Query 029155
Match_columns 198
No_of_seqs 176 out of 909
Neff 6.9
Searched_HMMs 46136
Date Fri Mar 29 08:22:46 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/029155.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/029155hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG1096 Predicted RNA-binding 100.0 1.5E-51 3.2E-56 330.3 19.9 177 6-196 3-182 (188)
2 KOG3409 Exosomal 3'-5' exoribo 100.0 1.7E-50 3.6E-55 319.1 16.6 185 7-197 4-190 (193)
3 PRK09521 exosome complex RNA-b 100.0 1.5E-49 3.2E-54 324.7 21.9 177 7-196 4-183 (189)
4 PRK04163 exosome complex RNA-b 100.0 1.5E-31 3.3E-36 225.2 17.1 137 6-163 6-144 (235)
5 COG1097 RRP4 RNA-binding prote 100.0 3.2E-30 6.9E-35 214.6 16.5 140 4-163 4-145 (239)
6 KOG3013 Exosomal 3'-5' exoribo 100.0 3.1E-29 6.8E-34 209.3 5.2 145 5-164 26-173 (301)
7 cd05791 S1_CSL4 S1_CSL4: CSL4, 100.0 2.8E-28 6.2E-33 177.9 9.7 91 72-162 2-92 (92)
8 PF10447 EXOSC1: Exosome compo 99.9 9.9E-23 2.1E-27 145.3 8.0 72 73-144 1-82 (82)
9 cd04454 S1_Rrp4_like S1_Rrp4_l 99.8 7.1E-19 1.5E-23 124.9 9.9 82 71-162 1-82 (82)
10 cd05789 S1_Rrp4 S1_Rrp4: Rrp4 99.7 2.3E-16 4.9E-21 112.8 9.2 84 71-162 1-86 (86)
11 cd05790 S1_Rrp40 S1_Rrp40: Rrp 99.6 2E-15 4.4E-20 108.6 9.7 76 71-157 1-76 (86)
12 KOG1004 Exosomal 3'-5' exoribo 99.5 5.2E-13 1.1E-17 109.4 13.2 145 9-176 2-154 (230)
13 PF14382 ECR1_N: Exosome compl 99.4 8.8E-14 1.9E-18 85.8 3.6 37 10-48 1-37 (39)
14 COG1098 VacB Predicted RNA bin 99.4 4.1E-13 8.8E-18 101.7 5.5 75 74-158 3-77 (129)
15 cd05704 S1_Rrp5_repeat_hs13 S1 99.4 2.2E-12 4.7E-17 89.7 8.4 70 75-155 2-72 (72)
16 cd05687 S1_RPS1_repeat_ec1_hs1 99.3 2.8E-11 6E-16 82.9 8.7 69 77-155 1-70 (70)
17 cd05706 S1_Rrp5_repeat_sc10 S1 99.2 1.1E-10 2.5E-15 80.5 9.9 71 75-155 2-73 (73)
18 cd05705 S1_Rrp5_repeat_hs14 S1 99.2 7.7E-11 1.7E-15 82.4 8.0 71 75-153 2-74 (74)
19 cd05691 S1_RPS1_repeat_ec6 S1_ 99.2 1.6E-10 3.5E-15 79.3 9.2 72 77-158 1-73 (73)
20 cd04452 S1_IF2_alpha S1_IF2_al 99.2 2.4E-10 5.1E-15 79.2 9.1 74 74-155 1-75 (76)
21 PRK08582 hypothetical protein; 99.2 4E-10 8.7E-15 88.0 10.7 75 74-158 3-77 (139)
22 cd05703 S1_Rrp5_repeat_hs12_sc 99.1 3.8E-10 8.2E-15 78.6 8.8 71 77-155 1-72 (73)
23 cd05693 S1_Rrp5_repeat_hs1_sc1 99.1 1.9E-10 4.1E-15 85.1 7.4 76 74-157 1-97 (100)
24 cd05692 S1_RPS1_repeat_hs4 S1_ 99.1 5.7E-10 1.2E-14 75.1 9.1 69 77-155 1-69 (69)
25 PF00575 S1: S1 RNA binding do 99.1 7.2E-10 1.6E-14 76.5 9.3 72 74-155 2-74 (74)
26 cd05702 S1_Rrp5_repeat_hs11_sc 99.1 4.3E-10 9.3E-15 77.3 7.8 65 77-149 1-65 (70)
27 cd05686 S1_pNO40 S1_pNO40: pNO 99.1 1.1E-09 2.4E-14 76.0 9.2 72 74-154 1-72 (73)
28 cd05707 S1_Rrp5_repeat_sc11 S1 99.1 5.9E-10 1.3E-14 76.0 7.7 67 77-153 1-68 (68)
29 cd05708 S1_Rrp5_repeat_sc12 S1 99.1 1.2E-09 2.7E-14 75.5 9.1 74 75-157 1-75 (77)
30 PTZ00248 eukaryotic translatio 99.0 9.9E-10 2.1E-14 96.2 9.1 77 72-157 13-91 (319)
31 PRK07252 hypothetical protein; 99.0 2.3E-09 4.9E-14 81.8 9.9 73 75-157 2-75 (120)
32 cd05698 S1_Rrp5_repeat_hs6_sc5 99.0 2.2E-09 4.8E-14 73.3 8.6 69 77-155 1-70 (70)
33 PRK05807 hypothetical protein; 99.0 3.6E-09 7.8E-14 82.4 10.5 73 74-157 3-75 (136)
34 smart00316 S1 Ribosomal protei 99.0 3.5E-09 7.7E-14 71.0 8.6 71 75-155 1-72 (72)
35 PRK08059 general stress protei 99.0 4.7E-09 1E-13 80.3 9.9 76 74-159 5-81 (123)
36 PRK03987 translation initiatio 98.9 4.5E-09 9.8E-14 90.1 9.6 78 72-157 4-82 (262)
37 cd05697 S1_Rrp5_repeat_hs5 S1_ 98.9 6.1E-09 1.3E-13 71.1 8.2 68 77-154 1-69 (69)
38 cd05696 S1_Rrp5_repeat_hs4 S1_ 98.9 6.8E-09 1.5E-13 71.8 8.4 68 77-154 1-71 (71)
39 cd04461 S1_Rrp5_repeat_hs8_sc7 98.9 7.6E-09 1.6E-13 73.3 8.5 72 73-154 11-83 (83)
40 COG0539 RpsA Ribosomal protein 98.9 3.7E-09 8E-14 98.1 8.5 75 73-158 189-264 (541)
41 cd05694 S1_Rrp5_repeat_hs2_sc2 98.9 2.7E-08 5.9E-13 69.5 9.6 68 74-157 2-71 (74)
42 cd05695 S1_Rrp5_repeat_hs3 S1_ 98.9 1.8E-08 3.9E-13 68.7 8.1 65 77-153 1-66 (66)
43 cd05688 S1_RPS1_repeat_ec3 S1_ 98.8 1.4E-08 3E-13 68.3 7.3 67 76-153 1-68 (68)
44 cd04472 S1_PNPase S1_PNPase: P 98.8 2.7E-08 5.9E-13 67.0 8.6 68 77-154 1-68 (68)
45 cd05685 S1_Tex S1_Tex: The C-t 98.8 1.8E-08 3.9E-13 67.5 7.2 67 77-153 1-68 (68)
46 cd04453 S1_RNase_E S1_RNase_E: 98.8 4E-08 8.8E-13 70.9 9.0 74 74-155 5-82 (88)
47 PHA02945 interferon resistance 98.7 8.6E-08 1.9E-12 68.7 8.9 73 72-156 7-83 (88)
48 PRK11824 polynucleotide phosph 98.7 1.4E-08 3.1E-13 97.5 5.8 100 33-156 592-691 (693)
49 COG1093 SUI2 Translation initi 98.7 2.9E-08 6.2E-13 84.2 6.3 78 71-156 6-84 (269)
50 PRK08563 DNA-directed RNA poly 98.7 1.8E-07 3.9E-12 76.2 10.8 83 72-163 77-174 (187)
51 PRK07400 30S ribosomal protein 98.7 9.3E-08 2E-12 84.1 9.7 76 72-158 192-268 (318)
52 cd05684 S1_DHX8_helicase S1_DH 98.7 1.8E-07 4E-12 65.5 9.1 72 77-156 1-73 (79)
53 cd05690 S1_RPS1_repeat_ec5 S1_ 98.7 9.1E-08 2E-12 64.9 7.1 66 77-152 1-68 (69)
54 cd04460 S1_RpoE S1_RpoE: RpoE, 98.6 1.5E-07 3.2E-12 69.0 7.9 77 78-163 1-92 (99)
55 TIGR00448 rpoE DNA-directed RN 98.6 1.8E-07 4E-12 75.7 8.8 84 71-163 76-174 (179)
56 TIGR02696 pppGpp_PNP guanosine 98.6 1.4E-07 3E-12 90.4 9.0 71 73-153 644-718 (719)
57 cd00164 S1_like S1_like: Ribos 98.6 2.7E-07 5.9E-12 60.5 6.5 64 80-153 1-65 (65)
58 cd05689 S1_RPS1_repeat_ec4 S1_ 98.5 6.3E-07 1.4E-11 61.4 8.3 69 75-152 2-71 (72)
59 PRK07400 30S ribosomal protein 98.5 4.3E-07 9.3E-12 79.9 8.7 76 72-157 27-103 (318)
60 PRK13806 rpsA 30S ribosomal pr 98.5 4.3E-07 9.4E-12 84.2 9.1 74 74-157 377-451 (491)
61 cd04465 S1_RPS1_repeat_ec2_hs2 98.5 1.3E-06 2.7E-11 59.3 8.4 66 77-155 1-67 (67)
62 cd04455 S1_NusA S1_NusA: N-uti 98.5 1.4E-06 3E-11 59.4 8.4 62 75-153 2-66 (67)
63 cd04473 S1_RecJ_like S1_RecJ_l 98.5 3.6E-06 7.8E-11 58.9 10.7 63 74-154 14-76 (77)
64 COG0539 RpsA Ribosomal protein 98.5 5.3E-07 1.1E-11 84.0 7.9 74 74-157 275-349 (541)
65 TIGR03591 polynuc_phos polyrib 98.5 5.2E-07 1.1E-11 86.8 8.1 91 38-150 592-682 (684)
66 PLN00207 polyribonucleotide nu 98.4 8.2E-07 1.8E-11 86.9 8.9 74 73-156 750-824 (891)
67 PRK13806 rpsA 30S ribosomal pr 98.4 9.2E-07 2E-11 82.0 8.8 75 73-157 199-278 (491)
68 COG1095 RPB7 DNA-directed RNA 98.4 7.7E-07 1.7E-11 72.1 7.2 83 72-163 77-174 (183)
69 PRK07899 rpsA 30S ribosomal pr 98.4 1.1E-06 2.5E-11 81.3 9.1 73 74-157 206-279 (486)
70 PRK12269 bifunctional cytidyla 98.4 1.1E-06 2.3E-11 86.4 8.6 74 74-156 576-650 (863)
71 PRK07899 rpsA 30S ribosomal pr 98.4 1.7E-06 3.8E-11 80.1 9.1 74 74-157 33-107 (486)
72 PRK06299 rpsA 30S ribosomal pr 98.4 1.7E-06 3.8E-11 81.2 8.9 74 74-157 458-532 (565)
73 PRK06676 rpsA 30S ribosomal pr 98.3 3.2E-06 6.9E-11 75.9 9.2 73 74-157 190-263 (390)
74 PRK06676 rpsA 30S ribosomal pr 98.3 4.1E-06 8.8E-11 75.2 9.7 75 74-158 275-350 (390)
75 PRK06299 rpsA 30S ribosomal pr 98.3 3.9E-06 8.5E-11 78.8 9.6 73 73-156 198-271 (565)
76 cd04471 S1_RNase_R S1_RNase_R: 98.2 1.1E-05 2.4E-10 56.3 8.9 71 76-154 1-82 (83)
77 TIGR00717 rpsA ribosomal prote 98.2 6.2E-06 1.4E-10 76.5 9.0 72 74-155 444-516 (516)
78 PRK00087 4-hydroxy-3-methylbut 98.2 7.6E-06 1.7E-10 78.3 9.8 75 74-158 560-635 (647)
79 PRK12269 bifunctional cytidyla 98.2 7.7E-06 1.7E-10 80.4 9.3 74 74-156 663-737 (863)
80 COG2183 Tex Transcriptional ac 98.1 8.3E-06 1.8E-10 78.4 7.3 77 73-159 655-732 (780)
81 PTZ00162 DNA-directed RNA poly 98.1 2E-05 4.4E-10 63.9 8.4 86 71-165 76-174 (176)
82 TIGR00717 rpsA ribosomal prote 98.1 1.9E-05 4.1E-10 73.3 9.1 73 73-156 184-257 (516)
83 PRK00087 4-hydroxy-3-methylbut 98.0 3.2E-05 6.8E-10 74.1 9.4 77 72-158 298-375 (647)
84 COG1185 Pnp Polyribonucleotide 97.8 5.2E-05 1.1E-09 72.0 7.1 75 73-157 616-690 (692)
85 PRK09202 nusA transcription el 97.7 8.2E-05 1.8E-09 68.8 7.2 71 72-159 130-203 (470)
86 PRK12327 nusA transcription el 97.6 0.0002 4.3E-09 64.2 7.1 72 71-159 129-203 (362)
87 TIGR01953 NusA transcription t 97.5 0.00025 5.3E-09 63.2 7.2 72 71-159 126-201 (341)
88 cd04462 S1_RNAPII_Rpb7 S1_RNAP 97.5 0.00097 2.1E-08 48.1 8.8 74 76-160 1-88 (88)
89 PHA02858 EIF2a-like PKR inhibi 97.4 0.00091 2E-08 47.7 7.1 73 71-154 11-85 (86)
90 TIGR00757 RNaseEG ribonuclease 97.2 0.0024 5.2E-08 58.3 9.7 74 74-155 23-109 (414)
91 TIGR02063 RNase_R ribonuclease 97.0 0.003 6.6E-08 61.2 9.1 74 73-154 624-708 (709)
92 PRK11642 exoribonuclease R; Pr 96.8 0.0068 1.5E-07 59.7 9.4 74 74-155 641-725 (813)
93 PRK12328 nusA transcription el 96.7 0.0044 9.6E-08 55.7 6.6 72 71-159 133-209 (374)
94 KOG1070 rRNA processing protei 96.7 0.0085 1.8E-07 61.2 9.1 76 74-159 1160-1236(1710)
95 PRK12329 nusA transcription el 96.6 0.0063 1.4E-07 55.8 6.9 77 71-159 147-228 (449)
96 KOG1070 rRNA processing protei 96.5 0.0036 7.7E-08 63.8 5.2 77 70-154 879-955 (1710)
97 TIGR00358 3_prime_RNase VacB a 96.5 0.015 3.2E-07 56.0 9.0 73 74-154 570-653 (654)
98 cd05699 S1_Rrp5_repeat_hs7 S1_ 96.4 0.017 3.7E-07 40.2 6.6 70 77-154 1-71 (72)
99 KOG1067 Predicted RNA-binding 96.2 0.0093 2E-07 56.1 5.5 74 73-156 660-738 (760)
100 COG2996 Predicted RNA-bindinin 95.9 0.033 7.1E-07 48.0 7.4 63 77-157 156-218 (287)
101 KOG1856 Transcription elongati 95.9 0.012 2.6E-07 59.1 5.0 81 73-160 982-1063(1299)
102 PF07754 DUF1610: Domain of un 95.7 0.007 1.5E-07 33.3 1.5 21 167-187 3-24 (24)
103 KOG2916 Translation initiation 95.4 0.016 3.5E-07 49.7 3.4 77 72-156 12-89 (304)
104 PRK11712 ribonuclease G; Provi 95.1 0.089 1.9E-06 49.1 7.9 73 74-154 36-121 (489)
105 PRK10811 rne ribonuclease E; R 95.0 0.095 2E-06 52.3 8.1 74 74-155 36-119 (1068)
106 PF09297 zf-NADH-PPase: NADH p 94.5 0.044 9.5E-07 31.9 2.8 25 165-189 5-31 (32)
107 PF01016 Ribosomal_L27: Riboso 94.4 0.077 1.7E-06 37.7 4.2 47 3-50 22-70 (81)
108 TIGR01384 TFS_arch transcripti 94.2 0.027 5.8E-07 41.4 1.7 29 165-194 2-31 (104)
109 COG1571 Predicted DNA-binding 93.4 0.19 4.2E-06 45.9 6.1 61 126-190 311-378 (421)
110 PF13509 S1_2: S1 domain; PDB: 93.3 0.84 1.8E-05 30.3 7.6 60 76-154 1-60 (61)
111 PRK05435 rpmA 50S ribosomal pr 93.1 0.24 5.1E-06 35.3 4.8 46 3-49 23-70 (82)
112 PRK14890 putative Zn-ribbon RN 93.0 0.083 1.8E-06 35.3 2.2 30 165-194 9-40 (59)
113 CHL00121 rpl27 ribosomal prote 93.0 0.19 4.2E-06 36.0 4.2 59 3-67 23-84 (86)
114 smart00661 RPOL9 RNA polymeras 92.9 0.096 2.1E-06 33.3 2.4 26 165-190 2-31 (52)
115 COG1645 Uncharacterized Zn-fin 92.1 0.13 2.8E-06 39.8 2.6 29 161-190 25-55 (131)
116 KOG3298 DNA-directed RNA polym 91.8 0.96 2.1E-05 36.3 7.3 85 72-162 77-170 (170)
117 PF09723 Zn-ribbon_8: Zinc rib 91.5 0.19 4E-06 31.1 2.4 29 165-193 7-40 (42)
118 smart00659 RPOLCX RNA polymera 91.0 0.36 7.8E-06 30.3 3.4 30 164-193 3-33 (44)
119 PRK05054 exoribonuclease II; P 90.7 1.6 3.4E-05 42.2 9.1 72 75-153 558-642 (644)
120 PF02150 RNA_POL_M_15KD: RNA p 90.7 0.35 7.7E-06 28.8 3.0 26 165-190 3-31 (35)
121 PRK00398 rpoP DNA-directed RNA 90.6 0.53 1.2E-05 29.4 3.9 33 163-195 3-37 (46)
122 PRK00420 hypothetical protein; 89.8 0.26 5.6E-06 37.2 2.3 27 164-190 24-51 (112)
123 smart00834 CxxC_CXXC_SSSS Puta 89.6 0.34 7.3E-06 29.1 2.4 28 165-193 7-39 (41)
124 KOG4600 Mitochondrial ribosoma 88.8 1.2 2.6E-05 34.6 5.4 62 3-68 50-114 (144)
125 TIGR00062 L27 ribosomal protei 88.6 0.87 1.9E-05 32.5 4.1 45 3-49 23-70 (83)
126 COG2888 Predicted Zn-ribbon RN 88.1 0.39 8.5E-06 32.1 2.0 31 163-193 9-41 (61)
127 TIGR02605 CxxC_CxxC_SSSS putat 87.4 0.52 1.1E-05 30.0 2.3 32 165-196 7-44 (52)
128 PF08792 A2L_zn_ribbon: A2L zi 87.4 0.87 1.9E-05 26.8 3.0 26 165-190 5-32 (33)
129 COG0557 VacB Exoribonuclease R 87.3 3.2 7E-05 40.5 8.6 74 75-155 621-704 (706)
130 COG1530 CafA Ribonucleases G a 87.3 1.3 2.8E-05 41.4 5.7 74 74-155 35-113 (487)
131 COG1545 Predicted nucleic-acid 87.3 0.64 1.4E-05 36.3 3.1 34 159-195 25-62 (140)
132 PF07282 OrfB_Zn_ribbon: Putat 87.2 0.45 9.8E-06 32.0 2.0 28 165-192 30-59 (69)
133 PF09538 FYDLN_acid: Protein o 87.0 0.32 7E-06 36.4 1.3 37 155-192 2-39 (108)
134 PRK07218 replication factor A; 86.3 2.8 6.1E-05 38.6 7.2 41 136-193 282-323 (423)
135 PRK00432 30S ribosomal protein 86.3 0.91 2E-05 29.2 2.9 28 163-191 20-49 (50)
136 COG1656 Uncharacterized conser 84.7 0.33 7.1E-06 39.0 0.3 28 161-188 95-139 (165)
137 PF06677 Auto_anti-p27: Sjogre 84.6 0.88 1.9E-05 28.1 2.2 24 163-186 17-41 (41)
138 PF03604 DNA_RNApol_7kD: DNA d 83.4 0.63 1.4E-05 27.2 1.1 28 165-192 2-30 (32)
139 PF01927 Mut7-C: Mut7-C RNAse 83.0 0.74 1.6E-05 35.9 1.7 32 158-189 86-134 (147)
140 TIGR02062 RNase_B exoribonucle 82.9 7.2 0.00016 37.7 8.6 65 75-146 554-630 (639)
141 PF08292 RNA_pol_Rbc25: RNA po 82.4 7.4 0.00016 29.7 6.9 70 74-144 1-74 (122)
142 PF01959 DHQS: 3-dehydroquinat 82.4 15 0.00033 33.1 9.8 96 10-146 246-341 (354)
143 PF14803 Nudix_N_2: Nudix N-te 82.3 1.1 2.3E-05 26.6 1.8 24 165-188 2-31 (34)
144 PRK03681 hypA hydrogenase nick 82.3 1.1 2.3E-05 33.8 2.2 32 162-193 69-101 (114)
145 PRK00564 hypA hydrogenase nick 81.6 0.81 1.8E-05 34.6 1.4 30 162-191 70-100 (117)
146 TIGR02300 FYDLN_acid conserved 81.2 0.75 1.6E-05 35.4 1.1 36 155-191 2-38 (129)
147 PRK02290 3-dehydroquinate synt 81.1 17 0.00036 32.7 9.6 95 10-145 236-330 (344)
148 COG2816 NPY1 NTP pyrophosphohy 81.0 0.94 2E-05 39.4 1.7 25 165-189 113-139 (279)
149 PTZ00248 eukaryotic translatio 80.7 2.5 5.5E-05 37.4 4.4 101 14-146 18-118 (319)
150 PF14446 Prok-RING_1: Prokaryo 80.0 0.99 2.1E-05 29.7 1.2 30 164-194 6-36 (54)
151 PHA02942 putative transposase; 79.7 1.3 2.7E-05 40.2 2.2 28 165-192 327-355 (383)
152 PRK08402 replication factor A; 78.5 22 0.00048 32.0 9.7 29 160-188 209-239 (355)
153 PF07497 Rho_RNA_bind: Rho ter 78.0 4 8.7E-05 28.8 3.9 42 61-102 30-74 (78)
154 COG1594 RPB9 DNA-directed RNA 77.6 1.9 4.2E-05 32.4 2.3 24 167-190 7-33 (113)
155 COG1996 RPC10 DNA-directed RNA 77.3 2.1 4.5E-05 27.6 2.0 29 163-191 6-36 (49)
156 PF13240 zinc_ribbon_2: zinc-r 76.7 0.76 1.6E-05 24.8 -0.1 20 166-188 2-22 (23)
157 PF01155 HypA: Hydrogenase exp 76.0 1.2 2.6E-05 33.4 0.8 29 162-191 69-98 (113)
158 KOG4134 DNA-dependent RNA poly 76.0 2.5 5.5E-05 35.7 2.8 61 72-147 103-163 (253)
159 PF10122 Mu-like_Com: Mu-like 75.6 2 4.3E-05 27.9 1.6 32 165-196 6-41 (51)
160 PRK11032 hypothetical protein; 75.5 2.2 4.8E-05 34.1 2.2 30 165-194 126-157 (160)
161 TIGR00100 hypA hydrogenase nic 75.0 2.1 4.6E-05 32.2 1.9 29 162-191 69-98 (115)
162 PRK12380 hydrogenase nickel in 74.8 2.1 4.7E-05 32.0 1.9 27 162-189 69-96 (113)
163 COG0211 RpmA Ribosomal protein 74.5 6.7 0.00015 28.0 4.2 60 3-67 23-84 (87)
164 PF10080 DUF2318: Predicted me 74.4 5.9 0.00013 29.3 4.1 36 155-190 27-63 (102)
165 PF07295 DUF1451: Protein of u 74.2 2.5 5.5E-05 33.3 2.2 30 165-194 114-145 (146)
166 TIGR01031 rpmF_bact ribosomal 73.9 2.6 5.6E-05 27.7 1.9 26 164-193 27-53 (55)
167 PF12172 DUF35_N: Rubredoxin-l 72.8 3.1 6.8E-05 24.6 1.9 27 160-189 8-35 (37)
168 COG0375 HybF Zn finger protein 72.6 2.9 6.3E-05 31.7 2.1 32 162-194 69-101 (115)
169 PRK06386 replication factor A; 72.6 31 0.00066 31.2 9.0 40 135-191 220-260 (358)
170 PF15616 TerY-C: TerY-C metal 72.2 4.9 0.00011 31.1 3.3 27 163-189 89-115 (131)
171 PF08274 PhnA_Zn_Ribbon: PhnA 72.1 2.5 5.5E-05 24.3 1.3 24 164-187 3-27 (30)
172 PRK03824 hypA hydrogenase nick 71.7 3.1 6.7E-05 32.2 2.2 30 162-191 69-119 (135)
173 PRK12286 rpmF 50S ribosomal pr 70.9 3.1 6.7E-05 27.5 1.7 27 164-194 28-55 (57)
174 PF10246 MRP-S35: Mitochondria 68.7 39 0.00085 25.1 7.3 53 75-144 22-74 (104)
175 PF13248 zf-ribbon_3: zinc-rib 68.5 2 4.4E-05 23.6 0.4 21 165-188 4-25 (26)
176 PF03966 Trm112p: Trm112p-like 68.4 7.3 0.00016 26.3 3.2 17 174-190 48-64 (68)
177 KOG3507 DNA-directed RNA polym 68.1 3.7 8E-05 27.4 1.6 28 161-188 18-46 (62)
178 PF01783 Ribosomal_L32p: Ribos 66.4 1.7 3.7E-05 28.5 -0.2 27 164-194 27-54 (56)
179 cd05790 S1_Rrp40 S1_Rrp40: Rrp 65.6 7.3 0.00016 27.9 2.9 29 71-100 47-75 (86)
180 PRK12366 replication factor A; 65.5 9.2 0.0002 37.0 4.4 29 162-191 531-560 (637)
181 COG0675 Transposase and inacti 65.5 4.1 8.8E-05 34.7 1.9 21 167-191 314-334 (364)
182 COG1107 Archaea-specific RecJ- 64.4 19 0.00041 34.7 6.1 68 71-154 117-185 (715)
183 PF08271 TF_Zn_Ribbon: TFIIB z 64.3 6.5 0.00014 24.0 2.2 26 165-190 2-30 (43)
184 cd05706 S1_Rrp5_repeat_sc10 S1 64.3 30 0.00064 22.9 5.7 19 72-90 46-64 (73)
185 cd04454 S1_Rrp4_like S1_Rrp4_l 64.2 16 0.00035 25.0 4.5 34 132-166 5-38 (82)
186 TIGR00686 phnA alkylphosphonat 63.8 5.3 0.00012 29.9 1.9 24 165-188 4-28 (109)
187 TIGR00767 rho transcription te 63.2 7.2 0.00016 35.8 3.1 129 23-171 48-182 (415)
188 PRK00241 nudC NADH pyrophospha 63.1 6.2 0.00013 33.7 2.5 30 163-192 99-130 (256)
189 PF04085 MreC: rod shape-deter 61.8 28 0.00061 27.1 5.9 60 80-139 36-102 (152)
190 KOG3297 DNA-directed RNA polym 61.8 66 0.0014 26.5 8.0 69 74-144 79-156 (202)
191 PF09953 DUF2187: Uncharacteri 61.7 21 0.00046 23.7 4.3 20 80-99 16-35 (57)
192 cd04476 RPA1_DBD_C RPA1_DBD_C: 59.9 21 0.00045 28.0 4.9 41 136-188 19-60 (166)
193 PF14319 Zn_Tnp_IS91: Transpos 59.6 5 0.00011 30.0 1.2 38 155-192 34-73 (111)
194 PRK09521 exosome complex RNA-b 59.6 14 0.00031 29.8 4.0 24 72-96 117-140 (189)
195 PF08646 Rep_fac-A_C: Replicat 58.7 25 0.00055 26.9 5.1 40 137-188 4-46 (146)
196 cd05791 S1_CSL4 S1_CSL4: CSL4, 58.7 25 0.00055 25.1 4.7 22 132-154 5-26 (92)
197 KOG1999 RNA polymerase II tran 58.2 94 0.002 31.7 9.8 113 72-194 406-549 (1024)
198 smart00293 PWWP domain with co 57.1 7.4 0.00016 25.8 1.6 14 131-144 1-14 (63)
199 PF10447 EXOSC1: Exosome compo 56.5 19 0.00041 25.5 3.7 15 132-146 3-17 (82)
200 COG1110 Reverse gyrase [DNA re 55.6 15 0.00033 37.6 4.0 53 132-189 653-718 (1187)
201 TIGR02098 MJ0042_CXXC MJ0042 f 55.4 14 0.0003 21.7 2.4 25 164-188 3-34 (38)
202 cd05705 S1_Rrp5_repeat_hs14 S1 55.3 30 0.00065 23.5 4.5 32 131-163 1-32 (74)
203 PRK13922 rod shape-determining 55.1 53 0.0011 27.9 7.0 91 38-138 120-222 (276)
204 PRK14892 putative transcriptio 53.7 19 0.00042 26.4 3.5 32 164-195 22-58 (99)
205 cd05789 S1_Rrp4 S1_Rrp4: Rrp4 53.7 30 0.00065 23.8 4.4 32 131-163 4-35 (86)
206 KOG1088 Uncharacterized conser 53.5 8.9 0.00019 29.2 1.7 13 178-190 97-109 (124)
207 PF08772 NOB1_Zn_bind: Nin one 53.4 6.3 0.00014 27.4 0.8 29 165-195 11-40 (73)
208 PRK10220 hypothetical protein; 53.3 12 0.00026 28.1 2.3 25 164-188 4-29 (111)
209 cd05704 S1_Rrp5_repeat_hs13 S1 53.1 34 0.00074 22.9 4.4 32 131-162 1-32 (72)
210 TIGR01206 lysW lysine biosynth 52.9 15 0.00033 24.0 2.5 25 164-188 3-31 (54)
211 PF08810 KapB: Kinase associat 52.1 25 0.00054 26.5 3.8 30 80-113 6-35 (112)
212 COG4416 Com Mu-like prophage p 52.0 4.4 9.5E-05 26.6 -0.2 27 165-191 6-36 (60)
213 COG0333 RpmF Ribosomal protein 52.0 12 0.00027 24.8 2.0 29 163-195 27-56 (57)
214 PF11781 RRN7: RNA polymerase 51.1 16 0.00035 21.7 2.2 23 166-188 11-34 (36)
215 TIGR02443 conserved hypothetic 50.9 15 0.00033 24.5 2.2 31 164-194 10-46 (59)
216 PF13597 NRDD: Anaerobic ribon 50.6 13 0.00028 35.3 2.6 29 163-195 491-520 (546)
217 PF09082 DUF1922: Domain of un 50.3 28 0.00061 23.9 3.5 26 164-190 4-30 (68)
218 cd05840 SPBC215_ISWI_like The 50.1 10 0.00023 27.3 1.5 14 131-144 1-14 (93)
219 PF12773 DZR: Double zinc ribb 49.6 6 0.00013 24.7 0.2 25 164-188 13-38 (50)
220 TIGR00515 accD acetyl-CoA carb 49.1 4.6 9.9E-05 35.2 -0.6 29 162-190 25-56 (285)
221 PTZ00329 eukaryotic translatio 48.9 30 0.00066 27.6 4.1 64 8-97 24-92 (155)
222 cd05836 N_Pac_NP60 The PWWP do 48.9 11 0.00024 26.7 1.5 14 131-144 1-14 (86)
223 PRK01110 rpmF 50S ribosomal pr 48.8 18 0.00038 24.1 2.3 29 163-196 27-56 (60)
224 COG0777 AccD Acetyl-CoA carbox 48.6 8.4 0.00018 33.6 1.0 28 162-189 27-57 (294)
225 PRK07217 replication factor A; 48.1 25 0.00054 31.1 3.8 38 137-191 174-214 (311)
226 COG1158 Rho Transcription term 47.6 27 0.00058 31.7 3.9 44 60-103 80-126 (422)
227 cd00350 rubredoxin_like Rubred 47.6 12 0.00027 21.6 1.3 23 165-188 3-26 (33)
228 TIGR00219 mreC rod shape-deter 47.3 77 0.0017 27.5 6.8 60 79-138 156-223 (283)
229 cd05834 HDGF_related The PWWP 47.3 13 0.00028 26.2 1.6 15 130-144 2-16 (83)
230 PF10571 UPF0547: Uncharacteri 47.2 8.3 0.00018 21.3 0.5 19 167-188 5-23 (26)
231 TIGR00739 yajC preprotein tran 46.1 47 0.001 23.5 4.4 23 74-96 38-66 (84)
232 PF03961 DUF342: Protein of un 45.4 49 0.0011 30.4 5.5 36 22-66 144-180 (451)
233 PF13717 zinc_ribbon_4: zinc-r 44.9 15 0.00032 21.8 1.4 17 172-188 18-34 (36)
234 PRK05654 acetyl-CoA carboxylas 44.4 6.3 0.00014 34.5 -0.4 29 162-190 26-57 (292)
235 CHL00174 accD acetyl-CoA carbo 44.1 5.8 0.00013 34.8 -0.7 29 162-190 37-68 (296)
236 PF03558 TBSV_P22: TBSV core p 43.4 1.6E+02 0.0035 23.7 7.3 78 106-187 73-157 (189)
237 PHA00626 hypothetical protein 43.1 27 0.0006 23.1 2.5 13 178-190 22-34 (59)
238 COG0361 InfA Translation initi 42.7 1.2E+02 0.0025 21.3 6.4 56 77-146 6-62 (75)
239 cd05693 S1_Rrp5_repeat_hs1_sc1 42.5 57 0.0012 23.6 4.5 30 131-161 1-30 (100)
240 PF01938 TRAM: TRAM domain; I 42.4 51 0.0011 21.2 3.9 24 73-96 37-60 (61)
241 PF09526 DUF2387: Probable met 41.9 27 0.00059 24.1 2.5 31 164-194 9-45 (71)
242 PRK06763 F0F1 ATP synthase sub 41.0 1E+02 0.0022 25.7 6.1 21 76-96 38-58 (213)
243 PRK12495 hypothetical protein; 40.6 16 0.00035 30.8 1.4 29 162-191 41-70 (226)
244 cd05835 Dnmt3b_related The PWW 40.5 18 0.0004 25.6 1.6 14 131-144 1-14 (87)
245 PF13375 RnfC_N: RnfC Barrel s 40.1 30 0.00065 25.4 2.7 12 38-49 69-80 (101)
246 PF01336 tRNA_anti-codon: OB-f 40.0 78 0.0017 20.4 4.6 63 79-154 2-69 (75)
247 COG3269 Predicted RNA-binding 39.5 55 0.0012 22.8 3.7 24 74-97 46-69 (73)
248 PF14205 Cys_rich_KTR: Cystein 38.9 19 0.0004 23.7 1.2 14 180-193 5-18 (55)
249 cd00729 rubredoxin_SM Rubredox 38.7 26 0.00057 20.4 1.8 23 165-188 4-27 (34)
250 COG3478 Predicted nucleic-acid 38.4 13 0.00029 25.3 0.5 10 180-189 5-14 (68)
251 COG1096 Predicted RNA-binding 38.3 86 0.0019 25.8 5.3 23 73-96 118-140 (188)
252 PRK05807 hypothetical protein; 38.3 1.1E+02 0.0023 23.5 5.7 69 13-98 5-74 (136)
253 COG2093 DNA-directed RNA polym 38.2 13 0.00028 25.1 0.4 21 166-189 7-28 (64)
254 COG1315 Uncharacterized conser 38.0 57 0.0012 30.9 4.7 48 22-80 220-270 (543)
255 PF09855 DUF2082: Nucleic-acid 38.0 23 0.00049 24.0 1.6 14 179-192 36-49 (64)
256 cd04459 Rho_CSD Rho_CSD: Rho p 37.8 19 0.00041 24.7 1.2 26 61-86 28-53 (68)
257 PRK11788 tetratricopeptide rep 37.8 19 0.00042 31.2 1.6 23 165-190 356-379 (389)
258 PRK00762 hypA hydrogenase nick 37.6 22 0.00047 27.0 1.7 29 163-191 70-104 (124)
259 PF09567 RE_MamI: MamI restric 37.3 14 0.0003 31.9 0.6 22 165-189 84-106 (314)
260 PF13453 zf-TFIIB: Transcripti 37.3 25 0.00054 21.1 1.6 20 167-186 4-26 (41)
261 PRK12496 hypothetical protein; 37.2 15 0.00032 29.3 0.7 31 164-195 128-159 (164)
262 PRK05886 yajC preprotein trans 37.0 74 0.0016 23.8 4.4 25 73-97 38-68 (109)
263 PRK09263 anaerobic ribonucleos 36.8 13 0.00029 36.5 0.4 28 163-191 641-671 (711)
264 TIGR00008 infA translation ini 36.7 1.2E+02 0.0025 20.8 5.0 52 80-145 7-59 (68)
265 COG1998 RPS31 Ribosomal protei 36.3 52 0.0011 21.3 2.9 28 164-192 20-50 (51)
266 COG4393 Predicted membrane pro 36.1 63 0.0014 29.1 4.5 34 156-189 327-361 (405)
267 PRK05585 yajC preprotein trans 36.0 78 0.0017 23.4 4.4 24 73-96 52-81 (106)
268 cd05162 PWWP The PWWP domain, 36.0 24 0.00052 24.6 1.6 14 131-144 1-14 (87)
269 PRK08582 hypothetical protein; 35.9 1.6E+02 0.0034 22.7 6.3 28 73-100 49-77 (139)
270 PRK00276 infA translation init 35.6 1.4E+02 0.003 20.2 7.1 53 80-146 9-62 (72)
271 PF13719 zinc_ribbon_5: zinc-r 35.5 29 0.00062 20.6 1.6 15 174-188 20-34 (37)
272 PRK14873 primosome assembly pr 35.4 28 0.00061 33.9 2.4 26 164-189 393-420 (665)
273 PF13913 zf-C2HC_2: zinc-finge 35.3 18 0.0004 19.6 0.7 11 179-189 2-12 (25)
274 COG0266 Nei Formamidopyrimidin 34.8 31 0.00066 30.0 2.3 23 165-187 247-273 (273)
275 cd05841 BS69_related The PWWP 34.5 29 0.00062 24.7 1.7 18 128-145 4-21 (83)
276 cd04322 LysRS_N LysRS_N: N-ter 33.9 1.5E+02 0.0032 21.3 5.6 55 79-140 3-59 (108)
277 PRK06556 vitamin B12-dependent 33.7 28 0.00061 35.4 2.2 23 165-188 926-949 (953)
278 cd03478 Rieske_AIFL_N AIFL (ap 33.3 1.6E+02 0.0035 20.4 5.6 55 129-190 7-67 (95)
279 PRK08579 anaerobic ribonucleos 33.3 18 0.0004 35.0 0.8 23 163-188 568-591 (625)
280 PRK05580 primosome assembly pr 33.2 28 0.0006 33.9 2.0 26 165-190 392-419 (679)
281 PF07191 zinc-ribbons_6: zinc- 32.8 68 0.0015 22.2 3.3 26 164-190 2-28 (70)
282 PRK12442 translation initiatio 32.5 1.5E+02 0.0032 21.3 5.1 52 80-145 9-61 (87)
283 PRK14810 formamidopyrimidine-D 32.4 36 0.00077 29.3 2.4 23 164-186 245-271 (272)
284 PF12508 DUF3714: Protein of u 32.4 2.9E+02 0.0063 22.8 8.0 55 36-100 53-111 (200)
285 smart00652 eIF1a eukaryotic tr 32.3 1.8E+02 0.0039 20.4 6.9 56 74-145 2-58 (83)
286 PLN00208 translation initiatio 32.1 1.4E+02 0.003 23.6 5.4 57 73-145 28-85 (145)
287 TIGR00595 priA primosomal prot 31.8 31 0.00068 32.3 2.0 26 165-190 224-251 (505)
288 PF00855 PWWP: PWWP domain; I 31.7 29 0.00063 23.7 1.4 12 131-142 1-12 (86)
289 PF10844 DUF2577: Protein of u 31.5 1.3E+02 0.0028 21.8 4.9 20 75-96 15-34 (100)
290 COG1592 Rubrerythrin [Energy p 31.4 24 0.00051 28.5 1.0 24 163-188 134-158 (166)
291 TIGR02827 RNR_anaer_Bdell anae 31.4 25 0.00054 33.8 1.3 24 163-189 532-556 (586)
292 TIGR00375 conserved hypothetic 30.8 17 0.00037 33.0 0.1 31 157-188 233-267 (374)
293 KOG2907 RNA polymerase I trans 30.8 29 0.00064 26.2 1.3 31 160-190 71-113 (116)
294 COG1792 MreC Cell shape-determ 30.6 2.2E+02 0.0049 24.6 7.0 20 80-99 156-175 (284)
295 PRK10445 endonuclease VIII; Pr 30.6 41 0.00088 28.8 2.4 22 165-186 237-262 (263)
296 PRK08665 ribonucleotide-diphos 30.5 29 0.00062 34.4 1.6 23 165-188 726-749 (752)
297 PF12760 Zn_Tnp_IS1595: Transp 30.4 33 0.00071 21.2 1.3 17 179-195 18-34 (46)
298 COG2824 PhnA Uncharacterized Z 30.3 40 0.00086 25.3 1.9 25 164-188 4-29 (112)
299 COG3809 Uncharacterized protei 30.2 42 0.00091 23.8 1.9 23 165-187 3-29 (88)
300 PRK04012 translation initiatio 30.1 2.2E+02 0.0048 20.8 7.1 58 73-146 17-75 (100)
301 PRK13945 formamidopyrimidine-D 29.9 38 0.00083 29.2 2.1 23 164-186 255-281 (282)
302 PRK00004 rplX 50S ribosomal pr 29.9 2.2E+02 0.0048 20.9 6.0 19 81-99 22-40 (105)
303 TIGR03779 Bac_Flav_CT_M Bacter 29.9 3.2E+02 0.007 25.2 8.1 56 35-100 255-314 (410)
304 TIGR00577 fpg formamidopyrimid 29.7 40 0.00087 28.9 2.2 21 165-185 247-271 (272)
305 PRK14350 ligA NAD-dependent DN 29.4 47 0.001 32.5 2.8 62 128-193 362-430 (669)
306 PF00096 zf-C2H2: Zinc finger, 29.4 29 0.00064 17.6 0.9 13 180-192 1-13 (23)
307 PF01835 A2M_N: MG2 domain; I 29.4 1.5E+02 0.0032 20.7 4.9 31 128-158 8-46 (99)
308 PRK08059 general stress protei 29.4 1.4E+02 0.003 22.3 4.9 33 129-162 3-35 (123)
309 COG2996 Predicted RNA-bindinin 29.3 1.9E+02 0.0041 25.3 6.2 25 73-97 70-95 (287)
310 TIGR00638 Mop molybdenum-pteri 29.0 1.3E+02 0.0028 19.4 4.2 54 78-143 7-61 (69)
311 cd06080 MUM1_like Mutated mela 28.9 38 0.00081 23.9 1.6 15 131-145 1-15 (80)
312 PRK09376 rho transcription ter 28.7 62 0.0013 29.9 3.3 71 23-103 48-123 (416)
313 cd03528 Rieske_RO_ferredoxin R 28.6 1.4E+02 0.003 20.7 4.6 56 131-190 10-68 (98)
314 PF02591 DUF164: Putative zinc 28.2 33 0.00072 22.0 1.1 12 177-188 44-55 (56)
315 COG4873 Uncharacterized protei 28.1 1.1E+02 0.0023 21.1 3.6 26 74-99 24-55 (81)
316 cd03474 Rieske_T4moC Toluene-4 28.1 2E+02 0.0044 20.4 5.5 57 131-190 10-69 (108)
317 PRK08270 anaerobic ribonucleos 28.1 26 0.00057 34.1 0.9 21 163-187 626-647 (656)
318 smart00440 ZnF_C2C2 C2C2 Zinc 28.1 27 0.00059 21.1 0.6 10 181-190 2-11 (40)
319 PRK11827 hypothetical protein; 28.1 58 0.0013 21.8 2.3 25 166-190 11-37 (60)
320 PRK14704 anaerobic ribonucleos 27.7 28 0.00061 33.7 1.0 23 163-189 559-582 (618)
321 PTZ00329 eukaryotic translatio 27.7 1.8E+02 0.004 23.1 5.4 56 73-144 28-84 (155)
322 TIGR01053 LSD1 zinc finger dom 27.5 67 0.0015 18.5 2.2 23 166-188 4-28 (31)
323 PF01176 eIF-1a: Translation i 27.4 1.9E+02 0.0041 19.1 5.7 51 78-143 3-54 (65)
324 PF09926 DUF2158: Uncharacteri 27.3 43 0.00094 21.7 1.5 24 131-158 1-24 (53)
325 PRK01103 formamidopyrimidine/5 27.2 50 0.0011 28.3 2.4 23 165-187 247-273 (274)
326 COG1862 YajC Preprotein transl 27.2 1.2E+02 0.0027 22.1 4.1 23 74-96 44-72 (97)
327 COG2051 RPS27A Ribosomal prote 26.2 1.2E+02 0.0025 20.8 3.5 29 160-188 16-47 (67)
328 PF00467 KOW: KOW motif; Inte 26.1 1E+02 0.0022 17.3 2.9 16 80-95 15-30 (32)
329 PF13901 DUF4206: Domain of un 26.1 21 0.00045 29.4 -0.2 24 165-188 157-181 (202)
330 PF05180 zf-DNL: DNL zinc fing 26.1 48 0.001 22.6 1.6 17 179-195 4-20 (66)
331 PRK14811 formamidopyrimidine-D 26.0 50 0.0011 28.3 2.2 24 165-188 237-264 (269)
332 PRK14351 ligA NAD-dependent DN 26.0 1.4E+02 0.003 29.4 5.4 58 128-189 387-452 (689)
333 PF01096 TFIIS_C: Transcriptio 26.0 28 0.00061 20.9 0.4 10 181-190 2-11 (39)
334 PF12647 RNHCP: RNHCP domain; 25.9 58 0.0012 23.7 2.1 30 167-196 46-84 (92)
335 CHL00010 infA translation init 25.9 2.3E+02 0.0049 19.6 6.8 52 80-145 9-61 (78)
336 PF11023 DUF2614: Protein of u 25.9 29 0.00063 26.2 0.6 26 162-188 68-94 (114)
337 PRK08271 anaerobic ribonucleos 25.3 32 0.00068 33.4 0.9 24 163-189 566-590 (623)
338 PRK04163 exosome complex RNA-b 25.3 1.2E+02 0.0027 25.4 4.4 32 132-164 62-93 (235)
339 PF11720 Inhibitor_I78: Peptid 25.2 99 0.0021 20.2 3.0 35 8-44 26-60 (60)
340 PF11520 Cren7: Chromatin prot 25.0 65 0.0014 21.5 2.0 26 168-195 32-57 (60)
341 PRK12678 transcription termina 24.8 90 0.002 30.5 3.7 43 61-103 320-371 (672)
342 COG4530 Uncharacterized protei 24.7 30 0.00065 26.2 0.5 36 155-191 2-38 (129)
343 COG1465 Predicted alternative 24.2 1.5E+02 0.0033 26.4 4.7 49 10-66 268-316 (376)
344 cd05793 S1_IF1A S1_IF1A: Trans 24.1 2.5E+02 0.0054 19.4 6.1 51 80-145 2-53 (77)
345 PRK01191 rpl24p 50S ribosomal 24.1 1E+02 0.0022 23.5 3.2 45 74-118 46-101 (120)
346 PRK04023 DNA polymerase II lar 23.9 36 0.00078 34.9 1.0 18 165-187 628-646 (1121)
347 cd01675 RNR_III Class III ribo 23.8 33 0.00071 32.7 0.7 22 165-189 520-542 (555)
348 PF01396 zf-C4_Topoisom: Topoi 23.8 55 0.0012 19.6 1.4 15 181-195 3-17 (39)
349 COG1439 Predicted nucleic acid 23.5 56 0.0012 26.6 1.9 29 165-196 141-170 (177)
350 PF12677 DUF3797: Domain of un 23.5 27 0.00059 22.4 0.0 15 174-188 8-22 (49)
351 PF00130 C1_1: Phorbol esters/ 23.5 88 0.0019 19.3 2.5 32 164-195 12-44 (53)
352 COG4049 Uncharacterized protei 23.1 19 0.00041 23.9 -0.8 13 179-191 17-29 (65)
353 TIGR02487 NrdD anaerobic ribon 23.1 37 0.0008 32.5 0.9 24 163-189 524-548 (579)
354 COG1097 RRP4 RNA-binding prote 23.1 81 0.0017 26.9 2.8 21 71-91 110-130 (239)
355 TIGR00074 hypC_hupF hydrogenas 22.8 2.3E+02 0.005 19.7 4.6 17 80-96 5-21 (76)
356 PTZ00194 60S ribosomal protein 22.7 1E+02 0.0023 24.2 3.1 38 81-118 64-102 (143)
357 PF14952 zf-tcix: Putative tre 22.6 37 0.00079 21.3 0.5 11 179-189 11-21 (44)
358 PRK03954 ribonuclease P protei 22.6 65 0.0014 24.6 2.0 13 177-189 91-103 (121)
359 cd05837 MSH6_like The PWWP dom 22.5 55 0.0012 24.2 1.5 15 130-144 2-16 (110)
360 PF08209 Sgf11: Sgf11 (transcr 22.4 63 0.0014 18.9 1.4 11 178-188 3-13 (33)
361 PRK14714 DNA polymerase II lar 22.2 40 0.00086 35.3 0.9 19 165-187 681-700 (1337)
362 PRK09462 fur ferric uptake reg 22.1 1.4E+02 0.003 22.9 3.8 13 178-190 89-101 (148)
363 PF13005 zf-IS66: zinc-finger 21.9 97 0.0021 18.8 2.4 10 167-176 7-16 (47)
364 TIGR02159 PA_CoA_Oxy4 phenylac 21.8 50 0.0011 25.9 1.2 19 179-197 105-123 (146)
365 PF04351 PilP: Pilus assembly 21.7 1.1E+02 0.0023 23.8 3.1 27 69-95 100-129 (149)
366 PF13408 Zn_ribbon_recom: Reco 21.5 85 0.0018 19.6 2.1 13 165-177 7-20 (58)
367 PF00394 Cu-oxidase: Multicopp 21.4 1.7E+02 0.0037 22.5 4.3 44 129-175 62-105 (159)
368 COG4956 Integral membrane prot 21.4 1.4E+02 0.0029 26.8 3.9 30 6-35 286-319 (356)
369 PRK13130 H/ACA RNA-protein com 21.3 65 0.0014 21.2 1.5 19 165-188 7-26 (56)
370 PRK07111 anaerobic ribonucleos 21.3 51 0.0011 32.6 1.4 21 163-187 680-701 (735)
371 PF14444 S1-like: S1-like 21.1 1E+02 0.0022 20.5 2.4 15 72-86 32-46 (58)
372 PF12073 DUF3553: Protein of u 21.1 2.5E+02 0.0054 18.3 4.7 16 81-96 17-32 (52)
373 PF14353 CpXC: CpXC protein 21.1 58 0.0013 24.3 1.4 15 175-189 34-48 (128)
374 COG2835 Uncharacterized conser 21.0 1.1E+02 0.0024 20.5 2.6 24 167-190 13-37 (60)
375 PRK14559 putative protein seri 21.0 37 0.00081 33.0 0.4 24 164-190 28-52 (645)
376 COG1379 PHP family phosphoeste 20.2 18 0.0004 32.4 -1.7 33 156-191 238-277 (403)
377 PF04319 NifZ: NifZ domain; I 20.2 1.4E+02 0.003 20.9 3.0 21 127-147 1-21 (75)
No 1
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.5e-51 Score=330.26 Aligned_cols=177 Identities=34% Similarity=0.503 Sum_probs=167.0
Q ss_pred cCCcEEecCCccCCCCCeeeCCCEEEeCCceEEEEeEeeeEEEcCCCCCCCCCCCeEEEecCCCCCCCCCCCCEEEEEEE
Q 029155 6 EEMVLVTPGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHKAHGPVPEPGSVVIARVT 85 (198)
Q Consensus 6 ~~~~iV~PGd~l~~~~e~~~G~Gty~~~g~~~i~asv~G~v~~~~~~~~~~~~~~~i~V~p~~~~~~~p~vGDiViG~V~ 85 (198)
.++.+|+|||.|+++|||++|.|||+++|+ |+|+.+|.+.. |++|.+++|.|.+..+.+|+.||+|+|+|+
T Consensus 3 ~~g~~v~PGd~~a~~EE~~~G~gt~~~~g~--i~Aa~~G~~~~-------d~~n~~~~V~p~~~~~~~~K~GdiV~grV~ 73 (188)
T COG1096 3 KDGTFVLPGDVLAVIEEFLPGEGTYEEGGE--IRAAATGVVRR-------DDKNRVISVKPGKKTPPLPKGGDIVYGRVT 73 (188)
T ss_pred ccCcEEcCcceeeeeeeeecCCCeEeECCE--EEEeecccEEE-------cccceEEEeccCCCCCCCCCCCCEEEEEEe
Confidence 578899999999999999999999999988 99999999999 356889999998876889999999999999
Q ss_pred EEecceEEEEEeeecccc--ccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeCCCccEEEEEecCCCeeeE
Q 029155 86 KVMTRMASADIMCVGAKS--VREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGDARAYFLSTAKNDLGVVS 163 (198)
Q Consensus 86 ~v~~~~~~V~I~~v~~~~--l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~~~~~~LSt~~~~lGvv~ 163 (198)
+++.+.|.|+|.++++.. +...+.|.||+||++..+.. +++++|+|||+|+|+|+|.+ .++.|||++++||||+
T Consensus 74 ~v~~~~a~V~i~~ve~~~r~~~~~~~~~ihvs~~~~~~~~--~~~d~f~~GDivrA~Vis~~--~~~~Lst~~~dlGVI~ 149 (188)
T COG1096 74 DVREQRALVRIVGVEGKERELATSGAADIHVSQVRDGYVE--KLSDAFRIGDIVRARVISTG--DPIQLSTKGNDLGVIY 149 (188)
T ss_pred eccceEEEEEEEEEecccccCCCCceeeEEEEeccccccc--ccccccccccEEEEEEEecC--CCeEEEecCCcceEEE
Confidence 999999999999999954 78899999999999998877 88999999999999999987 5899999999999999
Q ss_pred Eec-CCCceeEEccCCeEEeCCCCCEEeeeeCCC
Q 029155 164 AES-TAGGTMVPISWTEMQCPLTGQTEQRKVAKV 196 (198)
Q Consensus 164 a~~-~~g~~m~~~~~~~~~c~~cg~~e~RKva~~ 196 (198)
|+| +||++|.+ .|++|+||+||++|+||+|++
T Consensus 150 A~CsrC~~~L~~-~~~~l~Cp~Cg~tEkRKia~~ 182 (188)
T COG1096 150 ARCSRCRAPLVK-KGNMLKCPNCGNTEKRKIAKD 182 (188)
T ss_pred EEccCCCcceEE-cCcEEECCCCCCEEeeeeccc
Confidence 999 99999998 899999999999999999986
No 2
>KOG3409 consensus Exosomal 3'-5' exoribonuclease complex, subunit ski4 (Csl4) [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.7e-50 Score=319.08 Aligned_cols=185 Identities=45% Similarity=0.702 Sum_probs=167.0
Q ss_pred CCcEEecCCccCCCC-CeeeCCCEEEeCCceEEEEeEeeeEEEcCCCCCCCCCCCeEEEecCCCCCCCCCCCCEEEEEEE
Q 029155 7 EMVLVTPGEVLGKAT-EVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHKAHGPVPEPGSVVIARVT 85 (198)
Q Consensus 7 ~~~iV~PGd~l~~~~-e~~~G~Gty~~~g~~~i~asv~G~v~~~~~~~~~~~~~~~i~V~p~~~~~~~p~vGDiViG~V~ 85 (198)
...+++|||+++..+ +|..|.|||+.+++ |+||.+|...... ..+++++.++........+|.+||||+++|+
T Consensus 4 a~~~~lpG~~~c~~e~~~~~g~Gtye~~~y--I~aS~ag~~~~~~----~~~~~~v~~~~~~~~~~~LP~~G~IVtarV~ 77 (193)
T KOG3409|consen 4 AETLVLPGEVVCRAEGEYRMGEGTYERNGY--IFASVAGVNFRDN----LVQKIEVVSVEKQLFNELLPFVGAIVTARVS 77 (193)
T ss_pred ceEEEcccceeeecccccccccceeecCCe--EEeccccceeecC----CccceeeeeecccchhhcCCccCcEEEEEEE
Confidence 357899999999876 49999999999988 9999999554421 2234445555544456789999999999999
Q ss_pred EEecceEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeCCCccEEEEEecCCCeeeEEe
Q 029155 86 KVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGDARAYFLSTAKNDLGVVSAE 165 (198)
Q Consensus 86 ~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~~~~~~LSt~~~~lGvv~a~ 165 (198)
+++.++|.|+|+++++++|...|+|+||.+|+|++++|++++.++|+|||+|+|+|+|.+++.+|.|||+++|||||+|+
T Consensus 78 ~i~~rfAkv~I~~V~d~~lk~~FrglirkqdvR~tEkdrv~v~ksFrPgDiVlAkVis~~~~~~y~LTtAeneLGVV~a~ 157 (193)
T KOG3409|consen 78 RINLRFAKVDILSVGDKPLKKSFRGLIRKQDVRATEKDRVKVYKSFRPGDIVLAKVISLGDGSNYLLTTAENELGVVFAR 157 (193)
T ss_pred eeccceeeEEEEEEcCEEhhhhhcceeehhhccccccchhhhhhccCCCcEEEEEEeecCCCCcEEEEEecccceEEEEe
Confidence 99999999999999999999999999999999999999999999999999999999999989999999999999999999
Q ss_pred c-CCCceeEEccCCeEEeCCCCCEEeeeeCCCC
Q 029155 166 S-TAGGTMVPISWTEMQCPLTGQTEQRKVAKVG 197 (198)
Q Consensus 166 ~-~~g~~m~~~~~~~~~c~~cg~~e~RKva~~~ 197 (198)
. +.|.+|+|++|++|+||.+|.+|+||+||+.
T Consensus 158 as~~g~~M~pvdw~~mqsp~Tg~tE~RK~AKv~ 190 (193)
T KOG3409|consen 158 ASETGEPMVPVDWQEMQSPKTGKTEPRKCAKVP 190 (193)
T ss_pred ccccCCceeeccceeEEcCccCcccchhhccCC
Confidence 9 9999999999999999999999999999963
No 3
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=100.00 E-value=1.5e-49 Score=324.72 Aligned_cols=177 Identities=29% Similarity=0.414 Sum_probs=164.7
Q ss_pred CCcEEecCCccCCCCCeeeCCCEEEeCCceEEEEeEeeeEEEcCCCCCCCCCCCeEEEecCCCCCCCCCCCCEEEEEEEE
Q 029155 7 EMVLVTPGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHKAHGPVPEPGSVVIARVTK 86 (198)
Q Consensus 7 ~~~iV~PGd~l~~~~e~~~G~Gty~~~g~~~i~asv~G~v~~~~~~~~~~~~~~~i~V~p~~~~~~~p~vGDiViG~V~~ 86 (198)
++++|+|||.|+..++|++|+|||+++|. |||+++|.+++. ..++.|+|.|.....+.|++||+|+|+|++
T Consensus 4 ~~~~V~PGe~l~~~~e~~~G~Gty~~~~~--i~as~~G~~~id-------~~~~~Isv~P~~~~~~~~~~GdiV~GkV~~ 74 (189)
T PRK09521 4 QGDLVLPGDYLAVIEEYLPGEGTYEDNGE--VYASVVGKVFID-------DINRKISVIPFKKTPPLLKKGDIVYGRVVD 74 (189)
T ss_pred cCCEECCCCccccccceEcCCCEEeeCCE--EEEEeeEEEEEc-------CCCCEEEEecCcCCCCCCCCCCEEEEEEEE
Confidence 67899999999998999999999999988 999999999983 346789999987668999999999999999
Q ss_pred EecceEEEEEeeec--cccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeCCCccEEEEEecCCCeeeEE
Q 029155 87 VMTRMASADIMCVG--AKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGDARAYFLSTAKNDLGVVSA 164 (198)
Q Consensus 87 v~~~~~~V~I~~v~--~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~~~~~~LSt~~~~lGvv~a 164 (198)
+.+++|+|+|.+++ +.++..++.|+||.+|++..+.+ +|.+.|++||+|+|+|++++ +.+.||+++++||||+|
T Consensus 75 i~~~g~~V~I~~~~~~~~~l~~~~~G~l~~s~i~~~~~~--~~~~~~~~GD~V~akV~~i~--~~i~LS~k~~~lGvv~a 150 (189)
T PRK09521 75 VKEQRALVRIVSIEGSERELATSKLAYIHISQVSDGYVE--SLTDAFKIGDIVRAKVISYT--DPLQLSTKGKDLGVIYA 150 (189)
T ss_pred EcCCeEEEEEEEecccccccCCCceeeEEhhHcChhhhh--hHHhccCCCCEEEEEEEecC--CcEEEEEecCCceEEEE
Confidence 99999999999887 67788899999999999876655 89999999999999999997 68999999999999999
Q ss_pred ec-CCCceeEEccCCeEEeCCCCCEEeeeeCCC
Q 029155 165 ES-TAGGTMVPISWTEMQCPLTGQTEQRKVAKV 196 (198)
Q Consensus 165 ~~-~~g~~m~~~~~~~~~c~~cg~~e~RKva~~ 196 (198)
+| +||.+|+|.+|++|+||+||++|+||+|++
T Consensus 151 ~~~~~g~~~~~~~~~~~~c~~~~~~e~rkva~~ 183 (189)
T PRK09521 151 MCSRCRTPLVKKGENELKCPNCGNIETRKLSSY 183 (189)
T ss_pred EccccCCceEECCCCEEECCCCCCEEeeccchh
Confidence 99 799999999999999999999999999975
No 4
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=99.98 E-value=1.5e-31 Score=225.23 Aligned_cols=137 Identities=26% Similarity=0.439 Sum_probs=123.7
Q ss_pred cCCcEEecCCccCCCCCeeeCCCEEEeCCceEEEEeEeeeEEEcCCCCCCCCCCCeEEEecCCCCCCCCCCCCEEEEEEE
Q 029155 6 EEMVLVTPGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHKAHGPVPEPGSVVIARVT 85 (198)
Q Consensus 6 ~~~~iV~PGd~l~~~~e~~~G~Gty~~~g~~~i~asv~G~v~~~~~~~~~~~~~~~i~V~p~~~~~~~p~vGDiViG~V~ 85 (198)
.++++|+|||.|+ +++|.+|+|||+++|+ |+||++|.+... ++.++|.|... +|+|++||+|+|+|+
T Consensus 6 ~~~~~V~PGd~l~-~~~~~~G~Gty~~~g~--i~As~~G~~~~~---------~~~i~V~p~~~-~y~P~vGDiViG~V~ 72 (235)
T PRK04163 6 EDRKIVVPGDLLA-EGEFKAGRGTYKENGK--IYSTVVGLVDIK---------DDKVRVIPLEG-KYIPKVGDLVIGKVT 72 (235)
T ss_pred eCCcEECCCCCcC-cCCeecCCceEEeCCE--EEEEEeEEEEEE---------CCEEEEEECCC-cccCCCCCEEEEEEE
Confidence 3458999999997 5889999999999988 999999999984 25899999875 599999999999999
Q ss_pred EEecceEEEEEeeeccccccCcceeEEeccccccccc--cccccccCCCCCCEEEEEEEEeCCCccEEEEEecCCCeeeE
Q 029155 86 KVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEI--DKVDMHLSFRPGDIVRASVLSLGDARAYFLSTAKNDLGVVS 163 (198)
Q Consensus 86 ~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~--d~~~~~~~~~~GDiV~AkV~s~~~~~~~~LSt~~~~lGvv~ 163 (198)
++.+++|+|+| ..++.|+||.++++..+. |..+|+++|++||+|+|||+++++.+.+.||+++++||+|.
