Query psy12844
Match_columns 121
No_of_seqs 114 out of 1090
Neff 5.4
Searched_HMMs 46136
Date Fri Aug 16 21:13:31 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy12844.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/12844hhsearch_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 1.1E-26 2.4E-31 153.0 7.8 67 13-85 1-67 (67)
2 PRK09937 stationary phase/star 99.9 1.8E-25 3.8E-30 149.5 9.8 71 13-89 1-71 (74)
3 TIGR02381 cspD cold shock doma 99.9 2.9E-25 6.3E-30 145.7 8.8 67 13-85 1-67 (68)
4 PRK10943 cold shock-like prote 99.9 4.4E-25 9.6E-30 145.4 8.9 67 13-85 3-69 (69)
5 PRK14998 cold shock-like prote 99.9 6E-25 1.3E-29 146.5 9.4 69 13-87 1-69 (73)
6 PRK09507 cspE cold shock prote 99.9 8.5E-25 1.9E-29 144.0 9.0 67 13-85 3-69 (69)
7 PRK15464 cold shock-like prote 99.9 8.5E-25 1.8E-29 144.9 9.0 65 14-84 5-69 (70)
8 PRK10354 RNA chaperone/anti-te 99.9 1.5E-24 3.2E-29 143.1 9.4 65 15-85 6-70 (70)
9 PRK09890 cold shock protein Cs 99.9 2.9E-24 6.3E-29 141.8 9.5 66 14-85 5-70 (70)
10 PRK15463 cold shock-like prote 99.9 2.5E-24 5.3E-29 142.5 8.9 65 14-84 5-69 (70)
11 PF00313 CSD: 'Cold-shock' DNA 99.9 2.4E-22 5.1E-27 129.4 10.6 66 14-85 1-66 (66)
12 cd04458 CSP_CDS Cold-Shock Pro 99.9 4.9E-22 1.1E-26 127.6 8.8 65 14-84 1-65 (65)
13 KOG3070|consensus 99.4 5.7E-13 1.2E-17 105.8 5.3 76 7-88 50-129 (235)
14 smart00357 CSP Cold shock prot 99.2 1.3E-10 2.9E-15 72.0 8.5 63 15-85 1-64 (64)
15 PF14444 S1-like: S1-like 97.8 0.00012 2.7E-09 47.1 6.7 53 13-80 3-57 (58)
16 PF08206 OB_RNB: Ribonuclease 97.7 0.00021 4.6E-09 45.1 6.2 56 16-83 1-57 (58)
17 PF07497 Rho_RNA_bind: Rho ter 96.9 0.0055 1.2E-07 41.5 7.0 66 14-87 3-73 (78)
18 cd04459 Rho_CSD Rho_CSD: Rho p 96.4 0.015 3.2E-07 38.4 6.0 43 25-73 10-55 (68)
19 PRK11642 exoribonuclease R; Pr 95.3 0.081 1.8E-06 48.8 8.1 62 13-86 84-146 (813)
20 TIGR00358 3_prime_RNase VacB a 95.0 0.14 2.9E-06 46.0 8.3 63 12-86 15-79 (654)
21 PF13509 S1_2: S1 domain; PDB: 95.0 0.097 2.1E-06 33.1 5.4 55 14-80 5-59 (61)
22 cd04461 S1_Rrp5_repeat_hs8_sc7 94.7 0.23 4.9E-06 32.4 6.9 61 8-73 12-73 (83)
23 PF00575 S1: S1 RNA binding do 94.6 0.24 5.3E-06 31.2 6.7 57 12-73 6-63 (74)
24 PRK08582 hypothetical protein; 94.1 0.86 1.9E-05 33.4 9.4 78 1-89 1-80 (139)
25 cd00164 S1_like S1_like: Ribos 94.0 0.44 9.6E-06 28.1 6.6 54 15-73 2-56 (65)
26 cd04453 S1_RNase_E S1_RNase_E: 93.7 0.45 9.8E-06 32.1 6.8 60 11-73 8-71 (88)
27 COG1158 Rho Transcription term 93.6 0.2 4.4E-06 42.9 6.0 81 13-101 53-138 (422)
28 TIGR02063 RNase_R ribonuclease 93.5 0.41 8.9E-06 43.2 8.1 63 13-87 68-133 (709)
29 PRK07252 hypothetical protein; 93.5 1 2.2E-05 32.3 8.7 68 13-86 6-76 (120)
30 cd05698 S1_Rrp5_repeat_hs6_sc5 93.4 0.61 1.3E-05 29.1 6.7 57 13-74 3-60 (70)
31 cd05696 S1_Rrp5_repeat_hs4 S1_ 92.8 0.72 1.6E-05 29.5 6.5 54 16-73 7-61 (71)
32 PRK05054 exoribonuclease II; P 92.7 0.6 1.3E-05 42.0 8.0 61 12-86 20-80 (644)
33 PRK09376 rho transcription ter 91.9 0.63 1.4E-05 40.3 6.8 81 13-101 50-135 (416)
34 cd05697 S1_Rrp5_repeat_hs5 S1_ 91.7 1.4 3.1E-05 27.5 6.8 57 13-74 3-60 (69)
35 cd05691 S1_RPS1_repeat_ec6 S1_ 91.6 1.7 3.7E-05 26.9 7.1 56 14-74 4-60 (73)
36 cd05684 S1_DHX8_helicase S1_DH 91.3 2.6 5.7E-05 27.0 7.9 69 13-85 3-74 (79)
37 cd04472 S1_PNPase S1_PNPase: P 91.3 1.5 3.2E-05 26.7 6.5 56 13-73 3-59 (68)
38 cd05692 S1_RPS1_repeat_hs4 S1_ 91.2 2.1 4.6E-05 25.7 7.3 56 13-73 3-59 (69)
39 PRK05807 hypothetical protein; 91.2 4.4 9.6E-05 29.5 9.8 67 13-86 8-76 (136)
40 PRK12608 transcription termina 91.1 0.25 5.4E-06 42.2 3.5 51 13-71 18-71 (380)
41 smart00316 S1 Ribosomal protei 90.8 1.5 3.3E-05 26.2 6.1 57 13-74 5-62 (72)
42 cd05694 S1_Rrp5_repeat_hs2_sc2 90.7 2.2 4.8E-05 27.7 7.1 55 10-74 4-59 (74)
43 TIGR02062 RNase_B exoribonucle 90.6 1.5 3.3E-05 39.4 8.2 62 11-86 16-77 (639)
44 cd05704 S1_Rrp5_repeat_hs13 S1 90.5 3.1 6.7E-05 26.6 7.6 59 13-75 6-65 (72)
45 cd05690 S1_RPS1_repeat_ec5 S1_ 90.1 2.2 4.8E-05 26.2 6.6 56 13-73 3-60 (69)
46 cd05686 S1_pNO40 S1_pNO40: pNO 89.8 2.1 4.6E-05 27.3 6.4 56 13-73 6-63 (73)
47 cd04465 S1_RPS1_repeat_ec2_hs2 89.1 1.7 3.6E-05 27.1 5.4 52 13-73 3-56 (67)
48 cd05689 S1_RPS1_repeat_ec4 S1_ 89.1 3.8 8.3E-05 25.5 7.6 56 13-73 6-63 (72)
49 cd05705 S1_Rrp5_repeat_hs14 S1 89.1 3.4 7.3E-05 26.7 7.0 57 13-74 6-66 (74)
50 cd04473 S1_RecJ_like S1_RecJ_l 89.0 4.5 9.8E-05 26.1 7.9 51 10-72 16-66 (77)
51 cd05707 S1_Rrp5_repeat_sc11 S1 88.6 4 8.6E-05 25.3 6.9 56 13-73 3-59 (68)
52 cd05706 S1_Rrp5_repeat_sc10 S1 88.5 4.4 9.5E-05 25.3 8.2 57 13-74 6-63 (73)
53 TIGR00767 rho transcription te 88.3 0.98 2.1E-05 39.1 5.1 52 13-72 50-104 (415)
54 PRK12678 transcription termina 88.3 1.9 4.1E-05 39.4 7.0 76 14-98 296-380 (672)
55 PLN00207 polyribonucleotide nu 87.7 3 6.5E-05 39.4 8.1 66 15-86 759-826 (891)
56 cd04452 S1_IF2_alpha S1_IF2_al 87.6 5.1 0.00011 25.0 7.4 58 13-73 6-64 (76)
57 cd05687 S1_RPS1_repeat_ec1_hs1 86.4 4.6 0.0001 25.0 6.3 55 13-72 3-58 (70)
58 cd05702 S1_Rrp5_repeat_hs11_sc 86.4 5.3 0.00011 25.0 6.6 57 13-74 3-62 (70)
59 cd05703 S1_Rrp5_repeat_hs12_sc 84.8 8.1 0.00018 24.7 7.2 56 14-74 4-62 (73)
60 PF11604 CusF_Ec: Copper bindi 83.9 2.3 5E-05 27.6 4.0 28 57-84 41-68 (70)
61 cd04455 S1_NusA S1_NusA: N-uti 82.9 9.2 0.0002 23.9 6.5 51 12-73 5-55 (67)
62 PHA02945 interferon resistance 82.8 11 0.00024 26.1 7.2 58 12-74 13-72 (88)
63 cd05685 S1_Tex S1_Tex: The C-t 82.2 8.4 0.00018 23.0 6.6 56 13-73 3-59 (68)
64 PRK08059 general stress protei 81.1 15 0.00032 26.0 7.7 68 12-85 9-79 (123)
65 COG1098 VacB Predicted RNA bin 80.7 3.4 7.3E-05 30.5 4.3 58 13-76 8-68 (129)
66 PTZ00248 eukaryotic translatio 80.1 11 0.00023 31.7 7.6 74 13-90 20-96 (319)
67 cd05708 S1_Rrp5_repeat_sc12 S1 79.2 9.3 0.0002 23.7 5.6 57 13-73 5-62 (77)
68 COG2190 NagE Phosphotransferas 78.6 3.6 7.8E-05 31.2 4.0 57 2-66 39-100 (156)
69 TIGR02696 pppGpp_PNP guanosine 78.1 8.7 0.00019 35.5 7.0 58 13-75 650-713 (719)
70 PRK09838 periplasmic copper-bi 77.9 5.2 0.00011 28.7 4.5 63 13-84 44-113 (115)
71 cd05789 S1_Rrp4 S1_Rrp4: Rrp4 75.7 18 0.0004 23.2 7.1 56 13-73 9-69 (86)
72 PRK13806 rpsA 30S ribosomal pr 75.7 23 0.0005 30.8 8.7 74 11-89 293-369 (491)
73 cd05695 S1_Rrp5_repeat_hs3 S1_ 75.0 18 0.00038 22.6 6.5 55 13-73 3-57 (66)
74 cd04471 S1_RNase_R S1_RNase_R: 74.6 18 0.0004 22.7 7.6 56 13-73 4-72 (83)
75 PF03100 CcmE: CcmE; InterPro 72.9 32 0.00069 24.7 9.2 67 16-91 62-128 (131)
76 PRK07400 30S ribosomal protein 72.8 23 0.00051 29.2 7.7 72 12-90 198-272 (318)
77 TIGR01451 B_ant_repeat conserv 71.2 9.1 0.0002 23.4 3.8 33 57-89 6-38 (53)
78 COG2996 Predicted RNA-bindinin 70.8 27 0.00058 29.0 7.5 60 14-83 9-68 (287)
79 cd04460 S1_RpoE S1_RpoE: RpoE, 70.2 23 0.0005 23.7 6.0 54 14-73 3-68 (99)
80 TIGR03591 polynuc_phos polyrib 69.9 16 0.00034 33.3 6.6 59 12-75 620-680 (684)
81 PRK11642 exoribonuclease R; Pr 69.4 40 0.00087 31.5 9.1 57 13-73 646-714 (813)
82 PRK13806 rpsA 30S ribosomal pr 69.3 16 0.00035 31.7 6.3 56 13-73 382-438 (491)
83 cd05688 S1_RPS1_repeat_ec3 S1_ 69.2 22 0.00047 21.2 6.9 55 13-73 4-59 (68)
84 PRK11824 polynucleotide phosph 69.0 35 0.00077 31.1 8.6 58 13-75 624-683 (693)
85 PRK09202 nusA transcription el 68.4 17 0.00038 31.8 6.3 51 12-73 136-186 (470)
86 KOG4246|consensus 67.8 0.65 1.4E-05 43.7 -2.7 60 13-87 148-209 (1194)
87 TIGR00830 PTBA PTS system, glu 67.5 15 0.00033 26.5 4.9 55 4-66 34-93 (121)
88 PF05606 DUF777: Borrelia burg 67.3 8.7 0.00019 29.8 3.7 47 14-67 36-82 (181)
89 TIGR00757 RNaseEG ribonuclease 66.8 30 0.00066 29.7 7.4 71 13-86 28-114 (414)
90 PRK12269 bifunctional cytidyla 65.7 24 0.00053 33.2 7.0 57 11-73 494-551 (863)
91 PRK07899 rpsA 30S ribosomal pr 64.9 35 0.00076 30.0 7.5 57 10-72 208-265 (486)
92 PRK06299 rpsA 30S ribosomal pr 64.3 40 0.00086 29.4 7.8 69 12-85 375-446 (565)
93 COG0539 RpsA Ribosomal protein 64.2 27 0.00058 31.4 6.7 81 5-92 187-270 (541)
94 PRK07899 rpsA 30S ribosomal pr 63.2 49 0.0011 29.1 8.1 65 13-83 296-363 (486)
95 PF00358 PTS_EIIA_1: phosphoen 62.6 24 0.00052 25.7 5.2 55 4-66 38-97 (132)
96 cd04489 ExoVII_LU_OBF ExoVII_L 62.3 35 0.00077 21.2 7.1 53 14-72 4-59 (78)
97 PRK13150 cytochrome c-type bio 61.2 71 0.0015 24.3 8.5 69 15-92 68-136 (159)
98 PRK03987 translation initiatio 59.6 53 0.0012 26.5 7.2 68 13-85 11-82 (262)
99 PRK12269 bifunctional cytidyla 58.6 46 0.00099 31.5 7.4 69 12-85 580-651 (863)
100 cd00210 PTS_IIA_glc PTS_IIA, P 58.2 27 0.00059 25.2 4.8 54 5-66 35-93 (124)
101 cd04454 S1_Rrp4_like S1_Rrp4_l 58.1 46 0.001 21.2 6.4 58 13-75 9-67 (82)
102 PF04225 OapA: Opacity-associa 57.3 15 0.00032 24.7 3.1 28 55-84 39-66 (85)
103 PRK13165 cytochrome c-type bio 55.2 91 0.002 23.7 8.4 69 15-92 68-136 (160)
104 PF11948 DUF3465: Protein of u 55.1 45 0.00097 24.7 5.5 55 15-75 42-104 (131)
105 PF01345 DUF11: Domain of unkn 54.2 30 0.00066 21.8 4.1 31 57-87 35-65 (76)
106 COG0539 RpsA Ribosomal protein 53.9 43 0.00092 30.1 6.2 69 13-86 280-350 (541)
107 PRK06676 rpsA 30S ribosomal pr 53.7 68 0.0015 26.6 7.1 65 5-73 12-77 (390)
108 PRK06299 rpsA 30S ribosomal pr 53.6 1E+02 0.0022 26.9 8.5 68 10-84 201-271 (565)
109 TIGR00717 rpsA ribosomal prote 53.2 85 0.0018 26.9 7.8 55 13-72 362-418 (516)
110 PF03459 TOBE: TOBE domain; I 52.8 25 0.00054 21.3 3.4 53 13-71 6-59 (64)
111 COG4776 Rnb Exoribonuclease II 52.4 11 0.00024 33.8 2.3 47 12-71 20-66 (645)
112 PF12869 tRNA_anti-like: tRNA_ 51.3 20 0.00044 25.2 3.2 63 4-71 65-129 (144)
113 PRK09439 PTS system glucose-sp 50.7 43 0.00093 25.5 5.0 56 3-66 55-115 (169)
114 COG0557 VacB Exoribonuclease R 50.2 72 0.0016 29.1 7.2 62 13-86 69-134 (706)
115 TIGR02063 RNase_R ribonuclease 49.2 74 0.0016 28.9 7.1 57 13-73 630-698 (709)
116 PF01796 DUF35: DUF35 OB-fold 48.4 66 0.0014 20.1 5.2 38 26-69 30-67 (68)
117 PF05753 TRAP_beta: Translocon 47.6 62 0.0013 24.7 5.5 46 35-87 17-62 (181)
118 TIGR00358 3_prime_RNase VacB a 47.6 72 0.0016 28.9 6.7 57 13-73 575-643 (654)
119 COG1185 Pnp Polyribonucleotide 46.1 67 0.0014 29.8 6.3 63 12-79 621-685 (692)
120 cd03703 aeIF5B_II aeIF5B_II: T 45.4 78 0.0017 22.6 5.4 58 15-95 2-59 (110)
121 PRK10811 rne ribonuclease E; R 44.9 87 0.0019 30.5 7.0 58 13-73 41-108 (1068)
122 PRK12327 nusA transcription el 44.4 69 0.0015 27.2 5.8 50 13-73 137-186 (362)
123 TIGR01953 NusA transcription t 43.1 79 0.0017 26.6 5.9 52 12-73 133-184 (341)
124 PRK00087 4-hydroxy-3-methylbut 42.7 2E+02 0.0043 25.9 8.7 67 13-85 565-634 (647)
125 PRK07400 30S ribosomal protein 42.7 84 0.0018 25.9 5.9 53 12-73 120-172 (318)
126 PRK11712 ribonuclease G; Provi 42.6 1.1E+02 0.0024 27.0 7.0 71 13-86 41-127 (489)
127 TIGR00717 rpsA ribosomal prote 42.4 1.7E+02 0.0037 25.1 8.0 51 12-71 20-70 (516)
128 cd03470 Rieske_cytochrome_bc1 42.4 27 0.00058 25.0 2.7 16 95-110 82-97 (126)
129 COG2265 TrmA SAM-dependent met 42.1 2.2E+02 0.0049 24.6 8.7 59 13-89 4-62 (432)
130 COG5569 Uncharacterized conser 42.1 28 0.00061 24.9 2.6 27 56-83 81-107 (108)
131 COG2996 Predicted RNA-bindinin 42.0 1.9E+02 0.0041 24.1 7.8 52 24-80 85-136 (287)
132 PRK05054 exoribonuclease II; P 41.5 1.2E+02 0.0025 27.6 7.1 34 13-50 564-597 (644)
133 cd05693 S1_Rrp5_repeat_hs1_sc1 40.9 86 0.0019 21.4 5.0 57 13-74 6-82 (100)
134 TIGR00448 rpoE DNA-directed RN 40.8 1.2E+02 0.0027 22.5 6.2 54 13-72 84-149 (179)
135 PRK06676 rpsA 30S ribosomal pr 40.7 2.1E+02 0.0045 23.7 8.8 71 13-89 280-353 (390)
136 KOG0149|consensus 39.4 19 0.0004 29.3 1.6 26 5-32 36-61 (247)
137 PRK13254 cytochrome c-type bio 38.9 1.6E+02 0.0035 21.9 8.5 68 15-92 62-129 (148)
138 PRK08563 DNA-directed RNA poly 38.4 1.2E+02 0.0025 22.7 5.7 55 13-73 84-150 (187)
139 COG1093 SUI2 Translation initi 36.9 70 0.0015 26.4 4.5 61 11-74 12-73 (269)
140 PF01336 tRNA_anti-codon: OB-f 36.9 51 0.0011 19.9 3.0 52 14-71 3-57 (75)
141 TIGR00638 Mop molybdenum-pteri 36.6 98 0.0021 18.7 5.5 53 13-71 8-61 (69)
142 PRK00087 4-hydroxy-3-methylbut 35.9 2.2E+02 0.0047 25.7 7.9 65 10-79 302-369 (647)
143 PF01551 Peptidase_M23: Peptid 35.7 40 0.00088 22.0 2.6 53 13-69 19-73 (96)
144 COG1095 RPB7 DNA-directed RNA 34.6 83 0.0018 24.5 4.4 55 13-73 84-150 (183)
145 TIGR01416 Rieske_proteo ubiqui 33.2 51 0.0011 24.9 3.0 14 97-110 132-145 (174)
146 PF03657 UPF0113: Uncharacteri 32.9 15 0.00032 27.8 0.0 43 1-48 111-156 (162)
147 PLN00059 PsbP domain-containin 32.3 39 0.00085 28.0 2.4 29 16-44 108-140 (286)
148 PRK13168 rumA 23S rRNA m(5)U19 31.5 3.2E+02 0.007 23.1 8.8 61 12-90 14-74 (443)
149 cd03473 Rieske_CMP_Neu5Ac_hydr 31.2 58 0.0013 23.2 2.9 56 57-112 15-81 (107)
150 COG4942 Membrane-bound metallo 31.2 48 0.001 28.9 2.9 58 3-66 328-388 (420)
151 cd03477 Rieske_YhfW_C YhfW fam 29.2 1E+02 0.0022 20.5 3.7 13 97-109 54-66 (91)
152 TIGR02377 MocE_fam_FeS Rieske 28.6 83 0.0018 21.1 3.2 38 74-111 33-72 (101)
153 cd03528 Rieske_RO_ferredoxin R 28.3 70 0.0015 20.8 2.8 18 94-111 53-70 (98)
154 PRK11637 AmiB activator; Provi 26.5 1.9E+02 0.004 24.5 5.6 50 14-68 346-398 (428)
155 PRK09965 3-phenylpropionate di 26.2 79 0.0017 21.3 2.8 39 74-112 32-73 (106)
156 PRK09824 PTS system beta-gluco 25.6 1.6E+02 0.0034 26.9 5.2 56 3-66 513-573 (627)
157 CHL00010 infA translation init 25.5 2E+02 0.0044 18.8 6.2 52 14-72 9-60 (78)
158 TIGR02694 arsenite_ox_S arseni 25.5 58 0.0013 23.5 2.1 17 95-111 70-86 (129)
159 KOG3492|consensus 24.8 97 0.0021 23.9 3.2 49 1-49 114-170 (180)
160 TIGR01995 PTS-II-ABC-beta PTS 24.7 1.6E+02 0.0035 26.6 5.1 55 4-66 498-557 (610)
161 cd03474 Rieske_T4moC Toluene-4 24.2 1.6E+02 0.0034 19.6 4.0 39 74-112 32-72 (108)
162 KOG1671|consensus 24.2 32 0.00069 27.4 0.5 14 98-111 169-182 (210)
163 cd04451 S1_IF1 S1_IF1: Transla 23.7 1.9E+02 0.004 17.8 6.7 50 15-71 4-53 (64)
164 COG2183 Tex Transcriptional ac 23.4 1.3E+02 0.0029 28.3 4.4 66 14-85 662-730 (780)
165 PRK13159 cytochrome c-type bio 23.2 3.4E+02 0.0073 20.5 8.2 69 14-92 61-129 (155)
166 cd04486 YhcR_OBF_like YhcR_OBF 22.9 2.3E+02 0.0049 18.5 6.3 52 14-75 2-62 (78)
167 COG0723 QcrA Rieske Fe-S prote 22.4 34 0.00073 25.4 0.4 16 96-111 123-138 (177)
168 PRK00276 infA translation init 21.9 2.3E+02 0.0049 18.1 6.3 51 14-72 9-60 (72)
169 cd05701 S1_Rrp5_repeat_hs10 S1 21.8 2.4E+02 0.0053 18.6 4.3 45 24-73 12-60 (69)
170 cd03478 Rieske_AIFL_N AIFL (ap 21.3 1E+02 0.0022 20.1 2.5 16 96-111 54-69 (95)
171 smart00361 RRM_1 RNA recogniti 20.9 62 0.0013 20.0 1.3 9 24-32 36-44 (70)
No 1
>COG1278 CspC Cold shock proteins [Transcription]
Probab=99.94 E-value=1.1e-26 Score=153.01 Aligned_cols=67 Identities=33% Similarity=0.628 Sum_probs=63.9
Q ss_pred eeeeEEEEeeCCCCeEEEEecCCCCcccEEEEccccccCCCCcccCCCCCCEEEEEEEECCCCCceEEEEEEc
Q psy12844 13 YVSGVIQFFNKERGFGFINRIGDDGRKDYFFHFSEIQGGTDNILRAIKYSLLVIFDIGVTPGGRREAVHIKIF 85 (121)
Q Consensus 13 m~~G~Vkwfn~~kGfGFI~~~~d~g~~dVFfH~s~l~~~g~~~~~~l~~G~~V~F~i~~~~kGk~~A~~V~~~ 85 (121)
|..|+|||||++||||||++ ++|++|||+|+|+|+..|+ +.|.+||+|+|++..+++| ++|++|+++
T Consensus 1 ~~~GtVKwfn~~KGfGFI~p--~~G~~DvFVH~Sai~~~g~---~~L~eGQ~V~f~~~~g~kg-p~A~nv~~~ 67 (67)
T COG1278 1 MATGTVKWFNATKGFGFITP--EDGGKDVFVHISAIQRAGF---RTLREGQKVEFEVEQGRKG-PSAANVRAL 67 (67)
T ss_pred CCcceEEEeeCCCcceEcCC--CCCCcCEEEEeeeeccCCC---cccCCCCEEEEEEecCCCC-CceeEEEeC
Confidence 57899999999999999999 9998999999999999999 9999999999999999999 999999864
No 2
>PRK09937 stationary phase/starvation inducible regulatory protein CspD; Provisional
Probab=99.93 E-value=1.8e-25 Score=149.50 Aligned_cols=71 Identities=34% Similarity=0.562 Sum_probs=66.2
Q ss_pred eeeeEEEEeeCCCCeEEEEecCCCCcccEEEEccccccCCCCcccCCCCCCEEEEEEEECCCCCceEEEEEEcCCcc
Q psy12844 13 YVSGVIQFFNKERGFGFINRIGDDGRKDYFFHFSEIQGGTDNILRAIKYSLLVIFDIGVTPGGRREAVHIKIFDTRL 89 (121)
Q Consensus 13 m~~G~Vkwfn~~kGfGFI~~~~d~g~~dVFfH~s~l~~~g~~~~~~l~~G~~V~F~i~~~~kGk~~A~~V~~~~~~~ 89 (121)
|.+|+|||||.+||||||++ +++++|||||+|+|+..++ +.|.+|++|+|++..+++| ++|.+|.+++...
T Consensus 1 M~~G~Vkwfn~~KGfGFI~~--~~gg~dVFvH~s~i~~~g~---~~l~~G~~V~f~~~~~~~G-~~A~~V~~~~~~~ 71 (74)
T PRK09937 1 MEKGTVKWFNNAKGFGFICP--EGGGEDIFAHYSTIQMDGY---RTLKAGQSVQFDVHQGPKG-NHASVIVPVEVEA 71 (74)
T ss_pred CCCeEEEEEeCCCCeEEEee--CCCCccEEEEEeeccccCC---CCCCCCCEEEEEEEECCCC-ceeeEEEECCccc
Confidence 56899999999999999999 8988999999999999988 8999999999999999999 9999999985543
No 3
>TIGR02381 cspD cold shock domain protein CspD. This model represents what appears to be a phylogenetically distinct clade, containing E. coli CspD and related proteobacterial proteins within the larger family of cold shock domain proteins described by pfam model pfam00313. The gene symbol cspD may have been used idependently for other subfamilies of cold shock domain proteins, such as for B. subtilis CspD. These proteins typically are shorter than 70 amino acids. In E. coli, CspD is a stress response protein induced in stationary phase. This homodimer binds single-stranded DNA and appears to inhibit DNA replication.
Probab=99.92 E-value=2.9e-25 Score=145.68 Aligned_cols=67 Identities=34% Similarity=0.570 Sum_probs=63.4
Q ss_pred eeeeEEEEeeCCCCeEEEEecCCCCcccEEEEccccccCCCCcccCCCCCCEEEEEEEECCCCCceEEEEEEc
Q psy12844 13 YVSGVIQFFNKERGFGFINRIGDDGRKDYFFHFSEIQGGTDNILRAIKYSLLVIFDIGVTPGGRREAVHIKIF 85 (121)
Q Consensus 13 m~~G~Vkwfn~~kGfGFI~~~~d~g~~dVFfH~s~l~~~g~~~~~~l~~G~~V~F~i~~~~kGk~~A~~V~~~ 85 (121)
|.+|+|||||.+||||||.+ +++++|||||+|+|+..++ +.|.+|++|+|++..+++| ++|.+|.++
T Consensus 1 m~~G~Vk~f~~~kGfGFI~~--~~g~~dvfvH~s~~~~~g~---~~l~~G~~V~f~~~~~~~G-~~A~~V~~~ 67 (68)
T TIGR02381 1 MAIGIVKWFNNAKGFGFICP--EGVDGDIFAHYSTIQMDGY---RTLKAGQKVQFEVVQGPKG-AHATHIVPI 67 (68)
T ss_pred CCCeEEEEEeCCCCeEEEec--CCCCccEEEEHHHhhhcCC---CCCCCCCEEEEEEEECCCC-ceeEEEEEC
Confidence 56899999999999999999 8888999999999998887 8999999999999999999 999999875
No 4
>PRK10943 cold shock-like protein CspC; Provisional
Probab=99.92 E-value=4.4e-25 Score=145.39 Aligned_cols=67 Identities=37% Similarity=0.653 Sum_probs=62.9
Q ss_pred eeeeEEEEeeCCCCeEEEEecCCCCcccEEEEccccccCCCCcccCCCCCCEEEEEEEECCCCCceEEEEEEc
Q psy12844 13 YVSGVIQFFNKERGFGFINRIGDDGRKDYFFHFSEIQGGTDNILRAIKYSLLVIFDIGVTPGGRREAVHIKIF 85 (121)
Q Consensus 13 m~~G~Vkwfn~~kGfGFI~~~~d~g~~dVFfH~s~l~~~g~~~~~~l~~G~~V~F~i~~~~kGk~~A~~V~~~ 85 (121)
+++|+|||||.+||||||++ +++++|||||+|+|+..++ +.|.+|++|+|++..+++| ++|++|+.+
T Consensus 3 ~~~G~Vk~f~~~kGfGFI~~--~~g~~dvFvH~s~l~~~g~---~~l~~G~~V~f~~~~~~~g-~~A~~V~~~ 69 (69)
T PRK10943 3 KIKGQVKWFNESKGFGFITP--ADGSKDVFVHFSAIQGNGF---KTLAEGQNVEFEIQDGQKG-PAAVNVTAI 69 (69)
T ss_pred ccceEEEEEeCCCCcEEEec--CCCCeeEEEEhhHccccCC---CCCCCCCEEEEEEEECCCC-ceeEEEEcC
Confidence 46899999999999999999 8888999999999999887 8999999999999999998 999999864
No 5
>PRK14998 cold shock-like protein CspD; Provisional
Probab=99.92 E-value=6e-25 Score=146.51 Aligned_cols=69 Identities=35% Similarity=0.593 Sum_probs=64.9
Q ss_pred eeeeEEEEeeCCCCeEEEEecCCCCcccEEEEccccccCCCCcccCCCCCCEEEEEEEECCCCCceEEEEEEcCC
Q psy12844 13 YVSGVIQFFNKERGFGFINRIGDDGRKDYFFHFSEIQGGTDNILRAIKYSLLVIFDIGVTPGGRREAVHIKIFDT 87 (121)
Q Consensus 13 m~~G~Vkwfn~~kGfGFI~~~~d~g~~dVFfH~s~l~~~g~~~~~~l~~G~~V~F~i~~~~kGk~~A~~V~~~~~ 87 (121)
|.+|+|||||.+||||||++ +++++|||||+|+|+..++ +.|.+|++|+|++..+++| ++|++|..+..
