Query 047168
Match_columns 258
No_of_seqs 315 out of 2554
Neff 7.4
Searched_HMMs 46136
Date Fri Mar 29 08:22:52 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/047168.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/047168hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PTZ00368 universal minicircle 100.0 5.3E-29 1.1E-33 203.5 12.2 145 90-256 2-148 (148)
2 COG1278 CspC Cold shock protei 99.9 1.5E-25 3.2E-30 156.7 6.6 66 6-72 1-66 (67)
3 PRK10943 cold shock-like prote 99.9 5.9E-24 1.3E-28 151.7 7.5 68 5-73 2-69 (69)
4 PRK15464 cold shock-like prote 99.9 7.5E-24 1.6E-28 151.2 7.6 66 6-72 4-69 (70)
5 PTZ00368 universal minicircle 99.9 2.1E-23 4.5E-28 170.4 9.9 120 129-256 1-122 (148)
6 PRK15463 cold shock-like prote 99.9 1.7E-23 3.6E-28 149.6 7.5 67 5-72 3-69 (70)
7 PRK09507 cspE cold shock prote 99.9 2E-23 4.4E-28 149.0 7.5 67 5-72 2-68 (69)
8 PRK09890 cold shock protein Cs 99.9 2.4E-23 5.1E-28 149.0 7.8 68 5-73 3-70 (70)
9 PRK10354 RNA chaperone/anti-te 99.9 2.5E-23 5.3E-28 149.0 7.9 67 6-73 4-70 (70)
10 PRK14998 cold shock-like prote 99.9 4.4E-23 9.5E-28 148.6 7.8 69 7-76 2-70 (73)
11 PRK09937 stationary phase/star 99.9 4.5E-23 9.8E-28 148.8 7.8 68 7-75 2-69 (74)
12 TIGR02381 cspD cold shock doma 99.9 5.7E-23 1.2E-27 146.3 7.2 66 7-73 2-67 (68)
13 PF00313 CSD: 'Cold-shock' DNA 99.8 9.1E-21 2E-25 134.1 7.9 66 7-73 1-66 (66)
14 cd04458 CSP_CDS Cold-Shock Pro 99.8 3.6E-20 7.7E-25 130.7 7.5 65 7-72 1-65 (65)
15 COG5082 AIR1 Arginine methyltr 99.8 1.3E-19 2.8E-24 150.8 9.5 126 83-250 55-189 (190)
16 COG5082 AIR1 Arginine methyltr 99.8 4.3E-20 9.3E-25 153.7 6.0 104 128-257 60-174 (190)
17 KOG3070 Predicted RNA-binding 99.7 1.2E-17 2.6E-22 145.4 10.6 85 3-88 53-141 (235)
18 KOG4400 E3 ubiquitin ligase in 99.6 9.2E-15 2E-19 129.9 10.2 136 86-256 70-215 (261)
19 KOG4400 E3 ubiquitin ligase in 99.5 3E-14 6.5E-19 126.7 8.9 111 128-257 72-184 (261)
20 smart00357 CSP Cold shock prot 98.9 2.7E-09 5.8E-14 73.7 6.6 62 8-72 1-63 (64)
21 PF00098 zf-CCHC: Zinc knuckle 98.2 7.5E-07 1.6E-11 46.7 1.6 17 239-255 2-18 (18)
22 PF00098 zf-CCHC: Zinc knuckle 98.0 3E-06 6.6E-11 44.4 1.8 16 215-230 2-17 (18)
23 PF08206 OB_RNB: Ribonuclease 97.7 7.8E-05 1.7E-09 51.1 4.9 48 17-69 7-55 (58)
24 PF14444 S1-like: S1-like 97.2 0.00099 2.1E-08 45.4 5.3 47 6-62 3-49 (58)
25 PF13696 zf-CCHC_2: Zinc knuck 96.7 0.0014 2.9E-08 39.3 2.0 17 215-231 10-26 (32)
26 PF13696 zf-CCHC_2: Zinc knuck 96.7 0.0013 2.8E-08 39.4 1.9 21 186-206 7-27 (32)
27 PF07497 Rho_RNA_bind: Rho ter 96.4 0.0066 1.4E-07 44.1 4.6 63 8-75 4-73 (78)
28 cd04459 Rho_CSD Rho_CSD: Rho p 96.1 0.011 2.4E-07 41.8 4.6 48 9-61 3-55 (68)
29 PF13509 S1_2: S1 domain; PDB: 95.5 0.04 8.7E-07 38.0 5.2 55 7-68 5-59 (61)
30 PF13917 zf-CCHC_3: Zinc knuck 95.2 0.011 2.5E-07 37.7 1.6 16 239-254 6-21 (42)
31 KOG0119 Splicing factor 1/bran 94.7 0.025 5.5E-07 53.9 3.0 42 188-231 262-303 (554)
32 smart00343 ZnF_C2HC zinc finge 94.4 0.02 4.4E-07 32.4 1.1 15 240-254 2-16 (26)
33 KOG0109 RNA-binding protein LA 93.9 0.14 3E-06 46.0 5.9 22 6-27 24-45 (346)
34 KOG0119 Splicing factor 1/bran 93.5 0.075 1.6E-06 50.8 3.6 44 128-176 261-304 (554)
35 PRK11642 exoribonuclease R; Pr 93.4 0.11 2.5E-06 53.3 5.1 62 6-74 84-146 (813)
36 TIGR00358 3_prime_RNase VacB a 93.0 0.2 4.3E-06 50.4 6.0 63 5-74 15-79 (654)
37 smart00343 ZnF_C2HC zinc finge 92.8 0.052 1.1E-06 30.7 1.0 17 215-231 1-17 (26)
38 PF13917 zf-CCHC_3: Zinc knuck 92.8 0.059 1.3E-06 34.4 1.2 18 214-231 5-22 (42)
39 PF00575 S1: S1 RNA binding do 92.8 0.4 8.6E-06 33.5 5.8 56 4-62 5-64 (74)
40 cd04461 S1_Rrp5_repeat_hs8_sc7 91.6 0.67 1.4E-05 33.4 5.9 56 4-62 15-74 (83)
41 cd00164 S1_like S1_like: Ribos 91.3 0.84 1.8E-05 30.1 5.9 51 7-61 1-56 (65)
42 cd05698 S1_Rrp5_repeat_hs6_sc5 90.8 0.66 1.4E-05 32.0 5.0 55 5-62 2-60 (70)
43 cd05704 S1_Rrp5_repeat_hs13 S1 90.7 1.4 3E-05 31.0 6.7 61 3-65 3-67 (72)
44 cd04453 S1_RNase_E S1_RNase_E: 90.6 0.89 1.9E-05 33.6 5.8 57 4-61 8-71 (88)
45 PRK07252 hypothetical protein; 90.0 1.8 3.9E-05 34.0 7.4 57 2-61 2-62 (120)
46 PF14392 zf-CCHC_4: Zinc knuck 89.6 0.14 3E-06 33.7 0.6 20 185-204 29-48 (49)
47 cd05692 S1_RPS1_repeat_hs4 S1_ 89.4 1.6 3.6E-05 29.4 6.1 54 5-61 2-59 (69)
48 KOG0109 RNA-binding protein LA 89.3 0.2 4.3E-06 45.1 1.6 21 214-234 161-181 (346)
49 cd05706 S1_Rrp5_repeat_sc10 S1 89.2 1.9 4E-05 30.0 6.4 57 3-62 3-63 (73)
50 PRK05054 exoribonuclease II; P 89.1 0.65 1.4E-05 46.7 5.3 60 5-73 20-79 (644)
51 TIGR02063 RNase_R ribonuclease 89.1 0.69 1.5E-05 47.0 5.6 62 6-74 68-132 (709)
52 PRK12608 transcription termina 89.0 0.54 1.2E-05 44.2 4.3 51 4-59 16-71 (380)
53 cd05696 S1_Rrp5_repeat_hs4 S1_ 88.9 1.3 2.8E-05 31.1 5.3 52 7-60 4-60 (71)
54 cd05686 S1_pNO40 S1_pNO40: pNO 88.7 2 4.4E-05 30.2 6.3 56 4-62 4-64 (73)
55 TIGR02062 RNase_B exoribonucle 88.5 0.83 1.8E-05 45.9 5.6 61 4-73 16-76 (639)
56 smart00316 S1 Ribosomal protei 88.5 1.2 2.5E-05 30.1 4.8 56 4-62 3-62 (72)
57 cd05697 S1_Rrp5_repeat_hs5 S1_ 88.2 1.7 3.7E-05 29.9 5.6 55 5-62 2-60 (69)
58 PRK08582 hypothetical protein; 87.9 2.7 5.9E-05 33.8 7.3 65 5-73 7-76 (139)
59 cd05689 S1_RPS1_repeat_ec4 S1_ 87.8 2.9 6.3E-05 28.9 6.6 56 4-62 4-64 (72)
60 PRK09376 rho transcription ter 87.5 0.84 1.8E-05 43.2 4.5 66 6-76 50-122 (416)
61 PF15288 zf-CCHC_6: Zinc knuck 87.4 0.32 6.9E-06 30.7 1.2 20 214-233 2-23 (40)
62 cd05705 S1_Rrp5_repeat_hs14 S1 86.8 2.4 5.3E-05 30.0 5.7 56 3-62 3-66 (74)
63 COG5222 Uncharacterized conser 86.7 0.38 8.2E-06 43.4 1.7 23 184-206 173-195 (427)
64 PRK12678 transcription termina 86.7 0.92 2E-05 45.0 4.5 52 6-63 295-349 (672)
65 KOG0314 Predicted E3 ubiquitin 86.5 1.6 3.5E-05 41.8 5.9 66 128-206 112-177 (448)
66 cd04472 S1_PNPase S1_PNPase: P 86.1 2.8 6E-05 28.3 5.6 53 6-61 3-59 (68)
67 PF14392 zf-CCHC_4: Zinc knuck 85.9 0.31 6.7E-06 32.0 0.6 19 156-174 30-48 (49)
68 COG1158 Rho Transcription term 85.4 0.8 1.7E-05 42.4 3.1 68 9-81 56-130 (422)
69 cd05691 S1_RPS1_repeat_ec6 S1_ 84.9 3.2 6.8E-05 28.6 5.5 54 6-62 3-60 (73)
70 cd05707 S1_Rrp5_repeat_sc11 S1 84.9 2.9 6.4E-05 28.6 5.3 54 5-61 2-59 (68)
71 cd04465 S1_RPS1_repeat_ec2_hs2 84.7 1.8 4E-05 29.7 4.1 53 5-61 2-56 (67)
72 cd05694 S1_Rrp5_repeat_hs2_sc2 84.6 3.8 8.2E-05 29.1 5.8 55 3-62 4-59 (74)
73 cd04473 S1_RecJ_like S1_RecJ_l 84.3 4.4 9.5E-05 28.8 6.1 50 4-60 17-66 (77)
74 cd05690 S1_RPS1_repeat_ec5 S1_ 83.1 4.3 9.4E-05 27.6 5.5 53 6-61 3-60 (69)
75 COG5222 Uncharacterized conser 82.5 0.86 1.9E-05 41.2 2.1 23 126-148 174-196 (427)
76 PF15288 zf-CCHC_6: Zinc knuck 82.0 0.84 1.8E-05 28.8 1.3 19 238-256 2-22 (40)
77 KOG0314 Predicted E3 ubiquitin 80.8 3 6.4E-05 40.0 5.1 69 155-233 110-178 (448)
78 PF14787 zf-CCHC_5: GAG-polypr 80.7 0.86 1.9E-05 28.0 1.0 19 188-206 3-21 (36)
79 cd05684 S1_DHX8_helicase S1_DH 80.6 5.9 0.00013 28.0 5.6 55 6-63 3-65 (79)
80 cd05703 S1_Rrp5_repeat_hs12_sc 79.2 5.2 0.00011 28.2 4.9 53 6-61 3-61 (73)
81 cd04452 S1_IF2_alpha S1_IF2_al 79.0 8.6 0.00019 26.6 6.0 55 4-61 4-64 (76)
82 cd05702 S1_Rrp5_repeat_hs11_sc 78.6 7.2 0.00016 26.9 5.4 55 5-62 2-62 (70)
83 cd05687 S1_RPS1_repeat_ec1_hs1 77.9 7.3 0.00016 26.7 5.3 53 5-60 2-58 (70)
84 PF14787 zf-CCHC_5: GAG-polypr 77.9 1.3 2.7E-05 27.3 1.1 18 239-256 4-21 (36)
85 TIGR00767 rho transcription te 77.9 3 6.5E-05 39.6 4.2 50 7-61 51-105 (415)
86 cd04471 S1_RNase_R S1_RNase_R: 76.4 10 0.00022 26.7 5.8 54 5-61 3-72 (83)
87 cd04460 S1_RpoE S1_RpoE: RpoE, 76.2 7.1 0.00015 29.1 5.1 52 6-61 2-68 (99)
88 COG2996 Predicted RNA-bindinin 75.8 8.9 0.00019 34.4 6.3 62 5-72 7-69 (287)
89 PF11604 CusF_Ec: Copper bindi 75.7 15 0.00032 25.8 6.4 61 9-71 1-67 (70)
90 cd05685 S1_Tex S1_Tex: The C-t 75.7 9.7 0.00021 25.4 5.3 53 6-61 3-59 (68)
91 PF05606 DUF777: Borrelia burg 73.7 4.4 9.5E-05 33.6 3.5 45 8-54 37-81 (181)
92 PRK08059 general stress protei 73.4 11 0.00024 29.4 5.8 55 4-61 8-66 (123)
93 PRK09838 periplasmic copper-bi 73.4 16 0.00034 28.5 6.5 64 6-72 44-113 (115)
94 PRK05807 hypothetical protein; 73.3 11 0.00024 30.1 5.8 57 4-64 6-67 (136)
95 cd05695 S1_Rrp5_repeat_hs3 S1_ 72.7 12 0.00026 25.7 5.2 52 6-60 3-56 (66)
96 cd04455 S1_NusA S1_NusA: N-uti 72.2 13 0.00028 25.5 5.3 52 4-61 4-55 (67)
97 cd05688 S1_RPS1_repeat_ec3 S1_ 70.3 14 0.0003 24.7 5.1 53 5-61 3-59 (68)
98 cd05789 S1_Rrp4 S1_Rrp4: Rrp4 68.2 19 0.00041 25.7 5.7 55 4-61 7-69 (86)
99 cd04482 RPA2_OBF_like RPA2_OBF 58.1 62 0.0013 23.8 6.9 84 6-95 2-91 (91)
100 cd05708 S1_Rrp5_repeat_sc12 S1 56.6 38 0.00082 23.2 5.4 54 5-61 4-62 (77)
101 cd04489 ExoVII_LU_OBF ExoVII_L 56.4 29 0.00063 24.0 4.8 52 7-60 4-59 (78)
102 TIGR00757 RNaseEG ribonuclease 55.8 29 0.00064 33.1 6.0 69 5-74 27-114 (414)
103 PTZ00248 eukaryotic translatio 55.3 38 0.00082 31.2 6.4 70 4-77 18-95 (319)
104 TIGR02696 pppGpp_PNP guanosine 55.0 23 0.0005 36.1 5.4 57 5-64 649-714 (719)
105 COG1095 RPB7 DNA-directed RNA 54.2 21 0.00045 30.2 4.1 52 5-60 83-149 (183)
106 TIGR00448 rpoE DNA-directed RN 53.2 37 0.0008 28.2 5.6 52 5-60 83-149 (179)
107 PF01796 DUF35: DUF35 OB-fold 50.5 37 0.0008 23.4 4.4 37 20-57 31-67 (68)
108 PRK13806 rpsA 30S ribosomal pr 49.8 41 0.00088 32.7 6.0 54 4-60 203-260 (491)
109 COG1098 VacB Predicted RNA bin 49.7 35 0.00075 27.1 4.4 67 4-75 6-78 (129)
110 TIGR01451 B_ant_repeat conserv 49.2 17 0.00036 24.1 2.3 31 45-75 6-36 (53)
111 PRK13806 rpsA 30S ribosomal pr 48.9 37 0.00081 33.0 5.6 53 4-60 380-437 (491)
112 PLN00207 polyribonucleotide nu 48.2 40 0.00086 35.4 5.9 57 5-64 755-817 (891)
113 PRK07899 rpsA 30S ribosomal pr 47.1 39 0.00084 33.0 5.4 53 5-60 295-351 (486)
114 cd05701 S1_Rrp5_repeat_hs10 S1 46.8 31 0.00067 24.1 3.3 52 7-60 4-59 (69)
115 PRK11824 polynucleotide phosph 46.4 43 0.00093 34.1 5.8 54 5-61 623-680 (693)
116 cd04486 YhcR_OBF_like YhcR_OBF 45.1 78 0.0017 22.6 5.5 50 7-61 2-59 (78)
117 PRK08563 DNA-directed RNA poly 44.9 51 0.0011 27.4 5.2 53 5-61 83-150 (187)
118 PF03100 CcmE: CcmE; InterPro 43.9 62 0.0013 25.6 5.3 63 6-72 54-121 (131)
119 PF00358 PTS_EIIA_1: phosphoen 43.5 68 0.0015 25.6 5.4 48 6-54 45-97 (132)
120 TIGR00638 Mop molybdenum-pteri 43.5 66 0.0014 21.6 4.8 54 5-59 7-61 (69)
121 TIGR03591 polynuc_phos polyrib 43.4 43 0.00094 34.1 5.3 54 5-61 620-677 (684)
122 cd04454 S1_Rrp4_like S1_Rrp4_l 42.3 1E+02 0.0022 21.6 5.9 55 5-62 8-66 (82)
123 COG4776 Rnb Exoribonuclease II 41.1 36 0.00077 33.1 3.9 50 3-60 18-67 (645)
124 PHA02945 interferon resistance 40.4 1.2E+02 0.0026 22.5 5.9 53 5-63 13-73 (88)
125 cd05693 S1_Rrp5_repeat_hs1_sc1 39.9 66 0.0014 24.1 4.6 56 4-62 4-82 (100)
126 PRK03987 translation initiatio 39.2 56 0.0012 29.1 4.8 55 5-62 10-70 (262)
127 PF03459 TOBE: TOBE domain; I 39.0 32 0.0007 23.0 2.6 54 5-59 5-59 (64)
128 PRK07899 rpsA 30S ribosomal pr 38.8 65 0.0014 31.5 5.5 53 4-60 209-265 (486)
129 PRK06299 rpsA 30S ribosomal pr 38.7 70 0.0015 31.5 5.8 52 5-59 288-344 (565)
130 PF01336 tRNA_anti-codon: OB-f 38.6 23 0.00049 24.1 1.8 53 7-59 3-57 (75)
131 PF05753 TRAP_beta: Translocon 38.2 37 0.0008 28.6 3.3 47 24-74 15-61 (181)
132 PRK12269 bifunctional cytidyla 38.2 62 0.0014 33.9 5.5 53 5-61 495-551 (863)
133 PF11948 DUF3465: Protein of u 38.1 88 0.0019 25.0 5.2 56 7-63 41-104 (131)
134 PRK09202 nusA transcription el 37.9 52 0.0011 32.0 4.7 52 4-61 135-186 (470)
135 COG1185 Pnp Polyribonucleotide 37.9 67 0.0015 32.6 5.4 60 5-67 621-685 (692)
136 KOG0107 Alternative splicing f 37.8 24 0.00053 29.7 2.1 19 128-146 100-118 (195)
137 PRK06676 rpsA 30S ribosomal pr 37.6 86 0.0019 29.2 6.0 56 4-61 18-77 (390)
138 COG0539 RpsA Ribosomal protein 37.2 57 0.0012 32.2 4.8 54 4-60 278-335 (541)
139 KOG2813 Predicted molecular ch 37.0 55 0.0012 30.2 4.3 34 213-248 234-267 (406)
140 PRK10811 rne ribonuclease E; R 36.8 77 0.0017 33.7 5.8 69 5-74 40-124 (1068)
141 cd04451 S1_IF1 S1_IF1: Transla 36.8 1.3E+02 0.0029 20.2 5.8 51 7-59 3-53 (64)
142 TIGR00830 PTBA PTS system, glu 36.8 91 0.002 24.5 5.1 47 6-54 41-93 (121)
143 PF06523 DUF1106: Protein of u 36.8 99 0.0021 22.1 4.7 55 5-59 31-89 (91)
144 CHL00010 infA translation init 36.1 1.5E+02 0.0033 21.2 5.8 54 5-60 7-60 (78)
145 PF01345 DUF11: Domain of unkn 35.5 30 0.00064 24.2 2.0 31 45-75 35-65 (76)
146 COG0557 VacB Exoribonuclease R 35.3 67 0.0015 32.8 5.2 60 8-74 71-134 (706)
147 PRK12269 bifunctional cytidyla 35.1 67 0.0015 33.7 5.2 53 5-60 580-637 (863)
148 PRK13150 cytochrome c-type bio 34.7 1.4E+02 0.003 24.7 6.0 63 7-73 67-129 (159)
149 PRK13165 cytochrome c-type bio 34.3 1.4E+02 0.003 24.8 5.9 63 7-73 67-129 (160)
150 KOG3070 Predicted RNA-binding 34.2 2.6E+02 0.0057 24.5 8.1 61 9-71 71-134 (235)
151 cd00210 PTS_IIA_glc PTS_IIA, P 33.6 1.1E+02 0.0023 24.2 5.0 48 6-54 41-93 (124)
152 KOG3116 Predicted C3H1-type Zn 33.0 13 0.00028 30.3 -0.2 20 187-206 27-46 (177)
153 PF12353 eIF3g: Eukaryotic tra 32.9 23 0.0005 28.1 1.2 17 238-255 107-123 (128)
154 TIGR00717 rpsA ribosomal prote 32.5 91 0.002 30.2 5.5 51 5-59 274-330 (516)
155 PRK07400 30S ribosomal protein 31.9 89 0.0019 28.6 5.0 52 5-60 120-171 (318)
156 PRK06299 rpsA 30S ribosomal pr 31.8 92 0.002 30.7 5.4 54 4-60 374-432 (565)
157 TIGR02063 RNase_R ribonuclease 31.7 85 0.0018 32.0 5.3 54 5-61 629-698 (709)
158 TIGR01953 NusA transcription t 31.7 1E+02 0.0022 28.6 5.4 53 4-61 132-184 (341)
159 cd03524 RPA2_OBF_family RPA2_O 31.7 1.1E+02 0.0024 19.8 4.4 54 7-60 2-60 (75)
160 TIGR00358 3_prime_RNase VacB a 29.9 1.2E+02 0.0026 30.6 6.0 54 5-61 574-643 (654)
161 PRK00276 infA translation init 29.6 1.9E+02 0.0042 20.2 5.4 54 5-60 7-60 (72)
162 PRK11712 ribonuclease G; Provi 29.4 1.3E+02 0.0029 29.3 5.9 69 5-74 40-127 (489)
163 PF01551 Peptidase_M23: Peptid 29.1 46 0.00099 24.2 2.2 43 6-54 19-64 (96)
164 KOG0407 40S ribosomal protein 28.3 51 0.0011 25.5 2.3 40 20-59 16-56 (139)
165 PRK07400 30S ribosomal protein 27.5 1.6E+02 0.0035 26.9 5.9 52 5-59 33-88 (318)
166 PRK11642 exoribonuclease R; Pr 27.5 1.3E+02 0.0029 31.3 5.9 54 5-61 645-714 (813)
167 PF06483 ChiC: Chitinase C; I 27.2 89 0.0019 26.3 3.7 44 16-59 88-140 (180)
168 PF12353 eIF3g: Eukaryotic tra 26.1 34 0.00073 27.1 1.0 19 127-146 105-123 (128)
169 COG2190 NagE Phosphotransferas 25.9 1.4E+02 0.0031 24.6 4.6 47 6-54 48-100 (156)
170 PRK12327 nusA transcription el 25.5 1E+02 0.0022 28.9 4.2 52 4-61 135-186 (362)
171 COG2996 Predicted RNA-bindinin 25.2 2.4E+02 0.0052 25.5 6.2 40 29-70 97-138 (287)
172 PRK00087 4-hydroxy-3-methylbut 25.0 1.8E+02 0.004 29.3 6.2 61 4-67 303-369 (647)
173 KOG0956 PHD finger protein AF1 24.9 43 0.00094 34.0 1.7 28 187-223 117-144 (900)
174 TIGR00717 rpsA ribosomal prote 24.7 2.3E+02 0.005 27.4 6.8 57 4-64 19-77 (516)
175 PTZ00162 DNA-directed RNA poly 24.7 1.6E+02 0.0034 24.6 4.9 33 4-40 82-114 (176)
176 PRK06676 rpsA 30S ribosomal pr 24.1 1.7E+02 0.0037 27.2 5.6 54 5-61 279-336 (390)
177 KOG2673 Uncharacterized conser 23.6 41 0.0009 32.3 1.3 17 240-256 131-147 (485)
178 PRK05054 exoribonuclease II; P 23.0 1.7E+02 0.0036 29.6 5.5 33 6-41 564-597 (644)
179 COG5569 Uncharacterized conser 23.0 85 0.0018 23.9 2.6 63 6-71 39-107 (108)
180 COG1545 Predicted nucleic-acid 22.8 2E+02 0.0044 22.9 5.0 37 20-60 87-123 (140)
181 PF11548 Receptor_IA-2: Protei 22.7 80 0.0017 23.6 2.4 22 49-71 43-64 (91)
182 KOG2044 5'-3' exonuclease HKE1 22.5 39 0.00084 34.8 0.9 17 239-255 262-278 (931)
183 KOG4246 Predicted DNA-binding 22.3 15 0.00033 37.8 -1.9 62 5-76 147-210 (1194)
184 KOG2673 Uncharacterized conser 22.1 47 0.001 32.0 1.3 19 159-177 130-148 (485)
185 PRK04023 DNA polymerase II lar 22.0 1E+02 0.0022 32.9 3.7 8 189-196 640-647 (1121)
186 PRK00087 4-hydroxy-3-methylbut 21.7 1.9E+02 0.004 29.3 5.6 54 5-61 564-621 (647)
187 COG2183 Tex Transcriptional ac 21.6 1.2E+02 0.0026 31.3 4.1 70 4-77 659-734 (780)
188 KOG2044 5'-3' exonuclease HKE1 21.2 43 0.00092 34.6 0.9 22 185-206 258-279 (931)
189 PRK09439 PTS system glucose-sp 21.1 2.4E+02 0.0053 23.4 5.3 47 6-54 63-115 (169)
190 KOG0125 Ataxin 2-binding prote 21.0 44 0.00095 30.9 0.8 15 14-28 130-146 (376)
191 PF05938 Self-incomp_S1: Plant 20.7 2.1E+02 0.0046 21.4 4.5 34 27-60 10-44 (110)
No 1
>PTZ00368 universal minicircle sequence binding protein (UMSBP); Provisional
Probab=99.96 E-value=5.3e-29 Score=203.47 Aligned_cols=145 Identities=36% Similarity=0.906 Sum_probs=118.6
Q ss_pred CCccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcccccCCCCccccccccccCCCCCCCCCCCcccCCCCCCC
Q 047168 90 SGYNNNRGGRGGGGAGFGGYWKGNNDSRRNNGGGYGPGGVVCYNCDGVGHVARECTSNRRNSNYNNNSGGCYNCGDPEHF 169 (258)
Q Consensus 90 ~c~~c~~~g~~~~~~~~~~~~~~c~~~~~~~~~~~~~~~~~C~~Cg~~GH~a~~Cp~~~~~~~~~~~~~~C~~Cg~~GH~ 169 (258)
+|+||++.||++ .+||+.... ...+...||+|++.||++++||.... ......|++|++.||+
T Consensus 2 ~C~~C~~~GH~~---------~~c~~~~~~----~~~~~~~C~~Cg~~GH~~~~Cp~~~~----~~~~~~C~~Cg~~GH~ 64 (148)
T PTZ00368 2 VCYRCGGVGHQS---------RECPNSAPA----GAAKARPCYKCGEPGHLSRECPSAPG----GRGERSCYNCGKTGHL 64 (148)
T ss_pred cCCCCCCCCcCc---------ccCcCCCCC----CCCCCccCccCCCCCcCcccCcCCCC----CCCCcccCCCCCcCcC
Confidence 699999999998 899975431 12347899999999999999998432 1235689999999999
Q ss_pred CCCCCCCCCCCCCCCCCCCcccccCCcccCcccCCCCCCCCCCCCccccCCCCCccCCCCCCCCC--CCCCccccCCCCC
Q 047168 170 ARDCPRQQGGSNSYNNNSGGCFKCGGYGHLARDCITRGSGGGGGGRCYNCGKSGHLARDCGAGGA--GGGGSCFNCGKPG 247 (258)
Q Consensus 170 ~~~Cp~~~~~~~~~~~~~~~C~~Cg~~GH~~~~C~~~~~~~~~~~~C~~Cg~~GH~~~~Cp~~~~--~~~~~C~~Cg~~G 247 (258)
+++||+... ......|++|++.||++++||+..........||+|++.||++++||+.+. .....||+|++.|
T Consensus 65 ~~~Cp~~~~-----~~~~~~C~~Cg~~GH~~~~C~~~~~~~~~~~~C~~Cg~~gH~~~~C~~~~~~~~~~~~C~~Cg~~g 139 (148)
T PTZ00368 65 SRECPEAPP-----GSGPRSCYNCGQTGHISRECPNRAKGGAARRACYNCGGEGHISRDCPNAGKRPGGDKTCYNCGQTG 139 (148)
T ss_pred cccCCCccc-----CCCCcccCcCCCCCcccccCCCcccccccchhhcccCcCCcchhcCCCccccCCCCCccccCCCcC
Confidence 999998742 124578999999999999999975444455689999999999999999632 2356999999999
Q ss_pred ccCCCCCCC
Q 047168 248 HFARECTKV 256 (258)
Q Consensus 248 H~~~~Cp~~ 256 (258)
||++|||++
T Consensus 140 H~~~dCp~~ 148 (148)
T PTZ00368 140 HLSRDCPDK 148 (148)
T ss_pred cccccCCCC
Confidence 999999985
No 2
>COG1278 CspC Cold shock proteins [Transcription]
Probab=99.92 E-value=1.5e-25 Score=156.74 Aligned_cols=66 Identities=50% Similarity=0.928 Sum_probs=63.4
Q ss_pred ccceEEEEeeCCCceeEEecCCCCCceEEeccccccCCccccCCCCcEEEEEEeCCCccceeecccc
Q 047168 6 RSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGYRTLYENQSVEFDVQLEADGKYQALDVTA 72 (258)
Q Consensus 6 ~~~G~vk~f~~~kGfGFI~~~~~~~dvF~H~s~l~~~~~~~l~~G~~V~F~v~~~~~G~~~A~~V~~ 72 (258)
+++|+|||||.+||||||+++++++|||||+|+|...++++|.+|++|+|+++.+++| ++|.+|++
T Consensus 1 ~~~GtVKwfn~~KGfGFI~p~~G~~DvFVH~Sai~~~g~~~L~eGQ~V~f~~~~g~kg-p~A~nv~~ 66 (67)
T COG1278 1 MATGTVKWFNATKGFGFITPEDGGKDVFVHISAIQRAGFRTLREGQKVEFEVEQGRKG-PSAANVRA 66 (67)
T ss_pred CCcceEEEeeCCCcceEcCCCCCCcCEEEEeeeeccCCCcccCCCCEEEEEEecCCCC-CceeEEEe
Confidence 4689999999999999999999999999999999999999999999999999999998 89999975
No 3
>PRK10943 cold shock-like protein CspC; Provisional
Probab=99.90 E-value=5.9e-24 Score=151.72 Aligned_cols=68 Identities=46% Similarity=0.868 Sum_probs=64.3
Q ss_pred cccceEEEEeeCCCceeEEecCCCCCceEEeccccccCCccccCCCCcEEEEEEeCCCccceeeccccC
Q 047168 5 TRSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGYRTLYENQSVEFDVQLEADGKYQALDVTAP 73 (258)
Q Consensus 5 ~~~~G~vk~f~~~kGfGFI~~~~~~~dvF~H~s~l~~~~~~~l~~G~~V~F~v~~~~~G~~~A~~V~~~ 73 (258)
++++|+|||||.+||||||+++++++|||||+|+|...+++.|.+|++|+|+++.+++| ++|++|+.+
T Consensus 2 ~~~~G~Vk~f~~~kGfGFI~~~~g~~dvFvH~s~l~~~g~~~l~~G~~V~f~~~~~~~g-~~A~~V~~~ 69 (69)
T PRK10943 2 AKIKGQVKWFNESKGFGFITPADGSKDVFVHFSAIQGNGFKTLAEGQNVEFEIQDGQKG-PAAVNVTAI 69 (69)
T ss_pred CccceEEEEEeCCCCcEEEecCCCCeeEEEEhhHccccCCCCCCCCCEEEEEEEECCCC-ceeEEEEcC
Confidence 47899999999999999999999999999999999999999999999999999999998 899999864
No 4
>PRK15464 cold shock-like protein CspH; Provisional
Probab=99.90 E-value=7.5e-24 Score=151.18 Aligned_cols=66 Identities=32% Similarity=0.391 Sum_probs=62.8
Q ss_pred ccceEEEEeeCCCceeEEecCCCCCceEEeccccccCCccccCCCCcEEEEEEeCCCccceeecccc
Q 047168 6 RSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGYRTLYENQSVEFDVQLEADGKYQALDVTA 72 (258)
Q Consensus 6 ~~~G~vk~f~~~kGfGFI~~~~~~~dvF~H~s~l~~~~~~~l~~G~~V~F~v~~~~~G~~~A~~V~~ 72 (258)
+++|+|||||.+||||||+++++++|||||+++|...+++.|.+|++|+|+++++++| ++|++|..
T Consensus 4 ~~~G~Vk~fn~~KGfGFI~~~~g~~DvFvH~s~l~~~g~~~l~~G~~V~f~v~~~~kG-~~A~~v~~ 69 (70)
T PRK15464 4 KMTGIVKTFDRKSGKGFIIPSDGRKEVQVHISAFTPRDAEVLIPGLRVEFCRVNGLRG-PTAANVYL 69 (70)
T ss_pred cceEEEEEEECCCCeEEEccCCCCccEEEEehhehhcCCCCCCCCCEEEEEEEECCCC-ceeEEEEc
Confidence 4699999999999999999999999999999999999998999999999999999999 79999974
No 5
>PTZ00368 universal minicircle sequence binding protein (UMSBP); Provisional
Probab=99.89 E-value=2.1e-23 Score=170.41 Aligned_cols=120 Identities=41% Similarity=1.090 Sum_probs=98.4
Q ss_pred CcccccCCCCccccccccccCCCCCCCCCCCcccCCCCCCCCCCCCCCCCCCCCCCCCCCcccccCCcccCcccCCCCCC
Q 047168 129 VVCYNCDGVGHVARECTSNRRNSNYNNNSGGCYNCGDPEHFARDCPRQQGGSNSYNNNSGGCFKCGGYGHLARDCITRGS 208 (258)
Q Consensus 129 ~~C~~Cg~~GH~a~~Cp~~~~~~~~~~~~~~C~~Cg~~GH~~~~Cp~~~~~~~~~~~~~~~C~~Cg~~GH~~~~C~~~~~ 208 (258)
+.||+|++.||++++||+... ........|++|++.||++++||++.. ......||+|++.||++++||+...
T Consensus 1 ~~C~~C~~~GH~~~~c~~~~~--~~~~~~~~C~~Cg~~GH~~~~Cp~~~~-----~~~~~~C~~Cg~~GH~~~~Cp~~~~ 73 (148)
T PTZ00368 1 MVCYRCGGVGHQSRECPNSAP--AGAAKARPCYKCGEPGHLSRECPSAPG-----GRGERSCYNCGKTGHLSRECPEAPP 73 (148)
T ss_pred CcCCCCCCCCcCcccCcCCCC--CCCCCCccCccCCCCCcCcccCcCCCC-----CCCCcccCCCCCcCcCcccCCCccc
Confidence 479999999999999998332 234456799999999999999998742 1245689999999999999998643
Q ss_pred CCCCCCccccCCCCCccCCCCCCCCCC--CCCccccCCCCCccCCCCCCC
Q 047168 209 GGGGGGRCYNCGKSGHLARDCGAGGAG--GGGSCFNCGKPGHFARECTKV 256 (258)
Q Consensus 209 ~~~~~~~C~~Cg~~GH~~~~Cp~~~~~--~~~~C~~Cg~~GH~~~~Cp~~ 256 (258)
.. ....|++|++.||++++||+.... ....||+|+++||++++||+.
