. .+-++|+|+.. .++.|.|..... ..|. ++|..++ +-.+++||.|...
T Consensus 11 ~~~p~~~e~e~~g~V~~~lG~~~~~V~~~dG~~~la~-----i~GK~Rk-~iwI~~GD~VlVs 67 (99)
T TIGR00523 11 VRLPRKEEGEILGVIEQMLGAGRVKVRCLDGKTRLGR-----IPGKLKK-RIWIREGDVVIVK 67 (99)
T ss_pred eeCCCCCCCEEEEEEEEEcCCCEEEEEeCCCCEEEEE-----Echhhcc-cEEecCCCEEEEE
Confidence 345643 67899999999 457888887542 2233 3454444 7779999999984
No 143
>PRK12442 translation initiation factor IF-1; Reviewed
Probab=62.16 E-value=36 Score=25.09 Aligned_cols=53 Identities=19% Similarity=0.213 Sum_probs=37.3
Q ss_pred EEEEEEEE-ecceEEEEECCCCCeeeeccccccccccCCcCCCCCCEEEEEEEecCC
Q psy230 60 VIGVVTSR-VGDNYRVDIGSHDPAVLSYLAFEGATKKNPPKVETGDVVAGKLLTANK 115 (222)
Q Consensus 60 VIG~V~~v-~~~~~~VdI~~~~~a~L~~~~f~gatk~~r~~l~~GDlV~ArV~~~~~ 115 (222)
+-|+|++. .+..|+|.+..-..-.- -+.|-.++++-.+.+||.|..++...+.
T Consensus 9 ~~G~V~e~Lp~~~frV~LenG~~vla---~isGKmR~~rIrIl~GD~V~VE~spYDl 62 (87)
T PRK12442 9 LDGIVDEVLPDSRFRVTLENGVEVGA---YASGRMRKHRIRILAGDRVTLELSPYDL 62 (87)
T ss_pred EEEEEEEECCCCEEEEEeCCCCEEEE---EeccceeeeeEEecCCCEEEEEECcccC
Confidence 67999998 45788988864322111 1346667778889999999999876553
No 144
>cd05841 BS69_related The PWWP domain is part of BS69 protein, a nuclear protein that specifically binds adenoviral E1A and Epstein-Barr viral EBNA2 proteins, suppressing their transactivation functions. BS69 is a multi-domain protein, containing bromo, PHD, PWWP, and MYND domains. The specific role of the PWWP domain within BS69 is not clearly identified, but BS69 functions in chromatin remodeling, consistent with other PWWP-containing proteins. The PWWP domain, named for a conserved Pro-Trp-Trp-Pro motif, is a small domain consisting of 100-150 amino acids. The PWWP domain is found in numerous proteins that are involved in cell division, growth and differentiation. Most PWWP-domain proteins seem to be nuclear, often DNA-binding, proteins that function as transcription factors regulating a variety of developmental processes.
Probab=61.69 E-value=5.7 Score=29.00 Aligned_cols=18 Identities=22% Similarity=0.115 Sum_probs=15.3
Q ss_pred CcCCCCCCEEEEEEEecC
Q psy230 97 PPKVETGDVVAGKLLTAN 114 (222)
Q Consensus 97 r~~l~~GDlV~ArV~~~~ 114 (222)
+||..+||||.|++...-
T Consensus 4 ~pc~~p~dLVwAK~kGyp 21 (83)
T cd05841 4 EPCRPPHELVWAKLKGFP 21 (83)
T ss_pred cccCCCCCEEEEeCCCCC
Confidence 789999999999986543
No 145
>PF03625 DUF302: Domain of unknown function DUF302 ; InterPro: IPR005180 This domain is found in an undescribed set of proteins. It normally occurs uniquely within a sequence, but is found as a tandem repeat (Q9X8B8 from SWISSPROT). It has an interesting phylogenetic distribution with the majority of examples in bacteria and archaea, but it is also found in Drosophila melanogaster (e.g. Q9VA18 from SWISSPROT). The hypothetical protein TT1751 from Thermus thermophilus has a beta-alpha-beta(4)-alpha structural fold [].; PDB: 1Q9U_A 1J3M_B.
Probab=59.29 E-value=26 Score=23.57 Aligned_cols=42 Identities=14% Similarity=0.240 Sum_probs=28.1
Q ss_pred eEEEechhhhhhccCCChhHHHHhhhcCCCcEEEEEE--eCCeEEEeeCC
Q psy230 140 YLLHTSISLCRKLLNPKCPLLKQLAKRSRQKMELSIG--MNGKIWIRCES 187 (222)
Q Consensus 140 ~l~~v~~~~~~rl~~~~~~~l~~l~~~~~~~~ei~vG--~NG~iWi~~~~ 187 (222)
.+.-++|..+.+++..... ++- ..||.|.|= .+|.+||...+
T Consensus 21 i~~~cnp~~a~~ll~~~p~----~~~--~lPcrv~vye~~~G~~~v~~~~ 64 (65)
T PF03625_consen 21 ILEFCNPKIAYQLLKADPE----IGL--FLPCRVLVYEDEDGKVWVSYMN 64 (65)
T ss_dssp EEEEE-HHHHHHHHCC-GG----GGG--C-SEEEEEEE-ETTEEEEEEE-
T ss_pred EEEECChHHHHHHHHhhHH----HHH--hCCeEEEEEEecCCeEEEEEeC
Confidence 3456799999999975543 333 678888764 59999998754
No 146
>KOG4134|consensus
Probab=59.14 E-value=13 Score=32.19 Aligned_cols=69 Identities=12% Similarity=0.083 Sum_probs=53.8
Q ss_pred EEEEccccccCCCCCCEEEEEEEEEecceEEEEECCCCCeeeeccccccccccCCcCCCCCCEEEEEEEecCC
Q psy230 43 YYVDYIQRRYVPTRGDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFEGATKKNPPKVETGDVVAGKLLTANK 115 (222)
Q Consensus 43 v~V~~~~~~Y~P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~gatk~~r~~l~~GDlV~ArV~~~~~ 115 (222)
+|+...--.+.|++||+.-|+|--+.....-+=|-..+.|.+|..+.+ ..+.++.+++-.-++|...+.
T Consensus 94 lwi~adfyVf~Pk~Gd~LeG~Vn~vS~sHIglLIhg~FNASIpk~nip----~dw~fI~md~eee~~v~ntD~ 162 (253)
T KOG4134|consen 94 LWINADFYVFRPKAGDILEGVVNHVSRSHIGLLIHGVFNASIPKTNIP----ADWEFIAMDQEEEIRVKNTDI 162 (253)
T ss_pred EEEeeeEEEECCCCCCeeeeeeeecchhhhceeehhhhhccCCCCCCc----cceeeecCCchhhhceeeccc
Confidence 566665556899999999999999988877777777777777754432 445688999999999998864
No 147
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=57.55 E-value=24 Score=35.23 Aligned_cols=63 Identities=11% Similarity=0.149 Sum_probs=53.4
Q ss_pred CceEEEechhhhhhccCCChhHHHHhhhcCCCcEEEEEEeCCeEEEeeCCchhHHHHHHHHHHhh
Q psy230 138 DGYLLHTSISLCRKLLNPKCPLLKQLAKRSRQKMELSIGMNGKIWIRCESFSDTVRVGNLIMSCE 202 (222)
Q Consensus 138 ~G~l~~v~~~~~~rl~~~~~~~l~~l~~~~~~~~ei~vG~NG~iWi~~~~~~~~~~i~~~i~~~e 202 (222)
.=..+++++.+++-++|+++..++.|-+ .++..|-+.-.|.|.|.+.+...+..+.+.|..+.
T Consensus 552 ri~t~~i~~dKI~dvIG~gGk~I~~I~e--etg~~IdieddGtv~i~~s~~~~~~~ak~~I~~i~ 614 (692)
T COG1185 552 RIETIKIDPDKIRDVIGPGGKTIKAITE--ETGVKIDIEDDGTVKIAASDGESAKKAKERIEAIT 614 (692)
T ss_pred ceEEEccCHHHHhhccCCcccchhhhhh--hhCcEEEecCCCcEEEEecchHHHHHHHHHHHHHH
Confidence 3467899999999999999999999999 99999999999999999998775655555555554
No 148
>cd04489 ExoVII_LU_OBF ExoVII_LU_OBF: A subfamily of OB folds corresponding to the N-terminal OB-fold domain of Escherichia coli exodeoxyribonuclease VII (ExoVII) large subunit. E. coli ExoVII is composed of two non-identical subunits. E. coli ExoVII is a single-strand-specific exonuclease which degrades ssDNA from both 3-prime and 5-prime ends. ExoVII plays a role in methyl-directed mismatch repair in vivo. ExoVII may also guard the genome from mutagenesis by removing excess ssDNA, since the build up of ssDNA would lead to SOS induction and PolIV-dependent mutagenesis.
Probab=56.72 E-value=60 Score=22.07 Aligned_cols=63 Identities=10% Similarity=0.101 Sum_probs=37.4
Q ss_pred EEEEEEEEe---cceEEEEECCCCCeeeeccccccccccCCcCCCCCCEEEEEEEec-CC-CCeeEEEE
Q psy230 60 VIGVVTSRV---GDNYRVDIGSHDPAVLSYLAFEGATKKNPPKVETGDVVAGKLLTA-NK-DMESEMVC 123 (222)
Q Consensus 60 VIG~V~~v~---~~~~~VdI~~~~~a~L~~~~f~gatk~~r~~l~~GDlV~ArV~~~-~~-~~~~~Ls~ 123 (222)
|.|.|++++ ..+..+.+-.. .+.+....|+..-++.++.+..|+.|.++...- .. ...+.|.+
T Consensus 4 v~g~v~~i~~tk~g~~~~~L~D~-~~~i~~~~f~~~~~~~~~~l~~g~~v~v~g~v~~~~~~~~~~l~v 71 (78)
T cd04489 4 VEGEISNLKRPSSGHLYFTLKDE-DASIRCVMWRSNARRLGFPLEEGMEVLVRGKVSFYEPRGGYQLIV 71 (78)
T ss_pred EEEEEecCEECCCcEEEEEEEeC-CeEEEEEEEcchhhhCCCCCCCCCEEEEEEEEEEECCCCEEEEEE
Confidence 455555543 12455555442 366777777766678889999999876665432 21 23455554
No 149
>PF01436 NHL: NHL repeat; InterPro: IPR001258 The NHL repeat, named after NCL-1, HT2A and Lin-41, is found largely in a large number of eukaryotic and prokaryotic proteins. For example, the repeat is found in a variety of enzymes of the copper type II, ascorbate-dependent monooxygenase family which catalyse the C terminus alpha-amidation of biological peptides []. In many it occurs in tandem arrays, for example in the ringfinger beta-box, coiled-coil (RBCC) eukaryotic growth regulators []. The 'Brain Tumor' protein (Brat) is one such growth regulator that contains a 6-bladed NHL-repeat beta-propeller [, ]. The NHL repeats are also found in serine/threonine protein kinase (STPK) in diverse range of pathogenic bacteria. These STPK are transmembrane receptors with a intracellular N-terminal kinase domain and extracellular C-terminal sensor domain. In the STPK, PknD, from Mycobacterium tuberculosis, the sensor domain forms a rigid, six-bladed b-propeller composed of NHL repeats with a flexible tether to the transmembrane domain.; GO: 0005515 protein binding; PDB: 3FVZ_A 3FW0_A 1RWL_A 1RWI_A 1Q7F_A.
Probab=56.15 E-value=15 Score=20.70 Aligned_cols=19 Identities=11% Similarity=0.314 Sum_probs=16.0
Q ss_pred CCcEEEEEEeCCeEEEeeC
Q psy230 168 RQKMELSIGMNGKIWIRCE 186 (222)
Q Consensus 168 ~~~~ei~vG~NG~iWi~~~ 186 (222)
..|-.|++..||.|||.-.
T Consensus 2 ~~P~gvav~~~g~i~VaD~ 20 (28)
T PF01436_consen 2 NYPHGVAVDSDGNIYVADS 20 (28)
T ss_dssp SSEEEEEEETTSEEEEEEC
T ss_pred cCCcEEEEeCCCCEEEEEC
Confidence 4578899999999999753
No 150
>PTZ00329 eukaryotic translation initiation factor 1A; Provisional
Probab=55.08 E-value=53 Score=26.79 Aligned_cols=53 Identities=13% Similarity=0.093 Sum_probs=34.4
Q ss_pred CCCCCCEEEEEEEEE-ecceEEEEECCCCCeeeeccccccccccCCcCCCCCCEEEEEE
Q psy230 53 VPTRGDLVIGVVTSR-VGDNYRVDIGSHDPAVLSYLAFEGATKKNPPKVETGDVVAGKL 110 (222)
Q Consensus 53 ~P~vGDiVIG~V~~v-~~~~~~VdI~~~~~a~L~~~~f~gatk~~r~~l~~GDlV~ArV 110 (222)
.|..|. ++|+|+.. .+..+.|.......-.- .++|..++ +-.+++||+|..+.
T Consensus 28 ~~eegq-~~g~V~~~LGn~~f~V~c~dG~~rLa---~I~GKmRK-~IWI~~GD~VlVel 81 (155)
T PTZ00329 28 FKEEGQ-EYAQVLRMLGNGRLEAYCFDGVKRLC---HIRGKMRK-RVWINIGDIILVSL 81 (155)
T ss_pred cCCCCc-EEEEEEEEcCCCEEEEEECCCCEEEE---Eeecccee-eEEecCCCEEEEec
Confidence 355554 89999998 45778887754322221 23344444 57799999999875
No 151
>PF01835 A2M_N: MG2 domain; InterPro: IPR002890 The proteinase-binding alpha-macroglobulins (A2M) [] are large glycoproteins found in the plasma of vertebrates, in the hemolymph of some invertebrates and in reptilian and avian egg white. A2M-like proteins are able to inhibit all four classes of proteinases by a 'trapping' mechanism. They have a peptide stretch, called the 'bait region', which contains specific cleavage sites for different proteinases. When a proteinase cleaves the bait region, a conformational change is induced in the protein, thus trapping the proteinase. The entrapped enzyme remains active against low molecular weight substrates, whilst its activity toward larger substrates is greatly reduced, due to steric hindrance. Following cleavage in the bait region, a thiol ester bond, formed between the side chains of a cysteine and a glutamine, is cleaved and mediates the covalent binding of the A2M-like protein to the proteinase. This family includes the N-terminal region of the alpha-2-macroglobulin family. The inhibitor domains belong to MEROPS inhibitor family I39.; GO: 0004866 endopeptidase inhibitor activity; PDB: 2B39_B 3KLS_B 3PRX_C 3KM9_B 3PVM_C 3CU7_A 4E0S_A 4A5W_A 4ACQ_C 2P9R_B ....
Probab=53.82 E-value=15 Score=26.51 Aligned_cols=35 Identities=14% Similarity=0.282 Sum_probs=24.9
Q ss_pred cCCcCCCCCCEEEEEEE--ecCC------CCeeEEEEecCCCc
Q psy230 95 KNPPKVETGDVVAGKLL--TANK------DMESEMVCVDSRGK 129 (222)
Q Consensus 95 ~~r~~l~~GDlV~ArV~--~~~~------~~~~~Ls~~~~~~~ 129 (222)
..|+.++|||-|..++. ..+. ...+.++..+++|+
T Consensus 6 TDr~iYrPGetV~~~~~~~~~~~~~~~~~~~~~~v~i~dp~g~ 48 (99)
T PF01835_consen 6 TDRPIYRPGETVHFRAIVRDLDNDFKPPANSPVTVTIKDPSGN 48 (99)
T ss_dssp ESSSEE-TTSEEEEEEEEEEECTTCSCESSEEEEEEEEETTSE
T ss_pred CCccCcCCCCEEEEEEEEeccccccccccCCceEEEEECCCCC
Confidence 46899999999999998 4431 13578888886654
No 152
>COG1315 Uncharacterized conserved protein [Function unknown]
Probab=53.53 E-value=20 Score=34.62 Aligned_cols=100 Identities=21% Similarity=0.232 Sum_probs=66.8
Q ss_pred CeeeCCCe-EEeCCEEEEEEeeEEEEecCcEEEEEcc---ccccCCCCCCEE-EEEEEEE--ecceEEEEECC-------
Q psy230 13 RLILGPGL-RRESSAILVSQSGILRHAKPFTYYVDYI---QRRYVPTRGDLV-IGVVTSR--VGDNYRVDIGS------- 78 (222)
Q Consensus 13 ~~~~G~G~-y~~~~~i~as~~G~l~~~~~~~v~V~~~---~~~Y~P~vGDiV-IG~V~~v--~~~~~~VdI~~------- 78 (222)
.+.+|.|| ..+++.+.|+..|..-..+ ++++|.|. .+--.++.|++. +|.|.=. -.+.|.|.=.+
T Consensus 220 ~l~lG~nt~~kd~~tlvA~~~G~~~~s~-~tI~V~~iyeV~gdV~~kTGnI~F~G~VvI~G~V~dg~~VkA~g~I~V~G~ 298 (543)
T COG1315 220 KLNLGKNTAFKDNNTLVAKRDGQPIVSK-NTISVYPIYEVNGDVDVKTGNIKFVGNVVIHGDVEDGMVVKAEGNITVKGT 298 (543)
T ss_pred eeecCCCCccCCCCEEEEeeCCeEEecC-CeeEEEEEEEecCCccccccceeecceEEEeccCCCCcEEEecCceEEeeE
Confidence 47789999 6778899999999988774 78899883 345567777775 3544432 34666665332
Q ss_pred CCCeeeeccc--cc--cccccCCcCCCCCCEEEEEEEec
Q psy230 79 HDPAVLSYLA--FE--GATKKNPPKVETGDVVAGKLLTA 113 (222)
Q Consensus 79 ~~~a~L~~~~--f~--gatk~~r~~l~~GDlV~ArV~~~ 113 (222)
-..|.|.... |- |-.-+++.+++..-.+.|.-++.
T Consensus 299 Ve~A~v~A~G~I~vg~GI~G~g~~~i~ak~~v~a~fi~~ 337 (543)
T COG1315 299 VENANVSASGDIFVGKGIVGKGEGCIRAKGLVFAKFIEN 337 (543)
T ss_pred EeceEEeccCceEeccccccCCceeEeecceeeeeehhh
Confidence 3456665421 21 33457888888888888876654
No 153
>PRK00276 infA translation initiation factor IF-1; Validated
Probab=53.44 E-value=74 Score=22.12 Aligned_cols=52 Identities=21% Similarity=0.295 Sum_probs=32.1
Q ss_pred EEEEEEEEecc-eEEEEECCCCCeeeeccccccccccCCcCCCCCCEEEEEEEecC
Q psy230 60 VIGVVTSRVGD-NYRVDIGSHDPAVLSYLAFEGATKKNPPKVETGDVVAGKLLTAN 114 (222)
Q Consensus 60 VIG~V~~v~~~-~~~VdI~~~~~a~L~~~~f~gatk~~r~~l~~GDlV~ArV~~~~ 114 (222)
..|+|++..+. .|.|... .+.+-.-...|..++.+-...+||.|.-++...+
T Consensus 9 ~~G~Vi~~~~~~~y~V~~~---~g~~~~c~~~Gklr~~~i~i~vGD~V~ve~~~~~ 61 (72)
T PRK00276 9 MEGTVVEALPNAMFRVELE---NGHEVLAHISGKMRKNYIRILPGDKVTVELSPYD 61 (72)
T ss_pred EEEEEEEEcCCCEEEEEeC---CCCEEEEEEccceeeCCcccCCCCEEEEEEcccC
Confidence 45899998865 7887431 1211111244666655555889999988865543
No 154
>PRK05435 rpmA 50S ribosomal protein L27; Validated
Probab=53.03 E-value=40 Score=24.60 Aligned_cols=37 Identities=14% Similarity=0.348 Sum_probs=26.7
Q ss_pred CCCeecCCCCCCeeeCCCeEE-eCCEEEEEEeeEEEEe
Q psy230 2 AGDTLSLNAEPRLILGPGLRR-ESSAILVSQSGILRHA 38 (222)
Q Consensus 2 PGd~l~~~~~~~~~~G~G~y~-~~~~i~as~~G~l~~~ 38 (222)
||+.|..--...|-||.++-. .|..|+|.+.|.|+..