T Consensus 1 M~~G~Vkwfn~~kGfGFI~~--~~g~~dVFvH~s~l~~~g~---~~l~~G~~V~f~~~~~~~G-~~A~~V~~~~~ 69 (73)
T PRK14998 1 METGTVKWFNNAKGFGFICP--EGGGEDIFAHYSTIQMDGY---RTLKAGQSVRFDVHQGPKG-NHASVIVPIEA 69 (73)
T ss_pred CCCeEEEEEeCCCceEEEec--CCCCccEEEEeeeecccCC---CCCCCCCEEEEEEEECCCC-ceeEEEEECcc
Confidence 56899999999999999999 8988999999999999887 8999999999999999999 99999998754
No 6
>PRK09507 cspE cold shock protein CspE; Reviewed
Probab=99.92 E-value=8.5e-25 Score=144.03 Aligned_cols=67 Identities=34% Similarity=0.614 Sum_probs=63.0
Q ss_pred eeeeEEEEeeCCCCeEEEEecCCCCcccEEEEccccccCCCCcccCCCCCCEEEEEEEECCCCCceEEEEEEc
Q psy12844 13 YVSGVIQFFNKERGFGFINRIGDDGRKDYFFHFSEIQGGTDNILRAIKYSLLVIFDIGVTPGGRREAVHIKIF 85 (121)
Q Consensus 13 m~~G~Vkwfn~~kGfGFI~~~~d~g~~dVFfH~s~l~~~g~~~~~~l~~G~~V~F~i~~~~kGk~~A~~V~~~ 85 (121)
+.+|+|||||.+||||||++ +++++|||||+|+|...++ +.|.+|++|+|++..+++| ++|++|..+
T Consensus 3 ~~~G~Vk~f~~~kGyGFI~~--~~g~~dvfvH~s~l~~~g~---~~l~~G~~V~f~~~~~~~G-~~A~~V~~~ 69 (69)
T PRK09507 3 KIKGNVKWFNESKGFGFITP--EDGSKDVFVHFSAIQTNGF---KTLAEGQRVEFEITNGAKG-PSAANVIAL 69 (69)
T ss_pred ccceEEEEEeCCCCcEEEec--CCCCeeEEEEeecccccCC---CCCCCCCEEEEEEEECCCC-cccEEEEeC
Confidence 46899999999999999999 8988999999999998887 8999999999999999999 999999864
No 7
>PRK15464 cold shock-like protein CspH; Provisional
Probab=99.92 E-value=8.5e-25 Score=144.89 Aligned_cols=65 Identities=26% Similarity=0.396 Sum_probs=61.6
Q ss_pred eeeEEEEeeCCCCeEEEEecCCCCcccEEEEccccccCCCCcccCCCCCCEEEEEEEECCCCCceEEEEEE
Q psy12844 14 VSGVIQFFNKERGFGFINRIGDDGRKDYFFHFSEIQGGTDNILRAIKYSLLVIFDIGVTPGGRREAVHIKI 84 (121)
Q Consensus 14 ~~G~Vkwfn~~kGfGFI~~~~d~g~~dVFfH~s~l~~~g~~~~~~l~~G~~V~F~i~~~~kGk~~A~~V~~ 84 (121)
++|+|||||.+||||||++ +++++|||||+++|+..++ +.|.+||+|+|++.++++| ++|++|.+
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 MTGIVKTFDRKSGKGFIIP--SDGRKEVQVHISAFTPRDA---EVLIPGLRVEFCRVNGLRG-PTAANVYL 69 (70)
T ss_pred ceEEEEEEECCCCeEEEcc--CCCCccEEEEehhehhcCC---CCCCCCCEEEEEEEECCCC-ceeEEEEc
Confidence 4899999999999999999 8988999999999998887 7999999999999999999 99999974
No 8
>PRK10354 RNA chaperone/anti-terminator; Provisional
Probab=99.92 E-value=1.5e-24 Score=143.06 Aligned_cols=65 Identities=37% Similarity=0.685 Sum_probs=61.9
Q ss_pred eeEEEEeeCCCCeEEEEecCCCCcccEEEEccccccCCCCcccCCCCCCEEEEEEEECCCCCceEEEEEEc
Q psy12844 15 SGVIQFFNKERGFGFINRIGDDGRKDYFFHFSEIQGGTDNILRAIKYSLLVIFDIGVTPGGRREAVHIKIF 85 (121)
Q Consensus 15 ~G~Vkwfn~~kGfGFI~~~~d~g~~dVFfH~s~l~~~g~~~~~~l~~G~~V~F~i~~~~kGk~~A~~V~~~ 85 (121)
+|+|||||.++|||||.+ +++++|||||+|+|...++ +.|++|++|+|++..+++| ++|++|+.+
T Consensus 6 ~G~Vk~f~~~kGfGFI~~--~~g~~dvfvH~s~l~~~g~---~~l~~G~~V~f~~~~~~~G-~~A~~V~~~ 70 (70)
T PRK10354 6 TGIVKWFNADKGFGFITP--DDGSKDVFVHFSAIQNDGY---KSLDEGQKVSFTIESGAKG-PAAGNVTSL 70 (70)
T ss_pred eEEEEEEeCCCCcEEEec--CCCCccEEEEEeeccccCC---CCCCCCCEEEEEEEECCCC-ceeEEEEeC
Confidence 899999999999999999 8888999999999999887 8999999999999999999 999999863
No 9
>PRK09890 cold shock protein CspG; Provisional
Probab=99.91 E-value=2.9e-24 Score=141.83 Aligned_cols=66 Identities=36% Similarity=0.690 Sum_probs=62.4
Q ss_pred eeeEEEEeeCCCCeEEEEecCCCCcccEEEEccccccCCCCcccCCCCCCEEEEEEEECCCCCceEEEEEEc
Q psy12844 14 VSGVIQFFNKERGFGFINRIGDDGRKDYFFHFSEIQGGTDNILRAIKYSLLVIFDIGVTPGGRREAVHIKIF 85 (121)
Q Consensus 14 ~~G~Vkwfn~~kGfGFI~~~~d~g~~dVFfH~s~l~~~g~~~~~~l~~G~~V~F~i~~~~kGk~~A~~V~~~ 85 (121)
++|+|||||.+||||||++ +++++|||||+|+|+..++ +.|.+|++|+|++..+++| ++|.+|..+
T Consensus 5 ~~G~Vk~f~~~kGfGFI~~--~~g~~dvFvH~s~l~~~~~---~~l~~G~~V~f~~~~~~~G-~~A~~V~~~ 70 (70)
T PRK09890 5 MTGLVKWFNADKGFGFITP--DDGSKDVFVHFTAIQSNEF---RTLNENQKVEFSIEQGQRG-PAAANVVTL 70 (70)
T ss_pred ceEEEEEEECCCCcEEEec--CCCCceEEEEEeeeccCCC---CCCCCCCEEEEEEEECCCC-ceeEEEEeC
Confidence 4899999999999999999 8888899999999999987 8999999999999999999 999999864
No 10
>PRK15463 cold shock-like protein CspF; Provisional
Probab=99.91 E-value=2.5e-24 Score=142.46 Aligned_cols=65 Identities=26% Similarity=0.387 Sum_probs=61.5
Q ss_pred eeeEEEEeeCCCCeEEEEecCCCCcccEEEEccccccCCCCcccCCCCCCEEEEEEEECCCCCceEEEEEE
Q psy12844 14 VSGVIQFFNKERGFGFINRIGDDGRKDYFFHFSEIQGGTDNILRAIKYSLLVIFDIGVTPGGRREAVHIKI 84 (121)
Q Consensus 14 ~~G~Vkwfn~~kGfGFI~~~~d~g~~dVFfH~s~l~~~g~~~~~~l~~G~~V~F~i~~~~kGk~~A~~V~~ 84 (121)
++|+|||||.+||||||++ +++++|||||+++|+..++ +.|.+|++|+|++..+++| ++|++|.+
T Consensus 5 ~~G~Vk~fn~~kGfGFI~~--~~g~~DvFvH~sal~~~g~---~~l~~G~~V~f~v~~~~~G-~~A~~V~~ 69 (70)
T PRK15463 5 MTGIVKTFDGKSGKGLITP--SDGRKDVQVHISALNLRDA---EELTTGLRVEFCRINGLRG-PTAANVYL 69 (70)
T ss_pred ceEEEEEEeCCCceEEEec--CCCCccEEEEehhhhhcCC---CCCCCCCEEEEEEEECCCC-ceeEEEEc
Confidence 4899999999999999999 8988999999999998877 8999999999999999999 99999974
No 11
>PF00313 CSD: 'Cold-shock' DNA-binding domain; InterPro: IPR002059 When Escherichia coli is exposed to a temperature drop from 37 to 10 degrees centigrade, a 4-5 hour lag phase occurs, after which growth is resumed at a reduced rate []. During the lag phase, the expression of around 13 proteins, which contain specific DNA-binding regions [], is increased 2-10 fold. These so-called 'cold shock' proteins are thought to help the cell to survive in temperatures lower than optimum growth temperature, by contrast with heat shock proteins, which help the cell to survive in temperatures greater than the optimum, possibly by condensation of the chromosome and organisation of the prokaryotic nucleoid []. A conserved domain of about 70 amino acids has been found in prokaryotic and eukaryotic DNA-binding proteins [, , ]. This domain is known as the 'cold-shock domain' (CSD), part of which is highly similar [] to the RNP-1 RNA-binding motif.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1HZC_A 1I5F_A 1HZ9_B 1C9O_B 1HZB_B 1HZA_A 2HAX_B 2L15_A 2LSS_A 3I2Z_B ....
Probab=99.89 E-value=2.4e-22 Score=129.38 Aligned_cols=66 Identities=35% Similarity=0.729 Sum_probs=59.3
Q ss_pred eeeEEEEeeCCCCeEEEEecCCCCcccEEEEccccccCCCCcccCCCCCCEEEEEEEECCCCCceEEEEEEc
Q psy12844 14 VSGVIQFFNKERGFGFINRIGDDGRKDYFFHFSEIQGGTDNILRAIKYSLLVIFDIGVTPGGRREAVHIKIF 85 (121)
Q Consensus 14 ~~G~Vkwfn~~kGfGFI~~~~d~g~~dVFfH~s~l~~~g~~~~~~l~~G~~V~F~i~~~~kGk~~A~~V~~~ 85 (121)
++|+|+|||+++|||||.+ +++++|||||+++|...++ ..|.+|++|+|++..+++| ++|++|+.+
T Consensus 1 ~~G~V~~~~~~kgyGFI~~--~~~~~diFfh~s~~~~~~~---~~l~~G~~V~F~~~~~~~g-~~A~~V~~~ 66 (66)
T PF00313_consen 1 MTGTVKWFDDEKGYGFITS--DDGGEDIFFHISDLSGNGF---RSLKEGDRVEFEVEEGKKG-PQAVNVRKI 66 (66)
T ss_dssp EEEEEEEEETTTTEEEEEE--TTSSSEEEEEGGGBCSSSS---TS--TTSEEEEEEEECTTS-EEEEEEEE-
T ss_pred CeEEEEEEECCCCceEEEE--cccceeEEecccccccccc---ccCCCCCEEEEEEEECCCC-CEEEEEECc
Confidence 4799999999999999999 8888899999999999987 7999999999999998888 999999864
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=99.87 E-value=4.9e-22 Score=127.55 Aligned_cols=65 Identities=35% Similarity=0.719 Sum_probs=60.1
Q ss_pred eeeEEEEeeCCCCeEEEEecCCCCcccEEEEccccccCCCCcccCCCCCCEEEEEEEECCCCCceEEEEEE
Q psy12844 14 VSGVIQFFNKERGFGFINRIGDDGRKDYFFHFSEIQGGTDNILRAIKYSLLVIFDIGVTPGGRREAVHIKI 84 (121)
Q Consensus 14 ~~G~Vkwfn~~kGfGFI~~~~d~g~~dVFfH~s~l~~~g~~~~~~l~~G~~V~F~i~~~~kGk~~A~~V~~ 84 (121)
.+|+|+|||+++|||||++ +++++|||||+++|...++ ..|++|++|+|++..+++| ++|++|++
T Consensus 1 ~~G~Vk~~~~~kGfGFI~~--~~~g~diffh~~~~~~~~~---~~~~~G~~V~f~~~~~~~g-~~A~~V~~ 65 (65)
T cd04458 1 VTGTVKWFDDEKGFGFITP--DDGGEDVFVHISALEGDGF---RSLEEGDRVEFELEEGDKG-PQAVNVRL 65 (65)
T ss_pred CcEEEEEEECCCCeEEEec--CCCCcCEEEEhhHhhccCC---CcCCCCCEEEEEEEECCCC-CeEEEeEC
Confidence 3799999999999999999 8877899999999998876 7999999999999999888 99999873
No 13
>KOG3070|consensus
Probab=99.37 E-value=5.7e-13 Score=105.85 Aligned_cols=76 Identities=37% Similarity=0.538 Sum_probs=67.6
Q ss_pred ccceeeeeeeEEEEeeCCCCeEEEEecCCCCcccEEEEcccccc----CCCCcccCCCCCCEEEEEEEECCCCCceEEEE
Q psy12844 7 KIIEEVYVSGVIQFFNKERGFGFINRIGDDGRKDYFFHFSEIQG----GTDNILRAIKYSLLVIFDIGVTPGGRREAVHI 82 (121)
Q Consensus 7 ~~~~~~m~~G~Vkwfn~~kGfGFI~~~~d~g~~dVFfH~s~l~~----~g~~~~~~l~~G~~V~F~i~~~~kGk~~A~~V 82 (121)
+.......+|+|||||..+|||||++ +|+++|||||.++|.. .++ +.+..++.|.|.++.+.+| ..|++|
T Consensus 50 ~~~~~~~~~G~~k~fnv~~G~gFi~~--~d~~~D~fvhQs~i~~~~~~~~~---rs~~~~e~v~f~~~~~~~g-~~a~~v 123 (235)
T KOG3070|consen 50 KKVQGARVKGTVKWFNVGKGYGFITR--DDGPEDVFVHQSAITKYTPSEGF---RSLKEGEAVPFDIQEGNKG-TEAANV 123 (235)
T ss_pred cccccccccCcceeEeccCCcceecc--cCCCCceeEEeeeecccccccch---hhcccCCCccceecccCcc-ceeeee
Confidence 44444468999999999999999999 9999999999999999 777 8999999999999999999 999998
Q ss_pred EEcCCc
Q psy12844 83 KIFDTR 88 (121)
Q Consensus 83 ~~~~~~ 88 (121)
+-.+..
T Consensus 124 t~p~g~ 129 (235)
T KOG3070|consen 124 TGPDGV 129 (235)
T ss_pred cCCCCc
Confidence 876643
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=99.21 E-value=1.3e-10 Score=72.02 Aligned_cols=63 Identities=41% Similarity=0.711 Sum_probs=51.3
Q ss_pred eeEEEEeeCCCCeEEEEecCCCCcccEEEEccccccCCCCcccCCCCCCEEEEEEEEC-CCCCceEEEEEEc
Q psy12844 15 SGVIQFFNKERGFGFINRIGDDGRKDYFFHFSEIQGGTDNILRAIKYSLLVIFDIGVT-PGGRREAVHIKIF 85 (121)
Q Consensus 15 ~G~Vkwfn~~kGfGFI~~~~d~g~~dVFfH~s~l~~~g~~~~~~l~~G~~V~F~i~~~-~kGk~~A~~V~~~ 85 (121)
+|+|+|++ +|||||.+ ++...++|||.+++.. +. ..+..||.|.|.+... ..++++|..|.++
T Consensus 1 ~G~i~~~~--~g~gfv~~--~~~~~~i~v~~~~~~~-~~---~~~~~Gd~V~~~i~~~~~~~~~~a~~v~~~ 64 (64)
T smart00357 1 TGVVKWFN--KGFGFIRP--DDGGKDVFVHPSQIQG-GL---KSLREGDEVEFKVVSPRGGGKPEAENVVKL 64 (64)
T ss_pred CeEEEEEc--CCeeEEec--CCCCccEEEEhHHhhc-CC---CcCCCCCEEEEEEEEccCCCCcEEEEEEeC
Confidence 58999997 79999999 7654699999999887 55 6789999999999873 3344899887753
No 15
>PF14444 S1-like: S1-like
Probab=97.80 E-value=0.00012 Score=47.08 Aligned_cols=53 Identities=25% Similarity=0.419 Sum_probs=43.3
Q ss_pred eeeeEEEEeeCCCCeEEEEecCCCCcccEEEEccccccCCCCcccCCCCCCEEEEEEEECCC--CCceEE
Q psy12844 13 YVSGVIQFFNKERGFGFINRIGDDGRKDYFFHFSEIQGGTDNILRAIKYSLLVIFDIGVTPG--GRREAV 80 (121)
Q Consensus 13 m~~G~Vkwfn~~kGfGFI~~~~d~g~~dVFfH~s~l~~~g~~~~~~l~~G~~V~F~i~~~~k--Gk~~A~ 80 (121)
..+|.|+.+. ..||||+. +|||+.+.+.+. .|+.||+|..+...++. .++.|.
T Consensus 3 ~~~GvVTkl~--~~yG~IDe-------~vFF~~~vv~G~------~P~vGdrV~v~A~~n~~~~~kW~A~ 57 (58)
T PF14444_consen 3 VFTGVVTKLC--DDYGFIDE-------DVFFQTDVVKGN------VPKVGDRVLVEAIYNPNMPFKWNAT 57 (58)
T ss_pred eEEEEEEEEe--CCcceEcc-------cEEEEcccEecC------CCccCCEEEEEEEeCCCCCccceee
Confidence 3589999996 78999977 899999998744 57999999999998763 356664
No 16
>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=97.67 E-value=0.00021 Score=45.08 Aligned_cols=56 Identities=27% Similarity=0.464 Sum_probs=37.0
Q ss_pred eEEEEeeCCCCeEEEEecCCCCcccEEEEccccccCCCCcccCCCCCCEEEEEEEECCC-CCceEEEEE
Q psy12844 16 GVIQFFNKERGFGFINRIGDDGRKDYFFHFSEIQGGTDNILRAIKYSLLVIFDIGVTPG-GRREAVHIK 83 (121)
Q Consensus 16 G~Vkwfn~~kGfGFI~~~~d~g~~dVFfH~s~l~~~g~~~~~~l~~G~~V~F~i~~~~k-Gk~~A~~V~ 83 (121)
|+|+-- .+||||+.+ ++.++|||+...++.. .-.||.|...+....+ +++++.-|.
T Consensus 1 G~~~~~--~~GfGFv~~--~~~~~DifIp~~~l~~--------A~~gD~V~v~i~~~~~~~~~eg~vv~ 57 (58)
T PF08206_consen 1 GTLKIH--PKGFGFVIP--DDGGEDIFIPPRNLNG--------AMDGDKVLVRITPPSRGKRPEGEVVE 57 (58)
T ss_dssp EEEEE---SSS-EEEEE--CT-TEEEEE-HHHHTT--------S-TT-EEEEEEEESSSEEEEEEEEEE
T ss_pred CEEEEE--cCCCEEEEE--CCCCCCEEECHHHHCC--------CCCCCEEEEEEecCCCCCCCCEEEEe
Confidence 444432 799999999 8777899999998863 3679999999998433 346665443
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=96.94 E-value=0.0055 Score=41.49 Aligned_cols=66 Identities=18% Similarity=0.297 Sum_probs=40.2
Q ss_pred eeeEEEEeeCCCCeEEEEec--C-CCCcccEEEEccccccCCCCcccCCCCCCEEEEEEEECCCC-C-ceEEEEEEcCC
Q psy12844 14 VSGVIQFFNKERGFGFINRI--G-DDGRKDYFFHFSEIQGGTDNILRAIKYSLLVIFDIGVTPGG-R-REAVHIKIFDT 87 (121)
Q Consensus 14 ~~G~Vkwfn~~kGfGFI~~~--~-d~g~~dVFfH~s~l~~~g~~~~~~l~~G~~V~F~i~~~~kG-k-~~A~~V~~~~~ 87 (121)
..|.+--. .+||||+... + ..+..|||+..+.|+..+ |+.||.|+=.+.....| | +.-..|..++.
T Consensus 3 ~~GvLei~--~dGyGFLR~~~~~y~~~~~DvYVs~~qIrrf~------LR~GD~V~G~vr~p~~~ek~~aL~~V~~VNg 73 (78)
T PF07497_consen 3 VEGVLEIL--PDGYGFLRSPDNNYLPSPDDVYVSPSQIRRFG------LRTGDLVEGQVRPPREGEKYFALLRVESVNG 73 (78)
T ss_dssp EEEEEEE---TTS-EEEE-GGGTTS-STTSEEE-CCCCCCTT--------TTEEEEEEEE--STTSSSEEECEECEETT
T ss_pred EEEEEEEC--CCCcEEeECCCcCCCCCCCCEEECHHHHHHcC------CCCCCEEEEEEeCCCCCCcceeeEEEEeECC
Confidence 45666633 4799999993 1 145689999999999876 79999999888886544 3 23445555543
No 18
>cd04459 Rho_CSD Rho_CSD: Rho protein cold-shock domain (CSD). Rho protein is a transcription termination factor in most bacteria. In bacteria, there are two distinct mechanisms for mRNA transcription termination. In intrinsic termination, RNA polymerase and nascent mRNA are released from DNA template by an mRNA stem loop structure, which resembles the transcription termination mechanism used by eukaryotic pol III. The second mechanism is mediated by Rho factor. Rho factor terminates transcription by using energy from ATP hydrolysis to forcibly dissociate the transcripts from RNA polymerase. Rho protein contains an N-terminal S1-like domain, which binds single-stranded RNA. Rho has a C-terminal ATPase domain which hydrolyzes ATP to provide energy to strip RNA polymerase and mRNA from the DNA template. Rho functions as a homohexamer.
Probab=96.42 E-value=0.015 Score=38.39 Aligned_cols=43 Identities=26% Similarity=0.363 Sum_probs=34.9
Q ss_pred CCeEEEEecC---CCCcccEEEEccccccCCCCcccCCCCCCEEEEEEEECC
Q psy12844 25 RGFGFINRIG---DDGRKDYFFHFSEIQGGTDNILRAIKYSLLVIFDIGVTP 73 (121)
Q Consensus 25 kGfGFI~~~~---d~g~~dVFfH~s~l~~~g~~~~~~l~~G~~V~F~i~~~~ 73 (121)
+||||+...+ ..+..||||..+.|+..+ |+.||.|+=.+....
T Consensus 10 ~g~GFLR~~~~~y~~~~~DvyVs~~~Irr~~------LR~GD~V~G~vr~p~ 55 (68)
T cd04459 10 DGFGFLRSSGYNYLPGPDDIYVSPSQIRRFN------LRTGDTVVGQIRPPK 55 (68)
T ss_pred CCceEEecCCcCCCCCCCCEEECHHHHHHhC------CCCCCEEEEEEeCCC
Confidence 4999999831 135689999999999886 799999998877644
No 19
>PRK11642 exoribonuclease R; Provisional
Probab=95.33 E-value=0.081 Score=48.83 Aligned_cols=62 Identities=18% Similarity=0.309 Sum_probs=46.3
Q ss_pred eeeeEEEEeeCCCCeEEEEecCCCCcccEEEEccccccCCCCcccCCCCCCEEEEEEEE-CCCCCceEEEEEEcC
Q psy12844 13 YVSGVIQFFNKERGFGFINRIGDDGRKDYFFHFSEIQGGTDNILRAIKYSLLVIFDIGV-TPGGRREAVHIKIFD 86 (121)
Q Consensus 13 m~~G~Vkwfn~~kGfGFI~~~~d~g~~dVFfH~s~l~~~g~~~~~~l~~G~~V~F~i~~-~~kGk~~A~~V~~~~ 86 (121)
.+.|+|..= .+||||+.+ +++++|||+.-..+.+ .-.||+|...+.. +.+|++.|.-|.++.
T Consensus 84 ~~~G~v~~~--~~GfgFv~~--e~~~~difI~~~~l~~--------A~~GD~V~v~i~~~~~~~r~eg~Vv~Ile 146 (813)
T PRK11642 84 LLKGTVIGH--RDGYGFLRV--EGRKDDLYLSSEQMKT--------CIHGDQVLAQPLGADRKGRREARIVRVLV 146 (813)
T ss_pred eEEEEEEEC--CCccEEEEE--CCCCCCEEEChHHHcc--------CCCCCEEEEEEccCCCCCCcEEEEEEEEe
Confidence 467999953 699999999 7656799998776642 3459999988665 334667888777775
No 20
>TIGR00358 3_prime_RNase VacB and RNase II family 3'-5' exoribonucleases. This model is defined to identify a pair of paralogous 3-prime exoribonucleases in E. coli, plus the set of proteins apparently orthologous to one or the other in other eubacteria. VacB was characterized originally as required for the expression of virulence genes, but is now recognized as the exoribonuclease RNase R (Rnr). Its paralog in E. coli and H. influenzae is designated exoribonuclease II (Rnb). Both are involved in the degradation of mRNA, and consequently have strong pleiotropic effects that may be difficult to disentangle. Both these proteins share domain-level similarity (RNB, S1) with a considerable number of other proteins, and full-length similarity scoring below the trusted cutoff to proteins associated with various phenotypes but uncertain biochemistry; it may be that these latter proteins are also 3-prime exoribonucleases.
Probab=94.99 E-value=0.14 Score=46.03 Aligned_cols=63 Identities=32% Similarity=0.460 Sum_probs=47.1
Q ss_pred eeeeeEEEEeeCCCCeEEEEecCCC-CcccEEEEccccccCCCCcccCCCCCCEEEEEEEE-CCCCCceEEEEEEcC
Q psy12844 12 VYVSGVIQFFNKERGFGFINRIGDD-GRKDYFFHFSEIQGGTDNILRAIKYSLLVIFDIGV-TPGGRREAVHIKIFD 86 (121)
Q Consensus 12 ~m~~G~Vkwfn~~kGfGFI~~~~d~-g~~dVFfH~s~l~~~g~~~~~~l~~G~~V~F~i~~-~~kGk~~A~~V~~~~ 86 (121)
....|+|+.= .+||||+.+ ++ +++|+|+.-.++.. .-.||.|...+.. +.+|++.|.-+.++.
T Consensus 15 ~~~~G~i~~~--~~gfgFv~~--~~~~~~difI~~~~~~~--------a~~GD~V~v~i~~~~~~~~~~g~v~~il~ 79 (654)
T TIGR00358 15 DLVKGVVKAH--NKGFGFLRP--DDDDKKDYFIPPPQMKK--------VMHGDLVEACPLSQPQRGRFEAEVERILE 79 (654)
T ss_pred CeEEEEEEEC--CCccEEEEe--CCCCCCcEEEchHHhCc--------CCCCCEEEEEEeecCCCCCceEEEEEEec
Confidence 3468999964 699999999 65 35799998776642 3469999998754 446667888777775
No 21
>PF13509 S1_2: S1 domain; PDB: 3GO5_A.
Probab=94.98 E-value=0.097 Score=33.11 Aligned_cols=55 Identities=22% Similarity=0.166 Sum_probs=34.3
Q ss_pred eeeEEEEeeCCCCeEEEEecCCCCcccEEEEccccccCCCCcccCCCCCCEEEEEEEECCCCCceEE
Q psy12844 14 VSGVIQFFNKERGFGFINRIGDDGRKDYFFHFSEIQGGTDNILRAIKYSLLVIFDIGVTPGGRREAV 80 (121)
Q Consensus 14 ~~G~Vkwfn~~kGfGFI~~~~d~g~~dVFfH~s~l~~~g~~~~~~l~~G~~V~F~i~~~~kGk~~A~ 80 (121)
.+.+|...+ .+|+... .+.+.+||+|.+.+. ..+++||.|.-=+-.+.++++.|.
T Consensus 5 ~~L~V~~~~---~~g~fL~--~~~~~~vlLp~~e~~-------~~~~~Gd~v~VFvY~D~~~rl~AT 59 (61)
T PF13509_consen 5 NTLKVVDKN---EFGYFLD--DGEGKEVLLPKSEVP-------EPLKVGDEVEVFVYLDKEGRLVAT 59 (61)
T ss_dssp ----EEEE----SSEEEEE--ETT-EEEEEEGGG-------------TTSEEEEEEEE-TTS-EEEE
T ss_pred cceEEEEEe---CCEEEEE--CCCCCEEEechHHcC-------CCCCCCCEEEEEEEECCCCCEEEe
Confidence 345677764 5787777 555579999999886 358999999999999998878774
No 22
>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=94.70 E-value=0.23 Score=32.43 Aligned_cols=61 Identities=13% Similarity=-0.006 Sum_probs=44.7
Q ss_pred cceeeeeeeEEEEeeCCCCeEEEEecCCCCcccEEEEccccccCCCC-cccCCCCCCEEEEEEEECC
Q psy12844 8 IIEEVYVSGVIQFFNKERGFGFINRIGDDGRKDYFFHFSEIQGGTDN-ILRAIKYSLLVIFDIGVTP 73 (121)
Q Consensus 8 ~~~~~m~~G~Vkwfn~~kGfGFI~~~~d~g~~dVFfH~s~l~~~g~~-~~~~l~~G~~V~F~i~~~~ 73 (121)
+.+-..+.|+|+... .||++.. -.++-+.|+|.+++...... ....++.||.|++.+...+
T Consensus 12 ~~~G~i~~g~V~~v~---~~G~fv~--l~~~~~g~v~~~el~~~~~~~~~~~~~~Gd~v~vkV~~id 73 (83)
T cd04461 12 LKPGMVVHGYVRNIT---PYGVFVE--FLGGLTGLAPKSYISDEFVTDPSFGFKKGQSVTAKVTSVD 73 (83)
T ss_pred CCCCCEEEEEEEEEe---eceEEEE--cCCCCEEEEEHHHCCcccccCHHHhcCCCCEEEEEEEEEc
Confidence 334445789999875 5898888 55557999999999655331 2345788999999988755
No 23
>PF00575 S1: S1 RNA binding domain; InterPro: IPR003029 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. The S1 domain was originally identified in ribosomal protein S1 but is found in a large number of RNA-associated proteins. The structure of the S1 RNA-binding domain from the Escherichia coli polynucleotide phosphorylase has been determined using NMR methods and consists of a five-stranded antiparallel beta barrel. Conserved residues on one face of the barrel and adjacent loops form the putative RNA-binding site []. The structure of the S1 domain is very similar to that of cold shock proteins. This suggests that they may both be derived from an ancient nucleic acid-binding protein []. More information about these proteins can be found at Protein of the Month: RNA Exosomes []. This entry does not include translation initiation factor IF-1 S1 domains.; GO: 0003723 RNA binding; PDB: 3L7Z_F 2JE6_I 2JEA_I 2JEB_I 1E3P_A 2Y0S_E 1WI5_A 2BH8_A 2CQO_A 2EQS_A ....
Probab=94.63 E-value=0.24 Score=31.17 Aligned_cols=57 Identities=18% Similarity=0.163 Sum_probs=42.3
Q ss_pred eeeeeEEEEeeCCCCeEEEEecCCCCcccEEEEccccccCC-CCcccCCCCCCEEEEEEEECC
Q psy12844 12 VYVSGVIQFFNKERGFGFINRIGDDGRKDYFFHFSEIQGGT-DNILRAIKYSLLVIFDIGVTP 73 (121)
Q Consensus 12 ~m~~G~Vkwfn~~kGfGFI~~~~d~g~~dVFfH~s~l~~~g-~~~~~~l~~G~~V~F~i~~~~ 73 (121)
..+.|+|...++ +|++.. -.++-+.|+|.+++...- ......+..||.|.+.+..-+
T Consensus 6 ~iv~g~V~~v~~---~g~~V~--l~~~~~g~ip~~~l~~~~~~~~~~~~~~G~~v~v~v~~vd 63 (74)
T PF00575_consen 6 DIVEGKVTSVED---FGVFVD--LGNGIEGFIPISELSDDRIDDPSEVYKIGQTVRVKVIKVD 63 (74)
T ss_dssp SEEEEEEEEEET---TEEEEE--ESTSSEEEEEGGGSSSSEESSSHGTCETTCEEEEEEEEEE
T ss_pred CEEEEEEEEEEC---CEEEEE--ECCcEEEEEEeehhcCccccccccccCCCCEEEEEEEEEE
Confidence 357899999875 777777 345579999999998530 001267899999999988754
No 24
>PRK08582 hypothetical protein; Provisional
Probab=94.06 E-value=0.86 Score=33.38 Aligned_cols=78 Identities=21% Similarity=0.190 Sum_probs=52.5
Q ss_pred CcccccccceeeeeeeEEEEeeCCCCeEEEEecCCCCcccEEEEccccccCCCC-cccCCCCCCEEEEEEEECC-CCCce
Q psy12844 1 MKAHLGKIIEEVYVSGVIQFFNKERGFGFINRIGDDGRKDYFFHFSEIQGGTDN-ILRAIKYSLLVIFDIGVTP-GGRRE 78 (121)
Q Consensus 1 ~~~~~~~~~~~~m~~G~Vkwfn~~kGfGFI~~~~d~g~~dVFfH~s~l~~~g~~-~~~~l~~G~~V~F~i~~~~-kGk~~ 78 (121)
|....|.+ +.|+|+.. ..||+... .+++.+-|+|++++...-.. ....++.||.|...+...+ +| ..
T Consensus 1 m~~kvG~i-----v~G~V~~I---~~fG~fV~--L~~~~~GlVhiSels~~~v~~~~~~l~vGD~VkvkV~~id~~g-kI 69 (139)
T PRK08582 1 MSIEVGSK-----LQGKVTGI---TNFGAFVE--LPEGKTGLVHISEVADNYVKDINDHLKVGDEVEVKVLNVEDDG-KI 69 (139)
T ss_pred CCCcCCCE-----EEEEEEEE---ECCeEEEE--ECCCCEEEEEeeccCcccccccccccCCCCEEEEEEEEECCCC-cE
Confidence 44445544 67888886 45888877 44457899999999744221 1245889999999988754 56 55
Q ss_pred EEEEEEcCCcc
Q psy12844 79 AVHIKIFDTRL 89 (121)
Q Consensus 79 A~~V~~~~~~~ 89 (121)
...+..+...+
T Consensus 70 ~LSlk~~~~~~ 80 (139)
T PRK08582 70 GLSIKKAKDRP 80 (139)
T ss_pred EEEEEecccCc
Confidence 56666665443
No 25
>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=93.98 E-value=0.44 Score=28.08 Aligned_cols=54 Identities=15% Similarity=0.100 Sum_probs=37.5
Q ss_pred eeEEEEeeCCCCeEEEEecCCCCcccEEEEccccccCCCC-cccCCCCCCEEEEEEEECC
Q psy12844 15 SGVIQFFNKERGFGFINRIGDDGRKDYFFHFSEIQGGTDN-ILRAIKYSLLVIFDIGVTP 73 (121)
Q Consensus 15 ~G~Vkwfn~~kGfGFI~~~~d~g~~dVFfH~s~l~~~g~~-~~~~l~~G~~V~F~i~~~~ 73 (121)
.|+|+..+ .+|+... .+.+.+.|+|.+++...... ....+++||.|...+..-+
T Consensus 2 ~g~V~~v~---~~g~~v~--l~~~~~g~~~~~~~~~~~~~~~~~~~~~G~~v~~~v~~~d 56 (65)
T cd00164 2 TGKVVSIT---KFGVFVE--LEDGVEGLVHISELSDKFVKDPSEVFKVGDEVEVKVLEVD 56 (65)
T ss_pred EEEEEEEE---eeeEEEE--ecCCCEEEEEHHHCCCccccCHhhEeCCCCEEEEEEEEEc
Confidence 68899986 4554444 33346999999999754110 1146899999999988754
No 26
>cd04453 S1_RNase_E S1_RNase_E: RNase E and RNase G, S1-like RNA-binding domain. RNase E is an essential endoribonuclease in the processing and degradation of RNA. In addition to its role in mRNA degradation, RNase E has also been implicated in the processing of rRNA, and the maturation of tRNA, 10Sa RNA and the M1 precursor of RNase P. RNase E associates with PNPase (3' to 5' exonuclease), Rhl B (DEAD-box RNA helicase) and enolase (glycolytic enzyme) to form the RNA degradosome. RNase E tends to cut mRNA within single-stranded regions that are rich in A/U nucleotides. The N-terminal region of RNase E contains the catalytic site. Within the conserved N-terminal domain of RNAse E and RNase G, there is an S1-like subdomain, which is an ancient single-stranded RNA-binding domain. S1 domain is an RNA-binding module originally identified in the ribosomal protein S1. The S1 domain is required for RNA cleavage by RNase E. RNase G is paralogous to RNase E with an N-terminal catalytic domain th
Probab=93.65 E-value=0.45 Score=32.07 Aligned_cols=60 Identities=15% Similarity=0.107 Sum_probs=39.9
Q ss_pred eeeeeeEEEEeeCCCCeEEEEecCCCCcccEEEEccccccC---CC-CcccCCCCCCEEEEEEEECC
Q psy12844 11 EVYVSGVIQFFNKERGFGFINRIGDDGRKDYFFHFSEIQGG---TD-NILRAIKYSLLVIFDIGVTP 73 (121)
Q Consensus 11 ~~m~~G~Vkwfn~~kGfGFI~~~~d~g~~dVFfH~s~l~~~---g~-~~~~~l~~G~~V~F~i~~~~ 73 (121)
-..+.|+|+...+ .-||.+.. -.++.+-|+|++++... .. +.-..+++||.|...+..-+
T Consensus 8 G~iy~g~V~~i~~-~~~GaFV~--l~~g~~Gllh~seis~~~~~~v~~~~~~~~~Gd~v~VqV~~~~ 71 (88)
T cd04453 8 GNIYLGRVKKIVP-GLQAAFVD--IGLGKNGFLHLSDILPAYFKKHKKIAKLLKEGQEILVQVVKEP 71 (88)
T ss_pred CCEEEEEEEEecc-CCcEEEEE--eCCCCEEEEEhHHcCchhccccCCHHHcCCCCCEEEEEEEEec
Confidence 3467899999843 22465555 33347999999999531 10 01145899999999988754
No 27
>COG1158 Rho Transcription termination factor [Transcription]
Probab=93.59 E-value=0.2 Score=42.87 Aligned_cols=81 Identities=17% Similarity=0.227 Sum_probs=57.9
Q ss_pred eeeeEEEEeeCCCCeEEEEecC---CCCcccEEEEccccccCCCCcccCCCCCCEEEEEEEECCCC-CceE-EEEEEcCC
Q psy12844 13 YVSGVIQFFNKERGFGFINRIG---DDGRKDYFFHFSEIQGGTDNILRAIKYSLLVIFDIGVTPGG-RREA-VHIKIFDT 87 (121)
Q Consensus 13 m~~G~Vkwfn~~kGfGFI~~~~---d~g~~dVFfH~s~l~~~g~~~~~~l~~G~~V~F~i~~~~kG-k~~A-~~V~~~~~ 87 (121)
+..|++.-.. .||||+.+.+ ..+..|||+.-|.++..+ |+.||.|+=.+.....| |+-| .+|..++.
T Consensus 53 ~~~GvLeil~--dGfGFLR~~~~~yl~~~~DiYvSpSQIRrf~------LrtGD~v~G~vR~Pke~Ery~aLl~ve~vN~ 124 (422)
T COG1158 53 FGDGVLEILP--DGFGFLRSADSSYLPGPDDIYVSPSQIRRFN------LRTGDTVEGKVRPPKEGERYFALLKVEAVNG 124 (422)
T ss_pred eeeeEEEecc--CCcceeecCccccCCCCCceEECHHHHhhcc------CccCCEEeeeecCCCcccceeeeEEEeecCC
Confidence 3457777663 8999999842 235689999999999775 79999999888876655 3433 56777776
Q ss_pred cccccccccccccC
Q psy12844 88 RLYLEDLRTCSVDC 101 (121)
Q Consensus 88 ~~~~~~~~~~~~~~ 101 (121)
..+....++.-.+.
