Query 032460
Match_columns 140
No_of_seqs 129 out of 727
Neff 4.2
Searched_HMMs 46136
Date Fri Mar 29 14:22:57 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/032460.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/032460hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK12442 translation initiatio 100.0 1.6E-30 3.6E-35 187.0 10.5 75 63-137 1-75 (87)
2 COG0361 InfA Translation initi 100.0 7.6E-30 1.6E-34 179.2 9.5 75 63-137 1-75 (75)
3 TIGR00008 infA translation ini 100.0 6.7E-29 1.5E-33 171.5 9.6 68 65-132 1-68 (68)
4 CHL00010 infA translation init 99.9 9.1E-26 2E-30 157.8 11.2 78 63-140 1-78 (78)
5 PRK04012 translation initiatio 99.9 5.7E-25 1.2E-29 161.1 9.4 81 56-137 8-88 (100)
6 PRK00276 infA translation init 99.9 9E-24 1.9E-28 145.1 10.4 72 63-134 1-72 (72)
7 cd05793 S1_IF1A S1_IF1A: Trans 99.9 9.5E-24 2.1E-28 147.9 8.0 67 70-137 1-67 (77)
8 PTZ00329 eukaryotic translatio 99.9 4.2E-23 9E-28 161.7 8.9 78 59-137 22-99 (155)
9 smart00652 eIF1a eukaryotic tr 99.9 1.1E-22 2.4E-27 144.2 8.8 68 68-136 4-71 (83)
10 PLN00208 translation initiatio 99.9 1.2E-22 2.6E-27 157.7 9.0 78 59-137 22-99 (145)
11 cd04456 S1_IF1A_like S1_IF1A_l 99.9 1.6E-22 3.4E-27 142.1 8.3 66 71-137 2-68 (78)
12 TIGR00523 eIF-1A eukaryotic/ar 99.9 4.6E-22 9.9E-27 145.5 9.5 76 59-137 9-87 (99)
13 PF01176 eIF-1a: Translation i 99.9 4E-22 8.6E-27 134.6 7.8 64 68-132 2-65 (65)
14 cd04451 S1_IF1 S1_IF1: Transla 99.8 4.7E-18 1E-22 113.3 9.2 64 69-132 1-64 (64)
15 cd05792 S1_eIF1AD_like S1_eIF1 99.7 2.9E-16 6.3E-21 110.9 7.3 64 73-137 4-68 (78)
16 KOG3403 Translation initiation 99.5 6.6E-15 1.4E-19 113.3 -0.2 68 68-136 31-98 (145)
17 cd04466 S1_YloQ_GTPase S1_YloQ 99.0 1.9E-09 4.1E-14 70.8 8.1 62 72-136 2-63 (68)
18 PRK00098 GTPase RsgA; Reviewed 98.6 1.8E-07 4E-12 77.9 8.8 63 71-136 1-63 (298)
19 PRK12289 GTPase RsgA; Reviewed 98.5 6.2E-07 1.4E-11 77.4 8.2 66 70-136 8-79 (352)
20 cd01854 YjeQ_engC YjeQ/EngC. 98.4 1.6E-06 3.4E-11 72.0 8.1 60 73-136 1-60 (287)
21 PRK12288 GTPase RsgA; Reviewed 98.2 6.3E-06 1.4E-10 70.9 8.5 61 71-136 40-102 (347)
22 PRK01889 GTPase RsgA; Reviewed 97.9 4.8E-05 1E-09 65.3 7.9 60 71-136 29-92 (356)
23 COG1162 Predicted GTPases [Gen 97.9 3.2E-05 7E-10 66.5 6.6 64 70-137 4-70 (301)
24 KOG2925 Predicted translation 97.2 6.9E-05 1.5E-09 59.6 -0.5 62 71-133 24-89 (167)
25 cd05685 S1_Tex S1_Tex: The C-t 95.9 0.047 1E-06 34.3 6.3 59 70-130 3-66 (68)
26 cd00164 S1_like S1_like: Ribos 95.8 0.039 8.4E-07 33.8 5.5 58 72-130 2-63 (65)
27 cd05707 S1_Rrp5_repeat_sc11 S1 93.9 0.34 7.3E-06 31.4 6.3 60 70-130 3-66 (68)
28 PF04076 BOF: Bacterial OB fol 93.8 0.27 5.9E-06 36.2 6.2 55 62-118 30-84 (103)
29 PF11948 DUF3465: Protein of u 93.7 0.65 1.4E-05 36.1 8.4 67 69-136 39-114 (131)
30 PF12059 DUF3540: Protein of u 93.2 0.69 1.5E-05 37.6 8.3 62 71-138 2-63 (202)
31 cd05698 S1_Rrp5_repeat_hs6_sc5 93.2 0.63 1.4E-05 30.0 6.7 60 70-131 3-67 (70)
32 TIGR00638 Mop molybdenum-pteri 92.8 0.64 1.4E-05 29.9 6.3 52 70-122 8-62 (69)
33 smart00316 S1 Ribosomal protei 92.7 0.86 1.9E-05 28.1 6.6 61 70-132 5-70 (72)
34 cd05697 S1_Rrp5_repeat_hs5 S1_ 92.5 0.83 1.8E-05 29.6 6.6 61 70-131 3-67 (69)
35 PRK07252 hypothetical protein; 92.3 1.3 2.7E-05 33.1 8.1 66 70-137 6-76 (120)
36 cd05706 S1_Rrp5_repeat_sc10 S1 92.1 1.4 3.1E-05 28.6 7.3 59 70-130 6-69 (73)
37 cd05691 S1_RPS1_repeat_ec6 S1_ 91.9 1.4 3.1E-05 28.2 7.1 63 70-133 3-69 (73)
38 PF03459 TOBE: TOBE domain; I 91.6 0.53 1.2E-05 30.1 4.8 52 70-122 6-60 (64)
39 TIGR00156 conserved hypothetic 91.6 0.84 1.8E-05 35.0 6.6 56 62-119 53-108 (126)
40 PF07076 DUF1344: Protein of u 90.8 1.2 2.7E-05 30.5 6.1 46 70-120 4-49 (61)
41 cd04454 S1_Rrp4_like S1_Rrp4_l 90.8 1.9 4E-05 29.0 7.0 62 64-130 4-71 (82)
42 COG1098 VacB Predicted RNA bin 90.7 0.61 1.3E-05 36.2 5.0 58 70-130 8-70 (129)
43 PRK08582 hypothetical protein; 90.7 3.1 6.7E-05 31.7 8.9 63 70-135 8-75 (139)
44 cd05692 S1_RPS1_repeat_hs4 S1_ 90.5 2.7 5.8E-05 26.1 7.2 59 70-131 3-66 (69)
45 cd05704 S1_Rrp5_repeat_hs13 S1 90.3 2 4.4E-05 28.6 6.8 58 70-130 6-68 (72)
46 cd05789 S1_Rrp4 S1_Rrp4: Rrp4 90.2 3.4 7.3E-05 27.8 8.0 59 70-131 9-76 (86)
47 cd05688 S1_RPS1_repeat_ec3 S1_ 90.2 1.7 3.7E-05 27.2 6.1 57 70-130 4-66 (68)
48 PRK08059 general stress protei 90.1 2.3 5E-05 31.4 7.6 66 70-136 10-79 (123)
49 cd04461 S1_Rrp5_repeat_hs8_sc7 90.0 2.1 4.5E-05 28.8 6.8 59 70-130 17-80 (83)
50 cd04452 S1_IF2_alpha S1_IF2_al 90.0 3.1 6.8E-05 27.0 7.4 62 70-133 6-74 (76)
51 cd05696 S1_Rrp5_repeat_hs4 S1_ 89.8 2.8 6E-05 27.8 7.1 58 73-130 7-68 (71)
52 cd05705 S1_Rrp5_repeat_hs14 S1 89.6 3.2 6.9E-05 28.0 7.4 60 70-130 6-72 (74)
53 cd05690 S1_RPS1_repeat_ec5 S1_ 89.6 1.6 3.5E-05 27.8 5.7 60 70-130 3-67 (69)
54 PRK03987 translation initiatio 89.6 2.1 4.5E-05 36.1 7.8 70 62-134 4-80 (262)
55 cd04471 S1_RNase_R S1_RNase_R: 89.5 3.6 7.8E-05 27.0 7.5 62 70-132 4-81 (83)
56 PRK10053 hypothetical protein; 89.4 1.8 3.9E-05 33.3 6.7 55 63-119 58-112 (130)
57 cd05703 S1_Rrp5_repeat_hs12_sc 89.3 2.2 4.7E-05 28.6 6.4 61 70-131 3-69 (73)
58 PF00575 S1: S1 RNA binding do 89.2 2.3 5.1E-05 27.5 6.3 61 70-131 7-71 (74)
59 PF04717 Phage_base_V: Phage-r 89.1 2.1 4.6E-05 28.9 6.3 64 73-137 1-72 (79)
60 cd05687 S1_RPS1_repeat_ec1_hs1 88.9 2.7 5.9E-05 27.0 6.5 58 70-130 3-66 (70)
61 PHA02945 interferon resistance 88.9 3 6.5E-05 30.5 7.2 67 63-134 8-82 (88)
62 cd04472 S1_PNPase S1_PNPase: P 88.8 2.8 6.2E-05 26.3 6.4 58 70-130 3-65 (68)
63 PF15057 DUF4537: Domain of un 88.6 4.6 0.0001 30.3 8.3 66 65-131 9-80 (124)
64 cd05708 S1_Rrp5_repeat_sc12 S1 87.7 4.5 9.8E-05 26.0 7.0 63 70-134 5-73 (77)
65 cd04482 RPA2_OBF_like RPA2_OBF 86.8 2.2 4.9E-05 30.1 5.5 53 71-123 3-64 (91)
66 cd04455 S1_NusA S1_NusA: N-uti 86.7 5.3 0.00011 26.1 6.8 51 70-124 6-56 (67)
67 PF02736 Myosin_N: Myosin N-te 86.5 2 4.3E-05 26.5 4.5 33 64-97 7-39 (42)
68 cd05695 S1_Rrp5_repeat_hs3 S1_ 85.9 5.9 0.00013 25.9 6.8 58 70-130 3-64 (66)
69 cd05689 S1_RPS1_repeat_ec4 S1_ 85.8 6.9 0.00015 25.2 7.0 59 70-130 6-70 (72)
70 cd05791 S1_CSL4 S1_CSL4: CSL4, 85.2 3.3 7.2E-05 29.3 5.7 59 64-124 4-76 (92)
71 PF00313 CSD: 'Cold-shock' DNA 84.9 8 0.00017 25.0 7.0 51 71-121 1-53 (66)
72 PF12158 DUF3592: Protein of u 84.1 10 0.00022 27.3 7.9 62 68-130 36-113 (148)
73 cd04487 RecJ_OBF2_like RecJ_OB 82.7 7 0.00015 26.6 6.2 51 70-120 2-55 (73)
74 cd04453 S1_RNase_E S1_RNase_E: 82.6 7.9 0.00017 27.1 6.6 52 70-121 10-69 (88)
75 PRK07899 rpsA 30S ribosomal pr 82.3 5.9 0.00013 36.2 7.4 65 70-135 296-364 (486)
76 PTZ00248 eukaryotic translatio 82.2 7.8 0.00017 33.9 7.8 71 63-136 14-91 (319)
77 cd05684 S1_DHX8_helicase S1_DH 82.1 12 0.00026 24.7 7.3 63 70-135 3-73 (79)
78 PRK13806 rpsA 30S ribosomal pr 81.8 6.8 0.00015 35.3 7.5 66 69-135 294-364 (491)
79 cd04465 S1_RPS1_repeat_ec2_hs2 81.6 11 0.00025 24.1 6.9 57 70-130 3-63 (67)
80 cd05790 S1_Rrp40 S1_Rrp40: Rrp 81.2 5.5 0.00012 28.5 5.5 57 64-124 4-65 (86)
81 PRK05807 hypothetical protein; 81.2 12 0.00026 28.4 7.6 61 70-133 8-72 (136)
82 PRK13806 rpsA 30S ribosomal pr 80.5 5.7 0.00012 35.8 6.6 65 69-134 381-449 (491)
83 cd04486 YhcR_OBF_like YhcR_OBF 80.5 6.9 0.00015 27.0 5.6 48 71-118 2-54 (78)
84 cd05686 S1_pNO40 S1_pNO40: pNO 80.0 13 0.00028 24.5 6.7 58 70-130 6-69 (73)
85 PF10447 EXOSC1: Exosome compo 79.6 4.8 0.0001 28.6 4.7 51 64-116 2-64 (82)
86 TIGR00358 3_prime_RNase VacB a 79.4 6.6 0.00014 36.7 6.8 69 63-132 568-652 (654)
87 PF14444 S1-like: S1-like 78.9 4.6 0.0001 27.4 4.2 40 71-120 4-45 (58)
88 PF08402 TOBE_2: TOBE domain; 78.6 14 0.00029 23.2 6.6 51 70-122 17-70 (75)
89 cd04473 S1_RecJ_like S1_RecJ_l 77.9 18 0.00039 24.2 7.4 56 70-131 19-74 (77)
90 PRK12696 flgH flagellar basal 76.6 11 0.00025 31.4 6.8 59 69-133 150-213 (236)
91 cd05702 S1_Rrp5_repeat_hs11_sc 76.4 13 0.00029 24.1 5.9 54 70-125 3-63 (70)
92 PRK10354 RNA chaperone/anti-te 75.6 17 0.00037 24.5 6.3 51 71-121 5-57 (70)
93 PRK11824 polynucleotide phosph 75.3 14 0.00031 34.9 7.8 60 70-132 624-688 (693)
94 TIGR03591 polynuc_phos polyrib 73.3 9.7 0.00021 36.1 6.2 57 70-129 621-682 (684)
95 PRK12407 flgH flagellar basal 72.7 17 0.00036 30.2 6.8 59 69-133 134-197 (221)
96 PRK12700 flgH flagellar basal 72.0 17 0.00038 30.3 6.8 59 69-133 144-207 (230)
97 PRK00249 flgH flagellar basal 71.7 15 0.00032 30.4 6.2 58 69-132 136-198 (222)
98 PRK12788 flgH flagellar basal 71.6 17 0.00037 30.5 6.6 59 69-133 148-211 (234)
99 PRK06676 rpsA 30S ribosomal pr 71.5 23 0.0005 30.4 7.7 63 70-134 280-347 (390)
100 smart00318 SNc Staphylococcal 71.2 12 0.00025 27.1 5.0 59 70-129 2-82 (138)
101 PF01957 NfeD: NfeD-like C-ter 71.1 20 0.00044 25.6 6.3 42 69-118 90-131 (144)
102 COG1545 Predicted nucleic-acid 70.9 11 0.00024 28.8 5.0 47 85-134 89-137 (140)
103 PLN00207 polyribonucleotide nu 70.8 19 0.00041 35.7 7.6 59 73-134 760-823 (891)
104 PF13533 Biotin_lipoyl_2: Biot 70.5 2.6 5.6E-05 26.6 1.2 33 93-136 4-36 (50)
105 PRK12699 flgH flagellar basal 70.1 20 0.00043 30.3 6.8 59 69-134 161-224 (246)
106 PRK09890 cold shock protein Cs 70.1 25 0.00053 23.8 6.1 51 71-121 5-57 (70)
107 PRK12698 flgH flagellar basal 69.9 20 0.00044 29.7 6.7 59 69-133 137-200 (224)
108 PF08206 OB_RNB: Ribonuclease 69.8 15 0.00033 23.7 4.8 40 78-121 5-44 (58)
109 PRK12701 flgH flagellar basal 69.5 21 0.00044 29.9 6.7 59 69-133 143-206 (230)
110 PRK00087 4-hydroxy-3-methylbut 69.2 25 0.00053 32.9 7.8 68 69-137 564-635 (647)
111 TIGR02696 pppGpp_PNP guanosine 69.0 13 0.00029 35.8 6.1 58 70-129 650-715 (719)
112 PF12857 TOBE_3: TOBE-like dom 68.4 29 0.00062 22.3 6.4 47 71-119 7-57 (58)
113 PTZ00454 26S protease regulato 67.4 17 0.00036 32.2 6.1 47 70-118 67-113 (398)
114 PRK12697 flgH flagellar basal 67.2 25 0.00053 29.4 6.7 58 70-133 141-203 (226)
115 cd00319 Ribosomal_S12_like Rib 66.7 11 0.00025 27.8 4.1 32 83-118 37-68 (95)
116 TIGR02063 RNase_R ribonuclease 65.8 25 0.00054 33.1 7.2 64 68-132 628-707 (709)
117 COG1489 SfsA DNA-binding prote 65.6 37 0.0008 28.8 7.5 60 71-135 8-70 (235)
118 PF13742 tRNA_anti_2: OB-fold 65.1 45 0.00097 23.7 6.9 53 67-119 22-79 (99)
119 PF10844 DUF2577: Protein of u 64.9 49 0.0011 23.7 7.9 63 65-132 15-99 (100)
120 PRK15464 cold shock-like prote 64.8 29 0.00062 23.7 5.6 51 71-121 5-57 (70)
121 TIGR00981 rpsL_bact ribosomal 64.5 13 0.00028 28.7 4.2 32 83-118 52-83 (124)
122 PRK05163 rpsL 30S ribosomal pr 63.9 14 0.0003 28.6 4.3 32 83-118 52-83 (124)
123 cd04458 CSP_CDS Cold-Shock Pro 63.7 28 0.00061 22.3 5.2 51 72-122 2-54 (65)
124 COG0048 RpsL Ribosomal protein 63.4 14 0.00031 28.8 4.3 44 71-118 36-89 (129)
125 COG2063 FlgH Flagellar basal b 63.3 18 0.00039 30.5 5.2 58 69-132 147-209 (230)
126 TIGR00717 rpsA ribosomal prote 63.3 33 0.00071 30.5 7.1 64 69-133 274-342 (516)
127 PHA02858 EIF2a-like PKR inhibi 63.0 25 0.00055 25.6 5.3 66 63-132 13-84 (86)
128 smart00357 CSP Cold shock prot 62.3 29 0.00063 21.2 4.9 48 73-122 2-50 (64)
129 PRK10862 SoxR reducing system 62.2 9.6 0.00021 29.6 3.2 51 70-121 3-71 (154)
130 TIGR00358 3_prime_RNase VacB a 61.8 39 0.00085 31.7 7.7 64 70-137 16-82 (654)
131 cd03368 Ribosomal_S12 S12-like 61.3 17 0.00036 27.6 4.2 32 83-118 50-81 (108)
132 PRK11642 exoribonuclease R; Pr 60.6 40 0.00087 32.8 7.7 63 70-137 84-149 (813)
133 PRK07400 30S ribosomal protein 60.4 50 0.0011 28.3 7.5 66 70-137 199-268 (318)
134 COG3111 Periplasmic protein wi 60.2 54 0.0012 25.5 6.9 57 62-120 53-109 (128)
135 PF02107 FlgH: Flagellar L-rin 59.9 18 0.00039 28.7 4.4 59 69-133 94-157 (179)
136 PF01336 tRNA_anti-codon: OB-f 59.9 27 0.00059 21.9 4.6 49 70-118 2-54 (75)
137 CHL00141 rpl24 ribosomal prote 59.3 24 0.00052 25.0 4.6 30 106-135 6-35 (83)
138 PTZ00361 26 proteosome regulat 59.3 43 0.00092 30.2 7.2 57 70-133 105-161 (438)
139 TIGR02063 RNase_R ribonuclease 59.0 48 0.001 31.2 7.7 64 70-137 68-135 (709)
140 PRK06299 rpsA 30S ribosomal pr 58.2 41 0.0009 30.4 7.0 64 69-133 288-356 (565)
141 PRK10413 hydrogenase 2 accesso 58.1 39 0.00085 24.0 5.5 46 71-118 5-52 (82)
142 PRK11642 exoribonuclease R; Pr 57.9 51 0.0011 32.1 7.9 65 68-133 644-724 (813)
143 PRK09521 exosome complex RNA-b 57.9 43 0.00093 26.3 6.3 53 70-123 67-133 (189)
144 COG0539 RpsA Ribosomal protein 57.6 39 0.00084 31.8 6.8 68 69-137 279-350 (541)
145 PF00164 Ribosom_S12_S23: Ribo 57.0 22 0.00047 27.3 4.3 46 70-119 28-83 (122)
146 PRK10676 DNA-binding transcrip 57.0 33 0.00072 28.5 5.7 52 70-122 201-255 (263)
147 CHL00051 rps12 ribosomal prote 56.4 21 0.00046 27.6 4.1 32 83-118 52-83 (123)
148 PRK04163 exosome complex RNA-b 55.8 47 0.001 27.2 6.4 61 62-124 59-127 (235)
149 smart00739 KOW KOW (Kyprides, 55.6 30 0.00066 18.3 4.0 24 109-132 2-25 (28)
150 PF09038 53-BP1_Tudor: Tumour 55.6 45 0.00097 25.8 5.8 59 71-131 20-78 (122)
151 TIGR00717 rpsA ribosomal prote 54.4 56 0.0012 29.0 7.1 61 70-131 449-513 (516)
152 cd05693 S1_Rrp5_repeat_hs1_sc1 53.0 62 0.0013 23.1 5.9 60 70-130 6-91 (100)
153 PRK06299 rpsA 30S ribosomal pr 52.5 59 0.0013 29.4 7.0 64 69-133 375-443 (565)
154 PF01200 Ribosomal_S28e: Ribos 51.7 77 0.0017 22.2 6.0 40 71-117 9-58 (69)
155 PF11325 DUF3127: Domain of un 50.9 28 0.0006 25.0 3.8 13 108-120 52-64 (84)
156 PRK12327 nusA transcription el 50.6 79 0.0017 28.0 7.3 60 69-132 136-198 (362)
157 cd05694 S1_Rrp5_repeat_hs2_sc2 50.2 76 0.0016 21.3 7.5 62 70-134 7-69 (74)
158 PF08605 Rad9_Rad53_bind: Fung 50.2 41 0.00088 25.9 4.8 44 72-119 26-70 (131)
159 PTZ00067 40S ribosomal S23; Pr 49.6 37 0.0008 26.9 4.6 35 83-119 69-104 (143)
160 TIGR02381 cspD cold shock doma 48.0 45 0.00098 22.2 4.3 50 72-121 3-54 (68)
161 cd03367 Ribosomal_S23 S12-like 47.9 42 0.00091 25.7 4.5 35 83-119 44-79 (115)
162 PRK09202 nusA transcription el 47.6 66 0.0014 29.4 6.6 53 69-125 136-188 (470)
163 PF08661 Rep_fac-A_3: Replicat 47.5 69 0.0015 22.9 5.5 46 68-119 20-67 (109)
164 PF12869 tRNA_anti-like: tRNA_ 46.9 60 0.0013 23.5 5.2 54 65-118 66-126 (144)
165 smart00743 Agenet Tudor-like d 46.9 61 0.0013 20.4 4.6 23 68-90 17-39 (61)
166 COG1222 RPT1 ATP-dependent 26S 46.8 61 0.0013 29.6 6.1 47 70-118 73-119 (406)
167 TIGR01953 NusA transcription t 46.1 92 0.002 27.3 7.0 52 69-123 133-184 (341)
168 PRK05054 exoribonuclease II; P 45.5 1.1E+02 0.0025 28.7 7.9 62 70-132 564-642 (644)
169 PRK12269 bifunctional cytidyla 45.2 77 0.0017 31.3 6.9 65 69-134 754-825 (863)
170 PRK15463 cold shock-like prote 44.3 99 0.0021 20.9 5.6 51 71-121 5-57 (70)
171 PRK07400 30S ribosomal protein 44.2 79 0.0017 27.1 6.2 59 70-131 34-98 (318)
172 PF01796 DUF35: DUF35 OB-fold 44.1 76 0.0017 20.8 4.9 37 82-118 30-66 (68)
173 PRK04211 rps12P 30S ribosomal 44.0 47 0.001 26.4 4.4 35 83-119 70-105 (145)
174 cd04479 RPA3 RPA3: A subfamily 43.9 83 0.0018 22.5 5.4 46 67-118 16-61 (101)
175 TIGR00982 S23_S12_E_A ribosoma 43.9 48 0.001 26.1 4.4 34 83-118 64-98 (139)
176 PF08922 DUF1905: Domain of un 43.5 61 0.0013 22.3 4.5 27 92-119 54-80 (80)
177 PRK12281 rplX 50S ribosomal pr 43.2 62 0.0014 22.5 4.5 29 107-136 5-34 (76)
178 PRK12269 bifunctional cytidyla 42.5 79 0.0017 31.2 6.6 66 69-135 580-650 (863)
179 COG1585 Membrane protein impli 41.8 96 0.0021 23.8 5.8 41 70-118 88-128 (140)
180 PF00467 KOW: KOW motif; Inte 41.6 44 0.00095 19.1 3.0 26 111-136 1-26 (32)
181 TIGR02062 RNase_B exoribonucle 41.1 1.2E+02 0.0026 28.6 7.3 57 70-132 560-638 (639)
182 TIGR02062 RNase_B exoribonucle 40.8 1.6E+02 0.0034 27.8 8.1 61 70-136 18-79 (639)
183 PRK10676 DNA-binding transcrip 40.1 81 0.0018 26.2 5.5 53 70-123 129-185 (263)
184 TIGR03635 S17_bact 30S ribosom 40.1 1.2E+02 0.0027 20.8 5.6 44 71-120 4-60 (71)
185 PRK09507 cspE cold shock prote 40.0 1.1E+02 0.0025 20.4 6.3 51 71-121 4-56 (69)
186 PRK09974 putative regulator Pr 39.7 40 0.00086 25.5 3.3 24 96-120 20-43 (111)
187 PRK06676 rpsA 30S ribosomal pr 39.3 1.6E+02 0.0034 25.3 7.3 62 69-132 194-259 (390)
188 cd04460 S1_RpoE S1_RpoE: RpoE, 39.0 91 0.002 21.6 4.9 53 71-124 3-69 (99)
189 PF13437 HlyD_3: HlyD family s 38.5 1.3E+02 0.0027 20.5 6.3 53 80-135 24-79 (105)
190 COG1185 Pnp Polyribonucleotide 38.1 73 0.0016 31.0 5.5 59 70-130 622-684 (692)
191 PRK05054 exoribonuclease II; P 37.8 1.9E+02 0.0041 27.3 8.1 61 70-136 21-82 (644)
192 PRK01191 rpl24p 50S ribosomal 37.8 69 0.0015 24.5 4.4 30 106-135 43-72 (120)
193 PF01455 HupF_HypC: HupF/HypC 37.7 51 0.0011 22.4 3.3 41 71-118 5-47 (68)
194 PRK10943 cold shock-like prote 37.7 1.3E+02 0.0027 20.2 5.8 51 71-121 4-56 (69)
195 cd04489 ExoVII_LU_OBF ExoVII_L 37.4 1.1E+02 0.0024 19.6 7.2 49 71-119 4-56 (78)
196 PRK12329 nusA transcription el 37.3 1E+02 0.0022 28.5 6.1 54 68-122 153-209 (449)
197 PF00717 Peptidase_S24: Peptid 37.2 22 0.00048 22.5 1.4 13 108-120 24-36 (70)
198 cd06530 S26_SPase_I The S26 Ty 37.1 35 0.00075 22.6 2.4 12 109-120 32-43 (85)
199 PF11604 CusF_Ec: Copper bindi 36.9 52 0.0011 22.1 3.3 24 109-132 43-66 (70)
200 COG0557 VacB Exoribonuclease R 36.5 1.1E+02 0.0024 29.0 6.3 69 63-132 618-702 (706)
201 COG1093 SUI2 Translation initi 36.5 87 0.0019 27.1 5.2 70 62-132 7-81 (269)
202 TIGR00237 xseA exodeoxyribonuc 36.3 2.4E+02 0.0052 25.2 8.2 51 68-118 19-73 (432)
203 PRK00004 rplX 50S ribosomal pr 36.2 85 0.0018 23.0 4.5 28 108-136 4-32 (105)
204 COG3086 RseC Positive regulato 35.3 25 0.00054 28.1 1.7 50 72-123 5-73 (150)
205 smart00532 LIGANc Ligase N fam 35.0 1.2E+02 0.0026 27.5 6.2 90 23-120 272-374 (441)
206 PRK00087 4-hydroxy-3-methylbut 34.8 1.4E+02 0.0031 27.9 6.8 64 69-134 479-546 (647)
207 PRK00286 xseA exodeoxyribonucl 34.1 2.9E+02 0.0062 24.3 8.2 52 67-118 24-79 (438)
208 smart00306 HintN Hint (Hedgeho 33.8 1.1E+02 0.0025 20.0 4.6 33 85-117 65-98 (100)
209 cd04508 TUDOR Tudor domains ar 33.7 1E+02 0.0023 18.1 4.0 28 68-95 12-40 (48)
210 PRK12328 nusA transcription el 33.2 1.3E+02 0.0028 27.1 6.0 49 69-120 140-188 (374)
211 PRK11607 potG putrescine trans 33.1 1.8E+02 0.0039 25.4 6.8 51 71-121 316-369 (377)
212 TIGR00051 acyl-CoA thioester h 32.7 57 0.0012 22.0 3.0 25 109-133 62-86 (117)
213 TIGR01079 rplX_bact ribosomal 32.7 1E+02 0.0022 22.6 4.5 29 108-136 3-31 (104)
214 TIGR01843 type_I_hlyD type I s 32.5 1.9E+02 0.0042 24.1 6.7 53 81-136 298-356 (423)
215 PRK07899 rpsA 30S ribosomal pr 32.1 1.9E+02 0.0041 26.6 7.0 58 68-130 123-184 (486)
216 COG0298 HypC Hydrogenase matur 30.7 1.6E+02 0.0034 21.4 5.0 44 71-118 5-48 (82)
217 PRK09937 stationary phase/star 30.2 1.1E+02 0.0024 21.0 4.1 49 72-121 3-54 (74)
218 PF01302 CAP_GLY: CAP-Gly doma 30.2 62 0.0014 21.7 2.8 22 111-134 1-22 (69)
219 TIGR00230 sfsA sugar fermentat 29.9 2.4E+02 0.0051 23.5 6.7 46 71-121 10-58 (232)
220 KOG1999 RNA polymerase II tran 29.8 1.3E+02 0.0029 30.5 5.9 74 59-134 523-607 (1024)
221 PF04246 RseC_MucC: Positive r 29.8 44 0.00096 24.6 2.2 16 106-121 49-64 (135)
222 PF11518 DUF3221: Protein of u 29.7 2.2E+02 0.0049 20.7 6.3 51 67-120 21-90 (108)
223 PTZ00115 40S ribosomal protein 29.6 83 0.0018 27.5 4.0 45 70-118 125-179 (290)
224 COG2047 Uncharacterized protei 29.5 58 0.0013 28.0 3.0 31 16-50 50-80 (258)
225 PRK06461 single-stranded DNA-b 29.3 2.4E+02 0.0052 20.9 6.3 48 67-118 15-74 (129)
226 TIGR02754 sod_Ni_protease nick 29.3 71 0.0015 21.5 3.0 8 111-118 32-39 (90)
227 COG1363 FrvX Cellulase M and r 29.0 1.8E+02 0.0038 25.9 6.1 25 109-133 154-178 (355)
228 PF02362 B3: B3 DNA binding do 29.0 1.8E+02 0.0039 19.4 6.5 12 109-120 74-85 (100)
229 PF02598 Methyltrn_RNA_3: Puta 28.9 1.4E+02 0.003 25.5 5.2 50 70-130 117-168 (291)
230 TIGR03406 FeS_long_SufT probab 28.6 1.2E+02 0.0026 24.2 4.6 41 54-102 11-51 (174)
231 PRK04007 rps28e 30S ribosomal 28.6 2.1E+02 0.0046 20.1 5.6 40 72-118 8-58 (70)
232 PRK14998 cold shock-like prote 28.5 1.2E+02 0.0027 20.6 4.1 50 72-122 3-55 (73)
233 PF04014 Antitoxin-MazE: Antid 28.4 71 0.0015 19.5 2.6 26 94-120 7-32 (47)
234 PRK12278 50S ribosomal protein 28.2 3.2E+02 0.0069 22.8 7.1 30 109-138 53-82 (221)
235 PF02359 CDC48_N: Cell divisio 28.1 37 0.0008 23.3 1.4 28 93-123 58-85 (87)
236 COG2524 Predicted transcriptio 27.5 74 0.0016 27.9 3.4 40 90-133 112-153 (294)
237 PF13550 Phage-tail_3: Putativ 27.2 92 0.002 22.6 3.5 34 97-131 128-161 (164)
238 cd03698 eRF3_II_like eRF3_II_l 27.1 2E+02 0.0043 19.2 4.9 24 108-131 56-82 (83)
239 PRK09961 exoaminopeptidase; Pr 26.9 1.3E+02 0.0027 26.0 4.7 25 109-133 140-164 (344)
240 TIGR02988 YaaA_near_RecF S4 do 26.8 72 0.0016 20.2 2.5 14 104-117 45-58 (59)
241 PF03749 SfsA: Sugar fermentat 26.7 2.7E+02 0.0058 22.9 6.4 46 82-130 5-56 (215)
242 PF07359 LEAP-2: Liver-express 26.6 26 0.00056 25.1 0.4 17 41-57 36-52 (77)
243 COG1792 MreC Cell shape-determ 26.3 1.6E+02 0.0035 24.9 5.2 30 71-104 156-186 (284)
244 CHL00207 rpoB RNA polymerase b 26.2 1.8E+02 0.0039 29.6 6.2 14 5-18 539-552 (1077)
245 TIGR03689 pup_AAA proteasome A 26.2 1.4E+02 0.0031 27.6 5.2 45 73-119 110-154 (512)
246 PRK10861 signal peptidase I; P 25.7 86 0.0019 27.4 3.5 11 109-119 96-106 (324)
247 PRK03598 putative efflux pump 25.6 1.4E+02 0.0031 24.8 4.7 52 81-135 229-282 (331)
248 cd04474 RPA1_DBD_A RPA1_DBD_A: 25.3 2.5E+02 0.0054 19.8 6.3 33 86-118 41-74 (104)
249 cd04715 BAH_Orc1p_like BAH, or 25.3 1.2E+02 0.0027 23.7 4.0 11 108-118 29-39 (159)
250 COG1278 CspC Cold shock protei 25.1 2E+02 0.0042 19.9 4.5 51 71-121 2-54 (67)
251 cd03693 EF1_alpha_II EF1_alpha 25.1 2.3E+02 0.005 19.3 5.2 26 108-133 60-88 (91)
252 COG0539 RpsA Ribosomal protein 25.0 1.8E+02 0.0039 27.5 5.6 66 70-136 195-263 (541)
253 COG1570 XseA Exonuclease VII, 24.6 2.3E+02 0.0049 26.2 6.1 51 68-118 25-79 (440)
254 PF14890 Intein_splicing: Inte 24.4 1.2E+02 0.0025 25.3 4.0 38 81-118 50-92 (323)
255 cd06462 Peptidase_S24_S26 The 24.3 98 0.0021 19.7 2.8 13 108-120 28-40 (84)
256 KOG1214 Nidogen and related ba 24.2 1.8E+02 0.0039 29.8 5.7 72 29-104 1027-1103(1289)
257 TIGR02609 doc_partner putative 24.2 1.6E+02 0.0035 19.9 4.0 40 91-135 7-46 (74)
258 PTZ00202 tuzin; Provisional 24.1 1.3E+02 0.0028 28.6 4.5 68 27-95 18-90 (550)
259 TIGR02851 spore_V_T stage V sp 24.1 73 0.0016 25.3 2.6 23 97-120 16-38 (180)
260 cd00165 S4 S4/Hsp/ tRNA synthe 24.1 1.4E+02 0.003 17.6 3.4 14 106-119 39-52 (70)
261 smart00675 DM11 Domains in hyp 23.9 44 0.00094 26.5 1.3 41 82-127 33-74 (164)
262 PTZ00194 60S ribosomal protein 23.9 1E+02 0.0022 24.3 3.2 31 105-135 43-73 (143)
263 PRK06763 F0F1 ATP synthase sub 23.7 3.5E+02 0.0075 22.8 6.5 46 71-119 120-175 (213)
264 PF03658 Ub-RnfH: RnfH family 23.6 50 0.0011 23.7 1.4 21 97-117 50-70 (84)
265 cd04713 BAH_plant_3 BAH, or Br 23.6 2.1E+02 0.0046 21.7 5.0 30 68-99 13-43 (146)
266 TIGR00575 dnlj DNA ligase, NAD 23.4 2.2E+02 0.0048 27.1 5.9 91 22-120 264-367 (652)
267 TIGR00074 hypC_hupF hydrogenas 23.3 1.3E+02 0.0029 21.0 3.5 41 71-118 5-45 (76)
268 KOG3409 Exosomal 3'-5' exoribo 23.2 2.9E+02 0.0062 22.9 5.8 57 62-120 64-134 (193)
269 PF09874 DUF2101: Predicted me 23.2 1.9E+02 0.0041 24.2 4.9 46 72-120 146-193 (206)
270 PRK03992 proteasome-activating 22.6 2.8E+02 0.0061 24.1 6.1 46 71-118 54-99 (389)
271 PRK14132 riboflavin kinase; Pr 22.4 81 0.0018 24.2 2.5 20 70-89 2-21 (126)
272 TIGR01080 rplX_A_E ribosomal p 22.4 1.8E+02 0.0039 21.9 4.2 28 107-134 40-67 (114)
273 PRK11144 modC molybdate transp 22.3 2.8E+02 0.0061 23.6 6.0 49 71-120 296-346 (352)
274 PRK00347 putative DNA-binding 22.1 4.6E+02 0.0099 21.7 7.4 46 71-121 8-57 (234)
275 PF01828 Peptidase_A4: Peptida 22.0 69 0.0015 26.1 2.1 27 106-132 88-114 (208)
276 PRK07956 ligA NAD-dependent DN 21.9 2.6E+02 0.0056 26.7 6.1 91 22-120 276-379 (665)
277 PF01245 Ribosomal_L19: Riboso 21.9 96 0.0021 23.2 2.7 29 107-135 17-52 (113)
278 PRK09774 fec operon regulator 21.8 1.8E+02 0.004 24.5 4.7 47 71-118 172-225 (319)
279 PRK11507 ribosome-associated p 21.7 59 0.0013 22.7 1.4 12 107-118 51-62 (70)
280 PRK12370 invasion protein regu 21.6 74 0.0016 28.6 2.4 35 97-137 185-221 (553)
281 PRK10800 acyl-CoA thioesterase 21.3 1.1E+02 0.0023 21.7 2.8 20 109-128 67-86 (130)
282 PF07116 DUF1372: Protein of u 21.3 2.1E+02 0.0045 21.6 4.3 44 66-115 53-98 (104)
283 PRK05889 putative acetyl-CoA c 21.1 53 0.0011 21.6 1.1 20 94-115 5-24 (71)
284 PF10610 Tafi-CsgC: Thin aggre 21.0 94 0.002 23.5 2.5 33 100-135 69-101 (106)
285 TIGR02228 sigpep_I_arch signal 20.8 88 0.0019 24.3 2.4 12 108-119 60-71 (158)
286 PTZ00085 40S ribosomal protein 20.5 3.2E+02 0.007 19.4 5.5 40 72-118 12-63 (73)
287 TIGR00998 8a0101 efflux pump m 20.4 3E+02 0.0064 22.6 5.6 51 82-135 231-284 (334)
288 PRK10409 hydrogenase assembly 20.3 1.5E+02 0.0032 21.5 3.3 42 72-118 6-51 (90)
289 COG3908 Uncharacterized protei 20.1 1.7E+02 0.0038 20.8 3.5 26 75-102 14-39 (77)
290 KOG1999 RNA polymerase II tran 20.1 2.7E+02 0.0058 28.5 6.0 26 109-134 460-485 (1024)
291 PF06068 TIP49: TIP49 C-termin 20.0 1.5E+02 0.0032 27.1 3.9 60 65-130 112-187 (398)
No 1
>PRK12442 translation initiation factor IF-1; Reviewed
Probab=99.97 E-value=1.6e-30 Score=187.00 Aligned_cols=75 Identities=41% Similarity=0.673 Sum_probs=72.1
Q ss_pred ccCCcceEEEEEEEEeCCCceEEEEeCCCCEEEEEecccccccccccCCCCEEEEEeccCCCCeEEEEEEecCCC
Q 032460 63 GANSEKWVHEGFITESLPNGMFRVRLDNEDLILGYISGKIRQNFIRVLPGDRVRVEVSRYDTSKGRIIYRLRNKI 137 (140)
Q Consensus 63 ~~k~d~ie~~GvVik~l~n~~f~V~l~dG~~~lcrI~GKmRk~~IrI~vGDrV~VE~sp~D~~kGrIiyRy~r~~ 137 (140)
|+++|.++++|+|+++|||++|+|+|+||++++|+|+||||+++|||++||+|+||+||||+++|+|+|||+.+.
T Consensus 1 M~ke~~ie~~G~V~e~Lp~~~frV~LenG~~vla~isGKmR~~rIrIl~GD~V~VE~spYDltkGRIiyR~~~~~ 75 (87)
T PRK12442 1 MAKEELIELDGIVDEVLPDSRFRVTLENGVEVGAYASGRMRKHRIRILAGDRVTLELSPYDLTKGRINFRHKDER 75 (87)
T ss_pred CCccceEEEEEEEEEECCCCEEEEEeCCCCEEEEEeccceeeeeEEecCCCEEEEEECcccCCceeEEEEecCCC
Confidence 678899999999999999999999999999999999999999999999999999999999999999999998643
No 2
>COG0361 InfA Translation initiation factor 1 (IF-1) [Translation, ribosomal structure and biogenesis]
Probab=99.96 E-value=7.6e-30 Score=179.24 Aligned_cols=75 Identities=51% Similarity=0.765 Sum_probs=71.4
Q ss_pred ccCCcceEEEEEEEEeCCCceEEEEeCCCCEEEEEecccccccccccCCCCEEEEEeccCCCCeEEEEEEecCCC
Q 032460 63 GANSEKWVHEGFITESLPNGMFRVRLDNEDLILGYISGKIRQNFIRVLPGDRVRVEVSRYDTSKGRIIYRLRNKI 137 (140)
Q Consensus 63 ~~k~d~ie~~GvVik~l~n~~f~V~l~dG~~~lcrI~GKmRk~~IrI~vGDrV~VE~sp~D~~kGrIiyRy~r~~ 137 (140)
|+++|.++++|+|+++|||++|+|+|+||++++|||+||||+++|||++||+|+||+||||+++|+|+|||.+.+
T Consensus 1 m~~~d~~e~~g~V~e~L~~~~f~v~~edg~~~~ahI~GKmr~~~i~I~~GD~V~Ve~~~~d~~kg~I~~Ry~~~~ 75 (75)
T COG0361 1 MAKPDEIEMEGTVIEMLPNGRFRVELENGHERLAHISGKMRKNRIRILPGDVVLVELSPYDLTKGRIVYRYKKDE 75 (75)
T ss_pred CccccccEEEEEEEEecCCCEEEEEecCCcEEEEEccCcchheeEEeCCCCEEEEEecccccccccEEEEecCCC
Confidence 346688999999999999999999999999999999999999999999999999999999999999999998864
No 3
>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=99.96 E-value=6.7e-29 Score=171.47 Aligned_cols=68 Identities=57% Similarity=0.954 Sum_probs=66.2
Q ss_pred CCcceEEEEEEEEeCCCceEEEEeCCCCEEEEEecccccccccccCCCCEEEEEeccCCCCeEEEEEE
Q 032460 65 NSEKWVHEGFITESLPNGMFRVRLDNEDLILGYISGKIRQNFIRVLPGDRVRVEVSRYDTSKGRIIYR 132 (140)
Q Consensus 65 k~d~ie~~GvVik~l~n~~f~V~l~dG~~~lcrI~GKmRk~~IrI~vGDrV~VE~sp~D~~kGrIiyR 132 (140)
+++.++++|+|+++|||++|+|+|+||++++|||+||||+++|||.+||+|+||+||||+++|||+||
T Consensus 1 k~~~ie~~G~V~e~L~~~~f~V~l~ng~~vla~i~GKmr~~rI~I~~GD~V~Ve~spyd~tkgrIi~R 68 (68)
T TIGR00008 1 KEDKIEMEGKVTESLPNAMFRVELENGHEVLAHISGKIRMHYIRILPGDKVKVELSPYDLTRGRITYR 68 (68)
T ss_pred CCcEEEEEEEEEEECCCCEEEEEECCCCEEEEEecCcchhccEEECCCCEEEEEECcccCCcEeEEeC
Confidence 46789999999999999999999999999999999999999999999999999999999999999997
No 4
>CHL00010 infA translation initiation factor 1
Probab=99.93 E-value=9.1e-26 Score=157.81 Aligned_cols=78 Identities=69% Similarity=1.044 Sum_probs=75.3
Q ss_pred ccCCcceEEEEEEEEeCCCceEEEEeCCCCEEEEEecccccccccccCCCCEEEEEeccCCCCeEEEEEEecCCCCCC
Q 032460 63 GANSEKWVHEGFITESLPNGMFRVRLDNEDLILGYISGKIRQNFIRVLPGDRVRVEVSRYDTSKGRIIYRLRNKISSD 140 (140)
Q Consensus 63 ~~k~d~ie~~GvVik~l~n~~f~V~l~dG~~~lcrI~GKmRk~~IrI~vGDrV~VE~sp~D~~kGrIiyRy~r~~~~~ 140 (140)
|++++.++++|+|++.+|+++|.|+|+||+.++|+++||||++++||++||+|+||+|++++++|+|+|||+.+.++|
T Consensus 1 m~~~~~~~~~G~Vik~lg~~~y~V~~~~g~~~~c~~rGklr~~~i~~~vGD~V~ve~~~~~~~~g~Ii~r~~~~~~~~ 78 (78)
T CHL00010 1 MKKENKIEMEGLVTESLPNGMFRVRLDNGCQVLGYISGKIRRNSIRILPGDRVKVELSPYDLTKGRIIYRLRNKDSND 78 (78)
T ss_pred CCccceEEEEEEEEEEcCCCEEEEEeCCCCEEEEEeccceecCCcccCCCCEEEEEEcccCCCeEEEEEEecCCCCCC
Confidence 789999999999999999999999999999999999999999889999999999999999999999999999999886
No 5
>PRK04012 translation initiation factor IF-1A; Provisional
Probab=99.92 E-value=5.7e-25 Score=161.13 Aligned_cols=81 Identities=22% Similarity=0.243 Sum_probs=75.2
Q ss_pred CCcccccccCCcceEEEEEEEEeCCCceEEEEeCCCCEEEEEecccccccccccCCCCEEEEEeccCCCCeEEEEEEecC
Q 032460 56 GDRSSEEGANSEKWVHEGFITESLPNGMFRVRLDNEDLILGYISGKIRQNFIRVLPGDRVRVEVSRYDTSKGRIIYRLRN 135 (140)
Q Consensus 56 ~~~~~~~~~k~d~ie~~GvVik~l~n~~f~V~l~dG~~~lcrI~GKmRk~~IrI~vGDrV~VE~sp~D~~kGrIiyRy~r 135 (140)
......+++.++..++.|+|++++||+.|+|+|+||++++|+|+||||+ +|||.+||+|+|++|+||+++|+|+|||..
T Consensus 8 ~~~~~~~~~~p~e~e~~g~V~~~lG~~~~~V~~~dG~~~la~i~GK~Rk-~IwI~~GD~VlVe~~~~~~~kg~Iv~r~~~ 86 (100)
T PRK04012 8 EEVTRVRLPMPEEGEVFGVVEQMLGANRVRVRCMDGVERMGRIPGKMKK-RMWIREGDVVIVAPWDFQDEKADIIWRYTK 86 (100)
T ss_pred CCceeEEccCCCCCEEEEEEEEEcCCCEEEEEeCCCCEEEEEEchhhcc-cEEecCCCEEEEEecccCCCEEEEEEEcCH
Confidence 3347778889889999999999999999999999999999999999998 899999999999999999999999999976
Q ss_pred CC
Q 032460 136 KI 137 (140)
Q Consensus 136 ~~ 137 (140)
.+
T Consensus 87 ~q 88 (100)
T PRK04012 87 PQ 88 (100)
T ss_pred HH
Confidence 53
No 6
>PRK00276 infA translation initiation factor IF-1; Validated
Probab=99.91 E-value=9e-24 Score=145.14 Aligned_cols=72 Identities=53% Similarity=0.871 Sum_probs=68.9
Q ss_pred ccCCcceEEEEEEEEeCCCceEEEEeCCCCEEEEEecccccccccccCCCCEEEEEeccCCCCeEEEEEEec
Q 032460 63 GANSEKWVHEGFITESLPNGMFRVRLDNEDLILGYISGKIRQNFIRVLPGDRVRVEVSRYDTSKGRIIYRLR 134 (140)
Q Consensus 63 ~~k~d~ie~~GvVik~l~n~~f~V~l~dG~~~lcrI~GKmRk~~IrI~vGDrV~VE~sp~D~~kGrIiyRy~ 134 (140)
|++++.++++|+|++.+++++|.|+|+||+.++|+++||+|++++|+++||+|+||+|++++++|+|+|||+
T Consensus 1 ~~~~~~~~~~G~Vi~~~~~~~y~V~~~~g~~~~c~~~Gklr~~~i~i~vGD~V~ve~~~~~~~~g~Iv~r~~ 72 (72)
T PRK00276 1 MAKEDVIEMEGTVVEALPNAMFRVELENGHEVLAHISGKMRKNYIRILPGDKVTVELSPYDLTKGRITYRHK 72 (72)
T ss_pred CCccceEEEEEEEEEEcCCCEEEEEeCCCCEEEEEEccceeeCCcccCCCCEEEEEEcccCCCeEEEEEEeC
Confidence 678899999999999998889999999999999999999998899999999999999999999999999995
No 7
>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=99.90 E-value=9.5e-24 Score=147.86 Aligned_cols=67 Identities=28% Similarity=0.346 Sum_probs=63.5
Q ss_pred EEEEEEEEeCCCceEEEEeCCCCEEEEEecccccccccccCCCCEEEEEeccCCCCeEEEEEEecCCC
Q 032460 70 VHEGFITESLPNGMFRVRLDNEDLILGYISGKIRQNFIRVLPGDRVRVEVSRYDTSKGRIIYRLRNKI 137 (140)
Q Consensus 70 e~~GvVik~l~n~~f~V~l~dG~~~lcrI~GKmRk~~IrI~vGDrV~VE~sp~D~~kGrIiyRy~r~~ 137 (140)
++.|+|++++||+.|+|+|+||++++|+|+||||+ ++||.+||+|+||+||||+++|+|+|||...+
T Consensus 1 e~~g~V~~~~g~~~~~V~~~~g~~~la~i~gK~rk-~iwI~~GD~V~Ve~~~~d~~kg~Iv~r~~~~~ 67 (77)
T cd05793 1 EEYGQVEKMLGNGRLEVRCFDGKKRLCRIRGKMRK-RVWINEGDIVLVAPWDFQDDKADIIYKYTPDE 67 (77)
T ss_pred CEEEEEEEEcCCCEEEEEECCCCEEEEEEchhhcc-cEEEcCCCEEEEEeccccCCEEEEEEEcCHHH
Confidence 47899999999999999999999999999999997 79999999999999999999999999997643
No 8
>PTZ00329 eukaryotic translation initiation factor 1A; Provisional
Probab=99.89 E-value=4.2e-23 Score=161.70 Aligned_cols=78 Identities=21% Similarity=0.187 Sum_probs=72.8
Q ss_pred ccccccCCcceEEEEEEEEeCCCceEEEEeCCCCEEEEEecccccccccccCCCCEEEEEeccCCCCeEEEEEEecCCC
Q 032460 59 SSEEGANSEKWVHEGFITESLPNGMFRVRLDNEDLILGYISGKIRQNFIRVLPGDRVRVEVSRYDTSKGRIIYRLRNKI 137 (140)
Q Consensus 59 ~~~~~~k~d~ie~~GvVik~l~n~~f~V~l~dG~~~lcrI~GKmRk~~IrI~vGDrV~VE~sp~D~~kGrIiyRy~r~~ 137 (140)
+..+++.++..++.|+|++++||++|+|+|+||++++|+|+||||+ +|||.+||+|+|++|||++++|+|+|||...+
T Consensus 22 ~~rel~~~eegq~~g~V~~~LGn~~f~V~c~dG~~rLa~I~GKmRK-~IWI~~GD~VlVel~~yd~~KgdIi~Ry~~de 99 (155)
T PTZ00329 22 EKRELVFKEEGQEYAQVLRMLGNGRLEAYCFDGVKRLCHIRGKMRK-RVWINIGDIILVSLRDFQDSKADVILKYTPDE 99 (155)
T ss_pred ceeeeccCCCCcEEEEEEEEcCCCEEEEEECCCCEEEEEeecccee-eEEecCCCEEEEeccCCCCCEEEEEEEcCHHH
Confidence 5667787788899999999999999999999999999999999998 59999999999999999999999999997654
No 9
>smart00652 eIF1a eukaryotic translation initiation factor 1A.
Probab=99.88 E-value=1.1e-22 Score=144.23 Aligned_cols=68 Identities=25% Similarity=0.326 Sum_probs=64.8
Q ss_pred ceEEEEEEEEeCCCceEEEEeCCCCEEEEEecccccccccccCCCCEEEEEeccCCCCeEEEEEEecCC
Q 032460 68 KWVHEGFITESLPNGMFRVRLDNEDLILGYISGKIRQNFIRVLPGDRVRVEVSRYDTSKGRIIYRLRNK 136 (140)
Q Consensus 68 ~ie~~GvVik~l~n~~f~V~l~dG~~~lcrI~GKmRk~~IrI~vGDrV~VE~sp~D~~kGrIiyRy~r~ 136 (140)
..++.|+|++++||+.|+|+|+||++++|+|+||||+ +|||.+||+|+|++||||+++|+|+|||...
T Consensus 4 e~q~~g~V~~~lG~~~~~V~~~dG~~~la~ipgK~Rk-~iwI~~GD~VlVe~~~~~~~kg~Iv~r~~~~ 71 (83)
T smart00652 4 DGQEIAQVVKMLGNGRLEVMCADGKERLARIPGKMRK-KVWIRRGDIVLVDPWDFQDVKADIIYKYTKD 71 (83)
T ss_pred CCcEEEEEEEEcCCCEEEEEECCCCEEEEEEchhhcc-cEEEcCCCEEEEEecCCCCCEEEEEEEeCHH
Confidence 4578999999999999999999999999999999997 8999999999999999999999999999764
No 10
>PLN00208 translation initiation factor (eIF); Provisional
Probab=99.88 E-value=1.2e-22 Score=157.71 Aligned_cols=78 Identities=21% Similarity=0.195 Sum_probs=72.7
Q ss_pred ccccccCCcceEEEEEEEEeCCCceEEEEeCCCCEEEEEecccccccccccCCCCEEEEEeccCCCCeEEEEEEecCCC
Q 032460 59 SSEEGANSEKWVHEGFITESLPNGMFRVRLDNEDLILGYISGKIRQNFIRVLPGDRVRVEVSRYDTSKGRIIYRLRNKI 137 (140)
Q Consensus 59 ~~~~~~k~d~ie~~GvVik~l~n~~f~V~l~dG~~~lcrI~GKmRk~~IrI~vGDrV~VE~sp~D~~kGrIiyRy~r~~ 137 (140)
+..+++.++..++.|+|++++||+.|+|+|+||++++|+|+||||+ +|||.+||+|+|++|+|++++|+|+|||.+.+
T Consensus 22 ~~~el~~p~egq~~g~V~~~lGn~~~~V~c~dG~~rLa~IpGKmRK-rIWI~~GD~VlVel~~~d~~KgdIv~ry~~dq 99 (145)
T PLN00208 22 EKRELIFKEDGQEYAQVLRMLGNGRCEALCIDGTKRLCHIRGKMRK-KVWIAAGDIILVGLRDYQDDKADVILKYMPDE 99 (145)
T ss_pred ceeecccCCCCcEEEEEEEEcCCCEEEEEECCCCEEEEEEecccee-eEEecCCCEEEEEccCCCCCEEEEEEEcCHHH
Confidence 5567777778899999999999999999999999999999999998 69999999999999999999999999997654
No 11
>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=99.88 E-value=1.6e-22 Score=142.10 Aligned_cols=66 Identities=24% Similarity=0.238 Sum_probs=62.5
Q ss_pred EEEEEEEeCCCceEEEEeCCCCEEEEEecccccccccccCCCCEEEEEeccC-CCCeEEEEEEecCCC
Q 032460 71 HEGFITESLPNGMFRVRLDNEDLILGYISGKIRQNFIRVLPGDRVRVEVSRY-DTSKGRIIYRLRNKI 137 (140)
Q Consensus 71 ~~GvVik~l~n~~f~V~l~dG~~~lcrI~GKmRk~~IrI~vGDrV~VE~sp~-D~~kGrIiyRy~r~~ 137 (140)
+-|+|++++||+.|+|+|+||++++|+|+||||++ |||.+||+|+|++||| |+++|+|+|||.+.+
T Consensus 2 ~i~~V~~~lG~~~~~V~~~dg~~~l~~i~gK~Rk~-iwI~~GD~VlV~~~~~~~~~kg~Iv~r~~~~~ 68 (78)
T cd04456 2 QIVRVLRMLGNNRHEVECADGQRRLVSIPGKLRKN-IWIKRGDFLIVDPIEEGEDVKADIIFVYCKDH 68 (78)
T ss_pred eEEEEEEECCCCEEEEEECCCCEEEEEEchhhccC-EEEcCCCEEEEEecccCCCceEEEEEEeCHHH
Confidence 56999999999999999999999999999999986 9999999999999999 799999999998753
No 12
>TIGR00523 eIF-1A eukaryotic/archaeal initiation factor 1A. Recommended nomenclature: eIF-1A for eukaryotes, aIF-1A for Archaea. Also called eIF-4C
Probab=99.87 E-value=4.6e-22 Score=145.48 Aligned_cols=76 Identities=26% Similarity=0.318 Sum_probs=69.0
Q ss_pred ccccccCCcceEEEEEEEEeCCCceEEEEeCCCCEEEEEecccccccccccCCCCEEEEEeccCCCC---eEEEEEEecC
Q 032460 59 SSEEGANSEKWVHEGFITESLPNGMFRVRLDNEDLILGYISGKIRQNFIRVLPGDRVRVEVSRYDTS---KGRIIYRLRN 135 (140)
Q Consensus 59 ~~~~~~k~d~ie~~GvVik~l~n~~f~V~l~dG~~~lcrI~GKmRk~~IrI~vGDrV~VE~sp~D~~---kGrIiyRy~r 135 (140)
...+||..+..++.|+|++++||+.|+|+|+||++++|+|+||||+ +|||.+||+|+|+ |||.+ +|+|+|||..