T Consensus 73 ~i~~~~~~vdI--------~~~~~g~L~~s~i~~~~~~~d~~~~~~~~~~GDlV~akV~~i~~~~~~~LS~k~~~lG~L~ 144 (235)
T PRK04163 73 DVTFSGWEVDI--------NSPYKAYLPVSEVLGRPVNVEGTDLRKYLDIGDYIIAKVKDVDRTRDVVLTLKGKGLGKIE 144 (235)
T ss_pred EEeCceEEEEe--------CCCceeEEEHHHcCCCccccchhhhHhhCCCCCEEEEEEEEECCCCcEEEEEcCCCCCccC
Confidence 99999999999 678999999999986543 56699999999999999999998767799999999999995
No 5
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=99.97 E-value=3.2e-30 Score=214.62 Aligned_cols=140 Identities=24% Similarity=0.350 Sum_probs=127.0
Q ss_pred eccCCcEEecCCccCCCCCeeeCCCEEEeCCceEEEEeEeeeEEEcCCCCCCCCCCCeEEEecCCCCCCCCCCCCEEEEE
Q 029155 4 KEEEMVLVTPGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHKAHGPVPEPGSVVIAR 83 (198)
Q Consensus 4 ~~~~~~iV~PGd~l~~~~e~~~G~Gty~~~g~~~i~asv~G~v~~~~~~~~~~~~~~~i~V~p~~~~~~~p~vGDiViG~ 83 (198)
...++++|+|||.|...+.|..|+|||.++++ |||+++|++++. ++.+.|+|+.+ +|+|++||+|||+
T Consensus 4 ~~~~~~iV~PGd~vl~~~~~~~G~Gty~~~~~--iyssv~G~~~~~---------~~~v~VIpl~g-~YiP~~gD~VIG~ 71 (239)
T COG1097 4 SVSMRKIVLPGDLVLAEGSYKLGHGTYFEGGK--IYSSVVGLLDVK---------GKLVRVIPLEG-RYIPEVGDVVIGK 71 (239)
T ss_pred eccccceecCCCccCCCCCEecCCCcEecCCE--EEEEEEeEEEEe---------CCEEEEEeCCC-cccCCCCCEEEEE
Confidence 45678999999987777899999999999988 999999999995 46899999976 9999999999999
Q ss_pred EEEEecceEEEEEeeeccccccCcceeEEeccccc--cccccccccccCCCCCCEEEEEEEEeCCCccEEEEEecCCCee
Q 029155 84 VTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVR--ATEIDKVDMHLSFRPGDIVRASVLSLGDARAYFLSTAKNDLGV 161 (198)
Q Consensus 84 V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~--~~~~d~~~~~~~~~~GDiV~AkV~s~~~~~~~~LSt~~~~lGv 161 (198)
|+++.+++|.||| +++|.++||.|+.. ..+.++.+|+++|++||+|+|||.+++..+.+.|++++..||.
T Consensus 72 I~~v~~~~W~VDI--------~sp~~A~L~ls~~~~r~~~~~~~~~r~~l~vGD~v~AkV~~vd~~~~~~L~~k~~~~Gk 143 (239)
T COG1097 72 IIEVGPSGWKVDI--------GSPYPALLSLSDFLRRKFENAEKDLRPFLNVGDLVYAKVVDVDRDGEVELTLKDEGLGK 143 (239)
T ss_pred EEEEcccceEEEc--------CCccceEeehhhhhcccccccccccccccccCCEEEEEEEEccCCCceEEEeecCCCcc
Confidence 9999999999999 78999999999983 3334467999999999999999999998889999999999999
Q ss_pred eE
Q 029155 162 VS 163 (198)
Q Consensus 162 v~ 163 (198)
+.
T Consensus 144 L~ 145 (239)
T COG1097 144 LK 145 (239)
T ss_pred cc
Confidence 84
No 6
>KOG3013 consensus Exosomal 3'-5' exoribonuclease complex, subunit Rrp4 [RNA processing and modification]
Probab=99.95 E-value=3.1e-29 Score=209.29 Aligned_cols=145 Identities=25% Similarity=0.393 Sum_probs=126.7
Q ss_pred ccCCcEEecCCccCCCCCeeeCCCEEEeCCceEEEEeEeeeEEEcCCCCCCCCCCCeEEEecCCCCCCCCCCCCEEEEEE
Q 029155 5 EEEMVLVTPGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHKAHGPVPEPGSVVIARV 84 (198)
Q Consensus 5 ~~~~~iV~PGd~l~~~~e~~~G~Gty~~~g~~~i~asv~G~v~~~~~~~~~~~~~~~i~V~p~~~~~~~p~vGDiViG~V 84 (198)
+....+|+||+.+...+.|+.|||||..++. |+||++|.++.. |++|+|+|++ .+|.|++||+|+|||
T Consensus 26 ~~~~~ivtPG~~V~~d~~fmRGHGTy~~d~~--i~ssvaG~v~rv---------NkLi~V~plk-~rY~pEvGDvVVgRV 93 (301)
T KOG3013|consen 26 SDHSTIVTPGELVTDDPGFMRGHGTYVRDGE--IYSSVAGVVQRV---------NKLISVKPLK-SRYAPEVGDVVVGRV 93 (301)
T ss_pred ccCceeecCCccccCchhhhhcccceecCCe--EEEeecchhhhh---------cceEEEeehh-hhcCCccCCEEEEEe
Confidence 4556799999999998899999999999999 999999999984 6899999997 689999999999999
Q ss_pred EEEecceEEEEEeeeccccccC---cceeEEeccccccccccccccccCCCCCCEEEEEEEEeCCCccEEEEEecCCCee
Q 029155 85 TKVMTRMASADIMCVGAKSVRE---KFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGDARAYFLSTAKNDLGV 161 (198)
Q Consensus 85 ~~v~~~~~~V~I~~v~~~~l~~---~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~~~~~~LSt~~~~lGv 161 (198)
+.|.++.|+||+++-.+..|.. ++.|-+ +.|.+..|+..|+++|+.||+|.|+|+++...++..|+||+..||+
T Consensus 94 ~eVq~KRWkvd~nsk~d~vL~LsSvNLPGg~---~RRk~~~DEl~MR~fl~egDLi~AEVQ~v~~dGs~sLhTRS~KYGK 170 (301)
T KOG3013|consen 94 IEVQQKRWKVDLNSKQDAVLMLSSVNLPGGI---QRRKSEEDELQMRSFLKEGDLIVAEVQNVFHDGSLSLHTRSLKYGK 170 (301)
T ss_pred eeeecceeEEecccccceEEEeecccCCchh---hhccchhhHHHHHHHhhccCeehHHHHHhccCCeEEEEecchhccc
Confidence 9999999999998877655432 344432 3456778899999999999999999999987789999999999999
Q ss_pred eEE
Q 029155 162 VSA 164 (198)
Q Consensus 162 v~a 164 (198)
+..
T Consensus 171 L~~ 173 (301)
T KOG3013|consen 171 LGQ 173 (301)
T ss_pred ccC
Confidence 843
No 7
>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=99.95 E-value=2.8e-28 Score=177.88 Aligned_cols=91 Identities=60% Similarity=1.022 Sum_probs=88.4
Q ss_pred CCCCCCCEEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeCCCccEE
Q 029155 72 PVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGDARAYF 151 (198)
Q Consensus 72 ~~p~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~~~~~~ 151 (198)
|+|++||+|+|+|++++.++|.|+|++++++++..+|.|+||+||+++++.++.+|+++|++||+|+|||+++++.++++
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 78999999999999999999999999999999999999999999999999999999999999999999999999878899
Q ss_pred EEEecCCCeee
Q 029155 152 LSTAKNDLGVV 162 (198)
Q Consensus 152 LSt~~~~lGvv 162 (198)
|||++++||||
T Consensus 82 Lst~~~~lGVv 92 (92)
T cd05791 82 LSTAENELGVV 92 (92)
T ss_pred EEecCCCCccC
Confidence 99999999996
No 8
>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=99.88 E-value=9.9e-23 Score=145.31 Aligned_cols=72 Identities=61% Similarity=0.963 Sum_probs=52.4
Q ss_pred CCCCCCEEEEEEEEEecceEEEEEeee----------ccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEE
Q 029155 73 VPEPGSVVIARVTKVMTRMASADIMCV----------GAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVL 142 (198)
Q Consensus 73 ~p~vGDiViG~V~~v~~~~~~V~I~~v----------~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~ 142 (198)
+|++||+|+|+|+++++++|.|+|+++ ++.++..+|.|+||.+|+|+++.|+++|.++|+|||+|+|+|+
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 589999999999999999999999999 7778899999999999999999999999999999999999999
Q ss_pred Ee
Q 029155 143 SL 144 (198)
Q Consensus 143 s~ 144 (198)
|+
T Consensus 81 Sl 82 (82)
T PF10447_consen 81 SL 82 (82)
T ss_dssp EE
T ss_pred eC
Confidence 85
No 9
>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=99.79 E-value=7.1e-19 Score=124.93 Aligned_cols=82 Identities=33% Similarity=0.552 Sum_probs=74.6
Q ss_pred CCCCCCCCEEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeCCCccE
Q 029155 71 GPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGDARAY 150 (198)
Q Consensus 71 ~~~p~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~~~~~ 150 (198)
+|.|++||+|+|+|+++.+++|+|+| ...++|+||.+++...+.. ++.+.|++||+|.|+|+++++.+.+
T Consensus 1 ~y~p~~GdiV~G~V~~v~~~~~~V~i--------~~~~~g~l~~~~~~~~~~~--~~~~~~~~GD~i~~~V~~~~~~~~i 70 (82)
T cd04454 1 RYLPDVGDIVIGIVTEVNSRFWKVDI--------LSRGTARLEDSSATEKDKK--EIRKSLQPGDLILAKVISLGDDMNV 70 (82)
T ss_pred CCCCCCCCEEEEEEEEEcCCEEEEEe--------CCCceEEeechhccCcchH--HHHhcCCCCCEEEEEEEEeCCCCCE
Confidence 48999999999999999999999999 6679999999999754433 8899999999999999999866789
Q ss_pred EEEEecCCCeee
Q 029155 151 FLSTAKNDLGVV 162 (198)
Q Consensus 151 ~LSt~~~~lGvv 162 (198)
.||+++++||+|
T Consensus 71 ~LS~~~~~~Gvi 82 (82)
T cd04454 71 LLTTADNELGVI 82 (82)
T ss_pred EEEECCCCCccC
Confidence 999999999986
No 10
>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=99.68 E-value=2.3e-16 Score=112.80 Aligned_cols=84 Identities=27% Similarity=0.396 Sum_probs=73.3
Q ss_pred CCCCCCCCEEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccccc--cccccccccCCCCCCEEEEEEEEeCCCc
Q 029155 71 GPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRAT--EIDKVDMHLSFRPGDIVRASVLSLGDAR 148 (198)
Q Consensus 71 ~~~p~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~--~~d~~~~~~~~~~GDiV~AkV~s~~~~~ 148 (198)
+|.|++||+|.|+|+++.+++|+|+| ...+.|+||.+++... .....++.+.|++||.|.|+|+++++.+
T Consensus 1 ~y~p~~GdiV~g~V~~i~~~g~~v~i--------~~~~~G~l~~se~~~~~~~~~~~~~~~~l~vGd~i~~~V~~~~~~~ 72 (86)
T cd05789 1 RYIPEVGDVVIGRVTEVGFKRWKVDI--------NSPYDAVLPLSEVNLPRTDEDELNMRSYLDEGDLIVAEVQSVDSDG 72 (86)
T ss_pred CCcCCCCCEEEEEEEEECCCEEEEEC--------CCCeEEEEEHHHccCCCCccchHHHHhhCCCCCEEEEEEEEECCCC
Confidence 48899999999999999999999999 6789999999998631 1122377889999999999999997657
Q ss_pred cEEEEEecCCCeee
Q 029155 149 AYFLSTAKNDLGVV 162 (198)
Q Consensus 149 ~~~LSt~~~~lGvv 162 (198)
.+.||++.++||++
T Consensus 73 ~i~LS~~~~~~g~~ 86 (86)
T cd05789 73 SVSLHTRSLKYGKL 86 (86)
T ss_pred CEEEEeCcccccCC
Confidence 89999999999985
No 11
>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=99.63 E-value=2e-15 Score=108.62 Aligned_cols=76 Identities=20% Similarity=0.152 Sum_probs=64.6
Q ss_pred CCCCCCCCEEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeCCCccE
Q 029155 71 GPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGDARAY 150 (198)
Q Consensus 71 ~~~p~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~~~~~ 150 (198)
+|+|++||+|+|+|+++..+.|+||| ++++.|+||.++.... ...++..|++||+|+|||.+++.....
T Consensus 1 rY~P~~gD~VIG~V~~~~~~~~~VdI--------~s~~~a~L~~~~f~ga---tk~~rp~L~~GDlV~ArV~~~~~~~~~ 69 (86)
T cd05790 1 RYVPAKGDHVIGIVVAKAGDFFKVDI--------GGSEPASLSYLAFEGA---TKRNRPNLNVGDLVYARVVKANRDMEP 69 (86)
T ss_pred CCcCCCCCEEEEEEEEEcCCeEEEEc--------CCCcceEechHHcccc---cccccccCCCCCEEEEEEEecCCCCCe
Confidence 59999999999999999999999999 6778899998776322 125789999999999999999876678
Q ss_pred EEEEecC
Q 029155 151 FLSTAKN 157 (198)
Q Consensus 151 ~LSt~~~ 157 (198)
.||..++
T Consensus 70 eLtc~~~ 76 (86)
T cd05790 70 ELSCVDS 76 (86)
T ss_pred EEEEeCC
Confidence 8888653
No 12
>KOG1004 consensus Exosomal 3'-5' exoribonuclease complex subunit Rrp40 [Translation, ribosomal structure and biogenesis]
Probab=99.50 E-value=5.2e-13 Score=109.38 Aligned_cols=145 Identities=22% Similarity=0.286 Sum_probs=105.5
Q ss_pred cEEecCCccCC--CCCeeeCCCEEEeCCceEEEEeEeeeEEEcCCCCCCCCCCCeEEEecCCCCCCCCCCCCEEEEEEEE
Q 029155 9 VLVTPGEVLGK--ATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHKAHGPVPEPGSVVIARVTK 86 (198)
Q Consensus 9 ~iV~PGd~l~~--~~e~~~G~Gty~~~g~~~i~asv~G~v~~~~~~~~~~~~~~~i~V~p~~~~~~~p~vGDiViG~V~~ 86 (198)
++.+|||.+.. ..+..+|+|.|..++. +..+.+|.+....+ ....-.+.+|.. .+.+|+|.+||.|||+|+.
T Consensus 2 ~~~~pg~~~~~~~~~sv~~G~g~~~~g~~--~~~~~~G~~~~~~~---gk~~~~v~~vds-~~kRYiP~~~D~VIGiV~~ 75 (230)
T KOG1004|consen 2 TFYFPGDSIPRPRLCSVVLGPGLRRRGQE--RLVTKCGRLRHKEP---GKGGGGVYWVDS-QQKRYIPVKGDHVIGIVTS 75 (230)
T ss_pred ceecCCcccccCccCceeecCCccccCce--EEeccccceeeccC---CcccceeEEEec-ccceecCCCCCEEEEEEEe
Confidence 46789998764 2357899999998877 99999998877531 000112557765 4679999999999999999
Q ss_pred EecceEEEEEeeeccccccC-cceeEEeccccccccccccccccCCCCCCEEEEEEEEeCCCccEEEEEecC-----CCe
Q 029155 87 VMTRMASADIMCVGAKSVRE-KFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGDARAYFLSTAKN-----DLG 160 (198)
Q Consensus 87 v~~~~~~V~I~~v~~~~l~~-~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~~~~~~LSt~~~-----~lG 160 (198)
-..+++.|||...+-+.|+. +|+| +++.+ ++.|+.||+|+|||...+......|+--+. .+|
T Consensus 76 ~~gd~ykVDigg~~~a~L~~laFe~--------AtkrN----rPnl~vGdliyakv~~a~~~~Epel~Cids~graaGfG 143 (230)
T KOG1004|consen 76 KSGDIYKVDIGGSEPASLSYLAFEG--------ATKRN----RPNLQVGDLIYAKVVDANKDMEPELTCIDSTGRAAGFG 143 (230)
T ss_pred ccCceEEEecCCCCeeeeeeccccC--------ccccC----CCccccccEEEEEEEecCCCcCcceEEEcccCcccCcc
Confidence 99999999996544444443 4555 35544 688999999999999987544455554444 666
Q ss_pred eeEEecCCCceeEEcc
Q 029155 161 VVSAESTAGGTMVPIS 176 (198)
Q Consensus 161 vv~a~~~~g~~m~~~~ 176 (198)
++ .++.|.+++
T Consensus 144 ~L-----kdG~if~vs 154 (230)
T KOG1004|consen 144 VL-----KDGMIFKVS 154 (230)
T ss_pred cc-----cCceEEEec
Confidence 66 367777776
No 13
>PF14382 ECR1_N: Exosome complex exonuclease RRP4 N-terminal region; PDB: 2NN6_I 3M7N_C 2BA1_A 3M85_C.
Probab=99.44 E-value=8.8e-14 Score=85.78 Aligned_cols=37 Identities=41% Similarity=0.803 Sum_probs=33.8
Q ss_pred EEecCCccCCCCCeeeCCCEEEeCCceEEEEeEeeeEEE
Q 029155 10 LVTPGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRT 48 (198)
Q Consensus 10 iV~PGd~l~~~~e~~~G~Gty~~~g~~~i~asv~G~v~~ 48 (198)
||+|||+|+.+++|++|+|||+++|+ ||||++|.+++
T Consensus 1 iV~PG~~l~~~~e~~~G~GTY~~~g~--I~asv~G~v~~ 37 (39)
T PF14382_consen 1 IVVPGDRLGSSEEYMPGHGTYVRDGN--IYASVAGTVKI 37 (39)
T ss_dssp EE-TT-EEEETTTSEESTTEEEETTE--EEESSSEEEEE
T ss_pred CCCCCCEeecCCCEecCCCEEEeCCE--EEEEeeEEEEE
Confidence 69999999999999999999999999 99999999987
No 14
>COG1098 VacB Predicted RNA binding protein (contains ribosomal protein S1 domain) [Translation, ribosomal structure and biogenesis]
Probab=99.40 E-value=4.1e-13 Score=101.72 Aligned_cols=75 Identities=19% Similarity=0.290 Sum_probs=70.3
Q ss_pred CCCCCEEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeCCCccEEEE
Q 029155 74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGDARAYFLS 153 (198)
Q Consensus 74 p~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~~~~~~LS 153 (198)
+++|+++.|+||.|++.+|+|++ ...-+|++|+|++...++. ++.|.+++||.|.|+|+++++.+.+.||
T Consensus 3 ~kvG~~l~GkItgI~~yGAFV~l--------~~g~tGLVHISEIa~~fVk--dI~d~L~vG~eV~vKVl~ide~GKisLS 72 (129)
T COG1098 3 MKVGSKLKGKITGITPYGAFVEL--------EGGKTGLVHISEIADGFVK--DIHDHLKVGQEVKVKVLDIDENGKISLS 72 (129)
T ss_pred ccccceEEEEEEeeEecceEEEe--------cCCCcceEEehHhhhhhHH--hHHHHhcCCCEEEEEEEeeccCCCccee
Confidence 68999999999999999999999 6667899999999999988 9999999999999999999988899999
Q ss_pred EecCC
Q 029155 154 TAKND 158 (198)
Q Consensus 154 t~~~~ 158 (198)
+|..+
T Consensus 73 Ir~~~ 77 (129)
T COG1098 73 IRKLE 77 (129)
T ss_pred hHHhh
Confidence 98754
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=99.39 E-value=2.2e-12 Score=89.67 Aligned_cols=70 Identities=29% Similarity=0.408 Sum_probs=62.2
Q ss_pred CCCCEEEEEEEEEec-ceEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeCCCccEEEE
Q 029155 75 EPGSVVIARVTKVMT-RMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGDARAYFLS 153 (198)
Q Consensus 75 ~vGDiViG~V~~v~~-~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~~~~~~LS 153 (198)
++||+|.|+|+++.+ ..+++++ ..+..|++|+++++..+.. ++.+.|++||.|+|+|+++++ +.+.||
T Consensus 2 ~~G~iv~G~V~~i~~~~g~~v~l--------~~~~~Glvhis~~s~~~~~--~~~~~~~~Gd~v~~kV~~~~~-~~i~LS 70 (72)
T cd05704 2 EEGAVTLGMVTKVIPHSGLTVQL--------PFGKTGLVSIFHLSDSYTE--NPLEGFKPGKIVRCCILSKKD-GKYQLS 70 (72)
T ss_pred CCCCEEEEEEEEeeCCcEEEEEC--------CCCCEEEEEHHHhcCcccC--CHHHhCCCCCEEEEEEEEecC-CEEEEE
Confidence 689999999999986 7899998 7789999999999876655 677999999999999999975 689999
Q ss_pred Ee
Q 029155 154 TA 155 (198)
Q Consensus 154 t~ 155 (198)
++
T Consensus 71 l~ 72 (72)
T cd05704 71 LR 72 (72)
T ss_pred eC
Confidence 85
No 16
>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=99.28 E-value=2.8e-11 Score=82.93 Aligned_cols=69 Identities=26% Similarity=0.286 Sum_probs=60.6
Q ss_pred CCEEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeC-CCccEEEEEe
Q 029155 77 GSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLG-DARAYFLSTA 155 (198)
Q Consensus 77 GDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~-~~~~~~LSt~ 155 (198)
||+|.|+|+++.+++|+|++ ...+.|+||.+++...+.+ ++.+.|++||.|.|+|++++ +.+.+.||.+
T Consensus 1 G~iv~g~V~~i~~~~~~v~l--------~~~~~g~l~~~e~~~~~~~--~~~~~~~~Gd~i~~~i~~~~~~~~~i~lS~~ 70 (70)
T cd05687 1 GDIVKGTVVSVDDDEVLVDI--------GYKSEGIIPISEFSDDPIE--NGEDEVKVGDEVEVYVLRVEDEEGNVVLSKR 70 (70)
T ss_pred CCEEEEEEEEEeCCEEEEEe--------CCCceEEEEHHHhCccccC--CHhHcCCCCCEEEEEEEEEECCCCeEEEEeC
Confidence 89999999999999999999 5578999999999866655 78899999999999999997 4466888864
No 17
>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=99.23 E-value=1.1e-10 Score=80.48 Aligned_cols=71 Identities=30% Similarity=0.354 Sum_probs=61.8
Q ss_pred CCCCEEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeCC-CccEEEE
Q 029155 75 EPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGD-ARAYFLS 153 (198)
Q Consensus 75 ~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~-~~~~~LS 153 (198)
++|++|.|+|+++.+++++|++ ....+|++|.++++..+.. ++.+.|++||.|.|+|++++. .+.+.||
T Consensus 2 ~~G~iv~g~V~~v~~~gi~v~l--------~~~~~g~v~~s~l~~~~~~--~~~~~~~~Gd~v~~~V~~~d~~~~~i~ls 71 (73)
T cd05706 2 KVGDILPGRVTKVNDRYVLVQL--------GNKVTGPSFITDALDDYSE--ALPYKFKKNDIVRACVLSVDVPNKKIALS 71 (73)
T ss_pred CCCCEEEEEEEEEeCCeEEEEe--------CCCcEEEEEhhhccCcccc--ccccccCCCCEEEEEEEEEeCCCCEEEEE
Confidence 6899999999999999999999 6679999999999765433 567899999999999999974 4679998
Q ss_pred Ee
Q 029155 154 TA 155 (198)
Q Consensus 154 t~ 155 (198)
++
T Consensus 72 ~~ 73 (73)
T cd05706 72 LR 73 (73)
T ss_pred EC
Confidence 74
No 18
>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=99.21 E-value=7.7e-11 Score=82.42 Aligned_cols=71 Identities=18% Similarity=0.176 Sum_probs=59.6
Q ss_pred CCCCEEEEEEEEEecceEEEEEeeeccccccCcceeEEecccccccccc-ccccccCCCCCCEEEEEEEEeCC-CccEEE
Q 029155 75 EPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEID-KVDMHLSFRPGDIVRASVLSLGD-ARAYFL 152 (198)
Q Consensus 75 ~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d-~~~~~~~~~~GDiV~AkV~s~~~-~~~~~L 152 (198)
++||+|.|+|+++++++++|++ .....|+||.++++..... ..++.+.|++||.|.|+|+++++ .+.+.|
T Consensus 2 k~G~~V~g~V~~i~~~G~fV~l--------~~~v~G~v~~~~ls~~~~~~~~~~~~~~~~G~~v~~kVl~id~~~~~i~L 73 (74)
T cd05705 2 KEGQLLRGYVSSVTKQGVFFRL--------SSSIVGRVLFQNVTKYFVSDPSLYNKYLPEGKLLTAKVLSVNSEKNLVEL 73 (74)
T ss_pred CCCCEEEEEEEEEeCCcEEEEe--------CCCCEEEEEHHHccCccccChhhHhcccCCCCEEEEEEEEEECCCCEEec
Confidence 7899999999999999999999 6789999999999865533 12367999999999999999975 355666
Q ss_pred E
Q 029155 153 S 153 (198)
Q Consensus 153 S 153 (198)
|
T Consensus 74 S 74 (74)
T cd05705 74 S 74 (74)
T ss_pred C
Confidence 4
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=99.20 E-value=1.6e-10 Score=79.29 Aligned_cols=72 Identities=25% Similarity=0.439 Sum_probs=63.1
Q ss_pred CCEEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeCCC-ccEEEEEe
Q 029155 77 GSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGDA-RAYFLSTA 155 (198)
Q Consensus 77 GDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~~-~~~~LSt~ 155 (198)
|++|.|+|+++.+++|+|+| .....|++|.+++...+.. ++.+.|++||.|.|+|++++.. +.+.||++
T Consensus 1 G~~v~g~V~~v~~~g~~v~l--------~~~~~g~i~~~~~~~~~~~--~~~~~~~~Gd~v~~~v~~~d~~~~~i~ls~k 70 (73)
T cd05691 1 GSIVTGKVTEVDAKGATVKL--------GDGVEGFLRAAELSRDRVE--DATERFKVGDEVEAKITNVDRKNRKISLSIK 70 (73)
T ss_pred CCEEEEEEEEEECCeEEEEe--------CCCCEEEEEHHHCCCcccc--CHHHccCCCCEEEEEEEEEeCCCCEEEEEEE
Confidence 89999999999999999999 5678999999999866554 7789999999999999999854 67999998
Q ss_pred cCC
Q 029155 156 KND 158 (198)
Q Consensus 156 ~~~ 158 (198)
..+
T Consensus 71 ~~~ 73 (73)
T cd05691 71 AKE 73 (73)
T ss_pred EcC
Confidence 653
No 20
>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=99.17 E-value=2.4e-10 Score=79.24 Aligned_cols=74 Identities=18% Similarity=0.244 Sum_probs=62.6
Q ss_pred CCCCCEEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeCC-CccEEE
Q 029155 74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGD-ARAYFL 152 (198)
Q Consensus 74 p~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~-~~~~~L 152 (198)
|++|+++.|+|+++.+.+++|++... .+.+|+||.++++..+.. ++.+.|++||.|.|+|++++. .+.+.|
T Consensus 1 ~~~G~~~~g~V~~v~~~g~~v~l~~~------~~~~gll~~s~l~~~~~~--~~~~~~~~Gd~v~vkv~~~d~~~~~i~l 72 (76)
T cd04452 1 PEEGELVVVTVKSIADMGAYVSLLEY------GNIEGMILLSELSRRRIR--SIRKLVKVGRKEVVKVIRVDKEKGYIDL 72 (76)
T ss_pred CCCCCEEEEEEEEEEccEEEEEEcCC------CCeEEEEEhHHcCCcccC--CHHHeeCCCCEEEEEEEEEECCCCEEEE
Confidence 67899999999999999999999321 148999999999865544 778999999999999999975 356899
Q ss_pred EEe
Q 029155 153 STA 155 (198)
Q Consensus 153 St~ 155 (198)
|++
T Consensus 73 s~k 75 (76)
T cd04452 73 SKK 75 (76)
T ss_pred EEc
Confidence 876
No 21
>PRK08582 hypothetical protein; Provisional
Probab=99.16 E-value=4e-10 Score=88.04 Aligned_cols=75 Identities=25% Similarity=0.305 Sum_probs=66.4
Q ss_pred CCCCCEEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeCCCccEEEE
Q 029155 74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGDARAYFLS 153 (198)
Q Consensus 74 p~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~~~~~~LS 153 (198)
+++|++|.|+|+.|++.+++|+| .....|++|++++...+.. ++.+.|++||.|.|+|++++..+.+.||
T Consensus 3 ~kvG~iv~G~V~~I~~fG~fV~L--------~~~~~GlVhiSels~~~v~--~~~~~l~vGD~VkvkV~~id~~gkI~LS 72 (139)
T PRK08582 3 IEVGSKLQGKVTGITNFGAFVEL--------PEGKTGLVHISEVADNYVK--DINDHLKVGDEVEVKVLNVEDDGKIGLS 72 (139)
T ss_pred CcCCCEEEEEEEEEECCeEEEEE--------CCCCEEEEEeeccCccccc--ccccccCCCCEEEEEEEEECCCCcEEEE
Confidence 57899999999999999999999 5678999999999866654 6789999999999999999865789999
Q ss_pred EecCC
Q 029155 154 TAKND 158 (198)
Q Consensus 154 t~~~~ 158 (198)
++...
T Consensus 73 lk~~~ 77 (139)
T PRK08582 73 IKKAK 77 (139)
T ss_pred EEecc
Confidence 98653
No 22
>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=99.14 E-value=3.8e-10 Score=78.61 Aligned_cols=71 Identities=20% Similarity=0.181 Sum_probs=61.2
Q ss_pred CCEEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeCC-CccEEEEEe
Q 029155 77 GSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGD-ARAYFLSTA 155 (198)
Q Consensus 77 GDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~-~~~~~LSt~ 155 (198)
||+|.|+|+++.+++++|++ ....+|+||.++++.......+..+.|++||.|.|+|++++. .+.+.||.+
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 GQEVTGFVNNVSKEFVWLTI--------SPDVKGRIPLLDLSDDVSVLEHPEKKFPIGQALKAKVVGVDKEHKLLRLSAR 72 (73)
T ss_pred CCEEEEEEEEEeCCEEEEEe--------CCCcEEEEEHHHcCCccccccCHHHhCCCCCEEEEEEEEEeCCCCEEEEEec
Confidence 89999999999999999999 678999999999975432223778999999999999999984 467999976
No 23
>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=99.13 E-value=1.9e-10 Score=85.05 Aligned_cols=76 Identities=18% Similarity=0.291 Sum_probs=63.8
Q ss_pred CCCCCEEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccccccc-----------------cccccccCCCCCCE
Q 029155 74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEI-----------------DKVDMHLSFRPGDI 136 (198)
Q Consensus 74 p~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~-----------------d~~~~~~~~~~GDi 136 (198)
+++|++|.|+|+++.+..+++++ .....|++|.+|+...+. +..++.+.|++||+
T Consensus 1 L~~G~vV~G~V~~v~~~gl~v~L--------~~g~~G~v~~seis~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~vGd~ 72 (100)
T cd05693 1 LSEGMLVLGQVKEITKLDLVISL--------PNGLTGYVPITNISDAYTERLEELDEESEEEDDEEELPDLEDLFSVGQL 72 (100)
T ss_pred CCCCCEEEEEEEEEcCCCEEEEC--------CCCcEEEEEHHHhhHHHHHHHHHhhhhccccccccccCCHHHhccCCCE
Confidence 37899999999999999999988 667999999999975331 12357899999999
Q ss_pred EEEEEEEeCCC----ccEEEEEecC
Q 029155 137 VRASVLSLGDA----RAYFLSTAKN 157 (198)
Q Consensus 137 V~AkV~s~~~~----~~~~LSt~~~ 157 (198)
|+|+|+++++. +.+.||++..
T Consensus 73 V~~kVi~~d~~~~~~~~i~LSlr~~ 97 (100)
T cd05693 73 VRCKVVSLDKSKSGKKRIELSLEPE 97 (100)
T ss_pred EEEEEEEccCCcCCCcEEEEEecHH
Confidence 99999999863 5799998754
No 24
>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=99.13 E-value=5.7e-10 Score=75.05 Aligned_cols=69 Identities=26% Similarity=0.352 Sum_probs=59.8
Q ss_pred CCEEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeCCCccEEEEEe
Q 029155 77 GSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGDARAYFLSTA 155 (198)
Q Consensus 77 GDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~~~~~~LSt~ 155 (198)
||++.|+|+++.+.+|+|+| ...+.|+||.++++..+.. ++.+.|++||.|.++|++++..+.+.||++
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 GSVVEGTVTRLKPFGAFVEL--------GGGISGLVHISQIAHKRVK--DVKDVLKEGDKVKVKVLSIDARGRISLSIK 69 (69)
T ss_pred CCEEEEEEEEEEeeeEEEEE--------CCCCEEEEEhHHcCCcccC--CHHHccCCCCEEEEEEEEECCCCcEEEEEC
Confidence 79999999999999999999 5678999999999765543 667889999999999999976567888874
No 25
>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=99.11 E-value=7.2e-10 Score=76.48 Aligned_cols=72 Identities=24% Similarity=0.308 Sum_probs=63.6
Q ss_pred CCCCCEEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeCC-CccEEE
Q 029155 74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGD-ARAYFL 152 (198)
Q Consensus 74 p~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~-~~~~~L 152 (198)
+++||++.|+|+++.+++++|+| ..+..|+||.+++.....+ +..+.|++||.|.|+|++++. .+.+.|
T Consensus 2 ~~~G~iv~g~V~~v~~~g~~V~l--------~~~~~g~ip~~~l~~~~~~--~~~~~~~~G~~v~v~v~~vd~~~~~i~l 71 (74)
T PF00575_consen 2 LKEGDIVEGKVTSVEDFGVFVDL--------GNGIEGFIPISELSDDRID--DPSEVYKIGQTVRVKVIKVDKEKGRIRL 71 (74)
T ss_dssp SSTTSEEEEEEEEEETTEEEEEE--------STSSEEEEEGGGSSSSEES--SSHGTCETTCEEEEEEEEEETTTTEEEE
T ss_pred CCCCCEEEEEEEEEECCEEEEEE--------CCcEEEEEEeehhcCcccc--ccccccCCCCEEEEEEEEEECCCCeEEE
Confidence 68999999999999999999999 6689999999999866544 778999999999999999985 456899
Q ss_pred EEe
Q 029155 153 STA 155 (198)
Q Consensus 153 St~ 155 (198)
|+|
T Consensus 72 S~k 74 (74)
T PF00575_consen 72 SLK 74 (74)
T ss_dssp EST
T ss_pred EEC
Confidence 875
No 26
>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=99.11 E-value=4.3e-10 Score=77.34 Aligned_cols=65 Identities=23% Similarity=0.303 Sum_probs=55.9
Q ss_pred CCEEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeCCCcc
Q 029155 77 GSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGDARA 149 (198)
Q Consensus 77 GDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~~~~ 149 (198)
|++|.|+|+++.+++++|++ ...++|.||.++++..+.+..++.+.|++||.|.|+|+++++.+.
T Consensus 1 G~iV~g~V~~i~~~gi~v~l--------~~~i~g~i~~~~i~~~~~~~~~~~~~~~~Gd~i~~kVl~~d~~~~ 65 (70)
T cd05702 1 GDLVKAKVKSVKPTQLNVQL--------ADNVHGRIHVSEVFDEWPDGKNPLSKFKIGQKIKARVIGGHDAKT 65 (70)
T ss_pred CCEEEEEEEEEECCcEEEEe--------CCCcEEEEEHHHhccccccccChhHhCCCCCEEEEEEEEEeCccc
Confidence 89999999999999999999 678999999999976532233778999999999999999986543
No 27
>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=99.08 E-value=1.1e-09 Score=75.98 Aligned_cols=72 Identities=18% Similarity=0.160 Sum_probs=61.4
Q ss_pred CCCCCEEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeCCCccEEEE
Q 029155 74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGDARAYFLS 153 (198)
Q Consensus 74 p~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~~~~~~LS 153 (198)
|+.|+++.|+|+++.+.+++|++. ....+|++|.++++..+.+ +..+.|++||.|.++|++++..+.+.||
T Consensus 1 ~~~g~~~~g~V~~i~~fG~fv~l~-------~~~~eGlvh~sel~~~~~~--~~~~~~~~Gd~v~vkv~~vd~~~ki~ls 71 (73)
T cd05686 1 PALYQIFKGEVASVTEYGAFVKIP-------GCRKQGLVHKSHMSSCRVD--DPSEVVDVGEKVWVKVIGREMKDKMKLS 71 (73)
T ss_pred CcCCCEEEEEEEEEEeeeEEEEEC-------CCCeEEEEEchhhCCCccc--CHhhEECCCCEEEEEEEEECCCCcEEEE
Confidence 578999999999999999999992 1135899999999876655 7788999999999999999865578887
Q ss_pred E
Q 029155 154 T 154 (198)
Q Consensus 154 t 154 (198)
+
T Consensus 72 ~ 72 (73)
T cd05686 72 L 72 (73)
T ss_pred e
Confidence 5
No 28
>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=99.08 E-value=5.9e-10 Score=75.99 Aligned_cols=67 Identities=15% Similarity=0.283 Sum_probs=57.7
Q ss_pred CCEEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeCC-CccEEEE
Q 029155 77 GSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGD-ARAYFLS 153 (198)
Q Consensus 77 GDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~-~~~~~LS 153 (198)
|++|.|+|+++.+++++|++ ...+.|++|.++++..+.. ++.+.|++||.|.|+|++++. .+.+.||
T Consensus 1 G~~v~g~V~~v~~~Gv~V~l--------~~~~~G~v~~s~l~~~~~~--~~~~~~~~Gd~v~~~v~~~d~~~~~i~ls 68 (68)
T cd05707 1 GDVVRGFVKNIANNGVFVTL--------GRGVDARVRVSELSDSYLK--DWKKRFKVGQLVKGKIVSIDPDNGRIEMT 68 (68)
T ss_pred CCEEEEEEEEEECccEEEEe--------CCCCEEEEEHHHCCchhhc--CHhhccCCCCEEEEEEEEEeCCCCEEecC
Confidence 79999999999999999999 5569999999999765544 678999999999999999985 4556654
No 29
>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=99.07 E-value=1.2e-09 Score=75.50 Aligned_cols=74 Identities=24% Similarity=0.320 Sum_probs=62.7
Q ss_pred CCCCEEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeCC-CccEEEE
Q 029155 75 EPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGD-ARAYFLS 153 (198)
Q Consensus 75 ~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~-~~~~~LS 153 (198)
++|++|.|+|+++.+.+|+|++. .....|++|.++++..+.. ++.+.|++||.|.|+|.+++. .+.+.||
T Consensus 1 ~~g~~v~g~V~~i~~~g~~v~l~-------~~~~~g~i~~~~l~~~~~~--~~~~~~~~Gd~v~v~i~~vd~~~~~i~ls 71 (77)
T cd05708 1 KVGQKIDGTVRRVEDYGVFIDID-------GTNVSGLCHKSEISDNRVA--DASKLFRVGDKVRAKVLKIDAEKKRISLG 71 (77)
T ss_pred CCCCEEEEEEEEEEcceEEEEEC-------CCCeEEEEEHHHCCCCccC--CHhHeecCCCEEEEEEEEEeCCCCEEEEE
Confidence 46999999999999999999993 1368999999999765533 677899999999999999985 5789999
Q ss_pred EecC
Q 029155 154 TAKN 157 (198)
Q Consensus 154 t~~~ 157 (198)
++..
T Consensus 72 ~k~~ 75 (77)
T cd05708 72 LKAS 75 (77)
T ss_pred EEee
Confidence 8764
No 30
>PTZ00248 eukaryotic translation initiation factor 2 subunit 1; Provisional
Probab=99.04 E-value=9.9e-10 Score=96.23 Aligned_cols=77 Identities=18% Similarity=0.280 Sum_probs=67.7
Q ss_pred CCCCCCCEEEEEEEEEecceEEEEEeeecccccc-CcceeEEeccccccccccccccccCCCCCCEEEEEEEEeCC-Ccc
Q 029155 72 PVPEPGSVVIARVTKVMTRMASADIMCVGAKSVR-EKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGD-ARA 149 (198)
Q Consensus 72 ~~p~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~-~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~-~~~ 149 (198)
-.|++||+|.|+|++|.+.+++|+|. . .+..|+||.|++++.... ++++.|++||.|.++|++++. .+.
T Consensus 13 ~~P~~GdvV~g~V~~I~d~GafV~L~-------EY~gvEGlIhiSElS~~ri~--~i~d~vkvGd~v~vkVl~VD~ekg~ 83 (319)
T PTZ00248 13 KFPEEDDLVMVKVVRITEMGAYVSLL-------EYDDIEGMILMSELSKRRIR--SINKLIRVGRHEVVVVLRVDKEKGY 83 (319)
T ss_pred hCCCCCCEEEEEEEEEeCCeEEEEec-------CCCCcEEEEEHHHhcccccC--CHHHhcCCCCEEEEEEEEEeCCCCE
Confidence 46899999999999999999999993 2 268999999999877665 999999999999999999973 467
Q ss_pred EEEEEecC
Q 029155 150 YFLSTAKN 157 (198)
Q Consensus 150 ~~LSt~~~ 157 (198)
+.||.+.-
T Consensus 84 IdLS~K~v 91 (319)
T PTZ00248 84 IDLSKKRV 91 (319)
T ss_pred EEEEeeec
Confidence 99999864
No 31
>PRK07252 hypothetical protein; Provisional
Probab=99.03 E-value=2.3e-09 Score=81.85 Aligned_cols=73 Identities=18% Similarity=0.257 Sum_probs=63.5
Q ss_pred CCCCEEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeCC-CccEEEE
Q 029155 75 EPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGD-ARAYFLS 153 (198)
Q Consensus 75 ~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~-~~~~~LS 153 (198)
++|+++.|+|++|.+.+|+|+| .....|+||.++++..+.. +..+.|++||.|.|+|++++. .+.+.||
T Consensus 2 kvG~iv~G~V~~V~~~G~fVei--------~~~~~GllhiseLs~~~~~--~~~~~~~vGD~V~VkI~~iD~~~~ri~lS 71 (120)
T PRK07252 2 KIGDKLKGTITGIKPYGAFVAL--------ENGTTGLIHISEIKTGFID--NIHQLLKVGEEVLVQVVDFDEYTGKASLS 71 (120)
T ss_pred CCCCEEEEEEEEEeCcEEEEEE--------CCCCEEEEEHHHcCCcccc--ChhhccCCCCEEEEEEEEEeCCCCEEEEE
Confidence 5799999999999999999999 5568999999999865544 567889999999999999985 5678888
Q ss_pred EecC
Q 029155 154 TAKN 157 (198)
Q Consensus 154 t~~~ 157 (198)
++..
T Consensus 72 lk~~ 75 (120)
T PRK07252 72 LRTL 75 (120)
T ss_pred Eeec
Confidence 8765
No 32
>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=99.02 E-value=2.2e-09 Score=73.30 Aligned_cols=69 Identities=22% Similarity=0.316 Sum_probs=59.8
Q ss_pred CCEEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeCC-CccEEEEEe
Q 029155 77 GSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGD-ARAYFLSTA 155 (198)
Q Consensus 77 GDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~-~~~~~LSt~ 155 (198)
|+++.|+|+++.+.+++|++ .....|++|.+++...+.. +..+.|++||.|.++|++++. .+.+.||.+
T Consensus 1 g~~~~g~V~~v~~~G~~V~l--------~~~~~gli~~s~l~~~~~~--~~~~~~~~G~~i~v~v~~~d~~~~~i~ls~k 70 (70)
T cd05698 1 GLKTHGTIVKVKPNGCIVSF--------YNNVKGFLPKSELSEAFIK--DPEEHFRVGQVVKVKVLSCDPEQQRLLLSCK 70 (70)
T ss_pred CCEEEEEEEEEecCcEEEEE--------CCCCEEEEEHHHcChhhcC--CHHHcccCCCEEEEEEEEEcCCCCEEEEEeC
Confidence 89999999999999999999 4568999999999765544 677899999999999999985 467888864
No 33
>PRK05807 hypothetical protein; Provisional
Probab=99.01 E-value=3.6e-09 Score=82.37 Aligned_cols=73 Identities=21% Similarity=0.312 Sum_probs=64.3
Q ss_pred CCCCCEEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeCCCccEEEE
Q 029155 74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGDARAYFLS 153 (198)
Q Consensus 74 p~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~~~~~~LS 153 (198)
.++|++|.|+|+.+.+.+|+|+| . ...|+||+++++..+.. ++.+.|++||.|.++|++++..+.+.||
T Consensus 3 ~~vG~vv~G~Vt~i~~~GafV~L--------~-~~~Glvhiseis~~~v~--~~~~~~kvGd~V~VkV~~id~~gkI~LS 71 (136)
T PRK05807 3 LKAGSILEGTVVNITNFGAFVEV--------E-GKTGLVHISEVADTYVK--DIREHLKEQDKVKVKVISIDDNGKISLS 71 (136)
T ss_pred ccCCCEEEEEEEEEECCeEEEEE--------C-CEEEEEEhhhccccccc--CccccCCCCCEEEEEEEEECCCCcEEEE
Confidence 46899999999999999999999 2 34899999999876665 7789999999999999999866789999
Q ss_pred EecC
Q 029155 154 TAKN 157 (198)
Q Consensus 154 t~~~ 157 (198)
++..
T Consensus 72 lk~~ 75 (136)
T PRK05807 72 IKQA 75 (136)
T ss_pred EEec
Confidence 9874
No 34
>smart00316 S1 Ribosomal protein S1-like RNA-binding domain.
Probab=98.99 E-value=3.5e-09 Score=71.02 Aligned_cols=71 Identities=27% Similarity=0.356 Sum_probs=60.2
Q ss_pred CCCCEEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeCCC-ccEEEE
Q 029155 75 EPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGDA-RAYFLS 153 (198)
Q Consensus 75 ~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~~-~~~~LS 153 (198)
++|++|.|+|+++.+.++++++ ...+.|++|.+++...+.. ++.+.|++||.|.|+|.+++.. +.+.||
T Consensus 1 ~~G~~v~g~V~~v~~~g~~v~i--------~~~~~g~l~~~~~~~~~~~--~~~~~~~~G~~v~~~V~~~~~~~~~i~ls 70 (72)
T smart00316 1 EVGDVVEGTVTEITPFGAFVDL--------GNGVEGLIPISELSDKRVK--DPEEVLKVGDEVKVKVLSVDEEKGRIILS 70 (72)
T ss_pred CCCCEEEEEEEEEEccEEEEEe--------CCCCEEEEEHHHCCccccC--CHHHeecCCCEEEEEEEEEeCCCCEEEEE
Confidence 4699999999999999999999 5578999999998765433 5678899999999999999753 678887
Q ss_pred Ee
Q 029155 154 TA 155 (198)
Q Consensus 154 t~ 155 (198)
++
T Consensus 71 ~~ 72 (72)
T smart00316 71 LK 72 (72)
T ss_pred eC
Confidence 64
No 35
>PRK08059 general stress protein 13; Validated
Probab=98.98 E-value=4.7e-09 Score=80.25 Aligned_cols=76 Identities=26% Similarity=0.323 Sum_probs=65.8
Q ss_pred CCCCCEEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeCC-CccEEE
Q 029155 74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGD-ARAYFL 152 (198)
Q Consensus 74 p~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~-~~~~~L 152 (198)
+++|++|.|+|+++.+.+|+|+| ...+.|+||.++++..+.. ++.+.|++||.|.|+|++++. .+.+.|
T Consensus 5 ~k~G~iv~G~V~~i~~~G~fV~i--------~~~~~Gli~~sel~~~~~~--~~~~~~~vGD~I~vkI~~id~~~~~i~l 74 (123)
T PRK08059 5 YEVGSVVTGKVTGIQPYGAFVAL--------DEETQGLVHISEITHGFVK--DIHDFLSVGDEVKVKVLSVDEEKGKISL 74 (123)
T ss_pred CCCCCEEEEEEEEEecceEEEEE--------CCCCEEEEEHHHCCccccc--CHHHcCCCCCEEEEEEEEEECCCCeEEE
Confidence 57899999999999999999999 5678999999999765544 667899999999999999964 578999
Q ss_pred EEecCCC
Q 029155 153 STAKNDL 159 (198)
Q Consensus 153 St~~~~l 159 (198)
|++..+.
T Consensus 75 slk~~~~ 81 (123)
T PRK08059 75 SIRATEE 81 (123)
T ss_pred EEEEccc
Confidence 9987654
No 36
>PRK03987 translation initiation factor IF-2 subunit alpha; Validated
Probab=98.95 E-value=4.5e-09 Score=90.12 Aligned_cols=78 Identities=19% Similarity=0.192 Sum_probs=66.3
Q ss_pred CCCCCCCEEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeCC-CccE
Q 029155 72 PVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGD-ARAY 150 (198)
Q Consensus 72 ~~p~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~-~~~~ 150 (198)
-.|++||+|.|+|+++.+.+|+|++... .+..|+||.++++..... ++++.|++||.|.|+|++++. .+.+
T Consensus 4 ~~P~~GdiV~G~V~~I~~~G~fV~L~e~------~gieGlI~iSEls~~~i~--~i~~~~kvGd~V~vkVi~VD~~k~~I 75 (262)
T PRK03987 4 EWPEEGELVVGTVKEVKDFGAFVTLDEY------PGKEGFIHISEVASGWVK--NIRDHVKEGQKVVCKVIRVDPRKGHI 75 (262)
T ss_pred CCCCCCCEEEEEEEEEECCEEEEEECCC------CCcEEEEEHHHcCccccc--CHHHhCCCCCEEEEEEEEEecccCeE
Confidence 4689999999999999999999999311 157999999999765554 788999999999999999985 3679
Q ss_pred EEEEecC
Q 029155 151 FLSTAKN 157 (198)
Q Consensus 151 ~LSt~~~ 157 (198)
.||++.-
T Consensus 76 ~LSlK~v 82 (262)
T PRK03987 76 DLSLKRV 82 (262)
T ss_pred EEEEEec
Confidence 9999853
No 37
>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=98.94 E-value=6.1e-09 Score=71.13 Aligned_cols=68 Identities=19% Similarity=0.345 Sum_probs=58.5
Q ss_pred CCEEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeCC-CccEEEEE
Q 029155 77 GSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGD-ARAYFLST 154 (198)
Q Consensus 77 GDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~-~~~~~LSt 154 (198)
|+++.|+|+++.+.+++|++ .....|++|.++++..... ++.+.|++||.|.++|++++. .+.+.||.
T Consensus 1 G~~v~g~V~~v~~~Gv~V~l--------~~~v~g~i~~~~l~~~~~~--~~~~~~~~Gd~i~~~V~~id~~~~~i~ls~ 69 (69)
T cd05697 1 GQVVKGTIRKLRPSGIFVKL--------SDHIKGLVPPMHLADVRLK--HPEKKFKPGLKVKCRVLSVEPERKRLVLTL 69 (69)
T ss_pred CCEEEEEEEEEeccEEEEEe--------cCCcEEEEEHHHCCCcccc--CHHHcCCCCCEEEEEEEEEECCCCEEEEEC
Confidence 79999999999999999999 5679999999999765443 567889999999999999985 46788873
No 38
>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=98.94 E-value=6.8e-09 Score=71.79 Aligned_cols=68 Identities=21% Similarity=0.293 Sum_probs=58.2
Q ss_pred CCEEE-EEEEEE-ecceEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeCC-CccEEEE
Q 029155 77 GSVVI-ARVTKV-MTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGD-ARAYFLS 153 (198)
Q Consensus 77 GDiVi-G~V~~v-~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~-~~~~~LS 153 (198)
|+++- |+|+++ .+++++|++ ..+.+|++|.+++...+.+ ++.+.|++||.+.|+|++++. .+.+.||
T Consensus 1 G~v~~~g~V~~v~~~~G~~V~l--------~~gv~G~i~~s~l~~~~~~--~~~~~~~vG~~v~~kV~~id~~~~~i~lS 70 (71)
T cd05696 1 GAVVDSVKVTKVEPDLGAVFEL--------KDGLLGFVHISHLSDDKVP--SDTGPFKAGTTHKARIIGYSPMDGLLQLS 70 (71)
T ss_pred CcEeeeeEEEEEccCceEEEEe--------CCCCEEEEEHHHCCcchhc--CcccccCCCCEEEEEEEEEeCCCCEEEEe
Confidence 78888 999999 699999999 5679999999999765555 677889999999999999985 4578887
Q ss_pred E
Q 029155 154 T 154 (198)
Q Consensus 154 t 154 (198)
+
T Consensus 71 ~ 71 (71)
T cd05696 71 L 71 (71)
T ss_pred C
Confidence 4
No 39
>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=98.92 E-value=7.6e-09 Score=73.32 Aligned_cols=72 Identities=21% Similarity=0.319 Sum_probs=62.6
Q ss_pred CCCCCCEEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeCC-CccEE
Q 029155 73 VPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGD-ARAYF 151 (198)
Q Consensus 73 ~p~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~-~~~~~ 151 (198)
-+++|+++.|+|.++.+++++|++ .....|++|.++++..+.. ++.+.|++||.|.++|++++. .+.+.
T Consensus 11 ~~~~G~i~~g~V~~v~~~G~fv~l--------~~~~~g~v~~~el~~~~~~--~~~~~~~~Gd~v~vkV~~id~~~~~i~ 80 (83)
T cd04461 11 DLKPGMVVHGYVRNITPYGVFVEF--------LGGLTGLAPKSYISDEFVT--DPSFGFKKGQSVTAKVTSVDEEKQRFL 80 (83)
T ss_pred hCCCCCEEEEEEEEEeeceEEEEc--------CCCCEEEEEHHHCCccccc--CHHHhcCCCCEEEEEEEEEcCCCCEEE
Confidence 478999999999999999999999 4568999999999765544 778999999999999999975 46788
Q ss_pred EEE
Q 029155 152 LST 154 (198)
Q Consensus 152 LSt 154 (198)
||+
T Consensus 81 lsl 83 (83)
T cd04461 81 LSL 83 (83)
T ss_pred EeC
Confidence 874
No 40
>COG0539 RpsA Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]
Probab=98.92 E-value=3.7e-09 Score=98.13 Aligned_cols=75 Identities=24% Similarity=0.276 Sum_probs=68.8
Q ss_pred CCCCCCEEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeC-CCccEE
Q 029155 73 VPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLG-DARAYF 151 (198)
Q Consensus 73 ~p~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~-~~~~~~ 151 (198)
..++||+|.|+|++|++.+++|+| . ++.|++|++++++.+.+ .+++.|++||.|.++|++++ +.+.+.
T Consensus 189 ~l~~G~vV~G~V~~It~~GafVdi--------g-GvdGLlHiseiS~~rv~--~P~~vvkvGd~VkvkVi~~D~e~~RVs 257 (541)
T COG0539 189 KLEVGEVVEGVVKNITDYGAFVDI--------G-GVDGLLHISEISWKRVD--HPSEVVKVGDEVKVKVISLDEERGRVS 257 (541)
T ss_pred cCCCCceEEEEEEEeecCcEEEEe--------c-CeeeEEehhhccccccC--CHHHhcccCCEEEEEEEEEccCCCeEE
Confidence 478999999999999999999999 3 59999999999998888 99999999999999999998 457899
Q ss_pred EEEecCC
Q 029155 152 LSTAKND 158 (198)
Q Consensus 152 LSt~~~~ 158 (198)
||++...
T Consensus 258 LSlK~l~ 264 (541)
T COG0539 258 LSLKQLE 264 (541)
T ss_pred EEehhcc
Confidence 9998753
No 41
>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=98.87 E-value=2.7e-08 Score=69.54 Aligned_cols=68 Identities=21% Similarity=0.219 Sum_probs=58.7
Q ss_pred CCCCCEEEEEEEEEecceEEEEEeeecccccc-CcceeEEeccccccccccccccccCCCCCCEEEEEEEEeCC-CccEE
Q 029155 74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVR-EKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGD-ARAYF 151 (198)
Q Consensus 74 p~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~-~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~-~~~~~ 151 (198)
.+.|++|.|.|.+|.+.++++++ . ..+.|+||.+++... +.|++||.+.|+|++++. .+.+.
T Consensus 2 l~~G~~v~g~V~si~d~G~~v~~--------g~~gv~Gfl~~~~~~~~--------~~~~~Gq~v~~~V~~vd~~~~~v~ 65 (74)
T cd05694 2 LVEGMVLSGCVSSVEDHGYILDI--------GIPGTTGFLPKKDAGNF--------SKLKVGQLLLCVVEKVKDDGRVVS 65 (74)
T ss_pred CCCCCEEEEEEEEEeCCEEEEEe--------CCCCcEEEEEHHHCCcc--------cccCCCCEEEEEEEEEECCCCEEE
Confidence 46899999999999999999999 4 468999999997532 789999999999999974 46789
Q ss_pred EEEecC
Q 029155 152 LSTAKN 157 (198)
Q Consensus 152 LSt~~~ 157 (198)
||++..
T Consensus 66 ls~k~~ 71 (74)
T cd05694 66 LSADPS 71 (74)
T ss_pred EEEeec
Confidence 998754
No 42
>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=98.85 E-value=1.8e-08 Score=68.74 Aligned_cols=65 Identities=26% Similarity=0.377 Sum_probs=54.5
Q ss_pred CCEEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeCC-CccEEEE
Q 029155 77 GSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGD-ARAYFLS 153 (198)
Q Consensus 77 GDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~-~~~~~LS 153 (198)
||+|.|+|+++.+++++|++ ...+.|++|.+++..... . .+.|++||.|.|+|++++. .+.+.||
T Consensus 1 G~~V~g~V~~i~~~G~~v~l--------~~~v~g~v~~~~l~~~~~---~-~~~~~~G~~i~~kVi~id~~~~~i~LS 66 (66)
T cd05695 1 GMLVNARVKKVLSNGLILDF--------LSSFTGTVDFLHLDPEKS---S-KSTYKEGQKVRARILYVDPSTKVVGLS 66 (66)
T ss_pred CCEEEEEEEEEeCCcEEEEE--------cCCceEEEEHHHcCCccC---c-ccCcCCCCEEEEEEEEEeCCCCEEecC
Confidence 89999999999999999999 456999999999864332 2 7889999999999999984 4556665
No 43
>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=98.85 E-value=1.4e-08 Score=68.30 Aligned_cols=67 Identities=21% Similarity=0.256 Sum_probs=55.3
Q ss_pred CCCEEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeCC-CccEEEE
Q 029155 76 PGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGD-ARAYFLS 153 (198)
Q Consensus 76 vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~-~~~~~LS 153 (198)
+|+++.|+|+++.+.+|+|++ . ...|+||.++++..+.. .+.+.|++||.|+|+|.+++. .+.+.||
T Consensus 1 ~g~~~~g~V~~v~~~g~~v~l--------~-~~~g~l~~~e~~~~~~~--~~~~~~~~Gd~v~v~i~~vd~~~~~i~ls 68 (68)
T cd05688 1 EGDVVEGTVKSITDFGAFVDL--------G-GVDGLLHISDMSWGRVK--HPSEVVNVGDEVEVKVLKIDKERKRISLG 68 (68)
T ss_pred CCCEEEEEEEEEEeeeEEEEE--------C-CeEEEEEhHHCCCcccc--CHhHEECCCCEEEEEEEEEECCCCEEecC
Confidence 499999999999999999999 3 47899999998754443 567889999999999999974 3455554
No 44
>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=98.84 E-value=2.7e-08 Score=66.95 Aligned_cols=68 Identities=19% Similarity=0.299 Sum_probs=57.3
Q ss_pred CCEEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeCCCccEEEEE
Q 029155 77 GSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGDARAYFLST 154 (198)
Q Consensus 77 GDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~~~~~~LSt 154 (198)
|+++.|+|+++.+++|+|+| .....|++|.++++..+.. ...+.|++||.|.++|.+++..+.+.||+
T Consensus 1 g~~~~g~V~~v~~~G~~v~l--------~~~~~g~l~~~~l~~~~~~--~~~~~~~~Gd~v~v~v~~~d~~~~i~ls~ 68 (68)
T cd04472 1 GKIYEGKVVKIKDFGAFVEI--------LPGKDGLVHISELSDERVE--KVEDVLKVGDEVKVKVIEVDDRGRISLSR 68 (68)
T ss_pred CCEEEEEEEEEEEeEEEEEe--------CCCCEEEEEhHHcCCcccc--CHHHccCCCCEEEEEEEEECCCCcEEeeC
Confidence 78999999999999999999 5568999999999755443 55688999999999999997655677763
No 45
>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=98.82 E-value=1.8e-08 Score=67.54 Aligned_cols=67 Identities=28% Similarity=0.267 Sum_probs=56.3
Q ss_pred CCEEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeCC-CccEEEE
Q 029155 77 GSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGD-ARAYFLS 153 (198)
Q Consensus 77 GDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~-~~~~~LS 153 (198)
|+++.|+|+++.+.+|+|++ .....|++|.++++..... ++.+.|++||.|.|+|.+++. .+.+.||
T Consensus 1 g~~~~g~V~~i~~~G~fv~l--------~~~~~g~~~~~~l~~~~~~--~~~~~~~~Gd~v~v~i~~vd~~~~~i~ls 68 (68)
T cd05685 1 GMVLEGVVTNVTDFGAFVDI--------GVKQDGLIHISKMADRFVS--HPSDVVSVGDIVEVKVISIDEERGRISLS 68 (68)
T ss_pred CCEEEEEEEEEecccEEEEc--------CCCCEEEEEHHHCCCcccc--CHHHhcCCCCEEEEEEEEEECCCCEEecC
Confidence 78999999999999999999 5568999999999765444 667889999999999999974 3556554
No 46
>cd04453 S1_RNase_E S1_RNase_E: RNase E and RNase G, S1-like RNA-binding domain. RNase E is an essential endoribonuclease in the processing and degradation of RNA. In addition to its role in mRNA degradation, RNase E has also been implicated in the processing of rRNA, and the maturation of tRNA, 10Sa RNA and the M1 precursor of RNase P. RNase E associates with PNPase (3' to 5' exonuclease), Rhl B (DEAD-box RNA helicase) and enolase (glycolytic enzyme) to form the RNA degradosome. RNase E tends to cut mRNA within single-stranded regions that are rich in A/U nucleotides. The N-terminal region of RNase E contains the catalytic site. Within the conserved N-terminal domain of RNAse E and RNase G, there is an S1-like subdomain, which is an ancient single-stranded RNA-binding domain. S1 domain is an RNA-binding module originally identified in the ribosomal protein S1. The S1 domain is required for RNA cleavage by RNase E. RNase G is paralogous to RNase E with an N-terminal catalytic domain th
Probab=98.81 E-value=4e-08 Score=70.92 Aligned_cols=74 Identities=19% Similarity=0.239 Sum_probs=58.0
Q ss_pred CCCCCEEEEEEEEEecc--eEEEEEeeeccccccCcceeEEecccccccc-ccccccccCCCCCCEEEEEEEEeCC-Ccc
Q 029155 74 PEPGSVVIARVTKVMTR--MASADIMCVGAKSVREKFSGIIRQQDVRATE-IDKVDMHLSFRPGDIVRASVLSLGD-ARA 149 (198)
Q Consensus 74 p~vGDiViG~V~~v~~~--~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~-~d~~~~~~~~~~GDiV~AkV~s~~~-~~~ 149 (198)
+++|+++.|+|+++.+. .|+|+| ....+|+||.++++... ....++.+.|++||.|.++|+...- ...
T Consensus 5 ~~~G~iy~g~V~~i~~~~~GaFV~l--------~~g~~Gllh~seis~~~~~~v~~~~~~~~~Gd~v~VqV~~~~~~~K~ 76 (88)
T cd04453 5 PIVGNIYLGRVKKIVPGLQAAFVDI--------GLGKNGFLHLSDILPAYFKKHKKIAKLLKEGQEILVQVVKEPIGTKG 76 (88)
T ss_pred CCCCCEEEEEEEEeccCCcEEEEEe--------CCCCEEEEEhHHcCchhccccCCHHHcCCCCCEEEEEEEEecCCCCC
Confidence 57999999999999996 999999 55689999999986511 1122567899999999999999752 344
Q ss_pred EEEEEe
Q 029155 150 YFLSTA 155 (198)
Q Consensus 150 ~~LSt~ 155 (198)
..||+.
T Consensus 77 ~~lt~~ 82 (88)
T cd04453 77 PRLTTN 82 (88)
T ss_pred ceEEEE
Confidence 556554
No 47
>PHA02945 interferon resistance protein; Provisional
Probab=98.75 E-value=8.6e-08 Score=68.74 Aligned_cols=73 Identities=12% Similarity=0.128 Sum_probs=61.1
Q ss_pred CCCCCCCEEEEEEEEEecceEEEEEeeeccccccC-cceeEEecccc--ccccccccccccCCCCCCEEEEEEEEeCCC-
Q 029155 72 PVPEPGSVVIARVTKVMTRMASADIMCVGAKSVRE-KFSGIIRQQDV--RATEIDKVDMHLSFRPGDIVRASVLSLGDA- 147 (198)
Q Consensus 72 ~~p~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~-~~~G~l~~s~v--~~~~~d~~~~~~~~~~GDiV~AkV~s~~~~- 147 (198)
-.|++||+|+|+|.. .+..++|++. .+ ..+|+||.|++ ...-.. + ++.+ .|..|.|||+.++..
T Consensus 7 ~~P~~GelvigtV~~-~d~ga~v~L~-------EY~g~eg~i~~seveva~~wvK--~-rd~l-~GqkvV~KVirVd~~k 74 (88)
T PHA02945 7 SLPNVGDVLKGKVYE-NGYALYIDLF-------DYPHSEAILAESVQMHMNRYFK--Y-RDKL-VGKTVKVKVIRVDYTK 74 (88)
T ss_pred cCCCCCcEEEEEEEe-cCceEEEEec-------ccCCcEEEEEeehhhhccceEe--e-eeEe-cCCEEEEEEEEECCCC
Confidence 469999999999999 9999999994 23 67999999955 554444 5 8999 999999999999864
Q ss_pred ccEEEEEec
Q 029155 148 RAYFLSTAK 156 (198)
Q Consensus 148 ~~~~LSt~~ 156 (198)
+.+-||++.
