Query 030905
Match_columns 169
No_of_seqs 312 out of 2087
Neff 7.2
Searched_HMMs 46136
Date Fri Mar 29 06:21:26 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/030905.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/030905hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG1278 CspC Cold shock protei 99.9 9.9E-28 2.2E-32 157.6 8.0 67 6-73 1-67 (67)
2 PRK10943 cold shock-like prote 99.9 1.3E-26 2.9E-31 154.6 8.7 69 4-73 1-69 (69)
3 PRK15464 cold shock-like prote 99.9 1.8E-26 3.9E-31 154.2 9.1 69 1-72 1-69 (70)
4 PRK15463 cold shock-like prote 99.9 4.3E-26 9.4E-31 152.5 8.9 69 1-72 1-69 (70)
5 PRK10354 RNA chaperone/anti-te 99.9 7.5E-26 1.6E-30 151.4 9.5 70 1-73 1-70 (70)
6 PRK09890 cold shock protein Cs 99.9 8E-26 1.7E-30 151.3 9.5 69 1-72 1-69 (70)
7 PRK09507 cspE cold shock prote 99.9 9.5E-26 2.1E-30 150.5 8.9 67 5-72 2-68 (69)
8 PRK09937 stationary phase/star 99.9 2.1E-25 4.6E-30 150.6 9.3 67 7-74 2-68 (74)
9 TIGR02381 cspD cold shock doma 99.9 2.7E-25 5.8E-30 148.0 8.4 66 7-73 2-67 (68)
10 PRK14998 cold shock-like prote 99.9 4.4E-25 9.5E-30 148.7 9.4 68 7-75 2-69 (73)
11 PF00313 CSD: 'Cold-shock' DNA 99.9 1E-22 2.3E-27 134.3 9.2 66 7-73 1-66 (66)
12 cd04458 CSP_CDS Cold-Shock Pro 99.9 3E-22 6.4E-27 131.7 8.7 65 7-72 1-65 (65)
13 KOG3070 Predicted RNA-binding 99.8 9.2E-19 2E-23 141.5 11.0 157 4-168 54-217 (235)
14 smart00357 CSP Cold shock prot 99.2 2.4E-10 5.3E-15 73.4 8.0 62 8-72 1-63 (64)
15 PTZ00368 universal minicircle 98.8 3.5E-09 7.6E-14 80.0 3.4 47 116-169 102-148 (148)
16 COG5082 AIR1 Arginine methyltr 98.7 1.4E-08 2.9E-13 79.5 2.8 54 115-168 58-116 (190)
17 PF00098 zf-CCHC: Zinc knuckle 98.6 1.6E-08 3.4E-13 50.2 1.5 17 152-168 2-18 (18)
18 PTZ00368 universal minicircle 98.6 7.8E-08 1.7E-12 72.6 4.3 44 117-168 52-95 (148)
19 COG5082 AIR1 Arginine methyltr 98.3 3.7E-07 8.1E-12 71.4 2.5 41 117-168 97-138 (190)
20 PF00098 zf-CCHC: Zinc knuckle 98.2 7E-07 1.5E-11 44.2 1.5 18 118-135 1-18 (18)
21 KOG4400 E3 ubiquitin ligase in 98.2 1.1E-06 2.4E-11 72.2 2.7 40 118-169 144-183 (261)
22 KOG4400 E3 ubiquitin ligase in 98.1 2.8E-06 6E-11 69.8 3.3 53 116-169 91-162 (261)
23 PF14444 S1-like: S1-like 97.8 7.6E-05 1.6E-09 47.7 5.7 53 6-68 3-57 (58)
24 PF08206 OB_RNB: Ribonuclease 97.7 9.5E-05 2.1E-09 47.3 5.6 40 17-61 7-46 (58)
25 PF13696 zf-CCHC_2: Zinc knuck 97.7 1.2E-05 2.6E-10 45.4 0.7 20 150-169 8-27 (32)
26 PF07497 Rho_RNA_bind: Rho ter 97.0 0.0018 3.8E-08 44.1 5.2 66 8-78 4-76 (78)
27 KOG0119 Splicing factor 1/bran 96.7 0.0011 2.3E-08 58.7 2.8 45 116-169 260-304 (554)
28 smart00343 ZnF_C2HC zinc finge 96.6 0.00095 2.1E-08 35.7 1.0 17 152-168 1-17 (26)
29 PF13917 zf-CCHC_3: Zinc knuck 96.4 0.0016 3.4E-08 39.1 1.4 18 150-167 4-21 (42)
30 cd04459 Rho_CSD Rho_CSD: Rho p 96.3 0.011 2.4E-07 39.1 4.9 41 18-61 10-55 (68)
31 PF14787 zf-CCHC_5: GAG-polypr 96.2 0.0023 5E-08 36.9 1.3 18 151-168 3-20 (36)
32 PF13509 S1_2: S1 domain; PDB: 96.0 0.026 5.7E-07 36.2 5.7 55 7-68 5-59 (61)
33 KOG0109 RNA-binding protein LA 96.0 0.015 3.2E-07 48.7 5.2 22 117-138 160-181 (346)
34 KOG0109 RNA-binding protein LA 95.6 0.0044 9.5E-08 51.8 0.9 21 7-27 25-45 (346)
35 PF13696 zf-CCHC_2: Zinc knuck 95.5 0.0063 1.4E-07 34.4 1.0 20 117-136 8-27 (32)
36 PF13917 zf-CCHC_3: Zinc knuck 95.4 0.0078 1.7E-07 36.1 1.3 20 116-135 3-22 (42)
37 PRK11642 exoribonuclease R; Pr 94.8 0.086 1.9E-06 50.1 6.9 62 6-74 84-146 (813)
38 smart00343 ZnF_C2HC zinc finge 94.7 0.014 3E-07 31.0 0.9 18 119-136 1-18 (26)
39 PF00575 S1: S1 RNA binding do 94.7 0.12 2.6E-06 33.6 5.6 54 4-60 5-62 (74)
40 TIGR00358 3_prime_RNase VacB a 94.3 0.15 3.2E-06 47.3 7.2 63 5-74 15-79 (654)
41 PRK08582 hypothetical protein; 94.2 0.51 1.1E-05 35.3 8.7 69 4-76 6-79 (139)
42 PF15288 zf-CCHC_6: Zinc knuck 94.0 0.031 6.7E-07 33.1 1.3 16 152-167 3-20 (40)
43 cd04453 S1_RNase_E S1_RNase_E: 93.5 0.68 1.5E-05 31.8 7.7 56 4-60 8-70 (88)
44 cd05698 S1_Rrp5_repeat_hs6_sc5 93.5 0.43 9.4E-06 30.6 6.3 55 5-62 2-60 (70)
45 cd05704 S1_Rrp5_repeat_hs13 S1 93.4 0.63 1.4E-05 30.5 7.0 60 3-64 3-66 (72)
46 COG5222 Uncharacterized conser 93.1 0.039 8.5E-07 46.4 1.0 20 150-169 176-195 (427)
47 cd00164 S1_like S1_like: Ribos 93.0 0.51 1.1E-05 28.9 6.0 51 7-61 1-56 (65)
48 PF14392 zf-CCHC_4: Zinc knuck 92.8 0.036 7.8E-07 34.1 0.3 17 151-167 32-48 (49)
49 cd04461 S1_Rrp5_repeat_hs8_sc7 92.8 0.41 8.9E-06 32.0 5.6 55 4-61 15-73 (83)
50 cd05696 S1_Rrp5_repeat_hs4 S1_ 92.5 0.48 1E-05 31.0 5.5 52 6-59 3-59 (71)
51 PRK05054 exoribonuclease II; P 92.5 0.38 8.2E-06 44.6 6.7 61 5-74 20-80 (644)
52 PRK07252 hypothetical protein; 92.3 1.6 3.4E-05 31.9 8.5 70 1-74 1-76 (120)
53 TIGR02062 RNase_B exoribonucle 92.3 0.45 9.8E-06 44.1 6.9 61 4-73 16-76 (639)
54 cd05692 S1_RPS1_repeat_hs4 S1_ 92.3 0.63 1.4E-05 29.1 5.8 53 5-60 2-58 (69)
55 PRK12608 transcription termina 92.0 0.33 7.1E-06 42.3 5.3 70 4-79 16-90 (380)
56 cd05697 S1_Rrp5_repeat_hs5 S1_ 91.9 0.72 1.6E-05 29.6 5.7 54 5-61 2-59 (69)
57 smart00316 S1 Ribosomal protei 91.8 0.48 1E-05 29.6 4.7 55 4-61 3-61 (72)
58 cd05706 S1_Rrp5_repeat_sc10 S1 91.7 1.1 2.3E-05 29.0 6.4 56 3-61 3-62 (73)
59 PF14392 zf-CCHC_4: Zinc knuck 91.7 0.066 1.4E-06 32.9 0.5 20 116-135 30-49 (49)
60 TIGR02063 RNase_R ribonuclease 91.6 0.58 1.2E-05 43.8 6.8 62 6-74 68-132 (709)
61 cd05694 S1_Rrp5_repeat_hs2_sc2 91.6 1.3 2.8E-05 29.3 6.7 52 4-60 5-57 (74)
62 cd05689 S1_RPS1_repeat_ec4 S1_ 91.3 1.4 3.1E-05 28.3 6.7 54 4-60 4-62 (72)
63 cd05705 S1_Rrp5_repeat_hs14 S1 91.2 0.92 2E-05 30.0 5.8 54 4-61 4-65 (74)
64 COG1158 Rho Transcription term 91.2 0.35 7.7E-06 41.7 4.5 67 8-79 55-128 (422)
65 cd04472 S1_PNPase S1_PNPase: P 90.6 1.2 2.6E-05 27.9 5.8 53 6-61 3-59 (68)
66 cd05686 S1_pNO40 S1_pNO40: pNO 90.5 1.5 3.2E-05 28.6 6.3 54 4-60 4-62 (73)
67 PF15288 zf-CCHC_6: Zinc knuck 90.4 0.13 2.9E-06 30.4 0.9 20 118-137 2-23 (40)
68 PRK09376 rho transcription ter 89.9 0.87 1.9E-05 40.1 5.9 67 7-78 51-124 (416)
69 cd04465 S1_RPS1_repeat_ec2_hs2 89.7 0.73 1.6E-05 29.4 4.2 53 5-61 2-56 (67)
70 cd05707 S1_Rrp5_repeat_sc11 S1 89.0 1.6 3.4E-05 27.8 5.4 52 6-60 3-58 (68)
71 PRK05807 hypothetical protein; 89.0 3.2 6.9E-05 30.9 7.7 66 4-74 6-76 (136)
72 cd05684 S1_DHX8_helicase S1_DH 89.0 3.6 7.9E-05 27.0 7.3 55 6-63 3-65 (79)
73 cd05691 S1_RPS1_repeat_ec6 S1_ 88.9 2.8 6E-05 26.7 6.6 53 6-61 3-59 (73)
74 PF14787 zf-CCHC_5: GAG-polypr 88.9 0.25 5.4E-06 28.5 1.3 21 118-138 3-23 (36)
75 PRK12678 transcription termina 87.8 1.2 2.6E-05 41.2 5.6 66 7-78 296-372 (672)
76 cd04473 S1_RecJ_like S1_RecJ_l 87.5 2.7 5.8E-05 27.7 5.9 50 4-60 17-66 (77)
77 cd05687 S1_RPS1_repeat_ec1_hs1 86.5 2.8 6E-05 26.7 5.4 53 5-60 2-58 (70)
78 cd05690 S1_RPS1_repeat_ec5 S1_ 86.4 3.1 6.8E-05 26.2 5.6 52 6-60 3-59 (69)
79 cd05703 S1_Rrp5_repeat_hs12_sc 86.4 3.5 7.6E-05 27.0 5.9 51 6-60 3-60 (73)
80 cd04455 S1_NusA S1_NusA: N-uti 85.9 2.7 5.8E-05 27.0 5.1 51 4-60 4-54 (67)
81 cd05702 S1_Rrp5_repeat_hs11_sc 85.5 3.5 7.5E-05 26.5 5.5 55 5-62 2-62 (70)
82 cd04460 S1_RpoE S1_RpoE: RpoE, 84.5 5.1 0.00011 27.7 6.3 51 6-60 2-67 (99)
83 COG5222 Uncharacterized conser 84.3 0.47 1E-05 40.1 1.1 20 119-138 178-197 (427)
84 cd04452 S1_IF2_alpha S1_IF2_al 83.6 4.9 0.00011 25.8 5.7 54 4-60 4-63 (76)
85 PRK08059 general stress protei 83.6 11 0.00024 27.3 8.0 68 4-75 8-81 (123)
86 cd04471 S1_RNase_R S1_RNase_R: 83.3 10 0.00022 24.7 7.2 54 5-61 3-72 (83)
87 COG1098 VacB Predicted RNA bin 83.1 2.4 5.2E-05 31.3 4.3 70 4-78 6-81 (129)
88 cd05685 S1_Tex S1_Tex: The C-t 82.7 5 0.00011 24.8 5.3 52 6-60 3-58 (68)
89 PF11604 CusF_Ec: Copper bindi 82.4 2.3 4.9E-05 28.0 3.6 29 44-72 40-68 (70)
90 COG2996 Predicted RNA-bindinin 82.4 6 0.00013 33.1 6.8 61 5-71 7-68 (287)
91 TIGR00767 rho transcription te 82.0 1.5 3.3E-05 38.6 3.4 50 6-60 50-104 (415)
92 TIGR00757 RNaseEG ribonuclease 81.6 8.3 0.00018 34.0 7.8 71 4-75 26-115 (414)
93 cd05789 S1_Rrp4 S1_Rrp4: Rrp4 81.3 7.3 0.00016 25.9 6.0 55 4-61 7-69 (86)
94 PF05606 DUF777: Borrelia burg 79.8 3.4 7.4E-05 32.0 4.2 47 7-55 36-82 (181)
95 cd05688 S1_RPS1_repeat_ec3 S1_ 78.7 7.7 0.00017 24.0 5.1 52 5-60 3-58 (68)
96 cd05695 S1_Rrp5_repeat_hs3 S1_ 78.0 8.8 0.00019 24.5 5.3 52 5-59 2-55 (66)
97 PRK09838 periplasmic copper-bi 78.0 4.7 0.0001 29.3 4.4 63 6-72 44-113 (115)
98 PTZ00248 eukaryotic translatio 77.9 14 0.0003 31.6 7.8 70 4-77 18-95 (319)
99 KOG2044 5'-3' exonuclease HKE1 75.7 1.3 2.8E-05 42.0 1.0 20 149-168 259-278 (931)
100 KOG0314 Predicted E3 ubiquitin 75.6 2.5 5.3E-05 37.7 2.7 42 119-168 135-176 (448)
101 TIGR01451 B_ant_repeat conserv 74.6 4.6 0.0001 24.9 3.1 31 45-75 6-36 (53)
102 PRK13806 rpsA 30S ribosomal pr 74.6 16 0.00034 32.9 7.6 67 4-73 293-365 (491)
103 cd05708 S1_Rrp5_repeat_sc12 S1 73.1 13 0.00028 23.7 5.2 54 5-61 4-62 (77)
104 PHA02945 interferon resistance 72.6 26 0.00057 24.3 6.7 54 4-62 12-72 (88)
105 KOG0921 Dosage compensation co 71.2 17 0.00037 35.6 7.2 23 87-109 1186-1208(1282)
106 COG4776 Rnb Exoribonuclease II 71.1 5.7 0.00012 35.8 3.9 50 4-61 19-68 (645)
107 KOG0107 Alternative splicing f 70.0 2 4.3E-05 33.7 0.8 16 120-135 103-118 (195)
108 PF03100 CcmE: CcmE; InterPro 69.0 22 0.00048 26.0 6.2 63 6-72 54-121 (131)
109 KOG3116 Predicted C3H1-type Zn 69.0 1.4 2.9E-05 33.7 -0.3 22 116-137 26-47 (177)
110 TIGR02696 pppGpp_PNP guanosine 68.7 11 0.00024 35.6 5.5 58 4-64 648-714 (719)
111 PF01796 DUF35: DUF35 OB-fold 66.9 20 0.00044 22.9 5.0 37 20-57 31-67 (68)
112 PRK10811 rne ribonuclease E; R 66.6 25 0.00055 34.5 7.4 70 4-74 39-124 (1068)
113 PRK13806 rpsA 30S ribosomal pr 66.1 15 0.00032 33.0 5.6 54 4-60 380-437 (491)
114 PLN00207 polyribonucleotide nu 65.7 27 0.00059 33.9 7.5 63 5-71 755-823 (891)
115 PRK07899 rpsA 30S ribosomal pr 65.6 34 0.00073 30.9 7.7 68 4-75 294-367 (486)
116 PF05753 TRAP_beta: Translocon 65.6 14 0.00031 28.8 4.8 47 24-74 15-61 (181)
117 PRK13150 cytochrome c-type bio 65.1 42 0.00092 25.8 7.1 63 7-73 67-129 (159)
118 TIGR00448 rpoE DNA-directed RN 64.9 47 0.001 25.5 7.6 52 5-60 83-149 (179)
119 PRK11712 ribonuclease G; Provi 63.4 33 0.00071 31.1 7.2 71 4-75 39-128 (489)
120 PRK06299 rpsA 30S ribosomal pr 63.2 25 0.00054 31.9 6.6 65 4-71 287-357 (565)
121 PRK13165 cytochrome c-type bio 62.6 47 0.001 25.6 7.0 63 7-73 67-129 (160)
122 PRK07899 rpsA 30S ribosomal pr 62.0 36 0.00079 30.7 7.3 52 4-59 209-264 (486)
123 TIGR00717 rpsA ribosomal prote 61.6 34 0.00074 30.5 7.1 63 4-70 273-342 (516)
124 cd04489 ExoVII_LU_OBF ExoVII_L 61.6 40 0.00086 21.6 6.2 66 6-72 3-76 (78)
125 KOG2673 Uncharacterized conser 60.7 4.7 0.0001 36.0 1.3 22 117-138 128-149 (485)
126 PF01345 DUF11: Domain of unkn 60.5 12 0.00026 24.3 3.0 31 45-75 35-65 (76)
127 TIGR03591 polynuc_phos polyrib 60.1 21 0.00046 33.5 5.6 55 4-61 619-677 (684)
128 PRK06299 rpsA 30S ribosomal pr 59.6 42 0.0009 30.5 7.3 68 4-74 374-447 (565)
129 COG0539 RpsA Ribosomal protein 59.2 32 0.0007 31.5 6.5 68 4-74 278-350 (541)
130 PF12353 eIF3g: Eukaryotic tra 58.8 4.9 0.00011 29.7 1.0 20 149-169 105-124 (128)
131 PRK09202 nusA transcription el 58.3 19 0.00042 32.3 4.9 51 4-60 135-185 (470)
132 PRK11824 polynucleotide phosph 57.7 53 0.0011 31.0 7.8 58 4-64 622-684 (693)
133 TIGR00717 rpsA ribosomal prote 57.4 53 0.0011 29.3 7.6 65 4-72 360-431 (516)
134 PRK12269 bifunctional cytidyla 56.1 25 0.00054 34.1 5.5 52 5-60 495-550 (863)
135 PRK07400 30S ribosomal protein 55.8 47 0.001 28.1 6.6 67 4-75 197-269 (318)
136 PRK12269 bifunctional cytidyla 55.4 19 0.00041 34.9 4.5 67 4-74 579-652 (863)
137 cd05693 S1_Rrp5_repeat_hs1_sc1 54.4 50 0.0011 23.0 5.6 56 4-62 4-82 (100)
138 COG2996 Predicted RNA-bindinin 53.6 64 0.0014 27.1 6.8 49 19-69 87-137 (287)
139 TIGR00638 Mop molybdenum-pteri 53.0 54 0.0012 20.4 5.4 54 5-59 7-61 (69)
140 PF01336 tRNA_anti-codon: OB-f 52.7 17 0.00037 22.8 2.8 53 6-58 2-56 (75)
141 PRK08563 DNA-directed RNA poly 52.6 39 0.00085 26.0 5.3 52 5-60 83-149 (187)
142 PRK07400 30S ribosomal protein 52.3 35 0.00076 28.9 5.3 53 4-60 119-171 (318)
143 COG0539 RpsA Ribosomal protein 51.6 49 0.0011 30.4 6.3 54 4-61 193-250 (541)
144 COG1095 RPB7 DNA-directed RNA 49.9 25 0.00054 27.7 3.7 52 5-60 83-149 (183)
145 PF03459 TOBE: TOBE domain; I 49.7 28 0.00061 21.5 3.4 55 4-59 4-59 (64)
146 KOG2044 5'-3' exonuclease HKE1 49.6 7.8 0.00017 37.0 1.0 22 115-136 258-279 (931)
147 PF04225 OapA: Opacity-associa 49.5 27 0.00058 23.7 3.4 31 43-75 39-69 (85)
148 cd04486 YhcR_OBF_like YhcR_OBF 48.6 78 0.0017 21.0 5.7 49 7-60 2-58 (78)
149 PRK06676 rpsA 30S ribosomal pr 48.5 1E+02 0.0022 26.4 7.7 71 4-77 278-353 (390)
150 PRK06676 rpsA 30S ribosomal pr 48.4 77 0.0017 27.2 6.9 56 4-61 18-77 (390)
151 PF06523 DUF1106: Protein of u 46.6 66 0.0014 21.6 4.8 54 6-59 32-89 (91)
152 PF11948 DUF3465: Protein of u 46.5 79 0.0017 23.5 5.7 56 7-63 41-104 (131)
153 PF00358 PTS_EIIA_1: phosphoen 46.5 72 0.0016 23.6 5.6 46 7-54 46-97 (132)
154 TIGR00830 PTBA PTS system, glu 45.8 74 0.0016 23.2 5.5 46 7-54 42-93 (121)
155 KOG2673 Uncharacterized conser 45.8 10 0.00022 33.9 1.1 19 150-168 128-146 (485)
156 TIGR01953 NusA transcription t 45.1 42 0.0009 28.9 4.7 52 4-60 132-183 (341)
157 KOG0107 Alternative splicing f 45.1 11 0.00025 29.6 1.1 16 153-168 103-118 (195)
158 cd05701 S1_Rrp5_repeat_hs10 S1 44.8 56 0.0012 21.4 4.1 45 16-60 11-59 (69)
159 PRK03987 translation initiatio 44.7 50 0.0011 27.3 5.0 64 4-71 9-80 (262)
160 TIGR00358 3_prime_RNase VacB a 44.7 57 0.0012 30.4 5.9 53 5-60 574-642 (654)
161 PF01551 Peptidase_M23: Peptid 44.4 33 0.00071 23.1 3.3 51 6-56 19-72 (96)
162 cd00210 PTS_IIA_glc PTS_IIA, P 44.1 82 0.0018 23.1 5.5 46 7-54 42-93 (124)
163 PRK12327 nusA transcription el 43.4 41 0.00089 29.2 4.4 51 4-60 135-185 (362)
164 PRK00087 4-hydroxy-3-methylbut 43.1 88 0.0019 29.1 6.8 61 4-67 303-369 (647)
165 PRK13159 cytochrome c-type bio 42.9 1.5E+02 0.0032 22.7 6.9 63 6-73 60-122 (155)
166 KOG4246 Predicted DNA-binding 42.3 2.9 6.4E-05 39.9 -2.9 63 5-77 147-211 (1194)
167 KOG0407 40S ribosomal protein 41.7 30 0.00065 25.1 2.8 42 18-59 14-56 (139)
168 PRK13254 cytochrome c-type bio 40.2 1.6E+02 0.0035 22.2 7.1 60 9-73 63-122 (148)
169 cd04454 S1_Rrp4_like S1_Rrp4_l 40.2 1E+02 0.0022 20.0 7.2 56 4-62 7-66 (82)
170 KOG0119 Splicing factor 1/bran 40.0 14 0.0003 33.4 1.0 20 117-136 285-304 (554)
171 KOG3070 Predicted RNA-binding 39.7 1.9E+02 0.0042 23.5 7.5 54 9-63 71-127 (235)
172 KOG3262 H/ACA small nucleolar 39.0 1.3E+02 0.0029 23.9 6.1 8 46-53 118-125 (215)
173 PRK00087 4-hydroxy-3-methylbut 38.9 1.6E+02 0.0034 27.5 7.8 67 5-75 564-636 (647)
174 COG2183 Tex Transcriptional ac 36.7 95 0.0021 29.8 5.9 72 4-78 659-735 (780)
175 KOG0105 Alternative splicing f 36.7 24 0.00052 28.2 1.7 32 29-60 23-57 (241)
176 TIGR02063 RNase_R ribonuclease 36.6 77 0.0017 29.8 5.4 53 5-60 629-697 (709)
177 PRK11642 exoribonuclease R; Pr 35.4 1.5E+02 0.0032 28.6 7.2 54 4-60 644-713 (813)
178 COG1185 Pnp Polyribonucleotide 34.1 99 0.0021 29.2 5.5 59 4-65 620-683 (692)
179 COG1545 Predicted nucleic-acid 33.5 2E+02 0.0043 21.3 6.6 37 20-60 87-123 (140)
180 COG0557 VacB Exoribonuclease R 33.4 1.1E+02 0.0023 29.0 5.8 60 8-74 71-134 (706)
181 COG5569 Uncharacterized conser 33.1 58 0.0013 23.2 3.0 26 44-70 81-106 (108)
182 KOG3794 CBF1-interacting corep 32.7 18 0.00039 31.8 0.6 19 149-167 123-143 (453)
183 PTZ00162 DNA-directed RNA poly 31.8 1E+02 0.0022 23.8 4.6 34 4-41 82-115 (176)
184 PF13742 tRNA_anti_2: OB-fold 31.4 1.8E+02 0.0038 20.0 6.9 61 4-64 23-89 (99)
185 CHL00010 infA translation init 31.3 1.6E+02 0.0035 19.5 6.0 55 4-60 6-60 (78)
186 KOG0341 DEAD-box protein abstr 31.1 27 0.00058 31.2 1.3 20 149-168 569-588 (610)
187 PF01194 RNA_pol_N: RNA polyme 30.5 25 0.00055 22.6 0.8 10 150-159 4-13 (60)
188 COG1644 RPB10 DNA-directed RNA 29.4 22 0.00048 23.0 0.4 10 150-159 4-13 (63)
189 COG2190 NagE Phosphotransferas 29.2 1.6E+02 0.0036 22.5 5.2 45 8-54 50-100 (156)
190 COG5179 TAF1 Transcription ini 28.5 32 0.0007 32.3 1.4 12 151-162 938-949 (968)
191 COG1093 SUI2 Translation initi 28.2 1.4E+02 0.0031 24.8 5.0 59 4-63 12-74 (269)
192 PRK09439 PTS system glucose-sp 27.1 2.1E+02 0.0045 22.1 5.5 46 7-54 64-115 (169)
193 cd03524 RPA2_OBF_family RPA2_O 27.0 1.4E+02 0.0031 17.6 5.0 54 7-60 2-60 (75)
194 PRK05054 exoribonuclease II; P 26.7 1.9E+02 0.0041 27.0 6.2 33 6-41 564-597 (644)
195 PRK00276 infA translation init 25.6 1.9E+02 0.0042 18.7 6.2 55 4-60 6-60 (72)
196 PRK11637 AmiB activator; Provi 25.0 78 0.0017 27.7 3.2 35 6-40 345-382 (428)
197 cd04451 S1_IF1 S1_IF1: Transla 24.9 1.8E+02 0.004 18.1 6.4 51 7-59 3-53 (64)
198 PF14326 DUF4384: Domain of un 24.8 1.3E+02 0.0029 19.8 3.7 25 46-70 2-26 (83)
199 KOG2560 RNA splicing factor - 24.7 16 0.00035 32.7 -1.1 17 150-166 112-128 (529)
200 PRK04016 DNA-directed RNA poly 24.3 32 0.0007 22.3 0.5 10 150-159 4-13 (62)
201 PRK06958 single-stranded DNA-b 24.1 3.5E+02 0.0077 21.1 7.9 25 32-56 52-79 (182)
202 KOG3272 Predicted coiled-coil 23.8 52 0.0011 26.1 1.7 25 29-53 34-59 (207)
203 PF12353 eIF3g: Eukaryotic tra 23.6 36 0.00077 25.1 0.7 22 115-137 104-125 (128)
204 COG5179 TAF1 Transcription ini 23.4 49 0.0011 31.1 1.6 24 114-137 934-959 (968)
205 PF00498 FHA: FHA domain; Int 23.4 77 0.0017 19.6 2.2 47 7-55 21-67 (68)
206 PRK09521 exosome complex RNA-b 23.2 2.2E+02 0.0049 21.9 5.2 55 4-61 65-133 (189)
207 KOG0921 Dosage compensation co 23.0 1.3E+02 0.0028 29.9 4.3 11 33-43 1152-1162(1282)
208 KOG3497 DNA-directed RNA polym 22.8 30 0.00066 22.4 0.1 10 150-159 4-13 (69)
209 cd04318 EcAsnRS_like_N EcAsnRS 22.7 2.2E+02 0.0049 18.4 4.9 51 6-56 3-57 (82)
210 PF05938 Self-incomp_S1: Plant 22.3 2.6E+02 0.0056 19.3 5.0 34 28-61 11-45 (110)
211 PLN03134 glycine-rich RNA-bind 22.2 26 0.00056 26.1 -0.3 12 17-28 75-86 (144)
212 COG4384 Mu-like prophage prote 22.0 1.1E+02 0.0024 24.2 3.2 41 18-58 55-107 (203)
213 KOG2560 RNA splicing factor - 20.9 27 0.00059 31.4 -0.5 19 118-136 113-131 (529)
214 TIGR02038 protease_degS peripl 20.9 2.1E+02 0.0046 24.3 5.0 45 4-54 111-155 (351)
215 PF05741 zf-nanos: Nanos RNA b 20.5 43 0.00092 21.1 0.5 20 150-169 33-55 (55)
No 1
>COG1278 CspC Cold shock proteins [Transcription]
Probab=99.95 E-value=9.9e-28 Score=157.60 Aligned_cols=67 Identities=60% Similarity=1.072 Sum_probs=63.9
Q ss_pred ccceEEEEeeCCCCeeEEecCCCCccEEEEeeccccCCcccCCCCCEEEEEEeeCCCCceeEEEEEcC
Q 030905 6 RSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVGEDGRTKAVDVEAA 73 (169)
Q Consensus 6 ~~~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~~~~~~l~~G~~V~F~~~~~~kGr~~A~~V~~~ 73 (169)
|++|+|||||.+||||||+++++.+|||||+|+|+..++++|.+||+|+|+++++++| ++|.||+++
T Consensus 1 ~~~GtVKwfn~~KGfGFI~p~~G~~DvFVH~Sai~~~g~~~L~eGQ~V~f~~~~g~kg-p~A~nv~~~ 67 (67)
T COG1278 1 MATGTVKWFNATKGFGFITPEDGGKDVFVHISAIQRAGFRTLREGQKVEFEVEQGRKG-PSAANVRAL 67 (67)
T ss_pred CCcceEEEeeCCCcceEcCCCCCCcCEEEEeeeeccCCCcccCCCCEEEEEEecCCCC-CceeEEEeC
Confidence 4689999999999999999999999999999999999999999999999999999999 899999863
No 2
>PRK10943 cold shock-like protein CspC; Provisional
Probab=99.94 E-value=1.3e-26 Score=154.61 Aligned_cols=69 Identities=51% Similarity=0.983 Sum_probs=64.9
Q ss_pred ccccceEEEEeeCCCCeeEEecCCCCccEEEEeeccccCCcccCCCCCEEEEEEeeCCCCceeEEEEEcC
Q 030905 4 VQRSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVGEDGRTKAVDVEAA 73 (169)
Q Consensus 4 ~~~~~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~~~~~~l~~G~~V~F~~~~~~kGr~~A~~V~~~ 73 (169)
||+++|+|||||.+||||||+++++++|||||+|+|+..+++.|.+|++|+|+++++++| ++|++|+.+
T Consensus 1 ~~~~~G~Vk~f~~~kGfGFI~~~~g~~dvFvH~s~l~~~g~~~l~~G~~V~f~~~~~~~g-~~A~~V~~~ 69 (69)
T PRK10943 1 MAKIKGQVKWFNESKGFGFITPADGSKDVFVHFSAIQGNGFKTLAEGQNVEFEIQDGQKG-PAAVNVTAI 69 (69)
T ss_pred CCccceEEEEEeCCCCcEEEecCCCCeeEEEEhhHccccCCCCCCCCCEEEEEEEECCCC-ceeEEEEcC
Confidence 467999999999999999999999889999999999999889999999999999999998 799999853
No 3
>PRK15464 cold shock-like protein CspH; Provisional
Probab=99.94 E-value=1.8e-26 Score=154.17 Aligned_cols=69 Identities=33% Similarity=0.517 Sum_probs=64.3
Q ss_pred CCcccccceEEEEeeCCCCeeEEecCCCCccEEEEeeccccCCcccCCCCCEEEEEEeeCCCCceeEEEEEc
Q 030905 1 MAEVQRSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVGEDGRTKAVDVEA 72 (169)
Q Consensus 1 M~~~~~~~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~~~~~~l~~G~~V~F~~~~~~kGr~~A~~V~~ 72 (169)
|+ .+++|+|||||.+||||||+++++++|||||+++|+..+++.|.+|++|+|+++++++| ++|++|.+
T Consensus 1 m~--~~~~G~Vk~fn~~KGfGFI~~~~g~~DvFvH~s~l~~~g~~~l~~G~~V~f~v~~~~kG-~~A~~v~~ 69 (70)
T PRK15464 1 MS--RKMTGIVKTFDRKSGKGFIIPSDGRKEVQVHISAFTPRDAEVLIPGLRVEFCRVNGLRG-PTAANVYL 69 (70)
T ss_pred CC--ccceEEEEEEECCCCeEEEccCCCCccEEEEehhehhcCCCCCCCCCEEEEEEEECCCC-ceeEEEEc
Confidence 65 34699999999999999999999999999999999988888999999999999999999 79999975
No 4
>PRK15463 cold shock-like protein CspF; Provisional
Probab=99.93 E-value=4.3e-26 Score=152.47 Aligned_cols=69 Identities=33% Similarity=0.527 Sum_probs=64.5
Q ss_pred CCcccccceEEEEeeCCCCeeEEecCCCCccEEEEeeccccCCcccCCCCCEEEEEEeeCCCCceeEEEEEc
Q 030905 1 MAEVQRSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVGEDGRTKAVDVEA 72 (169)
Q Consensus 1 M~~~~~~~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~~~~~~l~~G~~V~F~~~~~~kGr~~A~~V~~ 72 (169)
|+ .+++|+|||||.+||||||+++++++|||||+++|+..+++.|.+|++|+|+++++++| ++|++|++
T Consensus 1 m~--~~~~G~Vk~fn~~kGfGFI~~~~g~~DvFvH~sal~~~g~~~l~~G~~V~f~v~~~~~G-~~A~~V~~ 69 (70)
T PRK15463 1 MS--RKMTGIVKTFDGKSGKGLITPSDGRKDVQVHISALNLRDAEELTTGLRVEFCRINGLRG-PTAANVYL 69 (70)
T ss_pred CC--ccceEEEEEEeCCCceEEEecCCCCccEEEEehhhhhcCCCCCCCCCEEEEEEEECCCC-ceeEEEEc
Confidence 66 34699999999999999999999999999999999988889999999999999999999 79999975
No 5
>PRK10354 RNA chaperone/anti-terminator; Provisional
Probab=99.93 E-value=7.5e-26 Score=151.41 Aligned_cols=70 Identities=46% Similarity=0.969 Sum_probs=64.9
Q ss_pred CCcccccceEEEEeeCCCCeeEEecCCCCccEEEEeeccccCCcccCCCCCEEEEEEeeCCCCceeEEEEEcC
Q 030905 1 MAEVQRSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVGEDGRTKAVDVEAA 73 (169)
Q Consensus 1 M~~~~~~~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~~~~~~l~~G~~V~F~~~~~~kGr~~A~~V~~~ 73 (169)
|+ .+++|+|||||.+||||||+++++++|||||+|+|...+++.|.+|++|+|+++++++| ++|++|+.+
T Consensus 1 m~--~~~~G~Vk~f~~~kGfGFI~~~~g~~dvfvH~s~l~~~g~~~l~~G~~V~f~~~~~~~G-~~A~~V~~~ 70 (70)
T PRK10354 1 MS--GKMTGIVKWFNADKGFGFITPDDGSKDVFVHFSAIQNDGYKSLDEGQKVSFTIESGAKG-PAAGNVTSL 70 (70)
T ss_pred CC--ccceEEEEEEeCCCCcEEEecCCCCccEEEEEeeccccCCCCCCCCCEEEEEEEECCCC-ceeEEEEeC
Confidence 77 33599999999999999999999989999999999999889999999999999999999 899999863
No 6
>PRK09890 cold shock protein CspG; Provisional
Probab=99.93 E-value=8e-26 Score=151.25 Aligned_cols=69 Identities=54% Similarity=0.983 Sum_probs=64.7
Q ss_pred CCcccccceEEEEeeCCCCeeEEecCCCCccEEEEeeccccCCcccCCCCCEEEEEEeeCCCCceeEEEEEc
Q 030905 1 MAEVQRSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVGEDGRTKAVDVEA 72 (169)
Q Consensus 1 M~~~~~~~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~~~~~~l~~G~~V~F~~~~~~kGr~~A~~V~~ 72 (169)
|+ ++++|+|||||.+||||||+++++++|||||+|+|+..+++.|.+|++|+|+++++++| ++|++|..