T Consensus 74 ~~-~~~~C~~Cg~~GH~~~~C~~~~~~~~~~~~C~~Cg~~gH~~~~C~~~ 122 (148)
T PTZ00368 74 GS-GPRSCYNCGQTGHISRECPNRAKGGAARRACYNCGGEGHISRDCPNA 122 (148)
T ss_pred CC-CCcccCcCCCCCcccccCCCcccccccchhhcccCcCCcchhcCCCc
Confidence 22 345799999999999999996632 345899999999999999985
No 6
>PRK15463 cold shock-like protein CspF; Provisional
Probab=99.89 E-value=1.7e-23 Score=149.65 Aligned_cols=67 Identities=33% Similarity=0.411 Sum_probs=63.2
Q ss_pred cccceEEEEeeCCCceeEEecCCCCCceEEeccccccCCccccCCCCcEEEEEEeCCCccceeecccc
Q 047168 5 TRSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGYRTLYENQSVEFDVQLEADGKYQALDVTA 72 (258)
Q Consensus 5 ~~~~G~vk~f~~~kGfGFI~~~~~~~dvF~H~s~l~~~~~~~l~~G~~V~F~v~~~~~G~~~A~~V~~ 72 (258)
.+++|+|||||.+||||||+++++++|||||+++|...+++.|.+|++|+|+++.+++| ++|++|.+
T Consensus 3 ~~~~G~Vk~fn~~kGfGFI~~~~g~~DvFvH~sal~~~g~~~l~~G~~V~f~v~~~~~G-~~A~~V~~ 69 (70)
T PRK15463 3 RKMTGIVKTFDGKSGKGLITPSDGRKDVQVHISALNLRDAEELTTGLRVEFCRINGLRG-PTAANVYL 69 (70)
T ss_pred ccceEEEEEEeCCCceEEEecCCCCccEEEEehhhhhcCCCCCCCCCEEEEEEEECCCC-ceeEEEEc
Confidence 34699999999999999999999999999999999988899999999999999999999 89999974
No 7
>PRK09507 cspE cold shock protein CspE; Reviewed
Probab=99.89 E-value=2e-23 Score=148.96 Aligned_cols=67 Identities=45% Similarity=0.886 Sum_probs=63.9
Q ss_pred cccceEEEEeeCCCceeEEecCCCCCceEEeccccccCCccccCCCCcEEEEEEeCCCccceeecccc
Q 047168 5 TRSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGYRTLYENQSVEFDVQLEADGKYQALDVTA 72 (258)
Q Consensus 5 ~~~~G~vk~f~~~kGfGFI~~~~~~~dvF~H~s~l~~~~~~~l~~G~~V~F~v~~~~~G~~~A~~V~~ 72 (258)
.+++|+|||||.+||||||+++++++|||||+++|...+++.|.+|++|+|+++.+++| ++|++|..
T Consensus 2 ~~~~G~Vk~f~~~kGyGFI~~~~g~~dvfvH~s~l~~~g~~~l~~G~~V~f~~~~~~~G-~~A~~V~~ 68 (69)
T PRK09507 2 SKIKGNVKWFNESKGFGFITPEDGSKDVFVHFSAIQTNGFKTLAEGQRVEFEITNGAKG-PSAANVIA 68 (69)
T ss_pred CccceEEEEEeCCCCcEEEecCCCCeeEEEEeecccccCCCCCCCCCEEEEEEEECCCC-cccEEEEe
Confidence 57889999999999999999999999999999999999999999999999999999999 89999975
No 8
>PRK09890 cold shock protein CspG; Provisional
Probab=99.89 E-value=2.4e-23 Score=149.01 Aligned_cols=68 Identities=47% Similarity=0.844 Sum_probs=63.8
Q ss_pred cccceEEEEeeCCCceeEEecCCCCCceEEeccccccCCccccCCCCcEEEEEEeCCCccceeeccccC
Q 047168 5 TRSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGYRTLYENQSVEFDVQLEADGKYQALDVTAP 73 (258)
Q Consensus 5 ~~~~G~vk~f~~~kGfGFI~~~~~~~dvF~H~s~l~~~~~~~l~~G~~V~F~v~~~~~G~~~A~~V~~~ 73 (258)
.+++|+|||||.+||||||+++++++|||||+++|...+++.|.+|++|+|+++.+++| ++|.+|..+
T Consensus 3 ~~~~G~Vk~f~~~kGfGFI~~~~g~~dvFvH~s~l~~~~~~~l~~G~~V~f~~~~~~~G-~~A~~V~~~ 70 (70)
T PRK09890 3 NKMTGLVKWFNADKGFGFITPDDGSKDVFVHFTAIQSNEFRTLNENQKVEFSIEQGQRG-PAAANVVTL 70 (70)
T ss_pred ccceEEEEEEECCCCcEEEecCCCCceEEEEEeeeccCCCCCCCCCCEEEEEEEECCCC-ceeEEEEeC
Confidence 35799999999999999999999999999999999999999999999999999999999 899999753
No 9
>PRK10354 RNA chaperone/anti-terminator; Provisional
Probab=99.89 E-value=2.5e-23 Score=149.01 Aligned_cols=67 Identities=48% Similarity=0.866 Sum_probs=63.4
Q ss_pred ccceEEEEeeCCCceeEEecCCCCCceEEeccccccCCccccCCCCcEEEEEEeCCCccceeeccccC
Q 047168 6 RSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGYRTLYENQSVEFDVQLEADGKYQALDVTAP 73 (258)
Q Consensus 6 ~~~G~vk~f~~~kGfGFI~~~~~~~dvF~H~s~l~~~~~~~l~~G~~V~F~v~~~~~G~~~A~~V~~~ 73 (258)
+|+|+|||||.+||||||+++++++|||||+++|...+++.|.+|++|+|+++.+++| ++|++|+.+
T Consensus 4 ~~~G~Vk~f~~~kGfGFI~~~~g~~dvfvH~s~l~~~g~~~l~~G~~V~f~~~~~~~G-~~A~~V~~~ 70 (70)
T PRK10354 4 KMTGIVKWFNADKGFGFITPDDGSKDVFVHFSAIQNDGYKSLDEGQKVSFTIESGAKG-PAAGNVTSL 70 (70)
T ss_pred cceEEEEEEeCCCCcEEEecCCCCccEEEEEeeccccCCCCCCCCCEEEEEEEECCCC-ceeEEEEeC
Confidence 4599999999999999999999999999999999999999999999999999999999 899999863
No 10
>PRK14998 cold shock-like protein CspD; Provisional
Probab=99.89 E-value=4.4e-23 Score=148.56 Aligned_cols=69 Identities=46% Similarity=0.840 Sum_probs=64.5
Q ss_pred cceEEEEeeCCCceeEEecCCCCCceEEeccccccCCccccCCCCcEEEEEEeCCCccceeeccccCCCC
Q 047168 7 STGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGYRTLYENQSVEFDVQLEADGKYQALDVTAPGGA 76 (258)
Q Consensus 7 ~~G~vk~f~~~kGfGFI~~~~~~~dvF~H~s~l~~~~~~~l~~G~~V~F~v~~~~~G~~~A~~V~~~~g~ 76 (258)
.+|+|||||.+||||||+++++++|||||+|+|...+++.|.+|++|+|+++.+++| ++|.+|..++.+
T Consensus 2 ~~G~Vkwfn~~kGfGFI~~~~g~~dVFvH~s~l~~~g~~~l~~G~~V~f~~~~~~~G-~~A~~V~~~~~~ 70 (73)
T PRK14998 2 ETGTVKWFNNAKGFGFICPEGGGEDIFAHYSTIQMDGYRTLKAGQSVRFDVHQGPKG-NHASVIVPIEAE 70 (73)
T ss_pred CCeEEEEEeCCCceEEEecCCCCccEEEEeeeecccCCCCCCCCCEEEEEEEECCCC-ceeEEEEECccc
Confidence 479999999999999999999999999999999999999999999999999999999 799999876543
No 11
>PRK09937 stationary phase/starvation inducible regulatory protein CspD; Provisional
Probab=99.89 E-value=4.5e-23 Score=148.80 Aligned_cols=68 Identities=46% Similarity=0.832 Sum_probs=64.2
Q ss_pred cceEEEEeeCCCceeEEecCCCCCceEEeccccccCCccccCCCCcEEEEEEeCCCccceeeccccCCC
Q 047168 7 STGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGYRTLYENQSVEFDVQLEADGKYQALDVTAPGG 75 (258)
Q Consensus 7 ~~G~vk~f~~~kGfGFI~~~~~~~dvF~H~s~l~~~~~~~l~~G~~V~F~v~~~~~G~~~A~~V~~~~g 75 (258)
.+|+|||||.+||||||+++++++|||||+|+|...+++.|.+|++|+|+++.+++| ++|++|..++.
T Consensus 2 ~~G~Vkwfn~~KGfGFI~~~~gg~dVFvH~s~i~~~g~~~l~~G~~V~f~~~~~~~G-~~A~~V~~~~~ 69 (74)
T PRK09937 2 EKGTVKWFNNAKGFGFICPEGGGEDIFAHYSTIQMDGYRTLKAGQSVQFDVHQGPKG-NHASVIVPVEV 69 (74)
T ss_pred CCeEEEEEeCCCCeEEEeeCCCCccEEEEEeeccccCCCCCCCCCEEEEEEEECCCC-ceeeEEEECCc
Confidence 379999999999999999999999999999999999999999999999999999999 79999998743
No 12
>TIGR02381 cspD cold shock domain protein CspD. This model represents what appears to be a phylogenetically distinct clade, containing E. coli CspD and related proteobacterial proteins within the larger family of cold shock domain proteins described by pfam model pfam00313. The gene symbol cspD may have been used idependently for other subfamilies of cold shock domain proteins, such as for B. subtilis CspD. These proteins typically are shorter than 70 amino acids. In E. coli, CspD is a stress response protein induced in stationary phase. This homodimer binds single-stranded DNA and appears to inhibit DNA replication.
Probab=99.88 E-value=5.7e-23 Score=146.32 Aligned_cols=66 Identities=41% Similarity=0.766 Sum_probs=62.6
Q ss_pred cceEEEEeeCCCceeEEecCCCCCceEEeccccccCCccccCCCCcEEEEEEeCCCccceeeccccC
Q 047168 7 STGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGYRTLYENQSVEFDVQLEADGKYQALDVTAP 73 (258)
Q Consensus 7 ~~G~vk~f~~~kGfGFI~~~~~~~dvF~H~s~l~~~~~~~l~~G~~V~F~v~~~~~G~~~A~~V~~~ 73 (258)
.+|+|||||.+||||||+++++++|||||+|+|...+++.|.+|++|+|+++.+++| ++|.+|..+
T Consensus 2 ~~G~Vk~f~~~kGfGFI~~~~g~~dvfvH~s~~~~~g~~~l~~G~~V~f~~~~~~~G-~~A~~V~~~ 67 (68)
T TIGR02381 2 AIGIVKWFNNAKGFGFICPEGVDGDIFAHYSTIQMDGYRTLKAGQKVQFEVVQGPKG-AHATHIVPI 67 (68)
T ss_pred CCeEEEEEeCCCCeEEEecCCCCccEEEEHHHhhhcCCCCCCCCCEEEEEEEECCCC-ceeEEEEEC
Confidence 479999999999999999999999999999999999999999999999999999999 899999854
No 13
>PF00313 CSD: 'Cold-shock' DNA-binding domain; InterPro: IPR002059 When Escherichia coli is exposed to a temperature drop from 37 to 10 degrees centigrade, a 4-5 hour lag phase occurs, after which growth is resumed at a reduced rate []. During the lag phase, the expression of around 13 proteins, which contain specific DNA-binding regions [], is increased 2-10 fold. These so-called 'cold shock' proteins are thought to help the cell to survive in temperatures lower than optimum growth temperature, by contrast with heat shock proteins, which help the cell to survive in temperatures greater than the optimum, possibly by condensation of the chromosome and organisation of the prokaryotic nucleoid []. A conserved domain of about 70 amino acids has been found in prokaryotic and eukaryotic DNA-binding proteins [, , ]. This domain is known as the 'cold-shock domain' (CSD), part of which is highly similar [] to the RNP-1 RNA-binding motif.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1HZC_A 1I5F_A 1HZ9_B 1C9O_B 1HZB_B 1HZA_A 2HAX_B 2L15_A 2LSS_A 3I2Z_B ....
Probab=99.84 E-value=9.1e-21 Score=134.10 Aligned_cols=66 Identities=47% Similarity=0.887 Sum_probs=60.0
Q ss_pred cceEEEEeeCCCceeEEecCCCCCceEEeccccccCCccccCCCCcEEEEEEeCCCccceeeccccC
Q 047168 7 STGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGYRTLYENQSVEFDVQLEADGKYQALDVTAP 73 (258)
Q Consensus 7 ~~G~vk~f~~~kGfGFI~~~~~~~dvF~H~s~l~~~~~~~l~~G~~V~F~v~~~~~G~~~A~~V~~~ 73 (258)
|+|+|+|||+.+|||||+++++.+|||||+++|...+++.|.+|++|+|++..++++ ++|++|+.+
T Consensus 1 ~~G~V~~~~~~kgyGFI~~~~~~~diFfh~s~~~~~~~~~l~~G~~V~F~~~~~~~g-~~A~~V~~~ 66 (66)
T PF00313_consen 1 MTGTVKWFDDEKGYGFITSDDGGEDIFFHISDLSGNGFRSLKEGDRVEFEVEEGKKG-PQAVNVRKI 66 (66)
T ss_dssp EEEEEEEEETTTTEEEEEETTSSSEEEEEGGGBCSSSSTS--TTSEEEEEEEECTTS-EEEEEEEE-
T ss_pred CeEEEEEEECCCCceEEEEcccceeEEeccccccccccccCCCCCEEEEEEEECCCC-CEEEEEECc
Confidence 689999999999999999999989999999999999889999999999999998887 899999853
No 14
>cd04458 CSP_CDS Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in eukaryotes, prokaryotes, and archaea. CSP's include the major cold-shock proteins CspA and CspB in bacteria and the eukaryotic gene regulatory factor Y-box protein. CSP expression is up-regulated by an abrupt drop in growth temperature. CSP's are also expressed under normal condition at lower level. The function of cold-shock proteins is not fully understood. They preferentially bind poly-pyrimidine region of single-stranded RNA and DNA. CSP's are thought to bind mRNA and regulate ribosomal translation, mRNA degradation, and the rate of transcription termination. The human Y-box protein, which contains a CSD, regulates transcription and translation of genes that contain the Y-box sequence in their promoters. This specific ssDNA-binding properties of CSD are required for the binding of Y-box protein to the promoter's Y-box sequence, thereby regulating transcription.
Probab=99.82 E-value=3.6e-20 Score=130.67 Aligned_cols=65 Identities=49% Similarity=0.957 Sum_probs=61.1
Q ss_pred cceEEEEeeCCCceeEEecCCCCCceEEeccccccCCccccCCCCcEEEEEEeCCCccceeecccc
Q 047168 7 STGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGYRTLYENQSVEFDVQLEADGKYQALDVTA 72 (258)
Q Consensus 7 ~~G~vk~f~~~kGfGFI~~~~~~~dvF~H~s~l~~~~~~~l~~G~~V~F~v~~~~~G~~~A~~V~~ 72 (258)
++|+|||||.+||||||+++++++|||||+++|...++..|.+|+.|+|++..+++| ++|++|+.
T Consensus 1 ~~G~Vk~~~~~kGfGFI~~~~~g~diffh~~~~~~~~~~~~~~G~~V~f~~~~~~~g-~~A~~V~~ 65 (65)
T cd04458 1 VTGTVKWFDDEKGFGFITPDDGGEDVFVHISALEGDGFRSLEEGDRVEFELEEGDKG-PQAVNVRL 65 (65)
T ss_pred CcEEEEEEECCCCeEEEecCCCCcCEEEEhhHhhccCCCcCCCCCEEEEEEEECCCC-CeEEEeEC
Confidence 579999999999999999999889999999999988889999999999999999887 89999863
No 15
>COG5082 AIR1 Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]
Probab=99.80 E-value=1.3e-19 Score=150.76 Aligned_cols=126 Identities=30% Similarity=0.689 Sum_probs=95.4
Q ss_pred CCCCCCCCCccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcccccCCCCccccccccccCCCCCCCCCCCccc
Q 047168 83 NNNTNNNSGYNNNRGGRGGGGAGFGGYWKGNNDSRRNNGGGYGPGGVVCYNCDGVGHVARECTSNRRNSNYNNNSGGCYN 162 (258)
Q Consensus 83 ~~~~g~~~c~~c~~~g~~~~~~~~~~~~~~c~~~~~~~~~~~~~~~~~C~~Cg~~GH~a~~Cp~~~~~~~~~~~~~~C~~ 162 (258)
.....++.|+||++.||+. ++|| ...||+|...+|.+..||. .+.|++
T Consensus 55 ~~~~~~~~C~nCg~~GH~~---------~DCP-------------~~iC~~C~~~~H~s~~C~~----------~~~C~~ 102 (190)
T COG5082 55 AIREENPVCFNCGQNGHLR---------RDCP-------------HSICYNCSWDGHRSNHCPK----------PKKCYN 102 (190)
T ss_pred cccccccccchhcccCccc---------ccCC-------------hhHhhhcCCCCcccccCCc----------cccccc
Confidence 4444566799999999988 8888 3588999778899999887 378999
Q ss_pred CCCCCCCCCCC-CCCCCCCCCCCCCCCcccccCCcccCcccCCCCCCCCC--------CCCccccCCCCCccCCCCCCCC
Q 047168 163 CGDPEHFARDC-PRQQGGSNSYNNNSGGCFKCGGYGHLARDCITRGSGGG--------GGGRCYNCGKSGHLARDCGAGG 233 (258)
Q Consensus 163 Cg~~GH~~~~C-p~~~~~~~~~~~~~~~C~~Cg~~GH~~~~C~~~~~~~~--------~~~~C~~Cg~~GH~~~~Cp~~~ 233 (258)
|++.||++++| |.+ .....|+.|....|++++||+.+.... ....||+|+..+|++++|++++
T Consensus 103 Cg~~GH~~~dC~P~~--------~~~~~C~~C~s~~H~s~~Cp~~~k~y~~~~~~~~~~~~~cy~c~~~~H~~~dc~~~~ 174 (190)
T COG5082 103 CGETGHLSRDCNPSK--------DQQKSCFDCNSTRHSSEDCPSIWKHYVLNNGDGHPIKKFCYSCGSAGHFGDDCKEPR 174 (190)
T ss_pred ccccCccccccCccc--------ccCcceeccCCCccccccCcccccccccccCCCcceeeeccccCCccccCCCCCCCc
Confidence 99999999999 454 335688999999999999988743221 1345888888888888888877
Q ss_pred CCCCCccccCCCCCccC
Q 047168 234 AGGGGSCFNCGKPGHFA 250 (258)
Q Consensus 234 ~~~~~~C~~Cg~~GH~~ 250 (258)
..... |.|+..+|+.
T Consensus 175 ~s~~~--~~~~~~~~~~ 189 (190)
T COG5082 175 SSRVP--YVCGKKGYVS 189 (190)
T ss_pred ccccc--ccccccccCC
Confidence 65444 7777776653
No 16
>COG5082 AIR1 Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]
Probab=99.80 E-value=4.3e-20 Score=153.66 Aligned_cols=104 Identities=35% Similarity=0.912 Sum_probs=92.0
Q ss_pred CCcccccCCCCccccccccccCCCCCCCCCCCcccCCCCCCCCCCCCCCCCCCCCCCCCCCcccccCCcccCcccC-CCC
Q 047168 128 GVVCYNCDGVGHVARECTSNRRNSNYNNNSGGCYNCGDPEHFARDCPRQQGGSNSYNNNSGGCFKCGGYGHLARDC-ITR 206 (258)
Q Consensus 128 ~~~C~~Cg~~GH~a~~Cp~~~~~~~~~~~~~~C~~Cg~~GH~~~~Cp~~~~~~~~~~~~~~~C~~Cg~~GH~~~~C-~~~ 206 (258)
..+||+|++.||++++||. .+|++|...+|.+..||.+ .+|++|++.||++++| |..
T Consensus 60 ~~~C~nCg~~GH~~~DCP~-----------~iC~~C~~~~H~s~~C~~~-----------~~C~~Cg~~GH~~~dC~P~~ 117 (190)
T COG5082 60 NPVCFNCGQNGHLRRDCPH-----------SICYNCSWDGHRSNHCPKP-----------KKCYNCGETGHLSRDCNPSK 117 (190)
T ss_pred ccccchhcccCcccccCCh-----------hHhhhcCCCCcccccCCcc-----------cccccccccCccccccCccc
Confidence 6899999999999999996 8999997799999999987 5999999999999999 554
Q ss_pred CCCCCCCCccccCCCCCccCCCCCCCCCCC----------CCccccCCCCCccCCCCCCCc
Q 047168 207 GSGGGGGGRCYNCGKSGHLARDCGAGGAGG----------GGSCFNCGKPGHFARECTKVA 257 (258)
Q Consensus 207 ~~~~~~~~~C~~Cg~~GH~~~~Cp~~~~~~----------~~~C~~Cg~~GH~~~~Cp~~~ 257 (258)
... ..|+.|...+|++++||+.|+.. ...||+|+..+||+.+|+++.
T Consensus 118 ~~~----~~C~~C~s~~H~s~~Cp~~~k~y~~~~~~~~~~~~~cy~c~~~~H~~~dc~~~~ 174 (190)
T COG5082 118 DQQ----KSCFDCNSTRHSSEDCPSIWKHYVLNNGDGHPIKKFCYSCGSAGHFGDDCKEPR 174 (190)
T ss_pred ccC----cceeccCCCccccccCcccccccccccCCCcceeeeccccCCccccCCCCCCCc
Confidence 332 37999999999999999988541 358999999999999999764
No 17
>KOG3070 consensus Predicted RNA-binding protein containing PIN domain and invovled in translation or RNA processing [Translation, ribosomal structure and biogenesis]
Probab=99.74 E-value=1.2e-17 Score=145.38 Aligned_cols=85 Identities=47% Similarity=0.821 Sum_probs=78.7
Q ss_pred CccccceEEEEeeCCCceeEEecCCCCCceEEecccccc----CCccccCCCCcEEEEEEeCCCccceeeccccCCCCcc
Q 047168 3 QLTRSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKS----DGYRTLYENQSVEFDVQLEADGKYQALDVTAPGGAPV 78 (258)
Q Consensus 3 ~~~~~~G~vk~f~~~kGfGFI~~~~~~~dvF~H~s~l~~----~~~~~l~~G~~V~F~v~~~~~G~~~A~~V~~~~g~~~ 78 (258)
++...+|+|||||+.+|||||+++|+.+||||||++|.. .+|++|.+++.|.|+++...++ .+|++|+.+++.++
T Consensus 53 ~~~~~~G~~k~fnv~~G~gFi~~~d~~~D~fvhQs~i~~~~~~~~~rs~~~~e~v~f~~~~~~~g-~~a~~vt~p~g~~~ 131 (235)
T KOG3070|consen 53 QGARVKGTVKWFNVGKGYGFITRDDGPEDVFVHQSAITKYTPSEGFRSLKEGEAVPFDIQEGNKG-TEAANVTGPDGVPV 131 (235)
T ss_pred ccccccCcceeEeccCCcceecccCCCCceeEEeeeecccccccchhhcccCCCccceecccCcc-ceeeeecCCCCccc
Confidence 456889999999999999999999999999999999999 8899999999999999999999 89999999999999
Q ss_pred cCCCCCCCCC
Q 047168 79 HSSKNNNTNN 88 (258)
Q Consensus 79 ~~s~~~~~g~ 88 (258)
..+++..+..
T Consensus 132 ~~s~~~~~~~ 141 (235)
T KOG3070|consen 132 RGSKGAVKGN 141 (235)
T ss_pred cccccccccc
Confidence 8887766543
No 18
>KOG4400 consensus E3 ubiquitin ligase interacting with arginine methyltransferase [Posttranslational modification, protein turnover, chaperones]
Probab=99.58 E-value=9.2e-15 Score=129.94 Aligned_cols=136 Identities=30% Similarity=0.698 Sum_probs=87.1
Q ss_pred CCCCCCccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcccccCCCCccccccccccCCCCCCCCCCCcccCCC
Q 047168 86 TNNNSGYNNNRGGRGGGGAGFGGYWKGNNDSRRNNGGGYGPGGVVCYNCDGVGHVARECTSNRRNSNYNNNSGGCYNCGD 165 (258)
Q Consensus 86 ~g~~~c~~c~~~g~~~~~~~~~~~~~~c~~~~~~~~~~~~~~~~~C~~Cg~~GH~a~~Cp~~~~~~~~~~~~~~C~~Cg~ 165 (258)
....+|++|++.+|.. .+|+.. ...|++|++.||++++||....... ....|+.|+.
T Consensus 70 ~~~~~c~~~g~~~~~~---------~~~~~~-----------~~~c~~C~~~gH~~~~c~~~~~~~~---~~~~~~~c~~ 126 (261)
T KOG4400|consen 70 CPEVSCYICGEKGHLG---------RRCTRI-----------AAACFNCGEGGHIERDCPEAGKEGS---SETSCYSCGK 126 (261)
T ss_pred CCCceeeecCCCCchh---------hcCccc-----------chhhhhCCCCccchhhCCcccCccc---ccceeeccCC
Confidence 3355788888888776 666641 4688888888888888886332111 3456788888
Q ss_pred CCCCC-CCCCCCCCCCCCCCCCCCcccccCCcccCcccCCCCCCCCCCCCccccCCCCCccCCCCCCCCCCC--------
Q 047168 166 PEHFA-RDCPRQQGGSNSYNNNSGGCFKCGGYGHLARDCITRGSGGGGGGRCYNCGKSGHLARDCGAGGAGG-------- 236 (258)
Q Consensus 166 ~GH~~-~~Cp~~~~~~~~~~~~~~~C~~Cg~~GH~~~~C~~~~~~~~~~~~C~~Cg~~GH~~~~Cp~~~~~~-------- 236 (258)
.+|.. +++.... .... ..||+|++.||++.+||++ ....||.|++.+|.+++||......
T Consensus 127 ~gh~~~~~~~~~~-----~~~~-~~Cy~Cg~~GH~s~~C~~~-----~~~~c~~c~~~~h~~~~C~~~~~~~~~~~~~~~ 195 (261)
T KOG4400|consen 127 TGHRGCPDADPVD-----GPKP-AKCYSCGEQGHISDDCPEN-----KGGTCFRCGKVGHGSRDCPSKQKSKSKQGGQRK 195 (261)
T ss_pred CccccCccccccc-----CCCC-CccCCCCcCCcchhhCCCC-----CCCccccCCCcceecccCCccccccccCccccc
Confidence 88887 3322221 1122 6688888888888888864 1237888888888888888765331
Q ss_pred -CCccccCCCCCccCCCCCCC
Q 047168 237 -GGSCFNCGKPGHFARECTKV 256 (258)
Q Consensus 237 -~~~C~~Cg~~GH~~~~Cp~~ 256 (258)
...|+ +...+|+.++|+..
T Consensus 196 ~~~~~~-~~~~~~~~~~~~~~ 215 (261)
T KOG4400|consen 196 GFGACY-DYPQGHKQRACGGS 215 (261)
T ss_pred ccccCc-cccccccccccCCC
Confidence 11233 44677777777653
No 19
>KOG4400 consensus E3 ubiquitin ligase interacting with arginine methyltransferase [Posttranslational modification, protein turnover, chaperones]
Probab=99.53 E-value=3e-14 Score=126.68 Aligned_cols=111 Identities=40% Similarity=1.017 Sum_probs=90.0
Q ss_pred CCcccccCCCCccccccccccCCCCCCCCCCCcccCCCCCCCCCCCCCCCCCCCCCCCCCCcccccCCcccCcccCCCCC
Q 047168 128 GVVCYNCDGVGHVARECTSNRRNSNYNNNSGGCYNCGDPEHFARDCPRQQGGSNSYNNNSGGCFKCGGYGHLARDCITRG 207 (258)
Q Consensus 128 ~~~C~~Cg~~GH~a~~Cp~~~~~~~~~~~~~~C~~Cg~~GH~~~~Cp~~~~~~~~~~~~~~~C~~Cg~~GH~~~~C~~~~ 207 (258)
...|+.|++.+|.++.|+. ....|++|++.||++++|+...... .....||.|+..+|.. |+...
T Consensus 72 ~~~c~~~g~~~~~~~~~~~---------~~~~c~~C~~~gH~~~~c~~~~~~~----~~~~~~~~c~~~gh~~--~~~~~ 136 (261)
T KOG4400|consen 72 EVSCYICGEKGHLGRRCTR---------IAAACFNCGEGGHIERDCPEAGKEG----SSETSCYSCGKTGHRG--CPDAD 136 (261)
T ss_pred CceeeecCCCCchhhcCcc---------cchhhhhCCCCccchhhCCcccCcc----cccceeeccCCCcccc--Ccccc
Confidence 6899999999999999984 4588999999999999999885321 1456899999999999 33322
Q ss_pred C--CCCCCCccccCCCCCccCCCCCCCCCCCCCccccCCCCCccCCCCCCCc
Q 047168 208 S--GGGGGGRCYNCGKSGHLARDCGAGGAGGGGSCFNCGKPGHFARECTKVA 257 (258)
Q Consensus 208 ~--~~~~~~~C~~Cg~~GH~~~~Cp~~~~~~~~~C~~Cg~~GH~~~~Cp~~~ 257 (258)
. .... +.||+|++.||++++||++ ....||.|++.+|.+++||++.
T Consensus 137 ~~~~~~~-~~Cy~Cg~~GH~s~~C~~~---~~~~c~~c~~~~h~~~~C~~~~ 184 (261)
T KOG4400|consen 137 PVDGPKP-AKCYSCGEQGHISDDCPEN---KGGTCFRCGKVGHGSRDCPSKQ 184 (261)
T ss_pred cccCCCC-CccCCCCcCCcchhhCCCC---CCCccccCCCcceecccCCccc
Confidence 1 1112 5799999999999999976 2568999999999999999875
No 20
>smart00357 CSP Cold shock protein domain. RNA-binding domain that functions as a RNA-chaperone in bacteria and is involved in regulating translation in eukaryotes. Contains sub-family of RNA-binding domains in the Rho transcription termination factor.
Probab=98.94 E-value=2.7e-09 Score=73.75 Aligned_cols=62 Identities=52% Similarity=0.945 Sum_probs=50.3
Q ss_pred ceEEEEeeCCCceeEEecCCCCCceEEeccccccCCccccCCCCcEEEEEEeC-CCccceeecccc
Q 047168 8 TGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGYRTLYENQSVEFDVQLE-ADGKYQALDVTA 72 (258)
Q Consensus 8 ~G~vk~f~~~kGfGFI~~~~~~~dvF~H~s~l~~~~~~~l~~G~~V~F~v~~~-~~G~~~A~~V~~ 72 (258)
+|+|+|++ +|||||.+++...|||||.+.|.. ++..+.+|+.|.|.+... .+++++|..|.+
T Consensus 1 ~G~i~~~~--~g~gfv~~~~~~~~i~v~~~~~~~-~~~~~~~Gd~V~~~i~~~~~~~~~~a~~v~~ 63 (64)
T smart00357 1 TGVVKWFN--KGFGFIRPDDGGKDVFVHPSQIQG-GLKSLREGDEVEFKVVSPRGGGKPEAENVVK 63 (64)
T ss_pred CeEEEEEc--CCeeEEecCCCCccEEEEhHHhhc-CCCcCCCCCEEEEEEEEccCCCCcEEEEEEe
Confidence 58999997 799999998765799999999876 566789999999999872 233478887654
No 21
>PF00098 zf-CCHC: Zinc knuckle; InterPro: IPR001878 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the CysCysHisCys (CCHC) type zinc finger domains, and have the sequence: C-X2-C-X4-H-X4-C where X can be any amino acid, and number indicates the number of residues. These 18 residues CCHC zinc finger domains are mainly found in the nucleocapsid protein of retroviruses. It is required for viral genome packaging and for early infection process [, , ]. It is also found in eukaryotic proteins involved in RNA binding or single-stranded DNA binding []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding; PDB: 2L44_A 1A1T_A 1WWG_A 1U6P_A 1WWD_A 1WWE_A 1A6B_B 1F6U_A 1MFS_A 1NCP_C ....
Probab=98.20 E-value=7.5e-07 Score=46.72 Aligned_cols=17 Identities=71% Similarity=1.712 Sum_probs=10.1
Q ss_pred ccccCCCCCccCCCCCC
Q 047168 239 SCFNCGKPGHFARECTK 255 (258)
Q Consensus 239 ~C~~Cg~~GH~~~~Cp~ 255 (258)
.||+|++.||++++||+
T Consensus 2 ~C~~C~~~GH~~~~Cp~ 18 (18)
T PF00098_consen 2 KCFNCGEPGHIARDCPK 18 (18)
T ss_dssp BCTTTSCSSSCGCTSSS
T ss_pred cCcCCCCcCcccccCcc
Confidence 46666666666666653
No 22
>PF00098 zf-CCHC: Zinc knuckle; InterPro: IPR001878 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the CysCysHisCys (CCHC) type zinc finger domains, and have the sequence: C-X2-C-X4-H-X4-C where X can be any amino acid, and number indicates the number of residues. These 18 residues CCHC zinc finger domains are mainly found in the nucleocapsid protein of retroviruses. It is required for viral genome packaging and for early infection process [, , ]. It is also found in eukaryotic proteins involved in RNA binding or single-stranded DNA binding []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding; PDB: 2L44_A 1A1T_A 1WWG_A 1U6P_A 1WWD_A 1WWE_A 1A6B_B 1F6U_A 1MFS_A 1NCP_C ....
Probab=98.03 E-value=3e-06 Score=44.40 Aligned_cols=16 Identities=63% Similarity=1.661 Sum_probs=9.7
Q ss_pred ccccCCCCCccCCCCC
Q 047168 215 RCYNCGKSGHLARDCG 230 (258)
Q Consensus 215 ~C~~Cg~~GH~~~~Cp 230 (258)
.||+|++.||++++||
T Consensus 2 ~C~~C~~~GH~~~~Cp 17 (18)
T PF00098_consen 2 KCFNCGEPGHIARDCP 17 (18)
T ss_dssp BCTTTSCSSSCGCTSS
T ss_pred cCcCCCCcCcccccCc
Confidence 4666666666666665
No 23
>PF08206 OB_RNB: Ribonuclease B OB domain; InterPro: IPR013223 This domain includes the N-terminal OB domain found in ribonuclease B proteins in one or two copies.; PDB: 2ID0_D 2IX1_A 2IX0_A.
Probab=97.70 E-value=7.8e-05 Score=51.14 Aligned_cols=48 Identities=25% Similarity=0.578 Sum_probs=33.9
Q ss_pred CCceeEEecCCCCCceEEeccccccCCccccCCCCcEEEEEEeCC-Cccceeec
Q 047168 17 AKGYGFIRPDDGGADLFVHQKSIKSDGYRTLYENQSVEFDVQLEA-DGKYQALD 69 (258)
Q Consensus 17 ~kGfGFI~~~~~~~dvF~H~s~l~~~~~~~l~~G~~V~F~v~~~~-~G~~~A~~ 69 (258)
.+||||+.+++..+|||+....+.. .-.||.|...+.... .+++++.-
T Consensus 7 ~~GfGFv~~~~~~~DifIp~~~l~~-----A~~gD~V~v~i~~~~~~~~~eg~v 55 (58)
T PF08206_consen 7 PKGFGFVIPDDGGEDIFIPPRNLNG-----AMDGDKVLVRITPPSRGKRPEGEV 55 (58)
T ss_dssp SSS-EEEEECT-TEEEEE-HHHHTT-----S-TT-EEEEEEEESSSEEEEEEEE
T ss_pred cCCCEEEEECCCCCCEEECHHHHCC-----CCCCCEEEEEEecCCCCCCCCEEE
Confidence 8999999999988999999999965 478999999998833 33344443
No 24
>PF14444 S1-like: S1-like
Probab=97.21 E-value=0.00099 Score=45.36 Aligned_cols=47 Identities=26% Similarity=0.400 Sum_probs=40.0
Q ss_pred ccceEEEEeeCCCceeEEecCCCCCceEEeccccccCCccccCCCCcEEEEEEeCCC
Q 047168 6 RSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGYRTLYENQSVEFDVQLEAD 62 (258)
Q Consensus 6 ~~~G~vk~f~~~kGfGFI~~~~~~~dvF~H~s~l~~~~~~~l~~G~~V~F~v~~~~~ 62 (258)
.++|.|+.+ ...||||. +||||..+++... .|++||+|..+....+.
T Consensus 3 ~~~GvVTkl--~~~yG~ID-----e~vFF~~~vv~G~---~P~vGdrV~v~A~~n~~ 49 (58)
T PF14444_consen 3 VFTGVVTKL--CDDYGFID-----EDVFFQTDVVKGN---VPKVGDRVLVEAIYNPN 49 (58)
T ss_pred eEEEEEEEE--eCCcceEc-----ccEEEEcccEecC---CCccCCEEEEEEEeCCC
Confidence 468999999 47899997 7999999998744 47999999999888754
No 25
>PF13696 zf-CCHC_2: Zinc knuckle
Probab=96.65 E-value=0.0014 Score=39.35 Aligned_cols=17 Identities=41% Similarity=1.079 Sum_probs=8.6
Q ss_pred ccccCCCCCccCCCCCC
Q 047168 215 RCYNCGKSGHLARDCGA 231 (258)
Q Consensus 215 ~C~~Cg~~GH~~~~Cp~ 231 (258)
.|+.|++.||+.+|||+
T Consensus 10 ~C~~C~~~GH~i~dCP~ 26 (32)
T PF13696_consen 10 VCHRCGQKGHWIQDCPT 26 (32)
T ss_pred EeecCCCCCccHhHCCC
Confidence 35555555555555554
No 26
>PF13696 zf-CCHC_2: Zinc knuckle
Probab=96.65 E-value=0.0013 Score=39.42 Aligned_cols=21 Identities=38% Similarity=0.798 Sum_probs=15.9
Q ss_pred CCCcccccCCcccCcccCCCC
Q 047168 186 NSGGCFKCGGYGHLARDCITR 206 (258)
Q Consensus 186 ~~~~C~~Cg~~GH~~~~C~~~ 206 (258)
...+|++|++.||+.++||++
T Consensus 7 ~~Y~C~~C~~~GH~i~dCP~~ 27 (32)
T PF13696_consen 7 PGYVCHRCGQKGHWIQDCPTN 27 (32)
T ss_pred CCCEeecCCCCCccHhHCCCC
Confidence 456788888888888888874
No 27
>PF07497 Rho_RNA_bind: Rho termination factor, RNA-binding domain; InterPro: IPR011113 The Rho termination factor disengages newly transcribed RNA from its DNA template at certain, specific transcripts. It is thought that two copies of Rho bind to RNA and that Rho functions as a hexamer of protomers [].; GO: 0003723 RNA binding, 0006353 transcription termination, DNA-dependent; PDB: 1A8V_B 1PVO_A 1PV4_D 3ICE_A 1XPU_C 1XPO_D 1XPR_F 2A8V_B 2HT1_B 1A63_A ....
