Query 032330
Match_columns 143
No_of_seqs 106 out of 404
Neff 5.9
Searched_HMMs 46136
Date Fri Mar 29 12:41:04 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/032330.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/032330hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3416 Predicted nucleic acid 99.9 4.1E-27 9E-32 173.8 9.9 108 15-137 5-112 (134)
2 PRK06461 single-stranded DNA-b 99.9 1.7E-26 3.7E-31 171.5 13.1 114 13-139 3-116 (129)
3 PRK06386 replication factor A; 99.9 3.4E-21 7.3E-26 164.1 12.7 104 14-130 2-105 (358)
4 PRK07217 replication factor A; 99.9 6.8E-21 1.5E-25 159.2 13.9 113 10-142 68-181 (311)
5 PRK06386 replication factor A; 99.9 1.1E-20 2.4E-25 160.9 13.6 102 12-129 105-206 (358)
6 PRK07218 replication factor A; 99.8 7E-21 1.5E-25 165.1 11.3 98 11-122 55-152 (423)
7 PRK07218 replication factor A; 99.8 1.5E-19 3.2E-24 156.9 13.0 102 13-128 161-262 (423)
8 PRK08402 replication factor A; 99.8 3E-19 6.4E-24 152.1 11.3 100 12-121 60-164 (355)
9 PRK07211 replication factor A; 99.8 5.5E-18 1.2E-22 149.1 11.1 100 12-121 159-261 (485)
10 PRK15491 replication factor A; 99.8 6.7E-18 1.4E-22 144.6 10.9 100 11-121 54-158 (374)
11 PRK14699 replication factor A; 99.7 5.9E-18 1.3E-22 149.1 10.7 113 12-136 55-173 (484)
12 PRK14699 replication factor A; 99.7 8.8E-18 1.9E-22 148.0 11.7 97 14-120 166-267 (484)
13 PRK12366 replication factor A; 99.7 1.5E-17 3.3E-22 150.5 12.4 101 10-120 59-162 (637)
14 cd04491 SoSSB_OBF SoSSB_OBF: A 99.7 4.3E-17 9.2E-22 111.2 10.9 80 28-118 1-81 (82)
15 PRK15491 replication factor A; 99.7 2E-16 4.4E-21 135.5 11.0 100 12-121 164-268 (374)
16 PRK12366 replication factor A; 99.6 6.1E-15 1.3E-19 133.6 10.8 100 11-120 392-495 (637)
17 PRK07211 replication factor A; 99.6 1.8E-14 3.9E-19 127.0 11.1 100 11-121 266-367 (485)
18 cd04475 RPA1_DBD_B RPA1_DBD_B: 99.3 5.4E-11 1.2E-15 83.7 9.5 85 27-121 2-89 (101)
19 COG1599 RFA1 Single-stranded D 99.3 1.6E-11 3.5E-16 105.9 8.1 110 8-127 43-154 (407)
20 cd04474 RPA1_DBD_A RPA1_DBD_A: 99.2 6.2E-11 1.4E-15 84.6 9.5 90 16-116 1-102 (104)
21 TIGR00617 rpa1 replication fac 99.0 4.5E-09 9.7E-14 95.2 12.1 98 13-121 179-287 (608)
22 TIGR00617 rpa1 replication fac 98.8 3.1E-08 6.8E-13 89.8 9.7 102 9-120 293-399 (608)
23 PF01336 tRNA_anti-codon: OB-f 98.4 1.9E-06 4.1E-11 56.1 7.7 67 27-113 1-72 (75)
24 cd04497 hPOT1_OB1_like hPOT1_O 98.3 6.1E-06 1.3E-10 61.6 9.9 87 12-112 1-95 (138)
25 cd04483 hOBFC1_like hOBFC1_lik 97.9 0.00012 2.6E-09 51.4 8.5 49 62-111 15-87 (92)
26 PRK13480 3'-5' exoribonuclease 97.7 0.00015 3.2E-09 61.4 8.2 80 16-112 4-86 (314)
27 cd04492 YhaM_OBF_like YhaM_OBF 97.7 0.0004 8.7E-09 45.8 8.6 50 61-111 19-71 (83)
28 cd04478 RPA2_DBD_D RPA2_DBD_D: 97.7 0.00077 1.7E-08 46.4 9.7 70 27-120 2-78 (95)
29 cd03524 RPA2_OBF_family RPA2_O 97.5 0.001 2.2E-08 41.6 7.9 65 29-111 2-71 (75)
30 cd04485 DnaE_OBF DnaE_OBF: A s 97.4 0.0012 2.6E-08 43.0 7.3 50 61-111 19-72 (84)
31 cd04488 RecG_wedge_OBF RecG_we 97.2 0.0034 7.4E-08 40.1 7.8 48 61-109 18-68 (75)
32 cd04481 RPA1_DBD_B_like RPA1_D 97.1 0.0041 8.8E-08 44.0 7.7 82 28-120 1-93 (106)
33 cd04480 RPA1_DBD_A_like RPA1_D 96.8 0.0058 1.3E-07 41.6 6.2 64 29-107 2-70 (86)
34 PF02765 POT1: Telomeric singl 96.8 0.012 2.5E-07 44.2 8.3 84 22-119 10-109 (146)
35 cd04489 ExoVII_LU_OBF ExoVII_L 96.7 0.023 5E-07 37.3 8.4 50 62-111 18-72 (78)
36 COG1599 RFA1 Single-stranded D 96.5 0.012 2.7E-07 51.0 8.0 65 30-109 173-238 (407)
37 cd04484 polC_OBF polC_OBF: A s 94.5 0.42 9.2E-06 32.5 8.1 71 26-111 1-77 (82)
38 cd04498 hPOT1_OB2 hPOT1_OB2: A 94.1 0.13 2.8E-06 38.3 5.1 32 73-104 61-95 (123)
39 COG4085 Predicted RNA-binding 93.9 0.52 1.1E-05 37.8 8.5 94 12-124 35-141 (204)
40 PRK10917 ATP-dependent DNA hel 93.1 0.42 9.2E-06 44.1 7.8 77 14-109 50-130 (681)
41 cd04487 RecJ_OBF2_like RecJ_OB 92.8 0.83 1.8E-05 30.5 7.0 48 63-111 17-68 (73)
42 PRK08402 replication factor A; 92.6 0.16 3.4E-06 43.9 4.1 72 12-86 182-270 (355)
43 PRK05673 dnaE DNA polymerase I 92.3 0.29 6.2E-06 48.0 5.9 86 15-116 966-1057(1135)
44 cd04490 PolII_SU_OBF PolII_SU_ 92.0 1.7 3.7E-05 29.3 7.8 53 27-98 2-60 (79)
45 TIGR00643 recG ATP-dependent D 91.9 0.89 1.9E-05 41.6 8.2 80 14-111 23-105 (630)
46 PRK07373 DNA polymerase III su 91.4 0.42 9E-06 42.4 5.4 82 15-112 269-356 (449)
47 PRK00448 polC DNA polymerase I 89.3 1.6 3.5E-05 44.0 7.9 86 12-112 224-316 (1437)
48 PF02721 DUF223: Domain of unk 88.2 1.5 3.3E-05 30.2 5.2 57 64-120 1-69 (95)
49 PF10451 Stn1: Telomere regula 87.2 3.8 8.3E-05 33.9 7.8 73 24-116 66-147 (256)
50 PRK05159 aspC aspartyl-tRNA sy 85.4 6 0.00013 34.7 8.6 86 14-119 4-100 (437)
51 cd04482 RPA2_OBF_like RPA2_OBF 84.4 4.1 9E-05 28.1 5.8 39 64-103 20-64 (91)
52 COG1200 RecG RecG-like helicas 84.1 7.1 0.00015 36.6 8.7 77 15-109 52-131 (677)
53 PF11325 DUF3127: Domain of un 82.6 12 0.00025 26.1 7.3 47 61-107 22-75 (84)
54 cd04494 BRCA2DBD_OB2 BRCA2DBD_ 82.2 4.1 8.9E-05 33.8 5.8 59 62-120 166-236 (251)
55 PF08646 Rep_fac-A_C: Replicat 81.8 0.58 1.3E-05 34.6 0.7 25 60-84 53-77 (146)
56 PRK07374 dnaE DNA polymerase I 81.4 3.3 7.1E-05 41.1 5.7 83 15-113 989-1077(1170)
57 PF13742 tRNA_anti_2: OB-fold 80.0 18 0.00038 25.3 9.1 68 24-111 21-95 (99)
58 PRK07459 single-stranded DNA-b 79.6 5.5 0.00012 29.0 5.2 62 24-99 3-75 (121)
59 cd04486 YhcR_OBF_like YhcR_OBF 79.5 5.2 0.00011 26.9 4.7 36 75-112 35-70 (78)
60 PRK02801 primosomal replicatio 79.1 7.2 0.00016 27.5 5.5 63 24-100 2-80 (101)
61 PTZ00401 aspartyl-tRNA synthet 78.3 26 0.00056 32.1 10.1 97 11-127 62-178 (550)
62 PRK06826 dnaE DNA polymerase I 78.2 7.9 0.00017 38.4 7.2 74 25-113 992-1069(1151)
63 PF02760 HIN: HIN-200/IF120x d 77.8 32 0.00069 27.0 9.4 77 29-120 5-83 (170)
64 COG5235 RFA2 Single-stranded D 77.4 5.7 0.00012 32.5 5.0 45 65-110 87-137 (258)
65 PRK06920 dnaE DNA polymerase I 76.4 5.4 0.00012 39.4 5.5 83 15-113 933-1020(1107)
66 PRK07279 dnaE DNA polymerase I 76.2 7.6 0.00016 38.1 6.4 83 14-112 875-961 (1034)
67 cd04320 AspRS_cyto_N AspRS_cyt 75.9 23 0.00049 24.4 7.4 56 61-116 17-89 (102)
68 TIGR00499 lysS_bact lysyl-tRNA 74.0 34 0.00073 30.8 9.6 60 60-119 69-137 (496)