T Consensus 125 ~~pe~~~~R~~F~~ 138 (422)
T COG1158 125 DDPEKAKNRVLFEN 138 (422)
T ss_pred CCHHHhhccCCccc
Confidence 66665555554444
No 28
>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=93.48 E-value=0.41 Score=43.22 Aligned_cols=63 Identities=30% Similarity=0.471 Sum_probs=45.9
Q ss_pred eeeeEEEEeeCCCCeEEEEecCCC-CcccEEEEccccccCCCCcccCCCCCCEEEEEEEECC--CCCceEEEEEEcCC
Q psy12844 13 YVSGVIQFFNKERGFGFINRIGDD-GRKDYFFHFSEIQGGTDNILRAIKYSLLVIFDIGVTP--GGRREAVHIKIFDT 87 (121)
Q Consensus 13 m~~G~Vkwfn~~kGfGFI~~~~d~-g~~dVFfH~s~l~~~g~~~~~~l~~G~~V~F~i~~~~--kGk~~A~~V~~~~~ 87 (121)
.+.|+++. ..+||||+.+ ++ ...|+|+...++. ....||.|...+.... ++++.|.-|.+++.
T Consensus 68 ~~~G~i~~--~~~g~gFv~~--~~~~~~di~I~~~~~~--------~a~~GD~Vlv~I~~~~~~~~~~eg~Vv~Il~r 133 (709)
T TIGR02063 68 LVKGTVIA--HRDGFGFLRP--EDDDEDDIFIPPRQMN--------GAMHGDRVLVRITGKPDGGDRFEARVIKILER 133 (709)
T ss_pred eEEEEEEE--CCCccEEEEE--CCCCCCcEEEChHHhC--------cCCCCCEEEEEEecccCCCCCceEEEEEEEee
Confidence 46798885 3789999999 65 3468999766553 3567999999987532 45578877777753
No 29
>PRK07252 hypothetical protein; Provisional
Probab=93.47 E-value=1 Score=32.30 Aligned_cols=68 Identities=18% Similarity=0.266 Sum_probs=47.3
Q ss_pred eeeeEEEEeeCCCCeEEEEecCCCCcccEEEEccccccCCCC-cccCCCCCCEEEEEEEECC--CCCceEEEEEEcC
Q psy12844 13 YVSGVIQFFNKERGFGFINRIGDDGRKDYFFHFSEIQGGTDN-ILRAIKYSLLVIFDIGVTP--GGRREAVHIKIFD 86 (121)
Q Consensus 13 m~~G~Vkwfn~~kGfGFI~~~~d~g~~dVFfH~s~l~~~g~~-~~~~l~~G~~V~F~i~~~~--kGk~~A~~V~~~~ 86 (121)
.+.|+|.... .||++.. -+++.+-|+|++++....+. ....++.||.|...+...+ .| ........+.
T Consensus 6 iv~G~V~~V~---~~G~fVe--i~~~~~GllhiseLs~~~~~~~~~~~~vGD~V~VkI~~iD~~~~-ri~lSlk~~~ 76 (120)
T PRK07252 6 KLKGTITGIK---PYGAFVA--LENGTTGLIHISEIKTGFIDNIHQLLKVGEEVLVQVVDFDEYTG-KASLSLRTLE 76 (120)
T ss_pred EEEEEEEEEe---CcEEEEE--ECCCCEEEEEHHHcCCccccChhhccCCCCEEEEEEEEEeCCCC-EEEEEEeecc
Confidence 4789999984 5898888 55557899999999754321 1245789999999988854 45 3333444443
No 30
>cd05698 S1_Rrp5_repeat_hs6_sc5 S1_Rrp5_repeat_hs6_sc5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 6 (hs6) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=93.38 E-value=0.61 Score=29.06 Aligned_cols=57 Identities=14% Similarity=-0.004 Sum_probs=41.1
Q ss_pred eeeeEEEEeeCCCCeEEEEecCCCCcccEEEEccccccCCC-CcccCCCCCCEEEEEEEECCC
Q psy12844 13 YVSGVIQFFNKERGFGFINRIGDDGRKDYFFHFSEIQGGTD-NILRAIKYSLLVIFDIGVTPG 74 (121)
Q Consensus 13 m~~G~Vkwfn~~kGfGFI~~~~d~g~~dVFfH~s~l~~~g~-~~~~~l~~G~~V~F~i~~~~k 74 (121)
.+.|+|+... .||.+.. -.++-+-|+|.+++..... +....++.||.|++.+..-+.
T Consensus 3 ~~~g~V~~v~---~~G~~V~--l~~~~~gli~~s~l~~~~~~~~~~~~~~G~~i~v~v~~~d~ 60 (70)
T cd05698 3 KTHGTIVKVK---PNGCIVS--FYNNVKGFLPKSELSEAFIKDPEEHFRVGQVVKVKVLSCDP 60 (70)
T ss_pred EEEEEEEEEe---cCcEEEE--ECCCCEEEEEHHHcChhhcCCHHHcccCCCEEEEEEEEEcC
Confidence 3689999984 4777777 4445789999999964422 112458899999999888554
No 31
>cd05696 S1_Rrp5_repeat_hs4 S1_Rrp5_repeat_hs4: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 4 (hs4). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=92.79 E-value=0.72 Score=29.50 Aligned_cols=54 Identities=13% Similarity=-0.017 Sum_probs=37.5
Q ss_pred eEEEEeeCCCCeEEEEecCCCCcccEEEEccccccCCCC-cccCCCCCCEEEEEEEECC
Q psy12844 16 GVIQFFNKERGFGFINRIGDDGRKDYFFHFSEIQGGTDN-ILRAIKYSLLVIFDIGVTP 73 (121)
Q Consensus 16 G~Vkwfn~~kGfGFI~~~~d~g~~dVFfH~s~l~~~g~~-~~~~l~~G~~V~F~i~~~~ 73 (121)
|+|+... ..||.+... .+ +-+-|+|+|++...... ....++.||.|+..+..-+
T Consensus 7 g~V~~v~--~~~G~~V~l-~~-gv~G~i~~s~l~~~~~~~~~~~~~vG~~v~~kV~~id 61 (71)
T cd05696 7 VKVTKVE--PDLGAVFEL-KD-GLLGFVHISHLSDDKVPSDTGPFKAGTTHKARIIGYS 61 (71)
T ss_pred eEEEEEc--cCceEEEEe-CC-CCEEEEEHHHCCcchhcCcccccCCCCEEEEEEEEEe
Confidence 8898874 457776662 34 47899999999643210 1245899999999977643
No 32
>PRK05054 exoribonuclease II; Provisional
Probab=92.69 E-value=0.6 Score=41.99 Aligned_cols=61 Identities=26% Similarity=0.361 Sum_probs=43.9
Q ss_pred eeeeeEEEEeeCCCCeEEEEecCCCCcccEEEEccccccCCCCcccCCCCCCEEEEEEEECCCCCceEEEEEEcC
Q psy12844 12 VYVSGVIQFFNKERGFGFINRIGDDGRKDYFFHFSEIQGGTDNILRAIKYSLLVIFDIGVTPGGRREAVHIKIFD 86 (121)
Q Consensus 12 ~m~~G~Vkwfn~~kGfGFI~~~~d~g~~dVFfH~s~l~~~g~~~~~~l~~G~~V~F~i~~~~kGk~~A~~V~~~~ 86 (121)
....|+|+.= .+||||+.+ ++. +|+|++-.++.+. -.||+|...+... +++..|.-+.++.
T Consensus 20 ~~~~G~~~~~--~~gfgFv~~--~~~-~difI~~~~l~~a--------~~GD~V~v~i~~~-~~r~~g~v~~il~ 80 (644)
T PRK05054 20 PRVEGVVKAT--EKGFGFLEV--DAQ-KSYFIPPPQMKKV--------MHGDRIIAVIHTE-KDREIAEPEELIE 80 (644)
T ss_pred CeEEEEEEEC--CCccEEEEE--CCC-CcEEEChHHHccC--------CCCCEEEEEEecC-CCCcEEEEEEEEe
Confidence 3567999963 699999988 553 5999988877533 3599999887543 4446666666554
No 33
>PRK09376 rho transcription termination factor Rho; Provisional
Probab=91.92 E-value=0.63 Score=40.29 Aligned_cols=81 Identities=17% Similarity=0.208 Sum_probs=57.0
Q ss_pred eeeeEEEEeeCCCCeEEEEecC---CCCcccEEEEccccccCCCCcccCCCCCCEEEEEEEECCCC-C-ceEEEEEEcCC
Q psy12844 13 YVSGVIQFFNKERGFGFINRIG---DDGRKDYFFHFSEIQGGTDNILRAIKYSLLVIFDIGVTPGG-R-REAVHIKIFDT 87 (121)
Q Consensus 13 m~~G~Vkwfn~~kGfGFI~~~~---d~g~~dVFfH~s~l~~~g~~~~~~l~~G~~V~F~i~~~~kG-k-~~A~~V~~~~~ 87 (121)
...|++.-.. .||||+.... ..+..|||+..+.++..+ |+.||.|+=.+.....| | +.-..|..++.
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--DGFGFLRSPDANYLPGPDDIYVSPSQIRRFN------LRTGDTVEGKIRPPKEGERYFALLKVETVNG 121 (416)
T ss_pred EEEEEEEEcC--CCCeEEeCCCcCCCCCCCCeeeCHHHHHhcC------CCCCCEEEEEeeCCCCCCCccceEEEeeeCC
Confidence 3578777653 4999999821 234579999999999876 79999999888774433 2 45667777777
Q ss_pred cccccccccccccC
Q psy12844 88 RLYLEDLRTCSVDC 101 (121)
Q Consensus 88 ~~~~~~~~~~~~~~ 101 (121)
..+.....+...+.
T Consensus 122 ~~~~~~~~r~~f~~ 135 (416)
T PRK09376 122 EDPEKARNRPLFEN 135 (416)
T ss_pred CCHHHhcCCCCccc
Confidence 66655555554444
No 34
>cd05697 S1_Rrp5_repeat_hs5 S1_Rrp5_repeat_hs5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 5 (hs5) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=91.72 E-value=1.4 Score=27.46 Aligned_cols=57 Identities=12% Similarity=-0.009 Sum_probs=41.8
Q ss_pred eeeeEEEEeeCCCCeEEEEecCCCCcccEEEEccccccCCCC-cccCCCCCCEEEEEEEECCC
Q psy12844 13 YVSGVIQFFNKERGFGFINRIGDDGRKDYFFHFSEIQGGTDN-ILRAIKYSLLVIFDIGVTPG 74 (121)
Q Consensus 13 m~~G~Vkwfn~~kGfGFI~~~~d~g~~dVFfH~s~l~~~g~~-~~~~l~~G~~V~F~i~~~~k 74 (121)
.+.|+|+... .||.+.. -+.+-+-|+|.+++...... +...++.||.|.+.+..-+.
T Consensus 3 ~v~g~V~~v~---~~Gv~V~--l~~~v~g~i~~~~l~~~~~~~~~~~~~~Gd~i~~~V~~id~ 60 (69)
T cd05697 3 VVKGTIRKLR---PSGIFVK--LSDHIKGLVPPMHLADVRLKHPEKKFKPGLKVKCRVLSVEP 60 (69)
T ss_pred EEEEEEEEEe---ccEEEEE--ecCCcEEEEEHHHCCCccccCHHHcCCCCCEEEEEEEEEEC
Confidence 3689999974 5888877 44457999999999754321 12458899999999887553
No 35
>cd05691 S1_RPS1_repeat_ec6 S1_RPS1_repeat_ec6: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 6 (ec6) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=91.60 E-value=1.7 Score=26.90 Aligned_cols=56 Identities=14% Similarity=0.042 Sum_probs=40.8
Q ss_pred eeeEEEEeeCCCCeEEEEecCCCCcccEEEEccccccCCCC-cccCCCCCCEEEEEEEECCC
Q psy12844 14 VSGVIQFFNKERGFGFINRIGDDGRKDYFFHFSEIQGGTDN-ILRAIKYSLLVIFDIGVTPG 74 (121)
Q Consensus 14 ~~G~Vkwfn~~kGfGFI~~~~d~g~~dVFfH~s~l~~~g~~-~~~~l~~G~~V~F~i~~~~k 74 (121)
+.|+|+.. +.+|.+.. -.++-+-|+|.+++....+. +...++.||.|.+.+...+.
T Consensus 4 v~g~V~~v---~~~g~~v~--l~~~~~g~i~~~~~~~~~~~~~~~~~~~Gd~v~~~v~~~d~ 60 (73)
T cd05691 4 VTGKVTEV---DAKGATVK--LGDGVEGFLRAAELSRDRVEDATERFKVGDEVEAKITNVDR 60 (73)
T ss_pred EEEEEEEE---ECCeEEEE--eCCCCEEEEEHHHCCCccccCHHHccCCCCEEEEEEEEEeC
Confidence 57999997 45787777 44446899999999754321 12347899999999888654
No 36
>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=91.33 E-value=2.6 Score=26.98 Aligned_cols=69 Identities=17% Similarity=0.204 Sum_probs=44.5
Q ss_pred eeeeEEEEeeCCCCeEEEEecCCC-CcccEEEEccccccCCC-C-cccCCCCCCEEEEEEEECCCCCceEEEEEEc
Q psy12844 13 YVSGVIQFFNKERGFGFINRIGDD-GRKDYFFHFSEIQGGTD-N-ILRAIKYSLLVIFDIGVTPGGRREAVHIKIF 85 (121)
Q Consensus 13 m~~G~Vkwfn~~kGfGFI~~~~d~-g~~dVFfH~s~l~~~g~-~-~~~~l~~G~~V~F~i~~~~kGk~~A~~V~~~ 85 (121)
.+.|+|.... .||+....++. .+.+-|+|.+++....+ . ....++.||.|...+...++| ........+
T Consensus 3 ~~~g~V~~v~---~~G~fv~l~~~~~~~~gll~~s~l~~~~~~~~~~~~~~~Gd~v~v~v~~vd~~-~i~~s~k~~ 74 (79)
T cd05684 3 IYKGKVTSIM---DFGCFVQLEGLKGRKEGLVHISQLSFEGRVANPSDVVKRGQKVKVKVISIQNG-KISLSMKDV 74 (79)
T ss_pred EEEEEEEEEE---eeeEEEEEeCCCCCcEEEEEhHhccCCCCcCChhheeCCCCEEEEEEEEEeCC-EEEEEEEec
Confidence 4678888874 58888873111 24689999999964421 1 223568999999988776555 334344333
No 37
>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=91.31 E-value=1.5 Score=26.65 Aligned_cols=56 Identities=18% Similarity=0.118 Sum_probs=40.5
Q ss_pred eeeeEEEEeeCCCCeEEEEecCCCCcccEEEEccccccCCCC-cccCCCCCCEEEEEEEECC
Q psy12844 13 YVSGVIQFFNKERGFGFINRIGDDGRKDYFFHFSEIQGGTDN-ILRAIKYSLLVIFDIGVTP 73 (121)
Q Consensus 13 m~~G~Vkwfn~~kGfGFI~~~~d~g~~dVFfH~s~l~~~g~~-~~~~l~~G~~V~F~i~~~~ 73 (121)
.+.|+|....+ ||+... -..+.+-|+|.+++...... ....++.||.|...+...+
T Consensus 3 ~~~g~V~~v~~---~G~~v~--l~~~~~g~l~~~~l~~~~~~~~~~~~~~Gd~v~v~v~~~d 59 (68)
T cd04472 3 IYEGKVVKIKD---FGAFVE--ILPGKDGLVHISELSDERVEKVEDVLKVGDEVKVKVIEVD 59 (68)
T ss_pred EEEEEEEEEEE---eEEEEE--eCCCCEEEEEhHHcCCccccCHHHccCCCCEEEEEEEEEC
Confidence 46889988864 998888 44447899999999754321 1134689999999877744
No 38
>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=91.18 E-value=2.1 Score=25.72 Aligned_cols=56 Identities=18% Similarity=0.154 Sum_probs=39.5
Q ss_pred eeeeEEEEeeCCCCeEEEEecCCCCcccEEEEccccccCCCC-cccCCCCCCEEEEEEEECC
Q psy12844 13 YVSGVIQFFNKERGFGFINRIGDDGRKDYFFHFSEIQGGTDN-ILRAIKYSLLVIFDIGVTP 73 (121)
Q Consensus 13 m~~G~Vkwfn~~kGfGFI~~~~d~g~~dVFfH~s~l~~~g~~-~~~~l~~G~~V~F~i~~~~ 73 (121)
.+.|+|.... .||+... .+.+.+.|+|.+++...... ....++.||.|...+...+
T Consensus 3 ~~~g~V~~i~---~~g~~v~--i~~~~~g~l~~~~l~~~~~~~~~~~~~~Gd~v~v~v~~~~ 59 (69)
T cd05692 3 VVEGTVTRLK---PFGAFVE--LGGGISGLVHISQIAHKRVKDVKDVLKEGDKVKVKVLSID 59 (69)
T ss_pred EEEEEEEEEE---eeeEEEE--ECCCCEEEEEhHHcCCcccCCHHHccCCCCEEEEEEEEEC
Confidence 4678998875 3788777 44457899999999754210 1134789999998886643
No 39
>PRK05807 hypothetical protein; Provisional
Probab=91.16 E-value=4.4 Score=29.47 Aligned_cols=67 Identities=21% Similarity=0.217 Sum_probs=46.4
Q ss_pred eeeeEEEEeeCCCCeEEEEecCCCCcccEEEEccccccCCCC-cccCCCCCCEEEEEEEECC-CCCceEEEEEEcC
Q psy12844 13 YVSGVIQFFNKERGFGFINRIGDDGRKDYFFHFSEIQGGTDN-ILRAIKYSLLVIFDIGVTP-GGRREAVHIKIFD 86 (121)
Q Consensus 13 m~~G~Vkwfn~~kGfGFI~~~~d~g~~dVFfH~s~l~~~g~~-~~~~l~~G~~V~F~i~~~~-kGk~~A~~V~~~~ 86 (121)
.+.|+|... ..||+... .++ .+-|+|++.+...-.. ....++.||.|...+...+ +| .....+..+.
T Consensus 8 vv~G~Vt~i---~~~GafV~--L~~-~~Glvhiseis~~~v~~~~~~~kvGd~V~VkV~~id~~g-kI~LSlk~~~ 76 (136)
T PRK05807 8 ILEGTVVNI---TNFGAFVE--VEG-KTGLVHISEVADTYVKDIREHLKEQDKVKVKVISIDDNG-KISLSIKQAM 76 (136)
T ss_pred EEEEEEEEE---ECCeEEEE--ECC-EEEEEEhhhcccccccCccccCCCCCEEEEEEEEECCCC-cEEEEEEecc
Confidence 467888886 46898888 544 5899999999642110 1145799999999977644 56 5555555554
No 40
>PRK12608 transcription termination factor Rho; Provisional
Probab=91.06 E-value=0.25 Score=42.16 Aligned_cols=51 Identities=22% Similarity=0.236 Sum_probs=40.1
Q ss_pred eeeeEEEEeeCCCCeEEEEec--C-CCCcccEEEEccccccCCCCcccCCCCCCEEEEEEEE
Q psy12844 13 YVSGVIQFFNKERGFGFINRI--G-DDGRKDYFFHFSEIQGGTDNILRAIKYSLLVIFDIGV 71 (121)
Q Consensus 13 m~~G~Vkwfn~~kGfGFI~~~--~-d~g~~dVFfH~s~l~~~g~~~~~~l~~G~~V~F~i~~ 71 (121)
...|++.-.. .||||+... + ..+..|||+..+.++..+ |+.|+.|.-....
T Consensus 18 ~~~g~l~~~~--~g~gflr~~~~~~~~~~~d~yv~~~~i~~~~------l~~Gd~V~~~~r~ 71 (380)
T PRK12608 18 EVLGVLEILG--DGFGFLRSARRNYLPSPDDVFVPPALIRRFN------LRTGDVVEGVARP 71 (380)
T ss_pred cceEEEEEcC--CCceEeecCccCCCCCCCCeeeCHHHHHHhC------CCCCCEEEeccCC
Confidence 3578888664 499999982 1 255689999999999886 7999999987655
No 41
>smart00316 S1 Ribosomal protein S1-like RNA-binding domain.
Probab=90.81 E-value=1.5 Score=26.15 Aligned_cols=57 Identities=14% Similarity=0.098 Sum_probs=40.2
Q ss_pred eeeeEEEEeeCCCCeEEEEecCCCCcccEEEEccccccCC-CCcccCCCCCCEEEEEEEECCC
Q psy12844 13 YVSGVIQFFNKERGFGFINRIGDDGRKDYFFHFSEIQGGT-DNILRAIKYSLLVIFDIGVTPG 74 (121)
Q Consensus 13 m~~G~Vkwfn~~kGfGFI~~~~d~g~~dVFfH~s~l~~~g-~~~~~~l~~G~~V~F~i~~~~k 74 (121)
.+.|+|...++ +|++.. ..++.+.|+|.+++.... .+....++.||.|.+.+...+.
T Consensus 5 ~v~g~V~~v~~---~g~~v~--i~~~~~g~l~~~~~~~~~~~~~~~~~~~G~~v~~~V~~~~~ 62 (72)
T smart00316 5 VVEGTVTEITP---FGAFVD--LGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDE 62 (72)
T ss_pred EEEEEEEEEEc---cEEEEE--eCCCCEEEEEHHHCCccccCCHHHeecCCCEEEEEEEEEeC
Confidence 46899999865 566666 443568999999997551 0011348999999999887543
No 42
>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=90.71 E-value=2.2 Score=27.71 Aligned_cols=55 Identities=15% Similarity=0.160 Sum_probs=41.5
Q ss_pred eeeeeeeEEEEeeCCCCeEEEEecCCC-CcccEEEEccccccCCCCcccCCCCCCEEEEEEEECCC
Q psy12844 10 EEVYVSGVIQFFNKERGFGFINRIGDD-GRKDYFFHFSEIQGGTDNILRAIKYSLLVIFDIGVTPG 74 (121)
Q Consensus 10 ~~~m~~G~Vkwfn~~kGfGFI~~~~d~-g~~dVFfH~s~l~~~g~~~~~~l~~G~~V~F~i~~~~k 74 (121)
+-....|+|+.. ..||++.. -. ++-+-|+|.+++... ..+++||.|...+..-++
T Consensus 4 ~G~~v~g~V~si---~d~G~~v~--~g~~gv~Gfl~~~~~~~~-----~~~~~Gq~v~~~V~~vd~ 59 (74)
T cd05694 4 EGMVLSGCVSSV---EDHGYILD--IGIPGTTGFLPKKDAGNF-----SKLKVGQLLLCVVEKVKD 59 (74)
T ss_pred CCCEEEEEEEEE---eCCEEEEE--eCCCCcEEEEEHHHCCcc-----cccCCCCEEEEEEEEEEC
Confidence 334579999997 57888777 32 345899999999854 268999999999876443
No 43
>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=90.59 E-value=1.5 Score=39.44 Aligned_cols=62 Identities=26% Similarity=0.374 Sum_probs=43.6
Q ss_pred eeeeeeEEEEeeCCCCeEEEEecCCCCcccEEEEccccccCCCCcccCCCCCCEEEEEEEECCCCCceEEEEEEcC
Q psy12844 11 EVYVSGVIQFFNKERGFGFINRIGDDGRKDYFFHFSEIQGGTDNILRAIKYSLLVIFDIGVTPGGRREAVHIKIFD 86 (121)
Q Consensus 11 ~~m~~G~Vkwfn~~kGfGFI~~~~d~g~~dVFfH~s~l~~~g~~~~~~l~~G~~V~F~i~~~~kGk~~A~~V~~~~ 86 (121)
.....|+|+.= .+||||+.+ ++ ++|||+.-..+... -.||+|...+... +++..|.-+.++.
T Consensus 16 ~~~~~G~i~~~--~kGfgFv~~--~~-~~difI~~~~l~~A--------~~GD~V~v~i~~~-~~r~~~~v~~ive 77 (639)
T TIGR02062 16 TPRVEGVVKAT--EKGFGFLEV--DA-QKSYFIPPPQMKKV--------MHGDKIIAVIHSE-KERESAEPEELIE 77 (639)
T ss_pred CceEEEEEEEC--CCccEEEEE--CC-CCcEEEChHHHccC--------CCCCEEEEEEecC-CCCcEEEEEEEEc
Confidence 34567999963 699999987 54 46999988877633 3599999887643 3445665555553
No 44
>cd05704 S1_Rrp5_repeat_hs13 S1_Rrp5_repeat_hs13: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 13 (hs13). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=90.54 E-value=3.1 Score=26.57 Aligned_cols=59 Identities=14% Similarity=0.015 Sum_probs=41.4
Q ss_pred eeeeEEEEeeCCCCeEEEEecCCCCcccEEEEccccccCCCC-cccCCCCCCEEEEEEEECCCC
Q psy12844 13 YVSGVIQFFNKERGFGFINRIGDDGRKDYFFHFSEIQGGTDN-ILRAIKYSLLVIFDIGVTPGG 75 (121)
Q Consensus 13 m~~G~Vkwfn~~kGfGFI~~~~d~g~~dVFfH~s~l~~~g~~-~~~~l~~G~~V~F~i~~~~kG 75 (121)
.+.|+|+...+ -||.+.. -..+.+-|+|++++...-.. ....+++||.|...+...++|
T Consensus 6 iv~G~V~~i~~--~~g~~v~--l~~~~~Glvhis~~s~~~~~~~~~~~~~Gd~v~~kV~~~~~~ 65 (72)
T cd05704 6 VTLGMVTKVIP--HSGLTVQ--LPFGKTGLVSIFHLSDSYTENPLEGFKPGKIVRCCILSKKDG 65 (72)
T ss_pred EEEEEEEEeeC--CcEEEEE--CCCCCEEEEEHHHhcCcccCCHHHhCCCCCEEEEEEEEecCC
Confidence 46899998642 3676766 44457999999999654321 113468899999998876655
No 45
>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=90.14 E-value=2.2 Score=26.20 Aligned_cols=56 Identities=25% Similarity=0.159 Sum_probs=39.7
Q ss_pred eeeeEEEEeeCCCCeEEEEecCCCCcccEEEEcccccc--CCCCcccCCCCCCEEEEEEEECC
Q psy12844 13 YVSGVIQFFNKERGFGFINRIGDDGRKDYFFHFSEIQG--GTDNILRAIKYSLLVIFDIGVTP 73 (121)
Q Consensus 13 m~~G~Vkwfn~~kGfGFI~~~~d~g~~dVFfH~s~l~~--~g~~~~~~l~~G~~V~F~i~~~~ 73 (121)
.+.|+|+.. ..||+... -+++.+-|+|.+++.. ..-+....++.||.|...+...+
T Consensus 3 ~~~g~V~~i---~~~G~fv~--l~~~~~Glv~~~~l~~~~~~~~~~~~~~~G~~v~v~v~~id 60 (69)
T cd05690 3 VVSGKIKSI---TDFGIFVG--LDGGIDGLVHISDISWTQRVRHPSEIYKKGQEVEAVVLNID 60 (69)
T ss_pred EEEEEEEEE---EeeeEEEE--eCCCCEEEEEHHHCCCccccCChhhEECCCCEEEEEEEEEE
Confidence 468899887 46898877 4445789999999963 11112234689999998877644
No 46
>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=89.84 E-value=2.1 Score=27.26 Aligned_cols=56 Identities=14% Similarity=0.122 Sum_probs=40.3
Q ss_pred eeeeEEEEeeCCCCeEEEEecCCCC-cccEEEEccccccCCCC-cccCCCCCCEEEEEEEECC
Q psy12844 13 YVSGVIQFFNKERGFGFINRIGDDG-RKDYFFHFSEIQGGTDN-ILRAIKYSLLVIFDIGVTP 73 (121)
Q Consensus 13 m~~G~Vkwfn~~kGfGFI~~~~d~g-~~dVFfH~s~l~~~g~~-~~~~l~~G~~V~F~i~~~~ 73 (121)
.+.|+|+... .||+... -++ ..+-|+|++++....+. +...++.||.|...+..-+
T Consensus 6 ~~~g~V~~i~---~fG~fv~--l~~~~~eGlvh~sel~~~~~~~~~~~~~~Gd~v~vkv~~vd 63 (73)
T cd05686 6 IFKGEVASVT---EYGAFVK--IPGCRKQGLVHKSHMSSCRVDDPSEVVDVGEKVWVKVIGRE 63 (73)
T ss_pred EEEEEEEEEE---eeeEEEE--ECCCCeEEEEEchhhCCCcccCHhhEECCCCEEEEEEEEEC
Confidence 4689999984 5998888 433 25899999999765431 1123688999999887754
No 47
>cd04465 S1_RPS1_repeat_ec2_hs2 S1_RPS1_repeat_ec2_hs2: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain.While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 2 of the Escherichia coli and Homo sapiens RPS1 (ec2 and hs2, respectively). Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=89.14 E-value=1.7 Score=27.05 Aligned_cols=52 Identities=15% Similarity=-0.001 Sum_probs=38.5
Q ss_pred eeeeEEEEeeCCCCeEEEEecCCCCcccEEEEccccccCCCCcccCC--CCCCEEEEEEEECC
Q psy12844 13 YVSGVIQFFNKERGFGFINRIGDDGRKDYFFHFSEIQGGTDNILRAI--KYSLLVIFDIGVTP 73 (121)
Q Consensus 13 m~~G~Vkwfn~~kGfGFI~~~~d~g~~dVFfH~s~l~~~g~~~~~~l--~~G~~V~F~i~~~~ 73 (121)
.+.|+|+..+ .+|++.. - ++-+.|+|.+.+..... ..+ ..|+.+.+.+..-+
T Consensus 3 iv~g~V~~v~---~~G~~v~--l-~g~~gfip~s~~~~~~~---~~~~~~vG~~i~~~i~~vd 56 (67)
T cd04465 3 IVEGKVTEKV---KGGLIVD--I-EGVRAFLPASQVDLRPV---EDLDEYVGKELKFKIIEID 56 (67)
T ss_pred EEEEEEEEEE---CCeEEEE--E-CCEEEEEEHHHCCCccc---CChHHhCCCEEEEEEEEEe
Confidence 3689999985 4788888 6 45789999999975432 122 37999999988754
No 48
>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=89.14 E-value=3.8 Score=25.52 Aligned_cols=56 Identities=11% Similarity=0.035 Sum_probs=39.8
Q ss_pred eeeeEEEEeeCCCCeEEEEecCCCCcccEEEEccccccCC--CCcccCCCCCCEEEEEEEECC
Q psy12844 13 YVSGVIQFFNKERGFGFINRIGDDGRKDYFFHFSEIQGGT--DNILRAIKYSLLVIFDIGVTP 73 (121)
Q Consensus 13 m~~G~Vkwfn~~kGfGFI~~~~d~g~~dVFfH~s~l~~~g--~~~~~~l~~G~~V~F~i~~~~ 73 (121)
.+.|+|+.. +.||+... -+.+.+-|+|.+++.... .+....++.||.|...+..-+
T Consensus 6 ~~~g~V~~i---~~~G~fv~--l~~~~~Gl~~~~~l~~~~~~~~~~~~~~~Gd~v~v~v~~id 63 (72)
T cd05689 6 RLFGKVTNL---TDYGCFVE--LEEGVEGLVHVSEMDWTNKNIHPSKVVSLGDEVEVMVLDID 63 (72)
T ss_pred EEEEEEEEE---EeeEEEEE--cCCCCEEEEEEEeccCcccccCcccEeCCCCEEEEEEEEee
Confidence 478999987 45998887 443478999999996321 112235688999998877654
No 49
>cd05705 S1_Rrp5_repeat_hs14 S1_Rrp5_repeat_hs14: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 14 (hs14). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=89.10 E-value=3.4 Score=26.74 Aligned_cols=57 Identities=9% Similarity=-0.035 Sum_probs=40.3
Q ss_pred eeeeEEEEeeCCCCeEEEEecCCCCcccEEEEccccccCCCC----cccCCCCCCEEEEEEEECCC
Q psy12844 13 YVSGVIQFFNKERGFGFINRIGDDGRKDYFFHFSEIQGGTDN----ILRAIKYSLLVIFDIGVTPG 74 (121)
Q Consensus 13 m~~G~Vkwfn~~kGfGFI~~~~d~g~~dVFfH~s~l~~~g~~----~~~~l~~G~~V~F~i~~~~k 74 (121)
...|+|+... .||.... -..+-+-|+|++++...... ....+++||.|.+.+..-+.
T Consensus 6 ~V~g~V~~i~---~~G~fV~--l~~~v~G~v~~~~ls~~~~~~~~~~~~~~~~G~~v~~kVl~id~ 66 (74)
T cd05705 6 LLRGYVSSVT---KQGVFFR--LSSSIVGRVLFQNVTKYFVSDPSLYNKYLPEGKLLTAKVLSVNS 66 (74)
T ss_pred EEEEEEEEEe---CCcEEEE--eCCCCEEEEEHHHccCccccChhhHhcccCCCCEEEEEEEEEEC
Confidence 4689999974 5665555 33457999999999765421 01456999999999887543
No 50
>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=88.96 E-value=4.5 Score=26.07 Aligned_cols=51 Identities=14% Similarity=0.094 Sum_probs=39.4
Q ss_pred eeeeeeeEEEEeeCCCCeEEEEecCCCCcccEEEEccccccCCCCcccCCCCCCEEEEEEEEC
Q psy12844 10 EEVYVSGVIQFFNKERGFGFINRIGDDGRKDYFFHFSEIQGGTDNILRAIKYSLLVIFDIGVT 72 (121)
Q Consensus 10 ~~~m~~G~Vkwfn~~kGfGFI~~~~d~g~~dVFfH~s~l~~~g~~~~~~l~~G~~V~F~i~~~ 72 (121)
+...+.|+|... ..||+... -+++.+-|+|.+++. ..++.||.|...+...
T Consensus 16 ~G~~~~g~V~~i---~~~G~fV~--l~~~~~Glv~~se~~-------~~~~iGd~v~v~I~~i 66 (77)
T cd04473 16 VGKLYKGKVNGV---AKYGVFVD--LNDHVRGLIHRSNLL-------RDYEVGDEVIVQVTDI 66 (77)
T ss_pred CCCEEEEEEEeE---ecceEEEE--ECCCcEEEEEchhcc-------CcCCCCCEEEEEEEEE
Confidence 334578999886 45898888 444578999999974 4689999999887665
No 51
>cd05707 S1_Rrp5_repeat_sc11 S1_Rrp5_repeat_sc11: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 11 (sc11). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=88.60 E-value=4 Score=25.29 Aligned_cols=56 Identities=18% Similarity=0.058 Sum_probs=40.0
Q ss_pred eeeeEEEEeeCCCCeEEEEecCCCCcccEEEEccccccCCCC-cccCCCCCCEEEEEEEECC
Q psy12844 13 YVSGVIQFFNKERGFGFINRIGDDGRKDYFFHFSEIQGGTDN-ILRAIKYSLLVIFDIGVTP 73 (121)
Q Consensus 13 m~~G~Vkwfn~~kGfGFI~~~~d~g~~dVFfH~s~l~~~g~~-~~~~l~~G~~V~F~i~~~~ 73 (121)
.+.|+|+... .||.+.. -.++-+-|+|.+.+...... +...++.||.|+..+..-+
T Consensus 3 ~v~g~V~~v~---~~Gv~V~--l~~~~~G~v~~s~l~~~~~~~~~~~~~~Gd~v~~~v~~~d 59 (68)
T cd05707 3 VVRGFVKNIA---NNGVFVT--LGRGVDARVRVSELSDSYLKDWKKRFKVGQLVKGKIVSID 59 (68)
T ss_pred EEEEEEEEEE---CccEEEE--eCCCCEEEEEHHHCCchhhcCHhhccCCCCEEEEEEEEEe
Confidence 3689999874 5777666 44457999999999644221 1245899999999987654
No 52
>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=88.47 E-value=4.4 Score=25.33 Aligned_cols=57 Identities=5% Similarity=-0.121 Sum_probs=39.7
Q ss_pred eeeeEEEEeeCCCCeEEEEecCCCCcccEEEEccccccCCC-CcccCCCCCCEEEEEEEECCC
Q psy12844 13 YVSGVIQFFNKERGFGFINRIGDDGRKDYFFHFSEIQGGTD-NILRAIKYSLLVIFDIGVTPG 74 (121)
Q Consensus 13 m~~G~Vkwfn~~kGfGFI~~~~d~g~~dVFfH~s~l~~~g~-~~~~~l~~G~~V~F~i~~~~k 74 (121)
.+.|+|+.. ..+|.+.. -+.+-+-|+|.+++..... +....++.||.|...+..-+.