Probab=96.37 E-value=0.0066 Score=44.13 Aligned_cols=63 Identities=29% Similarity=0.480 Sum_probs=39.2
Q ss_pred ceEEEEeeCCCceeEEecC-----CCCCceEEeccccccCCccccCCCCcEEEEEEeCCCcc--ceeeccccCCC
Q 047168 8 TGKVTWFDGAKGYGFIRPD-----DGGADLFVHQKSIKSDGYRTLYENQSVEFDVQLEADGK--YQALDVTAPGG 75 (258)
Q Consensus 8 ~G~vk~f~~~kGfGFI~~~-----~~~~dvF~H~s~l~~~~~~~l~~G~~V~F~v~~~~~G~--~~A~~V~~~~g 75 (258)
.|++-- ..+|||||..+ .+.+||||-.+.|+..+ |+.|+.|+=.+.....+. +..+.|..+.+
T Consensus 4 ~GvLei--~~dGyGFLR~~~~~y~~~~~DvYVs~~qIrrf~---LR~GD~V~G~vr~p~~~ek~~aL~~V~~VNg 73 (78)
T PF07497_consen 4 EGVLEI--LPDGYGFLRSPDNNYLPSPDDVYVSPSQIRRFG---LRTGDLVEGQVRPPREGEKYFALLRVESVNG 73 (78)
T ss_dssp EEEEEE---TTS-EEEE-GGGTTS-STTSEEE-CCCCCCTT-----TTEEEEEEEE--STTSSSEEECEECEETT
T ss_pred EEEEEE--CCCCcEEeECCCcCCCCCCCCEEECHHHHHHcC---CCCCCEEEEEEeCCCCCCcceeeEEEEeECC
Confidence 455553 25799999987 35799999999998875 899999998888865442 23445554444
No 28
>cd04459 Rho_CSD Rho_CSD: Rho protein cold-shock domain (CSD). Rho protein is a transcription termination factor in most bacteria. In bacteria, there are two distinct mechanisms for mRNA transcription termination. In intrinsic termination, RNA polymerase and nascent mRNA are released from DNA template by an mRNA stem loop structure, which resembles the transcription termination mechanism used by eukaryotic pol III. The second mechanism is mediated by Rho factor. Rho factor terminates transcription by using energy from ATP hydrolysis to forcibly dissociate the transcripts from RNA polymerase. Rho protein contains an N-terminal S1-like domain, which binds single-stranded RNA. Rho has a C-terminal ATPase domain which hydrolyzes ATP to provide energy to strip RNA polymerase and mRNA from the DNA template. Rho functions as a homohexamer.
Probab=96.14 E-value=0.011 Score=41.85 Aligned_cols=48 Identities=23% Similarity=0.467 Sum_probs=37.7
Q ss_pred eEEEEeeCCCceeEEecC-----CCCCceEEeccccccCCccccCCCCcEEEEEEeCC
Q 047168 9 GKVTWFDGAKGYGFIRPD-----DGGADLFVHQKSIKSDGYRTLYENQSVEFDVQLEA 61 (258)
Q Consensus 9 G~vk~f~~~kGfGFI~~~-----~~~~dvF~H~s~l~~~~~~~l~~G~~V~F~v~~~~ 61 (258)
|++--. ..|||||... .+.+||||..+.|+..+ |+.|+.|+=.+....
T Consensus 3 GiLdi~--~~g~GFLR~~~~~y~~~~~DvyVs~~~Irr~~---LR~GD~V~G~vr~p~ 55 (68)
T cd04459 3 GVLEIL--PDGFGFLRSSGYNYLPGPDDIYVSPSQIRRFN---LRTGDTVVGQIRPPK 55 (68)
T ss_pred EEEEEc--CCCceEEecCCcCCCCCCCCEEECHHHHHHhC---CCCCCEEEEEEeCCC
Confidence 444433 3499999866 36799999999998875 899999998887643
No 29
>PF13509 S1_2: S1 domain; PDB: 3GO5_A.
Probab=95.50 E-value=0.04 Score=37.97 Aligned_cols=55 Identities=24% Similarity=0.360 Sum_probs=34.4
Q ss_pred cceEEEEeeCCCceeEEecCCCCCceEEeccccccCCccccCCCCcEEEEEEeCCCccceee
Q 047168 7 STGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGYRTLYENQSVEFDVQLEADGKYQAL 68 (258)
Q Consensus 7 ~~G~vk~f~~~kGfGFI~~~~~~~dvF~H~s~l~~~~~~~l~~G~~V~F~v~~~~~G~~~A~ 68 (258)
.+-+|+..+ .+|++-..+...+||++.+.+.. .+.+|+.|+.-+..+.++++.|+
T Consensus 5 ~~L~V~~~~---~~g~fL~~~~~~~vlLp~~e~~~----~~~~Gd~v~VFvY~D~~~rl~AT 59 (61)
T PF13509_consen 5 NTLKVVDKN---EFGYFLDDGEGKEVLLPKSEVPE----PLKVGDEVEVFVYLDKEGRLVAT 59 (61)
T ss_dssp ----EEEE----SSEEEEEETT-EEEEEEGGG----------TTSEEEEEEEE-TTS-EEEE
T ss_pred cceEEEEEe---CCEEEEECCCCCEEEechHHcCC----CCCCCCEEEEEEEECCCCCEEEe
Confidence 345677765 46766666666999999999964 38999999999999998888776
No 30
>PF13917 zf-CCHC_3: Zinc knuckle
Probab=95.19 E-value=0.011 Score=37.70 Aligned_cols=16 Identities=44% Similarity=1.221 Sum_probs=8.2
Q ss_pred ccccCCCCCccCCCCC
Q 047168 239 SCFNCGKPGHFARECT 254 (258)
Q Consensus 239 ~C~~Cg~~GH~~~~Cp 254 (258)
.|.+|++.||+..+||
T Consensus 6 ~CqkC~~~GH~tyeC~ 21 (42)
T PF13917_consen 6 RCQKCGQKGHWTYECP 21 (42)
T ss_pred cCcccCCCCcchhhCC
Confidence 4555555555555555
No 31
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]
Probab=94.65 E-value=0.025 Score=53.90 Aligned_cols=42 Identities=36% Similarity=0.752 Sum_probs=18.4
Q ss_pred CcccccCCcccCcccCCCCCCCCCCCCccccCCCCCccCCCCCC
Q 047168 188 GGCFKCGGYGHLARDCITRGSGGGGGGRCYNCGKSGHLARDCGA 231 (258)
Q Consensus 188 ~~C~~Cg~~GH~~~~C~~~~~~~~~~~~C~~Cg~~GH~~~~Cp~ 231 (258)
..|..|+..+|-.-+||...... ...|..|+..||++.||+.
T Consensus 262 ~~c~~cg~~~H~q~~cp~r~~~~--~n~c~~cg~~gH~~~dc~~ 303 (554)
T KOG0119|consen 262 RACRNCGSTGHKQYDCPGRIPNT--TNVCKICGPLGHISIDCKV 303 (554)
T ss_pred ccccccCCCccccccCCcccccc--cccccccCCcccccccCCC
Confidence 44555555555555555431000 0144444444444444443
No 32
>smart00343 ZnF_C2HC zinc finger.
Probab=94.41 E-value=0.02 Score=32.42 Aligned_cols=15 Identities=67% Similarity=1.690 Sum_probs=9.7
Q ss_pred cccCCCCCccCCCCC
Q 047168 240 CFNCGKPGHFARECT 254 (258)
Q Consensus 240 C~~Cg~~GH~~~~Cp 254 (258)
|++|++.||++++||
T Consensus 2 C~~CG~~GH~~~~C~ 16 (26)
T smart00343 2 CYNCGKEGHIARDCP 16 (26)
T ss_pred CccCCCCCcchhhCC
Confidence 666666666666665
No 33
>KOG0109 consensus RNA-binding protein LARK, contains RRM and retroviral-type Zn-finger domains [RNA processing and modification; General function prediction only]
Probab=93.94 E-value=0.14 Score=46.02 Aligned_cols=22 Identities=41% Similarity=0.596 Sum_probs=18.8
Q ss_pred ccceEEEEeeCCCceeEEecCC
Q 047168 6 RSTGKVTWFDGAKGYGFIRPDD 27 (258)
Q Consensus 6 ~~~G~vk~f~~~kGfGFI~~~~ 27 (258)
...|+|..-|..|-|||+-.+|
T Consensus 24 e~ygkVlECDIvKNYgFVHiEd 45 (346)
T KOG0109|consen 24 EQYGKVLECDIVKNYGFVHIED 45 (346)
T ss_pred HhhCceEeeeeecccceEEeec
Confidence 3579999999999999997664
No 34
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]
Probab=93.46 E-value=0.075 Score=50.79 Aligned_cols=44 Identities=30% Similarity=0.670 Sum_probs=23.3
Q ss_pred CCcccccCCCCccccccccccCCCCCCCCCCCcccCCCCCCCCCCCCCC
Q 047168 128 GVVCYNCDGVGHVARECTSNRRNSNYNNNSGGCYNCGDPEHFARDCPRQ 176 (258)
Q Consensus 128 ~~~C~~Cg~~GH~a~~Cp~~~~~~~~~~~~~~C~~Cg~~GH~~~~Cp~~ 176 (258)
..+|.+|+..||...+||..- ......|..|+..||++.+|+..
T Consensus 261 ~~~c~~cg~~~H~q~~cp~r~-----~~~~n~c~~cg~~gH~~~dc~~~ 304 (554)
T KOG0119|consen 261 NRACRNCGSTGHKQYDCPGRI-----PNTTNVCKICGPLGHISIDCKVN 304 (554)
T ss_pred cccccccCCCccccccCCccc-----ccccccccccCCcccccccCCCc
Confidence 356666666666666666410 00111566666666666666544
No 35
>PRK11642 exoribonuclease R; Provisional
Probab=93.40 E-value=0.11 Score=53.33 Aligned_cols=62 Identities=23% Similarity=0.290 Sum_probs=45.8
Q ss_pred ccceEEEEeeCCCceeEEecCCCCCceEEeccccccCCccccCCCCcEEEEEEeC-CCccceeeccccCC
Q 047168 6 RSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGYRTLYENQSVEFDVQLE-ADGKYQALDVTAPG 74 (258)
Q Consensus 6 ~~~G~vk~f~~~kGfGFI~~~~~~~dvF~H~s~l~~~~~~~l~~G~~V~F~v~~~-~~G~~~A~~V~~~~ 74 (258)
.+.|+|..= .+||||+.+++..+|||+....+.. .-.||.|...+... .+++++|.-|.++.
T Consensus 84 ~~~G~v~~~--~~GfgFv~~e~~~~difI~~~~l~~-----A~~GD~V~v~i~~~~~~~r~eg~Vv~Ile 146 (813)
T PRK11642 84 LLKGTVIGH--RDGYGFLRVEGRKDDLYLSSEQMKT-----CIHGDQVLAQPLGADRKGRREARIVRVLV 146 (813)
T ss_pred eEEEEEEEC--CCccEEEEECCCCCCEEEChHHHcc-----CCCCCEEEEEEccCCCCCCcEEEEEEEEe
Confidence 367888843 8999999998767899998887754 35699998887652 34556777666655
No 36
>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=92.95 E-value=0.2 Score=50.41 Aligned_cols=63 Identities=27% Similarity=0.397 Sum_probs=46.5
Q ss_pred cccceEEEEeeCCCceeEEecCC-CCCceEEeccccccCCccccCCCCcEEEEEEe-CCCccceeeccccCC
Q 047168 5 TRSTGKVTWFDGAKGYGFIRPDD-GGADLFVHQKSIKSDGYRTLYENQSVEFDVQL-EADGKYQALDVTAPG 74 (258)
Q Consensus 5 ~~~~G~vk~f~~~kGfGFI~~~~-~~~dvF~H~s~l~~~~~~~l~~G~~V~F~v~~-~~~G~~~A~~V~~~~ 74 (258)
..+.|+|+.= .+||||+.+++ ..+|||+.-..+.. .-.||.|...+.. ..+++++|.-|.++.
T Consensus 15 ~~~~G~i~~~--~~gfgFv~~~~~~~~difI~~~~~~~-----a~~GD~V~v~i~~~~~~~~~~g~v~~il~ 79 (654)
T TIGR00358 15 DLVKGVVKAH--NKGFGFLRPDDDDKKDYFIPPPQMKK-----VMHGDLVEACPLSQPQRGRFEAEVERILE 79 (654)
T ss_pred CeEEEEEEEC--CCccEEEEeCCCCCCcEEEchHHhCc-----CCCCCEEEEEEeecCCCCCceEEEEEEec
Confidence 3578999964 89999999886 36899998877754 4679999988754 334545676666554
No 37
>smart00343 ZnF_C2HC zinc finger.
Probab=92.84 E-value=0.052 Score=30.71 Aligned_cols=17 Identities=71% Similarity=1.644 Sum_probs=14.6
Q ss_pred ccccCCCCCccCCCCCC
Q 047168 215 RCYNCGKSGHLARDCGA 231 (258)
Q Consensus 215 ~C~~Cg~~GH~~~~Cp~ 231 (258)
.|++|++.||++++||+
T Consensus 1 ~C~~CG~~GH~~~~C~~ 17 (26)
T smart00343 1 KCYNCGKEGHIARDCPK 17 (26)
T ss_pred CCccCCCCCcchhhCCc
Confidence 48899999999999984
No 38
>PF13917 zf-CCHC_3: Zinc knuckle
Probab=92.76 E-value=0.059 Score=34.44 Aligned_cols=18 Identities=39% Similarity=1.012 Sum_probs=16.0
Q ss_pred CccccCCCCCccCCCCCC
Q 047168 214 GRCYNCGKSGHLARDCGA 231 (258)
Q Consensus 214 ~~C~~Cg~~GH~~~~Cp~ 231 (258)
..|.+|++.||++.+||.
T Consensus 5 ~~CqkC~~~GH~tyeC~~ 22 (42)
T PF13917_consen 5 VRCQKCGQKGHWTYECPN 22 (42)
T ss_pred CcCcccCCCCcchhhCCC
Confidence 489999999999999993
No 39
>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=92.76 E-value=0.4 Score=33.55 Aligned_cols=56 Identities=20% Similarity=0.195 Sum_probs=44.0
Q ss_pred ccccceEEEEeeCCCceeEEecCCCCCceEEeccccccC----CccccCCCCcEEEEEEeCCC
Q 047168 4 LTRSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSD----GYRTLYENQSVEFDVQLEAD 62 (258)
Q Consensus 4 ~~~~~G~vk~f~~~kGfGFI~~~~~~~dvF~H~s~l~~~----~~~~l~~G~~V~F~v~~~~~ 62 (258)
.+.+.|+|...+. ||++.....+-+.|+|.+.|... ....+.+|+.|++.+..-+.
T Consensus 5 G~iv~g~V~~v~~---~g~~V~l~~~~~g~ip~~~l~~~~~~~~~~~~~~G~~v~v~v~~vd~ 64 (74)
T PF00575_consen 5 GDIVEGKVTSVED---FGVFVDLGNGIEGFIPISELSDDRIDDPSEVYKIGQTVRVKVIKVDK 64 (74)
T ss_dssp TSEEEEEEEEEET---TEEEEEESTSSEEEEEGGGSSSSEESSSHGTCETTCEEEEEEEEEET
T ss_pred CCEEEEEEEEEEC---CEEEEEECCcEEEEEEeehhcCccccccccccCCCCEEEEEEEEEEC
Confidence 4678999999975 66655555678999999999853 45678999999999887543
No 40
>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=91.57 E-value=0.67 Score=33.42 Aligned_cols=56 Identities=20% Similarity=0.088 Sum_probs=42.6
Q ss_pred ccccceEEEEeeCCCceeEEecCCCCCceEEeccccccCCc----cccCCCCcEEEEEEeCCC
Q 047168 4 LTRSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGY----RTLYENQSVEFDVQLEAD 62 (258)
Q Consensus 4 ~~~~~G~vk~f~~~kGfGFI~~~~~~~dvF~H~s~l~~~~~----~~l~~G~~V~F~v~~~~~ 62 (258)
.+.+.|+|+... -||++.....+.+.|+|.+.|....+ ..+.+|+.|++.+..-+.
T Consensus 15 G~i~~g~V~~v~---~~G~fv~l~~~~~g~v~~~el~~~~~~~~~~~~~~Gd~v~vkV~~id~ 74 (83)
T cd04461 15 GMVVHGYVRNIT---PYGVFVEFLGGLTGLAPKSYISDEFVTDPSFGFKKGQSVTAKVTSVDE 74 (83)
T ss_pred CCEEEEEEEEEe---eceEEEEcCCCCEEEEEHHHCCcccccCHHHhcCCCCEEEEEEEEEcC
Confidence 467889999886 37777766556899999999965533 247789999999877543
No 41
>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=91.31 E-value=0.84 Score=30.14 Aligned_cols=51 Identities=24% Similarity=0.328 Sum_probs=37.4
Q ss_pred cceEEEEeeCCCcee-EEecCCCCCceEEeccccccCC----ccccCCCCcEEEEEEeCC
Q 047168 7 STGKVTWFDGAKGYG-FIRPDDGGADLFVHQKSIKSDG----YRTLYENQSVEFDVQLEA 61 (258)
Q Consensus 7 ~~G~vk~f~~~kGfG-FI~~~~~~~dvF~H~s~l~~~~----~~~l~~G~~V~F~v~~~~ 61 (258)
++|+|+..+ .+| ||..+ ...+.|+|.+.+.... ...+++|+.|+..+..-+
T Consensus 1 v~g~V~~v~---~~g~~v~l~-~~~~g~~~~~~~~~~~~~~~~~~~~~G~~v~~~v~~~d 56 (65)
T cd00164 1 VTGKVVSIT---KFGVFVELE-DGVEGLVHISELSDKFVKDPSEVFKVGDEVEVKVLEVD 56 (65)
T ss_pred CEEEEEEEE---eeeEEEEec-CCCEEEEEHHHCCCccccCHhhEeCCCCEEEEEEEEEc
Confidence 468999996 344 45544 4589999999996531 245899999999988754
No 42
>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=90.76 E-value=0.66 Score=32.05 Aligned_cols=55 Identities=13% Similarity=0.064 Sum_probs=39.8
Q ss_pred cccceEEEEeeCCCceeEEecCCCCCceEEeccccccCC----ccccCCCCcEEEEEEeCCC
Q 047168 5 TRSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDG----YRTLYENQSVEFDVQLEAD 62 (258)
Q Consensus 5 ~~~~G~vk~f~~~kGfGFI~~~~~~~dvF~H~s~l~~~~----~~~l~~G~~V~F~v~~~~~ 62 (258)
+.+.|+|+...+ ||.+...++.-+-|+|.+.|.... ...+++|+.|++.+..-+.
T Consensus 2 ~~~~g~V~~v~~---~G~~V~l~~~~~gli~~s~l~~~~~~~~~~~~~~G~~i~v~v~~~d~ 60 (70)
T cd05698 2 LKTHGTIVKVKP---NGCIVSFYNNVKGFLPKSELSEAFIKDPEEHFRVGQVVKVKVLSCDP 60 (70)
T ss_pred CEEEEEEEEEec---CcEEEEECCCCEEEEEHHHcChhhcCCHHHcccCCCEEEEEEEEEcC
Confidence 357899999853 565555554589999999996432 2247899999999887544
No 43
>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=90.67 E-value=1.4 Score=31.00 Aligned_cols=61 Identities=18% Similarity=0.070 Sum_probs=43.0
Q ss_pred CccccceEEEEeeCCCceeEEecCCCCCceEEeccccccCCcc----ccCCCCcEEEEEEeCCCccc
Q 047168 3 QLTRSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGYR----TLYENQSVEFDVQLEADGKY 65 (258)
Q Consensus 3 ~~~~~~G~vk~f~~~kGfGFI~~~~~~~dvF~H~s~l~~~~~~----~l~~G~~V~F~v~~~~~G~~ 65 (258)
..+.+.|+|+..... ||.+.....+.+-|+|+|.+...-.. .+++||.|...+..-+++++
T Consensus 3 ~G~iv~G~V~~i~~~--~g~~v~l~~~~~Glvhis~~s~~~~~~~~~~~~~Gd~v~~kV~~~~~~~i 67 (72)
T cd05704 3 EGAVTLGMVTKVIPH--SGLTVQLPFGKTGLVSIFHLSDSYTENPLEGFKPGKIVRCCILSKKDGKY 67 (72)
T ss_pred CCCEEEEEEEEeeCC--cEEEEECCCCCEEEEEHHHhcCcccCCHHHhCCCCCEEEEEEEEecCCEE
Confidence 346789999997433 55555455568999999999664322 35789999988877655543
No 44
>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=90.60 E-value=0.89 Score=33.57 Aligned_cols=57 Identities=21% Similarity=0.145 Sum_probs=40.4
Q ss_pred ccccceEEEEeeCCCceeEEecCCCCCceEEecccccc-------CCccccCCCCcEEEEEEeCC
Q 047168 4 LTRSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKS-------DGYRTLYENQSVEFDVQLEA 61 (258)
Q Consensus 4 ~~~~~G~vk~f~~~kGfGFI~~~~~~~dvF~H~s~l~~-------~~~~~l~~G~~V~F~v~~~~ 61 (258)
...+.|+|+...+.-.==||...+ +.+-|+|++.+.. .--..|++||.|...+...+
T Consensus 8 G~iy~g~V~~i~~~~~GaFV~l~~-g~~Gllh~seis~~~~~~v~~~~~~~~~Gd~v~VqV~~~~ 71 (88)
T cd04453 8 GNIYLGRVKKIVPGLQAAFVDIGL-GKNGFLHLSDILPAYFKKHKKIAKLLKEGQEILVQVVKEP 71 (88)
T ss_pred CCEEEEEEEEeccCCcEEEEEeCC-CCEEEEEhHHcCchhccccCCHHHcCCCCCEEEEEEEEec
Confidence 356889999995332334556554 5899999999954 11235899999999988854
No 45
>PRK07252 hypothetical protein; Provisional
Probab=90.03 E-value=1.8 Score=33.98 Aligned_cols=57 Identities=19% Similarity=0.152 Sum_probs=43.6
Q ss_pred CCccccceEEEEeeCCCceeEEecCCCCCceEEeccccccCCc----cccCCCCcEEEEEEeCC
Q 047168 2 AQLTRSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGY----RTLYENQSVEFDVQLEA 61 (258)
Q Consensus 2 ~~~~~~~G~vk~f~~~kGfGFI~~~~~~~dvF~H~s~l~~~~~----~~l~~G~~V~F~v~~~~ 61 (258)
.....+.|+|.... -||++...+...+-|+|++.|....+ ..+..||.|+..|..-+
T Consensus 2 kvG~iv~G~V~~V~---~~G~fVei~~~~~GllhiseLs~~~~~~~~~~~~vGD~V~VkI~~iD 62 (120)
T PRK07252 2 KIGDKLKGTITGIK---PYGAFVALENGTTGLIHISEIKTGFIDNIHQLLKVGEEVLVQVVDFD 62 (120)
T ss_pred CCCCEEEEEEEEEe---CcEEEEEECCCCEEEEEHHHcCCccccChhhccCCCCEEEEEEEEEe
Confidence 34567899999985 38877766666899999999965432 34788999999988854
No 46
>PF14392 zf-CCHC_4: Zinc knuckle
Probab=89.62 E-value=0.14 Score=33.70 Aligned_cols=20 Identities=35% Similarity=0.858 Sum_probs=12.2
Q ss_pred CCCCcccccCCcccCcccCC
Q 047168 185 NNSGGCFKCGGYGHLARDCI 204 (258)
Q Consensus 185 ~~~~~C~~Cg~~GH~~~~C~ 204 (258)
..+..|+.|+..||..++||
T Consensus 29 ~lp~~C~~C~~~gH~~~~C~ 48 (49)
T PF14392_consen 29 RLPRFCFHCGRIGHSDKECP 48 (49)
T ss_pred CcChhhcCCCCcCcCHhHcC
Confidence 34456666666666666665
No 47
>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=89.42 E-value=1.6 Score=29.37 Aligned_cols=54 Identities=24% Similarity=0.267 Sum_probs=39.2
Q ss_pred cccceEEEEeeCCCceeEEecCCCCCceEEeccccccCCc----cccCCCCcEEEEEEeCC
Q 047168 5 TRSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGY----RTLYENQSVEFDVQLEA 61 (258)
Q Consensus 5 ~~~~G~vk~f~~~kGfGFI~~~~~~~dvF~H~s~l~~~~~----~~l~~G~~V~F~v~~~~ 61 (258)
..+.|+|+.... ||++...+...+.|+|.+.+..... ..++.||.|+..+..-+
T Consensus 2 ~~~~g~V~~i~~---~g~~v~i~~~~~g~l~~~~l~~~~~~~~~~~~~~Gd~v~v~v~~~~ 59 (69)
T cd05692 2 SVVEGTVTRLKP---FGAFVELGGGISGLVHISQIAHKRVKDVKDVLKEGDKVKVKVLSID 59 (69)
T ss_pred CEEEEEEEEEEe---eeEEEEECCCCEEEEEhHHcCCcccCCHHHccCCCCEEEEEEEEEC
Confidence 356789988763 6766655556899999999965422 34789999998876543
No 48
>KOG0109 consensus RNA-binding protein LARK, contains RRM and retroviral-type Zn-finger domains [RNA processing and modification; General function prediction only]
Probab=89.34 E-value=0.2 Score=45.06 Aligned_cols=21 Identities=38% Similarity=1.088 Sum_probs=14.4
Q ss_pred CccccCCCCCccCCCCCCCCC
Q 047168 214 GRCYNCGKSGHLARDCGAGGA 234 (258)
Q Consensus 214 ~~C~~Cg~~GH~~~~Cp~~~~ 234 (258)
..||+|++.||.+++||..+.
T Consensus 161 ~~cyrcGkeghwskEcP~~~~ 181 (346)
T KOG0109|consen 161 SGCYRCGKEGHWSKECPVDRT 181 (346)
T ss_pred HHheeccccccccccCCccCC
Confidence 357777777777777776553
No 49
>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=89.22 E-value=1.9 Score=30.03 Aligned_cols=57 Identities=12% Similarity=-0.142 Sum_probs=40.3
Q ss_pred CccccceEEEEeeCCCceeEEecCCCCCceEEeccccccCCc----cccCCCCcEEEEEEeCCC
Q 047168 3 QLTRSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGY----RTLYENQSVEFDVQLEAD 62 (258)
Q Consensus 3 ~~~~~~G~vk~f~~~kGfGFI~~~~~~~dvF~H~s~l~~~~~----~~l~~G~~V~F~v~~~~~ 62 (258)
..+.+.|+|+.... ||.+-..+..-+-|+|+++|..... ..+++||.|+..+..-+.
T Consensus 3 ~G~iv~g~V~~v~~---~gi~v~l~~~~~g~v~~s~l~~~~~~~~~~~~~~Gd~v~~~V~~~d~ 63 (73)
T cd05706 3 VGDILPGRVTKVND---RYVLVQLGNKVTGPSFITDALDDYSEALPYKFKKNDIVRACVLSVDV 63 (73)
T ss_pred CCCEEEEEEEEEeC---CeEEEEeCCCcEEEEEhhhccCccccccccccCCCCEEEEEEEEEeC
Confidence 45678899999843 4544444445899999999975421 237899999998877543
No 50
>PRK05054 exoribonuclease II; Provisional
Probab=89.14 E-value=0.65 Score=46.67 Aligned_cols=60 Identities=20% Similarity=0.257 Sum_probs=42.5
Q ss_pred cccceEEEEeeCCCceeEEecCCCCCceEEeccccccCCccccCCCCcEEEEEEeCCCccceeeccccC
Q 047168 5 TRSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGYRTLYENQSVEFDVQLEADGKYQALDVTAP 73 (258)
Q Consensus 5 ~~~~G~vk~f~~~kGfGFI~~~~~~~dvF~H~s~l~~~~~~~l~~G~~V~F~v~~~~~G~~~A~~V~~~ 73 (258)
..+.|+|+.= .+||||+.+++ .+|||+....+... -.||.|...+... +++.+|.-+.++
T Consensus 20 ~~~~G~~~~~--~~gfgFv~~~~-~~difI~~~~l~~a-----~~GD~V~v~i~~~-~~r~~g~v~~il 79 (644)
T PRK05054 20 PRVEGVVKAT--EKGFGFLEVDA-QKSYFIPPPQMKKV-----MHGDRIIAVIHTE-KDREIAEPEELI 79 (644)
T ss_pred CeEEEEEEEC--CCccEEEEECC-CCcEEEChHHHccC-----CCCCEEEEEEecC-CCCcEEEEEEEE
Confidence 4577999854 89999998755 46999998888653 5699998887653 233455544443
No 51
>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=89.14 E-value=0.69 Score=46.96 Aligned_cols=62 Identities=19% Similarity=0.412 Sum_probs=44.5
Q ss_pred ccceEEEEeeCCCceeEEecCC-CCCceEEeccccccCCccccCCCCcEEEEEEeCC--CccceeeccccCC
Q 047168 6 RSTGKVTWFDGAKGYGFIRPDD-GGADLFVHQKSIKSDGYRTLYENQSVEFDVQLEA--DGKYQALDVTAPG 74 (258)
Q Consensus 6 ~~~G~vk~f~~~kGfGFI~~~~-~~~dvF~H~s~l~~~~~~~l~~G~~V~F~v~~~~--~G~~~A~~V~~~~ 74 (258)
.+.|+++. ..+||||+.+++ ..+|||+....+. .+..||.|...+.... +++++|.-|.+++
T Consensus 68 ~~~G~i~~--~~~g~gFv~~~~~~~~di~I~~~~~~-----~a~~GD~Vlv~I~~~~~~~~~~eg~Vv~Il~ 132 (709)
T TIGR02063 68 LVKGTVIA--HRDGFGFLRPEDDDEDDIFIPPRQMN-----GAMHGDRVLVRITGKPDGGDRFEARVIKILE 132 (709)
T ss_pred eEEEEEEE--CCCccEEEEECCCCCCcEEEChHHhC-----cCCCCCEEEEEEecccCCCCCceEEEEEEEe
Confidence 46788875 489999999886 4579999876653 3578999999986532 3445666665554
No 52
>PRK12608 transcription termination factor Rho; Provisional
Probab=88.99 E-value=0.54 Score=44.16 Aligned_cols=51 Identities=24% Similarity=0.334 Sum_probs=41.3
Q ss_pred ccccceEEEEeeCCCceeEEecC-----CCCCceEEeccccccCCccccCCCCcEEEEEEe
Q 047168 4 LTRSTGKVTWFDGAKGYGFIRPD-----DGGADLFVHQKSIKSDGYRTLYENQSVEFDVQL 59 (258)
Q Consensus 4 ~~~~~G~vk~f~~~kGfGFI~~~-----~~~~dvF~H~s~l~~~~~~~l~~G~~V~F~v~~ 59 (258)
.....|++--.. .||||+... .+.+||||..+.|+..+ |..|+.|.-....
T Consensus 16 ~~~~~g~l~~~~--~g~gflr~~~~~~~~~~~d~yv~~~~i~~~~---l~~Gd~V~~~~r~ 71 (380)
T PRK12608 16 TEEVLGVLEILG--DGFGFLRSARRNYLPSPDDVFVPPALIRRFN---LRTGDVVEGVARP 71 (380)
T ss_pred CCcceEEEEEcC--CCceEeecCccCCCCCCCCeeeCHHHHHHhC---CCCCCEEEeccCC
Confidence 356778888664 499999985 45799999999998875 8999999987655
No 53
>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=88.91 E-value=1.3 Score=31.07 Aligned_cols=52 Identities=17% Similarity=0.079 Sum_probs=36.0
Q ss_pred cc-eEEEEeeCCCceeEEecCCCCCceEEeccccccCC----ccccCCCCcEEEEEEeC
Q 047168 7 ST-GKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDG----YRTLYENQSVEFDVQLE 60 (258)
Q Consensus 7 ~~-G~vk~f~~~kGfGFI~~~~~~~dvF~H~s~l~~~~----~~~l~~G~~V~F~v~~~ 60 (258)
+. |+|+... ..||.+.....+-+-|+|+|.|.... ...+++|+.|++.+..-
T Consensus 4 ~~~g~V~~v~--~~~G~~V~l~~gv~G~i~~s~l~~~~~~~~~~~~~vG~~v~~kV~~i 60 (71)
T cd05696 4 VDSVKVTKVE--PDLGAVFELKDGLLGFVHISHLSDDKVPSDTGPFKAGTTHKARIIGY 60 (71)
T ss_pred eeeeEEEEEc--cCceEEEEeCCCCEEEEEHHHCCcchhcCcccccCCCCEEEEEEEEE
Confidence 45 8888874 34665444433589999999995432 33488999999987653
No 54
>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=88.72 E-value=2 Score=30.15 Aligned_cols=56 Identities=18% Similarity=0.097 Sum_probs=40.4
Q ss_pred ccccceEEEEeeCCCceeEEecCCC-CCceEEeccccccCCccc----cCCCCcEEEEEEeCCC
Q 047168 4 LTRSTGKVTWFDGAKGYGFIRPDDG-GADLFVHQKSIKSDGYRT----LYENQSVEFDVQLEAD 62 (258)
Q Consensus 4 ~~~~~G~vk~f~~~kGfGFI~~~~~-~~dvF~H~s~l~~~~~~~----l~~G~~V~F~v~~~~~ 62 (258)
...+.|+|+... -||++...++ ..+-|+|++.|....+.. ++.||.|+..+..-+.
T Consensus 4 g~~~~g~V~~i~---~fG~fv~l~~~~~eGlvh~sel~~~~~~~~~~~~~~Gd~v~vkv~~vd~ 64 (73)
T cd05686 4 YQIFKGEVASVT---EYGAFVKIPGCRKQGLVHKSHMSSCRVDDPSEVVDVGEKVWVKVIGREM 64 (73)
T ss_pred CCEEEEEEEEEE---eeeEEEEECCCCeEEEEEchhhCCCcccCHhhEECCCCEEEEEEEEECC
Confidence 467889999986 3776655543 369999999997654322 5789999988776443
No 55
>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=88.54 E-value=0.83 Score=45.87 Aligned_cols=61 Identities=20% Similarity=0.244 Sum_probs=42.8
Q ss_pred ccccceEEEEeeCCCceeEEecCCCCCceEEeccccccCCccccCCCCcEEEEEEeCCCccceeeccccC
Q 047168 4 LTRSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGYRTLYENQSVEFDVQLEADGKYQALDVTAP 73 (258)
Q Consensus 4 ~~~~~G~vk~f~~~kGfGFI~~~~~~~dvF~H~s~l~~~~~~~l~~G~~V~F~v~~~~~G~~~A~~V~~~ 73 (258)
...+.|+|+.= .+||||+.+++ .+|||+.-..+... -.||.|...+.... ++.+|.-+.++
T Consensus 16 ~~~~~G~i~~~--~kGfgFv~~~~-~~difI~~~~l~~A-----~~GD~V~v~i~~~~-~r~~~~v~~iv 76 (639)
T TIGR02062 16 TPRVEGVVKAT--EKGFGFLEVDA-QKSYFIPPPQMKKV-----MHGDKIIAVIHSEK-ERESAEPEELI 76 (639)
T ss_pred CceEEEEEEEC--CCccEEEEECC-CCcEEEChHHHccC-----CCCCEEEEEEecCC-CCcEEEEEEEE
Confidence 34677999854 89999997654 57999999888654 56999988876543 33454444433
No 56
>smart00316 S1 Ribosomal protein S1-like RNA-binding domain.
Probab=88.46 E-value=1.2 Score=30.06 Aligned_cols=56 Identities=14% Similarity=0.117 Sum_probs=40.9
Q ss_pred ccccceEEEEeeCCCceeEEecCCCCCceEEeccccccCC----ccccCCCCcEEEEEEeCCC
Q 047168 4 LTRSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDG----YRTLYENQSVEFDVQLEAD 62 (258)
Q Consensus 4 ~~~~~G~vk~f~~~kGfGFI~~~~~~~dvF~H~s~l~~~~----~~~l~~G~~V~F~v~~~~~ 62 (258)
.+.+.|+|+..+. +|++-..+...+.|+|.+.+.... ...+++|+.|.+.+..-+.