T Consensus 9 ~~~~~p~~~e~e~~g~V~~~lG~~~~~V~~~dG~~~la~i~GK~Rk-~iwI~~GD~VlVs--p~d~~~~~kg~Iv~r~~~ 85 (99)
T TIGR00523 9 IRVRLPRKEEGEILGVIEQMLGAGRVKVRCLDGKTRLGRIPGKLKK-RIWIREGDVVIVK--PWEFQGDDKCDIVWRYTK 85 (99)
T ss_pred ceeeCCCCCCCEEEEEEEEEcCCCEEEEEeCCCCEEEEEEchhhcc-cEEecCCCEEEEE--EccCCCCccEEEEEEcCH
Confidence 6778998778899999999999999999999999999999999997 8999999999996 55655 9999999976
Q ss_pred CC
Q 032460 136 KI 137 (140)
Q Consensus 136 ~~ 137 (140)
.+
T Consensus 86 ~q 87 (99)
T TIGR00523 86 TQ 87 (99)
T ss_pred HH
Confidence 54
No 13
>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=99.87 E-value=4e-22 Score=134.61 Aligned_cols=64 Identities=42% Similarity=0.544 Sum_probs=57.0
Q ss_pred ceEEEEEEEEeCCCceEEEEeCCCCEEEEEecccccccccccCCCCEEEEEeccCCCCeEEEEEE
Q 032460 68 KWVHEGFITESLPNGMFRVRLDNEDLILGYISGKIRQNFIRVLPGDRVRVEVSRYDTSKGRIIYR 132 (140)
Q Consensus 68 ~ie~~GvVik~l~n~~f~V~l~dG~~~lcrI~GKmRk~~IrI~vGDrV~VE~sp~D~~kGrIiyR 132 (140)
.+++.|+|++++||+.|.|+|+||++++|+|+||+ ++++||.+||+|+|++|+||.++|+|+||
T Consensus 2 e~e~~~~V~~~lG~~~~~V~~~dg~~~l~~i~gK~-r~~iwI~~GD~V~V~~~~~d~~kG~Ii~r 65 (65)
T PF01176_consen 2 EGEVIGRVTEMLGNNLFEVECEDGEERLARIPGKF-RKRIWIKRGDFVLVEPSPYDKVKGRIIYR 65 (65)
T ss_dssp TTEEEEEEEEEESSSEEEEEETTSEEEEEEE-HHH-HTCC---TTEEEEEEESTTCTTEEEEEEE
T ss_pred CcEEEEEEEEECCCCEEEEEeCCCCEEEEEeccce-eeeEecCCCCEEEEEecccCCCeEEEEEC
Confidence 56899999999999999999999999999999995 56899999999999999999999999997
No 14
>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=99.76 E-value=4.7e-18 Score=113.27 Aligned_cols=64 Identities=61% Similarity=1.028 Sum_probs=60.0
Q ss_pred eEEEEEEEEeCCCceEEEEeCCCCEEEEEecccccccccccCCCCEEEEEeccCCCCeEEEEEE
Q 032460 69 WVHEGFITESLPNGMFRVRLDNEDLILGYISGKIRQNFIRVLPGDRVRVEVSRYDTSKGRIIYR 132 (140)
Q Consensus 69 ie~~GvVik~l~n~~f~V~l~dG~~~lcrI~GKmRk~~IrI~vGDrV~VE~sp~D~~kGrIiyR 132 (140)
++|+|+|++.++|++|.|++++|..+.|+++||+|++++++++||+|.++++++++++|+|+||
T Consensus 1 ~~~~G~Vi~~~~g~~~~V~~~~g~~~~c~~rGklr~~~~~~~vGD~V~~~~~~~~~~~g~I~~~ 64 (64)
T cd04451 1 IEMEGVVTEALPNAMFRVELENGHEVLAHISGKMRMNYIRILPGDRVKVELSPYDLTKGRIVYR 64 (64)
T ss_pred CeEEEEEEEEeCCCEEEEEeCCCCEEEEEECceeecCCcccCCCCEEEEEEeecCCCEEEEEEC
Confidence 4789999999977999999999999999999999977899999999999999888899999997
No 15
>cd05792 S1_eIF1AD_like S1_eIF1AD_like: eukaryotic translation initiation factor 1A domain containing protein (eIF1AD)-like, S1-like RNA-binding domain. eIF1AD is also known as MGC11102 protein. Little is known about the function of eIF1AD. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins, including translation initiation factor IF1A (also referred to as eIF1A in eukaryotes). eIF1A 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.
Probab=99.66 E-value=2.9e-16 Score=110.95 Aligned_cols=64 Identities=25% Similarity=0.167 Sum_probs=59.7
Q ss_pred EEEEEeCCCceEEEEeCCCCEEEEEecccccccccccCCCCEEEEEeccCCC-CeEEEEEEecCCC
Q 032460 73 GFITESLPNGMFRVRLDNEDLILGYISGKIRQNFIRVLPGDRVRVEVSRYDT-SKGRIIYRLRNKI 137 (140)
Q Consensus 73 GvVik~l~n~~f~V~l~dG~~~lcrI~GKmRk~~IrI~vGDrV~VE~sp~D~-~kGrIiyRy~r~~ 137 (140)
.+|+++.||+.|.|+|.||++++|+|+||||+ ++||..||+|+|++++++. .+|.|+|+|.+.+
T Consensus 4 ~rV~~~~G~n~~~V~~~dG~~~l~~iP~KfRk-~iWIkrGd~VlV~p~~~~~kvkgeIv~i~~~~q 68 (78)
T cd05792 4 VRVLGSKGNNLHEVETPNGSRYLVSMPTKFRK-NIWIKRGDFVLVEPIEEGDKVKAEIVKILTRDH 68 (78)
T ss_pred EEEEEcCCCcEEEEEcCCCCEEEEEechhhcc-cEEEEeCCEEEEEecccCCceEEEEEEEECHHH
Confidence 78999999999999999999999999999997 7999999999999998885 6999999998753
No 16
>KOG3403 consensus Translation initiation factor 1A (eIF-1A) [Translation, ribosomal structure and biogenesis]
Probab=99.46 E-value=6.6e-15 Score=113.27 Aligned_cols=68 Identities=21% Similarity=0.244 Sum_probs=64.1
Q ss_pred ceEEEEEEEEeCCCceEEEEeCCCCEEEEEecccccccccccCCCCEEEEEeccCCCCeEEEEEEecCC
Q 032460 68 KWVHEGFITESLPNGMFRVRLDNEDLILGYISGKIRQNFIRVLPGDRVRVEVSRYDTSKGRIIYRLRNK 136 (140)
Q Consensus 68 ~ie~~GvVik~l~n~~f~V~l~dG~~~lcrI~GKmRk~~IrI~vGDrV~VE~sp~D~~kGrIiyRy~r~ 136 (140)
..++.|.|+++||||.|.|.|.||..++|||+||+|+ ++||.+||.|+|.+-.|+..+|+|+-+|...
T Consensus 31 egqeYaQv~kmLGnGr~e~~CfDGvkR~~hiRGklrk-kVwi~~GDIiLv~lRD~qd~kaDvilKY~~d 98 (145)
T KOG3403|consen 31 EGQEYAQVIKMLGNGRLEASCFDGVKRLCHIRGKLRK-KVWINQGDIILVGLRDYQDDKADVILKYMPD 98 (145)
T ss_pred cchhHHHHHhhhcCCcEEEEEecchhhhhhhhcccee-eEeecCCCEEEEeeecccccccceehhhChH
Confidence 3778899999999999999999999999999999998 7999999999999999999999999999654
No 17
>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=99.03 E-value=1.9e-09 Score=70.78 Aligned_cols=62 Identities=29% Similarity=0.436 Sum_probs=52.4
Q ss_pred EEEEEEeCCCceEEEEeCCCCEEEEEecccccccccccCCCCEEEEEeccCCCCeEEEEEEecCC
Q 032460 72 EGFITESLPNGMFRVRLDNEDLILGYISGKIRQNFIRVLPGDRVRVEVSRYDTSKGRIIYRLRNK 136 (140)
Q Consensus 72 ~GvVik~l~n~~f~V~l~dG~~~lcrI~GKmRk~~IrI~vGDrV~VE~sp~D~~kGrIiyRy~r~ 136 (140)
.|.|++.. +++|.|.+++|..+.|.++|++++....+.+||+|.++++ +.+.|.|+-.++|+
T Consensus 2 ~grVv~~~-~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~VGD~V~~~~~--~~~~~~I~~vl~R~ 63 (68)
T cd04466 2 EGLIIKAI-GGFYYVETEDGKIYECRLRGKFRKDKNPPAVGDRVEFEPE--DDGEGVIEEILPRK 63 (68)
T ss_pred CEEEEEEE-CCEEEEEeCCCeEEEEEEccccccCCCCCCCCcEEEEEEC--CCCcEEEEEEeccc
Confidence 58999987 6899999877889999999999866678999999999864 45678998888775
No 18
>PRK00098 GTPase RsgA; Reviewed
Probab=98.62 E-value=1.8e-07 Score=77.88 Aligned_cols=63 Identities=25% Similarity=0.397 Sum_probs=53.8
Q ss_pred EEEEEEEeCCCceEEEEeCCCCEEEEEecccccccccccCCCCEEEEEeccCCCCeEEEEEEecCC
Q 032460 71 HEGFITESLPNGMFRVRLDNEDLILGYISGKIRQNFIRVLPGDRVRVEVSRYDTSKGRIIYRLRNK 136 (140)
Q Consensus 71 ~~GvVik~l~n~~f~V~l~dG~~~lcrI~GKmRk~~IrI~vGDrV~VE~sp~D~~kGrIiyRy~r~ 136 (140)
|+|+|++.. +++|.|..++|..+.|+++|++++....+.+||+|.|++. +++.|.|...++|.
T Consensus 1 ~~g~v~~~~-~~~~~v~~~~~~~~~~~~~g~~~~~~~~~~vGD~V~~~~~--~~~~g~i~~i~~R~ 63 (298)
T PRK00098 1 MEGLIIKAL-GGFYYVESEDGQVYQCRARGKFRKKTNTPAVGDRVEFSAE--NNDEGVILEIHERK 63 (298)
T ss_pred CeEEEEEEE-CCEEEEEECCCCEEEEEeccccccCCCCcCCCCEEEEEEC--CCCcEEEEEEeCCC
Confidence 479999997 8999999877899999999999976777999999999853 55779998777765
No 19
>PRK12289 GTPase RsgA; Reviewed
Probab=98.47 E-value=6.2e-07 Score=77.41 Aligned_cols=66 Identities=27% Similarity=0.374 Sum_probs=55.9
Q ss_pred EEEEEEEEeCCCceEEEEeCCC------CEEEEEecccccccccccCCCCEEEEEeccCCCCeEEEEEEecCC
Q 032460 70 VHEGFITESLPNGMFRVRLDNE------DLILGYISGKIRQNFIRVLPGDRVRVEVSRYDTSKGRIIYRLRNK 136 (140)
Q Consensus 70 e~~GvVik~l~n~~f~V~l~dG------~~~lcrI~GKmRk~~IrI~vGDrV~VE~sp~D~~kGrIiyRy~r~ 136 (140)
.+.|+|+... +++|.|.+++| ..++|..+|++++.+..+.+||+|.++..++...+|.|...++|+
T Consensus 8 ~~~g~V~~~~-~~~y~V~~~~~~~~~~~~~~~~~~r~~lk~~~~~~~vGD~V~~~~~~~~~~~~~I~~vlpR~ 79 (352)
T PRK12289 8 QLLGTVVAVQ-ANFYRVQLDEPQNLNPPSLLLCTRRTRLKKIGQQVMVGDRVIVEEPDWQGQRGAIAEVLPRK 79 (352)
T ss_pred cccEEEEEEE-CCEEEEEECCCcccCcceEEEEEcccccccCCCCcccCCEEEEeecCCCCCceEEEEEeccc
Confidence 3679999996 88999998654 579999999999877779999999999766656789999988876
No 20
>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=98.37 E-value=1.6e-06 Score=71.96 Aligned_cols=60 Identities=28% Similarity=0.398 Sum_probs=50.7
Q ss_pred EEEEEeCCCceEEEEeCCCCEEEEEecccccccccccCCCCEEEEEeccCCCCeEEEEEEecCC
Q 032460 73 GFITESLPNGMFRVRLDNEDLILGYISGKIRQNFIRVLPGDRVRVEVSRYDTSKGRIIYRLRNK 136 (140)
Q Consensus 73 GvVik~l~n~~f~V~l~dG~~~lcrI~GKmRk~~IrI~vGDrV~VE~sp~D~~kGrIiyRy~r~ 136 (140)
|+|++.. +++|.|.. ++..+.|+++|++++.+..+.+||+|.++.. +.++|.|+..++|+
T Consensus 1 g~v~~~~-~~~~~v~~-~~~~~~~~~~g~~~~~~~~~~vGD~V~~~~~--~~~~~~i~~i~~R~ 60 (287)
T cd01854 1 GRVIAVH-GGFYDVET-EGGELRCRARGKLRKKGIKPVVGDWVEVEPD--DDGEGVIVRVLPRK 60 (287)
T ss_pred CEEEEEE-CCEEEEEE-CCeEEEEEeccccccCCCCccCCCEEEEEec--CCCcEEEEEEECCC
Confidence 6788886 78999986 5789999999999976667999999998854 45689999999875
No 21
>PRK12288 GTPase RsgA; Reviewed
Probab=98.21 E-value=6.3e-06 Score=70.93 Aligned_cols=61 Identities=18% Similarity=0.210 Sum_probs=49.9
Q ss_pred EEEEEEEeCCCceEEEEeCCCCEEEEEecccccccccccCCCCEEEEEeccCCC--CeEEEEEEecCC
Q 032460 71 HEGFITESLPNGMFRVRLDNEDLILGYISGKIRQNFIRVLPGDRVRVEVSRYDT--SKGRIIYRLRNK 136 (140)
Q Consensus 71 ~~GvVik~l~n~~f~V~l~dG~~~lcrI~GKmRk~~IrI~vGDrV~VE~sp~D~--~kGrIiyRy~r~ 136 (140)
+.|+|++.. +++|.|.+++|..+.|.++|+++. +.+||+|.++....+. ..|.|+..++|.
T Consensus 40 ~~g~Vi~~~-~~~~~v~~~~g~~~~~~~~g~~~~----~~vGD~V~~~~~~~~~~~~~~~I~~il~R~ 102 (347)
T PRK12288 40 QEGIVISRF-GQHADVEAADGEVHRCNIRRTIRS----LVTGDRVVWRPGKEALEGVSGVVEAVHPRT 102 (347)
T ss_pred cceEEEEEE-CCEEEEEeCCCcEEEEEecccCCC----CCCCcEEEEEeCCCcccccceEEEEEeccc
Confidence 679999997 889999998999999999999863 9999999998432111 249998888775
No 22
>PRK01889 GTPase RsgA; Reviewed
Probab=97.90 E-value=4.8e-05 Score=65.33 Aligned_cols=60 Identities=25% Similarity=0.283 Sum_probs=47.3
Q ss_pred EEEEEEEeCCCceEEEEeCCCCEEEEEeccccccc----ccccCCCCEEEEEeccCCCCeEEEEEEecCC
Q 032460 71 HEGFITESLPNGMFRVRLDNEDLILGYISGKIRQN----FIRVLPGDRVRVEVSRYDTSKGRIIYRLRNK 136 (140)
Q Consensus 71 ~~GvVik~l~n~~f~V~l~dG~~~lcrI~GKmRk~----~IrI~vGDrV~VE~sp~D~~kGrIiyRy~r~ 136 (140)
+.|+|++.. +++|.|..++| ++.|.++||++.. ...+.+||+|.++. .+.|.|+..++|+
T Consensus 29 ~~g~v~~~~-~~~~~v~~~~~-~~~~~~~gk~~~~~~~~~~~~~vGD~V~~~~----~~~g~I~~i~pR~ 92 (356)
T PRK01889 29 EPGRVVEEH-RSGYVVATEEG-EVRAEVSGKWRHEAFPPGDRPAVGDWVLLDN----EKKARIVRLLPRR 92 (356)
T ss_pred ccEEEEEEE-CCEEEEEECCc-EEEEEecchhhccccccCCCCccCcEEEEec----CCceEEEEEECCC
Confidence 569999997 89999987554 6789999999852 23489999998873 3569999777765
No 23
>COG1162 Predicted GTPases [General function prediction only]
Probab=97.88 E-value=3.2e-05 Score=66.46 Aligned_cols=64 Identities=25% Similarity=0.361 Sum_probs=54.3
Q ss_pred EEEEEEEEeCCCceEEEEeCC---CCEEEEEecccccccccccCCCCEEEEEeccCCCCeEEEEEEecCCC
Q 032460 70 VHEGFITESLPNGMFRVRLDN---EDLILGYISGKIRQNFIRVLPGDRVRVEVSRYDTSKGRIIYRLRNKI 137 (140)
Q Consensus 70 e~~GvVik~l~n~~f~V~l~d---G~~~lcrI~GKmRk~~IrI~vGDrV~VE~sp~D~~kGrIiyRy~r~~ 137 (140)
.+.|.|++.+ .|+|.|.+++ ++.+.|..+|++|+....+++||+|.++..+. + |.|...++|+-
T Consensus 4 ~~~g~v~~~~-~g~y~v~~~~~~~~~~~~~~~r~~lr~~~~~~vVGD~V~~~~~~~--~-g~I~~i~~Rkn 70 (301)
T COG1162 4 LKRGRVVKVD-AGFYGVRLEEEVDGEVYRCRARGNLRKKDLKPVVGDRVVFEDENN--N-GVIEKILPRKN 70 (301)
T ss_pred ccCcEEEEee-CCEEEEEEccccccceeeeeeecceeccCccccccCeEEEecCCC--c-ceEEEEecccC
Confidence 3569999997 9999999864 77899999999999988999999998875532 2 99999998863
No 24
>KOG2925 consensus Predicted translation initiation factor related to eIF-1A [Translation, ribosomal structure and biogenesis]
Probab=97.19 E-value=6.9e-05 Score=59.64 Aligned_cols=62 Identities=23% Similarity=0.188 Sum_probs=53.2
Q ss_pred EEEEEEEeCCCceEEEEeCCCCEEEEEecccccccccccCCCCEEEEEeccC---C-CCeEEEEEEe
Q 032460 71 HEGFITESLPNGMFRVRLDNEDLILGYISGKIRQNFIRVLPGDRVRVEVSRY---D-TSKGRIIYRL 133 (140)
Q Consensus 71 ~~GvVik~l~n~~f~V~l~dG~~~lcrI~GKmRk~~IrI~vGDrV~VE~sp~---D-~~kGrIiyRy 133 (140)
+-+.|+++-|++-+.|...+|..+++..+-|+|+ .|||+-|+.|.|.++-. + .-+|.|.|-.
T Consensus 24 ~IaqVvqlrGsnlheV~danGq~~lvsmP~KfRk-siWiRRg~FvvVdpiee~~~g~KVkgeI~yVl 89 (167)
T KOG2925|consen 24 SIAQVVQLRGSNLHEVMDANGQNSLVSMPAKFRK-SIWIRRGSFVVVDPIEEEKSGSKVKGEICYVL 89 (167)
T ss_pred hHHHHHhcCCcchhhhhhcCCceeeeeCCHhhhh-ceEEeeCCEEEEccccccccCCccceEEEEEE
Confidence 3478888889999999999999999999999998 79999999999987655 2 2468888865
No 25
>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=95.89 E-value=0.047 Score=34.35 Aligned_cols=59 Identities=37% Similarity=0.447 Sum_probs=41.3
Q ss_pred EEEEEEEEeCCCceEEEEeCCCCEEEEEeccccccccc-----ccCCCCEEEEEeccCCCCeEEEE
Q 032460 70 VHEGFITESLPNGMFRVRLDNEDLILGYISGKIRQNFI-----RVLPGDRVRVEVSRYDTSKGRII 130 (140)
Q Consensus 70 e~~GvVik~l~n~~f~V~l~dG~~~lcrI~GKmRk~~I-----rI~vGDrV~VE~sp~D~~kGrIi 130 (140)
.+.|+|+++.+.|.| |++.++..-+++.+ .+....+ .+.+||.|.|.+..-|.++|+|.
T Consensus 3 ~~~g~V~~i~~~G~f-v~l~~~~~g~~~~~-~l~~~~~~~~~~~~~~Gd~v~v~i~~vd~~~~~i~ 66 (68)
T cd05685 3 VLEGVVTNVTDFGAF-VDIGVKQDGLIHIS-KMADRFVSHPSDVVSVGDIVEVKVISIDEERGRIS 66 (68)
T ss_pred EEEEEEEEEecccEE-EEcCCCCEEEEEHH-HCCCccccCHHHhcCCCCEEEEEEEEEECCCCEEe
Confidence 478999999766665 78877755555543 3322211 36899999999887777777774
No 26
>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=95.79 E-value=0.039 Score=33.75 Aligned_cols=58 Identities=28% Similarity=0.149 Sum_probs=41.5
Q ss_pred EEEEEEeCCCceEEEEeCCCCEEEEEecccccc----cccccCCCCEEEEEeccCCCCeEEEE
Q 032460 72 EGFITESLPNGMFRVRLDNEDLILGYISGKIRQ----NFIRVLPGDRVRVEVSRYDTSKGRII 130 (140)
Q Consensus 72 ~GvVik~l~n~~f~V~l~dG~~~lcrI~GKmRk----~~IrI~vGDrV~VE~sp~D~~kGrIi 130 (140)
.|+|+++. ++.+.|.+.+|..-.++.+.--.. ....+.+||.|.+.+...|.++|.|.
T Consensus 2 ~g~V~~v~-~~g~~v~l~~~~~g~~~~~~~~~~~~~~~~~~~~~G~~v~~~v~~~d~~~~~i~ 63 (65)
T cd00164 2 TGKVVSIT-KFGVFVELEDGVEGLVHISELSDKFVKDPSEVFKVGDEVEVKVLEVDPEKGRIS 63 (65)
T ss_pred EEEEEEEE-eeeEEEEecCCCEEEEEHHHCCCccccCHhhEeCCCCEEEEEEEEEcCCcCEEe
Confidence 68999986 555568888777766666543221 13458999999999888787777764
No 27
>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=93.92 E-value=0.34 Score=31.41 Aligned_cols=60 Identities=22% Similarity=0.181 Sum_probs=41.2
Q ss_pred EEEEEEEEeCCCceEEEEeCCCCEEEEEec----ccccccccccCCCCEEEEEeccCCCCeEEEE
Q 032460 70 VHEGFITESLPNGMFRVRLDNEDLILGYIS----GKIRQNFIRVLPGDRVRVEVSRYDTSKGRII 130 (140)
Q Consensus 70 e~~GvVik~l~n~~f~V~l~dG~~~lcrI~----GKmRk~~IrI~vGDrV~VE~sp~D~~kGrIi 130 (140)
.+.|+|+++.. .-..|++.++..=.++++ .......-.+.+||.|.+.+...|+.+++|.
T Consensus 3 ~v~g~V~~v~~-~Gv~V~l~~~~~G~v~~s~l~~~~~~~~~~~~~~Gd~v~~~v~~~d~~~~~i~ 66 (68)
T cd05707 3 VVRGFVKNIAN-NGVFVTLGRGVDARVRVSELSDSYLKDWKKRFKVGQLVKGKIVSIDPDNGRIE 66 (68)
T ss_pred EEEEEEEEEEC-ccEEEEeCCCCEEEEEHHHCCchhhcCHhhccCCCCEEEEEEEEEeCCCCEEe
Confidence 47899999974 446788877655444443 1222222238999999999888888888875
No 28
>PF04076 BOF: Bacterial OB fold (BOF) protein; InterPro: IPR005220 Proteins in this entry have an OB-fold fold (oligonucleotide/oligosaccharide binding motif). Analysis of the predicted nucleotide-binding site of the OB-fold suggests that they lack nucleic acid-binding properties. They contain an predicted N-terminal signal peptide which indicates that they localise to the periplasm where they may function to bind proteins, small molecules, or other typical OB-fold ligands. As hypothesised for the distantly related OB-fold containing bacterial enterotoxins, the loss of nucleotide-binding function and the rapid evolution of the OB-fold ligand-binding site may be associated with the presence of members in mobile genetic elements and their potential role in bacterial pathogenicity [].; PDB: 1NNX_A.
Probab=93.75 E-value=0.27 Score=36.24 Aligned_cols=55 Identities=22% Similarity=0.239 Sum_probs=41.7
Q ss_pred cccCCcceEEEEEEEEeCCCceEEEEeCCCCEEEEEecccccccccccCCCCEEEEE
Q 032460 62 EGANSEKWVHEGFITESLPNGMFRVRLDNEDLILGYISGKIRQNFIRVLPGDRVRVE 118 (140)
Q Consensus 62 ~~~k~d~ie~~GvVik~l~n~~f~V~l~dG~~~lcrI~GKmRk~~IrI~vGDrV~VE 118 (140)
.|+....++++|.|++-+++..|..+...| ++...|.-+.-. +..+-++|+|.+.
T Consensus 30 ~~~Dd~~V~L~G~Iv~~l~~d~Y~F~D~TG-~I~VeId~~~w~-g~~vt~~~~Vri~ 84 (103)
T PF04076_consen 30 NAKDDTPVTLEGNIVKQLGDDKYLFRDATG-EIEVEIDDDVWR-GQTVTPDDKVRIS 84 (103)
T ss_dssp TS-SSEEEEEEEEEEEEEETTEEEEEETTE-EEEEE--GGGST-T----TTSEEEEE
T ss_pred hCcCCCeEEEEEEEEEEecCCEEEEECCCC-cEEEEEChhhcC-CcccCCCCEEEEE
Confidence 456677889999999999999999998888 889999988765 6789999999775
No 29
>PF11948 DUF3465: Protein of unknown function (DUF3465); InterPro: IPR021856 This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 131 to 151 amino acids in length. This protein has a conserved HWTH sequence motif.
Probab=93.66 E-value=0.65 Score=36.11 Aligned_cols=67 Identities=21% Similarity=0.250 Sum_probs=46.0
Q ss_pred eEEEEEEEEeCCC-------ceEEEEeCCCCEEEEEeccccccccc-ccCCCCEEEEEec-cCCCCeEEEEEEecCC
Q 032460 69 WVHEGFITESLPN-------GMFRVRLDNEDLILGYISGKIRQNFI-RVLPGDRVRVEVS-RYDTSKGRIIYRLRNK 136 (140)
Q Consensus 69 ie~~GvVik~l~n-------~~f~V~l~dG~~~lcrI~GKmRk~~I-rI~vGDrV~VE~s-p~D~~kGrIiyRy~r~ 136 (140)
+.-.|+|+++|++ .+|.|++.+|.+++.-=-=-+- -++ ++.+||.|.|--. -|++..|.|-|-+.-+
T Consensus 39 v~g~G~V~~vLpdd~~GsrHQ~Fiv~l~~g~tllIahNIDla-prip~l~~GD~V~f~GeYe~n~kggvIHWTH~dp 114 (131)
T PF11948_consen 39 VSGCGTVVKVLPDDNKGSRHQRFIVRLSSGQTLLIAHNIDLA-PRIPWLQKGDQVEFYGEYEWNPKGGVIHWTHHDP 114 (131)
T ss_pred EeccEEEEEECcccCCCCcceEEEEEeCCCCEEEEEeccCcc-ccCcCcCCCCEEEEEEEEEECCCCCEEEeeccCC
Confidence 3458999999986 5899999999887654221221 233 4899999987632 4566668887766433
No 30
>PF12059 DUF3540: Protein of unknown function (DUF3540); InterPro: IPR021927 This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 212 to 238 amino acids in length. This protein has a conserved SCL sequence motif.
Probab=93.21 E-value=0.69 Score=37.63 Aligned_cols=62 Identities=16% Similarity=0.055 Sum_probs=45.9
Q ss_pred EEEEEEEeCCCceEEEEeCCCCEEEEEecccccccccccCCCCEEEEEeccCCCCeEEEEEEecCCCC
Q 032460 71 HEGFITESLPNGMFRVRLDNEDLILGYISGKIRQNFIRVLPGDRVRVEVSRYDTSKGRIIYRLRNKIS 138 (140)
Q Consensus 71 ~~GvVik~l~n~~f~V~l~dG~~~lcrI~GKmRk~~IrI~vGDrV~VE~sp~D~~kGrIiyRy~r~~~ 138 (140)
..|.|+... ++.|.|...+|. +.|+-.---.. .+.+||+|+|. .+-|....+|+.-.+|.+.
T Consensus 2 ~~g~V~~~~-~~~~~v~~~~G~-~~arrAaSCLl---~P~~GD~VLv~-~~~d~~~~yILAVL~r~~~ 63 (202)
T PF12059_consen 2 FSGTVVGRE-GDGLVVVDDDGE-WRARRAASCLL---EPAVGDTVLVS-GVADEERVYILAVLERADP 63 (202)
T ss_pred ceEEEEEEe-CCeEEEEcCCCE-EEEEecccccc---CCCCCCEEEEe-ecCCCCcEEEEEEEecCCC
Confidence 358999987 667777778888 88887655543 49999999982 2235566789888877654
No 31
>cd05698 S1_Rrp5_repeat_hs6_sc5 S1_Rrp5_repeat_hs6_sc5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 6 (hs6) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=93.19 E-value=0.63 Score=30.02 Aligned_cols=60 Identities=22% Similarity=0.198 Sum_probs=41.8
Q ss_pred EEEEEEEEeCCCceEEEEeCCCCEEEEEeccccccccc-----ccCCCCEEEEEeccCCCCeEEEEE
Q 032460 70 VHEGFITESLPNGMFRVRLDNEDLILGYISGKIRQNFI-----RVLPGDRVRVEVSRYDTSKGRIIY 131 (140)
Q Consensus 70 e~~GvVik~l~n~~f~V~l~dG~~~lcrI~GKmRk~~I-----rI~vGDrV~VE~sp~D~~kGrIiy 131 (140)
.+.|+|+++. +.-..|++.++..-+++++ .+...++ .+.+||.|.|.+...|.++++|..
T Consensus 3 ~~~g~V~~v~-~~G~~V~l~~~~~gli~~s-~l~~~~~~~~~~~~~~G~~i~v~v~~~d~~~~~i~l 67 (70)
T cd05698 3 KTHGTIVKVK-PNGCIVSFYNNVKGFLPKS-ELSEAFIKDPEEHFRVGQVVKVKVLSCDPEQQRLLL 67 (70)
T ss_pred EEEEEEEEEe-cCcEEEEECCCCEEEEEHH-HcChhhcCCHHHcccCCCEEEEEEEEEcCCCCEEEE
Confidence 4789999996 5555788877755555543 2222111 278999999999888888888764
No 32
>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=92.83 E-value=0.64 Score=29.90 Aligned_cols=52 Identities=13% Similarity=0.064 Sum_probs=38.3
Q ss_pred EEEEEEEEeCC-CceEEEEe--CCCCEEEEEecccccccccccCCCCEEEEEeccC
Q 032460 70 VHEGFITESLP-NGMFRVRL--DNEDLILGYISGKIRQNFIRVLPGDRVRVEVSRY 122 (140)
Q Consensus 70 e~~GvVik~l~-n~~f~V~l--~dG~~~lcrI~GKmRk~~IrI~vGDrV~VE~sp~ 122 (140)
.+.|+|.++.. +...+|.+ .++..+.|.++.+--. ...+.+||.|.+.+.+.
T Consensus 8 ~l~g~I~~i~~~g~~~~v~l~~~~~~~l~a~i~~~~~~-~l~l~~G~~v~~~ik~~ 62 (69)
T TIGR00638 8 QLKGKVVAIEDGDVNAEVDLLLGGGTKLTAVITLESVA-ELGLKPGKEVYAVIKAP 62 (69)
T ss_pred EEEEEEEEEEECCCeEEEEEEECCCCEEEEEecHHHHh-hCCCCCCCEEEEEEECc
Confidence 57899999843 44556665 4566899999976544 56799999999887654
No 33
>smart00316 S1 Ribosomal protein S1-like RNA-binding domain.
Probab=92.68 E-value=0.86 Score=28.07 Aligned_cols=61 Identities=36% Similarity=0.251 Sum_probs=40.6
Q ss_pred EEEEEEEEeCCCceEEEEeCCCCEEEEEecccccc-----cccccCCCCEEEEEeccCCCCeEEEEEE
Q 032460 70 VHEGFITESLPNGMFRVRLDNEDLILGYISGKIRQ-----NFIRVLPGDRVRVEVSRYDTSKGRIIYR 132 (140)
Q Consensus 70 e~~GvVik~l~n~~f~V~l~dG~~~lcrI~GKmRk-----~~IrI~vGDrV~VE~sp~D~~kGrIiyR 132 (140)
.+.|+|++.. ...+.|.+.++..-..+.+ .+.. ....+.+||.|.+.+...+.+++.|...
T Consensus 5 ~v~g~V~~v~-~~g~~v~i~~~~~g~l~~~-~~~~~~~~~~~~~~~~G~~v~~~V~~~~~~~~~i~ls 70 (72)
T smart00316 5 VVEGTVTEIT-PFGAFVDLGNGVEGLIPIS-ELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILS 70 (72)
T ss_pred EEEEEEEEEE-ccEEEEEeCCCCEEEEEHH-HCCccccCCHHHeecCCCEEEEEEEEEeCCCCEEEEE
Confidence 5789999995 5667888876544333332 1111 1234899999999988777776777643
No 34
>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=92.50 E-value=0.83 Score=29.61 Aligned_cols=61 Identities=18% Similarity=0.211 Sum_probs=41.3
Q ss_pred EEEEEEEEeCCCceEEEEeCCCCEEEEEe---cc-cccccccccCCCCEEEEEeccCCCCeEEEEE
Q 032460 70 VHEGFITESLPNGMFRVRLDNEDLILGYI---SG-KIRQNFIRVLPGDRVRVEVSRYDTSKGRIIY 131 (140)
Q Consensus 70 e~~GvVik~l~n~~f~V~l~dG~~~lcrI---~G-KmRk~~IrI~vGDrV~VE~sp~D~~kGrIiy 131 (140)
.+.|+|+++. +.-..|++++|.+-.+++ +. ..+...-.+.+||.+.+.+...|.++++|..
T Consensus 3 ~v~g~V~~v~-~~Gv~V~l~~~v~g~i~~~~l~~~~~~~~~~~~~~Gd~i~~~V~~id~~~~~i~l 67 (69)
T cd05697 3 VVKGTIRKLR-PSGIFVKLSDHIKGLVPPMHLADVRLKHPEKKFKPGLKVKCRVLSVEPERKRLVL 67 (69)
T ss_pred EEEEEEEEEe-ccEEEEEecCCcEEEEEHHHCCCccccCHHHcCCCCCEEEEEEEEEECCCCEEEE
Confidence 4789999986 556678887774444432 21 1222223489999999999888887887753
No 35
>PRK07252 hypothetical protein; Provisional
Probab=92.26 E-value=1.3 Score=33.12 Aligned_cols=66 Identities=27% Similarity=0.199 Sum_probs=44.8
Q ss_pred EEEEEEEEeCCCceEEEEeCCCCEEEEEeccccccc-----ccccCCCCEEEEEeccCCCCeEEEEEEecCCC
Q 032460 70 VHEGFITESLPNGMFRVRLDNEDLILGYISGKIRQN-----FIRVLPGDRVRVEVSRYDTSKGRIIYRLRNKI 137 (140)
Q Consensus 70 e~~GvVik~l~n~~f~V~l~dG~~~lcrI~GKmRk~-----~IrI~vGDrV~VE~sp~D~~kGrIiyRy~r~~ 137 (140)
.+.|+|+.+. ..-+.|++.++..-..+++ .+... .-.+.+||.|.|.+...|..+|+|.......+
T Consensus 6 iv~G~V~~V~-~~G~fVei~~~~~Gllhis-eLs~~~~~~~~~~~~vGD~V~VkI~~iD~~~~ri~lSlk~~~ 76 (120)
T PRK07252 6 KLKGTITGIK-PYGAFVALENGTTGLIHIS-EIKTGFIDNIHQLLKVGEEVLVQVVDFDEYTGKASLSLRTLE 76 (120)
T ss_pred EEEEEEEEEe-CcEEEEEECCCCEEEEEHH-HcCCccccChhhccCCCCEEEEEEEEEeCCCCEEEEEEeecc
Confidence 4889999997 4455677876655455443 12111 12378999999999888888899986655443
No 36
>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=92.05 E-value=1.4 Score=28.61 Aligned_cols=59 Identities=20% Similarity=0.197 Sum_probs=40.4
Q ss_pred EEEEEEEEeCCCceEEEEeCCCCEEEEEeccccccc-----ccccCCCCEEEEEeccCCCCeEEEE
Q 032460 70 VHEGFITESLPNGMFRVRLDNEDLILGYISGKIRQN-----FIRVLPGDRVRVEVSRYDTSKGRII 130 (140)
Q Consensus 70 e~~GvVik~l~n~~f~V~l~dG~~~lcrI~GKmRk~-----~IrI~vGDrV~VE~sp~D~~kGrIi 130 (140)
.+.|+|+++. +.-..|+++++.+-.++++ .+... .-...+||.|.+.+...|..++.|.
T Consensus 6 iv~g~V~~v~-~~gi~v~l~~~~~g~v~~s-~l~~~~~~~~~~~~~~Gd~v~~~V~~~d~~~~~i~ 69 (73)
T cd05706 6 ILPGRVTKVN-DRYVLVQLGNKVTGPSFIT-DALDDYSEALPYKFKKNDIVRACVLSVDVPNKKIA 69 (73)
T ss_pred EEEEEEEEEe-CCeEEEEeCCCcEEEEEhh-hccCccccccccccCCCCEEEEEEEEEeCCCCEEE
Confidence 5889999985 6667888887755555543 22111 1237899999999887777666665
No 37
>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=91.87 E-value=1.4 Score=28.21 Aligned_cols=63 Identities=17% Similarity=0.177 Sum_probs=41.0
Q ss_pred EEEEEEEEeCCCceEEEEeCCCCEEEEEecc----cccccccccCCCCEEEEEeccCCCCeEEEEEEe
Q 032460 70 VHEGFITESLPNGMFRVRLDNEDLILGYISG----KIRQNFIRVLPGDRVRVEVSRYDTSKGRIIYRL 133 (140)
Q Consensus 70 e~~GvVik~l~n~~f~V~l~dG~~~lcrI~G----KmRk~~IrI~vGDrV~VE~sp~D~~kGrIiyRy 133 (140)
.+.|+|+++- +.-..|++.++..-.++++= .++...-.+.+||.|.+.+...|..++.|..-.
T Consensus 3 ~v~g~V~~v~-~~g~~v~l~~~~~g~i~~~~~~~~~~~~~~~~~~~Gd~v~~~v~~~d~~~~~i~ls~ 69 (73)
T cd05691 3 IVTGKVTEVD-AKGATVKLGDGVEGFLRAAELSRDRVEDATERFKVGDEVEAKITNVDRKNRKISLSI 69 (73)
T ss_pred EEEEEEEEEE-CCeEEEEeCCCCEEEEEHHHCCCccccCHHHccCCCCEEEEEEEEEeCCCCEEEEEE
Confidence 3689999995 66677888776555554431 111111236899999998887777667665443
No 38
>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=91.65 E-value=0.53 Score=30.10 Aligned_cols=52 Identities=15% Similarity=0.197 Sum_probs=33.8
Q ss_pred EEEEEEEEeCCCc-eE--EEEeCCCCEEEEEecccccccccccCCCCEEEEEeccC
Q 032460 70 VHEGFITESLPNG-MF--RVRLDNEDLILGYISGKIRQNFIRVLPGDRVRVEVSRY 122 (140)
Q Consensus 70 e~~GvVik~l~n~-~f--~V~l~dG~~~lcrI~GKmRk~~IrI~vGDrV~VE~sp~ 122 (140)
.+.|+|..+-..| .. ++.+.++..+.|++...-.. +..+.+||.|.+.+.+.
T Consensus 6 ~l~g~V~~ie~~g~~~~v~~~~~~~~~l~a~it~~~~~-~L~L~~G~~V~~~ik~~ 60 (64)
T PF03459_consen 6 QLPGTVESIENLGSEVEVTLDLGGGETLTARITPESAE-ELGLKPGDEVYASIKAS 60 (64)
T ss_dssp EEEEEEEEEEESSSEEEEEEEETTSEEEEEEEEHHHHH-HCT-STT-EEEEEE-GG
T ss_pred EEEEEEEEEEECCCeEEEEEEECCCCEEEEEEcHHHHH-HcCCCCCCEEEEEEehh
Confidence 4678887665433 33 44445655599999987665 56799999999987753
No 39
>TIGR00156 conserved hypothetical protein TIGR00156. As of the last revision, this family consists only of two proteins from Escherichia coli and one from the related species Haemophilus influenzae.
Probab=91.64 E-value=0.84 Score=35.03 Aligned_cols=56 Identities=18% Similarity=0.149 Sum_probs=45.7
Q ss_pred cccCCcceEEEEEEEEeCCCceEEEEeCCCCEEEEEecccccccccccCCCCEEEEEe
Q 032460 62 EGANSEKWVHEGFITESLPNGMFRVRLDNEDLILGYISGKIRQNFIRVLPGDRVRVEV 119 (140)
Q Consensus 62 ~~~k~d~ie~~GvVik~l~n~~f~V~l~dG~~~lcrI~GKmRk~~IrI~vGDrV~VE~ 119 (140)
.|+.+..++++|.|++.+++..|..+...|. +.-.|.-+.= ++..+-|+|+|.+.-
T Consensus 53 ~~~Ddt~V~L~G~Iv~~l~~d~Y~F~D~TG~-I~VeId~~~w-~G~~v~p~d~V~I~G 108 (126)
T TIGR00156 53 SMHDGASVTLRGNIISHIGDDRYVFRDKSGE-INVVIPAAVW-NGREVQPKDMVNISG 108 (126)
T ss_pred hCCCCCEEEEEEEEEEEeCCceEEEECCCCC-EEEEECHHHc-CCCcCCCCCEEEEEE
Confidence 3556667899999999999999999987774 7888887765 467799999998863
No 40
>PF07076 DUF1344: Protein of unknown function (DUF1344); InterPro: IPR009780 This family consists of several short, hypothetical bacterial proteins of around 80 residues in length. Members of this family are found in Rhizobium, Agrobacterium and Brucella species. The function of this family is unknown.
Probab=90.82 E-value=1.2 Score=30.47 Aligned_cols=46 Identities=20% Similarity=0.120 Sum_probs=36.3
Q ss_pred EEEEEEEEeCCCceEEEEeCCCCEEEEEecccccccccccCCCCEEEEEec
Q 032460 70 VHEGFITESLPNGMFRVRLDNEDLILGYISGKIRQNFIRVLPGDRVRVEVS 120 (140)
Q Consensus 70 e~~GvVik~l~n~~f~V~l~dG~~~lcrI~GKmRk~~IrI~vGDrV~VE~s 120 (140)
+++|+|.++ -...+.+.|+||+.|.. ++-+.. -.+.+|..|.|..+
T Consensus 4 ~veG~I~~i-d~~~~titLdDGksy~l--p~ef~~--~~L~~G~kV~V~yd 49 (61)
T PF07076_consen 4 DVEGTIKSI-DPETMTITLDDGKSYKL--PEEFDF--DGLKPGMKVVVFYD 49 (61)
T ss_pred cceEEEEEE-cCCceEEEecCCCEEEC--CCcccc--cccCCCCEEEEEEE
Confidence 578999998 57888999999999864 555543 24999999999644
No 41
>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=90.75 E-value=1.9 Score=29.02 Aligned_cols=62 Identities=13% Similarity=0.214 Sum_probs=39.5
Q ss_pred cCCcceEEEEEEEEeCCCceEEEEeCCCCEEEEEeccc------ccccccccCCCCEEEEEeccCCCCeEEEE
Q 032460 64 ANSEKWVHEGFITESLPNGMFRVRLDNEDLILGYISGK------IRQNFIRVLPGDRVRVEVSRYDTSKGRII 130 (140)
Q Consensus 64 ~k~d~ie~~GvVik~l~n~~f~V~l~dG~~~lcrI~GK------mRk~~IrI~vGDrV~VE~sp~D~~kGrIi 130 (140)
|+... .+.|+|++. .++.+.|.+..+ ..+.++-. .+...-.+.+||.+.+.+...+.+ +.|.
T Consensus 4 p~~Gd-iV~G~V~~v-~~~~~~V~i~~~--~~g~l~~~~~~~~~~~~~~~~~~~GD~i~~~V~~~~~~-~~i~ 71 (82)
T cd04454 4 PDVGD-IVIGIVTEV-NSRFWKVDILSR--GTARLEDSSATEKDKKEIRKSLQPGDLILAKVISLGDD-MNVL 71 (82)
T ss_pred CCCCC-EEEEEEEEE-cCCEEEEEeCCC--ceEEeechhccCcchHHHHhcCCCCCEEEEEEEEeCCC-CCEE
Confidence 44433 478999999 588888988543 44444332 111123489999999998877764 4443
No 42
>COG1098 VacB Predicted RNA binding protein (contains ribosomal protein S1 domain) [Translation, ribosomal structure and biogenesis]
Probab=90.71 E-value=0.61 Score=36.23 Aligned_cols=58 Identities=33% Similarity=0.440 Sum_probs=44.7
Q ss_pred EEEEEEEEeCCCceEEEEeCCCCEEEEEecccccccccc-----cCCCCEEEEEeccCCCCeEEEE
Q 032460 70 VHEGFITESLPNGMFRVRLDNEDLILGYISGKIRQNFIR-----VLPGDRVRVEVSRYDTSKGRII 130 (140)
Q Consensus 70 e~~GvVik~l~n~~f~V~l~dG~~~lcrI~GKmRk~~Ir-----I~vGDrV~VE~sp~D~~kGrIi 130 (140)
.++|+|+.+.+-|-| |++++|.+=+-||+-- ..++++ +.+||.|.|.+-.-|. .|.|-
T Consensus 8 ~l~GkItgI~~yGAF-V~l~~g~tGLVHISEI-a~~fVkdI~d~L~vG~eV~vKVl~ide-~GKis 70 (129)
T COG1098 8 KLKGKITGITPYGAF-VELEGGKTGLVHISEI-ADGFVKDIHDHLKVGQEVKVKVLDIDE-NGKIS 70 (129)
T ss_pred eEEEEEEeeEecceE-EEecCCCcceEEehHh-hhhhHHhHHHHhcCCCEEEEEEEeecc-CCCcc
Confidence 488999999766664 7789999989998843 344555 9999999999876665 77764
No 43
>PRK08582 hypothetical protein; Provisional
Probab=90.68 E-value=3.1 Score=31.72 Aligned_cols=63 Identities=25% Similarity=0.246 Sum_probs=42.5
Q ss_pred EEEEEEEEeCCCceEEEEeCCCCEEEEEecccccccc-----cccCCCCEEEEEeccCCCCeEEEEEEecC
Q 032460 70 VHEGFITESLPNGMFRVRLDNEDLILGYISGKIRQNF-----IRVLPGDRVRVEVSRYDTSKGRIIYRLRN 135 (140)
Q Consensus 70 e~~GvVik~l~n~~f~V~l~dG~~~lcrI~GKmRk~~-----IrI~vGDrV~VE~sp~D~~kGrIiyRy~r 135 (140)
.+.|+|+.+. +.-+.|.++++..=+.+++ .+.... -.+.+||.|.|.+...|. .|.|..-..+
T Consensus 8 iv~G~V~~I~-~fG~fV~L~~~~~GlVhiS-els~~~v~~~~~~l~vGD~VkvkV~~id~-~gkI~LSlk~ 75 (139)
T PRK08582 8 KLQGKVTGIT-NFGAFVELPEGKTGLVHIS-EVADNYVKDINDHLKVGDEVEVKVLNVED-DGKIGLSIKK 75 (139)
T ss_pred EEEEEEEEEE-CCeEEEEECCCCEEEEEee-ccCcccccccccccCCCCEEEEEEEEECC-CCcEEEEEEe
Confidence 5899999986 4456678887777666665 222111 238899999999776665 3777755543
No 44
>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=90.48 E-value=2.7 Score=26.11 Aligned_cols=59 Identities=32% Similarity=0.237 Sum_probs=37.7
Q ss_pred EEEEEEEEeCCCceEEEEeCCCCEEEEEecccccccc-----cccCCCCEEEEEeccCCCCeEEEEE
Q 032460 70 VHEGFITESLPNGMFRVRLDNEDLILGYISGKIRQNF-----IRVLPGDRVRVEVSRYDTSKGRIIY 131 (140)
Q Consensus 70 e~~GvVik~l~n~~f~V~l~dG~~~lcrI~GKmRk~~-----IrI~vGDrV~VE~sp~D~~kGrIiy 131 (140)
.+.|+|+++. +.-+.|.+.++..-..+++ .+...+ -.+.+||.|.+.+..-|. +|+|..
T Consensus 3 ~~~g~V~~i~-~~g~~v~i~~~~~g~l~~~-~l~~~~~~~~~~~~~~Gd~v~v~v~~~~~-~~~i~l 66 (69)
T cd05692 3 VVEGTVTRLK-PFGAFVELGGGISGLVHIS-QIAHKRVKDVKDVLKEGDKVKVKVLSIDA-RGRISL 66 (69)
T ss_pred EEEEEEEEEE-eeeEEEEECCCCEEEEEhH-HcCCcccCCHHHccCCCCEEEEEEEEECC-CCcEEE
Confidence 4789999986 5555677777655454443 222111 126889999998866665 666653
No 45
>cd05704 S1_Rrp5_repeat_hs13 S1_Rrp5_repeat_hs13: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 13 (hs13). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=90.33 E-value=2 Score=28.58 Aligned_cols=58 Identities=22% Similarity=0.316 Sum_probs=40.6
Q ss_pred EEEEEEEEeCCCceEEEEeCCCCEEEEEecccccccccc-----cCCCCEEEEEeccCCCCeEEEE
Q 032460 70 VHEGFITESLPNGMFRVRLDNEDLILGYISGKIRQNFIR-----VLPGDRVRVEVSRYDTSKGRII 130 (140)
Q Consensus 70 e~~GvVik~l~n~~f~V~l~dG~~~lcrI~GKmRk~~Ir-----I~vGDrV~VE~sp~D~~kGrIi 130 (140)
.+.|+|+++.+.--..|++.+|..=++|++ .+..+++. +.+||.|.+.+...|. |+|.
T Consensus 6 iv~G~V~~i~~~~g~~v~l~~~~~Glvhis-~~s~~~~~~~~~~~~~Gd~v~~kV~~~~~--~~i~ 68 (72)
T cd05704 6 VTLGMVTKVIPHSGLTVQLPFGKTGLVSIF-HLSDSYTENPLEGFKPGKIVRCCILSKKD--GKYQ 68 (72)
T ss_pred EEEEEEEEeeCCcEEEEECCCCCEEEEEHH-HhcCcccCCHHHhCCCCCEEEEEEEEecC--CEEE
Confidence 478999998643345778888888888877 55433332 6889999998765442 5553
No 46
>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=90.24 E-value=3.4 Score=27.83 Aligned_cols=59 Identities=20% Similarity=0.158 Sum_probs=38.2
Q ss_pred EEEEEEEEeCCCceEEEEeCCCCEEEEEecccccc-------c--ccccCCCCEEEEEeccCCCCeEEEEE
Q 032460 70 VHEGFITESLPNGMFRVRLDNEDLILGYISGKIRQ-------N--FIRVLPGDRVRVEVSRYDTSKGRIIY 131 (140)
Q Consensus 70 e~~GvVik~l~n~~f~V~l~dG~~~lcrI~GKmRk-------~--~IrI~vGDrV~VE~sp~D~~kGrIiy 131 (140)
.+.|+|++.. +..+.|.+.++..=.++++ .+.. . .-.+.+||.|.+.+...+.+ |+|.-
T Consensus 9 iV~g~V~~i~-~~g~~v~i~~~~~G~l~~s-e~~~~~~~~~~~~~~~~l~vGd~i~~~V~~~~~~-~~i~L 76 (86)
T cd05789 9 VVIGRVTEVG-FKRWKVDINSPYDAVLPLS-EVNLPRTDEDELNMRSYLDEGDLIVAEVQSVDSD-GSVSL 76 (86)
T ss_pred EEEEEEEEEC-CCEEEEECCCCeEEEEEHH-HccCCCCccchHHHHhhCCCCCEEEEEEEEECCC-CCEEE
Confidence 4899999985 6667888876644444433 1110 0 11389999999998776654 66553
No 47
>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=90.22 E-value=1.7 Score=27.20 Aligned_cols=57 Identities=28% Similarity=0.328 Sum_probs=36.3
Q ss_pred EEEEEEEEeCCCceEEEEeCCCCEEEEEec------ccccccccccCCCCEEEEEeccCCCCeEEEE
Q 032460 70 VHEGFITESLPNGMFRVRLDNEDLILGYIS------GKIRQNFIRVLPGDRVRVEVSRYDTSKGRII 130 (140)
Q Consensus 70 e~~GvVik~l~n~~f~V~l~dG~~~lcrI~------GKmRk~~IrI~vGDrV~VE~sp~D~~kGrIi 130 (140)
.+.|+|+..- +.-+.|++. + ..+.++ .+++...-.+.+||.|.|.+...|.++++|.
T Consensus 4 ~~~g~V~~v~-~~g~~v~l~-~--~~g~l~~~e~~~~~~~~~~~~~~~Gd~v~v~i~~vd~~~~~i~ 66 (68)
T cd05688 4 VVEGTVKSIT-DFGAFVDLG-G--VDGLLHISDMSWGRVKHPSEVVNVGDEVEVKVLKIDKERKRIS 66 (68)
T ss_pred EEEEEEEEEE-eeeEEEEEC-C--eEEEEEhHHCCCccccCHhHEECCCCEEEEEEEEEECCCCEEe
Confidence 4789999986 445667774 3 344442 1122212237999999998877777777664
No 48
>PRK08059 general stress protein 13; Validated
Probab=90.09 E-value=2.3 Score=31.39 Aligned_cols=66 Identities=30% Similarity=0.244 Sum_probs=43.4
Q ss_pred EEEEEEEEeCCCceEEEEeCCCCEEEEEec---cc-ccccccccCCCCEEEEEeccCCCCeEEEEEEecCC
Q 032460 70 VHEGFITESLPNGMFRVRLDNEDLILGYIS---GK-IRQNFIRVLPGDRVRVEVSRYDTSKGRIIYRLRNK 136 (140)
Q Consensus 70 e~~GvVik~l~n~~f~V~l~dG~~~lcrI~---GK-mRk~~IrI~vGDrV~VE~sp~D~~kGrIiyRy~r~ 136 (140)
.+.|+|+++. ..-+.|.+.++..=+++++ .. ...-.-.+.+||.|.|.+...|.++|+|.......
T Consensus 10 iv~G~V~~i~-~~G~fV~i~~~~~Gli~~sel~~~~~~~~~~~~~vGD~I~vkI~~id~~~~~i~lslk~~ 79 (123)
T PRK08059 10 VVTGKVTGIQ-PYGAFVALDEETQGLVHISEITHGFVKDIHDFLSVGDEVKVKVLSVDEEKGKISLSIRAT 79 (123)
T ss_pred EEEEEEEEEe-cceEEEEECCCCEEEEEHHHCCcccccCHHHcCCCCCEEEEEEEEEECCCCeEEEEEEEc
Confidence 5889999996 4555677777655454443 11 11001137889999999887777788888766544
No 49
>cd04461 S1_Rrp5_repeat_hs8_sc7 S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 repeat 7 (sc7)-like domains. Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in S. cerevisiae Rrp5 and 14 S1 repeats in H. sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 8 and S. cerevisiae S1 repeat 7. Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=90.05 E-value=2.1 Score=28.83 Aligned_cols=59 Identities=22% Similarity=0.209 Sum_probs=40.8
Q ss_pred EEEEEEEEeCCCceEEEEeCCCCEEEEEeccccccccc-----ccCCCCEEEEEeccCCCCeEEEE
Q 032460 70 VHEGFITESLPNGMFRVRLDNEDLILGYISGKIRQNFI-----RVLPGDRVRVEVSRYDTSKGRII 130 (140)
Q Consensus 70 e~~GvVik~l~n~~f~V~l~dG~~~lcrI~GKmRk~~I-----rI~vGDrV~VE~sp~D~~kGrIi 130 (140)
.+.|+|.++. +.-+.|.+.+|..-..+++ .+...++ ...+||.|.|.+..-|..+|+|.
