Query psy3654
Match_columns 140
No_of_seqs 153 out of 1078
Neff 5.5
Searched_HMMs 46136
Date Fri Aug 16 22:14:24 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy3654.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/3654hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG1278 CspC Cold shock protei 99.9 2.8E-23 6E-28 139.8 7.7 65 58-125 1-67 (67)
2 PRK10943 cold shock-like prote 99.9 1.8E-22 3.9E-27 136.1 8.6 65 58-125 3-69 (69)
3 PRK15464 cold shock-like prote 99.9 2.8E-22 6.1E-27 135.9 9.2 63 59-124 5-69 (70)
4 PRK09937 stationary phase/star 99.9 3.1E-22 6.6E-27 136.9 8.9 66 58-126 1-68 (74)
5 TIGR02381 cspD cold shock doma 99.9 2.5E-22 5.4E-27 134.9 8.2 65 58-125 1-67 (68)
6 PRK10354 RNA chaperone/anti-te 99.9 4.6E-22 9.9E-27 134.3 9.5 64 59-125 5-70 (70)
7 PRK09507 cspE cold shock prote 99.9 3.8E-22 8.2E-27 134.5 8.9 65 58-125 3-69 (69)
8 PRK15463 cold shock-like prote 99.9 5.5E-22 1.2E-26 134.3 9.0 63 59-124 5-69 (70)
9 PRK14998 cold shock-like prote 99.9 8.5E-22 1.8E-26 134.4 9.0 66 58-126 1-68 (73)
10 PRK09890 cold shock protein Cs 99.9 1.3E-21 2.8E-26 132.2 9.3 64 59-125 5-70 (70)
11 PF00313 CSD: 'Cold-shock' DNA 99.8 1E-20 2.2E-25 124.8 9.5 64 59-125 1-66 (66)
12 cd04458 CSP_CDS Cold-Shock Pro 99.8 6.2E-20 1.4E-24 120.7 8.3 63 59-124 1-65 (65)
13 KOG3070|consensus 99.5 1.6E-14 3.5E-19 117.6 6.5 99 32-138 31-136 (235)
14 smart00357 CSP Cold shock prot 99.1 9.1E-10 2E-14 70.0 8.1 63 60-125 1-64 (64)
15 PF08206 OB_RNB: Ribonuclease 98.0 1.8E-05 3.8E-10 51.3 5.1 57 61-123 1-57 (58)
16 PF14444 S1-like: S1-like 97.9 8.9E-05 1.9E-09 48.8 7.0 54 58-119 3-56 (58)
17 PF07497 Rho_RNA_bind: Rho ter 96.6 0.0053 1.1E-07 42.5 4.9 65 59-126 3-72 (78)
18 PRK11642 exoribonuclease R; Pr 96.2 0.019 4E-07 54.4 7.6 67 57-129 83-149 (813)
19 TIGR00358 3_prime_RNase VacB a 95.9 0.043 9.3E-07 50.5 8.6 66 57-128 15-81 (654)
20 cd04459 Rho_CSD Rho_CSD: Rho p 95.8 0.04 8.6E-07 37.2 5.9 46 61-109 3-53 (68)
21 PRK05054 exoribonuclease II; P 95.6 0.054 1.2E-06 49.9 7.8 63 57-128 20-82 (644)
22 PF00575 S1: S1 RNA binding do 95.5 0.08 1.7E-06 34.3 6.6 56 54-112 3-64 (74)
23 TIGR02062 RNase_B exoribonucle 95.4 0.069 1.5E-06 49.2 7.9 63 56-127 16-78 (639)
24 cd04461 S1_Rrp5_repeat_hs8_sc7 95.3 0.09 2E-06 35.3 6.4 57 53-112 12-74 (83)
25 cd05696 S1_Rrp5_repeat_hs4 S1_ 95.3 0.12 2.6E-06 34.0 6.8 57 56-114 1-64 (71)
26 cd05698 S1_Rrp5_repeat_hs6_sc5 95.2 0.09 1.9E-06 33.8 5.9 54 56-112 1-60 (70)
27 cd04453 S1_RNase_E S1_RNase_E: 95.0 0.23 5E-06 34.4 7.8 63 54-117 6-77 (88)
28 smart00316 S1 Ribosomal protei 94.9 0.18 3.9E-06 31.2 6.6 55 55-112 2-62 (72)
29 TIGR02063 RNase_R ribonuclease 94.8 0.12 2.7E-06 47.9 7.8 67 57-128 67-134 (709)
30 cd05706 S1_Rrp5_repeat_sc10 S1 94.7 0.25 5.5E-06 32.0 7.1 55 55-112 3-63 (73)
31 cd05694 S1_Rrp5_repeat_hs2_sc2 94.6 0.2 4.4E-06 33.5 6.6 55 55-112 4-59 (74)
32 cd05692 S1_RPS1_repeat_hs4 S1_ 94.5 0.49 1.1E-05 29.4 7.9 53 56-111 1-59 (69)
33 cd04465 S1_RPS1_repeat_ec2_hs2 94.3 0.2 4.3E-06 32.2 5.8 53 56-112 1-57 (67)
34 PRK08582 hypothetical protein; 94.3 0.68 1.5E-05 34.8 9.5 70 55-129 5-80 (139)
35 PF13509 S1_2: S1 domain; PDB: 94.2 0.16 3.4E-06 32.9 5.1 58 56-120 2-59 (61)
36 cd05707 S1_Rrp5_repeat_sc11 S1 94.0 0.36 7.9E-06 30.9 6.5 54 56-112 1-60 (68)
37 cd05705 S1_Rrp5_repeat_hs14 S1 93.9 0.31 6.7E-06 32.5 6.3 55 55-112 3-66 (74)
38 cd05697 S1_Rrp5_repeat_hs5 S1_ 93.9 0.37 8.1E-06 31.0 6.5 54 56-112 1-60 (69)
39 cd05691 S1_RPS1_repeat_ec6 S1_ 93.8 0.4 8.6E-06 30.7 6.5 54 56-112 1-60 (73)
40 cd05689 S1_RPS1_repeat_ec4 S1_ 93.7 0.75 1.6E-05 29.6 7.8 55 55-112 3-64 (72)
41 cd04472 S1_PNPase S1_PNPase: P 93.4 0.84 1.8E-05 28.6 7.4 54 56-112 1-60 (68)
42 cd05703 S1_Rrp5_repeat_hs12_sc 93.4 0.41 8.8E-06 31.7 6.1 54 56-112 1-62 (73)
43 cd00164 S1_like S1_like: Ribos 93.1 0.49 1.1E-05 28.7 5.8 50 60-112 2-57 (65)
44 cd05684 S1_DHX8_helicase S1_DH 93.1 1.3 2.9E-05 29.1 8.4 64 56-125 1-74 (79)
45 cd05686 S1_pNO40 S1_pNO40: pNO 93.1 1.2 2.6E-05 29.1 8.1 55 55-112 3-64 (73)
46 cd05690 S1_RPS1_repeat_ec5 S1_ 93.0 0.74 1.6E-05 29.2 6.7 54 56-112 1-61 (69)
47 cd05685 S1_Tex S1_Tex: The C-t 92.4 0.9 1.9E-05 28.2 6.5 54 56-112 1-60 (68)
48 cd05704 S1_Rrp5_repeat_hs13 S1 92.4 1.6 3.5E-05 28.6 8.0 55 55-111 3-63 (72)
49 cd04452 S1_IF2_alpha S1_IF2_al 92.0 1.2 2.7E-05 28.7 7.0 55 55-112 3-65 (76)
50 PRK05807 hypothetical protein; 92.0 2 4.4E-05 32.1 9.0 66 55-126 5-76 (136)
51 PRK07252 hypothetical protein; 91.9 1.4 3E-05 32.4 7.8 55 55-112 3-63 (120)
52 COG1098 VacB Predicted RNA bin 91.9 0.39 8.4E-06 36.2 4.9 72 55-131 5-82 (129)
53 cd04455 S1_NusA S1_NusA: N-uti 91.5 1.4 2.9E-05 28.5 6.7 54 55-112 3-56 (67)
54 cd04473 S1_RecJ_like S1_RecJ_l 90.9 2.6 5.7E-05 27.9 7.8 53 53-110 14-66 (77)
55 cd05695 S1_Rrp5_repeat_hs3 S1_ 90.6 1.4 3E-05 28.5 6.1 55 56-113 1-59 (66)
56 cd05687 S1_RPS1_repeat_ec1_hs1 90.6 1.6 3.4E-05 27.9 6.3 53 56-111 1-59 (70)
57 PRK08059 general stress protei 90.2 3 6.5E-05 30.3 8.2 71 55-129 7-83 (123)
58 PRK09376 rho transcription ter 90.1 1.1 2.3E-05 39.9 6.7 67 58-127 50-121 (416)
59 PHA02945 interferon resistance 88.7 5.2 0.00011 28.4 8.2 70 51-125 7-84 (88)
60 cd04471 S1_RNase_R S1_RNase_R: 88.3 3.9 8.4E-05 26.6 7.0 53 56-111 2-72 (83)
61 cd05789 S1_Rrp4 S1_Rrp4: Rrp4 88.0 5.9 0.00013 26.3 8.3 55 55-112 6-70 (86)
62 PRK09202 nusA transcription el 87.6 2 4.4E-05 38.5 6.9 61 55-119 134-194 (470)
63 COG1158 Rho Transcription term 87.6 1.7 3.6E-05 38.3 6.1 65 59-127 54-124 (422)
64 cd05702 S1_Rrp5_repeat_hs11_sc 87.5 3.2 7E-05 26.7 6.2 53 56-111 1-61 (70)
65 PTZ00248 eukaryotic translatio 87.4 3.1 6.7E-05 35.7 7.5 72 54-129 16-95 (319)
66 cd05708 S1_Rrp5_repeat_sc12 S1 86.7 5 0.00011 25.6 6.8 54 56-112 3-63 (77)
67 PRK07899 rpsA 30S ribosomal pr 86.1 4.6 0.0001 36.4 8.3 66 55-124 293-364 (486)
68 cd05688 S1_RPS1_repeat_ec3 S1_ 85.6 4.8 0.0001 24.9 6.1 53 56-112 2-60 (68)
69 PRK12608 transcription termina 85.6 0.93 2E-05 39.7 3.6 52 55-109 15-71 (380)
70 PLN00207 polyribonucleotide nu 85.2 5.2 0.00011 38.8 8.6 67 55-126 753-826 (891)
71 PRK13806 rpsA 30S ribosomal pr 85.1 6.1 0.00013 35.3 8.6 72 54-129 291-369 (491)
72 PRK13806 rpsA 30S ribosomal pr 84.3 4.9 0.00011 35.9 7.6 57 53-112 200-262 (491)
73 PRK07899 rpsA 30S ribosomal pr 82.9 6.6 0.00014 35.4 7.8 69 53-126 206-280 (486)
74 TIGR00757 RNaseEG ribonuclease 82.8 7.6 0.00016 34.3 8.0 72 53-125 23-113 (414)
75 PRK07400 30S ribosomal protein 82.4 8.4 0.00018 32.6 7.9 73 53-130 194-272 (318)
76 TIGR00767 rho transcription te 80.1 3 6.4E-05 37.1 4.5 50 57-109 49-103 (415)
77 PRK11824 polynucleotide phosph 79.4 14 0.00029 34.7 8.9 56 54-112 620-681 (693)
78 PRK12269 bifunctional cytidyla 79.1 6 0.00013 38.1 6.5 66 54-123 664-736 (863)
79 TIGR02696 pppGpp_PNP guanosine 78.9 7.8 0.00017 36.7 7.1 57 53-112 645-711 (719)
80 COG2996 Predicted RNA-bindinin 78.5 8.6 0.00019 32.6 6.6 62 55-122 5-67 (287)
81 TIGR03591 polynuc_phos polyrib 78.2 8.2 0.00018 36.1 7.0 56 54-112 617-678 (684)
82 PRK07400 30S ribosomal protein 77.6 7.3 0.00016 33.0 6.0 54 55-112 118-173 (318)
83 cd04460 S1_RpoE S1_RpoE: RpoE, 77.5 15 0.00033 25.3 6.7 51 58-112 2-69 (99)
84 PRK12678 transcription termina 76.7 6.5 0.00014 36.9 5.8 48 58-109 295-345 (672)
85 PRK12269 bifunctional cytidyla 76.2 13 0.00028 35.9 7.9 66 55-125 493-564 (863)
86 PRK06299 rpsA 30S ribosomal pr 75.4 13 0.00028 33.4 7.3 66 54-123 285-357 (565)
87 PRK06299 rpsA 30S ribosomal pr 75.3 18 0.00038 32.5 8.1 68 55-126 373-447 (565)
88 TIGR00717 rpsA ribosomal prote 75.1 15 0.00034 32.3 7.7 56 53-111 270-332 (516)
89 cd05693 S1_Rrp5_repeat_hs1_sc1 74.2 20 0.00044 25.2 6.7 55 55-112 3-82 (100)
90 TIGR00717 rpsA ribosomal prote 74.0 20 0.00044 31.6 8.1 69 53-125 357-432 (516)
91 PRK03987 translation initiatio 74.0 28 0.00062 28.8 8.5 70 53-126 6-83 (262)
92 PRK06676 rpsA 30S ribosomal pr 73.3 20 0.00042 30.6 7.6 58 53-112 15-78 (390)
93 TIGR01953 NusA transcription t 72.8 13 0.00027 32.1 6.3 61 54-117 130-190 (341)
94 COG4776 Rnb Exoribonuclease II 72.4 2.8 6.1E-05 38.3 2.3 48 56-109 19-66 (645)
95 cd04462 S1_RNAPII_Rpb7 S1_RNAP 72.1 26 0.00057 24.1 6.8 35 56-94 2-36 (88)
96 COG0539 RpsA Ribosomal protein 71.9 12 0.00027 34.3 6.3 73 53-129 275-353 (541)
97 PRK00087 4-hydroxy-3-methylbut 71.7 29 0.00063 32.1 8.8 72 54-129 561-638 (647)
98 PRK12327 nusA transcription el 71.1 15 0.00032 32.0 6.4 60 54-117 133-192 (362)
99 cd04454 S1_Rrp4_like S1_Rrp4_l 70.7 27 0.00059 22.9 6.7 56 54-112 5-66 (82)
100 PF05606 DUF777: Borrelia burg 70.4 6.4 0.00014 31.2 3.7 46 58-104 35-81 (181)
101 PRK06676 rpsA 30S ribosomal pr 70.2 37 0.0008 28.9 8.6 74 53-130 275-354 (390)
102 PRK08563 DNA-directed RNA poly 69.1 30 0.00065 26.6 7.2 55 53-111 79-150 (187)
103 COG1095 RPB7 DNA-directed RNA 68.6 14 0.00031 29.4 5.4 73 54-130 80-169 (183)
104 TIGR00448 rpoE DNA-directed RN 67.5 48 0.001 25.5 8.0 55 53-111 79-150 (179)
105 TIGR00358 3_prime_RNase VacB a 67.5 23 0.0005 32.8 7.2 54 55-111 572-643 (654)
106 COG0557 VacB Exoribonuclease R 65.2 17 0.00037 33.9 6.0 64 58-126 69-134 (706)
107 KOG0407|consensus 64.3 10 0.00022 28.4 3.5 60 55-126 11-87 (139)
108 COG0539 RpsA Ribosomal protein 62.8 30 0.00066 31.8 6.9 72 53-129 190-267 (541)
109 PRK11712 ribonuclease G; Provi 62.5 40 0.00087 30.5 7.6 73 53-126 36-127 (489)
110 TIGR02063 RNase_R ribonuclease 61.0 28 0.00061 32.4 6.6 55 55-112 627-699 (709)
111 COG1185 Pnp Polyribonucleotide 61.0 16 0.00035 34.5 5.0 58 52-112 616-679 (692)
112 PRK09838 periplasmic copper-bi 60.2 65 0.0014 23.6 7.3 64 58-124 44-113 (115)
113 PRK11642 exoribonuclease R; Pr 60.1 45 0.00097 32.0 7.8 55 55-112 643-715 (813)
114 TIGR01451 B_ant_repeat conserv 57.9 21 0.00045 22.3 3.7 32 97-130 8-39 (53)
115 PRK10811 rne ribonuclease E; R 56.5 50 0.0011 32.8 7.5 65 54-119 37-116 (1068)
116 PF01336 tRNA_anti-codon: OB-f 56.0 26 0.00057 21.8 4.0 49 59-107 3-55 (75)
117 PRK00087 4-hydroxy-3-methylbut 55.4 55 0.0012 30.3 7.4 66 54-124 476-547 (647)
118 COG2183 Tex Transcriptional ac 55.2 37 0.0008 32.7 6.3 71 53-127 656-732 (780)
119 PRK04163 exosome complex RNA-b 51.6 1.3E+02 0.0027 24.3 8.2 56 54-112 62-127 (235)
120 COG2190 NagE Phosphotransferas 50.9 33 0.00072 26.6 4.5 45 59-104 49-100 (156)
121 KOG0125|consensus 49.4 31 0.00068 30.2 4.5 24 56-80 121-146 (376)
122 PF01345 DUF11: Domain of unkn 47.0 39 0.00084 21.9 3.8 33 96-130 36-68 (76)
123 COG1093 SUI2 Translation initi 46.1 64 0.0014 27.3 5.8 71 51-125 7-85 (269)
124 COG5569 Uncharacterized conser 45.1 90 0.0019 22.8 5.7 24 97-123 84-107 (108)
125 PF11604 CusF_Ec: Copper bindi 43.4 93 0.002 20.4 7.7 26 96-124 42-68 (70)
126 PF03459 TOBE: TOBE domain; I 39.9 76 0.0017 19.5 4.3 53 58-110 6-60 (64)
127 cd00210 PTS_IIA_glc PTS_IIA, P 39.1 65 0.0014 23.8 4.3 44 59-104 42-93 (124)
128 COG1545 Predicted nucleic-acid 38.7 1.7E+02 0.0036 21.9 7.0 38 72-111 87-124 (140)
129 PRK05054 exoribonuclease II; P 37.8 1.2E+02 0.0025 28.3 6.7 35 57-94 563-598 (644)
130 TIGR00830 PTBA PTS system, glu 37.7 72 0.0016 23.5 4.4 45 59-104 42-93 (121)
131 PRK13168 rumA 23S rRNA m(5)U19 37.6 2.4E+02 0.0052 24.6 8.3 62 56-130 13-74 (443)
132 PF05670 DUF814: Domain of unk 37.5 27 0.00059 23.9 2.0 16 80-95 28-43 (90)
133 PLN00059 PsbP domain-containin 37.1 31 0.00067 29.3 2.6 27 61-87 108-140 (286)
134 KOG4246|consensus 36.5 3.5 7.6E-05 40.0 -3.4 63 56-126 146-208 (1194)
135 PRK09439 PTS system glucose-sp 34.5 83 0.0018 24.5 4.5 44 59-104 64-115 (169)
136 PF00358 PTS_EIIA_1: phosphoen 33.8 68 0.0015 23.9 3.8 45 59-104 46-97 (132)
137 KOG0149|consensus 33.6 22 0.00047 29.7 1.1 24 56-79 37-63 (247)
138 cd04487 RecJ_OBF2_like RecJ_OB 33.5 1.4E+02 0.0031 19.6 5.0 53 58-110 2-57 (73)
139 PF11948 DUF3465: Protein of u 33.2 1.5E+02 0.0033 22.4 5.5 53 60-112 42-103 (131)
140 cd01212 JIP JNK-interacting pr 33.0 46 0.001 25.3 2.8 26 67-92 89-114 (148)
141 PF01796 DUF35: DUF35 OB-fold 31.7 1.4E+02 0.0031 19.0 5.0 35 72-107 31-67 (68)
142 KOG3716|consensus 30.1 41 0.00089 32.1 2.4 26 68-93 707-732 (764)
143 smart00361 RRM_1 RNA recogniti 28.9 36 0.00079 21.7 1.4 13 67-79 34-46 (70)
144 cd04489 ExoVII_LU_OBF ExoVII_L 27.3 1.7E+02 0.0036 18.5 5.1 51 59-110 4-59 (78)
145 PF14506 CppA_N: CppA N-termin 27.0 74 0.0016 24.0 2.9 27 64-90 89-115 (125)
146 PTZ00162 DNA-directed RNA poly 26.5 77 0.0017 24.6 3.1 39 52-94 78-116 (176)
147 CHL00010 infA translation init 23.6 2.4E+02 0.0051 18.9 6.6 51 59-111 9-61 (78)
148 PRK12328 nusA transcription el 23.1 3.2E+02 0.0069 24.1 6.6 62 54-118 137-199 (374)
149 PF13037 DUF3898: Domain of un 23.1 36 0.00078 24.2 0.6 26 86-111 47-73 (91)
150 PRK09521 exosome complex RNA-b 22.8 3.6E+02 0.0078 20.7 6.4 55 54-111 63-133 (189)
151 PF01551 Peptidase_M23: Peptid 22.1 97 0.0021 20.7 2.6 48 58-105 19-71 (96)
152 PF08292 RNA_pol_Rbc25: RNA po 22.0 2.2E+02 0.0048 20.9 4.7 52 55-109 3-73 (122)
153 KOG0124|consensus 21.6 45 0.00098 29.9 1.0 13 67-79 249-261 (544)
154 cd01268 Numb Numb Phosphotyros 21.6 1E+02 0.0022 23.3 2.8 25 68-92 89-113 (138)
155 KOG4208|consensus 21.2 82 0.0018 25.8 2.3 19 61-79 75-101 (214)
No 1
>COG1278 CspC Cold shock proteins [Transcription]
Probab=99.89 E-value=2.8e-23 Score=139.82 Aligned_cols=65 Identities=35% Similarity=0.592 Sum_probs=59.3
Q ss_pred eeeeEEEEeeCCCceeEEecCCCCCeEEEEEccccCC-C-cCCCCCEEEEEEEecCCCCCCceEEEEEec
Q psy3654 58 VETGKIKEFCRSKGHGFITPDSGEPAVFVHISDIEGC-Y-VPLPGDEVKYRLCPIPPKFEKNQAVHVEIV 125 (140)
Q Consensus 58 ~~~G~VK~f~~~KGfGFI~~~~g~~dIFfH~s~l~~~-~-~~l~Gd~V~F~v~~~~k~~~g~~A~~V~~~ 125 (140)
+.+|+|||||..||||||++++|++|||||+|+|+.. + .+.+||+|+|++..++ +|++|.||+++
T Consensus 1 ~~~GtVKwfn~~KGfGFI~p~~G~~DvFVH~Sai~~~g~~~L~eGQ~V~f~~~~g~---kgp~A~nv~~~ 67 (67)
T COG1278 1 MATGTVKWFNATKGFGFITPEDGGKDVFVHISAIQRAGFRTLREGQKVEFEVEQGR---KGPSAANVRAL 67 (67)
T ss_pred CCcceEEEeeCCCcceEcCCCCCCcCEEEEeeeeccCCCcccCCCCEEEEEEecCC---CCCceeEEEeC
Confidence 4679999999999999999999999999999999876 4 5669999999999998 59999999864
No 2
>PRK10943 cold shock-like protein CspC; Provisional
Probab=99.88 E-value=1.8e-22 Score=136.07 Aligned_cols=65 Identities=37% Similarity=0.598 Sum_probs=59.0
Q ss_pred eeeeEEEEeeCCCceeEEecCCCCCeEEEEEccccCC-C-cCCCCCEEEEEEEecCCCCCCceEEEEEec
Q psy3654 58 VETGKIKEFCRSKGHGFITPDSGEPAVFVHISDIEGC-Y-VPLPGDEVKYRLCPIPPKFEKNQAVHVEIV 125 (140)
Q Consensus 58 ~~~G~VK~f~~~KGfGFI~~~~g~~dIFfH~s~l~~~-~-~~l~Gd~V~F~v~~~~k~~~g~~A~~V~~~ 125 (140)
.++|+|||||.+||||||+++++++|||||+++|... + .+.+||.|+|++..++ +|++|.+|+.+
T Consensus 3 ~~~G~Vk~f~~~kGfGFI~~~~g~~dvFvH~s~l~~~g~~~l~~G~~V~f~~~~~~---~g~~A~~V~~~ 69 (69)
T PRK10943 3 KIKGQVKWFNESKGFGFITPADGSKDVFVHFSAIQGNGFKTLAEGQNVEFEIQDGQ---KGPAAVNVTAI 69 (69)
T ss_pred ccceEEEEEeCCCCcEEEecCCCCeeEEEEhhHccccCCCCCCCCCEEEEEEEECC---CCceeEEEEcC
Confidence 5789999999999999999999999999999999986 4 4669999999999988 48999999864
No 3
>PRK15464 cold shock-like protein CspH; Provisional
Probab=99.88 E-value=2.8e-22 Score=135.87 Aligned_cols=63 Identities=35% Similarity=0.465 Sum_probs=57.9
Q ss_pred eeeEEEEeeCCCceeEEecCCCCCeEEEEEccccCC-C-cCCCCCEEEEEEEecCCCCCCceEEEEEe
Q psy3654 59 ETGKIKEFCRSKGHGFITPDSGEPAVFVHISDIEGC-Y-VPLPGDEVKYRLCPIPPKFEKNQAVHVEI 124 (140)
Q Consensus 59 ~~G~VK~f~~~KGfGFI~~~~g~~dIFfH~s~l~~~-~-~~l~Gd~V~F~v~~~~k~~~g~~A~~V~~ 124 (140)
++|+|||||.+||||||+++++++|||||+++|... + .+.+||.|+|++.+++ +|++|.+|++
T Consensus 5 ~~G~Vk~fn~~KGfGFI~~~~g~~DvFvH~s~l~~~g~~~l~~G~~V~f~v~~~~---kG~~A~~v~~ 69 (70)
T PRK15464 5 MTGIVKTFDRKSGKGFIIPSDGRKEVQVHISAFTPRDAEVLIPGLRVEFCRVNGL---RGPTAANVYL 69 (70)
T ss_pred ceEEEEEEECCCCeEEEccCCCCccEEEEehhehhcCCCCCCCCCEEEEEEEECC---CCceeEEEEc
Confidence 489999999999999999999999999999999866 5 5779999999999998 4999999975
No 4
>PRK09937 stationary phase/starvation inducible regulatory protein CspD; Provisional
Probab=99.88 E-value=3.1e-22 Score=136.95 Aligned_cols=66 Identities=33% Similarity=0.553 Sum_probs=59.8
Q ss_pred eeeeEEEEeeCCCceeEEecCCCCCeEEEEEccccCC-C-cCCCCCEEEEEEEecCCCCCCceEEEEEecC
Q psy3654 58 VETGKIKEFCRSKGHGFITPDSGEPAVFVHISDIEGC-Y-VPLPGDEVKYRLCPIPPKFEKNQAVHVEIVH 126 (140)
Q Consensus 58 ~~~G~VK~f~~~KGfGFI~~~~g~~dIFfH~s~l~~~-~-~~l~Gd~V~F~v~~~~k~~~g~~A~~V~~~~ 126 (140)
|.+|+|||||.+||||||+++++++|||||+++|... + .+.+||.|+|++..+++ |.+|.+|..+.
T Consensus 1 M~~G~Vkwfn~~KGfGFI~~~~gg~dVFvH~s~i~~~g~~~l~~G~~V~f~~~~~~~---G~~A~~V~~~~ 68 (74)
T PRK09937 1 MEKGTVKWFNNAKGFGFICPEGGGEDIFAHYSTIQMDGYRTLKAGQSVQFDVHQGPK---GNHASVIVPVE 68 (74)
T ss_pred CCCeEEEEEeCCCCeEEEeeCCCCccEEEEEeeccccCCCCCCCCCEEEEEEEECCC---CceeeEEEECC
Confidence 3579999999999999999999999999999999876 4 56699999999999984 89999999883
No 5
>TIGR02381 cspD cold shock domain protein CspD. This model represents what appears to be a phylogenetically distinct clade, containing E. coli CspD and related proteobacterial proteins within the larger family of cold shock domain proteins described by pfam model pfam00313. The gene symbol cspD may have been used idependently for other subfamilies of cold shock domain proteins, such as for B. subtilis CspD. These proteins typically are shorter than 70 amino acids. In E. coli, CspD is a stress response protein induced in stationary phase. This homodimer binds single-stranded DNA and appears to inhibit DNA replication.
Probab=99.88 E-value=2.5e-22 Score=134.86 Aligned_cols=65 Identities=29% Similarity=0.536 Sum_probs=58.8
Q ss_pred eeeeEEEEeeCCCceeEEecCCCCCeEEEEEccccCC-C-cCCCCCEEEEEEEecCCCCCCceEEEEEec
Q psy3654 58 VETGKIKEFCRSKGHGFITPDSGEPAVFVHISDIEGC-Y-VPLPGDEVKYRLCPIPPKFEKNQAVHVEIV 125 (140)
Q Consensus 58 ~~~G~VK~f~~~KGfGFI~~~~g~~dIFfH~s~l~~~-~-~~l~Gd~V~F~v~~~~k~~~g~~A~~V~~~ 125 (140)
|.+|+|||||.+||||||+++++++|||||+|+|... + .+.+||.|+|++..++ +|++|.+|+.+
T Consensus 1 m~~G~Vk~f~~~kGfGFI~~~~g~~dvfvH~s~~~~~g~~~l~~G~~V~f~~~~~~---~G~~A~~V~~~ 67 (68)
T TIGR02381 1 MAIGIVKWFNNAKGFGFICPEGVDGDIFAHYSTIQMDGYRTLKAGQKVQFEVVQGP---KGAHATHIVPI 67 (68)
T ss_pred CCCeEEEEEeCCCCeEEEecCCCCccEEEEHHHhhhcCCCCCCCCCEEEEEEEECC---CCceeEEEEEC
Confidence 3579999999999999999999999999999999875 4 4669999999999998 49999999865
No 6
>PRK10354 RNA chaperone/anti-terminator; Provisional
Probab=99.88 E-value=4.6e-22 Score=134.27 Aligned_cols=64 Identities=38% Similarity=0.522 Sum_probs=58.1
Q ss_pred eeeEEEEeeCCCceeEEecCCCCCeEEEEEccccCC-C-cCCCCCEEEEEEEecCCCCCCceEEEEEec
Q psy3654 59 ETGKIKEFCRSKGHGFITPDSGEPAVFVHISDIEGC-Y-VPLPGDEVKYRLCPIPPKFEKNQAVHVEIV 125 (140)
Q Consensus 59 ~~G~VK~f~~~KGfGFI~~~~g~~dIFfH~s~l~~~-~-~~l~Gd~V~F~v~~~~k~~~g~~A~~V~~~ 125 (140)
++|+|||||.+||||||+++++++|||||+++|... + .+.+||.|+|++..+++ |++|.+|+.+
T Consensus 5 ~~G~Vk~f~~~kGfGFI~~~~g~~dvfvH~s~l~~~g~~~l~~G~~V~f~~~~~~~---G~~A~~V~~~ 70 (70)
T PRK10354 5 MTGIVKWFNADKGFGFITPDDGSKDVFVHFSAIQNDGYKSLDEGQKVSFTIESGAK---GPAAGNVTSL 70 (70)
T ss_pred ceEEEEEEeCCCCcEEEecCCCCccEEEEEeeccccCCCCCCCCCEEEEEEEECCC---CceeEEEEeC
Confidence 489999999999999999999999999999999976 4 46699999999999884 8999999863
No 7
>PRK09507 cspE cold shock protein CspE; Reviewed
Probab=99.87 E-value=3.8e-22 Score=134.50 Aligned_cols=65 Identities=34% Similarity=0.535 Sum_probs=58.8
Q ss_pred eeeeEEEEeeCCCceeEEecCCCCCeEEEEEccccCC-C-cCCCCCEEEEEEEecCCCCCCceEEEEEec
Q psy3654 58 VETGKIKEFCRSKGHGFITPDSGEPAVFVHISDIEGC-Y-VPLPGDEVKYRLCPIPPKFEKNQAVHVEIV 125 (140)
Q Consensus 58 ~~~G~VK~f~~~KGfGFI~~~~g~~dIFfH~s~l~~~-~-~~l~Gd~V~F~v~~~~k~~~g~~A~~V~~~ 125 (140)
..+|+|||||.+||||||+++++++|||||+++|... + .+.+||.|+|++..+++ |++|++|+.+
T Consensus 3 ~~~G~Vk~f~~~kGyGFI~~~~g~~dvfvH~s~l~~~g~~~l~~G~~V~f~~~~~~~---G~~A~~V~~~ 69 (69)
T PRK09507 3 KIKGNVKWFNESKGFGFITPEDGSKDVFVHFSAIQTNGFKTLAEGQRVEFEITNGAK---GPSAANVIAL 69 (69)
T ss_pred ccceEEEEEeCCCCcEEEecCCCCeeEEEEeecccccCCCCCCCCCEEEEEEEECCC---CcccEEEEeC
Confidence 5789999999999999999999999999999999876 4 46699999999999984 7999999854
No 8
>PRK15463 cold shock-like protein CspF; Provisional
Probab=99.87 E-value=5.5e-22 Score=134.29 Aligned_cols=63 Identities=30% Similarity=0.322 Sum_probs=57.5
Q ss_pred eeeEEEEeeCCCceeEEecCCCCCeEEEEEccccCC-C-cCCCCCEEEEEEEecCCCCCCceEEEEEe
Q psy3654 59 ETGKIKEFCRSKGHGFITPDSGEPAVFVHISDIEGC-Y-VPLPGDEVKYRLCPIPPKFEKNQAVHVEI 124 (140)
Q Consensus 59 ~~G~VK~f~~~KGfGFI~~~~g~~dIFfH~s~l~~~-~-~~l~Gd~V~F~v~~~~k~~~g~~A~~V~~ 124 (140)
++|+|||||.+||||||+++++++|||||+++|... + .+.+||.|+|++..+++ |++|++|++
T Consensus 5 ~~G~Vk~fn~~kGfGFI~~~~g~~DvFvH~sal~~~g~~~l~~G~~V~f~v~~~~~---G~~A~~V~~ 69 (70)
T PRK15463 5 MTGIVKTFDGKSGKGLITPSDGRKDVQVHISALNLRDAEELTTGLRVEFCRINGLR---GPTAANVYL 69 (70)
T ss_pred ceEEEEEEeCCCceEEEecCCCCccEEEEehhhhhcCCCCCCCCCEEEEEEEECCC---CceeEEEEc
Confidence 489999999999999999999999999999999875 4 56699999999999884 799999975
No 9
>PRK14998 cold shock-like protein CspD; Provisional
Probab=99.87 E-value=8.5e-22 Score=134.39 Aligned_cols=66 Identities=33% Similarity=0.570 Sum_probs=59.5
Q ss_pred eeeeEEEEeeCCCceeEEecCCCCCeEEEEEccccCC-C-cCCCCCEEEEEEEecCCCCCCceEEEEEecC
Q psy3654 58 VETGKIKEFCRSKGHGFITPDSGEPAVFVHISDIEGC-Y-VPLPGDEVKYRLCPIPPKFEKNQAVHVEIVH 126 (140)
Q Consensus 58 ~~~G~VK~f~~~KGfGFI~~~~g~~dIFfH~s~l~~~-~-~~l~Gd~V~F~v~~~~k~~~g~~A~~V~~~~ 126 (140)
|.+|+|||||.+||||||+++++++|||||+++|... + .+.+|+.|+|++..+++ |.+|.+|..+.