T Consensus 1 m~--~~~~G~Vk~f~~~kGfGFI~~~~g~~dvFvH~s~l~~~~~~~l~~G~~V~f~~~~~~~G-~~A~~V~~ 69 (70)
T PRK09890 1 MS--NKMTGLVKWFNADKGFGFITPDDGSKDVFVHFTAIQSNEFRTLNENQKVEFSIEQGQRG-PAAANVVT 69 (70)
T ss_pred CC--ccceEEEEEEECCCCcEEEecCCCCceEEEEEeeeccCCCCCCCCCCEEEEEEEECCCC-ceeEEEEe
Confidence 66 45699999999999999999999989999999999999999999999999999999999 79999975
No 7
>PRK09507 cspE cold shock protein CspE; Reviewed
Probab=99.93 E-value=9.5e-26 Score=150.50 Aligned_cols=67 Identities=52% Similarity=0.997 Sum_probs=63.8
Q ss_pred cccceEEEEeeCCCCeeEEecCCCCccEEEEeeccccCCcccCCCCCEEEEEEeeCCCCceeEEEEEc
Q 030905 5 QRSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVGEDGRTKAVDVEA 72 (169)
Q Consensus 5 ~~~~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~~~~~~l~~G~~V~F~~~~~~kGr~~A~~V~~ 72 (169)
.+++|+|||||.+||||||+++++++|||||+|+|...+++.|.+|++|+|+++++++| ++|++|+.
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 36899999999999999999999989999999999998899999999999999999999 79999975
No 8
>PRK09937 stationary phase/starvation inducible regulatory protein CspD; Provisional
Probab=99.93 E-value=2.1e-25 Score=150.55 Aligned_cols=67 Identities=49% Similarity=0.958 Sum_probs=63.7
Q ss_pred cceEEEEeeCCCCeeEEecCCCCccEEEEeeccccCCcccCCCCCEEEEEEeeCCCCceeEEEEEcCC
Q 030905 7 SSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVGEDGRTKAVDVEAAS 74 (169)
Q Consensus 7 ~~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~~~~~~l~~G~~V~F~~~~~~kGr~~A~~V~~~~ 74 (169)
.+|+|||||.+||||||+++++++|||||+|+|+..+++.|.+|++|+|+++++++| ++|++|..++
T Consensus 2 ~~G~Vkwfn~~KGfGFI~~~~gg~dVFvH~s~i~~~g~~~l~~G~~V~f~~~~~~~G-~~A~~V~~~~ 68 (74)
T PRK09937 2 EKGTVKWFNNAKGFGFICPEGGGEDIFAHYSTIQMDGYRTLKAGQSVQFDVHQGPKG-NHASVIVPVE 68 (74)
T ss_pred CCeEEEEEeCCCCeEEEeeCCCCccEEEEEeeccccCCCCCCCCCEEEEEEEECCCC-ceeeEEEECC
Confidence 479999999999999999999999999999999999999999999999999999999 6999999874
No 9
>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=99.92 E-value=2.7e-25 Score=147.95 Aligned_cols=66 Identities=44% Similarity=0.838 Sum_probs=62.7
Q ss_pred cceEEEEeeCCCCeeEEecCCCCccEEEEeeccccCCcccCCCCCEEEEEEeeCCCCceeEEEEEcC
Q 030905 7 SSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVGEDGRTKAVDVEAA 73 (169)
Q Consensus 7 ~~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~~~~~~l~~G~~V~F~~~~~~kGr~~A~~V~~~ 73 (169)
.+|+|||||.+||||||+++++++|||||+|+|+..+++.|.+|++|+|+++++++| ++|++|..+
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 479999999999999999999889999999999998899999999999999999999 799999864
No 10
>PRK14998 cold shock-like protein CspD; Provisional
Probab=99.92 E-value=4.4e-25 Score=148.70 Aligned_cols=68 Identities=49% Similarity=0.937 Sum_probs=64.0
Q ss_pred cceEEEEeeCCCCeeEEecCCCCccEEEEeeccccCCcccCCCCCEEEEEEeeCCCCceeEEEEEcCCC
Q 030905 7 SSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVGEDGRTKAVDVEAASR 75 (169)
Q Consensus 7 ~~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~~~~~~l~~G~~V~F~~~~~~kGr~~A~~V~~~~g 75 (169)
.+|+|||||.+||||||+++++++|||||+|+|+..+++.|.+|++|+|+++++++| ++|++|..++.
T Consensus 2 ~~G~Vkwfn~~kGfGFI~~~~g~~dVFvH~s~l~~~g~~~l~~G~~V~f~~~~~~~G-~~A~~V~~~~~ 69 (73)
T PRK14998 2 ETGTVKWFNNAKGFGFICPEGGGEDIFAHYSTIQMDGYRTLKAGQSVRFDVHQGPKG-NHASVIVPIEA 69 (73)
T ss_pred CCeEEEEEeCCCceEEEecCCCCccEEEEeeeecccCCCCCCCCCEEEEEEEECCCC-ceeEEEEECcc
Confidence 479999999999999999999999999999999999999999999999999999999 69999987653
No 11
>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=99.89 E-value=1e-22 Score=134.28 Aligned_cols=66 Identities=50% Similarity=1.018 Sum_probs=59.8
Q ss_pred cceEEEEeeCCCCeeEEecCCCCccEEEEeeccccCCcccCCCCCEEEEEEeeCCCCceeEEEEEcC
Q 030905 7 SSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVGEDGRTKAVDVEAA 73 (169)
Q Consensus 7 ~~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~~~~~~l~~G~~V~F~~~~~~kGr~~A~~V~~~ 73 (169)
|+|+|||||++||||||+++++.+|||||+++|....+..|.+|++|+|++..++++ ++|++|+++
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 689999999999999999999988999999999999888999999999999998887 899999864
No 12
>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=99.88 E-value=3e-22 Score=131.72 Aligned_cols=65 Identities=54% Similarity=1.112 Sum_probs=61.0
Q ss_pred cceEEEEeeCCCCeeEEecCCCCccEEEEeeccccCCcccCCCCCEEEEEEeeCCCCceeEEEEEc
Q 030905 7 SSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVGEDGRTKAVDVEA 72 (169)
Q Consensus 7 ~~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~~~~~~l~~G~~V~F~~~~~~kGr~~A~~V~~ 72 (169)
++|+|||||++||||||+++++++|||||+++|...++..|.+|+.|+|+++.+.+| ++|++|+.
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 479999999999999999999889999999999998889999999999999999888 79999973
No 13
>KOG3070 consensus Predicted RNA-binding protein containing PIN domain and invovled in translation or RNA processing [Translation, ribosomal structure and biogenesis]
Probab=99.79 E-value=9.2e-19 Score=141.55 Aligned_cols=157 Identities=40% Similarity=0.684 Sum_probs=105.5
Q ss_pred ccccceEEEEeeCCCCeeEEecCCCCccEEEEeecccc----CCcccCCCCCEEEEEEeeCCCCceeEEEEEcCCCcccc
Q 030905 4 VQRSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKS----EGFRTLSEGQTVEFSVDVGEDGRTKAVDVEAASRSRRF 79 (169)
Q Consensus 4 ~~~~~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~----~~~~~l~~G~~V~F~~~~~~kGr~~A~~V~~~~g~~~~ 79 (169)
....+|+|||||..+|||||+++++.+|||||+++|.. .+|++|.+++.|.|+++...++ ..|++|+-+++.++.
T Consensus 54 ~~~~~G~~k~fnv~~G~gFi~~~d~~~D~fvhQs~i~~~~~~~~~rs~~~~e~v~f~~~~~~~g-~~a~~vt~p~g~~~~ 132 (235)
T KOG3070|consen 54 GARVKGTVKWFNVGKGYGFITRDDGPEDVFVHQSAITKYTPSEGFRSLKEGEAVPFDIQEGNKG-TEAANVTGPDGVPVR 132 (235)
T ss_pred cccccCcceeEeccCCcceecccCCCCceeEEeeeecccccccchhhcccCCCccceecccCcc-ceeeeecCCCCcccc
Confidence 46789999999999999999999999999999999999 8899999999999999999999 899999999999998
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCC---CCCCCCCCCCCCccccCcCCeecccCCCCCCCCCCCCCCCCCCcccccc
Q 030905 80 GSRGGRSGGFYGGRGRGGGYGRGGRGGR---SVGSGGGAGSGACFNCGRTGHIARECYSRGRGGGRGYGGGRGGGGCYNC 156 (169)
Q Consensus 80 ~~~~~~~~~~~~~~~~~~~~~~~~~g~g---~~~gg~~~~~~~C~~Cg~~GH~a~~C~~~~~~~~~~~~g~~~~~~C~~C 156 (169)
++......-.+...........+.-... +...+.......|+.|+..+|.... +... -.+......|+.|
T Consensus 133 ~s~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~-~~r~------~~g~r~~~~~~~~ 205 (235)
T KOG3070|consen 133 GSKGAVKGNNERRVVGKSKVGHGGPIGQDDVRGEPGGEAVGVSGRACGGAGAAQRP-PVRK------CGGYRPASLCYTC 205 (235)
T ss_pred cccccccccccccccccccCCCCCCcccccccccccccccccccccccccccccCC-CCcc------cccCCCccccccc
Confidence 7754222111100000000000000000 1111222233344778877764422 1100 0011135679999
Q ss_pred CCCCccCCCCCC
Q 030905 157 GEEGHFARDCPN 168 (169)
Q Consensus 157 g~~GH~ardCp~ 168 (169)
++++|.+.+|++
T Consensus 206 ~~~g~~~~~~~e 217 (235)
T KOG3070|consen 206 GEPGHVADGCEE 217 (235)
T ss_pred Cccccccccccc
Confidence 999999999876
No 14
>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=99.16 E-value=2.4e-10 Score=73.39 Aligned_cols=62 Identities=50% Similarity=0.986 Sum_probs=50.7
Q ss_pred ceEEEEeeCCCCeeEEecCCCCccEEEEeeccccCCcccCCCCCEEEEEEeeC-CCCceeEEEEEc
Q 030905 8 SGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVG-EDGRTKAVDVEA 72 (169)
Q Consensus 8 ~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~~~~~~l~~G~~V~F~~~~~-~kGr~~A~~V~~ 72 (169)
+|+|+|++ +|||||.+++..+|||||.++|.. .+..+.+|+.|.|.+... .+++++|..|+.
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 58999998 799999998765699999999876 556789999999999873 334478887764
No 15
>PTZ00368 universal minicircle sequence binding protein (UMSBP); Provisional
Probab=98.80 E-value=3.5e-09 Score=80.02 Aligned_cols=47 Identities=49% Similarity=1.206 Sum_probs=36.7
Q ss_pred CCCCccccCcCCeecccCCCCCCCCCCCCCCCCCCccccccCCCCccCCCCCCC
Q 030905 116 GSGACFNCGRTGHIARECYSRGRGGGRGYGGGRGGGGCYNCGEEGHFARDCPNY 169 (169)
Q Consensus 116 ~~~~C~~Cg~~GH~a~~C~~~~~~~~~~~~g~~~~~~C~~Cg~~GH~ardCp~~ 169 (169)
....||+|++.+|++++||+.... ......||+|++.+||++|||++
T Consensus 102 ~~~~C~~Cg~~gH~~~~C~~~~~~-------~~~~~~C~~Cg~~gH~~~dCp~~ 148 (148)
T PTZ00368 102 ARRACYNCGGEGHISRDCPNAGKR-------PGGDKTCYNCGQTGHLSRDCPDK 148 (148)
T ss_pred cchhhcccCcCCcchhcCCCcccc-------CCCCCccccCCCcCcccccCCCC
Confidence 445799999999999999875211 11357899999999999999985
No 16
>COG5082 AIR1 Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]
Probab=98.66 E-value=1.4e-08 Score=79.46 Aligned_cols=54 Identities=39% Similarity=0.861 Sum_probs=36.0
Q ss_pred CCCCCccccCcCCeecccCCCCCC---CCCCCCCC-CCCCccccccCCCCccCCCC-CC
Q 030905 115 AGSGACFNCGRTGHIARECYSRGR---GGGRGYGG-GRGGGGCYNCGEEGHFARDC-PN 168 (169)
Q Consensus 115 ~~~~~C~~Cg~~GH~a~~C~~~~~---~~~~~~~g-~~~~~~C~~Cg~~GH~ardC-p~ 168 (169)
.....||+|++.||.++|||...- .--+++.. -...+.||+|++.||+++|| |+
T Consensus 58 ~~~~~C~nCg~~GH~~~DCP~~iC~~C~~~~H~s~~C~~~~~C~~Cg~~GH~~~dC~P~ 116 (190)
T COG5082 58 EENPVCFNCGQNGHLRRDCPHSICYNCSWDGHRSNHCPKPKKCYNCGETGHLSRDCNPS 116 (190)
T ss_pred ccccccchhcccCcccccCChhHhhhcCCCCcccccCCcccccccccccCccccccCcc
Confidence 456689999999999999991000 00001111 11247899999999999999 54
No 17
>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=98.63 E-value=1.6e-08 Score=50.18 Aligned_cols=17 Identities=71% Similarity=1.679 Sum_probs=14.3
Q ss_pred cccccCCCCccCCCCCC
Q 030905 152 GCYNCGEEGHFARDCPN 168 (169)
Q Consensus 152 ~C~~Cg~~GH~ardCp~ 168 (169)
.||+|+++||+++|||+
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 58888888888888885
No 18
>PTZ00368 universal minicircle sequence binding protein (UMSBP); Provisional
Probab=98.55 E-value=7.8e-08 Score=72.64 Aligned_cols=44 Identities=52% Similarity=1.312 Sum_probs=30.9
Q ss_pred CCCccccCcCCeecccCCCCCCCCCCCCCCCCCCccccccCCCCccCCCCCC
Q 030905 117 SGACFNCGRTGHIARECYSRGRGGGRGYGGGRGGGGCYNCGEEGHFARDCPN 168 (169)
Q Consensus 117 ~~~C~~Cg~~GH~a~~C~~~~~~~~~~~~g~~~~~~C~~Cg~~GH~ardCp~ 168 (169)
...||+|++.+|++++||...... ....||+|++.+|++++||+
T Consensus 52 ~~~C~~Cg~~GH~~~~Cp~~~~~~--------~~~~C~~Cg~~GH~~~~C~~ 95 (148)
T PTZ00368 52 ERSCYNCGKTGHLSRECPEAPPGS--------GPRSCYNCGQTGHISRECPN 95 (148)
T ss_pred CcccCCCCCcCcCcccCCCcccCC--------CCcccCcCCCCCcccccCCC
Confidence 345777777777777776643211 24579999999999999986
No 19
>COG5082 AIR1 Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]
Probab=98.29 E-value=3.7e-07 Score=71.44 Aligned_cols=41 Identities=39% Similarity=1.109 Sum_probs=29.5
Q ss_pred CCCccccCcCCeecccC-CCCCCCCCCCCCCCCCCccccccCCCCccCCCCCC
Q 030905 117 SGACFNCGRTGHIAREC-YSRGRGGGRGYGGGRGGGGCYNCGEEGHFARDCPN 168 (169)
Q Consensus 117 ~~~C~~Cg~~GH~a~~C-~~~~~~~~~~~~g~~~~~~C~~Cg~~GH~ardCp~ 168 (169)
...||+|++.||++++| |.... .+.||.|....|.+++||+
T Consensus 97 ~~~C~~Cg~~GH~~~dC~P~~~~-----------~~~C~~C~s~~H~s~~Cp~ 138 (190)
T COG5082 97 PKKCYNCGETGHLSRDCNPSKDQ-----------QKSCFDCNSTRHSSEDCPS 138 (190)
T ss_pred ccccccccccCccccccCccccc-----------CcceeccCCCccccccCcc
Confidence 36899999999999999 55432 3456666666666666664
No 20
>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=98.21 E-value=7e-07 Score=44.20 Aligned_cols=18 Identities=61% Similarity=1.376 Sum_probs=16.5
Q ss_pred CCccccCcCCeecccCCC
Q 030905 118 GACFNCGRTGHIARECYS 135 (169)
Q Consensus 118 ~~C~~Cg~~GH~a~~C~~ 135 (169)
+.||+|++.||++++||+
T Consensus 1 ~~C~~C~~~GH~~~~Cp~ 18 (18)
T PF00098_consen 1 RKCFNCGEPGHIARDCPK 18 (18)
T ss_dssp SBCTTTSCSSSCGCTSSS
T ss_pred CcCcCCCCcCcccccCcc
Confidence 379999999999999985
No 21
>KOG4400 consensus E3 ubiquitin ligase interacting with arginine methyltransferase [Posttranslational modification, protein turnover, chaperones]
Probab=98.16 E-value=1.1e-06 Score=72.21 Aligned_cols=40 Identities=45% Similarity=1.217 Sum_probs=35.5
Q ss_pred CCccccCcCCeecccCCCCCCCCCCCCCCCCCCccccccCCCCccCCCCCCC
Q 030905 118 GACFNCGRTGHIARECYSRGRGGGRGYGGGRGGGGCYNCGEEGHFARDCPNY 169 (169)
Q Consensus 118 ~~C~~Cg~~GH~a~~C~~~~~~~~~~~~g~~~~~~C~~Cg~~GH~ardCp~~ 169 (169)
..||+|++.||++.+||.+. ...||.|++.+|+++|||++
T Consensus 144 ~~Cy~Cg~~GH~s~~C~~~~------------~~~c~~c~~~~h~~~~C~~~ 183 (261)
T KOG4400|consen 144 AKCYSCGEQGHISDDCPENK------------GGTCFRCGKVGHGSRDCPSK 183 (261)
T ss_pred CccCCCCcCCcchhhCCCCC------------CCccccCCCcceecccCCcc
Confidence 67999999999999999751 56799999999999999974
No 22
>KOG4400 consensus E3 ubiquitin ligase interacting with arginine methyltransferase [Posttranslational modification, protein turnover, chaperones]
Probab=98.07 E-value=2.8e-06 Score=69.85 Aligned_cols=53 Identities=47% Similarity=1.105 Sum_probs=39.1
Q ss_pred CCCCccccCcCCeecccCCCCCCCCC-----------CCCC--------CCCCCccccccCCCCccCCCCCCC
Q 030905 116 GSGACFNCGRTGHIARECYSRGRGGG-----------RGYG--------GGRGGGGCYNCGEEGHFARDCPNY 169 (169)
Q Consensus 116 ~~~~C~~Cg~~GH~a~~C~~~~~~~~-----------~~~~--------g~~~~~~C~~Cg~~GH~ardCp~~ 169 (169)
....||+|++.||++++|+....... +... .... ..||+|++.|||+++||++
T Consensus 91 ~~~~c~~C~~~gH~~~~c~~~~~~~~~~~~~~~c~~~gh~~~~~~~~~~~~~~-~~Cy~Cg~~GH~s~~C~~~ 162 (261)
T KOG4400|consen 91 IAAACFNCGEGGHIERDCPEAGKEGSSETSCYSCGKTGHRGCPDADPVDGPKP-AKCYSCGEQGHISDDCPEN 162 (261)
T ss_pred cchhhhhCCCCccchhhCCcccCcccccceeeccCCCccccCcccccccCCCC-CccCCCCcCCcchhhCCCC
Confidence 46689999999999999998765330 0001 1112 6699999999999999953
No 23
>PF14444 S1-like: S1-like
Probab=97.81 E-value=7.6e-05 Score=47.69 Aligned_cols=53 Identities=23% Similarity=0.329 Sum_probs=42.9
Q ss_pred ccceEEEEeeCCCCeeEEecCCCCccEEEEeeccccCCcccCCCCCEEEEEEeeCCC--CceeEE
Q 030905 6 RSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVGED--GRTKAV 68 (169)
Q Consensus 6 ~~~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~~~~~~l~~G~~V~F~~~~~~k--Gr~~A~ 68 (169)
.++|.|+.+. ..||||. +||||+.+.+... .|++||+|..+...++. .+|.|.
T Consensus 3 ~~~GvVTkl~--~~yG~ID-----e~vFF~~~vv~G~---~P~vGdrV~v~A~~n~~~~~kW~A~ 57 (58)
T PF14444_consen 3 VFTGVVTKLC--DDYGFID-----EDVFFQTDVVKGN---VPKVGDRVLVEAIYNPNMPFKWNAT 57 (58)
T ss_pred eEEEEEEEEe--CCcceEc-----ccEEEEcccEecC---CCccCCEEEEEEEeCCCCCccceee
Confidence 4689999997 5899997 7899999998864 57999999999987753 245554
No 24
>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=97.75 E-value=9.5e-05 Score=47.31 Aligned_cols=40 Identities=35% Similarity=0.788 Sum_probs=30.8
Q ss_pred CCCeeEEecCCCCccEEEEeeccccCCcccCCCCCEEEEEEeeCC
Q 030905 17 QKGFGFIAPEDGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVGE 61 (169)
Q Consensus 17 ~kGfGFI~~~~~~~dvF~H~s~i~~~~~~~l~~G~~V~F~~~~~~ 61 (169)
.+||||+.+++..+|||+...++... ..||.|...+....
T Consensus 7 ~~GfGFv~~~~~~~DifIp~~~l~~A-----~~gD~V~v~i~~~~ 46 (58)
T PF08206_consen 7 PKGFGFVIPDDGGEDIFIPPRNLNGA-----MDGDKVLVRITPPS 46 (58)
T ss_dssp SSS-EEEEECT-TEEEEE-HHHHTTS------TT-EEEEEEEESS
T ss_pred cCCCEEEEECCCCCCEEECHHHHCCC-----CCCCEEEEEEecCC
Confidence 79999999999889999999999754 69999999998843
No 25
>PF13696 zf-CCHC_2: Zinc knuckle
Probab=97.70 E-value=1.2e-05 Score=45.42 Aligned_cols=20 Identities=45% Similarity=1.160 Sum_probs=17.4
Q ss_pred CccccccCCCCccCCCCCCC
Q 030905 150 GGGCYNCGEEGHFARDCPNY 169 (169)
Q Consensus 150 ~~~C~~Cg~~GH~ardCp~~ 169 (169)
.-.|+.|++.|||.+|||.|
T Consensus 8 ~Y~C~~C~~~GH~i~dCP~~ 27 (32)
T PF13696_consen 8 GYVCHRCGQKGHWIQDCPTN 27 (32)
T ss_pred CCEeecCCCCCccHhHCCCC
Confidence 45799999999999999975
No 26
>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=97.03 E-value=0.0018 Score=44.08 Aligned_cols=66 Identities=24% Similarity=0.449 Sum_probs=41.7
Q ss_pred ceEEEEeeCCCCeeEEecC-----CCCccEEEEeeccccCCcccCCCCCEEEEEEeeCCCC-c-eeEEEEEcCCCccc
Q 030905 8 SGTVKWFSAQKGFGFIAPE-----DGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVGEDG-R-TKAVDVEAASRSRR 78 (169)
Q Consensus 8 ~G~Vk~~~~~kGfGFI~~~-----~~~~dvF~H~s~i~~~~~~~l~~G~~V~F~~~~~~kG-r-~~A~~V~~~~g~~~ 78 (169)
.|.+-- ..+|||||..+ .+.+||||..+.|+..+ |+.|+.|+=.+.....+ | +..+.|..+++.++
T Consensus 4 ~GvLei--~~dGyGFLR~~~~~y~~~~~DvYVs~~qIrrf~---LR~GD~V~G~vr~p~~~ek~~aL~~V~~VNg~~p 76 (78)
T PF07497_consen 4 EGVLEI--LPDGYGFLRSPDNNYLPSPDDVYVSPSQIRRFG---LRTGDLVEGQVRPPREGEKYFALLRVESVNGRPP 76 (78)
T ss_dssp EEEEEE---TTS-EEEE-GGGTTS-STTSEEE-CCCCCCTT-----TTEEEEEEEE--STTSSSEEECEECEETTECT
T ss_pred EEEEEE--CCCCcEEeECCCcCCCCCCCCEEECHHHHHHcC---CCCCCEEEEEEeCCCCCCcceeeEEEEeECCcCC
Confidence 455542 34799999987 35689999999999864 88999999888876444 2 34566777776543
No 27
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]
Probab=96.72 E-value=0.0011 Score=58.74 Aligned_cols=45 Identities=38% Similarity=0.705 Sum_probs=36.7
Q ss_pred CCCCccccCcCCeecccCCCCCCCCCCCCCCCCCCccccccCCCCccCCCCCCC
Q 030905 116 GSGACFNCGRTGHIARECYSRGRGGGRGYGGGRGGGGCYNCGEEGHFARDCPNY 169 (169)
Q Consensus 116 ~~~~C~~Cg~~GH~a~~C~~~~~~~~~~~~g~~~~~~C~~Cg~~GH~ardCp~~ 169 (169)
....|.+|+..+|...+||..-..- ...|+.|+..+|+++||+.+
T Consensus 260 d~~~c~~cg~~~H~q~~cp~r~~~~---------~n~c~~cg~~gH~~~dc~~~ 304 (554)
T KOG0119|consen 260 DNRACRNCGSTGHKQYDCPGRIPNT---------TNVCKICGPLGHISIDCKVN 304 (554)
T ss_pred ccccccccCCCccccccCCcccccc---------cccccccCCcccccccCCCc
Confidence 4468999999999999999862211 23799999999999999864
No 28
>smart00343 ZnF_C2HC zinc finger.
Probab=96.59 E-value=0.00095 Score=35.66 Aligned_cols=17 Identities=76% Similarity=1.765 Sum_probs=14.0
Q ss_pred cccccCCCCccCCCCCC
Q 030905 152 GCYNCGEEGHFARDCPN 168 (169)
Q Consensus 152 ~C~~Cg~~GH~ardCp~ 168 (169)
.|++|++.+|++++||+
T Consensus 1 ~C~~CG~~GH~~~~C~~ 17 (26)
T smart00343 1 KCYNCGKEGHIARDCPK 17 (26)
T ss_pred CCccCCCCCcchhhCCc
Confidence 38888889998888873
No 29
>PF13917 zf-CCHC_3: Zinc knuckle
Probab=96.44 E-value=0.0016 Score=39.14 Aligned_cols=18 Identities=39% Similarity=1.167 Sum_probs=15.1
Q ss_pred CccccccCCCCccCCCCC
Q 030905 150 GGGCYNCGEEGHFARDCP 167 (169)
Q Consensus 150 ~~~C~~Cg~~GH~ardCp 167 (169)
...|.+|++.|||+.+||
T Consensus 4 ~~~CqkC~~~GH~tyeC~ 21 (42)
T PF13917_consen 4 RVRCQKCGQKGHWTYECP 21 (42)
T ss_pred CCcCcccCCCCcchhhCC
Confidence 466888888888888888
No 30
>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=96.29 E-value=0.011 Score=39.13 Aligned_cols=41 Identities=29% Similarity=0.558 Sum_probs=34.2
Q ss_pred CCeeEEecC-----CCCccEEEEeeccccCCcccCCCCCEEEEEEeeCC
Q 030905 18 KGFGFIAPE-----DGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVGE 61 (169)
Q Consensus 18 kGfGFI~~~-----~~~~dvF~H~s~i~~~~~~~l~~G~~V~F~~~~~~ 61 (169)
.|||||... .+.+||||..+.|+..+ |+.|+.|+=.+....
T Consensus 10 ~g~GFLR~~~~~y~~~~~DvyVs~~~Irr~~---LR~GD~V~G~vr~p~ 55 (68)
T cd04459 10 DGFGFLRSSGYNYLPGPDDIYVSPSQIRRFN---LRTGDTVVGQIRPPK 55 (68)
T ss_pred CCceEEecCCcCCCCCCCCEEECHHHHHHhC---CCCCCEEEEEEeCCC
Confidence 499999976 35689999999999864 899999998877643
No 31
>PF14787 zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB: 1CL4_A 1DSV_A.
Probab=96.24 E-value=0.0023 Score=36.91 Aligned_cols=18 Identities=39% Similarity=0.929 Sum_probs=10.9
Q ss_pred ccccccCCCCccCCCCCC
Q 030905 151 GGCYNCGEEGHFARDCPN 168 (169)
Q Consensus 151 ~~C~~Cg~~GH~ardCp~ 168 (169)
..|++|++..|||+||-+
T Consensus 3 ~~CprC~kg~Hwa~~C~s 20 (36)
T PF14787_consen 3 GLCPRCGKGFHWASECRS 20 (36)
T ss_dssp -C-TTTSSSCS-TTT---
T ss_pred ccCcccCCCcchhhhhhh
Confidence 469999999999999954
No 32
>PF13509 S1_2: S1 domain; PDB: 3GO5_A.
Probab=96.03 E-value=0.026 Score=36.22 Aligned_cols=55 Identities=22% Similarity=0.384 Sum_probs=34.7
Q ss_pred cceEEEEeeCCCCeeEEecCCCCccEEEEeeccccCCcccCCCCCEEEEEEeeCCCCceeEE
Q 030905 7 SSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVGEDGRTKAV 68 (169)
Q Consensus 7 ~~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~~~~~~l~~G~~V~F~~~~~~kGr~~A~ 68 (169)
.+-+|+..+ .+|++...+..++||+|.+.+.. .+++||.|+.-+-.+.++++.|+
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 455677776 46777666666899999999974 48999999999999999988875
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=95.96 E-value=0.015 Score=48.72 Aligned_cols=22 Identities=32% Similarity=0.951 Sum_probs=19.0
Q ss_pred CCCccccCcCCeecccCCCCCC
Q 030905 117 SGACFNCGRTGHIARECYSRGR 138 (169)
Q Consensus 117 ~~~C~~Cg~~GH~a~~C~~~~~ 138 (169)
...||.|++.|||+++||....
T Consensus 160 q~~cyrcGkeghwskEcP~~~~ 181 (346)
T KOG0109|consen 160 QSGCYRCGKEGHWSKECPVDRT 181 (346)
T ss_pred HHHheeccccccccccCCccCC
Confidence 3479999999999999998665
No 34
>KOG0109 consensus RNA-binding protein LARK, contains RRM and retroviral-type Zn-finger domains [RNA processing and modification; General function prediction only]
Probab=95.62 E-value=0.0044 Score=51.79 Aligned_cols=21 Identities=33% Similarity=0.472 Sum_probs=18.3
Q ss_pred cceEEEEeeCCCCeeEEecCC
Q 030905 7 SSGTVKWFSAQKGFGFIAPED 27 (169)
Q Consensus 7 ~~G~Vk~~~~~kGfGFI~~~~ 27 (169)
..|||..-|..|.|||+..++
T Consensus 25 ~ygkVlECDIvKNYgFVHiEd 45 (346)
T KOG0109|consen 25 QYGKVLECDIVKNYGFVHIED 45 (346)
T ss_pred hhCceEeeeeecccceEEeec
Confidence 468999999999999988765
No 35
>PF13696 zf-CCHC_2: Zinc knuckle
Probab=95.52 E-value=0.0063 Score=34.35 Aligned_cols=20 Identities=30% Similarity=0.871 Sum_probs=17.8
Q ss_pred CCCccccCcCCeecccCCCC
Q 030905 117 SGACFNCGRTGHIARECYSR 136 (169)
Q Consensus 117 ~~~C~~Cg~~GH~a~~C~~~ 136 (169)
.-.|+.|++.||+.++||..
T Consensus 8 ~Y~C~~C~~~GH~i~dCP~~ 27 (32)
T PF13696_consen 8 GYVCHRCGQKGHWIQDCPTN 27 (32)
T ss_pred CCEeecCCCCCccHhHCCCC
Confidence 34799999999999999984
No 36
>PF13917 zf-CCHC_3: Zinc knuckle
Probab=95.45 E-value=0.0078 Score=36.11 Aligned_cols=20 Identities=35% Similarity=0.805 Sum_probs=18.1
Q ss_pred CCCCccccCcCCeecccCCC
Q 030905 116 GSGACFNCGRTGHIARECYS 135 (169)
Q Consensus 116 ~~~~C~~Cg~~GH~a~~C~~ 135 (169)
....|.+|++.||+..+|++
T Consensus 3 ~~~~CqkC~~~GH~tyeC~~ 22 (42)
T PF13917_consen 3 ARVRCQKCGQKGHWTYECPN 22 (42)
T ss_pred CCCcCcccCCCCcchhhCCC
Confidence 56689999999999999994
No 37
>PRK11642 exoribonuclease R; Provisional
Probab=94.80 E-value=0.086 Score=50.10 Aligned_cols=62 Identities=26% Similarity=0.334 Sum_probs=45.8
Q ss_pred ccceEEEEeeCCCCeeEEecCCCCccEEEEeeccccCCcccCCCCCEEEEEEee-CCCCceeEEEEEcCC
Q 030905 6 RSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDV-GEDGRTKAVDVEAAS 74 (169)
Q Consensus 6 ~~~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~~~~~~l~~G~~V~F~~~~-~~kGr~~A~~V~~~~ 74 (169)
.+.|+|.. ..+||||+.+++..+|||+.-..+.. .-.||+|...+.. +.++++.|.=|.++.