T Consensus 6 iv~g~V~~v---~~~gi~v~--l~~~~~g~v~~s~l~~~~~~~~~~~~~~Gd~v~~~V~~~d~ 63 (73)
T cd05706 6 ILPGRVTKV---NDRYVLVQ--LGNKVTGPSFITDALDDYSEALPYKFKKNDIVRACVLSVDV 63 (73)
T ss_pred EEEEEEEEE---eCCeEEEE--eCCCcEEEEEhhhccCccccccccccCCCCEEEEEEEEEeC
Confidence 468999997 44666666 3434799999999975421 012447899999999887543
No 53
>TIGR00767 rho transcription termination factor Rho. Members of this family differ in the specificity of RNA binding.
Probab=88.34 E-value=0.98 Score=39.08 Aligned_cols=52 Identities=21% Similarity=0.342 Sum_probs=39.5
Q ss_pred eeeeEEEEeeCCCCeEEEEecC---CCCcccEEEEccccccCCCCcccCCCCCCEEEEEEEEC
Q psy12844 13 YVSGVIQFFNKERGFGFINRIG---DDGRKDYFFHFSEIQGGTDNILRAIKYSLLVIFDIGVT 72 (121)
Q Consensus 13 m~~G~Vkwfn~~kGfGFI~~~~---d~g~~dVFfH~s~l~~~g~~~~~~l~~G~~V~F~i~~~ 72 (121)
...|++.-.. .||||+.... ..+..|||+..+.++..+ |+.||.|+=.+...
T Consensus 50 ~~~g~le~~~--~g~gflr~~~~~~~~~~~d~yvs~~~i~~~~------lr~gd~v~g~~R~~ 104 (415)
T TIGR00767 50 FGEGVLEILP--DGFGFLRSPDSSYLPGPDDIYVSPSQIRRFN------LRTGDTIEGQIRSP 104 (415)
T ss_pred EEEEEEEEcC--CCCeEEeCCCcCCCCCCCCeeeCHHHHHhcC------CCCCCEEEEEEecc
Confidence 3578777553 5999999821 246689999999999876 79999999776543
No 54
>PRK12678 transcription termination factor Rho; Provisional
Probab=88.26 E-value=1.9 Score=39.36 Aligned_cols=76 Identities=13% Similarity=0.251 Sum_probs=51.5
Q ss_pred eeeEEEEeeCCCCeEEEEecC-CCCcccEEEEccccccCCCCcccCCCCCCEEEEEEEECCCC-------Cc-eEEEEEE
Q psy12844 14 VSGVIQFFNKERGFGFINRIG-DDGRKDYFFHFSEIQGGTDNILRAIKYSLLVIFDIGVTPGG-------RR-EAVHIKI 84 (121)
Q Consensus 14 ~~G~Vkwfn~~kGfGFI~~~~-d~g~~dVFfH~s~l~~~g~~~~~~l~~G~~V~F~i~~~~kG-------k~-~A~~V~~ 84 (121)
..|++--. .|||||...+ ..+..||||..+.|...+ |+.||.|.=.+.....| |. .-+.|..
T Consensus 296 ~~GiLdi~---dg~gFlR~~~y~~~~~Dvyvs~~qirr~~------Lr~Gd~v~G~vr~p~~~e~~~~r~k~~~l~~v~~ 366 (672)
T PRK12678 296 VAGILDVL---DNYAFVRTSGYLPGPNDVYVSMNQVRKNG------LRKGDAVTGAVRAPREGEQGNQRQKFNPLVRLDS 366 (672)
T ss_pred eeEEEEec---CCeeEeeCCCCCCCCCCeeeCHHHHHHcC------CCCCCEEEEeecCCCCCccccccceeeeeeeEee
Confidence 47877765 4999999743 356679999999999886 79999999777664433 22 3345666
Q ss_pred cCCccccccccccc
Q psy12844 85 FDTRLYLEDLRTCS 98 (121)
Q Consensus 85 ~~~~~~~~~~~~~~ 98 (121)
++...+.....+..
T Consensus 367 vNg~~~e~~~~r~~ 380 (672)
T PRK12678 367 VNGMSPEEAKKRPE 380 (672)
T ss_pred eCCCChHHhccCCC
Confidence 66544444433333
No 55
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=87.67 E-value=3 Score=39.36 Aligned_cols=66 Identities=12% Similarity=0.022 Sum_probs=45.1
Q ss_pred eeEEEEeeCCCCeEEEEecCCCCcccEEEEccccccCCCC-cccCCCCCCEEEEEEEECC-CCCceEEEEEEcC
Q psy12844 15 SGVIQFFNKERGFGFINRIGDDGRKDYFFHFSEIQGGTDN-ILRAIKYSLLVIFDIGVTP-GGRREAVHIKIFD 86 (121)
Q Consensus 15 ~G~Vkwfn~~kGfGFI~~~~d~g~~dVFfH~s~l~~~g~~-~~~~l~~G~~V~F~i~~~~-kGk~~A~~V~~~~ 86 (121)
.|+|+.. ..||+... -..+.+-|+|+|+|....+. ....++.||.|...+..-+ +| ........+.
T Consensus 759 ~g~V~~I---~~FGaFVe--L~~g~EGLVHISeLs~~rv~~~~dv~kvGD~V~VkVi~ID~~g-rI~LSlK~l~ 826 (891)
T PLN00207 759 NCEIKSI---APYGAFVE--IAPGREGLCHISELSSNWLAKPEDAFKVGDRIDVKLIEVNDKG-QLRLSRRALL 826 (891)
T ss_pred CcEEEEE---eccEEEEE--eCCCCEEEEEhhhcCCccccCHHHhcCCCCEEEEEEEEECCCC-cEEEEEeccc
Confidence 4689987 56998877 44447999999999754321 2235788999999988755 56 3344444333
No 56
>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=87.57 E-value=5.1 Score=25.03 Aligned_cols=58 Identities=12% Similarity=0.083 Sum_probs=40.6
Q ss_pred eeeeEEEEeeCCCCeEEEEecCCCCcccEEEEccccccCCCC-cccCCCCCCEEEEEEEECC
Q psy12844 13 YVSGVIQFFNKERGFGFINRIGDDGRKDYFFHFSEIQGGTDN-ILRAIKYSLLVIFDIGVTP 73 (121)
Q Consensus 13 m~~G~Vkwfn~~kGfGFI~~~~d~g~~dVFfH~s~l~~~g~~-~~~~l~~G~~V~F~i~~~~ 73 (121)
.+.|+|... ..||.+....+.++.+-|+|.+.+....+. ....++.||.|...+...+
T Consensus 6 ~~~g~V~~v---~~~g~~v~l~~~~~~~gll~~s~l~~~~~~~~~~~~~~Gd~v~vkv~~~d 64 (76)
T cd04452 6 LVVVTVKSI---ADMGAYVSLLEYGNIEGMILLSELSRRRIRSIRKLVKVGRKEVVKVIRVD 64 (76)
T ss_pred EEEEEEEEE---EccEEEEEEcCCCCeEEEEEhHHcCCcccCCHHHeeCCCCEEEEEEEEEE
Confidence 468999987 468988773111246899999999755321 1234789999999877654
No 57
>cd05687 S1_RPS1_repeat_ec1_hs1 S1_RPS1_repeat_ec1_hs1: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 1 of the Escherichia coli and Homo sapiens RPS1 (ec1 and hs1, respectively). Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=86.42 E-value=4.6 Score=25.01 Aligned_cols=55 Identities=11% Similarity=-0.045 Sum_probs=37.5
Q ss_pred eeeeEEEEeeCCCCeEEEEecCCCCcccEEEEccccccCCCC-cccCCCCCCEEEEEEEEC
Q psy12844 13 YVSGVIQFFNKERGFGFINRIGDDGRKDYFFHFSEIQGGTDN-ILRAIKYSLLVIFDIGVT 72 (121)
Q Consensus 13 m~~G~Vkwfn~~kGfGFI~~~~d~g~~dVFfH~s~l~~~g~~-~~~~l~~G~~V~F~i~~~ 72 (121)
.+.|+|....+ +|.+.. ..++.+-|+|.+++...... ....+++||.|.+.+..-
T Consensus 3 iv~g~V~~i~~---~~~~v~--l~~~~~g~l~~~e~~~~~~~~~~~~~~~Gd~i~~~i~~~ 58 (70)
T cd05687 3 IVKGTVVSVDD---DEVLVD--IGYKSEGIIPISEFSDDPIENGEDEVKVGDEVEVYVLRV 58 (70)
T ss_pred EEEEEEEEEeC---CEEEEE--eCCCceEEEEHHHhCccccCCHhHcCCCCCEEEEEEEEE
Confidence 46899999853 354444 33346899999999654210 113589999999998874
No 58
>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=86.41 E-value=5.3 Score=25.03 Aligned_cols=57 Identities=12% Similarity=-0.022 Sum_probs=38.7
Q ss_pred eeeeEEEEeeCCCCeEEEEecCCCCcccEEEEccccccC---CCCcccCCCCCCEEEEEEEECCC
Q psy12844 13 YVSGVIQFFNKERGFGFINRIGDDGRKDYFFHFSEIQGG---TDNILRAIKYSLLVIFDIGVTPG 74 (121)
Q Consensus 13 m~~G~Vkwfn~~kGfGFI~~~~d~g~~dVFfH~s~l~~~---g~~~~~~l~~G~~V~F~i~~~~k 74 (121)
.+.|+|+...+ +|.+.. ...+-+-++|++++... ..+....+++||.|...+..-+.
T Consensus 3 iV~g~V~~i~~---~gi~v~--l~~~i~g~i~~~~i~~~~~~~~~~~~~~~~Gd~i~~kVl~~d~ 62 (70)
T cd05702 3 LVKAKVKSVKP---TQLNVQ--LADNVHGRIHVSEVFDEWPDGKNPLSKFKIGQKIKARVIGGHD 62 (70)
T ss_pred EEEEEEEEEEC---CcEEEE--eCCCcEEEEEHHHhccccccccChhHhCCCCCEEEEEEEEEeC
Confidence 46899999853 455555 33347899999999643 11122457999999998876543
No 59
>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=84.79 E-value=8.1 Score=24.74 Aligned_cols=56 Identities=4% Similarity=-0.156 Sum_probs=38.5
Q ss_pred eeeEEEEeeCCCCeEEEEecCCCCcccEEEEccccccCC--C-CcccCCCCCCEEEEEEEECCC
Q psy12844 14 VSGVIQFFNKERGFGFINRIGDDGRKDYFFHFSEIQGGT--D-NILRAIKYSLLVIFDIGVTPG 74 (121)
Q Consensus 14 ~~G~Vkwfn~~kGfGFI~~~~d~g~~dVFfH~s~l~~~g--~-~~~~~l~~G~~V~F~i~~~~k 74 (121)
..|+|+.. ..+|.... ...+-+-|+|++++.... . +....+++||.|++.+..-+.
T Consensus 4 V~g~V~~i---~~~g~~V~--l~~~i~G~i~~~~ls~~~~~~~~~~~~~~vG~~v~~kV~~id~ 62 (73)
T cd05703 4 VTGFVNNV---SKEFVWLT--ISPDVKGRIPLLDLSDDVSVLEHPEKKFPIGQALKAKVVGVDK 62 (73)
T ss_pred EEEEEEEE---eCCEEEEE--eCCCcEEEEEHHHcCCccccccCHHHhCCCCCEEEEEEEEEeC
Confidence 57999998 35666555 333478999999996431 1 122458999999999877543
No 60
>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=83.95 E-value=2.3 Score=27.59 Aligned_cols=28 Identities=21% Similarity=0.108 Sum_probs=20.2
Q ss_pred cCCCCCCEEEEEEEECCCCCceEEEEEE
Q psy12844 57 RAIKYSLLVIFDIGVTPGGRREAVHIKI 84 (121)
Q Consensus 57 ~~l~~G~~V~F~i~~~~kGk~~A~~V~~ 84 (121)
..|++||+|.|.+...+.|.+.-..+++
T Consensus 41 ~~l~~Gd~V~F~~~~~~~~~~~I~~i~~ 68 (70)
T PF11604_consen 41 AGLKPGDKVRFTFERTDDGSYVITAIEP 68 (70)
T ss_dssp SS-STT-EEEEEEEEETTCEEEEEEEEE
T ss_pred hcCCCCCEEEEEEEECCCCcEEEEEEEE
Confidence 6789999999999998887555555543
No 61
>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=82.90 E-value=9.2 Score=23.91 Aligned_cols=51 Identities=10% Similarity=-0.005 Sum_probs=37.4
Q ss_pred eeeeeEEEEeeCCCCeEEEEecCCCCcccEEEEccccccCCCCcccCCCCCCEEEEEEEECC
Q psy12844 12 VYVSGVIQFFNKERGFGFINRIGDDGRKDYFFHFSEIQGGTDNILRAIKYSLLVIFDIGVTP 73 (121)
Q Consensus 12 ~m~~G~Vkwfn~~kGfGFI~~~~d~g~~dVFfH~s~l~~~g~~~~~~l~~G~~V~F~i~~~~ 73 (121)
.+..|+|...+. +|++.. .++ -+-|++.+.+... ..+++||.|.+.+..-+
T Consensus 5 ~iV~G~V~~~~~---~~~~vd--ig~-~eg~lp~~e~~~~-----~~~~~Gd~v~v~v~~v~ 55 (67)
T cd04455 5 EIVTGIVKRVDR---GNVIVD--LGK-VEAILPKKEQIPG-----ESYRPGDRIKAYVLEVR 55 (67)
T ss_pred CEEEEEEEEEcC---CCEEEE--cCC-eEEEeeHHHCCCC-----CcCCCCCEEEEEEEEEe
Confidence 357899999865 344444 333 6889999999743 35799999999988744
No 62
>PHA02945 interferon resistance protein; Provisional
Probab=82.84 E-value=11 Score=26.15 Aligned_cols=58 Identities=9% Similarity=-0.063 Sum_probs=39.8
Q ss_pred eeeeeEEEEeeCCCCeEEEEecCCCCcccEEEEcccc--ccCCCCcccCCCCCCEEEEEEEECCC
Q psy12844 12 VYVSGVIQFFNKERGFGFINRIGDDGRKDYFFHFSEI--QGGTDNILRAIKYSLLVIFDIGVTPG 74 (121)
Q Consensus 12 ~m~~G~Vkwfn~~kGfGFI~~~~d~g~~dVFfH~s~l--~~~g~~~~~~l~~G~~V~F~i~~~~k 74 (121)
....|+|+. +.||+-..+.+-++.+-|+|.|.+ ...=..+...+ +|+.|...+...++
T Consensus 13 elvigtV~~----~d~ga~v~L~EY~g~eg~i~~seveva~~wvK~rd~l-~GqkvV~KVirVd~ 72 (88)
T PHA02945 13 DVLKGKVYE----NGYALYIDLFDYPHSEAILAESVQMHMNRYFKYRDKL-VGKTVKVKVIRVDY 72 (88)
T ss_pred cEEEEEEEe----cCceEEEEecccCCcEEEEEeehhhhccceEeeeeEe-cCCEEEEEEEEECC
Confidence 456899987 678877664344678999999966 32211122567 99999999887553
No 63
>cd05685 S1_Tex S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has been characterized in Bordetella pertussis and Pseudomonas aeruginosa. The tex gene is essential in Bortella pertusis and is named for its role in toxin expression. Tex has two functional domains, an N-terminal domain homologous to the Escherichia coli maltose repression protein, which is a poorly defined transcriptional factor, and a C-terminal S1 RNA-binding domain. Tex is found in prokaryotes, eukaryotes, and archaea.
Probab=82.20 E-value=8.4 Score=22.99 Aligned_cols=56 Identities=14% Similarity=0.144 Sum_probs=39.2
Q ss_pred eeeeEEEEeeCCCCeEEEEecCCCCcccEEEEccccccCCCC-cccCCCCCCEEEEEEEECC
Q psy12844 13 YVSGVIQFFNKERGFGFINRIGDDGRKDYFFHFSEIQGGTDN-ILRAIKYSLLVIFDIGVTP 73 (121)
Q Consensus 13 m~~G~Vkwfn~~kGfGFI~~~~d~g~~dVFfH~s~l~~~g~~-~~~~l~~G~~V~F~i~~~~ 73 (121)
.+.|+|.... .||.... ...+.+-|+|.+++....+. ....++.||.|...+...+
T Consensus 3 ~~~g~V~~i~---~~G~fv~--l~~~~~g~~~~~~l~~~~~~~~~~~~~~Gd~v~v~i~~vd 59 (68)
T cd05685 3 VLEGVVTNVT---DFGAFVD--IGVKQDGLIHISKMADRFVSHPSDVVSVGDIVEVKVISID 59 (68)
T ss_pred EEEEEEEEEe---cccEEEE--cCCCCEEEEEHHHCCCccccCHHHhcCCCCEEEEEEEEEE
Confidence 3678898874 4787776 44447899999999754320 1124799999999887754
No 64
>PRK08059 general stress protein 13; Validated
Probab=81.13 E-value=15 Score=25.98 Aligned_cols=68 Identities=19% Similarity=0.179 Sum_probs=45.8
Q ss_pred eeeeeEEEEeeCCCCeEEEEecCCCCcccEEEEccccccCCCC-cccCCCCCCEEEEEEEECC--CCCceEEEEEEc
Q psy12844 12 VYVSGVIQFFNKERGFGFINRIGDDGRKDYFFHFSEIQGGTDN-ILRAIKYSLLVIFDIGVTP--GGRREAVHIKIF 85 (121)
Q Consensus 12 ~m~~G~Vkwfn~~kGfGFI~~~~d~g~~dVFfH~s~l~~~g~~-~~~~l~~G~~V~F~i~~~~--kGk~~A~~V~~~ 85 (121)
..+.|+|.... .||+... -+.+.+-|+|++++...-.. ....++.||.|...+...+ +| .....+..+
T Consensus 9 ~iv~G~V~~i~---~~G~fV~--i~~~~~Gli~~sel~~~~~~~~~~~~~vGD~I~vkI~~id~~~~-~i~lslk~~ 79 (123)
T PRK08059 9 SVVTGKVTGIQ---PYGAFVA--LDEETQGLVHISEITHGFVKDIHDFLSVGDEVKVKVLSVDEEKG-KISLSIRAT 79 (123)
T ss_pred CEEEEEEEEEe---cceEEEE--ECCCCEEEEEHHHCCcccccCHHHcCCCCCEEEEEEEEEECCCC-eEEEEEEEc
Confidence 35789999875 3888887 44457899999999643220 1245789999999988753 45 333344444
No 65
>COG1098 VacB Predicted RNA binding protein (contains ribosomal protein S1 domain) [Translation, ribosomal structure and biogenesis]
Probab=80.66 E-value=3.4 Score=30.55 Aligned_cols=58 Identities=24% Similarity=0.270 Sum_probs=41.3
Q ss_pred eeeeEEEEeeCCCCeEEEEecCCCCcccEEEEccccccCCC--CcccCCCCCCEEEEEEEE-CCCCC
Q psy12844 13 YVSGVIQFFNKERGFGFINRIGDDGRKDYFFHFSEIQGGTD--NILRAIKYSLLVIFDIGV-TPGGR 76 (121)
Q Consensus 13 m~~G~Vkwfn~~kGfGFI~~~~d~g~~dVFfH~s~l~~~g~--~~~~~l~~G~~V~F~i~~-~~kGk 76 (121)
.++|+|.-- ..||--.. .+++..=++|+|.+... | +.+..|++||.|.-.+.. +.+|+
T Consensus 8 ~l~GkItgI---~~yGAFV~--l~~g~tGLVHISEIa~~-fVkdI~d~L~vG~eV~vKVl~ide~GK 68 (129)
T COG1098 8 KLKGKITGI---TPYGAFVE--LEGGKTGLVHISEIADG-FVKDIHDHLKVGQEVKVKVLDIDENGK 68 (129)
T ss_pred eEEEEEEee---EecceEEE--ecCCCcceEEehHhhhh-hHHhHHHHhcCCCEEEEEEEeeccCCC
Confidence 357777764 66886555 45556889999999743 2 144679999999988776 44774
No 66
>PTZ00248 eukaryotic translation initiation factor 2 subunit 1; Provisional
Probab=80.13 E-value=11 Score=31.70 Aligned_cols=74 Identities=11% Similarity=-0.022 Sum_probs=51.9
Q ss_pred eeeeEEEEeeCCCCeEEEEecCCCCcccEEEEccccccCCCC-cccCCCCCCEEEEEEEEC--CCCCceEEEEEEcCCcc
Q psy12844 13 YVSGVIQFFNKERGFGFINRIGDDGRKDYFFHFSEIQGGTDN-ILRAIKYSLLVIFDIGVT--PGGRREAVHIKIFDTRL 89 (121)
Q Consensus 13 m~~G~Vkwfn~~kGfGFI~~~~d~g~~dVFfH~s~l~~~g~~-~~~~l~~G~~V~F~i~~~--~kGk~~A~~V~~~~~~~ 89 (121)
.+.|+|+.. ..||.+..++..++-+-|+|+|.|...... +-..+++||.|...+..- .+| .....++.+...+
T Consensus 20 vV~g~V~~I---~d~GafV~L~EY~gvEGlIhiSElS~~ri~~i~d~vkvGd~v~vkVl~VD~ekg-~IdLS~K~v~~~p 95 (319)
T PTZ00248 20 LVMVKVVRI---TEMGAYVSLLEYDDIEGMILMSELSKRRIRSINKLIRVGRHEVVVVLRVDKEKG-YIDLSKKRVSPED 95 (319)
T ss_pred EEEEEEEEE---eCCeEEEEecCCCCcEEEEEHHHhcccccCCHHHhcCCCCEEEEEEEEEeCCCC-EEEEEeeecccch
Confidence 568999997 469988773212457999999999754332 224479999999998864 356 6677777666544
Q ss_pred c
Q psy12844 90 Y 90 (121)
Q Consensus 90 ~ 90 (121)
+
T Consensus 96 w 96 (319)
T PTZ00248 96 I 96 (319)
T ss_pred H
Confidence 3
No 67
>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=79.18 E-value=9.3 Score=23.67 Aligned_cols=57 Identities=16% Similarity=0.145 Sum_probs=40.0
Q ss_pred eeeeEEEEeeCCCCeEEEEecCCCCcccEEEEccccccCCCC-cccCCCCCCEEEEEEEECC
Q psy12844 13 YVSGVIQFFNKERGFGFINRIGDDGRKDYFFHFSEIQGGTDN-ILRAIKYSLLVIFDIGVTP 73 (121)
Q Consensus 13 m~~G~Vkwfn~~kGfGFI~~~~d~g~~dVFfH~s~l~~~g~~-~~~~l~~G~~V~F~i~~~~ 73 (121)
.+.|+|+... .||++... .+.+.+-|+|.+++...... ....++.||.|...+...+
T Consensus 5 ~v~g~V~~i~---~~g~~v~l-~~~~~~g~i~~~~l~~~~~~~~~~~~~~Gd~v~v~i~~vd 62 (77)
T cd05708 5 KIDGTVRRVE---DYGVFIDI-DGTNVSGLCHKSEISDNRVADASKLFRVGDKVRAKVLKID 62 (77)
T ss_pred EEEEEEEEEE---cceEEEEE-CCCCeEEEEEHHHCCCCccCCHhHeecCCCEEEEEEEEEe
Confidence 4789999884 58887772 22246899999999754320 1234699999998887754
No 68
>COG2190 NagE Phosphotransferase system IIA components [Carbohydrate transport and metabolism]
Probab=78.60 E-value=3.6 Score=31.23 Aligned_cols=57 Identities=16% Similarity=0.297 Sum_probs=38.2
Q ss_pred cccccccceeeeeeeEEEEeeCCC-CeEEEEecCCCCcccEEEEcc----ccccCCCCcccCCCCCCEEE
Q psy12844 2 KAHLGKIIEEVYVSGVIQFFNKER-GFGFINRIGDDGRKDYFFHFS----EIQGGTDNILRAIKYSLLVI 66 (121)
Q Consensus 2 ~~~~~~~~~~~m~~G~Vkwfn~~k-GfGFI~~~~d~g~~dVFfH~s----~l~~~g~~~~~~l~~G~~V~ 66 (121)
+.+-|+|+++ ..|+|....+.+ -||+-+. + |-+|++|+- +|.+.||. ...++||.|.
T Consensus 39 ~P~~g~vvAP--vdG~v~~iFpTkHAigi~t~---~-GvEiLiHiGiDTV~L~GegF~--~~v~~Gd~Vk 100 (156)
T COG2190 39 KPSEGEVVAP--VDGTVVLIFPTKHAIGIETD---E-GVEILIHIGIDTVKLNGEGFE--SLVKEGDKVK 100 (156)
T ss_pred ecCCCeEEec--cCcEEEEEeeCCcEEEEEcC---C-CcEEEEEeceeeEEECCcceE--EEeeCCCEEc
Confidence 3456778877 689988887765 5666555 3 479999974 45666663 3445666664
No 69
>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=78.07 E-value=8.7 Score=35.54 Aligned_cols=58 Identities=19% Similarity=0.205 Sum_probs=41.5
Q ss_pred eeeeEEEEeeCCCCeEEEEecCCCCcccEEEEcccccc----CC-CCcccCCCCCCEEEEEEEECC-CC
Q psy12844 13 YVSGVIQFFNKERGFGFINRIGDDGRKDYFFHFSEIQG----GT-DNILRAIKYSLLVIFDIGVTP-GG 75 (121)
Q Consensus 13 m~~G~Vkwfn~~kGfGFI~~~~d~g~~dVFfH~s~l~~----~g-~~~~~~l~~G~~V~F~i~~~~-kG 75 (121)
.+.|+|+.. ..||.... -.++.+=|+|+|.|.. .. -+....+++||.|...+..-+ +|
T Consensus 650 i~~GkV~~I---~dfGaFVe--l~~G~eGLvHISeisdls~~~rv~~~~dv~kvGd~V~VKVl~ID~~g 713 (719)
T TIGR02696 650 RFLGTVVKT---TAFGAFVS--LLPGKDGLLHISQIRKLAGGKRVENVEDVLSVGQKIQVEIADIDDRG 713 (719)
T ss_pred EEEEEEEEE---ECceEEEE--ecCCceEEEEhhhccccccccCcCCHHHcCCCCCEEEEEEEEECCCC
Confidence 578999997 45998887 5455799999998831 11 112245889999999987744 56
No 70
>PRK09838 periplasmic copper-binding protein; Provisional
Probab=77.86 E-value=5.2 Score=28.71 Aligned_cols=63 Identities=17% Similarity=0.062 Sum_probs=37.9
Q ss_pred eeeeEEEEeeCCCCeEEEEecCCCCcccE-------EEEccccccCCCCcccCCCCCCEEEEEEEECCCCCceEEEEEE
Q psy12844 13 YVSGVIQFFNKERGFGFINRIGDDGRKDY-------FFHFSEIQGGTDNILRAIKYSLLVIFDIGVTPGGRREAVHIKI 84 (121)
Q Consensus 13 m~~G~Vkwfn~~kGfGFI~~~~d~g~~dV-------FfH~s~l~~~g~~~~~~l~~G~~V~F~i~~~~kGk~~A~~V~~ 84 (121)
...|+|+..|.+.+-=-|.- ..= +++ -|-..+ .. .+..|++|+.|.|++.....+ +...+|++
T Consensus 44 ~~~G~V~~vd~~~~~iti~H--~pI-p~l~wPaMTM~F~v~~--~~---~l~~lk~G~~V~F~~~~~~~~-~~i~~i~~ 113 (115)
T PRK09838 44 SGTGVVKGIDLESKKITIHH--EPI-PAVNWPEMTMRFTITP--QT---KMSEIKTGDKVAFNFVQQGNL-SLLQDIKV 113 (115)
T ss_pred EEEEEEEEEeCCCCEEEEee--ccc-ccCCCCCccccccCCC--hh---hhccCCCCCEEEEEEEEcCCc-EEEEEEee
Confidence 45899999987765544443 110 010 111111 01 125789999999999998777 66666654
No 71
>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=75.75 E-value=18 Score=23.24 Aligned_cols=56 Identities=13% Similarity=0.046 Sum_probs=38.1
Q ss_pred eeeeEEEEeeCCCCeEEEEecCCCCcccEEEEccccccCCC-----CcccCCCCCCEEEEEEEECC
Q psy12844 13 YVSGVIQFFNKERGFGFINRIGDDGRKDYFFHFSEIQGGTD-----NILRAIKYSLLVIFDIGVTP 73 (121)
Q Consensus 13 m~~G~Vkwfn~~kGfGFI~~~~d~g~~dVFfH~s~l~~~g~-----~~~~~l~~G~~V~F~i~~~~ 73 (121)
.+.|+|..- ..+|.... -+.+-+-|+|.+++..... +....+++||.|.+.+..-.
T Consensus 9 iV~g~V~~i---~~~g~~v~--i~~~~~G~l~~se~~~~~~~~~~~~~~~~l~vGd~i~~~V~~~~ 69 (86)
T cd05789 9 VVIGRVTEV---GFKRWKVD--INSPYDAVLPLSEVNLPRTDEDELNMRSYLDEGDLIVAEVQSVD 69 (86)
T ss_pred EEEEEEEEE---CCCEEEEE--CCCCeEEEEEHHHccCCCCccchHHHHhhCCCCCEEEEEEEEEC
Confidence 458899886 34555555 3445789999999964110 01135899999999988854
No 72
>PRK13806 rpsA 30S ribosomal protein S1; Provisional
Probab=75.67 E-value=23 Score=30.80 Aligned_cols=74 Identities=15% Similarity=0.055 Sum_probs=47.8
Q ss_pred eeeeeeEEEEeeCCCCeEEEEecCCCCcccEEEEccccccCC--CCcccCCCCCCEEEEEEEECC-CCCceEEEEEEcCC
Q psy12844 11 EVYVSGVIQFFNKERGFGFINRIGDDGRKDYFFHFSEIQGGT--DNILRAIKYSLLVIFDIGVTP-GGRREAVHIKIFDT 87 (121)
Q Consensus 11 ~~m~~G~Vkwfn~~kGfGFI~~~~d~g~~dVFfH~s~l~~~g--~~~~~~l~~G~~V~F~i~~~~-kGk~~A~~V~~~~~ 87 (121)
-..+.|+|+.. ..||+... ...+-+.|+|++++.... ......++.||.|...+..-+ ..+.....+.....
T Consensus 293 G~~v~G~V~~v---~~~G~fV~--l~~gv~Glvh~sels~~~~~~~~~~~~~~Gd~v~vkVl~iD~e~~ri~Ls~K~~~~ 367 (491)
T PRK13806 293 GDKVTGKVVRL---APFGAFVE--ILPGIEGLVHVSEMSWTRRVNKPEDVVAPGDAVAVKIKDIDPAKRRISLSLRDAEG 367 (491)
T ss_pred CCEEEEEEEEE---eCceEEEE--eCCCcEEEEEHHHcCcccccCCHHHcCCCCCEEEEEEEEEEccCCEEEEEEeeccc
Confidence 34578999987 45998877 444578999999986421 101135899999999987643 33244445544443
Q ss_pred cc
Q psy12844 88 RL 89 (121)
Q Consensus 88 ~~ 89 (121)
.+
T Consensus 368 ~p 369 (491)
T PRK13806 368 DP 369 (491)
T ss_pred Ch
Confidence 33
No 73
>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=75.05 E-value=18 Score=22.63 Aligned_cols=55 Identities=13% Similarity=-0.077 Sum_probs=37.1
Q ss_pred eeeeEEEEeeCCCCeEEEEecCCCCcccEEEEccccccCCCCcccCCCCCCEEEEEEEECC
Q psy12844 13 YVSGVIQFFNKERGFGFINRIGDDGRKDYFFHFSEIQGGTDNILRAIKYSLLVIFDIGVTP 73 (121)
Q Consensus 13 m~~G~Vkwfn~~kGfGFI~~~~d~g~~dVFfH~s~l~~~g~~~~~~l~~G~~V~F~i~~~~ 73 (121)
...|+|+... .+|.+.. ..++-+-|+|++++..... .-..+++|+.|.+.+..-+
T Consensus 3 ~V~g~V~~i~---~~G~~v~--l~~~v~g~v~~~~l~~~~~-~~~~~~~G~~i~~kVi~id 57 (66)
T cd05695 3 LVNARVKKVL---SNGLILD--FLSSFTGTVDFLHLDPEKS-SKSTYKEGQKVRARILYVD 57 (66)
T ss_pred EEEEEEEEEe---CCcEEEE--EcCCceEEEEHHHcCCccC-cccCcCCCCEEEEEEEEEe
Confidence 3578998874 5566555 3334689999999853211 0146899999999976643
No 74
>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=74.58 E-value=18 Score=22.66 Aligned_cols=56 Identities=16% Similarity=0.132 Sum_probs=38.0
Q ss_pred eeeeEEEEeeCCCCeEEEEecCCCC-cccEEEEccccccCCC------------CcccCCCCCCEEEEEEEECC
Q psy12844 13 YVSGVIQFFNKERGFGFINRIGDDG-RKDYFFHFSEIQGGTD------------NILRAIKYSLLVIFDIGVTP 73 (121)
Q Consensus 13 m~~G~Vkwfn~~kGfGFI~~~~d~g-~~dVFfH~s~l~~~g~------------~~~~~l~~G~~V~F~i~~~~ 73 (121)
.+.|+|... +.||+... -.. +.+-|+|++++....+ +....++.||.|.-.+...+
T Consensus 4 ~~~g~V~~v---~~~G~fv~--l~~~~~~G~v~~~~l~~~~~~~d~~~~~~~~~~~~~~~~~gd~v~v~v~~vd 72 (83)
T cd04471 4 EFDGVISGV---TSFGLFVE--LDNLTVEGLVHVSTLGDDYYEFDEENHALVGERTGKVFRLGDKVKVRVVRVD 72 (83)
T ss_pred EEEEEEEeE---EeeeEEEE--ecCCCEEEEEEEEecCCCcEEEcccceEEEeccCCCEEcCCCEEEEEEEEec
Confidence 467888887 44888888 443 4678999999864321 01145688999888877654
No 75
>PF03100 CcmE: CcmE; InterPro: IPR004329 CcmE is the product of one of a cluster of Ccm genes that are necessary for cytochrome c biosynthesis in eubacteria. Expression of these proteins is induced when the organisms are grown under anaerobic conditions with nitrate or nitrite as the final electron acceptor.; GO: 0017003 protein-heme linkage, 0017004 cytochrome complex assembly, 0005886 plasma membrane; PDB: 1SR3_A 2KCT_A 1J6Q_A 1LM0_A.
Probab=72.94 E-value=32 Score=24.69 Aligned_cols=67 Identities=15% Similarity=0.162 Sum_probs=44.8
Q ss_pred eEEEEeeCCCCeEEEEecCCCCcccEEEEccccccCCCCcccCCCCCCEEEEEEEECCCCCceEEEEEEcCCcccc
Q psy12844 16 GVIQFFNKERGFGFINRIGDDGRKDYFFHFSEIQGGTDNILRAIKYSLLVIFDIGVTPGGRREAVHIKIFDTRLYL 91 (121)
Q Consensus 16 G~Vkwfn~~kGfGFI~~~~d~g~~dVFfH~s~l~~~g~~~~~~l~~G~~V~F~i~~~~kGk~~A~~V~~~~~~~~~ 91 (121)
|.|.|=.....+=|+.. |.+ .++-|+++....+. .++|+.|.-+=.-+++|...|.+|..-.++.|.