T Consensus 1 M~~G~Vkwfn~~kGfGFI~~~~g~~dVFvH~s~l~~~g~~~l~~G~~V~f~~~~~~~---G~~A~~V~~~~ 68 (73)
T PRK14998 1 METGTVKWFNNAKGFGFICPEGGGEDIFAHYSTIQMDGYRTLKAGQSVRFDVHQGPK---GNHASVIVPIE 68 (73)
T ss_pred CCCeEEEEEeCCCceEEEecCCCCccEEEEeeeecccCCCCCCCCCEEEEEEEECCC---CceeEEEEECc
Confidence 3579999999999999999999999999999999876 4 46699999999999984 89999998764
No 10
>PRK09890 cold shock protein CspG; Provisional
Probab=99.86 E-value=1.3e-21 Score=132.22 Aligned_cols=64 Identities=33% Similarity=0.510 Sum_probs=58.3
Q ss_pred eeeEEEEeeCCCceeEEecCCCCCeEEEEEccccCC-C-cCCCCCEEEEEEEecCCCCCCceEEEEEec
Q psy3654 59 ETGKIKEFCRSKGHGFITPDSGEPAVFVHISDIEGC-Y-VPLPGDEVKYRLCPIPPKFEKNQAVHVEIV 125 (140)
Q Consensus 59 ~~G~VK~f~~~KGfGFI~~~~g~~dIFfH~s~l~~~-~-~~l~Gd~V~F~v~~~~k~~~g~~A~~V~~~ 125 (140)
++|+|||||.+||||||+++++++|||||+++|... + .+.+||.|+|++..++ +|++|.+|..+
T Consensus 5 ~~G~Vk~f~~~kGfGFI~~~~g~~dvFvH~s~l~~~~~~~l~~G~~V~f~~~~~~---~G~~A~~V~~~ 70 (70)
T PRK09890 5 MTGLVKWFNADKGFGFITPDDGSKDVFVHFTAIQSNEFRTLNENQKVEFSIEQGQ---RGPAAANVVTL 70 (70)
T ss_pred ceEEEEEEECCCCcEEEecCCCCceEEEEEeeeccCCCCCCCCCCEEEEEEEECC---CCceeEEEEeC
Confidence 589999999999999999999999999999999976 5 4569999999999988 49999999864
No 11
>PF00313 CSD: 'Cold-shock' DNA-binding domain; InterPro: IPR002059 When Escherichia coli is exposed to a temperature drop from 37 to 10 degrees centigrade, a 4-5 hour lag phase occurs, after which growth is resumed at a reduced rate []. During the lag phase, the expression of around 13 proteins, which contain specific DNA-binding regions [], is increased 2-10 fold. These so-called 'cold shock' proteins are thought to help the cell to survive in temperatures lower than optimum growth temperature, by contrast with heat shock proteins, which help the cell to survive in temperatures greater than the optimum, possibly by condensation of the chromosome and organisation of the prokaryotic nucleoid []. A conserved domain of about 70 amino acids has been found in prokaryotic and eukaryotic DNA-binding proteins [, , ]. This domain is known as the 'cold-shock domain' (CSD), part of which is highly similar [] to the RNP-1 RNA-binding motif.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1HZC_A 1I5F_A 1HZ9_B 1C9O_B 1HZB_B 1HZA_A 2HAX_B 2L15_A 2LSS_A 3I2Z_B ....
Probab=99.85 E-value=1e-20 Score=124.77 Aligned_cols=64 Identities=39% Similarity=0.589 Sum_probs=56.8
Q ss_pred eeeEEEEeeCCCceeEEecCCCCCeEEEEEccccCC-Cc-CCCCCEEEEEEEecCCCCCCceEEEEEec
Q psy3654 59 ETGKIKEFCRSKGHGFITPDSGEPAVFVHISDIEGC-YV-PLPGDEVKYRLCPIPPKFEKNQAVHVEIV 125 (140)
Q Consensus 59 ~~G~VK~f~~~KGfGFI~~~~g~~dIFfH~s~l~~~-~~-~l~Gd~V~F~v~~~~k~~~g~~A~~V~~~ 125 (140)
++|+|+||+..||||||+++++++|||||+++|... +. +..|++|+|++..++ +|++|++|+.+
T Consensus 1 ~~G~V~~~~~~kgyGFI~~~~~~~diFfh~s~~~~~~~~~l~~G~~V~F~~~~~~---~g~~A~~V~~~ 66 (66)
T PF00313_consen 1 MTGTVKWFDDEKGYGFITSDDGGEDIFFHISDLSGNGFRSLKEGDRVEFEVEEGK---KGPQAVNVRKI 66 (66)
T ss_dssp EEEEEEEEETTTTEEEEEETTSSSEEEEEGGGBCSSSSTS--TTSEEEEEEEECT---TSEEEEEEEE-
T ss_pred CeEEEEEEECCCCceEEEEcccceeEEeccccccccccccCCCCCEEEEEEEECC---CCCEEEEEECc
Confidence 589999999999999999999999999999999997 34 459999999999966 69999999874
No 12
>cd04458 CSP_CDS Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in eukaryotes, prokaryotes, and archaea. CSP's include the major cold-shock proteins CspA and CspB in bacteria and the eukaryotic gene regulatory factor Y-box protein. CSP expression is up-regulated by an abrupt drop in growth temperature. CSP's are also expressed under normal condition at lower level. The function of cold-shock proteins is not fully understood. They preferentially bind poly-pyrimidine region of single-stranded RNA and DNA. CSP's are thought to bind mRNA and regulate ribosomal translation, mRNA degradation, and the rate of transcription termination. The human Y-box protein, which contains a CSD, regulates transcription and translation of genes that contain the Y-box sequence in their promoters. This specific ssDNA-binding properties of CSD are required for the binding of Y-box protein to the promoter's Y-box sequence, thereby regulating transcription.
Probab=99.82 E-value=6.2e-20 Score=120.67 Aligned_cols=63 Identities=46% Similarity=0.637 Sum_probs=57.4
Q ss_pred eeeEEEEeeCCCceeEEecCCCCCeEEEEEccccCC--CcCCCCCEEEEEEEecCCCCCCceEEEEEe
Q psy3654 59 ETGKIKEFCRSKGHGFITPDSGEPAVFVHISDIEGC--YVPLPGDEVKYRLCPIPPKFEKNQAVHVEI 124 (140)
Q Consensus 59 ~~G~VK~f~~~KGfGFI~~~~g~~dIFfH~s~l~~~--~~~l~Gd~V~F~v~~~~k~~~g~~A~~V~~ 124 (140)
++|+||||+.+||||||+.+++++|||||+++|... ..+.+|+.|+|++..+. +|++|.+|+.
T Consensus 1 ~~G~Vk~~~~~kGfGFI~~~~~g~diffh~~~~~~~~~~~~~~G~~V~f~~~~~~---~g~~A~~V~~ 65 (65)
T cd04458 1 VTGTVKWFDDEKGFGFITPDDGGEDVFVHISALEGDGFRSLEEGDRVEFELEEGD---KGPQAVNVRL 65 (65)
T ss_pred CcEEEEEEECCCCeEEEecCCCCcCEEEEhhHhhccCCCcCCCCCEEEEEEEECC---CCCeEEEeEC
Confidence 369999999999999999999889999999999987 45679999999999996 6999999973
No 13
>KOG3070|consensus
Probab=99.52 E-value=1.6e-14 Score=117.57 Aligned_cols=99 Identities=29% Similarity=0.401 Sum_probs=81.0
Q ss_pred CcCCCCcccccccccccccccccCCceeeeEEEEeeCCCceeEEecCCCCCeEEEEEccccC----C-CcCC-CCCEEEE
Q psy3654 32 TLSLPSPIITRRTRTESISNRALQNPVETGKIKEFCRSKGHGFITPDSGEPAVFVHISDIEG----C-YVPL-PGDEVKY 105 (140)
Q Consensus 32 ~~~iPsplp~~r~rt~s~~~~~~~g~~~~G~VK~f~~~KGfGFI~~~~g~~dIFfH~s~l~~----~-~~~l-~Gd~V~F 105 (140)
..-.++++++.+.+..+ +.........+|+|||||..+|||||+++++.+|||||+++|.. . ++.+ +++.|.|
T Consensus 31 ~~~~~~~~~~~~~~~~s-~~~~~~~~~~~G~~k~fnv~~G~gFi~~~d~~~D~fvhQs~i~~~~~~~~~rs~~~~e~v~f 109 (235)
T KOG3070|consen 31 RSYSPKPLPTEVPEGLS-TAKKVQGARVKGTVKWFNVGKGYGFITRDDGPEDVFVHQSAITKYTPSEGFRSLKEGEAVPF 109 (235)
T ss_pred cccCCCcccccCcCCcc-cccccccccccCcceeEeccCCcceecccCCCCceeEEeeeecccccccchhhcccCCCccc
Confidence 45688999999999888 56667788999999999999999999999999999999999998 4 3444 9999999
Q ss_pred EEEecCCCCCCceEEEEEecCCCCc-cccccCCC
Q psy3654 106 RLCPIPPKFEKNQAVHVEIVHLTPE-VHLQWDSP 138 (140)
Q Consensus 106 ~v~~~~k~~~g~~A~~V~~~~~~p~-~~~~w~~~ 138 (140)
+++...+ +..|++|. .|+ .+++|+.+
T Consensus 110 ~~~~~~~---g~~a~~vt----~p~g~~~~~s~~ 136 (235)
T KOG3070|consen 110 DIQEGNK---GTEAANVT----GPDGVPVRGSKG 136 (235)
T ss_pred eecccCc---cceeeeec----CCCCcccccccc
Confidence 9999874 56666654 333 56667653
No 14
>smart00357 CSP Cold shock protein domain. RNA-binding domain that functions as a RNA-chaperone in bacteria and is involved in regulating translation in eukaryotes. Contains sub-family of RNA-binding domains in the Rho transcription termination factor.
Probab=99.08 E-value=9.1e-10 Score=70.04 Aligned_cols=63 Identities=41% Similarity=0.570 Sum_probs=50.3
Q ss_pred eeEEEEeeCCCceeEEecCCCCCeEEEEEccccCC-CcCCCCCEEEEEEEecCCCCCCceEEEEEec
Q psy3654 60 TGKIKEFCRSKGHGFITPDSGEPAVFVHISDIEGC-YVPLPGDEVKYRLCPIPPKFEKNQAVHVEIV 125 (140)
Q Consensus 60 ~G~VK~f~~~KGfGFI~~~~g~~dIFfH~s~l~~~-~~~l~Gd~V~F~v~~~~k~~~g~~A~~V~~~ 125 (140)
+|+|++++ +|||||.+++...|||||.++++.. ..+..||.|.|++.... ..++.+|..|+++
T Consensus 1 ~G~i~~~~--~g~gfv~~~~~~~~i~v~~~~~~~~~~~~~~Gd~V~~~i~~~~-~~~~~~a~~v~~~ 64 (64)
T smart00357 1 TGVVKWFN--KGFGFIRPDDGGKDVFVHPSQIQGGLKSLREGDEVEFKVVSPR-GGGKPEAENVVKL 64 (64)
T ss_pred CeEEEEEc--CCeeEEecCCCCccEEEEhHHhhcCCCcCCCCCEEEEEEEEcc-CCCCcEEEEEEeC
Confidence 48999997 7999999987657999999998663 34669999999997732 2357899988763
No 15
>PF08206 OB_RNB: Ribonuclease B OB domain; InterPro: IPR013223 This domain includes the N-terminal OB domain found in ribonuclease B proteins in one or two copies.; PDB: 2ID0_D 2IX1_A 2IX0_A.
Probab=97.98 E-value=1.8e-05 Score=51.28 Aligned_cols=57 Identities=33% Similarity=0.701 Sum_probs=38.0
Q ss_pred eEEEEeeCCCceeEEecCCCCCeEEEEEccccCCCcCCCCCEEEEEEEecCCCCCCceEEEEE
Q psy3654 61 GKIKEFCRSKGHGFITPDSGEPAVFVHISDIEGCYVPLPGDEVKYRLCPIPPKFEKNQAVHVE 123 (140)
Q Consensus 61 G~VK~f~~~KGfGFI~~~~g~~dIFfH~s~l~~~~~~l~Gd~V~F~v~~~~k~~~g~~A~~V~ 123 (140)
|+++. ..+||||+.+++.++|||+...++.+ ...||.|..++.. ....++..+.-|+
T Consensus 1 G~~~~--~~~GfGFv~~~~~~~DifIp~~~l~~---A~~gD~V~v~i~~-~~~~~~~eg~vv~ 57 (58)
T PF08206_consen 1 GTLKI--HPKGFGFVIPDDGGEDIFIPPRNLNG---AMDGDKVLVRITP-PSRGKRPEGEVVE 57 (58)
T ss_dssp EEEEE---SSS-EEEEECT-TEEEEE-HHHHTT---S-TT-EEEEEEEE-SSSEEEEEEEEEE
T ss_pred CEEEE--EcCCCEEEEECCCCCCEEECHHHHCC---CCCCCEEEEEEec-CCCCCCCCEEEEe
Confidence 44444 37899999999988999999988887 4589999999988 3333455554443
No 16
>PF14444 S1-like: S1-like
Probab=97.87 E-value=8.9e-05 Score=48.76 Aligned_cols=54 Identities=33% Similarity=0.424 Sum_probs=43.3
Q ss_pred eeeeEEEEeeCCCceeEEecCCCCCeEEEEEccccCCCcCCCCCEEEEEEEecCCCCCCceE
Q psy3654 58 VETGKIKEFCRSKGHGFITPDSGEPAVFVHISDIEGCYVPLPGDEVKYRLCPIPPKFEKNQA 119 (140)
Q Consensus 58 ~~~G~VK~f~~~KGfGFI~~~~g~~dIFfH~s~l~~~~~~l~Gd~V~F~v~~~~k~~~g~~A 119 (140)
.++|+|..++. .||||. +||||+.+.+.+. .+..||+|..+....+.-.-++.|
T Consensus 3 ~~~GvVTkl~~--~yG~ID-----e~vFF~~~vv~G~-~P~vGdrV~v~A~~n~~~~~kW~A 56 (58)
T PF14444_consen 3 VFTGVVTKLCD--DYGFID-----EDVFFQTDVVKGN-VPKVGDRVLVEAIYNPNMPFKWNA 56 (58)
T ss_pred eEEEEEEEEeC--CcceEc-----ccEEEEcccEecC-CCccCCEEEEEEEeCCCCCcccee
Confidence 46899999974 799997 6899999998875 568999999999887643234554
No 17
>PF07497 Rho_RNA_bind: Rho termination factor, RNA-binding domain; InterPro: IPR011113 The Rho termination factor disengages newly transcribed RNA from its DNA template at certain, specific transcripts. It is thought that two copies of Rho bind to RNA and that Rho functions as a hexamer of protomers [].; GO: 0003723 RNA binding, 0006353 transcription termination, DNA-dependent; PDB: 1A8V_B 1PVO_A 1PV4_D 3ICE_A 1XPU_C 1XPO_D 1XPR_F 2A8V_B 2HT1_B 1A63_A ....
Probab=96.57 E-value=0.0053 Score=42.54 Aligned_cols=65 Identities=23% Similarity=0.255 Sum_probs=39.3
Q ss_pred eeeEEEEeeCCCceeEEecC-----CCCCeEEEEEccccCCCcCCCCCEEEEEEEecCCCCCCceEEEEEecC
Q psy3654 59 ETGKIKEFCRSKGHGFITPD-----SGEPAVFVHISDIEGCYVPLPGDEVKYRLCPIPPKFEKNQAVHVEIVH 126 (140)
Q Consensus 59 ~~G~VK~f~~~KGfGFI~~~-----~g~~dIFfH~s~l~~~~~~l~Gd~V~F~v~~~~k~~~g~~A~~V~~~~ 126 (140)
..|++--. .+|||||+.. .+.+||||-.+.|+.. .++.||.|+=.+.....+.+-..-..|.-++
T Consensus 3 ~~GvLei~--~dGyGFLR~~~~~y~~~~~DvYVs~~qIrrf-~LR~GD~V~G~vr~p~~~ek~~aL~~V~~VN 72 (78)
T PF07497_consen 3 VEGVLEIL--PDGYGFLRSPDNNYLPSPDDVYVSPSQIRRF-GLRTGDLVEGQVRPPREGEKYFALLRVESVN 72 (78)
T ss_dssp EEEEEEE---TTS-EEEE-GGGTTS-STTSEEE-CCCCCCT-T--TTEEEEEEEE--STTSSSEEECEECEET
T ss_pred EEEEEEEC--CCCcEEeECCCcCCCCCCCCEEECHHHHHHc-CCCCCCEEEEEEeCCCCCCcceeeEEEEeEC
Confidence 45666533 5699999998 2668999999999764 5779999998887754322233445665554
No 18
>PRK11642 exoribonuclease R; Provisional
Probab=96.16 E-value=0.019 Score=54.38 Aligned_cols=67 Identities=13% Similarity=0.228 Sum_probs=49.8
Q ss_pred ceeeeEEEEeeCCCceeEEecCCCCCeEEEEEccccCCCcCCCCCEEEEEEEecCCCCCCceEEEEEecCCCC
Q psy3654 57 PVETGKIKEFCRSKGHGFITPDSGEPAVFVHISDIEGCYVPLPGDEVKYRLCPIPPKFEKNQAVHVEIVHLTP 129 (140)
Q Consensus 57 ~~~~G~VK~f~~~KGfGFI~~~~g~~dIFfH~s~l~~~~~~l~Gd~V~F~v~~~~k~~~g~~A~~V~~~~~~p 129 (140)
..+.|+|+. ..+||||+.++++++|||+.-..+.+ ...||.|..++..... .++..|.-|.++..+.
T Consensus 83 ~~~~G~v~~--~~~GfgFv~~e~~~~difI~~~~l~~---A~~GD~V~v~i~~~~~-~~r~eg~Vv~IleR~~ 149 (813)
T PRK11642 83 DLLKGTVIG--HRDGYGFLRVEGRKDDLYLSSEQMKT---CIHGDQVLAQPLGADR-KGRREARIVRVLVPKT 149 (813)
T ss_pred ceEEEEEEE--CCCccEEEEECCCCCCEEEChHHHcc---CCCCCEEEEEEccCCC-CCCcEEEEEEEEecCC
Confidence 457899995 57999999998767899998776655 4579999998764221 1456888888876543
No 19
>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=95.92 E-value=0.043 Score=50.54 Aligned_cols=66 Identities=23% Similarity=0.354 Sum_probs=48.9
Q ss_pred ceeeeEEEEeeCCCceeEEecCC-CCCeEEEEEccccCCCcCCCCCEEEEEEEecCCCCCCceEEEEEecCCC
Q psy3654 57 PVETGKIKEFCRSKGHGFITPDS-GEPAVFVHISDIEGCYVPLPGDEVKYRLCPIPPKFEKNQAVHVEIVHLT 128 (140)
Q Consensus 57 ~~~~G~VK~f~~~KGfGFI~~~~-g~~dIFfH~s~l~~~~~~l~Gd~V~F~v~~~~k~~~g~~A~~V~~~~~~ 128 (140)
....|+|+. ..+||||+..++ +++|||+.-.++.+ ...||.|..++....+ .++..|.-+.++..+
T Consensus 15 ~~~~G~i~~--~~~gfgFv~~~~~~~~difI~~~~~~~---a~~GD~V~v~i~~~~~-~~~~~g~v~~il~r~ 81 (654)
T TIGR00358 15 DLVKGVVKA--HNKGFGFLRPDDDDKKDYFIPPPQMKK---VMHGDLVEACPLSQPQ-RGRFEAEVERILEPA 81 (654)
T ss_pred CeEEEEEEE--CCCccEEEEeCCCCCCcEEEchHHhCc---CCCCCEEEEEEeecCC-CCCceEEEEEEeccC
Confidence 357899997 479999999986 35799998776655 4589999999854322 134678888877654
No 20
>cd04459 Rho_CSD Rho_CSD: Rho protein cold-shock domain (CSD). Rho protein is a transcription termination factor in most bacteria. In bacteria, there are two distinct mechanisms for mRNA transcription termination. In intrinsic termination, RNA polymerase and nascent mRNA are released from DNA template by an mRNA stem loop structure, which resembles the transcription termination mechanism used by eukaryotic pol III. The second mechanism is mediated by Rho factor. Rho factor terminates transcription by using energy from ATP hydrolysis to forcibly dissociate the transcripts from RNA polymerase. Rho protein contains an N-terminal S1-like domain, which binds single-stranded RNA. Rho has a C-terminal ATPase domain which hydrolyzes ATP to provide energy to strip RNA polymerase and mRNA from the DNA template. Rho functions as a homohexamer.
Probab=95.81 E-value=0.04 Score=37.16 Aligned_cols=46 Identities=26% Similarity=0.470 Sum_probs=35.6
Q ss_pred eEEEEeeCCCceeEEecC-----CCCCeEEEEEccccCCCcCCCCCEEEEEEEe
Q psy3654 61 GKIKEFCRSKGHGFITPD-----SGEPAVFVHISDIEGCYVPLPGDEVKYRLCP 109 (140)
Q Consensus 61 G~VK~f~~~KGfGFI~~~-----~g~~dIFfH~s~l~~~~~~l~Gd~V~F~v~~ 109 (140)
|++--. .+|||||... .+.+||||..+-|+.. .++.||.|+=.+..
T Consensus 3 GiLdi~--~~g~GFLR~~~~~y~~~~~DvyVs~~~Irr~-~LR~GD~V~G~vr~ 53 (68)
T cd04459 3 GVLEIL--PDGFGFLRSSGYNYLPGPDDIYVSPSQIRRF-NLRTGDTVVGQIRP 53 (68)
T ss_pred EEEEEc--CCCceEEecCCcCCCCCCCCEEECHHHHHHh-CCCCCCEEEEEEeC
Confidence 444433 3499999987 2678999999999874 57799999988875
No 21
>PRK05054 exoribonuclease II; Provisional
Probab=95.55 E-value=0.054 Score=49.92 Aligned_cols=63 Identities=21% Similarity=0.373 Sum_probs=46.7
Q ss_pred ceeeeEEEEeeCCCceeEEecCCCCCeEEEEEccccCCCcCCCCCEEEEEEEecCCCCCCceEEEEEecCCC
Q psy3654 57 PVETGKIKEFCRSKGHGFITPDSGEPAVFVHISDIEGCYVPLPGDEVKYRLCPIPPKFEKNQAVHVEIVHLT 128 (140)
Q Consensus 57 ~~~~G~VK~f~~~KGfGFI~~~~g~~dIFfH~s~l~~~~~~l~Gd~V~F~v~~~~k~~~g~~A~~V~~~~~~ 128 (140)
....|+|+. ..+||||+..++ .+|||+.-.++.+ ...||.|..++.... ++..|.-+.++..+
T Consensus 20 ~~~~G~~~~--~~~gfgFv~~~~-~~difI~~~~l~~---a~~GD~V~v~i~~~~---~r~~g~v~~il~r~ 82 (644)
T PRK05054 20 PRVEGVVKA--TEKGFGFLEVDA-QKSYFIPPPQMKK---VMHGDRIIAVIHTEK---DREIAEPEELIEPF 82 (644)
T ss_pred CeEEEEEEE--CCCccEEEEECC-CCcEEEChHHHcc---CCCCCEEEEEEecCC---CCcEEEEEEEEecC
Confidence 457799996 479999998755 4599998887776 457999999875432 35577777776644
No 22
>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=95.54 E-value=0.08 Score=34.34 Aligned_cols=56 Identities=16% Similarity=0.211 Sum_probs=44.6
Q ss_pred cCCceeeeEEEEeeCCCceeEEecCCCCCeEEEEEccccCC------CcCCCCCEEEEEEEecCC
Q psy3654 54 LQNPVETGKIKEFCRSKGHGFITPDSGEPAVFVHISDIEGC------YVPLPGDEVKYRLCPIPP 112 (140)
Q Consensus 54 ~~g~~~~G~VK~f~~~KGfGFI~~~~g~~dIFfH~s~l~~~------~~~l~Gd~V~F~v~~~~k 112 (140)
..|..+.|+|...+. +|++...+.+-+.|+|++++... .....||.|.+.+...++
T Consensus 3 ~~G~iv~g~V~~v~~---~g~~V~l~~~~~g~ip~~~l~~~~~~~~~~~~~~G~~v~v~v~~vd~ 64 (74)
T PF00575_consen 3 KEGDIVEGKVTSVED---FGVFVDLGNGIEGFIPISELSDDRIDDPSEVYKIGQTVRVKVIKVDK 64 (74)
T ss_dssp STTSEEEEEEEEEET---TEEEEEESTSSEEEEEGGGSSSSEESSSHGTCETTCEEEEEEEEEET
T ss_pred CCCCEEEEEEEEEEC---CEEEEEECCcEEEEEEeehhcCccccccccccCCCCEEEEEEEEEEC
Confidence 357899999999976 66666555678999999999864 234499999999988775
No 23
>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=95.40 E-value=0.069 Score=49.23 Aligned_cols=63 Identities=22% Similarity=0.409 Sum_probs=46.1
Q ss_pred CceeeeEEEEeeCCCceeEEecCCCCCeEEEEEccccCCCcCCCCCEEEEEEEecCCCCCCceEEEEEecCC
Q psy3654 56 NPVETGKIKEFCRSKGHGFITPDSGEPAVFVHISDIEGCYVPLPGDEVKYRLCPIPPKFEKNQAVHVEIVHL 127 (140)
Q Consensus 56 g~~~~G~VK~f~~~KGfGFI~~~~g~~dIFfH~s~l~~~~~~l~Gd~V~F~v~~~~k~~~g~~A~~V~~~~~ 127 (140)
.....|+|+. ..|||||+..++ .+|||+.-..+.+ ...||.|..++.... ++..|.-+.++..
T Consensus 16 ~~~~~G~i~~--~~kGfgFv~~~~-~~difI~~~~l~~---A~~GD~V~v~i~~~~---~r~~~~v~~iver 78 (639)
T TIGR02062 16 TPRVEGVVKA--TEKGFGFLEVDA-QKSYFIPPPQMKK---VMHGDKIIAVIHSEK---ERESAEPEELIEP 78 (639)
T ss_pred CceEEEEEEE--CCCccEEEEECC-CCcEEEChHHHcc---CCCCCEEEEEEecCC---CCcEEEEEEEEcc
Confidence 4467799996 579999997654 4699998887776 447999999876432 3456666666644
No 24
>cd04461 S1_Rrp5_repeat_hs8_sc7 S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 repeat 7 (sc7)-like domains. Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in S. cerevisiae Rrp5 and 14 S1 repeats in H. sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 8 and S. cerevisiae S1 repeat 7. Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=95.29 E-value=0.09 Score=35.29 Aligned_cols=57 Identities=14% Similarity=0.057 Sum_probs=45.5
Q ss_pred ccCCceeeeEEEEeeCCCceeEEecCCCCCeEEEEEccccCC-C-c----CCCCCEEEEEEEecCC
Q psy3654 53 ALQNPVETGKIKEFCRSKGHGFITPDSGEPAVFVHISDIEGC-Y-V----PLPGDEVKYRLCPIPP 112 (140)
Q Consensus 53 ~~~g~~~~G~VK~f~~~KGfGFI~~~~g~~dIFfH~s~l~~~-~-~----~l~Gd~V~F~v~~~~k 112 (140)
...|..+.|+|+... -||++....++-+.|+|++++..+ . . ...||.|++++...++
T Consensus 12 ~~~G~i~~g~V~~v~---~~G~fv~l~~~~~g~v~~~el~~~~~~~~~~~~~~Gd~v~vkV~~id~ 74 (83)
T cd04461 12 LKPGMVVHGYVRNIT---PYGVFVEFLGGLTGLAPKSYISDEFVTDPSFGFKKGQSVTAKVTSVDE 74 (83)
T ss_pred CCCCCEEEEEEEEEe---eceEEEEcCCCCEEEEEHHHCCcccccCHHHhcCCCCEEEEEEEEEcC
Confidence 346889999999886 488888776678999999999765 2 1 3499999999988764
No 25
>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=95.26 E-value=0.12 Score=34.02 Aligned_cols=57 Identities=21% Similarity=0.118 Sum_probs=40.0
Q ss_pred Cceee-eEEEEeeCCCceeEEecCCCCCeEEEEEccccCC-----C-cCCCCCEEEEEEEecCCCC
Q psy3654 56 NPVET-GKIKEFCRSKGHGFITPDSGEPAVFVHISDIEGC-----Y-VPLPGDEVKYRLCPIPPKF 114 (140)
Q Consensus 56 g~~~~-G~VK~f~~~KGfGFI~~~~g~~dIFfH~s~l~~~-----~-~~l~Gd~V~F~v~~~~k~~ 114 (140)
|.++. |+|+... ..||.+.....+-+-|+|++++..+ . .+..||.|++++...++++
T Consensus 1 G~v~~~g~V~~v~--~~~G~~V~l~~gv~G~i~~s~l~~~~~~~~~~~~~vG~~v~~kV~~id~~~ 64 (71)
T cd05696 1 GAVVDSVKVTKVE--PDLGAVFELKDGLLGFVHISHLSDDKVPSDTGPFKAGTTHKARIIGYSPMD 64 (71)
T ss_pred CcEeeeeEEEEEc--cCceEEEEeCCCCEEEEEHHHCCcchhcCcccccCCCCEEEEEEEEEeCCC
Confidence 34566 8898874 3476655554458999999999654 1 2459999999988776533
No 26
>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=95.22 E-value=0.09 Score=33.82 Aligned_cols=54 Identities=19% Similarity=0.156 Sum_probs=41.6
Q ss_pred CceeeeEEEEeeCCCceeEEecCCCCCeEEEEEccccCC--C----cCCCCCEEEEEEEecCC
Q psy3654 56 NPVETGKIKEFCRSKGHGFITPDSGEPAVFVHISDIEGC--Y----VPLPGDEVKYRLCPIPP 112 (140)
Q Consensus 56 g~~~~G~VK~f~~~KGfGFI~~~~g~~dIFfH~s~l~~~--~----~~l~Gd~V~F~v~~~~k 112 (140)
|..+.|+|+...+ ||.+....++-+-|+|++++..+ . ....||.|++++...++
T Consensus 1 g~~~~g~V~~v~~---~G~~V~l~~~~~gli~~s~l~~~~~~~~~~~~~~G~~i~v~v~~~d~ 60 (70)
T cd05698 1 GLKTHGTIVKVKP---NGCIVSFYNNVKGFLPKSELSEAFIKDPEEHFRVGQVVKVKVLSCDP 60 (70)
T ss_pred CCEEEEEEEEEec---CcEEEEECCCCEEEEEHHHcChhhcCCHHHcccCCCEEEEEEEEEcC
Confidence 4578899999864 66666655568999999999754 1 24599999999988765
No 27
>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=94.96 E-value=0.23 Score=34.40 Aligned_cols=63 Identities=16% Similarity=0.149 Sum_probs=43.8
Q ss_pred cCCceeeeEEEEeeCCCceeEEecCCCCCeEEEEEccccC-------C--CcCCCCCEEEEEEEecCCCCCCc
Q psy3654 54 LQNPVETGKIKEFCRSKGHGFITPDSGEPAVFVHISDIEG-------C--YVPLPGDEVKYRLCPIPPKFEKN 117 (140)
Q Consensus 54 ~~g~~~~G~VK~f~~~KGfGFI~~~~g~~dIFfH~s~l~~-------~--~~~l~Gd~V~F~v~~~~k~~~g~ 117 (140)
..|.++.|+|+...+. -+|.+...+.+.+-|+|++++.. . ..+..||.|..++...+-+.++.
