Query 032315
Match_columns 143
No_of_seqs 105 out of 425
Neff 6.3
Searched_HMMs 46136
Date Fri Mar 29 12:28:47 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/032315.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/032315hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PTZ00162 DNA-directed RNA poly 100.0 4.8E-44 1E-48 276.2 16.5 133 2-134 32-168 (176)
2 KOG3298 DNA-directed RNA polym 100.0 2.8E-39 6E-44 244.5 14.1 132 2-134 32-167 (170)
3 COG1095 RPB7 DNA-directed RNA 100.0 4.9E-39 1.1E-43 248.2 14.9 128 2-130 32-166 (183)
4 TIGR00448 rpoE DNA-directed RN 100.0 5.1E-34 1.1E-38 220.0 16.1 130 2-133 32-169 (179)
5 KOG3297 DNA-directed RNA polym 100.0 1.5E-34 3.3E-39 222.6 11.2 130 2-131 32-172 (202)
6 PRK08563 DNA-directed RNA poly 100.0 7.8E-33 1.7E-37 214.1 15.6 131 2-133 32-169 (187)
7 cd04462 S1_RNAPII_Rpb7 S1_RNAP 99.9 4.5E-23 9.8E-28 143.1 12.2 82 51-133 1-86 (88)
8 PF08292 RNA_pol_Rbc25: RNA po 99.8 8.3E-20 1.8E-24 133.9 11.7 71 49-119 1-77 (122)
9 cd04330 RNAP_III_Rpc25_N RNAP_ 99.8 3.3E-19 7.1E-24 121.8 5.9 50 2-51 31-80 (80)
10 cd04329 RNAP_II_Rpb7_N RNAP_II 99.8 4E-19 8.6E-24 121.4 5.3 50 2-51 31-80 (80)
11 cd00655 RNAP_Rpb7_N_like RNAP_ 99.8 6.8E-19 1.5E-23 120.2 6.1 50 2-51 31-80 (80)
12 cd04331 RNAP_E_N RNAP_E_N: Rpo 99.7 3.2E-18 7E-23 117.0 5.0 49 2-50 31-79 (80)
13 PF03876 SHS2_Rpb7-N: SHS2 dom 99.4 2.2E-13 4.8E-18 89.8 4.8 46 2-47 25-70 (70)
14 cd04328 RNAP_I_Rpa43_N RNAP_I_ 98.9 4.9E-09 1.1E-13 72.4 5.4 45 7-51 42-89 (89)
15 cd04471 S1_RNase_R S1_RNase_R: 98.9 3.7E-08 8E-13 65.6 9.4 71 51-122 1-77 (83)
16 cd04460 S1_RpoE S1_RpoE: RpoE, 98.6 3E-07 6.6E-12 64.2 9.1 79 53-132 1-86 (99)
17 PF00575 S1: S1 RNA binding do 98.6 1.5E-07 3.3E-12 61.7 6.7 65 48-123 1-69 (74)
18 cd05705 S1_Rrp5_repeat_hs14 S1 98.3 3.7E-06 8E-11 56.1 6.9 66 51-123 3-71 (74)
19 smart00316 S1 Ribosomal protei 98.2 1.4E-05 3.1E-10 50.3 7.8 61 51-122 2-66 (72)
20 cd05690 S1_RPS1_repeat_ec5 S1_ 98.2 1.3E-05 2.7E-10 51.6 7.3 61 52-122 1-65 (69)
21 cd05697 S1_Rrp5_repeat_hs5 S1_ 98.1 1.2E-05 2.6E-10 52.1 6.9 61 52-123 1-65 (69)
22 cd05706 S1_Rrp5_repeat_sc10 S1 98.1 2.2E-05 4.8E-10 51.3 7.9 62 50-122 2-67 (73)
23 cd05686 S1_pNO40 S1_pNO40: pNO 98.1 2.3E-05 5E-10 51.7 7.5 63 49-119 1-65 (73)
24 cd05698 S1_Rrp5_repeat_hs6_sc5 98.0 1.9E-05 4.1E-10 51.1 6.3 60 52-122 1-64 (70)
25 cd05707 S1_Rrp5_repeat_sc11 S1 98.0 2.7E-05 5.8E-10 50.3 6.7 60 52-122 1-64 (68)
26 TIGR02063 RNase_R ribonuclease 98.0 3.2E-05 7E-10 70.7 9.6 78 45-123 621-704 (709)
27 TIGR00358 3_prime_RNase VacB a 98.0 3.9E-05 8.5E-10 69.7 9.6 77 46-123 567-649 (654)
28 PRK11642 exoribonuclease R; Pr 98.0 4.1E-05 8.9E-10 71.3 9.5 77 45-122 637-719 (813)
29 cd05708 S1_Rrp5_repeat_sc12 S1 98.0 4.8E-05 1E-09 49.6 7.3 62 51-123 2-68 (77)
30 cd05703 S1_Rrp5_repeat_hs12_sc 98.0 3.4E-05 7.3E-10 51.2 6.5 62 52-122 1-66 (73)
31 cd05689 S1_RPS1_repeat_ec4 S1_ 97.9 0.0001 2.3E-09 47.9 8.3 63 51-123 3-69 (72)
32 cd04461 S1_Rrp5_repeat_hs8_sc7 97.9 4.1E-05 8.8E-10 51.5 6.4 64 49-123 12-79 (83)
33 cd05688 S1_RPS1_repeat_ec3 S1_ 97.9 7.8E-05 1.7E-09 47.3 7.3 64 51-122 1-64 (68)
34 cd05691 S1_RPS1_repeat_ec6 S1_ 97.9 6.6E-05 1.4E-09 48.6 7.0 60 52-122 1-64 (73)
35 cd05685 S1_Tex S1_Tex: The C-t 97.8 8.8E-05 1.9E-09 46.9 6.6 60 52-122 1-64 (68)
36 cd05692 S1_RPS1_repeat_hs4 S1_ 97.8 8.7E-05 1.9E-09 46.9 6.0 56 52-118 1-60 (69)
37 cd05694 S1_Rrp5_repeat_hs2_sc2 97.8 0.00019 4.1E-09 47.9 7.7 53 51-120 4-61 (74)
38 cd04452 S1_IF2_alpha S1_IF2_al 97.7 0.00019 4.1E-09 46.9 7.1 63 49-122 1-69 (76)
39 cd05684 S1_DHX8_helicase S1_DH 97.7 0.00055 1.2E-08 45.4 9.2 56 52-117 1-63 (79)
40 PRK08582 hypothetical protein; 97.7 0.00023 5.1E-09 53.1 7.8 59 49-118 3-65 (139)
41 KOG4134 DNA-dependent RNA poly 97.7 0.00016 3.5E-09 58.2 7.1 75 12-86 67-146 (253)
42 cd05789 S1_Rrp4 S1_Rrp4: Rrp4 97.7 8.7E-05 1.9E-09 50.0 4.7 68 47-118 2-70 (86)
43 cd05702 S1_Rrp5_repeat_hs11_sc 97.7 0.00025 5.4E-09 46.2 6.7 57 52-118 1-62 (70)
44 cd05687 S1_RPS1_repeat_ec1_hs1 97.7 0.00029 6.3E-09 45.5 6.9 57 52-119 1-61 (70)
45 cd04472 S1_PNPase S1_PNPase: P 97.7 0.00029 6.3E-09 44.7 6.8 56 52-118 1-60 (68)
46 cd05696 S1_Rrp5_repeat_hs4 S1_ 97.6 0.0004 8.6E-09 45.7 7.5 59 52-121 1-65 (71)
47 PRK07252 hypothetical protein; 97.6 0.00042 9.1E-09 50.5 7.6 62 51-123 3-68 (120)
48 cd05695 S1_Rrp5_repeat_hs3 S1_ 97.6 0.0006 1.3E-08 44.2 7.5 58 52-122 1-62 (66)
49 cd05704 S1_Rrp5_repeat_hs13 S1 97.5 0.00027 5.9E-09 46.6 5.7 56 51-117 3-63 (72)
50 cd04454 S1_Rrp4_like S1_Rrp4_l 97.5 0.00035 7.6E-09 46.8 5.9 62 47-119 2-67 (82)
51 PRK08059 general stress protei 97.5 0.00055 1.2E-08 49.8 7.0 63 49-122 5-71 (123)
52 cd00164 S1_like S1_like: Ribos 97.4 0.0008 1.7E-08 41.4 6.4 55 55-120 1-59 (65)
53 TIGR03591 polynuc_phos polyrib 97.4 0.00014 3.1E-09 66.6 3.4 88 20-118 585-678 (684)
54 PRK05807 hypothetical protein; 97.3 0.0012 2.5E-08 49.1 7.4 61 50-118 4-64 (136)
55 cd04453 S1_RNase_E S1_RNase_E: 97.3 0.0013 2.7E-08 45.3 6.7 72 48-124 4-78 (88)
56 cd05693 S1_Rrp5_repeat_hs1_sc1 97.2 0.0009 2E-08 47.2 5.4 68 50-119 2-83 (100)
57 cd04473 S1_RecJ_like S1_RecJ_l 97.2 0.0023 5E-08 42.6 7.1 59 47-122 12-71 (77)
58 PTZ00248 eukaryotic translatio 97.2 0.00086 1.9E-08 56.5 5.9 64 49-120 15-81 (319)
59 PRK04163 exosome complex RNA-b 97.1 0.0011 2.5E-08 53.3 5.6 65 47-118 59-127 (235)
60 cd04465 S1_RPS1_repeat_ec2_hs2 97.0 0.0052 1.1E-07 39.4 7.0 58 52-122 1-61 (67)
61 TIGR02696 pppGpp_PNP guanosine 97.0 0.0023 4.9E-08 59.1 6.9 65 48-117 644-710 (719)
62 PRK06299 rpsA 30S ribosomal pr 96.9 0.003 6.5E-08 56.2 6.9 63 51-123 373-439 (565)
63 cd04455 S1_NusA S1_NusA: N-uti 96.9 0.014 2.9E-07 37.8 8.2 57 50-120 2-58 (67)
64 PRK13806 rpsA 30S ribosomal pr 96.8 0.0028 6.2E-08 55.9 6.1 61 51-122 379-443 (491)
65 PRK11824 polynucleotide phosph 96.8 0.0058 1.3E-07 56.2 8.3 63 46-119 616-682 (693)
66 PRK07400 30S ribosomal protein 96.8 0.0054 1.2E-07 51.4 7.5 64 49-123 194-260 (318)
67 PHA02945 interferon resistance 96.8 0.012 2.5E-07 41.0 7.7 65 48-121 8-75 (88)
68 TIGR00717 rpsA ribosomal prote 96.8 0.0044 9.6E-08 54.4 6.9 66 51-123 359-425 (516)
69 COG0557 VacB Exoribonuclease R 96.7 0.0059 1.3E-07 56.2 7.8 73 50-123 621-699 (706)
70 PRK03987 translation initiatio 96.7 0.0052 1.1E-07 50.4 6.8 64 48-122 5-74 (262)
71 PRK05054 exoribonuclease II; P 96.7 0.015 3.2E-07 53.1 10.2 76 47-125 555-641 (644)
72 COG0539 RpsA Ribosomal protein 96.6 0.0058 1.2E-07 54.8 6.5 68 48-123 189-256 (541)
73 PRK13806 rpsA 30S ribosomal pr 96.6 0.0066 1.4E-07 53.6 6.9 66 51-123 292-358 (491)
74 PRK07899 rpsA 30S ribosomal pr 96.6 0.0062 1.3E-07 54.0 6.6 65 51-123 208-272 (486)
75 PRK09521 exosome complex RNA-b 96.4 0.006 1.3E-07 47.3 5.1 65 45-117 58-133 (189)
76 PRK12269 bifunctional cytidyla 96.4 0.013 2.9E-07 55.2 8.1 64 51-122 752-819 (863)
77 PRK07400 30S ribosomal protein 96.4 0.014 3.1E-07 48.9 7.3 61 49-120 29-93 (318)
78 PRK12269 bifunctional cytidyla 96.4 0.01 2.2E-07 56.0 7.0 66 51-123 665-731 (863)
79 PRK07899 rpsA 30S ribosomal pr 96.3 0.022 4.7E-07 50.6 8.3 62 51-123 293-358 (486)
80 PLN00207 polyribonucleotide nu 96.3 0.0071 1.5E-07 57.1 5.4 66 45-118 747-814 (891)
81 PRK06676 rpsA 30S ribosomal pr 96.3 0.014 3E-07 49.6 6.7 64 49-123 190-256 (390)
82 TIGR02062 RNase_B exoribonucle 96.1 0.042 9.2E-07 50.2 9.6 70 52-124 558-636 (639)
83 TIGR00717 rpsA ribosomal prote 96.0 0.028 6.1E-07 49.3 7.4 61 51-122 446-510 (516)
84 PRK06676 rpsA 30S ribosomal pr 95.9 0.044 9.4E-07 46.6 8.2 63 48-121 14-81 (390)
85 PRK06299 rpsA 30S ribosomal pr 95.9 0.024 5.1E-07 50.5 6.6 65 50-121 285-350 (565)
86 PRK00087 4-hydroxy-3-methylbut 95.8 0.03 6.5E-07 51.0 7.1 62 50-122 561-626 (647)
87 COG1098 VacB Predicted RNA bin 95.7 0.012 2.6E-07 43.5 3.4 62 49-118 3-65 (129)
88 cd05790 S1_Rrp40 S1_Rrp40: Rrp 95.7 0.045 9.8E-07 37.8 6.0 73 47-128 2-76 (86)
89 cd05791 S1_CSL4 S1_CSL4: CSL4, 95.5 0.026 5.7E-07 39.1 4.3 63 47-117 2-75 (92)
90 COG2183 Tex Transcriptional ac 95.5 0.026 5.6E-07 52.5 5.3 63 49-122 656-722 (780)
91 COG0539 RpsA Ribosomal protein 95.4 0.038 8.3E-07 49.7 6.0 70 47-124 273-343 (541)
92 PRK12327 nusA transcription el 95.3 0.093 2E-06 45.0 7.8 61 47-121 130-190 (362)
93 PRK09202 nusA transcription el 95.2 0.081 1.8E-06 46.8 7.5 61 47-121 130-190 (470)
94 PRK00087 4-hydroxy-3-methylbut 95.2 0.049 1.1E-06 49.7 6.2 61 51-122 477-540 (647)
95 COG1093 SUI2 Translation initi 94.7 0.027 5.8E-07 46.4 2.8 64 49-120 9-75 (269)
96 TIGR01953 NusA transcription t 94.1 0.22 4.9E-06 42.4 7.3 60 47-120 127-187 (341)
97 COG1097 RRP4 RNA-binding prote 93.6 1.1 2.4E-05 36.6 10.0 71 46-122 59-132 (239)
98 COG1185 Pnp Polyribonucleotide 93.1 0.22 4.8E-06 45.9 5.9 65 45-117 613-678 (692)
99 PF10447 EXOSC1: Exosome compo 91.5 0.29 6.3E-06 33.5 3.6 23 49-71 2-24 (82)
100 cd05699 S1_Rrp5_repeat_hs7 S1_ 88.0 1.2 2.7E-05 29.8 4.4 54 52-114 1-60 (72)
101 PRK12328 nusA transcription el 86.5 4.2 9.2E-05 35.2 7.9 61 47-121 134-195 (374)
102 KOG3409 Exosomal 3'-5' exoribo 86.2 2.5 5.5E-05 33.1 5.8 75 38-119 57-139 (193)
103 TIGR00757 RNaseEG ribonuclease 83.7 6.1 0.00013 34.5 7.8 75 48-122 22-103 (414)
104 PF13509 S1_2: S1 domain; PDB: 82.7 1.8 4E-05 27.5 3.1 28 51-78 1-29 (61)
105 PRK12329 nusA transcription el 78.7 7.7 0.00017 34.4 6.6 59 47-119 148-212 (449)
106 PF10246 MRP-S35: Mitochondria 78.1 12 0.00025 26.9 6.3 72 48-134 20-101 (104)
107 KOG1004 Exosomal 3'-5' exoribo 76.4 35 0.00075 27.7 9.1 85 36-129 50-136 (230)
108 COG1096 Predicted RNA-binding 73.3 16 0.00034 28.9 6.4 69 46-116 59-132 (188)
109 KOG1070 rRNA processing protei 70.3 18 0.00039 36.7 7.3 67 50-124 1161-1228(1710)
110 PRK11712 ribonuclease G; Provi 55.9 46 0.001 29.8 6.8 86 48-133 35-129 (489)
111 COG2996 Predicted RNA-bindinin 53.6 40 0.00087 28.2 5.6 54 51-120 155-209 (287)
112 COG4776 Rnb Exoribonuclease II 44.0 12 0.00026 33.8 1.3 74 48-123 558-639 (645)
113 PF07238 PilZ: PilZ domain; I 42.5 89 0.0019 19.9 5.5 34 38-71 8-41 (102)
114 PHA02858 EIF2a-like PKR inhibi 42.0 38 0.00083 23.5 3.2 64 48-120 13-78 (86)
115 cd04486 YhcR_OBF_like YhcR_OBF 40.1 1.1E+02 0.0024 20.2 6.1 58 55-118 2-60 (78)
116 KOG4078 Putative mitochondrial 38.4 58 0.0012 24.9 4.0 62 44-120 75-137 (173)
117 KOG1070 rRNA processing protei 37.7 1.3E+02 0.0028 31.0 7.1 71 50-126 508-578 (1710)
118 KOG1067 Predicted RNA-binding 33.2 69 0.0015 29.8 4.3 63 52-122 669-732 (760)
119 PRK10811 rne ribonuclease E; R 32.4 2.1E+02 0.0046 28.3 7.5 73 49-122 36-113 (1068)
120 KOG3013 Exosomal 3'-5' exoribo 30.5 89 0.0019 26.2 4.2 38 46-83 80-123 (301)
121 KOG2055 WD40 repeat protein [G 29.9 1.4E+02 0.003 27.0 5.5 100 25-132 354-458 (514)
122 PF00116 COX2: Cytochrome C ox 29.8 86 0.0019 22.4 3.6 18 98-115 45-62 (120)
123 PF01938 TRAM: TRAM domain; I 26.2 95 0.0021 19.0 3.0 23 48-70 37-59 (61)
124 PF01629 DUF22: Domain of unkn 25.4 2E+02 0.0043 20.7 4.8 33 91-123 37-69 (112)
125 PF05899 Cupin_3: Protein of u 24.7 1.9E+02 0.0041 18.6 4.3 28 53-81 30-57 (74)
126 PF01959 DHQS: 3-dehydroquinat 24.1 2.3E+02 0.005 24.5 5.7 58 14-83 194-251 (354)
127 COG2996 Predicted RNA-bindinin 24.0 1.2E+02 0.0026 25.5 3.8 29 50-78 72-102 (287)
128 PF12306 PixA: Inclusion body 22.4 1.8E+02 0.0038 22.2 4.4 30 100-129 59-88 (172)
129 PF07076 DUF1344: Protein of u 21.3 2.1E+02 0.0045 18.6 3.8 33 54-87 4-36 (61)
130 KOG2916 Translation initiation 21.3 92 0.002 26.2 2.7 31 48-78 13-46 (304)
131 PF01835 A2M_N: MG2 domain; I 21.2 1.4E+02 0.0031 19.7 3.3 20 100-119 8-27 (99)
132 PF07177 Neuralized: Neuralize 21.0 1.2E+02 0.0026 19.6 2.8 29 100-128 36-64 (69)
133 PRK10943 cold shock-like prote 20.9 2.4E+02 0.0052 18.1 4.5 45 24-69 15-63 (69)
134 PF15572 Imm26: Immunity prote 20.9 2.4E+02 0.0051 19.9 4.3 61 21-89 3-69 (96)
No 1
>PTZ00162 DNA-directed RNA polymerase II subunit 7; Provisional
Probab=100.00 E-value=4.8e-44 Score=276.23 Aligned_cols=133 Identities=32% Similarity=0.592 Sum_probs=127.5
Q ss_pred cceeEEEeCCeeEEEEEeecceecceeEEcCCccEEEEEEEEEEEEeecCCCEEEEEEEEEecccEEEEccccEEEE---
Q 032315 2 KDVEGTCSGRHGFAVAITGAESIGKGLIRNGTVLVTFLVRCQCIVFRPFKGEILGAGVTMVNKMGFLAEAGAVQIFC--- 78 (143)
Q Consensus 2 ~~~EG~~~~~~GliI~i~dI~~i~eG~I~~gdG~~~~~V~F~~lvFrPf~gEVv~G~V~~v~~~Gi~v~iGp~~ifI--- 78 (143)
+++||||++++||||+++|+.++++|+|.||||+++|+|+|||++||||+|||++|+|++++++|+|+++||+++||
T Consensus 32 ~~~egkv~~~~GliV~v~di~~i~~G~I~~gdG~~~~~V~FraivFrPf~gEVv~g~V~~v~~~G~~v~~Gp~~ifI~~~ 111 (176)
T PTZ00162 32 SQVEGQCTRKYGYVICVIRIIHNEPGRVQDGTGMIVVNVKYQAIVFKPFKDEVLDAIVTDVNKLGFFAQAGPLKAFVSRS 111 (176)
T ss_pred HHHCCCCcCcccEEEEEEEeeEecCCEEEcCCCCEEEEEEEEEEEEecCCCCEEEEEEEEEecceEEEEeeCeEEEEcHH
Confidence 57999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EcCCCceecCCC-CceEEcCCceEEEcCCCeEEEEEEEEEEccCCeEEEEEcccccc
Q 032315 79 LIPDDMELQTGD-LPSYTTSDGSVKIQKDCELWLKIIGTQVDVTEIEKARREVGKQR 134 (143)
Q Consensus 79 ~lp~~~~fd~~~-~~~~~~~~~~~~i~~g~~VR~RV~~v~~~~~~~~ai~~~~~~~~ 134 (143)
+||+++.||+++ .|+|.+++++.++++|+.|||||++++|+++++.|+|+|-+++-
T Consensus 112 ~l~~~~~fd~~~~~~~~~~~~~~~~i~~g~~VR~rV~~v~~~~~~~~~i~T~~~~~L 168 (176)
T PTZ00162 112 AIPPDFVYDSDSAYPCYISSDGQIQIKPNTEVRLRLQGVRYDASNLFAIATINSDYL 168 (176)
T ss_pred HCCCccEECCCCCcceEecCCCcEEECCCCEEEEEEEEEEecCCCcEEEEEecCCCc
Confidence 999999999875 59999778899999999999999999999999999999988864
No 2
>KOG3298 consensus DNA-directed RNA polymerase subunit E' [Transcription]
Probab=100.00 E-value=2.8e-39 Score=244.50 Aligned_cols=132 Identities=45% Similarity=0.757 Sum_probs=125.5
Q ss_pred cceeEEEeCCeeEEEEEeecceecceeEEcCCccEEEEEEEEEEEEeecCCCEEEEEEEEEecccEEEEccccEEEE---
Q 032315 2 KDVEGTCSGRHGFAVAITGAESIGKGLIRNGTVLVTFLVRCQCIVFRPFKGEILGAGVTMVNKMGFLAEAGAVQIFC--- 78 (143)
Q Consensus 2 ~~~EG~~~~~~GliI~i~dI~~i~eG~I~~gdG~~~~~V~F~~lvFrPf~gEVv~G~V~~v~~~Gi~v~iGp~~ifI--- 78 (143)
+++||+|.+++||+||++++.+|++|+|.+++|.+.|.|.|+|++||||+|||++|+|++++++|+|+++||+++|+
T Consensus 32 ~~veg~ctg~~Gyvi~vt~ld~Ig~g~I~~~~G~v~FpVky~av~FkpfKGEVvdgvV~~Vnk~G~F~~~GPl~~f~ssh 111 (170)
T KOG3298|consen 32 AEVEGKCTGKYGYVIAVTTLDNIGEGRIRPGTGFVTFPVKYKAVTFKPFKGEVVDGVVTKVNKMGVFARSGPLEVFYSSH 111 (170)
T ss_pred HHhhccccccccEEEEEEEhhhccCCccccCCceEEEEEEEEEEEEeecCCcEEEEEEEEEeeeeEEEeccceEeeeecc
Confidence 57999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EcCCCceecCCCC-ceEEcCCceEEEcCCCeEEEEEEEEEEccCCeEEEEEcccccc
Q 032315 79 LIPDDMELQTGDL-PSYTTSDGSVKIQKDCELWLKIIGTQVDVTEIEKARREVGKQR 134 (143)
Q Consensus 79 ~lp~~~~fd~~~~-~~~~~~~~~~~i~~g~~VR~RV~~v~~~~~~~~ai~~~~~~~~ 134 (143)
++|++++|+++++ ++|+.+|.. .|++|++||++|++++|+.++++|+|+|=|++-
T Consensus 112 l~ppd~~f~p~~n~P~f~~~d~s-~I~~~~~VR~kiigtr~~~~~i~algtl~~D~L 167 (170)
T KOG3298|consen 112 LKPPDYEFDPGENPPNFQTEDES-VIQKGVEVRLKIIGTRVDETEIFALGTLKGDYL 167 (170)
T ss_pred cCCCCcccCCCCCCCcccccccc-eeeeCcEEEEEEEEEEEeeeeEEEEEEecCccc
Confidence 8899999999875 778877654 999999999999999999999999999998863
No 3
>COG1095 RPB7 DNA-directed RNA polymerase, subunit E' [Transcription]
Probab=100.00 E-value=4.9e-39 Score=248.16 Aligned_cols=128 Identities=20% Similarity=0.354 Sum_probs=118.6
Q ss_pred cceeEEEeCCeeEEEEEeecceecceeEEcCCccEEEEEEEEEEEEeecCCCEEEEEEEEEecccEEEEccccEEEE---
Q 032315 2 KDVEGTCSGRHGFAVAITGAESIGKGLIRNGTVLVTFLVRCQCIVFRPFKGEILGAGVTMVNKMGFLAEAGAVQIFC--- 78 (143)
Q Consensus 2 ~~~EG~~~~~~GliI~i~dI~~i~eG~I~~gdG~~~~~V~F~~lvFrPf~gEVv~G~V~~v~~~Gi~v~iGp~~ifI--- 78 (143)
++|||||++++|+||+++|+.++++|+|.||||++||+|+||||+|+||+|||++|+|++++++|+|+++||+|+|+
T Consensus 32 ~k~eG~~~~~~G~~v~V~~v~~igeG~I~~GDG~~y~~V~f~al~fkP~~gEVV~GeVv~~~~~G~fV~igp~dglvh~s 111 (183)
T COG1095 32 EKYEGKLDGDVGLVVLVLDVKEIGEGIIVPGDGSTYHEVKFRALVFKPFRGEVVEGEVVEVVEFGAFVRIGPLDGLVHVS 111 (183)
T ss_pred HHhcceEccccCEEEEEEEeeEeeccEEecCCCcEEEEEEEEEEEEEeccccEEEEEEEEEeecceEEEeccccccccHh
Confidence 58999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EcCCC-ceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEEccCC---eEEEEEcc
Q 032315 79 LIPDD-MELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQVDVTE---IEKARREV 130 (143)
Q Consensus 79 ~lp~~-~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~~~~~---~~ai~~~~ 130 (143)
|++|+ +.||++ +|.|.++++++++++||.||+||+++++++.+ ..+.++|-
T Consensus 112 qi~dd~~~~d~~-~~~~~g~~tk~~i~~gd~VR~RIv~~s~~~~~~~~~~I~lTmr 166 (183)
T COG1095 112 QIMDDYIDYDEK-NKVLIGEETKRVLKVGDKVRARIVGVSLKSRRPRESKIGLTMR 166 (183)
T ss_pred hccCcccccCcc-cceeeecccceEEecCCEEEEEEEEEecccCccccceEEEEec
Confidence 88887 445555 68999999999999999999999999998864 77777664
No 4
>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=100.00 E-value=5.1e-34 Score=220.02 Aligned_cols=130 Identities=16% Similarity=0.203 Sum_probs=113.7
Q ss_pred cceeEEEeCCeeEEEEEeecceecceeEEcCCccEEEEEEEEEEEEeecCCCEEEEEEEEEecccEEEEccccEEEE---
Q 032315 2 KDVEGTCSGRHGFAVAITGAESIGKGLIRNGTVLVTFLVRCQCIVFRPFKGEILGAGVTMVNKMGFLAEAGAVQIFC--- 78 (143)
Q Consensus 2 ~~~EG~~~~~~GliI~i~dI~~i~eG~I~~gdG~~~~~V~F~~lvFrPf~gEVv~G~V~~v~~~Gi~v~iGp~~ifI--- 78 (143)
++|||||++++||||+++||.++++|+|.||||+++|+|+|||++|||++||+++|+|++++++|+|+++||++.++
T Consensus 32 ~~~~gk~~~~~G~~i~v~di~~i~~g~i~~gdG~~~~~V~f~~i~f~p~~gEvv~G~V~~v~~~GifV~lg~~~gi~~~~ 111 (179)
T TIGR00448 32 EKFEGRLDKNVGLCITIYDIEDIGEGKVIPGDGSAYHNVTFRALVFKPELGEIVEGEVIEIVEFGAFVSLGPFDGLFHVS 111 (179)
T ss_pred HHhcCcCcCCcCEEEEEEEeEEecCCEEECCCCCEEEEEEEEEEEEeccCCCEEEEEEEEEEeeEEEEEeCCceEEEEcH
Confidence 58999999999999999999999999999999999999999999999999999999999999999999999988555
Q ss_pred -EcCCCceecCCC-CceEEcCCceEEEcCCCeEEEEEEEEEEccC---CeEEEEEccccc
Q 032315 79 -LIPDDMELQTGD-LPSYTTSDGSVKIQKDCELWLKIIGTQVDVT---EIEKARREVGKQ 133 (143)