T Consensus 75 g~IDlSlK~ 83 (88)
T PHA02945 75 GYIDVNYKR 83 (88)
T ss_pred CEEEeEeeE
Confidence 678999874
No 48
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=98.73 E-value=1.4e-08 Score=97.54 Aligned_cols=100 Identities=17% Similarity=0.218 Sum_probs=79.3
Q ss_pred CCceEEEEeEeeeEEEcCCCCCCCCCCCeEEEecCCCCCCCCCCCCEEEEEEEEEecceEEEEEeeeccccccCcceeEE
Q 029155 33 KHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHKAHGPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGII 112 (198)
Q Consensus 33 ~g~~~i~asv~G~v~~~~~~~~~~~~~~~i~V~p~~~~~~~p~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l 112 (198)
+|. ++++..+..... ..+..|...+. .+++|+++.|+|+++.+++++|+| ....+|++
T Consensus 592 ~G~--v~i~~~~~~~~~-------~a~~~I~~~~~-----~~~vG~v~~G~V~~I~~fGafVei--------~~~~~Gll 649 (693)
T PRK11824 592 DGT--VKIAATDGEAAE-------AAKERIEGITA-----EPEVGEIYEGKVVRIVDFGAFVEI--------LPGKDGLV 649 (693)
T ss_pred Cce--EEEEcccHHHHH-------HHHHHHHHhcc-----cCcCCeEEEEEEEEEECCeEEEEE--------CCCCEEEE
Confidence 445 777777766652 12234444332 378999999999999999999999 45689999
Q ss_pred eccccccccccccccccCCCCCCEEEEEEEEeCCCccEEEEEec
Q 029155 113 RQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGDARAYFLSTAK 156 (198)
Q Consensus 113 ~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~~~~~~LSt~~ 156 (198)
|+++++..+.. +..+.|++||.|.++|++++..+.+.||++.
T Consensus 650 hiSels~~~v~--~~~~v~kvGD~V~VkV~~iD~~grI~LS~k~ 691 (693)
T PRK11824 650 HISEIADERVE--KVEDVLKEGDEVKVKVLEIDKRGRIRLSRKA 691 (693)
T ss_pred EeeeccCcccc--CccceeCCCCEEEEEEEEECCCCcEEEEEEe
Confidence 99999876655 7789999999999999999865789999875
No 49
>COG1093 SUI2 Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis]
Probab=98.70 E-value=2.9e-08 Score=84.19 Aligned_cols=78 Identities=22% Similarity=0.241 Sum_probs=68.0
Q ss_pred CCCCCCCCEEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeCCC-cc
Q 029155 71 GPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGDA-RA 149 (198)
Q Consensus 71 ~~~p~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~~-~~ 149 (198)
+-.|.+||+|+|+|.+|.+.+|+|.+.-. .+.+|++|+|++...-.. ++++.++.|..+.|+|++++.. +.
T Consensus 6 ~~~PeeGEiVv~tV~~V~~~GAyv~L~EY------~g~Eg~ihiSEvas~wVk--nIrd~vkegqkvV~kVlrVd~~rg~ 77 (269)
T COG1093 6 REYPEEGEIVVGTVKQVADYGAYVELDEY------PGKEGFIHISEVASGWVK--NIRDYVKEGQKVVAKVLRVDPKRGH 77 (269)
T ss_pred cCCCCCCcEEEEEEEEeeccccEEEeecc------CCeeeeEEHHHHHHHHHH--HHHHHhhcCCeEEEEEEEEcCCCCe
Confidence 45799999999999999999999999421 247899999999877766 9999999999999999999864 66
Q ss_pred EEEEEec
Q 029155 150 YFLSTAK 156 (198)
Q Consensus 150 ~~LSt~~ 156 (198)
+.||++.
T Consensus 78 IDLSlkr 84 (269)
T COG1093 78 IDLSLKR 84 (269)
T ss_pred Eeeehhh
Confidence 8999875
No 50
>PRK08563 DNA-directed RNA polymerase subunit E'; Provisional
Probab=98.70 E-value=1.8e-07 Score=76.16 Aligned_cols=83 Identities=22% Similarity=0.262 Sum_probs=66.8
Q ss_pred CCCCCCCEEEEEEEEEecceEEEEEeeeccccccCcceeEEecccccccccc--c-------cccccCCCCCCEEEEEEE
Q 029155 72 PVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEID--K-------VDMHLSFRPGDIVRASVL 142 (198)
Q Consensus 72 ~~p~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d--~-------~~~~~~~~~GDiV~AkV~ 142 (198)
+.|.+|++|.|+|+++...++++++ . +++|++|.+++...+.. . .+....|+.||.|++||.
T Consensus 77 f~P~~GEVv~g~V~~v~~~Gi~V~l--------g-~~~g~v~~~~l~~~~~~~d~~~~~~~~~~~~~~i~~Gd~VrvrV~ 147 (187)
T PRK08563 77 FKPELQEVVEGEVVEVVEFGAFVRI--------G-PVDGLLHISQIMDDYISYDPKNGRLIGKESKRVLKVGDVVRARIV 147 (187)
T ss_pred EeccCCCEEEEEEEEEEccEEEEEE--------e-CceEEEEcHHcCCCceEEccccceEEEccCCeEEcCCCEEEEEEE
Confidence 4588999999999999999999999 3 58999999988643211 0 124567899999999999
Q ss_pred EeCCC------ccEEEEEecCCCeeeE
Q 029155 143 SLGDA------RAYFLSTAKNDLGVVS 163 (198)
Q Consensus 143 s~~~~------~~~~LSt~~~~lGvv~ 163 (198)
+++-. ..+.||++++.||.+.
T Consensus 148 ~v~~~~~~~~~~~I~ls~~~~~LG~~~ 174 (187)
T PRK08563 148 AVSLKERRPRGSKIGLTMRQPGLGKLE 174 (187)
T ss_pred EEEcccCCCCCCEEEEEecCCCCCcHH
Confidence 98632 3689999999999874
No 51
>PRK07400 30S ribosomal protein S1; Reviewed
Probab=98.70 E-value=9.3e-08 Score=84.14 Aligned_cols=76 Identities=24% Similarity=0.290 Sum_probs=65.8
Q ss_pred CCCCCCCEEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeCC-CccE
Q 029155 72 PVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGD-ARAY 150 (198)
Q Consensus 72 ~~p~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~-~~~~ 150 (198)
.-+++|++|.|+|+++.+.+++|++. +..|++|+++++..+.. ++.+.|++||.|.|+|++++. .+.+
T Consensus 192 ~~~k~G~vv~G~V~~I~~~G~fV~i~---------gv~Gllhisels~~~~~--~~~~~~~vGd~VkvkVl~iD~e~~rI 260 (318)
T PRK07400 192 NRLEVGEVVVGTVRGIKPYGAFIDIG---------GVSGLLHISEISHEHIE--TPHSVFNVNDEMKVMIIDLDAERGRI 260 (318)
T ss_pred ccCCCCCEEEEEEEEEECCeEEEEEC---------CEEEEEEHHHccccccc--ChhhccCCCCEEEEEEEEEeCCCCEE
Confidence 34789999999999999999999982 46799999999876655 788999999999999999974 5789
Q ss_pred EEEEecCC
Q 029155 151 FLSTAKND 158 (198)
Q Consensus 151 ~LSt~~~~ 158 (198)
.||++..+
T Consensus 261 ~LS~K~l~ 268 (318)
T PRK07400 261 SLSTKQLE 268 (318)
T ss_pred EEEEeccc
Confidence 99998644
No 52
>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=98.69 E-value=1.8e-07 Score=65.47 Aligned_cols=72 Identities=15% Similarity=0.206 Sum_probs=59.5
Q ss_pred CCEEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccccccc-cccccccCCCCCCEEEEEEEEeCCCccEEEEEe
Q 029155 77 GSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEI-DKVDMHLSFRPGDIVRASVLSLGDARAYFLSTA 155 (198)
Q Consensus 77 GDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~-d~~~~~~~~~~GDiV~AkV~s~~~~~~~~LSt~ 155 (198)
|+++.|+|+++.+.+++|+|... ..+..|++|.++++.... + ++.+.|++||.|.++|++++ .+.+.||++
T Consensus 1 G~~~~g~V~~v~~~G~fv~l~~~-----~~~~~gll~~s~l~~~~~~~--~~~~~~~~Gd~v~v~v~~vd-~~~i~~s~k 72 (79)
T cd05684 1 GKIYKGKVTSIMDFGCFVQLEGL-----KGRKEGLVHISQLSFEGRVA--NPSDVVKRGQKVKVKVISIQ-NGKISLSMK 72 (79)
T ss_pred CCEEEEEEEEEEeeeEEEEEeCC-----CCCcEEEEEhHhccCCCCcC--ChhheeCCCCEEEEEEEEEe-CCEEEEEEE
Confidence 78999999999999999999310 035799999999975543 4 67789999999999999998 678888886
Q ss_pred c
Q 029155 156 K 156 (198)
Q Consensus 156 ~ 156 (198)
.
T Consensus 73 ~ 73 (79)
T cd05684 73 D 73 (79)
T ss_pred e
Confidence 5
No 53
>cd05690 S1_RPS1_repeat_ec5 S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 5 (ec5) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=98.68 E-value=9.1e-08 Score=64.90 Aligned_cols=66 Identities=17% Similarity=0.260 Sum_probs=54.2
Q ss_pred CCEEEEEEEEEecceEEEEEeeeccccccCcceeEEecccccc-ccccccccccCCCCCCEEEEEEEEeCC-CccEEE
Q 029155 77 GSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRA-TEIDKVDMHLSFRPGDIVRASVLSLGD-ARAYFL 152 (198)
Q Consensus 77 GDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~-~~~d~~~~~~~~~~GDiV~AkV~s~~~-~~~~~L 152 (198)
|+++.|+|+++.+.+++|++ ....+|++|.++++. .... +..+.|++||.|.|+|++++. .+.+.|
T Consensus 1 G~~~~g~V~~i~~~G~fv~l--------~~~~~Glv~~~~l~~~~~~~--~~~~~~~~G~~v~v~v~~id~~~~~i~l 68 (69)
T cd05690 1 GTVVSGKIKSITDFGIFVGL--------DGGIDGLVHISDISWTQRVR--HPSEIYKKGQEVEAVVLNIDVERERISL 68 (69)
T ss_pred CCEEEEEEEEEEeeeEEEEe--------CCCCEEEEEHHHCCCccccC--ChhhEECCCCEEEEEEEEEECCcCEEeC
Confidence 78999999999999999999 556899999999973 2222 557889999999999999974 344554
No 54
>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=98.64 E-value=1.5e-07 Score=69.02 Aligned_cols=77 Identities=21% Similarity=0.264 Sum_probs=61.4
Q ss_pred CEEEEEEEEEecceEEEEEeeeccccccCcceeEEecccccccccccc---------ccccCCCCCCEEEEEEEEeCCC-
Q 029155 78 SVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKV---------DMHLSFRPGDIVRASVLSLGDA- 147 (198)
Q Consensus 78 DiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~---------~~~~~~~~GDiV~AkV~s~~~~- 147 (198)
+++.|+|+++.+.+++|++ . +..|++|.++++..+.... ...+.|++||.|.++|.+++..
T Consensus 1 ~vv~g~V~~i~~~GifV~l--------~-~v~G~v~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~Gd~v~vkI~~vd~~~ 71 (99)
T cd04460 1 EVVEGEVVEVVDFGAFVRI--------G-PVDGLLHISQIMDDYISYDPKNKRLIGEETKRVLKVGDVVRARIVAVSLKE 71 (99)
T ss_pred CEEEEEEEEEEeccEEEEE--------c-CeEEEEEEEEccCCceEechhheeecccCcCCEECCCCEEEEEEEEEeHHH
Confidence 4789999999999999999 3 3789999999864432210 1236789999999999999732
Q ss_pred -----ccEEEEEecCCCeeeE
Q 029155 148 -----RAYFLSTAKNDLGVVS 163 (198)
Q Consensus 148 -----~~~~LSt~~~~lGvv~ 163 (198)
..+.||++++.||.+.
T Consensus 72 ~~~~~~~i~ls~k~~~~g~~~ 92 (99)
T cd04460 72 RRPRESKIGLTMRQPGLGKLE 92 (99)
T ss_pred CcCCCceEEEEEecCCCCcHH
Confidence 4799999999999864
No 55
>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=98.63 E-value=1.8e-07 Score=75.74 Aligned_cols=84 Identities=23% Similarity=0.294 Sum_probs=67.4
Q ss_pred CCCCCCCCEEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccccccc--ccc-------ccccCCCCCCEEEEEE
Q 029155 71 GPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEI--DKV-------DMHLSFRPGDIVRASV 141 (198)
Q Consensus 71 ~~~p~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~--d~~-------~~~~~~~~GDiV~AkV 141 (198)
.+.|.+|+++.|+|++++..++++++ . +++|++|.+++...+. |.. +....|+.||.|++||
T Consensus 76 ~f~p~~gEvv~G~V~~v~~~GifV~l--------g-~~~gi~~~~~l~~~~~~~d~~~~~~~~~~~~~~~~~Gd~VrvrV 146 (179)
T TIGR00448 76 VFKPELGEIVEGEVIEIVEFGAFVSL--------G-PFDGLFHVSQVTDDYCYYDPKESALIGKETKKVLDEGDKVRARI 146 (179)
T ss_pred EEeccCCCEEEEEEEEEEeeEEEEEe--------C-CceEEEEcHHhCCCceEEccccceEEEccCCeEEcCCCEEEEEE
Confidence 34588999999999999999999999 3 5899999998763321 110 2346799999999999
Q ss_pred EEeC------CCccEEEEEecCCCeeeE
Q 029155 142 LSLG------DARAYFLSTAKNDLGVVS 163 (198)
Q Consensus 142 ~s~~------~~~~~~LSt~~~~lGvv~ 163 (198)
.+++ +...+.||++++.||.+.
T Consensus 147 ~~v~~~~~~~~~~~I~lt~k~~~LG~~~ 174 (179)
T TIGR00448 147 VALSLKDRRPEGSKIGLTMRQPLLGKLE 174 (179)
T ss_pred EEEEccCCCCCcceEEEEeccCcCCccc
Confidence 9985 235699999999999874
No 56
>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=98.62 E-value=1.4e-07 Score=90.36 Aligned_cols=71 Identities=15% Similarity=0.281 Sum_probs=61.4
Q ss_pred CCCCCCEEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccc---c-ccccccccccCCCCCCEEEEEEEEeCCCc
Q 029155 73 VPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVR---A-TEIDKVDMHLSFRPGDIVRASVLSLGDAR 148 (198)
Q Consensus 73 ~p~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~---~-~~~d~~~~~~~~~~GDiV~AkV~s~~~~~ 148 (198)
.|++|+++.|+|++|.+++++|+| ..+.+|++|+|+++ + .+.. ++.+.|++||.|.++|+++++.+
T Consensus 644 ~~~vG~i~~GkV~~I~dfGaFVel--------~~G~eGLvHISeisdls~~~rv~--~~~dv~kvGd~V~VKVl~ID~~g 713 (719)
T TIGR02696 644 MPEVGERFLGTVVKTTAFGAFVSL--------LPGKDGLLHISQIRKLAGGKRVE--NVEDVLSVGQKIQVEIADIDDRG 713 (719)
T ss_pred cCCCCCEEEEEEEEEECceEEEEe--------cCCceEEEEhhhccccccccCcC--CHHHcCCCCCEEEEEEEEECCCC
Confidence 489999999999999999999999 56789999999885 2 2333 88999999999999999998666
Q ss_pred cEEEE
Q 029155 149 AYFLS 153 (198)
Q Consensus 149 ~~~LS 153 (198)
.+.|+
T Consensus 714 KI~L~ 718 (719)
T TIGR02696 714 KLSLV 718 (719)
T ss_pred Ceeec
Confidence 77775
No 57
>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=98.55 E-value=2.7e-07 Score=60.53 Aligned_cols=64 Identities=19% Similarity=0.283 Sum_probs=51.8
Q ss_pred EEEEEEEEecceEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeCC-CccEEEE
Q 029155 80 VIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGD-ARAYFLS 153 (198)
Q Consensus 80 ViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~-~~~~~LS 153 (198)
+.|+|+++.+.+++|++ .....|++|.++++..... ++.+.|++||.|+|+|++++. .+.+.||
T Consensus 1 v~g~V~~v~~~g~~v~l--------~~~~~g~~~~~~~~~~~~~--~~~~~~~~G~~v~~~v~~~d~~~~~i~ls 65 (65)
T cd00164 1 VTGKVVSITKFGVFVEL--------EDGVEGLVHISELSDKFVK--DPSEVFKVGDEVEVKVLEVDPEKGRISLS 65 (65)
T ss_pred CEEEEEEEEeeeEEEEe--------cCCCEEEEEHHHCCCcccc--CHhhEeCCCCEEEEEEEEEcCCcCEEecC
Confidence 47999999999999999 5568999999998754432 567889999999999999974 3445543
No 58
>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=98.54 E-value=6.3e-07 Score=61.42 Aligned_cols=69 Identities=19% Similarity=0.300 Sum_probs=55.3
Q ss_pred CCCCEEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeCCC-ccEEE
Q 029155 75 EPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGDA-RAYFL 152 (198)
Q Consensus 75 ~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~~-~~~~L 152 (198)
.+|+++.|+|+++.+.+++|++ ....+|++|.+++...+ ...+..+.|++||.|.++|++++.. +.+.|
T Consensus 2 ~~g~~~~g~V~~i~~~G~fv~l--------~~~~~Gl~~~~~l~~~~-~~~~~~~~~~~Gd~v~v~v~~id~~~~~i~~ 71 (72)
T cd05689 2 PEGTRLFGKVTNLTDYGCFVEL--------EEGVEGLVHVSEMDWTN-KNIHPSKVVSLGDEVEVMVLDIDEERRRISL 71 (72)
T ss_pred cCCCEEEEEEEEEEeeEEEEEc--------CCCCEEEEEEEeccCcc-cccCcccEeCCCCEEEEEEEEeeCCcCEEeC
Confidence 4799999999999999999999 45689999999996421 1225568899999999999999743 34443
No 59
>PRK07400 30S ribosomal protein S1; Reviewed
Probab=98.52 E-value=4.3e-07 Score=79.93 Aligned_cols=76 Identities=20% Similarity=0.202 Sum_probs=66.2
Q ss_pred CCCCCCCEEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeCC-CccE
Q 029155 72 PVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGD-ARAY 150 (198)
Q Consensus 72 ~~p~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~-~~~~ 150 (198)
+..++||+|.|+|+++.+++++|+| .....|+||.++++..+.. ++.+.|++||.|.++|++.++ .+.+
T Consensus 27 ~~~~~G~iv~G~V~~i~~~g~~Vdi--------g~k~~g~lp~sEis~~~~~--~~~~~~~~G~~v~~~Vi~~~~~~~~i 96 (318)
T PRK07400 27 YHFKPGDIVNGTVFSLEPRGALIDI--------GAKTAAFMPIQEMSINRVE--GPEEVLQPNETREFFILSDENEDGQL 96 (318)
T ss_pred hhcCCCCEEEEEEEEEECCEEEEEE--------CCCeEEEEEHHHhcccccc--CHHHccCCCCEEEEEEEEEeCCCCeE
Confidence 3479999999999999999999999 5667999999999876655 778999999999999999864 4679
Q ss_pred EEEEecC
Q 029155 151 FLSTAKN 157 (198)
Q Consensus 151 ~LSt~~~ 157 (198)
.||.+..
T Consensus 97 ~lS~k~~ 103 (318)
T PRK07400 97 TLSIRRI 103 (318)
T ss_pred EEehhhh
Confidence 9999864
No 60
>PRK13806 rpsA 30S ribosomal protein S1; Provisional
Probab=98.51 E-value=4.3e-07 Score=84.19 Aligned_cols=74 Identities=19% Similarity=0.215 Sum_probs=64.9
Q ss_pred CCCCCEEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeC-CCccEEE
Q 029155 74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLG-DARAYFL 152 (198)
Q Consensus 74 p~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~-~~~~~~L 152 (198)
.++|++|.|+|+++.+++++|++ ..++.|++|.+++...+.. +..+.|++||.|.|+|++++ +.+.+.|
T Consensus 377 ~~vG~~v~G~V~~i~~~G~FV~l--------~~gv~Gli~~se~s~~~~~--~~~~~~~~Gd~v~~~V~~id~e~~ri~L 446 (491)
T PRK13806 377 FAPGTTVTGTVEKRAQFGLFVNL--------APGVTGLLPASVISRAGKP--ATYEKLKPGDSVTLVVEEIDTAKRKISL 446 (491)
T ss_pred CCCCCEEEEEEEEEecCceEEEc--------CCCcEEEEEHHHcCccccc--chhhcCCCCCEEEEEEEEEeCCCCEEEE
Confidence 46899999999999999999999 5689999999999865554 67889999999999999997 3567999
Q ss_pred EEecC
Q 029155 153 STAKN 157 (198)
Q Consensus 153 St~~~ 157 (198)
|++..
T Consensus 447 s~~~~ 451 (491)
T PRK13806 447 APAGA 451 (491)
T ss_pred Eeehh
Confidence 99854
No 61
>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=98.48 E-value=1.3e-06 Score=59.29 Aligned_cols=66 Identities=17% Similarity=0.273 Sum_probs=53.8
Q ss_pred CCEEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeCC-CccEEEEEe
Q 029155 77 GSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGD-ARAYFLSTA 155 (198)
Q Consensus 77 GDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~-~~~~~LSt~ 155 (198)
|++|.|+|+++.+.+++|++ . .+.|+||.+++...+.. ++.+ .+||.+.|+|++++. .+.+.||.+
T Consensus 1 G~iv~g~V~~v~~~G~~v~l--------~-g~~gfip~s~~~~~~~~--~~~~--~vG~~i~~~i~~vd~~~~~i~lS~k 67 (67)
T cd04465 1 GEIVEGKVTEKVKGGLIVDI--------E-GVRAFLPASQVDLRPVE--DLDE--YVGKELKFKIIEIDRERNNIVLSRR 67 (67)
T ss_pred CCEEEEEEEEEECCeEEEEE--------C-CEEEEEEHHHCCCcccC--ChHH--hCCCEEEEEEEEEeCCCCEEEEEcC
Confidence 78999999999999999999 3 58999999998754433 3333 389999999999985 567888853
No 62
>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=98.47 E-value=1.4e-06 Score=59.43 Aligned_cols=62 Identities=26% Similarity=0.401 Sum_probs=51.3
Q ss_pred CCCCEEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeCCC---ccEE
Q 029155 75 EPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGDA---RAYF 151 (198)
Q Consensus 75 ~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~~---~~~~ 151 (198)
+.|++|.|+|.++.++.++|+| .. .+|+||.+++.. .+.|++||.|.+.|.++++. .++.
T Consensus 2 ~~g~iV~G~V~~~~~~~~~vdi--------g~-~eg~lp~~e~~~--------~~~~~~Gd~v~v~v~~v~~~~~~~~i~ 64 (67)
T cd04455 2 REGEIVTGIVKRVDRGNVIVDL--------GK-VEAILPKKEQIP--------GESYRPGDRIKAYVLEVRKTSKGPQII 64 (67)
T ss_pred CCCCEEEEEEEEEcCCCEEEEc--------CC-eEEEeeHHHCCC--------CCcCCCCCEEEEEEEEEecCCCCCEEE
Confidence 5799999999999999999999 44 799999988752 35689999999999999742 3455
Q ss_pred EE
Q 029155 152 LS 153 (198)
Q Consensus 152 LS 153 (198)
||
T Consensus 65 lS 66 (67)
T cd04455 65 LS 66 (67)
T ss_pred Ee
Confidence 55
No 63
>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=98.47 E-value=3.6e-06 Score=58.89 Aligned_cols=63 Identities=19% Similarity=0.258 Sum_probs=54.6
Q ss_pred CCCCCEEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeCCCccEEEE
Q 029155 74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGDARAYFLS 153 (198)
Q Consensus 74 p~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~~~~~~LS 153 (198)
+++|+.+.|+|+++++.++++++ .....|++|.+++ .+.|+.||.+.++|.++.+.+.+.||
T Consensus 14 ~~~G~~~~g~V~~i~~~G~fV~l--------~~~~~Glv~~se~----------~~~~~iGd~v~v~I~~i~e~~~i~l~ 75 (77)
T cd04473 14 LEVGKLYKGKVNGVAKYGVFVDL--------NDHVRGLIHRSNL----------LRDYEVGDEVIVQVTDIPENGNIDLI 75 (77)
T ss_pred CCCCCEEEEEEEeEecceEEEEE--------CCCcEEEEEchhc----------cCcCCCCCEEEEEEEEECCCCcEEEE
Confidence 78999999999999999999999 5569999999874 35699999999999999545677777
Q ss_pred E
Q 029155 154 T 154 (198)
Q Consensus 154 t 154 (198)
.
T Consensus 76 ~ 76 (77)
T cd04473 76 P 76 (77)
T ss_pred E
Confidence 4
No 64
>COG0539 RpsA Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]
Probab=98.45 E-value=5.3e-07 Score=83.96 Aligned_cols=74 Identities=20% Similarity=0.207 Sum_probs=67.6
Q ss_pred CCCCCEEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeCC-CccEEE
Q 029155 74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGD-ARAYFL 152 (198)
Q Consensus 74 p~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~-~~~~~L 152 (198)
..+|+.+.|+|+.+++++++|+| ..+.+|++|+|++++++.. ..++.++.||.|.++|++++. .+.+.|
T Consensus 275 ~~~g~~v~G~Vt~i~~~GafVei--------~~GvEGlvhvSEisw~~~~--~P~evv~~Gq~V~V~Vl~id~e~rRIsL 344 (541)
T COG0539 275 YPVGDKVEGKVTNLTDYGAFVEI--------EEGVEGLVHVSEISWTKKN--VPSEVVKVGQEVEVKVLDIDPERRRISL 344 (541)
T ss_pred cCCCCEEEEEEEEeecCcEEEEe--------cCCccceeechhhcccccC--CHHHhcccCCEEEEEEEeeCchhceEEe
Confidence 57899999999999999999999 7899999999999988876 499999999999999999984 578999
Q ss_pred EEecC
Q 029155 153 STAKN 157 (198)
Q Consensus 153 St~~~ 157 (198)
|++..
T Consensus 345 ~iKq~ 349 (541)
T COG0539 345 GLKQL 349 (541)
T ss_pred eehhh
Confidence 99863
No 65
>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=98.45 E-value=5.2e-07 Score=86.75 Aligned_cols=91 Identities=16% Similarity=0.224 Sum_probs=70.0
Q ss_pred EEEeEeeeEEEcCCCCCCCCCCCeEEEecCCCCCCCCCCCCEEEEEEEEEecceEEEEEeeeccccccCcceeEEecccc
Q 029155 38 VYASLTGLLRTLSPPPDSPDQRPTVEVTGHKAHGPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDV 117 (198)
Q Consensus 38 i~asv~G~v~~~~~~~~~~~~~~~i~V~p~~~~~~~p~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v 117 (198)
++++..+..... ..+..|.... ..|++|+++.|+|+++.+++++|+| ..+.+|+||+|++
T Consensus 592 V~i~~~~~~~~~-------~a~~~I~~~~-----~~~~~G~i~~G~V~~I~~~GafVei--------~~g~~GllHiSei 651 (684)
T TIGR03591 592 VKIAASDGEAAE-------AAIKMIEGIT-----AEPEVGKIYEGKVVRIMDFGAFVEI--------LPGKDGLVHISEI 651 (684)
T ss_pred EEEEECcHHHHH-------HHHHHHHhhh-----cccccCcEEEEEEEEEeCCEEEEEE--------CCCcEEEEEHHHc
Confidence 777666655442 1122344332 2479999999999999999999999 4568999999999
Q ss_pred ccccccccccccCCCCCCEEEEEEEEeCCCccE
Q 029155 118 RATEIDKVDMHLSFRPGDIVRASVLSLGDARAY 150 (198)
Q Consensus 118 ~~~~~d~~~~~~~~~~GDiV~AkV~s~~~~~~~ 150 (198)
+..+.+ ++.+.|++||.|+++|++++..+.+
T Consensus 652 ~~~~v~--~~~~~~kvGD~V~VkVi~id~~gki 682 (684)
T TIGR03591 652 ANERVE--KVEDVLKEGDEVKVKVLEIDKQGRI 682 (684)
T ss_pred CCCccc--ChhhccCCCCEEEEEEEEECCCCCc
Confidence 876655 7889999999999999999754444
No 66
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=98.43 E-value=8.2e-07 Score=86.86 Aligned_cols=74 Identities=16% Similarity=0.258 Sum_probs=65.2
Q ss_pred CCCCCCEEE-EEEEEEecceEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeCCCccEE
Q 029155 73 VPEPGSVVI-ARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGDARAYF 151 (198)
Q Consensus 73 ~p~vGDiVi-G~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~~~~~~ 151 (198)
.|++|+++. |+|++|.+++++|+| ....+|++|+|++.+.+.. +..+.|++||.|.++|++++..+.+.
T Consensus 750 ~~~vG~iy~~g~V~~I~~FGaFVeL--------~~g~EGLVHISeLs~~rv~--~~~dv~kvGD~V~VkVi~ID~~grI~ 819 (891)
T PLN00207 750 VPTVGDIYRNCEIKSIAPYGAFVEI--------APGREGLCHISELSSNWLA--KPEDAFKVGDRIDVKLIEVNDKGQLR 819 (891)
T ss_pred CcCCCcEEECcEEEEEeccEEEEEe--------CCCCEEEEEhhhcCCcccc--CHHHhcCCCCEEEEEEEEECCCCcEE
Confidence 479999995 699999999999999 4568999999999876655 67899999999999999998767899
Q ss_pred EEEec
Q 029155 152 LSTAK 156 (198)
Q Consensus 152 LSt~~ 156 (198)
||++.
T Consensus 820 LSlK~ 824 (891)
T PLN00207 820 LSRRA 824 (891)
T ss_pred EEEec
Confidence 99975
No 67
>PRK13806 rpsA 30S ribosomal protein S1; Provisional
Probab=98.42 E-value=9.2e-07 Score=82.03 Aligned_cols=75 Identities=21% Similarity=0.278 Sum_probs=64.7
Q ss_pred CCCCCCEEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeCCC-----
Q 029155 73 VPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGDA----- 147 (198)
Q Consensus 73 ~p~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~~----- 147 (198)
.+++|++|.|+|+++.+.+++|+| .....|+||.++++..+.. ++.+.|++||.|.|+|++++..
T Consensus 199 ~l~~G~iv~G~V~~v~~~G~fV~l--------~~gv~g~v~~sels~~~~~--~~~~~~~vGd~i~vkVl~id~~~~~~~ 268 (491)
T PRK13806 199 TVKEGDVVEGTVTRLAPFGAFVEL--------APGVEGMVHISELSWSRVQ--KADEAVSVGDTVRVKVLGIERAKKGKG 268 (491)
T ss_pred hCCCCCEEEEEEEEEeCCeEEEEc--------CCCcEEEEEHHHCCCcccc--ChhHhcCCCCEEEEEEEEEecccCCcc
Confidence 378999999999999999999999 5568999999999876655 7789999999999999999753
Q ss_pred ccEEEEEecC
Q 029155 148 RAYFLSTAKN 157 (198)
Q Consensus 148 ~~~~LSt~~~ 157 (198)
..+.||++..
T Consensus 269 ~ri~lS~K~~ 278 (491)
T PRK13806 269 LRISLSIKQA 278 (491)
T ss_pred eEEEEEehhh
Confidence 2588998664
No 68
>COG1095 RPB7 DNA-directed RNA polymerase, subunit E' [Transcription]
Probab=98.42 E-value=7.7e-07 Score=72.13 Aligned_cols=83 Identities=25% Similarity=0.303 Sum_probs=66.4
Q ss_pred CCCCCCCEEEEEEEEEecceEEEEEeeeccccccCcceeEEecccccccccc-----cccc----ccCCCCCCEEEEEEE
Q 029155 72 PVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEID-----KVDM----HLSFRPGDIVRASVL 142 (198)
Q Consensus 72 ~~p~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d-----~~~~----~~~~~~GDiV~AkV~ 142 (198)
+.|..|++|.|.|+++...+++|.| .++.|++|.+|+...+.+ ..-. ...|+.||.|+|||+
T Consensus 77 fkP~~gEVV~GeVv~~~~~G~fV~i---------gp~dglvh~sqi~dd~~~~d~~~~~~~g~~tk~~i~~gd~VR~RIv 147 (183)
T COG1095 77 FKPFRGEVVEGEVVEVVEFGAFVRI---------GPLDGLVHVSQIMDDYIDYDEKNKVLIGEETKRVLKVGDKVRARIV 147 (183)
T ss_pred EEeccccEEEEEEEEEeecceEEEe---------ccccccccHhhccCcccccCcccceeeecccceEEecCCEEEEEEE
Confidence 4588899999999999999999999 388999999998644221 1111 238999999999999
Q ss_pred EeCC-C-----ccEEEEEecCCCeeeE
Q 029155 143 SLGD-A-----RAYFLSTAKNDLGVVS 163 (198)
Q Consensus 143 s~~~-~-----~~~~LSt~~~~lGvv~ 163 (198)
+..- . ..+.||++++.||++.
T Consensus 148 ~~s~~~~~~~~~~I~lTmrq~~LGkle 174 (183)
T COG1095 148 GVSLKSRRPRESKIGLTMRQPGLGKLE 174 (183)
T ss_pred EEecccCccccceEEEEeccccCCcch
Confidence 9752 2 4589999999999874
No 69
>PRK07899 rpsA 30S ribosomal protein S1; Reviewed
Probab=98.41 E-value=1.1e-06 Score=81.33 Aligned_cols=73 Identities=19% Similarity=0.194 Sum_probs=64.0
Q ss_pred CCCCCEEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeCC-CccEEE
Q 029155 74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGD-ARAYFL 152 (198)
Q Consensus 74 p~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~-~~~~~L 152 (198)
.++|++|.|+|+++.+.+++|+| . ...|+||.++++..+.+ ++.+.|++||.|.++|++++. .+.+.|
T Consensus 206 lk~G~iv~G~V~~i~~~G~FVdl--------g-gv~Glv~~Sels~~~v~--~~~~~~kvGd~V~vkVl~iD~e~~rI~L 274 (486)
T PRK07899 206 LQKGQVRKGVVSSIVNFGAFVDL--------G-GVDGLVHVSELSWKHID--HPSEVVEVGQEVTVEVLDVDMDRERVSL 274 (486)
T ss_pred ccCCCEEEEEEEEEECCeEEEEE--------C-CEEEEEEHHHCCCcccC--CHHHhcCCCCEEEEEEEEEECCCCEEEE
Confidence 57999999999999999999999 3 47899999999876655 778899999999999999974 477999
Q ss_pred EEecC
Q 029155 153 STAKN 157 (198)
Q Consensus 153 St~~~ 157 (198)
|++..
T Consensus 275 SlK~~ 279 (486)
T PRK07899 275 SLKAT 279 (486)
T ss_pred EEeec
Confidence 98753
No 70
>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional
Probab=98.39 E-value=1.1e-06 Score=86.35 Aligned_cols=74 Identities=20% Similarity=0.151 Sum_probs=63.5
Q ss_pred CCCCCEEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeCC-CccEEE
Q 029155 74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGD-ARAYFL 152 (198)
Q Consensus 74 p~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~-~~~~~L 152 (198)
+++||+|.|+|+++.+++++|++ ..++.|++|++++++.. ...++.+.|++||.|.|+|++++. .+.+.|
T Consensus 576 ~~vG~iV~G~V~~I~~fG~fVeL--------~~gveGLvhiSEls~~~-~~~~p~~~~kvGd~V~vkVl~iD~e~~rIsL 646 (863)
T PRK12269 576 FGVNDVVKGRVTKIADFGAFIEL--------AEGIEGLAHISEFSWVK-KTSKPSDMVKIGDEVECMILGYDIQAGRVSL 646 (863)
T ss_pred CCCCCEEEEEEEEEeCCeEEEEe--------cCCceeeeEHHHhcCcc-ccCCHHHcCCCCCEEEEEEEEEecccCceEE
Confidence 67999999999999999999999 56789999999997522 122678899999999999999974 467999
Q ss_pred EEec
Q 029155 153 STAK 156 (198)
Q Consensus 153 St~~ 156 (198)
|++.
T Consensus 647 S~K~ 650 (863)
T PRK12269 647 GLKQ 650 (863)
T ss_pred Eehh
Confidence 9975
No 71
>PRK07899 rpsA 30S ribosomal protein S1; Reviewed
Probab=98.37 E-value=1.7e-06 Score=80.10 Aligned_cols=74 Identities=27% Similarity=0.250 Sum_probs=64.1
Q ss_pred CCCCCEEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeCC-CccEEE
Q 029155 74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGD-ARAYFL 152 (198)
Q Consensus 74 p~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~-~~~~~L 152 (198)
.+.||+|.|+|+++.++.++|+| .....|+||.++++..... ++.+.|++||.|.|+|+++++ .+.+.|
T Consensus 33 ~~~GdiV~G~V~~v~~~gv~VdI--------g~k~eG~Ip~~Els~~~~~--~~~~~~~vGd~Ie~~V~~~~~~~g~liL 102 (486)
T PRK07899 33 FNDGDIVEGTVVKVDRDEVLLDI--------GYKTEGVIPSRELSIKHDV--DPNEVVEVGDEVEALVLQKEDKEGRLIL 102 (486)
T ss_pred CCCCCEEEEEEEEEECCcEEEEE--------CCCcEEEEEHHHhcccccC--ChhhcCCCCCEEEEEEEEEECCCCeEEE
Confidence 68999999999999999999999 6678999999999764433 677889999999999999875 467999
Q ss_pred EEecC
Q 029155 153 STAKN 157 (198)
Q Consensus 153 St~~~ 157 (198)
|.+..
T Consensus 103 S~k~~ 107 (486)
T PRK07899 103 SKKRA 107 (486)
T ss_pred Eehhh
Confidence 99854
No 72
>PRK06299 rpsA 30S ribosomal protein S1; Reviewed
Probab=98.35 E-value=1.7e-06 Score=81.16 Aligned_cols=74 Identities=26% Similarity=0.397 Sum_probs=65.6
Q ss_pred CCCCCEEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeCC-CccEEE
Q 029155 74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGD-ARAYFL 152 (198)
Q Consensus 74 p~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~-~~~~~L 152 (198)
.++||+|.|+|+++.+.+++|.+ ..++.|++|.++++..+.. ++.+.|++||.|.|+|++++. .+.+.|
T Consensus 458 ~~~G~vV~G~V~~v~~~G~fV~l--------~~gi~g~i~~se~s~~~~~--~~~~~~~~Gd~v~~~V~~vd~~~~~i~L 527 (565)
T PRK06299 458 HKKGSIVTGTVTEVKDKGAFVEL--------EDGVEGLIRASELSRDRVE--DATEVLKVGDEVEAKVINIDRKNRRISL 527 (565)
T ss_pred cCCCCEEEEEEEEEecCceEEec--------CCCcEEEEEHHHhcchhcc--CccccCCCCCEEEEEEEEEccccCEEEE
Confidence 47899999999999999999999 4578999999999876665 788999999999999999974 578999
Q ss_pred EEecC
Q 029155 153 STAKN 157 (198)
Q Consensus 153 St~~~ 157 (198)
|++..
T Consensus 528 S~k~~ 532 (565)
T PRK06299 528 SIKAL 532 (565)
T ss_pred Eeeeh
Confidence 99864
No 73
>PRK06676 rpsA 30S ribosomal protein S1; Reviewed
Probab=98.31 E-value=3.2e-06 Score=75.93 Aligned_cols=73 Identities=21% Similarity=0.229 Sum_probs=63.0
Q ss_pred CCCCCEEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeCC-CccEEE
Q 029155 74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGD-ARAYFL 152 (198)
Q Consensus 74 p~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~-~~~~~L 152 (198)
+++|++|.|+|+++.+.+++|++ . ...|++|.++++..+.+ ++.+.|++||.|.|+|++++. .+.+.|
T Consensus 190 ~~~G~~v~g~V~~v~~~G~fV~l--------~-~v~g~v~~sels~~~~~--~~~~~~~vGd~i~~~Vl~vd~~~~~i~l 258 (390)
T PRK06676 190 LKEGDVVEGTVARLTDFGAFVDI--------G-GVDGLVHISELSHERVE--KPSEVVSVGQEVEVKVLSIDWETERISL 258 (390)
T ss_pred CCCCCEEEEEEEEEecceEEEEe--------C-CeEEEEEHHHcCccccC--CHHHhcCCCCEEEEEEEEEeCCCCEEEE
Confidence 58999999999999999999999 2 47899999999865544 778899999999999999974 467999
Q ss_pred EEecC
Q 029155 153 STAKN 157 (198)
Q Consensus 153 St~~~ 157 (198)
|++..
T Consensus 259 S~k~~ 263 (390)
T PRK06676 259 SLKDT 263 (390)
T ss_pred EEeec
Confidence 98753
No 74
>PRK06676 rpsA 30S ribosomal protein S1; Reviewed
Probab=98.30 E-value=4.1e-06 Score=75.23 Aligned_cols=75 Identities=16% Similarity=0.230 Sum_probs=64.3
Q ss_pred CCCCCEEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeCC-CccEEE
Q 029155 74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGD-ARAYFL 152 (198)
Q Consensus 74 p~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~-~~~~~L 152 (198)
.++|+++.|+|+++.+.+++|++ ..++.|++|.+++...+.. +..+.|++||.|.|+|++++. .+.+.|
T Consensus 275 ~~~G~~v~g~V~~i~~~G~fV~l--------~~gi~Glv~~se~~~~~~~--~~~~~~~~Gd~v~v~V~~id~e~~~i~l 344 (390)
T PRK06676 275 LPEGDVIEGTVKRLTDFGAFVEV--------LPGVEGLVHISQISHKHIA--TPSEVLEEGQEVKVKVLEVNEEEKRISL 344 (390)
T ss_pred hcCCcEEEEEEEEEeCceEEEEE--------CCCCeEEEEhHHcCccccC--ChhhccCCCCEEEEEEEEEECCCCEEEE
Confidence 57899999999999999999999 5578999999999765544 667889999999999999973 578999
Q ss_pred EEecCC
Q 029155 153 STAKND 158 (198)
Q Consensus 153 St~~~~ 158 (198)
|++...
T Consensus 345 s~k~~~ 350 (390)
T PRK06676 345 SIKALE 350 (390)
T ss_pred EEEecc
Confidence 988543
No 75
>PRK06299 rpsA 30S ribosomal protein S1; Reviewed
Probab=98.28 E-value=3.9e-06 Score=78.81 Aligned_cols=73 Identities=21% Similarity=0.255 Sum_probs=64.4
Q ss_pred CCCCCCEEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeCC-CccEE
Q 029155 73 VPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGD-ARAYF 151 (198)
Q Consensus 73 ~p~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~-~~~~~ 151 (198)
-+++|++|.|+|+++.+.+++|+| . ++.|++|.++++..+.. ++.+.|++||.|.|+|++++. .+.+.
T Consensus 198 ~l~~G~iv~g~V~~v~~~G~~V~i--------~-g~~glv~~se~s~~~~~--~~~~~~kvG~~v~v~V~~~d~~~~~i~ 266 (565)
T PRK06299 198 NLEEGQVVEGVVKNITDYGAFVDL--------G-GVDGLLHITDISWKRVN--HPSEVVNVGDEVKVKVLKFDKEKKRVS 266 (565)
T ss_pred cCCCCCEEEEEEEEEeCCeEEEEE--------C-CEEEEEEHHHhcccccC--CHhhcCCCCCEEEEEEEEEeCCCCeEE
Confidence 368999999999999999999999 5 78999999999866554 778999999999999999974 46799
Q ss_pred EEEec
Q 029155 152 LSTAK 156 (198)
Q Consensus 152 LSt~~ 156 (198)
||++.
T Consensus 267 lS~k~ 271 (565)
T PRK06299 267 LGLKQ 271 (565)
T ss_pred EEEEe
Confidence 99874
No 76
>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=98.24 E-value=1.1e-05 Score=56.27 Aligned_cols=71 Identities=15% Similarity=0.171 Sum_probs=54.8
Q ss_pred CCCEEEEEEEEEecceEEEEEeeeccccccC-cceeEEeccccccccc--cc-------cccccCCCCCCEEEEEEEEeC
Q 029155 76 PGSVVIARVTKVMTRMASADIMCVGAKSVRE-KFSGIIRQQDVRATEI--DK-------VDMHLSFRPGDIVRASVLSLG 145 (198)
Q Consensus 76 vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~-~~~G~l~~s~v~~~~~--d~-------~~~~~~~~~GDiV~AkV~s~~ 145 (198)
+|+++.|+|+++++.+++|++ .. ...|++|.++++.... +. ....+.|++||.|+++|.+++
T Consensus 1 ~g~~~~g~V~~v~~~G~fv~l--------~~~~~~G~v~~~~l~~~~~~~d~~~~~~~~~~~~~~~~~gd~v~v~v~~vd 72 (83)
T cd04471 1 VGEEFDGVISGVTSFGLFVEL--------DNLTVEGLVHVSTLGDDYYEFDEENHALVGERTGKVFRLGDKVKVRVVRVD 72 (83)
T ss_pred CCCEEEEEEEeEEeeeEEEEe--------cCCCEEEEEEEEecCCCcEEEcccceEEEeccCCCEEcCCCEEEEEEEEec
Confidence 489999999999999999999 33 5899999999863221 00 023478999999999999997
Q ss_pred C-CccEEEEE
Q 029155 146 D-ARAYFLST 154 (198)
Q Consensus 146 ~-~~~~~LSt 154 (198)
. .+.+.|++
T Consensus 73 ~~~~~i~~~l 82 (83)
T cd04471 73 LDRRKIDFEL 82 (83)
T ss_pred cccCEEEEEE
Confidence 4 35666664
No 77
>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=98.20 E-value=6.2e-06 Score=76.50 Aligned_cols=72 Identities=26% Similarity=0.334 Sum_probs=63.1
Q ss_pred CCCCCEEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeCC-CccEEE
Q 029155 74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGD-ARAYFL 152 (198)
Q Consensus 74 p~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~-~~~~~L 152 (198)
.++|++|.|+|+++++.+++|++ ...+.|++|.+++...+.+ ++.+.|++||.|.++|++++. .+.+.|
T Consensus 444 ~~~G~~v~g~V~~v~~~G~fV~l--------~~~~~Glv~~s~l~~~~~~--~~~~~~~~Gd~v~~~V~~id~~~~~i~l 513 (516)
T TIGR00717 444 YKVGSVVKGKVTEIKDFGAFVEL--------PGGVEGLIRNSELSENRDE--DKTDEIKVGDEVEAKVVDIDKKNRKVSL 513 (516)
T ss_pred cCcceEEEEEEEEEecceEEEEc--------CCCeEEEEEHHHcCccccc--cccccCCCCCEEEEEEEEEeCCCCEEEE
Confidence 46899999999999999999999 5679999999999876654 788999999999999999973 467888
Q ss_pred EEe
Q 029155 153 STA 155 (198)
Q Consensus 153 St~ 155 (198)
|++
T Consensus 514 s~k 516 (516)
T TIGR00717 514 SVK 516 (516)
T ss_pred EEC
Confidence 874
No 78
>PRK00087 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed
Probab=98.20 E-value=7.6e-06 Score=78.29 Aligned_cols=75 Identities=19% Similarity=0.298 Sum_probs=65.1
Q ss_pred CCCCCEEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeCC-CccEEE
Q 029155 74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGD-ARAYFL 152 (198)
Q Consensus 74 p~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~-~~~~~L 152 (198)
.++|++|.|+|+++.+.+++|++ ...+.|++|.++++..+.. ++.+.|++||.|.|+|++++. .+.+.|
T Consensus 560 ~~~G~~v~g~V~~i~~~G~fV~l--------~~~i~Gli~~sel~~~~~~--~~~~~~kvGd~V~vkV~~id~e~~rI~l 629 (647)
T PRK00087 560 YPVGSIVLGKVVRIAPFGAFVEL--------EPGVDGLVHISQISWKRID--KPEDVLSEGEEVKAKILEVDPEEKRIRL 629 (647)
T ss_pred ccCCeEEEEEEEEEECCeEEEEE--------CCCCEEEEEhhhcCccccC--CHhhcCCCCCEEEEEEEEEeCCCCEEEE
Confidence 46899999999999999999999 5679999999999865544 677899999999999999974 578999
Q ss_pred EEecCC
Q 029155 153 STAKND 158 (198)
Q Consensus 153 St~~~~ 158 (198)
|++...
T Consensus 630 slk~~~ 635 (647)
T PRK00087 630 SIKEVE 635 (647)
T ss_pred EEeecc
Confidence 998653
No 79
>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional
Probab=98.17 E-value=7.7e-06 Score=80.39 Aligned_cols=74 Identities=18% Similarity=0.205 Sum_probs=62.6
Q ss_pred CCCCCEEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeCC-CccEEE
Q 029155 74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGD-ARAYFL 152 (198)
Q Consensus 74 p~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~-~~~~~L 152 (198)
..+|++|.|+|+.+.+.+++|++ ..+..|+||.+|++..... ....+.|++||.|.++|++++. .+.+.|
T Consensus 663 ~~vG~~v~G~V~~i~~~G~fV~l--------~~gV~GlIh~sels~~~~~-~~~~~~~kvGq~VkvkVl~ID~e~rrI~L 733 (863)
T PRK12269 663 YPVGARFTRRIVKVTNAGAFIEM--------EEGIDGFLHVDDLSWVKRT-RPADHELEVGKEIECMVIECDPQARRIRL 733 (863)
T ss_pred CCCCCEEEEEEEEEecceEEEEe--------CCCcEEEEEhHHhhccccc-cchhhccCCCCEEEEEEEEEeccCCEEEE
Confidence 46899999999999999999999 6789999999999753322 2445689999999999999984 477999
Q ss_pred EEec
Q 029155 153 STAK 156 (198)
Q Consensus 153 St~~ 156 (198)
|++.
T Consensus 734 S~K~ 737 (863)
T PRK12269 734 GVKQ 737 (863)
T ss_pred Eecc
Confidence 9874
No 80
>COG2183 Tex Transcriptional accessory protein [Transcription]
Probab=98.09 E-value=8.3e-06 Score=78.37 Aligned_cols=77 Identities=21% Similarity=0.283 Sum_probs=68.4
Q ss_pred CCCCCCEEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeCC-CccEE
Q 029155 73 VPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGD-ARAYF 151 (198)
Q Consensus 73 ~p~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~-~~~~~ 151 (198)
-+++|.++.|.|+.+.+++++|+| .-.-.|++|+|+++..... +..+.+++||+|.++|++++. ...+.
T Consensus 655 dLk~Gm~leg~Vrnv~~fgafVdI--------gv~qDglvHis~ls~~fv~--~P~~vv~vGdiV~v~V~~vD~~r~rI~ 724 (780)
T COG2183 655 DLKPGMILEGTVRNVVDFGAFVDI--------GVHQDGLVHISQLSDKFVK--DPNEVVKVGDIVKVKVIEVDTARKRIA 724 (780)
T ss_pred hccCCCEEEEEEEEeeeccceEEe--------ccccceeeeHHHhhhhhcC--ChHHhcccCCEEEEEEEEEecccCeee
Confidence 469999999999999999999999 5567899999999877776 679999999999999999984 46799
Q ss_pred EEEecCCC
Q 029155 152 LSTAKNDL 159 (198)
Q Consensus 152 LSt~~~~l 159 (198)
||++..+.
T Consensus 725 Lsmr~~~~ 732 (780)
T COG2183 725 LSMRLDEE 732 (780)
T ss_pred eEeeccCC
Confidence 99998765
No 81
>PTZ00162 DNA-directed RNA polymerase II subunit 7; Provisional
Probab=98.07 E-value=2e-05 Score=63.86 Aligned_cols=86 Identities=17% Similarity=0.141 Sum_probs=64.4
Q ss_pred CCCCCCCCEEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccccc-ccc---c------cccccCCCCCCEEEEE
Q 029155 71 GPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRAT-EID---K------VDMHLSFRPGDIVRAS 140 (198)
Q Consensus 71 ~~~p~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~-~~d---~------~~~~~~~~~GDiV~Ak 140 (198)
.+.|-.|++|.|+|+++...++++++. ++++.+|.+++... .-| . .+-...++.||.|++|
T Consensus 76 vFrPf~gEVv~g~V~~v~~~G~~v~~G---------p~~ifI~~~~l~~~~~fd~~~~~~~~~~~~~~~~i~~g~~VR~r 146 (176)
T PTZ00162 76 VFKPFKDEVLDAIVTDVNKLGFFAQAG---------PLKAFVSRSAIPPDFVYDSDSAYPCYISSDGQIQIKPNTEVRLR 146 (176)
T ss_pred EEecCCCCEEEEEEEEEecceEEEEee---------CeEEEEcHHHCCCccEECCCCCcceEecCCCcEEECCCCEEEEE
Confidence 345889999999999999999999993 67788888877521 100 0 0113568999999999
Q ss_pred EEEeC-C--CccEEEEEecCCCeeeEEe
Q 029155 141 VLSLG-D--ARAYFLSTAKNDLGVVSAE 165 (198)
Q Consensus 141 V~s~~-~--~~~~~LSt~~~~lGvv~a~ 165 (198)
|.++. + ......|++++.||.+.|+
T Consensus 147 V~~v~~~~~~~~~i~T~~~~~LG~~~~~ 174 (176)
T PTZ00162 147 LQGVRYDASNLFAIATINSDYLGPIESS 174 (176)
T ss_pred EEEEEecCCCcEEEEEecCCCcCccccc
Confidence 98874 2 2346789999999999654
No 82
>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=98.06 E-value=1.9e-05 Score=73.29 Aligned_cols=73 Identities=18% Similarity=0.205 Sum_probs=63.0
Q ss_pred CCCCCCEEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeCC-CccEE
Q 029155 73 VPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGD-ARAYF 151 (198)
Q Consensus 73 ~p~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~-~~~~~ 151 (198)
-+++|++|.|+|+++.+.+++|++ . .+.|++|.++++..... ++.+.|++||.|.|+|++++. .+.+.
T Consensus 184 ~l~~G~~v~g~V~~i~~~G~~V~l--------~-g~~g~lp~~e~s~~~~~--~~~~~~~vG~~v~v~Vl~~d~~~~~i~ 252 (516)
T TIGR00717 184 NLKEGDVVKGVVKNITDFGAFVDL--------G-GVDGLLHITDMSWKRVK--HPSEYVKVGQEVKVKVIKFDKEKGRIS 252 (516)
T ss_pred hccCCCEEEEEEEEEECCeEEEEE--------C-CEEEEEEHHHcCCCCCC--CHHHhccCCCEEEEEEEEEECCCCcEE
Confidence 478999999999999999999998 3 47899999999765544 677889999999999999974 46799
Q ss_pred EEEec
Q 029155 152 LSTAK 156 (198)
Q Consensus 152 LSt~~ 156 (198)
||++.
T Consensus 253 lS~k~ 257 (516)
T TIGR00717 253 LSLKQ 257 (516)
T ss_pred EEEEe
Confidence 99885
No 83
>PRK00087 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed
Probab=97.99 E-value=3.2e-05 Score=74.11 Aligned_cols=77 Identities=26% Similarity=0.324 Sum_probs=65.3
Q ss_pred CCCCCCCEEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeCC-CccE
Q 029155 72 PVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGD-ARAY 150 (198)
Q Consensus 72 ~~p~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~-~~~~ 150 (198)
..+++|++|.|+|.++.+++++|++ .....|+|+.+++...... ++.+.|++||.|.++|+++++ .+.+
T Consensus 298 ~~l~~G~iV~G~V~~v~~~gv~Vdi--------g~~~~G~lp~~els~~~~~--~~~~~~~vGd~V~v~V~~vd~~~g~i 367 (647)
T PRK00087 298 KQIRRGDIVKGTVVSVNENEVFVDV--------GYKSEGVIPLRELTLDEIS--SLKESVKVGDEIEVKVLKLEDEDGYV 367 (647)
T ss_pred hhccCCCEEEEEEEEEECCEEEEEE--------CCCeEEEEEHHHhcccccC--ChhhccCCCCEEEEEEEEEECCCCcE
Confidence 3479999999999999999999999 5667899999998754333 677889999999999999864 4679
Q ss_pred EEEEecCC
Q 029155 151 FLSTAKND 158 (198)
Q Consensus 151 ~LSt~~~~ 158 (198)
.||.+..+
T Consensus 368 ~LS~k~~~ 375 (647)
T PRK00087 368 VLSKKEAD 375 (647)
T ss_pred EEEeehhc
Confidence 99999775
No 84
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=97.80 E-value=5.2e-05 Score=72.02 Aligned_cols=75 Identities=16% Similarity=0.224 Sum_probs=67.6
Q ss_pred CCCCCCEEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeCCCccEEE
Q 029155 73 VPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGDARAYFL 152 (198)
Q Consensus 73 ~p~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~~~~~~L 152 (198)
-+++|.+-.|+|+++.+.+++|++ ..+-.|++|+|++...+.+ +..+.++.||.|+.||+.+++.+.+.|
T Consensus 616 e~evg~iy~G~V~ri~~fGaFv~l--------~~gkdgl~hiS~~~~~rv~--kv~dvlk~Gd~v~Vkv~~iD~~Gri~l 685 (692)
T COG1185 616 EVEVGEVYEGTVVRIVDFGAFVEL--------LPGKDGLVHISQLAKERVE--KVEDVLKEGDEVKVKVIEIDKQGRIRL 685 (692)
T ss_pred hcccccEEEEEEEEEeecceEEEe--------cCCcceeEEehhhhhhhhh--cccceeecCceEEEEEeeecccCCccc
Confidence 479999999999999999999999 5677899999999877776 677999999999999999998788999
Q ss_pred EEecC
Q 029155 153 STAKN 157 (198)
Q Consensus 153 St~~~ 157 (198)
|++..
T Consensus 686 s~~~~ 690 (692)
T COG1185 686 SIKAV 690 (692)
T ss_pred eehhc
Confidence 98753
No 85
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=97.74 E-value=8.2e-05 Score=68.78 Aligned_cols=71 Identities=23% Similarity=0.329 Sum_probs=59.8
Q ss_pred CCCCCCCEEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeCC---Cc
Q 029155 72 PVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGD---AR 148 (198)
Q Consensus 72 ~~p~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~---~~ 148 (198)
|..+.|++|.|+|.++....++|++ . ...|+||.++.. .++.|++||.|+|.|+.++. +.
T Consensus 130 yk~~~GeIV~G~V~ri~~~giiVDL--------g-gvea~LP~sE~i--------p~E~~~~GdrIka~I~~Vd~~~kg~ 192 (470)
T PRK09202 130 YKDRVGEIITGVVKRVERGNIIVDL--------G-RAEAILPRKEQI--------PRENFRPGDRVRAYVYEVRKEARGP 192 (470)
T ss_pred HHhhcCCEEEEEEEEEecCCEEEEE--------C-CeEEEecHHHcC--------CCccCCCCCEEEEEEEEEecCCCCC
Confidence 5567999999999999999999999 2 579999998863 35789999999999999974 34
Q ss_pred cEEEEEecCCC
Q 029155 149 AYFLSTAKNDL 159 (198)
Q Consensus 149 ~~~LSt~~~~l 159 (198)
++.||-+.++|
T Consensus 193 qIilSRt~p~~ 203 (470)
T PRK09202 193 QIILSRTHPEF 203 (470)
T ss_pred eEEEEeCcHHH
Confidence 68899888754
No 86
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=97.58 E-value=0.0002 Score=64.23 Aligned_cols=72 Identities=15% Similarity=0.287 Sum_probs=58.6
Q ss_pred CCCCCCCCEEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeCC---C
Q 029155 71 GPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGD---A 147 (198)
Q Consensus 71 ~~~p~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~---~ 147 (198)
.|..+.|++|.|+|.++..+.++|+| . ...|+||.++... ++.|++||.|+|.|.+++. +
T Consensus 129 ef~~k~GeiV~G~V~~~~~~~~~Vdl--------g-~vEa~LP~~E~ip--------~e~~~~Gd~Ika~V~~V~~~~kg 191 (362)
T PRK12327 129 EFSEREGDIVTGVVQRRDNRFVYVNL--------G-KIEAVLPPAEQIP--------GETYKHGDRIKVYVVKVEKTTKG 191 (362)
T ss_pred HHHHhcCCEEEEEEEEEeCCcEEEEe--------C-CeEEEecHHHcCC--------CCCCCCCCEEEEEEEEEecCCCC
Confidence 36679999999999999999999999 3 3789999766432 5779999999999999973 3
Q ss_pred ccEEEEEecCCC
Q 029155 148 RAYFLSTAKNDL 159 (198)
Q Consensus 148 ~~~~LSt~~~~l 159 (198)
..+.||-..++|
T Consensus 192 p~IivSRt~p~~ 203 (362)
T PRK12327 192 PQIFVSRTHPGL 203 (362)
T ss_pred CeEEEEeCCHHH
Confidence 458888877654
No 87
>TIGR01953 NusA transcription termination factor NusA. This model describes NusA, or N utilization substance protein A, a bacterial transcription termination factor. It binds to RNA polymerase alpha subunit and promotes termination at certain RNA hairpin structures. It is named for the interaction in E. coli of phage lambda antitermination protein N with the N-utilization substance, consisting of NusA, NusB, NusE (ribosomal protein S10), and nusG. This model represents a region of NusA shared in all bacterial forms, and including an S1 (pfam00575) and a KH (pfam00013) RNA binding domains. Proteobacterial forms have an additional C-terminal region, not included in this model, with two repeats of 50-residue domain rich in acidic amino acids.
Probab=97.55 E-value=0.00025 Score=63.18 Aligned_cols=72 Identities=21% Similarity=0.319 Sum_probs=58.5
Q ss_pred CCCCCCCCEEEEEEEEEecce-EEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeCC---
Q 029155 71 GPVPEPGSVVIARVTKVMTRM-ASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGD--- 146 (198)
Q Consensus 71 ~~~p~vGDiViG~V~~v~~~~-~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~--- 146 (198)
.|..+.|++|.|+|.++..++ |+|+| . ...|+||.++... .+.|++||.|+|.|.++++
T Consensus 126 ey~~k~GeiV~G~V~~v~~~g~v~Vdi--------G-~~ea~LP~~E~ip--------~E~~~~Gd~ik~~V~~V~~~~k 188 (341)
T TIGR01953 126 EFSSKEGEIISGTVKRVNRRGNLYVEL--------G-KTEGILPKKEQIP--------GEKFRIGDRIKAYVYEVRKTAK 188 (341)
T ss_pred HHHhhcCCEEEEEEEEEecCCcEEEEE--------C-CeEEEecHHHcCC--------CcCCCCCCEEEEEEEEEEcCCC
Confidence 355689999999999998865 79999 3 5789999888642 3559999999999999974
Q ss_pred CccEEEEEecCCC
Q 029155 147 ARAYFLSTAKNDL 159 (198)
Q Consensus 147 ~~~~~LSt~~~~l 159 (198)
+.++.||.+.++|
T Consensus 189 g~qIivSRt~~~~ 201 (341)
T TIGR01953 189 GPQIILSRTHPEF 201 (341)
T ss_pred CCeEEEEeCcHHH
Confidence 3568999988765
No 88
>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=97.52 E-value=0.00097 Score=48.05 Aligned_cols=74 Identities=22% Similarity=0.183 Sum_probs=47.8
Q ss_pred CCCEEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccccc-----------cccccccccCCCCCCEEEEEEEEe
Q 029155 76 PGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRAT-----------EIDKVDMHLSFRPGDIVRASVLSL 144 (198)
Q Consensus 76 vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~-----------~~d~~~~~~~~~~GDiV~AkV~s~ 144 (198)
+|+++.|+|+++...++++.+. ++.+++|.+++.+. ..+ +-...+++||.|++||+++
T Consensus 1 kgEVi~g~V~~v~~~G~~v~~G---------pl~~f~~~~~ip~~~~~~~~~~~~~~~~--~~~~~i~~g~~VR~rV~~v 69 (88)
T cd04462 1 KGEVVDAIVTSVNKTGFFAEVG---------PLSIFISRHLIPSDMEFDPNASPPCFTS--NEDIVIKKDTEVRLKIIGT 69 (88)
T ss_pred CCcEEEEEEEEEeccEEEEEEc---------CceEEEEeeecCccceECCcCCCCeEeC--CCcEEECCCCEEEEEEEEE
Confidence 5899999999999999999995 23333333332210 111 1145689999999999987
Q ss_pred C-CCcc--EEEEEecCCCe
Q 029155 145 G-DARA--YFLSTAKNDLG 160 (198)
Q Consensus 145 ~-~~~~--~~LSt~~~~lG 160 (198)
. +.+. ..-|++++.||
T Consensus 70 ~~~~~~~~~igt~~~~~LG 88 (88)
T cd04462 70 RVDATDIFAIGTIKDDYLG 88 (88)
T ss_pred EEccCceEEEEEccCCCCC
Confidence 4 2222 23366666665
No 89
>PHA02858 EIF2a-like PKR inhibitor; Provisional
Probab=97.40 E-value=0.00091 Score=47.73 Aligned_cols=73 Identities=11% Similarity=0.131 Sum_probs=60.4
Q ss_pred CCCCCCCCEEEEEEEEEecceEEEEEeeeccccccCcceeEEe-ccccccccccccccccCCCCCCEEEEEEEEeCC-Cc
Q 029155 71 GPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIR-QQDVRATEIDKVDMHLSFRPGDIVRASVLSLGD-AR 148 (198)
Q Consensus 71 ~~~p~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~-~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~-~~ 148 (198)
...|++||+|. .|..+.+..+.|.++ .++.+|.|. .++++..... ++++.+ +|=.+.++|+.++. ++
T Consensus 11 y~~P~v~dvv~-~Vv~i~d~~~YV~Ll-------eY~iegmIl~~selsr~rir--si~kll-VGk~e~v~ViRVDk~KG 79 (86)
T PHA02858 11 YVFPNINEVTK-GIVFVKDNIFYVKLI-------DYGLEALIVNYVNVNADRAE--KLKKKL-VGKTINVQVIRTDKLKG 79 (86)
T ss_pred EecCCCCeEEE-EEEEEeccEEEEEEe-------cCccceEEecHHHHhHHHHH--hhhhhh-cCCeeEEEEEEECCCCC
Confidence 34699999999 899999999999995 556888888 8888776666 788888 99999999999984 35
Q ss_pred cEEEEE
Q 029155 149 AYFLST 154 (198)
Q Consensus 149 ~~~LSt 154 (198)
-+-||.