T Consensus 33 ~G~IivRQRGtk~~PG~nVg~GrD~TlfA~~~G~V~f~ 70 (82)
T PRK05435 33 AGNIIVRQRGTKFHPGVNVGRGKDHTLFALVDGVVKFE 70 (82)
T ss_pred CCcEEEEeCCCeECCCCCEeecCCceEEEecceEEEEE
Confidence 666665211135778888765 5789999999999876
No 155
>CHL00121 rpl27 ribosomal protein L27; Reviewed
Probab=52.84 E-value=32 Score=25.28 Aligned_cols=46 Identities=15% Similarity=0.157 Sum_probs=29.7
Q ss_pred CCCeecCCCCCCeeeCCCeEE-eCCEEEEEEeeEEEEec----CcEEEEEc
Q psy230 2 AGDTLSLNAEPRLILGPGLRR-ESSAILVSQSGILRHAK----PFTYYVDY 47 (222)
Q Consensus 2 PGd~l~~~~~~~~~~G~G~y~-~~~~i~as~~G~l~~~~----~~~v~V~~ 47 (222)
||+.|..--...|-+|.++-. .|..|+|...|.|+... ++.++|.|
T Consensus 33 ~G~IivRQRGtk~hPG~NVg~GrD~TlfAl~~G~V~f~~~~~~~~~vsv~~ 83 (86)
T CHL00121 33 AGNILIRQRGTKFKPGLNVGCGKDFTLYALIDGFVKFKKKNKKQKSINVIN 83 (86)
T ss_pred CCcEEEEcCCCeECCCCcccccCCceEEEccceEEEEEEeCCCCEEEEEee
Confidence 677665311134677776643 58899999999998752 23455555
No 156
>CHL00010 infA translation initiation factor 1
Probab=51.39 E-value=86 Score=22.27 Aligned_cols=52 Identities=21% Similarity=0.313 Sum_probs=32.4
Q ss_pred EEEEEEEEe-cceEEEEECCCCCeeeeccccccccccCCcCCCCCCEEEEEEEecC
Q psy230 60 VIGVVTSRV-GDNYRVDIGSHDPAVLSYLAFEGATKKNPPKVETGDVVAGKLLTAN 114 (222)
Q Consensus 60 VIG~V~~v~-~~~~~VdI~~~~~a~L~~~~f~gatk~~r~~l~~GDlV~ArV~~~~ 114 (222)
+.|+|++.. +..|.|... .+..-.-...|..++.+-...+||.|.-++...+
T Consensus 9 ~~G~Vik~lg~~~y~V~~~---~g~~~~c~~rGklr~~~i~~~vGD~V~ve~~~~~ 61 (78)
T CHL00010 9 MEGLVTESLPNGMFRVRLD---NGCQVLGYISGKIRRNSIRILPGDRVKVELSPYD 61 (78)
T ss_pred EEEEEEEEcCCCEEEEEeC---CCCEEEEEeccceecCCcccCCCCEEEEEEcccC
Confidence 569999998 588888642 1211111234555544455789999988864444
No 157
>cd04482 RPA2_OBF_like RPA2_OBF_like: A subgroup of uncharacterized archaeal OB folds with similarity to the OB fold of the central ssDNA-binding domain (DBD)-D of human RPA2 (also called RPA32). RPA2 is a subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B; RPA2 DBD-D is a weak ssDNA-binding domain. RPA2 DBD-D is also involved in trimerization. The ssDNA binding mechanism is believed to be multistep and to involve conformational change. N-terminal to human RPA2 DBD-D is a domain containing all the known phosphorylation sites of RPA. Human RPA2 is phosphorylated in a cell cycle depende
Probab=51.18 E-value=51 Score=24.01 Aligned_cols=49 Identities=20% Similarity=0.211 Sum_probs=32.5
Q ss_pred EEEEEEEEe----cceEEEEECCCCCeeeeccccccc--cccCCcCCCCCCEEEEE
Q psy230 60 VIGVVTSRV----GDNYRVDIGSHDPAVLSYLAFEGA--TKKNPPKVETGDVVAGK 109 (222)
Q Consensus 60 VIG~V~~v~----~~~~~VdI~~~~~a~L~~~~f~ga--tk~~r~~l~~GDlV~Ar 109 (222)
|-|.|+... +-.+...|.. ..|.++...|... .++....+++||.|.+.
T Consensus 3 v~GeVs~~~~~~~sGH~yFtlkD-~~~~i~cv~f~~~g~~~~~~~~l~~Gd~V~v~ 57 (91)
T cd04482 3 VTGKVVEEPRTIEGGHVFFKISD-GTGEIDCAAYEPTKEFRDVVRLLIPGDEVTVY 57 (91)
T ss_pred EEEEEeCCeecCCCCCEEEEEEC-CCcEEEEEEECcccccccccCCCCCCCEEEEE
Confidence 566666542 2235555644 3477887778765 56788899999987655
No 158
>smart00293 PWWP domain with conserved PWWP motif. conservation of Pro-Trp-Trp-Pro residues
Probab=49.97 E-value=11 Score=25.54 Aligned_cols=15 Identities=27% Similarity=0.321 Sum_probs=12.7
Q ss_pred CCCCCEEEEEEEecC
Q psy230 100 VETGDVVAGKLLTAN 114 (222)
Q Consensus 100 l~~GDlV~ArV~~~~ 114 (222)
|++||+|.||+...-
T Consensus 1 f~~GdlVwaK~~G~p 15 (63)
T smart00293 1 FKPGDLVWAKMKGFP 15 (63)
T ss_pred CCCCCEEEEECCCCC
Confidence 689999999997654
No 159
>PF12508 DUF3714: Protein of unknown function (DUF3714) ; InterPro: IPR022187 Proteins in this entry are designated TraM and are found in a proposed transfer region of a class of conjugative transposon found in the Bacteroides lineage.
Probab=49.12 E-value=99 Score=26.22 Aligned_cols=54 Identities=20% Similarity=0.253 Sum_probs=42.9
Q ss_pred eCCEEEEEEeeEEEEecCcEEEEEcc-----ccccCCCCCCEEEEEEEEEecceEEEEECC
Q psy230 23 ESSAILVSQSGILRHAKPFTYYVDYI-----QRRYVPTRGDLVIGVVTSRVGDNYRVDIGS 78 (222)
Q Consensus 23 ~~~~i~as~~G~l~~~~~~~v~V~~~-----~~~Y~P~vGDiVIG~V~~v~~~~~~VdI~~ 78 (222)
..+.|.|.+-|.....+...+.++-+ .+..+|+ |-++.| +.++.+++..+.|.+
T Consensus 51 ~~n~I~A~V~~~qtv~~Gs~vrlRLle~i~i~g~~IPk-gt~l~G-~~~~~~~Rl~i~I~S 109 (200)
T PF12508_consen 51 EKNTIRAVVDGTQTVVDGSRVRLRLLEDIQIGGILIPK-GTYLYG-VASFQGQRLLITITS 109 (200)
T ss_pred CCCeEEEEEecceEEeCCCEEEEEEcCceEECCEEeCC-CCEEEE-EEeeeccEEEEEEEE
Confidence 57789999999877665555555432 4567877 999999 999999999999987
No 160
>PF13014 KH_3: KH domain
Probab=49.05 E-value=11 Score=23.35 Aligned_cols=27 Identities=7% Similarity=0.212 Sum_probs=23.2
Q ss_pred hhhccCCChhHHHHhhhcCCCcEEEEEEe
Q psy230 149 CRKLLNPKCPLLKQLAKRSRQKMELSIGM 177 (222)
Q Consensus 149 ~~rl~~~~~~~l~~l~~~~~~~~ei~vG~ 177 (222)
+.+++|+++..++.|.+ .+++.|-|-.
T Consensus 2 vg~iIG~~G~~I~~I~~--~tg~~I~i~~ 28 (43)
T PF13014_consen 2 VGRIIGKGGSTIKEIRE--ETGAKIQIPP 28 (43)
T ss_pred cCeEECCCChHHHHHHH--HhCcEEEECC
Confidence 56789999999999999 8888887765
No 161
>COG1530 CafA Ribonucleases G and E [Translation, ribosomal structure and biogenesis]
Probab=48.34 E-value=36 Score=32.65 Aligned_cols=71 Identities=15% Similarity=0.133 Sum_probs=52.4
Q ss_pred CCCCEEEEEEEEEe--cceEEEEECCCCCeeeecccccccc-----ccCCcCCCCCCEEEEEEEecCCC-CeeEEEEec
Q psy230 55 TRGDLVIGVVTSRV--GDNYRVDIGSHDPAVLSYLAFEGAT-----KKNPPKVETGDVVAGKLLTANKD-MESEMVCVD 125 (222)
Q Consensus 55 ~vGDiVIG~V~~v~--~~~~~VdI~~~~~a~L~~~~f~gat-----k~~r~~l~~GDlV~ArV~~~~~~-~~~~Ls~~~ 125 (222)
.+||+-.|+|+++- -+.++|||+.--.|+||+....... .+.+..++.|+-+.-.|..-... .-+.||+.-
T Consensus 36 ~~gniy~grv~~i~p~~~aafvdig~~r~gfl~~~~~~~~~~~~~~~~i~~~lr~~~~~~Vqv~ke~~G~Kga~lT~~I 114 (487)
T COG1530 36 IVGNIYKGRVTRVLPSLEAAFVDIGLERNGFLHLSEIVPYFRAVLEEKIKVRLRGGQATLVQVVKEPRGTKGARLTTDI 114 (487)
T ss_pred eecCceEEEecccCccchhheeeccCCccceEEecccchhhhhcccccceeeecCCceEEEEEEeecCccccccceeEE
Confidence 57999999999995 4789999999999999976432221 14567899999999888765433 235666643
No 162
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=48.27 E-value=22 Score=35.70 Aligned_cols=59 Identities=10% Similarity=0.120 Sum_probs=48.3
Q ss_pred eEEEechhhhhhccCCChhHHHHhhhcCCCcEEEEEEeCCeEEEeeCCchhHHHHHHHHHHhhc
Q psy230 140 YLLHTSISLCRKLLNPKCPLLKQLAKRSRQKMELSIGMNGKIWIRCESFSDTVRVGNLIMSCEL 203 (222)
Q Consensus 140 ~l~~v~~~~~~rl~~~~~~~l~~l~~~~~~~~ei~vG~NG~iWi~~~~~~~~~~i~~~i~~~e~ 203 (222)
..+++++.+++.++|+++..++.|-+ .++..|=+--+|.|.|.+.+... +-.|...++.
T Consensus 556 ~~~~I~~~kI~~vIG~gg~~ik~I~~--~~~~~idi~d~G~v~i~~~~~~~---~~~a~~~I~~ 614 (693)
T PRK11824 556 ETIKIPPDKIRDVIGPGGKTIREITE--ETGAKIDIEDDGTVKIAATDGEA---AEAAKERIEG 614 (693)
T ss_pred eeecCCHHHHHHHhcCCchhHHHHHH--HHCCccccCCCceEEEEcccHHH---HHHHHHHHHH
Confidence 58899999999999999999999998 78888888999999999988763 3344444443
No 163
>PF03961 DUF342: Protein of unknown function (DUF342); InterPro: IPR005646 This family of bacterial proteins has no known function. The proteins are in the region of 500-600 amino acid residues in length.
Probab=47.17 E-value=46 Score=31.31 Aligned_cols=34 Identities=15% Similarity=0.050 Sum_probs=27.8
Q ss_pred CeeeCCCeEEe---CCEEEEEEeeEEEEecCcEEEEEc
Q psy230 13 RLILGPGLRRE---SSAILVSQSGILRHAKPFTYYVDY 47 (222)
Q Consensus 13 ~~~~G~G~y~~---~~~i~as~~G~l~~~~~~~v~V~~ 47 (222)
.+.+|+|+... +..++|++.|.+...+ +.++|.|
T Consensus 144 ~~~~g~~~~~~~~d~~~~~A~~~G~~~~~~-~~i~V~~ 180 (451)
T PF03961_consen 144 PLKAGKNTEVSEEDGNKLYAAIDGRPVFEN-GKISVDP 180 (451)
T ss_pred ceeCCCCEEEEcCCCCEEEEecCCEEEEEC-CEEEEEE
Confidence 57889999875 3589999999999884 6677776
No 164
>cd05834 HDGF_related The PWWP domain is an essential part of the Hepatoma Derived Growth Factor (HDGF) family of proteins, and is necessary for DNA binding by HDGF. This family of endogenous nuclear-targeted mitogens includes HRP (HDGF-related proteins 1, 2, 3, 4, or HPR1, HPR2, HPR3, HPR4, respectively) and lens epithelium-derived growth factor, LEDGF. Members of the HDGF family have been linked to human diseases, and HDGF is a prognostic factor in several types of cancer. The PWWP domain, named for a conserved Pro-Trp-Trp-Pro motif, is a small domain consisting of 100-150 amino acids. The PWWP domain is found in numerous proteins that are involved in cell division, growth and differentiation. Most PWWP-domain proteins seem to be nuclear, often DNA-binding, proteins that function as transcription factors regulating a variety of developmental processes.
Probab=46.42 E-value=13 Score=26.83 Aligned_cols=16 Identities=25% Similarity=0.351 Sum_probs=13.2
Q ss_pred CCCCCCEEEEEEEecC
Q psy230 99 KVETGDVVAGKLLTAN 114 (222)
Q Consensus 99 ~l~~GDlV~ArV~~~~ 114 (222)
.|++||||.|++...-
T Consensus 2 ~f~~GdlVwaK~kGyp 17 (83)
T cd05834 2 QFKAGDLVFAKVKGYP 17 (83)
T ss_pred CCCCCCEEEEecCCCC
Confidence 4889999999986554
No 165
>cd04491 SoSSB_OBF SoSSB_OBF: A subfamily of OB folds similar to the OB fold of the crenarchaeote Sulfolobus solfataricus single-stranded (ss) DNA-binding protein (SSoSSB). SSoSSB has a single OB fold, and it physically and functionally interacts with RNA polymerase. In vitro, SSoSSB can substitute for the basal transcription factor TBP, stimulating transcription from promoters under conditions in which TBP is limiting, and supporting transcription when TBP is absent. SSoSSB selectively melts the duplex DNA of promoter sequences. It also relieves transcriptional repression by the chromatin Alba. In addition, SSoSSB activates reverse gyrase activity, which involves DNA binding, DNA cleavage, strand passage and ligation. SSoSSB stimulates all these steps in the presence of the chromatin protein, Sul7d. SSoSSB antagonizes the inhibitory effect of Sul7d on reverse gyrase supercoiling activity. It also physically and functionally interacts with Mini-chromosome Maintenance (MCM), stimulating
Probab=45.55 E-value=1e+02 Score=21.43 Aligned_cols=25 Identities=28% Similarity=0.282 Sum_probs=17.7
Q ss_pred CcCCCCCCEEEEE---EEecCCCCeeEEEE
Q psy230 97 PPKVETGDVVAGK---LLTANKDMESEMVC 123 (222)
Q Consensus 97 r~~l~~GDlV~Ar---V~~~~~~~~~~Ls~ 123 (222)
.+.+.+||+|..+ |.... ..++|++
T Consensus 46 ~~~~~~G~vv~i~~~~v~~~~--g~~ql~i 73 (82)
T cd04491 46 ADDLEPGDVVRIENAYVREFN--GRLELSV 73 (82)
T ss_pred cccCCCCCEEEEEeEEEEecC--CcEEEEe
Confidence 5679999998766 44443 4577776
No 166
>cd04466 S1_YloQ_GTPase S1_YloQ_GTPase: YloQ GTase family (also known as YjeQ and CpgA), S1-like RNA-binding domain. Proteins in the YloQ GTase family bind the ribosome and have GTPase activity. The precise role of this family is unknown. The protein structure is composed of three domains: an N-terminal S1 domain, a central GTPase domain, and a C-terminal zinc finger domain. This N-terminal S1 domain binds ssRNA. The central GTPase domain contains nucleotide-binding signature motifs: G1 (walker A), G3 (walker B) and G4 motifs. Experiments show that the bacterial YloQ and YjeQ proteins have low intrinsic GTPase activity. The C-terminal zinc-finger domain has structural similarity to a portion of the DNA-repair protein Rad51. This suggests a possible role for this GTPase as a regulator of translation, perhaps as a translation initiation factor. This family is classified based on the N-terminal S1 domain.
Probab=45.09 E-value=74 Score=21.09 Aligned_cols=44 Identities=20% Similarity=0.292 Sum_probs=27.9
Q ss_pred EEEEEEecceEEEEECC--CCCeeeeccccccccccCCcCCCCCCEEEEEE
Q psy230 62 GVVTSRVGDNYRVDIGS--HDPAVLSYLAFEGATKKNPPKVETGDVVAGKL 110 (222)
Q Consensus 62 G~V~~v~~~~~~VdI~~--~~~a~L~~~~f~gatk~~r~~l~~GDlV~ArV 110 (222)
|+|+....++|.|.... ...+. ..+..++.....-+||.|..+.
T Consensus 3 grVv~~~~~~~~v~~~~~~~~~~~-----~~~~~~~~~~~~~VGD~V~~~~ 48 (68)
T cd04466 3 GLIIKAIGGFYYVETEDGKIYECR-----LRGKFRKDKNPPAVGDRVEFEP 48 (68)
T ss_pred EEEEEEECCEEEEEeCCCeEEEEE-----EccccccCCCCCCCCcEEEEEE
Confidence 78999988999887642 11222 2233333345678999997764
No 167
>PLN02800 imidazoleglycerol-phosphate dehydratase
Probab=43.72 E-value=76 Score=28.09 Aligned_cols=44 Identities=18% Similarity=0.389 Sum_probs=35.9
Q ss_pred hhHHHHhhhcCCCcEEEEEEeCCeEEEeeC--CchhHHHHHHHHHHhh
Q psy230 157 CPLLKQLAKRSRQKMELSIGMNGKIWIRCE--SFSDTVRVGNLIMSCE 202 (222)
Q Consensus 157 ~~~l~~l~~~~~~~~ei~vG~NG~iWi~~~--~~~~~~~i~~~i~~~e 202 (222)
.+||+++.+ +-.|++-|-.+|-+||+.+ .+.-.+.+.+||++.-
T Consensus 100 DHML~~~a~--Hg~fdL~V~a~GDl~vD~HHtvEDvgI~LG~Al~~AL 145 (261)
T PLN02800 100 DHMLDQLAS--HGLFDVHVKATGDLWIDDHHTNEDVALAIGTALLKAL 145 (261)
T ss_pred HHHHHHHHH--HcCCCeEEEEecCccccCCCchhhhhhhHHHHHHHHh
Confidence 589999999 9999999999999999965 2334567778887753
No 168
>cd05836 N_Pac_NP60 The PWWP domain is an essential part of the cytokine-like nuclear factor n-pac protein, or NP60, which enhances the activity of MAP2K4 and MAP2K6 kinases to phosphorylate p38-alpha. In a variety of cell lines, NP60 has been shown to localize to the nucleus. In addition to the PWWP domain, NP60 also contains an AT-hook and a C-terminal NAD-binding domain. The PWWP domain, named for a conserved Pro-Trp-Trp-Pro motif, is a small domain consisting of 100-150 amino acids. The PWWP domain is found in numerous proteins that are involved in cell division, growth and differentiation. Most PWWP-domain proteins seem to be nuclear, often DNA-binding proteins, that function as transcription factors regulating a variety of developmental processes.
Probab=43.51 E-value=15 Score=26.70 Aligned_cols=15 Identities=27% Similarity=0.328 Sum_probs=12.3
Q ss_pred CCCCCEEEEEEEecC
Q psy230 100 VETGDVVAGKLLTAN 114 (222)
Q Consensus 100 l~~GDlV~ArV~~~~ 114 (222)
|++||||.|++...-
T Consensus 1 f~~GDlVwaK~~g~P 15 (86)
T cd05836 1 LKLGDLVWAKMKGFP 15 (86)
T ss_pred CCCCCEEEEeCCCCC
Confidence 689999999987543
No 169
>cd05840 SPBC215_ISWI_like The PWWP domain is a component of the S. pombe hypothetical protein SPBC215, as well as ISWI complex protein 4. The ISWI (imitation switch) proteins are ATPases responsible for chromatin remodeling in eukaryotes, and SPBC215 is proposed to also bind chromatin. The PWWP domain, named for a conserved Pro-Trp-Trp-Pro motif, is a small domain consisting of 100-150 amino acids. The PWWP domain is found in numerous proteins that are involved in cell division, growth and differentiation. Most PWWP-domain proteins seem to be nuclear, often DNA-binding, proteins that function as transcription factors regulating a variety of developmental processes.
