Query 026458
Match_columns 238
No_of_seqs 149 out of 672
Neff 6.6
Searched_HMMs 46136
Date Fri Mar 29 08:18:06 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/026458.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/026458hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG1097 RRP4 RNA-binding prote 100.0 8.1E-58 1.7E-62 394.0 24.0 215 7-234 3-228 (239)
2 KOG1004 Exosomal 3'-5' exoribo 100.0 3.7E-56 8E-61 374.6 23.4 221 13-237 2-227 (230)
3 PRK04163 exosome complex RNA-b 100.0 9.1E-52 2E-56 361.5 24.3 211 11-235 7-228 (235)
4 KOG3013 Exosomal 3'-5' exoribo 100.0 1.7E-40 3.7E-45 286.9 11.4 175 10-202 27-212 (301)
5 cd05790 S1_Rrp40 S1_Rrp40: Rrp 100.0 3E-30 6.4E-35 192.6 10.2 86 69-154 1-86 (86)
6 PRK09521 exosome complex RNA-b 99.9 3.6E-26 7.8E-31 193.9 15.9 134 10-155 3-149 (189)
7 COG1096 Predicted RNA-binding 99.9 3.1E-25 6.7E-30 185.1 14.4 134 9-154 2-148 (188)
8 KOG3409 Exosomal 3'-5' exoribo 99.9 7E-22 1.5E-26 162.5 12.8 149 11-169 4-175 (193)
9 cd05791 S1_CSL4 S1_CSL4: CSL4, 99.8 6E-19 1.3E-23 133.5 8.6 80 70-154 2-92 (92)
10 cd04454 S1_Rrp4_like S1_Rrp4_l 99.8 5.3E-18 1.2E-22 124.9 9.5 81 69-154 1-82 (82)
11 cd05789 S1_Rrp4 S1_Rrp4: Rrp4 99.6 1.2E-14 2.5E-19 107.8 8.7 81 69-154 1-86 (86)
12 PF10447 EXOSC1: Exosome compo 99.3 8.6E-12 1.9E-16 92.4 6.1 61 71-131 1-82 (82)
13 PF14382 ECR1_N: Exosome compl 99.1 3.8E-11 8.1E-16 76.8 3.2 38 14-56 1-38 (39)
14 cd05687 S1_RPS1_repeat_ec1_hs1 98.7 6.4E-08 1.4E-12 68.6 7.5 67 75-141 1-69 (70)
15 cd05704 S1_Rrp5_repeat_hs13 S1 98.7 7.4E-08 1.6E-12 69.3 7.3 68 73-141 2-71 (72)
16 smart00316 S1 Ribosomal protei 98.6 1.3E-07 2.7E-12 65.7 7.4 69 73-141 1-71 (72)
17 cd04452 S1_IF2_alpha S1_IF2_al 98.6 2.3E-07 5E-12 66.5 7.9 71 72-142 1-75 (76)
18 cd05692 S1_RPS1_repeat_hs4 S1_ 98.6 2.8E-07 6.1E-12 64.0 8.0 68 75-142 1-69 (69)
19 cd05691 S1_RPS1_repeat_ec6 S1_ 98.6 2.5E-07 5.5E-12 65.6 7.8 69 75-143 1-71 (73)
20 PF00575 S1: S1 RNA binding do 98.5 5.2E-07 1.1E-11 64.4 8.0 70 72-141 2-73 (74)
21 cd05706 S1_Rrp5_repeat_sc10 S1 98.5 9.4E-07 2E-11 63.0 8.7 69 73-141 2-72 (73)
22 cd05702 S1_Rrp5_repeat_hs11_sc 98.5 6.6E-07 1.4E-11 63.6 7.0 62 75-136 1-65 (70)
23 cd05708 S1_Rrp5_repeat_sc12 S1 98.4 1.8E-06 3.9E-11 61.7 8.1 71 73-143 1-74 (77)
24 PRK08582 hypothetical protein; 98.4 3.1E-06 6.7E-11 68.7 9.7 72 72-143 3-75 (139)
25 PRK07252 hypothetical protein; 98.4 2.3E-06 5.1E-11 67.8 8.8 72 73-144 2-75 (120)
26 cd05707 S1_Rrp5_repeat_sc11 S1 98.3 1.8E-06 3.8E-11 60.9 6.6 65 75-139 1-67 (68)
27 PRK08059 general stress protei 98.3 3.2E-06 7E-11 67.0 8.3 73 72-144 5-79 (123)
28 cd05705 S1_Rrp5_repeat_hs14 S1 98.3 2.8E-06 6.1E-11 61.5 6.9 62 73-134 2-67 (74)
29 PRK08563 DNA-directed RNA poly 98.3 2.8E-06 6.1E-11 71.8 8.0 80 69-154 76-173 (187)
30 cd05693 S1_Rrp5_repeat_hs1_sc1 98.3 2.6E-06 5.7E-11 65.3 6.4 71 73-143 2-96 (100)
31 cd05686 S1_pNO40 S1_pNO40: pNO 98.2 1.1E-05 2.4E-10 57.9 8.6 70 72-141 1-72 (73)
32 cd04461 S1_Rrp5_repeat_hs8_sc7 98.2 7.9E-06 1.7E-10 59.9 7.3 72 70-141 10-83 (83)
33 cd05698 S1_Rrp5_repeat_hs6_sc5 98.2 1E-05 2.3E-10 57.0 7.4 67 75-141 1-69 (70)
34 TIGR00448 rpoE DNA-directed RN 98.2 9.8E-06 2.1E-10 68.2 8.4 81 69-155 76-174 (179)
35 cd05703 S1_Rrp5_repeat_hs12_sc 98.2 1.1E-05 2.4E-10 58.2 7.4 68 75-142 1-72 (73)
36 PRK03987 translation initiatio 98.1 1.1E-05 2.3E-10 72.1 8.5 74 70-143 4-81 (262)
37 PRK05807 hypothetical protein; 98.1 2.2E-05 4.7E-10 63.5 9.6 70 73-143 4-74 (136)
38 cd02393 PNPase_KH Polynucleoti 98.1 4.3E-06 9.4E-11 58.4 4.7 54 159-213 5-58 (61)
39 cd05688 S1_RPS1_repeat_ec3 S1_ 98.1 9.9E-06 2.1E-10 56.2 6.3 60 74-134 1-61 (68)
40 cd04472 S1_PNPase S1_PNPase: P 98.1 1.9E-05 4.2E-10 54.8 7.8 66 75-140 1-67 (68)
41 COG1098 VacB Predicted RNA bin 98.1 5.1E-06 1.1E-10 65.7 4.9 74 71-144 2-76 (129)
42 cd05694 S1_Rrp5_repeat_hs2_sc2 98.0 3.6E-05 7.9E-10 55.7 8.4 66 73-143 3-70 (74)
43 cd05697 S1_Rrp5_repeat_hs5 S1_ 98.0 2.8E-05 6E-10 54.9 7.3 66 75-140 1-68 (69)
44 cd05685 S1_Tex S1_Tex: The C-t 98.0 1.6E-05 3.4E-10 55.0 5.9 65 75-139 1-67 (68)
45 cd04453 S1_RNase_E S1_RNase_E: 98.0 4.7E-05 1E-09 57.0 8.6 71 72-142 5-82 (88)
46 PHA02945 interferon resistance 98.0 4.3E-05 9.3E-10 57.0 8.2 70 71-143 8-83 (88)
47 cd00164 S1_like S1_like: Ribos 98.0 1.7E-05 3.6E-10 53.8 5.5 56 78-133 1-57 (65)
48 cd04455 S1_NusA S1_NusA: N-uti 97.9 6.2E-05 1.3E-09 53.1 7.7 56 73-134 2-57 (67)
49 cd05695 S1_Rrp5_repeat_hs3 S1_ 97.9 5.4E-05 1.2E-09 53.4 7.0 59 75-134 1-59 (66)
50 PTZ00248 eukaryotic translatio 97.9 4.4E-05 9.5E-10 69.8 7.8 93 71-163 14-117 (319)
51 cd05684 S1_DHX8_helicase S1_DH 97.7 0.00021 4.6E-09 51.7 8.2 68 75-143 1-73 (79)
52 COG1095 RPB7 DNA-directed RNA 97.7 9.7E-05 2.1E-09 62.3 6.8 81 69-155 76-174 (183)
53 cd04460 S1_RpoE S1_RpoE: RpoE, 97.7 0.00018 3.9E-09 54.5 7.5 73 76-154 1-91 (99)
54 cd04465 S1_RPS1_repeat_ec2_hs2 97.6 0.00027 5.9E-09 49.5 7.2 65 75-141 1-66 (67)
55 cd05690 S1_RPS1_repeat_ec5 S1_ 97.6 0.00021 4.5E-09 50.0 6.4 60 75-134 1-62 (69)
56 cd05696 S1_Rrp5_repeat_hs4 S1_ 97.6 0.00031 6.7E-09 50.1 7.3 67 75-141 1-71 (71)
57 COG1093 SUI2 Translation initi 97.6 9E-05 1.9E-09 65.6 4.9 147 67-222 4-207 (269)
58 PRK07400 30S ribosomal protein 97.6 0.00022 4.8E-09 65.3 7.5 75 70-144 27-103 (318)
59 cd04473 S1_RecJ_like S1_RecJ_l 97.5 0.0012 2.6E-08 47.7 9.7 64 71-141 13-76 (77)
60 PRK11824 polynucleotide phosph 97.5 0.00052 1.1E-08 69.0 9.4 99 41-143 591-691 (693)
61 cd05689 S1_RPS1_repeat_ec4 S1_ 97.4 0.00098 2.1E-08 47.1 7.5 62 73-134 2-65 (72)
62 PTZ00162 DNA-directed RNA poly 97.4 0.00081 1.8E-08 56.7 8.0 81 69-155 76-172 (176)
63 TIGR02696 pppGpp_PNP guanosine 97.4 0.00059 1.3E-08 68.4 8.0 70 71-140 644-718 (719)
64 PRK07400 30S ribosomal protein 97.4 0.00089 1.9E-08 61.4 8.6 72 71-143 193-266 (318)
65 COG0539 RpsA Ribosomal protein 97.3 0.00057 1.2E-08 66.5 7.3 72 71-143 189-262 (541)
66 TIGR03591 polynuc_phos polyrib 97.2 0.0009 2E-08 67.2 7.6 92 41-136 588-681 (684)
67 PRK06676 rpsA 30S ribosomal pr 97.1 0.0022 4.9E-08 59.8 8.3 73 71-143 14-89 (390)
68 cd04471 S1_RNase_R S1_RNase_R: 97.0 0.0049 1.1E-07 44.3 8.2 67 74-140 1-81 (83)
69 PRK06676 rpsA 30S ribosomal pr 97.0 0.0024 5.2E-08 59.7 8.2 72 72-144 190-263 (390)
70 PRK06299 rpsA 30S ribosomal pr 97.0 0.0029 6.3E-08 61.9 9.1 72 73-144 372-446 (565)
71 PRK13806 rpsA 30S ribosomal pr 97.0 0.0031 6.7E-08 61.0 8.9 74 71-144 199-278 (491)
72 PRK06299 rpsA 30S ribosomal pr 97.0 0.007 1.5E-07 59.3 11.4 72 72-143 458-531 (565)
73 cd02394 vigilin_like_KH K homo 97.0 0.0013 2.8E-08 45.3 4.4 52 159-212 3-58 (62)
74 TIGR00717 rpsA ribosomal prote 97.0 0.0023 4.9E-08 61.9 7.6 68 72-143 16-84 (516)
75 PRK07899 rpsA 30S ribosomal pr 96.9 0.0043 9.3E-08 60.1 8.8 72 72-144 206-279 (486)
76 PRK07899 rpsA 30S ribosomal pr 96.9 0.0031 6.7E-08 61.0 7.8 73 72-144 33-107 (486)
77 PRK12327 nusA transcription el 96.8 0.0035 7.6E-08 58.5 7.2 69 69-143 129-200 (362)
78 PRK13806 rpsA 30S ribosomal pr 96.8 0.0073 1.6E-07 58.5 9.6 74 72-145 290-366 (491)
79 PRK00087 4-hydroxy-3-methylbut 96.8 0.0068 1.5E-07 60.6 9.5 75 70-144 298-374 (647)
80 COG0539 RpsA Ribosomal protein 96.7 0.0058 1.2E-07 59.7 7.5 94 68-163 15-126 (541)
81 PRK00087 4-hydroxy-3-methylbut 96.6 0.0098 2.1E-07 59.5 8.9 72 73-144 561-634 (647)
82 PLN00207 polyribonucleotide nu 96.6 0.0079 1.7E-07 61.8 8.1 73 71-143 750-824 (891)
83 TIGR00717 rpsA ribosomal prote 96.4 0.036 7.7E-07 53.6 11.6 69 73-141 445-515 (516)
84 PRK12269 bifunctional cytidyla 96.4 0.011 2.3E-07 61.0 8.1 64 72-143 319-382 (863)
85 COG2183 Tex Transcriptional ac 96.4 0.0072 1.6E-07 60.9 6.5 74 72-145 656-731 (780)
86 PRK09202 nusA transcription el 96.3 0.012 2.5E-07 56.8 7.3 70 69-144 129-201 (470)
87 TIGR00757 RNaseEG ribonuclease 96.2 0.066 1.4E-06 50.9 11.9 92 61-163 14-121 (414)
88 TIGR01953 NusA transcription t 96.2 0.016 3.4E-07 53.8 7.1 120 69-197 126-254 (341)
89 PRK12269 bifunctional cytidyla 96.1 0.036 7.8E-07 57.2 9.9 72 72-144 491-564 (863)
90 cd00105 KH-I K homology RNA-bi 95.8 0.017 3.7E-07 39.4 4.2 44 159-203 3-52 (64)
91 cd04462 S1_RNAPII_Rpb7 S1_RNAP 95.7 0.079 1.7E-06 39.5 8.0 59 74-132 1-70 (88)
92 PF00013 KH_1: KH domain syndr 95.7 0.016 3.4E-07 39.6 3.8 54 159-214 3-59 (60)
93 PRK12328 nusA transcription el 95.6 0.047 1E-06 51.1 7.7 69 69-143 133-206 (374)
94 PRK12329 nusA transcription el 95.3 0.076 1.7E-06 50.7 8.1 93 69-166 147-252 (449)
95 KOG1070 rRNA processing protei 94.5 0.25 5.3E-06 53.0 9.9 74 72-145 1160-1235(1710)
96 smart00322 KH K homology RNA-b 94.4 0.14 3E-06 34.4 5.7 58 158-217 5-66 (69)
97 KOG1856 Transcription elongati 94.3 0.058 1.3E-06 56.4 4.8 74 72-145 983-1061(1299)
98 TIGR03591 polynuc_phos polyrib 93.3 0.15 3.3E-06 51.4 5.8 59 158-217 553-611 (684)
99 PRK11642 exoribonuclease R; Pr 92.6 0.72 1.6E-05 47.6 9.5 83 72-154 641-737 (813)
100 PRK13763 putative RNA-processi 92.0 0.42 9.1E-06 40.3 5.9 62 158-220 5-70 (180)
101 TIGR02063 RNase_R ribonuclease 91.9 0.7 1.5E-05 46.8 8.4 70 71-140 624-707 (709)
102 TIGR03665 arCOG04150 arCOG0415 91.7 0.32 7E-06 40.7 4.9 60 160-220 2-64 (172)
103 PRK10811 rne ribonuclease E; R 91.2 1.3 2.8E-05 46.3 9.4 81 61-143 27-120 (1068)
104 cd02396 PCBP_like_KH K homolog 90.6 0.58 1.3E-05 32.4 4.6 36 160-196 4-39 (65)
105 cd02395 SF1_like-KH Splicing f 90.5 0.46 1E-05 37.6 4.4 55 164-219 14-93 (120)
106 TIGR02696 pppGpp_PNP guanosine 90.5 0.58 1.3E-05 47.5 6.1 60 158-218 580-639 (719)
107 COG1185 Pnp Polyribonucleotide 90.0 0.79 1.7E-05 46.0 6.5 73 71-143 616-689 (692)
108 PRK11712 ribonuclease G; Provi 89.4 5.3 0.00012 38.9 11.6 80 61-142 27-122 (489)
109 PF13509 S1_2: S1 domain; PDB: 89.4 2.6 5.6E-05 29.0 7.0 60 74-141 1-60 (61)
110 cd05699 S1_Rrp5_repeat_hs7 S1_ 88.1 2.2 4.7E-05 30.9 6.0 65 75-140 1-70 (72)
111 TIGR00358 3_prime_RNase VacB a 87.8 2.5 5.4E-05 42.6 8.4 70 71-140 569-652 (654)
112 KOG1070 rRNA processing protei 85.6 1.5 3.2E-05 47.4 5.6 70 67-137 878-951 (1710)
113 PRK04012 translation initiatio 83.9 6.7 0.00015 30.1 7.2 55 71-132 17-74 (100)
114 PF08292 RNA_pol_Rbc25: RNA po 83.8 5.3 0.00012 31.7 6.9 61 72-132 1-75 (122)
115 PHA02858 EIF2a-like PKR inhibi 83.6 3.5 7.7E-05 30.7 5.3 64 71-136 13-79 (86)
116 smart00652 eIF1a eukaryotic tr 83.5 6.7 0.00014 29.0 6.9 53 72-131 2-57 (83)
117 PF01176 eIF-1a: Translation i 82.9 4.5 9.8E-05 28.2 5.5 51 76-132 3-56 (65)
118 PRK13763 putative RNA-processi 82.7 5.7 0.00012 33.4 7.0 69 166-237 105-174 (180)
119 KOG3298 DNA-directed RNA polym 81.8 9 0.00019 32.0 7.6 63 69-131 76-149 (170)
120 PLN00208 translation initiatio 81.1 7 0.00015 32.0 6.7 56 71-131 28-84 (145)
121 cd04456 S1_IF1A_like S1_IF1A_l 81.0 13 0.00027 27.2 7.5 50 78-131 2-52 (78)
122 COG0361 InfA Translation initi 79.5 10 0.00023 27.6 6.5 55 75-132 6-61 (75)
123 TIGR03665 arCOG04150 arCOG0415 78.6 11 0.00025 31.3 7.5 68 166-236 99-167 (172)
124 TIGR00008 infA translation ini 78.3 13 0.00028 26.5 6.6 52 78-132 7-59 (68)
125 KOG3038 Histone acetyltransfer 78.1 9.3 0.0002 34.1 7.0 74 60-167 116-189 (264)
126 cd05793 S1_IF1A S1_IF1A: Trans 77.9 10 0.00022 27.6 6.1 50 78-131 2-52 (77)
127 COG2996 Predicted RNA-bindinin 76.7 10 0.00022 34.3 6.9 29 115-143 189-217 (287)
128 cd03524 RPA2_OBF_family RPA2_O 76.6 10 0.00022 25.0 5.7 64 78-141 2-70 (75)
129 CHL00121 rpl27 ribosomal prote 75.8 6.2 0.00013 29.5 4.5 44 10-56 26-70 (86)
130 PF01336 tRNA_anti-codon: OB-f 75.4 6.7 0.00014 26.8 4.5 63 78-142 3-70 (75)
131 KOG3297 DNA-directed RNA polym 74.6 18 0.00038 30.9 7.5 62 70-131 77-156 (202)
132 PF10246 MRP-S35: Mitochondria 73.6 21 0.00046 27.6 7.0 53 72-130 21-73 (104)
133 PF15057 DUF4537: Domain of un 73.2 36 0.00078 26.8 8.7 48 80-128 17-66 (124)
134 PF07494 Reg_prop: Two compone 72.6 4.1 8.9E-05 22.7 2.3 16 188-203 8-23 (24)
135 PRK12442 translation initiatio 71.3 21 0.00046 26.7 6.4 52 78-132 9-61 (87)
136 PF01959 DHQS: 3-dehydroquinat 71.3 46 0.00099 31.2 10.0 98 11-134 243-342 (354)
137 COG1094 Predicted RNA-binding 71.2 24 0.00051 30.3 7.6 71 159-230 11-87 (194)
138 PRK05435 rpmA 50S ribosomal pr 70.8 8.7 0.00019 28.4 4.2 45 9-56 25-70 (82)
139 KOG4600 Mitochondrial ribosoma 70.5 11 0.00024 30.5 5.1 56 9-69 52-116 (144)
140 PF03961 DUF342: Protein of un 70.4 8.9 0.00019 36.7 5.5 52 13-65 107-180 (451)
141 PF01016 Ribosomal_L27: Riboso 68.6 7.1 0.00015 28.9 3.4 45 9-56 24-69 (81)
142 KOG4134 DNA-dependent RNA poly 67.2 7 0.00015 34.4 3.6 70 60-133 93-162 (253)
143 PLN00207 polyribonucleotide nu 66.6 6.8 0.00015 40.9 4.0 60 158-218 687-747 (891)
144 TIGR00523 eIF-1A eukaryotic/ar 66.5 56 0.0012 24.9 8.5 53 69-127 11-67 (99)
145 PTZ00329 eukaryotic translatio 66.5 27 0.00059 28.9 6.8 76 71-171 28-104 (155)
146 PRK02290 3-dehydroquinate synt 66.0 77 0.0017 29.6 10.3 99 11-135 233-333 (344)
147 cd05791 S1_CSL4 S1_CSL4: CSL4, 65.4 6.8 0.00015 29.2 2.9 28 73-100 62-90 (92)
148 COG1185 Pnp Polyribonucleotide 64.2 15 0.00032 37.2 5.7 62 157-219 553-614 (692)
149 COG1096 Predicted RNA-binding 61.8 44 0.00096 28.5 7.3 29 115-144 59-87 (188)
150 TIGR00062 L27 ribosomal protei 60.3 14 0.0003 27.4 3.6 45 9-56 25-70 (83)
151 COG2932 Predicted transcriptio 60.2 79 0.0017 26.8 8.9 68 13-86 135-210 (214)
152 PRK00276 infA translation init 59.3 46 0.00099 23.6 6.1 52 78-132 9-61 (72)
153 PF01835 A2M_N: MG2 domain; I 59.1 8.8 0.00019 28.3 2.5 35 113-147 6-48 (99)
154 PF13014 KH_3: KH domain 57.4 5.8 0.00013 25.0 1.1 28 166-194 1-28 (43)
155 PF03625 DUF302: Domain of unk 55.9 31 0.00067 23.5 4.7 42 159-205 22-65 (65)
156 CHL00010 infA translation init 54.4 53 0.0012 23.7 5.9 52 78-132 9-61 (78)
157 COG1315 Uncharacterized conser 54.1 22 0.00048 34.8 4.8 100 31-131 220-337 (543)
158 cd05841 BS69_related The PWWP 53.6 9.1 0.0002 28.4 1.7 18 115-132 4-21 (83)
159 COG1530 CafA Ribonucleases G a 52.2 28 0.00062 33.9 5.3 71 73-143 36-114 (487)
160 PRK11824 polynucleotide phosph 51.2 17 0.00037 36.9 3.8 58 158-216 556-613 (693)
161 PF10447 EXOSC1: Exosome compo 50.5 13 0.00028 27.4 2.1 25 119-143 3-28 (82)
162 PF14398 ATPgrasp_YheCD: YheC/ 49.8 10 0.00022 33.7 1.7 16 185-200 211-226 (262)
163 smart00293 PWWP domain with co 47.5 12 0.00027 25.7 1.6 15 118-132 1-15 (63)
164 KOG1067 Predicted RNA-binding 46.8 42 0.00091 33.6 5.5 71 71-141 660-736 (760)
165 cd04489 ExoVII_LU_OBF ExoVII_L 46.5 95 0.0021 21.4 6.4 64 78-142 4-72 (78)
166 PF01436 NHL: NHL repeat; Int 46.3 24 0.00053 20.1 2.4 18 186-203 3-20 (28)
167 cd04482 RPA2_OBF_like RPA2_OBF 44.2 65 0.0014 23.8 5.1 49 78-127 3-57 (91)
168 cd04466 S1_YloQ_GTPase S1_YloQ 43.7 96 0.0021 20.8 5.7 44 80-128 3-48 (68)
169 cd05834 HDGF_related The PWWP 42.5 16 0.00035 26.8 1.6 16 117-132 2-17 (83)
170 PF12508 DUF3714: Protein of u 41.5 1.4E+02 0.003 25.7 7.4 56 40-97 50-110 (200)
171 PRK05054 exoribonuclease II; P 41.2 98 0.0021 31.2 7.4 62 72-133 557-634 (644)
172 PF08460 SH3_5: Bacterial SH3 40.9 30 0.00066 24.2 2.7 20 184-203 35-54 (65)
173 cd05839 BR140_related The PWWP 40.0 1E+02 0.0022 24.1 5.8 14 118-131 1-14 (111)
174 cd05836 N_Pac_NP60 The PWWP do 39.7 18 0.0004 26.6 1.5 14 118-131 1-14 (86)
175 cd05840 SPBC215_ISWI_like The 39.7 18 0.00039 27.1 1.5 15 118-132 1-15 (93)
176 PRK06763 F0F1 ATP synthase sub 39.7 73 0.0016 27.6 5.3 12 122-133 118-129 (213)
177 TIGR00182 plsX fatty acid/phos 39.6 44 0.00095 30.8 4.3 59 178-237 258-321 (322)
178 PF07497 Rho_RNA_bind: Rho ter 39.4 49 0.0011 24.2 3.7 29 58-86 28-57 (78)
179 PF13742 tRNA_anti_2: OB-fold 39.4 1.2E+02 0.0027 22.6 6.1 66 77-143 25-96 (99)
180 COG0557 VacB Exoribonuclease R 39.4 1.3E+02 0.0028 30.7 7.9 70 72-141 620-703 (706)
181 cd04454 S1_Rrp4_like S1_Rrp4_l 39.2 55 0.0012 23.1 4.0 31 70-100 49-80 (82)
182 cd05790 S1_Rrp40 S1_Rrp40: Rrp 38.0 36 0.00079 25.2 2.9 21 68-88 46-66 (86)
183 TIGR03319 YmdA_YtgF conserved 37.7 1E+02 0.0022 30.3 6.7 72 165-237 214-289 (514)
184 TIGR02554 PrgH type III secret 36.1 1E+02 0.0022 29.3 6.2 52 184-235 177-234 (389)
185 PHA00691 hypothetical protein 34.2 21 0.00046 24.7 1.0 8 194-201 11-18 (68)
186 cd05835 Dnmt3b_related The PWW 33.0 27 0.00059 25.7 1.5 15 118-132 1-15 (87)
187 PRK05585 yajC preprotein trans 33.0 73 0.0016 24.5 3.9 48 111-172 46-99 (106)
188 cd04451 S1_IF1 S1_IF1: Transla 31.5 1.7E+02 0.0036 19.8 6.4 51 78-131 3-54 (64)
189 PRK00106 hypothetical protein; 31.3 1.5E+02 0.0033 29.4 6.7 72 165-237 235-310 (535)
190 PF05257 CHAP: CHAP domain; I 31.0 60 0.0013 24.8 3.3 26 69-94 60-97 (124)
191 PRK00951 hisB imidazoleglycero 30.7 1.3E+02 0.0028 25.9 5.4 78 125-219 4-83 (195)
192 TIGR00739 yajC preprotein tran 30.6 76 0.0016 23.3 3.5 45 111-169 31-81 (84)
193 PF09480 PrgH: Type III secret 30.1 1.8E+02 0.0039 27.5 6.8 52 184-235 167-224 (375)
194 PF14444 S1-like: S1-like 30.0 92 0.002 21.6 3.6 17 69-85 31-47 (58)
195 PRK09521 exosome complex RNA-b 29.5 86 0.0019 26.2 4.2 32 72-104 119-150 (189)
196 PTZ00329 eukaryotic translatio 28.9 1.3E+02 0.0027 25.0 4.9 52 12-82 24-81 (155)
197 cd05789 S1_Rrp4 S1_Rrp4: Rrp4 28.5 1E+02 0.0022 21.9 3.9 26 72-97 55-81 (86)
198 TIGR00074 hypC_hupF hydrogenas 28.4 1.5E+02 0.0033 21.5 4.7 40 79-128 6-46 (76)
199 TIGR00498 lexA SOS regulatory 28.2 2.6E+02 0.0056 23.2 6.9 30 58-87 163-196 (199)
200 cd06080 MUM1_like Mutated mela 28.1 36 0.00078 25.0 1.4 15 118-132 1-15 (80)
201 cd05162 PWWP The PWWP domain, 28.1 38 0.00081 24.5 1.5 14 118-131 1-14 (87)
202 PF11763 DIPSY: Cell-wall adhe 28.1 55 0.0012 25.9 2.5 18 186-203 83-100 (123)
203 COG2147 RPL19A Ribosomal prote 27.9 48 0.001 27.2 2.2 31 192-232 17-47 (150)
204 PRK15327 type III secretion sy 27.9 1.7E+02 0.0037 27.9 6.2 52 184-235 182-239 (393)
205 PF13953 PapC_C: PapC C-termin 27.8 32 0.00069 23.9 1.0 19 187-205 23-41 (68)
206 PF10000 ACT_3: ACT domain; I 27.2 36 0.00078 24.4 1.2 47 112-169 12-61 (72)
207 cd04497 hPOT1_OB1_like hPOT1_O 26.1 1.6E+02 0.0035 23.3 5.0 22 111-132 62-86 (138)
208 COG1137 YhbG ABC-type (unclass 26.0 2.3E+02 0.005 25.0 6.2 47 152-204 17-67 (243)
209 PF04319 NifZ: NifZ domain; I 26.0 1.4E+02 0.003 21.7 4.1 20 114-133 1-20 (75)
210 PF00855 PWWP: PWWP domain; I 25.8 45 0.00097 23.7 1.6 13 118-130 1-13 (86)
211 KOG0147 Transcriptional coacti 25.7 93 0.002 30.8 4.1 39 178-216 470-511 (549)
212 PRK00215 LexA repressor; Valid 25.2 2.6E+02 0.0056 23.3 6.4 30 58-87 170-203 (205)
213 cd00900 PH-like Pleckstrin hom 25.0 1.3E+02 0.0029 20.2 3.9 33 185-217 64-98 (99)
214 KOG1004 Exosomal 3'-5' exoribo 24.9 1.8E+02 0.004 25.4 5.3 21 68-88 105-125 (230)
215 PRK04163 exosome complex RNA-b 24.5 1.1E+02 0.0024 26.7 4.0 32 72-103 112-144 (235)
216 PRK12704 phosphodiesterase; Pr 24.4 1.5E+02 0.0032 29.2 5.3 69 166-235 221-293 (520)
217 cd02414 jag_KH jag_K homology 24.4 1.3E+02 0.0028 21.3 3.8 39 158-197 26-74 (77)
218 PRK10553 assembly protein for 24.4 3E+02 0.0065 20.4 5.8 57 156-220 8-68 (87)
219 COG3822 ABC-type sugar transpo 24.1 1.6E+02 0.0034 25.5 4.7 39 50-88 152-191 (225)
220 PLN02800 imidazoleglycerol-pho 24.0 44 0.00095 30.0 1.4 43 177-219 101-145 (261)
221 PF09953 DUF2187: Uncharacteri 24.0 1.5E+02 0.0033 20.4 3.8 19 78-96 16-34 (57)
222 cd04491 SoSSB_OBF SoSSB_OBF: A 23.8 2.6E+02 0.0057 19.5 6.9 26 115-142 46-74 (82)
223 COG2810 Predicted type IV rest 23.7 69 0.0015 28.7 2.6 51 149-202 59-112 (284)
224 COG1792 MreC Cell shape-determ 23.3 1.8E+02 0.004 26.2 5.4 25 78-102 156-180 (284)
225 COG1158 Rho Transcription term 23.3 85 0.0019 29.7 3.2 67 30-108 49-123 (422)
226 KOG4078 Putative mitochondrial 23.2 2.1E+02 0.0045 23.5 5.0 78 71-167 79-156 (173)
227 TIGR00638 Mop molybdenum-pteri 23.2 2.3E+02 0.0049 18.9 4.7 49 76-130 7-61 (69)
228 PRK10861 signal peptidase I; P 23.1 2.9E+02 0.0063 25.5 6.7 75 111-203 89-170 (324)
229 PF14842 FliG_N: FliG N-termin 22.9 1.4E+02 0.0031 22.6 4.0 32 204-235 31-62 (108)
230 COG2996 Predicted RNA-bindinin 22.5 2.6E+02 0.0057 25.4 6.0 57 70-130 69-127 (287)
231 COG2106 Uncharacterized conser 22.0 2.7E+02 0.0058 25.2 6.0 49 71-131 102-150 (272)
232 cd04478 RPA2_DBD_D RPA2_DBD_D: 21.8 3.1E+02 0.0067 19.6 7.1 61 78-141 4-71 (95)
233 PF01873 eIF-5_eIF-2B: Domain 21.7 89 0.0019 24.8 2.7 46 158-203 31-76 (125)
234 cd04485 DnaE_OBF DnaE_OBF: A s 21.3 2E+02 0.0043 19.3 4.2 64 78-142 2-72 (84)
235 PF08869 XisI: XisI protein; 21.3 68 0.0015 25.1 1.9 17 187-206 60-76 (111)
236 PF03927 NapD: NapD protein; 21.2 3.2E+02 0.007 19.6 6.1 56 157-220 7-65 (79)
237 cd07914 IGPD Imidazoleglycerol 21.2 57 0.0012 27.9 1.5 43 177-219 35-79 (190)
238 COG3602 Uncharacterized protei 20.7 72 0.0016 25.3 1.9 33 112-144 12-47 (134)
239 COG0211 RpmA Ribosomal protein 20.7 2.7E+02 0.0058 20.8 4.7 54 10-66 26-84 (87)
240 PRK03988 translation initiatio 20.7 2.6E+02 0.0056 22.6 5.2 43 160-203 43-85 (138)
241 TIGR00617 rpa1 replication fac 20.6 2E+02 0.0043 28.9 5.4 66 77-143 194-278 (608)
242 cd04487 RecJ_OBF2_like RecJ_OB 20.5 3.2E+02 0.0069 19.2 5.2 62 78-142 3-68 (73)
243 PF07116 DUF1372: Protein of u 20.1 2.6E+02 0.0057 21.6 4.8 44 73-124 53-98 (104)
244 PTZ00400 DnaK-type molecular c 20.1 2.1E+02 0.0046 28.9 5.6 38 166-203 107-145 (663)
No 1
>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=8.1e-58 Score=394.00 Aligned_cols=215 Identities=31% Similarity=0.454 Sum_probs=201.0
Q ss_pred ccCCCCcEEecCCccCCCCCCCCCceeecCcEEEeCCEEEEEEeeEeEEecCCeEEEEccCCccCCCCCCEEEEEEEEec
Q 026458 7 TANLVDKIVVPGDVVLDLSSMTNQTIKLGGGLRQECDSVSVIKAGKLRFSKPNKYWVESSQKRYVPCVEDTVLGIVVDCK 86 (238)
Q Consensus 7 ~~~~~~~iV~PGd~l~~~~~~~~~~~~~G~G~y~~~g~i~as~~G~v~~~~~~~i~V~~~~~~Y~P~vGDiVIG~V~~v~ 86 (238)
.....+++|+|||.|.... .+..|||||.+++++||+++|.++.. ++.+.|+|++++|+|++||+|||+|+++.
T Consensus 3 ~~~~~~~iV~PGd~vl~~~-----~~~~G~Gty~~~~~iyssv~G~~~~~-~~~v~VIpl~g~YiP~~gD~VIG~I~~v~ 76 (239)
T COG1097 3 LSVSMRKIVLPGDLVLAEG-----SYKLGHGTYFEGGKIYSSVVGLLDVK-GKLVRVIPLEGRYIPEVGDVVIGKIIEVG 76 (239)
T ss_pred eeccccceecCCCccCCCC-----CEecCCCcEecCCEEEEEEEeEEEEe-CCEEEEEeCCCcccCCCCCEEEEEEEEEc
Confidence 4456789999999766554 79999999999999999999999996 88999999999999999999999999999
Q ss_pred CceEEEEecCCeeeeecCccc-----CCcccccccCcCCCCEEEEEEEecCCCCcceEEEecCCCccCCCcccCCeeEEE
Q 026458 87 ADNFFVDIRGPTIAFLPVLAF-----EGGTRRNIPKFEIGSLLYVRVVKANPGMNPELSCTDASGKAAEFGLLKDGYMFE 161 (238)
Q Consensus 87 ~~~~~VdI~~~~~a~L~~~~f-----~gatk~~r~~l~~GDlV~ArV~~~~~~~~~~Ls~~~~~~~~~~~G~L~~G~~~~ 161 (238)
++.|+|||++++.|+|++++| +.++++||++|++||+|+|||+.++++++++|+|++ .+||+|++|++++
T Consensus 77 ~~~W~VDI~sp~~A~L~ls~~~~r~~~~~~~~~r~~l~vGD~v~AkV~~vd~~~~~~L~~k~-----~~~GkL~~G~iv~ 151 (239)
T COG1097 77 PSGWKVDIGSPYPALLSLSDFLRRKFENAEKDLRPFLNVGDLVYAKVVDVDRDGEVELTLKD-----EGLGKLKNGQIVK 151 (239)
T ss_pred ccceEEEcCCccceEeehhhhhcccccccccccccccccCCEEEEEEEEccCCCceEEEeec-----CCCccccCCEEEE
Confidence 999999999999999999988 456899999999999999999999999999999988 9999999999999
Q ss_pred echhhhhhhcCCCCchhhHhhccccceEEEEeeCCeEEEecCChhHHHHHHHHHHHhcc------CCHHHHHHHHHHHH
Q 026458 162 TSTGLSRMLLSSPTCPVLEELGKQLSFEIAVGLNGRVWVNAESPSTVVLVSNAIMNSES------LSAVQQKIMVDKLL 234 (238)
Q Consensus 162 V~~~~v~rl~~~~~~~~l~~l~~~~~~ei~vG~NG~IWi~~~~~~~~~~i~~~i~~~e~------lt~~~~~~~~~~~~ 234 (238)
|+|++++|++++.++ |+++|+++++|+|+||+||||||++++...+.++..||++||+ +| +++++++++.+
T Consensus 152 i~p~kVpRvig~~~s-m~~~l~~~~~~~I~VG~NG~IWV~~~~~~~e~~~~~aI~~ie~ea~~~glt-dr~~~~i~~~~ 228 (239)
T COG1097 152 IPPSKVPRVIGKKGS-MLNMLKEKTGCEIIVGQNGRIWVDGENESLEELAIEAIRKIEREAHTSGLT-DRIKEFLKKLL 228 (239)
T ss_pred EchhhcceEecCCCc-HHHHhhhhcCeEEEEecCCEEEecCCCcchHHHHHHHHHHHhhhhhhhhHH-HHHHHHHHHHH
Confidence 999999999999998 9999999999999999999999999998889999999999997 66 78888877654
No 2
>KOG1004 consensus Exosomal 3'-5' exoribonuclease complex subunit Rrp40 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=3.7e-56 Score=374.65 Aligned_cols=221 Identities=47% Similarity=0.833 Sum_probs=206.6
Q ss_pred cEEecCCccCCCCCCCCCceeecCcEEEeCCEEEEEEeeEeEEec-CC----eEEEEccCCccCCCCCCEEEEEEEEecC
Q 026458 13 KIVVPGDVVLDLSSMTNQTIKLGGGLRQECDSVSVIKAGKLRFSK-PN----KYWVESSQKRYVPCVEDTVLGIVVDCKA 87 (238)
Q Consensus 13 ~iV~PGd~l~~~~~~~~~~~~~G~G~y~~~g~i~as~~G~v~~~~-~~----~i~V~~~~~~Y~P~vGDiVIG~V~~v~~ 87 (238)
.+.+|||.+..... .+..+|+|++..++.+..+.+|.++... ++ ..||...++||+|++||.|||+|++..+
T Consensus 2 ~~~~pg~~~~~~~~---~sv~~G~g~~~~g~~~~~~~~G~~~~~~~gk~~~~v~~vds~~kRYiP~~~D~VIGiV~~~~g 78 (230)
T KOG1004|consen 2 TFYFPGDSIPRPRL---CSVVLGPGLRRRGQERLVTKCGRLRHKEPGKGGGGVYWVDSQQKRYIPVKGDHVIGIVTSKSG 78 (230)
T ss_pred ceecCCcccccCcc---CceeecCCccccCceEEeccccceeeccCCcccceeEEEecccceecCCCCCEEEEEEEeccC
Confidence 46799999876532 2589999999999999999999887642 22 6799999999999999999999999999
Q ss_pred ceEEEEecCCeeeeecCcccCCcccccccCcCCCCEEEEEEEecCCCCcceEEEecCCCccCCCcccCCeeEEEechhhh
Q 026458 88 DNFFVDIRGPTIAFLPVLAFEGGTRRNIPKFEIGSLLYVRVVKANPGMNPELSCTDASGKAAEFGLLKDGYMFETSTGLS 167 (238)
Q Consensus 88 ~~~~VdI~~~~~a~L~~~~f~gatk~~r~~l~~GDlV~ArV~~~~~~~~~~Ls~~~~~~~~~~~G~L~~G~~~~V~~~~v 167 (238)
|.|+|||+.+..|.|++++|+||||+|||+|+.||+|||||..++++++++|+|.+++||+.+||+|+||+||+++++++
T Consensus 79 d~ykVDigg~~~a~L~~laFe~AtkrNrPnl~vGdliyakv~~a~~~~Epel~Cids~graaGfG~LkdG~if~vs~~~~ 158 (230)
T KOG1004|consen 79 DIYKVDIGGSEPASLSYLAFEGATKRNRPNLQVGDLIYAKVVDANKDMEPELTCIDSTGRAAGFGVLKDGMIFKVSLGLC 158 (230)
T ss_pred ceEEEecCCCCeeeeeeccccCccccCCCccccccEEEEEEEecCCCcCcceEEEcccCcccCcccccCceEEEecHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhhcCCCCchhhHhhccccceEEEEeeCCeEEEecCChhHHHHHHHHHHHhccCCHHHHHHHHHHHHhhc
Q 026458 168 RMLLSSPTCPVLEELGKQLSFEIAVGLNGRVWVNAESPSTVVLVSNAIMNSESLSAVQQKIMVDKLLQRI 237 (238)
Q Consensus 168 ~rl~~~~~~~~l~~l~~~~~~ei~vG~NG~IWi~~~~~~~~~~i~~~i~~~e~lt~~~~~~~~~~~~~~~ 237 (238)
|+|+. +.|++|+.++++++|||++|+||||||++++..++++++++|.+||+||.+|...|+++.++++
T Consensus 159 R~Ll~-p~~~iLq~vGk~~~FEia~GlNGriWV~ae~~~~t~~i~~~l~~~e~~td~~q~~~~k~~~~~~ 227 (230)
T KOG1004|consen 159 RKLLL-PDCPILQTVGKKYPFEIAFGLNGRIWVKAETLSDTLIIANILMNCEFMTDTQQRIMVKQLFKRL 227 (230)
T ss_pred HHHHc-CCCcHHHHhhcccceEEEEecCceEEEeccCcchHHHHHHHHHHhhccCcHHHHHHHHHHHHHH
Confidence 99997 7788999999999999999999999999999999999999999999999999888888888765
No 3
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=100.00 E-value=9.1e-52 Score=361.52 Aligned_cols=211 Identities=25% Similarity=0.383 Sum_probs=197.9
Q ss_pred CCcEEecCCccCCCCCCCCCceeecCcEEEeCCEEEEEEeeEeEEecCCeEEEEccCCccCCCCCCEEEEEEEEecCceE
Q 026458 11 VDKIVVPGDVVLDLSSMTNQTIKLGGGLRQECDSVSVIKAGKLRFSKPNKYWVESSQKRYVPCVEDTVLGIVVDCKADNF 90 (238)
Q Consensus 11 ~~~iV~PGd~l~~~~~~~~~~~~~G~G~y~~~g~i~as~~G~v~~~~~~~i~V~~~~~~Y~P~vGDiVIG~V~~v~~~~~ 90 (238)
.+++|+|||.|+. + +|.+|+|||.++|+|+||++|.++.+ ++.++|.|.+++|+|++||+|+|+|+++.++.|
T Consensus 7 ~~~~V~PGd~l~~-~-----~~~~G~Gty~~~g~i~As~~G~~~~~-~~~i~V~p~~~~y~P~vGDiViG~V~~i~~~~~ 79 (235)
T PRK04163 7 DRKIVVPGDLLAE-G-----EFKAGRGTYKENGKIYSTVVGLVDIK-DDKVRVIPLEGKYIPKVGDLVIGKVTDVTFSGW 79 (235)
T ss_pred CCcEECCCCCcCc-C-----CeecCCceEEeCCEEEEEEeEEEEEE-CCEEEEEECCCcccCCCCCEEEEEEEEEeCceE
Confidence 4589999999973 3 79999999999999999999999987 679999999989999999999999999999999
Q ss_pred EEEecCCeeeeecCcccCCc-----ccccccCcCCCCEEEEEEEecCCCCcceEEEecCCCccCCCcccCCeeEEEechh
Q 026458 91 FVDIRGPTIAFLPVLAFEGG-----TRRNIPKFEIGSLLYVRVVKANPGMNPELSCTDASGKAAEFGLLKDGYMFETSTG 165 (238)
Q Consensus 91 ~VdI~~~~~a~L~~~~f~ga-----tk~~r~~l~~GDlV~ArV~~~~~~~~~~Ls~~~~~~~~~~~G~L~~G~~~~V~~~ 165 (238)
+|||++++.|+||.+++.++ +++++++|++||+|+|||+++++++.++|||++ ++||+|.+|++++||+.