69 PRK05733 single-stranded DNA-b 73.7 30 0.00065 27.0 8.1 84 23-120 4-112 (172)
70 TIGR00621 ssb single stranded 72.8 10 0.00022 28.9 5.3 31 69-99 48-82 (164)
71 PRK07274 single-stranded DNA-b 72.7 9.2 0.0002 28.1 4.8 29 71-99 46-78 (131)
72 cd04476 RPA1_DBD_C RPA1_DBD_C: 72.2 2.3 5.1E-05 32.0 1.6 26 60-85 67-92 (166)
73 PRK09010 single-stranded DNA-b 72.2 39 0.00084 26.4 8.5 83 24-120 6-114 (177)
74 cd01491 Ube1_repeat1 Ubiquitin 72.2 18 0.0004 30.2 7.0 66 62-134 167-232 (286)
75 PRK00484 lysS lysyl-tRNA synth 71.3 46 0.001 29.8 9.8 60 60-119 70-137 (491)
76 TIGR01405 polC_Gram_pos DNA po 70.5 39 0.00086 33.9 9.9 82 19-115 2-90 (1213)
77 PF04076 BOF: Bacterial OB fol 70.4 11 0.00024 27.0 4.6 66 22-111 32-99 (103)
78 PRK05672 dnaE2 error-prone DNA 69.6 9.4 0.0002 37.5 5.3 50 62-112 974-1027(1046)
79 PRK06752 single-stranded DNA-b 69.5 13 0.00028 26.4 4.9 62 24-99 2-78 (112)
80 PRK12445 lysyl-tRNA synthetase 69.3 25 0.00054 31.7 7.7 60 60-119 81-149 (505)
81 cd04321 ScAspRS_mt_like_N ScAs 69.1 23 0.0005 23.7 5.9 51 60-110 16-78 (86)
82 PRK13732 single-stranded DNA-b 68.8 50 0.0011 25.8 8.4 83 23-119 5-112 (175)
83 cd04317 EcAspRS_like_N EcAspRS 67.0 45 0.00098 24.1 8.2 68 61-128 31-113 (135)
84 PRK06751 single-stranded DNA-b 66.5 15 0.00033 28.6 5.0 65 24-102 2-82 (173)
85 PLN02850 aspartate-tRNA ligase 66.5 64 0.0014 29.3 9.7 96 12-127 67-181 (530)
86 PRK05813 single-stranded DNA-b 65.9 22 0.00047 28.8 6.0 63 23-99 108-178 (219)
87 PRK08763 single-stranded DNA-b 65.6 16 0.00035 28.2 5.0 63 23-99 4-83 (164)
88 PRK07275 single-stranded DNA-b 65.5 14 0.0003 28.4 4.6 65 24-102 2-82 (162)
89 cd04100 Asp_Lys_Asn_RS_N Asp_L 64.9 38 0.00081 22.4 7.1 50 61-110 16-77 (85)
90 PF15072 DUF4539: Domain of un 64.1 20 0.00043 24.9 4.8 52 62-113 20-76 (86)
91 cd04316 ND_PkAspRS_like_N ND_P 64.0 46 0.001 23.1 7.0 58 61-118 29-96 (108)
92 PRK06293 single-stranded DNA-b 62.2 20 0.00043 27.7 5.0 65 24-102 1-78 (161)
93 PLN02502 lysyl-tRNA synthetase 62.0 39 0.00084 31.0 7.5 59 60-118 124-193 (553)
94 cd04322 LysRS_N LysRS_N: N-ter 61.3 42 0.00092 23.3 6.2 56 61-116 16-80 (108)
95 cd04496 SSB_OBF SSB_OBF: A sub 61.3 32 0.0007 22.8 5.4 30 70-99 42-75 (100)
96 PRK03932 asnC asparaginyl-tRNA 61.1 45 0.00098 29.5 7.6 73 24-116 16-97 (450)
97 PRK02983 lysS lysyl-tRNA synth 60.6 75 0.0016 31.6 9.6 59 60-118 667-734 (1094)
98 TIGR00458 aspS_arch aspartyl-t 60.3 69 0.0015 28.1 8.6 60 60-119 28-97 (428)
99 PRK08486 single-stranded DNA-b 60.3 24 0.00052 27.7 5.2 34 69-102 46-84 (182)
100 PF02760 HIN: HIN-200/IF120x d 59.5 14 0.0003 28.9 3.6 65 13-95 100-165 (170)
101 PRK06958 single-stranded DNA-b 59.4 23 0.0005 27.9 4.9 30 70-99 50-83 (182)
102 PF00436 SSB: Single-strand bi 59.3 6 0.00013 26.8 1.5 30 70-99 46-79 (104)
103 COG1107 Archaea-specific RecJ- 58.9 32 0.0007 32.2 6.4 50 65-115 234-287 (715)
104 COG1571 Predicted DNA-binding 58.1 38 0.00083 30.1 6.6 73 17-113 260-338 (421)
105 PRK08182 single-stranded DNA-b 57.4 28 0.0006 26.3 4.9 30 73-102 55-89 (148)
106 PTZ00385 lysyl-tRNA synthetase 57.3 1E+02 0.0022 29.1 9.5 59 60-118 123-191 (659)
107 KOG2012 Ubiquitin activating e 55.6 18 0.00039 35.1 4.3 56 76-136 197-252 (1013)
108 cd04318 EcAsnRS_like_N EcAsnRS 55.6 55 0.0012 21.4 5.7 51 61-111 16-75 (82)
109 PF07680 DoxA: TQO small subun 54.7 64 0.0014 24.2 6.5 72 60-141 46-119 (133)
110 TIGR00156 conserved hypothetic 54.4 25 0.00053 26.2 4.1 70 15-108 46-119 (126)
111 PRK09919 anti-adapter protein 54.0 23 0.00051 26.0 3.9 37 73-109 26-62 (114)
112 PRK10053 hypothetical protein; 53.6 34 0.00074 25.6 4.8 40 66-108 80-123 (130)
113 KOG3108 Single-stranded DNA-bi 51.7 39 0.00085 28.2 5.4 47 65-112 89-141 (265)
114 COG4393 Predicted membrane pro 50.0 1.1E+02 0.0024 26.9 7.9 88 3-120 271-376 (405)
115 PF05113 DUF693: Protein of un 49.0 46 0.00099 28.3 5.3 33 72-104 61-96 (314)
116 PRK07772 single-stranded DNA-b 48.6 51 0.0011 26.0 5.3 29 71-99 52-84 (186)
117 PRK00286 xseA exodeoxyribonucl 48.5 1.1E+02 0.0024 26.5 7.9 68 24-111 23-96 (438)
118 PRK07135 dnaE DNA polymerase I 46.0 40 0.00087 33.0 5.2 68 15-99 889-959 (973)
119 TIGR00457 asnS asparaginyl-tRN 46.0 1.4E+02 0.0031 26.4 8.3 60 60-119 32-102 (453)
120 PF09104 BRCA-2_OB3: BRCA2, ol 45.8 1.3E+02 0.0029 22.9 8.6 82 20-120 14-103 (143)
121 COG3481 Predicted HD-superfami 45.6 18 0.00039 30.6 2.5 58 62-120 22-82 (287)
122 PTZ00417 lysine-tRNA ligase; P 43.9 1.1E+02 0.0024 28.4 7.4 57 61-117 150-217 (585)
123 COG1376 ErfK Uncharacterized p 43.6 11 0.00023 29.9 0.8 27 70-96 202-230 (232)
124 PF11183 PmrD: Polymyxin resis 43.5 26 0.00057 24.3 2.6 38 62-99 16-55 (82)
125 PRK06863 single-stranded DNA-b 41.5 76 0.0016 24.6 5.2 28 72-99 52-83 (168)
126 cd04319 PhAsnRS_like_N PhAsnRS 40.4 1.2E+02 0.0026 20.8 6.9 58 61-118 16-82 (103)
127 PRK10260 L,D-transpeptidase; P 40.2 17 0.00037 31.0 1.6 41 70-110 207-252 (306)
128 TIGR00237 xseA exodeoxyribonuc 40.0 1.5E+02 0.0032 26.1 7.5 48 63-111 37-90 (432)
129 PF11213 DUF3006: Protein of u 39.9 83 0.0018 20.6 4.6 33 61-94 10-42 (71)
130 PRK10190 L,D-transpeptidase; P 39.8 19 0.00041 30.8 1.7 41 70-110 204-249 (310)
131 PRK04036 DNA polymerase II sma 39.5 1.1E+02 0.0023 27.5 6.6 66 15-99 144-215 (504)
132 PRK06642 single-stranded DNA-b 38.6 1E+02 0.0023 23.2 5.5 65 24-102 5-89 (152)
133 PRK05813 single-stranded DNA-b 38.5 2.1E+02 0.0046 23.1 8.1 65 23-101 7-78 (219)
134 COG1190 LysU Lysyl-tRNA synthe 37.6 1.8E+02 0.004 26.6 7.7 58 60-117 77-143 (502)
135 COG0017 AsnS Aspartyl/asparagi 37.3 3.1E+02 0.0067 24.6 9.8 87 14-120 4-101 (435)
136 PRK00476 aspS aspartyl-tRNA sy 34.2 1.6E+02 0.0035 27.2 6.9 66 61-126 34-113 (588)
137 TIGR00459 aspS_bact aspartyl-t 33.8 1.4E+02 0.0031 27.6 6.5 66 61-126 32-111 (583)
138 PLN02603 asparaginyl-tRNA synt 33.4 3.9E+02 0.0085 24.7 9.9 88 12-119 87-193 (565)
139 PF12869 tRNA_anti-like: tRNA_ 33.3 1E+02 0.0022 22.1 4.6 66 24-108 67-140 (144)
140 COG1917 Uncharacterized conser 32.7 44 0.00095 23.7 2.5 28 71-99 72-99 (131)
141 COG0587 DnaE DNA polymerase II 31.0 91 0.002 31.2 5.0 72 15-100 967-1042(1139)