T Consensus 62 gSv~~~~~~~~~~F~i~--D~~-~~i~V~Y~G~~Pd~------F~eg~~VVv~G~~~~~g~F~A~~lL~KcpskY~ 128 (131)
T PF03100_consen 62 GSVEYDPDGNTLTFTIT--DGG-KEIPVVYTGPLPDL------FREGQGVVVEGRLGEDGVFEATELLAKCPSKYM 128 (131)
T ss_dssp TTEEE-TTSSEEEEEEE---SS--EEEEEEES--CTT--------TTSEEEEEEEECCTSEEEEEEEEETS-----
T ss_pred CCEEEcCCCCEEEEEEE--ECC-cEEEEEECCCCCcc------ccCCCeEEEEEEECCCCEEEEEEEEeCCCCCCC
Confidence 34445436789999999 775 68999999987664 599999998888878888999999877666553
No 76
>PRK07400 30S ribosomal protein S1; Reviewed
Probab=72.78 E-value=23 Score=29.16 Aligned_cols=72 Identities=17% Similarity=0.092 Sum_probs=51.5
Q ss_pred eeeeeEEEEeeCCCCeEEEEecCCCCcccEEEEccccccCCCC-cccCCCCCCEEEEEEEECC--CCCceEEEEEEcCCc
Q psy12844 12 VYVSGVIQFFNKERGFGFINRIGDDGRKDYFFHFSEIQGGTDN-ILRAIKYSLLVIFDIGVTP--GGRREAVHIKIFDTR 88 (121)
Q Consensus 12 ~m~~G~Vkwfn~~kGfGFI~~~~d~g~~dVFfH~s~l~~~g~~-~~~~l~~G~~V~F~i~~~~--kGk~~A~~V~~~~~~ 88 (121)
..+.|+|+.. +.||+... ..| -+-|+|++.+...... ....++.||.|...+...+ +| .....+..+...
T Consensus 198 ~vv~G~V~~I---~~~G~fV~--i~g-v~Gllhisels~~~~~~~~~~~~vGd~VkvkVl~iD~e~~-rI~LS~K~l~~~ 270 (318)
T PRK07400 198 EVVVGTVRGI---KPYGAFID--IGG-VSGLLHISEISHEHIETPHSVFNVNDEMKVMIIDLDAERG-RISLSTKQLEPE 270 (318)
T ss_pred CEEEEEEEEE---ECCeEEEE--ECC-EEEEEEHHHcccccccChhhccCCCCEEEEEEEEEeCCCC-EEEEEEeccccC
Confidence 3578999987 56999888 544 5899999999754321 2245799999999988754 45 666666666655
Q ss_pred cc
Q psy12844 89 LY 90 (121)
Q Consensus 89 ~~ 90 (121)
++
T Consensus 271 P~ 272 (318)
T PRK07400 271 PG 272 (318)
T ss_pred hh
Confidence 44
No 77
>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=71.15 E-value=9.1 Score=23.39 Aligned_cols=33 Identities=18% Similarity=0.198 Sum_probs=26.3
Q ss_pred cCCCCCCEEEEEEEECCCCCceEEEEEEcCCcc
Q psy12844 57 RAIKYSLLVIFDIGVTPGGRREAVHIKIFDTRL 89 (121)
Q Consensus 57 ~~l~~G~~V~F~i~~~~kGk~~A~~V~~~~~~~ 89 (121)
..+.+||.|+|.+.....|...|.+|.+.+.-+
T Consensus 6 ~~~~~Gd~v~Yti~v~N~g~~~a~~v~v~D~lP 38 (53)
T TIGR01451 6 TVATIGDTITYTITVTNNGNVPATNVVVTDILP 38 (53)
T ss_pred cccCCCCEEEEEEEEEECCCCceEeEEEEEcCC
Confidence 467899999999999888867788888765433
No 78
>COG2996 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only]
Probab=70.81 E-value=27 Score=29.04 Aligned_cols=60 Identities=18% Similarity=0.101 Sum_probs=42.9
Q ss_pred eeeEEEEeeCCCCeEEEEecCCCCcccEEEEccccccCCCCcccCCCCCCEEEEEEEECCCCCceEEEEE
Q psy12844 14 VSGVIQFFNKERGFGFINRIGDDGRKDYFFHFSEIQGGTDNILRAIKYSLLVIFDIGVTPGGRREAVHIK 83 (121)
Q Consensus 14 ~~G~Vkwfn~~kGfGFI~~~~d~g~~dVFfH~s~l~~~g~~~~~~l~~G~~V~F~i~~~~kGk~~A~~V~ 83 (121)
....|..+ ..||..... +.+++.|+.|.++.... .+++||.|++=+-.+.++++.|.--.
T Consensus 9 ~~l~V~~~---~~~g~fL~~-~~~~~~ilL~k~~~~~~------e~evGdev~vFiY~D~~~rl~aTt~~ 68 (287)
T COG2996 9 NSLEVVEF---SDFGYFLDA-GEDGTTILLPKSEPEED------ELEVGDEVTVFIYVDSEDRLIATTRE 68 (287)
T ss_pred EEEEEEEe---eceeEEEec-CCCceEEeccccCCcCC------ccccCcEEEEEEEECCCCceeheeec
Confidence 45677776 456655541 44445899999988533 58999999999988888877775433
No 79
>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=70.16 E-value=23 Score=23.65 Aligned_cols=54 Identities=24% Similarity=0.190 Sum_probs=37.5
Q ss_pred eeeEEEEeeCCCCeEEEEecCCCCcccEEEEccccccCCCCc------------ccCCCCCCEEEEEEEECC
Q psy12844 14 VSGVIQFFNKERGFGFINRIGDDGRKDYFFHFSEIQGGTDNI------------LRAIKYSLLVIFDIGVTP 73 (121)
Q Consensus 14 ~~G~Vkwfn~~kGfGFI~~~~d~g~~dVFfH~s~l~~~g~~~------------~~~l~~G~~V~F~i~~~~ 73 (121)
+.|+|...+ .+|+... .++ .+.|+|++++....+.. ...++.||.|...+...+
T Consensus 3 v~g~V~~i~---~~GifV~--l~~-v~G~v~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~Gd~v~vkI~~vd 68 (99)
T cd04460 3 VEGEVVEVV---DFGAFVR--IGP-VDGLLHISQIMDDYISYDPKNKRLIGEETKRVLKVGDVVRARIVAVS 68 (99)
T ss_pred EEEEEEEEE---eccEEEE--EcC-eEEEEEEEEccCCceEechhheeecccCcCCEECCCCEEEEEEEEEe
Confidence 578888874 4777777 444 68999999986543310 134689999999987754
No 80
>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase. Members of this protein family are polyribonucleotide nucleotidyltransferase, also called polynucleotide phosphorylase. Some members have been shown also to have additional functions as guanosine pentaphosphate synthetase and as poly(A) polymerase (see model TIGR02696 for an exception clade, within this family).
Probab=69.86 E-value=16 Score=33.34 Aligned_cols=59 Identities=20% Similarity=0.112 Sum_probs=42.9
Q ss_pred eeeeeEEEEeeCCCCeEEEEecCCCCcccEEEEccccccCCCC-cccCCCCCCEEEEEEEECC-CC
Q psy12844 12 VYVSGVIQFFNKERGFGFINRIGDDGRKDYFFHFSEIQGGTDN-ILRAIKYSLLVIFDIGVTP-GG 75 (121)
Q Consensus 12 ~m~~G~Vkwfn~~kGfGFI~~~~d~g~~dVFfH~s~l~~~g~~-~~~~l~~G~~V~F~i~~~~-kG 75 (121)
..+.|+|+.. +.||.... -.++.+-|+|+|.+....+. ....++.||.|...+...+ +|
T Consensus 620 ~i~~G~V~~I---~~~GafVe--i~~g~~GllHiSei~~~~v~~~~~~~kvGD~V~VkVi~id~~g 680 (684)
T TIGR03591 620 KIYEGKVVRI---MDFGAFVE--ILPGKDGLVHISEIANERVEKVEDVLKEGDEVKVKVLEIDKQG 680 (684)
T ss_pred cEEEEEEEEE---eCCEEEEE--ECCCcEEEEEHHHcCCCcccChhhccCCCCEEEEEEEEECCCC
Confidence 3578999998 45998887 44457999999999654331 2234788999998877654 45
No 81
>PRK11642 exoribonuclease R; Provisional
Probab=69.42 E-value=40 Score=31.51 Aligned_cols=57 Identities=25% Similarity=0.290 Sum_probs=39.9
Q ss_pred eeeeEEEEeeCCCCeEEEEecCCCCcccEEEEccccccCCC------------CcccCCCCCCEEEEEEEECC
Q psy12844 13 YVSGVIQFFNKERGFGFINRIGDDGRKDYFFHFSEIQGGTD------------NILRAIKYSLLVIFDIGVTP 73 (121)
Q Consensus 13 m~~G~Vkwfn~~kGfGFI~~~~d~g~~dVFfH~s~l~~~g~------------~~~~~l~~G~~V~F~i~~~~ 73 (121)
.+.|+|... ..|||...+ ++.+-+-|+|+++|...-| ++...++.||.|...+..-+
T Consensus 646 ~f~G~Is~V---~~fGifVeL-~~~~vEGlV~vs~L~~d~y~~d~~~~~L~g~~~~~~~~lGD~V~VkV~~vD 714 (813)
T PRK11642 646 VFKGVISSV---TGFGFFVRL-DDLFIDGLVHVSSLDNDYYRFDQVGQRLIGESSGQTYRLGDRVEVRVEAVN 714 (813)
T ss_pred EEEEEEEEe---ecCceEEEE-CCCCeeeeEEEeecCCcceEecchheEEecccCCcEECCCCEEEEEEEEee
Confidence 367888875 568887763 4445789999998864311 01246889999999997654
No 82
>PRK13806 rpsA 30S ribosomal protein S1; Provisional
Probab=69.31 E-value=16 Score=31.72 Aligned_cols=56 Identities=14% Similarity=0.060 Sum_probs=40.3
Q ss_pred eeeeEEEEeeCCCCeEEEEecCCCCcccEEEEccccccCCC-CcccCCCCCCEEEEEEEECC
Q psy12844 13 YVSGVIQFFNKERGFGFINRIGDDGRKDYFFHFSEIQGGTD-NILRAIKYSLLVIFDIGVTP 73 (121)
Q Consensus 13 m~~G~Vkwfn~~kGfGFI~~~~d~g~~dVFfH~s~l~~~g~-~~~~~l~~G~~V~F~i~~~~ 73 (121)
...|+|+.. ..||.... .+.+-+-|+|.+.+..... +....+++||.|.+.+..-+
T Consensus 382 ~v~G~V~~i---~~~G~FV~--l~~gv~Gli~~se~s~~~~~~~~~~~~~Gd~v~~~V~~id 438 (491)
T PRK13806 382 TVTGTVEKR---AQFGLFVN--LAPGVTGLLPASVISRAGKPATYEKLKPGDSVTLVVEEID 438 (491)
T ss_pred EEEEEEEEE---ecCceEEE--cCCCcEEEEEHHHcCcccccchhhcCCCCCEEEEEEEEEe
Confidence 578999986 56887666 3345799999999964321 12257899999999877643
No 83
>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=69.17 E-value=22 Score=21.22 Aligned_cols=55 Identities=16% Similarity=0.150 Sum_probs=38.3
Q ss_pred eeeeEEEEeeCCCCeEEEEecCCCCcccEEEEccccccCCCC-cccCCCCCCEEEEEEEECC
Q psy12844 13 YVSGVIQFFNKERGFGFINRIGDDGRKDYFFHFSEIQGGTDN-ILRAIKYSLLVIFDIGVTP 73 (121)
Q Consensus 13 m~~G~Vkwfn~~kGfGFI~~~~d~g~~dVFfH~s~l~~~g~~-~~~~l~~G~~V~F~i~~~~ 73 (121)
.+.|+|...+ .+|++.. -+ +.+-|+|.+++...... ....++.||.|.+.+...+
T Consensus 4 ~~~g~V~~v~---~~g~~v~--l~-~~~g~l~~~e~~~~~~~~~~~~~~~Gd~v~v~i~~vd 59 (68)
T cd05688 4 VVEGTVKSIT---DFGAFVD--LG-GVDGLLHISDMSWGRVKHPSEVVNVGDEVEVKVLKID 59 (68)
T ss_pred EEEEEEEEEE---eeeEEEE--EC-CeEEEEEhHHCCCccccCHhHEECCCCEEEEEEEEEE
Confidence 4789999986 3677777 43 36899999998633220 1134699999999887754
No 84
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=69.02 E-value=35 Score=31.15 Aligned_cols=58 Identities=21% Similarity=0.119 Sum_probs=42.7
Q ss_pred eeeeEEEEeeCCCCeEEEEecCCCCcccEEEEccccccCCCC-cccCCCCCCEEEEEEEECC-CC
Q psy12844 13 YVSGVIQFFNKERGFGFINRIGDDGRKDYFFHFSEIQGGTDN-ILRAIKYSLLVIFDIGVTP-GG 75 (121)
Q Consensus 13 m~~G~Vkwfn~~kGfGFI~~~~d~g~~dVFfH~s~l~~~g~~-~~~~l~~G~~V~F~i~~~~-kG 75 (121)
.+.|+|+... .||+... -..+.+-|+|+|.+...... ....++.||.|.-.+...+ +|
T Consensus 624 v~~G~V~~I~---~fGafVe--i~~~~~GllhiSels~~~v~~~~~v~kvGD~V~VkV~~iD~~g 683 (693)
T PRK11824 624 IYEGKVVRIV---DFGAFVE--ILPGKDGLVHISEIADERVEKVEDVLKEGDEVKVKVLEIDKRG 683 (693)
T ss_pred EEEEEEEEEE---CCeEEEE--ECCCCEEEEEeeeccCccccCccceeCCCCEEEEEEEEECCCC
Confidence 5789999984 5998888 44557999999999754321 1234789999998877753 35
No 85
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=68.42 E-value=17 Score=31.80 Aligned_cols=51 Identities=14% Similarity=0.013 Sum_probs=39.4
Q ss_pred eeeeeEEEEeeCCCCeEEEEecCCCCcccEEEEccccccCCCCcccCCCCCCEEEEEEEECC
Q psy12844 12 VYVSGVIQFFNKERGFGFINRIGDDGRKDYFFHFSEIQGGTDNILRAIKYSLLVIFDIGVTP 73 (121)
Q Consensus 12 ~m~~G~Vkwfn~~kGfGFI~~~~d~g~~dVFfH~s~l~~~g~~~~~~l~~G~~V~F~i~~~~ 73 (121)
.+..|+|+... .+|++.. . |+-+-|+|.+.+... ..+++|++|.+.+..-.
T Consensus 136 eIV~G~V~ri~---~~giiVD--L-ggvea~LP~sE~ip~-----E~~~~GdrIka~I~~Vd 186 (470)
T PRK09202 136 EIITGVVKRVE---RGNIIVD--L-GRAEAILPRKEQIPR-----ENFRPGDRVRAYVYEVR 186 (470)
T ss_pred CEEEEEEEEEe---cCCEEEE--E-CCeEEEecHHHcCCC-----ccCCCCCEEEEEEEEEe
Confidence 36799999986 3466666 4 456999999999644 46899999999887754
No 86
>KOG4246|consensus
Probab=67.77 E-value=0.65 Score=43.74 Aligned_cols=60 Identities=23% Similarity=0.376 Sum_probs=45.8
Q ss_pred eeeeEEEEeeCCCCeEEEEecCCCCcccEEEEccccccCCCCcccCCCCCCEEEEEEEECCCC--CceEEEEEEcCC
Q psy12844 13 YVSGVIQFFNKERGFGFINRIGDDGRKDYFFHFSEIQGGTDNILRAIKYSLLVIFDIGVTPGG--RREAVHIKIFDT 87 (121)
Q Consensus 13 m~~G~Vkwfn~~kGfGFI~~~~d~g~~dVFfH~s~l~~~g~~~~~~l~~G~~V~F~i~~~~kG--k~~A~~V~~~~~ 87 (121)
.+.|.|... ..-||||.. ||||..+.+++. .+.+||+|--+..-.+.- ++.|.+|+.+++
T Consensus 148 ~f~gvvtk~--~DtygfVD~-------dvffQls~~~g~------hp~vgD~V~vea~Ynpsmpfkwnaqriq~l~~ 209 (1194)
T KOG4246|consen 148 RFAGVVTKQ--TDTYGFVDQ-------DVFFQLSKMQGL------HPSVGDAVNVEADYNPSMPFKWNAQRIQHLGG 209 (1194)
T ss_pred eeehhhhhh--ccccccccH-------HHHHHHHHHhcC------CCccccceeeecccCCCCCccccHHHHHhccc
Confidence 467888876 568999977 799999999866 489999998777665532 477777777764
No 87
>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=67.50 E-value=15 Score=26.50 Aligned_cols=55 Identities=24% Similarity=0.394 Sum_probs=34.8
Q ss_pred cccccceeeeeeeEEEEeeCCC-CeEEEEecCCCCcccEEEEcc----ccccCCCCcccCCCCCCEEE
Q psy12844 4 HLGKIIEEVYVSGVIQFFNKER-GFGFINRIGDDGRKDYFFHFS----EIQGGTDNILRAIKYSLLVI 66 (121)
Q Consensus 4 ~~~~~~~~~m~~G~Vkwfn~~k-GfGFI~~~~d~g~~dVFfH~s----~l~~~g~~~~~~l~~G~~V~ 66 (121)
+-|+|..+ ..|+|....+.+ -|| |.. ++| -+|.+|+- .+.+.+|. ...++||.|+
T Consensus 34 ~~~~v~AP--~~G~v~~v~~T~HA~g-i~~--~~G-~evLiHiGidTV~L~G~gF~--~~v~~Gd~V~ 93 (121)
T TIGR00830 34 TDGKVVAP--VDGKIGKIFPTKHAFG-IES--DSG-VEILIHIGIDTVKLNGEGFT--SHVEEGQRVK 93 (121)
T ss_pred CCCeEEcc--CCeEEEEEccCCCEEE-EEe--CCC-cEEEEEeeeceeecCCCceE--EEecCCCEEc
Confidence 44677666 589999976544 455 444 454 69999984 34555552 3355677765
No 88
>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=67.26 E-value=8.7 Score=29.77 Aligned_cols=47 Identities=17% Similarity=0.147 Sum_probs=40.7
Q ss_pred eeeEEEEeeCCCCeEEEEecCCCCcccEEEEccccccCCCCcccCCCCCCEEEE
Q psy12844 14 VSGVIQFFNKERGFGFINRIGDDGRKDYFFHFSEIQGGTDNILRAIKYSLLVIF 67 (121)
Q Consensus 14 ~~G~Vkwfn~~kGfGFI~~~~d~g~~dVFfH~s~l~~~g~~~~~~l~~G~~V~F 67 (121)
.-|+||.|+.+..=|.++- .+= +|+=+|-..+..-.+ .|.+||.|-.
T Consensus 36 rIG~iK~F~~~tQe~iVti--~e~-e~LeI~T~nISN~~l----eLs~~D~VlL 82 (181)
T PF05606_consen 36 RIGTIKSFKFQTQEGIVTI--PEY-EDLEIHTKNISNINL----ELSKGDEVLL 82 (181)
T ss_pred EEeeeeecccccceEEEEe--ecc-cCceEEeeeccccee----EecCCCEEEE
Confidence 3799999999999999998 553 689999999988886 8999999974
No 89
>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=66.83 E-value=30 Score=29.75 Aligned_cols=71 Identities=18% Similarity=0.223 Sum_probs=48.7
Q ss_pred eeeeEEEEeeCCCCeEEEEecCCCCcccEEEEccccccCCC-------------CcccCCCCCCEEEEEEEECC---CCC
Q psy12844 13 YVSGVIQFFNKERGFGFINRIGDDGRKDYFFHFSEIQGGTD-------------NILRAIKYSLLVIFDIGVTP---GGR 76 (121)
Q Consensus 13 m~~G~Vkwfn~~kGfGFI~~~~d~g~~dVFfH~s~l~~~g~-------------~~~~~l~~G~~V~F~i~~~~---kGk 76 (121)
.+.|+|+...+.-+--||+- ..+ +.-|+|++++..... +....|++||.|--.+...+ +|-
T Consensus 28 IY~GrV~~i~p~l~aAFVdi--G~~-k~gfL~~~d~~~~~~~~~~~~~~~~~~~~i~~~l~~G~~IlVQV~Ke~~~~Kgp 104 (414)
T TIGR00757 28 IYKGRVTRILPSLQAAFVDI--GLE-KNGFLHASDIGPNYECLAPAEAKREAGPSISELLRPGQSVLVQVVKEPRGNKGA 104 (414)
T ss_pred EEEEEEeeecCCCceEEEEc--CCC-ceEEEEHHHcCchhhccccccccccccCCHHHhCcCCCEEEEEEeeCCcCCCCC
Confidence 58999999987666889998 554 689999999853200 00124899999999999865 552
Q ss_pred ceEEEEEEcC
Q psy12844 77 REAVHIKIFD 86 (121)
Q Consensus 77 ~~A~~V~~~~ 86 (121)
.--.++.+.+
T Consensus 105 ~lT~~Isl~G 114 (414)
T TIGR00757 105 RLTTDISLPG 114 (414)
T ss_pred eEEEEEEecc
Confidence 2223444444
No 90
>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional
Probab=65.74 E-value=24 Score=33.23 Aligned_cols=57 Identities=21% Similarity=0.199 Sum_probs=40.7
Q ss_pred eeeeeeEEEEeeCCCCeEEEEecCCCCcccEEEEccccccCCCC-cccCCCCCCEEEEEEEECC
Q psy12844 11 EVYVSGVIQFFNKERGFGFINRIGDDGRKDYFFHFSEIQGGTDN-ILRAIKYSLLVIFDIGVTP 73 (121)
Q Consensus 11 ~~m~~G~Vkwfn~~kGfGFI~~~~d~g~~dVFfH~s~l~~~g~~-~~~~l~~G~~V~F~i~~~~ 73 (121)
-..+.|+|+... .||++.. -. +-+-|+|+|.+...... +...+++||.|++.+..-+
T Consensus 494 G~~V~G~Vk~i~---~~G~fVd--l~-Gv~Gfvp~SeiS~~~v~~~~~~~kvGq~v~vkVi~iD 551 (863)
T PRK12269 494 EDSVSGVVKSFT---SFGAFID--LG-GFDGLLHVNDMSWGHVARPREFVKKGQTIELKVIRLD 551 (863)
T ss_pred CCEEEEEEEEEe---CCcEEEE--EC-CEEEEEEchhccccccCCHHHhccCCCEEEEEEEEEe
Confidence 345799999984 5888887 54 46899999998643220 1134678999999987744
No 91
>PRK07899 rpsA 30S ribosomal protein S1; Reviewed
Probab=64.91 E-value=35 Score=30.01 Aligned_cols=57 Identities=16% Similarity=0.096 Sum_probs=40.6
Q ss_pred eeeeeeeEEEEeeCCCCeEEEEecCCCCcccEEEEccccccCCCC-cccCCCCCCEEEEEEEEC
Q psy12844 10 EEVYVSGVIQFFNKERGFGFINRIGDDGRKDYFFHFSEIQGGTDN-ILRAIKYSLLVIFDIGVT 72 (121)
Q Consensus 10 ~~~m~~G~Vkwfn~~kGfGFI~~~~d~g~~dVFfH~s~l~~~g~~-~~~~l~~G~~V~F~i~~~ 72 (121)
+-..+.|+|+.. ..||.+.. .. +-+.|+|+++|...... +...+++||.|++.+..-
T Consensus 208 ~G~iv~G~V~~i---~~~G~FVd--lg-gv~Glv~~Sels~~~v~~~~~~~kvGd~V~vkVl~i 265 (486)
T PRK07899 208 KGQVRKGVVSSI---VNFGAFVD--LG-GVDGLVHVSELSWKHIDHPSEVVEVGQEVTVEVLDV 265 (486)
T ss_pred CCCEEEEEEEEE---ECCeEEEE--EC-CEEEEEEHHHCCCcccCCHHHhcCCCCEEEEEEEEE
Confidence 334578999987 45787776 43 47999999999754321 113478999999997763
No 92
>PRK06299 rpsA 30S ribosomal protein S1; Reviewed
Probab=64.32 E-value=40 Score=29.44 Aligned_cols=69 Identities=20% Similarity=0.157 Sum_probs=45.3
Q ss_pred eeeeeEEEEeeCCCCeEEEEecCCCCcccEEEEccccccCC--CCcccCCCCCCEEEEEEEEC-CCCCceEEEEEEc
Q psy12844 12 VYVSGVIQFFNKERGFGFINRIGDDGRKDYFFHFSEIQGGT--DNILRAIKYSLLVIFDIGVT-PGGRREAVHIKIF 85 (121)
Q Consensus 12 ~m~~G~Vkwfn~~kGfGFI~~~~d~g~~dVFfH~s~l~~~g--~~~~~~l~~G~~V~F~i~~~-~kGk~~A~~V~~~ 85 (121)
..+.|+|+.. ..||+... .+.+-+.|+|.+++...- -+....+++||.|...+..- ...+.........
T Consensus 375 ~~v~g~V~~v---~~~G~fV~--l~~~v~g~i~~s~l~~~~~~~~~~~~~~~Gd~v~v~Il~vd~~~~~i~ls~k~~ 446 (565)
T PRK06299 375 DVVEGKVKNI---TDFGAFVG--LEGGIDGLVHLSDISWDKKGEEAVELYKKGDEVEAVVLKVDVEKERISLGIKQL 446 (565)
T ss_pred CEEEEEEEEE---ecceEEEE--CCCCCEEEEEHHHcCccccccChHhhCCCCCEEEEEEEEEeCCCCEEEEEEehh
Confidence 3578999996 46888777 444579999999997321 00125679999999976653 3332444444443
No 93
>COG0539 RpsA Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]
Probab=64.19 E-value=27 Score=31.39 Aligned_cols=81 Identities=21% Similarity=0.223 Sum_probs=58.0
Q ss_pred ccccceeeeeeeEEEEeeCCCCeEEEEecCCCCcccEEEEccccccCCCC-cccCCCCCCEEEEEEEECC--CCCceEEE
Q psy12844 5 LGKIIEEVYVSGVIQFFNKERGFGFINRIGDDGRKDYFFHFSEIQGGTDN-ILRAIKYSLLVIFDIGVTP--GGRREAVH 81 (121)
Q Consensus 5 ~~~~~~~~m~~G~Vkwfn~~kGfGFI~~~~d~g~~dVFfH~s~l~~~g~~-~~~~l~~G~~V~F~i~~~~--kGk~~A~~ 81 (121)
+.+|.+-....|+|+...+ ||.... ..| -|=++|++++.-.... +...+++||.|.-.+..-+ ++ .....
T Consensus 187 ~~~l~~G~vV~G~V~~It~---~GafVd--igG-vdGLlHiseiS~~rv~~P~~vvkvGd~VkvkVi~~D~e~~-RVsLS 259 (541)
T COG0539 187 LNKLEVGEVVEGVVKNITD---YGAFVD--IGG-VDGLLHISEISWKRVDHPSEVVKVGDEVKVKVISLDEERG-RVSLS 259 (541)
T ss_pred HhcCCCCceEEEEEEEeec---CcEEEE--ecC-eeeEEehhhccccccCCHHHhcccCCEEEEEEEEEccCCC-eEEEE
Confidence 5667777788999999854 997766 444 7899999999866542 4456789999998887754 45 55666
Q ss_pred EEEcCCccccc
Q psy12844 82 IKIFDTRLYLE 92 (121)
Q Consensus 82 V~~~~~~~~~~ 92 (121)
+..+...+|..
T Consensus 260 lK~l~~dPw~~ 270 (541)
T COG0539 260 LKQLEEDPWEG 270 (541)
T ss_pred ehhcccCcHHH
Confidence 66555555444
No 94
>PRK07899 rpsA 30S ribosomal protein S1; Reviewed
Probab=63.18 E-value=49 Score=29.09 Aligned_cols=65 Identities=17% Similarity=0.158 Sum_probs=45.0
Q ss_pred eeeeEEEEeeCCCCeEEEEecCCCCcccEEEEccccccCCCC-cccCCCCCCEEEEEEEECC--CCCceEEEEE
Q psy12844 13 YVSGVIQFFNKERGFGFINRIGDDGRKDYFFHFSEIQGGTDN-ILRAIKYSLLVIFDIGVTP--GGRREAVHIK 83 (121)
Q Consensus 13 m~~G~Vkwfn~~kGfGFI~~~~d~g~~dVFfH~s~l~~~g~~-~~~~l~~G~~V~F~i~~~~--kGk~~A~~V~ 83 (121)
.+.|+|+.. ..||+... .+.+-+-|+|++.+....+. +...++.||.|...+..-+ ++ .....+.
T Consensus 296 vv~G~V~~I---~~fGvFVe--L~~gieGLvh~SeLs~~~v~~~~~~~kvGd~V~VkIi~ID~e~r-rI~LSlK 363 (486)
T PRK07899 296 IVPGKVTKL---VPFGAFVR--VEEGIEGLVHISELAERHVEVPEQVVQVGDEVFVKVIDIDLERR-RISLSLK 363 (486)
T ss_pred EEEEEEEEE---eccEEEEE--eCCCcEEEEEHHHcCcccccCccceeCCCCEEEEEEEEEECCCC-EEEEEEE
Confidence 478999987 45998887 44457899999999754321 1134789999999987643 44 4444444
No 95
>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=62.60 E-value=24 Score=25.74 Aligned_cols=55 Identities=18% Similarity=0.323 Sum_probs=33.5
Q ss_pred cccccceeeeeeeEEEEeeCCC-CeEEEEecCCCCcccEEEEcc----ccccCCCCcccCCCCCCEEE
Q psy12844 4 HLGKIIEEVYVSGVIQFFNKER-GFGFINRIGDDGRKDYFFHFS----EIQGGTDNILRAIKYSLLVI 66 (121)
Q Consensus 4 ~~~~~~~~~m~~G~Vkwfn~~k-GfGFI~~~~d~g~~dVFfH~s----~l~~~g~~~~~~l~~G~~V~ 66 (121)
+-|+|.++ ..|+|....+.+ -||+-+. +| -+|.+|+- .+.+.+|. ...++||.|.
T Consensus 38 ~~~~v~AP--~~G~v~~i~~T~HAi~i~s~---~G-~eiLiHiGidTv~L~G~gF~--~~v~~G~~V~ 97 (132)
T PF00358_consen 38 SDGKVYAP--VDGTVTMIFPTKHAIGIRSD---NG-VEILIHIGIDTVKLNGEGFE--TLVKEGDKVK 97 (132)
T ss_dssp SSSEEEES--SSEEEEEE-TTSSEEEEEET---TS-EEEEEE-SBSGGGGTTTTEE--ESS-TTSEE-
T ss_pred CCCeEEEE--eeEEEEEEcCCCCEEEEEeC---CC-CEEEEEEccchhhcCCcceE--EEEeCCCEEE
Confidence 44666666 589999988755 3444443 44 69999974 35566652 4556888876
No 96
>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=62.33 E-value=35 Score=21.21 Aligned_cols=53 Identities=15% Similarity=0.118 Sum_probs=34.0
Q ss_pred eeeEEEEee-CCCCeEEEEecCCCCc--ccEEEEccccccCCCCcccCCCCCCEEEEEEEEC
Q psy12844 14 VSGVIQFFN-KERGFGFINRIGDDGR--KDYFFHFSEIQGGTDNILRAIKYSLLVIFDIGVT 72 (121)
Q Consensus 14 ~~G~Vkwfn-~~kGfGFI~~~~d~g~--~dVFfH~s~l~~~g~~~~~~l~~G~~V~F~i~~~ 72 (121)
..|.|..+. ..+|+.|++. .|.. -++-+.-+.+.... ..|++|+.|...-...
T Consensus 4 v~g~v~~i~~tk~g~~~~~L--~D~~~~i~~~~f~~~~~~~~----~~l~~g~~v~v~g~v~ 59 (78)
T cd04489 4 VEGEISNLKRPSSGHLYFTL--KDEDASIRCVMWRSNARRLG----FPLEEGMEVLVRGKVS 59 (78)
T ss_pred EEEEEecCEECCCcEEEEEE--EeCCeEEEEEEEcchhhhCC----CCCCCCCEEEEEEEEE
Confidence 456666665 4788999998 5543 23333334454443 5799999999886654
No 97
>PRK13150 cytochrome c-type biogenesis protein CcmE; Reviewed
Probab=61.20 E-value=71 Score=24.30 Aligned_cols=69 Identities=12% Similarity=0.035 Sum_probs=52.1
Q ss_pred eeEEEEeeCCCCeEEEEecCCCCcccEEEEccccccCCCCcccCCCCCCEEEEEEEECCCCCceEEEEEEcCCccccc
Q psy12844 15 SGVIQFFNKERGFGFINRIGDDGRKDYFFHFSEIQGGTDNILRAIKYSLLVIFDIGVTPGGRREAVHIKIFDTRLYLE 92 (121)
Q Consensus 15 ~G~Vkwfn~~kGfGFI~~~~d~g~~dVFfH~s~l~~~g~~~~~~l~~G~~V~F~i~~~~kGk~~A~~V~~~~~~~~~~ 92 (121)
.|.|+|-...-..=|... |.. ..|-|+++.+..+- .++|+.|.-+=.-.++|..+|.+|..-..+.|.+
T Consensus 68 ~GSv~r~~~~~~v~F~vt--D~~-~~v~V~Y~GilPDl------FrEG~gVVveG~~~~~g~F~A~evLAKhdekYmP 136 (159)
T PRK13150 68 PGSVRRDPDSLKVNFSLY--DAE-GSVTVSYEGILPDL------FREGQGVVVQGTLEKGNHVLAHEVLAKHDENYTP 136 (159)
T ss_pred CCcEEECCCCcEEEEEEE--cCC-cEEEEEEeccCCcc------ccCCCeEEEEEEECCCCEEEEeEEEeCCCCCCCC
Confidence 466666333335788888 654 58999999997664 5999999988777777889999999887766643
No 98
>PRK03987 translation initiation factor IF-2 subunit alpha; Validated
Probab=59.62 E-value=53 Score=26.52 Aligned_cols=68 Identities=24% Similarity=0.338 Sum_probs=45.9
Q ss_pred eeeeEEEEeeCCCCeEEEEecCCC-CcccEEEEccccccCCCC-cccCCCCCCEEEEEEEECC--CCCceEEEEEEc
Q psy12844 13 YVSGVIQFFNKERGFGFINRIGDD-GRKDYFFHFSEIQGGTDN-ILRAIKYSLLVIFDIGVTP--GGRREAVHIKIF 85 (121)
Q Consensus 13 m~~G~Vkwfn~~kGfGFI~~~~d~-g~~dVFfH~s~l~~~g~~-~~~~l~~G~~V~F~i~~~~--kGk~~A~~V~~~ 85 (121)
.+.|+|+.. ..||+.... ++ ++-+-|+|.+.+....+. ....++.||.|...+..-+ +| .....+..+
T Consensus 11 iV~G~V~~I---~~~G~fV~L-~e~~gieGlI~iSEls~~~i~~i~~~~kvGd~V~vkVi~VD~~k~-~I~LSlK~v 82 (262)
T PRK03987 11 LVVGTVKEV---KDFGAFVTL-DEYPGKEGFIHISEVASGWVKNIRDHVKEGQKVVCKVIRVDPRKG-HIDLSLKRV 82 (262)
T ss_pred EEEEEEEEE---ECCEEEEEE-CCCCCcEEEEEHHHcCcccccCHHHhCCCCCEEEEEEEEEecccC-eEEEEEEec
Confidence 468999987 568887774 32 257899999999754331 1134789999999988755 34 444444433
No 99
>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional
Probab=58.56 E-value=46 Score=31.46 Aligned_cols=69 Identities=19% Similarity=0.033 Sum_probs=45.7
Q ss_pred eeeeeEEEEeeCCCCeEEEEecCCCCcccEEEEccccccC--CCCcccCCCCCCEEEEEEEECC-CCCceEEEEEEc
Q psy12844 12 VYVSGVIQFFNKERGFGFINRIGDDGRKDYFFHFSEIQGG--TDNILRAIKYSLLVIFDIGVTP-GGRREAVHIKIF 85 (121)
Q Consensus 12 ~m~~G~Vkwfn~~kGfGFI~~~~d~g~~dVFfH~s~l~~~--g~~~~~~l~~G~~V~F~i~~~~-kGk~~A~~V~~~ 85 (121)
..+.|+|+... .||.+.. ...+-+-|+|+|++... ..++...+++||.|...+..-+ ..+.....+..+
T Consensus 580 ~iV~G~V~~I~---~fG~fVe--L~~gveGLvhiSEls~~~~~~~p~~~~kvGd~V~vkVl~iD~e~~rIsLS~K~l 651 (863)
T PRK12269 580 DVVKGRVTKIA---DFGAFIE--LAEGIEGLAHISEFSWVKKTSKPSDMVKIGDEVECMILGYDIQAGRVSLGLKQV 651 (863)
T ss_pred CEEEEEEEEEe---CCeEEEE--ecCCceeeeEHHHhcCccccCCHHHcCCCCCEEEEEEEEEecccCceEEEehhc
Confidence 45789999984 5998777 44446889999999741 1112245899999999987744 222444444433
No 100
>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=58.19 E-value=27 Score=25.22 Aligned_cols=54 Identities=22% Similarity=0.378 Sum_probs=32.9
Q ss_pred ccccceeeeeeeEEEEeeCCC-CeEEEEecCCCCcccEEEEcc----ccccCCCCcccCCCCCCEEE
Q psy12844 5 LGKIIEEVYVSGVIQFFNKER-GFGFINRIGDDGRKDYFFHFS----EIQGGTDNILRAIKYSLLVI 66 (121)
Q Consensus 5 ~~~~~~~~m~~G~Vkwfn~~k-GfGFI~~~~d~g~~dVFfH~s----~l~~~g~~~~~~l~~G~~V~ 66 (121)
-++|..+ ..|+|+...+.+ -|| |.. ++| -+|++|+. .+.+.+|. ...++||.|.