T Consensus 80 ~vdI~~~~~g~L~~s~i~~~~~~~d~~~~~~~~~~GDlV~akV~~i~~~~~~~LS~k~-----~~lG~L~~G~~~~V~~~ 154 (235)
T PRK04163 80 EVDINSPYKAYLPVSEVLGRPVNVEGTDLRKYLDIGDYIIAKVKDVDRTRDVVLTLKG-----KGLGKIEGGTIVEIKPV 154 (235)
T ss_pred EEEeCCCceeEEEHHHcCCCccccchhhhHhhCCCCCEEEEEEEEECCCCcEEEEEcC-----CCCCccCCCEEEEECHH
Confidence 99999999999999998764 488999999999999999999988889999988 89999999999999999
Q ss_pred hhhhhcCCCCchhhHhhccccceEEEEeeCCeEEEecCChhHHHHHHHHHHHhcc------CCHHHHHHHHHHHHh
Q 026458 166 LSRMLLSSPTCPVLEELGKQLSFEIAVGLNGRVWVNAESPSTVVLVSNAIMNSES------LSAVQQKIMVDKLLQ 235 (238)
Q Consensus 166 ~v~rl~~~~~~~~l~~l~~~~~~ei~vG~NG~IWi~~~~~~~~~~i~~~i~~~e~------lt~~~~~~~~~~~~~ 235 (238)
++++|+|+.+. +++.|.+.++|+|++|+||+|||.+++.+.+.++.++|+++|+ || +++++|+++..+
T Consensus 155 ~i~~lig~~g~-~i~~l~~~~~~~I~ig~NG~VwI~~~~~~~~~~a~~~I~~~e~~~~~~~l~-~~v~~~~~~~~~ 228 (235)
T PRK04163 155 KVPRVIGKKGS-MINMLKEETGCDIIVGQNGRIWIKGPDEEDEEIAIEAIKKIEREAHTSGLT-DRIKEFLEEELG 228 (235)
T ss_pred HHHhhcCCCCh-hHhhhhhhhCcEEEEcCCcEEEEeeCCHHHHHHHHHHHHHHHhhhhccChH-HHHHHHHHHhhh
Confidence 99999997765 9999999999999999999999999999999999999999997 99 999999986654
No 4
>KOG3013 consensus Exosomal 3'-5' exoribonuclease complex, subunit Rrp4 [RNA processing and modification]
Probab=100.00 E-value=1.7e-40 Score=286.91 Aligned_cols=175 Identities=22% Similarity=0.321 Sum_probs=159.1
Q ss_pred CCCcEEecCCccCCCCCCCCCceeecCcEEEeCCEEEEEEeeEeEEecCCeEEEEccCCccCCCCCCEEEEEEEEecCce
Q 026458 10 LVDKIVVPGDVVLDLSSMTNQTIKLGGGLRQECDSVSVIKAGKLRFSKPNKYWVESSQKRYVPCVEDTVLGIVVDCKADN 89 (238)
Q Consensus 10 ~~~~iV~PGd~l~~~~~~~~~~~~~G~G~y~~~g~i~as~~G~v~~~~~~~i~V~~~~~~Y~P~vGDiVIG~V~~v~~~~ 89 (238)
-..++|+||+.+...+ .|..|||||+.|+.|+||++|.+++. +++++|+|++.||.|++||+|+|+|+++.+++
T Consensus 27 ~~~~ivtPG~~V~~d~-----~fmRGHGTy~~d~~i~ssvaG~v~rv-NkLi~V~plk~rY~pEvGDvVVgRV~eVq~KR 100 (301)
T KOG3013|consen 27 DHSTIVTPGELVTDDP-----GFMRGHGTYVRDGEIYSSVAGVVQRV-NKLISVKPLKSRYAPEVGDVVVGRVIEVQQKR 100 (301)
T ss_pred cCceeecCCccccCch-----hhhhcccceecCCeEEEeecchhhhh-cceEEEeehhhhcCCccCCEEEEEeeeeecce
Confidence 3557999999999876 69999999999999999999999987 89999999999999999999999999999999
Q ss_pred EEEEecCCeeeeecCcc--cCCc---------ccccccCcCCCCEEEEEEEecCCCCcceEEEecCCCccCCCcccCCee
Q 026458 90 FFVDIRGPTIAFLPVLA--FEGG---------TRRNIPKFEIGSLLYVRVVKANPGMNPELSCTDASGKAAEFGLLKDGY 158 (238)
Q Consensus 90 ~~VdI~~~~~a~L~~~~--f~ga---------tk~~r~~l~~GDlV~ArV~~~~~~~~~~Ls~~~~~~~~~~~G~L~~G~ 158 (238)
|+||+++-.+|+|..++ .||. +..||.+|+.||+|.|+|+.+..++...|+++. ..||||..|+
T Consensus 101 Wkvd~nsk~d~vL~LsSvNLPGg~~RRk~~~DEl~MR~fl~egDLi~AEVQ~v~~dGs~sLhTRS-----~KYGKL~~G~ 175 (301)
T KOG3013|consen 101 WKVDLNSKQDAVLMLSSVNLPGGIQRRKSEEDELQMRSFLKEGDLIVAEVQNVFHDGSLSLHTRS-----LKYGKLGQGI 175 (301)
T ss_pred eEEecccccceEEEeecccCCchhhhccchhhHHHHHHHhhccCeehHHHHHhccCCeEEEEecc-----hhcccccCce
Confidence 99999999999998864 5764 446999999999999999999999999999988 9999999999
Q ss_pred EEEechhhhhhhcCCCCchhhHhhccccceEEEEeeCCeEEEec
Q 026458 159 MFETSTGLSRMLLSSPTCPVLEELGKQLSFEIAVGLNGRVWVNA 202 (238)
Q Consensus 159 ~~~V~~~~v~rl~~~~~~~~l~~l~~~~~~ei~vG~NG~IWi~~ 202 (238)
+++|||.+++|.. .++ ..+ .++.++|+|+||+|||..
T Consensus 176 lvkVpp~Lvkr~K--~hf---h~l--p~g~~vIlG~NGyIWv~~ 212 (301)
T KOG3013|consen 176 LVKVPPALVKRSK--THF---HNL--PGGVDVILGCNGYIWVGP 212 (301)
T ss_pred EEEeCHHHhhhhh--hhh---ccC--CCCeEEEEecCceEEecC
Confidence 9999999999975 332 223 479999999999999976
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=3e-30 Score=192.61 Aligned_cols=86 Identities=58% Similarity=0.888 Sum_probs=84.3
Q ss_pred ccCCCCCCEEEEEEEEecCceEEEEecCCeeeeecCcccCCcccccccCcCCCCEEEEEEEecCCCCcceEEEecCCCcc
Q 026458 69 RYVPCVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEGGTRRNIPKFEIGSLLYVRVVKANPGMNPELSCTDASGKA 148 (238)
Q Consensus 69 ~Y~P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~gatk~~r~~l~~GDlV~ArV~~~~~~~~~~Ls~~~~~~~~ 148 (238)
||+|++||+|||+|+++.+++|+|||++++.|+||.++|+|++++|||+|++||+|||||.+++++++++|||.+++||+
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 026458 149 AEFGLL 154 (238)
Q Consensus 149 ~~~G~L 154 (238)
.+||.|
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=99.94 E-value=3.6e-26 Score=193.90 Aligned_cols=134 Identities=22% Similarity=0.284 Sum_probs=118.4
Q ss_pred CCCcEEecCCccCCCCCCCCCceeecCcEEEeCCEEEEEEeeEeEEec-CCeEEEEccCC-ccCCCCCCEEEEEEEEecC
Q 026458 10 LVDKIVVPGDVVLDLSSMTNQTIKLGGGLRQECDSVSVIKAGKLRFSK-PNKYWVESSQK-RYVPCVEDTVLGIVVDCKA 87 (238)
Q Consensus 10 ~~~~iV~PGd~l~~~~~~~~~~~~~G~G~y~~~g~i~as~~G~v~~~~-~~~i~V~~~~~-~Y~P~vGDiVIG~V~~v~~ 87 (238)
..+++|+|||.|+..+ +|.+|+|||+++|+|+|+++|.++.++ ++.++|.|.+. .|.|++||+|+|+|+++..
T Consensus 3 ~~~~~V~PGe~l~~~~-----e~~~G~Gty~~~~~i~as~~G~~~id~~~~~Isv~P~~~~~~~~~~GdiV~GkV~~i~~ 77 (189)
T PRK09521 3 KQGDLVLPGDYLAVIE-----EYLPGEGTYEDNGEVYASVVGKVFIDDINRKISVIPFKKTPPLLKKGDIVYGRVVDVKE 77 (189)
T ss_pred ccCCEECCCCcccccc-----ceEcCCCEEeeCCEEEEEeeEEEEEcCCCCEEEEecCcCCCCCCCCCCEEEEEEEEEcC
Confidence 3568999999998866 799999999999999999999999864 45899999876 8999999999999999999
Q ss_pred ceEEEEecC----------CeeeeecCcccCC-cccccccCcCCCCEEEEEEEecCCCCcceEEEecCCCccCCCcccC
Q 026458 88 DNFFVDIRG----------PTIAFLPVLAFEG-GTRRNIPKFEIGSLLYVRVVKANPGMNPELSCTDASGKAAEFGLLK 155 (238)
Q Consensus 88 ~~~~VdI~~----------~~~a~L~~~~f~g-atk~~r~~l~~GDlV~ArV~~~~~~~~~~Ls~~~~~~~~~~~G~L~ 155 (238)
+.|.|||.+ +..|+||.+++.. ..+++++.|++||+|+|||++++ +.++|||++ ..||+|.
T Consensus 78 ~g~~V~I~~~~~~~~~l~~~~~G~l~~s~i~~~~~~~~~~~~~~GD~V~akV~~i~--~~i~LS~k~-----~~lGvv~ 149 (189)
T PRK09521 78 QRALVRIVSIEGSERELATSKLAYIHISQVSDGYVESLTDAFKIGDIVRAKVISYT--DPLQLSTKG-----KDLGVIY 149 (189)
T ss_pred CeEEEEEEEecccccccCCCceeeEEhhHcChhhhhhHHhccCCCCEEEEEEEecC--CcEEEEEec-----CCceEEE
Confidence 999999963 5789999887643 35567899999999999999998 789999998 8899993
No 7
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=99.93 E-value=3.1e-25 Score=185.13 Aligned_cols=134 Identities=24% Similarity=0.326 Sum_probs=120.3
Q ss_pred CCCCcEEecCCccCCCCCCCCCceeecCcEEEeCCEEEEEEeeEeEEec-CCeEEEEccCC-ccCCCCCCEEEEEEEEec
Q 026458 9 NLVDKIVVPGDVVLDLSSMTNQTIKLGGGLRQECDSVSVIKAGKLRFSK-PNKYWVESSQK-RYVPCVEDTVLGIVVDCK 86 (238)
Q Consensus 9 ~~~~~iV~PGd~l~~~~~~~~~~~~~G~G~y~~~g~i~as~~G~v~~~~-~~~i~V~~~~~-~Y~P~vGDiVIG~V~~v~ 86 (238)
...+.+|+|||.|+..| ||.+|.|||+++|.|+|+.+|.+.+|+ +..++|.|.++ ..+|+.||+|+|+|+++.
T Consensus 2 ~~~g~~v~PGd~~a~~E-----E~~~G~gt~~~~g~i~Aa~~G~~~~d~~n~~~~V~p~~~~~~~~K~GdiV~grV~~v~ 76 (188)
T COG1096 2 VKDGTFVLPGDVLAVIE-----EFLPGEGTYEEGGEIRAAATGVVRRDDKNRVISVKPGKKTPPLPKGGDIVYGRVTDVR 76 (188)
T ss_pred cccCcEEcCcceeeeee-----eeecCCCeEeECCEEEEeecccEEEcccceEEEeccCCCCCCCCCCCCEEEEEEeecc
Confidence 45679999999999988 899999999999999999999999874 46889999988 889999999999999999
Q ss_pred CceEEEEecC----------CeeeeecCcccC-CcccccccCcCCCCEEEEEEEecCCCCcceEEEecCCCccCCCccc
Q 026458 87 ADNFFVDIRG----------PTIAFLPVLAFE-GGTRRNIPKFEIGSLLYVRVVKANPGMNPELSCTDASGKAAEFGLL 154 (238)
Q Consensus 87 ~~~~~VdI~~----------~~~a~L~~~~f~-gatk~~r~~l~~GDlV~ArV~~~~~~~~~~Ls~~~~~~~~~~~G~L 154 (238)
.+.|.|.|-+ +..|.+|+++.. +..++.+++|++||+|+|||++.. ..++||+.+ +.||++
T Consensus 77 ~~~a~V~i~~ve~~~r~~~~~~~~~ihvs~~~~~~~~~~~d~f~~GDivrA~Vis~~--~~~~Lst~~-----~dlGVI 148 (188)
T COG1096 77 EQRALVRIVGVEGKERELATSGAADIHVSQVRDGYVEKLSDAFRIGDIVRARVISTG--DPIQLSTKG-----NDLGVI 148 (188)
T ss_pred ceEEEEEEEEEecccccCCCCceeeEEEEecccccccccccccccccEEEEEEEecC--CCeEEEecC-----CcceEE
Confidence 9999999843 567899998765 447778899999999999999987 679999998 899998
No 8
>KOG3409 consensus Exosomal 3'-5' exoribonuclease complex, subunit ski4 (Csl4) [Translation, ribosomal structure and biogenesis]
Probab=99.88 E-value=7e-22 Score=162.51 Aligned_cols=149 Identities=19% Similarity=0.217 Sum_probs=120.3
Q ss_pred CCcEEecCCccCCCCCCCCCceeecCcEEEeCCEEEEEEeeEeEEec-CCeEEEEcc----CCccCCCCCCEEEEEEEEe
Q 026458 11 VDKIVVPGDVVLDLSSMTNQTIKLGGGLRQECDSVSVIKAGKLRFSK-PNKYWVESS----QKRYVPCVEDTVLGIVVDC 85 (238)
Q Consensus 11 ~~~iV~PGd~l~~~~~~~~~~~~~G~G~y~~~g~i~as~~G~v~~~~-~~~i~V~~~----~~~Y~P~vGDiVIG~V~~v 85 (238)
...+|+|||+++..+ .++..|.|||+.++.|+||.+|....+. .+...|... ...-+|.+||||.++|+.+
T Consensus 4 a~~~~lpG~~~c~~e----~~~~~g~Gtye~~~yI~aS~ag~~~~~~~~~~~~v~~~~~~~~~~~LP~~G~IVtarV~~i 79 (193)
T KOG3409|consen 4 AETLVLPGEVVCRAE----GEYRMGEGTYERNGYIFASVAGVNFRDNLVQKIEVVSVEKQLFNELLPFVGAIVTARVSRI 79 (193)
T ss_pred ceEEEcccceeeecc----cccccccceeecCCeEEeccccceeecCCccceeeeeecccchhhcCCccCcEEEEEEEee
Confidence 347899999999887 5799999999999999999999665441 234444432 3457999999999999999
Q ss_pred cCceEEEEecC--------CeeeeecCcccCCcccccc----cCcCCCCEEEEEEEecCCCCcceEEEecCCCccCCCcc
Q 026458 86 KADNFFVDIRG--------PTIAFLPVLAFEGGTRRNI----PKFEIGSLLYVRVVKANPGMNPELSCTDASGKAAEFGL 153 (238)
Q Consensus 86 ~~~~~~VdI~~--------~~~a~L~~~~f~gatk~~r----~~l~~GDlV~ArV~~~~~~~~~~Ls~~~~~~~~~~~G~ 153 (238)
+..+++|||.+ .+.|+|+...+. +|+++| .+|+|||+|.|+|++.+...+|.||+.. +.||+
T Consensus 80 ~~rfAkv~I~~V~d~~lk~~FrglirkqdvR-~tEkdrv~v~ksFrPgDiVlAkVis~~~~~~y~LTtAe-----neLGV 153 (193)
T KOG3409|consen 80 NLRFAKVDILSVGDKPLKKSFRGLIRKQDVR-ATEKDRVKVYKSFRPGDIVLAKVISLGDGSNYLLTTAE-----NELGV 153 (193)
T ss_pred ccceeeEEEEEEcCEEhhhhhcceeehhhcc-ccccchhhhhhccCCCcEEEEEEeecCCCCcEEEEEec-----ccceE
Confidence 99999999976 456677665553 344444 4799999999999998888899999998 89998
Q ss_pred c------CCeeEEEechhhhhh
Q 026458 154 L------KDGYMFETSTGLSRM 169 (238)
Q Consensus 154 L------~~G~~~~V~~~~v~r 169 (238)
+ .++.|+.|++.....
T Consensus 154 V~a~as~~g~~M~pvdw~~mqs 175 (193)
T KOG3409|consen 154 VFARASETGEPMVPVDWQEMQS 175 (193)
T ss_pred EEEeccccCCceeeccceeEEc
Confidence 8 578899999987654
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=6e-19 Score=133.50 Aligned_cols=80 Identities=18% Similarity=0.203 Sum_probs=71.8
Q ss_pred cCCCCCCEEEEEEEEecCceEEEEe--------cCCeeeeecCcccCCc---ccccccCcCCCCEEEEEEEecCCCCcce
Q 026458 70 YVPCVEDTVLGIVVDCKADNFFVDI--------RGPTIAFLPVLAFEGG---TRRNIPKFEIGSLLYVRVVKANPGMNPE 138 (238)
Q Consensus 70 Y~P~vGDiVIG~V~~v~~~~~~VdI--------~~~~~a~L~~~~f~ga---tk~~r~~l~~GDlV~ArV~~~~~~~~~~ 138 (238)
|.|++||+|+|+|++++.++|.||| ++++.|+||.+++... ..+|+.+|++||+|+|||++.++.+.++
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 7789999998876432 2268999999999999999999888999
Q ss_pred EEEecCCCccCCCccc
Q 026458 139 LSCTDASGKAAEFGLL 154 (238)
Q Consensus 139 Ls~~~~~~~~~~~G~L 154 (238)
||+.+ ++||++
T Consensus 82 Lst~~-----~~lGVv 92 (92)
T cd05791 82 LSTAE-----NELGVV 92 (92)
T ss_pred EEecC-----CCCccC
Confidence 99998 888875
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=99.75 E-value=5.3e-18 Score=124.90 Aligned_cols=81 Identities=28% Similarity=0.413 Sum_probs=75.4
Q ss_pred ccCCCCCCEEEEEEEEecCceEEEEecCCeeeeecCcccCCc-ccccccCcCCCCEEEEEEEecCCCCcceEEEecCCCc
Q 026458 69 RYVPCVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEGG-TRRNIPKFEIGSLLYVRVVKANPGMNPELSCTDASGK 147 (238)
Q Consensus 69 ~Y~P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~ga-tk~~r~~l~~GDlV~ArV~~~~~~~~~~Ls~~~~~~~ 147 (238)
+|.|++||+|+|+|+++..+.|.|||++..+|+||.+++... .+++++.|++||+|.|+|+++++.+.+.|||.+
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 699999999999999999999999999999999999998754 778889999999999999999887889999998
Q ss_pred cCCCccc
Q 026458 148 AAEFGLL 154 (238)
Q Consensus 148 ~~~~G~L 154 (238)
++||+|
T Consensus 77 -~~~Gvi 82 (82)
T cd04454 77 -NELGVI 82 (82)
T ss_pred -CCCccC
Confidence 888875
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=99.57 E-value=1.2e-14 Score=107.77 Aligned_cols=81 Identities=26% Similarity=0.379 Sum_probs=72.9
Q ss_pred ccCCCCCCEEEEEEEEecCceEEEEecCCeeeeecCcccCC-----cccccccCcCCCCEEEEEEEecCCCCcceEEEec
Q 026458 69 RYVPCVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEG-----GTRRNIPKFEIGSLLYVRVVKANPGMNPELSCTD 143 (238)
Q Consensus 69 ~Y~P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~g-----atk~~r~~l~~GDlV~ArV~~~~~~~~~~Ls~~~ 143 (238)
+|.|++||+|.|+|+++.++.|.|+|+....|+||.+++.. ..+++++.|++||.|.|+|+++++++.+.||+..
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 69999999999999999999999999999999999998853 3456677899999999999999887889999988
Q ss_pred CCCccCCCccc
Q 026458 144 ASGKAAEFGLL 154 (238)
Q Consensus 144 ~~~~~~~~G~L 154 (238)
.+||+|
T Consensus 81 -----~~~g~~ 86 (86)
T cd05789 81 -----LKYGKL 86 (86)
T ss_pred -----ccccCC
Confidence 788876
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=99.27 E-value=8.6e-12 Score=92.39 Aligned_cols=61 Identities=18% Similarity=0.196 Sum_probs=38.5
Q ss_pred CCCCCCEEEEEEEEecCceEEEEecCC------------------eeeeecCcccCCc---ccccccCcCCCCEEEEEEE
Q 026458 71 VPCVEDTVLGIVVDCKADNFFVDIRGP------------------TIAFLPVLAFEGG---TRRNIPKFEIGSLLYVRVV 129 (238)
Q Consensus 71 ~P~vGDiVIG~V~~v~~~~~~VdI~~~------------------~~a~L~~~~f~ga---tk~~r~~l~~GDlV~ArV~ 129 (238)
+|++||+|+|+|++++..++.|+|.+. +.|+++.+..... .-+|..+|+|||+|+|||+
T Consensus 1 lP~vGdiV~~rVtrv~~~~a~v~Il~v~~~~~~~~~~~~~~l~~~f~GiIR~~DVR~te~Dkv~~~~~FrpGDIVrA~Vi 80 (82)
T PF10447_consen 1 LPKVGDIVIARVTRVNPRQAKVEILCVEGKGNDSINAGDRPLKEPFQGIIRKQDVRATEKDKVKMYDCFRPGDIVRARVI 80 (82)
T ss_dssp ---TT-EEEEEEEEE-SSEEEEEEEES----------SSS----SS-S-EEEEGGGT-SS----GGGT--SSSEEEEEEE
T ss_pred CCCCCCEEEEEEEEEeccEEEEEEEEEEeccccccccCCcccccccEEEEEeeeecccccchhhHHhccCCCCEEEEEEe
Confidence 599999999999999999999999765 2344444333211 1146789999999999999
Q ss_pred ec
Q 026458 130 KA 131 (238)
Q Consensus 130 ~~ 131 (238)
|+
T Consensus 81 Sl 82 (82)
T PF10447_consen 81 SL 82 (82)
T ss_dssp EE
T ss_pred eC
Confidence 84
No 13
>PF14382 ECR1_N: Exosome complex exonuclease RRP4 N-terminal region; PDB: 2NN6_I 3M7N_C 2BA1_A 3M85_C.
Probab=99.13 E-value=3.8e-11 Score=76.82 Aligned_cols=38 Identities=26% Similarity=0.330 Sum_probs=33.6
Q ss_pred EEecCCccCCCCCCCCCceeecCcEEEeCCEEEEEEeeEeEEe
Q 026458 14 IVVPGDVVLDLSSMTNQTIKLGGGLRQECDSVSVIKAGKLRFS 56 (238)
Q Consensus 14 iV~PGd~l~~~~~~~~~~~~~G~G~y~~~g~i~as~~G~v~~~ 56 (238)
+|+|||.|+..+ +|.+|+|||+++|+|+||++|.++++
T Consensus 1 iV~PG~~l~~~~-----e~~~G~GTY~~~g~I~asv~G~v~~~ 38 (39)
T PF14382_consen 1 IVVPGDRLGSSE-----EYMPGHGTYVRDGNIYASVAGTVKID 38 (39)
T ss_dssp EE-TT-EEEETT-----TSEESTTEEEETTEEEESSSEEEEEE
T ss_pred CCCCCCEeecCC-----CEecCCCEEEeCCEEEEEeeEEEEEc
Confidence 699999999876 89999999999999999999999875
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=98.71 E-value=6.4e-08 Score=68.57 Aligned_cols=67 Identities=25% Similarity=0.324 Sum_probs=56.0
Q ss_pred CCEEEEEEEEecCceEEEEecCCeeeeecCcccC-CcccccccCcCCCCEEEEEEEecCC-CCcceEEE
Q 026458 75 EDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFE-GGTRRNIPKFEIGSLLYVRVVKANP-GMNPELSC 141 (238)
Q Consensus 75 GDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~-gatk~~r~~l~~GDlV~ArV~~~~~-~~~~~Ls~ 141 (238)
||+|.|+|+++..+.|.||+++...|+||.+++. ...++....|++||.+.|+|.++++ ...+.||.
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 8999999999999999999998999999998774 3344456679999999999999974 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=98.69 E-value=7.4e-08 Score=69.27 Aligned_cols=68 Identities=13% Similarity=0.187 Sum_probs=58.2
Q ss_pred CCCCEEEEEEEEecC-ceEEEEecCCeeeeecCcccCC-cccccccCcCCCCEEEEEEEecCCCCcceEEE
Q 026458 73 CVEDTVLGIVVDCKA-DNFFVDIRGPTIAFLPVLAFEG-GTRRNIPKFEIGSLLYVRVVKANPGMNPELSC 141 (238)
Q Consensus 73 ~vGDiVIG~V~~v~~-~~~~VdI~~~~~a~L~~~~f~g-atk~~r~~l~~GDlV~ArV~~~~~~~~~~Ls~ 141 (238)
++||+|.|+|+++.+ ..+.|++.....|.+|++++.. ..++....|++||.|.|+|.++++ ..+.||+
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 5899999999999999998754 344455679999999999999975 7788886
No 16
>smart00316 S1 Ribosomal protein S1-like RNA-binding domain.
Probab=98.65 E-value=1.3e-07 Score=65.67 Aligned_cols=69 Identities=20% Similarity=0.260 Sum_probs=59.0
Q ss_pred CCCCEEEEEEEEecCceEEEEecCCeeeeecCcccCCc-ccccccCcCCCCEEEEEEEecCCC-CcceEEE
Q 026458 73 CVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEGG-TRRNIPKFEIGSLLYVRVVKANPG-MNPELSC 141 (238)
Q Consensus 73 ~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~ga-tk~~r~~l~~GDlV~ArV~~~~~~-~~~~Ls~ 141 (238)
++||+|.|+|+++....|.|++++...|.+|.+.+... .++....|++||.|.|+|.+++.+ ..+.||+
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 46999999999999999999999889999998876543 444556799999999999999876 6777776
No 17
>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=98.61 E-value=2.3e-07 Score=66.45 Aligned_cols=71 Identities=14% Similarity=0.110 Sum_probs=59.8
Q ss_pred CCCCCEEEEEEEEecCceEEEEecC--CeeeeecCcccCCc-ccccccCcCCCCEEEEEEEecCCC-CcceEEEe
Q 026458 72 PCVEDTVLGIVVDCKADNFFVDIRG--PTIAFLPVLAFEGG-TRRNIPKFEIGSLLYVRVVKANPG-MNPELSCT 142 (238)
Q Consensus 72 P~vGDiVIG~V~~v~~~~~~VdI~~--~~~a~L~~~~f~ga-tk~~r~~l~~GDlV~ArV~~~~~~-~~~~Ls~~ 142 (238)
|++|++|.|+|+++....+.|++.. ...|.||.+++... ..+....|++||.|.|+|.+++.. ..+.||++
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 37999999887543 445566799999999999999864 45788874
No 18
>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=98.60 E-value=2.8e-07 Score=64.02 Aligned_cols=68 Identities=18% Similarity=0.186 Sum_probs=57.6
Q ss_pred CCEEEEEEEEecCceEEEEecCCeeeeecCcccCCc-ccccccCcCCCCEEEEEEEecCCCCcceEEEe
Q 026458 75 EDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEGG-TRRNIPKFEIGSLLYVRVVKANPGMNPELSCT 142 (238)
Q Consensus 75 GDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~ga-tk~~r~~l~~GDlV~ArV~~~~~~~~~~Ls~~ 142 (238)
||+|.|+|+++....|.|+|.....|.||.+++... .......|++||.|.++|.+++..+.+.||++
T Consensus 1 G~~~~g~V~~i~~~g~~v~i~~~~~g~l~~~~l~~~~~~~~~~~~~~Gd~v~v~v~~~~~~~~i~ls~k 69 (69)
T cd05692 1 GSVVEGTVTRLKPFGAFVELGGGISGLVHISQIAHKRVKDVKDVLKEGDKVKVKVLSIDARGRISLSIK 69 (69)
T ss_pred CCEEEEEEEEEEeeeEEEEECCCCEEEEEhHHcCCcccCCHHHccCCCCEEEEEEEEECCCCcEEEEEC
Confidence 799999999999999999999999999999877543 22334569999999999999987667888873
No 19
>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=2.5e-07 Score=65.56 Aligned_cols=69 Identities=16% Similarity=0.234 Sum_probs=59.5
Q ss_pred CCEEEEEEEEecCceEEEEecCCeeeeecCcccCCc-ccccccCcCCCCEEEEEEEecCCC-CcceEEEec
Q 026458 75 EDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEGG-TRRNIPKFEIGSLLYVRVVKANPG-MNPELSCTD 143 (238)
Q Consensus 75 GDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~ga-tk~~r~~l~~GDlV~ArV~~~~~~-~~~~Ls~~~ 143 (238)
||+|.|+|+++.+..|.|+|.....|.+|.+.+... .++....|++||.|.|+|.+++.. ..+.||++.
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 899999999999999999999989999999877532 445566799999999999999876 568899875
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=98.53 E-value=5.2e-07 Score=64.36 Aligned_cols=70 Identities=23% Similarity=0.305 Sum_probs=61.4
Q ss_pred CCCCCEEEEEEEEecCceEEEEecCCeeeeecCcccCCc-ccccccCcCCCCEEEEEEEecCCCCc-ceEEE
Q 026458 72 PCVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEGG-TRRNIPKFEIGSLLYVRVVKANPGMN-PELSC 141 (238)
Q Consensus 72 P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~ga-tk~~r~~l~~GDlV~ArV~~~~~~~~-~~Ls~ 141 (238)
|++||+|-|+|+++....+.|+++....|++|.+++... .......|++||-|.|+|.+++.... +.||+
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 789999999999999999999999999999999988643 45566789999999999999987654 77775
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=98.51 E-value=9.4e-07 Score=63.02 Aligned_cols=69 Identities=14% Similarity=0.071 Sum_probs=59.0
Q ss_pred CCCCEEEEEEEEecCceEEEEecCCeeeeecCcccCCc-ccccccCcCCCCEEEEEEEecCCC-CcceEEE
Q 026458 73 CVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEGG-TRRNIPKFEIGSLLYVRVVKANPG-MNPELSC 141 (238)
Q Consensus 73 ~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~ga-tk~~r~~l~~GDlV~ArV~~~~~~-~~~~Ls~ 141 (238)
++||+|.|+|+++.+..+.|++.....|.+|.+.+... .++....|++||.|.|+|.+++.+ ..+.||+
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 58999999999999999999999999999999887532 334566799999999999999864 5778876
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=98.46 E-value=6.6e-07 Score=63.63 Aligned_cols=62 Identities=19% Similarity=0.231 Sum_probs=53.4
Q ss_pred CCEEEEEEEEecCceEEEEecCCeeeeecCcccCCc---ccccccCcCCCCEEEEEEEecCCCCc
Q 026458 75 EDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEGG---TRRNIPKFEIGSLLYVRVVKANPGMN 136 (238)
Q Consensus 75 GDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~ga---tk~~r~~l~~GDlV~ArV~~~~~~~~ 136 (238)
||+|.|+|+++....+.|++.+..+|.+|.+++... ..++...|++||.|.|+|++++....
T Consensus 1 G~iV~g~V~~i~~~gi~v~l~~~i~g~i~~~~i~~~~~~~~~~~~~~~~Gd~i~~kVl~~d~~~~ 65 (70)
T cd05702 1 GDLVKAKVKSVKPTQLNVQLADNVHGRIHVSEVFDEWPDGKNPLSKFKIGQKIKARVIGGHDAKT 65 (70)
T ss_pred CCEEEEEEEEEECCcEEEEeCCCcEEEEEHHHhccccccccChhHhCCCCCEEEEEEEEEeCccc
Confidence 899999999999999999999999999999877532 44556779999999999999876543
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=98.40 E-value=1.8e-06 Score=61.68 Aligned_cols=71 Identities=17% Similarity=0.214 Sum_probs=59.3
Q ss_pred CCCCEEEEEEEEecCceEEEEecC-CeeeeecCcccCC-cccccccCcCCCCEEEEEEEecCC-CCcceEEEec
Q 026458 73 CVEDTVLGIVVDCKADNFFVDIRG-PTIAFLPVLAFEG-GTRRNIPKFEIGSLLYVRVVKANP-GMNPELSCTD 143 (238)
Q Consensus 73 ~vGDiVIG~V~~v~~~~~~VdI~~-~~~a~L~~~~f~g-atk~~r~~l~~GDlV~ArV~~~~~-~~~~~Ls~~~ 143 (238)
++|++|.|+|+++....+.|++.. ...|.+|.+.+.. ...+....|++||.|.|+|.+++. ...+.|+++.
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 7899999887753 233445679999999999999986 4678888875
No 24
>PRK08582 hypothetical protein; Provisional
Probab=98.37 E-value=3.1e-06 Score=68.69 Aligned_cols=72 Identities=14% Similarity=0.137 Sum_probs=63.6
Q ss_pred CCCCCEEEEEEEEecCceEEEEecCCeeeeecCcccCC-cccccccCcCCCCEEEEEEEecCCCCcceEEEec
Q 026458 72 PCVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEG-GTRRNIPKFEIGSLLYVRVVKANPGMNPELSCTD 143 (238)
Q Consensus 72 P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~g-atk~~r~~l~~GDlV~ArV~~~~~~~~~~Ls~~~ 143 (238)
.++|++|.|+|+++....++|+|.....|.+|++++.. ...+....|.+||.|.|+|.+++..+.+.||+..
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 46899999999999999999999999999999998753 3455567899999999999999877889999876
No 25
>PRK07252 hypothetical protein; Provisional
Probab=98.37 E-value=2.3e-06 Score=67.76 Aligned_cols=72 Identities=18% Similarity=0.250 Sum_probs=61.5
Q ss_pred CCCCEEEEEEEEecCceEEEEecCCeeeeecCcccCCc-ccccccCcCCCCEEEEEEEecCC-CCcceEEEecC
Q 026458 73 CVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEGG-TRRNIPKFEIGSLLYVRVVKANP-GMNPELSCTDA 144 (238)
Q Consensus 73 ~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~ga-tk~~r~~l~~GDlV~ArV~~~~~-~~~~~Ls~~~~ 144 (238)
++||+|.|+|+++....+.|+|.....|.+|.+++... .......|++||.|.++|.+++. .+.+.||++..
T Consensus 2 kvG~iv~G~V~~V~~~G~fVei~~~~~GllhiseLs~~~~~~~~~~~~vGD~V~VkI~~iD~~~~ri~lSlk~~ 75 (120)
T PRK07252 2 KIGDKLKGTITGIKPYGAFVALENGTTGLIHISEIKTGFIDNIHQLLKVGEEVLVQVVDFDEYTGKASLSLRTL 75 (120)
T ss_pred CCCCEEEEEEEEEeCcEEEEEECCCCEEEEEHHHcCCccccChhhccCCCCEEEEEEEEEeCCCCEEEEEEeec
Confidence 47999999999999999999999889999999887532 33445679999999999999987 56788999874
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=98.34 E-value=1.8e-06 Score=60.87 Aligned_cols=65 Identities=22% Similarity=0.321 Sum_probs=54.7
Q ss_pred CCEEEEEEEEecCceEEEEecCCeeeeecCcccCCc-ccccccCcCCCCEEEEEEEecCCC-CcceE
Q 026458 75 EDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEGG-TRRNIPKFEIGSLLYVRVVKANPG-MNPEL 139 (238)
Q Consensus 75 GDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~ga-tk~~r~~l~~GDlV~ArV~~~~~~-~~~~L 139 (238)
||+|.|+|+++....+.|++.....|.+|.+.+... .++....|++||.|.|+|.++++. +.+.|
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 799999999999999999999889999999887543 445566799999999999999863 34444
No 27
>PRK08059 general stress protein 13; Validated
Probab=98.31 E-value=3.2e-06 Score=67.04 Aligned_cols=73 Identities=18% Similarity=0.185 Sum_probs=61.9
Q ss_pred CCCCCEEEEEEEEecCceEEEEecCCeeeeecCcccCCc-ccccccCcCCCCEEEEEEEecCC-CCcceEEEecC
Q 026458 72 PCVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEGG-TRRNIPKFEIGSLLYVRVVKANP-GMNPELSCTDA 144 (238)
Q Consensus 72 P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~ga-tk~~r~~l~~GDlV~ArV~~~~~-~~~~~Ls~~~~ 144 (238)
.++||+|.|+|+++....|.|+|.....|.+|.+++... ..+....|++||.|.|+|.+++. .+.+.||++..
T Consensus 5 ~k~G~iv~G~V~~i~~~G~fV~i~~~~~Gli~~sel~~~~~~~~~~~~~vGD~I~vkI~~id~~~~~i~lslk~~ 79 (123)
T PRK08059 5 YEVGSVVTGKVTGIQPYGAFVALDEETQGLVHISEITHGFVKDIHDFLSVGDEVKVKVLSVDEEKGKISLSIRAT 79 (123)
T ss_pred CCCCCEEEEEEEEEecceEEEEECCCCEEEEEHHHCCcccccCHHHcCCCCCEEEEEEEEEECCCCeEEEEEEEc
Confidence 468999999999999999999999999999999887543 33335679999999999999965 56899999873
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=98.29 E-value=2.8e-06 Score=61.48 Aligned_cols=62 Identities=13% Similarity=0.109 Sum_probs=52.7
Q ss_pred CCCCEEEEEEEEecCceEEEEecCCeeeeecCcccCCcc-cc---cccCcCCCCEEEEEEEecCCC
Q 026458 73 CVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEGGT-RR---NIPKFEIGSLLYVRVVKANPG 134 (238)
Q Consensus 73 ~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~gat-k~---~r~~l~~GDlV~ArV~~~~~~ 134 (238)
++||+|.|+|+++.+..+.|+++..-.|.+|.++..... ++ ....|++||.|.|+|++++++
T Consensus 2 k~G~~V~g~V~~i~~~G~fV~l~~~v~G~v~~~~ls~~~~~~~~~~~~~~~~G~~v~~kVl~id~~ 67 (74)
T cd05705 2 KEGQLLRGYVSSVTKQGVFFRLSSSIVGRVLFQNVTKYFVSDPSLYNKYLPEGKLLTAKVLSVNSE 67 (74)
T ss_pred CCCCEEEEEEEEEeCCcEEEEeCCCCEEEEEHHHccCccccChhhHhcccCCCCEEEEEEEEEECC
Confidence 689999999999999999999998899999987764332 22 346899999999999999764
No 29
>PRK08563 DNA-directed RNA polymerase subunit E'; Provisional
Probab=98.29 E-value=2.8e-06 Score=71.80 Aligned_cols=80 Identities=20% Similarity=0.308 Sum_probs=65.1
Q ss_pred ccCCCCCCEEEEEEEEecCceEEEEecCCeeeeecCcccCCc------------ccccccCcCCCCEEEEEEEecCCC--
Q 026458 69 RYVPCVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEGG------------TRRNIPKFEIGSLLYVRVVKANPG-- 134 (238)
Q Consensus 69 ~Y~P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~ga------------tk~~r~~l~~GDlV~ArV~~~~~~-- 134 (238)
.|.|.+|++|.|+|++++...+.|+++ +.+++++.++.+.. .++.+..++.||.|++||.+++.+
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 467999999999999999999999998 68888887665432 123456799999999999998753
Q ss_pred ----CcceEEEecCCCccCCCccc
Q 026458 135 ----MNPELSCTDASGKAAEFGLL 154 (238)
Q Consensus 135 ----~~~~Ls~~~~~~~~~~~G~L 154 (238)
..+.||+.+ ++||++
T Consensus 155 ~~~~~~I~ls~~~-----~~LG~~ 173 (187)
T PRK08563 155 RPRGSKIGLTMRQ-----PGLGKL 173 (187)
T ss_pred CCCCCEEEEEecC-----CCCCcH
Confidence 257789988 899987
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=98.26 E-value=2.6e-06 Score=65.27 Aligned_cols=71 Identities=18% Similarity=0.253 Sum_probs=58.4
Q ss_pred CCCCEEEEEEEEecCceEEEEecCCeeeeecCcccCCc--------------------ccccccCcCCCCEEEEEEEecC
Q 026458 73 CVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEGG--------------------TRRNIPKFEIGSLLYVRVVKAN 132 (238)
Q Consensus 73 ~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~ga--------------------tk~~r~~l~~GDlV~ArV~~~~ 132 (238)
++||+|.|+|+++......|++.....|.+|++++... ..+....|++||+|.|+|++++
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 68999999999999999999998888999998766421 1124567999999999999999
Q ss_pred CC----CcceEEEec
Q 026458 133 PG----MNPELSCTD 143 (238)
Q Consensus 133 ~~----~~~~Ls~~~ 143 (238)
+. ..+.||.+.
T Consensus 82 ~~~~~~~~i~LSlr~ 96 (100)
T cd05693 82 KSKSGKKRIELSLEP 96 (100)
T ss_pred CCcCCCcEEEEEecH
Confidence 74 467888754
No 31
>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=98.22 E-value=1.1e-05 Score=57.90 Aligned_cols=70 Identities=17% Similarity=0.221 Sum_probs=57.4
Q ss_pred CCCCCEEEEEEEEecCceEEEEecC-CeeeeecCcccCCc-ccccccCcCCCCEEEEEEEecCCCCcceEEE
Q 026458 72 PCVEDTVLGIVVDCKADNFFVDIRG-PTIAFLPVLAFEGG-TRRNIPKFEIGSLLYVRVVKANPGMNPELSC 141 (238)
Q Consensus 72 P~vGDiVIG~V~~v~~~~~~VdI~~-~~~a~L~~~~f~ga-tk~~r~~l~~GDlV~ArV~~~~~~~~~~Ls~ 141 (238)
|+.|+++-|+|+++.+-.++|++.. ...|.+|.+++... .++.+..|++||-|.++|.+++....+.||.
