Query 034382
Match_columns 96
No_of_seqs 100 out of 126
Neff 6.1
Searched_HMMs 46136
Date Fri Mar 29 12:51:19 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/034382.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/034382hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 TIGR00358 3_prime_RNase VacB a 98.9 5.9E-09 1.3E-13 86.9 9.3 89 2-92 542-652 (654)
2 TIGR02063 RNase_R ribonuclease 98.7 7.1E-08 1.5E-12 80.9 9.2 89 2-92 597-707 (709)
3 COG0557 VacB Exoribonuclease R 98.6 3E-07 6.6E-12 77.3 8.7 90 3-94 593-704 (706)
4 TIGR02062 RNase_B exoribonucle 98.5 1.1E-06 2.5E-11 73.4 9.2 89 3-92 526-638 (639)
5 PRK05054 exoribonuclease II; P 98.5 1.4E-06 3.1E-11 72.8 9.6 90 2-93 529-643 (644)
6 PRK11642 exoribonuclease R; Pr 97.9 8.7E-05 1.9E-09 63.8 9.2 89 3-93 614-724 (813)
7 KOG2102 Exosomal 3'-5' exoribo 97.1 0.0019 4.2E-08 56.5 7.4 91 2-95 820-927 (941)
8 cd04471 S1_RNase_R S1_RNase_R: 97.1 0.011 2.4E-07 35.9 8.6 58 34-92 2-81 (83)
9 cd05708 S1_Rrp5_repeat_sc12 S1 97.0 0.017 3.6E-07 34.6 8.8 58 34-92 3-71 (77)
10 smart00316 S1 Ribosomal protei 96.9 0.022 4.8E-07 32.7 8.5 57 34-92 3-70 (72)
11 PF00575 S1: S1 RNA binding do 96.8 0.032 7E-07 33.3 8.9 57 34-92 5-72 (74)
12 cd05692 S1_RPS1_repeat_hs4 S1_ 96.6 0.047 1E-06 31.5 8.4 56 34-92 1-67 (69)
13 cd05688 S1_RPS1_repeat_ec3 S1_ 96.5 0.039 8.4E-07 32.0 7.5 55 34-91 2-67 (68)
14 cd05706 S1_Rrp5_repeat_sc10 S1 96.4 0.08 1.7E-06 31.6 8.9 57 34-92 4-71 (73)
15 cd05685 S1_Tex S1_Tex: The C-t 96.4 0.045 9.7E-07 31.6 7.4 56 34-91 1-67 (68)
16 cd05703 S1_Rrp5_repeat_hs12_sc 96.4 0.073 1.6E-06 32.5 8.6 57 34-92 1-70 (73)
17 cd04472 S1_PNPase S1_PNPase: P 96.3 0.073 1.6E-06 30.9 8.2 56 34-92 1-67 (68)
18 cd05696 S1_Rrp5_repeat_hs4 S1_ 96.2 0.084 1.8E-06 32.0 8.2 58 34-92 1-70 (71)
19 cd05698 S1_Rrp5_repeat_hs6_sc5 96.2 0.097 2.1E-06 30.9 8.4 57 34-92 1-68 (70)
20 cd05687 S1_RPS1_repeat_ec1_hs1 96.2 0.12 2.5E-06 30.6 8.6 56 35-92 2-68 (70)
21 cd04452 S1_IF2_alpha S1_IF2_al 96.1 0.12 2.5E-06 31.0 8.5 58 34-92 4-73 (76)
22 cd05697 S1_Rrp5_repeat_hs5 S1_ 96.1 0.11 2.3E-06 30.9 8.2 57 34-92 1-68 (69)
23 cd05686 S1_pNO40 S1_pNO40: pNO 95.9 0.19 4.1E-06 30.4 8.8 57 34-92 4-71 (73)
24 cd05707 S1_Rrp5_repeat_sc11 S1 95.8 0.11 2.5E-06 30.6 7.5 56 34-91 1-67 (68)
25 cd04461 S1_Rrp5_repeat_hs8_sc7 95.6 0.18 3.9E-06 31.0 8.1 57 34-92 15-82 (83)
26 cd05684 S1_DHX8_helicase S1_DH 95.6 0.23 5.1E-06 30.2 8.5 56 34-92 1-70 (79)
27 cd05689 S1_RPS1_repeat_ec4 S1_ 95.4 0.28 6.1E-06 29.1 8.2 57 33-91 3-71 (72)
28 cd05695 S1_Rrp5_repeat_hs3 S1_ 95.2 0.27 5.9E-06 29.3 7.6 55 35-91 2-65 (66)
29 PRK07252 hypothetical protein; 95.2 0.35 7.7E-06 32.6 8.9 57 34-92 4-71 (120)
30 cd04465 S1_RPS1_repeat_ec2_hs2 95.1 0.34 7.3E-06 28.5 8.6 56 34-92 1-65 (67)
31 PRK05807 hypothetical protein; 95.0 0.42 9.1E-06 32.8 9.0 55 34-92 6-71 (136)
32 PRK08059 general stress protei 94.9 0.39 8.4E-06 32.2 8.4 57 34-92 8-75 (123)
33 cd05690 S1_RPS1_repeat_ec5 S1_ 94.8 0.34 7.4E-06 28.3 7.2 24 68-91 45-68 (69)
34 cd05705 S1_Rrp5_repeat_hs14 S1 94.8 0.44 9.6E-06 29.2 7.9 56 34-91 4-73 (74)
35 cd00164 S1_like S1_like: Ribos 94.8 0.31 6.6E-06 27.2 6.8 24 68-91 41-64 (65)
36 cd05691 S1_RPS1_repeat_ec6 S1_ 94.7 0.46 9.9E-06 27.9 8.6 57 34-92 1-68 (73)
37 PRK08582 hypothetical protein; 94.6 0.59 1.3E-05 32.2 9.1 56 34-92 6-72 (139)
38 cd04473 S1_RecJ_like S1_RecJ_l 94.4 0.66 1.4E-05 28.3 8.9 56 34-92 17-75 (77)
39 TIGR00008 infA translation ini 93.8 0.78 1.7E-05 28.4 7.5 56 35-91 5-67 (68)
40 PHA02945 interferon resistance 93.5 1.3 2.9E-05 28.8 8.3 55 34-91 12-79 (88)
41 PRK07899 rpsA 30S ribosomal pr 93.4 0.82 1.8E-05 37.7 9.0 68 22-92 283-361 (486)
42 PRK12269 bifunctional cytidyla 93.0 1.1 2.3E-05 39.5 9.6 68 22-92 742-823 (863)
43 PRK03987 translation initiatio 92.7 1.2 2.7E-05 33.8 8.5 58 34-92 9-78 (262)
44 cd05789 S1_Rrp4 S1_Rrp4: Rrp4 92.3 1.7 3.6E-05 26.7 8.9 56 34-92 7-77 (86)
45 PRK12442 translation initiatio 92.1 1.8 3.9E-05 28.1 7.5 57 35-92 7-70 (87)
46 cd05702 S1_Rrp5_repeat_hs11_sc 91.9 1.6 3.6E-05 25.8 7.3 52 34-87 1-65 (70)
47 cd04455 S1_NusA S1_NusA: N-uti 91.6 1.8 3.9E-05 25.7 8.4 55 34-91 4-65 (67)
48 PRK06676 rpsA 30S ribosomal pr 91.6 3 6.5E-05 32.6 9.8 68 21-92 181-259 (390)
49 PTZ00248 eukaryotic translatio 90.6 2.8 6E-05 33.0 8.6 64 28-92 11-87 (319)
50 PRK07899 rpsA 30S ribosomal pr 90.5 3 6.6E-05 34.4 9.2 63 27-92 202-275 (486)
51 cd05693 S1_Rrp5_repeat_hs1_sc1 89.3 4.3 9.3E-05 26.3 7.7 57 34-92 4-93 (100)
52 TIGR00717 rpsA ribosomal prote 89.1 3.7 8E-05 33.2 8.6 69 21-92 435-514 (516)
53 PRK06676 rpsA 30S ribosomal pr 89.1 4.5 9.7E-05 31.6 8.9 63 28-92 272-345 (390)
54 smart00743 Agenet Tudor-like d 88.9 1.7 3.7E-05 25.1 5.0 32 34-65 17-50 (61)
55 PRK13806 rpsA 30S ribosomal pr 88.9 4.1 8.9E-05 33.3 8.8 67 23-92 370-447 (491)
56 PRK00087 4-hydroxy-3-methylbut 88.7 4.5 9.7E-05 34.2 9.1 58 33-92 562-630 (647)
57 cd04466 S1_YloQ_GTPase S1_YloQ 87.9 3.8 8.1E-05 23.9 7.4 41 38-79 2-48 (68)
58 PRK13806 rpsA 30S ribosomal pr 87.5 6 0.00013 32.3 8.9 68 22-92 282-361 (491)
59 PRK12269 bifunctional cytidyla 87.4 5.5 0.00012 35.2 9.1 67 23-92 656-734 (863)
60 cd05694 S1_Rrp5_repeat_hs2_sc2 87.3 4.9 0.00011 24.5 8.8 58 34-92 5-67 (74)
61 cd05704 S1_Rrp5_repeat_hs13 S1 87.2 1.8 3.9E-05 26.0 4.5 55 34-92 4-70 (72)
62 PRK07400 30S ribosomal protein 86.6 9.9 0.00021 29.5 9.3 56 34-92 119-181 (318)
63 PRK11824 polynucleotide phosph 85.2 7.4 0.00016 33.4 8.6 58 31-92 620-688 (693)
64 TIGR01953 NusA transcription t 85.0 17 0.00037 28.7 10.0 65 25-92 124-195 (341)
65 PF02598 Methyltrn_RNA_3: Puta 84.3 2.5 5.5E-05 32.6 5.0 47 34-81 115-162 (291)
66 PLN00207 polyribonucleotide nu 84.2 2.6 5.6E-05 37.4 5.5 61 30-92 751-821 (891)
67 COG0539 RpsA Ribosomal protein 84.2 1.9 4.1E-05 36.2 4.5 65 27-92 186-259 (541)
68 PRK06299 rpsA 30S ribosomal pr 83.8 16 0.00034 30.1 9.7 58 31-92 200-268 (565)
69 PRK12327 nusA transcription el 83.6 19 0.00041 28.8 9.8 65 24-92 126-197 (362)
70 PRK00087 4-hydroxy-3-methylbut 83.2 13 0.00028 31.5 9.1 58 31-92 476-544 (647)
71 COG2996 Predicted RNA-bindinin 82.3 9 0.0002 29.8 7.2 56 34-92 156-214 (287)
72 PRK06299 rpsA 30S ribosomal pr 82.2 15 0.00031 30.3 8.9 57 34-92 31-95 (565)
73 cd04508 TUDOR Tudor domains ar 82.2 4.2 9.1E-05 22.1 4.2 33 34-66 12-44 (48)
74 PF10989 DUF2808: Protein of u 81.1 9.2 0.0002 26.3 6.4 45 48-92 78-124 (146)
75 PRK07400 30S ribosomal protein 80.4 5.2 0.00011 31.0 5.5 62 28-92 191-263 (318)
76 PRK09202 nusA transcription el 79.5 29 0.00063 28.6 9.8 64 25-92 127-197 (470)
77 COG2106 Uncharacterized conser 79.0 4.1 9E-05 31.5 4.4 45 34-82 106-150 (272)
78 cd04454 S1_Rrp4_like S1_Rrp4_l 77.9 13 0.00028 22.5 9.0 56 34-92 7-73 (82)
79 TIGR00717 rpsA ribosomal prote 77.6 30 0.00065 28.0 9.3 67 22-92 90-165 (516)
80 TIGR03591 polynuc_phos polyrib 76.1 12 0.00026 32.1 6.9 55 34-91 619-684 (684)
81 COG1098 VacB Predicted RNA bin 75.9 2.9 6.3E-05 29.0 2.6 44 48-92 29-72 (129)
82 PF11213 DUF3006: Protein of u 74.0 17 0.00037 22.1 5.9 37 41-77 3-42 (71)
83 TIGR00448 rpoE DNA-directed RN 73.9 20 0.00042 25.3 6.6 62 25-90 74-162 (179)
84 cd04460 S1_RpoE S1_RpoE: RpoE, 73.0 21 0.00045 22.5 7.7 18 69-86 54-71 (99)
85 PRK09521 exosome complex RNA-b 72.7 31 0.00068 24.5 8.2 49 34-83 65-133 (189)
86 cd05701 S1_Rrp5_repeat_hs10 S1 71.7 8.5 0.00018 23.9 3.7 52 36-88 3-65 (69)
87 cd04486 YhcR_OBF_like YhcR_OBF 71.5 21 0.00046 22.0 6.7 35 58-93 34-68 (78)
88 PF03459 TOBE: TOBE domain; I 71.2 17 0.00037 20.8 6.0 49 35-83 5-61 (64)
89 PRK00276 infA translation init 70.9 21 0.00045 21.7 7.8 57 35-91 7-69 (72)
90 PF07177 Neuralized: Neuralize 70.8 7.1 0.00015 23.8 3.2 26 66-91 36-62 (69)
91 TIGR02696 pppGpp_PNP guanosine 69.1 10 0.00022 33.0 4.8 56 34-92 648-718 (719)
92 COG1093 SUI2 Translation initi 68.0 22 0.00048 27.5 6.0 45 48-92 25-81 (269)
93 cd01854 YjeQ_engC YjeQ/EngC. 67.9 35 0.00075 25.7 7.1 51 39-90 1-64 (287)
94 cd05790 S1_Rrp40 S1_Rrp40: Rrp 65.2 20 0.00044 22.9 4.6 38 50-87 30-68 (86)
95 PRK12329 nusA transcription el 64.8 66 0.0014 26.7 8.5 60 24-85 144-212 (449)
96 COG0539 RpsA Ribosomal protein 62.6 82 0.0018 26.7 8.9 68 22-92 439-510 (541)
97 cd03447 FAS_MaoC FAS_MaoC, the 62.6 29 0.00062 23.0 5.2 29 61-89 73-101 (126)
98 cd05793 S1_IF1A S1_IF1A: Trans 62.6 35 0.00076 21.2 6.6 53 38-91 3-61 (77)
99 PRK04012 translation initiatio 62.6 41 0.0009 22.1 7.5 57 34-91 20-82 (100)
100 smart00333 TUDOR Tudor domain. 61.9 26 0.00056 19.5 5.1 34 33-66 15-48 (57)
101 PRK12288 GTPase RsgA; Reviewed 60.1 63 0.0014 25.4 7.5 53 37-90 40-106 (347)
102 PF14250 AbrB-like: AbrB-like 59.5 8.3 0.00018 24.2 2.0 15 67-81 51-65 (71)
103 CHL00010 infA translation init 58.2 42 0.00092 20.8 7.7 56 36-91 8-69 (78)
104 PF15057 DUF4537: Domain of un 57.4 55 0.0012 22.0 5.9 47 32-78 10-65 (124)
105 PF01176 eIF-1a: Translation i 57.2 39 0.00084 20.0 6.9 53 36-89 4-62 (65)
106 PF11604 CusF_Ec: Copper bindi 57.1 22 0.00048 21.5 3.6 31 54-84 25-58 (70)
107 TIGR00074 hypC_hupF hydrogenas 56.7 46 0.001 20.8 5.7 43 38-81 6-48 (76)
108 PRK00006 fabZ (3R)-hydroxymyri 55.5 32 0.00069 22.9 4.5 30 62-91 95-124 (147)
109 PRK00098 GTPase RsgA; Reviewed 55.2 90 0.0019 23.6 7.8 51 38-89 2-66 (298)
110 PF01938 TRAM: TRAM domain; I 54.4 40 0.00086 19.3 6.3 50 34-85 5-54 (61)
111 TIGR00638 Mop molybdenum-pteri 53.5 41 0.00089 19.2 6.5 48 35-82 7-62 (69)
112 PF09874 DUF2101: Predicted me 53.0 37 0.00081 25.3 4.8 53 27-82 135-195 (206)
113 COG0335 RplS Ribosomal protein 52.4 30 0.00065 23.6 3.9 27 67-93 19-45 (115)
114 PRK04424 fatty acid biosynthes 52.0 51 0.0011 23.4 5.4 32 61-92 131-162 (185)
115 PF00567 TUDOR: Tudor domain; 51.5 54 0.0012 20.0 4.9 33 34-66 66-98 (121)
116 TIGR01750 fabZ beta-hydroxyacy 48.3 56 0.0012 21.4 4.8 29 63-91 92-120 (140)
117 cd04453 S1_RNase_E S1_RNase_E: 48.0 67 0.0015 20.1 8.0 51 34-86 8-74 (88)
118 PF01828 Peptidase_A4: Peptida 47.6 26 0.00056 25.7 3.3 37 54-93 79-115 (208)
119 cd01288 FabZ FabZ is a 17kD be 47.5 46 0.00099 21.2 4.2 30 63-92 82-111 (131)
120 KOG1067 Predicted RNA-binding 47.4 17 0.00036 31.4 2.5 45 48-92 692-736 (760)
121 COG1185 Pnp Polyribonucleotide 46.3 27 0.00058 30.4 3.6 52 34-85 620-680 (692)
122 PF07703 A2M_N_2: Alpha-2-macr 46.3 69 0.0015 20.7 5.0 39 52-92 87-127 (136)
123 cd04456 S1_IF1A_like S1_IF1A_l 44.9 76 0.0016 19.8 6.5 51 39-90 4-61 (78)
124 PF00207 A2M: Alpha-2-macroglo 44.4 57 0.0012 20.2 4.2 34 59-92 56-89 (92)
125 COG2030 MaoC Acyl dehydratase 43.5 54 0.0012 22.5 4.3 24 62-85 100-123 (159)
126 cd03449 R_hydratase (R)-hydrat 43.5 82 0.0018 19.8 5.2 32 60-91 74-107 (128)
127 smart00588 NEUZ domain in neur 43.5 35 0.00076 22.9 3.2 19 66-84 37-55 (123)
128 smart00652 eIF1a eukaryotic tr 42.4 86 0.0019 19.7 7.3 55 35-90 5-65 (83)
129 PRK01889 GTPase RsgA; Reviewed 42.2 1.7E+02 0.0036 22.9 7.7 52 37-89 29-95 (356)
130 PF08605 Rad9_Rad53_bind: Fung 40.6 76 0.0016 21.8 4.6 45 35-79 23-70 (131)
131 cd04451 S1_IF1 S1_IF1: Transla 40.1 76 0.0016 18.4 7.0 52 37-89 3-61 (64)
132 PF02599 CsrA: Global regulato 40.1 37 0.0008 19.9 2.5 24 66-91 9-32 (54)
133 PF11454 DUF3016: Protein of u 40.0 33 0.00072 24.0 2.7 19 69-87 47-65 (141)
134 PRK13692 (3R)-hydroxyacyl-ACP 38.7 92 0.002 21.5 4.9 32 61-92 89-124 (159)
135 PF04246 RseC_MucC: Positive r 37.9 48 0.001 22.1 3.2 24 59-82 42-65 (135)
136 cd00493 FabA_FabZ FabA/Z, beta 37.6 92 0.002 19.6 4.5 29 63-91 83-111 (131)
137 PRK13901 ruvA Holliday junctio 37.6 1.6E+02 0.0035 21.5 6.3 54 37-92 5-60 (196)
138 PRK12289 GTPase RsgA; Reviewed 37.5 1.7E+02 0.0037 23.1 6.7 54 36-90 8-83 (352)
139 PHA02858 EIF2a-like PKR inhibi 37.3 1.2E+02 0.0025 19.7 6.5 44 48-92 29-84 (86)
140 PF01336 tRNA_anti-codon: OB-f 35.7 51 0.0011 18.7 2.7 24 67-91 43-67 (75)
141 cd03448 HDE_HSD HDE_HSD The R 35.1 1.2E+02 0.0027 19.8 4.9 28 62-92 76-103 (122)
142 PRK08563 DNA-directed RNA poly 34.9 1.6E+02 0.0035 20.6 7.3 55 29-87 78-154 (187)
143 PF01455 HupF_HypC: HupF/HypC 34.7 1.1E+02 0.0023 18.6 4.7 43 38-80 6-49 (68)
144 cd03452 MaoC_C MaoC_C The C-t 34.0 1.2E+02 0.0026 20.2 4.7 23 62-84 82-106 (142)
145 cd03440 hot_dog The hotdog fol 33.6 81 0.0018 16.8 5.4 30 63-92 52-81 (100)
146 COG0361 InfA Translation initi 33.2 1.3E+02 0.0027 18.9 7.4 57 34-91 6-69 (75)
147 PF05641 Agenet: Agenet domain 33.0 74 0.0016 18.8 3.2 27 34-60 18-44 (68)
148 PRK14600 ruvA Holliday junctio 32.6 1.9E+02 0.0041 20.8 6.4 54 37-92 5-61 (186)
149 PF12791 RsgI_N: Anti-sigma fa 31.6 1E+02 0.0022 17.3 4.0 34 48-82 6-39 (56)
150 KOG1004 Exosomal 3'-5' exoribo 30.7 1.1E+02 0.0025 23.1 4.4 51 36-86 68-126 (230)
151 PLN00208 translation initiatio 30.3 2E+02 0.0043 20.3 6.1 54 36-90 33-92 (145)
152 PF01245 Ribosomal_L19: Riboso 29.8 1.2E+02 0.0026 20.3 4.1 25 67-91 17-41 (113)
153 cd03441 R_hydratase_like (R)-h 29.8 1.4E+02 0.0031 18.5 4.8 26 60-85 72-97 (127)
154 PF13550 Phage-tail_3: Putativ 29.7 1.5E+02 0.0032 19.5 4.6 25 67-94 138-162 (164)
155 PRK01712 carbon storage regula 29.6 81 0.0018 19.2 2.9 24 66-91 9-32 (64)
156 PF07238 PilZ: PilZ domain; I 29.5 1.2E+02 0.0027 17.7 5.7 34 34-79 22-55 (102)
157 cd03451 FkbR2 FkbR2 is a Strep 28.3 1.4E+02 0.003 19.4 4.2 23 62-84 85-109 (146)
158 PF02563 Poly_export: Polysacc 28.3 27 0.00058 21.4 0.6 24 67-90 11-34 (82)
159 PF14345 GDYXXLXY: GDYXXLXY pr 28.0 46 0.001 22.5 1.8 20 68-87 16-35 (144)
160 COG4536 CorB Putative Mg2+ and 27.8 53 0.0012 26.9 2.4 44 19-65 284-327 (423)
161 PF01575 MaoC_dehydratas: MaoC 27.7 1E+02 0.0022 19.8 3.4 24 60-83 80-103 (122)
162 PF05683 Fumerase_C: Fumarase 27.5 36 0.00077 25.3 1.3 47 25-78 4-52 (205)
163 COG1162 Predicted GTPases [Gen 27.1 2.6E+02 0.0056 21.9 6.0 52 38-90 6-73 (301)
164 PTZ00329 eukaryotic translatio 27.1 2.4E+02 0.0051 20.1 6.1 53 37-90 34-92 (155)
165 COG4148 ModC ABC-type molybdat 26.9 1.9E+02 0.004 23.3 5.2 46 34-83 232-279 (352)
166 TIGR00757 RNaseEG ribonuclease 26.9 1.4E+02 0.003 24.2 4.6 18 68-86 83-100 (414)
167 PRK10862 SoxR reducing system 26.8 82 0.0018 21.9 3.0 24 59-82 49-72 (154)
168 CHL00084 rpl19 ribosomal prote 26.7 1.2E+02 0.0026 20.6 3.6 24 67-90 21-44 (117)
169 COG0764 FabA 3-hydroxymyristoy 26.5 1.8E+02 0.0039 20.2 4.6 23 63-85 94-116 (147)
170 COG5140 UFD1 Ubiquitin fusion- 26.3 50 0.0011 25.8 1.9 65 10-80 53-117 (331)
171 PRK12328 nusA transcription el 25.8 3.6E+02 0.0078 21.8 9.8 61 24-87 130-195 (374)
172 PRK09838 periplasmic copper-bi 25.4 94 0.002 20.8 3.0 51 36-86 44-106 (115)
173 COG3086 RseC Positive regulato 25.0 61 0.0013 23.1 2.0 25 60-84 50-74 (150)
174 PRK12281 rplX 50S ribosomal pr 24.6 1.4E+02 0.003 18.5 3.4 27 68-94 6-42 (76)
175 PF03061 4HBT: Thioesterase su 24.4 1.4E+02 0.0031 16.7 4.5 28 60-87 35-62 (79)
176 PF00181 Ribosomal_L2: Ribosom 24.3 1.8E+02 0.0039 17.8 4.3 39 37-76 33-76 (77)
177 TIGR00202 csrA carbon storage 24.1 1.1E+02 0.0024 18.9 2.8 25 65-91 8-32 (69)
178 CHL00141 rpl24 ribosomal prote 24.1 1.4E+02 0.003 18.8 3.4 26 68-93 8-43 (83)
179 PF08845 SymE_toxin: Toxin Sym 24.1 81 0.0018 18.6 2.2 15 67-81 36-50 (57)
180 cd01764 Urm1 Urm1-like ubuitin 24.0 98 0.0021 19.7 2.7 54 22-77 32-87 (94)
181 PRK06461 single-stranded DNA-b 23.7 2E+02 0.0043 19.2 4.4 44 49-92 41-88 (129)
182 cd03453 SAV4209_like SAV4209_l 23.0 2.1E+02 0.0046 18.3 4.3 20 63-82 75-94 (127)
183 PF12857 TOBE_3: TOBE-like dom 22.4 1.7E+02 0.0036 16.7 6.4 45 35-79 5-57 (58)
184 PRK00568 carbon storage regula 22.3 1.5E+02 0.0032 18.7 3.2 24 66-91 9-32 (76)
185 KOG3925 Uncharacterized conser 21.9 88 0.0019 25.3 2.6 45 37-82 184-230 (371)
186 PF00467 KOW: KOW motif; Inte 21.8 1.3E+02 0.0028 15.2 3.3 13 78-90 18-30 (32)
187 PRK04914 ATP-dependent helicas 21.7 4.5E+02 0.0098 23.9 7.2 64 27-92 8-83 (956)
188 PF07705 CARDB: CARDB; InterP 21.7 94 0.002 18.5 2.2 27 55-82 2-28 (101)
189 PF11535 Calci_bind_CcbP: Calc 21.5 1.8E+02 0.004 19.2 3.7 21 25-46 22-42 (106)
190 cd05751 Ig1_LILRB1_like First 21.2 1.7E+02 0.0037 17.7 3.4 20 67-86 11-30 (91)
191 PF10447 EXOSC1: Exosome compo 21.0 1.1E+02 0.0023 19.3 2.4 24 69-92 2-25 (82)
192 smart00739 KOW KOW (Kyprides, 20.9 96 0.0021 14.4 1.8 12 69-80 2-13 (28)
193 cd03455 SAV4209 SAV4209 is a S 20.9 2.4E+02 0.0051 17.9 5.0 23 62-84 73-95 (123)
194 COG3269 Predicted RNA-binding 20.7 2.3E+02 0.005 17.7 8.1 51 34-91 16-68 (73)
195 PF11874 DUF3394: Domain of un 20.6 1.3E+02 0.0028 21.9 3.1 25 67-91 70-94 (183)
196 PRK00004 rplX 50S ribosomal pr 20.4 1.8E+02 0.0038 19.0 3.5 26 68-93 4-39 (105)
197 cd03446 MaoC_like MoaC_like 20.4 1.7E+02 0.0037 18.8 3.4 21 62-82 84-104 (140)
198 COG1188 Ribosome-associated he 20.4 95 0.002 20.6 2.1 18 64-81 44-61 (100)
199 KOG1816 Ubiquitin fusion-degra 20.3 1.1E+02 0.0023 24.2 2.7 40 34-79 69-108 (308)
200 PRK10898 serine endoprotease; 20.2 4E+02 0.0087 20.7 6.0 43 34-77 111-156 (353)
201 TIGR02038 protease_degS peripl 20.1 4.2E+02 0.0091 20.5 6.2 43 34-77 111-156 (351)
202 PF14801 GCD14_N: tRNA methylt 20.1 81 0.0018 18.7 1.6 18 67-88 4-21 (54)
No 1
>TIGR00358 3_prime_RNase VacB and RNase II family 3'-5' exoribonucleases. This model is defined to identify a pair of paralogous 3-prime exoribonucleases in E. coli, plus the set of proteins apparently orthologous to one or the other in other eubacteria. VacB was characterized originally as required for the expression of virulence genes, but is now recognized as the exoribonuclease RNase R (Rnr). Its paralog in E. coli and H. influenzae is designated exoribonuclease II (Rnb). Both are involved in the degradation of mRNA, and consequently have strong pleiotropic effects that may be difficult to disentangle. Both these proteins share domain-level similarity (RNB, S1) with a considerable number of other proteins, and full-length similarity scoring below the trusted cutoff to proteins associated with various phenotypes but uncertain biochemistry; it may be that these latter proteins are also 3-prime exoribonucleases.
Probab=98.93 E-value=5.9e-09 Score=86.91 Aligned_cols=89 Identities=18% Similarity=0.201 Sum_probs=78.2
Q ss_pred cchhcHhHHHHHHhhhccccchHHHHhhhCCCCCeEEEEEEEEccCceEEEEeecceeeEEEeec---------------
Q 034382 2 ASIVNMQTRIARRLSNTSLRYWIIEFLRRQPKERQYRALVLRFIKDRTAALLLVEVGLQATAWVS--------------- 66 (96)
Q Consensus 2 ~~~~~~~~~~a~~ieR~s~RyW~l~YL~~~~~~~~~~AvVl~~~~~~~~~vlL~dl~le~~~~~~--------------- 66 (96)
+..++..-+.|.++||.+.+||+.+||+++. |++++|+|.+-.+ ...-|.|++.++|.-++.+
T Consensus 542 ~~~~~~~er~a~~aer~~~~~~~~~yl~~~i-G~~~~g~I~~v~~-~GifV~L~~~~veGlV~~s~l~~d~y~~d~~~~~ 619 (654)
T TIGR00358 542 AEHCSDTERRARDAERDVADWLKCRYLLDKV-GTEFSGEISSVTR-FGMFVRLDDNGIDGLIHISTLHNDYYVFDQEKMA 619 (654)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhhhhCC-CcEEEEEEEeEEc-CcEEEEecCCceEEEEEeEeCCCcceEEeccccE
Confidence 4567888899999999999999999999999 9999999999777 7788899988888844442
Q ss_pred -------CCCCCCCEEEEEEeeecCCCCeEEEE
Q 034382 67 -------VGAQIGDEVEVKVEEAHPRDDIIYLK 92 (96)
Q Consensus 67 -------~~~~~Gd~v~v~v~~vdP~~~~l~l~ 92 (96)
..+++||.|.|+|.+||+....|.|.
T Consensus 620 l~g~~~~~~~~lGD~V~Vki~~vd~~~~~I~f~ 652 (654)
T TIGR00358 620 LIGKGTGKVYRIGDRVTVKLTEVNMETRSIIFE 652 (654)
T ss_pred EEeccCCcEECCCCEEEEEEEEEecccCeEEEE
Confidence 34889999999999999999999886
No 2
>TIGR02063 RNase_R ribonuclease R. This family consists of an exoribonuclease, ribonuclease R, also called VacB. It is one of the eight exoribonucleases reported in E. coli and is broadly distributed throughout the bacteria. In E. coli, double mutants of this protein and polynucleotide phosphorylase are not viable. Scoring between trusted and noise cutoffs to the model are shorter, divergent forms from the Chlamydiae, and divergent forms from the Campylobacterales (including Helicobacter pylori) and Leptospira interrogans.
Probab=98.72 E-value=7.1e-08 Score=80.92 Aligned_cols=89 Identities=15% Similarity=0.150 Sum_probs=74.1
Q ss_pred cchhcHhHHHHHHhhhccccchHHHHhhhCCCCCeEEEEEEEEccCceEEEEeecceeeEEEeec---------------
Q 034382 2 ASIVNMQTRIARRLSNTSLRYWIIEFLRRQPKERQYRALVLRFIKDRTAALLLVEVGLQATAWVS--------------- 66 (96)
Q Consensus 2 ~~~~~~~~~~a~~ieR~s~RyW~l~YL~~~~~~~~~~AvVl~~~~~~~~~vlL~dl~le~~~~~~--------------- 66 (96)
+..++..-+.|.++||.+..+|+..|++.+. |++++|.|.+-.. ..+-|-|++.+.+.-++.+
T Consensus 597 ~~~~~~~er~a~~aer~~~~~~~~~yl~~~i-G~~~~g~V~~v~~-fGifV~L~~~~~eGlvhis~l~~d~~~~d~~~~~ 674 (709)
T TIGR02063 597 AEHSSKTERRADEAERDVNDWKKAEYMSEKI-GEEFEGVISGVTS-FGLFVELENNTIEGLVHISTLKDDYYVFDEKGLA 674 (709)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhhhccC-CcEEEEEEEEEEe-CCEEEEecCCceEEEEEeeecCCCcEEEcccceE
Confidence 4567888999999999999999999999999 9999999998665 5566666665555555432
Q ss_pred -------CCCCCCCEEEEEEeeecCCCCeEEEE
Q 034382 67 -------VGAQIGDEVEVKVEEAHPRDDIIYLK 92 (96)
Q Consensus 67 -------~~~~~Gd~v~v~v~~vdP~~~~l~l~ 92 (96)
..+++||.|.|+|.+||+.++.|.|.
T Consensus 675 l~g~~~~~~~~lGd~V~Vkv~~vd~~~~~I~~~ 707 (709)
T TIGR02063 675 LVGERTGKVFRLGDRVKVRVVKADLDTGKIDFE 707 (709)
T ss_pred EEeccCCcEECCCCEEEEEEEEEecccCeEEEE
Confidence 24789999999999999999999986
No 3
>COG0557 VacB Exoribonuclease R [Transcription]
Probab=98.57 E-value=3e-07 Score=77.30 Aligned_cols=90 Identities=20% Similarity=0.277 Sum_probs=81.7
Q ss_pred chhcHhHHHHHHhhhccccchHHHHhhhCCCCCeEEEEEEEEccCceEEEEeecceeeEEEeec--C-------------
Q 034382 3 SIVNMQTRIARRLSNTSLRYWIIEFLRRQPKERQYRALVLRFIKDRTAALLLVEVGLQATAWVS--V------------- 67 (96)
Q Consensus 3 ~~~~~~~~~a~~ieR~s~RyW~l~YL~~~~~~~~~~AvVl~~~~~~~~~vlL~dl~le~~~~~~--~------------- 67 (96)
...+.+-+.|.++||....||+++|+..+. |.+|+|+|+...+ ....|.||++++|..+..+ .
T Consensus 593 ~~~s~~er~a~~aer~~~~~~~~~~m~~~v-g~~f~g~V~~v~~-~g~~V~l~~~~ieglV~~s~L~~d~y~~~~~~~~l 670 (706)
T COG0557 593 AHISSAERRAQEAERDVIDLLKAEYMKKRV-GEEFDGVVTGVTS-FGFFVELPELGLEGLVHISSLPDDYYHFDERGQAL 670 (706)
T ss_pred HHhCHHHHHHHHHHHHHHHHHHHHHHHHhc-CCEEEEEEEEEEe-ccEEEEecccccccceEcccCCCceeeecccccee
Confidence 456788899999999999999999999999 8999999999999 9999999999999888775 2
Q ss_pred -------CCCCCCEEEEEEeeecCCCCeEEEEEe
Q 034382 68 -------GAQIGDEVEVKVEEAHPRDDIIYLKEV 94 (96)
Q Consensus 68 -------~~~~Gd~v~v~v~~vdP~~~~l~l~e~ 94 (96)
...+||.|.|++.+||+....+.|.-+
T Consensus 671 ~~~~~~~~~~lgd~v~v~v~~v~~~~~~i~~~~v 704 (706)
T COG0557 671 VGEKSGKVYRLGDEVKVKVTSVDLDERKIDFELV 704 (706)
T ss_pred eccccccccccCCEEEEEEEEEcccccceEEEec
Confidence 378999999999999999999988754
No 4
>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=98.46 E-value=1.1e-06 Score=73.35 Aligned_cols=89 Identities=17% Similarity=0.231 Sum_probs=69.4
Q ss_pred chhcHhHHHHHHhhhccccchHHHHhhhCCC-CCeEEEEEEEEccCceEEEEeecceeeEEE------------------
Q 034382 3 SIVNMQTRIARRLSNTSLRYWIIEFLRRQPK-ERQYRALVLRFIKDRTAALLLVEVGLQATA------------------ 63 (96)
Q Consensus 3 ~~~~~~~~~a~~ieR~s~RyW~l~YL~~~~~-~~~~~AvVl~~~~~~~~~vlL~dl~le~~~------------------ 63 (96)
..++..-+.|.++||.+..+|+.+||+++.. +++|+|+|.+... ....|-|++.+++.-+
T Consensus 526 ~~~s~~er~a~~aeR~~~~~~~~~yl~~~~g~~~~f~g~I~~v~~-~g~~v~l~~~~~~g~v~~~~l~~~~~~~~~~~~~ 604 (639)
T TIGR02062 526 VQLAERRRLNRIAERDVADWLYARFLADKAAKNTRFAAEIVDISR-GGMRVRLLENGAIAFIPAAFLHANREELVCNQEN 604 (639)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCCcEEEEEEEeeeC-CcEEEEEecCceEEEEEhhhcCCCCcceEEcccc
Confidence 3567778999999999999999999999972 3499999998777 5555555554444332
Q ss_pred ---eec--CCCCCCCEEEEEEeeecCCCCeEEEE
Q 034382 64 ---WVS--VGAQIGDEVEVKVEEAHPRDDIIYLK 92 (96)
Q Consensus 64 ---~~~--~~~~~Gd~v~v~v~~vdP~~~~l~l~ 92 (96)
... ..+.+||.|.|+|.+||+....|.|.
T Consensus 605 ~~~~l~g~~~~~lgd~v~V~v~~vd~~~~~i~~~ 638 (639)
T TIGR02062 605 GTVQIKGETVYKIGDVIDVVLTEVRMETRSIIAR 638 (639)
T ss_pred cEEEEeccEEEecCCEEEEEEEEeccccCcEeee
Confidence 221 24889999999999999999999875
No 5
>PRK05054 exoribonuclease II; Provisional
Probab=98.45 E-value=1.4e-06 Score=72.82 Aligned_cols=90 Identities=14% Similarity=0.208 Sum_probs=71.6
Q ss_pred cchhcHhHHHHHHhhhccccchHHHHhhhCCCC--CeEEEEEEEEccCceEEEEeecceeeEEEee--------------
Q 034382 2 ASIVNMQTRIARRLSNTSLRYWIIEFLRRQPKE--RQYRALVLRFIKDRTAALLLVEVGLQATAWV-------------- 65 (96)
Q Consensus 2 ~~~~~~~~~~a~~ieR~s~RyW~l~YL~~~~~~--~~~~AvVl~~~~~~~~~vlL~dl~le~~~~~-------------- 65 (96)
+..++...+.+.++||.+..+|+.+|++++. | ++|+|+|.+... ...-|.|++.+++.-++.