T Consensus 6 ~~G~iy~g~V~~i~~~-~~GaFV~l~~g~~Gllh~seis~~~~~~v~~~~~~~~~Gd~v~VqV~~~~~~~K~~ 77 (88)
T cd04453 6 IVGNIYLGRVKKIVPG-LQAAFVDIGLGKNGFLHLSDILPAYFKKHKKIAKLLKEGQEILVQVVKEPIGTKGP 77 (88)
T ss_pred CCCCEEEEEEEEeccC-CcEEEEEeCCCCEEEEEhHHcCchhccccCCHHHcCCCCCEEEEEEEEecCCCCCc
Confidence 4688999999998542 24555554445899999999843 1 23559999999998765433333
No 28
>smart00316 S1 Ribosomal protein S1-like RNA-binding domain.
Probab=94.92 E-value=0.18 Score=31.20 Aligned_cols=55 Identities=22% Similarity=0.259 Sum_probs=42.1
Q ss_pred CCceeeeEEEEeeCCCceeEEecCCCCCeEEEEEccccCCC------cCCCCCEEEEEEEecCC
Q psy3654 55 QNPVETGKIKEFCRSKGHGFITPDSGEPAVFVHISDIEGCY------VPLPGDEVKYRLCPIPP 112 (140)
Q Consensus 55 ~g~~~~G~VK~f~~~KGfGFI~~~~g~~dIFfH~s~l~~~~------~~l~Gd~V~F~v~~~~k 112 (140)
.|..+.|+|..... +|++-..+.+.+.|+|.+++...+ ....||.|.+.+...+.
T Consensus 2 ~G~~v~g~V~~v~~---~g~~v~i~~~~~g~l~~~~~~~~~~~~~~~~~~~G~~v~~~V~~~~~ 62 (72)
T smart00316 2 VGDVVEGTVTEITP---FGAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDE 62 (72)
T ss_pred CCCEEEEEEEEEEc---cEEEEEeCCCCEEEEEHHHCCccccCCHHHeecCCCEEEEEEEEEeC
Confidence 36789999999876 555555554578999999998752 24599999999988764
No 29
>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=94.82 E-value=0.12 Score=47.85 Aligned_cols=67 Identities=22% Similarity=0.466 Sum_probs=48.7
Q ss_pred ceeeeEEEEeeCCCceeEEecCC-CCCeEEEEEccccCCCcCCCCCEEEEEEEecCCCCCCceEEEEEecCCC
Q psy3654 57 PVETGKIKEFCRSKGHGFITPDS-GEPAVFVHISDIEGCYVPLPGDEVKYRLCPIPPKFEKNQAVHVEIVHLT 128 (140)
Q Consensus 57 ~~~~G~VK~f~~~KGfGFI~~~~-g~~dIFfH~s~l~~~~~~l~Gd~V~F~v~~~~k~~~g~~A~~V~~~~~~ 128 (140)
..+.|+++. ..+||||+.+++ ...|||+...++.+ ...||.|..++.......++..|.-|+++..+
T Consensus 67 ~~~~G~i~~--~~~g~gFv~~~~~~~~di~I~~~~~~~---a~~GD~Vlv~I~~~~~~~~~~eg~Vv~Il~r~ 134 (709)
T TIGR02063 67 KLVKGTVIA--HRDGFGFLRPEDDDEDDIFIPPRQMNG---AMHGDRVLVRITGKPDGGDRFEARVIKILERA 134 (709)
T ss_pred CeEEEEEEE--CCCccEEEEECCCCCCcEEEChHHhCc---CCCCCEEEEEEecccCCCCCceEEEEEEEeeC
Confidence 357898885 578999999876 45799997665544 55899999998653211246688877877654
No 30
>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=94.69 E-value=0.25 Score=31.99 Aligned_cols=55 Identities=11% Similarity=0.056 Sum_probs=42.3
Q ss_pred CCceeeeEEEEeeCCCceeEEecCCCCCeEEEEEccccCCC--c----CCCCCEEEEEEEecCC
Q psy3654 55 QNPVETGKIKEFCRSKGHGFITPDSGEPAVFVHISDIEGCY--V----PLPGDEVKYRLCPIPP 112 (140)
Q Consensus 55 ~g~~~~G~VK~f~~~KGfGFI~~~~g~~dIFfH~s~l~~~~--~----~l~Gd~V~F~v~~~~k 112 (140)
.|..+.|+|+... .+|.+-..+.+-+-|+|++++..++ . ...||.|+..+...+.
T Consensus 3 ~G~iv~g~V~~v~---~~gi~v~l~~~~~g~v~~s~l~~~~~~~~~~~~~~Gd~v~~~V~~~d~ 63 (73)
T cd05706 3 VGDILPGRVTKVN---DRYVLVQLGNKVTGPSFITDALDDYSEALPYKFKKNDIVRACVLSVDV 63 (73)
T ss_pred CCCEEEEEEEEEe---CCeEEEEeCCCcEEEEEhhhccCccccccccccCCCCEEEEEEEEEeC
Confidence 5788999999975 4666655555689999999997652 1 3499999999988764
No 31
>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=94.61 E-value=0.2 Score=33.51 Aligned_cols=55 Identities=15% Similarity=0.111 Sum_probs=43.1
Q ss_pred CCceeeeEEEEeeCCCceeEEecCC-CCCeEEEEEccccCCCcCCCCCEEEEEEEecCC
Q psy3654 55 QNPVETGKIKEFCRSKGHGFITPDS-GEPAVFVHISDIEGCYVPLPGDEVKYRLCPIPP 112 (140)
Q Consensus 55 ~g~~~~G~VK~f~~~KGfGFI~~~~-g~~dIFfH~s~l~~~~~~l~Gd~V~F~v~~~~k 112 (140)
+|..+.|+|+..- -||++-.-+ ++-+-|+|.+++.....+.+||.|...+...++
T Consensus 4 ~G~~v~g~V~si~---d~G~~v~~g~~gv~Gfl~~~~~~~~~~~~~Gq~v~~~V~~vd~ 59 (74)
T cd05694 4 EGMVLSGCVSSVE---DHGYILDIGIPGTTGFLPKKDAGNFSKLKVGQLLLCVVEKVKD 59 (74)
T ss_pred CCCEEEEEEEEEe---CCEEEEEeCCCCcEEEEEHHHCCcccccCCCCEEEEEEEEEEC
Confidence 5778999999985 478765553 456899999999875345699999999987664
No 32
>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=94.50 E-value=0.49 Score=29.44 Aligned_cols=53 Identities=28% Similarity=0.332 Sum_probs=40.9
Q ss_pred CceeeeEEEEeeCCCceeEEecCCCCCeEEEEEccccCCC------cCCCCCEEEEEEEecC
Q psy3654 56 NPVETGKIKEFCRSKGHGFITPDSGEPAVFVHISDIEGCY------VPLPGDEVKYRLCPIP 111 (140)
Q Consensus 56 g~~~~G~VK~f~~~KGfGFI~~~~g~~dIFfH~s~l~~~~------~~l~Gd~V~F~v~~~~ 111 (140)
|..+.|+|....+ ||+....+.+.+.|+|.+++..++ ....||.|..++...+
T Consensus 1 G~~~~g~V~~i~~---~g~~v~i~~~~~g~l~~~~l~~~~~~~~~~~~~~Gd~v~v~v~~~~ 59 (69)
T cd05692 1 GSVVEGTVTRLKP---FGAFVELGGGISGLVHISQIAHKRVKDVKDVLKEGDKVKVKVLSID 59 (69)
T ss_pred CCEEEEEEEEEEe---eeEEEEECCCCEEEEEhHHcCCcccCCHHHccCCCCEEEEEEEEEC
Confidence 4578899999764 777776665689999999997652 1358999999987765
No 33
>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=94.30 E-value=0.2 Score=32.18 Aligned_cols=53 Identities=21% Similarity=0.291 Sum_probs=40.3
Q ss_pred CceeeeEEEEeeCCCceeEEecCCCCCeEEEEEccccCCC--cC--CCCCEEEEEEEecCC
Q psy3654 56 NPVETGKIKEFCRSKGHGFITPDSGEPAVFVHISDIEGCY--VP--LPGDEVKYRLCPIPP 112 (140)
Q Consensus 56 g~~~~G~VK~f~~~KGfGFI~~~~g~~dIFfH~s~l~~~~--~~--l~Gd~V~F~v~~~~k 112 (140)
|..+.|+|+..++ +|++... ++-+.|+|.+.+...+ .+ ..||.+++.+..-++
T Consensus 1 G~iv~g~V~~v~~---~G~~v~l-~g~~gfip~s~~~~~~~~~~~~~vG~~i~~~i~~vd~ 57 (67)
T cd04465 1 GEIVEGKVTEKVK---GGLIVDI-EGVRAFLPASQVDLRPVEDLDEYVGKELKFKIIEIDR 57 (67)
T ss_pred CCEEEEEEEEEEC---CeEEEEE-CCEEEEEEHHHCCCcccCChHHhCCCEEEEEEEEEeC
Confidence 4568899999964 6666666 4578999999997542 12 389999999988775
No 34
>PRK08582 hypothetical protein; Provisional
Probab=94.30 E-value=0.68 Score=34.83 Aligned_cols=70 Identities=19% Similarity=0.272 Sum_probs=52.9
Q ss_pred CCceeeeEEEEeeCCCceeEEecCCCCCeEEEEEccccCCC------cCCCCCEEEEEEEecCCCCCCceEEEEEecCCC
Q psy3654 55 QNPVETGKIKEFCRSKGHGFITPDSGEPAVFVHISDIEGCY------VPLPGDEVKYRLCPIPPKFEKNQAVHVEIVHLT 128 (140)
Q Consensus 55 ~g~~~~G~VK~f~~~KGfGFI~~~~g~~dIFfH~s~l~~~~------~~l~Gd~V~F~v~~~~k~~~g~~A~~V~~~~~~ 128 (140)
.|..+.|+|+... .||+....+.+.+-++|+++|...+ .+..||.|+..+...+. .+.....++.+...
T Consensus 5 vG~iv~G~V~~I~---~fG~fV~L~~~~~GlVhiSels~~~v~~~~~~l~vGD~VkvkV~~id~--~gkI~LSlk~~~~~ 79 (139)
T PRK08582 5 VGSKLQGKVTGIT---NFGAFVELPEGKTGLVHISEVADNYVKDINDHLKVGDEVEVKVLNVED--DGKIGLSIKKAKDR 79 (139)
T ss_pred CCCEEEEEEEEEE---CCeEEEEECCCCEEEEEeeccCcccccccccccCCCCEEEEEEEEECC--CCcEEEEEEecccC
Confidence 5788999999975 4887777666789999999997652 23499999999988764 35566677666555
Q ss_pred C
Q psy3654 129 P 129 (140)
Q Consensus 129 p 129 (140)
|
T Consensus 80 ~ 80 (139)
T PRK08582 80 P 80 (139)
T ss_pred c
Confidence 4
No 35
>PF13509 S1_2: S1 domain; PDB: 3GO5_A.
Probab=94.16 E-value=0.16 Score=32.94 Aligned_cols=58 Identities=19% Similarity=0.161 Sum_probs=32.6
Q ss_pred CceeeeEEEEeeCCCceeEEecCCCCCeEEEEEccccCCCcCCCCCEEEEEEEecCCCCCCceEE
Q psy3654 56 NPVETGKIKEFCRSKGHGFITPDSGEPAVFVHISDIEGCYVPLPGDEVKYRLCPIPPKFEKNQAV 120 (140)
Q Consensus 56 g~~~~G~VK~f~~~KGfGFI~~~~g~~dIFfH~s~l~~~~~~l~Gd~V~F~v~~~~k~~~g~~A~ 120 (140)
|.+.+.+|+..+ .+|+.-..+.+.+||++.+++... +.+||+|+.-+..+.+ +.+.|+
T Consensus 2 G~~~~L~V~~~~---~~g~fL~~~~~~~vlLp~~e~~~~--~~~Gd~v~VFvY~D~~--~rl~AT 59 (61)
T PF13509_consen 2 GQINTLKVVDKN---EFGYFLDDGEGKEVLLPKSEVPEP--LKVGDEVEVFVYLDKE--GRLVAT 59 (61)
T ss_dssp -------EEEE----SSEEEEEETT-EEEEEEGGG--------TTSEEEEEEEE-TT--S-EEEE
T ss_pred CCCcceEEEEEe---CCEEEEECCCCCEEEechHHcCCC--CCCCCEEEEEEEECCC--CCEEEe
Confidence 445667788776 477776666668999999998754 6699999987777654 566664
No 36
>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=93.96 E-value=0.36 Score=30.94 Aligned_cols=54 Identities=20% Similarity=0.257 Sum_probs=41.2
Q ss_pred CceeeeEEEEeeCCCceeEEecCCCCCeEEEEEccccCC-C-----cCCCCCEEEEEEEecCC
Q psy3654 56 NPVETGKIKEFCRSKGHGFITPDSGEPAVFVHISDIEGC-Y-----VPLPGDEVKYRLCPIPP 112 (140)
Q Consensus 56 g~~~~G~VK~f~~~KGfGFI~~~~g~~dIFfH~s~l~~~-~-----~~l~Gd~V~F~v~~~~k 112 (140)
|..+.|+|+... .||.+....++-+-|+|++++..+ . ....||.|+.++...++
T Consensus 1 G~~v~g~V~~v~---~~Gv~V~l~~~~~G~v~~s~l~~~~~~~~~~~~~~Gd~v~~~v~~~d~ 60 (68)
T cd05707 1 GDVVRGFVKNIA---NNGVFVTLGRGVDARVRVSELSDSYLKDWKKRFKVGQLVKGKIVSIDP 60 (68)
T ss_pred CCEEEEEEEEEE---CccEEEEeCCCCEEEEEHHHCCchhhcCHhhccCCCCEEEEEEEEEeC
Confidence 456889999975 467666555568999999999764 1 24599999999988764
No 37
>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=93.91 E-value=0.31 Score=32.52 Aligned_cols=55 Identities=9% Similarity=0.100 Sum_probs=41.6
Q ss_pred CCceeeeEEEEeeCCCceeEEecCCCCCeEEEEEccccCCC--c-------CCCCCEEEEEEEecCC
Q psy3654 55 QNPVETGKIKEFCRSKGHGFITPDSGEPAVFVHISDIEGCY--V-------PLPGDEVKYRLCPIPP 112 (140)
Q Consensus 55 ~g~~~~G~VK~f~~~KGfGFI~~~~g~~dIFfH~s~l~~~~--~-------~l~Gd~V~F~v~~~~k 112 (140)
.|..+.|+|+... .||.......+-+-|+|++++...+ . ...||.|++.+...++
T Consensus 3 ~G~~V~g~V~~i~---~~G~fV~l~~~v~G~v~~~~ls~~~~~~~~~~~~~~~~G~~v~~kVl~id~ 66 (74)
T cd05705 3 EGQLLRGYVSSVT---KQGVFFRLSSSIVGRVLFQNVTKYFVSDPSLYNKYLPEGKLLTAKVLSVNS 66 (74)
T ss_pred CCCEEEEEEEEEe---CCcEEEEeCCCCEEEEEHHHccCccccChhhHhcccCCCCEEEEEEEEEEC
Confidence 5788999999985 4665544445689999999987642 1 2499999999988764
No 38
>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=93.89 E-value=0.37 Score=30.95 Aligned_cols=54 Identities=22% Similarity=0.273 Sum_probs=42.4
Q ss_pred CceeeeEEEEeeCCCceeEEecCCCCCeEEEEEccccCC-C-----cCCCCCEEEEEEEecCC
Q psy3654 56 NPVETGKIKEFCRSKGHGFITPDSGEPAVFVHISDIEGC-Y-----VPLPGDEVKYRLCPIPP 112 (140)
Q Consensus 56 g~~~~G~VK~f~~~KGfGFI~~~~g~~dIFfH~s~l~~~-~-----~~l~Gd~V~F~v~~~~k 112 (140)
|..+.|+|+... .||.+-..+.+-+-|+|++++... . ....||.|++++...++
T Consensus 1 G~~v~g~V~~v~---~~Gv~V~l~~~v~g~i~~~~l~~~~~~~~~~~~~~Gd~i~~~V~~id~ 60 (69)
T cd05697 1 GQVVKGTIRKLR---PSGIFVKLSDHIKGLVPPMHLADVRLKHPEKKFKPGLKVKCRVLSVEP 60 (69)
T ss_pred CCEEEEEEEEEe---ccEEEEEecCCcEEEEEHHHCCCccccCHHHcCCCCCEEEEEEEEEEC
Confidence 457889999986 478777666568999999999764 1 24599999999988764
No 39
>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=93.81 E-value=0.4 Score=30.67 Aligned_cols=54 Identities=19% Similarity=0.225 Sum_probs=41.7
Q ss_pred CceeeeEEEEeeCCCceeEEecCCCCCeEEEEEccccCC-C-----cCCCCCEEEEEEEecCC
Q psy3654 56 NPVETGKIKEFCRSKGHGFITPDSGEPAVFVHISDIEGC-Y-----VPLPGDEVKYRLCPIPP 112 (140)
Q Consensus 56 g~~~~G~VK~f~~~KGfGFI~~~~g~~dIFfH~s~l~~~-~-----~~l~Gd~V~F~v~~~~k 112 (140)
|..+.|+|+... .+|.+.....+-+-|+|++++..+ . ....||.|++.+...+.
T Consensus 1 G~~v~g~V~~v~---~~g~~v~l~~~~~g~i~~~~~~~~~~~~~~~~~~~Gd~v~~~v~~~d~ 60 (73)
T cd05691 1 GSIVTGKVTEVD---AKGATVKLGDGVEGFLRAAELSRDRVEDATERFKVGDEVEAKITNVDR 60 (73)
T ss_pred CCEEEEEEEEEE---CCeEEEEeCCCCEEEEEHHHCCCccccCHHHccCCCCEEEEEEEEEeC
Confidence 456889999985 477776665567999999999765 2 13599999999988764
No 40
>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=93.75 E-value=0.75 Score=29.63 Aligned_cols=55 Identities=22% Similarity=0.233 Sum_probs=41.8
Q ss_pred CCceeeeEEEEeeCCCceeEEecCCCCCeEEEEEccccCC-C------cCCCCCEEEEEEEecCC
Q psy3654 55 QNPVETGKIKEFCRSKGHGFITPDSGEPAVFVHISDIEGC-Y------VPLPGDEVKYRLCPIPP 112 (140)
Q Consensus 55 ~g~~~~G~VK~f~~~KGfGFI~~~~g~~dIFfH~s~l~~~-~------~~l~Gd~V~F~v~~~~k 112 (140)
.|..+.|+|+...+ ||+....+.+.+-|+|++++... . ....||.|+.++...+.
T Consensus 3 ~g~~~~g~V~~i~~---~G~fv~l~~~~~Gl~~~~~l~~~~~~~~~~~~~~~Gd~v~v~v~~id~ 64 (72)
T cd05689 3 EGTRLFGKVTNLTD---YGCFVELEEGVEGLVHVSEMDWTNKNIHPSKVVSLGDEVEVMVLDIDE 64 (72)
T ss_pred CCCEEEEEEEEEEe---eEEEEEcCCCCEEEEEEEeccCcccccCcccEeCCCCEEEEEEEEeeC
Confidence 46789999999764 88887766568999999999632 1 12489999998877653
No 41
>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=93.38 E-value=0.84 Score=28.56 Aligned_cols=54 Identities=24% Similarity=0.274 Sum_probs=42.2
Q ss_pred CceeeeEEEEeeCCCceeEEecCCCCCeEEEEEccccCC-C-----cCCCCCEEEEEEEecCC
Q psy3654 56 NPVETGKIKEFCRSKGHGFITPDSGEPAVFVHISDIEGC-Y-----VPLPGDEVKYRLCPIPP 112 (140)
Q Consensus 56 g~~~~G~VK~f~~~KGfGFI~~~~g~~dIFfH~s~l~~~-~-----~~l~Gd~V~F~v~~~~k 112 (140)
|..+.|+|....+ ||+......+.+-|+|++++... . ....||.|..++...+.
T Consensus 1 g~~~~g~V~~v~~---~G~~v~l~~~~~g~l~~~~l~~~~~~~~~~~~~~Gd~v~v~v~~~d~ 60 (68)
T cd04472 1 GKIYEGKVVKIKD---FGAFVEILPGKDGLVHISELSDERVEKVEDVLKVGDEVKVKVIEVDD 60 (68)
T ss_pred CCEEEEEEEEEEE---eEEEEEeCCCCEEEEEhHHcCCccccCHHHccCCCCEEEEEEEEECC
Confidence 3467899999875 88888766568999999999775 2 13589999999888763
No 42
>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=93.36 E-value=0.41 Score=31.75 Aligned_cols=54 Identities=11% Similarity=-0.004 Sum_probs=39.5
Q ss_pred CceeeeEEEEeeCCCceeEEecCCCCCeEEEEEccccCC--------CcCCCCCEEEEEEEecCC
Q psy3654 56 NPVETGKIKEFCRSKGHGFITPDSGEPAVFVHISDIEGC--------YVPLPGDEVKYRLCPIPP 112 (140)
Q Consensus 56 g~~~~G~VK~f~~~KGfGFI~~~~g~~dIFfH~s~l~~~--------~~~l~Gd~V~F~v~~~~k 112 (140)
|..+.|+|+... .+|.......+-+-|+|++++..+ .....||.|++++...++
T Consensus 1 G~~V~g~V~~i~---~~g~~V~l~~~i~G~i~~~~ls~~~~~~~~~~~~~~vG~~v~~kV~~id~ 62 (73)
T cd05703 1 GQEVTGFVNNVS---KEFVWLTISPDVKGRIPLLDLSDDVSVLEHPEKKFPIGQALKAKVVGVDK 62 (73)
T ss_pred CCEEEEEEEEEe---CCEEEEEeCCCcEEEEEHHHcCCccccccCHHHhCCCCCEEEEEEEEEeC
Confidence 456889999985 355544444458999999999532 124599999999988765
No 43
>cd00164 S1_like S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains are members of the Oligonucleotide/oligosaccharide Binding (OB) fold.
Probab=93.09 E-value=0.49 Score=28.66 Aligned_cols=50 Identities=28% Similarity=0.422 Sum_probs=36.4
Q ss_pred eeEEEEeeCCCceeEEecCCCCCeEEEEEccccCCC------cCCCCCEEEEEEEecCC
Q psy3654 60 TGKIKEFCRSKGHGFITPDSGEPAVFVHISDIEGCY------VPLPGDEVKYRLCPIPP 112 (140)
Q Consensus 60 ~G~VK~f~~~KGfGFI~~~~g~~dIFfH~s~l~~~~------~~l~Gd~V~F~v~~~~k 112 (140)
.|+|+... .+|++...+.+.+.|+|.+++...+ ....||.|.+++...+.
T Consensus 2 ~g~V~~v~---~~g~~v~l~~~~~g~~~~~~~~~~~~~~~~~~~~~G~~v~~~v~~~d~ 57 (65)
T cd00164 2 TGKVVSIT---KFGVFVELEDGVEGLVHISELSDKFVKDPSEVFKVGDEVEVKVLEVDP 57 (65)
T ss_pred EEEEEEEE---eeeEEEEecCCCEEEEEHHHCCCccccCHhhEeCCCCEEEEEEEEEcC
Confidence 58888886 3554444444579999999997641 24599999999987653
No 44
>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=93.09 E-value=1.3 Score=29.14 Aligned_cols=64 Identities=22% Similarity=0.287 Sum_probs=44.5
Q ss_pred CceeeeEEEEeeCCCceeEEecCC---CCCeEEEEEccccCC-C------cCCCCCEEEEEEEecCCCCCCceEEEEEec
Q psy3654 56 NPVETGKIKEFCRSKGHGFITPDS---GEPAVFVHISDIEGC-Y------VPLPGDEVKYRLCPIPPKFEKNQAVHVEIV 125 (140)
Q Consensus 56 g~~~~G~VK~f~~~KGfGFI~~~~---g~~dIFfH~s~l~~~-~------~~l~Gd~V~F~v~~~~k~~~g~~A~~V~~~ 125 (140)
|..+.|+|....+ ||+....+ .+.+-|+|++++... + ....||.|..++...+ .+.....++.+
T Consensus 1 G~~~~g~V~~v~~---~G~fv~l~~~~~~~~gll~~s~l~~~~~~~~~~~~~~~Gd~v~v~v~~vd---~~~i~~s~k~~ 74 (79)
T cd05684 1 GKIYKGKVTSIMD---FGCFVQLEGLKGRKEGLVHISQLSFEGRVANPSDVVKRGQKVKVKVISIQ---NGKISLSMKDV 74 (79)
T ss_pred CCEEEEEEEEEEe---eeEEEEEeCCCCCcEEEEEhHhccCCCCcCChhheeCCCCEEEEEEEEEe---CCEEEEEEEec
Confidence 3567899998864 78766655 257899999999765 2 1359999999988766 24444444443
No 45
>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=93.09 E-value=1.2 Score=29.12 Aligned_cols=55 Identities=16% Similarity=0.181 Sum_probs=42.4
Q ss_pred CCceeeeEEEEeeCCCceeEEecCCC-CCeEEEEEccccCC-C-c----CCCCCEEEEEEEecCC
Q psy3654 55 QNPVETGKIKEFCRSKGHGFITPDSG-EPAVFVHISDIEGC-Y-V----PLPGDEVKYRLCPIPP 112 (140)
Q Consensus 55 ~g~~~~G~VK~f~~~KGfGFI~~~~g-~~dIFfH~s~l~~~-~-~----~l~Gd~V~F~v~~~~k 112 (140)
.|..+.|+|+...+ ||.....++ ..+-|+|++++... . . ...||+|..++...+.
T Consensus 3 ~g~~~~g~V~~i~~---fG~fv~l~~~~~eGlvh~sel~~~~~~~~~~~~~~Gd~v~vkv~~vd~ 64 (73)
T cd05686 3 LYQIFKGEVASVTE---YGAFVKIPGCRKQGLVHKSHMSSCRVDDPSEVVDVGEKVWVKVIGREM 64 (73)
T ss_pred CCCEEEEEEEEEEe---eeEEEEECCCCeEEEEEchhhCCCcccCHhhEECCCCEEEEEEEEECC
Confidence 47789999999864 887766644 25899999999775 2 1 2489999999988764
No 46
>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=92.96 E-value=0.74 Score=29.19 Aligned_cols=54 Identities=31% Similarity=0.324 Sum_probs=41.0
Q ss_pred CceeeeEEEEeeCCCceeEEecCCCCCeEEEEEccccC-C--C----cCCCCCEEEEEEEecCC
Q psy3654 56 NPVETGKIKEFCRSKGHGFITPDSGEPAVFVHISDIEG-C--Y----VPLPGDEVKYRLCPIPP 112 (140)
Q Consensus 56 g~~~~G~VK~f~~~KGfGFI~~~~g~~dIFfH~s~l~~-~--~----~~l~Gd~V~F~v~~~~k 112 (140)
|..+.|+|+... -||+....+.+.+-++|++++.. . . ....||.|+.++...+.
T Consensus 1 G~~~~g~V~~i~---~~G~fv~l~~~~~Glv~~~~l~~~~~~~~~~~~~~~G~~v~v~v~~id~ 61 (69)
T cd05690 1 GTVVSGKIKSIT---DFGIFVGLDGGIDGLVHISDISWTQRVRHPSEIYKKGQEVEAVVLNIDV 61 (69)
T ss_pred CCEEEEEEEEEE---eeeEEEEeCCCCEEEEEHHHCCCccccCChhhEECCCCEEEEEEEEEEC
Confidence 456889999975 48888776667899999999973 2 1 12489999999887653
No 47
>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=92.43 E-value=0.9 Score=28.19 Aligned_cols=54 Identities=20% Similarity=0.221 Sum_probs=40.6
Q ss_pred CceeeeEEEEeeCCCceeEEecCCCCCeEEEEEccccCC-C-----cCCCCCEEEEEEEecCC
Q psy3654 56 NPVETGKIKEFCRSKGHGFITPDSGEPAVFVHISDIEGC-Y-----VPLPGDEVKYRLCPIPP 112 (140)
Q Consensus 56 g~~~~G~VK~f~~~KGfGFI~~~~g~~dIFfH~s~l~~~-~-----~~l~Gd~V~F~v~~~~k 112 (140)
|..+.|+|+.... ||.......+.+-|+|.+++..+ + .+..||.|..++...+.