T Consensus 3 G~~v~g~V~~v~~---~g~~v~i~~~~~g~l~~~~~~~~~~~~~~~~~~~G~~v~~~V~~~~~ 62 (72)
T smart00316 3 GDVVEGTVTEITP---FGAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDE 62 (72)
T ss_pred CCEEEEEEEEEEc---cEEEEEeCCCCEEEEEHHHCCccccCCHHHeecCCCEEEEEEEEEeC
Confidence 3567899999975 455544444589999999997541 2348999999999887543
No 57
>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=88.25 E-value=1.7 Score=29.94 Aligned_cols=55 Identities=9% Similarity=0.009 Sum_probs=40.5
Q ss_pred cccceEEEEeeCCCceeEEecCCCCCceEEeccccccCCc----cccCCCCcEEEEEEeCCC
Q 047168 5 TRSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGY----RTLYENQSVEFDVQLEAD 62 (258)
Q Consensus 5 ~~~~G~vk~f~~~kGfGFI~~~~~~~dvF~H~s~l~~~~~----~~l~~G~~V~F~v~~~~~ 62 (258)
+.+.|+|+... .||.+-..+.+-+-|+|.+.|....+ ..++.|+.|++.+..-+.
T Consensus 2 ~~v~g~V~~v~---~~Gv~V~l~~~v~g~i~~~~l~~~~~~~~~~~~~~Gd~i~~~V~~id~ 60 (69)
T cd05697 2 QVVKGTIRKLR---PSGIFVKLSDHIKGLVPPMHLADVRLKHPEKKFKPGLKVKCRVLSVEP 60 (69)
T ss_pred CEEEEEEEEEe---ccEEEEEecCCcEEEEEHHHCCCccccCHHHcCCCCCEEEEEEEEEEC
Confidence 35789999985 36766555555899999999965432 348899999999877543
No 58
>PRK08582 hypothetical protein; Provisional
Probab=87.93 E-value=2.7 Score=33.79 Aligned_cols=65 Identities=25% Similarity=0.293 Sum_probs=45.2
Q ss_pred cccceEEEEeeCCCceeEEecCCCCCceEEeccccccCCc----cccCCCCcEEEEEEeCC-CccceeeccccC
Q 047168 5 TRSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGY----RTLYENQSVEFDVQLEA-DGKYQALDVTAP 73 (258)
Q Consensus 5 ~~~~G~vk~f~~~kGfGFI~~~~~~~dvF~H~s~l~~~~~----~~l~~G~~V~F~v~~~~-~G~~~A~~V~~~ 73 (258)
..+.|+|+... .||++...+...+-|||++.|...-+ ..+.+||.|+..|..-+ ++++ ...+..+
T Consensus 7 ~iv~G~V~~I~---~fG~fV~L~~~~~GlVhiSels~~~v~~~~~~l~vGD~VkvkV~~id~~gkI-~LSlk~~ 76 (139)
T PRK08582 7 SKLQGKVTGIT---NFGAFVELPEGKTGLVHISEVADNYVKDINDHLKVGDEVEVKVLNVEDDGKI-GLSIKKA 76 (139)
T ss_pred CEEEEEEEEEE---CCeEEEEECCCCEEEEEeeccCcccccccccccCCCCEEEEEEEEECCCCcE-EEEEEec
Confidence 57889999874 46766555556899999999964432 35789999998887754 4543 3334333
No 59
>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=87.76 E-value=2.9 Score=28.92 Aligned_cols=56 Identities=25% Similarity=0.233 Sum_probs=40.1
Q ss_pred ccccceEEEEeeCCCceeEEecCCCCCceEEeccccccCCc-----cccCCCCcEEEEEEeCCC
Q 047168 4 LTRSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGY-----RTLYENQSVEFDVQLEAD 62 (258)
Q Consensus 4 ~~~~~G~vk~f~~~kGfGFI~~~~~~~dvF~H~s~l~~~~~-----~~l~~G~~V~F~v~~~~~ 62 (258)
.+.+.|+|+... -||+....+.+.+-|+|++.|..... ..++.||.|+..+..-+.
T Consensus 4 g~~~~g~V~~i~---~~G~fv~l~~~~~Gl~~~~~l~~~~~~~~~~~~~~~Gd~v~v~v~~id~ 64 (72)
T cd05689 4 GTRLFGKVTNLT---DYGCFVELEEGVEGLVHVSEMDWTNKNIHPSKVVSLGDEVEVMVLDIDE 64 (72)
T ss_pred CCEEEEEEEEEE---eeEEEEEcCCCCEEEEEEEeccCcccccCcccEeCCCCEEEEEEEEeeC
Confidence 456889999885 48877666556899999999963211 236789999888766543
No 60
>PRK09376 rho transcription termination factor Rho; Provisional
Probab=87.46 E-value=0.84 Score=43.24 Aligned_cols=66 Identities=26% Similarity=0.507 Sum_probs=46.6
Q ss_pred ccceEEEEeeCCCceeEEecCC-----CCCceEEeccccccCCccccCCCCcEEEEEEeCCCcc--ceeeccccCCCC
Q 047168 6 RSTGKVTWFDGAKGYGFIRPDD-----GGADLFVHQKSIKSDGYRTLYENQSVEFDVQLEADGK--YQALDVTAPGGA 76 (258)
Q Consensus 6 ~~~G~vk~f~~~kGfGFI~~~~-----~~~dvF~H~s~l~~~~~~~l~~G~~V~F~v~~~~~G~--~~A~~V~~~~g~ 76 (258)
...|++--.. .||||+...+ +.+||||-.+.|+..+ |+.|+.|+=.+....++. +..+.|..+.+.
T Consensus 50 ~~~g~le~~~--~g~gflr~~~~~y~~~~~d~yvs~~~ir~~~---lr~gd~v~g~~r~~~~~e~~~~l~~v~~vng~ 122 (416)
T PRK09376 50 FGEGVLEILP--DGFGFLRSPDANYLPGPDDIYVSPSQIRRFN---LRTGDTVEGKIRPPKEGERYFALLKVETVNGE 122 (416)
T ss_pred EEEEEEEEcC--CCCeEEeCCCcCCCCCCCCeeeCHHHHHhcC---CCCCCEEEEEeeCCCCCCCccceEEEeeeCCC
Confidence 3556666553 4999999853 4689999999998875 899999998887754331 234455555543
No 61
>PF15288 zf-CCHC_6: Zinc knuckle
Probab=87.42 E-value=0.32 Score=30.69 Aligned_cols=20 Identities=35% Similarity=0.798 Sum_probs=15.2
Q ss_pred CccccCCCCCccC--CCCCCCC
Q 047168 214 GRCYNCGKSGHLA--RDCGAGG 233 (258)
Q Consensus 214 ~~C~~Cg~~GH~~--~~Cp~~~ 233 (258)
++|.+|+..||+. +.||...
T Consensus 2 ~kC~~CG~~GH~~t~k~CP~~~ 23 (40)
T PF15288_consen 2 VKCKNCGAFGHMRTNKRCPMYC 23 (40)
T ss_pred ccccccccccccccCccCCCCC
Confidence 4788888888886 6788743
No 62
>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=86.83 E-value=2.4 Score=30.04 Aligned_cols=56 Identities=16% Similarity=0.013 Sum_probs=40.7
Q ss_pred CccccceEEEEeeCCCcee-EEecCCCCCceEEeccccccCCc-------cccCCCCcEEEEEEeCCC
Q 047168 3 QLTRSTGKVTWFDGAKGYG-FIRPDDGGADLFVHQKSIKSDGY-------RTLYENQSVEFDVQLEAD 62 (258)
Q Consensus 3 ~~~~~~G~vk~f~~~kGfG-FI~~~~~~~dvF~H~s~l~~~~~-------~~l~~G~~V~F~v~~~~~ 62 (258)
..+.+.|+|+... .|| |++.. .+-+-|+|+++|..... ..+++|+.|++.|..-+.
T Consensus 3 ~G~~V~g~V~~i~---~~G~fV~l~-~~v~G~v~~~~ls~~~~~~~~~~~~~~~~G~~v~~kVl~id~ 66 (74)
T cd05705 3 EGQLLRGYVSSVT---KQGVFFRLS-SSIVGRVLFQNVTKYFVSDPSLYNKYLPEGKLLTAKVLSVNS 66 (74)
T ss_pred CCCEEEEEEEEEe---CCcEEEEeC-CCCEEEEEHHHccCccccChhhHhcccCCCCEEEEEEEEEEC
Confidence 3467889999984 444 45544 46899999999976541 346999999999887543
No 63
>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=86.70 E-value=0.38 Score=43.42 Aligned_cols=23 Identities=30% Similarity=0.742 Sum_probs=19.5
Q ss_pred CCCCCcccccCCcccCcccCCCC
Q 047168 184 NNNSGGCFKCGGYGHLARDCITR 206 (258)
Q Consensus 184 ~~~~~~C~~Cg~~GH~~~~C~~~ 206 (258)
......||+||+.|||..+||.+
T Consensus 173 pPpgY~CyRCGqkgHwIqnCpTN 195 (427)
T COG5222 173 PPPGYVCYRCGQKGHWIQNCPTN 195 (427)
T ss_pred CCCceeEEecCCCCchhhcCCCC
Confidence 34567899999999999999876
No 64
>PRK12678 transcription termination factor Rho; Provisional
Probab=86.69 E-value=0.92 Score=45.04 Aligned_cols=52 Identities=23% Similarity=0.501 Sum_probs=41.1
Q ss_pred ccceEEEEeeCCCceeEEecC---CCCCceEEeccccccCCccccCCCCcEEEEEEeCCCc
Q 047168 6 RSTGKVTWFDGAKGYGFIRPD---DGGADLFVHQKSIKSDGYRTLYENQSVEFDVQLEADG 63 (258)
Q Consensus 6 ~~~G~vk~f~~~kGfGFI~~~---~~~~dvF~H~s~l~~~~~~~l~~G~~V~F~v~~~~~G 63 (258)
.+.|++--. .|||||... .+..||||..+.|...+ |..|+.|.=.|.....+
T Consensus 295 ~~~GiLdi~---dg~gFlR~~~y~~~~~Dvyvs~~qirr~~---Lr~Gd~v~G~vr~p~~~ 349 (672)
T PRK12678 295 PVAGILDVL---DNYAFVRTSGYLPGPNDVYVSMNQVRKNG---LRKGDAVTGAVRAPREG 349 (672)
T ss_pred EeeEEEEec---CCeeEeeCCCCCCCCCCeeeCHHHHHHcC---CCCCCEEEEeecCCCCC
Confidence 356766655 499999876 46799999999998875 89999999887765444
No 65
>KOG0314 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=86.48 E-value=1.6 Score=41.75 Aligned_cols=66 Identities=26% Similarity=0.387 Sum_probs=54.1
Q ss_pred CCcccccCCCCccccccccccCCCCCCCCCCCcccCCCCCCCCCCCCCCCCCCCCCCCCCCcccccCCcccCcccCCCC
Q 047168 128 GVVCYNCDGVGHVARECTSNRRNSNYNNNSGGCYNCGDPEHFARDCPRQQGGSNSYNNNSGGCFKCGGYGHLARDCITR 206 (258)
Q Consensus 128 ~~~C~~Cg~~GH~a~~Cp~~~~~~~~~~~~~~C~~Cg~~GH~~~~Cp~~~~~~~~~~~~~~~C~~Cg~~GH~~~~C~~~ 206 (258)
...+..++..+|..+.+.. .....|..|-.++|+...|.... .+.....|++|...|||.+.||..
T Consensus 112 ~q~~~~~~~~~~~~~~~t~--------~~~~~~~~~~~~~~~iq~~~~~g-----~Pppsy~c~rc~~~g~wikacptv 177 (448)
T KOG0314|consen 112 IQMNGRMGGRGFGMRRQTP--------PPGYVCHRCNSPGHFIQHCSTNG-----SPPPSYKCVKCPTPGPWIKACPTV 177 (448)
T ss_pred hhhccccccCCcccccCCC--------cccceeeecccCccccccccccC-----CCCCCcceecCCCCCccceecccc
Confidence 4578889999999888853 44578999999999999888763 345678999999999999999876
No 66
>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=86.12 E-value=2.8 Score=28.32 Aligned_cols=53 Identities=21% Similarity=0.182 Sum_probs=39.8
Q ss_pred ccceEEEEeeCCCceeEEecCCCCCceEEeccccccCCc----cccCCCCcEEEEEEeCC
Q 047168 6 RSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGY----RTLYENQSVEFDVQLEA 61 (258)
Q Consensus 6 ~~~G~vk~f~~~kGfGFI~~~~~~~dvF~H~s~l~~~~~----~~l~~G~~V~F~v~~~~ 61 (258)
.+.|+|..... ||++.......+-|+|++.|...-+ ..++.|+.|...+...+
T Consensus 3 ~~~g~V~~v~~---~G~~v~l~~~~~g~l~~~~l~~~~~~~~~~~~~~Gd~v~v~v~~~d 59 (68)
T cd04472 3 IYEGKVVKIKD---FGAFVEILPGKDGLVHISELSDERVEKVEDVLKVGDEVKVKVIEVD 59 (68)
T ss_pred EEEEEEEEEEE---eEEEEEeCCCCEEEEEhHHcCCccccCHHHccCCCCEEEEEEEEEC
Confidence 46788888864 8888776556899999999965432 23688999998877644
No 67
>PF14392 zf-CCHC_4: Zinc knuckle
Probab=85.94 E-value=0.31 Score=32.00 Aligned_cols=19 Identities=32% Similarity=0.891 Sum_probs=11.0
Q ss_pred CCCCcccCCCCCCCCCCCC
Q 047168 156 NSGGCYNCGDPEHFARDCP 174 (258)
Q Consensus 156 ~~~~C~~Cg~~GH~~~~Cp 174 (258)
.+..|+.|+..||..++||
T Consensus 30 lp~~C~~C~~~gH~~~~C~ 48 (49)
T PF14392_consen 30 LPRFCFHCGRIGHSDKECP 48 (49)
T ss_pred cChhhcCCCCcCcCHhHcC
Confidence 3455666666666666554
No 68
>COG1158 Rho Transcription termination factor [Transcription]
Probab=85.36 E-value=0.8 Score=42.40 Aligned_cols=68 Identities=28% Similarity=0.518 Sum_probs=47.7
Q ss_pred eEEEEeeCCCceeEEecCC-----CCCceEEeccccccCCccccCCCCcEEEEEEeCCCcc--ceeeccccCCCCcccCC
Q 047168 9 GKVTWFDGAKGYGFIRPDD-----GGADLFVHQKSIKSDGYRTLYENQSVEFDVQLEADGK--YQALDVTAPGGAPVHSS 81 (258)
Q Consensus 9 G~vk~f~~~kGfGFI~~~~-----~~~dvF~H~s~l~~~~~~~l~~G~~V~F~v~~~~~G~--~~A~~V~~~~g~~~~~s 81 (258)
|++--. ..||||+.+.+ +.+||||--|.|...+ |..||.|+=.|.....|. ..-+.|..+.+.+....
T Consensus 56 GvLeil--~dGfGFLR~~~~~yl~~~~DiYvSpSQIRrf~---LrtGD~v~G~vR~Pke~Ery~aLl~ve~vN~~~pe~~ 130 (422)
T COG1158 56 GVLEIL--PDGFGFLRSADSSYLPGPDDIYVSPSQIRRFN---LRTGDTVEGKVRPPKEGERYFALLKVEAVNGDDPEKA 130 (422)
T ss_pred eEEEec--cCCcceeecCccccCCCCCceEECHHHHhhcc---CccCCEEeeeecCCCcccceeeeEEEeecCCCCHHHh
Confidence 444444 48999998775 5699999999998774 889999998888776553 22345555555443333
No 69
>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=84.95 E-value=3.2 Score=28.59 Aligned_cols=54 Identities=22% Similarity=0.204 Sum_probs=39.8
Q ss_pred ccceEEEEeeCCCceeEEecCCCCCceEEeccccccCCc----cccCCCCcEEEEEEeCCC
Q 047168 6 RSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGY----RTLYENQSVEFDVQLEAD 62 (258)
Q Consensus 6 ~~~G~vk~f~~~kGfGFI~~~~~~~dvF~H~s~l~~~~~----~~l~~G~~V~F~v~~~~~ 62 (258)
.+.|+|+... .+|++...+..-+-|+|.+.+....+ ..+++||.|++.+..-+.
T Consensus 3 ~v~g~V~~v~---~~g~~v~l~~~~~g~i~~~~~~~~~~~~~~~~~~~Gd~v~~~v~~~d~ 60 (73)
T cd05691 3 IVTGKVTEVD---AKGATVKLGDGVEGFLRAAELSRDRVEDATERFKVGDEVEAKITNVDR 60 (73)
T ss_pred EEEEEEEEEE---CCeEEEEeCCCCEEEEEHHHCCCccccCHHHccCCCCEEEEEEEEEeC
Confidence 4679999985 46666555555899999999876433 236899999999887554
No 70
>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=84.93 E-value=2.9 Score=28.65 Aligned_cols=54 Identities=15% Similarity=0.053 Sum_probs=38.2
Q ss_pred cccceEEEEeeCCCceeEEecCCCCCceEEeccccccCCcc----ccCCCCcEEEEEEeCC
Q 047168 5 TRSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGYR----TLYENQSVEFDVQLEA 61 (258)
Q Consensus 5 ~~~~G~vk~f~~~kGfGFI~~~~~~~dvF~H~s~l~~~~~~----~l~~G~~V~F~v~~~~ 61 (258)
..+.|+|+... .||.+......-+-|+|++.|...... .+.+||.|+..+..-+
T Consensus 2 ~~v~g~V~~v~---~~Gv~V~l~~~~~G~v~~s~l~~~~~~~~~~~~~~Gd~v~~~v~~~d 59 (68)
T cd05707 2 DVVRGFVKNIA---NNGVFVTLGRGVDARVRVSELSDSYLKDWKKRFKVGQLVKGKIVSID 59 (68)
T ss_pred CEEEEEEEEEE---CccEEEEeCCCCEEEEEHHHCCchhhcCHhhccCCCCEEEEEEEEEe
Confidence 35789999985 355544444458999999999654322 3789999999877654
No 71
>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=84.71 E-value=1.8 Score=29.65 Aligned_cols=53 Identities=19% Similarity=0.158 Sum_probs=37.6
Q ss_pred cccceEEEEeeCCCceeEEecCCCCCceEEeccccccCCcc--ccCCCCcEEEEEEeCC
Q 047168 5 TRSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGYR--TLYENQSVEFDVQLEA 61 (258)
Q Consensus 5 ~~~~G~vk~f~~~kGfGFI~~~~~~~dvF~H~s~l~~~~~~--~l~~G~~V~F~v~~~~ 61 (258)
+.+.|+|+.+++ +|++... .+-+.|+|.+.+...... ...+|+.+++.+..-+
T Consensus 2 ~iv~g~V~~v~~---~G~~v~l-~g~~gfip~s~~~~~~~~~~~~~vG~~i~~~i~~vd 56 (67)
T cd04465 2 EIVEGKVTEKVK---GGLIVDI-EGVRAFLPASQVDLRPVEDLDEYVGKELKFKIIEID 56 (67)
T ss_pred CEEEEEEEEEEC---CeEEEEE-CCEEEEEEHHHCCCcccCChHHhCCCEEEEEEEEEe
Confidence 346899999963 5666555 458999999999754322 1247999999887754
No 72
>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=84.63 E-value=3.8 Score=29.11 Aligned_cols=55 Identities=20% Similarity=0.120 Sum_probs=41.2
Q ss_pred CccccceEEEEeeCCCceeEEecCC-CCCceEEeccccccCCccccCCCCcEEEEEEeCCC
Q 047168 3 QLTRSTGKVTWFDGAKGYGFIRPDD-GGADLFVHQKSIKSDGYRTLYENQSVEFDVQLEAD 62 (258)
Q Consensus 3 ~~~~~~G~vk~f~~~kGfGFI~~~~-~~~dvF~H~s~l~~~~~~~l~~G~~V~F~v~~~~~ 62 (258)
..+.+.|+|+... -||++.... .+-+-|+|.+++... ..+.+|+.|...+..-++
T Consensus 4 ~G~~v~g~V~si~---d~G~~v~~g~~gv~Gfl~~~~~~~~--~~~~~Gq~v~~~V~~vd~ 59 (74)
T cd05694 4 EGMVLSGCVSSVE---DHGYILDIGIPGTTGFLPKKDAGNF--SKLKVGQLLLCVVEKVKD 59 (74)
T ss_pred CCCEEEEEEEEEe---CCEEEEEeCCCCcEEEEEHHHCCcc--cccCCCCEEEEEEEEEEC
Confidence 3456889999985 567655443 346899999999765 569999999999875443
No 73
>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=84.32 E-value=4.4 Score=28.77 Aligned_cols=50 Identities=16% Similarity=0.100 Sum_probs=39.0
Q ss_pred ccccceEEEEeeCCCceeEEecCCCCCceEEeccccccCCccccCCCCcEEEEEEeC
Q 047168 4 LTRSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGYRTLYENQSVEFDVQLE 60 (258)
Q Consensus 4 ~~~~~G~vk~f~~~kGfGFI~~~~~~~dvF~H~s~l~~~~~~~l~~G~~V~F~v~~~ 60 (258)
.+.+.|+|.... -||+...-+...+-|+|.+.+.. .++.||.|...+..-
T Consensus 17 G~~~~g~V~~i~---~~G~fV~l~~~~~Glv~~se~~~----~~~iGd~v~v~I~~i 66 (77)
T cd04473 17 GKLYKGKVNGVA---KYGVFVDLNDHVRGLIHRSNLLR----DYEVGDEVIVQVTDI 66 (77)
T ss_pred CCEEEEEEEeEe---cceEEEEECCCcEEEEEchhccC----cCCCCCEEEEEEEEE
Confidence 356889998874 47777666666899999999853 489999999887664
No 74
>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=83.07 E-value=4.3 Score=27.63 Aligned_cols=53 Identities=26% Similarity=0.263 Sum_probs=38.4
Q ss_pred ccceEEEEeeCCCceeEEecCCCCCceEEecccccc-CC----ccccCCCCcEEEEEEeCC
Q 047168 6 RSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKS-DG----YRTLYENQSVEFDVQLEA 61 (258)
Q Consensus 6 ~~~G~vk~f~~~kGfGFI~~~~~~~dvF~H~s~l~~-~~----~~~l~~G~~V~F~v~~~~ 61 (258)
.+.|+|+... -||+....+...+-|+|++.|.. .. ...++.||.|+..+..-+
T Consensus 3 ~~~g~V~~i~---~~G~fv~l~~~~~Glv~~~~l~~~~~~~~~~~~~~~G~~v~v~v~~id 60 (69)
T cd05690 3 VVSGKIKSIT---DFGIFVGLDGGIDGLVHISDISWTQRVRHPSEIYKKGQEVEAVVLNID 60 (69)
T ss_pred EEEEEEEEEE---eeeEEEEeCCCCEEEEEHHHCCCccccCChhhEECCCCEEEEEEEEEE
Confidence 5678888874 58777666556899999999963 11 124688999998876643
No 75
>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=82.49 E-value=0.86 Score=41.20 Aligned_cols=23 Identities=43% Similarity=1.063 Sum_probs=17.3
Q ss_pred CCCCcccccCCCCcccccccccc
Q 047168 126 PGGVVCYNCDGVGHVARECTSNR 148 (258)
Q Consensus 126 ~~~~~C~~Cg~~GH~a~~Cp~~~ 148 (258)
..+..||.||+.|||..+||.+.
T Consensus 174 PpgY~CyRCGqkgHwIqnCpTN~ 196 (427)
T COG5222 174 PPGYVCYRCGQKGHWIQNCPTNQ 196 (427)
T ss_pred CCceeEEecCCCCchhhcCCCCC
Confidence 44667888888888888888744
No 76
>PF15288 zf-CCHC_6: Zinc knuckle
Probab=82.01 E-value=0.84 Score=28.79 Aligned_cols=19 Identities=37% Similarity=0.850 Sum_probs=16.3
Q ss_pred CccccCCCCCccC--CCCCCC
Q 047168 238 GSCFNCGKPGHFA--RECTKV 256 (258)
Q Consensus 238 ~~C~~Cg~~GH~~--~~Cp~~ 256 (258)
+.|.+|+..||+. +.||..
T Consensus 2 ~kC~~CG~~GH~~t~k~CP~~ 22 (40)
T PF15288_consen 2 VKCKNCGAFGHMRTNKRCPMY 22 (40)
T ss_pred ccccccccccccccCccCCCC
Confidence 4699999999998 779864
No 77
>KOG0314 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=80.76 E-value=3 Score=39.97 Aligned_cols=69 Identities=20% Similarity=0.319 Sum_probs=54.8
Q ss_pred CCCCCcccCCCCCCCCCCCCCCCCCCCCCCCCCCcccccCCcccCcccCCCCCCCCCCCCccccCCCCCccCCCCCCCC
Q 047168 155 NNSGGCYNCGDPEHFARDCPRQQGGSNSYNNNSGGCFKCGGYGHLARDCITRGSGGGGGGRCYNCGKSGHLARDCGAGG 233 (258)
Q Consensus 155 ~~~~~C~~Cg~~GH~~~~Cp~~~~~~~~~~~~~~~C~~Cg~~GH~~~~C~~~~~~~~~~~~C~~Cg~~GH~~~~Cp~~~ 233 (258)
+....+..++..+|..+.+... ...+|..|...+|+...|...... -....|++|...||....||...
T Consensus 110 p~~q~~~~~~~~~~~~~~~t~~---------~~~~~~~~~~~~~~iq~~~~~g~P-ppsy~c~rc~~~g~wikacptv~ 178 (448)
T KOG0314|consen 110 PLIQMNGRMGGRGFGMRRQTPP---------PGYVCHRCNSPGHFIQHCSTNGSP-PPSYKCVKCPTPGPWIKACPTVS 178 (448)
T ss_pred chhhhccccccCCcccccCCCc---------ccceeeecccCccccccccccCCC-CCCcceecCCCCCccceeccccC
Confidence 3445799999999999988554 368999999999999999876331 12347999999999999999854
No 78
>PF14787 zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB: 1CL4_A 1DSV_A.
Probab=80.70 E-value=0.86 Score=27.99 Aligned_cols=19 Identities=37% Similarity=0.770 Sum_probs=9.4
Q ss_pred CcccccCCcccCcccCCCC
Q 047168 188 GGCFKCGGYGHLARDCITR 206 (258)
Q Consensus 188 ~~C~~Cg~~GH~~~~C~~~ 206 (258)
..|++|++--|++.+|-..
T Consensus 3 ~~CprC~kg~Hwa~~C~sk 21 (36)
T PF14787_consen 3 GLCPRCGKGFHWASECRSK 21 (36)
T ss_dssp -C-TTTSSSCS-TTT---T
T ss_pred ccCcccCCCcchhhhhhhh
Confidence 3577777777777777554
No 79
>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=80.57 E-value=5.9 Score=28.00 Aligned_cols=55 Identities=24% Similarity=0.299 Sum_probs=38.6
Q ss_pred ccceEEEEeeCCCceeEEecCC---CCCceEEeccccccCCc-----cccCCCCcEEEEEEeCCCc
Q 047168 6 RSTGKVTWFDGAKGYGFIRPDD---GGADLFVHQKSIKSDGY-----RTLYENQSVEFDVQLEADG 63 (258)
Q Consensus 6 ~~~G~vk~f~~~kGfGFI~~~~---~~~dvF~H~s~l~~~~~-----~~l~~G~~V~F~v~~~~~G 63 (258)
.+.|+|+... -||+....+ .+.+-|+|++.|...-+ ..++.|+.|...+...+++
T Consensus 3 ~~~g~V~~v~---~~G~fv~l~~~~~~~~gll~~s~l~~~~~~~~~~~~~~~Gd~v~v~v~~vd~~ 65 (79)
T cd05684 3 IYKGKVTSIM---DFGCFVQLEGLKGRKEGLVHISQLSFEGRVANPSDVVKRGQKVKVKVISIQNG 65 (79)
T ss_pred EEEEEEEEEE---eeeEEEEEeCCCCCcEEEEEhHhccCCCCcCChhheeCCCCEEEEEEEEEeCC
Confidence 4678888885 367665444 25799999999965432 2458999998887775544
No 80
>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=79.17 E-value=5.2 Score=28.18 Aligned_cols=53 Identities=13% Similarity=0.060 Sum_probs=38.2
Q ss_pred ccceEEEEeeCCCceeEEecCCCCCceEEeccccccC------CccccCCCCcEEEEEEeCC
Q 047168 6 RSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSD------GYRTLYENQSVEFDVQLEA 61 (258)
Q Consensus 6 ~~~G~vk~f~~~kGfGFI~~~~~~~dvF~H~s~l~~~------~~~~l~~G~~V~F~v~~~~ 61 (258)
.+.|+|+... ...=||+..+ +-+-|+|+++|... ....+++|+.|++.+..-+
T Consensus 3 ~V~g~V~~i~--~~g~~V~l~~-~i~G~i~~~~ls~~~~~~~~~~~~~~vG~~v~~kV~~id 61 (73)
T cd05703 3 EVTGFVNNVS--KEFVWLTISP-DVKGRIPLLDLSDDVSVLEHPEKKFPIGQALKAKVVGVD 61 (73)
T ss_pred EEEEEEEEEe--CCEEEEEeCC-CcEEEEEHHHcCCccccccCHHHhCCCCCEEEEEEEEEe
Confidence 4679999984 3334566554 58999999999643 1334899999999987643
No 81
>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=79.02 E-value=8.6 Score=26.65 Aligned_cols=55 Identities=7% Similarity=-0.084 Sum_probs=39.9
Q ss_pred ccccceEEEEeeCCCceeEEecCC--CCCceEEeccccccCCc----cccCCCCcEEEEEEeCC
Q 047168 4 LTRSTGKVTWFDGAKGYGFIRPDD--GGADLFVHQKSIKSDGY----RTLYENQSVEFDVQLEA 61 (258)
Q Consensus 4 ~~~~~G~vk~f~~~kGfGFI~~~~--~~~dvF~H~s~l~~~~~----~~l~~G~~V~F~v~~~~ 61 (258)
...+.|+|+... .||++...+ .+.+-|+|.+.|...-+ ..+..||.|+..+..-+
T Consensus 4 G~~~~g~V~~v~---~~g~~v~l~~~~~~~gll~~s~l~~~~~~~~~~~~~~Gd~v~vkv~~~d 64 (76)
T cd04452 4 GELVVVTVKSIA---DMGAYVSLLEYGNIEGMILLSELSRRRIRSIRKLVKVGRKEVVKVIRVD 64 (76)
T ss_pred CCEEEEEEEEEE---ccEEEEEEcCCCCeEEEEEhHHcCCcccCCHHHeeCCCCEEEEEEEEEE
Confidence 457889999884 477765443 24799999999976533 23689999998877644
No 82
>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=78.58 E-value=7.2 Score=26.93 Aligned_cols=55 Identities=11% Similarity=0.001 Sum_probs=38.5
Q ss_pred cccceEEEEeeCCCceeEEecCCCCCceEEeccccccC--C----ccccCCCCcEEEEEEeCCC
Q 047168 5 TRSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSD--G----YRTLYENQSVEFDVQLEAD 62 (258)
Q Consensus 5 ~~~~G~vk~f~~~kGfGFI~~~~~~~dvF~H~s~l~~~--~----~~~l~~G~~V~F~v~~~~~ 62 (258)
+.+.|+|+..... .-|+..+ .+-+-|+|++++... . ...+.+||.|+..+..-++
T Consensus 2 ~iV~g~V~~i~~~--gi~v~l~-~~i~g~i~~~~i~~~~~~~~~~~~~~~~Gd~i~~kVl~~d~ 62 (70)
T cd05702 2 DLVKAKVKSVKPT--QLNVQLA-DNVHGRIHVSEVFDEWPDGKNPLSKFKIGQKIKARVIGGHD 62 (70)
T ss_pred CEEEEEEEEEECC--cEEEEeC-CCcEEEEEHHHhccccccccChhHhCCCCCEEEEEEEEEeC
Confidence 3568999998542 3445554 458999999999644 1 3447899999988876544
No 83
>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=77.93 E-value=7.3 Score=26.67 Aligned_cols=53 Identities=13% Similarity=0.024 Sum_probs=38.7
Q ss_pred cccceEEEEeeCCCceeEEecCCCCCceEEeccccccCC----ccccCCCCcEEEEEEeC
Q 047168 5 TRSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDG----YRTLYENQSVEFDVQLE 60 (258)
Q Consensus 5 ~~~~G~vk~f~~~kGfGFI~~~~~~~dvF~H~s~l~~~~----~~~l~~G~~V~F~v~~~ 60 (258)
..++|+|+.... .+-||... ...+-|+|.+.+.... ...+++||.|++.+..-
T Consensus 2 ~iv~g~V~~i~~--~~~~v~l~-~~~~g~l~~~e~~~~~~~~~~~~~~~Gd~i~~~i~~~ 58 (70)
T cd05687 2 DIVKGTVVSVDD--DEVLVDIG-YKSEGIIPISEFSDDPIENGEDEVKVGDEVEVYVLRV 58 (70)
T ss_pred CEEEEEEEEEeC--CEEEEEeC-CCceEEEEHHHhCccccCCHhHcCCCCCEEEEEEEEE
Confidence 357899999864 35566654 3579999999996542 13478999999998774
No 84
>PF14787 zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB: 1CL4_A 1DSV_A.
Probab=77.90 E-value=1.3 Score=27.27 Aligned_cols=18 Identities=44% Similarity=0.842 Sum_probs=10.7
Q ss_pred ccccCCCCCccCCCCCCC
Q 047168 239 SCFNCGKPGHFARECTKV 256 (258)
Q Consensus 239 ~C~~Cg~~GH~~~~Cp~~ 256 (258)
.|.+|++.-|++.||-.+
T Consensus 4 ~CprC~kg~Hwa~~C~sk 21 (36)
T PF14787_consen 4 LCPRCGKGFHWASECRSK 21 (36)
T ss_dssp C-TTTSSSCS-TTT---T
T ss_pred cCcccCCCcchhhhhhhh
Confidence 588888888888888644
No 85
>TIGR00767 rho transcription termination factor Rho. Members of this family differ in the specificity of RNA binding.
Probab=77.89 E-value=3 Score=39.63 Aligned_cols=50 Identities=22% Similarity=0.478 Sum_probs=39.3
Q ss_pred cceEEEEeeCCCceeEEecC-----CCCCceEEeccccccCCccccCCCCcEEEEEEeCC
Q 047168 7 STGKVTWFDGAKGYGFIRPD-----DGGADLFVHQKSIKSDGYRTLYENQSVEFDVQLEA 61 (258)
Q Consensus 7 ~~G~vk~f~~~kGfGFI~~~-----~~~~dvF~H~s~l~~~~~~~l~~G~~V~F~v~~~~ 61 (258)
..|++--. ..||||+... .+.+||||-.+.|+..+ |+.|+.|+=.+....