T Consensus 529 ~~~~s~~er~a~~aer~~~~~~~~~y~~~~~-G~~~~f~g~I~~v~~-~G~fV~l~~~~veglV~~~~l~~~~~~y~~~~ 606 (644)
T PRK05054 529 TVQLAERRRLNRMAERDVGDWLYARYLKDKA-GTDTRFAAEIIDISR-GGMRVRLLENGAVAFIPASFLHAVRDELVCNQ 606 (644)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhhcc-CCCeEEEEEEEeeec-CcEEEEEeCCceEEEEEccccCCCccceEEcc
Confidence 3456778889999999999999999999998 5 499999998777 555566655544444222
Q ss_pred -------c--CCCCCCCEEEEEEeeecCCCCeEEEEE
Q 034382 66 -------S--VGAQIGDEVEVKVEEAHPRDDIIYLKE 93 (96)
Q Consensus 66 -------~--~~~~~Gd~v~v~v~~vdP~~~~l~l~e 93 (96)
. ....+||+|.|+|.+||+....|.|.=
T Consensus 607 ~~~~~~~~~~~~~~lGd~V~V~v~~vd~~~~~i~~~~ 643 (644)
T PRK05054 607 ENGTVQIKGETVYKLGDVIDVTLAEVRMETRSIIARP 643 (644)
T ss_pred ccceEEEeCCEEEcCCCEEEEEEEEEccccCeEEEEE
Confidence 1 358899999999999999999998863
No 6
>PRK11642 exoribonuclease R; Provisional
Probab=97.89 E-value=8.7e-05 Score=63.84 Aligned_cols=89 Identities=18% Similarity=0.204 Sum_probs=74.8
Q ss_pred chhcHhHHHHHHhhhccccchHHHHhhhCCCCCeEEEEEEEEccCceEEEEeecceeeEEEeec----------------
Q 034382 3 SIVNMQTRIARRLSNTSLRYWIIEFLRRQPKERQYRALVLRFIKDRTAALLLVEVGLQATAWVS---------------- 66 (96)
Q Consensus 3 ~~~~~~~~~a~~ieR~s~RyW~l~YL~~~~~~~~~~AvVl~~~~~~~~~vlL~dl~le~~~~~~---------------- 66 (96)
..++..-+.|..+||....+=+..|++.+. |++++|+|.+-.. ...-|-|++.++|.-++.+
T Consensus 614 ~~~s~~er~A~~aeR~~~~~~~~~~m~~~i-Ge~f~G~Is~V~~-fGifVeL~~~~vEGlV~vs~L~~d~y~~d~~~~~L 691 (813)
T PRK11642 614 QHCSMTERRADEATRDVADWLKCDFMLDQV-GNVFKGVISSVTG-FGFFVRLDDLFIDGLVHVSSLDNDYYRFDQVGQRL 691 (813)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhhhccC-CcEEEEEEEEeec-CceEEEECCCCeeeeEEEeecCCcceEecchheEE
Confidence 456777889999999999888888888888 9999999999777 7788888888777766653
Q ss_pred ------CCCCCCCEEEEEEeeecCCCCeEEEEE
Q 034382 67 ------VGAQIGDEVEVKVEEAHPRDDIIYLKE 93 (96)
Q Consensus 67 ------~~~~~Gd~v~v~v~~vdP~~~~l~l~e 93 (96)
..+.+||.|.|+|.+||+....|.|.=
T Consensus 692 ~g~~~~~~~~lGD~V~VkV~~vD~~~rkI~f~l 724 (813)
T PRK11642 692 IGESSGQTYRLGDRVEVRVEAVNMDERKIDFSL 724 (813)
T ss_pred ecccCCcEECCCCEEEEEEEEeecCCCeEEEEE
Confidence 237899999999999999999998863
No 7
>KOG2102 consensus Exosomal 3'-5' exoribonuclease complex, subunit Rrp44/Dis3 [Translation, ribosomal structure and biogenesis]
Probab=97.10 E-value=0.0019 Score=56.55 Aligned_cols=91 Identities=20% Similarity=0.321 Sum_probs=73.3
Q ss_pred cchhcHhHHHHHHhhhccccchHHHHhhhCCCCCeEEEEEEEEccCceEEEEeecceeeEEEeec----C-CCCCC----
Q 034382 2 ASIVNMQTRIARRLSNTSLRYWIIEFLRRQPKERQYRALVLRFIKDRTAALLLVEVGLQATAWVS----V-GAQIG---- 72 (96)
Q Consensus 2 ~~~~~~~~~~a~~ieR~s~RyW~l~YL~~~~~~~~~~AvVl~~~~~~~~~vlL~dl~le~~~~~~----~-~~~~G---- 72 (96)
+..++..-+.+..+++.|..||...||+... ..-+|+|+.-.. +...|++|++|++.++..+ . .+-..
T Consensus 820 ~~~~N~r~~~a~~a~~~S~~l~~~~~~k~~~--~~~~a~v~~V~~-~~~~v~ipe~G~e~~v~l~~~~~~~~~~~~~~~~ 896 (941)
T KOG2102|consen 820 AANCNERKKAAKKAQEASTELYLCEYLKDKQ--VLEEAVVLFVRP-NGIDVVIPEYGLEGRVYLDLLKPSQTFFLDDEVS 896 (941)
T ss_pred HhhhhhhHHHHHHHHHhhHHHHHHHHHHhcc--cccceEEEEEec-CceEEEEcccCceEEEEecccCCccceeeccccc
Confidence 4567888999999999999999999999985 355899998777 9999999999999999987 1 11111
Q ss_pred ------CEEEEE--EeeecCCCCeEEEEEec
Q 034382 73 ------DEVEVK--VEEAHPRDDIIYLKEVV 95 (96)
Q Consensus 73 ------d~v~v~--v~~vdP~~~~l~l~e~~ 95 (96)
+.+.+. +.+.++..+.|++.++.
T Consensus 897 ~~~~~~~~v~~~~~~~~~~~~~~~l~~~~~~ 927 (941)
T KOG2102|consen 897 LRFEESDPVVVRIKLDKLVPQPDRLRIELVS 927 (941)
T ss_pred ccccccCCceeeecccccccCcceEEEEecc
Confidence 444444 67889999999988764
No 8
>cd04471 S1_RNase_R S1_RNase_R: RNase R C-terminal S1 domain. RNase R is a processive 3' to 5' exoribonuclease, which is a homolog of RNase II. RNase R degrades RNA with secondary structure having a 3' overhang of at least 7 nucleotides. RNase R and PNPase play an important role in the degradation of RNA with extensive secondary structure, such as rRNA, tRNA, and certain mRNA which contains repetitive extragenic palindromic sequences. The C-terminal S1 domain binds ssRNA.
Probab=97.05 E-value=0.011 Score=35.94 Aligned_cols=58 Identities=16% Similarity=0.181 Sum_probs=47.5
Q ss_pred CCeEEEEEEEEccCceEEEEeecceeeEEEeec----------------------CCCCCCCEEEEEEeeecCCCCeEEE
Q 034382 34 ERQYRALVLRFIKDRTAALLLVEVGLQATAWVS----------------------VGAQIGDEVEVKVEEAHPRDDIIYL 91 (96)
Q Consensus 34 ~~~~~AvVl~~~~~~~~~vlL~dl~le~~~~~~----------------------~~~~~Gd~v~v~v~~vdP~~~~l~l 91 (96)
|+.++|.|..-.+ ..+-|.|+.++.+..+..+ ..+++||.+.|++..+|+..+.+.+
T Consensus 2 g~~~~g~V~~v~~-~G~fv~l~~~~~~G~v~~~~l~~~~~~~d~~~~~~~~~~~~~~~~~gd~v~v~v~~vd~~~~~i~~ 80 (83)
T cd04471 2 GEEFDGVISGVTS-FGLFVELDNLTVEGLVHVSTLGDDYYEFDEENHALVGERTGKVFRLGDKVKVRVVRVDLDRRKIDF 80 (83)
T ss_pred CCEEEEEEEeEEe-eeEEEEecCCCEEEEEEEEecCCCcEEEcccceEEEeccCCCEEcCCCEEEEEEEEeccccCEEEE
Confidence 6789999999777 8888888887777666554 2248899999999999998888887
Q ss_pred E
Q 034382 92 K 92 (96)
Q Consensus 92 ~ 92 (96)
.
T Consensus 81 ~ 81 (83)
T cd04471 81 E 81 (83)
T ss_pred E
Confidence 5
No 9
>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=96.99 E-value=0.017 Score=34.59 Aligned_cols=58 Identities=17% Similarity=0.123 Sum_probs=47.4
Q ss_pred CCeEEEEEEEEccCceEEEEeecceeeEEEeec--C---------CCCCCCEEEEEEeeecCCCCeEEEE
Q 034382 34 ERQYRALVLRFIKDRTAALLLVEVGLQATAWVS--V---------GAQIGDEVEVKVEEAHPRDDIIYLK 92 (96)
Q Consensus 34 ~~~~~AvVl~~~~~~~~~vlL~dl~le~~~~~~--~---------~~~~Gd~v~v~v~~vdP~~~~l~l~ 92 (96)
|+.+.|.|.+-.+ ..+.|-|.+.+.+.-++.+ . .+.+||.+.++|.++|+-.+.+.|.
T Consensus 3 g~~v~g~V~~i~~-~g~~v~l~~~~~~g~i~~~~l~~~~~~~~~~~~~~Gd~v~v~i~~vd~~~~~i~ls 71 (77)
T cd05708 3 GQKIDGTVRRVED-YGVFIDIDGTNVSGLCHKSEISDNRVADASKLFRVGDKVRAKVLKIDAEKKRISLG 71 (77)
T ss_pred CCEEEEEEEEEEc-ceEEEEECCCCeEEEEEHHHCCCCccCCHhHeecCCCEEEEEEEEEeCCCCEEEEE
Confidence 7889999999877 7888888776777777765 1 2599999999999999998888765
No 10
>smart00316 S1 Ribosomal protein S1-like RNA-binding domain.
Probab=96.87 E-value=0.022 Score=32.68 Aligned_cols=57 Identities=25% Similarity=0.204 Sum_probs=45.9
Q ss_pred CCeEEEEEEEEccCceEEEEeecceeeEEEeec---CC--------CCCCCEEEEEEeeecCCCCeEEEE
Q 034382 34 ERQYRALVLRFIKDRTAALLLVEVGLQATAWVS---VG--------AQIGDEVEVKVEEAHPRDDIIYLK 92 (96)
Q Consensus 34 ~~~~~AvVl~~~~~~~~~vlL~dl~le~~~~~~---~~--------~~~Gd~v~v~v~~vdP~~~~l~l~ 92 (96)
|....|.|.+..+ ..+.+-+.. +++.-++.+ .. +++||.+.++|.++|+.++.+.+.
T Consensus 3 G~~v~g~V~~v~~-~g~~v~i~~-~~~g~l~~~~~~~~~~~~~~~~~~~G~~v~~~V~~~~~~~~~i~ls 70 (72)
T smart00316 3 GDVVEGTVTEITP-FGAFVDLGN-GVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILS 70 (72)
T ss_pred CCEEEEEEEEEEc-cEEEEEeCC-CCEEEEEHHHCCccccCCHHHeecCCCEEEEEEEEEeCCCCEEEEE
Confidence 7888999999877 777777753 577777664 23 799999999999999998888764
No 11
>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=96.77 E-value=0.032 Score=33.34 Aligned_cols=57 Identities=21% Similarity=0.095 Sum_probs=47.0
Q ss_pred CCeEEEEEEEEccCceEEEEeecceeeEEEeec-----------CCCCCCCEEEEEEeeecCCCCeEEEE
Q 034382 34 ERQYRALVLRFIKDRTAALLLVEVGLQATAWVS-----------VGAQIGDEVEVKVEEAHPRDDIIYLK 92 (96)
Q Consensus 34 ~~~~~AvVl~~~~~~~~~vlL~dl~le~~~~~~-----------~~~~~Gd~v~v~v~~vdP~~~~l~l~ 92 (96)
|...+|.|.+-.+ ..+.|-|. .+.+.-++.+ ..+.+||.+.++|.++|+-++.+.|.
T Consensus 5 G~iv~g~V~~v~~-~g~~V~l~-~~~~g~ip~~~l~~~~~~~~~~~~~~G~~v~v~v~~vd~~~~~i~lS 72 (74)
T PF00575_consen 5 GDIVEGKVTSVED-FGVFVDLG-NGIEGFIPISELSDDRIDDPSEVYKIGQTVRVKVIKVDKEKGRIRLS 72 (74)
T ss_dssp TSEEEEEEEEEET-TEEEEEES-TSSEEEEEGGGSSSSEESSSHGTCETTCEEEEEEEEEETTTTEEEEE
T ss_pred CCEEEEEEEEEEC-CEEEEEEC-CcEEEEEEeehhcCccccccccccCCCCEEEEEEEEEECCCCeEEEE
Confidence 7888999988777 77777777 6777777665 35789999999999999999999875
No 12
>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=96.56 E-value=0.047 Score=31.53 Aligned_cols=56 Identities=25% Similarity=0.178 Sum_probs=40.7
Q ss_pred CCeEEEEEEEEccCceEEEEeecceeeEEEeec-----------CCCCCCCEEEEEEeeecCCCCeEEEE
Q 034382 34 ERQYRALVLRFIKDRTAALLLVEVGLQATAWVS-----------VGAQIGDEVEVKVEEAHPRDDIIYLK 92 (96)
Q Consensus 34 ~~~~~AvVl~~~~~~~~~vlL~dl~le~~~~~~-----------~~~~~Gd~v~v~v~~vdP~~~~l~l~ 92 (96)
|..+.|.|.+-.+ ..+.|-|.+ +.+.-++.+ ..+.+||.+.+++.++|+ ++.+.+.
T Consensus 1 G~~~~g~V~~i~~-~g~~v~i~~-~~~g~l~~~~l~~~~~~~~~~~~~~Gd~v~v~v~~~~~-~~~i~ls 67 (69)
T cd05692 1 GSVVEGTVTRLKP-FGAFVELGG-GISGLVHISQIAHKRVKDVKDVLKEGDKVKVKVLSIDA-RGRISLS 67 (69)
T ss_pred CCEEEEEEEEEEe-eeEEEEECC-CCEEEEEhHHcCCcccCCHHHccCCCCEEEEEEEEECC-CCcEEEE
Confidence 4567888888666 666776653 355555544 126999999999999999 8888764
No 13
>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=96.45 E-value=0.039 Score=32.02 Aligned_cols=55 Identities=27% Similarity=0.222 Sum_probs=42.2
Q ss_pred CCeEEEEEEEEccCceEEEEeecceeeEEEeec-----------CCCCCCCEEEEEEeeecCCCCeEEE
Q 034382 34 ERQYRALVLRFIKDRTAALLLVEVGLQATAWVS-----------VGAQIGDEVEVKVEEAHPRDDIIYL 91 (96)
Q Consensus 34 ~~~~~AvVl~~~~~~~~~vlL~dl~le~~~~~~-----------~~~~~Gd~v~v~v~~vdP~~~~l~l 91 (96)
|...+|.|.+..+ ..+.|-|. ..+.-++.. ..+++||.+.+++.++|+-++.+.|
T Consensus 2 g~~~~g~V~~v~~-~g~~v~l~--~~~g~l~~~e~~~~~~~~~~~~~~~Gd~v~v~i~~vd~~~~~i~l 67 (68)
T cd05688 2 GDVVEGTVKSITD-FGAFVDLG--GVDGLLHISDMSWGRVKHPSEVVNVGDEVEVKVLKIDKERKRISL 67 (68)
T ss_pred CCEEEEEEEEEEe-eeEEEEEC--CeEEEEEhHHCCCccccCHhHEECCCCEEEEEEEEEECCCCEEec
Confidence 6778899998777 66666664 355555433 2269999999999999999988876
No 14
>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=96.41 E-value=0.08 Score=31.64 Aligned_cols=57 Identities=14% Similarity=0.088 Sum_probs=45.3
Q ss_pred CCeEEEEEEEEccCceEEEEeecceeeEEEeec-----------CCCCCCCEEEEEEeeecCCCCeEEEE
Q 034382 34 ERQYRALVLRFIKDRTAALLLVEVGLQATAWVS-----------VGAQIGDEVEVKVEEAHPRDDIIYLK 92 (96)
Q Consensus 34 ~~~~~AvVl~~~~~~~~~vlL~dl~le~~~~~~-----------~~~~~Gd~v~v~v~~vdP~~~~l~l~ 92 (96)
|...+|.|.+-.+ ..+.+-|+. +++.-++.+ ..+++||.+.++|.++|+..+.+.|.
T Consensus 4 G~iv~g~V~~v~~-~gi~v~l~~-~~~g~v~~s~l~~~~~~~~~~~~~~Gd~v~~~V~~~d~~~~~i~ls 71 (73)
T cd05706 4 GDILPGRVTKVND-RYVLVQLGN-KVTGPSFITDALDDYSEALPYKFKKNDIVRACVLSVDVPNKKIALS 71 (73)
T ss_pred CCEEEEEEEEEeC-CeEEEEeCC-CcEEEEEhhhccCccccccccccCCCCEEEEEEEEEeCCCCEEEEE
Confidence 7889999999766 777777765 466666653 23789999999999999999988875
No 15
>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=96.36 E-value=0.045 Score=31.59 Aligned_cols=56 Identities=21% Similarity=0.102 Sum_probs=41.2
Q ss_pred CCeEEEEEEEEccCceEEEEeecceeeEEEeec---C--------CCCCCCEEEEEEeeecCCCCeEEE
Q 034382 34 ERQYRALVLRFIKDRTAALLLVEVGLQATAWVS---V--------GAQIGDEVEVKVEEAHPRDDIIYL 91 (96)
Q Consensus 34 ~~~~~AvVl~~~~~~~~~vlL~dl~le~~~~~~---~--------~~~~Gd~v~v~v~~vdP~~~~l~l 91 (96)
|..+.|.|.+-.+ ..+.|-|.+ +.+.-++.+ . .+++||.+.+++.++|+..+.+.|
T Consensus 1 g~~~~g~V~~i~~-~G~fv~l~~-~~~g~~~~~~l~~~~~~~~~~~~~~Gd~v~v~i~~vd~~~~~i~l 67 (68)
T cd05685 1 GMVLEGVVTNVTD-FGAFVDIGV-KQDGLIHISKMADRFVSHPSDVVSVGDIVEVKVISIDEERGRISL 67 (68)
T ss_pred CCEEEEEEEEEec-ccEEEEcCC-CCEEEEEHHHCCCccccCHHHhcCCCCEEEEEEEEEECCCCEEec
Confidence 4578888888666 666666654 355555544 1 269999999999999998888765
No 16
>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=96.35 E-value=0.073 Score=32.52 Aligned_cols=57 Identities=14% Similarity=0.145 Sum_probs=44.3
Q ss_pred CCeEEEEEEEEccCceEEEEeecceeeEEEeec-------------CCCCCCCEEEEEEeeecCCCCeEEEE
Q 034382 34 ERQYRALVLRFIKDRTAALLLVEVGLQATAWVS-------------VGAQIGDEVEVKVEEAHPRDDIIYLK 92 (96)
Q Consensus 34 ~~~~~AvVl~~~~~~~~~vlL~dl~le~~~~~~-------------~~~~~Gd~v~v~v~~vdP~~~~l~l~ 92 (96)
|...+|.|.+-.. ..+.|.|.+ +++.-++.. ..+++||.+.++|..+|+-+..|.|.
T Consensus 1 G~~V~g~V~~i~~-~g~~V~l~~-~i~G~i~~~~ls~~~~~~~~~~~~~~vG~~v~~kV~~id~~~~~i~Ls 70 (73)
T cd05703 1 GQEVTGFVNNVSK-EFVWLTISP-DVKGRIPLLDLSDDVSVLEHPEKKFPIGQALKAKVVGVDKEHKLLRLS 70 (73)
T ss_pred CCEEEEEEEEEeC-CEEEEEeCC-CcEEEEEHHHcCCccccccCHHHhCCCCCEEEEEEEEEeCCCCEEEEE
Confidence 4567788888766 777777765 577666653 23899999999999999999998875
No 17
>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=96.31 E-value=0.073 Score=30.88 Aligned_cols=56 Identities=27% Similarity=0.317 Sum_probs=39.0
Q ss_pred CCeEEEEEEEEccCceEEEEeecceeeEEEeec-----------CCCCCCCEEEEEEeeecCCCCeEEEE
Q 034382 34 ERQYRALVLRFIKDRTAALLLVEVGLQATAWVS-----------VGAQIGDEVEVKVEEAHPRDDIIYLK 92 (96)
Q Consensus 34 ~~~~~AvVl~~~~~~~~~vlL~dl~le~~~~~~-----------~~~~~Gd~v~v~v~~vdP~~~~l~l~ 92 (96)
|+.+.|.|.+-.+ ..+.+-|++ ..+.-++.+ ..+++||.+.+++.++|+ ++.+.++
T Consensus 1 g~~~~g~V~~v~~-~G~~v~l~~-~~~g~l~~~~l~~~~~~~~~~~~~~Gd~v~v~v~~~d~-~~~i~ls 67 (68)
T cd04472 1 GKIYEGKVVKIKD-FGAFVEILP-GKDGLVHISELSDERVEKVEDVLKVGDEVKVKVIEVDD-RGRISLS 67 (68)
T ss_pred CCEEEEEEEEEEE-eEEEEEeCC-CCEEEEEhHHcCCccccCHHHccCCCCEEEEEEEEECC-CCcEEee
Confidence 3567777777666 666666653 244444432 236999999999999999 8888764
No 18
>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=96.19 E-value=0.084 Score=31.96 Aligned_cols=58 Identities=19% Similarity=0.193 Sum_probs=42.2
Q ss_pred CCeEE-EEEEEEccCceEEEEeecceeeEEEeec-----------CCCCCCCEEEEEEeeecCCCCeEEEE
Q 034382 34 ERQYR-ALVLRFIKDRTAALLLVEVGLQATAWVS-----------VGAQIGDEVEVKVEEAHPRDDIIYLK 92 (96)
Q Consensus 34 ~~~~~-AvVl~~~~~~~~~vlL~dl~le~~~~~~-----------~~~~~Gd~v~v~v~~vdP~~~~l~l~ 92 (96)
|..++ |-|.+-..+..+.|-|++ +++.-++.+ ..++.||.+.++|..+||.+..|.+.
T Consensus 1 G~v~~~g~V~~v~~~~G~~V~l~~-gv~G~i~~s~l~~~~~~~~~~~~~vG~~v~~kV~~id~~~~~i~lS 70 (71)
T cd05696 1 GAVVDSVKVTKVEPDLGAVFELKD-GLLGFVHISHLSDDKVPSDTGPFKAGTTHKARIIGYSPMDGLLQLS 70 (71)
T ss_pred CcEeeeeEEEEEccCceEEEEeCC-CCEEEEEHHHCCcchhcCcccccCCCCEEEEEEEEEeCCCCEEEEe
Confidence 35566 677775322556677766 566666543 34899999999999999999998874
No 19
>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=96.18 E-value=0.097 Score=30.94 Aligned_cols=57 Identities=14% Similarity=0.177 Sum_probs=40.8
Q ss_pred CCeEEEEEEEEccCceEEEEeecceeeEEEeec-----------CCCCCCCEEEEEEeeecCCCCeEEEE
Q 034382 34 ERQYRALVLRFIKDRTAALLLVEVGLQATAWVS-----------VGAQIGDEVEVKVEEAHPRDDIIYLK 92 (96)
Q Consensus 34 ~~~~~AvVl~~~~~~~~~vlL~dl~le~~~~~~-----------~~~~~Gd~v~v~v~~vdP~~~~l~l~ 92 (96)
|...+|.|.+-.+ ..+.|-|++ +++.-++.+ ..+++||.+.++|.++|+-++.+.|.
T Consensus 1 g~~~~g~V~~v~~-~G~~V~l~~-~~~gli~~s~l~~~~~~~~~~~~~~G~~i~v~v~~~d~~~~~i~ls 68 (70)
T cd05698 1 GLKTHGTIVKVKP-NGCIVSFYN-NVKGFLPKSELSEAFIKDPEEHFRVGQVVKVKVLSCDPEQQRLLLS 68 (70)
T ss_pred CCEEEEEEEEEec-CcEEEEECC-CCEEEEEHHHcChhhcCCHHHcccCCCEEEEEEEEEcCCCCEEEEE
Confidence 3456777777665 666666654 255555443 24899999999999999999888775
No 20
>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=96.15 E-value=0.12 Score=30.64 Aligned_cols=56 Identities=18% Similarity=0.138 Sum_probs=42.1
Q ss_pred CeEEEEEEEEccCceEEEEeecceeeEEEeec-----------CCCCCCCEEEEEEeeecCCCCeEEEE
Q 034382 35 RQYRALVLRFIKDRTAALLLVEVGLQATAWVS-----------VGAQIGDEVEVKVEEAHPRDDIIYLK 92 (96)
Q Consensus 35 ~~~~AvVl~~~~~~~~~vlL~dl~le~~~~~~-----------~~~~~Gd~v~v~v~~vdP~~~~l~l~ 92 (96)
....|.|.+..+ ..+.|-|.. ..+.-++.+ ..+++||.+.++|.++|+.++.+.|.
T Consensus 2 ~iv~g~V~~i~~-~~~~v~l~~-~~~g~l~~~e~~~~~~~~~~~~~~~Gd~i~~~i~~~~~~~~~i~lS 68 (70)
T cd05687 2 DIVKGTVVSVDD-DEVLVDIGY-KSEGIIPISEFSDDPIENGEDEVKVGDEVEVYVLRVEDEEGNVVLS 68 (70)
T ss_pred CEEEEEEEEEeC-CEEEEEeCC-CceEEEEHHHhCccccCCHhHcCCCCCEEEEEEEEEECCCCeEEEE
Confidence 456777877666 677777743 466666665 23899999999999999998888775
No 21
>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=96.11 E-value=0.12 Score=30.96 Aligned_cols=58 Identities=19% Similarity=0.138 Sum_probs=46.8
Q ss_pred CCeEEEEEEEEccCceEEEEeecc-eeeEEEeec-----------CCCCCCCEEEEEEeeecCCCCeEEEE
Q 034382 34 ERQYRALVLRFIKDRTAALLLVEV-GLQATAWVS-----------VGAQIGDEVEVKVEEAHPRDDIIYLK 92 (96)
Q Consensus 34 ~~~~~AvVl~~~~~~~~~vlL~dl-~le~~~~~~-----------~~~~~Gd~v~v~v~~vdP~~~~l~l~ 92 (96)
|....|.|.+-.+ ..+.|-|.+. +++.-++.+ .-+.+||.+.+++.++|+..+.+.|.
T Consensus 4 G~~~~g~V~~v~~-~g~~v~l~~~~~~~gll~~s~l~~~~~~~~~~~~~~Gd~v~vkv~~~d~~~~~i~ls 73 (76)
T cd04452 4 GELVVVTVKSIAD-MGAYVSLLEYGNIEGMILLSELSRRRIRSIRKLVKVGRKEVVKVIRVDKEKGYIDLS 73 (76)
T ss_pred CCEEEEEEEEEEc-cEEEEEEcCCCCeEEEEEhHHcCCcccCCHHHeeCCCCEEEEEEEEEECCCCEEEEE
Confidence 7889999999887 7788888765 477776665 11589999999999999998888774
No 22
>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=96.10 E-value=0.11 Score=30.85 Aligned_cols=57 Identities=11% Similarity=0.092 Sum_probs=42.7
Q ss_pred CCeEEEEEEEEccCceEEEEeecceeeEEEeec-----------CCCCCCCEEEEEEeeecCCCCeEEEE
Q 034382 34 ERQYRALVLRFIKDRTAALLLVEVGLQATAWVS-----------VGAQIGDEVEVKVEEAHPRDDIIYLK 92 (96)
Q Consensus 34 ~~~~~AvVl~~~~~~~~~vlL~dl~le~~~~~~-----------~~~~~Gd~v~v~v~~vdP~~~~l~l~ 92 (96)
|+..+|.|.+-.. ..+.|-|++ +++.-++.. ..+++||.+.++|.++|+.++.+.|.
T Consensus 1 G~~v~g~V~~v~~-~Gv~V~l~~-~v~g~i~~~~l~~~~~~~~~~~~~~Gd~i~~~V~~id~~~~~i~ls 68 (69)
T cd05697 1 GQVVKGTIRKLRP-SGIFVKLSD-HIKGLVPPMHLADVRLKHPEKKFKPGLKVKCRVLSVEPERKRLVLT 68 (69)
T ss_pred CCEEEEEEEEEec-cEEEEEecC-CcEEEEEHHHCCCccccCHHHcCCCCCEEEEEEEEEECCCCEEEEE
Confidence 4567788887666 666677754 366666432 34899999999999999999988764
No 23
>cd05686 S1_pNO40 S1_pNO40: pNO40 , S1-like RNA-binding domain. pNO40 is a nucleolar protein of unknown function with an N-terminal S1 RNA binding domain, a CCHC type zinc finger, and clusters of basic amino acids representing a potential nucleolar targeting signal. pNO40 was identified through a yeast two-hybrid interaction screen of a human kidney cDNA library using the pinin (pnn) protein as bait. pNO40 is thought to play a role in ribosome maturation and/or biogenesis.
Probab=95.87 E-value=0.19 Score=30.38 Aligned_cols=57 Identities=19% Similarity=0.137 Sum_probs=42.1
Q ss_pred CCeEEEEEEEEccCceEEEEeecceeeEEEeec-----------CCCCCCCEEEEEEeeecCCCCeEEEE
Q 034382 34 ERQYRALVLRFIKDRTAALLLVEVGLQATAWVS-----------VGAQIGDEVEVKVEEAHPRDDIIYLK 92 (96)
Q Consensus 34 ~~~~~AvVl~~~~~~~~~vlL~dl~le~~~~~~-----------~~~~~Gd~v~v~v~~vdP~~~~l~l~ 92 (96)
|..++|.|.+-.+ ..+-|-|++...+.-++.+ .-++.||.+.++|.++|+.. .++|.
T Consensus 4 g~~~~g~V~~i~~-fG~fv~l~~~~~eGlvh~sel~~~~~~~~~~~~~~Gd~v~vkv~~vd~~~-ki~ls 71 (73)
T cd05686 4 YQIFKGEVASVTE-YGAFVKIPGCRKQGLVHKSHMSSCRVDDPSEVVDVGEKVWVKVIGREMKD-KMKLS 71 (73)
T ss_pred CCEEEEEEEEEEe-eeEEEEECCCCeEEEEEchhhCCCcccCHhhEECCCCEEEEEEEEECCCC-cEEEE
Confidence 6788888888766 6677777766555555543 12588999999999999965 66664
No 24
>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=95.81 E-value=0.11 Score=30.64 Aligned_cols=56 Identities=21% Similarity=0.248 Sum_probs=41.4
Q ss_pred CCeEEEEEEEEccCceEEEEeecceeeEEEeec-----------CCCCCCCEEEEEEeeecCCCCeEEE
Q 034382 34 ERQYRALVLRFIKDRTAALLLVEVGLQATAWVS-----------VGAQIGDEVEVKVEEAHPRDDIIYL 91 (96)
Q Consensus 34 ~~~~~AvVl~~~~~~~~~vlL~dl~le~~~~~~-----------~~~~~Gd~v~v~v~~vdP~~~~l~l 91 (96)
|....|.|.+-.+ ..+.|-|++ +++.-++.+ ..+.+||.+.++|.++||..+.+.|
T Consensus 1 G~~v~g~V~~v~~-~Gv~V~l~~-~~~G~v~~s~l~~~~~~~~~~~~~~Gd~v~~~v~~~d~~~~~i~l 67 (68)
T cd05707 1 GDVVRGFVKNIAN-NGVFVTLGR-GVDARVRVSELSDSYLKDWKKRFKVGQLVKGKIVSIDPDNGRIEM 67 (68)
T ss_pred CCEEEEEEEEEEC-ccEEEEeCC-CCEEEEEHHHCCchhhcCHhhccCCCCEEEEEEEEEeCCCCEEec
Confidence 3566777777665 666666665 366655553 3389999999999999999988875
No 25
>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=95.63 E-value=0.18 Score=31.04 Aligned_cols=57 Identities=19% Similarity=0.166 Sum_probs=43.7
Q ss_pred CCeEEEEEEEEccCceEEEEeecceeeEEEeec-----------CCCCCCCEEEEEEeeecCCCCeEEEE
Q 034382 34 ERQYRALVLRFIKDRTAALLLVEVGLQATAWVS-----------VGAQIGDEVEVKVEEAHPRDDIIYLK 92 (96)
Q Consensus 34 ~~~~~AvVl~~~~~~~~~vlL~dl~le~~~~~~-----------~~~~~Gd~v~v~v~~vdP~~~~l~l~ 92 (96)
|+.++|.|..-.. ..+.|-|.+ +++.-++.+ ..+.+||.+.++|.++|+..+.+.+.
T Consensus 15 G~i~~g~V~~v~~-~G~fv~l~~-~~~g~v~~~el~~~~~~~~~~~~~~Gd~v~vkV~~id~~~~~i~ls 82 (83)
T cd04461 15 GMVVHGYVRNITP-YGVFVEFLG-GLTGLAPKSYISDEFVTDPSFGFKKGQSVTAKVTSVDEEKQRFLLS 82 (83)
T ss_pred CCEEEEEEEEEee-ceEEEEcCC-CCEEEEEHHHCCcccccCHHHhcCCCCEEEEEEEEEcCCCCEEEEe
Confidence 8899999988666 666666643 355555533 34889999999999999999998874
No 26
>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=95.61 E-value=0.23 Score=30.19 Aligned_cols=56 Identities=20% Similarity=0.210 Sum_probs=38.0
Q ss_pred CCeEEEEEEEEccCceEEEEeecc--eeeEEEeec------------CCCCCCCEEEEEEeeecCCCCeEEEE
Q 034382 34 ERQYRALVLRFIKDRTAALLLVEV--GLQATAWVS------------VGAQIGDEVEVKVEEAHPRDDIIYLK 92 (96)
Q Consensus 34 ~~~~~AvVl~~~~~~~~~vlL~dl--~le~~~~~~------------~~~~~Gd~v~v~v~~vdP~~~~l~l~ 92 (96)
|+.++|.|.+-.+ ..+-|-|.+. +.+.-++.+ .-+++||.+.+++.++| .+.+.|.
T Consensus 1 G~~~~g~V~~v~~-~G~fv~l~~~~~~~~gll~~s~l~~~~~~~~~~~~~~~Gd~v~v~v~~vd--~~~i~~s 70 (79)
T cd05684 1 GKIYKGKVTSIMD-FGCFVQLEGLKGRKEGLVHISQLSFEGRVANPSDVVKRGQKVKVKVISIQ--NGKISLS 70 (79)
T ss_pred CCEEEEEEEEEEe-eeEEEEEeCCCCCcEEEEEhHhccCCCCcCChhheeCCCCEEEEEEEEEe--CCEEEEE
Confidence 4567788877666 6666666644 344444433 12489999999999999 6676654
No 27
>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=95.40 E-value=0.28 Score=29.11 Aligned_cols=57 Identities=26% Similarity=0.255 Sum_probs=38.9
Q ss_pred CCCeEEEEEEEEccCceEEEEeecceeeEEEeec------------CCCCCCCEEEEEEeeecCCCCeEEE
Q 034382 33 KERQYRALVLRFIKDRTAALLLVEVGLQATAWVS------------VGAQIGDEVEVKVEEAHPRDDIIYL 91 (96)
Q Consensus 33 ~~~~~~AvVl~~~~~~~~~vlL~dl~le~~~~~~------------~~~~~Gd~v~v~v~~vdP~~~~l~l 91 (96)
.|..++|.|.+-.+ ..+-+-|++ +.+.-++.. ..++.||.+.+++.++|+-.+.+.+
T Consensus 3 ~g~~~~g~V~~i~~-~G~fv~l~~-~~~Gl~~~~~l~~~~~~~~~~~~~~~Gd~v~v~v~~id~~~~~i~~ 71 (72)
T cd05689 3 EGTRLFGKVTNLTD-YGCFVELEE-GVEGLVHVSEMDWTNKNIHPSKVVSLGDEVEVMVLDIDEERRRISL 71 (72)
T ss_pred CCCEEEEEEEEEEe-eEEEEEcCC-CCEEEEEEEeccCcccccCcccEeCCCCEEEEEEEEeeCCcCEEeC
Confidence 37788888888655 555555543 233322221 2368999999999999999888765
No 28
>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=95.20 E-value=0.27 Score=29.31 Aligned_cols=55 Identities=15% Similarity=0.151 Sum_probs=41.7
Q ss_pred CeEEEEEEEEccCceEEEEeecceeeEEEeec---------CCCCCCCEEEEEEeeecCCCCeEEE
Q 034382 35 RQYRALVLRFIKDRTAALLLVEVGLQATAWVS---------VGAQIGDEVEVKVEEAHPRDDIIYL 91 (96)
Q Consensus 35 ~~~~AvVl~~~~~~~~~vlL~dl~le~~~~~~---------~~~~~Gd~v~v~v~~vdP~~~~l~l 91 (96)
..-+|.|.+-.. .-+.|-|.+ +++.-++.+ ..+++||.+.++|..+||-+..+.|
T Consensus 2 ~~V~g~V~~i~~-~G~~v~l~~-~v~g~v~~~~l~~~~~~~~~~~~G~~i~~kVi~id~~~~~i~L 65 (66)
T cd05695 2 MLVNARVKKVLS-NGLILDFLS-SFTGTVDFLHLDPEKSSKSTYKEGQKVRARILYVDPSTKVVGL 65 (66)
T ss_pred CEEEEEEEEEeC-CcEEEEEcC-CceEEEEHHHcCCccCcccCcCCCCEEEEEEEEEeCCCCEEec
Confidence 345677777666 777777766 577666653 3489999999999999998887765
No 29
>PRK07252 hypothetical protein; Provisional
Probab=95.16 E-value=0.35 Score=32.60 Aligned_cols=57 Identities=18% Similarity=0.152 Sum_probs=43.5
Q ss_pred CCeEEEEEEEEccCceEEEEeecceeeEEEeec-----------CCCCCCCEEEEEEeeecCCCCeEEEE
Q 034382 34 ERQYRALVLRFIKDRTAALLLVEVGLQATAWVS-----------VGAQIGDEVEVKVEEAHPRDDIIYLK 92 (96)
Q Consensus 34 ~~~~~AvVl~~~~~~~~~vlL~dl~le~~~~~~-----------~~~~~Gd~v~v~v~~vdP~~~~l~l~ 92 (96)
|..+.|.|..-.+ ..+.|-|+. +.+.-++.+ ..+.+||.|.|+|.++|+-.+.+.|.
T Consensus 4 G~iv~G~V~~V~~-~G~fVei~~-~~~GllhiseLs~~~~~~~~~~~~vGD~V~VkI~~iD~~~~ri~lS 71 (120)
T PRK07252 4 GDKLKGTITGIKP-YGAFVALEN-GTTGLIHISEIKTGFIDNIHQLLKVGEEVLVQVVDFDEYTGKASLS 71 (120)
T ss_pred CCEEEEEEEEEeC-cEEEEEECC-CCEEEEEHHHcCCccccChhhccCCCCEEEEEEEEEeCCCCEEEEE
Confidence 7889999999777 777777764 345544443 23789999999999999988877654
No 30
>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=95.14 E-value=0.34 Score=28.53 Aligned_cols=56 Identities=21% Similarity=0.188 Sum_probs=43.6
Q ss_pred CCeEEEEEEEEccCceEEEEeecceeeEEEeec----CC-----CCCCCEEEEEEeeecCCCCeEEEE
Q 034382 34 ERQYRALVLRFIKDRTAALLLVEVGLQATAWVS----VG-----AQIGDEVEVKVEEAHPRDDIIYLK 92 (96)
Q Consensus 34 ~~~~~AvVl~~~~~~~~~vlL~dl~le~~~~~~----~~-----~~~Gd~v~v~v~~vdP~~~~l~l~ 92 (96)
|+..+|.|.+..+ .-+.|-+ + +++.-++.+ .. -.+||.+.++|.++|+.++.|.++
T Consensus 1 G~iv~g~V~~v~~-~G~~v~l-~-g~~gfip~s~~~~~~~~~~~~~vG~~i~~~i~~vd~~~~~i~lS 65 (67)
T cd04465 1 GEIVEGKVTEKVK-GGLIVDI-E-GVRAFLPASQVDLRPVEDLDEYVGKELKFKIIEIDRERNNIVLS 65 (67)
T ss_pred CCEEEEEEEEEEC-CeEEEEE-C-CEEEEEEHHHCCCcccCChHHhCCCEEEEEEEEEeCCCCEEEEE
Confidence 4567888888877 7788888 3 678777764 11 148999999999999998888775
No 31
>PRK05807 hypothetical protein; Provisional
Probab=94.96 E-value=0.42 Score=32.83 Aligned_cols=55 Identities=20% Similarity=0.141 Sum_probs=41.7
Q ss_pred CCeEEEEEEEEccCceEEEEeecceeeEEEeec-----------CCCCCCCEEEEEEeeecCCCCeEEEE
Q 034382 34 ERQYRALVLRFIKDRTAALLLVEVGLQATAWVS-----------VGAQIGDEVEVKVEEAHPRDDIIYLK 92 (96)
Q Consensus 34 ~~~~~AvVl~~~~~~~~~vlL~dl~le~~~~~~-----------~~~~~Gd~v~v~v~~vdP~~~~l~l~ 92 (96)
|+.++|.|.+..+ ..+.|-|+ +.+.-++.+ ..+++||.|.|+|.++|+ ++.|.|.