T Consensus 1 g~~~~g~V~~i~~---~G~fv~l~~~~~g~~~~~~l~~~~~~~~~~~~~~Gd~v~v~i~~vd~ 60 (68)
T cd05685 1 GMVLEGVVTNVTD---FGAFVDIGVKQDGLIHISKMADRFVSHPSDVVSVGDIVEVKVISIDE 60 (68)
T ss_pred CCEEEEEEEEEec---ccEEEEcCCCCEEEEEHHHCCCccccCHHHhcCCCCEEEEEEEEEEC
Confidence 3568899999753 67665555568899999999765 2 24599999999887653
No 48
>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=92.39 E-value=1.6 Score=28.61 Aligned_cols=55 Identities=16% Similarity=0.188 Sum_probs=42.5
Q ss_pred CCceeeeEEEEeeCCCceeEEecCCCCCeEEEEEccccCCC--c----CCCCCEEEEEEEecC
Q psy3654 55 QNPVETGKIKEFCRSKGHGFITPDSGEPAVFVHISDIEGCY--V----PLPGDEVKYRLCPIP 111 (140)
Q Consensus 55 ~g~~~~G~VK~f~~~KGfGFI~~~~g~~dIFfH~s~l~~~~--~----~l~Gd~V~F~v~~~~ 111 (140)
.|..+.|+|+..... ||.+.....+.+=|+|++++..++ . ...||.|..++...+
T Consensus 3 ~G~iv~G~V~~i~~~--~g~~v~l~~~~~Glvhis~~s~~~~~~~~~~~~~Gd~v~~kV~~~~ 63 (72)
T cd05704 3 EGAVTLGMVTKVIPH--SGLTVQLPFGKTGLVSIFHLSDSYTENPLEGFKPGKIVRCCILSKK 63 (72)
T ss_pred CCCEEEEEEEEeeCC--cEEEEECCCCCEEEEEHHHhcCcccCCHHHhCCCCCEEEEEEEEec
Confidence 578899999997533 666666666689999999997752 1 348999999998876
No 49
>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=92.03 E-value=1.2 Score=28.67 Aligned_cols=55 Identities=9% Similarity=0.108 Sum_probs=42.0
Q ss_pred CCceeeeEEEEeeCCCceeEEecCC--CCCeEEEEEccccCC-C-----cCCCCCEEEEEEEecCC
Q psy3654 55 QNPVETGKIKEFCRSKGHGFITPDS--GEPAVFVHISDIEGC-Y-----VPLPGDEVKYRLCPIPP 112 (140)
Q Consensus 55 ~g~~~~G~VK~f~~~KGfGFI~~~~--g~~dIFfH~s~l~~~-~-----~~l~Gd~V~F~v~~~~k 112 (140)
.|..+.|+|.... .||.+.... .+.+-|+|++++... + ....||.|+.++...+.
T Consensus 3 ~G~~~~g~V~~v~---~~g~~v~l~~~~~~~gll~~s~l~~~~~~~~~~~~~~Gd~v~vkv~~~d~ 65 (76)
T cd04452 3 EGELVVVTVKSIA---DMGAYVSLLEYGNIEGMILLSELSRRRIRSIRKLVKVGRKEVVKVIRVDK 65 (76)
T ss_pred CCCEEEEEEEEEE---ccEEEEEEcCCCCeEEEEEhHHcCCcccCCHHHeeCCCCEEEEEEEEEEC
Confidence 4778999999985 488766654 247899999999775 2 13599999999887653
No 50
>PRK05807 hypothetical protein; Provisional
Probab=92.01 E-value=2 Score=32.06 Aligned_cols=66 Identities=17% Similarity=0.264 Sum_probs=49.6
Q ss_pred CCceeeeEEEEeeCCCceeEEecCCCCCeEEEEEccccCCC------cCCCCCEEEEEEEecCCCCCCceEEEEEecC
Q psy3654 55 QNPVETGKIKEFCRSKGHGFITPDSGEPAVFVHISDIEGCY------VPLPGDEVKYRLCPIPPKFEKNQAVHVEIVH 126 (140)
Q Consensus 55 ~g~~~~G~VK~f~~~KGfGFI~~~~g~~dIFfH~s~l~~~~------~~l~Gd~V~F~v~~~~k~~~g~~A~~V~~~~ 126 (140)
.|..+.|+|.... .||++...+ +..-|+|++++...+ .+..||.|+..+...+. .+.....++.+.
T Consensus 5 vG~vv~G~Vt~i~---~~GafV~L~-~~~Glvhiseis~~~v~~~~~~~kvGd~V~VkV~~id~--~gkI~LSlk~~~ 76 (136)
T PRK05807 5 AGSILEGTVVNIT---NFGAFVEVE-GKTGLVHISEVADTYVKDIREHLKEQDKVKVKVISIDD--NGKISLSIKQAM 76 (136)
T ss_pred CCCEEEEEEEEEE---CCeEEEEEC-CEEEEEEhhhcccccccCccccCCCCCEEEEEEEEECC--CCcEEEEEEecc
Confidence 4788999999975 478777765 468999999997641 23599999999888764 355666666654
No 51
>PRK07252 hypothetical protein; Provisional
Probab=91.87 E-value=1.4 Score=32.39 Aligned_cols=55 Identities=18% Similarity=0.178 Sum_probs=44.3
Q ss_pred CCceeeeEEEEeeCCCceeEEecCCCCCeEEEEEccccCC-C-----cCCCCCEEEEEEEecCC
Q psy3654 55 QNPVETGKIKEFCRSKGHGFITPDSGEPAVFVHISDIEGC-Y-----VPLPGDEVKYRLCPIPP 112 (140)
Q Consensus 55 ~g~~~~G~VK~f~~~KGfGFI~~~~g~~dIFfH~s~l~~~-~-----~~l~Gd~V~F~v~~~~k 112 (140)
.|..+.|+|.... .||++...+++.+-|+|+++|..+ + ....||.|..++...+.
T Consensus 3 vG~iv~G~V~~V~---~~G~fVei~~~~~GllhiseLs~~~~~~~~~~~~vGD~V~VkI~~iD~ 63 (120)
T PRK07252 3 IGDKLKGTITGIK---PYGAFVALENGTTGLIHISEIKTGFIDNIHQLLKVGEEVLVQVVDFDE 63 (120)
T ss_pred CCCEEEEEEEEEe---CcEEEEEECCCCEEEEEHHHcCCccccChhhccCCCCEEEEEEEEEeC
Confidence 4778999999986 488887776668999999999764 2 23499999999988764
No 52
>COG1098 VacB Predicted RNA binding protein (contains ribosomal protein S1 domain) [Translation, ribosomal structure and biogenesis]
Probab=91.86 E-value=0.39 Score=36.24 Aligned_cols=72 Identities=24% Similarity=0.279 Sum_probs=53.3
Q ss_pred CCceeeeEEEEeeCCCceeEEecCCCCCeEEEEEccccCCC-----c-CCCCCEEEEEEEecCCCCCCceEEEEEecCCC
Q psy3654 55 QNPVETGKIKEFCRSKGHGFITPDSGEPAVFVHISDIEGCY-----V-PLPGDEVKYRLCPIPPKFEKNQAVHVEIVHLT 128 (140)
Q Consensus 55 ~g~~~~G~VK~f~~~KGfGFI~~~~g~~dIFfH~s~l~~~~-----~-~l~Gd~V~F~v~~~~k~~~g~~A~~V~~~~~~ 128 (140)
.|..++|+|.-.- -||--.-.++++.=+||||.|...| . +.+||+|.-.+-..+. .|-.-..|+-+...
T Consensus 5 vG~~l~GkItgI~---~yGAFV~l~~g~tGLVHISEIa~~fVkdI~d~L~vG~eV~vKVl~ide--~GKisLSIr~~~e~ 79 (129)
T COG1098 5 VGSKLKGKITGIT---PYGAFVELEGGKTGLVHISEIADGFVKDIHDHLKVGQEVKVKVLDIDE--NGKISLSIRKLEEE 79 (129)
T ss_pred ccceEEEEEEeeE---ecceEEEecCCCcceEEehHhhhhhHHhHHHHhcCCCEEEEEEEeecc--CCCcceehHHhhhC
Confidence 4778999988754 5774444445577899999998863 2 3499999999988775 45566777777777
Q ss_pred Ccc
Q psy3654 129 PEV 131 (140)
Q Consensus 129 p~~ 131 (140)
|+.
T Consensus 80 pe~ 82 (129)
T COG1098 80 PEK 82 (129)
T ss_pred ccc
Confidence 764
No 53
>cd04455 S1_NusA S1_NusA: N-utilizing substance A protein (NusA), S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. NusA is a transcription elongation factor containing an N-terminal catalytic domain and three RNA binding domains (RBD's). The RBD's include one S1 domain and two KH domains that form an RNA binding surface. DNA transcription by RNA polymerase (RNAP) includes three phases - initiation, elongation, and termination. During initiation, sigma factors bind RNAP and target RNAP to specific promoters. During elongation, N-utilization substances (NusA, B, E, and G) replace sigma factors and regulate pausing, termination, and antitermination. NusA is cold-shock-inducible.
Probab=91.55 E-value=1.4 Score=28.54 Aligned_cols=54 Identities=17% Similarity=0.188 Sum_probs=39.6
Q ss_pred CCceeeeEEEEeeCCCceeEEecCCCCCeEEEEEccccCCCcCCCCCEEEEEEEecCC
Q psy3654 55 QNPVETGKIKEFCRSKGHGFITPDSGEPAVFVHISDIEGCYVPLPGDEVKYRLCPIPP 112 (140)
Q Consensus 55 ~g~~~~G~VK~f~~~KGfGFI~~~~g~~dIFfH~s~l~~~~~~l~Gd~V~F~v~~~~k 112 (140)
.|..+.|+|...+. ++=||.. ++ -+-|++.+++........||.|++.+...++
T Consensus 3 ~g~iV~G~V~~~~~--~~~~vdi-g~-~eg~lp~~e~~~~~~~~~Gd~v~v~v~~v~~ 56 (67)
T cd04455 3 EGEIVTGIVKRVDR--GNVIVDL-GK-VEAILPKKEQIPGESYRPGDRIKAYVLEVRK 56 (67)
T ss_pred CCCEEEEEEEEEcC--CCEEEEc-CC-eEEEeeHHHCCCCCcCCCCCEEEEEEEEEec
Confidence 57789999999865 2334444 33 6889999998643345799999999987653
No 54
>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=90.88 E-value=2.6 Score=27.90 Aligned_cols=53 Identities=19% Similarity=0.160 Sum_probs=42.6
Q ss_pred ccCCceeeeEEEEeeCCCceeEEecCCCCCeEEEEEccccCCCcCCCCCEEEEEEEec
Q psy3654 53 ALQNPVETGKIKEFCRSKGHGFITPDSGEPAVFVHISDIEGCYVPLPGDEVKYRLCPI 110 (140)
Q Consensus 53 ~~~g~~~~G~VK~f~~~KGfGFI~~~~g~~dIFfH~s~l~~~~~~l~Gd~V~F~v~~~ 110 (140)
...|..+.|+|.... .||+...-+.+.+-|+|.+++.. ....||.|..++...
T Consensus 14 ~~~G~~~~g~V~~i~---~~G~fV~l~~~~~Glv~~se~~~--~~~iGd~v~v~I~~i 66 (77)
T cd04473 14 LEVGKLYKGKVNGVA---KYGVFVDLNDHVRGLIHRSNLLR--DYEVGDEVIVQVTDI 66 (77)
T ss_pred CCCCCEEEEEEEeEe---cceEEEEECCCcEEEEEchhccC--cCCCCCEEEEEEEEE
Confidence 335788999999975 48888777766899999999864 356999999988776
No 55
>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=90.63 E-value=1.4 Score=28.53 Aligned_cols=55 Identities=15% Similarity=0.167 Sum_probs=39.5
Q ss_pred CceeeeEEEEeeCCCceeEEecCCCCCeEEEEEccccCC----CcCCCCCEEEEEEEecCCC
Q psy3654 56 NPVETGKIKEFCRSKGHGFITPDSGEPAVFVHISDIEGC----YVPLPGDEVKYRLCPIPPK 113 (140)
Q Consensus 56 g~~~~G~VK~f~~~KGfGFI~~~~g~~dIFfH~s~l~~~----~~~l~Gd~V~F~v~~~~k~ 113 (140)
|....|+|+... .+|.+....++-+-|+|++.+... .....||.|.+++...+++
T Consensus 1 G~~V~g~V~~i~---~~G~~v~l~~~v~g~v~~~~l~~~~~~~~~~~~G~~i~~kVi~id~~ 59 (66)
T cd05695 1 GMLVNARVKKVL---SNGLILDFLSSFTGTVDFLHLDPEKSSKSTYKEGQKVRARILYVDPS 59 (66)
T ss_pred CCEEEEEEEEEe---CCcEEEEEcCCceEEEEHHHcCCccCcccCcCCCCEEEEEEEEEeCC
Confidence 456889999985 355544433357899999998653 1345999999998877653
No 56
>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=90.55 E-value=1.6 Score=27.94 Aligned_cols=53 Identities=13% Similarity=0.117 Sum_probs=38.9
Q ss_pred CceeeeEEEEeeCCCceeEEecCCCCCeEEEEEccccCCC------cCCCCCEEEEEEEecC
Q psy3654 56 NPVETGKIKEFCRSKGHGFITPDSGEPAVFVHISDIEGCY------VPLPGDEVKYRLCPIP 111 (140)
Q Consensus 56 g~~~~G~VK~f~~~KGfGFI~~~~g~~dIFfH~s~l~~~~------~~l~Gd~V~F~v~~~~ 111 (140)
|..+.|+|..... ..=||.. ..+.+-|+|.+++...+ ....||.|++.+...+
T Consensus 1 G~iv~g~V~~i~~--~~~~v~l-~~~~~g~l~~~e~~~~~~~~~~~~~~~Gd~i~~~i~~~~ 59 (70)
T cd05687 1 GDIVKGTVVSVDD--DEVLVDI-GYKSEGIIPISEFSDDPIENGEDEVKVGDEVEVYVLRVE 59 (70)
T ss_pred CCEEEEEEEEEeC--CEEEEEe-CCCceEEEEHHHhCccccCCHhHcCCCCCEEEEEEEEEE
Confidence 4678999999864 2445555 44578999999997541 2459999999998765
No 57
>PRK08059 general stress protein 13; Validated
Probab=90.21 E-value=3 Score=30.35 Aligned_cols=71 Identities=24% Similarity=0.327 Sum_probs=52.1
Q ss_pred CCceeeeEEEEeeCCCceeEEecCCCCCeEEEEEccccCCC------cCCCCCEEEEEEEecCCCCCCceEEEEEecCCC
Q psy3654 55 QNPVETGKIKEFCRSKGHGFITPDSGEPAVFVHISDIEGCY------VPLPGDEVKYRLCPIPPKFEKNQAVHVEIVHLT 128 (140)
Q Consensus 55 ~g~~~~G~VK~f~~~KGfGFI~~~~g~~dIFfH~s~l~~~~------~~l~Gd~V~F~v~~~~k~~~g~~A~~V~~~~~~ 128 (140)
.|..+.|+|..... ||+....+.+.+-|+|++++...+ ....||.|..++...+.. .+.....++.+...
T Consensus 7 ~G~iv~G~V~~i~~---~G~fV~i~~~~~Gli~~sel~~~~~~~~~~~~~vGD~I~vkI~~id~~-~~~i~lslk~~~~~ 82 (123)
T PRK08059 7 VGSVVTGKVTGIQP---YGAFVALDEETQGLVHISEITHGFVKDIHDFLSVGDEVKVKVLSVDEE-KGKISLSIRATEEA 82 (123)
T ss_pred CCCEEEEEEEEEec---ceEEEEECCCCEEEEEHHHCCcccccCHHHcCCCCCEEEEEEEEEECC-CCeEEEEEEEcccC
Confidence 57889999999764 787777766689999999997641 235899999999886532 34555566666555
Q ss_pred C
Q psy3654 129 P 129 (140)
Q Consensus 129 p 129 (140)
|
T Consensus 83 ~ 83 (123)
T PRK08059 83 P 83 (123)
T ss_pred c
Confidence 5
No 58
>PRK09376 rho transcription termination factor Rho; Provisional
Probab=90.11 E-value=1.1 Score=39.88 Aligned_cols=67 Identities=22% Similarity=0.288 Sum_probs=47.7
Q ss_pred eeeeEEEEeeCCCceeEEecCC-----CCCeEEEEEccccCCCcCCCCCEEEEEEEecCCCCCCceEEEEEecCC
Q psy3654 58 VETGKIKEFCRSKGHGFITPDS-----GEPAVFVHISDIEGCYVPLPGDEVKYRLCPIPPKFEKNQAVHVEIVHL 127 (140)
Q Consensus 58 ~~~G~VK~f~~~KGfGFI~~~~-----g~~dIFfH~s~l~~~~~~l~Gd~V~F~v~~~~k~~~g~~A~~V~~~~~ 127 (140)
...|++--.. +||||++..+ +.+||||-.+.|+.. .++.||.|.=.+..-..+.+.+.-..|..++.
T Consensus 50 ~~~g~le~~~--~g~gflr~~~~~y~~~~~d~yvs~~~ir~~-~lr~gd~v~g~~r~~~~~e~~~~l~~v~~vng 121 (416)
T PRK09376 50 FGEGVLEILP--DGFGFLRSPDANYLPGPDDIYVSPSQIRRF-NLRTGDTVEGKIRPPKEGERYFALLKVETVNG 121 (416)
T ss_pred EEEEEEEEcC--CCCeEEeCCCcCCCCCCCCeeeCHHHHHhc-CCCCCCEEEEEeeCCCCCCCccceEEEeeeCC
Confidence 5678777654 3999999853 458999999998774 57799999988876332223445567766653
No 59
>PHA02945 interferon resistance protein; Provisional
Probab=88.74 E-value=5.2 Score=28.37 Aligned_cols=70 Identities=16% Similarity=0.049 Sum_probs=48.5
Q ss_pred ccccCCceeeeEEEEeeCCCceeEEecCC--CCCeEEEEEccc--cCC----CcCCCCCEEEEEEEecCCCCCCceEEEE
Q psy3654 51 NRALQNPVETGKIKEFCRSKGHGFITPDS--GEPAVFVHISDI--EGC----YVPLPGDEVKYRLCPIPPKFEKNQAVHV 122 (140)
Q Consensus 51 ~~~~~g~~~~G~VK~f~~~KGfGFI~~~~--g~~dIFfH~s~l--~~~----~~~l~Gd~V~F~v~~~~k~~~g~~A~~V 122 (140)
.+...|+...|+|+. +.||+-...+ ++.+-|+|+|.+ ... ...++|+.|-.++-..++ .+|..-++.
T Consensus 7 ~~P~~GelvigtV~~----~d~ga~v~L~EY~g~eg~i~~seveva~~wvK~rd~l~GqkvV~KVirVd~-~kg~IDlSl 81 (88)
T PHA02945 7 SLPNVGDVLKGKVYE----NGYALYIDLFDYPHSEAILAESVQMHMNRYFKYRDKLVGKTVKVKVIRVDY-TKGYIDVNY 81 (88)
T ss_pred cCCCCCcEEEEEEEe----cCceEEEEecccCCcEEEEEeehhhhccceEeeeeEecCCEEEEEEEEECC-CCCEEEeEe
Confidence 355678999999998 4688655544 568899999966 443 223399999999988775 245554544
Q ss_pred Eec
Q psy3654 123 EIV 125 (140)
Q Consensus 123 ~~~ 125 (140)
+-+
T Consensus 82 K~V 84 (88)
T PHA02945 82 KRM 84 (88)
T ss_pred eEc
Confidence 433
No 60
>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=88.27 E-value=3.9 Score=26.60 Aligned_cols=53 Identities=25% Similarity=0.296 Sum_probs=38.8
Q ss_pred CceeeeEEEEeeCCCceeEEecCCC-CCeEEEEEccccCCC-----------------cCCCCCEEEEEEEecC
Q psy3654 56 NPVETGKIKEFCRSKGHGFITPDSG-EPAVFVHISDIEGCY-----------------VPLPGDEVKYRLCPIP 111 (140)
Q Consensus 56 g~~~~G~VK~f~~~KGfGFI~~~~g-~~dIFfH~s~l~~~~-----------------~~l~Gd~V~F~v~~~~ 111 (140)
|..+.|+|..... ||++..... +-+-|+|++++..++ ....||.|+-.+...+
T Consensus 2 g~~~~g~V~~v~~---~G~fv~l~~~~~~G~v~~~~l~~~~~~~d~~~~~~~~~~~~~~~~~gd~v~v~v~~vd 72 (83)
T cd04471 2 GEEFDGVISGVTS---FGLFVELDNLTVEGLVHVSTLGDDYYEFDEENHALVGERTGKVFRLGDKVKVRVVRVD 72 (83)
T ss_pred CCEEEEEEEeEEe---eeEEEEecCCCEEEEEEEEecCCCcEEEcccceEEEeccCCCEEcCCCEEEEEEEEec
Confidence 5678899998864 888877765 567899999987531 1237888888877765
No 61
>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=88.03 E-value=5.9 Score=26.32 Aligned_cols=55 Identities=11% Similarity=0.053 Sum_probs=40.5
Q ss_pred CCceeeeEEEEeeCCCceeEEecCCCCCeEEEEEccccC----C-----C-cCCCCCEEEEEEEecCC
Q psy3654 55 QNPVETGKIKEFCRSKGHGFITPDSGEPAVFVHISDIEG----C-----Y-VPLPGDEVKYRLCPIPP 112 (140)
Q Consensus 55 ~g~~~~G~VK~f~~~KGfGFI~~~~g~~dIFfH~s~l~~----~-----~-~~l~Gd~V~F~v~~~~k 112 (140)
.|..+.|+|.... .+|....-+.+-+-|+|++++.. . . .+..||.|.+++....+
T Consensus 6 ~GdiV~g~V~~i~---~~g~~v~i~~~~~G~l~~se~~~~~~~~~~~~~~~~l~vGd~i~~~V~~~~~ 70 (86)
T cd05789 6 VGDVVIGRVTEVG---FKRWKVDINSPYDAVLPLSEVNLPRTDEDELNMRSYLDEGDLIVAEVQSVDS 70 (86)
T ss_pred CCCEEEEEEEEEC---CCEEEEECCCCeEEEEEHHHccCCCCccchHHHHhhCCCCCEEEEEEEEECC
Confidence 5788999999964 34444444445789999999963 1 1 25699999999988764
No 62
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=87.64 E-value=2 Score=38.51 Aligned_cols=61 Identities=16% Similarity=0.140 Sum_probs=45.9
Q ss_pred CCceeeeEEEEeeCCCceeEEecCCCCCeEEEEEccccCCCcCCCCCEEEEEEEecCCCCCCceE
Q psy3654 55 QNPVETGKIKEFCRSKGHGFITPDSGEPAVFVHISDIEGCYVPLPGDEVKYRLCPIPPKFEKNQA 119 (140)
Q Consensus 55 ~g~~~~G~VK~f~~~KGfGFI~~~~g~~dIFfH~s~l~~~~~~l~Gd~V~F~v~~~~k~~~g~~A 119 (140)
.|.++.|+|+... + +|+|... ++-+-|+|.+++........||+|.+.+..-.+..+|.+.
T Consensus 134 ~GeIV~G~V~ri~--~-~giiVDL-ggvea~LP~sE~ip~E~~~~GdrIka~I~~Vd~~~kg~qI 194 (470)
T PRK09202 134 VGEIITGVVKRVE--R-GNIIVDL-GRAEAILPRKEQIPRENFRPGDRVRAYVYEVRKEARGPQI 194 (470)
T ss_pred cCCEEEEEEEEEe--c-CCEEEEE-CCeEEEecHHHcCCCccCCCCCEEEEEEEEEecCCCCCeE
Confidence 5899999999986 3 3565555 4578999999986544567999999999887654455443
No 63
>COG1158 Rho Transcription termination factor [Transcription]
Probab=87.57 E-value=1.7 Score=38.32 Aligned_cols=65 Identities=28% Similarity=0.408 Sum_probs=47.6
Q ss_pred eeeEEEEeeCCCceeEEecCC-----CCCeEEEEEccccCCCcCCCCCEEEEEEEecCCCCCCceE-EEEEecCC
Q psy3654 59 ETGKIKEFCRSKGHGFITPDS-----GEPAVFVHISDIEGCYVPLPGDEVKYRLCPIPPKFEKNQA-VHVEIVHL 127 (140)
Q Consensus 59 ~~G~VK~f~~~KGfGFI~~~~-----g~~dIFfH~s~l~~~~~~l~Gd~V~F~v~~~~k~~~g~~A-~~V~~~~~ 127 (140)
..|+.--.. .||||++..+ +.+||||--|.|+.. .++.||.|+=++.. +|..+++-| ..|..++.
T Consensus 54 ~~GvLeil~--dGfGFLR~~~~~yl~~~~DiYvSpSQIRrf-~LrtGD~v~G~vR~-Pke~Ery~aLl~ve~vN~ 124 (422)
T COG1158 54 GDGVLEILP--DGFGFLRSADSSYLPGPDDIYVSPSQIRRF-NLRTGDTVEGKVRP-PKEGERYFALLKVEAVNG 124 (422)
T ss_pred eeeEEEecc--CCcceeecCccccCCCCCceEECHHHHhhc-cCccCCEEeeeecC-CCcccceeeeEEEeecCC
Confidence 346666653 7999999866 568999999999874 56799999887754 444456666 56666653
No 64
>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=87.50 E-value=3.2 Score=26.72 Aligned_cols=53 Identities=13% Similarity=0.073 Sum_probs=38.5
Q ss_pred CceeeeEEEEeeCCCceeEEecCCCCCeEEEEEccccCCC--------cCCCCCEEEEEEEecC
Q psy3654 56 NPVETGKIKEFCRSKGHGFITPDSGEPAVFVHISDIEGCY--------VPLPGDEVKYRLCPIP 111 (140)
Q Consensus 56 g~~~~G~VK~f~~~KGfGFI~~~~g~~dIFfH~s~l~~~~--------~~l~Gd~V~F~v~~~~ 111 (140)
|..+.|+|+.... +|.+-..+.+-+-++|++++...+ ...+||.|...+...+
T Consensus 1 G~iV~g~V~~i~~---~gi~v~l~~~i~g~i~~~~i~~~~~~~~~~~~~~~~Gd~i~~kVl~~d 61 (70)
T cd05702 1 GDLVKAKVKSVKP---TQLNVQLADNVHGRIHVSEVFDEWPDGKNPLSKFKIGQKIKARVIGGH 61 (70)
T ss_pred CCEEEEEEEEEEC---CcEEEEeCCCcEEEEEHHHhccccccccChhHhCCCCCEEEEEEEEEe
Confidence 4678899999854 455544445689999999996431 2459999999987755
No 65
>PTZ00248 eukaryotic translation initiation factor 2 subunit 1; Provisional
Probab=87.42 E-value=3.1 Score=35.73 Aligned_cols=72 Identities=7% Similarity=-0.057 Sum_probs=55.1
Q ss_pred cCCceeeeEEEEeeCCCceeEEecCC--CCCeEEEEEccccCC--C---c-CCCCCEEEEEEEecCCCCCCceEEEEEec
Q psy3654 54 LQNPVETGKIKEFCRSKGHGFITPDS--GEPAVFVHISDIEGC--Y---V-PLPGDEVKYRLCPIPPKFEKNQAVHVEIV 125 (140)
Q Consensus 54 ~~g~~~~G~VK~f~~~KGfGFI~~~~--g~~dIFfH~s~l~~~--~---~-~l~Gd~V~F~v~~~~k~~~g~~A~~V~~~ 125 (140)
..|..+.|+|+... .||.+.... ++-+-|+|+|+|... . . +++||.|...+-..++ .+|.....++.+
T Consensus 16 ~~GdvV~g~V~~I~---d~GafV~L~EY~gvEGlIhiSElS~~ri~~i~d~vkvGd~v~vkVl~VD~-ekg~IdLS~K~v 91 (319)
T PTZ00248 16 EEDDLVMVKVVRIT---EMGAYVSLLEYDDIEGMILMSELSKRRIRSINKLIRVGRHEVVVVLRVDK-EKGYIDLSKKRV 91 (319)
T ss_pred CCCCEEEEEEEEEe---CCeEEEEecCCCCcEEEEEHHHhcccccCCHHHhcCCCCEEEEEEEEEeC-CCCEEEEEeeec
Confidence 36899999999986 488776664 468999999999664 1 2 3599999999988654 247778888877
Q ss_pred CCCC
Q psy3654 126 HLTP 129 (140)
Q Consensus 126 ~~~p 129 (140)
...|
T Consensus 92 ~~~p 95 (319)
T PTZ00248 92 SPED 95 (319)
T ss_pred ccch
Confidence 7655
No 66
>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=86.70 E-value=5 Score=25.59 Aligned_cols=54 Identities=17% Similarity=0.190 Sum_probs=41.2
Q ss_pred CceeeeEEEEeeCCCceeEEecCC-CCCeEEEEEccccCCC------cCCCCCEEEEEEEecCC
Q psy3654 56 NPVETGKIKEFCRSKGHGFITPDS-GEPAVFVHISDIEGCY------VPLPGDEVKYRLCPIPP 112 (140)
Q Consensus 56 g~~~~G~VK~f~~~KGfGFI~~~~-g~~dIFfH~s~l~~~~------~~l~Gd~V~F~v~~~~k 112 (140)
|..+.|+|+... .+|++.... .+.+-|+|++++..++ ....||.|+.++...+.
T Consensus 3 g~~v~g~V~~i~---~~g~~v~l~~~~~~g~i~~~~l~~~~~~~~~~~~~~Gd~v~v~i~~vd~ 63 (77)
T cd05708 3 GQKIDGTVRRVE---DYGVFIDIDGTNVSGLCHKSEISDNRVADASKLFRVGDKVRAKVLKIDA 63 (77)
T ss_pred CCEEEEEEEEEE---cceEEEEECCCCeEEEEEHHHCCCCccCCHhHeecCCCEEEEEEEEEeC
Confidence 667899999985 477666654 3578999999998652 23599999999887663
No 67
>PRK07899 rpsA 30S ribosomal protein S1; Reviewed
Probab=86.15 E-value=4.6 Score=36.36 Aligned_cols=66 Identities=20% Similarity=0.252 Sum_probs=48.6
Q ss_pred CCceeeeEEEEeeCCCceeEEecCCCCCeEEEEEccccCC-C-----cCCCCCEEEEEEEecCCCCCCceEEEEEe
Q psy3654 55 QNPVETGKIKEFCRSKGHGFITPDSGEPAVFVHISDIEGC-Y-----VPLPGDEVKYRLCPIPPKFEKNQAVHVEI 124 (140)
Q Consensus 55 ~g~~~~G~VK~f~~~KGfGFI~~~~g~~dIFfH~s~l~~~-~-----~~l~Gd~V~F~v~~~~k~~~g~~A~~V~~ 124 (140)
.|..+.|+|+... -||+....+.+-+-|+|+++|... . ....||.|+..+...+.. ++.....++.
T Consensus 293 vG~vv~G~V~~I~---~fGvFVeL~~gieGLvh~SeLs~~~v~~~~~~~kvGd~V~VkIi~ID~e-~rrI~LSlK~ 364 (486)
T PRK07899 293 IGQIVPGKVTKLV---PFGAFVRVEEGIEGLVHISELAERHVEVPEQVVQVGDEVFVKVIDIDLE-RRRISLSLKQ 364 (486)
T ss_pred CCCEEEEEEEEEe---ccEEEEEeCCCcEEEEEHHHcCcccccCccceeCCCCEEEEEEEEEECC-CCEEEEEEEE
Confidence 5889999999985 489877766668999999999764 1 235999999999876642 2334444443
No 68
>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=85.63 E-value=4.8 Score=24.92 Aligned_cols=53 Identities=26% Similarity=0.283 Sum_probs=39.2
Q ss_pred CceeeeEEEEeeCCCceeEEecCCCCCeEEEEEccccCC--C----cCCCCCEEEEEEEecCC
Q psy3654 56 NPVETGKIKEFCRSKGHGFITPDSGEPAVFVHISDIEGC--Y----VPLPGDEVKYRLCPIPP 112 (140)
Q Consensus 56 g~~~~G~VK~f~~~KGfGFI~~~~g~~dIFfH~s~l~~~--~----~~l~Gd~V~F~v~~~~k 112 (140)
|..+.|+|....+ +|++...+ +.+-|+|.+++... . ....||.|.+.+...+.
T Consensus 2 g~~~~g~V~~v~~---~g~~v~l~-~~~g~l~~~e~~~~~~~~~~~~~~~Gd~v~v~i~~vd~ 60 (68)
T cd05688 2 GDVVEGTVKSITD---FGAFVDLG-GVDGLLHISDMSWGRVKHPSEVVNVGDEVEVKVLKIDK 60 (68)
T ss_pred CCEEEEEEEEEEe---eeEEEEEC-CeEEEEEhHHCCCccccCHhHEECCCCEEEEEEEEEEC
Confidence 5678999999874 56665554 47899999998643 1 23599999999887653
No 69
>PRK12608 transcription termination factor Rho; Provisional
Probab=85.62 E-value=0.93 Score=39.73 Aligned_cols=52 Identities=23% Similarity=0.254 Sum_probs=40.1
Q ss_pred CCceeeeEEEEeeCCCceeEEecC-----CCCCeEEEEEccccCCCcCCCCCEEEEEEEe
Q psy3654 55 QNPVETGKIKEFCRSKGHGFITPD-----SGEPAVFVHISDIEGCYVPLPGDEVKYRLCP 109 (140)
Q Consensus 55 ~g~~~~G~VK~f~~~KGfGFI~~~-----~g~~dIFfH~s~l~~~~~~l~Gd~V~F~v~~ 109 (140)
......|++--.. +||||++.. .+.+||||..+.|+.. .+..||.|.-....