T Consensus 80 YIDLs~ 85 (86)
T PHA02858 80 YIDVRH 85 (86)
T ss_pred EEEeEc
Confidence 566763
No 90
>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=97.22 E-value=0.0024 Score=58.31 Aligned_cols=74 Identities=22% Similarity=0.280 Sum_probs=55.7
Q ss_pred CCCCCEEEEEEEEEecc--eEEEEEeeeccccccCcceeEEecccccccc----------ccccccccCCCCCCEEEEEE
Q 029155 74 PEPGSVVIARVTKVMTR--MASADIMCVGAKSVREKFSGIIRQQDVRATE----------IDKVDMHLSFRPGDIVRASV 141 (198)
Q Consensus 74 p~vGDiViG~V~~v~~~--~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~----------~d~~~~~~~~~~GDiV~AkV 141 (198)
..+|++..|+|+++.+. .|||+| ...-.|+||.+|+.... ....++.+.+++||.|.++|
T Consensus 23 ~~vGnIY~GrV~~i~p~l~aAFVdi--------G~~k~gfL~~~d~~~~~~~~~~~~~~~~~~~~i~~~l~~G~~IlVQV 94 (414)
T TIGR00757 23 QLKGNIYKGRVTRILPSLQAAFVDI--------GLEKNGFLHASDIGPNYECLAPAEAKREAGPSISELLRPGQSVLVQV 94 (414)
T ss_pred CCCCCEEEEEEeeecCCCceEEEEc--------CCCceEEEEHHHcCchhhccccccccccccCCHHHhCcCCCEEEEEE
Confidence 56899999999999998 899999 66778999999985321 01124667899999999999
Q ss_pred EEeC-CCccEEEEEe
Q 029155 142 LSLG-DARAYFLSTA 155 (198)
Q Consensus 142 ~s~~-~~~~~~LSt~ 155 (198)
..-. ......||+.
T Consensus 95 ~Ke~~~~Kgp~lT~~ 109 (414)
T TIGR00757 95 VKEPRGNKGARLTTD 109 (414)
T ss_pred eeCCcCCCCCeEEEE
Confidence 9832 1233555553
No 91
>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=97.04 E-value=0.003 Score=61.18 Aligned_cols=74 Identities=14% Similarity=0.152 Sum_probs=57.4
Q ss_pred CCCCCCEEEEEEEEEecceEEEEEeeeccccccC-cceeEEeccccccccc--cc-------cccccCCCCCCEEEEEEE
Q 029155 73 VPEPGSVVIARVTKVMTRMASADIMCVGAKSVRE-KFSGIIRQQDVRATEI--DK-------VDMHLSFRPGDIVRASVL 142 (198)
Q Consensus 73 ~p~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~-~~~G~l~~s~v~~~~~--d~-------~~~~~~~~~GDiV~AkV~ 142 (198)
..++|.++.|+|++|++.+++|++ .. ..+|++|++++...+. +. ......|++||.|.++|.
T Consensus 624 ~~~iG~~~~g~V~~v~~fGifV~L--------~~~~~eGlvhis~l~~d~~~~d~~~~~l~g~~~~~~~~lGd~V~Vkv~ 695 (709)
T TIGR02063 624 SEKIGEEFEGVISGVTSFGLFVEL--------ENNTIEGLVHISTLKDDYYVFDEKGLALVGERTGKVFRLGDRVKVRVV 695 (709)
T ss_pred hccCCcEEEEEEEEEEeCCEEEEe--------cCCceEEEEEeeecCCCcEEEcccceEEEeccCCcEECCCCEEEEEEE
Confidence 357899999999999999999999 33 5899999999863221 10 122467999999999999
Q ss_pred EeCC-CccEEEEE
Q 029155 143 SLGD-ARAYFLST 154 (198)
Q Consensus 143 s~~~-~~~~~LSt 154 (198)
+++. .+.+.+++
T Consensus 696 ~vd~~~~~I~~~l 708 (709)
T TIGR02063 696 KADLDTGKIDFEL 708 (709)
T ss_pred EEecccCeEEEEE
Confidence 9974 46677764
No 92
>PRK11642 exoribonuclease R; Provisional
Probab=96.81 E-value=0.0068 Score=59.72 Aligned_cols=74 Identities=18% Similarity=0.207 Sum_probs=57.5
Q ss_pred CCCCCEEEEEEEEEecceEEEEEeeeccccccC-cceeEEecccccccc--cccc-------ccccCCCCCCEEEEEEEE
Q 029155 74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVRE-KFSGIIRQQDVRATE--IDKV-------DMHLSFRPGDIVRASVLS 143 (198)
Q Consensus 74 p~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~-~~~G~l~~s~v~~~~--~d~~-------~~~~~~~~GDiV~AkV~s 143 (198)
.++|+++.|+|++|++.+++|+| .. ..+|++|++++...+ .+.. .....|++||.|.++|.+
T Consensus 641 ~~iGe~f~G~Is~V~~fGifVeL--------~~~~vEGlV~vs~L~~d~y~~d~~~~~L~g~~~~~~~~lGD~V~VkV~~ 712 (813)
T PRK11642 641 DQVGNVFKGVISSVTGFGFFVRL--------DDLFIDGLVHVSSLDNDYYRFDQVGQRLIGESSGQTYRLGDRVEVRVEA 712 (813)
T ss_pred ccCCcEEEEEEEEeecCceEEEE--------CCCCeeeeEEEeecCCcceEecchheEEecccCCcEECCCCEEEEEEEE
Confidence 36899999999999999999999 33 489999999886321 1110 224679999999999999
Q ss_pred eCC-CccEEEEEe
Q 029155 144 LGD-ARAYFLSTA 155 (198)
Q Consensus 144 ~~~-~~~~~LSt~ 155 (198)
++. .+.+.|++.
T Consensus 713 vD~~~rkI~f~l~ 725 (813)
T PRK11642 713 VNMDERKIDFSLI 725 (813)
T ss_pred eecCCCeEEEEEe
Confidence 873 467888874
No 93
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=96.70 E-value=0.0044 Score=55.72 Aligned_cols=72 Identities=17% Similarity=0.201 Sum_probs=56.2
Q ss_pred CCCCCCCCEEEEEEEEEec-ceEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeCC---
Q 029155 71 GPVPEPGSVVIARVTKVMT-RMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGD--- 146 (198)
Q Consensus 71 ~~~p~vGDiViG~V~~v~~-~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~--- 146 (198)
.|..++|++|.|+|.++.. ..++|++ . ...|+|+.++.- ..+.|++||.|+|-|..+..
T Consensus 133 ey~~~~Geiv~g~V~r~~~~~~i~vdl--------g-~~ea~LP~~eqi--------p~E~~~~Gdrik~~i~~V~~~~k 195 (374)
T PRK12328 133 KYKKKVGKIVFGTVVRVDNEENTFIEI--------D-EIRAVLPMKNRI--------KGEKFKVGDVVKAVLKRVKIDKN 195 (374)
T ss_pred HHHHhcCcEEEEEEEEEecCCCEEEEc--------C-CeEEEeCHHHcC--------CCCcCCCCCEEEEEEEEEecCCC
Confidence 4778999999999999986 4578888 3 478999877643 25779999999999999863
Q ss_pred -CccEEEEEecCCC
Q 029155 147 -ARAYFLSTAKNDL 159 (198)
Q Consensus 147 -~~~~~LSt~~~~l 159 (198)
+..+.||-..++|
T Consensus 196 ~gp~IilSRt~p~~ 209 (374)
T PRK12328 196 NGILIELSRTSPKF 209 (374)
T ss_pred CCCEEEEEcCCHHH
Confidence 2457777766544
No 94
>KOG1070 consensus rRNA processing protein Rrp5 [RNA processing and modification]
Probab=96.69 E-value=0.0085 Score=61.18 Aligned_cols=76 Identities=18% Similarity=0.223 Sum_probs=67.2
Q ss_pred CCCCCEEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeCC-CccEEE
Q 029155 74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGD-ARAYFL 152 (198)
Q Consensus 74 p~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~-~~~~~L 152 (198)
.+.||+|.|.|..+.+++.++.+ +..+.|..++++...+... .-+..|.+|+++.++|.+++. .+.+.|
T Consensus 1160 lk~g~iv~G~V~nv~~~glfi~l--------s~~v~a~v~is~~~ds~~k--~w~k~~~~gklv~~rv~~ve~~s~riel 1229 (1710)
T KOG1070|consen 1160 LKIGDIVRGFVKNVETKGLFIAL--------SRKVEAFVPISGLSDSFEK--EWEKHLPVGKLVTGRVLSVEEDSKRIEL 1229 (1710)
T ss_pred cccCceeEEEEEEecCCcEEEEE--------ccceEEEEEccccccchhh--hhhccCCccceeeeEEEEeeccCceEEE
Confidence 58899999999999999999999 7899999999999877755 677899999999999999974 467999
Q ss_pred EEecCCC
Q 029155 153 STAKNDL 159 (198)
Q Consensus 153 St~~~~l 159 (198)
+++..+-
T Consensus 1230 ~Lk~s~~ 1236 (1710)
T KOG1070|consen 1230 SLKNSDI 1236 (1710)
T ss_pred EEecccc
Confidence 9987654
No 95
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=96.60 E-value=0.0063 Score=55.77 Aligned_cols=77 Identities=12% Similarity=0.146 Sum_probs=58.1
Q ss_pred CCCCCCCCEEEEEEEEEecceEEEEEeeeccccccC-cceeEEeccccccccccccccccCCCCCCEEEEEEEEeCC---
Q 029155 71 GPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVRE-KFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGD--- 146 (198)
Q Consensus 71 ~~~p~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~-~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~--- 146 (198)
-|..++|++|.|+|.++..+.+.|++.+- +.. ...|+|+.++.- ..+.|++||.|+|-|..+..
T Consensus 147 ef~~~~GeIV~G~V~r~e~~~viv~l~~~----~g~~~~EaiLP~~Eqi--------p~E~y~~Gdrika~i~~V~~~~~ 214 (449)
T PRK12329 147 EFQDLEDTVLTARVLRFERQSVIMAVSSG----FGQPEVEAELPKREQL--------PNDNYRANATFKVFLKEVSEGPR 214 (449)
T ss_pred HHHHhcCcEEEEEEEEEcCCCEEEEeccc----CCCcceEEEecHHHcC--------CCCcCCCCCEEEEEEEEeecCCC
Confidence 46789999999999999999899888310 011 378899877642 25779999999999999953
Q ss_pred -CccEEEEEecCCC
Q 029155 147 -ARAYFLSTAKNDL 159 (198)
Q Consensus 147 -~~~~~LSt~~~~l 159 (198)
+..+.||-..++|
T Consensus 215 kGpqIilSRt~p~l 228 (449)
T PRK12329 215 RGPQLFVSRANAGL 228 (449)
T ss_pred CCCEEEEEcCCHHH
Confidence 2457788776654
No 96
>KOG1070 consensus rRNA processing protein Rrp5 [RNA processing and modification]
Probab=96.52 E-value=0.0036 Score=63.79 Aligned_cols=77 Identities=19% Similarity=0.145 Sum_probs=64.9
Q ss_pred CCCCCCCCCEEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeCCCcc
Q 029155 70 HGPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGDARA 149 (198)
Q Consensus 70 ~~~~p~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~~~~ 149 (198)
..+-..+|++|.|.|++|.+++..|.. ...+.|-||++++-.+...-.++.+-|+.||-|.|||+.-.|-.+
T Consensus 879 ~~~~~~igsiv~a~v~svKp~~L~v~l--------~~~~~gri~isev~d~~~eitDp~~k~~vG~~I~vrviG~~D~k~ 950 (1710)
T KOG1070|consen 879 STEDLSIGSIVRAYVKSVKPDQLNVLL--------AANHHGRIHISEVLDNLHEITDPLDKFKVGDGIFVRVIGGHDVKD 950 (1710)
T ss_pred cccceeeeeEEEEEEeeecccceEEec--------cccccCceehHHhhccccccCChhhhcccCCeEEEEEEcCCcccc
Confidence 457789999999999999999999998 678999999999987666666789999999999999998765444
Q ss_pred EEEEE
Q 029155 150 YFLST 154 (198)
Q Consensus 150 ~~LSt 154 (198)
+-.|+
T Consensus 951 lpith 955 (1710)
T KOG1070|consen 951 LPITH 955 (1710)
T ss_pred Ccccc
Confidence 43333
No 97
>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=96.47 E-value=0.015 Score=56.02 Aligned_cols=73 Identities=14% Similarity=0.203 Sum_probs=56.2
Q ss_pred CCCCCEEEEEEEEEecceEEEEEeeecccccc-CcceeEEecccccccc--ccc-------cccccCCCCCCEEEEEEEE
Q 029155 74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVR-EKFSGIIRQQDVRATE--IDK-------VDMHLSFRPGDIVRASVLS 143 (198)
Q Consensus 74 p~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~-~~~~G~l~~s~v~~~~--~d~-------~~~~~~~~~GDiV~AkV~s 143 (198)
-++|++..|+|+++++.+++|+| . ...+|++|.+++...+ .|+ ......|++||.|.++|.+
T Consensus 570 ~~iG~~~~g~I~~v~~~GifV~L--------~~~~veGlV~~s~l~~d~y~~d~~~~~l~g~~~~~~~~lGD~V~Vki~~ 641 (654)
T TIGR00358 570 DKVGTEFSGEISSVTRFGMFVRL--------DDNGIDGLIHISTLHNDYYVFDQEKMALIGKGTGKVYRIGDRVTVKLTE 641 (654)
T ss_pred hCCCcEEEEEEEeEEcCcEEEEe--------cCCceEEEEEeEeCCCcceEEeccccEEEeccCCcEECCCCEEEEEEEE
Confidence 36799999999999999999999 4 4689999999986432 111 1123679999999999999
Q ss_pred eCC-CccEEEEE
Q 029155 144 LGD-ARAYFLST 154 (198)
Q Consensus 144 ~~~-~~~~~LSt 154 (198)
++. .+.+.+++
T Consensus 642 vd~~~~~I~f~l 653 (654)
T TIGR00358 642 VNMETRSIIFEL 653 (654)
T ss_pred EecccCeEEEEE
Confidence 973 35666654
No 98
>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=96.41 E-value=0.017 Score=40.21 Aligned_cols=70 Identities=19% Similarity=0.177 Sum_probs=53.7
Q ss_pred CCEEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEE-EEEEEEeCCCccEEEEE
Q 029155 77 GSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIV-RASVLSLGDARAYFLST 154 (198)
Q Consensus 77 GDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV-~AkV~s~~~~~~~~LSt 154 (198)
|++|.|+|.+-+.+...|++. ..+..|.|+..+++........+...+++||.+ .+-|++. ..+.+.||.
T Consensus 1 G~lV~~~V~EKt~D~l~v~l~-------~~~l~a~l~~~HLsD~~~k~~~~~~klrvG~~L~~~lvL~~-~~r~i~lt~ 71 (72)
T cd05699 1 GKLVDARVLKKTLNGLEVAIL-------PEEIRAFLPTMHLSDHVSNCPLLWHCLQEGDTIPNLMCLSN-YKGRIILTK 71 (72)
T ss_pred CceEEEEEEEEcCCcEEEEec-------CCCcEEEEEccccCCchhhCHHHHhhhhcCCCccceEEEec-cccEEEEec
Confidence 789999999999999999994 457889998877765333334567889999999 8888832 235566653
No 99
>KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only]
Probab=96.16 E-value=0.0093 Score=56.07 Aligned_cols=74 Identities=9% Similarity=0.130 Sum_probs=61.9
Q ss_pred CCCCCCEE-----EEEEEEEecceEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeCCC
Q 029155 73 VPEPGSVV-----IARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGDA 147 (198)
Q Consensus 73 ~p~vGDiV-----iG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~~ 147 (198)
.++++|+. .|+|+.+++.+++|++ ...-.|+||.+|+.+.... +.++.+.+||.|..+-+..+..
T Consensus 660 ~~~~~~l~~g~vy~~tIt~~rd~G~~V~l--------~p~~~~Llh~sqL~~e~ia--kpsd~levGq~I~vk~ie~d~~ 729 (760)
T KOG1067|consen 660 DDQVQDLEFGGVYTATITEIRDTGVMVEL--------YPMQQGLLHNSQLDQEKIA--KPSDLLEVGQEIQVKYIERDPR 729 (760)
T ss_pred CccccceEeeeEEEEEEeeecccceEEEe--------cCCchhhccchhccccccc--ChHHHHhhcceeEEEEEeecCc
Confidence 35556655 5899999999999999 4567899999999877766 7889999999999999999877
Q ss_pred ccEEEEEec
Q 029155 148 RAYFLSTAK 156 (198)
Q Consensus 148 ~~~~LSt~~ 156 (198)
+.+.||-|.
T Consensus 730 g~~~ls~ra 738 (760)
T KOG1067|consen 730 GGIMLSSRA 738 (760)
T ss_pred cceeehhhh
Confidence 778887664
No 100
>COG2996 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only]
Probab=95.94 E-value=0.033 Score=48.05 Aligned_cols=63 Identities=17% Similarity=0.167 Sum_probs=47.8
Q ss_pred CCEEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeCCCccEEEEEec
Q 029155 77 GSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGDARAYFLSTAK 156 (198)
Q Consensus 77 GDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~~~~~~LSt~~ 156 (198)
++.|-|.|.++...+.+|-+ ...+.|+||.|++. ...+.|+.+.|+|+.+.+.+++.||++.
T Consensus 156 nq~v~~tVYr~~~~G~fv~~--------e~~~~GfIh~sEr~----------~~prlG~~l~~rVi~~reDg~lnLSl~p 217 (287)
T COG2996 156 NQEVDATVYRLLESGTFVIT--------ENGYLGFIHKSERF----------AEPRLGERLTARVIGVREDGKLNLSLRP 217 (287)
T ss_pred cCeeeeEEEEEeccceEEEE--------cCCeEEEEcchhhc----------ccccCCceEEEEEEEEccCCeeeccccc
Confidence 55566666666665555555 56789999988753 3467999999999999877899999975
Q ss_pred C
Q 029155 157 N 157 (198)
Q Consensus 157 ~ 157 (198)
-
T Consensus 218 ~ 218 (287)
T COG2996 218 R 218 (287)
T ss_pred c
Confidence 3
No 101
>KOG1856 consensus Transcription elongation factor SPT6 [RNA processing and modification]
Probab=95.86 E-value=0.012 Score=59.07 Aligned_cols=81 Identities=20% Similarity=0.239 Sum_probs=63.5
Q ss_pred CCCCCCEEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeCC-CccEE
Q 029155 73 VPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGD-ARAYF 151 (198)
Q Consensus 73 ~p~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~-~~~~~ 151 (198)
...+|.+|.+.|++++.....| + ...|..+..|+|+.++++..... .+.+-+++|+.|.+||++++. .-...
T Consensus 982 t~~~g~iV~~~V~~vt~rr~~C-v----~v~ld~G~~g~i~~~~~Sd~~v~--~p~~~v~vgq~v~~kvi~id~e~f~v~ 1054 (1299)
T KOG1856|consen 982 TFYEGAIVPVTVTKVTHRRGIC-V----RVRLDCGVTGFILAKNLSDRDVR--RPENRVKVGQTVYCKVIKIDKERFSVE 1054 (1299)
T ss_pred HhccCceEEEeeeEEEecccce-e----EEEecCCCceeeeccccChhhcc--CHHHhhccCceEEEEeeeeeHhhhhhh
Confidence 3578999999999999998555 1 11236789999999998764444 778889999999999999974 34578
Q ss_pred EEEecCCCe
Q 029155 152 LSTAKNDLG 160 (198)
Q Consensus 152 LSt~~~~lG 160 (198)
||++..+|-
T Consensus 1055 Ls~r~sdlk 1063 (1299)
T KOG1856|consen 1055 LSCRTSDLK 1063 (1299)
T ss_pred hhhhhHHhh
Confidence 888877764
No 102
>PF07754 DUF1610: Domain of unknown function (DUF1610); InterPro: IPR011668 This domain is found in archaeal species. It is likely to bind zinc via its four well-conserved cysteine residues.
Probab=95.69 E-value=0.007 Score=33.26 Aligned_cols=21 Identities=24% Similarity=0.518 Sum_probs=18.6
Q ss_pred CCCceeEEcc-CCeEEeCCCCC
Q 029155 167 TAGGTMVPIS-WTEMQCPLTGQ 187 (198)
Q Consensus 167 ~~g~~m~~~~-~~~~~c~~cg~ 187 (198)
.||..|.|.. ...+.||+||.
T Consensus 3 sC~~~i~~r~~~v~f~CPnCG~ 24 (24)
T PF07754_consen 3 SCGRPIAPREQAVPFPCPNCGF 24 (24)
T ss_pred cCCCcccCcccCceEeCCCCCC
Confidence 7899999887 78999999994
No 103
>KOG2916 consensus Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis]
Probab=95.38 E-value=0.016 Score=49.74 Aligned_cols=77 Identities=18% Similarity=0.228 Sum_probs=65.8
Q ss_pred CCCCCCCEEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeCCC-ccE
Q 029155 72 PVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGDA-RAY 150 (198)
Q Consensus 72 ~~p~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~~-~~~ 150 (198)
..|.++|+|++.|..|..-+|.|.++-.+ ..+|.|-.|+++..++. .++...++|-.=.+-|+.++.. +-+
T Consensus 12 kyPev~e~VmvnV~sIaemGayv~LlEYn------niEGmiLlsELSrRRIR--SI~klirVGr~E~vvVlrVDkekGYI 83 (304)
T KOG2916|consen 12 KYPEVEEIVMVNVRSIAEMGAYVKLLEYN------NIEGMILLSELSRRRIR--SIQKLIRVGRNEPVVVLRVDKEKGYI 83 (304)
T ss_pred cCCCcccEEEEEeeEehhccceEeeeecC------CcccchhhhHHHHHHHH--HHHHHHhcCCcceEEEEEEcCCCCce
Confidence 46999999999999999999999996432 47899999999876766 8889999999999999999854 567
Q ss_pred EEEEec
Q 029155 151 FLSTAK 156 (198)
Q Consensus 151 ~LSt~~ 156 (198)
.||.|.
T Consensus 84 DLSkrr 89 (304)
T KOG2916|consen 84 DLSKRR 89 (304)
T ss_pred echhcc
Confidence 899875
No 104
>PRK11712 ribonuclease G; Provisional
Probab=95.13 E-value=0.089 Score=49.14 Aligned_cols=73 Identities=19% Similarity=0.188 Sum_probs=53.1
Q ss_pred CCCCCEEEEEEEEEecc--eEEEEEeeeccccccCcceeEEecccccccc----------ccccccccCCCCCCEEEEEE
Q 029155 74 PEPGSVVIARVTKVMTR--MASADIMCVGAKSVREKFSGIIRQQDVRATE----------IDKVDMHLSFRPGDIVRASV 141 (198)
Q Consensus 74 p~vGDiViG~V~~v~~~--~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~----------~d~~~~~~~~~~GDiV~AkV 141 (198)
..+|+|-.|+|.+|.+. .||||| ...-.|+||.+|+.... .....+.+.+++||.|...|
T Consensus 36 ~~vGnIY~G~V~~v~pg~~AAFVdI--------G~~k~gFL~~~d~~~~~~~~~~~~~~~~~~~~i~~~l~~Gq~iLVQV 107 (489)
T PRK11712 36 GIVGNIYKGRVSRVLPGMQAAFVDI--------GLDKAAFLHASDIVPHTECVAGEEQKQFVVRDISELVRQGQDIMVQV 107 (489)
T ss_pred cccccEEEEEEeecCCCCceeEEee--------CCCccEEEEhhhccchhhhcccccccccccccHHHhccCCCEEEEEE
Confidence 46899999999999775 699999 67788999999874210 00113566799999999999
Q ss_pred EEeCC-CccEEEEE
Q 029155 142 LSLGD-ARAYFLST 154 (198)
Q Consensus 142 ~s~~~-~~~~~LSt 154 (198)
..-.- .....||+
T Consensus 108 ~Ke~~~~KG~~lT~ 121 (489)
T PRK11712 108 VKDPLGTKGARLTT 121 (489)
T ss_pred EeCCcCCCCCeEEE
Confidence 98431 23345555
No 105
>PRK10811 rne ribonuclease E; Reviewed
Probab=95.04 E-value=0.095 Score=52.34 Aligned_cols=74 Identities=12% Similarity=0.165 Sum_probs=54.0
Q ss_pred CCCCCEEEEEEEEEec--ceEEEEEeeeccccccCcceeEEecccccccc-cc------ccccccCCCCCCEEEEEEEEe
Q 029155 74 PEPGSVVIARVTKVMT--RMASADIMCVGAKSVREKFSGIIRQQDVRATE-ID------KVDMHLSFRPGDIVRASVLSL 144 (198)
Q Consensus 74 p~vGDiViG~V~~v~~--~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~-~d------~~~~~~~~~~GDiV~AkV~s~ 144 (198)
+.+|+|-.|+|.+|-+ +.+||+| ...-.|+||.+|+.... .. ...+.+.+++||.|...|..-
T Consensus 36 ~~vGnIYkGkVenIvPGInAAFVDI--------G~gknGFL~L~Di~~~~f~~~~~~~~~~~i~~~Lk~GqeILVQV~KE 107 (1068)
T PRK10811 36 QKKANIYKGKITRIEPSLEAAFVDY--------GAERHGFLPLKEIAREYFPANYSAHGRPNIKDVLREGQEVIVQIDKE 107 (1068)
T ss_pred cCccceEEEEEecccCCcceeEEEe--------cCCcceEEEhhhccccccccccccccccccccccCCCCEEEEEEeec
Confidence 4689999999999966 4699999 66788999999984211 11 113456799999999999984
Q ss_pred C-CCccEEEEEe
Q 029155 145 G-DARAYFLSTA 155 (198)
Q Consensus 145 ~-~~~~~~LSt~ 155 (198)
. .++...||++
T Consensus 108 a~gtKGp~LTt~ 119 (1068)
T PRK10811 108 ERGNKGAALTTF 119 (1068)
T ss_pred ccCCCCCceeee
Confidence 3 2234555554
No 106
>PF09297 zf-NADH-PPase: NADH pyrophosphatase zinc ribbon domain; InterPro: IPR015376 This domain has a zinc ribbon structure and is often found between two NUDIX domains.; GO: 0016787 hydrolase activity, 0046872 metal ion binding; PDB: 1VK6_A 2GB5_A.
Probab=94.54 E-value=0.044 Score=31.87 Aligned_cols=25 Identities=20% Similarity=0.341 Sum_probs=15.0
Q ss_pred ec-CCCceeEEccC-CeEEeCCCCCEE
Q 029155 165 ES-TAGGTMVPISW-TEMQCPLTGQTE 189 (198)
Q Consensus 165 ~~-~~g~~m~~~~~-~~~~c~~cg~~e 189 (198)
.| +||.+|.+..+ -.++||.||...
T Consensus 5 fC~~CG~~t~~~~~g~~r~C~~Cg~~~ 31 (32)
T PF09297_consen 5 FCGRCGAPTKPAPGGWARRCPSCGHEH 31 (32)
T ss_dssp B-TTT--BEEE-SSSS-EEESSSS-EE
T ss_pred ccCcCCccccCCCCcCEeECCCCcCEe
Confidence 47 89999988753 379999999764
No 107
>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=94.39 E-value=0.077 Score=37.73 Aligned_cols=47 Identities=17% Similarity=0.308 Sum_probs=38.4
Q ss_pred eeccCCcEEecCCccCC--CCCeeeCCCEEEeCCceEEEEeEeeeEEEcC
Q 029155 3 VKEEEMVLVTPGEVLGK--ATEVKAGKGAYVAKHNGLVYASLTGLLRTLS 50 (198)
Q Consensus 3 ~~~~~~~iV~PGd~l~~--~~e~~~G~Gty~~~g~~~i~asv~G~v~~~~ 50 (198)
+|..+.+.|.||+.|.. ...|-||.++..-.+ .+|||.+-|.|....
T Consensus 22 vK~~~G~~V~~G~IivRQRgtk~hPG~NVg~GrD-~TLfAl~~G~V~f~~ 70 (81)
T PF01016_consen 22 VKKFGGQFVKAGNIIVRQRGTKFHPGENVGMGRD-HTLFALVDGRVKFTK 70 (81)
T ss_dssp ESSSTTCEESSTSEEEEBSSSSSEEBTTEEEETT-SEEEESSSCEEEEEE
T ss_pred EEEeCCEEEcCCCEEEEeCCCcCcCCCCEEECCC-CcEEEecCEEEEEEE
Confidence 57788999999999874 246999999987743 359999999999864
No 108
>TIGR01384 TFS_arch transcription factor S, archaeal. There has been an apparent duplication event in the Halobacteriaceae lineage (Haloarcula, Haloferax, Haloquadratum, Halobacterium and Natromonas). There appears to be a separate duplication in Methanosphaera stadtmanae.
Probab=94.20 E-value=0.027 Score=41.39 Aligned_cols=29 Identities=24% Similarity=0.424 Sum_probs=24.8
Q ss_pred ec-CCCceeEEccCCeEEeCCCCCEEeeeeC
Q 029155 165 ES-TAGGTMVPISWTEMQCPLTGQTEQRKVA 194 (198)
Q Consensus 165 ~~-~~g~~m~~~~~~~~~c~~cg~~e~RKva 194 (198)
.| .||++|.|.+ +.+.|+.||..+.++.+
T Consensus 2 fC~~Cg~~l~~~~-~~~~C~~C~~~~~~~~~ 31 (104)
T TIGR01384 2 FCPKCGSLMTPKN-GVYVCPSCGYEKEKKPE 31 (104)
T ss_pred CCcccCcccccCC-CeEECcCCCCccccccc
Confidence 47 8999999876 68999999999998744
No 109
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=93.44 E-value=0.19 Score=45.91 Aligned_cols=61 Identities=20% Similarity=0.356 Sum_probs=41.3
Q ss_pred ccccCCCCCCEEEEE--E----EEeCCCccEEEEEecCCCeeeEEec-CCCceeEEccCCeEEeCCCCCEEe
Q 029155 126 DMHLSFRPGDIVRAS--V----LSLGDARAYFLSTAKNDLGVVSAES-TAGGTMVPISWTEMQCPLTGQTEQ 190 (198)
Q Consensus 126 ~~~~~~~~GDiV~Ak--V----~s~~~~~~~~LSt~~~~lGvv~a~~-~~g~~m~~~~~~~~~c~~cg~~e~ 190 (198)
++-.-+.+||.|.+- | +++. .+++..-.. +-...-+| .||..|.-.+.+-++|++||++-+
T Consensus 311 ~~a~~L~pGD~i~~~G~~~~~~~n~e---k~~v~~l~~-~~~~~p~Cp~Cg~~m~S~G~~g~rC~kCg~~~~ 378 (421)
T COG1571 311 ELARKLIPGDEITVYGSVKPGTLNLE---KFQVLKLAR-YERVNPVCPRCGGRMKSAGRNGFRCKKCGTRAR 378 (421)
T ss_pred HHHHhcCCCCEEEEecCccccceeEE---EEEEEEeee-eEEcCCCCCccCCchhhcCCCCcccccccccCC
Confidence 334567899998542 1 2221 233333344 77777899 999999877766899999998743
No 110
>PF13509 S1_2: S1 domain; PDB: 3GO5_A.
Probab=93.26 E-value=0.84 Score=30.30 Aligned_cols=60 Identities=17% Similarity=0.080 Sum_probs=31.3
Q ss_pred CCCEEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeCCCccEEEEE
Q 029155 76 PGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGDARAYFLST 154 (198)
Q Consensus 76 vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~~~~~~LSt 154 (198)
+|+++..+|.++++.+|+++. ...-.-+||.+++. ..+.+||.|.+-|=. +..+.+..||
T Consensus 1 iG~~~~L~V~~~~~~g~fL~~--------~~~~~vlLp~~e~~----------~~~~~Gd~v~VFvY~-D~~~rl~AT~ 60 (61)
T PF13509_consen 1 IGQINTLKVVDKNEFGYFLDD--------GEGKEVLLPKSEVP----------EPLKVGDEVEVFVYL-DKEGRLVATT 60 (61)
T ss_dssp --------EEEE-SSEEEEEE--------TT-EEEEEEGGG----------------TTSEEEEEEEE--TTS-EEEE-
T ss_pred CCCCcceEEEEEeCCEEEEEC--------CCCCEEEechHHcC----------CCCCCCCEEEEEEEE-CCCCCEEEec
Confidence 589999999999999999987 44456677766542 447899999998875 2234565555
No 111
>PRK05435 rpmA 50S ribosomal protein L27; Validated
Probab=93.09 E-value=0.24 Score=35.26 Aligned_cols=46 Identities=20% Similarity=0.278 Sum_probs=36.8
Q ss_pred eeccCCcEEecCCccCCC--CCeeeCCCEEEeCCceEEEEeEeeeEEEc
Q 029155 3 VKEEEMVLVTPGEVLGKA--TEVKAGKGAYVAKHNGLVYASLTGLLRTL 49 (198)
Q Consensus 3 ~~~~~~~iV~PGd~l~~~--~e~~~G~Gty~~~g~~~i~asv~G~v~~~ 49 (198)
+|....+.|.||+.|..- ..|-||.++-.-.+ .+|||.+.|.|...
T Consensus 23 vK~~~g~~V~~G~IivRQRGtk~~PG~nVg~GrD-~TlfA~~~G~V~f~ 70 (82)
T PRK05435 23 VKRFGGQFVKAGNIIVRQRGTKFHPGVNVGRGKD-HTLFALVDGVVKFE 70 (82)
T ss_pred eEecCCEEEcCCcEEEEeCCCeECCCCCEeecCC-ceEEEecceEEEEE
Confidence 567788999999998743 35899999976532 35999999999985
No 112
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=92.97 E-value=0.083 Score=35.28 Aligned_cols=30 Identities=17% Similarity=0.347 Sum_probs=23.2
Q ss_pred ec-CCCceeEEcc-CCeEEeCCCCCEEeeeeC
Q 029155 165 ES-TAGGTMVPIS-WTEMQCPLTGQTEQRKVA 194 (198)
Q Consensus 165 ~~-~~g~~m~~~~-~~~~~c~~cg~~e~RKva 194 (198)
.| .||..|.|.+ ...+.||+||..+-+..+
T Consensus 9 ~CtSCg~~i~~~~~~~~F~CPnCG~~~I~RC~ 40 (59)
T PRK14890 9 KCTSCGIEIAPREKAVKFLCPNCGEVIIYRCE 40 (59)
T ss_pred cccCCCCcccCCCccCEeeCCCCCCeeEeech
Confidence 46 7999998887 678999999987554443
No 113
>CHL00121 rpl27 ribosomal protein L27; Reviewed
Probab=92.95 E-value=0.19 Score=35.99 Aligned_cols=59 Identities=20% Similarity=0.288 Sum_probs=42.9
Q ss_pred eeccCCcEEecCCccCCC--CCeeeCCCEEEe-CCceEEEEeEeeeEEEcCCCCCCCCCCCeEEEecC
Q 029155 3 VKEEEMVLVTPGEVLGKA--TEVKAGKGAYVA-KHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGH 67 (198)
Q Consensus 3 ~~~~~~~iV~PGd~l~~~--~e~~~G~Gty~~-~g~~~i~asv~G~v~~~~~~~~~~~~~~~i~V~p~ 67 (198)
+|....+.|.||+.|..- ..|-||.++-.- |. +|||...|.|.... ...+++.|+|.|.
T Consensus 23 vK~~~gq~V~~G~IivRQRGtk~hPG~NVg~GrD~--TlfAl~~G~V~f~~----~~~~~~~vsv~~~ 84 (86)
T CHL00121 23 VKRFGGEKVSAGNILIRQRGTKFKPGLNVGCGKDF--TLYALIDGFVKFKK----KNKKQKSINVINI 84 (86)
T ss_pred eEEcCCEEEcCCcEEEEcCCCeECCCCcccccCCc--eEEEccceEEEEEE----eCCCCEEEEEeec
Confidence 467788999999998743 358899987544 43 59999999999853 1223456777764
No 114
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=92.89 E-value=0.096 Score=33.33 Aligned_cols=26 Identities=19% Similarity=0.351 Sum_probs=21.1
Q ss_pred ec-CCCceeEEccC---CeEEeCCCCCEEe
Q 029155 165 ES-TAGGTMVPISW---TEMQCPLTGQTEQ 190 (198)
Q Consensus 165 ~~-~~g~~m~~~~~---~~~~c~~cg~~e~ 190 (198)
.| .||+.|.+..+ +.+.||.||..+.
T Consensus 2 FCp~Cg~~l~~~~~~~~~~~vC~~Cg~~~~ 31 (52)
T smart00661 2 FCPKCGNMLIPKEGKEKRRFVCRKCGYEEP 31 (52)
T ss_pred CCCCCCCccccccCCCCCEEECCcCCCeEE
Confidence 47 89999988765 3799999998764
No 115
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=92.09 E-value=0.13 Score=39.83 Aligned_cols=29 Identities=24% Similarity=0.424 Sum_probs=22.0
Q ss_pred eeEEe-c-CCCceeEEccCCeEEeCCCCCEEe
Q 029155 161 VVSAE-S-TAGGTMVPISWTEMQCPLTGQTEQ 190 (198)
Q Consensus 161 vv~a~-~-~~g~~m~~~~~~~~~c~~cg~~e~ 190 (198)
+..+. | .||.||.... .+..||.||+++.
T Consensus 25 kML~~hCp~Cg~PLF~Kd-G~v~CPvC~~~~~ 55 (131)
T COG1645 25 KMLAKHCPKCGTPLFRKD-GEVFCPVCGYREV 55 (131)
T ss_pred HHHHhhCcccCCcceeeC-CeEECCCCCceEE
Confidence 33444 6 8999999866 4899999996553
No 116
>KOG3298 consensus DNA-directed RNA polymerase subunit E' [Transcription]
Probab=91.83 E-value=0.96 Score=36.27 Aligned_cols=85 Identities=20% Similarity=0.115 Sum_probs=52.2
Q ss_pred CCCCCCCEEEEEEEEEecceEEEEEeeecccccc------CcceeEEeccccccccccccccccCCCCCCEEEEEEEEeC
Q 029155 72 PVPEPGSVVIARVTKVMTRMASADIMCVGAKSVR------EKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLG 145 (198)
Q Consensus 72 ~~p~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~------~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~ 145 (198)
..|-.|++|-|.|+.+...++++++...+-..++ ..|. +-++- +.+.. .+++ ....|+.|+.+|+.+.
T Consensus 77 FkpfKGEVvdgvV~~Vnk~G~F~~~GPl~~f~sshl~ppd~~f~---p~~n~-P~f~~-~d~s-~I~~~~~VR~kiigtr 150 (170)
T KOG3298|consen 77 FKPFKGEVVDGVVTKVNKMGVFARSGPLEVFYSSHLKPPDYEFD---PGENP-PNFQT-EDES-VIQKGVEVRLKIIGTR 150 (170)
T ss_pred EeecCCcEEEEEEEEEeeeeEEEeccceEeeeecccCCCCcccC---CCCCC-Ccccc-cccc-eeeeCcEEEEEEEEEE
Confidence 4577899999999999999999999654432111 1121 22221 11111 1222 6889999999999864
Q ss_pred -CCcc-E-EEEEecCCCeee
Q 029155 146 -DARA-Y-FLSTAKNDLGVV 162 (198)
Q Consensus 146 -~~~~-~-~LSt~~~~lGvv 162 (198)
+... + .=|+.++-||.+
T Consensus 151 ~~~~~i~algtl~~D~LG~i 170 (170)
T KOG3298|consen 151 VDETEIFALGTLKGDYLGPI 170 (170)
T ss_pred EeeeeEEEEEEecCcccccC
Confidence 2222 3 335566667754
No 117
>PF09723 Zn-ribbon_8: Zinc ribbon domain; InterPro: IPR013429 This entry represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB []. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=91.52 E-value=0.19 Score=31.11 Aligned_cols=29 Identities=34% Similarity=0.558 Sum_probs=20.9
Q ss_pred ec-CCCce---eEEccC-CeEEeCCCCCEEeeee
Q 029155 165 ES-TAGGT---MVPISW-TEMQCPLTGQTEQRKV 193 (198)
Q Consensus 165 ~~-~~g~~---m~~~~~-~~~~c~~cg~~e~RKv 193 (198)
+| +||+. +.+.+. ....||+||..+-||+
T Consensus 7 ~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~~~~~r~ 40 (42)
T PF09723_consen 7 RCEECGHEFEVLQSISEDDPVPCPECGSTEVRRV 40 (42)
T ss_pred EeCCCCCEEEEEEEcCCCCCCcCCCCCCCceEEe
Confidence 46 78854 566653 6899999999666554
No 118
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=91.00 E-value=0.36 Score=30.29 Aligned_cols=30 Identities=17% Similarity=-0.002 Sum_probs=23.5
Q ss_pred Eec-CCCceeEEccCCeEEeCCCCCEEeeee
Q 029155 164 AES-TAGGTMVPISWTEMQCPLTGQTEQRKV 193 (198)
Q Consensus 164 a~~-~~g~~m~~~~~~~~~c~~cg~~e~RKv 193 (198)
-.| +||......+...++||+||..-.-|.
T Consensus 3 Y~C~~Cg~~~~~~~~~~irC~~CG~rIlyK~ 33 (44)
T smart00659 3 YICGECGRENEIKSKDVVRCRECGYRILYKK 33 (44)
T ss_pred EECCCCCCEeecCCCCceECCCCCceEEEEe
Confidence 367 899987665667999999998766554
No 119
>PRK05054 exoribonuclease II; Provisional
Probab=90.70 E-value=1.6 Score=42.22 Aligned_cols=72 Identities=11% Similarity=0.243 Sum_probs=51.6
Q ss_pred CCCC--EEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccccc---cc---c--cccc--ccCCCCCCEEEEEEE
Q 029155 75 EPGS--VVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRAT---EI---D--KVDM--HLSFRPGDIVRASVL 142 (198)
Q Consensus 75 ~vGD--iViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~---~~---d--~~~~--~~~~~~GDiV~AkV~ 142 (198)
++|+ ...|.|++++..+.+|+|. .....|++|.+.+... +. + ...+ ...|++||-|..+|.
T Consensus 558 ~~G~~~~f~g~I~~v~~~G~fV~l~-------~~~veglV~~~~l~~~~~~y~~~~~~~~~~~~~~~~~~lGd~V~V~v~ 630 (644)
T PRK05054 558 KAGTDTRFAAEIIDISRGGMRVRLL-------ENGAVAFIPASFLHAVRDELVCNQENGTVQIKGETVYKLGDVIDVTLA 630 (644)
T ss_pred ccCCCeEEEEEEEeeecCcEEEEEe-------CCceEEEEEccccCCCccceEEccccceEEEeCCEEEcCCCEEEEEEE
Confidence 4555 9999999999999999994 3467899999887431 10 0 0111 246999999999999
Q ss_pred EeCC-CccEEEE
Q 029155 143 SLGD-ARAYFLS 153 (198)
Q Consensus 143 s~~~-~~~~~LS 153 (198)
+++. .+.+..+
T Consensus 631 ~vd~~~~~i~~~ 642 (644)
T PRK05054 631 EVRMETRSIIAR 642 (644)
T ss_pred EEccccCeEEEE
Confidence 9973 3445443
No 120
>PF02150 RNA_POL_M_15KD: RNA polymerases M/15 Kd subunit; InterPro: IPR001529 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. In archaebacteria, there is generally a single form of RNA polymerase which also consist of an oligomeric assemblage of 10 to 13 polypeptides. It has recently been shown [], [] that small subunits of about 15 kDa, found in polymerase types I and II, are highly conserved. These proteins contain a probable zinc finger in their N-terminal region and a C-terminal zinc ribbon domain (see IPR001222 from INTERPRO).; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3H0G_I 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I ....
Probab=90.66 E-value=0.35 Score=28.78 Aligned_cols=26 Identities=19% Similarity=0.313 Sum_probs=19.6
Q ss_pred ec-CCCceeEEcc--CCeEEeCCCCCEEe
Q 029155 165 ES-TAGGTMVPIS--WTEMQCPLTGQTEQ 190 (198)
Q Consensus 165 ~~-~~g~~m~~~~--~~~~~c~~cg~~e~ 190 (198)
.| +||+.|+|.. +....|+.|+..++
T Consensus 3 FCp~C~nlL~p~~~~~~~~~C~~C~Y~~~ 31 (35)
T PF02150_consen 3 FCPECGNLLYPKEDKEKRVACRTCGYEEP 31 (35)
T ss_dssp BETTTTSBEEEEEETTTTEEESSSS-EEE
T ss_pred eCCCCCccceEcCCCccCcCCCCCCCccC
Confidence 47 8999999985 33347999999886
No 121
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=90.59 E-value=0.53 Score=29.43 Aligned_cols=33 Identities=15% Similarity=0.205 Sum_probs=23.4
Q ss_pred EEec-CCCceeEEccCC-eEEeCCCCCEEeeeeCC
Q 029155 163 SAES-TAGGTMVPISWT-EMQCPLTGQTEQRKVAK 195 (198)
Q Consensus 163 ~a~~-~~g~~m~~~~~~-~~~c~~cg~~e~RKva~ 195 (198)
.-.| .||..+.-.... .+.||.||.....|...
T Consensus 3 ~y~C~~CG~~~~~~~~~~~~~Cp~CG~~~~~~~~~ 37 (46)
T PRK00398 3 EYKCARCGREVELDEYGTGVRCPYCGYRILFKERP 37 (46)
T ss_pred EEECCCCCCEEEECCCCCceECCCCCCeEEEccCC
Confidence 3468 899987554433 79999999977665443
No 122
>PRK00420 hypothetical protein; Validated
Probab=89.77 E-value=0.26 Score=37.21 Aligned_cols=27 Identities=19% Similarity=0.368 Sum_probs=21.7
Q ss_pred Eec-CCCceeEEccCCeEEeCCCCCEEe
Q 029155 164 AES-TAGGTMVPISWTEMQCPLTGQTEQ 190 (198)
Q Consensus 164 a~~-~~g~~m~~~~~~~~~c~~cg~~e~ 190 (198)
..| .||.+|........+||.||....
T Consensus 24 ~~CP~Cg~pLf~lk~g~~~Cp~Cg~~~~ 51 (112)
T PRK00420 24 KHCPVCGLPLFELKDGEVVCPVHGKVYI 51 (112)
T ss_pred CCCCCCCCcceecCCCceECCCCCCeee
Confidence 567 899999875556899999998643
No 123
>smart00834 CxxC_CXXC_SSSS Putative regulatory protein. CxxC_CXXC_SSSS represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=89.64 E-value=0.34 Score=29.13 Aligned_cols=28 Identities=29% Similarity=0.463 Sum_probs=19.1
Q ss_pred ec-CCCce---eEEcc-CCeEEeCCCCCEEeeee
Q 029155 165 ES-TAGGT---MVPIS-WTEMQCPLTGQTEQRKV 193 (198)
Q Consensus 165 ~~-~~g~~---m~~~~-~~~~~c~~cg~~e~RKv 193 (198)
+| .||+. +.+.+ .....||.||. +-||+
T Consensus 7 ~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~-~~~r~ 39 (41)
T smart00834 7 RCEDCGHTFEVLQKISDDPLATCPECGG-DVRRL 39 (41)
T ss_pred EcCCCCCEEEEEEecCCCCCCCCCCCCC-cceec
Confidence 67 78884 34433 56789999999 44443
No 124
>KOG4600 consensus Mitochondrial ribosomal protein MRP7 (L2) [Translation, ribosomal structure and biogenesis]
Probab=88.82 E-value=1.2 Score=34.64 Aligned_cols=62 Identities=21% Similarity=0.276 Sum_probs=43.7
Q ss_pred eeccCCcEEecCCccCCCC--CeeeCCCEEEe-CCceEEEEeEeeeEEEcCCCCCCCCCCCeEEEecCC
Q 029155 3 VKEEEMVLVTPGEVLGKAT--EVKAGKGAYVA-KHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHK 68 (198)
Q Consensus 3 ~~~~~~~iV~PGd~l~~~~--e~~~G~Gty~~-~g~~~i~asv~G~v~~~~~~~~~~~~~~~i~V~p~~ 68 (198)
+|.++++.|.||+.|..-- .|-||.++=.- |. +|||..-|.|+......+ ..++.|.|.|..
T Consensus 50 vKk~egq~V~~G~IIvrQRgtkfHPG~nVGiGKDh--tifaL~eG~Vrf~k~~~~--~~Rk~i~V~~~~ 114 (144)
T KOG4600|consen 50 VKKYEGQSVIPGNIIVRQRGTKFHPGDNVGIGKDH--TIFALEEGRVRFEKSKIT--PPRKWIGVDPRG 114 (144)
T ss_pred ceecCCeeeecccEEEEecccccCCCcccccCCcc--eEEEeeccEEEEEEccCC--CCcceEEEeecC
Confidence 5788899999999997643 46677665433 43 599999999998653211 135678888754
No 125
>TIGR00062 L27 ribosomal protein L27. Eubacterial, chloroplast, and mitochondrial. Mitochondrial members have an additional C-terminal domain.
Probab=88.57 E-value=0.87 Score=32.49 Aligned_cols=45 Identities=20% Similarity=0.353 Sum_probs=36.4
Q ss_pred eeccCCcEEecCCccCCC--CCeeeCCCEEEe-CCceEEEEeEeeeEEEc
Q 029155 3 VKEEEMVLVTPGEVLGKA--TEVKAGKGAYVA-KHNGLVYASLTGLLRTL 49 (198)
Q Consensus 3 ~~~~~~~iV~PGd~l~~~--~e~~~G~Gty~~-~g~~~i~asv~G~v~~~ 49 (198)
+|....+.|.||+.|..- ..|-||.++-.- |. +|||.+.|.|...
T Consensus 23 vK~~~gq~V~~G~IivRQRGtk~hPG~nVg~GrD~--TlfAl~~G~V~f~ 70 (83)
T TIGR00062 23 VKRAGGQFVRAGSIIVRQRGTKFHPGNNVGMGKDH--TLFALSDGVVKFE 70 (83)
T ss_pred eEecCCEEEcCCcEEEEcCCceECCCCcccccCCC--eEEEecceEEEEE
Confidence 577788999999998743 358899998665 54 5999999999985
No 126
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=88.12 E-value=0.39 Score=32.12 Aligned_cols=31 Identities=19% Similarity=0.408 Sum_probs=19.4
Q ss_pred EEec-CCCceeEEcc-CCeEEeCCCCCEEeeee
Q 029155 163 SAES-TAGGTMVPIS-WTEMQCPLTGQTEQRKV 193 (198)
Q Consensus 163 ~a~~-~~g~~m~~~~-~~~~~c~~cg~~e~RKv 193 (198)
...| .||..+-|.. ...+.||+||..+-...
T Consensus 9 ~~~CtSCg~~i~p~e~~v~F~CPnCGe~~I~Rc 41 (61)
T COG2888 9 PPVCTSCGREIAPGETAVKFPCPNCGEVEIYRC 41 (61)
T ss_pred CceeccCCCEeccCCceeEeeCCCCCceeeehh
Confidence 3456 6777775543 45777888886665443
No 127
>TIGR02605 CxxC_CxxC_SSSS putative regulatory protein, FmdB family. This model represents a region of about 50 amino acids found in a number of small proteins in a wide range of bacteria. The region begins usually with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One member of this family is has been noted as a putative regulatory protein, designated FmdB (PubMed:8841393). Most members of this family have a C-terminal region containing highly degenerate sequence, such as SSTSESTKSSGSSGSSGSSESKASGSTEKSTSSTTAAAAV in Mycobacterium tuberculosis and VAVGGSAPAPSPAPRAGGGGGGCCGGGCCG in Streptomyces avermitilis. These low complexity regions, which are not included in the model, resemble low-complexity C-terminal regions of some heterocycle-containing bacteriocin precursors.
Probab=87.39 E-value=0.52 Score=30.01 Aligned_cols=32 Identities=22% Similarity=0.345 Sum_probs=20.9
Q ss_pred ec-CCCc---eeEEccC-CeEEeCCCCCEEe-eeeCCC
Q 029155 165 ES-TAGG---TMVPISW-TEMQCPLTGQTEQ-RKVAKV 196 (198)
Q Consensus 165 ~~-~~g~---~m~~~~~-~~~~c~~cg~~e~-RKva~~ 196 (198)
+| +||+ .+.+.+- ....||.||..+- |-+|.|
T Consensus 7 ~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~~~~~r~~s~~ 44 (52)
T TIGR02605 7 RCTACGHRFEVLQKMSDDPLATCPECGGEKLRRLLSAV 44 (52)
T ss_pred EeCCCCCEeEEEEecCCCCCCCCCCCCCCceeEEeccc
Confidence 57 7888 4554442 3567999999654 556644
No 128
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=87.36 E-value=0.87 Score=26.80 Aligned_cols=26 Identities=15% Similarity=0.190 Sum_probs=20.4
Q ss_pred ec-CCCceeEE-ccCCeEEeCCCCCEEe
Q 029155 165 ES-TAGGTMVP-ISWTEMQCPLTGQTEQ 190 (198)
Q Consensus 165 ~~-~~g~~m~~-~~~~~~~c~~cg~~e~ 190 (198)
.| .||+.++- .....+.|+.||....
T Consensus 5 ~C~~C~~~~i~~~~~~~~~C~~Cg~~~~ 32 (33)
T PF08792_consen 5 KCSKCGGNGIVNKEDDYEVCIFCGSSFP 32 (33)
T ss_pred EcCCCCCCeEEEecCCeEEcccCCcEee
Confidence 57 69988876 4557999999998764
No 129
>COG0557 VacB Exoribonuclease R [Transcription]
Probab=87.34 E-value=3.2 Score=40.48 Aligned_cols=74 Identities=16% Similarity=0.092 Sum_probs=53.8
Q ss_pred CCCCEEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccccccc---------cccccccCCCCCCEEEEEEEEeC
Q 029155 75 EPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEI---------DKVDMHLSFRPGDIVRASVLSLG 145 (198)
Q Consensus 75 ~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~---------d~~~~~~~~~~GDiV~AkV~s~~ 145 (198)
.+|+.-.|.|+++..++.+|.|. ...++|.+|++.+...+- ........|+.||-|.++|.+++
T Consensus 621 ~vg~~f~g~V~~v~~~g~~V~l~-------~~~ieglV~~s~L~~d~y~~~~~~~~l~~~~~~~~~~lgd~v~v~v~~v~ 693 (706)
T COG0557 621 RVGEEFDGVVTGVTSFGFFVELP-------ELGLEGLVHISSLPDDYYHFDERGQALVGEKSGKVYRLGDEVKVKVTSVD 693 (706)
T ss_pred hcCCEEEEEEEEEEeccEEEEec-------ccccccceEcccCCCceeeeccccceeeccccccccccCCEEEEEEEEEc
Confidence 67899999999999999999993 234788888887752110 01123457999999999999986
Q ss_pred C-CccEEEEEe
Q 029155 146 D-ARAYFLSTA 155 (198)
Q Consensus 146 ~-~~~~~LSt~ 155 (198)
. .+.+.++..
T Consensus 694 ~~~~~i~~~~v 704 (706)
T COG0557 694 LDERKIDFELV 704 (706)
T ss_pred ccccceEEEec
Confidence 3 355655543
No 130
>COG1530 CafA Ribonucleases G and E [Translation, ribosomal structure and biogenesis]
Probab=87.30 E-value=1.3 Score=41.44 Aligned_cols=74 Identities=19% Similarity=0.234 Sum_probs=54.1
Q ss_pred CCCCCEEEEEEEEEecc--eEEEEEeeeccccccCcceeEEecccccccccc--ccccccCCCCCCEEEEEEEEeCCC-c
Q 029155 74 PEPGSVVIARVTKVMTR--MASADIMCVGAKSVREKFSGIIRQQDVRATEID--KVDMHLSFRPGDIVRASVLSLGDA-R 148 (198)
Q Consensus 74 p~vGDiViG~V~~v~~~--~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d--~~~~~~~~~~GDiV~AkV~s~~~~-~ 148 (198)
-.+|++-.|+|++|.+. .|+||| ...-.|+||.+++.+.... ...++..++.|+.+...|..-..+ .
T Consensus 35 ~~~gniy~grv~~i~p~~~aafvdi--------g~~r~gfl~~~~~~~~~~~~~~~~i~~~lr~~~~~~Vqv~ke~~G~K 106 (487)
T COG1530 35 QIVGNIYKGRVTRVLPSLEAAFVDI--------GLERNGFLHLSEIVPYFRAVLEEKIKVRLRGGQATLVQVVKEPRGTK 106 (487)
T ss_pred eeecCceEEEecccCccchhheeec--------cCCccceEEecccchhhhhcccccceeeecCCceEEEEEEeecCccc
Confidence 46899999999999876 599999 5567899999998752111 113567999999999999986432 2
Q ss_pred cEEEEEe
Q 029155 149 AYFLSTA 155 (198)
Q Consensus 149 ~~~LSt~ 155 (198)
...||+.
T Consensus 107 ga~lT~~ 113 (487)
T COG1530 107 GARLTTD 113 (487)
T ss_pred cccceeE
Confidence 2444443
No 131
>COG1545 Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]
Probab=87.30 E-value=0.64 Score=36.25 Aligned_cols=34 Identities=18% Similarity=0.335 Sum_probs=26.7
Q ss_pred CeeeEEec-CCCceeEEccCCeEEeCCCCCE---EeeeeCC
Q 029155 159 LGVVSAES-TAGGTMVPISWTEMQCPLTGQT---EQRKVAK 195 (198)
Q Consensus 159 lGvv~a~~-~~g~~m~~~~~~~~~c~~cg~~---e~RKva~ 195 (198)
..-+-++| +||+...|-. ..||.||.. |...+|.
T Consensus 25 ~kl~g~kC~~CG~v~~PPr---~~Cp~C~~~~~~E~vels~ 62 (140)
T COG1545 25 GKLLGTKCKKCGRVYFPPR---AYCPKCGSETELEWVELSG 62 (140)
T ss_pred CcEEEEEcCCCCeEEcCCc---ccCCCCCCCCceEEEEeCC
Confidence 34455679 8999999954 889999998 7777765
No 132
>PF07282 OrfB_Zn_ribbon: Putative transposase DNA-binding domain; InterPro: IPR010095 This entry represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by IPR001959 from INTERPRO, and other proteins. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=87.22 E-value=0.45 Score=32.05 Aligned_cols=28 Identities=21% Similarity=0.236 Sum_probs=22.7
Q ss_pred ec-CCCceeEE-ccCCeEEeCCCCCEEeee
Q 029155 165 ES-TAGGTMVP-ISWTEMQCPLTGQTEQRK 192 (198)
Q Consensus 165 ~~-~~g~~m~~-~~~~~~~c~~cg~~e~RK 192 (198)
.| .||..+.. .++..+.||+||....|=
T Consensus 30 ~C~~CG~~~~~~~~~r~~~C~~Cg~~~~rD 59 (69)
T PF07282_consen 30 TCPRCGHRNKKRRSGRVFTCPNCGFEMDRD 59 (69)
T ss_pred CccCcccccccccccceEEcCCCCCEECcH
Confidence 36 79998876 577899999999987763
No 133
>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=87.03 E-value=0.32 Score=36.42 Aligned_cols=37 Identities=22% Similarity=0.419 Sum_probs=28.8
Q ss_pred ecCCCeeeEEec-CCCceeEEccCCeEEeCCCCCEEeee
Q 029155 155 AKNDLGVVSAES-TAGGTMVPISWTEMQCPLTGQTEQRK 192 (198)
Q Consensus 155 ~~~~lGvv~a~~-~~g~~m~~~~~~~~~c~~cg~~e~RK 192 (198)
..++||. .-.| .||...|=...+-..||.||.....-
T Consensus 2 akpelGt-KR~Cp~CG~kFYDLnk~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 2 AKPELGT-KRTCPSCGAKFYDLNKDPIVCPKCGTEFPPE 39 (108)
T ss_pred CccccCC-cccCCCCcchhccCCCCCccCCCCCCccCcc
Confidence 4567776 3468 89999888888899999999876543
No 134
>PRK07218 replication factor A; Provisional
Probab=86.32 E-value=2.8 Score=38.57 Aligned_cols=41 Identities=17% Similarity=0.249 Sum_probs=30.6
Q ss_pred EEEEEEEEeCCCccEEEEEecCCCeeeEEec-CCCceeEEccCCeEEeCCCCCEEeeee
Q 029155 136 IVRASVLSLGDARAYFLSTAKNDLGVVSAES-TAGGTMVPISWTEMQCPLTGQTEQRKV 193 (198)
Q Consensus 136 iV~AkV~s~~~~~~~~LSt~~~~lGvv~a~~-~~g~~m~~~~~~~~~c~~cg~~e~RKv 193 (198)
.|.+.|+++..+. -+..+| .|+..|.. -+||.||..|..+.
T Consensus 282 ev~G~Iv~i~~gs------------gli~rCP~C~r~v~~-----~~C~~hG~ve~~~d 323 (423)
T PRK07218 282 ELVGNIISVRDGS------------GLIERCPECGRVIQK-----GQCRSHGAVEGEDD 323 (423)
T ss_pred EEEEEEEEeccCC------------cceecCcCccccccC-----CcCCCCCCcCCeee
Confidence 4788888886542 236699 99999954 47999999987653
No 135
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=86.31 E-value=0.91 Score=29.24 Aligned_cols=28 Identities=21% Similarity=0.245 Sum_probs=22.3
Q ss_pred EEec-CCCc-eeEEccCCeEEeCCCCCEEee
Q 029155 163 SAES-TAGG-TMVPISWTEMQCPLTGQTEQR 191 (198)
Q Consensus 163 ~a~~-~~g~-~m~~~~~~~~~c~~cg~~e~R 191 (198)
+..| +||. .|.+-. +.+.|..||.++-.
T Consensus 20 ~~fCP~Cg~~~m~~~~-~r~~C~~Cgyt~~~ 49 (50)
T PRK00432 20 NKFCPRCGSGFMAEHL-DRWHCGKCGYTEFK 49 (50)
T ss_pred cCcCcCCCcchheccC-CcEECCCcCCEEec
Confidence 4467 8999 887765 78999999998754
No 136
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=84.69 E-value=0.33 Score=38.97 Aligned_cols=28 Identities=21% Similarity=0.442 Sum_probs=22.9
Q ss_pred eeEEec-CCCceeEEccCCeEE----------------eCCCCCE
Q 029155 161 VVSAES-TAGGTMVPISWTEMQ----------------CPLTGQT 188 (198)
Q Consensus 161 vv~a~~-~~g~~m~~~~~~~~~----------------c~~cg~~ 188 (198)
--+++| .|++++.+++-.+.+ ||+||+.
T Consensus 95 ~e~~RCp~CN~~L~~vs~eev~~~Vp~~~~~~~~~f~~C~~Cgki 139 (165)
T COG1656 95 PEFSRCPECNGELEKVSREEVKEKVPEKVYRNYEEFYRCPKCGKI 139 (165)
T ss_pred cccccCcccCCEeccCcHHHHhhccchhhhhcccceeECCCCccc
Confidence 348899 999999999866644 9999985
No 137
>PF06677 Auto_anti-p27: Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27); InterPro: IPR009563 The proteins in this entry are functionally uncharacterised and include several proteins that characterise Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27). It is thought that the potential association of anti-p27 with anti-centromere antibodies suggests that autoantigen p27 might play a role in mitosis [].
Probab=84.62 E-value=0.88 Score=28.15 Aligned_cols=24 Identities=13% Similarity=0.228 Sum_probs=18.6
Q ss_pred EEec-CCCceeEEccCCeEEeCCCC
Q 029155 163 SAES-TAGGTMVPISWTEMQCPLTG 186 (198)
Q Consensus 163 ~a~~-~~g~~m~~~~~~~~~c~~cg 186 (198)
...| .||.||.+.......|+.|+
T Consensus 17 ~~~Cp~C~~PL~~~k~g~~~Cv~C~ 41 (41)
T PF06677_consen 17 DEHCPDCGTPLMRDKDGKIYCVSCG 41 (41)
T ss_pred cCccCCCCCeeEEecCCCEECCCCC
Confidence 3467 89999987444689999996
No 138
>PF03604 DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa subunit; InterPro: IPR006591 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Each class of RNA polymerase is assembled from 9 to 15 different polypeptides. Rbp10 (RNA polymerase CX) is a domain found in RNA polymerase subunit 10; present in RNA polymerase I, II and III.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_Z 3HKZ_X 2NVX_L 3S1Q_L 2JA6_L 3S17_L 3HOW_L 3HOV_L 3PO2_L 3HOZ_L ....
Probab=83.40 E-value=0.63 Score=27.24 Aligned_cols=28 Identities=18% Similarity=0.246 Sum_probs=18.9
Q ss_pred ec-CCCceeEEccCCeEEeCCCCCEEeee
Q 029155 165 ES-TAGGTMVPISWTEMQCPLTGQTEQRK 192 (198)
Q Consensus 165 ~~-~~g~~m~~~~~~~~~c~~cg~~e~RK 192 (198)
.| +||....-...+.++|++||.+-.-|
T Consensus 2 ~C~~Cg~~~~~~~~~~irC~~CG~RIlyK 30 (32)
T PF03604_consen 2 ICGECGAEVELKPGDPIRCPECGHRILYK 30 (32)
T ss_dssp BESSSSSSE-BSTSSTSSBSSSS-SEEBE
T ss_pred CCCcCCCeeEcCCCCcEECCcCCCeEEEe
Confidence 46 78888764456789999999865433
No 139
>PF01927 Mut7-C: Mut7-C RNAse domain; InterPro: IPR002782 This prokaryotic family of proteins have no known function. The proteins contain four conserved cysteines that may be involved in metal binding or disulphide bridges.