T Consensus 6 G~vv~G~Vt~i~~-~GafV~L~--~~~Glvhiseis~~~v~~~~~~~kvGd~V~VkV~~id~-~gkI~LS 71 (136)
T PRK05807 6 GSILEGTVVNITN-FGAFVEVE--GKTGLVHISEVADTYVKDIREHLKEQDKVKVKVISIDD-NGKISLS 71 (136)
T ss_pred CCEEEEEEEEEEC-CeEEEEEC--CEEEEEEhhhcccccccCccccCCCCCEEEEEEEEECC-CCcEEEE
Confidence 7899999999777 77777774 344444443 236999999999999999 7777654
No 32
>PRK08059 general stress protein 13; Validated
Probab=94.86 E-value=0.39 Score=32.20 Aligned_cols=57 Identities=26% Similarity=0.160 Sum_probs=43.3
Q ss_pred CCeEEEEEEEEccCceEEEEeecceeeEEEeec-----------CCCCCCCEEEEEEeeecCCCCeEEEE
Q 034382 34 ERQYRALVLRFIKDRTAALLLVEVGLQATAWVS-----------VGAQIGDEVEVKVEEAHPRDDIIYLK 92 (96)
Q Consensus 34 ~~~~~AvVl~~~~~~~~~vlL~dl~le~~~~~~-----------~~~~~Gd~v~v~v~~vdP~~~~l~l~ 92 (96)
|..+.|.|.+-.+ ..+.|-|.+ +.+.-++.+ ..+.+||.+.++|.++|+-.+.+.|.
T Consensus 8 G~iv~G~V~~i~~-~G~fV~i~~-~~~Gli~~sel~~~~~~~~~~~~~vGD~I~vkI~~id~~~~~i~ls 75 (123)
T PRK08059 8 GSVVTGKVTGIQP-YGAFVALDE-ETQGLVHISEITHGFVKDIHDFLSVGDEVKVKVLSVDEEKGKISLS 75 (123)
T ss_pred CCEEEEEEEEEec-ceEEEEECC-CCEEEEEHHHCCcccccCHHHcCCCCCEEEEEEEEEECCCCeEEEE
Confidence 7899999999777 777777654 345544443 23689999999999999988777664
No 33
>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=94.78 E-value=0.34 Score=28.32 Aligned_cols=24 Identities=29% Similarity=0.210 Sum_probs=21.6
Q ss_pred CCCCCCEEEEEEeeecCCCCeEEE
Q 034382 68 GAQIGDEVEVKVEEAHPRDDIIYL 91 (96)
Q Consensus 68 ~~~~Gd~v~v~v~~vdP~~~~l~l 91 (96)
.+++||.+.+++.++|+..+.|.+
T Consensus 45 ~~~~G~~v~v~v~~id~~~~~i~l 68 (69)
T cd05690 45 IYKKGQEVEAVVLNIDVERERISL 68 (69)
T ss_pred EECCCCEEEEEEEEEECCcCEEeC
Confidence 469999999999999999988875
No 34
>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=94.77 E-value=0.44 Score=29.16 Aligned_cols=56 Identities=14% Similarity=0.141 Sum_probs=42.5
Q ss_pred CCeEEEEEEEEccCceEEEEeecceeeEEEeec--------------CCCCCCCEEEEEEeeecCCCCeEEE
Q 034382 34 ERQYRALVLRFIKDRTAALLLVEVGLQATAWVS--------------VGAQIGDEVEVKVEEAHPRDDIIYL 91 (96)
Q Consensus 34 ~~~~~AvVl~~~~~~~~~vlL~dl~le~~~~~~--------------~~~~~Gd~v~v~v~~vdP~~~~l~l 91 (96)
|+...|.|..-.. ..+-|-|.+ +++..++.. ..+++||.+.++|.++|+.++.|.|
T Consensus 4 G~~V~g~V~~i~~-~G~fV~l~~-~v~G~v~~~~ls~~~~~~~~~~~~~~~~G~~v~~kVl~id~~~~~i~L 73 (74)
T cd05705 4 GQLLRGYVSSVTK-QGVFFRLSS-SIVGRVLFQNVTKYFVSDPSLYNKYLPEGKLLTAKVLSVNSEKNLVEL 73 (74)
T ss_pred CCEEEEEEEEEeC-CcEEEEeCC-CCEEEEEHHHccCccccChhhHhcccCCCCEEEEEEEEEECCCCEEec
Confidence 6788888888665 556666653 677766622 2369999999999999999988876
No 35
>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=94.77 E-value=0.31 Score=27.24 Aligned_cols=24 Identities=50% Similarity=0.618 Sum_probs=21.6
Q ss_pred CCCCCCEEEEEEeeecCCCCeEEE
Q 034382 68 GAQIGDEVEVKVEEAHPRDDIIYL 91 (96)
Q Consensus 68 ~~~~Gd~v~v~v~~vdP~~~~l~l 91 (96)
.+++||.+.+++.++|+.++.+.+
T Consensus 41 ~~~~G~~v~~~v~~~d~~~~~i~l 64 (65)
T cd00164 41 VFKVGDEVEVKVLEVDPEKGRISL 64 (65)
T ss_pred EeCCCCEEEEEEEEEcCCcCEEec
Confidence 479999999999999998888775
No 36
>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=94.72 E-value=0.46 Score=27.93 Aligned_cols=57 Identities=21% Similarity=0.258 Sum_probs=40.2
Q ss_pred CCeEEEEEEEEccCceEEEEeecceeeEEEeec-----------CCCCCCCEEEEEEeeecCCCCeEEEE
Q 034382 34 ERQYRALVLRFIKDRTAALLLVEVGLQATAWVS-----------VGAQIGDEVEVKVEEAHPRDDIIYLK 92 (96)
Q Consensus 34 ~~~~~AvVl~~~~~~~~~vlL~dl~le~~~~~~-----------~~~~~Gd~v~v~v~~vdP~~~~l~l~ 92 (96)
|....|.|.+-.+ ..+.|-|.+ +++.-++.+ ..+.+||.+.+++.++|+.++.+.+.
T Consensus 1 G~~v~g~V~~v~~-~g~~v~l~~-~~~g~i~~~~~~~~~~~~~~~~~~~Gd~v~~~v~~~d~~~~~i~ls 68 (73)
T cd05691 1 GSIVTGKVTEVDA-KGATVKLGD-GVEGFLRAAELSRDRVEDATERFKVGDEVEAKITNVDRKNRKISLS 68 (73)
T ss_pred CCEEEEEEEEEEC-CeEEEEeCC-CCEEEEEHHHCCCccccCHHHccCCCCEEEEEEEEEeCCCCEEEEE
Confidence 3566777877666 666666643 255555553 23689999999999999988877654
No 37
>PRK08582 hypothetical protein; Provisional
Probab=94.64 E-value=0.59 Score=32.25 Aligned_cols=56 Identities=30% Similarity=0.283 Sum_probs=40.4
Q ss_pred CCeEEEEEEEEccCceEEEEeecceeeEEEeec-----------CCCCCCCEEEEEEeeecCCCCeEEEE
Q 034382 34 ERQYRALVLRFIKDRTAALLLVEVGLQATAWVS-----------VGAQIGDEVEVKVEEAHPRDDIIYLK 92 (96)
Q Consensus 34 ~~~~~AvVl~~~~~~~~~vlL~dl~le~~~~~~-----------~~~~~Gd~v~v~v~~vdP~~~~l~l~ 92 (96)
|..++|.|..-.+ ..+-|-|++ +.+.-++.+ ..+.+||.|.++|.++|+ ++.|.|.
T Consensus 6 G~iv~G~V~~I~~-fG~fV~L~~-~~~GlVhiSels~~~v~~~~~~l~vGD~VkvkV~~id~-~gkI~LS 72 (139)
T PRK08582 6 GSKLQGKVTGITN-FGAFVELPE-GKTGLVHISEVADNYVKDINDHLKVGDEVEVKVLNVED-DGKIGLS 72 (139)
T ss_pred CCEEEEEEEEEEC-CeEEEEECC-CCEEEEEeeccCcccccccccccCCCCEEEEEEEEECC-CCcEEEE
Confidence 7889999998666 566666654 344444443 348999999999999998 4777654
No 38
>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=94.38 E-value=0.66 Score=28.33 Aligned_cols=56 Identities=25% Similarity=0.270 Sum_probs=43.3
Q ss_pred CCeEEEEEEEEccCceEEEEeecceeeEEEeec---CCCCCCCEEEEEEeeecCCCCeEEEE
Q 034382 34 ERQYRALVLRFIKDRTAALLLVEVGLQATAWVS---VGAQIGDEVEVKVEEAHPRDDIIYLK 92 (96)
Q Consensus 34 ~~~~~AvVl~~~~~~~~~vlL~dl~le~~~~~~---~~~~~Gd~v~v~v~~vdP~~~~l~l~ 92 (96)
|+.++|.|.+-.+ ..+-+.|.+ +.+.-++.+ ..++.||.+.+++.++ ..++.+.+.
T Consensus 17 G~~~~g~V~~i~~-~G~fV~l~~-~~~Glv~~se~~~~~~iGd~v~v~I~~i-~e~~~i~l~ 75 (77)
T cd04473 17 GKLYKGKVNGVAK-YGVFVDLND-HVRGLIHRSNLLRDYEVGDEVIVQVTDI-PENGNIDLI 75 (77)
T ss_pred CCEEEEEEEeEec-ceEEEEECC-CcEEEEEchhccCcCCCCCEEEEEEEEE-CCCCcEEEE
Confidence 8899999999666 666777765 355555444 5689999999999999 777888765
No 39
>TIGR00008 infA translation initiation factor IF-1. This family consists of translation initiation factor IF-1 as found in bacteria and chloroplasts. This protein, about 70 residues in length, consists largely of an S1 RNA binding domain (pfam00575).
Probab=93.83 E-value=0.78 Score=28.43 Aligned_cols=56 Identities=18% Similarity=0.128 Sum_probs=44.4
Q ss_pred CeEEEEEEEEccCceEEEEeecceeeEEEeecC-------CCCCCCEEEEEEeeecCCCCeEEE
Q 034382 35 RQYRALVLRFIKDRTAALLLVEVGLQATAWVSV-------GAQIGDEVEVKVEEAHPRDDIIYL 91 (96)
Q Consensus 35 ~~~~AvVl~~~~~~~~~vlL~dl~le~~~~~~~-------~~~~Gd~v~v~v~~vdP~~~~l~l 91 (96)
-+.+|+|++-++.....|.|++ |.+.-+..+. .+-|||.|.|.+..-|+-.+.|-+
T Consensus 5 ie~~G~V~e~L~~~~f~V~l~n-g~~vla~i~GKmr~~rI~I~~GD~V~Ve~spyd~tkgrIi~ 67 (68)
T TIGR00008 5 IEMEGKVTESLPNAMFRVELEN-GHEVLAHISGKIRMHYIRILPGDKVKVELSPYDLTRGRITY 67 (68)
T ss_pred EEEEEEEEEECCCCEEEEEECC-CCEEEEEecCcchhccEEECCCCEEEEEECcccCCcEeEEe
Confidence 3678999999997788888876 6666666662 367999999999999988777654
No 40
>PHA02945 interferon resistance protein; Provisional
Probab=93.46 E-value=1.3 Score=28.79 Aligned_cols=55 Identities=18% Similarity=0.070 Sum_probs=45.5
Q ss_pred CCeEEEEEEEEccCceEEEEeecc-eeeEEEeec------------CCCCCCCEEEEEEeeecCCCCeEEE
Q 034382 34 ERQYRALVLRFIKDRTAALLLVEV-GLQATAWVS------------VGAQIGDEVEVKVEEAHPRDDIIYL 91 (96)
Q Consensus 34 ~~~~~AvVl~~~~~~~~~vlL~dl-~le~~~~~~------------~~~~~Gd~v~v~v~~vdP~~~~l~l 91 (96)
|.---|.|-+ .+ .-+.+.|+|+ ++|.-++.+ +-+ .|+.+.++|-+|||..+.|-+
T Consensus 12 GelvigtV~~-~d-~ga~v~L~EY~g~eg~i~~seveva~~wvK~rd~l-~GqkvV~KVirVd~~kg~IDl 79 (88)
T PHA02945 12 GDVLKGKVYE-NG-YALYIDLFDYPHSEAILAESVQMHMNRYFKYRDKL-VGKTVKVKVIRVDYTKGYIDV 79 (88)
T ss_pred CcEEEEEEEe-cC-ceEEEEecccCCcEEEEEeehhhhccceEeeeeEe-cCCEEEEEEEEECCCCCEEEe
Confidence 4555677777 55 8999999999 888877776 236 999999999999999999876
No 41
>PRK07899 rpsA 30S ribosomal protein S1; Reviewed
Probab=93.38 E-value=0.82 Score=37.66 Aligned_cols=68 Identities=26% Similarity=0.322 Sum_probs=52.0
Q ss_pred chHHHHhhhCCCCCeEEEEEEEEccCceEEEEeecceeeEEEeec-----------CCCCCCCEEEEEEeeecCCCCeEE
Q 034382 22 YWIIEFLRRQPKERQYRALVLRFIKDRTAALLLVEVGLQATAWVS-----------VGAQIGDEVEVKVEEAHPRDDIIY 90 (96)
Q Consensus 22 yW~l~YL~~~~~~~~~~AvVl~~~~~~~~~vlL~dl~le~~~~~~-----------~~~~~Gd~v~v~v~~vdP~~~~l~ 90 (96)
=| ..|...++.|..++|.|.+-.+ ..+-|-|++ +++.-++.+ ..+++||.|.++|.++|+-+..|.
T Consensus 283 Pw-~~~~~~~~vG~vv~G~V~~I~~-fGvFVeL~~-gieGLvh~SeLs~~~v~~~~~~~kvGd~V~VkIi~ID~e~rrI~ 359 (486)
T PRK07899 283 PW-QQFARTHAIGQIVPGKVTKLVP-FGAFVRVEE-GIEGLVHISELAERHVEVPEQVVQVGDEVFVKVIDIDLERRRIS 359 (486)
T ss_pred ch-hhhHHhcCCCCEEEEEEEEEec-cEEEEEeCC-CcEEEEEHHHcCcccccCccceeCCCCEEEEEEEEEECCCCEEE
Confidence 35 3577766558999999999776 666677755 566666554 237999999999999999998888
Q ss_pred EE
Q 034382 91 LK 92 (96)
Q Consensus 91 l~ 92 (96)
|.
T Consensus 360 LS 361 (486)
T PRK07899 360 LS 361 (486)
T ss_pred EE
Confidence 75
No 42
>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional
Probab=93.01 E-value=1.1 Score=39.50 Aligned_cols=68 Identities=12% Similarity=0.152 Sum_probs=55.3
Q ss_pred chHHHHhhhCCCCCeEEEEEEEEccCceEEEEeecceeeEEEeecC--------------CCCCCCEEEEEEeeecCCCC
Q 034382 22 YWIIEFLRRQPKERQYRALVLRFIKDRTAALLLVEVGLQATAWVSV--------------GAQIGDEVEVKVEEAHPRDD 87 (96)
Q Consensus 22 yW~l~YL~~~~~~~~~~AvVl~~~~~~~~~vlL~dl~le~~~~~~~--------------~~~~Gd~v~v~v~~vdP~~~ 87 (96)
-|.- |...++.|...+|.|.+-.+ ..+-|-|++ +++.-++.+. .+++||.|.++|.++|+...
T Consensus 742 pw~~-~~~~~~vG~iV~GkV~~v~~-~GvFVeL~~-gVeGlI~~s~lsdd~~~~~~~~~~~f~vGD~V~v~Vl~iD~~~r 818 (863)
T PRK12269 742 PWQV-FANAYGVGSTVEGEVSSVTD-FGIFVRVPG-GVEGLVRKQHLVENRDGDPGEALRKYAVGDRVKAVIVDMNVKDR 818 (863)
T ss_pred hHHH-HHhhCCCCCEEEEEEEEEec-CeEEEEcCC-CeEEEEEHHHcCCcccccchhhccccCCCCEEEEEEEEEEcCCC
Confidence 4764 66665449999999999766 777788987 7888887751 26899999999999999998
Q ss_pred eEEEE
Q 034382 88 IIYLK 92 (96)
Q Consensus 88 ~l~l~ 92 (96)
.|.|.
T Consensus 819 kI~LS 823 (863)
T PRK12269 819 KVAFS 823 (863)
T ss_pred EEEEE
Confidence 88875
No 43
>PRK03987 translation initiation factor IF-2 subunit alpha; Validated
Probab=92.66 E-value=1.2 Score=33.81 Aligned_cols=58 Identities=24% Similarity=0.163 Sum_probs=48.2
Q ss_pred CCeEEEEEEEEccCceEEEEeecc-eeeEEEeec-----------CCCCCCCEEEEEEeeecCCCCeEEEE
Q 034382 34 ERQYRALVLRFIKDRTAALLLVEV-GLQATAWVS-----------VGAQIGDEVEVKVEEAHPRDDIIYLK 92 (96)
Q Consensus 34 ~~~~~AvVl~~~~~~~~~vlL~dl-~le~~~~~~-----------~~~~~Gd~v~v~v~~vdP~~~~l~l~ 92 (96)
|....|.|.+-.+ ..+.|-|.+. +++.-++.+ ..+.+||.+.++|.++|+..+.+.|.
T Consensus 9 GdiV~G~V~~I~~-~G~fV~L~e~~gieGlI~iSEls~~~i~~i~~~~kvGd~V~vkVi~VD~~k~~I~LS 78 (262)
T PRK03987 9 GELVVGTVKEVKD-FGAFVTLDEYPGKEGFIHISEVASGWVKNIRDHVKEGQKVVCKVIRVDPRKGHIDLS 78 (262)
T ss_pred CCEEEEEEEEEEC-CEEEEEECCCCCcEEEEEHHHcCcccccCHHHhCCCCCEEEEEEEEEecccCeEEEE
Confidence 7888999999777 8899999887 788777765 13689999999999999998877653
No 44
>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=92.31 E-value=1.7 Score=26.70 Aligned_cols=56 Identities=13% Similarity=-0.025 Sum_probs=42.7
Q ss_pred CCeEEEEEEEEccCceEEEEeecceeeEEEeec--C-------------CCCCCCEEEEEEeeecCCCCeEEEE
Q 034382 34 ERQYRALVLRFIKDRTAALLLVEVGLQATAWVS--V-------------GAQIGDEVEVKVEEAHPRDDIIYLK 92 (96)
Q Consensus 34 ~~~~~AvVl~~~~~~~~~vlL~dl~le~~~~~~--~-------------~~~~Gd~v~v~v~~vdP~~~~l~l~ 92 (96)
|..-.|.|.+-.+ ..+.+-|.. +++.-++.+ . .+++||.+..+|.++|+- +.+.|.
T Consensus 7 GdiV~g~V~~i~~-~g~~v~i~~-~~~G~l~~se~~~~~~~~~~~~~~~~l~vGd~i~~~V~~~~~~-~~i~LS 77 (86)
T cd05789 7 GDVVIGRVTEVGF-KRWKVDINS-PYDAVLPLSEVNLPRTDEDELNMRSYLDEGDLIVAEVQSVDSD-GSVSLH 77 (86)
T ss_pred CCEEEEEEEEECC-CEEEEECCC-CeEEEEEHHHccCCCCccchHHHHhhCCCCCEEEEEEEEECCC-CCEEEE
Confidence 7888999999666 777777753 467666654 1 389999999999999986 666554
No 45
>PRK12442 translation initiation factor IF-1; Reviewed
Probab=92.07 E-value=1.8 Score=28.14 Aligned_cols=57 Identities=18% Similarity=0.275 Sum_probs=44.9
Q ss_pred CeEEEEEEEEccCceEEEEeecceeeEEEeec-------CCCCCCCEEEEEEeeecCCCCeEEEE
Q 034382 35 RQYRALVLRFIKDRTAALLLVEVGLQATAWVS-------VGAQIGDEVEVKVEEAHPRDDIIYLK 92 (96)
Q Consensus 35 ~~~~AvVl~~~~~~~~~vlL~dl~le~~~~~~-------~~~~~Gd~v~v~v~~vdP~~~~l~l~ 92 (96)
-+.+|+|++-++...+.|.|++ |.+.-+..+ ..+-|||.|.|.++--|+-.+.|.++
T Consensus 7 ie~~G~V~e~Lp~~~frV~Len-G~~vla~isGKmR~~rIrIl~GD~V~VE~spYDltkGRIiyR 70 (87)
T PRK12442 7 IELDGIVDEVLPDSRFRVTLEN-GVEVGAYASGRMRKHRIRILAGDRVTLELSPYDLTKGRINFR 70 (87)
T ss_pred EEEEEEEEEECCCCEEEEEeCC-CCEEEEEeccceeeeeEEecCCCEEEEEECcccCCceeEEEE
Confidence 4678999999997788888854 455445444 35789999999999999999888765
No 46
>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=91.91 E-value=1.6 Score=25.83 Aligned_cols=52 Identities=17% Similarity=0.215 Sum_probs=38.9
Q ss_pred CCeEEEEEEEEccCceEEEEeecceeeEEEeec-------------CCCCCCCEEEEEEeeecCCCC
Q 034382 34 ERQYRALVLRFIKDRTAALLLVEVGLQATAWVS-------------VGAQIGDEVEVKVEEAHPRDD 87 (96)
Q Consensus 34 ~~~~~AvVl~~~~~~~~~vlL~dl~le~~~~~~-------------~~~~~Gd~v~v~v~~vdP~~~ 87 (96)
|..-.|.|++-.. ..+.|-|+. +++..++.+ ..+++||.+.++|.++|....
T Consensus 1 G~iV~g~V~~i~~-~gi~v~l~~-~i~g~i~~~~i~~~~~~~~~~~~~~~~Gd~i~~kVl~~d~~~~ 65 (70)
T cd05702 1 GDLVKAKVKSVKP-TQLNVQLAD-NVHGRIHVSEVFDEWPDGKNPLSKFKIGQKIKARVIGGHDAKT 65 (70)
T ss_pred CCEEEEEEEEEEC-CcEEEEeCC-CcEEEEEHHHhccccccccChhHhCCCCCEEEEEEEEEeCccc
Confidence 3456788888666 777777764 677777653 227899999999999998654
No 47
>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=91.62 E-value=1.8 Score=25.66 Aligned_cols=55 Identities=18% Similarity=0.119 Sum_probs=41.8
Q ss_pred CCeEEEEEEEEccCceEEEEeecceeeEEEeec-----CCCCCCCEEEEEEeeecCCC--CeEEE
Q 034382 34 ERQYRALVLRFIKDRTAALLLVEVGLQATAWVS-----VGAQIGDEVEVKVEEAHPRD--DIIYL 91 (96)
Q Consensus 34 ~~~~~AvVl~~~~~~~~~vlL~dl~le~~~~~~-----~~~~~Gd~v~v~v~~vdP~~--~~l~l 91 (96)
|+.-+|.|+...+ +.+.|-+.. .+.-++.+ ..+++||.+.+.|.++|... ..|.+
T Consensus 4 g~iV~G~V~~~~~-~~~~vdig~--~eg~lp~~e~~~~~~~~~Gd~v~v~v~~v~~~~~~~~i~l 65 (67)
T cd04455 4 GEIVTGIVKRVDR-GNVIVDLGK--VEAILPKKEQIPGESYRPGDRIKAYVLEVRKTSKGPQIIL 65 (67)
T ss_pred CCEEEEEEEEEcC-CCEEEEcCC--eEEEeeHHHCCCCCcCCCCCEEEEEEEEEecCCCCCEEEE
Confidence 6788999998777 777776643 67777765 34799999999999999644 44554
No 48
>PRK06676 rpsA 30S ribosomal protein S1; Reviewed
Probab=91.60 E-value=3 Score=32.60 Aligned_cols=68 Identities=21% Similarity=0.101 Sum_probs=50.8
Q ss_pred cchHHHHhhhCCCCCeEEEEEEEEccCceEEEEeecceeeEEEeecC-----------CCCCCCEEEEEEeeecCCCCeE
Q 034382 21 RYWIIEFLRRQPKERQYRALVLRFIKDRTAALLLVEVGLQATAWVSV-----------GAQIGDEVEVKVEEAHPRDDII 89 (96)
Q Consensus 21 RyW~l~YL~~~~~~~~~~AvVl~~~~~~~~~vlL~dl~le~~~~~~~-----------~~~~Gd~v~v~v~~vdP~~~~l 89 (96)
..|...|-.-+. |...+|.|..-.+ ..+.|-|. +++.-++.+. -+.+||.+.++|..+|+.++.|
T Consensus 181 ~~~~~~~~~~~~-G~~v~g~V~~v~~-~G~fV~l~--~v~g~v~~sels~~~~~~~~~~~~vGd~i~~~Vl~vd~~~~~i 256 (390)
T PRK06676 181 AKKEELLSSLKE-GDVVEGTVARLTD-FGAFVDIG--GVDGLVHISELSHERVEKPSEVVSVGQEVEVKVLSIDWETERI 256 (390)
T ss_pred hHHHHHHhhCCC-CCEEEEEEEEEec-ceEEEEeC--CeEEEEEHHHcCccccCCHHHhcCCCCEEEEEEEEEeCCCCEE
Confidence 345544444456 8999999999766 66777775 5777777651 2679999999999999998877
Q ss_pred EEE
Q 034382 90 YLK 92 (96)
Q Consensus 90 ~l~ 92 (96)
.+.
T Consensus 257 ~lS 259 (390)
T PRK06676 257 SLS 259 (390)
T ss_pred EEE
Confidence 654
No 49
>PTZ00248 eukaryotic translation initiation factor 2 subunit 1; Provisional
Probab=90.55 E-value=2.8 Score=33.02 Aligned_cols=64 Identities=19% Similarity=0.190 Sum_probs=51.2
Q ss_pred hhhCC-CCCeEEEEEEEEccCceEEEEeecc-eeeEEEeec-----------CCCCCCCEEEEEEeeecCCCCeEEEE
Q 034382 28 LRRQP-KERQYRALVLRFIKDRTAALLLVEV-GLQATAWVS-----------VGAQIGDEVEVKVEEAHPRDDIIYLK 92 (96)
Q Consensus 28 L~~~~-~~~~~~AvVl~~~~~~~~~vlL~dl-~le~~~~~~-----------~~~~~Gd~v~v~v~~vdP~~~~l~l~ 92 (96)
-...| .|..-.|.|..-.. ..+-|-|.++ +++.-++.+ .-+++||.+.++|-+||+-.+.|.|+
T Consensus 11 ~~~~P~~GdvV~g~V~~I~d-~GafV~L~EY~gvEGlIhiSElS~~ri~~i~d~vkvGd~v~vkVl~VD~ekg~IdLS 87 (319)
T PTZ00248 11 EQKFPEEDDLVMVKVVRITE-MGAYVSLLEYDDIEGMILMSELSKRRIRSINKLIRVGRHEVVVVLRVDKEKGYIDLS 87 (319)
T ss_pred hhhCCCCCCEEEEEEEEEeC-CeEEEEecCCCCcEEEEEHHHhcccccCCHHHhcCCCCEEEEEEEEEeCCCCEEEEE
Confidence 34445 27788888888666 8888888877 888888776 23799999999999999999988774
No 50
>PRK07899 rpsA 30S ribosomal protein S1; Reviewed
Probab=90.46 E-value=3 Score=34.38 Aligned_cols=63 Identities=24% Similarity=0.295 Sum_probs=48.9
Q ss_pred HhhhCCCCCeEEEEEEEEccCceEEEEeecceeeEEEeec-----------CCCCCCCEEEEEEeeecCCCCeEEEE
Q 034382 27 FLRRQPKERQYRALVLRFIKDRTAALLLVEVGLQATAWVS-----------VGAQIGDEVEVKVEEAHPRDDIIYLK 92 (96)
Q Consensus 27 YL~~~~~~~~~~AvVl~~~~~~~~~vlL~dl~le~~~~~~-----------~~~~~Gd~v~v~v~~vdP~~~~l~l~ 92 (96)
++.....|...+|.|..-.+ ..+-|-|. +++.-++.+ .-+++||.|.++|.++|+.++.|.|.
T Consensus 202 ~~~~lk~G~iv~G~V~~i~~-~G~FVdlg--gv~Glv~~Sels~~~v~~~~~~~kvGd~V~vkVl~iD~e~~rI~LS 275 (486)
T PRK07899 202 FLNQLQKGQVRKGVVSSIVN-FGAFVDLG--GVDGLVHVSELSWKHIDHPSEVVEVGQEVTVEVLDVDMDRERVSLS 275 (486)
T ss_pred HHHhccCCCEEEEEEEEEEC-CeEEEEEC--CEEEEEEHHHCCCcccCCHHHhcCCCCEEEEEEEEEECCCCEEEEE
Confidence 44444459999999999766 66777774 577777755 13679999999999999999987765
No 51
>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=89.27 E-value=4.3 Score=26.27 Aligned_cols=57 Identities=19% Similarity=0.094 Sum_probs=43.2
Q ss_pred CCeEEEEEEEEccCceEEEEeecceeeEEEeec------------------------------CCCCCCCEEEEEEeeec
Q 034382 34 ERQYRALVLRFIKDRTAALLLVEVGLQATAWVS------------------------------VGAQIGDEVEVKVEEAH 83 (96)
Q Consensus 34 ~~~~~AvVl~~~~~~~~~vlL~dl~le~~~~~~------------------------------~~~~~Gd~v~v~v~~vd 83 (96)
|..-.|.|.+-.. ..+.|.||+ +++.-++.+ ..+.+||.+..+|..+|
T Consensus 4 G~vV~G~V~~v~~-~gl~v~L~~-g~~G~v~~seis~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~vGd~V~~kVi~~d 81 (100)
T cd05693 4 GMLVLGQVKEITK-LDLVISLPN-GLTGYVPITNISDAYTERLEELDEESEEEDDEEELPDLEDLFSVGQLVRCKVVSLD 81 (100)
T ss_pred CCEEEEEEEEEcC-CCEEEECCC-CcEEEEEHHHhhHHHHHHHHHhhhhccccccccccCCHHHhccCCCEEEEEEEEcc
Confidence 6777888888655 777778875 677776654 22799999999999999
Q ss_pred CC---CCeEEEE
Q 034382 84 PR---DDIIYLK 92 (96)
Q Consensus 84 P~---~~~l~l~ 92 (96)
+. ...|.+.
T Consensus 82 ~~~~~~~~i~LS 93 (100)
T cd05693 82 KSKSGKKRIELS 93 (100)
T ss_pred CCcCCCcEEEEE
Confidence 96 5666553
No 52
>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=89.12 E-value=3.7 Score=33.22 Aligned_cols=69 Identities=22% Similarity=0.256 Sum_probs=51.5
Q ss_pred cchHHHHhhhCCCCCeEEEEEEEEccCceEEEEeecceeeEEEeec-----------CCCCCCCEEEEEEeeecCCCCeE
Q 034382 21 RYWIIEFLRRQPKERQYRALVLRFIKDRTAALLLVEVGLQATAWVS-----------VGAQIGDEVEVKVEEAHPRDDII 89 (96)
Q Consensus 21 RyW~l~YL~~~~~~~~~~AvVl~~~~~~~~~vlL~dl~le~~~~~~-----------~~~~~Gd~v~v~v~~vdP~~~~l 89 (96)
..|. .+....+.|...+|.|.+-.+ ..+-|.|++ +++.-++.+ ..+++||.+.++|.++|+.++.|
T Consensus 435 ~p~~-~~~~~~~~G~~v~g~V~~v~~-~G~fV~l~~-~~~Glv~~s~l~~~~~~~~~~~~~~Gd~v~~~V~~id~~~~~i 511 (516)
T TIGR00717 435 NPWE-KFAAKYKVGSVVKGKVTEIKD-FGAFVELPG-GVEGLIRNSELSENRDEDKTDEIKVGDEVEAKVVDIDKKNRKV 511 (516)
T ss_pred Cchh-hhhhccCcceEEEEEEEEEec-ceEEEEcCC-CeEEEEEHHHcCccccccccccCCCCCEEEEEEEEEeCCCCEE
Confidence 3563 334444448999999999766 677777766 566666664 34799999999999999999998
Q ss_pred EEE
Q 034382 90 YLK 92 (96)
Q Consensus 90 ~l~ 92 (96)
.|.
T Consensus 512 ~ls 514 (516)
T TIGR00717 512 SLS 514 (516)
T ss_pred EEE
Confidence 875
No 53
>PRK06676 rpsA 30S ribosomal protein S1; Reviewed
Probab=89.12 E-value=4.5 Score=31.63 Aligned_cols=63 Identities=24% Similarity=0.270 Sum_probs=45.4
Q ss_pred hhhCCCCCeEEEEEEEEccCceEEEEeecceeeEEEeec-----------CCCCCCCEEEEEEeeecCCCCeEEEE
Q 034382 28 LRRQPKERQYRALVLRFIKDRTAALLLVEVGLQATAWVS-----------VGAQIGDEVEVKVEEAHPRDDIIYLK 92 (96)
Q Consensus 28 L~~~~~~~~~~AvVl~~~~~~~~~vlL~dl~le~~~~~~-----------~~~~~Gd~v~v~v~~vdP~~~~l~l~ 92 (96)
......|....|.|.+-.+ ..+-|-|++ +++.-++.+ ..+++||.|.++|.++|+-++.+.|.
T Consensus 272 ~~~~~~G~~v~g~V~~i~~-~G~fV~l~~-gi~Glv~~se~~~~~~~~~~~~~~~Gd~v~v~V~~id~e~~~i~ls 345 (390)
T PRK06676 272 EEKLPEGDVIEGTVKRLTD-FGAFVEVLP-GVEGLVHISQISHKHIATPSEVLEEGQEVKVKVLEVNEEEKRISLS 345 (390)
T ss_pred hhhhcCCcEEEEEEEEEeC-ceEEEEECC-CCeEEEEhHHcCccccCChhhccCCCCEEEEEEEEEECCCCEEEEE
Confidence 3444348899999998655 555555543 455555433 23689999999999999999988875
No 54
>smart00743 Agenet Tudor-like domain present in plant sequences. Domain in plant sequences with possible chromatin-associated functions.
Probab=88.94 E-value=1.7 Score=25.14 Aligned_cols=32 Identities=16% Similarity=0.144 Sum_probs=25.4
Q ss_pred CCeEEEEEEEEccCceEEEEeec--ceeeEEEee
Q 034382 34 ERQYRALVLRFIKDRTAALLLVE--VGLQATAWV 65 (96)
Q Consensus 34 ~~~~~AvVl~~~~~~~~~vlL~d--l~le~~~~~ 65 (96)
+.+|+|.|+...+++.+.|.+++ .+....+..
T Consensus 17 ~~W~~a~V~~~~~~~~~~V~~~~~~~~~~e~v~~ 50 (61)
T smart00743 17 DSWWEAVVTKVLGDGKYLVRYLTESEPLKETVDW 50 (61)
T ss_pred CEEEEEEEEEECCCCEEEEEECCCCcccEEEEeH
Confidence 68999999998887789999998 555555544
No 55
>PRK13806 rpsA 30S ribosomal protein S1; Provisional
Probab=88.88 E-value=4.1 Score=33.30 Aligned_cols=67 Identities=21% Similarity=0.150 Sum_probs=50.9
Q ss_pred hHHHHhhhCCCCCeEEEEEEEEccCceEEEEeecceeeEEEeec-----------CCCCCCCEEEEEEeeecCCCCeEEE
Q 034382 23 WIIEFLRRQPKERQYRALVLRFIKDRTAALLLVEVGLQATAWVS-----------VGAQIGDEVEVKVEEAHPRDDIIYL 91 (96)
Q Consensus 23 W~l~YL~~~~~~~~~~AvVl~~~~~~~~~vlL~dl~le~~~~~~-----------~~~~~Gd~v~v~v~~vdP~~~~l~l 91 (96)
|.- +....+.|+..+|.|.+-.+ ..+-|-|.+ +++.-++.+ ..+++||.|.++|..+|+-...|+|
T Consensus 370 ~~~-~~~~~~vG~~v~G~V~~i~~-~G~FV~l~~-gv~Gli~~se~s~~~~~~~~~~~~~Gd~v~~~V~~id~e~~ri~L 446 (491)
T PRK13806 370 WAD-VAERFAPGTTVTGTVEKRAQ-FGLFVNLAP-GVTGLLPASVISRAGKPATYEKLKPGDSVTLVVEEIDTAKRKISL 446 (491)
T ss_pred hHH-hhhhCCCCCEEEEEEEEEec-CceEEEcCC-CcEEEEEHHHcCcccccchhhcCCCCCEEEEEEEEEeCCCCEEEE
Confidence 544 33444448999999999666 666677765 777777654 3479999999999999999888887
Q ss_pred E
Q 034382 92 K 92 (96)
Q Consensus 92 ~ 92 (96)
.
T Consensus 447 s 447 (491)
T PRK13806 447 A 447 (491)
T ss_pred E
Confidence 6
No 56
>PRK00087 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed
Probab=88.73 E-value=4.5 Score=34.20 Aligned_cols=58 Identities=24% Similarity=0.231 Sum_probs=44.4
Q ss_pred CCCeEEEEEEEEccCceEEEEeecceeeEEEeec-----------CCCCCCCEEEEEEeeecCCCCeEEEE
Q 034382 33 KERQYRALVLRFIKDRTAALLLVEVGLQATAWVS-----------VGAQIGDEVEVKVEEAHPRDDIIYLK 92 (96)
Q Consensus 33 ~~~~~~AvVl~~~~~~~~~vlL~dl~le~~~~~~-----------~~~~~Gd~v~v~v~~vdP~~~~l~l~ 92 (96)
.|..+.|.|.+..+ ..+-|-|++ +++.-++.+ ..+++||.+.++|.++|+.++.|.|.
T Consensus 562 ~G~~v~g~V~~i~~-~G~fV~l~~-~i~Gli~~sel~~~~~~~~~~~~kvGd~V~vkV~~id~e~~rI~ls 630 (647)
T PRK00087 562 VGSIVLGKVVRIAP-FGAFVELEP-GVDGLVHISQISWKRIDKPEDVLSEGEEVKAKILEVDPEEKRIRLS 630 (647)
T ss_pred CCeEEEEEEEEEEC-CeEEEEECC-CCEEEEEhhhcCccccCCHhhcCCCCCEEEEEEEEEeCCCCEEEEE
Confidence 38999999999776 666666643 456555543 24799999999999999988888765
No 57
>cd04466 S1_YloQ_GTPase S1_YloQ_GTPase: YloQ GTase family (also known as YjeQ and CpgA), S1-like RNA-binding domain. Proteins in the YloQ GTase family bind the ribosome and have GTPase activity. The precise role of this family is unknown. The protein structure is composed of three domains: an N-terminal S1 domain, a central GTPase domain, and a C-terminal zinc finger domain. This N-terminal S1 domain binds ssRNA. The central GTPase domain contains nucleotide-binding signature motifs: G1 (walker A), G3 (walker B) and G4 motifs. Experiments show that the bacterial YloQ and YjeQ proteins have low intrinsic GTPase activity. The C-terminal zinc-finger domain has structural similarity to a portion of the DNA-repair protein Rad51. This suggests a possible role for this GTPase as a regulator of translation, perhaps as a translation initiation factor. This family is classified based on the N-terminal S1 domain.
Probab=87.88 E-value=3.8 Score=23.87 Aligned_cols=41 Identities=15% Similarity=0.075 Sum_probs=27.8
Q ss_pred EEEEEEEccCceEEEEee-cceeeEEEeec-----CCCCCCCEEEEEE
Q 034382 38 RALVLRFIKDRTAALLLV-EVGLQATAWVS-----VGAQIGDEVEVKV 79 (96)
Q Consensus 38 ~AvVl~~~~~~~~~vlL~-dl~le~~~~~~-----~~~~~Gd~v~v~v 79 (96)
+|.|+...+ +.+.|..+ +--+.+.++.. ..+..||.|.+..