T Consensus 15 ~~~~~~g~l~~~~--~g~gflr~~~~~~~~~~~d~yv~~~~i~~~-~l~~Gd~V~~~~r~ 71 (380)
T PRK12608 15 STEEVLGVLEILG--DGFGFLRSARRNYLPSPDDVFVPPALIRRF-NLRTGDVVEGVARP 71 (380)
T ss_pred CCCcceEEEEEcC--CCceEeecCccCCCCCCCCeeeCHHHHHHh-CCCCCCEEEeccCC
Confidence 3455779888764 499999985 3668999999999875 46699999876554
No 70
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=85.24 E-value=5.2 Score=38.76 Aligned_cols=67 Identities=13% Similarity=0.139 Sum_probs=48.6
Q ss_pred CCceee-eEEEEeeCCCceeEEecCCCCCeEEEEEccccCC-C-----cCCCCCEEEEEEEecCCCCCCceEEEEEecC
Q psy3654 55 QNPVET-GKIKEFCRSKGHGFITPDSGEPAVFVHISDIEGC-Y-----VPLPGDEVKYRLCPIPPKFEKNQAVHVEIVH 126 (140)
Q Consensus 55 ~g~~~~-G~VK~f~~~KGfGFI~~~~g~~dIFfH~s~l~~~-~-----~~l~Gd~V~F~v~~~~k~~~g~~A~~V~~~~ 126 (140)
.|..+. |+|+... .||+......+.+-|+|+|+|..+ + ....||.|..++...++ .|......+.+.
T Consensus 753 vG~iy~~g~V~~I~---~FGaFVeL~~g~EGLVHISeLs~~rv~~~~dv~kvGD~V~VkVi~ID~--~grI~LSlK~l~ 826 (891)
T PLN00207 753 VGDIYRNCEIKSIA---PYGAFVEIAPGREGLCHISELSSNWLAKPEDAFKVGDRIDVKLIEVND--KGQLRLSRRALL 826 (891)
T ss_pred CCcEEECcEEEEEe---ccEEEEEeCCCCEEEEEhhhcCCccccCHHHhcCCCCEEEEEEEEECC--CCcEEEEEeccc
Confidence 677884 6999875 599776666568999999999765 1 23489999999998874 344445554443
No 71
>PRK13806 rpsA 30S ribosomal protein S1; Provisional
Probab=85.09 E-value=6.1 Score=35.26 Aligned_cols=72 Identities=21% Similarity=0.262 Sum_probs=51.2
Q ss_pred cCCceeeeEEEEeeCCCceeEEecCCCCCeEEEEEccccCC---C----cCCCCCEEEEEEEecCCCCCCceEEEEEecC
Q psy3654 54 LQNPVETGKIKEFCRSKGHGFITPDSGEPAVFVHISDIEGC---Y----VPLPGDEVKYRLCPIPPKFEKNQAVHVEIVH 126 (140)
Q Consensus 54 ~~g~~~~G~VK~f~~~KGfGFI~~~~g~~dIFfH~s~l~~~---~----~~l~Gd~V~F~v~~~~k~~~g~~A~~V~~~~ 126 (140)
..|..+.|+|+... -||.+...+.+-+.|+|++++... . ....||.|+..+...++. ++.....++...
T Consensus 291 ~~G~~v~G~V~~v~---~~G~fV~l~~gv~Glvh~sels~~~~~~~~~~~~~~Gd~v~vkVl~iD~e-~~ri~Ls~K~~~ 366 (491)
T PRK13806 291 KAGDKVTGKVVRLA---PFGAFVEILPGIEGLVHVSEMSWTRRVNKPEDVVAPGDAVAVKIKDIDPA-KRRISLSLRDAE 366 (491)
T ss_pred CCCCEEEEEEEEEe---CceEEEEeCCCcEEEEEHHHcCcccccCCHHHcCCCCCEEEEEEEEEEcc-CCEEEEEEeecc
Confidence 46889999999985 489877766568899999998742 1 245999999999876542 344555555444
Q ss_pred CCC
Q psy3654 127 LTP 129 (140)
Q Consensus 127 ~~p 129 (140)
..|
T Consensus 367 ~~p 369 (491)
T PRK13806 367 GDP 369 (491)
T ss_pred cCh
Confidence 433
No 72
>PRK13806 rpsA 30S ribosomal protein S1; Provisional
Probab=84.35 E-value=4.9 Score=35.86 Aligned_cols=57 Identities=19% Similarity=0.229 Sum_probs=43.1
Q ss_pred ccCCceeeeEEEEeeCCCceeEEecCCCCCeEEEEEccccCCC------cCCCCCEEEEEEEecCC
Q psy3654 53 ALQNPVETGKIKEFCRSKGHGFITPDSGEPAVFVHISDIEGCY------VPLPGDEVKYRLCPIPP 112 (140)
Q Consensus 53 ~~~g~~~~G~VK~f~~~KGfGFI~~~~g~~dIFfH~s~l~~~~------~~l~Gd~V~F~v~~~~k 112 (140)
...|..+.|+|+.... ||.+...+++-+.|+|++++...+ ....||.|.+.+...++
T Consensus 200 l~~G~iv~G~V~~v~~---~G~fV~l~~gv~g~v~~sels~~~~~~~~~~~~vGd~i~vkVl~id~ 262 (491)
T PRK13806 200 VKEGDVVEGTVTRLAP---FGAFVELAPGVEGMVHISELSWSRVQKADEAVSVGDTVRVKVLGIER 262 (491)
T ss_pred CCCCCEEEEEEEEEeC---CeEEEEcCCCcEEEEEHHHCCCccccChhHhcCCCCEEEEEEEEEec
Confidence 3478899999999753 666555555689999999997642 13499999999987654
No 73
>PRK07899 rpsA 30S ribosomal protein S1; Reviewed
Probab=82.86 E-value=6.6 Score=35.40 Aligned_cols=69 Identities=14% Similarity=0.186 Sum_probs=47.9
Q ss_pred ccCCceeeeEEEEeeCCCceeEEecCCCCCeEEEEEccccCCC------cCCCCCEEEEEEEecCCCCCCceEEEEEecC
Q psy3654 53 ALQNPVETGKIKEFCRSKGHGFITPDSGEPAVFVHISDIEGCY------VPLPGDEVKYRLCPIPPKFEKNQAVHVEIVH 126 (140)
Q Consensus 53 ~~~g~~~~G~VK~f~~~KGfGFI~~~~g~~dIFfH~s~l~~~~------~~l~Gd~V~F~v~~~~k~~~g~~A~~V~~~~ 126 (140)
...|..+.|+|+... .||.+...+ +-+.|+|+++|.... .+..||.|++.+...++. .+.....++.+.
T Consensus 206 lk~G~iv~G~V~~i~---~~G~FVdlg-gv~Glv~~Sels~~~v~~~~~~~kvGd~V~vkVl~iD~e-~~rI~LSlK~~~ 280 (486)
T PRK07899 206 LQKGQVRKGVVSSIV---NFGAFVDLG-GVDGLVHVSELSWKHIDHPSEVVEVGQEVTVEVLDVDMD-RERVSLSLKATQ 280 (486)
T ss_pred ccCCCEEEEEEEEEE---CCeEEEEEC-CEEEEEEHHHCCCcccCCHHHhcCCCCEEEEEEEEEECC-CCEEEEEEeecc
Confidence 347899999999985 467655444 589999999997641 234999999998876542 244444444433
No 74
>TIGR00757 RNaseEG ribonuclease, Rne/Rng family. The C-terminal half of RNase E (excluded from the seed alignment for this model) lacks ribonuclease activity but participates in mRNA degradation by organizing the degradosome.
Probab=82.78 E-value=7.6 Score=34.27 Aligned_cols=72 Identities=18% Similarity=0.256 Sum_probs=53.5
Q ss_pred ccCCceeeeEEEEeeCCCceeEEecCCCCCeEEEEEccccCC-----------------C-cCCCCCEEEEEEEecCCCC
Q psy3654 53 ALQNPVETGKIKEFCRSKGHGFITPDSGEPAVFVHISDIEGC-----------------Y-VPLPGDEVKYRLCPIPPKF 114 (140)
Q Consensus 53 ~~~g~~~~G~VK~f~~~KGfGFI~~~~g~~dIFfH~s~l~~~-----------------~-~~l~Gd~V~F~v~~~~k~~ 114 (140)
...|.++.|+|+...+.-+-=||....+ .+-|+|++++... . .+.+||.|..++...+-+.
T Consensus 23 ~~vGnIY~GrV~~i~p~l~aAFVdiG~~-k~gfL~~~d~~~~~~~~~~~~~~~~~~~~i~~~l~~G~~IlVQV~Ke~~~~ 101 (414)
T TIGR00757 23 QLKGNIYKGRVTRILPSLQAAFVDIGLE-KNGFLHASDIGPNYECLAPAEAKREAGPSISELLRPGQSVLVQVVKEPRGN 101 (414)
T ss_pred CCCCCEEEEEEeeecCCCceEEEEcCCC-ceEEEEHHHcCchhhccccccccccccCCHHHhCcCCCEEEEEEeeCCcCC
Confidence 3468899999999988666889999764 7899999998532 0 2458999999999877555
Q ss_pred CCceEE-EEEec
Q psy3654 115 EKNQAV-HVEIV 125 (140)
Q Consensus 115 ~g~~A~-~V~~~ 125 (140)
+|...+ +|.+.
T Consensus 102 Kgp~lT~~Isl~ 113 (414)
T TIGR00757 102 KGARLTTDISLP 113 (414)
T ss_pred CCCeEEEEEEec
Confidence 565553 44433
No 75
>PRK07400 30S ribosomal protein S1; Reviewed
Probab=82.37 E-value=8.4 Score=32.62 Aligned_cols=73 Identities=16% Similarity=0.118 Sum_probs=55.3
Q ss_pred ccCCceeeeEEEEeeCCCceeEEecCCCCCeEEEEEccccCCC------cCCCCCEEEEEEEecCCCCCCceEEEEEecC
Q psy3654 53 ALQNPVETGKIKEFCRSKGHGFITPDSGEPAVFVHISDIEGCY------VPLPGDEVKYRLCPIPPKFEKNQAVHVEIVH 126 (140)
Q Consensus 53 ~~~g~~~~G~VK~f~~~KGfGFI~~~~g~~dIFfH~s~l~~~~------~~l~Gd~V~F~v~~~~k~~~g~~A~~V~~~~ 126 (140)
...|..+.|+|+... .||...... +-+-|+|++++...+ ....||.|+..+...+. ..+.....++.+.
T Consensus 194 ~k~G~vv~G~V~~I~---~~G~fV~i~-gv~Gllhisels~~~~~~~~~~~~vGd~VkvkVl~iD~-e~~rI~LS~K~l~ 268 (318)
T PRK07400 194 LEVGEVVVGTVRGIK---PYGAFIDIG-GVSGLLHISEISHEHIETPHSVFNVNDEMKVMIIDLDA-ERGRISLSTKQLE 268 (318)
T ss_pred CCCCCEEEEEEEEEE---CCeEEEEEC-CEEEEEEHHHcccccccChhhccCCCCEEEEEEEEEeC-CCCEEEEEEeccc
Confidence 346889999999985 588877664 468999999997651 23499999999988763 2466777777777
Q ss_pred CCCc
Q psy3654 127 LTPE 130 (140)
Q Consensus 127 ~~p~ 130 (140)
..|.
T Consensus 269 ~~P~ 272 (318)
T PRK07400 269 PEPG 272 (318)
T ss_pred cChh
Confidence 7765
No 76
>TIGR00767 rho transcription termination factor Rho. Members of this family differ in the specificity of RNA binding.
Probab=80.05 E-value=3 Score=37.08 Aligned_cols=50 Identities=20% Similarity=0.348 Sum_probs=38.3
Q ss_pred ceeeeEEEEeeCCCceeEEecC-----CCCCeEEEEEccccCCCcCCCCCEEEEEEEe
Q psy3654 57 PVETGKIKEFCRSKGHGFITPD-----SGEPAVFVHISDIEGCYVPLPGDEVKYRLCP 109 (140)
Q Consensus 57 ~~~~G~VK~f~~~KGfGFI~~~-----~g~~dIFfH~s~l~~~~~~l~Gd~V~F~v~~ 109 (140)
....|++--.. +||||++.. .+.+||||-.+.|+.. .++.||.|.=.+..
T Consensus 49 ~~~~g~le~~~--~g~gflr~~~~~~~~~~~d~yvs~~~i~~~-~lr~gd~v~g~~R~ 103 (415)
T TIGR00767 49 IFGEGVLEILP--DGFGFLRSPDSSYLPGPDDIYVSPSQIRRF-NLRTGDTIEGQIRS 103 (415)
T ss_pred eEEEEEEEEcC--CCCeEEeCCCcCCCCCCCCeeeCHHHHHhc-CCCCCCEEEEEEec
Confidence 35668777553 499999985 3678999999998774 56799999876653
No 77
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=79.43 E-value=14 Score=34.71 Aligned_cols=56 Identities=27% Similarity=0.267 Sum_probs=45.3
Q ss_pred cCCceeeeEEEEeeCCCceeEEecCCCCCeEEEEEccccCCC------cCCCCCEEEEEEEecCC
Q psy3654 54 LQNPVETGKIKEFCRSKGHGFITPDSGEPAVFVHISDIEGCY------VPLPGDEVKYRLCPIPP 112 (140)
Q Consensus 54 ~~g~~~~G~VK~f~~~KGfGFI~~~~g~~dIFfH~s~l~~~~------~~l~Gd~V~F~v~~~~k 112 (140)
..|..+.|+|+... .||+...-..+.+-++|++++...+ ....||.|.-++...+.
T Consensus 620 ~vG~v~~G~V~~I~---~fGafVei~~~~~GllhiSels~~~v~~~~~v~kvGD~V~VkV~~iD~ 681 (693)
T PRK11824 620 EVGEIYEGKVVRIV---DFGAFVEILPGKDGLVHISEIADERVEKVEDVLKEGDEVKVKVLEIDK 681 (693)
T ss_pred cCCeEEEEEEEEEE---CCeEEEEECCCCEEEEEeeeccCccccCccceeCCCCEEEEEEEEECC
Confidence 46889999999986 4888887666789999999997652 13599999999988764
No 78
>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional
Probab=79.08 E-value=6 Score=38.13 Aligned_cols=66 Identities=15% Similarity=0.146 Sum_probs=48.8
Q ss_pred cCCceeeeEEEEeeCCCceeEEecCCCCCeEEEEEccccCC-----C--cCCCCCEEEEEEEecCCCCCCceEEEEE
Q psy3654 54 LQNPVETGKIKEFCRSKGHGFITPDSGEPAVFVHISDIEGC-----Y--VPLPGDEVKYRLCPIPPKFEKNQAVHVE 123 (140)
Q Consensus 54 ~~g~~~~G~VK~f~~~KGfGFI~~~~g~~dIFfH~s~l~~~-----~--~~l~Gd~V~F~v~~~~k~~~g~~A~~V~ 123 (140)
..|..+.|+|+... .||++....++-+-|+|++++.-. . ....||.|++.+...++. ++.....++
T Consensus 664 ~vG~~v~G~V~~i~---~~G~fV~l~~gV~GlIh~sels~~~~~~~~~~~~kvGq~VkvkVl~ID~e-~rrI~LS~K 736 (863)
T PRK12269 664 PVGARFTRRIVKVT---NAGAFIEMEEGIDGFLHVDDLSWVKRTRPADHELEVGKEIECMVIECDPQ-ARRIRLGVK 736 (863)
T ss_pred CCCCEEEEEEEEEe---cceEEEEeCCCcEEEEEhHHhhccccccchhhccCCCCEEEEEEEEEecc-CCEEEEEec
Confidence 46889999999976 588887776678999999998542 1 245999999999888753 233444444
No 79
>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=78.92 E-value=7.8 Score=36.73 Aligned_cols=57 Identities=18% Similarity=0.155 Sum_probs=44.2
Q ss_pred ccCCceeeeEEEEeeCCCceeEEecCCCCCeEEEEEcccc----CC-----C-cCCCCCEEEEEEEecCC
Q psy3654 53 ALQNPVETGKIKEFCRSKGHGFITPDSGEPAVFVHISDIE----GC-----Y-VPLPGDEVKYRLCPIPP 112 (140)
Q Consensus 53 ~~~g~~~~G~VK~f~~~KGfGFI~~~~g~~dIFfH~s~l~----~~-----~-~~l~Gd~V~F~v~~~~k 112 (140)
...|..+.|+|+..- -||.......+.+-|+|+|+|. .. . ....||.|+.++...++
T Consensus 645 ~~vG~i~~GkV~~I~---dfGaFVel~~G~eGLvHISeisdls~~~rv~~~~dv~kvGd~V~VKVl~ID~ 711 (719)
T TIGR02696 645 PEVGERFLGTVVKTT---AFGAFVSLLPGKDGLLHISQIRKLAGGKRVENVEDVLSVGQKIQVEIADIDD 711 (719)
T ss_pred CCCCCEEEEEEEEEE---CceEEEEecCCceEEEEhhhccccccccCcCCHHHcCCCCCEEEEEEEEECC
Confidence 357899999999985 4997777666789999999883 11 1 24499999999988763
No 80
>COG2996 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only]
Probab=78.49 E-value=8.6 Score=32.63 Aligned_cols=62 Identities=18% Similarity=0.205 Sum_probs=44.4
Q ss_pred CCceeeeEEEEeeCCCcee-EEecCCCCCeEEEEEccccCCCcCCCCCEEEEEEEecCCCCCCceEEEE
Q psy3654 55 QNPVETGKIKEFCRSKGHG-FITPDSGEPAVFVHISDIEGCYVPLPGDEVKYRLCPIPPKFEKNQAVHV 122 (140)
Q Consensus 55 ~g~~~~G~VK~f~~~KGfG-FI~~~~g~~dIFfH~s~l~~~~~~l~Gd~V~F~v~~~~k~~~g~~A~~V 122 (140)
.|......|+.++ .|| |+.-...++.|+.|.++..+. .+.+||+|++=+..+.+ +.+.|+--
T Consensus 5 iG~~~~l~V~~~~---~~g~fL~~~~~~~~ilL~k~~~~~~-e~evGdev~vFiY~D~~--~rl~aTt~ 67 (287)
T COG2996 5 IGQINSLEVVEFS---DFGYFLDAGEDGTTILLPKSEPEED-ELEVGDEVTVFIYVDSE--DRLIATTR 67 (287)
T ss_pred ccceEEEEEEEee---ceeEEEecCCCceEEeccccCCcCC-ccccCcEEEEEEEECCC--Cceeheee
Confidence 3567788898886 355 566566556899999987543 46699999987777654 56777543
No 81
>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=78.22 E-value=8.2 Score=36.11 Aligned_cols=56 Identities=27% Similarity=0.262 Sum_probs=44.6
Q ss_pred cCCceeeeEEEEeeCCCceeEEecCCCCCeEEEEEccccCCC------cCCCCCEEEEEEEecCC
Q psy3654 54 LQNPVETGKIKEFCRSKGHGFITPDSGEPAVFVHISDIEGCY------VPLPGDEVKYRLCPIPP 112 (140)
Q Consensus 54 ~~g~~~~G~VK~f~~~KGfGFI~~~~g~~dIFfH~s~l~~~~------~~l~Gd~V~F~v~~~~k 112 (140)
..|..+.|+|+... .||....-.++.+-|+|+|.+...+ ....||.|..++...++
T Consensus 617 ~~G~i~~G~V~~I~---~~GafVei~~g~~GllHiSei~~~~v~~~~~~~kvGD~V~VkVi~id~ 678 (684)
T TIGR03591 617 EVGKIYEGKVVRIM---DFGAFVEILPGKDGLVHISEIANERVEKVEDVLKEGDEVKVKVLEIDK 678 (684)
T ss_pred ccCcEEEEEEEEEe---CCEEEEEECCCcEEEEEHHHcCCCcccChhhccCCCCEEEEEEEEECC
Confidence 46889999999986 4887777666689999999996652 13489999999988764
No 82
>PRK07400 30S ribosomal protein S1; Reviewed
Probab=77.59 E-value=7.3 Score=33.00 Aligned_cols=54 Identities=15% Similarity=0.143 Sum_probs=42.3
Q ss_pred CCceeeeEEEEeeCCCceeEEecCCCCCeEEEEEccccCC--CcCCCCCEEEEEEEecCC
Q psy3654 55 QNPVETGKIKEFCRSKGHGFITPDSGEPAVFVHISDIEGC--YVPLPGDEVKYRLCPIPP 112 (140)
Q Consensus 55 ~g~~~~G~VK~f~~~KGfGFI~~~~g~~dIFfH~s~l~~~--~~~l~Gd~V~F~v~~~~k 112 (140)
.+..++|+|+..+. +|++...+ |-+-|+|++.+... ...+.|+.|.+.+...++
T Consensus 118 ~~~~V~g~V~~~~~---~G~~V~l~-Gv~gfip~s~ls~~~~~~~~vG~~i~~kVl~id~ 173 (318)
T PRK07400 118 EDATVRSEVFATNR---GGALVRIE-GLRGFIPGSHISTRKPKEELVGEELPLKFLEVDE 173 (318)
T ss_pred CCCEEEEEEEEEEC---CeEEEEEC-CEEEEEEHHHcCccCCccccCCCEEEEEEEEEEc
Confidence 47889999999873 67777665 56889999999753 223599999999988765
No 83
>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=77.53 E-value=15 Score=25.26 Aligned_cols=51 Identities=24% Similarity=0.251 Sum_probs=37.3
Q ss_pred eeeeEEEEeeCCCceeEEecCCCCCeEEEEEccccCC-Cc----------------CCCCCEEEEEEEecCC
Q psy3654 58 VETGKIKEFCRSKGHGFITPDSGEPAVFVHISDIEGC-YV----------------PLPGDEVKYRLCPIPP 112 (140)
Q Consensus 58 ~~~G~VK~f~~~KGfGFI~~~~g~~dIFfH~s~l~~~-~~----------------~l~Gd~V~F~v~~~~k 112 (140)
.+.|+|..... +|+....++ .+.|+|++++..+ +. ...||.|...+...+.
T Consensus 2 vv~g~V~~i~~---~GifV~l~~-v~G~v~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~Gd~v~vkI~~vd~ 69 (99)
T cd04460 2 VVEGEVVEVVD---FGAFVRIGP-VDGLLHISQIMDDYISYDPKNKRLIGEETKRVLKVGDVVRARIVAVSL 69 (99)
T ss_pred EEEEEEEEEEe---ccEEEEEcC-eEEEEEEEEccCCceEechhheeecccCcCCEECCCCEEEEEEEEEeH
Confidence 46788888764 666655554 7899999999765 21 2589999999987753
No 84
>PRK12678 transcription termination factor Rho; Provisional
Probab=76.66 E-value=6.5 Score=36.88 Aligned_cols=48 Identities=17% Similarity=0.266 Sum_probs=37.6
Q ss_pred eeeeEEEEeeCCCceeEEecC---CCCCeEEEEEccccCCCcCCCCCEEEEEEEe
Q psy3654 58 VETGKIKEFCRSKGHGFITPD---SGEPAVFVHISDIEGCYVPLPGDEVKYRLCP 109 (140)
Q Consensus 58 ~~~G~VK~f~~~KGfGFI~~~---~g~~dIFfH~s~l~~~~~~l~Gd~V~F~v~~ 109 (140)
.+.|++--. .|||||... .+..||||..+.|+.. .+..||.|.=.+..
T Consensus 295 ~~~GiLdi~---dg~gFlR~~~y~~~~~Dvyvs~~qirr~-~Lr~Gd~v~G~vr~ 345 (672)
T PRK12678 295 PVAGILDVL---DNYAFVRTSGYLPGPNDVYVSMNQVRKN-GLRKGDAVTGAVRA 345 (672)
T ss_pred EeeEEEEec---CCeeEeeCCCCCCCCCCeeeCHHHHHHc-CCCCCCEEEEeecC
Confidence 356777665 399999986 3678999999998875 56799999877654
No 85
>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional
Probab=76.21 E-value=13 Score=35.89 Aligned_cols=66 Identities=12% Similarity=0.151 Sum_probs=46.5
Q ss_pred CCceeeeEEEEeeCCCceeEEecCCCCCeEEEEEccccCCC-----c-CCCCCEEEEEEEecCCCCCCceEEEEEec
Q psy3654 55 QNPVETGKIKEFCRSKGHGFITPDSGEPAVFVHISDIEGCY-----V-PLPGDEVKYRLCPIPPKFEKNQAVHVEIV 125 (140)
Q Consensus 55 ~g~~~~G~VK~f~~~KGfGFI~~~~g~~dIFfH~s~l~~~~-----~-~l~Gd~V~F~v~~~~k~~~g~~A~~V~~~ 125 (140)
.|..+.|+|+... .||++...+ |-+-|+|++++...+ . ...||.|++++...++.+ +......+.+
T Consensus 493 ~G~~V~G~Vk~i~---~~G~fVdl~-Gv~Gfvp~SeiS~~~v~~~~~~~kvGq~v~vkVi~iD~e~-~rI~LSlK~l 564 (863)
T PRK12269 493 IEDSVSGVVKSFT---SFGAFIDLG-GFDGLLHVNDMSWGHVARPREFVKKGQTIELKVIRLDQAE-KRINLSLKHF 564 (863)
T ss_pred CCCEEEEEEEEEe---CCcEEEEEC-CEEEEEEchhccccccCCHHHhccCCCEEEEEEEEEecCC-CeEEEEEecc
Confidence 5788999999986 477766664 568999999986541 1 348999999998877533 3344444433
No 86
>PRK06299 rpsA 30S ribosomal protein S1; Reviewed
Probab=75.39 E-value=13 Score=33.39 Aligned_cols=66 Identities=17% Similarity=0.184 Sum_probs=46.5
Q ss_pred cCCceeeeEEEEeeCCCceeEEecCCCCCeEEEEEccccCC---C----cCCCCCEEEEEEEecCCCCCCceEEEEE
Q psy3654 54 LQNPVETGKIKEFCRSKGHGFITPDSGEPAVFVHISDIEGC---Y----VPLPGDEVKYRLCPIPPKFEKNQAVHVE 123 (140)
Q Consensus 54 ~~g~~~~G~VK~f~~~KGfGFI~~~~g~~dIFfH~s~l~~~---~----~~l~Gd~V~F~v~~~~k~~~g~~A~~V~ 123 (140)
..|..+.|+|.... .||+....+.+-+.|+|++++... . .+..||.|.+.+...++. .+..+..++
T Consensus 285 ~~G~~v~g~V~~i~---~~G~fV~l~~~v~Glv~~sel~~~~~~~~~~~~~~~G~~v~v~V~~id~~-~~~i~ls~k 357 (565)
T PRK06299 285 PVGSKVKGKVTNIT---DYGAFVELEEGIEGLVHVSEMSWTKKNKHPSKVVSVGQEVEVMVLEIDEE-KRRISLGLK 357 (565)
T ss_pred CCCCEEEEEEEEEe---CCeEEEEeCCCCEEEEEHHHcCccccccCHHHhcCCCCEEEEEEEEEcCC-CCEEEEehH
Confidence 35889999999974 578776655568999999998642 1 135999999998776532 234444433
No 87
>PRK06299 rpsA 30S ribosomal protein S1; Reviewed
Probab=75.27 E-value=18 Score=32.55 Aligned_cols=68 Identities=22% Similarity=0.258 Sum_probs=48.4
Q ss_pred CCceeeeEEEEeeCCCceeEEecCCCCCeEEEEEccccCCC-------cCCCCCEEEEEEEecCCCCCCceEEEEEecC
Q psy3654 55 QNPVETGKIKEFCRSKGHGFITPDSGEPAVFVHISDIEGCY-------VPLPGDEVKYRLCPIPPKFEKNQAVHVEIVH 126 (140)
Q Consensus 55 ~g~~~~G~VK~f~~~KGfGFI~~~~g~~dIFfH~s~l~~~~-------~~l~Gd~V~F~v~~~~k~~~g~~A~~V~~~~ 126 (140)
.|..+.|+|+... .||+....+.+-+.|+|++++...+ ....||.|+..+...++. .+.....++...
T Consensus 373 ~G~~v~g~V~~v~---~~G~fV~l~~~v~g~i~~s~l~~~~~~~~~~~~~~~Gd~v~v~Il~vd~~-~~~i~ls~k~~~ 447 (565)
T PRK06299 373 VGDVVEGKVKNIT---DFGAFVGLEGGIDGLVHLSDISWDKKGEEAVELYKKGDEVEAVVLKVDVE-KERISLGIKQLE 447 (565)
T ss_pred CCCEEEEEEEEEe---cceEEEECCCCCEEEEEHHHcCccccccChHhhCCCCCEEEEEEEEEeCC-CCEEEEEEehhh
Confidence 5889999999975 5787766665689999999997431 235999999998776532 344445554443
No 88
>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=75.09 E-value=15 Score=32.34 Aligned_cols=56 Identities=21% Similarity=0.218 Sum_probs=40.9
Q ss_pred ccCCceeeeEEEEeeCCCceeEEecCCCCCeEEEEEccccCC---C----cCCCCCEEEEEEEecC
Q psy3654 53 ALQNPVETGKIKEFCRSKGHGFITPDSGEPAVFVHISDIEGC---Y----VPLPGDEVKYRLCPIP 111 (140)
Q Consensus 53 ~~~g~~~~G~VK~f~~~KGfGFI~~~~g~~dIFfH~s~l~~~---~----~~l~Gd~V~F~v~~~~ 111 (140)
...|..+.|+|+... .||.+-..+.+-+.|+|++++... . ....||.|++.+...+
T Consensus 270 ~~~G~i~~g~V~~v~---~~G~fV~l~~~v~g~v~~sels~~~~~~~~~~~~~vG~~v~v~V~~id 332 (516)
T TIGR00717 270 FPVGDKITGRVTNLT---DYGVFVEIEEGIEGLVHVSEMSWVKKNSHPSKVVKKGDEVEVMILDID 332 (516)
T ss_pred ccCCCEEEEEEEEee---CCcEEEEeCCCCEEEEEHHHcCCccccCCHHHhccCCCEEEEEEEEEc
Confidence 346899999999975 477444433357899999998643 1 1449999999987654
No 89
>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=74.23 E-value=20 Score=25.17 Aligned_cols=55 Identities=16% Similarity=0.294 Sum_probs=40.7
Q ss_pred CCceeeeEEEEeeCCCceeEEecCCCCCeEEEEEccccCCC-------------------------cCCCCCEEEEEEEe
Q psy3654 55 QNPVETGKIKEFCRSKGHGFITPDSGEPAVFVHISDIEGCY-------------------------VPLPGDEVKYRLCP 109 (140)
Q Consensus 55 ~g~~~~G~VK~f~~~KGfGFI~~~~g~~dIFfH~s~l~~~~-------------------------~~l~Gd~V~F~v~~ 109 (140)
.|..+.|+|+... .+|.+....++-+-|+|++++..++ ....||.|.+.+..