T Consensus 17 i~~g~V~~v~-~~G~fv~l~~~~~g~v~~~-el~~~~~~~~~~~~~~Gd~v~vkV~~id~~~~~i~ 80 (83)
T cd04461 17 VVHGYVRNIT-PYGVFVEFLGGLTGLAPKS-YISDEFVTDPSFGFKKGQSVTAKVTSVDEEKQRFL 80 (83)
T ss_pred EEEEEEEEEe-eceEEEEcCCCCEEEEEHH-HCCcccccCHHHhcCCCCEEEEEEEEEcCCCCEEE
Confidence 4789999996 5666787877755554433 2222222 27889999999887787788875
No 50
>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=90.00 E-value=3.1 Score=26.96 Aligned_cols=62 Identities=21% Similarity=0.059 Sum_probs=40.4
Q ss_pred EEEEEEEEeCCCceEEEEeCC--CCEEEEEeccccccccc-----ccCCCCEEEEEeccCCCCeEEEEEEe
Q 032460 70 VHEGFITESLPNGMFRVRLDN--EDLILGYISGKIRQNFI-----RVLPGDRVRVEVSRYDTSKGRIIYRL 133 (140)
Q Consensus 70 e~~GvVik~l~n~~f~V~l~d--G~~~lcrI~GKmRk~~I-----rI~vGDrV~VE~sp~D~~kGrIiyRy 133 (140)
.+.|+|+++. +.-+.|.+.+ |..-+++++ .+...++ .+.+||.|.+.+...|..+++|..-.
T Consensus 6 ~~~g~V~~v~-~~g~~v~l~~~~~~~gll~~s-~l~~~~~~~~~~~~~~Gd~v~vkv~~~d~~~~~i~ls~ 74 (76)
T cd04452 6 LVVVTVKSIA-DMGAYVSLLEYGNIEGMILLS-ELSRRRIRSIRKLVKVGRKEVVKVIRVDKEKGYIDLSK 74 (76)
T ss_pred EEEEEEEEEE-ccEEEEEEcCCCCeEEEEEhH-HcCCcccCCHHHeeCCCCEEEEEEEEEECCCCEEEEEE
Confidence 4789999997 5555677754 344454544 2322222 26899999999887777777776543
No 51
>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=89.80 E-value=2.8 Score=27.82 Aligned_cols=58 Identities=17% Similarity=0.105 Sum_probs=38.0
Q ss_pred EEEEEeCCCceEEEEeCCCCEEEEEec----ccccccccccCCCCEEEEEeccCCCCeEEEE
Q 032460 73 GFITESLPNGMFRVRLDNEDLILGYIS----GKIRQNFIRVLPGDRVRVEVSRYDTSKGRII 130 (140)
Q Consensus 73 GvVik~l~n~~f~V~l~dG~~~lcrI~----GKmRk~~IrI~vGDrV~VE~sp~D~~kGrIi 130 (140)
|+|+++..+.-..|++.+|..=..+++ .+.....-.+.+||.|.+.+...|..+++|.
T Consensus 7 g~V~~v~~~~G~~V~l~~gv~G~i~~s~l~~~~~~~~~~~~~vG~~v~~kV~~id~~~~~i~ 68 (71)
T cd05696 7 VKVTKVEPDLGAVFELKDGLLGFVHISHLSDDKVPSDTGPFKAGTTHKARIIGYSPMDGLLQ 68 (71)
T ss_pred eEEEEEccCceEEEEeCCCCEEEEEHHHCCcchhcCcccccCCCCEEEEEEEEEeCCCCEEE
Confidence 899997423335688888866555543 2222212238899999999888887777664
No 52
>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=89.58 E-value=3.2 Score=28.00 Aligned_cols=60 Identities=13% Similarity=0.205 Sum_probs=40.8
Q ss_pred EEEEEEEEeCCCceEEEEeCCCCEEEEE---eccccccc----ccccCCCCEEEEEeccCCCCeEEEE
Q 032460 70 VHEGFITESLPNGMFRVRLDNEDLILGY---ISGKIRQN----FIRVLPGDRVRVEVSRYDTSKGRII 130 (140)
Q Consensus 70 e~~GvVik~l~n~~f~V~l~dG~~~lcr---I~GKmRk~----~IrI~vGDrV~VE~sp~D~~kGrIi 130 (140)
.+.|.|.+....|.| |.+..|..=..+ ++-..-.+ .-...+||.|.+.+-..|.++++|.
T Consensus 6 ~V~g~V~~i~~~G~f-V~l~~~v~G~v~~~~ls~~~~~~~~~~~~~~~~G~~v~~kVl~id~~~~~i~ 72 (74)
T cd05705 6 LLRGYVSSVTKQGVF-FRLSSSIVGRVLFQNVTKYFVSDPSLYNKYLPEGKLLTAKVLSVNSEKNLVE 72 (74)
T ss_pred EEEEEEEEEeCCcEE-EEeCCCCEEEEEHHHccCccccChhhHhcccCCCCEEEEEEEEEECCCCEEe
Confidence 589999999766665 888766555555 33332111 1236899999998877777777764
No 53
>cd05690 S1_RPS1_repeat_ec5 S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 5 (ec5) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=89.57 E-value=1.6 Score=27.84 Aligned_cols=60 Identities=27% Similarity=0.120 Sum_probs=39.5
Q ss_pred EEEEEEEEeCCCceEEEEeCCCCEEEEEecc-----cccccccccCCCCEEEEEeccCCCCeEEEE
Q 032460 70 VHEGFITESLPNGMFRVRLDNEDLILGYISG-----KIRQNFIRVLPGDRVRVEVSRYDTSKGRII 130 (140)
Q Consensus 70 e~~GvVik~l~n~~f~V~l~dG~~~lcrI~G-----KmRk~~IrI~vGDrV~VE~sp~D~~kGrIi 130 (140)
.+.|.|.++.+ .-+.|++++|..-+++++= +.+...-...+||.|.|.+..-|.++++|.
T Consensus 3 ~~~g~V~~i~~-~G~fv~l~~~~~Glv~~~~l~~~~~~~~~~~~~~~G~~v~v~v~~id~~~~~i~ 67 (69)
T cd05690 3 VVSGKIKSITD-FGIFVGLDGGIDGLVHISDISWTQRVRHPSEIYKKGQEVEAVVLNIDVERERIS 67 (69)
T ss_pred EEEEEEEEEEe-eeEEEEeCCCCEEEEEHHHCCCccccCChhhEECCCCEEEEEEEEEECCcCEEe
Confidence 47899999864 4456777777666665431 111111236899999999877777777764
No 54
>PRK03987 translation initiation factor IF-2 subunit alpha; Validated
Probab=89.56 E-value=2.1 Score=36.05 Aligned_cols=70 Identities=26% Similarity=0.260 Sum_probs=47.8
Q ss_pred cccCCcceEEEEEEEEeCCCceEEEEeCC--CCEEEEEeccccccccc-----ccCCCCEEEEEeccCCCCeEEEEEEec
Q 032460 62 EGANSEKWVHEGFITESLPNGMFRVRLDN--EDLILGYISGKIRQNFI-----RVLPGDRVRVEVSRYDTSKGRIIYRLR 134 (140)
Q Consensus 62 ~~~k~d~ie~~GvVik~l~n~~f~V~l~d--G~~~lcrI~GKmRk~~I-----rI~vGDrV~VE~sp~D~~kGrIiyRy~ 134 (140)
..|+... .+.|+|+++. +.-+.|.+.+ |..=+++++ .+..+++ .+.+||.|.|.+...|..+|.|.--.+
T Consensus 4 ~~P~~Gd-iV~G~V~~I~-~~G~fV~L~e~~gieGlI~iS-Els~~~i~~i~~~~kvGd~V~vkVi~VD~~k~~I~LSlK 80 (262)
T PRK03987 4 EWPEEGE-LVVGTVKEVK-DFGAFVTLDEYPGKEGFIHIS-EVASGWVKNIRDHVKEGQKVVCKVIRVDPRKGHIDLSLK 80 (262)
T ss_pred CCCCCCC-EEEEEEEEEE-CCEEEEEECCCCCcEEEEEHH-HcCcccccCHHHhCCCCCEEEEEEEEEecccCeEEEEEE
Confidence 4566544 4889999996 5556677764 655555554 2222222 378999999999888888888876544
No 55
>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=89.46 E-value=3.6 Score=26.96 Aligned_cols=62 Identities=26% Similarity=0.233 Sum_probs=37.7
Q ss_pred EEEEEEEEeCCCceEEEEeCC-CCEEEEEec---cc-c-----------cccccccCCCCEEEEEeccCCCCeEEEEEE
Q 032460 70 VHEGFITESLPNGMFRVRLDN-EDLILGYIS---GK-I-----------RQNFIRVLPGDRVRVEVSRYDTSKGRIIYR 132 (140)
Q Consensus 70 e~~GvVik~l~n~~f~V~l~d-G~~~lcrI~---GK-m-----------Rk~~IrI~vGDrV~VE~sp~D~~kGrIiyR 132 (140)
.++|.|+++- +.-+.|++.+ |..=.++++ +. + +.....+.+||.|.|.+..-|.++++|...
T Consensus 4 ~~~g~V~~v~-~~G~fv~l~~~~~~G~v~~~~l~~~~~~~d~~~~~~~~~~~~~~~~~gd~v~v~v~~vd~~~~~i~~~ 81 (83)
T cd04471 4 EFDGVISGVT-SFGLFVELDNLTVEGLVHVSTLGDDYYEFDEENHALVGERTGKVFRLGDKVKVRVVRVDLDRRKIDFE 81 (83)
T ss_pred EEEEEEEeEE-eeeEEEEecCCCEEEEEEEEecCCCcEEEcccceEEEeccCCCEEcCCCEEEEEEEEeccccCEEEEE
Confidence 3678888875 4444566654 433333332 21 1 111235788999999988878778888764
No 56
>PRK10053 hypothetical protein; Provisional
Probab=89.35 E-value=1.8 Score=33.34 Aligned_cols=55 Identities=11% Similarity=0.051 Sum_probs=46.0
Q ss_pred ccCCcceEEEEEEEEeCCCceEEEEeCCCCEEEEEecccccccccccCCCCEEEEEe
Q 032460 63 GANSEKWVHEGFITESLPNGMFRVRLDNEDLILGYISGKIRQNFIRVLPGDRVRVEV 119 (140)
Q Consensus 63 ~~k~d~ie~~GvVik~l~n~~f~V~l~dG~~~lcrI~GKmRk~~IrI~vGDrV~VE~ 119 (140)
|..+..+.++|.|++.+++..|.-+...| ++.--|.-+.-. +..+-|.|+|.+.-
T Consensus 58 ~~Dd~~V~L~G~Iv~~lg~d~Y~F~D~tG-~I~VeID~~~w~-G~~v~p~~kV~I~G 112 (130)
T PRK10053 58 MHDGATVSLRGNLIDHKGDDRYVFRDKSG-EINVIIPAAVFD-GREVQPDQMINING 112 (130)
T ss_pred CcCCCeEEEEEEEEEEeCCceEEEECCCC-cEEEEeCHHHcC-CCcCCCCCEEEEEE
Confidence 55666789999999999999999997777 578889888764 67899999998763
No 57
>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=89.32 E-value=2.2 Score=28.60 Aligned_cols=61 Identities=8% Similarity=0.052 Sum_probs=41.2
Q ss_pred EEEEEEEEeCCCceEEEEeCCCCEEEEEec------ccccccccccCCCCEEEEEeccCCCCeEEEEE
Q 032460 70 VHEGFITESLPNGMFRVRLDNEDLILGYIS------GKIRQNFIRVLPGDRVRVEVSRYDTSKGRIIY 131 (140)
Q Consensus 70 e~~GvVik~l~n~~f~V~l~dG~~~lcrI~------GKmRk~~IrI~vGDrV~VE~sp~D~~kGrIiy 131 (140)
.+.|.|++.. +.-..|.+++|-.=.++++ .+.+.-.-...+||.|.+.+...|.++.+|.-
T Consensus 3 ~V~g~V~~i~-~~g~~V~l~~~i~G~i~~~~ls~~~~~~~~~~~~~~vG~~v~~kV~~id~~~~~i~L 69 (73)
T cd05703 3 EVTGFVNNVS-KEFVWLTISPDVKGRIPLLDLSDDVSVLEHPEKKFPIGQALKAKVVGVDKEHKLLRL 69 (73)
T ss_pred EEEEEEEEEe-CCEEEEEeCCCcEEEEEHHHcCCccccccCHHHhCCCCCEEEEEEEEEeCCCCEEEE
Confidence 4789999995 6666788877633333321 12333233489999999998888877766653
No 58
>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=89.16 E-value=2.3 Score=27.50 Aligned_cols=61 Identities=30% Similarity=0.145 Sum_probs=44.0
Q ss_pred EEEEEEEEeCCCceEEEEeCCCCEEEEEeccccc----ccccccCCCCEEEEEeccCCCCeEEEEE
Q 032460 70 VHEGFITESLPNGMFRVRLDNEDLILGYISGKIR----QNFIRVLPGDRVRVEVSRYDTSKGRIIY 131 (140)
Q Consensus 70 e~~GvVik~l~n~~f~V~l~dG~~~lcrI~GKmR----k~~IrI~vGDrV~VE~sp~D~~kGrIiy 131 (140)
.+.|+|+++- ..-+.|.+.+|..-.++++=--. ...-.+.+||.|.|.+...|.++++|.-
T Consensus 7 iv~g~V~~v~-~~g~~V~l~~~~~g~ip~~~l~~~~~~~~~~~~~~G~~v~v~v~~vd~~~~~i~l 71 (74)
T PF00575_consen 7 IVEGKVTSVE-DFGVFVDLGNGIEGFIPISELSDDRIDDPSEVYKIGQTVRVKVIKVDKEKGRIRL 71 (74)
T ss_dssp EEEEEEEEEE-TTEEEEEESTSSEEEEEGGGSSSSEESSSHGTCETTCEEEEEEEEEETTTTEEEE
T ss_pred EEEEEEEEEE-CCEEEEEECCcEEEEEEeehhcCccccccccccCCCCEEEEEEEEEECCCCeEEE
Confidence 4899999996 57778888877766665542211 1123488999999999888888887753
No 59
>PF04717 Phage_base_V: Phage-related baseplate assembly protein; InterPro: IPR006531 This domain occurs in a family of phage (and bacteriocin) proteins related to the phage P2 V gene product, which forms the small spike at the tip of the tail []. Homologs in general are annotated as baseplate assembly protein V. At least one member is encoded within a region of Pectobacterium carotovorum (Erwinia carotovora) described as a bacteriocin, a phage tail-derived module able to kill bacteria closely related to the host strain. It is also found in Vgr-related proteins. Genes encoding type VI secretion systems (T6SS) are widely distributed in pathogenic Gram-negative bacterial species. In Vibrio cholerae, T6SS have been found to secrete three related proteins extracellularly, VgrG-1, VgrG-2, and VgrG-3. VgrG-1 can covalently cross-link actin in vitro, and this activity was used to demonstrate that V. cholerae can translocate VgrG-1 into macrophages by a T6SS-dependent mechanism. VgrG-related proteins likely assemble into a trimeric complex that is analogous to that formed by the two trimeric proteins gp27 and gp5 that make up the baseplate "tail spike" of Escherichia coli bacteriophage T4. The VgrG components of the T6SS apparatus might assemble a "cell-puncturing device" analogous to phage tail spikes to deliver effector protein domains through membranes of target host cells []. Gp5 is an integral component of the virion baseplate of bacteriophage T4. T4 Gp5 consists of 3 domains connected via long linkers: the N-terminal oligosaccharide/oligonucleotide-binding (OB)-fold domain, the middle lysozyme domain, and the C-terminal triplestranded-helix. The equivalent of the Gp5 OB-fold domain in the structure of VgrG is the domain of unknown function comprising residues 380-470 and conserved in all known VgrGs. This entry represents the OB-fold domain which consists of a 5-stranded antiparallel-barrel with a Greek-key topology [].; PDB: 3AQJ_C 3QR8_A 2P5Z_X.
Probab=89.11 E-value=2.1 Score=28.87 Aligned_cols=64 Identities=22% Similarity=0.307 Sum_probs=35.2
Q ss_pred EEEEEeCC-CceEEEEeC-CCCEEEEE------ecccccccccccCCCCEEEEEeccCCCCeEEEEEEecCCC
Q 032460 73 GFITESLP-NGMFRVRLD-NEDLILGY------ISGKIRQNFIRVLPGDRVRVEVSRYDTSKGRIIYRLRNKI 137 (140)
Q Consensus 73 GvVik~l~-n~~f~V~l~-dG~~~lcr------I~GKmRk~~IrI~vGDrV~VE~sp~D~~kGrIiyRy~r~~ 137 (140)
|+|+..-. .++++|+++ ++....+- -.|..+. ..-+.+||.|.|....-|.++|.|+-.+-..+
T Consensus 1 G~V~~v~~~~grvrV~~~~~~~~~s~Wl~~~~~~ag~~g~-~~~P~iGeqV~v~~~~Gd~~~~~vlg~l~~~~ 72 (79)
T PF04717_consen 1 GTVTAVDPDKGRVRVRFPDDGDIVSDWLPVLQPRAGGWGF-WFPPEIGEQVLVLFPGGDPERPVVLGSLYSDA 72 (79)
T ss_dssp EEEEEEETTTTEEEEE-B-CTTEEEEEEEE--S-BSSSB-------TT-EEEEEEGGCTTTSEEEEEEE--SS
T ss_pred CeEEEEECCCCEEEEEEecCCCccceEEEeeehhccCCee-EccCCCCcEEEEEccCCcCCCCEEEEEECCCC
Confidence 45555443 479999973 34443332 3343332 34489999999999888889999997664433
No 60
>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=88.91 E-value=2.7 Score=27.04 Aligned_cols=58 Identities=21% Similarity=0.259 Sum_probs=37.1
Q ss_pred EEEEEEEEeCCCceEEEEeCCCCEEEEEeccc-ccccc-----cccCCCCEEEEEeccCCCCeEEEE
Q 032460 70 VHEGFITESLPNGMFRVRLDNEDLILGYISGK-IRQNF-----IRVLPGDRVRVEVSRYDTSKGRII 130 (140)
Q Consensus 70 e~~GvVik~l~n~~f~V~l~dG~~~lcrI~GK-mRk~~-----IrI~vGDrV~VE~sp~D~~kGrIi 130 (140)
.+.|+|+++- +....|.+..+ ..+.++-. +.... -.+.+||.|.+.+...+...+.|.
T Consensus 3 iv~g~V~~i~-~~~~~v~l~~~--~~g~l~~~e~~~~~~~~~~~~~~~Gd~i~~~i~~~~~~~~~i~ 66 (70)
T cd05687 3 IVKGTVVSVD-DDEVLVDIGYK--SEGIIPISEFSDDPIENGEDEVKVGDEVEVYVLRVEDEEGNVV 66 (70)
T ss_pred EEEEEEEEEe-CCEEEEEeCCC--ceEEEEHHHhCccccCCHhHcCCCCCEEEEEEEEEECCCCeEE
Confidence 4789999985 66677777544 34444422 21111 127899999999877776666664
No 61
>PHA02945 interferon resistance protein; Provisional
Probab=88.88 E-value=3 Score=30.48 Aligned_cols=67 Identities=21% Similarity=0.128 Sum_probs=48.9
Q ss_pred ccCCcceEEEEEEEEeCCCceEEEEeCC--CCEEEEEec------ccccccccccCCCCEEEEEeccCCCCeEEEEEEec
Q 032460 63 GANSEKWVHEGFITESLPNGMFRVRLDN--EDLILGYIS------GKIRQNFIRVLPGDRVRVEVSRYDTSKGRIIYRLR 134 (140)
Q Consensus 63 ~~k~d~ie~~GvVik~l~n~~f~V~l~d--G~~~lcrI~------GKmRk~~IrI~vGDrV~VE~sp~D~~kGrIiyRy~ 134 (140)
+|++..+ +.|+|.+ . +.-+.|.|++ |.+-..+++ |-++. +-.+ +|.+|.+.+---|..||.|=--++
T Consensus 8 ~P~~Gel-vigtV~~-~-d~ga~v~L~EY~g~eg~i~~seveva~~wvK~-rd~l-~GqkvV~KVirVd~~kg~IDlSlK 82 (88)
T PHA02945 8 LPNVGDV-LKGKVYE-N-GYALYIDLFDYPHSEAILAESVQMHMNRYFKY-RDKL-VGKTVKVKVIRVDYTKGYIDVNYK 82 (88)
T ss_pred CCCCCcE-EEEEEEe-c-CceEEEEecccCCcEEEEEeehhhhccceEee-eeEe-cCCEEEEEEEEECCCCCEEEeEee
Confidence 5666555 6799999 5 5566777754 677666665 66665 5557 999999998888999999865433
No 62
>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=88.82 E-value=2.8 Score=26.25 Aligned_cols=58 Identities=26% Similarity=0.172 Sum_probs=36.2
Q ss_pred EEEEEEEEeCCCceEEEEeCCCCEEEEEecccccccc-----cccCCCCEEEEEeccCCCCeEEEE
Q 032460 70 VHEGFITESLPNGMFRVRLDNEDLILGYISGKIRQNF-----IRVLPGDRVRVEVSRYDTSKGRII 130 (140)
Q Consensus 70 e~~GvVik~l~n~~f~V~l~dG~~~lcrI~GKmRk~~-----IrI~vGDrV~VE~sp~D~~kGrIi 130 (140)
.+.|+|+++.+ .-+.|++.++..-.+++. .+.... -.+.+||.|.|.+...|. .|.|.
T Consensus 3 ~~~g~V~~v~~-~G~~v~l~~~~~g~l~~~-~l~~~~~~~~~~~~~~Gd~v~v~v~~~d~-~~~i~ 65 (68)
T cd04472 3 IYEGKVVKIKD-FGAFVEILPGKDGLVHIS-ELSDERVEKVEDVLKVGDEVKVKVIEVDD-RGRIS 65 (68)
T ss_pred EEEEEEEEEEE-eEEEEEeCCCCEEEEEhH-HcCCccccCHHHccCCCCEEEEEEEEECC-CCcEE
Confidence 46799999874 444666666544444432 111111 136899999999877776 67665
No 63
>PF15057 DUF4537: Domain of unknown function (DUF4537)
Probab=88.61 E-value=4.6 Score=30.27 Aligned_cols=66 Identities=23% Similarity=0.270 Sum_probs=42.7
Q ss_pred CCcceEEEEEEEEeCCCceEEEEeCCCCEEEEEeccccccc---ccccCCCCEEEEEeccCCCC---eEEEEE
Q 032460 65 NSEKWVHEGFITESLPNGMFRVRLDNEDLILGYISGKIRQN---FIRVLPGDRVRVEVSRYDTS---KGRIIY 131 (140)
Q Consensus 65 k~d~ie~~GvVik~l~n~~f~V~l~dG~~~lcrI~GKmRk~---~IrI~vGDrV~VE~sp~D~~---kGrIiy 131 (140)
.+|..=-.|+|.+.+..+.|.|+.+++........--+... .-.+.+||.|+.- |+-+.. =|.|+.
T Consensus 9 ~~DG~YY~GtV~~~~~~~~~lV~f~~~~~~~v~~~~iI~~~~~~~~~L~~GD~VLA~-~~~~~~~Y~Pg~V~~ 80 (124)
T PF15057_consen 9 EEDGFYYPGTVKKCVSSGQFLVEFDDGDTQEVPISDIIALSDAMRHSLQVGDKVLAP-WEPDDCRYGPGTVIA 80 (124)
T ss_pred CCCCcEEeEEEEEccCCCEEEEEECCCCEEEeChHHeEEccCcccCcCCCCCEEEEe-cCcCCCEEeCEEEEE
Confidence 35566688999999999999999977666544332222211 1249999999875 432221 266664
No 64
>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=87.74 E-value=4.5 Score=26.01 Aligned_cols=63 Identities=25% Similarity=0.223 Sum_probs=40.2
Q ss_pred EEEEEEEEeCCCceEEEEeCC-CCEEEEEeccccccc-----ccccCCCCEEEEEeccCCCCeEEEEEEec
Q 032460 70 VHEGFITESLPNGMFRVRLDN-EDLILGYISGKIRQN-----FIRVLPGDRVRVEVSRYDTSKGRIIYRLR 134 (140)
Q Consensus 70 e~~GvVik~l~n~~f~V~l~d-G~~~lcrI~GKmRk~-----~IrI~vGDrV~VE~sp~D~~kGrIiyRy~ 134 (140)
.+.|.|+++- ..-..|++.+ +..=+++++ .+... .-.+.+||.|.+.+...|.++++|....+
T Consensus 5 ~v~g~V~~i~-~~g~~v~l~~~~~~g~i~~~-~l~~~~~~~~~~~~~~Gd~v~v~i~~vd~~~~~i~ls~k 73 (77)
T cd05708 5 KIDGTVRRVE-DYGVFIDIDGTNVSGLCHKS-EISDNRVADASKLFRVGDKVRAKVLKIDAEKKRISLGLK 73 (77)
T ss_pred EEEEEEEEEE-cceEEEEECCCCeEEEEEHH-HCCCCccCCHhHeecCCCEEEEEEEEEeCCCCEEEEEEE
Confidence 4789999996 5555667754 333333332 11111 11368999999998877888888876543
No 65
>cd04482 RPA2_OBF_like RPA2_OBF_like: A subgroup of uncharacterized archaeal OB folds with similarity to the OB fold of the central ssDNA-binding domain (DBD)-D of human RPA2 (also called RPA32). RPA2 is a subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B; RPA2 DBD-D is a weak ssDNA-binding domain. RPA2 DBD-D is also involved in trimerization. The ssDNA binding mechanism is believed to be multistep and to involve conformational change. N-terminal to human RPA2 DBD-D is a domain containing all the known phosphorylation sites of RPA. Human RPA2 is phosphorylated in a cell cycle depende
Probab=86.85 E-value=2.2 Score=30.10 Aligned_cols=53 Identities=23% Similarity=0.233 Sum_probs=32.4
Q ss_pred EEEEEEEeC---CCceEEEEe-CCCCEEEE-Eecc--cccccccccCCCCEEEEE--eccCC
Q 032460 71 HEGFITESL---PNGMFRVRL-DNEDLILG-YISG--KIRQNFIRVLPGDRVRVE--VSRYD 123 (140)
Q Consensus 71 ~~GvVik~l---~n~~f~V~l-~dG~~~lc-rI~G--KmRk~~IrI~vGDrV~VE--~sp~D 123 (140)
++|.|.+.- .+|+....+ +++-.+.| --++ ++++-...+.+||.|.|. ++.|.
T Consensus 3 v~GeVs~~~~~~~sGH~yFtlkD~~~~i~cv~f~~~g~~~~~~~~l~~Gd~V~v~G~v~~y~ 64 (91)
T cd04482 3 VTGKVVEEPRTIEGGHVFFKISDGTGEIDCAAYEPTKEFRDVVRLLIPGDEVTVYGSVRPGT 64 (91)
T ss_pred EEEEEeCCeecCCCCCEEEEEECCCcEEEEEEECcccccccccCCCCCCCEEEEEEEEecCC
Confidence 678877541 466555555 33334555 3343 376656679999999887 34443
No 66
>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=86.65 E-value=5.3 Score=26.09 Aligned_cols=51 Identities=20% Similarity=0.234 Sum_probs=35.5
Q ss_pred EEEEEEEEeCCCceEEEEeCCCCEEEEEecccccccccccCCCCEEEEEeccCCC
Q 032460 70 VHEGFITESLPNGMFRVRLDNEDLILGYISGKIRQNFIRVLPGDRVRVEVSRYDT 124 (140)
Q Consensus 70 e~~GvVik~l~n~~f~V~l~dG~~~lcrI~GKmRk~~IrI~vGDrV~VE~sp~D~ 124 (140)
.++|+|++.- .+.+.|.+ ++ ..+.++-+=...+-...+||.|.|-+...+.
T Consensus 6 iV~G~V~~~~-~~~~~vdi-g~--~eg~lp~~e~~~~~~~~~Gd~v~v~v~~v~~ 56 (67)
T cd04455 6 IVTGIVKRVD-RGNVIVDL-GK--VEAILPKKEQIPGESYRPGDRIKAYVLEVRK 56 (67)
T ss_pred EEEEEEEEEc-CCCEEEEc-CC--eEEEeeHHHCCCCCcCCCCCEEEEEEEEEec
Confidence 4899999995 55666776 33 6888884433322347999999998775554
No 67
>PF02736 Myosin_N: Myosin N-terminal SH3-like domain; InterPro: IPR004009 This domain has an SH3-like fold. It is found at the N terminus of many but not all myosins. The function of this domain is unknown.; GO: 0003774 motor activity, 0005524 ATP binding, 0016459 myosin complex; PDB: 2EC6_A 2W4H_M 1O1E_P 1O1D_D 1O18_A 1O1C_P 1O1B_D 1O1F_A 2W4A_M 2W4G_M ....
Probab=86.54 E-value=2 Score=26.53 Aligned_cols=33 Identities=12% Similarity=0.123 Sum_probs=26.1
Q ss_pred cCCcceEEEEEEEEeCCCceEEEEeCCCCEEEEE
Q 032460 64 ANSEKWVHEGFITESLPNGMFRVRLDNEDLILGY 97 (140)
Q Consensus 64 ~k~d~ie~~GvVik~l~n~~f~V~l~dG~~~lcr 97 (140)
|.+...-+.|.|++. .++.+.|++.||+++...
T Consensus 7 pD~~egfv~g~I~~~-~g~~vtV~~~~G~~~tv~ 39 (42)
T PF02736_consen 7 PDPKEGFVKGEIIEE-EGDKVTVKTEDGKEVTVK 39 (42)
T ss_dssp EESSSSEEEEEEEEE-ESSEEEEEETTTEEEEEE
T ss_pred eCCcccEEEEEEEEE-cCCEEEEEECCCCEEEeC
Confidence 444556688999987 699999999999887653
No 68
>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=85.89 E-value=5.9 Score=25.90 Aligned_cols=58 Identities=16% Similarity=0.167 Sum_probs=37.7
Q ss_pred EEEEEEEEeCCCceEEEEeCCCCEEEEEeccc----ccccccccCCCCEEEEEeccCCCCeEEEE
Q 032460 70 VHEGFITESLPNGMFRVRLDNEDLILGYISGK----IRQNFIRVLPGDRVRVEVSRYDTSKGRII 130 (140)
Q Consensus 70 e~~GvVik~l~n~~f~V~l~dG~~~lcrI~GK----mRk~~IrI~vGDrV~VE~sp~D~~kGrIi 130 (140)
.+.|+|+++..+| ..|++.+| +.+.++-. -+...-...+||.|.+.+.-.|+++.+|.
T Consensus 3 ~V~g~V~~i~~~G-~~v~l~~~--v~g~v~~~~l~~~~~~~~~~~~G~~i~~kVi~id~~~~~i~ 64 (66)
T cd05695 3 LVNARVKKVLSNG-LILDFLSS--FTGTVDFLHLDPEKSSKSTYKEGQKVRARILYVDPSTKVVG 64 (66)
T ss_pred EEEEEEEEEeCCc-EEEEEcCC--ceEEEEHHHcCCccCcccCcCCCCEEEEEEEEEeCCCCEEe
Confidence 4789999998555 56777765 44444311 11112348899999998877777666653
No 69
>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=85.77 E-value=6.9 Score=25.24 Aligned_cols=59 Identities=25% Similarity=0.115 Sum_probs=39.3
Q ss_pred EEEEEEEEeCCCceEEEEeCCCCEEEEEeccccc------ccccccCCCCEEEEEeccCCCCeEEEE
Q 032460 70 VHEGFITESLPNGMFRVRLDNEDLILGYISGKIR------QNFIRVLPGDRVRVEVSRYDTSKGRII 130 (140)
Q Consensus 70 e~~GvVik~l~n~~f~V~l~dG~~~lcrI~GKmR------k~~IrI~vGDrV~VE~sp~D~~kGrIi 130 (140)
.+.|+|.++. ..-+.|++++|..-+++++ .+. ...-.+.+||.|.|.+..-|.++++|.
T Consensus 6 ~~~g~V~~i~-~~G~fv~l~~~~~Gl~~~~-~l~~~~~~~~~~~~~~~Gd~v~v~v~~id~~~~~i~ 70 (72)
T cd05689 6 RLFGKVTNLT-DYGCFVELEEGVEGLVHVS-EMDWTNKNIHPSKVVSLGDEVEVMVLDIDEERRRIS 70 (72)
T ss_pred EEEEEEEEEE-eeEEEEEcCCCCEEEEEEE-eccCcccccCcccEeCCCCEEEEEEEEeeCCcCEEe
Confidence 4789999986 4445677777665555543 221 111236889999999887787777764
No 70
>cd05791 S1_CSL4 S1_CSL4: CSL4, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. ScCSL4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In S. cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".
Probab=85.21 E-value=3.3 Score=29.27 Aligned_cols=59 Identities=22% Similarity=0.216 Sum_probs=39.5
Q ss_pred cCCcceEEEEEEEEeCCCceEEEEe--CCCCEEEEEecccccccccc------------cCCCCEEEEEeccCCC
Q 032460 64 ANSEKWVHEGFITESLPNGMFRVRL--DNEDLILGYISGKIRQNFIR------------VLPGDRVRVEVSRYDT 124 (140)
Q Consensus 64 ~k~d~ie~~GvVik~l~n~~f~V~l--~dG~~~lcrI~GKmRk~~Ir------------I~vGDrV~VE~sp~D~ 124 (140)
|+...+ +.|+|+++ ......|.. -+++.......|-++...++ ..+||.|+-++..+++
T Consensus 4 P~~GDi-Vig~V~~v-~~~~~~v~I~~v~~~~l~~~~~g~l~~~dv~~~~~d~~~~~~~f~~GDiV~AkVis~~~ 76 (92)
T cd05791 4 PKVGSI-VIARVTRI-NPRFAKVDILCVGGRPLKESFRGVIRKEDIRATEKDKVEMYKCFRPGDIVRAKVISLGD 76 (92)
T ss_pred CCCCCE-EEEEEEEE-cCCEEEEEEEEecCeecCCCcccEEEHHHccccccchHHHHhhcCCCCEEEEEEEEcCC
Confidence 455444 78999998 477777765 35555565666666644332 6899999988765554
No 71
>PF00313 CSD: 'Cold-shock' DNA-binding domain; InterPro: IPR002059 When Escherichia coli is exposed to a temperature drop from 37 to 10 degrees centigrade, a 4-5 hour lag phase occurs, after which growth is resumed at a reduced rate []. During the lag phase, the expression of around 13 proteins, which contain specific DNA-binding regions [], is increased 2-10 fold. These so-called 'cold shock' proteins are thought to help the cell to survive in temperatures lower than optimum growth temperature, by contrast with heat shock proteins, which help the cell to survive in temperatures greater than the optimum, possibly by condensation of the chromosome and organisation of the prokaryotic nucleoid []. A conserved domain of about 70 amino acids has been found in prokaryotic and eukaryotic DNA-binding proteins [, , ]. This domain is known as the 'cold-shock domain' (CSD), part of which is highly similar [] to the RNP-1 RNA-binding motif.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1HZC_A 1I5F_A 1HZ9_B 1C9O_B 1HZB_B 1HZA_A 2HAX_B 2L15_A 2LSS_A 3I2Z_B ....
Probab=84.90 E-value=8 Score=25.02 Aligned_cols=51 Identities=25% Similarity=0.188 Sum_probs=35.2
Q ss_pred EEEEEEEeCC-CceEEEEeCCCC-EEEEEecccccccccccCCCCEEEEEecc
Q 032460 71 HEGFITESLP-NGMFRVRLDNED-LILGYISGKIRQNFIRVLPGDRVRVEVSR 121 (140)
Q Consensus 71 ~~GvVik~l~-n~~f~V~l~dG~-~~lcrI~GKmRk~~IrI~vGDrV~VE~sp 121 (140)
|+|+|...-. .++=.|.++++. .+-.|++--.....-.+.+||.|.+++..
T Consensus 1 ~~G~V~~~~~~kgyGFI~~~~~~~diFfh~s~~~~~~~~~l~~G~~V~F~~~~ 53 (66)
T PF00313_consen 1 MTGTVKWFDDEKGYGFITSDDGGEDIFFHISDLSGNGFRSLKEGDRVEFEVEE 53 (66)
T ss_dssp EEEEEEEEETTTTEEEEEETTSSSEEEEEGGGBCSSSSTS--TTSEEEEEEEE
T ss_pred CeEEEEEEECCCCceEEEEcccceeEEeccccccccccccCCCCCEEEEEEEE
Confidence 7899998865 345466666655 88999887444322468999999999875
No 72
>PF12158 DUF3592: Protein of unknown function (DUF3592); InterPro: IPR021994 This family of proteins is functionally uncharacterised.This family of proteins is found in bacteria, archaea, eukaryotes and viruses. Proteins in this family are typically between 150 and 242 amino acids in length.
Probab=84.06 E-value=10 Score=27.28 Aligned_cols=62 Identities=15% Similarity=0.105 Sum_probs=38.0
Q ss_pred ceEEEEEEEEeC-------CC--ceEEEEe----CCCCEEEEEeccc---ccccccccCCCCEEEEEeccCCCCeEEEE
Q 032460 68 KWVHEGFITESL-------PN--GMFRVRL----DNEDLILGYISGK---IRQNFIRVLPGDRVRVEVSRYDTSKGRII 130 (140)
Q Consensus 68 ~ie~~GvVik~l-------~n--~~f~V~l----~dG~~~lcrI~GK---mRk~~IrI~vGDrV~VE~sp~D~~kGrIi 130 (140)
-.+.+|+|+..- ++ ..|.+.. +||+.+. +.... .-...-...+||.|.|-.+|.+|+++++.
T Consensus 36 ~~~~~g~V~~~~~~~~~~~~~~~~~y~~~v~y~~~~G~~~~-~~~~~~~~~~~~~~~~~~G~~V~V~Y~P~~P~~~~l~ 113 (148)
T PF12158_consen 36 WQRVEGTVVSSETERERSDGSRSSSYRPVVEYTYQDGRTYS-RFYSGSDNFGSYWPKYPIGDTVTVYYNPNNPEEARLE 113 (148)
T ss_pred CcEEEEEEEEEEEEecccCCCCceEEEEEEEEEECCCcEEE-EeccCCcccccCCccCCCcCEEEEEECCcCCCeEEEe
Confidence 346778888775 11 3333222 4676655 33332 21111126699999999999999998887
No 73
>cd04487 RecJ_OBF2_like RecJ_OBF2_like: A subfamily of OB folds corresponding to the second OB fold (OBF2) of archaeal-specific proteins with similarity to eubacterial RecJ. RecJ is an ssDNA-specific exonuclease. Although the overall sequence similarity of these proteins to eubacterial RecJ proteins is marginal, they appear to carry motifs, which have been shown to be essential for nuclease function in Escherichia coli RecJ. In addition to this OB fold, most proteins in this subfamily contain: i) an N-terminal OB fold belonging to a different domain family (the ribosomal S1-like RNA-binding family); and ii) a domain, C-terminal to OBF2, characteristic of DHH family proteins. DHH family proteins include E. coli RecJ, and are predicted to have a phosphoesterase function.
Probab=82.65 E-value=7 Score=26.64 Aligned_cols=51 Identities=22% Similarity=0.164 Sum_probs=31.2
Q ss_pred EEEEEEEEe-CCCceEEEEe-CCCCEEEEEe-cccccccccccCCCCEEEEEec
Q 032460 70 VHEGFITES-LPNGMFRVRL-DNEDLILGYI-SGKIRQNFIRVLPGDRVRVEVS 120 (140)
Q Consensus 70 e~~GvVik~-l~n~~f~V~l-~dG~~~lcrI-~GKmRk~~IrI~vGDrV~VE~s 120 (140)
.++|.|.+. ..+|+.+..+ +++-.+.|-+ ++...+-...+.+||.|.+.-.
T Consensus 2 ~v~GeVs~~~~~~GHvyfsLkD~~a~i~cv~f~~~~~~~~~~l~~Gd~V~v~G~ 55 (73)
T cd04487 2 HIEGEVVQIKQTSGPTIFTLRDETGTVWAAAFEEAGVRAYPEVEVGDIVRVTGE 55 (73)
T ss_pred EEEEEEeccccCCCCEEEEEEcCCEEEEEEEEchhccCCcCCCCCCCEEEEEEE
Confidence 467777743 2577666666 3444556644 4433223457999999988744
No 74
>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=82.58 E-value=7.9 Score=27.08 Aligned_cols=52 Identities=13% Similarity=0.073 Sum_probs=36.2
Q ss_pred EEEEEEEEeCCC-ceEEEEeCCCCEEEEEeccc-------ccccccccCCCCEEEEEecc
Q 032460 70 VHEGFITESLPN-GMFRVRLDNEDLILGYISGK-------IRQNFIRVLPGDRVRVEVSR 121 (140)
Q Consensus 70 e~~GvVik~l~n-~~f~V~l~dG~~~lcrI~GK-------mRk~~IrI~vGDrV~VE~sp 121 (140)
...|+|+++.+. +-..|.+.+|..-+++++-- ...-.-.+.+||.|.|.+.-
T Consensus 10 iy~g~V~~i~~~~~GaFV~l~~g~~Gllh~seis~~~~~~v~~~~~~~~~Gd~v~VqV~~ 69 (88)
T cd04453 10 IYLGRVKKIVPGLQAAFVDIGLGKNGFLHLSDILPAYFKKHKKIAKLLKEGQEILVQVVK 69 (88)
T ss_pred EEEEEEEEeccCCcEEEEEeCCCCEEEEEhHHcCchhccccCCHHHcCCCCCEEEEEEEE
Confidence 588999999864 24567778888888887621 11112238899999998753
No 75
>PRK07899 rpsA 30S ribosomal protein S1; Reviewed
Probab=82.28 E-value=5.9 Score=36.17 Aligned_cols=65 Identities=29% Similarity=0.275 Sum_probs=47.4
Q ss_pred EEEEEEEEeCCCceEEEEeCCCCEEEEEec----ccccccccccCCCCEEEEEeccCCCCeEEEEEEecC
Q 032460 70 VHEGFITESLPNGMFRVRLDNEDLILGYIS----GKIRQNFIRVLPGDRVRVEVSRYDTSKGRIIYRLRN 135 (140)
Q Consensus 70 e~~GvVik~l~n~~f~V~l~dG~~~lcrI~----GKmRk~~IrI~vGDrV~VE~sp~D~~kGrIiyRy~r 135 (140)
.+.|+|+++.+.|. .|++.+|..-+++++ .++....-.+.+||.|.|.+...|.++++|..-.+.
T Consensus 296 vv~G~V~~I~~fGv-FVeL~~gieGLvh~SeLs~~~v~~~~~~~kvGd~V~VkIi~ID~e~rrI~LSlK~ 364 (486)
T PRK07899 296 IVPGKVTKLVPFGA-FVRVEEGIEGLVHISELAERHVEVPEQVVQVGDEVFVKVIDIDLERRRISLSLKQ 364 (486)
T ss_pred EEEEEEEEEeccEE-EEEeCCCcEEEEEHHHcCcccccCccceeCCCCEEEEEEEEEECCCCEEEEEEEE
Confidence 58999999975554 577888877777765 222222234789999999988888888898866543
No 76
>PTZ00248 eukaryotic translation initiation factor 2 subunit 1; Provisional
Probab=82.22 E-value=7.8 Score=33.88 Aligned_cols=71 Identities=17% Similarity=0.025 Sum_probs=47.8
Q ss_pred ccCCcceEEEEEEEEeCCCceEEEEeC--CCCEEEEEecccccccc---cc--cCCCCEEEEEeccCCCCeEEEEEEecC
Q 032460 63 GANSEKWVHEGFITESLPNGMFRVRLD--NEDLILGYISGKIRQNF---IR--VLPGDRVRVEVSRYDTSKGRIIYRLRN 135 (140)
Q Consensus 63 ~~k~d~ie~~GvVik~l~n~~f~V~l~--dG~~~lcrI~GKmRk~~---Ir--I~vGDrV~VE~sp~D~~kGrIiyRy~r 135 (140)
.|+... .+.|+|+++.. .-..|.+. +|..=+.+++= +..++ +. +.+||.|.|.+-..|..+|+|.--.++
T Consensus 14 ~P~~Gd-vV~g~V~~I~d-~GafV~L~EY~gvEGlIhiSE-lS~~ri~~i~d~vkvGd~v~vkVl~VD~ekg~IdLS~K~ 90 (319)
T PTZ00248 14 FPEEDD-LVMVKVVRITE-MGAYVSLLEYDDIEGMILMSE-LSKRRIRSINKLIRVGRHEVVVVLRVDKEKGYIDLSKKR 90 (319)
T ss_pred CCCCCC-EEEEEEEEEeC-CeEEEEecCCCCcEEEEEHHH-hcccccCCHHHhcCCCCEEEEEEEEEeCCCCEEEEEeee
Confidence 444433 38899999974 44457775 56666666653 22222 22 899999999988778889998765544
Q ss_pred C
Q 032460 136 K 136 (140)
Q Consensus 136 ~ 136 (140)
-
T Consensus 91 v 91 (319)
T PTZ00248 91 V 91 (319)
T ss_pred c
Confidence 3
No 77
>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=82.05 E-value=12 Score=24.72 Aligned_cols=63 Identities=22% Similarity=0.213 Sum_probs=38.0
Q ss_pred EEEEEEEEeCCCceEEEEeC---CCCEEEEEecc----cc-cccccccCCCCEEEEEeccCCCCeEEEEEEecC
Q 032460 70 VHEGFITESLPNGMFRVRLD---NEDLILGYISG----KI-RQNFIRVLPGDRVRVEVSRYDTSKGRIIYRLRN 135 (140)
Q Consensus 70 e~~GvVik~l~n~~f~V~l~---dG~~~lcrI~G----Km-Rk~~IrI~vGDrV~VE~sp~D~~kGrIiyRy~r 135 (140)
.+.|+|+++.+. -+.|+++ +|..-+.+++= +. ....-.+.+||.|.|.+..-| +|+|....+.
T Consensus 3 ~~~g~V~~v~~~-G~fv~l~~~~~~~~gll~~s~l~~~~~~~~~~~~~~~Gd~v~v~v~~vd--~~~i~~s~k~ 73 (79)
T cd05684 3 IYKGKVTSIMDF-GCFVQLEGLKGRKEGLVHISQLSFEGRVANPSDVVKRGQKVKVKVISIQ--NGKISLSMKD 73 (79)
T ss_pred EEEEEEEEEEee-eEEEEEeCCCCCcEEEEEhHhccCCCCcCChhheeCCCCEEEEEEEEEe--CCEEEEEEEe
Confidence 467899998644 4456665 34444444431 11 111123689999999987666 6777766543
No 78
>PRK13806 rpsA 30S ribosomal protein S1; Provisional
Probab=81.78 E-value=6.8 Score=35.35 Aligned_cols=66 Identities=27% Similarity=0.233 Sum_probs=47.1
Q ss_pred eEEEEEEEEeCCCceEEEEeCCCCEEEEEecc-----cccccccccCCCCEEEEEeccCCCCeEEEEEEecC
Q 032460 69 WVHEGFITESLPNGMFRVRLDNEDLILGYISG-----KIRQNFIRVLPGDRVRVEVSRYDTSKGRIIYRLRN 135 (140)
Q Consensus 69 ie~~GvVik~l~n~~f~V~l~dG~~~lcrI~G-----KmRk~~IrI~vGDrV~VE~sp~D~~kGrIiyRy~r 135 (140)
-.+.|+|+.+.+.| ..|.+.+|..-+++++- ++.+-.-++.+||.|.|.+...|.++++|.--...
T Consensus 294 ~~v~G~V~~v~~~G-~fV~l~~gv~Glvh~sels~~~~~~~~~~~~~~Gd~v~vkVl~iD~e~~ri~Ls~K~ 364 (491)
T PRK13806 294 DKVTGKVVRLAPFG-AFVEILPGIEGLVHVSEMSWTRRVNKPEDVVAPGDAVAVKIKDIDPAKRRISLSLRD 364 (491)
T ss_pred CEEEEEEEEEeCce-EEEEeCCCcEEEEEHHHcCcccccCCHHHcCCCCCEEEEEEEEEEccCCEEEEEEee
Confidence 36899999997544 45678778777777652 22222335899999999988788888888755443
No 79
>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=81.59 E-value=11 Score=24.08 Aligned_cols=57 Identities=16% Similarity=0.389 Sum_probs=37.6
Q ss_pred EEEEEEEEeCCCceEEEEeCCCCEEEEEecc-cccccc---cccCCCCEEEEEeccCCCCeEEEE
Q 032460 70 VHEGFITESLPNGMFRVRLDNEDLILGYISG-KIRQNF---IRVLPGDRVRVEVSRYDTSKGRII 130 (140)
Q Consensus 70 e~~GvVik~l~n~~f~V~l~dG~~~lcrI~G-KmRk~~---IrI~vGDrV~VE~sp~D~~kGrIi 130 (140)
.+.|+|++.. ++-+.|.+ +| +.+.++- .+.... ..-.+||.+.+.+...|...++|+
T Consensus 3 iv~g~V~~v~-~~G~~v~l-~g--~~gfip~s~~~~~~~~~~~~~vG~~i~~~i~~vd~~~~~i~ 63 (67)
T cd04465 3 IVEGKVTEKV-KGGLIVDI-EG--VRAFLPASQVDLRPVEDLDEYVGKELKFKIIEIDRERNNIV 63 (67)
T ss_pred EEEEEEEEEE-CCeEEEEE-CC--EEEEEEHHHCCCcccCChHHhCCCEEEEEEEEEeCCCCEEE
Confidence 3689999996 56677888 65 4555542 222111 122489999999888887667765
No 80
>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=81.19 E-value=5.5 Score=28.46 Aligned_cols=57 Identities=16% Similarity=0.221 Sum_probs=39.0
Q ss_pred cCCcceEEEEEEEEeCCCceEEEEeCCCCEEEEE-----ecccccccccccCCCCEEEEEeccCCC
Q 032460 64 ANSEKWVHEGFITESLPNGMFRVRLDNEDLILGY-----ISGKIRQNFIRVLPGDRVRVEVSRYDT 124 (140)
Q Consensus 64 ~k~d~ie~~GvVik~l~n~~f~V~l~dG~~~lcr-----I~GKmRk~~IrI~vGDrV~VE~sp~D~ 124 (140)
|+.+.+ +-|+|+.. .+..|+|.... ...|. ..|.-|+++-.+.+||.|.-++...+.
T Consensus 4 P~~gD~-VIG~V~~~-~~~~~~VdI~s--~~~a~L~~~~f~gatk~~rp~L~~GDlV~ArV~~~~~ 65 (86)
T cd05790 4 PAKGDH-VIGIVVAK-AGDFFKVDIGG--SEPASLSYLAFEGATKRNRPNLNVGDLVYARVVKANR 65 (86)
T ss_pred CCCCCE-EEEEEEEE-cCCeEEEEcCC--CcceEechHHcccccccccccCCCCCEEEEEEEecCC
Confidence 454444 67999998 58999998733 23333 344455556669999999988766554
No 81
>PRK05807 hypothetical protein; Provisional
Probab=81.19 E-value=12 Score=28.35 Aligned_cols=61 Identities=23% Similarity=0.244 Sum_probs=38.6
Q ss_pred EEEEEEEEeCCCceEEEEeCCCCEEEEEec----ccccccccccCCCCEEEEEeccCCCCeEEEEEEe
Q 032460 70 VHEGFITESLPNGMFRVRLDNEDLILGYIS----GKIRQNFIRVLPGDRVRVEVSRYDTSKGRIIYRL 133 (140)
Q Consensus 70 e~~GvVik~l~n~~f~V~l~dG~~~lcrI~----GKmRk~~IrI~vGDrV~VE~sp~D~~kGrIiyRy 133 (140)
.+.|+|+.+.+.| +.|.+ +|..-+.+++ +.++.-.-.+.+||.|.|.+...|. .|.|..-.
T Consensus 8 vv~G~Vt~i~~~G-afV~L-~~~~Glvhiseis~~~v~~~~~~~kvGd~V~VkV~~id~-~gkI~LSl 72 (136)
T PRK05807 8 ILEGTVVNITNFG-AFVEV-EGKTGLVHISEVADTYVKDIREHLKEQDKVKVKVISIDD-NGKISLSI 72 (136)
T ss_pred EEEEEEEEEECCe-EEEEE-CCEEEEEEhhhcccccccCccccCCCCCEEEEEEEEECC-CCcEEEEE
Confidence 5899999997544 45667 5665555554 1121111237899999999766565 57775443
No 82
>PRK13806 rpsA 30S ribosomal protein S1; Provisional
Probab=80.54 E-value=5.7 Score=35.82 Aligned_cols=65 Identities=23% Similarity=0.177 Sum_probs=46.7
Q ss_pred eEEEEEEEEeCCCceEEEEeCCCCEEEEEecc----cccccccccCCCCEEEEEeccCCCCeEEEEEEec
Q 032460 69 WVHEGFITESLPNGMFRVRLDNEDLILGYISG----KIRQNFIRVLPGDRVRVEVSRYDTSKGRIIYRLR 134 (140)
Q Consensus 69 ie~~GvVik~l~n~~f~V~l~dG~~~lcrI~G----KmRk~~IrI~vGDrV~VE~sp~D~~kGrIiyRy~ 134 (140)
-.+.|+|+++...|. .|++++|..=+|+++= +.....-.+.+||.|.+.+...|.++.+|.-...
T Consensus 381 ~~v~G~V~~i~~~G~-FV~l~~gv~Gli~~se~s~~~~~~~~~~~~~Gd~v~~~V~~id~e~~ri~Ls~~ 449 (491)
T PRK13806 381 TTVTGTVEKRAQFGL-FVNLAPGVTGLLPASVISRAGKPATYEKLKPGDSVTLVVEEIDTAKRKISLAPA 449 (491)
T ss_pred CEEEEEEEEEecCce-EEEcCCCcEEEEEHHHcCcccccchhhcCCCCCEEEEEEEEEeCCCCEEEEEee
Confidence 369999999986665 4688889888888752 1211123478999999988777777777765443
No 83
>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=80.52 E-value=6.9 Score=27.01 Aligned_cols=48 Identities=27% Similarity=0.257 Sum_probs=26.5
Q ss_pred EEEEEEEeCCC---ceEEEEeCCCCEEEEEeccccccc--ccccCCCCEEEEE
Q 032460 71 HEGFITESLPN---GMFRVRLDNEDLILGYISGKIRQN--FIRVLPGDRVRVE 118 (140)
Q Consensus 71 ~~GvVik~l~n---~~f~V~l~dG~~~lcrI~GKmRk~--~IrI~vGDrV~VE 118 (140)
++|+|+...++ +-|.++.+++---...-.|-+-.. .-.+.+||+|.|.
T Consensus 2 v~GvVTa~~~~~~~~GffiQd~~~d~~~~ts~gifV~~~~~~~~~~Gd~V~vt 54 (78)
T cd04486 2 VEGVVTAVFSGGGLGGFYIQDEDGDGDPATSEGIFVYTGSGADVAVGDLVRVT 54 (78)
T ss_pred eEEEEEEEcCCCCcCEEEEEcCCCCCCCcccceEEEecCCCCCCCCCCEEEEE
Confidence 68999998763 456688753211111111111100 2358899999885
No 84
>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=79.96 E-value=13 Score=24.51 Aligned_cols=58 Identities=17% Similarity=0.181 Sum_probs=36.1
Q ss_pred EEEEEEEEeCCCceEEEEeCC-CCEEEEEeccccccccc-----ccCCCCEEEEEeccCCCCeEEEE
Q 032460 70 VHEGFITESLPNGMFRVRLDN-EDLILGYISGKIRQNFI-----RVLPGDRVRVEVSRYDTSKGRII 130 (140)
Q Consensus 70 e~~GvVik~l~n~~f~V~l~d-G~~~lcrI~GKmRk~~I-----rI~vGDrV~VE~sp~D~~kGrIi 130 (140)
.+.|+|+++...|. .|++++ +..-+++++ .+...++ .+.+||.|.|.+-..|.++ +|.
T Consensus 6 ~~~g~V~~i~~fG~-fv~l~~~~~eGlvh~s-el~~~~~~~~~~~~~~Gd~v~vkv~~vd~~~-ki~ 69 (73)
T cd05686 6 IFKGEVASVTEYGA-FVKIPGCRKQGLVHKS-HMSSCRVDDPSEVVDVGEKVWVKVIGREMKD-KMK 69 (73)
T ss_pred EEEEEEEEEEeeeE-EEEECCCCeEEEEEch-hhCCCcccCHhhEECCCCEEEEEEEEECCCC-cEE
Confidence 47899999974444 456632 245666665 3322222 2688999999877666644 554
No 85
>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=79.57 E-value=4.8 Score=28.59 Aligned_cols=51 Identities=14% Similarity=0.129 Sum_probs=25.4
Q ss_pred cCCcceEEEEEEEEeCCCceEE--EEeC----------CCCEEEEEecccccccccccCCCCEEE
Q 032460 64 ANSEKWVHEGFITESLPNGMFR--VRLD----------NEDLILGYISGKIRQNFIRVLPGDRVR 116 (140)
Q Consensus 64 ~k~d~ie~~GvVik~l~n~~f~--V~l~----------dG~~~lcrI~GKmRk~~IrI~vGDrV~ 116 (140)
|+... .+.|+|+++- ..+-. +.+- ++.......+|-+|+..|+.-.-|+|.