Probab=82.96 E-value=0.74 Score=35.95 Aligned_cols=32 Identities=25% Similarity=0.468 Sum_probs=24.9
Q ss_pred CCeeeEEec-CCCceeEEccCCe----------------EEeCCCCCEE
Q 029155 158 DLGVVSAES-TAGGTMVPISWTE----------------MQCPLTGQTE 189 (198)
Q Consensus 158 ~lGvv~a~~-~~g~~m~~~~~~~----------------~~c~~cg~~e 189 (198)
++..++++| .|.+++.+++..+ .+||.||++.
T Consensus 86 ~~~~~~sRC~~CN~~L~~v~~~~v~~~vp~~v~~~~~~f~~C~~C~kiy 134 (147)
T PF01927_consen 86 RLDPIFSRCPKCNGPLRPVSKEEVKDRVPPYVYETYDEFWRCPGCGKIY 134 (147)
T ss_pred ccCCCCCccCCCCcEeeechhhccccccCccccccCCeEEECCCCCCEe
Confidence 345678999 8999998887553 4899999864
No 140
>TIGR02062 RNase_B exoribonuclease II. This family consists of exoribonuclease II, the product of the rnb gene, as found in a number of gamma proteobacteria. In Escherichia coli, it is one of eight different exoribonucleases. It is involved in mRNA degradation and tRNA precursor end processing.
Probab=82.89 E-value=7.2 Score=37.73 Aligned_cols=65 Identities=9% Similarity=0.168 Sum_probs=48.1
Q ss_pred CCCC--EEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccccc---c---ccc--cccc--cCCCCCCEEEEEEE
Q 029155 75 EPGS--VVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRAT---E---IDK--VDMH--LSFRPGDIVRASVL 142 (198)
Q Consensus 75 ~vGD--iViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~---~---~d~--~~~~--~~~~~GDiV~AkV~ 142 (198)
++|+ .-.|.|+++...+.+|++. ...+.|++|.+.+... + .+. ..+. ..|+.||-|..+|.
T Consensus 554 ~~g~~~~f~g~I~~v~~~g~~v~l~-------~~~~~g~v~~~~l~~~~~~~~~~~~~~~~~l~g~~~~~lgd~v~V~v~ 626 (639)
T TIGR02062 554 KAAKNTRFAAEIVDISRGGMRVRLL-------ENGAIAFIPAAFLHANREELVCNQENGTVQIKGETVYKIGDVIDVVLT 626 (639)
T ss_pred ccCCCcEEEEEEEeeeCCcEEEEEe-------cCceEEEEEhhhcCCCCcceEEcccccEEEEeccEEEecCCEEEEEEE
Confidence 4554 8899999999999999994 4568999998887531 1 011 1221 25999999999999
Q ss_pred EeCC
Q 029155 143 SLGD 146 (198)
Q Consensus 143 s~~~ 146 (198)
+++.
T Consensus 627 ~vd~ 630 (639)
T TIGR02062 627 EVRM 630 (639)
T ss_pred Eecc
Confidence 9973
No 141
>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=82.43 E-value=7.4 Score=29.65 Aligned_cols=70 Identities=17% Similarity=0.150 Sum_probs=38.1
Q ss_pred CCCCCEEEEEEEEEecceEEEEEeeeccccccC----cceeEEeccccccccccccccccCCCCCCEEEEEEEEe
Q 029155 74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVRE----KFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSL 144 (198)
Q Consensus 74 p~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~----~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~ 144 (198)
|-+|+++.|+|.+-+..+..|.+...++--+.. .-...=+.+++=-...+ .+-.-+|..|+.|+=||.+.
T Consensus 1 PF~gEvl~g~I~~~~~~Gi~vslgFFddI~IP~~~L~~ps~fd~~~~~W~W~~~-~~~~l~~d~ge~IRFRV~~~ 74 (122)
T PF08292_consen 1 PFVGEVLTGKIKSSTAEGIRVSLGFFDDIFIPPSLLPEPSRFDEEEQAWVWEYD-EEQELFFDIGEEIRFRVESE 74 (122)
T ss_dssp --TT-EEEEEEEEEETTEEEEEECCEEEEEEECCCC-TTEEEECCCTEEEEEES-SSEEEEE-TT-EEEEEEEEE
T ss_pred CCCCCEEEEEEEecCCCcEEEEecccccEEECHHHCCCCCccCccCCEEEEECC-CCceeEccCCCEEEEEEeEE
Confidence 568999999999999999999996555421110 00011011111001110 13345679999999999985
No 142
>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=82.42 E-value=15 Score=33.07 Aligned_cols=96 Identities=18% Similarity=0.371 Sum_probs=65.4
Q ss_pred EEecCCccCCCCCeeeCCCEEEeCCceEEEEeEeeeEEEcCCCCCCCCCCCeEEEecCCCCCCCCCCCCEEEEEEEEEec
Q 029155 10 LVTPGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHKAHGPVPEPGSVVIARVTKVMT 89 (198)
Q Consensus 10 iV~PGd~l~~~~e~~~G~Gty~~~g~~~i~asv~G~v~~~~~~~~~~~~~~~i~V~p~~~~~~~p~vGDiViG~V~~v~~ 89 (198)
+.+||+.=...+|...|.-+..-+..|.-+..++|++++. +++.+.|+-. + -| -++.-+..
T Consensus 246 v~~pg~kT~YLSEL~sG~~VlvVd~~G~tR~~~VGRvKIE--------~RPLllIeA~----~---~g----~~~svilQ 306 (354)
T PF01959_consen 246 VLMPGGKTRYLSELRSGDEVLVVDADGRTRTAIVGRVKIE--------RRPLLLIEAE----A---DG----KRISVILQ 306 (354)
T ss_pred EEcCCCceeehhhhcCCCEEEEEeCCCCEEEEEeeEEEEe--------ecceEEEEEE----e---CC----eEEEEEEe
Confidence 4678888777788889988776654455999999999994 4677777642 1 12 23444567
Q ss_pred ceEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeCC
Q 029155 90 RMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGD 146 (198)
Q Consensus 90 ~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~ 146 (198)
+-|.|.+...++.+++ --.+++||.|.+.+..-+.
T Consensus 307 naetIRlv~p~G~~vs----------------------Vt~Lk~GD~vL~~~~~~~R 341 (354)
T PF01959_consen 307 NAETIRLVGPDGEPVS----------------------VTELKPGDEVLVYLEEAGR 341 (354)
T ss_pred cCcEEEEECCCCCEee----------------------eeecCCCCEEEEEecCCCc
Confidence 8888888543322111 1236899999999987543
No 143
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=82.28 E-value=1.1 Score=26.61 Aligned_cols=24 Identities=25% Similarity=0.501 Sum_probs=13.0
Q ss_pred ec-CCCceeE---E--ccCCeEEeCCCCCE
Q 029155 165 ES-TAGGTMV---P--ISWTEMQCPLTGQT 188 (198)
Q Consensus 165 ~~-~~g~~m~---~--~~~~~~~c~~cg~~ 188 (198)
.| .||++|. | -+..-+.|+.||++
T Consensus 2 fC~~CG~~l~~~ip~gd~r~R~vC~~Cg~I 31 (34)
T PF14803_consen 2 FCPQCGGPLERRIPEGDDRERLVCPACGFI 31 (34)
T ss_dssp B-TTT--B-EEE--TT-SS-EEEETTTTEE
T ss_pred ccccccChhhhhcCCCCCccceECCCCCCE
Confidence 46 7898873 4 23457999999986
No 144
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=82.28 E-value=1.1 Score=33.79 Aligned_cols=32 Identities=16% Similarity=0.120 Sum_probs=22.1
Q ss_pred eEEec-CCCceeEEccCCeEEeCCCCCEEeeee
Q 029155 162 VSAES-TAGGTMVPISWTEMQCPLTGQTEQRKV 193 (198)
Q Consensus 162 v~a~~-~~g~~m~~~~~~~~~c~~cg~~e~RKv 193 (198)
..++| .||...-...+..+.||.||....+=+
T Consensus 69 ~~~~C~~Cg~~~~~~~~~~~~CP~Cgs~~~~i~ 101 (114)
T PRK03681 69 AECWCETCQQYVTLLTQRVRRCPQCHGDMLRIV 101 (114)
T ss_pred cEEEcccCCCeeecCCccCCcCcCcCCCCcEEc
Confidence 37889 799765444555588999997654433
No 145
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=81.63 E-value=0.81 Score=34.56 Aligned_cols=30 Identities=13% Similarity=0.083 Sum_probs=21.4
Q ss_pred eEEec-CCCceeEEccCCeEEeCCCCCEEee
Q 029155 162 VSAES-TAGGTMVPISWTEMQCPLTGQTEQR 191 (198)
Q Consensus 162 v~a~~-~~g~~m~~~~~~~~~c~~cg~~e~R 191 (198)
..++| .||...-+..+..+.||.||....+
T Consensus 70 ~~~~C~~Cg~~~~~~~~~~~~CP~Cgs~~~~ 100 (117)
T PRK00564 70 VELECKDCSHVFKPNALDYGVCEKCHSKNVI 100 (117)
T ss_pred CEEEhhhCCCccccCCccCCcCcCCCCCceE
Confidence 37889 7997765544555679999986544
No 146
>TIGR02300 FYDLN_acid conserved hypothetical protein TIGR02300. Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=81.15 E-value=0.75 Score=35.40 Aligned_cols=36 Identities=25% Similarity=0.350 Sum_probs=28.2
Q ss_pred ecCCCeeeEEec-CCCceeEEccCCeEEeCCCCCEEee
Q 029155 155 AKNDLGVVSAES-TAGGTMVPISWTEMQCPLTGQTEQR 191 (198)
Q Consensus 155 ~~~~lGvv~a~~-~~g~~m~~~~~~~~~c~~cg~~e~R 191 (198)
..++||. .-.| .||...+=....-..||.||.....
T Consensus 2 ~k~elGt-Kr~Cp~cg~kFYDLnk~p~vcP~cg~~~~~ 38 (129)
T TIGR02300 2 AKPDLGT-KRICPNTGSKFYDLNRRPAVSPYTGEQFPP 38 (129)
T ss_pred CchhhCc-cccCCCcCccccccCCCCccCCCcCCccCc
Confidence 3456775 3467 9999999888889999999987643
No 147
>PRK02290 3-dehydroquinate synthase; Provisional
Probab=81.09 E-value=17 Score=32.66 Aligned_cols=95 Identities=17% Similarity=0.362 Sum_probs=63.5
Q ss_pred EEecCCccCCCCCeeeCCCEEEeCCceEEEEeEeeeEEEcCCCCCCCCCCCeEEEecCCCCCCCCCCCCEEEEEEEEEec
Q 029155 10 LVTPGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHKAHGPVPEPGSVVIARVTKVMT 89 (198)
Q Consensus 10 iV~PGd~l~~~~e~~~G~Gty~~~g~~~i~asv~G~v~~~~~~~~~~~~~~~i~V~p~~~~~~~p~vGDiViG~V~~v~~ 89 (198)
+.+||+.=...+|...|.-+-.-+..|.-+..++|++++. .++.+-|+-. + -| -++.-+..
T Consensus 236 v~~pgg~T~YLsEL~sG~eVlvVd~~G~tR~~~VGRvKIE--------~RPL~lIeAe----~---~g----~~~~viLQ 296 (344)
T PRK02290 236 VRVPGDKTRYLSELRSGDEVLVVDADGNTREAIVGRVKIE--------KRPLLLIEAE----Y---GG----KRIRTILQ 296 (344)
T ss_pred EEcCCCcchhhHhhcCCCEEEEEeCCCCEEEEEeeEEEEe--------eccEEEEEEE----e---CC----eEEEEEEe
Confidence 4678998888788888988765544444999999999994 4677777642 1 13 23334467
Q ss_pred ceEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeC
Q 029155 90 RMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLG 145 (198)
Q Consensus 90 ~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~ 145 (198)
+-|.+.+...++++ +.+ -.+++||.|.+++...+
T Consensus 297 naetIrlv~~dG~~--------vsV--------------t~Lk~GD~VL~~~~~~~ 330 (344)
T PRK02290 297 NAETIRLVTPDGKP--------VSV--------------VDLKPGDEVLGYLEEAA 330 (344)
T ss_pred cCcEEEEECCCCCE--------eee--------------eecCCCCEEEEEecCCc
Confidence 77888885332221 111 23689999999998644
No 148
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=80.98 E-value=0.94 Score=39.38 Aligned_cols=25 Identities=20% Similarity=0.264 Sum_probs=19.9
Q ss_pred ec-CCCceeEEcc-CCeEEeCCCCCEE
Q 029155 165 ES-TAGGTMVPIS-WTEMQCPLTGQTE 189 (198)
Q Consensus 165 ~~-~~g~~m~~~~-~~~~~c~~cg~~e 189 (198)
.| +||++|.+.. .-.++|++||+..
T Consensus 113 FCg~CG~~~~~~~~g~~~~C~~cg~~~ 139 (279)
T COG2816 113 FCGRCGTKTYPREGGWARVCPKCGHEH 139 (279)
T ss_pred CCCCCCCcCccccCceeeeCCCCCCcc
Confidence 46 7999998874 2379999999864
No 149
>PTZ00248 eukaryotic translation initiation factor 2 subunit 1; Provisional
Probab=80.69 E-value=2.5 Score=37.44 Aligned_cols=101 Identities=13% Similarity=0.173 Sum_probs=58.5
Q ss_pred CCccCCCCCeeeCCCEEEeCCceEEEEeEeeeEEEcCCCCCCCCCCCeEEEecCCCCCCCCCCCCEEEEEEEEEecceEE
Q 029155 14 GEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHKAHGPVPEPGSVVIARVTKVMTRMAS 93 (198)
Q Consensus 14 Gd~l~~~~e~~~G~Gty~~~g~~~i~asv~G~v~~~~~~~~~~~~~~~i~V~p~~~~~~~p~vGDiViG~V~~v~~~~~~ 93 (198)
||.+-..-.-+.-.|.|++=+. |--+=|++.+++ ++-.......-..++||.|.++|.+|....-.
T Consensus 18 GdvV~g~V~~I~d~GafV~L~E---Y~gvEGlIhiSE-----------lS~~ri~~i~d~vkvGd~v~vkVl~VD~ekg~ 83 (319)
T PTZ00248 18 DDLVMVKVVRITEMGAYVSLLE---YDDIEGMILMSE-----------LSKRRIRSINKLIRVGRHEVVVVLRVDKEKGY 83 (319)
T ss_pred CCEEEEEEEEEeCCeEEEEecC---CCCcEEEEEHHH-----------hcccccCCHHHhcCCCCEEEEEEEEEeCCCCE
Confidence 6655332223445567755321 123456676642 11122223334579999999999999776555
Q ss_pred EEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeCC
Q 029155 94 ADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGD 146 (198)
Q Consensus 94 V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~ 146 (198)
+++ + ..++.... ...+.+.|..|++|.++|..+-+
T Consensus 84 IdL--------S--------~K~v~~~p--w~~~~e~~~~g~~v~~~V~~ia~ 118 (319)
T PTZ00248 84 IDL--------S--------KKRVSPED--IEACEEKFSKSKKVHSIMRHIAQ 118 (319)
T ss_pred EEE--------E--------eeecccch--HHHHHHhCcCCCEEEEEEEEchh
Confidence 555 1 11222221 12556889999999999999843
No 150
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=80.03 E-value=0.99 Score=29.65 Aligned_cols=30 Identities=17% Similarity=0.256 Sum_probs=24.5
Q ss_pred Eec-CCCceeEEccCCeEEeCCCCCEEeeeeC
Q 029155 164 AES-TAGGTMVPISWTEMQCPLTGQTEQRKVA 194 (198)
Q Consensus 164 a~~-~~g~~m~~~~~~~~~c~~cg~~e~RKva 194 (198)
.+| .||.++.+.+ +.+.||.||...-|-..
T Consensus 6 ~~C~~Cg~~~~~~d-DiVvCp~CgapyHR~C~ 36 (54)
T PF14446_consen 6 CKCPVCGKKFKDGD-DIVVCPECGAPYHRDCW 36 (54)
T ss_pred ccChhhCCcccCCC-CEEECCCCCCcccHHHH
Confidence 467 7999998765 79999999998877544
No 151
>PHA02942 putative transposase; Provisional
Probab=79.74 E-value=1.3 Score=40.20 Aligned_cols=28 Identities=29% Similarity=0.547 Sum_probs=22.3
Q ss_pred ec-CCCceeEEccCCeEEeCCCCCEEeee
Q 029155 165 ES-TAGGTMVPISWTEMQCPLTGQTEQRK 192 (198)
Q Consensus 165 ~~-~~g~~m~~~~~~~~~c~~cg~~e~RK 192 (198)
.| .||+.+.+.+...+.|++||....|=
T Consensus 327 ~Cs~CG~~~~~l~~r~f~C~~CG~~~drD 355 (383)
T PHA02942 327 SCPKCGHKMVEIAHRYFHCPSCGYENDRD 355 (383)
T ss_pred cCCCCCCccCcCCCCEEECCCCCCEeCcH
Confidence 46 69998876666689999999988763
No 152
>PRK08402 replication factor A; Reviewed
Probab=78.49 E-value=22 Score=32.00 Aligned_cols=29 Identities=14% Similarity=0.147 Sum_probs=21.0
Q ss_pred eeeEEec-CCCceeE-EccCCeEEeCCCCCE
Q 029155 160 GVVSAES-TAGGTMV-PISWTEMQCPLTGQT 188 (198)
Q Consensus 160 Gvv~a~~-~~g~~m~-~~~~~~~~c~~cg~~ 188 (198)
+-++..| .|.+.|. -...+...|++||..
T Consensus 209 ~~~y~aCp~CnKkv~~~~~~~~~~Ce~~~~v 239 (355)
T PRK08402 209 VLVYDACPECRRKVDYDPATDTWICPEHGEV 239 (355)
T ss_pred CeeEecCCCCCeEEEEecCCCCEeCCCCCCc
Confidence 4468889 8999986 333346799999953
No 153
>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=78.01 E-value=4 Score=28.77 Aligned_cols=42 Identities=17% Similarity=0.109 Sum_probs=27.9
Q ss_pred eEEEecCCCCCCCCCCCCEEEEEEEEEecc---eEEEEEeeeccc
Q 029155 61 TVEVTGHKAHGPVPEPGSVVIARVTKVMTR---MASADIMCVGAK 102 (198)
Q Consensus 61 ~i~V~p~~~~~~~p~vGDiViG~V~~v~~~---~~~V~I~~v~~~ 102 (198)
-|.|.|..-+++-++.||.|.|.|..=++. .+.+.|.++++.
T Consensus 30 DvYVs~~qIrrf~LR~GD~V~G~vr~p~~~ek~~aL~~V~~VNg~ 74 (78)
T PF07497_consen 30 DVYVSPSQIRRFGLRTGDLVEGQVRPPREGEKYFALLRVESVNGR 74 (78)
T ss_dssp SEEE-CCCCCCTT--TTEEEEEEEE--STTSSSEEECEECEETTE
T ss_pred CEEECHHHHHHcCCCCCCEEEEEEeCCCCCCcceeeEEEEeECCc
Confidence 578887666788899999999999987543 467777666654
No 154
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=77.62 E-value=1.9 Score=32.40 Aligned_cols=24 Identities=21% Similarity=0.407 Sum_probs=19.4
Q ss_pred CCCceeEEc---cCCeEEeCCCCCEEe
Q 029155 167 TAGGTMVPI---SWTEMQCPLTGQTEQ 190 (198)
Q Consensus 167 ~~g~~m~~~---~~~~~~c~~cg~~e~ 190 (198)
+||+.|+|. ....|.|++||..+.
T Consensus 7 ~Cgsll~p~~~~~~~~l~C~kCgye~~ 33 (113)
T COG1594 7 KCGSLLYPKKDDEGGKLVCRKCGYEEE 33 (113)
T ss_pred CccCeeEEeEcCCCcEEECCCCCcchh
Confidence 599999995 235899999998764
No 155
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=77.32 E-value=2.1 Score=27.58 Aligned_cols=29 Identities=14% Similarity=0.241 Sum_probs=21.0
Q ss_pred EEec-CCCceeE-EccCCeEEeCCCCCEEee
Q 029155 163 SAES-TAGGTMV-PISWTEMQCPLTGQTEQR 191 (198)
Q Consensus 163 ~a~~-~~g~~m~-~~~~~~~~c~~cg~~e~R 191 (198)
.-.| +||.... ........||.||.+-.=
T Consensus 6 ~Y~C~~Cg~~~~~~~~~~~irCp~Cg~rIl~ 36 (49)
T COG1996 6 EYKCARCGREVELDQETRGIRCPYCGSRILV 36 (49)
T ss_pred EEEhhhcCCeeehhhccCceeCCCCCcEEEE
Confidence 4468 8999875 334568999999986543
No 156
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=76.70 E-value=0.76 Score=24.78 Aligned_cols=20 Identities=20% Similarity=0.439 Sum_probs=15.0
Q ss_pred c-CCCceeEEccCCeEEeCCCCCE
Q 029155 166 S-TAGGTMVPISWTEMQCPLTGQT 188 (198)
Q Consensus 166 ~-~~g~~m~~~~~~~~~c~~cg~~ 188 (198)
| .||+.+.+ +...|++||..
T Consensus 2 Cp~CG~~~~~---~~~fC~~CG~~ 22 (23)
T PF13240_consen 2 CPNCGAEIED---DAKFCPNCGTP 22 (23)
T ss_pred CcccCCCCCC---cCcchhhhCCc
Confidence 6 78888853 45779999973
No 157
>PF01155 HypA: Hydrogenase expression/synthesis hypA family; InterPro: IPR000688 Bacterial membrane-bound nickel-dependent hydrogenases requires a number of accessory proteins which are involved in their maturation. The exact role of these proteins is not yet clear, but some seem to be required for the incorporation of the nickel ions []. One of these proteins is generally known as hypA. It is a protein of about 12 to 14 kDa that contains, in its C-terminal region, four conserved cysteines that form a zinc-finger like motif. Escherichia coli has two proteins that belong to this family, hypA and hybF. A homologue, MJ0214, has also been found in a number of archaeal species, including the genome of Methanocaldococcus jannaschii (Methanococcus jannaschii).; GO: 0016151 nickel ion binding, 0006464 protein modification process; PDB: 2KDX_A 3A44_D 3A43_B.
Probab=76.00 E-value=1.2 Score=33.38 Aligned_cols=29 Identities=21% Similarity=0.519 Sum_probs=20.3
Q ss_pred eEEec-CCCceeEEccCCeEEeCCCCCEEee
Q 029155 162 VSAES-TAGGTMVPISWTEMQCPLTGQTEQR 191 (198)
Q Consensus 162 v~a~~-~~g~~m~~~~~~~~~c~~cg~~e~R 191 (198)
+.++| .||...-+... .+.||.||....+
T Consensus 69 ~~~~C~~Cg~~~~~~~~-~~~CP~Cgs~~~~ 98 (113)
T PF01155_consen 69 ARARCRDCGHEFEPDEF-DFSCPRCGSPDVE 98 (113)
T ss_dssp -EEEETTTS-EEECHHC-CHH-SSSSSS-EE
T ss_pred CcEECCCCCCEEecCCC-CCCCcCCcCCCcE
Confidence 37899 89999887664 4889999987654
No 158
>KOG4134 consensus DNA-dependent RNA polymerase I [Transcription]
Probab=75.98 E-value=2.5 Score=35.67 Aligned_cols=61 Identities=16% Similarity=0.113 Sum_probs=49.3
Q ss_pred CCCCCCCEEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeCCC
Q 029155 72 PVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGDA 147 (198)
Q Consensus 72 ~~p~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~~ 147 (198)
..|++||+..|.|-.+.....-+-| ..-|.+.|+..++.+ + +.++..++...++|.+++++
T Consensus 103 f~Pk~Gd~LeG~Vn~vS~sHIglLI--------hg~FNASIpk~nip~---d----w~fI~md~eee~~v~ntD~g 163 (253)
T KOG4134|consen 103 FRPKAGDILEGVVNHVSRSHIGLLI--------HGVFNASIPKTNIPA---D----WEFIAMDQEEEIRVKNTDIG 163 (253)
T ss_pred ECCCCCCeeeeeeeecchhhhceee--------hhhhhccCCCCCCcc---c----eeeecCCchhhhceeecccc
Confidence 4599999999999999998887777 445788888776432 3 46788999999999999754
No 159
>PF10122 Mu-like_Com: Mu-like prophage protein Com; InterPro: IPR019294 Members of this entry belong to the Com family of proteins that act as translational regulators of mom [, ].
Probab=75.62 E-value=2 Score=27.86 Aligned_cols=32 Identities=9% Similarity=0.216 Sum_probs=21.7
Q ss_pred ec-CCCceeEEc-cC--CeEEeCCCCCEEeeeeCCC
Q 029155 165 ES-TAGGTMVPI-SW--TEMQCPLTGQTEQRKVAKV 196 (198)
Q Consensus 165 ~~-~~g~~m~~~-~~--~~~~c~~cg~~e~RKva~~ 196 (198)
+| .|+..|-.. +. -+++||.||....=+-+.|
T Consensus 6 RC~~CnklLa~~g~~~~leIKCpRC~tiN~~~a~~~ 41 (51)
T PF10122_consen 6 RCGHCNKLLAKAGEVIELEIKCPRCKTINHVRATSP 41 (51)
T ss_pred eccchhHHHhhhcCccEEEEECCCCCccceEeccCC
Confidence 56 677776552 22 3899999999876655554
No 160
>PRK11032 hypothetical protein; Provisional
Probab=75.52 E-value=2.2 Score=34.14 Aligned_cols=30 Identities=10% Similarity=0.106 Sum_probs=23.3
Q ss_pred ec-CCCceeEEc-cCCeEEeCCCCCEEeeeeC
Q 029155 165 ES-TAGGTMVPI-SWTEMQCPLTGQTEQRKVA 194 (198)
Q Consensus 165 ~~-~~g~~m~~~-~~~~~~c~~cg~~e~RKva 194 (198)
.| +||+.|.-. ....--||+||..+.+..+
T Consensus 126 vC~~Cg~~~~~~~p~~i~pCp~C~~~~F~R~~ 157 (160)
T PRK11032 126 VCEKCHHHLAFYTPEVLPLCPKCGHDQFQRRP 157 (160)
T ss_pred EecCCCCEEEecCCCcCCCCCCCCCCeeeeCC
Confidence 68 899998433 2457789999999988764
No 161
>TIGR00100 hypA hydrogenase nickel insertion protein HypA. In Hpylori, hypA mutant abolished hydrogenase activity and decrease in urease activity. Nickel supplementation in media restored urease activity and partial hydrogenase activity. HypA probably involved in inserting Ni in enzymes.
Probab=75.04 E-value=2.1 Score=32.16 Aligned_cols=29 Identities=17% Similarity=0.248 Sum_probs=21.0
Q ss_pred eEEec-CCCceeEEccCCeEEeCCCCCEEee
Q 029155 162 VSAES-TAGGTMVPISWTEMQCPLTGQTEQR 191 (198)
Q Consensus 162 v~a~~-~~g~~m~~~~~~~~~c~~cg~~e~R 191 (198)
+.++| .||..--+.. ..+.||.||....+
T Consensus 69 ~~~~C~~Cg~~~~~~~-~~~~CP~Cgs~~~~ 98 (115)
T TIGR00100 69 VECECEDCSEEVSPEI-DLYRCPKCHGIMLQ 98 (115)
T ss_pred cEEEcccCCCEEecCC-cCccCcCCcCCCcE
Confidence 36889 7997665434 46889999976544
No 162
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=74.84 E-value=2.1 Score=32.05 Aligned_cols=27 Identities=15% Similarity=0.156 Sum_probs=19.5
Q ss_pred eEEec-CCCceeEEccCCeEEeCCCCCEE
Q 029155 162 VSAES-TAGGTMVPISWTEMQCPLTGQTE 189 (198)
Q Consensus 162 v~a~~-~~g~~m~~~~~~~~~c~~cg~~e 189 (198)
..++| .||..--+.. ..+.||.||...
T Consensus 69 ~~~~C~~Cg~~~~~~~-~~~~CP~Cgs~~ 96 (113)
T PRK12380 69 AQAWCWDCSQVVEIHQ-HDAQCPHCHGER 96 (113)
T ss_pred cEEEcccCCCEEecCC-cCccCcCCCCCC
Confidence 37889 7997665433 467799999653
No 163
>COG0211 RpmA Ribosomal protein L27 [Translation, ribosomal structure and biogenesis]
Probab=74.54 E-value=6.7 Score=28.03 Aligned_cols=60 Identities=20% Similarity=0.275 Sum_probs=42.0
Q ss_pred eeccCCcEEecCCccCCC--CCeeeCCCEEEeCCceEEEEeEeeeEEEcCCCCCCCCCCCeEEEecC
Q 029155 3 VKEEEMVLVTPGEVLGKA--TEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGH 67 (198)
Q Consensus 3 ~~~~~~~iV~PGd~l~~~--~e~~~G~Gty~~~g~~~i~asv~G~v~~~~~~~~~~~~~~~i~V~p~ 67 (198)
+|..++++|.+|+.|-.- ..|-||.++=.-. ..+|||.+-|.|+... ...+++.++|.|.
T Consensus 23 vK~~~Gq~v~aG~IivRQRGTk~hpG~NVG~Gk-DhTlFAl~dG~Vkf~~----k~~~rk~vsV~~~ 84 (87)
T COG0211 23 VKKFGGQFVKAGSIIVRQRGTKFHPGVNVGRGK-DHTLFALVDGVVKFET----KGKNRKYVSVVPE 84 (87)
T ss_pred eeeeCCeEEecccEEEEeccccccCCcccccCC-CceEEEeeccEEEEEE----ccCCccEEEEEee
Confidence 466788999999988642 2467777764332 1459999999998753 1234568899875
No 164
>PF10080 DUF2318: Predicted membrane protein (DUF2318); InterPro: IPR018758 This domain of unknown function is found in hypothetical bacterial membrane proteins with no known function.
Probab=74.44 E-value=5.9 Score=29.34 Aligned_cols=36 Identities=11% Similarity=0.048 Sum_probs=28.5
Q ss_pred ecCCCeeeEEec-CCCceeEEccCCeEEeCCCCCEEe
Q 029155 155 AKNDLGVVSAES-TAGGTMVPISWTEMQCPLTGQTEQ 190 (198)
Q Consensus 155 ~~~~lGvv~a~~-~~g~~m~~~~~~~~~c~~cg~~e~ 190 (198)
....+++.+.-| -||..=+-...+.|.|.+||.+-.
T Consensus 27 ~dg~~~va~daCeiC~~~GY~q~g~~lvC~~C~~~~~ 63 (102)
T PF10080_consen 27 PDGSYRVAFDACEICGPKGYYQEGDQLVCKNCGVRFN 63 (102)
T ss_pred CCCCEEEEEEeccccCCCceEEECCEEEEecCCCEEe
Confidence 345678889999 787776667788999999998753
No 165
>PF07295 DUF1451: Protein of unknown function (DUF1451); InterPro: IPR009912 This family consists of several hypothetical bacterial proteins of around 160 residues in length. Members of this family contain four highly conserved cysteine resides toward the C-terminal region of the protein. The function of this family is unknown.
Probab=74.21 E-value=2.5 Score=33.28 Aligned_cols=30 Identities=20% Similarity=0.232 Sum_probs=22.9
Q ss_pred ec-CCCceeEEc-cCCeEEeCCCCCEEeeeeC
Q 029155 165 ES-TAGGTMVPI-SWTEMQCPLTGQTEQRKVA 194 (198)
Q Consensus 165 ~~-~~g~~m~~~-~~~~~~c~~cg~~e~RKva 194 (198)
.| +||+.+.-. .....-||+||..+.++.+
T Consensus 114 ~C~~Cg~~~~~~~~~~l~~Cp~C~~~~F~R~~ 145 (146)
T PF07295_consen 114 VCENCGHEVELTHPERLPPCPKCGHTEFTRQP 145 (146)
T ss_pred ecccCCCEEEecCCCcCCCCCCCCCCeeeeCC
Confidence 68 899998433 2357889999999987754
No 166
>TIGR01031 rpmF_bact ribosomal protein L32. This protein describes bacterial ribosomal protein L32. The noise cutoff is set low enough to include the equivalent protein from mitochondria and chloroplasts. No related proteins from the Archaea nor from the eukaryotic cytosol are detected by this model. This model is a fragment model; the putative L32 of some species shows similarity only toward the N-terminus.
Probab=73.87 E-value=2.6 Score=27.67 Aligned_cols=26 Identities=27% Similarity=0.480 Sum_probs=21.0
Q ss_pred Eec-CCCceeEEccCCeEEeCCCCCEEeeee
Q 029155 164 AES-TAGGTMVPISWTEMQCPLTGQTEQRKV 193 (198)
Q Consensus 164 a~~-~~g~~m~~~~~~~~~c~~cg~~e~RKv 193 (198)
+.| .||++..| +-.|+.||.--.|++
T Consensus 27 ~~C~~cG~~~~~----H~vc~~cG~Y~gr~v 53 (55)
T TIGR01031 27 VVCPNCGEFKLP----HRVCPSCGYYKGRQV 53 (55)
T ss_pred eECCCCCCcccC----eeECCccCeECCEEc
Confidence 558 79998864 789999998877765
No 167
>PF12172 DUF35_N: Rubredoxin-like zinc ribbon domain (DUF35_N); InterPro: IPR022002 This domain has no known function and is found in conserved hypothetical archaeal and bacterial proteins. The domain is duplicated in O53566 from SWISSPROT. The structure of a DUF35 representative reveals two long N-terminal helices followed by a rubredoxin-like zinc ribbon domain represented in this family and a C-terminal OB fold domain. Zinc is chelated by the four conserved cysteines in the alignment. ; PDB: 3IRB_A.
Probab=72.81 E-value=3.1 Score=24.59 Aligned_cols=27 Identities=22% Similarity=0.452 Sum_probs=14.9
Q ss_pred eeeEEec-CCCceeEEccCCeEEeCCCCCEE
Q 029155 160 GVVSAES-TAGGTMVPISWTEMQCPLTGQTE 189 (198)
Q Consensus 160 Gvv~a~~-~~g~~m~~~~~~~~~c~~cg~~e 189 (198)
-.+..+| .||....|-. ..||.||..+
T Consensus 8 ~l~~~rC~~Cg~~~~pPr---~~Cp~C~s~~ 35 (37)
T PF12172_consen 8 RLLGQRCRDCGRVQFPPR---PVCPHCGSDE 35 (37)
T ss_dssp -EEEEE-TTT--EEES-----SEETTTT---
T ss_pred EEEEEEcCCCCCEecCCC---cCCCCcCccc
Confidence 3456778 8999988744 7899999765
No 168
>COG0375 HybF Zn finger protein HypA/HybF (possibly regulating hydrogenase expression) [General function prediction only]
Probab=72.60 E-value=2.9 Score=31.69 Aligned_cols=32 Identities=16% Similarity=0.276 Sum_probs=25.1
Q ss_pred eEEec-CCCceeEEccCCeEEeCCCCCEEeeeeC
Q 029155 162 VSAES-TAGGTMVPISWTEMQCPLTGQTEQRKVA 194 (198)
Q Consensus 162 v~a~~-~~g~~m~~~~~~~~~c~~cg~~e~RKva 194 (198)
..+.| .|+++..+..|. ++||.||....|=++
T Consensus 69 ~~~~C~~C~~~~~~e~~~-~~CP~C~s~~~~i~~ 101 (115)
T COG0375 69 AECWCLDCGQEVELEELD-YRCPKCGSINLRIIG 101 (115)
T ss_pred cEEEeccCCCeecchhhe-eECCCCCCCceEEec
Confidence 36788 899999988885 669999987766443
No 169
>PRK06386 replication factor A; Reviewed
Probab=72.58 E-value=31 Score=31.18 Aligned_cols=40 Identities=8% Similarity=0.068 Sum_probs=27.6
Q ss_pred CEEEEEEEEeCCCccEEEEEecCCCeeeEEec-CCCceeEEccCCeEEeCCCCCEEee
Q 029155 135 DIVRASVLSLGDARAYFLSTAKNDLGVVSAES-TAGGTMVPISWTEMQCPLTGQTEQR 191 (198)
Q Consensus 135 DiV~AkV~s~~~~~~~~LSt~~~~lGvv~a~~-~~g~~m~~~~~~~~~c~~cg~~e~R 191 (198)
-.|.+.|+++..+. -++.+| .|+..|.. | +||+||..+..
T Consensus 220 v~i~G~iv~i~~gs------------gli~rCP~C~R~l~~--g---~C~~HG~v~~~ 260 (358)
T PRK06386 220 ITIMGFIVSVGQGS------------RIFTKCSVCNKIIED--G---VCKDHPDAPVY 260 (358)
T ss_pred EEEEEEEEEEcCCc------------EeEecCcCCCeEccC--C---cCCCCCCCCCe
Confidence 35556666654321 357899 99999973 4 89999987643
No 170
>PF15616 TerY-C: TerY-C metal binding domain
Probab=72.18 E-value=4.9 Score=31.15 Aligned_cols=27 Identities=22% Similarity=0.262 Sum_probs=21.6
Q ss_pred EEecCCCceeEEccCCeEEeCCCCCEE
Q 029155 163 SAESTAGGTMVPISWTEMQCPLTGQTE 189 (198)
Q Consensus 163 ~a~~~~g~~m~~~~~~~~~c~~cg~~e 189 (198)
+|.|.||+.|=--+-.+..||-||+.-
T Consensus 89 fa~C~CGkl~Ci~g~~~~~CPwCg~~g 115 (131)
T PF15616_consen 89 FAVCGCGKLFCIDGEGEVTCPWCGNEG 115 (131)
T ss_pred EEEecCCCEEEeCCCCCEECCCCCCee
Confidence 677899999964455689999999863
No 171
>PF08274 PhnA_Zn_Ribbon: PhnA Zinc-Ribbon ; InterPro: IPR013987 The PhnA protein family includes the uncharacterised Escherichia coli protein PhnA and its homologues. The E. coli phnA gene is part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage []. The protein is not related to the characterised phosphonoacetate hydrolase designated PhnA []. This entry represents the N-terminal domain of PhnA, which is predicted to form a zinc-ribbon.; PDB: 2AKL_A.
Probab=72.15 E-value=2.5 Score=24.34 Aligned_cols=24 Identities=17% Similarity=0.282 Sum_probs=12.6
Q ss_pred Eec-CCCceeEEccCCeEEeCCCCC
Q 029155 164 AES-TAGGTMVPISWTEMQCPLTGQ 187 (198)
Q Consensus 164 a~~-~~g~~m~~~~~~~~~c~~cg~ 187 (198)
..| .|+..-.-.+...|.||.|+.
T Consensus 3 p~Cp~C~se~~y~D~~~~vCp~C~~ 27 (30)
T PF08274_consen 3 PKCPLCGSEYTYEDGELLVCPECGH 27 (30)
T ss_dssp ---TTT-----EE-SSSEEETTTTE
T ss_pred CCCCCCCCcceeccCCEEeCCcccc
Confidence 356 677776556778999999985
No 172
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=71.67 E-value=3.1 Score=32.18 Aligned_cols=30 Identities=13% Similarity=0.276 Sum_probs=20.5
Q ss_pred eEEec-CCCceeEEcc--------------------CCeEEeCCCCCEEee
Q 029155 162 VSAES-TAGGTMVPIS--------------------WTEMQCPLTGQTEQR 191 (198)
Q Consensus 162 v~a~~-~~g~~m~~~~--------------------~~~~~c~~cg~~e~R 191 (198)
..++| .||..--... ...+.||.||....+
T Consensus 69 ~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~CP~Cgs~~~~ 119 (135)
T PRK03824 69 AVLKCRNCGNEWSLKEVKESLDEEIREAIHFIPEVVHAFLKCPKCGSRDFE 119 (135)
T ss_pred eEEECCCCCCEEecccccccccccccccccccccccccCcCCcCCCCCCcE
Confidence 57889 8997754321 345789999976543
No 173
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=70.92 E-value=3.1 Score=27.54 Aligned_cols=27 Identities=30% Similarity=0.556 Sum_probs=22.2
Q ss_pred Eec-CCCceeEEccCCeEEeCCCCCEEeeeeC
Q 029155 164 AES-TAGGTMVPISWTEMQCPLTGQTEQRKVA 194 (198)
Q Consensus 164 a~~-~~g~~m~~~~~~~~~c~~cg~~e~RKva 194 (198)
..| .||+...| +-.|+.||.--.|++-
T Consensus 28 ~~C~~CG~~~~~----H~vC~~CG~Y~gr~v~ 55 (57)
T PRK12286 28 VECPNCGEPKLP----HRVCPSCGYYKGREVV 55 (57)
T ss_pred eECCCCCCccCC----eEECCCCCcCCCEEee
Confidence 568 89999875 7899999998888764
No 174
>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=68.68 E-value=39 Score=25.10 Aligned_cols=53 Identities=23% Similarity=0.351 Sum_probs=42.4
Q ss_pred CCCCEEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEe
Q 029155 75 EPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSL 144 (198)
Q Consensus 75 ~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~ 144 (198)
-.|-+|+|+|..+-++-..+|. .-.|.++.+.... + .+.|..|+-|+.++...
T Consensus 22 ~~gk~V~G~I~hvv~ddLYIDf--------G~KFhcVc~rp~~-----~----~~~y~~G~rV~lrLkdl 74 (104)
T PF10246_consen 22 PEGKIVIGKIFHVVDDDLYIDF--------GGKFHCVCKRPAV-----N----GEKYVRGSRVRLRLKDL 74 (104)
T ss_pred ccCCEEEEEEEEEecCceEEEe--------CCceeEEEecccc-----c----ccccccCCEEEEEECCH
Confidence 4688999999999999888999 6778898875442 1 25588899999999864
No 175
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=68.54 E-value=2 Score=23.59 Aligned_cols=21 Identities=19% Similarity=0.270 Sum_probs=13.9
Q ss_pred ec-CCCceeEEccCCeEEeCCCCCE
Q 029155 165 ES-TAGGTMVPISWTEMQCPLTGQT 188 (198)
Q Consensus 165 ~~-~~g~~m~~~~~~~~~c~~cg~~ 188 (198)
.| .||..+. -+.-.||+||..
T Consensus 4 ~Cp~Cg~~~~---~~~~fC~~CG~~ 25 (26)
T PF13248_consen 4 FCPNCGAEID---PDAKFCPNCGAK 25 (26)
T ss_pred CCcccCCcCC---cccccChhhCCC
Confidence 46 7888543 245788888863
No 176
>PF03966 Trm112p: Trm112p-like protein; InterPro: IPR005651 This family of short proteins have no known function. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The function of this family is uncertain. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The entry contains 2 families: Trm112, which is required for tRNA methylation in Saccharomyces cerevisiae (Baker's yeast) and is found in complexes with 2 tRNA methylases (TRM9 and TRM11) also with putative methyltransferase YDR140W []. The zinc-finger protein Ynr046w is plurifunctional and a component of the eRF1 methyltransferase in yeast []. The crystal structure of Ynr046w has been determined to 1.7 A resolution. It comprises a zinc-binding domain built from both the N- and C-terminal sequences and an inserted domain, absent from bacterial and archaeal orthologs of the protein, composed of three alpha-helices []. UPF0434, which are proteins that are functionally uncharacterised. ; PDB: 3Q87_A 2KPI_A 2K5R_A 2HF1_A 2JS4_A 2J6A_A 2JR6_A 2PK7_A 2JNY_A.
Probab=68.38 E-value=7.3 Score=26.26 Aligned_cols=17 Identities=29% Similarity=0.442 Sum_probs=13.1
Q ss_pred EccCCeEEeCCCCCEEe
Q 029155 174 PISWTEMQCPLTGQTEQ 190 (198)
Q Consensus 174 ~~~~~~~~c~~cg~~e~ 190 (198)
-+-...|.||+||+..+
T Consensus 48 ~i~eg~L~Cp~c~r~YP 64 (68)
T PF03966_consen 48 EIVEGELICPECGREYP 64 (68)
T ss_dssp ETTTTEEEETTTTEEEE
T ss_pred cccCCEEEcCCCCCEEe
Confidence 44557999999998754
No 177
>KOG3507 consensus DNA-directed RNA polymerase, subunit RPB7.0 [Transcription]
Probab=68.12 E-value=3.7 Score=27.44 Aligned_cols=28 Identities=11% Similarity=0.054 Sum_probs=22.2
Q ss_pred eeEEec-CCCceeEEccCCeEEeCCCCCE
Q 029155 161 VVSAES-TAGGTMVPISWTEMQCPLTGQT 188 (198)
Q Consensus 161 vv~a~~-~~g~~m~~~~~~~~~c~~cg~~ 188 (198)
-+.-.| .||....-.+.+.++|.+||.+
T Consensus 18 ~miYiCgdC~~en~lk~~D~irCReCG~R 46 (62)
T KOG3507|consen 18 TMIYICGDCGQENTLKRGDVIRCRECGYR 46 (62)
T ss_pred cEEEEeccccccccccCCCcEehhhcchH
Confidence 345678 8998876667789999999974
No 178
>PF01783 Ribosomal_L32p: Ribosomal L32p protein family; InterPro: IPR002677 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 [, ]. Ribosomal protein L32p is part of the 50S ribosomal subunit. This family is found in both prokaryotes and eukaryotes. Ribosomal protein L32 of yeast binds to and regulates the splicing and the translation of the transcript of its own gene [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0015934 large ribosomal subunit; PDB: 3PYT_2 3F1F_5 3PYV_2 3D5B_5 3MRZ_2 3D5D_5 3F1H_5 1VSP_Y 3PYR_2 3MS1_2 ....
Probab=66.37 E-value=1.7 Score=28.52 Aligned_cols=27 Identities=26% Similarity=0.519 Sum_probs=20.3
Q ss_pred Eec-CCCceeEEccCCeEEeCCCCCEEeeeeC
Q 029155 164 AES-TAGGTMVPISWTEMQCPLTGQTEQRKVA 194 (198)
Q Consensus 164 a~~-~~g~~m~~~~~~~~~c~~cg~~e~RKva 194 (198)
+.| .||++..| +..|+.||....|.+-
T Consensus 27 ~~c~~cg~~~~~----H~vc~~cG~y~~r~v~ 54 (56)
T PF01783_consen 27 VKCPNCGEPKLP----HRVCPSCGYYKGRQVI 54 (56)
T ss_dssp EESSSSSSEEST----TSBCTTTBBSSSSSSS
T ss_pred eeeccCCCEecc----cEeeCCCCeECCEEEe
Confidence 567 79987754 5799999987777653
No 179
>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=65.57 E-value=7.3 Score=27.89 Aligned_cols=29 Identities=34% Similarity=0.550 Sum_probs=21.5
Q ss_pred CCCCCCCCEEEEEEEEEecceEEEEEeeec
Q 029155 71 GPVPEPGSVVIARVTKVMTRMASADIMCVG 100 (198)
Q Consensus 71 ~~~p~vGDiViG~V~~v~~~~~~V~I~~v~ 100 (198)
+...++||+|+++|..+...+ ..++.|++
T Consensus 47 rp~L~~GDlV~ArV~~~~~~~-~~eLtc~~ 75 (86)
T cd05790 47 RPNLNVGDLVYARVVKANRDM-EPELSCVD 75 (86)
T ss_pred cccCCCCCEEEEEEEecCCCC-CeEEEEeC
Confidence 456799999999999997753 35555544
No 180
>PRK12366 replication factor A; Reviewed
Probab=65.53 E-value=9.2 Score=37.00 Aligned_cols=29 Identities=14% Similarity=0.148 Sum_probs=22.9
Q ss_pred eEEec-CCCceeEEccCCeEEeCCCCCEEee
Q 029155 162 VSAES-TAGGTMVPISWTEMQCPLTGQTEQR 191 (198)
Q Consensus 162 v~a~~-~~g~~m~~~~~~~~~c~~cg~~e~R 191 (198)
++..| .|.+.|.. ......|++||+.+++
T Consensus 531 ~y~aCp~CnkKv~~-~~g~~~C~~c~~~~p~ 560 (637)
T PRK12366 531 ILYLCPNCRKRVEE-VDGEYICEFCGEVEPN 560 (637)
T ss_pred EEecccccCeEeEc-CCCcEECCCCCCCCCc
Confidence 57889 89999975 3357899999997544
No 181
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=65.48 E-value=4.1 Score=34.74 Aligned_cols=21 Identities=29% Similarity=0.520 Sum_probs=16.9
Q ss_pred CCCceeEEccCCeEEeCCCCCEEee
Q 029155 167 TAGGTMVPISWTEMQCPLTGQTEQR 191 (198)
Q Consensus 167 ~~g~~m~~~~~~~~~c~~cg~~e~R 191 (198)
.||. .+...+.||.||....|
T Consensus 314 ~cg~----~~~r~~~C~~cg~~~~r 334 (364)
T COG0675 314 CCGH----LSGRLFKCPRCGFVHDR 334 (364)
T ss_pred ccCC----ccceeEECCCCCCeehh
Confidence 5888 45678999999998766
No 182
>COG1107 Archaea-specific RecJ-like exonuclease, contains DnaJ-type Zn finger domain [DNA replication, recombination, and repair]
Probab=64.39 E-value=19 Score=34.74 Aligned_cols=68 Identities=15% Similarity=0.175 Sum_probs=54.9
Q ss_pred CCCCCCCCEEEEEEEEEecceEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeCCC-cc
Q 029155 71 GPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGDA-RA 149 (198)
Q Consensus 71 ~~~p~vGDiViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~~-~~ 149 (198)
..-.+.|.+=-|.|+++....+++++ ++-..|+||.++... ...|.+||.|..+|..+.+. +.
T Consensus 117 ~~Dve~g~~Y~g~v~~v~~~GvFv~L--------n~~v~GL~~~~d~~~--------~~~~~vgdeiiV~v~~vr~~~ge 180 (715)
T COG1107 117 MEDVEAGKYYKGIVSRVEKYGVFVEL--------NSHVRGLIHRRDLGG--------DPDYAVGDEIIVQVSDVRPEKGE 180 (715)
T ss_pred hhhcccceeeeccccchhhhcceeec--------ChhhhccccccccCC--------CCCCCCCCeEEEEeeccCCCCCc
Confidence 45568899999999999999999999 788999999888653 25588999999999998754 44
Q ss_pred EEEEE
Q 029155 150 YFLST 154 (198)
Q Consensus 150 ~~LSt 154 (198)
+.+..
T Consensus 181 idf~~ 185 (715)
T COG1107 181 IDFEP 185 (715)
T ss_pred cceee
Confidence 44433
No 183
>PF08271 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013137 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIB (TFIIB). In eukaryotes the initiation of transcription of protein encoding genes by the polymerase II complexe (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least seven different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, and -IIH []. TFIIB and TFIID are responsible for promoter recognition and interaction with pol II; together with Pol II, they form a minimal initiation complex capable of transcription under certain conditions. The TATA box of a Pol II promoter is bound in the initiation complex by the TBP subunit of TFIID, which bends the DNA around the C-terminal domain of TFIIB whereas the N-terminal zinc finger of TFIIB interacts with Pol II [, ]. The TFIIB zinc finger adopts a zinc ribbon fold characterised by two beta-hairpins forming two structurally similar zinc-binding sub-sites []. The zinc finger contacts the rbp1 subunit of Pol II through its dock domain, a conserved region of about 70 amino acids located close to the polymerase active site []. In the Pol II complex this surface is located near the RNA exit groove. Interestingly this sequence is best conserved in the three polymerases that utilise a TFIIB-like general transcription factor (Pol II, Pol III, and archaeal RNA polymerase) but not in Pol I []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1VD4_A 1PFT_A 3K1F_M 3K7A_M 1RO4_A 1RLY_A 1DL6_A.
Probab=64.34 E-value=6.5 Score=24.04 Aligned_cols=26 Identities=19% Similarity=0.375 Sum_probs=16.1
Q ss_pred ec-CCCceeE--EccCCeEEeCCCCCEEe
Q 029155 165 ES-TAGGTMV--PISWTEMQCPLTGQTEQ 190 (198)
Q Consensus 165 ~~-~~g~~m~--~~~~~~~~c~~cg~~e~ 190 (198)
.| .||...+ --...++.|++||.+-.
T Consensus 2 ~Cp~Cg~~~~~~D~~~g~~vC~~CG~Vl~ 30 (43)
T PF08271_consen 2 KCPNCGSKEIVFDPERGELVCPNCGLVLE 30 (43)
T ss_dssp SBTTTSSSEEEEETTTTEEEETTT-BBEE
T ss_pred CCcCCcCCceEEcCCCCeEECCCCCCEee
Confidence 36 6777542 22345899999997644
No 184
>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=64.26 E-value=30 Score=22.86 Aligned_cols=19 Identities=21% Similarity=-0.017 Sum_probs=16.1
Q ss_pred CCCCCCCEEEEEEEEEecc
Q 029155 72 PVPEPGSVVIARVTKVMTR 90 (198)
Q Consensus 72 ~~p~vGDiViG~V~~v~~~ 90 (198)
...++||.|.++|.++...
T Consensus 46 ~~~~~Gd~v~~~V~~~d~~ 64 (73)
T cd05706 46 YKFKKNDIVRACVLSVDVP 64 (73)
T ss_pred cccCCCCEEEEEEEEEeCC
Confidence 3468999999999999864
No 185
>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=64.20 E-value=16 Score=24.97 Aligned_cols=34 Identities=21% Similarity=0.231 Sum_probs=25.8
Q ss_pred CCCCEEEEEEEEeCCCccEEEEEecCCCeeeEEec
Q 029155 132 RPGDIVRASVLSLGDARAYFLSTAKNDLGVVSAES 166 (198)
Q Consensus 132 ~~GDiV~AkV~s~~~~~~~~LSt~~~~lGvv~a~~ 166 (198)
++||+|.++|+++.+ ..+.+.+.+.-.|.+...-
T Consensus 5 ~~GdiV~G~V~~v~~-~~~~V~i~~~~~g~l~~~~ 38 (82)
T cd04454 5 DVGDIVIGIVTEVNS-RFWKVDILSRGTARLEDSS 38 (82)
T ss_pred CCCCEEEEEEEEEcC-CEEEEEeCCCceEEeechh
Confidence 699999999999975 4677888766666665543
No 186
>TIGR00686 phnA alkylphosphonate utilization operon protein PhnA. The protein family includes an uncharacterized member designated phnA in Escherichia coli, part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage. This protein is not related to the characterized phosphonoacetate hydrolase designated PhnA by Kulakova, et al. (2001, 1997).
Probab=63.78 E-value=5.3 Score=29.91 Aligned_cols=24 Identities=13% Similarity=0.104 Sum_probs=18.7
Q ss_pred ec-CCCceeEEccCCeEEeCCCCCE
Q 029155 165 ES-TAGGTMVPISWTEMQCPLTGQT 188 (198)
Q Consensus 165 ~~-~~g~~m~~~~~~~~~c~~cg~~ 188 (198)
.| +|+..-.-..+..+.||+|+..
T Consensus 4 ~CP~C~seytY~dg~~~iCpeC~~E 28 (109)
T TIGR00686 4 PCPKCNSEYTYHDGTQLICPSCLYE 28 (109)
T ss_pred cCCcCCCcceEecCCeeECcccccc
Confidence 57 7877765566789999999964
No 187
>TIGR00767 rho transcription termination factor Rho. Members of this family differ in the specificity of RNA binding.
Probab=63.25 E-value=7.2 Score=35.85 Aligned_cols=129 Identities=16% Similarity=0.186 Sum_probs=74.2
Q ss_pred eeeCCCEEEe--CCceEEEEeEeeeEEEcCCCCCCCCCCCeEEEecCCCCCCCCCCCCEEEEEEEEEecc---eEEEEEe
Q 029155 23 VKAGKGAYVA--KHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHKAHGPVPEPGSVVIARVTKVMTR---MASADIM 97 (198)
Q Consensus 23 ~~~G~Gty~~--~g~~~i~asv~G~v~~~~~~~~~~~~~~~i~V~p~~~~~~~p~vGDiViG~V~~v~~~---~~~V~I~ 97 (198)
...+.|+.+- +|+|-+++.-.+.... ..-|+|.|..-+++-++.||.|.|.|...... +..+++.
T Consensus 48 ~~~~~g~le~~~~g~gflr~~~~~~~~~----------~~d~yvs~~~i~~~~lr~gd~v~g~~R~~~~~ER~~~Ll~v~ 117 (415)
T TIGR00767 48 LIFGEGVLEILPDGFGFLRSPDSSYLPG----------PDDIYVSPSQIRRFNLRTGDTIEGQIRSPKEGERYFALLKVE 117 (415)
T ss_pred ceEEEEEEEEcCCCCeEEeCCCcCCCCC----------CCCeeeCHHHHHhcCCCCCCEEEEEEeccccHhHHHHHhCCC
Confidence 4566676553 3454455544444322 13578887655678899999999999876443 3445555
Q ss_pred eeccccccCcceeEEeccccccccccccccccCCC-CCCEEEEEEEEeCCCccEEEEEecCCCeeeEEecCCCce
Q 029155 98 CVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFR-PGDIVRASVLSLGDARAYFLSTAKNDLGVVSAESTAGGT 171 (198)
Q Consensus 98 ~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~-~GDiV~AkV~s~~~~~~~~LSt~~~~lGvv~a~~~~g~~ 171 (198)
.+++.+. ....+-++.+++...+.++. ..+. -.+-+-.|++. +.+.+..-+.+.|.+...+|+-
T Consensus 118 ~vn~~~~-e~~~~ri~Fe~LTf~YP~er---~~Le~~~~~~~~R~id------~~~pig~Gq~~~IvG~~g~GKT 182 (415)
T TIGR00767 118 SVNGDDP-EKAKNRVLFENLTPLYPNER---LRLETSTEDLSTRVLD------LFAPIGKGQRGLIVAPPKAGKT 182 (415)
T ss_pred ccCCCCc-cccCCCeEEEEeeecCCCcc---ceeecCccccceeeee------eEEEeCCCCEEEEECCCCCChh
Confidence 5544432 23456777777776665421 1111 12445556654 4455555566666666666654
No 188
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=63.05 E-value=6.2 Score=33.71 Aligned_cols=30 Identities=20% Similarity=0.206 Sum_probs=22.6
Q ss_pred EEec-CCCceeEEc-cCCeEEeCCCCCEEeee
Q 029155 163 SAES-TAGGTMVPI-SWTEMQCPLTGQTEQRK 192 (198)
Q Consensus 163 ~a~~-~~g~~m~~~-~~~~~~c~~cg~~e~RK 192 (198)
.-.| .||.+|... +...+.|+.||...--.
T Consensus 99 ~~fC~~CG~~~~~~~~~~~~~C~~c~~~~yp~ 130 (256)
T PRK00241 99 HRFCGYCGHPMHPSKTEWAMLCPHCRERYYPR 130 (256)
T ss_pred CccccccCCCCeecCCceeEECCCCCCEECCC
Confidence 3478 899999765 34579999999877543
No 189
>PF04085 MreC: rod shape-determining protein MreC; InterPro: IPR007221 MreC (murein formation C) is involved in the rod shape determination in Escherichia coli, and more generally in cell shape determination of bacteria whether or not they are rod-shaped.; GO: 0008360 regulation of cell shape; PDB: 2J5U_B 2QF4_B 2QF5_A.
Probab=61.79 E-value=28 Score=27.12 Aligned_cols=60 Identities=20% Similarity=0.298 Sum_probs=32.9
Q ss_pred EEEEEEEEecceEEEEEeeecccc-----ccCcceeEEecccccc--ccccccccccCCCCCCEEEE
Q 029155 80 VIARVTKVMTRMASADIMCVGAKS-----VREKFSGIIRQQDVRA--TEIDKVDMHLSFRPGDIVRA 139 (198)
Q Consensus 80 ViG~V~~v~~~~~~V~I~~v~~~~-----l~~~~~G~l~~s~v~~--~~~d~~~~~~~~~~GDiV~A 139 (198)
++|+|+++.++.+.|..+.-.+.. ......|+++-..-.. -..........+++||.|.-
T Consensus 36 lVG~V~~V~~~~S~V~li~d~~~~v~v~i~~~~~~Gi~~G~~~~~~~~~l~~i~~~~~i~~GD~V~T 102 (152)
T PF04085_consen 36 LVGRVTEVGPNTSRVLLITDPNSRVSVKIERSGDRGILRGDGSNTGLLKLEYIPKDADIKKGDIVVT 102 (152)
T ss_dssp EEEEEEEE-SS-EEEEETTSSBCEEEEEEECTTEEEEEEEEETTTTEEEEEEECTTS---TT-EEEE
T ss_pred cEEEEEEECCCEEEEEEEeCCCceEEEEEecCCeeEEEEeCCCCCceEEEEECCCCCCCCCCCEEEE
Confidence 589999999999998886543321 2334568876554332 22233344567788998763
No 190
>KOG3297 consensus DNA-directed RNA polymerase subunit E' [Transcription]
Probab=61.76 E-value=66 Score=26.53 Aligned_cols=69 Identities=14% Similarity=0.153 Sum_probs=42.3
Q ss_pred CCCCCEEEEEEEEEecceEEEEEeeecccc-----ccC--cc--eeEEeccccccccccccccccCCCCCCEEEEEEEEe
Q 029155 74 PEPGSVVIARVTKVMTRMASADIMCVGAKS-----VRE--KF--SGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSL 144 (198)
Q Consensus 74 p~vGDiViG~V~~v~~~~~~V~I~~v~~~~-----l~~--~~--~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~ 144 (198)
|-+|.++.|+|..-...+..|.|...++-- |.. .| ....=+=+....+-. .-.-+|++|..|+=||.+.
T Consensus 79 PF~gEVi~gki~~cs~eG~rvtl~FFdDI~IP~~~L~~p~~f~~~e~vWVWey~~Edg~--~~~Ly~D~~e~IRFRV~~e 156 (202)
T KOG3297|consen 79 PFVGEVITGKIKECSEEGLRVTLGFFDDIFIPKEMLPEPCVFEPDEQVWVWEYEQEDGP--GTKLYFDVGEEIRFRVEDE 156 (202)
T ss_pred cccceEEEEEeecCCccceEEEEEeeeceeechhhCCCCcccccccEEEEEEecccCCC--CceeEecCCCeEEEEEeee
Confidence 678999999999999999999997665521 111 11 111111011100000 1234689999999999985
No 191
>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=61.71 E-value=21 Score=23.65 Aligned_cols=20 Identities=25% Similarity=0.220 Sum_probs=17.6
Q ss_pred EEEEEEEEecceEEEEEeee
Q 029155 80 VIARVTKVMTRMASADIMCV 99 (198)
Q Consensus 80 ViG~V~~v~~~~~~V~I~~v 99 (198)
..|+|..+..+.+.|+|...
T Consensus 16 ~~G~V~kv~eNSVIVdIT~m 35 (57)
T PF09953_consen 16 FTGIVEKVYENSVIVDITIM 35 (57)
T ss_pred cEEEEEEEecCcEEEEEEec
Confidence 58999999999999999543
No 192
>cd04476 RPA1_DBD_C RPA1_DBD_C: A subfamily of OB folds corresponding to the C-terminal OB fold, the ssDNA-binding domain (DBD)-C, of human RPA1 (also called RPA70). RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-C, RPA1 contains three other OB folds: DBD-A, DBD-B, and RPA1N. The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B. RPA1 DBD-C is involved in DNA binding and trimerization. It contains two structural insertions not found to date in other OB-folds: a zinc ribbon and a three-helix bundle. RPA1 DBD-C also contains a Cys4-type zinc-binding motif, which plays a role in the ssDNA binding fun
Probab=59.92 E-value=21 Score=27.98 Aligned_cols=41 Identities=10% Similarity=0.126 Sum_probs=30.1
Q ss_pred EEEEEEEEeCCCccEEEEEecCCCeeeEEec-CCCceeEEccCCeEEeCCCCCE
Q 029155 136 IVRASVLSLGDARAYFLSTAKNDLGVVSAES-TAGGTMVPISWTEMQCPLTGQT 188 (198)
Q Consensus 136 iV~AkV~s~~~~~~~~LSt~~~~lGvv~a~~-~~g~~m~~~~~~~~~c~~cg~~ 188 (198)
.|+|.|..+... +-.+.-| .|.+.|.+..-....|++|+..