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 36899999887543 3344556999999999999998766566664
No 32
>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=98.18 E-value=7.9e-06 Score=59.91 Aligned_cols=72 Identities=17% Similarity=0.086 Sum_probs=60.5
Q ss_pred cCCCCCCEEEEEEEEecCceEEEEecCCeeeeecCcccCCc-ccccccCcCCCCEEEEEEEecCCC-CcceEEE
Q 026458 70 YVPCVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEGG-TRRNIPKFEIGSLLYVRVVKANPG-MNPELSC 141 (238)
Q Consensus 70 Y~P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~ga-tk~~r~~l~~GDlV~ArV~~~~~~-~~~~Ls~ 141 (238)
..+++|+++-|+|+++......|++...-.|.+|.+.+... ..+....|++||.|.++|.+++.. +.+.||+
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 34789999999999999999999999889999999877543 445566799999999999999864 5677764
No 33
>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=98.16 E-value=1e-05 Score=56.99 Aligned_cols=67 Identities=22% Similarity=0.401 Sum_probs=56.4
Q ss_pred CCEEEEEEEEecCceEEEEecCCeeeeecCcccCCc-ccccccCcCCCCEEEEEEEecCCC-CcceEEE
Q 026458 75 EDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEGG-TRRNIPKFEIGSLLYVRVVKANPG-MNPELSC 141 (238)
Q Consensus 75 GDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~ga-tk~~r~~l~~GDlV~ArV~~~~~~-~~~~Ls~ 141 (238)
||+|.|+|+++....+.|++.....|.+|.+++... ..+.+..|++||.|.++|.++++. +.+.||+
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 899999999999999999998779999999887532 333445699999999999999874 5788886
No 34
>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=98.15 E-value=9.8e-06 Score=68.19 Aligned_cols=81 Identities=19% Similarity=0.269 Sum_probs=65.1
Q ss_pred ccCCCCCCEEEEEEEEecCceEEEEecCCeeeeecCcccCCc------------ccccccCcCCCCEEEEEEEecC----
Q 026458 69 RYVPCVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEGG------------TRRNIPKFEIGSLLYVRVVKAN---- 132 (238)
Q Consensus 69 ~Y~P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~ga------------tk~~r~~l~~GDlV~ArV~~~~---- 132 (238)
.|.|.+|+++.|+|++++...+.|+++ +..++++.++.... .++.+..++.||.|++||.+++
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 467999999999999999999999995 68888887654311 1234567999999999999986
Q ss_pred --CCCcceEEEecCCCccCCCcccC
Q 026458 133 --PGMNPELSCTDASGKAAEFGLLK 155 (238)
Q Consensus 133 --~~~~~~Ls~~~~~~~~~~~G~L~ 155 (238)
+...+.||++. ++||+++
T Consensus 155 ~~~~~~I~lt~k~-----~~LG~~~ 174 (179)
T TIGR00448 155 RPEGSKIGLTMRQ-----PLLGKLE 174 (179)
T ss_pred CCCcceEEEEecc-----CcCCccc
Confidence 23568899988 8999984
No 35
>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=1.1e-05 Score=58.15 Aligned_cols=68 Identities=22% Similarity=0.292 Sum_probs=56.9
Q ss_pred CCEEEEEEEEecCceEEEEecCCeeeeecCcccCCc---ccccccCcCCCCEEEEEEEecCCC-CcceEEEe
Q 026458 75 EDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEGG---TRRNIPKFEIGSLLYVRVVKANPG-MNPELSCT 142 (238)
Q Consensus 75 GDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~ga---tk~~r~~l~~GDlV~ArV~~~~~~-~~~~Ls~~ 142 (238)
||+|-|+|+++.+..+.|++...-.|.+|.+++... .++....|++||.|.|+|+++++. ..+.||.+
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 899999999999999999998889999999877532 334456799999999999999875 45778754
No 36
>PRK03987 translation initiation factor IF-2 subunit alpha; Validated
Probab=98.13 E-value=1.1e-05 Score=72.09 Aligned_cols=74 Identities=19% Similarity=0.253 Sum_probs=63.6
Q ss_pred cCCCCCCEEEEEEEEecCceEEEEecC--CeeeeecCcccC-CcccccccCcCCCCEEEEEEEecCCC-CcceEEEec
Q 026458 70 YVPCVEDTVLGIVVDCKADNFFVDIRG--PTIAFLPVLAFE-GGTRRNIPKFEIGSLLYVRVVKANPG-MNPELSCTD 143 (238)
Q Consensus 70 Y~P~vGDiVIG~V~~v~~~~~~VdI~~--~~~a~L~~~~f~-gatk~~r~~l~~GDlV~ArV~~~~~~-~~~~Ls~~~ 143 (238)
-.|++||+|.|+|+++....|.|++.. ...|.+|.+.+. +..+..+..|++||.|.|+|.+++.. +.+.||.+.
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 479999998774 34556677899999999999999875 468899975
No 37
>PRK05807 hypothetical protein; Provisional
Probab=98.13 E-value=2.2e-05 Score=63.49 Aligned_cols=70 Identities=13% Similarity=0.126 Sum_probs=60.8
Q ss_pred CCCCEEEEEEEEecCceEEEEecCCeeeeecCcccCC-cccccccCcCCCCEEEEEEEecCCCCcceEEEec
Q 026458 73 CVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEG-GTRRNIPKFEIGSLLYVRVVKANPGMNPELSCTD 143 (238)
Q Consensus 73 ~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~g-atk~~r~~l~~GDlV~ArV~~~~~~~~~~Ls~~~ 143 (238)
++||+|.|+|+++....++|+| ....|.+|.+.+.. ..++....|++||.|.++|.+++.++.+.||++.
T Consensus 4 ~vG~vv~G~Vt~i~~~GafV~L-~~~~Glvhiseis~~~v~~~~~~~kvGd~V~VkV~~id~~gkI~LSlk~ 74 (136)
T PRK05807 4 KAGSILEGTVVNITNFGAFVEV-EGKTGLVHISEVADTYVKDIREHLKEQDKVKVKVISIDDNGKISLSIKQ 74 (136)
T ss_pred cCCCEEEEEEEEEECCeEEEEE-CCEEEEEEhhhcccccccCccccCCCCCEEEEEEEEECCCCcEEEEEEe
Confidence 5799999999999999999999 45789999988753 3555567899999999999999877889999876
No 38
>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=98.13 E-value=4.3e-06 Score=58.36 Aligned_cols=54 Identities=9% Similarity=0.175 Sum_probs=47.2
Q ss_pred EEEechhhhhhhcCCCCchhhHhhccccceEEEEeeCCeEEEecCChhHHHHHHH
Q 026458 159 MFETSTGLSRMLLSSPTCPVLEELGKQLSFEIAVGLNGRVWVNAESPSTVVLVSN 213 (238)
Q Consensus 159 ~~~V~~~~v~rl~~~~~~~~l~~l~~~~~~ei~vG~NG~IWi~~~~~~~~~~i~~ 213 (238)
.+.||+.++.+++|+.++ .++.|.+.+++.|-+..||.|||.+.+.+....+..
T Consensus 5 ~i~Ip~~~ig~iIGkgG~-~ik~I~~~tg~~I~i~~~g~v~I~G~~~~~v~~A~~ 58 (61)
T cd02393 5 TMKIPPDKIRDVIGPGGK-TIKKIIEETGVKIDIEDDGTVYIAASDKEAAEKAKK 58 (61)
T ss_pred EEEeChhheeeeECCCch-HHHHHHHHHCCEEEeCCCCEEEEEeCCHHHHHHHHH
Confidence 589999999999999998 999999999999999999999999977754444433
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=98.11 E-value=9.9e-06 Score=56.23 Aligned_cols=60 Identities=20% Similarity=0.212 Sum_probs=49.6
Q ss_pred CCCEEEEEEEEecCceEEEEecCCeeeeecCcccCC-cccccccCcCCCCEEEEEEEecCCC
Q 026458 74 VEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEG-GTRRNIPKFEIGSLLYVRVVKANPG 134 (238)
Q Consensus 74 vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~g-atk~~r~~l~~GDlV~ArV~~~~~~ 134 (238)
+|++|.|+|+++....|.|+++ ...|.||.+.... .....+..|++||.|.++|.+++..
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 5999999999999999999998 5899999876642 2333445699999999999998754
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=98.10 E-value=1.9e-05 Score=54.80 Aligned_cols=66 Identities=18% Similarity=0.190 Sum_probs=54.5
Q ss_pred CCEEEEEEEEecCceEEEEecCCeeeeecCcccCCc-ccccccCcCCCCEEEEEEEecCCCCcceEE
Q 026458 75 EDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEGG-TRRNIPKFEIGSLLYVRVVKANPGMNPELS 140 (238)
Q Consensus 75 GDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~ga-tk~~r~~l~~GDlV~ArV~~~~~~~~~~Ls 140 (238)
|+++.|+|+++....+.|+|.....|.||.+.++.. .......|++||.|.++|.+++..+.+.||
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 789999999999999999999889999999887643 222234699999999999999875566665
No 41
>COG1098 VacB Predicted RNA binding protein (contains ribosomal protein S1 domain) [Translation, ribosomal structure and biogenesis]
Probab=98.09 E-value=5.1e-06 Score=65.72 Aligned_cols=74 Identities=15% Similarity=0.209 Sum_probs=68.4
Q ss_pred CCCCCCEEEEEEEEecCceEEEEecCCeeeeecCcccC-CcccccccCcCCCCEEEEEEEecCCCCcceEEEecC
Q 026458 71 VPCVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFE-GGTRRNIPKFEIGSLLYVRVVKANPGMNPELSCTDA 144 (238)
Q Consensus 71 ~P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~-gatk~~r~~l~~GDlV~ArV~~~~~~~~~~Ls~~~~ 144 (238)
.+++||+|-|+|+++.+=.++|++....+|..|+|.+. |..++..+.|.+||-|.++|+++++++.+.||++..
T Consensus 2 ~~kvG~~l~GkItgI~~yGAFV~l~~g~tGLVHISEIa~~fVkdI~d~L~vG~eV~vKVl~ide~GKisLSIr~~ 76 (129)
T COG1098 2 SMKVGSKLKGKITGITPYGAFVELEGGKTGLVHISEIADGFVKDIHDHLKVGQEVKVKVLDIDENGKISLSIRKL 76 (129)
T ss_pred CccccceEEEEEEeeEecceEEEecCCCcceEEehHhhhhhHHhHHHHhcCCCEEEEEEEeeccCCCcceehHHh
Confidence 36899999999999999999999999999999999874 568899999999999999999999999999999873
No 42
>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=98.04 E-value=3.6e-05 Score=55.70 Aligned_cols=66 Identities=24% Similarity=0.273 Sum_probs=56.0
Q ss_pred CCCCEEEEEEEEecCceEEEEec-CCeeeeecCcccCCcccccccCcCCCCEEEEEEEecCCC-CcceEEEec
Q 026458 73 CVEDTVLGIVVDCKADNFFVDIR-GPTIAFLPVLAFEGGTRRNIPKFEIGSLLYVRVVKANPG-MNPELSCTD 143 (238)
Q Consensus 73 ~vGDiVIG~V~~v~~~~~~VdI~-~~~~a~L~~~~f~gatk~~r~~l~~GDlV~ArV~~~~~~-~~~~Ls~~~ 143 (238)
..|++|-|.|.++.+..|.||++ ....|.||.++.... ..|++||.+.|+|.++++. ..+.||++.
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 467999998766421 7899999999999999865 457898865
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=98.02 E-value=2.8e-05 Score=54.87 Aligned_cols=66 Identities=18% Similarity=0.304 Sum_probs=54.9
Q ss_pred CCEEEEEEEEecCceEEEEecCCeeeeecCcccCCc-ccccccCcCCCCEEEEEEEecCCC-CcceEE
Q 026458 75 EDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEGG-TRRNIPKFEIGSLLYVRVVKANPG-MNPELS 140 (238)
Q Consensus 75 GDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~ga-tk~~r~~l~~GDlV~ArV~~~~~~-~~~~Ls 140 (238)
|++|-|+|+++....+.|++...-.|.+|.+.+... .++....|++||.+.++|.+++.+ +.+.||
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 799999999999999999998779999998877543 333445799999999999999864 566665
No 44
>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=98.02 E-value=1.6e-05 Score=54.99 Aligned_cols=65 Identities=15% Similarity=0.200 Sum_probs=52.5
Q ss_pred CCEEEEEEEEecCceEEEEecCCeeeeecCcccCCc-ccccccCcCCCCEEEEEEEecCCC-CcceE
Q 026458 75 EDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEGG-TRRNIPKFEIGSLLYVRVVKANPG-MNPEL 139 (238)
Q Consensus 75 GDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~ga-tk~~r~~l~~GDlV~ArV~~~~~~-~~~~L 139 (238)
|+++.|+|+++.+..+.|+++....|.+|.+.+... ..+....|++||.|.|+|.+++.. +.+.|
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 789999999999999999999889999998776532 233445699999999999998763 34444
No 45
>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=98.00 E-value=4.7e-05 Score=56.96 Aligned_cols=71 Identities=27% Similarity=0.313 Sum_probs=57.0
Q ss_pred CCCCCEEEEEEEEecCc--eEEEEecCCeeeeecCcccCC----cccccccCcCCCCEEEEEEEecCCC-CcceEEEe
Q 026458 72 PCVEDTVLGIVVDCKAD--NFFVDIRGPTIAFLPVLAFEG----GTRRNIPKFEIGSLLYVRVVKANPG-MNPELSCT 142 (238)
Q Consensus 72 P~vGDiVIG~V~~v~~~--~~~VdI~~~~~a~L~~~~f~g----atk~~r~~l~~GDlV~ArV~~~~~~-~~~~Ls~~ 142 (238)
|++||++.|+|+++.+. .++|||+....|+||.++... ...+....|++||.|.++|...... ..+.||+.
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 999999988899999987642 2233456799999999999986543 45667764
No 46
>PHA02945 interferon resistance protein; Provisional
Probab=98.00 E-value=4.3e-05 Score=57.04 Aligned_cols=70 Identities=17% Similarity=0.246 Sum_probs=58.9
Q ss_pred CCCCCCEEEEEEEEecCceEEEEecC--CeeeeecCccc---CCcccccccCcCCCCEEEEEEEecCCC-CcceEEEec
Q 026458 71 VPCVEDTVLGIVVDCKADNFFVDIRG--PTIAFLPVLAF---EGGTRRNIPKFEIGSLLYVRVVKANPG-MNPELSCTD 143 (238)
Q Consensus 71 ~P~vGDiVIG~V~~v~~~~~~VdI~~--~~~a~L~~~~f---~gatk~~r~~l~~GDlV~ArV~~~~~~-~~~~Ls~~~ 143 (238)
.|.+||+|+|+|+. .+..+.|++.- .-.|.+|.+.. .|..|. |+.+ .|..|.|+|+.+++. +-+.||.+.
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 46899999854 344666 9999 999999999999876 456788765
No 47
>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=97.99 E-value=1.7e-05 Score=53.77 Aligned_cols=56 Identities=20% Similarity=0.362 Sum_probs=47.8
Q ss_pred EEEEEEEecCceEEEEecCCeeeeecCcccCCc-ccccccCcCCCCEEEEEEEecCC
Q 026458 78 VLGIVVDCKADNFFVDIRGPTIAFLPVLAFEGG-TRRNIPKFEIGSLLYVRVVKANP 133 (238)
Q Consensus 78 VIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~ga-tk~~r~~l~~GDlV~ArV~~~~~ 133 (238)
|.|+|+++....+.|++.....|.+|.+.+... ..+.+..|++||.|.|+|.+++.
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 479999999999999999889999998877543 33456779999999999999875
No 48
>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=97.93 E-value=6.2e-05 Score=53.15 Aligned_cols=56 Identities=21% Similarity=0.206 Sum_probs=48.9
Q ss_pred CCCCEEEEEEEEecCceEEEEecCCeeeeecCcccCCcccccccCcCCCCEEEEEEEecCCC
Q 026458 73 CVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEGGTRRNIPKFEIGSLLYVRVVKANPG 134 (238)
Q Consensus 73 ~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~gatk~~r~~l~~GDlV~ArV~~~~~~ 134 (238)
..|++|-|+|.++..+.+.|||+. ..|+||.+.+. .+..|++||-|.+.|.+++++
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 89999987773 234689999999999998754
No 49
>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=97.91 E-value=5.4e-05 Score=53.39 Aligned_cols=59 Identities=12% Similarity=0.187 Sum_probs=50.1
Q ss_pred CCEEEEEEEEecCceEEEEecCCeeeeecCcccCCcccccccCcCCCCEEEEEEEecCCC
Q 026458 75 EDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEGGTRRNIPKFEIGSLLYVRVVKANPG 134 (238)
Q Consensus 75 GDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~gatk~~r~~l~~GDlV~ArV~~~~~~ 134 (238)
||+|-|+|+++......|++.....|.+|.+.+...... ...|++||-|.|||+.+++.
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 899999999999999999997778999998877422222 66799999999999999864
No 50
>PTZ00248 eukaryotic translation initiation factor 2 subunit 1; Provisional
Probab=97.88 E-value=4.4e-05 Score=69.84 Aligned_cols=93 Identities=15% Similarity=0.088 Sum_probs=72.9
Q ss_pred CCCCCCEEEEEEEEecCceEEEEec--CCeeeeecCcccC-CcccccccCcCCCCEEEEEEEecCCC-CcceEEEecCCC
Q 026458 71 VPCVEDTVLGIVVDCKADNFFVDIR--GPTIAFLPVLAFE-GGTRRNIPKFEIGSLLYVRVVKANPG-MNPELSCTDASG 146 (238)
Q Consensus 71 ~P~vGDiVIG~V~~v~~~~~~VdI~--~~~~a~L~~~~f~-gatk~~r~~l~~GDlV~ArV~~~~~~-~~~~Ls~~~~~~ 146 (238)
.|.+||+|.|+|+++....+.|+|. ....|++|.+.+. +..++.+..|++||-|.++|+++++. +.+.||.+.-+.
T Consensus 14 ~P~~GdvV~g~V~~I~d~GafV~L~EY~gvEGlIhiSElS~~ri~~i~d~vkvGd~v~vkVl~VD~ekg~IdLS~K~v~~ 93 (319)
T PTZ00248 14 FPEEDDLVMVKVVRITEMGAYVSLLEYDDIEGMILMSELSKRRIRSINKLIRVGRHEVVVVLRVDKEKGYIDLSKKRVSP 93 (319)
T ss_pred CCCCCCEEEEEEEEEeCCeEEEEecCCCCcEEEEEHHHhcccccCCHHHhcCCCCEEEEEEEEEeCCCCEEEEEeeeccc
Confidence 6999999999999999999999996 3579999998874 34666778899999999999999765 457899887431
Q ss_pred c-----cCC--CcccCCeeEEEec
Q 026458 147 K-----AAE--FGLLKDGYMFETS 163 (238)
Q Consensus 147 ~-----~~~--~G~L~~G~~~~V~ 163 (238)
. ... -|....|.+..+.
T Consensus 94 ~pw~~~~e~~~~g~~v~~~V~~ia 117 (319)
T PTZ00248 94 EDIEACEEKFSKSKKVHSIMRHIA 117 (319)
T ss_pred chHHHHHHhCcCCCEEEEEEEEch
Confidence 1 122 3666667766663
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=97.75 E-value=0.00021 Score=51.69 Aligned_cols=68 Identities=16% Similarity=0.150 Sum_probs=58.3
Q ss_pred CCEEEEEEEEecCceEEEEec---CCeeeeecCcccCCc-c-cccccCcCCCCEEEEEEEecCCCCcceEEEec
Q 026458 75 EDTVLGIVVDCKADNFFVDIR---GPTIAFLPVLAFEGG-T-RRNIPKFEIGSLLYVRVVKANPGMNPELSCTD 143 (238)
Q Consensus 75 GDiVIG~V~~v~~~~~~VdI~---~~~~a~L~~~~f~ga-t-k~~r~~l~~GDlV~ArV~~~~~~~~~~Ls~~~ 143 (238)
|+++-|+|+++.+..++|+|. ....|.+|.+.++.. . ++.+..|++||.|.++|.+++ ...+.+|++.
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 789999999999999999998 357999999888654 2 455567999999999999998 7788899865
No 52
>COG1095 RPB7 DNA-directed RNA polymerase, subunit E' [Transcription]
Probab=97.72 E-value=9.7e-05 Score=62.32 Aligned_cols=81 Identities=20% Similarity=0.249 Sum_probs=64.5
Q ss_pred ccCCCCCCEEEEEEEEecCceEEEEecCCeeeeecCcccCCc------------ccccccCcCCCCEEEEEEEecCCCC-
Q 026458 69 RYVPCVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEGG------------TRRNIPKFEIGSLLYVRVVKANPGM- 135 (238)
Q Consensus 69 ~Y~P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~ga------------tk~~r~~l~~GDlV~ArV~~~~~~~- 135 (238)
.|.|..|.+|-|.|+++..-.++|.|+ |.++.+|.++.... .+..+..|+.||.|+|||.......
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 478999999999999999999999999 88899988765321 2334558999999999999875432
Q ss_pred -----cceEEEecCCCccCCCcccC
Q 026458 136 -----NPELSCTDASGKAAEFGLLK 155 (238)
Q Consensus 136 -----~~~Ls~~~~~~~~~~~G~L~ 155 (238)
.+.||++. .++|+++
T Consensus 155 ~~~~~~I~lTmrq-----~~LGkle 174 (183)
T COG1095 155 RPRESKIGLTMRQ-----PGLGKLE 174 (183)
T ss_pred ccccceEEEEecc-----ccCCcch
Confidence 34566666 8999984
No 53
>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=97.70 E-value=0.00018 Score=54.54 Aligned_cols=73 Identities=21% Similarity=0.283 Sum_probs=58.3
Q ss_pred CEEEEEEEEecCceEEEEecCCeeeeecCcccCCc-c-----------cccccCcCCCCEEEEEEEecCCC------Ccc
Q 026458 76 DTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEGG-T-----------RRNIPKFEIGSLLYVRVVKANPG------MNP 137 (238)
Q Consensus 76 DiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~ga-t-----------k~~r~~l~~GDlV~ArV~~~~~~------~~~ 137 (238)
++|.|+|+++....+.|++. +..|.+|.+.+... . ++....|++||.|.++|.+++.. ..+
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 48899988766432 1 12245689999999999999754 468
Q ss_pred eEEEecCCCccCCCccc
Q 026458 138 ELSCTDASGKAAEFGLL 154 (238)
Q Consensus 138 ~Ls~~~~~~~~~~~G~L 154 (238)
.||... +++|++
T Consensus 80 ~ls~k~-----~~~g~~ 91 (99)
T cd04460 80 GLTMRQ-----PGLGKL 91 (99)
T ss_pred EEEEec-----CCCCcH
Confidence 899987 788887
No 54
>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=97.65 E-value=0.00027 Score=49.48 Aligned_cols=65 Identities=23% Similarity=0.241 Sum_probs=50.4
Q ss_pred CCEEEEEEEEecCceEEEEecCCeeeeecCcccCCcccccccCcCCCCEEEEEEEecCC-CCcceEEE
Q 026458 75 EDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEGGTRRNIPKFEIGSLLYVRVVKANP-GMNPELSC 141 (238)
Q Consensus 75 GDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~gatk~~r~~l~~GDlV~ArV~~~~~-~~~~~Ls~ 141 (238)
|++|.|+|+++....+.|++ ....|.+|.++......+. +.-.+||.+.|+|.++++ ...+.||.
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 5689999988764221111 122489999999999986 45667764
No 55
>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=97.63 E-value=0.00021 Score=49.97 Aligned_cols=60 Identities=13% Similarity=0.149 Sum_probs=51.2
Q ss_pred CCEEEEEEEEecCceEEEEecCCeeeeecCcccCC--cccccccCcCCCCEEEEEEEecCCC
Q 026458 75 EDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEG--GTRRNIPKFEIGSLLYVRVVKANPG 134 (238)
Q Consensus 75 GDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~g--atk~~r~~l~~GDlV~ArV~~~~~~ 134 (238)
|+++-|+|+++.+..++|++.....|.+|.+.++. ..++.+..|++||.|.++|.+++..
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 78999999999999999999988999999988763 2334456799999999999998754
No 56
>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=97.62 E-value=0.00031 Score=50.15 Aligned_cols=67 Identities=13% Similarity=0.135 Sum_probs=54.2
Q ss_pred CCEEE-EEEEEe-cCceEEEEecCCeeeeecCcccCC-cccccccCcCCCCEEEEEEEecCCC-CcceEEE
Q 026458 75 EDTVL-GIVVDC-KADNFFVDIRGPTIAFLPVLAFEG-GTRRNIPKFEIGSLLYVRVVKANPG-MNPELSC 141 (238)
Q Consensus 75 GDiVI-G~V~~v-~~~~~~VdI~~~~~a~L~~~~f~g-atk~~r~~l~~GDlV~ArV~~~~~~-~~~~Ls~ 141 (238)
|+++= |+|+++ ....+.|++....+|.+|.+.+.. ..++....|++||.+.|+|+++++. +.+.|||
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 67788 899998 688899999877899999988753 3444556799999999999999864 4566764
No 57
>COG1093 SUI2 Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis]
Probab=97.59 E-value=9e-05 Score=65.59 Aligned_cols=147 Identities=18% Similarity=0.278 Sum_probs=102.9
Q ss_pred CCccCCCCCCEEEEEEEEecCceEEEEecC--CeeeeecCcccC-CcccccccCcCCCCEEEEEEEecCCCC-cceEEEe
Q 026458 67 QKRYVPCVEDTVLGIVVDCKADNFFVDIRG--PTIAFLPVLAFE-GGTRRNIPKFEIGSLLYVRVVKANPGM-NPELSCT 142 (238)
Q Consensus 67 ~~~Y~P~vGDiVIG~V~~v~~~~~~VdI~~--~~~a~L~~~~f~-gatk~~r~~l~~GDlV~ArV~~~~~~~-~~~Ls~~ 142 (238)
..+-.|.+||+|||+|.++.+-.+.|.+.- .-.|++|+|.+. |..++.|+.+++|.-+.|+|+.+++.+ -+.||.+
T Consensus 4 ~~~~~PeeGEiVv~tV~~V~~~GAyv~L~EY~g~Eg~ihiSEvas~wVknIrd~vkegqkvV~kVlrVd~~rg~IDLSlk 83 (269)
T COG1093 4 KRREYPEEGEIVVGTVKQVADYGAYVELDEYPGKEGFIHISEVASGWVKNIRDYVKEGQKVVAKVLRVDPKRGHIDLSLK 83 (269)
T ss_pred cccCCCCCCcEEEEEEEEeeccccEEEeeccCCeeeeEEHHHHHHHHHHHHHHHhhcCCeEEEEEEEEcCCCCeEeeehh
Confidence 345579999999999999999999999975 358999998874 568899999999999999999999864 5779997
Q ss_pred cCCC--c---------------------------------------cCCCcccCCee---------EEEe-ch--hhhhh
Q 026458 143 DASG--K---------------------------------------AAEFGLLKDGY---------MFET-ST--GLSRM 169 (238)
Q Consensus 143 ~~~~--~---------------------------------------~~~~G~L~~G~---------~~~V-~~--~~v~r 169 (238)
.-+. + .+.||.+-++| .+.- .+ ..+
T Consensus 84 rV~~~q~~~k~~~wk~~qka~klle~aaekl~~~~ee~~~~vg~~L~e~fG~~y~aFE~aa~~g~~~l~~~~~~~~~~-- 161 (269)
T COG1093 84 RVTEHQRRKKIQEWKKEQKADKLLELAAEKLGKDLEEAYEEVGWKLEEEFGSLYDAFEAAAKEGGEVLDDEGVPEEWK-- 161 (269)
T ss_pred hCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCHHHHHHHHhHHHHHHhCCHHHHHHHHHhcCCcccccCCCCHHHH--
Confidence 7541 1 03356653222 1110 00 000
Q ss_pred hcCCCCchhhHhhccccceEEEEeeCCeEEEecCChhHHHHHHHHHHHhccCC
Q 026458 170 LLSSPTCPVLEELGKQLSFEIAVGLNGRVWVNAESPSTVVLVSNAIMNSESLS 222 (238)
Q Consensus 170 l~~~~~~~~l~~l~~~~~~ei~vG~NG~IWi~~~~~~~~~~i~~~i~~~e~lt 222 (238)
-.+++...+++.. =.|-.-|+|=+.|..+..+..|-.||...+...
T Consensus 162 ------~~l~e~a~e~i~~-~~VkI~g~vev~s~~~dGVe~IK~aL~~A~~~~ 207 (269)
T COG1093 162 ------EVLKEIARENIEP-PTVKIRGYVEVTSPAPDGVEKIKKALKAAEDNG 207 (269)
T ss_pred ------HHHHHHHHhcCCC-CceEEEEEEEEEecCCCcHHHHHHHHHHHHhcC
Confidence 0133333322110 124556899999999999999999999987633
No 58
>PRK07400 30S ribosomal protein S1; Reviewed
Probab=97.57 E-value=0.00022 Score=65.31 Aligned_cols=75 Identities=17% Similarity=0.133 Sum_probs=63.9
Q ss_pred cCCCCCCEEEEEEEEecCceEEEEecCCeeeeecCcccCC-cccccccCcCCCCEEEEEEEecCCC-CcceEEEecC
Q 026458 70 YVPCVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEG-GTRRNIPKFEIGSLLYVRVVKANPG-MNPELSCTDA 144 (238)
Q Consensus 70 Y~P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~g-atk~~r~~l~~GDlV~ArV~~~~~~-~~~~Ls~~~~ 144 (238)
|..++||+|-|+|+.+..+...|||+....|+||.+.+.. ..++....|++||.|.+.|++.++. +.+.|||+..
T Consensus 27 ~~~~~G~iv~G~V~~i~~~g~~Vdig~k~~g~lp~sEis~~~~~~~~~~~~~G~~v~~~Vi~~~~~~~~i~lS~k~~ 103 (318)
T PRK07400 27 YHFKPGDIVNGTVFSLEPRGALIDIGAKTAAFMPIQEMSINRVEGPEEVLQPNETREFFILSDENEDGQLTLSIRRI 103 (318)
T ss_pred hhcCCCCEEEEEEEEEECCEEEEEECCCeEEEEEHHHhccccccCHHHccCCCCEEEEEEEEEeCCCCeEEEehhhh
Confidence 4579999999999999999999999988899999988753 3455567799999999999998654 5789999864
No 59
>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=97.54 E-value=0.0012 Score=47.74 Aligned_cols=64 Identities=19% Similarity=0.188 Sum_probs=55.0
Q ss_pred CCCCCCEEEEEEEEecCceEEEEecCCeeeeecCcccCCcccccccCcCCCCEEEEEEEecCCCCcceEEE
Q 026458 71 VPCVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEGGTRRNIPKFEIGSLLYVRVVKANPGMNPELSC 141 (238)
Q Consensus 71 ~P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~gatk~~r~~l~~GDlV~ArV~~~~~~~~~~Ls~ 141 (238)
-.++|+.+.|+|+++....++|++.....|.+|.+.+ ...++.||.+.++|.++..++.+.|+.
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 3778999999999999999999999889999998765 346999999999999995556677664
No 60
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=97.48 E-value=0.00052 Score=69.01 Aligned_cols=99 Identities=14% Similarity=0.072 Sum_probs=76.7
Q ss_pred eCCEEEEEEeeEeEEecC-CeEEEEccCCccCCCCCCEEEEEEEEecCceEEEEecCCeeeeecCcccCC-cccccccCc
Q 026458 41 ECDSVSVIKAGKLRFSKP-NKYWVESSQKRYVPCVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEG-GTRRNIPKF 118 (238)
Q Consensus 41 ~~g~i~as~~G~v~~~~~-~~i~V~~~~~~Y~P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~g-atk~~r~~l 118 (238)
++|.++++..+....++- ..+...+ ..|++|+++.|+|+++....++|+|....+|.+|++.+.. ..++....|
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 467777777777665321 1222221 2378999999999999999999999988999999998853 345556779
Q ss_pred CCCCEEEEEEEecCCCCcceEEEec
Q 026458 119 EIGSLLYVRVVKANPGMNPELSCTD 143 (238)
Q Consensus 119 ~~GDlV~ArV~~~~~~~~~~Ls~~~ 143 (238)
++||.|.++|.+++..+.+.||++.
T Consensus 667 kvGD~V~VkV~~iD~~grI~LS~k~ 691 (693)
T PRK11824 667 KEGDEVKVKVLEIDKRGRIRLSRKA 691 (693)
T ss_pred CCCCEEEEEEEEECCCCcEEEEEEe
Confidence 9999999999999876888999864
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=0.00098 Score=47.10 Aligned_cols=62 Identities=13% Similarity=0.140 Sum_probs=52.0
Q ss_pred CCCCEEEEEEEEecCceEEEEecCCeeeeecCcccCC--cccccccCcCCCCEEEEEEEecCCC
Q 026458 73 CVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEG--GTRRNIPKFEIGSLLYVRVVKANPG 134 (238)
Q Consensus 73 ~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~g--atk~~r~~l~~GDlV~ArV~~~~~~ 134 (238)
.+|+++.|+|+++....++|++....+|.+|.+.++. ...+....|++||.|.++|.+++..
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 3699999999999999999999888999999988753 2223445699999999999998754
No 62
>PTZ00162 DNA-directed RNA polymerase II subunit 7; Provisional
Probab=97.38 E-value=0.00081 Score=56.66 Aligned_cols=81 Identities=15% Similarity=0.210 Sum_probs=61.7
Q ss_pred ccCCCCCCEEEEEEEEecCceEEEEecCCeeeeecCcccCC------c-------ccccccCcCCCCEEEEEEEecCC--
Q 026458 69 RYVPCVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEG------G-------TRRNIPKFEIGSLLYVRVVKANP-- 133 (238)
Q Consensus 69 ~Y~P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~g------a-------tk~~r~~l~~GDlV~ArV~~~~~-- 133 (238)
-|.|-.|.+|.|+|++++...+.|+++ +.++.+|.++.+. . .++.+..++.||.|++||..+.-
T Consensus 76 vFrPf~gEVv~g~V~~v~~~G~~v~~G-p~~ifI~~~~l~~~~~fd~~~~~~~~~~~~~~~~i~~g~~VR~rV~~v~~~~ 154 (176)
T PTZ00162 76 VFKPFKDEVLDAIVTDVNKLGFFAQAG-PLKAFVSRSAIPPDFVYDSDSAYPCYISSDGQIQIKPNTEVRLRLQGVRYDA 154 (176)
T ss_pred EEecCCCCEEEEEEEEEecceEEEEee-CeEEEEcHHHCCCccEECCCCCcceEecCCCcEEECCCCEEEEEEEEEEecC
Confidence 588999999999999999999999997 5558887765442 1 12234579999999999987642
Q ss_pred -CCcceEEEecCCCccCCCcccC
Q 026458 134 -GMNPELSCTDASGKAAEFGLLK 155 (238)
Q Consensus 134 -~~~~~Ls~~~~~~~~~~~G~L~ 155 (238)
+.....|+++ ++||+++
T Consensus 155 ~~~~~i~T~~~-----~~LG~~~ 172 (176)
T PTZ00162 155 SNLFAIATINS-----DYLGPIE 172 (176)
T ss_pred CCcEEEEEecC-----CCcCccc
Confidence 2335567766 8999983
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=97.36 E-value=0.00059 Score=68.43 Aligned_cols=70 Identities=19% Similarity=0.213 Sum_probs=60.1
Q ss_pred CCCCCCEEEEEEEEecCceEEEEecCCeeeeecCcccC-----CcccccccCcCCCCEEEEEEEecCCCCcceEE
Q 026458 71 VPCVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFE-----GGTRRNIPKFEIGSLLYVRVVKANPGMNPELS 140 (238)
Q Consensus 71 ~P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~-----gatk~~r~~l~~GDlV~ArV~~~~~~~~~~Ls 140 (238)
.|.+|++|.|+|+++.+-.++|+|....+|.||++++. ...++.+..|++||.|.++|.++++.+.+.|+
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 58999999999999999999999987789999999773 34556677899999999999999865556554
No 64
>PRK07400 30S ribosomal protein S1; Reviewed
Probab=97.36 E-value=0.00089 Score=61.38 Aligned_cols=72 Identities=18% Similarity=0.201 Sum_probs=60.6
Q ss_pred CCCCCCEEEEEEEEecCceEEEEecCCeeeeecCcccCCc-ccccccCcCCCCEEEEEEEecCC-CCcceEEEec
Q 026458 71 VPCVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEGG-TRRNIPKFEIGSLLYVRVVKANP-GMNPELSCTD 143 (238)
Q Consensus 71 ~P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~ga-tk~~r~~l~~GDlV~ArV~~~~~-~~~~~Ls~~~ 143 (238)
..++||+|.|+|+++....++|+++ ...|.+|.+.+... ..+....|++||.|.|+|.+++. .+.+.||++.
T Consensus 193 ~~k~G~vv~G~V~~I~~~G~fV~i~-gv~Gllhisels~~~~~~~~~~~~vGd~VkvkVl~iD~e~~rI~LS~K~ 266 (318)
T PRK07400 193 RLEVGEVVVGTVRGIKPYGAFIDIG-GVSGLLHISEISHEHIETPHSVFNVNDEMKVMIIDLDAERGRISLSTKQ 266 (318)
T ss_pred cCCCCCEEEEEEEEEECCeEEEEEC-CEEEEEEHHHcccccccChhhccCCCCEEEEEEEEEeCCCCEEEEEEec
Confidence 4788999999999999999999996 46899999877543 44556779999999999999975 4678899876
No 65
>COG0539 RpsA Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]
Probab=97.33 E-value=0.00057 Score=66.49 Aligned_cols=72 Identities=21% Similarity=0.233 Sum_probs=63.3
Q ss_pred CCCCCCEEEEEEEEecCceEEEEecCCeeeeecCcccC-CcccccccCcCCCCEEEEEEEecCCC-CcceEEEec
Q 026458 71 VPCVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFE-GGTRRNIPKFEIGSLLYVRVVKANPG-MNPELSCTD 143 (238)
Q Consensus 71 ~P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~-gatk~~r~~l~~GDlV~ArV~~~~~~-~~~~Ls~~~ 143 (238)
.-++||+|-|+|+++++-.++|||+. ..|.||++... ++.+.....|++||-|.++|++++.. ..+.||++.
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 46899999999999999999999999 99999998775 34566677899999999999999965 568899976
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=97.22 E-value=0.0009 Score=67.22 Aligned_cols=92 Identities=13% Similarity=0.036 Sum_probs=68.1
Q ss_pred eCCEEEEEEeeEeEEec-CCeEEEEccCCccCCCCCCEEEEEEEEecCceEEEEecCCeeeeecCcccCC-cccccccCc
Q 026458 41 ECDSVSVIKAGKLRFSK-PNKYWVESSQKRYVPCVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEG-GTRRNIPKF 118 (238)
Q Consensus 41 ~~g~i~as~~G~v~~~~-~~~i~V~~~~~~Y~P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~g-atk~~r~~l 118 (238)
++|.+++...+....++ ...+... ...|++|+++.|+|+++....++|+|.....|.||+++... ..++....|
T Consensus 588 ddG~V~i~~~~~~~~~~a~~~I~~~----~~~~~~G~i~~G~V~~I~~~GafVei~~g~~GllHiSei~~~~v~~~~~~~ 663 (684)
T TIGR03591 588 DDGTVKIAASDGEAAEAAIKMIEGI----TAEPEVGKIYEGKVVRIMDFGAFVEILPGKDGLVHISEIANERVEKVEDVL 663 (684)
T ss_pred cCeEEEEEECcHHHHHHHHHHHHhh----hcccccCcEEEEEEEEEeCCEEEEEECCCcEEEEEHHHcCCCcccChhhcc
Confidence 35666666655544331 1122222 12489999999999999999999999988999999998853 355667789
Q ss_pred CCCCEEEEEEEecCCCCc
Q 026458 119 EIGSLLYVRVVKANPGMN 136 (238)
Q Consensus 119 ~~GDlV~ArV~~~~~~~~ 136 (238)
++||.|.++|.+++..+.
T Consensus 664 kvGD~V~VkVi~id~~gk 681 (684)
T TIGR03591 664 KEGDEVKVKVLEIDKQGR 681 (684)
T ss_pred CCCCEEEEEEEEECCCCC
Confidence 999999999999876443
No 67
>PRK06676 rpsA 30S ribosomal protein S1; Reviewed
Probab=97.07 E-value=0.0022 Score=59.84 Aligned_cols=73 Identities=25% Similarity=0.248 Sum_probs=59.9
Q ss_pred CCCCCCEEEEEEEEecCceEEEEe-cCCeeeeecCcccCCc-ccccccCcCCCCEEEEEEEecCCC-CcceEEEec
Q 026458 71 VPCVEDTVLGIVVDCKADNFFVDI-RGPTIAFLPVLAFEGG-TRRNIPKFEIGSLLYVRVVKANPG-MNPELSCTD 143 (238)
Q Consensus 71 ~P~vGDiVIG~V~~v~~~~~~VdI-~~~~~a~L~~~~f~ga-tk~~r~~l~~GDlV~ArV~~~~~~-~~~~Ls~~~ 143 (238)
-.++||+|.|+|+++..+.+.||| +....|.||...+... .+.....|++||-|.|+|.+++.+ ..+.||.+.
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 468999999999999999999999 7788999998877532 333445699999999999999765 357888775
No 68
>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=97.05 E-value=0.0049 Score=44.33 Aligned_cols=67 Identities=18% Similarity=0.315 Sum_probs=52.7
Q ss_pred CCCEEEEEEEEecCceEEEEecC-CeeeeecCcccCCcc------------cccccCcCCCCEEEEEEEecCCC-CcceE
Q 026458 74 VEDTVLGIVVDCKADNFFVDIRG-PTIAFLPVLAFEGGT------------RRNIPKFEIGSLLYVRVVKANPG-MNPEL 139 (238)
Q Consensus 74 vGDiVIG~V~~v~~~~~~VdI~~-~~~a~L~~~~f~gat------------k~~r~~l~~GDlV~ArV~~~~~~-~~~~L 139 (238)
+|+++-|.|++++...+.|++.. ...|.++.+++++.. ++....|++||.|.++|.+++.. ..+.+
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 578999988775321 12346799999999999999763 34454
Q ss_pred E
Q 026458 140 S 140 (238)
Q Consensus 140 s 140 (238)
+
T Consensus 81 ~ 81 (83)
T cd04471 81 E 81 (83)
T ss_pred E
Confidence 4
No 69
>PRK06676 rpsA 30S ribosomal protein S1; Reviewed
Probab=97.04 E-value=0.0024 Score=59.66 Aligned_cols=72 Identities=21% Similarity=0.192 Sum_probs=60.0
Q ss_pred CCCCCEEEEEEEEecCceEEEEecCCeeeeecCcccCCc-ccccccCcCCCCEEEEEEEecCC-CCcceEEEecC
Q 026458 72 PCVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEGG-TRRNIPKFEIGSLLYVRVVKANP-GMNPELSCTDA 144 (238)
Q Consensus 72 P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~ga-tk~~r~~l~~GDlV~ArV~~~~~-~~~~~Ls~~~~ 144 (238)
.++||+|-|+|+++....+.|+++. ..|.+|.+.+... .++....|++||.|.|+|.++++ .+.+.||++..
T Consensus 190 ~~~G~~v~g~V~~v~~~G~fV~l~~-v~g~v~~sels~~~~~~~~~~~~vGd~i~~~Vl~vd~~~~~i~lS~k~~ 263 (390)
T PRK06676 190 LKEGDVVEGTVARLTDFGAFVDIGG-VDGLVHISELSHERVEKPSEVVSVGQEVEVKVLSIDWETERISLSLKDT 263 (390)
T ss_pred CCCCCEEEEEEEEEecceEEEEeCC-eEEEEEHHHcCccccCCHHHhcCCCCEEEEEEEEEeCCCCEEEEEEeec
Confidence 5899999999999999999999974 8899999877532 34445679999999999999976 46788998753
No 70
>PRK06299 rpsA 30S ribosomal protein S1; Reviewed
Probab=97.04 E-value=0.0029 Score=61.93 Aligned_cols=72 Identities=17% Similarity=0.158 Sum_probs=61.2
Q ss_pred CCCCEEEEEEEEecCceEEEEecCCeeeeecCcccCCc-c-cccccCcCCCCEEEEEEEecCCC-CcceEEEecC
Q 026458 73 CVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEGG-T-RRNIPKFEIGSLLYVRVVKANPG-MNPELSCTDA 144 (238)
Q Consensus 73 ~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~ga-t-k~~r~~l~~GDlV~ArV~~~~~~-~~~~Ls~~~~ 144 (238)
.+||+|-|+|+++....++|+|+....|.+|.+.+... . ++....|++||.|.|+|.+++.. +.+.||++..