T Consensus 2 P~vGd-iV~~rVtrv~-~~~a~v~Il~v~~~~~~~~~~~~~~l~~~f~GiIR~~DVR~te~Dkv~ 64 (82)
T PF10447_consen 2 PKVGD-IVIARVTRVN-PRQAKVEILCVEGKGNDSINAGDRPLKEPFQGIIRKQDVRATEKDKVK 64 (82)
T ss_dssp --TT--EEEEEEEEE--SSEEEEEEEES----------SSS----SS-S-EEEEGGGT-SS----
T ss_pred CCCCC-EEEEEEEEEe-ccEEEEEEEEEEeccccccccCCcccccccEEEEEeeeecccccchhh
Confidence 44444 4889999984 44433 4445 566777889999999988866666653
No 86
>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=79.40 E-value=6.6 Score=36.73 Aligned_cols=69 Identities=25% Similarity=0.156 Sum_probs=44.7
Q ss_pred ccCCcceEEEEEEEEeCCCceEEEEeC-CCCEEEEEe---cccc------------cccccccCCCCEEEEEeccCCCCe
Q 032460 63 GANSEKWVHEGFITESLPNGMFRVRLD-NEDLILGYI---SGKI------------RQNFIRVLPGDRVRVEVSRYDTSK 126 (140)
Q Consensus 63 ~~k~d~ie~~GvVik~l~n~~f~V~l~-dG~~~lcrI---~GKm------------Rk~~IrI~vGDrV~VE~sp~D~~k 126 (140)
|.+.-.-+..|+|+.+...| +.|+++ .|.+-+.++ .+.. ++.+....+||.|.|.+..-|..+
T Consensus 568 l~~~iG~~~~g~I~~v~~~G-ifV~L~~~~veGlV~~s~l~~d~y~~d~~~~~l~g~~~~~~~~lGD~V~Vki~~vd~~~ 646 (654)
T TIGR00358 568 LLDKVGTEFSGEISSVTRFG-MFVRLDDNGIDGLIHISTLHNDYYVFDQEKMALIGKGTGKVYRIGDRVTVKLTEVNMET 646 (654)
T ss_pred hhhCCCcEEEEEEEeEEcCc-EEEEecCCceEEEEEeEeCCCcceEEeccccEEEeccCCcEECCCCEEEEEEEEEeccc
Confidence 33333446899999987666 667775 443333333 2211 112345889999999998888888
Q ss_pred EEEEEE
Q 032460 127 GRIIYR 132 (140)
Q Consensus 127 GrIiyR 132 (140)
+.|.+.
T Consensus 647 ~~I~f~ 652 (654)
T TIGR00358 647 RSIIFE 652 (654)
T ss_pred CeEEEE
Confidence 888764
No 87
>PF14444 S1-like: S1-like
Probab=78.89 E-value=4.6 Score=27.45 Aligned_cols=40 Identities=23% Similarity=0.339 Sum_probs=25.3
Q ss_pred EEEEEEEeCCCceEEEEeCCCCEE--EEEecccccccccccCCCCEEEEEec
Q 032460 71 HEGFITESLPNGMFRVRLDNEDLI--LGYISGKIRQNFIRVLPGDRVRVEVS 120 (140)
Q Consensus 71 ~~GvVik~l~n~~f~V~l~dG~~~--lcrI~GKmRk~~IrI~vGDrV~VE~s 120 (140)
+.|+|+++. +.|=+-.++ +. ..-++|.+ +.+||+|+||..
T Consensus 4 ~~GvVTkl~--~~yG~IDe~--vFF~~~vv~G~~------P~vGdrV~v~A~ 45 (58)
T PF14444_consen 4 FTGVVTKLC--DDYGFIDED--VFFQTDVVKGNV------PKVGDRVLVEAI 45 (58)
T ss_pred EEEEEEEEe--CCcceEccc--EEEEcccEecCC------CccCCEEEEEEE
Confidence 689999995 555554333 21 11144543 568999999965
No 88
>PF08402 TOBE_2: TOBE domain; InterPro: IPR013611 The TOBE domain [] (Transport-associated OB) always occurs as a dimer as the C-terminal strand of each domain is supplied by the partner. Probably involved in the recognition of small ligands such as molybdenum (e.g. P46930 from SWISSPROT) and sulphate (P16676 from SWISSPROT). Found in ABC transporters immediately after the ATPase domain. A strong RPE motif is found at the presumed N terminus of the 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: 1Q12_A 1Q1B_C 2AWN_D 3RLF_B 3PUX_B 2R6G_B 3PUV_B 1Q1E_A 3PV0_B 2AWO_A ....
Probab=78.65 E-value=14 Score=23.20 Aligned_cols=51 Identities=20% Similarity=0.279 Sum_probs=32.8
Q ss_pred EEEEEEEEeCC-Cc--eEEEEeCCCCEEEEEecccccccccccCCCCEEEEEeccC
Q 032460 70 VHEGFITESLP-NG--MFRVRLDNEDLILGYISGKIRQNFIRVLPGDRVRVEVSRY 122 (140)
Q Consensus 70 e~~GvVik~l~-n~--~f~V~l~dG~~~lcrI~GKmRk~~IrI~vGDrV~VE~sp~ 122 (140)
.+.|+|+...- |+ .|.|+++++..........-. . ..+.+||.|.+.+.+.
T Consensus 17 ~~~g~V~~~~~~G~~~~~~v~~~~~~~~~~~~~~~~~-~-~~~~~G~~v~l~~~~~ 70 (75)
T PF08402_consen 17 RLPGTVVSVEFLGSETRYTVRLEGGEELVVRVPNSQR-D-SPLEPGDEVRLSWDPD 70 (75)
T ss_dssp EEEEEEEEEEEESSEEEEEEEETTSSEEEEEEESSG--T-TT--TTSEEEEEEEGG
T ss_pred eEEEEEEEEEECCCEEEEEEEECCCCEEEEEecCccc-c-CCCCCCCEEEEEECcc
Confidence 67888877642 33 445556888887777665543 1 4588999999987653
No 89
>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=77.95 E-value=18 Score=24.18 Aligned_cols=56 Identities=21% Similarity=0.102 Sum_probs=38.9
Q ss_pred EEEEEEEEeCCCceEEEEeCCCCEEEEEecccccccccccCCCCEEEEEeccCCCCeEEEEE
Q 032460 70 VHEGFITESLPNGMFRVRLDNEDLILGYISGKIRQNFIRVLPGDRVRVEVSRYDTSKGRIIY 131 (140)
Q Consensus 70 e~~GvVik~l~n~~f~V~l~dG~~~lcrI~GKmRk~~IrI~vGDrV~VE~sp~D~~kGrIiy 131 (140)
...|+|.+.. +.-+.|+++++..-+.+.+= +. -.+..||.|.|.+..- .++|+|..
T Consensus 19 ~~~g~V~~i~-~~G~fV~l~~~~~Glv~~se-~~---~~~~iGd~v~v~I~~i-~e~~~i~l 74 (77)
T cd04473 19 LYKGKVNGVA-KYGVFVDLNDHVRGLIHRSN-LL---RDYEVGDEVIVQVTDI-PENGNIDL 74 (77)
T ss_pred EEEEEEEeEe-cceEEEEECCCcEEEEEchh-cc---CcCCCCCEEEEEEEEE-CCCCcEEE
Confidence 5889999985 55567778777666666653 22 2488899999886554 45677654
No 90
>PRK12696 flgH flagellar basal body L-ring protein; Reviewed
Probab=76.63 E-value=11 Score=31.45 Aligned_cols=59 Identities=22% Similarity=0.267 Sum_probs=44.0
Q ss_pred eEEEEEEEEeCCCceEEEEe-----CCCCEEEEEecccccccccccCCCCEEEEEeccCCCCeEEEEEEe
Q 032460 69 WVHEGFITESLPNGMFRVRL-----DNEDLILGYISGKIRQNFIRVLPGDRVRVEVSRYDTSKGRIIYRL 133 (140)
Q Consensus 69 ie~~GvVik~l~n~~f~V~l-----~dG~~~lcrI~GKmRk~~IrI~vGDrV~VE~sp~D~~kGrIiyRy 133 (140)
..+.++|+++||||++.|+= -|+....-+++|-+|-.. |.++..|.=. ..-.++|.|.-
T Consensus 150 ~tIta~V~~VLPNGNLvI~G~k~v~vN~e~~~i~lsGvVRP~D--I~~~NtV~S~----~IAdArI~Y~G 213 (236)
T PRK12696 150 ATIAARVVRVLPGGLMQVEGARETRVNDETQYIVVSGLVRPRD--IGPDNSVMST----QLADARIEYYG 213 (236)
T ss_pred EEEEEEEEEECCCCCEEEEEEEEEEECCCEEEEEEEEEECHHH--CCCCCeEccc----eeeeeEEEEcc
Confidence 46899999999999999974 378888999999999754 6667766211 22447777753
No 91
>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=76.45 E-value=13 Score=24.10 Aligned_cols=54 Identities=9% Similarity=0.079 Sum_probs=33.9
Q ss_pred EEEEEEEEeCCCceEEEEeCCCCEEEEEeccccccc-------ccccCCCCEEEEEeccCCCC
Q 032460 70 VHEGFITESLPNGMFRVRLDNEDLILGYISGKIRQN-------FIRVLPGDRVRVEVSRYDTS 125 (140)
Q Consensus 70 e~~GvVik~l~n~~f~V~l~dG~~~lcrI~GKmRk~-------~IrI~vGDrV~VE~sp~D~~ 125 (140)
.+.|+|+++. .....|++.+|-+-..+++ .+... .-.+.+||.|.+.+...|..
T Consensus 3 iV~g~V~~i~-~~gi~v~l~~~i~g~i~~~-~i~~~~~~~~~~~~~~~~Gd~i~~kVl~~d~~ 63 (70)
T cd05702 3 LVKAKVKSVK-PTQLNVQLADNVHGRIHVS-EVFDEWPDGKNPLSKFKIGQKIKARVIGGHDA 63 (70)
T ss_pred EEEEEEEEEE-CCcEEEEeCCCcEEEEEHH-HhccccccccChhHhCCCCCEEEEEEEEEeCc
Confidence 4789999985 6667888877644333332 22211 12378999998887655543
No 92
>PRK10354 RNA chaperone/anti-terminator; Provisional
Probab=75.63 E-value=17 Score=24.49 Aligned_cols=51 Identities=12% Similarity=0.139 Sum_probs=34.9
Q ss_pred EEEEEEEeCC-CceEEEEeCCC-CEEEEEecccccccccccCCCCEEEEEecc
Q 032460 71 HEGFITESLP-NGMFRVRLDNE-DLILGYISGKIRQNFIRVLPGDRVRVEVSR 121 (140)
Q Consensus 71 ~~GvVik~l~-n~~f~V~l~dG-~~~lcrI~GKmRk~~IrI~vGDrV~VE~sp 121 (140)
|.|+|...-. .|+=.+..++| ..+--|++-=-....-.+.+||+|.+++..
T Consensus 5 ~~G~Vk~f~~~kGfGFI~~~~g~~dvfvH~s~l~~~g~~~l~~G~~V~f~~~~ 57 (70)
T PRK10354 5 MTGIVKWFNADKGFGFITPDDGSKDVFVHFSAIQNDGYKSLDEGQKVSFTIES 57 (70)
T ss_pred ceEEEEEEeCCCCcEEEecCCCCccEEEEEeeccccCCCCCCCCCEEEEEEEE
Confidence 5799988643 33324555554 778888886544322459999999998764
No 93
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=75.29 E-value=14 Score=34.95 Aligned_cols=60 Identities=27% Similarity=0.230 Sum_probs=44.1
Q ss_pred EEEEEEEEeCCCceEEEEeCCCCEEEEEeccccccccc-----ccCCCCEEEEEeccCCCCeEEEEEE
Q 032460 70 VHEGFITESLPNGMFRVRLDNEDLILGYISGKIRQNFI-----RVLPGDRVRVEVSRYDTSKGRIIYR 132 (140)
Q Consensus 70 e~~GvVik~l~n~~f~V~l~dG~~~lcrI~GKmRk~~I-----rI~vGDrV~VE~sp~D~~kGrIiyR 132 (140)
.+.|+|+++. +.-+.|++.+|..=+.|++ ++...++ .+.+||.|.|.+...|.. |+|..-
T Consensus 624 v~~G~V~~I~-~fGafVei~~~~~GllhiS-els~~~v~~~~~v~kvGD~V~VkV~~iD~~-grI~LS 688 (693)
T PRK11824 624 IYEGKVVRIV-DFGAFVEILPGKDGLVHIS-EIADERVEKVEDVLKEGDEVKVKVLEIDKR-GRIRLS 688 (693)
T ss_pred EEEEEEEEEE-CCeEEEEECCCCEEEEEee-eccCccccCccceeCCCCEEEEEEEEECCC-CcEEEE
Confidence 5899999997 4555677777888788876 4444333 279999999998777765 777643
No 94
>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=73.29 E-value=9.7 Score=36.08 Aligned_cols=57 Identities=28% Similarity=0.286 Sum_probs=41.7
Q ss_pred EEEEEEEEeCCCceEEEEeCCCCEEEEEecccccccccc-----cCCCCEEEEEeccCCCCeEEE
Q 032460 70 VHEGFITESLPNGMFRVRLDNEDLILGYISGKIRQNFIR-----VLPGDRVRVEVSRYDTSKGRI 129 (140)
Q Consensus 70 e~~GvVik~l~n~~f~V~l~dG~~~lcrI~GKmRk~~Ir-----I~vGDrV~VE~sp~D~~kGrI 129 (140)
...|+|+++. +--..|++.+|..=++|++ ++...++. +.+||.|.|.+...|. +|+|
T Consensus 621 i~~G~V~~I~-~~GafVei~~g~~GllHiS-ei~~~~v~~~~~~~kvGD~V~VkVi~id~-~gki 682 (684)
T TIGR03591 621 IYEGKVVRIM-DFGAFVEILPGKDGLVHIS-EIANERVEKVEDVLKEGDEVKVKVLEIDK-QGRI 682 (684)
T ss_pred EEEEEEEEEe-CCEEEEEECCCcEEEEEHH-HcCCCcccChhhccCCCCEEEEEEEEECC-CCCc
Confidence 4899999997 4455677777888888887 44433332 7889999999876665 5665
No 95
>PRK12407 flgH flagellar basal body L-ring protein; Reviewed
Probab=72.75 E-value=17 Score=30.24 Aligned_cols=59 Identities=20% Similarity=0.236 Sum_probs=44.2
Q ss_pred eEEEEEEEEeCCCceEEEEe-----CCCCEEEEEecccccccccccCCCCEEEEEeccCCCCeEEEEEEe
Q 032460 69 WVHEGFITESLPNGMFRVRL-----DNEDLILGYISGKIRQNFIRVLPGDRVRVEVSRYDTSKGRIIYRL 133 (140)
Q Consensus 69 ie~~GvVik~l~n~~f~V~l-----~dG~~~lcrI~GKmRk~~IrI~vGDrV~VE~sp~D~~kGrIiyRy 133 (140)
..+..+|+++||||.+.|+= -|+....-+++|-+|-. -|.++..|. -...--++|.|.-
T Consensus 134 gtIta~V~~VlpNGnL~I~GeK~i~vN~e~e~i~~sGvVRP~--DI~~~NtV~----S~~iAdArI~Y~G 197 (221)
T PRK12407 134 GSITVAVHQVLPNGVLVIRGEKWLTLNQGDEYMRVTGLVRAD--DIARDNSVS----SQRIANARISYAG 197 (221)
T ss_pred EEEEEEEEEECCCCCEEEEEEEEEEECCCEEEEEEEEEECHH--HCCCCCeEc----cceeeeeEEEEcc
Confidence 35889999999999999974 26778888999999875 466677762 1123457888864
No 96
>PRK12700 flgH flagellar basal body L-ring protein; Reviewed
Probab=71.97 E-value=17 Score=30.26 Aligned_cols=59 Identities=20% Similarity=0.222 Sum_probs=43.4
Q ss_pred eEEEEEEEEeCCCceEEEEeC-----CCCEEEEEecccccccccccCCCCEEEEEeccCCCCeEEEEEEe
Q 032460 69 WVHEGFITESLPNGMFRVRLD-----NEDLILGYISGKIRQNFIRVLPGDRVRVEVSRYDTSKGRIIYRL 133 (140)
Q Consensus 69 ie~~GvVik~l~n~~f~V~l~-----dG~~~lcrI~GKmRk~~IrI~vGDrV~VE~sp~D~~kGrIiyRy 133 (140)
..+..+|+++||||.+.|+=+ |+....-+++|-+|-.. |.++..|.= ...-.++|.|.=
T Consensus 144 ~tIta~V~~VlpNGNLvI~GeK~i~vN~~~e~irlsGiVRP~D--I~~~NtV~S----~~IAdArI~Y~G 207 (230)
T PRK12700 144 GTITTTVIGVLPNGNLQIAGEKQIAINRGSEYVRFSGVVDPRS--ITGSNTVSS----TRVADARIEYRS 207 (230)
T ss_pred EEEEEEEEEECCCCCEEEEEEEEEEECCCEEEEEEEEEECHHH--CCCCCeEcc----ceeeeEEEEEcc
Confidence 358899999999999998742 67778889999998754 666777621 123457787753
No 97
>PRK00249 flgH flagellar basal body L-ring protein; Reviewed
Probab=71.74 E-value=15 Score=30.42 Aligned_cols=58 Identities=22% Similarity=0.255 Sum_probs=43.1
Q ss_pred eEEEEEEEEeCCCceEEEEe-----CCCCEEEEEecccccccccccCCCCEEEEEeccCCCCeEEEEEE
Q 032460 69 WVHEGFITESLPNGMFRVRL-----DNEDLILGYISGKIRQNFIRVLPGDRVRVEVSRYDTSKGRIIYR 132 (140)
Q Consensus 69 ie~~GvVik~l~n~~f~V~l-----~dG~~~lcrI~GKmRk~~IrI~vGDrV~VE~sp~D~~kGrIiyR 132 (140)
..+..+|+++||||.+.|+= -|+....-+++|.+|-.. |.++..|.=. ....++|.|.
T Consensus 136 ~~Ita~V~~VlpNGnLvI~G~K~i~vN~e~~~i~lsGiVRP~D--I~~dNtV~S~----~iAdArI~Y~ 198 (222)
T PRK00249 136 GTITVTVTQVLPNGNLVIRGEKEVRVNQGTEFLRVSGVVRPRD--ISGDNTISST----RIADARISYG 198 (222)
T ss_pred EEEEEEEEEECCCCcEEEEEEEEEEECCCEEEEEEEEEECHHH--CCCCCeEchh----eeeeeEEEEc
Confidence 35889999999999999974 378888899999999864 5666666311 2244677775
No 98
>PRK12788 flgH flagellar basal body L-ring protein; Reviewed
Probab=71.58 E-value=17 Score=30.53 Aligned_cols=59 Identities=19% Similarity=0.291 Sum_probs=44.0
Q ss_pred eEEEEEEEEeCCCceEEEEe-----CCCCEEEEEecccccccccccCCCCEEEEEeccCCCCeEEEEEEe
Q 032460 69 WVHEGFITESLPNGMFRVRL-----DNEDLILGYISGKIRQNFIRVLPGDRVRVEVSRYDTSKGRIIYRL 133 (140)
Q Consensus 69 ie~~GvVik~l~n~~f~V~l-----~dG~~~lcrI~GKmRk~~IrI~vGDrV~VE~sp~D~~kGrIiyRy 133 (140)
..+.++|+++||||.+.|+= -|+....-+++|-+|-.. |..+..|.=. ..-.++|.|.=
T Consensus 148 ~tIaa~V~~VLPNGNLvI~G~kev~vN~e~~~i~vsGvVRP~D--I~~~NtV~S~----kIAdArI~Y~G 211 (234)
T PRK12788 148 FSVAAIVVDVLPNGNLLISGSQEVRVNYEMRVLNVGGIVRPLD--ITRNNTIAYE----KVAEARISYGG 211 (234)
T ss_pred EEEEEEEEEEcCCCCEEEEEEEEEEECCCEEEEEEEEEECHHH--CCCCCeEccc----eeeeeEEEEcc
Confidence 35899999999999999874 378888999999999754 6667766221 22457777753
No 99
>PRK06676 rpsA 30S ribosomal protein S1; Reviewed
Probab=71.53 E-value=23 Score=30.35 Aligned_cols=63 Identities=22% Similarity=0.130 Sum_probs=44.3
Q ss_pred EEEEEEEEeCCCceEEEEeCCCCEEEEEecccccccc-----cccCCCCEEEEEeccCCCCeEEEEEEec
Q 032460 70 VHEGFITESLPNGMFRVRLDNEDLILGYISGKIRQNF-----IRVLPGDRVRVEVSRYDTSKGRIIYRLR 134 (140)
Q Consensus 70 e~~GvVik~l~n~~f~V~l~dG~~~lcrI~GKmRk~~-----IrI~vGDrV~VE~sp~D~~kGrIiyRy~ 134 (140)
.+.|.|+++. +.-+.|++++|..=+++++- +...+ ..+.+||.|.+.+...|.++++|..-.+
T Consensus 280 ~v~g~V~~i~-~~G~fV~l~~gi~Glv~~se-~~~~~~~~~~~~~~~Gd~v~v~V~~id~e~~~i~ls~k 347 (390)
T PRK06676 280 VIEGTVKRLT-DFGAFVEVLPGVEGLVHISQ-ISHKHIATPSEVLEEGQEVKVKVLEVNEEEKRISLSIK 347 (390)
T ss_pred EEEEEEEEEe-CceEEEEECCCCeEEEEhHH-cCccccCChhhccCCCCEEEEEEEEEECCCCEEEEEEE
Confidence 5899999986 44456777777666666552 22212 2368999999998888888888876554
No 100
>smart00318 SNc Staphylococcal nuclease homologues.
Probab=71.18 E-value=12 Score=27.11 Aligned_cols=59 Identities=34% Similarity=0.508 Sum_probs=39.3
Q ss_pred EEEEEEEEeCCCceEEEEeCCCCEEEEEecccc----c-----------------cccc-ccCCCCEEEEEeccCCCCeE
Q 032460 70 VHEGFITESLPNGMFRVRLDNEDLILGYISGKI----R-----------------QNFI-RVLPGDRVRVEVSRYDTSKG 127 (140)
Q Consensus 70 e~~GvVik~l~n~~f~V~l~dG~~~lcrI~GKm----R-----------------k~~I-rI~vGDrV~VE~sp~D~~kG 127 (140)
.+.|+|++++.++.|.|.+.+|+...-++.|-= . +... .++.|-.|.+++...| .-|
T Consensus 2 ~~~~~V~~V~DGDT~~v~~~~~~~~~vrL~gIdaPe~~~~~~~~~~~~~~~g~~A~~~l~~~l~g~~V~~~~~~~D-~~g 80 (138)
T smart00318 2 EIRGVVERVLDGDTIRVRLPKNKLITIRLSGIDAPETARPNKGDGTTDEPFGEEAKEFLKKLLLGKKVQVEVDSKD-RYG 80 (138)
T ss_pred ceeEEEEEEecCCEEEEEeCCCCEEEEEEEeccCCccCCCCCCCccccCcHHHHHHHHHHHHhCCCEEEEEEeccC-CCC
Confidence 367999999999999999888766666665521 1 0111 1557888988876544 234
Q ss_pred EE
Q 032460 128 RI 129 (140)
Q Consensus 128 rI 129 (140)
++
T Consensus 81 r~ 82 (138)
T smart00318 81 RF 82 (138)
T ss_pred CE
Confidence 44
No 101
>PF01957 NfeD: NfeD-like C-terminal, partner-binding; InterPro: IPR002810 The nfe genes (nfeA, nfeB, and nfeD) are involved in the nodulation efficiency and competitiveness of Rhizobium meliloti (Sinorhizobium meliloti) (Rhizobium meliloti) on alfalfa roots []. The specific function of this family is unknown although it is unlikely that NfeD is specifically involved in nodulation as the family contains several different archaeal and bacterial species most of which are not symbionts. This entry describes archaeal and bacterial proteins which are variously described, examples are: nodulation protein, nodulation efficiency protein D (nfeD), hypothetical protein and membrane-bound serine protease (ClpP class). A number of these proteins are classified in MEROPS peptidase family S49 as non-peptidase homologues or as unassigned peptidases. ; PDB: 2K5H_A 3CP0_A 2EXD_A.
Probab=71.10 E-value=20 Score=25.62 Aligned_cols=42 Identities=31% Similarity=0.332 Sum_probs=29.7
Q ss_pred eEEEEEEEEeCCCceEEEEeCCCCEEEEEecccccccccccCCCCEEEEE
Q 032460 69 WVHEGFITESLPNGMFRVRLDNEDLILGYISGKIRQNFIRVLPGDRVRVE 118 (140)
Q Consensus 69 ie~~GvVik~l~n~~f~V~l~dG~~~lcrI~GKmRk~~IrI~vGDrV~VE 118 (140)
+=.+|+|+....++.-+|+. +|....|+-.+. |.+||+|.|.
T Consensus 90 iG~~g~v~~~~~~~~G~V~~-~G~~w~A~s~~~-------i~~G~~V~Vv 131 (144)
T PF01957_consen 90 IGKEGTVIEIPLNGSGRVKV-DGERWRARSEDE-------IPKGDRVRVV 131 (144)
T ss_dssp TTSEEEEEEEBSSS-EEEEE-TTEEEEEEESST-------B-TT-EEEEE
T ss_pred cCCeEEEEEeecCCcEEEEE-CCeEEEEEeCCC-------CCCCCEEEEE
Confidence 33568885445688889987 688999988776 7779999875
No 102
>COG1545 Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]
Probab=70.88 E-value=11 Score=28.80 Aligned_cols=47 Identities=26% Similarity=0.355 Sum_probs=32.2
Q ss_pred EEEeCCCCEEEEEecccccccccccCCCCEEEEEeccCC--CCeEEEEEEec
Q 032460 85 RVRLDNEDLILGYISGKIRQNFIRVLPGDRVRVEVSRYD--TSKGRIIYRLR 134 (140)
Q Consensus 85 ~V~l~dG~~~lcrI~GKmRk~~IrI~vGDrV~VE~sp~D--~~kGrIiyRy~ 134 (140)
-|++++|..++++|.| ..--.+.+|+.|....-+.. ...+.++|.++
T Consensus 89 iV~l~~~~~i~~~i~~---~~p~~v~iGm~V~~v~~~~~~~~~~~~~~~~~~ 137 (140)
T COG1545 89 IVELEEGGRILGQLVD---VDPDDVEIGMKVEAVFRKREEDGGRGYIIYGFK 137 (140)
T ss_pred EEEeCCCCceEEEEEe---cCcccccCCCEEEEEEEEccccCCceEEEEEEe
Confidence 4677777789999999 11234888999998876544 34556665543
No 103
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=70.78 E-value=19 Score=35.68 Aligned_cols=59 Identities=25% Similarity=0.318 Sum_probs=44.2
Q ss_pred EEEEEeCCCceEEEEeCCCCEEEEEeccccccccc-----ccCCCCEEEEEeccCCCCeEEEEEEec
Q 032460 73 GFITESLPNGMFRVRLDNEDLILGYISGKIRQNFI-----RVLPGDRVRVEVSRYDTSKGRIIYRLR 134 (140)
Q Consensus 73 GvVik~l~n~~f~V~l~dG~~~lcrI~GKmRk~~I-----rI~vGDrV~VE~sp~D~~kGrIiyRy~ 134 (140)
|+|+++...|. .|++.+|..-++||+ .+..+++ .+.+||.|.|.+-..|. +|+|-.-.+
T Consensus 760 g~V~~I~~FGa-FVeL~~g~EGLVHIS-eLs~~rv~~~~dv~kvGD~V~VkVi~ID~-~grI~LSlK 823 (891)
T PLN00207 760 CEIKSIAPYGA-FVEIAPGREGLCHIS-ELSSNWLAKPEDAFKVGDRIDVKLIEVND-KGQLRLSRR 823 (891)
T ss_pred cEEEEEeccEE-EEEeCCCCEEEEEhh-hcCCccccCHHHhcCCCCEEEEEEEEECC-CCcEEEEEe
Confidence 69999975555 567778899999988 5544333 28899999999887776 788876554
No 104
>PF13533 Biotin_lipoyl_2: Biotin-lipoyl like
Probab=70.45 E-value=2.6 Score=26.60 Aligned_cols=33 Identities=27% Similarity=0.494 Sum_probs=25.4
Q ss_pred EEEEEecccccccccccCCCCEEEEEeccCCCCeEEEEEEecCC
Q 032460 93 LILGYISGKIRQNFIRVLPGDRVRVEVSRYDTSKGRIIYRLRNK 136 (140)
Q Consensus 93 ~~lcrI~GKmRk~~IrI~vGDrV~VE~sp~D~~kGrIiyRy~r~ 136 (140)
.+.+.++|++.. +.+.+||.| .+|+++++....
T Consensus 4 ~I~~~~~G~V~~--v~V~~G~~V---------kkGd~L~~ld~~ 36 (50)
T PF13533_consen 4 TIQAPVSGRVES--VYVKEGQQV---------KKGDVLLVLDSP 36 (50)
T ss_pred EEeCCCCEEEEE--EEecCCCEE---------cCCCEEEEECcH
Confidence 356678888864 778899999 578998887654
No 105
>PRK12699 flgH flagellar basal body L-ring protein; Reviewed
Probab=70.14 E-value=20 Score=30.34 Aligned_cols=59 Identities=24% Similarity=0.235 Sum_probs=43.0
Q ss_pred eEEEEEEEEeCCCceEEEEeC-----CCCEEEEEecccccccccccCCCCEEEEEeccCCCCeEEEEEEec
Q 032460 69 WVHEGFITESLPNGMFRVRLD-----NEDLILGYISGKIRQNFIRVLPGDRVRVEVSRYDTSKGRIIYRLR 134 (140)
Q Consensus 69 ie~~GvVik~l~n~~f~V~l~-----dG~~~lcrI~GKmRk~~IrI~vGDrV~VE~sp~D~~kGrIiyRy~ 134 (140)
..+..+|+++||||.+.|+=+ |+....-+++|-+|-..|. +..| . -...-.++|.|.=+
T Consensus 161 gtItvtVv~VLPNGNLvI~GeK~i~vN~~~e~IrlsGvVRP~DI~---~NtV--~--St~IAdArI~Y~G~ 224 (246)
T PRK12699 161 GTITVTVVDILPNGNLLVSGEKQIGINQGHEFIRLSGVINPINVI---NNTV--S--SIQVADARIEYRGN 224 (246)
T ss_pred EEEEEEEEEECCCCCEEEEEEEEEEECCCeEEEEEEEEEChhhcc---CCeE--c--cceeeeeEEEEcce
Confidence 358899999999999998742 6777788999999987763 3444 1 22335588888643
No 106
>PRK09890 cold shock protein CspG; Provisional
Probab=70.12 E-value=25 Score=23.79 Aligned_cols=51 Identities=10% Similarity=0.133 Sum_probs=34.5
Q ss_pred EEEEEEEeCC-CceEEEEeCCC-CEEEEEecccccccccccCCCCEEEEEecc
Q 032460 71 HEGFITESLP-NGMFRVRLDNE-DLILGYISGKIRQNFIRVLPGDRVRVEVSR 121 (140)
Q Consensus 71 ~~GvVik~l~-n~~f~V~l~dG-~~~lcrI~GKmRk~~IrI~vGDrV~VE~sp 121 (140)
|.|+|...-. .|+=.+..++| ..+-.|++-=-+...-.+.+||+|.+++..
T Consensus 5 ~~G~Vk~f~~~kGfGFI~~~~g~~dvFvH~s~l~~~~~~~l~~G~~V~f~~~~ 57 (70)
T PRK09890 5 MTGLVKWFNADKGFGFITPDDGSKDVFVHFTAIQSNEFRTLNENQKVEFSIEQ 57 (70)
T ss_pred ceEEEEEEECCCCcEEEecCCCCceEEEEEeeeccCCCCCCCCCCEEEEEEEE
Confidence 5799988643 33335666554 788888885443322358999999998764
No 107
>PRK12698 flgH flagellar basal body L-ring protein; Reviewed
Probab=69.92 E-value=20 Score=29.71 Aligned_cols=59 Identities=20% Similarity=0.270 Sum_probs=43.6
Q ss_pred eEEEEEEEEeCCCceEEEEe-----CCCCEEEEEecccccccccccCCCCEEEEEeccCCCCeEEEEEEe
Q 032460 69 WVHEGFITESLPNGMFRVRL-----DNEDLILGYISGKIRQNFIRVLPGDRVRVEVSRYDTSKGRIIYRL 133 (140)
Q Consensus 69 ie~~GvVik~l~n~~f~V~l-----~dG~~~lcrI~GKmRk~~IrI~vGDrV~VE~sp~D~~kGrIiyRy 133 (140)
..+..+|+++||||.+.|+= -|+....-+++|-+|-. -|.++..|.= ...--++|.|.=
T Consensus 137 ~tIta~V~~VlpNGnL~I~GeK~i~vN~~~e~I~lsGvVRP~--DI~~~NtV~S----t~iAdArI~Y~G 200 (224)
T PRK12698 137 GSISANVMQVLPNGNLVIRGEKWISINNGDEFIRLTGIVRSQ--DITPDNTIDS----TRVANARIQYSG 200 (224)
T ss_pred EEEEEEEEEECCCCCEEEEEEEEEEECCCEEEEEEEEEECHH--HCCCCCeEcc----ceeeeEEEEEcc
Confidence 46889999999999999974 26777788999999975 4666777621 123457787753
No 108
>PF08206 OB_RNB: Ribonuclease B OB domain; InterPro: IPR013223 This domain includes the N-terminal OB domain found in ribonuclease B proteins in one or two copies.; PDB: 2ID0_D 2IX1_A 2IX0_A.
Probab=69.75 E-value=15 Score=23.74 Aligned_cols=40 Identities=23% Similarity=0.208 Sum_probs=24.7
Q ss_pred eCCCceEEEEeCCCCEEEEEecccccccccccCCCCEEEEEecc
Q 032460 78 SLPNGMFRVRLDNEDLILGYISGKIRQNFIRVLPGDRVRVEVSR 121 (140)
Q Consensus 78 ~l~n~~f~V~l~dG~~~lcrI~GKmRk~~IrI~vGDrV~VE~sp 121 (140)
+.++|+=.|.++| ....-.|+.+-.+ ....||+|.|++.+
T Consensus 5 ~~~~GfGFv~~~~-~~~DifIp~~~l~---~A~~gD~V~v~i~~ 44 (58)
T PF08206_consen 5 IHPKGFGFVIPDD-GGEDIFIPPRNLN---GAMDGDKVLVRITP 44 (58)
T ss_dssp E-SSS-EEEEECT--TEEEEE-HHHHT---TS-TT-EEEEEEEE
T ss_pred EEcCCCEEEEECC-CCCCEEECHHHHC---CCCCCCEEEEEEec
Confidence 3467777777766 4456677765554 37889999999987
No 109
>PRK12701 flgH flagellar basal body L-ring protein; Reviewed
Probab=69.53 E-value=21 Score=29.85 Aligned_cols=59 Identities=19% Similarity=0.159 Sum_probs=43.3
Q ss_pred eEEEEEEEEeCCCceEEEEe-----CCCCEEEEEecccccccccccCCCCEEEEEeccCCCCeEEEEEEe
Q 032460 69 WVHEGFITESLPNGMFRVRL-----DNEDLILGYISGKIRQNFIRVLPGDRVRVEVSRYDTSKGRIIYRL 133 (140)
Q Consensus 69 ie~~GvVik~l~n~~f~V~l-----~dG~~~lcrI~GKmRk~~IrI~vGDrV~VE~sp~D~~kGrIiyRy 133 (140)
..+..+|+++||||.+.|+= -|+....-+++|-+|-. -|-++..|.= ...-.++|.|.=
T Consensus 143 ~tItv~V~~VlpNGnL~I~GeK~v~vN~e~e~i~lsGvVRP~--DI~~~NtV~S----~~iAdArI~Y~G 206 (230)
T PRK12701 143 GSISVTVAKVLANGNMVVQGEKWVRINQGNEFVRLSGIVRPQ--DIKADNTITS----DRIANARISYGG 206 (230)
T ss_pred EEEEEEEEEECCCCCEEEEEEEEEEECCCeEEEEEEEEECHH--HCCCCCeEcc----ceeeeEEEEEcc
Confidence 35889999999999999974 26777788999999975 4666776621 123457787753
No 110
>PRK00087 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed
Probab=69.24 E-value=25 Score=32.88 Aligned_cols=68 Identities=19% Similarity=0.102 Sum_probs=47.7
Q ss_pred eEEEEEEEEeCCCceEEEEeCCCCEEEEEecc----cccccccccCCCCEEEEEeccCCCCeEEEEEEecCCC
Q 032460 69 WVHEGFITESLPNGMFRVRLDNEDLILGYISG----KIRQNFIRVLPGDRVRVEVSRYDTSKGRIIYRLRNKI 137 (140)
Q Consensus 69 ie~~GvVik~l~n~~f~V~l~dG~~~lcrI~G----KmRk~~IrI~vGDrV~VE~sp~D~~kGrIiyRy~r~~ 137 (140)
-.+.|+|+++.. .-+.|++.+|..-+++++- +...-.-.+.+||.|.+.+...|.++++|....++.+
T Consensus 564 ~~v~g~V~~i~~-~G~fV~l~~~i~Gli~~sel~~~~~~~~~~~~kvGd~V~vkV~~id~e~~rI~lslk~~~ 635 (647)
T PRK00087 564 SIVLGKVVRIAP-FGAFVELEPGVDGLVHISQISWKRIDKPEDVLSEGEEVKAKILEVDPEEKRIRLSIKEVE 635 (647)
T ss_pred eEEEEEEEEEEC-CeEEEEECCCCEEEEEhhhcCccccCCHhhcCCCCCEEEEEEEEEeCCCCEEEEEEeecc
Confidence 368999999964 4556778888777777642 1111112378999999998888888888887665544
No 111
>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase. Sohlberg, et al. present characterization of two proteins from Streptomyces coelicolor. The protein in this family was shown to have poly(A) polymerase activity and may be responsible for polyadenylating RNA in this species. Reference 2 showed that a nearly identical plasmid-encoded protein from Streptomyces antibioticus is a bifunctional enzyme that acts also as a guanosine pentaphosphate synthetase.
Probab=68.98 E-value=13 Score=35.84 Aligned_cols=58 Identities=21% Similarity=0.216 Sum_probs=41.7
Q ss_pred EEEEEEEEeCCCceEEEEeCCCCEEEEEec--------ccccccccccCCCCEEEEEeccCCCCeEEE
Q 032460 70 VHEGFITESLPNGMFRVRLDNEDLILGYIS--------GKIRQNFIRVLPGDRVRVEVSRYDTSKGRI 129 (140)
Q Consensus 70 e~~GvVik~l~n~~f~V~l~dG~~~lcrI~--------GKmRk~~IrI~vGDrV~VE~sp~D~~kGrI 129 (140)
.+.|+|+++..-|. .|++..|..=++|++ ++...-.--+.+||.|.|.+-..|. +|+|
T Consensus 650 i~~GkV~~I~dfGa-FVel~~G~eGLvHISeisdls~~~rv~~~~dv~kvGd~V~VKVl~ID~-~gKI 715 (719)
T TIGR02696 650 RFLGTVVKTTAFGA-FVSLLPGKDGLLHISQIRKLAGGKRVENVEDVLSVGQKIQVEIADIDD-RGKL 715 (719)
T ss_pred EEEEEEEEEECceE-EEEecCCceEEEEhhhccccccccCcCCHHHcCCCCCEEEEEEEEECC-CCCe
Confidence 58999999985555 466778889999988 2222211238899999998776663 6766
No 112
>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=68.42 E-value=29 Score=22.34 Aligned_cols=47 Identities=19% Similarity=0.221 Sum_probs=35.1
Q ss_pred EEEEEEEeCC-CceEEEEe--C-CCCEEEEEecccccccccccCCCCEEEEEe
Q 032460 71 HEGFITESLP-NGMFRVRL--D-NEDLILGYISGKIRQNFIRVLPGDRVRVEV 119 (140)
Q Consensus 71 ~~GvVik~l~-n~~f~V~l--~-dG~~~lcrI~GKmRk~~IrI~vGDrV~VE~ 119 (140)
+.|+|..+.. |...+|++ . +|..+.+-++..- . ...+.+||.|-+.+
T Consensus 7 l~a~V~~v~~~G~~vRlEl~~~~~~~~iEvel~~~~-~-~l~l~~G~~V~l~P 57 (58)
T PF12857_consen 7 LPARVRRVRPVGPEVRLELKRLDDGEPIEVELPRER-R-QLGLQPGDRVYLRP 57 (58)
T ss_pred EeEEEEEEEecCCeEEEEEEECCCCCEEEEEeCHhH-H-hcCCCCCCEEEEEe
Confidence 5677777665 67778887 3 6899999999766 2 45688899998753
No 113
>PTZ00454 26S protease regulatory subunit 6B-like protein; Provisional
Probab=67.36 E-value=17 Score=32.17 Aligned_cols=47 Identities=13% Similarity=0.069 Sum_probs=40.9
Q ss_pred EEEEEEEEeCCCceEEEEeCCCCEEEEEecccccccccccCCCCEEEEE
Q 032460 70 VHEGFITESLPNGMFRVRLDNEDLILGYISGKIRQNFIRVLPGDRVRVE 118 (140)
Q Consensus 70 e~~GvVik~l~n~~f~V~l~dG~~~lcrI~GKmRk~~IrI~vGDrV~VE 118 (140)
...|.|++.+.++++.|...+|..+...+.+.+.+. .+.+||.|.+.
T Consensus 67 ~~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~--~~~~~~~v~~~ 113 (398)
T PTZ00454 67 LVIGQFLEMIDSNYGIVSSTSGSNYYVRILSTLNRE--LLKPNASVALH 113 (398)
T ss_pred ceEEEEEEEEcCCEEEEEcCCCCEEEEecccccCHh--hCCCCCEEEee
Confidence 356999999999999999999999999999998653 48889999764
No 114
>PRK12697 flgH flagellar basal body L-ring protein; Reviewed
Probab=67.23 E-value=25 Score=29.41 Aligned_cols=58 Identities=24% Similarity=0.221 Sum_probs=42.6
Q ss_pred EEEEEEEEeCCCceEEEEe-----CCCCEEEEEecccccccccccCCCCEEEEEeccCCCCeEEEEEEe
Q 032460 70 VHEGFITESLPNGMFRVRL-----DNEDLILGYISGKIRQNFIRVLPGDRVRVEVSRYDTSKGRIIYRL 133 (140)
Q Consensus 70 e~~GvVik~l~n~~f~V~l-----~dG~~~lcrI~GKmRk~~IrI~vGDrV~VE~sp~D~~kGrIiyRy 133 (140)
.+..+|+++||||.+.|+= -|+....-+++|-+|-.. |.++..|.= ...-.++|.|.=
T Consensus 141 tItv~V~~VlpNGnL~I~GeK~i~vN~e~e~IrlsGvVRP~D--I~~~NtV~S----t~IAdArI~Y~G 203 (226)
T PRK12697 141 TITVTVTNVLPNGNLVVSGEKQMLINQGNEFVRFSGVVNPNT--ISGANSVYS----TQVADARIEYSA 203 (226)
T ss_pred EEEEEEEEECCCCCEEEEEEEEEEECCCEEEEEEEEEECHHH--CCCCCeEch----heeeeeEEEEcc
Confidence 5778999999999999974 267777889999998754 666777621 122457888763
No 115
>cd00319 Ribosomal_S12_like Ribosomal protein S12-like family; composed of prokaryotic 30S ribosomal protein S12, eukaryotic 40S ribosomal protein S23 and similar proteins. S12 and S23 are located at the interface of the large and small ribosomal subunits, adjacent to the decoding center. They play an important role in translocation during the peptide elongation step of protein synthesis. They are also involved in important RNA and protein interactions. Ribosomal protein S12 is essential for maintenance of a pretranslocation state and, together with S13, functions as a control element for the rRNA- and tRNA-driven movements of translocation. S23 interacts with domain III of the eukaryotic elongation factor 2 (eEF2), which catalyzes translocation. Mutations in S12 and S23 have been found to affect translational accuracy. Antibiotics such as streptomycin may also bind S12/S23 and cause the ribosome to misread the genetic code.
Probab=66.71 E-value=11 Score=27.79 Aligned_cols=32 Identities=22% Similarity=0.308 Sum_probs=26.9
Q ss_pred eEEEEeCCCCEEEEEecccccccccccCCCCEEEEE
Q 032460 83 MFRVRLDNEDLILGYISGKIRQNFIRVLPGDRVRVE 118 (140)
Q Consensus 83 ~f~V~l~dG~~~lcrI~GKmRk~~IrI~vGDrV~VE 118 (140)
..+|+|.||+++.|+|+|-= . -+.+-|.|+|+
T Consensus 37 ~arV~L~ngk~v~ayIPg~G-h---~lqeh~~VLvr 68 (95)
T cd00319 37 VAKVRLTSGYEVTAYIPGEG-H---NLQEHSVVLIR 68 (95)
T ss_pred EEEEEccCCCEEEEECCCCC-c---ccccccEEEEe
Confidence 46788999999999999976 2 38889999886
No 116
>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=65.84 E-value=25 Score=33.10 Aligned_cols=64 Identities=30% Similarity=0.274 Sum_probs=42.9
Q ss_pred ceEEEEEEEEeCCCceEEEEeCC-CCEEEEEec---ccc------------cccccccCCCCEEEEEeccCCCCeEEEEE
Q 032460 68 KWVHEGFITESLPNGMFRVRLDN-EDLILGYIS---GKI------------RQNFIRVLPGDRVRVEVSRYDTSKGRIIY 131 (140)
Q Consensus 68 ~ie~~GvVik~l~n~~f~V~l~d-G~~~lcrI~---GKm------------Rk~~IrI~vGDrV~VE~sp~D~~kGrIiy 131 (140)
.-...|+|+.+...| +.|++++ |.+-+.+++ +.. ++.+-...+||.|.|.+..-|..+|+|..
T Consensus 628 G~~~~g~V~~v~~fG-ifV~L~~~~~eGlvhis~l~~d~~~~d~~~~~l~g~~~~~~~~lGd~V~Vkv~~vd~~~~~I~~ 706 (709)
T TIGR02063 628 GEEFEGVISGVTSFG-LFVELENNTIEGLVHISTLKDDYYVFDEKGLALVGERTGKVFRLGDRVKVRVVKADLDTGKIDF 706 (709)
T ss_pred CcEEEEEEEEEEeCC-EEEEecCCceEEEEEeeecCCCcEEEcccceEEEeccCCcEECCCCEEEEEEEEEecccCeEEE
Confidence 346899999997555 5667765 555555543 110 11123478899999999888888888875
Q ss_pred E
Q 032460 132 R 132 (140)
Q Consensus 132 R 132 (140)
.
T Consensus 707 ~ 707 (709)
T TIGR02063 707 E 707 (709)
T ss_pred E
Confidence 4
No 117
>COG1489 SfsA DNA-binding protein, stimulates sugar fermentation [General function prediction only]
Probab=65.57 E-value=37 Score=28.75 Aligned_cols=60 Identities=17% Similarity=0.242 Sum_probs=42.3
Q ss_pred EEEEEEEeCCCceEEEEe-CCCCEEEEEec--ccccccccccCCCCEEEEEeccCCCCeEEEEEEecC
Q 032460 71 HEGFITESLPNGMFRVRL-DNEDLILGYIS--GKIRQNFIRVLPGDRVRVEVSRYDTSKGRIIYRLRN 135 (140)
Q Consensus 71 ~~GvVik~l~n~~f~V~l-~dG~~~lcrI~--GKmRk~~IrI~vGDrV~VE~sp~D~~kGrIiyRy~r 135 (140)
+.|+.++-+ ++|.|.. -||++++||++ |+|+- -+.+|+.|.+.-+.....|-.+.+-..+
T Consensus 8 ~~a~li~R~--nRFl~dv~l~G~~~~~H~~ntGrm~~---l~~pG~~v~l~~sd~~~rK~~~~~~~~~ 70 (235)
T COG1489 8 QEATLIKRY--NRFLADVELDGEEVTAHCPNTGRMTE---LLTPGNTVWLSRSDNPKRKYRYTLELVE 70 (235)
T ss_pred ceeEEEeee--cceEEEEEECCeEEEEEcCCCCcccc---ccCCCCEEEEEEecCCCccceEEEEEEE
Confidence 468888886 7777664 35999999985 77764 3889999999876544445555544433
No 118
>PF13742 tRNA_anti_2: OB-fold nucleic acid binding domain
Probab=65.07 E-value=45 Score=23.66 Aligned_cols=53 Identities=23% Similarity=0.128 Sum_probs=33.6
Q ss_pred cceEEEEEEEEeCC--CceEEEEeCC-CCEEEEEecccccc-cc-cccCCCCEEEEEe
Q 032460 67 EKWVHEGFITESLP--NGMFRVRLDN-EDLILGYISGKIRQ-NF-IRVLPGDRVRVEV 119 (140)
Q Consensus 67 d~ie~~GvVik~l~--n~~f~V~l~d-G~~~lcrI~GKmRk-~~-IrI~vGDrV~VE~ 119 (140)
..+-++|.|.+.-. +|+++..+-| .-.+.|.+=..-.. -. ..+..||.|+|.-
T Consensus 22 ~~vwV~GEIs~~~~~~~gh~YftLkD~~a~i~~~~~~~~~~~i~~~~l~~G~~V~v~g 79 (99)
T PF13742_consen 22 PNVWVEGEISNLKRHSSGHVYFTLKDEEASISCVIFRSRARRIRGFDLKDGDKVLVRG 79 (99)
T ss_pred CCEEEEEEEeecEECCCceEEEEEEcCCcEEEEEEEHHHHhhCCCCCCCCCCEEEEEE
Confidence 35678999988654 7777777744 34455554333222 12 4589999999863
No 119
>PF10844 DUF2577: Protein of unknown function (DUF2577); InterPro: IPR022555 This family of proteins has no known function
Probab=64.90 E-value=49 Score=23.71 Aligned_cols=63 Identities=14% Similarity=0.105 Sum_probs=35.6
Q ss_pred CCcceEEEEEEEEeCCCceEEEEeCC----------------CCEEEEEeccccccc------ccccCCCCEEEEEeccC
Q 032460 65 NSEKWVHEGFITESLPNGMFRVRLDN----------------EDLILGYISGKIRQN------FIRVLPGDRVRVEVSRY 122 (140)
Q Consensus 65 k~d~ie~~GvVik~l~n~~f~V~l~d----------------G~~~lcrI~GKmRk~------~IrI~vGDrV~VE~sp~ 122 (140)
++..+ +.|+|++..| .+|+.++ +.++.+.+.+..-.. .-.+.+||+|.+-.. .
T Consensus 15 ~p~~i-~~G~V~s~~P---L~I~i~~~liL~~~~L~i~~~l~~~~~~~~~~~~~~~~~~~i~~~~~Lk~GD~V~ll~~-~ 89 (100)
T PF10844_consen 15 NPVDI-VIGTVVSVPP---LKIKIDQKLILDKDFLIIPELLKDYTRDITIEHNSETDNITITFTDGLKVGDKVLLLRV-Q 89 (100)
T ss_pred CCcee-EEEEEEeccc---EEEEECCeEEEchHHEEeehhccceEEEEEEeccccccceeEEEecCCcCCCEEEEEEe-c
Confidence 34444 7799999754 6666655 333444444432221 114899999988642 2
Q ss_pred CCCeEEEEEE
Q 032460 123 DTSKGRIIYR 132 (140)
Q Consensus 123 D~~kGrIiyR 132 (140)
+-.+-.|+.|
T Consensus 90 ~gQ~yiVlDk 99 (100)
T PF10844_consen 90 GGQKYIVLDK 99 (100)
T ss_pred CCCEEEEEEe
Confidence 3346666655
No 120
>PRK15464 cold shock-like protein CspH; Provisional
Probab=64.85 E-value=29 Score=23.74 Aligned_cols=51 Identities=14% Similarity=0.031 Sum_probs=35.0
Q ss_pred EEEEEEEeCCCceE-EEEeCC-CCEEEEEecccccccccccCCCCEEEEEecc
Q 032460 71 HEGFITESLPNGMF-RVRLDN-EDLILGYISGKIRQNFIRVLPGDRVRVEVSR 121 (140)
Q Consensus 71 ~~GvVik~l~n~~f-~V~l~d-G~~~lcrI~GKmRk~~IrI~vGDrV~VE~sp 121 (140)
+.|+|..--...=| .|..++ |+.+-.|++-=-+...-.+.+||+|.+++..
T Consensus 5 ~~G~Vk~fn~~KGfGFI~~~~g~~DvFvH~s~l~~~g~~~l~~G~~V~f~v~~ 57 (70)
T PRK15464 5 MTGIVKTFDRKSGKGFIIPSDGRKEVQVHISAFTPRDAEVLIPGLRVEFCRVN 57 (70)
T ss_pred ceEEEEEEECCCCeEEEccCCCCccEEEEehhehhcCCCCCCCCCEEEEEEEE
Confidence 57999887542233 455545 5789999886544422369999999998764
No 121
>TIGR00981 rpsL_bact ribosomal protein S12, bacterial/organelle. This model recognizes ribosomal protein S12 of Bacteria, mitochondria, and chloroplasts. The homologous ribosomal proteins of Archaea and Eukarya, termed S23 in Eukarya and S12 or S23 in Archaea, score below the trusted cutoff.
Probab=64.49 E-value=13 Score=28.74 Aligned_cols=32 Identities=28% Similarity=0.341 Sum_probs=26.9
Q ss_pred eEEEEeCCCCEEEEEecccccccccccCCCCEEEEE
Q 032460 83 MFRVRLDNEDLILGYISGKIRQNFIRVLPGDRVRVE 118 (140)
Q Consensus 83 ~f~V~l~dG~~~lcrI~GKmRk~~IrI~vGDrV~VE 118 (140)
-.+|+|.||+++.|+|+|-= . -+.+-|.|+|+
T Consensus 52 varVrL~ngk~v~AyIPG~G-h---nlqehs~VLvr 83 (124)
T TIGR00981 52 VARVRLTNGFEVTAYIPGEG-H---NLQEHSVVLIR 83 (124)
T ss_pred eEEEEeCCCCEEEEEcCCCC-C---CccccCEEEEe
Confidence 46788999999999999976 2 38888898887
No 122
>PRK05163 rpsL 30S ribosomal protein S12; Validated
Probab=63.88 E-value=14 Score=28.59 Aligned_cols=32 Identities=28% Similarity=0.341 Sum_probs=26.8
Q ss_pred eEEEEeCCCCEEEEEecccccccccccCCCCEEEEE
Q 032460 83 MFRVRLDNEDLILGYISGKIRQNFIRVLPGDRVRVE 118 (140)
Q Consensus 83 ~f~V~l~dG~~~lcrI~GKmRk~~IrI~vGDrV~VE 118 (140)
..+|+|.||+++.|+|+|-= . -+.+-|.|+|.
T Consensus 52 varVrL~ngk~v~AyIPGeG-h---nlqehs~VLvr 83 (124)
T PRK05163 52 VARVRLTNGFEVTAYIPGEG-H---NLQEHSVVLIR 83 (124)
T ss_pred EEEEEeCCCCEEEEEcCCCC-C---CccccCEEEEe
Confidence 46788999999999999976 2 37888888886
No 123
>cd04458 CSP_CDS Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in eukaryotes, prokaryotes, and archaea. CSP's include the major cold-shock proteins CspA and CspB in bacteria and the eukaryotic gene regulatory factor Y-box protein. CSP expression is up-regulated by an abrupt drop in growth temperature. CSP's are also expressed under normal condition at lower level. The function of cold-shock proteins is not fully understood. They preferentially bind poly-pyrimidine region of single-stranded RNA and DNA. CSP's are thought to bind mRNA and regulate ribosomal translation, mRNA degradation, and the rate of transcription termination. The human Y-box protein, which contains a CSD, regulates transcription and translation of genes that contain the Y-box sequence in their promoters. This specific ssDNA-binding properties of CSD are required for the binding of Y-box protein to the promoter's Y-box sequence, thereby regulating transcription.
Probab=63.65 E-value=28 Score=22.31 Aligned_cols=51 Identities=22% Similarity=0.187 Sum_probs=32.7
Q ss_pred EEEEEEeCC-CceEEEEeCC-CCEEEEEecccccccccccCCCCEEEEEeccC
Q 032460 72 EGFITESLP-NGMFRVRLDN-EDLILGYISGKIRQNFIRVLPGDRVRVEVSRY 122 (140)
Q Consensus 72 ~GvVik~l~-n~~f~V~l~d-G~~~lcrI~GKmRk~~IrI~vGDrV~VE~sp~ 122 (140)
.|+|...-. .|+=.+..++ |+.+--|++-=-....-.+.+||.|.+++...