T Consensus 3 ~G~vV~G~V~~v~---~~gl~v~L~~g~~G~v~~seis~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~vGd~V~~kVi~ 79 (100)
T cd05693 3 EGMLVLGQVKEIT---KLDLVISLPNGLTGYVPITNISDAYTERLEELDEESEEEDDEEELPDLEDLFSVGQLVRCKVVS 79 (100)
T ss_pred CCCEEEEEEEEEc---CCCEEEECCCCcEEEEEHHHhhHHHHHHHHHhhhhccccccccccCCHHHhccCCCEEEEEEEE
Confidence 4778999999974 3454444445689999999996521 13599999999988
Q ss_pred cCC
Q psy3654 110 IPP 112 (140)
Q Consensus 110 ~~k 112 (140)
.++
T Consensus 80 ~d~ 82 (100)
T cd05693 80 LDK 82 (100)
T ss_pred ccC
Confidence 775
No 90
>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=74.03 E-value=20 Score=31.59 Aligned_cols=69 Identities=23% Similarity=0.253 Sum_probs=47.8
Q ss_pred ccCCceeeeEEEEeeCCCceeEEecCCCCCeEEEEEccccCC-------CcCCCCCEEEEEEEecCCCCCCceEEEEEec
Q psy3654 53 ALQNPVETGKIKEFCRSKGHGFITPDSGEPAVFVHISDIEGC-------YVPLPGDEVKYRLCPIPPKFEKNQAVHVEIV 125 (140)
Q Consensus 53 ~~~g~~~~G~VK~f~~~KGfGFI~~~~g~~dIFfH~s~l~~~-------~~~l~Gd~V~F~v~~~~k~~~g~~A~~V~~~ 125 (140)
...|..+.|+|+... .||+....+.+-+.|+|++++... .....||.|..++...++. .+.....++..
T Consensus 357 ~~~G~~v~g~V~~v~---~~G~fV~l~~~v~glv~~s~ls~~~~~~~~~~~~~~G~~V~~~Vl~vd~~-~~~i~ls~K~~ 432 (516)
T TIGR00717 357 HPVGDRVTGKIKKIT---DFGAFVELEGGIDGLIHLSDISWDKDGREADHLYKKGDEIEAVVLAVDKE-KKRISLGVKQL 432 (516)
T ss_pred CCCCCEEEEEEEEEe---cceEEEECCCCCEEEEEHHHCcCcccCCCHhHccCCCCEEEEEEEEEeCc-CCEEEEeeccc
Confidence 346889999999864 567776666678999999999643 1234999999987766532 23344444443
No 91
>PRK03987 translation initiation factor IF-2 subunit alpha; Validated
Probab=74.02 E-value=28 Score=28.82 Aligned_cols=70 Identities=17% Similarity=0.284 Sum_probs=49.6
Q ss_pred ccCCceeeeEEEEeeCCCceeEEecCCC--CCeEEEEEccccCC-C-----cCCCCCEEEEEEEecCCCCCCceEEEEEe
Q psy3654 53 ALQNPVETGKIKEFCRSKGHGFITPDSG--EPAVFVHISDIEGC-Y-----VPLPGDEVKYRLCPIPPKFEKNQAVHVEI 124 (140)
Q Consensus 53 ~~~g~~~~G~VK~f~~~KGfGFI~~~~g--~~dIFfH~s~l~~~-~-----~~l~Gd~V~F~v~~~~k~~~g~~A~~V~~ 124 (140)
...|..+.|+|+... .||+....+. +-+-|+|++++... . .+..||.|..++...++. ++.....++.
T Consensus 6 P~~GdiV~G~V~~I~---~~G~fV~L~e~~gieGlI~iSEls~~~i~~i~~~~kvGd~V~vkVi~VD~~-k~~I~LSlK~ 81 (262)
T PRK03987 6 PEEGELVVGTVKEVK---DFGAFVTLDEYPGKEGFIHISEVASGWVKNIRDHVKEGQKVVCKVIRVDPR-KGHIDLSLKR 81 (262)
T ss_pred CCCCCEEEEEEEEEE---CCEEEEEECCCCCcEEEEEHHHcCcccccCHHHhCCCCCEEEEEEEEEecc-cCeEEEEEEe
Confidence 346889999999985 4777665542 57899999999765 2 235999999999887742 3445555554
Q ss_pred cC
Q psy3654 125 VH 126 (140)
Q Consensus 125 ~~ 126 (140)
+.
T Consensus 82 v~ 83 (262)
T PRK03987 82 VN 83 (262)
T ss_pred cc
Confidence 44
No 92
>PRK06676 rpsA 30S ribosomal protein S1; Reviewed
Probab=73.27 E-value=20 Score=30.61 Aligned_cols=58 Identities=17% Similarity=0.169 Sum_probs=42.5
Q ss_pred ccCCceeeeEEEEeeCCCceeEEecCCCCCeEEEEEccccCC------CcCCCCCEEEEEEEecCC
Q psy3654 53 ALQNPVETGKIKEFCRSKGHGFITPDSGEPAVFVHISDIEGC------YVPLPGDEVKYRLCPIPP 112 (140)
Q Consensus 53 ~~~g~~~~G~VK~f~~~KGfGFI~~~~g~~dIFfH~s~l~~~------~~~l~Gd~V~F~v~~~~k 112 (140)
...|..+.|+|+.... .+=||..+.++.+.|+|.+++... ....+||.|++.+.....
T Consensus 15 ~~~G~iv~G~V~~i~~--~g~~V~i~~~~~~g~lp~~e~~~~~~~~~~~~~~vGd~v~~~V~~v~~ 78 (390)
T PRK06676 15 VEVGDVVTGEVLKVED--KQVFVNIEGYKVEGVIPISELSNDHIEDINDVVKVGDELEVYVLKVED 78 (390)
T ss_pred ccCCCEEEEEEEEEEC--CeEEEEEecCCcEEEEEHHHhccccccCcccccCCCCEEEEEEEEEEC
Confidence 4568899999999964 234454424457899999999652 124599999999988764
No 93
>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=72.82 E-value=13 Score=32.12 Aligned_cols=61 Identities=13% Similarity=0.160 Sum_probs=43.5
Q ss_pred cCCceeeeEEEEeeCCCceeEEecCCCCCeEEEEEccccCCCcCCCCCEEEEEEEecCCCCCCc
Q psy3654 54 LQNPVETGKIKEFCRSKGHGFITPDSGEPAVFVHISDIEGCYVPLPGDEVKYRLCPIPPKFEKN 117 (140)
Q Consensus 54 ~~g~~~~G~VK~f~~~KGfGFI~~~~g~~dIFfH~s~l~~~~~~l~Gd~V~F~v~~~~k~~~g~ 117 (140)
..|.+++|+|+..+. +||=||.. |+-+-|++.+++........||+|.+.+..-....+|.
T Consensus 130 k~GeiV~G~V~~v~~-~g~v~Vdi--G~~ea~LP~~E~ip~E~~~~Gd~ik~~V~~V~~~~kg~ 190 (341)
T TIGR01953 130 KEGEIISGTVKRVNR-RGNLYVEL--GKTEGILPKKEQIPGEKFRIGDRIKAYVYEVRKTAKGP 190 (341)
T ss_pred hcCCEEEEEEEEEec-CCcEEEEE--CCeEEEecHHHcCCCcCCCCCCEEEEEEEEEEcCCCCC
Confidence 368999999999853 34434444 45788999988875544669999999988765433343
No 94
>COG4776 Rnb Exoribonuclease II [Transcription]
Probab=72.44 E-value=2.8 Score=38.29 Aligned_cols=48 Identities=23% Similarity=0.451 Sum_probs=30.4
Q ss_pred CceeeeEEEEeeCCCceeEEecCCCCCeEEEEEccccCCCcCCCCCEEEEEEEe
Q psy3654 56 NPVETGKIKEFCRSKGHGFITPDSGEPAVFVHISDIEGCYVPLPGDEVKYRLCP 109 (140)
Q Consensus 56 g~~~~G~VK~f~~~KGfGFI~~~~g~~dIFfH~s~l~~~~~~l~Gd~V~F~v~~ 109 (140)
.+.+.|+||. .+|||||+..+.. ..+|+---..+. ..-||.|.-.+..
T Consensus 19 ~prvEGvVK~--tekgfGFLEvD~q-kSYFIpPp~MKk---vMHGDkIiA~i~t 66 (645)
T COG4776 19 TPRVEGVVKA--TEKGFGFLEVDAQ-KSYFIPPPQMKK---VMHGDKIIAVIHT 66 (645)
T ss_pred Ccccceeeee--ccccceeEEEcCc-cccccCCHHHhh---hcccCeEEEEEEe
Confidence 4567899998 5899999999863 456643222221 2256666554443
No 95
>cd04462 S1_RNAPII_Rpb7 S1_RNAPII_Rpb7: Eukaryotic RNA polymerase II (RNAPII) Rpb7 subunit C-terminal S1 domain. RNAPII is composed of 12 subunits (Rpb1-12). Rpb4 and Rpb7 form a heterodimer that associate with the RNAPII core. Rpb7 is a homolog of the Rpc25 of RNA polymerase III, RpoE of the archaeal RNA polymerase, and Rpa43 of eukaryotic RNA polymerase I. Rpb7 has two domains, an N-terminal ribonucleoprotein (RNP) domain and a C-terminal S1 domain, both of which bind single-stranded RNA. It is possible that the S1 domain interacts with the nascent RNA transcript, assisted by the RNP domain. In yeast, Rpb4/Rpb7 is necessary for promoter-directed transcription initiation. They also play a role in regulating transcription-coupled repair in the Rad26-dependent pathway, in efficient mRNA export, and in transcription termination.
Probab=72.13 E-value=26 Score=24.09 Aligned_cols=35 Identities=14% Similarity=0.196 Sum_probs=26.7
Q ss_pred CceeeeEEEEeeCCCceeEEecCCCCCeEEEEEccccCC
Q psy3654 56 NPVETGKIKEFCRSKGHGFITPDSGEPAVFVHISDIEGC 94 (140)
Q Consensus 56 g~~~~G~VK~f~~~KGfGFI~~~~g~~dIFfH~s~l~~~ 94 (140)
++++.|+|+.-+. +||....++ -++|||.+.+..+
T Consensus 2 gEVi~g~V~~v~~---~G~~v~~Gp-l~~f~~~~~ip~~ 36 (88)
T cd04462 2 GEVVDAIVTSVNK---TGFFAEVGP-LSIFISRHLIPSD 36 (88)
T ss_pred CcEEEEEEEEEec---cEEEEEEcC-ceEEEEeeecCcc
Confidence 5688999999875 677766654 6799999888654
No 96
>COG0539 RpsA Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]
Probab=71.93 E-value=12 Score=34.33 Aligned_cols=73 Identities=19% Similarity=0.230 Sum_probs=52.7
Q ss_pred ccCCceeeeEEEEeeCCCceeEEecCCCCCeEEEEEccccCC--Cc----CCCCCEEEEEEEecCCCCCCceEEEEEecC
Q psy3654 53 ALQNPVETGKIKEFCRSKGHGFITPDSGEPAVFVHISDIEGC--YV----PLPGDEVKYRLCPIPPKFEKNQAVHVEIVH 126 (140)
Q Consensus 53 ~~~g~~~~G~VK~f~~~KGfGFI~~~~g~~dIFfH~s~l~~~--~~----~l~Gd~V~F~v~~~~k~~~g~~A~~V~~~~ 126 (140)
...|....|+|..+-+ ||.+.--..|-+=|+|+|++.-. .. +..||+|+..+-..++.+ +..-..++.+.
T Consensus 275 ~~~g~~v~G~Vt~i~~---~GafVei~~GvEGlvhvSEisw~~~~~P~evv~~Gq~V~V~Vl~id~e~-rRIsL~iKq~~ 350 (541)
T COG0539 275 YPVGDKVEGKVTNLTD---YGAFVEIEEGVEGLVHVSEISWTKKNVPSEVVKVGQEVEVKVLDIDPER-RRISLGLKQLK 350 (541)
T ss_pred cCCCCEEEEEEEEeec---CcEEEEecCCccceeechhhcccccCCHHHhcccCCEEEEEEEeeCchh-ceEEeeehhhh
Confidence 3458899999999864 88766666678899999988654 12 349999999998877543 44445555555
Q ss_pred CCC
Q psy3654 127 LTP 129 (140)
Q Consensus 127 ~~p 129 (140)
.+|
T Consensus 351 ~~p 353 (541)
T COG0539 351 ENP 353 (541)
T ss_pred cCh
Confidence 555
No 97
>PRK00087 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed
Probab=71.69 E-value=29 Score=32.06 Aligned_cols=72 Identities=25% Similarity=0.294 Sum_probs=52.2
Q ss_pred cCCceeeeEEEEeeCCCceeEEecCCCCCeEEEEEccccCCC------cCCCCCEEEEEEEecCCCCCCceEEEEEecCC
Q psy3654 54 LQNPVETGKIKEFCRSKGHGFITPDSGEPAVFVHISDIEGCY------VPLPGDEVKYRLCPIPPKFEKNQAVHVEIVHL 127 (140)
Q Consensus 54 ~~g~~~~G~VK~f~~~KGfGFI~~~~g~~dIFfH~s~l~~~~------~~l~Gd~V~F~v~~~~k~~~g~~A~~V~~~~~ 127 (140)
..|..+.|+|+...+ ||+....+++-+-|+|++++...+ .+..||.|+..+...++. ++.....++.+..
T Consensus 561 ~~G~~v~g~V~~i~~---~G~fV~l~~~i~Gli~~sel~~~~~~~~~~~~kvGd~V~vkV~~id~e-~~rI~lslk~~~~ 636 (647)
T PRK00087 561 PVGSIVLGKVVRIAP---FGAFVELEPGVDGLVHISQISWKRIDKPEDVLSEGEEVKAKILEVDPE-EKRIRLSIKEVEE 636 (647)
T ss_pred cCCeEEEEEEEEEEC---CeEEEEECCCCEEEEEhhhcCccccCCHhhcCCCCCEEEEEEEEEeCC-CCEEEEEEeeccc
Confidence 357889999999864 777665555688999999997641 245999999998887642 3555566666655
Q ss_pred CC
Q psy3654 128 TP 129 (140)
Q Consensus 128 ~p 129 (140)
+|
T Consensus 637 ~~ 638 (647)
T PRK00087 637 EP 638 (647)
T ss_pred Cc
Confidence 55
No 98
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=71.12 E-value=15 Score=32.01 Aligned_cols=60 Identities=10% Similarity=0.005 Sum_probs=42.6
Q ss_pred cCCceeeeEEEEeeCCCceeEEecCCCCCeEEEEEccccCCCcCCCCCEEEEEEEecCCCCCCc
Q psy3654 54 LQNPVETGKIKEFCRSKGHGFITPDSGEPAVFVHISDIEGCYVPLPGDEVKYRLCPIPPKFEKN 117 (140)
Q Consensus 54 ~~g~~~~G~VK~f~~~KGfGFI~~~~g~~dIFfH~s~l~~~~~~l~Gd~V~F~v~~~~k~~~g~ 117 (140)
..|.+++|+|+.... | |++... |+-+-|++.+++........||+|.+.+..-.+..+|.
T Consensus 133 k~GeiV~G~V~~~~~--~-~~~Vdl-g~vEa~LP~~E~ip~e~~~~Gd~Ika~V~~V~~~~kgp 192 (362)
T PRK12327 133 REGDIVTGVVQRRDN--R-FVYVNL-GKIEAVLPPAEQIPGETYKHGDRIKVYVVKVEKTTKGP 192 (362)
T ss_pred hcCCEEEEEEEEEeC--C-cEEEEe-CCeEEEecHHHcCCCCCCCCCCEEEEEEEEEecCCCCC
Confidence 468999999999854 3 444433 34678999888765545669999999998766433443
No 99
>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=70.67 E-value=27 Score=22.92 Aligned_cols=56 Identities=11% Similarity=-0.010 Sum_probs=41.0
Q ss_pred cCCceeeeEEEEeeCCCceeEEecCCCCCeEEEEEccccCC------CcCCCCCEEEEEEEecCC
Q psy3654 54 LQNPVETGKIKEFCRSKGHGFITPDSGEPAVFVHISDIEGC------YVPLPGDEVKYRLCPIPP 112 (140)
Q Consensus 54 ~~g~~~~G~VK~f~~~KGfGFI~~~~g~~dIFfH~s~l~~~------~~~l~Gd~V~F~v~~~~k 112 (140)
..|..+.|+|..... ..-++... ..-+-|+|++++... ..+..||.|.+++...++
T Consensus 5 ~~GdiV~G~V~~v~~--~~~~V~i~-~~~~g~l~~~~~~~~~~~~~~~~~~~GD~i~~~V~~~~~ 66 (82)
T cd04454 5 DVGDIVIGIVTEVNS--RFWKVDIL-SRGTARLEDSSATEKDKKEIRKSLQPGDLILAKVISLGD 66 (82)
T ss_pred CCCCEEEEEEEEEcC--CEEEEEeC-CCceEEeechhccCcchHHHHhcCCCCCEEEEEEEEeCC
Confidence 357889999999843 23345554 457899999999653 124599999999998764
No 100
>PF05606 DUF777: Borrelia burgdorferi protein of unknown function (DUF777); InterPro: IPR008495 This family consists of several hypothetical proteins of unknown function, found in Borrelia burgdorferi and Borrelia garinii.
Probab=70.40 E-value=6.4 Score=31.18 Aligned_cols=46 Identities=26% Similarity=0.311 Sum_probs=39.3
Q ss_pred eeeeEEEEeeCCCceeEEecCCCCCeEEEEEccccCC-CcCCCCCEEE
Q psy3654 58 VETGKIKEFCRSKGHGFITPDSGEPAVFVHISDIEGC-YVPLPGDEVK 104 (140)
Q Consensus 58 ~~~G~VK~f~~~KGfGFI~~~~g~~dIFfH~s~l~~~-~~~l~Gd~V~ 104 (140)
+--|+||.|+.+..=|.++..+ .+|+=+|-..+..- +++.+||+|-
T Consensus 35 ~rIG~iK~F~~~tQe~iVti~e-~e~LeI~T~nISN~~leLs~~D~Vl 81 (181)
T PF05606_consen 35 CRIGTIKSFKFQTQEGIVTIPE-YEDLEIHTKNISNINLELSKGDEVL 81 (181)
T ss_pred EEEeeeeecccccceEEEEeec-ccCceEEeeecccceeEecCCCEEE
Confidence 4569999999999999999887 57899999888876 6777999885
No 101
>PRK06676 rpsA 30S ribosomal protein S1; Reviewed
Probab=70.17 E-value=37 Score=28.92 Aligned_cols=74 Identities=23% Similarity=0.274 Sum_probs=52.4
Q ss_pred ccCCceeeeEEEEeeCCCceeEEecCCCCCeEEEEEccccCCC------cCCCCCEEEEEEEecCCCCCCceEEEEEecC
Q psy3654 53 ALQNPVETGKIKEFCRSKGHGFITPDSGEPAVFVHISDIEGCY------VPLPGDEVKYRLCPIPPKFEKNQAVHVEIVH 126 (140)
Q Consensus 53 ~~~g~~~~G~VK~f~~~KGfGFI~~~~g~~dIFfH~s~l~~~~------~~l~Gd~V~F~v~~~~k~~~g~~A~~V~~~~ 126 (140)
...|..+.|+|+...+ ||+....+++-+-++|++++.... ....||.|...+...+.. .+.....++...
T Consensus 275 ~~~G~~v~g~V~~i~~---~G~fV~l~~gi~Glv~~se~~~~~~~~~~~~~~~Gd~v~v~V~~id~e-~~~i~ls~k~~~ 350 (390)
T PRK06676 275 LPEGDVIEGTVKRLTD---FGAFVEVLPGVEGLVHISQISHKHIATPSEVLEEGQEVKVKVLEVNEE-EKRISLSIKALE 350 (390)
T ss_pred hcCCcEEEEEEEEEeC---ceEEEEECCCCeEEEEhHHcCccccCChhhccCCCCEEEEEEEEEECC-CCEEEEEEEecc
Confidence 3468899999999753 887666555578899999996541 235999999998887642 345556666555
Q ss_pred CCCc
Q psy3654 127 LTPE 130 (140)
Q Consensus 127 ~~p~ 130 (140)
.+|.
T Consensus 351 ~~~~ 354 (390)
T PRK06676 351 EAPA 354 (390)
T ss_pred cChh
Confidence 5554
No 102
>PRK08563 DNA-directed RNA polymerase subunit E'; Provisional
Probab=69.11 E-value=30 Score=26.57 Aligned_cols=55 Identities=24% Similarity=0.254 Sum_probs=42.1
Q ss_pred ccCCceeeeEEEEeeCCCceeEEecCCCCCeEEEEEccccCC-C----------------cCCCCCEEEEEEEecC
Q psy3654 53 ALQNPVETGKIKEFCRSKGHGFITPDSGEPAVFVHISDIEGC-Y----------------VPLPGDEVKYRLCPIP 111 (140)
Q Consensus 53 ~~~g~~~~G~VK~f~~~KGfGFI~~~~g~~dIFfH~s~l~~~-~----------------~~l~Gd~V~F~v~~~~ 111 (140)
...|+.+.|+|+.-+. +|+....+. -+.|+|.+++..+ . ....||.|.|++....
T Consensus 79 P~~GEVv~g~V~~v~~---~Gi~V~lg~-~~g~v~~~~l~~~~~~~d~~~~~~~~~~~~~~i~~Gd~VrvrV~~v~ 150 (187)
T PRK08563 79 PELQEVVEGEVVEVVE---FGAFVRIGP-VDGLLHISQIMDDYISYDPKNGRLIGKESKRVLKVGDVVRARIVAVS 150 (187)
T ss_pred ccCCCEEEEEEEEEEc---cEEEEEEeC-ceEEEEcHHcCCCceEEccccceEEEccCCeEEcCCCEEEEEEEEEE
Confidence 4468899999999874 677766654 6899999998654 1 1248999999998765
No 103
>COG1095 RPB7 DNA-directed RNA polymerase, subunit E' [Transcription]
Probab=68.61 E-value=14 Score=29.40 Aligned_cols=73 Identities=21% Similarity=0.274 Sum_probs=50.3
Q ss_pred cCCceeeeEEEEeeCCCceeEEecCCCCCeEEEEEccccCC----------C-------cCCCCCEEEEEEEecCCCCCC
Q psy3654 54 LQNPVETGKIKEFCRSKGHGFITPDSGEPAVFVHISDIEGC----------Y-------VPLPGDEVKYRLCPIPPKFEK 116 (140)
Q Consensus 54 ~~g~~~~G~VK~f~~~KGfGFI~~~~g~~dIFfH~s~l~~~----------~-------~~l~Gd~V~F~v~~~~k~~~g 116 (140)
..++++.|.|..-+ .||+-..-.. .|+|+|++.+-++ + .+..||.|.+++.....+...
T Consensus 80 ~~gEVV~GeVv~~~---~~G~fV~igp-~dglvh~sqi~dd~~~~d~~~~~~~g~~tk~~i~~gd~VR~RIv~~s~~~~~ 155 (183)
T COG1095 80 FRGEVVEGEVVEVV---EFGAFVRIGP-LDGLVHVSQIMDDYIDYDEKNKVLIGEETKRVLKVGDKVRARIVGVSLKSRR 155 (183)
T ss_pred ccccEEEEEEEEEe---ecceEEEecc-ccccccHhhccCcccccCcccceeeecccceEEecCCEEEEEEEEEecccCc
Confidence 35788999999865 5887777664 7999999988664 0 123799999999876543344
Q ss_pred ceEEEEEecCCCCc
Q psy3654 117 NQAVHVEIVHLTPE 130 (140)
Q Consensus 117 ~~A~~V~~~~~~p~ 130 (140)
.+...|.+.-.-|+
T Consensus 156 ~~~~~I~lTmrq~~ 169 (183)
T COG1095 156 PRESKIGLTMRQPG 169 (183)
T ss_pred cccceEEEEecccc
Confidence 45566665544444
No 104
>TIGR00448 rpoE DNA-directed RNA polymerase (rpoE), archaeal and eukaryotic form. This family seems to be confined to the archea and eukaryotic taxa and are quite dissimilar to E.coli rpoE.
Probab=67.50 E-value=48 Score=25.45 Aligned_cols=55 Identities=18% Similarity=0.253 Sum_probs=41.1
Q ss_pred ccCCceeeeEEEEeeCCCceeEEecCCCCCeEEEEEccccCC-C----------------cCCCCCEEEEEEEecC
Q psy3654 53 ALQNPVETGKIKEFCRSKGHGFITPDSGEPAVFVHISDIEGC-Y----------------VPLPGDEVKYRLCPIP 111 (140)
Q Consensus 53 ~~~g~~~~G~VK~f~~~KGfGFI~~~~g~~dIFfH~s~l~~~-~----------------~~l~Gd~V~F~v~~~~ 111 (140)
...|+.+.|+|+.-+. +|+....+. -+-+||.+++..+ + ....||.|.|++...+
T Consensus 79 p~~gEvv~G~V~~v~~---~GifV~lg~-~~gi~~~~~l~~~~~~~d~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~ 150 (179)
T TIGR00448 79 PELGEIVEGEVIEIVE---FGAFVSLGP-FDGLFHVSQVTDDYCYYDPKESALIGKETKKVLDEGDKVRARIVALS 150 (179)
T ss_pred ccCCCEEEEEEEEEEe---eEEEEEeCC-ceEEEEcHHhCCCceEEccccceEEEccCCeEEcCCCEEEEEEEEEE
Confidence 4468899999999874 888877654 6788899988643 1 1238999999997654
No 105
>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=67.48 E-value=23 Score=32.85 Aligned_cols=54 Identities=26% Similarity=0.380 Sum_probs=38.9
Q ss_pred CCceeeeEEEEeeCCCceeE-EecCCCCCeEEEEEccccCC-C----------------cCCCCCEEEEEEEecC
Q psy3654 55 QNPVETGKIKEFCRSKGHGF-ITPDSGEPAVFVHISDIEGC-Y----------------VPLPGDEVKYRLCPIP 111 (140)
Q Consensus 55 ~g~~~~G~VK~f~~~KGfGF-I~~~~g~~dIFfH~s~l~~~-~----------------~~l~Gd~V~F~v~~~~ 111 (140)
.|..+.|+|..... ||+ +..++.+.+-|+|++++..+ | ....||.|..++...+
T Consensus 572 iG~~~~g~I~~v~~---~GifV~L~~~~veGlV~~s~l~~d~y~~d~~~~~l~g~~~~~~~~lGD~V~Vki~~vd 643 (654)
T TIGR00358 572 VGTEFSGEISSVTR---FGMFVRLDDNGIDGLIHISTLHNDYYVFDQEKMALIGKGTGKVYRIGDRVTVKLTEVN 643 (654)
T ss_pred CCcEEEEEEEeEEc---CcEEEEecCCceEEEEEeEeCCCcceEEeccccEEEeccCCcEECCCCEEEEEEEEEe
Confidence 47889999999753 666 56665678999999999764 1 1226777777776654
No 106
>COG0557 VacB Exoribonuclease R [Transcription]
Probab=65.23 E-value=17 Score=33.94 Aligned_cols=64 Identities=28% Similarity=0.480 Sum_probs=45.3
Q ss_pred eeeeEEEEeeCCCceeEEecCC--CCCeEEEEEccccCCCcCCCCCEEEEEEEecCCCCCCceEEEEEecC
Q psy3654 58 VETGKIKEFCRSKGHGFITPDS--GEPAVFVHISDIEGCYVPLPGDEVKYRLCPIPPKFEKNQAVHVEIVH 126 (140)
Q Consensus 58 ~~~G~VK~f~~~KGfGFI~~~~--g~~dIFfH~s~l~~~~~~l~Gd~V~F~v~~~~k~~~g~~A~~V~~~~ 126 (140)
...|++.+ ..+||||+.+++ ...|||+-...+.. ...||.|..++....+..++..|.-|.++.
T Consensus 69 ~~~~~~~~--~~~gf~f~~~~~~~~~~d~~v~~~~~~~---a~~gD~V~v~~~~~~~~~~~~~~~v~~il~ 134 (706)
T COG0557 69 LVEGIVEA--SAKGFGFLSPDDSKDADDIFVPKDPLNR---ALHGDRVLVELLPSDKRGRFKEAAVVRILE 134 (706)
T ss_pred cccceEEe--ccCCceeeccCccCCCCcEEeccccccc---cccCCEEEEEECcccccCCCceEEEEeeec
Confidence 45676666 478999999998 66899987766333 458999999987665421125666666665
No 107
>KOG0407|consensus
Probab=64.32 E-value=10 Score=28.39 Aligned_cols=60 Identities=23% Similarity=0.236 Sum_probs=39.8
Q ss_pred CCceeeeEEEEeeCCCceeEEecCCCCCeEEEEEccccCC--C-cCCCCCEEEEEEEecCC--------------CCCCc
Q psy3654 55 QNPVETGKIKEFCRSKGHGFITPDSGEPAVFVHISDIEGC--Y-VPLPGDEVKYRLCPIPP--------------KFEKN 117 (140)
Q Consensus 55 ~g~~~~G~VK~f~~~KGfGFI~~~~g~~dIFfH~s~l~~~--~-~~l~Gd~V~F~v~~~~k--------------~~~g~ 117 (140)
+++.+.|+..-|- .-+|-|||+.|+.+. . +..-|+.|.-+-.++.+ +..|.
T Consensus 11 e~~~vfgvahi~a------------sfndtfvhitdlsg~eti~rvtggmkvkadrdesspyaamlaaqdva~kck~~gi 78 (139)
T KOG0407|consen 11 EGEQVFGVAHIFA------------SFNDTFVHVTDLSGKETIVRVTGGMKVKADRDESSPYAAMLAAQDVAAKCKELGI 78 (139)
T ss_pred ccceeeeEEEEEe------------ecccceEEEeccCCceEEEEecCCeEEecccccCChHHHHHHHHHHHHHHHhcCe
Confidence 4556667665543 236899999999986 2 33488888876655443 23477
Q ss_pred eEEEEEecC
Q psy3654 118 QAVHVEIVH 126 (140)
Q Consensus 118 ~A~~V~~~~ 126 (140)
.|.+|++-.
T Consensus 79 ~alh~klra 87 (139)
T KOG0407|consen 79 TALHIKLRA 87 (139)
T ss_pred eEEEEEEEe
Confidence 788877654
No 108
>COG0539 RpsA Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]
Probab=62.75 E-value=30 Score=31.84 Aligned_cols=72 Identities=22% Similarity=0.238 Sum_probs=53.3
Q ss_pred ccCCceeeeEEEEeeCCCceeEEecCCCCCeEEEEEccccCCC------cCCCCCEEEEEEEecCCCCCCceEEEEEecC
Q psy3654 53 ALQNPVETGKIKEFCRSKGHGFITPDSGEPAVFVHISDIEGCY------VPLPGDEVKYRLCPIPPKFEKNQAVHVEIVH 126 (140)
Q Consensus 53 ~~~g~~~~G~VK~f~~~KGfGFI~~~~g~~dIFfH~s~l~~~~------~~l~Gd~V~F~v~~~~k~~~g~~A~~V~~~~ 126 (140)
...|..+.|+|+...+ ||-....+| -|=++|++++...+ ....||.|.-.+-.-++ .++.....++.+.
T Consensus 190 l~~G~vV~G~V~~It~---~GafVdigG-vdGLlHiseiS~~rv~~P~~vvkvGd~VkvkVi~~D~-e~~RVsLSlK~l~ 264 (541)
T COG0539 190 LEVGEVVEGVVKNITD---YGAFVDIGG-VDGLLHISEISWKRVDHPSEVVKVGDEVKVKVISLDE-ERGRVSLSLKQLE 264 (541)
T ss_pred CCCCceEEEEEEEeec---CcEEEEecC-eeeEEehhhccccccCCHHHhcccCCEEEEEEEEEcc-CCCeEEEEehhcc
Confidence 4579999999999975 886666555 79999999998751 23499999999988774 2455666665555
Q ss_pred CCC
Q psy3654 127 LTP 129 (140)
Q Consensus 127 ~~p 129 (140)
..|
T Consensus 265 ~dP 267 (541)
T COG0539 265 EDP 267 (541)
T ss_pred cCc
Confidence 444
No 109
>PRK11712 ribonuclease G; Provisional
Probab=62.51 E-value=40 Score=30.53 Aligned_cols=73 Identities=14% Similarity=0.231 Sum_probs=54.5
Q ss_pred ccCCceeeeEEEEeeCCCceeEEecCCCCCeEEEEEccccCC-------------C-----cCCCCCEEEEEEEecCCCC
Q psy3654 53 ALQNPVETGKIKEFCRSKGHGFITPDSGEPAVFVHISDIEGC-------------Y-----VPLPGDEVKYRLCPIPPKF 114 (140)
Q Consensus 53 ~~~g~~~~G~VK~f~~~KGfGFI~~~~g~~dIFfH~s~l~~~-------------~-----~~l~Gd~V~F~v~~~~k~~ 114 (140)
...|.++.|+|+..-+.-.==||....+ .+-|.|++++... . .+.+||.|-.++...+-+.