T Consensus 372 ~~G~~v~g~V~~v~~~G~fV~l~~~v~g~i~~s~l~~~~~~~~~~~~~~~Gd~v~v~Il~vd~~~~~i~ls~k~~ 446 (565)
T PRK06299 372 PVGDVVEGKVKNITDFGAFVGLEGGIDGLVHLSDISWDKKGEEAVELYKKGDEVEAVVLKVDVEKERISLGIKQL 446 (565)
T ss_pred CCCCEEEEEEEEEecceEEEECCCCCEEEEEHHHcCccccccChHhhCCCCCEEEEEEEEEeCCCCEEEEEEehh
Confidence 57999999999999999999999889999999877532 2 45567799999999999999854 6789998764
No 71
>PRK13806 rpsA 30S ribosomal protein S1; Provisional
Probab=97.02 E-value=0.0031 Score=61.02 Aligned_cols=74 Identities=16% Similarity=0.150 Sum_probs=61.6
Q ss_pred CCCCCCEEEEEEEEecCceEEEEecCCeeeeecCcccCC-cccccccCcCCCCEEEEEEEecCCCC-----cceEEEecC
Q 026458 71 VPCVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEG-GTRRNIPKFEIGSLLYVRVVKANPGM-----NPELSCTDA 144 (238)
Q Consensus 71 ~P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~g-atk~~r~~l~~GDlV~ArV~~~~~~~-----~~~Ls~~~~ 144 (238)
..++||+|-|+|+++....++|||+....|.+|.+.+.. ...+....|++||.|.|+|.+++... .+.||++..
T Consensus 199 ~l~~G~iv~G~V~~v~~~G~fV~l~~gv~g~v~~sels~~~~~~~~~~~~vGd~i~vkVl~id~~~~~~~~ri~lS~K~~ 278 (491)
T PRK13806 199 TVKEGDVVEGTVTRLAPFGAFVELAPGVEGMVHISELSWSRVQKADEAVSVGDTVRVKVLGIERAKKGKGLRISLSIKQA 278 (491)
T ss_pred hCCCCCEEEEEEEEEeCCeEEEEcCCCcEEEEEHHHCCCccccChhHhcCCCCEEEEEEEEEecccCCcceEEEEEehhh
Confidence 478999999999999999999999877899999988754 23455667999999999999998753 477887653
No 72
>PRK06299 rpsA 30S ribosomal protein S1; Reviewed
Probab=97.01 E-value=0.007 Score=59.28 Aligned_cols=72 Identities=14% Similarity=0.198 Sum_probs=61.8
Q ss_pred CCCCCEEEEEEEEecCceEEEEecCCeeeeecCcccC-CcccccccCcCCCCEEEEEEEecCCC-CcceEEEec
Q 026458 72 PCVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFE-GGTRRNIPKFEIGSLLYVRVVKANPG-MNPELSCTD 143 (238)
Q Consensus 72 P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~-gatk~~r~~l~~GDlV~ArV~~~~~~-~~~~Ls~~~ 143 (238)
.++||+|.|+|+++....++|.+.....|.+|.++.. ...++....|++||.|.|+|.+++.+ ..+.||+..
T Consensus 458 ~~~G~vV~G~V~~v~~~G~fV~l~~gi~g~i~~se~s~~~~~~~~~~~~~Gd~v~~~V~~vd~~~~~i~LS~k~ 531 (565)
T PRK06299 458 HKKGSIVTGTVTEVKDKGAFVELEDGVEGLIRASELSRDRVEDATEVLKVGDEVEAKVINIDRKNRRISLSIKA 531 (565)
T ss_pred cCCCCEEEEEEEEEecCceEEecCCCcEEEEEHHHhcchhccCccccCCCCCEEEEEEEEEccccCEEEEEeee
Confidence 3789999999999999999999987889999988764 23456677899999999999999864 678899976
No 73
>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=96.98 E-value=0.0013 Score=45.31 Aligned_cols=52 Identities=10% Similarity=0.140 Sum_probs=44.3
Q ss_pred EEEechhhhhhhcCCCCchhhHhhccccceEEEEee----CCeEEEecCChhHHHHHH
Q 026458 159 MFETSTGLSRMLLSSPTCPVLEELGKQLSFEIAVGL----NGRVWVNAESPSTVVLVS 212 (238)
Q Consensus 159 ~~~V~~~~v~rl~~~~~~~~l~~l~~~~~~ei~vG~----NG~IWi~~~~~~~~~~i~ 212 (238)
-+.||+.++++++|++++ .++.|.+.+++.|-+.. ++.|||.++ .+.+..+.
T Consensus 3 ~i~Vp~~~~~~iIG~~G~-~i~~i~~~~g~~I~i~~~~~~~~~v~I~G~-~~~v~~A~ 58 (62)
T cd02394 3 EVEIPKKLHRFIIGKKGS-NIRKIMEETGVKIRFPDPGSKSDTITITGP-KENVEKAK 58 (62)
T ss_pred EEEeCHHHhhhccCCCCC-cHHHHHHHhCCEEEcCCCCCCCCEEEEEcC-HHHHHHHH
Confidence 478999999999999998 89999999999999999 899999996 44444333
No 74
>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=96.98 E-value=0.0023 Score=61.87 Aligned_cols=68 Identities=21% Similarity=0.176 Sum_probs=59.5
Q ss_pred CCCCCEEEEEEEEecCceEEEEecCCeeeeecCcccCCcccccccCcCCCCEEEEEEEecCC-CCcceEEEec
Q 026458 72 PCVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEGGTRRNIPKFEIGSLLYVRVVKANP-GMNPELSCTD 143 (238)
Q Consensus 72 P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~gatk~~r~~l~~GDlV~ArV~~~~~-~~~~~Ls~~~ 143 (238)
.++|++|-|.|+++..+.+.|||+....|++|..++.. ..+.|++||.|.++|.+.++ .+.+.||+..
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 58899999999999999999999999999999888753 23679999999999998865 4678999864
No 75
>PRK07899 rpsA 30S ribosomal protein S1; Reviewed
Probab=96.91 E-value=0.0043 Score=60.06 Aligned_cols=72 Identities=18% Similarity=0.145 Sum_probs=60.1
Q ss_pred CCCCCEEEEEEEEecCceEEEEecCCeeeeecCcccCCc-ccccccCcCCCCEEEEEEEecCCC-CcceEEEecC
Q 026458 72 PCVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEGG-TRRNIPKFEIGSLLYVRVVKANPG-MNPELSCTDA 144 (238)
Q Consensus 72 P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~ga-tk~~r~~l~~GDlV~ArV~~~~~~-~~~~Ls~~~~ 144 (238)
-++||+|-|+|+++.+..++|||+. ..|.+|.+.+... .++....|++||.|.++|..++.. ..+.||++..
T Consensus 206 lk~G~iv~G~V~~i~~~G~FVdlgg-v~Glv~~Sels~~~v~~~~~~~kvGd~V~vkVl~iD~e~~rI~LSlK~~ 279 (486)
T PRK07899 206 LQKGQVRKGVVSSIVNFGAFVDLGG-VDGLVHVSELSWKHIDHPSEVVEVGQEVTVEVLDVDMDRERVSLSLKAT 279 (486)
T ss_pred ccCCCEEEEEEEEEECCeEEEEECC-EEEEEEHHHCCCcccCCHHHhcCCCCEEEEEEEEEECCCCEEEEEEeec
Confidence 4589999999999999999999974 8999999887642 344455799999999999999864 6788998753
No 76
>PRK07899 rpsA 30S ribosomal protein S1; Reviewed
Probab=96.91 E-value=0.0031 Score=61.04 Aligned_cols=73 Identities=22% Similarity=0.130 Sum_probs=59.7
Q ss_pred CCCCCEEEEEEEEecCceEEEEecCCeeeeecCcccCCc-ccccccCcCCCCEEEEEEEecCCC-CcceEEEecC
Q 026458 72 PCVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEGG-TRRNIPKFEIGSLLYVRVVKANPG-MNPELSCTDA 144 (238)
Q Consensus 72 P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~ga-tk~~r~~l~~GDlV~ArV~~~~~~-~~~~Ls~~~~ 144 (238)
.+.||+|.|+|+++..+.+.|||+....|+||.+.+... ..+....|.+||-|.|.|++.++. +.+.||.+..
T Consensus 33 ~~~GdiV~G~V~~v~~~gv~VdIg~k~eG~Ip~~Els~~~~~~~~~~~~vGd~Ie~~V~~~~~~~g~liLS~k~~ 107 (486)
T PRK07899 33 FNDGDIVEGTVVKVDRDEVLLDIGYKTEGVIPSRELSIKHDVDPNEVVEVGDEVEALVLQKEDKEGRLILSKKRA 107 (486)
T ss_pred CCCCCEEEEEEEEEECCcEEEEECCCcEEEEEHHHhcccccCChhhcCCCCCEEEEEEEEEECCCCeEEEEehhh
Confidence 689999999999999999999999888999998877532 223344699999999999998653 5688888753
No 77
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=96.82 E-value=0.0035 Score=58.50 Aligned_cols=69 Identities=22% Similarity=0.187 Sum_probs=56.4
Q ss_pred ccCCCCCCEEEEEEEEecCceEEEEecCCeeeeecCcccCCcccccccCcCCCCEEEEEEEecCCCC---cceEEEec
Q 026458 69 RYVPCVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEGGTRRNIPKFEIGSLLYVRVVKANPGM---NPELSCTD 143 (238)
Q Consensus 69 ~Y~P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~gatk~~r~~l~~GDlV~ArV~~~~~~~---~~~Ls~~~ 143 (238)
.|..+.|++|.|+|.++....|.|||+. ..|+||..... .+..|++||-|.|.|.++.... .+.||-.+
T Consensus 129 ef~~k~GeiV~G~V~~~~~~~~~Vdlg~-vEa~LP~~E~i-----p~e~~~~Gd~Ika~V~~V~~~~kgp~IivSRt~ 200 (362)
T PRK12327 129 EFSEREGDIVTGVVQRRDNRFVYVNLGK-IEAVLPPAEQI-----PGETYKHGDRIKVYVVKVEKTTKGPQIFVSRTH 200 (362)
T ss_pred HHHHhcCCEEEEEEEEEeCCcEEEEeCC-eEEEecHHHcC-----CCCCCCCCCEEEEEEEEEecCCCCCeEEEEeCC
Confidence 3899999999999999999999999987 79999964431 2567999999999999998543 35666555
No 78
>PRK13806 rpsA 30S ribosomal protein S1; Provisional
Probab=96.82 E-value=0.0073 Score=58.47 Aligned_cols=74 Identities=22% Similarity=0.179 Sum_probs=62.1
Q ss_pred CCCCCEEEEEEEEecCceEEEEecCCeeeeecCcccCC--cccccccCcCCCCEEEEEEEecCCC-CcceEEEecCC
Q 026458 72 PCVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEG--GTRRNIPKFEIGSLLYVRVVKANPG-MNPELSCTDAS 145 (238)
Q Consensus 72 P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~g--atk~~r~~l~~GDlV~ArV~~~~~~-~~~~Ls~~~~~ 145 (238)
-.+|++|-|+|+++....++|++.....|.+|.+.+.. ...+....|++||.|.++|.+++.. +.+.||++...
T Consensus 290 ~~~G~~v~G~V~~v~~~G~fV~l~~gv~Glvh~sels~~~~~~~~~~~~~~Gd~v~vkVl~iD~e~~ri~Ls~K~~~ 366 (491)
T PRK13806 290 LKAGDKVTGKVVRLAPFGAFVEILPGIEGLVHVSEMSWTRRVNKPEDVVAPGDAVAVKIKDIDPAKRRISLSLRDAE 366 (491)
T ss_pred CCCCCEEEEEEEEEeCceEEEEeCCCcEEEEEHHHcCcccccCCHHHcCCCCCEEEEEEEEEEccCCEEEEEEeecc
Confidence 46899999999999999999999877899999987753 2344556899999999999999864 67889998643
No 79
>PRK00087 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed
Probab=96.80 E-value=0.0068 Score=60.57 Aligned_cols=75 Identities=21% Similarity=0.207 Sum_probs=62.7
Q ss_pred cCCCCCCEEEEEEEEecCceEEEEecCCeeeeecCcccCC-cccccccCcCCCCEEEEEEEecCC-CCcceEEEecC
Q 026458 70 YVPCVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEG-GTRRNIPKFEIGSLLYVRVVKANP-GMNPELSCTDA 144 (238)
Q Consensus 70 Y~P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~g-atk~~r~~l~~GDlV~ArV~~~~~-~~~~~Ls~~~~ 144 (238)
+..++|++|-|+|+++..+.+.||++....|.||.+.+.. ..+.....|++||.|.++|.++++ .+.+.||.+.+
T Consensus 298 ~~l~~G~iV~G~V~~v~~~gv~Vdig~~~~G~lp~~els~~~~~~~~~~~~vGd~V~v~V~~vd~~~g~i~LS~k~~ 374 (647)
T PRK00087 298 KQIRRGDIVKGTVVSVNENEVFVDVGYKSEGVIPLRELTLDEISSLKESVKVGDEIEVKVLKLEDEDGYVVLSKKEA 374 (647)
T ss_pred hhccCCCEEEEEEEEEECCEEEEEECCCeEEEEEHHHhcccccCChhhccCCCCEEEEEEEEEECCCCcEEEEeehh
Confidence 5689999999999999999999999988899999877653 233445679999999999999864 46788998765
No 80
>COG0539 RpsA Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]
Probab=96.66 E-value=0.0058 Score=59.65 Aligned_cols=94 Identities=23% Similarity=0.304 Sum_probs=74.2
Q ss_pred CccCCCCCCEEEEEEEEecCceEEEEecCCeeeeecCcccCCcccccccCcCCCCEEEEEEEecCCC-CcceEEEecCC-
Q 026458 68 KRYVPCVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEGGTRRNIPKFEIGSLLYVRVVKANPG-MNPELSCTDAS- 145 (238)
Q Consensus 68 ~~Y~P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~gatk~~r~~l~~GDlV~ArV~~~~~~-~~~~Ls~~~~~- 145 (238)
..+.+++||+|-|.|+++..++..|||+.-..|++|.++|.+.-... .|++||.|-+.|...... +.+.||-....
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 45789999999999999999999999999999999999997543222 799999999999987654 35677754322
Q ss_pred Cc----------------cCCCcccCCeeEEEec
Q 026458 146 GK----------------AAEFGLLKDGYMFETS 163 (238)
Q Consensus 146 ~~----------------~~~~G~L~~G~~~~V~ 163 (238)
-+ ..-.|+++||+++.+.
T Consensus 93 ~~~w~~l~~~~e~~~~V~~~v~~~vKGG~~Vdi~ 126 (541)
T COG0539 93 ERAWEKLEEAFENGEIVEGKITGKVKGGLTVDIE 126 (541)
T ss_pred HHhHHHHHHHHhcCCeEEEEEEEEecCcEEEEEC
Confidence 00 1225778999999995
No 81
>PRK00087 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed
Probab=96.59 E-value=0.0098 Score=59.45 Aligned_cols=72 Identities=17% Similarity=0.194 Sum_probs=61.6
Q ss_pred CCCCEEEEEEEEecCceEEEEecCCeeeeecCcccCC-cccccccCcCCCCEEEEEEEecCC-CCcceEEEecC
Q 026458 73 CVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEG-GTRRNIPKFEIGSLLYVRVVKANP-GMNPELSCTDA 144 (238)
Q Consensus 73 ~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~g-atk~~r~~l~~GDlV~ArV~~~~~-~~~~~Ls~~~~ 144 (238)
++|++|-|.|+++....++|++.....|.+|.+.+.. ..++....|++||.|.|+|.+++. .+.+.||++..
T Consensus 561 ~~G~~v~g~V~~i~~~G~fV~l~~~i~Gli~~sel~~~~~~~~~~~~kvGd~V~vkV~~id~e~~rI~lslk~~ 634 (647)
T PRK00087 561 PVGSIVLGKVVRIAPFGAFVELEPGVDGLVHISQISWKRIDKPEDVLSEGEEVKAKILEVDPEEKRIRLSIKEV 634 (647)
T ss_pred cCCeEEEEEEEEEECCeEEEEECCCCEEEEEhhhcCccccCCHhhcCCCCCEEEEEEEEEeCCCCEEEEEEeec
Confidence 5899999999999999999999888999999987753 244555679999999999999985 47788999874
No 82
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=96.55 E-value=0.0079 Score=61.84 Aligned_cols=73 Identities=18% Similarity=0.187 Sum_probs=63.2
Q ss_pred CCCCCCEEE-EEEEEecCceEEEEecCCeeeeecCcccCC-cccccccCcCCCCEEEEEEEecCCCCcceEEEec
Q 026458 71 VPCVEDTVL-GIVVDCKADNFFVDIRGPTIAFLPVLAFEG-GTRRNIPKFEIGSLLYVRVVKANPGMNPELSCTD 143 (238)
Q Consensus 71 ~P~vGDiVI-G~V~~v~~~~~~VdI~~~~~a~L~~~~f~g-atk~~r~~l~~GDlV~ArV~~~~~~~~~~Ls~~~ 143 (238)
.|++|+++- |+|+++.+-.++|+|....+|.+|++.+.. ..++....|++||.|..+|.+++..+.+.||.+.
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 699999999999999877899999998854 3555667899999999999999877788999865
No 83
>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=96.45 E-value=0.036 Score=53.62 Aligned_cols=69 Identities=19% Similarity=0.243 Sum_probs=58.3
Q ss_pred CCCCEEEEEEEEecCceEEEEecCCeeeeecCcccCC-cccccccCcCCCCEEEEEEEecCC-CCcceEEE
Q 026458 73 CVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEG-GTRRNIPKFEIGSLLYVRVVKANP-GMNPELSC 141 (238)
Q Consensus 73 ~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~g-atk~~r~~l~~GDlV~ArV~~~~~-~~~~~Ls~ 141 (238)
.+||+|-|+|+++....++|.+.....|.+|.+.+.. ..++....|++||.|.++|.+++. ...+.||.
T Consensus 445 ~~G~~v~g~V~~v~~~G~fV~l~~~~~Glv~~s~l~~~~~~~~~~~~~~Gd~v~~~V~~id~~~~~i~ls~ 515 (516)
T TIGR00717 445 KVGSVVKGKVTEIKDFGAFVELPGGVEGLIRNSELSENRDEDKTDEIKVGDEVEAKVVDIDKKNRKVSLSV 515 (516)
T ss_pred CcceEEEEEEEEEecceEEEEcCCCeEEEEEHHHcCccccccccccCCCCCEEEEEEEEEeCCCCEEEEEE
Confidence 5799999999999999999999888999999987643 244567789999999999999975 35666764
No 84
>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional
Probab=96.41 E-value=0.011 Score=61.00 Aligned_cols=64 Identities=36% Similarity=0.444 Sum_probs=56.0
Q ss_pred CCCCCEEEEEEEEecCceEEEEecCCeeeeecCcccCCcccccccCcCCCCEEEEEEEecCCCCcceEEEec
Q 026458 72 PCVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEGGTRRNIPKFEIGSLLYVRVVKANPGMNPELSCTD 143 (238)
Q Consensus 72 P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~gatk~~r~~l~~GDlV~ArV~~~~~~~~~~Ls~~~ 143 (238)
++.||+|-|+|+++..+...|||+.-.+|++|...|.. .+++||-|.|.|.+.+..+ +.||-..
T Consensus 319 ~~~G~iV~G~Vv~i~~~~v~VdiG~K~eGiI~~~E~~~-------~~kvGd~i~~~V~~~~~~~-~~LS~~~ 382 (863)
T PRK12269 319 PEPGSVRMGTVVQVNAGTVFVDIGGKSEGRVPVEEFEA-------PPKAGDGVRVYVERVTPYG-PELSKTK 382 (863)
T ss_pred CCCCCEEEEEEEEEECCEEEEEeCCCceEEeEHHHhcc-------CCCCCCEEEEEEEEEcCCc-eEEEehH
Confidence 89999999999999999999999999999999888831 2589999999999987654 7888654
No 85
>COG2183 Tex Transcriptional accessory protein [Transcription]
Probab=96.39 E-value=0.0072 Score=60.90 Aligned_cols=74 Identities=15% Similarity=0.130 Sum_probs=64.5
Q ss_pred CCCCCEEEEEEEEecCceEEEEecCCeeeeecCcccCCc-ccccccCcCCCCEEEEEEEecCCC-CcceEEEecCC
Q 026458 72 PCVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEGG-TRRNIPKFEIGSLLYVRVVKANPG-MNPELSCTDAS 145 (238)
Q Consensus 72 P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~ga-tk~~r~~l~~GDlV~ArV~~~~~~-~~~~Ls~~~~~ 145 (238)
-++|-++.|.|+.+.+-.++|||+....|.+|++...+. .+.-...+++||+|.++|.+++.. ..+.||++.+.
T Consensus 656 Lk~Gm~leg~Vrnv~~fgafVdIgv~qDglvHis~ls~~fv~~P~~vv~vGdiV~v~V~~vD~~r~rI~Lsmr~~~ 731 (780)
T COG2183 656 LKPGMILEGTVRNVVDFGAFVDIGVHQDGLVHISQLSDKFVKDPNEVVKVGDIVKVKVIEVDTARKRIALSMRLDE 731 (780)
T ss_pred ccCCCEEEEEEEEeeeccceEEeccccceeeeHHHhhhhhcCChHHhcccCCEEEEEEEEEecccCeeeeEeeccC
Confidence 488999999999999999999999999999999887654 444567899999999999999865 46899999864
No 86
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=96.32 E-value=0.012 Score=56.84 Aligned_cols=70 Identities=23% Similarity=0.239 Sum_probs=57.4
Q ss_pred ccCCCCCCEEEEEEEEecCceEEEEecCCeeeeecCcccCCcccccccCcCCCCEEEEEEEecCCCC---cceEEEecC
Q 026458 69 RYVPCVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEGGTRRNIPKFEIGSLLYVRVVKANPGM---NPELSCTDA 144 (238)
Q Consensus 69 ~Y~P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~gatk~~r~~l~~GDlV~ArV~~~~~~~---~~~Ls~~~~ 144 (238)
.|..++|++|.|+|.++....+.||++ ...|+||.+.. -.+..|++||-|.|.|..+++.. .+.||-.+|
T Consensus 129 eyk~~~GeIV~G~V~ri~~~giiVDLg-gvea~LP~sE~-----ip~E~~~~GdrIka~I~~Vd~~~kg~qIilSRt~p 201 (470)
T PRK09202 129 EYKDRVGEIITGVVKRVERGNIIVDLG-RAEAILPRKEQ-----IPRENFRPGDRVRAYVYEVRKEARGPQIILSRTHP 201 (470)
T ss_pred HHHhhcCCEEEEEEEEEecCCEEEEEC-CeEEEecHHHc-----CCCccCCCCCEEEEEEEEEecCCCCCeEEEEeCcH
Confidence 488999999999999999999999996 47999997654 24567999999999999997642 456776553
No 87
>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=96.25 E-value=0.066 Score=50.93 Aligned_cols=92 Identities=18% Similarity=0.140 Sum_probs=64.5
Q ss_pred EEEEccCCccCCCCCCEEEEEEEEecCc--eEEEEecCCeeeeecCcccCCc-------------ccccccCcCCCCEEE
Q 026458 61 YWVESSQKRYVPCVEDTVLGIVVDCKAD--NFFVDIRGPTIAFLPVLAFEGG-------------TRRNIPKFEIGSLLY 125 (238)
Q Consensus 61 i~V~~~~~~Y~P~vGDiVIG~V~~v~~~--~~~VdI~~~~~a~L~~~~f~ga-------------tk~~r~~l~~GDlV~ 125 (238)
+++++... .+.+||+..|+|.++.+. .++|||+...+|+||+++.... .++....+.+||-|.
T Consensus 14 ~~ie~~~~--~~~vGnIY~GrV~~i~p~l~aAFVdiG~~k~gfL~~~d~~~~~~~~~~~~~~~~~~~~i~~~l~~G~~Il 91 (414)
T TIGR00757 14 LIIERPKS--RQLKGNIYKGRVTRILPSLQAAFVDIGLEKNGFLHASDIGPNYECLAPAEAKREAGPSISELLRPGQSVL 91 (414)
T ss_pred EEEecCcC--cCCCCCEEEEEEeeecCCCceEEEEcCCCceEEEEHHHcCchhhccccccccccccCCHHHhCcCCCEEE
Confidence 45554433 346899999999999887 9999999999999999875311 112233599999999
Q ss_pred EEEEecCC-CCcceEEEecCCCccCCCcccCCeeEEEec
Q 026458 126 VRVVKANP-GMNPELSCTDASGKAAEFGLLKDGYMFETS 163 (238)
Q Consensus 126 ArV~~~~~-~~~~~Ls~~~~~~~~~~~G~L~~G~~~~V~ 163 (238)
.+|..-.. ...+.||+.- .|.|.+++-.|
T Consensus 92 VQV~Ke~~~~Kgp~lT~~I---------sl~GrylVl~P 121 (414)
T TIGR00757 92 VQVVKEPRGNKGARLTTDI---------SLPGRYLVLMP 121 (414)
T ss_pred EEEeeCCcCCCCCeEEEEE---------EeccceEEEec
Confidence 99998432 3457777743 14555555554
No 88
>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=96.16 E-value=0.016 Score=53.78 Aligned_cols=120 Identities=19% Similarity=0.144 Sum_probs=75.1
Q ss_pred ccCCCCCCEEEEEEEEecCce-EEEEecCCeeeeecCcccCCcccccccCcCCCCEEEEEEEecCCC---CcceEEEecC
Q 026458 69 RYVPCVEDTVLGIVVDCKADN-FFVDIRGPTIAFLPVLAFEGGTRRNIPKFEIGSLLYVRVVKANPG---MNPELSCTDA 144 (238)
Q Consensus 69 ~Y~P~vGDiVIG~V~~v~~~~-~~VdI~~~~~a~L~~~~f~gatk~~r~~l~~GDlV~ArV~~~~~~---~~~~Ls~~~~ 144 (238)
.|..++|++|.|+|.++..+. |.|||+ ...|+||.+... .+..|++||-|.|.|.++.+. ..+.||-..|
T Consensus 126 ey~~k~GeiV~G~V~~v~~~g~v~VdiG-~~ea~LP~~E~i-----p~E~~~~Gd~ik~~V~~V~~~~kg~qIivSRt~~ 199 (341)
T TIGR01953 126 EFSSKEGEIISGTVKRVNRRGNLYVELG-KTEGILPKKEQI-----PGEKFRIGDRIKAYVYEVRKTAKGPQIILSRTHP 199 (341)
T ss_pred HHHhhcCCEEEEEEEEEecCCcEEEEEC-CeEEEecHHHcC-----CCcCCCCCCEEEEEEEEEEcCCCCCeEEEEeCcH
Confidence 488999999999999998854 799996 579999976542 233499999999999999754 3466776553
Q ss_pred C-Cc---cCCCcccCCeeEEEechhhhhhhcCCCCc-hhhHhhccccceEEEEeeCCe
Q 026458 145 S-GK---AAEFGLLKDGYMFETSTGLSRMLLSSPTC-PVLEELGKQLSFEIAVGLNGR 197 (238)
Q Consensus 145 ~-~~---~~~~G~L~~G~~~~V~~~~v~rl~~~~~~-~~l~~l~~~~~~ei~vG~NG~ 197 (238)
. -+ +..--.+.+|.+-=.+.+..+ |.+.- .+...=..-=|.-.|||++|.
T Consensus 200 ~~v~~Lfe~EVPEI~dG~VeI~~iaR~p---G~RtKvAV~s~~~~iDpvga~vG~~G~ 254 (341)
T TIGR01953 200 EFVKELLKLEVPEIADGIIEIKKIAREP---GYRTKIAVESNDENIDPVGACVGPKGS 254 (341)
T ss_pred HHHHHHHHHhCccccCCeEEEEEEeeCC---cceeEEEEEcCCCCCCcceeeECCCCc
Confidence 1 00 122244567776544433322 21111 011111111356678888773
No 89
>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional
Probab=96.10 E-value=0.036 Score=57.22 Aligned_cols=72 Identities=19% Similarity=0.203 Sum_probs=60.5
Q ss_pred CCCCCEEEEEEEEecCceEEEEecCCeeeeecCcccCC-cccccccCcCCCCEEEEEEEecCC-CCcceEEEecC
Q 026458 72 PCVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEG-GTRRNIPKFEIGSLLYVRVVKANP-GMNPELSCTDA 144 (238)
Q Consensus 72 P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~g-atk~~r~~l~~GDlV~ArV~~~~~-~~~~~Ls~~~~ 144 (238)
.++||+|.|+|..+....++||++ ...|.+|.+.+.. ...+.+..|.+||-|.++|+++++ .+.+.||++..
T Consensus 491 l~~G~~V~G~Vk~i~~~G~fVdl~-Gv~Gfvp~SeiS~~~v~~~~~~~kvGq~v~vkVi~iD~e~~rI~LSlK~l 564 (863)
T PRK12269 491 VHIEDSVSGVVKSFTSFGAFIDLG-GFDGLLHVNDMSWGHVARPREFVKKGQTIELKVIRLDQAEKRINLSLKHF 564 (863)
T ss_pred CCCCCEEEEEEEEEeCCcEEEEEC-CEEEEEEchhccccccCCHHHhccCCCEEEEEEEEEecCCCeEEEEEecc
Confidence 568999999999999999999996 4789999987752 345556779999999999999986 46789998753
No 90
>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=95.77 E-value=0.017 Score=39.43 Aligned_cols=44 Identities=9% Similarity=0.112 Sum_probs=39.4
Q ss_pred EEEechhhhhhhcCCCCchhhHhhccccceEEEEee------CCeEEEecC
Q 026458 159 MFETSTGLSRMLLSSPTCPVLEELGKQLSFEIAVGL------NGRVWVNAE 203 (238)
Q Consensus 159 ~~~V~~~~v~rl~~~~~~~~l~~l~~~~~~ei~vG~------NG~IWi~~~ 203 (238)
-+.||..++++++|++++ .++.|.+.+++.|.+.. +..|||.+.
T Consensus 3 ~i~ip~~~~~~vIG~~G~-~i~~I~~~s~~~I~i~~~~~~~~~~~v~i~G~ 52 (64)
T cd00105 3 RVLVPSSLVGRIIGKGGS-TIKEIREETGAKIKIPDSGSGSEERIVTITGT 52 (64)
T ss_pred EEEEchhhcceeECCCCH-HHHHHHHHHCCEEEEcCCCCCCCceEEEEEcC
Confidence 478999999999999998 99999999999999987 467999985
No 91
>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=95.74 E-value=0.079 Score=39.54 Aligned_cols=59 Identities=14% Similarity=0.242 Sum_probs=41.0
Q ss_pred CCCEEEEEEEEecCceEEEEecC----CeeeeecCc-ccCC-c-----ccccccCcCCCCEEEEEEEecC
Q 026458 74 VEDTVLGIVVDCKADNFFVDIRG----PTIAFLPVL-AFEG-G-----TRRNIPKFEIGSLLYVRVVKAN 132 (238)
Q Consensus 74 vGDiVIG~V~~v~~~~~~VdI~~----~~~a~L~~~-~f~g-a-----tk~~r~~l~~GDlV~ArV~~~~ 132 (238)
+|.+|.|+|++++...+.|+++. -....+|.. .|.. . ..+.+..+++||.|++||....
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 222222211 1211 1 1123567999999999998874
No 92
>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=95.69 E-value=0.016 Score=39.56 Aligned_cols=54 Identities=15% Similarity=0.224 Sum_probs=45.8
Q ss_pred EEEechhhhhhhcCCCCchhhHhhccccceEEEEeeC---CeEEEecCChhHHHHHHHH
Q 026458 159 MFETSTGLSRMLLSSPTCPVLEELGKQLSFEIAVGLN---GRVWVNAESPSTVVLVSNA 214 (238)
Q Consensus 159 ~~~V~~~~v~rl~~~~~~~~l~~l~~~~~~ei~vG~N---G~IWi~~~~~~~~~~i~~~ 214 (238)
-+.||..++.+++|++++ .++.|.+.+++.|-+-.+ ..|.|.+ +++....+.+.
T Consensus 3 ~i~vp~~~~~~iIG~~G~-~i~~I~~~t~~~I~i~~~~~~~~v~I~G-~~~~v~~A~~~ 59 (60)
T PF00013_consen 3 RIEVPSSLVGRIIGKKGS-NIKEIEEETGVKIQIPDDDERDIVTISG-SPEQVEKAKKM 59 (60)
T ss_dssp EEEEEHHHHHHHHTGGGH-HHHHHHHHHTSEEEEESTTEEEEEEEEE-SHHHHHHHHHH
T ss_pred EEEECHHHcCEEECCCCC-cHHHhhhhcCeEEEEcCCCCcEEEEEEe-CHHHHHHHHhh
Confidence 478999999999999998 999999999999999875 6899998 77665555543
No 93
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=95.60 E-value=0.047 Score=51.12 Aligned_cols=69 Identities=28% Similarity=0.353 Sum_probs=53.0
Q ss_pred ccCCCCCCEEEEEEEEecC-ceEEEEecCCeeeeecCcccCCcccccccCcCCCCEEEEEEEecCCCC----cceEEEec
Q 026458 69 RYVPCVEDTVLGIVVDCKA-DNFFVDIRGPTIAFLPVLAFEGGTRRNIPKFEIGSLLYVRVVKANPGM----NPELSCTD 143 (238)
Q Consensus 69 ~Y~P~vGDiVIG~V~~v~~-~~~~VdI~~~~~a~L~~~~f~gatk~~r~~l~~GDlV~ArV~~~~~~~----~~~Ls~~~ 143 (238)
.|.+++|++|.|+|.++.. ..+.||++ ...|+||...- -.+..|++||-|.|-|..+.+.. .+.||..+
T Consensus 133 ey~~~~Geiv~g~V~r~~~~~~i~vdlg-~~ea~LP~~eq-----ip~E~~~~Gdrik~~i~~V~~~~k~gp~IilSRt~ 206 (374)
T PRK12328 133 KYKKKVGKIVFGTVVRVDNEENTFIEID-EIRAVLPMKNR-----IKGEKFKVGDVVKAVLKRVKIDKNNGILIELSRTS 206 (374)
T ss_pred HHHHhcCcEEEEEEEEEecCCCEEEEcC-CeEEEeCHHHc-----CCCCcCCCCCEEEEEEEEEecCCCCCCEEEEEcCC
Confidence 4899999999999999985 56889998 48999996432 23456999999999999986543 23455444
No 94
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=95.29 E-value=0.076 Score=50.71 Aligned_cols=93 Identities=11% Similarity=0.084 Sum_probs=64.0
Q ss_pred ccCCCCCCEEEEEEEEecCceEEEEecC-----CeeeeecCcccCCcccccccCcCCCCEEEEEEEecCCC--C--cceE
Q 026458 69 RYVPCVEDTVLGIVVDCKADNFFVDIRG-----PTIAFLPVLAFEGGTRRNIPKFEIGSLLYVRVVKANPG--M--NPEL 139 (238)
Q Consensus 69 ~Y~P~vGDiVIG~V~~v~~~~~~VdI~~-----~~~a~L~~~~f~gatk~~r~~l~~GDlV~ArV~~~~~~--~--~~~L 139 (238)
.|.+++|++|.|+|.++..+.+.||+++ ...|+||...- --+..|++||-|+|-|..+... . .+.|
T Consensus 147 ef~~~~GeIV~G~V~r~e~~~viv~l~~~~g~~~~EaiLP~~Eq-----ip~E~y~~Gdrika~i~~V~~~~~kGpqIil 221 (449)
T PRK12329 147 EFQDLEDTVLTARVLRFERQSVIMAVSSGFGQPEVEAELPKREQ-----LPNDNYRANATFKVFLKEVSEGPRRGPQLFV 221 (449)
T ss_pred HHHHhcCcEEEEEEEEEcCCCEEEEecccCCCcceEEEecHHHc-----CCCCcCCCCCEEEEEEEEeecCCCCCCEEEE
Confidence 3899999999999999999999999953 26899996432 1235699999999999999654 2 2445
Q ss_pred EEecCC-Cc---cCCCcccCCeeEEEechhh
Q 026458 140 SCTDAS-GK---AAEFGLLKDGYMFETSTGL 166 (238)
Q Consensus 140 s~~~~~-~~---~~~~G~L~~G~~~~V~~~~ 166 (238)
|-.+|. -+ ...--.+.+|.+-=...+.
T Consensus 222 SRt~p~lv~~Lfe~EVPEI~dG~VeIk~IAR 252 (449)
T PRK12329 222 SRANAGLVVYLFENEVPEIEEGVVRIVAVAR 252 (449)
T ss_pred EcCCHHHHHHHHHhhCcccccCeEEEEEEEe
Confidence 543321 00 1223555778766555444
No 95
>KOG1070 consensus rRNA processing protein Rrp5 [RNA processing and modification]
Probab=94.53 E-value=0.25 Score=52.99 Aligned_cols=74 Identities=20% Similarity=0.327 Sum_probs=65.4
Q ss_pred CCCCCEEEEEEEEecCceEEEEecCCeeeeecCcccC-CcccccccCcCCCCEEEEEEEecCCC-CcceEEEecCC
Q 026458 72 PCVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFE-GGTRRNIPKFEIGSLLYVRVVKANPG-MNPELSCTDAS 145 (238)
Q Consensus 72 P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~-gatk~~r~~l~~GDlV~ArV~~~~~~-~~~~Ls~~~~~ 145 (238)
-++||+|.|.|..+.....++-+.....|.++++.+- ...+.-++.|.+|++|-+||.+++.+ ..++|+..+..
T Consensus 1160 lk~g~iv~G~V~nv~~~glfi~ls~~v~a~v~is~~~ds~~k~w~k~~~~gklv~~rv~~ve~~s~riel~Lk~s~ 1235 (1710)
T KOG1070|consen 1160 LKIGDIVRGFVKNVETKGLFIALSRKVEAFVPISGLSDSFEKEWEKHLPVGKLVTGRVLSVEEDSKRIELSLKNSD 1235 (1710)
T ss_pred cccCceeEEEEEEecCCcEEEEEccceEEEEEccccccchhhhhhccCCccceeeeEEEEeeccCceEEEEEeccc
Confidence 4789999999999999999999999999999988764 34677888999999999999999866 47999998864
No 96
>smart00322 KH K homology RNA-binding domain.
Probab=94.44 E-value=0.14 Score=34.35 Aligned_cols=58 Identities=9% Similarity=0.165 Sum_probs=48.3
Q ss_pred eEEEechhhhhhhcCCCCchhhHhhccccceEEEEeeC----CeEEEecCChhHHHHHHHHHHH
Q 026458 158 YMFETSTGLSRMLLSSPTCPVLEELGKQLSFEIAVGLN----GRVWVNAESPSTVVLVSNAIMN 217 (238)
Q Consensus 158 ~~~~V~~~~v~rl~~~~~~~~l~~l~~~~~~ei~vG~N----G~IWi~~~~~~~~~~i~~~i~~ 217 (238)
.-+.|+..+...++|++++ .++.|.+.+++.|.+..+ ..++|.++ ..+...+..+|..
T Consensus 5 ~~i~i~~~~~~~liG~~G~-~i~~i~~~~~~~i~~~~~~~~~~~v~i~g~-~~~v~~a~~~i~~ 66 (69)
T smart00322 5 IEVLIPADKVGLIIGKGGS-TIKKIEEETGVKIDIPEDGSEERVVEITGP-PENVEKAAELILE 66 (69)
T ss_pred EEEEEcchhcceeECCCch-HHHHHHHHHCCEEEECCCCCCccEEEEEcC-HHHHHHHHHHHHH
Confidence 4578999999999999998 889999999999998885 78999985 6667777766654
No 97
>KOG1856 consensus Transcription elongation factor SPT6 [RNA processing and modification]
Probab=94.26 E-value=0.058 Score=56.36 Aligned_cols=74 Identities=19% Similarity=0.260 Sum_probs=60.9
Q ss_pred CCCCCEEEEEEEEecCce---EEEEecCCeeeeecCcccCCc-ccccccCcCCCCEEEEEEEecCCCC-cceEEEecCC
Q 026458 72 PCVEDTVLGIVVDCKADN---FFVDIRGPTIAFLPVLAFEGG-TRRNIPKFEIGSLLYVRVVKANPGM-NPELSCTDAS 145 (238)
Q Consensus 72 P~vGDiVIG~V~~v~~~~---~~VdI~~~~~a~L~~~~f~ga-tk~~r~~l~~GDlV~ArV~~~~~~~-~~~Ls~~~~~ 145 (238)
-.+|-+|.+.|+++.... ..|-..|..+++++..+..++ .++.-..+++|+.|+|||++++... ..+|||+++.
T Consensus 983 ~~~g~iV~~~V~~vt~rr~~Cv~v~ld~G~~g~i~~~~~Sd~~v~~p~~~v~vgq~v~~kvi~id~e~f~v~Ls~r~sd 1061 (1299)
T KOG1856|consen 983 FYEGAIVPVTVTKVTHRRGICVRVRLDCGVTGFILAKNLSDRDVRRPENRVKVGQTVYCKVIKIDKERFSVELSCRTSD 1061 (1299)
T ss_pred hccCceEEEeeeEEEecccceeEEEecCCCceeeeccccChhhccCHHHhhccCceEEEEeeeeeHhhhhhhhhhhhHH
Confidence 458999999999999999 555899999999998877663 4445556889999999999998764 6889998754
No 98
>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=93.33 E-value=0.15 Score=51.40 Aligned_cols=59 Identities=14% Similarity=0.134 Sum_probs=50.1
Q ss_pred eEEEechhhhhhhcCCCCchhhHhhccccceEEEEeeCCeEEEecCChhHHHHHHHHHHH
Q 026458 158 YMFETSTGLSRMLLSSPTCPVLEELGKQLSFEIAVGLNGRVWVNAESPSTVVLVSNAIMN 217 (238)
Q Consensus 158 ~~~~V~~~~v~rl~~~~~~~~l~~l~~~~~~ei~vG~NG~IWi~~~~~~~~~~i~~~i~~ 217 (238)
..++|+|.+++.+||+.+. +++.|.+++++.|-+-.+|.|+|.+.+......+.+.|+.
T Consensus 553 ~~~~I~~~kI~~vIG~gGk-~Ik~I~~~tg~~I~i~ddG~V~i~~~~~~~~~~a~~~I~~ 611 (684)
T TIGR03591 553 ETIKINPDKIRDVIGPGGK-VIREITEETGAKIDIEDDGTVKIAASDGEAAEAAIKMIEG 611 (684)
T ss_pred EEEecCHHHHHhhcCCCcH-HHHHHHHHHCCEEEEecCeEEEEEECcHHHHHHHHHHHHh
Confidence 4689999999999999987 9999999999999999999999999887555544444443
No 99
>PRK11642 exoribonuclease R; Provisional
Probab=92.58 E-value=0.72 Score=47.56 Aligned_cols=83 Identities=16% Similarity=0.228 Sum_probs=62.8
Q ss_pred CCCCCEEEEEEEEecCceEEEEecCC-eeeeecCcccCCc------------ccccccCcCCCCEEEEEEEecCCC-Ccc
Q 026458 72 PCVEDTVLGIVVDCKADNFFVDIRGP-TIAFLPVLAFEGG------------TRRNIPKFEIGSLLYVRVVKANPG-MNP 137 (238)
Q Consensus 72 P~vGDiVIG~V~~v~~~~~~VdI~~~-~~a~L~~~~f~ga------------tk~~r~~l~~GDlV~ArV~~~~~~-~~~ 137 (238)
..+|+.+-|+|+++....++|.|... -+|.+|++.+.+. -++....|++||-|..+|.+++.. +.+
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 7899998766431 113346799999999999998754 568
Q ss_pred eEEEecCCCccCCCccc
Q 026458 138 ELSCTDASGKAAEFGLL 154 (238)
Q Consensus 138 ~Ls~~~~~~~~~~~G~L 154 (238)
.++....+-+..+.|+-
T Consensus 721 ~f~l~~~~~~~~~~~~~ 737 (813)
T PRK11642 721 DFSLISSERAPRNVGKT 737 (813)
T ss_pred EEEEecccccCCCCCcc
Confidence 88876543344455543
No 100
>PRK13763 putative RNA-processing protein; Provisional
Probab=92.04 E-value=0.42 Score=40.28 Aligned_cols=62 Identities=11% Similarity=0.198 Sum_probs=53.0
Q ss_pred eEEEechhhhhhhcCCCCchhhHhhccccceEEEEeeC-CeEEEe---cCChhHHHHHHHHHHHhcc
Q 026458 158 YMFETSTGLSRMLLSSPTCPVLEELGKQLSFEIAVGLN-GRVWVN---AESPSTVVLVSNAIMNSES 220 (238)
Q Consensus 158 ~~~~V~~~~v~rl~~~~~~~~l~~l~~~~~~ei~vG~N-G~IWi~---~~~~~~~~~i~~~i~~~e~ 220 (238)
..+.||+.++..++|+.+. .++.|.+.+++.|-+-.+ |.|-|. +.|+.....+.+.|+.+-.