Probab=42.84 E-value=15 Score=27.09 Aligned_cols=15 Identities=27% Similarity=0.279 Sum_probs=12.6
Q ss_pred CCCCCEEEEEEEecC
Q psy230 100 VETGDVVAGKLLTAN 114 (222)
Q Consensus 100 l~~GDlV~ArV~~~~ 114 (222)
|++||+|.||+-..-
T Consensus 1 f~~GDlVwaK~~GyP 15 (93)
T cd05840 1 FQPGDRVLAKVKGFP 15 (93)
T ss_pred CCCCCEEEEeCCCCC
Confidence 689999999997654
No 170
>PF01016 Ribosomal_L27: Ribosomal L27 protein; InterPro: IPR001684 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. L27 is a protein from the large (50S) subunit; it is essential for ribosome function, but its exact role is unclear. It belongs to a family of ribosomal proteins, examples of which are found in bacteria, chloroplasts of plants and red algae and the mitochondria of fungi (e.g. MRP7 from yeast mitochondria). The schematic relationship between these groups of proteins is shown below. Bacterial L27 Nxxxxxxxxx Algal L27 Nxxxxxxxxx Plant L27 tttttNxxxxxxxxxxxxx Yeast MRP7 tttNxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx 't': transit peptide. 'N': N-terminal of mature protein. ; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2ZJQ_T 2ZJP_T 3PIP_T 3DLL_T 3PIO_T 1Y69_U 3CF5_T 2ZJR_T 1VSA_U 3PYT_W ....
Probab=42.74 E-value=43 Score=24.35 Aligned_cols=38 Identities=11% Similarity=0.232 Sum_probs=28.2
Q ss_pred CCCCeecCCCCCCeeeCCCeEE-eCCEEEEEEeeEEEEe
Q psy230 1 MAGDTLSLNAEPRLILGPGLRR-ESSAILVSQSGILRHA 38 (222)
Q Consensus 1 ~PGd~l~~~~~~~~~~G~G~y~-~~~~i~as~~G~l~~~ 38 (222)
.||+.|..--...|-||.++.. .|..|+|...|.|...
T Consensus 31 ~~G~IivRQRgtk~hPG~NVg~GrD~TLfAl~~G~V~f~ 69 (81)
T PF01016_consen 31 KAGNIIVRQRGTKFHPGENVGMGRDHTLFALVDGRVKFT 69 (81)
T ss_dssp SSTSEEEEBSSSSSEEBTTEEEETTSEEEESSSCEEEEE
T ss_pred cCCCEEEEeCCCcCcCCCCEEECCCCcEEEecCEEEEEE
Confidence 3677776311135889999876 4789999999999875
No 171
>PF13742 tRNA_anti_2: OB-fold nucleic acid binding domain
Probab=42.19 E-value=1.4e+02 Score=21.98 Aligned_cols=65 Identities=12% Similarity=0.122 Sum_probs=45.4
Q ss_pred EEEEEEEEEec---ceEEEEECCCCCeeeeccccccccccCC-cCCCCCCEEEEEEE--ecCCCCeeEEEEe
Q psy230 59 LVIGVVTSRVG---DNYRVDIGSHDPAVLSYLAFEGATKKNP-PKVETGDVVAGKLL--TANKDMESEMVCV 124 (222)
Q Consensus 59 iVIG~V~~v~~---~~~~VdI~~~~~a~L~~~~f~gatk~~r-~~l~~GDlV~ArV~--~~~~~~~~~Ls~~ 124 (222)
-|.|.|++.+. ..+..++-. ..|.++...|.+..+++. ..++.||-|.++.. -..+.+.+.|.+.
T Consensus 25 wV~GEIs~~~~~~~gh~YftLkD-~~a~i~~~~~~~~~~~i~~~~l~~G~~V~v~g~~~~y~~~G~~sl~v~ 95 (99)
T PF13742_consen 25 WVEGEISNLKRHSSGHVYFTLKD-EEASISCVIFRSRARRIRGFDLKDGDKVLVRGRVSFYEPRGSLSLIVE 95 (99)
T ss_pred EEEEEEeecEECCCceEEEEEEc-CCcEEEEEEEHHHHhhCCCCCCCCCCEEEEEEEEEEECCCcEEEEEEE
Confidence 57788887754 455666655 348888777877777777 88999999887754 2334556777664
No 172
>COG0557 VacB Exoribonuclease R [Transcription]
Probab=42.06 E-value=1.3e+02 Score=30.16 Aligned_cols=69 Identities=17% Similarity=0.167 Sum_probs=52.1
Q ss_pred CCCCEEEEEEEEEecceEEEEECCC-CCeeeecccccc------------ccccCCcCCCCCCEEEEEEEecCCC-CeeE
Q psy230 55 TRGDLVIGVVTSRVGDNYRVDIGSH-DPAVLSYLAFEG------------ATKKNPPKVETGDVVAGKLLTANKD-MESE 120 (222)
Q Consensus 55 ~vGDiVIG~V~~v~~~~~~VdI~~~-~~a~L~~~~f~g------------atk~~r~~l~~GDlV~ArV~~~~~~-~~~~ 120 (222)
.+|..--|.|+++....+.|.+... -.+..+.+.+++ .-++....++.||-|..+|.+++.. +.+.
T Consensus 621 ~vg~~f~g~V~~v~~~g~~V~l~~~~ieglV~~s~L~~d~y~~~~~~~~l~~~~~~~~~~lgd~v~v~v~~v~~~~~~i~ 700 (706)
T COG0557 621 RVGEEFDGVVTGVTSFGFFVELPELGLEGLVHISSLPDDYYHFDERGQALVGEKSGKVYRLGDEVKVKVTSVDLDERKID 700 (706)
T ss_pred hcCCEEEEEEEEEEeccEEEEecccccccceEcccCCCceeeeccccceeeccccccccccCCEEEEEEEEEcccccceE
Confidence 6789999999999999999999774 566666655443 2246677899999999999998753 3344
Q ss_pred EEE
Q psy230 121 MVC 123 (222)
Q Consensus 121 Ls~ 123 (222)
++.
T Consensus 701 ~~~ 703 (706)
T COG0557 701 FEL 703 (706)
T ss_pred EEe
Confidence 443
No 173
>cd07914 IGPD Imidazoleglycerol-phosphate dehydratase. Imidazoleglycerol-phosphate dehydratase (IGPD; EC 4.2.1.19) catalyzes the dehydration of imidazole glycerol phosphate to imidazole acetol phosphate, the sixth step of histidine biosynthesis in plants and microorganisms where the histidine is synthesized de novo. There is an internal repeat in the protein domain that is related by pseudo-dyad symmetry, perhaps as a result of an ancient gene duplication. The apo-form of IGPD exists as a catalytically inactive trimer which, in the presence of specific divalent metal cations such as manganese (Mn2+), cobalt (Co2+), cadmium (Cd2+), nickel (Ni2+), iron (Fe2+) and zinc (Zn2+), assembles to form a biologically active high molecular weight metalloenzyme; a 24-mer with 4-3-2 symmetry. Each 24-mer has 24 active sites, and contains around 1.5 metal ions per monomer, each monomer contributing residues to three separate active sites. IGPD enzymes are monofunctional in fungi, plants, archaea and s
Probab=41.33 E-value=66 Score=27.14 Aligned_cols=44 Identities=11% Similarity=0.189 Sum_probs=35.7
Q ss_pred hhHHHHhhhcCCCcEEEEEEeCCeEEEeeCC--chhHHHHHHHHHHhh
Q psy230 157 CPLLKQLAKRSRQKMELSIGMNGKIWIRCES--FSDTVRVGNLIMSCE 202 (222)
Q Consensus 157 ~~~l~~l~~~~~~~~ei~vG~NG~iWi~~~~--~~~~~~i~~~i~~~e 202 (222)
.+||+++.+ +..|++.|-.+|-+||+.+- +.-.+.+.+|+++.-
T Consensus 34 DHML~~~a~--H~~~dL~v~a~GDl~vD~HHtvEDvgI~LG~al~~aL 79 (190)
T cd07914 34 DHMLTLFAR--HGGFDLTVKAKGDLEVDDHHTVEDVGIVLGQALKKAL 79 (190)
T ss_pred HHHHHHHHH--HcCCCeEEEEecCccccCCcchhhhHhhHHHHHHHHh
Confidence 589999999 99999999999999998652 334566778887654
No 174
>PF14398 ATPgrasp_YheCD: YheC/D like ATP-grasp
Probab=41.26 E-value=16 Score=31.98 Aligned_cols=16 Identities=44% Similarity=0.929 Sum_probs=14.8
Q ss_pred CCcEEEEEEeCCeEEE
Q psy230 168 RQKMELSIGMNGKIWI 183 (222)
Q Consensus 168 ~~~~ei~vG~NG~iWi 183 (222)
+.++|++|..||+||+
T Consensus 211 ElGiDl~iD~~g~iWl 226 (262)
T PF14398_consen 211 ELGIDLGIDKNGKIWL 226 (262)
T ss_pred EEEEEEEEcCCCCEEE
Confidence 5789999999999998
No 175
>PRK00951 hisB imidazoleglycerol-phosphate dehydratase; Validated
Probab=40.46 E-value=96 Score=26.25 Aligned_cols=44 Identities=16% Similarity=0.251 Sum_probs=35.1
Q ss_pred hhHHHHhhhcCCCcEEEEEEeCCeEEEeeCC--chhHHHHHHHHHHhh
Q psy230 157 CPLLKQLAKRSRQKMELSIGMNGKIWIRCES--FSDTVRVGNLIMSCE 202 (222)
Q Consensus 157 ~~~l~~l~~~~~~~~ei~vG~NG~iWi~~~~--~~~~~~i~~~i~~~e 202 (222)
.+||.++.+ +..|++-|-.+|-+||+.+- +.-.+.+.+|+++.-
T Consensus 38 DHML~~~a~--H~~~dL~v~a~GDl~vD~HHtvEDvgI~LG~al~~aL 83 (195)
T PRK00951 38 DHMLDQFAR--HGLFDLTVKAKGDLHIDDHHTVEDVGIVLGQALKEAL 83 (195)
T ss_pred HHHHHHHHH--HcCCCeEEEEecCccccCCchHHHHHHHHHHHHHHHh
Confidence 589999999 99999999999999999753 233456677777643
No 176
>PRK06763 F0F1 ATP synthase subunit alpha; Validated
Probab=40.05 E-value=1.5e+02 Score=25.34 Aligned_cols=21 Identities=10% Similarity=-0.092 Sum_probs=12.9
Q ss_pred CCEEEEEEEEEecceEEEEEC
Q psy230 57 GDLVIGVVTSRVGDNYRVDIG 77 (222)
Q Consensus 57 GDiVIG~V~~v~~~~~~VdI~ 77 (222)
-+.+=|+|+++....+.+..-
T Consensus 39 ~~tiEGrVvEV~~~~i~iesk 59 (213)
T PRK06763 39 FSTIEGRVVEVDNGVIVIKSK 59 (213)
T ss_pred cceeeeEEEEEeCCEEEEEec
Confidence 445666666666666666554
No 177
>COG2810 Predicted type IV restriction endonuclease [Defense mechanisms]
Probab=39.83 E-value=45 Score=29.36 Aligned_cols=54 Identities=17% Similarity=0.239 Sum_probs=32.7
Q ss_pred ccCcccCCceEEEechhhhhhccCCChhHHHHhhhcCCCcEEEEEEeCCeEEEee
Q psy230 131 FIMGILNDGYLLHTSISLCRKLLNPKCPLLKQLAKRSRQKMELSIGMNGKIWIRC 185 (222)
Q Consensus 131 ~~~G~L~~G~l~~v~~~~~~rl~~~~~~~l~~l~~~~~~~~ei~vG~NG~iWi~~ 185 (222)
..|-.+.+|-+|-.-..+.-..+ +...+.+.++=....++|+.+=-|||+||--
T Consensus 59 aDyalikd~kvfafieak~ls~~-~akd~qq~~~Yav~~Gv~~~iVtnGrvWiV~ 112 (284)
T COG2810 59 ADYALIKDGKVFAFIEAKNLSVN-PAKDVQQLAKYAVDKGVEVGIVTNGRVWIVV 112 (284)
T ss_pred cceEEEecCcEEEEEeccccCcC-chHHHHHHHHHHHhcCcEEEEEeCCeEEEEE
Confidence 45777777777766554433222 2233333332111569999999999999943
No 178
>PF07208 DUF1414: Protein of unknown function (DUF1414); InterPro: IPR009857 This family consists of several hypothetical bacterial proteins of around 70 residues in length. Members of this family are often referred to as YejL. The function of this family is unknown.; PDB: 2JPQ_A 2JUZ_B 2JUW_B 2QTI_A 2OTA_A 2JR2_A 2JRX_A.
Probab=39.53 E-value=62 Score=20.82 Aligned_cols=31 Identities=10% Similarity=0.145 Sum_probs=24.0
Q ss_pred HHHHHHHHHhh--cCCHHHHHHHHHHHHHHhcC
Q psy230 192 VRVGNLIMSCE--LLSYEEILNLCESIHIRFLQ 222 (222)
Q Consensus 192 ~~i~~~i~~~e--~~~~~~~~~~~~~~~~~l~~ 222 (222)
..+.|++.++- ..+.+|...+.++|.+.|++
T Consensus 10 MvLGN~vTniln~~V~~~qR~~iAe~Fa~AL~~ 42 (44)
T PF07208_consen 10 MVLGNMVTNILNTSVPPAQRQAIAEKFAQALKS 42 (44)
T ss_dssp HHHHHHHHHHHHHCS-HHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHhhcCCHHHHHHHHHHHHHHHHh
Confidence 45677777665 57899999999999999864
No 179
>PF14069 SpoVIF: Stage VI sporulation protein F
Probab=39.39 E-value=48 Score=23.96 Aligned_cols=34 Identities=12% Similarity=0.187 Sum_probs=27.7
Q ss_pred CchhHHHHHHHHHHhhcCCHHHHHHHHHHHHHHh
Q psy230 187 SFSDTVRVGNLIMSCELLSYEEILNLCESIHIRF 220 (222)
Q Consensus 187 ~~~~~~~i~~~i~~~e~~~~~~~~~~~~~~~~~l 220 (222)
+.++...+++.+...+.-++++++.|+.++++.+
T Consensus 11 ~~~~i~kLA~sv~~adlqdE~~vR~lIk~vs~~a 44 (79)
T PF14069_consen 11 NKEDIFKLANSVQKADLQDEKKVRQLIKQVSQIA 44 (79)
T ss_pred CHHHHHHHHHhcchhhcccHHHHHHHHHHHHHHh
Confidence 4567788888888888888999999988887754
No 180
>KOG1067|consensus
Probab=39.00 E-value=70 Score=31.62 Aligned_cols=72 Identities=13% Similarity=0.090 Sum_probs=56.2
Q ss_pred cCCCCCCEEE-----EEEEEEecceEEEEECCCCCeeeecccccc-ccccCCcCCCCCCEEEEEEEecCCCCeeEEEE
Q psy230 52 YVPTRGDLVI-----GVVTSRVGDNYRVDIGSHDPAVLSYLAFEG-ATKKNPPKVETGDVVAGKLLTANKDMESEMVC 123 (222)
Q Consensus 52 Y~P~vGDiVI-----G~V~~v~~~~~~VdI~~~~~a~L~~~~f~g-atk~~r~~l~~GDlV~ArV~~~~~~~~~~Ls~ 123 (222)
-.|+++|++. +.|+++.+-...|.+-.-..+.||.+++.. -..+-...|.+||-|--+-+..+......|+-
T Consensus 659 ~~~~~~~l~~g~vy~~tIt~~rd~G~~V~l~p~~~~Llh~sqL~~e~iakpsd~levGq~I~vk~ie~d~~g~~~ls~ 736 (760)
T KOG1067|consen 659 KDDQVQDLEFGGVYTATITEIRDTGVMVELYPMQQGLLHNSQLDQEKIAKPSDLLEVGQEIQVKYIERDPRGGIMLSS 736 (760)
T ss_pred cCccccceEeeeEEEEEEeeecccceEEEecCCchhhccchhcccccccChHHHHhhcceeEEEEEeecCccceeehh
Confidence 4688999987 688899999999999998899999887753 33455666999999888877776655555554
No 181
>COG0131 HisB Imidazoleglycerol-phosphate dehydratase [Amino acid transport and metabolism]
Probab=38.23 E-value=1.4e+02 Score=25.32 Aligned_cols=76 Identities=16% Similarity=0.185 Sum_probs=52.4
Q ss_pred EEEEEecCCCCeeEEEEecCCCccccCccc--CCceEEEechhhhhhccCCChhHHHHhhhcCCCcEEEEEEeCCeEEEe
Q psy230 107 AGKLLTANKDMESEMVCVDSRGKEFIMGIL--NDGYLLHTSISLCRKLLNPKCPLLKQLAKRSRQKMELSIGMNGKIWIR 184 (222)
Q Consensus 107 ~ArV~~~~~~~~~~Ls~~~~~~~~~~~G~L--~~G~l~~v~~~~~~rl~~~~~~~l~~l~~~~~~~~ei~vG~NG~iWi~ 184 (222)
.|+|..-.+..+++++.-- ++-|+. .-| ++=-.+||.+|++ +..|++-|-.-|-+||+
T Consensus 5 ~a~v~R~T~ET~I~V~i~l-----Dg~G~~~i~TG-------------v~FfDHML~~~a~--H~~~dl~V~a~GDl~iD 64 (195)
T COG0131 5 TAEVTRKTKETDIEVSLDL-----DGTGKSKIDTG-------------VGFFDHMLDQLAR--HGGFDLEVSAKGDLHID 64 (195)
T ss_pred eeEEEecccceEEEEEEEc-----CCCCceeecCC-------------CchHHHHHHHHHH--hCCCceEEEEccCcccc
Confidence 4677777776677777632 232332 333 1212589999999 99999999999999998
Q ss_pred eCC--chhHHHHHHHHHHhh
Q psy230 185 CES--FSDTVRVGNLIMSCE 202 (222)
Q Consensus 185 ~~~--~~~~~~i~~~i~~~e 202 (222)
.+- +...+.+..||++.-
T Consensus 65 dHHtvED~gIaLGqAl~~Al 84 (195)
T COG0131 65 DHHTVEDTGIALGQALKEAL 84 (195)
T ss_pred ccchHHHHHHHHHHHHHHHh
Confidence 752 334567788887765
No 182
>PF04319 NifZ: NifZ domain; InterPro: IPR007415 NifZ is a short protein is found in the nif (nitrogen fixation) operon. It is required for the maturation of the nitrogenase MoFe protein. In the absence of NifZ, only one of the two P-clusters of the MoFe protein is matured to the ultimate [8Fe-7S] structure. The other P-cluster site in the protein contains a [4Fe-4S] cluster pair, suggesting that NifZ is specifically required for the formation of the second P-cluster [, , ].; GO: 0009399 nitrogen fixation
Probab=38.18 E-value=67 Score=22.99 Aligned_cols=21 Identities=33% Similarity=0.455 Sum_probs=17.3
Q ss_pred CCcCCCCCCEEEEEEEecCCC
Q psy230 96 NPPKVETGDVVAGKLLTANKD 116 (222)
Q Consensus 96 ~r~~l~~GDlV~ArV~~~~~~ 116 (222)
|.|.|+.||.|+|+-.-.|+.
T Consensus 1 ~~p~f~~G~~V~a~~~irNDG 21 (75)
T PF04319_consen 1 MPPRFEWGDKVRARKDIRNDG 21 (75)
T ss_pred CCCccCCCCEEEEEEEeEcCC
Confidence 578999999999998766643
No 183
>PF07116 DUF1372: Protein of unknown function (DUF1372); InterPro: IPR010779 This entry is represented by Streptococcus phage Sfi11, Gp93. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family consists of several Streptococcus bacteriophage sequences and related proteins from Streptococcus species. Members of this family are typically around 100 residues in length and their function is unknown.