142 PF04775 Bile_Hydr_Trans: Acyl 30.2 96 0.0021 22.5 4.0 47 11-77 3-49 (126)
143 COG4013 Uncharacterized protei 29.5 1.4E+02 0.003 21.0 4.4 32 85-116 20-61 (91)
144 TIGR00594 polc DNA-directed DN 29.3 1.1E+02 0.0025 30.0 5.4 40 26-79 983-1022(1022)
145 COG2176 PolC DNA polymerase II 28.9 2.2E+02 0.0047 29.2 7.1 90 13-117 228-324 (1444)
146 KOG1816 Ubiquitin fusion-degra 28.9 45 0.00098 28.5 2.3 30 69-98 81-110 (308)
147 PF01957 NfeD: NfeD-like C-ter 28.4 72 0.0016 22.6 3.1 31 66-96 99-132 (144)
148 COG1570 XseA Exonuclease VII, 27.0 3.7E+02 0.0081 24.2 7.8 68 24-111 23-96 (440)
149 PLN02221 asparaginyl-tRNA synt 26.6 2.7E+02 0.0058 25.8 7.0 58 62-119 70-137 (572)
150 KOG0851 Single-stranded DNA-bi 26.3 1.7E+02 0.0037 22.5 5.1 81 13-108 3-88 (246)
151 cd04457 S1_S28E S1_S28E: S28E, 26.1 2E+02 0.0043 18.9 4.9 36 58-96 14-51 (60)
152 smart00350 MCM minichromosome 25.3 90 0.0019 27.9 3.7 29 73-101 105-133 (509)
153 KOG4757 Predicted telomere bin 25.0 2.5E+02 0.0055 25.5 6.3 81 12-106 7-95 (522)
154 TIGR02656 cyanin_plasto plasto 24.8 91 0.002 21.3 2.9 30 65-97 3-32 (99)
155 PRK06341 single-stranded DNA-b 24.7 1.8E+02 0.004 22.4 4.9 32 71-102 52-89 (166)
156 PF09356 Phage_BR0599: Phage c 24.3 1E+02 0.0022 20.8 3.0 22 74-95 29-50 (80)
157 PF08696 Dna2: DNA replication 23.7 2.5E+02 0.0055 22.1 5.6 24 73-96 11-35 (209)
158 cd05706 S1_Rrp5_repeat_sc10 S1 22.8 1.6E+02 0.0036 18.3 3.7 27 84-110 46-72 (73)
159 cd04472 S1_PNPase S1_PNPase: P 21.5 1.3E+02 0.0029 18.1 3.0 24 85-109 44-67 (68)
160 PF01200 Ribosomal_S28e: Ribos 21.4 2.7E+02 0.0058 18.7 5.3 36 59-97 23-61 (69)
161 cd05692 S1_RPS1_repeat_hs4 S1_ 21.3 1.5E+02 0.0033 17.6 3.3 26 84-110 43-68 (69)
162 TIGR01439 lp_hng_hel_AbrB loop 21.2 1.1E+02 0.0023 17.2 2.3 26 69-95 4-30 (43)
163 cd03702 IF2_mtIF2_II This fami 20.4 3.1E+02 0.0066 19.0 6.3 27 68-95 36-65 (95)
164 cd05691 S1_RPS1_repeat_ec6 S1_ 20.3 1.8E+02 0.0039 17.9 3.5 27 84-110 43-69 (73)
165 COG4880 Secreted protein conta 20.0 1.3E+02 0.0029 27.4 3.6 54 67-120 488-542 (603)
No 1
>KOG3416 consensus Predicted nucleic acid binding protein [General function prediction only]
Probab=99.94 E-value=4.1e-27 Score=173.83 Aligned_cols=108 Identities=22% Similarity=0.406 Sum_probs=100.5
Q ss_pred eeeccCCCCCCCceEEEEEEecCcceeccCCCccccCCCCCCCCCCeeEEEEEeeCcceEEEEEecCCCCCCCCCCEEEE
Q 032330 15 IKVDQLKPGTTGHTLTVKVVSSKPVQVNKPRGARSLSSLSQPSRPPRIAECLVGDDTGAIYFTARNDQVDIMTPGTTVIL 94 (143)
Q Consensus 15 ~kI~dL~p~~~~v~i~~kVl~~~~~~~~~~R~~~~~~~DG~~~~~~~v~~~lVgDeTG~I~ltlW~~~~~~i~~Gd~v~I 94 (143)
+.|+||+|+++|++++++||+.+.++ .++ || +.|+.++|||+||+|.+++|||..+.+++||+|++
T Consensus 5 i~ikdi~P~~kN~~v~fIvl~~g~~t-kTk--------dg-----~~v~~~kVaD~TgsI~isvW~e~~~~~~PGDIirL 70 (134)
T KOG3416|consen 5 IFIKDIKPGLKNINVTFIVLEYGRAT-KTK--------DG-----HEVRSCKVADETGSINISVWDEEGCLIQPGDIIRL 70 (134)
T ss_pred hhHhhcChhhhcceEEEEEEeeceee-ecc--------CC-----CEEEEEEEecccceEEEEEecCcCcccCCccEEEe
Confidence 46899999999999999999999766 333 66 68999999999999999999999999999999999
Q ss_pred eceEEceeCCeEEEEeCCceeEEEcCCCceEEcCCCCccccce
Q 032330 95 RNAKIDMFKGSMRLAVDKWGRIEVTEPADFEVKESNNLSLVEY 137 (143)
Q Consensus 95 ~na~~~~~~g~~~L~ig~~g~I~~~~~~~~~v~e~~n~S~~ey 137 (143)
++||+++|+|++.|++||.|.++++++|++.|+|++|+| +.|
T Consensus 71 t~Gy~Si~qg~LtL~~GK~Ge~~KiGef~~vf~etpn~S-~~~ 112 (134)
T KOG3416|consen 71 TGGYASIFQGCLTLYVGKGGEVQKIGEFCMVFSETPNIS-IQW 112 (134)
T ss_pred cccchhhhcCceEEEecCCceEeEeeeeEEeeecCCCcc-ccc
Confidence 999999999999999999999999999999999999999 444
No 2
>PRK06461 single-stranded DNA-binding protein; Reviewed
Probab=99.94 E-value=1.7e-26 Score=171.46 Aligned_cols=114 Identities=28% Similarity=0.458 Sum_probs=102.4
Q ss_pred ceeeeccCCCCCCCceEEEEEEecCcceeccCCCccccCCCCCCCCCCeeEEEEEeeCcceEEEEEecCCCCCCCCCCEE
Q 032330 13 VFIKVDQLKPGTTGHTLTVKVVSSKPVQVNKPRGARSLSSLSQPSRPPRIAECLVGDDTGAIYFTARNDQVDIMTPGTTV 92 (143)
Q Consensus 13 ~~~kI~dL~p~~~~v~i~~kVl~~~~~~~~~~R~~~~~~~DG~~~~~~~v~~~lVgDeTG~I~ltlW~~~~~~i~~Gd~v 92 (143)
.++||+||+|++.+++++++|+++++.. ++++ +| +.+.+.+++|+|+||+|+|++|+++++.+++||+|
T Consensus 3 ~~~kI~dL~~g~~~v~~~~~V~~i~~~~-~~~~-------k~---~~~~v~~~~l~D~TG~I~~tlW~~~a~~l~~GdvV 71 (129)
T PRK06461 3 MITKIKDLKPGMERVNVTVRVLEVGEPK-VIQT-------KG---GPRTISEAVVGDETGRVKLTLWGEQAGSLKEGEVV 71 (129)
T ss_pred CceEHHHcCCCCCceEEEEEEEEcCCce-EEEe-------CC---CceEEEEEEEECCCCEEEEEEeCCccccCCCCCEE
Confidence 4789999999999999999999998754 2233 32 25789999999999999999999999999999999
Q ss_pred EEeceEEceeCCeEEEEeCCceeEEEcCCCceEEcCCCCccccceee
Q 032330 93 ILRNAKIDMFKGSMRLAVDKWGRIEVTEPADFEVKESNNLSLVEYEL 139 (143)
Q Consensus 93 ~I~na~~~~~~g~~~L~ig~~g~I~~~~~~~~~v~e~~n~S~~eye~ 139 (143)
+|+||++++|+|+++|+++++|.|+.+++. +|+..++||+.+||.
T Consensus 72 ~I~na~v~~f~G~lqL~i~~~~~i~~~~~~--~v~~~~~i~~~~~~~ 116 (129)
T PRK06461 72 EIENAWTTLYRGKVQLNVGKYGSISESDDE--EVPEAEEIPEETPEA 116 (129)
T ss_pred EEECcEEeeeCCEEEEEECCCEEEEECCcc--ccCCCCccCccCccc
Confidence 999999999999999999999999999764 899999999999985
No 3
>PRK06386 replication factor A; Reviewed
Probab=99.86 E-value=3.4e-21 Score=164.07 Aligned_cols=104 Identities=20% Similarity=0.335 Sum_probs=90.0
Q ss_pred eeeeccCCCCCCCceEEEEEEecCcceeccCCCccccCCCCCCCCCCeeEEEEEeeCcceEEEEEecCCCCCCCCCCEEE
Q 032330 14 FIKVDQLKPGTTGHTLTVKVVSSKPVQVNKPRGARSLSSLSQPSRPPRIAECLVGDDTGAIYFTARNDQVDIMTPGTTVI 93 (143)
Q Consensus 14 ~~kI~dL~p~~~~v~i~~kVl~~~~~~~~~~R~~~~~~~DG~~~~~~~v~~~lVgDeTG~I~ltlW~~~~~~i~~Gd~v~ 93 (143)
..||+||.|++.+|++++|||+++++.+. .+ || +..+.+++|||+||+|+||+|+ +.+.+++||+|+
T Consensus 2 ~~kI~DI~~~~~~V~v~akVl~~~~r~i~-~~-------~g----~~~~~~gllgDeTG~I~fT~W~-~~~~l~~Gd~v~ 68 (358)
T PRK06386 2 LSKISDINAARQNVDLKVKVLSLNKRTIK-ND-------RG----ETIYYYGIIGDETGTVPFTAWE-FPDAVKSGDVIE 68 (358)
T ss_pred CcchhhcCCCCCcEEEEEEEEEccceEEe-cC-------CC----CeEEEEEEEECCcceEEEEecC-CcccCCCCCEEE
Confidence 36899999999999999999999976532 32 55 4678899999999999999999 456799999999
Q ss_pred EeceEEceeCCeEEEEeCCceeEEEcCCCceEEcCCC
Q 032330 94 LRNAKIDMFKGSMRLAVDKWGRIEVTEPADFEVKESN 130 (143)
Q Consensus 94 I~na~~~~~~g~~~L~ig~~g~I~~~~~~~~~v~e~~ 130 (143)
|.||++++|+|.++|+++++++|...++..++++++.