T Consensus 84 ~~~G~v~~--~~~GfgFv~~e~~~~difI~~~~l~~-----A~~GD~V~v~i~~~~~~~r~eg~Vv~Ile 146 (813)
T PRK11642 84 LLKGTVIG--HRDGYGFLRVEGRKDDLYLSSEQMKT-----CIHGDQVLAQPLGADRKGRREARIVRVLV 146 (813)
T ss_pred eEEEEEEE--CCCccEEEEECCCCCCEEEChHHHcc-----CCCCCEEEEEEccCCCCCCcEEEEEEEEe
Confidence 46788884 46999999998766899998887754 3689999988765 234556666555554
No 38
>smart00343 ZnF_C2HC zinc finger.
Probab=94.74 E-value=0.014 Score=31.05 Aligned_cols=18 Identities=56% Similarity=1.392 Sum_probs=16.0
Q ss_pred CccccCcCCeecccCCCC
Q 030905 119 ACFNCGRTGHIARECYSR 136 (169)
Q Consensus 119 ~C~~Cg~~GH~a~~C~~~ 136 (169)
.|++|+..+|++++||..
T Consensus 1 ~C~~CG~~GH~~~~C~~~ 18 (26)
T smart00343 1 KCYNCGKEGHIARDCPKX 18 (26)
T ss_pred CCccCCCCCcchhhCCcc
Confidence 499999999999999843
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=94.74 E-value=0.12 Score=33.63 Aligned_cols=54 Identities=20% Similarity=0.212 Sum_probs=43.3
Q ss_pred ccccceEEEEeeCCCCeeEEecCCCCccEEEEeeccccC----CcccCCCCCEEEEEEeeC
Q 030905 4 VQRSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSE----GFRTLSEGQTVEFSVDVG 60 (169)
Q Consensus 4 ~~~~~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~~----~~~~l~~G~~V~F~~~~~ 60 (169)
.+.+.|+|+..++ ||++..-..+-+.|+|+++|... ....+.+||.|.+.+..-
T Consensus 5 G~iv~g~V~~v~~---~g~~V~l~~~~~g~ip~~~l~~~~~~~~~~~~~~G~~v~v~v~~v 62 (74)
T PF00575_consen 5 GDIVEGKVTSVED---FGVFVDLGNGIEGFIPISELSDDRIDDPSEVYKIGQTVRVKVIKV 62 (74)
T ss_dssp TSEEEEEEEEEET---TEEEEEESTSSEEEEEGGGSSSSEESSSHGTCETTCEEEEEEEEE
T ss_pred CCEEEEEEEEEEC---CEEEEEECCcEEEEEEeehhcCccccccccccCCCCEEEEEEEEE
Confidence 4678999999986 66666655668999999999863 346789999999988764
No 40
>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=94.33 E-value=0.15 Score=47.32 Aligned_cols=63 Identities=30% Similarity=0.450 Sum_probs=46.4
Q ss_pred cccceEEEEeeCCCCeeEEecCC-CCccEEEEeeccccCCcccCCCCCEEEEEEee-CCCCceeEEEEEcCC
Q 030905 5 QRSSGTVKWFSAQKGFGFIAPED-GGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDV-GEDGRTKAVDVEAAS 74 (169)
Q Consensus 5 ~~~~G~Vk~~~~~kGfGFI~~~~-~~~dvF~H~s~i~~~~~~~l~~G~~V~F~~~~-~~kGr~~A~~V~~~~ 74 (169)
..++|+|+.= .+||||+.+++ ..+|||+.-..+.. .-.||.|...+.. ..++++.|.=|.++.
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 3578999963 69999999986 35799999887754 4689999998754 345555666555554
No 41
>PRK08582 hypothetical protein; Provisional
Probab=94.22 E-value=0.51 Score=35.30 Aligned_cols=69 Identities=22% Similarity=0.304 Sum_probs=48.9
Q ss_pred ccccceEEEEeeCCCCeeEEecCCCCccEEEEeeccccCCc----ccCCCCCEEEEEEeeC-CCCceeEEEEEcCCCc
Q 030905 4 VQRSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGF----RTLSEGQTVEFSVDVG-EDGRTKAVDVEAASRS 76 (169)
Q Consensus 4 ~~~~~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~~~~----~~l~~G~~V~F~~~~~-~kGr~~A~~V~~~~g~ 76 (169)
...+.|+|+... .||++..-+...+-|+|++.|...-+ ..+.+||.|+..|... .+++ ..+.+..+...
T Consensus 6 G~iv~G~V~~I~---~fG~fV~L~~~~~GlVhiSels~~~v~~~~~~l~vGD~VkvkV~~id~~gk-I~LSlk~~~~~ 79 (139)
T PRK08582 6 GSKLQGKVTGIT---NFGAFVELPEGKTGLVHISEVADNYVKDINDHLKVGDEVEVKVLNVEDDGK-IGLSIKKAKDR 79 (139)
T ss_pred CCEEEEEEEEEE---CCeEEEEECCCCEEEEEeeccCcccccccccccCCCCEEEEEEEEECCCCc-EEEEEEecccC
Confidence 457899999865 47776665555899999999975422 4588999999887764 3564 55666655443
No 42
>PF15288 zf-CCHC_6: Zinc knuckle
Probab=94.02 E-value=0.031 Score=33.12 Aligned_cols=16 Identities=50% Similarity=1.277 Sum_probs=8.0
Q ss_pred cccccCCCCccC--CCCC
Q 030905 152 GCYNCGEEGHFA--RDCP 167 (169)
Q Consensus 152 ~C~~Cg~~GH~a--rdCp 167 (169)
+|.+||..||++ +.||
T Consensus 3 kC~~CG~~GH~~t~k~CP 20 (40)
T PF15288_consen 3 KCKNCGAFGHMRTNKRCP 20 (40)
T ss_pred cccccccccccccCccCC
Confidence 355555555544 3444
No 43
>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=93.55 E-value=0.68 Score=31.77 Aligned_cols=56 Identities=23% Similarity=0.191 Sum_probs=39.6
Q ss_pred ccccceEEEEeeCCCCeeEEecCCCCccEEEEeecccc-------CCcccCCCCCEEEEEEeeC
Q 030905 4 VQRSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKS-------EGFRTLSEGQTVEFSVDVG 60 (169)
Q Consensus 4 ~~~~~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~-------~~~~~l~~G~~V~F~~~~~ 60 (169)
...+.|+|+...+.-.==||...+ +.+-|+|++++.. .--..|++||.|...+...
T Consensus 8 G~iy~g~V~~i~~~~~GaFV~l~~-g~~Gllh~seis~~~~~~v~~~~~~~~~Gd~v~VqV~~~ 70 (88)
T cd04453 8 GNIYLGRVKKIVPGLQAAFVDIGL-GKNGFLHLSDILPAYFKKHKKIAKLLKEGQEILVQVVKE 70 (88)
T ss_pred CCEEEEEEEEeccCCcEEEEEeCC-CCEEEEEhHHcCchhccccCCHHHcCCCCCEEEEEEEEe
Confidence 457899999986432233555554 4799999999954 1124589999999998864
No 44
>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=93.46 E-value=0.43 Score=30.59 Aligned_cols=55 Identities=16% Similarity=0.140 Sum_probs=40.2
Q ss_pred cccceEEEEeeCCCCeeEEecCCCCccEEEEeeccccCC----cccCCCCCEEEEEEeeCCC
Q 030905 5 QRSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEG----FRTLSEGQTVEFSVDVGED 62 (169)
Q Consensus 5 ~~~~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~~~----~~~l~~G~~V~F~~~~~~k 62 (169)
+.+.|+|+...+ ||.+..-...-+-|+|+++|.... ...+++||.|++.+..-..
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 357899999864 666555444479999999997532 1348899999999887543
No 45
>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=93.37 E-value=0.63 Score=30.48 Aligned_cols=60 Identities=17% Similarity=0.142 Sum_probs=42.9
Q ss_pred cccccceEEEEeeCCCCeeEEecCCCCccEEEEeeccccCCc----ccCCCCCEEEEEEeeCCCCc
Q 030905 3 EVQRSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGF----RTLSEGQTVEFSVDVGEDGR 64 (169)
Q Consensus 3 ~~~~~~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~~~~----~~l~~G~~V~F~~~~~~kGr 64 (169)
..+.+.|+|+...+. ||.+..-..+.+-|+|+|++...-. ..+++||.|...+..-.+++
T Consensus 3 ~G~iv~G~V~~i~~~--~g~~v~l~~~~~Glvhis~~s~~~~~~~~~~~~~Gd~v~~kV~~~~~~~ 66 (72)
T cd05704 3 EGAVTLGMVTKVIPH--SGLTVQLPFGKTGLVSIFHLSDSYTENPLEGFKPGKIVRCCILSKKDGK 66 (72)
T ss_pred CCCEEEEEEEEeeCC--cEEEEECCCCCEEEEEHHHhcCcccCCHHHhCCCCCEEEEEEEEecCCE
Confidence 356789999997543 5555555455799999999976432 33688999998887765554
No 46
>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=93.08 E-value=0.039 Score=46.45 Aligned_cols=20 Identities=45% Similarity=1.285 Sum_probs=17.7
Q ss_pred CccccccCCCCccCCCCCCC
Q 030905 150 GGGCYNCGEEGHFARDCPNY 169 (169)
Q Consensus 150 ~~~C~~Cg~~GH~ardCp~~ 169 (169)
+-.||+||+.|||..+||-|
T Consensus 176 gY~CyRCGqkgHwIqnCpTN 195 (427)
T COG5222 176 GYVCYRCGQKGHWIQNCPTN 195 (427)
T ss_pred ceeEEecCCCCchhhcCCCC
Confidence 45699999999999999865
No 47
>cd00164 S1_like S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains are members of the Oligonucleotide/oligosaccharide Binding (OB) fold.
Probab=93.04 E-value=0.51 Score=28.85 Aligned_cols=51 Identities=25% Similarity=0.361 Sum_probs=37.1
Q ss_pred cceEEEEeeCCCCee-EEecCCCCccEEEEeeccccCC----cccCCCCCEEEEEEeeCC
Q 030905 7 SSGTVKWFSAQKGFG-FIAPEDGGEDLFVHQTSIKSEG----FRTLSEGQTVEFSVDVGE 61 (169)
Q Consensus 7 ~~G~Vk~~~~~kGfG-FI~~~~~~~dvF~H~s~i~~~~----~~~l~~G~~V~F~~~~~~ 61 (169)
+.|+|+..+ .+| ||..+ ...+.|+|.+.+.... ...+++||.|.+.+..-.
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 368899997 344 45544 4479999999997531 245899999999987643
No 48
>PF14392 zf-CCHC_4: Zinc knuckle
Probab=92.79 E-value=0.036 Score=34.08 Aligned_cols=17 Identities=41% Similarity=1.202 Sum_probs=10.0
Q ss_pred ccccccCCCCccCCCCC
Q 030905 151 GGCYNCGEEGHFARDCP 167 (169)
Q Consensus 151 ~~C~~Cg~~GH~ardCp 167 (169)
..|+.|+..||.+++||
T Consensus 32 ~~C~~C~~~gH~~~~C~ 48 (49)
T PF14392_consen 32 RFCFHCGRIGHSDKECP 48 (49)
T ss_pred hhhcCCCCcCcCHhHcC
Confidence 34666666666666665
No 49
>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=92.78 E-value=0.41 Score=32.01 Aligned_cols=55 Identities=20% Similarity=0.189 Sum_probs=42.3
Q ss_pred ccccceEEEEeeCCCCeeEEecCCCCccEEEEeeccccCCc----ccCCCCCEEEEEEeeCC
Q 030905 4 VQRSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGF----RTLSEGQTVEFSVDVGE 61 (169)
Q Consensus 4 ~~~~~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~~~~----~~l~~G~~V~F~~~~~~ 61 (169)
.+.+.|+|+...+ ||++..-..+-+.|+|++++....+ ..+++||.|++.+..-.
T Consensus 15 G~i~~g~V~~v~~---~G~fv~l~~~~~g~v~~~el~~~~~~~~~~~~~~Gd~v~vkV~~id 73 (83)
T cd04461 15 GMVVHGYVRNITP---YGVFVEFLGGLTGLAPKSYISDEFVTDPSFGFKKGQSVTAKVTSVD 73 (83)
T ss_pred CCEEEEEEEEEee---ceEEEEcCCCCEEEEEHHHCCcccccCHHHhcCCCCEEEEEEEEEc
Confidence 4678899998864 8887775555899999999965532 34788999999987644
No 50
>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=92.54 E-value=0.48 Score=30.97 Aligned_cols=52 Identities=15% Similarity=0.102 Sum_probs=36.3
Q ss_pred ccc-eEEEEeeCCCCeeEEecCCCCccEEEEeeccccCC----cccCCCCCEEEEEEee
Q 030905 6 RSS-GTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEG----FRTLSEGQTVEFSVDV 59 (169)
Q Consensus 6 ~~~-G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~~~----~~~l~~G~~V~F~~~~ 59 (169)
.+. |+|+... ..||.+..-..+-+-|+|+|.|.... ...+++||.|++.+..
T Consensus 3 v~~~g~V~~v~--~~~G~~V~l~~gv~G~i~~s~l~~~~~~~~~~~~~vG~~v~~kV~~ 59 (71)
T cd05696 3 VVDSVKVTKVE--PDLGAVFELKDGLLGFVHISHLSDDKVPSDTGPFKAGTTHKARIIG 59 (71)
T ss_pred EeeeeEEEEEc--cCceEEEEeCCCCEEEEEHHHCCcchhcCcccccCCCCEEEEEEEE
Confidence 345 8999875 34666544433479999999996432 2458999999998764
No 51
>PRK05054 exoribonuclease II; Provisional
Probab=92.53 E-value=0.38 Score=44.64 Aligned_cols=61 Identities=25% Similarity=0.395 Sum_probs=43.2
Q ss_pred cccceEEEEeeCCCCeeEEecCCCCccEEEEeeccccCCcccCCCCCEEEEEEeeCCCCceeEEEEEcCC
Q 030905 5 QRSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVGEDGRTKAVDVEAAS 74 (169)
Q Consensus 5 ~~~~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~~~~~~l~~G~~V~F~~~~~~kGr~~A~~V~~~~ 74 (169)
..+.|+|+. ..+||||+.+++ .+|||++-..+... -.||.|...+... +++..|.=+..+.
T Consensus 20 ~~~~G~~~~--~~~gfgFv~~~~-~~difI~~~~l~~a-----~~GD~V~v~i~~~-~~r~~g~v~~il~ 80 (644)
T PRK05054 20 PRVEGVVKA--TEKGFGFLEVDA-QKSYFIPPPQMKKV-----MHGDRIIAVIHTE-KDREIAEPEELIE 80 (644)
T ss_pred CeEEEEEEE--CCCccEEEEECC-CCcEEEChHHHccC-----CCCCEEEEEEecC-CCCcEEEEEEEEe
Confidence 457788885 469999998855 46999999888653 5799999887643 3444554444433
No 52
>PRK07252 hypothetical protein; Provisional
Probab=92.34 E-value=1.6 Score=31.85 Aligned_cols=70 Identities=19% Similarity=0.276 Sum_probs=48.8
Q ss_pred CCcccccceEEEEeeCCCCeeEEecCCCCccEEEEeeccccCCc----ccCCCCCEEEEEEeeCC--CCceeEEEEEcCC
Q 030905 1 MAEVQRSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGF----RTLSEGQTVEFSVDVGE--DGRTKAVDVEAAS 74 (169)
Q Consensus 1 M~~~~~~~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~~~~----~~l~~G~~V~F~~~~~~--kGr~~A~~V~~~~ 74 (169)
|.....+.|+|+...+ ||++..-....+-|+|+++|...-+ ..+.+||.|+..+..-. +++ ..+.+..+.
T Consensus 1 ~kvG~iv~G~V~~V~~---~G~fVei~~~~~GllhiseLs~~~~~~~~~~~~vGD~V~VkI~~iD~~~~r-i~lSlk~~~ 76 (120)
T PRK07252 1 MKIGDKLKGTITGIKP---YGAFVALENGTTGLIHISEIKTGFIDNIHQLLKVGEEVLVQVVDFDEYTGK-ASLSLRTLE 76 (120)
T ss_pred CCCCCEEEEEEEEEeC---cEEEEEECCCCEEEEEHHHcCCccccChhhccCCCCEEEEEEEEEeCCCCE-EEEEEeecc
Confidence 3445678999999864 8877766555799999999975432 34789999999988743 443 334444443
No 53
>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=92.33 E-value=0.45 Score=44.10 Aligned_cols=61 Identities=25% Similarity=0.401 Sum_probs=43.5
Q ss_pred ccccceEEEEeeCCCCeeEEecCCCCccEEEEeeccccCCcccCCCCCEEEEEEeeCCCCceeEEEEEcC
Q 030905 4 VQRSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVGEDGRTKAVDVEAA 73 (169)
Q Consensus 4 ~~~~~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~~~~~~l~~G~~V~F~~~~~~kGr~~A~~V~~~ 73 (169)
...+.|+|+. ..+||||+.+++ .+|||+.-..+... -.||.|...+.... ++..|.=+..+
T Consensus 16 ~~~~~G~i~~--~~kGfgFv~~~~-~~difI~~~~l~~A-----~~GD~V~v~i~~~~-~r~~~~v~~iv 76 (639)
T TIGR02062 16 TPRVEGVVKA--TEKGFGFLEVDA-QKSYFIPPPQMKKV-----MHGDKIIAVIHSEK-ERESAEPEELI 76 (639)
T ss_pred CceEEEEEEE--CCCccEEEEECC-CCcEEEChHHHccC-----CCCCEEEEEEecCC-CCcEEEEEEEE
Confidence 3457799985 469999997665 46999999888653 57999998876543 44455444444
No 54
>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=92.30 E-value=0.63 Score=29.14 Aligned_cols=53 Identities=28% Similarity=0.349 Sum_probs=39.0
Q ss_pred cccceEEEEeeCCCCeeEEecCCCCccEEEEeeccccCCc----ccCCCCCEEEEEEeeC
Q 030905 5 QRSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGF----RTLSEGQTVEFSVDVG 60 (169)
Q Consensus 5 ~~~~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~~~~----~~l~~G~~V~F~~~~~ 60 (169)
..+.|+|+...+ ||++..-+...+.|+|++++..... ..+++||.|+..+..-
T Consensus 2 ~~~~g~V~~i~~---~g~~v~i~~~~~g~l~~~~l~~~~~~~~~~~~~~Gd~v~v~v~~~ 58 (69)
T cd05692 2 SVVEGTVTRLKP---FGAFVELGGGISGLVHISQIAHKRVKDVKDVLKEGDKVKVKVLSI 58 (69)
T ss_pred CEEEEEEEEEEe---eeEEEEECCCCEEEEEhHHcCCcccCCHHHccCCCCEEEEEEEEE
Confidence 357889998764 7776665555799999999975422 3478999999887553
No 55
>PRK12608 transcription termination factor Rho; Provisional
Probab=91.99 E-value=0.33 Score=42.30 Aligned_cols=70 Identities=21% Similarity=0.341 Sum_probs=49.0
Q ss_pred ccccceEEEEeeCCCCeeEEecC-----CCCccEEEEeeccccCCcccCCCCCEEEEEEeeCCCCceeEEEEEcCCCccc
Q 030905 4 VQRSSGTVKWFSAQKGFGFIAPE-----DGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVGEDGRTKAVDVEAASRSRR 78 (169)
Q Consensus 4 ~~~~~G~Vk~~~~~kGfGFI~~~-----~~~~dvF~H~s~i~~~~~~~l~~G~~V~F~~~~~~kGr~~A~~V~~~~g~~~ 78 (169)
.....|++--.. .||||+... .+.+||||..+.|+..+ |+.|+.|.-.... +-+...-..|.-+.+.|+
T Consensus 16 ~~~~~g~l~~~~--~g~gflr~~~~~~~~~~~d~yv~~~~i~~~~---l~~Gd~V~~~~r~-~~~~~~LgrV~~~~G~p~ 89 (380)
T PRK12608 16 TEEVLGVLEILG--DGFGFLRSARRNYLPSPDDVFVPPALIRRFN---LRTGDVVEGVARP-RERYRVLVRVDSVNGTDP 89 (380)
T ss_pred CCcceEEEEEcC--CCceEeecCccCCCCCCCCeeeCHHHHHHhC---CCCCCEEEeccCC-CCChhheEEEeccCCcCc
Confidence 345677777554 499999985 45689999999999864 8899999987665 333223345555555554
Q ss_pred c
Q 030905 79 F 79 (169)
Q Consensus 79 ~ 79 (169)
.
T Consensus 90 d 90 (380)
T PRK12608 90 E 90 (380)
T ss_pred h
Confidence 3
No 56
>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=91.91 E-value=0.72 Score=29.59 Aligned_cols=54 Identities=17% Similarity=0.148 Sum_probs=40.4
Q ss_pred cccceEEEEeeCCCCeeEEecCCCCccEEEEeeccccCCc----ccCCCCCEEEEEEeeCC
Q 030905 5 QRSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGF----RTLSEGQTVEFSVDVGE 61 (169)
Q Consensus 5 ~~~~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~~~~----~~l~~G~~V~F~~~~~~ 61 (169)
+.++|+|+... .||.+..-+.+-+-|+|++.+....+ ..+++||.|++.+..-+
T Consensus 2 ~~v~g~V~~v~---~~Gv~V~l~~~v~g~i~~~~l~~~~~~~~~~~~~~Gd~i~~~V~~id 59 (69)
T cd05697 2 QVVKGTIRKLR---PSGIFVKLSDHIKGLVPPMHLADVRLKHPEKKFKPGLKVKCRVLSVE 59 (69)
T ss_pred CEEEEEEEEEe---ccEEEEEecCCcEEEEEHHHCCCccccCHHHcCCCCCEEEEEEEEEE
Confidence 35789999986 36777665445899999999975422 35889999999987653
No 57
>smart00316 S1 Ribosomal protein S1-like RNA-binding domain.
Probab=91.77 E-value=0.48 Score=29.59 Aligned_cols=55 Identities=18% Similarity=0.210 Sum_probs=40.4
Q ss_pred ccccceEEEEeeCCCCeeEEecCCCCccEEEEeeccccCC----cccCCCCCEEEEEEeeCC
Q 030905 4 VQRSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEG----FRTLSEGQTVEFSVDVGE 61 (169)
Q Consensus 4 ~~~~~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~~~----~~~l~~G~~V~F~~~~~~ 61 (169)
...+.|+|+..+. +|++..-....+.|+|.+++.... ...+++||.|.+.+..-.
T Consensus 3 G~~v~g~V~~v~~---~g~~v~i~~~~~g~l~~~~~~~~~~~~~~~~~~~G~~v~~~V~~~~ 61 (72)
T smart00316 3 GDVVEGTVTEITP---FGAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVD 61 (72)
T ss_pred CCEEEEEEEEEEc---cEEEEEeCCCCEEEEEHHHCCccccCCHHHeecCCCEEEEEEEEEe
Confidence 3567899999976 455554443578999999997641 134899999999887653
No 58
>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=91.72 E-value=1.1 Score=29.01 Aligned_cols=56 Identities=9% Similarity=-0.146 Sum_probs=39.9
Q ss_pred cccccceEEEEeeCCCCeeEEecCCCCccEEEEeeccccCC----cccCCCCCEEEEEEeeCC
Q 030905 3 EVQRSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEG----FRTLSEGQTVEFSVDVGE 61 (169)
Q Consensus 3 ~~~~~~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~~~----~~~l~~G~~V~F~~~~~~ 61 (169)
..+.+.|+|+.... ||.+..-+.+-+-|+|+++|.... ...+++||.|+..+..-.
T Consensus 3 ~G~iv~g~V~~v~~---~gi~v~l~~~~~g~v~~s~l~~~~~~~~~~~~~~Gd~v~~~V~~~d 62 (73)
T cd05706 3 VGDILPGRVTKVND---RYVLVQLGNKVTGPSFITDALDDYSEALPYKFKKNDIVRACVLSVD 62 (73)
T ss_pred CCCEEEEEEEEEeC---CeEEEEeCCCcEEEEEhhhccCccccccccccCCCCEEEEEEEEEe
Confidence 34678999999753 555544444489999999997542 134789999999887643
No 59
>PF14392 zf-CCHC_4: Zinc knuckle
Probab=91.71 E-value=0.066 Score=32.89 Aligned_cols=20 Identities=45% Similarity=0.997 Sum_probs=17.2
Q ss_pred CCCCccccCcCCeecccCCC
Q 030905 116 GSGACFNCGRTGHIARECYS 135 (169)
Q Consensus 116 ~~~~C~~Cg~~GH~a~~C~~ 135 (169)
-+..|++|+..||...+||.
T Consensus 30 lp~~C~~C~~~gH~~~~C~k 49 (49)
T PF14392_consen 30 LPRFCFHCGRIGHSDKECPK 49 (49)
T ss_pred cChhhcCCCCcCcCHhHcCC
Confidence 34479999999999999984
No 60
>TIGR02063 RNase_R ribonuclease R. This family consists of an exoribonuclease, ribonuclease R, also called VacB. It is one of the eight exoribonucleases reported in E. coli and is broadly distributed throughout the bacteria. In E. coli, double mutants of this protein and polynucleotide phosphorylase are not viable. Scoring between trusted and noise cutoffs to the model are shorter, divergent forms from the Chlamydiae, and divergent forms from the Campylobacterales (including Helicobacter pylori) and Leptospira interrogans.
Probab=91.58 E-value=0.58 Score=43.81 Aligned_cols=62 Identities=26% Similarity=0.431 Sum_probs=44.0
Q ss_pred ccceEEEEeeCCCCeeEEecCC-CCccEEEEeeccccCCcccCCCCCEEEEEEeeCC--CCceeEEEEEcCC
Q 030905 6 RSSGTVKWFSAQKGFGFIAPED-GGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVGE--DGRTKAVDVEAAS 74 (169)
Q Consensus 6 ~~~G~Vk~~~~~kGfGFI~~~~-~~~dvF~H~s~i~~~~~~~l~~G~~V~F~~~~~~--kGr~~A~~V~~~~ 74 (169)
.+.|+|+. ..+||||+.+++ ..+|||+....+.. ...||.|...+.... ++++.|.=|.+++
T Consensus 68 ~~~G~i~~--~~~g~gFv~~~~~~~~di~I~~~~~~~-----a~~GD~Vlv~I~~~~~~~~~~eg~Vv~Il~ 132 (709)
T TIGR02063 68 LVKGTVIA--HRDGFGFLRPEDDDEDDIFIPPRQMNG-----AMHGDRVLVRITGKPDGGDRFEARVIKILE 132 (709)
T ss_pred eEEEEEEE--CCCccEEEEECCCCCCcEEEChHHhCc-----CCCCCEEEEEEecccCCCCCceEEEEEEEe
Confidence 46788875 478999999886 35799998776643 578999999986542 3445665445443
No 61
>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=91.56 E-value=1.3 Score=29.35 Aligned_cols=52 Identities=21% Similarity=0.165 Sum_probs=40.5
Q ss_pred ccccceEEEEeeCCCCeeEEecCC-CCccEEEEeeccccCCcccCCCCCEEEEEEeeC
Q 030905 4 VQRSSGTVKWFSAQKGFGFIAPED-GGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVG 60 (169)
Q Consensus 4 ~~~~~G~Vk~~~~~kGfGFI~~~~-~~~dvF~H~s~i~~~~~~~l~~G~~V~F~~~~~ 60 (169)
.+.++|+|+..- -||++..-. .+-+-|+|.+++... ..+.+||.|...+..-
T Consensus 5 G~~v~g~V~si~---d~G~~v~~g~~gv~Gfl~~~~~~~~--~~~~~Gq~v~~~V~~v 57 (74)
T cd05694 5 GMVLSGCVSSVE---DHGYILDIGIPGTTGFLPKKDAGNF--SKLKVGQLLLCVVEKV 57 (74)
T ss_pred CCEEEEEEEEEe---CCEEEEEeCCCCcEEEEEHHHCCcc--cccCCCCEEEEEEEEE
Confidence 467899999985 577766543 346899999999865 5689999999997643
No 62
>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=91.30 E-value=1.4 Score=28.31 Aligned_cols=54 Identities=22% Similarity=0.231 Sum_probs=38.8
Q ss_pred ccccceEEEEeeCCCCeeEEecCCCCccEEEEeeccccCCc-----ccCCCCCEEEEEEeeC
Q 030905 4 VQRSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGF-----RTLSEGQTVEFSVDVG 60 (169)
Q Consensus 4 ~~~~~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~~~~-----~~l~~G~~V~F~~~~~ 60 (169)
.+.+.|+|+...+ ||+...-+.+.+-|+|+++|..... ..++.||.|+..+..-
T Consensus 4 g~~~~g~V~~i~~---~G~fv~l~~~~~Gl~~~~~l~~~~~~~~~~~~~~~Gd~v~v~v~~i 62 (72)
T cd05689 4 GTRLFGKVTNLTD---YGCFVELEEGVEGLVHVSEMDWTNKNIHPSKVVSLGDEVEVMVLDI 62 (72)
T ss_pred CCEEEEEEEEEEe---eEEEEEcCCCCEEEEEEEeccCcccccCcccEeCCCCEEEEEEEEe
Confidence 4568899998754 8887665545899999999963211 2467888888877654
No 63
>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=91.20 E-value=0.92 Score=29.98 Aligned_cols=54 Identities=17% Similarity=-0.018 Sum_probs=39.5
Q ss_pred ccccceEEEEeeCCCCeeE-EecCCCCccEEEEeeccccCCc-------ccCCCCCEEEEEEeeCC
Q 030905 4 VQRSSGTVKWFSAQKGFGF-IAPEDGGEDLFVHQTSIKSEGF-------RTLSEGQTVEFSVDVGE 61 (169)
Q Consensus 4 ~~~~~G~Vk~~~~~kGfGF-I~~~~~~~dvF~H~s~i~~~~~-------~~l~~G~~V~F~~~~~~ 61 (169)
...+.|+|+... .||. +... .+-+-|+|+++|..... ..+++||.|++.+..-+
T Consensus 4 G~~V~g~V~~i~---~~G~fV~l~-~~v~G~v~~~~ls~~~~~~~~~~~~~~~~G~~v~~kVl~id 65 (74)
T cd05705 4 GQLLRGYVSSVT---KQGVFFRLS-SSIVGRVLFQNVTKYFVSDPSLYNKYLPEGKLLTAKVLSVN 65 (74)
T ss_pred CCEEEEEEEEEe---CCcEEEEeC-CCCEEEEEHHHccCccccChhhHhcccCCCCEEEEEEEEEE
Confidence 467899999985 4554 4544 35799999999876531 35699999999887643
No 64
>COG1158 Rho Transcription termination factor [Transcription]
Probab=91.18 E-value=0.35 Score=41.72 Aligned_cols=67 Identities=33% Similarity=0.541 Sum_probs=49.8
Q ss_pred ceEEEEeeCCCCeeEEecCC-----CCccEEEEeeccccCCcccCCCCCEEEEEEeeCCCC-ceeE-EEEEcCCCcccc
Q 030905 8 SGTVKWFSAQKGFGFIAPED-----GGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVGEDG-RTKA-VDVEAASRSRRF 79 (169)
Q Consensus 8 ~G~Vk~~~~~kGfGFI~~~~-----~~~dvF~H~s~i~~~~~~~l~~G~~V~F~~~~~~kG-r~~A-~~V~~~~g~~~~ 79 (169)
.|++--.. .||||+.+.+ +.+||||.-|.|.... |+.||.|+=.+.....| |+.| +.|..+++.++.
T Consensus 55 ~GvLeil~--dGfGFLR~~~~~yl~~~~DiYvSpSQIRrf~---LrtGD~v~G~vR~Pke~Ery~aLl~ve~vN~~~pe 128 (422)
T COG1158 55 DGVLEILP--DGFGFLRSADSSYLPGPDDIYVSPSQIRRFN---LRTGDTVEGKVRPPKEGERYFALLKVEAVNGDDPE 128 (422)
T ss_pred eeEEEecc--CCcceeecCccccCCCCCceEECHHHHhhcc---CccCCEEeeeecCCCcccceeeeEEEeecCCCCHH
Confidence 35555443 7999999865 4589999999999864 88999999998877665 3444 567777766643
No 65
>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=90.61 E-value=1.2 Score=27.93 Aligned_cols=53 Identities=25% Similarity=0.265 Sum_probs=40.1
Q ss_pred ccceEEEEeeCCCCeeEEecCCCCccEEEEeeccccCCc----ccCCCCCEEEEEEeeCC
Q 030905 6 RSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGF----RTLSEGQTVEFSVDVGE 61 (169)
Q Consensus 6 ~~~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~~~~----~~l~~G~~V~F~~~~~~ 61 (169)
.+.|+|....+ ||++..-....+-|+|++++...-+ ..++.||.|...+....
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 57889998875 8888775555899999999976432 24689999998877643
No 66
>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=90.48 E-value=1.5 Score=28.60 Aligned_cols=54 Identities=20% Similarity=0.201 Sum_probs=39.6
Q ss_pred ccccceEEEEeeCCCCeeEEecCCC-CccEEEEeeccccCCcc----cCCCCCEEEEEEeeC
Q 030905 4 VQRSSGTVKWFSAQKGFGFIAPEDG-GEDLFVHQTSIKSEGFR----TLSEGQTVEFSVDVG 60 (169)
Q Consensus 4 ~~~~~G~Vk~~~~~kGfGFI~~~~~-~~dvF~H~s~i~~~~~~----~l~~G~~V~F~~~~~ 60 (169)
...+.|+|+...+ ||++..-++ ..+-|+|++++...-+. .+++||.|...+..-
T Consensus 4 g~~~~g~V~~i~~---fG~fv~l~~~~~eGlvh~sel~~~~~~~~~~~~~~Gd~v~vkv~~v 62 (73)
T cd05686 4 YQIFKGEVASVTE---YGAFVKIPGCRKQGLVHKSHMSSCRVDDPSEVVDVGEKVWVKVIGR 62 (73)
T ss_pred CCEEEEEEEEEEe---eeEEEEECCCCeEEEEEchhhCCCcccCHhhEECCCCEEEEEEEEE
Confidence 4568899999864 887666533 35899999999765432 257899999887654
No 67
>PF15288 zf-CCHC_6: Zinc knuckle
Probab=90.40 E-value=0.13 Score=30.40 Aligned_cols=20 Identities=35% Similarity=0.740 Sum_probs=16.7
Q ss_pred CCccccCcCCeec--ccCCCCC
Q 030905 118 GACFNCGRTGHIA--RECYSRG 137 (169)
Q Consensus 118 ~~C~~Cg~~GH~a--~~C~~~~ 137 (169)
..|.+||.+||.+ +.||...