T Consensus 51 ~~g~le~~--~~g~gflr~~~~~~~~~~~d~yvs~~~i~~~~---lr~gd~v~g~~R~~~ 105 (415)
T TIGR00767 51 GEGVLEIL--PDGFGFLRSPDSSYLPGPDDIYVSPSQIRRFN---LRTGDTIEGQIRSPK 105 (415)
T ss_pred EEEEEEEc--CCCCeEEeCCCcCCCCCCCCeeeCHHHHHhcC---CCCCCEEEEEEeccc
Confidence 55666644 3599999985 36799999999998875 899999998876643
No 86
>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=76.37 E-value=10 Score=26.68 Aligned_cols=54 Identities=15% Similarity=0.174 Sum_probs=37.6
Q ss_pred cccceEEEEeeCCCceeEEecCCC-CCceEEeccccccCC---------------ccccCCCCcEEEEEEeCC
Q 047168 5 TRSTGKVTWFDGAKGYGFIRPDDG-GADLFVHQKSIKSDG---------------YRTLYENQSVEFDVQLEA 61 (258)
Q Consensus 5 ~~~~G~vk~f~~~kGfGFI~~~~~-~~dvF~H~s~l~~~~---------------~~~l~~G~~V~F~v~~~~ 61 (258)
..+.|+|+... -||++..... +.+-|+|++++.... ...++.|+.|+..+...+
T Consensus 3 ~~~~g~V~~v~---~~G~fv~l~~~~~~G~v~~~~l~~~~~~~d~~~~~~~~~~~~~~~~~gd~v~v~v~~vd 72 (83)
T cd04471 3 EEFDGVISGVT---SFGLFVELDNLTVEGLVHVSTLGDDYYEFDEENHALVGERTGKVFRLGDKVKVRVVRVD 72 (83)
T ss_pred CEEEEEEEeEE---eeeEEEEecCCCEEEEEEEEecCCCcEEEcccceEEEeccCCCEEcCCCEEEEEEEEec
Confidence 45678888885 3777766554 578899999986432 135678888887776654
No 87
>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=76.16 E-value=7.1 Score=29.06 Aligned_cols=52 Identities=19% Similarity=0.135 Sum_probs=36.9
Q ss_pred ccceEEEEeeCCCceeEEecCCCCCceEEeccccccCCc---------------cccCCCCcEEEEEEeCC
Q 047168 6 RSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGY---------------RTLYENQSVEFDVQLEA 61 (258)
Q Consensus 6 ~~~G~vk~f~~~kGfGFI~~~~~~~dvF~H~s~l~~~~~---------------~~l~~G~~V~F~v~~~~ 61 (258)
.+.|+|+..+. ||++...+. .+.|+|+++|....+ ..++.|+.|...+..-+
T Consensus 2 vv~g~V~~i~~---~GifV~l~~-v~G~v~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~Gd~v~vkI~~vd 68 (99)
T cd04460 2 VVEGEVVEVVD---FGAFVRIGP-VDGLLHISQIMDDYISYDPKNKRLIGEETKRVLKVGDVVRARIVAVS 68 (99)
T ss_pred EEEEEEEEEEe---ccEEEEEcC-eEEEEEEEEccCCceEechhheeecccCcCCEECCCCEEEEEEEEEe
Confidence 36788888853 565554453 789999999865543 34688999998887654
No 88
>COG2996 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only]
Probab=75.79 E-value=8.9 Score=34.40 Aligned_cols=62 Identities=15% Similarity=0.300 Sum_probs=46.8
Q ss_pred cccceEEEEeeCCCcee-EEecCCCCCceEEeccccccCCccccCCCCcEEEEEEeCCCccceeecccc
Q 047168 5 TRSTGKVTWFDGAKGYG-FIRPDDGGADLFVHQKSIKSDGYRTLYENQSVEFDVQLEADGKYQALDVTA 72 (258)
Q Consensus 5 ~~~~G~vk~f~~~kGfG-FI~~~~~~~dvF~H~s~l~~~~~~~l~~G~~V~F~v~~~~~G~~~A~~V~~ 72 (258)
...+..|+.++ .|| |+..+..++.||+|.+..... .+.+|+.|++-+..+.++++.|+.-++
T Consensus 7 ~~~~l~V~~~~---~~g~fL~~~~~~~~ilL~k~~~~~~---e~evGdev~vFiY~D~~~rl~aTt~~p 69 (287)
T COG2996 7 QINSLEVVEFS---DFGYFLDAGEDGTTILLPKSEPEED---ELEVGDEVTVFIYVDSEDRLIATTREP 69 (287)
T ss_pred ceEEEEEEEee---ceeEEEecCCCceEEeccccCCcCC---ccccCcEEEEEEEECCCCceeheeecc
Confidence 45677777774 455 555555556999999988554 589999999999999998888876443
No 89
>PF11604 CusF_Ec: Copper binding periplasmic protein CusF; InterPro: IPR021647 CusF is a periplasmic protein involved in copper and silver resistance in Escherichia coil. CusF forms a five-stranded beta-barrel OB fold. Cu(I) binds to H36, M47 and M49 which are conserved residues in the protein []. ; PDB: 2L55_A 2VB3_X 1ZEQ_X 2QCP_X 3E6Z_X 2VB2_X.
Probab=75.72 E-value=15 Score=25.82 Aligned_cols=61 Identities=18% Similarity=0.152 Sum_probs=32.1
Q ss_pred eEEEEeeCCCceeEEecCCCCC------ceEEeccccccCCccccCCCCcEEEEEEeCCCccceeeccc
Q 047168 9 GKVTWFDGAKGYGFIRPDDGGA------DLFVHQKSIKSDGYRTLYENQSVEFDVQLEADGKYQALDVT 71 (258)
Q Consensus 9 G~vk~f~~~kGfGFI~~~~~~~------dvF~H~s~l~~~~~~~l~~G~~V~F~v~~~~~G~~~A~~V~ 71 (258)
|+|+..+...+-=-|+-+.-.+ ---|.+. ....+..|++|+.|.|.++..+.+.+.-+.|.
T Consensus 1 G~V~~vd~~~~~iti~H~pIp~l~wpaMTM~F~v~--~~~~l~~l~~Gd~V~F~~~~~~~~~~~I~~i~ 67 (70)
T PF11604_consen 1 GVVKSVDPEAGTITISHEPIPELGWPAMTMDFPVA--DPVDLAGLKPGDKVRFTFERTDDGSYVITAIE 67 (70)
T ss_dssp EEEEEEETTTTEEEEEE--BCCCTB-SEEEEEE----TTSEESS-STT-EEEEEEEEETTCEEEEEEEE
T ss_pred CEEEEEecCCCEEEEecCccccCCCCCeEEEEEcC--ChhhhhcCCCCCEEEEEEEECCCCcEEEEEEE
Confidence 5677776655554444332111 1112221 12234569999999999999888745555443
No 90
>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=75.65 E-value=9.7 Score=25.37 Aligned_cols=53 Identities=17% Similarity=0.062 Sum_probs=38.0
Q ss_pred ccceEEEEeeCCCceeEEecCCCCCceEEeccccccCCc----cccCCCCcEEEEEEeCC
Q 047168 6 RSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGY----RTLYENQSVEFDVQLEA 61 (258)
Q Consensus 6 ~~~G~vk~f~~~kGfGFI~~~~~~~dvF~H~s~l~~~~~----~~l~~G~~V~F~v~~~~ 61 (258)
.+.|+|+.... ||+........+-|+|.+.+....+ ..++.||.|+..+..-+
T Consensus 3 ~~~g~V~~i~~---~G~fv~l~~~~~g~~~~~~l~~~~~~~~~~~~~~Gd~v~v~i~~vd 59 (68)
T cd05685 3 VLEGVVTNVTD---FGAFVDIGVKQDGLIHISKMADRFVSHPSDVVSVGDIVEVKVISID 59 (68)
T ss_pred EEEEEEEEEec---ccEEEEcCCCCEEEEEHHHCCCccccCHHHhcCCCCEEEEEEEEEE
Confidence 57789988853 5655544555899999999965432 13689999998877654
No 91
>PF05606 DUF777: Borrelia burgdorferi protein of unknown function (DUF777); InterPro: IPR008495 This family consists of several hypothetical proteins of unknown function, found in Borrelia burgdorferi and Borrelia garinii.
Probab=73.68 E-value=4.4 Score=33.58 Aligned_cols=45 Identities=22% Similarity=0.267 Sum_probs=40.3
Q ss_pred ceEEEEeeCCCceeEEecCCCCCceEEeccccccCCccccCCCCcEE
Q 047168 8 TGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGYRTLYENQSVE 54 (258)
Q Consensus 8 ~G~vk~f~~~kGfGFI~~~~~~~dvF~H~s~l~~~~~~~l~~G~~V~ 54 (258)
-|+||.|+.+.--|.++.++- +|+=+|-..|..-.|. |.+||.|.
T Consensus 37 IG~iK~F~~~tQe~iVti~e~-e~LeI~T~nISN~~le-Ls~~D~Vl 81 (181)
T PF05606_consen 37 IGTIKSFKFQTQEGIVTIPEY-EDLEIHTKNISNINLE-LSKGDEVL 81 (181)
T ss_pred EeeeeecccccceEEEEeecc-cCceEEeeecccceeE-ecCCCEEE
Confidence 599999999999999998875 8999999999888765 99999986
No 92
>PRK08059 general stress protein 13; Validated
Probab=73.41 E-value=11 Score=29.38 Aligned_cols=55 Identities=25% Similarity=0.157 Sum_probs=40.8
Q ss_pred ccccceEEEEeeCCCceeEEecCCCCCceEEeccccccCCc----cccCCCCcEEEEEEeCC
Q 047168 4 LTRSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGY----RTLYENQSVEFDVQLEA 61 (258)
Q Consensus 4 ~~~~~G~vk~f~~~kGfGFI~~~~~~~dvF~H~s~l~~~~~----~~l~~G~~V~F~v~~~~ 61 (258)
...+.|+|..... ||++...+...+-|+|++.|...-. ..+..|+.|+..|..-+
T Consensus 8 G~iv~G~V~~i~~---~G~fV~i~~~~~Gli~~sel~~~~~~~~~~~~~vGD~I~vkI~~id 66 (123)
T PRK08059 8 GSVVTGKVTGIQP---YGAFVALDEETQGLVHISEITHGFVKDIHDFLSVGDEVKVKVLSVD 66 (123)
T ss_pred CCEEEEEEEEEec---ceEEEEECCCCEEEEEHHHCCcccccCHHHcCCCCCEEEEEEEEEE
Confidence 3578899998853 7776666666899999999954322 24689999999888753
No 93
>PRK09838 periplasmic copper-binding protein; Provisional
Probab=73.35 E-value=16 Score=28.53 Aligned_cols=64 Identities=13% Similarity=0.035 Sum_probs=39.4
Q ss_pred ccceEEEEeeCCCceeEEecCCCC------CceEEeccccccCCccccCCCCcEEEEEEeCCCccceeecccc
Q 047168 6 RSTGKVTWFDGAKGYGFIRPDDGG------ADLFVHQKSIKSDGYRTLYENQSVEFDVQLEADGKYQALDVTA 72 (258)
Q Consensus 6 ~~~G~vk~f~~~kGfGFI~~~~~~------~dvF~H~s~l~~~~~~~l~~G~~V~F~v~~~~~G~~~A~~V~~ 72 (258)
..+|+|+.+|.+.+-=.|+-..-. .---|-.. ....+..|++|+.|.|+++....+ +..+.|+.
T Consensus 44 ~~~G~V~~vd~~~~~iti~H~pIp~l~wPaMTM~F~v~--~~~~l~~lk~G~~V~F~~~~~~~~-~~i~~i~~ 113 (115)
T PRK09838 44 SGTGVVKGIDLESKKITIHHEPIPAVNWPEMTMRFTIT--PQTKMSEIKTGDKVAFNFVQQGNL-SLLQDIKV 113 (115)
T ss_pred EEEEEEEEEeCCCCEEEEeecccccCCCCCccccccCC--ChhhhccCCCCCEEEEEEEEcCCc-EEEEEEee
Confidence 458999999887766666533210 00111111 111235689999999999998887 56666653
No 94
>PRK05807 hypothetical protein; Provisional
Probab=73.31 E-value=11 Score=30.12 Aligned_cols=57 Identities=21% Similarity=0.228 Sum_probs=41.0
Q ss_pred ccccceEEEEeeCCCceeEEecCCCCCceEEeccccccCCc----cccCCCCcEEEEEEeCC-Ccc
Q 047168 4 LTRSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGY----RTLYENQSVEFDVQLEA-DGK 64 (258)
Q Consensus 4 ~~~~~G~vk~f~~~kGfGFI~~~~~~~dvF~H~s~l~~~~~----~~l~~G~~V~F~v~~~~-~G~ 64 (258)
...+.|+|+-.. .||++...+ ..+-|+|++.|...-+ ..+.+|+.|+..|...+ +++
T Consensus 6 G~vv~G~Vt~i~---~~GafV~L~-~~~Glvhiseis~~~v~~~~~~~kvGd~V~VkV~~id~~gk 67 (136)
T PRK05807 6 GSILEGTVVNIT---NFGAFVEVE-GKTGLVHISEVADTYVKDIREHLKEQDKVKVKVISIDDNGK 67 (136)
T ss_pred CCEEEEEEEEEE---CCeEEEEEC-CEEEEEEhhhcccccccCccccCCCCCEEEEEEEEECCCCc
Confidence 367899999974 467666554 4689999999964322 34799999998876644 453
No 95
>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=72.70 E-value=12 Score=25.71 Aligned_cols=52 Identities=13% Similarity=0.001 Sum_probs=36.0
Q ss_pred ccceEEEEeeCCCceeEEecCCCCCceEEeccccccC--CccccCCCCcEEEEEEeC
Q 047168 6 RSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSD--GYRTLYENQSVEFDVQLE 60 (258)
Q Consensus 6 ~~~G~vk~f~~~kGfGFI~~~~~~~dvF~H~s~l~~~--~~~~l~~G~~V~F~v~~~ 60 (258)
.+.|+|+... ++| -|+...+ .-|-|+|++.|... ....+++|+.|.+.+..-
T Consensus 3 ~V~g~V~~i~-~~G-~~v~l~~-~v~g~v~~~~l~~~~~~~~~~~~G~~i~~kVi~i 56 (66)
T cd05695 3 LVNARVKKVL-SNG-LILDFLS-SFTGTVDFLHLDPEKSSKSTYKEGQKVRARILYV 56 (66)
T ss_pred EEEEEEEEEe-CCc-EEEEEcC-CceEEEEHHHcCCccCcccCcCCCCEEEEEEEEE
Confidence 4678999985 333 3344444 58999999988532 134589999999987654
No 96
>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=72.24 E-value=13 Score=25.49 Aligned_cols=52 Identities=13% Similarity=0.056 Sum_probs=38.6
Q ss_pred ccccceEEEEeeCCCceeEEecCCCCCceEEeccccccCCccccCCCCcEEEEEEeCC
Q 047168 4 LTRSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGYRTLYENQSVEFDVQLEA 61 (258)
Q Consensus 4 ~~~~~G~vk~f~~~kGfGFI~~~~~~~dvF~H~s~l~~~~~~~l~~G~~V~F~v~~~~ 61 (258)
...++|+|...+. .+=||... . .+-|++.+.+... ..+++|+.|++.+..-+
T Consensus 4 g~iV~G~V~~~~~--~~~~vdig-~-~eg~lp~~e~~~~--~~~~~Gd~v~v~v~~v~ 55 (67)
T cd04455 4 GEIVTGIVKRVDR--GNVIVDLG-K-VEAILPKKEQIPG--ESYRPGDRIKAYVLEVR 55 (67)
T ss_pred CCEEEEEEEEEcC--CCEEEEcC-C-eEEEeeHHHCCCC--CcCCCCCEEEEEEEEEe
Confidence 3567999999964 34445443 3 7889999999754 35799999999988754
No 97
>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=70.29 E-value=14 Score=24.69 Aligned_cols=53 Identities=17% Similarity=0.167 Sum_probs=37.0
Q ss_pred cccceEEEEeeCCCceeEEecCCCCCceEEeccccccCCc----cccCCCCcEEEEEEeCC
Q 047168 5 TRSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGY----RTLYENQSVEFDVQLEA 61 (258)
Q Consensus 5 ~~~~G~vk~f~~~kGfGFI~~~~~~~dvF~H~s~l~~~~~----~~l~~G~~V~F~v~~~~ 61 (258)
..+.|+|...+. ||++...+ ..+-|+|.+.+..... ..++.||.|.+.+..-+
T Consensus 3 ~~~~g~V~~v~~---~g~~v~l~-~~~g~l~~~e~~~~~~~~~~~~~~~Gd~v~v~i~~vd 59 (68)
T cd05688 3 DVVEGTVKSITD---FGAFVDLG-GVDGLLHISDMSWGRVKHPSEVVNVGDEVEVKVLKID 59 (68)
T ss_pred CEEEEEEEEEEe---eeEEEEEC-CeEEEEEhHHCCCccccCHhHEECCCCEEEEEEEEEE
Confidence 457899999863 45554444 4789999998863222 23689999998877654
No 98
>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=68.18 E-value=19 Score=25.75 Aligned_cols=55 Identities=15% Similarity=-0.020 Sum_probs=38.2
Q ss_pred ccccceEEEEeeCCCceeEEecCCCCCceEEeccccccC----C----ccccCCCCcEEEEEEeCC
Q 047168 4 LTRSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSD----G----YRTLYENQSVEFDVQLEA 61 (258)
Q Consensus 4 ~~~~~G~vk~f~~~kGfGFI~~~~~~~dvF~H~s~l~~~----~----~~~l~~G~~V~F~v~~~~ 61 (258)
.+.+.|+|+... .+|++...+..-+-|+|+++|... . ...+++||.|.+.+..-+
T Consensus 7 GdiV~g~V~~i~---~~g~~v~i~~~~~G~l~~se~~~~~~~~~~~~~~~~l~vGd~i~~~V~~~~ 69 (86)
T cd05789 7 GDVVIGRVTEVG---FKRWKVDINSPYDAVLPLSEVNLPRTDEDELNMRSYLDEGDLIVAEVQSVD 69 (86)
T ss_pred CCEEEEEEEEEC---CCEEEEECCCCeEEEEEHHHccCCCCccchHHHHhhCCCCCEEEEEEEEEC
Confidence 356789999973 234443334458999999999641 1 124899999999988754
No 99
>cd04482 RPA2_OBF_like RPA2_OBF_like: A subgroup of uncharacterized archaeal OB folds with similarity to the OB fold of the central ssDNA-binding domain (DBD)-D of human RPA2 (also called RPA32). RPA2 is a subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B; RPA2 DBD-D is a weak ssDNA-binding domain. RPA2 DBD-D is also involved in trimerization. The ssDNA binding mechanism is believed to be multistep and to involve conformational change. N-terminal to human RPA2 DBD-D is a domain containing all the known phosphorylation sites of RPA. Human RPA2 is phosphorylated in a cell cycle depende
Probab=58.10 E-value=62 Score=23.80 Aligned_cols=84 Identities=17% Similarity=0.099 Sum_probs=46.2
Q ss_pred ccceEEEEeeC--CCceeEEecCCCCCc--eEEeccc--cccCCccccCCCCcEEEEEEeCCCccceeeccccCCCCccc
Q 047168 6 RSTGKVTWFDG--AKGYGFIRPDDGGAD--LFVHQKS--IKSDGYRTLYENQSVEFDVQLEADGKYQALDVTAPGGAPVH 79 (258)
Q Consensus 6 ~~~G~vk~f~~--~kGfGFI~~~~~~~d--vF~H~s~--l~~~~~~~l~~G~~V~F~v~~~~~G~~~A~~V~~~~g~~~~ 79 (258)
.+.|.|..+.. ..|.=|++..|.... ..+-... +... ...|.+||.|+..=..+....+.+..+++.+.....
T Consensus 2 ~v~GeVs~~~~~~~sGH~yFtlkD~~~~i~cv~f~~~g~~~~~-~~~l~~Gd~V~v~G~v~~y~ql~ve~l~~~glg~~~ 80 (91)
T cd04482 2 RVTGKVVEEPRTIEGGHVFFKISDGTGEIDCAAYEPTKEFRDV-VRLLIPGDEVTVYGSVRPGTTLNLEKLRVIRLARLY 80 (91)
T ss_pred EEEEEEeCCeecCCCCCEEEEEECCCcEEEEEEECcccccccc-cCCCCCCCEEEEEEEEecCCEEEEEEEEECCCcceE
Confidence 46788888865 567777776553222 2222222 3222 245999999986655443324566666655443321
Q ss_pred CCCCCCCCCCCCccCC
Q 047168 80 SSKNNNTNNNSGYNNN 95 (258)
Q Consensus 80 ~s~~~~~g~~~c~~c~ 95 (258)
. ..+|.|-.|+
T Consensus 81 ~-----~~np~C~~C~ 91 (91)
T cd04482 81 E-----RENPVCPKCG 91 (91)
T ss_pred E-----EcCCcCCCCC
Confidence 1 1245677664
No 100
>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=56.59 E-value=38 Score=23.18 Aligned_cols=54 Identities=17% Similarity=0.219 Sum_probs=38.7
Q ss_pred cccceEEEEeeCCCceeEEecCC-CCCceEEeccccccCCc----cccCCCCcEEEEEEeCC
Q 047168 5 TRSTGKVTWFDGAKGYGFIRPDD-GGADLFVHQKSIKSDGY----RTLYENQSVEFDVQLEA 61 (258)
Q Consensus 5 ~~~~G~vk~f~~~kGfGFI~~~~-~~~dvF~H~s~l~~~~~----~~l~~G~~V~F~v~~~~ 61 (258)
..+.|+|+... .||++...+ ...+-|+|.+.+..... ..+..||.|+..+..-+
T Consensus 4 ~~v~g~V~~i~---~~g~~v~l~~~~~~g~i~~~~l~~~~~~~~~~~~~~Gd~v~v~i~~vd 62 (77)
T cd05708 4 QKIDGTVRRVE---DYGVFIDIDGTNVSGLCHKSEISDNRVADASKLFRVGDKVRAKVLKID 62 (77)
T ss_pred CEEEEEEEEEE---cceEEEEECCCCeEEEEEHHHCCCCccCCHhHeecCCCEEEEEEEEEe
Confidence 46789999885 366555444 35789999999975432 24689999998877654
No 101
>cd04489 ExoVII_LU_OBF ExoVII_LU_OBF: A subfamily of OB folds corresponding to the N-terminal OB-fold domain of Escherichia coli exodeoxyribonuclease VII (ExoVII) large subunit. E. coli ExoVII is composed of two non-identical subunits. E. coli ExoVII is a single-strand-specific exonuclease which degrades ssDNA from both 3-prime and 5-prime ends. ExoVII plays a role in methyl-directed mismatch repair in vivo. ExoVII may also guard the genome from mutagenesis by removing excess ssDNA, since the build up of ssDNA would lead to SOS induction and PolIV-dependent mutagenesis.
Probab=56.42 E-value=29 Score=24.05 Aligned_cols=52 Identities=15% Similarity=0.191 Sum_probs=33.9
Q ss_pred cceEEEEee-CCCceeEEecCCCCCc---eEEeccccccCCccccCCCCcEEEEEEeC
Q 047168 7 STGKVTWFD-GAKGYGFIRPDDGGAD---LFVHQKSIKSDGYRTLYENQSVEFDVQLE 60 (258)
Q Consensus 7 ~~G~vk~f~-~~kGfGFI~~~~~~~d---vF~H~s~l~~~~~~~l~~G~~V~F~v~~~ 60 (258)
+.|.|..+. ..+|+.|++.+|.... ++|. ..+.... ..|++|+.|.......
T Consensus 4 v~g~v~~i~~tk~g~~~~~L~D~~~~i~~~~f~-~~~~~~~-~~l~~g~~v~v~g~v~ 59 (78)
T cd04489 4 VEGEISNLKRPSSGHLYFTLKDEDASIRCVMWR-SNARRLG-FPLEEGMEVLVRGKVS 59 (78)
T ss_pred EEEEEecCEECCCcEEEEEEEeCCeEEEEEEEc-chhhhCC-CCCCCCCEEEEEEEEE
Confidence 557777776 4889999998876433 2443 3333322 4589999988776554
No 102
>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=55.77 E-value=29 Score=33.06 Aligned_cols=69 Identities=25% Similarity=0.256 Sum_probs=51.1
Q ss_pred cccceEEEEeeCCCceeEEecCCCCCceEEeccccccCC----------------ccccCCCCcEEEEEEeCC---Cccc
Q 047168 5 TRSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDG----------------YRTLYENQSVEFDVQLEA---DGKY 65 (258)
Q Consensus 5 ~~~~G~vk~f~~~kGfGFI~~~~~~~dvF~H~s~l~~~~----------------~~~l~~G~~V~F~v~~~~---~G~~ 65 (258)
..+.|+|+...+...--||.-.++ .+-|+|++++...- ...|++|+.|...|...+ +|..
T Consensus 27 nIY~GrV~~i~p~l~aAFVdiG~~-k~gfL~~~d~~~~~~~~~~~~~~~~~~~~i~~~l~~G~~IlVQV~Ke~~~~Kgp~ 105 (414)
T TIGR00757 27 NIYKGRVTRILPSLQAAFVDIGLE-KNGFLHASDIGPNYECLAPAEAKREAGPSISELLRPGQSVLVQVVKEPRGNKGAR 105 (414)
T ss_pred CEEEEEEeeecCCCceEEEEcCCC-ceEEEEHHHcCchhhccccccccccccCCHHHhCcCCCEEEEEEeeCCcCCCCCe
Confidence 468899999988877899998764 79999999985320 113889999999999964 5633
Q ss_pred eeeccccCC
Q 047168 66 QALDVTAPG 74 (258)
Q Consensus 66 ~A~~V~~~~ 74 (258)
...+|++++
T Consensus 106 lT~~Isl~G 114 (414)
T TIGR00757 106 LTTDISLPG 114 (414)
T ss_pred EEEEEEecc
Confidence 344555554
No 103
>PTZ00248 eukaryotic translation initiation factor 2 subunit 1; Provisional
Probab=55.32 E-value=38 Score=31.19 Aligned_cols=70 Identities=10% Similarity=-0.029 Sum_probs=47.1
Q ss_pred ccccceEEEEeeCCCceeEEecCC--CCCceEEeccccccCCc----cccCCCCcEEEEEEeC--CCccceeeccccCCC
Q 047168 4 LTRSTGKVTWFDGAKGYGFIRPDD--GGADLFVHQKSIKSDGY----RTLYENQSVEFDVQLE--ADGKYQALDVTAPGG 75 (258)
Q Consensus 4 ~~~~~G~vk~f~~~kGfGFI~~~~--~~~dvF~H~s~l~~~~~----~~l~~G~~V~F~v~~~--~~G~~~A~~V~~~~g 75 (258)
...+.|+|+... -||.+...+ ++-+-|+|+|.|...-. ..+++|+.|...|..- .+| .....+..+..
T Consensus 18 GdvV~g~V~~I~---d~GafV~L~EY~gvEGlIhiSElS~~ri~~i~d~vkvGd~v~vkVl~VD~ekg-~IdLS~K~v~~ 93 (319)
T PTZ00248 18 DDLVMVKVVRIT---EMGAYVSLLEYDDIEGMILMSELSKRRIRSINKLIRVGRHEVVVVLRVDKEKG-YIDLSKKRVSP 93 (319)
T ss_pred CCEEEEEEEEEe---CCeEEEEecCCCCcEEEEEHHHhcccccCCHHHhcCCCCEEEEEEEEEeCCCC-EEEEEeeeccc
Confidence 356789999985 477664442 46899999999966432 2378999999888863 445 34554444444
Q ss_pred Cc
Q 047168 76 AP 77 (258)
Q Consensus 76 ~~ 77 (258)
.+
T Consensus 94 ~p 95 (319)
T PTZ00248 94 ED 95 (319)
T ss_pred ch
Confidence 34
No 104
>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=55.03 E-value=23 Score=36.14 Aligned_cols=57 Identities=21% Similarity=0.228 Sum_probs=41.3
Q ss_pred cccceEEEEeeCCCceeEEecCCCCCceEEeccccc---c-----CCccccCCCCcEEEEEEeCC-Ccc
Q 047168 5 TRSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIK---S-----DGYRTLYENQSVEFDVQLEA-DGK 64 (258)
Q Consensus 5 ~~~~G~vk~f~~~kGfGFI~~~~~~~dvF~H~s~l~---~-----~~~~~l~~G~~V~F~v~~~~-~G~ 64 (258)
..+.|+|+..- -||.+.....+.|-|+|+|.|. . +-...+++||.|+..+..-+ +++
T Consensus 649 ~i~~GkV~~I~---dfGaFVel~~G~eGLvHISeisdls~~~rv~~~~dv~kvGd~V~VKVl~ID~~gK 714 (719)
T TIGR02696 649 ERFLGTVVKTT---AFGAFVSLLPGKDGLLHISQIRKLAGGKRVENVEDVLSVGQKIQVEIADIDDRGK 714 (719)
T ss_pred CEEEEEEEEEE---CceEEEEecCCceEEEEhhhccccccccCcCCHHHcCCCCCEEEEEEEEECCCCC
Confidence 56889999984 4887766656689999999884 1 11224888999998876643 454
No 105
>COG1095 RPB7 DNA-directed RNA polymerase, subunit E' [Transcription]
Probab=54.23 E-value=21 Score=30.19 Aligned_cols=52 Identities=21% Similarity=0.104 Sum_probs=36.0
Q ss_pred cccceEEEEeeCCCceeEEecCCCCCceEEeccccccCC---------------ccccCCCCcEEEEEEeC
Q 047168 5 TRSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDG---------------YRTLYENQSVEFDVQLE 60 (258)
Q Consensus 5 ~~~~G~vk~f~~~kGfGFI~~~~~~~dvF~H~s~l~~~~---------------~~~l~~G~~V~F~v~~~ 60 (258)
+.+.|.|+.-+ .||+-..-. ..|+|+|++.|..+- =+.|+.|+.|.+.++..
T Consensus 83 EVV~GeVv~~~---~~G~fV~ig-p~dglvh~sqi~dd~~~~d~~~~~~~g~~tk~~i~~gd~VR~RIv~~ 149 (183)
T COG1095 83 EVVEGEVVEVV---EFGAFVRIG-PLDGLVHVSQIMDDYIDYDEKNKVLIGEETKRVLKVGDKVRARIVGV 149 (183)
T ss_pred cEEEEEEEEEe---ecceEEEec-cccccccHhhccCcccccCcccceeeecccceEEecCCEEEEEEEEE
Confidence 45678887764 577665554 689999999986651 12567777777777664
No 106
>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=53.20 E-value=37 Score=28.24 Aligned_cols=52 Identities=17% Similarity=0.129 Sum_probs=37.0
Q ss_pred cccceEEEEeeCCCceeEEecCCCCCceEEeccccccCCc---------------cccCCCCcEEEEEEeC
Q 047168 5 TRSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGY---------------RTLYENQSVEFDVQLE 60 (258)
Q Consensus 5 ~~~~G~vk~f~~~kGfGFI~~~~~~~dvF~H~s~l~~~~~---------------~~l~~G~~V~F~v~~~ 60 (258)
+.+.|+|+..+. |||..... .-|-+||.+++....+ ..++.|+.|.|.|..-
T Consensus 83 Evv~G~V~~v~~---~GifV~lg-~~~gi~~~~~l~~~~~~~d~~~~~~~~~~~~~~~~~Gd~VrvrV~~v 149 (179)
T TIGR00448 83 EIVEGEVIEIVE---FGAFVSLG-PFDGLFHVSQVTDDYCYYDPKESALIGKETKKVLDEGDKVRARIVAL 149 (179)
T ss_pred CEEEEEEEEEEe---eEEEEEeC-CceEEEEcHHhCCCceEEccccceEEEccCCeEEcCCCEEEEEEEEE
Confidence 467899998864 77776654 4788889888864332 3477888888887654
No 107
>PF01796 DUF35: DUF35 OB-fold domain; InterPro: IPR002878 This domain has no known function and is found in conserved hypothetical archaeal and bacterial proteins. The domain is approximately 70 amino acids long. The domain is duplicated in O53566 from SWISSPROT. The structure of a DUF35 representative reveals two long N-terminal helices followed by a rubredoxin-like zinc ribbon domain and a C-terminal OB fold domain represented in this entry. OB-folds are frequently found to bind nucleic acids suggesting this domain might bind to DNA or RNA.
Probab=50.49 E-value=37 Score=23.39 Aligned_cols=37 Identities=11% Similarity=0.195 Sum_probs=26.5
Q ss_pred eeEEecCCCCCceEEeccccccCCccccCCCCcEEEEE
Q 047168 20 YGFIRPDDGGADLFVHQKSIKSDGYRTLYENQSVEFDV 57 (258)
Q Consensus 20 fGFI~~~~~~~dvF~H~s~l~~~~~~~l~~G~~V~F~v 57 (258)
++.|..|+ +--|+.++......+...|+.|++|+..+
T Consensus 31 v~~V~lde-g~rv~~~i~~~~~~~~~~l~iG~~V~~vf 67 (68)
T PF01796_consen 31 VAIVELDE-GVRVMARIVDVDPEDPDELRIGMRVRLVF 67 (68)
T ss_pred EEEEEeCC-CCEEEEEEecCCCCCcccCCCCCEEEEEE
Confidence 56777765 46788888876544556688999998664
No 108
>PRK13806 rpsA 30S ribosomal protein S1; Provisional
Probab=49.83 E-value=41 Score=32.73 Aligned_cols=54 Identities=17% Similarity=0.119 Sum_probs=38.5
Q ss_pred ccccceEEEEeeCCCceeEEecCCCCCceEEeccccccCCc----cccCCCCcEEEEEEeC
Q 047168 4 LTRSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGY----RTLYENQSVEFDVQLE 60 (258)
Q Consensus 4 ~~~~~G~vk~f~~~kGfGFI~~~~~~~dvF~H~s~l~~~~~----~~l~~G~~V~F~v~~~ 60 (258)
.+.+.|+|+.... ||.+.....+.+.|+|++.|...-. ..+.+|+.|.+.|..-
T Consensus 203 G~iv~G~V~~v~~---~G~fV~l~~gv~g~v~~sels~~~~~~~~~~~~vGd~i~vkVl~i 260 (491)
T PRK13806 203 GDVVEGTVTRLAP---FGAFVELAPGVEGMVHISELSWSRVQKADEAVSVGDTVRVKVLGI 260 (491)
T ss_pred CCEEEEEEEEEeC---CeEEEEcCCCcEEEEEHHHCCCccccChhHhcCCCCEEEEEEEEE
Confidence 3568899999842 5555444445899999999965422 2367999999988654
No 109
>COG1098 VacB Predicted RNA binding protein (contains ribosomal protein S1 domain) [Translation, ribosomal structure and biogenesis]
Probab=49.68 E-value=35 Score=27.08 Aligned_cols=67 Identities=27% Similarity=0.364 Sum_probs=44.3
Q ss_pred ccccceEEEEeeCCCcee-EEecCCCCCceEEeccccccCC----ccccCCCCcEEEEEEe-CCCccceeeccccCCC
Q 047168 4 LTRSTGKVTWFDGAKGYG-FIRPDDGGADLFVHQKSIKSDG----YRTLYENQSVEFDVQL-EADGKYQALDVTAPGG 75 (258)
Q Consensus 4 ~~~~~G~vk~f~~~kGfG-FI~~~~~~~dvF~H~s~l~~~~----~~~l~~G~~V~F~v~~-~~~G~~~A~~V~~~~g 75 (258)
...++|+|+-. +-|| |+.. ++++.=+||+|.|...- -..|.+|+.|...|.. +++|++ ...|.....
T Consensus 6 G~~l~GkItgI---~~yGAFV~l-~~g~tGLVHISEIa~~fVkdI~d~L~vG~eV~vKVl~ide~GKi-sLSIr~~~e 78 (129)
T COG1098 6 GSKLKGKITGI---TPYGAFVEL-EGGKTGLVHISEIADGFVKDIHDHLKVGQEVKVKVLDIDENGKI-SLSIRKLEE 78 (129)
T ss_pred cceEEEEEEee---EecceEEEe-cCCCcceEEehHhhhhhHHhHHHHhcCCCEEEEEEEeeccCCCc-ceehHHhhh
Confidence 35678888765 4566 5554 45578999999996532 2358899999987765 456753 444444433
No 110
>TIGR01451 B_ant_repeat conserved repeat domain. This model represents the conserved region of about 53 amino acids shared between regions, usually repeated, of proteins from a small number of phylogenetically distant prokaryotes. Examples include a 132-residue region found repeated in three of the five longest proteins of Bacillus anthracis, a 131-residue repeat in a cell wall-anchored protein of Enterococcus faecalis, and a 120-residue repeat in Methanobacterium thermoautotrophicum. A similar region is found in some Chlamydial outer membrane proteins.
Probab=49.24 E-value=17 Score=24.08 Aligned_cols=31 Identities=10% Similarity=0.219 Sum_probs=24.1
Q ss_pred cccCCCCcEEEEEEeCCCccceeeccccCCC
Q 047168 45 RTLYENQSVEFDVQLEADGKYQALDVTAPGG 75 (258)
Q Consensus 45 ~~l~~G~~V~F~v~~~~~G~~~A~~V~~~~g 75 (258)
..+.+||.|+|.+.....|...|.+|.+.+.