T Consensus 19 ~v~a~I~~I~~~------------~~~Y~aC~~C~kkv~~~~~~~~~C~~C~~~ 60 (166)
T cd04476 19 TVKATIVFIKPD------------NWWYPACPGCNKKVVEEGNGTYRCEKCNKS 60 (166)
T ss_pred EEEEEEEEEcCC------------CeEEccccccCcccEeCCCCcEECCCCCCc
Confidence 466777776532 4457778 8999998765357999999986
No 193
>PF14319 Zn_Tnp_IS91: Transposase zinc-binding domain
Probab=59.64 E-value=5 Score=29.99 Aligned_cols=38 Identities=18% Similarity=0.278 Sum_probs=30.7
Q ss_pred ecCCCeeeEEec-CCCce-eEEccCCeEEeCCCCCEEeee
Q 029155 155 AKNDLGVVSAES-TAGGT-MVPISWTEMQCPLTGQTEQRK 192 (198)
Q Consensus 155 ~~~~lGvv~a~~-~~g~~-m~~~~~~~~~c~~cg~~e~RK 192 (198)
+...+|.....| .||.. .++.|...=.||.||....++
T Consensus 34 rt~~~G~~~~~C~~Cg~~~~~~~SCk~R~CP~C~~~~~~~ 73 (111)
T PF14319_consen 34 RTEALGFHRYRCEDCGHEKIVYNSCKNRHCPSCQAKATEQ 73 (111)
T ss_pred CCccCCcceeecCCCCceEEecCcccCcCCCCCCChHHHH
Confidence 457789999999 89987 477787777999999886543
No 194
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=59.59 E-value=14 Score=29.85 Aligned_cols=24 Identities=17% Similarity=0.095 Sum_probs=19.7
Q ss_pred CCCCCCCEEEEEEEEEecceEEEEE
Q 029155 72 PVPEPGSVVIARVTKVMTRMASADI 96 (198)
Q Consensus 72 ~~p~vGDiViG~V~~v~~~~~~V~I 96 (198)
...++||+|.++|.++. ..+.+.+
T Consensus 117 ~~~~~GD~V~akV~~i~-~~i~LS~ 140 (189)
T PRK09521 117 DAFKIGDIVRAKVISYT-DPLQLST 140 (189)
T ss_pred hccCCCCEEEEEEEecC-CcEEEEE
Confidence 34699999999999999 6666666
No 195
>PF08646 Rep_fac-A_C: Replication factor-A C terminal domain; InterPro: IPR013955 Replication factor A (RP-A) binds and subsequently stabilises single-stranded DNA intermediates and thus prevents complementary DNA from reannealing. It also plays an essential role in several cellular processes in DNA metabolism including replication, recombination and repair of DNA []. Replication factor-A protein is also known as Replication protein A 70 kDa DNA-binding subunit. This entry is found at the C terminus of Replication factor A.; PDB: 1L1O_F 3U50_C.
Probab=58.73 E-value=25 Score=26.92 Aligned_cols=40 Identities=13% Similarity=0.176 Sum_probs=26.6
Q ss_pred EEEEEEEeCCCccEEEEEecCCCeeeEEecC---CCceeEEccCCeEEeCCCCCE
Q 029155 137 VRASVLSLGDARAYFLSTAKNDLGVVSAEST---AGGTMVPISWTEMQCPLTGQT 188 (198)
Q Consensus 137 V~AkV~s~~~~~~~~LSt~~~~lGvv~a~~~---~g~~m~~~~~~~~~c~~cg~~ 188 (198)
++|.|..+... +-.+.-|. |+..+.+.+.+.+.|++|++.
T Consensus 4 v~a~I~~I~~~------------~~~Y~aC~~~~C~kKv~~~~~~~y~C~~C~~~ 46 (146)
T PF08646_consen 4 VRATIVEIKSD------------NWYYPACPNEKCNKKVTENGDGSYRCEKCNKT 46 (146)
T ss_dssp EEEEEEEEETT------------TTEEEE-TSTTTS-B-EEETTTEEEETTTTEE
T ss_pred EEEEEEEEECC------------CcEECCCCCccCCCEeecCCCcEEECCCCCCc
Confidence 56777776432 23466674 999898886568999999976
No 196
>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=58.65 E-value=25 Score=25.08 Aligned_cols=22 Identities=27% Similarity=0.277 Sum_probs=18.1
Q ss_pred CCCCEEEEEEEEeCCCccEEEEE
Q 029155 132 RPGDIVRASVLSLGDARAYFLST 154 (198)
Q Consensus 132 ~~GDiV~AkV~s~~~~~~~~LSt 154 (198)
++||+|.|+|.++.. ....+.+
T Consensus 5 ~~GDiVig~V~~v~~-~~~~v~I 26 (92)
T cd05791 5 KVGSIVIARVTRINP-RFAKVDI 26 (92)
T ss_pred CCCCEEEEEEEEEcC-CEEEEEE
Confidence 799999999999974 4566666
No 197
>KOG1999 consensus RNA polymerase II transcription elongation factor DSIF/SUPT5H/SPT5 [Transcription]
Probab=58.15 E-value=94 Score=31.72 Aligned_cols=113 Identities=19% Similarity=0.212 Sum_probs=66.7
Q ss_pred CCCCCCCEEEEEEEEEecceEEEEEeeecccc--cc---CcceeEEeccccccccccccccccCCCCCCEEEE-------
Q 029155 72 PVPEPGSVVIARVTKVMTRMASADIMCVGAKS--VR---EKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRA------- 139 (198)
Q Consensus 72 ~~p~vGDiViG~V~~v~~~~~~V~I~~v~~~~--l~---~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~A------- 139 (198)
...++||.|+-.+-+..+-+..| ..+.+.. .. ..+.+-| ......|+.+|++||.|+.
T Consensus 406 ~~F~~GD~VeV~~Gel~glkG~v--e~vdg~~vti~~~~e~l~~pl--------~~~~~eLrKyF~~GDhVKVi~G~~eG 475 (1024)
T KOG1999|consen 406 HLFSPGDAVEVIVGELKGLKGKV--ESVDGTIVTIMSKHEDLKGPL--------EVPASELRKYFEPGDHVKVIAGRYEG 475 (1024)
T ss_pred cccCCCCeEEEeeeeeccceeEE--EeccCceEEEeeccccCCCcc--------ccchHhhhhhccCCCeEEEEeccccC
Confidence 34689999987766665533222 2222210 00 1122211 1112267899999998764
Q ss_pred ---EEEEeCCCccEEEEEecCCCeeeEEec-C-C--------------CceeEEccCCeEEeCCCCCEEeeeeC
Q 029155 140 ---SVLSLGDARAYFLSTAKNDLGVVSAES-T-A--------------GGTMVPISWTEMQCPLTGQTEQRKVA 194 (198)
Q Consensus 140 ---kV~s~~~~~~~~LSt~~~~lGvv~a~~-~-~--------------g~~m~~~~~~~~~c~~cg~~e~RKva 194 (198)
-|+.+..+.-+.||.-..+-..|++.- . | -+.|+..+.+..-|..|.-.|.+++-
T Consensus 476 ~tGlVvrVe~~~vi~~Sd~t~eel~Vf~~dlq~c~ev~~gv~~~ge~e~hdlVqLd~~~vgvI~rle~e~~~vl 549 (1024)
T KOG1999|consen 476 DTGLVVRVEQGDVILLSDLTMEELKVFARDLQLCSEVTLGVEKSGEYELHDLVQLDNQNVGVIVRLERETFQVL 549 (1024)
T ss_pred CcceEEEEeCCeEEEEecCccceeeEEehhcccchheeecccccccccccceeecCCCcEEEEEEecchheeee
Confidence 245555555578888777777777753 1 2 24577777777888887777777654
No 198
>smart00293 PWWP domain with conserved PWWP motif. conservation of Pro-Trp-Trp-Pro residues
Probab=57.07 E-value=7.4 Score=25.78 Aligned_cols=14 Identities=43% Similarity=0.895 Sum_probs=12.4
Q ss_pred CCCCCEEEEEEEEe
Q 029155 131 FRPGDIVRASVLSL 144 (198)
Q Consensus 131 ~~~GDiV~AkV~s~ 144 (198)
|++||+|-||+-+.
T Consensus 1 f~~GdlVwaK~~G~ 14 (63)
T smart00293 1 FKPGDLVWAKMKGF 14 (63)
T ss_pred CCCCCEEEEECCCC
Confidence 68999999999874
No 199
>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=56.52 E-value=19 Score=25.52 Aligned_cols=15 Identities=40% Similarity=0.507 Sum_probs=11.2
Q ss_pred CCCCEEEEEEEEeCC
Q 029155 132 RPGDIVRASVLSLGD 146 (198)
Q Consensus 132 ~~GDiV~AkV~s~~~ 146 (198)
++||+|.|||+++..
T Consensus 3 ~vGdiV~~rVtrv~~ 17 (82)
T PF10447_consen 3 KVGDIVIARVTRVNP 17 (82)
T ss_dssp -TT-EEEEEEEEE-S
T ss_pred CCCCEEEEEEEEEec
Confidence 489999999999975
No 200
>COG1110 Reverse gyrase [DNA replication, recombination, and repair]
Probab=55.58 E-value=15 Score=37.58 Aligned_cols=53 Identities=26% Similarity=0.348 Sum_probs=39.4
Q ss_pred CCCCEEEEEEEEeCCCccEEEEEecCCCeeeEE------------ec-CCCceeEEccCCeEEeCCCCCEE
Q 029155 132 RPGDIVRASVLSLGDARAYFLSTAKNDLGVVSA------------ES-TAGGTMVPISWTEMQCPLTGQTE 189 (198)
Q Consensus 132 ~~GDiV~AkV~s~~~~~~~~LSt~~~~lGvv~a------------~~-~~g~~m~~~~~~~~~c~~cg~~e 189 (198)
..||.|.--..|. ++-+.|.|...-+||+.- +| .||...+ +| .-.||.||...
T Consensus 653 ~~gD~vL~ItAS~--GHv~DLvt~~g~hGvl~~~~~~vPvY~tIKrC~dcg~q~~--~~-~~~cP~Cgs~~ 718 (1187)
T COG1110 653 AIGDLVLTITASG--GHVFDLVTEPGVHGVLVKDGKYVPVYDTIKRCRDCGEQFV--DS-EDKCPRCGSRN 718 (1187)
T ss_pred ecCCeEEEEEecC--CeeEEeecccccceeeccCCceEehHHHHHHHhhcCceec--cc-cccCCCCCCcc
Confidence 5889876655553 467899999988887643 67 6898874 66 34999999843
No 201
>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain. This domain contains a CXXCX(19)CXXC motif suggestive of both zinc fingers and thioredoxin, usually found at the N-terminus of prokaryotic proteins. One partially characterized gene, agmX, is among a large set in Myxococcus whose interruption affects adventurous gliding motility.
Probab=55.41 E-value=14 Score=21.72 Aligned_cols=25 Identities=12% Similarity=0.256 Sum_probs=15.2
Q ss_pred Eec-CCCcee-E-----EccCCeEEeCCCCCE
Q 029155 164 AES-TAGGTM-V-----PISWTEMQCPLTGQT 188 (198)
Q Consensus 164 a~~-~~g~~m-~-----~~~~~~~~c~~cg~~ 188 (198)
..| .|+... + +.....+.||+||..
T Consensus 3 ~~CP~C~~~~~v~~~~~~~~~~~v~C~~C~~~ 34 (38)
T TIGR02098 3 IQCPNCKTSFRVVDSQLGANGGKVRCGKCGHV 34 (38)
T ss_pred EECCCCCCEEEeCHHHcCCCCCEEECCCCCCE
Confidence 456 676642 1 122346999999975
No 202
>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=55.30 E-value=30 Score=23.51 Aligned_cols=32 Identities=22% Similarity=0.376 Sum_probs=22.3
Q ss_pred CCCCCEEEEEEEEeCCCccEEEEEecCCCeeeE
Q 029155 131 FRPGDIVRASVLSLGDARAYFLSTAKNDLGVVS 163 (198)
Q Consensus 131 ~~~GDiV~AkV~s~~~~~~~~LSt~~~~lGvv~ 163 (198)
|++||+|.++|.++.+. .+.+++...--|-|.
T Consensus 1 ~k~G~~V~g~V~~i~~~-G~fV~l~~~v~G~v~ 32 (74)
T cd05705 1 IKEGQLLRGYVSSVTKQ-GVFFRLSSSIVGRVL 32 (74)
T ss_pred CCCCCEEEEEEEEEeCC-cEEEEeCCCCEEEEE
Confidence 57999999999999764 466776543334443
No 203
>PRK13922 rod shape-determining protein MreC; Provisional
Probab=55.13 E-value=53 Score=27.93 Aligned_cols=91 Identities=13% Similarity=0.168 Sum_probs=51.6
Q ss_pred EEEeEeeeEEEcCCCCCCCCCCCeEEEecCCCCCCCCCCCCE------EEEEEEEEecceEEEEEeeecccc-----ccC
Q 029155 38 VYASLTGLLRTLSPPPDSPDQRPTVEVTGHKAHGPVPEPGSV------VIARVTKVMTRMASADIMCVGAKS-----VRE 106 (198)
Q Consensus 38 i~asv~G~v~~~~~~~~~~~~~~~i~V~p~~~~~~~p~vGDi------ViG~V~~v~~~~~~V~I~~v~~~~-----l~~ 106 (198)
+.|.+.+.-.. .-.+.+.+.- +...=.++|+. ++|+|+++.+..+.|..+.-.+.. -..
T Consensus 120 i~A~Vi~~~~~--------~~~~~i~Id~--G~~~Gv~~g~~Vv~~~GlVG~V~~v~~~~s~V~li~d~~~~v~v~i~~~ 189 (276)
T PRK13922 120 ITARVISRSPD--------PWSQQVTIDK--GSNDGVKKGMPVIDPGGLVGRVIEVSPNTSRVLLLTDPNSRVPVQVGRN 189 (276)
T ss_pred EEEEEEEeCCC--------CceeEEEEcc--CcccCCCCCCceEcCCCCeEEEEEECCCeeEEEEEEcCCCceEEEEEcC
Confidence 66666665421 1234555532 22333566666 599999999999888887643321 133
Q ss_pred cceeEEecccccc-ccccccccccCCCCCCEEE
Q 029155 107 KFSGIIRQQDVRA-TEIDKVDMHLSFRPGDIVR 138 (198)
Q Consensus 107 ~~~G~l~~s~v~~-~~~d~~~~~~~~~~GDiV~ 138 (198)
...|+++-+.-.. -..+-..-...+++||.|.
T Consensus 190 ~~~gi~~G~g~~~~l~l~~i~~~~~i~~GD~Vv 222 (276)
T PRK13922 190 GIRGILSGNGSGDNLKLEFIPRSADIKVGDLVV 222 (276)
T ss_pred CceEEEEecCCCCceEEEecCCCCCCCCCCEEE
Confidence 4567777663211 1222223345689999863
No 204
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=53.73 E-value=19 Score=26.45 Aligned_cols=32 Identities=16% Similarity=0.260 Sum_probs=23.1
Q ss_pred Eec-CCCceeEEc----cCCeEEeCCCCCEEeeeeCC
Q 029155 164 AES-TAGGTMVPI----SWTEMQCPLTGQTEQRKVAK 195 (198)
Q Consensus 164 a~~-~~g~~m~~~----~~~~~~c~~cg~~e~RKva~ 195 (198)
..| .||+..+++ .--+..|++||..-.|++..
T Consensus 22 f~CP~Cge~~v~v~~~k~~~h~~C~~CG~y~~~~V~~ 58 (99)
T PRK14892 22 FECPRCGKVSISVKIKKNIAIITCGNCGLYTEFEVPS 58 (99)
T ss_pred eECCCCCCeEeeeecCCCcceEECCCCCCccCEECCc
Confidence 347 889765542 12379999999998888764
No 205
>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=53.73 E-value=30 Score=23.76 Aligned_cols=32 Identities=19% Similarity=0.173 Sum_probs=22.6
Q ss_pred CCCCCEEEEEEEEeCCCccEEEEEecCCCeeeE
Q 029155 131 FRPGDIVRASVLSLGDARAYFLSTAKNDLGVVS 163 (198)
Q Consensus 131 ~~~GDiV~AkV~s~~~~~~~~LSt~~~~lGvv~ 163 (198)
.++||+|.|+|.++.+. .+.+.+...-.|.+.
T Consensus 4 p~~GdiV~g~V~~i~~~-g~~v~i~~~~~G~l~ 35 (86)
T cd05789 4 PEVGDVVIGRVTEVGFK-RWKVDINSPYDAVLP 35 (86)
T ss_pred CCCCCEEEEEEEEECCC-EEEEECCCCeEEEEE
Confidence 47999999999999753 466666544445544
No 206
>KOG1088 consensus Uncharacterized conserved protein [Function unknown]
Probab=53.48 E-value=8.9 Score=29.17 Aligned_cols=13 Identities=38% Similarity=0.682 Sum_probs=11.2
Q ss_pred CeEEeCCCCCEEe
Q 029155 178 TEMQCPLTGQTEQ 190 (198)
Q Consensus 178 ~~~~c~~cg~~e~ 190 (198)
.+|+||+||++-+
T Consensus 97 G~l~CpetG~vfp 109 (124)
T KOG1088|consen 97 GELVCPETGRVFP 109 (124)
T ss_pred ceEecCCCCcEee
Confidence 5899999999865
No 207
>PF08772 NOB1_Zn_bind: Nin one binding (NOB1) Zn-ribbon like; InterPro: IPR014881 This entry corresponds to a zinc ribbon and is found on the RNA binding protein NOB1. ; PDB: 2CON_A.
Probab=53.37 E-value=6.3 Score=27.45 Aligned_cols=29 Identities=17% Similarity=0.265 Sum_probs=12.0
Q ss_pred ec-CCCceeEEccCCeEEeCCCCCEEeeeeCC
Q 029155 165 ES-TAGGTMVPISWTEMQCPLTGQTEQRKVAK 195 (198)
Q Consensus 165 ~~-~~g~~m~~~~~~~~~c~~cg~~e~RKva~ 195 (198)
+| .|=.... +-..+.||+||+.-.+|+|-
T Consensus 11 rC~aCf~~t~--~~~k~FCp~CGn~TL~rvsv 40 (73)
T PF08772_consen 11 RCHACFKITK--DMTKQFCPKCGNATLKRVSV 40 (73)
T ss_dssp E-SSS--EES---SS--S-SSS--S--EEEE-
T ss_pred EccccccCcC--CCCceeCcccCCCcceEEEE
Confidence 46 4544442 23578999999999999985
No 208
>PRK10220 hypothetical protein; Provisional
Probab=53.34 E-value=12 Score=28.14 Aligned_cols=25 Identities=8% Similarity=0.072 Sum_probs=19.1
Q ss_pred Eec-CCCceeEEccCCeEEeCCCCCE
Q 029155 164 AES-TAGGTMVPISWTEMQCPLTGQT 188 (198)
Q Consensus 164 a~~-~~g~~m~~~~~~~~~c~~cg~~ 188 (198)
..| +|.....--....+.||+|+..
T Consensus 4 P~CP~C~seytY~d~~~~vCpeC~hE 29 (111)
T PRK10220 4 PHCPKCNSEYTYEDNGMYICPECAHE 29 (111)
T ss_pred CcCCCCCCcceEcCCCeEECCcccCc
Confidence 357 7877766566689999999864
No 209
>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=53.12 E-value=34 Score=22.94 Aligned_cols=32 Identities=13% Similarity=0.142 Sum_probs=20.8
Q ss_pred CCCCCEEEEEEEEeCCCccEEEEEecCCCeee
Q 029155 131 FRPGDIVRASVLSLGDARAYFLSTAKNDLGVV 162 (198)
Q Consensus 131 ~~~GDiV~AkV~s~~~~~~~~LSt~~~~lGvv 162 (198)
+++||++.|+|.++.+...+.+.+...--|-+
T Consensus 1 l~~G~iv~G~V~~i~~~~g~~v~l~~~~~Glv 32 (72)
T cd05704 1 LEEGAVTLGMVTKVIPHSGLTVQLPFGKTGLV 32 (72)
T ss_pred CCCCCEEEEEEEEeeCCcEEEEECCCCCEEEE
Confidence 46999999999998642335555544433444
No 210
>TIGR01206 lysW lysine biosynthesis protein LysW. This very small, poorly characterized protein has been shown essential in Thermus thermophilus for an unusual pathway of Lys biosynthesis from aspartate by way of alpha-aminoadipate (AAA) rather than diaminopimelate. It is found also in Deinococcus radiodurans and Pyrococcus horikoshii, which appear to share the AAA pathway.
Probab=52.93 E-value=15 Score=23.99 Aligned_cols=25 Identities=16% Similarity=0.122 Sum_probs=17.2
Q ss_pred Eec-CCCceeEEc---cCCeEEeCCCCCE
Q 029155 164 AES-TAGGTMVPI---SWTEMQCPLTGQT 188 (198)
Q Consensus 164 a~~-~~g~~m~~~---~~~~~~c~~cg~~ 188 (198)
+.| .||..+.-- ....+.||.||..
T Consensus 3 ~~CP~CG~~iev~~~~~GeiV~Cp~CGae 31 (54)
T TIGR01206 3 FECPDCGAEIELENPELGELVICDECGAE 31 (54)
T ss_pred cCCCCCCCEEecCCCccCCEEeCCCCCCE
Confidence 567 788876321 2468899999975
No 211
>PF08810 KapB: Kinase associated protein B; InterPro: IPR014916 This bacterial protein forms an anti-parallel beta sheet with an extending alpha helical region. ; PDB: 1Y71_B.
Probab=52.13 E-value=25 Score=26.47 Aligned_cols=30 Identities=13% Similarity=0.164 Sum_probs=19.1
Q ss_pred EEEEEEEEecceEEEEEeeeccccccCcceeEEe
Q 029155 80 VIARVTKVMTRMASADIMCVGAKSVREKFSGIIR 113 (198)
Q Consensus 80 ViG~V~~v~~~~~~V~I~~v~~~~l~~~~~G~l~ 113 (198)
=+|.|++++++.+.|.|.+|- ..+.+|-||
T Consensus 6 Yigei~e~~~~~~lVkVlaVl----KHP~QGDLH 35 (112)
T PF08810_consen 6 YIGEITEERPQHYLVKVLAVL----KHPKQGDLH 35 (112)
T ss_dssp EEEEEEEEETTEEEEEEEEEE----E--------
T ss_pred eEEEEEeecCCeEEEEEEEEe----cCCCccCCC
Confidence 479999999999999998873 334455554
No 212
>COG4416 Com Mu-like prophage protein Com [General function prediction only]
Probab=52.02 E-value=4.4 Score=26.65 Aligned_cols=27 Identities=11% Similarity=0.212 Sum_probs=19.4
Q ss_pred ec-CCCceeEEccCC---eEEeCCCCCEEee
Q 029155 165 ES-TAGGTMVPISWT---EMQCPLTGQTEQR 191 (198)
Q Consensus 165 ~~-~~g~~m~~~~~~---~~~c~~cg~~e~R 191 (198)
+| .|+..|-..+.+ +.+||.|.....=
T Consensus 6 RC~~CnKlLa~a~~~~yle~KCPrCK~vN~~ 36 (60)
T COG4416 6 RCAKCNKLLAEAEGQAYLEKKCPRCKEVNEF 36 (60)
T ss_pred ehHHHhHHHHhcccceeeeecCCccceeeee
Confidence 57 788887666544 7899999876543
No 213
>COG0333 RpmF Ribosomal protein L32 [Translation, ribosomal structure and biogenesis]
Probab=52.01 E-value=12 Score=24.77 Aligned_cols=29 Identities=21% Similarity=0.313 Sum_probs=22.9
Q ss_pred EEec-CCCceeEEccCCeEEeCCCCCEEeeeeCC
Q 029155 163 SAES-TAGGTMVPISWTEMQCPLTGQTEQRKVAK 195 (198)
Q Consensus 163 ~a~~-~~g~~m~~~~~~~~~c~~cg~~e~RKva~ 195 (198)
...| .||+.-.| +-.|+.||...-|++..
T Consensus 27 ~~~c~~cG~~~l~----Hrvc~~cg~Y~g~~v~~ 56 (57)
T COG0333 27 LSVCPNCGEYKLP----HRVCLKCGYYKGRQVIE 56 (57)
T ss_pred ceeccCCCCcccC----ceEcCCCCCccCeEecc
Confidence 4567 78887764 57899999999998764
No 214
>PF11781 RRN7: RNA polymerase I-specific transcription initiation factor Rrn7; InterPro: IPR021752 Rrn7 is a transcription binding factor that associates strongly with both Rrn6 and Rrn11 to form a complex which itself binds the TATA-binding protein and is required for transcription by the core domain of the RNA PolI promoter [],[].
Probab=51.10 E-value=16 Score=21.73 Aligned_cols=23 Identities=13% Similarity=0.088 Sum_probs=17.6
Q ss_pred c-CCCceeEEccCCeEEeCCCCCE
Q 029155 166 S-TAGGTMVPISWTEMQCPLTGQT 188 (198)
Q Consensus 166 ~-~~g~~m~~~~~~~~~c~~cg~~ 188 (198)
| .||..........++|..||+.
T Consensus 11 C~~C~~~~~~~~dG~~yC~~cG~~ 34 (36)
T PF11781_consen 11 CPVCGSRWFYSDDGFYYCDRCGHQ 34 (36)
T ss_pred CCCCCCeEeEccCCEEEhhhCceE
Confidence 5 6888876666668999999875
No 215
>TIGR02443 conserved hypothetical metal-binding protein. Members of this family are small proteins, about 70 residues in length, with a basic triplet near the N-terminus and a probable metal-binding motif CPXCX(18)CXXC. Members are found in various Proteobacteria.
Probab=50.95 E-value=15 Score=24.54 Aligned_cols=31 Identities=23% Similarity=0.214 Sum_probs=20.4
Q ss_pred Eec-CCCce----eEEc-cCCeEEeCCCCCEEeeeeC
Q 029155 164 AES-TAGGT----MVPI-SWTEMQCPLTGQTEQRKVA 194 (198)
Q Consensus 164 a~~-~~g~~----m~~~-~~~~~~c~~cg~~e~RKva 194 (198)
|.| +|+.. |+.- .-....|..||..|.|.-.
T Consensus 10 A~CP~C~~~Dtl~~~~e~~~e~vECv~Cg~~~~~~~~ 46 (59)
T TIGR02443 10 AVCPACSAQDTLAMWKENNIELVECVECGYQEQQKDQ 46 (59)
T ss_pred ccCCCCcCccEEEEEEeCCceEEEeccCCCccccCCc
Confidence 567 67654 3322 2236899999999988543
No 216
>PF13597 NRDD: Anaerobic ribonucleoside-triphosphate reductase; PDB: 1HK8_A 1H78_A 1H7A_A 1H79_A 1H7B_A.
Probab=50.61 E-value=13 Score=35.31 Aligned_cols=29 Identities=14% Similarity=0.142 Sum_probs=13.3
Q ss_pred EEec-CCCceeEEccCCeEEeCCCCCEEeeeeCC
Q 029155 163 SAES-TAGGTMVPISWTEMQCPLTGQTEQRKVAK 195 (198)
Q Consensus 163 ~a~~-~~g~~m~~~~~~~~~c~~cg~~e~RKva~ 195 (198)
++.| .||.... ....||.||..+-.-+++
T Consensus 491 ~~~C~~CG~~~~----~~~~CP~CGs~~~~~~~R 520 (546)
T PF13597_consen 491 IDICPDCGYIGG----EGDKCPKCGSENIEVYSR 520 (546)
T ss_dssp EEEETTT---S------EEE-CCC----EEEEB-
T ss_pred cccccCCCcCCC----CCCCCCCCCCcccceEEE
Confidence 6789 8998654 268999999986544443
No 217
>PF09082 DUF1922: Domain of unknown function (DUF1922); InterPro: IPR015166 Members of this family consist of a beta-sheet region followed by an alpha-helix and an unstructured C terminus. The beta-sheet region contains a CXCX...XCXC sequence with Cys residues located in two proximal loops and pointing towards each other. This precise function of this set of bacterial proteins is, as yet, unknown []. ; PDB: 1GH9_A.
Probab=50.30 E-value=28 Score=23.91 Aligned_cols=26 Identities=15% Similarity=0.275 Sum_probs=17.8
Q ss_pred EecCCCceeEEc-cCCeEEeCCCCCEEe
Q 029155 164 AESTAGGTMVPI-SWTEMQCPLTGQTEQ 190 (198)
Q Consensus 164 a~~~~g~~m~~~-~~~~~~c~~cg~~e~ 190 (198)
=+|.||..|+-. +-.+=+| .||++-+
T Consensus 4 frC~Cgr~lya~e~~kTkkC-~CG~~l~ 30 (68)
T PF09082_consen 4 FRCDCGRYLYAKEGAKTKKC-VCGKTLK 30 (68)
T ss_dssp EEETTS--EEEETT-SEEEE-TTTEEEE
T ss_pred EEecCCCEEEecCCcceeEe-cCCCeee
Confidence 468999999765 4558899 9998754
No 218
>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=50.09 E-value=10 Score=27.34 Aligned_cols=14 Identities=50% Similarity=0.771 Sum_probs=12.3
Q ss_pred CCCCCEEEEEEEEe
Q 029155 131 FRPGDIVRASVLSL 144 (198)
Q Consensus 131 ~~~GDiV~AkV~s~ 144 (198)
|++||+|.||+-+.
T Consensus 1 f~~GDlVwaK~~Gy 14 (93)
T cd05840 1 FQPGDRVLAKVKGF 14 (93)
T ss_pred CCCCCEEEEeCCCC
Confidence 68999999999764
No 219
>PF12773 DZR: Double zinc ribbon
Probab=49.61 E-value=6 Score=24.69 Aligned_cols=25 Identities=20% Similarity=0.357 Sum_probs=16.3
Q ss_pred Eec-CCCceeEEccCCeEEeCCCCCE
Q 029155 164 AES-TAGGTMVPISWTEMQCPLTGQT 188 (198)
Q Consensus 164 a~~-~~g~~m~~~~~~~~~c~~cg~~ 188 (198)
..| .||.+|.......+.|+.||..
T Consensus 13 ~fC~~CG~~l~~~~~~~~~C~~Cg~~ 38 (50)
T PF12773_consen 13 KFCPHCGTPLPPPDQSKKICPNCGAE 38 (50)
T ss_pred cCChhhcCChhhccCCCCCCcCCcCC
Confidence 346 6787776333346788888875
No 220
>TIGR00515 accD acetyl-CoA carboxylase, carboxyl transferase, beta subunit. The enzyme acetyl-CoA carboxylase contains a biotin carboxyl carrier protein or domain, a biotin carboxylase, and a carboxyl transferase. This model represents the beta chain of the carboxyl transferase for cases in which the architecture of the protein is as in E. coli, in which the carboxyltransferase portion consists of two non-identical subnits, alpha and beta.
Probab=49.07 E-value=4.6 Score=35.25 Aligned_cols=29 Identities=14% Similarity=0.216 Sum_probs=22.9
Q ss_pred eEEec-CCCceeEEccC--CeEEeCCCCCEEe
Q 029155 162 VSAES-TAGGTMVPISW--TEMQCPLTGQTEQ 190 (198)
Q Consensus 162 v~a~~-~~g~~m~~~~~--~~~~c~~cg~~e~ 190 (198)
+...| .|+..++...+ +...||+||.-.+
T Consensus 25 ~~~~c~~c~~~~~~~~l~~~~~vc~~c~~h~r 56 (285)
T TIGR00515 25 VWTKCPKCGQVLYTKELERNLEVCPKCDHHMR 56 (285)
T ss_pred CeeECCCCcchhhHHHHHhhCCCCCCCCCcCc
Confidence 58889 89999877643 5689999998643
No 221
>PTZ00329 eukaryotic translation initiation factor 1A; Provisional
Probab=48.89 E-value=30 Score=27.56 Aligned_cols=64 Identities=17% Similarity=0.255 Sum_probs=38.3
Q ss_pred CcEEec--CCccCCCCCeeeCCCEEE---eCCceEEEEeEeeeEEEcCCCCCCCCCCCeEEEecCCCCCCCCCCCCEEEE
Q 029155 8 MVLVTP--GEVLGKATEVKAGKGAYV---AKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHKAHGPVPEPGSVVIA 82 (198)
Q Consensus 8 ~~iV~P--Gd~l~~~~e~~~G~Gty~---~~g~~~i~asv~G~v~~~~~~~~~~~~~~~i~V~p~~~~~~~p~vGDiViG 82 (198)
+.+++| ||.++... -..|.|.|. .+|. .+.|.+.|.++. .|||. +||+|+.
T Consensus 24 rel~~~eegq~~g~V~-~~LGn~~f~V~c~dG~-~rLa~I~GKmRK------------~IWI~----------~GD~VlV 79 (155)
T PTZ00329 24 RELVFKEEGQEYAQVL-RMLGNGRLEAYCFDGV-KRLCHIRGKMRK------------RVWIN----------IGDIILV 79 (155)
T ss_pred eeeccCCCCcEEEEEE-EEcCCCEEEEEECCCC-EEEEEeecccee------------eEEec----------CCCEEEE
Confidence 456676 66666533 356777765 2442 478888888865 36664 4788877
Q ss_pred EEEEEecceEEEEEe
Q 029155 83 RVTKVMTRMASADIM 97 (198)
Q Consensus 83 ~V~~v~~~~~~V~I~ 97 (198)
....-. .-..+|.
T Consensus 80 el~~yd--~~KgdIi 92 (155)
T PTZ00329 80 SLRDFQ--DSKADVI 92 (155)
T ss_pred eccCCC--CCEEEEE
Confidence 553332 2344453
No 222
>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=48.85 E-value=11 Score=26.70 Aligned_cols=14 Identities=29% Similarity=0.541 Sum_probs=12.0
Q ss_pred CCCCCEEEEEEEEe
Q 029155 131 FRPGDIVRASVLSL 144 (198)
Q Consensus 131 ~~~GDiV~AkV~s~ 144 (198)
|++||+|-||+-..
T Consensus 1 f~~GDlVwaK~~g~ 14 (86)
T cd05836 1 LKLGDLVWAKMKGF 14 (86)
T ss_pred CCCCCEEEEeCCCC
Confidence 68999999998754
No 223
>PRK01110 rpmF 50S ribosomal protein L32; Validated
Probab=48.76 E-value=18 Score=24.15 Aligned_cols=29 Identities=31% Similarity=0.379 Sum_probs=22.4
Q ss_pred EEec-CCCceeEEccCCeEEeCCCCCEEeeeeCCC
Q 029155 163 SAES-TAGGTMVPISWTEMQCPLTGQTEQRKVAKV 196 (198)
Q Consensus 163 ~a~~-~~g~~m~~~~~~~~~c~~cg~~e~RKva~~ 196 (198)
...| .||....| +-.|+ ||..-.|++..+
T Consensus 27 ~~~c~~cg~~~~p----H~vc~-cG~Y~gr~v~~~ 56 (60)
T PRK01110 27 LSVDKTTGEYHLP----HHVSP-KGYYKGRKVLKK 56 (60)
T ss_pred eeEcCCCCceecc----ceecC-CcccCCeEeecc
Confidence 4668 79998876 45699 999888887654
No 224
>COG0777 AccD Acetyl-CoA carboxylase beta subunit [Lipid metabolism]
Probab=48.55 E-value=8.4 Score=33.58 Aligned_cols=28 Identities=14% Similarity=0.240 Sum_probs=22.3
Q ss_pred eEEec-CCCceeEEcc--CCeEEeCCCCCEE
Q 029155 162 VSAES-TAGGTMVPIS--WTEMQCPLTGQTE 189 (198)
Q Consensus 162 v~a~~-~~g~~m~~~~--~~~~~c~~cg~~e 189 (198)
+...| .||..|+..+ -|...||+|+.-.
T Consensus 27 lw~KCp~c~~~~y~~eL~~n~~vcp~c~~h~ 57 (294)
T COG0777 27 LWTKCPSCGEMLYRKELESNLKVCPKCGHHM 57 (294)
T ss_pred ceeECCCccceeeHHHHHhhhhcccccCccc
Confidence 47889 8999998763 4678999999754
No 225
>PRK07217 replication factor A; Reviewed
Probab=48.11 E-value=25 Score=31.14 Aligned_cols=38 Identities=11% Similarity=0.225 Sum_probs=26.5
Q ss_pred EEEEEEEeCCCccEEEEEecCCCeeeEEec-C--CCceeEEccCCeEEeCCCCCEEee
Q 029155 137 VRASVLSLGDARAYFLSTAKNDLGVVSAES-T--AGGTMVPISWTEMQCPLTGQTEQR 191 (198)
Q Consensus 137 V~AkV~s~~~~~~~~LSt~~~~lGvv~a~~-~--~g~~m~~~~~~~~~c~~cg~~e~R 191 (198)
+.+.++.+..+. -+..+| . |+..|.. -+||.||..|..
T Consensus 174 i~G~lVdi~~Gs------------glI~rCP~~~C~Rvl~~-----g~C~~HG~ve~~ 214 (311)
T PRK07217 174 VEGALVDIQSGS------------GLIKRCPEEDCTRVLQN-----GRCSEHGKVEGE 214 (311)
T ss_pred ceeEEEEEeCCC------------CCeecCCccccCccccC-----CCCCCCCCcCCc
Confidence 666677765432 236789 7 9999942 379999988753
No 226
>COG1158 Rho Transcription termination factor [Transcription]
Probab=47.59 E-value=27 Score=31.72 Aligned_cols=44 Identities=14% Similarity=0.092 Sum_probs=34.2
Q ss_pred CeEEEecCCCCCCCCCCCCEEEEEEEEEec---ceEEEEEeeecccc
Q 029155 60 PTVEVTGHKAHGPVPEPGSVVIARVTKVMT---RMASADIMCVGAKS 103 (198)
Q Consensus 60 ~~i~V~p~~~~~~~p~vGDiViG~V~~v~~---~~~~V~I~~v~~~~ 103 (198)
.-|+|.|..-+++-++.||.|.|+|-.=.. .++.+.+.++++.+
T Consensus 80 ~DiYvSpSQIRrf~LrtGD~v~G~vR~Pke~Ery~aLl~ve~vN~~~ 126 (422)
T COG1158 80 DDIYVSPSQIRRFNLRTGDTVEGKVRPPKEGERYFALLKVEAVNGDD 126 (422)
T ss_pred CceEECHHHHhhccCccCCEEeeeecCCCcccceeeeEEEeecCCCC
Confidence 358898876677889999999999987644 46778888887644
No 227
>cd00350 rubredoxin_like Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center. The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=47.56 E-value=12 Score=21.57 Aligned_cols=23 Identities=17% Similarity=0.263 Sum_probs=15.9
Q ss_pred ec-CCCceeEEccCCeEEeCCCCCE
Q 029155 165 ES-TAGGTMVPISWTEMQCPLTGQT 188 (198)
Q Consensus 165 ~~-~~g~~m~~~~~~~~~c~~cg~~ 188 (198)
+| .||....+.. ..-.||.||..
T Consensus 3 ~C~~CGy~y~~~~-~~~~CP~Cg~~ 26 (33)
T cd00350 3 VCPVCGYIYDGEE-APWVCPVCGAP 26 (33)
T ss_pred ECCCCCCEECCCc-CCCcCcCCCCc
Confidence 46 6888776543 34589999874
No 228
>TIGR00219 mreC rod shape-determining protein MreC. MreC (murein formation C) is involved in the rod shape determination in E. coli, and more generally in cell shape determination of bacteria whether or not they are rod-shaped. Cells defective in MreC are round. Species with MreC include many of the Proteobacteria, Gram-positives, and spirochetes.
Probab=47.30 E-value=77 Score=27.45 Aligned_cols=60 Identities=13% Similarity=0.241 Sum_probs=36.8
Q ss_pred EEEEEEEEEecceEEEEEeeecccc-----ccCcceeEEecccccc---ccccccccccCCCCCCEEE
Q 029155 79 VVIARVTKVMTRMASADIMCVGAKS-----VREKFSGIIRQQDVRA---TEIDKVDMHLSFRPGDIVR 138 (198)
Q Consensus 79 iViG~V~~v~~~~~~V~I~~v~~~~-----l~~~~~G~l~~s~v~~---~~~d~~~~~~~~~~GDiV~ 138 (198)
=++|+|+++.+....|..+.-.+.. ......|+++-.+-.. .......-...+++||.|.
T Consensus 156 GLVG~V~~V~~~~S~V~litd~~~~v~v~v~~t~~~gi~~G~~~g~~~~l~l~~~~~~~~v~~GD~Vv 223 (283)
T TIGR00219 156 GLVGKVVSVGSNTSRVLLLTDYTNFVPAQILRSDFRGLIEGNGYGKTLEMNLVNRPAEKDIKKGDLIV 223 (283)
T ss_pred ceEEEEEEECCCeEEEEEEEcCCCceEEEEecCCceEEEEecCCCCCcEEEEEECCCCCCCCCCCEEE
Confidence 3789999999999999887643321 2345678887664111 0111112245688999764
No 229
>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=47.28 E-value=13 Score=26.24 Aligned_cols=15 Identities=40% Similarity=0.638 Sum_probs=12.7
Q ss_pred CCCCCCEEEEEEEEe
Q 029155 130 SFRPGDIVRASVLSL 144 (198)
Q Consensus 130 ~~~~GDiV~AkV~s~ 144 (198)
.|.+||+|-||+...
T Consensus 2 ~f~~GdlVwaK~kGy 16 (83)
T cd05834 2 QFKAGDLVFAKVKGY 16 (83)
T ss_pred CCCCCCEEEEecCCC
Confidence 489999999998664
No 230
>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines. Several members are annotated as putative helicases.
Probab=47.17 E-value=8.3 Score=21.35 Aligned_cols=19 Identities=32% Similarity=0.592 Sum_probs=12.9
Q ss_pred CCCceeEEccCCeEEeCCCCCE
Q 029155 167 TAGGTMVPISWTEMQCPLTGQT 188 (198)
Q Consensus 167 ~~g~~m~~~~~~~~~c~~cg~~ 188 (198)
.|+... |.+ ...||.||..
T Consensus 5 ~C~~~V-~~~--~~~Cp~CG~~ 23 (26)
T PF10571_consen 5 ECGAEV-PES--AKFCPHCGYD 23 (26)
T ss_pred CCcCCc-hhh--cCcCCCCCCC
Confidence 566554 443 6899999974
No 231
>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=46.12 E-value=47 Score=23.48 Aligned_cols=23 Identities=26% Similarity=0.369 Sum_probs=20.4
Q ss_pred CCCCCEE------EEEEEEEecceEEEEE
Q 029155 74 PEPGSVV------IARVTKVMTRMASADI 96 (198)
Q Consensus 74 p~vGDiV------iG~V~~v~~~~~~V~I 96 (198)
.++||-| +|+|.++.++.+.+++
T Consensus 38 L~~Gd~VvT~gGi~G~V~~i~d~~v~vei 66 (84)
T TIGR00739 38 LKKGDKVLTIGGIIGTVTKIAENTIVIEL 66 (84)
T ss_pred CCCCCEEEECCCeEEEEEEEeCCEEEEEE
Confidence 6889987 8999999999888888
No 232
>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=45.37 E-value=49 Score=30.41 Aligned_cols=36 Identities=25% Similarity=0.328 Sum_probs=26.7
Q ss_pred CeeeCCCEEEe-CCceEEEEeEeeeEEEcCCCCCCCCCCCeEEEec
Q 029155 22 EVKAGKGAYVA-KHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTG 66 (198)
Q Consensus 22 e~~~G~Gty~~-~g~~~i~asv~G~v~~~~~~~~~~~~~~~i~V~p 66 (198)
.+.+|+||... ++...++|++.|.+.... ..++|.|
T Consensus 144 ~~~~g~~~~~~~~d~~~~~A~~~G~~~~~~---------~~i~V~~ 180 (451)
T PF03961_consen 144 PLKAGKNTEVSEEDGNKLYAAIDGRPVFEN---------GKISVDP 180 (451)
T ss_pred ceeCCCCEEEEcCCCCEEEEecCCEEEEEC---------CEEEEEE
Confidence 47789999987 322348999999999953 4577766
No 233
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=44.86 E-value=15 Score=21.78 Aligned_cols=17 Identities=18% Similarity=0.471 Sum_probs=13.2
Q ss_pred eEEccCCeEEeCCCCCE
Q 029155 172 MVPISWTEMQCPLTGQT 188 (198)
Q Consensus 172 m~~~~~~~~~c~~cg~~ 188 (198)
.+|.....++|++||++
T Consensus 18 ~ip~~g~~v~C~~C~~~ 34 (36)
T PF13717_consen 18 KIPPKGRKVRCSKCGHV 34 (36)
T ss_pred HCCCCCcEEECCCCCCE
Confidence 35556678999999975
No 234
>PRK05654 acetyl-CoA carboxylase subunit beta; Validated
Probab=44.39 E-value=6.3 Score=34.50 Aligned_cols=29 Identities=14% Similarity=0.274 Sum_probs=23.1
Q ss_pred eEEec-CCCceeEEccC--CeEEeCCCCCEEe
Q 029155 162 VSAES-TAGGTMVPISW--TEMQCPLTGQTEQ 190 (198)
Q Consensus 162 v~a~~-~~g~~m~~~~~--~~~~c~~cg~~e~ 190 (198)
+...| .|+..++...+ +...||+||.-.+
T Consensus 26 ~~~~c~~c~~~~~~~~l~~~~~vc~~c~~h~r 57 (292)
T PRK05654 26 LWTKCPSCGQVLYRKELEANLNVCPKCGHHMR 57 (292)
T ss_pred CeeECCCccchhhHHHHHhcCCCCCCCCCCee
Confidence 48889 89999877654 5679999998653
No 235
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=44.07 E-value=5.8 Score=34.82 Aligned_cols=29 Identities=10% Similarity=-0.004 Sum_probs=22.8
Q ss_pred eEEec-CCCceeEEccC--CeEEeCCCCCEEe
Q 029155 162 VSAES-TAGGTMVPISW--TEMQCPLTGQTEQ 190 (198)
Q Consensus 162 v~a~~-~~g~~m~~~~~--~~~~c~~cg~~e~ 190 (198)
+...| .|+..++...+ +...||+||.-.+
T Consensus 37 lw~kc~~C~~~~~~~~l~~~~~vcp~c~~h~r 68 (296)
T CHL00174 37 LWVQCENCYGLNYKKFLKSKMNICEQCGYHLK 68 (296)
T ss_pred CeeECCCccchhhHHHHHHcCCCCCCCCCCcC
Confidence 58899 89999887754 4579999998543
No 236
>PF03558 TBSV_P22: TBSV core protein P21/P22; InterPro: IPR005332 Two small nested genes (p19 and p22) are located near the 3' end of the genome of tomato bushy stunt virus (TBSV) - the p19 gene encodes a soluble protein, whereas the p22 gene specifies a membrane-associated protein. p22 is required for cell-to-cell movement in all plants tested [].; GO: 0019028 viral capsid
Probab=43.36 E-value=1.6e+02 Score=23.73 Aligned_cols=78 Identities=22% Similarity=0.331 Sum_probs=51.3
Q ss_pred CcceeEEeccccccccccccccccCCCCCCEEEEEEEEeCCCccEEEEEecC---CCeeeEEec--CCCceeEEc--cCC
Q 029155 106 EKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGDARAYFLSTAKN---DLGVVSAES--TAGGTMVPI--SWT 178 (198)
Q Consensus 106 ~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~~~~~~LSt~~~---~lGvv~a~~--~~g~~m~~~--~~~ 178 (198)
.+..|.+..-|++...-.+.--.+.|+.|--|+.+-.-+ ++.|++++. .+|+=..++ ..|..|.-. .|+
T Consensus 73 AgV~g~l~L~D~sD~ssr~L~~Tk~fnLG~~i~le~~qL----~F~l~~~gd~PI~F~~t~l~S~F~e~r~LfStSleWq 148 (189)
T PF03558_consen 73 AGVSGVLKLRDISDTSSRKLHCTKEFNLGHGIRLEGSQL----PFCLPTRGDYPIVFEVTVLVSQFREGRELFSTSLEWQ 148 (189)
T ss_pred cCceEEEEEEEccccccceeeeehhccCCcceEEeeccC----ceeeecCCCcceEEEEEEeechhhccceeEEeEeEEE
Confidence 356666666666544433333457888898887665433 478888765 467777777 689998665 598
Q ss_pred eEEeCCCCC
Q 029155 179 EMQCPLTGQ 187 (198)
Q Consensus 179 ~~~c~~cg~ 187 (198)
.|..+.|-.
T Consensus 149 ~~~S~t~~S 157 (189)
T PF03558_consen 149 MMLSPTPYS 157 (189)
T ss_pred eeccCCccc
Confidence 776666643
No 237
>PHA00626 hypothetical protein
Probab=43.09 E-value=27 Score=23.13 Aligned_cols=13 Identities=15% Similarity=0.340 Sum_probs=10.4
Q ss_pred CeEEeCCCCCEEe
Q 029155 178 TEMQCPLTGQTEQ 190 (198)
Q Consensus 178 ~~~~c~~cg~~e~ 190 (198)
+...|+.||....
T Consensus 22 nrYkCkdCGY~ft 34 (59)
T PHA00626 22 DDYVCCDCGYNDS 34 (59)
T ss_pred cceEcCCCCCeec
Confidence 6899999997643
No 238
>COG0361 InfA Translation initiation factor 1 (IF-1) [Translation, ribosomal structure and biogenesis]
Probab=42.72 E-value=1.2e+02 Score=21.27 Aligned_cols=56 Identities=9% Similarity=0.141 Sum_probs=33.2
Q ss_pred CCEEEEEEEEEecc-eEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeCC
Q 029155 77 GSVVIARVTKVMTR-MASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGD 146 (198)
Q Consensus 77 GDiViG~V~~v~~~-~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~ 146 (198)
...+.|+|++..++ .+.|.+ ..++.-.-|++.- -+ ..+=.+.+||+|..+....++
T Consensus 6 ~~e~~g~V~e~L~~~~f~v~~--------edg~~~~ahI~GK--mr----~~~i~I~~GD~V~Ve~~~~d~ 62 (75)
T COG0361 6 EIEMEGTVIEMLPNGRFRVEL--------ENGHERLAHISGK--MR----KNRIRILPGDVVLVELSPYDL 62 (75)
T ss_pred ccEEEEEEEEecCCCEEEEEe--------cCCcEEEEEccCc--ch----heeEEeCCCCEEEEEeccccc
Confidence 34588999998654 555655 3333333333321 01 113457899999999887653
No 239
>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=42.48 E-value=57 Score=23.59 Aligned_cols=30 Identities=17% Similarity=0.194 Sum_probs=21.6
Q ss_pred CCCCCEEEEEEEEeCCCccEEEEEecCCCee
Q 029155 131 FRPGDIVRASVLSLGDARAYFLSTAKNDLGV 161 (198)
Q Consensus 131 ~~~GDiV~AkV~s~~~~~~~~LSt~~~~lGv 161 (198)
+++||+|.|+|.++.+. .+.+++...--|-
T Consensus 1 L~~G~vV~G~V~~v~~~-gl~v~L~~g~~G~ 30 (100)
T cd05693 1 LSEGMLVLGQVKEITKL-DLVISLPNGLTGY 30 (100)
T ss_pred CCCCCEEEEEEEEEcCC-CEEEECCCCcEEE
Confidence 57999999999999753 5777765433333
No 240
>PF01938 TRAM: TRAM domain; InterPro: IPR002792 The TRAM (after TRM2 and miaB) domain is a 60-70-residue-long module that is found in: Two distinct classes of tRNA-modifying enzymes, namely uridine methylases of the TRM2 family and enzymes of the miaB family that are involved in 2- methylthioadenine formation In several other proteins associated with the translation machinery In a family of small uncharacterised archaeal proteins that are predicted to have a role in the regulation of tRNA modification and/or translation The TRAM domain can be found alone or in association with other domains, such as the catalytic biotin/lipoate synthetase-like domain, the RNA methylase domain, the ribosomal S2 domain and the eIF2-beta domain. The TRAM domain is predicted to bind tRNA and deliver the RNA-modifying enzymatic domain to their targets []. Secondary structure prediction indicates that the TRAM domain adopts a simple beta-barrel fold. The conservation pattern of the TRAM domain consists primarily of small and hydrophobic residues that correspond to five beta-strands in the predicted secondary structure [].; PDB: 1YEZ_A 2BH2_A 1UWV_A 1YVC_A.
Probab=42.41 E-value=51 Score=21.23 Aligned_cols=24 Identities=25% Similarity=0.372 Sum_probs=17.7
Q ss_pred CCCCCCEEEEEEEEEecceEEEEE
Q 029155 73 VPEPGSVVIARVTKVMTRMASADI 96 (198)
Q Consensus 73 ~p~vGDiViG~V~~v~~~~~~V~I 96 (198)
.|.+||.|..+|++.....++-++
T Consensus 37 ~~~iG~~v~v~I~~~~~~~l~G~~ 60 (61)
T PF01938_consen 37 LPLIGEFVKVRITKAKKNYLFGEL 60 (61)
T ss_dssp -T--TEEEEEEEEEE-SSEEEEEE
T ss_pred CCCCCCEEEEEEEEeeCCcEEEEE
Confidence 355899999999999999887665
No 241
>PF09526 DUF2387: Probable metal-binding protein (DUF2387); InterPro: IPR012658 Members of this family are small proteins, about 70 residues in length, with a basic triplet near the N terminus and a probable metal-binding motif CPXCX(18)CXXC. Members are found in various proteobacteria.
Probab=41.87 E-value=27 Score=24.06 Aligned_cols=31 Identities=19% Similarity=0.147 Sum_probs=20.9
Q ss_pred Eec-CCCce----eE-EccCCeEEeCCCCCEEeeeeC
Q 029155 164 AES-TAGGT----MV-PISWTEMQCPLTGQTEQRKVA 194 (198)
Q Consensus 164 a~~-~~g~~----m~-~~~~~~~~c~~cg~~e~RKva 194 (198)
|.| +|... |+ .-+-..+.|..||..+.|.-.
T Consensus 9 a~CP~C~~~D~i~~~~e~~ve~vECV~CGy~e~~~~~ 45 (71)
T PF09526_consen 9 AVCPKCQAMDTIMMWRENGVEYVECVECGYTERQPDQ 45 (71)
T ss_pred ccCCCCcCccEEEEEEeCCceEEEecCCCCeeccCCc
Confidence 567 66654 22 223457899999999988655
No 242
>PRK06763 F0F1 ATP synthase subunit alpha; Validated
Probab=40.98 E-value=1e+02 Score=25.74 Aligned_cols=21 Identities=19% Similarity=0.064 Sum_probs=15.7
Q ss_pred CCCEEEEEEEEEecceEEEEE
Q 029155 76 PGSVVIARVTKVMTRMASADI 96 (198)
Q Consensus 76 vGDiViG~V~~v~~~~~~V~I 96 (198)
--+.+.|+|..+......++.
T Consensus 38 n~~tiEGrVvEV~~~~i~ies 58 (213)
T PRK06763 38 NFSTIEGRVVEVDNGVIVIKS 58 (213)
T ss_pred ccceeeeEEEEEeCCEEEEEe
Confidence 356788888888887777666
No 243
>PRK12495 hypothetical protein; Provisional
Probab=40.58 E-value=16 Score=30.79 Aligned_cols=29 Identities=17% Similarity=0.251 Sum_probs=22.1
Q ss_pred eEEec-CCCceeEEccCCeEEeCCCCCEEee
Q 029155 162 VSAES-TAGGTMVPISWTEMQCPLTGQTEQR 191 (198)
Q Consensus 162 v~a~~-~~g~~m~~~~~~~~~c~~cg~~e~R 191 (198)
..-.| .||.|+-.+.| ...|+.|+....+
T Consensus 41 sa~hC~~CG~PIpa~pG-~~~Cp~CQ~~~~~ 70 (226)
T PRK12495 41 TNAHCDECGDPIFRHDG-QEFCPTCQQPVTE 70 (226)
T ss_pred chhhcccccCcccCCCC-eeECCCCCCcccc
Confidence 34458 89999987764 6999999987543
No 244
>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=40.47 E-value=18 Score=25.56 Aligned_cols=14 Identities=29% Similarity=0.605 Sum_probs=12.0
Q ss_pred CCCCCEEEEEEEEe
Q 029155 131 FRPGDIVRASVLSL 144 (198)
Q Consensus 131 ~~~GDiV~AkV~s~ 144 (198)
|.+||+|-||+-..
T Consensus 1 f~vGDlVWaK~kg~ 14 (87)
T cd05835 1 FNVGDLVWGKIKGF 14 (87)
T ss_pred CCCCCEEEEecCCC
Confidence 68999999998664
No 245
>PF13375 RnfC_N: RnfC Barrel sandwich hybrid domain
Probab=40.07 E-value=30 Score=25.37 Aligned_cols=12 Identities=25% Similarity=0.531 Sum_probs=10.6
Q ss_pred EEEeEeeeEEEc
Q 029155 38 VYASLTGLLRTL 49 (198)
Q Consensus 38 i~asv~G~v~~~ 49 (198)
|+||+.|++.-.
T Consensus 69 iHAsvSG~V~~I 80 (101)
T PF13375_consen 69 IHASVSGTVTAI 80 (101)
T ss_pred EEcCCCeEEEEE
Confidence 999999999875
No 246
>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=40.01 E-value=78 Score=20.42 Aligned_cols=63 Identities=21% Similarity=0.173 Sum_probs=31.4
Q ss_pred EEEEEEEEEe---cceEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEE--EEEeCCCccEEEE
Q 029155 79 VVIARVTKVM---TRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRAS--VLSLGDARAYFLS 153 (198)
Q Consensus 79 iViG~V~~v~---~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~Ak--V~s~~~~~~~~LS 153 (198)
.|.|+|+++. ...+++.|. + .+|.+..-- .........+.+++||.|.++ |....+ +.++|+
T Consensus 2 ~v~G~V~~~~~~~~~~~~~~l~---D------~tg~i~~~~---~~~~~~~~~~~l~~g~~v~v~G~v~~~~~-~~~~l~ 68 (75)
T PF01336_consen 2 TVEGRVTSIRRSGGKIVFFTLE---D------GTGSIQVVF---FNEEYERFREKLKEGDIVRVRGKVKRYNG-GELELI 68 (75)
T ss_dssp EEEEEEEEEEEEETTEEEEEEE---E------TTEEEEEEE---ETHHHHHHHHTS-TTSEEEEEEEEEEETT-SSEEEE
T ss_pred EEEEEEEEEEcCCCCEEEEEEE---E------CCccEEEEE---ccHHhhHHhhcCCCCeEEEEEEEEEEECC-ccEEEE
Confidence 3678888883 334555552 1 123332211 111122567889999998765 444322 235555
Q ss_pred E
Q 029155 154 T 154 (198)
Q Consensus 154 t 154 (198)
.
T Consensus 69 ~ 69 (75)
T PF01336_consen 69 V 69 (75)
T ss_dssp E
T ss_pred E
Confidence 4
No 247
>COG3269 Predicted RNA-binding protein, contains TRAM domain [General function prediction only]
Probab=39.46 E-value=55 Score=22.80 Aligned_cols=24 Identities=33% Similarity=0.468 Sum_probs=21.7
Q ss_pred CCCCCEEEEEEEEEecceEEEEEe
Q 029155 74 PEPGSVVIARVTKVMTRMASADIM 97 (198)
Q Consensus 74 p~vGDiViG~V~~v~~~~~~V~I~ 97 (198)
-++||.|.-+|+++.+++++-++.
T Consensus 46 a~~Gd~V~vkI~~v~~~~afaevv 69 (73)
T COG3269 46 AEVGDEVKVKITKVKPNFAFAEVV 69 (73)
T ss_pred CCCCCeeeEEEEEeeccceeeEEe
Confidence 378999999999999999998884
No 248
>PF14205 Cys_rich_KTR: Cysteine-rich KTR
Probab=38.88 E-value=19 Score=23.72 Aligned_cols=14 Identities=29% Similarity=0.838 Sum_probs=10.0
Q ss_pred EEeCCCCCEEeeee
Q 029155 180 MQCPLTGQTEQRKV 193 (198)
Q Consensus 180 ~~c~~cg~~e~RKv 193 (198)
+.||.||++-+=|+
T Consensus 5 i~CP~CgnKTR~ki 18 (55)
T PF14205_consen 5 ILCPICGNKTRLKI 18 (55)
T ss_pred EECCCCCCccceee
Confidence 78888887765444
No 249
>cd00729 rubredoxin_SM Rubredoxin, Small Modular nonheme iron binding domain containing a [Fe(SCys)4] center, present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=38.73 E-value=26 Score=20.42 Aligned_cols=23 Identities=17% Similarity=0.281 Sum_probs=14.9
Q ss_pred ec-CCCceeEEccCCeEEeCCCCCE
Q 029155 165 ES-TAGGTMVPISWTEMQCPLTGQT 188 (198)
Q Consensus 165 ~~-~~g~~m~~~~~~~~~c~~cg~~ 188 (198)
+| .||..+.- ..-.-.||.||..
T Consensus 4 ~C~~CG~i~~g-~~~p~~CP~Cg~~ 27 (34)
T cd00729 4 VCPVCGYIHEG-EEAPEKCPICGAP 27 (34)
T ss_pred ECCCCCCEeEC-CcCCCcCcCCCCc
Confidence 57 78877652 2123589999874
No 250
>COG3478 Predicted nucleic-acid-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=38.39 E-value=13 Score=25.28 Aligned_cols=10 Identities=40% Similarity=1.009 Sum_probs=7.1
Q ss_pred EEeCCCCCEE
Q 029155 180 MQCPLTGQTE 189 (198)
Q Consensus 180 ~~c~~cg~~e 189 (198)
.+||+||..+
T Consensus 5 ~kCpKCgn~~ 14 (68)
T COG3478 5 FKCPKCGNTN 14 (68)
T ss_pred ccCCCcCCcc
Confidence 3488888764
No 251
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=38.29 E-value=86 Score=25.78 Aligned_cols=23 Identities=22% Similarity=0.106 Sum_probs=19.5
Q ss_pred CCCCCCEEEEEEEEEecceEEEEE
Q 029155 73 VPEPGSVVIARVTKVMTRMASADI 96 (198)
Q Consensus 73 ~p~vGDiViG~V~~v~~~~~~V~I 96 (198)
-.++||+|.|+|++.. +...+.+
T Consensus 118 ~f~~GDivrA~Vis~~-~~~~Lst 140 (188)
T COG1096 118 AFRIGDIVRARVISTG-DPIQLST 140 (188)
T ss_pred ccccccEEEEEEEecC-CCeEEEe
Confidence 3589999999999998 6667777
No 252
>PRK05807 hypothetical protein; Provisional
Probab=38.28 E-value=1.1e+02 Score=23.53 Aligned_cols=69 Identities=19% Similarity=0.135 Sum_probs=38.5
Q ss_pred cCCccCCCCCeeeCCCEEEeCCceEEEEeEeeeEEEcCCCCCCCCCCCeEEEecCCCCCCCCCCCCEEEEEEEEEec-ce
Q 029155 13 PGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHKAHGPVPEPGSVVIARVTKVMT-RM 91 (198)
Q Consensus 13 PGd~l~~~~e~~~G~Gty~~~g~~~i~asv~G~v~~~~~~~~~~~~~~~i~V~p~~~~~~~p~vGDiViG~V~~v~~-~~ 91 (198)
+||.+--.-.-....|.|++-.. ..|++.+.+-. ... +. .....+++||.|.++|.++.. ..
T Consensus 5 vG~vv~G~Vt~i~~~GafV~L~~------~~Glvhiseis------~~~--v~---~~~~~~kvGd~V~VkV~~id~~gk 67 (136)
T PRK05807 5 AGSILEGTVVNITNFGAFVEVEG------KTGLVHISEVA------DTY--VK---DIREHLKEQDKVKVKVISIDDNGK 67 (136)
T ss_pred CCCEEEEEEEEEECCeEEEEECC------EEEEEEhhhcc------ccc--cc---CccccCCCCCEEEEEEEEECCCCc
Confidence 45554321122445677776422 26888774310 111 11 112346999999999999986 45
Q ss_pred EEEEEee
Q 029155 92 ASADIMC 98 (198)
Q Consensus 92 ~~V~I~~ 98 (198)
+.+.+-.
T Consensus 68 I~LSlk~ 74 (136)
T PRK05807 68 ISLSIKQ 74 (136)
T ss_pred EEEEEEe
Confidence 6666643
No 253
>COG2093 DNA-directed RNA polymerase, subunit E'' [Transcription]
Probab=38.23 E-value=13 Score=25.15 Aligned_cols=21 Identities=19% Similarity=0.310 Sum_probs=14.1
Q ss_pred c-CCCceeEEccCCeEEeCCCCCEE
Q 029155 166 S-TAGGTMVPISWTEMQCPLTGQTE 189 (198)
Q Consensus 166 ~-~~g~~m~~~~~~~~~c~~cg~~e 189 (198)
| +|...|- .++-+||.||..+
T Consensus 7 C~~Ck~l~~---~d~e~CP~Cgs~~ 28 (64)
T COG2093 7 CKNCKRLTP---EDTEICPVCGSTD 28 (64)
T ss_pred HhhccccCC---CCCccCCCCCCcc
Confidence 5 5666553 2456899999864
No 254
>COG1315 Uncharacterized conserved protein [Function unknown]
Probab=38.04 E-value=57 Score=30.92 Aligned_cols=48 Identities=15% Similarity=0.165 Sum_probs=33.7
Q ss_pred CeeeCCCE-EEeCCceEEEEeEeeeEEEcCCCCCCCCCCCeEEEecCC--CCCCCCCCCCEE
Q 029155 22 EVKAGKGA-YVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHK--AHGPVPEPGSVV 80 (198)
Q Consensus 22 e~~~G~Gt-y~~~g~~~i~asv~G~v~~~~~~~~~~~~~~~i~V~p~~--~~~~~p~vGDiV 80 (198)
.+.+|.|| +.+++. +.|+..|.+-+. +++|+|.|.- ..-.-++.|+|.
T Consensus 220 ~l~lG~nt~~kd~~t--lvA~~~G~~~~s---------~~tI~V~~iyeV~gdV~~kTGnI~ 270 (543)
T COG1315 220 KLNLGKNTAFKDNNT--LVAKRDGQPIVS---------KNTISVYPIYEVNGDVDVKTGNIK 270 (543)
T ss_pred eeecCCCCccCCCCE--EEEeeCCeEEec---------CCeeEEEEEEEecCCcccccccee
Confidence 37789999 777766 999999999884 4689998741 112334555554
No 255
>PF09855 DUF2082: Nucleic-acid-binding protein containing Zn-ribbon domain (DUF2082); InterPro: IPR018652 This family of proteins contains various hypothetical prokaryotic proteins as well as some Zn-ribbon nucleic-acid-binding proteins.