T Consensus 2 ~kC~~CG~~GH~~t~k~CP~~~ 23 (40)
T PF15288_consen 2 VKCKNCGAFGHMRTNKRCPMYC 23 (40)
T ss_pred ccccccccccccccCccCCCCC
Confidence 5799999999987 6788754
No 68
>PRK09376 rho transcription termination factor Rho; Provisional
Probab=89.89 E-value=0.87 Score=40.11 Aligned_cols=67 Identities=28% Similarity=0.541 Sum_probs=48.4
Q ss_pred cceEEEEeeCCCCeeEEecCC-----CCccEEEEeeccccCCcccCCCCCEEEEEEeeCCCC-c-eeEEEEEcCCCccc
Q 030905 7 SSGTVKWFSAQKGFGFIAPED-----GGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVGEDG-R-TKAVDVEAASRSRR 78 (169)
Q Consensus 7 ~~G~Vk~~~~~kGfGFI~~~~-----~~~dvF~H~s~i~~~~~~~l~~G~~V~F~~~~~~kG-r-~~A~~V~~~~g~~~ 78 (169)
..|++--.. .|||||.+.+ +.+||||-.+.|+..+ |+.|+.|+=.+.....+ | +.-+.|..+++.++
T Consensus 51 ~~g~le~~~--~g~gflr~~~~~y~~~~~d~yvs~~~ir~~~---lr~gd~v~g~~r~~~~~e~~~~l~~v~~vng~~~ 124 (416)
T PRK09376 51 GEGVLEILP--DGFGFLRSPDANYLPGPDDIYVSPSQIRRFN---LRTGDTVEGKIRPPKEGERYFALLKVETVNGEDP 124 (416)
T ss_pred EEEEEEEcC--CCCeEEeCCCcCCCCCCCCeeeCHHHHHhcC---CCCCCEEEEEeeCCCCCCCccceEEEeeeCCCCH
Confidence 556665443 3999999853 4589999999999864 88999999888865433 2 34567777776553
No 69
>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=89.72 E-value=0.73 Score=29.42 Aligned_cols=53 Identities=15% Similarity=0.171 Sum_probs=37.9
Q ss_pred cccceEEEEeeCCCCeeEEecCCCCccEEEEeeccccCCcc--cCCCCCEEEEEEeeCC
Q 030905 5 QRSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGFR--TLSEGQTVEFSVDVGE 61 (169)
Q Consensus 5 ~~~~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~~~~~--~l~~G~~V~F~~~~~~ 61 (169)
..++|+|+..++ +|++..-+ +-+.|+|.+.+...... ...+|+.+.+.+..-.
T Consensus 2 ~iv~g~V~~v~~---~G~~v~l~-g~~gfip~s~~~~~~~~~~~~~vG~~i~~~i~~vd 56 (67)
T cd04465 2 EIVEGKVTEKVK---GGLIVDIE-GVRAFLPASQVDLRPVEDLDEYVGKELKFKIIEID 56 (67)
T ss_pred CEEEEEEEEEEC---CeEEEEEC-CEEEEEEHHHCCCcccCChHHhCCCEEEEEEEEEe
Confidence 357899999964 66666653 57899999999754321 1247999999887643
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=88.99 E-value=1.6 Score=27.84 Aligned_cols=52 Identities=19% Similarity=0.153 Sum_probs=37.3
Q ss_pred ccceEEEEeeCCCCeeEEecCCCCccEEEEeeccccCCc----ccCCCCCEEEEEEeeC
Q 030905 6 RSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGF----RTLSEGQTVEFSVDVG 60 (169)
Q Consensus 6 ~~~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~~~~----~~l~~G~~V~F~~~~~ 60 (169)
.+.|+|+... .||.+..-...-+-|+|++.|..... ..+++||.|+..+..-
T Consensus 3 ~v~g~V~~v~---~~Gv~V~l~~~~~G~v~~s~l~~~~~~~~~~~~~~Gd~v~~~v~~~ 58 (68)
T cd05707 3 VVRGFVKNIA---NNGVFVTLGRGVDARVRVSELSDSYLKDWKKRFKVGQLVKGKIVSI 58 (68)
T ss_pred EEEEEEEEEE---CccEEEEeCCCCEEEEEHHHCCchhhcCHhhccCCCCEEEEEEEEE
Confidence 4789999985 35555444444799999999965422 3478999999987654
No 71
>PRK05807 hypothetical protein; Provisional
Probab=88.96 E-value=3.2 Score=30.87 Aligned_cols=66 Identities=21% Similarity=0.287 Sum_probs=46.5
Q ss_pred ccccceEEEEeeCCCCeeEEecCCCCccEEEEeeccccCCc----ccCCCCCEEEEEEeeC-CCCceeEEEEEcCC
Q 030905 4 VQRSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGF----RTLSEGQTVEFSVDVG-EDGRTKAVDVEAAS 74 (169)
Q Consensus 4 ~~~~~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~~~~----~~l~~G~~V~F~~~~~-~kGr~~A~~V~~~~ 74 (169)
...+.|+|+... .||++..-+ ..+-|+|++.|...-+ ..+++||.|+..+... .+++ ..+.+..+.
T Consensus 6 G~vv~G~Vt~i~---~~GafV~L~-~~~Glvhiseis~~~v~~~~~~~kvGd~V~VkV~~id~~gk-I~LSlk~~~ 76 (136)
T PRK05807 6 GSILEGTVVNIT---NFGAFVEVE-GKTGLVHISEVADTYVKDIREHLKEQDKVKVKVISIDDNGK-ISLSIKQAM 76 (136)
T ss_pred CCEEEEEEEEEE---CCeEEEEEC-CEEEEEEhhhcccccccCccccCCCCCEEEEEEEEECCCCc-EEEEEEecc
Confidence 567899999975 477766654 3689999999965322 4579999999887653 4564 555565543
No 72
>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=88.96 E-value=3.6 Score=26.99 Aligned_cols=55 Identities=25% Similarity=0.364 Sum_probs=39.6
Q ss_pred ccceEEEEeeCCCCeeEEecCC---CCccEEEEeeccccCCc-----ccCCCCCEEEEEEeeCCCC
Q 030905 6 RSSGTVKWFSAQKGFGFIAPED---GGEDLFVHQTSIKSEGF-----RTLSEGQTVEFSVDVGEDG 63 (169)
Q Consensus 6 ~~~G~Vk~~~~~kGfGFI~~~~---~~~dvF~H~s~i~~~~~-----~~l~~G~~V~F~~~~~~kG 63 (169)
.+.|+|+...+ ||+...-+ .+.+-|+|+++|...-+ ..++.||.|...+...+++
T Consensus 3 ~~~g~V~~v~~---~G~fv~l~~~~~~~~gll~~s~l~~~~~~~~~~~~~~~Gd~v~v~v~~vd~~ 65 (79)
T cd05684 3 IYKGKVTSIMD---FGCFVQLEGLKGRKEGLVHISQLSFEGRVANPSDVVKRGQKVKVKVISIQNG 65 (79)
T ss_pred EEEEEEEEEEe---eeEEEEEeCCCCCcEEEEEhHhccCCCCcCChhheeCCCCEEEEEEEEEeCC
Confidence 46788888864 67666544 24789999999975432 2468999999887765555
No 73
>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=88.91 E-value=2.8 Score=26.73 Aligned_cols=53 Identities=15% Similarity=0.208 Sum_probs=39.2
Q ss_pred ccceEEEEeeCCCCeeEEecCCCCccEEEEeeccccCCc----ccCCCCCEEEEEEeeCC
Q 030905 6 RSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGF----RTLSEGQTVEFSVDVGE 61 (169)
Q Consensus 6 ~~~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~~~~----~~l~~G~~V~F~~~~~~ 61 (169)
.+.|+|+... .+|++..-...-+-|+|++++....+ ..+++||.|++.+..-.
T Consensus 3 ~v~g~V~~v~---~~g~~v~l~~~~~g~i~~~~~~~~~~~~~~~~~~~Gd~v~~~v~~~d 59 (73)
T cd05691 3 IVTGKVTEVD---AKGATVKLGDGVEGFLRAAELSRDRVEDATERFKVGDEVEAKITNVD 59 (73)
T ss_pred EEEEEEEEEE---CCeEEEEeCCCCEEEEEHHHCCCccccCHHHccCCCCEEEEEEEEEe
Confidence 4789999985 46666654445789999999876432 34689999999987654
No 74
>PF14787 zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB: 1CL4_A 1DSV_A.
Probab=88.88 E-value=0.25 Score=28.51 Aligned_cols=21 Identities=43% Similarity=0.811 Sum_probs=13.3
Q ss_pred CCccccCcCCeecccCCCCCC
Q 030905 118 GACFNCGRTGHIARECYSRGR 138 (169)
Q Consensus 118 ~~C~~Cg~~GH~a~~C~~~~~ 138 (169)
..|++|+...|+|.+|.+..+
T Consensus 3 ~~CprC~kg~Hwa~~C~sk~d 23 (36)
T PF14787_consen 3 GLCPRCGKGFHWASECRSKTD 23 (36)
T ss_dssp -C-TTTSSSCS-TTT---TCC
T ss_pred ccCcccCCCcchhhhhhhhhc
Confidence 479999999999999987654
No 75
>PRK12678 transcription termination factor Rho; Provisional
Probab=87.84 E-value=1.2 Score=41.16 Aligned_cols=66 Identities=18% Similarity=0.434 Sum_probs=47.7
Q ss_pred cceEEEEeeCCCCeeEEecC---CCCccEEEEeeccccCCcccCCCCCEEEEEEeeCCCC-------ce-eEEEEEcCCC
Q 030905 7 SSGTVKWFSAQKGFGFIAPE---DGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVGEDG-------RT-KAVDVEAASR 75 (169)
Q Consensus 7 ~~G~Vk~~~~~kGfGFI~~~---~~~~dvF~H~s~i~~~~~~~l~~G~~V~F~~~~~~kG-------r~-~A~~V~~~~g 75 (169)
+.|++--. .+||||... .+..||||..+.|+..+ |..|+.|+=.+.....+ |+ .-+.|..+++
T Consensus 296 ~~GiLdi~---dg~gFlR~~~y~~~~~Dvyvs~~qirr~~---Lr~Gd~v~G~vr~p~~~e~~~~r~k~~~l~~v~~vNg 369 (672)
T PRK12678 296 VAGILDVL---DNYAFVRTSGYLPGPNDVYVSMNQVRKNG---LRKGDAVTGAVRAPREGEQGNQRQKFNPLVRLDSVNG 369 (672)
T ss_pred eeEEEEec---CCeeEeeCCCCCCCCCCeeeCHHHHHHcC---CCCCCEEEEeecCCCCCccccccceeeeeeeEeeeCC
Confidence 55666655 399999976 45689999999999875 88999999887764433 22 2356666776
Q ss_pred ccc
Q 030905 76 SRR 78 (169)
Q Consensus 76 ~~~ 78 (169)
.++
T Consensus 370 ~~~ 372 (672)
T PRK12678 370 MSP 372 (672)
T ss_pred CCh
Confidence 553
No 76
>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=87.51 E-value=2.7 Score=27.73 Aligned_cols=50 Identities=16% Similarity=0.189 Sum_probs=39.0
Q ss_pred ccccceEEEEeeCCCCeeEEecCCCCccEEEEeeccccCCcccCCCCCEEEEEEeeC
Q 030905 4 VQRSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVG 60 (169)
Q Consensus 4 ~~~~~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~~~~~~l~~G~~V~F~~~~~ 60 (169)
...+.|+|.... -||+...-+...+-|+|.+++. ..++.||.|...+..-
T Consensus 17 G~~~~g~V~~i~---~~G~fV~l~~~~~Glv~~se~~----~~~~iGd~v~v~I~~i 66 (77)
T cd04473 17 GKLYKGKVNGVA---KYGVFVDLNDHVRGLIHRSNLL----RDYEVGDEVIVQVTDI 66 (77)
T ss_pred CCEEEEEEEeEe---cceEEEEECCCcEEEEEchhcc----CcCCCCCEEEEEEEEE
Confidence 456889998864 4887777655589999999985 3589999999887654
No 77
>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=86.51 E-value=2.8 Score=26.72 Aligned_cols=53 Identities=13% Similarity=0.016 Sum_probs=38.6
Q ss_pred cccceEEEEeeCCCCeeEEecCCCCccEEEEeeccccCC----cccCCCCCEEEEEEeeC
Q 030905 5 QRSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEG----FRTLSEGQTVEFSVDVG 60 (169)
Q Consensus 5 ~~~~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~~~----~~~l~~G~~V~F~~~~~ 60 (169)
..++|+|+.... ..=||.... ..+-|+|++++.... ...+++||.|++.+..-
T Consensus 2 ~iv~g~V~~i~~--~~~~v~l~~-~~~g~l~~~e~~~~~~~~~~~~~~~Gd~i~~~i~~~ 58 (70)
T cd05687 2 DIVKGTVVSVDD--DEVLVDIGY-KSEGIIPISEFSDDPIENGEDEVKVGDEVEVYVLRV 58 (70)
T ss_pred CEEEEEEEEEeC--CEEEEEeCC-CceEEEEHHHhCccccCCHhHcCCCCCEEEEEEEEE
Confidence 357899999865 245555543 478999999997542 13489999999998763
No 78
>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=86.43 E-value=3.1 Score=26.24 Aligned_cols=52 Identities=33% Similarity=0.355 Sum_probs=37.8
Q ss_pred ccceEEEEeeCCCCeeEEecCCCCccEEEEeecccc-CC----cccCCCCCEEEEEEeeC
Q 030905 6 RSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKS-EG----FRTLSEGQTVEFSVDVG 60 (169)
Q Consensus 6 ~~~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~-~~----~~~l~~G~~V~F~~~~~ 60 (169)
.+.|+|+... -||+...-+...+-|+|+++|.. .. ...+++||.|...+..-
T Consensus 3 ~~~g~V~~i~---~~G~fv~l~~~~~Glv~~~~l~~~~~~~~~~~~~~~G~~v~v~v~~i 59 (69)
T cd05690 3 VVSGKIKSIT---DFGIFVGLDGGIDGLVHISDISWTQRVRHPSEIYKKGQEVEAVVLNI 59 (69)
T ss_pred EEEEEEEEEE---eeeEEEEeCCCCEEEEEHHHCCCccccCChhhEECCCCEEEEEEEEE
Confidence 5788998875 48877665555899999999973 11 13468899998877653
No 79
>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=86.41 E-value=3.5 Score=27.00 Aligned_cols=51 Identities=12% Similarity=-0.007 Sum_probs=37.1
Q ss_pred ccceEEEEeeCCCCee-EEecCCCCccEEEEeeccccCC------cccCCCCCEEEEEEeeC
Q 030905 6 RSSGTVKWFSAQKGFG-FIAPEDGGEDLFVHQTSIKSEG------FRTLSEGQTVEFSVDVG 60 (169)
Q Consensus 6 ~~~G~Vk~~~~~kGfG-FI~~~~~~~dvF~H~s~i~~~~------~~~l~~G~~V~F~~~~~ 60 (169)
.++|+|+... -|| ||+..+ +-+-|+|+++|.... ...+++||.|++.+..-
T Consensus 3 ~V~g~V~~i~---~~g~~V~l~~-~i~G~i~~~~ls~~~~~~~~~~~~~~vG~~v~~kV~~i 60 (73)
T cd05703 3 EVTGFVNNVS---KEFVWLTISP-DVKGRIPLLDLSDDVSVLEHPEKKFPIGQALKAKVVGV 60 (73)
T ss_pred EEEEEEEEEe---CCEEEEEeCC-CcEEEEEHHHcCCccccccCHHHhCCCCCEEEEEEEEE
Confidence 4789999985 344 455544 479999999996431 24589999999997753
No 80
>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=85.93 E-value=2.7 Score=26.97 Aligned_cols=51 Identities=12% Similarity=0.066 Sum_probs=37.9
Q ss_pred ccccceEEEEeeCCCCeeEEecCCCCccEEEEeeccccCCcccCCCCCEEEEEEeeC
Q 030905 4 VQRSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVG 60 (169)
Q Consensus 4 ~~~~~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~~~~~~l~~G~~V~F~~~~~ 60 (169)
...++|+|...+. .+=||.. +. -+-|++.+.+... ..+++|+.|.+.+..-
T Consensus 4 g~iV~G~V~~~~~--~~~~vdi-g~-~eg~lp~~e~~~~--~~~~~Gd~v~v~v~~v 54 (67)
T cd04455 4 GEIVTGIVKRVDR--GNVIVDL-GK-VEAILPKKEQIPG--ESYRPGDRIKAYVLEV 54 (67)
T ss_pred CCEEEEEEEEEcC--CCEEEEc-CC-eEEEeeHHHCCCC--CcCCCCCEEEEEEEEE
Confidence 4567999999976 2334444 33 6889999999754 4579999999988764
No 81
>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=85.52 E-value=3.5 Score=26.50 Aligned_cols=55 Identities=18% Similarity=0.138 Sum_probs=38.0
Q ss_pred cccceEEEEeeCCCCeeEEecCCCCccEEEEeeccccC--C----cccCCCCCEEEEEEeeCCC
Q 030905 5 QRSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSE--G----FRTLSEGQTVEFSVDVGED 62 (169)
Q Consensus 5 ~~~~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~~--~----~~~l~~G~~V~F~~~~~~k 62 (169)
..+.|+|+..... .=|+..+. +-+-++|++++... . ...+++||.|...+..-.+
T Consensus 2 ~iV~g~V~~i~~~--gi~v~l~~-~i~g~i~~~~i~~~~~~~~~~~~~~~~Gd~i~~kVl~~d~ 62 (70)
T cd05702 2 DLVKAKVKSVKPT--QLNVQLAD-NVHGRIHVSEVFDEWPDGKNPLSKFKIGQKIKARVIGGHD 62 (70)
T ss_pred CEEEEEEEEEECC--cEEEEeCC-CcEEEEEHHHhccccccccChhHhCCCCCEEEEEEEEEeC
Confidence 3578999998652 23444444 57999999999653 1 2447899999988765433
No 82
>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=84.54 E-value=5.1 Score=27.65 Aligned_cols=51 Identities=22% Similarity=0.203 Sum_probs=36.7
Q ss_pred ccceEEEEeeCCCCeeEEecCCCCccEEEEeeccccCCc---------------ccCCCCCEEEEEEeeC
Q 030905 6 RSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGF---------------RTLSEGQTVEFSVDVG 60 (169)
Q Consensus 6 ~~~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~~~~---------------~~l~~G~~V~F~~~~~ 60 (169)
.+.|+|+..+. +|++..-+. .+.|+|++++....+ ..++.||.|...+..-
T Consensus 2 vv~g~V~~i~~---~GifV~l~~-v~G~v~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~Gd~v~vkI~~v 67 (99)
T cd04460 2 VVEGEVVEVVD---FGAFVRIGP-VDGLLHISQIMDDYISYDPKNKRLIGEETKRVLKVGDVVRARIVAV 67 (99)
T ss_pred EEEEEEEEEEe---ccEEEEEcC-eEEEEEEEEccCCceEechhheeecccCcCCEECCCCEEEEEEEEE
Confidence 36788888864 566555443 789999999975433 3468999999988754
No 83
>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=84.34 E-value=0.47 Score=40.12 Aligned_cols=20 Identities=30% Similarity=0.966 Sum_probs=17.8
Q ss_pred CccccCcCCeecccCCCCCC
Q 030905 119 ACFNCGRTGHIARECYSRGR 138 (169)
Q Consensus 119 ~C~~Cg~~GH~a~~C~~~~~ 138 (169)
.||+||+.||+-++||...+
T Consensus 178 ~CyRCGqkgHwIqnCpTN~D 197 (427)
T COG5222 178 VCYRCGQKGHWIQNCPTNQD 197 (427)
T ss_pred eEEecCCCCchhhcCCCCCC
Confidence 59999999999999997654
No 84
>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=83.65 E-value=4.9 Score=25.83 Aligned_cols=54 Identities=13% Similarity=0.044 Sum_probs=39.5
Q ss_pred ccccceEEEEeeCCCCeeEEecCC--CCccEEEEeeccccCCc----ccCCCCCEEEEEEeeC
Q 030905 4 VQRSSGTVKWFSAQKGFGFIAPED--GGEDLFVHQTSIKSEGF----RTLSEGQTVEFSVDVG 60 (169)
Q Consensus 4 ~~~~~G~Vk~~~~~kGfGFI~~~~--~~~dvF~H~s~i~~~~~----~~l~~G~~V~F~~~~~ 60 (169)
...+.|+|+... .||.+..-. .+.+-|+|++.|...-+ ..++.||.|+..+..-
T Consensus 4 G~~~~g~V~~v~---~~g~~v~l~~~~~~~gll~~s~l~~~~~~~~~~~~~~Gd~v~vkv~~~ 63 (76)
T cd04452 4 GELVVVTVKSIA---DMGAYVSLLEYGNIEGMILLSELSRRRIRSIRKLVKVGRKEVVKVIRV 63 (76)
T ss_pred CCEEEEEEEEEE---ccEEEEEEcCCCCeEEEEEhHHcCCcccCCHHHeeCCCCEEEEEEEEE
Confidence 356789999885 488766543 23689999999976532 2478999999887754
No 85
>PRK08059 general stress protein 13; Validated
Probab=83.59 E-value=11 Score=27.28 Aligned_cols=68 Identities=22% Similarity=0.250 Sum_probs=47.1
Q ss_pred ccccceEEEEeeCCCCeeEEecCCCCccEEEEeeccccCCc----ccCCCCCEEEEEEeeC--CCCceeEEEEEcCCC
Q 030905 4 VQRSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGF----RTLSEGQTVEFSVDVG--EDGRTKAVDVEAASR 75 (169)
Q Consensus 4 ~~~~~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~~~~----~~l~~G~~V~F~~~~~--~kGr~~A~~V~~~~g 75 (169)
...+.|+|+...+ ||++..-....+-|+|++++...-. ..+.+||.|...+..- .+++ ....+..+..
T Consensus 8 G~iv~G~V~~i~~---~G~fV~i~~~~~Gli~~sel~~~~~~~~~~~~~vGD~I~vkI~~id~~~~~-i~lslk~~~~ 81 (123)
T PRK08059 8 GSVVTGKVTGIQP---YGAFVALDEETQGLVHISEITHGFVKDIHDFLSVGDEVKVKVLSVDEEKGK-ISLSIRATEE 81 (123)
T ss_pred CCEEEEEEEEEec---ceEEEEECCCCEEEEEHHHCCcccccCHHHcCCCCCEEEEEEEEEECCCCe-EEEEEEEccc
Confidence 4678899998764 7777765555799999999965322 3468999999988764 2453 4444554443
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=83.26 E-value=10 Score=24.66 Aligned_cols=54 Identities=17% Similarity=0.263 Sum_probs=37.4
Q ss_pred cccceEEEEeeCCCCeeEEecCCC-CccEEEEeeccccCC---------------cccCCCCCEEEEEEeeCC
Q 030905 5 QRSSGTVKWFSAQKGFGFIAPEDG-GEDLFVHQTSIKSEG---------------FRTLSEGQTVEFSVDVGE 61 (169)
Q Consensus 5 ~~~~G~Vk~~~~~kGfGFI~~~~~-~~dvF~H~s~i~~~~---------------~~~l~~G~~V~F~~~~~~ 61 (169)
..+.|+|+.... ||++..-.. +.+-|+|++++.... ...+++||.|.-.+....
T Consensus 3 ~~~~g~V~~v~~---~G~fv~l~~~~~~G~v~~~~l~~~~~~~d~~~~~~~~~~~~~~~~~gd~v~v~v~~vd 72 (83)
T cd04471 3 EEFDGVISGVTS---FGLFVELDNLTVEGLVHVSTLGDDYYEFDEENHALVGERTGKVFRLGDKVKVRVVRVD 72 (83)
T ss_pred CEEEEEEEeEEe---eeEEEEecCCCEEEEEEEEecCCCcEEEcccceEEEeccCCCEEcCCCEEEEEEEEec
Confidence 457788888854 787776553 467899999986431 135677888887776553
No 87
>COG1098 VacB Predicted RNA binding protein (contains ribosomal protein S1 domain) [Translation, ribosomal structure and biogenesis]
Probab=83.12 E-value=2.4 Score=31.32 Aligned_cols=70 Identities=21% Similarity=0.333 Sum_probs=49.0
Q ss_pred ccccceEEEEeeCCCCee-EEecCCCCccEEEEeeccccCC----cccCCCCCEEEEEEee-CCCCceeEEEEEcCCCcc
Q 030905 4 VQRSSGTVKWFSAQKGFG-FIAPEDGGEDLFVHQTSIKSEG----FRTLSEGQTVEFSVDV-GEDGRTKAVDVEAASRSR 77 (169)
Q Consensus 4 ~~~~~G~Vk~~~~~kGfG-FI~~~~~~~dvF~H~s~i~~~~----~~~l~~G~~V~F~~~~-~~kGr~~A~~V~~~~g~~ 77 (169)
...++|+|+-. +-|| |+..++ ++.=+||||.|...- ...|.+||.|.-.+.. +.+|+ .-..|+.+..+|
T Consensus 6 G~~l~GkItgI---~~yGAFV~l~~-g~tGLVHISEIa~~fVkdI~d~L~vG~eV~vKVl~ide~GK-isLSIr~~~e~p 80 (129)
T COG1098 6 GSKLKGKITGI---TPYGAFVELEG-GKTGLVHISEIADGFVKDIHDHLKVGQEVKVKVLDIDENGK-ISLSIRKLEEEP 80 (129)
T ss_pred cceEEEEEEee---EecceEEEecC-CCcceEEehHhhhhhHHhHHHHhcCCCEEEEEEEeeccCCC-cceehHHhhhCc
Confidence 45678888865 4577 555554 478899999998642 2578999999987664 56786 556676665544
Q ss_pred c
Q 030905 78 R 78 (169)
Q Consensus 78 ~ 78 (169)
.
T Consensus 81 e 81 (129)
T COG1098 81 E 81 (129)
T ss_pred c
Confidence 4
No 88
>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=82.66 E-value=5 Score=24.80 Aligned_cols=52 Identities=21% Similarity=0.190 Sum_probs=37.6
Q ss_pred ccceEEEEeeCCCCeeEEecCCCCccEEEEeeccccCCc----ccCCCCCEEEEEEeeC
Q 030905 6 RSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGF----RTLSEGQTVEFSVDVG 60 (169)
Q Consensus 6 ~~~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~~~~----~~l~~G~~V~F~~~~~ 60 (169)
.+.|+|+...+ ||....-....+-|+|.+++....+ ..+++||.|...+..-
T Consensus 3 ~~~g~V~~i~~---~G~fv~l~~~~~g~~~~~~l~~~~~~~~~~~~~~Gd~v~v~i~~v 58 (68)
T cd05685 3 VLEGVVTNVTD---FGAFVDIGVKQDGLIHISKMADRFVSHPSDVVSVGDIVEVKVISI 58 (68)
T ss_pred EEEEEEEEEec---ccEEEEcCCCCEEEEEHHHCCCccccCHHHhcCCCCEEEEEEEEE
Confidence 47889998864 6655554445789999999975422 2478999999887754
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=82.43 E-value=2.3 Score=27.97 Aligned_cols=29 Identities=24% Similarity=0.456 Sum_probs=20.9
Q ss_pred cccCCCCCEEEEEEeeCCCCceeEEEEEc
Q 030905 44 FRTLSEGQTVEFSVDVGEDGRTKAVDVEA 72 (169)
Q Consensus 44 ~~~l~~G~~V~F~~~~~~kGr~~A~~V~~ 72 (169)
+..|++||+|.|+++....+.+.-+.|+.
T Consensus 40 l~~l~~Gd~V~F~~~~~~~~~~~I~~i~~ 68 (70)
T PF11604_consen 40 LAGLKPGDKVRFTFERTDDGSYVITAIEP 68 (70)
T ss_dssp ESS-STT-EEEEEEEEETTCEEEEEEEEE
T ss_pred hhcCCCCCEEEEEEEECCCCcEEEEEEEE
Confidence 46799999999999998887455555543
No 90
>COG2996 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only]
Probab=82.39 E-value=6 Score=33.09 Aligned_cols=61 Identities=26% Similarity=0.368 Sum_probs=45.3
Q ss_pred cccceEEEEeeCCCCee-EEecCCCCccEEEEeeccccCCcccCCCCCEEEEEEeeCCCCceeEEEEE
Q 030905 5 QRSSGTVKWFSAQKGFG-FIAPEDGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVGEDGRTKAVDVE 71 (169)
Q Consensus 5 ~~~~G~Vk~~~~~kGfG-FI~~~~~~~dvF~H~s~i~~~~~~~l~~G~~V~F~~~~~~kGr~~A~~V~ 71 (169)
...+..|+.++ .|| |+..+..++.|++|.+.... ..+++||.|++-|-.+.+.++.|+-..
T Consensus 7 ~~~~l~V~~~~---~~g~fL~~~~~~~~ilL~k~~~~~---~e~evGdev~vFiY~D~~~rl~aTt~~ 68 (287)
T COG2996 7 QINSLEVVEFS---DFGYFLDAGEDGTTILLPKSEPEE---DELEVGDEVTVFIYVDSEDRLIATTRE 68 (287)
T ss_pred ceEEEEEEEee---ceeEEEecCCCceEEeccccCCcC---CccccCcEEEEEEEECCCCceeheeec
Confidence 34566777765 455 44445555589999998865 468999999999999999988886544
No 91
>TIGR00767 rho transcription termination factor Rho. Members of this family differ in the specificity of RNA binding.
Probab=81.97 E-value=1.5 Score=38.63 Aligned_cols=50 Identities=26% Similarity=0.536 Sum_probs=38.3
Q ss_pred ccceEEEEeeCCCCeeEEecC-----CCCccEEEEeeccccCCcccCCCCCEEEEEEeeC
Q 030905 6 RSSGTVKWFSAQKGFGFIAPE-----DGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVG 60 (169)
Q Consensus 6 ~~~G~Vk~~~~~kGfGFI~~~-----~~~~dvF~H~s~i~~~~~~~l~~G~~V~F~~~~~ 60 (169)
...|.+--.. .||||+... .+.+||||-.+.|+..+ |+.||.|+=.+...
T Consensus 50 ~~~g~le~~~--~g~gflr~~~~~~~~~~~d~yvs~~~i~~~~---lr~gd~v~g~~R~~ 104 (415)
T TIGR00767 50 FGEGVLEILP--DGFGFLRSPDSSYLPGPDDIYVSPSQIRRFN---LRTGDTIEGQIRSP 104 (415)
T ss_pred EEEEEEEEcC--CCCeEEeCCCcCCCCCCCCeeeCHHHHHhcC---CCCCCEEEEEEecc
Confidence 3456665443 499999985 35689999999999864 88999999776643
No 92
>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=81.57 E-value=8.3 Score=34.01 Aligned_cols=71 Identities=20% Similarity=0.193 Sum_probs=53.7
Q ss_pred ccccceEEEEeeCCCCeeEEecCCCCccEEEEeeccccCC----------------cccCCCCCEEEEEEeeC---CCCc
Q 030905 4 VQRSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEG----------------FRTLSEGQTVEFSVDVG---EDGR 64 (169)
Q Consensus 4 ~~~~~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~~~----------------~~~l~~G~~V~F~~~~~---~kGr 64 (169)
...+.|+|+...+.-.--||.-..+ +.-|+|++++...- ...|++||.|..++... .||.
T Consensus 26 GnIY~GrV~~i~p~l~aAFVdiG~~-k~gfL~~~d~~~~~~~~~~~~~~~~~~~~i~~~l~~G~~IlVQV~Ke~~~~Kgp 104 (414)
T TIGR00757 26 GNIYKGRVTRILPSLQAAFVDIGLE-KNGFLHASDIGPNYECLAPAEAKREAGPSISELLRPGQSVLVQVVKEPRGNKGA 104 (414)
T ss_pred CCEEEEEEeeecCCCceEEEEcCCC-ceEEEEHHHcCchhhccccccccccccCCHHHhCcCCCEEEEEEeeCCcCCCCC
Confidence 3568999999988777899998765 78999999985310 11489999999999986 4675
Q ss_pred eeEEEEEcCCC
Q 030905 65 TKAVDVEAASR 75 (169)
Q Consensus 65 ~~A~~V~~~~g 75 (169)
....+|++++.
T Consensus 105 ~lT~~Isl~Gr 115 (414)
T TIGR00757 105 RLTTDISLPGR 115 (414)
T ss_pred eEEEEEEeccc
Confidence 45567776653
No 93
>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=81.30 E-value=7.3 Score=25.89 Aligned_cols=55 Identities=13% Similarity=0.035 Sum_probs=37.9
Q ss_pred ccccceEEEEeeCCCCeeEEecCCCCccEEEEeeccccC----C----cccCCCCCEEEEEEeeCC
Q 030905 4 VQRSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSE----G----FRTLSEGQTVEFSVDVGE 61 (169)
Q Consensus 4 ~~~~~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~~----~----~~~l~~G~~V~F~~~~~~ 61 (169)
...+.|+|+...+ +|.+..-...-+-|+|+++|... . ...|++||.|.+.+..-.
T Consensus 7 GdiV~g~V~~i~~---~g~~v~i~~~~~G~l~~se~~~~~~~~~~~~~~~~l~vGd~i~~~V~~~~ 69 (86)
T cd05789 7 GDVVIGRVTEVGF---KRWKVDINSPYDAVLPLSEVNLPRTDEDELNMRSYLDEGDLIVAEVQSVD 69 (86)
T ss_pred CCEEEEEEEEECC---CEEEEECCCCeEEEEEHHHccCCCCccchHHHHhhCCCCCEEEEEEEEEC
Confidence 3567899999643 44444334447899999999631 1 124899999999988753
No 94
>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=79.79 E-value=3.4 Score=32.01 Aligned_cols=47 Identities=32% Similarity=0.432 Sum_probs=40.8
Q ss_pred cceEEEEeeCCCCeeEEecCCCCccEEEEeeccccCCcccCCCCCEEEE
Q 030905 7 SSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGFRTLSEGQTVEF 55 (169)
Q Consensus 7 ~~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~~~~~~l~~G~~V~F 55 (169)
.-|+||.|+.+..-|.++-++= +|+=+|-..|..-.|. |.+||.|..