T Consensus 69 i~na~v~~~~G~~~Lnv~~~t~v~~~~d~~iev~~~~ 105 (358)
T PRK06386 69 IKYCYSKEYNGKIRIYFDSRSEVMLKPDENIEVKRTY 105 (358)
T ss_pred EEeEEEeeECCEEEEEEcCceEEEecCcccccccccc
Confidence 9999999999999999999999987766767777653
No 4
>PRK07217 replication factor A; Reviewed
Probab=99.86 E-value=6.8e-21 Score=159.19 Aligned_cols=113 Identities=23% Similarity=0.326 Sum_probs=94.3
Q ss_pred CCCceeeeccCCCCCCCceEEEEEEecCcceeccCCCccccCCCCCCCCCCeeEEEEEeeCcceEEEEEecC-CCCCCCC
Q 032330 10 RKPVFIKVDQLKPGTTGHTLTVKVVSSKPVQVNKPRGARSLSSLSQPSRPPRIAECLVGDDTGAIYFTARND-QVDIMTP 88 (143)
Q Consensus 10 ~~~~~~kI~dL~p~~~~v~i~~kVl~~~~~~~~~~R~~~~~~~DG~~~~~~~v~~~lVgDeTG~I~ltlW~~-~~~~i~~ 88 (143)
..+..+||+||.|+..+|+|++||++++++. ++ .....++||||||+|+||+|++ ....+++
T Consensus 68 ~~~~~~kI~Di~~~~~~VsV~aKVl~l~e~~------------~~-----si~qvGllgDETG~IkfT~W~~s~~~~lee 130 (311)
T PRK07217 68 GGSELVNIADIDEPEQWVDVTAKVVQLWEPS------------SD-----SIAQVGLLGDETGTIKFTKWAKSDLPELEE 130 (311)
T ss_pred CCCCceeeeecCCCCCcEEEEEEEEEecCCC------------CC-----ceEEEEEEEcCCceEEEEEccCCCCCcccC
Confidence 3567889999999999999999999999632 22 2344599999999999999995 5666999
Q ss_pred CCEEEEeceEEceeCCeEEEEeCCceeEEEcCCCceEEcCCCCccccceeeeec
Q 032330 89 GTTVILRNAKIDMFKGSMRLAVDKWGRIEVTEPADFEVKESNNLSLVEYELVNV 142 (143)
Q Consensus 89 Gd~v~I~na~~~~~~g~~~L~ig~~g~I~~~~~~~~~v~e~~n~S~~eye~v~~ 142 (143)
|++|+|.||++++|+|+++|++++++.|+.+ +..+++++.. .++...+|+|
T Consensus 131 Gd~~rI~na~v~ey~G~~~lnlg~~t~I~~~-de~IeV~~~~--vei~G~lVdi 181 (311)
T PRK07217 131 GKSYLLKNVVTDEYQGRFSVKLNRTTSIEEL-DEDIEVGDDE--VEVEGALVDI 181 (311)
T ss_pred CCEEEEEeEEEeeECCEEEEEeCCceEEEeC-CCCccccCcc--ccceeEEEEE
Confidence 9999999999999999999999999999998 5666777554 5566666654
No 5
>PRK06386 replication factor A; Reviewed
Probab=99.85 E-value=1.1e-20 Score=160.93 Aligned_cols=102 Identities=14% Similarity=0.197 Sum_probs=89.0
Q ss_pred CceeeeccCCCCCCCceEEEEEEecCcceeccCCCccccCCCCCCCCCCeeEEEEEeeCcceEEEEEecCCCCCCCCCCE
Q 032330 12 PVFIKVDQLKPGTTGHTLTVKVVSSKPVQVNKPRGARSLSSLSQPSRPPRIAECLVGDDTGAIYFTARNDQVDIMTPGTT 91 (143)
Q Consensus 12 ~~~~kI~dL~p~~~~v~i~~kVl~~~~~~~~~~R~~~~~~~DG~~~~~~~v~~~lVgDeTG~I~ltlW~~~~~~i~~Gd~ 91 (143)
....||+||.|++.+++++++|++++++. +.+ || +++.+++++|||+||+|+||+|+++ +++||+
T Consensus 105 ~~~~KI~DL~~g~~~v~V~akVle~~e~e--~~~-------~g---~~~~v~sg~lgDeTGrIr~TlW~~~---l~eGd~ 169 (358)
T PRK06386 105 YKLVKIRDLSLVTPYVSVIGKITGITKKE--YDS-------DG---TSKIVYQGYIEDDTARVRISSFGKP---LEDNRF 169 (358)
T ss_pred cCccEeEeccCCCCceEEEEEEEEccCce--Eec-------CC---CccEEEEEEEEcCCCeEEEEEcccc---ccCCCE
Confidence 35679999999999999999999998865 333 45 3699999999999999999999974 799999
Q ss_pred EEEeceEEceeCCeEEEEeCCceeEEEcCCCceEEcCC
Q 032330 92 VILRNAKIDMFKGSMRLAVDKWGRIEVTEPADFEVKES 129 (143)
Q Consensus 92 v~I~na~~~~~~g~~~L~ig~~g~I~~~~~~~~~v~e~ 129 (143)
|+|.||++++|+|+++|+++++++|+.+ +..+++...
T Consensus 170 v~i~na~v~e~~G~~el~v~~~t~I~~~-~~~iev~~~ 206 (358)
T PRK06386 170 VRIENARVSQYNGYIEISVGNKSVIKEV-ESDINLESR 206 (358)
T ss_pred EEEeeeEEEccCCeEEEEeCCeEEEEEC-CCCcccCcc
Confidence 9999999999999999999999999998 455555443
No 6
>PRK07218 replication factor A; Provisional
Probab=99.85 E-value=7e-21 Score=165.15 Aligned_cols=98 Identities=22% Similarity=0.326 Sum_probs=89.1
Q ss_pred CCceeeeccCCCCCCCceEEEEEEecCcceeccCCCccccCCCCCCCCCCeeEEEEEeeCcceEEEEEecCCCCCCCCCC
Q 032330 11 KPVFIKVDQLKPGTTGHTLTVKVVSSKPVQVNKPRGARSLSSLSQPSRPPRIAECLVGDDTGAIYFTARNDQVDIMTPGT 90 (143)
Q Consensus 11 ~~~~~kI~dL~p~~~~v~i~~kVl~~~~~~~~~~R~~~~~~~DG~~~~~~~v~~~lVgDeTG~I~ltlW~~~~~~i~~Gd 90 (143)
.+...||+||.|++.+|+|++|||+++++. +++ ||+ +++|++++|||+||+|+||+|+++. +++||
T Consensus 55 ~~~~~kI~Di~~~~~~V~v~~kVl~i~~rt--~r~-------dg~---~g~v~~~~igDeTG~Ir~tlW~~~~--l~~Gd 120 (423)
T PRK07218 55 TPSSKDIKELSTDDKNVTVTGRVLTIGERS--IRY-------QGD---DHVIYEGILADETGTISYTAWKDFG--LSPGD 120 (423)
T ss_pred CCCCccHhhCCCCCceeEEEEEEEEeccee--Eec-------CCC---ceEEEEEEEECCCCeEEEEEECCCC--CCCCC
Confidence 467889999999999999999999999854 455 774 7999999999999999999999774 99999
Q ss_pred EEEEeceEEceeCCeEEEEeCCceeEEEcCCC
Q 032330 91 TVILRNAKIDMFKGSMRLAVDKWGRIEVTEPA 122 (143)
Q Consensus 91 ~v~I~na~~~~~~g~~~L~ig~~g~I~~~~~~ 122 (143)
+|+|.||++++|+|+++|++|+.+.|+..++.
T Consensus 121 vv~I~na~vre~~g~~el~ig~~t~I~~~de~ 152 (423)
T PRK07218 121 TVTIGNAGVREWDGRPELNIGESTTVSLLDDS 152 (423)
T ss_pred EEEEeccEeeccCCceEEeccCcceEEEcCcc
Confidence 99999999999999999999999999988644
No 7
>PRK07218 replication factor A; Provisional
Probab=99.82 E-value=1.5e-19 Score=156.95 Aligned_cols=102 Identities=20% Similarity=0.311 Sum_probs=88.5
Q ss_pred ceeeeccCCCCCCCceEEEEEEecCcceeccCCCccccCCCCCCCCCCeeEEEEEeeCcceEEEEEecCCCCCCCCCCEE
Q 032330 13 VFIKVDQLKPGTTGHTLTVKVVSSKPVQVNKPRGARSLSSLSQPSRPPRIAECLVGDDTGAIYFTARNDQVDIMTPGTTV 92 (143)
Q Consensus 13 ~~~kI~dL~p~~~~v~i~~kVl~~~~~~~~~~R~~~~~~~DG~~~~~~~v~~~lVgDeTG~I~ltlW~~~~~~i~~Gd~v 92 (143)
...+|.||.|++.+++|+++|++++++. +.+| || +..|++++|||+||+|+||+|++++ .+++||+|
T Consensus 161 ~~~kI~DL~~g~~~V~v~g~Vl~~~~r~-f~~~-------dg----~~~v~~giigDeTG~Ir~tlW~~~~-~l~~Gd~v 227 (423)
T PRK07218 161 GDKKLIDLGPGDRGVNVEARVLELEHRE-IDGR-------DG----ETTILSGVLADETGRLPFTDWDPLP-EIEIGASI 227 (423)
T ss_pred CccchhhccCCCCceEEEEEEEEeccee-EEcC-------CC----CeEEEEEEEECCCceEEEEEecccc-cCCCCCEE
Confidence 4568999999999999999999998866 3343 55 3679999999999999999999875 48999999
Q ss_pred EEeceEEceeCCeEEEEeCCceeEEEcCCCceEEcC
Q 032330 93 ILRNAKIDMFKGSMRLAVDKWGRIEVTEPADFEVKE 128 (143)
Q Consensus 93 ~I~na~~~~~~g~~~L~ig~~g~I~~~~~~~~~v~e 128 (143)
+|.||++++|+|.++|++++++.|+.++ ...++.+
T Consensus 228 ~I~na~v~e~~G~~elnv~~~t~I~~~d-~~i~v~~ 262 (423)
T PRK07218 228 RIEDAYVREFRGVPSVNVSEFTTVEALD-REVSVSK 262 (423)
T ss_pred EEeeeEEeccCCeEEEEECCceEEEECC-CCccccC
Confidence 9999999999999999999999999985 3445543
No 8
>PRK08402 replication factor A; Reviewed
Probab=99.80 E-value=3e-19 Score=152.12 Aligned_cols=100 Identities=19% Similarity=0.298 Sum_probs=87.9
Q ss_pred CceeeeccCCCCCCCceEEEEEEecCcceeccCCCccccCCCCCCCCCCeeEEEEEeeCcceEEEEEecCCCC----CCC
Q 032330 12 PVFIKVDQLKPGTTGHTLTVKVVSSKPVQVNKPRGARSLSSLSQPSRPPRIAECLVGDDTGAIYFTARNDQVD----IMT 87 (143)
Q Consensus 12 ~~~~kI~dL~p~~~~v~i~~kVl~~~~~~~~~~R~~~~~~~DG~~~~~~~v~~~lVgDeTG~I~ltlW~~~~~----~i~ 87 (143)
....||+||.|++++|+++++|+++++...+.+| || ++++|++++|+|+||.|+||||+++++ .++
T Consensus 60 ~~~~kI~dl~~g~~~V~v~~rVl~~~~~r~f~rr-------dG---~~~~V~~i~l~DeTG~ir~TlW~~~a~~~~~~l~ 129 (355)
T PRK08402 60 APLMHISDLVPGMRGVNIVGRVLRKYPPREYTKK-------DG---STGRVASLIIYDDTGRARVVLWDAKVAKYYNKIN 129 (355)
T ss_pred cCccCHHHccCCCceeeEEEEEEEccCCceeecc-------CC---CcceEEEEEEEcCCCeEEEEEechhhhhhcccCC
Confidence 3588999999999999999999999874424445 77 479999999999999999999998764 489
Q ss_pred CCCEEEEeceEEcee-CCeEEEEeCCceeEEEcCC
Q 032330 88 PGTTVILRNAKIDMF-KGSMRLAVDKWGRIEVTEP 121 (143)
Q Consensus 88 ~Gd~v~I~na~~~~~-~g~~~L~ig~~g~I~~~~~ 121 (143)