T Consensus 36 ~~vGnIY~G~V~~v~pg~~AAFVdIG~~-k~gFL~~~d~~~~~~~~~~~~~~~~~~~~i~~~l~~Gq~iLVQV~Ke~~~~ 114 (489)
T PRK11712 36 GIVGNIYKGRVSRVLPGMQAAFVDIGLD-KAAFLHASDIVPHTECVAGEEQKQFVVRDISELVRQGQDIMVQVVKDPLGT 114 (489)
T ss_pred cccccEEEEEEeecCCCCceeEEeeCCC-ccEEEEhhhccchhhhcccccccccccccHHHhccCCCEEEEEEEeCCcCC
Confidence 3468899999999998888889999874 7899999998321 0 1458999999999877555
Q ss_pred CCceEE-EEEecC
Q psy3654 115 EKNQAV-HVEIVH 126 (140)
Q Consensus 115 ~g~~A~-~V~~~~ 126 (140)
+|...+ +|.+.+
T Consensus 115 KG~~lT~~Isl~G 127 (489)
T PRK11712 115 KGARLTTDITLPS 127 (489)
T ss_pred CCCeEEEEEEecc
Confidence 555543 444443
No 110
>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=61.00 E-value=28 Score=32.44 Aligned_cols=55 Identities=25% Similarity=0.248 Sum_probs=39.6
Q ss_pred CCceeeeEEEEeeCCCceeEEecCCC-CCeEEEEEccccCC-C----------------cCCCCCEEEEEEEecCC
Q psy3654 55 QNPVETGKIKEFCRSKGHGFITPDSG-EPAVFVHISDIEGC-Y----------------VPLPGDEVKYRLCPIPP 112 (140)
Q Consensus 55 ~g~~~~G~VK~f~~~KGfGFI~~~~g-~~dIFfH~s~l~~~-~----------------~~l~Gd~V~F~v~~~~k 112 (140)
.|..+.|+|..-. .||+....++ +.+-++|+++|.++ + ....||.|+.++...+.
T Consensus 627 iG~~~~g~V~~v~---~fGifV~L~~~~~eGlvhis~l~~d~~~~d~~~~~l~g~~~~~~~~lGd~V~Vkv~~vd~ 699 (709)
T TIGR02063 627 IGEEFEGVISGVT---SFGLFVELENNTIEGLVHISTLKDDYYVFDEKGLALVGERTGKVFRLGDRVKVRVVKADL 699 (709)
T ss_pred CCcEEEEEEEEEE---eCCEEEEecCCceEEEEEeeecCCCcEEEcccceEEEeccCCcEECCCCEEEEEEEEEec
Confidence 4788999999875 5887544433 57899999999753 1 12378888888877653
No 111
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=61.00 E-value=16 Score=34.51 Aligned_cols=58 Identities=24% Similarity=0.213 Sum_probs=45.7
Q ss_pred cccCCceeeeEEEEeeCCCceeEEecCCCCCeEEEEEccccCC------CcCCCCCEEEEEEEecCC
Q psy3654 52 RALQNPVETGKIKEFCRSKGHGFITPDSGEPAVFVHISDIEGC------YVPLPGDEVKYRLCPIPP 112 (140)
Q Consensus 52 ~~~~g~~~~G~VK~f~~~KGfGFI~~~~g~~dIFfH~s~l~~~------~~~l~Gd~V~F~v~~~~k 112 (140)
....|..+.|+|+.-.. ||-....-++.|-++|+|.+... ..+..||.|.-++...++
T Consensus 616 e~evg~iy~G~V~ri~~---fGaFv~l~~gkdgl~hiS~~~~~rv~kv~dvlk~Gd~v~Vkv~~iD~ 679 (692)
T COG1185 616 EVEVGEVYEGTVVRIVD---FGAFVELLPGKDGLVHISQLAKERVEKVEDVLKEGDEVKVKVIEIDK 679 (692)
T ss_pred hcccccEEEEEEEEEee---cceEEEecCCcceeEEehhhhhhhhhcccceeecCceEEEEEeeecc
Confidence 34568899999999864 88655555568999999999875 234599999999988775
No 112
>PRK09838 periplasmic copper-binding protein; Provisional
Probab=60.16 E-value=65 Score=23.57 Aligned_cols=64 Identities=14% Similarity=0.100 Sum_probs=36.4
Q ss_pred eeeeEEEEeeCCCceeEEecCC------CCCeEEEEEccccCCCcCCCCCEEEEEEEecCCCCCCceEEEEEe
Q psy3654 58 VETGKIKEFCRSKGHGFITPDS------GEPAVFVHISDIEGCYVPLPGDEVKYRLCPIPPKFEKNQAVHVEI 124 (140)
Q Consensus 58 ~~~G~VK~f~~~KGfGFI~~~~------g~~dIFfH~s~l~~~~~~l~Gd~V~F~v~~~~k~~~g~~A~~V~~ 124 (140)
...|+|+..+.+.|-=.|.-.. +..-.-|-..+=..-..+.+||.|.|++.... +++..++|+.
T Consensus 44 ~~~G~V~~vd~~~~~iti~H~pIp~l~wPaMTM~F~v~~~~~l~~lk~G~~V~F~~~~~~---~~~~i~~i~~ 113 (115)
T PRK09838 44 SGTGVVKGIDLESKKITIHHEPIPAVNWPEMTMRFTITPQTKMSEIKTGDKVAFNFVQQG---NLSLLQDIKV 113 (115)
T ss_pred EEEEEEEEEeCCCCEEEEeecccccCCCCCccccccCCChhhhccCCCCCEEEEEEEEcC---CcEEEEEEee
Confidence 5689999998876533333322 01111111111000013459999999999876 5777777765
No 113
>PRK11642 exoribonuclease R; Provisional
Probab=60.07 E-value=45 Score=32.03 Aligned_cols=55 Identities=25% Similarity=0.289 Sum_probs=41.4
Q ss_pred CCceeeeEEEEeeCCCceeEEecC-CCCCeEEEEEccccCC-C----------------cCCCCCEEEEEEEecCC
Q psy3654 55 QNPVETGKIKEFCRSKGHGFITPD-SGEPAVFVHISDIEGC-Y----------------VPLPGDEVKYRLCPIPP 112 (140)
Q Consensus 55 ~g~~~~G~VK~f~~~KGfGFI~~~-~g~~dIFfH~s~l~~~-~----------------~~l~Gd~V~F~v~~~~k 112 (140)
.|..+.|+|.... .|||.... +.+-+-|+|+++|..+ | ....||.|+.++...+.
T Consensus 643 iGe~f~G~Is~V~---~fGifVeL~~~~vEGlV~vs~L~~d~y~~d~~~~~L~g~~~~~~~~lGD~V~VkV~~vD~ 715 (813)
T PRK11642 643 VGNVFKGVISSVT---GFGFFVRLDDLFIDGLVHVSSLDNDYYRFDQVGQRLIGESSGQTYRLGDRVEVRVEAVNM 715 (813)
T ss_pred CCcEEEEEEEEee---cCceEEEECCCCeeeeEEEeecCCcceEecchheEEecccCCcEECCCCEEEEEEEEeec
Confidence 5889999999864 58876554 4558999999998654 1 12379999999977654
No 114
>TIGR01451 B_ant_repeat conserved repeat domain. This model represents the conserved region of about 53 amino acids shared between regions, usually repeated, of proteins from a small number of phylogenetically distant prokaryotes. Examples include a 132-residue region found repeated in three of the five longest proteins of Bacillus anthracis, a 131-residue repeat in a cell wall-anchored protein of Enterococcus faecalis, and a 120-residue repeat in Methanobacterium thermoautotrophicum. A similar region is found in some Chlamydial outer membrane proteins.
Probab=57.85 E-value=21 Score=22.29 Aligned_cols=32 Identities=19% Similarity=0.335 Sum_probs=25.1
Q ss_pred CCCCCEEEEEEEecCCCCCCceEEEEEecCCCCc
Q psy3654 97 PLPGDEVKYRLCPIPPKFEKNQAVHVEIVHLTPE 130 (140)
Q Consensus 97 ~l~Gd~V~F~v~~~~k~~~g~~A~~V~~~~~~p~ 130 (140)
...||.|+|++.-... +...|.+|.+.+.-|.
T Consensus 8 ~~~Gd~v~Yti~v~N~--g~~~a~~v~v~D~lP~ 39 (53)
T TIGR01451 8 ATIGDTITYTITVTNN--GNVPATNVVVTDILPS 39 (53)
T ss_pred cCCCCEEEEEEEEEEC--CCCceEeEEEEEcCCC
Confidence 4599999999988664 5677888998876554
No 115
>PRK10811 rne ribonuclease E; Reviewed
Probab=56.50 E-value=50 Score=32.81 Aligned_cols=65 Identities=17% Similarity=0.117 Sum_probs=50.4
Q ss_pred cCCceeeeEEEEeeCCCceeEEecCCCCCeEEEEEccccCC---------------CcCCCCCEEEEEEEecCCCCCCce
Q psy3654 54 LQNPVETGKIKEFCRSKGHGFITPDSGEPAVFVHISDIEGC---------------YVPLPGDEVKYRLCPIPPKFEKNQ 118 (140)
Q Consensus 54 ~~g~~~~G~VK~f~~~KGfGFI~~~~g~~dIFfH~s~l~~~---------------~~~l~Gd~V~F~v~~~~k~~~g~~ 118 (140)
..|.++.|+|+.--..-+==||...++ ..-|+|++++... ..+.+||.|..++...+-+.+|..
T Consensus 37 ~vGnIYkGkVenIvPGInAAFVDIG~g-knGFL~L~Di~~~~f~~~~~~~~~~~i~~~Lk~GqeILVQV~KEa~gtKGp~ 115 (1068)
T PRK10811 37 KKANIYKGKITRIEPSLEAAFVDYGAE-RHGFLPLKEIAREYFPANYSAHGRPNIKDVLREGQEVIVQIDKEERGNKGAA 115 (1068)
T ss_pred CccceEEEEEecccCCcceeEEEecCC-cceEEEhhhccccccccccccccccccccccCCCCEEEEEEeecccCCCCCc
Confidence 358899999999988777779999875 7899999998532 124489999999988765555554
Q ss_pred E
Q psy3654 119 A 119 (140)
Q Consensus 119 A 119 (140)
.
T Consensus 116 L 116 (1068)
T PRK10811 116 L 116 (1068)
T ss_pred e
Confidence 4
No 116
>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=56.02 E-value=26 Score=21.81 Aligned_cols=49 Identities=20% Similarity=0.194 Sum_probs=34.5
Q ss_pred eeeEEEEe-eCCCceeEEecCCCCCeEEEEEcc--ccCCC-cCCCCCEEEEEE
Q psy3654 59 ETGKIKEF-CRSKGHGFITPDSGEPAVFVHISD--IEGCY-VPLPGDEVKYRL 107 (140)
Q Consensus 59 ~~G~VK~f-~~~KGfGFI~~~~g~~dIFfH~s~--l~~~~-~~l~Gd~V~F~v 107 (140)
+.|.|..- ...+++-|++-.|+...|-+.+-. ..... .+.+|+.|...=
T Consensus 3 v~G~V~~~~~~~~~~~~~~l~D~tg~i~~~~~~~~~~~~~~~l~~g~~v~v~G 55 (75)
T PF01336_consen 3 VEGRVTSIRRSGGKIVFFTLEDGTGSIQVVFFNEEYERFREKLKEGDIVRVRG 55 (75)
T ss_dssp EEEEEEEEEEEETTEEEEEEEETTEEEEEEEETHHHHHHHHTS-TTSEEEEEE
T ss_pred EEEEEEEEEcCCCCEEEEEEEECCccEEEEEccHHhhHHhhcCCCCeEEEEEE
Confidence 56888887 888899999998877666666655 11222 355999998873
No 117
>PRK00087 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed
Probab=55.38 E-value=55 Score=30.30 Aligned_cols=66 Identities=23% Similarity=0.296 Sum_probs=45.4
Q ss_pred cCCceeeeEEEEeeCCCceeEEecCCCCCeEEEEEccccCCC------cCCCCCEEEEEEEecCCCCCCceEEEEEe
Q psy3654 54 LQNPVETGKIKEFCRSKGHGFITPDSGEPAVFVHISDIEGCY------VPLPGDEVKYRLCPIPPKFEKNQAVHVEI 124 (140)
Q Consensus 54 ~~g~~~~G~VK~f~~~KGfGFI~~~~g~~dIFfH~s~l~~~~------~~l~Gd~V~F~v~~~~k~~~g~~A~~V~~ 124 (140)
..|..+.|+|+... .||++... ++-+.|+|++++...+ .+..||.|.+.+...++. .+.....++.
T Consensus 476 ~~G~iV~g~V~~v~---~~G~fV~l-~gv~Gll~~sels~~~~~~~~~~~~vGd~V~vkV~~id~~-~~~I~lS~K~ 547 (647)
T PRK00087 476 EEGDVVEGEVKRLT---DFGAFVDI-GGVDGLLHVSEISWGRVEKPSDVLKVGDEIKVYILDIDKE-NKKLSLSLKK 547 (647)
T ss_pred CCCCEEEEEEEEEe---CCcEEEEE-CCEEEEEEHHHcCccccCCHHHhcCCCCEEEEEEEEEECC-CCEEEEEeec
Confidence 36899999999975 36655444 4578999999987531 234999999998776432 2444444443
No 118
>COG2183 Tex Transcriptional accessory protein [Transcription]
Probab=55.21 E-value=37 Score=32.67 Aligned_cols=71 Identities=18% Similarity=0.203 Sum_probs=50.7
Q ss_pred ccCCceeeeEEEEeeCCCceeEEecCCCCCeEEEEEccccCC--CcC----CCCCEEEEEEEecCCCCCCceEEEEEecC
Q psy3654 53 ALQNPVETGKIKEFCRSKGHGFITPDSGEPAVFVHISDIEGC--YVP----LPGDEVKYRLCPIPPKFEKNQAVHVEIVH 126 (140)
Q Consensus 53 ~~~g~~~~G~VK~f~~~KGfGFI~~~~g~~dIFfH~s~l~~~--~~~----l~Gd~V~F~v~~~~k~~~g~~A~~V~~~~ 126 (140)
...|+...|+|+..- -||-+..-+-.+|..+|+|.+.+. ..+ ..||.|+-.+...+- .++..+...+...
T Consensus 656 Lk~Gm~leg~Vrnv~---~fgafVdIgv~qDglvHis~ls~~fv~~P~~vv~vGdiV~v~V~~vD~-~r~rI~Lsmr~~~ 731 (780)
T COG2183 656 LKPGMILEGTVRNVV---DFGAFVDIGVHQDGLVHISQLSDKFVKDPNEVVKVGDIVKVKVIEVDT-ARKRIALSMRLDE 731 (780)
T ss_pred ccCCCEEEEEEEEee---eccceEEeccccceeeeHHHhhhhhcCChHHhcccCCEEEEEEEEEec-ccCeeeeEeeccC
Confidence 346888999999874 477666666668999999999886 222 399999998887663 2455555555444
Q ss_pred C
Q psy3654 127 L 127 (140)
Q Consensus 127 ~ 127 (140)
.
T Consensus 732 ~ 732 (780)
T COG2183 732 E 732 (780)
T ss_pred C
Confidence 3
No 119
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=51.63 E-value=1.3e+02 Score=24.34 Aligned_cols=56 Identities=14% Similarity=0.098 Sum_probs=40.5
Q ss_pred cCCceeeeEEEEeeCCCceeEEecCCCCCeEEEEEccccCCC---------c-CCCCCEEEEEEEecCC
Q psy3654 54 LQNPVETGKIKEFCRSKGHGFITPDSGEPAVFVHISDIEGCY---------V-PLPGDEVKYRLCPIPP 112 (140)
Q Consensus 54 ~~g~~~~G~VK~f~~~KGfGFI~~~~g~~dIFfH~s~l~~~~---------~-~l~Gd~V~F~v~~~~k 112 (140)
..|+.+.|+|+.-... +.|+.... .-+-|+|++++...+ . +.+||.|.-++....+
T Consensus 62 ~vGDiViG~V~~i~~~--~~~vdI~~-~~~g~L~~s~i~~~~~~~d~~~~~~~~~~GDlV~akV~~i~~ 127 (235)
T PRK04163 62 KVGDLVIGKVTDVTFS--GWEVDINS-PYKAYLPVSEVLGRPVNVEGTDLRKYLDIGDYIIAKVKDVDR 127 (235)
T ss_pred CCCCEEEEEEEEEeCc--eEEEEeCC-CceeEEEHHHcCCCccccchhhhHhhCCCCCEEEEEEEEECC
Confidence 4688999999987542 24555544 357899999997531 1 3489999999987653
No 120
>COG2190 NagE Phosphotransferase system IIA components [Carbohydrate transport and metabolism]
Probab=50.86 E-value=33 Score=26.65 Aligned_cols=45 Identities=22% Similarity=0.396 Sum_probs=28.5
Q ss_pred eeeEEEEeeCCCceeEEecCCCCCeEEEEE----ccccCC-CcCC--CCCEEE
Q psy3654 59 ETGKIKEFCRSKGHGFITPDSGEPAVFVHI----SDIEGC-YVPL--PGDEVK 104 (140)
Q Consensus 59 ~~G~VK~f~~~KGfGFI~~~~g~~dIFfH~----s~l~~~-~~~l--~Gd~V~ 104 (140)
..|+|....+. +|.|.-..+.|-+|++|+ -.|.++ +..+ +||.|.
T Consensus 49 vdG~v~~iFpT-kHAigi~t~~GvEiLiHiGiDTV~L~GegF~~~v~~Gd~Vk 100 (156)
T COG2190 49 VDGTVVLIFPT-KHAIGIETDEGVEILIHIGIDTVKLNGEGFESLVKEGDKVK 100 (156)
T ss_pred cCcEEEEEeeC-CcEEEEEcCCCcEEEEEeceeeEEECCcceEEEeeCCCEEc
Confidence 34777777654 455555555568999998 355665 5432 777663
No 121
>KOG0125|consensus
Probab=49.43 E-value=31 Score=30.21 Aligned_cols=24 Identities=38% Similarity=0.508 Sum_probs=15.2
Q ss_pred CceeeeEEEEeeC--CCceeEEecCCC
Q psy3654 56 NPVETGKIKEFCR--SKGHGFITPDSG 80 (140)
Q Consensus 56 g~~~~G~VK~f~~--~KGfGFI~~~~g 80 (140)
|.+..-.|. ||+ .|||||++.++.
T Consensus 121 G~VldVEII-fNERGSKGFGFVTmen~ 146 (376)
T KOG0125|consen 121 GKVLDVEII-FNERGSKGFGFVTMENP 146 (376)
T ss_pred CceeeEEEE-eccCCCCccceEEecCh
Confidence 333333333 444 599999999875
No 122
>PF01345 DUF11: Domain of unknown function DUF11; InterPro: IPR001434 This group of sequences is represented by a conserved region of about 53 amino acids shared between regions, usually repeated, of proteins from a small number of phylogenetically distant prokaryotes. Examples include a 132-residue region found repeated in three of the five longest proteins of Bacillus anthracis, a 131-residue repeat in a cell wall-anchored protein of Enterococcus faecalis (Streptococcus faecalis), and a 120-residue repeat in Methanobacterium thermoautotrophicum. A similar region is found in some Chlamydia trachomatis outer membrane proteins. In C. trachomatis, three cysteine-rich proteins (also believed to be lipoproteins), MOMP, OMP6 and OMP3, make up the extracellular matrix of the outer membrane []. They are involved in the essential structural integrity of both the elementary body (EB) and recticulate body (RB) phase. They are thought to be involved in porin formation and, as these bacteria lack the peptidoglycan layer common to most Gram-negative microbes, such proteins are highly important in the pathogenicity of the organism.; GO: 0005727 extrachromosomal circular DNA
Probab=47.02 E-value=39 Score=21.88 Aligned_cols=33 Identities=24% Similarity=0.385 Sum_probs=25.8
Q ss_pred cCCCCCEEEEEEEecCCCCCCceEEEEEecCCCCc
Q psy3654 96 VPLPGDEVKYRLCPIPPKFEKNQAVHVEIVHLTPE 130 (140)
Q Consensus 96 ~~l~Gd~V~F~v~~~~k~~~g~~A~~V~~~~~~p~ 130 (140)
....||.|+|.+.-.-. +...|.+|.+.+.-|.
T Consensus 36 ~~~~Gd~v~ytitvtN~--G~~~a~nv~v~D~lp~ 68 (76)
T PF01345_consen 36 TANPGDTVTYTITVTNT--GPAPATNVVVTDTLPA 68 (76)
T ss_pred cccCCCEEEEEEEEEEC--CCCeeEeEEEEEcCCC
Confidence 35699999999988765 6677899998875443
No 123
>COG1093 SUI2 Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis]
Probab=46.13 E-value=64 Score=27.26 Aligned_cols=71 Identities=18% Similarity=0.323 Sum_probs=48.0
Q ss_pred ccccCCceeeeEEEEeeCCCcee-EEecCC-CCCeEEEEEccccCC-----Cc-CCCCCEEEEEEEecCCCCCCceEEEE
Q psy3654 51 NRALQNPVETGKIKEFCRSKGHG-FITPDS-GEPAVFVHISDIEGC-----YV-PLPGDEVKYRLCPIPPKFEKNQAVHV 122 (140)
Q Consensus 51 ~~~~~g~~~~G~VK~f~~~KGfG-FI~~~~-g~~dIFfH~s~l~~~-----~~-~l~Gd~V~F~v~~~~k~~~g~~A~~V 122 (140)
.+..+|+.+-|+|+.-. .|| |+.-++ +|.+-|+|+|.|... +. +++|+.|-+.+-.-+++ +|..-...
T Consensus 7 ~~PeeGEiVv~tV~~V~---~~GAyv~L~EY~g~Eg~ihiSEvas~wVknIrd~vkegqkvV~kVlrVd~~-rg~IDLSl 82 (269)
T COG1093 7 EYPEEGEIVVGTVKQVA---DYGAYVELDEYPGKEGFIHISEVASGWVKNIRDYVKEGQKVVAKVLRVDPK-RGHIDLSL 82 (269)
T ss_pred CCCCCCcEEEEEEEEee---ccccEEEeeccCCeeeeEEHHHHHHHHHHHHHHHhhcCCeEEEEEEEEcCC-CCeEeeeh
Confidence 35668999999999875 455 333333 457899999999875 12 45999999998776642 34444443
Q ss_pred Eec
Q psy3654 123 EIV 125 (140)
Q Consensus 123 ~~~ 125 (140)
+-+
T Consensus 83 krV 85 (269)
T COG1093 83 KRV 85 (269)
T ss_pred hhC
Confidence 333
No 124
>COG5569 Uncharacterized conserved protein [Function unknown]
Probab=45.05 E-value=90 Score=22.84 Aligned_cols=24 Identities=21% Similarity=0.271 Sum_probs=18.0
Q ss_pred CCCCCEEEEEEEecCCCCCCceEEEEE
Q psy3654 97 PLPGDEVKYRLCPIPPKFEKNQAVHVE 123 (140)
Q Consensus 97 ~l~Gd~V~F~v~~~~k~~~g~~A~~V~ 123 (140)
+++||.|+|..++-. +.+...+|+
T Consensus 84 lKeGdkV~fvferv~---gk~tv~qvk 107 (108)
T COG5569 84 LKEGDKVEFVFERVN---GKLTVQQVK 107 (108)
T ss_pred cccCCcEEEEEEeeC---CEEEEEEec
Confidence 559999999998865 566666654
No 125
>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=43.41 E-value=93 Score=20.39 Aligned_cols=26 Identities=19% Similarity=0.276 Sum_probs=18.7
Q ss_pred cCCCCCEEEEEEEecCCCCCC-ceEEEEEe
Q psy3654 96 VPLPGDEVKYRLCPIPPKFEK-NQAVHVEI 124 (140)
Q Consensus 96 ~~l~Gd~V~F~v~~~~k~~~g-~~A~~V~~ 124 (140)
.+.+||.|.|.+...+ .+ +.-+.|+.
T Consensus 42 ~l~~Gd~V~F~~~~~~---~~~~~I~~i~~ 68 (70)
T PF11604_consen 42 GLKPGDKVRFTFERTD---DGSYVITAIEP 68 (70)
T ss_dssp S-STT-EEEEEEEEET---TCEEEEEEEEE
T ss_pred cCCCCCEEEEEEEECC---CCcEEEEEEEE
Confidence 3559999999999987 35 77777664
No 126
>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=39.88 E-value=76 Score=19.55 Aligned_cols=53 Identities=19% Similarity=0.116 Sum_probs=33.0
Q ss_pred eeeeEEEEeeCCCceeEEecCCCCCe-EEEEEccccCC-CcCCCCCEEEEEEEec
Q psy3654 58 VETGKIKEFCRSKGHGFITPDSGEPA-VFVHISDIEGC-YVPLPGDEVKYRLCPI 110 (140)
Q Consensus 58 ~~~G~VK~f~~~KGfGFI~~~~g~~d-IFfH~s~l~~~-~~~l~Gd~V~F~v~~~ 110 (140)
...|+|...-.....-+|...-++.. +...++.-... ..+.+||+|.+.+...
T Consensus 6 ~l~g~V~~ie~~g~~~~v~~~~~~~~~l~a~it~~~~~~L~L~~G~~V~~~ik~~ 60 (64)
T PF03459_consen 6 QLPGTVESIENLGSEVEVTLDLGGGETLTARITPESAEELGLKPGDEVYASIKAS 60 (64)
T ss_dssp EEEEEEEEEEESSSEEEEEEEETTSEEEEEEEEHHHHHHCT-STT-EEEEEE-GG
T ss_pred EEEEEEEEEEECCCeEEEEEEECCCCEEEEEEcHHHHHHcCCCCCCEEEEEEehh
Confidence 47788888877766666666544444 66666542222 3466999999888653
No 127
>cd00210 PTS_IIA_glc PTS_IIA, PTS system, glucose/sucrose specific IIA subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. This family is one of four structurally and functionally distinct group IIA PTS system cytoplasmic enzymes, necessary for the uptake of carbohydrates across the cytoplasmic membrane and their phosphorylation.
Probab=39.11 E-value=65 Score=23.85 Aligned_cols=44 Identities=27% Similarity=0.503 Sum_probs=26.7
Q ss_pred eeeEEEEeeCCCceeE-EecCCCCCeEEEEEc----cccCC-CcC--CCCCEEE
Q psy3654 59 ETGKIKEFCRSKGHGF-ITPDSGEPAVFVHIS----DIEGC-YVP--LPGDEVK 104 (140)
Q Consensus 59 ~~G~VK~f~~~KGfGF-I~~~~g~~dIFfH~s----~l~~~-~~~--l~Gd~V~ 104 (140)
..|+|+...+ .++-| |+.++ |-+|.+|+- .+.++ +.. .+||.|+
T Consensus 42 ~~G~v~~i~~-T~HA~~i~~~~-G~eiLiHiGidTv~l~g~gF~~~vk~Gd~V~ 93 (124)
T cd00210 42 VDGTIVQIFP-TKHAIGIESDS-GVEILIHIGIDTVKLNGEGFTSHVEEGQRVK 93 (124)
T ss_pred CCeEEEEEcc-CCCEEEEEeCC-CcEEEEEeeeeeeecCCCceEEEecCCCEEc
Confidence 4699988754 45556 44444 479999984 33443 332 2676664
No 128
>COG1545 Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]
Probab=38.67 E-value=1.7e+02 Score=21.89 Aligned_cols=38 Identities=11% Similarity=0.014 Sum_probs=28.1
Q ss_pred eeEEecCCCCCeEEEEEccccCCCcCCCCCEEEEEEEecC
Q psy3654 72 HGFITPDSGEPAVFVHISDIEGCYVPLPGDEVKYRLCPIP 111 (140)
Q Consensus 72 fGFI~~~~g~~dIFfH~s~l~~~~~~l~Gd~V~F~v~~~~ 111 (140)
.|.|+.++++ .|+.|+.+ ........|+.|+-......
T Consensus 87 iaiV~l~~~~-~i~~~i~~-~~p~~v~iGm~V~~v~~~~~ 124 (140)
T COG1545 87 IAIVELEEGG-RILGQLVD-VDPDDVEIGMKVEAVFRKRE 124 (140)
T ss_pred EEEEEeCCCC-ceEEEEEe-cCcccccCCCEEEEEEEEcc
Confidence 5677777665 89999999 22245779999998887644
No 129
>PRK05054 exoribonuclease II; Provisional
Probab=37.82 E-value=1.2e+02 Score=28.33 Aligned_cols=35 Identities=11% Similarity=0.088 Sum_probs=25.9
Q ss_pred ceeeeEEEEeeCCCceeEE-ecCCCCCeEEEEEccccCC
Q psy3654 57 PVETGKIKEFCRSKGHGFI-TPDSGEPAVFVHISDIEGC 94 (140)
Q Consensus 57 ~~~~G~VK~f~~~KGfGFI-~~~~g~~dIFfH~s~l~~~ 94 (140)
..+.|+|.... .|||. ..++.+-+.|||+++|.++
T Consensus 563 ~~f~g~I~~v~---~~G~fV~l~~~~veglV~~~~l~~~ 598 (644)
T PRK05054 563 TRFAAEIIDIS---RGGMRVRLLENGAVAFIPASFLHAV 598 (644)
T ss_pred eEEEEEEEeee---cCcEEEEEeCCceEEEEEccccCCC
Confidence 48899998764 47744 4456668899999999663
No 130
>TIGR00830 PTBA PTS system, glucose subfamily, IIA component. These are part of the The PTS Glucose-Glucoside (Glc) SuperFamily. The Glc family includes permeases specific for glucose, N-acetylglucosamine and a large variety of a- and b-glucosides. However, not all b-glucoside PTS permeases are in this class, as the cellobiose (Cel) b-glucoside PTS permease is in the Lac family (TC #4.A.3). The IIA, IIB and IIC domains of all of the permeases listed below are demonstrably homologous. These permeases show limited sequence similarity with members of the Fru family (TC #4.A.2). Several of the PTS permeases in the Glc family lack their own IIA domains and instead use the glucose IIA protein (IIAglc or Crr). Most of these permeases have the B and C domains linked together in a single polypeptide chain, and a cysteyl residue in the IIB domain is phosphorylated by direct phosphoryl transfer from IIAglc(his~P). Those permeases which lack a IIA domain include the maltose (Mal), arbutin-salicin-c
Probab=37.72 E-value=72 Score=23.54 Aligned_cols=45 Identities=24% Similarity=0.446 Sum_probs=26.3
Q ss_pred eeeEEEEeeCCCceeEEecCCCCCeEEEEEc----cccCC-CcC--CCCCEEE
Q psy3654 59 ETGKIKEFCRSKGHGFITPDSGEPAVFVHIS----DIEGC-YVP--LPGDEVK 104 (140)
Q Consensus 59 ~~G~VK~f~~~KGfGFI~~~~g~~dIFfH~s----~l~~~-~~~--l~Gd~V~ 104 (140)
..|+|....+ .++-|.-..+.|-+|.+|+- .|.++ +.. .+||.|+
T Consensus 42 ~~G~v~~v~~-T~HA~gi~~~~G~evLiHiGidTV~L~G~gF~~~v~~Gd~V~ 93 (121)
T TIGR00830 42 VDGKIGKIFP-TKHAFGIESDSGVEILIHIGIDTVKLNGEGFTSHVEEGQRVK 93 (121)
T ss_pred CCeEEEEEcc-CCCEEEEEeCCCcEEEEEeeeceeecCCCceEEEecCCCEEc
Confidence 4589988764 45555333333578999983 33444 332 2666664
No 131
>PRK13168 rumA 23S rRNA m(5)U1939 methyltransferase; Reviewed
Probab=37.64 E-value=2.4e+02 Score=24.59 Aligned_cols=62 Identities=24% Similarity=0.381 Sum_probs=45.5
Q ss_pred CceeeeEEEEeeCCCceeEEecCCCCCeEEEEEccccCCCcCCCCCEEEEEEEecCCCCCCceEEEEEecCCCCc
Q psy3654 56 NPVETGKIKEFCRSKGHGFITPDSGEPAVFVHISDIEGCYVPLPGDEVKYRLCPIPPKFEKNQAVHVEIVHLTPE 130 (140)
Q Consensus 56 g~~~~G~VK~f~~~KGfGFI~~~~g~~dIFfH~s~l~~~~~~l~Gd~V~F~v~~~~k~~~g~~A~~V~~~~~~p~ 130 (140)
-.++..+|..+. ..|+|.-..+ +.-|||- ..++||+|+.++....+ +-..|.-++++..+|.