T Consensus 6 ~~~~~Gd~v~Yti~v~N~g~~~a~~v~v~D~ 36 (53)
T TIGR01451 6 TVATIGDTITYTITVTNNGNVPATNVVVTDI 36 (53)
T ss_pred cccCCCCEEEEEEEEEECCCCceEeEEEEEc
Confidence 4578999999999998888656777765543
No 111
>PRK13806 rpsA 30S ribosomal protein S1; Provisional
Probab=48.90 E-value=37 Score=32.99 Aligned_cols=53 Identities=23% Similarity=0.233 Sum_probs=39.1
Q ss_pred ccccceEEEEeeCCCceeE-EecCCCCCceEEeccccccC----CccccCCCCcEEEEEEeC
Q 047168 4 LTRSTGKVTWFDGAKGYGF-IRPDDGGADLFVHQKSIKSD----GYRTLYENQSVEFDVQLE 60 (258)
Q Consensus 4 ~~~~~G~vk~f~~~kGfGF-I~~~~~~~dvF~H~s~l~~~----~~~~l~~G~~V~F~v~~~ 60 (258)
...+.|+|+..- -||. |+.++ +-+-|+|.+.|... ....|++||.|++.|..-
T Consensus 380 G~~v~G~V~~i~---~~G~FV~l~~-gv~Gli~~se~s~~~~~~~~~~~~~Gd~v~~~V~~i 437 (491)
T PRK13806 380 GTTVTGTVEKRA---QFGLFVNLAP-GVTGLLPASVISRAGKPATYEKLKPGDSVTLVVEEI 437 (491)
T ss_pred CCEEEEEEEEEe---cCceEEEcCC-CcEEEEEHHHcCcccccchhhcCCCCCEEEEEEEEE
Confidence 356889999874 4665 45544 68999999998643 235689999999887664
No 112
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=48.20 E-value=40 Score=35.39 Aligned_cols=57 Identities=11% Similarity=0.134 Sum_probs=41.1
Q ss_pred ccc-ceEEEEeeCCCceeEEecCCCCCceEEeccccccCCc----cccCCCCcEEEEEEeCC-Ccc
Q 047168 5 TRS-TGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGY----RTLYENQSVEFDVQLEA-DGK 64 (258)
Q Consensus 5 ~~~-~G~vk~f~~~kGfGFI~~~~~~~dvF~H~s~l~~~~~----~~l~~G~~V~F~v~~~~-~G~ 64 (258)
+.+ .|+|+... -||++.....+.|-|+|+|.|...-+ ..+++||.|+..|..-+ +++
T Consensus 755 ~iy~~g~V~~I~---~FGaFVeL~~g~EGLVHISeLs~~rv~~~~dv~kvGD~V~VkVi~ID~~gr 817 (891)
T PLN00207 755 DIYRNCEIKSIA---PYGAFVEIAPGREGLCHISELSSNWLAKPEDAFKVGDRIDVKLIEVNDKGQ 817 (891)
T ss_pred cEEECcEEEEEe---ccEEEEEeCCCCEEEEEhhhcCCccccCHHHhcCCCCEEEEEEEEECCCCc
Confidence 345 36888874 58877655556899999999965432 35788999999887754 454
No 113
>PRK07899 rpsA 30S ribosomal protein S1; Reviewed
Probab=47.11 E-value=39 Score=32.95 Aligned_cols=53 Identities=19% Similarity=0.145 Sum_probs=40.4
Q ss_pred cccceEEEEeeCCCceeEEecCCCCCceEEeccccccCCc----cccCCCCcEEEEEEeC
Q 047168 5 TRSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGY----RTLYENQSVEFDVQLE 60 (258)
Q Consensus 5 ~~~~G~vk~f~~~kGfGFI~~~~~~~dvF~H~s~l~~~~~----~~l~~G~~V~F~v~~~ 60 (258)
..+.|+|+... -||++...+.+.+-|+|++.|....+ ..+++|+.|+..|..-
T Consensus 295 ~vv~G~V~~I~---~fGvFVeL~~gieGLvh~SeLs~~~v~~~~~~~kvGd~V~VkIi~I 351 (486)
T PRK07899 295 QIVPGKVTKLV---PFGAFVRVEEGIEGLVHISELAERHVEVPEQVVQVGDEVFVKVIDI 351 (486)
T ss_pred CEEEEEEEEEe---ccEEEEEeCCCcEEEEEHHHcCcccccCccceeCCCCEEEEEEEEE
Confidence 56889999884 48887666556899999999965432 2478999999888664
No 114
>cd05701 S1_Rrp5_repeat_hs10 S1_Rrp5_repeat_hs10: 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 10 (hs10). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=46.83 E-value=31 Score=24.12 Aligned_cols=52 Identities=13% Similarity=0.063 Sum_probs=36.8
Q ss_pred cceEEEEeeCCCceeEEecCCCCCceEEeccc----cccCCccccCCCCcEEEEEEeC
Q 047168 7 STGKVTWFDGAKGYGFIRPDDGGADLFVHQKS----IKSDGYRTLYENQSVEFDVQLE 60 (258)
Q Consensus 7 ~~G~vk~f~~~kGfGFI~~~~~~~dvF~H~s~----l~~~~~~~l~~G~~V~F~v~~~ 60 (258)
.+.+|... ++.|-.|+.++++.-.+|..++ +-..+.+.|++|+.|..++...
T Consensus 4 htA~VQh~--~kdfAvvSL~~t~~L~a~p~~sHLNdtfrf~seklkvG~~l~v~lk~~ 59 (69)
T cd05701 4 HTAIVQHA--DKDFAIVSLATTGDLAAFPTRSHLNDTFRFDSEKLSVGQCLDVTLKDP 59 (69)
T ss_pred cchhhhhh--hhceEEEEeeccccEEEEEchhhccccccccceeeeccceEEEEEecC
Confidence 34444444 6889999999988888885544 4334446799999998887654
No 115
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=46.43 E-value=43 Score=34.15 Aligned_cols=54 Identities=24% Similarity=0.204 Sum_probs=41.1
Q ss_pred cccceEEEEeeCCCceeEEecCCCCCceEEeccccccCCc----cccCCCCcEEEEEEeCC
Q 047168 5 TRSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGY----RTLYENQSVEFDVQLEA 61 (258)
Q Consensus 5 ~~~~G~vk~f~~~kGfGFI~~~~~~~dvF~H~s~l~~~~~----~~l~~G~~V~F~v~~~~ 61 (258)
+.+.|+|+... -||++..-..+.+-|+|+|.|...-+ ..+++||.|+..+..-+
T Consensus 623 ~v~~G~V~~I~---~fGafVei~~~~~GllhiSels~~~v~~~~~v~kvGD~V~VkV~~iD 680 (693)
T PRK11824 623 EIYEGKVVRIV---DFGAFVEILPGKDGLVHISEIADERVEKVEDVLKEGDEVKVKVLEID 680 (693)
T ss_pred eEEEEEEEEEE---CCeEEEEECCCCEEEEEeeeccCccccCccceeCCCCEEEEEEEEEC
Confidence 56889999985 48877766667999999999965432 23688999988877643
No 116
>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=45.05 E-value=78 Score=22.60 Aligned_cols=50 Identities=20% Similarity=0.142 Sum_probs=31.9
Q ss_pred cceEEEEeeCCC-ceeEEecCCC-------CCceEEeccccccCCccccCCCCcEEEEEEeCC
Q 047168 7 STGKVTWFDGAK-GYGFIRPDDG-------GADLFVHQKSIKSDGYRTLYENQSVEFDVQLEA 61 (258)
Q Consensus 7 ~~G~vk~f~~~k-GfGFI~~~~~-------~~dvF~H~s~l~~~~~~~l~~G~~V~F~v~~~~ 61 (258)
++|+|....... ..||-..++. .+-|||.... . ..|.+|+.|+..=...+
T Consensus 2 v~GvVTa~~~~~~~~GffiQd~~~d~~~~ts~gifV~~~~-~----~~~~~Gd~V~vtG~v~e 59 (78)
T cd04486 2 VEGVVTAVFSGGGLGGFYIQDEDGDGDPATSEGIFVYTGS-G----ADVAVGDLVRVTGTVTE 59 (78)
T ss_pred eEEEEEEEcCCCCcCEEEEEcCCCCCCCcccceEEEecCC-C----CCCCCCCEEEEEEEEEe
Confidence 567887775543 2355444431 3569998876 2 34899999998755554
No 117
>PRK08563 DNA-directed RNA polymerase subunit E'; Provisional
Probab=44.92 E-value=51 Score=27.44 Aligned_cols=53 Identities=19% Similarity=0.127 Sum_probs=38.1
Q ss_pred cccceEEEEeeCCCceeEEecCCCCCceEEeccccccCCc---------------cccCCCCcEEEEEEeCC
Q 047168 5 TRSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGY---------------RTLYENQSVEFDVQLEA 61 (258)
Q Consensus 5 ~~~~G~vk~f~~~kGfGFI~~~~~~~dvF~H~s~l~~~~~---------------~~l~~G~~V~F~v~~~~ 61 (258)
+.+.|+|+..+. +|++.... .-+.|+|.+.+....+ ..++.|+.|.|.+..-+
T Consensus 83 EVv~g~V~~v~~---~Gi~V~lg-~~~g~v~~~~l~~~~~~~d~~~~~~~~~~~~~~i~~Gd~VrvrV~~v~ 150 (187)
T PRK08563 83 EVVEGEVVEVVE---FGAFVRIG-PVDGLLHISQIMDDYISYDPKNGRLIGKESKRVLKVGDVVRARIVAVS 150 (187)
T ss_pred CEEEEEEEEEEc---cEEEEEEe-CceEEEEcHHcCCCceEEccccceEEEccCCeEEcCCCEEEEEEEEEE
Confidence 467899999863 56665554 4789999999865422 34688999998887653
No 118
>PF03100 CcmE: CcmE; InterPro: IPR004329 CcmE is the product of one of a cluster of Ccm genes that are necessary for cytochrome c biosynthesis in eubacteria. Expression of these proteins is induced when the organisms are grown under anaerobic conditions with nitrate or nitrite as the final electron acceptor.; GO: 0017003 protein-heme linkage, 0017004 cytochrome complex assembly, 0005886 plasma membrane; PDB: 1SR3_A 2KCT_A 1J6Q_A 1LM0_A.
Probab=43.92 E-value=62 Score=25.56 Aligned_cols=63 Identities=25% Similarity=0.307 Sum_probs=43.5
Q ss_pred ccceEEE-----EeeCCCceeEEecCCCCCceEEeccccccCCccccCCCCcEEEEEEeCCCccceeecccc
Q 047168 6 RSTGKVT-----WFDGAKGYGFIRPDDGGADLFVHQKSIKSDGYRTLYENQSVEFDVQLEADGKYQALDVTA 72 (258)
Q Consensus 6 ~~~G~vk-----~f~~~kGfGFI~~~~~~~dvF~H~s~l~~~~~~~l~~G~~V~F~v~~~~~G~~~A~~V~~ 72 (258)
++.|.|+ |=.....+=|+..|. ..+|-|+...+..+. .++|+.|.-+=.-.++|.++|.+|-.
T Consensus 54 rv~G~V~~gSv~~~~~~~~~~F~i~D~-~~~i~V~Y~G~~Pd~---F~eg~~VVv~G~~~~~g~F~A~~lL~ 121 (131)
T PF03100_consen 54 RVGGLVVEGSVEYDPDGNTLTFTITDG-GKEIPVVYTGPLPDL---FREGQGVVVEGRLGEDGVFEATELLA 121 (131)
T ss_dssp EEEEEEECTTEEE-TTSSEEEEEEE-S-S-EEEEEEES--CTT-----TTSEEEEEEEECCTSEEEEEEEEE
T ss_pred EEeeEEccCCEEEcCCCCEEEEEEEEC-CcEEEEEECCCCCcc---ccCCCeEEEEEEECCCCEEEEEEEEe
Confidence 4455555 444788899999887 478999999998775 57899998887777777788988764
No 119
>PF00358 PTS_EIIA_1: phosphoenolpyruvate-dependent sugar phosphotransferase system, EIIA 1; InterPro: IPR001127 The phosphoenolpyruvate-dependent sugar phosphotransferase system (PTS) [, ] is a major carbohydrate transport system in bacteria. The PTS catalyses the phosphorylation of incoming sugar substrates and coupled with translocation across the cell membrane, makes the PTS a link between the uptake and metabolism of sugars. The general mechanism of the PTS is the following: a phosphoryl group from phosphoenolpyruvate (PEP) is transferred via a signal transduction pathway, to enzyme I (EI) which in turn transfers it to a phosphoryl carrier, the histidine protein (HPr). Phospho-HPr then transfers the phosphoryl group to a sugar-specific permease, a membrane-bound complex known as enzyme 2 (EII), which transports the sugar to the cell. EII consists of at least three structurally distinct domains IIA, IIB and IIC []. These can either be fused together in a single polypeptide chain or exist as two or three interactive chains, formerly called enzymes II (EII) and III (EIII). The first domain (IIA or EIIA) carries the first permease-specific phosphorylation site, a histidine which is phosphorylated by phospho-HPr. The second domain (IIB or EIIB) is phosphorylated by phospho-IIA on a cysteinyl or histidyl residue, depending on the sugar transported. Finally, the phosphoryl group is transferred from the IIB domain to the sugar substrate concomitantly with the sugar uptake processed by the IIC domain. This third domain (IIC or EIIC) forms the translocation channel and the specific substrate-binding site. An additional transmembrane domain IID, homologous to IIC, can be found in some PTSs, e.g. for mannose [, , , ]. ; GO: 0005351 sugar:hydrogen symporter activity, 0006810 transport, 0009401 phosphoenolpyruvate-dependent sugar phosphotransferase system, 0016020 membrane; PDB: 3OUR_D 1GPR_A 1F3G_A 2F3G_B 1F3Z_A 1O2F_A 1GLB_F 1GGR_A 1GLA_F 1GLE_F ....
Probab=43.50 E-value=68 Score=25.55 Aligned_cols=48 Identities=29% Similarity=0.448 Sum_probs=29.4
Q ss_pred ccceEEEEeeCCCceeEEecCCCCCceEEecc----ccccCCcccc-CCCCcEE
Q 047168 6 RSTGKVTWFDGAKGYGFIRPDDGGADLFVHQK----SIKSDGYRTL-YENQSVE 54 (258)
Q Consensus 6 ~~~G~vk~f~~~kGfGFI~~~~~~~dvF~H~s----~l~~~~~~~l-~~G~~V~ 54 (258)
...|+|.+..+.+..=-|+.++ +-+|++|+- .|...+|..+ ++|+.|.
T Consensus 45 P~~G~v~~i~~T~HAi~i~s~~-G~eiLiHiGidTv~L~G~gF~~~v~~G~~V~ 97 (132)
T PF00358_consen 45 PVDGTVTMIFPTKHAIGIRSDN-GVEILIHIGIDTVKLNGEGFETLVKEGDKVK 97 (132)
T ss_dssp SSSEEEEEE-TTSSEEEEEETT-SEEEEEE-SBSGGGGTTTTEEESS-TTSEE-
T ss_pred EeeEEEEEEcCCCCEEEEEeCC-CCEEEEEEccchhhcCCcceEEEEeCCCEEE
Confidence 4679999988765544444454 489999984 3555666643 4777765
No 120
>TIGR00638 Mop molybdenum-pterin binding domain. This model describes a multigene family of molybdenum-pterin binding proteins of about 70 amino acids in Clostridium pasteurianum, as a tandemly-repeated domain C-terminal to an unrelated domain in ModE, a molybdate transport gene repressor of E. coli, and in single or tandemly paired domains in several related proteins.
Probab=43.47 E-value=66 Score=21.59 Aligned_cols=54 Identities=15% Similarity=0.023 Sum_probs=33.7
Q ss_pred cccceEEEEeeCCCceeEEecCCCCC-ceEEeccccccCCccccCCCCcEEEEEEe
Q 047168 5 TRSTGKVTWFDGAKGYGFIRPDDGGA-DLFVHQKSIKSDGYRTLYENQSVEFDVQL 59 (258)
Q Consensus 5 ~~~~G~vk~f~~~kGfGFI~~~~~~~-dvF~H~s~l~~~~~~~l~~G~~V~F~v~~ 59 (258)
....|+|++......+=-|..+-++. .+...++.-.... ..|.+|+.|...+..
T Consensus 7 N~l~g~I~~i~~~g~~~~v~l~~~~~~~l~a~i~~~~~~~-l~l~~G~~v~~~ik~ 61 (69)
T TIGR00638 7 NQLKGKVVAIEDGDVNAEVDLLLGGGTKLTAVITLESVAE-LGLKPGKEVYAVIKA 61 (69)
T ss_pred cEEEEEEEEEEECCCeEEEEEEECCCCEEEEEecHHHHhh-CCCCCCCEEEEEEEC
Confidence 45889999997665555455443333 5555555432222 248899999877754
No 121
>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=43.44 E-value=43 Score=34.06 Aligned_cols=54 Identities=24% Similarity=0.207 Sum_probs=40.6
Q ss_pred cccceEEEEeeCCCceeEEecCCCCCceEEeccccccCCc----cccCCCCcEEEEEEeCC
Q 047168 5 TRSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGY----RTLYENQSVEFDVQLEA 61 (258)
Q Consensus 5 ~~~~G~vk~f~~~kGfGFI~~~~~~~dvF~H~s~l~~~~~----~~l~~G~~V~F~v~~~~ 61 (258)
..+.|+|+.+. .||.+..-..+.+-|+|+|.|...-+ ..+++||.|...+..-+
T Consensus 620 ~i~~G~V~~I~---~~GafVei~~g~~GllHiSei~~~~v~~~~~~~kvGD~V~VkVi~id 677 (684)
T TIGR03591 620 KIYEGKVVRIM---DFGAFVEILPGKDGLVHISEIANERVEKVEDVLKEGDEVKVKVLEID 677 (684)
T ss_pred cEEEEEEEEEe---CCEEEEEECCCcEEEEEHHHcCCCcccChhhccCCCCEEEEEEEEEC
Confidence 56889999995 48877666556899999999965432 23678999988877654
No 122
>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=42.34 E-value=1e+02 Score=21.62 Aligned_cols=55 Identities=13% Similarity=0.016 Sum_probs=39.2
Q ss_pred cccceEEEEeeCCCceeEEecCCCCCceEEeccccccCC----ccccCCCCcEEEEEEeCCC
Q 047168 5 TRSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDG----YRTLYENQSVEFDVQLEAD 62 (258)
Q Consensus 5 ~~~~G~vk~f~~~kGfGFI~~~~~~~dvF~H~s~l~~~~----~~~l~~G~~V~F~v~~~~~ 62 (258)
..+.|+|.... ...-++... ...+-|+|+++|.... ...+++||.|.+.+..-++
T Consensus 8 diV~G~V~~v~--~~~~~V~i~-~~~~g~l~~~~~~~~~~~~~~~~~~~GD~i~~~V~~~~~ 66 (82)
T cd04454 8 DIVIGIVTEVN--SRFWKVDIL-SRGTARLEDSSATEKDKKEIRKSLQPGDLILAKVISLGD 66 (82)
T ss_pred CEEEEEEEEEc--CCEEEEEeC-CCceEEeechhccCcchHHHHhcCCCCCEEEEEEEEeCC
Confidence 56789999883 334445543 4589999999996442 2347999999999887654
No 123
>COG4776 Rnb Exoribonuclease II [Transcription]
Probab=41.05 E-value=36 Score=33.06 Aligned_cols=50 Identities=24% Similarity=0.404 Sum_probs=35.7
Q ss_pred CccccceEEEEeeCCCceeEEecCCCCCceEEeccccccCCccccCCCCcEEEEEEeC
Q 047168 3 QLTRSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGYRTLYENQSVEFDVQLE 60 (258)
Q Consensus 3 ~~~~~~G~vk~f~~~kGfGFI~~~~~~~dvF~H~s~l~~~~~~~l~~G~~V~F~v~~~ 60 (258)
+..++.|+||.= +|||||+..|. .+.+|+.--.++ .+--||+|.-.+...
T Consensus 18 ~~prvEGvVK~t--ekgfGFLEvD~-qkSYFIpPp~MK-----kvMHGDkIiA~i~te 67 (645)
T COG4776 18 QTPRVEGVVKAT--EKGFGFLEVDA-QKSYFIPPPQMK-----KVMHGDKIIAVIHTE 67 (645)
T ss_pred cCcccceeeeec--cccceeEEEcC-ccccccCCHHHh-----hhcccCeEEEEEEec
Confidence 457899999975 89999999875 477886655543 345677776555544
No 124
>PHA02945 interferon resistance protein; Provisional
Probab=40.44 E-value=1.2e+02 Score=22.49 Aligned_cols=53 Identities=15% Similarity=0.060 Sum_probs=36.3
Q ss_pred cccceEEEEeeCCCceeEE-ecC-CCCCceEEecccc--cc----CCccccCCCCcEEEEEEeCCCc
Q 047168 5 TRSTGKVTWFDGAKGYGFI-RPD-DGGADLFVHQKSI--KS----DGYRTLYENQSVEFDVQLEADG 63 (258)
Q Consensus 5 ~~~~G~vk~f~~~kGfGFI-~~~-~~~~dvF~H~s~l--~~----~~~~~l~~G~~V~F~v~~~~~G 63 (258)
+.+.|+|+. +.||+- +.+ .++.+-|+|+|.+ .. . ...| +|+.|...+..-++.
T Consensus 13 elvigtV~~----~d~ga~v~L~EY~g~eg~i~~seveva~~wvK~-rd~l-~GqkvV~KVirVd~~ 73 (88)
T PHA02945 13 DVLKGKVYE----NGYALYIDLFDYPHSEAILAESVQMHMNRYFKY-RDKL-VGKTVKVKVIRVDYT 73 (88)
T ss_pred cEEEEEEEe----cCceEEEEecccCCcEEEEEeehhhhccceEee-eeEe-cCCEEEEEEEEECCC
Confidence 456788876 566654 444 3689999999966 21 2 3446 999999988876543
No 125
>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=39.94 E-value=66 Score=24.11 Aligned_cols=56 Identities=16% Similarity=-0.026 Sum_probs=39.2
Q ss_pred ccccceEEEEeeCCCceeEEecCCCCCceEEeccccccC-----------------------CccccCCCCcEEEEEEeC
Q 047168 4 LTRSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSD-----------------------GYRTLYENQSVEFDVQLE 60 (258)
Q Consensus 4 ~~~~~G~vk~f~~~kGfGFI~~~~~~~dvF~H~s~l~~~-----------------------~~~~l~~G~~V~F~v~~~ 60 (258)
.+.+.|+|+... .. -=||..+. +-+-|+|+++|... -...+.+||.|.+.|..-
T Consensus 4 G~vV~G~V~~v~-~~-gl~v~L~~-g~~G~v~~seis~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~vGd~V~~kVi~~ 80 (100)
T cd05693 4 GMLVLGQVKEIT-KL-DLVISLPN-GLTGYVPITNISDAYTERLEELDEESEEEDDEEELPDLEDLFSVGQLVRCKVVSL 80 (100)
T ss_pred CCEEEEEEEEEc-CC-CEEEECCC-CcEEEEEHHHhhHHHHHHHHHhhhhccccccccccCCHHHhccCCCEEEEEEEEc
Confidence 467889999974 22 33455444 58999999999642 123468999999988876
Q ss_pred CC
Q 047168 61 AD 62 (258)
Q Consensus 61 ~~ 62 (258)
++
T Consensus 81 d~ 82 (100)
T cd05693 81 DK 82 (100)
T ss_pred cC
Confidence 54
No 126
>PRK03987 translation initiation factor IF-2 subunit alpha; Validated
Probab=39.23 E-value=56 Score=29.14 Aligned_cols=55 Identities=20% Similarity=0.210 Sum_probs=39.7
Q ss_pred cccceEEEEeeCCCceeEEecC-C-CCCceEEeccccccCCcc----ccCCCCcEEEEEEeCCC
Q 047168 5 TRSTGKVTWFDGAKGYGFIRPD-D-GGADLFVHQKSIKSDGYR----TLYENQSVEFDVQLEAD 62 (258)
Q Consensus 5 ~~~~G~vk~f~~~kGfGFI~~~-~-~~~dvF~H~s~l~~~~~~----~l~~G~~V~F~v~~~~~ 62 (258)
+.+.|+|+... .||++... + .+.+-|+|++.|...-++ .+++|+.|...|..-+.
T Consensus 10 diV~G~V~~I~---~~G~fV~L~e~~gieGlI~iSEls~~~i~~i~~~~kvGd~V~vkVi~VD~ 70 (262)
T PRK03987 10 ELVVGTVKEVK---DFGAFVTLDEYPGKEGFIHISEVASGWVKNIRDHVKEGQKVVCKVIRVDP 70 (262)
T ss_pred CEEEEEEEEEE---CCEEEEEECCCCCcEEEEEHHHcCcccccCHHHhCCCCCEEEEEEEEEec
Confidence 56789999884 46655443 3 257999999999654432 46899999999887553
No 127
>PF03459 TOBE: TOBE domain; InterPro: IPR005116 The TOBE domain [] (Transport-associated OB) always occurs as a dimer as the C-terminal strand of each domain is supplied by the partner. It is probably involved in the recognition of small ligands such as molybdenum (P46930 from SWISSPROT) and sulphate (P16676 from SWISSPROT), and is found in ABC transporters immediately after the ATPase domain.; GO: 0005215 transporter activity, 0005524 ATP binding, 0016820 hydrolase activity, acting on acid anhydrides, catalyzing transmembrane movement of substances, 0006810 transport, 0043190 ATP-binding cassette (ABC) transporter complex; PDB: 1G29_2 1H9M_B 1H9J_A 1H9K_A 1H9R_B 1O7L_C 1H9S_A 1B9N_A 1B9M_A 1GUS_C ....
Probab=38.99 E-value=32 Score=22.95 Aligned_cols=54 Identities=15% Similarity=0.126 Sum_probs=34.6
Q ss_pred cccceEEEEeeCCCceeEEecCCCCCc-eEEeccccccCCccccCCCCcEEEEEEe
Q 047168 5 TRSTGKVTWFDGAKGYGFIRPDDGGAD-LFVHQKSIKSDGYRTLYENQSVEFDVQL 59 (258)
Q Consensus 5 ~~~~G~vk~f~~~kGfGFI~~~~~~~d-vF~H~s~l~~~~~~~l~~G~~V~F~v~~ 59 (258)
....|+|.........=+|+.+-++.. +...++.-.... -.|.+|+.|.+.+..
T Consensus 5 N~l~g~V~~ie~~g~~~~v~~~~~~~~~l~a~it~~~~~~-L~L~~G~~V~~~ik~ 59 (64)
T PF03459_consen 5 NQLPGTVESIENLGSEVEVTLDLGGGETLTARITPESAEE-LGLKPGDEVYASIKA 59 (64)
T ss_dssp EEEEEEEEEEEESSSEEEEEEEETTSEEEEEEEEHHHHHH-CT-STT-EEEEEE-G
T ss_pred cEEEEEEEEEEECCCeEEEEEEECCCCEEEEEEcHHHHHH-cCCCCCCEEEEEEeh
Confidence 457899999987777777776655445 666664433222 238899999988854
No 128
>PRK07899 rpsA 30S ribosomal protein S1; Reviewed
Probab=38.78 E-value=65 Score=31.45 Aligned_cols=53 Identities=19% Similarity=0.130 Sum_probs=38.1
Q ss_pred ccccceEEEEeeCCCceeEEecCCCCCceEEeccccccCCc----cccCCCCcEEEEEEeC
Q 047168 4 LTRSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGY----RTLYENQSVEFDVQLE 60 (258)
Q Consensus 4 ~~~~~G~vk~f~~~kGfGFI~~~~~~~dvF~H~s~l~~~~~----~~l~~G~~V~F~v~~~ 60 (258)
...+.|+|+... .||.+.... +-+.|+|++.|..... ..+++|+.|++.|..-
T Consensus 209 G~iv~G~V~~i~---~~G~FVdlg-gv~Glv~~Sels~~~v~~~~~~~kvGd~V~vkVl~i 265 (486)
T PRK07899 209 GQVRKGVVSSIV---NFGAFVDLG-GVDGLVHVSELSWKHIDHPSEVVEVGQEVTVEVLDV 265 (486)
T ss_pred CCEEEEEEEEEE---CCeEEEEEC-CEEEEEEHHHCCCcccCCHHHhcCCCCEEEEEEEEE
Confidence 356889999984 356544333 4899999999975432 2468999999987663
No 129
>PRK06299 rpsA 30S ribosomal protein S1; Reviewed
Probab=38.67 E-value=70 Score=31.48 Aligned_cols=52 Identities=25% Similarity=0.275 Sum_probs=37.8
Q ss_pred cccceEEEEeeCCCceeEEecCCCCCceEEeccccccCC-----ccccCCCCcEEEEEEe
Q 047168 5 TRSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDG-----YRTLYENQSVEFDVQL 59 (258)
Q Consensus 5 ~~~~G~vk~f~~~kGfGFI~~~~~~~dvF~H~s~l~~~~-----~~~l~~G~~V~F~v~~ 59 (258)
..+.|+|+... .||++.....+.+.|+|+++|.... ...+.+|+.|++.+..
T Consensus 288 ~~v~g~V~~i~---~~G~fV~l~~~v~Glv~~sel~~~~~~~~~~~~~~~G~~v~v~V~~ 344 (565)
T PRK06299 288 SKVKGKVTNIT---DYGAFVELEEGIEGLVHVSEMSWTKKNKHPSKVVSVGQEVEVMVLE 344 (565)
T ss_pred CEEEEEEEEEe---CCeEEEEeCCCCEEEEEHHHcCccccccCHHHhcCCCCEEEEEEEE
Confidence 56789999874 4676655544589999999986321 1347899999998765
No 130
>PF01336 tRNA_anti-codon: OB-fold nucleic acid binding domain; InterPro: IPR004365 The OB-fold (oligonucleotide/oligosaccharide-binding fold) is found in all three kingdoms and its common architecture presents a binding face that has adapted to bind different ligands. The OB-fold is a five/six-stranded closed beta-barrel formed by 70-80 amino acid residues. The strands are connected by loops of varying length which form the functional appendages of the protein. The majority of OB-fold proteins use the same face for ligand binding or as an active site. Different OB-fold proteins use this 'fold-related binding face' to, variously, bind oligosaccharides, oligonucleotides, proteins, metal ions and catalytic substrates. This entry contains OB-fold domains that bind to nucleic acids []. It includes the anti-codon binding domain of lysyl, aspartyl, and asparaginyl-tRNA synthetases (See IPR004364 from INTERPRO). Aminoacyl-tRNA synthetases catalyse the addition of an amino acid to the appropriate tRNA molecule 6.1.1 from EC. This domain is found in RecG helicase involved in DNA repair. Replication factor A is a heterotrimeric complex, that contains a subunit in this family [, ]. This domain is also found at the C terminus of bacterial DNA polymerase III alpha chain.; GO: 0003676 nucleic acid binding; PDB: 1BBU_A 1KRS_A 1BBW_A 1KRT_A 1EQR_B 1IL2_B 1C0A_A 3KFU_A 1EOV_A 1ASY_A ....
Probab=38.59 E-value=23 Score=24.06 Aligned_cols=53 Identities=19% Similarity=0.124 Sum_probs=36.5
Q ss_pred cceEEEEe-eCCCceeEEecCCCCCceEEeccc-cccCCccccCCCCcEEEEEEe
Q 047168 7 STGKVTWF-DGAKGYGFIRPDDGGADLFVHQKS-IKSDGYRTLYENQSVEFDVQL 59 (258)
Q Consensus 7 ~~G~vk~f-~~~kGfGFI~~~~~~~dvF~H~s~-l~~~~~~~l~~G~~V~F~v~~ 59 (258)
+.|+|..- ...+.+-|++.+|+...|-+.+-. ....-...|.+|+.|...=..
T Consensus 3 v~G~V~~~~~~~~~~~~~~l~D~tg~i~~~~~~~~~~~~~~~l~~g~~v~v~G~v 57 (75)
T PF01336_consen 3 VEGRVTSIRRSGGKIVFFTLEDGTGSIQVVFFNEEYERFREKLKEGDIVRVRGKV 57 (75)
T ss_dssp EEEEEEEEEEEETTEEEEEEEETTEEEEEEEETHHHHHHHHTS-TTSEEEEEEEE
T ss_pred EEEEEEEEEcCCCCEEEEEEEECCccEEEEEccHHhhHHhhcCCCCeEEEEEEEE
Confidence 56888888 888999999988876665555544 222234679999999877333
No 131
>PF05753 TRAP_beta: Translocon-associated protein beta (TRAPB); InterPro: IPR008856 This family consists of several eukaryotic translocon-associated protein beta (TRAPB) or signal sequence receptor beta subunit (SSR-beta) proteins. The normal translocation of nascent polypeptides into the lumen of the endoplasmic reticulum (ER) is thought to be aided in part by a translocon-associated protein (TRAP) complex consisting of 4 protein subunits. The association of mature proteins with the ER and Golgi, or other intracellular locales, such as lysosomes, depends on the initial targeting of the nascent polypeptide to the ER membrane. A similar scenario must also exist for proteins destined for secretion [].; GO: 0005783 endoplasmic reticulum, 0016021 integral to membrane
Probab=38.23 E-value=37 Score=28.58 Aligned_cols=47 Identities=23% Similarity=0.294 Sum_probs=34.3
Q ss_pred ecCCCCCceEEeccccccCCccccCCCCcEEEEEEeCCCccceeeccccCC
Q 047168 24 RPDDGGADLFVHQKSIKSDGYRTLYENQSVEFDVQLEADGKYQALDVTAPG 74 (258)
Q Consensus 24 ~~~~~~~dvF~H~s~l~~~~~~~l~~G~~V~F~v~~~~~G~~~A~~V~~~~ 74 (258)
..+|..-.|+++.+.+... +.+|+.|++++..-..|.-.|.+|++.+
T Consensus 15 ~~~~~~a~llv~K~il~~~----~v~g~~v~V~~~iyN~G~~~A~dV~l~D 61 (181)
T PF05753_consen 15 AQEDSPARLLVSKQILNKY----LVEGEDVTVTYTIYNVGSSAAYDVKLTD 61 (181)
T ss_pred ccCCCCcEEEEEEeecccc----ccCCcEEEEEEEEEECCCCeEEEEEEEC
Confidence 4455556677777766543 7888988877777667767899999888
No 132
>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional
Probab=38.19 E-value=62 Score=33.91 Aligned_cols=53 Identities=19% Similarity=0.231 Sum_probs=38.3
Q ss_pred cccceEEEEeeCCCceeEEecCCCCCceEEeccccccCCc----cccCCCCcEEEEEEeCC
Q 047168 5 TRSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGY----RTLYENQSVEFDVQLEA 61 (258)
Q Consensus 5 ~~~~G~vk~f~~~kGfGFI~~~~~~~dvF~H~s~l~~~~~----~~l~~G~~V~F~v~~~~ 61 (258)
..+.|+|+... .||++.... +-+-|+|+|.|...-. ..+++|+.|++.|..-+
T Consensus 495 ~~V~G~Vk~i~---~~G~fVdl~-Gv~Gfvp~SeiS~~~v~~~~~~~kvGq~v~vkVi~iD 551 (863)
T PRK12269 495 DSVSGVVKSFT---SFGAFIDLG-GFDGLLHVNDMSWGHVARPREFVKKGQTIELKVIRLD 551 (863)
T ss_pred CEEEEEEEEEe---CCcEEEEEC-CEEEEEEchhccccccCCHHHhccCCCEEEEEEEEEe
Confidence 46799999885 366665443 5789999999864322 23678999999987643
No 133
>PF11948 DUF3465: Protein of unknown function (DUF3465); InterPro: IPR021856 This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 131 to 151 amino acids in length. This protein has a conserved HWTH sequence motif.
Probab=38.08 E-value=88 Score=24.99 Aligned_cols=56 Identities=20% Similarity=0.226 Sum_probs=36.0
Q ss_pred cceEEEEeeCCCc-----eeEEecCCCCCceEEe-ccccccCCccccCCCCcEEEE--EEeCCCc
Q 047168 7 STGKVTWFDGAKG-----YGFIRPDDGGADLFVH-QKSIKSDGYRTLYENQSVEFD--VQLEADG 63 (258)
Q Consensus 7 ~~G~vk~f~~~kG-----fGFI~~~~~~~dvF~H-~s~l~~~~~~~l~~G~~V~F~--v~~~~~G 63 (258)
..|+|+...++.- -=||.....+..|+|= --+|. .-+..|++||.|+|. .+-+++|
T Consensus 41 g~G~V~~vLpdd~~GsrHQ~Fiv~l~~g~tllIahNIDla-prip~l~~GD~V~f~GeYe~n~kg 104 (131)
T PF11948_consen 41 GCGTVVKVLPDDNKGSRHQRFIVRLSSGQTLLIAHNIDLA-PRIPWLQKGDQVEFYGEYEWNPKG 104 (131)
T ss_pred ccEEEEEECcccCCCCcceEEEEEeCCCCEEEEEeccCcc-ccCcCcCCCCEEEEEEEEEECCCC
Confidence 4788888877633 3388777666666654 33332 445669999999986 3334454
No 134
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=37.93 E-value=52 Score=31.96 Aligned_cols=52 Identities=19% Similarity=0.133 Sum_probs=39.3
Q ss_pred ccccceEEEEeeCCCceeEEecCCCCCceEEeccccccCCccccCCCCcEEEEEEeCC
Q 047168 4 LTRSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGYRTLYENQSVEFDVQLEA 61 (258)
Q Consensus 4 ~~~~~G~vk~f~~~kGfGFI~~~~~~~dvF~H~s~l~~~~~~~l~~G~~V~F~v~~~~ 61 (258)
...++|+|+.+. ++ |+|... ++-+.|+|.+.+... ..+.+|++|.+.|..-+
T Consensus 135 GeIV~G~V~ri~--~~-giiVDL-ggvea~LP~sE~ip~--E~~~~GdrIka~I~~Vd 186 (470)
T PRK09202 135 GEIITGVVKRVE--RG-NIIVDL-GRAEAILPRKEQIPR--ENFRPGDRVRAYVYEVR 186 (470)
T ss_pred CCEEEEEEEEEe--cC-CEEEEE-CCeEEEecHHHcCCC--ccCCCCCEEEEEEEEEe
Confidence 356899999996 33 555533 457999999999755 56899999998877653
No 135
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=37.86 E-value=67 Score=32.58 Aligned_cols=60 Identities=20% Similarity=0.202 Sum_probs=43.1
Q ss_pred cccceEEEEeeCCCceeEEecCCCCCceEEeccccccCC----ccccCCCCcEEEEEEeC-CCcccee
Q 047168 5 TRSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDG----YRTLYENQSVEFDVQLE-ADGKYQA 67 (258)
Q Consensus 5 ~~~~G~vk~f~~~kGfGFI~~~~~~~dvF~H~s~l~~~~----~~~l~~G~~V~F~v~~~-~~G~~~A 67 (258)
..+.|+|+.-.+ ||-....-.+.|-++|+|.+...- -..|++||.|...+..- ++|+...