T Consensus 36 rIG~iK~F~~~tQe~iVti~e~-e~LeI~T~nISN~~le-Ls~~D~VlL 82 (181)
T PF05606_consen 36 RIGTIKSFKFQTQEGIVTIPEY-EDLEIHTKNISNINLE-LSKGDEVLL 82 (181)
T ss_pred EEeeeeecccccceEEEEeecc-cCceEEeeecccceeE-ecCCCEEEE
Confidence 4699999999999999998875 7999999999887765 899999964
No 95
>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=78.68 E-value=7.7 Score=24.04 Aligned_cols=52 Identities=25% Similarity=0.279 Sum_probs=36.9
Q ss_pred cccceEEEEeeCCCCeeEEecCCCCccEEEEeeccccCCc----ccCCCCCEEEEEEeeC
Q 030905 5 QRSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGF----RTLSEGQTVEFSVDVG 60 (169)
Q Consensus 5 ~~~~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~~~~----~~l~~G~~V~F~~~~~ 60 (169)
..++|+|...++ ||++..-. ..+-|+|.+++..... ..+++||.|.+.+..-
T Consensus 3 ~~~~g~V~~v~~---~g~~v~l~-~~~g~l~~~e~~~~~~~~~~~~~~~Gd~v~v~i~~v 58 (68)
T cd05688 3 DVVEGTVKSITD---FGAFVDLG-GVDGLLHISDMSWGRVKHPSEVVNVGDEVEVKVLKI 58 (68)
T ss_pred CEEEEEEEEEEe---eeEEEEEC-CeEEEEEhHHCCCccccCHhHEECCCCEEEEEEEEE
Confidence 457899999874 55555444 4789999999863321 2368999999887654
No 96
>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=78.03 E-value=8.8 Score=24.47 Aligned_cols=52 Identities=21% Similarity=0.049 Sum_probs=35.7
Q ss_pred cccceEEEEeeCCCCeeEEecCCCCccEEEEeeccccC--CcccCCCCCEEEEEEee
Q 030905 5 QRSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSE--GFRTLSEGQTVEFSVDV 59 (169)
Q Consensus 5 ~~~~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~~--~~~~l~~G~~V~F~~~~ 59 (169)
..+.|+|+... -||.+..-.+.-+-|+|++.+... ....+++|+.|.+.+..
T Consensus 2 ~~V~g~V~~i~---~~G~~v~l~~~v~g~v~~~~l~~~~~~~~~~~~G~~i~~kVi~ 55 (66)
T cd05695 2 MLVNARVKKVL---SNGLILDFLSSFTGTVDFLHLDPEKSSKSTYKEGQKVRARILY 55 (66)
T ss_pred CEEEEEEEEEe---CCcEEEEEcCCceEEEEHHHcCCccCcccCcCCCCEEEEEEEE
Confidence 35689999985 344444322247899999988532 13458999999998654
No 97
>PRK09838 periplasmic copper-binding protein; Provisional
Probab=78.03 E-value=4.7 Score=29.28 Aligned_cols=63 Identities=16% Similarity=0.100 Sum_probs=38.2
Q ss_pred ccceEEEEeeCCCCeeEEecCCCCccE-------EEEeeccccCCcccCCCCCEEEEEEeeCCCCceeEEEEEc
Q 030905 6 RSSGTVKWFSAQKGFGFIAPEDGGEDL-------FVHQTSIKSEGFRTLSEGQTVEFSVDVGEDGRTKAVDVEA 72 (169)
Q Consensus 6 ~~~G~Vk~~~~~kGfGFI~~~~~~~dv-------F~H~s~i~~~~~~~l~~G~~V~F~~~~~~kGr~~A~~V~~ 72 (169)
..+|+|+..|.+.+-=.|+-+.- +.+ -|-..+= ..+..|++|+.|.|++++...+ +..++|++
T Consensus 44 ~~~G~V~~vd~~~~~iti~H~pI-p~l~wPaMTM~F~v~~~--~~l~~lk~G~~V~F~~~~~~~~-~~i~~i~~ 113 (115)
T PRK09838 44 SGTGVVKGIDLESKKITIHHEPI-PAVNWPEMTMRFTITPQ--TKMSEIKTGDKVAFNFVQQGNL-SLLQDIKV 113 (115)
T ss_pred EEEEEEEEEeCCCCEEEEeeccc-ccCCCCCccccccCCCh--hhhccCCCCCEEEEEEEEcCCc-EEEEEEee
Confidence 34788888887665544442211 111 1111110 1245689999999999998887 57777765
No 98
>PTZ00248 eukaryotic translation initiation factor 2 subunit 1; Provisional
Probab=77.88 E-value=14 Score=31.56 Aligned_cols=70 Identities=10% Similarity=0.011 Sum_probs=50.1
Q ss_pred ccccceEEEEeeCCCCeeEEecCC--CCccEEEEeeccccCCc----ccCCCCCEEEEEEeeC--CCCceeEEEEEcCCC
Q 030905 4 VQRSSGTVKWFSAQKGFGFIAPED--GGEDLFVHQTSIKSEGF----RTLSEGQTVEFSVDVG--EDGRTKAVDVEAASR 75 (169)
Q Consensus 4 ~~~~~G~Vk~~~~~kGfGFI~~~~--~~~dvF~H~s~i~~~~~----~~l~~G~~V~F~~~~~--~kGr~~A~~V~~~~g 75 (169)
...+.|+|+... -||.+..-. ++-+-|+|+|.|...-. ..+++|+.|...+..- .+| ...++++.+..
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 457889999986 488776553 35799999999976432 3579999999888753 456 46777766654
Q ss_pred cc
Q 030905 76 SR 77 (169)
Q Consensus 76 ~~ 77 (169)
.|
T Consensus 94 ~p 95 (319)
T PTZ00248 94 ED 95 (319)
T ss_pred ch
Confidence 43
No 99
>KOG2044 consensus 5'-3' exonuclease HKE1/RAT1 [Replication, recombination and repair; RNA processing and modification]
Probab=75.73 E-value=1.3 Score=41.99 Aligned_cols=20 Identities=40% Similarity=0.974 Sum_probs=17.3
Q ss_pred CCccccccCCCCccCCCCCC
Q 030905 149 GGGGCYNCGEEGHFARDCPN 168 (169)
Q Consensus 149 ~~~~C~~Cg~~GH~ardCp~ 168 (169)
....|+.|++.||.+.||..
T Consensus 259 ~~~~C~~cgq~gh~~~dc~g 278 (931)
T KOG2044|consen 259 KPRRCFLCGQTGHEAKDCEG 278 (931)
T ss_pred CcccchhhcccCCcHhhcCC
Confidence 46779999999999999964
No 100
>KOG0314 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=75.64 E-value=2.5 Score=37.66 Aligned_cols=42 Identities=26% Similarity=0.778 Sum_probs=28.1
Q ss_pred CccccCcCCeecccCCCCCCCCCCCCCCCCCCccccccCCCCccCCCCCC
Q 030905 119 ACFNCGRTGHIARECYSRGRGGGRGYGGGRGGGGCYNCGEEGHFARDCPN 168 (169)
Q Consensus 119 ~C~~Cg~~GH~a~~C~~~~~~~~~~~~g~~~~~~C~~Cg~~GH~ardCp~ 168 (169)
.|-.|-...|+-.-|..... ......|++|..++||.+.||.
T Consensus 135 ~~~~~~~~~~~iq~~~~~g~--------Pppsy~c~rc~~~g~wikacpt 176 (448)
T KOG0314|consen 135 VCHRCNSPGHFIQHCSTNGS--------PPPSYKCVKCPTPGPWIKACPT 176 (448)
T ss_pred eeeecccCccccccccccCC--------CCCCcceecCCCCCccceeccc
Confidence 35555555555555544332 2236789999999999999985
No 101
>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=74.61 E-value=4.6 Score=24.94 Aligned_cols=31 Identities=19% Similarity=0.396 Sum_probs=25.0
Q ss_pred ccCCCCCEEEEEEeeCCCCceeEEEEEcCCC
Q 030905 45 RTLSEGQTVEFSVDVGEDGRTKAVDVEAASR 75 (169)
Q Consensus 45 ~~l~~G~~V~F~~~~~~kGr~~A~~V~~~~g 75 (169)
..+.+||.|+|.|.....|...|.+|.+.+-
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 4578999999999988888667888876553
No 102
>PRK13806 rpsA 30S ribosomal protein S1; Provisional
Probab=74.56 E-value=16 Score=32.87 Aligned_cols=67 Identities=16% Similarity=0.196 Sum_probs=45.5
Q ss_pred ccccceEEEEeeCCCCeeEEecCCCCccEEEEeeccccCC-----cccCCCCCEEEEEEeeC-CCCceeEEEEEcC
Q 030905 4 VQRSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEG-----FRTLSEGQTVEFSVDVG-EDGRTKAVDVEAA 73 (169)
Q Consensus 4 ~~~~~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~~~-----~~~l~~G~~V~F~~~~~-~kGr~~A~~V~~~ 73 (169)
...++|+|+... -||++..-..+-+.|+|+++|.... -..+++||.|+..+..- +..+.....+..+
T Consensus 293 G~~v~G~V~~v~---~~G~fV~l~~gv~Glvh~sels~~~~~~~~~~~~~~Gd~v~vkVl~iD~e~~ri~Ls~K~~ 365 (491)
T PRK13806 293 GDKVTGKVVRLA---PFGAFVEILPGIEGLVHVSEMSWTRRVNKPEDVVAPGDAVAVKIKDIDPAKRRISLSLRDA 365 (491)
T ss_pred CCEEEEEEEEEe---CceEEEEeCCCcEEEEEHHHcCcccccCCHHHcCCCCCEEEEEEEEEEccCCEEEEEEeec
Confidence 457889999885 4887766544578999999987421 12578999999988743 3222344555443
No 103
>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=73.05 E-value=13 Score=23.71 Aligned_cols=54 Identities=20% Similarity=0.292 Sum_probs=38.8
Q ss_pred cccceEEEEeeCCCCeeEEecCC-CCccEEEEeeccccCCc----ccCCCCCEEEEEEeeCC
Q 030905 5 QRSSGTVKWFSAQKGFGFIAPED-GGEDLFVHQTSIKSEGF----RTLSEGQTVEFSVDVGE 61 (169)
Q Consensus 5 ~~~~G~Vk~~~~~kGfGFI~~~~-~~~dvF~H~s~i~~~~~----~~l~~G~~V~F~~~~~~ 61 (169)
..+.|+|+... .||++..-. ...+-|+|++++..... ..+++||.|+..+..-.
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 45789999886 366666543 35689999999976422 34699999998876543
No 104
>PHA02945 interferon resistance protein; Provisional
Probab=72.58 E-value=26 Score=24.26 Aligned_cols=54 Identities=17% Similarity=0.102 Sum_probs=36.9
Q ss_pred ccccceEEEEeeCCCCeeEEec-CC-CCccEEEEeecc--ccC---CcccCCCCCEEEEEEeeCCC
Q 030905 4 VQRSSGTVKWFSAQKGFGFIAP-ED-GGEDLFVHQTSI--KSE---GFRTLSEGQTVEFSVDVGED 62 (169)
Q Consensus 4 ~~~~~G~Vk~~~~~kGfGFI~~-~~-~~~dvF~H~s~i--~~~---~~~~l~~G~~V~F~~~~~~k 62 (169)
.....|+|+. +.||+-.. ++ ++.+-|+|+|.+ ... ....| +|+.|...+..-.+
T Consensus 12 GelvigtV~~----~d~ga~v~L~EY~g~eg~i~~seveva~~wvK~rd~l-~GqkvV~KVirVd~ 72 (88)
T PHA02945 12 GDVLKGKVYE----NGYALYIDLFDYPHSEAILAESVQMHMNRYFKYRDKL-VGKTVKVKVIRVDY 72 (88)
T ss_pred CcEEEEEEEe----cCceEEEEecccCCcEEEEEeehhhhccceEeeeeEe-cCCEEEEEEEEECC
Confidence 4567788887 56776554 33 467999999966 221 13457 99999998876543
No 105
>KOG0921 consensus Dosage compensation complex, subunit MLE [Transcription]
Probab=71.19 E-value=17 Score=35.57 Aligned_cols=23 Identities=48% Similarity=0.963 Sum_probs=11.6
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCC
Q 030905 87 GGFYGGRGRGGGYGRGGRGGRSV 109 (169)
Q Consensus 87 ~~~~~~~~~~~~~~~~~~g~g~~ 109 (169)
+.+|.+||.++.++++|||.|+.
T Consensus 1186 gssysgGGYGggys~gGygsGGY 1208 (1282)
T KOG0921|consen 1186 GSSYSGGGYGGGYSGGGYGSGGY 1208 (1282)
T ss_pred CCCCCCCCcCCCCCCCCcCCCCC
Confidence 34555555555555555554433
No 106
>COG4776 Rnb Exoribonuclease II [Transcription]
Probab=71.10 E-value=5.7 Score=35.81 Aligned_cols=50 Identities=24% Similarity=0.497 Sum_probs=38.2
Q ss_pred ccccceEEEEeeCCCCeeEEecCCCCccEEEEeeccccCCcccCCCCCEEEEEEeeCC
Q 030905 4 VQRSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVGE 61 (169)
Q Consensus 4 ~~~~~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~~~~~~l~~G~~V~F~~~~~~ 61 (169)
.+++.|+||. .+|||||++.|.. +.+|+--..++ .+--||+|.-.+....
T Consensus 19 ~prvEGvVK~--tekgfGFLEvD~q-kSYFIpPp~MK-----kvMHGDkIiA~i~te~ 68 (645)
T COG4776 19 TPRVEGVVKA--TEKGFGFLEVDAQ-KSYFIPPPQMK-----KVMHGDKIIAVIHTEK 68 (645)
T ss_pred Ccccceeeee--ccccceeEEEcCc-cccccCCHHHh-----hhcccCeEEEEEEecC
Confidence 5789999997 5799999999864 67887655554 4568899887776543
No 107
>KOG0107 consensus Alternative splicing factor SRp20/9G8 (RRM superfamily) [RNA processing and modification]
Probab=70.04 E-value=2 Score=33.73 Aligned_cols=16 Identities=50% Similarity=1.410 Sum_probs=14.9
Q ss_pred ccccCcCCeecccCCC
Q 030905 120 CFNCGRTGHIARECYS 135 (169)
Q Consensus 120 C~~Cg~~GH~a~~C~~ 135 (169)
|+.|++.+|+.++|..
T Consensus 103 ~~r~G~rg~~~r~~~~ 118 (195)
T KOG0107|consen 103 CYRCGERGHIGRNCKD 118 (195)
T ss_pred cccCCCcccccccccc
Confidence 9999999999999876
No 108
>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=69.03 E-value=22 Score=26.05 Aligned_cols=63 Identities=27% Similarity=0.361 Sum_probs=44.2
Q ss_pred ccceEEE----Eee-CCCCeeEEecCCCCccEEEEeeccccCCcccCCCCCEEEEEEeeCCCCceeEEEEEc
Q 030905 6 RSSGTVK----WFS-AQKGFGFIAPEDGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVGEDGRTKAVDVEA 72 (169)
Q Consensus 6 ~~~G~Vk----~~~-~~kGfGFI~~~~~~~dvF~H~s~i~~~~~~~l~~G~~V~F~~~~~~kGr~~A~~V~~ 72 (169)
++.|.|+ .|+ ....+=|+..|.. .+|-|+++.+... .+++|+.|.-+=.-..+|...|.+|..
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 RVGGLVVEGSVEYDPDGNTLTFTITDGG-KEIPVVYTGPLPD---LFREGQGVVVEGRLGEDGVFEATELLA 121 (131)
T ss_dssp EEEEEEECTTEEE-TTSSEEEEEEE-SS--EEEEEEES--CT---T--TTSEEEEEEEECCTSEEEEEEEEE
T ss_pred EEeeEEccCCEEEcCCCCEEEEEEEECC-cEEEEEECCCCCc---cccCCCeEEEEEEECCCCEEEEEEEEe
Confidence 4555555 344 6788999999885 6899999998775 467999998887777888889998864
No 109
>KOG3116 consensus Predicted C3H1-type Zn-finger protein [General function prediction only]
Probab=69.02 E-value=1.4 Score=33.66 Aligned_cols=22 Identities=32% Similarity=0.706 Sum_probs=17.6
Q ss_pred CCCCccccCcCCeecccCCCCC
Q 030905 116 GSGACFNCGRTGHIARECYSRG 137 (169)
Q Consensus 116 ~~~~C~~Cg~~GH~a~~C~~~~ 137 (169)
....|.+|.+.|||..+|.+..
T Consensus 26 ~~~rCQKClq~GHWtYECk~kR 47 (177)
T KOG3116|consen 26 SSARCQKCLQAGHWTYECKNKR 47 (177)
T ss_pred cchhHHHHHhhccceeeecCce
Confidence 3458999999999999998643
No 110
>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=68.68 E-value=11 Score=35.59 Aligned_cols=58 Identities=26% Similarity=0.347 Sum_probs=42.0
Q ss_pred ccccceEEEEeeCCCCeeEEecCCCCccEEEEeecccc---C----C-cccCCCCCEEEEEEee-CCCCc
Q 030905 4 VQRSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKS---E----G-FRTLSEGQTVEFSVDV-GEDGR 64 (169)
Q Consensus 4 ~~~~~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~---~----~-~~~l~~G~~V~F~~~~-~~kGr 64 (169)
...++|+|+..- -||.+..-..+.+-|+|+|.|.. . . ...+++||.|...+.. ++++|
T Consensus 648 G~i~~GkV~~I~---dfGaFVel~~G~eGLvHISeisdls~~~rv~~~~dv~kvGd~V~VKVl~ID~~gK 714 (719)
T TIGR02696 648 GERFLGTVVKTT---AFGAFVSLLPGKDGLLHISQIRKLAGGKRVENVEDVLSVGQKIQVEIADIDDRGK 714 (719)
T ss_pred CCEEEEEEEEEE---CceEEEEecCCceEEEEhhhccccccccCcCCHHHcCCCCCEEEEEEEEECCCCC
Confidence 467899999985 49977665556899999998841 1 1 2358899999988765 34565
No 111
>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=66.85 E-value=20 Score=22.94 Aligned_cols=37 Identities=14% Similarity=0.270 Sum_probs=27.0
Q ss_pred eeEEecCCCCccEEEEeeccccCCcccCCCCCEEEEEE
Q 030905 20 FGFIAPEDGGEDLFVHQTSIKSEGFRTLSEGQTVEFSV 57 (169)
Q Consensus 20 fGFI~~~~~~~dvF~H~s~i~~~~~~~l~~G~~V~F~~ 57 (169)
++.|+.|+ +-.|+.++.+........|+.|++|+..+
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 57777765 45788888877644456688999998654
No 112
>PRK10811 rne ribonuclease E; Reviewed
Probab=66.57 E-value=25 Score=34.48 Aligned_cols=70 Identities=20% Similarity=0.235 Sum_probs=53.1
Q ss_pred ccccceEEEEeeCCCCeeEEecCCCCccEEEEeeccccCCc-------------ccCCCCCEEEEEEeeC---CCCceeE
Q 030905 4 VQRSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGF-------------RTLSEGQTVEFSVDVG---EDGRTKA 67 (169)
Q Consensus 4 ~~~~~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~~~~-------------~~l~~G~~V~F~~~~~---~kGr~~A 67 (169)
...+.|+|+.-.+.-.==||....+ ..-|+|++++....| ..|++||.|..++... .||....
T Consensus 39 GnIYkGkVenIvPGInAAFVDIG~g-knGFL~L~Di~~~~f~~~~~~~~~~~i~~~Lk~GqeILVQV~KEa~gtKGp~LT 117 (1068)
T PRK10811 39 ANIYKGKITRIEPSLEAAFVDYGAE-RHGFLPLKEIAREYFPANYSAHGRPNIKDVLREGQEVIVQIDKEERGNKGAALT 117 (1068)
T ss_pred cceEEEEEecccCCcceeEEEecCC-cceEEEhhhccccccccccccccccccccccCCCCEEEEEEeecccCCCCCcee
Confidence 3468899999988888889998875 789999999853211 1388999999999875 4665566
Q ss_pred EEEEcCC
Q 030905 68 VDVEAAS 74 (169)
Q Consensus 68 ~~V~~~~ 74 (169)
.+|++++
T Consensus 118 t~ISLpG 124 (1068)
T PRK10811 118 TFISLAG 124 (1068)
T ss_pred eeEEecc
Confidence 6777665
No 113
>PRK13806 rpsA 30S ribosomal protein S1; Provisional
Probab=66.08 E-value=15 Score=33.02 Aligned_cols=54 Identities=22% Similarity=0.318 Sum_probs=39.1
Q ss_pred ccccceEEEEeeCCCCeeEEecCCCCccEEEEeeccccCC----cccCCCCCEEEEEEeeC
Q 030905 4 VQRSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEG----FRTLSEGQTVEFSVDVG 60 (169)
Q Consensus 4 ~~~~~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~~~----~~~l~~G~~V~F~~~~~ 60 (169)
...++|+|+..- -||.+..-..+-+-|+|++.|.... ...|++||.|++.+..-
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---QFGLFVNLAPGVTGLLPASVISRAGKPATYEKLKPGDSVTLVVEEI 437 (491)
T ss_pred CCEEEEEEEEEe---cCceEEEcCCCcEEEEEHHHcCcccccchhhcCCCCCEEEEEEEEE
Confidence 357889999874 4665444333589999999987532 35689999999986643
No 114
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=65.74 E-value=27 Score=33.93 Aligned_cols=63 Identities=11% Similarity=0.199 Sum_probs=43.5
Q ss_pred ccc-ceEEEEeeCCCCeeEEecCCCCccEEEEeeccccCCc----ccCCCCCEEEEEEeeC-CCCceeEEEEE
Q 030905 5 QRS-SGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGF----RTLSEGQTVEFSVDVG-EDGRTKAVDVE 71 (169)
Q Consensus 5 ~~~-~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~~~~----~~l~~G~~V~F~~~~~-~kGr~~A~~V~ 71 (169)
+.+ .|+|+... -||++..-..+.+-|+|+|.|...-+ ..+++||.|...+..- .+++ ....+.
T Consensus 755 ~iy~~g~V~~I~---~FGaFVeL~~g~EGLVHISeLs~~rv~~~~dv~kvGD~V~VkVi~ID~~gr-I~LSlK 823 (891)
T PLN00207 755 DIYRNCEIKSIA---PYGAFVEIAPGREGLCHISELSSNWLAKPEDAFKVGDRIDVKLIEVNDKGQ-LRLSRR 823 (891)
T ss_pred cEEECcEEEEEe---ccEEEEEeCCCCEEEEEhhhcCCccccCHHHhcCCCCEEEEEEEEECCCCc-EEEEEe
Confidence 445 36899875 59977655445899999999965422 3588999999987754 3564 333443
No 115
>PRK07899 rpsA 30S ribosomal protein S1; Reviewed
Probab=65.64 E-value=34 Score=30.90 Aligned_cols=68 Identities=19% Similarity=0.207 Sum_probs=47.1
Q ss_pred ccccceEEEEeeCCCCeeEEecCCCCccEEEEeeccccCCc----ccCCCCCEEEEEEeeC--CCCceeEEEEEcCCC
Q 030905 4 VQRSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGF----RTLSEGQTVEFSVDVG--EDGRTKAVDVEAASR 75 (169)
Q Consensus 4 ~~~~~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~~~~----~~l~~G~~V~F~~~~~--~kGr~~A~~V~~~~g 75 (169)
...++|+|+...+ ||++..-..+.+-|+|++.|...-+ ..+++||.|...+..- .+. .....+..+..
T Consensus 294 G~vv~G~V~~I~~---fGvFVeL~~gieGLvh~SeLs~~~v~~~~~~~kvGd~V~VkIi~ID~e~r-rI~LSlK~~~~ 367 (486)
T PRK07899 294 GQIVPGKVTKLVP---FGAFVRVEEGIEGLVHISELAERHVEVPEQVVQVGDEVFVKVIDIDLERR-RISLSLKQANE 367 (486)
T ss_pred CCEEEEEEEEEec---cEEEEEeCCCcEEEEEHHHcCcccccCccceeCCCCEEEEEEEEEECCCC-EEEEEEEEccc
Confidence 3568899998854 8887765545899999999975422 2478999999997653 244 34555554443
No 116
>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=65.58 E-value=14 Score=28.82 Aligned_cols=47 Identities=28% Similarity=0.381 Sum_probs=36.3
Q ss_pred ecCCCCccEEEEeeccccCCcccCCCCCEEEEEEeeCCCCceeEEEEEcCC
Q 030905 24 APEDGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVGEDGRTKAVDVEAAS 74 (169)
Q Consensus 24 ~~~~~~~dvF~H~s~i~~~~~~~l~~G~~V~F~~~~~~kGr~~A~~V~~~~ 74 (169)
..++....|.++.+.+.. .+.+|+.|++++..-..|...|.+|++.+
T Consensus 15 ~~~~~~a~llv~K~il~~----~~v~g~~v~V~~~iyN~G~~~A~dV~l~D 61 (181)
T PF05753_consen 15 AQEDSPARLLVSKQILNK----YLVEGEDVTVTYTIYNVGSSAAYDVKLTD 61 (181)
T ss_pred ccCCCCcEEEEEEeeccc----cccCCcEEEEEEEEEECCCCeEEEEEEEC
Confidence 334455677777777654 47899999998888888877899999988
No 117
>PRK13150 cytochrome c-type biogenesis protein CcmE; Reviewed
Probab=65.07 E-value=42 Score=25.78 Aligned_cols=63 Identities=19% Similarity=0.166 Sum_probs=46.6
Q ss_pred cceEEEEeeCCCCeeEEecCCCCccEEEEeeccccCCcccCCCCCEEEEEEeeCCCCceeEEEEEcC
Q 030905 7 SSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVGEDGRTKAVDVEAA 73 (169)
Q Consensus 7 ~~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~~~~~~l~~G~~V~F~~~~~~kGr~~A~~V~~~ 73 (169)
..|.|+|-...-..=|...|.. ..|-|+++-+... .+++|+.|.-+=.-.+++..+|.+|-.-
T Consensus 67 ~~GSv~r~~~~~~v~F~vtD~~-~~v~V~Y~GilPD---lFrEG~gVVveG~~~~~g~F~A~evLAK 129 (159)
T PRK13150 67 MPGSVRRDPDSLKVNFSLYDAE-GSVTVSYEGILPD---LFREGQGVVVQGTLEKGNHVLAHEVLAK 129 (159)
T ss_pred eCCcEEECCCCcEEEEEEEcCC-cEEEEEEeccCCc---cccCCCeEEEEEEECCCCEEEEeEEEeC
Confidence 4566665433335788888875 5899999988764 5789999988877777787889998743
No 118
>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=64.86 E-value=47 Score=25.51 Aligned_cols=52 Identities=19% Similarity=0.210 Sum_probs=37.6
Q ss_pred cccceEEEEeeCCCCeeEEecCCCCccEEEEeeccccCCc---------------ccCCCCCEEEEEEeeC
Q 030905 5 QRSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGF---------------RTLSEGQTVEFSVDVG 60 (169)
Q Consensus 5 ~~~~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~~~~---------------~~l~~G~~V~F~~~~~ 60 (169)
..+.|+|+..+. |||...-. .-+-+||.+++....+ ..++.|+.|.|.+..-
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 467899998875 78877664 4688889888764321 3578888888887643
No 119
>PRK11712 ribonuclease G; Provisional
Probab=63.40 E-value=33 Score=31.05 Aligned_cols=71 Identities=18% Similarity=0.202 Sum_probs=53.9
Q ss_pred ccccceEEEEeeCCCCeeEEecCCCCccEEEEeeccccC----------C------cccCCCCCEEEEEEeeCC---CCc
Q 030905 4 VQRSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSE----------G------FRTLSEGQTVEFSVDVGE---DGR 64 (169)
Q Consensus 4 ~~~~~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~~----------~------~~~l~~G~~V~F~~~~~~---kGr 64 (169)
...+.|+|+...+.-.=-||.-..+ +.-|+|++++... . -..|++||.|..++...+ ||.
T Consensus 39 GnIY~G~V~~v~pg~~AAFVdIG~~-k~gFL~~~d~~~~~~~~~~~~~~~~~~~~i~~~l~~Gq~iLVQV~Ke~~~~KG~ 117 (489)
T PRK11712 39 GNIYKGRVSRVLPGMQAAFVDIGLD-KAAFLHASDIVPHTECVAGEEQKQFVVRDISELVRQGQDIMVQVVKDPLGTKGA 117 (489)
T ss_pred ccEEEEEEeecCCCCceeEEeeCCC-ccEEEEhhhccchhhhcccccccccccccHHHhccCCCEEEEEEEeCCcCCCCC
Confidence 3468899999999888899998865 7999999998321 0 012889999999999874 675
Q ss_pred eeEEEEEcCCC
Q 030905 65 TKAVDVEAASR 75 (169)
Q Consensus 65 ~~A~~V~~~~g 75 (169)
....+|++++.
T Consensus 118 ~lT~~Isl~Gr 128 (489)
T PRK11712 118 RLTTDITLPSR 128 (489)
T ss_pred eEEEEEEeccc
Confidence 55667777663
No 120
>PRK06299 rpsA 30S ribosomal protein S1; Reviewed
Probab=63.22 E-value=25 Score=31.88 Aligned_cols=65 Identities=22% Similarity=0.294 Sum_probs=43.1
Q ss_pred ccccceEEEEeeCCCCeeEEecCCCCccEEEEeeccccCC-----cccCCCCCEEEEEEee-CCCCceeEEEEE
Q 030905 4 VQRSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEG-----FRTLSEGQTVEFSVDV-GEDGRTKAVDVE 71 (169)
Q Consensus 4 ~~~~~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~~~-----~~~l~~G~~V~F~~~~-~~kGr~~A~~V~ 71 (169)
...++|+|+... .||++..-..+.+.|+|++++.... ...+.+|+.|.+.+.. ++..+..+..+.
T Consensus 287 G~~v~g~V~~i~---~~G~fV~l~~~v~Glv~~sel~~~~~~~~~~~~~~~G~~v~v~V~~id~~~~~i~ls~k 357 (565)
T PRK06299 287 GSKVKGKVTNIT---DYGAFVELEEGIEGLVHVSEMSWTKKNKHPSKVVSVGQEVEVMVLEIDEEKRRISLGLK 357 (565)
T ss_pred CCEEEEEEEEEe---CCeEEEEeCCCCEEEEEHHHcCccccccCHHHhcCCCCEEEEEEEEEcCCCCEEEEehH
Confidence 456789999974 4777765444579999999986321 1347899999998654 443323444443
No 121
>PRK13165 cytochrome c-type biogenesis protein CcmE; Reviewed
Probab=62.58 E-value=47 Score=25.56 Aligned_cols=63 Identities=21% Similarity=0.204 Sum_probs=46.3
Q ss_pred cceEEEEeeCCCCeeEEecCCCCccEEEEeeccccCCcccCCCCCEEEEEEeeCCCCceeEEEEEcC
Q 030905 7 SSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVGEDGRTKAVDVEAA 73 (169)
Q Consensus 7 ~~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~~~~~~l~~G~~V~F~~~~~~kGr~~A~~V~~~ 73 (169)
..|.|+|-...-.+=|...|.. ..|.|+++-+... .+++|+.|.-+=.-.+.+..+|.+|-.-
T Consensus 67 ~~GSi~r~~~~l~v~F~vtD~~-~~v~V~Y~GilPD---lFrEG~gVVveG~~~~~g~F~A~~vLAK 129 (160)
T PRK13165 67 MPGSVQRDPNSLKVSFTLYDAG-GSVTVTYEGILPD---LFREGQGIVAQGVLEEGNHIEAKEVLAK 129 (160)
T ss_pred eCCcEEECCCCeEEEEEEEcCC-eEEEEEEcccCCc---cccCCCeEEEEEEECCCCeEEEEEEEec
Confidence 4566666323335788888764 6899999988764 5789999988877777777889988743
No 122
>PRK07899 rpsA 30S ribosomal protein S1; Reviewed
Probab=61.99 E-value=36 Score=30.70 Aligned_cols=52 Identities=25% Similarity=0.260 Sum_probs=38.6
Q ss_pred ccccceEEEEeeCCCCeeEEecCCCCccEEEEeeccccCCc----ccCCCCCEEEEEEee
Q 030905 4 VQRSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGF----RTLSEGQTVEFSVDV 59 (169)
Q Consensus 4 ~~~~~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~~~~----~~l~~G~~V~F~~~~ 59 (169)
...++|+|+... .||.+..-. +-+.|+|+++|...-. ..+++||.|++.+..
T Consensus 209 G~iv~G~V~~i~---~~G~FVdlg-gv~Glv~~Sels~~~v~~~~~~~kvGd~V~vkVl~ 264 (486)
T PRK07899 209 GQVRKGVVSSIV---NFGAFVDLG-GVDGLVHVSELSWKHIDHPSEVVEVGQEVTVEVLD 264 (486)
T ss_pred CCEEEEEEEEEE---CCeEEEEEC-CEEEEEEHHHCCCcccCCHHHhcCCCCEEEEEEEE
Confidence 456899999985 467655444 4799999999986432 246899999998664
No 123
>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=61.63 E-value=34 Score=30.53 Aligned_cols=63 Identities=19% Similarity=0.384 Sum_probs=41.0
Q ss_pred ccccceEEEEeeCCCCee-EEecCCCCccEEEEeeccccCC-----cccCCCCCEEEEEEe-eCCCCceeEEEE
Q 030905 4 VQRSSGTVKWFSAQKGFG-FIAPEDGGEDLFVHQTSIKSEG-----FRTLSEGQTVEFSVD-VGEDGRTKAVDV 70 (169)
Q Consensus 4 ~~~~~G~Vk~~~~~kGfG-FI~~~~~~~dvF~H~s~i~~~~-----~~~l~~G~~V~F~~~-~~~kGr~~A~~V 70 (169)
...++|+|+... .|| |+...+ +.+.|+|++++.... ...+.+||.|.+.+. .++..+..+..+
T Consensus 273 G~i~~g~V~~v~---~~G~fV~l~~-~v~g~v~~sels~~~~~~~~~~~~~vG~~v~v~V~~id~~~~~i~lS~ 342 (516)
T TIGR00717 273 GDKITGRVTNLT---DYGVFVEIEE-GIEGLVHVSEMSWVKKNSHPSKVVKKGDEVEVMILDIDPERRRLSLGL 342 (516)
T ss_pred CCEEEEEEEEee---CCcEEEEeCC-CCEEEEEHHHcCCccccCCHHHhccCCCEEEEEEEEEcCCCCEEEEEe
Confidence 356789999875 467 444444 478999999986421 124789999999975 344332344433
No 124
>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=61.61 E-value=40 Score=21.56 Aligned_cols=66 Identities=17% Similarity=0.238 Sum_probs=39.8
Q ss_pred ccceEEEEee-CCCCeeEEecCCCCc--cEEEEeeccccCCcccCCCCCEEEEEEeeCC---CC--ceeEEEEEc
Q 030905 6 RSSGTVKWFS-AQKGFGFIAPEDGGE--DLFVHQTSIKSEGFRTLSEGQTVEFSVDVGE---DG--RTKAVDVEA 72 (169)
Q Consensus 6 ~~~G~Vk~~~-~~kGfGFI~~~~~~~--dvF~H~s~i~~~~~~~l~~G~~V~F~~~~~~---kG--r~~A~~V~~ 72 (169)
.+.|.|..+. ..+|+-|++.+|... ++-+.-+.+.... ..|++|+.|...-.... .+ ++.|.+|..