Probab=38.11 E-value=72 Score=24.23 Aligned_cols=44 Identities=30% Similarity=0.520 Sum_probs=32.5
Q ss_pred CCCCEEEEEEEEE--ecceEEEEECCCCCeeeeccccccccccCCcCCCCCCEE
Q psy230 55 TRGDLVIGVVTSR--VGDNYRVDIGSHDPAVLSYLAFEGATKKNPPKVETGDVV 106 (222)
Q Consensus 55 ~vGDiVIG~V~~v--~~~~~~VdI~~~~~a~L~~~~f~gatk~~r~~l~~GDlV 106 (222)
..|-...|+|+++ -+..|.|++++...-.. ||.....+++||=|
T Consensus 53 N~G~ei~GkVt~K~~ig~~yTvti~~YGkFlV--------tkeqY~~i~iGDdi 98 (104)
T PF07116_consen 53 NAGAEIFGKVTEKEIIGGLYTVTIGAYGKFLV--------TKEQYESIKIGDDI 98 (104)
T ss_pred CCCcEEEEEEeeceeECCEEEEEecCceEEEE--------ehhhcceeecCCcc
Confidence 5678899999987 57999999998533333 36667778888743
No 184
>PRK10553 assembly protein for periplasmic nitrate reductase; Provisional
Probab=37.46 E-value=1.6e+02 Score=21.47 Aligned_cols=56 Identities=13% Similarity=0.105 Sum_probs=36.5
Q ss_pred CceEEEechhhhhhccCCChhHHHHhhhcCCCcEEEEEE--eCCeEEEeeCCchhHHHHHHHHHHhhc
Q psy230 138 DGYLLHTSISLCRKLLNPKCPLLKQLAKRSRQKMELSIG--MNGKIWIRCESFSDTVRVGNLIMSCEL 203 (222)
Q Consensus 138 ~G~l~~v~~~~~~rl~~~~~~~l~~l~~~~~~~~ei~vG--~NG~iWi~~~~~~~~~~i~~~i~~~e~ 203 (222)
.|.++.+.|..... +.+.|.+ --+|||..- -+|++-|--+... ...+.+.|..++.
T Consensus 8 sSlVV~~~Pe~~~~-------V~~~l~~--ipg~Evh~~d~~~GKiVVtiE~~~-~~~~~~~i~~I~~ 65 (87)
T PRK10553 8 CSLVVQAKSERISD-------ISTQLNA--FPGCEVAVSDAPSGQLIVVVEAED-SETLLQTIESVRN 65 (87)
T ss_pred eEEEEEeChHHHHH-------HHHHHHc--CCCcEEEeecCCCCeEEEEEEeCC-hHHHHHHHHHHHc
Confidence 46778888887654 4556666 679999875 6899988755442 3344444444443
No 185
>PF10844 DUF2577: Protein of unknown function (DUF2577); InterPro: IPR022555 This family of proteins has no known function
Probab=36.83 E-value=85 Score=23.29 Aligned_cols=22 Identities=32% Similarity=0.434 Sum_probs=17.1
Q ss_pred CCCCEEEEEEEEEecceEEEEECC
Q psy230 55 TRGDLVIGVVTSRVGDNYRVDIGS 78 (222)
Q Consensus 55 ~vGDiVIG~V~~v~~~~~~VdI~~ 78 (222)
.+=++++|+|++..+ .++.++.
T Consensus 15 ~p~~i~~G~V~s~~P--L~I~i~~ 36 (100)
T PF10844_consen 15 NPVDIVIGTVVSVPP--LKIKIDQ 36 (100)
T ss_pred CCceeEEEEEEeccc--EEEEECC
Confidence 445678999999888 7777776
No 186
>cd05835 Dnmt3b_related The PWWP domain is an essential component of DNA methyltransferase 3 B (Dnmt3b) which is responsible for establishing DNA methylation patterns during embryogenesis and gametogenesis. In tumorigenesis, DNA methylation by Dnmt3b is known to play a role in the inactivation of tumor suppressor genes. In addition, a point mutation in the PWWP domain of Dnmt3b has been identified in patients with ICF syndrome (immunodeficiency, centromeric instability, and facial anomalies), a rare autosomal recessive disorder characterized by hypomethylation of classical satellite DNA. The PWWP domain, named for a conserved Pro-Trp-Trp-Pro motif, is a small domain consisting of 100-150 amino acids. The PWWP domain is found in numerous proteins that are involved in cell division, growth and differentiation. Most PWWP-domain proteins seem to be nuclear, often DNA-binding, proteins that function as transcription factors regulating a variety of developmental processes.
Probab=36.47 E-value=23 Score=25.72 Aligned_cols=15 Identities=33% Similarity=0.448 Sum_probs=12.2
Q ss_pred CCCCCEEEEEEEecC
Q psy230 100 VETGDVVAGKLLTAN 114 (222)
Q Consensus 100 l~~GDlV~ArV~~~~ 114 (222)
|.+||||-|++....
T Consensus 1 f~vGDlVWaK~kg~p 15 (87)
T cd05835 1 FNVGDLVWGKIKGFP 15 (87)
T ss_pred CCCCCEEEEecCCCC
Confidence 679999999986543
No 187
>TIGR00638 Mop molybdenum-pterin binding domain. This model describes a multigene family of molybdenum-pterin binding proteins of about 70 amino acids in Clostridium pasteurianum, as a tandemly-repeated domain C-terminal to an unrelated domain in ModE, a molybdate transport gene repressor of E. coli, and in single or tandemly paired domains in several related proteins.
Probab=36.18 E-value=1.1e+02 Score=20.20 Aligned_cols=50 Identities=18% Similarity=0.104 Sum_probs=28.4
Q ss_pred CCEEEEEEEEE--ecceEEEEECCC----CCeeeeccccccccccCCcCCCCCCEEEEEEEe
Q psy230 57 GDLVIGVVTSR--VGDNYRVDIGSH----DPAVLSYLAFEGATKKNPPKVETGDVVAGKLLT 112 (222)
Q Consensus 57 GDiVIG~V~~v--~~~~~~VdI~~~----~~a~L~~~~f~gatk~~r~~l~~GDlV~ArV~~ 112 (222)
....-|+|.++ .+..+.|.+... ..|.++..++ .+-.|++||-|+|.+.+
T Consensus 6 ~N~l~g~I~~i~~~g~~~~v~l~~~~~~~l~a~i~~~~~------~~l~l~~G~~v~~~ik~ 61 (69)
T TIGR00638 6 RNQLKGKVVAIEDGDVNAEVDLLLGGGTKLTAVITLESV------AELGLKPGKEVYAVIKA 61 (69)
T ss_pred ccEEEEEEEEEEECCCeEEEEEEECCCCEEEEEecHHHH------hhCCCCCCCEEEEEEEC
Confidence 34567888888 344444444322 2233332111 22348899999999864
No 188
>cd04454 S1_Rrp4_like S1_Rrp4_like: Rrp4-like, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein, and Rrp40 and Csl4 proteins, also represented in this group, are subunits of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In Saccharomyces cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".
Probab=36.13 E-value=76 Score=22.04 Aligned_cols=31 Identities=19% Similarity=0.164 Sum_probs=22.9
Q ss_pred cCCCCCCEEEEEEEEEec-ceEEEEECCCCCe
Q psy230 52 YVPTRGDLVIGVVTSRVG-DNYRVDIGSHDPA 82 (222)
Q Consensus 52 Y~P~vGDiVIG~V~~v~~-~~~~VdI~~~~~a 82 (222)
...++||.+.++|.++.. ....+.+.++..+
T Consensus 49 ~~~~~GD~i~~~V~~~~~~~~i~LS~~~~~~G 80 (82)
T cd04454 49 KSLQPGDLILAKVISLGDDMNVLLTTADNELG 80 (82)
T ss_pred hcCCCCCEEEEEEEEeCCCCCEEEEECCCCCc
Confidence 345999999999999976 4566666655444
No 189
>PRK05054 exoribonuclease II; Provisional
Probab=35.89 E-value=1.1e+02 Score=30.33 Aligned_cols=63 Identities=14% Similarity=0.118 Sum_probs=47.0
Q ss_pred CCCCC--EEEEEEEEEecceEEEEECC-CCCeeeeccccccc-------------cccCCcCCCCCCEEEEEEEecCCC
Q psy230 54 PTRGD--LVIGVVTSRVGDNYRVDIGS-HDPAVLSYLAFEGA-------------TKKNPPKVETGDVVAGKLLTANKD 116 (222)
Q Consensus 54 P~vGD--iVIG~V~~v~~~~~~VdI~~-~~~a~L~~~~f~ga-------------tk~~r~~l~~GDlV~ArV~~~~~~ 116 (222)
..+|+ ..-|+|++++...+.|.|.. .-.+.+|.+.+.+. ..+.+..|+.||-|.-+|.+++..
T Consensus 557 ~~~G~~~~f~g~I~~v~~~G~fV~l~~~~veglV~~~~l~~~~~~y~~~~~~~~~~~~~~~~~~lGd~V~V~v~~vd~~ 635 (644)
T PRK05054 557 DKAGTDTRFAAEIIDISRGGMRVRLLENGAVAFIPASFLHAVRDELVCNQENGTVQIKGETVYKLGDVIDVTLAEVRME 635 (644)
T ss_pred hccCCCeEEEEEEEeeecCcEEEEEeCCceEEEEEccccCCCccceEEccccceEEEeCCEEEcCCCEEEEEEEEEccc
Confidence 45665 99999999999999999965 35677776554321 113345799999999999998753
No 190
>PF05257 CHAP: CHAP domain; InterPro: IPR007921 The CHAP (cysteine, histidine-dependent amidohydrolases/peptidases) domain is a region between 110 and 140 amino acids that is found in proteins from bacteria, bacteriophages, archaea and eukaryotes of the Trypanosomidae family. Many of these proteins are uncharacterised, but it has been proposed that they may function mainly in peptidoglycan hydrolysis. The CHAP domain is found in a wide range of protein architectures; it is commonly associated with bacterial type SH3 domains and with several families of amidase domains. It has been suggested that CHAP domain containing proteins utilise a catalytic cysteine residue in a nucleophilic-attack mechanism [, ]. The CHAP domain contains two invariant residues, a cysteine and a histidine. These residues form part of the putative active site of CHAP domain containing proteins. Secondary structure predictions show that the CHAP domain belongs to the alpha + beta structural class, with the N-terminal half largely containing predicted alpha helices and the C-terminal half principally composed of predicted beta strands [, ]. Some proteins known to contain a CHAP domain are listed below: Bacterial and trypanosomal glutathionylspermidine amidases. A variety of bacterial autolysins. A Nocardia aerocolonigenes putative esterase. Streptococcus pneumoniae choline-binding protein D. Methanosarcina mazei protein MM2478, a putative chloride channel. Several phage-encoded peptidoglycan hydrolases. Cysteine peptidases belonging to MEROPS peptidase family C51 (D-alanyl-glycyl endopeptidase, clan CA). ; PDB: 2LRJ_A 2VPM_B 2VOB_B 2VPS_A 2K3A_A 2IO9_A 2IO8_A 2IOB_A 2IOA_B 2IO7_B ....
Probab=35.76 E-value=42 Score=25.32 Aligned_cols=27 Identities=26% Similarity=0.329 Sum_probs=15.8
Q ss_pred cccCCCCCCEE------------EEEEEEEecceEEEEE
Q psy230 50 RRYVPTRGDLV------------IGVVTSRVGDNYRVDI 76 (222)
Q Consensus 50 ~~Y~P~vGDiV------------IG~V~~v~~~~~~VdI 76 (222)
....|++||+| +|+|+++..+.+..-+
T Consensus 59 ~~~~P~~Gdivv~~~~~~~~~GHVaIV~~v~~~~~i~v~ 97 (124)
T PF05257_consen 59 TGSTPQPGDIVVWDSGSGGGYGHVAIVESVNDGGTITVI 97 (124)
T ss_dssp ECS---TTEEEEEEECTTTTT-EEEEEEEE-TTSEEEEE
T ss_pred cCcccccceEEEeccCCCCCCCeEEEEEEECCCCEEEEE
Confidence 44789999999 4899999444444444
No 191
>PF01938 TRAM: TRAM domain; InterPro: IPR002792 The TRAM (after TRM2 and miaB) domain is a 60-70-residue-long module that is found in: Two distinct classes of tRNA-modifying enzymes, namely uridine methylases of the TRM2 family and enzymes of the miaB family that are involved in 2- methylthioadenine formation In several other proteins associated with the translation machinery In a family of small uncharacterised archaeal proteins that are predicted to have a role in the regulation of tRNA modification and/or translation The TRAM domain can be found alone or in association with other domains, such as the catalytic biotin/lipoate synthetase-like domain, the RNA methylase domain, the ribosomal S2 domain and the eIF2-beta domain. The TRAM domain is predicted to bind tRNA and deliver the RNA-modifying enzymatic domain to their targets []. Secondary structure prediction indicates that the TRAM domain adopts a simple beta-barrel fold. The conservation pattern of the TRAM domain consists primarily of small and hydrophobic residues that correspond to five beta-strands in the predicted secondary structure [].; PDB: 1YEZ_A 2BH2_A 1UWV_A 1YVC_A.
Probab=34.33 E-value=1.4e+02 Score=19.62 Aligned_cols=23 Identities=17% Similarity=0.180 Sum_probs=16.4
Q ss_pred CCCCCCEEEEEEEEEecceEEEE
Q psy230 53 VPTRGDLVIGVVTSRVGDNYRVD 75 (222)
Q Consensus 53 ~P~vGDiVIG~V~~v~~~~~~Vd 75 (222)
.|.+||.|--+|++....+..-+
T Consensus 37 ~~~iG~~v~v~I~~~~~~~l~G~ 59 (61)
T PF01938_consen 37 LPLIGEFVKVRITKAKKNYLFGE 59 (61)
T ss_dssp -T--TEEEEEEEEEE-SSEEEEE
T ss_pred CCCCCCEEEEEEEEeeCCcEEEE
Confidence 56689999999999998877644
No 192
>PHA00691 hypothetical protein
Probab=34.27 E-value=21 Score=24.29 Aligned_cols=9 Identities=33% Similarity=0.981 Sum_probs=7.1
Q ss_pred eCCeEEEee
Q psy230 177 MNGKIWIRC 185 (222)
Q Consensus 177 ~NG~iWi~~ 185 (222)
-||++|+--
T Consensus 11 ENGr~WVL~ 19 (68)
T PHA00691 11 ENGRVWVLK 19 (68)
T ss_pred cCCeEEEEE
Confidence 499999943
No 193
>PF07497 Rho_RNA_bind: Rho termination factor, RNA-binding domain; InterPro: IPR011113 The Rho termination factor disengages newly transcribed RNA from its DNA template at certain, specific transcripts. It is thought that two copies of Rho bind to RNA and that Rho functions as a hexamer of protomers [].; GO: 0003723 RNA binding, 0006353 transcription termination, DNA-dependent; PDB: 1A8V_B 1PVO_A 1PV4_D 3ICE_A 1XPU_C 1XPO_D 1XPR_F 2A8V_B 2HT1_B 1A63_A ....
Probab=34.23 E-value=58 Score=23.45 Aligned_cols=36 Identities=42% Similarity=0.544 Sum_probs=21.7
Q ss_pred eEEEEec------CcEEEEEccc-cccCCCCCCEEEEEEEEEe
Q psy230 33 GILRHAK------PFTYYVDYIQ-RRYVPTRGDLVIGVVTSRV 68 (222)
Q Consensus 33 G~l~~~~------~~~v~V~~~~-~~Y~P~vGDiVIG~V~~v~ 68 (222)
|+|+..+ +.=++|-+.+ ++|--+.||.|.|.|..-.
T Consensus 15 GFLR~~~~~y~~~~~DvYVs~~qIrrf~LR~GD~V~G~vr~p~ 57 (78)
T PF07497_consen 15 GFLRSPDNNYLPSPDDVYVSPSQIRRFGLRTGDLVEGQVRPPR 57 (78)
T ss_dssp EEEE-GGGTTS-STTSEEE-CCCCCCTT--TTEEEEEEEE--S
T ss_pred EEeECCCcCCCCCCCCEEECHHHHHHcCCCCCCEEEEEEeCCC
Confidence 6666651 2346788754 6799999999999998853
No 194
>PF08460 SH3_5: Bacterial SH3 domain; InterPro: IPR013667 SH3 (src Homology-3) domains are small protein modules containing approximately 50 amino acid residues [, ]. They are found in a great variety of intracellular or membrane-associated proteins [, , ] for example, in a variety of proteins with enzymatic activity, in adaptor proteins that lack catalytic sequences and in cytoskeletal proteins, such as fodrin and yeast actin binding protein ABP-1. The SH3 domain has a characteristic fold which consists of five or six beta-strands arranged as two tightly packed anti-parallel beta sheets. The linker regions may contain short helices []. The surface of the SH3-domain bears a flat, hydrophobic ligand-binding pocket which consists of three shallow grooves defined by conservative aromatic residues in which the ligand adopts an extended left-handed helical arrangement. The ligand binds with low affinity but this may be enhanced by multiple interactions. The region bound by the SH3 domain is in all cases proline-rich and contains PXXP as a core-conserved binding motif. The function of the SH3 domain is not well understood but they may mediate many diverse processes such as increasing local concentration of proteins, altering their subcellular location and mediating the assembly of large multiprotein complexes []. The SH3 domain has been found in a number of different bacterial proteins including glycyl-glycine endopeptidase, bacteriocin and some hypothetical proteins.; GO: 0016787 hydrolase activity; PDB: 1R77_B.
Probab=33.45 E-value=41 Score=23.16 Aligned_cols=20 Identities=25% Similarity=0.468 Sum_probs=16.5
Q ss_pred CCcEEEEEEeCCeEEEeeCC
Q psy230 168 RQKMELSIGMNGKIWIRCES 187 (222)
Q Consensus 168 ~~~~ei~vG~NG~iWi~~~~ 187 (222)
...++=.+-.||++||+-.+
T Consensus 36 ~V~YD~~~~~dGy~Wisy~~ 55 (65)
T PF08460_consen 36 SVNYDQVIKADGYVWISYIS 55 (65)
T ss_dssp EEEEEEEEEETTEEEEEEE-
T ss_pred EEEEEEEEEeCCEEEEEEEC
Confidence 57888999999999998543
No 195
>PRK00215 LexA repressor; Validated
Probab=33.43 E-value=1.7e+02 Score=24.03 Aligned_cols=30 Identities=13% Similarity=0.031 Sum_probs=19.2
Q ss_pred CcEEEEEccccccCCCC----CCEEEEEEEEEec
Q psy230 40 PFTYYVDYIQRRYVPTR----GDLVIGVVTSRVG 69 (222)
Q Consensus 40 ~~~v~V~~~~~~Y~P~v----GDiVIG~V~~v~~ 69 (222)
++.+++.|....|-|.. .-.|+|+|+.+..
T Consensus 170 ~~~~~L~s~Np~y~~~~~~~~~~~IiG~Vv~~~r 203 (205)
T PRK00215 170 GGHIRLEPENPAYEPIIVDPDRVTIEGKVVGLIR 203 (205)
T ss_pred CCEEEEEcCCCCCCCEEeCCCcEEEEEEEEEEEE
Confidence 34567888666564421 4588888887643
No 196
>KOG4078|consensus
Probab=32.38 E-value=85 Score=25.40 Aligned_cols=80 Identities=24% Similarity=0.263 Sum_probs=52.9
Q ss_pred cCCCCCCEEEEEEEEEecceEEEEECCCCCeeeeccccccccccCCcCCCCCCEEEEEEEecCCCCeeEEEEecCCCccc
Q psy230 52 YVPTRGDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFEGATKKNPPKVETGDVVAGKLLTANKDMESEMVCVDSRGKEF 131 (222)
Q Consensus 52 Y~P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~gatk~~r~~l~~GDlV~ArV~~~~~~~~~~Ls~~~~~~~~~ 131 (222)
.-|..|-+|+|+|-.+..+-..+|-+.-+.++-..- ..+-..++-|.-|.-|++ +++||. .
T Consensus 78 lg~a~gklV~GkIfhiV~~DlYIDFG~KFhcVC~rP------~~n~e~Y~~GaRVrlRl~------DlELs~-------r 138 (173)
T KOG4078|consen 78 LGDAKGKLVIGKIFHIVEEDLYIDFGGKFHCVCKRP------ALNGEAYQKGARVRLRLI------DLELSE-------R 138 (173)
T ss_pred ccCcCCcEEEeeeeeeeccceEEecCCeEEEEEcCc------CcCHHHhhcCceEEEEEc------ChhHhh-------h
Confidence 357889999999999988888889887666655421 234456778888888875 355664 3
Q ss_pred cCcccCCceEEEechhhhh
Q psy230 132 IMGILNDGYLLHTSISLCR 150 (222)
Q Consensus 132 ~~G~L~~G~l~~v~~~~~~ 150 (222)
-+|--.+=.+++..-.++.
T Consensus 139 FLGs~~D~T~LEAdavLlg 157 (173)
T KOG4078|consen 139 FLGSKHDLTLLEADAVLLG 157 (173)
T ss_pred hhcCCccceEEecceeeee
Confidence 3455555555554444443
No 197
>cd05790 S1_Rrp40 S1_Rrp40: Rrp40 S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In Saccharomyces cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".