T Consensus 5 ~~i~IP~~kig~iIG~gGk-~Ik~I~e~tg~~I~i~~~~g~V~I~~~~~~d~~~i~kA~~~I~ai~~ 70 (180)
T PRK13763 5 EYVKIPKDRIGVLIGKKGE-TKKEIEERTGVKLEIDSETGEVIIEPTDGEDPLAVLKARDIVKAIGR 70 (180)
T ss_pred EEEEcCHHHhhhHhccchh-HHHHHHHHHCcEEEEECCCCeEEEEeCCCCCHHHHHHHHHHHHHHhc
Confidence 3578999999999998887 999999999999999999 999999 7788777777777765443
No 101
>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=91.93 E-value=0.7 Score=46.79 Aligned_cols=70 Identities=17% Similarity=0.302 Sum_probs=55.8
Q ss_pred CCCCCCEEEEEEEEecCceEEEEecC-CeeeeecCcccCCc------------ccccccCcCCCCEEEEEEEecCCC-Cc
Q 026458 71 VPCVEDTVLGIVVDCKADNFFVDIRG-PTIAFLPVLAFEGG------------TRRNIPKFEIGSLLYVRVVKANPG-MN 136 (238)
Q Consensus 71 ~P~vGDiVIG~V~~v~~~~~~VdI~~-~~~a~L~~~~f~ga------------tk~~r~~l~~GDlV~ArV~~~~~~-~~ 136 (238)
.+.+|.++-|+|+++..-.++|++.. ...|.+|++++.+. .++....|++||-|..+|.+++.. +.
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 47889999999999999999999986 58999999877532 122345799999999999999753 45
Q ss_pred ceEE
Q 026458 137 PELS 140 (238)
Q Consensus 137 ~~Ls 140 (238)
+.++
T Consensus 704 I~~~ 707 (709)
T TIGR02063 704 IDFE 707 (709)
T ss_pred EEEE
Confidence 5554
No 102
>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=91.73 E-value=0.32 Score=40.66 Aligned_cols=60 Identities=12% Similarity=0.196 Sum_probs=51.8
Q ss_pred EEechhhhhhhcCCCCchhhHhhccccceEEEEeeC-CeEEE--ecCChhHHHHHHHHHHHhcc
Q 026458 160 FETSTGLSRMLLSSPTCPVLEELGKQLSFEIAVGLN-GRVWV--NAESPSTVVLVSNAIMNSES 220 (238)
Q Consensus 160 ~~V~~~~v~rl~~~~~~~~l~~l~~~~~~ei~vG~N-G~IWi--~~~~~~~~~~i~~~i~~~e~ 220 (238)
+.||+.++..++|+.+. .++.|.+.+++.|-+-.+ |.|-| .+.|+.....+...|+.+-.
T Consensus 2 i~Ip~~kig~vIG~gG~-~Ik~I~~~tgv~I~Id~~~g~V~I~~~t~d~~~i~kA~~~I~~i~~ 64 (172)
T TIGR03665 2 VKIPKDRIGVLIGKGGE-TKKEIEERTGVKLDIDSETGEVKIEEEDEDPLAVMKAREVVKAIGR 64 (172)
T ss_pred ccCCHHHhhhHhCCchh-HHHHHHHHhCcEEEEEcCCceEEEecCCCCHHHHHHHHHHHHHHHc
Confidence 67999999999999988 999999999999999999 99999 67888777777777766443
No 103
>PRK10811 rne ribonuclease E; Reviewed
Probab=91.22 E-value=1.3 Score=46.31 Aligned_cols=81 Identities=16% Similarity=0.137 Sum_probs=56.1
Q ss_pred EEEEccCCccCCCCCCEEEEEEEEe--cCceEEEEecCCeeeeecCcccCCc----------ccccccCcCCCCEEEEEE
Q 026458 61 YWVESSQKRYVPCVEDTVLGIVVDC--KADNFFVDIRGPTIAFLPVLAFEGG----------TRRNIPKFEIGSLLYVRV 128 (238)
Q Consensus 61 i~V~~~~~~Y~P~vGDiVIG~V~~v--~~~~~~VdI~~~~~a~L~~~~f~ga----------tk~~r~~l~~GDlV~ArV 128 (238)
+.|++... -+.+|+|-+|+|.++ +-+.++|||+....|+|++...... ..+....|++||-|.-.|
T Consensus 27 L~IEr~~~--e~~vGnIYkGkVenIvPGInAAFVDIG~gknGFL~L~Di~~~~f~~~~~~~~~~~i~~~Lk~GqeILVQV 104 (1068)
T PRK10811 27 LDIESPGH--EQKKANIYKGKITRIEPSLEAAFVDYGAERHGFLPLKEIAREYFPANYSAHGRPNIKDVLREGQEVIVQI 104 (1068)
T ss_pred EEeccCcc--ccCccceEEEEEecccCCcceeEEEecCCcceEEEhhhccccccccccccccccccccccCCCCEEEEEE
Confidence 45555333 235899999999998 4578999999999999997654210 012234599999999999
Q ss_pred EecC-CCCcceEEEec
Q 026458 129 VKAN-PGMNPELSCTD 143 (238)
Q Consensus 129 ~~~~-~~~~~~Ls~~~ 143 (238)
..-. ...-+.||+.-
T Consensus 105 ~KEa~gtKGp~LTt~I 120 (1068)
T PRK10811 105 DKEERGNKGAALTTFI 120 (1068)
T ss_pred eecccCCCCCceeeeE
Confidence 9733 23446666543
No 104
>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=90.63 E-value=0.58 Score=32.45 Aligned_cols=36 Identities=8% Similarity=0.142 Sum_probs=33.5
Q ss_pred EEechhhhhhhcCCCCchhhHhhccccceEEEEeeCC
Q 026458 160 FETSTGLSRMLLSSPTCPVLEELGKQLSFEIAVGLNG 196 (238)
Q Consensus 160 ~~V~~~~v~rl~~~~~~~~l~~l~~~~~~ei~vG~NG 196 (238)
+.||..++.+++|++++ .++.|.+.+++.|-+..|.
T Consensus 4 ~~ip~~~vg~iIG~~G~-~i~~i~~~tga~I~i~~~~ 39 (65)
T cd02396 4 LLVPSSQAGSIIGKGGS-TIKEIREETGAKIRVSKSV 39 (65)
T ss_pred EEECHHHcCeeECCCcH-HHHHHHHHHCCEEEEcCCC
Confidence 67999999999999998 9999999999999999887
No 105
>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=90.53 E-value=0.46 Score=37.57 Aligned_cols=55 Identities=18% Similarity=0.197 Sum_probs=42.5
Q ss_pred hhhhhhhcCCCCchhhHhhccccceEEEEeeC-----------------------CeEEEecCC--hhHHHHHHHHHHHh
Q 026458 164 TGLSRMLLSSPTCPVLEELGKQLSFEIAVGLN-----------------------GRVWVNAES--PSTVVLVSNAIMNS 218 (238)
Q Consensus 164 ~~~v~rl~~~~~~~~l~~l~~~~~~ei~vG~N-----------------------G~IWi~~~~--~~~~~~i~~~i~~~ 218 (238)
-.++.++||.+++ -++.|.+.++|.|.|--. |.|.|.+.+ .+....+...|+.+
T Consensus 14 ~N~IG~IIGPgG~-tiK~i~~eTg~kI~Irg~gs~~~~~~~~~~~~~~~~~~~eplhV~I~a~~~~~e~~~~A~~~I~~l 92 (120)
T cd02395 14 YNFVGLILGPRGN-TLKQLEKETGAKISIRGKGSMKDGKKEEELRGPKYAHLNEPLHVLITAETPPEEALAKAVEAIEEL 92 (120)
T ss_pred CCeeEEEECCCCh-HHHHHHHHHCCEEEEecCcccccccccccccCcccccCCCCcEEEEEeCCcHHHHHHHHHHHHHHH
Confidence 3577888999988 899999999999998766 899999988 55555555555444
Q ss_pred c
Q 026458 219 E 219 (238)
Q Consensus 219 e 219 (238)
-
T Consensus 93 l 93 (120)
T cd02395 93 L 93 (120)
T ss_pred h
Confidence 3
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=90.52 E-value=0.58 Score=47.46 Aligned_cols=60 Identities=10% Similarity=0.153 Sum_probs=51.5
Q ss_pred eEEEechhhhhhhcCCCCchhhHhhccccceEEEEeeCCeEEEecCChhHHHHHHHHHHHh
Q 026458 158 YMFETSTGLSRMLLSSPTCPVLEELGKQLSFEIAVGLNGRVWVNAESPSTVVLVSNAIMNS 218 (238)
Q Consensus 158 ~~~~V~~~~v~rl~~~~~~~~l~~l~~~~~~ei~vG~NG~IWi~~~~~~~~~~i~~~i~~~ 218 (238)
..++|+|.+++.+||..+. .++.|.+.++++|=+-.+|.|.|.+.+.+....+...|+.+
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 ITVKIPVDKIGEVIGPKGK-MINQIQDETGAEISIEDDGTVYIGAADGPSAEAARAMINAI 639 (719)
T ss_pred EEEEeChHHhhheeCCCcH-hHHHHHHHHCCEEEEecCcEEEEEeCCHHHHHHHHHHHHHh
Confidence 5789999999999998887 99999999999999999999999999986665555555443
No 107
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=90.04 E-value=0.79 Score=45.99 Aligned_cols=73 Identities=15% Similarity=0.102 Sum_probs=64.4
Q ss_pred CCCCCCEEEEEEEEecCceEEEEecCCeeeeecCcccCC-cccccccCcCCCCEEEEEEEecCCCCcceEEEec
Q 026458 71 VPCVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEG-GTRRNIPKFEIGSLLYVRVVKANPGMNPELSCTD 143 (238)
Q Consensus 71 ~P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~g-atk~~r~~l~~GDlV~ArV~~~~~~~~~~Ls~~~ 143 (238)
-|++|.+=.|+|+++..=.++|.+...-.|.+|++.... ...+-.+.++.||.|+.||..+++.+.+.||.+.
T Consensus 616 e~evg~iy~G~V~ri~~fGaFv~l~~gkdgl~hiS~~~~~rv~kv~dvlk~Gd~v~Vkv~~iD~~Gri~ls~~~ 689 (692)
T COG1185 616 EVEVGEVYEGTVVRIVDFGAFVELLPGKDGLVHISQLAKERVEKVEDVLKEGDEVKVKVIEIDKQGRIRLSIKA 689 (692)
T ss_pred hcccccEEEEEEEEEeecceEEEecCCcceeEEehhhhhhhhhcccceeecCceEEEEEeeecccCCccceehh
Confidence 589999999999999999999999999999999987642 3555668899999999999999998999998764
No 108
>PRK11712 ribonuclease G; Provisional
Probab=89.42 E-value=5.3 Score=38.94 Aligned_cols=80 Identities=23% Similarity=0.163 Sum_probs=56.0
Q ss_pred EEEEccCCccCCCCCCEEEEEEEEecC--ceEEEEecCCeeeeecCccc-CC------cc------cccccCcCCCCEEE
Q 026458 61 YWVESSQKRYVPCVEDTVLGIVVDCKA--DNFFVDIRGPTIAFLPVLAF-EG------GT------RRNIPKFEIGSLLY 125 (238)
Q Consensus 61 i~V~~~~~~Y~P~vGDiVIG~V~~v~~--~~~~VdI~~~~~a~L~~~~f-~g------at------k~~r~~l~~GDlV~ 125 (238)
+++++.. ....+|+|-.|+|.++.+ +.++|||+..-.|+||+... +. .. ......+++||-|.
T Consensus 27 ~~iE~~~--~~~~vGnIY~G~V~~v~pg~~AAFVdIG~~k~gFL~~~d~~~~~~~~~~~~~~~~~~~~i~~~l~~Gq~iL 104 (489)
T PRK11712 27 IHIEREA--KRGIVGNIYKGRVSRVLPGMQAAFVDIGLDKAAFLHASDIVPHTECVAGEEQKQFVVRDISELVRQGQDIM 104 (489)
T ss_pred EEEecCC--cccccccEEEEEEeecCCCCceeEEeeCCCccEEEEhhhccchhhhcccccccccccccHHHhccCCCEEE
Confidence 3445433 345689999999999955 78999999999999998754 11 00 01123499999999
Q ss_pred EEEEecCC-CCcceEEEe
Q 026458 126 VRVVKANP-GMNPELSCT 142 (238)
Q Consensus 126 ArV~~~~~-~~~~~Ls~~ 142 (238)
.+|..-.. ...+.||+.
T Consensus 105 VQV~Ke~~~~KG~~lT~~ 122 (489)
T PRK11712 105 VQVVKDPLGTKGARLTTD 122 (489)
T ss_pred EEEEeCCcCCCCCeEEEE
Confidence 99997432 345677764
No 109
>PF13509 S1_2: S1 domain; PDB: 3GO5_A.
Probab=89.37 E-value=2.6 Score=29.03 Aligned_cols=60 Identities=17% Similarity=0.105 Sum_probs=33.9
Q ss_pred CCCEEEEEEEEecCceEEEEecCCeeeeecCcccCCcccccccCcCCCCEEEEEEEecCCCCcceEEE
Q 026458 74 VEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEGGTRRNIPKFEIGSLLYVRVVKANPGMNPELSC 141 (238)
Q Consensus 74 vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~gatk~~r~~l~~GDlV~ArV~~~~~~~~~~Ls~ 141 (238)
+|+++-.+|++++...|.+|-+......||..+.+ ..+.+||-|..-|=. ++......||
T Consensus 1 iG~~~~L~V~~~~~~g~fL~~~~~~~vlLp~~e~~-------~~~~~Gd~v~VFvY~-D~~~rl~AT~ 60 (61)
T PF13509_consen 1 IGQINTLKVVDKNEFGYFLDDGEGKEVLLPKSEVP-------EPLKVGDEVEVFVYL-DKEGRLVATT 60 (61)
T ss_dssp --------EEEE-SSEEEEEETT-EEEEEEGGG-------------TTSEEEEEEEE--TTS-EEEE-
T ss_pred CCCCcceEEEEEeCCEEEEECCCCCEEEechHHcC-------CCCCCCCEEEEEEEE-CCCCCEEEec
Confidence 58899999999999999999888899999976553 348899999988765 3334455554
No 110
>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=88.10 E-value=2.2 Score=30.86 Aligned_cols=65 Identities=17% Similarity=0.108 Sum_probs=46.3
Q ss_pred CCEEEEEEEEecCceEEEEecC-CeeeeecCcccCCcccccc---cCcCCCCEE-EEEEEecCCCCcceEE
Q 026458 75 EDTVLGIVVDCKADNFFVDIRG-PTIAFLPVLAFEGGTRRNI---PKFEIGSLL-YVRVVKANPGMNPELS 140 (238)
Q Consensus 75 GDiVIG~V~~v~~~~~~VdI~~-~~~a~L~~~~f~gatk~~r---~~l~~GDlV-~ArV~~~~~~~~~~Ls 140 (238)
|++|-|+|.+++.|...|++.. .-.|+||.........+++ ..+++||-+ -+=|.. .....+.||
T Consensus 1 G~lV~~~V~EKt~D~l~v~l~~~~l~a~l~~~HLsD~~~k~~~~~~klrvG~~L~~~lvL~-~~~r~i~lt 70 (72)
T cd05699 1 GKLVDARVLKKTLNGLEVAILPEEIRAFLPTMHLSDHVSNCPLLWHCLQEGDTIPNLMCLS-NYKGRIILT 70 (72)
T ss_pred CceEEEEEEEEcCCcEEEEecCCCcEEEEEccccCCchhhCHHHHhhhhcCCCccceEEEe-ccccEEEEe
Confidence 7899999999999999999976 6689998765544322332 358999988 666662 223344454
No 111
>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=87.77 E-value=2.5 Score=42.56 Aligned_cols=70 Identities=11% Similarity=0.157 Sum_probs=54.5
Q ss_pred CCCCCCEEEEEEEEecCceEEEEec-CCeeeeecCcccCCc------------ccccccCcCCCCEEEEEEEecCCC-Cc
Q 026458 71 VPCVEDTVLGIVVDCKADNFFVDIR-GPTIAFLPVLAFEGG------------TRRNIPKFEIGSLLYVRVVKANPG-MN 136 (238)
Q Consensus 71 ~P~vGDiVIG~V~~v~~~~~~VdI~-~~~~a~L~~~~f~ga------------tk~~r~~l~~GDlV~ArV~~~~~~-~~ 136 (238)
...+|..+-|+|+++....++|+|. ...+|.+|++++++. .++....|++||.|..+|.+++.. ..
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 3567999999999999999999997 568999999877542 122346799999999999999753 33
Q ss_pred ceEE
Q 026458 137 PELS 140 (238)
Q Consensus 137 ~~Ls 140 (238)
+.++
T Consensus 649 I~f~ 652 (654)
T TIGR00358 649 IIFE 652 (654)
T ss_pred EEEE
Confidence 4443
No 112
>KOG1070 consensus rRNA processing protein Rrp5 [RNA processing and modification]
Probab=85.56 E-value=1.5 Score=47.35 Aligned_cols=70 Identities=17% Similarity=0.187 Sum_probs=57.2
Q ss_pred CCccCCCCCCEEEEEEEEecCceEEEEecCCeeeeecCccc----CCcccccccCcCCCCEEEEEEEecCCCCcc
Q 026458 67 QKRYVPCVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAF----EGGTRRNIPKFEIGSLLYVRVVKANPGMNP 137 (238)
Q Consensus 67 ~~~Y~P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f----~gatk~~r~~l~~GDlV~ArV~~~~~~~~~ 137 (238)
+..|.-++|++|-+.|+++.++.-.|++.+...|-+|++.. +..+. .-..|+.||-|.|||+.-++..+.
T Consensus 878 k~~~~~~igsiv~a~v~svKp~~L~v~l~~~~~gri~isev~d~~~eitD-p~~k~~vG~~I~vrviG~~D~k~l 951 (1710)
T KOG1070|consen 878 KSTEDLSIGSIVRAYVKSVKPDQLNVLLAANHHGRIHISEVLDNLHEITD-PLDKFKVGDGIFVRVIGGHDVKDL 951 (1710)
T ss_pred ccccceeeeeEEEEEEeeecccceEEeccccccCceehHHhhccccccCC-hhhhcccCCeEEEEEEcCCccccC
Confidence 45688899999999999999999999999999999998753 22233 445799999999999987654443
No 113
>PRK04012 translation initiation factor IF-1A; Provisional
Probab=83.86 E-value=6.7 Score=30.07 Aligned_cols=55 Identities=18% Similarity=0.220 Sum_probs=39.2
Q ss_pred CCCCCCEEEEEEEEe-cCceEEEEecCCe--eeeecCcccCCcccccccCcCCCCEEEEEEEecC
Q 026458 71 VPCVEDTVLGIVVDC-KADNFFVDIRGPT--IAFLPVLAFEGGTRRNIPKFEIGSLLYVRVVKAN 132 (238)
Q Consensus 71 ~P~vGDiVIG~V~~v-~~~~~~VdI~~~~--~a~L~~~~f~gatk~~r~~l~~GDlV~ArV~~~~ 132 (238)
.|. .+-++|+|+.. .++.|.|.+.... .|.+ +|.-++ +-.+++||.|..+....+
T Consensus 17 ~p~-e~e~~g~V~~~lG~~~~~V~~~dG~~~la~i-----~GK~Rk-~IwI~~GD~VlVe~~~~~ 74 (100)
T PRK04012 17 MPE-EGEVFGVVEQMLGANRVRVRCMDGVERMGRI-----PGKMKK-RMWIREGDVVIVAPWDFQ 74 (100)
T ss_pred CCC-CCEEEEEEEEEcCCCEEEEEeCCCCEEEEEE-----chhhcc-cEEecCCCEEEEEecccC
Confidence 454 55699999997 5678888886533 3333 455455 778999999999986654
No 114
>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=83.79 E-value=5.3 Score=31.66 Aligned_cols=61 Identities=21% Similarity=0.267 Sum_probs=41.5
Q ss_pred CCCCCEEEEEEEEecCceEEEEecCCeeeeecCcc------cCCc-------c-cccccCcCCCCEEEEEEEecC
Q 026458 72 PCVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLA------FEGG-------T-RRNIPKFEIGSLLYVRVVKAN 132 (238)
Q Consensus 72 P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~------f~ga-------t-k~~r~~l~~GDlV~ArV~~~~ 132 (238)
|-+|.++.|+|.+.+.+..+|.++--.+-.+|... |... . ...+-+++.|+-|+=||.+..
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 67899999999999999999999764444444433 3211 2 455667999999999999753
No 115
>PHA02858 EIF2a-like PKR inhibitor; Provisional
Probab=83.65 E-value=3.5 Score=30.70 Aligned_cols=64 Identities=16% Similarity=0.269 Sum_probs=46.4
Q ss_pred CCCCCCEEEEEEEEecCceEEEEecC-Ceeee-ecCcccCC-cccccccCcCCCCEEEEEEEecCCCCc
Q 026458 71 VPCVEDTVLGIVVDCKADNFFVDIRG-PTIAF-LPVLAFEG-GTRRNIPKFEIGSLLYVRVVKANPGMN 136 (238)
Q Consensus 71 ~P~vGDiVIG~V~~v~~~~~~VdI~~-~~~a~-L~~~~f~g-atk~~r~~l~~GDlV~ArV~~~~~~~~ 136 (238)
.|++||+|. .|..+....+.|.+-- ..+|. |+.++..- .-++.+..+ +|-.+.++|+.+++..-
T Consensus 13 ~P~v~dvv~-~Vv~i~d~~~YV~LleY~iegmIl~~selsr~rirsi~kll-VGk~e~v~ViRVDk~KG 79 (86)
T PHA02858 13 FPNINEVTK-GIVFVKDNIFYVKLIDYGLEALIVNYVNVNADRAEKLKKKL-VGKTINVQVIRTDKLKG 79 (86)
T ss_pred cCCCCeEEE-EEEEEeccEEEEEEecCccceEEecHHHHhHHHHHhhhhhh-cCCeeEEEEEEECCCCC
Confidence 699999999 8888999999998853 24444 43655532 233445567 99999999999987643
No 116
>smart00652 eIF1a eukaryotic translation initiation factor 1A.
Probab=83.55 E-value=6.7 Score=28.96 Aligned_cols=53 Identities=15% Similarity=0.105 Sum_probs=36.9
Q ss_pred CCCCCEEEEEEEEe-cCceEEEEecCCe--eeeecCcccCCcccccccCcCCCCEEEEEEEec
Q 026458 72 PCVEDTVLGIVVDC-KADNFFVDIRGPT--IAFLPVLAFEGGTRRNIPKFEIGSLLYVRVVKA 131 (238)
Q Consensus 72 P~vGDiVIG~V~~v-~~~~~~VdI~~~~--~a~L~~~~f~gatk~~r~~l~~GDlV~ArV~~~ 131 (238)
|. .+-++|+|+.. .++.|.|...... .|.+ +|.-++ +-.++.||+|..+....
T Consensus 2 p~-e~q~~g~V~~~lG~~~~~V~~~dG~~~la~i-----pgK~Rk-~iwI~~GD~VlVe~~~~ 57 (83)
T smart00652 2 KE-DGQEIAQVVKMLGNGRLEVMCADGKERLARI-----PGKMRK-KVWIRRGDIVLVDPWDF 57 (83)
T ss_pred CC-CCcEEEEEEEEcCCCEEEEEECCCCEEEEEE-----chhhcc-cEEEcCCCEEEEEecCC
Confidence 54 44589999997 5688888886533 3444 344443 67899999999987543
No 117
>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=82.94 E-value=4.5 Score=28.23 Aligned_cols=51 Identities=22% Similarity=0.283 Sum_probs=34.7
Q ss_pred CEEEEEEEEe-cCceEEEEecCCe--eeeecCcccCCcccccccCcCCCCEEEEEEEecC
Q 026458 76 DTVLGIVVDC-KADNFFVDIRGPT--IAFLPVLAFEGGTRRNIPKFEIGSLLYVRVVKAN 132 (238)
Q Consensus 76 DiVIG~V~~v-~~~~~~VdI~~~~--~a~L~~~~f~gatk~~r~~l~~GDlV~ArV~~~~ 132 (238)
+-++|+|+.. .++.|.|.+.... .+.+| |. .+.+-.+++||.|...+...+
T Consensus 3 ~e~~~~V~~~lG~~~~~V~~~dg~~~l~~i~-----gK-~r~~iwI~~GD~V~V~~~~~d 56 (65)
T PF01176_consen 3 GEVIGRVTEMLGNNLFEVECEDGEERLARIP-----GK-FRKRIWIKRGDFVLVEPSPYD 56 (65)
T ss_dssp TEEEEEEEEEESSSEEEEEETTSEEEEEEE------HH-HHTCC---TTEEEEEEESTTC
T ss_pred cEEEEEEEEECCCCEEEEEeCCCCEEEEEec-----cc-eeeeEecCCCCEEEEEecccC
Confidence 5689999997 6688999886643 34443 55 577888999999999885443
No 118
>PRK13763 putative RNA-processing protein; Provisional
Probab=82.66 E-value=5.7 Score=33.42 Aligned_cols=69 Identities=10% Similarity=0.055 Sum_probs=53.7
Q ss_pred hhhhhcCCCCchhhHhhccccceEEEEeeCCeEEEecCChhHHHHHHHHHHHhcc-CCHHHHHHHHHHHHhhc
Q 026458 166 LSRMLLSSPTCPVLEELGKQLSFEIAVGLNGRVWVNAESPSTVVLVSNAIMNSES-LSAVQQKIMVDKLLQRI 237 (238)
Q Consensus 166 ~v~rl~~~~~~~~l~~l~~~~~~ei~vG~NG~IWi~~~~~~~~~~i~~~i~~~e~-lt~~~~~~~~~~~~~~~ 237 (238)
...|++|+.+. .++.|.+.++|.|.|.-+ .|-|.+ +++....+.++|..+-. -..+.+-.+++...+++
T Consensus 105 ~~griIG~~G~-~~k~ie~~t~~~i~i~~~-~v~i~G-~~~~~~~A~~~I~~li~g~~~~~~~~~l~~~~~~~ 174 (180)
T PRK13763 105 IKGRIIGEGGK-TRRIIEELTGVDISVYGK-TVAIIG-DPEQVEIAREAIEMLIEGAPHGTVYKFLERKKREL 174 (180)
T ss_pred HhhheeCCCcH-HHHHHHHHHCcEEEEcCC-EEEEEe-CHHHHHHHHHHHHHHHcCCCcHHHHHHHHHHHHHH
Confidence 56788999987 999999999999999754 477775 99989998998887664 44466666677666554
No 119
>KOG3298 consensus DNA-directed RNA polymerase subunit E' [Transcription]
Probab=81.82 E-value=9 Score=32.01 Aligned_cols=63 Identities=14% Similarity=0.277 Sum_probs=46.3
Q ss_pred ccCCCCCCEEEEEEEEecCceEEEEecCCeeeeecCc-----cc-CCcc-----cccccCcCCCCEEEEEEEec
Q 026458 69 RYVPCVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVL-----AF-EGGT-----RRNIPKFEIGSLLYVRVVKA 131 (238)
Q Consensus 69 ~Y~P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~-----~f-~gat-----k~~r~~l~~GDlV~ArV~~~ 131 (238)
.+.|-.|++|=|.|+.++...+.++++.-...+++.+ .| ||.. ..+-...+.|+-|+-+|+..
T Consensus 76 ~FkpfKGEVvdgvV~~Vnk~G~F~~~GPl~~f~sshl~ppd~~f~p~~n~P~f~~~d~s~I~~~~~VR~kiigt 149 (170)
T KOG3298|consen 76 TFKPFKGEVVDGVVTKVNKMGVFARSGPLEVFYSSHLKPPDYEFDPGENPPNFQTEDESVIQKGVEVRLKIIGT 149 (170)
T ss_pred EEeecCCcEEEEEEEEEeeeeEEEeccceEeeeecccCCCCcccCCCCCCCcccccccceeeeCcEEEEEEEEE
Confidence 4789999999999999999999999998666665543 23 2321 11112578888899888875
No 120
>PLN00208 translation initiation factor (eIF); Provisional
Probab=81.14 E-value=7 Score=32.02 Aligned_cols=56 Identities=11% Similarity=-0.005 Sum_probs=37.9
Q ss_pred CCCCCCEEEEEEEEe-cCceEEEEecCCeeeeecCcccCCcccccccCcCCCCEEEEEEEec
Q 026458 71 VPCVEDTVLGIVVDC-KADNFFVDIRGPTIAFLPVLAFEGGTRRNIPKFEIGSLLYVRVVKA 131 (238)
Q Consensus 71 ~P~vGDiVIG~V~~v-~~~~~~VdI~~~~~a~L~~~~f~gatk~~r~~l~~GDlV~ArV~~~ 131 (238)
.|..|. ++|+|+.. .+..+.|.......-.-+ ++|.-++ +-.+++||+|..+....
T Consensus 28 ~p~egq-~~g~V~~~lGn~~~~V~c~dG~~rLa~---IpGKmRK-rIWI~~GD~VlVel~~~ 84 (145)
T PLN00208 28 FKEDGQ-EYAQVLRMLGNGRCEALCIDGTKRLCH---IRGKMRK-KVWIAAGDIILVGLRDY 84 (145)
T ss_pred cCCCCc-EEEEEEEEcCCCEEEEEECCCCEEEEE---Eecccee-eEEecCCCEEEEEccCC
Confidence 466655 89999997 567888887653332222 2454444 67899999999996544
No 121
>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=80.96 E-value=13 Score=27.17 Aligned_cols=50 Identities=16% Similarity=0.191 Sum_probs=33.9
Q ss_pred EEEEEEEe-cCceEEEEecCCeeeeecCcccCCcccccccCcCCCCEEEEEEEec
Q 026458 78 VLGIVVDC-KADNFFVDIRGPTIAFLPVLAFEGGTRRNIPKFEIGSLLYVRVVKA 131 (238)
Q Consensus 78 VIG~V~~v-~~~~~~VdI~~~~~a~L~~~~f~gatk~~r~~l~~GDlV~ArV~~~ 131 (238)
++|+|++. .++.|.|.......-..+ ++|.-++. -.+++||.|..+....
T Consensus 2 ~i~~V~~~lG~~~~~V~~~dg~~~l~~---i~gK~Rk~-iwI~~GD~VlV~~~~~ 52 (78)
T cd04456 2 QIVRVLRMLGNNRHEVECADGQRRLVS---IPGKLRKN-IWIKRGDFLIVDPIEE 52 (78)
T ss_pred eEEEEEEECCCCEEEEEECCCCEEEEE---EchhhccC-EEEcCCCEEEEEeccc
Confidence 68999997 568889888653322222 23443333 6799999999987665
No 122
>COG0361 InfA Translation initiation factor 1 (IF-1) [Translation, ribosomal structure and biogenesis]
Probab=79.47 E-value=10 Score=27.57 Aligned_cols=55 Identities=18% Similarity=0.278 Sum_probs=40.5
Q ss_pred CCEEEEEEEEe-cCceEEEEecCCeeeeecCcccCCcccccccCcCCCCEEEEEEEecC
Q 026458 75 EDTVLGIVVDC-KADNFFVDIRGPTIAFLPVLAFEGGTRRNIPKFEIGSLLYVRVVKAN 132 (238)
Q Consensus 75 GDiVIG~V~~v-~~~~~~VdI~~~~~a~L~~~~f~gatk~~r~~l~~GDlV~ArV~~~~ 132 (238)
..-+.|+|++. .+..+.|.+.....-.=+ .+|.-++++-.+.+||+|..+....+
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 45688999996 678899988664432222 24666777889999999999987654
No 123
>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=78.58 E-value=11 Score=31.30 Aligned_cols=68 Identities=10% Similarity=0.020 Sum_probs=51.1
Q ss_pred hhhhhcCCCCchhhHhhccccceEEEEeeCCeEEEecCChhHHHHHHHHHHHhcc-CCHHHHHHHHHHHHhh
Q 026458 166 LSRMLLSSPTCPVLEELGKQLSFEIAVGLNGRVWVNAESPSTVVLVSNAIMNSES-LSAVQQKIMVDKLLQR 236 (238)
Q Consensus 166 ~v~rl~~~~~~~~l~~l~~~~~~ei~vG~NG~IWi~~~~~~~~~~i~~~i~~~e~-lt~~~~~~~~~~~~~~ 236 (238)
.+.|++|+.+. .++.|...+++.|.|.- ..|-|.+ ++++...+.++|..+-. -...-+=.++++..++
T Consensus 99 ~~griIG~~G~-t~~~ie~~t~~~i~i~~-~~v~i~G-~~~~~~~A~~~i~~li~~~~~~~vy~~l~~~~~~ 167 (172)
T TIGR03665 99 IKGRIIGEGGK-TRRIIEELTGVSISVYG-KTVGIIG-DPEQVQIAREAIEMLIEGAPHGTVYKFLERKRRE 167 (172)
T ss_pred HHhhhcCCCcH-HHHHHHHHHCCeEEEcC-CEEEEEC-CHHHHHHHHHHHHHHHcCCCChhHHHHHHHHHHH
Confidence 67889999887 99999999999999975 6888887 89888888888877654 2223444555544443
No 124
>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=78.30 E-value=13 Score=26.52 Aligned_cols=52 Identities=15% Similarity=0.187 Sum_probs=37.2
Q ss_pred EEEEEEEe-cCceEEEEecCCeeeeecCcccCCcccccccCcCCCCEEEEEEEecC
Q 026458 78 VLGIVVDC-KADNFFVDIRGPTIAFLPVLAFEGGTRRNIPKFEIGSLLYVRVVKAN 132 (238)
Q Consensus 78 VIG~V~~v-~~~~~~VdI~~~~~a~L~~~~f~gatk~~r~~l~~GDlV~ArV~~~~ 132 (238)
+.|.|++. .+..|.|.+.....-.-+ .+|.-++++-.+.+||.|..+....+
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 MEGKVTESLPNAMFRVELENGHEVLAH---ISGKIRMHYIRILPGDKVKVELSPYD 59 (68)
T ss_pred EEEEEEEECCCCEEEEEECCCCEEEEE---ecCcchhccEEECCCCEEEEEECccc
Confidence 67899987 567888888653332222 24667777888999999999887654
No 125
>KOG3038 consensus Histone acetyltransferase SAGA associated factor SGF29 [General function prediction only]
Probab=78.05 E-value=9.3 Score=34.13 Aligned_cols=74 Identities=20% Similarity=0.157 Sum_probs=51.1
Q ss_pred eEEEEccCCccCCCCCCEEEEEEEEecCceEEEEecCCeeeeecCcccCCcccccccCcCCCCEEEEEEEecCCCCcceE
Q 026458 60 KYWVESSQKRYVPCVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEGGTRRNIPKFEIGSLLYVRVVKANPGMNPEL 139 (238)
Q Consensus 60 ~i~V~~~~~~Y~P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~gatk~~r~~l~~GDlV~ArV~~~~~~~~~~L 139 (238)
...-.|.++-|.+..||-|-.+|++.+. -||+|.|+|+++..+..++.
T Consensus 116 ~~gaip~~~~~~~~~gd~VAa~v~~~~~--------------------------------dg~WIlaeVv~~~~~~~ye~ 163 (264)
T KOG3038|consen 116 LCGAIPAQGDYVLLKGDEVAARVKAVSE--------------------------------DGDWILAEVVKVSSETRYEF 163 (264)
T ss_pred ccccccccCCccccCCceeeeeeeeccC--------------------------------CCCEEEEEEEEEecCCceEe
Confidence 3344556667888888888888877654 47899999999887766888
Q ss_pred EEecCCCccCCCcccCCeeEEEechhhh
Q 026458 140 SCTDASGKAAEFGLLKDGYMFETSTGLS 167 (238)
Q Consensus 140 s~~~~~~~~~~~G~L~~G~~~~V~~~~v 167 (238)
...|++.|.... ...|.+++.+-+.+
T Consensus 164 ev~D~Epk~d~~--g~r~~~yklp~~~~ 189 (264)
T KOG3038|consen 164 EVVDPEPKKDEV--GNRGQLYKLPRWKL 189 (264)
T ss_pred EecCCCcccccc--ccccceecccHhhc
Confidence 888865433332 24566777766554
No 126
>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=77.94 E-value=10 Score=27.57 Aligned_cols=50 Identities=14% Similarity=0.063 Sum_probs=34.7
Q ss_pred EEEEEEEe-cCceEEEEecCCeeeeecCcccCCcccccccCcCCCCEEEEEEEec
Q 026458 78 VLGIVVDC-KADNFFVDIRGPTIAFLPVLAFEGGTRRNIPKFEIGSLLYVRVVKA 131 (238)
Q Consensus 78 VIG~V~~v-~~~~~~VdI~~~~~a~L~~~~f~gatk~~r~~l~~GDlV~ArV~~~ 131 (238)
++|+|+.. .++.|.|.......-.- .++|.-++ +-.+++||.|..+....
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 68999997 56888888865333221 23454444 67899999999996654
No 127
>COG2996 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only]
Probab=76.66 E-value=10 Score=34.32 Aligned_cols=29 Identities=21% Similarity=0.214 Sum_probs=25.7
Q ss_pred ccCcCCCCEEEEEEEecCCCCcceEEEec
Q 026458 115 IPKFEIGSLLYVRVVKANPGMNPELSCTD 143 (238)
Q Consensus 115 r~~l~~GDlV~ArV~~~~~~~~~~Ls~~~ 143 (238)
....+.|+-+-|||+.+..++++.||+..
T Consensus 189 ~~~prlG~~l~~rVi~~reDg~lnLSl~p 217 (287)
T COG2996 189 FAEPRLGERLTARVIGVREDGKLNLSLRP 217 (287)
T ss_pred cccccCCceEEEEEEEEccCCeeeccccc
Confidence 34579999999999999999999999865
No 128
>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=76.58 E-value=10 Score=24.98 Aligned_cols=64 Identities=16% Similarity=0.160 Sum_probs=38.9
Q ss_pred EEEEEEEecC-----ceEEEEecCCeeeeecCcccCCcccccccCcCCCCEEEEEEEecCCCCcceEEE
Q 026458 78 VLGIVVDCKA-----DNFFVDIRGPTIAFLPVLAFEGGTRRNIPKFEIGSLLYVRVVKANPGMNPELSC 141 (238)
Q Consensus 78 VIG~V~~v~~-----~~~~VdI~~~~~a~L~~~~f~gatk~~r~~l~~GDlV~ArV~~~~~~~~~~Ls~ 141 (238)
|.|+|.++.. .++.+.|.....+.+....|+....+....+.+|+.++.+..--.....+.|.+
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 6778888764 456666765443666666665444445567999999887733322223455554
No 129
>CHL00121 rpl27 ribosomal protein L27; Reviewed
Probab=75.82 E-value=6.2 Score=29.46 Aligned_cols=44 Identities=14% Similarity=0.219 Sum_probs=32.2
Q ss_pred CCCcEEecCCccCCCCCCCCCceeecCcEEE-eCCEEEEEEeeEeEEe
Q 026458 10 LVDKIVVPGDVVLDLSSMTNQTIKLGGGLRQ-ECDSVSVIKAGKLRFS 56 (238)
Q Consensus 10 ~~~~iV~PGd~l~~~~~~~~~~~~~G~G~y~-~~g~i~as~~G~v~~~ 56 (238)
+..+.|.||+.|.--- +-.|-+|.++-. .|..|+|...|.|+..
T Consensus 26 ~~gq~V~~G~IivRQR---Gtk~hPG~NVg~GrD~TlfAl~~G~V~f~ 70 (86)
T CHL00121 26 FGGEKVSAGNILIRQR---GTKFKPGLNVGCGKDFTLYALIDGFVKFK 70 (86)
T ss_pred cCCEEEcCCcEEEEcC---CCeECCCCcccccCCceEEEccceEEEEE
Confidence 4567899999885321 014667776654 5889999999999875
No 130
>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=75.45 E-value=6.7 Score=26.82 Aligned_cols=63 Identities=27% Similarity=0.309 Sum_probs=41.2
Q ss_pred EEEEEEEe---cCceEEEEecCCeeeeecCcccCCcccccccCcCCCCEEEEE--EEecCCCCcceEEEe
Q 026458 78 VLGIVVDC---KADNFFVDIRGPTIAFLPVLAFEGGTRRNIPKFEIGSLLYVR--VVKANPGMNPELSCT 142 (238)
Q Consensus 78 VIG~V~~v---~~~~~~VdI~~~~~a~L~~~~f~gatk~~r~~l~~GDlV~Ar--V~~~~~~~~~~Ls~~ 142 (238)
|.|+|+++ ......++|.... +.+....|.....+....+++||.|..+ |.... ..+++|++.
T Consensus 3 v~G~V~~~~~~~~~~~~~~l~D~t-g~i~~~~~~~~~~~~~~~l~~g~~v~v~G~v~~~~-~~~~~l~~~ 70 (75)
T PF01336_consen 3 VEGRVTSIRRSGGKIVFFTLEDGT-GSIQVVFFNEEYERFREKLKEGDIVRVRGKVKRYN-GGELELIVP 70 (75)
T ss_dssp EEEEEEEEEEEETTEEEEEEEETT-EEEEEEEETHHHHHHHHTS-TTSEEEEEEEEEEET-TSSEEEEEE
T ss_pred EEEEEEEEEcCCCCEEEEEEEECC-ccEEEEEccHHhhHHhhcCCCCeEEEEEEEEEEEC-CccEEEEEC
Confidence 67888877 5677777876544 6666666654455677789999998655 55542 234777654
No 131
>KOG3297 consensus DNA-directed RNA polymerase subunit E' [Transcription]
Probab=74.59 E-value=18 Score=30.93 Aligned_cols=62 Identities=21% Similarity=0.375 Sum_probs=44.2
Q ss_pred cCCCCCCEEEEEEEEecCceEEEEecCCeeeeecCc------ccCCc---------c---cccccCcCCCCEEEEEEEec
Q 026458 70 YVPCVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVL------AFEGG---------T---RRNIPKFEIGSLLYVRVVKA 131 (238)
Q Consensus 70 Y~P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~------~f~ga---------t---k~~r~~l~~GDlV~ArV~~~ 131 (238)
+.|-+|.+|.|+|.+...+.-.|.|+--.+-.+|.. .|.-+ . ...+-+|++|.-|+=||.+.
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 679999999999999999999998874222333322 22111 1 23455899999999999875
No 132
>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=73.59 E-value=21 Score=27.58 Aligned_cols=53 Identities=21% Similarity=0.268 Sum_probs=43.1
Q ss_pred CCCCCEEEEEEEEecCceEEEEecCCeeeeecCcccCCcccccccCcCCCCEEEEEEEe
Q 026458 72 PCVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEGGTRRNIPKFEIGSLLYVRVVK 130 (238)
Q Consensus 72 P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~gatk~~r~~l~~GDlV~ArV~~ 130 (238)
+..|-+|+|+|..+..+---+|.+.-++++.+.-+. +-..|..|+-|.-|+..