T Consensus 3 ~v~g~v~~i~~tk~g~~~~~L~D~~~~i~~~~f~~~~~~~~-~~l~~g~~v~v~g~v~~~~~~~~~~l~v~~i~~ 76 (78)
T cd04489 3 WVEGEISNLKRPSSGHLYFTLKDEDASIRCVMWRSNARRLG-FPLEEGMEVLVRGKVSFYEPRGGYQLIVEEIEP 76 (78)
T ss_pred EEEEEEecCEECCCcEEEEEEEeCCeEEEEEEEcchhhhCC-CCCCCCCEEEEEEEEEEECCCCEEEEEEEEEEE
Confidence 3567777776 488899999876543 2323323343322 56899999988765431 23 345655543
No 125
>KOG2673 consensus Uncharacterized conserved protein, contains PSP domain [Function unknown]
Probab=60.70 E-value=4.7 Score=35.96 Aligned_cols=22 Identities=41% Similarity=0.803 Sum_probs=18.9
Q ss_pred CCCccccCcCCeecccCCCCCC
Q 030905 117 SGACFNCGRTGHIARECYSRGR 138 (169)
Q Consensus 117 ~~~C~~Cg~~GH~a~~C~~~~~ 138 (169)
-..||||+..-|..++||.+..
T Consensus 128 ~~~CFNC~g~~hsLrdC~rp~d 149 (485)
T KOG2673|consen 128 CDPCFNCGGTPHSLRDCPRPFD 149 (485)
T ss_pred CccccccCCCCCccccCCCccc
Confidence 3459999999999999998765
No 126
>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=60.53 E-value=12 Score=24.34 Aligned_cols=31 Identities=26% Similarity=0.437 Sum_probs=26.1
Q ss_pred ccCCCCCEEEEEEeeCCCCceeEEEEEcCCC
Q 030905 45 RTLSEGQTVEFSVDVGEDGRTKAVDVEAASR 75 (169)
Q Consensus 45 ~~l~~G~~V~F~~~~~~kGr~~A~~V~~~~g 75 (169)
..+.+||.|+|.|.....|...|.+|.+.+-
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 5689999999999998888767888987664
No 127
>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=60.14 E-value=21 Score=33.53 Aligned_cols=55 Identities=27% Similarity=0.278 Sum_probs=40.5
Q ss_pred ccccceEEEEeeCCCCeeEEecCCCCccEEEEeeccccCCc----ccCCCCCEEEEEEeeCC
Q 030905 4 VQRSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGF----RTLSEGQTVEFSVDVGE 61 (169)
Q Consensus 4 ~~~~~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~~~~----~~l~~G~~V~F~~~~~~ 61 (169)
...+.|+|+...+ ||.+..-..+.+-|+|+|.|...-+ ..+++||.|...+..-.
T Consensus 619 G~i~~G~V~~I~~---~GafVei~~g~~GllHiSei~~~~v~~~~~~~kvGD~V~VkVi~id 677 (684)
T TIGR03591 619 GKIYEGKVVRIMD---FGAFVEILPGKDGLVHISEIANERVEKVEDVLKEGDEVKVKVLEID 677 (684)
T ss_pred CcEEEEEEEEEeC---CEEEEEECCCcEEEEEHHHcCCCcccChhhccCCCCEEEEEEEEEC
Confidence 3568899999864 8877765555899999999965422 34688999988776543
No 128
>PRK06299 rpsA 30S ribosomal protein S1; Reviewed
Probab=59.58 E-value=42 Score=30.46 Aligned_cols=68 Identities=22% Similarity=0.277 Sum_probs=45.3
Q ss_pred ccccceEEEEeeCCCCeeEEecCCCCccEEEEeeccccCC-----cccCCCCCEEEEEEee-CCCCceeEEEEEcCC
Q 030905 4 VQRSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEG-----FRTLSEGQTVEFSVDV-GEDGRTKAVDVEAAS 74 (169)
Q Consensus 4 ~~~~~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~~~-----~~~l~~G~~V~F~~~~-~~kGr~~A~~V~~~~ 74 (169)
...+.|+|+... .||++..-...-+.|+|+++|...- ...+++||.|...+.. +...+...+.+....
T Consensus 374 G~~v~g~V~~v~---~~G~fV~l~~~v~g~i~~s~l~~~~~~~~~~~~~~~Gd~v~v~Il~vd~~~~~i~ls~k~~~ 447 (565)
T PRK06299 374 GDVVEGKVKNIT---DFGAFVGLEGGIDGLVHLSDISWDKKGEEAVELYKKGDEVEAVVLKVDVEKERISLGIKQLE 447 (565)
T ss_pred CCEEEEEEEEEe---cceEEEECCCCCEEEEEHHHcCccccccChHhhCCCCCEEEEEEEEEeCCCCEEEEEEehhh
Confidence 356889999975 4677655544589999999997421 2457899999997554 433333555555443
No 129
>COG0539 RpsA Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]
Probab=59.22 E-value=32 Score=31.50 Aligned_cols=68 Identities=19% Similarity=0.229 Sum_probs=45.8
Q ss_pred ccccceEEEEeeCCCCeeEEecCCCCccEEEEeeccccCCcc----cCCCCCEEEEEEeeC-CCCceeEEEEEcCC
Q 030905 4 VQRSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGFR----TLSEGQTVEFSVDVG-EDGRTKAVDVEAAS 74 (169)
Q Consensus 4 ~~~~~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~~~~~----~l~~G~~V~F~~~~~-~kGr~~A~~V~~~~ 74 (169)
..++.|+|+.+-+ ||.+..-..+-+=|+|+|.|...-.. .|++||.|+..+-.- +.-+..-+.+....
T Consensus 278 g~~v~G~Vt~i~~---~GafVei~~GvEGlvhvSEisw~~~~~P~evv~~Gq~V~V~Vl~id~e~rRIsL~iKq~~ 350 (541)
T COG0539 278 GDKVEGKVTNLTD---YGAFVEIEEGVEGLVHVSEISWTKKNVPSEVVKVGQEVEVKVLDIDPERRRISLGLKQLK 350 (541)
T ss_pred CCEEEEEEEEeec---CcEEEEecCCccceeechhhcccccCCHHHhcccCCEEEEEEEeeCchhceEEeeehhhh
Confidence 4578899999864 77666555557899999988665433 479999999887753 33332333444433
No 130
>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=58.77 E-value=4.9 Score=29.70 Aligned_cols=20 Identities=25% Similarity=0.627 Sum_probs=15.7
Q ss_pred CCccccccCCCCccCCCCCCC
Q 030905 149 GGGGCYNCGEEGHFARDCPNY 169 (169)
Q Consensus 149 ~~~~C~~Cg~~GH~ardCp~~ 169 (169)
....|..|+ -.||...||-+
T Consensus 105 ~~v~CR~Ck-GdH~T~~CPyK 124 (128)
T PF12353_consen 105 SKVKCRICK-GDHWTSKCPYK 124 (128)
T ss_pred ceEEeCCCC-CCcccccCCcc
Confidence 357799995 88999999853
No 131
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=58.35 E-value=19 Score=32.32 Aligned_cols=51 Identities=14% Similarity=0.084 Sum_probs=39.2
Q ss_pred ccccceEEEEeeCCCCeeEEecCCCCccEEEEeeccccCCcccCCCCCEEEEEEeeC
Q 030905 4 VQRSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVG 60 (169)
Q Consensus 4 ~~~~~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~~~~~~l~~G~~V~F~~~~~ 60 (169)
...++|+|+... + +|+|...+ +-+.|+|.+.+... ..+.+|++|.+.+..-
T Consensus 135 GeIV~G~V~ri~--~-~giiVDLg-gvea~LP~sE~ip~--E~~~~GdrIka~I~~V 185 (470)
T PRK09202 135 GEIITGVVKRVE--R-GNIIVDLG-RAEAILPRKEQIPR--ENFRPGDRVRAYVYEV 185 (470)
T ss_pred CCEEEEEEEEEe--c-CCEEEEEC-CeEEEecHHHcCCC--ccCCCCCEEEEEEEEE
Confidence 467899999997 3 35655543 46899999999654 5689999999887754
No 132
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=57.71 E-value=53 Score=30.97 Aligned_cols=58 Identities=29% Similarity=0.322 Sum_probs=42.7
Q ss_pred ccccceEEEEeeCCCCeeEEecCCCCccEEEEeeccccCCc----ccCCCCCEEEEEEeeC-CCCc
Q 030905 4 VQRSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGF----RTLSEGQTVEFSVDVG-EDGR 64 (169)
Q Consensus 4 ~~~~~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~~~~----~~l~~G~~V~F~~~~~-~kGr 64 (169)
.+.+.|+|+... -||++..-..+.+-|+|+|.|...-+ ..+++||.|.-.+..- .+++
T Consensus 622 G~v~~G~V~~I~---~fGafVei~~~~~GllhiSels~~~v~~~~~v~kvGD~V~VkV~~iD~~gr 684 (693)
T PRK11824 622 GEIYEGKVVRIV---DFGAFVEILPGKDGLVHISEIADERVEKVEDVLKEGDEVKVKVLEIDKRGR 684 (693)
T ss_pred CeEEEEEEEEEE---CCeEEEEECCCCEEEEEeeeccCccccCccceeCCCCEEEEEEEEECCCCc
Confidence 357899999986 48887775556899999999975432 3468999999877654 3353
No 133
>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=57.43 E-value=53 Score=29.32 Aligned_cols=65 Identities=23% Similarity=0.353 Sum_probs=42.8
Q ss_pred ccccceEEEEeeCCCCeeEEecCCCCccEEEEeeccccCC-----cccCCCCCEEEEEEee-CC-CCceeEEEEEc
Q 030905 4 VQRSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEG-----FRTLSEGQTVEFSVDV-GE-DGRTKAVDVEA 72 (169)
Q Consensus 4 ~~~~~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~~~-----~~~l~~G~~V~F~~~~-~~-kGr~~A~~V~~ 72 (169)
.+.++|+|+... -||+...-+.+.+.|+|+++|...- -..+++|+.|...+.. ++ +++ ....+..
T Consensus 360 G~~v~g~V~~v~---~~G~fV~l~~~v~glv~~s~ls~~~~~~~~~~~~~~G~~V~~~Vl~vd~~~~~-i~ls~K~ 431 (516)
T TIGR00717 360 GDRVTGKIKKIT---DFGAFVELEGGIDGLIHLSDISWDKDGREADHLYKKGDEIEAVVLAVDKEKKR-ISLGVKQ 431 (516)
T ss_pred CCEEEEEEEEEe---cceEEEECCCCCEEEEEHHHCcCcccCCCHhHccCCCCEEEEEEEEEeCcCCE-EEEeecc
Confidence 456789999863 5666655544589999999986321 1457899999987553 33 343 4444443
No 134
>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional
Probab=56.13 E-value=25 Score=34.06 Aligned_cols=52 Identities=29% Similarity=0.344 Sum_probs=38.3
Q ss_pred cccceEEEEeeCCCCeeEEecCCCCccEEEEeeccccCCc----ccCCCCCEEEEEEeeC
Q 030905 5 QRSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGF----RTLSEGQTVEFSVDVG 60 (169)
Q Consensus 5 ~~~~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~~~~----~~l~~G~~V~F~~~~~ 60 (169)
..++|+|+... .||++..-. +-+-|+|+|.|...-. ..+++|+.|++.+..-
T Consensus 495 ~~V~G~Vk~i~---~~G~fVdl~-Gv~Gfvp~SeiS~~~v~~~~~~~kvGq~v~vkVi~i 550 (863)
T PRK12269 495 DSVSGVVKSFT---SFGAFIDLG-GFDGLLHVNDMSWGHVARPREFVKKGQTIELKVIRL 550 (863)
T ss_pred CEEEEEEEEEe---CCcEEEEEC-CEEEEEEchhccccccCCHHHhccCCCEEEEEEEEE
Confidence 46799999886 367666554 4689999999864321 3367899999998654
No 135
>PRK07400 30S ribosomal protein S1; Reviewed
Probab=55.83 E-value=47 Score=28.12 Aligned_cols=67 Identities=15% Similarity=0.188 Sum_probs=47.3
Q ss_pred ccccceEEEEeeCCCCeeEEecCCCCccEEEEeeccccCC----cccCCCCCEEEEEEeeCC--CCceeEEEEEcCCC
Q 030905 4 VQRSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEG----FRTLSEGQTVEFSVDVGE--DGRTKAVDVEAASR 75 (169)
Q Consensus 4 ~~~~~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~~~----~~~l~~G~~V~F~~~~~~--kGr~~A~~V~~~~g 75 (169)
...+.|+|+... .||++.... +-+-|+|++.|.... ...+++||.|...+..-. +++ ....+..+..
T Consensus 197 G~vv~G~V~~I~---~~G~fV~i~-gv~Gllhisels~~~~~~~~~~~~vGd~VkvkVl~iD~e~~r-I~LS~K~l~~ 269 (318)
T PRK07400 197 GEVVVGTVRGIK---PYGAFIDIG-GVSGLLHISEISHEHIETPHSVFNVNDEMKVMIIDLDAERGR-ISLSTKQLEP 269 (318)
T ss_pred CCEEEEEEEEEE---CCeEEEEEC-CEEEEEEHHHcccccccChhhccCCCCEEEEEEEEEeCCCCE-EEEEEecccc
Confidence 356889999885 488777654 468999999997642 235799999999987653 453 5555554443
No 136
>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional
Probab=55.38 E-value=19 Score=34.85 Aligned_cols=67 Identities=16% Similarity=0.173 Sum_probs=46.1
Q ss_pred ccccceEEEEeeCCCCeeEEecCCCCccEEEEeeccccC-C----cccCCCCCEEEEEEeeC--CCCceeEEEEEcCC
Q 030905 4 VQRSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSE-G----FRTLSEGQTVEFSVDVG--EDGRTKAVDVEAAS 74 (169)
Q Consensus 4 ~~~~~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~~-~----~~~l~~G~~V~F~~~~~--~kGr~~A~~V~~~~ 74 (169)
...++|+|+... -||.+..-..+-+-|+|+|+|... . ...+++||.|++.+..- .+++ ....+..+.
T Consensus 579 G~iV~G~V~~I~---~fG~fVeL~~gveGLvhiSEls~~~~~~~p~~~~kvGd~V~vkVl~iD~e~~r-IsLS~K~l~ 652 (863)
T PRK12269 579 NDVVKGRVTKIA---DFGAFIELAEGIEGLAHISEFSWVKKTSKPSDMVKIGDEVECMILGYDIQAGR-VSLGLKQVT 652 (863)
T ss_pred CCEEEEEEEEEe---CCeEEEEecCCceeeeEHHHhcCccccCCHHHcCCCCCEEEEEEEEEecccCc-eEEEehhcc
Confidence 367899999995 488766655457899999999752 1 23589999999987763 2343 455554333
No 137
>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=54.36 E-value=50 Score=22.98 Aligned_cols=56 Identities=23% Similarity=0.060 Sum_probs=38.7
Q ss_pred ccccceEEEEeeCCCCeeEEecCCCCccEEEEeeccccC-----------------------CcccCCCCCEEEEEEeeC
Q 030905 4 VQRSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSE-----------------------GFRTLSEGQTVEFSVDVG 60 (169)
Q Consensus 4 ~~~~~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~~-----------------------~~~~l~~G~~V~F~~~~~ 60 (169)
.+.+.|+|+...+ . -=||..+. +-+-|+|++++... -...+.+||.|.+.+..-
T Consensus 4 G~vV~G~V~~v~~-~-gl~v~L~~-g~~G~v~~seis~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~vGd~V~~kVi~~ 80 (100)
T cd05693 4 GMLVLGQVKEITK-L-DLVISLPN-GLTGYVPITNISDAYTERLEELDEESEEEDDEEELPDLEDLFSVGQLVRCKVVSL 80 (100)
T ss_pred CCEEEEEEEEEcC-C-CEEEECCC-CcEEEEEHHHhhHHHHHHHHHhhhhccccccccccCCHHHhccCCCEEEEEEEEc
Confidence 4668899999743 2 23444444 47999999999652 124578999999988865
Q ss_pred CC
Q 030905 61 ED 62 (169)
Q Consensus 61 ~k 62 (169)
.+
T Consensus 81 d~ 82 (100)
T cd05693 81 DK 82 (100)
T ss_pred cC
Confidence 43
No 138
>COG2996 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only]
Probab=53.65 E-value=64 Score=27.11 Aligned_cols=49 Identities=16% Similarity=0.172 Sum_probs=36.2
Q ss_pred CeeEEecCCCCccEEEEeeccccCCccc--CCCCCEEEEEEeeCCCCceeEEE
Q 030905 19 GFGFIAPEDGGEDLFVHQTSIKSEGFRT--LSEGQTVEFSVDVGEDGRTKAVD 69 (169)
Q Consensus 19 GfGFI~~~~~~~dvF~H~s~i~~~~~~~--l~~G~~V~F~~~~~~kGr~~A~~ 69 (169)
.-|.-..-.-.+||+|-++++... +. |++|+.+.+.+..++++|..|+-
T Consensus 87 ~lGaFlD~Gl~KDl~vp~~elp~~--~~~wpq~Gd~l~v~l~~Dkk~Ri~g~~ 137 (287)
T COG2996 87 DLGAFLDWGLPKDLLVPLDELPTL--KSLWPQKGDKLLVYLYVDKKGRIWGTL 137 (287)
T ss_pred CcceEEecCCCcceeeehhhcccc--cccCCCCCCEEEEEEEEccCCcEEEEe
Confidence 344333333347999999999764 34 89999999999999999866643
No 139
>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=52.98 E-value=54 Score=20.39 Aligned_cols=54 Identities=17% Similarity=0.037 Sum_probs=33.6
Q ss_pred cccceEEEEeeCCCCeeEEecCCCCc-cEEEEeeccccCCcccCCCCCEEEEEEee
Q 030905 5 QRSSGTVKWFSAQKGFGFIAPEDGGE-DLFVHQTSIKSEGFRTLSEGQTVEFSVDV 59 (169)
Q Consensus 5 ~~~~G~Vk~~~~~kGfGFI~~~~~~~-dvF~H~s~i~~~~~~~l~~G~~V~F~~~~ 59 (169)
.+..|+|++......+=-|..+-++. .+...++.-.-.. ..|++|++|...+..
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 45899999997665554455443222 5655654422221 348899999877754
No 140
>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=52.71 E-value=17 Score=22.84 Aligned_cols=53 Identities=21% Similarity=0.146 Sum_probs=37.0
Q ss_pred ccceEEEEe-eCCCCeeEEecCCCCccEEEEeec-cccCCcccCCCCCEEEEEEe
Q 030905 6 RSSGTVKWF-SAQKGFGFIAPEDGGEDLFVHQTS-IKSEGFRTLSEGQTVEFSVD 58 (169)
Q Consensus 6 ~~~G~Vk~~-~~~kGfGFI~~~~~~~dvF~H~s~-i~~~~~~~l~~G~~V~F~~~ 58 (169)
.+.|+|..- ...+.+-|++.+|....|-+.+-. ....-...|.+|+.|...=.
T Consensus 2 ~v~G~V~~~~~~~~~~~~~~l~D~tg~i~~~~~~~~~~~~~~~l~~g~~v~v~G~ 56 (75)
T PF01336_consen 2 TVEGRVTSIRRSGGKIVFFTLEDGTGSIQVVFFNEEYERFREKLKEGDIVRVRGK 56 (75)
T ss_dssp EEEEEEEEEEEEETTEEEEEEEETTEEEEEEEETHHHHHHHHTS-TTSEEEEEEE
T ss_pred EEEEEEEEEEcCCCCEEEEEEEECCccEEEEEccHHhhHHhhcCCCCeEEEEEEE
Confidence 367888888 888999999988766656555555 22222467999999988633
No 141
>PRK08563 DNA-directed RNA polymerase subunit E'; Provisional
Probab=52.60 E-value=39 Score=26.02 Aligned_cols=52 Identities=21% Similarity=0.212 Sum_probs=37.9
Q ss_pred cccceEEEEeeCCCCeeEEecCCCCccEEEEeeccccCCc---------------ccCCCCCEEEEEEeeC
Q 030905 5 QRSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGF---------------RTLSEGQTVEFSVDVG 60 (169)
Q Consensus 5 ~~~~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~~~~---------------~~l~~G~~V~F~~~~~ 60 (169)
..+.|+|+.-+. +|++..-. .-+.|+|.+++....+ ..++.|+.|.|.+..-
T Consensus 83 EVv~g~V~~v~~---~Gi~V~lg-~~~g~v~~~~l~~~~~~~d~~~~~~~~~~~~~~i~~Gd~VrvrV~~v 149 (187)
T PRK08563 83 EVVEGEVVEVVE---FGAFVRIG-PVDGLLHISQIMDDYISYDPKNGRLIGKESKRVLKVGDVVRARIVAV 149 (187)
T ss_pred CEEEEEEEEEEc---cEEEEEEe-CceEEEEcHHcCCCceEEccccceEEEccCCeEEcCCCEEEEEEEEE
Confidence 467899999874 67666654 3789999999865421 2468899999988754
No 142
>PRK07400 30S ribosomal protein S1; Reviewed
Probab=52.35 E-value=35 Score=28.91 Aligned_cols=53 Identities=11% Similarity=-0.002 Sum_probs=38.5
Q ss_pred ccccceEEEEeeCCCCeeEEecCCCCccEEEEeeccccCCcccCCCCCEEEEEEeeC
Q 030905 4 VQRSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVG 60 (169)
Q Consensus 4 ~~~~~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~~~~~~l~~G~~V~F~~~~~ 60 (169)
...++|+|+..+. +|++..-. +-+-|+|+|.|.........+|+.|.+.+..-
T Consensus 119 ~~~V~g~V~~~~~---~G~~V~l~-Gv~gfip~s~ls~~~~~~~~vG~~i~~kVl~i 171 (318)
T PRK07400 119 DATVRSEVFATNR---GGALVRIE-GLRGFIPGSHISTRKPKEELVGEELPLKFLEV 171 (318)
T ss_pred CCEEEEEEEEEEC---CeEEEEEC-CEEEEEEHHHcCccCCccccCCCEEEEEEEEE
Confidence 3567899999873 56666554 46789999999764333345999999988753
No 143
>COG0539 RpsA Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]
Probab=51.59 E-value=49 Score=30.38 Aligned_cols=54 Identities=20% Similarity=0.247 Sum_probs=42.6
Q ss_pred ccccceEEEEeeCCCCeeEEecCCCCccEEEEeeccccCCc----ccCCCCCEEEEEEeeCC
Q 030905 4 VQRSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGF----RTLSEGQTVEFSVDVGE 61 (169)
Q Consensus 4 ~~~~~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~~~~----~~l~~G~~V~F~~~~~~ 61 (169)
...+.|+|+...+ ||-...-.+ -|=++|+|+|..... ..+++||.|.-.+..-+
T Consensus 193 G~vV~G~V~~It~---~GafVdigG-vdGLlHiseiS~~rv~~P~~vvkvGd~VkvkVi~~D 250 (541)
T COG0539 193 GEVVEGVVKNITD---YGAFVDIGG-VDGLLHISEISWKRVDHPSEVVKVGDEVKVKVISLD 250 (541)
T ss_pred CceEEEEEEEeec---CcEEEEecC-eeeEEehhhccccccCCHHHhcccCCEEEEEEEEEc
Confidence 4678899999975 887776665 799999999987643 46789999998877643
No 144
>COG1095 RPB7 DNA-directed RNA polymerase, subunit E' [Transcription]
Probab=49.94 E-value=25 Score=27.68 Aligned_cols=52 Identities=23% Similarity=0.165 Sum_probs=37.4
Q ss_pred cccceEEEEeeCCCCeeEEecCCCCccEEEEeeccccCC---------------cccCCCCCEEEEEEeeC
Q 030905 5 QRSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEG---------------FRTLSEGQTVEFSVDVG 60 (169)
Q Consensus 5 ~~~~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~~~---------------~~~l~~G~~V~F~~~~~ 60 (169)
..+.|.|+.-+ -||+-..-. ..|+|+|+|.|-+.- -+.|.+|+.|.|.|...
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 35677787765 578777665 479999999986641 12577888888888754
No 145
>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=49.75 E-value=28 Score=21.52 Aligned_cols=55 Identities=22% Similarity=0.174 Sum_probs=34.9
Q ss_pred ccccceEEEEeeCCCCeeEEecCCCCcc-EEEEeeccccCCcccCCCCCEEEEEEee
Q 030905 4 VQRSSGTVKWFSAQKGFGFIAPEDGGED-LFVHQTSIKSEGFRTLSEGQTVEFSVDV 59 (169)
Q Consensus 4 ~~~~~G~Vk~~~~~kGfGFI~~~~~~~d-vF~H~s~i~~~~~~~l~~G~~V~F~~~~ 59 (169)
.....|+|...-.....=+|+.+-++.. |...++.-.... -.|++|+.|.+.+..
T Consensus 4 ~N~l~g~V~~ie~~g~~~~v~~~~~~~~~l~a~it~~~~~~-L~L~~G~~V~~~ik~ 59 (64)
T PF03459_consen 4 RNQLPGTVESIENLGSEVEVTLDLGGGETLTARITPESAEE-LGLKPGDEVYASIKA 59 (64)
T ss_dssp SEEEEEEEEEEEESSSEEEEEEEETTSEEEEEEEEHHHHHH-CT-STT-EEEEEE-G
T ss_pred CcEEEEEEEEEEECCCeEEEEEEECCCCEEEEEEcHHHHHH-cCCCCCCEEEEEEeh
Confidence 3567899999888777777776544444 666664433322 238899999988864
No 146
>KOG2044 consensus 5'-3' exonuclease HKE1/RAT1 [Replication, recombination and repair; RNA processing and modification]
Probab=49.62 E-value=7.8 Score=36.97 Aligned_cols=22 Identities=41% Similarity=0.978 Sum_probs=19.2
Q ss_pred CCCCCccccCcCCeecccCCCC
Q 030905 115 AGSGACFNCGRTGHIARECYSR 136 (169)
Q Consensus 115 ~~~~~C~~Cg~~GH~a~~C~~~ 136 (169)
+....|+.|+++||.+.+|...
T Consensus 258 ~~~~~C~~cgq~gh~~~dc~g~ 279 (931)
T KOG2044|consen 258 NKPRRCFLCGQTGHEAKDCEGK 279 (931)
T ss_pred CCcccchhhcccCCcHhhcCCc
Confidence 4666799999999999999865
No 147
>PF04225 OapA: Opacity-associated protein A LysM-like domain; InterPro: IPR007340 This entry includes the Haemophilus influenzae opacity-associated protein. This protein is required for efficient nasopharyngeal mucosal colonization, and its expression is associated with a distinctive transparent colony phenotype. OapA is thought to be a secreted protein, and its expression exhibits high-frequency phase variation [].; PDB: 2GU1_A.
Probab=49.52 E-value=27 Score=23.72 Aligned_cols=31 Identities=35% Similarity=0.583 Sum_probs=19.2
Q ss_pred CcccCCCCCEEEEEEeeCCCCceeEEEEEcCCC
Q 030905 43 GFRTLSEGQTVEFSVDVGEDGRTKAVDVEAASR 75 (169)
Q Consensus 43 ~~~~l~~G~~V~F~~~~~~kGr~~A~~V~~~~g 75 (169)
.+..|++||.|+|.+.. .|.+.+..+.....
T Consensus 39 ~L~~L~pGq~l~f~~d~--~g~L~~L~~~~~~~ 69 (85)
T PF04225_consen 39 PLTRLKPGQTLEFQLDE--DGQLTALRYERSPK 69 (85)
T ss_dssp -GGG--TT-EEEEEE-T--TS-EEEEEEEEETT
T ss_pred hHhhCCCCCEEEEEECC--CCCEEEEEEEcCCc
Confidence 46789999999999975 47688887765443
No 148
>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=48.60 E-value=78 Score=20.98 Aligned_cols=49 Identities=22% Similarity=0.256 Sum_probs=31.4
Q ss_pred cceEEEEeeCCC-CeeEEecCCC-------CccEEEEeeccccCCcccCCCCCEEEEEEeeC
Q 030905 7 SSGTVKWFSAQK-GFGFIAPEDG-------GEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVG 60 (169)
Q Consensus 7 ~~G~Vk~~~~~k-GfGFI~~~~~-------~~dvF~H~s~i~~~~~~~l~~G~~V~F~~~~~ 60 (169)
++|.|..-.... ..||-..+.. .+-||+.... . ..|++||.|...=...
T Consensus 2 v~GvVTa~~~~~~~~GffiQd~~~d~~~~ts~gifV~~~~--~---~~~~~Gd~V~vtG~v~ 58 (78)
T cd04486 2 VEGVVTAVFSGGGLGGFYIQDEDGDGDPATSEGIFVYTGS--G---ADVAVGDLVRVTGTVT 58 (78)
T ss_pred eEEEEEEEcCCCCcCEEEEEcCCCCCCCcccceEEEecCC--C---CCCCCCCEEEEEEEEE
Confidence 567777766543 2455554432 2469998876 1 4589999999874443
No 149
>PRK06676 rpsA 30S ribosomal protein S1; Reviewed
Probab=48.50 E-value=1e+02 Score=26.43 Aligned_cols=71 Identities=24% Similarity=0.302 Sum_probs=45.6
Q ss_pred ccccceEEEEeeCCCCeeEEecCCCCccEEEEeeccccCCc----ccCCCCCEEEEEEeeCC-CCceeEEEEEcCCCcc
Q 030905 4 VQRSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGF----RTLSEGQTVEFSVDVGE-DGRTKAVDVEAASRSR 77 (169)
Q Consensus 4 ~~~~~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~~~~----~~l~~G~~V~F~~~~~~-kGr~~A~~V~~~~g~~ 77 (169)
...++|+|+...+ ||+...-+.+-+-|+|++.+..... ..+++||.|...+..-. ..+...+.+..+...|
T Consensus 278 G~~v~g~V~~i~~---~G~fV~l~~gi~Glv~~se~~~~~~~~~~~~~~~Gd~v~v~V~~id~e~~~i~ls~k~~~~~~ 353 (390)
T PRK06676 278 GDVIEGTVKRLTD---FGAFVEVLPGVEGLVHISQISHKHIATPSEVLEEGQEVKVKVLEVNEEEKRISLSIKALEEAP 353 (390)
T ss_pred CcEEEEEEEEEeC---ceEEEEECCCCeEEEEhHHcCccccCChhhccCCCCEEEEEEEEEECCCCEEEEEEEecccCh
Confidence 3568899998753 7776554444678999999865321 34789999998876543 2223455555444433
No 150
>PRK06676 rpsA 30S ribosomal protein S1; Reviewed
Probab=48.40 E-value=77 Score=27.20 Aligned_cols=56 Identities=14% Similarity=0.033 Sum_probs=39.5
Q ss_pred ccccceEEEEeeCCCCeeEEecCCCCccEEEEeeccccC----CcccCCCCCEEEEEEeeCC
Q 030905 4 VQRSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSE----GFRTLSEGQTVEFSVDVGE 61 (169)
Q Consensus 4 ~~~~~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~~----~~~~l~~G~~V~F~~~~~~ 61 (169)
.+.++|+|+..++ .+=||..+....+.|+|.+++... .-..+++|+.|++.+....
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 4678999999974 334454424456899999999652 1234789999999887653
No 151
>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=46.60 E-value=66 Score=21.60 Aligned_cols=54 Identities=17% Similarity=0.404 Sum_probs=38.5
Q ss_pred ccceEEEEeeCCCCeeEEec---CCCCccEEE-EeeccccCCcccCCCCCEEEEEEee
Q 030905 6 RSSGTVKWFSAQKGFGFIAP---EDGGEDLFV-HQTSIKSEGFRTLSEGQTVEFSVDV 59 (169)
Q Consensus 6 ~~~G~Vk~~~~~kGfGFI~~---~~~~~dvF~-H~s~i~~~~~~~l~~G~~V~F~~~~ 59 (169)
+..|.|..+.-.+|-=++.. ++...-||+ |..+..-.-++.+-+.+.++|.++-
T Consensus 32 rlrgiv~t~kcs~g~iylsi~v~pnn~~hi~ly~kk~yi~dklkeifpde~iefsiey 89 (91)
T PF06523_consen 32 RLRGIVLTIKCSNGIIYLSIKVNPNNSNHIFLYHKKNYIFDKLKEIFPDEAIEFSIEY 89 (91)
T ss_pred ceeeEEEEEEecCcEEEEEEEeCCCCcceEEEEecchhHHHHHHHhCCCCceEEEEEe
Confidence 57788888888888666542 334456774 5566555556788899999999873
No 152
>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=46.50 E-value=79 Score=23.53 Aligned_cols=56 Identities=25% Similarity=0.376 Sum_probs=36.9
Q ss_pred cceEEEEeeCCCC-----eeEEecCCCCccEEE-EeeccccCCcccCCCCCEEEEEE--eeCCCC
Q 030905 7 SSGTVKWFSAQKG-----FGFIAPEDGGEDLFV-HQTSIKSEGFRTLSEGQTVEFSV--DVGEDG 63 (169)
Q Consensus 7 ~~G~Vk~~~~~kG-----fGFI~~~~~~~dvF~-H~s~i~~~~~~~l~~G~~V~F~~--~~~~kG 63 (169)
-.|+|+.--++.- -=||.....+..|+| |--++. .-+..|++||.|+|.= +-+++|
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 348887766666664 444444 3356799999999953 344454
No 153
>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=46.47 E-value=72 Score=23.60 Aligned_cols=46 Identities=28% Similarity=0.580 Sum_probs=27.3
Q ss_pred cceEEEEeeCCCC-eeEEecCCCCccEEEEee----ccccCCcc-cCCCCCEEE
Q 030905 7 SSGTVKWFSAQKG-FGFIAPEDGGEDLFVHQT----SIKSEGFR-TLSEGQTVE 54 (169)
Q Consensus 7 ~~G~Vk~~~~~kG-fGFI~~~~~~~dvF~H~s----~i~~~~~~-~l~~G~~V~ 54 (169)
..|+|....+.+. |||.+ ++ +-+|.+|+- .|...+|. .+++||.|+
T Consensus 46 ~~G~v~~i~~T~HAi~i~s-~~-G~eiLiHiGidTv~L~G~gF~~~v~~G~~V~ 97 (132)
T PF00358_consen 46 VDGTVTMIFPTKHAIGIRS-DN-GVEILIHIGIDTVKLNGEGFETLVKEGDKVK 97 (132)
T ss_dssp SSEEEEEE-TTSSEEEEEE-TT-SEEEEEE-SBSGGGGTTTTEEESS-TTSEE-
T ss_pred eeEEEEEEcCCCCEEEEEe-CC-CCEEEEEEccchhhcCCcceEEEEeCCCEEE
Confidence 4688988876554 44444 44 379999983 35555665 455888874
No 154
>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=45.85 E-value=74 Score=23.19 Aligned_cols=46 Identities=26% Similarity=0.587 Sum_probs=27.8
Q ss_pred cceEEEEeeCC-CCeeEEecCCCCccEEEEee----ccccCCcc-cCCCCCEEE
Q 030905 7 SSGTVKWFSAQ-KGFGFIAPEDGGEDLFVHQT----SIKSEGFR-TLSEGQTVE 54 (169)
Q Consensus 7 ~~G~Vk~~~~~-kGfGFI~~~~~~~dvF~H~s----~i~~~~~~-~l~~G~~V~ 54 (169)
..|+|++..+. .-||+ +.+++ -+|.+|+- .|...+|. ..++||.|+
T Consensus 42 ~~G~v~~v~~T~HA~gi-~~~~G-~evLiHiGidTV~L~G~gF~~~v~~Gd~V~ 93 (121)
T TIGR00830 42 VDGKIGKIFPTKHAFGI-ESDSG-VEILIHIGIDTVKLNGEGFTSHVEEGQRVK 93 (121)
T ss_pred CCeEEEEEccCCCEEEE-EeCCC-cEEEEEeeeceeecCCCceEEEecCCCEEc
Confidence 36888886554 34554 44443 68999984 34444554 345666664
No 155
>KOG2673 consensus Uncharacterized conserved protein, contains PSP domain [Function unknown]
Probab=45.79 E-value=10 Score=33.85 Aligned_cols=19 Identities=47% Similarity=1.109 Sum_probs=16.4
Q ss_pred CccccccCCCCccCCCCCC
Q 030905 150 GGGCYNCGEEGHFARDCPN 168 (169)
Q Consensus 150 ~~~C~~Cg~~GH~ardCp~ 168 (169)
...||+|+..-|-.||||.