Probab=31.65 E-value=49 Score=24.15 Aligned_cols=20 Identities=35% Similarity=0.277 Sum_probs=16.8
Q ss_pred ccCCCCCCEEEEEEEEEecc
Q psy230 51 RYVPTRGDLVIGVVTSRVGD 70 (222)
Q Consensus 51 ~Y~P~vGDiVIG~V~~v~~~ 70 (222)
|..-++||+|+++|.++..+
T Consensus 47 rp~L~~GDlV~ArV~~~~~~ 66 (86)
T cd05790 47 RPNLNVGDLVYARVVKANRD 66 (86)
T ss_pred cccCCCCCEEEEEEEecCCC
Confidence 45568999999999999765
No 198
>cd04497 hPOT1_OB1_like hPOT1_OB1_like: A subfamily of OB folds similar to the first OB fold (OB1) of human protection of telomeres 1 protein (hPOT1), the single OB fold of the N-terminal domain of Schizosaccharomyces pombe POT1 (SpPOT1), and the first OB fold of the N-terminal domain of the alpha subunit (OB1Nalpha) of Oxytricha nova telomere end binding protein (OnTEBP). POT1 proteins recognize single-stranded (ss) 3-prime ends of the telomere. A 3-prime ss overhang is conserved in ciliated protozoa, yeast, and mammals. SpPOT1 is essential for telomere maintenance. It binds specifically to the ss G-rich telomeric sequence (GGTTAC) of S. pombe. hPOT1 binds specifically to ss telomeric DNA repeats ending with the sequence GGTTAG. Deletion of the S. pombe pot1+ gene results in a rapid loss of telomere sequences, chromosome mis-segregation and chromosome circularization. hPOT1 is implicated in telomere length regulation. The hPOT1 monomer consists of two closely connected OB folds (OB1-OB
Probab=31.61 E-value=1.5e+02 Score=23.02 Aligned_cols=61 Identities=23% Similarity=0.335 Sum_probs=31.2
Q ss_pred EEEEEEEEec------ceEEEEEC--CCCC---eeeeccccccccccCCcCCCCCCEEEE---EEEecCCCCeeEEEE
Q psy230 60 VIGVVTSRVG------DNYRVDIG--SHDP---AVLSYLAFEGATKKNPPKVETGDVVAG---KLLTANKDMESEMVC 123 (222)
Q Consensus 60 VIG~V~~v~~------~~~~VdI~--~~~~---a~L~~~~f~gatk~~r~~l~~GDlV~A---rV~~~~~~~~~~Ls~ 123 (222)
|||.|++... +-|.+++. .+.. ..|.+.-|. .++..-|.+.+||+|.. +|++.+. ...+.+
T Consensus 19 vigVV~~~~~p~~s~g~d~~~tl~i~D~S~~~~~~l~v~~F~-~~~~~LP~v~~GDVIll~~~kv~~~~g--~~~~~~ 93 (138)
T cd04497 19 VIGVVVDAGPPVRSKGTDYCCTLTITDPSLANSDGLTVKLFR-PNEESLPIVKVGDIILLRRVKIQSYNG--KPQGIS 93 (138)
T ss_pred EEEEEeecCCCcccCCCcEEEEEEEECCCCCCCCcEEEEEEC-CChhhCCCCCCCCEEEEEEEEEEEECC--ceEEEE
Confidence 4555555432 34666653 2211 334433332 23344455699999965 5666653 344443
No 199
>PRK13598 hisB imidazoleglycerol-phosphate dehydratase; Provisional
Probab=31.41 E-value=1.6e+02 Score=24.96 Aligned_cols=44 Identities=11% Similarity=0.019 Sum_probs=35.2
Q ss_pred hhHHHHhhhcCCCcEEEEEEeCCeEEEeeC-C-chhHHHHHHHHHHhh
Q psy230 157 CPLLKQLAKRSRQKMELSIGMNGKIWIRCE-S-FSDTVRVGNLIMSCE 202 (222)
Q Consensus 157 ~~~l~~l~~~~~~~~ei~vG~NG~iWi~~~-~-~~~~~~i~~~i~~~e 202 (222)
.+||+++.+ +..|++-|-..|-+||+.+ . +.-.+.+.+|+++.-
T Consensus 38 DHML~~~a~--H~~~dL~v~a~GDl~vD~HHtvEDvgI~LG~al~~Al 83 (193)
T PRK13598 38 NHMLITLLT--YMNSTATVSATDKLPYDDHHIVEDVAITLGLAIKEAL 83 (193)
T ss_pred HHHHHHHHH--HcCCCeEEEEecCccccCCCchhhhhhhHHHHHHHHh
Confidence 589999999 9999999999999999864 2 233466777777653
No 200
>PF13953 PapC_C: PapC C-terminal domain; PDB: 3L48_E 2XET_A 3RFZ_E 2KT6_A.
Probab=31.31 E-value=23 Score=24.23 Aligned_cols=21 Identities=10% Similarity=0.151 Sum_probs=15.0
Q ss_pred CcEEEEEEeCCeEEEeeCCch
Q psy230 169 QKMELSIGMNGKIWIRCESFS 189 (222)
Q Consensus 169 ~~~ei~vG~NG~iWi~~~~~~ 189 (222)
-..--+||.+|++|++.....
T Consensus 22 g~~~g~Vg~~G~vyl~~~~~~ 42 (68)
T PF13953_consen 22 GNNIGIVGQDGQVYLSGLPPK 42 (68)
T ss_dssp SSEEEEB-GCGEEEEEEE-TC
T ss_pred CCEEEEEcCCCEEEEECCCCC
Confidence 356679999999999986644
No 201
>COG3439 Uncharacterized conserved protein [Function unknown]
Probab=31.15 E-value=2.7e+02 Score=22.13 Aligned_cols=72 Identities=14% Similarity=0.106 Sum_probs=40.5
Q ss_pred eEEEechhhhhhccCCChhHHHHhhhcCCCcEEEEEEe--CCeEEEeeCCchhHHHHHHHHHHhhcCCHHHHHHHHHHHH
Q psy230 140 YLLHTSISLCRKLLNPKCPLLKQLAKRSRQKMELSIGM--NGKIWIRCESFSDTVRVGNLIMSCELLSYEEILNLCESIH 217 (222)
Q Consensus 140 ~l~~v~~~~~~rl~~~~~~~l~~l~~~~~~~~ei~vG~--NG~iWi~~~~~~~~~~i~~~i~~~e~~~~~~~~~~~~~~~ 217 (222)
.+.-+.|.....++..... ++- ..||.|.|=. +|++|+.-.+.. ..+-.......+- .+.+++..+.+.
T Consensus 62 Il~~cnP~~g~~ll~~~p~----~gl--~lPcrv~V~e~~~~~v~~~~~~~~-~l~~~~~~~~~e~--a~~~e~~~~~v~ 132 (137)
T COG3439 62 ILVFCNPKAGTPLLSKNPE----FGL--LLPCRVLVYEDEDGKVRVSYIPIE-ALIEGSKDLLSEV--ADIIENTIEDVI 132 (137)
T ss_pred EEEEcCCcccchhhccChh----hhc--cCCeEEEEEEcCCCeEEEEEechH-HHHhHhhccCHHH--HHHHHHHHHHHH
Confidence 4555677777777754432 333 5799998765 899999887654 2222223332222 444444455555
Q ss_pred HHh
Q psy230 218 IRF 220 (222)
Q Consensus 218 ~~l 220 (222)
+.+
T Consensus 133 k~~ 135 (137)
T COG3439 133 KTL 135 (137)
T ss_pred Hhh
Confidence 443
No 202
>cd05693 S1_Rrp5_repeat_hs1_sc1 S1_Rrp5_repeat_hs1_sc1: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 1 (hs1) and S. cerevisiae S1 repeat 1 (sc1). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=31.08 E-value=53 Score=24.37 Aligned_cols=23 Identities=17% Similarity=0.216 Sum_probs=17.8
Q ss_pred CCCCCEEEEEEEecCCCCeeEEEE
Q psy230 100 VETGDVVAGKLLTANKDMESEMVC 123 (222)
Q Consensus 100 l~~GDlV~ArV~~~~~~~~~~Ls~ 123 (222)
|++||+|.|+|.++.+. .+.+++
T Consensus 1 L~~G~vV~G~V~~v~~~-gl~v~L 23 (100)
T cd05693 1 LSEGMLVLGQVKEITKL-DLVISL 23 (100)
T ss_pred CCCCCEEEEEEEEEcCC-CEEEEC
Confidence 57999999999999754 455554
No 203
>cd05162 PWWP The PWWP domain, named for a conserved Pro-Trp-Trp-Pro motif, is a small domain consisting of 100-150 amino acids. The PWWP domain is found in numerous proteins that are involved in cell division, growth and differentiation. Most PWWP-domain proteins seem to be nuclear, often DNA-binding, proteins that function as transcription factors regulating a variety of developmental processes. The function of the PWWP domain is still not known precisely; however, based on the fact that other regions of PWWP-domain proteins are responsible for nuclear localization and DNA-binding, is likely that the PWWP domain acts as a site for protein-protein binding interactions, influencing chromatin remodeling and thereby regulating transcriptional processes. Some PWWP-domain proteins have been linked to cancer or other diseases; some are known to function as growth factors.
Probab=31.06 E-value=31 Score=24.54 Aligned_cols=15 Identities=27% Similarity=0.306 Sum_probs=12.5
Q ss_pred CCCCCEEEEEEEecC
Q psy230 100 VETGDVVAGKLLTAN 114 (222)
Q Consensus 100 l~~GDlV~ArV~~~~ 114 (222)
|++||+|.|++.+.-
T Consensus 1 f~~GdlVwaK~~g~p 15 (87)
T cd05162 1 FRPGDLVWAKMKGYP 15 (87)
T ss_pred CCCCCEEEEeCCCCC
Confidence 689999999997653
No 204
>cd06080 MUM1_like Mutated melanoma-associated antigen 1 (MUM-1) is a melanoma-associated antigen (MAA). MUM-1 belongs to the mutated or aberrantly expressed type of MAAs, along with antigens such as CDK4, beta-catenin, gp100-in4, p15, and N-acetylglucosaminyltransferase V. It is highly expressed in several types of human cancers. The PWWP domain, named for a conserved Pro-Trp-Trp-Pro motif, is a small domain consisting of 100-150 amino acids. The PWWP domain is found in numerous proteins that are involved in cell division, growth and differentiation. Most PWWP-domain proteins seem to be nuclear, often DNA-binding, proteins that function as transcription factors regulating a variety of developmental processes.
Probab=30.85 E-value=29 Score=25.07 Aligned_cols=15 Identities=27% Similarity=0.251 Sum_probs=12.4
Q ss_pred CCCCCEEEEEEEecC
Q psy230 100 VETGDVVAGKLLTAN 114 (222)
Q Consensus 100 l~~GDlV~ArV~~~~ 114 (222)
|.+||||.|++...-
T Consensus 1 f~~gdlVWaK~~g~P 15 (80)
T cd06080 1 FEKNDLVWAKIQGYP 15 (80)
T ss_pred CCCCCEEEEeCCCCC
Confidence 679999999987654
No 205
>TIGR00062 L27 ribosomal protein L27. Eubacterial, chloroplast, and mitochondrial. Mitochondrial members have an additional C-terminal domain.
Probab=30.85 E-value=74 Score=23.27 Aligned_cols=37 Identities=11% Similarity=0.299 Sum_probs=25.8
Q ss_pred CCCeecCCCCCCeeeCCCeEE-eCCEEEEEEeeEEEEe
Q psy230 2 AGDTLSLNAEPRLILGPGLRR-ESSAILVSQSGILRHA 38 (222)
Q Consensus 2 PGd~l~~~~~~~~~~G~G~y~-~~~~i~as~~G~l~~~ 38 (222)
||+.|..--...|-||.++-. .|..|+|.+.|.|+..
T Consensus 33 ~G~IivRQRGtk~hPG~nVg~GrD~TlfAl~~G~V~f~ 70 (83)
T TIGR00062 33 AGSIIVRQRGTKFHPGNNVGMGKDHTLFALSDGVVKFE 70 (83)
T ss_pred CCcEEEEcCCceECCCCcccccCCCeEEEecceEEEEE
Confidence 666665211134778877754 5789999999999875
No 206
>PF03927 NapD: NapD protein; InterPro: IPR005623 This entry represents NapD, the twin-arginine signal-peptide-binding chaperone for NapA, functioning as an assembly protein for the periplasmic nitrate reductase NapABC. The periplasmic NapABC enzyme likely functions during growth in nitrate-limited environments [].; PDB: 2JSX_A 2PQ4_A.
Probab=30.64 E-value=2e+02 Score=20.39 Aligned_cols=55 Identities=20% Similarity=0.176 Sum_probs=34.6
Q ss_pred ceEEEechhhhhhccCCChhHHHHhhhcCCCcEEEEEE-eCCeEEEeeCCchhHHHHHHHHHHhhc
Q psy230 139 GYLLHTSISLCRKLLNPKCPLLKQLAKRSRQKMELSIG-MNGKIWIRCESFSDTVRVGNLIMSCEL 203 (222)
Q Consensus 139 G~l~~v~~~~~~rl~~~~~~~l~~l~~~~~~~~ei~vG-~NG~iWi~~~~~~~~~~i~~~i~~~e~ 203 (222)
|+++.+.|.... .+.+.|.+ --++||--. -+|++-+-.++.. ...+...+..++.
T Consensus 7 s~vV~~~p~~~~-------~v~~~l~~--~~gvEVh~~~~~GKiVVtiE~~~-~~~~~~~~~~i~~ 62 (79)
T PF03927_consen 7 SLVVHARPERLE-------EVAEALAA--IPGVEVHAVDEDGKIVVTIEAES-SEEEVDLIDAINA 62 (79)
T ss_dssp EEEEEE-CCCHH-------HHHHHHCC--STTEEEEEEETTTEEEEEEEESS-HHHHHHHHHHHCC
T ss_pred EEEEEECchhHH-------HHHHHHHc--CCCcEEEeeCCCCeEEEEEEeCC-hHHHHHHHHHHHc
Confidence 667777776553 56777877 789999655 4499998765442 3444444444443
No 207
>PF04085 MreC: rod shape-determining protein MreC; InterPro: IPR007221 MreC (murein formation C) is involved in the rod shape determination in Escherichia coli, and more generally in cell shape determination of bacteria whether or not they are rod-shaped.; GO: 0008360 regulation of cell shape; PDB: 2J5U_B 2QF4_B 2QF5_A.
Probab=30.57 E-value=2.1e+02 Score=22.69 Aligned_cols=30 Identities=23% Similarity=0.185 Sum_probs=19.5
Q ss_pred CCEEEEEEEEEecceEEEEECCCCCeeeec
Q psy230 57 GDLVIGVVTSRVGDNYRVDIGSHDPAVLSY 86 (222)
Q Consensus 57 GDiVIG~V~~v~~~~~~VdI~~~~~a~L~~ 86 (222)
++-++|+|+++.+.+.+|..-......++.
T Consensus 33 ~~glVG~V~~V~~~~S~V~li~d~~~~v~v 62 (152)
T PF04085_consen 33 GGGLVGRVTEVGPNTSRVLLITDPNSRVSV 62 (152)
T ss_dssp TTEEEEEEEEE-SS-EEEEETTSSBCEEEE
T ss_pred CCCcEEEEEEECCCEEEEEEEeCCCceEEE
Confidence 344789999999998888876544444443
No 208
>PF02216 B: B domain; InterPro: IPR003132 This entry represents the immunoglobulin-binding domain found in the Staphylococcus aureus virulence factor protein A (SpA). Protein A contains five highly homologous Ig-binding domains in tandem (designated domains E, D, A, B and C), which share a common structure consisting of three helices in a closed left-handed twist. Protein A can exist in both secreted and membrane-bound forms, and has two distinct Ig-binding activities: each domain can bind Fc-gamma (the constant region of IgG involved in effector functions) and Fab (the Ig fragment responsible for antigen recognition) [].; GO: 0019865 immunoglobulin binding, 0009405 pathogenesis; PDB: 1EDL_A 1EDI_A 1EDJ_A 1EDK_A 2B88_A 2B87_A 2B89_A 1FC2_C 1DEE_H 1ZXG_A ....
Probab=30.41 E-value=55 Score=21.90 Aligned_cols=21 Identities=14% Similarity=0.110 Sum_probs=16.3
Q ss_pred HHHhhcCCHHHHHHHHHHHHH
Q psy230 198 IMSCELLSYEEILNLCESIHI 218 (222)
Q Consensus 198 i~~~e~~~~~~~~~~~~~~~~ 218 (222)
|...+.++++|..+++++++.
T Consensus 16 vl~~~nLteeQrn~yI~~lKd 36 (54)
T PF02216_consen 16 VLHMPNLTEEQRNGYIQSLKD 36 (54)
T ss_dssp HHCSTTS-HHHHHHHHHHHHH
T ss_pred HHcCCCcCHHHHHhHHHHHhh
Confidence 345567889999999999875
No 209
>KOG0147|consensus
Probab=30.23 E-value=89 Score=30.45 Aligned_cols=40 Identities=15% Similarity=0.306 Sum_probs=31.7
Q ss_pred hHHHHhhhcCCC-cEEEEEEeC--CeEEEeeCCchhHHHHHHHHH
Q psy230 158 PLLKQLAKRSRQ-KMELSIGMN--GKIWIRCESFSDTVRVGNLIM 199 (222)
Q Consensus 158 ~~l~~l~~~~~~-~~ei~vG~N--G~iWi~~~~~~~~~~i~~~i~ 199 (222)
.+++..++ ++ -+.|.|..| |.|+|+|++...+..+.+||-
T Consensus 469 dV~Eec~k--~g~v~hi~vd~ns~g~VYvrc~s~~~A~~a~~alh 511 (549)
T KOG0147|consen 469 DVIEECGK--HGKVCHIFVDKNSAGCVYVRCPSAEAAGTAVKALH 511 (549)
T ss_pred HHHHHHHh--cCCeeEEEEccCCCceEEEecCcHHHHHHHHHHHh
Confidence 46666665 44 578888888 899999999988888888774
No 210
>cd04485 DnaE_OBF DnaE_OBF: A subfamily of OB folds corresponding to the C-terminal OB-fold nucleic acid binding domain of Thermus aquaticus and Escherichia coli type C replicative DNA polymerase III alpha subunit (DnaE). The DNA polymerase holoenzyme of E. coli contains two copies of this replicative polymerase, each of which copies a different DNA strand. This group also contains Bacillus subtilis DnaE. Replication in B. subtilis and Staphylococcus aureus requires two different type C polymerases, polC and DnaE, both of which are thought to be included in the DNA polymerase holoenzyme. At the B. subtilis replication fork, polC appears to be involved in leading strand synthesis and DnaE in lagging strand synthesis.
Probab=29.83 E-value=1.4e+02 Score=19.85 Aligned_cols=63 Identities=14% Similarity=0.107 Sum_probs=34.1
Q ss_pred EEEEEEEEec-------ceEEEEECCCCCeeeeccccccccccCCcCCCCCCEEEEEEEecCCCCeeEEEE
Q psy230 60 VIGVVTSRVG-------DNYRVDIGSHDPAVLSYLAFEGATKKNPPKVETGDVVAGKLLTANKDMESEMVC 123 (222)
Q Consensus 60 VIG~V~~v~~-------~~~~VdI~~~~~a~L~~~~f~gatk~~r~~l~~GDlV~ArV~~~~~~~~~~Ls~ 123 (222)
+.|.|+++.. .++.+.+.. ..+.+.+..|+..-++.++.+.+|..+...-.--.....++|++
T Consensus 2 i~g~v~~~~~~~~k~g~~~~~~~l~D-~tg~~~~~~f~~~~~~~~~~l~~g~~v~v~G~v~~~~~~~~l~~ 71 (84)
T cd04485 2 VAGLVTSVRRRRTKKGKRMAFVTLED-LTGSIEVVVFPETYEKYRDLLKEDALLLVEGKVERRDGGLRLIA 71 (84)
T ss_pred EEEEEEEeEEEEcCCCCEEEEEEEEe-CCCeEEEEECHHHHHHHHHHhcCCCEEEEEEEEEecCCceEEEe
Confidence 5566655321 135555543 34556655665443456778999998765533222223456665
No 211
>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF.