+||+|+|.||+++.| +|.++|+++++|.|...|+
T Consensus 130 ~Gdvi~I~~a~V~e~~~G~~eLsvg~~s~i~~~pd 164 (355)
T PRK08402 130 VGDVIKVIDAQVRESLSGLPELHINFRARIILNPD 164 (355)
T ss_pred CCCEEEEECCEEeecCCCcEEEEECCCceEEeCCC
Confidence 999999999999986 8999999999999988864
No 9
>PRK07211 replication factor A; Reviewed
Probab=99.75 E-value=5.5e-18 Score=149.06 Aligned_cols=100 Identities=25% Similarity=0.363 Sum_probs=89.8
Q ss_pred CceeeeccCCCCCCCceEEEEEEecCcceeccCCCccccCCCCCCCCCCeeEEEEEeeCcceEEEEEecCCCCC---CCC
Q 032330 12 PVFIKVDQLKPGTTGHTLTVKVVSSKPVQVNKPRGARSLSSLSQPSRPPRIAECLVGDDTGAIYFTARNDQVDI---MTP 88 (143)
Q Consensus 12 ~~~~kI~dL~p~~~~v~i~~kVl~~~~~~~~~~R~~~~~~~DG~~~~~~~v~~~lVgDeTG~I~ltlW~~~~~~---i~~ 88 (143)
..|.+|++|.|++.+++|+++|+++.+++ ++.| . || +++++.++.|+|+||+||||||+++++. +++
T Consensus 159 ~~~~~I~dL~~~~~~v~I~grV~~v~~iR-tf~r---~---dG---seGkv~sv~L~DeTG~IR~TlW~d~Ad~~~~le~ 228 (485)
T PRK07211 159 GDTYTVEDLSLGLSDVTLVGVVLDTDSVR-TFDR---D---DG---SEGRVSNLTVGDETGRVRVTLWDDRADLAEELDA 228 (485)
T ss_pred cCCccHHHcCCCCCceEEEEEEEEcCCCe-EEEC---C---CC---CeeEEEEEEEEcCCCeEEEEEechhhhhhccCCC
Confidence 37889999999999999999999999966 3454 2 76 4799999999999999999999988655 679
Q ss_pred CCEEEEeceEEceeCCeEEEEeCCceeEEEcCC
Q 032330 89 GTTVILRNAKIDMFKGSMRLAVDKWGRIEVTEP 121 (143)
Q Consensus 89 Gd~v~I~na~~~~~~g~~~L~ig~~g~I~~~~~ 121 (143)
|++|+|.||++++|+|.++|+++..+.|++.++
T Consensus 229 G~Vv~I~~a~Vre~~g~~ELsl~~~s~I~~~~d 261 (485)
T PRK07211 229 GESVEIVDGYVRERDGSLELHVGDRGAVEEVDE 261 (485)
T ss_pred CCEEEEEeeEEEecCCcEEEEECCCceEEECCc
Confidence 999999999999999999999999999999865
No 10
>PRK15491 replication factor A; Provisional
Probab=99.75 E-value=6.7e-18 Score=144.62 Aligned_cols=100 Identities=20% Similarity=0.326 Sum_probs=85.8
Q ss_pred CCceeeeccCCCCCCCceEEEEEEecCcceeccCCCccccCCCCCCCCCCeeEEEEEeeCcceEEEEEecCCCC-----C
Q 032330 11 KPVFIKVDQLKPGTTGHTLTVKVVSSKPVQVNKPRGARSLSSLSQPSRPPRIAECLVGDDTGAIYFTARNDQVD-----I 85 (143)
Q Consensus 11 ~~~~~kI~dL~p~~~~v~i~~kVl~~~~~~~~~~R~~~~~~~DG~~~~~~~v~~~lVgDeTG~I~ltlW~~~~~-----~ 85 (143)
.....||+||.|++.+++|++||+++++++ ++.| . ||+ ++++.+++|||+||+||||||+++++ .
T Consensus 54 ~~~~~kI~dL~~~~~~v~i~arVl~~~~~R-~f~r---~---dGs---~g~v~~~~v~DeTG~ir~tlW~~~a~~~~~~~ 123 (374)
T PRK15491 54 GVDTTKIADINESSSNVNFTAKVVSIFEPK-EFNR---N---DGT---TGRVGNIIVADETGSIRLTLWDDLADLIKTGD 123 (374)
T ss_pred ccccccHHHCCCCCCceEEEEEEeeccCCe-eeec---C---CCC---ceEEEEEEEEcCCCeEEEEEECchhhhhccCC
Confidence 457789999999999999999999998866 4444 2 774 79999999999999999999998864 4
Q ss_pred CCCCCEEEEeceEEceeCCeEEEEeCCceeEEEcCC
Q 032330 86 MTPGTTVILRNAKIDMFKGSMRLAVDKWGRIEVTEP 121 (143)
Q Consensus 86 i~~Gd~v~I~na~~~~~~g~~~L~ig~~g~I~~~~~ 121 (143)
+++|++|+|.++..+.|+| ++|++++.+.|.+.++
T Consensus 124 le~G~v~~I~~~~~~~y~g-~Ei~i~~~~~i~~~~~ 158 (374)
T PRK15491 124 IEVGKSLNISGYAKEGYSG-IEVNIGRYGGISESDE 158 (374)
T ss_pred cCCCCEEEEeeeeccCccc-EEEEeCCCceeeeccc
Confidence 6789999998776667777 8999999999988853
No 11
>PRK14699 replication factor A; Provisional
Probab=99.75 E-value=5.9e-18 Score=149.06 Aligned_cols=113 Identities=19% Similarity=0.315 Sum_probs=91.3
Q ss_pred CceeeeccCCCCCCCceEEEEEEecCcceeccCCCccccCCCCCCCCCCeeEEEEEeeCcceEEEEEecCCCCC-----C
Q 032330 12 PVFIKVDQLKPGTTGHTLTVKVVSSKPVQVNKPRGARSLSSLSQPSRPPRIAECLVGDDTGAIYFTARNDQVDI-----M 86 (143)
Q Consensus 12 ~~~~kI~dL~p~~~~v~i~~kVl~~~~~~~~~~R~~~~~~~DG~~~~~~~v~~~lVgDeTG~I~ltlW~~~~~~-----i 86 (143)
+...||+||.|++.+++|++||+++++++ +|.| . ||+ .++++++.|||+||+|+||||++.++. +
T Consensus 55 ~~~~kI~di~~~~~~v~i~~rVl~i~~~r-~f~r---~---dG~---~g~v~~~~iaDeTG~ir~tlW~~~a~~~~~g~l 124 (484)
T PRK14699 55 RDSVKIENITPESGPVNFIARVVSVFDTK-EFTR---N---DGT---IGRVGNLIVGDETGKIKLTLWDNMADLIKAGKI 124 (484)
T ss_pred cccccHhHccCCCceEEEEEEEEEecCce-EEec---C---CCC---ceEEEEEEEecCCCeEEEEEecCccchhhhcCC
Confidence 56689999999999999999999999766 5655 2 774 799999999999999999999988865 8
Q ss_pred CCCCEEEEeceEEceeCCeEEEEeCCceeEEEcCCCceEEc-CCCCccccc
Q 032330 87 TPGTTVILRNAKIDMFKGSMRLAVDKWGRIEVTEPADFEVK-ESNNLSLVE 136 (143)
Q Consensus 87 ~~Gd~v~I~na~~~~~~g~~~L~ig~~g~I~~~~~~~~~v~-e~~n~S~~e 136 (143)
++||+|+|.|+ ++.+.+.++|++++.+.+...+ ..+++. ...+++++.
T Consensus 125 ~~GDvv~I~~~-~r~~~~g~el~~~~~~~i~~~~-~~i~v~~~~~~I~dL~ 173 (484)
T PRK14699 125 KAGQTLQISGY-AKQGYSGVEVNIGNNGVLTESE-EEIDVAANSQKIKDIK 173 (484)
T ss_pred CCCCEEEEcce-eccCCCCceEEeCCCceeeccC-cccccCCCCcchhhcC
Confidence 99999999995 6666666999999998888864 333432 234555543
No 12
>PRK14699 replication factor A; Provisional
Probab=99.75 E-value=8.8e-18 Score=147.98 Aligned_cols=97 Identities=28% Similarity=0.363 Sum_probs=85.4
Q ss_pred eeeeccCCCCCCCceEEEEEEecCcceeccCCCccccCCCCCCCCCCeeEEEEEeeCcceEEEEEecCCCCC---CCCCC
Q 032330 14 FIKVDQLKPGTTGHTLTVKVVSSKPVQVNKPRGARSLSSLSQPSRPPRIAECLVGDDTGAIYFTARNDQVDI---MTPGT 90 (143)
Q Consensus 14 ~~kI~dL~p~~~~v~i~~kVl~~~~~~~~~~R~~~~~~~DG~~~~~~~v~~~lVgDeTG~I~ltlW~~~~~~---i~~Gd 90 (143)
..+|.||.|++.+|+|.++|+++++++ ++.| . || .+++|.+++|||+||+|+||+|+++++. +++||
T Consensus 166 ~~~I~dL~~~~~~V~i~gkVl~~~~~R-~f~~---~---dG---~~g~v~~~~igDeTG~ir~tlW~~~a~~~~~l~~Gd 235 (484)
T PRK14699 166 SQKIKDIKDGMGDLNLTGKVLEISEIR-TFQR---K---DG---TSGKVGNLLLGDETGTLRVTLWDDKTDFLNQIEYGD 235 (484)
T ss_pred CcchhhcCCCCCceEEEEEEEeccCce-EEec---C---CC---CceEEEEEEEEcCCceEEEEEECcccccccccCCCC
Confidence 469999999999999999999999955 3444 2 76 4799999999999999999999987655 79999
Q ss_pred EEEEeceEEce--eCCeEEEEeCCceeEEEcC
Q 032330 91 TVILRNAKIDM--FKGSMRLAVDKWGRIEVTE 120 (143)
Q Consensus 91 ~v~I~na~~~~--~~g~~~L~ig~~g~I~~~~ 120 (143)
+|+|.|||++. |+|.++|++++.+.|...+
T Consensus 236 ~v~I~~a~vr~~~~~~~~el~~~~~s~i~~~~ 267 (484)
T PRK14699 236 TVELINAYARENAFTQKVELQVGNRSIIRKSE 267 (484)
T ss_pred EEEEecceEeecccCCceEEEecCceEeeccc
Confidence 99999999975 7799999999999988775
No 13
>PRK12366 replication factor A; Reviewed
Probab=99.74 E-value=1.5e-17 Score=150.45 Aligned_cols=101 Identities=19% Similarity=0.330 Sum_probs=90.0
Q ss_pred CCCceeeeccCCCCCCCceEEEEEEecCcceeccCCCccccCCCCCCCCCCeeEEEEEeeCcceEEEEEecCCCCC---C
Q 032330 10 RKPVFIKVDQLKPGTTGHTLTVKVVSSKPVQVNKPRGARSLSSLSQPSRPPRIAECLVGDDTGAIYFTARNDQVDI---M 86 (143)
Q Consensus 10 ~~~~~~kI~dL~p~~~~v~i~~kVl~~~~~~~~~~R~~~~~~~DG~~~~~~~v~~~lVgDeTG~I~ltlW~~~~~~---i 86 (143)
..+.+.+|+||.|++.+++|++||+++++.+ .+.| . || ++++|+++.|+|+||+|+||+|++.++. +
T Consensus 59 ~~~~~~~I~dl~p~~~~v~i~arV~~~~~~r-~~~~---~---~G---~eGkv~~~~v~DetG~Ir~t~W~~~~~~~~~l 128 (637)
T PRK12366 59 EEEEDFKISDIEEGQINVEITGRIIEISNIK-TFTR---K---DG---STGKLANITIADNTGTIRLTLWNDNAKLLKGL 128 (637)
T ss_pred cccceeEHHHCcCCCcceEEEEEEEEccCCe-EEEC---C---CC---CccEEEEEEEEcCCCEEEEEEEchhhhhhccC
Confidence 3467899999999999999999999999855 3433 1 66 4799999999999999999999987654 7
Q ss_pred CCCCEEEEeceEEceeCCeEEEEeCCceeEEEcC
Q 032330 87 TPGTTVILRNAKIDMFKGSMRLAVDKWGRIEVTE 120 (143)
Q Consensus 87 ~~Gd~v~I~na~~~~~~g~~~L~ig~~g~I~~~~ 120 (143)