T Consensus 2 ~G~Vk~~~~~kGfGFI~~~~~g~diffh~~~~~~~~~~~~~~G~~V~f~~~~~ 54 (65)
T cd04458 2 TGTVKWFDDEKGFGFITPDDGGEDVFVHISALEGDGFRSLEEGDRVEFELEEG 54 (65)
T ss_pred cEEEEEEECCCCeEEEecCCCCcCEEEEhhHhhccCCCcCCCCCEEEEEEEEC
Confidence 577776654 3444555555 67777776643322134699999999997754
No 124
>COG0048 RpsL Ribosomal protein S12 [Translation, ribosomal structure and biogenesis]
Probab=63.43 E-value=14 Score=28.75 Aligned_cols=44 Identities=27% Similarity=0.349 Sum_probs=33.2
Q ss_pred EEEEEEEeCC------C----ceEEEEeCCCCEEEEEecccccccccccCCCCEEEEE
Q 032460 71 HEGFITESLP------N----GMFRVRLDNEDLILGYISGKIRQNFIRVLPGDRVRVE 118 (140)
Q Consensus 71 ~~GvVik~l~------n----~~f~V~l~dG~~~lcrI~GKmRk~~IrI~vGDrV~VE 118 (140)
-.|+|++.++ | -..+|+|.||.++.|+|+|-=-. |.+-|.|+|+
T Consensus 36 ~RGv~~~v~~~~pKkPNSAlRK~~RVrL~NG~~VtAyiPg~Gh~----lqEH~~Vli~ 89 (129)
T COG0048 36 ARGVCTRVYTVTPKKPNSALRKVARVRLINGKEVTAYIPGEGHN----LQEHSEVLIR 89 (129)
T ss_pred cceEEEEEEecccCCCChhhheeEEEEeeCCcEEEEEcCCCCcc----ccccCEEEEe
Confidence 3466666542 2 25789999999999999996432 8888999887
No 125
>COG2063 FlgH Flagellar basal body L-ring protein [Cell motility and secretion]
Probab=63.28 E-value=18 Score=30.50 Aligned_cols=58 Identities=21% Similarity=0.243 Sum_probs=41.2
Q ss_pred eEEEEEEEEeCCCceEEEEe-----CCCCEEEEEecccccccccccCCCCEEEEEeccCCCCeEEEEEE
Q 032460 69 WVHEGFITESLPNGMFRVRL-----DNEDLILGYISGKIRQNFIRVLPGDRVRVEVSRYDTSKGRIIYR 132 (140)
Q Consensus 69 ie~~GvVik~l~n~~f~V~l-----~dG~~~lcrI~GKmRk~~IrI~vGDrV~VE~sp~D~~kGrIiyR 132 (140)
..+.++|+++|+||.+.|+= -|+....-+++|.+|-..| --...|. -.....+||.|.
T Consensus 147 ~tIta~V~~VLpNGNL~I~G~Kev~vN~~~e~i~vsGvVRP~DI--~~~NtI~----S~~IAdARI~Y~ 209 (230)
T COG2063 147 GTITATVVQVLPNGNLVIEGEKEVRVNGEKEIIRVSGVVRPDDI--SGDNTIS----STRIADARIEYG 209 (230)
T ss_pred EEEEEEEEEEcCCCCEEEEEEEEEEECCceEEEEEeeeEccccc--CCCCeec----chheeeeEEEEc
Confidence 45899999999999999874 3788889999999997643 3333331 112245777775
No 126
>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=63.26 E-value=33 Score=30.48 Aligned_cols=64 Identities=23% Similarity=0.141 Sum_probs=42.7
Q ss_pred eEEEEEEEEeCCCceEEEEeCCCCEEEEEecc-----cccccccccCCCCEEEEEeccCCCCeEEEEEEe
Q 032460 69 WVHEGFITESLPNGMFRVRLDNEDLILGYISG-----KIRQNFIRVLPGDRVRVEVSRYDTSKGRIIYRL 133 (140)
Q Consensus 69 ie~~GvVik~l~n~~f~V~l~dG~~~lcrI~G-----KmRk~~IrI~vGDrV~VE~sp~D~~kGrIiyRy 133 (140)
-.+.|+|+++.+.| +.|++.+|..-.++++= ....-.-.+.+||.|.|.+...|.++++|.--.
T Consensus 274 ~i~~g~V~~v~~~G-~fV~l~~~v~g~v~~sels~~~~~~~~~~~~~vG~~v~v~V~~id~~~~~i~lS~ 342 (516)
T TIGR00717 274 DKITGRVTNLTDYG-VFVEIEEGIEGLVHVSEMSWVKKNSHPSKVVKKGDEVEVMILDIDPERRRLSLGL 342 (516)
T ss_pred CEEEEEEEEeeCCc-EEEEeCCCCEEEEEHHHcCCccccCCHHHhccCCCEEEEEEEEEcCCCCEEEEEe
Confidence 35789999996444 56778777776666431 111111127799999999877788788876543
No 127
>PHA02858 EIF2a-like PKR inhibitor; Provisional
Probab=63.04 E-value=25 Score=25.63 Aligned_cols=66 Identities=24% Similarity=0.293 Sum_probs=43.3
Q ss_pred ccCCcceEEEEEEEEeCCCceEEEEeCCCCEEEEEec--ccccccccc----cCCCCEEEEEeccCCCCeEEEEEE
Q 032460 63 GANSEKWVHEGFITESLPNGMFRVRLDNEDLILGYIS--GKIRQNFIR----VLPGDRVRVEVSRYDTSKGRIIYR 132 (140)
Q Consensus 63 ~~k~d~ie~~GvVik~l~n~~f~V~l~dG~~~lcrI~--GKmRk~~Ir----I~vGDrV~VE~sp~D~~kGrIiyR 132 (140)
+|+.+.+.+ |+|.-. ++-++|.|-+=. ..|-|- -.+.+++++ ..+|=...|.+---|..||.|=-+
T Consensus 13 ~P~v~dvv~-~Vv~i~--d~~~YV~LleY~-iegmIl~~selsr~rirsi~kllVGk~e~v~ViRVDk~KGYIDLs 84 (86)
T PHA02858 13 FPNINEVTK-GIVFVK--DNIFYVKLIDYG-LEALIVNYVNVNADRAEKLKKKLVGKTINVQVIRTDKLKGYIDVR 84 (86)
T ss_pred cCCCCeEEE-EEEEEe--ccEEEEEEecCc-cceEEecHHHHhHHHHHhhhhhhcCCeeEEEEEEECCCCCEEEeE
Confidence 678777777 666543 788889884422 444444 333333333 449998888887788899998543
No 128
>smart00357 CSP Cold shock protein domain. RNA-binding domain that functions as a RNA-chaperone in bacteria and is involved in regulating translation in eukaryotes. Contains sub-family of RNA-binding domains in the Rho transcription termination factor.
Probab=62.34 E-value=29 Score=21.16 Aligned_cols=48 Identities=17% Similarity=0.176 Sum_probs=24.4
Q ss_pred EEEEEeCCCceEEEEeCCCCEEEEEecccc-cccccccCCCCEEEEEeccC
Q 032460 73 GFITESLPNGMFRVRLDNEDLILGYISGKI-RQNFIRVLPGDRVRVEVSRY 122 (140)
Q Consensus 73 GvVik~l~n~~f~V~l~dG~~~lcrI~GKm-Rk~~IrI~vGDrV~VE~sp~ 122 (140)
|+|... ..++-.|..+++. -..++.-+- +...-.+..||+|.+.+..+
T Consensus 2 G~i~~~-~~g~gfv~~~~~~-~~i~v~~~~~~~~~~~~~~Gd~V~~~i~~~ 50 (64)
T smart00357 2 GVVKWF-NKGFGFIRPDDGG-KDVFVHPSQIQGGLKSLREGDEVEFKVVSP 50 (64)
T ss_pred eEEEEE-cCCeeEEecCCCC-ccEEEEhHHhhcCCCcCCCCCEEEEEEEEc
Confidence 455543 3444445554432 133343222 11122488899999998654
No 129
>PRK10862 SoxR reducing system protein RseC; Provisional
Probab=62.17 E-value=9.6 Score=29.56 Aligned_cols=51 Identities=12% Similarity=0.141 Sum_probs=30.3
Q ss_pred EEEEEEEEeCCCceEEEEeCC-CCEEEEEe-------------ccc---cc-ccccccCCCCEEEEEecc
Q 032460 70 VHEGFITESLPNGMFRVRLDN-EDLILGYI-------------SGK---IR-QNFIRVLPGDRVRVEVSR 121 (140)
Q Consensus 70 e~~GvVik~l~n~~f~V~l~d-G~~~lcrI-------------~GK---mR-k~~IrI~vGDrV~VE~sp 121 (140)
+-.|+|++. .+++..|++.. .-.=-|.. .++ ++ .+.....+||.|.|++..
T Consensus 3 ee~~~Vv~v-~~~~a~Ve~~r~saCg~C~a~~gCG~~~l~~~~~~~~~~~~v~~~~~~~vGD~V~v~i~e 71 (154)
T PRK10862 3 KEWATVVSW-QNGIALLRCEVKAGCSSCASRAGCGSRLLNKLGPQTTHQLVVPSSQPLVPGQKVELGIAE 71 (154)
T ss_pred ceEEEEEEE-ECCEEEEEEecCCCCcCcCCCCCchhhHHHHhcCCCceEEEecCCCCCCCCCEEEEecch
Confidence 456999998 58899999743 10011221 111 11 122348999999998763
No 130
>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=61.84 E-value=39 Score=31.70 Aligned_cols=64 Identities=17% Similarity=0.199 Sum_probs=42.9
Q ss_pred EEEEEEEEeCCCceEEEEeCCCCEEEEEecccccccccccCCCCEEEEEeccCCC-C--eEEEEEEecCCC
Q 032460 70 VHEGFITESLPNGMFRVRLDNEDLILGYISGKIRQNFIRVLPGDRVRVEVSRYDT-S--KGRIIYRLRNKI 137 (140)
Q Consensus 70 e~~GvVik~l~n~~f~V~l~dG~~~lcrI~GKmRk~~IrI~vGDrV~VE~sp~D~-~--kGrIiyRy~r~~ 137 (140)
.+.|+|.-. +.|+=.|..+++..-..+|++.-.. ....||+|+|++.+.+. . +|+|+.-.+|+.
T Consensus 16 ~~~G~i~~~-~~gfgFv~~~~~~~~difI~~~~~~---~a~~GD~V~v~i~~~~~~~~~~g~v~~il~r~~ 82 (654)
T TIGR00358 16 LVKGVVKAH-NKGFGFLRPDDDDKKDYFIPPPQMK---KVMHGDLVEACPLSQPQRGRFEAEVERILEPAL 82 (654)
T ss_pred eEEEEEEEC-CCccEEEEeCCCCCCcEEEchHHhC---cCCCCCEEEEEEeecCCCCCceEEEEEEeccCC
Confidence 467999876 6776666655421226788775433 37889999999765432 2 599988777654
No 131
>cd03368 Ribosomal_S12 S12-like family, 30S ribosomal protein S12 subfamily; S12 is located at the interface of the large and small ribosomal subunits of prokaryotes, chloroplasts and mitochondria, where it plays an important role in both tRNA and ribosomal subunit interactions. S12 is essential for maintenance of a pretranslocation state and, together with S13, functions as a control element for the rRNA- and tRNA-driven movements of translocation. Antibiotics such as streptomycin bind S12 and cause the ribosome to misread the genetic code.
Probab=61.34 E-value=17 Score=27.56 Aligned_cols=32 Identities=31% Similarity=0.401 Sum_probs=26.9
Q ss_pred eEEEEeCCCCEEEEEecccccccccccCCCCEEEEE
Q 032460 83 MFRVRLDNEDLILGYISGKIRQNFIRVLPGDRVRVE 118 (140)
Q Consensus 83 ~f~V~l~dG~~~lcrI~GKmRk~~IrI~vGDrV~VE 118 (140)
-.+|+|.||+++.|+|+|-= . .+.+-|.|+|+
T Consensus 50 varV~L~ngk~v~AyIPG~G-h---nlqehs~VLvr 81 (108)
T cd03368 50 VARVRLSNGKEVTAYIPGEG-H---NLQEHSVVLVR 81 (108)
T ss_pred eEEEEecCCCEEEEEcCCCC-C---CccccCEEEEe
Confidence 46788999999999999976 2 38888999886
No 132
>PRK11642 exoribonuclease R; Provisional
Probab=60.55 E-value=40 Score=32.80 Aligned_cols=63 Identities=21% Similarity=0.247 Sum_probs=44.1
Q ss_pred EEEEEEEEeCCCceEEEEeCCCCEEEEEecccccccccccCCCCEEEEEeccCCC---CeEEEEEEecCCC
Q 032460 70 VHEGFITESLPNGMFRVRLDNEDLILGYISGKIRQNFIRVLPGDRVRVEVSRYDT---SKGRIIYRLRNKI 137 (140)
Q Consensus 70 e~~GvVik~l~n~~f~V~l~dG~~~lcrI~GKmRk~~IrI~vGDrV~VE~sp~D~---~kGrIiyRy~r~~ 137 (140)
.+.|+|.-. +.|+-.|..+++.. ..+|+..-.. ....||+|+|.+.+.+. ..|+|+...+|..
T Consensus 84 ~~~G~v~~~-~~GfgFv~~e~~~~-difI~~~~l~---~A~~GD~V~v~i~~~~~~~r~eg~Vv~IleR~~ 149 (813)
T PRK11642 84 LLKGTVIGH-RDGYGFLRVEGRKD-DLYLSSEQMK---TCIHGDQVLAQPLGADRKGRREARIVRVLVPKT 149 (813)
T ss_pred eEEEEEEEC-CCccEEEEECCCCC-CEEEChHHHc---cCCCCCEEEEEEccCCCCCCcEEEEEEEEecCC
Confidence 488999876 67776776655333 6778766543 27789999999775331 3699998887764
No 133
>PRK07400 30S ribosomal protein S1; Reviewed
Probab=60.42 E-value=50 Score=28.34 Aligned_cols=66 Identities=21% Similarity=0.184 Sum_probs=42.8
Q ss_pred EEEEEEEEeCCCceEEEEeCCCCEEEEEecc----cccccccccCCCCEEEEEeccCCCCeEEEEEEecCCC
Q 032460 70 VHEGFITESLPNGMFRVRLDNEDLILGYISG----KIRQNFIRVLPGDRVRVEVSRYDTSKGRIIYRLRNKI 137 (140)
Q Consensus 70 e~~GvVik~l~n~~f~V~l~dG~~~lcrI~G----KmRk~~IrI~vGDrV~VE~sp~D~~kGrIiyRy~r~~ 137 (140)
.+.|+|+++-+.|. .|.+ .|..=+++++- +...-.-.+.+||.|.+.+...|..+|+|..-.+..+
T Consensus 199 vv~G~V~~I~~~G~-fV~i-~gv~Gllhisels~~~~~~~~~~~~vGd~VkvkVl~iD~e~~rI~LS~K~l~ 268 (318)
T PRK07400 199 VVVGTVRGIKPYGA-FIDI-GGVSGLLHISEISHEHIETPHSVFNVNDEMKVMIIDLDAERGRISLSTKQLE 268 (318)
T ss_pred EEEEEEEEEECCeE-EEEE-CCEEEEEEHHHcccccccChhhccCCCCEEEEEEEEEeCCCCEEEEEEeccc
Confidence 58999999965444 4555 45444444431 1111112378999999998888888899987665544
No 134
>COG3111 Periplasmic protein with OB-fold [Function unknown]
Probab=60.22 E-value=54 Score=25.54 Aligned_cols=57 Identities=23% Similarity=0.173 Sum_probs=45.4
Q ss_pred cccCCcceEEEEEEEEeCCCceEEEEeCCCCEEEEEecccccccccccCCCCEEEEEec
Q 032460 62 EGANSEKWVHEGFITESLPNGMFRVRLDNEDLILGYISGKIRQNFIRVLPGDRVRVEVS 120 (140)
Q Consensus 62 ~~~k~d~ie~~GvVik~l~n~~f~V~l~dG~~~lcrI~GKmRk~~IrI~vGDrV~VE~s 120 (140)
.+..+-.+.++|-+++-+++..|.-+...| ++.--|.-+.= ++..+-|-|+|.++-+
T Consensus 53 ~~~Dda~V~l~GnIv~qi~~D~y~FrD~sG-eI~VeIdd~~w-~g~tv~P~dkV~I~Ge 109 (128)
T COG3111 53 TLHDDAWVSLEGNIVRQIGDDRYVFRDASG-EINVDIDDKVW-NGQTVTPKDKVRIQGE 109 (128)
T ss_pred ccccCCeEEEEeeEEEeeCCceEEEEcCCc-cEEEEeccccc-CCcccCcccEEEEEeE
Confidence 355666788999999999999999998777 66777876664 3677999999988643
No 135
>PF02107 FlgH: Flagellar L-ring protein; InterPro: IPR000527 The flgH, flgI and fliF genes of Salmonella typhimurium encode the major proteins for the L, P and M rings of the flagellar basal body []. In fact, the basal body consists of four rings (L,P,S and M) surrounding the flagellar rod, which is believed to transmit motor rotation to the filament []. The M ring is integral to the inner membrane of the cell, and may be connected to the rod via the S (supramembrane) ring, which lies just distal to it. The L and P rings reside in the outer membrane and periplasmic space, respectively. FlgH and FlgI, which are exported across the cell membrane to their destinations in the outer membrane and periplasmic space, have typical N-terminal cleaved signal-peptide sequences. FlgH is predicted to have an extensive beta-sheet structure, in keeping with other outer membrane proteins [].; GO: 0003774 motor activity, 0001539 ciliary or flagellar motility, 0009427 bacterial-type flagellum basal body, distal rod, L ring
Probab=59.88 E-value=18 Score=28.68 Aligned_cols=59 Identities=24% Similarity=0.235 Sum_probs=42.6
Q ss_pred eEEEEEEEEeCCCceEEEEe-----CCCCEEEEEecccccccccccCCCCEEEEEeccCCCCeEEEEEEe
Q 032460 69 WVHEGFITESLPNGMFRVRL-----DNEDLILGYISGKIRQNFIRVLPGDRVRVEVSRYDTSKGRIIYRL 133 (140)
Q Consensus 69 ie~~GvVik~l~n~~f~V~l-----~dG~~~lcrI~GKmRk~~IrI~vGDrV~VE~sp~D~~kGrIiyRy 133 (140)
..+.++|++++|||.+.|+= -|+....-+++|-+|... |.....|.-. ...-++|.|.-
T Consensus 94 ~~ita~Vv~VlpNGnL~I~G~k~i~vn~e~~~i~lsGiVRp~D--I~~~NtV~S~----~IAda~I~y~G 157 (179)
T PF02107_consen 94 GTITARVVEVLPNGNLVIEGEKQIRVNGEEQYIRLSGIVRPED--IDPDNTVLSS----KIADARIEYSG 157 (179)
T ss_pred EEEEEEEEEECCCCcEEEEEEEEEEECCCEEEEEEEEEECHHH--CCCCCeEchh----eeEeEEEEEcc
Confidence 36999999999999999873 367777779999999764 5667766321 22346666653
No 136
>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=59.85 E-value=27 Score=21.93 Aligned_cols=49 Identities=20% Similarity=0.156 Sum_probs=29.8
Q ss_pred EEEEEEEEe--CCCceEEEEeCCC-CEEEEEecc-cccccccccCCCCEEEEE
Q 032460 70 VHEGFITES--LPNGMFRVRLDNE-DLILGYISG-KIRQNFIRVLPGDRVRVE 118 (140)
Q Consensus 70 e~~GvVik~--l~n~~f~V~l~dG-~~~lcrI~G-KmRk~~IrI~vGDrV~VE 118 (140)
.+.|.|... -++....+.++|+ ..+.|.+-+ .+....-.+.+||.|.|.
T Consensus 2 ~v~G~V~~~~~~~~~~~~~~l~D~tg~i~~~~~~~~~~~~~~~l~~g~~v~v~ 54 (75)
T PF01336_consen 2 TVEGRVTSIRRSGGKIVFFTLEDGTGSIQVVFFNEEYERFREKLKEGDIVRVR 54 (75)
T ss_dssp EEEEEEEEEEEEETTEEEEEEEETTEEEEEEEETHHHHHHHHTS-TTSEEEEE
T ss_pred EEEEEEEEEEcCCCCEEEEEEEECCccEEEEEccHHhhHHhhcCCCCeEEEEE
Confidence 466777766 2345555555443 456777776 343333459999999986
No 137
>CHL00141 rpl24 ribosomal protein L24; Validated
Probab=59.32 E-value=24 Score=24.98 Aligned_cols=30 Identities=17% Similarity=0.275 Sum_probs=19.2
Q ss_pred ccccCCCCEEEEEeccCCCCeEEEEEEecC
Q 032460 106 FIRVLPGDRVRVEVSRYDTSKGRIIYRLRN 135 (140)
Q Consensus 106 ~IrI~vGDrV~VE~sp~D~~kGrIiyRy~r 135 (140)
.+.|.+||+|.|--=++--..|.|..-+..
T Consensus 6 ~~~I~~GD~V~Vi~G~dKGK~G~V~~V~~~ 35 (83)
T CHL00141 6 KMHVKIGDTVKIISGSDKGKIGEVLKIIKK 35 (83)
T ss_pred eCcccCCCEEEEeEcCCCCcEEEEEEEEcC
Confidence 456899999988433322346777766544
No 138
>PTZ00361 26 proteosome regulatory subunit 4-like protein; Provisional
Probab=59.30 E-value=43 Score=30.24 Aligned_cols=57 Identities=14% Similarity=0.083 Sum_probs=45.2
Q ss_pred EEEEEEEEeCCCceEEEEeCCCCEEEEEecccccccccccCCCCEEEEEeccCCCCeEEEEEEe
Q 032460 70 VHEGFITESLPNGMFRVRLDNEDLILGYISGKIRQNFIRVLPGDRVRVEVSRYDTSKGRIIYRL 133 (140)
Q Consensus 70 e~~GvVik~l~n~~f~V~l~dG~~~lcrI~GKmRk~~IrI~vGDrV~VE~sp~D~~kGrIiyRy 133 (140)
...|.|++++.++++-|....|..+..++.+.+-+ ..+.+|+.|.+. ...+.|+...
T Consensus 105 ~~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~--~~l~~~~~v~l~-----~~~~~~~~~~ 161 (438)
T PTZ00361 105 LSVGTLEEIIDENHAIVSSSVGPEYYVNILSFVDK--EQLEPGCSVLLH-----NKTHSVVGIL 161 (438)
T ss_pred cEEEEEEEEeCCCeEEEEeCCCCEEEEeccCcCCH--hhCCCCCEEEEc-----CCCCceEecC
Confidence 36699999999999999999999999999998865 458899999653 2345555544
No 139
>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=59.00 E-value=48 Score=31.24 Aligned_cols=64 Identities=20% Similarity=0.252 Sum_probs=40.8
Q ss_pred EEEEEEEEeCCCceEEEEeCCCCEEEEEecccccccccccCCCCEEEEEeccCC----CCeEEEEEEecCCC
Q 032460 70 VHEGFITESLPNGMFRVRLDNEDLILGYISGKIRQNFIRVLPGDRVRVEVSRYD----TSKGRIIYRLRNKI 137 (140)
Q Consensus 70 e~~GvVik~l~n~~f~V~l~dG~~~lcrI~GKmRk~~IrI~vGDrV~VE~sp~D----~~kGrIiyRy~r~~ 137 (140)
.+.|++... ++|+-.|..++.....-.|+..-.. ....||+|+|++..+. ...|+|+....|..
T Consensus 68 ~~~G~i~~~-~~g~gFv~~~~~~~~di~I~~~~~~---~a~~GD~Vlv~I~~~~~~~~~~eg~Vv~Il~r~~ 135 (709)
T TIGR02063 68 LVKGTVIAH-RDGFGFLRPEDDDEDDIFIPPRQMN---GAMHGDRVLVRITGKPDGGDRFEARVIKILERAN 135 (709)
T ss_pred eEEEEEEEC-CCccEEEEECCCCCCcEEEChHHhC---cCCCCCEEEEEEecccCCCCCceEEEEEEEeeCC
Confidence 478988764 4555555554421235666654322 3788999999986542 24699998887764
No 140
>PRK06299 rpsA 30S ribosomal protein S1; Reviewed
Probab=58.19 E-value=41 Score=30.38 Aligned_cols=64 Identities=27% Similarity=0.089 Sum_probs=43.5
Q ss_pred eEEEEEEEEeCCCceEEEEeCCCCEEEEEecc-----cccccccccCCCCEEEEEeccCCCCeEEEEEEe
Q 032460 69 WVHEGFITESLPNGMFRVRLDNEDLILGYISG-----KIRQNFIRVLPGDRVRVEVSRYDTSKGRIIYRL 133 (140)
Q Consensus 69 ie~~GvVik~l~n~~f~V~l~dG~~~lcrI~G-----KmRk~~IrI~vGDrV~VE~sp~D~~kGrIiyRy 133 (140)
-.+.|+|+++.+ .-+.|++.+|..-+++++= +...-.-.+.+||.|.|.+-..|.++++|.-..
T Consensus 288 ~~v~g~V~~i~~-~G~fV~l~~~v~Glv~~sel~~~~~~~~~~~~~~~G~~v~v~V~~id~~~~~i~ls~ 356 (565)
T PRK06299 288 SKVKGKVTNITD-YGAFVELEEGIEGLVHVSEMSWTKKNKHPSKVVSVGQEVEVMVLEIDEEKRRISLGL 356 (565)
T ss_pred CEEEEEEEEEeC-CeEEEEeCCCCEEEEEHHHcCccccccCHHHhcCCCCEEEEEEEEEcCCCCEEEEeh
Confidence 358899999964 4467778888777776531 111111236899999998877787778886544
No 141
>PRK10413 hydrogenase 2 accessory protein HypG; Provisional
Probab=58.13 E-value=39 Score=24.03 Aligned_cols=46 Identities=13% Similarity=-0.161 Sum_probs=25.5
Q ss_pred EEEEEEEeCCCceEEEEe-CCCCEEEEEeccccccc-ccccCCCCEEEEE
Q 032460 71 HEGFITESLPNGMFRVRL-DNEDLILGYISGKIRQN-FIRVLPGDRVRVE 118 (140)
Q Consensus 71 ~~GvVik~l~n~~f~V~l-~dG~~~lcrI~GKmRk~-~IrI~vGDrV~VE 118 (140)
+-|+|+++-+++.....+ ..|.++...+. +--. ...+.+||+|+|-
T Consensus 5 iP~kVi~i~~~~~~~A~vd~~Gv~r~V~l~--Lv~~~~~~~~vGDyVLVH 52 (82)
T PRK10413 5 VPGQVLAVGEDIHQLAQVEVCGIKRDVNIA--LICEGNPADLLGQWVLVH 52 (82)
T ss_pred cceEEEEECCCCCcEEEEEcCCeEEEEEee--eeccCCcccccCCEEEEe
Confidence 347888886443233333 35666665543 1100 0136789999984
No 142
>PRK11642 exoribonuclease R; Provisional
Probab=57.91 E-value=51 Score=32.12 Aligned_cols=65 Identities=29% Similarity=0.275 Sum_probs=42.6
Q ss_pred ceEEEEEEEEeCCCceEEEEeCCC-CEEEEEec---cc---c---------cccccccCCCCEEEEEeccCCCCeEEEEE
Q 032460 68 KWVHEGFITESLPNGMFRVRLDNE-DLILGYIS---GK---I---------RQNFIRVLPGDRVRVEVSRYDTSKGRIIY 131 (140)
Q Consensus 68 ~ie~~GvVik~l~n~~f~V~l~dG-~~~lcrI~---GK---m---------Rk~~IrI~vGDrV~VE~sp~D~~kGrIiy 131 (140)
.-++.|+|+.+...| +.|+++++ .+=+.+++ .- + ++.+-....||.|.|.+...|..++.|..
T Consensus 644 Ge~f~G~Is~V~~fG-ifVeL~~~~vEGlV~vs~L~~d~y~~d~~~~~L~g~~~~~~~~lGD~V~VkV~~vD~~~rkI~f 722 (813)
T PRK11642 644 GNVFKGVISSVTGFG-FFVRLDDLFIDGLVHVSSLDNDYYRFDQVGQRLIGESSGQTYRLGDRVEVRVEAVNMDERKIDF 722 (813)
T ss_pred CcEEEEEEEEeecCc-eEEEECCCCeeeeEEEeecCCcceEecchheEEecccCCcEECCCCEEEEEEEEeecCCCeEEE
Confidence 346899999996444 56888653 33333332 21 0 11123478899999999888888888887
Q ss_pred Ee
Q 032460 132 RL 133 (140)
Q Consensus 132 Ry 133 (140)
..
T Consensus 723 ~l 724 (813)
T PRK11642 723 SL 724 (813)
T ss_pred EE
Confidence 65
No 143
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=57.91 E-value=43 Score=26.28 Aligned_cols=53 Identities=23% Similarity=0.123 Sum_probs=30.7
Q ss_pred EEEEEEEEeCCCceEEEEeC----------CCCEEEEEeccccccc----ccccCCCCEEEEEeccCC
Q 032460 70 VHEGFITESLPNGMFRVRLD----------NEDLILGYISGKIRQN----FIRVLPGDRVRVEVSRYD 123 (140)
Q Consensus 70 e~~GvVik~l~n~~f~V~l~----------dG~~~lcrI~GKmRk~----~IrI~vGDrV~VE~sp~D 123 (140)
.+.|+|+++. +..+.|.+. ++-.-..+++-.-... .-.+.+||.|.+.+...+
T Consensus 67 iV~GkV~~i~-~~g~~V~I~~~~~~~~~l~~~~~G~l~~s~i~~~~~~~~~~~~~~GD~V~akV~~i~ 133 (189)
T PRK09521 67 IVYGRVVDVK-EQRALVRIVSIEGSERELATSKLAYIHISQVSDGYVESLTDAFKIGDIVRAKVISYT 133 (189)
T ss_pred EEEEEEEEEc-CCeEEEEEEEecccccccCCCceeeEEhhHcChhhhhhHHhccCCCCEEEEEEEecC
Confidence 4899999995 666677752 1222222222111000 122899999999976555
No 144
>COG0539 RpsA Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]
Probab=57.62 E-value=39 Score=31.76 Aligned_cols=68 Identities=25% Similarity=0.134 Sum_probs=51.2
Q ss_pred eEEEEEEEEeCCCceEEEEeCCCCEEEEEec----ccccccccccCCCCEEEEEeccCCCCeEEEEEEecCCC
Q 032460 69 WVHEGFITESLPNGMFRVRLDNEDLILGYIS----GKIRQNFIRVLPGDRVRVEVSRYDTSKGRIIYRLRNKI 137 (140)
Q Consensus 69 ie~~GvVik~l~n~~f~V~l~dG~~~lcrI~----GKmRk~~IrI~vGDrV~VE~sp~D~~kGrIiyRy~r~~ 137 (140)
-.+.|+|+.+.+.|- .|++.+|-.=++|++ .+...-.--+.+||.|.|.+-..|+++.||.-=.++..
T Consensus 279 ~~v~G~Vt~i~~~Ga-fVei~~GvEGlvhvSEisw~~~~~P~evv~~Gq~V~V~Vl~id~e~rRIsL~iKq~~ 350 (541)
T COG0539 279 DKVEGKVTNLTDYGA-FVEIEEGVEGLVHVSEISWTKKNVPSEVVKVGQEVEVKVLDIDPERRRISLGLKQLK 350 (541)
T ss_pred CEEEEEEEEeecCcE-EEEecCCccceeechhhcccccCCHHHhcccCCEEEEEEEeeCchhceEEeeehhhh
Confidence 358999999986665 578899999999998 22222122379999999999999999999876554443
No 145
>PF00164 Ribosom_S12_S23: Ribosomal protein S12/S23; InterPro: IPR006032 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 S12 is one of the proteins from the small ribosomal subunit. In Escherichia coli, S12 is known to be involved in the translation initiation step. It is a very basic protein of 120 to 150 amino-acid residues. S12 belongs to a family of ribosomal proteins which are grouped on the basis of sequence similarities. This protein is known typically as S12 in bacteria, S23 in eukaryotes and as either S12 or S23 in the Archaea []. Bacterial S12 molecules contain a conserved aspartic acid residue which undergoes a novel post-translational modification, beta-methylthiolation, to form the corresponding 3-methylthioaspartic acid.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2ZKQ_l 3BBN_L 3PYU_L 3D5A_L 3MS0_L 3MR8_L 3F1G_L 2OW8_m 3PYS_L 2QNH_m ....
Probab=56.99 E-value=22 Score=27.33 Aligned_cols=46 Identities=26% Similarity=0.346 Sum_probs=34.4
Q ss_pred EEEEEEEEeCC------Cc----eEEEEeCCCCEEEEEecccccccccccCCCCEEEEEe
Q 032460 70 VHEGFITESLP------NG----MFRVRLDNEDLILGYISGKIRQNFIRVLPGDRVRVEV 119 (140)
Q Consensus 70 e~~GvVik~l~------n~----~f~V~l~dG~~~lcrI~GKmRk~~IrI~vGDrV~VE~ 119 (140)
+..|+|++.++ |. ..+|+|.||+.+.|+|+|-= . -+.+-|.|+|+-
T Consensus 28 q~kGi~l~~~~~~pKKPNSA~RK~arVrL~n~k~v~AyIPg~G-h---nlqehs~VLVrG 83 (122)
T PF00164_consen 28 QKKGICLKVVTVKPKKPNSAIRKVARVRLSNGKKVTAYIPGEG-H---NLQEHSVVLVRG 83 (122)
T ss_dssp EEEEEEEEEEEEEESTTTCSEEEEEEEEETTSEEEEEEC-SSS-C---CSTTTSEEEEEE
T ss_pred ccCcEEeecccccccCccchhhhcceeeeccCceEEEEecCCc-c---cccccceEEEec
Confidence 56677777652 22 46889999999999999976 2 388999999973
No 146
>PRK10676 DNA-binding transcriptional regulator ModE; Provisional
Probab=56.99 E-value=33 Score=28.53 Aligned_cols=52 Identities=12% Similarity=0.063 Sum_probs=38.3
Q ss_pred EEEEEEEEeC-CCceEEEEe--CCCCEEEEEecccccccccccCCCCEEEEEeccC
Q 032460 70 VHEGFITESL-PNGMFRVRL--DNEDLILGYISGKIRQNFIRVLPGDRVRVEVSRY 122 (140)
Q Consensus 70 e~~GvVik~l-~n~~f~V~l--~dG~~~lcrI~GKmRk~~IrI~vGDrV~VE~sp~ 122 (140)
.+.|+|.++. ++....|.+ .+|..+.|.|...=-. ...+.+||.|.+.+.+.
T Consensus 201 ~l~g~V~~i~~~~~~~~V~l~l~~g~~l~A~IT~~s~~-~L~L~~G~~V~a~iKas 255 (263)
T PRK10676 201 QLPGTISHIERGAEQSEVLMALPDGQTLCATVPNNEAA-RLSLQQGDAVTAYFNAD 255 (263)
T ss_pred eEEEEEEEEEeCCCcEEEEEEeCCCCEEEEEecHHHHH-hcCCCCCCEEEEEEEcc
Confidence 5889999986 344455554 5788899999865433 46799999999877643
No 147
>CHL00051 rps12 ribosomal protein S12
Probab=56.35 E-value=21 Score=27.57 Aligned_cols=32 Identities=31% Similarity=0.283 Sum_probs=26.8
Q ss_pred eEEEEeCCCCEEEEEecccccccccccCCCCEEEEE
Q 032460 83 MFRVRLDNEDLILGYISGKIRQNFIRVLPGDRVRVE 118 (140)
Q Consensus 83 ~f~V~l~dG~~~lcrI~GKmRk~~IrI~vGDrV~VE 118 (140)
..+|+|.||+++.|+|+|-=- -+.+-|.|+|+
T Consensus 52 varVrLsngk~v~AyIPGeGh----nlqehs~VLvr 83 (123)
T CHL00051 52 VARVRLTSGFEITAYIPGIGH----NLQEHSVVLVR 83 (123)
T ss_pred EEEEEccCCCEEEEEcCCCCc----cccccCEEEEe
Confidence 467889999999999999752 48888888886
No 148
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=55.76 E-value=47 Score=27.20 Aligned_cols=61 Identities=15% Similarity=0.077 Sum_probs=37.0
Q ss_pred cccCCcceEEEEEEEEeCCCceEEEEeCCCCEEEEEec---cc-c----cccccccCCCCEEEEEeccCCC
Q 032460 62 EGANSEKWVHEGFITESLPNGMFRVRLDNEDLILGYIS---GK-I----RQNFIRVLPGDRVRVEVSRYDT 124 (140)
Q Consensus 62 ~~~k~d~ie~~GvVik~l~n~~f~V~l~dG~~~lcrI~---GK-m----Rk~~IrI~vGDrV~VE~sp~D~ 124 (140)
-.|+... .+.|+|++.. +..+.|.+..+..-..+++ ++ . +..+-.+.+||.|...+...+.
T Consensus 59 y~P~vGD-iViG~V~~i~-~~~~~vdI~~~~~g~L~~s~i~~~~~~~d~~~~~~~~~~GDlV~akV~~i~~ 127 (235)
T PRK04163 59 YIPKVGD-LVIGKVTDVT-FSGWEVDINSPYKAYLPVSEVLGRPVNVEGTDLRKYLDIGDYIIAKVKDVDR 127 (235)
T ss_pred ccCCCCC-EEEEEEEEEe-CceEEEEeCCCceeEEEHHHcCCCccccchhhhHhhCCCCCEEEEEEEEECC
Confidence 3555544 4889999985 7778888865433222322 21 1 1112237999999988765554
No 149
>smart00739 KOW KOW (Kyprides, Ouzounis, Woese) motif. Motif in ribosomal proteins, NusG, Spt5p, KIN17 and T54.
Probab=55.60 E-value=30 Score=18.31 Aligned_cols=24 Identities=25% Similarity=0.396 Sum_probs=18.8
Q ss_pred cCCCCEEEEEeccCCCCeEEEEEE
Q 032460 109 VLPGDRVRVEVSRYDTSKGRIIYR 132 (140)
Q Consensus 109 I~vGDrV~VE~sp~D~~kGrIiyR 132 (140)
+.+||.|.|.--++.-..|.|+..
T Consensus 2 ~~~G~~V~I~~G~~~g~~g~i~~i 25 (28)
T smart00739 2 FEVGDTVRVIAGPFKGKVGKVLEV 25 (28)
T ss_pred CCCCCEEEEeECCCCCcEEEEEEE
Confidence 568999999877777777888754
No 150
>PF09038 53-BP1_Tudor: Tumour suppressor p53-binding protein-1 Tudor; InterPro: IPR015125 This domain consist of ten beta-strands and a carboxy-terminal alpha-helix. The amino-terminal five beta-strands and the C-terminal five beta-strands adopt folds that are identical to each other. The domain is essential for the recruitment of proteins to double stranded breaks in DNA, which is mediated by interaction with methylated Lys 79 of histone H3 []. ; PDB: 3LGL_A 1XNI_B 3LGF_A 2G3R_A 2IG0_A 3LH0_A 1SSF_A.
Probab=55.57 E-value=45 Score=25.75 Aligned_cols=59 Identities=19% Similarity=0.036 Sum_probs=37.1
Q ss_pred EEEEEEEeCCCceEEEEeCCCCEEEEEecccccccccccCCCCEEEEEeccCCCCeEEEEE
Q 032460 71 HEGFITESLPNGMFRVRLDNEDLILGYISGKIRQNFIRVLPGDRVRVEVSRYDTSKGRIIY 131 (140)
Q Consensus 71 ~~GvVik~l~n~~f~V~l~dG~~~lcrI~GKmRk~~IrI~vGDrV~VE~sp~D~~kGrIiy 131 (140)
--|+|+.-.+++.|+|..+||.+ |++.+|--.-.+.+.+|--|.-+....-.+-|.|+-
T Consensus 20 Y~G~I~~~~~~~kykv~FdDG~~--~~v~~~div~~dplpl~~eV~A~~eddY~~~GvV~~ 78 (122)
T PF09038_consen 20 YPGKITSDKGKNKYKVLFDDGYE--CRVLGKDIVVCDPLPLGTEVTALSEDDYFSPGVVKG 78 (122)
T ss_dssp EEEEEEEEETTTEEEEEETTS-E--EEEECCCEEEESSS-TTEEEEECCTTCTSEEEEEEE
T ss_pred cCceEeecCCCCeEEEEecCCcc--ceeccCcEEEEcceeccceeEEeecCCcccccEEEE
Confidence 46998888899999999999975 555555433335666777776542221124566654
No 151
>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=54.42 E-value=56 Score=29.04 Aligned_cols=61 Identities=21% Similarity=0.076 Sum_probs=41.5
Q ss_pred EEEEEEEEeCCCceEEEEeCCCCEEEEEecc----cccccccccCCCCEEEEEeccCCCCeEEEEE
Q 032460 70 VHEGFITESLPNGMFRVRLDNEDLILGYISG----KIRQNFIRVLPGDRVRVEVSRYDTSKGRIIY 131 (140)
Q Consensus 70 e~~GvVik~l~n~~f~V~l~dG~~~lcrI~G----KmRk~~IrI~vGDrV~VE~sp~D~~kGrIiy 131 (140)
.+.|.|++.. +.-+.|.+++|-.=+|+++= +...-.-.+.+||.|.+.+...|.++++|.-
T Consensus 449 ~v~g~V~~v~-~~G~fV~l~~~~~Glv~~s~l~~~~~~~~~~~~~~Gd~v~~~V~~id~~~~~i~l 513 (516)
T TIGR00717 449 VVKGKVTEIK-DFGAFVELPGGVEGLIRNSELSENRDEDKTDEIKVGDEVEAKVVDIDKKNRKVSL 513 (516)
T ss_pred EEEEEEEEEe-cceEEEEcCCCeEEEEEHHHcCccccccccccCCCCCEEEEEEEEEeCCCCEEEE
Confidence 6899999986 44456778777555555532 1111223478999999998877877788754
No 152
>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=52.98 E-value=62 Score=23.08 Aligned_cols=60 Identities=23% Similarity=0.056 Sum_probs=38.8
Q ss_pred EEEEEEEEeCCCceEEEEeCCCCEEEEEeccccc-------c----------------cccccCCCCEEEEEeccCCCC-
Q 032460 70 VHEGFITESLPNGMFRVRLDNEDLILGYISGKIR-------Q----------------NFIRVLPGDRVRVEVSRYDTS- 125 (140)
Q Consensus 70 e~~GvVik~l~n~~f~V~l~dG~~~lcrI~GKmR-------k----------------~~IrI~vGDrV~VE~sp~D~~- 125 (140)
.+.|+|+++- +.-..|.+.+|..=.+++.=--. . -.-...+||.|.+.+...|..
T Consensus 6 vV~G~V~~v~-~~gl~v~L~~g~~G~v~~seis~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~vGd~V~~kVi~~d~~~ 84 (100)
T cd05693 6 LVLGQVKEIT-KLDLVISLPNGLTGYVPITNISDAYTERLEELDEESEEEDDEEELPDLEDLFSVGQLVRCKVVSLDKSK 84 (100)
T ss_pred EEEEEEEEEc-CCCEEEECCCCcEEEEEHHHhhHHHHHHHHHhhhhccccccccccCCHHHhccCCCEEEEEEEEccCCc
Confidence 5889999985 55667788877655554421110 0 012378999999998777765
Q ss_pred --eEEEE
Q 032460 126 --KGRII 130 (140)
Q Consensus 126 --kGrIi 130 (140)
+++|.
T Consensus 85 ~~~~~i~ 91 (100)
T cd05693 85 SGKKRIE 91 (100)
T ss_pred CCCcEEE
Confidence 55654
No 153
>PRK06299 rpsA 30S ribosomal protein S1; Reviewed
Probab=52.55 E-value=59 Score=29.40 Aligned_cols=64 Identities=23% Similarity=0.074 Sum_probs=43.8
Q ss_pred eEEEEEEEEeCCCceEEEEeCCCCEEEEEeccc----c-cccccccCCCCEEEEEeccCCCCeEEEEEEe
Q 032460 69 WVHEGFITESLPNGMFRVRLDNEDLILGYISGK----I-RQNFIRVLPGDRVRVEVSRYDTSKGRIIYRL 133 (140)
Q Consensus 69 ie~~GvVik~l~n~~f~V~l~dG~~~lcrI~GK----m-Rk~~IrI~vGDrV~VE~sp~D~~kGrIiyRy 133 (140)
-.+.|+|...- +.-+.|.+.+|..-.++++=- . +...-+..+||.|.+-+...|.++++|.--.
T Consensus 375 ~~v~g~V~~v~-~~G~fV~l~~~v~g~i~~s~l~~~~~~~~~~~~~~~Gd~v~v~Il~vd~~~~~i~ls~ 443 (565)
T PRK06299 375 DVVEGKVKNIT-DFGAFVGLEGGIDGLVHLSDISWDKKGEEAVELYKKGDEVEAVVLKVDVEKERISLGI 443 (565)
T ss_pred CEEEEEEEEEe-cceEEEECCCCCEEEEEHHHcCccccccChHhhCCCCCEEEEEEEEEeCCCCEEEEEE
Confidence 36899999985 555668887776666665421 1 2222357899999998777777777776544
No 154
>PF01200 Ribosomal_S28e: Ribosomal protein S28e; InterPro: IPR000289 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 [, ]. A number of eukaryotic and archaebacterial ribosomal proteins can be grouped on the basis of sequence similarities. Examples are: Mammalian S28 [] Plant S28 [] Fungi S33 [] Archaebacterial S28e. These proteins have from 64 to 78 amino acids and a highly conserved C-terminal region.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3IZ6_Y 2XZN_1 2XZM_1 1NY4_A 1NE3_A 3U5C_c 3U5G_c 3O30_R 3O2Z_R 3IZB_Y.
Probab=51.71 E-value=77 Score=22.22 Aligned_cols=40 Identities=20% Similarity=0.365 Sum_probs=25.5
Q ss_pred EEEEEEEeCC-----CceEE--EEe-CC--CCEEEEEecccccccccccCCCCEEEE
Q 032460 71 HEGFITESLP-----NGMFR--VRL-DN--EDLILGYISGKIRQNFIRVLPGDRVRV 117 (140)
Q Consensus 71 ~~GvVik~l~-----n~~f~--V~l-~d--G~~~lcrI~GKmRk~~IrI~vGDrV~V 117 (140)
..+.|+++++ ++.-. |++ ++ |..++..++|=+|. ||.+.+
T Consensus 9 ~~A~V~kVlgRtGs~G~~tQVrv~~l~~~~gR~i~RNVkGPVr~-------GDil~L 58 (69)
T PF01200_consen 9 KLARVIKVLGRTGSRGQVTQVRVEFLDGDKGRSIIRNVKGPVRE-------GDILTL 58 (69)
T ss_dssp EEEEEEEEECCCTSSSSEEEEEEEESSSSSS-EEEEEECSTTST-------T-EEEE
T ss_pred eeEEEEEEcccccCcccEEEEEEEEecCCcceEEeecccCCccc-------CcEEEE
Confidence 4588888885 33444 444 33 58888888887765 999865
No 155
>PF11325 DUF3127: Domain of unknown function (DUF3127); InterPro: IPR021474 This bacterial family of proteins has no known function.
Probab=50.87 E-value=28 Score=25.02 Aligned_cols=13 Identities=31% Similarity=0.498 Sum_probs=11.1
Q ss_pred ccCCCCEEEEEec
Q 032460 108 RVLPGDRVRVEVS 120 (140)
Q Consensus 108 rI~vGDrV~VE~s 120 (140)
.+.+||.|.|.+.
T Consensus 52 ~~~~Gd~V~Vsf~ 64 (84)
T PF11325_consen 52 NFQVGDEVKVSFN 64 (84)
T ss_pred cCCCCCEEEEEEE
Confidence 5889999999865
No 156
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=50.62 E-value=79 Score=28.04 Aligned_cols=60 Identities=22% Similarity=0.237 Sum_probs=40.7
Q ss_pred eEEEEEEEEeCCCceEEEEeCCCCEEEEEecccccccccccCCCCEEEEEeccCCCC-eE--EEEEE
Q 032460 69 WVHEGFITESLPNGMFRVRLDNEDLILGYISGKIRQNFIRVLPGDRVRVEVSRYDTS-KG--RIIYR 132 (140)
Q Consensus 69 ie~~GvVik~l~n~~f~V~l~dG~~~lcrI~GKmRk~~IrI~vGDrV~VE~sp~D~~-kG--rIiyR 132 (140)
-.+.|+|.+.- ++.+.|.+ |. ..|.++-+-...+-...+||+|.+-+...+.+ +| .++.|
T Consensus 136 eiV~G~V~~~~-~~~~~Vdl--g~-vEa~LP~~E~ip~e~~~~Gd~Ika~V~~V~~~~kgp~IivSR 198 (362)
T PRK12327 136 DIVTGVVQRRD-NRFVYVNL--GK-IEAVLPPAEQIPGETYKHGDRIKVYVVKVEKTTKGPQIFVSR 198 (362)
T ss_pred CEEEEEEEEEe-CCcEEEEe--CC-eEEEecHHHcCCCCCCCCCCEEEEEEEEEecCCCCCeEEEEe
Confidence 35899999985 66677876 33 68888855444456689999998876544432 33 44444
No 157
>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=50.24 E-value=76 Score=21.29 Aligned_cols=62 Identities=13% Similarity=0.191 Sum_probs=40.9
Q ss_pred EEEEEEEEeCCCceEEEEeC-CCCEEEEEecccccccccccCCCCEEEEEeccCCCCeEEEEEEec
Q 032460 70 VHEGFITESLPNGMFRVRLD-NEDLILGYISGKIRQNFIRVLPGDRVRVEVSRYDTSKGRIIYRLR 134 (140)
Q Consensus 70 e~~GvVik~l~n~~f~V~l~-dG~~~lcrI~GKmRk~~IrI~vGDrV~VE~sp~D~~kGrIiyRy~ 134 (140)
.+.|.|.++. +-=+.|.+. +| +.+.++=+---..-.+.+||.|.+.+...|.++.+|.--.+
T Consensus 7 ~v~g~V~si~-d~G~~v~~g~~g--v~Gfl~~~~~~~~~~~~~Gq~v~~~V~~vd~~~~~v~ls~k 69 (74)
T cd05694 7 VLSGCVSSVE-DHGYILDIGIPG--TTGFLPKKDAGNFSKLKVGQLLLCVVEKVKDDGRVVSLSAD 69 (74)
T ss_pred EEEEEEEEEe-CCEEEEEeCCCC--cEEEEEHHHCCcccccCCCCEEEEEEEEEECCCCEEEEEEe
Confidence 4899999997 444557663 44 56666633222123489999999988777777777654433
No 158
>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=50.16 E-value=41 Score=25.86 Aligned_cols=44 Identities=16% Similarity=0.135 Sum_probs=29.0
Q ss_pred EEEEEEeCC-CceEEEEeCCCCEEEEEecccccccccccCCCCEEEEEe
Q 032460 72 EGFITESLP-NGMFRVRLDNEDLILGYISGKIRQNFIRVLPGDRVRVEV 119 (140)
Q Consensus 72 ~GvVik~l~-n~~f~V~l~dG~~~lcrI~GKmRk~~IrI~vGDrV~VE~ 119 (140)
-|+++..-. ...+.|+.+||. ..-.... ++ ..-|++||.|.|..
T Consensus 26 Pa~~~~~~~~~~~~~V~Fedg~-~~i~~~d-v~--~LDlRIGD~Vkv~~ 70 (131)
T PF08605_consen 26 PATCVGSGVDRDRSLVRFEDGT-YEIKNED-VK--YLDLRIGDTVKVDG 70 (131)
T ss_pred eEEEEeecCCCCeEEEEEecCc-eEeCccc-Ee--eeeeecCCEEEECC
Confidence 466666632 225999999988 4444444 32 34588899999965
No 159
>PTZ00067 40S ribosomal S23; Provisional
Probab=49.62 E-value=37 Score=26.90 Aligned_cols=35 Identities=26% Similarity=0.211 Sum_probs=28.3
Q ss_pred eEEEEeC-CCCEEEEEecccccccccccCCCCEEEEEe
Q 032460 83 MFRVRLD-NEDLILGYISGKIRQNFIRVLPGDRVRVEV 119 (140)
Q Consensus 83 ~f~V~l~-dG~~~lcrI~GKmRk~~IrI~vGDrV~VE~ 119 (140)
-.+|+|. ||+++.|+|+|-=-.+ -|.+-|.|+|+-
T Consensus 69 ~~rV~L~kngk~vtAyiPg~G~lh--~lqEh~~VLV~G 104 (143)
T PTZ00067 69 CVRVQLIKNGKKITAFVPNDGCLN--FINENDEVLVSG 104 (143)
T ss_pred EEEEEEccCCcEEEEEeCCCCccc--ccccCCEEEEEe
Confidence 4678886 9999999999976433 388899999983
No 160
>TIGR02381 cspD cold shock domain protein CspD. This model represents what appears to be a phylogenetically distinct clade, containing E. coli CspD and related proteobacterial proteins within the larger family of cold shock domain proteins described by pfam model pfam00313. The gene symbol cspD may have been used idependently for other subfamilies of cold shock domain proteins, such as for B. subtilis CspD. These proteins typically are shorter than 70 amino acids. In E. coli, CspD is a stress response protein induced in stationary phase. This homodimer binds single-stranded DNA and appears to inhibit DNA replication.
Probab=47.95 E-value=45 Score=22.25 Aligned_cols=50 Identities=16% Similarity=0.160 Sum_probs=33.0
Q ss_pred EEEEEEeCC-CceEEEEeCC-CCEEEEEecccccccccccCCCCEEEEEecc
Q 032460 72 EGFITESLP-NGMFRVRLDN-EDLILGYISGKIRQNFIRVLPGDRVRVEVSR 121 (140)
Q Consensus 72 ~GvVik~l~-n~~f~V~l~d-G~~~lcrI~GKmRk~~IrI~vGDrV~VE~sp 121 (140)
+|+|..--. .|+=.|..++ |..+-.|++.=-....-.+.+||+|.+++..
T Consensus 3 ~G~Vk~f~~~kGfGFI~~~~g~~dvfvH~s~~~~~g~~~l~~G~~V~f~~~~ 54 (68)
T TIGR02381 3 IGIVKWFNNAKGFGFICPEGVDGDIFAHYSTIQMDGYRTLKAGQKVQFEVVQ 54 (68)
T ss_pred CeEEEEEeCCCCeEEEecCCCCccEEEEHHHhhhcCCCCCCCCCEEEEEEEE
Confidence 477777543 3333555555 6788899887432222469999999998764
No 161
>cd03367 Ribosomal_S23 S12-like family, 40S ribosomal protein S23 subfamily; S23 is located at the interface of the large and small ribosomal subunits of eukaryotes, adjacent to the decoding center. It interacts with domain III of the eukaryotic elongation factor 2 (eEF2), which catalyzes the translocation of the growing peptidyl-tRNA to the P site to make room for the next aminoacyl-tRNA at the A (acceptor) site. Through its interaction with eEF2, S23 may play an important role in translocation. Also members of this subfamily are the archaeal 30S ribosomal S12 proteins. Prokaryotic S12 is essential for maintenance of a pretranslocation state and, together with S13, functions as control element for the rRNA- and tRNA-driven movements of translocation. S12 and S23 are also implicated in translation accuracy. Antibiotics such as streptomycin bind S12/S23 and cause the ribosome to misread the genetic code.
Probab=47.86 E-value=42 Score=25.67 Aligned_cols=35 Identities=29% Similarity=0.300 Sum_probs=28.1
Q ss_pred eEEEEe-CCCCEEEEEecccccccccccCCCCEEEEEe
Q 032460 83 MFRVRL-DNEDLILGYISGKIRQNFIRVLPGDRVRVEV 119 (140)
Q Consensus 83 ~f~V~l-~dG~~~lcrI~GKmRk~~IrI~vGDrV~VE~ 119 (140)
-.+|+| .||+++.|+|+|-=-.+ -+.+-|.|+|+-
T Consensus 44 ~~rV~L~~ngk~itAyIPG~G~~~--~lqeh~~VLV~G 79 (115)
T cd03367 44 CVRVQLIKNGKKITAFVPGDGCLN--FIDENDEVLVAG 79 (115)
T ss_pred EEEEEEccCCeEEEEEeCCCCccc--ccccCCEEEEEe
Confidence 467888 69999999999976433 388899999983
No 162
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=47.63 E-value=66 Score=29.45 Aligned_cols=53 Identities=23% Similarity=0.216 Sum_probs=40.5
Q ss_pred eEEEEEEEEeCCCceEEEEeCCCCEEEEEecccccccccccCCCCEEEEEeccCCCC
Q 032460 69 WVHEGFITESLPNGMFRVRLDNEDLILGYISGKIRQNFIRVLPGDRVRVEVSRYDTS 125 (140)
Q Consensus 69 ie~~GvVik~l~n~~f~V~l~dG~~~lcrI~GKmRk~~IrI~vGDrV~VE~sp~D~~ 125 (140)
-.+.|+|.+.- ++.+.|.+ +| ..|.++.+-.-.+....+||+|.+-+...+.+
T Consensus 136 eIV~G~V~ri~-~~giiVDL-gg--vea~LP~sE~ip~E~~~~GdrIka~I~~Vd~~ 188 (470)
T PRK09202 136 EIITGVVKRVE-RGNIIVDL-GR--AEAILPRKEQIPRENFRPGDRVRAYVYEVRKE 188 (470)
T ss_pred CEEEEEEEEEe-cCCEEEEE-CC--eEEEecHHHcCCCccCCCCCEEEEEEEEEecC
Confidence 35899999986 77788887 33 58888877666566799999999987665553
No 163
>PF08661 Rep_fac-A_3: Replication factor A protein 3; InterPro: IPR013970 Replication factor A is involved in eukaryotic DNA replication, recombination and repair. ; PDB: 2PI2_H 1L1O_D 3KDF_A 2Z6K_D 1QUQ_D 2PQA_D.