Probab=29.82 E-value=1.8e+02 Score=28.16 Aligned_cols=71 Identities=7% Similarity=-0.001 Sum_probs=55.3
Q ss_pred hhhhccCCChhHHHHhhhcCCCcEEEEEEeCC-eEEEeeCCchhHHHHHHHHHHhh---cCCHHHHHHHHHHHHHHh
Q psy230 148 LCRKLLNPKCPLLKQLAKRSRQKMELSIGMNG-KIWIRCESFSDTVRVGNLIMSCE---LLSYEEILNLCESIHIRF 220 (222)
Q Consensus 148 ~~~rl~~~~~~~l~~l~~~~~~~~ei~vG~NG-~iWi~~~~~~~~~~i~~~i~~~e---~~~~~~~~~~~~~~~~~l 220 (222)
+--|++|+.+.-+++|.. .|++++||.-.- -|-++|-||-.-..+-.+|.+.- +..++.++.++++..+.+
T Consensus 215 ~kgriigreGrnir~~e~--~tgvd~iiddtp~~v~ls~fdp~rreia~~~l~~li~dgrihp~riee~~~~~~~~~ 289 (514)
T TIGR03319 215 MKGRIIGREGRNIRALET--LTGVDLIIDDTPEAVILSGFDPVRREIARMALEKLIQDGRIHPARIEEMVEKATKEV 289 (514)
T ss_pred hhccccCCCcchHHHHHH--HhCceEEEcCCCCeEEecCCchHHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHH
Confidence 344678999999999988 999999998764 78889988876667777776654 466888888888776654
No 212
>PF14444 S1-like: S1-like
Probab=29.79 E-value=54 Score=22.36 Aligned_cols=18 Identities=28% Similarity=0.324 Sum_probs=14.2
Q ss_pred cccCCCCCCEEEEEEEEE
Q psy230 50 RRYVPTRGDLVIGVVTSR 67 (222)
Q Consensus 50 ~~Y~P~vGDiVIG~V~~v 67 (222)
+-++|++||.|+..-+.-
T Consensus 30 ~G~~P~vGdrV~v~A~~n 47 (58)
T PF14444_consen 30 KGNVPKVGDRVLVEAIYN 47 (58)
T ss_pred ecCCCccCCEEEEEEEeC
Confidence 357999999999876543
No 213
>TIGR00074 hypC_hupF hydrogenase assembly chaperone HypC/HupF. An additional proposed function is to shuttle the iron atom that has been liganded at the HypC/HypD complex to the precursor of the large hydrogenase (HycE) subunit. PubMed:12441107.
Probab=29.59 E-value=1e+02 Score=21.97 Aligned_cols=39 Identities=21% Similarity=0.181 Sum_probs=25.5
Q ss_pred EEEEEEecceEEEEECCC-CCeeeeccccccccccCCcCCCCCCEEEEEE
Q psy230 62 GVVTSRVGDNYRVDIGSH-DPAVLSYLAFEGATKKNPPKVETGDVVAGKL 110 (222)
Q Consensus 62 G~V~~v~~~~~~VdI~~~-~~a~L~~~~f~gatk~~r~~l~~GDlV~ArV 110 (222)
|+|.++.++...||.++. ....|.+. +..++||.|.-..
T Consensus 7 ~~V~~i~~~~A~v~~~G~~~~v~l~lv----------~~~~vGD~VLVH~ 46 (76)
T TIGR00074 7 GQVVEIDENIALVEFCGIKRDVSLDLV----------GEVKVGDYVLVHV 46 (76)
T ss_pred eEEEEEcCCEEEEEcCCeEEEEEEEee----------CCCCCCCEEEEec
Confidence 788889888889888752 12222221 3477999887653
No 214
>KOG0207|consensus
Probab=29.52 E-value=49 Score=34.28 Aligned_cols=53 Identities=21% Similarity=0.355 Sum_probs=41.0
Q ss_pred CCcEEE---EEEeCCeEEEeeCCchhHHHHHHHHHHhhc--CCHHHHHHHHHHHHHHh
Q psy230 168 RQKMEL---SIGMNGKIWIRCESFSDTVRVGNLIMSCEL--LSYEEILNLCESIHIRF 220 (222)
Q Consensus 168 ~~~~ei---~vG~NG~iWi~~~~~~~~~~i~~~i~~~e~--~~~~~~~~~~~~~~~~l 220 (222)
+.+..+ .+-.||++.++....-..-.+++.++..|+ ++.+-++++.|++..++
T Consensus 439 k~gs~ViaGsiN~nG~l~VkaT~~g~dttla~IvkLVEEAQ~sKapiQq~aDkia~yF 496 (951)
T KOG0207|consen 439 KKGSTVIAGSINLNGTLLVKATKVGGDTTLAQIVKLVEEAQLSKAPIQQLADKIAGYF 496 (951)
T ss_pred CCCCeeeeeeecCCceEEEEEEeccccchHHHHHHHHHHHHcccchHHHHHHHhhhcC
Confidence 445555 466899999998766656677777887774 78999999999998764
No 215
>PF15533 Toxin_54: Putative toxin 54
Probab=29.06 E-value=63 Score=22.54 Aligned_cols=29 Identities=28% Similarity=0.424 Sum_probs=21.2
Q ss_pred hHHHHhhhcCCCcEEEEEEeCCeEEEeeC
Q psy230 158 PLLKQLAKRSRQKMELSIGMNGKIWIRCE 186 (222)
Q Consensus 158 ~~l~~l~~~~~~~~ei~vG~NG~iWi~~~ 186 (222)
+=|+.|+.+-...++|-.-.||.|||...
T Consensus 24 H~lK~~g~~~~s~yDlykD~~gni~ik~K 52 (66)
T PF15533_consen 24 HELKRLGKKNISNYDLYKDREGNIYIKPK 52 (66)
T ss_pred HHHHhhccCCcccceeEEcCCCCEEEecC
Confidence 34444554336799999999999999753
No 216
>cd04478 RPA2_DBD_D RPA2_DBD_D: A subfamily of OB folds corresponding to the OB fold of the central ssDNA-binding domain (DBD)-D of human RPA2 (also called RPA32). RPA2 is a subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B; RPA2 DBD-D is a weak ssDNA-binding domain. RPA2 DBD-D is also involved in trimerization. The ssDNA binding mechanism is believed to be multistep and to involve conformational change. N-terminal to human RPA2 DBD-D is a domain containing all the known phosphorylation sites of RPA. Human RPA2 is phosphorylated in a cell cycle dependent manner in response to DNA dam
Probab=28.96 E-value=2.1e+02 Score=20.19 Aligned_cols=61 Identities=15% Similarity=0.181 Sum_probs=37.2
Q ss_pred EEEEEEEEe--cceEEEEECCCCCeeeeccccccccc---cCCcCCCCCCEEEEE--EEecCCCCeeEEEE
Q psy230 60 VIGVVTSRV--GDNYRVDIGSHDPAVLSYLAFEGATK---KNPPKVETGDVVAGK--LLTANKDMESEMVC 123 (222)
Q Consensus 60 VIG~V~~v~--~~~~~VdI~~~~~a~L~~~~f~gatk---~~r~~l~~GDlV~Ar--V~~~~~~~~~~Ls~ 123 (222)
++|.|.++. +.++...+.... +.+....+..... ...+.+.+|++|..+ +.... ...+|.+
T Consensus 4 ~vG~V~~~~~~~~~~~~tL~D~T-G~I~~~~W~~~~~~~~~~~~~~~~g~~v~v~G~v~~~~--g~~ql~i 71 (95)
T cd04478 4 LVGVVRNVEEQSTNITYTIDDGT-GTIEVRQWLDDDNDDSSEVEPIEEGTYVRVFGNLKSFQ--GKKSIMA 71 (95)
T ss_pred EEEEEEeeeEcccEEEEEEECCC-CcEEEEEeCCCCCcccccccccccCCEEEEEEEEcccC--CeeEEEE
Confidence 689999986 457777787633 4555443332222 467789999988554 43333 3455554
No 217
>TIGR00182 plsX fatty acid/phospholipid synthesis protein PlsX. This protein of fatty acid/phospholipid biosynthesis, called PlsX after the member in Streptococcus pneumoniae, is proposed to be a phosphate acyltransferase that partners with PlsY (TIGR00023) in a two-step 1-acylglycerol-3-phosphate biosynthesis pathway alternative to the one-step PlsB (EC 2.3.1.15) pathway.
Probab=28.70 E-value=1.2e+02 Score=27.43 Aligned_cols=57 Identities=18% Similarity=0.193 Sum_probs=37.4
Q ss_pred hHHHHhhhcCCCcEE-----EEEEeCCeEEEeeCCchhHHHHHHHHHHhhcCCHHHHHHHHHHHHHHh
Q psy230 158 PLLKQLAKRSRQKME-----LSIGMNGKIWIRCESFSDTVRVGNLIMSCELLSYEEILNLCESIHIRF 220 (222)
Q Consensus 158 ~~l~~l~~~~~~~~e-----i~vG~NG~iWi~~~~~~~~~~i~~~i~~~e~~~~~~~~~~~~~~~~~l 220 (222)
..|+.+++ ++.++ ..+|.||-+.+.-.+. +...+.|||+.+..+-+.+ +.+++.+.|
T Consensus 257 ~~l~~~~~--~~d~~~~gGa~llG~~g~vvk~HG~s-~~~a~~~ai~~a~~~~~~~---~~~~i~~~~ 318 (322)
T TIGR00182 257 PILKSLKQ--KFDYANYGGAVLFGLNKLVIKSHGSS-DSRAFFSAIRQAHEAVKSQ---VINRIKSSL 318 (322)
T ss_pred HHHHHHHH--hcCccccCCeEEecCCceEEEEcCCC-CHHHHHHHHHHHHHHHHhC---HHHHHHHHH
Confidence 34556666 44444 7999999887764444 5789999999988755444 444444433
No 218
>cd04474 RPA1_DBD_A RPA1_DBD_A: A subfamily of OB folds corresponding to the second OB fold, the ssDNA-binding domain (DBD)-A, of human RPA1 (also called RPA70). RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-A, RPA1 contains three other OB folds: DBD-B, DBD-C, and RPA1N. The major DNA binding activity of human RPA (hRPA) and Saccharomyces cerevisiae RPA (ScRPA) is associated with DBD-A and DBD-B of RPA1. RPA1 DBD-C is involved in trimerization. The ssDNA-binding mechanism is believed to be multistep and to involve conformational change. Although ScRPA and the hRPA have similar ssDNA-binding properties, they differ funct
Probab=28.58 E-value=79 Score=23.38 Aligned_cols=35 Identities=23% Similarity=0.193 Sum_probs=16.6
Q ss_pred EEEECCCCCeeeeccccccccccCCcCCCCCCEEE
Q psy230 73 RVDIGSHDPAVLSYLAFEGATKKNPPKVETGDVVA 107 (222)
Q Consensus 73 ~VdI~~~~~a~L~~~~f~gatk~~r~~l~~GDlV~ 107 (222)
.++|.....+.+....|.....+..+.|++|++++
T Consensus 38 ~~~l~De~~~~I~~t~~~~~~~~f~~~l~eG~vy~ 72 (104)
T cd04474 38 SFDLLDEDGGEIRATFFNDAVDKFYDLLEVGKVYY 72 (104)
T ss_pred EEEEEECCCCEEEEEEehHHHHHhhcccccccEEE
Confidence 44444433444444444444445555556665553
No 219
>COG3822 ABC-type sugar transport system, auxiliary component [General function prediction only]
Probab=28.08 E-value=1.2e+02 Score=25.82 Aligned_cols=43 Identities=14% Similarity=0.118 Sum_probs=31.1
Q ss_pred EEEeeEEEEecCcEEEEEcc-ccccCCCCCCEEEEEEEEEecce
Q psy230 29 VSQSGILRHAKPFTYYVDYI-QRRYVPTRGDLVIGVVTSRVGDN 71 (222)
Q Consensus 29 as~~G~l~~~~~~~v~V~~~-~~~Y~P~vGDiVIG~V~~v~~~~ 71 (222)
-+.-|.++.++...+.+.|. .+.+-.+.|++++|.|..++.|.
T Consensus 149 ~~ag~~lkL~PGesitL~Pg~~HsFwae~g~vlvgEvSsvndD~ 192 (225)
T COG3822 149 HTAGSQLKLSPGESITLPPGLYHSFWAEEGGVLVGEVSSVNDDL 192 (225)
T ss_pred eccceeEEECCCCcEecCCCceeeeeecCCcEEEEEEeeccCcc
Confidence 33444566665566777774 45678899999999999998763
No 220
>TIGR00617 rpa1 replication factor-a protein 1 (rpa1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=27.95 E-value=1.4e+02 Score=29.43 Aligned_cols=64 Identities=25% Similarity=0.332 Sum_probs=46.3
Q ss_pred EEEEEEEEEe-----------cceEEEEECCCCCeeeeccccccccccCCcCCCCCCEE---EEEEEecCC-----CCee
Q psy230 59 LVIGVVTSRV-----------GDNYRVDIGSHDPAVLSYLAFEGATKKNPPKVETGDVV---AGKLLTANK-----DMES 119 (222)
Q Consensus 59 iVIG~V~~v~-----------~~~~~VdI~~~~~a~L~~~~f~gatk~~r~~l~~GDlV---~ArV~~~~~-----~~~~ 119 (222)
.+-|+|+.+. +..+.++|.. ..+.+....|.....+..+.|++|++. .++|..+++ ..++
T Consensus 194 tIkaRV~~Ks~ir~~~~~~gegkvfsv~L~D-egg~Irat~f~~~~dkf~~~l~eG~VY~Is~~~Vk~an~~y~~~~~~y 272 (608)
T TIGR00617 194 TIKARVTNKSEIRTWSNARGEGKLFNVELLD-ESGEIRATAFNEQADKFYDIIQEGKVYYISKGSLKPANKQFTNLGNDY 272 (608)
T ss_pred EEEEEEEeccccceecCCCCCceeeEEEEec-CCCeEEEEECchHHHHHhhhcccCCEEEECceEEEEccccccCCCCCE
Confidence 5678898754 2357777776 667778777877778889999999999 467776643 2356
Q ss_pred EEEE
Q psy230 120 EMVC 123 (222)
Q Consensus 120 ~Ls~ 123 (222)
+|+.
T Consensus 273 ei~f 276 (608)
T TIGR00617 273 EMTL 276 (608)
T ss_pred EEEE
Confidence 7764
No 221
>COG3602 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=27.63 E-value=47 Score=25.93 Aligned_cols=18 Identities=22% Similarity=0.287 Sum_probs=16.5
Q ss_pred ccCCcCCCCCCEEEEEEE
Q psy230 94 KKNPPKVETGDVVAGKLL 111 (222)
Q Consensus 94 k~~r~~l~~GDlV~ArV~ 111 (222)
..|.|.+..||.|+|.|.
T Consensus 12 ~smtPeL~~G~yVfcT~~ 29 (134)
T COG3602 12 ASMTPELLDGDYVFCTVA 29 (134)
T ss_pred HhcCccccCCceEEEEec
Confidence 479999999999999997
No 222
>PF00855 PWWP: PWWP domain; InterPro: IPR000313 Upon characterisation of WHSC1, a gene mapping to the Wolf-Hirschhornsyndrome critical region and at its C terminus similar to the Drosophila melanogaster ASH1/trithorax group proteins, a novel protein domain designated PWWP domain was identified []. The PWWP domain is named after a conserved Pro-Trp-Trp-Pro motif. It is present in proteins of nuclear origin and plays a role in cell growth and differentiation. Due to its position, the composition of amino acids close to the PWWP motif and the pattern of other domains present it has been suggested that the domain is involved in protein-protein interactions [].; PDB: 3LYI_B 2L89_A 2NLU_A 1RI0_A 1KHC_A 3QKJ_C 2DAQ_A 1N27_A 3PFS_B 3QJ6_A ....
Probab=27.11 E-value=39 Score=23.62 Aligned_cols=13 Identities=38% Similarity=0.463 Sum_probs=10.2
Q ss_pred CCCCCEEEEEEEe
Q psy230 100 VETGDVVAGKLLT 112 (222)
Q Consensus 100 l~~GDlV~ArV~~ 112 (222)
|.+||+|-||+..
T Consensus 1 f~~GdlVWaK~~g 13 (86)
T PF00855_consen 1 FRPGDLVWAKLKG 13 (86)
T ss_dssp -STTEEEEEEETT
T ss_pred CCCCCEEEEEeCC
Confidence 6799999999843
No 223
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=26.39 E-value=1.1e+02 Score=25.29 Aligned_cols=32 Identities=25% Similarity=0.240 Sum_probs=26.8
Q ss_pred CCCCCEEEEEEEEEecceEEEEECCCCCeeeec
Q psy230 54 PTRGDLVIGVVTSRVGDNYRVDIGSHDPAVLSY 86 (222)
Q Consensus 54 P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~ 86 (222)
-++||+|.++|.++. ..+.+.+-.+..+.|..
T Consensus 119 ~~~GD~V~akV~~i~-~~i~LS~k~~~lGvv~a 150 (189)
T PRK09521 119 FKIGDIVRAKVISYT-DPLQLSTKGKDLGVIYA 150 (189)
T ss_pred cCCCCEEEEEEEecC-CcEEEEEecCCceEEEE
Confidence 388999999999999 78888887777777764
No 224
>PF07385 DUF1498: Protein of unknown function (DUF1498); InterPro: IPR010864 This family consists of several hypothetical bacterial proteins of around 225 residues in length. The function of this family is unknown.; PDB: 3MPB_B 3KMH_A.
Probab=26.37 E-value=1e+02 Score=26.67 Aligned_cols=51 Identities=18% Similarity=0.097 Sum_probs=28.8
Q ss_pred eEEeCCEEEEEEee-EEEEecCcEEEEEcc-ccccCCCCCCEEEEEEEEEecc
Q psy230 20 LRRESSAILVSQSG-ILRHAKPFTYYVDYI-QRRYVPTRGDLVIGVVTSRVGD 70 (222)
Q Consensus 20 ~y~~~~~i~as~~G-~l~~~~~~~v~V~~~-~~~Y~P~vGDiVIG~V~~v~~~ 70 (222)
+...||..+.-.+| .++......+.+.|. -+++-.+.|+++||.|..++.|
T Consensus 140 ~V~~DG~~~t~~aG~~l~L~PGESiTL~Pg~yH~Fw~e~g~vLigEVStvNDD 192 (225)
T PF07385_consen 140 TVPVDGIRRTVPAGTQLRLNPGESITLPPGIYHWFWGEGGDVLIGEVSTVNDD 192 (225)
T ss_dssp EEEETTEEEEE-TT-EEEE-TT-EEEE-TTEEEEEEE-TTSEEEEEEEE---T
T ss_pred EEecCCcEEEecCCceEEeCCCCeEeeCCCCeeeEEecCCCEEEEeeecccCC
Confidence 33445554444444 345555566778874 4678889999999999999875
No 225
>cd04451 S1_IF1 S1_IF1: Translation Initiation Factor IF1, S1-like RNA-binding domain. IF1 contains an S1-like RNA-binding domain, which is found in a wide variety of RNA-associated proteins. Translation initiation includes a number of interrelated steps preceding the formation of the first peptide bond. In Escherichia coli, the initiation mechanism requires, in addition to mRNA, fMet-tRNA, and ribosomal subunits, the presence of three additional proteins (initiation factors IF1, IF2, and IF3) and at least one GTP molecule. The three initiation factors influence both the kinetics and the stability of ternary complex formation. IF1 is the smallest of the three factors. IF1 enhances the rate of 70S ribosome subunit association and dissociation and the interaction of 30S ribosomal subunit with IF2 and IF3. It stimulates 30S complex formation. In addition, by binding to the A-site of the 30S ribosomal subunit, IF1 may contribute to the fidelity of the selection of the initiation site of th
Probab=25.85 E-value=2.1e+02 Score=19.06 Aligned_cols=51 Identities=24% Similarity=0.288 Sum_probs=30.4
Q ss_pred EEEEEEEEec-ceEEEEECCCCCeeeeccccccccccCCcCCCCCCEEEEEEEec
Q psy230 60 VIGVVTSRVG-DNYRVDIGSHDPAVLSYLAFEGATKKNPPKVETGDVVAGKLLTA 113 (222)
Q Consensus 60 VIG~V~~v~~-~~~~VdI~~~~~a~L~~~~f~gatk~~r~~l~~GDlV~ArV~~~ 113 (222)
.-|+|++..+ .+|.|..... .... -...|..++.+..+.+||.|..+....
T Consensus 3 ~~G~Vi~~~~g~~~~V~~~~g--~~~~-c~~rGklr~~~~~~~vGD~V~~~~~~~ 54 (64)
T cd04451 3 MEGVVTEALPNAMFRVELENG--HEVL-AHISGKMRMNYIRILPGDRVKVELSPY 54 (64)
T ss_pred EEEEEEEEeCCCEEEEEeCCC--CEEE-EEECceeecCCcccCCCCEEEEEEeec
Confidence 3588888884 8888754211 1111 123454444455588999998886543
No 226
>COG1107 Archaea-specific RecJ-like exonuclease, contains DnaJ-type Zn finger domain [DNA replication, recombination, and repair]
Probab=25.77 E-value=2.2e+02 Score=28.43 Aligned_cols=44 Identities=25% Similarity=0.413 Sum_probs=32.6
Q ss_pred CCCeeeeccccccccccCCcCCCCCCEEE--EEEEecCCCCeeEEEEe
Q psy230 79 HDPAVLSYLAFEGATKKNPPKVETGDVVA--GKLLTANKDMESEMVCV 124 (222)
Q Consensus 79 ~~~a~L~~~~f~gatk~~r~~l~~GDlV~--ArV~~~~~~~~~~Ls~~ 124 (222)
-..+..+.-+|+.+-.+-.|.+++||+|. .+|. .+++..++.+.