T Consensus 35 ~~~v~AP--~~G~v~~i~~T~HA~~-i~~--~~G-~eiLiHiGidTv~l~g~gF~--~~vk~Gd~V~ 93 (124)
T cd00210 35 DGKVVAP--VDGTIVQIFPTKHAIG-IES--DSG-VEILIHIGIDTVKLNGEGFT--SHVEEGQRVK 93 (124)
T ss_pred CCeEECc--CCeEEEEEccCCCEEE-EEe--CCC-cEEEEEeeeeeeecCCCceE--EEecCCCEEc
Confidence 3566655 589999976543 344 444 454 69999985 33445542 3355677765
No 101
>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=58.07 E-value=46 Score=21.20 Aligned_cols=58 Identities=12% Similarity=0.006 Sum_probs=38.3
Q ss_pred eeeeEEEEeeCCCCeEEEEecCCCCcccEEEEccccccCCCC-cccCCCCCCEEEEEEEECCCC
Q psy12844 13 YVSGVIQFFNKERGFGFINRIGDDGRKDYFFHFSEIQGGTDN-ILRAIKYSLLVIFDIGVTPGG 75 (121)
Q Consensus 13 m~~G~Vkwfn~~kGfGFI~~~~d~g~~dVFfH~s~l~~~g~~-~~~~l~~G~~V~F~i~~~~kG 75 (121)
...|+|.... ..|.+.. ..+..+-|+|.+++...... ....+++||.|.+.+..-+++
T Consensus 9 iV~G~V~~v~---~~~~~V~--i~~~~~g~l~~~~~~~~~~~~~~~~~~~GD~i~~~V~~~~~~ 67 (82)
T cd04454 9 IVIGIVTEVN---SRFWKVD--ILSRGTARLEDSSATEKDKKEIRKSLQPGDLILAKVISLGDD 67 (82)
T ss_pred EEEEEEEEEc---CCEEEEE--eCCCceEEeechhccCcchHHHHhcCCCCCEEEEEEEEeCCC
Confidence 3578888873 3344444 33346899999999654210 124589999999999876543
No 102
>PF04225 OapA: Opacity-associated protein A LysM-like domain; InterPro: IPR007340 This entry includes the Haemophilus influenzae opacity-associated protein. This protein is required for efficient nasopharyngeal mucosal colonization, and its expression is associated with a distinctive transparent colony phenotype. OapA is thought to be a secreted protein, and its expression exhibits high-frequency phase variation [].; PDB: 2GU1_A.
Probab=57.34 E-value=15 Score=24.72 Aligned_cols=28 Identities=18% Similarity=0.214 Sum_probs=17.1
Q ss_pred cccCCCCCCEEEEEEEECCCCCceEEEEEE
Q psy12844 55 ILRAIKYSLLVIFDIGVTPGGRREAVHIKI 84 (121)
Q Consensus 55 ~~~~l~~G~~V~F~i~~~~kGk~~A~~V~~ 84 (121)
.+..|++||.|+|.+.. .|++.+.++..
T Consensus 39 ~L~~L~pGq~l~f~~d~--~g~L~~L~~~~ 66 (85)
T PF04225_consen 39 PLTRLKPGQTLEFQLDE--DGQLTALRYER 66 (85)
T ss_dssp -GGG--TT-EEEEEE-T--TS-EEEEEEEE
T ss_pred hHhhCCCCCEEEEEECC--CCCEEEEEEEc
Confidence 34789999999999875 57788777553
No 103
>PRK13165 cytochrome c-type biogenesis protein CcmE; Reviewed
Probab=55.18 E-value=91 Score=23.70 Aligned_cols=69 Identities=13% Similarity=0.054 Sum_probs=51.8
Q ss_pred eeEEEEeeCCCCeEEEEecCCCCcccEEEEccccccCCCCcccCCCCCCEEEEEEEECCCCCceEEEEEEcCCccccc
Q psy12844 15 SGVIQFFNKERGFGFINRIGDDGRKDYFFHFSEIQGGTDNILRAIKYSLLVIFDIGVTPGGRREAVHIKIFDTRLYLE 92 (121)
Q Consensus 15 ~G~Vkwfn~~kGfGFI~~~~d~g~~dVFfH~s~l~~~g~~~~~~l~~G~~V~F~i~~~~kGk~~A~~V~~~~~~~~~~ 92 (121)
.|.|.|-...-..=|... |. ...|-|+++.+..+- .++|+.|.-+=.-.+.|..+|.+|..-.++.|.+
T Consensus 68 ~GSi~r~~~~l~v~F~vt--D~-~~~v~V~Y~GilPDl------FrEG~gVVveG~~~~~g~F~A~~vLAKhdekYmP 136 (160)
T PRK13165 68 PGSVQRDPNSLKVSFTLY--DA-GGSVTVTYEGILPDL------FREGQGIVAQGVLEEGNHIEAKEVLAKHDENYTP 136 (160)
T ss_pred CCcEEECCCCeEEEEEEE--cC-CeEEEEEEcccCCcc------ccCCCeEEEEEEECCCCeEEEEEEEecCCCCCCC
Confidence 567766322225788888 65 468999999988664 5899999988777777889999999887776643
No 104
>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=55.09 E-value=45 Score=24.71 Aligned_cols=55 Identities=16% Similarity=0.090 Sum_probs=37.1
Q ss_pred eeEEEEeeCCCCe-----EEEEecCCCCcccEE-EEccccccCCCCcccCCCCCCEEEEEE--EECCCC
Q psy12844 15 SGVIQFFNKERGF-----GFINRIGDDGRKDYF-FHFSEIQGGTDNILRAIKYSLLVIFDI--GVTPGG 75 (121)
Q Consensus 15 ~G~Vkwfn~~kGf-----GFI~~~~d~g~~dVF-fH~s~l~~~g~~~~~~l~~G~~V~F~i--~~~~kG 75 (121)
.|+|+..-++..- =||.. ...+..|+ .|=-++. ... ..|++||.|+|.= +.+++|
T Consensus 42 ~G~V~~vLpdd~~GsrHQ~Fiv~--l~~g~tllIahNIDla-pri---p~l~~GD~V~f~GeYe~n~kg 104 (131)
T PF11948_consen 42 CGTVVKVLPDDNKGSRHQRFIVR--LSSGQTLLIAHNIDLA-PRI---PWLQKGDQVEFYGEYEWNPKG 104 (131)
T ss_pred cEEEEEECcccCCCCcceEEEEE--eCCCCEEEEEeccCcc-ccC---cCcCCCCEEEEEEEEEECCCC
Confidence 7999988776433 38888 55555666 5655665 223 6899999999973 345555
No 105
>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=54.18 E-value=30 Score=21.81 Aligned_cols=31 Identities=26% Similarity=0.268 Sum_probs=26.2
Q ss_pred cCCCCCCEEEEEEEECCCCCceEEEEEEcCC
Q psy12844 57 RAIKYSLLVIFDIGVTPGGRREAVHIKIFDT 87 (121)
Q Consensus 57 ~~l~~G~~V~F~i~~~~kGk~~A~~V~~~~~ 87 (121)
..+.+||.|+|.+.....|..-|.+|.+.+.
T Consensus 35 ~~~~~Gd~v~ytitvtN~G~~~a~nv~v~D~ 65 (76)
T PF01345_consen 35 STANPGDTVTYTITVTNTGPAPATNVVVTDT 65 (76)
T ss_pred CcccCCCEEEEEEEEEECCCCeeEeEEEEEc
Confidence 4689999999999998888677888887754
No 106
>COG0539 RpsA Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]
Probab=53.88 E-value=43 Score=30.14 Aligned_cols=69 Identities=19% Similarity=0.168 Sum_probs=46.2
Q ss_pred eeeeEEEEeeCCCCeEEEEecCCCCcccEEEEccccccCCCC-cccCCCCCCEEEEEEEECC-CCCceEEEEEEcC
Q psy12844 13 YVSGVIQFFNKERGFGFINRIGDDGRKDYFFHFSEIQGGTDN-ILRAIKYSLLVIFDIGVTP-GGRREAVHIKIFD 86 (121)
Q Consensus 13 m~~G~Vkwfn~~kGfGFI~~~~d~g~~dVFfH~s~l~~~g~~-~~~~l~~G~~V~F~i~~~~-kGk~~A~~V~~~~ 86 (121)
...|+|+.+ .-||.+.. -..+-+=|+|+|.+.-...+ +-..+++||.|+..+-.-+ .-+..-..+....
T Consensus 280 ~v~G~Vt~i---~~~GafVe--i~~GvEGlvhvSEisw~~~~~P~evv~~Gq~V~V~Vl~id~e~rRIsL~iKq~~ 350 (541)
T COG0539 280 KVEGKVTNL---TDYGAFVE--IEEGVEGLVHVSEISWTKKNVPSEVVKVGQEVEVKVLDIDPERRRISLGLKQLK 350 (541)
T ss_pred EEEEEEEEe---ecCcEEEE--ecCCccceeechhhcccccCCHHHhcccCCEEEEEEEeeCchhceEEeeehhhh
Confidence 578999998 56887776 45557899999988654431 2245799999999887744 3333333444343
No 107
>PRK06676 rpsA 30S ribosomal protein S1; Reviewed
Probab=53.71 E-value=68 Score=26.57 Aligned_cols=65 Identities=11% Similarity=0.012 Sum_probs=42.4
Q ss_pred ccccceeeeeeeEEEEeeCCCCeEEEEecCCCCcccEEEEccccccCCCC-cccCCCCCCEEEEEEEECC
Q psy12844 5 LGKIIEEVYVSGVIQFFNKERGFGFINRIGDDGRKDYFFHFSEIQGGTDN-ILRAIKYSLLVIFDIGVTP 73 (121)
Q Consensus 5 ~~~~~~~~m~~G~Vkwfn~~kGfGFI~~~~d~g~~dVFfH~s~l~~~g~~-~~~~l~~G~~V~F~i~~~~ 73 (121)
+.++.+-....|+|+..++ +|++... +.++-+.|+|.+++...... +-..+++|+.|++.+....
T Consensus 12 ~~~~~~G~iv~G~V~~i~~---~g~~V~i-~~~~~~g~lp~~e~~~~~~~~~~~~~~vGd~v~~~V~~v~ 77 (390)
T PRK06676 12 VKEVEVGDVVTGEVLKVED---KQVFVNI-EGYKVEGVIPISELSNDHIEDINDVVKVGDELEVYVLKVE 77 (390)
T ss_pred hhcccCCCEEEEEEEEEEC---CeEEEEE-ecCCcEEEEEHHHhccccccCcccccCCCCEEEEEEEEEE
Confidence 3445555567899999964 3444441 24456899999999642110 1145789999999988754
No 108
>PRK06299 rpsA 30S ribosomal protein S1; Reviewed
Probab=53.62 E-value=1e+02 Score=26.91 Aligned_cols=68 Identities=18% Similarity=0.152 Sum_probs=44.3
Q ss_pred eeeeeeeEEEEeeCCCCeEEEEecCCCCcccEEEEccccccCCCC-cccCCCCCCEEEEEEEE-CC-CCCceEEEEEE
Q psy12844 10 EEVYVSGVIQFFNKERGFGFINRIGDDGRKDYFFHFSEIQGGTDN-ILRAIKYSLLVIFDIGV-TP-GGRREAVHIKI 84 (121)
Q Consensus 10 ~~~m~~G~Vkwfn~~kGfGFI~~~~d~g~~dVFfH~s~l~~~g~~-~~~~l~~G~~V~F~i~~-~~-kGk~~A~~V~~ 84 (121)
+-..+.|+|+... .||.... .. +-+.|+|.+++...... +-..+++||.|.+.+.. ++ ++ ..+.....
T Consensus 201 ~G~iv~g~V~~v~---~~G~~V~--i~-g~~glv~~se~s~~~~~~~~~~~kvG~~v~v~V~~~d~~~~-~i~lS~k~ 271 (565)
T PRK06299 201 EGQVVEGVVKNIT---DYGAFVD--LG-GVDGLLHITDISWKRVNHPSEVVNVGDEVKVKVLKFDKEKK-RVSLGLKQ 271 (565)
T ss_pred CCCEEEEEEEEEe---CCeEEEE--EC-CEEEEEEHHHhcccccCCHhhcCCCCCEEEEEEEEEeCCCC-eEEEEEEe
Confidence 3345689999874 4787777 44 57999999998644221 11347899999999765 33 45 44444443
No 109
>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=53.25 E-value=85 Score=26.95 Aligned_cols=55 Identities=20% Similarity=0.147 Sum_probs=38.6
Q ss_pred eeeeEEEEeeCCCCeEEEEecCCCCcccEEEEccccccCC--CCcccCCCCCCEEEEEEEEC
Q psy12844 13 YVSGVIQFFNKERGFGFINRIGDDGRKDYFFHFSEIQGGT--DNILRAIKYSLLVIFDIGVT 72 (121)
Q Consensus 13 m~~G~Vkwfn~~kGfGFI~~~~d~g~~dVFfH~s~l~~~g--~~~~~~l~~G~~V~F~i~~~ 72 (121)
...|+|+.. ..||+... -+.+-+.|+|.+++...- -+....+++|+.|...+..-
T Consensus 362 ~v~g~V~~v---~~~G~fV~--l~~~v~glv~~s~ls~~~~~~~~~~~~~~G~~V~~~Vl~v 418 (516)
T TIGR00717 362 RVTGKIKKI---TDFGAFVE--LEGGIDGLIHLSDISWDKDGREADHLYKKGDEIEAVVLAV 418 (516)
T ss_pred EEEEEEEEE---ecceEEEE--CCCCCEEEEEHHHCcCcccCCCHhHccCCCCEEEEEEEEE
Confidence 468999986 56787777 444579999999986321 00114678999999986654
No 110
>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=52.84 E-value=25 Score=21.28 Aligned_cols=53 Identities=11% Similarity=-0.006 Sum_probs=33.1
Q ss_pred eeeeEEEEeeCCCCeEEEEecCCCCccc-EEEEccccccCCCCcccCCCCCCEEEEEEEE
Q psy12844 13 YVSGVIQFFNKERGFGFINRIGDDGRKD-YFFHFSEIQGGTDNILRAIKYSLLVIFDIGV 71 (121)
Q Consensus 13 m~~G~Vkwfn~~kGfGFI~~~~d~g~~d-VFfH~s~l~~~g~~~~~~l~~G~~V~F~i~~ 71 (121)
...|+|.........-+|.- +-++.. +...++.-....+ .|++|+.|.+.+..
T Consensus 6 ~l~g~V~~ie~~g~~~~v~~--~~~~~~~l~a~it~~~~~~L----~L~~G~~V~~~ik~ 59 (64)
T PF03459_consen 6 QLPGTVESIENLGSEVEVTL--DLGGGETLTARITPESAEEL----GLKPGDEVYASIKA 59 (64)
T ss_dssp EEEEEEEEEEESSSEEEEEE--EETTSEEEEEEEEHHHHHHC----T-STT-EEEEEE-G
T ss_pred EEEEEEEEEEECCCeEEEEE--EECCCCEEEEEEcHHHHHHc----CCCCCCEEEEEEeh
Confidence 46889988887777777776 444334 6655544333333 58999999998764
No 111
>COG4776 Rnb Exoribonuclease II [Transcription]
Probab=52.35 E-value=11 Score=33.80 Aligned_cols=47 Identities=30% Similarity=0.504 Sum_probs=30.6
Q ss_pred eeeeeEEEEeeCCCCeEEEEecCCCCcccEEEEccccccCCCCcccCCCCCCEEEEEEEE
Q psy12844 12 VYVSGVIQFFNKERGFGFINRIGDDGRKDYFFHFSEIQGGTDNILRAIKYSLLVIFDIGV 71 (121)
Q Consensus 12 ~m~~G~Vkwfn~~kGfGFI~~~~d~g~~dVFfH~s~l~~~g~~~~~~l~~G~~V~F~i~~ 71 (121)
+...|+||.= +|||||+.. |. .+..|+-=-.. ...--||+|.-.+..
T Consensus 20 prvEGvVK~t--ekgfGFLEv--D~-qkSYFIpPp~M--------KkvMHGDkIiA~i~t 66 (645)
T COG4776 20 PRVEGVVKAT--EKGFGFLEV--DA-QKSYFIPPPQM--------KKVMHGDKIIAVIHT 66 (645)
T ss_pred cccceeeeec--cccceeEEE--cC-ccccccCCHHH--------hhhcccCeEEEEEEe
Confidence 4578999974 899999999 54 45666432222 233357777766554
No 112
>PF12869 tRNA_anti-like: tRNA_anti-like; InterPro: IPR024422 The function of the proteins in this entry is not known, but they contain a novel variant of the nucleic acid-binding OB fold [].; PDB: 3F1Z_I.
Probab=51.31 E-value=20 Score=25.17 Aligned_cols=63 Identities=22% Similarity=0.188 Sum_probs=31.1
Q ss_pred cccccceeeeeeeEEEEeeC--CCCeEEEEecCCCCcccEEEEccccccCCCCcccCCCCCCEEEEEEEE
Q psy12844 4 HLGKIIEEVYVSGVIQFFNK--ERGFGFINRIGDDGRKDYFFHFSEIQGGTDNILRAIKYSLLVIFDIGV 71 (121)
Q Consensus 4 ~~~~~~~~~m~~G~Vkwfn~--~kGfGFI~~~~d~g~~dVFfH~s~l~~~g~~~~~~l~~G~~V~F~i~~ 71 (121)
..||+|+ .+|+|...+. ...| ++....+++...|++++++=..... ....|+.||.|...-..
T Consensus 65 Y~gK~i~---vtG~V~~I~~~~~~~~-~~~~~~~~~~~~v~~~~~~~~~~~~-~~~~l~~G~~Vti~G~~ 129 (144)
T PF12869_consen 65 YKGKIIE---VTGTVSSIDKGFGDNY-VVLLGTENGFAGVQCYFSNDQEKRA-SVAKLKKGQKVTIKGIC 129 (144)
T ss_dssp HTT-EEE---EEEEEEEEEE-STT-E-EEEEE-TT-S-S--EEEEEEGGGHH-HHHH--TTSEEEEEEE-
T ss_pred cCCCEEE---EEEEEEEEEEcCCCcE-EEEccCCCCceeEEEEEccchhhhh-hHhcCCCCCEEEEEEEE
Confidence 3577765 5799999965 3344 5544212344567777766552211 00238999999976444
No 113
>PRK09439 PTS system glucose-specific transporter subunit; Provisional
Probab=50.66 E-value=43 Score=25.50 Aligned_cols=56 Identities=25% Similarity=0.390 Sum_probs=35.5
Q ss_pred ccccccceeeeeeeEEEEeeCC-CCeEEEEecCCCCcccEEEEcc----ccccCCCCcccCCCCCCEEE
Q psy12844 3 AHLGKIIEEVYVSGVIQFFNKE-RGFGFINRIGDDGRKDYFFHFS----EIQGGTDNILRAIKYSLLVI 66 (121)
Q Consensus 3 ~~~~~~~~~~m~~G~Vkwfn~~-kGfGFI~~~~d~g~~dVFfH~s----~l~~~g~~~~~~l~~G~~V~ 66 (121)
.+-|+|.++ ..|+|....+. .-||+ .. ++| -+|.+|+- .|.+.||. ...++||+|.
T Consensus 55 P~~~~v~AP--~dG~V~~vf~T~HAigi-~t--~~G-~eiLIHiGiDTV~L~G~gF~--~~Vk~Gd~Vk 115 (169)
T PRK09439 55 PTGNKMVAP--VDGTIGKIFETNHAFSI-ES--DSG-VELFVHFGIDTVELKGEGFK--RIAEEGQRVK 115 (169)
T ss_pred ccCCEEEec--CCeEEEEEcCCCCEEEE-Ee--CCC-cEEEEEEeecccccCCCceE--EEecCCCEEe
Confidence 345777776 69999986553 35554 44 454 69999984 45556652 3345677765
No 114
>COG0557 VacB Exoribonuclease R [Transcription]
Probab=50.20 E-value=72 Score=29.08 Aligned_cols=62 Identities=26% Similarity=0.494 Sum_probs=43.9
Q ss_pred eeeeEEEEeeCCCCeEEEEecCCC--CcccEEEEccccccCCCCcccCCCCCCEEEEEEEECC-CCC-ceEEEEEEcC
Q psy12844 13 YVSGVIQFFNKERGFGFINRIGDD--GRKDYFFHFSEIQGGTDNILRAIKYSLLVIFDIGVTP-GGR-REAVHIKIFD 86 (121)
Q Consensus 13 m~~G~Vkwfn~~kGfGFI~~~~d~--g~~dVFfH~s~l~~~g~~~~~~l~~G~~V~F~i~~~~-kGk-~~A~~V~~~~ 86 (121)
...|++.+= .+||||+.+ ++ ...|+|+-...+. .--.||.|..++.... +++ +.|.-+.++.
T Consensus 69 ~~~~~~~~~--~~gf~f~~~--~~~~~~~d~~v~~~~~~--------~a~~gD~V~v~~~~~~~~~~~~~~~v~~il~ 134 (706)
T COG0557 69 LVEGIVEAS--AKGFGFLSP--DDSKDADDIFVPKDPLN--------RALHGDRVLVELLPSDKRGRFKEAAVVRILE 134 (706)
T ss_pred cccceEEec--cCCceeecc--CccCCCCcEEecccccc--------ccccCCEEEEEECcccccCCCceEEEEeeec
Confidence 456777664 699999999 66 5579998877733 3467999999975543 453 6666666665
No 115
>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=49.18 E-value=74 Score=28.92 Aligned_cols=57 Identities=14% Similarity=0.191 Sum_probs=38.2
Q ss_pred eeeeEEEEeeCCCCeEEEEecCCCCcccEEEEccccccCCC------------CcccCCCCCCEEEEEEEECC
Q psy12844 13 YVSGVIQFFNKERGFGFINRIGDDGRKDYFFHFSEIQGGTD------------NILRAIKYSLLVIFDIGVTP 73 (121)
Q Consensus 13 m~~G~Vkwfn~~kGfGFI~~~~d~g~~dVFfH~s~l~~~g~------------~~~~~l~~G~~V~F~i~~~~ 73 (121)
.+.|+|..- ..||+.... ++.+.+-++|+++|....+ +....++.||.|.-.+..-+
T Consensus 630 ~~~g~V~~v---~~fGifV~L-~~~~~eGlvhis~l~~d~~~~d~~~~~l~g~~~~~~~~lGd~V~Vkv~~vd 698 (709)
T TIGR02063 630 EFEGVISGV---TSFGLFVEL-ENNTIEGLVHISTLKDDYYVFDEKGLALVGERTGKVFRLGDRVKVRVVKAD 698 (709)
T ss_pred EEEEEEEEE---EeCCEEEEe-cCCceEEEEEeeecCCCcEEEcccceEEEeccCCcEECCCCEEEEEEEEEe
Confidence 368888886 468886652 3324689999999974311 01135788999998887754
No 116
>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=48.42 E-value=66 Score=20.12 Aligned_cols=38 Identities=8% Similarity=0.187 Sum_probs=27.0
Q ss_pred CeEEEEecCCCCcccEEEEccccccCCCCcccCCCCCCEEEEEE
Q psy12844 26 GFGFINRIGDDGRKDYFFHFSEIQGGTDNILRAIKYSLLVIFDI 69 (121)
Q Consensus 26 GfGFI~~~~d~g~~dVFfH~s~l~~~g~~~~~~l~~G~~V~F~i 69 (121)
-+|.|.. |+| -.++.++.+...... ..++.|++|+..+
T Consensus 30 ~v~~V~l--deg-~rv~~~i~~~~~~~~---~~l~iG~~V~~vf 67 (68)
T PF01796_consen 30 VVAIVEL--DEG-VRVMARIVDVDPEDP---DELRIGMRVRLVF 67 (68)
T ss_pred EEEEEEe--CCC-CEEEEEEecCCCCCc---ccCCCCCEEEEEE
Confidence 3577777 665 488888887654443 5688999998654
No 117
>PF05753 TRAP_beta: Translocon-associated protein beta (TRAPB); InterPro: IPR008856 This family consists of several eukaryotic translocon-associated protein beta (TRAPB) or signal sequence receptor beta subunit (SSR-beta) proteins. The normal translocation of nascent polypeptides into the lumen of the endoplasmic reticulum (ER) is thought to be aided in part by a translocon-associated protein (TRAP) complex consisting of 4 protein subunits. The association of mature proteins with the ER and Golgi, or other intracellular locales, such as lysosomes, depends on the initial targeting of the nascent polypeptide to the ER membrane. A similar scenario must also exist for proteins destined for secretion [].; GO: 0005783 endoplasmic reticulum, 0016021 integral to membrane
Probab=47.58 E-value=62 Score=24.72 Aligned_cols=46 Identities=13% Similarity=0.117 Sum_probs=36.3
Q ss_pred CCCcccEEEEccccccCCCCcccCCCCCCEEEEEEEECCCCCceEEEEEEcCC
Q psy12844 35 DDGRKDYFFHFSEIQGGTDNILRAIKYSLLVIFDIGVTPGGRREAVHIKIFDT 87 (121)
Q Consensus 35 d~g~~dVFfH~s~l~~~g~~~~~~l~~G~~V~F~i~~~~kGk~~A~~V~~~~~ 87 (121)
++.+..+.++.+-+. +.+.+|+.|.+.+.--..|.-.|.+|++.+.
T Consensus 17 ~~~~a~llv~K~il~-------~~~v~g~~v~V~~~iyN~G~~~A~dV~l~D~ 62 (181)
T PF05753_consen 17 EDSPARLLVSKQILN-------KYLVEGEDVTVTYTIYNVGSSAAYDVKLTDD 62 (181)
T ss_pred CCCCcEEEEEEeecc-------ccccCCcEEEEEEEEEECCCCeEEEEEEECC
Confidence 344567777777765 3478899999999988888889999999884
No 118
>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=47.55 E-value=72 Score=28.86 Aligned_cols=57 Identities=21% Similarity=0.248 Sum_probs=37.8
Q ss_pred eeeeEEEEeeCCCCeEEEEecCCCCcccEEEEccccccCCC------------CcccCCCCCCEEEEEEEECC
Q psy12844 13 YVSGVIQFFNKERGFGFINRIGDDGRKDYFFHFSEIQGGTD------------NILRAIKYSLLVIFDIGVTP 73 (121)
Q Consensus 13 m~~G~Vkwfn~~kGfGFI~~~~d~g~~dVFfH~s~l~~~g~------------~~~~~l~~G~~V~F~i~~~~ 73 (121)
.+.|+|.... .||+.... ++.+-+-|+|++++....+ +....++.||.|...+..-+
T Consensus 575 ~~~g~I~~v~---~~GifV~L-~~~~veGlV~~s~l~~d~y~~d~~~~~l~g~~~~~~~~lGD~V~Vki~~vd 643 (654)
T TIGR00358 575 EFSGEISSVT---RFGMFVRL-DDNGIDGLIHISTLHNDYYVFDQEKMALIGKGTGKVYRIGDRVTVKLTEVN 643 (654)
T ss_pred EEEEEEEeEE---cCcEEEEe-cCCceEEEEEeEeCCCcceEEeccccEEEeccCCcEECCCCEEEEEEEEEe
Confidence 3678998874 47765442 4455799999999964321 01145778998888877654
No 119
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=46.05 E-value=67 Score=29.83 Aligned_cols=63 Identities=17% Similarity=0.093 Sum_probs=44.8
Q ss_pred eeeeeEEEEeeCCCCeEEEEecCCCCcccEEEEccccccCCCC-cccCCCCCCEEEEEEEECC-CCCceE
Q psy12844 12 VYVSGVIQFFNKERGFGFINRIGDDGRKDYFFHFSEIQGGTDN-ILRAIKYSLLVIFDIGVTP-GGRREA 79 (121)
Q Consensus 12 ~m~~G~Vkwfn~~kGfGFI~~~~d~g~~dVFfH~s~l~~~g~~-~~~~l~~G~~V~F~i~~~~-kGk~~A 79 (121)
..+.|+|+.-.+ ||-... --+++|-++|+|.+...-.. --..+++||.|.-.+..-+ +|+...
T Consensus 621 ~iy~G~V~ri~~---fGaFv~--l~~gkdgl~hiS~~~~~rv~kv~dvlk~Gd~v~Vkv~~iD~~Gri~l 685 (692)
T COG1185 621 EVYEGTVVRIVD---FGAFVE--LLPGKDGLVHISQLAKERVEKVEDVLKEGDEVKVKVIEIDKQGRIRL 685 (692)
T ss_pred cEEEEEEEEEee---cceEEE--ecCCcceeEEehhhhhhhhhcccceeecCceEEEEEeeecccCCccc
Confidence 368999999754 986666 45567999999999754110 0146889999998887754 585443
No 120
>cd03703 aeIF5B_II aeIF5B_II: This family represents the domain II of archeal and eukaryotic aeIF5B. aeIF5B is a homologue of prokaryotic Initiation Factor 2 (IF2). Disruption of the eIF5B gene (FUN12) in yeast causes a severe slow-growth phenotype, associated with a defect in translation. eIF5B has a function analogous to prokaryotic IF2 in mediating the joining of joining of 60S subunits. The eIF5B consists of three N-terminal domains (I, II, II) connected by a long helix to domain IV. Domain I is a G domain, domain II and IV are beta-barrels and domain III has a novel alpha-beta-alpha sandwich fold. The G domain and the beta-barrel domain II display a similar structure and arrangement to the homologous domains of EF1A, eEF1A and aeIF2gamma.
Probab=45.39 E-value=78 Score=22.57 Aligned_cols=58 Identities=16% Similarity=0.184 Sum_probs=40.5
Q ss_pred eeEEEEeeCCCCeEEEEecCCCCcccEEEEccccccCCCCcccCCCCCCEEEEEEEECCCCCceEEEEEEcCCccccccc
Q psy12844 15 SGVIQFFNKERGFGFINRIGDDGRKDYFFHFSEIQGGTDNILRAIKYSLLVIFDIGVTPGGRREAVHIKIFDTRLYLEDL 94 (121)
Q Consensus 15 ~G~Vkwfn~~kGfGFI~~~~d~g~~dVFfH~s~l~~~g~~~~~~l~~G~~V~F~i~~~~kGk~~A~~V~~~~~~~~~~~~ 94 (121)
.|+|..-..++|+|.... .|-.+| .|+.||.|-+- +..| +...+|+.+-.+.++..+
T Consensus 2 ~gtVlEvk~~~G~G~t~d--------------vIl~~G-----tL~~GD~Iv~g---~~~G-pi~tkVRaLl~~~~~~E~ 58 (110)
T cd03703 2 QGTVLEVKEEEGLGTTID--------------VILYDG-----TLREGDTIVVC---GLNG-PIVTKVRALLKPQPLKEL 58 (110)
T ss_pred cEEEEEEEEcCCCceEEE--------------EEEECC-----eEecCCEEEEc---cCCC-CceEEEeEecCCCCchhh
Confidence 577888888899998765 122355 58999987643 3466 777788888777777666
Q ss_pred c
Q psy12844 95 R 95 (121)
Q Consensus 95 ~ 95 (121)
|
T Consensus 59 r 59 (110)
T cd03703 59 R 59 (110)
T ss_pred c
Confidence 5
No 121
>PRK10811 rne ribonuclease E; Reviewed
Probab=44.95 E-value=87 Score=30.48 Aligned_cols=58 Identities=17% Similarity=0.165 Sum_probs=43.8
Q ss_pred eeeeEEEEeeCCCCeEEEEecCCCCcccEEEEccccccCCCC----------cccCCCCCCEEEEEEEECC
Q psy12844 13 YVSGVIQFFNKERGFGFINRIGDDGRKDYFFHFSEIQGGTDN----------ILRAIKYSLLVIFDIGVTP 73 (121)
Q Consensus 13 m~~G~Vkwfn~~kGfGFI~~~~d~g~~dVFfH~s~l~~~g~~----------~~~~l~~G~~V~F~i~~~~ 73 (121)
.+.|+|+.--+.-+=-||.. .++ ..-|+|++++....|. .-..|++||.|--.+....
T Consensus 41 IYkGkVenIvPGInAAFVDI--G~g-knGFL~L~Di~~~~f~~~~~~~~~~~i~~~Lk~GqeILVQV~KEa 108 (1068)
T PRK10811 41 IYKGKITRIEPSLEAAFVDY--GAE-RHGFLPLKEIAREYFPANYSAHGRPNIKDVLREGQEVIVQIDKEE 108 (1068)
T ss_pred eEEEEEecccCCcceeEEEe--cCC-cceEEEhhhccccccccccccccccccccccCCCCEEEEEEeecc
Confidence 58899999887778889998 654 6999999999532210 0024889999999998865
No 122
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=44.40 E-value=69 Score=27.20 Aligned_cols=50 Identities=16% Similarity=0.043 Sum_probs=36.6
Q ss_pred eeeeEEEEeeCCCCeEEEEecCCCCcccEEEEccccccCCCCcccCCCCCCEEEEEEEECC
Q psy12844 13 YVSGVIQFFNKERGFGFINRIGDDGRKDYFFHFSEIQGGTDNILRAIKYSLLVIFDIGVTP 73 (121)
Q Consensus 13 m~~G~Vkwfn~~kGfGFI~~~~d~g~~dVFfH~s~l~~~g~~~~~~l~~G~~V~F~i~~~~ 73 (121)
+.+|+|+..+. | |++.. . |+-+-|++.+..... ..+++||+|.+-+..-.