Probab=47.50 E-value=69 Score=22.92 Aligned_cols=46 Identities=9% Similarity=-0.075 Sum_probs=31.2
Q ss_pred ceEEEEEEEEeCC--CceEEEEeCCCCEEEEEecccccccccccCCCCEEEEEe
Q 032460 68 KWVHEGFITESLP--NGMFRVRLDNEDLILGYISGKIRQNFIRVLPGDRVRVEV 119 (140)
Q Consensus 68 ~ie~~GvVik~l~--n~~f~V~l~dG~~~lcrI~GKmRk~~IrI~vGDrV~VE~ 119 (140)
.+.+-|+|.+. . ++.+.+++.||..+.+.+..-.- ...+.+|+|.-
T Consensus 20 ~VrivGkv~~~-~~~g~~~~l~~~d~~~V~v~l~~~~~-----~~~~~~vEviG 67 (109)
T PF08661_consen 20 TVRIVGKVESV-DPDGGSATLSTSDGGQVTVSLNPPSD-----EELSKYVEVIG 67 (109)
T ss_dssp EEEEEEEEEEE--TTSSEEEEE-TTS-EEEEEESS--S-----S---SEEEEEE
T ss_pred eEEEEEEEeeE-cCCCCEEEEEcCCCCEEEEEeCCCCC-----CCCCCEEEEEE
Confidence 56788999997 5 89999999999999999885542 34578887653
No 164
>PF12869 tRNA_anti-like: tRNA_anti-like; InterPro: IPR024422 The function of the proteins in this entry is not known, but they contain a novel variant of the nucleic acid-binding OB fold [].; PDB: 3F1Z_I.
Probab=46.88 E-value=60 Score=23.54 Aligned_cols=54 Identities=13% Similarity=0.145 Sum_probs=29.4
Q ss_pred CCcceEEEEEEEEeC--CCceEEEEeC---CCCEEEEEeccccccc--ccccCCCCEEEEE
Q 032460 65 NSEKWVHEGFITESL--PNGMFRVRLD---NEDLILGYISGKIRQN--FIRVLPGDRVRVE 118 (140)
Q Consensus 65 k~d~ie~~GvVik~l--~n~~f~V~l~---dG~~~lcrI~GKmRk~--~IrI~vGDrV~VE 118 (140)
+...++++|+|.++- .++.|.+... +...+.|.+.-.-... -..+..||.|.|.
T Consensus 66 ~gK~i~vtG~V~~I~~~~~~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~l~~G~~Vti~ 126 (144)
T PF12869_consen 66 KGKIIEVTGTVSSIDKGFGDNYVVLLGTENGFAGVQCYFSNDQEKRASVAKLKKGQKVTIK 126 (144)
T ss_dssp TT-EEEEEEEEEEEEE-STT-EEEEEE-TT-S-S--EEEEEEGGGHHHHHH--TTSEEEEE
T ss_pred CCCEEEEEEEEEEEEEcCCCcEEEEccCCCCceeEEEEEccchhhhhhHhcCCCCCEEEEE
Confidence 345689999999982 2455544432 2334678887555321 1138899999986
No 165
>smart00743 Agenet Tudor-like domain present in plant sequences. Domain in plant sequences with possible chromatin-associated functions.
Probab=46.88 E-value=61 Score=20.44 Aligned_cols=23 Identities=26% Similarity=0.307 Sum_probs=18.7
Q ss_pred ceEEEEEEEEeCCCceEEEEeCC
Q 032460 68 KWVHEGFITESLPNGMFRVRLDN 90 (140)
Q Consensus 68 ~ie~~GvVik~l~n~~f~V~l~d 90 (140)
..=-.|+|++..+++.|.|...+
T Consensus 17 ~~W~~a~V~~~~~~~~~~V~~~~ 39 (61)
T smart00743 17 DSWWEAVVTKVLGDGKYLVRYLT 39 (61)
T ss_pred CEEEEEEEEEECCCCEEEEEECC
Confidence 34477999999987899999865
No 166
>COG1222 RPT1 ATP-dependent 26S proteasome regulatory subunit [Posttranslational modification, protein turnover, chaperones]
Probab=46.79 E-value=61 Score=29.58 Aligned_cols=47 Identities=21% Similarity=0.210 Sum_probs=40.1
Q ss_pred EEEEEEEEeCCCceEEEEeCCCCEEEEEecccccccccccCCCCEEEEE
Q 032460 70 VHEGFITESLPNGMFRVRLDNEDLILGYISGKIRQNFIRVLPGDRVRVE 118 (140)
Q Consensus 70 e~~GvVik~l~n~~f~V~l~dG~~~lcrI~GKmRk~~IrI~vGDrV~VE 118 (140)
.+.|+|++.+.++.+-|....|-.+.-.+..-+-+ -.+.||++|-+-
T Consensus 73 l~vg~v~e~id~~~~iVks~~g~~~vV~i~~~vd~--~~L~pG~rVal~ 119 (406)
T COG1222 73 LIVGTVLEVLDDGRAIVKSSTGPKFVVNILSFVDR--DLLEPGMRVALN 119 (406)
T ss_pred ceEEEEEEEcCCceEEEEeCCCCeEEEeccCCcCH--HHcCCCCEEEEc
Confidence 36699999998888999999999999999887765 469999999764
No 167
>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=46.05 E-value=92 Score=27.33 Aligned_cols=52 Identities=19% Similarity=0.151 Sum_probs=37.6
Q ss_pred eEEEEEEEEeCCCceEEEEeCCCCEEEEEecccccccccccCCCCEEEEEeccCC
Q 032460 69 WVHEGFITESLPNGMFRVRLDNEDLILGYISGKIRQNFIRVLPGDRVRVEVSRYD 123 (140)
Q Consensus 69 ie~~GvVik~l~n~~f~V~l~dG~~~lcrI~GKmRk~~IrI~vGDrV~VE~sp~D 123 (140)
-.+.|+|.+.-.++.+.|.+ | ...+.++.+-.-.+-...+||+|.+-+..-+
T Consensus 133 eiV~G~V~~v~~~g~v~Vdi--G-~~ea~LP~~E~ip~E~~~~Gd~ik~~V~~V~ 184 (341)
T TIGR01953 133 EIISGTVKRVNRRGNLYVEL--G-KTEGILPKKEQIPGEKFRIGDRIKAYVYEVR 184 (341)
T ss_pred CEEEEEEEEEecCCcEEEEE--C-CeEEEecHHHcCCCcCCCCCCEEEEEEEEEE
Confidence 35899999986446557876 4 3588888666555556899999988765444
No 168
>PRK05054 exoribonuclease II; Provisional
Probab=45.50 E-value=1.1e+02 Score=28.74 Aligned_cols=62 Identities=23% Similarity=0.176 Sum_probs=38.8
Q ss_pred EEEEEEEEeCCCceEEEEeC-CCCEEEEEecc---------------ccc-ccccccCCCCEEEEEeccCCCCeEEEEEE
Q 032460 70 VHEGFITESLPNGMFRVRLD-NEDLILGYISG---------------KIR-QNFIRVLPGDRVRVEVSRYDTSKGRIIYR 132 (140)
Q Consensus 70 e~~GvVik~l~n~~f~V~l~-dG~~~lcrI~G---------------KmR-k~~IrI~vGDrV~VE~sp~D~~kGrIiyR 132 (140)
+..|+|+.+.+.| |.|+++ +|.+-+-++++ .+. +.+-....||+|.|.+..-|..++.|..+
T Consensus 564 ~f~g~I~~v~~~G-~fV~l~~~~veglV~~~~l~~~~~~y~~~~~~~~~~~~~~~~~~lGd~V~V~v~~vd~~~~~i~~~ 642 (644)
T PRK05054 564 RFAAEIIDISRGG-MRVRLLENGAVAFIPASFLHAVRDELVCNQENGTVQIKGETVYKLGDVIDVTLAEVRMETRSIIAR 642 (644)
T ss_pred EEEEEEEeeecCc-EEEEEeCCceEEEEEccccCCCccceEEccccceEEEeCCEEEcCCCEEEEEEEEEccccCeEEEE
Confidence 6899999986544 455553 32222211111 011 11124788999999999889888888765
No 169
>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional
Probab=45.16 E-value=77 Score=31.26 Aligned_cols=65 Identities=15% Similarity=0.129 Sum_probs=43.9
Q ss_pred eEEEEEEEEeCCCceEEEEeCCCCEEEEEec---ccccc----cccccCCCCEEEEEeccCCCCeEEEEEEec
Q 032460 69 WVHEGFITESLPNGMFRVRLDNEDLILGYIS---GKIRQ----NFIRVLPGDRVRVEVSRYDTSKGRIIYRLR 134 (140)
Q Consensus 69 ie~~GvVik~l~n~~f~V~l~dG~~~lcrI~---GKmRk----~~IrI~vGDrV~VE~sp~D~~kGrIiyRy~ 134 (140)
-.+.|+|+++. +.-+.|++++|..-+++++ -.... ..-+..+||.|.|.+...|..+.+|..-.+
T Consensus 754 ~iV~GkV~~v~-~~GvFVeL~~gVeGlI~~s~lsdd~~~~~~~~~~~f~vGD~V~v~Vl~iD~~~rkI~LSlk 825 (863)
T PRK12269 754 STVEGEVSSVT-DFGIFVRVPGGVEGLVRKQHLVENRDGDPGEALRKYAVGDRVKAVIVDMNVKDRKVAFSVR 825 (863)
T ss_pred CEEEEEEEEEe-cCeEEEEcCCCeEEEEEHHHcCCcccccchhhccccCCCCEEEEEEEEEEcCCCEEEEEEe
Confidence 36999999985 5556788888766666554 11000 012478999999998877777777776544
No 170
>PRK15463 cold shock-like protein CspF; Provisional
Probab=44.27 E-value=99 Score=20.93 Aligned_cols=51 Identities=14% Similarity=0.001 Sum_probs=34.0
Q ss_pred EEEEEEEeCC-CceEEEEeCC-CCEEEEEecccccccccccCCCCEEEEEecc
Q 032460 71 HEGFITESLP-NGMFRVRLDN-EDLILGYISGKIRQNFIRVLPGDRVRVEVSR 121 (140)
Q Consensus 71 ~~GvVik~l~-n~~f~V~l~d-G~~~lcrI~GKmRk~~IrI~vGDrV~VE~sp 121 (140)
|.|+|..--. .|+=.+..++ |..+-.|++-=-+...-.+.+||+|.+++..
T Consensus 5 ~~G~Vk~fn~~kGfGFI~~~~g~~DvFvH~sal~~~g~~~l~~G~~V~f~v~~ 57 (70)
T PRK15463 5 MTGIVKTFDGKSGKGLITPSDGRKDVQVHISALNLRDAEELTTGLRVEFCRIN 57 (70)
T ss_pred ceEEEEEEeCCCceEEEecCCCCccEEEEehhhhhcCCCCCCCCCEEEEEEEE
Confidence 5789988754 2332455544 5688888875433223359999999998764
No 171
>PRK07400 30S ribosomal protein S1; Reviewed
Probab=44.18 E-value=79 Score=27.10 Aligned_cols=59 Identities=7% Similarity=0.073 Sum_probs=37.4
Q ss_pred EEEEEEEEeCCCceEEEEeCCCCEEEEEeccc-ccccc-----cccCCCCEEEEEeccCCCCeEEEEE
Q 032460 70 VHEGFITESLPNGMFRVRLDNEDLILGYISGK-IRQNF-----IRVLPGDRVRVEVSRYDTSKGRIIY 131 (140)
Q Consensus 70 e~~GvVik~l~n~~f~V~l~dG~~~lcrI~GK-mRk~~-----IrI~vGDrV~VE~sp~D~~kGrIiy 131 (140)
.+.|+|+++. .+...|.+ |....+.++=. +...+ ..+.+||.|.|.+...+..+|+|+-
T Consensus 34 iv~G~V~~i~-~~g~~Vdi--g~k~~g~lp~sEis~~~~~~~~~~~~~G~~v~~~Vi~~~~~~~~i~l 98 (318)
T PRK07400 34 IVNGTVFSLE-PRGALIDI--GAKTAAFMPIQEMSINRVEGPEEVLQPNETREFFILSDENEDGQLTL 98 (318)
T ss_pred EEEEEEEEEE-CCEEEEEE--CCCeEEEEEHHHhccccccCHHHccCCCCEEEEEEEEEeCCCCeEEE
Confidence 4899999984 66677877 44446665411 11111 1267899999887655666666654
No 172
>PF01796 DUF35: DUF35 OB-fold domain; InterPro: IPR002878 This domain has no known function and is found in conserved hypothetical archaeal and bacterial proteins. The domain is approximately 70 amino acids long. The domain is duplicated in O53566 from SWISSPROT. The structure of a DUF35 representative reveals two long N-terminal helices followed by a rubredoxin-like zinc ribbon domain and a C-terminal OB fold domain represented in this entry. OB-folds are frequently found to bind nucleic acids suggesting this domain might bind to DNA or RNA.
Probab=44.13 E-value=76 Score=20.76 Aligned_cols=37 Identities=22% Similarity=0.114 Sum_probs=25.0
Q ss_pred ceEEEEeCCCCEEEEEecccccccccccCCCCEEEEE
Q 032460 82 GMFRVRLDNEDLILGYISGKIRQNFIRVLPGDRVRVE 118 (140)
Q Consensus 82 ~~f~V~l~dG~~~lcrI~GKmRk~~IrI~vGDrV~VE 118 (140)
..-.|++++|-.++++|-|---..--.+..|++|.+.
T Consensus 30 ~v~~V~ldeg~rv~~~i~~~~~~~~~~l~iG~~V~~v 66 (68)
T PF01796_consen 30 VVAIVELDEGVRVMARIVDVDPEDPDELRIGMRVRLV 66 (68)
T ss_pred EEEEEEeCCCCEEEEEEecCCCCCcccCCCCCEEEEE
Confidence 3346788779999999998321111136789999765
No 173
>PRK04211 rps12P 30S ribosomal protein S12P; Reviewed
Probab=43.99 E-value=47 Score=26.38 Aligned_cols=35 Identities=26% Similarity=0.284 Sum_probs=28.1
Q ss_pred eEEEEe-CCCCEEEEEecccccccccccCCCCEEEEEe
Q 032460 83 MFRVRL-DNEDLILGYISGKIRQNFIRVLPGDRVRVEV 119 (140)
Q Consensus 83 ~f~V~l-~dG~~~lcrI~GKmRk~~IrI~vGDrV~VE~ 119 (140)
-.+|+| .||+++.|+|+|-=-.+ -|.+-|.|+|+-
T Consensus 70 ~arV~L~~Ngk~vtAyIPg~G~~~--~lqEh~~VLV~G 105 (145)
T PRK04211 70 CVRVQLIKNGKQVTAFCPGDGAIN--FIDEHDEVVIEG 105 (145)
T ss_pred eEEEEEccCCeEEEEEeCCCcccc--ccccCCEEEEee
Confidence 468889 69999999999975432 388899999973
No 174
>cd04479 RPA3 RPA3: A subfamily of OB folds similar to human RPA3 (also called RPA14). RPA3 is the smallest subunit of Replication protein A (RPA). RPA is a nuclear ssDNA binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). RPA3 is believed to have a structural role in assembly of the RPA heterotrimer.
Probab=43.94 E-value=83 Score=22.45 Aligned_cols=46 Identities=7% Similarity=-0.071 Sum_probs=34.1
Q ss_pred cceEEEEEEEEeCCCceEEEEeCCCCEEEEEecccccccccccCCCCEEEEE
Q 032460 67 EKWVHEGFITESLPNGMFRVRLDNEDLILGYISGKIRQNFIRVLPGDRVRVE 118 (140)
Q Consensus 67 d~ie~~GvVik~l~n~~f~V~l~dG~~~lcrI~GKmRk~~IrI~vGDrV~VE 118 (140)
..+.+-|+|++.- ++.+.+++.||+.+.|.+..-. -..+|=+|+|.
T Consensus 16 k~V~ivGkV~~~~-~~~~~~~~~Dg~~v~v~l~~~~-----~~~~~~~vEVi 61 (101)
T cd04479 16 KTVRIVGKVEKVD-GDSLTLISSDGVNVTVELNRPL-----DLPISGYVEVI 61 (101)
T ss_pred CEEEEEEEEEEec-CCeEEEEcCCCCEEEEEeCCCC-----CcccCCEEEEE
Confidence 3577889999985 5589999999999999977533 24455566554
No 175
>TIGR00982 S23_S12_E_A ribosomal protein S23 (S12). This model represents the eukaryotic and archaeal homologs of bacterial ribosomal protein S12. This protein is known typically as S23 in eukaryotes and as either S12 or S23 in the Archaea.
Probab=43.90 E-value=48 Score=26.14 Aligned_cols=34 Identities=26% Similarity=0.354 Sum_probs=27.6
Q ss_pred eEEEEe-CCCCEEEEEecccccccccccCCCCEEEEE
Q 032460 83 MFRVRL-DNEDLILGYISGKIRQNFIRVLPGDRVRVE 118 (140)
Q Consensus 83 ~f~V~l-~dG~~~lcrI~GKmRk~~IrI~vGDrV~VE 118 (140)
-.+|+| .||+++.|+|+|-=-.+ -+.+-|.|+|+
T Consensus 64 ~~rV~L~~ngk~vtAyiPg~G~~~--~lqeh~~VLV~ 98 (139)
T TIGR00982 64 CVRVQLIKNGKVVTAFCPGDGAIN--FIDEHDEVIIE 98 (139)
T ss_pred EEEEEEccCCeEEEEEeCCCcccc--ccccCCEEEEE
Confidence 467889 79999999999865432 38889999997
No 176
>PF08922 DUF1905: Domain of unknown function (DUF1905); InterPro: IPR015018 This family consist of hypothetical bacterial proteins. ; PDB: 2D9R_A.
Probab=43.45 E-value=61 Score=22.32 Aligned_cols=27 Identities=22% Similarity=0.241 Sum_probs=18.1
Q ss_pred CEEEEEecccccccccccCCCCEEEEEe
Q 032460 92 DLILGYISGKIRQNFIRVLPGDRVRVEV 119 (140)
Q Consensus 92 ~~~lcrI~GKmRk~~IrI~vGDrV~VE~ 119 (140)
..+.--++-.+|+ .+.+.+||.|.|++
T Consensus 54 G~~~Lpv~~~vRk-~~g~~~Gd~V~v~l 80 (80)
T PF08922_consen 54 GGYILPVKAAVRK-AIGKEAGDTVEVTL 80 (80)
T ss_dssp T-EEEEE-HHHHH-HHT--TTSEEEEEE
T ss_pred CCEEEEEcHHHHH-HcCCCCCCEEEEEC
Confidence 4566667778887 68899999999875
No 177
>PRK12281 rplX 50S ribosomal protein L24; Reviewed
Probab=43.24 E-value=62 Score=22.52 Aligned_cols=29 Identities=31% Similarity=0.495 Sum_probs=18.8
Q ss_pred cccCCCCEEEEEeccCCC-CeEEEEEEecCC
Q 032460 107 IRVLPGDRVRVEVSRYDT-SKGRIIYRLRNK 136 (140)
Q Consensus 107 IrI~vGDrV~VE~sp~D~-~kGrIiyRy~r~ 136 (140)
+.|..||+|.|- +--|. ..|.|+.-+..+
T Consensus 5 ~~I~kGD~V~Vi-~G~dKGK~G~V~~V~~~~ 34 (76)
T PRK12281 5 LKVKKGDMVKVI-AGDDKGKTGKVLAVLPKK 34 (76)
T ss_pred ccccCCCEEEEe-EcCCCCcEEEEEEEEcCC
Confidence 468889999874 43343 457777766543
No 178
>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional
Probab=42.50 E-value=79 Score=31.19 Aligned_cols=66 Identities=27% Similarity=0.220 Sum_probs=45.9
Q ss_pred eEEEEEEEEeCCCceEEEEeCCCCEEEEEec-----ccccccccccCCCCEEEEEeccCCCCeEEEEEEecC
Q 032460 69 WVHEGFITESLPNGMFRVRLDNEDLILGYIS-----GKIRQNFIRVLPGDRVRVEVSRYDTSKGRIIYRLRN 135 (140)
Q Consensus 69 ie~~GvVik~l~n~~f~V~l~dG~~~lcrI~-----GKmRk~~IrI~vGDrV~VE~sp~D~~kGrIiyRy~r 135 (140)
-.+.|+|+++.+.| ..|++.+|..=+.|++ .+...-.-.+.+||.|.+.+-..|.++++|.-..+.
T Consensus 580 ~iV~G~V~~I~~fG-~fVeL~~gveGLvhiSEls~~~~~~~p~~~~kvGd~V~vkVl~iD~e~~rIsLS~K~ 650 (863)
T PRK12269 580 DVVKGRVTKIADFG-AFIELAEGIEGLAHISEFSWVKKTSKPSDMVKIGDEVECMILGYDIQAGRVSLGLKQ 650 (863)
T ss_pred CEEEEEEEEEeCCe-EEEEecCCceeeeEHHHhcCccccCCHHHcCCCCCEEEEEEEEEecccCceEEEehh
Confidence 35899999997555 4577777777777764 122111123789999999988888888888655443
No 179
>COG1585 Membrane protein implicated in regulation of membrane protease activity [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]
Probab=41.80 E-value=96 Score=23.79 Aligned_cols=41 Identities=24% Similarity=0.352 Sum_probs=30.5
Q ss_pred EEEEEEEEeCCCceEEEEeCCCCEEEEEecccccccccccCCCCEEEEE
Q 032460 70 VHEGFITESLPNGMFRVRLDNEDLILGYISGKIRQNFIRVLPGDRVRVE 118 (140)
Q Consensus 70 e~~GvVik~l~n~~f~V~l~dG~~~lcrI~GKmRk~~IrI~vGDrV~VE 118 (140)
-..|+|++-+.+++++|+. +|..=.++-..... +||.|.|.
T Consensus 88 G~~g~v~e~i~~g~g~Vkv-~g~~Wra~~~~~l~-------~G~~V~Vv 128 (140)
T COG1585 88 GRRGVVVEDIVEGRGRVKV-EGESWRARSDEDLP-------AGDRVEVV 128 (140)
T ss_pred CcEEEEEeeccCCeEEEEE-CCeEeEEecCCCCC-------CCCEEEEE
Confidence 3678999987899999997 45666666544443 79999875
No 180
>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=41.59 E-value=44 Score=19.14 Aligned_cols=26 Identities=31% Similarity=0.427 Sum_probs=19.8
Q ss_pred CCCEEEEEeccCCCCeEEEEEEecCC
Q 032460 111 PGDRVRVEVSRYDTSKGRIIYRLRNK 136 (140)
Q Consensus 111 vGDrV~VE~sp~D~~kGrIiyRy~r~ 136 (140)
+||.|.|--=||.-..|.|+.....+
T Consensus 1 ~Gd~V~V~~G~~~G~~G~I~~i~~~~ 26 (32)
T PF00467_consen 1 VGDTVKVISGPFKGKIGKIVEIDRSK 26 (32)
T ss_dssp TTSEEEESSSTTTTEEEEEEEEETTT
T ss_pred CCCEEEEeEcCCCCceEEEEEEECCC
Confidence 69999886556666788888877654
No 181
>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=41.11 E-value=1.2e+02 Score=28.62 Aligned_cols=57 Identities=26% Similarity=0.284 Sum_probs=37.7
Q ss_pred EEEEEEEEeCCCceEEEEeC-CCCEEE---------------------EEecccccccccccCCCCEEEEEeccCCCCeE
Q 032460 70 VHEGFITESLPNGMFRVRLD-NEDLIL---------------------GYISGKIRQNFIRVLPGDRVRVEVSRYDTSKG 127 (140)
Q Consensus 70 e~~GvVik~l~n~~f~V~l~-dG~~~l---------------------crI~GKmRk~~IrI~vGDrV~VE~sp~D~~kG 127 (140)
+..|+|+.....| +.|+++ +|.+-+ -.+.|+ + ....||.|.|.+..-|..++
T Consensus 560 ~f~g~I~~v~~~g-~~v~l~~~~~~g~v~~~~l~~~~~~~~~~~~~~~~~l~g~-~----~~~lgd~v~V~v~~vd~~~~ 633 (639)
T TIGR02062 560 RFAAEIVDISRGG-MRVRLLENGAIAFIPAAFLHANREELVCNQENGTVQIKGE-T----VYKIGDVIDVVLTEVRMETR 633 (639)
T ss_pred EEEEEEEeeeCCc-EEEEEecCceEEEEEhhhcCCCCcceEEcccccEEEEecc-E----EEecCCEEEEEEEEeccccC
Confidence 6889999885444 455553 322221 133344 1 47779999999998888888
Q ss_pred EEEEE
Q 032460 128 RIIYR 132 (140)
Q Consensus 128 rIiyR 132 (140)
.|...
T Consensus 634 ~i~~~ 638 (639)
T TIGR02062 634 SIIAR 638 (639)
T ss_pred cEeee
Confidence 88754
No 182
>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=40.77 E-value=1.6e+02 Score=27.84 Aligned_cols=61 Identities=13% Similarity=0.148 Sum_probs=41.1
Q ss_pred EEEEEEEEeCCCceEEEEeCCCCEEEEEecccccccccccCCCCEEEEEeccCC-CCeEEEEEEecCC
Q 032460 70 VHEGFITESLPNGMFRVRLDNEDLILGYISGKIRQNFIRVLPGDRVRVEVSRYD-TSKGRIIYRLRNK 136 (140)
Q Consensus 70 e~~GvVik~l~n~~f~V~l~dG~~~lcrI~GKmRk~~IrI~vGDrV~VE~sp~D-~~kGrIiyRy~r~ 136 (140)
.++|+|... +.|+-.|..+ |.+ ..+|+..-... ...||+|+|.+...+ ..+|.|+.-.+|+
T Consensus 18 ~~~G~i~~~-~kGfgFv~~~-~~~-difI~~~~l~~---A~~GD~V~v~i~~~~~r~~~~v~~iver~ 79 (639)
T TIGR02062 18 RVEGVVKAT-EKGFGFLEVD-AQK-SYFIPPPQMKK---VMHGDKIIAVIHSEKERESAEPEELIEPF 79 (639)
T ss_pred eEEEEEEEC-CCccEEEEEC-CCC-cEEEChHHHcc---CCCCCEEEEEEecCCCCcEEEEEEEEccC
Confidence 467999876 6777777543 333 67887776542 677999999976433 2457777666554
No 183
>PRK10676 DNA-binding transcriptional regulator ModE; Provisional
Probab=40.14 E-value=81 Score=26.20 Aligned_cols=53 Identities=17% Similarity=0.026 Sum_probs=37.6
Q ss_pred EEEEEEEEeCC---CceEEEEeCCCC-EEEEEecccccccccccCCCCEEEEEeccCC
Q 032460 70 VHEGFITESLP---NGMFRVRLDNED-LILGYISGKIRQNFIRVLPGDRVRVEVSRYD 123 (140)
Q Consensus 70 e~~GvVik~l~---n~~f~V~l~dG~-~~lcrI~GKmRk~~IrI~vGDrV~VE~sp~D 123 (140)
.+.|+|.++-+ ++...|.++.|. .+.|.|.-+=-. ...+.+||.|.+.+.+.+
T Consensus 129 ~l~g~V~~i~~~~~~~~v~v~l~~g~~~l~a~IT~~s~~-~L~l~~G~~v~~~Ika~~ 185 (263)
T PRK10676 129 QWFGTITARDHQQVQQHVDVLLADGKTRLKVAITAQSAE-RLGLDEGKEVLVLIKAPW 185 (263)
T ss_pred cceeEEEEEEeCCcccEEEEEEcCCCcEEEEEeCHHHHh-hcCCCCCCeEEEEEECCE
Confidence 57799998854 366677777664 688999765543 466889998887765443
No 184
>TIGR03635 S17_bact 30S ribosomal protein S17. This model describes the bacterial ribosomal small subunit protein S17, while excluding cytosolic eukaryotic homologs and archaeal homologs. The model finds many, but not, chloroplast and mitochondrial counterparts to bacterial S17.
Probab=40.08 E-value=1.2e+02 Score=20.81 Aligned_cols=44 Identities=14% Similarity=0.129 Sum_probs=25.9
Q ss_pred EEEEEEEeCCCceEEEEeCC-------------CCEEEEEecccccccccccCCCCEEEEEec
Q 032460 71 HEGFITESLPNGMFRVRLDN-------------EDLILGYISGKIRQNFIRVLPGDRVRVEVS 120 (140)
Q Consensus 71 ~~GvVik~l~n~~f~V~l~d-------------G~~~lcrI~GKmRk~~IrI~vGDrV~VE~s 120 (140)
+.|+|+..-.+....|+.+- -+.+.||-+.. ...+||.|.++-+
T Consensus 4 l~G~Vvs~km~KTvvV~v~~~~~h~ky~k~~~r~kk~~aHD~~~------~~k~GD~V~I~ec 60 (71)
T TIGR03635 4 LQGVVVSDKMDKTIVVLVERRVKHPLYGKIVKRTKKYHAHDENN------ECKVGDVVRIIET 60 (71)
T ss_pred EEEEEEcccCCceEEEEEEEEEEeccccEEEEccEEEEEECCCC------CCCCCCEEEEEEc
Confidence 56777766545555554321 24455555521 2788999988743
No 185
>PRK09507 cspE cold shock protein CspE; Reviewed
Probab=39.99 E-value=1.1e+02 Score=20.42 Aligned_cols=51 Identities=16% Similarity=0.182 Sum_probs=34.2
Q ss_pred EEEEEEEeCC-CceEEEEeCC-CCEEEEEecccccccccccCCCCEEEEEecc
Q 032460 71 HEGFITESLP-NGMFRVRLDN-EDLILGYISGKIRQNFIRVLPGDRVRVEVSR 121 (140)
Q Consensus 71 ~~GvVik~l~-n~~f~V~l~d-G~~~lcrI~GKmRk~~IrI~vGDrV~VE~sp 121 (140)
.+|+|..--. .|+=.|..+| |..+-.|++-=-....-.+.+||+|.+++..
T Consensus 4 ~~G~Vk~f~~~kGyGFI~~~~g~~dvfvH~s~l~~~g~~~l~~G~~V~f~~~~ 56 (69)
T PRK09507 4 IKGNVKWFNESKGFGFITPEDGSKDVFVHFSAIQTNGFKTLAEGQRVEFEITN 56 (69)
T ss_pred cceEEEEEeCCCCcEEEecCCCCeeEEEEeecccccCCCCCCCCCEEEEEEEE
Confidence 4588887643 3443455555 4688889886544322459999999998764
No 186
>PRK09974 putative regulator PrlF; Provisional
Probab=39.70 E-value=40 Score=25.51 Aligned_cols=24 Identities=13% Similarity=0.317 Sum_probs=19.3
Q ss_pred EEecccccccccccCCCCEEEEEec
Q 032460 96 GYISGKIRQNFIRVLPGDRVRVEVS 120 (140)
Q Consensus 96 crI~GKmRk~~IrI~vGDrV~VE~s 120 (140)
-.|+-.+|+ ...+.+||+|.|++.
T Consensus 20 vTIPk~IR~-~Lgl~~GdkI~f~i~ 43 (111)
T PRK09974 20 TTVPAPVRK-ALKLKKRDSIHYEIL 43 (111)
T ss_pred EeccHHHHH-HcCCCCCCEEEEEEe
Confidence 467777876 688999999999765
No 187
>PRK06676 rpsA 30S ribosomal protein S1; Reviewed
Probab=39.27 E-value=1.6e+02 Score=25.26 Aligned_cols=62 Identities=26% Similarity=0.123 Sum_probs=37.2
Q ss_pred eEEEEEEEEeCCCceEEEEeCCCCEEEEEec---c-cccccccccCCCCEEEEEeccCCCCeEEEEEE
Q 032460 69 WVHEGFITESLPNGMFRVRLDNEDLILGYIS---G-KIRQNFIRVLPGDRVRVEVSRYDTSKGRIIYR 132 (140)
Q Consensus 69 ie~~GvVik~l~n~~f~V~l~dG~~~lcrI~---G-KmRk~~IrI~vGDrV~VE~sp~D~~kGrIiyR 132 (140)
-.+.|+|+.....| +.|.+ +|..-.++++ - .+..-.-.+.+||.|.+.+...|..+++|..-
T Consensus 194 ~~v~g~V~~v~~~G-~fV~l-~~v~g~v~~sels~~~~~~~~~~~~vGd~i~~~Vl~vd~~~~~i~lS 259 (390)
T PRK06676 194 DVVEGTVARLTDFG-AFVDI-GGVDGLVHISELSHERVEKPSEVVSVGQEVEVKVLSIDWETERISLS 259 (390)
T ss_pred CEEEEEEEEEecce-EEEEe-CCeEEEEEHHHcCccccCCHHHhcCCCCEEEEEEEEEeCCCCEEEEE
Confidence 46899999986545 45555 3433232222 1 11111113689999999987777777887643
No 188
>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=38.95 E-value=91 Score=21.58 Aligned_cols=53 Identities=23% Similarity=0.159 Sum_probs=28.9
Q ss_pred EEEEEEEeCCCceEEEEeC--CCCEEEEEeccc-ccc-----------cccccCCCCEEEEEeccCCC
Q 032460 71 HEGFITESLPNGMFRVRLD--NEDLILGYISGK-IRQ-----------NFIRVLPGDRVRVEVSRYDT 124 (140)
Q Consensus 71 ~~GvVik~l~n~~f~V~l~--dG~~~lcrI~GK-mRk-----------~~IrI~vGDrV~VE~sp~D~ 124 (140)
+.|+|+.+- +.-+.|++. +|-.....++.. +.. ..-.+.+||.|.|.+...|.
T Consensus 3 v~g~V~~i~-~~GifV~l~~v~G~v~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~Gd~v~vkI~~vd~ 69 (99)
T cd04460 3 VEGEVVEVV-DFGAFVRIGPVDGLLHISQIMDDYISYDPKNKRLIGEETKRVLKVGDVVRARIVAVSL 69 (99)
T ss_pred EEEEEEEEE-eccEEEEEcCeEEEEEEEEccCCceEechhheeecccCcCCEECCCCEEEEEEEEEeH
Confidence 567788775 444456663 122222233322 111 12347899999998876654
No 189
>PF13437 HlyD_3: HlyD family secretion protein
Probab=38.53 E-value=1.3e+02 Score=20.48 Aligned_cols=53 Identities=17% Similarity=0.235 Sum_probs=33.5
Q ss_pred CCceEEEEeCCCCEEEEEecccccccccccC-CCCEEEEEeccCC--CCeEEEEEEecC
Q 032460 80 PNGMFRVRLDNEDLILGYISGKIRQNFIRVL-PGDRVRVEVSRYD--TSKGRIIYRLRN 135 (140)
Q Consensus 80 ~n~~f~V~l~dG~~~lcrI~GKmRk~~IrI~-vGDrV~VE~sp~D--~~kGrIiyRy~r 135 (140)
+...+.|...+.-.+.+.++-+-.. +|. +||.|.+.+.++. .-+|.|.+-...
T Consensus 24 g~~l~~i~~~~~~~v~~~v~~~~~~---~i~~~g~~v~v~~~~~~~~~~~g~V~~I~~~ 79 (105)
T PF13437_consen 24 GQPLAEIVDTDDLWVEAYVPEKDIA---RIKDPGQKVTVRLDPGPEKTIEGKVSSISPS 79 (105)
T ss_pred CCEEEEEEccceEEEEEEEChHhhc---ceEeCCCEEEEEECCCCCcEEEEEEEEEeCc
Confidence 3444555545555666777765544 475 8999999887443 236888877653
No 190
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=38.07 E-value=73 Score=30.97 Aligned_cols=59 Identities=31% Similarity=0.234 Sum_probs=42.6
Q ss_pred EEEEEEEEeCCCceEEEEeCCCCEEEEEecccccc----cccccCCCCEEEEEeccCCCCeEEEE
Q 032460 70 VHEGFITESLPNGMFRVRLDNEDLILGYISGKIRQ----NFIRVLPGDRVRVEVSRYDTSKGRII 130 (140)
Q Consensus 70 e~~GvVik~l~n~~f~V~l~dG~~~lcrI~GKmRk----~~IrI~vGDrV~VE~sp~D~~kGrIi 130 (140)
..+|+|+++.+-|- .|.+.+|+.-+|||+=.-.. -.-.+.+||.|.|.+...| .+|+|-
T Consensus 622 iy~G~V~ri~~fGa-Fv~l~~gkdgl~hiS~~~~~rv~kv~dvlk~Gd~v~Vkv~~iD-~~Gri~ 684 (692)
T COG1185 622 VYEGTVVRIVDFGA-FVELLPGKDGLVHISQLAKERVEKVEDVLKEGDEVKVKVIEID-KQGRIR 684 (692)
T ss_pred EEEEEEEEEeecce-EEEecCCcceeEEehhhhhhhhhcccceeecCceEEEEEeeec-ccCCcc
Confidence 37899999986554 46678999999999843332 1123899999999987666 467663
No 191
>PRK05054 exoribonuclease II; Provisional
Probab=37.83 E-value=1.9e+02 Score=27.32 Aligned_cols=61 Identities=15% Similarity=0.146 Sum_probs=40.4
Q ss_pred EEEEEEEEeCCCceEEEEeCCCCEEEEEecccccccccccCCCCEEEEEeccCC-CCeEEEEEEecCC
Q 032460 70 VHEGFITESLPNGMFRVRLDNEDLILGYISGKIRQNFIRVLPGDRVRVEVSRYD-TSKGRIIYRLRNK 136 (140)
Q Consensus 70 e~~GvVik~l~n~~f~V~l~dG~~~lcrI~GKmRk~~IrI~vGDrV~VE~sp~D-~~kGrIiyRy~r~ 136 (140)
.+.|+|... ++|+-.|..++ .. ..+|+..-... ...||+|+|.+...+ ..+|.|+.-..|.
T Consensus 21 ~~~G~~~~~-~~gfgFv~~~~-~~-difI~~~~l~~---a~~GD~V~v~i~~~~~r~~g~v~~il~r~ 82 (644)
T PRK05054 21 RVEGVVKAT-EKGFGFLEVDA-QK-SYFIPPPQMKK---VMHGDRIIAVIHTEKDREIAEPEELIEPF 82 (644)
T ss_pred eEEEEEEEC-CCccEEEEECC-CC-cEEEChHHHcc---CCCCCEEEEEEecCCCCcEEEEEEEEecC
Confidence 467998876 67766665433 32 66787665442 677999999976432 2368887766654
No 192
>PRK01191 rpl24p 50S ribosomal protein L24P; Validated
Probab=37.76 E-value=69 Score=24.49 Aligned_cols=30 Identities=20% Similarity=0.309 Sum_probs=19.7
Q ss_pred ccccCCCCEEEEEeccCCCCeEEEEEEecC
Q 032460 106 FIRVLPGDRVRVEVSRYDTSKGRIIYRLRN 135 (140)
Q Consensus 106 ~IrI~vGDrV~VE~sp~D~~kGrIiyRy~r 135 (140)
.+.|..||.|.|.-=++--.+|.|+.-.+.
T Consensus 43 ~~~IkkGD~V~VisG~~KGk~GkV~~V~~~ 72 (120)
T PRK01191 43 SLPVRKGDTVKVMRGDFKGEEGKVVEVDLK 72 (120)
T ss_pred cceEeCCCEEEEeecCCCCceEEEEEEEcC
Confidence 345888999988533333356888876544
No 193
>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=37.73 E-value=51 Score=22.40 Aligned_cols=41 Identities=24% Similarity=0.122 Sum_probs=21.2
Q ss_pred EEEEEEEe-CCCceEEEEeCCCCEEEEEecccccccccc-cCCCCEEEEE
Q 032460 71 HEGFITES-LPNGMFRVRLDNEDLILGYISGKIRQNFIR-VLPGDRVRVE 118 (140)
Q Consensus 71 ~~GvVik~-l~n~~f~V~l~dG~~~lcrI~GKmRk~~Ir-I~vGDrV~VE 118 (140)
+-++|+++ .+++.-.|. .+|..+...+. -+. +.+||+|+|-
T Consensus 5 iP~~Vv~v~~~~~~A~v~-~~G~~~~V~~~------lv~~v~~Gd~VLVH 47 (68)
T PF01455_consen 5 IPGRVVEVDEDGGMAVVD-FGGVRREVSLA------LVPDVKVGDYVLVH 47 (68)
T ss_dssp EEEEEEEEETTTTEEEEE-ETTEEEEEEGT------TCTSB-TT-EEEEE
T ss_pred ccEEEEEEeCCCCEEEEE-cCCcEEEEEEE------EeCCCCCCCEEEEe
Confidence 34677777 224444443 23555554443 111 8899999984
No 194
>PRK10943 cold shock-like protein CspC; Provisional
Probab=37.66 E-value=1.3e+02 Score=20.22 Aligned_cols=51 Identities=14% Similarity=0.119 Sum_probs=34.5
Q ss_pred EEEEEEEeCC-CceEEEEeCC-CCEEEEEecccccccccccCCCCEEEEEecc
Q 032460 71 HEGFITESLP-NGMFRVRLDN-EDLILGYISGKIRQNFIRVLPGDRVRVEVSR 121 (140)
Q Consensus 71 ~~GvVik~l~-n~~f~V~l~d-G~~~lcrI~GKmRk~~IrI~vGDrV~VE~sp 121 (140)
+.|+|..--. .|+=.+..++ |..+-.|++.=-....-.+.+||+|.+++..
T Consensus 4 ~~G~Vk~f~~~kGfGFI~~~~g~~dvFvH~s~l~~~g~~~l~~G~~V~f~~~~ 56 (69)
T PRK10943 4 IKGQVKWFNESKGFGFITPADGSKDVFVHFSAIQGNGFKTLAEGQNVEFEIQD 56 (69)
T ss_pred cceEEEEEeCCCCcEEEecCCCCeeEEEEhhHccccCCCCCCCCCEEEEEEEE
Confidence 5688887643 3332455444 5689999887654433469999999999764
No 195
>cd04489 ExoVII_LU_OBF ExoVII_LU_OBF: A subfamily of OB folds corresponding to the N-terminal OB-fold domain of Escherichia coli exodeoxyribonuclease VII (ExoVII) large subunit. E. coli ExoVII is composed of two non-identical subunits. E. coli ExoVII is a single-strand-specific exonuclease which degrades ssDNA from both 3-prime and 5-prime ends. ExoVII plays a role in methyl-directed mismatch repair in vivo. ExoVII may also guard the genome from mutagenesis by removing excess ssDNA, since the build up of ssDNA would lead to SOS induction and PolIV-dependent mutagenesis.
Probab=37.40 E-value=1.1e+02 Score=19.60 Aligned_cols=49 Identities=22% Similarity=0.135 Sum_probs=29.6
Q ss_pred EEEEEEEeC--CCceEEEEeCCC-CEEEEEeccc-ccccccccCCCCEEEEEe
Q 032460 71 HEGFITESL--PNGMFRVRLDNE-DLILGYISGK-IRQNFIRVLPGDRVRVEV 119 (140)
Q Consensus 71 ~~GvVik~l--~n~~f~V~l~dG-~~~lcrI~GK-mRk~~IrI~vGDrV~VE~ 119 (140)
+.|.|.+.- .+|+..+.++|+ ..+.|.+-.. ..+.+-.+.+|+.|.|+-
T Consensus 4 v~g~v~~i~~tk~g~~~~~L~D~~~~i~~~~f~~~~~~~~~~l~~g~~v~v~g 56 (78)
T cd04489 4 VEGEISNLKRPSSGHLYFTLKDEDASIRCVMWRSNARRLGFPLEEGMEVLVRG 56 (78)
T ss_pred EEEEEecCEECCCcEEEEEEEeCCeEEEEEEEcchhhhCCCCCCCCCEEEEEE
Confidence 445555442 355677777553 3556666555 333345699999998873
No 196
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=37.34 E-value=1e+02 Score=28.49 Aligned_cols=54 Identities=4% Similarity=-0.106 Sum_probs=41.2
Q ss_pred ceEEEEEEEEeCCCceEEEEeCC--CC-EEEEEecccccccccccCCCCEEEEEeccC
Q 032460 68 KWVHEGFITESLPNGMFRVRLDN--ED-LILGYISGKIRQNFIRVLPGDRVRVEVSRY 122 (140)
Q Consensus 68 ~ie~~GvVik~l~n~~f~V~l~d--G~-~~lcrI~GKmRk~~IrI~vGDrV~VE~sp~ 122 (140)
.-.+.|+|.+.- .+...|.+.+ |+ ...|.++-+=...+-...+||+|.+-+-.-
T Consensus 153 GeIV~G~V~r~e-~~~viv~l~~~~g~~~~EaiLP~~Eqip~E~y~~Gdrika~i~~V 209 (449)
T PRK12329 153 DTVLTARVLRFE-RQSVIMAVSSGFGQPEVEAELPKREQLPNDNYRANATFKVFLKEV 209 (449)
T ss_pred CcEEEEEEEEEc-CCCEEEEecccCCCcceEEEecHHHcCCCCcCCCCCEEEEEEEEe
Confidence 345999999984 5666787743 54 578999988777778899999998876533
No 197
>PF00717 Peptidase_S24: Peptidase S24-like peptidase classification. ; InterPro: IPR019759 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. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ].; PDB: 1KCA_H 3BDN_A 1F39_A 1JHH_A 1JHE_B 3JSP_A 1JHF_B 1JHC_A 3JSO_B 1B12_D ....
Probab=37.16 E-value=22 Score=22.48 Aligned_cols=13 Identities=31% Similarity=0.368 Sum_probs=6.5
Q ss_pred ccCCCCEEEEEec
Q 032460 108 RVLPGDRVRVEVS 120 (140)
Q Consensus 108 rI~vGDrV~VE~s 120 (140)
.+..||.|.+...
T Consensus 24 ~~~~gdivv~~~~ 36 (70)
T PF00717_consen 24 EPKDGDIVVVKID 36 (70)
T ss_dssp ---TTSEEEEEET
T ss_pred CCccCeEEEEEEC
Confidence 4666777776543
No 198
>cd06530 S26_SPase_I The S26 Type I signal peptidase (SPase; LepB; leader peptidase B; leader peptidase I; EC 3.4.21.89) family members are essential membrane-bound serine proteases that function to cleave the amino-terminal signal peptide extension from proteins that are translocated across biological membranes. The bacterial signal peptidase I, which is the most intensively studied, has two N-terminal transmembrane segments inserted in the plasma membrane and a hydrophilic, C-terminal catalytic region that is located in the periplasmic space. Although the bacterial signal peptidase I is monomeric, signal peptidases of eukaryotic cells commonly function as oligomeric complexes containing two divergent copies of the catalytic monomer. These are the IMP1 and IMP2 signal peptidases of the mitochondrial inner membrane that remove leader peptides from nuclear- and mitochondrial-encoded proteins. Also, two components of the endoplasmic reticulum signal peptidase in mammals (18-kDa and 21-kDa
Probab=37.06 E-value=35 Score=22.60 Aligned_cols=12 Identities=25% Similarity=0.185 Sum_probs=7.6
Q ss_pred cCCCCEEEEEec
Q 032460 109 VLPGDRVRVEVS 120 (140)
Q Consensus 109 I~vGDrV~VE~s 120 (140)
+..||.|.+...
T Consensus 32 ~~~GDiv~~~~~ 43 (85)
T cd06530 32 PKRGDVVVFKSP 43 (85)
T ss_pred CCCCCEEEEeCC
Confidence 556777777643
No 199
>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=36.94 E-value=52 Score=22.11 Aligned_cols=24 Identities=33% Similarity=0.425 Sum_probs=16.4
Q ss_pred cCCCCEEEEEeccCCCCeEEEEEE
Q 032460 109 VLPGDRVRVEVSRYDTSKGRIIYR 132 (140)
Q Consensus 109 I~vGDrV~VE~sp~D~~kGrIiyR 132 (140)
+.+||.|.|++...+...-+|+-.
T Consensus 43 l~~Gd~V~F~~~~~~~~~~~I~~i 66 (70)
T PF11604_consen 43 LKPGDKVRFTFERTDDGSYVITAI 66 (70)
T ss_dssp -STT-EEEEEEEEETTCEEEEEEE
T ss_pred CCCCCEEEEEEEECCCCcEEEEEE
Confidence 889999999998766554566644
No 200
>COG0557 VacB Exoribonuclease R [Transcription]
Probab=36.47 E-value=1.1e+02 Score=29.05 Aligned_cols=69 Identities=19% Similarity=0.176 Sum_probs=47.0
Q ss_pred ccCCcceEEEEEEEEeCCCceEEEEe----CCCCEEEEEecc------------cccccccccCCCCEEEEEeccCCCCe
Q 032460 63 GANSEKWVHEGFITESLPNGMFRVRL----DNEDLILGYISG------------KIRQNFIRVLPGDRVRVEVSRYDTSK 126 (140)
Q Consensus 63 ~~k~d~ie~~GvVik~l~n~~f~V~l----~dG~~~lcrI~G------------KmRk~~IrI~vGDrV~VE~sp~D~~k 126 (140)
|.+-..-+..|+|+.+...|.| |.+ .+|.+....+.+ .-.+.......||.|.|++..-+...
T Consensus 618 m~~~vg~~f~g~V~~v~~~g~~-V~l~~~~ieglV~~s~L~~d~y~~~~~~~~l~~~~~~~~~~lgd~v~v~v~~v~~~~ 696 (706)
T COG0557 618 MKKRVGEEFDGVVTGVTSFGFF-VELPELGLEGLVHISSLPDDYYHFDERGQALVGEKSGKVYRLGDEVKVKVTSVDLDE 696 (706)
T ss_pred HHHhcCCEEEEEEEEEEeccEE-EEecccccccceEcccCCCceeeeccccceeeccccccccccCCEEEEEEEEEcccc
Confidence 3344444688999999755554 544 257777888776 33333445889999999987666667
Q ss_pred EEEEEE
Q 032460 127 GRIIYR 132 (140)
Q Consensus 127 GrIiyR 132 (140)
+.|.+.
T Consensus 697 ~~i~~~ 702 (706)
T COG0557 697 RKIDFE 702 (706)
T ss_pred cceEEE
Confidence 777654
No 201
>COG1093 SUI2 Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis]
Probab=36.46 E-value=87 Score=27.14 Aligned_cols=70 Identities=20% Similarity=0.139 Sum_probs=50.2
Q ss_pred cccCCcceEEEEEEEEeCCCceEEEEeC-CCCEEEEEec----ccccccccccCCCCEEEEEeccCCCCeEEEEEE
Q 032460 62 EGANSEKWVHEGFITESLPNGMFRVRLD-NEDLILGYIS----GKIRQNFIRVLPGDRVRVEVSRYDTSKGRIIYR 132 (140)
Q Consensus 62 ~~~k~d~ie~~GvVik~l~n~~f~V~l~-dG~~~lcrI~----GKmRk~~IrI~vGDrV~VE~sp~D~~kGrIiyR 132 (140)
+.|.++.+ +-|+|.++..-|-|-..++ +|.+=+.+|+ |.+|.=+-.+.+|-+|.+-+---|+.+|.|---
T Consensus 7 ~~PeeGEi-Vv~tV~~V~~~GAyv~L~EY~g~Eg~ihiSEvas~wVknIrd~vkegqkvV~kVlrVd~~rg~IDLS 81 (269)
T COG1093 7 EYPEEGEI-VVGTVKQVADYGAYVELDEYPGKEGFIHISEVASGWVKNIRDYVKEGQKVVAKVLRVDPKRGHIDLS 81 (269)
T ss_pred CCCCCCcE-EEEEEEEeeccccEEEeeccCCeeeeEEHHHHHHHHHHHHHHHhhcCCeEEEEEEEEcCCCCeEeee
Confidence 46777766 6699999986666555443 5777777764 566532223999999999988889999988543
No 202
>TIGR00237 xseA exodeoxyribonuclease VII, large subunit. This family consist of exodeoxyribonuclease VII, large subunit XseA which catalyses exonucleolytic cleavage in either the 5'-3' or 3'-5' direction to yield 5'-phosphomononucleotides. Exonuclease VII consists of one large subunit and four small subunits.
Probab=36.28 E-value=2.4e+02 Score=25.17 Aligned_cols=51 Identities=20% Similarity=0.205 Sum_probs=34.4
Q ss_pred ceEEEEEEEEeC--CCceEEEEe-CCCCEEEEEe-cccccccccccCCCCEEEEE
Q 032460 68 KWVHEGFITESL--PNGMFRVRL-DNEDLILGYI-SGKIRQNFIRVLPGDRVRVE 118 (140)
Q Consensus 68 ~ie~~GvVik~l--~n~~f~V~l-~dG~~~lcrI-~GKmRk~~IrI~vGDrV~VE 118 (140)
.+-++|.|...- ++|+++-.+ +++-.+.|.+ ++..++-...+..||.|+|.
T Consensus 19 ~v~V~GEisn~~~~~sGH~YFtLkD~~a~i~~vmf~~~~~~l~f~~~~G~~V~v~ 73 (432)
T TIGR00237 19 QVWIQGEISNFTQPVSGHWYFTLKDENAQVRCVMFRGNNNRLKFRPQNGQQVLVR 73 (432)
T ss_pred cEEEEEEecCCeeCCCceEEEEEEcCCcEEEEEEEcChhhCCCCCCCCCCEEEEE
Confidence 567889998762 467777776 4455556654 44444434569999999986
No 203
>PRK00004 rplX 50S ribosomal protein L24; Reviewed
Probab=36.16 E-value=85 Score=22.98 Aligned_cols=28 Identities=29% Similarity=0.474 Sum_probs=18.6
Q ss_pred ccCCCCEEEEEeccCCC-CeEEEEEEecCC
Q 032460 108 RVLPGDRVRVEVSRYDT-SKGRIIYRLRNK 136 (140)
Q Consensus 108 rI~vGDrV~VE~sp~D~-~kGrIiyRy~r~ 136 (140)
.|..||+|.|- +--|. ..|.|+.-+..+
T Consensus 4 ~i~kGD~V~Vi-~G~dKGk~G~V~~V~~~~ 32 (105)
T PRK00004 4 KIKKGDTVIVI-AGKDKGKRGKVLKVLPKK 32 (105)
T ss_pred cccCCCEEEEe-EcCCCCcEEEEEEEEcCC
Confidence 58889999884 43333 458887776543
No 204
>COG3086 RseC Positive regulator of sigma E activity [Signal transduction mechanisms]
Probab=35.33 E-value=25 Score=28.05 Aligned_cols=50 Identities=18% Similarity=0.305 Sum_probs=32.1
Q ss_pred EEEEEEeCCCceEEEEeCC-------------CCEEEEEecccccccccc------cCCCCEEEEEeccCC
Q 032460 72 EGFITESLPNGMFRVRLDN-------------EDLILGYISGKIRQNFIR------VLPGDRVRVEVSRYD 123 (140)
Q Consensus 72 ~GvVik~l~n~~f~V~l~d-------------G~~~lcrI~GKmRk~~Ir------I~vGDrV~VE~sp~D 123 (140)
.++|+... +|...|+|+- |...+-++ |+--.+..+ +.+||.|++.+...+
T Consensus 5 ~a~vv~~q-~G~a~V~c~~~S~CgsC~a~~~CGs~~l~kL-g~~~~h~~~~~t~~pL~~Gq~VeiGi~Eks 73 (150)
T COG3086 5 WATVVSWQ-NGQAKVSCQRQSACGSCAARAGCGSGLLSKL-GPQTEHIFRVETDEPLEPGQKVELGIEEKS 73 (150)
T ss_pred eEEEEEcc-CCeEEEEeeccCccccchhhcccchHHHHHh-ccccceEEEEecCCcCCCCCEEEEccCccc
Confidence 47888875 8899999964 33333344 332222332 899999999877544
No 205
>smart00532 LIGANc Ligase N family.
Probab=35.00 E-value=1.2e+02 Score=27.50 Aligned_cols=90 Identities=13% Similarity=0.134 Sum_probs=46.7
Q ss_pred CCceeccceeEeeeccceEeeeeehhhhhcccCCCc--ccccccC-CcceEEEEEEEEeCCCceEEEEe--C----CCCE
Q 032460 23 SPISFPINHVKFNVNKEFVKITKIWTAIGAKKGGDR--SSEEGAN-SEKWVHEGFITESLPNGMFRVRL--D----NEDL 93 (140)
Q Consensus 23 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~k-~d~ie~~GvVik~l~n~~f~V~l--~----dG~~ 93 (140)
....+.|.|+-+++|+.- .|..+|.....-+ .+.-.|. +-...+.+++.++--.|.++-.. + +|.+
T Consensus 272 ~~l~y~iDGiViKvn~~~-----~~~~lG~ts~~PrwaiA~Kf~~~~~~T~l~~I~~qVGRTG~iTPvA~lePV~l~G~t 346 (441)
T smart00532 272 AELPYEIDGVVVKVDDLA-----LQRELGFTSKAPRWAIAYKFPAEEAETKLLDIIVQVGRTGKITPVAELEPVFLAGST 346 (441)
T ss_pred ccCCCCcCcEEEEecCHH-----HHHHhCccCCCCCeeEEECCCCceeEEEEEEEEEecCCCceeeEEEEEEeEEECCEE
Confidence 444567777777766543 5667765554333 2222333 33445777777763344444221 1 2333
Q ss_pred EEEEec----ccccccccccCCCCEEEEEec
Q 032460 94 ILGYIS----GKIRQNFIRVLPGDRVRVEVS 120 (140)
Q Consensus 94 ~lcrI~----GKmRk~~IrI~vGDrV~VE~s 120 (140)
+ .++. .-+++ ..|.+||.|.|+-.