T Consensus 21 ~~~gk~V~G~I~hvv~ddLYIDfG~KFhcVc~rp~~------~~~~y~~G~rV~lrLkd 73 (104)
T PF10246_consen 21 DPEGKIVIGKIFHVVDDDLYIDFGGKFHCVCKRPAV------NGEKYVRGSRVRLRLKD 73 (104)
T ss_pred CccCCEEEEEEEEEecCceEEEeCCceeEEEecccc------cccccccCCEEEEEECC
Confidence 457899999999999998999999999999874332 33468889999998853
No 133
>PF15057 DUF4537: Domain of unknown function (DUF4537)
Probab=73.23 E-value=36 Score=26.84 Aligned_cols=48 Identities=15% Similarity=0.302 Sum_probs=28.0
Q ss_pred EEEEEe-cCceEEEEecCCeeeeecCcc-cCCcccccccCcCCCCEEEEEE
Q 026458 80 GIVVDC-KADNFFVDIRGPTIAFLPVLA-FEGGTRRNIPKFEIGSLLYVRV 128 (238)
Q Consensus 80 G~V~~v-~~~~~~VdI~~~~~a~L~~~~-f~gatk~~r~~l~~GDlV~ArV 128 (238)
|+|.+. ....+.|+-.....-..+... +.. ...+++.|++||-|.|+.
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 455443 667777777443333333221 111 123488999999999984
No 134
>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=72.57 E-value=4.1 Score=22.73 Aligned_cols=16 Identities=19% Similarity=0.619 Sum_probs=12.4
Q ss_pred eEEEEeeCCeEEEecC
Q 026458 188 FEIAVGLNGRVWVNAE 203 (238)
Q Consensus 188 ~ei~vG~NG~IWi~~~ 203 (238)
..|+...||++||.+.
T Consensus 8 ~~i~~D~~G~lWigT~ 23 (24)
T PF07494_consen 8 YSIYEDSDGNLWIGTY 23 (24)
T ss_dssp EEEEE-TTSCEEEEET
T ss_pred EEEEEcCCcCEEEEeC
Confidence 4588899999999864
No 135
>PRK12442 translation initiation factor IF-1; Reviewed
Probab=71.31 E-value=21 Score=26.73 Aligned_cols=52 Identities=15% Similarity=0.146 Sum_probs=37.7
Q ss_pred EEEEEEEe-cCceEEEEecCCeeeeecCcccCCcccccccCcCCCCEEEEEEEecC
Q 026458 78 VLGIVVDC-KADNFFVDIRGPTIAFLPVLAFEGGTRRNIPKFEIGSLLYVRVVKAN 132 (238)
Q Consensus 78 VIG~V~~v-~~~~~~VdI~~~~~a~L~~~~f~gatk~~r~~l~~GDlV~ArV~~~~ 132 (238)
+-|.|++. .+..|.|.+.....-.-+ +.|.-++++-.+.+||.|..++...+
T Consensus 9 ~~G~V~e~Lp~~~frV~LenG~~vla~---isGKmR~~rIrIl~GD~V~VE~spYD 61 (87)
T PRK12442 9 LDGIVDEVLPDSRFRVTLENGVEVGAY---ASGRMRKHRIRILAGDRVTLELSPYD 61 (87)
T ss_pred EEEEEEEECCCCEEEEEeCCCCEEEEE---eccceeeeeEEecCCCEEEEEECccc
Confidence 67999997 567899988653332222 24667777888999999999887654
No 136
>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=71.27 E-value=46 Score=31.23 Aligned_cols=98 Identities=13% Similarity=0.184 Sum_probs=72.0
Q ss_pred CCcEEecCCccCCCCCCCCCceeecCcEEE--eCCEEEEEEeeEeEEecCCeEEEEccCCccCCCCCCEEEEEEEEecCc
Q 026458 11 VDKIVVPGDVVLDLSSMTNQTIKLGGGLRQ--ECDSVSVIKAGKLRFSKPNKYWVESSQKRYVPCVEDTVLGIVVDCKAD 88 (238)
Q Consensus 11 ~~~iV~PGd~l~~~~~~~~~~~~~G~G~y~--~~g~i~as~~G~v~~~~~~~i~V~~~~~~Y~P~vGDiVIG~V~~v~~~ 88 (238)
+.-+..||+.-.+.+ ++..|.-+.. .+|+-+....|.+++.+..++-|+... ++ -++.-+-++
T Consensus 243 HaYv~~pg~kT~YLS-----EL~sG~~VlvVd~~G~tR~~~VGRvKIE~RPLllIeA~~-------~g---~~~svilQn 307 (354)
T PF01959_consen 243 HAYVLMPGGKTRYLS-----ELRSGDEVLVVDADGRTRTAIVGRVKIERRPLLLIEAEA-------DG---KRISVILQN 307 (354)
T ss_pred eeEEEcCCCceeehh-----hhcCCCEEEEEeCCCCEEEEEeeEEEEeecceEEEEEEe-------CC---eEEEEEEec
Confidence 445788999887775 7888887664 368999999999999866677777432 33 233344678
Q ss_pred eEEEEecCCeeeeecCcccCCcccccccCcCCCCEEEEEEEecCCC
Q 026458 89 NFFVDIRGPTIAFLPVLAFEGGTRRNIPKFEIGSLLYVRVVKANPG 134 (238)
Q Consensus 89 ~~~VdI~~~~~a~L~~~~f~gatk~~r~~l~~GDlV~ArV~~~~~~ 134 (238)
.|.|.+-.+....++.. .|++||-|.+++....++
T Consensus 308 aetIRlv~p~G~~vsVt-----------~Lk~GD~vL~~~~~~~RH 342 (354)
T PF01959_consen 308 AETIRLVGPDGEPVSVT-----------ELKPGDEVLVYLEEAGRH 342 (354)
T ss_pred CcEEEEECCCCCEeeee-----------ecCCCCEEEEEecCCCcc
Confidence 88998887765555543 468999999999987775
No 137
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=71.21 E-value=24 Score=30.33 Aligned_cols=71 Identities=7% Similarity=0.137 Sum_probs=57.3
Q ss_pred EEEechhhhhhhcCCCCchhhHhhccccceEEEEeeC-CeEEEecC----ChhHHHHHHHHHHHhcc-CCHHHHHHHH
Q 026458 159 MFETSTGLSRMLLSSPTCPVLEELGKQLSFEIAVGLN-GRVWVNAE----SPSTVVLVSNAIMNSES-LSAVQQKIMV 230 (238)
Q Consensus 159 ~~~V~~~~v~rl~~~~~~~~l~~l~~~~~~ei~vG~N-G~IWi~~~----~~~~~~~i~~~i~~~e~-lt~~~~~~~~ 230 (238)
.+.||+....-|+++.+. +...|-+++++++.+.-. |.|||.+. ||-....+.+.++.+-. .+.++--+++
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 AVKIPKDRIGVLIGKWGE-VKKAIEEKTGVKLRIDSKTGSVTIRTTRKTEDPLALLKARDVVKAIGRGFPPEKALKLL 87 (194)
T ss_pred eeecCchhheeeeccccc-chHHHHhhcCeEEEEECCCCeEEEEecCCCCChHHHHHHHHHHHHHhcCCCHHHHHHHh
Confidence 478899999999998886 888998889999998766 99999997 78888888888888775 5555544444
No 138
>PRK05435 rpmA 50S ribosomal protein L27; Validated
Probab=70.80 E-value=8.7 Score=28.43 Aligned_cols=45 Identities=11% Similarity=0.302 Sum_probs=34.2
Q ss_pred CCCCcEEecCCccCCCCCCCCCceeecCcEEE-eCCEEEEEEeeEeEEe
Q 026458 9 NLVDKIVVPGDVVLDLSSMTNQTIKLGGGLRQ-ECDSVSVIKAGKLRFS 56 (238)
Q Consensus 9 ~~~~~iV~PGd~l~~~~~~~~~~~~~G~G~y~-~~g~i~as~~G~v~~~ 56 (238)
.+..+.|.||..|.--- +-.+.||.++-. .|..|+|.+.|.|+..
T Consensus 25 ~~~g~~V~~G~IivRQR---Gtk~~PG~nVg~GrD~TlfA~~~G~V~f~ 70 (82)
T PRK05435 25 RFGGQFVKAGNIIVRQR---GTKFHPGVNVGRGKDHTLFALVDGVVKFE 70 (82)
T ss_pred ecCCEEEcCCcEEEEeC---CCeECCCCCEeecCCceEEEecceEEEEE
Confidence 34668899999885321 025778888875 6899999999999876
No 139
>KOG4600 consensus Mitochondrial ribosomal protein MRP7 (L2) [Translation, ribosomal structure and biogenesis]
Probab=70.48 E-value=11 Score=30.54 Aligned_cols=56 Identities=18% Similarity=0.321 Sum_probs=37.2
Q ss_pred CCCCcEEecCCccCCCCCCCCCceeecCcEEE---eCCEEEEEEeeEeEEec------CCeEEEEccCCc
Q 026458 9 NLVDKIVVPGDVVLDLSSMTNQTIKLGGGLRQ---ECDSVSVIKAGKLRFSK------PNKYWVESSQKR 69 (238)
Q Consensus 9 ~~~~~iV~PGd~l~~~~~~~~~~~~~G~G~y~---~~g~i~as~~G~v~~~~------~~~i~V~~~~~~ 69 (238)
-+..+.|.||+.|.--- ..+.=||-|+ .|-.|||-.-|.|+..+ .+.+.|.|....
T Consensus 52 k~egq~V~~G~IIvrQR-----gtkfHPG~nVGiGKDhtifaL~eG~Vrf~k~~~~~~Rk~i~V~~~~~~ 116 (144)
T KOG4600|consen 52 KYEGQSVIPGNIIVRQR-----GTKFHPGDNVGIGKDHTIFALEEGRVRFEKSKITPPRKWIGVDPRGGL 116 (144)
T ss_pred ecCCeeeecccEEEEec-----ccccCCCcccccCCcceEEEeeccEEEEEEccCCCCcceEEEeecCCc
Confidence 45678999999886421 2233333333 47789999999999863 257788776543
No 140
>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=70.45 E-value=8.9 Score=36.68 Aligned_cols=52 Identities=19% Similarity=0.222 Sum_probs=38.0
Q ss_pred cEEecCCccCCCCCC-------------------CCCceeecCcEEEe---CCEEEEEEeeEeEEecCCeEEEEc
Q 026458 13 KIVVPGDVVLDLSSM-------------------TNQTIKLGGGLRQE---CDSVSVIKAGKLRFSKPNKYWVES 65 (238)
Q Consensus 13 ~iV~PGd~l~~~~~~-------------------~~~~~~~G~G~y~~---~g~i~as~~G~v~~~~~~~i~V~~ 65 (238)
..|-+||+|+...++ ....+.+|+|+... +..++|++.|.+... ++.+.|.|
T Consensus 107 ~~V~~G~~la~~~p~~~G~~G~~V~G~~I~~~~~~~~~~~~g~~~~~~~~d~~~~~A~~~G~~~~~-~~~i~V~~ 180 (451)
T PF03961_consen 107 PSVKKGDVLAEKIPPTPGEPGRDVFGEPIPAKPGKDIPLKAGKNTEVSEEDGNKLYAAIDGRPVFE-NGKISVDP 180 (451)
T ss_pred eEECCCCEEEEEccCCCCCCCcccCCCCcCCCCCCccceeCCCCEEEEcCCCCEEEEecCCEEEEE-CCEEEEEE
Confidence 348888888743221 02367889999975 358999999999987 66777776
No 141
>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=68.59 E-value=7.1 Score=28.87 Aligned_cols=45 Identities=11% Similarity=0.341 Sum_probs=35.6
Q ss_pred CCCCcEEecCCccCCCCCCCCCceeecCcEEE-eCCEEEEEEeeEeEEe
Q 026458 9 NLVDKIVVPGDVVLDLSSMTNQTIKLGGGLRQ-ECDSVSVIKAGKLRFS 56 (238)
Q Consensus 9 ~~~~~iV~PGd~l~~~~~~~~~~~~~G~G~y~-~~g~i~as~~G~v~~~ 56 (238)
.+..+.|.||+.|.--- +-.|-||.++.. .|..|+|.+.|.|...
T Consensus 24 ~~~G~~V~~G~IivRQR---gtk~hPG~NVg~GrD~TLfAl~~G~V~f~ 69 (81)
T PF01016_consen 24 KFGGQFVKAGNIIVRQR---GTKFHPGENVGMGRDHTLFALVDGRVKFT 69 (81)
T ss_dssp SSTTCEESSTSEEEEBS---SSSSEEBTTEEEETTSEEEESSSCEEEEE
T ss_pred EeCCEEEcCCCEEEEeC---CCcCcCCCCEEECCCCcEEEecCEEEEEE
Confidence 45678999999885311 126899999986 5899999999999876
No 142
>KOG4134 consensus DNA-dependent RNA polymerase I [Transcription]
Probab=67.17 E-value=7 Score=34.35 Aligned_cols=70 Identities=16% Similarity=0.210 Sum_probs=56.3
Q ss_pred eEEEEccCCccCCCCCCEEEEEEEEecCceEEEEecCCeeeeecCcccCCcccccccCcCCCCEEEEEEEecCC
Q 026458 60 KYWVESSQKRYVPCVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEGGTRRNIPKFEIGSLLYVRVVKANP 133 (238)
Q Consensus 60 ~i~V~~~~~~Y~P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~gatk~~r~~l~~GDlV~ArV~~~~~ 133 (238)
.+||...--.+.|++||+.-|.|--++....-+=|-..++|.++.-+.+ ....++.+++-..++|...+.
T Consensus 93 hlwi~adfyVf~Pk~Gd~LeG~Vn~vS~sHIglLIhg~FNASIpk~nip----~dw~fI~md~eee~~v~ntD~ 162 (253)
T KOG4134|consen 93 HLWINADFYVFRPKAGDILEGVVNHVSRSHIGLLIHGVFNASIPKTNIP----ADWEFIAMDQEEEIRVKNTDI 162 (253)
T ss_pred EEEEeeeEEEECCCCCCeeeeeeeecchhhhceeehhhhhccCCCCCCc----cceeeecCCchhhhceeeccc
Confidence 4677766667899999999999999999888888877888888765543 345578899999999998874
No 143
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=66.56 E-value=6.8 Score=40.88 Aligned_cols=60 Identities=15% Similarity=0.145 Sum_probs=50.2
Q ss_pred eEEEechhhhhhhcCCCCchhhHhhccccceE-EEEeeCCeEEEecCChhHHHHHHHHHHHh
Q 026458 158 YMFETSTGLSRMLLSSPTCPVLEELGKQLSFE-IAVGLNGRVWVNAESPSTVVLVSNAIMNS 218 (238)
Q Consensus 158 ~~~~V~~~~v~rl~~~~~~~~l~~l~~~~~~e-i~vG~NG~IWi~~~~~~~~~~i~~~i~~~ 218 (238)
..++|+|.+++.+||..+. .++.|.+.++.. |=+.-.|.|-|-+.|.+....+...|+.+
T Consensus 687 ~~~~i~~~ki~~vIG~GGk-tIk~I~eetg~~~Idi~ddg~V~I~a~d~~~i~~A~~~I~~l 747 (891)
T PLN00207 687 HIMKVKPEKVNMIIGSGGK-KVKSIIEETGVEAIDTQDDGTVKITAKDLSSLEKSKAIISSL 747 (891)
T ss_pred EEEEcCHHHHHHHhcCCch-hHHHHHHHHCCCccCcCCCeeEEEEeCCHHHHHHHHHHHHHH
Confidence 4789999999999998876 999999999999 99999999999999986555554444443
No 144
>TIGR00523 eIF-1A eukaryotic/archaeal initiation factor 1A. Recommended nomenclature: eIF-1A for eukaryotes, aIF-1A for Archaea. Also called eIF-4C
Probab=66.52 E-value=56 Score=24.93 Aligned_cols=53 Identities=17% Similarity=0.241 Sum_probs=36.4
Q ss_pred ccCCC-CCCEEEEEEEEe-cCceEEEEecCC--eeeeecCcccCCcccccccCcCCCCEEEEE
Q 026458 69 RYVPC-VEDTVLGIVVDC-KADNFFVDIRGP--TIAFLPVLAFEGGTRRNIPKFEIGSLLYVR 127 (238)
Q Consensus 69 ~Y~P~-vGDiVIG~V~~v-~~~~~~VdI~~~--~~a~L~~~~f~gatk~~r~~l~~GDlV~Ar 127 (238)
+-+|. ..+-++|+|+.. .++.|.|.+... ..|.+ +|.-++ +-.+.+||+|...
T Consensus 11 ~~~p~~~e~e~~g~V~~~lG~~~~~V~~~dG~~~la~i-----~GK~Rk-~iwI~~GD~VlVs 67 (99)
T TIGR00523 11 VRLPRKEEGEILGVIEQMLGAGRVKVRCLDGKTRLGRI-----PGKLKK-RIWIREGDVVIVK 67 (99)
T ss_pred eeCCCCCCCEEEEEEEEEcCCCEEEEEeCCCCEEEEEE-----chhhcc-cEEecCCCEEEEE
Confidence 34564 367799999998 567888887542 23333 454444 7789999999973
No 145
>PTZ00329 eukaryotic translation initiation factor 1A; Provisional
Probab=66.47 E-value=27 Score=28.92 Aligned_cols=76 Identities=13% Similarity=0.083 Sum_probs=47.5
Q ss_pred CCCCCCEEEEEEEEe-cCceEEEEecCCeeeeecCcccCCcccccccCcCCCCEEEEEEEecCCCCcceEEEecCCCccC
Q 026458 71 VPCVEDTVLGIVVDC-KADNFFVDIRGPTIAFLPVLAFEGGTRRNIPKFEIGSLLYVRVVKANPGMNPELSCTDASGKAA 149 (238)
Q Consensus 71 ~P~vGDiVIG~V~~v-~~~~~~VdI~~~~~a~L~~~~f~gatk~~r~~l~~GDlV~ArV~~~~~~~~~~Ls~~~~~~~~~ 149 (238)
.|..|. ++|+|+.. .+..+.|.+.....-.- .++|.-++ +-.+.+||+|..+.... .++
T Consensus 28 ~~eegq-~~g~V~~~LGn~~f~V~c~dG~~rLa---~I~GKmRK-~IWI~~GD~VlVel~~y------d~~--------- 87 (155)
T PTZ00329 28 FKEEGQ-EYAQVLRMLGNGRLEAYCFDGVKRLC---HIRGKMRK-RVWINIGDIILVSLRDF------QDS--------- 87 (155)
T ss_pred cCCCCc-EEEEEEEEcCCCEEEEEECCCCEEEE---Eeecccee-eEEecCCCEEEEeccCC------CCC---------
Confidence 466555 89999997 56778887754333222 22454444 57899999999865332 222
Q ss_pred CCcccCCeeEEEechhhhhhhc
Q 026458 150 EFGLLKDGYMFETSTGLSRMLL 171 (238)
Q Consensus 150 ~~G~L~~G~~~~V~~~~v~rl~ 171 (238)
.+=+++.-.+..++.|.
T Consensus 88 -----KgdIi~Ry~~devr~Lk 104 (155)
T PTZ00329 88 -----KADVILKYTPDEARALK 104 (155)
T ss_pred -----EEEEEEEcCHHHHHHHH
Confidence 12236677777777776
No 146
>PRK02290 3-dehydroquinate synthase; Provisional
Probab=65.96 E-value=77 Score=29.62 Aligned_cols=99 Identities=15% Similarity=0.173 Sum_probs=70.0
Q ss_pred CCcEEecCCccCCCCCCCCCceeecCcEEE--eCCEEEEEEeeEeEEecCCeEEEEccCCccCCCCCCEEEEEEEEecCc
Q 026458 11 VDKIVVPGDVVLDLSSMTNQTIKLGGGLRQ--ECDSVSVIKAGKLRFSKPNKYWVESSQKRYVPCVEDTVLGIVVDCKAD 88 (238)
Q Consensus 11 ~~~iV~PGd~l~~~~~~~~~~~~~G~G~y~--~~g~i~as~~G~v~~~~~~~i~V~~~~~~Y~P~vGDiVIG~V~~v~~~ 88 (238)
+.-+..||+.-.+.+ ++..|.-+.. .+|+-+..+.|.+++.+..++-|+.. | ++ -++.-+-++
T Consensus 233 haYv~~pgg~T~YLs-----EL~sG~eVlvVd~~G~tR~~~VGRvKIE~RPL~lIeAe---~----~g---~~~~viLQn 297 (344)
T PRK02290 233 HAYVRVPGDKTRYLS-----ELRSGDEVLVVDADGNTREAIVGRVKIEKRPLLLIEAE---Y----GG---KRIRTILQN 297 (344)
T ss_pred eeEEEcCCCcchhhH-----hhcCCCEEEEEeCCCCEEEEEeeEEEEeeccEEEEEEE---e----CC---eEEEEEEec
Confidence 345788999887775 7778876653 37999999999999986667777743 1 22 222334478
Q ss_pred eEEEEecCCeeeeecCcccCCcccccccCcCCCCEEEEEEEecCCCC
Q 026458 89 NFFVDIRGPTIAFLPVLAFEGGTRRNIPKFEIGSLLYVRVVKANPGM 135 (238)
Q Consensus 89 ~~~VdI~~~~~a~L~~~~f~gatk~~r~~l~~GDlV~ArV~~~~~~~ 135 (238)
-|.+.+-.+....++.. .|++||-|.+++....++.
T Consensus 298 aetIrlv~~dG~~vsVt-----------~Lk~GD~VL~~~~~~~RHf 333 (344)
T PRK02290 298 AETIRLVTPDGKPVSVV-----------DLKPGDEVLGYLEEAARHF 333 (344)
T ss_pred CcEEEEECCCCCEeeee-----------ecCCCCEEEEEecCCcccc
Confidence 88888887754444432 4689999999998877653
No 147
>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=65.41 E-value=6.8 Score=29.22 Aligned_cols=28 Identities=11% Similarity=0.207 Sum_probs=22.2
Q ss_pred CCCCEEEEEEEEecC-ceEEEEecCCeee
Q 026458 73 CVEDTVLGIVVDCKA-DNFFVDIRGPTIA 100 (238)
Q Consensus 73 ~vGDiVIG~V~~v~~-~~~~VdI~~~~~a 100 (238)
++||+|.++|.+... ..|.+.+.....|
T Consensus 62 ~~GDiV~AkVis~~~~~~~~Lst~~~~lG 90 (92)
T cd05791 62 RPGDIVRAKVISLGDASSYYLSTAENELG 90 (92)
T ss_pred CCCCEEEEEEEEcCCCCCcEEEecCCCCc
Confidence 899999999999975 6677777655444
No 148
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=64.23 E-value=15 Score=37.24 Aligned_cols=62 Identities=10% Similarity=0.079 Sum_probs=52.0
Q ss_pred eeEEEechhhhhhhcCCCCchhhHhhccccceEEEEeeCCeEEEecCChhHHHHHHHHHHHhc
Q 026458 157 GYMFETSTGLSRMLLSSPTCPVLEELGKQLSFEIAVGLNGRVWVNAESPSTVVLVSNAIMNSE 219 (238)
Q Consensus 157 G~~~~V~~~~v~rl~~~~~~~~l~~l~~~~~~ei~vG~NG~IWi~~~~~~~~~~i~~~i~~~e 219 (238)
=..+++++.+++-++|+.+. .++.|-++++..|-+.-.|.|.|.+.+.+.+..+-+.|..+.
T Consensus 553 i~t~~i~~dKI~dvIG~gGk-~I~~I~eetg~~IdieddGtv~i~~s~~~~~~~ak~~I~~i~ 614 (692)
T COG1185 553 IETIKIDPDKIRDVIGPGGK-TIKAITEETGVKIDIEDDGTVKIAASDGESAKKAKERIEAIT 614 (692)
T ss_pred eEEEccCHHHHhhccCCccc-chhhhhhhhCcEEEecCCCcEEEEecchHHHHHHHHHHHHHH
Confidence 35789999999999998887 888899999999999999999999988766665555555443
No 149
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=61.77 E-value=44 Score=28.54 Aligned_cols=29 Identities=17% Similarity=0.209 Sum_probs=22.0
Q ss_pred ccCcCCCCEEEEEEEecCCCCcceEEEecC
Q 026458 115 IPKFEIGSLLYVRVVKANPGMNPELSCTDA 144 (238)
Q Consensus 115 r~~l~~GDlV~ArV~~~~~~~~~~Ls~~~~ 144 (238)
.+..++||+|+|||+++.. ..+.+.+..-
T Consensus 59 ~~~~K~GdiV~grV~~v~~-~~a~V~i~~v 87 (188)
T COG1096 59 PPLPKGGDIVYGRVTDVRE-QRALVRIVGV 87 (188)
T ss_pred CCCCCCCCEEEEEEeeccc-eEEEEEEEEE
Confidence 4578899999999999865 4566666553
No 150
>TIGR00062 L27 ribosomal protein L27. Eubacterial, chloroplast, and mitochondrial. Mitochondrial members have an additional C-terminal domain.
Probab=60.35 E-value=14 Score=27.42 Aligned_cols=45 Identities=11% Similarity=0.285 Sum_probs=33.5
Q ss_pred CCCCcEEecCCccCCCCCCCCCceeecCcEEE-eCCEEEEEEeeEeEEe
Q 026458 9 NLVDKIVVPGDVVLDLSSMTNQTIKLGGGLRQ-ECDSVSVIKAGKLRFS 56 (238)
Q Consensus 9 ~~~~~iV~PGd~l~~~~~~~~~~~~~G~G~y~-~~g~i~as~~G~v~~~ 56 (238)
.+..+.|.||+.|.--- +-.|-||.++-. .|..|+|.+.|.|...
T Consensus 25 ~~~gq~V~~G~IivRQR---Gtk~hPG~nVg~GrD~TlfAl~~G~V~f~ 70 (83)
T TIGR00062 25 RAGGQFVRAGSIIVRQR---GTKFHPGNNVGMGKDHTLFALSDGVVKFE 70 (83)
T ss_pred ecCCEEEcCCcEEEEcC---CceECCCCcccccCCCeEEEecceEEEEE
Confidence 34667899999885321 025778887765 6899999999999875
No 151
>COG2932 Predicted transcriptional regulator [Transcription]
Probab=60.17 E-value=79 Score=26.79 Aligned_cols=68 Identities=19% Similarity=0.159 Sum_probs=36.5
Q ss_pred cEEecCCccCCCCCCCCCceeecCcEEEe--CCEEEEEEeeEeEEecCCeEEEEccCCcc----CCCCCC-E-EEEEEEE
Q 026458 13 KIVVPGDVVLDLSSMTNQTIKLGGGLRQE--CDSVSVIKAGKLRFSKPNKYWVESSQKRY----VPCVED-T-VLGIVVD 84 (238)
Q Consensus 13 ~iV~PGd~l~~~~~~~~~~~~~G~G~y~~--~g~i~as~~G~v~~~~~~~i~V~~~~~~Y----~P~vGD-i-VIG~V~~ 84 (238)
....|||.+..... .....|.++|+. +|..+....... .++.+.+.++.+.| .+...| + +||+|..
T Consensus 135 P~~~~Gd~ilVd~~---~~~~~gd~v~v~~~g~~~~VK~l~~~---~~~~~~l~S~N~~~~~~~~~~~~~~v~iIgrVv~ 208 (214)
T COG2932 135 PTYEDGDTLLVDPG---VNTRRGDRVYVETDGGELYVKKLQRE---PGGLLRLVSLNPDYYPDEIFSEDDDVEIIGRVVW 208 (214)
T ss_pred ccccCCCEEEECCC---CceeeCCEEEEEEeCCeEEEEEEEEe---cCCeEEEEeCCCCCCcccccCccceEEEEEEEEE
Confidence 34567776654321 133444445532 334444333222 34566677765443 566677 5 8999987
Q ss_pred ec
Q 026458 85 CK 86 (238)
Q Consensus 85 v~ 86 (238)
..
T Consensus 209 ~~ 210 (214)
T COG2932 209 VS 210 (214)
T ss_pred Ee
Confidence 64
No 152
>PRK00276 infA translation initiation factor IF-1; Validated
Probab=59.34 E-value=46 Score=23.57 Aligned_cols=52 Identities=19% Similarity=0.259 Sum_probs=32.2
Q ss_pred EEEEEEEecCc-eEEEEecCCeeeeecCcccCCcccccccCcCCCCEEEEEEEecC
Q 026458 78 VLGIVVDCKAD-NFFVDIRGPTIAFLPVLAFEGGTRRNIPKFEIGSLLYVRVVKAN 132 (238)
Q Consensus 78 VIG~V~~v~~~-~~~VdI~~~~~a~L~~~~f~gatk~~r~~l~~GDlV~ArV~~~~ 132 (238)
..|+|++..++ +|.|... ++.+-.-...|..++.+....+||.|.-++...+
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 45899998755 8887431 1211112245665655556789999988875543
No 153
>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=59.12 E-value=8.8 Score=28.28 Aligned_cols=35 Identities=17% Similarity=0.302 Sum_probs=25.1
Q ss_pred ccccCcCCCCEEEEEEEecCCC--------CcceEEEecCCCc
Q 026458 113 RNIPKFEIGSLLYVRVVKANPG--------MNPELSCTDASGK 147 (238)
Q Consensus 113 ~~r~~l~~GDlV~ArV~~~~~~--------~~~~Ls~~~~~~~ 147 (238)
.+|+.++|||-|..++.-.+.+ ..+.++..+|+|+
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 4789999999999999833222 3567888887653
No 154
>PF13014 KH_3: KH domain
Probab=57.36 E-value=5.8 Score=24.99 Aligned_cols=28 Identities=7% Similarity=0.182 Sum_probs=23.9
Q ss_pred hhhhhcCCCCchhhHhhccccceEEEEee
Q 026458 166 LSRMLLSSPTCPVLEELGKQLSFEIAVGL 194 (238)
Q Consensus 166 ~v~rl~~~~~~~~l~~l~~~~~~ei~vG~ 194 (238)
++.+++|++++ .++.|.+.+++.|-|-.
T Consensus 1 ~vg~iIG~~G~-~I~~I~~~tg~~I~i~~ 28 (43)
T PF13014_consen 1 FVGRIIGKGGS-TIKEIREETGAKIQIPP 28 (43)
T ss_pred CcCeEECCCCh-HHHHHHHHhCcEEEECC
Confidence 35678999998 89999999999988866
No 155
>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=55.94 E-value=31 Score=23.52 Aligned_cols=42 Identities=24% Similarity=0.375 Sum_probs=28.2
Q ss_pred EEEechhhhhhhcCCCCchhhHhhccccceEEEEe--eCCeEEEecCCh
Q 026458 159 MFETSTGLSRMLLSSPTCPVLEELGKQLSFEIAVG--LNGRVWVNAESP 205 (238)
Q Consensus 159 ~~~V~~~~v~rl~~~~~~~~l~~l~~~~~~ei~vG--~NG~IWi~~~~~ 205 (238)
++-++|..+.+++...- . ++-..||.|+|= .+|.+||...+|
T Consensus 22 ~~~cnp~~a~~ll~~~p--~---~~~~lPcrv~vye~~~G~~~v~~~~P 65 (65)
T PF03625_consen 22 LEFCNPKIAYQLLKADP--E---IGLFLPCRVLVYEDEDGKVWVSYMNP 65 (65)
T ss_dssp EEEE-HHHHHHHHCC-G--G---GGGC-SEEEEEEE-ETTEEEEEEE-H
T ss_pred EEECChHHHHHHHHhhH--H---HHHhCCeEEEEEEecCCeEEEEEeCc
Confidence 45679999999995321 2 445689999875 599999987553
No 156
>CHL00010 infA translation initiation factor 1
Probab=54.40 E-value=53 Score=23.72 Aligned_cols=52 Identities=19% Similarity=0.213 Sum_probs=32.6
Q ss_pred EEEEEEEec-CceEEEEecCCeeeeecCcccCCcccccccCcCCCCEEEEEEEecC
Q 026458 78 VLGIVVDCK-ADNFFVDIRGPTIAFLPVLAFEGGTRRNIPKFEIGSLLYVRVVKAN 132 (238)
Q Consensus 78 VIG~V~~v~-~~~~~VdI~~~~~a~L~~~~f~gatk~~r~~l~~GDlV~ArV~~~~ 132 (238)
+.|+|++.. +.+|.|.... +..-.-...|..++.+....+||.|.-++...+
T Consensus 9 ~~G~Vik~lg~~~y~V~~~~---g~~~~c~~rGklr~~~i~~~vGD~V~ve~~~~~ 61 (78)
T CHL00010 9 MEGLVTESLPNGMFRVRLDN---GCQVLGYISGKIRRNSIRILPGDRVKVELSPYD 61 (78)
T ss_pred EEEEEEEEcCCCEEEEEeCC---CCEEEEEeccceecCCcccCCCCEEEEEEcccC
Confidence 569999988 6888886421 111111234555544555789999988865543
No 157
>COG1315 Uncharacterized conserved protein [Function unknown]
Probab=54.06 E-value=22 Score=34.82 Aligned_cols=100 Identities=16% Similarity=0.156 Sum_probs=64.4
Q ss_pred ceeecCcE-EEeCCEEEEEEeeEeEEecCCeEEEEcc---CCccCCCCCCEE-EEEEEE--ecCceEEEEecC-------
Q 026458 31 TIKLGGGL-RQECDSVSVIKAGKLRFSKPNKYWVESS---QKRYVPCVEDTV-LGIVVD--CKADNFFVDIRG------- 96 (238)
Q Consensus 31 ~~~~G~G~-y~~~g~i~as~~G~v~~~~~~~i~V~~~---~~~Y~P~vGDiV-IG~V~~--v~~~~~~VdI~~------- 96 (238)
.+.+|.|| ..+++.+.|+..|..-.. +++++|.|. .+.-.++.|+|. +|.|.= --.+.|.|.=..
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 KLNLGKNTAFKDNNTLVAKRDGQPIVS-KNTISVYPIYEVNGDVDVKTGNIKFVGNVVIHGDVEDGMVVKAEGNITVKGT 298 (543)
T ss_pred eeecCCCCccCCCCEEEEeeCCeEEec-CCeeEEEEEEEecCCccccccceeecceEEEeccCCCCcEEEecCceEEeeE
Confidence 57889999 567889999999999885 789999984 445567777775 344432 234556654322
Q ss_pred CeeeeecCcc--cC--CcccccccCcCCCCEEEEEEEec
Q 026458 97 PTIAFLPVLA--FE--GGTRRNIPKFEIGSLLYVRVVKA 131 (238)
Q Consensus 97 ~~~a~L~~~~--f~--gatk~~r~~l~~GDlV~ArV~~~ 131 (238)
...|.|..+. |- |-.-+++.+++..-.+.|.-++.
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 3455555421 21 22456667777777777766554
No 158
>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=53.60 E-value=9.1 Score=28.35 Aligned_cols=18 Identities=11% Similarity=0.060 Sum_probs=15.5
Q ss_pred ccCcCCCCEEEEEEEecC
Q 026458 115 IPKFEIGSLLYVRVVKAN 132 (238)
Q Consensus 115 r~~l~~GDlV~ArV~~~~ 132 (238)
+|+..+||||.|++...-
T Consensus 4 ~pc~~p~dLVwAK~kGyp 21 (83)
T cd05841 4 EPCRPPHELVWAKLKGFP 21 (83)
T ss_pred cccCCCCCEEEEeCCCCC
Confidence 689999999999987643
No 159
>COG1530 CafA Ribonucleases G and E [Translation, ribosomal structure and biogenesis]
Probab=52.20 E-value=28 Score=33.88 Aligned_cols=71 Identities=23% Similarity=0.188 Sum_probs=53.5
Q ss_pred CCCCEEEEEEEEec--CceEEEEecCCeeeeecCcccCCc-----ccccccCcCCCCEEEEEEEecCCC-CcceEEEec
Q 026458 73 CVEDTVLGIVVDCK--ADNFFVDIRGPTIAFLPVLAFEGG-----TRRNIPKFEIGSLLYVRVVKANPG-MNPELSCTD 143 (238)
Q Consensus 73 ~vGDiVIG~V~~v~--~~~~~VdI~~~~~a~L~~~~f~ga-----tk~~r~~l~~GDlV~ArV~~~~~~-~~~~Ls~~~ 143 (238)
.+|++-.|+|+++- -+.++|||+.--+|+||....... ..+.+..++.|+-+.-.|..-... .-+.||+.-
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 57999999999984 578999999999999998754321 113467899999999999875443 235666654
No 160
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=51.20 E-value=17 Score=36.95 Aligned_cols=58 Identities=12% Similarity=0.122 Sum_probs=48.0
Q ss_pred eEEEechhhhhhhcCCCCchhhHhhccccceEEEEeeCCeEEEecCChhHHHHHHHHHH
Q 026458 158 YMFETSTGLSRMLLSSPTCPVLEELGKQLSFEIAVGLNGRVWVNAESPSTVVLVSNAIM 216 (238)
Q Consensus 158 ~~~~V~~~~v~rl~~~~~~~~l~~l~~~~~~ei~vG~NG~IWi~~~~~~~~~~i~~~i~ 216 (238)
..++|+|.++..++|..+. .++.|-++++..|=+--+|.|.|.+.+.+....+.+.|+
T Consensus 556 ~~~~I~~~kI~~vIG~gg~-~ik~I~~~~~~~idi~d~G~v~i~~~~~~~~~~a~~~I~ 613 (693)
T PRK11824 556 ETIKIPPDKIRDVIGPGGK-TIREITEETGAKIDIEDDGTVKIAATDGEAAEAAKERIE 613 (693)
T ss_pred eeecCCHHHHHHHhcCCch-hHHHHHHHHCCccccCCCceEEEEcccHHHHHHHHHHHH
Confidence 4789999999999998876 899998999999999999999999988755444444443
No 161
>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=50.55 E-value=13 Score=27.42 Aligned_cols=25 Identities=28% Similarity=0.709 Sum_probs=17.0
Q ss_pred CCCCEEEEEEEecCCCC-cceEEEec
Q 026458 119 EIGSLLYVRVVKANPGM-NPELSCTD 143 (238)
Q Consensus 119 ~~GDlV~ArV~~~~~~~-~~~Ls~~~ 143 (238)
++||+|.|||.+++... ..++-|.+
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 58999999999998653 46677773
No 162
>PF14398 ATPgrasp_YheCD: YheC/D like ATP-grasp
Probab=49.82 E-value=10 Score=33.67 Aligned_cols=16 Identities=25% Similarity=0.966 Sum_probs=15.0
Q ss_pred ccceEEEEeeCCeEEE
Q 026458 185 QLSFEIAVGLNGRVWV 200 (238)
Q Consensus 185 ~~~~ei~vG~NG~IWi 200 (238)
++++|++|..||+||+
T Consensus 211 ElGiDl~iD~~g~iWl 226 (262)
T PF14398_consen 211 ELGIDLGIDKNGKIWL 226 (262)
T ss_pred EEEEEEEEcCCCCEEE
Confidence 5799999999999998
No 163
>smart00293 PWWP domain with conserved PWWP motif. conservation of Pro-Trp-Trp-Pro residues
Probab=47.46 E-value=12 Score=25.65 Aligned_cols=15 Identities=20% Similarity=0.468 Sum_probs=12.7
Q ss_pred cCCCCEEEEEEEecC
Q 026458 118 FEIGSLLYVRVVKAN 132 (238)
Q Consensus 118 l~~GDlV~ArV~~~~ 132 (238)
|++||+|.||+...-
T Consensus 1 f~~GdlVwaK~~G~p 15 (63)
T smart00293 1 FKPGDLVWAKMKGFP 15 (63)
T ss_pred CCCCCEEEEECCCCC
Confidence 689999999998753
No 164
>KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only]
Probab=46.85 E-value=42 Score=33.58 Aligned_cols=71 Identities=14% Similarity=0.202 Sum_probs=55.1
Q ss_pred CCCCCCEEE-----EEEEEecCceEEEEecCCeeeeecCcccCCc-ccccccCcCCCCEEEEEEEecCCCCcceEEE
Q 026458 71 VPCVEDTVL-----GIVVDCKADNFFVDIRGPTIAFLPVLAFEGG-TRRNIPKFEIGSLLYVRVVKANPGMNPELSC 141 (238)
Q Consensus 71 ~P~vGDiVI-----G~V~~v~~~~~~VdI~~~~~a~L~~~~f~ga-tk~~r~~l~~GDlV~ArV~~~~~~~~~~Ls~ 141 (238)
.|+++|++. |.|+++..-..+|.+-.-..+.||.++.... ..+-...|.+||-|-.+-+..+..+...|+-
T Consensus 660 ~~~~~~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 660 DDQVQDLEFGGVYTATITEIRDTGVMVELYPMQQGLLHNSQLDQEKIAKPSDLLEVGQEIQVKYIERDPRGGIMLSS 736 (760)
T ss_pred CccccceEeeeEEEEEEeeecccceEEEecCCchhhccchhcccccccChHHHHhhcceeEEEEEeecCccceeehh
Confidence 588999887 7889999999999999988999999887532 3334446999999988887776655555554
No 165
>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=46.45 E-value=95 Score=21.36 Aligned_cols=64 Identities=17% Similarity=0.164 Sum_probs=35.8
Q ss_pred EEEEEEEec---CceEEEEecCCeeeeecCcccCCcccccccCcCCCCEEEEEEEec-CC-CCcceEEEe
Q 026458 78 VLGIVVDCK---ADNFFVDIRGPTIAFLPVLAFEGGTRRNIPKFEIGSLLYVRVVKA-NP-GMNPELSCT 142 (238)
Q Consensus 78 VIG~V~~v~---~~~~~VdI~~~~~a~L~~~~f~gatk~~r~~l~~GDlV~ArV~~~-~~-~~~~~Ls~~ 142 (238)
|.|.|++++ ..++.+.+... .|.+....|+..-++.++.+..|+.|.++...- +. ...+.|.+.
T Consensus 4 v~g~v~~i~~tk~g~~~~~L~D~-~~~i~~~~f~~~~~~~~~~l~~g~~v~v~g~v~~~~~~~~~~l~v~ 72 (78)
T cd04489 4 VEGEISNLKRPSSGHLYFTLKDE-DASIRCVMWRSNARRLGFPLEEGMEVLVRGKVSFYEPRGGYQLIVE 72 (78)
T ss_pred EEEEEecCEECCCcEEEEEEEeC-CeEEEEEEEcchhhhCCCCCCCCCEEEEEEEEEEECCCCEEEEEEE
Confidence 555555543 22455555432 255655566655566788999999876655432 21 234555543
No 166
>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=46.29 E-value=24 Score=20.14 Aligned_cols=18 Identities=22% Similarity=0.477 Sum_probs=15.0
Q ss_pred cceEEEEeeCCeEEEecC
Q 026458 186 LSFEIAVGLNGRVWVNAE 203 (238)
Q Consensus 186 ~~~ei~vG~NG~IWi~~~ 203 (238)
.|-.|++..||.|||.-.
T Consensus 3 ~P~gvav~~~g~i~VaD~ 20 (28)
T PF01436_consen 3 YPHGVAVDSDGNIYVADS 20 (28)
T ss_dssp SEEEEEEETTSEEEEEEC
T ss_pred CCcEEEEeCCCCEEEEEC
Confidence 467899999999999753
No 167
>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=44.17 E-value=65 Score=23.80 Aligned_cols=49 Identities=22% Similarity=0.224 Sum_probs=31.6
Q ss_pred EEEEEEEec----CceEEEEecCCeeeeecCcccCCc--ccccccCcCCCCEEEEE
Q 026458 78 VLGIVVDCK----ADNFFVDIRGPTIAFLPVLAFEGG--TRRNIPKFEIGSLLYVR 127 (238)
Q Consensus 78 VIG~V~~v~----~~~~~VdI~~~~~a~L~~~~f~ga--tk~~r~~l~~GDlV~Ar 127 (238)
|-|.|+... +-.+...|.. ..|.++...|... ..+....+++||.|.+.
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 667777542 3346666654 3367776677654 45677789999977554
No 168
>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=43.66 E-value=96 Score=20.84 Aligned_cols=44 Identities=14% Similarity=0.249 Sum_probs=28.2
Q ss_pred EEEEEecCceEEEEecC--CeeeeecCcccCCcccccccCcCCCCEEEEEE
Q 026458 80 GIVVDCKADNFFVDIRG--PTIAFLPVLAFEGGTRRNIPKFEIGSLLYVRV 128 (238)
Q Consensus 80 G~V~~v~~~~~~VdI~~--~~~a~L~~~~f~gatk~~r~~l~~GDlV~ArV 128 (238)
|+|+....++|.|.... ...+.++ +..++.....-+||.|..+.