T Consensus 13 ~~~~~l~i~~l~-~~G~Gv~~~~--~~~vfV~--------~~lPGe~v~v~i~~~~~--~~~~~~~~~vl~~sp~ 74 (443)
T PRK13168 13 RQIITVTIESLD-HDGRGVARHN--GKTVFIE--------GALPGERVEVQVTEDKK--QYARAKVVRILKPSPE 74 (443)
T ss_pred CcEEEEEEEEcC-CCCceEEEEC--CEEEEeC--------CCCCCCEEEEEEEEecC--cEEEEEEEEEecCCcc
Confidence 346778999996 7899997753 2456641 25699999999987543 4568888888887776
No 132
>PF05670 DUF814: Domain of unknown function (DUF814); InterPro: IPR008532 This domain occurs in proteins that have been annotated as Fibronectin/fibrinogen binding protein by similarity. This annotation comes from O34693 from SWISSPROT where the N-terminal region is involved in this activity []. Hence the activity of this C-terminal domain is unknown. This domain contains a conserved motif D/E-X-W/Y-X-H that may be functionally important.
Probab=37.45 E-value=27 Score=23.89 Aligned_cols=16 Identities=19% Similarity=0.314 Sum_probs=13.1
Q ss_pred CCCeEEEEEccccCCC
Q psy3654 80 GEPAVFVHISDIEGCY 95 (140)
Q Consensus 80 g~~dIFfH~s~l~~~~ 95 (140)
..+|+|||..++.+..
T Consensus 28 ~~~D~wfH~~~~pg~h 43 (90)
T PF05670_consen 28 RPNDLWFHADDFPGPH 43 (90)
T ss_pred hhcceeEeccCCCCCE
Confidence 3579999999998873
No 133
>PLN00059 PsbP domain-containing protein 1; Provisional
Probab=37.06 E-value=31 Score=29.32 Aligned_cols=27 Identities=15% Similarity=0.156 Sum_probs=19.4
Q ss_pred eEEEEeeCCCceeEEecCC------CCCeEEEE
Q psy3654 61 GKIKEFCRSKGHGFITPDS------GEPAVFVH 87 (140)
Q Consensus 61 G~VK~f~~~KGfGFI~~~~------g~~dIFfH 87 (140)
|--..-+...||.|.-+.+ .|.|||||
T Consensus 108 ~l~~y~D~~DGY~FlYP~GWi~V~~~G~DVvFr 140 (286)
T PLN00059 108 VFREYIDTFDGYSFKYPQNWIQVRGAGADIFFR 140 (286)
T ss_pred ccceeEcCCCCeEEeCCCCCeEeccCCCceEEe
Confidence 5444556678999988865 56788877
No 134
>KOG4246|consensus
Probab=36.52 E-value=3.5 Score=39.97 Aligned_cols=63 Identities=22% Similarity=0.269 Sum_probs=43.2
Q ss_pred CceeeeEEEEeeCCCceeEEecCCCCCeEEEEEccccCCCcCCCCCEEEEEEEecCCCCCCceEEEEEecC
Q psy3654 56 NPVETGKIKEFCRSKGHGFITPDSGEPAVFVHISDIEGCYVPLPGDEVKYRLCPIPPKFEKNQAVHVEIVH 126 (140)
Q Consensus 56 g~~~~G~VK~f~~~KGfGFI~~~~g~~dIFfH~s~l~~~~~~l~Gd~V~F~v~~~~k~~~g~~A~~V~~~~ 126 (140)
...+.|+|...- .-||||. +||||..+.+.+- .+..||.|--+..-.+----++.|-.|..++
T Consensus 146 qR~f~gvvtk~~--DtygfVD-----~dvffQls~~~g~-hp~vgD~V~vea~Ynpsmpfkwnaqriq~l~ 208 (1194)
T KOG4246|consen 146 QRRFAGVVTKQT--DTYGFVD-----QDVFFQLSKMQGL-HPSVGDAVNVEADYNPSMPFKWNAQRIQHLG 208 (1194)
T ss_pred ceeeehhhhhhc--ccccccc-----HHHHHHHHHHhcC-CCccccceeeecccCCCCCccccHHHHHhcc
Confidence 347889888874 4799997 5899998988885 3668998876554333111466666665554
No 135
>PRK09439 PTS system glucose-specific transporter subunit; Provisional
Probab=34.49 E-value=83 Score=24.52 Aligned_cols=44 Identities=32% Similarity=0.616 Sum_probs=27.3
Q ss_pred eeeEEEEeeCCCceeE-EecCCCCCeEEEEEc----cccCC-CcCC--CCCEEE
Q psy3654 59 ETGKIKEFCRSKGHGF-ITPDSGEPAVFVHIS----DIEGC-YVPL--PGDEVK 104 (140)
Q Consensus 59 ~~G~VK~f~~~KGfGF-I~~~~g~~dIFfH~s----~l~~~-~~~l--~Gd~V~ 104 (140)
..|+|....+ .+|-| |+.++ |-+|.+|+- .|.++ +..+ +||.|+
T Consensus 64 ~dG~V~~vf~-T~HAigi~t~~-G~eiLIHiGiDTV~L~G~gF~~~Vk~Gd~Vk 115 (169)
T PRK09439 64 VDGTIGKIFE-TNHAFSIESDS-GVELFVHFGIDTVELKGEGFKRIAEEGQRVK 115 (169)
T ss_pred CCeEEEEEcC-CCCEEEEEeCC-CcEEEEEEeecccccCCCceEEEecCCCEEe
Confidence 4599988654 45666 44444 579999993 34454 4433 777664
No 136
>PF00358 PTS_EIIA_1: phosphoenolpyruvate-dependent sugar phosphotransferase system, EIIA 1; InterPro: IPR001127 The phosphoenolpyruvate-dependent sugar phosphotransferase system (PTS) [, ] is a major carbohydrate transport system in bacteria. The PTS catalyses the phosphorylation of incoming sugar substrates and coupled with translocation across the cell membrane, makes the PTS a link between the uptake and metabolism of sugars. The general mechanism of the PTS is the following: a phosphoryl group from phosphoenolpyruvate (PEP) is transferred via a signal transduction pathway, to enzyme I (EI) which in turn transfers it to a phosphoryl carrier, the histidine protein (HPr). Phospho-HPr then transfers the phosphoryl group to a sugar-specific permease, a membrane-bound complex known as enzyme 2 (EII), which transports the sugar to the cell. EII consists of at least three structurally distinct domains IIA, IIB and IIC []. These can either be fused together in a single polypeptide chain or exist as two or three interactive chains, formerly called enzymes II (EII) and III (EIII). The first domain (IIA or EIIA) carries the first permease-specific phosphorylation site, a histidine which is phosphorylated by phospho-HPr. The second domain (IIB or EIIB) is phosphorylated by phospho-IIA on a cysteinyl or histidyl residue, depending on the sugar transported. Finally, the phosphoryl group is transferred from the IIB domain to the sugar substrate concomitantly with the sugar uptake processed by the IIC domain. This third domain (IIC or EIIC) forms the translocation channel and the specific substrate-binding site. An additional transmembrane domain IID, homologous to IIC, can be found in some PTSs, e.g. for mannose [, , , ]. ; GO: 0005351 sugar:hydrogen symporter activity, 0006810 transport, 0009401 phosphoenolpyruvate-dependent sugar phosphotransferase system, 0016020 membrane; PDB: 3OUR_D 1GPR_A 1F3G_A 2F3G_B 1F3Z_A 1O2F_A 1GLB_F 1GGR_A 1GLA_F 1GLE_F ....
Probab=33.78 E-value=68 Score=23.94 Aligned_cols=45 Identities=20% Similarity=0.388 Sum_probs=25.5
Q ss_pred eeeEEEEeeCCCceeEEecCCCCCeEEEEEc----cccCC-CcC--CCCCEEE
Q psy3654 59 ETGKIKEFCRSKGHGFITPDSGEPAVFVHIS----DIEGC-YVP--LPGDEVK 104 (140)
Q Consensus 59 ~~G~VK~f~~~KGfGFI~~~~g~~dIFfH~s----~l~~~-~~~--l~Gd~V~ 104 (140)
..|+|....+. ++-|.-..+.|-+|.+|+- .+.+. +.. .+||.|.
T Consensus 46 ~~G~v~~i~~T-~HAi~i~s~~G~eiLiHiGidTv~L~G~gF~~~v~~G~~V~ 97 (132)
T PF00358_consen 46 VDGTVTMIFPT-KHAIGIRSDNGVEILIHIGIDTVKLNGEGFETLVKEGDKVK 97 (132)
T ss_dssp SSEEEEEE-TT-SSEEEEEETTSEEEEEE-SBSGGGGTTTTEEESS-TTSEE-
T ss_pred eeEEEEEEcCC-CCEEEEEeCCCCEEEEEEccchhhcCCcceEEEEeCCCEEE
Confidence 35999888753 4444444344579999982 24554 433 3888774
No 137
>KOG0149|consensus
Probab=33.59 E-value=22 Score=29.67 Aligned_cols=24 Identities=29% Similarity=0.385 Sum_probs=16.0
Q ss_pred CceeeeEEE---EeeCCCceeEEecCC
Q psy3654 56 NPVETGKIK---EFCRSKGHGFITPDS 79 (140)
Q Consensus 56 g~~~~G~VK---~f~~~KGfGFI~~~~ 79 (140)
|+++.-+|. .=.+.||||||+.-|
T Consensus 37 GeI~eavvitd~~t~rskGyGfVTf~d 63 (247)
T KOG0149|consen 37 GEIVEAVVITDKNTGRSKGYGFVTFRD 63 (247)
T ss_pred CceEEEEEEeccCCccccceeeEEeec
Confidence 444444443 345789999999866
No 138
>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=33.49 E-value=1.4e+02 Score=19.65 Aligned_cols=53 Identities=13% Similarity=0.040 Sum_probs=31.4
Q ss_pred eeeeEEEEeeCCCceeEEecCCCCCeE---EEEEccccCCCcCCCCCEEEEEEEec
Q psy3654 58 VETGKIKEFCRSKGHGFITPDSGEPAV---FVHISDIEGCYVPLPGDEVKYRLCPI 110 (140)
Q Consensus 58 ~~~G~VK~f~~~KGfGFI~~~~g~~dI---FfH~s~l~~~~~~l~Gd~V~F~v~~~ 110 (140)
.++|.|..+....|+=|++..|.+..| +|--....-.+.+.+||+|+..=..+
T Consensus 2 ~v~GeVs~~~~~~GHvyfsLkD~~a~i~cv~f~~~~~~~~~~l~~Gd~V~v~G~v~ 57 (73)
T cd04487 2 HIEGEVVQIKQTSGPTIFTLRDETGTVWAAAFEEAGVRAYPEVEVGDIVRVTGEVE 57 (73)
T ss_pred EEEEEEeccccCCCCEEEEEEcCCEEEEEEEEchhccCCcCCCCCCCEEEEEEEEe
Confidence 367888887667788888775543233 22222212124567999988654433
No 139
>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=33.20 E-value=1.5e+02 Score=22.43 Aligned_cols=53 Identities=21% Similarity=0.283 Sum_probs=34.1
Q ss_pred eeEEEEeeCCCcee-----EEecCCCCCeEEE-EEccccCCC-cCCCCCEEEEE--EEecCC
Q psy3654 60 TGKIKEFCRSKGHG-----FITPDSGEPAVFV-HISDIEGCY-VPLPGDEVKYR--LCPIPP 112 (140)
Q Consensus 60 ~G~VK~f~~~KGfG-----FI~~~~g~~dIFf-H~s~l~~~~-~~l~Gd~V~F~--v~~~~k 112 (140)
.|+|+...+++--| ||.....+..|+| |=-|+.... .+..||.|+|. .+-+++
T Consensus 42 ~G~V~~vLpdd~~GsrHQ~Fiv~l~~g~tllIahNIDlaprip~l~~GD~V~f~GeYe~n~k 103 (131)
T PF11948_consen 42 CGTVVKVLPDDNKGSRHQRFIVRLSSGQTLLIAHNIDLAPRIPWLQKGDQVEFYGEYEWNPK 103 (131)
T ss_pred cEEEEEECcccCCCCcceEEEEEeCCCCEEEEEeccCccccCcCcCCCCEEEEEEEEEECCC
Confidence 68888887764433 8887777777765 334443332 35599999984 445553
No 140
>cd01212 JIP JNK-interacting protein (JIP) Phosphotyrosine-binding (PTB) domain. JNK-interacting protein (JIP) Phosphotyrosine-binding (PTB) domain. JIP is a mitogen-activated protein kinase scaffold protein. JIP consists of a C-terminal SH3 domain, followed by a PTB domain. PTB domains have a PH-like fold and are found in various eukaryotic signaling molecules. They were initially identified based upon their ability to recognize phosphorylated tyrosine residues In contrast to SH2 domains, which recognize phosphotyrosine and adjacent carboxy-terminal residues, PTB-domain binding specificity is conferred by residues amino-terminal to the phosphotyrosine. More recent studies have found that some types of PTB domains can bind to peptides which are not tyrosine phosphorylated or lack tyrosine residues altogether.
Probab=33.03 E-value=46 Score=25.32 Aligned_cols=26 Identities=19% Similarity=0.146 Sum_probs=20.1
Q ss_pred eCCCceeEEecCCCCCeEEEEEcccc
Q psy3654 67 CRSKGHGFITPDSGEPAVFVHISDIE 92 (140)
Q Consensus 67 ~~~KGfGFI~~~~g~~dIFfH~s~l~ 92 (140)
++.|.||||..+...+...+|+-.-.
T Consensus 89 ~~~r~F~FIak~~~~~~~~CHVF~s~ 114 (148)
T cd01212 89 RDHRYFGFITKHPLLQRFACHVFKSS 114 (148)
T ss_pred CCCcEEEEEeccCCCCceEEEEEEeC
Confidence 45688999999877778888886543
No 141
>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=31.67 E-value=1.4e+02 Score=19.05 Aligned_cols=35 Identities=17% Similarity=0.143 Sum_probs=25.0
Q ss_pred eeEEecCCCCCeEEEEEccccCC--CcCCCCCEEEEEE
Q psy3654 72 HGFITPDSGEPAVFVHISDIEGC--YVPLPGDEVKYRL 107 (140)
Q Consensus 72 fGFI~~~~g~~dIFfH~s~l~~~--~~~l~Gd~V~F~v 107 (140)
+|.|+.++ |-.|+.++.+.... .++..|++|+...
T Consensus 31 v~~V~lde-g~rv~~~i~~~~~~~~~~l~iG~~V~~vf 67 (68)
T PF01796_consen 31 VAIVELDE-GVRVMARIVDVDPEDPDELRIGMRVRLVF 67 (68)
T ss_pred EEEEEeCC-CCEEEEEEecCCCCCcccCCCCCEEEEEE
Confidence 57777765 46899999886533 3466999998654
No 142
>KOG3716|consensus
Probab=30.10 E-value=41 Score=32.06 Aligned_cols=26 Identities=35% Similarity=0.451 Sum_probs=21.3
Q ss_pred CCCceeEEecCCCCCeEEEEEccccC
Q psy3654 68 RSKGHGFITPDSGEPAVFVHISDIEG 93 (140)
Q Consensus 68 ~~KGfGFI~~~~g~~dIFfH~s~l~~ 93 (140)
.+.|||.--.-.|..-|||||++-..
T Consensus 707 addGYGVsY~~~G~~~I~fHIsSk~S 732 (764)
T KOG3716|consen 707 ADDGYGVSYIFAGENAIFFHISSKHS 732 (764)
T ss_pred cCCCceeEEEEecCceEEEEeecccc
Confidence 57899987777777889999998765
No 143
>smart00361 RRM_1 RNA recognition motif.
Probab=28.90 E-value=36 Score=21.70 Aligned_cols=13 Identities=23% Similarity=0.422 Sum_probs=9.9
Q ss_pred eCCCceeEEecCC
Q psy3654 67 CRSKGHGFITPDS 79 (140)
Q Consensus 67 ~~~KGfGFI~~~~ 79 (140)
...+|||||+..+
T Consensus 34 ~~~rG~~fV~f~~ 46 (70)
T smart00361 34 NHKRGNVYITFER 46 (70)
T ss_pred CCCcEEEEEEECC
Confidence 3458999998876
No 144
>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=27.29 E-value=1.7e+02 Score=18.49 Aligned_cols=51 Identities=24% Similarity=0.222 Sum_probs=31.5
Q ss_pred eeeEEEEee-CCCceeEEecCCCCCe---EEEEEccccCC-CcCCCCCEEEEEEEec
Q psy3654 59 ETGKIKEFC-RSKGHGFITPDSGEPA---VFVHISDIEGC-YVPLPGDEVKYRLCPI 110 (140)
Q Consensus 59 ~~G~VK~f~-~~KGfGFI~~~~g~~d---IFfH~s~l~~~-~~~l~Gd~V~F~v~~~ 110 (140)
+.|.|..+. ..+|+.|++..|.... ++|. +.+... ..+..|+.|..+-...
T Consensus 4 v~g~v~~i~~tk~g~~~~~L~D~~~~i~~~~f~-~~~~~~~~~l~~g~~v~v~g~v~ 59 (78)
T cd04489 4 VEGEISNLKRPSSGHLYFTLKDEDASIRCVMWR-SNARRLGFPLEEGMEVLVRGKVS 59 (78)
T ss_pred EEEEEecCEECCCcEEEEEEEeCCeEEEEEEEc-chhhhCCCCCCCCCEEEEEEEEE
Confidence 456676666 4789999999775433 2333 333332 3345999888766543
No 145
>PF14506 CppA_N: CppA N-terminal; PDB: 3E0R_D.
Probab=26.96 E-value=74 Score=23.95 Aligned_cols=27 Identities=15% Similarity=0.274 Sum_probs=16.6
Q ss_pred EEeeCCCceeEEecCCCCCeEEEEEcc
Q psy3654 64 KEFCRSKGHGFITPDSGEPAVFVHISD 90 (140)
Q Consensus 64 K~f~~~KGfGFI~~~~g~~dIFfH~s~ 90 (140)
+-|...+||+|.....-++.+.+|..+
T Consensus 89 ~l~kg~~gyAfe~vSPEgd~~llhaEd 115 (125)
T PF14506_consen 89 RLYKGKNGYAFEAVSPEGDRFLLHAED 115 (125)
T ss_dssp EEEE-SSSEEEEEE-TT--EEEEE--S
T ss_pred eeEEcCCceEEEEECCCCCEEEEEEcC
Confidence 446678999999997777777788754
No 146
>PTZ00162 DNA-directed RNA polymerase II subunit 7; Provisional
Probab=26.46 E-value=77 Score=24.62 Aligned_cols=39 Identities=18% Similarity=0.271 Sum_probs=30.7
Q ss_pred cccCCceeeeEEEEeeCCCceeEEecCCCCCeEEEEEccccCC
Q psy3654 52 RALQNPVETGKIKEFCRSKGHGFITPDSGEPAVFVHISDIEGC 94 (140)
Q Consensus 52 ~~~~g~~~~G~VK~f~~~KGfGFI~~~~g~~dIFfH~s~l~~~ 94 (140)
+...|++..|+|+.-+. +||....+. -|||+|.+.+..+
T Consensus 78 rPf~gEVv~g~V~~v~~---~G~~v~~Gp-~~ifI~~~~l~~~ 116 (176)
T PTZ00162 78 KPFKDEVLDAIVTDVNK---LGFFAQAGP-LKAFVSRSAIPPD 116 (176)
T ss_pred ecCCCCEEEEEEEEEec---ceEEEEeeC-eEEEEcHHHCCCc
Confidence 45578999999999875 788777765 4599999998743
No 147
>CHL00010 infA translation initiation factor 1
Probab=23.59 E-value=2.4e+02 Score=18.94 Aligned_cols=51 Identities=31% Similarity=0.286 Sum_probs=31.3
Q ss_pred eeeEEEEeeCCCceeEEecCCCCCeEEEEEccccCC--CcCCCCCEEEEEEEecC
Q psy3654 59 ETGKIKEFCRSKGHGFITPDSGEPAVFVHISDIEGC--YVPLPGDEVKYRLCPIP 111 (140)
Q Consensus 59 ~~G~VK~f~~~KGfGFI~~~~g~~dIFfH~s~l~~~--~~~l~Gd~V~F~v~~~~ 111 (140)
+.|+|...-. .||=.+..+++ ..+-+|+.---.. ..+++||.|+|++...+
T Consensus 9 ~~G~Vik~lg-~~~y~V~~~~g-~~~~c~~rGklr~~~i~~~vGD~V~ve~~~~~ 61 (78)
T CHL00010 9 MEGLVTESLP-NGMFRVRLDNG-CQVLGYISGKIRRNSIRILPGDRVKVELSPYD 61 (78)
T ss_pred EEEEEEEEcC-CCEEEEEeCCC-CEEEEEeccceecCCcccCCCCEEEEEEcccC
Confidence 5687776431 35555665554 5676776543222 34679999999975543
No 148
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=23.15 E-value=3.2e+02 Score=24.12 Aligned_cols=62 Identities=15% Similarity=-0.002 Sum_probs=38.1
Q ss_pred cCCceeeeEEEEeeCCCceeEEecCCCCCeEEEEEccccCCCcCCCCCEEEEEEEecCCCCC-Cce
Q psy3654 54 LQNPVETGKIKEFCRSKGHGFITPDSGEPAVFVHISDIEGCYVPLPGDEVKYRLCPIPPKFE-KNQ 118 (140)
Q Consensus 54 ~~g~~~~G~VK~f~~~KGfGFI~~~~g~~dIFfH~s~l~~~~~~l~Gd~V~F~v~~~~k~~~-g~~ 118 (140)
..|.+++|+|..++.. |+=||.. |+-+.++-.++.........||.|.+.+..-.+..+ |++
T Consensus 137 ~~Geiv~g~V~r~~~~-~~i~vdl--g~~ea~LP~~eqip~E~~~~Gdrik~~i~~V~~~~k~gp~ 199 (374)
T PRK12328 137 KVGKIVFGTVVRVDNE-ENTFIEI--DEIRAVLPMKNRIKGEKFKVGDVVKAVLKRVKIDKNNGIL 199 (374)
T ss_pred hcCcEEEEEEEEEecC-CCEEEEc--CCeEEEeCHHHcCCCCcCCCCCEEEEEEEEEecCCCCCCE
Confidence 3689999999998543 3224433 234555555544433345699999988877654333 443
No 149
>PF13037 DUF3898: Domain of unknown function (DUF3898)
Probab=23.08 E-value=36 Score=24.24 Aligned_cols=26 Identities=31% Similarity=0.606 Sum_probs=21.4
Q ss_pred EEEccccCCCcCC-CCCEEEEEEEecC
Q psy3654 86 VHISDIEGCYVPL-PGDEVKYRLCPIP 111 (140)
Q Consensus 86 fH~s~l~~~~~~l-~Gd~V~F~v~~~~ 111 (140)
+|+.-+.+-|..+ +||.+.|+.+-++
T Consensus 47 iHiAKv~~RYv~liEgd~~~FEKG~SP 73 (91)
T PF13037_consen 47 IHIAKVNDRYVLLIEGDSLQFEKGFSP 73 (91)
T ss_pred eeEEEECCEEEEEEEcceEEEccCCCc
Confidence 6888888877654 9999999987766
No 150
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=22.80 E-value=3.6e+02 Score=20.73 Aligned_cols=55 Identities=13% Similarity=0.190 Sum_probs=39.0
Q ss_pred cCCceeeeEEEEeeCCCceeEE-ecC---------CCCCeEEEEEccccCC-----C-cCCCCCEEEEEEEecC
Q psy3654 54 LQNPVETGKIKEFCRSKGHGFI-TPD---------SGEPAVFVHISDIEGC-----Y-VPLPGDEVKYRLCPIP 111 (140)
Q Consensus 54 ~~g~~~~G~VK~f~~~KGfGFI-~~~---------~g~~dIFfH~s~l~~~-----~-~~l~Gd~V~F~v~~~~ 111 (140)
..|..+.|+|+.... +|++ ... ..+-+-|+|++++... . ...+||.|..++....
T Consensus 63 ~~GdiV~GkV~~i~~---~g~~V~I~~~~~~~~~l~~~~~G~l~~s~i~~~~~~~~~~~~~~GD~V~akV~~i~ 133 (189)
T PRK09521 63 KKGDIVYGRVVDVKE---QRALVRIVSIEGSERELATSKLAYIHISQVSDGYVESLTDAFKIGDIVRAKVISYT 133 (189)
T ss_pred CCCCEEEEEEEEEcC---CeEEEEEEEecccccccCCCceeeEEhhHcChhhhhhHHhccCCCCEEEEEEEecC
Confidence 368899999999853 5554 321 1235799999999753 1 2459999999998764
No 151
>PF01551 Peptidase_M23: Peptidase family M23; InterPro: IPR016047 Members of this family are zinc metallopeptidases with a range of specificities. The peptidase family M23 is included in this family, these are Gly-Gly endopeptidases. Peptidase family M23 are also endopeptidases. This family also includes some bacterial lipoproteins such as Swiss:P33648 for which no proteolytic activity has been demonstrated. This family also includes leukocyte cell-derived chemotaxin 2 (LECT2) proteins. LECT2 is a liver-specific protein which is thought to be linked to hepatocyte growth although the exact function of this protein is unknown.; PDB: 3IT5_A 3IT7_B 2GU1_A 3NYY_A 2HSI_B 3SLU_B 3UZ0_D 3TUF_B 1QWY_A 2B44_B ....
Probab=22.05 E-value=97 Score=20.68 Aligned_cols=48 Identities=17% Similarity=0.147 Sum_probs=27.5
Q ss_pred eeeeEEEEeeCCCceeEEec---CCCCCeEEEEEccccCC--CcCCCCCEEEE
Q psy3654 58 VETGKIKEFCRSKGHGFITP---DSGEPAVFVHISDIEGC--YVPLPGDEVKY 105 (140)
Q Consensus 58 ~~~G~VK~f~~~KGfGFI~~---~~g~~dIFfH~s~l~~~--~~~l~Gd~V~F 105 (140)
...|+|......+++|-... .++..-+|.|...+.-. .....||.+-.
T Consensus 19 ~~~G~V~~~~~~~~~g~~V~i~~~~g~~~~y~~l~~~~v~~G~~V~~G~~IG~ 71 (96)
T PF01551_consen 19 PADGKVVFVGEDPGYGNYVIIQHGNGYITVYGHLDSVSVKVGDRVKAGQVIGT 71 (96)
T ss_dssp SSSEEEEEEEEETTTEEEEEEEETTSEEEEEEEESEESS-TTSEE-TTCEEEE
T ss_pred CccEEEEEEEeccCCccEEEEEeCCcCCEEEeccccccceecccccCCCEEEe
Confidence 35588888877666665444 33335578888775422 23346665543
No 152
>PF08292 RNA_pol_Rbc25: RNA polymerase III subunit Rpc25; InterPro: IPR013238 Rpc25 is a strongly conserved subunit of RNA polymerase III and has homology to Rpa43 in RNA polymerase I, Rpb7 in RNA polymerase II and the archaeal RpoE subunit. Rpc25 is required for transcription initiation and is not essential for the elongating properties of RNA polymerase III [].; PDB: 2CKZ_D 3AYH_B.
Probab=22.03 E-value=2.2e+02 Score=20.88 Aligned_cols=52 Identities=23% Similarity=0.231 Sum_probs=30.7
Q ss_pred CCceeeeEEEEeeCCCceeEEecCCCCCeEEEEEccccCC--C-----------------cCCCCCEEEEEEEe
Q psy3654 55 QNPVETGKIKEFCRSKGHGFITPDSGEPAVFVHISDIEGC--Y-----------------VPLPGDEVKYRLCP 109 (140)
Q Consensus 55 ~g~~~~G~VK~f~~~KGfGFI~~~~g~~dIFfH~s~l~~~--~-----------------~~l~Gd~V~F~v~~ 109 (140)
.|+++.|+|+.=+. -|.....+--+|||+=.+.|... | -...|++|.|++..
T Consensus 3 ~gEvl~g~I~~~~~---~Gi~vslgFFddI~IP~~~L~~ps~fd~~~~~W~W~~~~~~~l~~d~ge~IRFRV~~ 73 (122)
T PF08292_consen 3 VGEVLTGKIKSSTA---EGIRVSLGFFDDIFIPPSLLPEPSRFDEEEQAWVWEYDEEQELFFDIGEEIRFRVES 73 (122)
T ss_dssp TT-EEEEEEEEEET---TEEEEEECCEEEEEEECCCC-TTEEEECCCTEEEEEESSSEEEEE-TT-EEEEEEEE
T ss_pred CCCEEEEEEEecCC---CcEEEEecccccEEECHHHCCCCCccCccCCEEEEECCCCceeEccCCCEEEEEEeE
Confidence 47789999999874 34444444445777777776632 1 11278888888764
No 153
>KOG0124|consensus
Probab=21.65 E-value=45 Score=29.87 Aligned_cols=13 Identities=38% Similarity=0.557 Sum_probs=10.7
Q ss_pred eCCCceeEEecCC
Q psy3654 67 CRSKGHGFITPDS 79 (140)
Q Consensus 67 ~~~KGfGFI~~~~ 79 (140)
...||||||..++
T Consensus 249 ~~HkGyGfiEy~n 261 (544)
T KOG0124|consen 249 RGHKGYGFIEYNN 261 (544)
T ss_pred CCccceeeEEecc
Confidence 3468999999976
No 154
>cd01268 Numb Numb Phosphotyrosine-binding (PTB) domain. Numb Phosphotyrosine-binding (PTB) domain. Numb is a membrane associated adaptor protein, which is a determinant of asymmetric cell division. Numb has an N-terminal PTB domain. PTB domains have a PH-like fold and are found in various eukaryotic signaling molecules. They were initially identified based upon their ability to recognize phosphorylated tyrosine residues. In contrast to SH2 domains, which recognize phosphotyrosine and adjacent carboxy-terminal residues, PTB-domain binding specificity is conferred by residues amino-terminal to the phosphotyrosine. More recent studies have found that some types of PTB domains can bind to peptides which are not tyrosine phosphorylated or lack tyrosine residues altogether.
Probab=21.58 E-value=1e+02 Score=23.31 Aligned_cols=25 Identities=16% Similarity=0.109 Sum_probs=19.5
Q ss_pred CCCceeEEecCCCCCeEEEEEcccc
Q psy3654 68 RSKGHGFITPDSGEPAVFVHISDIE 92 (140)
Q Consensus 68 ~~KGfGFI~~~~g~~dIFfH~s~l~ 92 (140)
+.|.|+||..+...+...+|.-.-.
T Consensus 89 d~r~FayIakd~~~~r~~CHvF~~~ 113 (138)
T cd01268 89 FDRGFSYICRDGTTRRWMCHGFLAV 113 (138)
T ss_pred CCcEEEEEecCCCcccEEEEEEEee
Confidence 4678999999887777888875543
No 155
>KOG4208|consensus
Probab=21.18 E-value=82 Score=25.78 Aligned_cols=19 Identities=37% Similarity=0.646 Sum_probs=14.4
Q ss_pred eEEEEee--------CCCceeEEecCC
Q psy3654 61 GKIKEFC--------RSKGHGFITPDS 79 (140)
Q Consensus 61 G~VK~f~--------~~KGfGFI~~~~ 79 (140)
|+|+.|- ..||||||..++
T Consensus 75 g~v~r~rlsRnkrTGNSKgYAFVEFEs 101 (214)
T KOG4208|consen 75 GTVTRFRLSRNKRTGNSKGYAFVEFES 101 (214)
T ss_pred CeeEEEEeecccccCCcCceEEEEecc
Confidence 6665553 479999999977
Done!