T Consensus 347 V-srATLhN~~~i~~--~~i~iGd~V~V~ra 374 (441)
T smart00532 347 V-SRATLHNEDEIEE--KDIRIGDTVVVRKA 374 (441)
T ss_pred E-EecccCCHHHHHH--cCCCCCCEEEEEEC
Confidence 2 2222 22222 23888999999854
No 206
>PRK00087 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed
Probab=34.79 E-value=1.4e+02 Score=27.90 Aligned_cols=64 Identities=20% Similarity=0.172 Sum_probs=40.1
Q ss_pred eEEEEEEEEeCCCceEEEEeCCCCEEEEEec----ccccccccccCCCCEEEEEeccCCCCeEEEEEEec
Q 032460 69 WVHEGFITESLPNGMFRVRLDNEDLILGYIS----GKIRQNFIRVLPGDRVRVEVSRYDTSKGRIIYRLR 134 (140)
Q Consensus 69 ie~~GvVik~l~n~~f~V~l~dG~~~lcrI~----GKmRk~~IrI~vGDrV~VE~sp~D~~kGrIiyRy~ 134 (140)
-.+.|+|++....| +.|.+ +|..-.++++ .++..-.-.+.+||.|.+.+...|..+++|.--.+
T Consensus 479 ~iV~g~V~~v~~~G-~fV~l-~gv~Gll~~sels~~~~~~~~~~~~vGd~V~vkV~~id~~~~~I~lS~K 546 (647)
T PRK00087 479 DVVEGEVKRLTDFG-AFVDI-GGVDGLLHVSEISWGRVEKPSDVLKVGDEIKVYILDIDKENKKLSLSLK 546 (647)
T ss_pred CEEEEEEEEEeCCc-EEEEE-CCEEEEEEHHHcCccccCCHHHhcCCCCEEEEEEEEEECCCCEEEEEee
Confidence 35899999997555 45666 6654444433 11111112377999999987766776777766543
No 207
>PRK00286 xseA exodeoxyribonuclease VII large subunit; Reviewed
Probab=34.15 E-value=2.9e+02 Score=24.26 Aligned_cols=52 Identities=19% Similarity=0.162 Sum_probs=34.3
Q ss_pred cceEEEEEEEEeC--CCceEEEEeC-CCCEEEEEe-cccccccccccCCCCEEEEE
Q 032460 67 EKWVHEGFITESL--PNGMFRVRLD-NEDLILGYI-SGKIRQNFIRVLPGDRVRVE 118 (140)
Q Consensus 67 d~ie~~GvVik~l--~n~~f~V~l~-dG~~~lcrI-~GKmRk~~IrI~vGDrV~VE 118 (140)
..+-+.|.|...- ++|+++..+. +.-.+.|.+ ++..++-...+..||.|+|.
T Consensus 24 ~~v~v~gEis~~~~~~sGH~Yf~Lkd~~a~i~~~~~~~~~~~~~~~~~~G~~v~v~ 79 (438)
T PRK00286 24 GQVWVRGEISNFTRHSSGHWYFTLKDEIAQIRCVMFKGSARRLKFKPEEGMKVLVR 79 (438)
T ss_pred CcEEEEEEeCCCeeCCCCeEEEEEEcCCcEEEEEEEcChhhcCCCCCCCCCEEEEE
Confidence 4577999988752 3677777773 334455554 34444445679999999986
No 208
>smart00306 HintN Hint (Hedgehog/Intein) domain N-terminal region. Hedgehog/Intein domain, N-terminal region. Domain has been split to accommodate large insertions of endonucleases.
Probab=33.85 E-value=1.1e+02 Score=20.03 Aligned_cols=33 Identities=30% Similarity=0.357 Sum_probs=16.9
Q ss_pred EEEeCCCCEEEEEeccccccc-ccccCCCCEEEE
Q 032460 85 RVRLDNEDLILGYISGKIRQN-FIRVLPGDRVRV 117 (140)
Q Consensus 85 ~V~l~dG~~~lcrI~GKmRk~-~IrI~vGDrV~V 117 (140)
.+.+..+|.+...-.|+++-. --.+.+||.|.+
T Consensus 65 ~i~~T~~H~~~~~~~~~~~w~~a~~l~~gd~v~~ 98 (100)
T smart00306 65 EITLTPDHLLLVRDGGKLVWVFASELKPGDYVLV 98 (100)
T ss_pred EEEECCCCEEEEecCCcEEEEEHHHCCCCCEEEe
Confidence 344444555555544432211 123888998865
No 209
>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=33.69 E-value=1e+02 Score=18.12 Aligned_cols=28 Identities=18% Similarity=0.075 Sum_probs=18.9
Q ss_pred ceEEEEEEEEeCCCceEEEEeCC-CCEEE
Q 032460 68 KWVHEGFITESLPNGMFRVRLDN-EDLIL 95 (140)
Q Consensus 68 ~ie~~GvVik~l~n~~f~V~l~d-G~~~l 95 (140)
..--.|+|++..+++.+.|...| |..-.
T Consensus 12 ~~wyra~V~~~~~~~~~~V~f~DyG~~~~ 40 (48)
T cd04508 12 GKWYRAKITSILSDGKVEVFFVDYGNTEV 40 (48)
T ss_pred CeEEEEEEEEECCCCcEEEEEEcCCCcEE
Confidence 44466788887667778887755 65543
No 210
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=33.20 E-value=1.3e+02 Score=27.05 Aligned_cols=49 Identities=14% Similarity=0.042 Sum_probs=38.3
Q ss_pred eEEEEEEEEeCCCceEEEEeCCCCEEEEEecccccccccccCCCCEEEEEec
Q 032460 69 WVHEGFITESLPNGMFRVRLDNEDLILGYISGKIRQNFIRVLPGDRVRVEVS 120 (140)
Q Consensus 69 ie~~GvVik~l~n~~f~V~l~dG~~~lcrI~GKmRk~~IrI~vGDrV~VE~s 120 (140)
-.+.|+|.+.-.++.+.|.+ | ...|.++-+-...+-...+||++.+-+.
T Consensus 140 eiv~g~V~r~~~~~~i~vdl--g-~~ea~LP~~eqip~E~~~~Gdrik~~i~ 188 (374)
T PRK12328 140 KIVFGTVVRVDNEENTFIEI--D-EIRAVLPMKNRIKGEKFKVGDVVKAVLK 188 (374)
T ss_pred cEEEEEEEEEecCCCEEEEc--C-CeEEEeCHHHcCCCCcCCCCCEEEEEEE
Confidence 35999999985445566776 3 3799999888777888999999988664
No 211
>PRK11607 potG putrescine transporter ATP-binding subunit; Provisional
Probab=33.08 E-value=1.8e+02 Score=25.40 Aligned_cols=51 Identities=20% Similarity=0.160 Sum_probs=31.8
Q ss_pred EEEEEEEeCC-Cc--eEEEEeCCCCEEEEEecccccccccccCCCCEEEEEecc
Q 032460 71 HEGFITESLP-NG--MFRVRLDNEDLILGYISGKIRQNFIRVLPGDRVRVEVSR 121 (140)
Q Consensus 71 ~~GvVik~l~-n~--~f~V~l~dG~~~lcrI~GKmRk~~IrI~vGDrV~VE~sp 121 (140)
+.|+|..+.. ++ .+.|.++.|..+.+++.+......-.+.+||.|.+.+.+
T Consensus 316 ~~~~v~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~v~~~~~~ 369 (377)
T PRK11607 316 AVGEVIHIAYLGDLSIYHVRLKSGQMISAQLQNAHRYRKGLPTWGDEVRLCWEA 369 (377)
T ss_pred EEEEEEEEEEcCCeEEEEEEECCCCEEEEEecCccccccccCCCCCEEEEEEeh
Confidence 5677776642 33 355666667777888876443222235789999887654
No 212
>TIGR00051 acyl-CoA thioester hydrolase, YbgC/YbaW family. This model describes a subset of related acyl-CoA thioesterases that include several at least partially characterized proteins. YbgC is an acyl-CoA thioesterase associated with the Tol-Pal system. YbaW is part of the FadM regulon.
Probab=32.73 E-value=57 Score=21.97 Aligned_cols=25 Identities=4% Similarity=0.034 Sum_probs=16.1
Q ss_pred cCCCCEEEEEeccCCCCeEEEEEEe
Q 032460 109 VLPGDRVRVEVSRYDTSKGRIIYRL 133 (140)
Q Consensus 109 I~vGDrV~VE~sp~D~~kGrIiyRy 133 (140)
+..||.|.|+.+....++-.+.+.+
T Consensus 62 ~~~gd~v~v~~~~~~~~~~s~~~~~ 86 (117)
T TIGR00051 62 ARLDDVLEIRTQIEELNGFSFVFSQ 86 (117)
T ss_pred ccCCCEEEEEEEEEecCcEEEEEEE
Confidence 6668888888776665544444443
No 213
>TIGR01079 rplX_bact ribosomal protein L24, bacterial/organelle. This model recognizes bacterial and organellar forms of ribosomal protein L24. It excludes eukaryotic and archaeal forms, designated L26 in eukaryotes.
Probab=32.67 E-value=1e+02 Score=22.61 Aligned_cols=29 Identities=21% Similarity=0.433 Sum_probs=17.8
Q ss_pred ccCCCCEEEEEeccCCCCeEEEEEEecCC
Q 032460 108 RVLPGDRVRVEVSRYDTSKGRIIYRLRNK 136 (140)
Q Consensus 108 rI~vGDrV~VE~sp~D~~kGrIiyRy~r~ 136 (140)
.|..||+|.|--=++--..|.|+.-+..+
T Consensus 3 ~ikkGD~V~Vi~G~dKGK~G~V~~V~~~~ 31 (104)
T TIGR01079 3 KIKKGDTVKVISGKDKGKRGKVLKVLPKT 31 (104)
T ss_pred cccCCCEEEEeEcCCCCcEEEEEEEEcCC
Confidence 57889999874222222458787765543
No 214
>TIGR01843 type_I_hlyD type I secretion membrane fusion protein, HlyD family. Type I secretion is an ABC transport process that exports proteins, without cleavage of any signal sequence, from the cytosol to extracellular medium across both inner and outer membranes. The secretion signal is found in the C-terminus of the transported protein. This model represents the adaptor protein between the ATP-binding cassette (ABC) protein of the inner membrane and the outer membrane protein, and is called the membrane fusion protein. This model selects a subfamily closely related to HlyD; it is defined narrowly and excludes, for example, colicin V secretion protein CvaA and multidrug efflux proteins.
Probab=32.49 E-value=1.9e+02 Score=24.15 Aligned_cols=53 Identities=13% Similarity=0.115 Sum_probs=33.0
Q ss_pred CceEEEEeC-CCCEEEEEecccccccccccCCCCEEEEEeccCCCC-----eEEEEEEecCC
Q 032460 81 NGMFRVRLD-NEDLILGYISGKIRQNFIRVLPGDRVRVEVSRYDTS-----KGRIIYRLRNK 136 (140)
Q Consensus 81 n~~f~V~l~-dG~~~lcrI~GKmRk~~IrI~vGDrV~VE~sp~D~~-----kGrIiyRy~r~ 136 (140)
...+.+... +.-.+.+.++=+-.. .|.+|+.|.|.+..|... .|.|++..+..
T Consensus 298 ~~l~~i~~~~~~~~v~~~v~~~~~~---~i~~G~~v~v~~~~~~~~~~~~~~g~V~~i~~~~ 356 (423)
T TIGR01843 298 ETLMEIVPEDDPLEIEAKLSPKDIG---FVHVGQPAEIKFSAFPYRRYGILNGKVKSISPDT 356 (423)
T ss_pred CeeEEEecCCCcEEEEEEEChhhhh---hhCCCCceEEEEecCCCcccCCccEEEEEECCCc
Confidence 344444432 344566777643332 488999999987655432 69999886543
No 215
>PRK07899 rpsA 30S ribosomal protein S1; Reviewed
Probab=32.09 E-value=1.9e+02 Score=26.61 Aligned_cols=58 Identities=14% Similarity=0.326 Sum_probs=38.3
Q ss_pred ceEEEEEEEEeCCCceEEEEeCCCCEEEEEeccc---cc-ccccccCCCCEEEEEeccCCCCeEEEE
Q 032460 68 KWVHEGFITESLPNGMFRVRLDNEDLILGYISGK---IR-QNFIRVLPGDRVRVEVSRYDTSKGRII 130 (140)
Q Consensus 68 ~ie~~GvVik~l~n~~f~V~l~dG~~~lcrI~GK---mR-k~~IrI~vGDrV~VE~sp~D~~kGrIi 130 (140)
...++|+|++.. .+-+.|.+ |. .+.++-. ++ .....-.+||.|.|.+...|.++++|+
T Consensus 123 g~~V~G~V~~v~-k~G~~Vdl--Gi--~gflP~Sel~~~~~~~~~~~vGq~V~vkVleid~~~~~iv 184 (486)
T PRK07899 123 DGVVTGTVIEVV-KGGLILDI--GL--RGFLPASLVEMRRVRDLQPYIGQEIEAKIIELDKNRNNVV 184 (486)
T ss_pred CCEEEEEEEEEE-CCeEEEEE--CC--EEEEEhhHhcccccCChhhcCCCEEEEEEEEEECCCCEEE
Confidence 446899999996 45568887 53 4555432 11 112335689999999887777766655
No 216
>COG0298 HypC Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=30.66 E-value=1.6e+02 Score=21.36 Aligned_cols=44 Identities=20% Similarity=-0.060 Sum_probs=24.8
Q ss_pred EEEEEEEeCCCceEEEEeCCCCEEEEEecccccccccccCCCCEEEEE
Q 032460 71 HEGFITESLPNGMFRVRLDNEDLILGYISGKIRQNFIRVLPGDRVRVE 118 (140)
Q Consensus 71 ~~GvVik~l~n~~f~V~l~dG~~~lcrI~GKmRk~~IrI~vGDrV~VE 118 (140)
+-|.|+++-.++.+-+-.--|.++..++. .. .--+.+||+|+|-
T Consensus 5 iPgqI~~I~~~~~~A~Vd~gGvkreV~l~---Lv-~~~v~~GdyVLVH 48 (82)
T COG0298 5 IPGQIVEIDDNNHLAIVDVGGVKREVNLD---LV-GEEVKVGDYVLVH 48 (82)
T ss_pred cccEEEEEeCCCceEEEEeccEeEEEEee---ee-cCccccCCEEEEE
Confidence 34788888654432222235666555543 11 0147789999984
No 217
>PRK09937 stationary phase/starvation inducible regulatory protein CspD; Provisional
Probab=30.18 E-value=1.1e+02 Score=20.98 Aligned_cols=49 Identities=16% Similarity=0.129 Sum_probs=32.0
Q ss_pred EEEEEEeCC-CceEEEEe-CCCCEEEEEecccccccc-cccCCCCEEEEEecc
Q 032460 72 EGFITESLP-NGMFRVRL-DNEDLILGYISGKIRQNF-IRVLPGDRVRVEVSR 121 (140)
Q Consensus 72 ~GvVik~l~-n~~f~V~l-~dG~~~lcrI~GKmRk~~-IrI~vGDrV~VE~sp 121 (140)
.|+|...-. .|+=.|.. ++|..+-.|++- ++... -.+.+||+|.+++..
T Consensus 3 ~G~Vkwfn~~KGfGFI~~~~gg~dVFvH~s~-i~~~g~~~l~~G~~V~f~~~~ 54 (74)
T PRK09937 3 KGTVKWFNNAKGFGFICPEGGGEDIFAHYST-IQMDGYRTLKAGQSVQFDVHQ 54 (74)
T ss_pred CeEEEEEeCCCCeEEEeeCCCCccEEEEEee-ccccCCCCCCCCCEEEEEEEE
Confidence 477776533 33323444 446888888886 34333 359999999999764
No 218
>PF01302 CAP_GLY: CAP-Gly domain; InterPro: IPR000938 Cytoskeleton-associated proteins (CAP) are made of three distinct parts, an N-terminal section that is most probably globular and contains the CAP-Gly domain, a large central region predicted to be in an alpha-helical coiled-coil conformation and, finally, a short C-terminal globular domain. The CAP-Gly domain is a conserved, glycine-rich domain of about 42 residues found in some CAPs []. Proteins known to contain this domain include restin (also known as cytoplasmic linker protein-170 or CLIP-170), a 160 kDa protein associated with intermediate filaments and that links endocytic vesicles to microtubules; vertebrate dynactin (150 kDa dynein-associated polypeptide; DAP) and Drosophila glued, a major component of activator I; yeast protein BIK1, which seems to be required for the formation or stabilisation of microtubules during mitosis and for spindle pole body fusion during conjugation; yeast protein NIP100 (NIP80); human protein CKAP1/TFCB; Schizosaccharomyces pombe protein alp11 and Caenorhabditis elegans hypothetical protein F53F4.3. The latter proteins contain a N-terminal ubiquitin domain and a C-terminal CAP-Gly domain. The crystal structure of the CAP-Gly domain of C. elegans F53F4.3 protein, solved by single wavelength sulphur-anomalous phasing, revealed a novel protein fold containing three beta-sheets. The most conserved sequence, GKNDG, is located in two consecutive sharp turns on the surface, forming the entrance to a groove. Residues in the groove are highly conserved as measured from the information content of the aligned sequences. The C-terminal tail of another molecule in the crystal is bound in this groove []. ; PDB: 2CP6_A 2E4H_A 2E3H_A 3E2U_B 2HL3_B 3TQ7_Q 2HKQ_B 2HQH_A 2HKN_B 2HL5_C ....
Probab=30.17 E-value=62 Score=21.72 Aligned_cols=22 Identities=36% Similarity=0.478 Sum_probs=15.6
Q ss_pred CCCEEEEEeccCCCCeEEEEEEec
Q 032460 111 PGDRVRVEVSRYDTSKGRIIYRLR 134 (140)
Q Consensus 111 vGDrV~VE~sp~D~~kGrIiyRy~ 134 (140)
+||+|.| ..-....|.|-|.=+
T Consensus 1 VG~rV~v--~~~~~~~G~vryiG~ 22 (69)
T PF01302_consen 1 VGDRVRV--DDPGGRRGTVRYIGP 22 (69)
T ss_dssp TTSEEEE--SSTTTEEEEEEEEEE
T ss_pred CCCEEEE--eeCCCCEEEEEEEee
Confidence 5999988 344556888888643
No 219
>TIGR00230 sfsA sugar fermentation stimulation protein. probable regulatory factor involved in maltose metabolism contains a putative DNA binding domain. Isolated as a gene which enabled E.coli strain MK2001 to use maltose.
Probab=29.88 E-value=2.4e+02 Score=23.55 Aligned_cols=46 Identities=17% Similarity=0.319 Sum_probs=36.4
Q ss_pred EEEEEEEeCCCceEEEEeC-CCCEEEEEec--ccccccccccCCCCEEEEEecc
Q 032460 71 HEGFITESLPNGMFRVRLD-NEDLILGYIS--GKIRQNFIRVLPGDRVRVEVSR 121 (140)
Q Consensus 71 ~~GvVik~l~n~~f~V~l~-dG~~~lcrI~--GKmRk~~IrI~vGDrV~VE~sp 121 (140)
+.|+.++-. ++|.+.++ ||++..||++ |+|.- -+.||-.|.+..++
T Consensus 10 ~~~~fi~R~--nRF~~~V~~~G~~~~aH~pNtGrl~e---ll~pG~~vll~~~~ 58 (232)
T TIGR00230 10 VRGRLIGRY--NRFLVDVEVDGRRETAHCPNTGRLTE---LIFPGNDVGLSKSD 58 (232)
T ss_pred eEEEEEeec--CCEEEEEEECCeEEEEEcCCCCCChh---hcCCCCEEEEEECC
Confidence 469999985 78988864 8999999985 77754 37799999998664
No 220
>KOG1999 consensus RNA polymerase II transcription elongation factor DSIF/SUPT5H/SPT5 [Transcription]
Probab=29.81 E-value=1.3e+02 Score=30.51 Aligned_cols=74 Identities=16% Similarity=0.107 Sum_probs=52.6
Q ss_pred ccccccCCcceEEEEEEEEeCCCceEEEEeCCCCEEEEEecccccccccc-----------cCCCCEEEEEeccCCCCeE
Q 032460 59 SSEEGANSEKWVHEGFITESLPNGMFRVRLDNEDLILGYISGKIRQNFIR-----------VLPGDRVRVEVSRYDTSKG 127 (140)
Q Consensus 59 ~~~~~~k~d~ie~~GvVik~l~n~~f~V~l~dG~~~lcrI~GKmRk~~Ir-----------I~vGDrV~VE~sp~D~~kG 127 (140)
+..++..-+.. =.|+|+++ ....|.|.-.+|+++.++-.--+++...+ |+++|.|+|.--|.--..|
T Consensus 523 e~hdlVqLd~~-~vgvI~rl-e~e~~~vl~~~g~v~~i~~~~i~~kk~~r~~~~~D~~~n~I~~kD~Vkvi~Gp~~g~~G 600 (1024)
T KOG1999|consen 523 ELHDLVQLDNQ-NVGVIVRL-ERETFQVLGMNGKVVTIRKSSITKKKDNRKAVAVDRNGNEIRVKDTVKVIGGPSKGREG 600 (1024)
T ss_pred cccceeecCCC-cEEEEEEe-cchheeeecCcCceEEEeechhhhhhhhhhheeecccCCeecccceEEEecCCCCCccC
Confidence 55555555544 45999997 69999998889988888766665553322 9999999986555444447
Q ss_pred EEEEEec
Q 032460 128 RIIYRLR 134 (140)
Q Consensus 128 rIiyRy~ 134 (140)
-|.|.|+
T Consensus 601 ~v~~i~r 607 (1024)
T KOG1999|consen 601 EVLHIYR 607 (1024)
T ss_pred ccceeec
Confidence 8887775
No 221
>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=29.76 E-value=44 Score=24.62 Aligned_cols=16 Identities=44% Similarity=0.545 Sum_probs=13.0
Q ss_pred ccccCCCCEEEEEecc
Q 032460 106 FIRVLPGDRVRVEVSR 121 (140)
Q Consensus 106 ~IrI~vGDrV~VE~sp 121 (140)
.+...+||.|+|+++.
T Consensus 49 ~~~~~~GD~V~v~i~~ 64 (135)
T PF04246_consen 49 PIGAKVGDRVEVEIPE 64 (135)
T ss_pred CCCCCCCCEEEEEecc
Confidence 4458999999999874
No 222
>PF11518 DUF3221: Protein of unknown function (DUF3221); InterPro: IPR021598 This family of proteins with unknown function appears to be restricted to Bacillus. Some members in this family of proteins are annotated as YobA however this cannot be confirmed. YobA is a protein with unknown function. ; PDB: 2JQO_A.
Probab=29.67 E-value=2.2e+02 Score=20.72 Aligned_cols=51 Identities=24% Similarity=0.392 Sum_probs=27.8
Q ss_pred cceEEEEEEEEeCCCceEEEEeCC-------------------CCEEEEEecccccccccccCCCCEEEEEec
Q 032460 67 EKWVHEGFITESLPNGMFRVRLDN-------------------EDLILGYISGKIRQNFIRVLPGDRVRVEVS 120 (140)
Q Consensus 67 d~ie~~GvVik~l~n~~f~V~l~d-------------------G~~~lcrI~GKmRk~~IrI~vGDrV~VE~s 120 (140)
....++|.|+..-.++.|.|...+ +..++ ++.++-- .-.+..||+|.|-.+
T Consensus 21 ~~~~~eGYVI~k~~~~~~lV~d~~~~~~d~~~~~~~el~~~~~~~~il-~~~~~~~--~~~lk~G~KVkVw~~ 90 (108)
T PF11518_consen 21 KKFPFEGYVISKDNDNVILVVDKDFETKDLQNYSEEELNEEYPSDIIL-FFKDKDS--YDNLKVGQKVKVWSS 90 (108)
T ss_dssp --EEEEEEEEEE-SSEEEEE-SS----TTGGGS-HHHHHHHSTTTEEE-E-TT-TT--GGG--TTEEEEEEEE
T ss_pred cccceeEEEEEecCCcEEEEecCCcChHHHHHHHHHHHHHhCCCceEE-Eeecccc--hhhcccCCEEEEEeC
Confidence 346799977776346777776321 45555 6666633 345888999988543
No 223
>PTZ00115 40S ribosomal protein S12; Provisional
Probab=29.63 E-value=83 Score=27.46 Aligned_cols=45 Identities=24% Similarity=0.246 Sum_probs=33.8
Q ss_pred EEEEEEEEeCC------C----ceEEEEeCCCCEEEEEecccccccccccCCCCEEEEE
Q 032460 70 VHEGFITESLP------N----GMFRVRLDNEDLILGYISGKIRQNFIRVLPGDRVRVE 118 (140)
Q Consensus 70 e~~GvVik~l~------n----~~f~V~l~dG~~~lcrI~GKmRk~~IrI~vGDrV~VE 118 (140)
+..|+|++.++ | -..+|+|.||+++.|+|+|-=- -+.+-|.|+|.
T Consensus 125 QkKGIclkv~~~tPKKPNSA~RKvarVrLsNGk~VtAyIPGeGH----nLQEHs~VLVR 179 (290)
T PTZ00115 125 QKKGICVKVRVQTPRKPNSGLRKVARVRLSTGRTVTVYIPGIGH----NLNTHSVVLVR 179 (290)
T ss_pred ccCeEEEEeeecCCCCCCccccceEEEEecCCCEEEEEcCCCCc----ccccCCEEEEe
Confidence 45678877653 2 3568899999999999999652 47788888874
No 224
>COG2047 Uncharacterized protein (ATP-grasp superfamily) [General function prediction only]
Probab=29.47 E-value=58 Score=27.98 Aligned_cols=31 Identities=13% Similarity=0.221 Sum_probs=25.7
Q ss_pred ccCCcCCCCceeccceeEeeeccceEeeeeehhhh
Q 032460 16 LLPRHYLSPISFPINHVKFNVNKEFVKITKIWTAI 50 (140)
Q Consensus 16 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 50 (140)
|+.|+||||..+.-..+..-..++|| .|+.-
T Consensus 50 l~S~yfPPQV~V~dD~~vel~~ne~Y----~~k~~ 80 (258)
T COG2047 50 LFSPYFPPQVLVNDDSTVELMRNEFY----YWKSP 80 (258)
T ss_pred hhccCCCCeeEecCCceEEeeeceeE----EEecC
Confidence 34558999999999999999999999 66543
No 225
>PRK06461 single-stranded DNA-binding protein; Reviewed
Probab=29.32 E-value=2.4e+02 Score=20.91 Aligned_cols=48 Identities=15% Similarity=0.063 Sum_probs=25.7
Q ss_pred cceEEEEEEEEeCC-------Cc---eEEEEeCC--CCEEEEEecccccccccccCCCCEEEEE
Q 032460 67 EKWVHEGFITESLP-------NG---MFRVRLDN--EDLILGYISGKIRQNFIRVLPGDRVRVE 118 (140)
Q Consensus 67 d~ie~~GvVik~l~-------n~---~f~V~l~d--G~~~lcrI~GKmRk~~IrI~vGDrV~VE 118 (140)
..+.+.|+|+++-. ++ .+.+.+.| | .+.+.+=+.- .-.+.+||.|.|.
T Consensus 15 ~~v~~~~~V~~i~~~~~~~~k~~~~~v~~~~l~D~TG-~I~~tlW~~~---a~~l~~GdvV~I~ 74 (129)
T PRK06461 15 ERVNVTVRVLEVGEPKVIQTKGGPRTISEAVVGDETG-RVKLTLWGEQ---AGSLKEGEVVEIE 74 (129)
T ss_pred CceEEEEEEEEcCCceEEEeCCCceEEEEEEEECCCC-EEEEEEeCCc---cccCCCCCEEEEE
Confidence 45677788886532 11 22233322 3 2444444431 1237889999887
No 226
>TIGR02754 sod_Ni_protease nickel-type superoxide dismutase maturation protease. Members of this protein family are apparent proteases encoded adjacent to the genes for a nickel-type superoxide dismutase. This family belongs to the same larger family (see Pfam model pfam00717) as signal peptidase I, an unusual serine protease suggested to have a Ser/Lys catalytic dyad.
Probab=29.26 E-value=71 Score=21.50 Aligned_cols=8 Identities=38% Similarity=0.393 Sum_probs=5.5
Q ss_pred CCCEEEEE
Q 032460 111 PGDRVRVE 118 (140)
Q Consensus 111 vGDrV~VE 118 (140)
+||.|.+.
T Consensus 32 ~Gdivv~~ 39 (90)
T TIGR02754 32 IGNVVVVR 39 (90)
T ss_pred CCeEEEEe
Confidence 47777665
No 227
>COG1363 FrvX Cellulase M and related proteins [Carbohydrate transport and metabolism]
Probab=29.03 E-value=1.8e+02 Score=25.90 Aligned_cols=25 Identities=20% Similarity=0.332 Sum_probs=19.8
Q ss_pred cCCCCEEEEEeccCCCCeEEEEEEe
Q 032460 109 VLPGDRVRVEVSRYDTSKGRIIYRL 133 (140)
Q Consensus 109 I~vGDrV~VE~sp~D~~kGrIiyRy 133 (140)
|.+||+|.+...+.-...|+|..|+
T Consensus 154 I~vGd~v~~~~~~~~l~~~~i~ska 178 (355)
T COG1363 154 IRVGDFVVFDPRFRELANGRVVSKA 178 (355)
T ss_pred CCCCCEEEEcCceEEecCCcEEeee
Confidence 8999999887666555558888876
No 228
>PF02362 B3: B3 DNA binding domain; InterPro: IPR003340 Two DNA binding proteins, RAV1 and RAV2 from Arabidopsis thaliana contain two distinct amino acid sequence domains found only in higher plant species. The N-terminal regions of RAV1 and RAV2 are homologous to the AP2 DNA-binding domain (see IPR001471 from INTERPRO) present in a family of transcription factors, while the C-terminal region exhibits homology to the highly conserved C-terminal domain, designated B3, of VP1/ABI3 transcription factors []. The AP2 and B3-like domains of RAV1 bind autonomously to the CAACA and CACCTG motifs, respectively, and together achieve a high affinity and specificity of binding. It has been suggested that the AP2 and B3-like domains of RAV1 are connected by a highly flexible structure enabling the two domains to bind to the CAACA and CACCTG motifs in various spacings and orientations [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1WID_A 1YEL_A.
Probab=28.96 E-value=1.8e+02 Score=19.42 Aligned_cols=12 Identities=25% Similarity=0.285 Sum_probs=7.6
Q ss_pred cCCCCEEEEEec
Q 032460 109 VLPGDRVRVEVS 120 (140)
Q Consensus 109 I~vGDrV~VE~s 120 (140)
+.+||.+.+++.
T Consensus 74 L~~GD~~~F~~~ 85 (100)
T PF02362_consen 74 LKEGDVCVFELI 85 (100)
T ss_dssp --TT-EEEEEE-
T ss_pred CCCCCEEEEEEe
Confidence 999999999976
No 229
>PF02598 Methyltrn_RNA_3: Putative RNA methyltransferase; InterPro: IPR003750 This entry describes proteins of unknown function.; PDB: 1K3R_B.
Probab=28.89 E-value=1.4e+02 Score=25.55 Aligned_cols=50 Identities=24% Similarity=0.298 Sum_probs=29.8
Q ss_pred EEEEEEEEeCCCce--EEEEeCCCCEEEEEecccccccccccCCCCEEEEEeccCCCCeEEEE
Q 032460 70 VHEGFITESLPNGM--FRVRLDNEDLILGYISGKIRQNFIRVLPGDRVRVEVSRYDTSKGRII 130 (140)
Q Consensus 70 e~~GvVik~l~n~~--f~V~l~dG~~~lcrI~GKmRk~~IrI~vGDrV~VE~sp~D~~kGrIi 130 (140)
--+|+|+..-+.+. ..|.+ |......+.+ ..+.+|.||+|.+.. .+|.++
T Consensus 117 yREGvv~~~~~~~~~~~~Vdi--Gl~~~v~i~~------~~l~~g~RVTV~~~~---~~~~vV 168 (291)
T PF02598_consen 117 YREGVVVRKPSKGGKGSYVDI--GLDKPVEIDK------QELPPGTRVTVRIKS---LKGKVV 168 (291)
T ss_dssp EEEEEEEEE-SSS---EEEES--SSSEEEESSS----------SS-EEEEEEEE---SSS-EE
T ss_pred eeEEEEEeCCCCCCceEEEEe--CCCcEEeecc------cccCCCCEEEEEecC---CcCCEe
Confidence 37899999865443 66765 6666777776 247789999998775 334554
No 230
>TIGR03406 FeS_long_SufT probable FeS assembly SUF system protein SufT. The function is unknown for this protein family, but members are found almost always in operons for the the SUF system of iron-sulfur cluster biosynthesis. The SUF system is present elsewhere on the chromosome for those few species where SUF genes are not adjacent. This family shares this property of association with the SUF system with a related family, TIGR02945. TIGR02945 consists largely of a DUF59 domain (see Pfam family pfam01883), while this protein is about double the length, with a unique N-terminal domain and DUF59 C-terminal domain. A location immediately downstream of the cysteine desulfurase gene sufS in many contexts suggests the gene symbol sufT. Note that some other homologs of this family and of TIGR02945, but no actual members of this family, are found in operons associated with phenylacetic acid (or other ring-hydroxylating) degradation pathways.
Probab=28.59 E-value=1.2e+02 Score=24.16 Aligned_cols=41 Identities=24% Similarity=0.221 Sum_probs=26.3
Q ss_pred cCCCcccccccCCcceEEEEEEEEeCCCceEEEEeCCCCEEEEEecccc
Q 032460 54 KGGDRSSEEGANSEKWVHEGFITESLPNGMFRVRLDNEDLILGYISGKI 102 (140)
Q Consensus 54 ~~~~~~~~~~~k~d~ie~~GvVik~l~n~~f~V~l~dG~~~lcrI~GKm 102 (140)
..-+.+...+|+.. ...|++.| ||.|+|.. +|. +.||.|+=
T Consensus 11 ~~p~g~~~~~~~~~----~~~~~q~l-gg~~t~~~-~g~--~~r~~~~~ 51 (174)
T TIGR03406 11 LVPSGDPITLPAGT----EVTITQAL-GGNFTVVV-EGN--MARIDGKD 51 (174)
T ss_pred EccCCCeEEcCCCC----EEEEEEcc-CCeEEEEE-cCe--EEEecCcC
Confidence 33333444455543 37899999 88899964 454 77888764
No 231
>PRK04007 rps28e 30S ribosomal protein S28e; Validated
Probab=28.57 E-value=2.1e+02 Score=20.13 Aligned_cols=40 Identities=18% Similarity=0.304 Sum_probs=23.4
Q ss_pred EEEEEEeCC-----CceEEEE--eCC----CCEEEEEecccccccccccCCCCEEEEE
Q 032460 72 EGFITESLP-----NGMFRVR--LDN----EDLILGYISGKIRQNFIRVLPGDRVRVE 118 (140)
Q Consensus 72 ~GvVik~l~-----n~~f~V~--l~d----G~~~lcrI~GKmRk~~IrI~vGDrV~VE 118 (140)
.+.|+++++ +....|+ +-+ |++++..++|-+| +||.+.+.
T Consensus 8 ~A~VikVlGRTG~~G~~tQVrv~~l~~~~~~R~i~RNVkGPVR-------~GDIl~L~ 58 (70)
T PRK04007 8 PAEVIEIIGRTGMTGEVTQVKCRILEGRDKGRIITRNVKGPVR-------VGDILMLR 58 (70)
T ss_pred eEEEEEEeccccccccEEEEEEEEecCCCcCcEEEEeccCCcc-------cCcEEEEh
Confidence 366666664 3333444 323 5566766766555 49998654
No 232
>PRK14998 cold shock-like protein CspD; Provisional
Probab=28.51 E-value=1.2e+02 Score=20.65 Aligned_cols=50 Identities=18% Similarity=0.130 Sum_probs=33.0
Q ss_pred EEEEEEeCC-CceEEEEeC-CCCEEEEEecccccccc-cccCCCCEEEEEeccC
Q 032460 72 EGFITESLP-NGMFRVRLD-NEDLILGYISGKIRQNF-IRVLPGDRVRVEVSRY 122 (140)
Q Consensus 72 ~GvVik~l~-n~~f~V~l~-dG~~~lcrI~GKmRk~~-IrI~vGDrV~VE~sp~ 122 (140)
.|+|..--. .|+=.|..+ +|..+-.|++. ++..+ -.+.+||+|.+++..-
T Consensus 3 ~G~Vkwfn~~kGfGFI~~~~g~~dVFvH~s~-l~~~g~~~l~~G~~V~f~~~~~ 55 (73)
T PRK14998 3 TGTVKWFNNAKGFGFICPEGGGEDIFAHYST-IQMDGYRTLKAGQSVRFDVHQG 55 (73)
T ss_pred CeEEEEEeCCCceEEEecCCCCccEEEEeee-ecccCCCCCCCCCEEEEEEEEC
Confidence 477777533 333245444 45788999887 44433 4599999999997643
No 233
>PF04014 Antitoxin-MazE: Antidote-toxin recognition MazE; InterPro: IPR007159 This domain is found in AbrB from Bacillus subtilis. The product of the abrB gene is an ambiactive repressor and activator of the transcription of genes expressed during the transition state between vegetative growth and the onset of stationary phase and sporulation []. AbrB is thought to interact directly with the transcription initiation regions of genes under its control []. AbrB contains a helix-turn-helix structure, but this domain ends before the helix-turn-helix begins []. The product of the B. subtilis gene spoVT is another member of this family and is also a transcriptional regulator []. DNA-binding activity in this AbrB homologue requires hexamerisation []. Another family member has been isolated from the Sulfolobus solfataricus and has been identified as a homologue of bacterial repressor-like proteins. The Escherichia coli family member SohA or Prl1F appears to be bifunctional and is able to regulate its own expression as well as relieve the export block imposed by high-level synthesis of beta-galactosidase hybrid proteins [].; PDB: 2L66_A 2GLW_A 3TND_D 2W1T_B 2RO5_B 2FY9_A 2RO3_B 1UB4_C 3ZVK_G 1YFB_B ....
Probab=28.45 E-value=71 Score=19.54 Aligned_cols=26 Identities=35% Similarity=0.452 Sum_probs=18.3
Q ss_pred EEEEecccccccccccCCCCEEEEEec
Q 032460 94 ILGYISGKIRQNFIRVLPGDRVRVEVS 120 (140)
Q Consensus 94 ~lcrI~GKmRk~~IrI~vGDrV~VE~s 120 (140)
..-+|+-.++. ...+.+||.|.++..
T Consensus 7 ~~v~iPk~~~~-~l~l~~Gd~v~i~~~ 32 (47)
T PF04014_consen 7 GQVTIPKEIRE-KLGLKPGDEVEIEVE 32 (47)
T ss_dssp SEEEE-HHHHH-HTTSSTTTEEEEEEE
T ss_pred ceEECCHHHHH-HcCCCCCCEEEEEEe
Confidence 34566767765 467999999988765
No 234
>PRK12278 50S ribosomal protein L21/unknown domain fusion protein; Provisional
Probab=28.24 E-value=3.2e+02 Score=22.79 Aligned_cols=30 Identities=23% Similarity=0.284 Sum_probs=21.9
Q ss_pred cCCCCEEEEEeccCCCCeEEEEEEecCCCC
Q 032460 109 VLPGDRVRVEVSRYDTSKGRIIYRLRNKIS 138 (140)
Q Consensus 109 I~vGDrV~VE~sp~D~~kGrIiyRy~r~~~ 138 (140)
.+.|..|..++-....++=.|+|+++|+.+
T Consensus 53 ~v~~a~V~A~V~~~~kg~Ki~vfK~krRK~ 82 (221)
T PRK12278 53 FVDGAAVQAEVIEQIKGDKVIHFKKRRRQS 82 (221)
T ss_pred EecCCEEEEEEEeecCCCCEEEEEeCCCCC
Confidence 445777877776655667788999988775
No 235
>PF02359 CDC48_N: Cell division protein 48 (CDC48), N-terminal domain; InterPro: IPR003338 AAA ATPases (ATPases Associated with diverse cellular Activities) form a large protein family and play a number of roles in the cell including cell-cycle regulation, protein proteolysis and disaggregation, organelle biogenesis and intracellular transport. Some of them function as molecular chaperones, subunits of proteolytic complexes or independent proteases (FtsH, Lon). They also act as DNA helicases and transcription factors []. AAA ATPases belong to the AAA+ superfamily of ringshaped P-loop NTPases, which act via the energy-dependent unfolding of macromolecules [, ]. There are six major clades of AAA domains (proteasome subunits, metalloproteases, domains D1 and D2 of ATPases with two AAA domains, the MSP1/katanin/spastin group and BCS1 and it homologues), as well as a number of deeply branching minor clades []. They assemble into oligomeric assemblies (often hexamers) that form a ring-shaped structure with a central pore. These proteins produce a molecular motor that couples ATP binding and hydrolysis to changes in conformational states that act upon a target substrate, either translocating or remodelling it []. They are found in all living organisms and share the common feature of the presence of a highly conserved AAA domain called the AAA module. This domain is responsible for ATP binding and hydrolysis. It contains 200-250 residues, among them there are two classical motifs, Walker A (GX4GKT) and Walker B (HyDE) []. The VAT protein of the archaebacterium Thermoplasma acidophilum, like all other members of the Cdc48/p97 family of AAA ATPases, has two ATPase domains and a 185-residue amino-terminal substrate-recognition domain, VAT-N. VAT shows activity in protein folding and unfolding and thus shares the common function of these ATPases in disassembly and/or degradation of protein complexes. VAT-N is composed of two equally sized subdomains. The amino-terminal subdomain VAT-Nn forms a double-psi beta-barrel whose pseudo-twofold symmetry is mirrored by an internal sequence repeat of 42 residues. The carboxy-terminal subdomain VAT-Nc forms a novel six-stranded beta-clam fold []. Together, VAT-Nn and VAT-Nc form a kidney-shaped structure, in close agreement with results from electron microscopy. VAT-Nn is related to numerous proteins including prokaryotic transcription factors, metabolic enzymes, the protease cofactors UFD1 and PrlF, and aspartic proteinases. ; GO: 0005524 ATP binding; PDB: 1CZ4_A 1CZ5_A 3CF3_C 3CF1_A 3CF2_A 1S3S_D 1E32_A 1R7R_A 2PJH_B 1CR5_B ....
Probab=28.08 E-value=37 Score=23.32 Aligned_cols=28 Identities=39% Similarity=0.369 Sum_probs=18.9
Q ss_pred EEEEEecccccccccccCCCCEEEEEeccCC
Q 032460 93 LILGYISGKIRQNFIRVLPGDRVRVEVSRYD 123 (140)
Q Consensus 93 ~~lcrI~GKmRk~~IrI~vGDrV~VE~sp~D 123 (140)
.-..++.|-+|+ ...+..||.|.|. +++
T Consensus 58 ~g~I~l~~~~R~-n~~v~igd~V~V~--~~~ 85 (87)
T PF02359_consen 58 PGVIRLSGIQRK-NAGVSIGDRVTVR--PYD 85 (87)
T ss_dssp TTEEEE-HHHHH-HCT--TTSEEEEE--EET
T ss_pred CCEEEECHHHHh-hCCcCCCCEEEEE--ECC
Confidence 445678888887 5889999999886 544
No 236
>COG2524 Predicted transcriptional regulator, contains C-terminal CBS domains [Transcription]
Probab=27.51 E-value=74 Score=27.88 Aligned_cols=40 Identities=28% Similarity=0.364 Sum_probs=29.3
Q ss_pred CCCEEEEEecccccccccccCCCCEEEEEeccCCC--CeEEEEEEe
Q 032460 90 NEDLILGYISGKIRQNFIRVLPGDRVRVEVSRYDT--SKGRIIYRL 133 (140)
Q Consensus 90 dG~~~lcrI~GKmRk~~IrI~vGDrV~VE~sp~D~--~kGrIiyRy 133 (140)
+-..-.-++.|-+|+ +..||.|.|.+.|+.. =.|.|+-|-
T Consensus 112 ~~c~a~i~v~Gdi~~----~~~gD~VrVGPtP~~klvv~G~V~g~D 153 (294)
T COG2524 112 DACRAVIRVVGDIRK----INIGDSVRVGPTPVNKLVVEGKVIGRD 153 (294)
T ss_pred cccceEEEEEecccc----CCCCCeEEECCcccceEEEEeEEeccc
Confidence 334556678888876 7889999999998873 357776553
No 237
>PF13550 Phage-tail_3: Putative phage tail protein
Probab=27.23 E-value=92 Score=22.55 Aligned_cols=34 Identities=18% Similarity=0.143 Sum_probs=20.7
Q ss_pred EecccccccccccCCCCEEEEEeccCCCCeEEEEE
Q 032460 97 YISGKIRQNFIRVLPGDRVRVEVSRYDTSKGRIIY 131 (140)
Q Consensus 97 rI~GKmRk~~IrI~vGDrV~VE~sp~D~~kGrIiy 131 (140)
.++-++-.....+.|||.|.|.-. ......||..
T Consensus 128 t~~f~~~~~~~~l~pGDvi~l~~~-~~~~~~RI~~ 161 (164)
T PF13550_consen 128 TVSFTLPPDGLALEPGDVIALSDD-GRDMRFRITE 161 (164)
T ss_pred EEEEEEChhhccCCCCCEEEEEeC-CCceEEEEEE
Confidence 444455555677999999988633 2233455543
No 238
>cd03698 eRF3_II_like eRF3_II_like: domain similar to domain II of the eukaryotic class II release factor (eRF3). In eukaryotes, translation termination is mediated by two interacting release factors, eRF1 and eRF3, which act as class I and II factors, respectively. eRF1 functions as an omnipotent release factor, decoding all three stop codons and triggering the release of the nascent peptide catalyzed by the ribsome. eRF3 is a GTPase, which enhances the termination efficiency by stimulating the eRF1 activity in a GTP-dependent manner. Sequence comparison of class II release factors with elongation factors shows that eRF3 is more similar to eEF1alpha whereas prokaryote RF3 is more similar to EF-G, implying that their precise function may differ. Only eukaryote RF3s are found in this group. Saccharomyces cerevisiae eRF3 (Sup35p) is a translation termination factor which is divided into three regions N, M and a C-terminal eEF1a-like region essential for translation termination. Sup35NM
Probab=27.07 E-value=2e+02 Score=19.23 Aligned_cols=24 Identities=25% Similarity=0.538 Sum_probs=18.1
Q ss_pred ccCCCCEEEEEeccC---CCCeEEEEE
Q 032460 108 RVLPGDRVRVEVSRY---DTSKGRIIY 131 (140)
Q Consensus 108 rI~vGDrV~VE~sp~---D~~kGrIiy 131 (140)
...+||.|.+.+... +..+|.|+.
T Consensus 56 ~a~aGd~v~~~l~~~~~~~v~~G~vl~ 82 (83)
T cd03698 56 YAVAGENVRLKLKGIDEEDISPGDVLC 82 (83)
T ss_pred EECCCCEEEEEECCCCHHHCCCCCEEe
Confidence 488999999888743 357888763
No 239
>PRK09961 exoaminopeptidase; Provisional
Probab=26.89 E-value=1.3e+02 Score=26.00 Aligned_cols=25 Identities=24% Similarity=0.410 Sum_probs=18.9
Q ss_pred cCCCCEEEEEeccCCCCeEEEEEEe
Q 032460 109 VLPGDRVRVEVSRYDTSKGRIIYRL 133 (140)
Q Consensus 109 I~vGDrV~VE~sp~D~~kGrIiyRy 133 (140)
|.+||.|.++...+....++|.-|.
T Consensus 140 I~~Gd~v~~~~~~~~~~~~~i~gka 164 (344)
T PRK09961 140 IRPGDRVTFDTTFQVLPHQRVMGKA 164 (344)
T ss_pred CCCCCEEEEcceeEEecCCEEEEee
Confidence 8899999988776665667777654
No 240
>TIGR02988 YaaA_near_RecF S4 domain protein YaaA. This small protein has a single S4 domain (pfam01479), as do bacterial ribosomal protein S4, some pseudouridine synthases, tyrosyl-tRNA synthetases. The S4 domain may bind RNA. Members of this protein family are found almost exclusively in the Firmicutes, and almost invariably just a few nucleotides upstream of the gene for the DNA replication and repair protein RecF. The few members of this family that are not near recF are found instead near dnaA and/or dnaN, the usual neighbors of recF, near the origin of replication. The conserved location suggests a possible role in replication in the Firmicutes lineage.
Probab=26.83 E-value=72 Score=20.24 Aligned_cols=14 Identities=21% Similarity=0.536 Sum_probs=10.4
Q ss_pred ccccccCCCCEEEE
Q 032460 104 QNFIRVLPGDRVRV 117 (140)
Q Consensus 104 k~~IrI~vGDrV~V 117 (140)
+...++..||.|.|
T Consensus 45 ~~~~~l~~Gd~v~i 58 (59)
T TIGR02988 45 RRGKKLYPGDVIEI 58 (59)
T ss_pred CCCCCCCCCCEEEe
Confidence 33567889999865
No 241
>PF03749 SfsA: Sugar fermentation stimulation protein; InterPro: IPR005224 The sugar fermentation stimulation protein is a probable regulatory factor involved in maltose metabolism. It contains a putative DNA-binding domain, and was isolated as a gene which enabled Escherichia coli W3110 (strain MK2001) to use maltose [].
Probab=26.71 E-value=2.7e+02 Score=22.87 Aligned_cols=46 Identities=20% Similarity=0.356 Sum_probs=31.4
Q ss_pred ceEEEEe--CCCCEEEEEec--ccccccccccCCCCEEEEEeccCC--CCeEEEE
Q 032460 82 GMFRVRL--DNEDLILGYIS--GKIRQNFIRVLPGDRVRVEVSRYD--TSKGRII 130 (140)
Q Consensus 82 ~~f~V~l--~dG~~~lcrI~--GKmRk~~IrI~vGDrV~VE~sp~D--~~kGrIi 130 (140)
++|.+.+ +||++..||++ |+|+- -+.||-.|.+..++.. .++..++
T Consensus 5 nRF~~~v~l~~g~~~~~H~pntGRl~e---ll~pG~~v~l~~~~~~~RKt~y~l~ 56 (215)
T PF03749_consen 5 NRFLADVELDDGEEVTAHCPNTGRLKE---LLVPGARVLLSKSDNPKRKTKYTLE 56 (215)
T ss_pred CcEEEEEEECCCCEEEEEcCCCCcchh---hccCCCEEEEEECCCCCCCCcEEEE
Confidence 5566554 66999999996 77764 3669999999876533 2444444
No 242
>PF07359 LEAP-2: Liver-expressed antimicrobial peptide 2 precursor (LEAP-2); InterPro: IPR009955 This family consists of several mammalian liver-expressed antimicrobial peptide 2 (LEAP-2) sequences. LEAP-2 is a cysteine-rich, and cationic protein. LEAP-2 contains a core structure with two disulphide bonds formed by cysteine residues in relative 1-3 and 2-4 positions. LEAP-2 is synthesised as a 77-residue precursor, which is predominantly expressed in the liver and highly conserved among mammals. The largest native LEAP-2 form of 40 amino acid residues is generated from the precursor at a putative cleavage site for a furin-like endoprotease. In contrast to smaller LEAP-2 variants, this peptide exhibits dose-dependent antimicrobial activity against selected microbial model organisms []. The exact function of this family is unclear.; GO: 0042742 defense response to bacterium; PDB: 2L1Q_A.
Probab=26.61 E-value=26 Score=25.12 Aligned_cols=17 Identities=24% Similarity=0.577 Sum_probs=7.7
Q ss_pred EeeeeehhhhhcccCCC
Q 032460 41 VKITKIWTAIGAKKGGD 57 (140)
Q Consensus 41 ~~~~~~~~~~~~~~~~~ 57 (140)
-..||+|++|+-|-.|+
T Consensus 36 ~RMTP~WR~~s~kP~GA 52 (77)
T PF07359_consen 36 ARMTPFWRGVSLKPIGA 52 (77)
T ss_dssp -----TTSS-SSB-TTS
T ss_pred hccChHHHhhcCCcCcc
Confidence 46789999999665544
No 243
>COG1792 MreC Cell shape-determining protein [Cell envelope biogenesis, outer membrane]
Probab=26.28 E-value=1.6e+02 Score=24.93 Aligned_cols=30 Identities=27% Similarity=0.268 Sum_probs=20.1
Q ss_pred EEEEEEEeCCCceEEEEe-CCCCEEEEEecccccc
Q 032460 71 HEGFITESLPNGMFRVRL-DNEDLILGYISGKIRQ 104 (140)
Q Consensus 71 ~~GvVik~l~n~~f~V~l-~dG~~~lcrI~GKmRk 104 (140)
+-|.|+++ ..+.=+|.+ .| ..++|++++-+
T Consensus 156 LVG~V~~V-~~~tS~V~Lltd---~~~~i~v~i~r 186 (284)
T COG1792 156 LVGKVVEV-SKNTSRVLLLTD---VNSKIPVKINR 186 (284)
T ss_pred eEEEEEEE-cCceeEEEEeec---cccceeEEecc
Confidence 77999998 577778876 34 44455555544
No 244
>CHL00207 rpoB RNA polymerase beta subunit; Provisional
Probab=26.25 E-value=1.8e+02 Score=29.63 Aligned_cols=14 Identities=43% Similarity=0.847 Sum_probs=12.1
Q ss_pred cccccCCCCccccC
Q 032460 5 SCNLHRPSQPLLLP 18 (140)
Q Consensus 5 ~~~~~~~~~~~~~~ 18 (140)
..|-|||.-|||.|
T Consensus 539 GsnMqrQaVPll~~ 552 (1077)
T CHL00207 539 GSNMQRQAVPLLYP 552 (1077)
T ss_pred hhcccccccccccc
Confidence 36889999999998
No 245
>TIGR03689 pup_AAA proteasome ATPase. In the Actinobacteria, as shown for Mycobacterium tuberculosis, some proteins are modified by ligation between an epsilon-amino group of a lysine side chain and the C-terminal carboxylate of the ubiquitin-like protein Pup. This modification leads to protein degradation by the archaeal-like proteasome found in the Actinobacteria. Members of this protein family belong to the AAA family of ATPases and tend to be clustered with the genes for Pup, the Pup ligase PafA, and structural components of the proteasome. This protein forms hexameric rings with ATPase activity.
Probab=26.17 E-value=1.4e+02 Score=27.64 Aligned_cols=45 Identities=18% Similarity=0.214 Sum_probs=38.9
Q ss_pred EEEEEeCCCceEEEEeCCCCEEEEEecccccccccccCCCCEEEEEe
Q 032460 73 GFITESLPNGMFRVRLDNEDLILGYISGKIRQNFIRVLPGDRVRVEV 119 (140)
Q Consensus 73 GvVik~l~n~~f~V~l~dG~~~lcrI~GKmRk~~IrI~vGDrV~VE~ 119 (140)
.+|.+.++++++.|...+|..+..++.+.+... .+.+||.|.+..
T Consensus 110 ~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~--~~~~g~~~~~~~ 154 (512)
T TIGR03689 110 ATLKEVLGDGRALVVDHSGEERVVKLAGALADE--LIRAGDSLLVDP 154 (512)
T ss_pred EEEEEEeCCCeEEEEeCCCCeEEeehhhhhCHh--hCCCCCEEEEcc
Confidence 488888889999999999999999999999864 478999998763
No 246
>PRK10861 signal peptidase I; Provisional
Probab=25.71 E-value=86 Score=27.43 Aligned_cols=11 Identities=45% Similarity=0.531 Sum_probs=5.0
Q ss_pred cCCCCEEEEEe
Q 032460 109 VLPGDRVRVEV 119 (140)
Q Consensus 109 I~vGDrV~VE~ 119 (140)
+.+||+|.|.-
T Consensus 96 L~~GD~IlVnK 106 (324)
T PRK10861 96 LLIGDFILVEK 106 (324)
T ss_pred ccCCCEEEEEE
Confidence 44444444443
No 247
>PRK03598 putative efflux pump membrane fusion protein; Provisional
Probab=25.56 E-value=1.4e+02 Score=24.75 Aligned_cols=52 Identities=15% Similarity=0.263 Sum_probs=34.4
Q ss_pred CceEEEEeCCCCEEEEEecccccccccccCCCCEEEEEeccC--CCCeEEEEEEecC
Q 032460 81 NGMFRVRLDNEDLILGYISGKIRQNFIRVLPGDRVRVEVSRY--DTSKGRIIYRLRN 135 (140)
Q Consensus 81 n~~f~V~l~dG~~~lcrI~GKmRk~~IrI~vGDrV~VE~sp~--D~~kGrIiyRy~r 135 (140)
...+.+...+.-.+.+.++-+-.. .+.+||.|.|.+..+ ..-.|.|.+..+-
T Consensus 229 ~~l~~I~~~~~~~v~~~V~e~~~~---~i~~Gq~v~v~~~~~~~~~~~g~V~~Is~~ 282 (331)
T PRK03598 229 STVFTLSLTRPVWVRAYVDERNLG---QAQPGRKVLLYTDGRPDKPYHGQIGFVSPT 282 (331)
T ss_pred CeEEEEecCCceEEEEEECHHHHh---hCCCCCEEEEEEcCCCCcEEEEEEEEEcCc
Confidence 444555545556677777765433 488999999987643 3457888877654
No 248
>cd04474 RPA1_DBD_A RPA1_DBD_A: A subfamily of OB folds corresponding to the second OB fold, the ssDNA-binding domain (DBD)-A, of human RPA1 (also called RPA70). RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-A, RPA1 contains three other OB folds: DBD-B, DBD-C, and RPA1N. The major DNA binding activity of human RPA (hRPA) and Saccharomyces cerevisiae RPA (ScRPA) is associated with DBD-A and DBD-B of RPA1. RPA1 DBD-C is involved in trimerization. The ssDNA-binding mechanism is believed to be multistep and to involve conformational change. Although ScRPA and the hRPA have similar ssDNA-binding properties, they differ funct
Probab=25.33 E-value=2.5e+02 Score=19.78 Aligned_cols=33 Identities=6% Similarity=-0.059 Sum_probs=23.3
Q ss_pred EEeCCCCEEEEEeccccc-ccccccCCCCEEEEE
Q 032460 86 VRLDNEDLILGYISGKIR-QNFIRVLPGDRVRVE 118 (140)
Q Consensus 86 V~l~dG~~~lcrI~GKmR-k~~IrI~vGDrV~VE 118 (140)
+.+++|..+.|.+-|..- +..-.|.+|+.+.+.