T Consensus 3 grVv~~~~~~~~v~~~~~~~~~~~~~-----~~~~~~~~~~~VGD~V~~~~ 48 (68)
T cd04466 3 GLIIKAIGGFYYVETEDGKIYECRLR-----GKFRKDKNPPAVGDRVEFEP 48 (68)
T ss_pred EEEEEEECCEEEEEeCCCeEEEEEEc-----cccccCCCCCCCCcEEEEEE
Confidence 78999988988887642 2233332 22222345678999997764
No 169
>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=42.51 E-value=16 Score=26.77 Aligned_cols=16 Identities=25% Similarity=0.567 Sum_probs=13.2
Q ss_pred CcCCCCEEEEEEEecC
Q 026458 117 KFEIGSLLYVRVVKAN 132 (238)
Q Consensus 117 ~l~~GDlV~ArV~~~~ 132 (238)
.|++||+|.|++...-
T Consensus 2 ~f~~GdlVwaK~kGyp 17 (83)
T cd05834 2 QFKAGDLVFAKVKGYP 17 (83)
T ss_pred CCCCCCEEEEecCCCC
Confidence 4789999999997643
No 170
>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=41.53 E-value=1.4e+02 Score=25.74 Aligned_cols=56 Identities=11% Similarity=0.208 Sum_probs=44.7
Q ss_pred EeCCEEEEEEeeEeEEecCCeEEEEcc-----CCccCCCCCCEEEEEEEEecCceEEEEecCC
Q 026458 40 QECDSVSVIKAGKLRFSKPNKYWVESS-----QKRYVPCVEDTVLGIVVDCKADNFFVDIRGP 97 (238)
Q Consensus 40 ~~~g~i~as~~G~v~~~~~~~i~V~~~-----~~~Y~P~vGDiVIG~V~~v~~~~~~VdI~~~ 97 (238)
.+.+.|+|.+-|......+..+.++=+ .+..+|+ |-+++| +..+.+++..+.|.+.
T Consensus 50 ~~~n~I~A~V~~~qtv~~Gs~vrlRLle~i~i~g~~IPk-gt~l~G-~~~~~~~Rl~i~I~SI 110 (200)
T PF12508_consen 50 TEKNTIRAVVDGTQTVVDGSRVRLRLLEDIQIGGILIPK-GTYLYG-VASFQGQRLLITITSI 110 (200)
T ss_pred CCCCeEEEEEecceEEeCCCEEEEEEcCceEECCEEeCC-CCEEEE-EEeeeccEEEEEEEEE
Confidence 357889999999987765566666532 4678887 999999 9999999999999873
No 171
>PRK05054 exoribonuclease II; Provisional
Probab=41.23 E-value=98 Score=31.23 Aligned_cols=62 Identities=11% Similarity=0.217 Sum_probs=47.7
Q ss_pred CCCCC--EEEEEEEEecCceEEEEecCC-eeeeecCcccCCc-------------ccccccCcCCCCEEEEEEEecCC
Q 026458 72 PCVED--TVLGIVVDCKADNFFVDIRGP-TIAFLPVLAFEGG-------------TRRNIPKFEIGSLLYVRVVKANP 133 (238)
Q Consensus 72 P~vGD--iVIG~V~~v~~~~~~VdI~~~-~~a~L~~~~f~ga-------------tk~~r~~l~~GDlV~ArV~~~~~ 133 (238)
..+|+ ..-|.|++++...+.|.|... ..|.+|.+.+.+. ..+.+..|+.||-|.-+|.+++.
T Consensus 557 ~~~G~~~~f~g~I~~v~~~G~fV~l~~~~veglV~~~~l~~~~~~y~~~~~~~~~~~~~~~~~~lGd~V~V~v~~vd~ 634 (644)
T PRK05054 557 DKAGTDTRFAAEIIDISRGGMRVRLLENGAVAFIPASFLHAVRDELVCNQENGTVQIKGETVYKLGDVIDVTLAEVRM 634 (644)
T ss_pred hccCCCeEEEEEEEeeecCcEEEEEeCCceEEEEEccccCCCccceEEccccceEEEeCCEEEcCCCEEEEEEEEEcc
Confidence 55665 999999999999999999753 6788887765431 11223469999999999999875
No 172
>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=40.86 E-value=30 Score=24.19 Aligned_cols=20 Identities=15% Similarity=0.582 Sum_probs=16.6
Q ss_pred cccceEEEEeeCCeEEEecC
Q 026458 184 KQLSFEIAVGLNGRVWVNAE 203 (238)
Q Consensus 184 ~~~~~ei~vG~NG~IWi~~~ 203 (238)
+.+.++=.+-.||++||+-.
T Consensus 35 ~~V~YD~~~~~dGy~Wisy~ 54 (65)
T PF08460_consen 35 QSVNYDQVIKADGYVWISYI 54 (65)
T ss_dssp -EEEEEEEEEETTEEEEEEE
T ss_pred CEEEEEEEEEeCCEEEEEEE
Confidence 45789999999999999753
No 173
>cd05839 BR140_related The PWWP domain is found in the BR140 family, which includes peregrin and BR140-like proteins 1 and 2. BR140 is the only family to contain the PWWP domain at the C terminus, with PHD and bromo domains in the N-terminal region. In myeloid leukemias, BR140 is disrupted by chromosomal translocations, similar to translocations of WHSC1 in lymphoid multiple myeloma. 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=39.97 E-value=1e+02 Score=24.06 Aligned_cols=14 Identities=14% Similarity=0.180 Sum_probs=11.6
Q ss_pred cCCCCEEEEEEEec
Q 026458 118 FEIGSLLYVRVVKA 131 (238)
Q Consensus 118 l~~GDlV~ArV~~~ 131 (238)
+.+||+|.|++...
T Consensus 1 ~~pg~lVwaK~~g~ 14 (111)
T cd05839 1 LEPLTLVWAKCRGY 14 (111)
T ss_pred CCCcCEeeeeecCC
Confidence 57999999999654
No 174
>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=39.69 E-value=18 Score=26.65 Aligned_cols=14 Identities=14% Similarity=0.532 Sum_probs=12.1
Q ss_pred cCCCCEEEEEEEec
Q 026458 118 FEIGSLLYVRVVKA 131 (238)
Q Consensus 118 l~~GDlV~ArV~~~ 131 (238)
|++||||-|++...
T Consensus 1 f~~GDlVwaK~~g~ 14 (86)
T cd05836 1 LKLGDLVWAKMKGF 14 (86)
T ss_pred CCCCCEEEEeCCCC
Confidence 68999999999754
No 175
>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=39.68 E-value=18 Score=27.13 Aligned_cols=15 Identities=20% Similarity=0.290 Sum_probs=12.7
Q ss_pred cCCCCEEEEEEEecC
Q 026458 118 FEIGSLLYVRVVKAN 132 (238)
Q Consensus 118 l~~GDlV~ArV~~~~ 132 (238)
|++||+|.||+-..-
T Consensus 1 f~~GDlVwaK~~GyP 15 (93)
T cd05840 1 FQPGDRVLAKVKGFP 15 (93)
T ss_pred CCCCCEEEEeCCCCC
Confidence 689999999998653
No 176
>PRK06763 F0F1 ATP synthase subunit alpha; Validated
Probab=39.66 E-value=73 Score=27.60 Aligned_cols=12 Identities=17% Similarity=0.088 Sum_probs=7.5
Q ss_pred CEEEEEEEecCC
Q 026458 122 SLLYVRVVKANP 133 (238)
Q Consensus 122 DlV~ArV~~~~~ 133 (238)
|.+..+|..+++
T Consensus 118 dYvIG~Iskv~k 129 (213)
T PRK06763 118 DYVIGEVSKVYT 129 (213)
T ss_pred ceEEEEEEEecc
Confidence 666666666654
No 177
>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=39.59 E-value=44 Score=30.79 Aligned_cols=59 Identities=19% Similarity=0.222 Sum_probs=42.0
Q ss_pred hhHhhccccceE-----EEEeeCCeEEEecCChhHHHHHHHHHHHhccCCHHHHHHHHHHHHhhc
Q 026458 178 VLEELGKQLSFE-----IAVGLNGRVWVNAESPSTVVLVSNAIMNSESLSAVQQKIMVDKLLQRI 237 (238)
Q Consensus 178 ~l~~l~~~~~~e-----i~vG~NG~IWi~~~~~~~~~~i~~~i~~~e~lt~~~~~~~~~~~~~~~ 237 (238)
.|+.+++.++++ ..+|.||-+.+.-.+. +...+.|||+.+..+-+.++-.-+++.++++
T Consensus 258 ~l~~~~~~~d~~~~gGa~llG~~g~vvk~HG~s-~~~a~~~ai~~a~~~~~~~~~~~i~~~~~~~ 321 (322)
T TIGR00182 258 ILKSLKQKFDYANYGGAVLFGLNKLVIKSHGSS-DSRAFFSAIRQAHEAVKSQVINRIKSSLESL 321 (322)
T ss_pred HHHHHHHhcCccccCCeEEecCCceEEEEcCCC-CHHHHHHHHHHHHHHHHhCHHHHHHHHHHhc
Confidence 455566556555 7899999988865444 4679999999988866666666666666655
No 178
>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=39.42 E-value=49 Score=24.22 Aligned_cols=29 Identities=31% Similarity=0.405 Sum_probs=19.4
Q ss_pred CCeEEEEccC-CccCCCCCCEEEEEEEEec
Q 026458 58 PNKYWVESSQ-KRYVPCVEDTVLGIVVDCK 86 (238)
Q Consensus 58 ~~~i~V~~~~-~~Y~P~vGDiVIG~V~~v~ 86 (238)
+.-++|-+.. ++|-.+.||.|.|.|..-.
T Consensus 28 ~~DvYVs~~qIrrf~LR~GD~V~G~vr~p~ 57 (78)
T PF07497_consen 28 PDDVYVSPSQIRRFGLRTGDLVEGQVRPPR 57 (78)
T ss_dssp TTSEEE-CCCCCCTT--TTEEEEEEEE--S
T ss_pred CCCEEECHHHHHHcCCCCCCEEEEEEeCCC
Confidence 3468888765 6899999999999998853
No 179
>PF13742 tRNA_anti_2: OB-fold nucleic acid binding domain
Probab=39.39 E-value=1.2e+02 Score=22.57 Aligned_cols=66 Identities=20% Similarity=0.217 Sum_probs=44.0
Q ss_pred EEEEEEEEecC---ceEEEEecCCeeeeecCcccCCcccccc-cCcCCCCEEEEEEEe--cCCCCcceEEEec
Q 026458 77 TVLGIVVDCKA---DNFFVDIRGPTIAFLPVLAFEGGTRRNI-PKFEIGSLLYVRVVK--ANPGMNPELSCTD 143 (238)
Q Consensus 77 iVIG~V~~v~~---~~~~VdI~~~~~a~L~~~~f~gatk~~r-~~l~~GDlV~ArV~~--~~~~~~~~Ls~~~ 143 (238)
-|.|.|++.+. ..+..++.. ..|.++..-|.....+.. ..++.||-|.++..- -.+.+.+.|.+.+
T Consensus 25 wV~GEIs~~~~~~~gh~YftLkD-~~a~i~~~~~~~~~~~i~~~~l~~G~~V~v~g~~~~y~~~G~~sl~v~~ 96 (99)
T PF13742_consen 25 WVEGEISNLKRHSSGHVYFTLKD-EEASISCVIFRSRARRIRGFDLKDGDKVLVRGRVSFYEPRGSLSLIVED 96 (99)
T ss_pred EEEEEEeecEECCCceEEEEEEc-CCcEEEEEEEHHHHhhCCCCCCCCCCEEEEEEEEEEECCCcEEEEEEEE
Confidence 47788887643 556666665 337777766766666677 789999998777643 3344556666643
No 180
>COG0557 VacB Exoribonuclease R [Transcription]
Probab=39.38 E-value=1.3e+02 Score=30.70 Aligned_cols=70 Identities=13% Similarity=0.218 Sum_probs=52.1
Q ss_pred CCCCCEEEEEEEEecCceEEEEecCC-eeeeecCcccCC------------cccccccCcCCCCEEEEEEEecCCC-Ccc
Q 026458 72 PCVEDTVLGIVVDCKADNFFVDIRGP-TIAFLPVLAFEG------------GTRRNIPKFEIGSLLYVRVVKANPG-MNP 137 (238)
Q Consensus 72 P~vGDiVIG~V~~v~~~~~~VdI~~~-~~a~L~~~~f~g------------atk~~r~~l~~GDlV~ArV~~~~~~-~~~ 137 (238)
=++|..--|.|+++......|.+... ..|..+.+.+++ ..++....++.||-|..+|.+++.. +.+
T Consensus 620 ~~vg~~f~g~V~~v~~~g~~V~l~~~~ieglV~~s~L~~d~y~~~~~~~~l~~~~~~~~~~lgd~v~v~v~~v~~~~~~i 699 (706)
T COG0557 620 KRVGEEFDGVVTGVTSFGFFVELPELGLEGLVHISSLPDDYYHFDERGQALVGEKSGKVYRLGDEVKVKVTSVDLDERKI 699 (706)
T ss_pred HhcCCEEEEEEEEEEeccEEEEecccccccceEcccCCCceeeeccccceeeccccccccccCCEEEEEEEEEcccccce
Confidence 46789999999999999999999775 566666665543 2344555799999999999998653 344
Q ss_pred eEEE
Q 026458 138 ELSC 141 (238)
Q Consensus 138 ~Ls~ 141 (238)
.++.
T Consensus 700 ~~~~ 703 (706)
T COG0557 700 DFEL 703 (706)
T ss_pred EEEe
Confidence 4443
No 181
>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=39.16 E-value=55 Score=23.13 Aligned_cols=31 Identities=13% Similarity=0.094 Sum_probs=22.7
Q ss_pred cCCCCCCEEEEEEEEecC-ceEEEEecCCeee
Q 026458 70 YVPCVEDTVLGIVVDCKA-DNFFVDIRGPTIA 100 (238)
Q Consensus 70 Y~P~vGDiVIG~V~~v~~-~~~~VdI~~~~~a 100 (238)
...++||.+.++|.++.. ....+.+..+..|
T Consensus 49 ~~~~~GD~i~~~V~~~~~~~~i~LS~~~~~~G 80 (82)
T cd04454 49 KSLQPGDLILAKVISLGDDMNVLLTTADNELG 80 (82)
T ss_pred hcCCCCCEEEEEEEEeCCCCCEEEEECCCCCc
Confidence 346999999999999876 4566666654443
No 182
>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=38.00 E-value=36 Score=25.25 Aligned_cols=21 Identities=33% Similarity=0.260 Sum_probs=17.5
Q ss_pred CccCCCCCCEEEEEEEEecCc
Q 026458 68 KRYVPCVEDTVLGIVVDCKAD 88 (238)
Q Consensus 68 ~~Y~P~vGDiVIG~V~~v~~~ 88 (238)
.|..-++||+|+++|..+..+
T Consensus 46 ~rp~L~~GDlV~ArV~~~~~~ 66 (86)
T cd05790 46 NRPNLNVGDLVYARVVKANRD 66 (86)
T ss_pred ccccCCCCCEEEEEEEecCCC
Confidence 356679999999999999765
No 183
>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF.
Probab=37.69 E-value=1e+02 Score=30.29 Aligned_cols=72 Identities=10% Similarity=0.129 Sum_probs=56.9
Q ss_pred hhhhhhcCCCCchhhHhhccccceEEEEeeC-CeEEEecCChhHHHHHHHHHHHhcc---CCHHHHHHHHHHHHhhc
Q 026458 165 GLSRMLLSSPTCPVLEELGKQLSFEIAVGLN-GRVWVNAESPSTVVLVSNAIMNSES---LSAVQQKIMVDKLLQRI 237 (238)
Q Consensus 165 ~~v~rl~~~~~~~~l~~l~~~~~~ei~vG~N-G~IWi~~~~~~~~~~i~~~i~~~e~---lt~~~~~~~~~~~~~~~ 237 (238)
.+--|+||+.|- =++.|...|+++++|.-. +-|-++|-||-.-..+-.+|.+.-. .-+.+|++++++..+.+
T Consensus 214 ~~kgriigreGr-nir~~e~~tgvd~iiddtp~~v~ls~fdp~rreia~~~l~~li~dgrihp~riee~~~~~~~~~ 289 (514)
T TIGR03319 214 EMKGRIIGREGR-NIRALETLTGVDLIIDDTPEAVILSGFDPVRREIARMALEKLIQDGRIHPARIEEMVEKATKEV 289 (514)
T ss_pred hhhccccCCCcc-hHHHHHHHhCceEEEcCCCCeEEecCCchHHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHH
Confidence 344466898886 788888889999999876 4788899999877888888877653 77799999998877654
No 184
>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=36.15 E-value=1e+02 Score=29.32 Aligned_cols=52 Identities=19% Similarity=0.328 Sum_probs=40.5
Q ss_pred cccceEEEEeeCCeEEEecCChhHHHHHHHHHHHhcc------CCHHHHHHHHHHHHh
Q 026458 184 KQLSFEIAVGLNGRVWVNAESPSTVVLVSNAIMNSES------LSAVQQKIMVDKLLQ 235 (238)
Q Consensus 184 ~~~~~ei~vG~NG~IWi~~~~~~~~~~i~~~i~~~e~------lt~~~~~~~~~~~~~ 235 (238)
+..+++|.=|+||.++|-+.+.+++.-..+++.+... ...++.++-+++.++
T Consensus 177 ~~~p~~il~grDg~iyVla~~qrd~~W~~Q~Llk~~~~e~v~v~~i~~~~~~i~~~L~ 234 (389)
T TIGR02554 177 APVRFAVLPGRDGRIYVAAASQRDAEWARQALLRAALPEKIEVAVIGAERQRVSRWLD 234 (389)
T ss_pred CCCCeEEEeCCCCcEEEEEccccHhHHHHHHHhhcCCCCCeEEechHHHHHHHHHHHH
Confidence 5689999999999999999999999999999998643 344455554454443
No 185
>PHA00691 hypothetical protein
Probab=34.22 E-value=21 Score=24.69 Aligned_cols=8 Identities=75% Similarity=1.261 Sum_probs=6.6
Q ss_pred eCCeEEEe
Q 026458 194 LNGRVWVN 201 (238)
Q Consensus 194 ~NG~IWi~ 201 (238)
-|||+|+-
T Consensus 11 ENGr~WVL 18 (68)
T PHA00691 11 ENGRVWVL 18 (68)
T ss_pred cCCeEEEE
Confidence 49999983
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=32.96 E-value=27 Score=25.67 Aligned_cols=15 Identities=20% Similarity=0.545 Sum_probs=12.3
Q ss_pred cCCCCEEEEEEEecC
Q 026458 118 FEIGSLLYVRVVKAN 132 (238)
Q Consensus 118 l~~GDlV~ArV~~~~ 132 (238)
|.+||||-|++....
T Consensus 1 f~vGDlVWaK~kg~p 15 (87)
T cd05835 1 FNVGDLVWGKIKGFP 15 (87)
T ss_pred CCCCCEEEEecCCCC
Confidence 679999999997643
No 187
>PRK05585 yajC preprotein translocase subunit YajC; Validated
Probab=32.96 E-value=73 Score=24.52 Aligned_cols=48 Identities=10% Similarity=0.105 Sum_probs=35.5
Q ss_pred ccccccCcCCCCEE------EEEEEecCCCCcceEEEecCCCccCCCcccCCeeEEEechhhhhhhcC
Q 026458 111 TRRNIPKFEIGSLL------YVRVVKANPGMNPELSCTDASGKAAEFGLLKDGYMFETSTGLSRMLLS 172 (238)
Q Consensus 111 tk~~r~~l~~GDlV------~ArV~~~~~~~~~~Ls~~~~~~~~~~~G~L~~G~~~~V~~~~v~rl~~ 172 (238)
.+++...|++||-| +++|.++++ ..+.|.+ .+|..+++.-+.+.+.+.
T Consensus 46 ~~~~~~~Lk~Gd~VvT~gGi~G~Vv~i~~-~~v~lei-------------~~g~~i~~~r~aI~~v~~ 99 (106)
T PRK05585 46 HKKMLSSLAKGDEVVTNGGIIGKVTKVSE-DFVIIEL-------------NDDTEIKIQKSAIAAVLP 99 (106)
T ss_pred HHHHHHhcCCCCEEEECCCeEEEEEEEeC-CEEEEEE-------------CCCeEEEEEhHHhhhhcC
Confidence 45677889999998 899999975 4555554 356778888777777664
No 188
>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=31.52 E-value=1.7e+02 Score=19.84 Aligned_cols=51 Identities=18% Similarity=0.197 Sum_probs=30.0
Q ss_pred EEEEEEEecC-ceEEEEecCCeeeeecCcccCCcccccccCcCCCCEEEEEEEec
Q 026458 78 VLGIVVDCKA-DNFFVDIRGPTIAFLPVLAFEGGTRRNIPKFEIGSLLYVRVVKA 131 (238)
Q Consensus 78 VIG~V~~v~~-~~~~VdI~~~~~a~L~~~~f~gatk~~r~~l~~GDlV~ArV~~~ 131 (238)
.-|+|++..+ .+|.|..... .... -...|..++.+..+.+||.|..+....
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 4588888874 8888754211 1111 123354443455589999998886543
No 189
>PRK00106 hypothetical protein; Provisional
Probab=31.28 E-value=1.5e+02 Score=29.35 Aligned_cols=72 Identities=7% Similarity=0.081 Sum_probs=57.0
Q ss_pred hhhhhhcCCCCchhhHhhccccceEEEEeeC-CeEEEecCChhHHHHHHHHHHHhcc---CCHHHHHHHHHHHHhhc
Q 026458 165 GLSRMLLSSPTCPVLEELGKQLSFEIAVGLN-GRVWVNAESPSTVVLVSNAIMNSES---LSAVQQKIMVDKLLQRI 237 (238)
Q Consensus 165 ~~v~rl~~~~~~~~l~~l~~~~~~ei~vG~N-G~IWi~~~~~~~~~~i~~~i~~~e~---lt~~~~~~~~~~~~~~~ 237 (238)
.+--|+||+.|- =+++|...|+++++|.-. .-|-++|-||-.-..+-.+|.+.-. .-+.+|++++++..+.+
T Consensus 235 emkGriIGreGr-Nir~~E~~tGvdliiddtp~~v~lS~fdpvRReiAr~~le~Li~dgrIhp~rIEe~v~k~~~e~ 310 (535)
T PRK00106 235 NMKGRIIGREGR-NIRTLESLTGIDVIIDDTPEVVVLSGFDPIRREIARMTLESLIKDGRIHPARIEELVEKNRLEM 310 (535)
T ss_pred HhhcceeCCCcc-hHHHHHHHhCceEEEcCCCCeEEEeCCChHHHHHHHHHHHHHHHcCCcCHHHHHHHHHHHHHHH
Confidence 344466898886 788888889999999765 5677899899888888888877654 77799999998877654
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=31.05 E-value=60 Score=24.84 Aligned_cols=26 Identities=23% Similarity=0.212 Sum_probs=15.1
Q ss_pred ccCCCCCCEE------------EEEEEEecCceEEEEe
Q 026458 69 RYVPCVEDTV------------LGIVVDCKADNFFVDI 94 (238)
Q Consensus 69 ~Y~P~vGDiV------------IG~V~~v~~~~~~VdI 94 (238)
...|++||+| +|+|+++..+.+..-+
T Consensus 60 ~~~P~~Gdivv~~~~~~~~~GHVaIV~~v~~~~~i~v~ 97 (124)
T PF05257_consen 60 GSTPQPGDIVVWDSGSGGGYGHVAIVESVNDGGTITVI 97 (124)
T ss_dssp CS---TTEEEEEEECTTTTT-EEEEEEEE-TTSEEEEE
T ss_pred CcccccceEEEeccCCCCCCCeEEEEEEECCCCEEEEE
Confidence 4679999999 4788888444444444
No 191
>PRK00951 hisB imidazoleglycerol-phosphate dehydratase; Validated
Probab=30.65 E-value=1.3e+02 Score=25.87 Aligned_cols=78 Identities=12% Similarity=0.206 Sum_probs=49.7
Q ss_pred EEEEEecCCCCcceEEEecCCCccCCCcccCCeeEEEechhhhhhhcCCCCchhhHhhccccceEEEEeeCCeEEEecCC
Q 026458 125 YVRVVKANPGMNPELSCTDASGKAAEFGLLKDGYMFETSTGLSRMLLSSPTCPVLEELGKQLSFEIAVGLNGRVWVNAES 204 (238)
Q Consensus 125 ~ArV~~~~~~~~~~Ls~~~~~~~~~~~G~L~~G~~~~V~~~~v~rl~~~~~~~~l~~l~~~~~~ei~vG~NG~IWi~~~~ 204 (238)
.|+|..-.+.-+++++..- ++-|+. -++...++. -+||+++.++-.|++.|-.+|-+||....
T Consensus 4 ~a~v~R~T~ET~I~v~l~L-----DG~g~~----~i~TGi~Fl--------DHML~~~a~H~~~dL~v~a~GDl~vD~HH 66 (195)
T PRK00951 4 TAEVERKTKETDISVELNL-----DGTGKS----DIDTGVGFL--------DHMLDQFARHGLFDLTVKAKGDLHIDDHH 66 (195)
T ss_pred eEEEEEcccceEEEEEEEe-----CCCCcc----ceeCCccHH--------HHHHHHHHHHcCCCeEEEEecCccccCCc
Confidence 3666666665666666543 333332 133333331 25999999999999999999999998753
Q ss_pred h-hH-HHHHHHHHHHhc
Q 026458 205 P-ST-VVLVSNAIMNSE 219 (238)
Q Consensus 205 ~-~~-~~~i~~~i~~~e 219 (238)
. ++ .+.+.+|+++.-
T Consensus 67 tvEDvgI~LG~al~~aL 83 (195)
T PRK00951 67 TVEDVGIVLGQALKEAL 83 (195)
T ss_pred hHHHHHHHHHHHHHHHh
Confidence 3 33 345567776643
No 192
>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=30.63 E-value=76 Score=23.33 Aligned_cols=45 Identities=13% Similarity=0.067 Sum_probs=29.8
Q ss_pred ccccccCcCCCCEE------EEEEEecCCCCcceEEEecCCCccCCCcccCCeeEEEechhhhhh
Q 026458 111 TRRNIPKFEIGSLL------YVRVVKANPGMNPELSCTDASGKAAEFGLLKDGYMFETSTGLSRM 169 (238)
Q Consensus 111 tk~~r~~l~~GDlV------~ArV~~~~~~~~~~Ls~~~~~~~~~~~G~L~~G~~~~V~~~~v~r 169 (238)
.+++...|++||-| +++|.+++++ ..+|.. ..|..++++-+.+.+
T Consensus 31 ~~~m~~~L~~Gd~VvT~gGi~G~V~~i~d~-~v~vei-------------~~g~~i~~~r~aI~~ 81 (84)
T TIGR00739 31 HKKLIESLKKGDKVLTIGGIIGTVTKIAEN-TIVIEL-------------NDNTEITFSKNAIVE 81 (84)
T ss_pred HHHHHHhCCCCCEEEECCCeEEEEEEEeCC-EEEEEE-------------CCCeEEEEEhHHhhh
Confidence 45678899999996 7899998753 344442 345666666554433
No 193
>PF09480 PrgH: Type III secretion system protein PrgH-EprH (PrgH); InterPro: IPR019029 In Salmonella, the gene encoding this protein is part of a four-gene operon PrgHIJK, while in other organisms it is found in type III secretion operons. PrgH has been shown to be required for type III secretion and is a structural component of the needle complex, which is the core component of type III secretion systems. ; GO: 0016021 integral to membrane; PDB: 4A4Y_A 2XXS_A 2Y9J_C 3GR1_F 3GR0_D.
Probab=30.09 E-value=1.8e+02 Score=27.48 Aligned_cols=52 Identities=17% Similarity=0.291 Sum_probs=38.5
Q ss_pred cccceEEEEeeCCeEEEecCChhHHHHHHHHHHHhcc------CCHHHHHHHHHHHHh
Q 026458 184 KQLSFEIAVGLNGRVWVNAESPSTVVLVSNAIMNSES------LSAVQQKIMVDKLLQ 235 (238)
Q Consensus 184 ~~~~~ei~vG~NG~IWi~~~~~~~~~~i~~~i~~~e~------lt~~~~~~~~~~~~~ 235 (238)
+..+++|.=|+||.++|=+.+.+++.=..+++.+... +..+|.++=+++.+.
T Consensus 167 ~~~p~~Il~g~d~~iyVla~~qrd~~W~rQ~L~k~~~~~~v~v~~i~~e~~~I~~~L~ 224 (375)
T PF09480_consen 167 SPSPYTILPGRDGKIYVLASTQRDAEWARQALLKEHYNEPVVVLWIDQEEKRIESWLS 224 (375)
T ss_dssp GTTTEEEEE-TTS-EEEEESSHHHHHHHHHHHHHHTGTTTEEEE-HHHHHHHHHHHHH
T ss_pred CCCceEEEeCCCccEEEEECcchHHHHHHHHHHhCCCCCceEEechHHHHHHHHHHHH
Confidence 5689999999999999999999999999999988665 444554444555443
No 194
>PF14444 S1-like: S1-like
Probab=30.00 E-value=92 Score=21.56 Aligned_cols=17 Identities=35% Similarity=0.255 Sum_probs=13.6
Q ss_pred ccCCCCCCEEEEEEEEe
Q 026458 69 RYVPCVEDTVLGIVVDC 85 (238)
Q Consensus 69 ~Y~P~vGDiVIG~V~~v 85 (238)
-++|++||.|+..-+.-
T Consensus 31 G~~P~vGdrV~v~A~~n 47 (58)
T PF14444_consen 31 GNVPKVGDRVLVEAIYN 47 (58)
T ss_pred cCCCccCCEEEEEEEeC
Confidence 47999999999876543
No 195
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=29.46 E-value=86 Score=26.25 Aligned_cols=32 Identities=16% Similarity=0.239 Sum_probs=26.6
Q ss_pred CCCCCEEEEEEEEecCceEEEEecCCeeeeecC
Q 026458 72 PCVEDTVLGIVVDCKADNFFVDIRGPTIAFLPV 104 (238)
Q Consensus 72 P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~ 104 (238)
-++||+|.++|.++. +.+.+.+..+..|.|..
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 488999999999999 78888887777777654
No 196
>PTZ00329 eukaryotic translation initiation factor 1A; Provisional
Probab=28.87 E-value=1.3e+02 Score=25.02 Aligned_cols=52 Identities=21% Similarity=0.351 Sum_probs=33.3
Q ss_pred CcEEec--CCccCCCCCCCCCceeecCcEEE----eCCEEEEEEeeEeEEecCCeEEEEccCCccCCCCCCEEEEEE
Q 026458 12 DKIVVP--GDVVLDLSSMTNQTIKLGGGLRQ----ECDSVSVIKAGKLRFSKPNKYWVESSQKRYVPCVEDTVLGIV 82 (238)
Q Consensus 12 ~~iV~P--Gd~l~~~~~~~~~~~~~G~G~y~----~~g~i~as~~G~v~~~~~~~i~V~~~~~~Y~P~vGDiVIG~V 82 (238)
..+++| ||.++... -.+|.|.|. ++..+.|.+.|.++. .+||. +||+|+-..
T Consensus 24 rel~~~eegq~~g~V~------~~LGn~~f~V~c~dG~~rLa~I~GKmRK----~IWI~---------~GD~VlVel 81 (155)
T PTZ00329 24 RELVFKEEGQEYAQVL------RMLGNGRLEAYCFDGVKRLCHIRGKMRK----RVWIN---------IGDIILVSL 81 (155)
T ss_pred eeeccCCCCcEEEEEE------EEcCCCEEEEEECCCCEEEEEeecccee----eEEec---------CCCEEEEec
Confidence 456666 66666542 356777774 235788889998875 37775 466666544
No 197
>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=28.48 E-value=1e+02 Score=21.90 Aligned_cols=26 Identities=15% Similarity=0.120 Sum_probs=19.0
Q ss_pred CCCCCEEEEEEEEecCc-eEEEEecCC
Q 026458 72 PCVEDTVLGIVVDCKAD-NFFVDIRGP 97 (238)
Q Consensus 72 P~vGDiVIG~V~~v~~~-~~~VdI~~~ 97 (238)
-++||.|.++|.++..+ ...+.+..+
T Consensus 55 l~vGd~i~~~V~~~~~~~~i~LS~~~~ 81 (86)
T cd05789 55 LDEGDLIVAEVQSVDSDGSVSLHTRSL 81 (86)
T ss_pred CCCCCEEEEEEEEECCCCCEEEEeCcc
Confidence 48999999999999764 445554443
No 198
>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=28.41 E-value=1.5e+02 Score=21.47 Aligned_cols=40 Identities=23% Similarity=0.336 Sum_probs=26.6
Q ss_pred EEEEEEecCceEEEEecCCe-eeeecCcccCCcccccccCcCCCCEEEEEE
Q 026458 79 LGIVVDCKADNFFVDIRGPT-IAFLPVLAFEGGTRRNIPKFEIGSLLYVRV 128 (238)
Q Consensus 79 IG~V~~v~~~~~~VdI~~~~-~a~L~~~~f~gatk~~r~~l~~GDlV~ArV 128 (238)
=|+|+++.++.+.||.+... ...|.+. +...+||+|.--.
T Consensus 6 P~~V~~i~~~~A~v~~~G~~~~v~l~lv----------~~~~vGD~VLVH~ 46 (76)
T TIGR00074 6 PGQVVEIDENIALVEFCGIKRDVSLDLV----------GEVKVGDYVLVHV 46 (76)
T ss_pred ceEEEEEcCCEEEEEcCCeEEEEEEEee----------CCCCCCCEEEEec
Confidence 37899999999999987532 2333221 3467999887543
No 199
>TIGR00498 lexA SOS regulatory protein LexA. LexA acts as a homodimer to repress a number of genes involved in the response to DNA damage (SOS response), including itself and RecA. RecA, in the presence of single-stranded DNA, acts as a co-protease to activate a latent autolytic protease activity (EC 3.4.21.88) of LexA, where the active site Ser is part of LexA. The autolytic cleavage site is an Ala-Gly bond in LexA (at position 84-85 in E. coli LexA; this sequence is replaced by Gly-Gly in Synechocystis). The cleavage leads to derepression of the SOS regulon and eventually to DNA repair. LexA in Bacillus subtilis is called DinR. LexA is much less broadly distributed than RecA.
Probab=28.17 E-value=2.6e+02 Score=23.16 Aligned_cols=30 Identities=27% Similarity=0.346 Sum_probs=20.8
Q ss_pred CCeEEEEccCCccCCCC----CCEEEEEEEEecC
Q 026458 58 PNKYWVESSQKRYVPCV----EDTVLGIVVDCKA 87 (238)
Q Consensus 58 ~~~i~V~~~~~~Y~P~v----GDiVIG~V~~v~~ 87 (238)
++.+++.|....|-|.. .-.|+|+|+.+..
T Consensus 163 ~~~i~L~s~N~~y~~i~~~~~~~~IiG~Vv~~~r 196 (199)
T TIGR00498 163 GTKVELKPENPEFDPIVLNAEDVTILGKVVGVIR 196 (199)
T ss_pred CCEEEEEcCCCCCcCCcCCCCcEEEEEEEEEEEE
Confidence 56788888776664332 4588999987643
No 200
>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=28.10 E-value=36 Score=24.97 Aligned_cols=15 Identities=20% Similarity=0.434 Sum_probs=12.6
Q ss_pred cCCCCEEEEEEEecC
Q 026458 118 FEIGSLLYVRVVKAN 132 (238)
Q Consensus 118 l~~GDlV~ArV~~~~ 132 (238)
|.+||+|.|++...-
T Consensus 1 f~~gdlVWaK~~g~P 15 (80)
T cd06080 1 FEKNDLVWAKIQGYP 15 (80)
T ss_pred CCCCCEEEEeCCCCC
Confidence 679999999988753
No 201
>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=28.10 E-value=38 Score=24.51 Aligned_cols=14 Identities=21% Similarity=0.506 Sum_probs=12.3
Q ss_pred cCCCCEEEEEEEec
Q 026458 118 FEIGSLLYVRVVKA 131 (238)
Q Consensus 118 l~~GDlV~ArV~~~ 131 (238)
|++||+|.||+...
T Consensus 1 f~~GdlVwaK~~g~ 14 (87)
T cd05162 1 FRPGDLVWAKMKGY 14 (87)
T ss_pred CCCCCEEEEeCCCC
Confidence 68999999999865
No 202
>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=28.10 E-value=55 Score=25.93 Aligned_cols=18 Identities=17% Similarity=0.578 Sum_probs=15.9
Q ss_pred cceEEEEeeCCeEEEecC
Q 026458 186 LSFEIAVGLNGRVWVNAE 203 (238)
Q Consensus 186 ~~~ei~vG~NG~IWi~~~ 203 (238)
.++++-+-.+||||++++
T Consensus 83 ep~~l~~l~dgri~~ts~ 100 (123)
T PF11763_consen 83 EPLDLHTLSDGRIWFTSN 100 (123)
T ss_pred CcEEEEEecCCcEEEEcc
Confidence 488899999999999984
No 203
>COG2147 RPL19A Ribosomal protein L19E [Translation, ribosomal structure and biogenesis]
Probab=27.89 E-value=48 Score=27.25 Aligned_cols=31 Identities=23% Similarity=0.597 Sum_probs=19.4
Q ss_pred EeeCCeEEEecCChhHHHHHHHHHHHhccCCHHHHHHHHHH
Q 026458 192 VGLNGRVWVNAESPSTVVLVSNAIMNSESLSAVQQKIMVDK 232 (238)
Q Consensus 192 vG~NG~IWi~~~~~~~~~~i~~~i~~~e~lt~~~~~~~~~~ 232 (238)
||.| ||||+.+. ..-|++| .|-++|++|+++
T Consensus 17 vG~~-Rvwidp~~---~eei~~A------~TR~dIr~LIk~ 47 (150)
T COG2147 17 VGEN-RVWIDPNE---IEEIASA------ITREDIRALIKD 47 (150)
T ss_pred cCcc-eeeeChHH---HHHHHHh------hhHHHHHHHHHC
Confidence 4444 89998732 2333333 577888888764
No 204
>PRK15327 type III secretion system needle complex protein PrgH; Provisional
Probab=27.89 E-value=1.7e+02 Score=27.89 Aligned_cols=52 Identities=12% Similarity=0.272 Sum_probs=40.6
Q ss_pred cccceEEEEeeCCeEEEecCChhHHHHHHHHHHHhcc------CCHHHHHHHHHHHHh
Q 026458 184 KQLSFEIAVGLNGRVWVNAESPSTVVLVSNAIMNSES------LSAVQQKIMVDKLLQ 235 (238)
Q Consensus 184 ~~~~~ei~vG~NG~IWi~~~~~~~~~~i~~~i~~~e~------lt~~~~~~~~~~~~~ 235 (238)
+..+++|.=|+||.++|=+.+.+++.-..+++.+... +..++.++-+++.++
T Consensus 182 ~~~p~~Il~grD~~iyVLa~~qrd~~W~~Q~L~k~~~~~~v~v~~~~~~~~~ie~~L~ 239 (393)
T PRK15327 182 EKERFQVLPGRDKMLYVAAQNERDTLWARQSLARGDYDKNARVINENEENKRVSTWLD 239 (393)
T ss_pred CCCceEEEeCCCCcEEEEEccccHhHHHHHHHhhCCCcCceEEechHHHHHHHHHHHH
Confidence 5689999999999999999999999999999988664 334454444454443
No 205
>PF13953 PapC_C: PapC C-terminal domain; PDB: 3L48_E 2XET_A 3RFZ_E 2KT6_A.
Probab=27.81 E-value=32 Score=23.94 Aligned_cols=19 Identities=26% Similarity=0.429 Sum_probs=13.9
Q ss_pred ceEEEEeeCCeEEEecCCh
Q 026458 187 SFEIAVGLNGRVWVNAESP 205 (238)
Q Consensus 187 ~~ei~vG~NG~IWi~~~~~ 205 (238)
..--+||.+|++|++....
T Consensus 23 ~~~g~Vg~~G~vyl~~~~~ 41 (68)
T PF13953_consen 23 NNIGIVGQDGQVYLSGLPP 41 (68)
T ss_dssp SEEEEB-GCGEEEEEEE-T
T ss_pred CEEEEEcCCCEEEEECCCC
Confidence 4567899999999998554
No 206
>PF10000 ACT_3: ACT domain; InterPro: IPR018717 This domain has no known function.; PDB: 1ZVP_C.
Probab=27.24 E-value=36 Score=24.39 Aligned_cols=47 Identities=15% Similarity=0.331 Sum_probs=25.3
Q ss_pred cccccCcCCCCEEEEEEE-ecC--CCCcceEEEecCCCccCCCcccCCeeEEEechhhhhh
Q 026458 112 RRNIPKFEIGSLLYVRVV-KAN--PGMNPELSCTDASGKAAEFGLLKDGYMFETSTGLSRM 169 (238)
Q Consensus 112 k~~r~~l~~GDlV~ArV~-~~~--~~~~~~Ls~~~~~~~~~~~G~L~~G~~~~V~~~~v~r 169 (238)
..|+|.+++|++|+|.+. ... ...++..+.++ ..|.-+-++-..+.+
T Consensus 12 ~~m~P~L~~~~yVF~t~~~~~~~~~~l~pi~~frE-----------~EGlTlIl~~~~A~~ 61 (72)
T PF10000_consen 12 ASMSPELNPGEYVFCTVPGDLADPPGLEPIATFRE-----------AEGLTLILPKEEADA 61 (72)
T ss_dssp ST-EEEE-SS-EEEEEE-S-GGGGGGG--SEEEEE-----------TTEEEEEEEHHHHHC
T ss_pred hhCCcEeCCCCEEEEEecCcccCccCCcceEEEEe-----------cCceEEEEEHHHHHH
Confidence 468999999999999998 211 12234455555 356666666555543
No 207
>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=26.11 E-value=1.6e+02 Score=23.31 Aligned_cols=22 Identities=14% Similarity=0.537 Sum_probs=14.8
Q ss_pred ccccccCcCCCCEEEE---EEEecC
Q 026458 111 TRRNIPKFEIGSLLYV---RVVKAN 132 (238)
Q Consensus 111 tk~~r~~l~~GDlV~A---rV~~~~ 132 (238)
++..-|.+.+||+|.. +|+..+
T Consensus 62 ~~~~LP~v~~GDVIll~~~kv~~~~ 86 (138)
T cd04497 62 NEESLPIVKVGDIILLRRVKIQSYN 86 (138)
T ss_pred ChhhCCCCCCCCEEEEEEEEEEEEC
Confidence 3344565699999964 566665
No 208
>COG1137 YhbG ABC-type (unclassified) transport system, ATPase component [General function prediction only]
Probab=26.05 E-value=2.3e+02 Score=25.03 Aligned_cols=47 Identities=26% Similarity=0.420 Sum_probs=39.5
Q ss_pred cccCCeeEEEechhhhhhhcCCCCchhhHhhccccceEEEEee----CCeEEEecCC
Q 026458 152 GLLKDGYMFETSTGLSRMLLSSPTCPVLEELGKQLSFEIAVGL----NGRVWVNAES 204 (238)
Q Consensus 152 G~L~~G~~~~V~~~~v~rl~~~~~~~~l~~l~~~~~~ei~vG~----NG~IWi~~~~ 204 (238)
.++.+|+-+.|.++-+=-|+|..+. ++-+-|-+++|. -|+||+++.|
T Consensus 17 r~Vv~~Vsl~v~~GEiVGLLGPNGA------GKTT~Fymi~Glv~~d~G~i~ld~~d 67 (243)
T COG1137 17 RKVVNDVSLEVNSGEIVGLLGPNGA------GKTTTFYMIVGLVRPDSGKILLDDED 67 (243)
T ss_pred eeeeeeeeEEEcCCcEEEEECCCCC------CceeEEEEEEEEEecCCceEEECCcc
Confidence 4567899999999999999997775 667889999986 7999999865
No 209
>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=25.97 E-value=1.4e+02 Score=21.72 Aligned_cols=20 Identities=30% Similarity=0.333 Sum_probs=16.9
Q ss_pred cccCcCCCCEEEEEEEecCC
Q 026458 114 NIPKFEIGSLLYVRVVKANP 133 (238)
Q Consensus 114 ~r~~l~~GDlV~ArV~~~~~ 133 (238)
|.|.|++||.|+|+-.-.|+
T Consensus 1 ~~p~f~~G~~V~a~~~irND 20 (75)
T PF04319_consen 1 MPPRFEWGDKVRARKDIRND 20 (75)
T ss_pred CCCccCCCCEEEEEEEeEcC
Confidence 56899999999999877665
No 210
>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=25.77 E-value=45 Score=23.68 Aligned_cols=13 Identities=23% Similarity=0.606 Sum_probs=10.4
Q ss_pred cCCCCEEEEEEEe
Q 026458 118 FEIGSLLYVRVVK 130 (238)
Q Consensus 118 l~~GDlV~ArV~~ 130 (238)
|.+||+|-||+..