Q Consensus 79 -~lp~~~~fd~~~-~~~~~~~~~~~~i~~g~~VR~RV~~v~~~~~---~~~ai~~~~~~~ 133 (143)
.+|+++.||+++ .|.| ++++.+++.|+.||+||.++++++. .....++|-.++
T Consensus 112 ~l~~~~~~~d~~~~~~~~--~~~~~~~~~Gd~VrvrV~~v~~~~~~~~~~~I~lt~k~~~ 169 (179)
T TIGR00448 112 QVTDDYCYYDPKESALIG--KETKKVLDEGDKVRARIVALSLKDRRPEGSKIGLTMRQPL 169 (179)
T ss_pred HhCCCceEEccccceEEE--ccCCeEEcCCCEEEEEEEEEEccCCCCCcceEEEEeccCc
Confidence 567778899876 4555 5667999999999999999998543 233466665444
No 5
>KOG3297 consensus DNA-directed RNA polymerase subunit E' [Transcription]
Probab=100.00 E-value=1.5e-34 Score=222.58 Aligned_cols=130 Identities=14% Similarity=0.271 Sum_probs=115.3
Q ss_pred cceeEEEeCCeeEEEEEeecceecceeEEcCCccEEEEEEEEEEEEeecCCCEEEEEEEEEecccEEEEccc-cEEEE--
Q 032315 2 KDVEGTCSGRHGFAVAITGAESIGKGLIRNGTVLVTFLVRCQCIVFRPFKGEILGAGVTMVNKMGFLAEAGA-VQIFC-- 78 (143)
Q Consensus 2 ~~~EG~~~~~~GliI~i~dI~~i~eG~I~~gdG~~~~~V~F~~lvFrPf~gEVv~G~V~~v~~~Gi~v~iGp-~~ifI-- 78 (143)
+++-+|+++|+|||||++||+++++|+|.||||+++.+|.||++|||||.|||+.|+|++|+++|+++++|| .||||
T Consensus 32 ~k~anKvl~nvGLCI~vyDi~~v~e~~v~pGDGas~~~V~FR~vVFrPF~gEVi~gki~~cs~eG~rvtl~FFdDI~IP~ 111 (202)
T KOG3297|consen 32 RKLANKVLPNVGLCICVYDILEVEEGIVLPGDGASYARVWFRVVVFRPFVGEVITGKIKECSEEGLRVTLGFFDDIFIPK 111 (202)
T ss_pred HHHHhhhcccccEEEEEeEeeeecceEEecCCCceEEEEEEEEEEEecccceEEEEEeecCCccceEEEEEeeeceeech
Confidence 356789999999999999999999999999999999999999999999999999999999999999999998 66999
Q ss_pred -EcCCCceecCCC-CceEEcC-----CceEEEcCCCeEEEEEEEEEEcc-CCeEEEEEccc
Q 032315 79 -LIPDDMELQTGD-LPSYTTS-----DGSVKIQKDCELWLKIIGTQVDV-TEIEKARREVG 131 (143)
Q Consensus 79 -~lp~~~~fd~~~-~~~~~~~-----~~~~~i~~g~~VR~RV~~v~~~~-~~~~ai~~~~~ 131 (143)
.||+++.|++++ .|.|.++ .+++|++.|++|||||.+++|.. +...+-..++|
T Consensus 112 ~~L~~p~~f~~~e~vWVWey~~Edg~~~~Ly~D~~e~IRFRV~~e~f~d~~p~~~~~~~t~ 172 (202)
T KOG3297|consen 112 EMLPEPCVFEPDEQVWVWEYEQEDGPGTKLYFDVGEEIRFRVEDESFVDVSPEGNSTAITG 172 (202)
T ss_pred hhCCCCcccccccEEEEEEecccCCCCceeEecCCCeEEEEEeeecccccCcccccccccc
Confidence 999999999887 5999986 57899999999999999999833 33333333444
No 6
>PRK08563 DNA-directed RNA polymerase subunit E'; Provisional
Probab=100.00 E-value=7.8e-33 Score=214.13 Aligned_cols=131 Identities=18% Similarity=0.215 Sum_probs=115.5
Q ss_pred cceeEEEeCCeeEEEEEeecceecceeEEcCCccEEEEEEEEEEEEeecCCCEEEEEEEEEecccEEEEccccEEEE---
Q 032315 2 KDVEGTCSGRHGFAVAITGAESIGKGLIRNGTVLVTFLVRCQCIVFRPFKGEILGAGVTMVNKMGFLAEAGAVQIFC--- 78 (143)
Q Consensus 2 ~~~EG~~~~~~GliI~i~dI~~i~eG~I~~gdG~~~~~V~F~~lvFrPf~gEVv~G~V~~v~~~Gi~v~iGp~~ifI--- 78 (143)
++|||||++++||||+++||.++++|+|.||||+++|+|+|||++|+|++||+++|+|++++++|+|+++||.+.|+
T Consensus 32 ~~~~~k~~~~~G~~v~v~di~~i~~g~i~~gdg~~~~~v~f~~lvf~P~~GEVv~g~V~~v~~~Gi~V~lg~~~g~v~~~ 111 (187)
T PRK08563 32 EKYEGRIDKELGIIVAVLDVKVIGEGKIVPGDGATYHEVEFDALVFKPELQEVVEGEVVEVVEFGAFVRIGPVDGLLHIS 111 (187)
T ss_pred HHhhCcCcCCcCEEEEEEEeEEecccEEecCCCCcEEEEEEEEEEEeccCCCEEEEEEEEEEccEEEEEEeCceEEEEcH
Confidence 57999999999999999999999999999999999999999999999999999999999999999999999999888
Q ss_pred EcC-CCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEEccCCe--EEEE-Eccccc
Q 032315 79 LIP-DDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQVDVTEI--EKAR-REVGKQ 133 (143)
Q Consensus 79 ~lp-~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~~~~~~--~ai~-~~~~~~ 133 (143)
+++ +++.||+++. .|..++.+.+++.|+.||+||.+++++..+. .+|+ +|-+++
T Consensus 112 ~l~~~~~~~d~~~~-~~~~~~~~~~i~~Gd~VrvrV~~v~~~~~~~~~~~I~ls~~~~~ 169 (187)
T PRK08563 112 QIMDDYISYDPKNG-RLIGKESKRVLKVGDVVRARIVAVSLKERRPRGSKIGLTMRQPG 169 (187)
T ss_pred HcCCCceEEccccc-eEEEccCCeEEcCCCEEEEEEEEEEcccCCCCCCEEEEEecCCC
Confidence 555 4588998853 5666677899999999999999999987654 3444 665553
No 7
>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=99.90 E-value=4.5e-23 Score=143.13 Aligned_cols=82 Identities=46% Similarity=0.690 Sum_probs=76.4
Q ss_pred CCCEEEEEEEEEecccEEEEccccEEEE---EcCCCceecCC-CCceEEcCCceEEEcCCCeEEEEEEEEEEccCCeEEE
Q 032315 51 KGEILGAGVTMVNKMGFLAEAGAVQIFC---LIPDDMELQTG-DLPSYTTSDGSVKIQKDCELWLKIIGTQVDVTEIEKA 126 (143)
Q Consensus 51 ~gEVv~G~V~~v~~~Gi~v~iGp~~ifI---~lp~~~~fd~~-~~~~~~~~~~~~~i~~g~~VR~RV~~v~~~~~~~~ai 126 (143)
+|||++|+|++++++|+|+++||+++|+ ++|+++.|+++ +.|+|.. +++++|++|+.|||||.+++|++++++|+
T Consensus 1 kgEVi~g~V~~v~~~G~~v~~Gpl~~f~~~~~ip~~~~~~~~~~~~~~~~-~~~~~i~~g~~VR~rV~~v~~~~~~~~~i 79 (88)
T cd04462 1 KGEVVDAIVTSVNKTGFFAEVGPLSIFISRHLIPSDMEFDPNASPPCFTS-NEDIVIKKDTEVRLKIIGTRVDATDIFAI 79 (88)
T ss_pred CCcEEEEEEEEEeccEEEEEEcCceEEEEeeecCccceECCcCCCCeEeC-CCcEEECCCCEEEEEEEEEEEccCceEEE
Confidence 6999999999999999999999999999 99999999985 5789974 46899999999999999999999999999
Q ss_pred EEccccc
Q 032315 127 RREVGKQ 133 (143)
Q Consensus 127 ~~~~~~~ 133 (143)
|+|-+++
T Consensus 80 gt~~~~~ 86 (88)
T cd04462 80 GTIKDDY 86 (88)
T ss_pred EEccCCC
Confidence 9999886
No 8
>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=99.83 E-value=8.3e-20 Score=133.85 Aligned_cols=71 Identities=17% Similarity=0.303 Sum_probs=60.9
Q ss_pred ecCCCEEEEEEEEEecccEEEEccc-cEEEE---EcCCCceecCCC-CceEEc-CCceEEEcCCCeEEEEEEEEEEc
Q 032315 49 PFKGEILGAGVTMVNKMGFLAEAGA-VQIFC---LIPDDMELQTGD-LPSYTT-SDGSVKIQKDCELWLKIIGTQVD 119 (143)
Q Consensus 49 Pf~gEVv~G~V~~v~~~Gi~v~iGp-~~ifI---~lp~~~~fd~~~-~~~~~~-~~~~~~i~~g~~VR~RV~~v~~~ 119 (143)
||+|||+.|+|++++++|+++++|| .|||| +||+++.||+++ .|.|.+ ++++++++.|++|||||.+++|.
T Consensus 1 PF~gEvl~g~I~~~~~~Gi~vslgFFddI~IP~~~L~~ps~fd~~~~~W~W~~~~~~~l~~d~ge~IRFRV~~~~f~ 77 (122)
T PF08292_consen 1 PFVGEVLTGKIKSSTAEGIRVSLGFFDDIFIPPSLLPEPSRFDEEEQAWVWEYDEEQELFFDIGEEIRFRVESEIFP 77 (122)
T ss_dssp --TT-EEEEEEEEEETTEEEEEECCEEEEEEECCCC-TTEEEECCCTEEEEEESSSEEEEE-TT-EEEEEEEEEEE-
T ss_pred CCCCCEEEEEEEecCCCcEEEEecccccEEECHHHCCCCCccCccCCEEEEECCCCceeEccCCCEEEEEEeEEEEe
Confidence 8999999999999999999999998 66999 999999999886 599999 88899999999999999999993
No 9
>cd04330 RNAP_III_Rpc25_N RNAP_III_Rpc25_N: Rpc25, N-terminal ribonucleoprotein (RNP) domain. Rpc25 is a subunit of eukaryotic RNA polymerase (RNAP) III and is homologous to Rpa43 of eukaryotic RNAP I, Rpb7 of eukaryotic RNAP II, and RpoE of archaeal RNAP. Rpc25 has two domains, an N-terminal RNP domain and a C-terminal oligonucleotide-binding (OB) domain, both of which are thought to bind single-stranded RNA. Rpc25 heterodimerizes with Rpc17 and plays an important role in transcription initiation. RNAP III transcribes diverse structural and catalytic RNAs including 5S ribosomal RNAs, tRNAs, and a small number of snRNAs involved in RNA and protein synthesis.
Probab=99.78 E-value=3.3e-19 Score=121.84 Aligned_cols=50 Identities=22% Similarity=0.382 Sum_probs=48.7
Q ss_pred cceeEEEeCCeeEEEEEeecceecceeEEcCCccEEEEEEEEEEEEeecC
Q 032315 2 KDVEGTCSGRHGFAVAITGAESIGKGLIRNGTVLVTFLVRCQCIVFRPFK 51 (143)
Q Consensus 2 ~~~EG~~~~~~GliI~i~dI~~i~eG~I~~gdG~~~~~V~F~~lvFrPf~ 51 (143)
++||||+++++|+||+++|+.++++|+|.||||+++|+|+|||++||||+
T Consensus 31 ~ky~gkv~~~~Gl~v~v~di~~i~eG~I~~gdG~~~~~V~Fr~lvFrPf~ 80 (80)
T cd04330 31 KKYANKVIQNVGLCICLYDILEVEDGYILPGDGASHYKVTFRMVVFRPFV 80 (80)
T ss_pred HHhCCcEeCCccEEEEEEEeEEEcCCEEECCCCCEEEEEEEEEEEEECCC
Confidence 58999999999999999999999999999999999999999999999985
No 10
>cd04329 RNAP_II_Rpb7_N RNAP_II_Rpb7_N: Rpb7, N-terminal ribonucleoprotein (RNP) domain. Rpb7 is a subunit of eukaryotic RNA polymerase (RNAP) II that is homologous to Rpc25 of RNAP III, RpoE of archaeal RNAP, and Rpa43 of eukaryotic RNAP I. Rpb7 heterodimerizes with Rpb4 and this heterodimer binds the 10-subunit core of RNAP II, forming part of the floor of the DNA-binding cleft. Rpb7 has two domains, an N-terminal RNP domain and a C-terminal oligonucleotide-binding (OB) domain, both of which bind single-stranded RNA. Rpb7 is thought to interact with the nascent RNA strand as it exits the RNAP II complex during transcription elongation. The Rpb7/Rpb4 heterodimer is also thought to serve as an upstream interface between the C-terminal domain of Rpb1 and the transcription factor IIB (TFIIB), recruiting pol II to the pol II promoter.
Probab=99.77 E-value=4e-19 Score=121.41 Aligned_cols=50 Identities=48% Similarity=0.886 Sum_probs=48.7
Q ss_pred cceeEEEeCCeeEEEEEeecceecceeEEcCCccEEEEEEEEEEEEeecC
Q 032315 2 KDVEGTCSGRHGFAVAITGAESIGKGLIRNGTVLVTFLVRCQCIVFRPFK 51 (143)
Q Consensus 2 ~~~EG~~~~~~GliI~i~dI~~i~eG~I~~gdG~~~~~V~F~~lvFrPf~ 51 (143)
+++||||.+++|+|||++|+.++++|+|.||||+++|+|+|||++||||+
T Consensus 31 ~~~egk~~~~~G~iv~v~di~~i~~G~I~~gdG~~~~~V~F~aivfrPf~ 80 (80)
T cd04329 31 EEVEGTCTGDYGYIIAVTDIDDIGEGKILPGTGSVEFPVKYKAIVFKPFK 80 (80)
T ss_pred HHhCCcCcCceeEEEEEEEeeEecCcEEEcCCCCEEEEEEEEEEEEEccC
Confidence 58999999999999999999999999999999999999999999999996
No 11
>cd00655 RNAP_Rpb7_N_like RNAP_Rpb7_N_like: This conserved domain represents the N-terminal ribonucleoprotein (RNP) domain of the Rpb7 subunit of eukaryotic RNA polymerase (RNAP) II and its homologs, Rpa43 of eukaryotic RNAP I, Rpc25 of eukaryotic RNAP III, and RpoE (subunit E) of archaeal RNAP. These proteins have, in addition to their N-terminal RNP domain, a C-terminal oligonucleotide-binding (OB) domain. Each of these subunits heterodimerizes with another RNAP subunit (Rpb7 to Rpb4, Rpc25 to Rpc17, RpoE to RpoF, and Rpa43 to Rpa14). The heterodimer is thought to tether the RNAP to a given promoter via its interactions with a promoter-bound transcription factor.The heterodimer is also thought to bind and position nascent RNA as it exits the polymerase complex.
Probab=99.77 E-value=6.8e-19 Score=120.20 Aligned_cols=50 Identities=30% Similarity=0.457 Sum_probs=48.6
Q ss_pred cceeEEEeCCeeEEEEEeecceecceeEEcCCccEEEEEEEEEEEEeecC
Q 032315 2 KDVEGTCSGRHGFAVAITGAESIGKGLIRNGTVLVTFLVRCQCIVFRPFK 51 (143)
Q Consensus 2 ~~~EG~~~~~~GliI~i~dI~~i~eG~I~~gdG~~~~~V~F~~lvFrPf~ 51 (143)
+++||||++++|+||+++|+.++++|+|.||||+++|+|+|||++||||+
T Consensus 31 ~k~~gkv~~~~G~~v~v~di~~i~~G~I~~gdG~~~~~V~F~~ivFrPf~ 80 (80)
T cd00655 31 EKGEGDRTPVVGIILAIKDTKDIPEGAIRPGDGSAYVNVSFRAVVFKPFS 80 (80)
T ss_pred HHhCCeEeCCccEEEEEEEeEEEcCCEEECCCCCEEEEEEEEEEEEEcCC
Confidence 58999999999999999999999999999999999999999999999985
No 12
>cd04331 RNAP_E_N RNAP_E_N: RpoE, N-terminal ribonucleoprotein (RNP) domain. RpoE (subunit E) is a subunit of the archaeal RNA polymerase (RNAP) that is homologous to Rpb7 of eukaryotic RNAP II, Rpc25 of eukaryotic RNAP III, and Rpa43 of eukaryotic RNAP I. RpoE heterodimerizes with RpoF, another RNA polymerase subunit. RpoE has an elongated two-domain structure that includes an N-terminal RNP domain and a C-terminal oligonucleotide-binding (OB) domain. Both domains of RpoE bind single-stranded RNA.
Probab=99.73 E-value=3.2e-18 Score=116.99 Aligned_cols=49 Identities=29% Similarity=0.441 Sum_probs=47.8
Q ss_pred cceeEEEeCCeeEEEEEeecceecceeEEcCCccEEEEEEEEEEEEeec
Q 032315 2 KDVEGTCSGRHGFAVAITGAESIGKGLIRNGTVLVTFLVRCQCIVFRPF 50 (143)
Q Consensus 2 ~~~EG~~~~~~GliI~i~dI~~i~eG~I~~gdG~~~~~V~F~~lvFrPf 50 (143)
+++||||++++|+||+++||.++++|+|.||||+++|+|+|||++|||.
T Consensus 31 ~~~egk~~~~~G~iv~v~di~~i~eG~I~~gdG~~~~~V~F~~ivFrP~ 79 (80)
T cd04331 31 EKYEGRLDKDLGKIVSVLDVKDVGEGKIVHGDGAVYHEVRFDALVFKPE 79 (80)
T ss_pred HHhcCcCcCCCCEEEEEEEEEEecCCEEEcCCCCEEEEEEEEEEEEecC
Confidence 6899999999999999999999999999999999999999999999996
No 13
>PF03876 SHS2_Rpb7-N: SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397; InterPro: IPR005576 The eukaryotic RNA polymerase subunits RPB4 and RPB7 form a heterodimer that reversibly associates with the RNA polymerase II core. Archaeal cells contain a single RNAP made up of about 12 subunits, displaying considerable homology to the eukaryotic RNAPII subunits. The RPB4 and RPB7 homologs are called subunits F and E, respectively, and have been shown to form a stable heterodimer. While the RPB7 homologue is reasonably well conserved, the similarity between the eukaryotic RPB4 and the archaeal F subunit is barely detectable []. This entry represents the N-terminal, heterodimerisation domain of RPB7.; GO: 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2C35_F 3HKZ_E 2PMZ_T 2CKZ_D 2Y0S_E 2RF4_A 2JA7_G 1Y1V_G 2JA5_G 4A3D_G ....
Probab=99.42 E-value=2.2e-13 Score=89.82 Aligned_cols=46 Identities=30% Similarity=0.461 Sum_probs=43.7
Q ss_pred cceeEEEeCCeeEEEEEeecceecceeEEcCCccEEEEEEEEEEEE
Q 032315 2 KDVEGTCSGRHGFAVAITGAESIGKGLIRNGTVLVTFLVRCQCIVF 47 (143)
Q Consensus 2 ~~~EG~~~~~~GliI~i~dI~~i~eG~I~~gdG~~~~~V~F~~lvF 47 (143)
+++|||+.+++|+||+++||..+++|+|.+|||+++|+|+|+|++|
T Consensus 25 ~~~~~k~~~~~G~~i~v~~i~~~~~g~I~~~~g~~~~~V~f~~lvF 70 (70)
T PF03876_consen 25 DKYEGKYIPELGVVIAVTDIKEISEGKIIPGDGFVYFKVTFRALVF 70 (70)
T ss_dssp HHHTTEEETTTEEEEEEEEEEEESCEEE-TTTSSEEEEEEEEEEEE
T ss_pred HHHhCcCcCCceEEEEEeeeeEecCcEEECCCCCEEEEEEEEEEEC
Confidence 5789999999999999999999999999999999999999999998
No 14
>cd04328 RNAP_I_Rpa43_N RNAP_I_Rpa43_N: Rpa43, N-terminal ribonucleoprotein (RNP) domain. Rpa43 is a subunit of eukaryotic RNA polymerase (RNAP) I that is homologous to Rpb7 of eukaryotic RNAP II, Rpc25 of eukaryotic RNP III, and RpoE of archaeal RNAP. Rpa43 has two domains, an N-terminal RNP domain and a C-terminal oligonucleotide-binding (OB) domain. Rpa43 heterodimerizes with Rpa14 and this heterodimer has genetic and biochemical characteristics similar to those of the Rpb7/Rpb4 heterodimer of RNAP II. In addition, the Rpa43/Rpa14 heterodimer binds single-stranded RNA, as is the case for the Rpb7/Rpb4 and the archaeal E/F complexes. The position of Rpa43/Rpa14 in the three-dimensional structure of RNAP I is similar to that of Rpb4/Rpb7, which forms an upstream interface between the C-terminal domain of Rpb1 and the transcription factor IIB (TFIIB), recruiting pol II to the pol II promoter. Rpb43 binds Rrn3, an rDNA-specific transcription factor, functionally equivalent to TFIIB, invo
Probab=98.86 E-value=4.9e-09 Score=72.44 Aligned_cols=45 Identities=18% Similarity=0.303 Sum_probs=41.9
Q ss_pred EEeCCe-eEEEEEeecceecc--eeEEcCCccEEEEEEEEEEEEeecC
Q 032315 7 TCSGRH-GFAVAITGAESIGK--GLIRNGTVLVTFLVRCQCIVFRPFK 51 (143)
Q Consensus 7 ~~~~~~-GliI~i~dI~~i~e--G~I~~gdG~~~~~V~F~~lvFrPf~ 51 (143)
|+.+++ |+|++.+|+..+++ |+|.+++|.++++|+||++||||+.
T Consensus 42 ky~~~l~Gv~l~~~di~~~~~~~~~i~~~~~~~~~~V~~~~lVFrP~~ 89 (89)
T cd04328 42 KYSPKLKGVVLAYSNIKLLEGELAKIVDDSPFIFVWISADFLVFRPKI 89 (89)
T ss_pred hhcccCCeEEEEecceEeccccceeeeCCCcEEEEEEEEEEEEEecCC
Confidence 677889 99999999988867 9999999999999999999999984
No 15
>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=98.85 E-value=3.7e-08 Score=65.63 Aligned_cols=71 Identities=14% Similarity=0.245 Sum_probs=57.5
Q ss_pred CCCEEEEEEEEEecccEEEEccc--cEEEE---EcCCC-ceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEEccCC
Q 032315 51 KGEILGAGVTMVNKMGFLAEAGA--VQIFC---LIPDD-MELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQVDVTE 122 (143)
Q Consensus 51 ~gEVv~G~V~~v~~~Gi~v~iGp--~~ifI---~lp~~-~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~~~~~ 122 (143)
.|++++|+|++++++|+|+.+++ .++++ .++++ +.||+.. +.+..+.....++.||.|++||.++......
T Consensus 1 ~g~~~~g~V~~v~~~G~fv~l~~~~~~G~v~~~~l~~~~~~~d~~~-~~~~~~~~~~~~~~gd~v~v~v~~vd~~~~~ 77 (83)
T cd04471 1 VGEEFDGVISGVTSFGLFVELDNLTVEGLVHVSTLGDDYYEFDEEN-HALVGERTGKVFRLGDKVKVRVVRVDLDRRK 77 (83)
T ss_pred CCCEEEEEEEeEEeeeEEEEecCCCEEEEEEEEecCCCcEEEcccc-eEEEeccCCCEEcCCCEEEEEEEEeccccCE
Confidence 38999999999999999999997 77888 67654 6777664 4566666678999999999999999864444
No 16
>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=3e-07 Score=64.18 Aligned_cols=79 Identities=13% Similarity=0.122 Sum_probs=61.6
Q ss_pred CEEEEEEEEEecccEEEEccccEEEE---EcCC-CceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEEccCC--eEEE
Q 032315 53 EILGAGVTMVNKMGFLAEAGAVQIFC---LIPD-DMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQVDVTE--IEKA 126 (143)
Q Consensus 53 EVv~G~V~~v~~~Gi~v~iGp~~ifI---~lp~-~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~~~~~--~~ai 126 (143)
|++.|+|+++++.|+|+.+++.++++ .+++ .+.|++.. .+|.+++.+..|+.||.|+++|.++..+... +..+
T Consensus 1 ~vv~g~V~~i~~~GifV~l~~v~G~v~~~~l~~~~~~~~~~~-~~~~~~~~~~~~~~Gd~v~vkI~~vd~~~~~~~~~~i 79 (99)
T cd04460 1 EVVEGEVVEVVDFGAFVRIGPVDGLLHISQIMDDYISYDPKN-KRLIGEETKRVLKVGDVVRARIVAVSLKERRPRESKI 79 (99)
T ss_pred CEEEEEEEEEEeccEEEEEcCeEEEEEEEEccCCceEechhh-eeecccCcCCEECCCCEEEEEEEEEeHHHCcCCCceE
Confidence 68999999999999999999888888 5554 46677664 4788877778999999999999999876543 4444
Q ss_pred E-Ecccc
Q 032315 127 R-REVGK 132 (143)
Q Consensus 127 ~-~~~~~ 132 (143)
+ ++-++
T Consensus 80 ~ls~k~~ 86 (99)
T cd04460 80 GLTMRQP 86 (99)
T ss_pred EEEEecC
Confidence 4 44433
No 17
>PF00575 S1: S1 RNA binding domain; InterPro: IPR003029 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. The S1 domain was originally identified in ribosomal protein S1 but is found in a large number of RNA-associated proteins. The structure of the S1 RNA-binding domain from the Escherichia coli polynucleotide phosphorylase has been determined using NMR methods and consists of a five-stranded antiparallel beta barrel. Conserved residues on one face of the barrel and adjacent loops form the putative RNA-binding site []. The structure of the S1 domain is very similar to that of cold shock proteins. This suggests that they may both be derived from an ancient nucleic acid-binding protein []. More information about these proteins can be found at Protein of the Month: RNA Exosomes []. This entry does not include translation initiation factor IF-1 S1 domains.; GO: 0003723 RNA binding; PDB: 3L7Z_F 2JE6_I 2JEA_I 2JEB_I 1E3P_A 2Y0S_E 1WI5_A 2BH8_A 2CQO_A 2EQS_A ....