T Consensus 621 ~iy~G~V~ri~~---fGaFv~l~~gkdgl~hiS~~~~~rv~kv~dvlk~Gd~v~Vkv~~iD~~Gri~l 685 (692)
T COG1185 621 EVYEGTVVRIVD---FGAFVELLPGKDGLVHISQLAKERVEKVEDVLKEGDEVKVKVIEIDKQGRIRL 685 (692)
T ss_pred cEEEEEEEEEee---cceEEEecCCcceeEEehhhhhhhhhcccceeecCceEEEEEeeecccCCccc
Confidence 568999999865 885555555689999999997641 13578888888777664 4575433
No 136
>KOG0107 consensus Alternative splicing factor SRp20/9G8 (RRM superfamily) [RNA processing and modification]
Probab=37.84 E-value=24 Score=29.71 Aligned_cols=19 Identities=37% Similarity=1.018 Sum_probs=14.4
Q ss_pred CCcccccCCCCcccccccc
Q 047168 128 GVVCYNCDGVGHVARECTS 146 (258)
Q Consensus 128 ~~~C~~Cg~~GH~a~~Cp~ 146 (258)
...|+.|++.||+.+.|-.
T Consensus 100 ~~~~~r~G~rg~~~r~~~~ 118 (195)
T KOG0107|consen 100 RGFCYRCGERGHIGRNCKD 118 (195)
T ss_pred ccccccCCCcccccccccc
Confidence 3458888888888888754
No 137
>PRK06676 rpsA 30S ribosomal protein S1; Reviewed
Probab=37.55 E-value=86 Score=29.22 Aligned_cols=56 Identities=13% Similarity=0.031 Sum_probs=39.7
Q ss_pred ccccceEEEEeeCCCceeEEecCCCCCceEEeccccccC----CccccCCCCcEEEEEEeCC
Q 047168 4 LTRSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSD----GYRTLYENQSVEFDVQLEA 61 (258)
Q Consensus 4 ~~~~~G~vk~f~~~kGfGFI~~~~~~~dvF~H~s~l~~~----~~~~l~~G~~V~F~v~~~~ 61 (258)
.+.+.|+|+..+. .+=||..+....+.|+|.+.+... ....+.+|+.|++.|....
T Consensus 18 G~iv~G~V~~i~~--~g~~V~i~~~~~~g~lp~~e~~~~~~~~~~~~~~vGd~v~~~V~~v~ 77 (390)
T PRK06676 18 GDVVTGEVLKVED--KQVFVNIEGYKVEGVIPISELSNDHIEDINDVVKVGDELEVYVLKVE 77 (390)
T ss_pred CCEEEEEEEEEEC--CeEEEEEecCCcEEEEEHHHhccccccCcccccCCCCEEEEEEEEEE
Confidence 3568899999963 334555424457899999999642 1234789999999887754
No 138
>COG0539 RpsA Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]
Probab=37.17 E-value=57 Score=32.24 Aligned_cols=54 Identities=26% Similarity=0.230 Sum_probs=41.0
Q ss_pred ccccceEEEEeeCCCceeEEecCCCCCceEEeccccccCCccc----cCCCCcEEEEEEeC
Q 047168 4 LTRSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGYRT----LYENQSVEFDVQLE 60 (258)
Q Consensus 4 ~~~~~G~vk~f~~~kGfGFI~~~~~~~dvF~H~s~l~~~~~~~----l~~G~~V~F~v~~~ 60 (258)
...+.|+|+.+- -||.+..-..+-+=|+|+|.|....... |.+||.|+..+..-
T Consensus 278 g~~v~G~Vt~i~---~~GafVei~~GvEGlvhvSEisw~~~~~P~evv~~Gq~V~V~Vl~i 335 (541)
T COG0539 278 GDKVEGKVTNLT---DYGAFVEIEEGVEGLVHVSEISWTKKNVPSEVVKVGQEVEVKVLDI 335 (541)
T ss_pred CCEEEEEEEEee---cCcEEEEecCCccceeechhhcccccCCHHHhcccCCEEEEEEEee
Confidence 356789999884 5776666666789999999886655443 78999999887664
No 139
>KOG2813 consensus Predicted molecular chaperone, contains DnaJ domain [Posttranslational modification, protein turnover, chaperones]
Probab=36.98 E-value=55 Score=30.24 Aligned_cols=34 Identities=26% Similarity=0.698 Sum_probs=24.7
Q ss_pred CCccccCCCCCccCCCCCCCCCCCCCccccCCCCCc
Q 047168 213 GGRCYNCGKSGHLARDCGAGGAGGGGSCFNCGKPGH 248 (258)
Q Consensus 213 ~~~C~~Cg~~GH~~~~Cp~~~~~~~~~C~~Cg~~GH 248 (258)
...||+|...|- +.|+.-...+...|-.|...|-
T Consensus 234 ~~~C~~C~G~G~--~~C~tC~grG~k~C~TC~gtgs 267 (406)
T KOG2813|consen 234 HDLCYMCHGRGI--KECHTCKGRGKKPCTTCSGTGS 267 (406)
T ss_pred cchhhhccCCCc--ccCCcccCCCCcccccccCccc
Confidence 347999988874 5677766556778888887763
No 140
>PRK10811 rne ribonuclease E; Reviewed
Probab=36.83 E-value=77 Score=33.66 Aligned_cols=69 Identities=20% Similarity=0.246 Sum_probs=49.8
Q ss_pred cccceEEEEeeCCCceeEEecCCCCCceEEeccccccCCc-------------cccCCCCcEEEEEEeCC---Cccceee
Q 047168 5 TRSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGY-------------RTLYENQSVEFDVQLEA---DGKYQAL 68 (258)
Q Consensus 5 ~~~~G~vk~f~~~kGfGFI~~~~~~~dvF~H~s~l~~~~~-------------~~l~~G~~V~F~v~~~~---~G~~~A~ 68 (258)
.-|.|+|+......+=-||...++ ..-|+|++++....| ..|.+|+.|...|...+ ||.....
T Consensus 40 nIYkGkVenIvPGInAAFVDIG~g-knGFL~L~Di~~~~f~~~~~~~~~~~i~~~Lk~GqeILVQV~KEa~gtKGp~LTt 118 (1068)
T PRK10811 40 NIYKGKITRIEPSLEAAFVDYGAE-RHGFLPLKEIAREYFPANYSAHGRPNIKDVLREGQEVIVQIDKEERGNKGAALTT 118 (1068)
T ss_pred ceEEEEEecccCCcceeEEEecCC-cceEEEhhhccccccccccccccccccccccCCCCEEEEEEeecccCCCCCceee
Confidence 457899999988888889998874 899999988853211 13889999999998864 4433344
Q ss_pred ccccCC
Q 047168 69 DVTAPG 74 (258)
Q Consensus 69 ~V~~~~ 74 (258)
+|++++
T Consensus 119 ~ISLpG 124 (1068)
T PRK10811 119 FISLAG 124 (1068)
T ss_pred eEEecc
Confidence 555443
No 141
>cd04451 S1_IF1 S1_IF1: Translation Initiation Factor IF1, S1-like RNA-binding domain. IF1 contains an S1-like RNA-binding domain, which is found in a wide variety of RNA-associated proteins. Translation initiation includes a number of interrelated steps preceding the formation of the first peptide bond. In Escherichia coli, the initiation mechanism requires, in addition to mRNA, fMet-tRNA, and ribosomal subunits, the presence of three additional proteins (initiation factors IF1, IF2, and IF3) and at least one GTP molecule. The three initiation factors influence both the kinetics and the stability of ternary complex formation. IF1 is the smallest of the three factors. IF1 enhances the rate of 70S ribosome subunit association and dissociation and the interaction of 30S ribosomal subunit with IF2 and IF3. It stimulates 30S complex formation. In addition, by binding to the A-site of the 30S ribosomal subunit, IF1 may contribute to the fidelity of the selection of the initiation site of th
Probab=36.80 E-value=1.3e+02 Score=20.24 Aligned_cols=51 Identities=14% Similarity=0.160 Sum_probs=28.9
Q ss_pred cceEEEEeeCCCceeEEecCCCCCceEEeccccccCCccccCCCCcEEEEEEe
Q 047168 7 STGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGYRTLYENQSVEFDVQL 59 (258)
Q Consensus 7 ~~G~vk~f~~~kGfGFI~~~~~~~dvF~H~s~l~~~~~~~l~~G~~V~F~v~~ 59 (258)
++|+|...- ..+|=.|..+++ +.+-.+..-........+.+||.|+|++..
T Consensus 3 ~~G~Vi~~~-~g~~~~V~~~~g-~~~~c~~rGklr~~~~~~~vGD~V~~~~~~ 53 (64)
T cd04451 3 MEGVVTEAL-PNAMFRVELENG-HEVLAHISGKMRMNYIRILPGDRVKVELSP 53 (64)
T ss_pred EEEEEEEEe-CCCEEEEEeCCC-CEEEEEECceeecCCcccCCCCEEEEEEee
Confidence 567776541 135666765443 444455443221112348999999999764
No 142
>TIGR00830 PTBA PTS system, glucose subfamily, IIA component. These are part of the The PTS Glucose-Glucoside (Glc) SuperFamily. The Glc family includes permeases specific for glucose, N-acetylglucosamine and a large variety of a- and b-glucosides. However, not all b-glucoside PTS permeases are in this class, as the cellobiose (Cel) b-glucoside PTS permease is in the Lac family (TC #4.A.3). The IIA, IIB and IIC domains of all of the permeases listed below are demonstrably homologous. These permeases show limited sequence similarity with members of the Fru family (TC #4.A.2). Several of the PTS permeases in the Glc family lack their own IIA domains and instead use the glucose IIA protein (IIAglc or Crr). Most of these permeases have the B and C domains linked together in a single polypeptide chain, and a cysteyl residue in the IIB domain is phosphorylated by direct phosphoryl transfer from IIAglc(his~P). Those permeases which lack a IIA domain include the maltose (Mal), arbutin-salicin-c
Probab=36.79 E-value=91 Score=24.47 Aligned_cols=47 Identities=26% Similarity=0.551 Sum_probs=28.9
Q ss_pred ccceEEEEeeCCC-ceeEEecCCCCCceEEecc----ccccCCccc-cCCCCcEE
Q 047168 6 RSTGKVTWFDGAK-GYGFIRPDDGGADLFVHQK----SIKSDGYRT-LYENQSVE 54 (258)
Q Consensus 6 ~~~G~vk~f~~~k-GfGFI~~~~~~~dvF~H~s----~l~~~~~~~-l~~G~~V~ 54 (258)
...|+|++..+.+ -|| |+.++ +-+|++|+. .|...+|.. +++||.|+
T Consensus 41 P~~G~v~~v~~T~HA~g-i~~~~-G~evLiHiGidTV~L~G~gF~~~v~~Gd~V~ 93 (121)
T TIGR00830 41 PVDGKIGKIFPTKHAFG-IESDS-GVEILIHIGIDTVKLNGEGFTSHVEEGQRVK 93 (121)
T ss_pred cCCeEEEEEccCCCEEE-EEeCC-CcEEEEEeeeceeecCCCceEEEecCCCEEc
Confidence 4679999876544 344 44444 589999984 444455543 34566654
No 143
>PF06523 DUF1106: Protein of unknown function (DUF1106); InterPro: IPR009490 This family consists of several hypothetical bacterial proteins found in Escherichia coli and Citrobacter rodentium. The function of this family is unknown.
Probab=36.76 E-value=99 Score=22.14 Aligned_cols=55 Identities=18% Similarity=0.425 Sum_probs=40.0
Q ss_pred cccceEEEEeeCCCceeEEec---CCCCCceEE-eccccccCCccccCCCCcEEEEEEe
Q 047168 5 TRSTGKVTWFDGAKGYGFIRP---DDGGADLFV-HQKSIKSDGYRTLYENQSVEFDVQL 59 (258)
Q Consensus 5 ~~~~G~vk~f~~~kGfGFI~~---~~~~~dvF~-H~s~l~~~~~~~l~~G~~V~F~v~~ 59 (258)
-+..|+|..+.-.+|--+++. +.....||+ |..+..-+-++.+-+.+.++|.++-
T Consensus 31 grlrgiv~t~kcs~g~iylsi~v~pnn~~hi~ly~kk~yi~dklkeifpde~iefsiey 89 (91)
T PF06523_consen 31 GRLRGIVLTIKCSNGIIYLSIKVNPNNSNHIFLYHKKNYIFDKLKEIFPDEAIEFSIEY 89 (91)
T ss_pred eceeeEEEEEEecCcEEEEEEEeCCCCcceEEEEecchhHHHHHHHhCCCCceEEEEEe
Confidence 467899999999999877652 234466776 4455555556778899999999874
No 144
>CHL00010 infA translation initiation factor 1
Probab=36.12 E-value=1.5e+02 Score=21.18 Aligned_cols=54 Identities=15% Similarity=0.071 Sum_probs=32.4
Q ss_pred cccceEEEEeeCCCceeEEecCCCCCceEEeccccccCCccccCCCCcEEEEEEeC
Q 047168 5 TRSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGYRTLYENQSVEFDVQLE 60 (258)
Q Consensus 5 ~~~~G~vk~f~~~kGfGFI~~~~~~~dvF~H~s~l~~~~~~~l~~G~~V~F~v~~~ 60 (258)
..++|+|...-. .+|=.|..+++ ..+-.++.-........+.+||.|+|++..-
T Consensus 7 ~~~~G~Vik~lg-~~~y~V~~~~g-~~~~c~~rGklr~~~i~~~vGD~V~ve~~~~ 60 (78)
T CHL00010 7 IEMEGLVTESLP-NGMFRVRLDNG-CQVLGYISGKIRRNSIRILPGDRVKVELSPY 60 (78)
T ss_pred EEEEEEEEEEcC-CCEEEEEeCCC-CEEEEEeccceecCCcccCCCCEEEEEEccc
Confidence 357888887632 34445554443 5666665543222223478999999996443
No 145
>PF01345 DUF11: Domain of unknown function DUF11; InterPro: IPR001434 This group of sequences is represented by a conserved region of about 53 amino acids shared between regions, usually repeated, of proteins from a small number of phylogenetically distant prokaryotes. Examples include a 132-residue region found repeated in three of the five longest proteins of Bacillus anthracis, a 131-residue repeat in a cell wall-anchored protein of Enterococcus faecalis (Streptococcus faecalis), and a 120-residue repeat in Methanobacterium thermoautotrophicum. A similar region is found in some Chlamydia trachomatis outer membrane proteins. In C. trachomatis, three cysteine-rich proteins (also believed to be lipoproteins), MOMP, OMP6 and OMP3, make up the extracellular matrix of the outer membrane []. They are involved in the essential structural integrity of both the elementary body (EB) and recticulate body (RB) phase. They are thought to be involved in porin formation and, as these bacteria lack the peptidoglycan layer common to most Gram-negative microbes, such proteins are highly important in the pathogenicity of the organism.; GO: 0005727 extrachromosomal circular DNA
Probab=35.49 E-value=30 Score=24.16 Aligned_cols=31 Identities=16% Similarity=0.264 Sum_probs=25.6
Q ss_pred cccCCCCcEEEEEEeCCCccceeeccccCCC
Q 047168 45 RTLYENQSVEFDVQLEADGKYQALDVTAPGG 75 (258)
Q Consensus 45 ~~l~~G~~V~F~v~~~~~G~~~A~~V~~~~g 75 (258)
..+.+||.|+|.|.....|...|.+|.+.+.
T Consensus 35 ~~~~~Gd~v~ytitvtN~G~~~a~nv~v~D~ 65 (76)
T PF01345_consen 35 STANPGDTVTYTITVTNTGPAPATNVVVTDT 65 (76)
T ss_pred CcccCCCEEEEEEEEEECCCCeeEeEEEEEc
Confidence 4589999999999998888777888876654
No 146
>COG0557 VacB Exoribonuclease R [Transcription]
Probab=35.27 E-value=67 Score=32.78 Aligned_cols=60 Identities=28% Similarity=0.459 Sum_probs=42.5
Q ss_pred ceEEEEeeCCCceeEEecCC--CCCceEEeccccccCCccccCCCCcEEEEEEeCC-Ccc-ceeeccccCC
Q 047168 8 TGKVTWFDGAKGYGFIRPDD--GGADLFVHQKSIKSDGYRTLYENQSVEFDVQLEA-DGK-YQALDVTAPG 74 (258)
Q Consensus 8 ~G~vk~f~~~kGfGFI~~~~--~~~dvF~H~s~l~~~~~~~l~~G~~V~F~v~~~~-~G~-~~A~~V~~~~ 74 (258)
.|++.+= .+||+|+.+++ ...||||-...+.. ...|+.|..++.... +++ .+|.-|.++.
T Consensus 71 ~~~~~~~--~~gf~f~~~~~~~~~~d~~v~~~~~~~-----a~~gD~V~v~~~~~~~~~~~~~~~v~~il~ 134 (706)
T COG0557 71 EGIVEAS--AKGFGFLSPDDSKDADDIFVPKDPLNR-----ALHGDRVLVELLPSDKRGRFKEAAVVRILE 134 (706)
T ss_pred cceEEec--cCCceeeccCccCCCCcEEeccccccc-----cccCCEEEEEECcccccCCCceEEEEeeec
Confidence 4555543 89999999998 67899999888533 478999998865543 331 4566666555
No 147
>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional
Probab=35.11 E-value=67 Score=33.69 Aligned_cols=53 Identities=15% Similarity=0.063 Sum_probs=40.2
Q ss_pred cccceEEEEeeCCCceeEEecCCCCCceEEeccccccC-C----ccccCCCCcEEEEEEeC
Q 047168 5 TRSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSD-G----YRTLYENQSVEFDVQLE 60 (258)
Q Consensus 5 ~~~~G~vk~f~~~kGfGFI~~~~~~~dvF~H~s~l~~~-~----~~~l~~G~~V~F~v~~~ 60 (258)
+.++|+|+... -||.+.....+-+-|+|+|.|... . ...+++|+.|+..|..-
T Consensus 580 ~iV~G~V~~I~---~fG~fVeL~~gveGLvhiSEls~~~~~~~p~~~~kvGd~V~vkVl~i 637 (863)
T PRK12269 580 DVVKGRVTKIA---DFGAFIELAEGIEGLAHISEFSWVKKTSKPSDMVKIGDEVECMILGY 637 (863)
T ss_pred CEEEEEEEEEe---CCeEEEEecCCceeeeEHHHhcCccccCCHHHcCCCCCEEEEEEEEE
Confidence 56889999985 488766555567899999999752 1 23578999999988774
No 148
>PRK13150 cytochrome c-type biogenesis protein CcmE; Reviewed
Probab=34.74 E-value=1.4e+02 Score=24.71 Aligned_cols=63 Identities=24% Similarity=0.151 Sum_probs=45.7
Q ss_pred cceEEEEeeCCCceeEEecCCCCCceEEeccccccCCccccCCCCcEEEEEEeCCCccceeeccccC
Q 047168 7 STGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGYRTLYENQSVEFDVQLEADGKYQALDVTAP 73 (258)
Q Consensus 7 ~~G~vk~f~~~kGfGFI~~~~~~~dvF~H~s~l~~~~~~~l~~G~~V~F~v~~~~~G~~~A~~V~~~ 73 (258)
..|.|+|-...-..=|...|. ..+|.|..+-+..+- ..+|+.|.-+=...++|.++|.+|-.-
T Consensus 67 ~~GSv~r~~~~~~v~F~vtD~-~~~v~V~Y~GilPDl---FrEG~gVVveG~~~~~g~F~A~evLAK 129 (159)
T PRK13150 67 MPGSVRRDPDSLKVNFSLYDA-EGSVTVSYEGILPDL---FREGQGVVVQGTLEKGNHVLAHEVLAK 129 (159)
T ss_pred eCCcEEECCCCcEEEEEEEcC-CcEEEEEEeccCCcc---ccCCCeEEEEEEECCCCEEEEeEEEeC
Confidence 345555543344577887775 578999999998774 578999988877777777888887654
No 149
>PRK13165 cytochrome c-type biogenesis protein CcmE; Reviewed
Probab=34.30 E-value=1.4e+02 Score=24.75 Aligned_cols=63 Identities=24% Similarity=0.197 Sum_probs=45.6
Q ss_pred cceEEEEeeCCCceeEEecCCCCCceEEeccccccCCccccCCCCcEEEEEEeCCCccceeeccccC
Q 047168 7 STGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGYRTLYENQSVEFDVQLEADGKYQALDVTAP 73 (258)
Q Consensus 7 ~~G~vk~f~~~kGfGFI~~~~~~~dvF~H~s~l~~~~~~~l~~G~~V~F~v~~~~~G~~~A~~V~~~ 73 (258)
..|.|.|-...-.+=|...|. ...|.|..+-+..+- ..+|+.|.-+=...+++.++|.+|-.-
T Consensus 67 ~~GSi~r~~~~l~v~F~vtD~-~~~v~V~Y~GilPDl---FrEG~gVVveG~~~~~g~F~A~~vLAK 129 (160)
T PRK13165 67 MPGSVQRDPNSLKVSFTLYDA-GGSVTVTYEGILPDL---FREGQGIVAQGVLEEGNHIEAKEVLAK 129 (160)
T ss_pred eCCcEEECCCCeEEEEEEEcC-CeEEEEEEcccCCcc---ccCCCeEEEEEEECCCCeEEEEEEEec
Confidence 345666633333578887765 578999999998875 578999987777776677888887643
No 150
>KOG3070 consensus Predicted RNA-binding protein containing PIN domain and invovled in translation or RNA processing [Translation, ribosomal structure and biogenesis]
Probab=34.16 E-value=2.6e+02 Score=24.54 Aligned_cols=61 Identities=10% Similarity=-0.083 Sum_probs=38.0
Q ss_pred eEEEEeeCCCceeEEecCCCCCceEEeccccccCC---ccccCCCCcEEEEEEeCCCccceeeccc
Q 047168 9 GKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDG---YRTLYENQSVEFDVQLEADGKYQALDVT 71 (258)
Q Consensus 9 G~vk~f~~~kGfGFI~~~~~~~dvF~H~s~l~~~~---~~~l~~G~~V~F~v~~~~~G~~~A~~V~ 71 (258)
|-|..=|....+.++.++... |++++...+...+ .-.+.++..+++.+....-+ -..+..+
T Consensus 71 gFi~~~d~~~D~fvhQs~i~~-~~~~~~~rs~~~~e~v~f~~~~~~~g~~a~~vt~p~-g~~~~~s 134 (235)
T KOG3070|consen 71 GFITRDDGPEDVFVHQSAITK-YTPSEGFRSLKEGEAVPFDIQEGNKGTEAANVTGPD-GVPVRGS 134 (235)
T ss_pred ceecccCCCCceeEEeeeecc-cccccchhhcccCCCccceecccCccceeeeecCCC-Ccccccc
Confidence 334444677788888888877 9998877765554 12345666667777666544 2344433
No 151
>cd00210 PTS_IIA_glc PTS_IIA, PTS system, glucose/sucrose specific IIA subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. This family is one of four structurally and functionally distinct group IIA PTS system cytoplasmic enzymes, necessary for the uptake of carbohydrates across the cytoplasmic membrane and their phosphorylation.
Probab=33.56 E-value=1.1e+02 Score=24.17 Aligned_cols=48 Identities=21% Similarity=0.342 Sum_probs=28.5
Q ss_pred ccceEEEEeeCCCceeEEecCCCCCceEEeccc----cccCCccc-cCCCCcEE
Q 047168 6 RSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKS----IKSDGYRT-LYENQSVE 54 (258)
Q Consensus 6 ~~~G~vk~f~~~kGfGFI~~~~~~~dvF~H~s~----l~~~~~~~-l~~G~~V~ 54 (258)
...|+|++..+.+-.=-|+.++ +-+|++|+.. |...+|.. +++|+.|.
T Consensus 41 P~~G~v~~i~~T~HA~~i~~~~-G~eiLiHiGidTv~l~g~gF~~~vk~Gd~V~ 93 (124)
T cd00210 41 PVDGTIVQIFPTKHAIGIESDS-GVEILIHIGIDTVKLNGEGFTSHVEEGQRVK 93 (124)
T ss_pred cCCeEEEEEccCCCEEEEEeCC-CcEEEEEeeeeeeecCCCceEEEecCCCEEc
Confidence 4679999876544332244444 4899999843 34445442 34666654
No 152
>KOG3116 consensus Predicted C3H1-type Zn-finger protein [General function prediction only]
Probab=33.04 E-value=13 Score=30.34 Aligned_cols=20 Identities=35% Similarity=0.728 Sum_probs=16.9
Q ss_pred CCcccccCCcccCcccCCCC
Q 047168 187 SGGCFKCGGYGHLARDCITR 206 (258)
Q Consensus 187 ~~~C~~Cg~~GH~~~~C~~~ 206 (258)
...|.+|-+.|||..+|.+.
T Consensus 27 ~~rCQKClq~GHWtYECk~k 46 (177)
T KOG3116|consen 27 SARCQKCLQAGHWTYECKNK 46 (177)
T ss_pred chhHHHHHhhccceeeecCc
Confidence 46899999999999999876
No 153
>PF12353 eIF3g: Eukaryotic translation initiation factor 3 subunit G ; InterPro: IPR024675 At least eleven different protein factors are involved in initiation of protein synthesis in eukaryotes. Binding of initiator tRNA and mRNA to the 40S subunit requires the presence of the translation initiation factors eIF-2 and eIF-3, with eIF-3 being particularly important for 80S ribosome dissociation and mRNA binding []. eIF-3 is the most complex translation inititation factor, consisting of about 13 putative subunits and having a molecular weight of between 550 - 700 kDa in mammalian cells. Subunits are designated eIF-3a - eIF-3m; the large number of subunits means that the interactions between the individual subunits that make up the eIF-3 complex are complex and varied. Subunit G is required for eIF3 integrity. This entry represents a domain of approximately 130 amino acids in length found at the N terminus of eukaryotic translation initiation factor 3 subunit G. This domain is commonly found in association with the RNA recognition domain PF00076 from PFAM.
Probab=32.90 E-value=23 Score=28.07 Aligned_cols=17 Identities=24% Similarity=0.626 Sum_probs=8.7
Q ss_pred CccccCCCCCccCCCCCC
Q 047168 238 GSCFNCGKPGHFARECTK 255 (258)
Q Consensus 238 ~~C~~Cg~~GH~~~~Cp~ 255 (258)
+.|..|+ ..||...||-
T Consensus 107 v~CR~Ck-GdH~T~~CPy 123 (128)
T PF12353_consen 107 VKCRICK-GDHWTSKCPY 123 (128)
T ss_pred EEeCCCC-CCcccccCCc
Confidence 3455553 5555555554
No 154
>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=32.47 E-value=91 Score=30.20 Aligned_cols=51 Identities=24% Similarity=0.388 Sum_probs=36.5
Q ss_pred cccceEEEEeeCCCcee-EEecCCCCCceEEeccccccCC-----ccccCCCCcEEEEEEe
Q 047168 5 TRSTGKVTWFDGAKGYG-FIRPDDGGADLFVHQKSIKSDG-----YRTLYENQSVEFDVQL 59 (258)
Q Consensus 5 ~~~~G~vk~f~~~kGfG-FI~~~~~~~dvF~H~s~l~~~~-----~~~l~~G~~V~F~v~~ 59 (258)
..+.|+|+... .|| |+...+ +-+.|+|++.+.... ...+.+|+.|++.|..
T Consensus 274 ~i~~g~V~~v~---~~G~fV~l~~-~v~g~v~~sels~~~~~~~~~~~~~vG~~v~v~V~~ 330 (516)
T TIGR00717 274 DKITGRVTNLT---DYGVFVEIEE-GIEGLVHVSEMSWVKKNSHPSKVVKKGDEVEVMILD 330 (516)
T ss_pred CEEEEEEEEee---CCcEEEEeCC-CCEEEEEHHHcCCccccCCHHHhccCCCEEEEEEEE
Confidence 56789999874 466 454443 579999999986421 1237899999999754
No 155
>PRK07400 30S ribosomal protein S1; Reviewed
Probab=31.89 E-value=89 Score=28.60 Aligned_cols=52 Identities=10% Similarity=0.028 Sum_probs=37.5
Q ss_pred cccceEEEEeeCCCceeEEecCCCCCceEEeccccccCCccccCCCCcEEEEEEeC
Q 047168 5 TRSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGYRTLYENQSVEFDVQLE 60 (258)
Q Consensus 5 ~~~~G~vk~f~~~kGfGFI~~~~~~~dvF~H~s~l~~~~~~~l~~G~~V~F~v~~~ 60 (258)
..++|+|+..+ .+|++.... +-+-|+|+|.|.........+|+.|++.|..-
T Consensus 120 ~~V~g~V~~~~---~~G~~V~l~-Gv~gfip~s~ls~~~~~~~~vG~~i~~kVl~i 171 (318)
T PRK07400 120 ATVRSEVFATN---RGGALVRIE-GLRGFIPGSHISTRKPKEELVGEELPLKFLEV 171 (318)
T ss_pred CEEEEEEEEEE---CCeEEEEEC-CEEEEEEHHHcCccCCccccCCCEEEEEEEEE
Confidence 56788998886 346665444 57889999999754334456999999888764
No 156
>PRK06299 rpsA 30S ribosomal protein S1; Reviewed
Probab=31.83 E-value=92 Score=30.65 Aligned_cols=54 Identities=26% Similarity=0.225 Sum_probs=38.7
Q ss_pred ccccceEEEEeeCCCceeEEecCCCCCceEEeccccccC-----CccccCCCCcEEEEEEeC
Q 047168 4 LTRSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSD-----GYRTLYENQSVEFDVQLE 60 (258)
Q Consensus 4 ~~~~~G~vk~f~~~kGfGFI~~~~~~~dvF~H~s~l~~~-----~~~~l~~G~~V~F~v~~~ 60 (258)
.+.+.|+|+... .||++...+..-+.|+|+++|... ....+++|+.|+..+..-
T Consensus 374 G~~v~g~V~~v~---~~G~fV~l~~~v~g~i~~s~l~~~~~~~~~~~~~~~Gd~v~v~Il~v 432 (565)
T PRK06299 374 GDVVEGKVKNIT---DFGAFVGLEGGIDGLVHLSDISWDKKGEEAVELYKKGDEVEAVVLKV 432 (565)
T ss_pred CCEEEEEEEEEe---cceEEEECCCCCEEEEEHHHcCccccccChHhhCCCCCEEEEEEEEE
Confidence 356889999874 466655555458999999999642 124578999999876553
No 157
>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=31.70 E-value=85 Score=32.02 Aligned_cols=54 Identities=17% Similarity=0.305 Sum_probs=37.8
Q ss_pred cccceEEEEeeCCCceeEE-ecCCCCCceEEeccccccCCc---------------cccCCCCcEEEEEEeCC
Q 047168 5 TRSTGKVTWFDGAKGYGFI-RPDDGGADLFVHQKSIKSDGY---------------RTLYENQSVEFDVQLEA 61 (258)
Q Consensus 5 ~~~~G~vk~f~~~kGfGFI-~~~~~~~dvF~H~s~l~~~~~---------------~~l~~G~~V~F~v~~~~ 61 (258)
..+.|+|+... .|||. ..++...+-|||++.|....| +.++.||.|+..|..-+
T Consensus 629 ~~~~g~V~~v~---~fGifV~L~~~~~eGlvhis~l~~d~~~~d~~~~~l~g~~~~~~~~lGd~V~Vkv~~vd 698 (709)
T TIGR02063 629 EEFEGVISGVT---SFGLFVELENNTIEGLVHISTLKDDYYVFDEKGLALVGERTGKVFRLGDRVKVRVVKAD 698 (709)
T ss_pred cEEEEEEEEEE---eCCEEEEecCCceEEEEEeeecCCCcEEEcccceEEEeccCCcEECCCCEEEEEEEEEe
Confidence 46889999874 47774 444435899999999974322 34678888888877653
No 158
>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=31.70 E-value=1e+02 Score=28.60 Aligned_cols=53 Identities=11% Similarity=0.097 Sum_probs=39.6
Q ss_pred ccccceEEEEeeCCCceeEEecCCCCCceEEeccccccCCccccCCCCcEEEEEEeCC
Q 047168 4 LTRSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGYRTLYENQSVEFDVQLEA 61 (258)
Q Consensus 4 ~~~~~G~vk~f~~~kGfGFI~~~~~~~dvF~H~s~l~~~~~~~l~~G~~V~F~v~~~~ 61 (258)
...++|+|+.++ ..+|=||.. +.-+-|++.+.+... ..+.+|++|++-+..-+
T Consensus 132 GeiV~G~V~~v~-~~g~v~Vdi--G~~ea~LP~~E~ip~--E~~~~Gd~ik~~V~~V~ 184 (341)
T TIGR01953 132 GEIISGTVKRVN-RRGNLYVEL--GKTEGILPKKEQIPG--EKFRIGDRIKAYVYEVR 184 (341)
T ss_pred CCEEEEEEEEEe-cCCcEEEEE--CCeEEEecHHHcCCC--cCCCCCCEEEEEEEEEE
Confidence 356799999985 445545544 467999999999755 45899999998877654
No 159
>cd03524 RPA2_OBF_family RPA2_OBF_family: A family of oligonucleotide binding (OB) folds with similarity to the OB fold of the single strand (ss) DNA-binding domain (DBD)-D of human RPA2 (also called RPA32). RPA2 is a subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). RPA contains six OB folds, which are involved in ssDNA binding and in trimerization. The ssDNA binding mechanism is believed to be multistep and to involve conformational change. This family also includes OB folds similar to those found in Escherichia coli SSB, the wedge domain of E. coli RecG (a branched-DNA-specific helicase), E. coli ssDNA specific exodeoxyribonuclease VII large subunit, Pyroco
Probab=31.67 E-value=1.1e+02 Score=19.77 Aligned_cols=54 Identities=17% Similarity=0.087 Sum_probs=33.5
Q ss_pred cceEEEEeeCCC---ceeEEecCCCC-CceEEeccccccCC-ccccCCCCcEEEEEEeC
Q 047168 7 STGKVTWFDGAK---GYGFIRPDDGG-ADLFVHQKSIKSDG-YRTLYENQSVEFDVQLE 60 (258)
Q Consensus 7 ~~G~vk~f~~~k---GfGFI~~~~~~-~dvF~H~s~l~~~~-~~~l~~G~~V~F~v~~~ 60 (258)
+.|.|......+ .|.+++.+|.. ..+-+-+-.-.... ...+.+|+.|.+.....
T Consensus 2 v~g~v~~~~~~~~~~~~~~~~l~D~~~~~i~~~~~~~~~~~~~~~~~~g~~v~v~g~v~ 60 (75)
T cd03524 2 IVGIVVAVEEIRTEGKVLIFTLTDGTGGTIRVTLFGELAEELENLLKEGQVVYIKGKVK 60 (75)
T ss_pred eEEEEEeecccccCCeEEEEEEEcCCCCEEEEEEEchHHHHHHhhccCCCEEEEEEEEE
Confidence 567888887665 78999988865 55443332211111 13578888888775554
No 160
>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=29.86 E-value=1.2e+02 Score=30.63 Aligned_cols=54 Identities=22% Similarity=0.421 Sum_probs=38.4
Q ss_pred cccceEEEEeeCCCceeE-EecCCCCCceEEeccccccCCc---------------cccCCCCcEEEEEEeCC
Q 047168 5 TRSTGKVTWFDGAKGYGF-IRPDDGGADLFVHQKSIKSDGY---------------RTLYENQSVEFDVQLEA 61 (258)
Q Consensus 5 ~~~~G~vk~f~~~kGfGF-I~~~~~~~dvF~H~s~l~~~~~---------------~~l~~G~~V~F~v~~~~ 61 (258)
..+.|+|+... -||| |..++...+-|||+++|....| +.++.||.|+..+..-+
T Consensus 574 ~~~~g~I~~v~---~~GifV~L~~~~veGlV~~s~l~~d~y~~d~~~~~l~g~~~~~~~~lGD~V~Vki~~vd 643 (654)
T TIGR00358 574 TEFSGEISSVT---RFGMFVRLDDNGIDGLIHISTLHNDYYVFDQEKMALIGKGTGKVYRIGDRVTVKLTEVN 643 (654)
T ss_pred cEEEEEEEeEE---cCcEEEEecCCceEEEEEeEeCCCcceEEeccccEEEeccCCcEECCCCEEEEEEEEEe
Confidence 46789999885 3555 6666567999999999965421 34678888887776643
No 161
>PRK00276 infA translation initiation factor IF-1; Validated
Probab=29.64 E-value=1.9e+02 Score=20.15 Aligned_cols=54 Identities=11% Similarity=0.145 Sum_probs=31.4
Q ss_pred cccceEEEEeeCCCceeEEecCCCCCceEEeccccccCCccccCCCCcEEEEEEeC
Q 047168 5 TRSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGYRTLYENQSVEFDVQLE 60 (258)
Q Consensus 5 ~~~~G~vk~f~~~kGfGFI~~~~~~~dvF~H~s~l~~~~~~~l~~G~~V~F~v~~~ 60 (258)
..+.|+|...- ..+|=.|..+++ ..+-.+..-........+.+||.|+|++..-
T Consensus 7 ~~~~G~Vi~~~-~~~~y~V~~~~g-~~~~c~~~Gklr~~~i~i~vGD~V~ve~~~~ 60 (72)
T PRK00276 7 IEMEGTVVEAL-PNAMFRVELENG-HEVLAHISGKMRKNYIRILPGDKVTVELSPY 60 (72)
T ss_pred EEEEEEEEEEc-CCCEEEEEeCCC-CEEEEEEccceeeCCcccCCCCEEEEEEccc
Confidence 46789988763 222445554443 4555555433221112388999999996553
No 162
>PRK11712 ribonuclease G; Provisional
Probab=29.35 E-value=1.3e+02 Score=29.34 Aligned_cols=69 Identities=17% Similarity=0.223 Sum_probs=50.9
Q ss_pred cccceEEEEeeCCCceeEEecCCCCCceEEeccccccC----------C------ccccCCCCcEEEEEEeCC---Cccc
Q 047168 5 TRSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSD----------G------YRTLYENQSVEFDVQLEA---DGKY 65 (258)
Q Consensus 5 ~~~~G~vk~f~~~kGfGFI~~~~~~~dvF~H~s~l~~~----------~------~~~l~~G~~V~F~v~~~~---~G~~ 65 (258)
.-+.|+|+...+...=-||.-.. +..-|+|++++... . -..|++|+.|-.+|...+ +|..