T Consensus 1 f~~GdlVWaK~~g 13 (86)
T PF00855_consen 1 FRPGDLVWAKLKG 13 (86)
T ss_dssp -STTEEEEEEETT
T ss_pred CCCCCEEEEEeCC
Confidence 6799999999954
No 211
>KOG0147 consensus Transcriptional coactivator CAPER (RRM superfamily) [Transcription]
Probab=25.70 E-value=93 Score=30.76 Aligned_cols=39 Identities=33% Similarity=0.362 Sum_probs=29.8
Q ss_pred hhHhhcccc-ceEEEEeeC--CeEEEecCChhHHHHHHHHHH
Q 026458 178 VLEELGKQL-SFEIAVGLN--GRVWVNAESPSTVVLVSNAIM 216 (238)
Q Consensus 178 ~l~~l~~~~-~~ei~vG~N--G~IWi~~~~~~~~~~i~~~i~ 216 (238)
++++.+++. =|.|.|..| |.|+|+|++.+.+..+.+||-
T Consensus 470 V~Eec~k~g~v~hi~vd~ns~g~VYvrc~s~~~A~~a~~alh 511 (549)
T KOG0147|consen 470 VIEECGKHGKVCHIFVDKNSAGCVYVRCPSAEAAGTAVKALH 511 (549)
T ss_pred HHHHHHhcCCeeEEEEccCCCceEEEecCcHHHHHHHHHHHh
Confidence 455555554 367888887 899999999988888888774
No 212
>PRK00215 LexA repressor; Validated
Probab=25.23 E-value=2.6e+02 Score=23.31 Aligned_cols=30 Identities=23% Similarity=0.286 Sum_probs=20.6
Q ss_pred CCeEEEEccCCccCCCC----CCEEEEEEEEecC
Q 026458 58 PNKYWVESSQKRYVPCV----EDTVLGIVVDCKA 87 (238)
Q Consensus 58 ~~~i~V~~~~~~Y~P~v----GDiVIG~V~~v~~ 87 (238)
++.+++.|....|-|.. .-.|+|+|+.+..
T Consensus 170 ~~~~~L~s~Np~y~~~~~~~~~~~IiG~Vv~~~r 203 (205)
T PRK00215 170 GGHIRLEPENPAYEPIIVDPDRVTIEGKVVGLIR 203 (205)
T ss_pred CCEEEEEcCCCCCCCEEeCCCcEEEEEEEEEEEE
Confidence 55788888766664421 4588999887643
No 213
>cd00900 PH-like Pleckstrin homology-like domain. Pleckstrin homology-like domain. This family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. The PH domain is commonly found in eukaryotic signaling proteins. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins.
Probab=24.95 E-value=1.3e+02 Score=20.24 Aligned_cols=33 Identities=15% Similarity=0.037 Sum_probs=27.5
Q ss_pred ccceEEEEee--CCeEEEecCChhHHHHHHHHHHH
Q 026458 185 QLSFEIAVGL--NGRVWVNAESPSTVVLVSNAIMN 217 (238)
Q Consensus 185 ~~~~ei~vG~--NG~IWi~~~~~~~~~~i~~~i~~ 217 (238)
...|.|.... +..+++.+++.++.....+||+.
T Consensus 64 ~~~F~i~~~~~~~~~~~~~~~~~~~~~~W~~al~~ 98 (99)
T cd00900 64 PNCFAIVTKDRGRRVFVFQADSEEEAQEWVEALQQ 98 (99)
T ss_pred CceEEEECCCCCcEEEEEEcCCHHHHHHHHHHHhc
Confidence 4577777775 89999999999999988888875
No 214
>KOG1004 consensus Exosomal 3'-5' exoribonuclease complex subunit Rrp40 [Translation, ribosomal structure and biogenesis]
Probab=24.91 E-value=1.8e+02 Score=25.44 Aligned_cols=21 Identities=33% Similarity=0.320 Sum_probs=17.0
Q ss_pred CccCCCCCCEEEEEEEEecCc
Q 026458 68 KRYVPCVEDTVLGIVVDCKAD 88 (238)
Q Consensus 68 ~~Y~P~vGDiVIG~V~~v~~~ 88 (238)
+|..-++||+|+++|.+-..+
T Consensus 105 NrPnl~vGdliyakv~~a~~~ 125 (230)
T KOG1004|consen 105 NRPNLQVGDLIYAKVVDANKD 125 (230)
T ss_pred CCCccccccEEEEEEEecCCC
Confidence 467779999999999887543
No 215
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=24.46 E-value=1.1e+02 Score=26.72 Aligned_cols=32 Identities=13% Similarity=0.284 Sum_probs=23.9
Q ss_pred CCCCCEEEEEEEEecCc-eEEEEecCCeeeeec
Q 026458 72 PCVEDTVLGIVVDCKAD-NFFVDIRGPTIAFLP 103 (238)
Q Consensus 72 P~vGDiVIG~V~~v~~~-~~~VdI~~~~~a~L~ 103 (238)
-++||+|.++|.++..+ .+.+.+.....|.|.
T Consensus 112 ~~~GDlV~akV~~i~~~~~~~LS~k~~~lG~L~ 144 (235)
T PRK04163 112 LDIGDYIIAKVKDVDRTRDVVLTLKGKGLGKIE 144 (235)
T ss_pred CCCCCEEEEEEEEECCCCcEEEEEcCCCCCccC
Confidence 48899999999999754 467777666555554
No 216
>PRK12704 phosphodiesterase; Provisional
Probab=24.45 E-value=1.5e+02 Score=29.23 Aligned_cols=69 Identities=10% Similarity=0.113 Sum_probs=48.0
Q ss_pred hhhhhcCCCCchhhHhhccccceEEEEeeC-CeEEEecCChhHHHHHHHHHHHhcc---CCHHHHHHHHHHHHh
Q 026458 166 LSRMLLSSPTCPVLEELGKQLSFEIAVGLN-GRVWVNAESPSTVVLVSNAIMNSES---LSAVQQKIMVDKLLQ 235 (238)
Q Consensus 166 ~v~rl~~~~~~~~l~~l~~~~~~ei~vG~N-G~IWi~~~~~~~~~~i~~~i~~~e~---lt~~~~~~~~~~~~~ 235 (238)
+--|+||+.|- =+++|...|+++++|.-. +.|.++|-||-.-..+..++...-. .-+.++++++.+..+
T Consensus 221 mkgriigreGr-nir~~e~~tgvd~iiddtp~~v~ls~~~~~rre~a~~~l~~l~~dg~i~P~~iee~~~~~~~ 293 (520)
T PRK12704 221 MKGRIIGREGR-NIRALETLTGVDLIIDDTPEAVILSGFDPIRREIARLALEKLVQDGRIHPARIEEMVEKARK 293 (520)
T ss_pred hhcceeCCCcc-hHHHHHHHhCCeEEEcCCCCeEEEecCChhhHHHHHHHHHHHHhcCCcCCCCHHHHHHHHHH
Confidence 44466898886 788888889999999887 7888999888765555666655432 333555665555443
No 217
>cd02414 jag_KH jag_K homology RNA-binding domain. The KH domain is found in proteins homologous to the Bacillus subtilis protein Jag, which is associated with SpoIIIJ and is necessary for the third stage of sporulation. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. 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=24.43 E-value=1.3e+02 Score=21.26 Aligned_cols=39 Identities=15% Similarity=0.135 Sum_probs=22.0
Q ss_pred eEEEechhhhhhhcCCCCchhhHhhc----------cccceEEEEeeCCe
Q 026458 158 YMFETSTGLSRMLLSSPTCPVLEELG----------KQLSFEIAVGLNGR 197 (238)
Q Consensus 158 ~~~~V~~~~v~rl~~~~~~~~l~~l~----------~~~~~ei~vG~NG~ 197 (238)
+.+.+++.-..+|||+++. .|+.|. ....+.|.+..|||
T Consensus 26 i~i~i~~~~~g~LIGk~G~-tL~AlQ~L~~~~~~~~~~~~~~v~lDv~~Y 74 (77)
T cd02414 26 VEVNISGDDIGLLIGKRGK-TLDALQYLANLVLNRNTGEYVRITLDVEGY 74 (77)
T ss_pred EEEEEecCCCCeEECCCCc-cHHHHHHHHHHHHhhccCCceEEEEECccc
Confidence 3455555555566777665 444431 12466777777765
No 218
>PRK10553 assembly protein for periplasmic nitrate reductase; Provisional
Probab=24.39 E-value=3e+02 Score=20.39 Aligned_cols=57 Identities=18% Similarity=0.203 Sum_probs=37.7
Q ss_pred CeeEEEechhhhhhhcCCCCchhhHhhccccceEEEEe--eCCeEEEec--CChhHHHHHHHHHHHhcc
Q 026458 156 DGYMFETSTGLSRMLLSSPTCPVLEELGKQLSFEIAVG--LNGRVWVNA--ESPSTVVLVSNAIMNSES 220 (238)
Q Consensus 156 ~G~~~~V~~~~v~rl~~~~~~~~l~~l~~~~~~ei~vG--~NG~IWi~~--~~~~~~~~i~~~i~~~e~ 220 (238)
-|.++.+.|..+..+. +.|.+--+|||..- .+|+|-|.. ++.+......+.|+.++.
T Consensus 8 sSlVV~~~Pe~~~~V~--------~~l~~ipg~Evh~~d~~~GKiVVtiE~~~~~~~~~~i~~I~~l~G 68 (87)
T PRK10553 8 CSLVVQAKSERISDIS--------TQLNAFPGCEVAVSDAPSGQLIVVVEAEDSETLLQTIESVRNVEG 68 (87)
T ss_pred eEEEEEeChHHHHHHH--------HHHHcCCCcEEEeecCCCCeEEEEEEeCChHHHHHHHHHHHcCCC
Confidence 3678889888876654 44445569999975 689998865 444555555555555544
No 219
>COG3822 ABC-type sugar transport system, auxiliary component [General function prediction only]
Probab=24.11 E-value=1.6e+02 Score=25.53 Aligned_cols=39 Identities=13% Similarity=0.186 Sum_probs=28.8
Q ss_pred eeEeEEecCCeEEEEcc-CCccCCCCCCEEEEEEEEecCc
Q 026458 50 AGKLRFSKPNKYWVESS-QKRYVPCVEDTVLGIVVDCKAD 88 (238)
Q Consensus 50 ~G~v~~~~~~~i~V~~~-~~~Y~P~vGDiVIG~V~~v~~~ 88 (238)
-|.++.+....+.+-|. ...+-...|++++|.|..++.|
T Consensus 152 g~~lkL~PGesitL~Pg~~HsFwae~g~vlvgEvSsvndD 191 (225)
T COG3822 152 GSQLKLSPGESITLPPGLYHSFWAEEGGVLVGEVSSVNDD 191 (225)
T ss_pred ceeEEECCCCcEecCCCceeeeeecCCcEEEEEEeeccCc
Confidence 34455554567777775 3567789999999999999876
No 220
>PLN02800 imidazoleglycerol-phosphate dehydratase
Probab=24.03 E-value=44 Score=30.01 Aligned_cols=43 Identities=16% Similarity=0.469 Sum_probs=34.0
Q ss_pred hhhHhhccccceEEEEeeCCeEEEecCC-hhH-HHHHHHHHHHhc
Q 026458 177 PVLEELGKQLSFEIAVGLNGRVWVNAES-PST-VVLVSNAIMNSE 219 (238)
Q Consensus 177 ~~l~~l~~~~~~ei~vG~NG~IWi~~~~-~~~-~~~i~~~i~~~e 219 (238)
+||+++.++-.|++.|-.+|-+||+... .++ .+.+.+||++.-
T Consensus 101 HML~~~a~Hg~fdL~V~a~GDl~vD~HHtvEDvgI~LG~Al~~AL 145 (261)
T PLN02800 101 HMLDQLASHGLFDVHVKATGDLWIDDHHTNEDVALAIGTALLKAL 145 (261)
T ss_pred HHHHHHHHHcCCCeEEEEecCccccCCCchhhhhhhHHHHHHHHh
Confidence 5999999999999999999999998643 233 455677777653
No 221
>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=23.99 E-value=1.5e+02 Score=20.43 Aligned_cols=19 Identities=32% Similarity=0.368 Sum_probs=17.3
Q ss_pred EEEEEEEecCceEEEEecC
Q 026458 78 VLGIVVDCKADNFFVDIRG 96 (238)
Q Consensus 78 VIG~V~~v~~~~~~VdI~~ 96 (238)
.-|+|..+..+...|||..
T Consensus 16 ~~G~V~kv~eNSVIVdIT~ 34 (57)
T PF09953_consen 16 FTGIVEKVYENSVIVDITI 34 (57)
T ss_pred cEEEEEEEecCcEEEEEEe
Confidence 5899999999999999975
No 222
>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=23.78 E-value=2.6e+02 Score=19.55 Aligned_cols=26 Identities=27% Similarity=0.280 Sum_probs=17.8
Q ss_pred ccCcCCCCEEEEE---EEecCCCCcceEEEe
Q 026458 115 IPKFEIGSLLYVR---VVKANPGMNPELSCT 142 (238)
Q Consensus 115 r~~l~~GDlV~Ar---V~~~~~~~~~~Ls~~ 142 (238)
.+.+.+||+|..+ |...+ +.++|++.
T Consensus 46 ~~~~~~G~vv~i~~~~v~~~~--g~~ql~i~ 74 (82)
T cd04491 46 ADDLEPGDVVRIENAYVREFN--GRLELSVG 74 (82)
T ss_pred cccCCCCCEEEEEeEEEEecC--CcEEEEeC
Confidence 5679999998765 44432 56777763
No 223
>COG2810 Predicted type IV restriction endonuclease [Defense mechanisms]
Probab=23.70 E-value=69 Score=28.65 Aligned_cols=51 Identities=27% Similarity=0.514 Sum_probs=28.0
Q ss_pred CCCcccCCeeEEEechhhhhhhcCCCCchhhHhhcc---ccceEEEEeeCCeEEEec
Q 026458 149 AEFGLLKDGYMFETSTGLSRMLLSSPTCPVLEELGK---QLSFEIAVGLNGRVWVNA 202 (238)
Q Consensus 149 ~~~G~L~~G~~~~V~~~~v~rl~~~~~~~~l~~l~~---~~~~ei~vG~NG~IWi~~ 202 (238)
..|-.+.||-+|-.-..+.-..+-.. =..++.+ ..+.|+.+=-|||+||--
T Consensus 59 aDyalikd~kvfafieak~ls~~~ak---d~qq~~~Yav~~Gv~~~iVtnGrvWiV~ 112 (284)
T COG2810 59 ADYALIKDGKVFAFIEAKNLSVNPAK---DVQQLAKYAVDKGVEVGIVTNGRVWIVV 112 (284)
T ss_pred cceEEEecCcEEEEEeccccCcCchH---HHHHHHHHHHhcCcEEEEEeCCeEEEEE
Confidence 45666666666554333322221111 1122222 258999999999999943
No 224
>COG1792 MreC Cell shape-determining protein [Cell envelope biogenesis, outer membrane]
Probab=23.35 E-value=1.8e+02 Score=26.17 Aligned_cols=25 Identities=16% Similarity=0.135 Sum_probs=19.9
Q ss_pred EEEEEEEecCceEEEEecCCeeeee
Q 026458 78 VLGIVVDCKADNFFVDIRGPTIAFL 102 (238)
Q Consensus 78 VIG~V~~v~~~~~~VdI~~~~~a~L 102 (238)
++|+|+.+.....+|.+-+.....+
T Consensus 156 LVG~V~~V~~~tS~V~Lltd~~~~i 180 (284)
T COG1792 156 LVGKVVEVSKNTSRVLLLTDVNSKI 180 (284)
T ss_pred eEEEEEEEcCceeEEEEeeccccce
Confidence 8999999999999998866443333
No 225
>COG1158 Rho Transcription termination factor [Transcription]
Probab=23.35 E-value=85 Score=29.66 Aligned_cols=67 Identities=28% Similarity=0.339 Sum_probs=42.9
Q ss_pred CceeecCcEEEeCCEEEEEEeeEeEEec------CCeEEEEccC-CccCCCCCCEEEEEEEEe-cCceEEEEecCCeeee
Q 026458 30 QTIKLGGGLRQECDSVSVIKAGKLRFSK------PNKYWVESSQ-KRYVPCVEDTVLGIVVDC-KADNFFVDIRGPTIAF 101 (238)
Q Consensus 30 ~~~~~G~G~y~~~g~i~as~~G~v~~~~------~~~i~V~~~~-~~Y~P~vGDiVIG~V~~v-~~~~~~VdI~~~~~a~ 101 (238)
+++..+.|+.+. ..-=+|.++... .+-++|.|.+ +||-.+.||.|.|+|-.= .++.| .|.
T Consensus 49 g~~~~~~GvLei----l~dGfGFLR~~~~~yl~~~~DiYvSpSQIRrf~LrtGD~v~G~vR~Pke~Ery--------~aL 116 (422)
T COG1158 49 GEEIFGDGVLEI----LPDGFGFLRSADSSYLPGPDDIYVSPSQIRRFNLRTGDTVEGKVRPPKEGERY--------FAL 116 (422)
T ss_pred CceEeeeeEEEe----ccCCcceeecCccccCCCCCceEECHHHHhhccCccCCEEeeeecCCCcccce--------eee
Confidence 456777777642 222267776531 3568999876 689999999999999763 33333 355
Q ss_pred ecCcccC
Q 026458 102 LPVLAFE 108 (238)
Q Consensus 102 L~~~~f~ 108 (238)
|.+..+.
T Consensus 117 l~ve~vN 123 (422)
T COG1158 117 LKVEAVN 123 (422)
T ss_pred EEEeecC
Confidence 5554443
No 226
>KOG4078 consensus Putative mitochondrial ribosomal protein mRpS35 [Translation, ribosomal structure and biogenesis]
Probab=23.16 E-value=2.1e+02 Score=23.55 Aligned_cols=78 Identities=19% Similarity=0.229 Sum_probs=54.0
Q ss_pred CCCCCCEEEEEEEEecCceEEEEecCCeeeeecCcccCCcccccccCcCCCCEEEEEEEecCCCCcceEEEecCCCccCC
Q 026458 71 VPCVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEGGTRRNIPKFEIGSLLYVRVVKANPGMNPELSCTDASGKAAE 150 (238)
Q Consensus 71 ~P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~gatk~~r~~l~~GDlV~ArV~~~~~~~~~~Ls~~~~~~~~~~ 150 (238)
=|..|-+|+|+|-.+..+-..+|.+.-++.+-..-+ .|-..++-|.-|+-|++. ++||. .-
T Consensus 79 g~a~gklV~GkIfhiV~~DlYIDFG~KFhcVC~rP~------~n~e~Y~~GaRVrlRl~D------lELs~-------rF 139 (173)
T KOG4078|consen 79 GDAKGKLVIGKIFHIVEEDLYIDFGGKFHCVCKRPA------LNGEAYQKGARVRLRLID------LELSE-------RF 139 (173)
T ss_pred cCcCCcEEEeeeeeeeccceEEecCCeEEEEEcCcC------cCHHHhhcCceEEEEEcC------hhHhh-------hh
Confidence 488899999999999888888899888877765322 244567788888888753 56664 34
Q ss_pred CcccCCeeEEEechhhh
Q 026458 151 FGLLKDGYMFETSTGLS 167 (238)
Q Consensus 151 ~G~L~~G~~~~V~~~~v 167 (238)
+|--.+=.+++-+-.++
T Consensus 140 LGs~~D~T~LEAdavLl 156 (173)
T KOG4078|consen 140 LGSKHDLTLLEADAVLL 156 (173)
T ss_pred hcCCccceEEecceeee
Confidence 55555555555554444
No 227
>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=23.16 E-value=2.3e+02 Score=18.89 Aligned_cols=49 Identities=18% Similarity=0.133 Sum_probs=29.7
Q ss_pred CEEEEEEEEe--cCceEEEEecC----CeeeeecCcccCCcccccccCcCCCCEEEEEEEe
Q 026458 76 DTVLGIVVDC--KADNFFVDIRG----PTIAFLPVLAFEGGTRRNIPKFEIGSLLYVRVVK 130 (238)
Q Consensus 76 DiVIG~V~~v--~~~~~~VdI~~----~~~a~L~~~~f~gatk~~r~~l~~GDlV~ArV~~ 130 (238)
...-|+|.++ .+..+.|.+.. ...|.++..++ .+-.|++||-|+|.+.+
T Consensus 7 N~l~g~I~~i~~~g~~~~v~l~~~~~~~l~a~i~~~~~------~~l~l~~G~~v~~~ik~ 61 (69)
T TIGR00638 7 NQLKGKVVAIEDGDVNAEVDLLLGGGTKLTAVITLESV------AELGLKPGKEVYAVIKA 61 (69)
T ss_pred cEEEEEEEEEEECCCeEEEEEEECCCCEEEEEecHHHH------hhCCCCCCCEEEEEEEC
Confidence 4567888888 44555554432 23344443222 23457899999999865
No 228
>PRK10861 signal peptidase I; Provisional
Probab=23.13 E-value=2.9e+02 Score=25.55 Aligned_cols=75 Identities=16% Similarity=0.181 Sum_probs=44.1
Q ss_pred ccccccCcCCCCEEEEEEEecCCCCcceEEEecCCCccCCCcccCCe--eEEEec----hhhhhhhcCCCCchhhHhhcc
Q 026458 111 TRRNIPKFEIGSLLYVRVVKANPGMNPELSCTDASGKAAEFGLLKDG--YMFETS----TGLSRMLLSSPTCPVLEELGK 184 (238)
Q Consensus 111 tk~~r~~l~~GDlV~ArV~~~~~~~~~~Ls~~~~~~~~~~~G~L~~G--~~~~V~----~~~v~rl~~~~~~~~l~~l~~ 184 (238)
+..|.|.|..||.|.+.=.+.+-.... ....- -..+..+-| ++|+.| ..+++|++|.++-
T Consensus 89 s~SM~PTL~~GD~IlVnK~~yg~~~p~-~~~~~-----~~~~~p~RGDIVVF~~P~~~~~~yIKRVIGlPGD-------- 154 (324)
T PRK10861 89 SGSMMPTLLIGDFILVEKFAYGIKDPI-TQTTL-----IETGHPKRGDIVVFKYPEDPKLDYIKRVVGLPGD-------- 154 (324)
T ss_pred CCcCcCcccCCCEEEEEEeecCccCcc-ccccc-----cccCCCCCCCEEEEecCCCCCCcEEEEeeecCCc--------
Confidence 457999999999999887665421111 11000 112333333 344442 2588999987765
Q ss_pred ccceEEEE-eeCCeEEEecC
Q 026458 185 QLSFEIAV-GLNGRVWVNAE 203 (238)
Q Consensus 185 ~~~~ei~v-G~NG~IWi~~~ 203 (238)
.|.+ ..||.++|++.
T Consensus 155 ----~I~~~~~~~~l~iNg~ 170 (324)
T PRK10861 155 ----KVTYDPVSKEVTIQPG 170 (324)
T ss_pred ----EEEEEeCCCEEEEcCc
Confidence 2334 35899999874
No 229
>PF14842 FliG_N: FliG N-terminal domain; PDB: 3HJL_A 3AJC_A 3USY_B.
Probab=22.94 E-value=1.4e+02 Score=22.63 Aligned_cols=32 Identities=9% Similarity=0.188 Sum_probs=23.9
Q ss_pred ChhHHHHHHHHHHHhccCCHHHHHHHHHHHHh
Q 026458 204 SPSTVVLVSNAIMNSESLSAVQQKIMVDKLLQ 235 (238)
Q Consensus 204 ~~~~~~~i~~~i~~~e~lt~~~~~~~~~~~~~ 235 (238)
++++...+.+++..+..++.++++..+++|..
T Consensus 31 ~~~ei~~i~~~ma~l~~v~~~~~~~Vl~EF~~ 62 (108)
T PF14842_consen 31 DEEEIERISREMAKLGSVSPEEVEEVLEEFYD 62 (108)
T ss_dssp -HHHHHHHHHHHHT-----HHHHHHHHHHHHH
T ss_pred CHHHHHHHHHHHHccCCCCHHHHHHHHHHHHH
Confidence 67889999999999999999999999999876
No 230
>COG2996 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only]
Probab=22.55 E-value=2.6e+02 Score=25.43 Aligned_cols=57 Identities=18% Similarity=0.039 Sum_probs=45.2
Q ss_pred cCCCCCCEEEEEEEEec-CceEEEEecCCeeeeecCcccCCccccc-ccCcCCCCEEEEEEEe
Q 026458 70 YVPCVEDTVLGIVVDCK-ADNFFVDIRGPTIAFLPVLAFEGGTRRN-IPKFEIGSLLYVRVVK 130 (238)
Q Consensus 70 Y~P~vGDiVIG~V~~v~-~~~~~VdI~~~~~a~L~~~~f~gatk~~-r~~l~~GDlV~ArV~~ 130 (238)
..-.+|+.=-++|++++ .-.+++|.+-+-+..+|.+..| .. +-..++||-++..+--
T Consensus 69 p~~tvg~~g~~~Vv~v~~~lGaFlD~Gl~KDl~vp~~elp----~~~~~wpq~Gd~l~v~l~~ 127 (287)
T COG2996 69 PKATVGEYGWLKVVEVNKDLGAFLDWGLPKDLLVPLDELP----TLKSLWPQKGDKLLVYLYV 127 (287)
T ss_pred ceEeecceeEEEEEEEcCCcceEEecCCCcceeeehhhcc----cccccCCCCCCEEEEEEEE
Confidence 45688999999999999 8899999999999999987665 22 2247788877777654
No 231
>COG2106 Uncharacterized conserved protein [Function unknown]
Probab=22.03 E-value=2.7e+02 Score=25.23 Aligned_cols=49 Identities=22% Similarity=0.240 Sum_probs=42.0
Q ss_pred CCCCCCEEEEEEEEecCceEEEEecCCeeeeecCcccCCcccccccCcCCCCEEEEEEEec
Q 026458 71 VPCVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEGGTRRNIPKFEIGSLLYVRVVKA 131 (238)
Q Consensus 71 ~P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~gatk~~r~~l~~GDlV~ArV~~~ 131 (238)
.|.+|.+=-|.|++...+...||||....+.|+-. +.+|+.|--|+.+.
T Consensus 102 ~~~~Ge~ReG~v~~~~~~~~~v~iG~~~~~~l~~~------------~~~~~RvTvri~~~ 150 (272)
T COG2106 102 SPKEGEYREGLVIRRGKKGNLVDIGKDKLAKLSSP------------APPGARVTVRIISR 150 (272)
T ss_pred CccceeecceEEEEecCCceEEEecCCcceeccCC------------CCCCceEEEEEEec
Confidence 79999999999999999999999999999998742 45777777777765
No 232
>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=21.83 E-value=3.1e+02 Score=19.62 Aligned_cols=61 Identities=15% Similarity=0.210 Sum_probs=34.9
Q ss_pred EEEEEEEec--CceEEEEecCCeeeeecCcccCCcc---cccccCcCCCCEEEEE--EEecCCCCcceEEE
Q 026458 78 VLGIVVDCK--ADNFFVDIRGPTIAFLPVLAFEGGT---RRNIPKFEIGSLLYVR--VVKANPGMNPELSC 141 (238)
Q Consensus 78 VIG~V~~v~--~~~~~VdI~~~~~a~L~~~~f~gat---k~~r~~l~~GDlV~Ar--V~~~~~~~~~~Ls~ 141 (238)
++|.|.++. +.++...+.... |.+....+.... ....+.+.+|++|+.+ +...+ +..+|.+
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 688998886 457777776532 344433332222 1356779999987544 43332 3445554
No 233
>PF01873 eIF-5_eIF-2B: Domain found in IF2B/IF5; InterPro: IPR002735 The beta subunit of archaeal and eukaryotic translation initiation factor 2 (IF2beta) and the N-terminal domain of translation initiation factor 5 (IF5) show significant sequence homology []. Archaeal IF2beta contains two independent structural domains: an N-terminal mixed alpha/beta core domain (topological similarity to the common core of ribosomal proteins L23 and L15e), and a C-terminal domain consisting of a zinc-binding C4 finger []. Archaeal IF2beta is a ribosome-dependent GTPase that stimulates the binding of initiator Met-tRNA(i)(Met) to the ribosomes, even in the absence of other factors []. The C-terminal domain of eukaryotic IF5 is involved in the formation of the multi-factor complex (MFC), an important intermediate for the 43S pre-initiation complex assembly []. IF5 interacts directly with IF1, IF2beta and IF3c, which together with IF2-bound Met-tRNA(i)(Met) form the MFC. This entry represents both the N-terminal and zinc-binding domains of IF2, as well as a domain in IF5.; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 2DCU_B 2D74_B 2E9H_A 2G2K_A 1NEE_A 3CW2_L 2QMU_C 3V11_C 2NXU_A 2QN6_C ....
Probab=21.75 E-value=89 Score=24.78 Aligned_cols=46 Identities=20% Similarity=0.133 Sum_probs=36.1
Q ss_pred eEEEechhhhhhhcCCCCchhhHhhccccceEEEEeeCCeEEEecC
Q 026458 158 YMFETSTGLSRMLLSSPTCPVLEELGKQLSFEIAVGLNGRVWVNAE 203 (238)
Q Consensus 158 ~~~~V~~~~v~rl~~~~~~~~l~~l~~~~~~ei~vG~NG~IWi~~~ 203 (238)
-.+-++..-+-..|.++..++++-|..+++..--+.-+|+.||++.
T Consensus 31 KTvi~Nf~dI~~~L~R~p~~~~ky~~~ELgt~~~id~~~~lii~G~ 76 (125)
T PF01873_consen 31 KTVIVNFVDICKALNRDPEHVLKYFGKELGTQGSIDGKGRLIINGR 76 (125)
T ss_dssp EEEETTHHHHHHHHTSSHHHHHHHHHHHSSSEEEEETTTEEEEESS
T ss_pred eeeeecHHHHHHHHCCCHHHHHHHHHHHHCCceEECCCCEEEEEEe
Confidence 3455566666666777777888888888899988888899999984
No 234
>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=21.35 E-value=2e+02 Score=19.29 Aligned_cols=64 Identities=17% Similarity=0.180 Sum_probs=32.2
Q ss_pred EEEEEEEec------C-ceEEEEecCCeeeeecCcccCCcccccccCcCCCCEEEEEEEecCCCCcceEEEe
Q 026458 78 VLGIVVDCK------A-DNFFVDIRGPTIAFLPVLAFEGGTRRNIPKFEIGSLLYVRVVKANPGMNPELSCT 142 (238)
Q Consensus 78 VIG~V~~v~------~-~~~~VdI~~~~~a~L~~~~f~gatk~~r~~l~~GDlV~ArV~~~~~~~~~~Ls~~ 142 (238)
|.|.|+++. + .++.+.+.. ..+.+...-|+..-++.++.+.+|..+...-.--...+.++|++.
T Consensus 2 i~g~v~~~~~~~~k~g~~~~~~~l~D-~tg~~~~~~f~~~~~~~~~~l~~g~~v~v~G~v~~~~~~~~l~~~ 72 (84)
T cd04485 2 VAGLVTSVRRRRTKKGKRMAFVTLED-LTGSIEVVVFPETYEKYRDLLKEDALLLVEGKVERRDGGLRLIAE 72 (84)
T ss_pred EEEEEEEeEEEEcCCCCEEEEEEEEe-CCCeEEEEECHHHHHHHHHHhcCCCEEEEEEEEEecCCceEEEee
Confidence 566665532 1 134444433 344455555543323456778899987654332212244566653
No 235
>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=21.31 E-value=68 Score=25.09 Aligned_cols=17 Identities=18% Similarity=0.853 Sum_probs=12.9
Q ss_pred ceEEEEeeCCeEEEecCChh
Q 026458 187 SFEIAVGLNGRVWVNAESPS 206 (238)
Q Consensus 187 ~~ei~vG~NG~IWi~~~~~~ 206 (238)
.++|. ||+|||.....+
T Consensus 60 H~dI~---dgKIWIq~d~TE 76 (111)
T PF08869_consen 60 HLDIK---DGKIWIQRDGTE 76 (111)
T ss_dssp EEEEE---TTEEEEEEESSS
T ss_pred EEEEE---CCeEEEEcCchh
Confidence 55664 999999886654
No 236
>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=21.23 E-value=3.2e+02 Score=19.59 Aligned_cols=56 Identities=20% Similarity=0.137 Sum_probs=36.3
Q ss_pred eeEEEechhhhhhhcCCCCchhhHhhccccceEEEEeeC-CeEEEec--CChhHHHHHHHHHHHhcc
Q 026458 157 GYMFETSTGLSRMLLSSPTCPVLEELGKQLSFEIAVGLN-GRVWVNA--ESPSTVVLVSNAIMNSES 220 (238)
Q Consensus 157 G~~~~V~~~~v~rl~~~~~~~~l~~l~~~~~~ei~vG~N-G~IWi~~--~~~~~~~~i~~~i~~~e~ 220 (238)
|+++.+.|..... +.+.|..--++||.-.-+ |++-+.. ++.+......++|+.++.
T Consensus 7 s~vV~~~p~~~~~--------v~~~l~~~~gvEVh~~~~~GKiVVtiE~~~~~~~~~~~~~i~~l~G 65 (79)
T PF03927_consen 7 SLVVHARPERLEE--------VAEALAAIPGVEVHAVDEDGKIVVTIEAESSEEEVDLIDAINALPG 65 (79)
T ss_dssp EEEEEE-CCCHHH--------HHHHHCCSTTEEEEEEETTTEEEEEEEESSHHHHHHHHHHHCCSTT
T ss_pred EEEEEECchhHHH--------HHHHHHcCCCcEEEeeCCCCeEEEEEEeCChHHHHHHHHHHHcCCC
Confidence 6778888876544 556676677999975555 9998865 445555555555555443
No 237
>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=21.19 E-value=57 Score=27.93 Aligned_cols=43 Identities=14% Similarity=0.266 Sum_probs=33.9
Q ss_pred hhhHhhccccceEEEEeeCCeEEEecCC-hhH-HHHHHHHHHHhc
Q 026458 177 PVLEELGKQLSFEIAVGLNGRVWVNAES-PST-VVLVSNAIMNSE 219 (238)
Q Consensus 177 ~~l~~l~~~~~~ei~vG~NG~IWi~~~~-~~~-~~~i~~~i~~~e 219 (238)
+||+++.++-.|++.|-.+|-+||.... .++ .+.+.+|+++.-
T Consensus 35 HML~~~a~H~~~dL~v~a~GDl~vD~HHtvEDvgI~LG~al~~aL 79 (190)
T cd07914 35 HMLTLFARHGGFDLTVKAKGDLEVDDHHTVEDVGIVLGQALKKAL 79 (190)
T ss_pred HHHHHHHHHcCCCeEEEEecCccccCCcchhhhHhhHHHHHHHHh
Confidence 5999999999999999999999998643 222 455667777654
No 238
>COG3602 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=20.70 E-value=72 Score=25.30 Aligned_cols=33 Identities=15% Similarity=0.289 Sum_probs=22.9
Q ss_pred cccccCcCCCCEEEEEEEe-c--CCCCcceEEEecC
Q 026458 112 RRNIPKFEIGSLLYVRVVK-A--NPGMNPELSCTDA 144 (238)
Q Consensus 112 k~~r~~l~~GDlV~ArV~~-~--~~~~~~~Ls~~~~ 144 (238)
..|.|.|..||.|+|.|.. + +...+|.-+.+++
T Consensus 12 ~smtPeL~~G~yVfcT~~~ga~~~~~lePla~FRE~ 47 (134)
T COG3602 12 ASMTPELLDGDYVFCTVAPGALQPKNLEPLATFRER 47 (134)
T ss_pred HhcCccccCCceEEEEecCCcCCCcCCChHhhhccc
Confidence 3588999999999999972 2 2234555555554
No 239
>COG0211 RpmA Ribosomal protein L27 [Translation, ribosomal structure and biogenesis]
Probab=20.68 E-value=2.7e+02 Score=20.78 Aligned_cols=54 Identities=11% Similarity=0.212 Sum_probs=33.6
Q ss_pred CCCcEEecCCccCCCCCCCCCceeecCcEEE-eCCEEEEEEeeEeEEec----CCeEEEEcc
Q 026458 10 LVDKIVVPGDVVLDLSSMTNQTIKLGGGLRQ-ECDSVSVIKAGKLRFSK----PNKYWVESS 66 (238)
Q Consensus 10 ~~~~iV~PGd~l~~~~~~~~~~~~~G~G~y~-~~g~i~as~~G~v~~~~----~~~i~V~~~ 66 (238)
+..+.|.+|+.|---- +-.+-+|.++=. .|..|+|.+.|.|+... .+.++|.|.
T Consensus 26 ~~Gq~v~aG~IivRQR---GTk~hpG~NVG~GkDhTlFAl~dG~Vkf~~k~~~rk~vsV~~~ 84 (87)
T COG0211 26 FGGQFVKAGSIIVRQR---GTKFHPGVNVGRGKDHTLFALVDGVVKFETKGKNRKYVSVVPE 84 (87)
T ss_pred eCCeEEecccEEEEec---cccccCCcccccCCCceEEEeeccEEEEEEccCCccEEEEEee
Confidence 4567788888774211 012445544432 47899999999997652 246777764
No 240
>PRK03988 translation initiation factor IF-2 subunit beta; Validated
Probab=20.68 E-value=2.6e+02 Score=22.56 Aligned_cols=43 Identities=16% Similarity=0.026 Sum_probs=29.5
Q ss_pred EEechhhhhhhcCCCCchhhHhhccccceEEEEeeCCeEEEecC
Q 026458 160 FETSTGLSRMLLSSPTCPVLEELGKQLSFEIAVGLNGRVWVNAE 203 (238)
Q Consensus 160 ~~V~~~~v~rl~~~~~~~~l~~l~~~~~~ei~vG~NG~IWi~~~ 203 (238)
+-++..-+-+.+.++..++++-|..+++..--+ -||+.+|++.
T Consensus 43 vi~Nf~~I~~~L~R~~~hv~ky~~~ELgt~g~i-~~~~lii~G~ 85 (138)
T PRK03988 43 IIRNFKEIADRLNRDPKHVAKFLLKELGTAGNI-EGGRLILQGK 85 (138)
T ss_pred EEecHHHHHHHHCCCHHHHHHHHHHHhCCceee-cCCEEEEEEe
Confidence 344555555556677667777777666666666 5899999984
No 241
>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=20.60 E-value=2e+02 Score=28.91 Aligned_cols=66 Identities=17% Similarity=0.159 Sum_probs=46.1
Q ss_pred EEEEEEEEec-----------CceEEEEecCCeeeeecCcccCCcccccccCcCCCCEE---EEEEEecCC-----CCcc
Q 026458 77 TVLGIVVDCK-----------ADNFFVDIRGPTIAFLPVLAFEGGTRRNIPKFEIGSLL---YVRVVKANP-----GMNP 137 (238)
Q Consensus 77 iVIG~V~~v~-----------~~~~~VdI~~~~~a~L~~~~f~gatk~~r~~l~~GDlV---~ArV~~~~~-----~~~~ 137 (238)
.+-|+|+.+. +..+.++|.. ..+.++...|.....+..+.|.+|++. .++|..+++ ..++
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 5778888755 2346666665 566677777776677788999999999 467876643 3567
Q ss_pred eEEEec
Q 026458 138 ELSCTD 143 (238)
Q Consensus 138 ~Ls~~~ 143 (238)
+|+...
T Consensus 273 ei~f~~ 278 (608)
T TIGR00617 273 EMTLDR 278 (608)
T ss_pred EEEECC
Confidence 777644
No 242
>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=20.47 E-value=3.2e+02 Score=19.24 Aligned_cols=62 Identities=19% Similarity=0.251 Sum_probs=34.7
Q ss_pred EEEEEEEe--cCceEEEEecCCeeeeecCcccCCcccccccCcCCCCEE--EEEEEecCCCCcceEEEe
Q 026458 78 VLGIVVDC--KADNFFVDIRGPTIAFLPVLAFEGGTRRNIPKFEIGSLL--YVRVVKANPGMNPELSCT 142 (238)
Q Consensus 78 VIG~V~~v--~~~~~~VdI~~~~~a~L~~~~f~gatk~~r~~l~~GDlV--~ArV~~~~~~~~~~Ls~~ 142 (238)
|-|.|++. .+..+...+.. ..|.++.-.|.+...+....+++||.| ++++.. +.+.++|...
T Consensus 3 v~GeVs~~~~~~GHvyfsLkD-~~a~i~cv~f~~~~~~~~~~l~~Gd~V~v~G~v~~--~~G~~ql~v~ 68 (73)
T cd04487 3 IEGEVVQIKQTSGPTIFTLRD-ETGTVWAAAFEEAGVRAYPEVEVGDIVRVTGEVEP--RDGQLQIEVE 68 (73)
T ss_pred EEEEEeccccCCCCEEEEEEc-CCEEEEEEEEchhccCCcCCCCCCCEEEEEEEEec--CCeEEEEEEe
Confidence 44555543 22235555533 335566555654444566778999965 455553 5566777654
No 243
>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=20.13 E-value=2.6e+02 Score=21.55 Aligned_cols=44 Identities=14% Similarity=0.194 Sum_probs=31.3
Q ss_pred CCCCEEEEEEEEe--cCceEEEEecCCeeeeecCcccCCcccccccCcCCCCEE
Q 026458 73 CVEDTVLGIVVDC--KADNFFVDIRGPTIAFLPVLAFEGGTRRNIPKFEIGSLL 124 (238)
Q Consensus 73 ~vGDiVIG~V~~v--~~~~~~VdI~~~~~a~L~~~~f~gatk~~r~~l~~GDlV 124 (238)
..|-...|+|++. -+..|.+++++..--+.+ +.....+++||=|
T Consensus 53 N~G~ei~GkVt~K~~ig~~yTvti~~YGkFlVt--------keqY~~i~iGDdi 98 (104)
T PF07116_consen 53 NAGAEIFGKVTEKEIIGGLYTVTIGAYGKFLVT--------KEQYESIKIGDDI 98 (104)
T ss_pred CCCcEEEEEEeeceeECCEEEEEecCceEEEEe--------hhhcceeecCCcc
Confidence 5688899999986 689999999985444443 4444566777743
No 244
>PTZ00400 DnaK-type molecular chaperone; Provisional
Probab=20.06 E-value=2.1e+02 Score=28.89 Aligned_cols=38 Identities=21% Similarity=0.387 Sum_probs=27.8
Q ss_pred hhhhhcCCCCc-hhhHhhccccceEEEEeeCCeEEEecC
Q 026458 166 LSRMLLSSPTC-PVLEELGKQLSFEIAVGLNGRVWVNAE 203 (238)
Q Consensus 166 ~v~rl~~~~~~-~~l~~l~~~~~~ei~vG~NG~IWi~~~ 203 (238)
.++|++|++.. ..+....+..+|++.-+.||.+|+...
T Consensus 107 ~~KrliG~~~~d~~~~~~~~~~p~~~~~~~~~~~~~~~~ 145 (663)
T PTZ00400 107 ATKRLIGRRYDEDATKKEQKILPYKIVRASNGDAWIEAQ 145 (663)
T ss_pred hhhhhcCCCcCcHHHHhhhccCCeEEEecCCCceEEEEC
Confidence 57899987532 234444567899999999999998764
Done!