T Consensus 137 iV~G~V~~~~~--~-~~~Vd--l-g~vEa~LP~~E~ip~-----e~~~~Gd~Ika~V~~V~ 186 (362)
T PRK12327 137 IVTGVVQRRDN--R-FVYVN--L-GKIEAVLPPAEQIPG-----ETYKHGDRIKVYVVKVE 186 (362)
T ss_pred EEEEEEEEEeC--C-cEEEE--e-CCeEEEecHHHcCCC-----CCCCCCCEEEEEEEEEe
Confidence 57999999854 3 45544 3 346889998887643 47899999999887644
No 123
>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=43.07 E-value=79 Score=26.57 Aligned_cols=52 Identities=15% Similarity=0.188 Sum_probs=37.6
Q ss_pred eeeeeEEEEeeCCCCeEEEEecCCCCcccEEEEccccccCCCCcccCCCCCCEEEEEEEECC
Q psy12844 12 VYVSGVIQFFNKERGFGFINRIGDDGRKDYFFHFSEIQGGTDNILRAIKYSLLVIFDIGVTP 73 (121)
Q Consensus 12 ~m~~G~Vkwfn~~kGfGFI~~~~d~g~~dVFfH~s~l~~~g~~~~~~l~~G~~V~F~i~~~~ 73 (121)
.+.+|+|...+. +||=|+.- |+-+-|++.+..... ..+++||+|.+-+..-.
T Consensus 133 eiV~G~V~~v~~-~g~v~Vdi----G~~ea~LP~~E~ip~-----E~~~~Gd~ik~~V~~V~ 184 (341)
T TIGR01953 133 EIISGTVKRVNR-RGNLYVEL----GKTEGILPKKEQIPG-----EKFRIGDRIKAYVYEVR 184 (341)
T ss_pred CEEEEEEEEEec-CCcEEEEE----CCeEEEecHHHcCCC-----cCCCCCCEEEEEEEEEE
Confidence 367999999853 34323433 456899999988743 46899999999887644
No 124
>PRK00087 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed
Probab=42.71 E-value=2e+02 Score=25.94 Aligned_cols=67 Identities=19% Similarity=0.055 Sum_probs=44.7
Q ss_pred eeeeEEEEeeCCCCeEEEEecCCCCcccEEEEccccccCCCC-cccCCCCCCEEEEEEEECC--CCCceEEEEEEc
Q psy12844 13 YVSGVIQFFNKERGFGFINRIGDDGRKDYFFHFSEIQGGTDN-ILRAIKYSLLVIFDIGVTP--GGRREAVHIKIF 85 (121)
Q Consensus 13 m~~G~Vkwfn~~kGfGFI~~~~d~g~~dVFfH~s~l~~~g~~-~~~~l~~G~~V~F~i~~~~--kGk~~A~~V~~~ 85 (121)
.+.|+|+... .||+... -+++-+-|+|.+++...... ....++.||.|...+..-+ ++ .....+..+
T Consensus 565 ~v~g~V~~i~---~~G~fV~--l~~~i~Gli~~sel~~~~~~~~~~~~kvGd~V~vkV~~id~e~~-rI~lslk~~ 634 (647)
T PRK00087 565 IVLGKVVRIA---PFGAFVE--LEPGVDGLVHISQISWKRIDKPEDVLSEGEEVKAKILEVDPEEK-RIRLSIKEV 634 (647)
T ss_pred EEEEEEEEEE---CCeEEEE--ECCCCEEEEEhhhcCccccCCHhhcCCCCCEEEEEEEEEeCCCC-EEEEEEeec
Confidence 4789999975 4788776 44457899999998754211 1135799999999877754 34 444444433
No 125
>PRK07400 30S ribosomal protein S1; Reviewed
Probab=42.66 E-value=84 Score=25.89 Aligned_cols=53 Identities=13% Similarity=-0.075 Sum_probs=38.5
Q ss_pred eeeeeEEEEeeCCCCeEEEEecCCCCcccEEEEccccccCCCCcccCCCCCCEEEEEEEECC
Q psy12844 12 VYVSGVIQFFNKERGFGFINRIGDDGRKDYFFHFSEIQGGTDNILRAIKYSLLVIFDIGVTP 73 (121)
Q Consensus 12 ~m~~G~Vkwfn~~kGfGFI~~~~d~g~~dVFfH~s~l~~~g~~~~~~l~~G~~V~F~i~~~~ 73 (121)
....|+|+..+ .+|++.. -. +-+-|+|+|.+..... .....|+.|.+.+..-+
T Consensus 120 ~~V~g~V~~~~---~~G~~V~--l~-Gv~gfip~s~ls~~~~---~~~~vG~~i~~kVl~id 172 (318)
T PRK07400 120 ATVRSEVFATN---RGGALVR--IE-GLRGFIPGSHISTRKP---KEELVGEELPLKFLEVD 172 (318)
T ss_pred CEEEEEEEEEE---CCeEEEE--EC-CEEEEEEHHHcCccCC---ccccCCCEEEEEEEEEE
Confidence 45689999985 4677777 54 4578999999975322 33458999999987643
No 126
>PRK11712 ribonuclease G; Provisional
Probab=42.60 E-value=1.1e+02 Score=27.03 Aligned_cols=71 Identities=17% Similarity=0.187 Sum_probs=49.5
Q ss_pred eeeeEEEEeeCCCCeEEEEecCCCCcccEEEEccccccC----------CC---CcccCCCCCCEEEEEEEECC---CCC
Q psy12844 13 YVSGVIQFFNKERGFGFINRIGDDGRKDYFFHFSEIQGG----------TD---NILRAIKYSLLVIFDIGVTP---GGR 76 (121)
Q Consensus 13 m~~G~Vkwfn~~kGfGFI~~~~d~g~~dVFfH~s~l~~~----------g~---~~~~~l~~G~~V~F~i~~~~---kGk 76 (121)
.+.|+|+..-+.-.=-||+- ..+ +.-|+|++++... .. +.-..|++||.|-..+...+ +|-
T Consensus 41 IY~G~V~~v~pg~~AAFVdI--G~~-k~gFL~~~d~~~~~~~~~~~~~~~~~~~~i~~~l~~Gq~iLVQV~Ke~~~~KG~ 117 (489)
T PRK11712 41 IYKGRVSRVLPGMQAAFVDI--GLD-KAAFLHASDIVPHTECVAGEEQKQFVVRDISELVRQGQDIMVQVVKDPLGTKGA 117 (489)
T ss_pred EEEEEEeecCCCCceeEEee--CCC-ccEEEEhhhccchhhhcccccccccccccHHHhccCCCEEEEEEEeCCcCCCCC
Confidence 58899999988888899998 554 7999999998421 00 00023889999999999865 552
Q ss_pred ceEEEEEEcC
Q psy12844 77 REAVHIKIFD 86 (121)
Q Consensus 77 ~~A~~V~~~~ 86 (121)
.--.++.+.+
T Consensus 118 ~lT~~Isl~G 127 (489)
T PRK11712 118 RLTTDITLPS 127 (489)
T ss_pred eEEEEEEecc
Confidence 2333555544
No 127
>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=42.37 E-value=1.7e+02 Score=25.08 Aligned_cols=51 Identities=14% Similarity=-0.030 Sum_probs=36.7
Q ss_pred eeeeeEEEEeeCCCCeEEEEecCCCCcccEEEEccccccCCCCcccCCCCCCEEEEEEEE
Q psy12844 12 VYVSGVIQFFNKERGFGFINRIGDDGRKDYFFHFSEIQGGTDNILRAIKYSLLVIFDIGV 71 (121)
Q Consensus 12 ~m~~G~Vkwfn~~kGfGFI~~~~d~g~~dVFfH~s~l~~~g~~~~~~l~~G~~V~F~i~~ 71 (121)
....|+|...++ .|.+.. -.+..+-|+..+++.... ..+++||.|++.+..
T Consensus 20 ~~v~g~V~~i~~---~~~~v~--~g~k~~g~i~~~E~~~~~----~~~~vGd~i~~~V~~ 70 (516)
T TIGR00717 20 SIVKGTVVAINK---DTVFVD--VGLKSEGRIPKEEFLDAP----LEIQVGDEVEVYLDR 70 (516)
T ss_pred CEEEEEEEEEEC---CEEEEE--cCCCcEEEEEHHHhcCCc----cCCCCCCEEEEEEEE
Confidence 346899999964 344444 233457899999987654 368999999999874
No 128
>cd03470 Rieske_cytochrome_bc1 Iron-sulfur protein (ISP) component of the bc(1) complex family, Rieske domain; The Rieske domain is a [2Fe-2S] cluster binding domain involved in electron transfer. The bc(1) complex is a multisubunit enzyme found in many different organisms including uni- and multi-cellular eukaryotes, plants (in their mitochondria) and bacteria. The cytochrome bc(1) and b6f complexes are central components of the respiratory and photosynthetic electron transport chains, respectively, which carry out similar core electron and proton transfer steps. The bc(1) and b6f complexes share a common core structure of three catalytic subunits: cyt b, the Rieske ISP, and either a cyt c1 in the bc(1) complex or cyt f in the b6f complex, which are arranged in an integral membrane-bound dimeric complex. While the core of the b6f complex is similar to that of the bc(1) complex, the domain arrangement outside the core and the complement of prosthetic groups are strikingly different.
Probab=42.37 E-value=27 Score=25.03 Aligned_cols=16 Identities=25% Similarity=0.588 Sum_probs=12.5
Q ss_pred ccccccCCCccccccc
Q psy12844 95 RTCSVDCPCRDSKLNV 110 (121)
Q Consensus 95 ~~~~~~~~~~~s~~~~ 110 (121)
....+.||||+|.=..
T Consensus 82 ~~~~~~CPcHgs~Fdl 97 (126)
T cd03470 82 DYGGFFCPCHGSHYDA 97 (126)
T ss_pred CCCEEEecCcCCEECC
Confidence 4567999999997554
No 129
>COG2265 TrmA SAM-dependent methyltransferases related to tRNA (uracil-5-)-methyltransferase [Translation, ribosomal structure and biogenesis]
Probab=42.12 E-value=2.2e+02 Score=24.58 Aligned_cols=59 Identities=17% Similarity=0.131 Sum_probs=45.7
Q ss_pred eeeeEEEEeeCCCCeEEEEecCCCCcccEEEEccccccCCCCcccCCCCCCEEEEEEEECCCCCceEEEEEEcCCcc
Q psy12844 13 YVSGVIQFFNKERGFGFINRIGDDGRKDYFFHFSEIQGGTDNILRAIKYSLLVIFDIGVTPGGRREAVHIKIFDTRL 89 (121)
Q Consensus 13 m~~G~Vkwfn~~kGfGFI~~~~d~g~~dVFfH~s~l~~~g~~~~~~l~~G~~V~F~i~~~~kGk~~A~~V~~~~~~~ 89 (121)
....+|+..+ ..|.|.... ++ .-||+ ...-+|+.|+..+....+....|..+.++..++
T Consensus 4 ~~~~~I~~l~-~~G~Gva~~--~~--~~vfV-------------p~alPge~v~~~~~~~~~~~~~a~~~~i~~~Sp 62 (432)
T COG2265 4 IIEVTIEDLG-HNGEGVARH--DG--KVVFV-------------PGALPGEEVEVRVTKVKKKYAEAKLVKVLEASP 62 (432)
T ss_pred eEEEEEEEcC-CCCeeEEEe--cC--ceEEe-------------CCCCCCcEEEEEEEeccccceeeEeeeeccCCh
Confidence 4678999987 689999988 53 36773 235689999999999988878888888776543
No 130
>COG5569 Uncharacterized conserved protein [Function unknown]
Probab=42.07 E-value=28 Score=24.89 Aligned_cols=27 Identities=22% Similarity=0.229 Sum_probs=19.8
Q ss_pred ccCCCCCCEEEEEEEECCCCCceEEEEE
Q psy12844 56 LRAIKYSLLVIFDIGVTPGGRREAVHIK 83 (121)
Q Consensus 56 ~~~l~~G~~V~F~i~~~~kGk~~A~~V~ 83 (121)
+..|++||.|+|..+.- +|++.-.+|.
T Consensus 81 lsglKeGdkV~fvferv-~gk~tv~qvk 107 (108)
T COG5569 81 LSGLKEGDKVEFVFERV-NGKLTVQQVK 107 (108)
T ss_pred hhccccCCcEEEEEEee-CCEEEEEEec
Confidence 46789999999998875 5546555543
No 131
>COG2996 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only]
Probab=41.99 E-value=1.9e+02 Score=24.14 Aligned_cols=52 Identities=15% Similarity=0.086 Sum_probs=37.7
Q ss_pred CCCeEEEEecCCCCcccEEEEccccccCCCCcccCCCCCCEEEEEEEECCCCCceEE
Q psy12844 24 ERGFGFINRIGDDGRKDYFFHFSEIQGGTDNILRAIKYSLLVIFDIGVTPGGRREAV 80 (121)
Q Consensus 24 ~kGfGFI~~~~d~g~~dVFfH~s~l~~~g~~~~~~l~~G~~V~F~i~~~~kGk~~A~ 80 (121)
.+.-|.-..+|. .+|+++-.+++...-- -.|++||++-+.+..+.+||..|.
T Consensus 85 ~~~lGaFlD~Gl--~KDl~vp~~elp~~~~---~wpq~Gd~l~v~l~~Dkk~Ri~g~ 136 (287)
T COG2996 85 NKDLGAFLDWGL--PKDLLVPLDELPTLKS---LWPQKGDKLLVYLYVDKKGRIWGT 136 (287)
T ss_pred cCCcceEEecCC--Ccceeeehhhcccccc---cCCCCCCEEEEEEEEccCCcEEEE
Confidence 345554444333 2799999999986421 369999999999999999965553
No 132
>PRK05054 exoribonuclease II; Provisional
Probab=41.48 E-value=1.2e+02 Score=27.60 Aligned_cols=34 Identities=15% Similarity=0.015 Sum_probs=25.2
Q ss_pred eeeeEEEEeeCCCCeEEEEecCCCCcccEEEEcccccc
Q psy12844 13 YVSGVIQFFNKERGFGFINRIGDDGRKDYFFHFSEIQG 50 (121)
Q Consensus 13 m~~G~Vkwfn~~kGfGFI~~~~d~g~~dVFfH~s~l~~ 50 (121)
...|+|... ..|||...+ ++.+-+.|+|.++|..
T Consensus 564 ~f~g~I~~v---~~~G~fV~l-~~~~veglV~~~~l~~ 597 (644)
T PRK05054 564 RFAAEIIDI---SRGGMRVRL-LENGAVAFIPASFLHA 597 (644)
T ss_pred EEEEEEEee---ecCcEEEEE-eCCceEEEEEccccCC
Confidence 478999876 457877664 4455789999999864
No 133
>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=40.91 E-value=86 Score=21.35 Aligned_cols=57 Identities=9% Similarity=0.060 Sum_probs=38.0
Q ss_pred eeeeEEEEeeCCCCeEEEEecCCCCcccEEEEccccccCC--------------------CCcccCCCCCCEEEEEEEEC
Q psy12844 13 YVSGVIQFFNKERGFGFINRIGDDGRKDYFFHFSEIQGGT--------------------DNILRAIKYSLLVIFDIGVT 72 (121)
Q Consensus 13 m~~G~Vkwfn~~kGfGFI~~~~d~g~~dVFfH~s~l~~~g--------------------~~~~~~l~~G~~V~F~i~~~ 72 (121)
...|+|+.-. .+|.... ..++-+-|+|++++...- .+....+++||.|.+.+..-
T Consensus 6 vV~G~V~~v~---~~gl~v~--L~~g~~G~v~~seis~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~vGd~V~~kVi~~ 80 (100)
T cd05693 6 LVLGQVKEIT---KLDLVIS--LPNGLTGYVPITNISDAYTERLEELDEESEEEDDEEELPDLEDLFSVGQLVRCKVVSL 80 (100)
T ss_pred EEEEEEEEEc---CCCEEEE--CCCCcEEEEEHHHhhHHHHHHHHHhhhhccccccccccCCHHHhccCCCEEEEEEEEc
Confidence 3589999963 4455555 344579999999996420 00113578999999998885
Q ss_pred CC
Q psy12844 73 PG 74 (121)
Q Consensus 73 ~k 74 (121)
++
T Consensus 81 d~ 82 (100)
T cd05693 81 DK 82 (100)
T ss_pred cC
Confidence 54
No 134
>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=40.82 E-value=1.2e+02 Score=22.51 Aligned_cols=54 Identities=19% Similarity=0.102 Sum_probs=36.8
Q ss_pred eeeeEEEEeeCCCCeEEEEecCCCCcccEEEEccccccCCCC------------cccCCCCCCEEEEEEEEC
Q psy12844 13 YVSGVIQFFNKERGFGFINRIGDDGRKDYFFHFSEIQGGTDN------------ILRAIKYSLLVIFDIGVT 72 (121)
Q Consensus 13 m~~G~Vkwfn~~kGfGFI~~~~d~g~~dVFfH~s~l~~~g~~------------~~~~l~~G~~V~F~i~~~ 72 (121)
...|+|+.-++ +|+... -. .-+-++|.+++....+. ....++.||.|.|.+..-
T Consensus 84 vv~G~V~~v~~---~GifV~--lg-~~~gi~~~~~l~~~~~~~d~~~~~~~~~~~~~~~~~Gd~VrvrV~~v 149 (179)
T TIGR00448 84 IVEGEVIEIVE---FGAFVS--LG-PFDGLFHVSQVTDDYCYYDPKESALIGKETKKVLDEGDKVRARIVAL 149 (179)
T ss_pred EEEEEEEEEEe---eEEEEE--eC-CceEEEEcHHhCCCceEEccccceEEEccCCeEEcCCCEEEEEEEEE
Confidence 46789988754 898888 53 36788899888643220 013577888888887654
No 135
>PRK06676 rpsA 30S ribosomal protein S1; Reviewed
Probab=40.71 E-value=2.1e+02 Score=23.66 Aligned_cols=71 Identities=14% Similarity=0.110 Sum_probs=45.7
Q ss_pred eeeeEEEEeeCCCCeEEEEecCCCCcccEEEEccccccCCCC-cccCCCCCCEEEEEEEECC--CCCceEEEEEEcCCcc
Q psy12844 13 YVSGVIQFFNKERGFGFINRIGDDGRKDYFFHFSEIQGGTDN-ILRAIKYSLLVIFDIGVTP--GGRREAVHIKIFDTRL 89 (121)
Q Consensus 13 m~~G~Vkwfn~~kGfGFI~~~~d~g~~dVFfH~s~l~~~g~~-~~~~l~~G~~V~F~i~~~~--kGk~~A~~V~~~~~~~ 89 (121)
.+.|+|+... .||+... .+++-+-++|.+.+...... .-..++.||.|...+..-+ ++ .....+......+
T Consensus 280 ~v~g~V~~i~---~~G~fV~--l~~gi~Glv~~se~~~~~~~~~~~~~~~Gd~v~v~V~~id~e~~-~i~ls~k~~~~~~ 353 (390)
T PRK06676 280 VIEGTVKRLT---DFGAFVE--VLPGVEGLVHISQISHKHIATPSEVLEEGQEVKVKVLEVNEEEK-RISLSIKALEEAP 353 (390)
T ss_pred EEEEEEEEEe---CceEEEE--ECCCCeEEEEhHHcCccccCChhhccCCCCEEEEEEEEEECCCC-EEEEEEEecccCh
Confidence 4789999874 4888776 44446789999998643210 1134799999998877754 34 4444555444333
No 136
>KOG0149|consensus
Probab=39.35 E-value=19 Score=29.35 Aligned_cols=26 Identities=27% Similarity=0.701 Sum_probs=17.4
Q ss_pred ccccceeeeeeeEEEEeeCCCCeEEEEe
Q psy12844 5 LGKIIEEVYVSGVIQFFNKERGFGFINR 32 (121)
Q Consensus 5 ~~~~~~~~m~~G~Vkwfn~~kGfGFI~~ 32 (121)
.|.|+|-..+.-+-. ...|||||++-
T Consensus 36 fGeI~eavvitd~~t--~rskGyGfVTf 61 (247)
T KOG0149|consen 36 FGEIVEAVVITDKNT--GRSKGYGFVTF 61 (247)
T ss_pred hCceEEEEEEeccCC--ccccceeeEEe
Confidence 578888765432222 33689999997
No 137
>PRK13254 cytochrome c-type biogenesis protein CcmE; Reviewed
Probab=38.93 E-value=1.6e+02 Score=21.86 Aligned_cols=68 Identities=15% Similarity=0.092 Sum_probs=51.0
Q ss_pred eeEEEEeeCCCCeEEEEecCCCCcccEEEEccccccCCCCcccCCCCCCEEEEEEEECCCCCceEEEEEEcCCccccc
Q psy12844 15 SGVIQFFNKERGFGFINRIGDDGRKDYFFHFSEIQGGTDNILRAIKYSLLVIFDIGVTPGGRREAVHIKIFDTRLYLE 92 (121)
Q Consensus 15 ~G~Vkwfn~~kGfGFI~~~~d~g~~dVFfH~s~l~~~g~~~~~~l~~G~~V~F~i~~~~kGk~~A~~V~~~~~~~~~~ 92 (121)
.|.|.|- +...+=|... |.+ ..|=++++.+..+. .++|+.|.-+=.-.++|...|.+|..-.++.+.+
T Consensus 62 ~gSi~~~-~~~~~~F~lt--D~~-~~i~V~Y~G~lPd~------F~eg~~VVv~G~~~~~g~F~A~~vLaKc~skY~p 129 (148)
T PRK13254 62 KGSVQRG-DGLTVRFVVT--DGN-ATVPVVYTGILPDL------FREGQGVVAEGRLQDGGVFVADEVLAKHDENYMP 129 (148)
T ss_pred cCcEEeC-CCCEEEEEEE--eCC-eEEEEEECCCCCcc------ccCCCEEEEEEEECCCCeEEEEEEEecCCCCCCC
Confidence 3444443 5567889988 664 68889999887554 5899999988777777779999998887766643
No 138
>PRK08563 DNA-directed RNA polymerase subunit E'; Provisional
Probab=38.37 E-value=1.2e+02 Score=22.67 Aligned_cols=55 Identities=24% Similarity=0.172 Sum_probs=38.0
Q ss_pred eeeeEEEEeeCCCCeEEEEecCCCCcccEEEEccccccCCCC------------cccCCCCCCEEEEEEEECC
Q psy12844 13 YVSGVIQFFNKERGFGFINRIGDDGRKDYFFHFSEIQGGTDN------------ILRAIKYSLLVIFDIGVTP 73 (121)
Q Consensus 13 m~~G~Vkwfn~~kGfGFI~~~~d~g~~dVFfH~s~l~~~g~~------------~~~~l~~G~~V~F~i~~~~ 73 (121)
...|+|+.-+ .+|+... -+ .-+.|+|.+++...... ....++.||.|.|.+....
T Consensus 84 Vv~g~V~~v~---~~Gi~V~--lg-~~~g~v~~~~l~~~~~~~d~~~~~~~~~~~~~~i~~Gd~VrvrV~~v~ 150 (187)
T PRK08563 84 VVEGEVVEVV---EFGAFVR--IG-PVDGLLHISQIMDDYISYDPKNGRLIGKESKRVLKVGDVVRARIVAVS 150 (187)
T ss_pred EEEEEEEEEE---ccEEEEE--Ee-CceEEEEcHHcCCCceEEccccceEEEccCCeEEcCCCEEEEEEEEEE
Confidence 4689999885 4788877 43 36899999998644210 0134688999999887643
No 139
>COG1093 SUI2 Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis]
Probab=36.92 E-value=70 Score=26.38 Aligned_cols=61 Identities=20% Similarity=0.220 Sum_probs=41.2
Q ss_pred eeeeeeEEEEeeCCCCeEEEEecCCCCcccEEEEccccccCCCC-cccCCCCCCEEEEEEEECCC
Q psy12844 11 EVYVSGVIQFFNKERGFGFINRIGDDGRKDYFFHFSEIQGGTDN-ILRAIKYSLLVIFDIGVTPG 74 (121)
Q Consensus 11 ~~m~~G~Vkwfn~~kGfGFI~~~~d~g~~dVFfH~s~l~~~g~~-~~~~l~~G~~V~F~i~~~~k 74 (121)
-...-|||+.- ..||--..+..-++.+=|+|+|.+...-.. ....+++|+.|.+.+-.-+.
T Consensus 12 GEiVv~tV~~V---~~~GAyv~L~EY~g~Eg~ihiSEvas~wVknIrd~vkegqkvV~kVlrVd~ 73 (269)
T COG1093 12 GEIVVGTVKQV---ADYGAYVELDEYPGKEGFIHISEVASGWVKNIRDYVKEGQKVVAKVLRVDP 73 (269)
T ss_pred CcEEEEEEEEe---eccccEEEeeccCCeeeeEEHHHHHHHHHHHHHHHhhcCCeEEEEEEEEcC
Confidence 34568999986 455544332233567999999999754211 23568999999999877543
No 140
>PF01336 tRNA_anti-codon: OB-fold nucleic acid binding domain; InterPro: IPR004365 The OB-fold (oligonucleotide/oligosaccharide-binding fold) is found in all three kingdoms and its common architecture presents a binding face that has adapted to bind different ligands. The OB-fold is a five/six-stranded closed beta-barrel formed by 70-80 amino acid residues. The strands are connected by loops of varying length which form the functional appendages of the protein. The majority of OB-fold proteins use the same face for ligand binding or as an active site. Different OB-fold proteins use this 'fold-related binding face' to, variously, bind oligosaccharides, oligonucleotides, proteins, metal ions and catalytic substrates. This entry contains OB-fold domains that bind to nucleic acids []. It includes the anti-codon binding domain of lysyl, aspartyl, and asparaginyl-tRNA synthetases (See IPR004364 from INTERPRO). Aminoacyl-tRNA synthetases catalyse the addition of an amino acid to the appropriate tRNA molecule 6.1.1 from EC. This domain is found in RecG helicase involved in DNA repair. Replication factor A is a heterotrimeric complex, that contains a subunit in this family [, ]. This domain is also found at the C terminus of bacterial DNA polymerase III alpha chain.; GO: 0003676 nucleic acid binding; PDB: 1BBU_A 1KRS_A 1BBW_A 1KRT_A 1EQR_B 1IL2_B 1C0A_A 3KFU_A 1EOV_A 1ASY_A ....
Probab=36.90 E-value=51 Score=19.88 Aligned_cols=52 Identities=17% Similarity=0.128 Sum_probs=33.7
Q ss_pred eeeEEEEe-eCCCCeEEEEecCCCCcccEEEEccc--cccCCCCcccCCCCCCEEEEEEEE
Q psy12844 14 VSGVIQFF-NKERGFGFINRIGDDGRKDYFFHFSE--IQGGTDNILRAIKYSLLVIFDIGV 71 (121)
Q Consensus 14 ~~G~Vkwf-n~~kGfGFI~~~~d~g~~dVFfH~s~--l~~~g~~~~~~l~~G~~V~F~i~~ 71 (121)
..|+|..- ...+++-|++- .|+...+-+.+-. .... . ..|++|+.|...-..
T Consensus 3 v~G~V~~~~~~~~~~~~~~l--~D~tg~i~~~~~~~~~~~~-~---~~l~~g~~v~v~G~v 57 (75)
T PF01336_consen 3 VEGRVTSIRRSGGKIVFFTL--EDGTGSIQVVFFNEEYERF-R---EKLKEGDIVRVRGKV 57 (75)
T ss_dssp EEEEEEEEEEEETTEEEEEE--EETTEEEEEEEETHHHHHH-H---HTS-TTSEEEEEEEE
T ss_pred EEEEEEEEEcCCCCEEEEEE--EECCccEEEEEccHHhhHH-h---hcCCCCeEEEEEEEE
Confidence 46777777 77889999998 5554454444443 2222 1 679999999988443
No 141
>TIGR00638 Mop molybdenum-pterin binding domain. This model describes a multigene family of molybdenum-pterin binding proteins of about 70 amino acids in Clostridium pasteurianum, as a tandemly-repeated domain C-terminal to an unrelated domain in ModE, a molybdate transport gene repressor of E. coli, and in single or tandemly paired domains in several related proteins.
Probab=36.61 E-value=98 Score=18.68 Aligned_cols=53 Identities=9% Similarity=-0.109 Sum_probs=32.5
Q ss_pred eeeeEEEEeeCCCCeEEEEecCCC-CcccEEEEccccccCCCCcccCCCCCCEEEEEEEE
Q psy12844 13 YVSGVIQFFNKERGFGFINRIGDD-GRKDYFFHFSEIQGGTDNILRAIKYSLLVIFDIGV 71 (121)
Q Consensus 13 m~~G~Vkwfn~~kGfGFI~~~~d~-g~~dVFfH~s~l~~~g~~~~~~l~~G~~V~F~i~~ 71 (121)
...|+|.+......+--|.- +- ++..+...++.=.-.. -.|++|++|...+..
T Consensus 8 ~l~g~I~~i~~~g~~~~v~l--~~~~~~~l~a~i~~~~~~~----l~l~~G~~v~~~ik~ 61 (69)
T TIGR00638 8 QLKGKVVAIEDGDVNAEVDL--LLGGGTKLTAVITLESVAE----LGLKPGKEVYAVIKA 61 (69)
T ss_pred EEEEEEEEEEECCCeEEEEE--EECCCCEEEEEecHHHHhh----CCCCCCCEEEEEEEC
Confidence 47899999976555444544 32 3335665554432223 258999999877654
No 142
>PRK00087 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed
Probab=35.87 E-value=2.2e+02 Score=25.73 Aligned_cols=65 Identities=9% Similarity=-0.005 Sum_probs=40.7
Q ss_pred eeeeeeeEEEEeeCCCCeEEEEecCCCCcccEEEEccccccCCCC-cccCCCCCCEEEEEEEE--CCCCCceE
Q psy12844 10 EEVYVSGVIQFFNKERGFGFINRIGDDGRKDYFFHFSEIQGGTDN-ILRAIKYSLLVIFDIGV--TPGGRREA 79 (121)
Q Consensus 10 ~~~m~~G~Vkwfn~~kGfGFI~~~~d~g~~dVFfH~s~l~~~g~~-~~~~l~~G~~V~F~i~~--~~kGk~~A 79 (121)
+-....|+|...++ .|.+.. ..+..+-|++.+++...... +...+++|+.|++.+.. ..+|+..+
T Consensus 302 ~G~iV~G~V~~v~~---~gv~Vd--ig~~~~G~lp~~els~~~~~~~~~~~~vGd~V~v~V~~vd~~~g~i~L 369 (647)
T PRK00087 302 RGDIVKGTVVSVNE---NEVFVD--VGYKSEGVIPLRELTLDEISSLKESVKVGDEIEVKVLKLEDEDGYVVL 369 (647)
T ss_pred CCCEEEEEEEEEEC---CEEEEE--ECCCeEEEEEHHHhcccccCChhhccCCCCEEEEEEEEEECCCCcEEE
Confidence 33456899999964 234443 23335789999988633221 11457899999999876 34564433
No 143
>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=35.74 E-value=40 Score=22.00 Aligned_cols=53 Identities=15% Similarity=0.194 Sum_probs=31.2
Q ss_pred eeeeEEEEeeCCCCeEEEEecC-CCCcccEEEEccccc-cCCCCcccCCCCCCEEEEEE
Q psy12844 13 YVSGVIQFFNKERGFGFINRIG-DDGRKDYFFHFSEIQ-GGTDNILRAIKYSLLVIFDI 69 (121)
Q Consensus 13 m~~G~Vkwfn~~kGfGFI~~~~-d~g~~dVFfH~s~l~-~~g~~~~~~l~~G~~V~F~i 69 (121)
+..|+|.......++|-...+. .++-.-+|.|.+.+. ..| ..++.||.+-..-
T Consensus 19 ~~~G~V~~~~~~~~~g~~V~i~~~~g~~~~y~~l~~~~v~~G----~~V~~G~~IG~~g 73 (96)
T PF01551_consen 19 PADGKVVFVGEDPGYGNYVIIQHGNGYITVYGHLDSVSVKVG----DRVKAGQVIGTVG 73 (96)
T ss_dssp SSSEEEEEEEEETTTEEEEEEEETTSEEEEEEEESEESS-TT----SEE-TTCEEEEEB
T ss_pred CccEEEEEEEeccCCccEEEEEeCCcCCEEEeccccccceec----ccccCCCEEEecC
Confidence 3689999988877777655521 222345778877753 122 4566666655443
No 144
>COG1095 RPB7 DNA-directed RNA polymerase, subunit E' [Transcription]
Probab=34.56 E-value=83 Score=24.53 Aligned_cols=55 Identities=24% Similarity=0.125 Sum_probs=36.7
Q ss_pred eeeeEEEEeeCCCCeEEEEecCCCCcccEEEEccccccCCCC------------cccCCCCCCEEEEEEEECC
Q psy12844 13 YVSGVIQFFNKERGFGFINRIGDDGRKDYFFHFSEIQGGTDN------------ILRAIKYSLLVIFDIGVTP 73 (121)
Q Consensus 13 m~~G~Vkwfn~~kGfGFI~~~~d~g~~dVFfH~s~l~~~g~~------------~~~~l~~G~~V~F~i~~~~ 73 (121)
...|.|..- ..||+-.. -. ..|.|+|.+.+-..-+. +-..++.|+.|.+.+....
T Consensus 84 VV~GeVv~~---~~~G~fV~--ig-p~dglvh~sqi~dd~~~~d~~~~~~~g~~tk~~i~~gd~VR~RIv~~s 150 (183)
T COG1095 84 VVEGEVVEV---VEFGAFVR--IG-PLDGLVHVSQIMDDYIDYDEKNKVLIGEETKRVLKVGDKVRARIVGVS 150 (183)
T ss_pred EEEEEEEEE---eecceEEE--ec-cccccccHhhccCcccccCcccceeeecccceEEecCCEEEEEEEEEe
Confidence 457888875 56888777 33 46899999998655110 1135777888888777644
No 145
>TIGR01416 Rieske_proteo ubiquinol-cytochrome c reductase, iron-sulfur subunit. Most members of this family have a recognizable twin-arginine translocation (tat) signal sequence (DeltaPh-dependent translocation in chloroplast) for transport across the membrane with the 2Fe-2S group already bound. These signal sequences include a motif resembling RRxFLK before the transmembrane helix.
Probab=33.17 E-value=51 Score=24.89 Aligned_cols=14 Identities=29% Similarity=0.721 Sum_probs=10.6
Q ss_pred ccccCCCccccccc
Q psy12844 97 CSVDCPCRDSKLNV 110 (121)
Q Consensus 97 ~~~~~~~~~s~~~~ 110 (121)
.-+.||||.|.=..
T Consensus 132 ~~~~CPcHgs~Fd~ 145 (174)
T TIGR01416 132 GGFFCPCHGSHYDT 145 (174)
T ss_pred CEEEeCCCCCEECC
Confidence 35889999997544
No 146
>PF03657 UPF0113: Uncharacterised protein family (UPF0113); InterPro: IPR005155 This entry represents PUA (PseudoUridine synthase and Archaeosine transglycosylase) domain containing proteins such as the ribosomal biogenesis factor NIP7 [, ]. PUA domains are predicted to bind RNA molecules with complex folded structures []. NIP7 is required for efficient 60S ribosome subunit biogenesis and has been shown to interact with another essential nucleolar protein, Nop8p, and the exosome subunit Rrp43p. These three proteins are required for 60S subunit synthesis and may be part of a dynamic complex involved in this process.; PDB: 1T5Y_A 1SQW_A 2P38_A.