T Consensus 40 nIY~G~V~~v~pg~~AAFVdIG~-~k~gFL~~~d~~~~~~~~~~~~~~~~~~~~i~~~l~~Gq~iLVQV~Ke~~~~KG~~ 118 (489)
T PRK11712 40 NIYKGRVSRVLPGMQAAFVDIGL-DKAAFLHASDIVPHTECVAGEEQKQFVVRDISELVRQGQDIMVQVVKDPLGTKGAR 118 (489)
T ss_pred cEEEEEEeecCCCCceeEEeeCC-CccEEEEhhhccchhhhcccccccccccccHHHhccCCCEEEEEEEeCCcCCCCCe
Confidence 45789999999999999999876 48999999998421 0 012889999999999975 5543
Q ss_pred eeeccccCC
Q 047168 66 QALDVTAPG 74 (258)
Q Consensus 66 ~A~~V~~~~ 74 (258)
...+|++++
T Consensus 119 lT~~Isl~G 127 (489)
T PRK11712 119 LTTDITLPS 127 (489)
T ss_pred EEEEEEecc
Confidence 344555554
No 163
>PF01551 Peptidase_M23: Peptidase family M23; InterPro: IPR016047 Members of this family are zinc metallopeptidases with a range of specificities. The peptidase family M23 is included in this family, these are Gly-Gly endopeptidases. Peptidase family M23 are also endopeptidases. This family also includes some bacterial lipoproteins such as Swiss:P33648 for which no proteolytic activity has been demonstrated. This family also includes leukocyte cell-derived chemotaxin 2 (LECT2) proteins. LECT2 is a liver-specific protein which is thought to be linked to hepatocyte growth although the exact function of this protein is unknown.; PDB: 3IT5_A 3IT7_B 2GU1_A 3NYY_A 2HSI_B 3SLU_B 3UZ0_D 3TUF_B 1QWY_A 2B44_B ....
Probab=29.08 E-value=46 Score=24.19 Aligned_cols=43 Identities=23% Similarity=0.346 Sum_probs=25.6
Q ss_pred ccceEEEEeeCCCceeEEecCC---CCCceEEeccccccCCccccCCCCcEE
Q 047168 6 RSTGKVTWFDGAKGYGFIRPDD---GGADLFVHQKSIKSDGYRTLYENQSVE 54 (258)
Q Consensus 6 ~~~G~vk~f~~~kGfGFI~~~~---~~~dvF~H~s~l~~~~~~~l~~G~~V~ 54 (258)
...|+|........+|-+..-+ +-.-+|.|+..+. +++|+.|+
T Consensus 19 ~~~G~V~~~~~~~~~g~~V~i~~~~g~~~~y~~l~~~~------v~~G~~V~ 64 (96)
T PF01551_consen 19 PADGKVVFVGEDPGYGNYVIIQHGNGYITVYGHLDSVS------VKVGDRVK 64 (96)
T ss_dssp SSSEEEEEEEEETTTEEEEEEEETTSEEEEEEEESEES------S-TTSEE-
T ss_pred CccEEEEEEEeccCCccEEEEEeCCcCCEEEecccccc------ceeccccc
Confidence 5679999998876666554333 2345677766653 44555553
No 164
>KOG0407 consensus 40S ribosomal protein S14 [Translation, ribosomal structure and biogenesis]
Probab=28.29 E-value=51 Score=25.54 Aligned_cols=40 Identities=18% Similarity=0.167 Sum_probs=25.4
Q ss_pred eeEEecCCCCCceEEeccccccCC-ccccCCCCcEEEEEEe
Q 047168 20 YGFIRPDDGGADLFVHQKSIKSDG-YRTLYENQSVEFDVQL 59 (258)
Q Consensus 20 fGFI~~~~~~~dvF~H~s~l~~~~-~~~l~~G~~V~F~v~~ 59 (258)
||....-..-.|-|||+++|.... +-.+.-|+.|.-+-.+
T Consensus 16 fgvahi~asfndtfvhitdlsg~eti~rvtggmkvkadrde 56 (139)
T KOG0407|consen 16 FGVAHIFASFNDTFVHVTDLSGKETIVRVTGGMKVKADRDE 56 (139)
T ss_pred eeEEEEEeecccceEEEeccCCceEEEEecCCeEEeccccc
Confidence 444443445578999999996653 3346677777655433
No 165
>PRK07400 30S ribosomal protein S1; Reviewed
Probab=27.53 E-value=1.6e+02 Score=26.90 Aligned_cols=52 Identities=15% Similarity=0.145 Sum_probs=37.1
Q ss_pred cccceEEEEeeCCCceeEEecCCCCCceEEeccccccCC----ccccCCCCcEEEEEEe
Q 047168 5 TRSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDG----YRTLYENQSVEFDVQL 59 (258)
Q Consensus 5 ~~~~G~vk~f~~~kGfGFI~~~~~~~dvF~H~s~l~~~~----~~~l~~G~~V~F~v~~ 59 (258)
+.+.|+|+... +.+=||.. ....+-|+|.+.|.... ...+.+|+.|+|.|..
T Consensus 33 ~iv~G~V~~i~--~~g~~Vdi-g~k~~g~lp~sEis~~~~~~~~~~~~~G~~v~~~Vi~ 88 (318)
T PRK07400 33 DIVNGTVFSLE--PRGALIDI-GAKTAAFMPIQEMSINRVEGPEEVLQPNETREFFILS 88 (318)
T ss_pred CEEEEEEEEEE--CCEEEEEE-CCCeEEEEEHHHhccccccCHHHccCCCCEEEEEEEE
Confidence 56789999985 33445554 44568999999996542 2236899999999875
No 166
>PRK11642 exoribonuclease R; Provisional
Probab=27.49 E-value=1.3e+02 Score=31.29 Aligned_cols=54 Identities=30% Similarity=0.324 Sum_probs=38.9
Q ss_pred cccceEEEEeeCCCceeEE-ecCCCCCceEEeccccccCC---------------ccccCCCCcEEEEEEeCC
Q 047168 5 TRSTGKVTWFDGAKGYGFI-RPDDGGADLFVHQKSIKSDG---------------YRTLYENQSVEFDVQLEA 61 (258)
Q Consensus 5 ~~~~G~vk~f~~~kGfGFI-~~~~~~~dvF~H~s~l~~~~---------------~~~l~~G~~V~F~v~~~~ 61 (258)
..+.|+|+... .|||. ..++...+-|||+++|..+- -+.++.||.|+..|..-+
T Consensus 645 e~f~G~Is~V~---~fGifVeL~~~~vEGlV~vs~L~~d~y~~d~~~~~L~g~~~~~~~~lGD~V~VkV~~vD 714 (813)
T PRK11642 645 NVFKGVISSVT---GFGFFVRLDDLFIDGLVHVSSLDNDYYRFDQVGQRLIGESSGQTYRLGDRVEVRVEAVN 714 (813)
T ss_pred cEEEEEEEEee---cCceEEEECCCCeeeeEEEeecCCcceEecchheEEecccCCcEECCCCEEEEEEEEee
Confidence 46789999874 47765 44555689999999986431 135788999999986653
No 167
>PF06483 ChiC: Chitinase C; InterPro: IPR009470 This ~170 aa region is found at the C-terminal to the catalytic domain (IPR001223 from INTERPRO) found in members of glycoside hydrolase family 18.
Probab=27.23 E-value=89 Score=26.33 Aligned_cols=44 Identities=23% Similarity=0.317 Sum_probs=32.5
Q ss_pred CCCceeEEecCCCC---------CceEEeccccccCCccccCCCCcEEEEEEe
Q 047168 16 GAKGYGFIRPDDGG---------ADLFVHQKSIKSDGYRTLYENQSVEFDVQL 59 (258)
Q Consensus 16 ~~kGfGFI~~~~~~---------~dvF~H~s~l~~~~~~~l~~G~~V~F~v~~ 59 (258)
++.|||+-....+. -+-=||..+|....+++|.+|+.|+.++.-
T Consensus 88 dqSG~g~~vi~sght~~g~NiGGL~gdfHrvs~tlp~wqslapG~s~~~~~~Y 140 (180)
T PF06483_consen 88 DQSGFGLKVISSGHTAAGNNIGGLKGDFHRVSFTLPAWQSLAPGASVELDMVY 140 (180)
T ss_pred cccCCcEEEEecCCcccCCcccccCCceEEEEEECCCccccCCCCEEEEeEEE
Confidence 45677765544322 256689999998889999999999977654
No 168
>PF12353 eIF3g: Eukaryotic translation initiation factor 3 subunit G ; InterPro: IPR024675 At least eleven different protein factors are involved in initiation of protein synthesis in eukaryotes. Binding of initiator tRNA and mRNA to the 40S subunit requires the presence of the translation initiation factors eIF-2 and eIF-3, with eIF-3 being particularly important for 80S ribosome dissociation and mRNA binding []. eIF-3 is the most complex translation inititation factor, consisting of about 13 putative subunits and having a molecular weight of between 550 - 700 kDa in mammalian cells. Subunits are designated eIF-3a - eIF-3m; the large number of subunits means that the interactions between the individual subunits that make up the eIF-3 complex are complex and varied. Subunit G is required for eIF3 integrity. This entry represents a domain of approximately 130 amino acids in length found at the N terminus of eukaryotic translation initiation factor 3 subunit G. This domain is commonly found in association with the RNA recognition domain PF00076 from PFAM.
Probab=26.11 E-value=34 Score=27.14 Aligned_cols=19 Identities=26% Similarity=0.552 Sum_probs=15.5
Q ss_pred CCCcccccCCCCcccccccc
Q 047168 127 GGVVCYNCDGVGHVARECTS 146 (258)
Q Consensus 127 ~~~~C~~Cg~~GH~a~~Cp~ 146 (258)
..+.|+.|. ..|+...||.
T Consensus 105 ~~v~CR~Ck-GdH~T~~CPy 123 (128)
T PF12353_consen 105 SKVKCRICK-GDHWTSKCPY 123 (128)
T ss_pred ceEEeCCCC-CCcccccCCc
Confidence 368899995 7799999986
No 169
>COG2190 NagE Phosphotransferase system IIA components [Carbohydrate transport and metabolism]
Probab=25.85 E-value=1.4e+02 Score=24.55 Aligned_cols=47 Identities=23% Similarity=0.471 Sum_probs=29.9
Q ss_pred ccceEEEEeeCCC-ceeEEecCCCCCceEEec----cccccCCcccc-CCCCcEE
Q 047168 6 RSTGKVTWFDGAK-GYGFIRPDDGGADLFVHQ----KSIKSDGYRTL-YENQSVE 54 (258)
Q Consensus 6 ~~~G~vk~f~~~k-GfGFI~~~~~~~dvF~H~----s~l~~~~~~~l-~~G~~V~ 54 (258)
...|+|....+.| -||+.+ +.+-+|++|+ ..|...+|..+ ++||.|.
T Consensus 48 PvdG~v~~iFpTkHAigi~t--~~GvEiLiHiGiDTV~L~GegF~~~v~~Gd~Vk 100 (156)
T COG2190 48 PVDGTVVLIFPTKHAIGIET--DEGVEILIHIGIDTVKLNGEGFESLVKEGDKVK 100 (156)
T ss_pred ccCcEEEEEeeCCcEEEEEc--CCCcEEEEEeceeeEEECCcceEEEeeCCCEEc
Confidence 4567776665444 466655 3358999998 45666666643 4666654
No 170
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=25.46 E-value=1e+02 Score=28.92 Aligned_cols=52 Identities=13% Similarity=-0.013 Sum_probs=37.1
Q ss_pred ccccceEEEEeeCCCceeEEecCCCCCceEEeccccccCCccccCCCCcEEEEEEeCC
Q 047168 4 LTRSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGYRTLYENQSVEFDVQLEA 61 (258)
Q Consensus 4 ~~~~~G~vk~f~~~kGfGFI~~~~~~~dvF~H~s~l~~~~~~~l~~G~~V~F~v~~~~ 61 (258)
...++|+|+..+. + +++. +-++-+-|++.+.+... ..+.+|++|.+-+..-.
T Consensus 135 GeiV~G~V~~~~~--~-~~~V-dlg~vEa~LP~~E~ip~--e~~~~Gd~Ika~V~~V~ 186 (362)
T PRK12327 135 GDIVTGVVQRRDN--R-FVYV-NLGKIEAVLPPAEQIPG--ETYKHGDRIKVYVVKVE 186 (362)
T ss_pred CCEEEEEEEEEeC--C-cEEE-EeCCeEEEecHHHcCCC--CCCCCCCEEEEEEEEEe
Confidence 3567999999853 3 3443 22447889998888654 56899999998877644
No 171
>COG2996 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only]
Probab=25.19 E-value=2.4e+02 Score=25.52 Aligned_cols=40 Identities=10% Similarity=0.125 Sum_probs=32.2
Q ss_pred CCceEEeccccccCCccc--cCCCCcEEEEEEeCCCccceeecc
Q 047168 29 GADLFVHQKSIKSDGYRT--LYENQSVEFDVQLEADGKYQALDV 70 (258)
Q Consensus 29 ~~dvF~H~s~l~~~~~~~--l~~G~~V~F~v~~~~~G~~~A~~V 70 (258)
..||||-.+.+... ++ |++|+.+-+.+..+.++++-|+-.
T Consensus 97 ~KDl~vp~~elp~~--~~~wpq~Gd~l~v~l~~Dkk~Ri~g~~a 138 (287)
T COG2996 97 PKDLLVPLDELPTL--KSLWPQKGDKLLVYLYVDKKGRIWGTLA 138 (287)
T ss_pred Ccceeeehhhcccc--cccCCCCCCEEEEEEEEccCCcEEEEec
Confidence 58999999998654 34 899999999999999997655543
No 172
>PRK00087 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed
Probab=24.96 E-value=1.8e+02 Score=29.30 Aligned_cols=61 Identities=13% Similarity=0.110 Sum_probs=40.7
Q ss_pred ccccceEEEEeeCCCceeEEecCCCCCceEEeccccccCC----ccccCCCCcEEEEEEe--CCCcccee
Q 047168 4 LTRSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDG----YRTLYENQSVEFDVQL--EADGKYQA 67 (258)
Q Consensus 4 ~~~~~G~vk~f~~~kGfGFI~~~~~~~dvF~H~s~l~~~~----~~~l~~G~~V~F~v~~--~~~G~~~A 67 (258)
.+.+.|+|+.++. .+=||.. ....+-|++.+.+.... ...+.+|+.|++.|.. ..++++.+
T Consensus 303 G~iV~G~V~~v~~--~gv~Vdi-g~~~~G~lp~~els~~~~~~~~~~~~vGd~V~v~V~~vd~~~g~i~L 369 (647)
T PRK00087 303 GDIVKGTVVSVNE--NEVFVDV-GYKSEGVIPLRELTLDEISSLKESVKVGDEIEVKVLKLEDEDGYVVL 369 (647)
T ss_pred CCEEEEEEEEEEC--CEEEEEE-CCCeEEEEEHHHhcccccCChhhccCCCCEEEEEEEEEECCCCcEEE
Confidence 3568899999964 2334543 33457899999887432 2347899999998876 34554433
No 173
>KOG0956 consensus PHD finger protein AF10 [General function prediction only]
Probab=24.88 E-value=43 Score=33.97 Aligned_cols=28 Identities=32% Similarity=0.829 Sum_probs=15.9
Q ss_pred CCcccccCCcccCcccCCCCCCCCCCCCccccCCCCC
Q 047168 187 SGGCFKCGGYGHLARDCITRGSGGGGGGRCYNCGKSG 223 (258)
Q Consensus 187 ~~~C~~Cg~~GH~~~~C~~~~~~~~~~~~C~~Cg~~G 223 (258)
..+||.|.|.|--.+.- ...|..|++.+
T Consensus 117 nKtCYIC~E~GrpnkA~---------~GACMtCNKs~ 144 (900)
T KOG0956|consen 117 NKTCYICNEEGRPNKAA---------KGACMTCNKSG 144 (900)
T ss_pred cceeeeecccCCccccc---------cccceeccccc
Confidence 46677777776543221 12677666654
No 174
>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=24.73 E-value=2.3e+02 Score=27.38 Aligned_cols=57 Identities=11% Similarity=0.044 Sum_probs=40.5
Q ss_pred ccccceEEEEeeCCCceeEEecCCCCCceEEeccccccCCccccCCCCcEEEEEEe--CCCcc
Q 047168 4 LTRSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGYRTLYENQSVEFDVQL--EADGK 64 (258)
Q Consensus 4 ~~~~~G~vk~f~~~kGfGFI~~~~~~~dvF~H~s~l~~~~~~~l~~G~~V~F~v~~--~~~G~ 64 (258)
.+.+.|+|...++ .+=||.. ....+-|+..+.+.... ..+.+|+.|++.+.. ...|+
T Consensus 19 G~~v~g~V~~i~~--~~~~v~~-g~k~~g~i~~~E~~~~~-~~~~vGd~i~~~V~~~~~~~g~ 77 (516)
T TIGR00717 19 GSIVKGTVVAINK--DTVFVDV-GLKSEGRIPKEEFLDAP-LEIQVGDEVEVYLDRVEDRFGE 77 (516)
T ss_pred CCEEEEEEEEEEC--CEEEEEc-CCCcEEEEEHHHhcCCc-cCCCCCCEEEEEEEEEeCCCCc
Confidence 3568899999964 4445554 45578899998886543 458999999999874 34454
No 175
>PTZ00162 DNA-directed RNA polymerase II subunit 7; Provisional
Probab=24.72 E-value=1.6e+02 Score=24.58 Aligned_cols=33 Identities=21% Similarity=0.189 Sum_probs=23.9
Q ss_pred ccccceEEEEeeCCCceeEEecCCCCCceEEeccccc
Q 047168 4 LTRSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIK 40 (258)
Q Consensus 4 ~~~~~G~vk~f~~~kGfGFI~~~~~~~dvF~H~s~l~ 40 (258)
.+.+.|+|+.-+. +||..... .-|||+|.+.|.
T Consensus 82 gEVv~g~V~~v~~---~G~~v~~G-p~~ifI~~~~l~ 114 (176)
T PTZ00162 82 DEVLDAIVTDVNK---LGFFAQAG-PLKAFVSRSAIP 114 (176)
T ss_pred CCEEEEEEEEEec---ceEEEEee-CeEEEEcHHHCC
Confidence 4567899998864 57666554 456999998885
No 176
>PRK06676 rpsA 30S ribosomal protein S1; Reviewed
Probab=24.12 E-value=1.7e+02 Score=27.18 Aligned_cols=54 Identities=22% Similarity=0.211 Sum_probs=38.5
Q ss_pred cccceEEEEeeCCCceeEEecCCCCCceEEeccccccCCc----cccCCCCcEEEEEEeCC
Q 047168 5 TRSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGY----RTLYENQSVEFDVQLEA 61 (258)
Q Consensus 5 ~~~~G~vk~f~~~kGfGFI~~~~~~~dvF~H~s~l~~~~~----~~l~~G~~V~F~v~~~~ 61 (258)
+.+.|+|+... -||+....+.+-+-|+|.+.+..... ..+++|+.|...+..-+
T Consensus 279 ~~v~g~V~~i~---~~G~fV~l~~gi~Glv~~se~~~~~~~~~~~~~~~Gd~v~v~V~~id 336 (390)
T PRK06676 279 DVIEGTVKRLT---DFGAFVEVLPGVEGLVHISQISHKHIATPSEVLEEGQEVKVKVLEVN 336 (390)
T ss_pred cEEEEEEEEEe---CceEEEEECCCCeEEEEhHHcCccccCChhhccCCCCEEEEEEEEEE
Confidence 46789999875 37776555545788999999864321 24689999998876653
No 177
>KOG2673 consensus Uncharacterized conserved protein, contains PSP domain [Function unknown]
Probab=23.65 E-value=41 Score=32.35 Aligned_cols=17 Identities=47% Similarity=1.169 Sum_probs=10.5
Q ss_pred cccCCCCCccCCCCCCC
Q 047168 240 CFNCGKPGHFARECTKV 256 (258)
Q Consensus 240 C~~Cg~~GH~~~~Cp~~ 256 (258)
||||+..-|-.+|||.+
T Consensus 131 CFNC~g~~hsLrdC~rp 147 (485)
T KOG2673|consen 131 CFNCGGTPHSLRDCPRP 147 (485)
T ss_pred ccccCCCCCccccCCCc
Confidence 56666666666666654
No 178
>PRK05054 exoribonuclease II; Provisional
Probab=22.98 E-value=1.7e+02 Score=29.63 Aligned_cols=33 Identities=18% Similarity=0.219 Sum_probs=24.1
Q ss_pred ccceEEEEeeCCCcee-EEecCCCCCceEEecccccc
Q 047168 6 RSTGKVTWFDGAKGYG-FIRPDDGGADLFVHQKSIKS 41 (258)
Q Consensus 6 ~~~G~vk~f~~~kGfG-FI~~~~~~~dvF~H~s~l~~ 41 (258)
.+.|+|.... .|| |+..++..-+.|||+++|..
T Consensus 564 ~f~g~I~~v~---~~G~fV~l~~~~veglV~~~~l~~ 597 (644)
T PRK05054 564 RFAAEIIDIS---RGGMRVRLLENGAVAFIPASFLHA 597 (644)
T ss_pred EEEEEEEeee---cCcEEEEEeCCceEEEEEccccCC
Confidence 6788888774 366 44555667899999999855
No 179
>COG5569 Uncharacterized conserved protein [Function unknown]
Probab=22.97 E-value=85 Score=23.88 Aligned_cols=63 Identities=19% Similarity=0.134 Sum_probs=33.6
Q ss_pred ccceEEEEeeCCCceeEEecCCC------CCceEEeccccccCCccccCCCCcEEEEEEeCCCccceeeccc
Q 047168 6 RSTGKVTWFDGAKGYGFIRPDDG------GADLFVHQKSIKSDGYRTLYENQSVEFDVQLEADGKYQALDVT 71 (258)
Q Consensus 6 ~~~G~vk~f~~~kGfGFI~~~~~------~~dvF~H~s~l~~~~~~~l~~G~~V~F~v~~~~~G~~~A~~V~ 71 (258)
.-+|.||-+|.+-+-=-|.-++- ..-.-|-+.+= .-+..|++|+.|+|..++-.. ++..++|.
T Consensus 39 ~at~~VkkvD~~akKVTl~He~i~~l~mp~MTM~F~Vkd~--a~lsglKeGdkV~fvferv~g-k~tv~qvk 107 (108)
T COG5569 39 KATGVVKKVDLEAKKVTLHHEPIKNLNMPAMTMVFRVKDQ--AKLSGLKEGDKVEFVFERVNG-KLTVQQVK 107 (108)
T ss_pred cCccceeeeccccceEEEeccchhhCCCcceEEEEEeccH--HHhhccccCCcEEEEEEeeCC-EEEEEEec
Confidence 34556888877665544432221 11111111111 114568999999999987643 45555543
No 180
>COG1545 Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]
Probab=22.75 E-value=2e+02 Score=22.95 Aligned_cols=37 Identities=11% Similarity=0.107 Sum_probs=27.2
Q ss_pred eeEEecCCCCCceEEeccccccCCccccCCCCcEEEEEEeC
Q 047168 20 YGFIRPDDGGADLFVHQKSIKSDGYRTLYENQSVEFDVQLE 60 (258)
Q Consensus 20 fGFI~~~~~~~dvF~H~s~l~~~~~~~l~~G~~V~F~v~~~ 60 (258)
.+.|..+++. .|+.|+.+ .....+.+|++|+-.+..-
T Consensus 87 iaiV~l~~~~-~i~~~i~~---~~p~~v~iGm~V~~v~~~~ 123 (140)
T COG1545 87 IAIVELEEGG-RILGQLVD---VDPDDVEIGMKVEAVFRKR 123 (140)
T ss_pred EEEEEeCCCC-ceEEEEEe---cCcccccCCCEEEEEEEEc
Confidence 4666666654 89999998 2234699999999888764
No 181
>PF11548 Receptor_IA-2: Protein-tyrosine phosphatase receptor IA-2; InterPro: IPR021613 IA-2 is a protein-tyrosine phosphatase receptor that upon exocytosis, the cytoplasmic domain is cleaved and moves to the nucleus where it enhances transcription of the insulin gene. The mature exodomain of IA-2 participates in adhesion to the extracellular matrix and is self-proteolyzed in vitro by reactive oxygen species which may be a new shedding mechanism. ; PDB: 2QT7_B 3N01_B 3N4W_B 3NG8_A.
Probab=22.73 E-value=80 Score=23.62 Aligned_cols=22 Identities=27% Similarity=0.356 Sum_probs=12.3
Q ss_pred CCCcEEEEEEeCCCccceeeccc
Q 047168 49 ENQSVEFDVQLEADGKYQALDVT 71 (258)
Q Consensus 49 ~G~~V~F~v~~~~~G~~~A~~V~ 71 (258)
.|-.|+|.|...+++ +.|.+|-
T Consensus 43 ~g~avTFrv~~N~~n-~taadVa 64 (91)
T PF11548_consen 43 VGPAVTFRVRPNNKN-LTAADVA 64 (91)
T ss_dssp ETTEEEEEE---TT----HHHHH
T ss_pred cCceEEEEeccCcCC-CCHHHHH
Confidence 456799999999998 7777664
No 182
>KOG2044 consensus 5'-3' exonuclease HKE1/RAT1 [Replication, recombination and repair; RNA processing and modification]
Probab=22.52 E-value=39 Score=34.84 Aligned_cols=17 Identities=47% Similarity=1.210 Sum_probs=8.8
Q ss_pred ccccCCCCCccCCCCCC
Q 047168 239 SCFNCGKPGHFARECTK 255 (258)
Q Consensus 239 ~C~~Cg~~GH~~~~Cp~ 255 (258)
.|+.|++.||.++||..
T Consensus 262 ~C~~cgq~gh~~~dc~g 278 (931)
T KOG2044|consen 262 RCFLCGQTGHEAKDCEG 278 (931)
T ss_pred cchhhcccCCcHhhcCC
Confidence 35555555555555543
No 183
>KOG4246 consensus Predicted DNA-binding protein, contains SAP domain [General function prediction only]
Probab=22.25 E-value=15 Score=37.79 Aligned_cols=62 Identities=23% Similarity=0.347 Sum_probs=43.6
Q ss_pred cccceEEEEeeCCCceeEEecCCCCCceEEeccccccCCccccCCCCcEEEEEEeC--CCccceeeccccCCCC
Q 047168 5 TRSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGYRTLYENQSVEFDVQLE--ADGKYQALDVTAPGGA 76 (258)
Q Consensus 5 ~~~~G~vk~f~~~kGfGFI~~~~~~~dvF~H~s~l~~~~~~~l~~G~~V~F~v~~~--~~G~~~A~~V~~~~g~ 76 (258)
.++.|+|... .--||||. +||||..+.|... .+.+|+.|-.+..-. .--+|.|..|..+++.
T Consensus 147 R~f~gvvtk~--~DtygfVD-----~dvffQls~~~g~---hp~vgD~V~vea~Ynpsmpfkwnaqriq~l~~~ 210 (1194)
T KOG4246|consen 147 RRFAGVVTKQ--TDTYGFVD-----QDVFFQLSKMQGL---HPSVGDAVNVEADYNPSMPFKWNAQRIQHLGGR 210 (1194)
T ss_pred eeeehhhhhh--cccccccc-----HHHHHHHHHHhcC---CCccccceeeecccCCCCCccccHHHHHhcccc
Confidence 4567777665 55799996 7999999998764 478999976554332 3345777777776654
No 184
>KOG2673 consensus Uncharacterized conserved protein, contains PSP domain [Function unknown]
Probab=22.12 E-value=47 Score=31.96 Aligned_cols=19 Identities=53% Similarity=1.209 Sum_probs=15.4
Q ss_pred CcccCCCCCCCCCCCCCCC
Q 047168 159 GCYNCGDPEHFARDCPRQQ 177 (258)
Q Consensus 159 ~C~~Cg~~GH~~~~Cp~~~ 177 (258)
.||+|+..-|..++||.+.
T Consensus 130 ~CFNC~g~~hsLrdC~rp~ 148 (485)
T KOG2673|consen 130 PCFNCGGTPHSLRDCPRPF 148 (485)
T ss_pred cccccCCCCCccccCCCcc
Confidence 3888888888888888775
No 185
>PRK04023 DNA polymerase II large subunit; Validated
Probab=21.99 E-value=1e+02 Score=32.92 Aligned_cols=8 Identities=38% Similarity=0.758 Sum_probs=4.1
Q ss_pred cccccCCc
Q 047168 189 GCFKCGGY 196 (258)
Q Consensus 189 ~C~~Cg~~ 196 (258)
.|-.||..
T Consensus 640 rCP~CG~~ 647 (1121)
T PRK04023 640 RCPFCGTH 647 (1121)
T ss_pred cCCCCCCC
Confidence 45555554
No 186
>PRK00087 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed
Probab=21.66 E-value=1.9e+02 Score=29.26 Aligned_cols=54 Identities=22% Similarity=0.223 Sum_probs=38.9
Q ss_pred cccceEEEEeeCCCceeEEecCCCCCceEEeccccccCCc----cccCCCCcEEEEEEeCC
Q 047168 5 TRSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGY----RTLYENQSVEFDVQLEA 61 (258)
Q Consensus 5 ~~~~G~vk~f~~~kGfGFI~~~~~~~dvF~H~s~l~~~~~----~~l~~G~~V~F~v~~~~ 61 (258)
..+.|+|+...+ ||++...+.+-+-|+|++.+..... ..+++|+.|+..+..-+
T Consensus 564 ~~v~g~V~~i~~---~G~fV~l~~~i~Gli~~sel~~~~~~~~~~~~kvGd~V~vkV~~id 621 (647)
T PRK00087 564 SIVLGKVVRIAP---FGAFVELEPGVDGLVHISQISWKRIDKPEDVLSEGEEVKAKILEVD 621 (647)
T ss_pred eEEEEEEEEEEC---CeEEEEECCCCEEEEEhhhcCccccCCHhhcCCCCCEEEEEEEEEe
Confidence 457889988853 6665544556899999999875321 24689999998877643
No 187
>COG2183 Tex Transcriptional accessory protein [Transcription]
Probab=21.59 E-value=1.2e+02 Score=31.34 Aligned_cols=70 Identities=14% Similarity=0.010 Sum_probs=46.7
Q ss_pred ccccceEEEEeeCCCceeEEecCCCCCceEEeccccccC----CccccCCCCcEEEEEEeCC--CccceeeccccCCCCc
Q 047168 4 LTRSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSD----GYRTLYENQSVEFDVQLEA--DGKYQALDVTAPGGAP 77 (258)
Q Consensus 4 ~~~~~G~vk~f~~~kGfGFI~~~~~~~dvF~H~s~l~~~----~~~~l~~G~~V~F~v~~~~--~G~~~A~~V~~~~g~~ 77 (258)
.|...|+|..+- -||-+..-.-..|.+||+|.+... ....+++|+.|+-.|..-+ +. ..+......+...
T Consensus 659 Gm~leg~Vrnv~---~fgafVdIgv~qDglvHis~ls~~fv~~P~~vv~vGdiV~v~V~~vD~~r~-rI~Lsmr~~~~~~ 734 (780)
T COG2183 659 GMILEGTVRNVV---DFGAFVDIGVHQDGLVHISQLSDKFVKDPNEVVKVGDIVKVKVIEVDTARK-RIALSMRLDEEEG 734 (780)
T ss_pred CCEEEEEEEEee---eccceEEeccccceeeeHHHhhhhhcCChHHhcccCCEEEEEEEEEecccC-eeeeEeeccCCcc
Confidence 467889998873 455444445568999999999662 2456889999998877753 33 2444444444443
No 188
>KOG2044 consensus 5'-3' exonuclease HKE1/RAT1 [Replication, recombination and repair; RNA processing and modification]
Probab=21.23 E-value=43 Score=34.55 Aligned_cols=22 Identities=45% Similarity=0.978 Sum_probs=18.1
Q ss_pred CCCCcccccCCcccCcccCCCC
Q 047168 185 NNSGGCFKCGGYGHLARDCITR 206 (258)
Q Consensus 185 ~~~~~C~~Cg~~GH~~~~C~~~ 206 (258)
.....|+.|++.||.+++|...
T Consensus 258 ~~~~~C~~cgq~gh~~~dc~g~ 279 (931)
T KOG2044|consen 258 NKPRRCFLCGQTGHEAKDCEGK 279 (931)
T ss_pred CCcccchhhcccCCcHhhcCCc
Confidence 4456799999999999999765
No 189
>PRK09439 PTS system glucose-specific transporter subunit; Provisional
Probab=21.14 E-value=2.4e+02 Score=23.42 Aligned_cols=47 Identities=26% Similarity=0.493 Sum_probs=29.6
Q ss_pred ccceEEEEeeCC-CceeEEecCCCCCceEEec----cccccCCccc-cCCCCcEE
Q 047168 6 RSTGKVTWFDGA-KGYGFIRPDDGGADLFVHQ----KSIKSDGYRT-LYENQSVE 54 (258)
Q Consensus 6 ~~~G~vk~f~~~-kGfGFI~~~~~~~dvF~H~----s~l~~~~~~~-l~~G~~V~ 54 (258)
...|+|+...+. --||+ +.++ +-+|++|+ ..|...+|.. +++||.|+
T Consensus 63 P~dG~V~~vf~T~HAigi-~t~~-G~eiLIHiGiDTV~L~G~gF~~~Vk~Gd~Vk 115 (169)
T PRK09439 63 PVDGTIGKIFETNHAFSI-ESDS-GVELFVHFGIDTVELKGEGFKRIAEEGQRVK 115 (169)
T ss_pred cCCeEEEEEcCCCCEEEE-EeCC-CcEEEEEEeecccccCCCceEEEecCCCEEe
Confidence 467999886543 34454 4444 58999998 3455566654 35677765
No 190
>KOG0125 consensus Ataxin 2-binding protein (RRM superfamily) [General function prediction only]
Probab=20.95 E-value=44 Score=30.91 Aligned_cols=15 Identities=33% Similarity=0.928 Sum_probs=11.6
Q ss_pred eeC--CCceeEEecCCC
Q 047168 14 FDG--AKGYGFIRPDDG 28 (258)
Q Consensus 14 f~~--~kGfGFI~~~~~ 28 (258)
||+ .|||||+|.+..
T Consensus 130 fNERGSKGFGFVTmen~ 146 (376)
T KOG0125|consen 130 FNERGSKGFGFVTMENP 146 (376)
T ss_pred eccCCCCccceEEecCh
Confidence 554 599999998864
No 191
>PF05938 Self-incomp_S1: Plant self-incompatibility protein S1; InterPro: IPR010264 This family consists of a series of plant proteins which are related to the Papaver rhoeas S1 self-incompatibility protein. Self-incompatibility (SI) is the single most important outbreeding device found in angiosperms and is a mechanism that regulates the acceptance or rejection of pollen. S1 is known to exhibit specific pollen-inhibitory properties [].
Probab=20.74 E-value=2.1e+02 Score=21.37 Aligned_cols=34 Identities=35% Similarity=0.411 Sum_probs=26.5
Q ss_pred CCCCceEEeccccccC-CccccCCCCcEEEEEEeC
Q 047168 27 DGGADLFVHQKSIKSD-GYRTLYENQSVEFDVQLE 60 (258)
Q Consensus 27 ~~~~dvF~H~s~l~~~-~~~~l~~G~~V~F~v~~~ 60 (258)
....+|.||=.+-..+ +...|.+|+..+|.....
T Consensus 10 ~~~~~L~vhC~S~d~Dlg~~~l~~g~~~~~~F~~~ 44 (110)
T PF05938_consen 10 GPGKILTVHCKSKDDDLGWHVLKPGQSYSFSFRDN 44 (110)
T ss_pred CCCCeEEEEeeCCCccCCCEECCCCCEEEEEEecC
Confidence 3567899998888554 678899999999888665
Done!