T Consensus 238 Detg~i~aAAFe~aGvRAyP~IevGdiV~ViG~V~--~r~g~lQiE~~ 283 (715)
T COG1107 238 DETGAIWAAAFEEAGVRAYPEIEVGDIVEVIGEVT--RRDGRLQIEIE 283 (715)
T ss_pred cCCCceehhhhccCCcccCCCCCCCceEEEEEEEe--ecCCcEEEeeh
Confidence 34677777889988899999999999985 3443 34566777764
No 227
>KOG2916|consensus
Probab=25.68 E-value=60 Score=28.97 Aligned_cols=73 Identities=11% Similarity=0.060 Sum_probs=48.7
Q ss_pred CCCCCCEEEEEEEEEecceEEEEECC--CCCeeeeccccc-cccccCCcCCCCCCEEEEEEEecCCCCe-eEEEEec
Q psy230 53 VPTRGDLVIGVVTSRVGDNYRVDIGS--HDPAVLSYLAFE-GATKKNPPKVETGDVVAGKLLTANKDME-SEMVCVD 125 (222)
Q Consensus 53 ~P~vGDiVIG~V~~v~~~~~~VdI~~--~~~a~L~~~~f~-gatk~~r~~l~~GDlV~ArV~~~~~~~~-~~Ls~~~ 125 (222)
.|.++|+|++.|..+....+.|.+.- .-.|.+-++.+. -..+......++|-.=.+-|+.+++..- +.||-..
T Consensus 13 yPev~e~VmvnV~sIaemGayv~LlEYnniEGmiLlsELSrRRIRSI~klirVGr~E~vvVlrVDkekGYIDLSkrr 89 (304)
T KOG2916|consen 13 YPEVEEIVMVNVRSIAEMGAYVKLLEYNNIEGMILLSELSRRRIRSIQKLIRVGRNEPVVVLRVDKEKGYIDLSKRR 89 (304)
T ss_pred CCCcccEEEEEeeEehhccceEeeeecCCcccchhhhHHHHHHHHHHHHHHhcCCcceEEEEEEcCCCCceechhcc
Confidence 59999999999999998888777643 112222222221 1234455678899888888998887644 5777644
No 228
>PRK12704 phosphodiesterase; Provisional
Probab=25.26 E-value=1.5e+02 Score=28.75 Aligned_cols=71 Identities=7% Similarity=0.003 Sum_probs=48.4
Q ss_pred hhhhccCCChhHHHHhhhcCCCcEEEEEEeC-CeEEEeeCCchhHHHHHHHHHHhh---cCCHHHHHHHHHHHHHHh
Q psy230 148 LCRKLLNPKCPLLKQLAKRSRQKMELSIGMN-GKIWIRCESFSDTVRVGNLIMSCE---LLSYEEILNLCESIHIRF 220 (222)
Q Consensus 148 ~~~rl~~~~~~~l~~l~~~~~~~~ei~vG~N-G~iWi~~~~~~~~~~i~~~i~~~e---~~~~~~~~~~~~~~~~~l 220 (222)
+--|++|+.+.-+++|.. .|++++||.-. +.|.++|-|+-.-..+-.++...- ...+..++.++.++.+.+
T Consensus 221 mkgriigreGrnir~~e~--~tgvd~iiddtp~~v~ls~~~~~rre~a~~~l~~l~~dg~i~P~~iee~~~~~~~~~ 295 (520)
T PRK12704 221 MKGRIIGREGRNIRALET--LTGVDLIIDDTPEAVILSGFDPIRREIARLALEKLVQDGRIHPARIEEMVEKARKEV 295 (520)
T ss_pred hhcceeCCCcchHHHHHH--HhCCeEEEcCCCCeEEEecCChhhHHHHHHHHHHHHhcCCcCCCCHHHHHHHHHHHH
Confidence 344678999999999988 99999999887 788889988765444555554442 233445555555554433
No 229
>PRK15491 replication factor A; Provisional
Probab=25.18 E-value=3.3e+02 Score=25.17 Aligned_cols=63 Identities=24% Similarity=0.302 Sum_probs=35.4
Q ss_pred EEEEEEEEec-ceEEEEECC----------CCCeeeeccccccccccCCcCCCCCCEEEE---EEEecCCCCeeEEEE
Q psy230 60 VIGVVTSRVG-DNYRVDIGS----------HDPAVLSYLAFEGATKKNPPKVETGDVVAG---KLLTANKDMESEMVC 123 (222)
Q Consensus 60 VIG~V~~v~~-~~~~VdI~~----------~~~a~L~~~~f~gatk~~r~~l~~GDlV~A---rV~~~~~~~~~~Ls~ 123 (222)
|.|+|+++.+ ..|.-.=+. ...+.+++..|....... +.|.+||.|+- .+..-+-.+.++|++
T Consensus 181 I~g~V~~~~~~r~~~~~~G~~~~v~~~~l~DetG~Ir~t~W~~~a~~~-~~l~~Gd~V~i~~~~~r~~~~~g~~El~~ 257 (374)
T PRK15491 181 IVGKVLDISDVRTFQKKDGSQGRVRNITIGDETGKIRVTLWDGKTDLA-DKLENGDSVEIINGYARTNNYSQEVEIQI 257 (374)
T ss_pred EEEEEEEccCceEEEecCCCeEEEEEEEEECCCCeEEEEEecchhccc-ccCCCCCEEEEEeceEEEeccCCCEEEEe
Confidence 5999999975 555432121 234445555554332333 67999999863 332111224788886
No 230
>PF09953 DUF2187: Uncharacterized protein conserved in bacteria (DUF2187); InterPro: IPR018690 This family consists of various hypothetical bacterial proteins with known function. It includes the uncharacterised YkvS protein from Bacillus subtilis.
Probab=24.93 E-value=1.5e+02 Score=20.09 Aligned_cols=19 Identities=26% Similarity=0.309 Sum_probs=17.4
Q ss_pred EEEEEEEEecceEEEEECC
Q psy230 60 VIGVVTSRVGDNYRVDIGS 78 (222)
Q Consensus 60 VIG~V~~v~~~~~~VdI~~ 78 (222)
.-|+|..+..++..|||..
T Consensus 16 ~~G~V~kv~eNSVIVdIT~ 34 (57)
T PF09953_consen 16 FTGIVEKVYENSVIVDITI 34 (57)
T ss_pred cEEEEEEEecCcEEEEEEe
Confidence 5899999999999999976
No 231
>PRK05331 putative phosphate acyltransferase; Provisional
Probab=24.42 E-value=2.2e+02 Score=25.93 Aligned_cols=57 Identities=28% Similarity=0.299 Sum_probs=38.5
Q ss_pred hHHHHhhhcCCCcEE-----EEEEeCCeEEEeeCCchhHHHHHHHHHHhhcCCHHHHHHHHHHHHHHh
Q psy230 158 PLLKQLAKRSRQKME-----LSIGMNGKIWIRCESFSDTVRVGNLIMSCELLSYEEILNLCESIHIRF 220 (222)
Q Consensus 158 ~~l~~l~~~~~~~~e-----i~vG~NG~iWi~~~~~~~~~~i~~~i~~~e~~~~~~~~~~~~~~~~~l 220 (222)
..|+.+++ .+.++ +.+|.||-+.+.-.+. +...+.|||+.+..+-+ .++.+++.+.|
T Consensus 270 ~~l~~~~~--~~d~~~~gGa~llG~~g~vik~HG~s-~~~a~~~ai~~a~~~~~---~~~~~~i~~~l 331 (334)
T PRK05331 270 PALKRLKK--KLDPREYGGAVLLGLNGIVIKSHGSS-DAKAFANAIRQAKEAVE---NNVPERIAERL 331 (334)
T ss_pred HHHHHHHH--hCCccccCCeeEccCCceEEEECCCC-ChHHHHHHHHHHHHHHH---hCHHHHHHHHH
Confidence 34566666 44444 7999999887754444 57899999999887444 34455555544
No 232
>PF11763 DIPSY: Cell-wall adhesin ligand-binding C-terminal; InterPro: IPR021746 The DIPSY domain is characterised by the distinctive D*I*PSY motif at the very C terminus of yeast cell-wall glycoproteins. It appears not to be conserved in any other species, however. In fungi, cell adhesion is required for flocculation, mating and virulence, and is mediated by covalently bound cell wall proteins termed adhesins. Map4, an adhesin required for mating in Schizosaccharomyces pombe, is N-glycosylated and O-glycosylated, and is an endogenous substrate for the mannosyl transferase Oma4p. Map4 has a modular structure with an N-terminal signal peptide, a serine and threonine (S/T)-rich domain that includes nine repeats of 36 amino acids (rich in serine and threonine residues, but lacking glutamines), and a C-terminal DIPSY domain with no glycosyl-phosphatidyl inositol (GPI)-anchor signal. The N-terminal S/T-rich regions, are required for cell wall attachment, but the C-terminal DIPSY domain is required for agglutination and mating in liquid and solid media [].
Probab=24.32 E-value=84 Score=24.51 Aligned_cols=19 Identities=21% Similarity=0.620 Sum_probs=16.9
Q ss_pred CCcEEEEEEeCCeEEEeeC
Q psy230 168 RQKMELSIGMNGKIWIRCE 186 (222)
Q Consensus 168 ~~~~ei~vG~NG~iWi~~~ 186 (222)
..++++-+-.+||||+++.
T Consensus 82 ~ep~~l~~l~dgri~~ts~ 100 (123)
T PF11763_consen 82 SEPLDLHTLSDGRIWFTSN 100 (123)
T ss_pred CCcEEEEEecCCcEEEEcc
Confidence 4699999999999999984
No 233
>TIGR03779 Bac_Flav_CT_M Bacteroides conjugative transposon TraM protein. Members of this protein family are designated TraM and are found in a proposed transfer region of a class of conjugative transposon found in the Bacteroides lineage.
Probab=24.07 E-value=3e+02 Score=26.02 Aligned_cols=55 Identities=15% Similarity=0.222 Sum_probs=42.8
Q ss_pred EeCCEEEEEEeeEEEEecCcEEEEEcc-----ccccCCCCCCEEEEEEEEEecceEEEEECC
Q psy230 22 RESSAILVSQSGILRHAKPFTYYVDYI-----QRRYVPTRGDLVIGVVTSRVGDNYRVDIGS 78 (222)
Q Consensus 22 ~~~~~i~as~~G~l~~~~~~~v~V~~~-----~~~Y~P~vGDiVIG~V~~v~~~~~~VdI~~ 78 (222)
.+.+.|+|++-|.....+...+..+-+ .+..+|+ |-+|+|. .++.+++..+.|.+
T Consensus 253 ~~~n~I~A~V~~~qtv~~G~~vrlRLle~~~v~~~~ipk-gt~l~g~-~~~~g~R~~i~I~s 312 (410)
T TIGR03779 253 SERNTIRACVHETQTVVDGSAVKLRLLEPIQAGDLVIPK-GTVLYGT-AKIQGERLDIKISS 312 (410)
T ss_pred cCCCceEEEEcCceEEecCCEEEEEEcCceeeCCEEecC-CCEEEEE-eeeccceEEEEEEE
Confidence 346789999999887765555555532 3467776 9999999 99999999998877
No 234
>PF02541 Ppx-GppA: Ppx/GppA phosphatase family; InterPro: IPR003695 Exopolyphosphate phosphatase (Ppx) 3.6.1.11 from EC and guanosine pentaphosphate phosphatase (GppA) 3.6.1.40 from EC belong to the sugar kinase/actin/hsp70 superfamily [].; PDB: 3MDQ_A 1U6Z_A 1T6D_B 2J4R_B 1T6C_A 2FLO_B 3CER_B 3HI0_A.
Probab=24.05 E-value=1.8e+02 Score=25.25 Aligned_cols=54 Identities=22% Similarity=0.155 Sum_probs=39.0
Q ss_pred CCcEEEEEEeCCeEEEeeCCchhHHHHHHHHHHhhcCCHHHHHHHHHHHHHHhc
Q psy230 168 RQKMELSIGMNGKIWIRCESFSDTVRVGNLIMSCELLSYEEILNLCESIHIRFL 221 (222)
Q Consensus 168 ~~~~ei~vG~NG~iWi~~~~~~~~~~i~~~i~~~e~~~~~~~~~~~~~~~~~l~ 221 (222)
..++|++.+.||.++-...=+--++.+.+.....+..+.++.+.+-+.+.+.|.
T Consensus 121 GGStEl~~~~~~~~~~~~Sl~lG~vrl~e~~~~~~~~~~~~~~~~~~~i~~~l~ 174 (285)
T PF02541_consen 121 GGSTELILFENGKVVFSQSLPLGAVRLTERFFKSDPPTAEELEKLREFIRKELE 174 (285)
T ss_dssp SSEEEEEEEETTEEEEEEEES--HHHHHHHHSGCSS-HHHHHHHHHHHHHHHHC
T ss_pred CCceEEEEEECCeeeEeeeeehHHHHHHHHHhccCcchHHHHHHHHHHHHHHHH
Confidence 579999999999997766555567888888777776667777777666666654
No 235
>COG1792 MreC Cell shape-determining protein [Cell envelope biogenesis, outer membrane]
Probab=23.92 E-value=2e+02 Score=25.49 Aligned_cols=27 Identities=15% Similarity=0.153 Sum_probs=22.1
Q ss_pred EEEEEEEEecceEEEEECCCCCeeeec
Q psy230 60 VIGVVTSRVGDNYRVDIGSHDPAVLSY 86 (222)
Q Consensus 60 VIG~V~~v~~~~~~VdI~~~~~a~L~~ 86 (222)
++|+|+.+.....+|.+-+.....+|.
T Consensus 156 LVG~V~~V~~~tS~V~Lltd~~~~i~v 182 (284)
T COG1792 156 LVGKVVEVSKNTSRVLLLTDVNSKIPV 182 (284)
T ss_pred eEEEEEEEcCceeEEEEeeccccceeE
Confidence 899999999999999987755555554
No 236
>PRK05585 yajC preprotein translocase subunit YajC; Validated
Probab=23.90 E-value=1.7e+02 Score=22.19 Aligned_cols=26 Identities=31% Similarity=0.394 Sum_probs=22.0
Q ss_pred CCCCCCEE------EEEEEEEecceEEEEECC
Q psy230 53 VPTRGDLV------IGVVTSRVGDNYRVDIGS 78 (222)
Q Consensus 53 ~P~vGDiV------IG~V~~v~~~~~~VdI~~ 78 (222)
.-++||.| +|+|+++..+...++|+.
T Consensus 52 ~Lk~Gd~VvT~gGi~G~Vv~i~~~~v~lei~~ 83 (106)
T PRK05585 52 SLAKGDEVVTNGGIIGKVTKVSEDFVIIELND 83 (106)
T ss_pred hcCCCCEEEECCCeEEEEEEEeCCEEEEEECC
Confidence 45889998 699999999988888854
No 237
>PRK06531 yajC preprotein translocase subunit YajC; Validated
Probab=23.69 E-value=1.8e+02 Score=22.41 Aligned_cols=47 Identities=15% Similarity=0.290 Sum_probs=33.6
Q ss_pred ccCCcCCCCCCEE------EEEEEecCCC-CeeEEEEecCCCccccCcccCCceEEEechhhhhhccC
Q psy230 94 KKNPPKVETGDVV------AGKLLTANKD-MESEMVCVDSRGKEFIMGILNDGYLLHTSISLCRKLLN 154 (222)
Q Consensus 94 k~~r~~l~~GDlV------~ArV~~~~~~-~~~~Ls~~~~~~~~~~~G~L~~G~l~~v~~~~~~rl~~ 154 (222)
++|...|++||-| +++|.+++.+ ..+.|.+ +|..+++.-+.+.+++.
T Consensus 31 ~em~~sLk~GD~VvT~GGi~G~V~~I~~~~~~v~le~--------------~gv~i~v~r~AI~~Vv~ 84 (113)
T PRK06531 31 QNQLNAIQKGDEVVTIGGLYGTVDEVDTEAKTIVLDV--------------DGVYLTFELAAIKRVVP 84 (113)
T ss_pred HHHHHhcCCCCEEEECCCcEEEEEEEecCCCEEEEEE--------------CCEEEEEEhhHhhhhcC
Confidence 4788899999997 6889888754 2344443 45677777777776664
No 238
>cd04487 RecJ_OBF2_like RecJ_OBF2_like: A subfamily of OB folds corresponding to the second OB fold (OBF2) of archaeal-specific proteins with similarity to eubacterial RecJ. RecJ is an ssDNA-specific exonuclease. Although the overall sequence similarity of these proteins to eubacterial RecJ proteins is marginal, they appear to carry motifs, which have been shown to be essential for nuclease function in Escherichia coli RecJ. In addition to this OB fold, most proteins in this subfamily contain: i) an N-terminal OB fold belonging to a different domain family (the ribosomal S1-like RNA-binding family); and ii) a domain, C-terminal to OBF2, characteristic of DHH family proteins. DHH family proteins include E. coli RecJ, and are predicted to have a phosphoesterase function.
Probab=23.56 E-value=2.6e+02 Score=19.39 Aligned_cols=49 Identities=24% Similarity=0.365 Sum_probs=30.5
Q ss_pred EEEEECCCCCeeeeccccccccccCCcCCCCCCEEE--EEEEecCCCCeeEEEE
Q psy230 72 YRVDIGSHDPAVLSYLAFEGATKKNPPKVETGDVVA--GKLLTANKDMESEMVC 123 (222)
Q Consensus 72 ~~VdI~~~~~a~L~~~~f~gatk~~r~~l~~GDlV~--ArV~~~~~~~~~~Ls~ 123 (222)
+...+.. ..|.++...|.+...+....+++||.|. +++. + +.+.++|..
T Consensus 17 vyfsLkD-~~a~i~cv~f~~~~~~~~~~l~~Gd~V~v~G~v~-~-~~G~~ql~v 67 (73)
T cd04487 17 TIFTLRD-ETGTVWAAAFEEAGVRAYPEVEVGDIVRVTGEVE-P-RDGQLQIEV 67 (73)
T ss_pred EEEEEEc-CCEEEEEEEEchhccCCcCCCCCCCEEEEEEEEe-c-CCeEEEEEE
Confidence 4444433 3466776667654455777899999764 4554 3 556677765
No 239
>PF08869 XisI: XisI protein; InterPro: IPR014968 The fdxN element, along with two other DNA elements, is excised from the chromosome during heterocyst differentiation in cyanobacteria. The xisH as well as the xisF and xisI genes are required []. ; PDB: 3D7Q_A 2NWV_A 2NVM_A 2NLV_B.
Probab=23.54 E-value=83 Score=24.21 Aligned_cols=18 Identities=28% Similarity=0.772 Sum_probs=13.2
Q ss_pred CcEEEEEEeCCeEEEeeCCch
Q psy230 169 QKMELSIGMNGKIWIRCESFS 189 (222)
Q Consensus 169 ~~~ei~vG~NG~iWi~~~~~~ 189 (222)
..++|. ||+|||.....+
T Consensus 59 iH~dI~---dgKIWIq~d~TE 76 (111)
T PF08869_consen 59 IHLDIK---DGKIWIQRDGTE 76 (111)
T ss_dssp EEEEEE---TTEEEEEEESSS
T ss_pred EEEEEE---CCeEEEEcCchh
Confidence 355564 999999887654
No 240
>PF05402 PqqD: Coenzyme PQQ synthesis protein D (PqqD); InterPro: IPR008792 This family contains several bacterial coenzyme PQQ synthesis protein D (PqqD) sequences. This protein is required for coenzyme pyrrolo-quinoline-quinone (PQQ) biosynthesis.; PDB: 3G2B_A.
Probab=23.43 E-value=42 Score=22.43 Aligned_cols=42 Identities=12% Similarity=0.008 Sum_probs=27.6
Q ss_pred eEEEeeCCchhHHHHHHHHHHhhcCCHHHHHHHHHHHHHHhc
Q psy230 180 KIWIRCESFSDTVRVGNLIMSCELLSYEEILNLCESIHIRFL 221 (222)
Q Consensus 180 ~iWi~~~~~~~~~~i~~~i~~~e~~~~~~~~~~~~~~~~~l~ 221 (222)
.||=.+..+.....|++++..-...+.++++.=+.++.+.|.