++||+|+|.||+++.|++.++|+++..++|++.+
T Consensus 129 e~G~v~~i~~~~v~~~~~~~el~~~~~t~I~~~~ 162 (637)
T PRK12366 129 KEGDVIKIENARSRKWNNDVELNSGSETRIDKLE 162 (637)
T ss_pred CCCCEEEEeccEecccCCceEEEcCCcceEEEcc
Confidence 9999999999999999999999999999999886
No 14
>cd04491 SoSSB_OBF SoSSB_OBF: A subfamily of OB folds similar to the OB fold of the crenarchaeote Sulfolobus solfataricus single-stranded (ss) DNA-binding protein (SSoSSB). SSoSSB has a single OB fold, and it physically and functionally interacts with RNA polymerase. In vitro, SSoSSB can substitute for the basal transcription factor TBP, stimulating transcription from promoters under conditions in which TBP is limiting, and supporting transcription when TBP is absent. SSoSSB selectively melts the duplex DNA of promoter sequences. It also relieves transcriptional repression by the chromatin Alba. In addition, SSoSSB activates reverse gyrase activity, which involves DNA binding, DNA cleavage, strand passage and ligation. SSoSSB stimulates all these steps in the presence of the chromatin protein, Sul7d. SSoSSB antagonizes the inhibitory effect of Sul7d on reverse gyrase supercoiling activity. It also physically and functionally interacts with Mini-chromosome Maintenance (MCM), stimulating
Probab=99.73 E-value=4.3e-17 Score=111.18 Aligned_cols=80 Identities=33% Similarity=0.476 Sum_probs=71.3
Q ss_pred eEEEEEEecCcceeccCCCccccCCCCCCCCCCeeEEEEEeeCcceEEEEEecCC-CCCCCCCCEEEEeceEEceeCCeE
Q 032330 28 TLTVKVVSSKPVQVNKPRGARSLSSLSQPSRPPRIAECLVGDDTGAIYFTARNDQ-VDIMTPGTTVILRNAKIDMFKGSM 106 (143)
Q Consensus 28 ~i~~kVl~~~~~~~~~~R~~~~~~~DG~~~~~~~v~~~lVgDeTG~I~ltlW~~~-~~~i~~Gd~v~I~na~~~~~~g~~ 106 (143)
+|+++|++++++. ++.+ || +.+.+.++.|+|+||+|++++|++. .+.+++|++|+|+||+++.|+|.+
T Consensus 1 ~v~~~V~~~~~~~-~~~~-------~g---~~~~~~~~~l~D~TG~i~~~~W~~~~~~~~~~G~vv~i~~~~v~~~~g~~ 69 (82)
T cd04491 1 SVEGKVLSISEPR-EFTR-------DG---SEGKVQSGLVGDETGTIRFTLWDEKAADDLEPGDVVRIENAYVREFNGRL 69 (82)
T ss_pred CEEEEEEEccCCe-Eecc-------CC---CeeEEEEEEEECCCCEEEEEEECchhcccCCCCCEEEEEeEEEEecCCcE
Confidence 5899999999866 3335 65 4799999999999999999999976 667899999999999999999999
Q ss_pred EEEeCCceeEEE
Q 032330 107 RLAVDKWGRIEV 118 (143)
Q Consensus 107 ~L~ig~~g~I~~ 118 (143)
+|+++++|.|+.
T Consensus 70 ql~i~~~~~i~~ 81 (82)
T cd04491 70 ELSVGKNSEIEK 81 (82)
T ss_pred EEEeCCceEEEE
Confidence 999999999975
No 15
>PRK15491 replication factor A; Provisional
Probab=99.68 E-value=2e-16 Score=135.50 Aligned_cols=100 Identities=19% Similarity=0.307 Sum_probs=86.1
Q ss_pred CceeeeccCCCCCCCceEEEEEEecCcceeccCCCccccCCCCCCCCCCeeEEEEEeeCcceEEEEEecCCCC---CCCC
Q 032330 12 PVFIKVDQLKPGTTGHTLTVKVVSSKPVQVNKPRGARSLSSLSQPSRPPRIAECLVGDDTGAIYFTARNDQVD---IMTP 88 (143)
Q Consensus 12 ~~~~kI~dL~p~~~~v~i~~kVl~~~~~~~~~~R~~~~~~~DG~~~~~~~v~~~lVgDeTG~I~ltlW~~~~~---~i~~ 88 (143)
+.|.+|+||.+++.+++|+++|+++++.....+| +| .+++++++.|+|+||.|++|+|+++++ .+++
T Consensus 164 ~~~~~I~dl~~~~~~V~I~g~V~~~~~~r~~~~~-------~G---~~~~v~~~~l~DetG~Ir~t~W~~~a~~~~~l~~ 233 (374)
T PRK15491 164 INSQKISDIKDGDSDINIVGKVLDISDVRTFQKK-------DG---SQGRVRNITIGDETGKIRVTLWDGKTDLADKLEN 233 (374)
T ss_pred cCcccHHHcCCCCccEEEEEEEEEccCceEEEec-------CC---CeEEEEEEEEECCCCeEEEEEecchhcccccCCC
Confidence 4578999999999999999999999985423333 65 468999999999999999999998766 4789
Q ss_pred CCEEEEeceEEce--eCCeEEEEeCCceeEEEcCC
Q 032330 89 GTTVILRNAKIDM--FKGSMRLAVDKWGRIEVTEP 121 (143)
Q Consensus 89 Gd~v~I~na~~~~--~~g~~~L~ig~~g~I~~~~~ 121 (143)
||.|+|.||+++. |+|.++|++++.+.|++.++
T Consensus 234 Gd~V~i~~~~~r~~~~~g~~El~~~~~s~I~~~~~ 268 (374)
T PRK15491 234 GDSVEIINGYARTNNYSQEVEIQIGNHGSLRKTDR 268 (374)
T ss_pred CCEEEEEeceEEEeccCCCEEEEeCCCceEEECCc
Confidence 9999999999874 67899999999999998853
No 16
>PRK12366 replication factor A; Reviewed
Probab=99.59 E-value=6.1e-15 Score=133.56 Aligned_cols=100 Identities=21% Similarity=0.371 Sum_probs=86.8
Q ss_pred CCceeeeccCC---CCCCCceEEEEEEecCcceeccCCCccccCCCCCCCCCCeeEEEEEeeCcceEEEEEecCCCCC-C
Q 032330 11 KPVFIKVDQLK---PGTTGHTLTVKVVSSKPVQVNKPRGARSLSSLSQPSRPPRIAECLVGDDTGAIYFTARNDQVDI-M 86 (143)
Q Consensus 11 ~~~~~kI~dL~---p~~~~v~i~~kVl~~~~~~~~~~R~~~~~~~DG~~~~~~~v~~~lVgDeTG~I~ltlW~~~~~~-i 86 (143)
...|++|++|. ++...++|.|+|++++++. ++.| . +| ++..+++++|+|+||+|+||||++++.. +
T Consensus 392 ~~~~~~i~dI~~~~~~~~~VdVig~V~~v~~~~-~i~~---k---~G---~~~~~r~i~l~D~TG~I~vtlWg~~a~~~~ 461 (637)
T PRK12366 392 EEKIYKIKDILNLEEDDNDITVIARVVEDYPVN-EFER---S---DG---SKGKVRNIELADGTGSIRLTLWDDDAEIEI 461 (637)
T ss_pred eeccccHHHhhcccCCCcEEEEEEEEEEccCce-EEEe---c---CC---CEeEEEEEEEEeCCCEEEEEEeccccccCC
Confidence 34578888887 5677899999999999965 3333 1 66 4789999999999999999999998875 7
Q ss_pred CCCCEEEEeceEEceeCCeEEEEeCCceeEEEcC
Q 032330 87 TPGTTVILRNAKIDMFKGSMRLAVDKWGRIEVTE 120 (143)
Q Consensus 87 ~~Gd~v~I~na~~~~~~g~~~L~ig~~g~I~~~~ 120 (143)
.+|++|.|.||++++|+|+++|++++.|+|+..|
T Consensus 462 ~~G~vi~i~~~~V~~~~g~~~Ls~~~~s~i~~~p 495 (637)
T PRK12366 462 KEGDAIKILHPYVKENGDYLDLSIGRYGRIEINP 495 (637)
T ss_pred CCCCEEEEEeeEEEeCCCeeEEEecCcceEEECC
Confidence 8999999999999999999999999999999886
No 17
>PRK07211 replication factor A; Reviewed
Probab=99.57 E-value=1.8e-14 Score=126.99 Aligned_cols=100 Identities=17% Similarity=0.226 Sum_probs=88.0
Q ss_pred CCceeeeccCCCCCCCceEEEEEEecCcceeccCCCccccCCCCCCCCCCeeEEEEEeeCcceEEEEEecCCCCC-CCCC
Q 032330 11 KPVFIKVDQLKPGTTGHTLTVKVVSSKPVQVNKPRGARSLSSLSQPSRPPRIAECLVGDDTGAIYFTARNDQVDI-MTPG 89 (143)
Q Consensus 11 ~~~~~kI~dL~p~~~~v~i~~kVl~~~~~~~~~~R~~~~~~~DG~~~~~~~v~~~lVgDeTG~I~ltlW~~~~~~-i~~G 89 (143)
.|.+.+|.+|.|+. .++|.+.|+++.++. ++.| . || +++.+++++|+|+||+||||||+++++. +.+|
T Consensus 266 vp~~~~I~dl~~g~-~vdV~GvV~~v~~~r-tf~r---~---dG---~~~~vr~l~l~D~TG~IrvTLWg~~A~~~i~~G 334 (485)
T PRK07211 266 VPDTTPIESLEIDE-TVDIAGVVRSADPKR-TFDR---D---DG---SEGQVRNVRIQDDTGDIRVALWGEKADLDIGPG 334 (485)
T ss_pred ccccccHhhcCCCC-ceeEEEEEEEccCcE-EEEc---C---CC---CEeEEEEEEEEcCCCcEEEEEeCccccCCCCCC
Confidence 45668999999988 599999999999977 4455 2 66 4799999999999999999999988764 7999
Q ss_pred CEEEEeceEEceeC-CeEEEEeCCceeEEEcCC
Q 032330 90 TTVILRNAKIDMFK-GSMRLAVDKWGRIEVTEP 121 (143)
Q Consensus 90 d~v~I~na~~~~~~-g~~~L~ig~~g~I~~~~~ 121 (143)
++|+|.|++++.|. |.++|+++..|.|..+++
T Consensus 335 dvV~Ikg~~V~dg~~ggleLS~g~~s~i~~~~~ 367 (485)
T PRK07211 335 DEVVAADVEIQDGWQDDLEASAGWQSTVVVLDD 367 (485)
T ss_pred CEEEEEccEEEecCCCCEEEEecCCceEEEccc
Confidence 99999999999986 899999999999998865
No 18
>cd04475 RPA1_DBD_B RPA1_DBD_B: A subfamily of OB folds corresponding to the third OB fold, the ssDNA-binding domain (DBD)-B, of human RPA1 (also called RPA70). RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-B, RPA1 contains three other OB folds: DBD-A, DBD-C, and RPA1N. The major DNA binding activity of human RPA (hRPA) and Saccharomyces cerevisiae RPA (ScRPA) is associated with RPA1 DBD-A and DBD-B. RPA1 DBD-C is involved in trimerization. The ssDNA binding mechanism is believed to be multistep and to involve conformational change. Although ScRPA and the hRPA have similar ssDNA-binding properties, they differ functiona