Probab=98.62 E-value=1.5e-07 Score=61.65 Aligned_cols=65 Identities=23% Similarity=0.346 Sum_probs=51.9
Q ss_pred eecCCCEEEEEEEEEecccEEEEcc-ccEEEE---EcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEEccCCe
Q 032315 48 RPFKGEILGAGVTMVNKMGFLAEAG-AVQIFC---LIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQVDVTEI 123 (143)
Q Consensus 48 rPf~gEVv~G~V~~v~~~Gi~v~iG-p~~ifI---~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~~~~~~ 123 (143)
+|..|+++.|+|+++++.|+|+.+| ..++|| +++++ + .++....++.|+.|++||.++..+.+.+
T Consensus 1 k~~~G~iv~g~V~~v~~~g~~V~l~~~~~g~ip~~~l~~~----------~-~~~~~~~~~~G~~v~v~v~~vd~~~~~i 69 (74)
T PF00575_consen 1 KLKEGDIVEGKVTSVEDFGVFVDLGNGIEGFIPISELSDD----------R-IDDPSEVYKIGQTVRVKVIKVDKEKGRI 69 (74)
T ss_dssp -SSTTSEEEEEEEEEETTEEEEEESTSSEEEEEGGGSSSS----------E-ESSSHGTCETTCEEEEEEEEEETTTTEE
T ss_pred CCCCCCEEEEEEEEEECCEEEEEECCcEEEEEEeehhcCc----------c-ccccccccCCCCEEEEEEEEEECCCCeE
Confidence 5789999999999999999999999 799999 44322 1 2233457899999999999998876654
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=98.29 E-value=3.7e-06 Score=56.12 Aligned_cols=66 Identities=15% Similarity=0.172 Sum_probs=48.9
Q ss_pred CCCEEEEEEEEEecccEEEEccc-cEEEEEcCCCceecCCCCceE-Ec-CCceEEEcCCCeEEEEEEEEEEccCCe
Q 032315 51 KGEILGAGVTMVNKMGFLAEAGA-VQIFCLIPDDMELQTGDLPSY-TT-SDGSVKIQKDCELWLKIIGTQVDVTEI 123 (143)
Q Consensus 51 ~gEVv~G~V~~v~~~Gi~v~iGp-~~ifI~lp~~~~fd~~~~~~~-~~-~~~~~~i~~g~~VR~RV~~v~~~~~~~ 123 (143)
.|+++.|+|++++++|+|++++| .++||.+.+ + .|.| .. ++-...+++|+.|++||+++.-+.+.+
T Consensus 3 ~G~~V~g~V~~i~~~G~fV~l~~~v~G~v~~~~-l------s~~~~~~~~~~~~~~~~G~~v~~kVl~id~~~~~i 71 (74)
T cd05705 3 EGQLLRGYVSSVTKQGVFFRLSSSIVGRVLFQN-V------TKYFVSDPSLYNKYLPEGKLLTAKVLSVNSEKNLV 71 (74)
T ss_pred CCCEEEEEEEEEeCCcEEEEeCCCCEEEEEHHH-c------cCccccChhhHhcccCCCCEEEEEEEEEECCCCEE
Confidence 68999999999999999999998 889993210 0 1112 11 111367899999999999998765543
No 19
>smart00316 S1 Ribosomal protein S1-like RNA-binding domain.
Probab=98.19 E-value=1.4e-05 Score=50.33 Aligned_cols=61 Identities=16% Similarity=0.280 Sum_probs=47.6
Q ss_pred CCCEEEEEEEEEecccEEEEccc-cEEEE---EcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEEccCC
Q 032315 51 KGEILGAGVTMVNKMGFLAEAGA-VQIFC---LIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQVDVTE 122 (143)
Q Consensus 51 ~gEVv~G~V~~v~~~Gi~v~iGp-~~ifI---~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~~~~~ 122 (143)
.|+++.|+|.++++.|+++.+++ .++|+ .++++. .++....++.|+.++++|..+..+...
T Consensus 2 ~G~~v~g~V~~v~~~g~~v~i~~~~~g~l~~~~~~~~~-----------~~~~~~~~~~G~~v~~~V~~~~~~~~~ 66 (72)
T smart00316 2 VGDVVEGTVTEITPFGAFVDLGNGVEGLIPISELSDKR-----------VKDPEEVLKVGDEVKVKVLSVDEEKGR 66 (72)
T ss_pred CCCEEEEEEEEEEccEEEEEeCCCCEEEEEHHHCCccc-----------cCCHHHeecCCCEEEEEEEEEeCCCCE
Confidence 58999999999999999999985 88888 443221 122335689999999999999875543
No 20
>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=98.17 E-value=1.3e-05 Score=51.63 Aligned_cols=61 Identities=11% Similarity=0.173 Sum_probs=46.5
Q ss_pred CCEEEEEEEEEecccEEEEccc-cEEEE---EcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEEccCC
Q 032315 52 GEILGAGVTMVNKMGFLAEAGA-VQIFC---LIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQVDVTE 122 (143)
Q Consensus 52 gEVv~G~V~~v~~~Gi~v~iGp-~~ifI---~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~~~~~ 122 (143)
|+++.|+|++++++|+|+.+.+ .+.++ .++ |.....+....++.|+.|++||.++..+...
T Consensus 1 G~~~~g~V~~i~~~G~fv~l~~~~~Glv~~~~l~----------~~~~~~~~~~~~~~G~~v~v~v~~id~~~~~ 65 (69)
T cd05690 1 GTVVSGKIKSITDFGIFVGLDGGIDGLVHISDIS----------WTQRVRHPSEIYKKGQEVEAVVLNIDVERER 65 (69)
T ss_pred CCEEEEEEEEEEeeeEEEEeCCCCEEEEEHHHCC----------CccccCChhhEECCCCEEEEEEEEEECCcCE
Confidence 6899999999999999999976 78888 332 1111223346789999999999998866544
No 21
>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=98.15 E-value=1.2e-05 Score=52.10 Aligned_cols=61 Identities=7% Similarity=0.211 Sum_probs=47.4
Q ss_pred CCEEEEEEEEEecccEEEEccc-cEEEE---EcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEEccCCe
Q 032315 52 GEILGAGVTMVNKMGFLAEAGA-VQIFC---LIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQVDVTEI 123 (143)
Q Consensus 52 gEVv~G~V~~v~~~Gi~v~iGp-~~ifI---~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~~~~~~ 123 (143)
|++++|+|+++++.|+++++++ .++|| .++++. + ++....++.|+.+.+||.++..+.+.+
T Consensus 1 G~~v~g~V~~v~~~Gv~V~l~~~v~g~i~~~~l~~~~---------~--~~~~~~~~~Gd~i~~~V~~id~~~~~i 65 (69)
T cd05697 1 GQVVKGTIRKLRPSGIFVKLSDHIKGLVPPMHLADVR---------L--KHPEKKFKPGLKVKCRVLSVEPERKRL 65 (69)
T ss_pred CCEEEEEEEEEeccEEEEEecCCcEEEEEHHHCCCcc---------c--cCHHHcCCCCCEEEEEEEEEECCCCEE
Confidence 6899999999999999999975 88988 443220 1 122357899999999999988766553
No 22
>cd05706 S1_Rrp5_repeat_sc10 S1_Rrp5_repeat_sc10: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 10 (sc10). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=98.12 E-value=2.2e-05 Score=51.26 Aligned_cols=62 Identities=24% Similarity=0.165 Sum_probs=47.5
Q ss_pred cCCCEEEEEEEEEecccEEEEccc-cEEEE---EcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEEccCC
Q 032315 50 FKGEILGAGVTMVNKMGFLAEAGA-VQIFC---LIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQVDVTE 122 (143)
Q Consensus 50 f~gEVv~G~V~~v~~~Gi~v~iGp-~~ifI---~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~~~~~ 122 (143)
.+|+++.|+|+++++.|+++++++ .++|+ .++++ |+. +-...++.||.++++|.++..+...
T Consensus 2 ~~G~iv~g~V~~v~~~gi~v~l~~~~~g~v~~s~l~~~--~~~---------~~~~~~~~Gd~v~~~V~~~d~~~~~ 67 (73)
T cd05706 2 KVGDILPGRVTKVNDRYVLVQLGNKVTGPSFITDALDD--YSE---------ALPYKFKKNDIVRACVLSVDVPNKK 67 (73)
T ss_pred CCCCEEEEEEEEEeCCeEEEEeCCCcEEEEEhhhccCc--ccc---------ccccccCCCCEEEEEEEEEeCCCCE
Confidence 379999999999999999999986 88988 44322 111 1135689999999999998775443
No 23
>cd05686 S1_pNO40 S1_pNO40: pNO40 , S1-like RNA-binding domain. pNO40 is a nucleolar protein of unknown function with an N-terminal S1 RNA binding domain, a CCHC type zinc finger, and clusters of basic amino acids representing a potential nucleolar targeting signal. pNO40 was identified through a yeast two-hybrid interaction screen of a human kidney cDNA library using the pinin (pnn) protein as bait. pNO40 is thought to play a role in ribosome maturation and/or biogenesis.
Probab=98.09 E-value=2.3e-05 Score=51.67 Aligned_cols=63 Identities=21% Similarity=0.306 Sum_probs=46.0
Q ss_pred ecCCCEEEEEEEEEecccEEEEccc--cEEEEEcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEEc
Q 032315 49 PFKGEILGAGVTMVNKMGFLAEAGA--VQIFCLIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQVD 119 (143)
Q Consensus 49 Pf~gEVv~G~V~~v~~~Gi~v~iGp--~~ifI~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~~ 119 (143)
|-.|++++|+|++++++|+|+.+.. .+.|+.+.+ + .|. ..++.+..++.||.|++||.++..+
T Consensus 1 ~~~g~~~~g~V~~i~~fG~fv~l~~~~~eGlvh~se-l------~~~-~~~~~~~~~~~Gd~v~vkv~~vd~~ 65 (73)
T cd05686 1 PALYQIFKGEVASVTEYGAFVKIPGCRKQGLVHKSH-M------SSC-RVDDPSEVVDVGEKVWVKVIGREMK 65 (73)
T ss_pred CcCCCEEEEEEEEEEeeeEEEEECCCCeEEEEEchh-h------CCC-cccCHhhEECCCCEEEEEEEEECCC
Confidence 5689999999999999999999932 578882210 0 111 1123346789999999999888764
No 24
>cd05698 S1_Rrp5_repeat_hs6_sc5 S1_Rrp5_repeat_hs6_sc5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 6 (hs6) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=98.04 E-value=1.9e-05 Score=51.10 Aligned_cols=60 Identities=12% Similarity=0.101 Sum_probs=45.9
Q ss_pred CCEEEEEEEEEecccEEEEccc-cEEEE---EcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEEccCC
Q 032315 52 GEILGAGVTMVNKMGFLAEAGA-VQIFC---LIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQVDVTE 122 (143)
Q Consensus 52 gEVv~G~V~~v~~~Gi~v~iGp-~~ifI---~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~~~~~ 122 (143)
|+++.|+|+++++.|+|+++++ .+.|+ +|+++..+ +-...+++|+.+++||.++..+...
T Consensus 1 g~~~~g~V~~v~~~G~~V~l~~~~~gli~~s~l~~~~~~-----------~~~~~~~~G~~i~v~v~~~d~~~~~ 64 (70)
T cd05698 1 GLKTHGTIVKVKPNGCIVSFYNNVKGFLPKSELSEAFIK-----------DPEEHFRVGQVVKVKVLSCDPEQQR 64 (70)
T ss_pred CCEEEEEEEEEecCcEEEEECCCCEEEEEHHHcChhhcC-----------CHHHcccCCCEEEEEEEEEcCCCCE
Confidence 6899999999999999999975 88888 45432111 1125689999999999998765544
No 25
>cd05707 S1_Rrp5_repeat_sc11 S1_Rrp5_repeat_sc11: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 11 (sc11). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=98.02 E-value=2.7e-05 Score=50.32 Aligned_cols=60 Identities=17% Similarity=0.178 Sum_probs=46.2
Q ss_pred CCEEEEEEEEEecccEEEEccc-cEEEE---EcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEEccCC
Q 032315 52 GEILGAGVTMVNKMGFLAEAGA-VQIFC---LIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQVDVTE 122 (143)
Q Consensus 52 gEVv~G~V~~v~~~Gi~v~iGp-~~ifI---~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~~~~~ 122 (143)
|+++.|+|+++.+.|+|+++++ .++|+ +++++. .++....+++|+.+++||.++......
T Consensus 1 G~~v~g~V~~v~~~Gv~V~l~~~~~G~v~~s~l~~~~-----------~~~~~~~~~~Gd~v~~~v~~~d~~~~~ 64 (68)
T cd05707 1 GDVVRGFVKNIANNGVFVTLGRGVDARVRVSELSDSY-----------LKDWKKRFKVGQLVKGKIVSIDPDNGR 64 (68)
T ss_pred CCEEEEEEEEEECccEEEEeCCCCEEEEEHHHCCchh-----------hcCHhhccCCCCEEEEEEEEEeCCCCE
Confidence 6899999999999999999976 88888 554321 112235689999999999988765443
No 26
>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=98.02 E-value=3.2e-05 Score=70.72 Aligned_cols=78 Identities=13% Similarity=0.199 Sum_probs=62.9
Q ss_pred EEEeecCCCEEEEEEEEEecccEEEEccc--cEEEE---EcCCC-ceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEE
Q 032315 45 IVFRPFKGEILGAGVTMVNKMGFLAEAGA--VQIFC---LIPDD-MELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQV 118 (143)
Q Consensus 45 lvFrPf~gEVv~G~V~~v~~~Gi~v~iGp--~~ifI---~lp~~-~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~ 118 (143)
.-.++..|++.+|+|++++++|+|+.+.+ .+++| .|+++ +.||+... .+..+..+..++.||.|++||.++..
T Consensus 621 ~yl~~~iG~~~~g~V~~v~~fGifV~L~~~~~eGlvhis~l~~d~~~~d~~~~-~l~g~~~~~~~~lGd~V~Vkv~~vd~ 699 (709)
T TIGR02063 621 EYMSEKIGEEFEGVISGVTSFGLFVELENNTIEGLVHISTLKDDYYVFDEKGL-ALVGERTGKVFRLGDRVKVRVVKADL 699 (709)
T ss_pred HhhhccCCcEEEEEEEEEEeCCEEEEecCCceEEEEEeeecCCCcEEEcccce-EEEeccCCcEECCCCEEEEEEEEEec
Confidence 34567889999999999999999999975 78888 77655 55776643 46666667889999999999999987
Q ss_pred ccCCe
Q 032315 119 DVTEI 123 (143)
Q Consensus 119 ~~~~~ 123 (143)
....+
T Consensus 700 ~~~~I 704 (709)
T TIGR02063 700 DTGKI 704 (709)
T ss_pred ccCeE
Confidence 66554
No 27
>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=98.00 E-value=3.9e-05 Score=69.74 Aligned_cols=77 Identities=8% Similarity=0.157 Sum_probs=63.5
Q ss_pred EEeecCCCEEEEEEEEEecccEEEEcc-c-cEEEE---EcCCC-ceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEEc
Q 032315 46 VFRPFKGEILGAGVTMVNKMGFLAEAG-A-VQIFC---LIPDD-MELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQVD 119 (143)
Q Consensus 46 vFrPf~gEVv~G~V~~v~~~Gi~v~iG-p-~~ifI---~lp~~-~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~~ 119 (143)
.++...|++.+|+|+++++.|+|+.+. + .+++| +|+++ +.||+... .+..++++..++.||.|++||.++...
T Consensus 567 yl~~~iG~~~~g~I~~v~~~GifV~L~~~~veGlV~~s~l~~d~y~~d~~~~-~l~g~~~~~~~~lGD~V~Vki~~vd~~ 645 (654)
T TIGR00358 567 YLLDKVGTEFSGEISSVTRFGMFVRLDDNGIDGLIHISTLHNDYYVFDQEKM-ALIGKGTGKVYRIGDRVTVKLTEVNME 645 (654)
T ss_pred hhhhCCCcEEEEEEEeEEcCcEEEEecCCceEEEEEeEeCCCcceEEecccc-EEEeccCCcEECCCCEEEEEEEEEecc
Confidence 355677999999999999999999996 5 88888 78765 67887753 566667778999999999999999877
Q ss_pred cCCe
Q 032315 120 VTEI 123 (143)
Q Consensus 120 ~~~~ 123 (143)
...+
T Consensus 646 ~~~I 649 (654)
T TIGR00358 646 TRSI 649 (654)
T ss_pred cCeE
Confidence 6654
No 28
>PRK11642 exoribonuclease R; Provisional
Probab=97.98 E-value=4.1e-05 Score=71.30 Aligned_cols=77 Identities=8% Similarity=0.139 Sum_probs=63.1
Q ss_pred EEEeecCCCEEEEEEEEEecccEEEEccc--cEEEE---EcCCC-ceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEE
Q 032315 45 IVFRPFKGEILGAGVTMVNKMGFLAEAGA--VQIFC---LIPDD-MELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQV 118 (143)
Q Consensus 45 lvFrPf~gEVv~G~V~~v~~~Gi~v~iGp--~~ifI---~lp~~-~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~ 118 (143)
-..+...|++++|+|++++++|+||.+.. .+++| .|+++ +.||+... .+..++++..++.||.|++||..+..
T Consensus 637 ~~m~~~iGe~f~G~Is~V~~fGifVeL~~~~vEGlV~vs~L~~d~y~~d~~~~-~L~g~~~~~~~~lGD~V~VkV~~vD~ 715 (813)
T PRK11642 637 DFMLDQVGNVFKGVISSVTGFGFFVRLDDLFIDGLVHVSSLDNDYYRFDQVGQ-RLIGESSGQTYRLGDRVEVRVEAVNM 715 (813)
T ss_pred hhhhccCCcEEEEEEEEeecCceEEEECCCCeeeeEEEeecCCcceEecchhe-EEecccCCcEECCCCEEEEEEEEeec
Confidence 34566789999999999999999999964 88888 77766 56776643 56677777899999999999999988
Q ss_pred ccCC
Q 032315 119 DVTE 122 (143)
Q Consensus 119 ~~~~ 122 (143)
....
T Consensus 716 ~~rk 719 (813)
T PRK11642 716 DERK 719 (813)
T ss_pred CCCe
Confidence 7765
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=97.98 E-value=4.8e-05 Score=49.63 Aligned_cols=62 Identities=19% Similarity=0.316 Sum_probs=47.5
Q ss_pred CCCEEEEEEEEEecccEEEEcc--ccEEEE---EcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEEccCCe
Q 032315 51 KGEILGAGVTMVNKMGFLAEAG--AVQIFC---LIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQVDVTEI 123 (143)
Q Consensus 51 ~gEVv~G~V~~v~~~Gi~v~iG--p~~ifI---~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~~~~~~ 123 (143)
.|+++.|+|+++++.|+|+.+. ..++++ .++++. ..+....+++||.|++||..+..+...+
T Consensus 2 ~g~~v~g~V~~i~~~g~~v~l~~~~~~g~i~~~~l~~~~-----------~~~~~~~~~~Gd~v~v~i~~vd~~~~~i 68 (77)
T cd05708 2 VGQKIDGTVRRVEDYGVFIDIDGTNVSGLCHKSEISDNR-----------VADASKLFRVGDKVRAKVLKIDAEKKRI 68 (77)
T ss_pred CCCEEEEEEEEEEcceEEEEECCCCeEEEEEHHHCCCCc-----------cCCHhHeecCCCEEEEEEEEEeCCCCEE
Confidence 5899999999999999999997 478888 443211 1123467899999999999988765543
No 30
>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=97.97 E-value=3.4e-05 Score=51.19 Aligned_cols=62 Identities=18% Similarity=0.084 Sum_probs=46.6
Q ss_pred CCEEEEEEEEEecccEEEEccc-cEEEE---EcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEEccCC
Q 032315 52 GEILGAGVTMVNKMGFLAEAGA-VQIFC---LIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQVDVTE 122 (143)
Q Consensus 52 gEVv~G~V~~v~~~Gi~v~iGp-~~ifI---~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~~~~~ 122 (143)
|.++.|+|+++++.|+|++++| .+.|| .++++... . ++-...+++|+.|.+||+++..+.+.
T Consensus 1 G~~V~g~V~~i~~~g~~V~l~~~i~G~i~~~~ls~~~~~--~-------~~~~~~~~vG~~v~~kV~~id~~~~~ 66 (73)
T cd05703 1 GQEVTGFVNNVSKEFVWLTISPDVKGRIPLLDLSDDVSV--L-------EHPEKKFPIGQALKAKVVGVDKEHKL 66 (73)
T ss_pred CCEEEEEEEEEeCCEEEEEeCCCcEEEEEHHHcCCcccc--c-------cCHHHhCCCCCEEEEEEEEEeCCCCE
Confidence 6789999999999999999998 88998 44321000 1 11235689999999999988776554
No 31
>cd05689 S1_RPS1_repeat_ec4 S1_RPS1_repeat_ec4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 4 (ec4) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=97.93 E-value=0.0001 Score=47.90 Aligned_cols=63 Identities=16% Similarity=0.110 Sum_probs=47.5
Q ss_pred CCCEEEEEEEEEecccEEEEccc-cEEEE---EcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEEccCCe
Q 032315 51 KGEILGAGVTMVNKMGFLAEAGA-VQIFC---LIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQVDVTEI 123 (143)
Q Consensus 51 ~gEVv~G~V~~v~~~Gi~v~iGp-~~ifI---~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~~~~~~ 123 (143)
.|+++.|+|++++++|+|+.+.+ .++|+ .++. +.. ..+....++.|+.|+++|.++..+...+
T Consensus 3 ~g~~~~g~V~~i~~~G~fv~l~~~~~Gl~~~~~l~~----~~~------~~~~~~~~~~Gd~v~v~v~~id~~~~~i 69 (72)
T cd05689 3 EGTRLFGKVTNLTDYGCFVELEEGVEGLVHVSEMDW----TNK------NIHPSKVVSLGDEVEVMVLDIDEERRRI 69 (72)
T ss_pred CCCEEEEEEEEEEeeEEEEEcCCCCEEEEEEEeccC----ccc------ccCcccEeCCCCEEEEEEEEeeCCcCEE
Confidence 68999999999999999999976 78888 4421 100 1133467999999999999988655443
No 32
>cd04461 S1_Rrp5_repeat_hs8_sc7 S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 repeat 7 (sc7)-like domains. Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in S. cerevisiae Rrp5 and 14 S1 repeats in H. sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 8 and S. cerevisiae S1 repeat 7. Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=97.92 E-value=4.1e-05 Score=51.48 Aligned_cols=64 Identities=16% Similarity=0.206 Sum_probs=49.5
Q ss_pred ecCCCEEEEEEEEEecccEEEEcc-ccEEEE---EcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEEccCCe
Q 032315 49 PFKGEILGAGVTMVNKMGFLAEAG-AVQIFC---LIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQVDVTEI 123 (143)
Q Consensus 49 Pf~gEVv~G~V~~v~~~Gi~v~iG-p~~ifI---~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~~~~~~ 123 (143)
+..|+++.|+|++++++|+|+.++ ..++|+ .++++ + ..+-...++.|+.|++||.++..+.+.+
T Consensus 12 ~~~G~i~~g~V~~v~~~G~fv~l~~~~~g~v~~~el~~~----------~-~~~~~~~~~~Gd~v~vkV~~id~~~~~i 79 (83)
T cd04461 12 LKPGMVVHGYVRNITPYGVFVEFLGGLTGLAPKSYISDE----------F-VTDPSFGFKKGQSVTAKVTSVDEEKQRF 79 (83)
T ss_pred CCCCCEEEEEEEEEeeceEEEEcCCCCEEEEEHHHCCcc----------c-ccCHHHhcCCCCEEEEEEEEEcCCCCEE
Confidence 568999999999999999999996 488988 44321 1 1133467899999999999988765443
No 33
>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=97.92 E-value=7.8e-05 Score=47.29 Aligned_cols=64 Identities=17% Similarity=0.248 Sum_probs=46.2
Q ss_pred CCCEEEEEEEEEecccEEEEccccEEEEEcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEEccCC
Q 032315 51 KGEILGAGVTMVNKMGFLAEAGAVQIFCLIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQVDVTE 122 (143)
Q Consensus 51 ~gEVv~G~V~~v~~~Gi~v~iGp~~ifI~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~~~~~ 122 (143)
.|+++.|+|+++++.|+++.++..++|+...+ . .|.+ ..+....++.||.|+++|.++....+.
T Consensus 1 ~g~~~~g~V~~v~~~g~~v~l~~~~g~l~~~e-~------~~~~-~~~~~~~~~~Gd~v~v~i~~vd~~~~~ 64 (68)
T cd05688 1 EGDVVEGTVKSITDFGAFVDLGGVDGLLHISD-M------SWGR-VKHPSEVVNVGDEVEVKVLKIDKERKR 64 (68)
T ss_pred CCCEEEEEEEEEEeeeEEEEECCeEEEEEhHH-C------CCcc-ccCHhHEECCCCEEEEEEEEEECCCCE
Confidence 48999999999999999999998888882211 0 0111 112235689999999999998765443
No 34
>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=97.91 E-value=6.6e-05 Score=48.56 Aligned_cols=60 Identities=23% Similarity=0.267 Sum_probs=46.0
Q ss_pred CCEEEEEEEEEecccEEEEccc-cEEEE---EcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEEccCC
Q 032315 52 GEILGAGVTMVNKMGFLAEAGA-VQIFC---LIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQVDVTE 122 (143)
Q Consensus 52 gEVv~G~V~~v~~~Gi~v~iGp-~~ifI---~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~~~~~ 122 (143)
|+++.|+|+++++.|+++.+++ .+.|+ .+.++. .++....+++|+.+++||..+......
T Consensus 1 G~~v~g~V~~v~~~g~~v~l~~~~~g~i~~~~~~~~~-----------~~~~~~~~~~Gd~v~~~v~~~d~~~~~ 64 (73)
T cd05691 1 GSIVTGKVTEVDAKGATVKLGDGVEGFLRAAELSRDR-----------VEDATERFKVGDEVEAKITNVDRKNRK 64 (73)
T ss_pred CCEEEEEEEEEECCeEEEEeCCCCEEEEEHHHCCCcc-----------ccCHHHccCCCCEEEEEEEEEeCCCCE
Confidence 6899999999999999999964 88888 333211 112235689999999999998876543
No 35
>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=97.84 E-value=8.8e-05 Score=46.85 Aligned_cols=60 Identities=20% Similarity=0.178 Sum_probs=45.2
Q ss_pred CCEEEEEEEEEecccEEEEccc-cEEEE---EcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEEccCC
Q 032315 52 GEILGAGVTMVNKMGFLAEAGA-VQIFC---LIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQVDVTE 122 (143)
Q Consensus 52 gEVv~G~V~~v~~~Gi~v~iGp-~~ifI---~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~~~~~ 122 (143)
|+++.|+|++++++|+|+.+++ .++|+ .++++ + + .+....++.|+.+++||..+..+...
T Consensus 1 g~~~~g~V~~i~~~G~fv~l~~~~~g~~~~~~l~~~--------~-~--~~~~~~~~~Gd~v~v~i~~vd~~~~~ 64 (68)
T cd05685 1 GMVLEGVVTNVTDFGAFVDIGVKQDGLIHISKMADR--------F-V--SHPSDVVSVGDIVEVKVISIDEERGR 64 (68)
T ss_pred CCEEEEEEEEEecccEEEEcCCCCEEEEEHHHCCCc--------c-c--cCHHHhcCCCCEEEEEEEEEECCCCE
Confidence 6889999999999999999986 77887 33321 1 1 12235689999999999998865443
No 36
>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=97.80 E-value=8.7e-05 Score=46.92 Aligned_cols=56 Identities=16% Similarity=0.283 Sum_probs=43.1
Q ss_pred CCEEEEEEEEEecccEEEEcc-ccEEEE---EcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEE
Q 032315 52 GEILGAGVTMVNKMGFLAEAG-AVQIFC---LIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQV 118 (143)
Q Consensus 52 gEVv~G~V~~v~~~Gi~v~iG-p~~ifI---~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~ 118 (143)
|+++.|+|++++++|+|+.++ +.++|+ .++++. . .+....++.|+.+++||..+..
T Consensus 1 G~~~~g~V~~i~~~g~~v~i~~~~~g~l~~~~l~~~~----------~-~~~~~~~~~Gd~v~v~v~~~~~ 60 (69)
T cd05692 1 GSVVEGTVTRLKPFGAFVELGGGISGLVHISQIAHKR----------V-KDVKDVLKEGDKVKVKVLSIDA 60 (69)
T ss_pred CCEEEEEEEEEEeeeEEEEECCCCEEEEEhHHcCCcc----------c-CCHHHccCCCCEEEEEEEEECC
Confidence 689999999999999999997 488888 443221 1 1122568999999999988765
No 37
>cd05694 S1_Rrp5_repeat_hs2_sc2 S1_Rrp5_repeat_hs2_sc2: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 2 (hs2) and S. cerevisiae S1 repeat 2 (sc2). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=97.78 E-value=0.00019 Score=47.88 Aligned_cols=53 Identities=19% Similarity=0.190 Sum_probs=42.8
Q ss_pred CCCEEEEEEEEEecccEEEEccc--cEEEE---EcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEEcc
Q 032315 51 KGEILGAGVTMVNKMGFLAEAGA--VQIFC---LIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQVDV 120 (143)
Q Consensus 51 ~gEVv~G~V~~v~~~Gi~v~iGp--~~ifI---~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~~~ 120 (143)
+|+++.|.|+++.++|+|+++|. ++.|+ .++ |. ..+++|+.+.+||.++.-+.