T Consensus 128 ~~~CFNC~g~~hsLrdC~r 146 (485)
T KOG2673|consen 128 CDPCFNCGGTPHSLRDCPR 146 (485)
T ss_pred CccccccCCCCCccccCCC
Confidence 3449999999999999985
No 156
>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=45.13 E-value=42 Score=28.90 Aligned_cols=52 Identities=17% Similarity=0.155 Sum_probs=38.5
Q ss_pred ccccceEEEEeeCCCCeeEEecCCCCccEEEEeeccccCCcccCCCCCEEEEEEeeC
Q 030905 4 VQRSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVG 60 (169)
Q Consensus 4 ~~~~~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~~~~~~l~~G~~V~F~~~~~ 60 (169)
...++|+|+..+. .+|=||.. ++-+.|++.+.+... ..+.+|++|.+.+..-
T Consensus 132 GeiV~G~V~~v~~-~g~v~Vdi--G~~ea~LP~~E~ip~--E~~~~Gd~ik~~V~~V 183 (341)
T TIGR01953 132 GEIISGTVKRVNR-RGNLYVEL--GKTEGILPKKEQIPG--EKFRIGDRIKAYVYEV 183 (341)
T ss_pred CCEEEEEEEEEec-CCcEEEEE--CCeEEEecHHHcCCC--cCCCCCCEEEEEEEEE
Confidence 4678999999864 34434443 456899999988754 4589999999887754
No 157
>KOG0107 consensus Alternative splicing factor SRp20/9G8 (RRM superfamily) [RNA processing and modification]
Probab=45.05 E-value=11 Score=29.57 Aligned_cols=16 Identities=56% Similarity=1.576 Sum_probs=14.3
Q ss_pred ccccCCCCccCCCCCC
Q 030905 153 CYNCGEEGHFARDCPN 168 (169)
Q Consensus 153 C~~Cg~~GH~ardCp~ 168 (169)
|+.|++.||+.+.|.+
T Consensus 103 ~~r~G~rg~~~r~~~~ 118 (195)
T KOG0107|consen 103 CYRCGERGHIGRNCKD 118 (195)
T ss_pred cccCCCcccccccccc
Confidence 8999999999999864
No 158
>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=44.83 E-value=56 Score=21.44 Aligned_cols=45 Identities=20% Similarity=0.224 Sum_probs=33.3
Q ss_pred CCCCeeEEecCCCCccEEE----EeeccccCCcccCCCCCEEEEEEeeC
Q 030905 16 AQKGFGFIAPEDGGEDLFV----HQTSIKSEGFRTLSEGQTVEFSVDVG 60 (169)
Q Consensus 16 ~~kGfGFI~~~~~~~dvF~----H~s~i~~~~~~~l~~G~~V~F~~~~~ 60 (169)
.++-|-.|.-.+++.-.+| |.+++-..+-+.|++|+.|.-++...
T Consensus 11 ~~kdfAvvSL~~t~~L~a~p~~sHLNdtfrf~seklkvG~~l~v~lk~~ 59 (69)
T cd05701 11 ADKDFAIVSLATTGDLAAFPTRSHLNDTFRFDSEKLSVGQCLDVTLKDP 59 (69)
T ss_pred hhhceEEEEeeccccEEEEEchhhccccccccceeeeccceEEEEEecC
Confidence 3578888988888776776 45555555557899999998877654
No 159
>PRK03987 translation initiation factor IF-2 subunit alpha; Validated
Probab=44.74 E-value=50 Score=27.29 Aligned_cols=64 Identities=27% Similarity=0.328 Sum_probs=43.7
Q ss_pred ccccceEEEEeeCCCCeeEEecCC--CCccEEEEeeccccCCc----ccCCCCCEEEEEEeeCC--CCceeEEEEE
Q 030905 4 VQRSSGTVKWFSAQKGFGFIAPED--GGEDLFVHQTSIKSEGF----RTLSEGQTVEFSVDVGE--DGRTKAVDVE 71 (169)
Q Consensus 4 ~~~~~G~Vk~~~~~kGfGFI~~~~--~~~dvF~H~s~i~~~~~----~~l~~G~~V~F~~~~~~--kGr~~A~~V~ 71 (169)
...+.|+|+... .||++..-. .+.+-|+|+|.|...-+ ..+++||.|.+.+..-. ++ ...+.+.
T Consensus 9 GdiV~G~V~~I~---~~G~fV~L~e~~gieGlI~iSEls~~~i~~i~~~~kvGd~V~vkVi~VD~~k~-~I~LSlK 80 (262)
T PRK03987 9 GELVVGTVKEVK---DFGAFVTLDEYPGKEGFIHISEVASGWVKNIRDHVKEGQKVVCKVIRVDPRKG-HIDLSLK 80 (262)
T ss_pred CCEEEEEEEEEE---CCEEEEEECCCCCcEEEEEHHHcCcccccCHHHhCCCCCEEEEEEEEEecccC-eEEEEEE
Confidence 356789999885 477666543 24789999999975432 34789999999987654 34 2444444
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=44.65 E-value=57 Score=30.43 Aligned_cols=53 Identities=19% Similarity=0.392 Sum_probs=37.1
Q ss_pred cccceEEEEeeCCCCeeE-EecCCCCccEEEEeeccccCCc---------------ccCCCCCEEEEEEeeC
Q 030905 5 QRSSGTVKWFSAQKGFGF-IAPEDGGEDLFVHQTSIKSEGF---------------RTLSEGQTVEFSVDVG 60 (169)
Q Consensus 5 ~~~~G~Vk~~~~~kGfGF-I~~~~~~~dvF~H~s~i~~~~~---------------~~l~~G~~V~F~~~~~ 60 (169)
..+.|+|+.... ||| |..++...+-|+|+++|....| ..++.||.|...+..-
T Consensus 574 ~~~~g~I~~v~~---~GifV~L~~~~veGlV~~s~l~~d~y~~d~~~~~l~g~~~~~~~~lGD~V~Vki~~v 642 (654)
T TIGR00358 574 TEFSGEISSVTR---FGMFVRLDDNGIDGLIHISTLHNDYYVFDQEKMALIGKGTGKVYRIGDRVTVKLTEV 642 (654)
T ss_pred cEEEEEEEeEEc---CcEEEEecCCceEEEEEeEeCCCcceEEeccccEEEeccCCcEECCCCEEEEEEEEE
Confidence 457899998754 665 5556566899999999965321 3467788888777654
No 161
>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=44.40 E-value=33 Score=23.11 Aligned_cols=51 Identities=18% Similarity=0.262 Sum_probs=28.0
Q ss_pred ccceEEEEeeCCCCeeEEecC---CCCccEEEEeeccccCCcccCCCCCEEEEE
Q 030905 6 RSSGTVKWFSAQKGFGFIAPE---DGGEDLFVHQTSIKSEGFRTLSEGQTVEFS 56 (169)
Q Consensus 6 ~~~G~Vk~~~~~kGfGFI~~~---~~~~dvF~H~s~i~~~~~~~l~~G~~V~F~ 56 (169)
...|+|........+|-+..- ++-.-+|.|++.+.-.--..++.||.+-..
T Consensus 19 ~~~G~V~~~~~~~~~g~~V~i~~~~g~~~~y~~l~~~~v~~G~~V~~G~~IG~~ 72 (96)
T PF01551_consen 19 PADGKVVFVGEDPGYGNYVIIQHGNGYITVYGHLDSVSVKVGDRVKAGQVIGTV 72 (96)
T ss_dssp SSSEEEEEEEEETTTEEEEEEEETTSEEEEEEEESEESS-TTSEE-TTCEEEEE
T ss_pred CccEEEEEEEeccCCccEEEEEeCCcCCEEEeccccccceecccccCCCEEEec
Confidence 467999998887676755442 223456777766542211334444444433
No 162
>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=44.06 E-value=82 Score=23.05 Aligned_cols=46 Identities=28% Similarity=0.548 Sum_probs=27.3
Q ss_pred cceEEEEeeCCC-CeeEEecCCCCccEEEEeec----cccCCcc-cCCCCCEEE
Q 030905 7 SSGTVKWFSAQK-GFGFIAPEDGGEDLFVHQTS----IKSEGFR-TLSEGQTVE 54 (169)
Q Consensus 7 ~~G~Vk~~~~~k-GfGFI~~~~~~~dvF~H~s~----i~~~~~~-~l~~G~~V~ 54 (169)
..|+|+...+.+ -|++- .+++ -+|++|+.- |...+|. .+++||.|+
T Consensus 42 ~~G~v~~i~~T~HA~~i~-~~~G-~eiLiHiGidTv~l~g~gF~~~vk~Gd~V~ 93 (124)
T cd00210 42 VDGTIVQIFPTKHAIGIE-SDSG-VEILIHIGIDTVKLNGEGFTSHVEEGQRVK 93 (124)
T ss_pred CCeEEEEEccCCCEEEEE-eCCC-cEEEEEeeeeeeecCCCceEEEecCCCEEc
Confidence 368888865543 44444 4443 689999843 3444443 345666664
No 163
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=43.37 E-value=41 Score=29.21 Aligned_cols=51 Identities=12% Similarity=0.017 Sum_probs=37.1
Q ss_pred ccccceEEEEeeCCCCeeEEecCCCCccEEEEeeccccCCcccCCCCCEEEEEEeeC
Q 030905 4 VQRSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVG 60 (169)
Q Consensus 4 ~~~~~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~~~~~~l~~G~~V~F~~~~~ 60 (169)
...++|+|+..+. + +++... ++-+-|++.+++... ..+++|++|.+.+..-
T Consensus 135 GeiV~G~V~~~~~--~-~~~Vdl-g~vEa~LP~~E~ip~--e~~~~Gd~Ika~V~~V 185 (362)
T PRK12327 135 GDIVTGVVQRRDN--R-FVYVNL-GKIEAVLPPAEQIPG--ETYKHGDRIKVYVVKV 185 (362)
T ss_pred CCEEEEEEEEEeC--C-cEEEEe-CCeEEEecHHHcCCC--CCCCCCCEEEEEEEEE
Confidence 4678999999864 3 444433 336889998887654 5689999999887754
No 164
>PRK00087 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed
Probab=43.12 E-value=88 Score=29.13 Aligned_cols=61 Identities=16% Similarity=0.122 Sum_probs=41.0
Q ss_pred ccccceEEEEeeCCCCeeEEecCCCCccEEEEeeccccCC----cccCCCCCEEEEEEee--CCCCceeE
Q 030905 4 VQRSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEG----FRTLSEGQTVEFSVDV--GEDGRTKA 67 (169)
Q Consensus 4 ~~~~~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~~~----~~~l~~G~~V~F~~~~--~~kGr~~A 67 (169)
.+.++|+|+..+.. +=||.. ...-+-|++.+++.... ...+++|+.|++.+.. ..++++.+
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 GDIVKGTVVSVNEN--EVFVDV-GYKSEGVIPLRELTLDEISSLKESVKVGDEIEVKVLKLEDEDGYVVL 369 (647)
T ss_pred CCEEEEEEEEEECC--EEEEEE-CCCeEEEEEHHHhcccccCChhhccCCCCEEEEEEEEEECCCCcEEE
Confidence 46788999999752 223433 33357899999887432 2457899999998876 45665433
No 165
>PRK13159 cytochrome c-type biogenesis protein CcmE; Reviewed
Probab=42.87 E-value=1.5e+02 Score=22.72 Aligned_cols=63 Identities=19% Similarity=0.196 Sum_probs=45.6
Q ss_pred ccceEEEEeeCCCCeeEEecCCCCccEEEEeeccccCCcccCCCCCEEEEEEeeCCCCceeEEEEEcC
Q 030905 6 RSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVGEDGRTKAVDVEAA 73 (169)
Q Consensus 6 ~~~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~~~~~~l~~G~~V~F~~~~~~kGr~~A~~V~~~ 73 (169)
...|.|+|-...-..=|...|.. ..|=|+++-|..+ .+++|+.|.-+=.-. +|..+|.+|-.-
T Consensus 60 V~~GSv~r~~~~~~v~F~vtD~~-~~v~V~Y~GilPD---lFrEGqgVVaeG~~~-~g~F~A~~vLAK 122 (155)
T PRK13159 60 VKAGSIQRAADSLKVSFTVIDKN-AATQVEYTGILPD---LFRDNQSVIANGRMQ-GGRFVANEVLAK 122 (155)
T ss_pred EecCcEEEcCCCcEEEEEEEcCC-cEEEEEEccCCCc---cccCCCeEEEEEEEc-CCEEEEeEEEec
Confidence 35677777444446788888764 6899999988654 468999998776655 477889988743
No 166
>KOG4246 consensus Predicted DNA-binding protein, contains SAP domain [General function prediction only]
Probab=42.27 E-value=2.9 Score=39.92 Aligned_cols=63 Identities=19% Similarity=0.302 Sum_probs=43.8
Q ss_pred cccceEEEEeeCCCCeeEEecCCCCccEEEEeeccccCCcccCCCCCEEEEEEeeCC--CCceeEEEEEcCCCcc
Q 030905 5 QRSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVGE--DGRTKAVDVEAASRSR 77 (169)
Q Consensus 5 ~~~~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~~~~~~l~~G~~V~F~~~~~~--kGr~~A~~V~~~~g~~ 77 (169)
.++.|+|...-. -||||. +||||..+.|+.. .+.+|++|.-+..-.+ --+|.|..|+.++++.
T Consensus 147 R~f~gvvtk~~D--tygfVD-----~dvffQls~~~g~---hp~vgD~V~vea~Ynpsmpfkwnaqriq~l~~~~ 211 (1194)
T KOG4246|consen 147 RRFAGVVTKQTD--TYGFVD-----QDVFFQLSKMQGL---HPSVGDAVNVEADYNPSMPFKWNAQRIQHLGGRL 211 (1194)
T ss_pred eeeehhhhhhcc--cccccc-----HHHHHHHHHHhcC---CCccccceeeecccCCCCCccccHHHHHhccccc
Confidence 356676666543 699996 6899999999874 5899999876655332 2346777777665543
No 167
>KOG0407 consensus 40S ribosomal protein S14 [Translation, ribosomal structure and biogenesis]
Probab=41.71 E-value=30 Score=25.12 Aligned_cols=42 Identities=24% Similarity=0.281 Sum_probs=28.1
Q ss_pred CCeeEEecCCCCccEEEEeeccccCC-cccCCCCCEEEEEEee
Q 030905 18 KGFGFIAPEDGGEDLFVHQTSIKSEG-FRTLSEGQTVEFSVDV 59 (169)
Q Consensus 18 kGfGFI~~~~~~~dvF~H~s~i~~~~-~~~l~~G~~V~F~~~~ 59 (169)
.=||....-..-.|-|||+.+|.... +..+.-|.+|.-+-.+
T Consensus 14 ~vfgvahi~asfndtfvhitdlsg~eti~rvtggmkvkadrde 56 (139)
T KOG0407|consen 14 QVFGVAHIFASFNDTFVHVTDLSGKETIVRVTGGMKVKADRDE 56 (139)
T ss_pred eeeeEEEEEeecccceEEEeccCCceEEEEecCCeEEeccccc
Confidence 34555555455679999999998763 3456678888765443
No 168
>PRK13254 cytochrome c-type biogenesis protein CcmE; Reviewed
Probab=40.19 E-value=1.6e+02 Score=22.20 Aligned_cols=60 Identities=23% Similarity=0.208 Sum_probs=44.4
Q ss_pred eEEEEeeCCCCeeEEecCCCCccEEEEeeccccCCcccCCCCCEEEEEEeeCCCCceeEEEEEcC
Q 030905 9 GTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVGEDGRTKAVDVEAA 73 (169)
Q Consensus 9 G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~~~~~~l~~G~~V~F~~~~~~kGr~~A~~V~~~ 73 (169)
|.|.+- ....+=|...|.. ..|=|++..+... .+++|+.|.-+=.-..+|...|.+|..-
T Consensus 63 gSi~~~-~~~~~~F~ltD~~-~~i~V~Y~G~lPd---~F~eg~~VVv~G~~~~~g~F~A~~vLaK 122 (148)
T PRK13254 63 GSVQRG-DGLTVRFVVTDGN-ATVPVVYTGILPD---LFREGQGVVAEGRLQDGGVFVADEVLAK 122 (148)
T ss_pred CcEEeC-CCCEEEEEEEeCC-eEEEEEECCCCCc---cccCCCEEEEEEEECCCCeEEEEEEEec
Confidence 444443 5567889888874 7899999887754 4679999988777776777899988753
No 169
>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=40.18 E-value=1e+02 Score=19.99 Aligned_cols=56 Identities=14% Similarity=0.031 Sum_probs=39.1
Q ss_pred ccccceEEEEeeCCCCeeEEecCCCCccEEEEeeccccCC----cccCCCCCEEEEEEeeCCC
Q 030905 4 VQRSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEG----FRTLSEGQTVEFSVDVGED 62 (169)
Q Consensus 4 ~~~~~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~~~----~~~l~~G~~V~F~~~~~~k 62 (169)
...+.|+|..... ..-++... ...+-|+|++++.... ...+++||.|.+.+..-.+
T Consensus 7 GdiV~G~V~~v~~--~~~~V~i~-~~~~g~l~~~~~~~~~~~~~~~~~~~GD~i~~~V~~~~~ 66 (82)
T cd04454 7 GDIVIGIVTEVNS--RFWKVDIL-SRGTARLEDSSATEKDKKEIRKSLQPGDLILAKVISLGD 66 (82)
T ss_pred CCEEEEEEEEEcC--CEEEEEeC-CCceEEeechhccCcchHHHHhcCCCCCEEEEEEEEeCC
Confidence 3457889988853 33345543 3478999999996532 2348999999999887554
No 170
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]
Probab=40.00 E-value=14 Score=33.41 Aligned_cols=20 Identities=35% Similarity=0.833 Sum_probs=17.9
Q ss_pred CCCccccCcCCeecccCCCC
Q 030905 117 SGACFNCGRTGHIARECYSR 136 (169)
Q Consensus 117 ~~~C~~Cg~~GH~a~~C~~~ 136 (169)
...|+.|+..+|++.+|+..
T Consensus 285 ~n~c~~cg~~gH~~~dc~~~ 304 (554)
T KOG0119|consen 285 TNVCKICGPLGHISIDCKVN 304 (554)
T ss_pred cccccccCCcccccccCCCc
Confidence 33899999999999999976
No 171
>KOG3070 consensus Predicted RNA-binding protein containing PIN domain and invovled in translation or RNA processing [Translation, ribosomal structure and biogenesis]
Probab=39.65 E-value=1.9e+02 Score=23.53 Aligned_cols=54 Identities=11% Similarity=-0.064 Sum_probs=33.6
Q ss_pred eEEEEeeCCCCeeEEecCCCCccEEEEeeccccCC---cccCCCCCEEEEEEeeCCCC
Q 030905 9 GTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEG---FRTLSEGQTVEFSVDVGEDG 63 (169)
Q Consensus 9 G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~~~---~~~l~~G~~V~F~~~~~~kG 63 (169)
|-|..=|....+-++.+.... ++++|...+...+ .-.+.++..+++.+.....+
T Consensus 71 gFi~~~d~~~D~fvhQs~i~~-~~~~~~~rs~~~~e~v~f~~~~~~~g~~a~~vt~p~ 127 (235)
T KOG3070|consen 71 GFITRDDGPEDVFVHQSAITK-YTPSEGFRSLKEGEAVPFDIQEGNKGTEAANVTGPD 127 (235)
T ss_pred ceecccCCCCceeEEeeeecc-cccccchhhcccCCCccceecccCccceeeeecCCC
Confidence 334444667778888888776 8888876655543 12355666666776665433
No 172
>KOG3262 consensus H/ACA small nucleolar RNP component GAR1 [Translation, ribosomal structure and biogenesis]
Probab=38.97 E-value=1.3e+02 Score=23.90 Aligned_cols=8 Identities=13% Similarity=0.522 Sum_probs=4.2
Q ss_pred cCCCCCEE
Q 030905 46 TLSEGQTV 53 (169)
Q Consensus 46 ~l~~G~~V 53 (169)
+.+++|++
T Consensus 118 sfk~g~k~ 125 (215)
T KOG3262|consen 118 SFKPGDKL 125 (215)
T ss_pred cccCCCeE
Confidence 44555554
No 173
>PRK00087 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed
Probab=38.94 E-value=1.6e+02 Score=27.50 Aligned_cols=67 Identities=22% Similarity=0.300 Sum_probs=44.7
Q ss_pred cccceEEEEeeCCCCeeEEecCCCCccEEEEeeccccCCc----ccCCCCCEEEEEEeeCC--CCceeEEEEEcCCC
Q 030905 5 QRSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGF----RTLSEGQTVEFSVDVGE--DGRTKAVDVEAASR 75 (169)
Q Consensus 5 ~~~~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~~~~----~~l~~G~~V~F~~~~~~--kGr~~A~~V~~~~g 75 (169)
..++|+|+...+ ||++..-..+-+-|+|++++...-. ..+++||.|+..+..-. +++ ....+..+..
T Consensus 564 ~~v~g~V~~i~~---~G~fV~l~~~i~Gli~~sel~~~~~~~~~~~~kvGd~V~vkV~~id~e~~r-I~lslk~~~~ 636 (647)
T PRK00087 564 SIVLGKVVRIAP---FGAFVELEPGVDGLVHISQISWKRIDKPEDVLSEGEEVKAKILEVDPEEKR-IRLSIKEVEE 636 (647)
T ss_pred eEEEEEEEEEEC---CeEEEEECCCCEEEEEhhhcCccccCCHhhcCCCCCEEEEEEEEEeCCCCE-EEEEEeeccc
Confidence 457889998864 6765554445789999999875421 35799999998876543 443 4445554443
No 174
>COG2183 Tex Transcriptional accessory protein [Transcription]
Probab=36.69 E-value=95 Score=29.79 Aligned_cols=72 Identities=17% Similarity=0.151 Sum_probs=49.7
Q ss_pred ccccceEEEEeeCCCCeeEEecCCCCccEEEEeeccccCC----cccCCCCCEEEEEEeeCC-CCceeEEEEEcCCCccc
Q 030905 4 VQRSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEG----FRTLSEGQTVEFSVDVGE-DGRTKAVDVEAASRSRR 78 (169)
Q Consensus 4 ~~~~~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~~~----~~~l~~G~~V~F~~~~~~-kGr~~A~~V~~~~g~~~ 78 (169)
.|.+.|+|...- -||-+..-+-.+|.+||+|.+...- ...+++||.|+-.+..-. +-+..+......+.+..
T Consensus 659 Gm~leg~Vrnv~---~fgafVdIgv~qDglvHis~ls~~fv~~P~~vv~vGdiV~v~V~~vD~~r~rI~Lsmr~~~~~~~ 735 (780)
T COG2183 659 GMILEGTVRNVV---DFGAFVDIGVHQDGLVHISQLSDKFVKDPNEVVKVGDIVKVKVIEVDTARKRIALSMRLDEEEGK 735 (780)
T ss_pred CCEEEEEEEEee---eccceEEeccccceeeeHHHhhhhhcCChHHhcccCCEEEEEEEEEecccCeeeeEeeccCCccc
Confidence 577899999874 5776666666689999999998732 356789999997766532 22235666665555444
No 175
>KOG0105 consensus Alternative splicing factor ASF/SF2 (RRM superfamily) [RNA processing and modification]
Probab=36.66 E-value=24 Score=28.17 Aligned_cols=32 Identities=25% Similarity=0.179 Sum_probs=18.3
Q ss_pred CccEEEEeeccccCCcc---cCCCCCEEEEEEeeC
Q 030905 29 GEDLFVHQTSIKSEGFR---TLSEGQTVEFSVDVG 60 (169)
Q Consensus 29 ~~dvF~H~s~i~~~~~~---~l~~G~~V~F~~~~~ 60 (169)
-+|||..+..|....++ .|.+=.-|+|+-..+
T Consensus 23 ieDlFyKyg~i~~ieLK~r~g~ppfafVeFEd~RD 57 (241)
T KOG0105|consen 23 IEDLFYKYGRIREIELKNRPGPPPFAFVEFEDPRD 57 (241)
T ss_pred HHHHHhhhcceEEEEeccCCCCCCeeEEEecCccc
Confidence 36888777666554332 233445677765544
No 176
>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=36.60 E-value=77 Score=29.83 Aligned_cols=53 Identities=19% Similarity=0.377 Sum_probs=36.6
Q ss_pred cccceEEEEeeCCCCeeEEec-CCCCccEEEEeeccccCCc---------------ccCCCCCEEEEEEeeC
Q 030905 5 QRSSGTVKWFSAQKGFGFIAP-EDGGEDLFVHQTSIKSEGF---------------RTLSEGQTVEFSVDVG 60 (169)
Q Consensus 5 ~~~~G~Vk~~~~~kGfGFI~~-~~~~~dvF~H~s~i~~~~~---------------~~l~~G~~V~F~~~~~ 60 (169)
..+.|+|+... .||+... ++...+-++|+++|...-+ ..++.||.|...+..-
T Consensus 629 ~~~~g~V~~v~---~fGifV~L~~~~~eGlvhis~l~~d~~~~d~~~~~l~g~~~~~~~~lGd~V~Vkv~~v 697 (709)
T TIGR02063 629 EEFEGVISGVT---SFGLFVELENNTIEGLVHISTLKDDYYVFDEKGLALVGERTGKVFRLGDRVKVRVVKA 697 (709)
T ss_pred cEEEEEEEEEE---eCCEEEEecCCceEEEEEeeecCCCcEEEcccceEEEeccCCcEECCCCEEEEEEEEE
Confidence 46789998875 4787444 4424789999999974321 3467888888777654
No 177
>PRK11642 exoribonuclease R; Provisional
Probab=35.38 E-value=1.5e+02 Score=28.63 Aligned_cols=54 Identities=28% Similarity=0.329 Sum_probs=38.8
Q ss_pred ccccceEEEEeeCCCCeeEEec-CCCCccEEEEeeccccCC---------------cccCCCCCEEEEEEeeC
Q 030905 4 VQRSSGTVKWFSAQKGFGFIAP-EDGGEDLFVHQTSIKSEG---------------FRTLSEGQTVEFSVDVG 60 (169)
Q Consensus 4 ~~~~~G~Vk~~~~~kGfGFI~~-~~~~~dvF~H~s~i~~~~---------------~~~l~~G~~V~F~~~~~ 60 (169)
...+.|+|+... .|||+.. ++...+-|+|+++|...- -..++.||.|...|..-
T Consensus 644 Ge~f~G~Is~V~---~fGifVeL~~~~vEGlV~vs~L~~d~y~~d~~~~~L~g~~~~~~~~lGD~V~VkV~~v 713 (813)
T PRK11642 644 GNVFKGVISSVT---GFGFFVRLDDLFIDGLVHVSSLDNDYYRFDQVGQRLIGESSGQTYRLGDRVEVRVEAV 713 (813)
T ss_pred CcEEEEEEEEee---cCceEEEECCCCeeeeEEEeecCCcceEecchheEEecccCCcEECCCCEEEEEEEEe
Confidence 356789999874 4776654 455579999999986431 14578999999999654
No 178
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=34.14 E-value=99 Score=29.25 Aligned_cols=59 Identities=29% Similarity=0.328 Sum_probs=44.0
Q ss_pred ccccceEEEEeeCCCCeeEEecCCCCccEEEEeeccccCC----cccCCCCCEEEEEEee-CCCCce
Q 030905 4 VQRSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEG----FRTLSEGQTVEFSVDV-GEDGRT 65 (169)
Q Consensus 4 ~~~~~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~~~----~~~l~~G~~V~F~~~~-~~kGr~ 65 (169)
...+.|+|+.-.. ||-...--.++|-++|+|.+...- -..|++||.|.-.+.. +++|+.
T Consensus 620 g~iy~G~V~ri~~---fGaFv~l~~gkdgl~hiS~~~~~rv~kv~dvlk~Gd~v~Vkv~~iD~~Gri 683 (692)
T COG1185 620 GEVYEGTVVRIVD---FGAFVELLPGKDGLVHISQLAKERVEKVEDVLKEGDEVKVKVIEIDKQGRI 683 (692)
T ss_pred ccEEEEEEEEEee---cceEEEecCCcceeEEehhhhhhhhhcccceeecCceEEEEEeeecccCCc
Confidence 4678999999876 886665555689999999997641 1468899999877665 456763
No 179
>COG1545 Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]
Probab=33.53 E-value=2e+02 Score=21.31 Aligned_cols=37 Identities=16% Similarity=0.223 Sum_probs=27.8
Q ss_pred eeEEecCCCCccEEEEeeccccCCcccCCCCCEEEEEEeeC
Q 030905 20 FGFIAPEDGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVG 60 (169)
Q Consensus 20 fGFI~~~~~~~dvF~H~s~i~~~~~~~l~~G~~V~F~~~~~ 60 (169)
.+.|..+++. .|+.|+.+ .. ...+++|++|+-.+..-
T Consensus 87 iaiV~l~~~~-~i~~~i~~-~~--p~~v~iGm~V~~v~~~~ 123 (140)
T COG1545 87 IAIVELEEGG-RILGQLVD-VD--PDDVEIGMKVEAVFRKR 123 (140)
T ss_pred EEEEEeCCCC-ceEEEEEe-cC--cccccCCCEEEEEEEEc
Confidence 5667777664 89999998 22 25689999999888753
No 180
>COG0557 VacB Exoribonuclease R [Transcription]
Probab=33.37 E-value=1.1e+02 Score=28.96 Aligned_cols=60 Identities=30% Similarity=0.554 Sum_probs=40.4
Q ss_pred ceEEEEeeCCCCeeEEecCC--CCccEEEEeeccccCCcccCCCCCEEEEEEeeC-CCCc-eeEEEEEcCC
Q 030905 8 SGTVKWFSAQKGFGFIAPED--GGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVG-EDGR-TKAVDVEAAS 74 (169)
Q Consensus 8 ~G~Vk~~~~~kGfGFI~~~~--~~~dvF~H~s~i~~~~~~~l~~G~~V~F~~~~~-~kGr-~~A~~V~~~~ 74 (169)
.+++.+ ..+||+|+.+++ ...||||-...+.. ...|+.|..++... ++++ ..|.=|..+.
T Consensus 71 ~~~~~~--~~~gf~f~~~~~~~~~~d~~v~~~~~~~-----a~~gD~V~v~~~~~~~~~~~~~~~v~~il~ 134 (706)
T COG0557 71 EGIVEA--SAKGFGFLSPDDSKDADDIFVPKDPLNR-----ALHGDRVLVELLPSDKRGRFKEAAVVRILE 134 (706)
T ss_pred cceEEe--ccCCceeeccCccCCCCcEEeccccccc-----cccCCEEEEEECcccccCCCceEEEEeeec
Confidence 444443 368999999998 56799999888544 46899999986544 3442 3444444333
No 181
>COG5569 Uncharacterized conserved protein [Function unknown]
Probab=33.12 E-value=58 Score=23.18 Aligned_cols=26 Identities=31% Similarity=0.510 Sum_probs=18.2
Q ss_pred cccCCCCCEEEEEEeeCCCCceeEEEE
Q 030905 44 FRTLSEGQTVEFSVDVGEDGRTKAVDV 70 (169)
Q Consensus 44 ~~~l~~G~~V~F~~~~~~kGr~~A~~V 70 (169)
+..|++|+.|+|..++- +|++.-.+|
T Consensus 81 lsglKeGdkV~fvferv-~gk~tv~qv 106 (108)
T COG5569 81 LSGLKEGDKVEFVFERV-NGKLTVQQV 106 (108)
T ss_pred hhccccCCcEEEEEEee-CCEEEEEEe
Confidence 45689999999988874 454544444
No 182
>KOG3794 consensus CBF1-interacting corepressor CIR and related proteins [Transcription]
Probab=32.74 E-value=18 Score=31.80 Aligned_cols=19 Identities=37% Similarity=0.950 Sum_probs=13.6
Q ss_pred CCccccccCCCCccC--CCCC
Q 030905 149 GGGGCYNCGEEGHFA--RDCP 167 (169)
Q Consensus 149 ~~~~C~~Cg~~GH~a--rdCp 167 (169)
+.+.|++|++-||+. ++||
T Consensus 123 RNVrC~kChkwGH~n~DreCp 143 (453)
T KOG3794|consen 123 RNVRCLKCHKWGHINTDRECP 143 (453)
T ss_pred eeeeEEeecccccccCCccCc
Confidence 467788888888875 4676
No 183
>PTZ00162 DNA-directed RNA polymerase II subunit 7; Provisional
Probab=31.85 E-value=1e+02 Score=23.83 Aligned_cols=34 Identities=21% Similarity=0.256 Sum_probs=25.9
Q ss_pred ccccceEEEEeeCCCCeeEEecCCCCccEEEEeecccc
Q 030905 4 VQRSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKS 41 (169)
Q Consensus 4 ~~~~~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~ 41 (169)
.+.+.|+|+.-+. +||...-.. -|||+|.+.|..