Probab=32.92 E-value=15 Score=27.83 Aligned_cols=43 Identities=23% Similarity=0.451 Sum_probs=27.0
Q ss_pred CcccccccceeeeeeeEEEEeeCCC---CeEEEEecCCCCcccEEEEcccc
Q psy12844 1 MKAHLGKIIEEVYVSGVIQFFNKER---GFGFINRIGDDGRKDYFFHFSEI 48 (121)
Q Consensus 1 ~~~~~~~~~~~~m~~G~Vkwfn~~k---GfGFI~~~~d~g~~dVFfH~s~l 48 (121)
+|+|+++|-|+.... |.=||... |||.+.. +.+ .-+.+|+.|+
T Consensus 111 ~ks~i~~i~e~~~~~--VvV~n~~d~~LGfG~~~~--~~~-~~vv~~~~Di 156 (162)
T PF03657_consen 111 LKSSIGRITEDTPQN--VVVYNMNDVPLGFGCRKS--DPD-GKVVKNQADI 156 (162)
T ss_dssp EGGGEEEEETTS-TC--EEEEETTS-EEEEEECST--CHC-CCCCECCEEG
T ss_pred hHhhcEEecCCCCce--EEEEeCCCCeEEEEEecc--CCC-CEEEEEcCcc
Confidence 478999999986444 55555443 6775544 433 3566687776
No 147
>PLN00059 PsbP domain-containing protein 1; Provisional
Probab=32.27 E-value=39 Score=28.03 Aligned_cols=29 Identities=17% Similarity=0.358 Sum_probs=19.8
Q ss_pred eEEEEeeCCCCeEEEEecC----CCCcccEEEE
Q psy12844 16 GVIQFFNKERGFGFINRIG----DDGRKDYFFH 44 (121)
Q Consensus 16 G~Vkwfn~~kGfGFI~~~~----d~g~~dVFfH 44 (121)
|-=..-|...||.|.-|.| ...|.|||||
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 4333446677999988865 3446789887
No 148
>PRK13168 rumA 23S rRNA m(5)U1939 methyltransferase; Reviewed
Probab=31.50 E-value=3.2e+02 Score=23.13 Aligned_cols=61 Identities=15% Similarity=0.159 Sum_probs=44.4
Q ss_pred eeeeeEEEEeeCCCCeEEEEecCCCCcccEEEEccccccCCCCcccCCCCCCEEEEEEEECCCCCceEEEEEEcCCccc
Q psy12844 12 VYVSGVIQFFNKERGFGFINRIGDDGRKDYFFHFSEIQGGTDNILRAIKYSLLVIFDIGVTPGGRREAVHIKIFDTRLY 90 (121)
Q Consensus 12 ~m~~G~Vkwfn~~kGfGFI~~~~d~g~~dVFfH~s~l~~~g~~~~~~l~~G~~V~F~i~~~~kGk~~A~~V~~~~~~~~ 90 (121)
.+...+|..+. ..|+|.-.. + | .-||+ ...-+||.|+..+....++...|.-+.++..++.
T Consensus 14 ~~~~l~i~~l~-~~G~Gv~~~--~-~-~~vfV-------------~~~lPGe~v~v~i~~~~~~~~~~~~~~vl~~sp~ 74 (443)
T PRK13168 14 QIITVTIESLD-HDGRGVARH--N-G-KTVFI-------------EGALPGERVEVQVTEDKKQYARAKVVRILKPSPE 74 (443)
T ss_pred cEEEEEEEEcC-CCCceEEEE--C-C-EEEEe-------------CCCCCCCEEEEEEEEecCcEEEEEEEEEecCCcc
Confidence 34578899987 799999776 4 2 46774 2246999999999987666577877777765443
No 149
>cd03473 Rieske_CMP_Neu5Ac_hydrolase_N Cytidine monophosphate-N-acetylneuraminic acid (CMP Neu5Ac) hydroxylase family, N-terminal Rieske domain; The Rieske domain is a [2Fe-2S] cluster binding domain involved in electron transfer. CMP Neu5Ac hydroxylase is the key enzyme for the synthesis of N-glycolylneuraminic acid (NeuGc) from N-acetylneuraminic acid (Neu5Ac), NeuGc and Neu5Ac are members of a family of cell surface sugars called sialic acids. All mammals except humans have both NeuGc variants on their cell surfaces. In humans, the gene encoding CMP Neu5Ac hydroxylase has a mutation within its coding region that abolishes NeuGc production.
Probab=31.25 E-value=58 Score=23.17 Aligned_cols=56 Identities=18% Similarity=0.116 Sum_probs=32.6
Q ss_pred cCCCCCCEEEEEE-------EECCCCCceEEEEEEcCCccccc----ccccccccCCCccccccccc
Q psy12844 57 RAIKYSLLVIFDI-------GVTPGGRREAVHIKIFDTRLYLE----DLRTCSVDCPCRDSKLNVKT 112 (121)
Q Consensus 57 ~~l~~G~~V~F~i-------~~~~kGk~~A~~V~~~~~~~~~~----~~~~~~~~~~~~~s~~~~~~ 112 (121)
..|.+|....+.+ .-..+|++.|.+=.=.....+++ ++...-|.||.|+.+-+..+
T Consensus 15 ~eL~~G~~~~v~v~~g~~I~V~~~~G~~~A~~n~CpH~g~pL~~g~g~~~g~~V~CP~Hg~~FDLrT 81 (107)
T cd03473 15 ANLKEGINFFRNKEDGKKYIIYKSKSELKACKNQCKHQGGLFIKDIEDLDGRTVRCTKHNWKLDVST 81 (107)
T ss_pred hcCCCCceEEEEecCCcEEEEEEECCEEEEEcCCCCCCCccccCCcceEeCCEEEeCCCCCEEEcCC
Confidence 4566676666666 11235556665544333333433 35566789999988766654
No 150
>COG4942 Membrane-bound metallopeptidase [Cell division and chromosome partitioning]
Probab=31.15 E-value=48 Score=28.93 Aligned_cols=58 Identities=17% Similarity=0.264 Sum_probs=36.5
Q ss_pred ccccccceeeeeeeEEEEeeCCCCeEEEEecCCCCccc--EEEEccccc-cCCCCcccCCCCCCEEE
Q psy12844 3 AHLGKIIEEVYVSGVIQFFNKERGFGFINRIGDDGRKD--YFFHFSEIQ-GGTDNILRAIKYSLLVI 66 (121)
Q Consensus 3 ~~~~~~~~~~m~~G~Vkwfn~~kGfGFI~~~~d~g~~d--VFfH~s~l~-~~g~~~~~~l~~G~~V~ 66 (121)
+-+|-+|.. ..-|+|.+=+.-+|||.+... |.|+.+ ||-+...|. ..| ..+..|++|-
T Consensus 328 a~~Ga~V~A-~AdG~VvyA~~l~GYG~vvIl-dhG~gy~slyg~~~~i~v~~G----~~V~AGepIa 388 (420)
T COG4942 328 ASAGATVKA-IADGRVVYADWLRGYGLVVIL-DHGGGYHSLYGGNQSILVNPG----QFVKAGEPIA 388 (420)
T ss_pred cCCCCeeee-ecCceEEechhhccCceEEEE-EcCCccEEEecccceeeecCC----CEeecCCchh
Confidence 456777776 478999998999999999885 444333 554444442 233 2444555543
No 151
>cd03477 Rieske_YhfW_C YhfW family, C-terminal Rieske domain; YhfW is a protein of unknown function with an N-terminal DadA-like (glycine/D-amino acid dehydrogenase) domain and a C-terminal Rieske domain. The Rieske domain is a [2Fe-2S] cluster binding domain involved in electron transfer. It is commonly found in Rieske non-heme iron oxygenase (RO) systems such as naphthalene and biphenyl dioxygenases, as well as in plant/cyanobacterial chloroplast b6f and mitochondrial cytochrome bc(1) complexes. YhfW is found in bacteria, some eukaryotes and archaea.
Probab=29.20 E-value=1e+02 Score=20.51 Aligned_cols=13 Identities=46% Similarity=1.040 Sum_probs=10.4
Q ss_pred ccccCCCcccccc
Q psy12844 97 CSVDCPCRDSKLN 109 (121)
Q Consensus 97 ~~~~~~~~~s~~~ 109 (121)
..+.||+|.|+=+
T Consensus 54 ~~i~CP~Hg~~Fd 66 (91)
T cd03477 54 KSWDCPCHGSRFS 66 (91)
T ss_pred CEEECCCCCCEEC
Confidence 4689999998755
No 152
>TIGR02377 MocE_fam_FeS Rieske [2Fe-2S] domain protein, MocE subfamily. This model describes a subfamily of the Rieske-like [2Fe-2S] family of ferredoxins that includes MocE, part of the rhizopine (3-O-methyl-scyllo-inosamine) catabolic cluster in Rhizobium. Members of this family are related to, yet distinct from, the small subunit of nitrite reductase [NAD(P)H].
Probab=28.61 E-value=83 Score=21.08 Aligned_cols=38 Identities=13% Similarity=0.111 Sum_probs=21.8
Q ss_pred CCCceEEEEEEcCCccccc--ccccccccCCCcccccccc
Q psy12844 74 GGRREAVHIKIFDTRLYLE--DLRTCSVDCPCRDSKLNVK 111 (121)
Q Consensus 74 kGk~~A~~V~~~~~~~~~~--~~~~~~~~~~~~~s~~~~~ 111 (121)
+|+..|.+-.=.....+++ .+.-..|.||.|++.=+..
T Consensus 33 ~g~~~A~~~~CpH~g~~L~~G~~~~~~i~CP~Hg~~Fdl~ 72 (101)
T TIGR02377 33 DDQYYATDGLCTHEYAHLADGLVMDTTVECPKHAGCFDYR 72 (101)
T ss_pred CCEEEEEcCcCCCCCCCCCCCEEcCCEEECCccCCEEECC
Confidence 4445554433333333444 4445679999998876654
No 153
>cd03528 Rieske_RO_ferredoxin Rieske non-heme iron oxygenase (RO) family, Rieske ferredoxin component; composed of the Rieske ferredoxin component of some three-component RO systems including biphenyl dioxygenase (BPDO) and carbazole 1,9a-dioxygenase (CARDO). The RO family comprise a large class of aromatic ring-hydroxylating dioxygenases found predominantly in microorganisms. These enzymes enable microorganisms to tolerate and even exclusively utilize aromatic compounds for growth. ROs consist of two or three components: reductase, oxygenase, and ferredoxin (in some cases) components. The ferredoxin component contains either a plant-type or Rieske-type [2Fe-2S] cluster. The Rieske ferredoxin component in this family carries an electron from the RO reductase component to the terminal RO oxygenase component. BPDO degrades biphenyls and polychlorinated biphenyls. BPDO ferredoxin (BphF) has structural features consistent with a minimal and perhaps archetypical Rieske protein in that the in
Probab=28.33 E-value=70 Score=20.81 Aligned_cols=18 Identities=11% Similarity=0.630 Sum_probs=12.6
Q ss_pred cccccccCCCcccccccc
Q psy12844 94 LRTCSVDCPCRDSKLNVK 111 (121)
Q Consensus 94 ~~~~~~~~~~~~s~~~~~ 111 (121)
.....+.||+|++.=+..
T Consensus 53 ~~~~~i~Cp~Hg~~fd~~ 70 (98)
T cd03528 53 VEGGVIECPLHGGRFDLR 70 (98)
T ss_pred EeCCEEEeCCcCCEEECC
Confidence 344578899998876653
No 154
>PRK11637 AmiB activator; Provisional
Probab=26.52 E-value=1.9e+02 Score=24.46 Aligned_cols=50 Identities=8% Similarity=0.181 Sum_probs=30.8
Q ss_pred eeeEEEEeeCCCCeEEEEecCCCCc--ccEEEEccccc-cCCCCcccCCCCCCEEEEE
Q psy12844 14 VSGVIQFFNKERGFGFINRIGDDGR--KDYFFHFSEIQ-GGTDNILRAIKYSLLVIFD 68 (121)
Q Consensus 14 ~~G~Vkwfn~~kGfGFI~~~~d~g~--~dVFfH~s~l~-~~g~~~~~~l~~G~~V~F~ 68 (121)
..|+|.+-+...|||-+..+ +.|+ --+|-|.+.+. ..| ..+..|+.|-+.
T Consensus 346 ~~G~V~~~~~~~~~G~~vii-~hg~g~~t~Y~~~~~~~v~~G----~~V~~G~~ig~~ 398 (428)
T PRK11637 346 ADGRVLLADWLQGYGLVVVV-EHGKGDMSLYGYNQSALVSVG----AQVRAGQPIALV 398 (428)
T ss_pred CCeEEEEeeccCCcccEEEE-EeCCCcEEEccCCCcCCCCCc----CEECCCCeEEee
Confidence 57999988878899965552 3332 23555765553 334 466677766543
No 155
>PRK09965 3-phenylpropionate dioxygenase ferredoxin subunit; Provisional
Probab=26.23 E-value=79 Score=21.32 Aligned_cols=39 Identities=23% Similarity=0.388 Sum_probs=22.3
Q ss_pred CCCceEEEEEEcCCccccc--cccc-ccccCCCccccccccc
Q psy12844 74 GGRREAVHIKIFDTRLYLE--DLRT-CSVDCPCRDSKLNVKT 112 (121)
Q Consensus 74 kGk~~A~~V~~~~~~~~~~--~~~~-~~~~~~~~~s~~~~~~ 112 (121)
+|+..|.+=.=.....+|+ .+.- ..|.||+|.+.=+..+
T Consensus 32 ~g~~~A~~~~CpH~g~~L~~G~~~~~~~i~Cp~Hg~~Fd~~t 73 (106)
T PRK09965 32 GGEFYAIDDRCSHGNASLSEGYLEDDATVECPLHAASFCLRT 73 (106)
T ss_pred CCEEEEEeCcCCCCCCCCCceEECCCCEEEcCCCCCEEEcCC
Confidence 4545665544334444443 2223 4688999998876653
No 156
>PRK09824 PTS system beta-glucoside-specific transporter subunits IIABC; Provisional
Probab=25.59 E-value=1.6e+02 Score=26.91 Aligned_cols=56 Identities=18% Similarity=0.317 Sum_probs=35.7
Q ss_pred ccccccceeeeeeeEEEEeeCCC-CeEEEEecCCCCcccEEEEcc----ccccCCCCcccCCCCCCEEE
Q psy12844 3 AHLGKIIEEVYVSGVIQFFNKER-GFGFINRIGDDGRKDYFFHFS----EIQGGTDNILRAIKYSLLVI 66 (121)
Q Consensus 3 ~~~~~~~~~~m~~G~Vkwfn~~k-GfGFI~~~~d~g~~dVFfH~s----~l~~~g~~~~~~l~~G~~V~ 66 (121)
.+-|+|..+ ..|+|+...+.+ -|| |.. ++| -+|.+|+- .+.+.+|. ...++||+|+
T Consensus 513 P~~~~v~AP--~~G~v~~vf~T~HAig-i~t--~~G-~eiLiHiGiDTV~L~G~gF~--~~v~~Gd~V~ 573 (627)
T PRK09824 513 PSVGEVRSP--VAGRVASLFATLHAIG-LES--DDG-VEVLIHVGIDTVKLDGKFFT--AHVNVGDKVN 573 (627)
T ss_pred CCCCeEEcc--CCeEEEEEcCCCcEEE-EEe--CCC-cEEEEEechhhhhcCCCCce--EEecCCCEEc
Confidence 344677776 589999976533 445 455 555 69999973 45556652 3455677765
No 157
>CHL00010 infA translation initiation factor 1
Probab=25.47 E-value=2e+02 Score=18.80 Aligned_cols=52 Identities=13% Similarity=0.005 Sum_probs=31.4
Q ss_pred eeeEEEEeeCCCCeEEEEecCCCCcccEEEEccccccCCCCcccCCCCCCEEEEEEEEC
Q psy12844 14 VSGVIQFFNKERGFGFINRIGDDGRKDYFFHFSEIQGGTDNILRAIKYSLLVIFDIGVT 72 (121)
Q Consensus 14 ~~G~Vkwfn~~kGfGFI~~~~d~g~~dVFfH~s~l~~~g~~~~~~l~~G~~V~F~i~~~ 72 (121)
..|+|..--. .+|=.+.. ++| ..+-.|+.---.... -.|.+||.|.|++..-
T Consensus 9 ~~G~Vik~lg-~~~y~V~~--~~g-~~~~c~~rGklr~~~---i~~~vGD~V~ve~~~~ 60 (78)
T CHL00010 9 MEGLVTESLP-NGMFRVRL--DNG-CQVLGYISGKIRRNS---IRILPGDRVKVELSPY 60 (78)
T ss_pred EEEEEEEEcC-CCEEEEEe--CCC-CEEEEEeccceecCC---cccCCCCEEEEEEccc
Confidence 4688887532 35545555 555 455577654322211 3588999999996543
No 158
>TIGR02694 arsenite_ox_S arsenite oxidase, small subunit. This model represents the small subunit of an arsenite oxidase complex. It is a Rieske protein and appears to rely on the Tat (twin-arginine translocation) system to cross the membrane. Although this enzyme could run in the direction of arsenate reduction to arsenite in principle, the relevant biological function is arsenite oxidation for energy metabolism, not arsenic resistance. Homologs to both large (TIGR02693) and small subunits that score in the gray zone between the set trusted and noise bit score cutoffs for the respective models are found in Aeropyrum pernix K1 and in Sulfolobus tokodaii str. 7.
Probab=25.46 E-value=58 Score=23.49 Aligned_cols=17 Identities=24% Similarity=0.628 Sum_probs=13.2
Q ss_pred ccccccCCCcccccccc
Q psy12844 95 RTCSVDCPCRDSKLNVK 111 (121)
Q Consensus 95 ~~~~~~~~~~~s~~~~~ 111 (121)
....|.||+|.+.=...
T Consensus 70 ~~~~i~CP~Hga~Fdl~ 86 (129)
T TIGR02694 70 DNKTFNCPCHFSVFDPE 86 (129)
T ss_pred CCCEEEcCCCCCEECCC
Confidence 45679999999876655
No 159
>KOG3492|consensus
Probab=24.84 E-value=97 Score=23.93 Aligned_cols=49 Identities=22% Similarity=0.427 Sum_probs=32.0
Q ss_pred Ccccccccceeeee-eeEEEEeeCC--CCeEEEEecC-----CCCcccEEEEccccc
Q psy12844 1 MKAHLGKIIEEVYV-SGVIQFFNKE--RGFGFINRIG-----DDGRKDYFFHFSEIQ 49 (121)
Q Consensus 1 ~~~~~~~~~~~~m~-~G~Vkwfn~~--kGfGFI~~~~-----d~g~~dVFfH~s~l~ 49 (121)
+|+|+|+|-|.... +|+|.+=-.+ -|||.....- -++..-|-||.+|+-
T Consensus 114 lKs~vgRitd~~p~~~GVvVysm~DvPLGFGv~Akst~d~r~~dp~aiv~~hQaDiG 170 (180)
T KOG3492|consen 114 LKSGVGRITDGIPQHQGVVVYSMNDVPLGFGVTAKSTQDCRKADPTAIVVLHQADIG 170 (180)
T ss_pred hhcccceecCCCCCcceEEEEeccCCccccceeecCcccccccCCcEEEEEEecchH
Confidence 48999999998764 7888765333 3777765420 222234778888874
No 160
>TIGR01995 PTS-II-ABC-beta PTS system, beta-glucoside-specific IIABC component. This model represents a family of PTS enzyme II proteins in which all three domains are found in the same polypeptide chain and which appear to have a broad specificity for beta-glucosides including salicin (beta-D-glucose-1-salicylate) and arbutin (Hydroquinone-O-beta-D-glucopyranoside). These are distinct from the closely related sucrose-specific and trehalose-specific PTS transporters.
Probab=24.72 E-value=1.6e+02 Score=26.56 Aligned_cols=55 Identities=20% Similarity=0.339 Sum_probs=34.4
Q ss_pred cccccceeeeeeeEEEEeeCCC-CeEEEEecCCCCcccEEEEcc----ccccCCCCcccCCCCCCEEE
Q psy12844 4 HLGKIIEEVYVSGVIQFFNKER-GFGFINRIGDDGRKDYFFHFS----EIQGGTDNILRAIKYSLLVI 66 (121)
Q Consensus 4 ~~~~~~~~~m~~G~Vkwfn~~k-GfGFI~~~~d~g~~dVFfH~s----~l~~~g~~~~~~l~~G~~V~ 66 (121)
.-|+|..+ ..|+|....+.+ -||+- . ++| -++.+|+- .+.+.+|. ...++||+|+
T Consensus 498 ~~~~v~aP--~~G~v~~~~~t~Ha~gi~-~--~~G-~eiliHiGidTv~l~g~gF~--~~v~~g~~V~ 557 (610)
T TIGR01995 498 TEGEVVAP--VDGTVTAVFPTKHAIGIR-S--DNG-IEILIHVGIDTVELNGEGFE--ILVKVGDHVK 557 (610)
T ss_pred CCCEEECC--CCeEEEEEcCCCCEEEEE-E--CCC-cEEEEEeccchhccCCCCeE--EEecCcCEEc
Confidence 44666666 589999976543 55554 4 454 69999973 45555552 3345666664
No 161
>cd03474 Rieske_T4moC Toluene-4-monooxygenase effector protein complex (T4mo), Rieske ferredoxin subunit; The Rieske domain is a [2Fe-2S] cluster binding domain involved in electron transfer. T4mo is a four-protein complex that catalyzes the NADH- and O2-dependent hydroxylation of toluene to form p-cresol. T4mo consists of an NADH oxidoreductase (T4moF), a diiron hydroxylase (T4moH), a catalytic effector protein (T4moD), and a Rieske ferredoxin (T4moC). T4moC contains a Rieske domain and functions as an obligate electron carrier between T4moF and T4moH. Rieske ferredoxins are found as subunits of membrane oxidase complexes, cis-dihydrodiol-forming aromatic dioxygenases, bacterial assimilatory nitrite reductases, and arsenite oxidase. Rieske ferredoxins are also found as soluble electron carriers in bacterial dioxygenase and monooxygenase complexes.
Probab=24.25 E-value=1.6e+02 Score=19.64 Aligned_cols=39 Identities=15% Similarity=0.175 Sum_probs=19.7
Q ss_pred CCCceEEEEEEcCCccccc--ccccccccCCCccccccccc
Q psy12844 74 GGRREAVHIKIFDTRLYLE--DLRTCSVDCPCRDSKLNVKT 112 (121)
Q Consensus 74 kGk~~A~~V~~~~~~~~~~--~~~~~~~~~~~~~s~~~~~~ 112 (121)
+|+..|..=.=.....+++ ...-..|-||.|++.=+..+
T Consensus 32 ~g~~~A~~n~CpH~g~~L~~g~~~g~~i~CP~Hg~~Fdl~~ 72 (108)
T cd03474 32 GGEFRAFQGICPHQEIPLAEGGFDGGVLTCRAHLWQFDADT 72 (108)
T ss_pred CCeEEEEcCcCCCCCCCcccCcccCCEEEeCCcCCEEECCC
Confidence 4445554333223333333 22334688999887665543
No 162
>KOG1671|consensus
Probab=24.18 E-value=32 Score=27.37 Aligned_cols=14 Identities=29% Similarity=0.786 Sum_probs=11.9
Q ss_pred cccCCCcccccccc
Q psy12844 98 SVDCPCRDSKLNVK 111 (121)
Q Consensus 98 ~~~~~~~~s~~~~~ 111 (121)
.+.||||+|+.+-.
T Consensus 169 g~~CPCHGSHYdas 182 (210)
T KOG1671|consen 169 GYYCPCHGSHYDAS 182 (210)
T ss_pred ceeccccccccccc
Confidence 68999999997754
No 163
>cd04451 S1_IF1 S1_IF1: Translation Initiation Factor IF1, S1-like RNA-binding domain. IF1 contains an S1-like RNA-binding domain, which is found in a wide variety of RNA-associated proteins. Translation initiation includes a number of interrelated steps preceding the formation of the first peptide bond. In Escherichia coli, the initiation mechanism requires, in addition to mRNA, fMet-tRNA, and ribosomal subunits, the presence of three additional proteins (initiation factors IF1, IF2, and IF3) and at least one GTP molecule. The three initiation factors influence both the kinetics and the stability of ternary complex formation. IF1 is the smallest of the three factors. IF1 enhances the rate of 70S ribosome subunit association and dissociation and the interaction of 30S ribosomal subunit with IF2 and IF3. It stimulates 30S complex formation. In addition, by binding to the A-site of the 30S ribosomal subunit, IF1 may contribute to the fidelity of the selection of the initiation site of th
Probab=23.66 E-value=1.9e+02 Score=17.77 Aligned_cols=50 Identities=14% Similarity=0.048 Sum_probs=28.4
Q ss_pred eeEEEEeeCCCCeEEEEecCCCCcccEEEEccccccCCCCcccCCCCCCEEEEEEEE
Q psy12844 15 SGVIQFFNKERGFGFINRIGDDGRKDYFFHFSEIQGGTDNILRAIKYSLLVIFDIGV 71 (121)
Q Consensus 15 ~G~Vkwfn~~kGfGFI~~~~d~g~~dVFfH~s~l~~~g~~~~~~l~~G~~V~F~i~~ 71 (121)
.|+|..-- ..+|-.+.. +++ +.+-.+...--.... ..+.+||.|.|++..
T Consensus 4 ~G~Vi~~~-~g~~~~V~~--~~g-~~~~c~~rGklr~~~---~~~~vGD~V~~~~~~ 53 (64)
T cd04451 4 EGVVTEAL-PNAMFRVEL--ENG-HEVLAHISGKMRMNY---IRILPGDRVKVELSP 53 (64)
T ss_pred EEEEEEEe-CCCEEEEEe--CCC-CEEEEEECceeecCC---cccCCCCEEEEEEee
Confidence 56665431 135666666 554 344455443221111 358999999999764
No 164
>COG2183 Tex Transcriptional accessory protein [Transcription]
Probab=23.42 E-value=1.3e+02 Score=28.30 Aligned_cols=66 Identities=15% Similarity=0.150 Sum_probs=44.8
Q ss_pred eeeEEEEeeCCCCeEEEEecCCCCcccEEEEccccccCCCC-cccCCCCCCEEEEEEEECC--CCCceEEEEEEc
Q psy12844 14 VSGVIQFFNKERGFGFINRIGDDGRKDYFFHFSEIQGGTDN-ILRAIKYSLLVIFDIGVTP--GGRREAVHIKIF 85 (121)
Q Consensus 14 ~~G~Vkwfn~~kGfGFI~~~~d~g~~dVFfH~s~l~~~g~~-~~~~l~~G~~V~F~i~~~~--kGk~~A~~V~~~ 85 (121)
..|+|+.. ..||-+.. .+=.+|.++|+|.+...=+. ++..+++||-|+-.+..-+ ++ ..+......
T Consensus 662 leg~Vrnv---~~fgafVd--Igv~qDglvHis~ls~~fv~~P~~vv~vGdiV~v~V~~vD~~r~-rI~Lsmr~~ 730 (780)
T COG2183 662 LEGTVRNV---VDFGAFVD--IGVHQDGLVHISQLSDKFVKDPNEVVKVGDIVKVKVIEVDTARK-RIALSMRLD 730 (780)
T ss_pred EEEEEEEe---eeccceEE--eccccceeeeHHHhhhhhcCChHHhcccCCEEEEEEEEEecccC-eeeeEeecc
Confidence 58999986 56776666 33347999999999764221 3467889999998877644 33 444444433
No 165
>PRK13159 cytochrome c-type biogenesis protein CcmE; Reviewed
Probab=23.18 E-value=3.4e+02 Score=20.54 Aligned_cols=69 Identities=19% Similarity=0.162 Sum_probs=50.5
Q ss_pred eeeEEEEeeCCCCeEEEEecCCCCcccEEEEccccccCCCCcccCCCCCCEEEEEEEECCCCCceEEEEEEcCCccccc
Q psy12844 14 VSGVIQFFNKERGFGFINRIGDDGRKDYFFHFSEIQGGTDNILRAIKYSLLVIFDIGVTPGGRREAVHIKIFDTRLYLE 92 (121)
Q Consensus 14 ~~G~Vkwfn~~kGfGFI~~~~d~g~~dVFfH~s~l~~~g~~~~~~l~~G~~V~F~i~~~~kGk~~A~~V~~~~~~~~~~ 92 (121)
..|.|+|-.+.-..=|... |. ...|=++++.+..+- .++|+.|.-+=.-. +|..+|.+|..-..+.|..
T Consensus 61 ~~GSv~r~~~~~~v~F~vt--D~-~~~v~V~Y~GilPDl------FrEGqgVVaeG~~~-~g~F~A~~vLAKHde~YmP 129 (155)
T PRK13159 61 KAGSIQRAADSLKVSFTVI--DK-NAATQVEYTGILPDL------FRDNQSVIANGRMQ-GGRFVANEVLAKHDETYMP 129 (155)
T ss_pred ecCcEEEcCCCcEEEEEEE--cC-CcEEEEEEccCCCcc------ccCCCeEEEEEEEc-CCEEEEeEEEecCCCcCCC
Confidence 3577877433336788888 65 458999999887554 58999998776665 4779999999887766643
No 166
>cd04486 YhcR_OBF_like YhcR_OBF_like: A subfamily of OB-fold domains similar to the OB folds of Bacillus subtilis YhcR. YhcR is a sugar-nonspecific nuclease, which is active in the presence of Ca2+ and Mn2+. It cleaves RNA endonucleolytically, producing 3'-monophosphate nucleosides. YhcR appears to be the major Ca2+ activated nuclease of B. subtilis. YhcR may be localized in the cell wall.
Probab=22.89 E-value=2.3e+02 Score=18.45 Aligned_cols=52 Identities=23% Similarity=0.171 Sum_probs=33.0
Q ss_pred eeeEEEEeeCCC-CeEEEEecCCCC-------cccEEEEccccccCCCCcccCCCCCCEEEEEEEECC-CC
Q psy12844 14 VSGVIQFFNKER-GFGFINRIGDDG-------RKDYFFHFSEIQGGTDNILRAIKYSLLVIFDIGVTP-GG 75 (121)
Q Consensus 14 ~~G~Vkwfn~~k-GfGFI~~~~d~g-------~~dVFfH~s~l~~~g~~~~~~l~~G~~V~F~i~~~~-kG 75 (121)
..|+|.--.+.. ..||-.. +.. .+-||+.... . ..+++||.|...=...+ .|
T Consensus 2 v~GvVTa~~~~~~~~GffiQ--d~~~d~~~~ts~gifV~~~~----~----~~~~~Gd~V~vtG~v~ey~g 62 (78)
T cd04486 2 VEGVVTAVFSGGGLGGFYIQ--DEDGDGDPATSEGIFVYTGS----G----ADVAVGDLVRVTGTVTEYYG 62 (78)
T ss_pred eEEEEEEEcCCCCcCEEEEE--cCCCCCCCcccceEEEecCC----C----CCCCCCCEEEEEEEEEeeCC
Confidence 467777765443 3576666 331 2358888766 2 36899999998755544 44
No 167
>COG0723 QcrA Rieske Fe-S protein [Energy production and conversion]
Probab=22.38 E-value=34 Score=25.42 Aligned_cols=16 Identities=25% Similarity=0.646 Sum_probs=12.3
Q ss_pred cccccCCCcccccccc
Q psy12844 96 TCSVDCPCRDSKLNVK 111 (121)
Q Consensus 96 ~~~~~~~~~~s~~~~~ 111 (121)
..-|.||||.|+-.+.
T Consensus 123 ~~~~~CPCHGS~yd~~ 138 (177)
T COG0723 123 EGGFFCPCHGSRYDPD 138 (177)
T ss_pred CCeEEccCCCCeEcCC
Confidence 3558999999986654
No 168
>PRK00276 infA translation initiation factor IF-1; Validated
Probab=21.85 E-value=2.3e+02 Score=18.10 Aligned_cols=51 Identities=12% Similarity=0.051 Sum_probs=30.5
Q ss_pred eeeEEEEeeCCCCeEEEEecCCCCcccEEEEcccccc-CCCCcccCCCCCCEEEEEEEEC
Q psy12844 14 VSGVIQFFNKERGFGFINRIGDDGRKDYFFHFSEIQG-GTDNILRAIKYSLLVIFDIGVT 72 (121)
Q Consensus 14 ~~G~Vkwfn~~kGfGFI~~~~d~g~~dVFfH~s~l~~-~g~~~~~~l~~G~~V~F~i~~~ 72 (121)
+.|+|...-. .+|=.+.. ++| ..+-.|..---. .. ..+.+||.|.|++...
T Consensus 9 ~~G~Vi~~~~-~~~y~V~~--~~g-~~~~c~~~Gklr~~~----i~i~vGD~V~ve~~~~ 60 (72)
T PRK00276 9 MEGTVVEALP-NAMFRVEL--ENG-HEVLAHISGKMRKNY----IRILPGDKVTVELSPY 60 (72)
T ss_pred EEEEEEEEcC-CCEEEEEe--CCC-CEEEEEEccceeeCC----cccCCCCEEEEEEccc
Confidence 3688877532 22444555 454 355566554322 23 3589999999997553
No 169
>cd05701 S1_Rrp5_repeat_hs10 S1_Rrp5_repeat_hs10: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 10 (hs10). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=21.84 E-value=2.4e+02 Score=18.65 Aligned_cols=45 Identities=7% Similarity=0.079 Sum_probs=32.2
Q ss_pred CCCeEEEEecCCCCcccEEE----EccccccCCCCcccCCCCCCEEEEEEEECC
Q psy12844 24 ERGFGFINRIGDDGRKDYFF----HFSEIQGGTDNILRAIKYSLLVIFDIGVTP 73 (121)
Q Consensus 24 ~kGfGFI~~~~d~g~~dVFf----H~s~l~~~g~~~~~~l~~G~~V~F~i~~~~ 73 (121)
++.|-.|.- .+.+.-.+| |.++.-..+- +.|++|+.+.-++....
T Consensus 12 ~kdfAvvSL--~~t~~L~a~p~~sHLNdtfrf~s---eklkvG~~l~v~lk~~~ 60 (69)
T cd05701 12 DKDFAIVSL--ATTGDLAAFPTRSHLNDTFRFDS---EKLSVGQCLDVTLKDPN 60 (69)
T ss_pred hhceEEEEe--eccccEEEEEchhhccccccccc---eeeeccceEEEEEecCc
Confidence 577888887 776655565 5555555554 78999999998887653
No 170
>cd03478 Rieske_AIFL_N AIFL (apoptosis-inducing factor like) family, N-terminal Rieske domain; members of this family show similarity to human AIFL, containing an N-terminal Rieske domain and a C-terminal pyridine nucleotide-disulfide oxidoreductase domain (Pyr_redox). The Rieske domain is a [2Fe-2S] cluster binding domain involved in electron transfer. AIFL shares 35% homology with human AIF (apoptosis-inducing factor), mainly in the Pyr_redox domain. AIFL is predominantly localized to the mitochondria. AIFL induces apoptosis in a caspase-dependent manner.
Probab=21.31 E-value=1e+02 Score=20.09 Aligned_cols=16 Identities=19% Similarity=0.584 Sum_probs=12.0
Q ss_pred cccccCCCcccccccc
Q psy12844 96 TCSVDCPCRDSKLNVK 111 (121)
Q Consensus 96 ~~~~~~~~~~s~~~~~ 111 (121)
-..|.||+|.+.=+..
T Consensus 54 ~~~i~CP~Hg~~Fdl~ 69 (95)
T cd03478 54 DGRIRCPWHGACFNLR 69 (95)
T ss_pred CCEEEcCCCCCEEECC
Confidence 4568899998876654
No 171
>smart00361 RRM_1 RNA recognition motif.
Probab=20.92 E-value=62 Score=20.04 Aligned_cols=9 Identities=33% Similarity=0.464 Sum_probs=7.9
Q ss_pred CCCeEEEEe
Q psy12844 24 ERGFGFINR 32 (121)
Q Consensus 24 ~kGfGFI~~ 32 (121)
.+|||||.-
T Consensus 36 ~rG~~fV~f 44 (70)
T smart00361 36 KRGNVYITF 44 (70)
T ss_pred CcEEEEEEE
Confidence 589999998
Done!