T Consensus 4 ~G~~v~g~V~si~d~G~~v~~g~~gv~Gfl~~~~~~------------~~-----~~~~~Gq~v~~~V~~vd~~~ 61 (74)
T cd05694 4 EGMVLSGCVSSVEDHGYILDIGIPGTTGFLPKKDAG------------NF-----SKLKVGQLLLCVVEKVKDDG 61 (74)
T ss_pred CCCEEEEEEEEEeCCEEEEEeCCCCcEEEEEHHHCC------------cc-----cccCCCCEEEEEEEEEECCC
Confidence 68999999999999999999984 67887 221 11 56899999999999876443
No 38
>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=97.74 E-value=0.00019 Score=46.87 Aligned_cols=63 Identities=13% Similarity=0.101 Sum_probs=47.0
Q ss_pred ecCCCEEEEEEEEEecccEEEEcc--c-cEEEE---EcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEEccCC
Q 032315 49 PFKGEILGAGVTMVNKMGFLAEAG--A-VQIFC---LIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQVDVTE 122 (143)
Q Consensus 49 Pf~gEVv~G~V~~v~~~Gi~v~iG--p-~~ifI---~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~~~~~ 122 (143)
|-.|+++.|+|+++.++|+|+.+. + .++++ ++.++ + ..+-...++.||.|++||.++....+.
T Consensus 1 ~~~G~~~~g~V~~v~~~g~~v~l~~~~~~~gll~~s~l~~~----------~-~~~~~~~~~~Gd~v~vkv~~~d~~~~~ 69 (76)
T cd04452 1 PEEGELVVVTVKSIADMGAYVSLLEYGNIEGMILLSELSRR----------R-IRSIRKLVKVGRKEVVKVIRVDKEKGY 69 (76)
T ss_pred CCCCCEEEEEEEEEEccEEEEEEcCCCCeEEEEEhHHcCCc----------c-cCCHHHeeCCCCEEEEEEEEEECCCCE
Confidence 567999999999999999999995 2 67887 33211 1 112245689999999999988775443
No 39
>cd05684 S1_DHX8_helicase S1_DHX8_helicase: The N-terminal S1 domain of human ATP-dependent RNA helicase DHX8, a DEAH (Asp-Glu-Ala-His) box polypeptide. The DEAH-box RNA helicases are thought to play key roles in pre-mRNA splicing and DHX8 facilitates nuclear export of spliced mRNA by releasing the RNA from the spliceosome. DHX8 is also known as HRH1 (human RNA helicase 1) in Homo sapiens and PRP22 in Saccharomyces cerevisiae.
Probab=97.72 E-value=0.00055 Score=45.44 Aligned_cols=56 Identities=16% Similarity=0.217 Sum_probs=43.0
Q ss_pred CCEEEEEEEEEecccEEEEcc----ccEEEE---EcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEE
Q 032315 52 GEILGAGVTMVNKMGFLAEAG----AVQIFC---LIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQ 117 (143)
Q Consensus 52 gEVv~G~V~~v~~~Gi~v~iG----p~~ifI---~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~ 117 (143)
|+++.|+|+++.++|+|+.++ +.+.|+ .++++ |..++....++.|+.|+++|.++.
T Consensus 1 G~~~~g~V~~v~~~G~fv~l~~~~~~~~gll~~s~l~~~----------~~~~~~~~~~~~Gd~v~v~v~~vd 63 (79)
T cd05684 1 GKIYKGKVTSIMDFGCFVQLEGLKGRKEGLVHISQLSFE----------GRVANPSDVVKRGQKVKVKVISIQ 63 (79)
T ss_pred CCEEEEEEEEEEeeeEEEEEeCCCCCcEEEEEhHhccCC----------CCcCChhheeCCCCEEEEEEEEEe
Confidence 689999999999999999998 367887 33211 111233467899999999999987
No 40
>PRK08582 hypothetical protein; Provisional
Probab=97.69 E-value=0.00023 Score=53.08 Aligned_cols=59 Identities=19% Similarity=0.201 Sum_probs=45.7
Q ss_pred ecCCCEEEEEEEEEecccEEEEccc-cEEEE---EcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEE
Q 032315 49 PFKGEILGAGVTMVNKMGFLAEAGA-VQIFC---LIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQV 118 (143)
Q Consensus 49 Pf~gEVv~G~V~~v~~~Gi~v~iGp-~~ifI---~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~ 118 (143)
.-.|++++|+|++++++|+||.+++ .+++| .+.++ |. .+-...+++||.|+++|+++..
T Consensus 3 ~kvG~iv~G~V~~I~~fG~fV~L~~~~~GlVhiSels~~----------~v-~~~~~~l~vGD~VkvkV~~id~ 65 (139)
T PRK08582 3 IEVGSKLQGKVTGITNFGAFVELPEGKTGLVHISEVADN----------YV-KDINDHLKVGDEVEVKVLNVED 65 (139)
T ss_pred CcCCCEEEEEEEEEECCeEEEEECCCCEEEEEeeccCcc----------cc-cccccccCCCCEEEEEEEEECC
Confidence 3479999999999999999999987 77887 33321 11 1223578999999999999875
No 41
>KOG4134 consensus DNA-dependent RNA polymerase I [Transcription]
Probab=97.68 E-value=0.00016 Score=58.19 Aligned_cols=75 Identities=23% Similarity=0.340 Sum_probs=58.8
Q ss_pred eeEEEEEeeccee-cceeEEcCCccEEEEEEEEEEEEeecCCCEEEEEEEEEecccEEEEc-cccEEEE---EcCCCcee
Q 032315 12 HGFAVAITGAESI-GKGLIRNGTVLVTFLVRCQCIVFRPFKGEILGAGVTMVNKMGFLAEA-GAVQIFC---LIPDDMEL 86 (143)
Q Consensus 12 ~GliI~i~dI~~i-~eG~I~~gdG~~~~~V~F~~lvFrPf~gEVv~G~V~~v~~~Gi~v~i-Gp~~ifI---~lp~~~~f 86 (143)
.|++++.-+|.-. ..++|.+.++..+.+++-...||+|..|.+|+|.|-.++...|-+-+ |-+..-| ++|.+++|
T Consensus 67 ~GivLgydnIKvLg~~aki~~D~pf~hlwi~adfyVf~Pk~Gd~LeG~Vn~vS~sHIglLIhg~FNASIpk~nip~dw~f 146 (253)
T KOG4134|consen 67 DGIVLGYDNIKVLGQTAKIRADDPFMHLWINADFYVFRPKAGDILEGVVNHVSRSHIGLLIHGVFNASIPKTNIPADWEF 146 (253)
T ss_pred CceEEeecceEeeccccceecCCCceEEEEeeeEEEECCCCCCeeeeeeeecchhhhceeehhhhhccCCCCCCccceee
Confidence 3677787777655 46999999999999999999999999999999999999988776554 4444444 45555544
No 42
>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=97.67 E-value=8.7e-05 Score=50.04 Aligned_cols=68 Identities=10% Similarity=0.101 Sum_probs=47.7
Q ss_pred EeecCCCEEEEEEEEEecccEEEEccc-cEEEEEcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEE
Q 032315 47 FRPFKGEILGAGVTMVNKMGFLAEAGA-VQIFCLIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQV 118 (143)
Q Consensus 47 FrPf~gEVv~G~V~~v~~~Gi~v~iGp-~~ifI~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~ 118 (143)
|.|-+|+++.|+|+++++.|+++.+++ .++++.+.+ +..+.-+. + .++-...+++||.+++||.+..-
T Consensus 2 y~p~~GdiV~g~V~~i~~~g~~v~i~~~~~G~l~~se-~~~~~~~~--~-~~~~~~~l~vGd~i~~~V~~~~~ 70 (86)
T cd05789 2 YIPEVGDVVIGRVTEVGFKRWKVDINSPYDAVLPLSE-VNLPRTDE--D-ELNMRSYLDEGDLIVAEVQSVDS 70 (86)
T ss_pred CcCCCCCEEEEEEEEECCCEEEEECCCCeEEEEEHHH-ccCCCCcc--c-hHHHHhhCCCCCEEEEEEEEECC
Confidence 578999999999999999999999985 888882210 00000001 1 12223568999999999998743
No 43
>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=97.66 E-value=0.00025 Score=46.20 Aligned_cols=57 Identities=16% Similarity=0.177 Sum_probs=42.9
Q ss_pred CCEEEEEEEEEecccEEEEccc-cEEEE---EcCCCceecCCCCceE-EcCCceEEEcCCCeEEEEEEEEEE
Q 032315 52 GEILGAGVTMVNKMGFLAEAGA-VQIFC---LIPDDMELQTGDLPSY-TTSDGSVKIQKDCELWLKIIGTQV 118 (143)
Q Consensus 52 gEVv~G~V~~v~~~Gi~v~iGp-~~ifI---~lp~~~~fd~~~~~~~-~~~~~~~~i~~g~~VR~RV~~v~~ 118 (143)
|+++.|+|+++++.|+++++++ .++++ .+.+ .| ..++-...+++|+.|++||+++.-
T Consensus 1 G~iV~g~V~~i~~~gi~v~l~~~i~g~i~~~~i~~----------~~~~~~~~~~~~~~Gd~i~~kVl~~d~ 62 (70)
T cd05702 1 GDLVKAKVKSVKPTQLNVQLADNVHGRIHVSEVFD----------EWPDGKNPLSKFKIGQKIKARVIGGHD 62 (70)
T ss_pred CCEEEEEEEEEECCcEEEEeCCCcEEEEEHHHhcc----------ccccccChhHhCCCCCEEEEEEEEEeC
Confidence 6899999999999999999976 88888 3321 12 111223557999999999998754
No 44
>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=97.65 E-value=0.00029 Score=45.50 Aligned_cols=57 Identities=18% Similarity=0.254 Sum_probs=42.8
Q ss_pred CCEEEEEEEEEecccEEEEccc-cEEEE---EcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEEc
Q 032315 52 GEILGAGVTMVNKMGFLAEAGA-VQIFC---LIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQVD 119 (143)
Q Consensus 52 gEVv~G~V~~v~~~Gi~v~iGp-~~ifI---~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~~ 119 (143)
|+++.|+|.++++.|++++++. .+.++ .+.++ +. ++-...+++||.++++|.++.-+
T Consensus 1 G~iv~g~V~~i~~~~~~v~l~~~~~g~l~~~e~~~~----------~~-~~~~~~~~~Gd~i~~~i~~~~~~ 61 (70)
T cd05687 1 GDIVKGTVVSVDDDEVLVDIGYKSEGIIPISEFSDD----------PI-ENGEDEVKVGDEVEVYVLRVEDE 61 (70)
T ss_pred CCEEEEEEEEEeCCEEEEEeCCCceEEEEHHHhCcc----------cc-CCHhHcCCCCCEEEEEEEEEECC
Confidence 7899999999999999999975 77887 23211 11 11234579999999999998743
No 45
>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=97.65 E-value=0.00029 Score=44.69 Aligned_cols=56 Identities=16% Similarity=0.180 Sum_probs=42.8
Q ss_pred CCEEEEEEEEEecccEEEEccc-cEEEE---EcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEE
Q 032315 52 GEILGAGVTMVNKMGFLAEAGA-VQIFC---LIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQV 118 (143)
Q Consensus 52 gEVv~G~V~~v~~~Gi~v~iGp-~~ifI---~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~ 118 (143)
|+++.|+|+++.++|+|+.++. .+.|+ .++++ +. ......++.||.|+++|.++..
T Consensus 1 g~~~~g~V~~v~~~G~~v~l~~~~~g~l~~~~l~~~----------~~-~~~~~~~~~Gd~v~v~v~~~d~ 60 (68)
T cd04472 1 GKIYEGKVVKIKDFGAFVEILPGKDGLVHISELSDE----------RV-EKVEDVLKVGDEVKVKVIEVDD 60 (68)
T ss_pred CCEEEEEEEEEEEeEEEEEeCCCCEEEEEhHHcCCc----------cc-cCHHHccCCCCEEEEEEEEECC
Confidence 6889999999999999999976 77888 33211 11 1223578999999999998764
No 46
>cd05696 S1_Rrp5_repeat_hs4 S1_Rrp5_repeat_hs4: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 4 (hs4). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=97.64 E-value=0.0004 Score=45.65 Aligned_cols=59 Identities=20% Similarity=0.201 Sum_probs=44.3
Q ss_pred CCEEE-EEEEEE-ecccEEEEccc-cEEEE---EcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEEccC
Q 032315 52 GEILG-AGVTMV-NKMGFLAEAGA-VQIFC---LIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQVDVT 121 (143)
Q Consensus 52 gEVv~-G~V~~v-~~~Gi~v~iGp-~~ifI---~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~~~~ 121 (143)
||+++ |+|+++ .+.|+|+++.+ .++|+ +++++ ... .-...+++|+.+.+||.++.-..+
T Consensus 1 G~v~~~g~V~~v~~~~G~~V~l~~gv~G~i~~s~l~~~----~~~-------~~~~~~~vG~~v~~kV~~id~~~~ 65 (71)
T cd05696 1 GAVVDSVKVTKVEPDLGAVFELKDGLLGFVHISHLSDD----KVP-------SDTGPFKAGTTHKARIIGYSPMDG 65 (71)
T ss_pred CcEeeeeEEEEEccCceEEEEeCCCCEEEEEHHHCCcc----hhc-------CcccccCCCCEEEEEEEEEeCCCC
Confidence 78999 999999 69999999987 88998 45421 001 112558999999999988765443
No 47
>PRK07252 hypothetical protein; Provisional
Probab=97.58 E-value=0.00042 Score=50.53 Aligned_cols=62 Identities=10% Similarity=0.090 Sum_probs=47.4
Q ss_pred CCCEEEEEEEEEecccEEEEccc-cEEEE---EcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEEccCCe
Q 032315 51 KGEILGAGVTMVNKMGFLAEAGA-VQIFC---LIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQVDVTEI 123 (143)
Q Consensus 51 ~gEVv~G~V~~v~~~Gi~v~iGp-~~ifI---~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~~~~~~ 123 (143)
.|+++.|+|++++++|+|+.+.+ .++|+ .|+++. + ++-...++.||.|++||.++....+.+
T Consensus 3 vG~iv~G~V~~V~~~G~fVei~~~~~GllhiseLs~~~---------~--~~~~~~~~vGD~V~VkI~~iD~~~~ri 68 (120)
T PRK07252 3 IGDKLKGTITGIKPYGAFVALENGTTGLIHISEIKTGF---------I--DNIHQLLKVGEEVLVQVVDFDEYTGKA 68 (120)
T ss_pred CCCEEEEEEEEEeCcEEEEEECCCCEEEEEHHHcCCcc---------c--cChhhccCCCCEEEEEEEEEeCCCCEE
Confidence 58999999999999999999964 88888 443210 1 112356899999999999988765554
No 48
>cd05695 S1_Rrp5_repeat_hs3 S1_Rrp5_repeat_hs3: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 3 (hs3). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=97.57 E-value=0.0006 Score=44.23 Aligned_cols=58 Identities=10% Similarity=0.072 Sum_probs=44.0
Q ss_pred CCEEEEEEEEEecccEEEEcc-ccEEEE---EcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEEccCC
Q 032315 52 GEILGAGVTMVNKMGFLAEAG-AVQIFC---LIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQVDVTE 122 (143)
Q Consensus 52 gEVv~G~V~~v~~~Gi~v~iG-p~~ifI---~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~~~~~ 122 (143)
|.+++|+|+++.+.|+++++- -.+.|+ ++++ ... . ...+++|+.|.+||+.+..+.+.
T Consensus 1 G~~V~g~V~~i~~~G~~v~l~~~v~g~v~~~~l~~------~~~------~-~~~~~~G~~i~~kVi~id~~~~~ 62 (66)
T cd05695 1 GMLVNARVKKVLSNGLILDFLSSFTGTVDFLHLDP------EKS------S-KSTYKEGQKVRARILYVDPSTKV 62 (66)
T ss_pred CCEEEEEEEEEeCCcEEEEEcCCceEEEEHHHcCC------ccC------c-ccCcCCCCEEEEEEEEEeCCCCE
Confidence 679999999999999999984 388888 3321 111 1 35689999999999987765544
No 49
>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=97.55 E-value=0.00027 Score=46.57 Aligned_cols=56 Identities=16% Similarity=0.112 Sum_probs=42.6
Q ss_pred CCCEEEEEEEEEec-ccEEEEccc-cEEEE---EcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEE
Q 032315 51 KGEILGAGVTMVNK-MGFLAEAGA-VQIFC---LIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQ 117 (143)
Q Consensus 51 ~gEVv~G~V~~v~~-~Gi~v~iGp-~~ifI---~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~ 117 (143)
.|+++.|+|+++.+ .|+|++++| .+.++ ++.++ |.. +-...+++||.||+||.+..
T Consensus 3 ~G~iv~G~V~~i~~~~g~~v~l~~~~~Glvhis~~s~~----------~~~-~~~~~~~~Gd~v~~kV~~~~ 63 (72)
T cd05704 3 EGAVTLGMVTKVIPHSGLTVQLPFGKTGLVSIFHLSDS----------YTE-NPLEGFKPGKIVRCCILSKK 63 (72)
T ss_pred CCCEEEEEEEEeeCCcEEEEECCCCCEEEEEHHHhcCc----------ccC-CHHHhCCCCCEEEEEEEEec
Confidence 69999999999986 899999988 78888 33321 211 11246799999999998874
No 50
>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=97.51 E-value=0.00035 Score=46.78 Aligned_cols=62 Identities=18% Similarity=0.052 Sum_probs=47.2
Q ss_pred EeecCCCEEEEEEEEEecccEEEEcc-ccEEEE---EcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEEc
Q 032315 47 FRPFKGEILGAGVTMVNKMGFLAEAG-AVQIFC---LIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQVD 119 (143)
Q Consensus 47 FrPf~gEVv~G~V~~v~~~Gi~v~iG-p~~ifI---~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~~ 119 (143)
|.|.+|.++.|+|++++..++++.++ ..+.++ ++..+ + .++....+++||.+++||..+.-+
T Consensus 2 y~p~~GdiV~G~V~~v~~~~~~V~i~~~~~g~l~~~~~~~~----------~-~~~~~~~~~~GD~i~~~V~~~~~~ 67 (82)
T cd04454 2 YLPDVGDIVIGIVTEVNSRFWKVDILSRGTARLEDSSATEK----------D-KKEIRKSLQPGDLILAKVISLGDD 67 (82)
T ss_pred CCCCCCCEEEEEEEEEcCCEEEEEeCCCceEEeechhccCc----------c-hHHHHhcCCCCCEEEEEEEEeCCC
Confidence 57999999999999999999999996 578877 22211 0 112234579999999999987553
No 51
>PRK08059 general stress protein 13; Validated
Probab=97.47 E-value=0.00055 Score=49.80 Aligned_cols=63 Identities=14% Similarity=0.132 Sum_probs=47.8
Q ss_pred ecCCCEEEEEEEEEecccEEEEccc-cEEEE---EcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEEccCC
Q 032315 49 PFKGEILGAGVTMVNKMGFLAEAGA-VQIFC---LIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQVDVTE 122 (143)
Q Consensus 49 Pf~gEVv~G~V~~v~~~Gi~v~iGp-~~ifI---~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~~~~~ 122 (143)
.-.|+++.|+|+++++.|+|+.+++ .++++ .++++ +. .+-...+++||.|++||.++......
T Consensus 5 ~k~G~iv~G~V~~i~~~G~fV~i~~~~~Gli~~sel~~~----------~~-~~~~~~~~vGD~I~vkI~~id~~~~~ 71 (123)
T PRK08059 5 YEVGSVVTGKVTGIQPYGAFVALDEETQGLVHISEITHG----------FV-KDIHDFLSVGDEVKVKVLSVDEEKGK 71 (123)
T ss_pred CCCCCEEEEEEEEEecceEEEEECCCCEEEEEHHHCCcc----------cc-cCHHHcCCCCCEEEEEEEEEECCCCe
Confidence 4579999999999999999999986 78888 44322 11 12235789999999999998765444
No 52
>cd00164 S1_like S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains are members of the Oligonucleotide/oligosaccharide Binding (OB) fold.
Probab=97.42 E-value=0.0008 Score=41.40 Aligned_cols=55 Identities=18% Similarity=0.245 Sum_probs=41.0
Q ss_pred EEEEEEEEecccEEEEccc-cEEEE---EcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEEcc
Q 032315 55 LGAGVTMVNKMGFLAEAGA-VQIFC---LIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQVDV 120 (143)
Q Consensus 55 v~G~V~~v~~~Gi~v~iGp-~~ifI---~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~~~ 120 (143)
+.|+|+++++.|+++.+++ .++|+ .+++.. + .+....+++|+.|++||.++..+.
T Consensus 1 v~g~V~~v~~~g~~v~l~~~~~g~~~~~~~~~~~---------~--~~~~~~~~~G~~v~~~v~~~d~~~ 59 (65)
T cd00164 1 VTGKVVSITKFGVFVELEDGVEGLVHISELSDKF---------V--KDPSEVFKVGDEVEVKVLEVDPEK 59 (65)
T ss_pred CEEEEEEEEeeeEEEEecCCCEEEEEHHHCCCcc---------c--cCHhhEeCCCCEEEEEEEEEcCCc
Confidence 4799999999999999984 78888 332110 1 223467899999999999986543
No 53
>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase. Members of this protein family are polyribonucleotide nucleotidyltransferase, also called polynucleotide phosphorylase. Some members have been shown also to have additional functions as guanosine pentaphosphate synthetase and as poly(A) polymerase (see model TIGR02696 for an exception clade, within this family).
Probab=97.36 E-value=0.00014 Score=66.56 Aligned_cols=88 Identities=15% Similarity=0.088 Sum_probs=65.0
Q ss_pred ecceecceeEEcCCccEEEEE--EEEEEEEeecCCCEEEEEEEEEecccEEEEccc-cEEEE---EcCCCceecCCCCce
Q 032315 20 GAESIGKGLIRNGTVLVTFLV--RCQCIVFRPFKGEILGAGVTMVNKMGFLAEAGA-VQIFC---LIPDDMELQTGDLPS 93 (143)
Q Consensus 20 dI~~i~eG~I~~gdG~~~~~V--~F~~lvFrPf~gEVv~G~V~~v~~~Gi~v~iGp-~~ifI---~lp~~~~fd~~~~~~ 93 (143)
||.+-+..+|...++..+.++ .++.++..|.+|+++.|+|+++.++|+|+.+.| .++|+ ++.+.
T Consensus 585 ~i~ddG~V~i~~~~~~~~~~a~~~I~~~~~~~~~G~i~~G~V~~I~~~GafVei~~g~~GllHiSei~~~---------- 654 (684)
T TIGR03591 585 DIEDDGTVKIAASDGEAAEAAIKMIEGITAEPEVGKIYEGKVVRIMDFGAFVEILPGKDGLVHISEIANE---------- 654 (684)
T ss_pred EEecCeEEEEEECcHHHHHHHHHHHHhhhcccccCcEEEEEEEEEeCCEEEEEECCCcEEEEEHHHcCCC----------
Confidence 344445666666666666555 566677889999999999999999999999977 88888 33211
Q ss_pred EEcCCceEEEcCCCeEEEEEEEEEE
Q 032315 94 YTTSDGSVKIQKDCELWLKIIGTQV 118 (143)
Q Consensus 94 ~~~~~~~~~i~~g~~VR~RV~~v~~ 118 (143)
+ .++-...++.||.|++||.++..
T Consensus 655 ~-v~~~~~~~kvGD~V~VkVi~id~ 678 (684)
T TIGR03591 655 R-VEKVEDVLKEGDEVKVKVLEIDK 678 (684)
T ss_pred c-ccChhhccCCCCEEEEEEEEECC
Confidence 1 12334578999999999998764
No 54
>PRK05807 hypothetical protein; Provisional
Probab=97.33 E-value=0.0012 Score=49.11 Aligned_cols=61 Identities=18% Similarity=0.240 Sum_probs=44.1
Q ss_pred cCCCEEEEEEEEEecccEEEEccccEEEEEcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEE
Q 032315 50 FKGEILGAGVTMVNKMGFLAEAGAVQIFCLIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQV 118 (143)
Q Consensus 50 f~gEVv~G~V~~v~~~Gi~v~iGp~~ifI~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~ 118 (143)
-.|+++.|+|+.++++|+||.+.-.+++|.+.+- .+.|.. +-..++++|+.|+++|..+.-
T Consensus 4 ~vG~vv~G~Vt~i~~~GafV~L~~~~Glvhisei-------s~~~v~-~~~~~~kvGd~V~VkV~~id~ 64 (136)
T PRK05807 4 KAGSILEGTVVNITNFGAFVEVEGKTGLVHISEV-------ADTYVK-DIREHLKEQDKVKVKVISIDD 64 (136)
T ss_pred cCCCEEEEEEEEEECCeEEEEECCEEEEEEhhhc-------cccccc-CccccCCCCCEEEEEEEEECC
Confidence 3699999999999999999999546787722110 011211 223568999999999999865
No 55
>cd04453 S1_RNase_E S1_RNase_E: RNase E and RNase G, S1-like RNA-binding domain. RNase E is an essential endoribonuclease in the processing and degradation of RNA. In addition to its role in mRNA degradation, RNase E has also been implicated in the processing of rRNA, and the maturation of tRNA, 10Sa RNA and the M1 precursor of RNase P. RNase E associates with PNPase (3' to 5' exonuclease), Rhl B (DEAD-box RNA helicase) and enolase (glycolytic enzyme) to form the RNA degradosome. RNase E tends to cut mRNA within single-stranded regions that are rich in A/U nucleotides. The N-terminal region of RNase E contains the catalytic site. Within the conserved N-terminal domain of RNAse E and RNase G, there is an S1-like subdomain, which is an ancient single-stranded RNA-binding domain. S1 domain is an RNA-binding module originally identified in the ribosomal protein S1. The S1 domain is required for RNA cleavage by RNase E. RNase G is paralogous to RNase E with an N-terminal catalytic domain th
Probab=97.28 E-value=0.0013 Score=45.32 Aligned_cols=72 Identities=11% Similarity=0.088 Sum_probs=50.1
Q ss_pred eecCCCEEEEEEEEEecc--cEEEEccc-cEEEEEcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEEccCCeE
Q 032315 48 RPFKGEILGAGVTMVNKM--GFLAEAGA-VQIFCLIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQVDVTEIE 124 (143)
Q Consensus 48 rPf~gEVv~G~V~~v~~~--Gi~v~iGp-~~ifI~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~~~~~~~ 124 (143)
+|-.|+++.|+|+++.+. |+|+++++ .+.|+.+.+- .+..- .+. ..-...+++||.|.++|..+-++...-.
T Consensus 4 ~~~~G~iy~g~V~~i~~~~~GaFV~l~~g~~Gllh~sei-s~~~~---~~v-~~~~~~~~~Gd~v~VqV~~~~~~~K~~~ 78 (88)
T cd04453 4 EPIVGNIYLGRVKKIVPGLQAAFVDIGLGKNGFLHLSDI-LPAYF---KKH-KKIAKLLKEGQEILVQVVKEPIGTKGPR 78 (88)
T ss_pred cCCCCCEEEEEEEEeccCCcEEEEEeCCCCEEEEEhHHc-Cchhc---ccc-CCHHHcCCCCCEEEEEEEEecCCCCCce
Confidence 356899999999999996 99999998 7898833211 01000 000 1113578999999999999877665533
No 56
>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=97.21 E-value=0.0009 Score=47.15 Aligned_cols=68 Identities=10% Similarity=0.070 Sum_probs=46.6
Q ss_pred cCCCEEEEEEEEEecccEEEEccc-cEEEE---EcCCCceecCC--C-----Cce---EEcCCceEEEcCCCeEEEEEEE
Q 032315 50 FKGEILGAGVTMVNKMGFLAEAGA-VQIFC---LIPDDMELQTG--D-----LPS---YTTSDGSVKIQKDCELWLKIIG 115 (143)
Q Consensus 50 f~gEVv~G~V~~v~~~Gi~v~iGp-~~ifI---~lp~~~~fd~~--~-----~~~---~~~~~~~~~i~~g~~VR~RV~~ 115 (143)
..|.++.|+|+++++.|+++++.+ .++|+ .+.++ |... + +.. -...+-...+++|+.||++|++
T Consensus 2 ~~G~vV~G~V~~v~~~gl~v~L~~g~~G~v~~seis~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~f~vGd~V~~kVi~ 79 (100)
T cd05693 2 SEGMLVLGQVKEITKLDLVISLPNGLTGYVPITNISDA--YTERLEELDEESEEEDDEEELPDLEDLFSVGQLVRCKVVS 79 (100)
T ss_pred CCCCEEEEEEEEEcCCCEEEECCCCcEEEEEHHHhhHH--HHHHHHHhhhhccccccccccCCHHHhccCCCEEEEEEEE
Confidence 368999999999999999999965 88998 44322 2100 0 000 0011123568999999999999
Q ss_pred EEEc
Q 032315 116 TQVD 119 (143)
Q Consensus 116 v~~~ 119 (143)
+.-+
T Consensus 80 ~d~~ 83 (100)
T cd05693 80 LDKS 83 (100)
T ss_pred ccCC
Confidence 8865
No 57
>cd04473 S1_RecJ_like S1_RecJ_like: The S1 domain of the archaea-specific RecJ-like exonuclease. The function of this family is not fully understood. In Escherichia coli, RecJ degrades single-stranded DNA in the 5'-3' direction and participates in homologous recombination and mismatch repair.