T Consensus 2 ~grVv~~~~-~~~~v~~~~~~~~~~~~~~~~~~~~~~~~VGD~V~~~~ 48 (68)
T cd04466 2 EGLIIKAIG-GFYYVETEDGKIYECRLRGKFRKDKNPPAVGDRVEFEP 48 (68)
T ss_pred CEEEEEEEC-CEEEEEeCCCeEEEEEEccccccCCCCCCCCcEEEEEE
Confidence 477888788 78888776 34455554443 3478999998753
No 58
>PRK13806 rpsA 30S ribosomal protein S1; Provisional
Probab=87.46 E-value=6 Score=32.35 Aligned_cols=68 Identities=24% Similarity=0.280 Sum_probs=47.9
Q ss_pred chHHHHhhhCCCCCeEEEEEEEEccCceEEEEeecceeeEEEeec------------CCCCCCCEEEEEEeeecCCCCeE
Q 034382 22 YWIIEFLRRQPKERQYRALVLRFIKDRTAALLLVEVGLQATAWVS------------VGAQIGDEVEVKVEEAHPRDDII 89 (96)
Q Consensus 22 yW~l~YL~~~~~~~~~~AvVl~~~~~~~~~vlL~dl~le~~~~~~------------~~~~~Gd~v~v~v~~vdP~~~~l 89 (96)
-|. .+....+.|...+|.|.+-.+ .-+-|-|.+ +++.-++.+ .-+++||.|.++|.++|+.+..|
T Consensus 282 p~~-~~~~~~~~G~~v~G~V~~v~~-~G~fV~l~~-gv~Glvh~sels~~~~~~~~~~~~~~Gd~v~vkVl~iD~e~~ri 358 (491)
T PRK13806 282 PWD-TVGDRLKAGDKVTGKVVRLAP-FGAFVEILP-GIEGLVHVSEMSWTRRVNKPEDVVAPGDAVAVKIKDIDPAKRRI 358 (491)
T ss_pred cch-hhhccCCCCCEEEEEEEEEeC-ceEEEEeCC-CcEEEEEHHHcCcccccCCHHHcCCCCCEEEEEEEEEEccCCEE
Confidence 353 333444448999999998766 555555532 455555543 23789999999999999999988
Q ss_pred EEE
Q 034382 90 YLK 92 (96)
Q Consensus 90 ~l~ 92 (96)
.+.
T Consensus 359 ~Ls 361 (491)
T PRK13806 359 SLS 361 (491)
T ss_pred EEE
Confidence 775
No 59
>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional
Probab=87.37 E-value=5.5 Score=35.18 Aligned_cols=67 Identities=22% Similarity=0.360 Sum_probs=49.8
Q ss_pred hHHHHhhhCCCCCeEEEEEEEEccCceEEEEeecceeeEEEeec------------CCCCCCCEEEEEEeeecCCCCeEE
Q 034382 23 WIIEFLRRQPKERQYRALVLRFIKDRTAALLLVEVGLQATAWVS------------VGAQIGDEVEVKVEEAHPRDDIIY 90 (96)
Q Consensus 23 W~l~YL~~~~~~~~~~AvVl~~~~~~~~~vlL~dl~le~~~~~~------------~~~~~Gd~v~v~v~~vdP~~~~l~ 90 (96)
|.- +..+.+.|...+|.|..-.+ .-+-|-|.+ +++.-++.+ ..+++||.|.++|..+||.+..|.
T Consensus 656 w~~-~~~~~~vG~~v~G~V~~i~~-~G~fV~l~~-gV~GlIh~sels~~~~~~~~~~~~kvGq~VkvkVl~ID~e~rrI~ 732 (863)
T PRK12269 656 WEE-IEARYPVGARFTRRIVKVTN-AGAFIEMEE-GIDGFLHVDDLSWVKRTRPADHELEVGKEIECMVIECDPQARRIR 732 (863)
T ss_pred hHH-HHHhCCCCCEEEEEEEEEec-ceEEEEeCC-CcEEEEEhHHhhccccccchhhccCCCCEEEEEEEEEeccCCEEE
Confidence 533 35555559999999998777 666666653 555555543 248899999999999999999988
Q ss_pred EE
Q 034382 91 LK 92 (96)
Q Consensus 91 l~ 92 (96)
|.
T Consensus 733 LS 734 (863)
T PRK12269 733 LG 734 (863)
T ss_pred EE
Confidence 75
No 60
>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=87.29 E-value=4.9 Score=24.52 Aligned_cols=58 Identities=12% Similarity=0.005 Sum_probs=44.0
Q ss_pred CCeEEEEEEEEccCceEEEEeecceeeEEEeec-----CCCCCCCEEEEEEeeecCCCCeEEEE
Q 034382 34 ERQYRALVLRFIKDRTAALLLVEVGLQATAWVS-----VGAQIGDEVEVKVEEAHPRDDIIYLK 92 (96)
Q Consensus 34 ~~~~~AvVl~~~~~~~~~vlL~dl~le~~~~~~-----~~~~~Gd~v~v~v~~vdP~~~~l~l~ 92 (96)
|....|.|-..-. .-+.|-+.-=+++.-++.+ ..+.+||.+.++|.++|+-...+.+.
T Consensus 5 G~~v~g~V~si~d-~G~~v~~g~~gv~Gfl~~~~~~~~~~~~~Gq~v~~~V~~vd~~~~~v~ls 67 (74)
T cd05694 5 GMVLSGCVSSVED-HGYILDIGIPGTTGFLPKKDAGNFSKLKVGQLLLCVVEKVKDDGRVVSLS 67 (74)
T ss_pred CCEEEEEEEEEeC-CEEEEEeCCCCcEEEEEHHHCCcccccCCCCEEEEEEEEEECCCCEEEEE
Confidence 5677788777655 6677776323677777765 35899999999999999999887764
No 61
>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=87.21 E-value=1.8 Score=26.04 Aligned_cols=55 Identities=15% Similarity=0.106 Sum_probs=32.9
Q ss_pred CCeEEEEEEEEccCce-EEEEeecceeeEEEeec-----------CCCCCCCEEEEEEeeecCCCCeEEEE
Q 034382 34 ERQYRALVLRFIKDRT-AALLLVEVGLQATAWVS-----------VGAQIGDEVEVKVEEAHPRDDIIYLK 92 (96)
Q Consensus 34 ~~~~~AvVl~~~~~~~-~~vlL~dl~le~~~~~~-----------~~~~~Gd~v~v~v~~vdP~~~~l~l~ 92 (96)
|....|.|.+-.. .. +.+-| .-+.+.-++.+ .-+++||.+.++|.++|. +.++|.
T Consensus 4 G~iv~G~V~~i~~-~~g~~v~l-~~~~~Glvhis~~s~~~~~~~~~~~~~Gd~v~~kV~~~~~--~~i~LS 70 (72)
T cd05704 4 GAVTLGMVTKVIP-HSGLTVQL-PFGKTGLVSIFHLSDSYTENPLEGFKPGKIVRCCILSKKD--GKYQLS 70 (72)
T ss_pred CCEEEEEEEEeeC-CcEEEEEC-CCCCEEEEEHHHhcCcccCCHHHhCCCCCEEEEEEEEecC--CEEEEE
Confidence 6677777777443 22 22222 22233333322 337899999999999985 666654
No 62
>PRK07400 30S ribosomal protein S1; Reviewed
Probab=86.57 E-value=9.9 Score=29.51 Aligned_cols=56 Identities=20% Similarity=0.207 Sum_probs=46.6
Q ss_pred CCeEEEEEEEEccCceEEEEeecceeeEEEeec-------CCCCCCCEEEEEEeeecCCCCeEEEE
Q 034382 34 ERQYRALVLRFIKDRTAALLLVEVGLQATAWVS-------VGAQIGDEVEVKVEEAHPRDDIIYLK 92 (96)
Q Consensus 34 ~~~~~AvVl~~~~~~~~~vlL~dl~le~~~~~~-------~~~~~Gd~v~v~v~~vdP~~~~l~l~ 92 (96)
|..-++.|....+ +-+.|-|+ |++.-+|.+ .+...|+.+.++|..+||..+.|.+.
T Consensus 119 ~~~V~g~V~~~~~-~G~~V~l~--Gv~gfip~s~ls~~~~~~~~vG~~i~~kVl~id~~~~~i~lS 181 (318)
T PRK07400 119 DATVRSEVFATNR-GGALVRIE--GLRGFIPGSHISTRKPKEELVGEELPLKFLEVDEERNRLVLS 181 (318)
T ss_pred CCEEEEEEEEEEC-CeEEEEEC--CEEEEEEHHHcCccCCccccCCCEEEEEEEEEEcccCEEEEE
Confidence 6889999999998 88888885 778777776 12348999999999999999988775
No 63
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=85.24 E-value=7.4 Score=33.36 Aligned_cols=58 Identities=29% Similarity=0.324 Sum_probs=41.3
Q ss_pred CCCCCeEEEEEEEEccCceEEEEeecceeeEEEeec-----------CCCCCCCEEEEEEeeecCCCCeEEEE
Q 034382 31 QPKERQYRALVLRFIKDRTAALLLVEVGLQATAWVS-----------VGAQIGDEVEVKVEEAHPRDDIIYLK 92 (96)
Q Consensus 31 ~~~~~~~~AvVl~~~~~~~~~vlL~dl~le~~~~~~-----------~~~~~Gd~v~v~v~~vdP~~~~l~l~ 92 (96)
+. |..++|.|.+-.+ ..+.|-|.. +.+.-++.+ .-+++||.|.|+|.++|+. +.++|.
T Consensus 620 ~v-G~v~~G~V~~I~~-fGafVei~~-~~~GllhiSels~~~v~~~~~v~kvGD~V~VkV~~iD~~-grI~LS 688 (693)
T PRK11824 620 EV-GEIYEGKVVRIVD-FGAFVEILP-GKDGLVHISEIADERVEKVEDVLKEGDEVKVKVLEIDKR-GRIRLS 688 (693)
T ss_pred cC-CeEEEEEEEEEEC-CeEEEEECC-CCEEEEEeeeccCccccCccceeCCCCEEEEEEEEECCC-CcEEEE
Confidence 44 8999999988766 555555542 333333332 3379999999999999997 887764
No 64
>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=85.01 E-value=17 Score=28.71 Aligned_cols=65 Identities=15% Similarity=0.088 Sum_probs=46.7
Q ss_pred HHHhhhCCCCCeEEEEEEEEccCceEEEEeecceeeEEEeec-----CCCCCCCEEEEEEeeec--CCCCeEEEE
Q 034382 25 IEFLRRQPKERQYRALVLRFIKDRTAALLLVEVGLQATAWVS-----VGAQIGDEVEVKVEEAH--PRDDIIYLK 92 (96)
Q Consensus 25 l~YL~~~~~~~~~~AvVl~~~~~~~~~vlL~dl~le~~~~~~-----~~~~~Gd~v~v~v~~vd--P~~~~l~l~ 92 (96)
+.-+..+. |..-.|.|.+..+.+.+.|-|- +.+.-+|.+ ..+.+||++.+-|.+|+ +....|.++
T Consensus 124 ~~ey~~k~-GeiV~G~V~~v~~~g~v~VdiG--~~ea~LP~~E~ip~E~~~~Gd~ik~~V~~V~~~~kg~qIivS 195 (341)
T TIGR01953 124 YDEFSSKE-GEIISGTVKRVNRRGNLYVELG--KTEGILPKKEQIPGEKFRIGDRIKAYVYEVRKTAKGPQIILS 195 (341)
T ss_pred HHHHHhhc-CCEEEEEEEEEecCCcEEEEEC--CeEEEecHHHcCCCcCCCCCCEEEEEEEEEEcCCCCCeEEEE
Confidence 33344456 8899999999766233456552 677778775 45899999999999999 545566654
No 65
>PF02598 Methyltrn_RNA_3: Putative RNA methyltransferase; InterPro: IPR003750 This entry describes proteins of unknown function.; PDB: 1K3R_B.
Probab=84.32 E-value=2.5 Score=32.55 Aligned_cols=47 Identities=17% Similarity=0.222 Sum_probs=32.9
Q ss_pred CCeEEEEEEEEccCceEEEEeecceeeEEEeecC-CCCCCCEEEEEEee
Q 034382 34 ERQYRALVLRFIKDRTAALLLVEVGLQATAWVSV-GAQIGDEVEVKVEE 81 (96)
Q Consensus 34 ~~~~~AvVl~~~~~~~~~vlL~dl~le~~~~~~~-~~~~Gd~v~v~v~~ 81 (96)
+.-=+|+|+++.. +...=.+-|+|+.-.+.++. .+.+|.+|+|++..
T Consensus 115 ~~yREGvv~~~~~-~~~~~~~VdiGl~~~v~i~~~~l~~g~RVTV~~~~ 162 (291)
T PF02598_consen 115 GPYREGVVVRKPS-KGGKGSYVDIGLDKPVEIDKQELPPGTRVTVRIKS 162 (291)
T ss_dssp T-EEEEEEEEE-S-SS---EEEESSSSEEEESSS----SS-EEEEEEEE
T ss_pred cceeEEEEEeCCC-CCCceEEEEeCCCcEEeecccccCCCCEEEEEecC
Confidence 3344799999887 44333788999999999998 99999999999988
No 66
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=84.22 E-value=2.6 Score=37.39 Aligned_cols=61 Identities=18% Similarity=0.194 Sum_probs=37.1
Q ss_pred hCCCCCeEE-EEEEEEcc---------CceEEEEeecceeeEEEeecCCCCCCCEEEEEEeeecCCCCeEEEE
Q 034382 30 RQPKERQYR-ALVLRFIK---------DRTAALLLVEVGLQATAWVSVGAQIGDEVEVKVEEAHPRDDIIYLK 92 (96)
Q Consensus 30 ~~~~~~~~~-AvVl~~~~---------~~~~~vlL~dl~le~~~~~~~~~~~Gd~v~v~v~~vdP~~~~l~l~ 92 (96)
-+. |..++ |.|..-.. ..-++|++-++.-+-.-....-++.||.|.|+|.++|+ .+.|+|.
T Consensus 751 ~~v-G~iy~~g~V~~I~~FGaFVeL~~g~EGLVHISeLs~~rv~~~~dv~kvGD~V~VkVi~ID~-~grI~LS 821 (891)
T PLN00207 751 PTV-GDIYRNCEIKSIAPYGAFVEIAPGREGLCHISELSSNWLAKPEDAFKVGDRIDVKLIEVND-KGQLRLS 821 (891)
T ss_pred cCC-CcEEECcEEEEEeccEEEEEeCCCCEEEEEhhhcCCccccCHHHhcCCCCEEEEEEEEECC-CCcEEEE
Confidence 345 88885 35554333 13444444444322211112458999999999999998 6777765
No 67
>COG0539 RpsA Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]
Probab=84.15 E-value=1.9 Score=36.19 Aligned_cols=65 Identities=20% Similarity=0.197 Sum_probs=47.4
Q ss_pred HhhhCCCCCeEEEEEEE---------EccCceEEEEeecceeeEEEeecCCCCCCCEEEEEEeeecCCCCeEEEE
Q 034382 27 FLRRQPKERQYRALVLR---------FIKDRTAALLLVEVGLQATAWVSVGAQIGDEVEVKVEEAHPRDDIIYLK 92 (96)
Q Consensus 27 YL~~~~~~~~~~AvVl~---------~~~~~~~~vlL~dl~le~~~~~~~~~~~Gd~v~v~v~~vdP~~~~l~l~ 92 (96)
.|.+...|+.-+++|-. -.+ =-++|++.++.-.-.-....-+++||.|.|+|-++|+-++.+.|.
T Consensus 186 ~~~~l~~G~vV~G~V~~It~~GafVdigG-vdGLlHiseiS~~rv~~P~~vvkvGd~VkvkVi~~D~e~~RVsLS 259 (541)
T COG0539 186 LLNKLEVGEVVEGVVKNITDYGAFVDIGG-VDGLLHISEISWKRVDHPSEVVKVGDEVKVKVISLDEERGRVSLS 259 (541)
T ss_pred HHhcCCCCceEEEEEEEeecCcEEEEecC-eeeEEehhhccccccCCHHHhcccCCEEEEEEEEEccCCCeEEEE
Confidence 34444447777765544 333 456677777777766666678999999999999999999998874
No 68
>PRK06299 rpsA 30S ribosomal protein S1; Reviewed
Probab=83.77 E-value=16 Score=30.07 Aligned_cols=58 Identities=21% Similarity=0.223 Sum_probs=46.6
Q ss_pred CCCCCeEEEEEEEEccCceEEEEeecceeeEEEeec-----------CCCCCCCEEEEEEeeecCCCCeEEEE
Q 034382 31 QPKERQYRALVLRFIKDRTAALLLVEVGLQATAWVS-----------VGAQIGDEVEVKVEEAHPRDDIIYLK 92 (96)
Q Consensus 31 ~~~~~~~~AvVl~~~~~~~~~vlL~dl~le~~~~~~-----------~~~~~Gd~v~v~v~~vdP~~~~l~l~ 92 (96)
++ |...+|.|..-.+ ..+.|-|. +++.-++.+ .-+++||.+.++|.++|+.++.+.|.
T Consensus 200 ~~-G~iv~g~V~~v~~-~G~~V~i~--g~~glv~~se~s~~~~~~~~~~~kvG~~v~v~V~~~d~~~~~i~lS 268 (565)
T PRK06299 200 EE-GQVVEGVVKNITD-YGAFVDLG--GVDGLLHITDISWKRVNHPSEVVNVGDEVKVKVLKFDKEKKRVSLG 268 (565)
T ss_pred CC-CCEEEEEEEEEeC-CeEEEEEC--CEEEEEEHHHhcccccCCHhhcCCCCCEEEEEEEEEeCCCCeEEEE
Confidence 45 8999999998666 67777775 788777765 12789999999999999999888765
No 69
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=83.61 E-value=19 Score=28.77 Aligned_cols=65 Identities=17% Similarity=0.146 Sum_probs=47.5
Q ss_pred HHHHhhhCCCCCeEEEEEEEEccCceEEEEeecceeeEEEeec-----CCCCCCCEEEEEEeeecC--CCCeEEEE
Q 034382 24 IIEFLRRQPKERQYRALVLRFIKDRTAALLLVEVGLQATAWVS-----VGAQIGDEVEVKVEEAHP--RDDIIYLK 92 (96)
Q Consensus 24 ~l~YL~~~~~~~~~~AvVl~~~~~~~~~vlL~dl~le~~~~~~-----~~~~~Gd~v~v~v~~vdP--~~~~l~l~ 92 (96)
.+.-|..+. |..-.|.|.+..+ +.+.|-|-. .++-+|.+ ..+.+||++.+-|.+|+. ..-.|.++
T Consensus 126 v~~ef~~k~-GeiV~G~V~~~~~-~~~~Vdlg~--vEa~LP~~E~ip~e~~~~Gd~Ika~V~~V~~~~kgp~IivS 197 (362)
T PRK12327 126 IYNEFSERE-GDIVTGVVQRRDN-RFVYVNLGK--IEAVLPPAEQIPGETYKHGDRIKVYVVKVEKTTKGPQIFVS 197 (362)
T ss_pred HHHHHHHhc-CCEEEEEEEEEeC-CcEEEEeCC--eEEEecHHHcCCCCCCCCCCEEEEEEEEEecCCCCCeEEEE
Confidence 455566667 8999999999777 666665543 77778743 678999999999999994 33345543
No 70
>PRK00087 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed
Probab=83.16 E-value=13 Score=31.47 Aligned_cols=58 Identities=19% Similarity=0.200 Sum_probs=46.1
Q ss_pred CCCCCeEEEEEEEEccCceEEEEeecceeeEEEeec-----------CCCCCCCEEEEEEeeecCCCCeEEEE
Q 034382 31 QPKERQYRALVLRFIKDRTAALLLVEVGLQATAWVS-----------VGAQIGDEVEVKVEEAHPRDDIIYLK 92 (96)
Q Consensus 31 ~~~~~~~~AvVl~~~~~~~~~vlL~dl~le~~~~~~-----------~~~~~Gd~v~v~v~~vdP~~~~l~l~ 92 (96)
+. |....|.|.+-.+ ..+.|-|+ +++.-++.+ ..+.+||.+.++|.++|+.++.+.+.
T Consensus 476 ~~-G~iV~g~V~~v~~-~G~fV~l~--gv~Gll~~sels~~~~~~~~~~~~vGd~V~vkV~~id~~~~~I~lS 544 (647)
T PRK00087 476 EE-GDVVEGEVKRLTD-FGAFVDIG--GVDGLLHVSEISWGRVEKPSDVLKVGDEIKVYILDIDKENKKLSLS 544 (647)
T ss_pred CC-CCEEEEEEEEEeC-CcEEEEEC--CEEEEEEHHHcCccccCCHHHhcCCCCEEEEEEEEEECCCCEEEEE
Confidence 45 8999999999776 66666673 577777654 23789999999999999999887764
No 71
>COG2996 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only]
Probab=82.27 E-value=9 Score=29.84 Aligned_cols=56 Identities=18% Similarity=0.341 Sum_probs=44.7
Q ss_pred CCeEEEEEEEEccCceEEEEeecceeeEEEeec---CCCCCCCEEEEEEeeecCCCCeEEEE
Q 034382 34 ERQYRALVLRFIKDRTAALLLVEVGLQATAWVS---VGAQIGDEVEVKVEEAHPRDDIIYLK 92 (96)
Q Consensus 34 ~~~~~AvVl~~~~~~~~~vlL~dl~le~~~~~~---~~~~~Gd~v~v~v~~vdP~~~~l~l~ 92 (96)
++.|+|+|-+... .+++.+.|=++-.-+..+ ..+..|++++.+|-.+.. ++.|-++
T Consensus 156 nq~v~~tVYr~~~--~G~fv~~e~~~~GfIh~sEr~~~prlG~~l~~rVi~~re-Dg~lnLS 214 (287)
T COG2996 156 NQEVDATVYRLLE--SGTFVITENGYLGFIHKSERFAEPRLGERLTARVIGVRE-DGKLNLS 214 (287)
T ss_pred cCeeeeEEEEEec--cceEEEEcCCeEEEEcchhhcccccCCceEEEEEEEEcc-CCeeecc
Confidence 6899999999755 444444487887777776 689999999999999999 8877654
No 72
>PRK06299 rpsA 30S ribosomal protein S1; Reviewed
Probab=82.20 E-value=15 Score=30.28 Aligned_cols=57 Identities=19% Similarity=0.123 Sum_probs=46.9
Q ss_pred CCeEEEEEEEEccCceEEEEeecceeeEEEeec---C-----CCCCCCEEEEEEeeecCCCCeEEEE
Q 034382 34 ERQYRALVLRFIKDRTAALLLVEVGLQATAWVS---V-----GAQIGDEVEVKVEEAHPRDDIIYLK 92 (96)
Q Consensus 34 ~~~~~AvVl~~~~~~~~~vlL~dl~le~~~~~~---~-----~~~~Gd~v~v~v~~vdP~~~~l~l~ 92 (96)
|..-+|.|+...+ +.+.|-+ ....+.-++.+ . .+.+||.+.+.|.++|+..+.+.+.
T Consensus 31 G~~v~G~V~~v~~-~~~~Vdi-g~k~~g~lp~~e~~~~~~~~~~~vG~~i~~~V~~~~~~~~~i~lS 95 (565)
T PRK06299 31 GSIVKGTVVAIDK-DYVLVDV-GLKSEGRIPLEEFKNEQGELEVKVGDEVEVYVERIEDGFGETVLS 95 (565)
T ss_pred CCEEEEEEEEEEC-CEEEEEe-CCCeEEEEEHHHhcCccccccCCCCCEEEEEEEEEECCCCcEEEe
Confidence 8888999999888 8888887 55567777765 1 4799999999999999998877654
No 73
>cd04508 TUDOR Tudor domains are found in many eukaryotic organisms and have been implicated in protein-protein interactions in which methylated protein substrates bind to these domains. For example, the Tudor domain of Survival of Motor Neuron (SMN) binds to symmetrically dimethylated arginines of arginine-glycine (RG) rich sequences found in the C-terminal tails of Sm proteins. The SMN protein is linked to spinal muscular atrophy. Another example is the tandem tudor domains of 53BP1, which bind to histone H4 specifically dimethylated at Lys20 (H4-K20me2). 53BP1 is a key transducer of the DNA damage checkpoint signal.
Probab=82.16 E-value=4.2 Score=22.08 Aligned_cols=33 Identities=21% Similarity=0.354 Sum_probs=28.1
Q ss_pred CCeEEEEEEEEccCceEEEEeecceeeEEEeec
Q 034382 34 ERQYRALVLRFIKDRTAALLLVEVGLQATAWVS 66 (96)
Q Consensus 34 ~~~~~AvVl~~~~~~~~~vlL~dl~le~~~~~~ 66 (96)
+.+++|.|++..+++.+.|.+.|+|-...++.+
T Consensus 12 ~~wyra~V~~~~~~~~~~V~f~DyG~~~~v~~~ 44 (48)
T cd04508 12 GKWYRAKITSILSDGKVEVFFVDYGNTEVVPLS 44 (48)
T ss_pred CeEEEEEEEEECCCCcEEEEEEcCCCcEEEeHH
Confidence 789999999988448999999999988877653
No 74
>PF10989 DUF2808: Protein of unknown function (DUF2808); InterPro: IPR021256 This family of proteins with unknown function appears to be restricted to Cyanobacteria.
Probab=81.11 E-value=9.2 Score=26.26 Aligned_cols=45 Identities=20% Similarity=0.147 Sum_probs=35.0
Q ss_pred ceEEEEeecceeeEEEeecCCCCCCCEEEEEEeee-cCCC-CeEEEE
Q 034382 48 RTAALLLVEVGLQATAWVSVGAQIGDEVEVKVEEA-HPRD-DIIYLK 92 (96)
Q Consensus 48 ~~~~vlL~dl~le~~~~~~~~~~~Gd~v~v~v~~v-dP~~-~~l~l~ 92 (96)
..+.+....-+=.+.+.++.++.||+.+.|.+..+ +|.. |...|.
T Consensus 78 pl~~v~~~~~~~~i~I~f~~PV~pG~tv~V~l~~v~NP~~~G~Y~f~ 124 (146)
T PF10989_consen 78 PLAEVEWDEDGRTITITFDEPVPPGTTVTVVLSPVRNPRSGGTYQFN 124 (146)
T ss_pred CceEEEEcCCCCEEEEEeCCCCCCCCEEEEEEEeeeCCCCCCeEEEE
Confidence 34556666666677788889999999999999888 9988 655553
No 75
>PRK07400 30S ribosomal protein S1; Reviewed
Probab=80.44 E-value=5.2 Score=31.04 Aligned_cols=62 Identities=16% Similarity=0.113 Sum_probs=46.1
Q ss_pred hhhCCCCCeEEEEEEEEccCceEEEEeecceeeEEEeec-----------CCCCCCCEEEEEEeeecCCCCeEEEE
Q 034382 28 LRRQPKERQYRALVLRFIKDRTAALLLVEVGLQATAWVS-----------VGAQIGDEVEVKVEEAHPRDDIIYLK 92 (96)
Q Consensus 28 L~~~~~~~~~~AvVl~~~~~~~~~vlL~dl~le~~~~~~-----------~~~~~Gd~v~v~v~~vdP~~~~l~l~ 92 (96)
+..-..|...+|.|..-.+ ..+-|-+. +++.-++.+ ..+++||.+.++|.++|+-.+.|.|.
T Consensus 191 ~~~~k~G~vv~G~V~~I~~-~G~fV~i~--gv~Gllhisels~~~~~~~~~~~~vGd~VkvkVl~iD~e~~rI~LS 263 (318)
T PRK07400 191 MNRLEVGEVVVGTVRGIKP-YGAFIDIG--GVSGLLHISEISHEHIETPHSVFNVNDEMKVMIIDLDAERGRISLS 263 (318)
T ss_pred hccCCCCCEEEEEEEEEEC-CeEEEEEC--CEEEEEEHHHcccccccChhhccCCCCEEEEEEEEEeCCCCEEEEE
Confidence 3443448999999998766 66666664 556655443 23799999999999999988888775
No 76
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=79.54 E-value=29 Score=28.64 Aligned_cols=64 Identities=19% Similarity=0.076 Sum_probs=48.2
Q ss_pred HHHhhhCCCCCeEEEEEEEEccCceEEEEeecceeeEEEeec-----CCCCCCCEEEEEEeeecCCCC--eEEEE
Q 034382 25 IEFLRRQPKERQYRALVLRFIKDRTAALLLVEVGLQATAWVS-----VGAQIGDEVEVKVEEAHPRDD--IIYLK 92 (96)
Q Consensus 25 l~YL~~~~~~~~~~AvVl~~~~~~~~~vlL~dl~le~~~~~~-----~~~~~Gd~v~v~v~~vdP~~~--~l~l~ 92 (96)
+.-+..+. |..-.|.|.+..+ +.+.|-|. +.++-+|.+ ..+.+||++.+.|.+||+... .|-++
T Consensus 127 ~~eyk~~~-GeIV~G~V~ri~~-~giiVDLg--gvea~LP~sE~ip~E~~~~GdrIka~I~~Vd~~~kg~qIilS 197 (470)
T PRK09202 127 YEEYKDRV-GEIITGVVKRVER-GNIIVDLG--RAEAILPRKEQIPRENFRPGDRVRAYVYEVRKEARGPQIILS 197 (470)
T ss_pred HHHHHhhc-CCEEEEEEEEEec-CCEEEEEC--CeEEEecHHHcCCCccCCCCCEEEEEEEEEecCCCCCeEEEE
Confidence 34444446 7899999999887 66666662 677777775 578999999999999999766 55443
No 77
>COG2106 Uncharacterized conserved protein [Function unknown]
Probab=78.99 E-value=4.1 Score=31.48 Aligned_cols=45 Identities=29% Similarity=0.290 Sum_probs=38.5
Q ss_pred CCeEEEEEEEEccCceEEEEeecceeeEEEeecCCCCCCCEEEEEEeee
Q 034382 34 ERQYRALVLRFIKDRTAALLLVEVGLQATAWVSVGAQIGDEVEVKVEEA 82 (96)
Q Consensus 34 ~~~~~AvVl~~~~~~~~~vlL~dl~le~~~~~~~~~~~Gd~v~v~v~~v 82 (96)
|.-=+|+|.++.+ +. .+-++|++-.+.++.++.+|++|+|++...
T Consensus 106 Ge~ReG~v~~~~~-~~---~~v~iG~~~~~~l~~~~~~~~RvTvri~~~ 150 (272)
T COG2106 106 GEYREGLVIRRGK-KG---NLVDIGKDKLAKLSSPAPPGARVTVRIISR 150 (272)
T ss_pred eeecceEEEEecC-Cc---eEEEecCCcceeccCCCCCCceEEEEEEec
Confidence 4455799999888 44 677889999999998899999999999988
No 78
>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=77.91 E-value=13 Score=22.50 Aligned_cols=56 Identities=18% Similarity=-0.024 Sum_probs=41.3
Q ss_pred CCeEEEEEEEEccCceEEEEeecceeeEEEeec-----------CCCCCCCEEEEEEeeecCCCCeEEEE
Q 034382 34 ERQYRALVLRFIKDRTAALLLVEVGLQATAWVS-----------VGAQIGDEVEVKVEEAHPRDDIIYLK 92 (96)
Q Consensus 34 ~~~~~AvVl~~~~~~~~~vlL~dl~le~~~~~~-----------~~~~~Gd~v~v~v~~vdP~~~~l~l~ 92 (96)
|..-.|.|++-.. +.+.|-+- -.++..++.. ..+.+||.+..+|.++|.- +.+.|.
T Consensus 7 GdiV~G~V~~v~~-~~~~V~i~-~~~~g~l~~~~~~~~~~~~~~~~~~~GD~i~~~V~~~~~~-~~i~LS 73 (82)
T cd04454 7 GDIVIGIVTEVNS-RFWKVDIL-SRGTARLEDSSATEKDKKEIRKSLQPGDLILAKVISLGDD-MNVLLT 73 (82)
T ss_pred CCEEEEEEEEEcC-CEEEEEeC-CCceEEeechhccCcchHHHHhcCCCCCEEEEEEEEeCCC-CCEEEE
Confidence 5677889998777 88887773 2455555554 2389999999999999985 666654
No 79
>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=77.64 E-value=30 Score=27.98 Aligned_cols=67 Identities=16% Similarity=0.157 Sum_probs=50.8
Q ss_pred chHHHHhhhCCCCCeEEEEEEEEccCceEEEEeecceeeEEEeec---------CCCCCCCEEEEEEeeecCCCCeEEEE
Q 034382 22 YWIIEFLRRQPKERQYRALVLRFIKDRTAALLLVEVGLQATAWVS---------VGAQIGDEVEVKVEEAHPRDDIIYLK 92 (96)
Q Consensus 22 yW~l~YL~~~~~~~~~~AvVl~~~~~~~~~vlL~dl~le~~~~~~---------~~~~~Gd~v~v~v~~vdP~~~~l~l~ 92 (96)
-|....-.... |..-+|.|++..+ +-+.|-+. +++.-+|.+ ....+|+.+.++|.++|+..+.+-+.
T Consensus 90 ~~~~l~~a~~~-g~~v~g~V~~~~~-~g~~V~i~--g~~~flP~s~~~~~~~~~~~~~vG~~i~~~v~~~~~~~~~iv~S 165 (516)
T TIGR00717 90 LWIKLEKAYEE-GSIVEGKIVGKVK-GGFIVDLN--GVEAFLPGSQVDVKPIKDLDSLIGKTLKFKIIKLDQKRNNIVVS 165 (516)
T ss_pred HHHHHHHHhhC-CCeEEEEEEEEEC-CEEEEEEC--CEEEEEeHHHhcCcccCchhhhCCCEEEEEEEEEECCCCcEEEE
Confidence 57654444455 7899999999988 77777775 677777765 12458999999999999988876553
No 80
>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=76.10 E-value=12 Score=32.05 Aligned_cols=55 Identities=29% Similarity=0.328 Sum_probs=39.4
Q ss_pred CCeEEEEEEEEccCceEEEEeecceeeEEEeec-----------CCCCCCCEEEEEEeeecCCCCeEEE
Q 034382 34 ERQYRALVLRFIKDRTAALLLVEVGLQATAWVS-----------VGAQIGDEVEVKVEEAHPRDDIIYL 91 (96)
Q Consensus 34 ~~~~~AvVl~~~~~~~~~vlL~dl~le~~~~~~-----------~~~~~Gd~v~v~v~~vdP~~~~l~l 91 (96)
|..+.|.|.+-.+ ..+-|-|.. +.+.-++.+ .-++.||.|.|+|.++|+ .+.++|
T Consensus 619 G~i~~G~V~~I~~-~GafVei~~-g~~GllHiSei~~~~v~~~~~~~kvGD~V~VkVi~id~-~gki~L 684 (684)
T TIGR03591 619 GKIYEGKVVRIMD-FGAFVEILP-GKDGLVHISEIANERVEKVEDVLKEGDEVKVKVLEIDK-QGRIKL 684 (684)
T ss_pred CcEEEEEEEEEeC-CEEEEEECC-CcEEEEEHHHcCCCcccChhhccCCCCEEEEEEEEECC-CCCccC
Confidence 8999999998766 555555533 344444433 337899999999999998 676653
No 81
>COG1098 VacB Predicted RNA binding protein (contains ribosomal protein S1 domain) [Translation, ribosomal structure and biogenesis]
Probab=75.95 E-value=2.9 Score=28.99 Aligned_cols=44 Identities=23% Similarity=0.256 Sum_probs=35.5
Q ss_pred ceEEEEeecceeeEEEeecCCCCCCCEEEEEEeeecCCCCeEEEE
Q 034382 48 RTAALLLVEVGLQATAWVSVGAQIGDEVEVKVEEAHPRDDIIYLK 92 (96)
Q Consensus 48 ~~~~vlL~dl~le~~~~~~~~~~~Gd~v~v~v~~vdP~~~~l~l~ 92 (96)
..++|+|-+++=.-.=...+-++.||.|.|+|-.+|- ++-|.|.
T Consensus 29 ~tGLVHISEIa~~fVkdI~d~L~vG~eV~vKVl~ide-~GKisLS 72 (129)
T COG1098 29 KTGLVHISEIADGFVKDIHDHLKVGQEVKVKVLDIDE-NGKISLS 72 (129)
T ss_pred CcceEEehHhhhhhHHhHHHHhcCCCEEEEEEEeecc-CCCccee
Confidence 7788888887755554555779999999999999999 8877764
No 82
>PF11213 DUF3006: Protein of unknown function (DUF3006); InterPro: IPR021377 This family of proteins has no known function.
Probab=74.04 E-value=17 Score=22.05 Aligned_cols=37 Identities=27% Similarity=0.243 Sum_probs=28.1
Q ss_pred EEEEccCceEEEEeecceeeEEEeec---CCCCCCCEEEE
Q 034382 41 VLRFIKDRTAALLLVEVGLQATAWVS---VGAQIGDEVEV 77 (96)
Q Consensus 41 Vl~~~~~~~~~vlL~dl~le~~~~~~---~~~~~Gd~v~v 77 (96)
|++...++.|.+++++-.-+..++.+ .+++.||.+.+
T Consensus 3 ivDRiE~~~AVl~~~~~~~~~~vp~~~LP~~~keGDvl~i 42 (71)
T PF11213_consen 3 IVDRIEGDYAVLELEDGEKEIDVPRSRLPEGAKEGDVLEI 42 (71)
T ss_pred EEEEEeCCEEEEEECCCeEEEEEEHHHCCCCCCcccEEEE
Confidence 56666658888888888845556654 78999999888
No 83
>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=73.86 E-value=20 Score=25.32 Aligned_cols=62 Identities=13% Similarity=0.096 Sum_probs=39.3
Q ss_pred HHHhhhCCCCCeEEEEEEEEccCceEEEEeecceeeEEEe----------e------------cCCCCCCCEEEEEEeee
Q 034382 25 IEFLRRQPKERQYRALVLRFIKDRTAALLLVEVGLQATAW----------V------------SVGAQIGDEVEVKVEEA 82 (96)
Q Consensus 25 l~YL~~~~~~~~~~AvVl~~~~~~~~~vlL~dl~le~~~~----------~------------~~~~~~Gd~v~v~v~~v 82 (96)
+.||+... |+.++|.|.+-.. .-.-+-|.- ++.-+. . ...++.||.|+++|.++
T Consensus 74 ~i~f~p~~-gEvv~G~V~~v~~-~GifV~lg~--~~gi~~~~~l~~~~~~~d~~~~~~~~~~~~~~~~~Gd~VrvrV~~v 149 (179)
T TIGR00448 74 ALVFKPEL-GEIVEGEVIEIVE-FGAFVSLGP--FDGLFHVSQVTDDYCYYDPKESALIGKETKKVLDEGDKVRARIVAL 149 (179)
T ss_pred EEEEeccC-CCEEEEEEEEEEe-eEEEEEeCC--ceEEEEcHHhCCCceEEccccceEEEccCCeEEcCCCEEEEEEEEE
Confidence 34667777 8999999988666 433333311 121111 0 13488999999999999
Q ss_pred c-----CCCCeEE
Q 034382 83 H-----PRDDIIY 90 (96)
Q Consensus 83 d-----P~~~~l~ 90 (96)
| |....|.
T Consensus 150 ~~~~~~~~~~~I~ 162 (179)
T TIGR00448 150 SLKDRRPEGSKIG 162 (179)
T ss_pred EccCCCCCcceEE
Confidence 9 5555553
No 84
>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=73.01 E-value=21 Score=22.51 Aligned_cols=18 Identities=17% Similarity=0.438 Sum_probs=16.1
Q ss_pred CCCCCEEEEEEeeecCCC
Q 034382 69 AQIGDEVEVKVEEAHPRD 86 (96)
Q Consensus 69 ~~~Gd~v~v~v~~vdP~~ 86 (96)
+++||.+.++|..+|+..
T Consensus 54 ~~~Gd~v~vkI~~vd~~~ 71 (99)
T cd04460 54 LKVGDVVRARIVAVSLKE 71 (99)
T ss_pred ECCCCEEEEEEEEEeHHH
Confidence 599999999999999754
No 85
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=72.70 E-value=31 Score=24.48 Aligned_cols=49 Identities=22% Similarity=0.165 Sum_probs=39.1
Q ss_pred CCeEEEEEEEEccCceEEEEeecc---------eeeEEEeec-----------CCCCCCCEEEEEEeeec
Q 034382 34 ERQYRALVLRFIKDRTAALLLVEV---------GLQATAWVS-----------VGAQIGDEVEVKVEEAH 83 (96)
Q Consensus 34 ~~~~~AvVl~~~~~~~~~vlL~dl---------~le~~~~~~-----------~~~~~Gd~v~v~v~~vd 83 (96)
|..-.|.|.+-.+ ..+.|-|.+. +++.-++.+ ..+.+||.|..+|.++|
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 7888999999887 8888888643 356666654 23899999999999999
No 86
>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=71.69 E-value=8.5 Score=23.88 Aligned_cols=52 Identities=17% Similarity=0.079 Sum_probs=35.8
Q ss_pred eEEEEEEEEccCceEEEEeecceeeEEEeec-----------CCCCCCCEEEEEEeeecCCCCe
Q 034382 36 QYRALVLRFIKDRTAALLLVEVGLQATAWVS-----------VGAQIGDEVEVKVEEAHPRDDI 88 (96)
Q Consensus 36 ~~~AvVl~~~~~~~~~vlL~dl~le~~~~~~-----------~~~~~Gd~v~v~v~~vdP~~~~ 88 (96)
+++|+|=.--+ .+|.|.|.+-+=-+..+.. .+++.|+.+.|++...++..+.