T Consensus 41 l~De~~~~I~~t~~~~~~~~f~~~l~eG~vy~i~ 74 (104)
T cd04474 41 LLDEDGGEIRATFFNDAVDKFYDLLEVGKVYYIS 74 (104)
T ss_pred EEECCCCEEEEEEehHHHHHhhcccccccEEEEe
Confidence 334558899999998742 223358899999774
No 249
>cd04715 BAH_Orc1p_like BAH, or Bromo Adjacent Homology domain, as present in the Schizosaccharomyces pombe homolog of Saccharomyces cerevisiae Orc1p and similar proteins. Orc1 is part of the Yeast Sir1-origin recognition complex, the Orc1p BAH doman functions in epigenetic silencing. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=25.32 E-value=1.2e+02 Score=23.72 Aligned_cols=11 Identities=27% Similarity=0.021 Sum_probs=5.4
Q ss_pred ccCCCCEEEEE
Q 032460 108 RVLPGDRVRVE 118 (140)
Q Consensus 108 rI~vGDrV~VE 118 (140)
.+.+||.|+|.
T Consensus 29 ~y~lGD~Vlv~ 39 (159)
T cd04715 29 EYRLYDDVYVH 39 (159)
T ss_pred EEeCCCEEEEe
Confidence 34445555554
No 250
>COG1278 CspC Cold shock proteins [Transcription]
Probab=25.15 E-value=2e+02 Score=19.92 Aligned_cols=51 Identities=20% Similarity=0.212 Sum_probs=32.1
Q ss_pred EEEEEEEeCC-CceEEEEeCCC-CEEEEEecccccccccccCCCCEEEEEecc
Q 032460 71 HEGFITESLP-NGMFRVRLDNE-DLILGYISGKIRQNFIRVLPGDRVRVEVSR 121 (140)
Q Consensus 71 ~~GvVik~l~-n~~f~V~l~dG-~~~lcrI~GKmRk~~IrI~vGDrV~VE~sp 121 (140)
+.|+|-..-. -|+=.+.-+|| +.+-.|++---+...-.+.+|++|.+++..
T Consensus 2 ~~GtVKwfn~~KGfGFI~p~~G~~DvFVH~Sai~~~g~~~L~eGQ~V~f~~~~ 54 (67)
T COG1278 2 ATGTVKWFNATKGFGFITPEDGGKDVFVHISAIQRAGFRTLREGQKVEFEVEQ 54 (67)
T ss_pred CcceEEEeeCCCcceEcCCCCCCcCEEEEeeeeccCCCcccCCCCEEEEEEec
Confidence 3456655432 22333444666 688888886544433359999999998763
No 251
>cd03693 EF1_alpha_II EF1_alpha_II: this family represents the domain II of elongation factor 1-alpha (EF-1a) that is found in archaea and all eukaryotic lineages. EF-1A is very abundant in the cytosol, where it is involved in the GTP-dependent binding of aminoacyl-tRNAs to the A site of the ribosomes in the second step of translation from mRNAs to proteins. Both domain II of EF1A and domain IV of IF2/eIF5B have been implicated in recognition of the 3'-ends of tRNA. More than 61% of eukaryotic elongation factor 1A (eEF-1A) in cells is estimated to be associated with actin cytoskeleton. The binding of eEF1A to actin is a noncanonical function that may link two distinct cellular processes, cytoskeleton organization and gene expression.
Probab=25.08 E-value=2.3e+02 Score=19.34 Aligned_cols=26 Identities=31% Similarity=0.500 Sum_probs=19.6
Q ss_pred ccCCCCEEEEEeccC---CCCeEEEEEEe
Q 032460 108 RVLPGDRVRVEVSRY---DTSKGRIIYRL 133 (140)
Q Consensus 108 rI~vGDrV~VE~sp~---D~~kGrIiyRy 133 (140)
+..+||.|.+.+... +..+|.|+-..
T Consensus 60 ~a~aG~~v~i~l~~i~~~~v~~G~vl~~~ 88 (91)
T cd03693 60 EALPGDNVGFNVKNVSKKDIKRGDVAGDS 88 (91)
T ss_pred EECCCCEEEEEECCCCHHHcCCcCEEccC
Confidence 478899999998753 34789887653
No 252
>COG0539 RpsA Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]
Probab=24.96 E-value=1.8e+02 Score=27.48 Aligned_cols=66 Identities=30% Similarity=0.361 Sum_probs=43.6
Q ss_pred EEEEEEEEeCCCceEEEEeC--CCCEEEEEecccccc-cccccCCCCEEEEEeccCCCCeEEEEEEecCC
Q 032460 70 VHEGFITESLPNGMFRVRLD--NEDLILGYISGKIRQ-NFIRVLPGDRVRVEVSRYDTSKGRIIYRLRNK 136 (140)
Q Consensus 70 e~~GvVik~l~n~~f~V~l~--dG~~~lcrI~GKmRk-~~IrI~vGDrV~VE~sp~D~~kGrIiyRy~r~ 136 (140)
.+.|+|.++-+.|.| |.+. ||-.....|+-+--. -.-.+.+||.|.|.+-.+|..++||.--.+..
T Consensus 195 vV~G~V~~It~~Gaf-VdigGvdGLlHiseiS~~rv~~P~~vvkvGd~VkvkVi~~D~e~~RVsLSlK~l 263 (541)
T COG0539 195 VVEGVVKNITDYGAF-VDIGGVDGLLHISEISWKRVDHPSEVVKVGDEVKVKVISLDEERGRVSLSLKQL 263 (541)
T ss_pred eEEEEEEEeecCcEE-EEecCeeeEEehhhccccccCCHHHhcccCCEEEEEEEEEccCCCeEEEEehhc
Confidence 589999999765554 5452 344444444433222 12238999999999999999999997554443
No 253
>COG1570 XseA Exonuclease VII, large subunit [DNA replication, recombination, and repair]
Probab=24.61 E-value=2.3e+02 Score=26.19 Aligned_cols=51 Identities=20% Similarity=0.192 Sum_probs=35.5
Q ss_pred ceEEEEEEEEeC--CCce--EEEEeCCCCEEEEEecccccccccccCCCCEEEEE
Q 032460 68 KWVHEGFITESL--PNGM--FRVRLDNEDLILGYISGKIRQNFIRVLPGDRVRVE 118 (140)
Q Consensus 68 ~ie~~GvVik~l--~n~~--f~V~l~dG~~~lcrI~GKmRk~~IrI~vGDrV~VE 118 (140)
.+-+.|.|-..- ++|+ |.++.+...+.-+--+|+.++-+.++..||.|+|.
T Consensus 25 ~V~v~GEISn~t~~~sgH~YFtLKD~~A~i~c~mf~~~~~~l~f~p~eG~~V~v~ 79 (440)
T COG1570 25 QVWVRGEISNFTRPASGHLYFTLKDERAQIRCVMFKGNNRRLKFRPEEGMQVLVR 79 (440)
T ss_pred eEEEEEEecCCccCCCccEEEEEccCCceEEEEEEcCcccccCCCccCCCEEEEE
Confidence 456888887653 3444 44444444555556789988877889999999996
No 254
>PF14890 Intein_splicing: Intein splicing domain; PDB: 1MI8_A 2CW7_A 2CW8_A.
Probab=24.45 E-value=1.2e+02 Score=25.34 Aligned_cols=38 Identities=21% Similarity=0.232 Sum_probs=21.7
Q ss_pred CceEEEEeCCCCEEEEEecccccccccc-----cCCCCEEEEE
Q 032460 81 NGMFRVRLDNEDLILGYISGKIRQNFIR-----VLPGDRVRVE 118 (140)
Q Consensus 81 n~~f~V~l~dG~~~lcrI~GKmRk~~Ir-----I~vGDrV~VE 118 (140)
...|+|++.+|.++.+..-=++.-..-| +.+||+|.+-
T Consensus 50 k~v~ri~t~~GreI~~T~~H~~lt~~~wk~~~~Lk~GD~I~v~ 92 (323)
T PF14890_consen 50 KPVYRIRTRSGREIKATPDHPFLTPDGWKRLEELKPGDRIAVP 92 (323)
T ss_dssp EEEEEEEETTS-EEEEETT-EEEECCCCCECCC--TT-EEEEE
T ss_pred ceEEEEEeCCCCEEEEcCCCcEEEccCCEEhHHhhcccccccc
Confidence 4467888888877777655444433223 8899999874
No 255
>cd06462 Peptidase_S24_S26 The S24, S26 LexA/signal peptidase superfamily contains LexA-related and type I signal peptidase families. The S24 LexA protein domains include: the lambda repressor CI/C2 family and related bacterial prophage repressor proteins; LexA (EC 3.4.21.88), the repressor of genes in the cellular SOS response to DNA damage; MucA and the related UmuD proteins, which are lesion-bypass DNA polymerases, induced in response to mitogenic DNA damage; RulA, a component of the rulAB locus that confers resistance to UV, and RuvA, which is a component of the RuvABC resolvasome that catalyzes the resolution of Holliday junctions that arise during genetic recombination and DNA repair. The S26 type I signal peptidase (SPase) family also includes mitochondrial inner membrane protease (IMP)-like members. SPases are essential membrane-bound proteases which function to cleave away the amino-terminal signal peptide from the translocated pre-protein, thus playing a crucial role in the tr
Probab=24.27 E-value=98 Score=19.67 Aligned_cols=13 Identities=23% Similarity=0.222 Sum_probs=8.6
Q ss_pred ccCCCCEEEEEec
Q 032460 108 RVLPGDRVRVEVS 120 (140)
Q Consensus 108 rI~vGDrV~VE~s 120 (140)
.+..||.|.+...
T Consensus 28 ~~~~G~iv~~~~~ 40 (84)
T cd06462 28 EPKRGDIVVFRLP 40 (84)
T ss_pred CCcCCEEEEEEcC
Confidence 3666787777644
No 256
>KOG1214 consensus Nidogen and related basement membrane protein proteins [Cell wall/membrane/envelope biogenesis; Extracellular structures]
Probab=24.23 E-value=1.8e+02 Score=29.76 Aligned_cols=72 Identities=19% Similarity=0.323 Sum_probs=53.6
Q ss_pred cceeEeeeccceEeeeeehhhhhcccCCCccccc-----ccCCcceEEEEEEEEeCCCceEEEEeCCCCEEEEEeccccc
Q 032460 29 INHVKFNVNKEFVKITKIWTAIGAKKGGDRSSEE-----GANSEKWVHEGFITESLPNGMFRVRLDNEDLILGYISGKIR 103 (140)
Q Consensus 29 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----~~k~d~ie~~GvVik~l~n~~f~V~l~dG~~~lcrI~GKmR 103 (140)
|-+|.|.--+..| .|+-|+.+...--+.+- .-+.+.+.-+|+-+.-++-++|...-.+.++-.|.+-|+.|
T Consensus 1027 iVGidfDC~e~mv----yWtDv~g~SI~rasL~G~Ep~ti~n~~L~SPEGiAVDh~~Rn~ywtDS~lD~IevA~LdG~~r 1102 (1289)
T KOG1214|consen 1027 IVGIDFDCRERMV----YWTDVAGRSISRASLEGAEPETIVNSGLISPEGIAVDHIRRNMYWTDSVLDKIEVALLDGSER 1102 (1289)
T ss_pred eeeeecccccceE----EEeecCCCccccccccCCCCceeecccCCCccceeeeeccceeeeeccccchhheeecCCcee
Confidence 4567788778877 89999887764433321 22344556788888888899999877777899999999999
Q ss_pred c
Q 032460 104 Q 104 (140)
Q Consensus 104 k 104 (140)
|
T Consensus 1103 k 1103 (1289)
T KOG1214|consen 1103 K 1103 (1289)
T ss_pred e
Confidence 7
No 257
>TIGR02609 doc_partner putative addiction module antidote. Members of this protein family are putative addiction module antidote proteins that appear recurringly in two-gene operons with members of the Doc (death-on-curing) family TIGR01550. Members of this family contain a SpoVT/AbrB-like domain (pfam04014). Note that the gene pairs with a member of this family tend to be found on bacterial chromosomes, not on plasmids.
Probab=24.21 E-value=1.6e+02 Score=19.89 Aligned_cols=40 Identities=13% Similarity=0.233 Sum_probs=26.8
Q ss_pred CCEEEEEecccccccccccCCCCEEEEEeccCCCCeEEEEEEecC
Q 032460 91 EDLILGYISGKIRQNFIRVLPGDRVRVEVSRYDTSKGRIIYRLRN 135 (140)
Q Consensus 91 G~~~lcrI~GKmRk~~IrI~vGDrV~VE~sp~D~~kGrIiyRy~r 135 (140)
|...--+|+-.++. ...+.+||.|.|+.. +.+.|+-+...
T Consensus 7 GNS~~vtIPk~i~~-~lgl~~Gd~v~v~~~----~~~iii~~~~~ 46 (74)
T TIGR02609 7 GNSLVVTLPKEVLE-SLGLKEGDTLYVDEE----EGGLKLKRFDE 46 (74)
T ss_pred CCeeEEEECHHHHH-HcCcCCCCEEEEEEE----CCEEEEEECCC
Confidence 44556677777765 577999999987755 23566655543
No 258
>PTZ00202 tuzin; Provisional
Probab=24.12 E-value=1.3e+02 Score=28.59 Aligned_cols=68 Identities=25% Similarity=0.238 Sum_probs=40.6
Q ss_pred eccceeEeeeccceEeeeeehhhh--hcccCCCccccc---ccCCcceEEEEEEEEeCCCceEEEEeCCCCEEE
Q 032460 27 FPINHVKFNVNKEFVKITKIWTAI--GAKKGGDRSSEE---GANSEKWVHEGFITESLPNGMFRVRLDNEDLIL 95 (140)
Q Consensus 27 ~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~---~~k~d~ie~~GvVik~l~n~~f~V~l~dG~~~l 95 (140)
+-+-+|+-..+.++|+.-- ...- .--..+++...+ -+......|.|+|.++-|||.|-|.++||..=+
T Consensus 18 ~a~g~i~~~~s~~~yav~~-~~~~~~~~~~~~~rv~~~~~~~~~~~g~~vgG~v~rVNgNgT~gvLlDnn~~dl 90 (550)
T PTZ00202 18 IAGGHVKAQIAGSVYAVHL-QHLFLSPIVEVGSRVYVEYGRDAENEGAVVGGLVVRVNGNGTLGVLLDNNRFDL 90 (550)
T ss_pred ccceeEEeeccCceeeeeh-hhcCCccccccccceeeecCCCcccCceEeeeEEEEEcCCceEEEEecCCcccc
Confidence 4566778888888776421 0000 011222332222 222335579999999999999999998865433
No 259
>TIGR02851 spore_V_T stage V sporulation protein T. Members of this protein family are the stage V sporulation protein T (SpoVT), a protein of the sporulation/germination program in Bacillus subtilis and related species. The amino-terminal 50 amino acids are nearly perfectly conserved across all endospore-forming bacteria. SpoVT is a DNA-binding transcriptional regulator related to AbrB (See PFAM model pfam04014).
Probab=24.07 E-value=73 Score=25.33 Aligned_cols=23 Identities=26% Similarity=0.459 Sum_probs=18.6
Q ss_pred EecccccccccccCCCCEEEEEec
Q 032460 97 YISGKIRQNFIRVLPGDRVRVEVS 120 (140)
Q Consensus 97 rI~GKmRk~~IrI~vGDrV~VE~s 120 (140)
.|+-.+|+ ...|.+||.|.+...
T Consensus 16 ~iP~~iR~-~l~i~~gd~~~~~~~ 38 (180)
T TIGR02851 16 VIPKEIRR-TLRIREGDPLEIFTD 38 (180)
T ss_pred EEeHHHHH-HcCCCCCCeEEEEEe
Confidence 47778886 688999999988654
No 260
>cd00165 S4 S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, charged residues that define a likely RNA-binding site; Found in stress proteins, ribosomal proteins and tRNA synthetases; This may imply a hitherto unrecognized functional similarity between these three protein classes.
Probab=24.06 E-value=1.4e+02 Score=17.65 Aligned_cols=14 Identities=36% Similarity=0.565 Sum_probs=8.5
Q ss_pred ccccCCCCEEEEEe
Q 032460 106 FIRVLPGDRVRVEV 119 (140)
Q Consensus 106 ~IrI~vGDrV~VE~ 119 (140)
...+.+||.|.+..
T Consensus 39 ~~~v~~~d~i~i~~ 52 (70)
T cd00165 39 SYKVKPGDVIEVDG 52 (70)
T ss_pred ccCcCCCCEEEEcC
Confidence 34466677776654
No 261
>smart00675 DM11 Domains in hypothetical proteins in Drosophila including 2 in CG15241 and CG9329.
Probab=23.95 E-value=44 Score=26.55 Aligned_cols=41 Identities=34% Similarity=0.445 Sum_probs=27.2
Q ss_pred ceEEEEeCCCCEEEEEecccccccccc-cCCCCEEEEEeccCCCCeE
Q 032460 82 GMFRVRLDNEDLILGYISGKIRQNFIR-VLPGDRVRVEVSRYDTSKG 127 (140)
Q Consensus 82 ~~f~V~l~dG~~~lcrI~GKmRk~~Ir-I~vGDrV~VE~sp~D~~kG 127 (140)
..+.+..+++. -+++|.+.- +| +.|+|++.+.++.+..++|
T Consensus 33 S~l~~~~d~~~---i~vsGn~t~--~wdi~P~DrI~~~~~~~~~eRG 74 (164)
T smart00675 33 SNLVVDMDPDG---LHISGNITV--IWDVQPTDRISARVSVMHFERG 74 (164)
T ss_pred hheEEEEcCCe---EEEeeeEEE--EEecCCCCeEEEEEEEEEecCC
Confidence 34455543333 358899875 55 8899999988776555554
No 262
>PTZ00194 60S ribosomal protein L26; Provisional
Probab=23.87 E-value=1e+02 Score=24.35 Aligned_cols=31 Identities=19% Similarity=0.200 Sum_probs=17.7
Q ss_pred cccccCCCCEEEEEeccCCCCeEEEEEEecC
Q 032460 105 NFIRVLPGDRVRVEVSRYDTSKGRIIYRLRN 135 (140)
Q Consensus 105 ~~IrI~vGDrV~VE~sp~D~~kGrIiyRy~r 135 (140)
+.+.|..||.|.|--=.+--.+|.|+..+..
T Consensus 43 Rs~~IkkGD~V~Vi~Gk~KGk~GkV~~V~~k 73 (143)
T PTZ00194 43 RSMPVRKDDEVMVVRGHHKGREGKVTAVYRK 73 (143)
T ss_pred ccceeecCCEEEEecCCCCCCceEEEEEEcC
Confidence 3445777888877422222245777766543
No 263
>PRK06763 F0F1 ATP synthase subunit alpha; Validated
Probab=23.74 E-value=3.5e+02 Score=22.81 Aligned_cols=46 Identities=15% Similarity=0.082 Sum_probs=30.5
Q ss_pred EEEEEEEeCCC--------ceEEEEe--CCCCEEEEEecccccccccccCCCCEEEEEe
Q 032460 71 HEGFITESLPN--------GMFRVRL--DNEDLILGYISGKIRQNFIRVLPGDRVRVEV 119 (140)
Q Consensus 71 ~~GvVik~l~n--------~~f~V~l--~dG~~~lcrI~GKmRk~~IrI~vGDrV~VE~ 119 (140)
+.|.|++.... ++..|+- .+|+...-++. .-++-...+||.|+|++
T Consensus 120 vIG~Iskv~k~~~~~~~~~dyVvV~YP~~~G~~~~V~V~---LT~GQkFnVGDkVKV~~ 175 (213)
T PRK06763 120 VIGEVSKVYTMEDDGDGATKYVVVEYPSLNGKKLIIDVF---LTKGQVFHVGDKVKVDM 175 (213)
T ss_pred EEEEEEEecccccCCCCcccEEEEEcCCCCCCeeEEEEE---eccCCEEecCCEEEEEe
Confidence 67999998431 3455665 35666555443 12456789999999995
No 264
>PF03658 Ub-RnfH: RnfH family Ubiquitin; InterPro: IPR005346 This is a small family of proteins of unknown function.; PDB: 2HJ1_B.
Probab=23.61 E-value=50 Score=23.68 Aligned_cols=21 Identities=33% Similarity=0.335 Sum_probs=9.7
Q ss_pred EecccccccccccCCCCEEEE
Q 032460 97 YISGKIRQNFIRVLPGDRVRV 117 (140)
Q Consensus 97 rI~GKmRk~~IrI~vGDrV~V 117 (140)
=|=||..+-.-.+..||||++
T Consensus 50 GIfGk~~~~d~~L~~GDRVEI 70 (84)
T PF03658_consen 50 GIFGKLVKLDTVLRDGDRVEI 70 (84)
T ss_dssp EEEE-S--TT-B--TT-EEEE
T ss_pred eeeeeEcCCCCcCCCCCEEEE
Confidence 345666665666999999965
No 265
>cd04713 BAH_plant_3 BAH, or Bromo Adjacent Homology domain, plant-specific sub-family with unknown function. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=23.59 E-value=2.1e+02 Score=21.74 Aligned_cols=30 Identities=7% Similarity=0.104 Sum_probs=14.6
Q ss_pred ceEEEEEEEEeCCCceEEEEeCC-CCEEEEEec
Q 032460 68 KWVHEGFITESLPNGMFRVRLDN-EDLILGYIS 99 (140)
Q Consensus 68 ~ie~~GvVik~l~n~~f~V~l~d-G~~~lcrI~ 99 (140)
.++..|++.++ |....|..++ ...+.|+|.
T Consensus 13 s~~~dg~~y~v--gD~Vlv~~~~~~~pyI~~I~ 43 (146)
T cd04713 13 SFEKDGNKYRL--EDCVLLVPEDDQKPYIAIIK 43 (146)
T ss_pred eEEECCEEEEC--CCEEEEeCCCCCCCEEEEEE
Confidence 34555666554 4555555433 334455443
No 266
>TIGR00575 dnlj DNA ligase, NAD-dependent. The member of this family from Treponema pallidum differs in having three rather than just one copy of the BRCT (BRCA1 C Terminus) domain (pfam00533) at the C-terminus. It is included in the seed.
Probab=23.35 E-value=2.2e+02 Score=27.09 Aligned_cols=91 Identities=13% Similarity=0.140 Sum_probs=46.8
Q ss_pred CCCceeccceeEeeeccceEeeeeehhhhhcccCCCc--ccccccC-CcceEEEEEEEEeCCCceEEEE--eC----CCC
Q 032460 22 LSPISFPINHVKFNVNKEFVKITKIWTAIGAKKGGDR--SSEEGAN-SEKWVHEGFITESLPNGMFRVR--LD----NED 92 (140)
Q Consensus 22 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~k-~d~ie~~GvVik~l~n~~f~V~--l~----dG~ 92 (140)
+.+..+.|.|+-+++|+- +.|..+|.....-+ .+.-.|. +-...+.+++.++--.|..+-. ++ +|.
T Consensus 264 R~~l~y~iDGiViKvn~~-----~~~~~lG~t~~~PrwaiA~Kf~~~~~~T~l~~I~~qVGRTG~iTPvA~lePV~l~G~ 338 (652)
T TIGR00575 264 RDSLPYEIDGVVVKVDDL-----ALQDELGFTSKAPRWAIAYKFPAEEAQTKLLDVVVQVGRTGAITPVAKLEPVFVAGT 338 (652)
T ss_pred hhcCCCCCCcEEEEecCH-----HHHHHhCccCCCCCceEEEcCCCceeeEEEEEEEEecCCCceeeeEEEEeeEEECCE
Confidence 445567777777777653 24666665443333 2222333 3344577777776334444322 21 233
Q ss_pred EEEEEe----cccccccccccCCCCEEEEEec
Q 032460 93 LILGYI----SGKIRQNFIRVLPGDRVRVEVS 120 (140)
Q Consensus 93 ~~lcrI----~GKmRk~~IrI~vGDrV~VE~s 120 (140)
++ .++ ..-+++. .|.+||.|.|+-.
T Consensus 339 ~V-srAtLhN~~~i~~~--~i~iGD~V~V~ra 367 (652)
T TIGR00575 339 TV-SRATLHNEDEIEEL--DIRIGDTVVVRKA 367 (652)
T ss_pred EE-EEeecCCHHHHHHc--CCCCCCEEEEEec
Confidence 32 222 2223322 3788999999854
No 267
>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=23.27 E-value=1.3e+02 Score=20.98 Aligned_cols=41 Identities=20% Similarity=-0.068 Sum_probs=24.7
Q ss_pred EEEEEEEeCCCceEEEEeCCCCEEEEEecccccccccccCCCCEEEEE
Q 032460 71 HEGFITESLPNGMFRVRLDNEDLILGYISGKIRQNFIRVLPGDRVRVE 118 (140)
Q Consensus 71 ~~GvVik~l~n~~f~V~l~dG~~~lcrI~GKmRk~~IrI~vGDrV~VE 118 (140)
+-|+|+++- ++.-.|. ..|..+...+.=- - .+.+||+|+|-
T Consensus 5 iP~~V~~i~-~~~A~v~-~~G~~~~v~l~lv--~---~~~vGD~VLVH 45 (76)
T TIGR00074 5 IPGQVVEID-ENIALVE-FCGIKRDVSLDLV--G---EVKVGDYVLVH 45 (76)
T ss_pred cceEEEEEc-CCEEEEE-cCCeEEEEEEEee--C---CCCCCCEEEEe
Confidence 347888874 4444443 3566666554311 1 38899999984
No 268
>KOG3409 consensus Exosomal 3'-5' exoribonuclease complex, subunit ski4 (Csl4) [Translation, ribosomal structure and biogenesis]
Probab=23.18 E-value=2.9e+02 Score=22.94 Aligned_cols=57 Identities=18% Similarity=0.088 Sum_probs=37.8
Q ss_pred cccCCcceEEEEEEEEeCCCceEEE--EeCCCCEEEEEecccccccccc------------cCCCCEEEEEec
Q 032460 62 EGANSEKWVHEGFITESLPNGMFRV--RLDNEDLILGYISGKIRQNFIR------------VLPGDRVRVEVS 120 (140)
Q Consensus 62 ~~~k~d~ie~~GvVik~l~n~~f~V--~l~dG~~~lcrI~GKmRk~~Ir------------I~vGDrV~VE~s 120 (140)
-+|....| +.++|..+ +--+-+| .+-+.+.+.-+.+|-+|++.+| .+|||.|+-.+.
T Consensus 64 ~LP~~G~I-VtarV~~i-~~rfAkv~I~~V~d~~lk~~FrglirkqdvR~tEkdrv~v~ksFrPgDiVlAkVi 134 (193)
T KOG3409|consen 64 LLPFVGAI-VTARVSRI-NLRFAKVDILSVGDKPLKKSFRGLIRKQDVRATEKDRVKVYKSFRPGDIVLAKVI 134 (193)
T ss_pred cCCccCcE-EEEEEEee-ccceeeEEEEEEcCEEhhhhhcceeehhhccccccchhhhhhccCCCcEEEEEEe
Confidence 36666554 88899886 3333333 3445567777888999988887 567887776543
No 269
>PF09874 DUF2101: Predicted membrane protein (DUF2101); InterPro: IPR018663 This family of conserved hypothetical proteins has no known function.
Probab=23.17 E-value=1.9e+02 Score=24.23 Aligned_cols=46 Identities=24% Similarity=0.297 Sum_probs=27.9
Q ss_pred EEEEEEeCCCceEEEEeCCCCEEEEEe-ccccccc-ccccCCCCEEEEEec
Q 032460 72 EGFITESLPNGMFRVRLDNEDLILGYI-SGKIRQN-FIRVLPGDRVRVEVS 120 (140)
Q Consensus 72 ~GvVik~l~n~~f~V~l~dG~~~lcrI-~GKmRk~-~IrI~vGDrV~VE~s 120 (140)
-|+|.++ ++|..+|..+| .+.|.+ +|..=-. .--+.+||.|++.+.
T Consensus 146 yG~VeEv-~~~~v~V~V~d--DI~ANVkPg~YwV~~~~d~~~G~vVKl~VE 193 (206)
T PF09874_consen 146 YGVVEEV-KENLVRVFVHD--DIAANVKPGYYWVEAVPDVEEGDVVKLLVE 193 (206)
T ss_pred eEEEEEe-cCCEEEEEEcc--chhhcCCCCeEEecCCCCCCCCceEEEEEe
Confidence 4999998 68888998765 222322 2221111 112678999988765
No 270
>PRK03992 proteasome-activating nucleotidase; Provisional
Probab=22.55 E-value=2.8e+02 Score=24.10 Aligned_cols=46 Identities=24% Similarity=0.281 Sum_probs=36.5
Q ss_pred EEEEEEEeCCCceEEEEeCCCCEEEEEecccccccccccCCCCEEEEE
Q 032460 71 HEGFITESLPNGMFRVRLDNEDLILGYISGKIRQNFIRVLPGDRVRVE 118 (140)
Q Consensus 71 ~~GvVik~l~n~~f~V~l~dG~~~lcrI~GKmRk~~IrI~vGDrV~VE 118 (140)
..|.|.+.+..+...|...+|..+...+...+-. -.+.+|+.|.+.
T Consensus 54 ~~~~i~~~~~~~~~~v~~~~g~~~~~~~~~~~~~--~~l~~g~~v~~~ 99 (389)
T PRK03992 54 IVATVLEVLDDGRVVVKSSGGPQFLVNVSPFIDR--EKLKPGARVALN 99 (389)
T ss_pred eEEEEEEEeCCCeEEEEECCCCEEEEeccccCCH--hHCCCCCEEEEc
Confidence 5689999998888889888888888888876544 347889999654
No 271
>PRK14132 riboflavin kinase; Provisional
Probab=22.41 E-value=81 Score=24.24 Aligned_cols=20 Identities=20% Similarity=0.257 Sum_probs=17.8
Q ss_pred EEEEEEEEeCCCceEEEEeC
Q 032460 70 VHEGFITESLPNGMFRVRLD 89 (140)
Q Consensus 70 e~~GvVik~l~n~~f~V~l~ 89 (140)
+++|+|++.||-|.|+|.++
T Consensus 2 ~l~G~VvSGlGEG~yyvsl~ 21 (126)
T PRK14132 2 KIFGRVVSGLGEGAYFLSLP 21 (126)
T ss_pred EEEEEEecccccceEEEeCH
Confidence 58899999999999999873
No 272
>TIGR01080 rplX_A_E ribosomal protein L24p/L26e, archaeal/eukaryotic. This model represents the archaeal and eukaryotic branch of the ribosomal protein L24p/L26e family. Bacterial and organellar forms are represented by the related TIGR01079.
Probab=22.40 E-value=1.8e+02 Score=21.92 Aligned_cols=28 Identities=21% Similarity=0.354 Sum_probs=17.5
Q ss_pred cccCCCCEEEEEeccCCCCeEEEEEEec
Q 032460 107 IRVLPGDRVRVEVSRYDTSKGRIIYRLR 134 (140)
Q Consensus 107 IrI~vGDrV~VE~sp~D~~kGrIiyRy~ 134 (140)
+.|..||.|.|.-=.+.-.+|.|+.-..
T Consensus 40 ~~IkkGD~V~Vi~Gk~KGk~GkV~~V~~ 67 (114)
T TIGR01080 40 LPVRKGDKVRIMRGDFKGHEGKVSKVDL 67 (114)
T ss_pred ceeecCCEEEEecCCCCCCEEEEEEEEc
Confidence 4577788887743333335677776653
No 273
>PRK11144 modC molybdate transporter ATP-binding protein; Provisional
Probab=22.32 E-value=2.8e+02 Score=23.64 Aligned_cols=49 Identities=18% Similarity=0.300 Sum_probs=32.2
Q ss_pred EEEEEEEeCC-CceEEEEeC-CCCEEEEEecccccccccccCCCCEEEEEec
Q 032460 71 HEGFITESLP-NGMFRVRLD-NEDLILGYISGKIRQNFIRVLPGDRVRVEVS 120 (140)
Q Consensus 71 ~~GvVik~l~-n~~f~V~l~-dG~~~lcrI~GKmRk~~IrI~vGDrV~VE~s 120 (140)
+.|+|..+.. ++.+.|.++ +|..+.+.+...-.. ...+.+||.|.+.+.
T Consensus 296 ~~~~v~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~-~~~l~~g~~v~~~~~ 346 (352)
T PRK11144 296 LRAKVVEIYDDNGQVEVKLEVGGKTLWARITPWARD-ELALKPGQWLYAQIK 346 (352)
T ss_pred eEEEEEEEEcCCCEEEEEEEeCCcEEEEEecHHHHH-hcCCCCCCEEEEEEE
Confidence 6788888743 445656553 466778888754321 235789999988754
No 274
>PRK00347 putative DNA-binding transcriptional regulator; Reviewed
Probab=22.14 E-value=4.6e+02 Score=21.73 Aligned_cols=46 Identities=17% Similarity=0.333 Sum_probs=37.0
Q ss_pred EEEEEEEeCCCceEEEEe--CCCCEEEEEec--ccccccccccCCCCEEEEEecc
Q 032460 71 HEGFITESLPNGMFRVRL--DNEDLILGYIS--GKIRQNFIRVLPGDRVRVEVSR 121 (140)
Q Consensus 71 ~~GvVik~l~n~~f~V~l--~dG~~~lcrI~--GKmRk~~IrI~vGDrV~VE~sp 121 (140)
+.|+.++=. ++|.+.+ +||++..||++ |+|+- -+.||-.|.+...+
T Consensus 8 ~~g~fi~R~--nRF~~~V~~~~g~~~~aH~pntGRl~e---ll~pG~~v~l~~~~ 57 (234)
T PRK00347 8 QEATLIKRY--KRFLADVELDDGEELTAHCPNTGRMTG---LLTPGNTVWLSTSD 57 (234)
T ss_pred eEEEEEEec--CCEEEEEEECCCCEEEEEcCCCCCChh---hccCCCEEEEEECC
Confidence 689999986 8998886 36999999995 77754 47799999988654
No 275
>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=22.03 E-value=69 Score=26.07 Aligned_cols=27 Identities=33% Similarity=0.535 Sum_probs=18.3
Q ss_pred ccccCCCCEEEEEeccCCCCeEEEEEE
Q 032460 106 FIRVLPGDRVRVEVSRYDTSKGRIIYR 132 (140)
Q Consensus 106 ~IrI~vGDrV~VE~sp~D~~kGrIiyR 132 (140)
.+.|.+||.|.+.+.....+.|.++..
T Consensus 88 ~~~v~~GD~i~~~V~a~s~~~g~~~l~ 114 (208)
T PF01828_consen 88 NFPVSPGDTIRVTVTATSNTSGTITLE 114 (208)
T ss_dssp T----TT-EEEEEEEEEETTEEEEEEE
T ss_pred cceECCCCEEEEEEEecCCCCEEEEEE
Confidence 467999999999998888888887654
No 276
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated
Probab=21.86 E-value=2.6e+02 Score=26.74 Aligned_cols=91 Identities=13% Similarity=0.096 Sum_probs=44.7
Q ss_pred CCCceeccceeEeeeccceEeeeeehhhhhcccCCCc--ccccccC-CcceEEEEEEEEeCCCceEEEE--eC----CCC
Q 032460 22 LSPISFPINHVKFNVNKEFVKITKIWTAIGAKKGGDR--SSEEGAN-SEKWVHEGFITESLPNGMFRVR--LD----NED 92 (140)
Q Consensus 22 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~k-~d~ie~~GvVik~l~n~~f~V~--l~----dG~ 92 (140)
+.+..+.|.|+-+++|+-- .|..+|.....-+ .+.-.|. +-...+.+++.++--.|..+.. ++ +|.
T Consensus 276 R~~l~y~iDGiViKvn~~~-----~~~~lG~t~~~PrWaiA~Kf~~~~~~T~l~~I~~qVGRTG~iTPVA~l~PV~l~G~ 350 (665)
T PRK07956 276 RHDLPYDIDGVVIKVDDLA-----LQEELGFTAKAPRWAIAYKFPAEEATTKLLDIEVQVGRTGAVTPVARLEPVEVAGV 350 (665)
T ss_pred hccCCCCCCcEEEEecCHH-----HHHhcCccCCCCCceeEecCCCceeEEEEEEEEEecCCCceeeeEEEEEeEEECCE
Confidence 4555677888888877632 2444443322222 1111222 2344577777776334444322 11 233
Q ss_pred EEEEEec----ccccccccccCCCCEEEEEec
Q 032460 93 LILGYIS----GKIRQNFIRVLPGDRVRVEVS 120 (140)
Q Consensus 93 ~~lcrI~----GKmRk~~IrI~vGDrV~VE~s 120 (140)
++ .++. .-+++ -.|.+||.|.|+-.
T Consensus 351 tV-srAtLhN~~~i~~--~~i~iGD~V~V~ra 379 (665)
T PRK07956 351 TV-SRATLHNADEIER--KDIRIGDTVVVRRA 379 (665)
T ss_pred EE-EEeecCCHHHHHH--cCCCCCCEEEEEEC
Confidence 32 1221 12222 23888999999854
No 277
>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=21.85 E-value=96 Score=23.19 Aligned_cols=29 Identities=31% Similarity=0.324 Sum_probs=20.1
Q ss_pred cccCCCCEEEEEeccCCC-------CeEEEEEEecC
Q 032460 107 IRVLPGDRVRVEVSRYDT-------SKGRIIYRLRN 135 (140)
Q Consensus 107 IrI~vGDrV~VE~sp~D~-------~kGrIiyRy~r 135 (140)
-.+.+||.|.|....-+. -.|.++.+..+
T Consensus 17 p~f~~GD~v~V~~~i~e~~k~r~q~f~GvvIa~~~~ 52 (113)
T PF01245_consen 17 PEFRVGDTVRVTYKISEGNKERIQVFEGVVIARRRR 52 (113)
T ss_dssp SSSSSSSEEEEEEEEESSSSEEEEEEEEEEEEEEBS
T ss_pred CCcCCCCEEEEEEEEecCCCceeEEEEEEEEEEECC
Confidence 358999999999753322 34777777654
No 278
>PRK09774 fec operon regulator FecR; Reviewed
Probab=21.78 E-value=1.8e+02 Score=24.50 Aligned_cols=47 Identities=15% Similarity=0.077 Sum_probs=33.6
Q ss_pred EEEEEEEeCCCceEEEEeCCCCEEEEEecccccc-------cccccCCCCEEEEE
Q 032460 71 HEGFITESLPNGMFRVRLDNEDLILGYISGKIRQ-------NFIRVLPGDRVRVE 118 (140)
Q Consensus 71 ~~GvVik~l~n~~f~V~l~dG~~~lcrI~GKmRk-------~~IrI~vGDrV~VE 118 (140)
..+.-++.+ |+.|.|...++....+-..|+.+. ..+.+.+|+.+.+.
T Consensus 172 t~~~~v~vl-GT~F~V~~~~~~~~V~V~eG~V~v~~~~~~~~~~~L~~Gq~~~~~ 225 (319)
T PRK09774 172 TRQGQLTAL-GTEFTVRQQDNFTQLAVQQHAVEVLLASAPAQKRIVNAGESLQFS 225 (319)
T ss_pred eCCcEEEEe-eeEEEEEEcCCCceEEEEEEEEEEEECCCCCcceEECCCcEEEEc
Confidence 344456666 889999987777777778888764 13458899998764
No 279
>PRK11507 ribosome-associated protein; Provisional
Probab=21.65 E-value=59 Score=22.68 Aligned_cols=12 Identities=17% Similarity=0.484 Sum_probs=9.3
Q ss_pred cccCCCCEEEEE
Q 032460 107 IRVLPGDRVRVE 118 (140)
Q Consensus 107 IrI~vGDrV~VE 118 (140)
-++.+||.|.+.
T Consensus 51 kKl~~GD~V~~~ 62 (70)
T PRK11507 51 CKIVAGQTVSFA 62 (70)
T ss_pred CCCCCCCEEEEC
Confidence 358899999773
No 280
>PRK12370 invasion protein regulator; Provisional
Probab=21.61 E-value=74 Score=28.63 Aligned_cols=35 Identities=17% Similarity=0.280 Sum_probs=26.2
Q ss_pred EecccccccccccCCCCEEEEEeccCCCCeEEEEE--EecCCC
Q 032460 97 YISGKIRQNFIRVLPGDRVRVEVSRYDTSKGRIIY--RLRNKI 137 (140)
Q Consensus 97 rI~GKmRk~~IrI~vGDrV~VE~sp~D~~kGrIiy--Ry~r~~ 137 (140)
-+.|.+|+. ||+|.|...-.|...|.++| ||.+..
T Consensus 185 vl~Gsvrr~------g~~vri~~qLida~~~~~~w~~~~d~~~ 221 (553)
T PRK12370 185 YISGQMIPD------GNDNIVQIEIVRVKGYHLLHQESIKLIE 221 (553)
T ss_pred EEEeEEEEc------CCEEEEEEEEEecCCCcEEehhhccccc
Confidence 466777764 89998887777777888886 777653
No 281
>PRK10800 acyl-CoA thioesterase YbgC; Provisional
Probab=21.34 E-value=1.1e+02 Score=21.69 Aligned_cols=20 Identities=10% Similarity=-0.027 Sum_probs=11.3
Q ss_pred cCCCCEEEEEeccCCCCeEE
Q 032460 109 VLPGDRVRVEVSRYDTSKGR 128 (140)
Q Consensus 109 I~vGDrV~VE~sp~D~~kGr 128 (140)
+..||.|.|+.+....++..
T Consensus 67 ~~~~d~i~v~t~v~~~~~~s 86 (130)
T PRK10800 67 ARLDDMLEVQSEITSMRGTS 86 (130)
T ss_pred ccCCCEEEEEEEEEeeCcEE
Confidence 44566666666655544443
No 282
>PF07116 DUF1372: Protein of unknown function (DUF1372); InterPro: IPR010779 This entry is represented by Streptococcus phage Sfi11, Gp93. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family consists of several Streptococcus bacteriophage sequences and related proteins from Streptococcus species. Members of this family are typically around 100 residues in length and their function is unknown.
Probab=21.28 E-value=2.1e+02 Score=21.63 Aligned_cols=44 Identities=16% Similarity=0.354 Sum_probs=28.7
Q ss_pred CcceEEEEEEEEe-CCCceEEEEeCC-CCEEEEEecccccccccccCCCCEE
Q 032460 66 SEKWVHEGFITES-LPNGMFRVRLDN-EDLILGYISGKIRQNFIRVLPGDRV 115 (140)
Q Consensus 66 ~d~ie~~GvVik~-l~n~~f~V~l~d-G~~~lcrI~GKmRk~~IrI~vGDrV 115 (140)
.-..+|.|+|++- .-++.|+|.|.+ |+-+.. +-+.-.+.+||-|
T Consensus 53 N~G~ei~GkVt~K~~ig~~yTvti~~YGkFlVt------keqY~~i~iGDdi 98 (104)
T PF07116_consen 53 NAGAEIFGKVTEKEIIGGLYTVTIGAYGKFLVT------KEQYESIKIGDDI 98 (104)
T ss_pred CCCcEEEEEEeeceeECCEEEEEecCceEEEEe------hhhcceeecCCcc
Confidence 3346899999863 238999998865 544332 2233458889876
No 283
>PRK05889 putative acetyl-CoA carboxylase biotin carboxyl carrier protein subunit; Provisional
Probab=21.12 E-value=53 Score=21.55 Aligned_cols=20 Identities=20% Similarity=0.365 Sum_probs=9.6
Q ss_pred EEEEecccccccccccCCCCEE
Q 032460 94 ILGYISGKIRQNFIRVLPGDRV 115 (140)
Q Consensus 94 ~lcrI~GKmRk~~IrI~vGDrV 115 (140)
+.+.++|++.+ +.+.+||.|
T Consensus 5 v~a~~~G~i~~--~~v~~Gd~V 24 (71)
T PRK05889 5 VRAEIVASVLE--VVVNEGDQI 24 (71)
T ss_pred EeCCCCEEEEE--EEeCCCCEE
Confidence 45555666554 233444443
No 284
>PF10610 Tafi-CsgC: Thin aggregative fimbriae synthesis protein; InterPro: IPR014491 Thin aggressive fibres known as curli fibres or fimbriae (curli; Tafi) are cell-surface protein polymers found in Salmonella typhimurium and Escherichia coli that mediate interactions important for host and environmental persistence, development of biofilms, motility, colonisation and invasion of cells, and conjugation []. Four general assembly pathways for different fimbriae have been proposed, one of which is extracellular nucleation-precipitation (ENP), which differs from the others in that fibre-growth occurs extracellularly. Thin aggregative fimbriae are the only fimbriae dependent on the ENP pathway. Tafi were first identified in Salmonella spp and the controlling operon termed agf; however subsequent isolation of the homologous operon in E coli led to its being called csg. Tafi are known as curli because, in the absence of extracellular polysaccharides, their morphology appears curled; however, when expressed with such polysaccharides their morphology appears as a tangled amorphous matrix. The gene agfC is found to be transcribed at low levels, localised to the periplasm in a mature form, and in combination with AgfE is important for AgfA extracellular assembly, which facilitates the synthesis of Tafi. The genes involved in Tafi production are organised into two adjacent divergently transcribed operons, agfBAC and agfDEFG, both of which are required for biosynthesis and assembly [].; PDB: 2XSK_A 2Y2T_A 2Y2Y_A.
Probab=21.04 E-value=94 Score=23.51 Aligned_cols=33 Identities=18% Similarity=0.323 Sum_probs=18.2
Q ss_pred ccccccccccCCCCEEEEEeccCCCCeEEEEEEecC
Q 032460 100 GKIRQNFIRVLPGDRVRVEVSRYDTSKGRIIYRLRN 135 (140)
Q Consensus 100 GKmRk~~IrI~vGDrV~VE~sp~D~~kGrIiyRy~r 135 (140)
|||.. -|.+||.|.+.++--|-.+-...++.+.
T Consensus 69 ~rls~---ni~p~D~v~I~VtvSDG~sl~LsqQw~~ 101 (106)
T PF10610_consen 69 SRLSF---NISPGDKVKIIVTVSDGKSLHLSQQWPP 101 (106)
T ss_dssp --EEE---E--TT-EEEEEEEEE-SSS-EEEEEE--
T ss_pred ceEEE---EeCCCCeEEEEEEEcCCCeEEeEeccCC
Confidence 44444 4899999998887777777777777744
No 285
>TIGR02228 sigpep_I_arch signal peptidase I, archaeal type. This model represents signal peptidase I from most archaea, a subunit of the eukaryotic endoplasmic reticulum signal peptidase I complex, and an apparent signal peptidase I from a small number of bacteria. It is related to but does not overlap in hits with TIGR02227, the bacterial and mitochondrial signal peptidase I.
Probab=20.75 E-value=88 Score=24.31 Aligned_cols=12 Identities=17% Similarity=0.299 Sum_probs=8.8
Q ss_pred ccCCCCEEEEEe
Q 032460 108 RVLPGDRVRVEV 119 (140)
Q Consensus 108 rI~vGDrV~VE~ 119 (140)
.+..||.|.+..
T Consensus 60 ~~~~GDIVvf~~ 71 (158)
T TIGR02228 60 DIQVGDVITYKS 71 (158)
T ss_pred CCCCCCEEEEEE
Confidence 467789888763
No 286
>PTZ00085 40S ribosomal protein S28; Provisional
Probab=20.53 E-value=3.2e+02 Score=19.37 Aligned_cols=40 Identities=20% Similarity=0.354 Sum_probs=23.1
Q ss_pred EEEEEEeCC-----CceEEEEe--CC-----CCEEEEEecccccccccccCCCCEEEEE
Q 032460 72 EGFITESLP-----NGMFRVRL--DN-----EDLILGYISGKIRQNFIRVLPGDRVRVE 118 (140)
Q Consensus 72 ~GvVik~l~-----n~~f~V~l--~d-----G~~~lcrI~GKmRk~~IrI~vGDrV~VE 118 (140)
.+.|++++| +....|+| -+ |..++..++|=.| +||.+.+.
T Consensus 12 ~A~VikVlGRTG~~G~~tQVrv~~l~~~~d~~r~i~RNVkGPVr-------~GDIl~L~ 63 (73)
T PTZ00085 12 LAKVIKVLGRTGSRGGVTQVRVQLMGEEGDAGRTLIRNVKGPVR-------EGDILSLM 63 (73)
T ss_pred eEEEEEEeccccCcccEEEEEEEEccCCcccCcEEEEeccCCcc-------cCcEEeeh
Confidence 356666654 44444444 22 4566666666554 49998653
No 287
>TIGR00998 8a0101 efflux pump membrane protein (multidrug resistance protein A).
Probab=20.43 E-value=3e+02 Score=22.56 Aligned_cols=51 Identities=12% Similarity=0.104 Sum_probs=32.0
Q ss_pred ceEEEEeCCCCEEEEEecccccccccccCCCCEEEEEeccCC-C--CeEEEEEEecC
Q 032460 82 GMFRVRLDNEDLILGYISGKIRQNFIRVLPGDRVRVEVSRYD-T--SKGRIIYRLRN 135 (140)
Q Consensus 82 ~~f~V~l~dG~~~lcrI~GKmRk~~IrI~vGDrV~VE~sp~D-~--~kGrIiyRy~r 135 (140)
..+.+...+.-.+.+.++-+--. +|.+|+.|.|.++.|. . -+|.|.+.-+.
T Consensus 231 ~l~~i~~~~~~~v~~~v~e~~~~---~i~~G~~v~v~~~~~~~~~~~~G~V~~Is~~ 284 (334)
T TIGR00998 231 PLMAVVPAEQMYVEANFKETQLK---NVRIGQPVTIRSDLYGSDVVFEGKVTGISMG 284 (334)
T ss_pred eeEEEEcCCcEEEEEecCHHHHh---hCCCCCEEEEEEecCCCCCEEEEEEEEECCC
Confidence 34555444555666777644332 4788999999876554 1 36888877653
No 288
>PRK10409 hydrogenase assembly chaperone; Provisional
Probab=20.30 E-value=1.5e+02 Score=21.51 Aligned_cols=42 Identities=14% Similarity=-0.143 Sum_probs=24.2
Q ss_pred EEEEEEeCCCceEEEEeCCCCEEEEEecccccccc----cccCCCCEEEEE
Q 032460 72 EGFITESLPNGMFRVRLDNEDLILGYISGKIRQNF----IRVLPGDRVRVE 118 (140)
Q Consensus 72 ~GvVik~l~n~~f~V~l~dG~~~lcrI~GKmRk~~----IrI~vGDrV~VE 118 (140)
-|+|+++- ++.-.|. ..|..+...+. ..-. -.+.+||+|+|-
T Consensus 6 P~kVv~i~-~~~A~vd-~~Gv~reV~l~---Lv~~~~~~~~~~vGDyVLVH 51 (90)
T PRK10409 6 PGQIRTID-GNQAKVD-VCGIQRDVDLT---LVGSCDENGQPRVGQWVLVH 51 (90)
T ss_pred ceEEEEEc-CCeEEEE-cCCeEEEEEEe---eecccCCCCccCCCCEEEEe
Confidence 47888874 4443333 45666665543 1100 036899999984
No 289
>COG3908 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=20.13 E-value=1.7e+02 Score=20.81 Aligned_cols=26 Identities=27% Similarity=0.471 Sum_probs=20.9
Q ss_pred EEEeCCCceEEEEeCCCCEEEEEecccc
Q 032460 75 ITESLPNGMFRVRLDNEDLILGYISGKI 102 (140)
Q Consensus 75 Vik~l~n~~f~V~l~dG~~~lcrI~GKm 102 (140)
|++-| +|.|.|. .-|.-++|-+.||-
T Consensus 14 ~iryl-dgdf~vv-~~GsfV~CAVtgk~ 39 (77)
T COG3908 14 VIRYL-DGDFQVV-SPGSFVLCAVTGKP 39 (77)
T ss_pred EEEEe-cCceEEE-cCCcEEEEEecCCc
Confidence 55666 8889995 67899999999983
No 290
>KOG1999 consensus RNA polymerase II transcription elongation factor DSIF/SUPT5H/SPT5 [Transcription]
Probab=20.13 E-value=2.7e+02 Score=28.45 Aligned_cols=26 Identities=31% Similarity=0.569 Sum_probs=21.7
Q ss_pred cCCCCEEEEEeccCCCCeEEEEEEec
Q 032460 109 VLPGDRVRVEVSRYDTSKGRIIYRLR 134 (140)
Q Consensus 109 I~vGDrV~VE~sp~D~~kGrIiyRy~ 134 (140)
+.+||.|+|.-=+|.-..|.|+--+.
T Consensus 460 F~~GDhVKVi~G~~eG~tGlVvrVe~ 485 (1024)
T KOG1999|consen 460 FEPGDHVKVIAGRYEGDTGLVVRVEQ 485 (1024)
T ss_pred ccCCCeEEEEeccccCCcceEEEEeC
Confidence 88999999988788888899886543
No 291
>PF06068 TIP49: TIP49 C-terminus; InterPro: IPR010339 This family consists of the C-terminal region of several eukaryotic and archaeal RuvB-like 1 (Pontin or TIP49a) and RuvB-like 2 (Reptin or TIP49b) proteins. The N-terminal domain contains the AAA ATPase, central region IPR003959 from INTERPRO domain. In zebrafish, the liebeskummer (lik) mutation, causes development of hyperplastic embryonic hearts. lik encodes Reptin, a component of a DNA-stimulated ATPase complex. Beta-catenin and Pontin, a DNA-stimulated ATPase that is often part of complexes with Reptin, are in the same genetic pathways. The Reptin/Pontin ratio serves to regulate heart growth during development, at least in part via the beta-catenin pathway []. TBP-interacting protein 49 (TIP49) was originally identified as a TBP-binding protein, and two related proteins are encoded by individual genes, tip49a and b. Although the function of this gene family has not been elucidated, they are supposed to play a critical role in nuclear events because they interact with various kinds of nuclear factors and have DNA helicase activities. TIP49a has been suggested to act as an autoantigen in some patients with autoimmune diseases [].; GO: 0003678 DNA helicase activity, 0005524 ATP binding; PDB: 2XSZ_E 2CQA_A 2C9O_C.
Probab=20.03 E-value=1.5e+02 Score=27.09 Aligned_cols=60 Identities=23% Similarity=0.281 Sum_probs=34.3
Q ss_pred CCcceEEEEEEEEeCCC--------------ceEEEEeCCCCEEEEEeccccccccc--ccCCCCEEEEEeccCCCCeEE
Q 032460 65 NSEKWVHEGFITESLPN--------------GMFRVRLDNEDLILGYISGKIRQNFI--RVLPGDRVRVEVSRYDTSKGR 128 (140)
Q Consensus 65 k~d~ie~~GvVik~l~n--------------~~f~V~l~dG~~~lcrI~GKmRk~~I--rI~vGDrV~VE~sp~D~~kGr 128 (140)
++..-..+|.|+++... +....+..|+ +..-.+..+|-.+-+ +|.+||++.++ .+.|.
T Consensus 112 kE~~eV~EGeVvei~~~~~~~~~~~~~~~~~~~i~LkT~~~-~~~l~l~~~i~~~l~kekV~~GDVI~Id-----~~tG~ 185 (398)
T PF06068_consen 112 KEEKEVYEGEVVEIKIEEAENPLNYGKTIKHGKITLKTTDM-EKTLKLGPKIYEQLQKEKVRVGDVIYID-----KNTGR 185 (398)
T ss_dssp EEEECEEEEEEEEEEE---E-TTS-SSSS-EEEEEEEETTC-EEEEEE-CHHHHHHHHTT--TTCEEEEE-----TTTTE
T ss_pred EEEEEEEEEEEEEEEEeeccCccccCCcceEEEEEEEEcCC-ceEecCCHHHHHHHHHhCCccCcEEEEE-----CCCCe
Confidence 34444588999988541 3334444443 445567777765433 49999999885 34566
Q ss_pred EE
Q 032460 129 II 130 (140)
Q Consensus 129 Ii 130 (140)
|.
T Consensus 186 V~ 187 (398)
T PF06068_consen 186 VK 187 (398)
T ss_dssp EE
T ss_pred EE
Confidence 65
Done!