Probab=97.20 E-value=0.0023 Score=42.56 Aligned_cols=59 Identities=12% Similarity=0.055 Sum_probs=45.1
Q ss_pred EeecCCCEEEEEEEEEecccEEEEccc-cEEEEEcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEEccCC
Q 032315 47 FRPFKGEILGAGVTMVNKMGFLAEAGA-VQIFCLIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQVDVTE 122 (143)
Q Consensus 47 FrPf~gEVv~G~V~~v~~~Gi~v~iGp-~~ifI~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~~~~~ 122 (143)
..+-.|+.++|+|++++++|+|+.+.+ .++++...+- ...++.|+.+++||.++ .+.+.
T Consensus 12 ~~~~~G~~~~g~V~~i~~~G~fV~l~~~~~Glv~~se~----------------~~~~~iGd~v~v~I~~i-~e~~~ 71 (77)
T cd04473 12 EDLEVGKLYKGKVNGVAKYGVFVDLNDHVRGLIHRSNL----------------LRDYEVGDEVIVQVTDI-PENGN 71 (77)
T ss_pred hhCCCCCEEEEEEEeEecceEEEEECCCcEEEEEchhc----------------cCcCCCCCEEEEEEEEE-CCCCc
Confidence 345579999999999999999999976 7777733210 13489999999999998 44333
No 58
>PTZ00248 eukaryotic translation initiation factor 2 subunit 1; Provisional
Probab=97.18 E-value=0.00086 Score=56.52 Aligned_cols=64 Identities=9% Similarity=0.071 Sum_probs=48.9
Q ss_pred ecCCCEEEEEEEEEecccEEEEcc--c-cEEEEEcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEEcc
Q 032315 49 PFKGEILGAGVTMVNKMGFLAEAG--A-VQIFCLIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQVDV 120 (143)
Q Consensus 49 Pf~gEVv~G~V~~v~~~Gi~v~iG--p-~~ifI~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~~~ 120 (143)
|..|+++.|+|+++.++|+||+++ + .++||.+.+ -.|.|. ++=+..+++|+.|.++|+.+.-+.
T Consensus 15 P~~GdvV~g~V~~I~d~GafV~L~EY~gvEGlIhiSE-------lS~~ri-~~i~d~vkvGd~v~vkVl~VD~ek 81 (319)
T PTZ00248 15 PEEDDLVMVKVVRITEMGAYVSLLEYDDIEGMILMSE-------LSKRRI-RSINKLIRVGRHEVVVVLRVDKEK 81 (319)
T ss_pred CCCCCEEEEEEEEEeCCeEEEEecCCCCcEEEEEHHH-------hccccc-CCHHHhcCCCCEEEEEEEEEeCCC
Confidence 667999999999999999999995 3 889884421 123343 233467899999999999986544
No 59
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=97.09 E-value=0.0011 Score=53.25 Aligned_cols=65 Identities=14% Similarity=0.155 Sum_probs=48.9
Q ss_pred EeecCCCEEEEEEEEEecccEEEEcc-ccEEEEEcCCCceecCCCCceEE---cCCceEEEcCCCeEEEEEEEEEE
Q 032315 47 FRPFKGEILGAGVTMVNKMGFLAEAG-AVQIFCLIPDDMELQTGDLPSYT---TSDGSVKIQKDCELWLKIIGTQV 118 (143)
Q Consensus 47 FrPf~gEVv~G~V~~v~~~Gi~v~iG-p~~ifI~lp~~~~fd~~~~~~~~---~~~~~~~i~~g~~VR~RV~~v~~ 118 (143)
+.|..|++|.|+|++++..|++++++ +.+.++.+.+ + .|.+. ..+-+..+++||.|++||+.+.-
T Consensus 59 y~P~vGDiViG~V~~i~~~~~~vdI~~~~~g~L~~s~---i----~~~~~~~d~~~~~~~~~~GDlV~akV~~i~~ 127 (235)
T PRK04163 59 YIPKVGDLVIGKVTDVTFSGWEVDINSPYKAYLPVSE---V----LGRPVNVEGTDLRKYLDIGDYIIAKVKDVDR 127 (235)
T ss_pred ccCCCCCEEEEEEEEEeCceEEEEeCCCceeEEEHHH---c----CCCccccchhhhHhhCCCCCEEEEEEEEECC
Confidence 89999999999999999999999998 5888882211 0 11121 12234568999999999998753
No 60
>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=96.98 E-value=0.0052 Score=39.40 Aligned_cols=58 Identities=24% Similarity=0.208 Sum_probs=41.6
Q ss_pred CCEEEEEEEEEecccEEEEccccEEEE---EcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEEccCC
Q 032315 52 GEILGAGVTMVNKMGFLAEAGAVQIFC---LIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQVDVTE 122 (143)
Q Consensus 52 gEVv~G~V~~v~~~Gi~v~iGp~~ifI---~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~~~~~ 122 (143)
|+++.|+|+++++.|++++++=.++|+ +|+.. +..+-. . .+|+.+.+||.++.-+.+.
T Consensus 1 G~iv~g~V~~v~~~G~~v~l~g~~gfip~s~~~~~----------~~~~~~-~--~vG~~i~~~i~~vd~~~~~ 61 (67)
T cd04465 1 GEIVEGKVTEKVKGGLIVDIEGVRAFLPASQVDLR----------PVEDLD-E--YVGKELKFKIIEIDRERNN 61 (67)
T ss_pred CCEEEEEEEEEECCeEEEEECCEEEEEEHHHCCCc----------ccCChH-H--hCCCEEEEEEEEEeCCCCE
Confidence 789999999999999999994478888 34211 100001 1 3899999999998865443
No 61
>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=96.95 E-value=0.0023 Score=59.10 Aligned_cols=65 Identities=11% Similarity=-0.033 Sum_probs=48.5
Q ss_pred eecCCCEEEEEEEEEecccEEEEccc-cEEEEEcCCCceecCCCCceEE-cCCceEEEcCCCeEEEEEEEEE
Q 032315 48 RPFKGEILGAGVTMVNKMGFLAEAGA-VQIFCLIPDDMELQTGDLPSYT-TSDGSVKIQKDCELWLKIIGTQ 117 (143)
Q Consensus 48 rPf~gEVv~G~V~~v~~~Gi~v~iGp-~~ifI~lp~~~~fd~~~~~~~~-~~~~~~~i~~g~~VR~RV~~v~ 117 (143)
.|-.|+++.|+|+++.++|+|++++| .++||.+.+=+ +-.| |. .++-...+++||.|.+||+++.
T Consensus 644 ~~~vG~i~~GkV~~I~dfGaFVel~~G~eGLvHISeis----dls~-~~rv~~~~dv~kvGd~V~VKVl~ID 710 (719)
T TIGR02696 644 MPEVGERFLGTVVKTTAFGAFVSLLPGKDGLLHISQIR----KLAG-GKRVENVEDVLSVGQKIQVEIADID 710 (719)
T ss_pred cCCCCCEEEEEEEEEECceEEEEecCCceEEEEhhhcc----cccc-ccCcCCHHHcCCCCCEEEEEEEEEC
Confidence 58999999999999999999999988 88988332100 0012 11 1222457899999999999987
No 62
>PRK06299 rpsA 30S ribosomal protein S1; Reviewed
Probab=96.87 E-value=0.003 Score=56.18 Aligned_cols=63 Identities=13% Similarity=0.151 Sum_probs=47.7
Q ss_pred CCCEEEEEEEEEecccEEEEcc-ccEEEE---EcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEEccCCe
Q 032315 51 KGEILGAGVTMVNKMGFLAEAG-AVQIFC---LIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQVDVTEI 123 (143)
Q Consensus 51 ~gEVv~G~V~~v~~~Gi~v~iG-p~~ifI---~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~~~~~~ 123 (143)
.|+++.|+|++++++|+|++++ ..++|+ .++. .+..++....++.|+.|++||..+..+.+.+
T Consensus 373 ~G~~v~g~V~~v~~~G~fV~l~~~v~g~i~~s~l~~----------~~~~~~~~~~~~~Gd~v~v~Il~vd~~~~~i 439 (565)
T PRK06299 373 VGDVVEGKVKNITDFGAFVGLEGGIDGLVHLSDISW----------DKKGEEAVELYKKGDEVEAVVLKVDVEKERI 439 (565)
T ss_pred CCCEEEEEEEEEecceEEEECCCCCEEEEEHHHcCc----------cccccChHhhCCCCCEEEEEEEEEeCCCCEE
Confidence 5999999999999999999998 488988 3431 1111233456899999999999887655443
No 63
>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=96.87 E-value=0.014 Score=37.77 Aligned_cols=57 Identities=14% Similarity=0.128 Sum_probs=42.7
Q ss_pred cCCCEEEEEEEEEecccEEEEccccEEEEEcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEEcc
Q 032315 50 FKGEILGAGVTMVNKMGFLAEAGAVQIFCLIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQVDV 120 (143)
Q Consensus 50 f~gEVv~G~V~~v~~~Gi~v~iGp~~ifI~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~~~ 120 (143)
..|+++.|+|.++++.|+++.+|..+.|+... ++. .. ..+++|+.|++.|.++.-+.
T Consensus 2 ~~g~iV~G~V~~~~~~~~~vdig~~eg~lp~~---e~~--------~~---~~~~~Gd~v~v~v~~v~~~~ 58 (67)
T cd04455 2 REGEIVTGIVKRVDRGNVIVDLGKVEAILPKK---EQI--------PG---ESYRPGDRIKAYVLEVRKTS 58 (67)
T ss_pred CCCCEEEEEEEEEcCCCEEEEcCCeEEEeeHH---HCC--------CC---CcCCCCCEEEEEEEEEecCC
Confidence 57999999999999999999998777766110 000 01 23599999999999987543
No 64
>PRK13806 rpsA 30S ribosomal protein S1; Provisional
Probab=96.81 E-value=0.0028 Score=55.89 Aligned_cols=61 Identities=11% Similarity=0.116 Sum_probs=47.2
Q ss_pred CCCEEEEEEEEEecccEEEEccc-cEEEE---EcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEEccCC
Q 032315 51 KGEILGAGVTMVNKMGFLAEAGA-VQIFC---LIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQVDVTE 122 (143)
Q Consensus 51 ~gEVv~G~V~~v~~~Gi~v~iGp-~~ifI---~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~~~~~ 122 (143)
+|+++.|+|++++++|+|+.+.| +++|| .+++ +.. ++....++.|+.|++||+.+..+...
T Consensus 379 vG~~v~G~V~~i~~~G~FV~l~~gv~Gli~~se~s~----~~~-------~~~~~~~~~Gd~v~~~V~~id~e~~r 443 (491)
T PRK13806 379 PGTTVTGTVEKRAQFGLFVNLAPGVTGLLPASVISR----AGK-------PATYEKLKPGDSVTLVVEEIDTAKRK 443 (491)
T ss_pred CCCEEEEEEEEEecCceEEEcCCCcEEEEEHHHcCc----ccc-------cchhhcCCCCCEEEEEEEEEeCCCCE
Confidence 69999999999999999999987 88988 3331 111 12235679999999999988876655
No 65
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=96.80 E-value=0.0058 Score=56.23 Aligned_cols=63 Identities=17% Similarity=0.172 Sum_probs=48.8
Q ss_pred EEeecCCCEEEEEEEEEecccEEEEccc-cEEEE---EcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEEc
Q 032315 46 VFRPFKGEILGAGVTMVNKMGFLAEAGA-VQIFC---LIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQVD 119 (143)
Q Consensus 46 vFrPf~gEVv~G~V~~v~~~Gi~v~iGp-~~ifI---~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~~ 119 (143)
+..|..|+++.|+|+++.++|+|+++.+ .++++ ++++. + .++-...++.||.|++||.++...
T Consensus 616 ~~~~~vG~v~~G~V~~I~~fGafVei~~~~~GllhiSels~~----------~-v~~~~~v~kvGD~V~VkV~~iD~~ 682 (693)
T PRK11824 616 TAEPEVGEIYEGKVVRIVDFGAFVEILPGKDGLVHISEIADE----------R-VEKVEDVLKEGDEVKVKVLEIDKR 682 (693)
T ss_pred cccCcCCeEEEEEEEEEECCeEEEEECCCCEEEEEeeeccCc----------c-ccCccceeCCCCEEEEEEEEECCC
Confidence 3468899999999999999999999987 78888 44311 1 112236789999999999998643
No 66
>PRK07400 30S ribosomal protein S1; Reviewed
Probab=96.80 E-value=0.0054 Score=51.43 Aligned_cols=64 Identities=17% Similarity=0.168 Sum_probs=48.8
Q ss_pred ecCCCEEEEEEEEEecccEEEEccccEEEE---EcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEEccCCe
Q 032315 49 PFKGEILGAGVTMVNKMGFLAEAGAVQIFC---LIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQVDVTEI 123 (143)
Q Consensus 49 Pf~gEVv~G~V~~v~~~Gi~v~iGp~~ifI---~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~~~~~~ 123 (143)
.-.|+++.|+|++++++|+|+.++..++++ .++++ +. .+....+++|+.|+++|.++..+...+
T Consensus 194 ~k~G~vv~G~V~~I~~~G~fV~i~gv~Gllhisels~~----------~~-~~~~~~~~vGd~VkvkVl~iD~e~~rI 260 (318)
T PRK07400 194 LEVGEVVVGTVRGIKPYGAFIDIGGVSGLLHISEISHE----------HI-ETPHSVFNVNDEMKVMIIDLDAERGRI 260 (318)
T ss_pred CCCCCEEEEEEEEEECCeEEEEECCEEEEEEHHHcccc----------cc-cChhhccCCCCEEEEEEEEEeCCCCEE
Confidence 456999999999999999999998888888 33211 11 122356899999999999988765554
No 67
>PHA02945 interferon resistance protein; Provisional
Probab=96.78 E-value=0.012 Score=41.00 Aligned_cols=65 Identities=12% Similarity=0.015 Sum_probs=47.1
Q ss_pred eecCCCEEEEEEEEEecccEEEEcc--c-cEEEEEcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEEccC
Q 032315 48 RPFKGEILGAGVTMVNKMGFLAEAG--A-VQIFCLIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQVDVT 121 (143)
Q Consensus 48 rPf~gEVv~G~V~~v~~~Gi~v~iG--p-~~ifI~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~~~~ 121 (143)
-|-.||++.|+|++ ..+|+|+++- | ++.||.+.+. ...+.| ... +.++ .|++|-+||+.+....+
T Consensus 8 ~P~~GelvigtV~~-~d~ga~v~L~EY~g~eg~i~~sev---eva~~w--vK~--rd~l-~GqkvV~KVirVd~~kg 75 (88)
T PHA02945 8 LPNVGDVLKGKVYE-NGYALYIDLFDYPHSEAILAESVQ---MHMNRY--FKY--RDKL-VGKTVKVKVIRVDYTKG 75 (88)
T ss_pred CCCCCcEEEEEEEe-cCceEEEEecccCCcEEEEEeehh---hhccce--Eee--eeEe-cCCEEEEEEEEECCCCC
Confidence 38999999999999 9999999995 3 7788833210 112344 332 4566 99999999998876543
No 68
>TIGR00717 rpsA ribosomal protein S1. This model provides trusted hits to most long form (6 repeat) examples of RpsA. Among homologs with only four repeats are some to which other (perhaps secondary) functions have been assigned.
Probab=96.75 E-value=0.0044 Score=54.37 Aligned_cols=66 Identities=11% Similarity=0.159 Sum_probs=48.6
Q ss_pred CCCEEEEEEEEEecccEEEEccc-cEEEEEcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEEccCCe
Q 032315 51 KGEILGAGVTMVNKMGFLAEAGA-VQIFCLIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQVDVTEI 123 (143)
Q Consensus 51 ~gEVv~G~V~~v~~~Gi~v~iGp-~~ifI~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~~~~~~ 123 (143)
.|+++.|+|+++++.|+|+.+++ .++|+.+.+ + .|.+...+....+++|+.|.+||+.+....+.+
T Consensus 359 ~G~~v~g~V~~v~~~G~fV~l~~~v~glv~~s~-l------s~~~~~~~~~~~~~~G~~V~~~Vl~vd~~~~~i 425 (516)
T TIGR00717 359 VGDRVTGKIKKITDFGAFVELEGGIDGLIHLSD-I------SWDKDGREADHLYKKGDEIEAVVLAVDKEKKRI 425 (516)
T ss_pred CCCEEEEEEEEEecceEEEECCCCCEEEEEHHH-C------cCcccCCCHhHccCCCCEEEEEEEEEeCcCCEE
Confidence 69999999999999999999996 889983321 0 111111222367899999999999988765554
No 69
>COG0557 VacB Exoribonuclease R [Transcription]
Probab=96.74 E-value=0.0059 Score=56.15 Aligned_cols=73 Identities=21% Similarity=0.275 Sum_probs=59.2
Q ss_pred cCCCEEEEEEEEEecccEEEEcc-c-cEEEE---EcCCC-ceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEEccCCe
Q 032315 50 FKGEILGAGVTMVNKMGFLAEAG-A-VQIFC---LIPDD-MELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQVDVTEI 123 (143)
Q Consensus 50 f~gEVv~G~V~~v~~~Gi~v~iG-p-~~ifI---~lp~~-~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~~~~~~ 123 (143)
..||..+|+|++++.+|+|+.+- + ++.+| .|+++ +.|++.. .....+.+...+..|+.|++|+.++......+
T Consensus 621 ~vg~~f~g~V~~v~~~g~~V~l~~~~ieglV~~s~L~~d~y~~~~~~-~~l~~~~~~~~~~lgd~v~v~v~~v~~~~~~i 699 (706)
T COG0557 621 RVGEEFDGVVTGVTSFGFFVELPELGLEGLVHISSLPDDYYHFDERG-QALVGEKSGKVYRLGDEVKVKVTSVDLDERKI 699 (706)
T ss_pred hcCCEEEEEEEEEEeccEEEEecccccccceEcccCCCceeeecccc-ceeeccccccccccCCEEEEEEEEEcccccce
Confidence 46899999999999999999994 4 78888 77754 6777764 24566777889999999999999998866553
No 70
>PRK03987 translation initiation factor IF-2 subunit alpha; Validated
Probab=96.74 E-value=0.0052 Score=50.40 Aligned_cols=64 Identities=14% Similarity=0.175 Sum_probs=48.3
Q ss_pred eecCCCEEEEEEEEEecccEEEEcc---ccEEEE---EcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEEccC
Q 032315 48 RPFKGEILGAGVTMVNKMGFLAEAG---AVQIFC---LIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQVDVT 121 (143)
Q Consensus 48 rPf~gEVv~G~V~~v~~~Gi~v~iG---p~~ifI---~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~~~~ 121 (143)
.|-+|+++.|+|+++.++|+|+++. ..++|+ .+++ . |.. +-...++.|+.|++||..+..+..
T Consensus 5 ~P~~GdiV~G~V~~I~~~G~fV~L~e~~gieGlI~iSEls~--------~--~i~-~i~~~~kvGd~V~vkVi~VD~~k~ 73 (262)
T PRK03987 5 WPEEGELVVGTVKEVKDFGAFVTLDEYPGKEGFIHISEVAS--------G--WVK-NIRDHVKEGQKVVCKVIRVDPRKG 73 (262)
T ss_pred CCCCCCEEEEEEEEEECCEEEEEECCCCCcEEEEEHHHcCc--------c--ccc-CHHHhCCCCCEEEEEEEEEecccC
Confidence 4889999999999999999999995 267887 3321 1 211 123578999999999999877654
Q ss_pred C
Q 032315 122 E 122 (143)
Q Consensus 122 ~ 122 (143)
.
T Consensus 74 ~ 74 (262)
T PRK03987 74 H 74 (262)
T ss_pred e
Confidence 4
No 71
>PRK05054 exoribonuclease II; Provisional
Probab=96.72 E-value=0.015 Score=53.14 Aligned_cols=76 Identities=8% Similarity=0.080 Sum_probs=55.0
Q ss_pred EeecCC--CEEEEEEEEEecccEEEEccc--cEEEE---EcCCC---ceecCCCC-ceEEcCCceEEEcCCCeEEEEEEE
Q 032315 47 FRPFKG--EILGAGVTMVNKMGFLAEAGA--VQIFC---LIPDD---MELQTGDL-PSYTTSDGSVKIQKDCELWLKIIG 115 (143)
Q Consensus 47 FrPf~g--EVv~G~V~~v~~~Gi~v~iGp--~~ifI---~lp~~---~~fd~~~~-~~~~~~~~~~~i~~g~~VR~RV~~ 115 (143)
.+...| +..+|.|+.++++|+||.+.. .+++| .|+++ +.|+.++. -.+ .++..++.||.|++||.+
T Consensus 555 ~~~~~G~~~~f~g~I~~v~~~G~fV~l~~~~veglV~~~~l~~~~~~y~~~~~~~~~~~---~~~~~~~lGd~V~V~v~~ 631 (644)
T PRK05054 555 LKDKAGTDTRFAAEIIDISRGGMRVRLLENGAVAFIPASFLHAVRDELVCNQENGTVQI---KGETVYKLGDVIDVTLAE 631 (644)
T ss_pred HhhccCCCeEEEEEEEeeecCcEEEEEeCCceEEEEEccccCCCccceEEccccceEEE---eCCEEEcCCCEEEEEEEE
Confidence 344555 499999999999999999963 77888 66654 33444431 122 234789999999999999
Q ss_pred EEEccCCeEE
Q 032315 116 TQVDVTEIEK 125 (143)
Q Consensus 116 v~~~~~~~~a 125 (143)
+......+-+
T Consensus 632 vd~~~~~i~~ 641 (644)
T PRK05054 632 VRMETRSIIA 641 (644)
T ss_pred EccccCeEEE
Confidence 9887766543
No 72
>COG0539 RpsA Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]
Probab=96.60 E-value=0.0058 Score=54.84 Aligned_cols=68 Identities=19% Similarity=0.278 Sum_probs=49.6
Q ss_pred eecCCCEEEEEEEEEecccEEEEccccEEEEEcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEEccCCe
Q 032315 48 RPFKGEILGAGVTMVNKMGFLAEAGAVQIFCLIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQVDVTEI 123 (143)
Q Consensus 48 rPf~gEVv~G~V~~v~~~Gi~v~iGp~~ifI~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~~~~~~ 123 (143)
.--.|++++|+|++++++|+|+.+|=.|.++.+. ++.|..-..+ ..++++||+|.+||+.+.-..+++
T Consensus 189 ~l~~G~vV~G~V~~It~~GafVdigGvdGLlHis-eiS~~rv~~P-------~~vvkvGd~VkvkVi~~D~e~~RV 256 (541)
T COG0539 189 KLEVGEVVEGVVKNITDYGAFVDIGGVDGLLHIS-EISWKRVDHP-------SEVVKVGDEVKVKVISLDEERGRV 256 (541)
T ss_pred cCCCCceEEEEEEEeecCcEEEEecCeeeEEehh-hccccccCCH-------HHhcccCCEEEEEEEEEccCCCeE
Confidence 3467999999999999999999997799888221 1111111111 367899999999999987766553
No 73
>PRK13806 rpsA 30S ribosomal protein S1; Provisional
Probab=96.59 E-value=0.0066 Score=53.60 Aligned_cols=66 Identities=12% Similarity=0.137 Sum_probs=47.8
Q ss_pred CCCEEEEEEEEEecccEEEEccc-cEEEEEcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEEccCCe
Q 032315 51 KGEILGAGVTMVNKMGFLAEAGA-VQIFCLIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQVDVTEI 123 (143)
Q Consensus 51 ~gEVv~G~V~~v~~~Gi~v~iGp-~~ifI~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~~~~~~ 123 (143)
.|+++.|+|++++++|+|+.++| .++|+.+.+ +.+.. ...+-...+++|+.|.+||.++..+.+.+
T Consensus 292 ~G~~v~G~V~~v~~~G~fV~l~~gv~Glvh~se-ls~~~------~~~~~~~~~~~Gd~v~vkVl~iD~e~~ri 358 (491)
T PRK13806 292 AGDKVTGKVVRLAPFGAFVEILPGIEGLVHVSE-MSWTR------RVNKPEDVVAPGDAVAVKIKDIDPAKRRI 358 (491)
T ss_pred CCCEEEEEEEEEeCceEEEEeCCCcEEEEEHHH-cCccc------ccCCHHHcCCCCCEEEEEEEEEEccCCEE
Confidence 59999999999999999999987 889883321 11100 01122356899999999999887765543
No 74
>PRK07899 rpsA 30S ribosomal protein S1; Reviewed
Probab=96.58 E-value=0.0062 Score=53.99 Aligned_cols=65 Identities=14% Similarity=0.246 Sum_probs=48.1
Q ss_pred CCCEEEEEEEEEecccEEEEccccEEEEEcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEEccCCe
Q 032315 51 KGEILGAGVTMVNKMGFLAEAGAVQIFCLIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQVDVTEI 123 (143)
Q Consensus 51 ~gEVv~G~V~~v~~~Gi~v~iGp~~ifI~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~~~~~~ 123 (143)
.|+++.|+|++++++|+|+.+|..++||.+.+ + .|.+. ++-...+++|+.|.+||+.+..+.+++
T Consensus 208 ~G~iv~G~V~~i~~~G~FVdlggv~Glv~~Se-l------s~~~v-~~~~~~~kvGd~V~vkVl~iD~e~~rI 272 (486)
T PRK07899 208 KGQVRKGVVSSIVNFGAFVDLGGVDGLVHVSE-L------SWKHI-DHPSEVVEVGQEVTVEVLDVDMDRERV 272 (486)
T ss_pred CCCEEEEEEEEEECCeEEEEECCEEEEEEHHH-C------CCccc-CCHHHhcCCCCEEEEEEEEEECCCCEE
Confidence 69999999999999999999988888882210 0 12111 122356899999999999988765553
No 75
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=96.45 E-value=0.006 Score=47.35 Aligned_cols=65 Identities=15% Similarity=0.031 Sum_probs=45.2
Q ss_pred EEEeecCCCEEEEEEEEEecccEEEEccc-----------cEEEEEcCCCceecCCCCceEEcCCceEEEcCCCeEEEEE
Q 032315 45 IVFRPFKGEILGAGVTMVNKMGFLAEAGA-----------VQIFCLIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKI 113 (143)
Q Consensus 45 lvFrPf~gEVv~G~V~~v~~~Gi~v~iGp-----------~~ifI~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV 113 (143)
....|..|+++.|+|++++..|++++++. .+.++...+- .|.+. ++-...+++||.|++||
T Consensus 58 ~~~~~~~GdiV~GkV~~i~~~g~~V~I~~~~~~~~~l~~~~~G~l~~s~i-------~~~~~-~~~~~~~~~GD~V~akV 129 (189)
T PRK09521 58 TPPLLKKGDIVYGRVVDVKEQRALVRIVSIEGSERELATSKLAYIHISQV-------SDGYV-ESLTDAFKIGDIVRAKV 129 (189)
T ss_pred CCCCCCCCCEEEEEEEEEcCCeEEEEEEEecccccccCCCceeeEEhhHc-------Chhhh-hhHHhccCCCCEEEEEE
Confidence 35778899999999999999999999852 4455511100 01010 11235689999999999
Q ss_pred EEEE
Q 032315 114 IGTQ 117 (143)
Q Consensus 114 ~~v~ 117 (143)
..+.