Probab=38.04 E-value=23 Score=24.00 Aligned_cols=14 Identities=36% Similarity=0.468 Sum_probs=11.5
Q ss_pred eEEeCCCCCEEeee
Q 029155 179 EMQCPLTGQTEQRK 192 (198)
Q Consensus 179 ~~~c~~cg~~e~RK 192 (198)
.+.|++||.+|.=|
T Consensus 36 ~v~C~~CGYTE~Y~ 49 (64)
T PF09855_consen 36 TVSCTNCGYTEFYK 49 (64)
T ss_pred EEECCCCCCEEEEe
Confidence 67899999999644
No 256
>cd04459 Rho_CSD Rho_CSD: Rho protein cold-shock domain (CSD). Rho protein is a transcription termination factor in most bacteria. In bacteria, there are two distinct mechanisms for mRNA transcription termination. In intrinsic termination, RNA polymerase and nascent mRNA are released from DNA template by an mRNA stem loop structure, which resembles the transcription termination mechanism used by eukaryotic pol III. The second mechanism is mediated by Rho factor. Rho factor terminates transcription by using energy from ATP hydrolysis to forcibly dissociate the transcripts from RNA polymerase. Rho protein contains an N-terminal S1-like domain, which binds single-stranded RNA. Rho has a C-terminal ATPase domain which hydrolyzes ATP to provide energy to strip RNA polymerase and mRNA from the DNA template. Rho functions as a homohexamer.
Probab=37.82 E-value=19 Score=24.65 Aligned_cols=26 Identities=12% Similarity=0.180 Sum_probs=20.2
Q ss_pred eEEEecCCCCCCCCCCCCEEEEEEEE
Q 029155 61 TVEVTGHKAHGPVPEPGSVVIARVTK 86 (198)
Q Consensus 61 ~i~V~p~~~~~~~p~vGDiViG~V~~ 86 (198)
-+.|.+..-+++-++.||.|.|.|..
T Consensus 28 DvyVs~~~Irr~~LR~GD~V~G~vr~ 53 (68)
T cd04459 28 DIYVSPSQIRRFNLRTGDTVVGQIRP 53 (68)
T ss_pred CEEECHHHHHHhCCCCCCEEEEEEeC
Confidence 46776654457889999999998875
No 257
>PRK11788 tetratricopeptide repeat protein; Provisional
Probab=37.76 E-value=19 Score=31.22 Aligned_cols=23 Identities=22% Similarity=0.238 Sum_probs=18.0
Q ss_pred ec-CCCceeEEccCCeEEeCCCCCEEe
Q 029155 165 ES-TAGGTMVPISWTEMQCPLTGQTEQ 190 (198)
Q Consensus 165 ~~-~~g~~m~~~~~~~~~c~~cg~~e~ 190 (198)
.| .||..+. .| ...||+||..+.
T Consensus 356 ~c~~cg~~~~--~~-~~~c~~c~~~~~ 379 (389)
T PRK11788 356 RCRNCGFTAR--TL-YWHCPSCKAWET 379 (389)
T ss_pred ECCCCCCCCc--cc-eeECcCCCCccC
Confidence 37 7998884 68 599999998653
No 258
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=37.64 E-value=22 Score=27.02 Aligned_cols=29 Identities=24% Similarity=0.439 Sum_probs=16.7
Q ss_pred EEecCCCceeE----EccCC--eEEeCCCCCEEee
Q 029155 163 SAESTAGGTMV----PISWT--EMQCPLTGQTEQR 191 (198)
Q Consensus 163 ~a~~~~g~~m~----~~~~~--~~~c~~cg~~e~R 191 (198)
.++|.||..-- +.... .+.||.||....+
T Consensus 70 ~~~C~Cg~~~~~~~~~~~~~~~~~~CP~Cgs~~~~ 104 (124)
T PRK00762 70 EIECECGYEGVVDEDEIDHYAAVIECPVCGNKRAH 104 (124)
T ss_pred eEEeeCcCcccccccchhccccCCcCcCCCCCCCE
Confidence 66777776522 11111 2679999965544
No 259
>PF09567 RE_MamI: MamI restriction endonuclease; InterPro: IPR019067 There are four classes of restriction endonucleases: types I, II,III and IV. All types of enzymes recognise specific short DNA sequences and carry out the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. They differ in their recognition sequence, subunit composition, cleavage position, and cofactor requirements [, ], as summarised below: Type I enzymes (3.1.21.3 from EC) cleave at sites remote from recognition site; require both ATP and S-adenosyl-L-methionine to function; multifunctional protein with both restriction and methylase (2.1.1.72 from EC) activities. Type II enzymes (3.1.21.4 from EC) cleave within or at short specific distances from recognition site; most require magnesium; single function (restriction) enzymes independent of methylase. Type III enzymes (3.1.21.5 from EC) cleave at sites a short distance from recognition site; require ATP (but doesn't hydrolyse it); S-adenosyl-L-methionine stimulates reaction but is not required; exists as part of a complex with a modification methylase methylase (2.1.1.72 from EC). Type IV enzymes target methylated DNA. Type II restriction endonucleases (3.1.21.4 from EC) are components of prokaryotic DNA restriction-modification mechanisms that protect the organism against invading foreign DNA. These site-specific deoxyribonucleases catalyse the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. Of the 3000 restriction endonucleases that have been characterised, most are homodimeric or tetrameric enzymes that cleave target DNA at sequence-specific sites close to the recognition site. For homodimeric enzymes, the recognition site is usually a palindromic sequence 4-8 bp in length. Most enzymes require magnesium ions as a cofactor for catalysis. Although they can vary in their mode of recognition, many restriction endonucleases share a similar structural core comprising four beta-strands and one alpha-helix, as well as a similar mechanism of cleavage, suggesting a common ancestral origin []. However, there is still considerable diversity amongst restriction endonucleases [, ]. The target site recognition process triggers large conformational changes of the enzyme and the target DNA, leading to the activation of the catalytic centres. Like other DNA binding proteins, restriction enzymes are capable of non-specific DNA binding as well, which is the prerequisite for efficient target site location by facilitated diffusion. Non-specific binding usually does not involve interactions with the bases but only with the DNA backbone []. This entry includes the MamI restriction endonuclease which recognises and cleaves GATNN^NNATC. ; GO: 0003677 DNA binding, 0009036 Type II site-specific deoxyribonuclease activity, 0009307 DNA restriction-modification system
Probab=37.28 E-value=14 Score=31.89 Aligned_cols=22 Identities=27% Similarity=0.564 Sum_probs=17.0
Q ss_pred ec-CCCceeEEccCCeEEeCCCCCEE
Q 029155 165 ES-TAGGTMVPISWTEMQCPLTGQTE 189 (198)
Q Consensus 165 ~~-~~g~~m~~~~~~~~~c~~cg~~e 189 (198)
.| +||.... .| +..||+||...
T Consensus 84 ~C~~CGa~V~--~~-e~~Cp~C~Stn 106 (314)
T PF09567_consen 84 KCNNCGANVS--RL-EESCPNCGSTN 106 (314)
T ss_pred hhccccceee--eh-hhcCCCCCccc
Confidence 47 7998874 46 58999999764
No 260
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=37.26 E-value=25 Score=21.14 Aligned_cols=20 Identities=25% Similarity=0.521 Sum_probs=11.5
Q ss_pred CCCceeEEccCC---eEEeCCCC
Q 029155 167 TAGGTMVPISWT---EMQCPLTG 186 (198)
Q Consensus 167 ~~g~~m~~~~~~---~~~c~~cg 186 (198)
+|+..|.+.... ...|+.||
T Consensus 4 ~C~~~l~~~~~~~~~id~C~~C~ 26 (41)
T PF13453_consen 4 RCGTELEPVRLGDVEIDVCPSCG 26 (41)
T ss_pred CCCcccceEEECCEEEEECCCCC
Confidence 566666555432 34577776
No 261
>PRK12496 hypothetical protein; Provisional
Probab=37.17 E-value=15 Score=29.30 Aligned_cols=31 Identities=19% Similarity=0.371 Sum_probs=21.2
Q ss_pred Eec-CCCceeEEccCCeEEeCCCCCEEeeeeCC
Q 029155 164 AES-TAGGTMVPISWTEMQCPLTGQTEQRKVAK 195 (198)
Q Consensus 164 a~~-~~g~~m~~~~~~~~~c~~cg~~e~RKva~ 195 (198)
-+| -||.. ++.....-.||.||..-+||..+
T Consensus 128 ~~C~gC~~~-~~~~~~~~~C~~CG~~~~r~~~~ 159 (164)
T PRK12496 128 KVCKGCKKK-YPEDYPDDVCEICGSPVKRKMVK 159 (164)
T ss_pred EECCCCCcc-ccCCCCCCcCCCCCChhhhcchh
Confidence 568 57744 44332345799999998888654
No 262
>PRK05886 yajC preprotein translocase subunit YajC; Validated
Probab=37.02 E-value=74 Score=23.82 Aligned_cols=25 Identities=20% Similarity=0.319 Sum_probs=21.4
Q ss_pred CCCCCCEE------EEEEEEEecceEEEEEe
Q 029155 73 VPEPGSVV------IARVTKVMTRMASADIM 97 (198)
Q Consensus 73 ~p~vGDiV------iG~V~~v~~~~~~V~I~ 97 (198)
-+++||-| +|+|+++.++.+.++|.
T Consensus 38 ~Lk~GD~VvT~gGi~G~V~~I~d~~v~leia 68 (109)
T PRK05886 38 SLQPGDRVHTTSGLQATIVGITDDTVDLEIA 68 (109)
T ss_pred hcCCCCEEEECCCeEEEEEEEeCCEEEEEEC
Confidence 36889988 79999999998888883
No 263
>PRK09263 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=36.80 E-value=13 Score=36.46 Aligned_cols=28 Identities=21% Similarity=0.379 Sum_probs=17.1
Q ss_pred EEec-CCCce--eEEccCCeEEeCCCCCEEee
Q 029155 163 SAES-TAGGT--MVPISWTEMQCPLTGQTEQR 191 (198)
Q Consensus 163 ~a~~-~~g~~--m~~~~~~~~~c~~cg~~e~R 191 (198)
+.+| .||.. +.... ....||.||..+.+
T Consensus 641 ~~~C~~CG~~Ge~~~~~-~~~~CP~CG~~~~~ 671 (711)
T PRK09263 641 IDECYECGFTGEFECTE-KGFTCPKCGNHDPK 671 (711)
T ss_pred CcccCCCCCCccccCCC-CCCcCcCCCCCCCc
Confidence 5678 89962 11111 22579999986633
No 264
>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=36.73 E-value=1.2e+02 Score=20.79 Aligned_cols=52 Identities=13% Similarity=0.261 Sum_probs=28.6
Q ss_pred EEEEEEEEecc-eEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeC
Q 029155 80 VIARVTKVMTR-MASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLG 145 (198)
Q Consensus 80 ViG~V~~v~~~-~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~ 145 (198)
+.|+|++..++ .+.|.+ ..+..-+-|++-- -... +-.+.+||.|..+...++
T Consensus 7 ~~G~V~e~L~~~~f~V~l--------~ng~~vla~i~GK--mr~~----rI~I~~GD~V~Ve~spyd 59 (68)
T TIGR00008 7 MEGKVTESLPNAMFRVEL--------ENGHEVLAHISGK--IRMH----YIRILPGDKVKVELSPYD 59 (68)
T ss_pred EEEEEEEECCCCEEEEEE--------CCCCEEEEEecCc--chhc----cEEECCCCEEEEEECccc
Confidence 67999998654 455565 2222222222220 0111 233679999999987654
No 265
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=36.27 E-value=52 Score=21.26 Aligned_cols=28 Identities=25% Similarity=0.177 Sum_probs=19.5
Q ss_pred Eec-CCC--ceeEEccCCeEEeCCCCCEEeee
Q 029155 164 AES-TAG--GTMVPISWTEMQCPLTGQTEQRK 192 (198)
Q Consensus 164 a~~-~~g--~~m~~~~~~~~~c~~cg~~e~RK 192 (198)
-.| +|| ..|- --.+.+.|-+||.+|.-+
T Consensus 20 ~~CPrCG~gvfmA-~H~dR~~CGkCgyTe~~~ 50 (51)
T COG1998 20 RFCPRCGPGVFMA-DHKDRWACGKCGYTEFKK 50 (51)
T ss_pred ccCCCCCCcchhh-hcCceeEeccccceEeec
Confidence 357 788 4553 223578999999999754
No 266
>COG4393 Predicted membrane protein [Function unknown]
Probab=36.08 E-value=63 Score=29.11 Aligned_cols=34 Identities=15% Similarity=0.149 Sum_probs=25.8
Q ss_pred cCCCeeeEEec-CCCceeEEccCCeEEeCCCCCEE
Q 029155 156 KNDLGVVSAES-TAGGTMVPISWTEMQCPLTGQTE 189 (198)
Q Consensus 156 ~~~lGvv~a~~-~~g~~m~~~~~~~~~c~~cg~~e 189 (198)
+..||.++--| -||..=+-...+++.|..|+.+.
T Consensus 327 r~s~~avfDAC~iCGd~GYv~e~dqvICv~C~Vrm 361 (405)
T COG4393 327 RLSLGAVFDACDICGDQGYVMEGDQVICVRCDVRM 361 (405)
T ss_pred CCCceeeehHHHhccccceEeECCEEEEEEccEEE
Confidence 45678888888 78776544456899999998764
No 267
>PRK05585 yajC preprotein translocase subunit YajC; Validated
Probab=36.01 E-value=78 Score=23.42 Aligned_cols=24 Identities=29% Similarity=0.379 Sum_probs=21.3
Q ss_pred CCCCCCEE------EEEEEEEecceEEEEE
Q 029155 73 VPEPGSVV------IARVTKVMTRMASADI 96 (198)
Q Consensus 73 ~p~vGDiV------iG~V~~v~~~~~~V~I 96 (198)
-.++||.| +|+|.++.++.+.++|
T Consensus 52 ~Lk~Gd~VvT~gGi~G~Vv~i~~~~v~lei 81 (106)
T PRK05585 52 SLAKGDEVVTNGGIIGKVTKVSEDFVIIEL 81 (106)
T ss_pred hcCCCCEEEECCCeEEEEEEEeCCEEEEEE
Confidence 36889998 8999999999888888
No 268
>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=35.99 E-value=24 Score=24.56 Aligned_cols=14 Identities=50% Similarity=0.895 Sum_probs=12.3
Q ss_pred CCCCCEEEEEEEEe
Q 029155 131 FRPGDIVRASVLSL 144 (198)
Q Consensus 131 ~~~GDiV~AkV~s~ 144 (198)
|++||+|-||+-+.
T Consensus 1 f~~GdlVwaK~~g~ 14 (87)
T cd05162 1 FRPGDLVWAKMKGY 14 (87)
T ss_pred CCCCCEEEEeCCCC
Confidence 78999999999764
No 269
>PRK08582 hypothetical protein; Provisional
Probab=35.87 E-value=1.6e+02 Score=22.73 Aligned_cols=28 Identities=18% Similarity=0.043 Sum_probs=21.1
Q ss_pred CCCCCCEEEEEEEEEec-ceEEEEEeeec
Q 029155 73 VPEPGSVVIARVTKVMT-RMASADIMCVG 100 (198)
Q Consensus 73 ~p~vGDiViG~V~~v~~-~~~~V~I~~v~ 100 (198)
..++||.|.++|.++.. ..+.+.+....
T Consensus 49 ~l~vGD~VkvkV~~id~~gkI~LSlk~~~ 77 (139)
T PRK08582 49 HLKVGDEVEVKVLNVEDDGKIGLSIKKAK 77 (139)
T ss_pred ccCCCCEEEEEEEEECCCCcEEEEEEecc
Confidence 46999999999999975 45666664443
No 270
>PRK00276 infA translation initiation factor IF-1; Validated
Probab=35.62 E-value=1.4e+02 Score=20.17 Aligned_cols=53 Identities=19% Similarity=0.305 Sum_probs=30.0
Q ss_pred EEEEEEEEecc-eEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeCC
Q 029155 80 VIARVTKVMTR-MASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGD 146 (198)
Q Consensus 80 ViG~V~~v~~~-~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~ 146 (198)
..|+|++..+. .+.|.. .++........|-++.+. ....+||.|..++...++
T Consensus 9 ~~G~Vi~~~~~~~y~V~~--~~g~~~~c~~~Gklr~~~------------i~i~vGD~V~ve~~~~~~ 62 (72)
T PRK00276 9 MEGTVVEALPNAMFRVEL--ENGHEVLAHISGKMRKNY------------IRILPGDKVTVELSPYDL 62 (72)
T ss_pred EEEEEEEEcCCCEEEEEe--CCCCEEEEEEccceeeCC------------cccCCCCEEEEEEcccCC
Confidence 46899998765 666643 223222233444433211 125799999998765543
No 271
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=35.54 E-value=29 Score=20.57 Aligned_cols=15 Identities=27% Similarity=0.702 Sum_probs=11.5
Q ss_pred EccCCeEEeCCCCCE
Q 029155 174 PISWTEMQCPLTGQT 188 (198)
Q Consensus 174 ~~~~~~~~c~~cg~~ 188 (198)
|.....++|++|+.+
T Consensus 20 ~~~~~~vrC~~C~~~ 34 (37)
T PF13719_consen 20 PAGGRKVRCPKCGHV 34 (37)
T ss_pred ccCCcEEECCCCCcE
Confidence 344568999999975
No 272
>PRK14873 primosome assembly protein PriA; Provisional
Probab=35.36 E-value=28 Score=33.94 Aligned_cols=26 Identities=15% Similarity=0.222 Sum_probs=18.6
Q ss_pred Eec-CCCceeEE-ccCCeEEeCCCCCEE
Q 029155 164 AES-TAGGTMVP-ISWTEMQCPLTGQTE 189 (198)
Q Consensus 164 a~~-~~g~~m~~-~~~~~~~c~~cg~~e 189 (198)
++| .|..+|.- .+.+.|.|..||..+
T Consensus 393 ~~C~~C~~~L~~h~~~~~l~Ch~CG~~~ 420 (665)
T PRK14873 393 ARCRHCTGPLGLPSAGGTPRCRWCGRAA 420 (665)
T ss_pred eECCCCCCceeEecCCCeeECCCCcCCC
Confidence 467 68888853 345689999999754
No 273
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=35.31 E-value=18 Score=19.56 Aligned_cols=11 Identities=27% Similarity=0.736 Sum_probs=8.9
Q ss_pred eEEeCCCCCEE
Q 029155 179 EMQCPLTGQTE 189 (198)
Q Consensus 179 ~~~c~~cg~~e 189 (198)
...||.||+.-
T Consensus 2 l~~C~~CgR~F 12 (25)
T PF13913_consen 2 LVPCPICGRKF 12 (25)
T ss_pred CCcCCCCCCEE
Confidence 46899999875
No 274
>COG0266 Nei Formamidopyrimidine-DNA glycosylase [DNA replication, recombination, and repair]
Probab=34.78 E-value=31 Score=30.03 Aligned_cols=23 Identities=17% Similarity=0.443 Sum_probs=17.5
Q ss_pred ec-CCCceeEEc---cCCeEEeCCCCC
Q 029155 165 ES-TAGGTMVPI---SWTEMQCPLTGQ 187 (198)
Q Consensus 165 ~~-~~g~~m~~~---~~~~~~c~~cg~ 187 (198)
.| .||.++.+. +-+...||.|-+
T Consensus 247 pC~~CGt~I~k~~~~gR~t~~CP~CQ~ 273 (273)
T COG0266 247 PCRRCGTPIEKIKLGGRSTFYCPVCQK 273 (273)
T ss_pred CCCccCCEeEEEEEcCCcCEeCCCCCC
Confidence 47 799998655 456899999963
No 275
>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=34.45 E-value=29 Score=24.70 Aligned_cols=18 Identities=17% Similarity=0.198 Sum_probs=15.0
Q ss_pred ccCCCCCCEEEEEEEEeC
Q 029155 128 HLSFRPGDIVRASVLSLG 145 (198)
Q Consensus 128 ~~~~~~GDiV~AkV~s~~ 145 (198)
..|+.+||+|-||+-..-
T Consensus 4 ~pc~~p~dLVwAK~kGyp 21 (83)
T cd05841 4 EPCRPPHELVWAKLKGFP 21 (83)
T ss_pred cccCCCCCEEEEeCCCCC
Confidence 478999999999987653
No 276
>cd04322 LysRS_N LysRS_N: N-terminal, anticodon recognition domain of lysyl-tRNA synthetases (LysRS). These enzymes are homodimeric class 2b aminoacyl-tRNA synthetases (aaRSs). This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop. aaRSs catalyze the specific attachment of amino acids (AAs) to their cognate tRNAs during protein biosynthesis. This 2-step reaction involves i) the activation of the AA by ATP in the presence of magnesium ions, followed by ii) the transfer of the activated AA to the terminal ribose of tRNA. In the case of the class2b aaRSs, the activated AA is attached to the 3'OH of the terminal ribose. Included in this group are E. coli LysS and LysU. These two isoforms of LysRS are encoded by distinct genes which are differently regulated. Eukaryotes contain 2 sets of aaRSs, both of which encoded by the nuclear genome. One set concerns with cytoplasmic protein synthesis, whereas the other exclusively with mitochondrial protein
Probab=33.86 E-value=1.5e+02 Score=21.30 Aligned_cols=55 Identities=18% Similarity=0.248 Sum_probs=30.4
Q ss_pred EEEEEEEEEecc--eEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEE
Q 029155 79 VVIARVTKVMTR--MASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRAS 140 (198)
Q Consensus 79 iViG~V~~v~~~--~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~Ak 140 (198)
.|.|+|..++.. .+|++|.. + ....+.++..++.... .-.+....+..||.|.++
T Consensus 3 ~v~GwV~~~R~~g~~~Fi~lrd--~---~~~lQ~v~~~~~~~~~--~~~~~~~~l~~g~~V~v~ 59 (108)
T cd04322 3 SVAGRIMSKRGSGKLSFADLQD--E---SGKIQVYVNKDDLGEE--EFEDFKKLLDLGDIIGVT 59 (108)
T ss_pred EEEEEEEEEecCCCeEEEEEEE--C---CeEEEEEEECCCCCHH--HHHHHHhcCCCCCEEEEE
Confidence 478999999754 57777732 1 1245555543332110 001222348999998764
No 277
>PRK06556 vitamin B12-dependent ribonucleotide reductase; Validated
Probab=33.66 E-value=28 Score=35.40 Aligned_cols=23 Identities=30% Similarity=0.328 Sum_probs=19.4
Q ss_pred ec-CCCceeEEccCCeEEeCCCCCE
Q 029155 165 ES-TAGGTMVPISWTEMQCPLTGQT 188 (198)
Q Consensus 165 ~~-~~g~~m~~~~~~~~~c~~cg~~ 188 (198)
.| .||..|+|.+ .=..|..||.+
T Consensus 926 ~c~~c~~~~~~~g-~c~~c~~cg~t 949 (953)
T PRK06556 926 LCPTCGTKMVRNG-SCYVCEGCGST 949 (953)
T ss_pred cCCCccCeeeECC-ceEeccCCCCC
Confidence 38 8999999866 67999999975
No 278
>cd03478 Rieske_AIFL_N AIFL (apoptosis-inducing factor like) family, N-terminal Rieske domain; members of this family show similarity to human AIFL, containing an N-terminal Rieske domain and a C-terminal pyridine nucleotide-disulfide oxidoreductase domain (Pyr_redox). The Rieske domain is a [2Fe-2S] cluster binding domain involved in electron transfer. AIFL shares 35% homology with human AIF (apoptosis-inducing factor), mainly in the Pyr_redox domain. AIFL is predominantly localized to the mitochondria. AIFL induces apoptosis in a caspase-dependent manner.
Probab=33.34 E-value=1.6e+02 Score=20.41 Aligned_cols=55 Identities=20% Similarity=0.376 Sum_probs=30.9
Q ss_pred cCCCCCCEEEEEEEEeCCCccEEEEEecCCCeeeEEec-CC---CceeEE--ccCCeEEeCCCCCEEe
Q 029155 129 LSFRPGDIVRASVLSLGDARAYFLSTAKNDLGVVSAES-TA---GGTMVP--ISWTEMQCPLTGQTEQ 190 (198)
Q Consensus 129 ~~~~~GDiV~AkV~s~~~~~~~~LSt~~~~lGvv~a~~-~~---g~~m~~--~~~~~~~c~~cg~~e~ 190 (198)
+.+..|+....++ + +..+.|.-.+ |.++|.. .| |.+|.. ...+.+.||--|+.-.
T Consensus 7 ~~l~~g~~~~~~~---~-~~~v~v~r~~---g~~~A~~~~CpH~g~~L~~g~~~~~~i~CP~Hg~~Fd 67 (95)
T cd03478 7 SDLGDGEMKEVDV---G-DGKVLLVRQG---GEVHAIGAKCPHYGAPLAKGVLTDGRIRCPWHGACFN 67 (95)
T ss_pred hhCCCCCEEEEEe---C-CcEEEEEEEC---CEEEEEcCcCcCCCCccCCCeEeCCEEEcCCCCCEEE
Confidence 3456777666555 2 3456554333 5667765 44 444431 1246799997766543
No 279
>PRK08579 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=33.32 E-value=18 Score=34.98 Aligned_cols=23 Identities=17% Similarity=0.314 Sum_probs=17.1
Q ss_pred EEec-CCCceeEEccCCeEEeCCCCCE
Q 029155 163 SAES-TAGGTMVPISWTEMQCPLTGQT 188 (198)
Q Consensus 163 ~a~~-~~g~~m~~~~~~~~~c~~cg~~ 188 (198)
+++| .||..+ ......||.||..
T Consensus 568 ~~~C~~CG~~~---~g~~~~CP~CGs~ 591 (625)
T PRK08579 568 ITVCNKCGRST---TGLYTRCPRCGSE 591 (625)
T ss_pred CccCCCCCCcc---CCCCCcCcCCCCc
Confidence 6688 899855 2346799999974
No 280
>PRK05580 primosome assembly protein PriA; Validated
Probab=33.25 E-value=28 Score=33.92 Aligned_cols=26 Identities=15% Similarity=0.266 Sum_probs=16.4
Q ss_pred ec-CCCceeE-EccCCeEEeCCCCCEEe
Q 029155 165 ES-TAGGTMV-PISWTEMQCPLTGQTEQ 190 (198)
Q Consensus 165 ~~-~~g~~m~-~~~~~~~~c~~cg~~e~ 190 (198)
.| .|+.+|. ....+.|.|..||..+.
T Consensus 392 ~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~ 419 (679)
T PRK05580 392 ECPHCDASLTLHRFQRRLRCHHCGYQEP 419 (679)
T ss_pred CCCCCCCceeEECCCCeEECCCCcCCCC
Confidence 45 4666664 23456788888887653
No 281
>PF07191 zinc-ribbons_6: zinc-ribbons; InterPro: IPR010807 This family consists of several short, hypothetical bacterial proteins of around 70 residues in length. Members of this family 8 highly conserved cysteine residues. The function of the family is unknown.; PDB: 2JRP_A 2JNE_A.
Probab=32.79 E-value=68 Score=22.16 Aligned_cols=26 Identities=4% Similarity=0.022 Sum_probs=14.3
Q ss_pred Eec-CCCceeEEccCCeEEeCCCCCEEe
Q 029155 164 AES-TAGGTMVPISWTEMQCPLTGQTEQ 190 (198)
Q Consensus 164 a~~-~~g~~m~~~~~~~~~c~~cg~~e~ 190 (198)
+.| .|..+|.+.+ ....|..|.....
T Consensus 2 ~~CP~C~~~L~~~~-~~~~C~~C~~~~~ 28 (70)
T PF07191_consen 2 NTCPKCQQELEWQG-GHYHCEACQKDYK 28 (70)
T ss_dssp -B-SSS-SBEEEET-TEEEETTT--EEE
T ss_pred CcCCCCCCccEEeC-CEEECccccccce
Confidence 456 6777777766 5677777776443
No 282
>PRK12442 translation initiation factor IF-1; Reviewed
Probab=32.47 E-value=1.5e+02 Score=21.35 Aligned_cols=52 Identities=17% Similarity=0.199 Sum_probs=29.3
Q ss_pred EEEEEEEEec-ceEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeC
Q 029155 80 VIARVTKVMT-RMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLG 145 (198)
Q Consensus 80 ViG~V~~v~~-~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~ 145 (198)
+.|.|+.+.+ ..+.|.+. ++.......+|=++.. +--+.+||.|..++...+
T Consensus 9 ~~G~V~e~Lp~~~frV~Le--nG~~vla~isGKmR~~------------rIrIl~GD~V~VE~spYD 61 (87)
T PRK12442 9 LDGIVDEVLPDSRFRVTLE--NGVEVGAYASGRMRKH------------RIRILAGDRVTLELSPYD 61 (87)
T ss_pred EEEEEEEECCCCEEEEEeC--CCCEEEEEeccceeee------------eEEecCCCEEEEEECccc
Confidence 6799999855 45666661 2222122223322211 123569999999987665
No 283
>PRK14810 formamidopyrimidine-DNA glycosylase; Provisional
Probab=32.42 E-value=36 Score=29.27 Aligned_cols=23 Identities=9% Similarity=0.211 Sum_probs=15.8
Q ss_pred Eec-CCCceeEEc---cCCeEEeCCCC
Q 029155 164 AES-TAGGTMVPI---SWTEMQCPLTG 186 (198)
Q Consensus 164 a~~-~~g~~m~~~---~~~~~~c~~cg 186 (198)
..| +||.++... +-....||+|.
T Consensus 245 ~pCprCG~~I~~~~~~gR~t~~CP~CQ 271 (272)
T PRK14810 245 EPCLNCKTPIRRVVVAGRSSHYCPHCQ 271 (272)
T ss_pred CcCCCCCCeeEEEEECCCccEECcCCc
Confidence 357 788887544 35578888885
No 284
>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=32.42 E-value=2.9e+02 Score=22.84 Aligned_cols=55 Identities=13% Similarity=0.155 Sum_probs=40.1
Q ss_pred eEEEEeEeeeEEEcCCCCCCCCCCCeEEEecCC----CCCCCCCCCCEEEEEEEEEecceEEEEEeeec
Q 029155 36 GLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHK----AHGPVPEPGSVVIARVTKVMTRMASADIMCVG 100 (198)
Q Consensus 36 ~~i~asv~G~v~~~~~~~~~~~~~~~i~V~p~~----~~~~~p~vGDiViG~V~~v~~~~~~V~I~~v~ 100 (198)
..|+|.+-|...... ...|..+=+. ....+|+ |-.++| +.++.+....+.|.++.
T Consensus 53 n~I~A~V~~~qtv~~--------Gs~vrlRLle~i~i~g~~IPk-gt~l~G-~~~~~~~Rl~i~I~SI~ 111 (200)
T PF12508_consen 53 NTIRAVVDGTQTVVD--------GSRVRLRLLEDIQIGGILIPK-GTYLYG-VASFQGQRLLITITSIE 111 (200)
T ss_pred CeEEEEEecceEEeC--------CCEEEEEEcCceEECCEEeCC-CCEEEE-EEeeeccEEEEEEEEEE
Confidence 349999999888853 2344433111 3356666 999999 99999999999998764
No 285
>smart00652 eIF1a eukaryotic translation initiation factor 1A.
Probab=32.33 E-value=1.8e+02 Score=20.44 Aligned_cols=56 Identities=23% Similarity=0.207 Sum_probs=31.1
Q ss_pred CCCCCEEEEEEEEEecc-eEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeC
Q 029155 74 PEPGSVVIARVTKVMTR-MASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLG 145 (198)
Q Consensus 74 p~vGDiViG~V~~v~~~-~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~ 145 (198)
|..| -++|+|++..++ .+.|.. .++. .+.+.|+.. ... +=.++.||.|.+.....+
T Consensus 2 p~e~-q~~g~V~~~lG~~~~~V~~--~dG~----~~la~ipgK-----~Rk----~iwI~~GD~VlVe~~~~~ 58 (83)
T smart00652 2 KEDG-QEIAQVVKMLGNGRLEVMC--ADGK----ERLARIPGK-----MRK----KVWIRRGDIVLVDPWDFQ 58 (83)
T ss_pred CCCC-cEEEEEEEEcCCCEEEEEE--CCCC----EEEEEEchh-----hcc----cEEEcCCCEEEEEecCCC
Confidence 4434 489999998664 455555 2221 222333211 111 244679999999876554
No 286
>PLN00208 translation initiation factor (eIF); Provisional
Probab=32.13 E-value=1.4e+02 Score=23.56 Aligned_cols=57 Identities=14% Similarity=0.176 Sum_probs=31.7
Q ss_pred CCCCCCEEEEEEEEEecc-eEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeC
Q 029155 73 VPEPGSVVIARVTKVMTR-MASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLG 145 (198)
Q Consensus 73 ~p~vGDiViG~V~~v~~~-~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~ 145 (198)
+|..|+ ++|+|++..++ ...|.. .++ ..-+.|++- -. ..+=.+++||+|.+..-..+
T Consensus 28 ~p~egq-~~g~V~~~lGn~~~~V~c--~dG------~~rLa~IpG---Km----RKrIWI~~GD~VlVel~~~d 85 (145)
T PLN00208 28 FKEDGQ-EYAQVLRMLGNGRCEALC--IDG------TKRLCHIRG---KM----RKKVWIAAGDIILVGLRDYQ 85 (145)
T ss_pred cCCCCc-EEEEEEEEcCCCEEEEEE--CCC------CEEEEEEec---cc----eeeEEecCCCEEEEEccCCC
Confidence 466665 89999999665 444444 222 222222211 01 11344679999999865554
No 287
>TIGR00595 priA primosomal protein N'. All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=31.81 E-value=31 Score=32.33 Aligned_cols=26 Identities=12% Similarity=0.161 Sum_probs=15.6
Q ss_pred ec-CCCceeEE-ccCCeEEeCCCCCEEe
Q 029155 165 ES-TAGGTMVP-ISWTEMQCPLTGQTEQ 190 (198)
Q Consensus 165 ~~-~~g~~m~~-~~~~~~~c~~cg~~e~ 190 (198)
.| .|+.+|.- .+.+.|.|..||..++
T Consensus 224 ~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~ 251 (505)
T TIGR00595 224 CCPNCDVSLTYHKKEGKLRCHYCGYQEP 251 (505)
T ss_pred CCCCCCCceEEecCCCeEEcCCCcCcCC
Confidence 45 56666642 2446787777776653
No 288
>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=31.67 E-value=29 Score=23.70 Aligned_cols=12 Identities=58% Similarity=1.038 Sum_probs=9.8
Q ss_pred CCCCCEEEEEEE
Q 029155 131 FRPGDIVRASVL 142 (198)
Q Consensus 131 ~~~GDiV~AkV~ 142 (198)
|.+||+|-||+-
T Consensus 1 f~~GdlVWaK~~ 12 (86)
T PF00855_consen 1 FRPGDLVWAKLK 12 (86)
T ss_dssp -STTEEEEEEET
T ss_pred CCCCCEEEEEeC
Confidence 689999999984
No 289
>PF10844 DUF2577: Protein of unknown function (DUF2577); InterPro: IPR022555 This family of proteins has no known function
Probab=31.53 E-value=1.3e+02 Score=21.80 Aligned_cols=20 Identities=30% Similarity=0.396 Sum_probs=14.8
Q ss_pred CCCCEEEEEEEEEecceEEEEE
Q 029155 75 EPGSVVIARVTKVMTRMASADI 96 (198)
Q Consensus 75 ~vGDiViG~V~~v~~~~~~V~I 96 (198)
++=++++|+|+++.+ ..+.|
T Consensus 15 ~p~~i~~G~V~s~~P--L~I~i 34 (100)
T PF10844_consen 15 NPVDIVIGTVVSVPP--LKIKI 34 (100)
T ss_pred CCceeEEEEEEeccc--EEEEE
Confidence 344668999999998 55665
No 290
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=31.42 E-value=24 Score=28.46 Aligned_cols=24 Identities=21% Similarity=0.205 Sum_probs=17.9
Q ss_pred EEec-CCCceeEEccCCeEEeCCCCCE
Q 029155 163 SAES-TAGGTMVPISWTEMQCPLTGQT 188 (198)
Q Consensus 163 ~a~~-~~g~~m~~~~~~~~~c~~cg~~ 188 (198)
.=+| .||....- -.--+||.||..
T Consensus 134 ~~vC~vCGy~~~g--e~P~~CPiCga~ 158 (166)
T COG1592 134 VWVCPVCGYTHEG--EAPEVCPICGAP 158 (166)
T ss_pred EEEcCCCCCcccC--CCCCcCCCCCCh
Confidence 5578 89988753 356789999954
No 291
>TIGR02827 RNR_anaer_Bdell anaerobic ribonucleoside-triphosphate reductase. Members of this family belong to the class III anaerobic ribonucleoside-triphosphate reductases (RNR). These glycine-radical-containing enzymes are oxygen-sensitive and operate under anaerobic conditions. The genes for this family are pair with genes for an acitivating protein that creates a glycine radical. Members of this family, though related, fall outside the scope of TIGR02487, a functionally equivalent protein set; no genome has members in both familes. Identification as RNR is supported by gene pairing with the activating protein, lack of other anaerobic RNR, and presence of an upstream regulatory element strongly conserved upstream of most RNR operons.
Probab=31.38 E-value=25 Score=33.83 Aligned_cols=24 Identities=17% Similarity=0.243 Sum_probs=16.5
Q ss_pred EEec-CCCceeEEccCCeEEeCCCCCEE
Q 029155 163 SAES-TAGGTMVPISWTEMQCPLTGQTE 189 (198)
Q Consensus 163 ~a~~-~~g~~m~~~~~~~~~c~~cg~~e 189 (198)
+++| .||... +...-.||.||..+
T Consensus 532 ~siC~~CGy~~---g~~~~~CP~CGs~~ 556 (586)
T TIGR02827 532 ITICNDCHHID---KRTLHRCPVCGSAN 556 (586)
T ss_pred CeecCCCCCcC---CCcCCcCcCCCCcc
Confidence 7789 899831 21236999999643
No 292
>TIGR00375 conserved hypothetical protein TIGR00375. The member of this family from Methanococcus jannaschii, MJ0043, is considerably longer and appears to contain an intein N-terminal to the region of homology.
Probab=30.81 E-value=17 Score=32.98 Aligned_cols=31 Identities=23% Similarity=0.309 Sum_probs=21.5
Q ss_pred CCCeeeEE-ec-CCCceeEEcc--CCeEEeCCCCCE
Q 029155 157 NDLGVVSA-ES-TAGGTMVPIS--WTEMQCPLTGQT 188 (198)
Q Consensus 157 ~~lGvv~a-~~-~~g~~m~~~~--~~~~~c~~cg~~ 188 (198)
+++|+=.- .| +|+..+.|.. -...+|| ||..
T Consensus 233 P~~GKYh~~~c~~C~~~~~~~~~~~~~~~Cp-CG~~ 267 (374)
T TIGR00375 233 PLLGKYHQTACEACGEPAVSEDAETACANCP-CGGR 267 (374)
T ss_pred cCCCccchhhhcccCCcCCchhhhhcCCCCC-CCCc
Confidence 56776544 36 8999887754 1137899 9987
No 293
>KOG2907 consensus RNA polymerase I transcription factor TFIIS, subunit A12.2/RPA12 [Transcription]
Probab=30.78 E-value=29 Score=26.19 Aligned_cols=31 Identities=16% Similarity=0.156 Sum_probs=20.9
Q ss_pred eeeEEec-CCCce------eEEccC---C--eEEeCCCCCEEe
Q 029155 160 GVVSAES-TAGGT------MVPISW---T--EMQCPLTGQTEQ 190 (198)
Q Consensus 160 Gvv~a~~-~~g~~------m~~~~~---~--~~~c~~cg~~e~ 190 (198)
-||.-+| +||++ |+-+|- + -..||+|+.++.
T Consensus 71 a~I~~kCpkCghe~m~Y~T~QlRSADEGQTVFYTC~kC~~k~~ 113 (116)
T KOG2907|consen 71 AVIKHKCPKCGHEEMSYHTLQLRSADEGQTVFYTCPKCKYKFT 113 (116)
T ss_pred cchhccCcccCCchhhhhhhhcccccCCceEEEEcCccceeee
Confidence 4788889 89987 333331 2 246999998874
No 294
>COG1792 MreC Cell shape-determining protein [Cell envelope biogenesis, outer membrane]
Probab=30.64 E-value=2.2e+02 Score=24.62 Aligned_cols=20 Identities=10% Similarity=0.230 Sum_probs=18.1
Q ss_pred EEEEEEEEecceEEEEEeee
Q 029155 80 VIARVTKVMTRMASADIMCV 99 (198)
Q Consensus 80 ViG~V~~v~~~~~~V~I~~v 99 (198)
++|+|+.|..+...|.++.-
T Consensus 156 LVG~V~~V~~~tS~V~Lltd 175 (284)
T COG1792 156 LVGKVVEVSKNTSRVLLLTD 175 (284)
T ss_pred eEEEEEEEcCceeEEEEeec
Confidence 79999999999999999764
No 295
>PRK10445 endonuclease VIII; Provisional
Probab=30.61 E-value=41 Score=28.76 Aligned_cols=22 Identities=23% Similarity=0.297 Sum_probs=14.7
Q ss_pred ec-CCCceeEEc---cCCeEEeCCCC
Q 029155 165 ES-TAGGTMVPI---SWTEMQCPLTG 186 (198)
Q Consensus 165 ~~-~~g~~m~~~---~~~~~~c~~cg 186 (198)
.| .||.++... +-.+..||+|.
T Consensus 237 ~Cp~Cg~~I~~~~~~gR~t~~CP~CQ 262 (263)
T PRK10445 237 ACERCGGIIEKTTLSSRPFYWCPGCQ 262 (263)
T ss_pred CCCCCCCEeEEEEECCCCcEECCCCc
Confidence 46 688776544 34578888885
No 296
>PRK08665 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=30.53 E-value=29 Score=34.39 Aligned_cols=23 Identities=13% Similarity=0.169 Sum_probs=19.3
Q ss_pred ec-CCCceeEEccCCeEEeCCCCCE
Q 029155 165 ES-TAGGTMVPISWTEMQCPLTGQT 188 (198)
Q Consensus 165 ~~-~~g~~m~~~~~~~~~c~~cg~~ 188 (198)
.| .||..|+..++ =+.|+.||+.
T Consensus 726 ~Cp~Cg~~l~~~~G-C~~C~~CG~s 749 (752)
T PRK08665 726 ACPECGSILEHEEG-CVVCHSCGYS 749 (752)
T ss_pred CCCCCCcccEECCC-CCcCCCCCCC
Confidence 59 99999998775 4899999974
No 297
>PF12760 Zn_Tnp_IS1595: Transposase zinc-ribbon domain; InterPro: IPR024442 This zinc binding domain is found in a range of transposase proteins such as ISSPO8, ISSOD11, ISRSSP2 etc. It may be a zinc-binding beta ribbon domain that could bind DNA.
Probab=30.35 E-value=33 Score=21.18 Aligned_cols=17 Identities=24% Similarity=0.591 Sum_probs=12.9
Q ss_pred eEEeCCCCCEEeeeeCC
Q 029155 179 EMQCPLTGQTEQRKVAK 195 (198)
Q Consensus 179 ~~~c~~cg~~e~RKva~ 195 (198)
.+.||.||..+-.+++.
T Consensus 18 g~~CP~Cg~~~~~~~~~ 34 (46)
T PF12760_consen 18 GFVCPHCGSTKHYRLKT 34 (46)
T ss_pred CCCCCCCCCeeeEEeCC
Confidence 47799999887666654
No 298
>COG2824 PhnA Uncharacterized Zn-ribbon-containing protein involved in phosphonate metabolism [Inorganic ion transport and metabolism]
Probab=30.26 E-value=40 Score=25.27 Aligned_cols=25 Identities=8% Similarity=0.143 Sum_probs=18.2
Q ss_pred Eec-CCCceeEEccCCeEEeCCCCCE
Q 029155 164 AES-TAGGTMVPISWTEMQCPLTGQT 188 (198)
Q Consensus 164 a~~-~~g~~m~~~~~~~~~c~~cg~~ 188 (198)
..| .|...-+--....|.||+|++.
T Consensus 4 p~cp~c~sEytYed~~~~~cpec~~e 29 (112)
T COG2824 4 PPCPKCNSEYTYEDGGQLICPECAHE 29 (112)
T ss_pred CCCCccCCceEEecCceEeCchhccc
Confidence 357 6776665566668999999864
No 299
>COG3809 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=30.15 E-value=42 Score=23.84 Aligned_cols=23 Identities=17% Similarity=0.085 Sum_probs=15.4
Q ss_pred ec-CCCceeEEcc---CCeEEeCCCCC
Q 029155 165 ES-TAGGTMVPIS---WTEMQCPLTGQ 187 (198)
Q Consensus 165 ~~-~~g~~m~~~~---~~~~~c~~cg~ 187 (198)
+| .|+..|++.. -..=+||.|+-
T Consensus 3 lCP~C~v~l~~~~rs~vEiD~CPrCrG 29 (88)
T COG3809 3 LCPICGVELVMSVRSGVEIDYCPRCRG 29 (88)
T ss_pred ccCcCCceeeeeeecCceeeeCCcccc
Confidence 47 7888877652 22458999874
No 300
>PRK04012 translation initiation factor IF-1A; Provisional
Probab=30.11 E-value=2.2e+02 Score=20.82 Aligned_cols=58 Identities=21% Similarity=0.330 Sum_probs=33.0
Q ss_pred CCCCCCEEEEEEEEEecc-eEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeCC
Q 029155 73 VPEPGSVVIARVTKVMTR-MASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGD 146 (198)
Q Consensus 73 ~p~vGDiViG~V~~v~~~-~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~~ 146 (198)
.|..| -++|+|+...++ .+.|.. -++. ...+.|+ . ... .+=.+++||.|.+.....++
T Consensus 17 ~p~e~-e~~g~V~~~lG~~~~~V~~--~dG~----~~la~i~--G----K~R---k~IwI~~GD~VlVe~~~~~~ 75 (100)
T PRK04012 17 MPEEG-EVFGVVEQMLGANRVRVRC--MDGV----ERMGRIP--G----KMK---KRMWIREGDVVIVAPWDFQD 75 (100)
T ss_pred CCCCC-EEEEEEEEEcCCCEEEEEe--CCCC----EEEEEEc--h----hhc---ccEEecCCCEEEEEecccCC
Confidence 35544 589999999664 455555 2221 1222222 1 111 13446799999999877653
No 301
>PRK13945 formamidopyrimidine-DNA glycosylase; Provisional
Probab=29.92 E-value=38 Score=29.21 Aligned_cols=23 Identities=17% Similarity=0.290 Sum_probs=16.1
Q ss_pred Eec-CCCceeEEc---cCCeEEeCCCC
Q 029155 164 AES-TAGGTMVPI---SWTEMQCPLTG 186 (198)
Q Consensus 164 a~~-~~g~~m~~~---~~~~~~c~~cg 186 (198)
..| .||.++... +-....||.|.
T Consensus 255 ~pC~~Cg~~I~~~~~~gR~t~~CP~CQ 281 (282)
T PRK13945 255 KPCRKCGTPIERIKLAGRSTHWCPNCQ 281 (282)
T ss_pred CCCCcCCCeeEEEEECCCccEECCCCc
Confidence 357 788887543 35688898885
No 302
>PRK00004 rplX 50S ribosomal protein L24; Reviewed
Probab=29.91 E-value=2.2e+02 Score=20.87 Aligned_cols=19 Identities=21% Similarity=0.218 Sum_probs=13.9
Q ss_pred EEEEEEEecceEEEEEeee
Q 029155 81 IARVTKVMTRMASADIMCV 99 (198)
Q Consensus 81 iG~V~~v~~~~~~V~I~~v 99 (198)
+|+|.+|......|-+-.+
T Consensus 22 ~G~V~~V~~~~~~V~Vegv 40 (105)
T PRK00004 22 RGKVLKVLPKKNKVIVEGV 40 (105)
T ss_pred EEEEEEEEcCCCEEEEcCc
Confidence 5999999877666666443
No 303
>TIGR03779 Bac_Flav_CT_M Bacteroides conjugative transposon TraM protein. Members of this protein family are designated TraM and are found in a proposed transfer region of a class of conjugative transposon found in the Bacteroides lineage.
Probab=29.90 E-value=3.2e+02 Score=25.22 Aligned_cols=56 Identities=13% Similarity=0.201 Sum_probs=40.4
Q ss_pred ceEEEEeEeeeEEEcCCCCCCCCCCCeEEEe---cCC-CCCCCCCCCCEEEEEEEEEecceEEEEEeeec
Q 029155 35 NGLVYASLTGLLRTLSPPPDSPDQRPTVEVT---GHK-AHGPVPEPGSVVIARVTKVMTRMASADIMCVG 100 (198)
Q Consensus 35 ~~~i~asv~G~v~~~~~~~~~~~~~~~i~V~---p~~-~~~~~p~vGDiViG~V~~v~~~~~~V~I~~v~ 100 (198)
..+|+|.+-|......+ ..|..+ |.. ....+|+ |..|+|. .++......+.|.++.
T Consensus 255 ~n~I~A~V~~~qtv~~G--------~~vrlRLle~~~v~~~~ipk-gt~l~g~-~~~~g~R~~i~I~si~ 314 (410)
T TIGR03779 255 RNTIRACVHETQTVVDG--------SAVKLRLLEPIQAGDLVIPK-GTVLYGT-AKIQGERLDIKISSIE 314 (410)
T ss_pred CCceEEEEcCceEEecC--------CEEEEEEcCceeeCCEEecC-CCEEEEE-eeeccceEEEEEEEEE
Confidence 35699999999888642 344433 221 2345655 9999999 9999999999998764
No 304
>TIGR00577 fpg formamidopyrimidine-DNA glycosylase (fpg). All proteins in the FPG family with known functions are FAPY-DNA glycosylases that function in base excision repair. Homologous to endonuclease VIII (nei). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=29.70 E-value=40 Score=28.93 Aligned_cols=21 Identities=19% Similarity=0.322 Sum_probs=14.1
Q ss_pred ec-CCCceeEEc---cCCeEEeCCC
Q 029155 165 ES-TAGGTMVPI---SWTEMQCPLT 185 (198)
Q Consensus 165 ~~-~~g~~m~~~---~~~~~~c~~c 185 (198)
.| .||.++... +-....||.|
T Consensus 247 pC~~Cg~~I~~~~~~gR~t~~CP~C 271 (272)
T TIGR00577 247 PCRRCGTPIEKIKVGGRGTHFCPQC 271 (272)
T ss_pred CCCCCCCeeEEEEECCCCCEECCCC
Confidence 46 688776443 3457888888
No 305
>PRK14350 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=29.44 E-value=47 Score=32.50 Aligned_cols=62 Identities=10% Similarity=0.193 Sum_probs=36.7
Q ss_pred ccCCCCCCEEEEEEEEeCCCccEE----EEEecCCCeeeEEec-CCCceeEEccCCeEEeCC--CCCEEeeee
Q 029155 128 HLSFRPGDIVRASVLSLGDARAYF----LSTAKNDLGVVSAES-TAGGTMVPISWTEMQCPL--TGQTEQRKV 193 (198)
Q Consensus 128 ~~~~~~GDiV~AkV~s~~~~~~~~----LSt~~~~lGvv~a~~-~~g~~m~~~~~~~~~c~~--cg~~e~RKv 193 (198)
+.-+++||.|. |...++--+.. ...+...+ ++-..| .||.+++. +...+.|++ |-..-.+++
T Consensus 362 ~~di~iGD~V~--V~raGdVIP~I~~v~~~~r~~~~-~~P~~CP~C~s~l~~-~~~~~~C~n~~C~aq~~~~i 430 (669)
T PRK14350 362 SIGLNVGDVVK--ISRRGDVIPAVELVIEKLSVGFF-KIPDNCPSCKTALIK-EGAHLFCVNNHCPSVIVERI 430 (669)
T ss_pred HcCCCCCCEEE--EEecCCCCCceeeecccccCCCC-CCCCCCCCCCCEeee-CCEEEEECCCCCHHHHHhhh
Confidence 34578999984 55555542222 22232222 234468 89999986 346899974 765555544
No 306
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=29.43 E-value=29 Score=17.56 Aligned_cols=13 Identities=31% Similarity=0.810 Sum_probs=10.1
Q ss_pred EEeCCCCCEEeee
Q 029155 180 MQCPLTGQTEQRK 192 (198)
Q Consensus 180 ~~c~~cg~~e~RK 192 (198)
..|+.|++.-.++
T Consensus 1 y~C~~C~~~f~~~ 13 (23)
T PF00096_consen 1 YKCPICGKSFSSK 13 (23)
T ss_dssp EEETTTTEEESSH
T ss_pred CCCCCCCCccCCH
Confidence 3799999887665
No 307
>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=29.42 E-value=1.5e+02 Score=20.67 Aligned_cols=31 Identities=16% Similarity=0.353 Sum_probs=20.9
Q ss_pred ccCCCCCCEEEEEEE--EeCC------CccEEEEEecCC
Q 029155 128 HLSFRPGDIVRASVL--SLGD------ARAYFLSTAKND 158 (198)
Q Consensus 128 ~~~~~~GDiV~AkV~--s~~~------~~~~~LSt~~~~ 158 (198)
+..++|||.|..+++ ..+. ...+.|.+..++
T Consensus 8 r~iYrPGetV~~~~~~~~~~~~~~~~~~~~~~v~i~dp~ 46 (99)
T PF01835_consen 8 RPIYRPGETVHFRAIVRDLDNDFKPPANSPVTVTIKDPS 46 (99)
T ss_dssp SSEE-TTSEEEEEEEEEEECTTCSCESSEEEEEEEEETT
T ss_pred ccCcCCCCEEEEEEEEeccccccccccCCceEEEEECCC
Confidence 578899999999998 4431 134677777763
No 308
>PRK08059 general stress protein 13; Validated
Probab=29.41 E-value=1.4e+02 Score=22.28 Aligned_cols=33 Identities=18% Similarity=0.366 Sum_probs=22.8
Q ss_pred cCCCCCCEEEEEEEEeCCCccEEEEEecCCCeee
Q 029155 129 LSFRPGDIVRASVLSLGDARAYFLSTAKNDLGVV 162 (198)
Q Consensus 129 ~~~~~GDiV~AkV~s~~~~~~~~LSt~~~~lGvv 162 (198)
..+++||++.|+|.++.+. .+.+.+...--|.+
T Consensus 3 ~~~k~G~iv~G~V~~i~~~-G~fV~i~~~~~Gli 35 (123)
T PRK08059 3 SQYEVGSVVTGKVTGIQPY-GAFVALDEETQGLV 35 (123)
T ss_pred ccCCCCCEEEEEEEEEecc-eEEEEECCCCEEEE
Confidence 4478999999999999753 46666654333433
No 309
>COG2996 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only]
Probab=29.34 E-value=1.9e+02 Score=25.30 Aligned_cols=25 Identities=20% Similarity=-0.041 Sum_probs=22.2
Q ss_pred CCCCCCEEEEEEEEEe-cceEEEEEe
Q 029155 73 VPEPGSVVIARVTKVM-TRMASADIM 97 (198)
Q Consensus 73 ~p~vGDiViG~V~~v~-~~~~~V~I~ 97 (198)
..++|+.-.++|++++ .-++++|..
T Consensus 70 ~~tvg~~g~~~Vv~v~~~lGaFlD~G 95 (287)
T COG2996 70 KATVGEYGWLKVVEVNKDLGAFLDWG 95 (287)
T ss_pred eEeecceeEEEEEEEcCCcceEEecC
Confidence 4589999999999999 789999993
No 310
>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=29.03 E-value=1.3e+02 Score=19.36 Aligned_cols=54 Identities=20% Similarity=0.365 Sum_probs=32.6
Q ss_pred CEEEEEEEEEecceEEEEEee-eccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEE
Q 029155 78 SVVIARVTKVMTRMASADIMC-VGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLS 143 (198)
Q Consensus 78 DiViG~V~~v~~~~~~V~I~~-v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s 143 (198)
...-|+|.++......+++.. .++ ...+.+.++.+.+. +-.|++||-|.|.+.+
T Consensus 7 N~l~g~I~~i~~~g~~~~v~l~~~~---~~~l~a~i~~~~~~---------~l~l~~G~~v~~~ik~ 61 (69)
T TIGR00638 7 NQLKGKVVAIEDGDVNAEVDLLLGG---GTKLTAVITLESVA---------ELGLKPGKEVYAVIKA 61 (69)
T ss_pred cEEEEEEEEEEECCCeEEEEEEECC---CCEEEEEecHHHHh---------hCCCCCCCEEEEEEEC
Confidence 457899999966655555532 111 11355555443321 2447899999999865
No 311
>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=28.87 E-value=38 Score=23.91 Aligned_cols=15 Identities=27% Similarity=0.430 Sum_probs=12.5
Q ss_pred CCCCCEEEEEEEEeC
Q 029155 131 FRPGDIVRASVLSLG 145 (198)
Q Consensus 131 ~~~GDiV~AkV~s~~ 145 (198)
|.+||+|-||+...-
T Consensus 1 f~~gdlVWaK~~g~P 15 (80)
T cd06080 1 FEKNDLVWAKIQGYP 15 (80)
T ss_pred CCCCCEEEEeCCCCC
Confidence 689999999987653
No 312
>PRK09376 rho transcription termination factor Rho; Provisional
Probab=28.68 E-value=62 Score=29.86 Aligned_cols=71 Identities=13% Similarity=0.096 Sum_probs=45.6
Q ss_pred eeeCCCEEEe--CCceEEEEeEeeeEEEcCCCCCCCCCCCeEEEecCCCCCCCCCCCCEEEEEEEEEe---cceEEEEEe
Q 029155 23 VKAGKGAYVA--KHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHKAHGPVPEPGSVVIARVTKVM---TRMASADIM 97 (198)
Q Consensus 23 ~~~G~Gty~~--~g~~~i~asv~G~v~~~~~~~~~~~~~~~i~V~p~~~~~~~p~vGDiViG~V~~v~---~~~~~V~I~ 97 (198)
...+.|+.+. +|+|-+++.-.+.... ..-|+|.|..-+++-++.||.|.|.|..-. ...+.+.|.
T Consensus 48 ~~~~~g~le~~~~g~gflr~~~~~y~~~----------~~d~yvs~~~ir~~~lr~gd~v~g~~r~~~~~e~~~~l~~v~ 117 (416)
T PRK09376 48 DIFGEGVLEILPDGFGFLRSPDANYLPG----------PDDIYVSPSQIRRFNLRTGDTVEGKIRPPKEGERYFALLKVE 117 (416)
T ss_pred ceEEEEEEEEcCCCCeEEeCCCcCCCCC----------CCCeeeCHHHHHhcCCCCCCEEEEEeeCCCCCCCccceEEEe
Confidence 4456666543 3444455544443322 124788876556788999999999998642 335888888
Q ss_pred eecccc
Q 029155 98 CVGAKS 103 (198)
Q Consensus 98 ~v~~~~ 103 (198)
.+++.+
T Consensus 118 ~vng~~ 123 (416)
T PRK09376 118 TVNGED 123 (416)
T ss_pred eeCCCC
Confidence 888754
No 313
>cd03528 Rieske_RO_ferredoxin Rieske non-heme iron oxygenase (RO) family, Rieske ferredoxin component; composed of the Rieske ferredoxin component of some three-component RO systems including biphenyl dioxygenase (BPDO) and carbazole 1,9a-dioxygenase (CARDO). The RO family comprise a large class of aromatic ring-hydroxylating dioxygenases found predominantly in microorganisms. These enzymes enable microorganisms to tolerate and even exclusively utilize aromatic compounds for growth. ROs consist of two or three components: reductase, oxygenase, and ferredoxin (in some cases) components. The ferredoxin component contains either a plant-type or Rieske-type [2Fe-2S] cluster. The Rieske ferredoxin component in this family carries an electron from the RO reductase component to the terminal RO oxygenase component. BPDO degrades biphenyls and polychlorinated biphenyls. BPDO ferredoxin (BphF) has structural features consistent with a minimal and perhaps archetypical Rieske protein in that the in
Probab=28.55 E-value=1.4e+02 Score=20.70 Aligned_cols=56 Identities=14% Similarity=0.244 Sum_probs=30.9
Q ss_pred CCCCCEEEEEEEEeCCCccEEEEEecCCCeeeEEec-CCCceeEE--ccCCeEEeCCCCCEEe
Q 029155 131 FRPGDIVRASVLSLGDARAYFLSTAKNDLGVVSAES-TAGGTMVP--ISWTEMQCPLTGQTEQ 190 (198)
Q Consensus 131 ~~~GDiV~AkV~s~~~~~~~~LSt~~~~lGvv~a~~-~~g~~m~~--~~~~~~~c~~cg~~e~ 190 (198)
|.+|+.+..++. +..+.|.-.+.++-.+.++| -.|.+|.. ...+.+.||--|+.-.
T Consensus 10 l~~g~~~~~~~~----g~~~~v~r~~~~~~a~~~~CpH~g~~L~~g~~~~~~i~Cp~Hg~~fd 68 (98)
T cd03528 10 LPEGEPKRVDVG----GRPIAVYRVDGEFYATDDLCTHGDASLSEGYVEGGVIECPLHGGRFD 68 (98)
T ss_pred cCCCCEEEEEEC----CeEEEEEEECCEEEEECCcCCCCCCCCCCCeEeCCEEEeCCcCCEEE
Confidence 467887766553 34555543333333444445 34555532 2345899998777653
No 314
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=28.23 E-value=33 Score=22.00 Aligned_cols=12 Identities=25% Similarity=0.393 Sum_probs=9.7
Q ss_pred CCeEEeCCCCCE
Q 029155 177 WTEMQCPLTGQT 188 (198)
Q Consensus 177 ~~~~~c~~cg~~ 188 (198)
.....||+||+.
T Consensus 44 ~~i~~Cp~CgRi 55 (56)
T PF02591_consen 44 DEIVFCPNCGRI 55 (56)
T ss_pred CCeEECcCCCcc
Confidence 357999999974
No 315
>COG4873 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=28.14 E-value=1.1e+02 Score=21.13 Aligned_cols=26 Identities=19% Similarity=0.304 Sum_probs=21.4
Q ss_pred CCCCCEE------EEEEEEEecceEEEEEeee
Q 029155 74 PEPGSVV------IARVTKVMTRMASADIMCV 99 (198)
Q Consensus 74 p~vGDiV------iG~V~~v~~~~~~V~I~~v 99 (198)
.++|+++ .|+|.+++.+.+.||+.--
T Consensus 24 a~vgniief~dgl~g~vek~nensvivdlt~m 55 (81)
T COG4873 24 AKVGNIIEFKDGLTGVVEKVNENSVIVDLTIM 55 (81)
T ss_pred eeccceEEEcccceeeeeeecCCcEEEEEEee
Confidence 4667776 7999999999999999543
No 316
>cd03474 Rieske_T4moC Toluene-4-monooxygenase effector protein complex (T4mo), Rieske ferredoxin subunit; The Rieske domain is a [2Fe-2S] cluster binding domain involved in electron transfer. T4mo is a four-protein complex that catalyzes the NADH- and O2-dependent hydroxylation of toluene to form p-cresol. T4mo consists of an NADH oxidoreductase (T4moF), a diiron hydroxylase (T4moH), a catalytic effector protein (T4moD), and a Rieske ferredoxin (T4moC). T4moC contains a Rieske domain and functions as an obligate electron carrier between T4moF and T4moH. Rieske ferredoxins are found as subunits of membrane oxidase complexes, cis-dihydrodiol-forming aromatic dioxygenases, bacterial assimilatory nitrite reductases, and arsenite oxidase. Rieske ferredoxins are also found as soluble electron carriers in bacterial dioxygenase and monooxygenase complexes.
Probab=28.13 E-value=2e+02 Score=20.41 Aligned_cols=57 Identities=5% Similarity=0.059 Sum_probs=29.3
Q ss_pred CCCCCEEEEEEEEeCCCccEEEEEecCCCeeeEEec-CCCceeEE--ccCCeEEeCCCCCEEe
Q 029155 131 FRPGDIVRASVLSLGDARAYFLSTAKNDLGVVSAES-TAGGTMVP--ISWTEMQCPLTGQTEQ 190 (198)
Q Consensus 131 ~~~GDiV~AkV~s~~~~~~~~LSt~~~~lGvv~a~~-~~g~~m~~--~~~~~~~c~~cg~~e~ 190 (198)
|..|+.+..++ ++...+.+...+.++-.+...| --|.+|.. .+.+.+.||--|+.-.