Probab=99.26 E-value=5.4e-11 Score=83.75 Aligned_cols=85 Identities=18% Similarity=0.250 Sum_probs=71.8
Q ss_pred ceEEEEEEecCcceeccCCCccccCCCCCCCCCCeeEEEEEeeCcc-eEEEEEecCCCCCCCC--CCEEEEeceEEceeC
Q 032330 27 HTLTVKVVSSKPVQVNKPRGARSLSSLSQPSRPPRIAECLVGDDTG-AIYFTARNDQVDIMTP--GTTVILRNAKIDMFK 103 (143)
Q Consensus 27 v~i~~kVl~~~~~~~~~~R~~~~~~~DG~~~~~~~v~~~lVgDeTG-~I~ltlW~~~~~~i~~--Gd~v~I~na~~~~~~ 103 (143)
++|.|.|.++++......| . .| ++...++..|+|+|| .+.+|||+++++.+.. |+++.|.+++++.|+
T Consensus 2 vDvig~V~~v~~~~~i~~k---~---~g---~~~~~r~v~i~D~t~~~i~vtLWg~~a~~~~~~~~~vv~~~~~~i~~~~ 72 (101)
T cd04475 2 VDVIGVVKSVGPVTTITTK---S---TG---RELDKREITLVDESGHSVELTLWGEQAELFDGSENPVIAIKGVKVSEFN 72 (101)
T ss_pred EeEEEEEeEccCcEEEEEe---c---CC---CceeEEEEEEEeCCCCEEEEEEEHHHhhhcccCCCCEEEEEeeEEEecC
Confidence 6899999999986523333 1 25 468899999999999 9999999998877644 999999999999999
Q ss_pred CeEEEEeCCceeEEEcCC
Q 032330 104 GSMRLAVDKWGRIEVTEP 121 (143)
Q Consensus 104 g~~~L~ig~~g~I~~~~~ 121 (143)
+.+|+.+..+.|...++
T Consensus 73 -~~~l~~~~~s~i~~np~ 89 (101)
T cd04475 73 -GKSLSTGSSSTIIINPD 89 (101)
T ss_pred -CeEEeecCceeEEECCC
Confidence 58999999999988864
No 19
>COG1599 RFA1 Single-stranded DNA-binding replication protein A (RPA), large (70 kD) subunit and related ssDNA-binding proteins [DNA replication, recombination, and repair]
Probab=99.26 E-value=1.6e-11 Score=105.91 Aligned_cols=110 Identities=23% Similarity=0.341 Sum_probs=93.3
Q ss_pred cCCCCceeeeccCCCCCCCceEEEEEEecCcceeccCCCccccCCCCCCCCCCeeEEEEEeeCcceEEE-EEecCCCC-C
Q 032330 8 AKRKPVFIKVDQLKPGTTGHTLTVKVVSSKPVQVNKPRGARSLSSLSQPSRPPRIAECLVGDDTGAIYF-TARNDQVD-I 85 (143)
Q Consensus 8 ~~~~~~~~kI~dL~p~~~~v~i~~kVl~~~~~~~~~~R~~~~~~~DG~~~~~~~v~~~lVgDeTG~I~l-tlW~~~~~-~ 85 (143)
.+..+...+|.++.+++.+++++++|+++++......+ +|. .+.+.+.++||+||.+++ ++|...+. .
T Consensus 43 ~~~~~~~~~i~~~~~~~~~~~v~~~V~~~~e~~~~~~k-------~g~---~~~l~~~~v~Detg~v~~~~~~~~~a~~~ 112 (407)
T COG1599 43 VLAMESIGKISDISEASSRVNVTGRVLSIGEKKTFDRK-------RGA---EGKLAEVLVGDETGSVKTVTLWNIAALEK 112 (407)
T ss_pred hhchhhcccccccchhhccccEEEEECccccceeeecc-------ccc---ccceEEEEEecCCCCEEEEeecccccccc
Confidence 45567888999999999999999999999974423333 553 489999999999999999 79998775 6
Q ss_pred CCCCCEEEEeceEEceeCCeEEEEeCCceeEEEcCCCceEEc
Q 032330 86 MTPGTTVILRNAKIDMFKGSMRLAVDKWGRIEVTEPADFEVK 127 (143)
Q Consensus 86 i~~Gd~v~I~na~~~~~~g~~~L~ig~~g~I~~~~~~~~~v~ 127 (143)
+++||+++|.|++++.|+|+.++++++.+.+...++....+.
T Consensus 113 ~e~Gdv~~i~~~~~~~~~~~~~~~~~~~~~v~~~~~~~~~~~ 154 (407)
T COG1599 113 LEPGDVIRIRNAYTSLYRGGKRLSVGRVGSVADVDDEEDEAR 154 (407)
T ss_pred CCccceEEecCcccccccCceeeecccccccccCchhhcccc
Confidence 899999999999999999999999999999988876544433
No 20
>cd04474 RPA1_DBD_A RPA1_DBD_A: A subfamily of OB folds corresponding to the second OB fold, the ssDNA-binding domain (DBD)-A, of human RPA1 (also called RPA70). RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-A, RPA1 contains three other OB folds: DBD-B, DBD-C, and RPA1N. The major DNA binding activity of human RPA (hRPA) and Saccharomyces cerevisiae RPA (ScRPA) is associated with DBD-A and DBD-B of RPA1. RPA1 DBD-C is involved in trimerization. The ssDNA-binding mechanism is believed to be multistep and to involve conformational change. Although ScRPA and the hRPA have similar ssDNA-binding properties, they differ funct
Probab=99.25 E-value=6.2e-11 Score=84.61 Aligned_cols=90 Identities=16% Similarity=0.243 Sum_probs=71.0
Q ss_pred eeccCCCCCCCceEEEEEEecCcceeccCCCccccCCCCCCCCCCeeEEEEEeeC-cceEEEEEecCCCC----CCCCCC
Q 032330 16 KVDQLKPGTTGHTLTVKVVSSKPVQVNKPRGARSLSSLSQPSRPPRIAECLVGDD-TGAIYFTARNDQVD----IMTPGT 90 (143)
Q Consensus 16 kI~dL~p~~~~v~i~~kVl~~~~~~~~~~R~~~~~~~DG~~~~~~~v~~~lVgDe-TG~I~ltlW~~~~~----~i~~Gd 90 (143)
+|++|.|++.+..|.|+|+.+++.. .++.+ ++ .+++.++.|.|+ +|.|+.++|++.++ .|++|+
T Consensus 1 pI~~L~p~~~~~~I~~rV~~k~~~~-~f~~~------~~----~g~~~~~~l~De~~~~I~~t~~~~~~~~f~~~l~eG~ 69 (104)
T cd04474 1 PISSLNPYQNKWTIKARVTNKSDIR-TWSNA------RG----EGKLFSFDLLDEDGGEIRATFFNDAVDKFYDLLEVGK 69 (104)
T ss_pred ChhHccCCCCcEEEEEEEeeccccc-cccCC------CC----CcEEEEEEEEECCCCEEEEEEehHHHHHhhccccccc
Confidence 4899999999999999999999855 44431 22 578999999999 99999999987654 689999
Q ss_pred EEEEeceEEceeCC-------eEEEEeCCceeE
Q 032330 91 TVILRNAKIDMFKG-------SMRLAVDKWGRI 116 (143)
Q Consensus 91 ~v~I~na~~~~~~g-------~~~L~ig~~g~I 116 (143)
++.|.++.++..++ ..++.+++++.|
T Consensus 70 vy~i~~~~V~~a~~~y~~~~~~yeI~f~~~t~~ 102 (104)
T cd04474 70 VYYISKGSVKVANKKFNTLKNDYEITFNRDTSI 102 (104)
T ss_pred EEEEeccEEeeccccCCCCCCcEEEEECCCcEE
Confidence 99999999977643 344555544443
No 21
>TIGR00617 rpa1 replication factor-a protein 1 (rpa1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=99.00 E-value=4.5e-09 Score=95.22 Aligned_cols=98 Identities=18% Similarity=0.269 Sum_probs=82.8
Q ss_pred ceeeeccCCCCCCCceEEEEEEecCcceeccCCCccccCCCCCCCCCCeeEEEEEeeCcceEEEEEecCCC----CCCCC
Q 032330 13 VFIKVDQLKPGTTGHTLTVKVVSSKPVQVNKPRGARSLSSLSQPSRPPRIAECLVGDDTGAIYFTARNDQV----DIMTP 88 (143)
Q Consensus 13 ~~~kI~dL~p~~~~v~i~~kVl~~~~~~~~~~R~~~~~~~DG~~~~~~~v~~~lVgDeTG~I~ltlW~~~~----~~i~~ 88 (143)
.+.+|++|.|.+.+..|.++|+.+++.+ .+.+ . +| .+++.++.+.|++|.|+.++|++++ +.|++
T Consensus 179 ~~~pI~~L~py~~~wtIkaRV~~Ks~ir-~~~~---~---~g----egkvfsv~L~Degg~Irat~f~~~~dkf~~~l~e 247 (608)
T TIGR00617 179 RVMPIASLSPYQNKWTIKARVTNKSEIR-TWSN---A---RG----EGKLFNVELLDESGEIRATAFNEQADKFYDIIQE 247 (608)
T ss_pred ceEEHHHCCCCCCceEEEEEEEeccccc-eecC---C---CC----CceeeEEEEecCCCeEEEEECchHHHHHhhhccc
Confidence 5899999999999999999999999855 3433 1 33 5789999999999999999999866 45789
Q ss_pred CCEEEEeceEEceeC-------CeEEEEeCCceeEEEcCC
Q 032330 89 GTTVILRNAKIDMFK-------GSMRLAVDKWGRIEVTEP 121 (143)
Q Consensus 89 Gd~v~I~na~~~~~~-------g~~~L~ig~~g~I~~~~~ 121 (143)
|+++.|.++.++..+ ...+|.+++++.|++.++
T Consensus 248 G~VY~Is~~~Vk~an~~y~~~~~~yei~f~~~T~I~~~~d 287 (608)
T TIGR00617 248 GKVYYISKGSLKPANKQFTNLGNDYEMTLDRDTVIEECED 287 (608)
T ss_pred CCEEEECceEEEEccccccCCCCCEEEEECCCeEEEECCC
Confidence 999999999987653 357999999999998753
No 22
>TIGR00617 rpa1 replication factor-a protein 1 (rpa1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=98.79 E-value=3.1e-08 Score=89.77 Aligned_cols=102 Identities=19% Similarity=0.214 Sum_probs=82.8
Q ss_pred CCCCceeeeccCCCCC--CCceEEEEEEecCcceeccCCCccccCCCCCCCCCCeeEEEEEeeCcc-eEEEEEecCCCCC
Q 032330 9 KRKPVFIKVDQLKPGT--TGHTLTVKVVSSKPVQVNKPRGARSLSSLSQPSRPPRIAECLVGDDTG-AIYFTARNDQVDI 85 (143)
Q Consensus 9 ~~~~~~~kI~dL~p~~--~~v~i~~kVl~~~~~~~~~~R~~~~~~~DG~~~~~~~v~~~lVgDeTG-~I~ltlW~~~~~~ 85 (143)
+..-.|++|.||.... ..|+|.|.|.++++......| . +| .....++..|.|+|| +|++|||++++..