T Consensus 130 ~~i~ 133 (189)
T PRK09521 130 ISYT 133 (189)
T ss_pred EecC
Confidence 9886
No 76
>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional
Probab=96.43 E-value=0.013 Score=55.22 Aligned_cols=64 Identities=14% Similarity=0.191 Sum_probs=48.6
Q ss_pred CCCEEEEEEEEEecccEEEEccc-cEEEE---EcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEEccCC
Q 032315 51 KGEILGAGVTMVNKMGFLAEAGA-VQIFC---LIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQVDVTE 122 (143)
Q Consensus 51 ~gEVv~G~V~~v~~~Gi~v~iGp-~~ifI---~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~~~~~ 122 (143)
.|.++.|+|++++++|+|+++++ .++|+ .++++...+.. +....|+.|+.|+++|+++..+...
T Consensus 752 vG~iV~GkV~~v~~~GvFVeL~~gVeGlI~~s~lsdd~~~~~~--------~~~~~f~vGD~V~v~Vl~iD~~~rk 819 (863)
T PRK12269 752 VGSTVEGEVSSVTDFGIFVRVPGGVEGLVRKQHLVENRDGDPG--------EALRKYAVGDRVKAVIVDMNVKDRK 819 (863)
T ss_pred CCCEEEEEEEEEecCeEEEEcCCCeEEEEEHHHcCCcccccch--------hhccccCCCCEEEEEEEEEEcCCCE
Confidence 69999999999999999999965 88888 56543211111 1135689999999999988776554
No 77
>PRK07400 30S ribosomal protein S1; Reviewed
Probab=96.39 E-value=0.014 Score=48.95 Aligned_cols=61 Identities=16% Similarity=0.142 Sum_probs=45.0
Q ss_pred ecCCCEEEEEEEEEecccEEEEccc-cEEEE---EcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEEcc
Q 032315 49 PFKGEILGAGVTMVNKMGFLAEAGA-VQIFC---LIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQVDV 120 (143)
Q Consensus 49 Pf~gEVv~G~V~~v~~~Gi~v~iGp-~~ifI---~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~~~ 120 (143)
.-.|+++.|+|.++++.|+++.+|. .++|+ .+.+. +. ++....+++|++|+++|+++.-+.
T Consensus 29 ~~~G~iv~G~V~~i~~~g~~Vdig~k~~g~lp~sEis~~----------~~-~~~~~~~~~G~~v~~~Vi~~~~~~ 93 (318)
T PRK07400 29 FKPGDIVNGTVFSLEPRGALIDIGAKTAAFMPIQEMSIN----------RV-EGPEEVLQPNETREFFILSDENED 93 (318)
T ss_pred cCCCCEEEEEEEEEECCEEEEEECCCeEEEEEHHHhccc----------cc-cCHHHccCCCCEEEEEEEEEeCCC
Confidence 5789999999999999999999997 78988 23211 11 111245788899999998865443
No 78
>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional
Probab=96.37 E-value=0.01 Score=55.96 Aligned_cols=66 Identities=15% Similarity=0.148 Sum_probs=48.8
Q ss_pred CCCEEEEEEEEEecccEEEEccc-cEEEEEcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEEccCCe
Q 032315 51 KGEILGAGVTMVNKMGFLAEAGA-VQIFCLIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQVDVTEI 123 (143)
Q Consensus 51 ~gEVv~G~V~~v~~~Gi~v~iGp-~~ifI~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~~~~~~ 123 (143)
.|+++.|+|++++++|+|++++| .++||.+.+ + .|....+.....+++|+.|.++|+++..+.+.+
T Consensus 665 vG~~v~G~V~~i~~~G~fV~l~~gV~GlIh~se-l------s~~~~~~~~~~~~kvGq~VkvkVl~ID~e~rrI 731 (863)
T PRK12269 665 VGARFTRRIVKVTNAGAFIEMEEGIDGFLHVDD-L------SWVKRTRPADHELEVGKEIECMVIECDPQARRI 731 (863)
T ss_pred CCCEEEEEEEEEecceEEEEeCCCcEEEEEhHH-h------hccccccchhhccCCCCEEEEEEEEEeccCCEE
Confidence 49999999999999999999998 889884321 1 121111112346899999999999998766554
No 79
>PRK07899 rpsA 30S ribosomal protein S1; Reviewed
Probab=96.29 E-value=0.022 Score=50.58 Aligned_cols=62 Identities=16% Similarity=0.246 Sum_probs=47.7
Q ss_pred CCCEEEEEEEEEecccEEEEccc-cEEEE---EcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEEccCCe
Q 032315 51 KGEILGAGVTMVNKMGFLAEAGA-VQIFC---LIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQVDVTEI 123 (143)
Q Consensus 51 ~gEVv~G~V~~v~~~Gi~v~iGp-~~ifI---~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~~~~~~ 123 (143)
.|+++.|+|++++++|+|+.+.+ .++++ .|+++. + +..+..++.|+.|++||..+..+...+
T Consensus 293 vG~vv~G~V~~I~~fGvFVeL~~gieGLvh~SeLs~~~---------v--~~~~~~~kvGd~V~VkIi~ID~e~rrI 358 (486)
T PRK07899 293 IGQIVPGKVTKLVPFGAFVRVEEGIEGLVHISELAERH---------V--EVPEQVVQVGDEVFVKVIDIDLERRRI 358 (486)
T ss_pred CCCEEEEEEEEEeccEEEEEeCCCcEEEEEHHHcCccc---------c--cCccceeCCCCEEEEEEEEEECCCCEE
Confidence 59999999999999999999975 88888 443210 1 112367899999999999988765553
No 80
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=96.28 E-value=0.0071 Score=57.08 Aligned_cols=66 Identities=14% Similarity=0.264 Sum_probs=48.8
Q ss_pred EEEeecCCCEEE-EEEEEEecccEEEEccc-cEEEEEcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEE
Q 032315 45 IVFRPFKGEILG-AGVTMVNKMGFLAEAGA-VQIFCLIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQV 118 (143)
Q Consensus 45 lvFrPf~gEVv~-G~V~~v~~~Gi~v~iGp-~~ifI~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~ 118 (143)
++..|..|++++ |+|+++.++|+|+.+.| .+++|.+.+ + .|-|. +.-...++.||.|++||+++..
T Consensus 747 l~~~~~vG~iy~~g~V~~I~~FGaFVeL~~g~EGLVHISe-L------s~~rv-~~~~dv~kvGD~V~VkVi~ID~ 814 (891)
T PLN00207 747 LTMVPTVGDIYRNCEIKSIAPYGAFVEIAPGREGLCHISE-L------SSNWL-AKPEDAFKVGDRIDVKLIEVND 814 (891)
T ss_pred HhcCcCCCcEEECcEEEEEeccEEEEEeCCCCEEEEEhhh-c------CCccc-cCHHHhcCCCCEEEEEEEEECC
Confidence 445799999996 69999999999999988 788883321 0 11111 1223578999999999999874
No 81
>PRK06676 rpsA 30S ribosomal protein S1; Reviewed
Probab=96.26 E-value=0.014 Score=49.61 Aligned_cols=64 Identities=14% Similarity=0.239 Sum_probs=46.7
Q ss_pred ecCCCEEEEEEEEEecccEEEEccccEEEE---EcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEEccCCe
Q 032315 49 PFKGEILGAGVTMVNKMGFLAEAGAVQIFC---LIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQVDVTEI 123 (143)
Q Consensus 49 Pf~gEVv~G~V~~v~~~Gi~v~iGp~~ifI---~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~~~~~~ 123 (143)
.-.|+++.|+|+++++.|+|+.++-.++|+ .+++ .+. ++-...+++|+.|++||.++..+.+.+
T Consensus 190 ~~~G~~v~g~V~~v~~~G~fV~l~~v~g~v~~sels~----------~~~-~~~~~~~~vGd~i~~~Vl~vd~~~~~i 256 (390)
T PRK06676 190 LKEGDVVEGTVARLTDFGAFVDIGGVDGLVHISELSH----------ERV-EKPSEVVSVGQEVEVKVLSIDWETERI 256 (390)
T ss_pred CCCCCEEEEEEEEEecceEEEEeCCeEEEEEHHHcCc----------ccc-CCHHHhcCCCCEEEEEEEEEeCCCCEE
Confidence 346999999999999999999998788888 3331 111 122345788999999998876654443
No 82
>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=96.14 E-value=0.042 Score=50.18 Aligned_cols=70 Identities=6% Similarity=0.055 Sum_probs=53.2
Q ss_pred CCEEEEEEEEEecccEEEEc-cc-cEEEE---EcCC---CceecCCCC-ceEEcCCceEEEcCCCeEEEEEEEEEEccCC
Q 032315 52 GEILGAGVTMVNKMGFLAEA-GA-VQIFC---LIPD---DMELQTGDL-PSYTTSDGSVKIQKDCELWLKIIGTQVDVTE 122 (143)
Q Consensus 52 gEVv~G~V~~v~~~Gi~v~i-Gp-~~ifI---~lp~---~~~fd~~~~-~~~~~~~~~~~i~~g~~VR~RV~~v~~~~~~ 122 (143)
++..+|.|+.++++|+|+.+ .. .++|| .|++ .+.||.++. -.+.++ ..++.|+.|+++|.++......
T Consensus 558 ~~~f~g~I~~v~~~g~~v~l~~~~~~g~v~~~~l~~~~~~~~~~~~~~~~~l~g~---~~~~lgd~v~V~v~~vd~~~~~ 634 (639)
T TIGR02062 558 NTRFAAEIVDISRGGMRVRLLENGAIAFIPAAFLHANREELVCNQENGTVQIKGE---TVYKIGDVIDVVLTEVRMETRS 634 (639)
T ss_pred CcEEEEEEEeeeCCcEEEEEecCceEEEEEhhhcCCCCcceEEcccccEEEEecc---EEEecCCEEEEEEEEeccccCc
Confidence 45899999999999999999 33 88888 5654 355777642 223322 4899999999999999887766
Q ss_pred eE
Q 032315 123 IE 124 (143)
Q Consensus 123 ~~ 124 (143)
+-
T Consensus 635 i~ 636 (639)
T TIGR02062 635 II 636 (639)
T ss_pred Ee
Confidence 54
No 83
>TIGR00717 rpsA ribosomal protein S1. This model provides trusted hits to most long form (6 repeat) examples of RpsA. Among homologs with only four repeats are some to which other (perhaps secondary) functions have been assigned.
Probab=95.95 E-value=0.028 Score=49.31 Aligned_cols=61 Identities=16% Similarity=0.234 Sum_probs=47.0
Q ss_pred CCCEEEEEEEEEecccEEEEccc-cEEEE---EcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEEccCC
Q 032315 51 KGEILGAGVTMVNKMGFLAEAGA-VQIFC---LIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQVDVTE 122 (143)
Q Consensus 51 ~gEVv~G~V~~v~~~Gi~v~iGp-~~ifI---~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~~~~~ 122 (143)
.|+++.|.|++++++|+|+.++. .++|+ .++++ + .++....++.|+.+++||..+..+...
T Consensus 446 ~G~~v~g~V~~v~~~G~fV~l~~~~~Glv~~s~l~~~----------~-~~~~~~~~~~Gd~v~~~V~~id~~~~~ 510 (516)
T TIGR00717 446 VGSVVKGKVTEIKDFGAFVELPGGVEGLIRNSELSEN----------R-DEDKTDEIKVGDEVEAKVVDIDKKNRK 510 (516)
T ss_pred cceEEEEEEEEEecceEEEEcCCCeEEEEEHHHcCcc----------c-cccccccCCCCCEEEEEEEEEeCCCCE
Confidence 69999999999999999999977 78888 44321 1 112346789999999999988765444
No 84
>PRK06676 rpsA 30S ribosomal protein S1; Reviewed
Probab=95.93 E-value=0.044 Score=46.58 Aligned_cols=63 Identities=14% Similarity=0.097 Sum_probs=43.8
Q ss_pred eecCCCEEEEEEEEEecccEEEEc-cc-cEEEE---EcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEEccC
Q 032315 48 RPFKGEILGAGVTMVNKMGFLAEA-GA-VQIFC---LIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQVDVT 121 (143)
Q Consensus 48 rPf~gEVv~G~V~~v~~~Gi~v~i-Gp-~~ifI---~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~~~~ 121 (143)
....|+++.|+|+++++.|+++.+ |+ .++|+ .+.+. .. ++-...+++|+.|+++|..+.-+.+
T Consensus 14 ~~~~G~iv~G~V~~i~~~g~~V~i~~~~~~g~lp~~e~~~~----~~-------~~~~~~~~vGd~v~~~V~~v~~~~~ 81 (390)
T PRK06676 14 EVEVGDVVTGEVLKVEDKQVFVNIEGYKVEGVIPISELSND----HI-------EDINDVVKVGDELEVYVLKVEDGEG 81 (390)
T ss_pred cccCCCEEEEEEEEEECCeEEEEEecCCcEEEEEHHHhccc----cc-------cCcccccCCCCEEEEEEEEEECCCC
Confidence 456899999999999999999999 75 77888 33211 00 1112346777777777777765444
No 85
>PRK06299 rpsA 30S ribosomal protein S1; Reviewed
Probab=95.87 E-value=0.024 Score=50.51 Aligned_cols=65 Identities=12% Similarity=0.124 Sum_probs=44.0
Q ss_pred cCCCEEEEEEEEEecccEEEEccc-cEEEEEcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEEccC
Q 032315 50 FKGEILGAGVTMVNKMGFLAEAGA-VQIFCLIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQVDVT 121 (143)
Q Consensus 50 f~gEVv~G~V~~v~~~Gi~v~iGp-~~ifI~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~~~~ 121 (143)
..|+++.|+|+++++.|+|+.+++ .++|+.+.+ +. |.....+....+++|+.|++||.++..+.+
T Consensus 285 ~~G~~v~g~V~~i~~~G~fV~l~~~v~Glv~~se-l~------~~~~~~~~~~~~~~G~~v~v~V~~id~~~~ 350 (565)
T PRK06299 285 PVGSKVKGKVTNITDYGAFVELEEGIEGLVHVSE-MS------WTKKNKHPSKVVSVGQEVEVMVLEIDEEKR 350 (565)
T ss_pred CCCCEEEEEEEEEeCCeEEEEeCCCCEEEEEHHH-cC------ccccccCHHHhcCCCCEEEEEEEEEcCCCC
Confidence 359999999999999999999987 788882210 00 100011112456888888888888765433
No 86
>PRK00087 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed
Probab=95.80 E-value=0.03 Score=51.03 Aligned_cols=62 Identities=16% Similarity=0.118 Sum_probs=46.6
Q ss_pred cCCCEEEEEEEEEecccEEEEccc-cEEEE---EcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEEccCC
Q 032315 50 FKGEILGAGVTMVNKMGFLAEAGA-VQIFC---LIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQVDVTE 122 (143)
Q Consensus 50 f~gEVv~G~V~~v~~~Gi~v~iGp-~~ifI---~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~~~~~ 122 (143)
..|+++.|+|++++++|+|+.+.+ .++|+ .++++ . .++.+..++.|+.|++||.++..+...
T Consensus 561 ~~G~~v~g~V~~i~~~G~fV~l~~~i~Gli~~sel~~~------~-----~~~~~~~~kvGd~V~vkV~~id~e~~r 626 (647)
T PRK00087 561 PVGSIVLGKVVRIAPFGAFVELEPGVDGLVHISQISWK------R-----IDKPEDVLSEGEEVKAKILEVDPEEKR 626 (647)
T ss_pred cCCeEEEEEEEEEECCeEEEEECCCCEEEEEhhhcCcc------c-----cCCHhhcCCCCCEEEEEEEEEeCCCCE
Confidence 369999999999999999999976 78887 33211 0 112235689999999999988765544
No 87
>COG1098 VacB Predicted RNA binding protein (contains ribosomal protein S1 domain) [Translation, ribosomal structure and biogenesis]
Probab=95.71 E-value=0.012 Score=43.48 Aligned_cols=62 Identities=16% Similarity=0.133 Sum_probs=43.4
Q ss_pred ecCCCEEEEEEEEEecccEEEEcc-ccEEEEEcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEE
Q 032315 49 PFKGEILGAGVTMVNKMGFLAEAG-AVQIFCLIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQV 118 (143)
Q Consensus 49 Pf~gEVv~G~V~~v~~~Gi~v~iG-p~~ifI~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~ 118 (143)
+-.|+++.|+|+.++++|+||.+- =...+|.+.+-. .+ |. ++-.-.+.+|++|-++|+++.-
T Consensus 3 ~kvG~~l~GkItgI~~yGAFV~l~~g~tGLVHISEIa-----~~--fV-kdI~d~L~vG~eV~vKVl~ide 65 (129)
T COG1098 3 MKVGSKLKGKITGITPYGAFVELEGGKTGLVHISEIA-----DG--FV-KDIHDHLKVGQEVKVKVLDIDE 65 (129)
T ss_pred ccccceEEEEEEeeEecceEEEecCCCcceEEehHhh-----hh--hH-HhHHHHhcCCCEEEEEEEeecc
Confidence 567999999999999999999884 355666332100 00 11 1223467999999999998765
No 88
>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=95.69 E-value=0.045 Score=37.81 Aligned_cols=73 Identities=12% Similarity=0.154 Sum_probs=54.1
Q ss_pred EeecCCCEEEEEEEEEecccEEEEcc-ccEEEEEcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEEcc-CCeE
Q 032315 47 FRPFKGEILGAGVTMVNKMGFLAEAG-AVQIFCLIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQVDV-TEIE 124 (143)
Q Consensus 47 FrPf~gEVv~G~V~~v~~~Gi~v~iG-p~~ifI~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~~~-~~~~ 124 (143)
|.|..|.+|.|+|++++....+++++ |...++ | .+.|... .++.+-.+++||.|-+||..+.-+. -++-
T Consensus 2 Y~P~~gD~VIG~V~~~~~~~~~VdI~s~~~a~L--~-~~~f~ga------tk~~rp~L~~GDlV~ArV~~~~~~~~~eLt 72 (86)
T cd05790 2 YVPAKGDHVIGIVVAKAGDFFKVDIGGSEPASL--S-YLAFEGA------TKRNRPNLNVGDLVYARVVKANRDMEPELS 72 (86)
T ss_pred CcCCCCCEEEEEEEEEcCCeEEEEcCCCcceEe--c-hHHcccc------cccccccCCCCCEEEEEEEecCCCCCeEEE
Confidence 67999999999999999999999996 455544 2 1334322 2345678999999999998886542 3466
Q ss_pred EEEE
Q 032315 125 KARR 128 (143)
Q Consensus 125 ai~~ 128 (143)
|+..
T Consensus 73 c~~~ 76 (86)
T cd05790 73 CVDS 76 (86)
T ss_pred EeCC
Confidence 7663
No 89
>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=95.49 E-value=0.026 Score=39.05 Aligned_cols=63 Identities=16% Similarity=-0.030 Sum_probs=40.8
Q ss_pred EeecCCCEEEEEEEEEecccEEEEcc---------ccEEEEEcCCCceecCCCCceEEcC--CceEEEcCCCeEEEEEEE
Q 032315 47 FRPFKGEILGAGVTMVNKMGFLAEAG---------AVQIFCLIPDDMELQTGDLPSYTTS--DGSVKIQKDCELWLKIIG 115 (143)
Q Consensus 47 FrPf~gEVv~G~V~~v~~~Gi~v~iG---------p~~ifI~lp~~~~fd~~~~~~~~~~--~~~~~i~~g~~VR~RV~~ 115 (143)
+-|..|.++.|.|++++..-+.+.+- |...++...+-. + ...+ +-...|++||.||+||.+
T Consensus 2 ~~P~~GDiVig~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~~dv~---~-----~~~d~~~~~~~f~~GDiV~AkVis 73 (92)
T cd05791 2 VLPKVGSIVIARVTRINPRFAKVDILCVGGRPLKESFRGVIRKEDIR---A-----TEKDKVEMYKCFRPGDIVRAKVIS 73 (92)
T ss_pred CCCCCCCEEEEEEEEEcCCEEEEEEEEecCeecCCCcccEEEHHHcc---c-----cccchHHHHhhcCCCCEEEEEEEE
Confidence 56899999999999999999999661 122222110000 0 0001 112568999999999998
Q ss_pred EE
Q 032315 116 TQ 117 (143)
Q Consensus 116 v~ 117 (143)
..
T Consensus 74 ~~ 75 (92)
T cd05791 74 LG 75 (92)
T ss_pred cC
Confidence 64
No 90
>COG2183 Tex Transcriptional accessory protein [Transcription]
Probab=95.46 E-value=0.026 Score=52.54 Aligned_cols=63 Identities=16% Similarity=0.157 Sum_probs=49.1
Q ss_pred ecCCCEEEEEEEEEecccEEEEccc-cEEEE---EcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEEccCC
Q 032315 49 PFKGEILGAGVTMVNKMGFLAEAGA-VQIFC---LIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQVDVTE 122 (143)
Q Consensus 49 Pf~gEVv~G~V~~v~~~Gi~v~iGp-~~ifI---~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~~~~~ 122 (143)
-..|.++.|+|+++.++|+||.+|- .|++| .+.+.+.+++. .++++|+.|.++|..+-.+..+
T Consensus 656 Lk~Gm~leg~Vrnv~~fgafVdIgv~qDglvHis~ls~~fv~~P~-----------~vv~vGdiV~v~V~~vD~~r~r 722 (780)
T COG2183 656 LKPGMILEGTVRNVVDFGAFVDIGVHQDGLVHISQLSDKFVKDPN-----------EVVKVGDIVKVKVIEVDTARKR 722 (780)
T ss_pred ccCCCEEEEEEEEeeeccceEEeccccceeeeHHHhhhhhcCChH-----------HhcccCCEEEEEEEEEecccCe
Confidence 4679999999999999999999998 67888 44433333332 4678999999999988776544
No 91
>COG0539 RpsA Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]
Probab=95.38 E-value=0.038 Score=49.67 Aligned_cols=70 Identities=14% Similarity=0.134 Sum_probs=53.0
Q ss_pred EeecCCCEEEEEEEEEecccEEEEccc-cEEEEEcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEEccCCeE
Q 032315 47 FRPFKGEILGAGVTMVNKMGFLAEAGA-VQIFCLIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQVDVTEIE 124 (143)
Q Consensus 47 FrPf~gEVv~G~V~~v~~~Gi~v~iGp-~~ifI~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~~~~~~~ 124 (143)
-+--.|.++.|+|+..+++|+|+.++| .+.|+.+++ + .|..... -+.+++.|++|-++|+++..+..++.
T Consensus 273 ~~~~~g~~v~G~Vt~i~~~GafVei~~GvEGlvhvSE-i------sw~~~~~-P~evv~~Gq~V~V~Vl~id~e~rRIs 343 (541)
T COG0539 273 KKYPVGDKVEGKVTNLTDYGAFVEIEEGVEGLVHVSE-I------SWTKKNV-PSEVVKVGQEVEVKVLDIDPERRRIS 343 (541)
T ss_pred hhcCCCCEEEEEEEEeecCcEEEEecCCccceeechh-h------cccccCC-HHHhcccCCEEEEEEEeeCchhceEE
Confidence 344578999999999999999999999 999883321 0 1222112 24678999999999999998877754
No 92
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=95.27 E-value=0.093 Score=45.04 Aligned_cols=61 Identities=10% Similarity=0.171 Sum_probs=46.8
Q ss_pred EeecCCCEEEEEEEEEecccEEEEccccEEEEEcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEEccC
Q 032315 47 FRPFKGEILGAGVTMVNKMGFLAEAGAVQIFCLIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQVDVT 121 (143)
Q Consensus 47 FrPf~gEVv~G~V~~v~~~Gi~v~iGp~~ifI~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~~~~ 121 (143)
|++..|+++.|+|.+.++.|+++.+|=.+.|+ |. .+ + .. +..+++|+.+++-|..+..+.+
T Consensus 130 f~~k~GeiV~G~V~~~~~~~~~Vdlg~vEa~L--P~------~E-~--ip---~e~~~~Gd~Ika~V~~V~~~~k 190 (362)
T PRK12327 130 FSEREGDIVTGVVQRRDNRFVYVNLGKIEAVL--PP------AE-Q--IP---GETYKHGDRIKVYVVKVEKTTK 190 (362)
T ss_pred HHHhcCCEEEEEEEEEeCCcEEEEeCCeEEEe--cH------HH-c--CC---CCCCCCCCEEEEEEEEEecCCC
Confidence 66789999999999999999999998777766 21 00 0 00 1347899999999999987653
No 93
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=95.23 E-value=0.081 Score=46.84 Aligned_cols=61 Identities=11% Similarity=0.189 Sum_probs=46.0
Q ss_pred EeecCCCEEEEEEEEEecccEEEEccccEEEEEcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEEccC
Q 032315 47 FRPFKGEILGAGVTMVNKMGFLAEAGAVQIFCLIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQVDVT 121 (143)
Q Consensus 47 FrPf~gEVv~G~V~~v~~~Gi~v~iGp~~ifI~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~~~~ 121 (143)
|+...||++.|+|.++++.|+++.+|=.+.|+ |. +.. . -+..+++|+.||+.|..+.-+.+
T Consensus 130 yk~~~GeIV~G~V~ri~~~giiVDLggvea~L--P~-------sE~--i---p~E~~~~GdrIka~I~~Vd~~~k 190 (470)
T PRK09202 130 YKDRVGEIITGVVKRVERGNIIVDLGRAEAIL--PR-------KEQ--I---PRENFRPGDRVRAYVYEVRKEAR 190 (470)
T ss_pred HHhhcCCEEEEEEEEEecCCEEEEECCeEEEe--cH-------HHc--C---CCccCCCCCEEEEEEEEEecCCC
Confidence 44457999999999999999999998777776 20 000 0 11346999999999999987654
No 94
>PRK00087 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed
Probab=95.19 E-value=0.049 Score=49.69 Aligned_cols=61 Identities=15% Similarity=0.206 Sum_probs=45.3
Q ss_pred CCCEEEEEEEEEecccEEEEccccEEEE---EcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEEccCC
Q 032315 51 KGEILGAGVTMVNKMGFLAEAGAVQIFC---LIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQVDVTE 122 (143)
Q Consensus 51 ~gEVv~G~V~~v~~~Gi~v~iGp~~ifI---~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~~~~~ 122 (143)
.|+++.|+|+++++.|+|+.++..++|+ .+++ .+. .+-...+++|+.|++||.++....+.
T Consensus 477 ~G~iV~g~V~~v~~~G~fV~l~gv~Gll~~sels~----------~~~-~~~~~~~~vGd~V~vkV~~id~~~~~ 540 (647)
T PRK00087 477 EGDVVEGEVKRLTDFGAFVDIGGVDGLLHVSEISW----------GRV-EKPSDVLKVGDEIKVYILDIDKENKK 540 (647)
T ss_pred CCCEEEEEEEEEeCCcEEEEECCEEEEEEHHHcCc----------ccc-CCHHHhcCCCCEEEEEEEEEECCCCE
Confidence 6999999999999999999997788888 3321 111 11234578999999999887655443
No 95
>COG1093 SUI2 Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis]
Probab=94.69 E-value=0.027 Score=46.38 Aligned_cols=64 Identities=17% Similarity=0.149 Sum_probs=49.3
Q ss_pred ecCCCEEEEEEEEEecccEEEEcc--c-cEEEEEcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEEcc
Q 032315 49 PFKGEILGAGVTMVNKMGFLAEAG--A-VQIFCLIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQVDV 120 (143)
Q Consensus 49 Pf~gEVv~G~V~~v~~~Gi~v~iG--p-~~ifI~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~~~ 120 (143)
|-.||+|-|+|.++.++|+|+++- | .+.||.+.+ -.+.|. ++-+.+++.|..+-++|+.+.-..