T Consensus 3 ~htA~VQh~~k-dfAvvSL~~t~~L~a~p~~sHLNdtfrf~seklkvG~~l~v~lk~~~~~~~g 65 (69)
T cd05701 3 RHTAIVQHADK-DFAIVSLATTGDLAAFPTRSHLNDTFRFDSEKLSVGQCLDVTLKDPNCLAGG 65 (69)
T ss_pred ccchhhhhhhh-ceEEEEeeccccEEEEEchhhccccccccceeeeccceEEEEEecCccCccc
Confidence 44555544333 7777777776655554432 6899999999999998886543
No 87
>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=71.52 E-value=21 Score=22.03 Aligned_cols=35 Identities=17% Similarity=0.178 Sum_probs=26.5
Q ss_pred eeeEEEeecCCCCCCCEEEEEEeeecCCCCeEEEEE
Q 034382 58 GLQATAWVSVGAQIGDEVEVKVEEAHPRDDIIYLKE 93 (96)
Q Consensus 58 ~le~~~~~~~~~~~Gd~v~v~v~~vdP~~~~l~l~e 93 (96)
++.+..+....+++||.|.|+ +.|....+..+|..
T Consensus 34 gifV~~~~~~~~~~Gd~V~vt-G~v~ey~g~tql~~ 68 (78)
T cd04486 34 GIFVYTGSGADVAVGDLVRVT-GTVTEYYGLTQLTA 68 (78)
T ss_pred eEEEecCCCCCCCCCCEEEEE-EEEEeeCCeEEEcc
Confidence 455444434678999999998 99999888877754
No 88
>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=71.23 E-value=17 Score=20.77 Aligned_cols=49 Identities=22% Similarity=0.141 Sum_probs=30.1
Q ss_pred CeEEEEEEEEccC-c--eEEEEeecce-eeEEEeec----CCCCCCCEEEEEEeeec
Q 034382 35 RQYRALVLRFIKD-R--TAALLLVEVG-LQATAWVS----VGAQIGDEVEVKVEEAH 83 (96)
Q Consensus 35 ~~~~AvVl~~~~~-~--~~~vlL~dl~-le~~~~~~----~~~~~Gd~v~v~v~~vd 83 (96)
..|+|.|...-.. . .+.+.+.+-. +.+.+... -++++||.+.+.+...+
T Consensus 5 N~l~g~V~~ie~~g~~~~v~~~~~~~~~l~a~it~~~~~~L~L~~G~~V~~~ik~~~ 61 (64)
T PF03459_consen 5 NQLPGTVESIENLGSEVEVTLDLGGGETLTARITPESAEELGLKPGDEVYASIKASS 61 (64)
T ss_dssp EEEEEEEEEEEESSSEEEEEEEETTSEEEEEEEEHHHHHHCT-STT-EEEEEE-GGG
T ss_pred cEEEEEEEEEEECCCeEEEEEEECCCCEEEEEEcHHHHHHcCCCCCCEEEEEEehhh
Confidence 4677777754332 3 4555566666 77777665 46889999999886543
No 89
>PRK00276 infA translation initiation factor IF-1; Validated
Probab=70.89 E-value=21 Score=21.68 Aligned_cols=57 Identities=14% Similarity=0.060 Sum_probs=39.1
Q ss_pred CeEEEEEEEEccCceEEEEee-cceeeEEEeec-----CCCCCCCEEEEEEeeecCCCCeEEE
Q 034382 35 RQYRALVLRFIKDRTAALLLV-EVGLQATAWVS-----VGAQIGDEVEVKVEEAHPRDDIIYL 91 (96)
Q Consensus 35 ~~~~AvVl~~~~~~~~~vlL~-dl~le~~~~~~-----~~~~~Gd~v~v~v~~vdP~~~~l~l 91 (96)
-+.+|.|++.++.+.+.|.++ .--+.+.++-. ..+.+||.|.+.+...|+-.+.|-.
T Consensus 7 ~~~~G~Vi~~~~~~~y~V~~~~g~~~~c~~~Gklr~~~i~i~vGD~V~ve~~~~~~~~g~Iv~ 69 (72)
T PRK00276 7 IEMEGTVVEALPNAMFRVELENGHEVLAHISGKMRKNYIRILPGDKVTVELSPYDLTKGRITY 69 (72)
T ss_pred EEEEEEEEEEcCCCEEEEEeCCCCEEEEEEccceeeCCcccCCCCEEEEEEcccCCCeEEEEE
Confidence 467899999997238888653 33444555533 2367899999998887776666544
No 90
>PF07177 Neuralized: Neuralized; InterPro: IPR006573 NEUZ is a domain of unknown function found in neuralized proteins, i.e. proteins involved in the specification of the neuroblast during cellular differentiation. ; PDB: 2YUE_A 2E63_A.
Probab=70.83 E-value=7.1 Score=23.84 Aligned_cols=26 Identities=27% Similarity=0.553 Sum_probs=15.7
Q ss_pred cCCCCCCCEEEEEEeeecCC-CCeEEE
Q 034382 66 SVGAQIGDEVEVKVEEAHPR-DDIIYL 91 (96)
Q Consensus 66 ~~~~~~Gd~v~v~v~~vdP~-~~~l~l 91 (96)
++++.+||.+.|+|.++++. .+-|++
T Consensus 36 ~rPl~~~E~~~v~I~~~~~~wsG~L~~ 62 (69)
T PF07177_consen 36 SRPLRIGEKFEVRIDEVEPSWSGSLRI 62 (69)
T ss_dssp SS-B-TT-EEEEEEEEE-SSSSS--EE
T ss_pred cCCccCCCEEEEEEEecCCCceeEEEE
Confidence 47899999999999999863 444444
No 91
>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=69.06 E-value=10 Score=33.02 Aligned_cols=56 Identities=14% Similarity=0.210 Sum_probs=36.5
Q ss_pred CCeEEEEEEEEccCceEEEEeecceeeEEEeec---------------CCCCCCCEEEEEEeeecCCCCeEEEE
Q 034382 34 ERQYRALVLRFIKDRTAALLLVEVGLQATAWVS---------------VGAQIGDEVEVKVEEAHPRDDIIYLK 92 (96)
Q Consensus 34 ~~~~~AvVl~~~~~~~~~vlL~dl~le~~~~~~---------------~~~~~Gd~v~v~v~~vdP~~~~l~l~ 92 (96)
|..++|.|..-.. --+-|-|. -+.+.=++.+ .-++.||.|.|+|.++|+ ++.|+|.
T Consensus 648 G~i~~GkV~~I~d-fGaFVel~-~G~eGLvHISeisdls~~~rv~~~~dv~kvGd~V~VKVl~ID~-~gKI~L~ 718 (719)
T TIGR02696 648 GERFLGTVVKTTA-FGAFVSLL-PGKDGLLHISQIRKLAGGKRVENVEDVLSVGQKIQVEIADIDD-RGKLSLV 718 (719)
T ss_pred CCEEEEEEEEEEC-ceEEEEec-CCceEEEEhhhccccccccCcCCHHHcCCCCCEEEEEEEEECC-CCCeeec
Confidence 8889988877554 33333332 1223222222 348999999999999996 6777763
No 92
>COG1093 SUI2 Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis]
Probab=68.03 E-value=22 Score=27.49 Aligned_cols=45 Identities=24% Similarity=0.151 Sum_probs=38.1
Q ss_pred ceEEEEeecce-eeEEEeec-----------CCCCCCCEEEEEEeeecCCCCeEEEE
Q 034382 48 RTAALLLVEVG-LQATAWVS-----------VGAQIGDEVEVKVEEAHPRDDIIYLK 92 (96)
Q Consensus 48 ~~~~vlL~dl~-le~~~~~~-----------~~~~~Gd~v~v~v~~vdP~~~~l~l~ 92 (96)
--|.+.|.+++ +|.-++.+ +=+..|+.+..+|-+|||..+.|-|+
T Consensus 25 ~GAyv~L~EY~g~Eg~ihiSEvas~wVknIrd~vkegqkvV~kVlrVd~~rg~IDLS 81 (269)
T COG1093 25 YGAYVELDEYPGKEGFIHISEVASGWVKNIRDYVKEGQKVVAKVLRVDPKRGHIDLS 81 (269)
T ss_pred cccEEEeeccCCeeeeEEHHHHHHHHHHHHHHHhhcCCeEEEEEEEEcCCCCeEeee
Confidence 56778888887 88888876 34899999999999999999998764
No 93
>cd01854 YjeQ_engC YjeQ/EngC. YjeQ (YloQ in Bacillus subtilis) represents a protein family whose members are broadly conserved in bacteria and have been shown to be essential to the growth of E. coli and B. subtilis. Proteins of the YjeQ family contain all sequence motifs typical of the vast class of P-loop-containing GTPases, but show a circular permutation, with a G4-G1-G3 pattern of motifs as opposed to the regular G1-G3-G4 pattern seen in most GTPases. All YjeQ family proteins display a unique domain architecture, which includes an N-terminal OB-fold RNA-binding domain, the central permuted GTPase domain, and a zinc knuckle-like C-terminal cysteine domain. This domain architecture suggests a role for YjeQ as a regulator of translation.
Probab=67.86 E-value=35 Score=25.74 Aligned_cols=51 Identities=20% Similarity=0.200 Sum_probs=33.6
Q ss_pred EEEEEEccCceEEEEeecceeeEEEeec-----CCCCCCCEEEEE--------EeeecCCCCeEE
Q 034382 39 ALVLRFIKDRTAALLLVEVGLQATAWVS-----VGAQIGDEVEVK--------VEEAHPRDDIIY 90 (96)
Q Consensus 39 AvVl~~~~~~~~~vlL~dl~le~~~~~~-----~~~~~Gd~v~v~--------v~~vdP~~~~l~ 90 (96)
|.|+...+ +.+.|.-++--+++.++.. ..+..||.|.+. |.++-||.+.|.
T Consensus 1 g~v~~~~~-~~~~v~~~~~~~~~~~~g~~~~~~~~~~vGD~V~~~~~~~~~~~i~~i~~R~~~l~ 64 (287)
T cd01854 1 GRVIAVHG-GFYDVETEGGELRCRARGKLRKKGIKPVVGDWVEVEPDDDGEGVIVRVLPRKNLLS 64 (287)
T ss_pred CEEEEEEC-CEEEEEECCeEEEEEeccccccCCCCccCCCEEEEEecCCCcEEEEEEECCCceEE
Confidence 35666666 7777765543445555544 258999999875 667778877663
No 94
>cd05790 S1_Rrp40 S1_Rrp40: Rrp40 S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In Saccharomyces cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".
Probab=65.24 E-value=20 Score=22.88 Aligned_cols=38 Identities=16% Similarity=0.164 Sum_probs=27.0
Q ss_pred EEEEeecceeeEEEeec-CCCCCCCEEEEEEeeecCCCC
Q 034382 50 AALLLVEVGLQATAWVS-VGAQIGDEVEVKVEEAHPRDD 87 (96)
Q Consensus 50 ~~vlL~dl~le~~~~~~-~~~~~Gd~v~v~v~~vdP~~~ 87 (96)
..-.||-++++-.-+.. ..+.+||.|.-+|..+|+..+
T Consensus 30 ~~a~L~~~~f~gatk~~rp~L~~GDlV~ArV~~~~~~~~ 68 (86)
T cd05790 30 EPASLSYLAFEGATKRNRPNLNVGDLVYARVVKANRDME 68 (86)
T ss_pred cceEechHHcccccccccccCCCCCEEEEEEEecCCCCC
Confidence 34456666666443333 579999999999999998644
No 95
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=64.76 E-value=66 Score=26.68 Aligned_cols=60 Identities=18% Similarity=0.189 Sum_probs=45.9
Q ss_pred HHHHhhhCCCCCeEEEEEEEEccCceEEEEee-cce---eeEEEeec-----CCCCCCCEEEEEEeeecCC
Q 034382 24 IIEFLRRQPKERQYRALVLRFIKDRTAALLLV-EVG---LQATAWVS-----VGAQIGDEVEVKVEEAHPR 85 (96)
Q Consensus 24 ~l~YL~~~~~~~~~~AvVl~~~~~~~~~vlL~-dl~---le~~~~~~-----~~~~~Gd~v~v~v~~vdP~ 85 (96)
.+.-|..+. |..-.|.|.+.-+ +.+.|-|. ++| .++-++.+ ..+.+||++.+-+.+|+.-
T Consensus 144 i~~ef~~~~-GeIV~G~V~r~e~-~~viv~l~~~~g~~~~EaiLP~~Eqip~E~y~~Gdrika~i~~V~~~ 212 (449)
T PRK12329 144 IQEEFQDLE-DTVLTARVLRFER-QSVIMAVSSGFGQPEVEAELPKREQLPNDNYRANATFKVFLKEVSEG 212 (449)
T ss_pred HHHHHHHhc-CcEEEEEEEEEcC-CCEEEEecccCCCcceEEEecHHHcCCCCcCCCCCEEEEEEEEeecC
Confidence 556666767 8999999999766 65555553 334 77777775 6799999999999999764
No 96
>COG0539 RpsA Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]
Probab=62.64 E-value=82 Score=26.69 Aligned_cols=68 Identities=24% Similarity=0.214 Sum_probs=50.0
Q ss_pred chHHHHhhhCCCCCeEEEEEEEEccCceEEEEeecceeeEEEeec----CCCCCCCEEEEEEeeecCCCCeEEEE
Q 034382 22 YWIIEFLRRQPKERQYRALVLRFIKDRTAALLLVEVGLQATAWVS----VGAQIGDEVEVKVEEAHPRDDIIYLK 92 (96)
Q Consensus 22 yW~l~YL~~~~~~~~~~AvVl~~~~~~~~~vlL~dl~le~~~~~~----~~~~~Gd~v~v~v~~vdP~~~~l~l~ 92 (96)
.|. .|-..+++|..-.|.|...-. ..+.+.|++-- +.-++.+ ..+++||.+..+|..+|+-+..+.+.
T Consensus 439 p~~-~~~~~~~~~~~v~~~v~~i~~-~G~~v~l~~~v-~G~i~~~~~~~~~~~~gd~v~a~v~~id~k~~ki~lS 510 (541)
T COG0539 439 PWE-EFSEKYKKGSVVKGKVKSVKD-KGAFVELGGGV-EGLIRLSELSRDVLKVGDEVEAVVVSIDKKNRKILLS 510 (541)
T ss_pred chh-hhHhhccCCCeEEEEEEEEcc-CceEEEecCce-eeeeecchhhhhhccCCCEEEEEEEEEcCCCCEEEEE
Confidence 453 355556668888888888555 66677777633 4444443 47999999999999999999998875
No 97
>cd03447 FAS_MaoC FAS_MaoC, the MaoC-like hot dog fold of the fatty acid synthase, beta subunit. Other enzymes with this fold include MaoC dehydratase, Hydratase-Dehydrogenase-Epimerase protein (HDE), and 17-beta-hydroxysteriod dehydrogenase (HSD).
Probab=62.63 E-value=29 Score=23.01 Aligned_cols=29 Identities=28% Similarity=0.095 Sum_probs=20.6
Q ss_pred EEEeecCCCCCCCEEEEEEeeecCCCCeE
Q 034382 61 ATAWVSVGAQIGDEVEVKVEEAHPRDDII 89 (96)
Q Consensus 61 ~~~~~~~~~~~Gd~v~v~v~~vdP~~~~l 89 (96)
..+++..++.+||.|.+++..++...+..
T Consensus 73 ~~~rf~~PV~~gdtl~~~~~v~~~~~~~~ 101 (126)
T cd03447 73 FTASFVGMVLPNDELEVRLEHVGMVDGRK 101 (126)
T ss_pred EEEEEcccCcCCCEEEEEEEEEEEeCCeE
Confidence 35556679999999998777666554443
No 98
>cd05793 S1_IF1A S1_IF1A: Translation initiation factor IF1A, also referred to as eIF1A in eukaryotes and aIF1A in archaea, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. IF1A is essential for translation initiation. eIF1A acts synergistically with eIF1 to mediate assembly of ribosomal initiation complexes at the initiation codon and maintain the accuracy of this process by recognizing and destabilizing aberrant preinitiation complexes from the mRNA. Without eIF1A and eIF1, 43S ribosomal preinitiation complexes can bind to the cap-proximal region, but are unable to reach the initiation codon. eIF1a also enhances the formation of 5'-terminal complexes in the presence of other translation initiation factors. This protein family is only found in eukaryotes and archaea.
Probab=62.61 E-value=35 Score=21.22 Aligned_cols=53 Identities=15% Similarity=0.086 Sum_probs=38.9
Q ss_pred EEEEEEEccCceEEEEeecceeeEEEeec------CCCCCCCEEEEEEeeecCCCCeEEE
Q 034382 38 RALVLRFIKDRTAALLLVEVGLQATAWVS------VGAQIGDEVEVKVEEAHPRDDIIYL 91 (96)
Q Consensus 38 ~AvVl~~~~~~~~~vlL~dl~le~~~~~~------~~~~~Gd~v~v~v~~vdP~~~~l~l 91 (96)
.|.|++-++.+...|.+++ |-+.-+..+ --+.+||.|.|....-|+-.+.|..
T Consensus 3 ~g~V~~~~g~~~~~V~~~~-g~~~la~i~gK~rk~iwI~~GD~V~Ve~~~~d~~kg~Iv~ 61 (77)
T cd05793 3 YGQVEKMLGNGRLEVRCFD-GKKRLCRIRGKMRKRVWINEGDIVLVAPWDFQDDKADIIY 61 (77)
T ss_pred EEEEEEEcCCCEEEEEECC-CCEEEEEEchhhcccEEEcCCCEEEEEeccccCCEEEEEE
Confidence 5788888887888888876 555555554 3478999999998877776665543
No 99
>PRK04012 translation initiation factor IF-1A; Provisional
Probab=62.59 E-value=41 Score=22.07 Aligned_cols=57 Identities=14% Similarity=0.140 Sum_probs=42.5
Q ss_pred CCeEEEEEEEEccCceEEEEeecceeeEEEeec------CCCCCCCEEEEEEeeecCCCCeEEE
Q 034382 34 ERQYRALVLRFIKDRTAALLLVEVGLQATAWVS------VGAQIGDEVEVKVEEAHPRDDIIYL 91 (96)
Q Consensus 34 ~~~~~AvVl~~~~~~~~~vlL~dl~le~~~~~~------~~~~~Gd~v~v~v~~vdP~~~~l~l 91 (96)
+-+-.|.|++-++.+.+.|.+++ |-+.-+..+ --+.+||.|.|.+..-|+-.+.|..
T Consensus 20 e~e~~g~V~~~lG~~~~~V~~~d-G~~~la~i~GK~Rk~IwI~~GD~VlVe~~~~~~~kg~Iv~ 82 (100)
T PRK04012 20 EGEVFGVVEQMLGANRVRVRCMD-GVERMGRIPGKMKKRMWIREGDVVIVAPWDFQDEKADIIW 82 (100)
T ss_pred CCEEEEEEEEEcCCCEEEEEeCC-CCEEEEEEchhhcccEEecCCCEEEEEecccCCCEEEEEE
Confidence 34668999999887899999886 555555554 3478999999998888866655543
No 100
>smart00333 TUDOR Tudor domain. Domain of unknown function present in several RNA-binding proteins. 10 copies in the Drosophila Tudor protein. Initial proposal that the survival motor neuron gene product contain a Tudor domain are corroborated by more recent database search techniques such as PSI-BLAST (unpublished).
Probab=61.87 E-value=26 Score=19.47 Aligned_cols=34 Identities=15% Similarity=0.256 Sum_probs=28.9
Q ss_pred CCCeEEEEEEEEccCceEEEEeecceeeEEEeec
Q 034382 33 KERQYRALVLRFIKDRTAALLLVEVGLQATAWVS 66 (96)
Q Consensus 33 ~~~~~~AvVl~~~~~~~~~vlL~dl~le~~~~~~ 66 (96)
++.+++|.|++..+++.+.|.+.|.|-...++..
T Consensus 15 d~~wyra~I~~~~~~~~~~V~f~D~G~~~~v~~~ 48 (57)
T smart00333 15 DGEWYRARIIKVDGEQLYEVFFIDYGNEEVVPPS 48 (57)
T ss_pred CCCEEEEEEEEECCCCEEEEEEECCCccEEEeHH
Confidence 3789999999987768899999999988877764
No 101
>PRK12288 GTPase RsgA; Reviewed
Probab=60.08 E-value=63 Score=25.35 Aligned_cols=53 Identities=19% Similarity=0.256 Sum_probs=36.9
Q ss_pred EEEEEEEEccCceEEEEeecce-eeEEEeec-CCCCCCCEEEEE------------EeeecCCCCeEE
Q 034382 37 YRALVLRFIKDRTAALLLVEVG-LQATAWVS-VGAQIGDEVEVK------------VEEAHPRDDIIY 90 (96)
Q Consensus 37 ~~AvVl~~~~~~~~~vlL~dl~-le~~~~~~-~~~~~Gd~v~v~------------v~~vdP~~~~l~ 90 (96)
-+|.|+...+ +.+.|.-.+=. +.+.++.. ..+..||.|.+. |.++.||.+.|.
T Consensus 40 ~~g~Vi~~~~-~~~~v~~~~g~~~~~~~~g~~~~~~vGD~V~~~~~~~~~~~~~~~I~~il~R~n~L~ 106 (347)
T PRK12288 40 QEGIVISRFG-QHADVEAADGEVHRCNIRRTIRSLVTGDRVVWRPGKEALEGVSGVVEAVHPRTSVLT 106 (347)
T ss_pred cceEEEEEEC-CEEEEEeCCCcEEEEEecccCCCCCCCcEEEEEeCCCcccccceEEEEEecccceEE
Confidence 5799999999 88888754422 34444444 357889999874 557777777665
No 102
>PF14250 AbrB-like: AbrB-like transcriptional regulator
Probab=59.51 E-value=8.3 Score=24.16 Aligned_cols=15 Identities=40% Similarity=0.716 Sum_probs=13.4
Q ss_pred CCCCCCCEEEEEEee
Q 034382 67 VGAQIGDEVEVKVEE 81 (96)
Q Consensus 67 ~~~~~Gd~v~v~v~~ 81 (96)
-.++|||++.+++.+
T Consensus 51 m~L~PGdEFeI~Lgr 65 (71)
T PF14250_consen 51 MGLKPGDEFEIKLGR 65 (71)
T ss_pred hCCCCCCEEEEEeCc
Confidence 578999999999986
No 103
>CHL00010 infA translation initiation factor 1
Probab=58.17 E-value=42 Score=20.76 Aligned_cols=56 Identities=14% Similarity=0.084 Sum_probs=37.7
Q ss_pred eEEEEEEEEccCceEEEEe-ecceeeEEEeec-----CCCCCCCEEEEEEeeecCCCCeEEE
Q 034382 36 QYRALVLRFIKDRTAALLL-VEVGLQATAWVS-----VGAQIGDEVEVKVEEAHPRDDIIYL 91 (96)
Q Consensus 36 ~~~AvVl~~~~~~~~~vlL-~dl~le~~~~~~-----~~~~~Gd~v~v~v~~vdP~~~~l~l 91 (96)
+.+|.|++.++.+.+.|.+ ..--+.+.++-. ..+.+||.|.+.+...|+..+.|-.
T Consensus 8 ~~~G~Vik~lg~~~y~V~~~~g~~~~c~~rGklr~~~i~~~vGD~V~ve~~~~~~~~g~Ii~ 69 (78)
T CHL00010 8 EMEGLVTESLPNGMFRVRLDNGCQVLGYISGKIRRNSIRILPGDRVKVELSPYDLTKGRIIY 69 (78)
T ss_pred EEEEEEEEEcCCCEEEEEeCCCCEEEEEeccceecCCcccCCCCEEEEEEcccCCCeEEEEE
Confidence 4579999999337777765 333455555543 2357899999998777776665543
No 104
>PF15057 DUF4537: Domain of unknown function (DUF4537)
Probab=57.36 E-value=55 Score=21.99 Aligned_cols=47 Identities=15% Similarity=0.106 Sum_probs=33.9
Q ss_pred CCCCeEEEEEEEEccCceEEEEeecceeeEEEee---------cCCCCCCCEEEEE
Q 034382 32 PKERQYRALVLRFIKDRTAALLLVEVGLQATAWV---------SVGAQIGDEVEVK 78 (96)
Q Consensus 32 ~~~~~~~AvVl~~~~~~~~~vlL~dl~le~~~~~---------~~~~~~Gd~v~v~ 78 (96)
.+|.-++|.|....+.+.++|-+++-..+..-.. ..++++||.|...
T Consensus 10 ~DG~YY~GtV~~~~~~~~~lV~f~~~~~~~v~~~~iI~~~~~~~~~L~~GD~VLA~ 65 (124)
T PF15057_consen 10 EDGFYYPGTVKKCVSSGQFLVEFDDGDTQEVPISDIIALSDAMRHSLQVGDKVLAP 65 (124)
T ss_pred CCCcEEeEEEEEccCCCEEEEEECCCCEEEeChHHeEEccCcccCcCCCCCEEEEe
Confidence 4588999999998765788888855444332221 3689999999888
No 105
>PF01176 eIF-1a: Translation initiation factor 1A / IF-1; InterPro: IPR006196 The S1 domain of around 70 amino acids, originally identified in ribosomal protein S1, is found in a large number of RNA-associated proteins. It has been shown that S1 proteins bind RNA through their S1 domains with some degree of sequence specificity. This type of S1 domain is found in translation initiation factor 1. The solution structure of one S1 RNA-binding domain from Escherichia coli polynucleotide phosphorylase has been determined []. It displays some similarity with the cold shock domain (CSD) (IPR002059 from INTERPRO). Both the S1 and the CSD domain consist of an antiparallel beta barrel of the same topology with 5 beta strands. This fold is also shared by many other proteins of unrelated function and is known as the OB fold. However, the S1 and CSD fold can be distinguished from the other OB folds by the presence of a short 3(10) helix at the end of strand 3. This unique feature is likely to form a part of the DNA/RNA-binding site. This entry is specific for bacterial, chloroplastic and eukaryotic IF-1 type S1 domains.; GO: 0003723 RNA binding, 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 1JT8_A 3I4O_A 1AH9_A 1ZO1_W 1D7Q_A 2OQK_A 2DGY_A 1HR0_W.
Probab=57.21 E-value=39 Score=20.04 Aligned_cols=53 Identities=15% Similarity=0.085 Sum_probs=37.9
Q ss_pred eEEEEEEEEccCceEEEEeecceeeEEEeec------CCCCCCCEEEEEEeeecCCCCeE
Q 034382 36 QYRALVLRFIKDRTAALLLVEVGLQATAWVS------VGAQIGDEVEVKVEEAHPRDDII 89 (96)
Q Consensus 36 ~~~AvVl~~~~~~~~~vlL~dl~le~~~~~~------~~~~~Gd~v~v~v~~vdP~~~~l 89 (96)
+-.|.|++-++.+.+.|.+++ |-+.-+..+ --+.+||.|.|.+..-|+-.+.|
T Consensus 4 e~~~~V~~~lG~~~~~V~~~d-g~~~l~~i~gK~r~~iwI~~GD~V~V~~~~~d~~kG~I 62 (65)
T PF01176_consen 4 EVIGRVTEMLGNNLFEVECED-GEERLARIPGKFRKRIWIKRGDFVLVEPSPYDKVKGRI 62 (65)
T ss_dssp EEEEEEEEEESSSEEEEEETT-SEEEEEEE-HHHHTCC---TTEEEEEEESTTCTTEEEE
T ss_pred EEEEEEEEECCCCEEEEEeCC-CCEEEEEeccceeeeEecCCCCEEEEEecccCCCeEEE
Confidence 457999999987899999887 666656655 45899999999987777555544
No 106
>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=57.15 E-value=22 Score=21.46 Aligned_cols=31 Identities=16% Similarity=0.204 Sum_probs=18.4
Q ss_pred eecceeeEEEeec---CCCCCCCEEEEEEeeecC
Q 034382 54 LVEVGLQATAWVS---VGAQIGDEVEVKVEEAHP 84 (96)
Q Consensus 54 L~dl~le~~~~~~---~~~~~Gd~v~v~v~~vdP 84 (96)
.|..-|+.++.-+ ..+++||.|...+...+-
T Consensus 25 wpaMTM~F~v~~~~~l~~l~~Gd~V~F~~~~~~~ 58 (70)
T PF11604_consen 25 WPAMTMDFPVADPVDLAGLKPGDKVRFTFERTDD 58 (70)
T ss_dssp B-SEEEEEE--TTSEESS-STT-EEEEEEEEETT
T ss_pred CCCeEEEEEcCChhhhhcCCCCCEEEEEEEECCC
Confidence 3444455555433 789999999999998664
No 107
>TIGR00074 hypC_hupF hydrogenase assembly chaperone HypC/HupF. An additional proposed function is to shuttle the iron atom that has been liganded at the HypC/HypD complex to the precursor of the large hydrogenase (HycE) subunit. PubMed:12441107.
Probab=56.71 E-value=46 Score=20.77 Aligned_cols=43 Identities=16% Similarity=0.098 Sum_probs=32.4
Q ss_pred EEEEEEEccCceEEEEeecceeeEEEeecCCCCCCCEEEEEEee
Q 034382 38 RALVLRFIKDRTAALLLVEVGLQATAWVSVGAQIGDEVEVKVEE 81 (96)
Q Consensus 38 ~AvVl~~~~~~~~~vlL~dl~le~~~~~~~~~~~Gd~v~v~v~~ 81 (96)
|+-|++..+ +.+.+-....--++.+..-.+++|||-|.|-.+-
T Consensus 6 P~~V~~i~~-~~A~v~~~G~~~~v~l~lv~~~~vGD~VLVH~G~ 48 (76)
T TIGR00074 6 PGQVVEIDE-NIALVEFCGIKRDVSLDLVGEVKVGDYVLVHVGF 48 (76)
T ss_pred ceEEEEEcC-CEEEEEcCCeEEEEEEEeeCCCCCCCEEEEecCh
Confidence 677788666 7888877766666666665789999999987653
No 108
>PRK00006 fabZ (3R)-hydroxymyristoyl-ACP dehydratase; Reviewed
Probab=55.52 E-value=32 Score=22.89 Aligned_cols=30 Identities=23% Similarity=0.209 Sum_probs=22.2
Q ss_pred EEeecCCCCCCCEEEEEEeeecCCCCeEEE
Q 034382 62 TAWVSVGAQIGDEVEVKVEEAHPRDDIIYL 91 (96)
Q Consensus 62 ~~~~~~~~~~Gd~v~v~v~~vdP~~~~l~l 91 (96)
.+++..++.|||.+.+++.-.+-..+.+.+
T Consensus 95 ~~kF~~pv~pGd~l~i~~~i~~~~~~~v~~ 124 (147)
T PRK00006 95 KARFKRPVVPGDQLILEVELLKQRRGIWKF 124 (147)
T ss_pred EEEEccccCCCCEEEEEEEEEEeeCCEEEE
Confidence 456667899999999998866655665544
No 109
>PRK00098 GTPase RsgA; Reviewed
Probab=55.23 E-value=90 Score=23.63 Aligned_cols=51 Identities=20% Similarity=0.235 Sum_probs=33.9
Q ss_pred EEEEEEEccCceEEEEee-cceeeEEEeec-----CCCCCCCEEEEE--------EeeecCCCCeE
Q 034382 38 RALVLRFIKDRTAALLLV-EVGLQATAWVS-----VGAQIGDEVEVK--------VEEAHPRDDII 89 (96)
Q Consensus 38 ~AvVl~~~~~~~~~vlL~-dl~le~~~~~~-----~~~~~Gd~v~v~--------v~~vdP~~~~l 89 (96)
+|.|+...+ +.+.|..+ .--+.+.++.. ..+..||.|.+. +.++.||.+.+
T Consensus 2 ~g~v~~~~~-~~~~v~~~~~~~~~~~~~g~~~~~~~~~~vGD~V~~~~~~~~~g~i~~i~~R~~~l 66 (298)
T PRK00098 2 EGLIIKALG-GFYYVESEDGQVYQCRARGKFRKKTNTPAVGDRVEFSAENNDEGVILEIHERKNLL 66 (298)
T ss_pred eEEEEEEEC-CEEEEEECCCCEEEEEeccccccCCCCcCCCCEEEEEECCCCcEEEEEEeCCCceE
Confidence 578888888 88888765 22355555543 236889999886 34566666655
No 110
>PF01938 TRAM: TRAM domain; InterPro: IPR002792 The TRAM (after TRM2 and miaB) domain is a 60-70-residue-long module that is found in: Two distinct classes of tRNA-modifying enzymes, namely uridine methylases of the TRM2 family and enzymes of the miaB family that are involved in 2- methylthioadenine formation In several other proteins associated with the translation machinery In a family of small uncharacterised archaeal proteins that are predicted to have a role in the regulation of tRNA modification and/or translation The TRAM domain can be found alone or in association with other domains, such as the catalytic biotin/lipoate synthetase-like domain, the RNA methylase domain, the ribosomal S2 domain and the eIF2-beta domain. The TRAM domain is predicted to bind tRNA and deliver the RNA-modifying enzymatic domain to their targets []. Secondary structure prediction indicates that the TRAM domain adopts a simple beta-barrel fold. The conservation pattern of the TRAM domain consists primarily of small and hydrophobic residues that correspond to five beta-strands in the predicted secondary structure [].; PDB: 1YEZ_A 2BH2_A 1UWV_A 1YVC_A.
Probab=54.44 E-value=40 Score=19.28 Aligned_cols=50 Identities=16% Similarity=0.109 Sum_probs=28.1
Q ss_pred CCeEEEEEEEEccCceEEEEeecceeeEEEeecCCCCCCCEEEEEEeeecCC
Q 034382 34 ERQYRALVLRFIKDRTAALLLVEVGLQATAWVSVGAQIGDEVEVKVEEAHPR 85 (96)
Q Consensus 34 ~~~~~AvVl~~~~~~~~~vlL~dl~le~~~~~~~~~~~Gd~v~v~v~~vdP~ 85 (96)
|++.+.+|-+...++...=..+. +.-+-++...+. .||.+.++|.++++.
T Consensus 5 G~~~~VlVe~~~~~g~~~gr~~~-~~~V~v~~~~~~-iG~~v~v~I~~~~~~ 54 (61)
T PF01938_consen 5 GKTLEVLVEELGDEGQGIGRTDN-GKVVFVPGGLPL-IGEFVKVRITKAKKN 54 (61)
T ss_dssp TEEEEEEEEEE-TTSEEEEEET--TEEEEETT--T---TEEEEEEEEEE-SS
T ss_pred CcEEEEEEEEecCCCEEEEEeCC-CeEEEECCCCCC-CCCEEEEEEEEeeCC
Confidence 67778777776654555555554 222222222222 599999999999884
No 111
>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=53.50 E-value=41 Score=19.22 Aligned_cols=48 Identities=21% Similarity=0.185 Sum_probs=31.4
Q ss_pred CeEEEEEEEEccC-ceEEEE--eecc-eeeEEEeec----CCCCCCCEEEEEEeee
Q 034382 35 RQYRALVLRFIKD-RTAALL--LVEV-GLQATAWVS----VGAQIGDEVEVKVEEA 82 (96)
Q Consensus 35 ~~~~AvVl~~~~~-~~~~vl--L~dl-~le~~~~~~----~~~~~Gd~v~v~v~~v 82 (96)
..++|.|.+-... ....|. +++- -+.+.++.. ..+++|+.+.+.+...
T Consensus 7 N~l~g~I~~i~~~g~~~~v~l~~~~~~~l~a~i~~~~~~~l~l~~G~~v~~~ik~~ 62 (69)
T TIGR00638 7 NQLKGKVVAIEDGDVNAEVDLLLGGGTKLTAVITLESVAELGLKPGKEVYAVIKAP 62 (69)
T ss_pred cEEEEEEEEEEECCCeEEEEEEECCCCEEEEEecHHHHhhCCCCCCCEEEEEEECc
Confidence 4689999876443 444444 4444 455555553 4688999999988654
No 112
>PF09874 DUF2101: Predicted membrane protein (DUF2101); InterPro: IPR018663 This family of conserved hypothetical proteins has no known function.
Probab=53.04 E-value=37 Score=25.29 Aligned_cols=53 Identities=21% Similarity=0.326 Sum_probs=33.8
Q ss_pred HhhhCCCCCeEE-EEEEEEccCceEEEEeecceeeEEEeec-------CCCCCCCEEEEEEeee
Q 034382 27 FLRRQPKERQYR-ALVLRFIKDRTAALLLVEVGLQATAWVS-------VGAQIGDEVEVKVEEA 82 (96)
Q Consensus 27 YL~~~~~~~~~~-AvVl~~~~~~~~~vlL~dl~le~~~~~~-------~~~~~Gd~v~v~v~~v 82 (96)
||+.+= |+.|. |+|.|-.+ +.+.|...| .+-+.+..+ .++++||.|.+.|++-
T Consensus 135 ~Fr~ky-~RdyTyG~VeEv~~-~~v~V~V~d-DI~ANVkPg~YwV~~~~d~~~G~vVKl~VE~r 195 (206)
T PF09874_consen 135 YFRSKY-GRDYTYGVVEEVKE-NLVRVFVHD-DIAANVKPGYYWVEAVPDVEEGDVVKLLVEER 195 (206)
T ss_pred heeeee-cccceeEEEEEecC-CEEEEEEcc-chhhcCCCCeEEecCCCCCCCCceEEEEEecc
Confidence 566655 67777 77766555 887776643 222222221 5788999999999863
No 113
>COG0335 RplS Ribosomal protein L19 [Translation, ribosomal structure and biogenesis]
Probab=52.37 E-value=30 Score=23.58 Aligned_cols=27 Identities=22% Similarity=0.201 Sum_probs=22.4
Q ss_pred CCCCCCCEEEEEEeeecCCCCeEEEEE
Q 034382 67 VGAQIGDEVEVKVEEAHPRDDIIYLKE 93 (96)
Q Consensus 67 ~~~~~Gd~v~v~v~~vdP~~~~l~l~e 93 (96)
.++.|||+|.|.+.=+..-...++.+|
T Consensus 19 P~f~~GDtvrv~vki~Eg~keR~Q~Fe 45 (115)
T COG0335 19 PSFRPGDTVRVHVKIVEGSKERVQAFE 45 (115)
T ss_pred CCCCCCCEEEEEEEEEeCCeEEEeeee
Confidence 368999999999988888877777665
No 114
>PRK04424 fatty acid biosynthesis transcriptional regulator; Provisional
Probab=52.04 E-value=51 Score=23.40 Aligned_cols=32 Identities=16% Similarity=0.235 Sum_probs=25.5
Q ss_pred EEEeecCCCCCCCEEEEEEeeecCCCCeEEEE
Q 034382 61 ATAWVSVGAQIGDEVEVKVEEAHPRDDIIYLK 92 (96)
Q Consensus 61 ~~~~~~~~~~~Gd~v~v~v~~vdP~~~~l~l~ 92 (96)
..+++..++.|||.+.+.+.-+....+...+.
T Consensus 131 ~~irF~kPV~pGD~L~~ea~v~~~~~~~~~v~ 162 (185)
T PRK04424 131 ANIRFKRPVKLGERVVAKAEVVRKKGNKYIVE 162 (185)
T ss_pred eeEEEccCCCCCCEEEEEEEEEEccCCEEEEE
Confidence 45666789999999999999888887765443
No 115
>PF00567 TUDOR: Tudor domain; InterPro: IPR008191 There are multiple copies of this domain in the Drosophila melanogaster tudor protein and it has been identified in several RNA-binding proteins []. Although the function of this domain is unknown, in Drosophila melanogaster the tudor protein is required during oogenesis for the formation of primordial germ cells and for normal abdominal segmentation [].; PDB: 3NTI_A 3NTK_B 3NTH_A 2DIQ_A 3FDR_A 3PNW_O 3S6W_A 3PMT_A 2WAC_A 2O4X_A ....