T Consensus 10 l~~g~~~~~~~---~~~~~~~~~~~~g~~~A~~n~CpH~g~~L~~g~~~g~~i~CP~Hg~~Fd 69 (108)
T cd03474 10 VWEGEMELVDV---DGEEVLLVAPEGGEFRAFQGICPHQEIPLAEGGFDGGVLTCRAHLWQFD 69 (108)
T ss_pred cCCCceEEEEE---CCeEEEEEEccCCeEEEEcCcCCCCCCCcccCcccCCEEEeCCcCCEEE
Confidence 45677666554 2222233333344455555555 23444432 2345899997776543
No 317
>PRK08270 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=28.11 E-value=26 Score=34.07 Aligned_cols=21 Identities=24% Similarity=0.240 Sum_probs=15.6
Q ss_pred EEec-CCCceeEEccCCeEEeCCCCC
Q 029155 163 SAES-TAGGTMVPISWTEMQCPLTGQ 187 (198)
Q Consensus 163 ~a~~-~~g~~m~~~~~~~~~c~~cg~ 187 (198)
+..| .||.. ......||.||+
T Consensus 626 ~~~C~~CG~~----~g~~~~CP~CG~ 647 (656)
T PRK08270 626 FSICPKHGYL----SGEHEFCPKCGE 647 (656)
T ss_pred CcccCCCCCc----CCCCCCCcCCcC
Confidence 5678 89973 234678999995
No 318
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=28.08 E-value=27 Score=21.11 Aligned_cols=10 Identities=40% Similarity=0.893 Sum_probs=7.5
Q ss_pred EeCCCCCEEe
Q 029155 181 QCPLTGQTEQ 190 (198)
Q Consensus 181 ~c~~cg~~e~ 190 (198)
.||+||..|-
T Consensus 2 ~Cp~C~~~~a 11 (40)
T smart00440 2 PCPKCGNREA 11 (40)
T ss_pred cCCCCCCCeE
Confidence 6888887664
No 319
>PRK11827 hypothetical protein; Provisional
Probab=28.08 E-value=58 Score=21.75 Aligned_cols=25 Identities=16% Similarity=0.181 Sum_probs=18.0
Q ss_pred c-CCCceeEEc-cCCeEEeCCCCCEEe
Q 029155 166 S-TAGGTMVPI-SWTEMQCPLTGQTEQ 190 (198)
Q Consensus 166 ~-~~g~~m~~~-~~~~~~c~~cg~~e~ 190 (198)
| .|.+++... ..+++.|..|+...+
T Consensus 11 CP~ckg~L~~~~~~~~Lic~~~~laYP 37 (60)
T PRK11827 11 CPVCNGKLWYNQEKQELICKLDNLAFP 37 (60)
T ss_pred CCCCCCcCeEcCCCCeEECCccCeecc
Confidence 6 787777653 346899999987543
No 320
>PRK14704 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=27.75 E-value=28 Score=33.66 Aligned_cols=23 Identities=13% Similarity=0.242 Sum_probs=15.9
Q ss_pred EEec-CCCceeEEccCCeEEeCCCCCEE
Q 029155 163 SAES-TAGGTMVPISWTEMQCPLTGQTE 189 (198)
Q Consensus 163 ~a~~-~~g~~m~~~~~~~~~c~~cg~~e 189 (198)
+.+| .||. . +.....||.||..+
T Consensus 559 ~~~C~~CGy-~---g~~~~~CP~CG~~d 582 (618)
T PRK14704 559 VDRCKCCSY-H---GVIGNECPSCGNED 582 (618)
T ss_pred CeecCCCCC-C---CCcCccCcCCCCCC
Confidence 5688 8996 2 21236899999764
No 321
>PTZ00329 eukaryotic translation initiation factor 1A; Provisional
Probab=27.70 E-value=1.8e+02 Score=23.12 Aligned_cols=56 Identities=20% Similarity=0.192 Sum_probs=29.9
Q ss_pred CCCCCCEEEEEEEEEecce-EEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEe
Q 029155 73 VPEPGSVVIARVTKVMTRM-ASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSL 144 (198)
Q Consensus 73 ~p~vGDiViG~V~~v~~~~-~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~ 144 (198)
.|..|+ ++|+|++..++. ..|.+ .++.. ..+.|+ - ... .+=.+.+||+|.+..-..
T Consensus 28 ~~eegq-~~g~V~~~LGn~~f~V~c--~dG~~----rLa~I~--G----KmR---K~IWI~~GD~VlVel~~y 84 (155)
T PTZ00329 28 FKEEGQ-EYAQVLRMLGNGRLEAYC--FDGVK----RLCHIR--G----KMR---KRVWINIGDIILVSLRDF 84 (155)
T ss_pred cCCCCc-EEEEEEEEcCCCEEEEEE--CCCCE----EEEEee--c----cce---eeEEecCCCEEEEeccCC
Confidence 356666 799999997653 44444 23221 222221 1 100 123467899998876443
No 322
>TIGR01053 LSD1 zinc finger domain, LSD1 subclass. This model describes a putative zinc finger domain found in three closely spaced copies in Arabidopsis protein LSD1 and in two copies in other proteins from the same species. The motif resembles CxxCRxxLMYxxGASxVxCxxC
Probab=27.49 E-value=67 Score=18.45 Aligned_cols=23 Identities=17% Similarity=0.297 Sum_probs=18.2
Q ss_pred c-CCCce-eEEccCCeEEeCCCCCE
Q 029155 166 S-TAGGT-MVPISWTEMQCPLTGQT 188 (198)
Q Consensus 166 ~-~~g~~-m~~~~~~~~~c~~cg~~ 188 (198)
| .|+.. |+|.+-...+|..|..+
T Consensus 4 C~~C~t~L~yP~gA~~vrCs~C~~v 28 (31)
T TIGR01053 4 CGGCRTLLMYPRGASSVRCALCQTV 28 (31)
T ss_pred cCCCCcEeecCCCCCeEECCCCCeE
Confidence 5 57766 48888889999999765
No 323
>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=27.37 E-value=1.9e+02 Score=19.10 Aligned_cols=51 Identities=20% Similarity=0.208 Sum_probs=27.6
Q ss_pred CEEEEEEEEEecc-eEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEE
Q 029155 78 SVVIARVTKVMTR-MASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLS 143 (198)
Q Consensus 78 DiViG~V~~v~~~-~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s 143 (198)
+-++|+|++..++ .+.|.. .++ ....+.|+.. ... +=.+++||.|.+.+-.
T Consensus 3 ~e~~~~V~~~lG~~~~~V~~--~dg----~~~l~~i~gK-----~r~----~iwI~~GD~V~V~~~~ 54 (65)
T PF01176_consen 3 GEVIGRVTEMLGNNLFEVEC--EDG----EERLARIPGK-----FRK----RIWIKRGDFVLVEPSP 54 (65)
T ss_dssp TEEEEEEEEEESSSEEEEEE--TTS----EEEEEEE-HH-----HHT----CC---TTEEEEEEEST
T ss_pred cEEEEEEEEECCCCEEEEEe--CCC----CEEEEEeccc-----eee----eEecCCCCEEEEEecc
Confidence 4588999998664 555555 222 1233444432 112 2347899999888743
No 324
>PF09926 DUF2158: Uncharacterized small protein (DUF2158); InterPro: IPR019226 This entry represents a family of predominantly prokaryotic proteins with no known function.
Probab=27.25 E-value=43 Score=21.71 Aligned_cols=24 Identities=17% Similarity=0.342 Sum_probs=15.0
Q ss_pred CCCCCEEEEEEEEeCCCccEEEEEecCC
Q 029155 131 FRPGDIVRASVLSLGDARAYFLSTAKND 158 (198)
Q Consensus 131 ~~~GDiV~AkV~s~~~~~~~~LSt~~~~ 158 (198)
|++||+|+-|= .++.+.++..++.
T Consensus 1 f~~GDvV~LKS----GGp~MTV~~v~~~ 24 (53)
T PF09926_consen 1 FKIGDVVQLKS----GGPRMTVTEVGPN 24 (53)
T ss_pred CCCCCEEEEcc----CCCCeEEEEcccc
Confidence 78999987652 3455666654443
No 325
>PRK01103 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated
Probab=27.23 E-value=50 Score=28.32 Aligned_cols=23 Identities=17% Similarity=0.372 Sum_probs=15.3
Q ss_pred ec-CCCceeEEc---cCCeEEeCCCCC
Q 029155 165 ES-TAGGTMVPI---SWTEMQCPLTGQ 187 (198)
Q Consensus 165 ~~-~~g~~m~~~---~~~~~~c~~cg~ 187 (198)
.| .||.++... +-.+..||.|-.
T Consensus 247 pC~~Cg~~I~~~~~~gR~t~~CP~CQ~ 273 (274)
T PRK01103 247 PCRRCGTPIEKIKQGGRSTFFCPRCQK 273 (274)
T ss_pred CCCCCCCeeEEEEECCCCcEECcCCCC
Confidence 37 788776544 345788888864
No 326
>COG1862 YajC Preprotein translocase subunit YajC [Intracellular trafficking and secretion]
Probab=27.20 E-value=1.2e+02 Score=22.15 Aligned_cols=23 Identities=26% Similarity=0.341 Sum_probs=19.3
Q ss_pred CCCCCEE------EEEEEEEecceEEEEE
Q 029155 74 PEPGSVV------IARVTKVMTRMASADI 96 (198)
Q Consensus 74 p~vGDiV------iG~V~~v~~~~~~V~I 96 (198)
.++||-| .|+|++|.++...+++
T Consensus 44 L~kGD~VvT~gGi~G~V~~v~d~~v~I~l 72 (97)
T COG1862 44 LKKGDEVVTIGGIVGTVTKVGDDTVEIEL 72 (97)
T ss_pred ccCCCEEEEcCCeEEEEEEEecCcEEEEE
Confidence 5788887 7999999998866666
No 327
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]
Probab=26.17 E-value=1.2e+02 Score=20.80 Aligned_cols=29 Identities=24% Similarity=0.378 Sum_probs=18.7
Q ss_pred eeeEEec-CCCceeEEcc--CCeEEeCCCCCE
Q 029155 160 GVVSAES-TAGGTMVPIS--WTEMQCPLTGQT 188 (198)
Q Consensus 160 Gvv~a~~-~~g~~m~~~~--~~~~~c~~cg~~ 188 (198)
.=+.-.| .||+.-+=-+ -....|..||.+
T Consensus 16 ~Fl~VkCpdC~N~q~vFshast~V~C~~CG~~ 47 (67)
T COG2051 16 RFLRVKCPDCGNEQVVFSHASTVVTCLICGTT 47 (67)
T ss_pred eEEEEECCCCCCEEEEeccCceEEEecccccE
Confidence 3345567 7887754332 347888888876
No 328
>PF00467 KOW: KOW motif; InterPro: IPR005824 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 KOW (Kyprides, Ouzounis, Woese) motif is found in a variety of ribosomal proteins and the bacterial transcription antitermination proteins NusG []. ; PDB: 3BBO_W 2HGJ_X 2HGQ_X 2HGU_X 1NPP_B 1M1G_D 1NPR_A 2XHC_A 2KVQ_G 2JVV_A ....
Probab=26.14 E-value=1e+02 Score=17.33 Aligned_cols=16 Identities=6% Similarity=0.171 Sum_probs=11.5
Q ss_pred EEEEEEEEecceEEEE
Q 029155 80 VIARVTKVMTRMASAD 95 (198)
Q Consensus 80 ViG~V~~v~~~~~~V~ 95 (198)
-+|+|.++..+.+.|-
T Consensus 15 ~~G~I~~i~~~~~~V~ 30 (32)
T PF00467_consen 15 KIGKIVEIDRSKVRVT 30 (32)
T ss_dssp EEEEEEEEETTTTEEE
T ss_pred ceEEEEEEECCCCEEE
Confidence 4788888887765544
No 329
>PF13901 DUF4206: Domain of unknown function (DUF4206)
Probab=26.12 E-value=21 Score=29.40 Aligned_cols=24 Identities=17% Similarity=0.408 Sum_probs=10.7
Q ss_pred ecCCCceeEEccC-CeEEeCCCCCE
Q 029155 165 ESTAGGTMVPISW-TEMQCPLTGQT 188 (198)
Q Consensus 165 ~~~~g~~m~~~~~-~~~~c~~cg~~ 188 (198)
.|....++.|-.- +..+|++|+..
T Consensus 157 ~C~~~~~IfPF~~~~~~~C~~C~~v 181 (202)
T PF13901_consen 157 ICNSDDIIFPFQIDTTVRCPKCKSV 181 (202)
T ss_pred cCCCCCCCCCCCCCCeeeCCcCccc
Confidence 3333344555433 34555555543
No 330
>PF05180 zf-DNL: DNL zinc finger; InterPro: IPR007853 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The DNL-type zinc finger is found in Tim15, a zinc finger protein essential for protein import into mitochondria. Mitochondrial functions rely on the correct transport of resident proteins synthesized in the cytosol to mitochondria. Protein import into mitochondria is mediated by membrane protein complexes, protein translocators, in the outer and inner mitochondrial membranes, in cooperation with their assistant proteins in the cytosol, intermembrane space and matrix. Proteins destined to the mitochondrial matrix cross the outer membrane with the aid of the outer membrane translocator, the tOM40 complex, and then the inner membrane with the aid of the inner membrane translocator, the TIM23 complex, and mitochondrial motor and chaperone (MMC) proteins including mitochondrial heat- shock protein 70 (mtHsp70), and translocase in the inner mitochondrial membrane (Tim)15. Tim15 is also known as zinc finger motif (Zim)17 or mtHsp70 escort protein (Hep)1. Tim15 contains a zinc-finger motif (CXXC and CXXC) of ~100 residues, which has been named DNL after a short C-terminal motif of D(N/H)L [, , ]. The DNL-type zinc finger is an L-shaped molecule. The two CXXC motifs are located at the end of the L, and are sandwiched by two- stranded antiparallel beta-sheets. Two short alpha-helices constitute another leg of the L. The outer (convex) face of the L has a large acidic groove, which is lined with five acidic residues, whereas the inner (concave) face of the L has two positively charged residues, next to the CXXC motifs []. This entry represents the DNL-type zinc finger.; GO: 0008270 zinc ion binding; PDB: 2E2Z_A.
Probab=26.06 E-value=48 Score=22.60 Aligned_cols=17 Identities=18% Similarity=0.425 Sum_probs=13.6
Q ss_pred eEEeCCCCCEEeeeeCC
Q 029155 179 EMQCPLTGQTEQRKVAK 195 (198)
Q Consensus 179 ~~~c~~cg~~e~RKva~ 195 (198)
.+.|..|+.+..|.+|+
T Consensus 4 ~FTC~~C~~Rs~~~~sk 20 (66)
T PF05180_consen 4 TFTCNKCGTRSAKMFSK 20 (66)
T ss_dssp EEEETTTTEEEEEEEEH
T ss_pred EEEcCCCCCccceeeCH
Confidence 46788888888888876
No 331
>PRK14811 formamidopyrimidine-DNA glycosylase; Provisional
Probab=26.02 E-value=50 Score=28.32 Aligned_cols=24 Identities=17% Similarity=0.248 Sum_probs=17.6
Q ss_pred ec-CCCceeEEc---cCCeEEeCCCCCE
Q 029155 165 ES-TAGGTMVPI---SWTEMQCPLTGQT 188 (198)
Q Consensus 165 ~~-~~g~~m~~~---~~~~~~c~~cg~~ 188 (198)
.| +||.++... +-.+..||.|...
T Consensus 237 pC~~Cg~~I~~~~~~gR~ty~Cp~CQ~~ 264 (269)
T PRK14811 237 PCPRCGTPIEKIVVGGRGTHFCPQCQPL 264 (269)
T ss_pred CCCcCCCeeEEEEECCCCcEECCCCcCC
Confidence 47 799887544 3568899999754
No 332
>PRK14351 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=26.02 E-value=1.4e+02 Score=29.41 Aligned_cols=58 Identities=16% Similarity=0.161 Sum_probs=33.5
Q ss_pred ccCCCCCCEEEEEEEEeCCCccEEEE----EecCCCeeeEEec-CCCceeEEccCCeEEeCC---CCCEE
Q 029155 128 HLSFRPGDIVRASVLSLGDARAYFLS----TAKNDLGVVSAES-TAGGTMVPISWTEMQCPL---TGQTE 189 (198)
Q Consensus 128 ~~~~~~GDiV~AkV~s~~~~~~~~LS----t~~~~lGvv~a~~-~~g~~m~~~~~~~~~c~~---cg~~e 189 (198)
+.-+++||.|.. ...++--+.... .+...+ .+-..| .||++++. +...+.|++ |-..-
T Consensus 387 ~~di~iGD~V~V--~raGdVIPkI~~vv~~~~~~~~-~~P~~CP~C~~~l~~-~~~~~~C~n~~~Cpaq~ 452 (689)
T PRK14351 387 ELGVNVGDRVRV--KRAGDVIPYVEEVVEKDSEGTF-EFPDTCPVCDSAVER-DGPLAFCTGGLACPAQL 452 (689)
T ss_pred HcCCCCCCEEEE--EecCCccceeeeeecccCCCCC-cCCCCCCCCCCEeee-CCceEEcCCCCCCHHHH
Confidence 355789999864 344443222222 222223 344578 89999986 446788975 65433
No 333
>PF01096 TFIIS_C: Transcription factor S-II (TFIIS); InterPro: IPR001222 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIs (TFIIS). In eukaryotes the initiation of transcription of protein encoding genes by polymerase II (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least eight different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, -IIH and -IIS []. During mRNA elongation, Pol II can encounter DNA sequences that cause reverse movement of the enzyme. Such backtracking involves extrusion of the RNA 3'-end into the pore, and can lead to transcriptional arrest. Escape from arrest requires cleavage of the extruded RNA with the help of TFIIS, which induces mRNA cleavage by enhancing the intrinsic nuclease activity of RNA polymerase (Pol) II, past template-encoded pause sites []. TFIIS extends from the polymerase surface via a pore to the internal active site. Two essential and invariant acidic residues in a TFIIS loop complement the Pol II active site and could position a metal ion and a water molecule for hydrolytic RNA cleavage. TFIIS also induces extensive structural changes in Pol II that would realign nucleic acids in the active centre. TFIIS is a protein of about 300 amino acids. It contains three regions: a variable N-terminal domain not required for TFIIS activity; a conserved central domain required for Pol II binding; and a conserved C-terminal C4-type zinc finger essential for RNA cleavage. The zinc finger folds in a conformation termed a zinc ribbon [] characterised by a three-stranded antiparallel beta-sheet and two beta-hairpins. A backbone model for Pol II-TFIIS complex was obtained from X-ray analysis. It shows that a beta hairpin protrudes from the zinc finger and complements the pol II active site []. Some viral proteins also contain the TFIIS zinc ribbon C-terminal domain. The Vaccinia virus protein, unlike its eukaryotic homologue, is an integral RNA polymerase subunit rather than a readily separable transcription factor []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding, 0006351 transcription, DNA-dependent; PDB: 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I 3I4M_I ....
Probab=26.01 E-value=28 Score=20.90 Aligned_cols=10 Identities=40% Similarity=0.989 Sum_probs=5.5
Q ss_pred EeCCCCCEEe
Q 029155 181 QCPLTGQTEQ 190 (198)
Q Consensus 181 ~c~~cg~~e~ 190 (198)
.||+||..|-
T Consensus 2 ~Cp~Cg~~~a 11 (39)
T PF01096_consen 2 KCPKCGHNEA 11 (39)
T ss_dssp --SSS-SSEE
T ss_pred CCcCCCCCeE
Confidence 6999998764
No 334
>PF12647 RNHCP: RNHCP domain; InterPro: IPR024439 This domain is found in uncharacterised bacterial proteins. It is typically between 94 and 143 amino acids in length and has a conserved RNHCP sequence motif.
Probab=25.95 E-value=58 Score=23.71 Aligned_cols=30 Identities=30% Similarity=0.682 Sum_probs=19.5
Q ss_pred CCCceeEEcc--------CC-eEEeCCCCCEEeeeeCCC
Q 029155 167 TAGGTMVPIS--------WT-EMQCPLTGQTEQRKVAKV 196 (198)
Q Consensus 167 ~~g~~m~~~~--------~~-~~~c~~cg~~e~RKva~~ 196 (198)
.||+.|.|++ |. .-+|..||....=++|..
T Consensus 46 ~C~g~M~Pi~v~~~~~g~w~iiHrC~~Cg~l~~Nr~a~D 84 (92)
T PF12647_consen 46 DCGGRMEPIAVWVRRDGEWMIIHRCTRCGELRSNRIAAD 84 (92)
T ss_pred cCCCeeeEEEEEEEcCCCEEEEEecCCCCCcccCCCCCC
Confidence 4788887653 43 346888888766666543
No 335
>CHL00010 infA translation initiation factor 1
Probab=25.91 E-value=2.3e+02 Score=19.56 Aligned_cols=52 Identities=23% Similarity=0.300 Sum_probs=29.7
Q ss_pred EEEEEEEEe-cceEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeC
Q 029155 80 VIARVTKVM-TRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLG 145 (198)
Q Consensus 80 ViG~V~~v~-~~~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~ 145 (198)
+.|+|+++. ...+.|.. -++........|-++.+ .-...+||.|..++...+
T Consensus 9 ~~G~Vik~lg~~~y~V~~--~~g~~~~c~~rGklr~~------------~i~~~vGD~V~ve~~~~~ 61 (78)
T CHL00010 9 MEGLVTESLPNGMFRVRL--DNGCQVLGYISGKIRRN------------SIRILPGDRVKVELSPYD 61 (78)
T ss_pred EEEEEEEEcCCCEEEEEe--CCCCEEEEEeccceecC------------CcccCCCCEEEEEEcccC
Confidence 578999988 46676643 22222223344443311 122468999998875544
No 336
>PF11023 DUF2614: Protein of unknown function (DUF2614); InterPro: IPR020912 This entry describes proteins of unknown function, which are thought to be membrane proteins.; GO: 0005887 integral to plasma membrane
Probab=25.90 E-value=29 Score=26.19 Aligned_cols=26 Identities=15% Similarity=0.188 Sum_probs=17.4
Q ss_pred eEEec-CCCceeEEccCCeEEeCCCCCE
Q 029155 162 VSAES-TAGGTMVPISWTEMQCPLTGQT 188 (198)
Q Consensus 162 v~a~~-~~g~~m~~~~~~~~~c~~cg~~ 188 (198)
+.-.| .|+++-.-.+ .+-.|..|++.
T Consensus 68 v~V~CP~C~K~TKmLG-r~D~CM~C~~p 94 (114)
T PF11023_consen 68 VQVECPNCGKQTKMLG-RVDACMHCKEP 94 (114)
T ss_pred eeeECCCCCChHhhhc-hhhccCcCCCc
Confidence 34458 8888865444 45688888864
No 337
>PRK08271 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=25.34 E-value=32 Score=33.39 Aligned_cols=24 Identities=17% Similarity=0.249 Sum_probs=17.4
Q ss_pred EEec-CCCceeEEccCCeEEeCCCCCEE
Q 029155 163 SAES-TAGGTMVPISWTEMQCPLTGQTE 189 (198)
Q Consensus 163 ~a~~-~~g~~m~~~~~~~~~c~~cg~~e 189 (198)
+.+| .||.... ...-.||.||...
T Consensus 566 ~~iC~~CG~~~~---g~~~~CP~CGs~~ 590 (623)
T PRK08271 566 ITICNDCHHIDK---RTGKRCPICGSEN 590 (623)
T ss_pred CccCCCCCCcCC---CCCcCCcCCCCcc
Confidence 5678 8997642 2467899999753
No 338
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=25.30 E-value=1.2e+02 Score=25.35 Aligned_cols=32 Identities=13% Similarity=0.141 Sum_probs=23.8
Q ss_pred CCCCEEEEEEEEeCCCccEEEEEecCCCeeeEE
Q 029155 132 RPGDIVRASVLSLGDARAYFLSTAKNDLGVVSA 164 (198)
Q Consensus 132 ~~GDiV~AkV~s~~~~~~~~LSt~~~~lGvv~a 164 (198)
++||+|.++|.++.. ..+.+.+.+.-.|.+..
T Consensus 62 ~vGDiViG~V~~i~~-~~~~vdI~~~~~g~L~~ 93 (235)
T PRK04163 62 KVGDLVIGKVTDVTF-SGWEVDINSPYKAYLPV 93 (235)
T ss_pred CCCCEEEEEEEEEeC-ceEEEEeCCCceeEEEH
Confidence 799999999999965 35777776655555443
No 339
>PF11720 Inhibitor_I78: Peptidase inhibitor I78 family; InterPro: IPR021719 This family includes Aspergillus elastase inhibitor and belongs to MEROPS peptidase inhibitor family I78.
Probab=25.16 E-value=99 Score=20.22 Aligned_cols=35 Identities=11% Similarity=0.346 Sum_probs=22.8
Q ss_pred CcEEecCCccCCCCCeeeCCCEEEeCCceEEEEeEee
Q 029155 8 MVLVTPGEVLGKATEVKAGKGAYVAKHNGLVYASLTG 44 (198)
Q Consensus 8 ~~iV~PGd~l~~~~e~~~G~Gty~~~g~~~i~asv~G 44 (198)
-.++-||+.+. .+|.+..=....|..|.|.+.-+|
T Consensus 26 ~Rvi~Pg~~vT--mDyr~dRLnv~~D~~g~I~~v~CG 60 (60)
T PF11720_consen 26 VRVIRPGDAVT--MDYRPDRLNVEVDDDGVITRVRCG 60 (60)
T ss_pred eEEeCCCCcCc--ccCCCCcEEEEECCCCcEEEEecC
Confidence 35788999864 568888854444334447776665
No 340
>PF11520 Cren7: Chromatin protein Cren7; InterPro: IPR020906 Cren7 is a chromatin protein found in Crenarchaeota and has a higher affinity for double-stranded DNA than for single-stranded DNA. The protein contains negative DNA supercoils and is associated with genomic DNA in vivo. Cren7 interacts with duplex DNA through a beta-sheet and a long flexible loop. Its binding to double-stranded DNA is without sequence specificity. There is approximately 1 Cren7 molecule for 12 bp of DNA. The function of Cren7 has not been completely determined but it is thought that the protein may have a role similar to that of archaeal proteins in Euryarchaea [].; GO: 0003690 double-stranded DNA binding, 0005737 cytoplasm; PDB: 3KXT_A 3LWH_A 3LWI_A 2JTM_A.
Probab=24.99 E-value=65 Score=21.50 Aligned_cols=26 Identities=31% Similarity=0.351 Sum_probs=14.6
Q ss_pred CCceeEEccCCeEEeCCCCCEEeeeeCC
Q 029155 168 AGGTMVPISWTEMQCPLTGQTEQRKVAK 195 (198)
Q Consensus 168 ~g~~m~~~~~~~~~c~~cg~~e~RKva~ 195 (198)
.|..=+.++ .++||++|+.-++|+++
T Consensus 32 kGrkGV~ig--LFk~P~tGk~fR~~v~~ 57 (60)
T PF11520_consen 32 KGRKGVKIG--LFKDPETGKYFRKKVPD 57 (60)
T ss_dssp TTS--EEEE--EEE-TTT--EEEEEE-T
T ss_pred CCCCceEEE--EEeCCCCCcchhhhccc
Confidence 343333344 69999999999999976
No 341
>PRK12678 transcription termination factor Rho; Provisional
Probab=24.83 E-value=90 Score=30.47 Aligned_cols=43 Identities=16% Similarity=0.054 Sum_probs=32.3
Q ss_pred eEEEecCCCCCCCCCCCCEEEEEEEEEecc---------eEEEEEeeecccc
Q 029155 61 TVEVTGHKAHGPVPEPGSVVIARVTKVMTR---------MASADIMCVGAKS 103 (198)
Q Consensus 61 ~i~V~p~~~~~~~p~vGDiViG~V~~v~~~---------~~~V~I~~v~~~~ 103 (198)
-|+|.+..-+++-++.||.|.|.|..-... .+.+.|..|++.+
T Consensus 320 Dvyvs~~qirr~~Lr~Gd~v~G~vr~p~~~e~~~~r~k~~~l~~v~~vNg~~ 371 (672)
T PRK12678 320 DVYVSMNQVRKNGLRKGDAVTGAVRAPREGEQGNQRQKFNPLVRLDSVNGMS 371 (672)
T ss_pred CeeeCHHHHHHcCCCCCCEEEEeecCCCCCccccccceeeeeeeEeeeCCCC
Confidence 477776544577899999999999875433 4788888888754
No 342
>COG4530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=24.75 E-value=30 Score=26.16 Aligned_cols=36 Identities=25% Similarity=0.405 Sum_probs=27.8
Q ss_pred ecCCCeeeEEec-CCCceeEEccCCeEEeCCCCCEEee
Q 029155 155 AKNDLGVVSAES-TAGGTMVPISWTEMQCPLTGQTEQR 191 (198)
Q Consensus 155 ~~~~lGvv~a~~-~~g~~m~~~~~~~~~c~~cg~~e~R 191 (198)
+.++||-- -+| .||+..+-....-..||.||...+|
T Consensus 2 Ak~eLGtK-ridPetg~KFYDLNrdPiVsPytG~s~P~ 38 (129)
T COG4530 2 AKPELGTK-RIDPETGKKFYDLNRDPIVSPYTGKSYPR 38 (129)
T ss_pred Cccccccc-ccCccccchhhccCCCccccCcccccchH
Confidence 34566653 346 8999998888889999999998766
No 343
>COG1465 Predicted alternative 3-dehydroquinate synthase [Amino acid transport and metabolism]
Probab=24.23 E-value=1.5e+02 Score=26.39 Aligned_cols=49 Identities=20% Similarity=0.399 Sum_probs=32.2
Q ss_pred EEecCCccCCCCCeeeCCCEEEeCCceEEEEeEeeeEEEcCCCCCCCCCCCeEEEec
Q 029155 10 LVTPGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTG 66 (198)
Q Consensus 10 iV~PGd~l~~~~e~~~G~Gty~~~g~~~i~asv~G~v~~~~~~~~~~~~~~~i~V~p 66 (198)
+-+||..=-...|..+|.-+-.-+..|.-+++++|.+++. +++.+-|+.
T Consensus 268 i~vPg~kTkYLaEL~aGDeV~iVD~dGr~R~aiVGRvKIE--------rRPl~lIeA 316 (376)
T COG1465 268 IRVPGGKTKYLAELKAGDEVLIVDFDGRTRSAIVGRVKIE--------RRPLMLIEA 316 (376)
T ss_pred EEcCCCceEEhhhhcCCCeEEEEecCCceeEEEEEEEEee--------cCceEEEEE
Confidence 3467775444456667776554443344999999999994 466666653
No 344
>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=24.14 E-value=2.5e+02 Score=19.41 Aligned_cols=51 Identities=20% Similarity=0.165 Sum_probs=28.6
Q ss_pred EEEEEEEEecc-eEEEEEeeeccccccCcceeEEeccccccccccccccccCCCCCCEEEEEEEEeC
Q 029155 80 VIARVTKVMTR-MASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLG 145 (198)
Q Consensus 80 ViG~V~~v~~~-~~~V~I~~v~~~~l~~~~~G~l~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~ 145 (198)
++|+|++..++ .+.|.. -++. ...+.|+.. . ..+=.+++||.|.++....+
T Consensus 2 ~~g~V~~~~g~~~~~V~~--~~g~----~~la~i~gK-----~----rk~iwI~~GD~V~Ve~~~~d 53 (77)
T cd05793 2 EYGQVEKMLGNGRLEVRC--FDGK----KRLCRIRGK-----M----RKRVWINEGDIVLVAPWDFQ 53 (77)
T ss_pred EEEEEEEEcCCCEEEEEE--CCCC----EEEEEEchh-----h----cccEEEcCCCEEEEEecccc
Confidence 68999998664 455555 2221 222333211 1 11344679999999876554
No 345
>PRK01191 rpl24p 50S ribosomal protein L24P; Validated
Probab=24.06 E-value=1e+02 Score=23.52 Aligned_cols=45 Identities=18% Similarity=0.141 Sum_probs=27.2
Q ss_pred CCCCCEE----------EEEEEEEecceEEEEEeeeccc-cccCcceeEEeccccc
Q 029155 74 PEPGSVV----------IARVTKVMTRMASADIMCVGAK-SVREKFSGIIRQQDVR 118 (198)
Q Consensus 74 p~vGDiV----------iG~V~~v~~~~~~V~I~~v~~~-~l~~~~~G~l~~s~v~ 118 (198)
.++||.| .|+|++|......|-+-.++-. +-....++-||+|++.
T Consensus 46 IkkGD~V~VisG~~KGk~GkV~~V~~~~~~V~VeGvn~~k~~G~~~e~pIh~SNV~ 101 (120)
T PRK01191 46 VRKGDTVKVMRGDFKGEEGKVVEVDLKRGRIYVEGVTVKKADGTEVPRPIHPSNVM 101 (120)
T ss_pred EeCCCEEEEeecCCCCceEEEEEEEcCCCEEEEeCcEEECCCCeEEEcccchhHeE
Confidence 4566666 5999999777666666433311 1123456677777764
No 346
>PRK04023 DNA polymerase II large subunit; Validated
Probab=23.91 E-value=36 Score=34.86 Aligned_cols=18 Identities=22% Similarity=0.560 Sum_probs=0.0
Q ss_pred ec-CCCceeEEccCCeEEeCCCCC
Q 029155 165 ES-TAGGTMVPISWTEMQCPLTGQ 187 (198)
Q Consensus 165 ~~-~~g~~m~~~~~~~~~c~~cg~ 187 (198)
.| .||... ....||+||.
T Consensus 628 fCpsCG~~t-----~~frCP~CG~ 646 (1121)
T PRK04023 628 KCPSCGKET-----FYRRCPFCGT 646 (1121)
T ss_pred cCCCCCCcC-----CcccCCCCCC
No 347
>cd01675 RNR_III Class III ribonucleotide reductase. Ribonucleotide reductase (RNR) catalyzes the reductive synthesis of deoxyribonucleotides from their corresponding ribonucleotides. It provides the precursors necessary for DNA synthesis. RNRs are separated into three classes based on their metallocofactor usage. Class I RNRs, found in eukaryotes, bacteria, and bacteriophage, use a diiron-tyrosyl radical. Class II RNRs, found in bacteria, bacteriophage, algae and archaea, use coenzyme B12 (adenosylcobalamin, AdoCbl). Class III RNRs, found in strict or facultative anaerobic bacteria, bacteriophage, and archaea, use an FeS cluster and S-adenosylmethionine to generate a glycyl radical. Many organisms have more than one class of RNR present in their genomes. All three RNRs have a ten-stranded alpha-beta barrel domain that is structurally similar to the domain of PFL (pyruvate formate lyase). The class III enzyme from phage T4 consists of two subunits, this model covers the larger subunit w
Probab=23.84 E-value=33 Score=32.65 Aligned_cols=22 Identities=18% Similarity=0.283 Sum_probs=16.0
Q ss_pred ec-CCCceeEEccCCeEEeCCCCCEE
Q 029155 165 ES-TAGGTMVPISWTEMQCPLTGQTE 189 (198)
Q Consensus 165 ~~-~~g~~m~~~~~~~~~c~~cg~~e 189 (198)
+| .||.... ...-.||.||+..
T Consensus 520 ~C~~CG~~~~---~~~~~CP~CGs~~ 542 (555)
T cd01675 520 ICNDCGYIGE---GEGFKCPKCGSED 542 (555)
T ss_pred cCCCCCCCCc---CCCCCCcCCCCcC
Confidence 78 7997554 2457899999763
No 348
>PF01396 zf-C4_Topoisom: Topoisomerase DNA binding C4 zinc finger; InterPro: IPR013498 DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks []. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis [, ]. DNA topoisomerases are divided into two classes: type I enzymes (5.99.1.2 from EC; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (5.99.1.3 from EC; topoisomerases II, IV and VI) break double-strand DNA []. Type I topoisomerases are ATP-independent enzymes (except for reverse gyrase), and can be subdivided according to their structure and reaction mechanisms: type IA (bacterial and archaeal topoisomerase I, topoisomerase III and reverse gyrase) and type IB (eukaryotic topoisomerase I and topoisomerase V). These enzymes are primarily responsible for relaxing positively and/or negatively supercoiled DNA, except for reverse gyrase, which can introduce positive supercoils into DNA. This entry represents the zinc-finger domain found in type IA topoisomerases, including bacterial and archaeal topoisomerase I and III enzymes, and in eukaryotic topoisomerase III enzymes. Escherichia coli topoisomerase I proteins contain five copies of a zinc-ribbon-like domain at their C terminus, two of which have lost their cysteine residues and are therefore probably not able to bind zinc []. This domain is still considered to be a member of the zinc-ribbon superfamily despite not being able to bind zinc. More information about this protein can be found at Protein of the Month: DNA Topoisomerase [].; GO: 0003677 DNA binding, 0003916 DNA topoisomerase activity, 0006265 DNA topological change, 0005694 chromosome
Probab=23.75 E-value=55 Score=19.63 Aligned_cols=15 Identities=27% Similarity=0.481 Sum_probs=8.9
Q ss_pred EeCCCCCEEeeeeCC
Q 029155 181 QCPLTGQTEQRKVAK 195 (198)
Q Consensus 181 ~c~~cg~~e~RKva~ 195 (198)
.||.||.....|-++
T Consensus 3 ~CP~Cg~~lv~r~~k 17 (39)
T PF01396_consen 3 KCPKCGGPLVLRRGK 17 (39)
T ss_pred CCCCCCceeEEEECC
Confidence 477777655555544
No 349
>COG1439 Predicted nucleic acid-binding protein, consists of a PIN domain and a Zn-ribbon module [General function prediction only]
Probab=23.53 E-value=56 Score=26.60 Aligned_cols=29 Identities=21% Similarity=0.273 Sum_probs=21.3
Q ss_pred ec-CCCceeEEccCCeEEeCCCCCEEeeeeCCC
Q 029155 165 ES-TAGGTMVPISWTEMQCPLTGQTEQRKVAKV 196 (198)
Q Consensus 165 ~~-~~g~~m~~~~~~~~~c~~cg~~e~RKva~~ 196 (198)
+| -|+...- ...=.||.||..-+||..+-
T Consensus 141 rC~GC~~~f~---~~~~~Cp~CG~~~~~~~~~~ 170 (177)
T COG1439 141 RCHGCKRIFP---EPKDFCPICGSPLKRKRVKS 170 (177)
T ss_pred EEecCceecC---CCCCcCCCCCCceEEeeech
Confidence 56 5776653 34568999999999987653
No 350
>PF12677 DUF3797: Domain of unknown function (DUF3797); InterPro: IPR024256 This presumed domain is functionally uncharacterised. This domain family is found in bacteria and viruses, and is approximately 50 amino acids in length. There is a conserved CGN sequence motif.
Probab=23.46 E-value=27 Score=22.39 Aligned_cols=15 Identities=27% Similarity=0.503 Sum_probs=10.3
Q ss_pred EccCCeEEeCCCCCE
Q 029155 174 PISWTEMQCPLTGQT 188 (198)
Q Consensus 174 ~~~~~~~~c~~cg~~ 188 (198)
|++..--+||+||+-
T Consensus 8 ~L~~kY~~Cp~CGN~ 22 (49)
T PF12677_consen 8 KLSNKYCKCPKCGND 22 (49)
T ss_pred chhhhhccCcccCCc
Confidence 344456789999973
No 351
>PF00130 C1_1: Phorbol esters/diacylglycerol binding domain (C1 domain); InterPro: IPR002219 Diacylglycerol (DAG) is an important second messenger. Phorbol esters (PE) are analogues of DAG and potent tumour promoters that cause a variety of physiological changes when administered to both cells and tissues. DAG activates a family of serine/threonine protein kinases, collectively known as protein kinase C (PKC) []. Phorbol esters can directly stimulate PKC. The N-terminal region of PKC, known as C1, has been shown [] to bind PE and DAG in a phospholipid and zinc-dependent fashion. The C1 region contains one or two copies (depending on the isozyme of PKC) of a cysteine-rich domain, which is about 50 amino-acid residues long, and which is essential for DAG/PE-binding. The DAG/PE-binding domain binds two zinc ions; the ligands of these metal ions are probably the six cysteines and two histidines that are conserved in this domain.; GO: 0035556 intracellular signal transduction; PDB: 1RFH_A 2FNF_X 3PFQ_A 1PTQ_A 1PTR_A 2VRW_B 1XA6_A 2ENN_A 1TBN_A 1TBO_A ....
Probab=23.46 E-value=88 Score=19.32 Aligned_cols=32 Identities=13% Similarity=0.200 Sum_probs=22.2
Q ss_pred Eec-CCCceeEEccCCeEEeCCCCCEEeeeeCC
Q 029155 164 AES-TAGGTMVPISWTEMQCPLTGQTEQRKVAK 195 (198)
Q Consensus 164 a~~-~~g~~m~~~~~~~~~c~~cg~~e~RKva~ 195 (198)
+.| .|+..|.....+.++|..|+..-=+|.+.
T Consensus 12 ~~C~~C~~~i~g~~~~g~~C~~C~~~~H~~C~~ 44 (53)
T PF00130_consen 12 TYCDVCGKFIWGLGKQGYRCSWCGLVCHKKCLS 44 (53)
T ss_dssp EB-TTSSSBECSSSSCEEEETTTT-EEETTGGC
T ss_pred CCCcccCcccCCCCCCeEEECCCCChHhhhhhh
Confidence 467 79999955556789999999876665543
No 352
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=23.13 E-value=19 Score=23.94 Aligned_cols=13 Identities=31% Similarity=0.634 Sum_probs=9.4
Q ss_pred eEEeCCCCCEEee
Q 029155 179 EMQCPLTGQTEQR 191 (198)
Q Consensus 179 ~~~c~~cg~~e~R 191 (198)
-+.||.||..-++
T Consensus 17 ~lrCPRC~~~FR~ 29 (65)
T COG4049 17 FLRCPRCGMVFRR 29 (65)
T ss_pred eeeCCchhHHHHH
Confidence 5789999876543
No 353
>TIGR02487 NrdD anaerobic ribonucleoside-triphosphate reductase. This model represents the oxygen-sensitive (anaerobic, class III) ribonucleotide reductase. The mechanism of the enzyme involves a glycine-centered radical, a C-terminal zinc binding site, and a set of conserved active site cysteines and asparagines. This enzyme requires an activating component, NrdG, a radical-SAM domain containing enzyme (TIGR02491). Together the two form an alpha-2/beta-2 heterodimer.
Probab=23.08 E-value=37 Score=32.50 Aligned_cols=24 Identities=21% Similarity=0.265 Sum_probs=15.3
Q ss_pred EEec-CCCceeEEccCCeEEeCCCCCEE
Q 029155 163 SAES-TAGGTMVPISWTEMQCPLTGQTE 189 (198)
Q Consensus 163 ~a~~-~~g~~m~~~~~~~~~c~~cg~~e 189 (198)
+.+| .||..- ......||+||...
T Consensus 524 ~~~C~~CG~~g---~~~~~~CP~Cgs~~ 548 (579)
T TIGR02487 524 VDVCEDCGYTG---EGLNDKCPKCGSHD 548 (579)
T ss_pred CccCCCCCCCC---CCCCCcCcCCCCcc
Confidence 5678 799621 11125899999753
No 354
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=23.06 E-value=81 Score=26.93 Aligned_cols=21 Identities=29% Similarity=0.327 Sum_probs=17.5
Q ss_pred CCCCCCCCEEEEEEEEEecce
Q 029155 71 GPVPEPGSVVIARVTKVMTRM 91 (198)
Q Consensus 71 ~~~p~vGDiViG~V~~v~~~~ 91 (198)
+...++||.|+++|.++...+
T Consensus 110 r~~l~vGD~v~AkV~~vd~~~ 130 (239)
T COG1097 110 RPFLNVGDLVYAKVVDVDRDG 130 (239)
T ss_pred ccccccCCEEEEEEEEccCCC
Confidence 456799999999999997654
No 355
>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=22.75 E-value=2.3e+02 Score=19.68 Aligned_cols=17 Identities=12% Similarity=0.276 Sum_probs=13.7
Q ss_pred EEEEEEEEecceEEEEE
Q 029155 80 VIARVTKVMTRMASADI 96 (198)
Q Consensus 80 ViG~V~~v~~~~~~V~I 96 (198)
|-|+|.++.++.+.|+.
T Consensus 5 iP~~V~~i~~~~A~v~~ 21 (76)
T TIGR00074 5 IPGQVVEIDENIALVEF 21 (76)
T ss_pred cceEEEEEcCCEEEEEc
Confidence 34789999888888887
No 356
>PTZ00194 60S ribosomal protein L26; Provisional
Probab=22.66 E-value=1e+02 Score=24.20 Aligned_cols=38 Identities=21% Similarity=0.082 Sum_probs=24.8
Q ss_pred EEEEEEEecceEEEEEeeecc-ccccCcceeEEeccccc
Q 029155 81 IARVTKVMTRMASADIMCVGA-KSVREKFSGIIRQQDVR 118 (198)
Q Consensus 81 iG~V~~v~~~~~~V~I~~v~~-~~l~~~~~G~l~~s~v~ 118 (198)
.|+|+.|......|-|-.++- +.-..+..+-||+|++.
T Consensus 64 ~GkV~~V~~k~~~ViVEgvn~~Kk~gk~~e~PIh~SNV~ 102 (143)
T PTZ00194 64 EGKVTAVYRKKWVIHIEKITREKANGEPVQIGIHPSNVI 102 (143)
T ss_pred ceEEEEEEcCCCEEEEeCeEEEecCCCEeecCcCchheE
Confidence 499999977776666644432 11234567788888775
No 357
>PF14952 zf-tcix: Putative treble-clef, zinc-finger, Zn-binding
Probab=22.64 E-value=37 Score=21.32 Aligned_cols=11 Identities=27% Similarity=0.582 Sum_probs=8.2
Q ss_pred eEEeCCCCCEE
Q 029155 179 EMQCPLTGQTE 189 (198)
Q Consensus 179 ~~~c~~cg~~e 189 (198)
.-+||+||...
T Consensus 11 irkCp~CGt~N 21 (44)
T PF14952_consen 11 IRKCPKCGTYN 21 (44)
T ss_pred cccCCcCcCcc
Confidence 45799999753
No 358
>PRK03954 ribonuclease P protein component 4; Validated
Probab=22.59 E-value=65 Score=24.56 Aligned_cols=13 Identities=15% Similarity=0.281 Sum_probs=7.7
Q ss_pred CCeEEeCCCCCEE
Q 029155 177 WTEMQCPLTGQTE 189 (198)
Q Consensus 177 ~~~~~c~~cg~~e 189 (198)
|-...|..||++-
T Consensus 91 ~vvitCl~CG~~k 103 (121)
T PRK03954 91 HVVITCLECGHIM 103 (121)
T ss_pred eEEEECccCCCEE
Confidence 3345677777653
No 359
>cd05837 MSH6_like The PWWP domain is present in MSH6, a mismatch repair protein homologous to bacterial MutS. The PWWP domain of histone-lysine N-methyltransferase, also known as Nuclear SET domain-containing protein 3, is also included. Mutations in MSH6 have been linked to increased cancer susceptibility, particularly in hereditary nonpolyposis colorectal cancer in humans. The role of the PWWP domain in MSH6 is not clear; MSH6 orthologs found in S. cerevisiae, Caenorhabditis elegans and Arabidopsis thaliana lack the PWWP domain. Histone methyltransferases (HMTases) induce the posttranslational methylation of lysine residues in histones and play a role in apoptosis. In the HMTase Whistle, the PWWP domain is necessary for HMTase activity. The PWWP domain, named for a conserved Pro-Trp-Trp-Pro motif, is a small domain consisting of 100-150 amino acids. The PWWP domain is found in numerous proteins that are involved in cell division, growth and differentiation. Most PWWP-domain pro
Probab=22.47 E-value=55 Score=24.17 Aligned_cols=15 Identities=33% Similarity=0.556 Sum_probs=12.8
Q ss_pred CCCCCCEEEEEEEEe
Q 029155 130 SFRPGDIVRASVLSL 144 (198)
Q Consensus 130 ~~~~GDiV~AkV~s~ 144 (198)
.|.+||+|-||+-+.
T Consensus 2 ~~~~GdlVWaK~~g~ 16 (110)
T cd05837 2 KYQVGDLVWAKVSGY 16 (110)
T ss_pred CCCCCCEEEEeCCCC
Confidence 378999999999864
No 360
>PF08209 Sgf11: Sgf11 (transcriptional regulation protein); InterPro: IPR013246 The Sgf11 family is a SAGA complex subunit in Saccharomyces cerevisiae (Baker's yeast). The SAGA complex is a multisubunit protein complex involved in transcriptional regulation. SAGA combines proteins involved in interactions with DNA-bound activators and TATA-binding protein (TBP), as well as enzymes for histone acetylation and deubiquitylation [].; PDB: 3M99_B 2LO2_A 3MHH_C 3MHS_C.
Probab=22.35 E-value=63 Score=18.92 Aligned_cols=11 Identities=27% Similarity=0.742 Sum_probs=7.5
Q ss_pred CeEEeCCCCCE
Q 029155 178 TEMQCPLTGQT 188 (198)
Q Consensus 178 ~~~~c~~cg~~ 188 (198)
....||+|++.
T Consensus 3 ~~~~C~nC~R~ 13 (33)
T PF08209_consen 3 PYVECPNCGRP 13 (33)
T ss_dssp -EEE-TTTSSE
T ss_pred CeEECCCCcCC
Confidence 46899999974
No 361
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=22.17 E-value=40 Score=35.33 Aligned_cols=19 Identities=26% Similarity=0.504 Sum_probs=0.0
Q ss_pred ec-CCCceeEEccCCeEEeCCCCC
Q 029155 165 ES-TAGGTMVPISWTEMQCPLTGQ 187 (198)
Q Consensus 165 ~~-~~g~~m~~~~~~~~~c~~cg~ 187 (198)
+| .||..+.| ...||.||.
T Consensus 681 fCP~CGs~te~----vy~CPsCGa 700 (1337)
T PRK14714 681 RCPDCGTHTEP----VYVCPDCGA 700 (1337)
T ss_pred cCcccCCcCCC----ceeCccCCC
No 362
>PRK09462 fur ferric uptake regulator; Provisional
Probab=22.06 E-value=1.4e+02 Score=22.87 Aligned_cols=13 Identities=15% Similarity=0.337 Sum_probs=10.3
Q ss_pred CeEEeCCCCCEEe
Q 029155 178 TEMQCPLTGQTEQ 190 (198)
Q Consensus 178 ~~~~c~~cg~~e~ 190 (198)
.++.|..||++..
T Consensus 89 ~H~iC~~Cg~i~~ 101 (148)
T PRK09462 89 DHLICLDCGKVIE 101 (148)
T ss_pred CceEECCCCCEEE
Confidence 4699999998764
No 363
>PF13005 zf-IS66: zinc-finger binding domain of transposase IS66 ; InterPro: IPR024474 This entry represents a predicted helix-turn-helix domain from insertion element IS66 transposases [].
Probab=21.88 E-value=97 Score=18.76 Aligned_cols=10 Identities=30% Similarity=0.621 Sum_probs=4.8
Q ss_pred CCCceeEEcc
Q 029155 167 TAGGTMVPIS 176 (198)
Q Consensus 167 ~~g~~m~~~~ 176 (198)
.||..|.+++
T Consensus 7 ~Cg~~l~~ig 16 (47)
T PF13005_consen 7 DCGGELKEIG 16 (47)
T ss_pred CCCceeeECC
Confidence 3555554443
No 364
>TIGR02159 PA_CoA_Oxy4 phenylacetate-CoA oxygenase, PaaJ subunit. Phenylacetate-CoA oxygenase is comprised of a five gene complex responsible for the hydroxylation of phenylacetate-CoA (PA-CoA) as the second catabolic step in phenylacetic acid (PA) degradation. Although the exact function of this enzyme has not been determined, it has been shown to be required for phenylacetic acid degradation and has been proposed to function in a multicomponent oxygenase acting on phenylacetate-CoA.
Probab=21.81 E-value=50 Score=25.86 Aligned_cols=19 Identities=26% Similarity=0.604 Sum_probs=17.0
Q ss_pred eEEeCCCCCEEeeeeCCCC
Q 029155 179 EMQCPLTGQTEQRKVAKVG 197 (198)
Q Consensus 179 ~~~c~~cg~~e~RKva~~~ 197 (198)
...||.||....|.+|.+.
T Consensus 105 ~~~cp~c~s~~t~~~s~fg 123 (146)
T TIGR02159 105 SVQCPRCGSADTTITSIFG 123 (146)
T ss_pred CCcCCCCCCCCcEeecCCC
Confidence 5899999999999998764
No 365
>PF04351 PilP: Pilus assembly protein, PilP; InterPro: IPR007446 The PilP family are periplasmic proteins involved in the biogenesis of type IV pili [].; PDB: 2Y4Y_B 2Y4X_A 2IVW_A 2LC4_A.
Probab=21.73 E-value=1.1e+02 Score=23.80 Aligned_cols=27 Identities=11% Similarity=0.062 Sum_probs=18.9
Q ss_pred CCCCCCCCCCEE---EEEEEEEecceEEEE
Q 029155 69 AHGPVPEPGSVV---IARVTKVMTRMASAD 95 (198)
Q Consensus 69 ~~~~~p~vGDiV---iG~V~~v~~~~~~V~ 95 (198)
+..|..++||-+ .|+|++|+.+.+.+.
T Consensus 100 g~v~~V~~G~yiG~n~G~I~~Is~~~I~l~ 129 (149)
T PF04351_consen 100 GKVYRVKVGDYIGQNYGRITSISEDSIELV 129 (149)
T ss_dssp TEEEEEETTEEETTTTEEEEEEETTEEEEE
T ss_pred CCEEEecCCCEeccCCCEEEEEeCCeEEEE
Confidence 344555666665 799999999876554
No 366
>PF13408 Zn_ribbon_recom: Recombinase zinc beta ribbon domain
Probab=21.47 E-value=85 Score=19.55 Aligned_cols=13 Identities=15% Similarity=0.189 Sum_probs=6.5
Q ss_pred ec-CCCceeEEccC
Q 029155 165 ES-TAGGTMVPISW 177 (198)
Q Consensus 165 ~~-~~g~~m~~~~~ 177 (198)
.| .||..|....|
T Consensus 7 ~C~~CG~~m~~~~~ 20 (58)
T PF13408_consen 7 RCGHCGSKMTRRKR 20 (58)
T ss_pred EcccCCcEeEEEEC
Confidence 34 45555554443
No 367
>PF00394 Cu-oxidase: Multicopper oxidase; InterPro: IPR001117 Copper is one of the most prevalent transition metals in living organisms and its biological function is intimately related to its redox properties. Since free copper is toxic, even at very low concentrations, its homeostasis in living organisms is tightly controlled by subtle molecular mechanisms. In eukaryotes, before being transported inside the cell via the high-affinity copper transporters of the CTR family, the copper (II) ion is reduced to copper (I). In blue copper proteins such as cupredoxin, the copper (I) ion form is stabilised by a constrained His2Cys coordination environment. Multicopper oxidases oxidise their substrate by accepting electrons at a mononuclear copper centre and transferring them to a trinuclear copper centre; dioxygen binds to the trinuclear centre and, following the transfer of four electrons, is reduced to two molecules of water []. There are three spectroscopically different copper centres found in multicopper oxidases: type 1 (or blue), type 2 (or normal) and type 3 (or coupled binuclear) [, ]. Multicopper oxidases consist of 2, 3 or 6 of these homologous domains, which also share homology to the cupredoxins azurin and plastocyanin. Structurally, these domains consist of a cupredoxin-like fold, a beta-sandwich consisting of 7 strands in 2 beta-sheets, arranged in a Greek-key beta-barrel []. Multicopper oxidases include: Ceruloplasmin (1.16.3.1 from EC) (ferroxidase), a 6-domain enzyme found in the serum of mammals and birds that oxidizes different inorganic and organic substances; exhibits internal sequence homology that appears to have evolved from the triplication of a Cu-binding domain similar to that of laccase and ascorbate oxidase. Laccase (1.10.3.2 from EC) (urishiol oxidase), a 3-domain enzyme found in fungi and plants, which oxidizes different phenols and diamines. CueO is a laccase found in Escherichia coli that is involved in copper-resistance []. Ascorbate oxidase (1.10.3.3 from EC), a 3-domain enzyme found in higher plants. Nitrite reductase (1.7.2.1 from EC), a 2-domain enzyme containing type-1 and type-2 copper centres [, ]. In addition to the above enzymes there are a number of other proteins that are similar to the multi-copper oxidases in terms of structure and sequence, some of which have lost the ability to bind copper. These include: copper resistance protein A (copA) from a plasmid in Pseudomonas syringae; domain A of (non-copper binding) blood coagulation factors V (Fa V) and VIII (Fa VIII) []; yeast FET3 required for ferrous iron uptake []; yeast hypothetical protein YFL041w; and the fission yeast homologue SpAC1F7.08. This entry represents multicopper oxidase type 1 (blue) domains. These domains are also present in proteins that have lost the ability to bind copper.; GO: 0016491 oxidoreductase activity, 0055114 oxidation-reduction process; PDB: 1RZP_A 2AVF_D 1NIA_A 1KCB_A 2NRD_A 1NIB_A 2BW4_A 1RZQ_C 2BWD_A 2BWI_A ....
Probab=21.39 E-value=1.7e+02 Score=22.50 Aligned_cols=44 Identities=20% Similarity=0.464 Sum_probs=33.3
Q ss_pred cCCCCCCEEEEEEEEeCCCccEEEEEecCCCeeeEEecCCCceeEEc
Q 029155 129 LSFRPGDIVRASVLSLGDARAYFLSTAKNDLGVVSAESTAGGTMVPI 175 (198)
Q Consensus 129 ~~~~~GDiV~AkV~s~~~~~~~~LSt~~~~lGvv~a~~~~g~~m~~~ 175 (198)
-.+++|+.++-|+++.+....+.|++.+..+-||.+ -|.++.|.
T Consensus 62 ~~v~~g~~~rlRliNa~~~~~~~~~i~gh~~~Via~---DG~~v~p~ 105 (159)
T PF00394_consen 62 IKVKPGERYRLRLINAGASTSFNFSIDGHPMTVIAA---DGVPVEPY 105 (159)
T ss_dssp EEEETTTEEEEEEEEESSS-BEEEEETTBCEEEEEE---TTEEEEEE
T ss_pred EEEcCCcEEEEEEEeccCCeeEEEEeeccceeEeee---cccccccc
Confidence 346899999999999986667899998888777755 45555544
No 368
>COG4956 Integral membrane protein (PIN domain superfamily) [General function prediction only]
Probab=21.36 E-value=1.4e+02 Score=26.82 Aligned_cols=30 Identities=27% Similarity=0.426 Sum_probs=21.3
Q ss_pred cCCcEEecCCccCC---CCCeeeCCCE-EEeCCc
Q 029155 6 EEMVLVTPGEVLGK---ATEVKAGKGA-YVAKHN 35 (198)
Q Consensus 6 ~~~~iV~PGd~l~~---~~e~~~G~Gt-y~~~g~ 35 (198)
+-+-.|+|||.+.. -+.-.+|.|+ |.+||.
T Consensus 286 AVkP~vlpGe~l~v~iiK~GkE~~QGVgYLdDGT 319 (356)
T COG4956 286 AVKPVVLPGEELTVQIIKDGKEPGQGVGYLDDGT 319 (356)
T ss_pred HhCCcccCCCeeEEEEeecCcccCCceEEecCCe
Confidence 34567999998753 1345688886 888876
No 369
>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed
Probab=21.30 E-value=65 Score=21.21 Aligned_cols=19 Identities=21% Similarity=0.490 Sum_probs=10.1
Q ss_pred ec-CCCceeEEccCCeEEeCCCCCE
Q 029155 165 ES-TAGGTMVPISWTEMQCPLTGQT 188 (198)
Q Consensus 165 ~~-~~g~~m~~~~~~~~~c~~cg~~ 188 (198)
.| +||..-. ...||.||..
T Consensus 7 ~C~~CgvYTL-----k~~CP~CG~~ 26 (56)
T PRK13130 7 KCPKCGVYTL-----KEICPVCGGK 26 (56)
T ss_pred ECCCCCCEEc-----cccCcCCCCC
Confidence 34 5555443 2467777643
No 370
>PRK07111 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=21.29 E-value=51 Score=32.59 Aligned_cols=21 Identities=29% Similarity=0.409 Sum_probs=14.6
Q ss_pred EEec-CCCceeEEccCCeEEeCCCCC
Q 029155 163 SAES-TAGGTMVPISWTEMQCPLTGQ 187 (198)
Q Consensus 163 ~a~~-~~g~~m~~~~~~~~~c~~cg~ 187 (198)
+.+| .||..-. -.-.||+||.
T Consensus 680 ~~~C~~CG~~~~----~~~~CP~CG~ 701 (735)
T PRK07111 680 VDRCPVCGYLGV----IEDKCPKCGS 701 (735)
T ss_pred CeecCCCCCCCC----cCccCcCCCC
Confidence 5688 7994221 2478999997
No 371
>PF14444 S1-like: S1-like
Probab=21.15 E-value=1e+02 Score=20.49 Aligned_cols=15 Identities=27% Similarity=0.417 Sum_probs=11.9
Q ss_pred CCCCCCCEEEEEEEE
Q 029155 72 PVPEPGSVVIARVTK 86 (198)
Q Consensus 72 ~~p~vGDiViG~V~~ 86 (198)
++|++||.|.+.-+.
T Consensus 32 ~~P~vGdrV~v~A~~ 46 (58)
T PF14444_consen 32 NVPKVGDRVLVEAIY 46 (58)
T ss_pred CCCccCCEEEEEEEe
Confidence 589999999876543
No 372
>PF12073 DUF3553: Protein of unknown function (DUF3553); InterPro: IPR021938 This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are about 60 amino acids in length. This protein has two conserved sequence motifs: GQVQS and TVNF.
Probab=21.13 E-value=2.5e+02 Score=18.26 Aligned_cols=16 Identities=13% Similarity=0.229 Sum_probs=12.5
Q ss_pred EEEEEEEecceEEEEE
Q 029155 81 IARVTKVMTRMASADI 96 (198)
Q Consensus 81 iG~V~~v~~~~~~V~I 96 (198)
+|+|.+.....+.|+-
T Consensus 17 ~GqVqS~i~~rvTVnF 32 (52)
T PF12073_consen 17 IGQVQSNIGGRVTVNF 32 (52)
T ss_pred ceEEEEecCCeEEEee
Confidence 7899888777776665
No 373
>PF14353 CpXC: CpXC protein
Probab=21.09 E-value=58 Score=24.33 Aligned_cols=15 Identities=27% Similarity=0.381 Sum_probs=11.6
Q ss_pred ccCCeEEeCCCCCEE
Q 029155 175 ISWTEMQCPLTGQTE 189 (198)
Q Consensus 175 ~~~~~~~c~~cg~~e 189 (198)
.+.....||.||..-
T Consensus 34 g~l~~~~CP~Cg~~~ 48 (128)
T PF14353_consen 34 GSLFSFTCPSCGHKF 48 (128)
T ss_pred CCcCEEECCCCCCce
Confidence 456788999999764
No 374
>COG2835 Uncharacterized conserved protein [Function unknown]
Probab=20.99 E-value=1.1e+02 Score=20.46 Aligned_cols=24 Identities=21% Similarity=0.252 Sum_probs=16.8
Q ss_pred CCCceeEEc-cCCeEEeCCCCCEEe
Q 029155 167 TAGGTMVPI-SWTEMQCPLTGQTEQ 190 (198)
Q Consensus 167 ~~g~~m~~~-~~~~~~c~~cg~~e~ 190 (198)
.|.++|.-. +.+++.|+.|+...+
T Consensus 13 ~~kg~L~~~~~~~~L~c~~~~~aYp 37 (60)
T COG2835 13 VCKGPLVYDEEKQELICPRCKLAYP 37 (60)
T ss_pred CcCCcceEeccCCEEEecccCceee
Confidence 576666433 467999999987543
No 375
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=20.98 E-value=37 Score=33.02 Aligned_cols=24 Identities=21% Similarity=0.397 Sum_probs=17.4
Q ss_pred Eec-CCCceeEEccCCeEEeCCCCCEEe
Q 029155 164 AES-TAGGTMVPISWTEMQCPLTGQTEQ 190 (198)
Q Consensus 164 a~~-~~g~~m~~~~~~~~~c~~cg~~e~ 190 (198)
..| .||..+-+ + .-.|++||..-.
T Consensus 28 ~~Cp~CG~~~~~-~--~~fC~~CG~~~~ 52 (645)
T PRK14559 28 KPCPQCGTEVPV-D--EAHCPNCGAETG 52 (645)
T ss_pred CcCCCCCCCCCc-c--cccccccCCccc
Confidence 358 89998643 3 469999998643
No 376
>COG1379 PHP family phosphoesterase with a Zn ribbon [General function prediction only]
Probab=20.22 E-value=18 Score=32.41 Aligned_cols=33 Identities=15% Similarity=0.263 Sum_probs=21.7
Q ss_pred cCCCeeeEEe-c-CCC-----ceeEEccCCeEEeCCCCCEEee
Q 029155 156 KNDLGVVSAE-S-TAG-----GTMVPISWTEMQCPLTGQTEQR 191 (198)
Q Consensus 156 ~~~lGvv~a~-~-~~g-----~~m~~~~~~~~~c~~cg~~e~R 191 (198)
.+.||+-.-. | +|. .++.... +.||+||-+-+.
T Consensus 238 dP~LGKY~~TAC~rC~t~y~le~A~~~~---wrCpkCGg~ikK 277 (403)
T COG1379 238 DPRLGKYHLTACSRCYTRYSLEEAKSLR---WRCPKCGGKIKK 277 (403)
T ss_pred CccccchhHHHHHHhhhccCcchhhhhc---ccCcccccchhh
Confidence 4677775544 5 788 5555434 579999986544
No 377
>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=20.15 E-value=1.4e+02 Score=20.89 Aligned_cols=21 Identities=38% Similarity=0.295 Sum_probs=17.4
Q ss_pred cccCCCCCCEEEEEEEEeCCC
Q 029155 127 MHLSFRPGDIVRASVLSLGDA 147 (198)
Q Consensus 127 ~~~~~~~GDiV~AkV~s~~~~ 147 (198)
|...|.+||.|+|.-.-.+|+
T Consensus 1 ~~p~f~~G~~V~a~~~irNDG 21 (75)
T PF04319_consen 1 MPPRFEWGDKVRARKDIRNDG 21 (75)
T ss_pred CCCccCCCCEEEEEEEeEcCC
Confidence 457799999999998877775
Done!