T Consensus 9 PeeGEiVv~tV~~V~~~GAyv~L~EY~g~Eg~ihiSE-----vas~wV---knIrd~vkegqkvV~kVlrVd~~r 75 (269)
T COG1093 9 PEEGEIVVGTVKQVADYGAYVELDEYPGKEGFIHISE-----VASGWV---KNIRDYVKEGQKVVAKVLRVDPKR 75 (269)
T ss_pred CCCCcEEEEEEEEeeccccEEEeeccCCeeeeEEHHH-----HHHHHH---HHHHHHhhcCCeEEEEEEEEcCCC
Confidence 889999999999999999999995 4 778885531 112342 223468899999999999886544
No 96
>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=94.15 E-value=0.22 Score=42.35 Aligned_cols=60 Identities=20% Similarity=0.268 Sum_probs=44.0
Q ss_pred EeecCCCEEEEEEEEEeccc-EEEEccccEEEEEcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEEcc
Q 032315 47 FRPFKGEILGAGVTMVNKMG-FLAEAGAVQIFCLIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQVDV 120 (143)
Q Consensus 47 FrPf~gEVv~G~V~~v~~~G-i~v~iGp~~ifI~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~~~ 120 (143)
|+...||++.|+|.++++.| +++.+|=.+.|+ |. +.+ ... ..+++|+.+++-|..+.-++
T Consensus 127 y~~k~GeiV~G~V~~v~~~g~v~VdiG~~ea~L--P~-------~E~--ip~---E~~~~Gd~ik~~V~~V~~~~ 187 (341)
T TIGR01953 127 FSSKEGEIISGTVKRVNRRGNLYVELGKTEGIL--PK-------KEQ--IPG---EKFRIGDRIKAYVYEVRKTA 187 (341)
T ss_pred HHhhcCCEEEEEEEEEecCCcEEEEECCeEEEe--cH-------HHc--CCC---cCCCCCCEEEEEEEEEEcCC
Confidence 55569999999999999998 599998767766 20 000 001 12789999999999998654
No 97
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=93.57 E-value=1.1 Score=36.56 Aligned_cols=71 Identities=13% Similarity=0.182 Sum_probs=53.1
Q ss_pred EEeecCCCEEEEEEEEEecccEEEEcc-ccEEEEEcCCC--ceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEEccCC
Q 032315 46 VFRPFKGEILGAGVTMVNKMGFLAEAG-AVQIFCLIPDD--MELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQVDVTE 122 (143)
Q Consensus 46 vFrPf~gEVv~G~V~~v~~~Gi~v~iG-p~~ifI~lp~~--~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~~~~~ 122 (143)
-|.|-.|.+|.|.|.++...+..++++ |...++.+.+- -.++.. ..+-+.++++||.|-+||..+.-+..-
T Consensus 59 ~YiP~~gD~VIG~I~~v~~~~W~VDI~sp~~A~L~ls~~~~r~~~~~------~~~~r~~l~vGD~v~AkV~~vd~~~~~ 132 (239)
T COG1097 59 RYIPEVGDVVIGKIIEVGPSGWKVDIGSPYPALLSLSDFLRRKFENA------EKDLRPFLNVGDLVYAKVVDVDRDGEV 132 (239)
T ss_pred cccCCCCCEEEEEEEEEcccceEEEcCCccceEeehhhhhccccccc------ccccccccccCCEEEEEEEEccCCCce
Confidence 588999999999999999999999996 78887733211 011111 234568899999999999987654433
No 98
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=93.13 E-value=0.22 Score=45.91 Aligned_cols=65 Identities=15% Similarity=0.097 Sum_probs=47.9
Q ss_pred EEEeecCCCEEEEEEEEEecccEEEEccc-cEEEEEcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEE
Q 032315 45 IVFRPFKGEILGAGVTMVNKMGFLAEAGA-VQIFCLIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQ 117 (143)
Q Consensus 45 lvFrPf~gEVv~G~V~~v~~~Gi~v~iGp-~~ifI~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~ 117 (143)
++=.|.+||+..|+|+.+..+|+|+++-| -++++.++.-. .. .-++-..+++.||.|++|+..+.
T Consensus 613 i~~e~evg~iy~G~V~ri~~fGaFv~l~~gkdgl~hiS~~~---~~-----rv~kv~dvlk~Gd~v~Vkv~~iD 678 (692)
T COG1185 613 ITREVEVGEVYEGTVVRIVDFGAFVELLPGKDGLVHISQLA---KE-----RVEKVEDVLKEGDEVKVKVIEID 678 (692)
T ss_pred HHhhcccccEEEEEEEEEeecceEEEecCCcceeEEehhhh---hh-----hhhcccceeecCceEEEEEeeec
Confidence 45668899999999999999999999988 66777322110 00 11223368899999999998764
No 99
>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=91.51 E-value=0.29 Score=33.52 Aligned_cols=23 Identities=39% Similarity=0.309 Sum_probs=17.1
Q ss_pred ecCCCEEEEEEEEEecccEEEEc
Q 032315 49 PFKGEILGAGVTMVNKMGFLAEA 71 (143)
Q Consensus 49 Pf~gEVv~G~V~~v~~~Gi~v~i 71 (143)
|..|-++.|.|+++++.-+.+.+
T Consensus 2 P~vGdiV~~rVtrv~~~~a~v~I 24 (82)
T PF10447_consen 2 PKVGDIVIARVTRVNPRQAKVEI 24 (82)
T ss_dssp --TT-EEEEEEEEE-SSEEEEEE
T ss_pred CCCCCEEEEEEEEEeccEEEEEE
Confidence 88999999999999999988843
No 100
>cd05699 S1_Rrp5_repeat_hs7 S1_Rrp5_repeat_hs7: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 7 (hs7). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=88.01 E-value=1.2 Score=29.80 Aligned_cols=54 Identities=15% Similarity=0.172 Sum_probs=39.5
Q ss_pred CCEEEEEEEEEecccEEEEccc--cEEEE---EcCCCceecCCCCceEEcCCceEEEcCCCeE-EEEEE
Q 032315 52 GEILGAGVTMVNKMGFLAEAGA--VQIFC---LIPDDMELQTGDLPSYTTSDGSVKIQKDCEL-WLKII 114 (143)
Q Consensus 52 gEVv~G~V~~v~~~Gi~v~iGp--~~ifI---~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~V-R~RV~ 114 (143)
|.+++|+|.+=++.++.+.+++ +..++ +|+| .+..+. ..| ..+++|+++ +.=|.
T Consensus 1 G~lV~~~V~EKt~D~l~v~l~~~~l~a~l~~~HLsD--~~~k~~-~~~------~klrvG~~L~~~lvL 60 (72)
T cd05699 1 GKLVDARVLKKTLNGLEVAILPEEIRAFLPTMHLSD--HVSNCP-LLW------HCLQEGDTIPNLMCL 60 (72)
T ss_pred CceEEEEEEEEcCCcEEEEecCCCcEEEEEccccCC--chhhCH-HHH------hhhhcCCCccceEEE
Confidence 6789999999999999999998 66777 7765 333332 123 457788877 66665
No 101
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=86.46 E-value=4.2 Score=35.21 Aligned_cols=61 Identities=13% Similarity=0.145 Sum_probs=43.7
Q ss_pred EeecCCCEEEEEEEEEecc-cEEEEccccEEEEEcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEEccC
Q 032315 47 FRPFKGEILGAGVTMVNKM-GFLAEAGAVQIFCLIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQVDVT 121 (143)
Q Consensus 47 FrPf~gEVv~G~V~~v~~~-Gi~v~iGp~~ifI~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~~~~ 121 (143)
|++..||++.|+|..++.. ++++.+|=.+.++ |.. ++ .. +..|++|+.+|+=|..+.-++.
T Consensus 134 y~~~~Geiv~g~V~r~~~~~~i~vdlg~~ea~L--P~~------eq---ip---~E~~~~Gdrik~~i~~V~~~~k 195 (374)
T PRK12328 134 YKKKVGKIVFGTVVRVDNEENTFIEIDEIRAVL--PMK------NR---IK---GEKFKVGDVVKAVLKRVKIDKN 195 (374)
T ss_pred HHHhcCcEEEEEEEEEecCCCEEEEcCCeEEEe--CHH------Hc---CC---CCcCCCCCEEEEEEEEEecCCC
Confidence 7889999999999999975 5899998655544 411 10 00 1346888888888888887665
No 102
>KOG3409 consensus Exosomal 3'-5' exoribonuclease complex, subunit ski4 (Csl4) [Translation, ribosomal structure and biogenesis]
Probab=86.23 E-value=2.5 Score=33.11 Aligned_cols=75 Identities=16% Similarity=0.025 Sum_probs=44.5
Q ss_pred EEEEEEEEEEeecCCCEEEEEEEEEecccEEEEccccEEEE--EcCCCceecCCC--CceEEcCCc----eEEEcCCCeE
Q 032315 38 FLVRCQCIVFRPFKGEILGAGVTMVNKMGFLAEAGAVQIFC--LIPDDMELQTGD--LPSYTTSDG----SVKIQKDCEL 109 (143)
Q Consensus 38 ~~V~F~~lvFrPf~gEVv~G~V~~v~~~Gi~v~iGp~~ifI--~lp~~~~fd~~~--~~~~~~~~~----~~~i~~g~~V 109 (143)
.+..|..+ -|+.|.|+.+.|+.++..=+.+ +|+. .+|-...|..-- +-.-..+.+ -..|++||.|
T Consensus 57 ~~~~~~~~--LP~~G~IVtarV~~i~~rfAkv-----~I~~V~d~~lk~~FrglirkqdvR~tEkdrv~v~ksFrPgDiV 129 (193)
T KOG3409|consen 57 EKQLFNEL--LPFVGAIVTARVSRINLRFAKV-----DILSVGDKPLKKSFRGLIRKQDVRATEKDRVKVYKSFRPGDIV 129 (193)
T ss_pred cccchhhc--CCccCcEEEEEEEeeccceeeE-----EEEEEcCEEhhhhhcceeehhhccccccchhhhhhccCCCcEE
Confidence 33444444 4999999999999999888877 4444 333222222100 000001111 1467899999
Q ss_pred EEEEEEEEEc
Q 032315 110 WLKIIGTQVD 119 (143)
Q Consensus 110 R~RV~~v~~~ 119 (143)
|+||++..-.
T Consensus 130 lAkVis~~~~ 139 (193)
T KOG3409|consen 130 LAKVISLGDG 139 (193)
T ss_pred EEEEeecCCC
Confidence 9999994433
No 103
>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=83.70 E-value=6.1 Score=34.51 Aligned_cols=75 Identities=15% Similarity=0.110 Sum_probs=47.9
Q ss_pred eecCCCEEEEEEEEEecc--cEEEEccc-cEEEE---EcCCCceecCCCCceE-EcCCceEEEcCCCeEEEEEEEEEEcc
Q 032315 48 RPFKGEILGAGVTMVNKM--GFLAEAGA-VQIFC---LIPDDMELQTGDLPSY-TTSDGSVKIQKDCELWLKIIGTQVDV 120 (143)
Q Consensus 48 rPf~gEVv~G~V~~v~~~--Gi~v~iGp-~~ifI---~lp~~~~fd~~~~~~~-~~~~~~~~i~~g~~VR~RV~~v~~~~ 120 (143)
.+..|.+..|+|.++.+. |+||.+|. -++|+ .+.++..+........ ...+-...+++|+.|.++|...-...
T Consensus 22 ~~~vGnIY~GrV~~i~p~l~aAFVdiG~~k~gfL~~~d~~~~~~~~~~~~~~~~~~~~i~~~l~~G~~IlVQV~Ke~~~~ 101 (414)
T TIGR00757 22 RQLKGNIYKGRVTRILPSLQAAFVDIGLEKNGFLHASDIGPNYECLAPAEAKREAGPSISELLRPGQSVLVQVVKEPRGN 101 (414)
T ss_pred cCCCCCEEEEEEeeecCCCceEEEEcCCCceEEEEHHHcCchhhccccccccccccCCHHHhCcCCCEEEEEEeeCCcCC
Confidence 356899999999999999 99999999 56999 3322211111000000 00011235889999999999866654
Q ss_pred CC
Q 032315 121 TE 122 (143)
Q Consensus 121 ~~ 122 (143)
..
T Consensus 102 Kg 103 (414)
T TIGR00757 102 KG 103 (414)
T ss_pred CC
Confidence 44
No 104
>PF13509 S1_2: S1 domain; PDB: 3GO5_A.
Probab=82.67 E-value=1.8 Score=27.47 Aligned_cols=28 Identities=21% Similarity=0.408 Sum_probs=17.3
Q ss_pred CCCEEEEEEEEEecccEEEEccc-cEEEE
Q 032315 51 KGEILGAGVTMVNKMGFLAEAGA-VQIFC 78 (143)
Q Consensus 51 ~gEVv~G~V~~v~~~Gi~v~iGp-~~ifI 78 (143)
.|++...+|++.++.|+|+..|- .++++
T Consensus 1 iG~~~~L~V~~~~~~g~fL~~~~~~~vlL 29 (61)
T PF13509_consen 1 IGQINTLKVVDKNEFGYFLDDGEGKEVLL 29 (61)
T ss_dssp --------EEEE-SSEEEEEETT-EEEEE
T ss_pred CCCCcceEEEEEeCCEEEEECCCCCEEEe
Confidence 37888999999999999999987 77887
No 105
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=78.65 E-value=7.7 Score=34.41 Aligned_cols=59 Identities=12% Similarity=0.192 Sum_probs=41.7
Q ss_pred EeecCCCEEEEEEEEEecccEEEEc----cc--cEEEEEcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEEc
Q 032315 47 FRPFKGEILGAGVTMVNKMGFLAEA----GA--VQIFCLIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQVD 119 (143)
Q Consensus 47 FrPf~gEVv~G~V~~v~~~Gi~v~i----Gp--~~ifI~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~~ 119 (143)
|++..||++.|+|..+...++++.+ |- .+.++ |. .++ .. +-.|++|+.||+=|..|+-.
T Consensus 148 f~~~~GeIV~G~V~r~e~~~viv~l~~~~g~~~~EaiL--P~------~Eq---ip---~E~y~~Gdrika~i~~V~~~ 212 (449)
T PRK12329 148 FQDLEDTVLTARVLRFERQSVIMAVSSGFGQPEVEAEL--PK------REQ---LP---NDNYRANATFKVFLKEVSEG 212 (449)
T ss_pred HHHhcCcEEEEEEEEEcCCCEEEEecccCCCcceEEEe--cH------HHc---CC---CCcCCCCCEEEEEEEEeecC
Confidence 7889999999999999999999887 42 44443 31 000 00 13468888888888888765
No 106
>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=78.13 E-value=12 Score=26.88 Aligned_cols=72 Identities=15% Similarity=0.231 Sum_probs=48.8
Q ss_pred eecCCCEEEEEEEEEecccEEEEccc-cEEEEEcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEEcc------
Q 032315 48 RPFKGEILGAGVTMVNKMGFLAEAGA-VQIFCLIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQVDV------ 120 (143)
Q Consensus 48 rPf~gEVv~G~V~~v~~~Gi~v~iGp-~~ifI~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~~~------ 120 (143)
-|++|-+|.|+|..+.+.-+++..|- +.+.+.-|. - + ...+..|+.||+|+.+....+
T Consensus 20 G~~~gk~V~G~I~hvv~ddLYIDfG~KFhcVc~rp~-----------~---~-~~~y~~G~rV~lrLkdlELs~~FLG~~ 84 (104)
T PF10246_consen 20 GDPEGKIVIGKIFHVVDDDLYIDFGGKFHCVCKRPA-----------V---N-GEKYVRGSRVRLRLKDLELSAHFLGAS 84 (104)
T ss_pred CCccCCEEEEEEEEEecCceEEEeCCceeEEEeccc-----------c---c-ccccccCCEEEEEECCHhhhhhhccCC
Confidence 46789999999999999988888775 555443321 0 1 134678999999998876533
Q ss_pred ---CCeEEEEEcccccc
Q 032315 121 ---TEIEKARREVGKQR 134 (143)
Q Consensus 121 ---~~~~ai~~~~~~~~ 134 (143)
+-.-|=|.++|-.+
T Consensus 85 ~d~TllEAd~~Llgl~~ 101 (104)
T PF10246_consen 85 KDTTLLEADATLLGLLK 101 (104)
T ss_pred CCcEEEEeeeEEEeeec
Confidence 11556666665443
No 107
>KOG1004 consensus Exosomal 3'-5' exoribonuclease complex subunit Rrp40 [Translation, ribosomal structure and biogenesis]
Probab=76.40 E-value=35 Score=27.65 Aligned_cols=85 Identities=14% Similarity=0.152 Sum_probs=63.6
Q ss_pred EEEEEEEEEEEEeecCCCEEEEEEEEEecccEEEEccc-cEEEEEcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEE
Q 032315 36 VTFLVRCQCIVFRPFKGEILGAGVTMVNKMGFLAEAGA-VQIFCLIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKII 114 (143)
Q Consensus 36 ~~~~V~F~~lvFrPf~gEVv~G~V~~v~~~Gi~v~iGp-~~ifI~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~ 114 (143)
=.+.+..+-.=|-|-++..|.|.|++.+.....+++|= .-.-+ | -..|...+ +.++-.+++||.|-.||.
T Consensus 50 ~v~~vds~~kRYiP~~~D~VIGiV~~~~gd~ykVDigg~~~a~L--~-~laFe~At------krNrPnl~vGdliyakv~ 120 (230)
T KOG1004|consen 50 GVYWVDSQQKRYIPVKGDHVIGIVTSKSGDIYKVDIGGSEPASL--S-YLAFEGAT------KRNRPNLQVGDLIYAKVV 120 (230)
T ss_pred eeEEEecccceecCCCCCEEEEEEEeccCceEEEecCCCCeeee--e-eccccCcc------ccCCCccccccEEEEEEE
Confidence 36688888899999999999999999999999999964 33432 2 23344332 234456899999999999
Q ss_pred EEEEcc-CCeEEEEEc
Q 032315 115 GTQVDV-TEIEKARRE 129 (143)
Q Consensus 115 ~v~~~~-~~~~ai~~~ 129 (143)
.-.-+. -++.|+.+-
T Consensus 121 ~a~~~~Epel~Cids~ 136 (230)
T KOG1004|consen 121 DANKDMEPELTCIDST 136 (230)
T ss_pred ecCCCcCcceEEEccc
Confidence 876543 447888775
No 108
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=73.31 E-value=16 Score=28.89 Aligned_cols=69 Identities=16% Similarity=0.037 Sum_probs=40.9
Q ss_pred EEeecCCCEEEEEEEEEecccEEEEccc-cEEEEEcCCC----ceecCCCCceEEcCCceEEEcCCCeEEEEEEEE
Q 032315 46 VFRPFKGEILGAGVTMVNKMGFLAEAGA-VQIFCLIPDD----MELQTGDLPSYTTSDGSVKIQKDCELWLKIIGT 116 (143)
Q Consensus 46 vFrPf~gEVv~G~V~~v~~~Gi~v~iGp-~~ifI~lp~~----~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v 116 (143)
-.-|-.|-++-|.|+++.+..+.+++-. .+-=-.+++. .+...... .+ .++..-.|++||.||+||++.
T Consensus 59 ~~~~K~GdiV~grV~~v~~~~a~V~i~~ve~~~r~~~~~~~~~ihvs~~~~-~~-~~~~~d~f~~GDivrA~Vis~ 132 (188)
T COG1096 59 PPLPKGGDIVYGRVTDVREQRALVRIVGVEGKERELATSGAADIHVSQVRD-GY-VEKLSDAFRIGDIVRARVIST 132 (188)
T ss_pred CCCCCCCCEEEEEEeeccceEEEEEEEEEecccccCCCCceeeEEEEeccc-cc-ccccccccccccEEEEEEEec
Confidence 4456677999999999999999987632 1100011111 11111110 01 122235789999999999995
No 109
>KOG1070 consensus rRNA processing protein Rrp5 [RNA processing and modification]
Probab=70.28 E-value=18 Score=36.66 Aligned_cols=67 Identities=16% Similarity=0.177 Sum_probs=49.9
Q ss_pred cCCCEEEEEEEEEecccEEEEccc-cEEEEEcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEEccCCeE
Q 032315 50 FKGEILGAGVTMVNKMGFLAEAGA-VQIFCLIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQVDVTEIE 124 (143)
Q Consensus 50 f~gEVv~G~V~~v~~~Gi~v~iGp-~~ifI~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~~~~~~~ 124 (143)
-.|++++|.|.+++.+|+|+.+++ .+.|+-+.+- ||.-.. .| +..+..|+.|-.||..+.-+++++.
T Consensus 1161 k~g~iv~G~V~nv~~~glfi~ls~~v~a~v~is~~--~ds~~k-~w-----~k~~~~gklv~~rv~~ve~~s~rie 1228 (1710)
T KOG1070|consen 1161 KIGDIVRGFVKNVETKGLFIALSRKVEAFVPISGL--SDSFEK-EW-----EKHLPVGKLVTGRVLSVEEDSKRIE 1228 (1710)
T ss_pred ccCceeEEEEEEecCCcEEEEEccceEEEEEcccc--ccchhh-hh-----hccCCccceeeeEEEEeeccCceEE
Confidence 468999999999999999999999 8888833211 222221 23 3567888899999999888876654
No 110
>PRK11712 ribonuclease G; Provisional
Probab=55.92 E-value=46 Score=29.82 Aligned_cols=86 Identities=13% Similarity=0.169 Sum_probs=51.6
Q ss_pred eecCCCEEEEEEEEEec--ccEEEEccc-cEEEEEcCC---Ccee-cCCCCceEEcCCceEEEcCCCeEEEEEEEEEEcc
Q 032315 48 RPFKGEILGAGVTMVNK--MGFLAEAGA-VQIFCLIPD---DMEL-QTGDLPSYTTSDGSVKIQKDCELWLKIIGTQVDV 120 (143)
Q Consensus 48 rPf~gEVv~G~V~~v~~--~Gi~v~iGp-~~ifI~lp~---~~~f-d~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~~~ 120 (143)
+...|.+..|.|.++-+ +++||.+|. -++|+.+.| +.++ ..+.........-...++.|+.|-+.|...-...
T Consensus 35 ~~~vGnIY~G~V~~v~pg~~AAFVdIG~~k~gFL~~~d~~~~~~~~~~~~~~~~~~~~i~~~l~~Gq~iLVQV~Ke~~~~ 114 (489)
T PRK11712 35 RGIVGNIYKGRVSRVLPGMQAAFVDIGLDKAAFLHASDIVPHTECVAGEEQKQFVVRDISELVRQGQDIMVQVVKDPLGT 114 (489)
T ss_pred ccccccEEEEEEeecCCCCceeEEeeCCCccEEEEhhhccchhhhcccccccccccccHHHhccCCCEEEEEEEeCCcCC
Confidence 45689999999999986 479999998 559992221 1111 1110000000001234899999999999877765
Q ss_pred CCeEEEE--Eccccc
Q 032315 121 TEIEKAR--REVGKQ 133 (143)
Q Consensus 121 ~~~~ai~--~~~~~~ 133 (143)
..-...+ ++.|+|
T Consensus 115 KG~~lT~~Isl~Gry 129 (489)
T PRK11712 115 KGARLTTDITLPSRY 129 (489)
T ss_pred CCCeEEEEEEeccce
Confidence 5533333 355554
No 111
>COG2996 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only]
Probab=53.63 E-value=40 Score=28.23 Aligned_cols=54 Identities=17% Similarity=0.136 Sum_probs=37.6
Q ss_pred CCCEEEEEEEEEecccEEEEc-cccEEEEEcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEEcc
Q 032315 51 KGEILGAGVTMVNKMGFLAEA-GAVQIFCLIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQVDV 120 (143)
Q Consensus 51 ~gEVv~G~V~~v~~~Gi~v~i-Gp~~ifI~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~~~ 120 (143)
+++.++|+|-...+.|.|+-+ +-.-+|| +.+. ++ ...+.|+.+-.||++++.+.
T Consensus 155 ~nq~v~~tVYr~~~~G~fv~~e~~~~GfI---------h~sE-r~------~~prlG~~l~~rVi~~reDg 209 (287)
T COG2996 155 KNQEVDATVYRLLESGTFVITENGYLGFI---------HKSE-RF------AEPRLGERLTARVIGVREDG 209 (287)
T ss_pred hcCeeeeEEEEEeccceEEEEcCCeEEEE---------cchh-hc------ccccCCceEEEEEEEEccCC
Confidence 489999999999999999855 1122222 1110 11 34688999999999998843
No 112
>COG4776 Rnb Exoribonuclease II [Transcription]
Probab=44.05 E-value=12 Score=33.76 Aligned_cols=74 Identities=9% Similarity=0.110 Sum_probs=50.3
Q ss_pred eecCCCEEEEEEEEEecccEEEEccc--cEEEE---Ec---CCCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEEc
Q 032315 48 RPFKGEILGAGVTMVNKMGFLAEAGA--VQIFC---LI---PDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQVD 119 (143)
Q Consensus 48 rPf~gEVv~G~V~~v~~~Gi~v~iGp--~~ifI---~l---p~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~~ 119 (143)
++..+....++|.+++.-|+++++=- -..|| .+ .+...++.++...++ ++...++.||.|-+++.+++-+
T Consensus 558 k~~~~~~F~AEI~Di~R~G~RvrLleNGA~~FIPa~lih~~reei~~n~e~gtv~I--~ge~~Yk~~D~i~V~l~eVr~e 635 (645)
T COG4776 558 KAGTNTRFAAEIQDISRGGMRVRLLENGAIAFIPAPLIHANREELVCNQENGTVQI--KGETVYKVGDVIDVTLAEVRME 635 (645)
T ss_pred ccccCchhhhhhhhhccCceEEEeccCCcceecchhhhccchhheEecCCCceEEE--ccEEEEeeccEEEEEeHHHHHh
Confidence 45556667788999999999999832 34566 22 223445544433333 3458899999999999998887
Q ss_pred cCCe
Q 032315 120 VTEI 123 (143)
Q Consensus 120 ~~~~ 123 (143)
..++
T Consensus 636 tRsi 639 (645)
T COG4776 636 TRSI 639 (645)
T ss_pred hhhh
Confidence 6654
No 113
>PF07238 PilZ: PilZ domain; InterPro: IPR009875 The ubiquitous bacterial second messenger cyclic-di-GMP (c-di-GMP) is associated with the regulation of biofilm formation, the control of exopolysaccharide synthesis, flagellar- and pili-based motility, gene expression, interactions of bacteria with eukaryotic hosts and multicellular behaviour in diverse bacteria. With the exception of bacterial cellulose synthases, the identities of c-di-GMP receptors and end targets of the proteins having one or more PilZ domains are mostly uncharacterised. However it was suggested that the PilZ domains present in the BcsA subunits of bacterial cellulose synthases function in c-di-GMP binding []. More recently YcgR (see IPR023787 from INTERPRO) was found to bind c-di-GMP tightly and specifically; also isolated PilZ domains from YcgR and BcsA bound c-di-GMP indicating that the PilZ domain was sufficient for binding of c-di-GMP and significantly that site-directed mutagenesis performed on YcgR implicated the most conserved residues in the PilZ domain directly in c-di-GMP binding []. It was suggested that c-di-GMP binding to PilZ brings about conformational changes in the protein that stabilise the bound ligand and probability initiates the downstream signal transduction cascade. In the case of YcgR, c-di-GMP binding regulates flagellum-based motility in a c-di-GMP-dependent manner (see IPR023787 from INTERPRO) []. The association of the PilZ domain with a variety of other domains, including likely components of bacterial multidrug secretion system, could provide clues to multiple functions of the c-di-GMP in bacterial pathogenesis and cell development. Binding and mutagenesis studies of several PilZ domain proteins have confirmed this observation and demonstrated that c-di-GMP binding depends on residues in RxxxR and D/NxSxxG sequence motifs. The crystal structure, at 1.7 A, of a PilZ domain::c-di-GMP complex from Vibrio cholerae shows c-di-GMP contacting seven of nine strongly conserved residues. Binding of c-di-GMP causes a conformational switch whereby the C- and N-terminal domains are brought into close opposition forming a new allosteric interaction surface that spans these domains and the c-di-GMP at their interface []. ; GO: 0035438 cyclic-di-GMP binding; PDB: 2RDE_B 1YLN_A 3KYG_A 3DSG_B 2GJG_A 3KYF_A 1YWU_A 2L74_A 2L1T_A 3CNR_A ....