Probab=51.49 E-value=54 Score=20.04 Aligned_cols=33 Identities=24% Similarity=0.339 Sum_probs=26.7
Q ss_pred CCeEEEEEEEEccCceEEEEeecceeeEEEeec
Q 034382 34 ERQYRALVLRFIKDRTAALLLVEVGLQATAWVS 66 (96)
Q Consensus 34 ~~~~~AvVl~~~~~~~~~vlL~dl~le~~~~~~ 66 (96)
+.++.|.|.....++.+.|.+-|+|....+..+
T Consensus 66 ~~w~Ra~I~~~~~~~~~~V~~iD~G~~~~v~~~ 98 (121)
T PF00567_consen 66 GRWYRAVITVDIDENQYKVFLIDYGNTEKVSAS 98 (121)
T ss_dssp SEEEEEEEEEEECTTEEEEEETTTTEEEEEEGG
T ss_pred CceeeEEEEEecccceeEEEEEecCceEEEcHH
Confidence 678899993334439999999999999988775
No 116
>TIGR01750 fabZ beta-hydroxyacyl-[acyl carrier protein] dehydratase FabZ. This enzyme, FabZ, shows overlapping substrate specificity with FabA with regard to chain length in fatty acid biosynthesis. FabZ works preferentially on shorter chains and is often designated (3R)-hydroxymyristoyl-[acyl carrier protein] dehydratase, although its actual specificity is broader. Unlike FabA, FabZ does not function as an isomerase and cannot initiate unsaturated fatty acid biosynthesis. However, only FabZ can act during the elongation of unsaturated fatty acid chains.
Probab=48.34 E-value=56 Score=21.43 Aligned_cols=29 Identities=21% Similarity=0.101 Sum_probs=21.1
Q ss_pred EeecCCCCCCCEEEEEEeeecCCCCeEEE
Q 034382 63 AWVSVGAQIGDEVEVKVEEAHPRDDIIYL 91 (96)
Q Consensus 63 ~~~~~~~~~Gd~v~v~v~~vdP~~~~l~l 91 (96)
+++..++.|||.+.+.+.-..-..+...+
T Consensus 92 ~kF~~~v~pGd~l~i~~~i~~~~~~~~~~ 120 (140)
T TIGR01750 92 AKFRRPVVPGDQLILHAEFLKKRRKIGKF 120 (140)
T ss_pred eEECCccCCCCEEEEEEEEEEccCCEEEE
Confidence 56667899999999888866555554443
No 117
>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=48.03 E-value=67 Score=20.05 Aligned_cols=51 Identities=18% Similarity=0.097 Sum_probs=32.0
Q ss_pred CCeEEEEEEEEccCc--eEEEEeecceeeEEEeec--------------CCCCCCCEEEEEEeeecCCC
Q 034382 34 ERQYRALVLRFIKDR--TAALLLVEVGLQATAWVS--------------VGAQIGDEVEVKVEEAHPRD 86 (96)
Q Consensus 34 ~~~~~AvVl~~~~~~--~~~vlL~dl~le~~~~~~--------------~~~~~Gd~v~v~v~~vdP~~ 86 (96)
|..+.|.|.+-.+ . -+-|-|.+ +.+.-++.+ ..++.||.|.|+|.+..--.
T Consensus 8 G~iy~g~V~~i~~-~~~GaFV~l~~-g~~Gllh~seis~~~~~~v~~~~~~~~~Gd~v~VqV~~~~~~~ 74 (88)
T cd04453 8 GNIYLGRVKKIVP-GLQAAFVDIGL-GKNGFLHLSDILPAYFKKHKKIAKLLKEGQEILVQVVKEPIGT 74 (88)
T ss_pred CCEEEEEEEEecc-CCcEEEEEeCC-CCEEEEEhHHcCchhccccCCHHHcCCCCCEEEEEEEEecCCC
Confidence 6677777777655 3 44444433 344444432 35899999999999854433
No 118
>PF01828 Peptidase_A4: Peptidase A4 family; InterPro: IPR000250 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. The peptidases in family G1 form a subset of what were formerly termed 'pepstatin-insensitive carboxyl proteinases'. After its discovery in about 1970, the pentapeptide pepstatin soon came to be thought of as a very general inhibitor of the endopeptidases that are active at acidic pH. But more recently several acid-acting endopeptidases from bacteria and fungi had been found to be resistant to pepstatin. The unusual active sites of the 'pepstatin-insensitive carboxyl peptidases' proved difficult to characterise, but it has now been established that the enzymes from bacteria are acid-acting serine peptidases in family S53 (clan SB), IPR000209 from INTERPRO, whereas the fungal enzymes are in family G1 (formerly A4). The importance of glutamate ('E') and glutamine ('Q') residues in the active sites of the family G1 enzymes led to the family name, Eqolisin []. This group of glutamate/glutamine peptidases belong to MEROPS peptidase family G1 (eqolisin family, clan GA). An example of this group is scytalidoglutamic peptidase. The proteins are thermostable, pepstatin insensitive and are active at low pH ranges []. The enzyme has a unique heterodimeric structure, with a 39-residue light chain and a 173-residue heavy chain bound to each other non-covalently []. The tertiary structure of the active site of scytalidoglutamic peptidase (MEROPS G01.001) with a bound tripeptide product has been interpreted as showing that Glu136 is the primary catalytic residue. The most likely mechanism is suggested to be nucleophilic attack by a water molecule activated by the Glu136 side chain on the si-face of the scissile peptide bond carbon atom to form the tetrahedral intermediate. Electrophilic assistance, and oxyanion stabilisation, are provided by the side-chain amide of Gln53. Both scytalidoglutamic peptidase (MEROPS G01.001) and aspergilloglutamic peptidase (MEROPS G01.002) cleave the Tyr26 Thr27 bond in the B chain of oxidized insulin; a bond not cleaved by other acid-acting endopeptidases. Scytalidoglutamic peptidase is most active on casein at pH 2 and is inhibited by 1,2-epoxy-3-(p-nitrophenoxy)propane (EPNP), a compound that also inhibits pepsin. ; GO: 0004190 aspartic-type endopeptidase activity, 0006508 proteolysis; PDB: 1Y43_B 1S2B_A 2IFR_A 1S2K_A 2IFW_A.
Probab=47.59 E-value=26 Score=25.75 Aligned_cols=37 Identities=16% Similarity=0.240 Sum_probs=23.0
Q ss_pred eecceeeEEEeecCCCCCCCEEEEEEeeecCCCCeEEEEE
Q 034382 54 LVEVGLQATAWVSVGAQIGDEVEVKVEEAHPRDDIIYLKE 93 (96)
Q Consensus 54 L~dl~le~~~~~~~~~~~Gd~v~v~v~~vdP~~~~l~l~e 93 (96)
+|+-+.+.. +-+++|||.|.+.|....+..+.+.++-
T Consensus 79 ~P~~a~~~~---~~~v~~GD~i~~~V~a~s~~~g~~~l~N 115 (208)
T PF01828_consen 79 YPDYAYDFS---NFPVSPGDTIRVTVTATSNTSGTITLEN 115 (208)
T ss_dssp ETS-EEEET---T----TT-EEEEEEEEEETTEEEEEEEE
T ss_pred cCCcccccc---cceECCCCEEEEEEEecCCCCEEEEEEe
Confidence 355554321 3579999999999999999888887764
No 119
>cd01288 FabZ FabZ is a 17kD beta-hydroxyacyl-acyl carrier protein (ACP) dehydratase that primarily catalyzes the dehydration of beta-hydroxyacyl-ACP to trans-2-acyl-ACP, the third step in the elongation phase of the bacterial/ plastid, type II, fatty-acid biosynthesis pathway.
Probab=47.49 E-value=46 Score=21.17 Aligned_cols=30 Identities=27% Similarity=0.190 Sum_probs=21.5
Q ss_pred EeecCCCCCCCEEEEEEeeecCCCCeEEEE
Q 034382 63 AWVSVGAQIGDEVEVKVEEAHPRDDIIYLK 92 (96)
Q Consensus 63 ~~~~~~~~~Gd~v~v~v~~vdP~~~~l~l~ 92 (96)
+++..++.|||.+.+++.-+.-..+...+.
T Consensus 82 ~kf~~pv~pgd~l~i~~~v~~~~~~~~~~~ 111 (131)
T cd01288 82 ARFRKPVVPGDQLILEVELLKLRRGIGKFK 111 (131)
T ss_pred cEEccccCCCCEEEEEEEEEEeeCCEEEEE
Confidence 555578999999999888776555554443
No 120
>KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only]
Probab=47.38 E-value=17 Score=31.41 Aligned_cols=45 Identities=24% Similarity=0.271 Sum_probs=32.6
Q ss_pred ceEEEEeecceeeEEEeecCCCCCCCEEEEEEeeecCCCCeEEEE
Q 034382 48 RTAALLLVEVGLQATAWVSVGAQIGDEVEVKVEEAHPRDDIIYLK 92 (96)
Q Consensus 48 ~~~~vlL~dl~le~~~~~~~~~~~Gd~v~v~v~~vdP~~~~l~l~ 92 (96)
..++++..+|.-+--...+.-++.||+|.|+.-..||+.+.-+..
T Consensus 692 ~~~Llh~sqL~~e~iakpsd~levGq~I~vk~ie~d~~g~~~ls~ 736 (760)
T KOG1067|consen 692 QQGLLHNSQLDQEKIAKPSDLLEVGQEIQVKYIERDPRGGIMLSS 736 (760)
T ss_pred chhhccchhcccccccChHHHHhhcceeEEEEEeecCccceeehh
Confidence 344555555555555555566899999999999999999876553
No 121
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=46.32 E-value=27 Score=30.39 Aligned_cols=52 Identities=23% Similarity=0.314 Sum_probs=41.5
Q ss_pred CCeEEEEEEE---------EccCceEEEEeecceeeEEEeecCCCCCCCEEEEEEeeecCC
Q 034382 34 ERQYRALVLR---------FIKDRTAALLLVEVGLQATAWVSVGAQIGDEVEVKVEEAHPR 85 (96)
Q Consensus 34 ~~~~~AvVl~---------~~~~~~~~vlL~dl~le~~~~~~~~~~~Gd~v~v~v~~vdP~ 85 (96)
|+.|.+.|.. ..+.+.+++++..++=+..-.+.+-++.||.+.||+..+|+.
T Consensus 620 g~iy~G~V~ri~~fGaFv~l~~gkdgl~hiS~~~~~rv~kv~dvlk~Gd~v~Vkv~~iD~~ 680 (692)
T COG1185 620 GEVYEGTVVRIVDFGAFVELLPGKDGLVHISQLAKERVEKVEDVLKEGDEVKVKVIEIDKQ 680 (692)
T ss_pred ccEEEEEEEEEeecceEEEecCCcceeEEehhhhhhhhhcccceeecCceEEEEEeeeccc
Confidence 7788877654 333367788888888886667778899999999999999985
No 122
>PF07703 A2M_N_2: Alpha-2-macroglobulin family N-terminal region; InterPro: IPR011625 This is a domain of the alpha-2-macroglobulin family. The alpha-macroglobulin (aM) family of proteins includes protease inhibitors [], typified by the human tetrameric a2-macroglobulin (a2M); they belong to the MEROPS proteinase inhibitor family I39, clan IL. These protease inhibitors share several defining properties, which include (i) the ability to inhibit proteases from all catalytic classes, (ii) the presence of a 'bait region' and a thiol ester, (iii) a similar protease inhibitory mechanism and (iv) the inactivation of the inhibitory capacity by reaction of the thiol ester with small primary amines. aM protease inhibitors inhibit by steric hindrance []. The mechanism involves protease cleavage of the bait region, a segment of the aM that is particularly susceptible to proteolytic cleavage, which initiates a conformational change such that the aM collapses about the protease. In the resulting aM-protease complex, the active site of the protease is sterically shielded, thus substantially decreasing access to protein substrates. Two additional events occur as a consequence of bait region cleavage, namely (i) the h-cysteinyl-g-glutamyl thiol ester becomes highly reactive and (ii) a major conformational change exposes a conserved COOH-terminal receptor binding domain [] (RBD). RBD exposure allows the aM protease complex to bind to clearance receptors and be removed from circulation []. Tetrameric, dimeric, and, more recently, monomeric aM protease inhibitors have been identified [, ].; PDB: 2QKI_D 3L3O_D 3NMS_A 2ICF_A 2A73_A 2ICE_D 2HR0_A 2A74_A 2XWJ_G 3OHX_A ....
Probab=46.31 E-value=69 Score=20.68 Aligned_cols=39 Identities=15% Similarity=0.287 Sum_probs=27.0
Q ss_pred EEeec-ceeeEEEee-cCCCCCCCEEEEEEeeecCCCCeEEEE
Q 034382 52 LLLVE-VGLQATAWV-SVGAQIGDEVEVKVEEAHPRDDIIYLK 92 (96)
Q Consensus 52 vlL~d-l~le~~~~~-~~~~~~Gd~v~v~v~~vdP~~~~l~l~ 92 (96)
+-++. ..+.+.+.. +...+||+.+.+++.. |....+.+.
T Consensus 87 i~V~~~~~~~v~l~~~~~~~~Pg~~~~~~i~~--~~~s~v~l~ 127 (136)
T PF07703_consen 87 IEVEPCFELKVELTASPDEYKPGEEVTLRIKA--PPNSLVGLS 127 (136)
T ss_dssp EEBGCSGSSSEEEEESSSSBTTTSEEEEEEEE--STTEEEEEE
T ss_pred EEecccccceEEEEEecceeCCCCEEEEEEEe--CCCCEEEEE
Confidence 33433 556666766 4789999999999988 555555443
No 123
>cd04456 S1_IF1A_like S1_IF1A_like: Translation initiation factor IF1A-like, S1-like RNA-binding domain. IF1A is also referred to as eIF1A in eukaryotes and aIF1A in archaea. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. IF1A is essential for translation initiation. eIF1A acts synergistically with eIF1 to mediate assembly of ribosomal initiation complexes at the initiation codon and maintain the accuracy of this process by recognizing and destabilizing aberrant preinitiation complexes from the mRNA. Without eIF1A and eIF1, 43S ribosomal preinitiation complexes can bind to the cap-proximal region, but are unable to reach the initiation codon. eIF1a also enhances the formation of 5'-terminal complexes in the presence of other translation initiation factors. This protein family is only found in eukaryotes and archaea.
Probab=44.92 E-value=76 Score=19.76 Aligned_cols=51 Identities=18% Similarity=0.161 Sum_probs=35.6
Q ss_pred EEEEEEccCceEEEEeecceeeEEEeec------CCCCCCCEEEEEEeee-cCCCCeEE
Q 034382 39 ALVLRFIKDRTAALLLVEVGLQATAWVS------VGAQIGDEVEVKVEEA-HPRDDIIY 90 (96)
Q Consensus 39 AvVl~~~~~~~~~vlL~dl~le~~~~~~------~~~~~Gd~v~v~v~~v-dP~~~~l~ 90 (96)
|.|++-++.++..|.++| |-+.-+..+ --+.+||.|.|....- |+-.+.|.
T Consensus 4 ~~V~~~lG~~~~~V~~~d-g~~~l~~i~gK~Rk~iwI~~GD~VlV~~~~~~~~~kg~Iv 61 (78)
T cd04456 4 VRVLRMLGNNRHEVECAD-GQRRLVSIPGKLRKNIWIKRGDFLIVDPIEEGEDVKADII 61 (78)
T ss_pred EEEEEECCCCEEEEEECC-CCEEEEEEchhhccCEEEcCCCEEEEEecccCCCceEEEE
Confidence 678887776888888876 444444444 3378999999988776 55555554
No 124
>PF00207 A2M: Alpha-2-macroglobulin family; InterPro: IPR001599 This entry contains serum complement C3 and C4 precursors and alpha-macrogrobulins. The alpha-macroglobulin (aM) family of proteins includes protease inhibitors [], typified by the human tetrameric a2-macroglobulin (a2M); they belong to the MEROPS proteinase inhibitor family I39, clan IL. These protease inhibitors share several defining properties, which include (i) the ability to inhibit proteases from all catalytic classes, (ii) the presence of a 'bait region' and a thiol ester, (iii) a similar protease inhibitory mechanism and (iv) the inactivation of the inhibitory capacity by reaction of the thiol ester with small primary amines. aM protease inhibitors inhibit by steric hindrance []. The mechanism involves protease cleavage of the bait region, a segment of the aM that is particularly susceptible to proteolytic cleavage, which initiates a conformational change such that the aM collapses about the protease. In the resulting aM-protease complex, the active site of the protease is sterically shielded, thus substantially decreasing access to protein substrates. Two additional events occur as a consequence of bait region cleavage, namely (i) the h-cysteinyl-g-glutamyl thiol ester becomes highly reactive and (ii) a major conformational change exposes a conserved COOH-terminal receptor binding domain [] (RBD). RBD exposure allows the aM protease complex to bind to clearance receptors and be removed from circulation []. Tetrameric, dimeric, and, more recently, monomeric aM protease inhibitors have been identified [, ].; GO: 0004866 endopeptidase inhibitor activity; PDB: 3KLS_B 3PRX_C 3KM9_B 3PVM_C 3CU7_A 4E0S_A 4A5W_A 2PN5_A 3FRP_G 3HRZ_B ....
Probab=44.38 E-value=57 Score=20.17 Aligned_cols=34 Identities=12% Similarity=0.084 Sum_probs=23.0
Q ss_pred eeEEEeecCCCCCCCEEEEEEeeecCCCCeEEEE
Q 034382 59 LQATAWVSVGAQIGDEVEVKVEEAHPRDDIIYLK 92 (96)
Q Consensus 59 le~~~~~~~~~~~Gd~v~v~v~~vdP~~~~l~l~ 92 (96)
+.+....|..+..||.+.+.+.=-|-.+..+.+.
T Consensus 56 ~~i~~~lP~~l~~GD~~~i~v~v~N~~~~~~~v~ 89 (92)
T PF00207_consen 56 FFIQLNLPRSLRRGDQIQIPVTVFNYTDKDQEVT 89 (92)
T ss_dssp EEEEEE--SEEETTSEEEEEEEEEE-SSS-EEEE
T ss_pred EEEEcCCCcEEecCCEEEEEEEEEeCCCCCEEEE
Confidence 3334444568999999999999888887777654
No 125
>COG2030 MaoC Acyl dehydratase [Lipid metabolism]
Probab=43.55 E-value=54 Score=22.54 Aligned_cols=24 Identities=21% Similarity=0.192 Sum_probs=19.8
Q ss_pred EEeecCCCCCCCEEEEEEeeecCC
Q 034382 62 TAWVSVGAQIGDEVEVKVEEAHPR 85 (96)
Q Consensus 62 ~~~~~~~~~~Gd~v~v~v~~vdP~ 85 (96)
.+++..++.|||.|.+++...|.+
T Consensus 100 ~vRF~~PV~~Gdtl~~~~~v~~~~ 123 (159)
T COG2030 100 EVRFVKPVFPGDTLRARVEVLDKR 123 (159)
T ss_pred ceEecCCCCCCCEEEEEEEEEEee
Confidence 366778999999999999888654
No 126
>cd03449 R_hydratase (R)-hydratase [(R)-specific enoyl-CoA hydratase] catalyzes the hydration of trans-2-enoyl CoA to (R)-3-hydroxyacyl-CoA as part of the PHA (polyhydroxyalkanoate) biosynthetic pathway. (R)-hydratase contains a hot-dog fold similar to those of thioesterase II, and beta-hydroxydecanoyl-ACP dehydratase, MaoC dehydratase, Hydratase-Dehydrogenase-Epimerase protein (HDE), and the fatty acid synthase beta subunit. The active site lies within a substrate-binding tunnel formed by the (R)-hydratase homodimer. A subset of the bacterial (R)-hydratases contain a C-terminal phosphotransacetylase (PTA) domain.
Probab=43.50 E-value=82 Score=19.75 Aligned_cols=32 Identities=19% Similarity=0.155 Sum_probs=21.1
Q ss_pred eEEEeecCCCCCCCEEEEEEeeec--CCCCeEEE
Q 034382 60 QATAWVSVGAQIGDEVEVKVEEAH--PRDDIIYL 91 (96)
Q Consensus 60 e~~~~~~~~~~~Gd~v~v~v~~vd--P~~~~l~l 91 (96)
...++...++.+||.+.++..-++ +..+.+.+
T Consensus 74 ~~~~~f~~Pv~~gd~l~~~~~v~~~~~~~~~v~~ 107 (128)
T cd03449 74 SQSLRFLRPVFIGDTVTATVTVTEKREDKKRVTL 107 (128)
T ss_pred EEEEEECCCccCCCEEEEEEEEEEEecCCCEEEE
Confidence 346667789999999887665543 43355544
No 127
>smart00588 NEUZ domain in neuralized proteins.
Probab=43.49 E-value=35 Score=22.90 Aligned_cols=19 Identities=26% Similarity=0.309 Sum_probs=16.4
Q ss_pred cCCCCCCCEEEEEEeeecC
Q 034382 66 SVGAQIGDEVEVKVEEAHP 84 (96)
Q Consensus 66 ~~~~~~Gd~v~v~v~~vdP 84 (96)
++++.+||.+.|+|.++++
T Consensus 37 ~rPl~~~E~~~v~i~~~~~ 55 (123)
T smart00588 37 ARPLRINELFEVKIEKVVR 55 (123)
T ss_pred CCCCcCCCEEEEEEEEecC
Confidence 3789999999999998754
No 128
>smart00652 eIF1a eukaryotic translation initiation factor 1A.
Probab=42.44 E-value=86 Score=19.71 Aligned_cols=55 Identities=20% Similarity=0.161 Sum_probs=39.4
Q ss_pred CeEEEEEEEEccCceEEEEeecceeeEEEeec------CCCCCCCEEEEEEeeecCCCCeEE
Q 034382 35 RQYRALVLRFIKDRTAALLLVEVGLQATAWVS------VGAQIGDEVEVKVEEAHPRDDIIY 90 (96)
Q Consensus 35 ~~~~AvVl~~~~~~~~~vlL~dl~le~~~~~~------~~~~~Gd~v~v~v~~vdP~~~~l~ 90 (96)
.+-.|.|++-++.+.+.|.+++ |-+.-+..+ --+.+||.|.|....-|+-.+.|.
T Consensus 5 ~q~~g~V~~~lG~~~~~V~~~d-G~~~la~ipgK~Rk~iwI~~GD~VlVe~~~~~~~kg~Iv 65 (83)
T smart00652 5 GQEIAQVVKMLGNGRLEVMCAD-GKERLARIPGKMRKKVWIRRGDIVLVDPWDFQDVKADII 65 (83)
T ss_pred CcEEEEEEEEcCCCEEEEEECC-CCEEEEEEchhhcccEEEcCCCEEEEEecCCCCCEEEEE
Confidence 3558999998887899988875 444444444 347899999998877666555554
No 129
>PRK01889 GTPase RsgA; Reviewed
Probab=42.16 E-value=1.7e+02 Score=22.92 Aligned_cols=52 Identities=15% Similarity=0.089 Sum_probs=34.3
Q ss_pred EEEEEEEEccCceEEEEeecceeeEEEeec---------CCCCCCCEEEEE------EeeecCCCCeE
Q 034382 37 YRALVLRFIKDRTAALLLVEVGLQATAWVS---------VGAQIGDEVEVK------VEEAHPRDDII 89 (96)
Q Consensus 37 ~~AvVl~~~~~~~~~vlL~dl~le~~~~~~---------~~~~~Gd~v~v~------v~~vdP~~~~l 89 (96)
-+|.|+...+ +.+.|.-.+=-+.+.++.. ..+..||.|.+. |.++-||.+.+
T Consensus 29 ~~g~v~~~~~-~~~~v~~~~~~~~~~~~gk~~~~~~~~~~~~~vGD~V~~~~~~~g~I~~i~pR~~~L 95 (356)
T PRK01889 29 EPGRVVEEHR-SGYVVATEEGEVRAEVSGKWRHEAFPPGDRPAVGDWVLLDNEKKARIVRLLPRRSLF 95 (356)
T ss_pred ccEEEEEEEC-CEEEEEECCcEEEEEecchhhccccccCCCCccCcEEEEecCCceEEEEEECCCceE
Confidence 3799999999 8888875442233333331 236789999885 45566777754
No 130
>PF08605 Rad9_Rad53_bind: Fungal Rad9-like Rad53-binding; InterPro: IPR013914 In Saccharomyces cerevisiae (Baker s yeast), the Rad9 is a key adaptor protein in DNA damage checkpoint pathways. DNA damage induces Rad9 phosphorylation, and Rad53 specifically associates with this region of Rad9, when phosphorylated, via the Rad53 IPR000253 from INTERPRO domain []. There is no clear higher eukaryotic ortholog to Rad9.
Probab=40.57 E-value=76 Score=21.82 Aligned_cols=45 Identities=18% Similarity=0.136 Sum_probs=33.3
Q ss_pred CeEEEEEEEEccC-ceEEEEeecceeeEEEeec--CCCCCCCEEEEEE
Q 034382 35 RQYRALVLRFIKD-RTAALLLVEVGLQATAWVS--VGAQIGDEVEVKV 79 (96)
Q Consensus 35 ~~~~AvVl~~~~~-~~~~vlL~dl~le~~~~~~--~~~~~Gd~v~v~v 79 (96)
.-++|.++....+ .+..|.++|-..+....-= -++..||.|.|.-
T Consensus 23 ~yYPa~~~~~~~~~~~~~V~Fedg~~~i~~~dv~~LDlRIGD~Vkv~~ 70 (131)
T PF08605_consen 23 KYYPATCVGSGVDRDRSLVRFEDGTYEIKNEDVKYLDLRIGDTVKVDG 70 (131)
T ss_pred eEeeEEEEeecCCCCeEEEEEecCceEeCcccEeeeeeecCCEEEECC
Confidence 5789999998553 4699999998844433221 5789999998865
No 131
>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=40.09 E-value=76 Score=18.41 Aligned_cols=52 Identities=15% Similarity=0.091 Sum_probs=31.9
Q ss_pred EEEEEEEEc-cCceEEEEeec-ceeeEEEeec-----CCCCCCCEEEEEEeeecCCCCeE
Q 034382 37 YRALVLRFI-KDRTAALLLVE-VGLQATAWVS-----VGAQIGDEVEVKVEEAHPRDDII 89 (96)
Q Consensus 37 ~~AvVl~~~-~~~~~~vlL~d-l~le~~~~~~-----~~~~~Gd~v~v~v~~vdP~~~~l 89 (96)
.+|+|+... + +.+.|...+ --+.+.++-. ..+.+||.|.+.+...++..+.|
T Consensus 3 ~~G~Vi~~~~g-~~~~V~~~~g~~~~c~~rGklr~~~~~~~vGD~V~~~~~~~~~~~g~I 61 (64)
T cd04451 3 MEGVVTEALPN-AMFRVELENGHEVLAHISGKMRMNYIRILPGDRVKVELSPYDLTKGRI 61 (64)
T ss_pred EEEEEEEEeCC-CEEEEEeCCCCEEEEEECceeecCCcccCCCCEEEEEEeecCCCEEEE
Confidence 468888877 4 666665422 2333333332 24789999999987666554444
No 132
>PF02599 CsrA: Global regulator protein family; InterPro: IPR003751 The RNA-binding protein CsrA (carbon storage regulator) is a new kind of global regulator, which facilitates specific mRNA decay []. CsrA is entirely contained within a globular complex of approximately 18 CsrA-H6 subunits and a single RNA, CsrB. CsrA binds to the CsrB RNA molecule to form the Csr regulatory system which has a strong negative regulatory effect on glycogen biosynthesis, glyconeogenesis and glycogen catabolism and a positive regulatory effect on glycolysis [].; GO: 0003723 RNA binding, 0006109 regulation of carbohydrate metabolic process, 0006402 mRNA catabolic process; PDB: 1Y00_B 2JPP_A 1T3O_A 1VPZ_A.
Probab=40.06 E-value=37 Score=19.93 Aligned_cols=24 Identities=29% Similarity=0.432 Sum_probs=17.1
Q ss_pred cCCCCCCCEEEEEEeeecCCCCeEEE
Q 034382 66 SVGAQIGDEVEVKVEEAHPRDDIIYL 91 (96)
Q Consensus 66 ~~~~~~Gd~v~v~v~~vdP~~~~l~l 91 (96)
+..+..||.+.++|.+++ .|.+++
T Consensus 9 gE~I~Ig~~I~I~Vl~i~--~~~Vkl 32 (54)
T PF02599_consen 9 GESIVIGDDIEITVLEIS--GGQVKL 32 (54)
T ss_dssp T-EEEETTTEEEEEEEEE--TTEEEE
T ss_pred CCEEEECCCEEEEEEEEc--CCEEEE
Confidence 356667888899998888 555554
No 133
>PF11454 DUF3016: Protein of unknown function (DUF3016); InterPro: IPR021557 This is a bacterial family of uncharacterised proteins.
Probab=40.03 E-value=33 Score=23.96 Aligned_cols=19 Identities=26% Similarity=0.365 Sum_probs=14.5
Q ss_pred CCCCCEEEEEEeeecCCCC
Q 034382 69 AQIGDEVEVKVEEAHPRDD 87 (96)
Q Consensus 69 ~~~Gd~v~v~v~~vdP~~~ 87 (96)
+.||+.+.|.|..||...+
T Consensus 47 Lp~gq~L~v~VtDvDLAG~ 65 (141)
T PF11454_consen 47 LPPGQTLEVTVTDVDLAGD 65 (141)
T ss_pred CCCCCEEEEEEEecccCcc
Confidence 7888888888888875443
No 134
>PRK13692 (3R)-hydroxyacyl-ACP dehydratase subunit HadA; Provisional
Probab=38.71 E-value=92 Score=21.53 Aligned_cols=32 Identities=19% Similarity=0.102 Sum_probs=20.1
Q ss_pred EEEeecCCCCCCCEEEEEEee--ecCCC--CeEEEE
Q 034382 61 ATAWVSVGAQIGDEVEVKVEE--AHPRD--DIIYLK 92 (96)
Q Consensus 61 ~~~~~~~~~~~Gd~v~v~v~~--vdP~~--~~l~l~ 92 (96)
-.++...++.+||.|..++.= +.+.. +.++++
T Consensus 89 q~~~f~~PV~~GDtL~~~~eV~~~~~~~~~giv~~~ 124 (159)
T PRK13692 89 QVLKFEKPIVAGDKLYCDVYVDSVREAHGTQIIVTK 124 (159)
T ss_pred eEEEEeCCccCCCEEEEEEEEEEEEEcCCceEEEEE
Confidence 456666899999999655543 33332 455554
No 135
>PF04246 RseC_MucC: Positive regulator of sigma(E), RseC/MucC; InterPro: IPR007359 This bacterial family of integral membrane proteins represents a positive regulator of the sigma(E) transcription factor, namely RseC/MucC. The sigma(E) transcription factor is up-regulated by cell envelope protein misfolding, and regulates the expression of genes that are collectively termed ECF (devoted to Extra-Cellular Functions) []. In Pseudomonas aeruginosa, derepression of sigma(E) is associated with the alginate-overproducing phenotype characteristic of chronic respiratory tract colonization in cystic fibrosis patients. The mechanism by which RseC/MucC positively regulates the sigma(E) transcription factor is unknown. RseC is also thought to have a role in thiamine biosynthesis in Salmonella typhimurium []. In addition, this family also includes an N-terminal part of RnfF, a Rhodobacter capsulatus protein, of unknown function, that is essential for nitrogen fixation. This protein also contains a domain found in ApbE protein IPR003374 from INTERPRO, which is itself involved in thiamine biosynthesis.
Probab=37.89 E-value=48 Score=22.09 Aligned_cols=24 Identities=38% Similarity=0.600 Sum_probs=18.5
Q ss_pred eeEEEeecCCCCCCCEEEEEEeee
Q 034382 59 LQATAWVSVGAQIGDEVEVKVEEA 82 (96)
Q Consensus 59 le~~~~~~~~~~~Gd~v~v~v~~v 82 (96)
.+..+..+.++++||.|.|.+..-
T Consensus 42 ~~~~~~~~~~~~~GD~V~v~i~~~ 65 (135)
T PF04246_consen 42 ITFRAPNPIGAKVGDRVEVEIPES 65 (135)
T ss_pred EEEEecCCCCCCCCCEEEEEeccc
Confidence 455556668999999999988754
No 136
>cd00493 FabA_FabZ FabA/Z, beta-hydroxyacyl-acyl carrier protein (ACP)-dehydratases: One of several distinct enzyme types of the dissociative, type II, fatty acid synthase system (found in bacteria and plants) required to complete successive cycles of fatty acid elongation. The third step of the elongation cycle, the dehydration of beta-hydroxyacyl-ACP to trans-2-acyl-ACP, is catalyzed by FabA or FabZ. FabA is bifunctional and catalyzes an additional isomerization reaction of trans-2-acyl-ACP to cis-3-acyl-ACP, an essential reaction to unsaturated fatty acid synthesis. FabZ is the primary dehydratase that participates in the elongation cycles of saturated as well as unsaturated fatty acid biosynthesis, whereas FabA is more active in the dehydration of beta-hydroxydecanoyl-ACP. The FabA structure is homodimeric with two independent active sites located at the dimer interface.
Probab=37.62 E-value=92 Score=19.59 Aligned_cols=29 Identities=17% Similarity=0.093 Sum_probs=20.2
Q ss_pred EeecCCCCCCCEEEEEEeeecCCCCeEEE
Q 034382 63 AWVSVGAQIGDEVEVKVEEAHPRDDIIYL 91 (96)
Q Consensus 63 ~~~~~~~~~Gd~v~v~v~~vdP~~~~l~l 91 (96)
+++..++.|||.+.+++.-..-..+.+.+
T Consensus 83 ~kf~~~v~pgd~l~i~~~i~~~~~~~~~~ 111 (131)
T cd00493 83 VKFRGPVLPGDTLTLEVELLKVRRGLGKF 111 (131)
T ss_pred eEECCCcCCCCEEEEEEEEEEeeCCEEEE
Confidence 55567889999998888766544444444
No 137
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=37.57 E-value=1.6e+02 Score=21.52 Aligned_cols=54 Identities=9% Similarity=0.076 Sum_probs=40.9
Q ss_pred EEEEEEEEccCceEEEEeecceeeEEEeec--CCCCCCCEEEEEEeeecCCCCeEEEE
Q 034382 37 YRALVLRFIKDRTAALLLVEVGLQATAWVS--VGAQIGDEVEVKVEEAHPRDDIIYLK 92 (96)
Q Consensus 37 ~~AvVl~~~~~~~~~vlL~dl~le~~~~~~--~~~~~Gd~v~v~v~~vdP~~~~l~l~ 92 (96)
..|.+++... +.+.|-.-.+|+++.++.+ ..+.+|+.+.+-+..+ -++|.++|.
T Consensus 5 l~G~v~~~~~-~~vvidv~GVGY~v~vs~~~~~~l~~g~~v~l~t~~~-vrED~~~LY 60 (196)
T PRK13901 5 IYGKIIEKKE-SSIVIMATPFEFELLVSSFCLAELRLLEDVEILTYLH-TREDELKLF 60 (196)
T ss_pred EEEEEEEEeC-CEEEEEeCCEEEEEEecHHHHHhcCCCCcEEEEEEEE-EecCCceee
Confidence 4677888766 8888888899999999876 5567899998876544 377766653
No 138
>PRK12289 GTPase RsgA; Reviewed
Probab=37.50 E-value=1.7e+02 Score=23.05 Aligned_cols=54 Identities=24% Similarity=0.192 Sum_probs=35.2
Q ss_pred eEEEEEEEEccCceEEEEeecc-------eeeEEEeec-----CCCCCCCEEEEE----------EeeecCCCCeEE
Q 034382 36 QYRALVLRFIKDRTAALLLVEV-------GLQATAWVS-----VGAQIGDEVEVK----------VEEAHPRDDIIY 90 (96)
Q Consensus 36 ~~~AvVl~~~~~~~~~vlL~dl-------~le~~~~~~-----~~~~~Gd~v~v~----------v~~vdP~~~~l~ 90 (96)
...|.|+.-.+ +.+.|...+- -+.+..+.. ..+..||.|.+. |.+|-||.+.|.
T Consensus 8 ~~~g~V~~~~~-~~y~V~~~~~~~~~~~~~~~~~~r~~lk~~~~~~~vGD~V~~~~~~~~~~~~~I~~vlpR~~~L~ 83 (352)
T PRK12289 8 QLLGTVVAVQA-NFYRVQLDEPQNLNPPSLLLCTRRTRLKKIGQQVMVGDRVIVEEPDWQGQRGAIAEVLPRKTELD 83 (352)
T ss_pred cccEEEEEEEC-CEEEEEECCCcccCcceEEEEEcccccccCCCCcccCCEEEEeecCCCCCceEEEEEecccccee
Confidence 35799999899 9998887531 244444432 337889999875 345556665553
No 139
>PHA02858 EIF2a-like PKR inhibitor; Provisional
Probab=37.33 E-value=1.2e+02 Score=19.71 Aligned_cols=44 Identities=18% Similarity=0.248 Sum_probs=37.0
Q ss_pred ceEEEEeecceeeEEEe-e-----------cCCCCCCCEEEEEEeeecCCCCeEEEE
Q 034382 48 RTAALLLVEVGLQATAW-V-----------SVGAQIGDEVEVKVEEAHPRDDIIYLK 92 (96)
Q Consensus 48 ~~~~vlL~dl~le~~~~-~-----------~~~~~~Gd~v~v~v~~vdP~~~~l~l~ 92 (96)
.-+-|.|.|+++|.=+. . +..+ .|-...++|-+||+..|-|-++
T Consensus 29 ~~~YV~LleY~iegmIl~~selsr~rirsi~kll-VGk~e~v~ViRVDk~KGYIDLs 84 (86)
T PHA02858 29 NIFYVKLIDYGLEALIVNYVNVNADRAEKLKKKL-VGKTINVQVIRTDKLKGYIDVR 84 (86)
T ss_pred cEEEEEEecCccceEEecHHHHhHHHHHhhhhhh-cCCeeEEEEEEECCCCCEEEeE
Confidence 88999999999888766 1 1345 9999999999999999988775
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=35.71 E-value=51 Score=18.72 Aligned_cols=24 Identities=21% Similarity=0.188 Sum_probs=19.5
Q ss_pred CCCCCCCEEEEEEeeecCCCCe-EEE
Q 034382 67 VGAQIGDEVEVKVEEAHPRDDI-IYL 91 (96)
Q Consensus 67 ~~~~~Gd~v~v~v~~vdP~~~~-l~l 91 (96)
..+++|+.+.|+ +++....+. +++
T Consensus 43 ~~l~~g~~v~v~-G~v~~~~~~~~~l 67 (75)
T PF01336_consen 43 EKLKEGDIVRVR-GKVKRYNGGELEL 67 (75)
T ss_dssp HTS-TTSEEEEE-EEEEEETTSSEEE
T ss_pred hcCCCCeEEEEE-EEEEEECCccEEE
Confidence 689999999999 999888776 655
No 141
>cd03448 HDE_HSD HDE_HSD The R-hydratase-like hot dog fold of the 17-beta-hydroxysteriod dehydrogenase (HSD), and Hydratase-Dehydrogenase-Epimerase (HDE) proteins. Other enzymes with this fold include MaoC dehydratase, and the fatty acid synthase beta subunit.