T Consensus 21 ~Iw~~~~g~~t~~ei~~~l~~~y~~~~~~~~~dv~~fl~~L~ 62 (68)
T PF05402_consen 21 FIWELLDGPRTVEEIVDALAEEYDVDPEEAEEDVEEFLEQLR 62 (68)
T ss_dssp HHHHH--SSS-HHHHHHHHHHHTT--HHHHHHHHHHHHHHHH
T ss_pred HHHHHccCCCCHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHH
Confidence 345555555667788888888888888888888888887775
No 241
>TIGR00739 yajC preprotein translocase, YajC subunit. While this protein is part of the preprotein translocase in Escherichia coli, it is not essential for viability or protein secretion. The N-terminus region contains a predicted membrane-spanning region followed by a region consisting almost entirely of residues with charged (acidic, basic, or zwitterionic) side chains. This small protein is about 100 residues in length, and is restricted to bacteria; however, this protein is absent from some lineages, including spirochetes and Mycoplasmas.
Probab=23.42 E-value=1.9e+02 Score=20.91 Aligned_cols=26 Identities=27% Similarity=0.451 Sum_probs=21.1
Q ss_pred CCCCCCEE------EEEEEEEecceEEEEECC
Q psy230 53 VPTRGDLV------IGVVTSRVGDNYRVDIGS 78 (222)
Q Consensus 53 ~P~vGDiV------IG~V~~v~~~~~~VdI~~ 78 (222)
--++||.| +|+|+++..+...++++.
T Consensus 37 ~L~~Gd~VvT~gGi~G~V~~i~d~~v~vei~~ 68 (84)
T TIGR00739 37 SLKKGDKVLTIGGIIGTVTKIAENTIVIELND 68 (84)
T ss_pred hCCCCCEEEECCCeEEEEEEEeCCEEEEEECC
Confidence 35789987 599999999988888853
No 242
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=23.11 E-value=1.4e+02 Score=25.71 Aligned_cols=32 Identities=13% Similarity=0.146 Sum_probs=23.7
Q ss_pred CCCCCEEEEEEEEEecc-eEEEEECCCCCeeee
Q psy230 54 PTRGDLVIGVVTSRVGD-NYRVDIGSHDPAVLS 85 (222)
Q Consensus 54 P~vGDiVIG~V~~v~~~-~~~VdI~~~~~a~L~ 85 (222)
-++||+|.++|.++..+ .+.+.+..+..+.|.
T Consensus 112 ~~~GDlV~akV~~i~~~~~~~LS~k~~~lG~L~ 144 (235)
T PRK04163 112 LDIGDYIIAKVKDVDRTRDVVLTLKGKGLGKIE 144 (235)
T ss_pred CCCCCEEEEEEEEECCCCcEEEEEcCCCCCccC
Confidence 38899999999999764 466777666555554
No 243
>COG0093 RplN Ribosomal protein L14 [Translation, ribosomal structure and biogenesis]
Probab=22.99 E-value=3.7e+02 Score=21.00 Aligned_cols=45 Identities=24% Similarity=0.258 Sum_probs=31.1
Q ss_pred EEEEccccccCCCCCCEEEEEEEEEecceEEEEECCCCCeeeeccccccccccCCcCCCCCCEEEEEEEecC
Q psy230 43 YYVDYIQRRYVPTRGDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFEGATKKNPPKVETGDVVAGKLLTAN 114 (222)
Q Consensus 43 v~V~~~~~~Y~P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~gatk~~r~~l~~GDlV~ArV~~~~ 114 (222)
+.|..-.+|....+||+|+..|.+-.+ +...+-||+++|-|....
T Consensus 22 I~V~gg~~r~~A~vGD~ivvsVKka~P---------------------------~~~vKkg~V~~AViVRtk 66 (122)
T COG0093 22 IKVLGGSRRRYAGVGDIIVVSVKKAIP---------------------------RGMVKKGDVVKAVVVRTK 66 (122)
T ss_pred EEEeccccccccCCCCEEEEEEeeccC---------------------------CcceeccceEEEEEEEeC
Confidence 445544445567999999999887665 123457899999887654
No 244
>TIGR02554 PrgH type III secretion system protein PrgH/EprH. In Samonella, this gene is part of a four-gene operon PrgHIJK and in general is found in type III secretion operons. PrgH has been shown to be required for secretion, as well as being a structural component of the needle complex.
Probab=22.83 E-value=1.3e+02 Score=28.24 Aligned_cols=35 Identities=14% Similarity=0.308 Sum_probs=32.2
Q ss_pred CCcEEEEEEeCCeEEEeeCCchhHHHHHHHHHHhh
Q psy230 168 RQKMELSIGMNGKIWIRCESFSDTVRVGNLIMSCE 202 (222)
Q Consensus 168 ~~~~ei~vG~NG~iWi~~~~~~~~~~i~~~i~~~e 202 (222)
..+++|.=|+||.++|-..+.+++.=.-.++.+..
T Consensus 178 ~~p~~il~grDg~iyVla~~qrd~~W~~Q~Llk~~ 212 (389)
T TIGR02554 178 PVRFAVLPGRDGRIYVAAASQRDAEWARQALLRAA 212 (389)
T ss_pred CCCeEEEeCCCCcEEEEEccccHhHHHHHHHhhcC
Confidence 78999999999999999999999999988888853
No 245
>PRK00106 hypothetical protein; Provisional
Probab=22.48 E-value=3e+02 Score=26.93 Aligned_cols=71 Identities=8% Similarity=0.024 Sum_probs=55.2
Q ss_pred hhhhccCCChhHHHHhhhcCCCcEEEEEEeC-CeEEEeeCCchhHHHHHHHHHHhh---cCCHHHHHHHHHHHHHHh
Q psy230 148 LCRKLLNPKCPLLKQLAKRSRQKMELSIGMN-GKIWIRCESFSDTVRVGNLIMSCE---LLSYEEILNLCESIHIRF 220 (222)
Q Consensus 148 ~~~rl~~~~~~~l~~l~~~~~~~~ei~vG~N-G~iWi~~~~~~~~~~i~~~i~~~e---~~~~~~~~~~~~~~~~~l 220 (222)
+--|++|+.+.-+.+|.. .|+++++|.-. .-|-++|-||-.-..+-.+|.+.- +..++.++.++++..+.+
T Consensus 236 mkGriIGreGrNir~~E~--~tGvdliiddtp~~v~lS~fdpvRReiAr~~le~Li~dgrIhp~rIEe~v~k~~~e~ 310 (535)
T PRK00106 236 MKGRIIGREGRNIRTLES--LTGIDVIIDDTPEVVVLSGFDPIRREIARMTLESLIKDGRIHPARIEELVEKNRLEM 310 (535)
T ss_pred hhcceeCCCcchHHHHHH--HhCceEEEcCCCCeEEEeCCChHHHHHHHHHHHHHHHcCCcCHHHHHHHHHHHHHHH
Confidence 344678999999999988 99999999865 567788888876667777776654 466888888888776654
No 246
>PRK05446 imidazole glycerol-phosphate dehydratase/histidinol phosphatase; Provisional
Probab=22.42 E-value=2.4e+02 Score=25.97 Aligned_cols=44 Identities=18% Similarity=0.279 Sum_probs=35.2
Q ss_pred hhHHHHhhhcCCCcEEEEEEeCCeEEEeeCC--chhHHHHHHHHHHhh
Q psy230 157 CPLLKQLAKRSRQKMELSIGMNGKIWIRCES--FSDTVRVGNLIMSCE 202 (222)
Q Consensus 157 ~~~l~~l~~~~~~~~ei~vG~NG~iWi~~~~--~~~~~~i~~~i~~~e 202 (222)
.+||.++.+ +..|++-|-.+|-+||+.+- +.-.+.+.+|+++.-
T Consensus 201 dhml~~~~~--h~~~~l~v~~~gd~~vd~hh~~ed~~i~lG~a~~~al 246 (354)
T PRK05446 201 DHMLDQIAT--HGGFRLEIKVKGDLHIDDHHTVEDTALALGEALKQAL 246 (354)
T ss_pred HHHHHHHHH--HcCCCeEEEEecCccccCCchHHHHHHHHHHHHHHHh
Confidence 589999999 99999999999999999753 233456677777653
No 247
>cd04459 Rho_CSD Rho_CSD: Rho protein cold-shock domain (CSD). Rho protein is a transcription termination factor in most bacteria. In bacteria, there are two distinct mechanisms for mRNA transcription termination. In intrinsic termination, RNA polymerase and nascent mRNA are released from DNA template by an mRNA stem loop structure, which resembles the transcription termination mechanism used by eukaryotic pol III. The second mechanism is mediated by Rho factor. Rho factor terminates transcription by using energy from ATP hydrolysis to forcibly dissociate the transcripts from RNA polymerase. Rho protein contains an N-terminal S1-like domain, which binds single-stranded RNA. Rho has a C-terminal ATPase domain which hydrolyzes ATP to provide energy to strip RNA polymerase and mRNA from the DNA template. Rho functions as a homohexamer.
Probab=22.25 E-value=72 Score=22.29 Aligned_cols=25 Identities=36% Similarity=0.578 Sum_probs=19.9
Q ss_pred EEEEEccc-cccCCCCCCEEEEEEEE
Q psy230 42 TYYVDYIQ-RRYVPTRGDLVIGVVTS 66 (222)
Q Consensus 42 ~v~V~~~~-~~Y~P~vGDiVIG~V~~ 66 (222)
=++|-+.. ++|--+.||.|.|.|-.
T Consensus 28 DvyVs~~~Irr~~LR~GD~V~G~vr~ 53 (68)
T cd04459 28 DIYVSPSQIRRFNLRTGDTVVGQIRP 53 (68)
T ss_pred CEEECHHHHHHhCCCCCCEEEEEEeC
Confidence 35677744 67999999999999875
No 248
>PF00475 IGPD: Imidazoleglycerol-phosphate dehydratase; InterPro: IPR000807 Imidazoleglycerol-phosphate dehydratase is the enzyme that catalyses the seventh step in the biosynthesis of histidine in bacteria, fungi and plants. In most organisms it is a monofunctional protein of about 22 to 29 kD. In some bacteria such as Escherichia coli, it is the C-terminal domain of a bifunctional protein that include a histidinol-phosphatase domain [].; GO: 0004424 imidazoleglycerol-phosphate dehydratase activity, 0000105 histidine biosynthetic process; PDB: 2F1D_G 2AE8_A 1RHY_B.
Probab=22.07 E-value=27 Score=28.15 Aligned_cols=43 Identities=21% Similarity=0.274 Sum_probs=31.9
Q ss_pred hhHHHHhhhcCCCcEEEEEEeCCeEEEeeC--CchhHHHHHHHHHHh
Q psy230 157 CPLLKQLAKRSRQKMELSIGMNGKIWIRCE--SFSDTVRVGNLIMSC 201 (222)
Q Consensus 157 ~~~l~~l~~~~~~~~ei~vG~NG~iWi~~~--~~~~~~~i~~~i~~~ 201 (222)
.+||+++.+ +..|++-|-..|-+||+.+ .+...+.+.+|+.++
T Consensus 7 DHML~~la~--h~~~dl~v~a~GDl~vD~HHtvEDvgI~LG~al~~a 51 (145)
T PF00475_consen 7 DHMLEQLAK--HGGFDLSVKAKGDLEVDDHHTVEDVGIVLGQALRQA 51 (145)
T ss_dssp HHHHHHHHH--HHT-EEEEEEEC-TTT-CHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHH--HCCCCEEEEEeCCCCcCcceehhhHHHHHHHHHHHH
Confidence 479999999 9999999999999999764 233456777888776
No 249
>COG2996 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only]
Probab=21.66 E-value=3e+02 Score=24.71 Aligned_cols=56 Identities=14% Similarity=-0.037 Sum_probs=41.9
Q ss_pred cCCCCCCEEEEEEEEEe-cceEEEEECCCCCeeeeccccccccccC-CcCCCCCCEEEEEEE
Q psy230 52 YVPTRGDLVIGVVTSRV-GDNYRVDIGSHDPAVLSYLAFEGATKKN-PPKVETGDVVAGKLL 111 (222)
Q Consensus 52 Y~P~vGDiVIG~V~~v~-~~~~~VdI~~~~~a~L~~~~f~gatk~~-r~~l~~GDlV~ArV~ 111 (222)
..-++|+.=-++|++++ .-..++|.+-+-+..+|....| .. +-..++||-++..+-
T Consensus 69 p~~tvg~~g~~~Vv~v~~~lGaFlD~Gl~KDl~vp~~elp----~~~~~wpq~Gd~l~v~l~ 126 (287)
T COG2996 69 PKATVGEYGWLKVVEVNKDLGAFLDWGLPKDLLVPLDELP----TLKSLWPQKGDKLLVYLY 126 (287)
T ss_pred ceEeecceeEEEEEEEcCCcceEEecCCCcceeeehhhcc----cccccCCCCCCEEEEEEE
Confidence 45689999999999999 8899999999999998876544 11 123556666665554
No 250
>KOG3409|consensus
Probab=21.50 E-value=1.3e+02 Score=25.23 Aligned_cols=25 Identities=16% Similarity=0.307 Sum_probs=20.0
Q ss_pred CCCCEEEEEEEecCCC-CeeEEEEec
Q psy230 101 ETGDVVAGKLLTANKD-MESEMVCVD 125 (222)
Q Consensus 101 ~~GDlV~ArV~~~~~~-~~~~Ls~~~ 125 (222)
..||+|.|||..++.. -...+.|++
T Consensus 67 ~~G~IVtarV~~i~~rfAkv~I~~V~ 92 (193)
T KOG3409|consen 67 FVGAIVTARVSRINLRFAKVDILSVG 92 (193)
T ss_pred ccCcEEEEEEEeeccceeeEEEEEEc
Confidence 4899999999999843 357788876
No 251
>PF14842 FliG_N: FliG N-terminal domain; PDB: 3HJL_A 3AJC_A 3USY_B.
Probab=21.33 E-value=1.5e+02 Score=22.10 Aligned_cols=33 Identities=15% Similarity=0.093 Sum_probs=23.8
Q ss_pred CchhHHHHHHHHHHhhcCCHHHHHHHHHHHHHH
Q psy230 187 SFSDTVRVGNLIMSCELLSYEEILNLCESIHIR 219 (222)
Q Consensus 187 ~~~~~~~i~~~i~~~e~~~~~~~~~~~~~~~~~ 219 (222)
++++...|.+++..+...+.++++..++.+...
T Consensus 31 ~~~ei~~i~~~ma~l~~v~~~~~~~Vl~EF~~~ 63 (108)
T PF14842_consen 31 DEEEIERISREMAKLGSVSPEEVEEVLEEFYDE 63 (108)
T ss_dssp -HHHHHHHHHHHHT-----HHHHHHHHHHHHHH
T ss_pred CHHHHHHHHHHHHccCCCCHHHHHHHHHHHHHH
Confidence 456788999999999999999999999988874
No 252
>PF02765 POT1: Telomeric single stranded DNA binding POT1/CDC13; InterPro: IPR011564 This entry represents a domain that binds single stranded telomeric DNA and adopts an OB fold []. It includes the proteins POT1 and CDC13 which have been shown to regulate telomere length, replication and capping [, , ]. ; GO: 0003677 DNA binding, 0000723 telomere maintenance, 0000784 nuclear chromosome, telomeric region; PDB: 1S40_A 1KXL_A 1PH7_A 1PH9_A 1PH2_A 1OTC_A 1PHJ_A 1JB7_A 1PA6_A 1PH1_A ....
Probab=20.37 E-value=3.5e+02 Score=21.15 Aligned_cols=39 Identities=18% Similarity=0.215 Sum_probs=20.2
Q ss_pred eeeccccccccccCCcCCCCCCEEE---EEEEecCCCCeeEEEE
Q psy230 83 VLSYLAFEGATKKNPPKVETGDVVA---GKLLTANKDMESEMVC 123 (222)
Q Consensus 83 ~L~~~~f~gatk~~r~~l~~GDlV~---ArV~~~~~~~~~~Ls~ 123 (222)
.|.+.-|......+...-.+||+|+ ++|++.+. .+.+-+
T Consensus 57 ~l~v~iF~~~~~~LP~v~~~GDii~l~r~kv~~~~~--~~~~~~ 98 (146)
T PF02765_consen 57 GLTVNIFRPHKESLPNVKSVGDIIRLRRVKVQSYNG--KPQGLS 98 (146)
T ss_dssp EEEEEEEESSHHHSCTTCSTTHEEEEEEEEEEEETT--EEEEEE
T ss_pred CEEEEEECCCHHHCCCCCCCCCEEEEEEEEEEEECC--EEEEEe
Confidence 3444444322234433444599994 55777764 444444
No 253
>PRK13689 hypothetical protein; Provisional
Probab=20.30 E-value=1.9e+02 Score=20.71 Aligned_cols=32 Identities=13% Similarity=0.152 Sum_probs=25.2
Q ss_pred HHHHHHHHHHhh--cCCHHHHHHHHHHHHHHhcC
Q psy230 191 TVRVGNLIMSCE--LLSYEEILNLCESIHIRFLQ 222 (222)
Q Consensus 191 ~~~i~~~i~~~e--~~~~~~~~~~~~~~~~~l~~ 222 (222)
-..++|++-++- ..+.+|...+.++|.+.|++
T Consensus 34 LMvLGN~vTnlln~~V~~~qR~~iAe~Fa~AL~~ 67 (75)
T PRK13689 34 LMVLGNMVTNLLNTSVAPAQRQAIAESFARALQS 67 (75)
T ss_pred HHHHHHHHHHHHhhcCCHHHHHHHHHHHHHHHHH
Confidence 456677777765 35699999999999999874
No 254
>PTZ00329 eukaryotic translation initiation factor 1A; Provisional
Probab=20.07 E-value=2.5e+02 Score=22.91 Aligned_cols=36 Identities=22% Similarity=0.471 Sum_probs=21.3
Q ss_pred eCCCeEE----eCCEEEEEEeeEEEEecCcEEEEEccccccCCCCCCEEEEEE
Q psy230 16 LGPGLRR----ESSAILVSQSGILRHAKPFTYYVDYIQRRYVPTRGDLVIGVV 64 (222)
Q Consensus 16 ~G~G~y~----~~~~i~as~~G~l~~~~~~~v~V~~~~~~Y~P~vGDiVIG~V 64 (222)
+|.|.|. ++..+.|.+.|.++. .+||.+ ||+|+-..
T Consensus 42 LGn~~f~V~c~dG~~rLa~I~GKmRK----~IWI~~---------GD~VlVel 81 (155)
T PTZ00329 42 LGNGRLEAYCFDGVKRLCHIRGKMRK----RVWINI---------GDIILVSL 81 (155)
T ss_pred cCCCEEEEEECCCCEEEEEeecccee----eEEecC---------CCEEEEec
Confidence 5667664 234667777777653 256654 66666543
No 255
>cd05837 MSH6_like The PWWP domain is present in MSH6, a mismatch repair protein homologous to bacterial MutS. The PWWP domain of histone-lysine N-methyltransferase, also known as Nuclear SET domain-containing protein 3, is also included. Mutations in MSH6 have been linked to increased cancer susceptibility, particularly in hereditary nonpolyposis colorectal cancer in humans. The role of the PWWP domain in MSH6 is not clear; MSH6 orthologs found in S. cerevisiae, Caenorhabditis elegans and Arabidopsis thaliana lack the PWWP domain. Histone methyltransferases (HMTases) induce the posttranslational methylation of lysine residues in histones and play a role in apoptosis. In the HMTase Whistle, the PWWP domain is necessary for HMTase activity. The PWWP domain, named for a conserved Pro-Trp-Trp-Pro motif, is a small domain consisting of 100-150 amino acids. The PWWP domain is found in numerous proteins that are involved in cell division, growth and differentiation. Most PWWP-domain pro
Probab=20.07 E-value=65 Score=24.37 Aligned_cols=15 Identities=33% Similarity=0.375 Sum_probs=12.8
Q ss_pred CCCCCCEEEEEEEec
Q psy230 99 KVETGDVVAGKLLTA 113 (222)
Q Consensus 99 ~l~~GDlV~ArV~~~ 113 (222)
.|.+||||-|++...
T Consensus 2 ~~~~GdlVWaK~~g~ 16 (110)
T cd05837 2 KYQVGDLVWAKVSGY 16 (110)
T ss_pred CCCCCCEEEEeCCCC
Confidence 478999999999764
Done!