Probab=42.54 E-value=89 Score=19.92 Aligned_cols=34 Identities=12% Similarity=0.041 Sum_probs=27.1
Q ss_pred EEEEEEEEEEeecCCCEEEEEEEEEecccEEEEc
Q 032315 38 FLVRCQCIVFRPFKGEILGAGVTMVNKMGFLAEA 71 (143)
Q Consensus 38 ~~V~F~~lvFrPf~gEVv~G~V~~v~~~Gi~v~i 71 (143)
+.+...+.......+..+.|.+.+++..|+.+.+
T Consensus 8 ~~~~~~~~~~~~~~~~~~~~~~~diS~~G~~~~~ 41 (102)
T PF07238_consen 8 VPVNLPIRVILDPGGSSFQGTIVDISEGGCAFRS 41 (102)
T ss_dssp EEEEEEEE-EEEETTEEEEEEEEEETTSEEEEEE
T ss_pred EeccceEEEEEecCCcEEEEEEEEECccceEEEE
Confidence 4455555567888899999999999999999876
No 114
>PHA02858 EIF2a-like PKR inhibitor; Provisional
Probab=41.97 E-value=38 Score=23.46 Aligned_cols=64 Identities=13% Similarity=0.100 Sum_probs=39.9
Q ss_pred eecCCCEEEEEEEEEecccEEEEcc-c-cEEEEEcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEEcc
Q 032315 48 RPFKGEILGAGVTMVNKMGFLAEAG-A-VQIFCLIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQVDV 120 (143)
Q Consensus 48 rPf~gEVv~G~V~~v~~~Gi~v~iG-p-~~ifI~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~~~ 120 (143)
-|-.|+++. .|..+.+.|+++++= . ++..| ++.++..... . +.=+..+ +|-.+.++|+.+....
T Consensus 13 ~P~v~dvv~-~Vv~i~d~~~YV~LleY~iegmI--l~~selsr~r---i--rsi~kll-VGk~e~v~ViRVDk~K 78 (86)
T PHA02858 13 FPNINEVTK-GIVFVKDNIFYVKLIDYGLEALI--VNYVNVNADR---A--EKLKKKL-VGKTINVQVIRTDKLK 78 (86)
T ss_pred cCCCCeEEE-EEEEEeccEEEEEEecCccceEE--ecHHHHhHHH---H--Hhhhhhh-cCCeeEEEEEEECCCC
Confidence 499999999 889999999999872 2 34333 2122222111 1 1112344 8888888888776543
No 115
>cd04486 YhcR_OBF_like YhcR_OBF_like: A subfamily of OB-fold domains similar to the OB folds of Bacillus subtilis YhcR. YhcR is a sugar-nonspecific nuclease, which is active in the presence of Ca2+ and Mn2+. It cleaves RNA endonucleolytically, producing 3'-monophosphate nucleosides. YhcR appears to be the major Ca2+ activated nuclease of B. subtilis. YhcR may be localized in the cell wall.
Probab=40.15 E-value=1.1e+02 Score=20.21 Aligned_cols=58 Identities=12% Similarity=0.004 Sum_probs=30.4
Q ss_pred EEEEEEEEecccEEEEccccEEEEEcCCCceecCCC-CceEEcCCceEEEcCCCeEEEEEEEEEE
Q 032315 55 LGAGVTMVNKMGFLAEAGAVQIFCLIPDDMELQTGD-LPSYTTSDGSVKIQKDCELWLKIIGTQV 118 (143)
Q Consensus 55 v~G~V~~v~~~Gi~v~iGp~~ifI~lp~~~~fd~~~-~~~~~~~~~~~~i~~g~~VR~RV~~v~~ 118 (143)
++|+|+.....+ |..-.||+-+ +...++.. .-.+.+......+++||.||+.=.-.+|
T Consensus 2 v~GvVTa~~~~~-----~~~GffiQd~-~~d~~~~ts~gifV~~~~~~~~~~Gd~V~vtG~v~ey 60 (78)
T cd04486 2 VEGVVTAVFSGG-----GLGGFYIQDE-DGDGDPATSEGIFVYTGSGADVAVGDLVRVTGTVTEY 60 (78)
T ss_pred eEEEEEEEcCCC-----CcCEEEEEcC-CCCCCCcccceEEEecCCCCCCCCCCEEEEEEEEEee
Confidence 688898888743 2233444443 11122221 1234433224567899999887444444
No 116
>KOG4078 consensus Putative mitochondrial ribosomal protein mRpS35 [Translation, ribosomal structure and biogenesis]
Probab=38.37 E-value=58 Score=24.88 Aligned_cols=62 Identities=15% Similarity=0.273 Sum_probs=42.8
Q ss_pred EEEEeecCCCEEEEEEEEEecccEEEEccc-cEEEEEcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEEcc
Q 032315 44 CIVFRPFKGEILGAGVTMVNKMGFLAEAGA-VQIFCLIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQVDV 120 (143)
Q Consensus 44 ~lvFrPf~gEVv~G~V~~v~~~Gi~v~iGp-~~ifI~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~~~ 120 (143)
++=.-|++|-+|.|.|-.+.++-+++..|- +..-+.-|. . +...|+.|..||.|+++....+
T Consensus 75 l~qlg~a~gklV~GkIfhiV~~DlYIDFG~KFhcVC~rP~-----------~----n~e~Y~~GaRVrlRl~DlELs~ 137 (173)
T KOG4078|consen 75 LMQLGDAKGKLVIGKIFHIVEEDLYIDFGGKFHCVCKRPA-----------L----NGEAYQKGARVRLRLIDLELSE 137 (173)
T ss_pred cccccCcCCcEEEeeeeeeeccceEEecCCeEEEEEcCcC-----------c----CHHHhhcCceEEEEEcChhHhh
Confidence 445568899999999999998888887664 333223321 1 1234688999999999876643
No 117
>KOG1070 consensus rRNA processing protein Rrp5 [RNA processing and modification]
Probab=37.68 E-value=1.3e+02 Score=30.97 Aligned_cols=71 Identities=11% Similarity=0.108 Sum_probs=46.9
Q ss_pred cCCCEEEEEEEEEecccEEEEccccEEEEEcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEEccCCeEEE
Q 032315 50 FKGEILGAGVTMVNKMGFLAEAGAVQIFCLIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQVDVTEIEKA 126 (143)
Q Consensus 50 f~gEVv~G~V~~v~~~Gi~v~iGp~~ifI~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~~~~~~~ai 126 (143)
-.|+.|+|+|.++++.|+-+.+-|-+|-=.+|...--|...+ +..-.+.+..|.++ ||+.+.-+.+++.+.
T Consensus 508 ~iG~~V~~~I~~vt~~Gv~v~v~~~ni~g~lp~~hlsd~~~~----~p~~~f~v~~~~k~--RVl~~~~~~~~v~l~ 578 (1710)
T KOG1070|consen 508 EIGQLVPGVIRKVTPQGVEVLVTFGNIKGVLPKEHLSDHPLQ----PPLRDFKVGSGVKL--RVLSVNRDRNRVALT 578 (1710)
T ss_pred cccceeeeEEEEecCCcEEEEEecCceeeecChHhhhhcccc----cccceeeeccccEE--EEEEEEccCCeeEEE
Confidence 579999999999999999999877552115554322233322 22223555555555 999998888776554
No 118
>KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only]
Probab=33.17 E-value=69 Score=29.81 Aligned_cols=63 Identities=16% Similarity=0.153 Sum_probs=42.0
Q ss_pred CCEEEEEEEEEecccEEEEccccE-EEEEcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEEccCC
Q 032315 52 GEILGAGVTMVNKMGFLAEAGAVQ-IFCLIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQVDVTE 122 (143)
Q Consensus 52 gEVv~G~V~~v~~~Gi~v~iGp~~-ifI~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~~~~~ 122 (143)
|-|..|+|+++.++|+||.+-|.. .++.+ ++-|. .|...-+.. +++|++|-+|-.+.....+-
T Consensus 669 g~vy~~tIt~~rd~G~~V~l~p~~~~Llh~---sqL~~----e~iakpsd~-levGq~I~vk~ie~d~~g~~ 732 (760)
T KOG1067|consen 669 GGVYTATITEIRDTGVMVELYPMQQGLLHN---SQLDQ----EKIAKPSDL-LEVGQEIQVKYIERDPRGGI 732 (760)
T ss_pred eeEEEEEEeeecccceEEEecCCchhhccc---hhccc----ccccChHHH-HhhcceeEEEEEeecCccce
Confidence 556689999999999999998844 43311 11121 234433335 89999999998887654443
No 119
>PRK10811 rne ribonuclease E; Reviewed
Probab=32.40 E-value=2.1e+02 Score=28.27 Aligned_cols=73 Identities=11% Similarity=0.041 Sum_probs=46.6
Q ss_pred ecCCCEEEEEEEEEec--ccEEEEccc-cEEEEEcCCCc--eecCCCCceEEcCCceEEEcCCCeEEEEEEEEEEccCC
Q 032315 49 PFKGEILGAGVTMVNK--MGFLAEAGA-VQIFCLIPDDM--ELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQVDVTE 122 (143)
Q Consensus 49 Pf~gEVv~G~V~~v~~--~Gi~v~iGp-~~ifI~lp~~~--~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~~~~~ 122 (143)
+..|.|..|+|.++-+ .++||.+|. -.+|+.|.+.. .|...... -....-+..++.|+.|-+.|...-.....
T Consensus 36 ~~vGnIYkGkVenIvPGInAAFVDIG~gknGFL~L~Di~~~~f~~~~~~-~~~~~i~~~Lk~GqeILVQV~KEa~gtKG 113 (1068)
T PRK10811 36 QKKANIYKGKITRIEPSLEAAFVDYGAERHGFLPLKEIAREYFPANYSA-HGRPNIKDVLREGQEVIVQIDKEERGNKG 113 (1068)
T ss_pred cCccceEEEEEecccCCcceeEEEecCCcceEEEhhhcccccccccccc-ccccccccccCCCCEEEEEEeecccCCCC
Confidence 4579999999999985 479999998 46998554321 11111000 00001134588999999999986665543
No 120
>KOG3013 consensus Exosomal 3'-5' exoribonuclease complex, subunit Rrp4 [RNA processing and modification]
Probab=30.49 E-value=89 Score=26.18 Aligned_cols=38 Identities=13% Similarity=0.250 Sum_probs=31.7
Q ss_pred EEeecCCCEEEEEEEEEecccEEEEccc-cEEEE-----EcCCC
Q 032315 46 VFRPFKGEILGAGVTMVNKMGFLAEAGA-VQIFC-----LIPDD 83 (143)
Q Consensus 46 vFrPf~gEVv~G~V~~v~~~Gi~v~iGp-~~ifI-----~lp~~ 83 (143)
=|.|..|.++.|.|.++.+.=..+.++. .|..+ +||..
T Consensus 80 rY~pEvGDvVVgRV~eVq~KRWkvd~nsk~d~vL~LsSvNLPGg 123 (301)
T KOG3013|consen 80 RYAPEVGDVVVGRVIEVQQKRWKVDLNSKQDAVLMLSSVNLPGG 123 (301)
T ss_pred hcCCccCCEEEEEeeeeecceeEEecccccceEEEeecccCCch
Confidence 4678899999999999999999999998 66544 77743
No 121
>KOG2055 consensus WD40 repeat protein [General function prediction only]
Probab=29.94 E-value=1.4e+02 Score=26.95 Aligned_cols=100 Identities=15% Similarity=0.078 Sum_probs=68.1
Q ss_pred cceeEE---cCCccEE-EEEEEEEEEEeecCCCEEEEEEEEEecccEEEEccccEEEEEcCCCceecCCCCceEEcCCce
Q 032315 25 GKGLIR---NGTVLVT-FLVRCQCIVFRPFKGEILGAGVTMVNKMGFLAEAGAVQIFCLIPDDMELQTGDLPSYTTSDGS 100 (143)
Q Consensus 25 ~eG~I~---~gdG~~~-~~V~F~~lvFrPf~gEVv~G~V~~v~~~Gi~v~iGp~~ifI~lp~~~~fd~~~~~~~~~~~~~ 100 (143)
++|+.+ .|+|.+| ++++=+-++.|-...--+.|+=...+.+|-++-.|-..++|++ ||-++ ++.+ ...
T Consensus 354 Sdsk~l~~~~~~GeV~v~nl~~~~~~~rf~D~G~v~gts~~~S~ng~ylA~GS~~GiVNI-----Yd~~s--~~~s-~~P 425 (514)
T KOG2055|consen 354 SDSKELLASGGTGEVYVWNLRQNSCLHRFVDDGSVHGTSLCISLNGSYLATGSDSGIVNI-----YDGNS--CFAS-TNP 425 (514)
T ss_pred cCCcEEEEEcCCceEEEEecCCcceEEEEeecCccceeeeeecCCCceEEeccCcceEEE-----eccch--hhcc-CCC
Confidence 455443 4678777 5666666666666666778888888889989888988888866 33222 1111 122
Q ss_pred EEEcCCCeEEEEEEEEEEccCC-eEEEEEcccc
Q 032315 101 VKIQKDCELWLKIIGTQVDVTE-IEKARREVGK 132 (143)
Q Consensus 101 ~~i~~g~~VR~RV~~v~~~~~~-~~ai~~~~~~ 132 (143)
..++.=+.++..|..+.|++.. ++||++-.-|
T Consensus 426 kPik~~dNLtt~Itsl~Fn~d~qiLAiaS~~~k 458 (514)
T KOG2055|consen 426 KPIKTVDNLTTAITSLQFNHDAQILAIASRVKK 458 (514)
T ss_pred CchhhhhhhheeeeeeeeCcchhhhhhhhhccc
Confidence 4455556789999999998855 8999876554
No 122
>PF00116 COX2: Cytochrome C oxidase subunit II, periplasmic domain This family corresponds to chains b and o.; InterPro: IPR002429 Cytochrome c oxidase (1.9.3.1 from EC) [, ] is an oligomeric enzymatic complex which is a component of the respiratory chain and is involved in the transfer of electrons from cytochrome c to oxygen. In eukaryotes this enzyme complex is located in the mitochondrial inner membrane; in aerobic prokaryotes it is found in the plasma membrane. The number of polypeptides in the complex ranges from 3-4 (prokaryotes), up to 13(mammals). Subunit 2 (CO II) transfers the electrons from cytochrome c to the catalytic subunit 1. It contains two adjacent transmembrane regions in its N terminus and the major part of the protein is exposed to the periplasmic or to the mitochondrial intermembrane space, respectively. CO II provides the substrate-binding site and contains a copper centre called Cu(A), probably the primary acceptor in cytochrome c oxidase. An exception is the corresponding subunit of the cbb3-type oxidase which lacks the copper A redox-centre. Several bacterial CO II have a C-terminal extension that contains a covalently bound haem c.; GO: 0004129 cytochrome-c oxidase activity, 0005507 copper ion binding, 0016020 membrane; PDB: 3OMN_D 3OMA_B 3OMI_D 3OM3_B 3EHB_B 1AR1_B 1QLE_B 3HB3_B 2IWK_B 2IWF_A ....
Probab=29.83 E-value=86 Score=22.38 Aligned_cols=18 Identities=6% Similarity=0.191 Sum_probs=15.9
Q ss_pred CceEEEcCCCeEEEEEEE
Q 032315 98 DGSVKIQKDCELWLKIIG 115 (143)
Q Consensus 98 ~~~~~i~~g~~VR~RV~~ 115 (143)
++.+.+..|+.||+++.+
T Consensus 45 ~~~l~lp~g~~v~~~ltS 62 (120)
T PF00116_consen 45 DNELVLPAGQPVRFHLTS 62 (120)
T ss_dssp SSEEEEETTSEEEEEEEE
T ss_pred cceecccccceEeEEEEc
Confidence 457899999999999988
No 123
>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=26.15 E-value=95 Score=19.00 Aligned_cols=23 Identities=26% Similarity=0.385 Sum_probs=16.7
Q ss_pred eecCCCEEEEEEEEEecccEEEE
Q 032315 48 RPFKGEILGAGVTMVNKMGFLAE 70 (143)
Q Consensus 48 rPf~gEVv~G~V~~v~~~Gi~v~ 70 (143)
.|..||.+...|++.+++-++..
T Consensus 37 ~~~iG~~v~v~I~~~~~~~l~G~ 59 (61)
T PF01938_consen 37 LPLIGEFVKVRITKAKKNYLFGE 59 (61)
T ss_dssp -T--TEEEEEEEEEE-SSEEEEE
T ss_pred CCCCCCEEEEEEEEeeCCcEEEE
Confidence 45669999999999999887764
No 124
>PF01629 DUF22: Domain of unknown function DUF22; InterPro: IPR002572 This region is found in 1 to 3 copies in archaeal proteins whose function is unknown. It only appears in multiple copies in proteins from Archaeoglobus fulgidus.
Probab=25.37 E-value=2e+02 Score=20.71 Aligned_cols=33 Identities=18% Similarity=0.112 Sum_probs=25.7
Q ss_pred CceEEcCCceEEEcCCCeEEEEEEEEEEccCCe
Q 032315 91 LPSYTTSDGSVKIQKDCELWLKIIGTQVDVTEI 123 (143)
Q Consensus 91 ~~~~~~~~~~~~i~~g~~VR~RV~~v~~~~~~~ 123 (143)
+|.-.-.+.+..++.|+..++||..+.+.++.+
T Consensus 37 ~wepiIAdEdvevk~Ge~~~IkIk~I~iP~~tI 69 (112)
T PF01629_consen 37 KWEPIIADEDVEVKKGEVKIIKIKKIEIPPNTI 69 (112)
T ss_pred eEEEEEEcCeeEEecCCEEEEEEEEEecCCCCE
Confidence 443333455689999999999999999998763
No 125
>PF05899 Cupin_3: Protein of unknown function (DUF861); InterPro: IPR008579 The function of the proteins in this entry are unknown. They contain the conserved barrel domain of the 'cupin' superfamily and members are specific to plants and bacteria.; PDB: 1RC6_A 3MYX_A 1O5U_A 2K9Z_A 1LKN_A 3ES4_A 1SFN_B 3BCW_A.
Probab=24.74 E-value=1.9e+02 Score=18.59 Aligned_cols=28 Identities=25% Similarity=0.310 Sum_probs=22.4
Q ss_pred CEEEEEEEEEecccEEEEccccEEEEEcC
Q 032315 53 EILGAGVTMVNKMGFLAEAGAVQIFCLIP 81 (143)
Q Consensus 53 EVv~G~V~~v~~~Gi~v~iGp~~ifI~lp 81 (143)
-||+|.|+=..+.|-...++|=|.|+ +|
T Consensus 30 ~vleG~v~it~~~G~~~~~~aGD~~~-~p 57 (74)
T PF05899_consen 30 YVLEGEVTITDEDGETVTFKAGDAFF-LP 57 (74)
T ss_dssp EEEEEEEEEEETTTEEEEEETTEEEE-E-
T ss_pred EEEEeEEEEEECCCCEEEEcCCcEEE-EC
Confidence 47899999999999999999978665 44
No 126
>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=24.08 E-value=2.3e+02 Score=24.52 Aligned_cols=58 Identities=26% Similarity=0.380 Sum_probs=41.2
Q ss_pred EEEEEeecceecceeEEcCCccEEEEEEEEEEEEeecCCCEEEEEEEEEecccEEEEccccEEEEEcCCC
Q 032315 14 FAVAITGAESIGKGLIRNGTVLVTFLVRCQCIVFRPFKGEILGAGVTMVNKMGFLAEAGAVQIFCLIPDD 83 (143)
Q Consensus 14 liI~i~dI~~i~eG~I~~gdG~~~~~V~F~~lvFrPf~gEVv~G~V~~v~~~Gi~v~iGp~~ifI~lp~~ 83 (143)
.||...++++-+||.+.-...+..|-|+=+..-- | -+...=|+++.||.-.|+.+|++
T Consensus 194 VCVDtcsll~~gEGmLVGs~s~glfLVhsEt~~~-p-----------Yva~RPFRVNAGaVHaYv~~pg~ 251 (354)
T PF01959_consen 194 VCVDTCSLLRPGEGMLVGSSSSGLFLVHSETHES-P-----------YVASRPFRVNAGAVHAYVLMPGG 251 (354)
T ss_pred EEEEccccCCCCCeEEEcccCceEEEEEeccccC-C-----------CCCCCCceEecCcceeEEEcCCC
Confidence 5788888899999999977777778777332100 0 01112288999999999988876
No 127
>COG2996 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only]
Probab=23.98 E-value=1.2e+02 Score=25.52 Aligned_cols=29 Identities=24% Similarity=0.253 Sum_probs=25.8
Q ss_pred cCCCEEEEEEEEEe-cccEEEEcc-ccEEEE
Q 032315 50 FKGEILGAGVTMVN-KMGFLAEAG-AVQIFC 78 (143)
Q Consensus 50 f~gEVv~G~V~~v~-~~Gi~v~iG-p~~ifI 78 (143)
.+||---++|++++ ..|+|+..| |-|++|
T Consensus 72 tvg~~g~~~Vv~v~~~lGaFlD~Gl~KDl~v 102 (287)
T COG2996 72 TVGEYGWLKVVEVNKDLGAFLDWGLPKDLLV 102 (287)
T ss_pred eecceeEEEEEEEcCCcceEEecCCCcceee
Confidence 46777889999999 999999999 788999
No 128
>PF12306 PixA: Inclusion body protein; InterPro: IPR021087 This entry represents bacterial proteins that are typically between 173 and 191 amino acids in length. PixA is thought to be specifically produced in Xenorhabdus nematophila. It is an inclusion body protein []. This signature also identifies AidA.
Probab=22.39 E-value=1.8e+02 Score=22.17 Aligned_cols=30 Identities=7% Similarity=-0.111 Sum_probs=22.8
Q ss_pred eEEEcCCCeEEEEEEEEEEccCCeEEEEEc
Q 032315 100 SVKIQKDCELWLKIIGTQVDVTEIEKARRE 129 (143)
Q Consensus 100 ~~~i~~g~~VR~RV~~v~~~~~~~~ai~~~ 129 (143)
.....+||.||+|..+++-+...-..+=.+
T Consensus 59 ~i~a~~GD~Irwr~tSls~n~~y~v~ly~~ 88 (172)
T PF12306_consen 59 SIKANVGDTIRWRATSLSGNSEYSVILYKF 88 (172)
T ss_pred EEeccCCCEEEEEEEeeccCCceeEEEEEe
Confidence 356789999999999999988774333333
No 129
>PF07076 DUF1344: Protein of unknown function (DUF1344); InterPro: IPR009780 This family consists of several short, hypothetical bacterial proteins of around 80 residues in length. Members of this family are found in Rhizobium, Agrobacterium and Brucella species. The function of this family is unknown.
Probab=21.34 E-value=2.1e+02 Score=18.56 Aligned_cols=33 Identities=3% Similarity=0.208 Sum_probs=21.8
Q ss_pred EEEEEEEEEecccEEEEccccEEEEEcCCCceec
Q 032315 54 ILGAGVTMVNKMGFLAEAGAVQIFCLIPDDMELQ 87 (143)
Q Consensus 54 Vv~G~V~~v~~~Gi~v~iGp~~ifI~lp~~~~fd 87 (143)
-++|+|+++++....+.+.=-+-| .+|+++.|+
T Consensus 4 ~veG~I~~id~~~~titLdDGksy-~lp~ef~~~ 36 (61)
T PF07076_consen 4 DVEGTIKSIDPETMTITLDDGKSY-KLPEEFDFD 36 (61)
T ss_pred cceEEEEEEcCCceEEEecCCCEE-ECCCccccc
Confidence 368999999999988876422222 355555544
No 130
>KOG2916 consensus Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis]
Probab=21.27 E-value=92 Score=26.15 Aligned_cols=31 Identities=19% Similarity=0.178 Sum_probs=25.7
Q ss_pred eecCCCEEEEEEEEEecccEEEEcc---ccEEEE
Q 032315 48 RPFKGEILGAGVTMVNKMGFLAEAG---AVQIFC 78 (143)
Q Consensus 48 rPf~gEVv~G~V~~v~~~Gi~v~iG---p~~ifI 78 (143)
.|-.+|++-+-|.++-++|+++++= -+++.|
T Consensus 13 yPev~e~VmvnV~sIaemGayv~LlEYnniEGmi 46 (304)
T KOG2916|consen 13 YPEVEEIVMVNVRSIAEMGAYVKLLEYNNIEGMI 46 (304)
T ss_pred CCCcccEEEEEeeEehhccceEeeeecCCcccch
Confidence 3889999999999999999999873 244555
No 131
>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=21.16 E-value=1.4e+02 Score=19.73 Aligned_cols=20 Identities=10% Similarity=0.101 Sum_probs=15.2
Q ss_pred eEEEcCCCeEEEEEEEEEEc
Q 032315 100 SVKIQKDCELWLKIIGTQVD 119 (143)
Q Consensus 100 ~~~i~~g~~VR~RV~~v~~~ 119 (143)
+-.+++|++|++|+....-+
T Consensus 8 r~iYrPGetV~~~~~~~~~~ 27 (99)
T PF01835_consen 8 RPIYRPGETVHFRAIVRDLD 27 (99)
T ss_dssp SSEE-TTSEEEEEEEEEEEC
T ss_pred ccCcCCCCEEEEEEEEeccc
Confidence 35679999999999966665
No 132
>PF07177 Neuralized: Neuralized; InterPro: IPR006573 NEUZ is a domain of unknown function found in neuralized proteins, i.e. proteins involved in the specification of the neuroblast during cellular differentiation. ; PDB: 2YUE_A 2E63_A.
Probab=20.95 E-value=1.2e+02 Score=19.65 Aligned_cols=29 Identities=7% Similarity=-0.060 Sum_probs=17.7
Q ss_pred eEEEcCCCeEEEEEEEEEEccCCeEEEEE
Q 032315 100 SVKIQKDCELWLKIIGTQVDVTEIEKARR 128 (143)
Q Consensus 100 ~~~i~~g~~VR~RV~~v~~~~~~~~ai~~ 128 (143)
...++.|+.+.+||..+.-.-+.-..+|-
T Consensus 36 ~rPl~~~E~~~v~I~~~~~~wsG~L~~Gv 64 (69)
T PF07177_consen 36 SRPLRIGEKFEVRIDEVEPSWSGSLRIGV 64 (69)
T ss_dssp SS-B-TT-EEEEEEEEE-SSSSS--EEEE
T ss_pred cCCccCCCEEEEEEEecCCCceeEEEEee
Confidence 37899999999999998765555555554
No 133
>PRK10943 cold shock-like protein CspC; Provisional
Probab=20.94 E-value=2.4e+02 Score=18.06 Aligned_cols=45 Identities=20% Similarity=0.105 Sum_probs=34.1
Q ss_pred ecceeEEcCCccEEEEEEEEEEEE----eecCCCEEEEEEEEEecccEEE
Q 032315 24 IGKGLIRNGTVLVTFLVRCQCIVF----RPFKGEILGAGVTMVNKMGFLA 69 (143)
Q Consensus 24 i~eG~I~~gdG~~~~~V~F~~lvF----rPf~gEVv~G~V~~v~~~Gi~v 69 (143)
-+-|.|.+.+|.--+-++++++-- +|..|+.|.=.+..-.+ |..+
T Consensus 15 kGfGFI~~~~g~~dvFvH~s~l~~~g~~~l~~G~~V~f~~~~~~~-g~~A 63 (69)
T PRK10943 15 KGFGFITPADGSKDVFVHFSAIQGNGFKTLAEGQNVEFEIQDGQK-GPAA 63 (69)
T ss_pred CCcEEEecCCCCeeEEEEhhHccccCCCCCCCCCEEEEEEEECCC-Ccee
Confidence 467899998888888888888874 47889999887776554 6543
No 134
>PF15572 Imm26: Immunity protein 26
Probab=20.85 E-value=2.4e+02 Score=19.91 Aligned_cols=61 Identities=18% Similarity=0.265 Sum_probs=42.6
Q ss_pred cceecceeEEcCCccEEEEEEEEEEEEeecCCCEEEEEEEEEec----ccEEEEccccEEEE--EcCCCceecCC
Q 032315 21 AESIGKGLIRNGTVLVTFLVRCQCIVFRPFKGEILGAGVTMVNK----MGFLAEAGAVQIFC--LIPDDMELQTG 89 (143)
Q Consensus 21 I~~i~eG~I~~gdG~~~~~V~F~~lvFrPf~gEVv~G~V~~v~~----~Gi~v~iGp~~ifI--~lp~~~~fd~~ 89 (143)
+++..+..|..|+ .||+-.=.|+. +++|=.|.+... .|+-+..|..-+.+ .+|.++..+..
T Consensus 3 L~dy~~~~l~rG~-------i~R~~~~ypye-~~VDFmV~e~~~~~~~~~L~v~sG~kAG~i~~~fP~Ea~~~~~ 69 (96)
T PF15572_consen 3 LIDYKEKYLWRGT-------IFRCPGVYPYE-EVVDFMVFEDPDFGRGFGLVVISGYKAGLILVKFPKEAESKEG 69 (96)
T ss_pred ceecCCccEecce-------EEEecccCCCc-ccEEEEEEeccCCCCceeEEEEeeEecceEEEeCCHHHhhccc
Confidence 3444555555543 46666668998 999988888776 56788889866555 88988777765
Done!