Probab=35.10 E-value=1.2e+02 Score=19.83 Aligned_cols=28 Identities=7% Similarity=0.105 Sum_probs=20.7
Q ss_pred EEeecCCCCCCCEEEEEEeeecCCCCeEEEE
Q 034382 62 TAWVSVGAQIGDEVEVKVEEAHPRDDIIYLK 92 (96)
Q Consensus 62 ~~~~~~~~~~Gd~v~v~v~~vdP~~~~l~l~ 92 (96)
.+++..++.+||.|.+++...+ +.+.++
T Consensus 76 ~~rF~~PV~~gDtl~~~~~~~~---~~v~~~ 103 (122)
T cd03448 76 KVRFSSPVFPGETLRTEMWKEG---NRVIFQ 103 (122)
T ss_pred EEEEcCCccCCCEEEEEEEEeC---CEEEEE
Confidence 5667789999999999998554 345444
No 142
>PRK08563 DNA-directed RNA polymerase subunit E'; Provisional
Probab=34.85 E-value=1.6e+02 Score=20.61 Aligned_cols=55 Identities=11% Similarity=0.162 Sum_probs=36.2
Q ss_pred hhCCCCCeEEEEEEEEccCceEEEEeecceeeEEEeec----------------------CCCCCCCEEEEEEeeecCCC
Q 034382 29 RRQPKERQYRALVLRFIKDRTAALLLVEVGLQATAWVS----------------------VGAQIGDEVEVKVEEAHPRD 86 (96)
Q Consensus 29 ~~~~~~~~~~AvVl~~~~~~~~~vlL~dl~le~~~~~~----------------------~~~~~Gd~v~v~v~~vdP~~ 86 (96)
+-.. |...+|.|.+-.+ ..+.+-|.- ++.-+..+ ..++.||.|+++|.++|...
T Consensus 78 ~P~~-GEVv~g~V~~v~~-~Gi~V~lg~--~~g~v~~~~l~~~~~~~d~~~~~~~~~~~~~~i~~Gd~VrvrV~~v~~~~ 153 (187)
T PRK08563 78 KPEL-QEVVEGEVVEVVE-FGAFVRIGP--VDGLLHISQIMDDYISYDPKNGRLIGKESKRVLKVGDVVRARIVAVSLKE 153 (187)
T ss_pred eccC-CCEEEEEEEEEEc-cEEEEEEeC--ceEEEEcHHcCCCceEEccccceEEEccCCeEEcCCCEEEEEEEEEEccc
Confidence 3344 7899999998777 655555531 22222211 23588999999999999754
Q ss_pred C
Q 034382 87 D 87 (96)
Q Consensus 87 ~ 87 (96)
.
T Consensus 154 ~ 154 (187)
T PRK08563 154 R 154 (187)
T ss_pred C
Confidence 3
No 143
>PF01455 HupF_HypC: HupF/HypC family; InterPro: IPR001109 The large subunit of [NiFe]-hydrogenase, as well as other nickel metalloenzymes, is synthesised as a precursor devoid of the metalloenzyme active site. This precursor then undergoes a complex post-translational maturation process that requires a number of accessory proteins. The hydrogenase expression/formation proteins (HupF/HypC) form a family of small proteins that are hydrogenase precursor-specific chaperones required for this maturation process []. They are believed to keep the hydrogenase precursor in a conformation accessible for metal incorporation [, ].; PDB: 3D3R_A 2Z1C_C 2OT2_A.
Probab=34.71 E-value=1.1e+02 Score=18.56 Aligned_cols=43 Identities=16% Similarity=0.097 Sum_probs=27.3
Q ss_pred EEEEEEEcc-CceEEEEeecceeeEEEeecCCCCCCCEEEEEEe
Q 034382 38 RALVLRFIK-DRTAALLLVEVGLQATAWVSVGAQIGDEVEVKVE 80 (96)
Q Consensus 38 ~AvVl~~~~-~~~~~vlL~dl~le~~~~~~~~~~~Gd~v~v~v~ 80 (96)
|+-|++.-. ++.|.+-....--++.+..=.+++|||-|.|-.+
T Consensus 6 P~~Vv~v~~~~~~A~v~~~G~~~~V~~~lv~~v~~Gd~VLVHaG 49 (68)
T PF01455_consen 6 PGRVVEVDEDGGMAVVDFGGVRREVSLALVPDVKVGDYVLVHAG 49 (68)
T ss_dssp EEEEEEEETTTTEEEEEETTEEEEEEGTTCTSB-TT-EEEEETT
T ss_pred cEEEEEEeCCCCEEEEEcCCcEEEEEEEEeCCCCCCCEEEEecC
Confidence 677888741 2888887765444444444477999999988654
No 144
>cd03452 MaoC_C MaoC_C The C-terminal hot dog fold of the MaoC (monoamine oxidase C) dehydratase regulatory protein. Orthologs of MaoC include PaaZ [Escherichia coli] and PaaN [Pseudomonas putida], which are putative ring-opening enzymes involved in phenylacetic acid degradation. The C-terminal domain of MaoC has sequence similarity to (R)-specific enoyl-CoA hydratase,Hydratase-Dehydrogenase-Epimerase (HDE) protein, and the fatty acid synthase beta subunit. MaoC also has an N-terminal PutA domain like that found in the E. coli PutA proline dehydrogenase and other members of the aldehyde dehydrogenase family.
Probab=34.05 E-value=1.2e+02 Score=20.15 Aligned_cols=23 Identities=17% Similarity=0.244 Sum_probs=16.2
Q ss_pred EEeecCCCCCCCEEEEE--EeeecC
Q 034382 62 TAWVSVGAQIGDEVEVK--VEEAHP 84 (96)
Q Consensus 62 ~~~~~~~~~~Gd~v~v~--v~~vdP 84 (96)
.+++..++.|||.|.++ |..+++
T Consensus 82 ~~rf~~PV~~GDtl~~~~~V~~~~~ 106 (142)
T cd03452 82 NLRFLEPVYPGDTIQVRLTCKRKIP 106 (142)
T ss_pred eEEECCCCCCCCEEEEEEEEEEEee
Confidence 56667899999999655 444443
No 145
>cd03440 hot_dog The hotdog fold was initially identified in the E. coli FabA (beta-hydroxydecanoyl-acyl carrier protein (ACP)-dehydratase) structure and subsequently in 4HBT (4-hydroxybenzoyl-CoA thioesterase) from Pseudomonas. A number of other seemingly unrelated proteins also share the hotdog fold. These proteins have related, but distinct, catalytic activities that include metabolic roles such as thioester hydrolysis in fatty acid metabolism, and degradation of phenylacetic acid and the environmental pollutant 4-chlorobenzoate. This superfamily also includes the PaaI-like protein FapR, a non-catalytic bacterial homolog involved in transcriptional regulation of fatty acid biosynthesis.
Probab=33.57 E-value=81 Score=16.81 Aligned_cols=30 Identities=13% Similarity=0.132 Sum_probs=22.4
Q ss_pred EeecCCCCCCCEEEEEEeeecCCCCeEEEE
Q 034382 63 AWVSVGAQIGDEVEVKVEEAHPRDDIIYLK 92 (96)
Q Consensus 63 ~~~~~~~~~Gd~v~v~v~~vdP~~~~l~l~ 92 (96)
+....++.+||.+.++..-.+.....+.+.
T Consensus 52 ~~~~~~~~~g~~v~~~~~~~~~~~~~~~~~ 81 (100)
T cd03440 52 VRFLRPVRPGDTLTVEAEVVRVGRSSVTVE 81 (100)
T ss_pred eEEecCCCCCCEEEEEEEEEeccccEEEEE
Confidence 444468888999999998888877665554
No 146
>COG0361 InfA Translation initiation factor 1 (IF-1) [Translation, ribosomal structure and biogenesis]
Probab=33.22 E-value=1.3e+02 Score=18.94 Aligned_cols=57 Identities=19% Similarity=0.202 Sum_probs=42.5
Q ss_pred CCeEEEEEEEEccCceEEEEeecceeeEEEeec-------CCCCCCCEEEEEEeeecCCCCeEEE
Q 034382 34 ERQYRALVLRFIKDRTAALLLVEVGLQATAWVS-------VGAQIGDEVEVKVEEAHPRDDIIYL 91 (96)
Q Consensus 34 ~~~~~AvVl~~~~~~~~~vlL~dl~le~~~~~~-------~~~~~Gd~v~v~v~~vdP~~~~l~l 91 (96)
.-+.+|.|++-++.+...|.+.+ |.+.-++.+ -.+.|||.|.|....-|+-.+.|..
T Consensus 6 ~~e~~g~V~e~L~~~~f~v~~ed-g~~~~ahI~GKmr~~~i~I~~GD~V~Ve~~~~d~~kg~I~~ 69 (75)
T COG0361 6 EIEMEGTVIEMLPNGRFRVELEN-GHERLAHISGKMRKNRIRILPGDVVLVELSPYDLTKGRIVY 69 (75)
T ss_pred ccEEEEEEEEecCCCEEEEEecC-CcEEEEEccCcchheeEEeCCCCEEEEEecccccccccEEE
Confidence 34678999999997788888655 555555555 2367999999999999876665543
No 147
>PF05641 Agenet: Agenet domain; InterPro: IPR008395 This domain is related to the TUDOR domain IPR008191 from INTERPRO []. The function of the agenet domain is unknown. This signature matches one of the two Agenet domains in the FMR proteins [].; GO: 0003723 RNA binding; PDB: 2BKD_N 3O8V_A 3KUF_A 3H8Z_A.
Probab=33.04 E-value=74 Score=18.82 Aligned_cols=27 Identities=15% Similarity=0.019 Sum_probs=19.6
Q ss_pred CCeEEEEEEEEccCceEEEEeecceee
Q 034382 34 ERQYRALVLRFIKDRTAALLLVEVGLQ 60 (96)
Q Consensus 34 ~~~~~AvVl~~~~~~~~~vlL~dl~le 60 (96)
|.+|.|.|+...+.+.+.|--.++..+
T Consensus 18 gaWf~a~V~~~~~~~~~~V~Y~~~~~~ 44 (68)
T PF05641_consen 18 GAWFPATVLKENGDDKYLVEYDDLPDE 44 (68)
T ss_dssp -EEEEEEEEEEETT-EEEEEETT-SS-
T ss_pred cEEEEEEEEEeCCCcEEEEEECCcccc
Confidence 789999999999933888888777655
No 148
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=32.60 E-value=1.9e+02 Score=20.80 Aligned_cols=54 Identities=20% Similarity=0.266 Sum_probs=41.5
Q ss_pred EEEEEEEEccCceEEEEeecceeeEEEeec--CCCCCCCEEEEEEee-ecCCCCeEEEE
Q 034382 37 YRALVLRFIKDRTAALLLVEVGLQATAWVS--VGAQIGDEVEVKVEE-AHPRDDIIYLK 92 (96)
Q Consensus 37 ~~AvVl~~~~~~~~~vlL~dl~le~~~~~~--~~~~~Gd~v~v~v~~-vdP~~~~l~l~ 92 (96)
-.|.+.+... +.+.+-.-.+|+++.++.+ ..+++|+.+.|-+.. ++ ++|.+++.
T Consensus 5 l~G~v~~~~~-~~~ii~~~GvGY~v~v~~~~~~~l~~g~~v~l~t~~~v~-rEd~~~Ly 61 (186)
T PRK14600 5 LSGIVEEVRS-DYIILNVGNVGYIVYLSAKVLSTCKIGDNIKLYIETYVN-RDNVTQLY 61 (186)
T ss_pred EEEEEEEEcC-CEEEEEECCEEEEEEecHHHHHhhCCCCeEEEEEEEEEe-ecCCceee
Confidence 4677777766 8888888899999999886 457899999988764 45 77766653
No 149
>PF12791 RsgI_N: Anti-sigma factor N-terminus; InterPro: IPR024449 The heat shock genes in Bacillus subtilis can be classified into several groups according to their regulation [], and the sigma gene, sigI, of Bacillus subtilis belongs to the group IV heat-shock response genes and has many orthologues in the bacterial phylum Firmicutes []. Regulation of sigma factor I is carried out by RsgI from the same operon. This entry represents the N-terminal cytoplasmic portion of RsgI ('upstream' of the single transmembrane helix) which has been shown to interact directly with Sigma-I [].
Probab=31.56 E-value=1e+02 Score=17.34 Aligned_cols=34 Identities=18% Similarity=0.225 Sum_probs=22.8
Q ss_pred ceEEEEeecceeeEEEeecCCCCCCCEEEEEEeee
Q 034382 48 RTAALLLVEVGLQATAWVSVGAQIGDEVEVKVEEA 82 (96)
Q Consensus 48 ~~~~vlL~dl~le~~~~~~~~~~~Gd~v~v~v~~v 82 (96)
+.+.|+=+|-. ...++.+.+.+.||.+.+.-...
T Consensus 6 ~~aiVlT~dGe-F~~ik~~~~~~vG~eI~~~~~~~ 39 (56)
T PF12791_consen 6 KYAIVLTPDGE-FIKIKRKPGMEVGQEIEFDEKDI 39 (56)
T ss_pred CEEEEEcCCCc-EEEEeCCCCCcccCEEEEechhh
Confidence 44555555544 45577776699999999876543
No 150
>KOG1004 consensus Exosomal 3'-5' exoribonuclease complex subunit Rrp40 [Translation, ribosomal structure and biogenesis]
Probab=30.71 E-value=1.1e+02 Score=23.10 Aligned_cols=51 Identities=18% Similarity=0.143 Sum_probs=41.1
Q ss_pred eEEEEEEEEccC-------ceEEEEeecceeeEEEeec-CCCCCCCEEEEEEeeecCCC
Q 034382 36 QYRALVLRFIKD-------RTAALLLVEVGLQATAWVS-VGAQIGDEVEVKVEEAHPRD 86 (96)
Q Consensus 36 ~~~AvVl~~~~~-------~~~~vlL~dl~le~~~~~~-~~~~~Gd~v~v~v~~vdP~~ 86 (96)
.-=|+|+...+| +--..+|+-+++|-.-+.+ .+++.||-|.-||..+++..
T Consensus 68 ~VIGiV~~~~gd~ykVDigg~~~a~L~~laFe~AtkrNrPnl~vGdliyakv~~a~~~~ 126 (230)
T KOG1004|consen 68 HVIGIVTSKSGDIYKVDIGGSEPASLSYLAFEGATKRNRPNLQVGDLIYAKVVDANKDM 126 (230)
T ss_pred EEEEEEEeccCceEEEecCCCCeeeeeeccccCccccCCCccccccEEEEEEEecCCCc
Confidence 446889888885 2234788889999888888 67999999999999998754
No 151
>PLN00208 translation initiation factor (eIF); Provisional
Probab=30.35 E-value=2e+02 Score=20.28 Aligned_cols=54 Identities=20% Similarity=0.255 Sum_probs=38.7
Q ss_pred eEEEEEEEEccCceEEEEeecceeeEEEeec------CCCCCCCEEEEEEeeecCCCCeEE
Q 034382 36 QYRALVLRFIKDRTAALLLVEVGLQATAWVS------VGAQIGDEVEVKVEEAHPRDDIIY 90 (96)
Q Consensus 36 ~~~AvVl~~~~~~~~~vlL~dl~le~~~~~~------~~~~~Gd~v~v~v~~vdP~~~~l~ 90 (96)
+--|.|+.-++.+...|.+.+ |-+.-++.+ .-+.+||.|.|.+..-|+-.+.|.
T Consensus 33 q~~g~V~~~lGn~~~~V~c~d-G~~rLa~IpGKmRKrIWI~~GD~VlVel~~~d~~KgdIv 92 (145)
T PLN00208 33 QEYAQVLRMLGNGRCEALCID-GTKRLCHIRGKMRKKVWIAAGDIILVGLRDYQDDKADVI 92 (145)
T ss_pred cEEEEEEEEcCCCEEEEEECC-CCEEEEEEeccceeeEEecCCCEEEEEccCCCCCEEEEE
Confidence 346899998887788888776 555555554 337899999999777776555554
No 152
>PF01245 Ribosomal_L19: Ribosomal protein L19; InterPro: IPR001857 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein L19 is one of the proteins from the large ribosomal subunit [, ]. In Escherichia coli, L19 is known to be located at the 30S-50S ribosomal subunit interface [] and may play a role in the structure and function of the aminoacyl-tRNA binding site. It belongs to a family of ribosomal proteins, including L19 from bacteria and the chloroplasts of red algae. L19 is a protein of 120 to 130 amino-acid residues.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3HUZ_T 3V2D_T 3I8I_R 2XG2_T 2V49_T 2XUX_T 3HUX_T 3I9C_R 3V25_T 3UZ2_R ....
Probab=29.83 E-value=1.2e+02 Score=20.28 Aligned_cols=25 Identities=20% Similarity=0.278 Sum_probs=19.4
Q ss_pred CCCCCCCEEEEEEeeecCCCCeEEE
Q 034382 67 VGAQIGDEVEVKVEEAHPRDDIIYL 91 (96)
Q Consensus 67 ~~~~~Gd~v~v~v~~vdP~~~~l~l 91 (96)
.++.+||.|.|.+.-...-.+.++.
T Consensus 17 p~f~~GD~v~V~~~i~e~~k~r~q~ 41 (113)
T PF01245_consen 17 PEFRVGDTVRVTYKISEGNKERIQV 41 (113)
T ss_dssp SSSSSSSEEEEEEEEESSSSEEEEE
T ss_pred CCcCCCCEEEEEEEEecCCCceeEE
Confidence 5799999999999877665555553
No 153
>cd03441 R_hydratase_like (R)-hydratase [(R)-specific enoyl-CoA hydratase]. Catalyzes the hydration of trans-2-enoyl CoA to (R)-3-hydroxyacyl-CoA as part of the PHA (polyhydroxyalkanoate) biosynthetic pathway. The structure of the monomer includes a five-strand antiparallel beta-sheet wrapped around a central alpha helix, referred to as a hot dog fold. The active site lies within a substrate-binding tunnel formed by the homodimer. Other enzymes with this fold include MaoC dehydratase, Hydratase-Dehydrogenase-Epimerase protein (HDE), and the fatty acid synthase beta subunit.
Probab=29.81 E-value=1.4e+02 Score=18.46 Aligned_cols=26 Identities=23% Similarity=0.207 Sum_probs=19.1
Q ss_pred eEEEeecCCCCCCCEEEEEEeeecCC
Q 034382 60 QATAWVSVGAQIGDEVEVKVEEAHPR 85 (96)
Q Consensus 60 e~~~~~~~~~~~Gd~v~v~v~~vdP~ 85 (96)
...+++..++.+||.|.++..-++-.
T Consensus 72 ~~~~~f~~Pv~~Gd~l~~~~~v~~~~ 97 (127)
T cd03441 72 SQSVRFLAPVFPGDTLRVEVEVLGKR 97 (127)
T ss_pred EeEEEEeCCcCCCCEEEEEEEEEEee
Confidence 34555668999999999887665544
No 154
>PF13550 Phage-tail_3: Putative phage tail protein
Probab=29.73 E-value=1.5e+02 Score=19.49 Aligned_cols=25 Identities=20% Similarity=0.343 Sum_probs=17.4
Q ss_pred CCCCCCCEEEEEEeeecCCCCeEEEEEe
Q 034382 67 VGAQIGDEVEVKVEEAHPRDDIIYLKEV 94 (96)
Q Consensus 67 ~~~~~Gd~v~v~v~~vdP~~~~l~l~e~ 94 (96)
..++|||.|.|.-. -..-..|+.++
T Consensus 138 ~~l~pGDvi~l~~~---~~~~~~RI~~i 162 (164)
T PF13550_consen 138 LALEPGDVIALSDD---GRDMRFRITEI 162 (164)
T ss_pred ccCCCCCEEEEEeC---CCceEEEEEEE
Confidence 56999999998766 33555555554
No 155
>PRK01712 carbon storage regulator; Provisional
Probab=29.62 E-value=81 Score=19.25 Aligned_cols=24 Identities=25% Similarity=0.416 Sum_probs=16.4
Q ss_pred cCCCCCCCEEEEEEeeecCCCCeEEE
Q 034382 66 SVGAQIGDEVEVKVEEAHPRDDIIYL 91 (96)
Q Consensus 66 ~~~~~~Gd~v~v~v~~vdP~~~~l~l 91 (96)
+..+..||-+.|+|..++ .|.+++
T Consensus 9 gE~I~Igd~I~I~V~~i~--~~~Vrl 32 (64)
T PRK01712 9 GESLMIGDDIEVTVLGVK--GNQVRI 32 (64)
T ss_pred CCEEEeCCCEEEEEEEEe--CCEEEE
Confidence 356777888888887776 455554
No 156
>PF07238 PilZ: PilZ domain; InterPro: IPR009875 The ubiquitous bacterial second messenger cyclic-di-GMP (c-di-GMP) is associated with the regulation of biofilm formation, the control of exopolysaccharide synthesis, flagellar- and pili-based motility, gene expression, interactions of bacteria with eukaryotic hosts and multicellular behaviour in diverse bacteria. With the exception of bacterial cellulose synthases, the identities of c-di-GMP receptors and end targets of the proteins having one or more PilZ domains are mostly uncharacterised. However it was suggested that the PilZ domains present in the BcsA subunits of bacterial cellulose synthases function in c-di-GMP binding []. More recently YcgR (see IPR023787 from INTERPRO) was found to bind c-di-GMP tightly and specifically; also isolated PilZ domains from YcgR and BcsA bound c-di-GMP indicating that the PilZ domain was sufficient for binding of c-di-GMP and significantly that site-directed mutagenesis performed on YcgR implicated the most conserved residues in the PilZ domain directly in c-di-GMP binding []. It was suggested that c-di-GMP binding to PilZ brings about conformational changes in the protein that stabilise the bound ligand and probability initiates the downstream signal transduction cascade. In the case of YcgR, c-di-GMP binding regulates flagellum-based motility in a c-di-GMP-dependent manner (see IPR023787 from INTERPRO) []. The association of the PilZ domain with a variety of other domains, including likely components of bacterial multidrug secretion system, could provide clues to multiple functions of the c-di-GMP in bacterial pathogenesis and cell development. Binding and mutagenesis studies of several PilZ domain proteins have confirmed this observation and demonstrated that c-di-GMP binding depends on residues in RxxxR and D/NxSxxG sequence motifs. The crystal structure, at 1.7 A, of a PilZ domain::c-di-GMP complex from Vibrio cholerae shows c-di-GMP contacting seven of nine strongly conserved residues. Binding of c-di-GMP causes a conformational switch whereby the C- and N-terminal domains are brought into close opposition forming a new allosteric interaction surface that spans these domains and the c-di-GMP at their interface []. ; GO: 0035438 cyclic-di-GMP binding; PDB: 2RDE_B 1YLN_A 3KYG_A 3DSG_B 2GJG_A 3KYF_A 1YWU_A 2L74_A 2L1T_A 3CNR_A ....
Probab=29.49 E-value=1.2e+02 Score=17.70 Aligned_cols=34 Identities=12% Similarity=0.215 Sum_probs=20.1
Q ss_pred CCeEEEEEEEEccCceEEEEeecceeeEEEeecCCCCCCCEEEEEE
Q 034382 34 ERQYRALVLRFIKDRTAALLLVEVGLQATAWVSVGAQIGDEVEVKV 79 (96)
Q Consensus 34 ~~~~~AvVl~~~~~~~~~vlL~dl~le~~~~~~~~~~~Gd~v~v~v 79 (96)
+..|.|.+++--. +-+.+..++ ++.+|+.+.+++
T Consensus 22 ~~~~~~~~~diS~-~G~~~~~~~-----------~~~~~~~v~l~~ 55 (102)
T PF07238_consen 22 GSSFQGTIVDISE-GGCAFRSPK-----------PLEPGDRVRLSF 55 (102)
T ss_dssp TEEEEEEEEEETT-SEEEEEECT-----------G--TTSEEEEEE
T ss_pred CcEEEEEEEEECc-cceEEEECC-----------CCCCCCEEEEEE
Confidence 5677777777555 544444433 667777777766
No 157
>cd03451 FkbR2 FkbR2 is a Streptomyces hygroscopicus protein with a hot dog fold that belongs to a conserved family of proteins found in prokaryotes and archaea but not in eukaryotes. FkbR2 has sequence similarity to (R)-specific enoyl-CoA hydratase, the peroxisomal Hydratase-Dehydrogenase-Epimerase (HDE) protein, and the fatty acid synthase beta subunit. The function of FkbR2 is unknown.
Probab=28.31 E-value=1.4e+02 Score=19.43 Aligned_cols=23 Identities=13% Similarity=0.072 Sum_probs=16.6
Q ss_pred EEeecCCCCCCCEEEE--EEeeecC
Q 034382 62 TAWVSVGAQIGDEVEV--KVEEAHP 84 (96)
Q Consensus 62 ~~~~~~~~~~Gd~v~v--~v~~vdP 84 (96)
.+++..++.|||.|.+ +|.++++
T Consensus 85 ~~~f~~pv~~GDtl~~~~~v~~~~~ 109 (146)
T cd03451 85 EVRFPAPVFHGDTLYAESEVLSKRE 109 (146)
T ss_pred EEEecCCCCCCCEEEEEEEEEEEec
Confidence 4666689999999976 4555554
No 158
>PF02563 Poly_export: Polysaccharide biosynthesis/export protein; InterPro: IPR003715 The extracellular polysaccharide colanic acid (CA) is produced by species of the family Enterobacteriaceae. In Escherichia coli (strain K12) the CA cluster comprises 19 genes. The wzx gene encodes a protein with multiple transmembrane segments that may function in export of the CA repeat unit from the cytoplasm into the periplasm in a process analogous to O-unit export. The CA gene clusters may be involved in the export of polysaccharide from the cell [].; GO: 0015159 polysaccharide transmembrane transporter activity, 0015774 polysaccharide transport, 0016020 membrane; PDB: 2W8I_E 2W8H_E 2J58_D.
Probab=28.29 E-value=27 Score=21.42 Aligned_cols=24 Identities=13% Similarity=-0.074 Sum_probs=13.0
Q ss_pred CCCCCCCEEEEEEeeecCCCCeEE
Q 034382 67 VGAQIGDEVEVKVEEAHPRDDIIY 90 (96)
Q Consensus 67 ~~~~~Gd~v~v~v~~vdP~~~~l~ 90 (96)
-.+.|||.|.|.+-.-++.+..++
T Consensus 11 y~l~pGD~l~i~v~~~~~l~~~~~ 34 (82)
T PF02563_consen 11 YRLGPGDVLRISVFGWPELSGEYT 34 (82)
T ss_dssp ----TT-EEEEEETT-HHHCCSEE
T ss_pred CEECCCCEEEEEEecCCCcccceE
Confidence 358999999999976665544333
No 159
>PF14345 GDYXXLXY: GDYXXLXY protein
Probab=28.00 E-value=46 Score=22.52 Aligned_cols=20 Identities=35% Similarity=0.405 Sum_probs=17.5
Q ss_pred CCCCCCEEEEEEeeecCCCC
Q 034382 68 GAQIGDEVEVKVEEAHPRDD 87 (96)
Q Consensus 68 ~~~~Gd~v~v~v~~vdP~~~ 87 (96)
-+.-|+.|.+++.=|||++-
T Consensus 16 ~l~~G~~v~L~~~PvDPRdl 35 (144)
T PF14345_consen 16 ILAQGKEVTLKTAPVDPRDL 35 (144)
T ss_pred HHhCCCEEEEEecccCcccc
Confidence 46789999999999999863
No 160
>COG4536 CorB Putative Mg2+ and Co2+ transporter CorB [Inorganic ion transport and metabolism]
Probab=27.82 E-value=53 Score=26.94 Aligned_cols=44 Identities=16% Similarity=-0.011 Sum_probs=33.4
Q ss_pred cccchHHHHhhhCCCCCeEEEEEEEEccCceEEEEeecceeeEEEee
Q 034382 19 SLRYWIIEFLRRQPKERQYRALVLRFIKDRTAALLLVEVGLQATAWV 65 (96)
Q Consensus 19 s~RyW~l~YL~~~~~~~~~~AvVl~~~~~~~~~vlL~dl~le~~~~~ 65 (96)
++--|+|.+|+++++ -=|+|++..++=++.|-|+|+-=|....+
T Consensus 284 Tpl~~QL~~F~~~k~---hialVVDEYG~i~GLVTLEDIlEEIVGdf 327 (423)
T COG4536 284 TPLSDQLVAFQRNKK---HIALVVDEYGDIQGLVTLEDILEEIVGDF 327 (423)
T ss_pred CcHHHHHHHHHHhcc---eEEEEEeccCcEEeeeeHHHHHHHHhccc
Confidence 345689999999882 35999999997789999998755544443
No 161
>PF01575 MaoC_dehydratas: MaoC like domain; InterPro: IPR002539 The C terminus of the MaoC protein is found to share similarity with a wide variety of enzymes. All these enzymes contain multiple domains. This domain is found in parts of two enzymes that have been assigned dehydratase activities. A deletion mutant of the C-terminal 271 amino acids in Q02207 from SWISSPROT abolished its 2-enoyl-CoA hydratase activity, suggesting that this region may be a hydratase enzyme []. The maoC gene is part of a operon with maoA which is involved in the synthesis of monoamine oxidase [].; GO: 0016491 oxidoreductase activity, 0008152 metabolic process; PDB: 3HMJ_H 2UV8_I 2VKZ_G 1PN4_C 1PN2_B 1S9C_K 3OML_A 1Q6W_B 2B3M_A 3K67_B ....
Probab=27.69 E-value=1e+02 Score=19.76 Aligned_cols=24 Identities=17% Similarity=0.166 Sum_probs=17.3
Q ss_pred eEEEeecCCCCCCCEEEEEEeeec
Q 034382 60 QATAWVSVGAQIGDEVEVKVEEAH 83 (96)
Q Consensus 60 e~~~~~~~~~~~Gd~v~v~v~~vd 83 (96)
...+++..++.|||.+.+++..++
T Consensus 80 ~~~~rF~~PV~~gdtl~~~~~v~~ 103 (122)
T PF01575_consen 80 RFNVRFRAPVFPGDTLTAEVEVTE 103 (122)
T ss_dssp EEEEEESS--BTTEEEEEEEEEEE
T ss_pred EEEEEEeccccCCCEEEEEEEEEE
Confidence 455666689999999999887765
No 162
>PF05683 Fumerase_C: Fumarase C-terminus; InterPro: IPR004647 This entry represents various Fe-S type hydro-lyases, including the beta subunit from both L-tartrate dehydratase (TtdB; EC:4.2.1.32) and class 2 fumarate hydratase (FumC; (4.2.1.2 from EC) []. A number of Fe-S cluster-containing hydro-lyases share a conserved motif, including argininosuccinate lyase, adenylosuccinate lyase, aspartase, class I fumarate hydratase (fumarase), and tartrate dehydratase (see IPR000362 from INTERPRO). Proteins in this group represent a subset of closely related proteins or modules, including the Escherichia coli tartrate dehydratase beta chain and the C-terminal region of the class I fumarase (where the N-terminal region is homologous to the tartrate dehydratase alpha chain). The activity of the archaeal proteins in this group is unknown.; GO: 0016836 hydro-lyase activity; PDB: 2ISB_A.
Probab=27.46 E-value=36 Score=25.30 Aligned_cols=47 Identities=19% Similarity=0.208 Sum_probs=10.0
Q ss_pred HHHhhhCCCCCeEEEEEEEEccCceEEEEeecceeeEEEeec--CCCCCCCEEEEE
Q 034382 25 IEFLRRQPKERQYRALVLRFIKDRTAALLLVEVGLQATAWVS--VGAQIGDEVEVK 78 (96)
Q Consensus 25 l~YL~~~~~~~~~~AvVl~~~~~~~~~vlL~dl~le~~~~~~--~~~~~Gd~v~v~ 78 (96)
++.|++++ .+.|+++..+...+ . ..+-|.+++.-. .+++.||.|.+.
T Consensus 4 ~~~l~~~~-~~~~p~~~~~~~~~-~-----~~~~L~tPlt~e~i~~L~vGD~V~Ls 52 (205)
T PF05683_consen 4 PEKLEHDP-AQYLPDIELDETAE-A-----REIELTTPLTEEDIRKLKVGDTVYLS 52 (205)
T ss_dssp -------------------------------EEEEESS--HHHHHH--TT-EEEEE
T ss_pred cccccccc-cccccccccccccc-e-----EEEEcCCCCCHHHHhhCCCCCEEEEe
Confidence 46788888 89999997765531 1 112222333333 689999999875
No 163
>COG1162 Predicted GTPases [General function prediction only]
Probab=27.14 E-value=2.6e+02 Score=21.93 Aligned_cols=52 Identities=21% Similarity=0.250 Sum_probs=35.8
Q ss_pred EEEEEEEccCceEEEEeec----ceeeEEEeec-----CCCCCCCEEEEEEe-------eecCCCCeEE
Q 034382 38 RALVLRFIKDRTAALLLVE----VGLQATAWVS-----VGAQIGDEVEVKVE-------EAHPRDDIIY 90 (96)
Q Consensus 38 ~AvVl~~~~~~~~~vlL~d----l~le~~~~~~-----~~~~~Gd~v~v~v~-------~vdP~~~~l~ 90 (96)
++.|+.... +++.+.... --+.+..+.+ .++-.||.|.+... ++-||.+.|.
T Consensus 6 ~g~v~~~~~-g~y~v~~~~~~~~~~~~~~~r~~lr~~~~~~vVGD~V~~~~~~~~g~I~~i~~Rkn~L~ 73 (301)
T COG1162 6 RGRVVKVDA-GFYGVRLEEEVDGEVYRCRARGNLRKKDLKPVVGDRVVFEDENNNGVIEKILPRKNVLI 73 (301)
T ss_pred CcEEEEeeC-CEEEEEEccccccceeeeeeecceeccCccccccCeEEEecCCCcceEEEEecccCcee
Confidence 567777777 888777762 2344444443 56788999988876 7788887764
No 164
>PTZ00329 eukaryotic translation initiation factor 1A; Provisional
Probab=27.11 E-value=2.4e+02 Score=20.13 Aligned_cols=53 Identities=19% Similarity=0.251 Sum_probs=36.4
Q ss_pred EEEEEEEEccCceEEEEeecceeeEEEeec------CCCCCCCEEEEEEeeecCCCCeEE
Q 034382 37 YRALVLRFIKDRTAALLLVEVGLQATAWVS------VGAQIGDEVEVKVEEAHPRDDIIY 90 (96)
Q Consensus 37 ~~AvVl~~~~~~~~~vlL~dl~le~~~~~~------~~~~~Gd~v~v~v~~vdP~~~~l~ 90 (96)
--|.|++-++.++..|.+.+ |.+.-++.+ .-+.+||.|.|.+..-|+-.+.|.
T Consensus 34 ~~g~V~~~LGn~~f~V~c~d-G~~rLa~I~GKmRK~IWI~~GD~VlVel~~yd~~KgdIi 92 (155)
T PTZ00329 34 EYAQVLRMLGNGRLEAYCFD-GVKRLCHIRGKMRKRVWINIGDIILVSLRDFQDSKADVI 92 (155)
T ss_pred EEEEEEEEcCCCEEEEEECC-CCEEEEEeeccceeeEEecCCCEEEEeccCCCCCEEEEE
Confidence 36899998886778777765 444444444 347899999998766665555443
No 165
>COG4148 ModC ABC-type molybdate transport system, ATPase component [Inorganic ion transport and metabolism]
Probab=26.90 E-value=1.9e+02 Score=23.27 Aligned_cols=46 Identities=20% Similarity=0.369 Sum_probs=33.6
Q ss_pred CCeEEEEEEEEccC-ceEEEEeecceeeEEEeec-CCCCCCCEEEEEEeeec
Q 034382 34 ERQYRALVLRFIKD-RTAALLLVEVGLQATAWVS-VGAQIGDEVEVKVEEAH 83 (96)
Q Consensus 34 ~~~~~AvVl~~~~~-~~~~vlL~dl~le~~~~~~-~~~~~Gd~v~v~v~~vd 83 (96)
+...++.|.+.-.. ++..+-|.+ ..++++ .+.++|.+++++|..-|
T Consensus 232 ~~vl~~~V~~hd~~y~lt~l~l~~----~~l~v~~~~a~~g~~~R~~I~a~D 279 (352)
T COG4148 232 SSVLEGTVLEHDPRYGLTALALGD----QHLWVPKLDAPVGARLRIRIQARD 279 (352)
T ss_pred ceEEEEEehhcCCCcceEEEecCc----eEEEeeccCCCCCCcEEEEEEccc
Confidence 67788888885553 566676664 445555 57899999999998765
No 166
>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=26.88 E-value=1.4e+02 Score=24.22 Aligned_cols=18 Identities=33% Similarity=0.409 Sum_probs=14.8
Q ss_pred CCCCCCEEEEEEeeecCCC
Q 034382 68 GAQIGDEVEVKVEEAHPRD 86 (96)
Q Consensus 68 ~~~~Gd~v~v~v~~vdP~~ 86 (96)
.+++||.|.|+|.+ +|..
T Consensus 83 ~l~~G~~IlVQV~K-e~~~ 100 (414)
T TIGR00757 83 LLRPGQSVLVQVVK-EPRG 100 (414)
T ss_pred hCcCCCEEEEEEee-CCcC
Confidence 48999999999998 5543
No 167
>PRK10862 SoxR reducing system protein RseC; Provisional
Probab=26.78 E-value=82 Score=21.91 Aligned_cols=24 Identities=25% Similarity=0.156 Sum_probs=18.0
Q ss_pred eeEEEeecCCCCCCCEEEEEEeee
Q 034382 59 LQATAWVSVGAQIGDEVEVKVEEA 82 (96)
Q Consensus 59 le~~~~~~~~~~~Gd~v~v~v~~v 82 (96)
...++..+.++++||.|.|-+.+-
T Consensus 49 ~~~~v~~~~~~~vGD~V~v~i~e~ 72 (154)
T PRK10862 49 HQLVVPSSQPLVPGQKVELGIAEG 72 (154)
T ss_pred eEEEecCCCCCCCCCEEEEecchh
Confidence 345566667899999999987653
No 168
>CHL00084 rpl19 ribosomal protein L19
Probab=26.68 E-value=1.2e+02 Score=20.59 Aligned_cols=24 Identities=21% Similarity=0.252 Sum_probs=17.0
Q ss_pred CCCCCCCEEEEEEeeecCCCCeEE
Q 034382 67 VGAQIGDEVEVKVEEAHPRDDIIY 90 (96)
Q Consensus 67 ~~~~~Gd~v~v~v~~vdP~~~~l~ 90 (96)
.++.+||.|.|.+.-.+.-...++
T Consensus 21 p~f~~GDtV~V~~~i~eg~k~R~q 44 (117)
T CHL00084 21 PKIRVGDTVKVGVLIQEGNKERVQ 44 (117)
T ss_pred CccCCCCEEEEEEEEecCCeeEec
Confidence 469999999998865554444444
No 169
>COG0764 FabA 3-hydroxymyristoyl/3-hydroxydecanoyl-(acyl carrier protein) dehydratases [Lipid metabolism]
Probab=26.50 E-value=1.8e+02 Score=20.23 Aligned_cols=23 Identities=26% Similarity=0.279 Sum_probs=19.6
Q ss_pred EeecCCCCCCCEEEEEEeeecCC
Q 034382 63 AWVSVGAQIGDEVEVKVEEAHPR 85 (96)
Q Consensus 63 ~~~~~~~~~Gd~v~v~v~~vdP~ 85 (96)
+++.+++.|||.+.+.++.+-.+
T Consensus 94 ~kF~~~V~PGd~l~l~~~~~~~~ 116 (147)
T COG0764 94 AKFKRPVLPGDQLELEVKLLKSR 116 (147)
T ss_pred eeecCccCCCCEEEEEEEEEEec
Confidence 45668999999999999988777
No 170
>COG5140 UFD1 Ubiquitin fusion-degradation protein [Posttranslational modification, protein turnover, chaperones]
Probab=26.26 E-value=50 Score=25.78 Aligned_cols=65 Identities=18% Similarity=0.191 Sum_probs=46.0
Q ss_pred HHHHHhhhccccchHHHHhhhCCCCCeEEEEEEEEccCceEEEEeecceeeEEEeecCCCCCCCEEEEEEe
Q 034382 10 RIARRLSNTSLRYWIIEFLRRQPKERQYRALVLRFIKDRTAALLLVEVGLQATAWVSVGAQIGDEVEVKVE 80 (96)
Q Consensus 10 ~~a~~ieR~s~RyW~l~YL~~~~~~~~~~AvVl~~~~~~~~~vlL~dl~le~~~~~~~~~~~Gd~v~v~v~ 80 (96)
++..++.+..-+|=.|-=|..+..+..=.+=||++.. -.+.|+||..+|++- +++|||.|.++-.