T Consensus 82 gEVv~g~V~~v~~---~G~~v~~Gp-~~ifI~~~~l~~ 115 (176)
T PTZ00162 82 DEVLDAIVTDVNK---LGFFAQAGP-LKAFVSRSAIPP 115 (176)
T ss_pred CCEEEEEEEEEec---ceEEEEeeC-eEEEEcHHHCCC
Confidence 3567899999876 677777653 569999999864
No 184
>PF13742 tRNA_anti_2: OB-fold nucleic acid binding domain
Probab=31.45 E-value=1.8e+02 Score=20.05 Aligned_cols=61 Identities=13% Similarity=0.151 Sum_probs=38.5
Q ss_pred ccccceEEEEeeC-CCCeeEEecCCCCccEEE--EeeccccCCcccCCCCCEEEEEEeeC---CCCc
Q 030905 4 VQRSSGTVKWFSA-QKGFGFIAPEDGGEDLFV--HQTSIKSEGFRTLSEGQTVEFSVDVG---EDGR 64 (169)
Q Consensus 4 ~~~~~G~Vk~~~~-~kGfGFI~~~~~~~dvF~--H~s~i~~~~~~~l~~G~~V~F~~~~~---~kGr 64 (169)
...+.|.|..++. .+|.=|.+--|....|-. -.+.+..-.-..|++|++|......+ +.|+
T Consensus 23 ~vwV~GEIs~~~~~~~gh~YftLkD~~a~i~~~~~~~~~~~i~~~~l~~G~~V~v~g~~~~y~~~G~ 89 (99)
T PF13742_consen 23 NVWVEGEISNLKRHSSGHVYFTLKDEEASISCVIFRSRARRIRGFDLKDGDKVLVRGRVSFYEPRGS 89 (99)
T ss_pred CEEEEEEEeecEECCCceEEEEEEcCCcEEEEEEEHHHHhhCCCCCCCCCCEEEEEEEEEEECCCcE
Confidence 4567899999998 888888887654332222 22222221103589999999877654 5664
No 185
>CHL00010 infA translation initiation factor 1
Probab=31.27 E-value=1.6e+02 Score=19.53 Aligned_cols=55 Identities=11% Similarity=0.026 Sum_probs=33.2
Q ss_pred ccccceEEEEeeCCCCeeEEecCCCCccEEEEeeccccCCcccCCCCCEEEEEEeeC
Q 030905 4 VQRSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVG 60 (169)
Q Consensus 4 ~~~~~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~~~~~~l~~G~~V~F~~~~~ 60 (169)
...++|+|..--. .+|=.|..+++ +.+-.|+.-.-......|.+||.|.|++...
T Consensus 6 ~~~~~G~Vik~lg-~~~y~V~~~~g-~~~~c~~rGklr~~~i~~~vGD~V~ve~~~~ 60 (78)
T CHL00010 6 KIEMEGLVTESLP-NGMFRVRLDNG-CQVLGYISGKIRRNSIRILPGDRVKVELSPY 60 (78)
T ss_pred eEEEEEEEEEEcC-CCEEEEEeCCC-CEEEEEeccceecCCcccCCCCEEEEEEccc
Confidence 4457888887643 34445555544 5566676543222123478999999996443
No 186
>KOG0341 consensus DEAD-box protein abstrakt [RNA processing and modification]
Probab=31.13 E-value=27 Score=31.18 Aligned_cols=20 Identities=50% Similarity=1.110 Sum_probs=17.8
Q ss_pred CCccccccCCCCccCCCCCC
Q 030905 149 GGGGCYNCGEEGHFARDCPN 168 (169)
Q Consensus 149 ~~~~C~~Cg~~GH~ardCp~ 168 (169)
..+.|-.|+.-||...|||.
T Consensus 569 ~~kGCayCgGLGHRItdCPK 588 (610)
T KOG0341|consen 569 GEKGCAYCGGLGHRITDCPK 588 (610)
T ss_pred CccccccccCCCcccccCch
Confidence 36789999999999999995
No 187
>PF01194 RNA_pol_N: RNA polymerases N / 8 kDa subunit; InterPro: IPR000268 In eukaryotes, there are three different forms of DNA-dependent RNA polymerases (2.7.7.6 from EC) transcribing different sets of genes. Each class of RNA polymerase is an assemblage of ten to twelve different polypeptides. In archaebacteria, there is generally a single form of RNA polymerase which also consists of an oligomeric assemblage of 10 to 13 polypeptides. Archaebacterial subunit N (gene rpoN) [] is a small protein of about 8 kDa, it is evolutionary related [] to a 8.3 kDa component shared by all three forms of eukaryotic RNA polymerases (gene RPB10 in yeast and POLR2J in mammals) as well as to African swine fever virus (ASFV) protein CP80R []. There is a conserved region which is located at the N-terminal extremity of these polymerase subunits; this region contains two cysteines that binds a zinc ion [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_N 3HKZ_N 1EF4_A 3H0G_V 2Y0S_N 2R92_J 3M4O_J 3S2D_J 1R9S_J 1Y1W_J ....
Probab=30.52 E-value=25 Score=22.58 Aligned_cols=10 Identities=30% Similarity=0.953 Sum_probs=6.6
Q ss_pred CccccccCCC
Q 030905 150 GGGCYNCGEE 159 (169)
Q Consensus 150 ~~~C~~Cg~~ 159 (169)
+..||.||+.
T Consensus 4 PVRCFTCGkv 13 (60)
T PF01194_consen 4 PVRCFTCGKV 13 (60)
T ss_dssp SSS-STTTSB
T ss_pred ceecCCCCCC
Confidence 4668888876
No 188
>COG1644 RPB10 DNA-directed RNA polymerase, subunit N (RpoN/RPB10) [Transcription]
Probab=29.40 E-value=22 Score=23.00 Aligned_cols=10 Identities=30% Similarity=0.966 Sum_probs=7.6
Q ss_pred CccccccCCC
Q 030905 150 GGGCYNCGEE 159 (169)
Q Consensus 150 ~~~C~~Cg~~ 159 (169)
+..||.||++
T Consensus 4 PiRCFsCGkv 13 (63)
T COG1644 4 PVRCFSCGKV 13 (63)
T ss_pred ceEeecCCCC
Confidence 4678888876
No 189
>COG2190 NagE Phosphotransferase system IIA components [Carbohydrate transport and metabolism]
Probab=29.16 E-value=1.6e+02 Score=22.50 Aligned_cols=45 Identities=29% Similarity=0.575 Sum_probs=28.2
Q ss_pred ceEEEEeeC-CCCeeEEecCCCCccEEEEee----ccccCCcc-cCCCCCEEE
Q 030905 8 SGTVKWFSA-QKGFGFIAPEDGGEDLFVHQT----SIKSEGFR-TLSEGQTVE 54 (169)
Q Consensus 8 ~G~Vk~~~~-~kGfGFI~~~~~~~dvF~H~s----~i~~~~~~-~l~~G~~V~ 54 (169)
.|+|....+ ..-||+.+.+ +-+|++|+- +|...+|. -+++||.|.
T Consensus 50 dG~v~~iFpTkHAigi~t~~--GvEiLiHiGiDTV~L~GegF~~~v~~Gd~Vk 100 (156)
T COG2190 50 DGTVVLIFPTKHAIGIETDE--GVEILIHIGIDTVKLNGEGFESLVKEGDKVK 100 (156)
T ss_pred CcEEEEEeeCCcEEEEEcCC--CcEEEEEeceeeEEECCcceEEEeeCCCEEc
Confidence 466665554 4457766644 469999983 56666665 345666664
No 190
>COG5179 TAF1 Transcription initiation factor TFIID, subunit TAF1 [Transcription]
Probab=28.51 E-value=32 Score=32.29 Aligned_cols=12 Identities=50% Similarity=1.146 Sum_probs=5.9
Q ss_pred ccccccCCCCcc
Q 030905 151 GGCYNCGEEGHF 162 (169)
Q Consensus 151 ~~C~~Cg~~GH~ 162 (169)
.+|-+||+.||+
T Consensus 938 r~C~nCGQvGHm 949 (968)
T COG5179 938 RTCGNCGQVGHM 949 (968)
T ss_pred eecccccccccc
Confidence 445555555554
No 191
>COG1093 SUI2 Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis]
Probab=28.17 E-value=1.4e+02 Score=24.83 Aligned_cols=59 Identities=22% Similarity=0.155 Sum_probs=38.8
Q ss_pred ccccceEEEEeeCCCCeeEEecCCCCccEEEEeeccccCC----cccCCCCCEEEEEEeeCCCC
Q 030905 4 VQRSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEG----FRTLSEGQTVEFSVDVGEDG 63 (169)
Q Consensus 4 ~~~~~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~~~----~~~l~~G~~V~F~~~~~~kG 63 (169)
...+-|||+.--.---|.-+.- -++.+-|+|+|.|...= ...+++|+.|.+.+-.-...
T Consensus 12 GEiVv~tV~~V~~~GAyv~L~E-Y~g~Eg~ihiSEvas~wVknIrd~vkegqkvV~kVlrVd~~ 74 (269)
T COG1093 12 GEIVVGTVKQVADYGAYVELDE-YPGKEGFIHISEVASGWVKNIRDYVKEGQKVVAKVLRVDPK 74 (269)
T ss_pred CcEEEEEEEEeeccccEEEeec-cCCeeeeEEHHHHHHHHHHHHHHHhhcCCeEEEEEEEEcCC
Confidence 4456788887654333333322 24578999999997642 24689999999987764433
No 192
>PRK09439 PTS system glucose-specific transporter subunit; Provisional
Probab=27.07 E-value=2.1e+02 Score=22.11 Aligned_cols=46 Identities=35% Similarity=0.600 Sum_probs=28.2
Q ss_pred cceEEEEeeC-CCCeeEEecCCCCccEEEEee----ccccCCcc-cCCCCCEEE
Q 030905 7 SSGTVKWFSA-QKGFGFIAPEDGGEDLFVHQT----SIKSEGFR-TLSEGQTVE 54 (169)
Q Consensus 7 ~~G~Vk~~~~-~kGfGFI~~~~~~~dvF~H~s----~i~~~~~~-~l~~G~~V~ 54 (169)
..|+|+...+ ..-||+- .++ +-+|.+|+- .|...+|. ..++||.|+
T Consensus 64 ~dG~V~~vf~T~HAigi~-t~~-G~eiLIHiGiDTV~L~G~gF~~~Vk~Gd~Vk 115 (169)
T PRK09439 64 VDGTIGKIFETNHAFSIE-SDS-GVELFVHFGIDTVELKGEGFKRIAEEGQRVK 115 (169)
T ss_pred CCeEEEEEcCCCCEEEEE-eCC-CcEEEEEEeecccccCCCceEEEecCCCEEe
Confidence 4688887544 4456644 444 368999983 34555554 345677664
No 193
>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=27.01 E-value=1.4e+02 Score=17.61 Aligned_cols=54 Identities=22% Similarity=0.116 Sum_probs=33.6
Q ss_pred cceEEEEeeCCC---CeeEEecCCCC-ccEEEEeeccccCC-cccCCCCCEEEEEEeeC
Q 030905 7 SSGTVKWFSAQK---GFGFIAPEDGG-EDLFVHQTSIKSEG-FRTLSEGQTVEFSVDVG 60 (169)
Q Consensus 7 ~~G~Vk~~~~~k---GfGFI~~~~~~-~dvF~H~s~i~~~~-~~~l~~G~~V~F~~~~~ 60 (169)
+.|+|......+ .|-+++..|.. ..+-+.+-.-.... ...+.+|+.|.+.....
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 78999887765 44443332211111 14588999888876554
No 194
>PRK05054 exoribonuclease II; Provisional
Probab=26.68 E-value=1.9e+02 Score=27.02 Aligned_cols=33 Identities=15% Similarity=0.147 Sum_probs=23.6
Q ss_pred ccceEEEEeeCCCCeeEE-ecCCCCccEEEEeecccc
Q 030905 6 RSSGTVKWFSAQKGFGFI-APEDGGEDLFVHQTSIKS 41 (169)
Q Consensus 6 ~~~G~Vk~~~~~kGfGFI-~~~~~~~dvF~H~s~i~~ 41 (169)
...|+|..... |||. +.++..-+.|||+++|..
T Consensus 564 ~f~g~I~~v~~---~G~fV~l~~~~veglV~~~~l~~ 597 (644)
T PRK05054 564 RFAAEIIDISR---GGMRVRLLENGAVAFIPASFLHA 597 (644)
T ss_pred EEEEEEEeeec---CcEEEEEeCCceEEEEEccccCC
Confidence 67888887653 6644 445556789999999865
No 195
>PRK00276 infA translation initiation factor IF-1; Validated
Probab=25.57 E-value=1.9e+02 Score=18.66 Aligned_cols=55 Identities=16% Similarity=0.196 Sum_probs=32.6
Q ss_pred ccccceEEEEeeCCCCeeEEecCCCCccEEEEeeccccCCcccCCCCCEEEEEEeeC
Q 030905 4 VQRSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVG 60 (169)
Q Consensus 4 ~~~~~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~~~~~~l~~G~~V~F~~~~~ 60 (169)
...++|+|...-. .+|=.|..+++ +.+-.|+.-.-...-..+.+||.|.|++...
T Consensus 6 ~~~~~G~Vi~~~~-~~~y~V~~~~g-~~~~c~~~Gklr~~~i~i~vGD~V~ve~~~~ 60 (72)
T PRK00276 6 VIEMEGTVVEALP-NAMFRVELENG-HEVLAHISGKMRKNYIRILPGDKVTVELSPY 60 (72)
T ss_pred eEEEEEEEEEEcC-CCEEEEEeCCC-CEEEEEEccceeeCCcccCCCCEEEEEEccc
Confidence 4567899987643 22444555444 4555665533221113488999999996543
No 196
>PRK11637 AmiB activator; Provisional
Probab=24.95 E-value=78 Score=27.68 Aligned_cols=35 Identities=20% Similarity=0.322 Sum_probs=21.3
Q ss_pred ccceEEEEeeCCCCeeEEecCCCCc---cEEEEeeccc
Q 030905 6 RSSGTVKWFSAQKGFGFIAPEDGGE---DLFVHQTSIK 40 (169)
Q Consensus 6 ~~~G~Vk~~~~~kGfGFI~~~~~~~---dvF~H~s~i~ 40 (169)
...|+|++-....+||-+..-+.+. -||-|.+++.
T Consensus 345 ~~~G~V~~~~~~~~~G~~vii~hg~g~~t~Y~~~~~~~ 382 (428)
T PRK11637 345 IADGRVLLADWLQGYGLVVVVEHGKGDMSLYGYNQSAL 382 (428)
T ss_pred cCCeEEEEeeccCCcccEEEEEeCCCcEEEccCCCcCC
Confidence 3579999888889999544332223 3444555443
No 197
>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=24.87 E-value=1.8e+02 Score=18.09 Aligned_cols=51 Identities=14% Similarity=0.206 Sum_probs=29.5
Q ss_pred cceEEEEeeCCCCeeEEecCCCCccEEEEeeccccCCcccCCCCCEEEEEEee
Q 030905 7 SSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDV 59 (169)
Q Consensus 7 ~~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~~~~~~l~~G~~V~F~~~~ 59 (169)
++|+|..--. .+|=.|..+++ +.+-.+..---......|.+||.|.|++..
T Consensus 3 ~~G~Vi~~~~-g~~~~V~~~~g-~~~~c~~rGklr~~~~~~~vGD~V~~~~~~ 53 (64)
T cd04451 3 MEGVVTEALP-NAMFRVELENG-HEVLAHISGKMRMNYIRILPGDRVKVELSP 53 (64)
T ss_pred EEEEEEEEeC-CCEEEEEeCCC-CEEEEEECceeecCCcccCCCCEEEEEEee
Confidence 5677765321 25666766554 444455543221112348999999999764
No 198
>PF14326 DUF4384: Domain of unknown function (DUF4384)
Probab=24.76 E-value=1.3e+02 Score=19.80 Aligned_cols=25 Identities=24% Similarity=0.336 Sum_probs=18.0
Q ss_pred cCCCCCEEEEEEeeCCCCceeEEEE
Q 030905 46 TLSEGQTVEFSVDVGEDGRTKAVDV 70 (169)
Q Consensus 46 ~l~~G~~V~F~~~~~~kGr~~A~~V 70 (169)
.+++||+|.|.+.....+-+.-.++
T Consensus 2 ~~~~Ge~v~~~~~~~~~~Yl~l~~~ 26 (83)
T PF14326_consen 2 VYRVGERVRFRVTSNRDGYLYLFYI 26 (83)
T ss_pred cccCCCEEEEEEEeCCCeEEEEEEE
Confidence 3678999999998877774444444
No 199
>KOG2560 consensus RNA splicing factor - Slu7p [RNA processing and modification]
Probab=24.72 E-value=16 Score=32.72 Aligned_cols=17 Identities=47% Similarity=1.083 Sum_probs=12.7
Q ss_pred CccccccCCCCccCCCC
Q 030905 150 GGGCYNCGEEGHFARDC 166 (169)
Q Consensus 150 ~~~C~~Cg~~GH~ardC 166 (169)
...|-+||..+|..+||
T Consensus 112 KGACeNCGAmtHk~KDC 128 (529)
T KOG2560|consen 112 KGACENCGAMTHKVKDC 128 (529)
T ss_pred hhhhhhhhhhhcchHHH
Confidence 35588888888888877
No 200
>PRK04016 DNA-directed RNA polymerase subunit N; Provisional
Probab=24.30 E-value=32 Score=22.25 Aligned_cols=10 Identities=30% Similarity=0.953 Sum_probs=7.6
Q ss_pred CccccccCCC
Q 030905 150 GGGCYNCGEE 159 (169)
Q Consensus 150 ~~~C~~Cg~~ 159 (169)
+..||.||+.
T Consensus 4 PvRCFTCGkv 13 (62)
T PRK04016 4 PVRCFTCGKV 13 (62)
T ss_pred CeEecCCCCC
Confidence 4668888876
No 201
>PRK06958 single-stranded DNA-binding protein; Provisional
Probab=24.10 E-value=3.5e+02 Score=21.14 Aligned_cols=25 Identities=12% Similarity=-0.023 Sum_probs=16.1
Q ss_pred EEEEeeccccC---CcccCCCCCEEEEE
Q 030905 32 LFVHQTSIKSE---GFRTLSEGQTVEFS 56 (169)
Q Consensus 32 vF~H~s~i~~~---~~~~l~~G~~V~F~ 56 (169)
-|+.++.+-.. -...|+.|+.|.-+
T Consensus 52 ~w~~V~~fGk~AE~v~~~LkKGs~V~Ve 79 (182)
T PRK06958 52 EWHRVAFFGRLAEIVGEYLKKGSSVYIE 79 (182)
T ss_pred eEEEEEEehHHHHHHHHHhCCCCEEEEE
Confidence 46777766432 12568999999754
No 202
>KOG3272 consensus Predicted coiled-coil protein [General function prediction only]
Probab=23.83 E-value=52 Score=26.14 Aligned_cols=25 Identities=36% Similarity=0.607 Sum_probs=18.0
Q ss_pred CccEEEEeeccccCC-cccCCCCCEE
Q 030905 29 GEDLFVHQTSIKSEG-FRTLSEGQTV 53 (169)
Q Consensus 29 ~~dvF~H~s~i~~~~-~~~l~~G~~V 53 (169)
.++||||++++.... +..|.+++.|
T Consensus 34 ~e~Vwfhv~~~sS~hvyl~l~~~qti 59 (207)
T KOG3272|consen 34 PEDVWFHVDKLSSAHVYLRLREGQTI 59 (207)
T ss_pred ccceEEEeecccccceeeeecCCCCc
Confidence 357999999987764 4557778733
No 203
>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=23.61 E-value=36 Score=25.08 Aligned_cols=22 Identities=18% Similarity=0.401 Sum_probs=18.1
Q ss_pred CCCCCccccCcCCeecccCCCCC
Q 030905 115 AGSGACFNCGRTGHIARECYSRG 137 (169)
Q Consensus 115 ~~~~~C~~Cg~~GH~a~~C~~~~ 137 (169)
.....|..|. -.||...||...
T Consensus 104 ~~~v~CR~Ck-GdH~T~~CPyKd 125 (128)
T PF12353_consen 104 KSKVKCRICK-GDHWTSKCPYKD 125 (128)
T ss_pred CceEEeCCCC-CCcccccCCccc
Confidence 4667899996 789999999753
No 204
>COG5179 TAF1 Transcription initiation factor TFIID, subunit TAF1 [Transcription]
Probab=23.42 E-value=49 Score=31.14 Aligned_cols=24 Identities=29% Similarity=0.714 Sum_probs=18.7
Q ss_pred CCCCCCccccCcCCeec--ccCCCCC
Q 030905 114 GAGSGACFNCGRTGHIA--RECYSRG 137 (169)
Q Consensus 114 ~~~~~~C~~Cg~~GH~a--~~C~~~~ 137 (169)
....++|-+||+.||+. ..||...
T Consensus 934 K~Ttr~C~nCGQvGHmkTNK~CP~f~ 959 (968)
T COG5179 934 KNTTRTCGNCGQVGHMKTNKACPKFS 959 (968)
T ss_pred CCcceecccccccccccccccCcccc
Confidence 45678999999999975 5677644
No 205
>PF00498 FHA: FHA domain; InterPro: IPR000253 The forkhead-associated (FHA) domain [] is a phosphopeptide recognition domain found in many regulatory proteins. It displays specificity for phosphothreonine-containing epitopes but will also recognise phosphotyrosine with relatively high affinity. It spans approximately 80-100 amino acid residues folded into an 11-stranded beta sandwich, which sometimes contain small helical insertions between the loops connecting the strands []. To date, genes encoding FHA-containing proteins have been identified in eubacterial and eukaryotic but not archaeal genomes. The domain is present in a diverse range of proteins, such as kinases, phosphatases, kinesins, transcription factors, RNA-binding proteins and metabolic enzymes which partake in many different cellular processes - DNA repair, signal transduction, vesicular transport and protein degradation are just a few examples.; GO: 0005515 protein binding; PDB: 1LGQ_B 1LGP_A 2CSW_A 2PIE_A 3FM8_A 3MDB_B 3GQS_B 1UHT_A 1WLN_A 3POA_A ....
Probab=23.38 E-value=77 Score=19.57 Aligned_cols=47 Identities=17% Similarity=0.314 Sum_probs=25.4
Q ss_pred cceEEEEeeCCCCeeEEecCCCCccEEEEeeccccCCcccCCCCCEEEE
Q 030905 7 SSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGFRTLSEGQTVEF 55 (169)
Q Consensus 7 ~~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~~~~~~l~~G~~V~F 55 (169)
.+.+|. |+.. +-=+|+......-+|+.-..|.......|..|+.|.|
T Consensus 21 ~Ha~i~-~~~~-~~~~i~d~~s~ngt~vng~~l~~~~~~~L~~gd~i~~ 67 (68)
T PF00498_consen 21 RHARIS-FDDD-GQFYIEDLGSTNGTFVNGQRLGPGEPVPLKDGDIIRF 67 (68)
T ss_dssp TSEEEE-EETT-EEEEEEESSSSS-EEETTEEESSTSEEEE-TTEEEEE
T ss_pred eeeEEE-Eece-eeEEEEeCCCCCcEEECCEEcCCCCEEECCCCCEEEc
Confidence 444553 3332 2334444344567888777776644456778887765
No 206
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=23.18 E-value=2.2e+02 Score=21.88 Aligned_cols=55 Identities=11% Similarity=-0.024 Sum_probs=37.0
Q ss_pred ccccceEEEEeeCCCCeeEE-ecC---------CCCccEEEEeeccccCC----cccCCCCCEEEEEEeeCC
Q 030905 4 VQRSSGTVKWFSAQKGFGFI-APE---------DGGEDLFVHQTSIKSEG----FRTLSEGQTVEFSVDVGE 61 (169)
Q Consensus 4 ~~~~~G~Vk~~~~~kGfGFI-~~~---------~~~~dvF~H~s~i~~~~----~~~l~~G~~V~F~~~~~~ 61 (169)
...+.|+|+.... ++++ ... ...-+-|+|++++.... ...+++||.|...+..-.
T Consensus 65 GdiV~GkV~~i~~---~g~~V~I~~~~~~~~~l~~~~~G~l~~s~i~~~~~~~~~~~~~~GD~V~akV~~i~ 133 (189)
T PRK09521 65 GDIVYGRVVDVKE---QRALVRIVSIEGSERELATSKLAYIHISQVSDGYVESLTDAFKIGDIVRAKVISYT 133 (189)
T ss_pred CCEEEEEEEEEcC---CeEEEEEEEecccccccCCCceeeEEhhHcChhhhhhHHhccCCCCEEEEEEEecC
Confidence 3467888888854 3333 321 12357999999986432 245899999999988765
No 207
>KOG0921 consensus Dosage compensation complex, subunit MLE [Transcription]
Probab=22.99 E-value=1.3e+02 Score=29.86 Aligned_cols=11 Identities=9% Similarity=0.383 Sum_probs=5.2
Q ss_pred EEEeeccccCC
Q 030905 33 FVHQTSIKSEG 43 (169)
Q Consensus 33 F~H~s~i~~~~ 43 (169)
..|.|.....+
T Consensus 1152 l~~~StrygDG 1162 (1282)
T KOG0921|consen 1152 LLTDSTRYGDG 1162 (1282)
T ss_pred cccccccccCC
Confidence 44555554443
No 208
>KOG3497 consensus DNA-directed RNA polymerase, subunit RPB10 [Transcription]
Probab=22.76 E-value=30 Score=22.38 Aligned_cols=10 Identities=30% Similarity=0.913 Sum_probs=6.9
Q ss_pred CccccccCCC
Q 030905 150 GGGCYNCGEE 159 (169)
Q Consensus 150 ~~~C~~Cg~~ 159 (169)
+..||.||+.
T Consensus 4 PiRCFtCGKv 13 (69)
T KOG3497|consen 4 PIRCFTCGKV 13 (69)
T ss_pred eeEeeecccc
Confidence 3568888775
No 209
>cd04318 EcAsnRS_like_N EcAsnRS_like_N: N-terminal, anticodon recognition domain of the type found in Escherichia coli asparaginyl-tRNA synthetase (AsnRS) and, in Arabidopsis thaliana and Saccharomyces cerevisiae mitochondrial (mt) AsnRS. This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop. The enzymes in this group are homodimeric class2b aminoacyl-tRNA synthetases (aaRSs). aaRSs catalyze the specific attachment of amino acids (AAs) to their cognate tRNAs during protein biosynthesis. This 2-step reaction involves i) the activation of the AA by ATP in the presence of magnesium ions, followed by ii) the transfer of the activated AA to the terminal ribose of tRNA. In the case of the class2b aaRSs, the activated AA is attached to the 3'OH of the terminal ribose. Eukaryotes contain 2 sets of aaRSs, both of which are encoded by the nuclear genome. One set concerns with cytoplasmic protein synthesis, whereas the other exclusively with mitochondrial
Probab=22.73 E-value=2.2e+02 Score=18.36 Aligned_cols=51 Identities=22% Similarity=0.301 Sum_probs=32.7
Q ss_pred ccceEEEEeeCCCCeeEEecCCC-C---ccEEEEeeccccCCcccCCCCCEEEEE
Q 030905 6 RSSGTVKWFSAQKGFGFIAPEDG-G---EDLFVHQTSIKSEGFRTLSEGQTVEFS 56 (169)
Q Consensus 6 ~~~G~Vk~~~~~kGfGFI~~~~~-~---~dvF~H~s~i~~~~~~~l~~G~~V~F~ 56 (169)
.+.|.|...-..+..-||.-.|+ . -.+.+..+.....-+..|..++.|..+
T Consensus 3 ~v~Gwv~~~R~~g~~~Fi~LrD~s~~~~lQvv~~~~~~~~~~~~~l~~gs~V~v~ 57 (82)
T cd04318 3 TVNGWVRSVRDSKKISFIELNDGSCLKNLQVVVDKELTNFKEILKLSTGSSIRVE 57 (82)
T ss_pred EEEEeEEEEEcCCcEEEEEEECCCCccCEEEEEeCcccCHHHHhcCCCceEEEEE
Confidence 46788888888888999998443 2 355554432211123467888888765
No 210
>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=22.25 E-value=2.6e+02 Score=19.28 Aligned_cols=34 Identities=32% Similarity=0.413 Sum_probs=26.6
Q ss_pred CCccEEEEeeccccC-CcccCCCCCEEEEEEeeCC
Q 030905 28 GGEDLFVHQTSIKSE-GFRTLSEGQTVEFSVDVGE 61 (169)
Q Consensus 28 ~~~dvF~H~s~i~~~-~~~~l~~G~~V~F~~~~~~ 61 (169)
...+|.||=.+-... +...|.+|+.++|.....-
T Consensus 11 ~~~~L~vhC~S~d~Dlg~~~l~~g~~~~~~F~~~~ 45 (110)
T PF05938_consen 11 PGKILTVHCKSKDDDLGWHVLKPGQSYSFSFRDNF 45 (110)
T ss_pred CCCeEEEEeeCCCccCCCEECCCCCEEEEEEecCc
Confidence 456789998777654 6788999999999987653
No 211
>PLN03134 glycine-rich RNA-binding protein 4; Provisional
Probab=22.22 E-value=26 Score=26.08 Aligned_cols=12 Identities=42% Similarity=0.941 Sum_probs=8.5
Q ss_pred CCCeeEEecCCC
Q 030905 17 QKGFGFIAPEDG 28 (169)
Q Consensus 17 ~kGfGFI~~~~~ 28 (169)
.|||+||+-.+.
T Consensus 75 ~kGfaFV~F~~~ 86 (144)
T PLN03134 75 SRGFGFVNFNDE 86 (144)
T ss_pred cceEEEEEECCH
Confidence 378888887653
No 212
>COG4384 Mu-like prophage protein gp45 [Function unknown]
Probab=22.00 E-value=1.1e+02 Score=24.25 Aligned_cols=41 Identities=22% Similarity=0.403 Sum_probs=26.2
Q ss_pred CCeeEEecCCCCccEEEE--------eecccc--CC--cccCCCCCEEEEEEe
Q 030905 18 KGFGFIAPEDGGEDLFVH--------QTSIKS--EG--FRTLSEGQTVEFSVD 58 (169)
Q Consensus 18 kGfGFI~~~~~~~dvF~H--------~s~i~~--~~--~~~l~~G~~V~F~~~ 58 (169)
.-|||++.+..+.|+|+= --.|.. .. ..-|.+||.|.|..+
T Consensus 55 q~yGf~S~ppaGse~vvv~lGG~rShgviv~~~~~syR~~GL~aGeT~iY~~e 107 (203)
T COG4384 55 QEYGFASVPPAGSEAVVVPLGGKRSHGVIVVSQHGSYRITGLKAGETVIYNHE 107 (203)
T ss_pred HhcCcccCCCCCCeEEEEecCCccceeEEEEecCCccccccccCCceEEEecc
Confidence 469999987766677762 211211 11 246899999999754
No 213
>KOG2560 consensus RNA splicing factor - Slu7p [RNA processing and modification]
Probab=20.93 E-value=27 Score=31.36 Aligned_cols=19 Identities=47% Similarity=1.083 Sum_probs=16.5
Q ss_pred CCccccCcCCeecccCCCC
Q 030905 118 GACFNCGRTGHIARECYSR 136 (169)
Q Consensus 118 ~~C~~Cg~~GH~a~~C~~~ 136 (169)
..|-|||..+|..++|-..
T Consensus 113 GACeNCGAmtHk~KDCmER 131 (529)
T KOG2560|consen 113 GACENCGAMTHKVKDCMER 131 (529)
T ss_pred hhhhhhhhhhcchHHHhhc
Confidence 3699999999999999653
No 214
>TIGR02038 protease_degS periplasmic serine pepetdase DegS. This family consists of the periplasmic serine protease DegS (HhoB), a shorter paralog of protease DO (HtrA, DegP) and DegQ (HhoA). It is found in E. coli and several other Proteobacteria of the gamma subdivision. It contains a trypsin domain and a single copy of PDZ domain (in contrast to DegP with two copies). A critical role of this DegS is to sense stress in the periplasm and partially degrade an inhibitor of sigma(E).
Probab=20.90 E-value=2.1e+02 Score=24.35 Aligned_cols=45 Identities=9% Similarity=0.088 Sum_probs=32.4
Q ss_pred ccccceEEEEeeCCCCeeEEecCCCCccEEEEeeccccCCcccCCCCCEEE
Q 030905 4 VQRSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGFRTLSEGQTVE 54 (169)
Q Consensus 4 ~~~~~G~Vk~~~~~kGfGFI~~~~~~~dvF~H~s~i~~~~~~~l~~G~~V~ 54 (169)
...+.++|+++|+...+.+|+.+... ++...|... ..+++||.|.
T Consensus 111 g~~~~a~vv~~d~~~DlAvlkv~~~~----~~~~~l~~s--~~~~~G~~V~ 155 (351)
T TIGR02038 111 GRKFEAELVGSDPLTDLAVLKIEGDN----LPTIPVNLD--RPPHVGDVVL 155 (351)
T ss_pred CCEEEEEEEEecCCCCEEEEEecCCC----CceEeccCc--CccCCCCEEE
Confidence 35678999999999999999998642 222233322 4689999984
No 215
>PF05741 zf-nanos: Nanos RNA binding domain; InterPro: IPR024161 Nanos is a highly conserved RNA-binding protein in higher eukaryotes and functions as a key regulatory protein in translational control using a 3' untranslated region during the development and maintenance of germ cells. Nanos comprises a non-conserved amino-terminus and highly conserved carboxy- terminal regions. The C-terminal region has two conserved Cys-Cys-His-Cys (CCHC)-type zinc-finger motifs that are indispensable for nanos function [, , ]. The structure of the nanos-type zinc finger is composed of two independent zinc-finger (ZF) lobes, the N-terminal ZF1 and the C-terminal ZF2, which are connected by a linker helix []. These lobes create a large cleft. Zinc ions in ZF1 and ZF2 are bound to the CCHC motif by tetrahedral coordination.; PDB: 3ALR_B.
Probab=20.53 E-value=43 Score=21.14 Aligned_cols=20 Identities=35% Similarity=0.708 Sum_probs=7.6
Q ss_pred CccccccCCCC---ccCCCCCCC
Q 030905 150 GGGCYNCGEEG---HFARDCPNY 169 (169)
Q Consensus 150 ~~~C~~Cg~~G---H~ardCp~~ 169 (169)
.-.|-.|+..| |-.+-||.|
T Consensus 33 ~y~Cp~CgAtGd~AHT~~yCP~k 55 (55)
T PF05741_consen 33 KYVCPICGATGDNAHTIKYCPKK 55 (55)
T ss_dssp G---TTT---GGG---GGG-TT-
T ss_pred cCcCCCCcCcCccccccccCcCC
Confidence 45688888876 777788875
Done!