T Consensus 53 SaL~kLs~lni~yPmlF~~s~~~~~~~THgGVLEFia-EEGrVylP~WMm~tL-----s~epgdlv~~~~t 117 (331)
T COG5140 53 SALVKLSSLNIQYPMLFEISHSDGIYRTHGGVLEFIA-EEGRVYLPSWMMQTL-----SMEPGDLVVLRYT 117 (331)
T ss_pred HHHHHHHhhccCCceEEEEecccceeEecccEEEEee-cCCcEeehHHHHHhc-----cCCCCcEEEEEec
Confidence 4455666666677666556665544555688999999 788899999998852 5677777776644
No 171
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=25.77 E-value=3.6e+02 Score=21.82 Aligned_cols=61 Identities=13% Similarity=0.172 Sum_probs=44.0
Q ss_pred HHHHhhhCCCCCeEEEEEEEEccCceEEEEeecceeeEEEeec-----CCCCCCCEEEEEEeeecCCCC
Q 034382 24 IIEFLRRQPKERQYRALVLRFIKDRTAALLLVEVGLQATAWVS-----VGAQIGDEVEVKVEEAHPRDD 87 (96)
Q Consensus 24 ~l~YL~~~~~~~~~~AvVl~~~~~~~~~vlL~dl~le~~~~~~-----~~~~~Gd~v~v~v~~vdP~~~ 87 (96)
.+.-+..+- |+.-.|.|.+.-+.+...|-|. +.++-+|.+ ..+.+||++.+=+.+|+....
T Consensus 130 i~~ey~~~~-Geiv~g~V~r~~~~~~i~vdlg--~~ea~LP~~eqip~E~~~~Gdrik~~i~~V~~~~k 195 (374)
T PRK12328 130 IFEKYKKKV-GKIVFGTVVRVDNEENTFIEID--EIRAVLPMKNRIKGEKFKVGDVVKAVLKRVKIDKN 195 (374)
T ss_pred HHHHHHHhc-CcEEEEEEEEEecCCCEEEEcC--CeEEEeCHHHcCCCCcCCCCCEEEEEEEEEecCCC
Confidence 455556666 8899999998664233444443 477777765 679999999999999987654
No 172
>PRK09838 periplasmic copper-binding protein; Provisional
Probab=25.40 E-value=94 Score=20.82 Aligned_cols=51 Identities=12% Similarity=0.085 Sum_probs=31.2
Q ss_pred eEEEEEEEEccC-ceEEEE---eecc-----eeeEEEeec---CCCCCCCEEEEEEeeecCCC
Q 034382 36 QYRALVLRFIKD-RTAALL---LVEV-----GLQATAWVS---VGAQIGDEVEVKVEEAHPRD 86 (96)
Q Consensus 36 ~~~AvVl~~~~~-~~~~vl---L~dl-----~le~~~~~~---~~~~~Gd~v~v~v~~vdP~~ 86 (96)
+-+|+|...-.+ +..+|. ||++ .|+..+.-+ ..+++||.|...+..-+...
T Consensus 44 ~~~G~V~~vd~~~~~iti~H~pIp~l~wPaMTM~F~v~~~~~l~~lk~G~~V~F~~~~~~~~~ 106 (115)
T PRK09838 44 SGTGVVKGIDLESKKITIHHEPIPAVNWPEMTMRFTITPQTKMSEIKTGDKVAFNFVQQGNLS 106 (115)
T ss_pred EEEEEEEEEeCCCCEEEEeecccccCCCCCccccccCCChhhhccCCCCCEEEEEEEEcCCcE
Confidence 336777765443 444443 4555 444444443 57899999999988654433
No 173
>COG3086 RseC Positive regulator of sigma E activity [Signal transduction mechanisms]
Probab=24.98 E-value=61 Score=23.05 Aligned_cols=25 Identities=20% Similarity=0.137 Sum_probs=18.9
Q ss_pred eEEEeecCCCCCCCEEEEEEeeecC
Q 034382 60 QATAWVSVGAQIGDEVEVKVEEAHP 84 (96)
Q Consensus 60 e~~~~~~~~~~~Gd~v~v~v~~vdP 84 (96)
..++.+..+++|||.|.+-+.+=|+
T Consensus 50 ~~~~~t~~pL~~Gq~VeiGi~Eksl 74 (150)
T COG3086 50 IFRVETDEPLEPGQKVELGIEEKSL 74 (150)
T ss_pred EEEEecCCcCCCCCEEEEccCcccH
Confidence 3455667899999999998766443
No 174
>PRK12281 rplX 50S ribosomal protein L24; Reviewed
Probab=24.59 E-value=1.4e+02 Score=18.54 Aligned_cols=27 Identities=30% Similarity=0.449 Sum_probs=19.6
Q ss_pred CCCCCCEEEE----------EEeeecCCCCeEEEEEe
Q 034382 68 GAQIGDEVEV----------KVEEAHPRDDIIYLKEV 94 (96)
Q Consensus 68 ~~~~Gd~v~v----------~v~~vdP~~~~l~l~e~ 94 (96)
.+..||+|.| +|.+||+.++.+.++.+
T Consensus 6 ~I~kGD~V~Vi~G~dKGK~G~V~~V~~~~~~V~Vegv 42 (76)
T PRK12281 6 KVKKGDMVKVIAGDDKGKTGKVLAVLPKKNRVIVEGV 42 (76)
T ss_pred cccCCCEEEEeEcCCCCcEEEEEEEEcCCCEEEEcCc
Confidence 5678888876 57778888887766543
No 175
>PF03061 4HBT: Thioesterase superfamily; InterPro: IPR006683 This family contains a wide variety of enzymes, principally thioesterases. This family includes 4HBT (3.1.2.23 from EC) which catalyses the final step in the biosynthesis of 4-hydroxybenzoate from 4-chlorobenzoate in the soil dwelling microbe Pseudomonas CBS-3. This family includes various cytosolic long-chain acyl-CoA thioester hydrolases. Long-chain acyl-CoA hydrolases hydrolyse palmitoyl-CoA to CoA and palmitate, they also catalyse the hydrolysis of other long chain fatty acyl-CoA thioesters. ; PDB: 3F5O_F 2F0X_D 2H4U_C 2PRX_A 2OV9_D 1YLI_B 3BJK_F 1IXL_A 3DKZ_B 2EIS_B ....
Probab=24.38 E-value=1.4e+02 Score=16.70 Aligned_cols=28 Identities=11% Similarity=0.051 Sum_probs=18.0
Q ss_pred eEEEeecCCCCCCCEEEEEEeeecCCCC
Q 034382 60 QATAWVSVGAQIGDEVEVKVEEAHPRDD 87 (96)
Q Consensus 60 e~~~~~~~~~~~Gd~v~v~v~~vdP~~~ 87 (96)
+..+..-.++.+||.+.++..-+.--..
T Consensus 35 ~~~i~f~~p~~~gd~l~~~~~v~~~g~~ 62 (79)
T PF03061_consen 35 ELSIDFLRPVRPGDTLRVEARVVRVGRK 62 (79)
T ss_dssp EEEEEESS-BBTTSEEEEEEEEEEEESS
T ss_pred EEEEEEccccCCCeEEEEEEEEEEECCE
Confidence 3445555789999999887765544333
No 176
>PF00181 Ribosomal_L2: Ribosomal Proteins L2, RNA binding domain; InterPro: IPR022666 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein L2 is one of the proteins from the large ribosomal subunit. This entry represents the best conserved region located in the C-terminal section of these proteins.In Escherichia coli, L2 is known to bind to the 23S rRNA and to have peptidyltransferase activity. It belongs to a family of ribosomal proteins which, on the basis of sequence similarities [, ], groups: Eubacterial L2. Algal and plant chloroplast L2. Cyanelle L2. Archaebacterial L2. Plant L2. Slime mold L2. Marchantia polymorpha mitochondrial L2. Paramecium tetraurelia mitochondrial L2. Fission yeast K5, K37 and KD4. Yeast YL6. Vertebrate L8. ; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 1YIT_A 1Q7Y_C 1YJN_A 3CPW_A 3I56_A 1VQ9_A 1M1K_C 3CC7_A 1YIJ_A 1K9M_C ....
Probab=24.29 E-value=1.8e+02 Score=17.77 Aligned_cols=39 Identities=21% Similarity=0.317 Sum_probs=29.4
Q ss_pred EEEEEEEEccC-----ceEEEEeecceeeEEEeecCCCCCCCEEE
Q 034382 37 YRALVLRFIKD-----RTAALLLVEVGLQATAWVSVGAQIGDEVE 76 (96)
Q Consensus 37 ~~AvVl~~~~~-----~~~~vlL~dl~le~~~~~~~~~~~Gd~v~ 76 (96)
-.++|++-.-+ ..|+|..++ +-..=+..+..+.+||.|.
T Consensus 33 ~~g~V~~i~~DP~Rsa~iAlV~~~~-g~~~yiiA~eg~~vGd~I~ 76 (77)
T PF00181_consen 33 IKGIVIDIEYDPNRSAPIALVKYED-GEKRYIIAPEGMKVGDIIE 76 (77)
T ss_dssp EEEEEEEEEEETTTSSEEEEEEETT-SEEEEEEEBTTEBTTEEEE
T ss_pred CcEEEEEEEecCCcCccEEEEEecC-CcEEEEEeECCCcCCCEEE
Confidence 57777765443 688888888 6666677778999999874
No 177
>TIGR00202 csrA carbon storage regulator (csrA). Modulates the expression of genes in the glycogen biosynthesis and gluconeogenesis pathways by accelerating the 5'-to-3' degradation of these transcripts through selective RNA binding. The N-terminal end of the sequence (AA 11-45) contains the KH motif which is characteristic of a set of RNA-binding proteins.
Probab=24.15 E-value=1.1e+02 Score=18.95 Aligned_cols=25 Identities=44% Similarity=0.606 Sum_probs=16.5
Q ss_pred ecCCCCCCCEEEEEEeeecCCCCeEEE
Q 034382 65 VSVGAQIGDEVEVKVEEAHPRDDIIYL 91 (96)
Q Consensus 65 ~~~~~~~Gd~v~v~v~~vdP~~~~l~l 91 (96)
.+..+..||-+.++|..+. .|.+++
T Consensus 8 ~gE~I~Igd~I~I~Vl~i~--g~~Vrl 32 (69)
T TIGR00202 8 VNESIQIGDDIEVKVLSVK--GDQVKL 32 (69)
T ss_pred CCCEEEeCCCEEEEEEEEc--CCeEEE
Confidence 3456777888888887766 444444
No 178
>CHL00141 rpl24 ribosomal protein L24; Validated
Probab=24.11 E-value=1.4e+02 Score=18.79 Aligned_cols=26 Identities=23% Similarity=0.417 Sum_probs=19.0
Q ss_pred CCCCCCEEEE----------EEeeecCCCCeEEEEE
Q 034382 68 GAQIGDEVEV----------KVEEAHPRDDIIYLKE 93 (96)
Q Consensus 68 ~~~~Gd~v~v----------~v~~vdP~~~~l~l~e 93 (96)
.+.+||+|.| +|.+||+..+.+.++.
T Consensus 8 ~I~~GD~V~Vi~G~dKGK~G~V~~V~~~~~~V~Veg 43 (83)
T CHL00141 8 HVKIGDTVKIISGSDKGKIGEVLKIIKKSNKVIVKG 43 (83)
T ss_pred cccCCCEEEEeEcCCCCcEEEEEEEEcCCCEEEEcC
Confidence 6788888887 5667777777766654
No 179
>PF08845 SymE_toxin: Toxin SymE, type I toxin-antitoxin system; InterPro: IPR014944 This entry represents a SOS-induced gene whose product shows homology to the antitoxin MazE (SymE), the coding region contains a cis-encoded antisense RNA. The small antisense RNA and the gene have the all the hallmarks of a toxin-antitoxin module. The synthesis of the SymE is tightly repressed at multiple levels; at the transcriptional level by the LexA repressor, at the level of mRNA stability and translation by the SymR RNA and at the level of protein stability by the Lon protease. SymE co-purifies with ribosomes and overproduction of the protein leads to cell growth inhibition, decreased protein synthesis and increased RNA degradation. These properties are shared with several RNA endonuclease toxins of toxin-antitoxin modules. It seems probable that the SymE protein represents an evolutionary derivative of a toxin containing the AbrB fold, whose representatives are typically antitoxins. The SymE promoted cleavage of RNA cleavage may be important for the recycling of RNAs damaged under SOS-inducing conditions []. ; GO: 0003723 RNA binding, 0016788 hydrolase activity, acting on ester bonds, 0016070 RNA metabolic process, 0005737 cytoplasm
Probab=24.10 E-value=81 Score=18.56 Aligned_cols=15 Identities=47% Similarity=0.685 Sum_probs=12.5
Q ss_pred CCCCCCCEEEEEEee
Q 034382 67 VGAQIGDEVEVKVEE 81 (96)
Q Consensus 67 ~~~~~Gd~v~v~v~~ 81 (96)
.++.+|+.|.|++..
T Consensus 36 aGF~~G~~v~V~v~~ 50 (57)
T PF08845_consen 36 AGFTIGDPVKVRVMP 50 (57)
T ss_pred hCCCCCCEEEEEEEC
Confidence 568999999999863
No 180
>cd01764 Urm1 Urm1-like ubuitin domain. Urm1 (Ubiquitin-Related Modifier1) The Urm1 fold, like those of two closely related proteins MoaD (molybdopterin synthase) and ThiS (sulfur carrier protein), is similar to that of ubiquitin although there is little or no sequence similarity. The C-terminal glycines of Urm1 are conjugated to an E1-like protein Uba4 as part of a novel conjugation system in yeast. The Urm1 fold is found only in eukaryotes.
Probab=24.01 E-value=98 Score=19.71 Aligned_cols=54 Identities=9% Similarity=0.086 Sum_probs=36.3
Q ss_pred chHHHHhhhCCCCCeEEEEEEE--EccCceEEEEeecceeeEEEeecCCCCCCCEEEE
Q 034382 22 YWIIEFLRRQPKERQYRALVLR--FIKDRTAALLLVEVGLQATAWVSVGAQIGDEVEV 77 (96)
Q Consensus 22 yW~l~YL~~~~~~~~~~AvVl~--~~~~~~~~vlL~dl~le~~~~~~~~~~~Gd~v~v 77 (96)
-..+.||..+- ...-+.++.+ .++ +...|++-+-..+.---.+..++.||.|.+
T Consensus 32 ~dll~~L~~~~-~~~~~~lf~~~g~lr-~~i~VlvN~~di~~l~g~~t~L~dgD~v~i 87 (94)
T cd01764 32 GDLLDYVASNL-LEERPDLFIEGGSVR-PGIIVLINDTDWELLGEEDYILEDGDHVVF 87 (94)
T ss_pred HHHHHHHHHhC-chhhhhhEecCCccc-CCEEEEECCccccccCCcccCCCCcCEEEE
Confidence 35678887754 2233444443 344 788899988887665555678999999876
No 181
>PRK06461 single-stranded DNA-binding protein; Reviewed
Probab=23.72 E-value=2e+02 Score=19.16 Aligned_cols=44 Identities=14% Similarity=0.160 Sum_probs=28.7
Q ss_pred eEEEEeecce--eeEEEeec--CCCCCCCEEEEEEeeecCCCCeEEEE
Q 034382 49 TAALLLVEVG--LQATAWVS--VGAQIGDEVEVKVEEAHPRDDIIYLK 92 (96)
Q Consensus 49 ~~~vlL~dl~--le~~~~~~--~~~~~Gd~v~v~v~~vdP~~~~l~l~ 92 (96)
...+.|-|-- +.+.++-+ ..+++||.|.|+=..++-.++.++|.
T Consensus 41 v~~~~l~D~TG~I~~tlW~~~a~~l~~GdvV~I~na~v~~f~G~lqL~ 88 (129)
T PRK06461 41 ISEAVVGDETGRVKLTLWGEQAGSLKEGEVVEIENAWTTLYRGKVQLN 88 (129)
T ss_pred EEEEEEECCCCEEEEEEeCCccccCCCCCEEEEECcEEeeeCCEEEEE
Confidence 3334444432 34444443 46899999999988888888876653
No 182
>cd03453 SAV4209_like SAV4209_like. Similar in sequence to the Streptomyces avermitilis SAV4209 protein, with a hot dog fold that is similar to those of (R)-specific enoyl-CoA hydratase, the peroxisomal Hydratase-Dehydrogenase-Epimerase (HDE) protein, and the fatty acid synthase beta subunit.
Probab=22.99 E-value=2.1e+02 Score=18.33 Aligned_cols=20 Identities=5% Similarity=-0.050 Sum_probs=15.0
Q ss_pred EeecCCCCCCCEEEEEEeee
Q 034382 63 AWVSVGAQIGDEVEVKVEEA 82 (96)
Q Consensus 63 ~~~~~~~~~Gd~v~v~v~~v 82 (96)
+++..++.+||.+.++..-+
T Consensus 75 ~rf~~Pv~~Gdtl~~~~~v~ 94 (127)
T cd03453 75 VRFTKPVPVPDTLTCTGIVV 94 (127)
T ss_pred EEECCcCcCCCEEEEEEEEE
Confidence 56667999999988765443
No 183
>PF12857 TOBE_3: TOBE-like domain; InterPro: IPR024765 The TOBE (transport-associated OB) domain [] always occurs as a dimer and it is found in ABC transporters immediately after the ATPase domain. This entry represents a TOBE-like domain, found in the C terminus of ATPase subunit CysA. CysA is part of the CysATWP ABC transporter complex, involved in sulphate/thiosulphate import [, ].
Probab=22.42 E-value=1.7e+02 Score=16.71 Aligned_cols=45 Identities=22% Similarity=0.078 Sum_probs=29.1
Q ss_pred CeEEEEEEEEccC-ceEEEEee----cceeeEEEeecC---CCCCCCEEEEEE
Q 034382 35 RQYRALVLRFIKD-RTAALLLV----EVGLQATAWVSV---GAQIGDEVEVKV 79 (96)
Q Consensus 35 ~~~~AvVl~~~~~-~~~~vlL~----dl~le~~~~~~~---~~~~Gd~v~v~v 79 (96)
.-++|.|..-..= ..+.+-|. +--+|+.++... ++.+||+|.++-
T Consensus 5 ~~l~a~V~~v~~~G~~vRlEl~~~~~~~~iEvel~~~~~~l~l~~G~~V~l~P 57 (58)
T PF12857_consen 5 GGLPARVRRVRPVGPEVRLELKRLDDGEPIEVELPRERRQLGLQPGDRVYLRP 57 (58)
T ss_pred CcEeEEEEEEEecCCeEEEEEEECCCCCEEEEEeCHhHHhcCCCCCCEEEEEe
Confidence 4567777643331 55555552 235777777776 788899998873
No 184
>PRK00568 carbon storage regulator; Provisional
Probab=22.27 E-value=1.5e+02 Score=18.74 Aligned_cols=24 Identities=25% Similarity=0.371 Sum_probs=16.7
Q ss_pred cCCCCCCCEEEEEEeeecCCCCeEEE
Q 034382 66 SVGAQIGDEVEVKVEEAHPRDDIIYL 91 (96)
Q Consensus 66 ~~~~~~Gd~v~v~v~~vdP~~~~l~l 91 (96)
+..+..||-+.++|.+++ .|.+++
T Consensus 9 gEsI~Igd~I~I~Vl~i~--g~~Vrl 32 (76)
T PRK00568 9 NEGIVIDDNIHIKVISID--RGSVRL 32 (76)
T ss_pred CCeEEeCCCeEEEEEEEc--CCEEEE
Confidence 366778888888887665 455554
No 185
>KOG3925 consensus Uncharacterized conserved protein [Function unknown]
Probab=21.94 E-value=88 Score=25.33 Aligned_cols=45 Identities=13% Similarity=0.319 Sum_probs=34.2
Q ss_pred EEEEEEEEccCceEEEEeecceeeEEEeec-CCCC-CCCEEEEEEeee
Q 034382 37 YRALVLRFIKDRTAALLLVEVGLQATAWVS-VGAQ-IGDEVEVKVEEA 82 (96)
Q Consensus 37 ~~AvVl~~~~~~~~~vlL~dl~le~~~~~~-~~~~-~Gd~v~v~v~~v 82 (96)
=+|+|++... .-..=.+-+.||.-.+-.+ ..++ ||.+++|++..=
T Consensus 184 REGvvi~~~~-~~g~~~~in~gL~k~v~I~~~~v~~p~~RvtV~l~aq 230 (371)
T KOG3925|consen 184 REGVVIKRKS-PAGHGYIINAGLKKEVYIDSKAVEAPGTRVTVRLNAQ 230 (371)
T ss_pred ccceeeccCC-CCCCcceecccceeeEEecchhhcCCcceEEEecCCc
Confidence 3799998766 5555566778888888777 5566 999999998854
No 186
>PF00467 KOW: KOW motif; InterPro: IPR005824 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. The KOW (Kyprides, Ouzounis, Woese) motif is found in a variety of ribosomal proteins and the bacterial transcription antitermination proteins NusG []. ; PDB: 3BBO_W 2HGJ_X 2HGQ_X 2HGU_X 1NPP_B 1M1G_D 1NPR_A 2XHC_A 2KVQ_G 2JVV_A ....
Probab=21.76 E-value=1.3e+02 Score=15.17 Aligned_cols=13 Identities=15% Similarity=0.077 Sum_probs=8.1
Q ss_pred EEeeecCCCCeEE
Q 034382 78 KVEEAHPRDDIIY 90 (96)
Q Consensus 78 ~v~~vdP~~~~l~ 90 (96)
+|.++|+..+.+.
T Consensus 18 ~I~~i~~~~~~V~ 30 (32)
T PF00467_consen 18 KIVEIDRSKVRVT 30 (32)
T ss_dssp EEEEEETTTTEEE
T ss_pred EEEEEECCCCEEE
Confidence 5667777665544
No 187
>PRK04914 ATP-dependent helicase HepA; Validated
Probab=21.67 E-value=4.5e+02 Score=23.85 Aligned_cols=64 Identities=19% Similarity=0.187 Sum_probs=45.4
Q ss_pred HhhhCCCCCeEEEEEEEEccCceEEEEeecceeeEEEeec------CCCCCCCEEEE------EEeeecCCCCeEEEE
Q 034382 27 FLRRQPKERQYRALVLRFIKDRTAALLLVEVGLQATAWVS------VGAQIGDEVEV------KVEEAHPRDDIIYLK 92 (96)
Q Consensus 27 YL~~~~~~~~~~AvVl~~~~~~~~~vlL~dl~le~~~~~~------~~~~~Gd~v~v------~v~~vdP~~~~l~l~ 92 (96)
|+.... ..-.=|+|++--+ +.++|++|.-+=+=....+ ..+.+||+|.. +|..|...+|.+...
T Consensus 8 w~s~~e-~eLGlG~v~~~d~-r~vtv~fpas~e~R~ya~~~apl~Rv~~~~g~~v~~~~~~~~~v~~v~~~~gl~~y~ 83 (956)
T PRK04914 8 WISDTE-SELGLGTVVAVDG-RTVTLLFPATGENRLYARNDAPLTRVMFNPGDTITSHEGWQLTVEEVEEENGLLTYH 83 (956)
T ss_pred cccCCC-CcCCcEEEEEEeC-CEEEEEecCCCCceeeecCCCCceeeecCCCCEEEecCCCEEEEEEEeccCCcEEEE
Confidence 444433 3455699999766 9999999998855433332 46899999986 588888877766653
No 188
>PF07705 CARDB: CARDB; InterPro: IPR011635 The APHP (acidic peptide-dependent hydrolases/peptidase) domain is found in a variety of different proteins.; PDB: 2KUT_A 2L0D_A 3IDU_A 2KL6_A.
Probab=21.66 E-value=94 Score=18.51 Aligned_cols=27 Identities=11% Similarity=0.163 Sum_probs=15.2
Q ss_pred ecceeeEEEeecCCCCCCCEEEEEEeee
Q 034382 55 VEVGLQATAWVSVGAQIGDEVEVKVEEA 82 (96)
Q Consensus 55 ~dl~le~~~~~~~~~~~Gd~v~v~v~~v 82 (96)
|||.+ .....+..+.+|+.+.+.+.=-
T Consensus 2 pDL~v-~~~~~~~~~~~g~~~~i~~~V~ 28 (101)
T PF07705_consen 2 PDLTV-SITVSPSNVVPGEPVTITVTVK 28 (101)
T ss_dssp --EEE--EEEC-SEEETTSEEEEEEEEE
T ss_pred CCEEE-EEeeCCCcccCCCEEEEEEEEE
Confidence 56666 3333346778888888877533
No 189
>PF11535 Calci_bind_CcbP: Calcium binding; InterPro: IPR020994 CcbP is a Ca(2+) binding protein found in bacteria which is thought to bind Ca(2+) by protein surface charge. When bound to Ca(2+), the protein becomes more compact and the level of free calcium decreases. Within the bacteria, Ca(2+) has a role in the early stages of heterocyst differentiation. The free Ca(2+) concentration which is regulated by CcbP is critical for the differentiation process []. Calcium signalling is widespread in bacterial species, and prokaryotic cells like eukaryotes are equipped with all the elements to maintain Ca2+ homeostasis [].; PDB: 2P0P_A 2K2V_A 2P0Q_A.
Probab=21.53 E-value=1.8e+02 Score=19.18 Aligned_cols=21 Identities=14% Similarity=0.238 Sum_probs=16.3
Q ss_pred HHHhhhCCCCCeEEEEEEEEcc
Q 034382 25 IEFLRRQPKERQYRALVLRFIK 46 (96)
Q Consensus 25 l~YL~~~~~~~~~~AvVl~~~~ 46 (96)
..||+++- .-.|+|.+++...
T Consensus 22 ~~yLee~L-~fPF~a~~~~~~~ 42 (106)
T PF11535_consen 22 YTYLEEHL-QFPFEATVIEEQE 42 (106)
T ss_dssp HHHHHHH---SSEEEEEEEEES
T ss_pred HHHHhhhc-CCceEEEEEeeec
Confidence 46899999 7899999999766
No 190
>cd05751 Ig1_LILRB1_like First immunoglobulin (Ig)-like domain found in Leukocyte Ig-like receptors (LILR)B1 (also known as LIR-1) and similar proteins. Ig1_LILRB1_like: domain similar to the first immunoglobulin (Ig)-like domain found in Leukocyte Ig-like receptors (LILR)B1 (also known as LIR-1). This group includes, LILRA5 (LIR9), an activating natural cytotoxicity receptor NKp46, and the immune-type receptor glycoprotein VI (GPVI). LILRs are a family of immunoreceptors expressed on expressed on T and B cells, on monocytes, dendritic cells, and subgroups of natural killer (NK) cells. The human LILR family contains nine proteins (LILRA1-3,and 5, and LILRB1-5). From functional assays, and as the cytoplasmic domains of various LILRs, for example LILRB1 (LIR-1), LILRB2 (LIR-2), and LILRB3 (LIR-3) contain immunoreceptor tyrosine-based inhibitory motifs (ITIMs) it is thought that LIR proteins are inhibitory receptors. Of the eight LIR family proteins, only LIR-1(LILRB1), and LIR-2 (LILRB2),
Probab=21.18 E-value=1.7e+02 Score=17.66 Aligned_cols=20 Identities=10% Similarity=0.114 Sum_probs=14.1
Q ss_pred CCCCCCCEEEEEEeeecCCC
Q 034382 67 VGAQIGDEVEVKVEEAHPRD 86 (96)
Q Consensus 67 ~~~~~Gd~v~v~v~~vdP~~ 86 (96)
.-+.+|+.|++++..-+|..
T Consensus 11 ~vV~~G~~VtL~C~~~~~~~ 30 (91)
T cd05751 11 SVVPLGKPVTLRCQGPYGAV 30 (91)
T ss_pred CccCCCCcEEEEEecCCCCC
Confidence 45788888888887655433
No 191
>PF10447 EXOSC1: Exosome component EXOSC1/CSL4; InterPro: IPR019495 The exosome mediates degradation of unstable mRNAs that contain AU-rich elements (AREs) within their 3' untranslated regions []. The proteins in this entry are components of the exosome 3'->5' exoribonuclease complex. They do not have exonuclease activity, but are required for the 3'-processing of the 7S pre-RNA to the mature 5.8S rRNA and for mRNA decay [, ].; PDB: 2NN6_I.
Probab=21.03 E-value=1.1e+02 Score=19.34 Aligned_cols=24 Identities=25% Similarity=0.472 Sum_probs=15.6
Q ss_pred CCCCCEEEEEEeeecCCCCeEEEE
Q 034382 69 AQIGDEVEVKVEEAHPRDDIIYLK 92 (96)
Q Consensus 69 ~~~Gd~v~v~v~~vdP~~~~l~l~ 92 (96)
+++||-|..||.++.|+.-...+.
T Consensus 2 P~vGdiV~~rVtrv~~~~a~v~Il 25 (82)
T PF10447_consen 2 PKVGDIVIARVTRVNPRQAKVEIL 25 (82)
T ss_dssp --TT-EEEEEEEEE-SSEEEEEEE
T ss_pred CCCCCEEEEEEEEEeccEEEEEEE
Confidence 478999999999998876555443
No 192
>smart00739 KOW KOW (Kyprides, Ouzounis, Woese) motif. Motif in ribosomal proteins, NusG, Spt5p, KIN17 and T54.
Probab=20.94 E-value=96 Score=14.43 Aligned_cols=12 Identities=33% Similarity=0.504 Sum_probs=9.2
Q ss_pred CCCCCEEEEEEe
Q 034382 69 AQIGDEVEVKVE 80 (96)
Q Consensus 69 ~~~Gd~v~v~v~ 80 (96)
+++||.+.|.-+
T Consensus 2 ~~~G~~V~I~~G 13 (28)
T smart00739 2 FEVGDTVRVIAG 13 (28)
T ss_pred CCCCCEEEEeEC
Confidence 578999888654
No 193
>cd03455 SAV4209 SAV4209 is a Streptomyces avermitilis protein with a hot dog fold that is similar to those of (R)-specific enoyl-CoA hydratase, the peroxisomal Hydratase-Dehydrogenase-Epimerase (HDE) protein, and the fatty acid synthase beta subunit. The alpha- and gamma-proteobacterial members of this CD have, in addition to a hot dog fold, an N-terminal extension.
Probab=20.89 E-value=2.4e+02 Score=17.94 Aligned_cols=23 Identities=9% Similarity=0.010 Sum_probs=17.2
Q ss_pred EEeecCCCCCCCEEEEEEeeecC
Q 034382 62 TAWVSVGAQIGDEVEVKVEEAHP 84 (96)
Q Consensus 62 ~~~~~~~~~~Gd~v~v~v~~vdP 84 (96)
.++...++.+||.|.++..-++-
T Consensus 73 ~~rf~~pv~~Gdtl~~~~~v~~~ 95 (123)
T cd03455 73 AFRLGAPLYAGDTLRFGGRVTAK 95 (123)
T ss_pred EEEeeccccCCCEEEEEEEEEee
Confidence 56666789999999887765543
No 194
>COG3269 Predicted RNA-binding protein, contains TRAM domain [General function prediction only]
Probab=20.74 E-value=2.3e+02 Score=17.73 Aligned_cols=51 Identities=24% Similarity=0.340 Sum_probs=30.8
Q ss_pred CCeEEEEEEEEccC--ceEEEEeecceeeEEEeecCCCCCCCEEEEEEeeecCCCCeEEE
Q 034382 34 ERQYRALVLRFIKD--RTAALLLVEVGLQATAWVSVGAQIGDEVEVKVEEAHPRDDIIYL 91 (96)
Q Consensus 34 ~~~~~AvVl~~~~~--~~~~vlL~dl~le~~~~~~~~~~~Gd~v~v~v~~vdP~~~~l~l 91 (96)
|.+++--+-+..+. +.+.+- |+-+-+ .+.++||.+.++|.++-|--..-..
T Consensus 16 Ge~y~V~I~d~g~~GDGiarve----GfvVFV---p~a~~Gd~V~vkI~~v~~~~afaev 68 (73)
T COG3269 16 GETYEVEIEDVGDQGDGIARVE----GFVVFV---PGAEVGDEVKVKITKVKPNFAFAEV 68 (73)
T ss_pred CCEEEEEEEEeccCCCceEEEE----EEEEEe---CCCCCCCeeeEEEEEeeccceeeEE
Confidence 44555555554443 344333 333333 3689999999999999876554433
No 195
>PF11874 DUF3394: Domain of unknown function (DUF3394); InterPro: IPR021814 This domain is functionally uncharacterised. This domain is found in bacteria. This presumed domain is about 190 amino acids in length. This domain is found associated with PF06808 from PFAM.
Probab=20.62 E-value=1.3e+02 Score=21.94 Aligned_cols=25 Identities=16% Similarity=0.161 Sum_probs=20.9
Q ss_pred CCCCCCCEEEEEEeeecCCCCeEEE
Q 034382 67 VGAQIGDEVEVKVEEAHPRDDIIYL 91 (96)
Q Consensus 67 ~~~~~Gd~v~v~v~~vdP~~~~l~l 91 (96)
..+.+|+.++++|+..|.-.+.++.
T Consensus 70 ~~~~~g~~lrl~V~G~~~~G~~~~k 94 (183)
T PF11874_consen 70 EQLPPGSSLRLRVEGPDFEGDPVTK 94 (183)
T ss_pred hcCCCCCEEEEEEEccCCCCCceEE
Confidence 4688999999999999997776654
No 196
>PRK00004 rplX 50S ribosomal protein L24; Reviewed
Probab=20.43 E-value=1.8e+02 Score=19.04 Aligned_cols=26 Identities=27% Similarity=0.405 Sum_probs=18.9
Q ss_pred CCCCCCEEEE----------EEeeecCCCCeEEEEE
Q 034382 68 GAQIGDEVEV----------KVEEAHPRDDIIYLKE 93 (96)
Q Consensus 68 ~~~~Gd~v~v----------~v~~vdP~~~~l~l~e 93 (96)
++..||+|.| +|.+|++..+.+.++-
T Consensus 4 ~i~kGD~V~Vi~G~dKGk~G~V~~V~~~~~~V~Veg 39 (105)
T PRK00004 4 KIKKGDTVIVIAGKDKGKRGKVLKVLPKKNKVIVEG 39 (105)
T ss_pred cccCCCEEEEeEcCCCCcEEEEEEEEcCCCEEEEcC
Confidence 5677888876 5777888888776653
No 197
>cd03446 MaoC_like MoaC_like Similar to the MaoC (monoamine oxidase C) dehydratase regulatory protein but without the N-terminal PutA domain. This protein family has a hot-dog fold similar to that of (R)-specific enoyl-CoA hydratase, the peroxisomal Hydratase-Dehydrogenase-Epimerase (HDE) protein, and the fatty acid synthase beta subunit.
Probab=20.38 E-value=1.7e+02 Score=18.80 Aligned_cols=21 Identities=19% Similarity=0.181 Sum_probs=15.4
Q ss_pred EEeecCCCCCCCEEEEEEeee
Q 034382 62 TAWVSVGAQIGDEVEVKVEEA 82 (96)
Q Consensus 62 ~~~~~~~~~~Gd~v~v~v~~v 82 (96)
.+++..++.+||.|.++..-+
T Consensus 84 ~~~f~~pv~~GD~l~~~~~v~ 104 (140)
T cd03446 84 NLRFLNPVFIGDTIRAEAEVV 104 (140)
T ss_pred eEEEcCCCCCCCEEEEEEEEE
Confidence 456667999999997766443
No 198
>COG1188 Ribosome-associated heat shock protein implicated in the recycling of the 50S subunit (S4 paralog) [Translation, ribosomal structure and biogenesis]
Probab=20.36 E-value=95 Score=20.59 Aligned_cols=18 Identities=17% Similarity=0.287 Sum_probs=14.0
Q ss_pred eecCCCCCCCEEEEEEee
Q 034382 64 WVSVGAQIGDEVEVKVEE 81 (96)
Q Consensus 64 ~~~~~~~~Gd~v~v~v~~ 81 (96)
..+..+++||.|.|++.+
T Consensus 44 KpS~~VK~GD~l~i~~~~ 61 (100)
T COG1188 44 KPSKEVKVGDILTIRFGN 61 (100)
T ss_pred ccccccCCCCEEEEEeCC
Confidence 344689999999998764
No 199
>KOG1816 consensus Ubiquitin fusion-degradation protein [Posttranslational modification, protein turnover, chaperones]
Probab=20.25 E-value=1.1e+02 Score=24.21 Aligned_cols=40 Identities=23% Similarity=0.230 Sum_probs=30.7
Q ss_pred CCeEEEEEEEEccCceEEEEeecceeeEEEeecCCCCCCCEEEEEE
Q 034382 34 ERQYRALVLRFIKDRTAALLLVEVGLQATAWVSVGAQIGDEVEVKV 79 (96)
Q Consensus 34 ~~~~~AvVl~~~~~~~~~vlL~dl~le~~~~~~~~~~~Gd~v~v~v 79 (96)
+++=.+=||++.. .-+.++||-.+|+. ..+++||.|+|+-
T Consensus 69 ~r~THcGVLEF~A-eEG~vyLP~WMmq~-----L~le~gdlv~i~~ 108 (308)
T KOG1816|consen 69 DRVTHCGVLEFTA-EEGRVYLPYWMMQN-----LLLEEGDLVRIRS 108 (308)
T ss_pred ceeeeeeEEEEEe-cCceEEeehHhhhh-----ccCCCCCeEEEEE
Confidence 3444688999999 88899999887763 4678899877653
No 200
>PRK10898 serine endoprotease; Provisional
Probab=20.17 E-value=4e+02 Score=20.74 Aligned_cols=43 Identities=23% Similarity=0.177 Sum_probs=26.4
Q ss_pred CCeEEEEEEEEccC-ceEEEEeecceeeEEEeec--CCCCCCCEEEE
Q 034382 34 ERQYRALVLRFIKD-RTAALLLVEVGLQATAWVS--VGAQIGDEVEV 77 (96)
Q Consensus 34 ~~~~~AvVl~~~~~-~~~~vlL~dl~le~~~~~~--~~~~~Gd~v~v 77 (96)
|.+++|-++..-.. ++|.+-+++..+.. +++. ..+++||.+..
T Consensus 111 g~~~~a~vv~~d~~~DlAvl~v~~~~l~~-~~l~~~~~~~~G~~V~a 156 (353)
T PRK10898 111 GRVFEALLVGSDSLTDLAVLKINATNLPV-IPINPKRVPHIGDVVLA 156 (353)
T ss_pred CCEEEEEEEEEcCCCCEEEEEEcCCCCCe-eeccCcCcCCCCCEEEE
Confidence 66788877754433 78888877654422 3332 45778877654
No 201
>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=20.14 E-value=4.2e+02 Score=20.54 Aligned_cols=43 Identities=23% Similarity=0.140 Sum_probs=28.1
Q ss_pred CCeEEEEEEEEccC-ceEEEEeecceeeEEEee--cCCCCCCCEEEE
Q 034382 34 ERQYRALVLRFIKD-RTAALLLVEVGLQATAWV--SVGAQIGDEVEV 77 (96)
Q Consensus 34 ~~~~~AvVl~~~~~-~~~~vlL~dl~le~~~~~--~~~~~~Gd~v~v 77 (96)
|.+++|-++..-.. ++|.+-+++-.+. .+++ +..+++||.+..
T Consensus 111 g~~~~a~vv~~d~~~DlAvlkv~~~~~~-~~~l~~s~~~~~G~~V~a 156 (351)
T TIGR02038 111 GRKFEAELVGSDPLTDLAVLKIEGDNLP-TIPVNLDRPPHVGDVVLA 156 (351)
T ss_pred CCEEEEEEEEecCCCCEEEEEecCCCCc-eEeccCcCccCCCCEEEE
Confidence 67788888865444 7888888765543 2233 256788887743
No 202
>PF14801 GCD14_N: tRNA methyltransferase complex GCD14 subunit N-term; PDB: 1I9G_A.
Probab=20.08 E-value=81 Score=18.70 Aligned_cols=18 Identities=22% Similarity=0.383 Sum_probs=8.6
Q ss_pred CCCCCCCEEEEEEeeecCCCCe
Q 034382 67 VGAQIGDEVEVKVEEAHPRDDI 88 (96)
Q Consensus 67 ~~~~~Gd~v~v~v~~vdP~~~~ 88 (96)
.++..||+|+++ ||..-.
T Consensus 4 Gpf~~GdrVQlT----D~Kgr~ 21 (54)
T PF14801_consen 4 GPFRAGDRVQLT----DPKGRK 21 (54)
T ss_dssp -S--TT-EEEEE----ETT--E
T ss_pred CCCCCCCEEEEc----cCCCCe
Confidence 578999998875 554443
Done!