T Consensus 293 ~~~~~f~~i~dI~~~~~~~~VDVIGvV~~v~~~~~i~~k---~---~g---~~~~kR~i~L~D~sg~sI~vTLWG~~A~~ 363 (608)
T TIGR00617 293 KIQFNFVKIDDIGGYEGNSLVDVIGIVQSVSPTQTITSR---K---NN---KEFPKRDITLVDDSGKSVRVTLWGDDATK 363 (608)
T ss_pred cccccceEHHHhhhhcCCCCccEEEEEeEecCceEEEEc---C---CC---CeeeeEEEEEEeCCCCEEEEEEEhhhhhh
Confidence 3356789999997543 378999999999996623324 2 55 467889999999999 6999999988755
Q ss_pred C--CCCCEEEEeceEEceeCCeEEEEeCCceeEEEcC
Q 032330 86 M--TPGTTVILRNAKIDMFKGSMRLAVDKWGRIEVTE 120 (143)
Q Consensus 86 i--~~Gd~v~I~na~~~~~~g~~~L~ig~~g~I~~~~ 120 (143)
+ .+|++|.|.+++++.|+| .+|+.+..++|...+
T Consensus 364 ~~~~~~~Vva~kg~~V~~f~g-~sLs~~~~S~i~iNP 399 (608)
T TIGR00617 364 FDVSVQPVIAIKGVRVSDFGG-KSLSTGGSSTIIVNP 399 (608)
T ss_pred cCCCCCCEEEEEeEEEEecCC-ceEeccCCceEEECC
Confidence 4 589999999999999955 699999999997765
No 23
>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=98.41 E-value=1.9e-06 Score=56.06 Aligned_cols=67 Identities=25% Similarity=0.324 Sum_probs=54.0
Q ss_pred ceEEEEEEecCcceeccCCCccccCCCCCCCCCCeeEEEEEeeCcceEEEEEec----CCCCCCCCCCEEEEeceEEcee
Q 032330 27 HTLTVKVVSSKPVQVNKPRGARSLSSLSQPSRPPRIAECLVGDDTGAIYFTARN----DQVDIMTPGTTVILRNAKIDMF 102 (143)
Q Consensus 27 v~i~~kVl~~~~~~~~~~R~~~~~~~DG~~~~~~~v~~~lVgDeTG~I~ltlW~----~~~~~i~~Gd~v~I~na~~~~~ 102 (143)
|.|.|+|.++. . . .+.+..+.|.|+||.+.+.+|+ ...+.+++|+.|+++ |.++.+
T Consensus 1 V~v~G~V~~~~--~---~--------------~~~~~~~~l~D~tg~i~~~~~~~~~~~~~~~l~~g~~v~v~-G~v~~~ 60 (75)
T PF01336_consen 1 VTVEGRVTSIR--R---S--------------GGKIVFFTLEDGTGSIQVVFFNEEYERFREKLKEGDIVRVR-GKVKRY 60 (75)
T ss_dssp EEEEEEEEEEE--E---E--------------ETTEEEEEEEETTEEEEEEEETHHHHHHHHTS-TTSEEEEE-EEEEEE
T ss_pred CEEEEEEEEEE--c---C--------------CCCEEEEEEEECCccEEEEEccHHhhHHhhcCCCCeEEEEE-EEEEEE
Confidence 56888888876 1 1 1458999999999999999999 345678999999999 888999
Q ss_pred CCe-EEEEeCCc
Q 032330 103 KGS-MRLAVDKW 113 (143)
Q Consensus 103 ~g~-~~L~ig~~ 113 (143)
++. ++|.+.+.
T Consensus 61 ~~~~~~l~~~~i 72 (75)
T PF01336_consen 61 NGGELELIVPKI 72 (75)
T ss_dssp TTSSEEEEEEEE
T ss_pred CCccEEEEECEE
Confidence 987 99987653
No 24
>cd04497 hPOT1_OB1_like hPOT1_OB1_like: A subfamily of OB folds similar to the first OB fold (OB1) of human protection of telomeres 1 protein (hPOT1), the single OB fold of the N-terminal domain of Schizosaccharomyces pombe POT1 (SpPOT1), and the first OB fold of the N-terminal domain of the alpha subunit (OB1Nalpha) of Oxytricha nova telomere end binding protein (OnTEBP). POT1 proteins recognize single-stranded (ss) 3-prime ends of the telomere. A 3-prime ss overhang is conserved in ciliated protozoa, yeast, and mammals. SpPOT1 is essential for telomere maintenance. It binds specifically to the ss G-rich telomeric sequence (GGTTAC) of S. pombe. hPOT1 binds specifically to ss telomeric DNA repeats ending with the sequence GGTTAG. Deletion of the S. pombe pot1+ gene results in a rapid loss of telomere sequences, chromosome mis-segregation and chromosome circularization. hPOT1 is implicated in telomere length regulation. The hPOT1 monomer consists of two closely connected OB folds (OB1-OB
Probab=98.34 E-value=6.1e-06 Score=61.60 Aligned_cols=87 Identities=14% Similarity=0.161 Sum_probs=70.4
Q ss_pred CceeeeccCC-CCCCCceEEEEEEecCcceeccCCCccccCCCCCCCCCCeeEEEEEeeCcce----EEEEEecCC---C
Q 032330 12 PVFIKVDQLK-PGTTGHTLTVKVVSSKPVQVNKPRGARSLSSLSQPSRPPRIAECLVGDDTGA----IYFTARNDQ---V 83 (143)
Q Consensus 12 ~~~~kI~dL~-p~~~~v~i~~kVl~~~~~~~~~~R~~~~~~~DG~~~~~~~v~~~lVgDeTG~----I~ltlW~~~---~ 83 (143)
+.|++|++|. .....+|+.+.|++..++. .. .| +...+...|.|+|+. +++.+|.+. .
T Consensus 1 ~~f~~i~~~~~~~~~~v~vigVV~~~~~p~--~s--------~g----~d~~~tl~i~D~S~~~~~~l~v~~F~~~~~~L 66 (138)
T cd04497 1 YKYTPLSSALKESGGSVNVIGVVVDAGPPV--RS--------KG----TDYCCTLTITDPSLANSDGLTVKLFRPNEESL 66 (138)
T ss_pred CceEeHHHHHhccCCeEEEEEEEeecCCCc--cc--------CC----CcEEEEEEEECCCCCCCCcEEEEEECCChhhC
Confidence 3588899998 4556699999999999754 22 23 247899999999875 999999864 3
Q ss_pred CCCCCCCEEEEeceEEceeCCeEEEEeCC
Q 032330 84 DIMTPGTTVILRNAKIDMFKGSMRLAVDK 112 (143)
Q Consensus 84 ~~i~~Gd~v~I~na~~~~~~g~~~L~ig~ 112 (143)
..+++||+|.++++.++.|+|++.+....
T Consensus 67 P~v~~GDVIll~~~kv~~~~g~~~~~~~~ 95 (138)
T cd04497 67 PIVKVGDIILLRRVKIQSYNGKPQGISND 95 (138)
T ss_pred CCCCCCCEEEEEEEEEEEECCceEEEECC
Confidence 43588999999999999999998888777
No 25
>cd04483 hOBFC1_like hOBFC1_like: A subfamily of OB folds similar to that found in human OB fold containing protein 1 (hOBFC1). Members of this group belong to the Replication protein A subunit 2 (RPA2) family of OB folds. RPA is a nuclear ssDNA binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). The OB fold domain of RPA2 has dual roles in ssDNA binding and trimerization.
Probab=97.89 E-value=0.00012 Score=51.40 Aligned_cols=49 Identities=16% Similarity=0.325 Sum_probs=41.0
Q ss_pred eEEEEEeeCcceEEEEEecCC------------------------CCCCCCCCEEEEeceEEceeCCeEEEEeC
Q 032330 62 IAECLVGDDTGAIYFTARNDQ------------------------VDIMTPGTTVILRNAKIDMFKGSMRLAVD 111 (143)
Q Consensus 62 v~~~lVgDeTG~I~ltlW~~~------------------------~~~i~~Gd~v~I~na~~~~~~g~~~L~ig 111 (143)
-....|.|.||+|...+|... .+.+++|+.++++ |.++.|+|.++|++.
T Consensus 15 ~~~~tLdDgTG~Ie~~~W~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~G~vvrV~-G~i~~frg~~ql~i~ 87 (92)
T cd04483 15 FYSFGVDDGTGVVNCVCWKNLSYAEVSSRSDAARILKSALMALKQAKVLEIGDLLRVR-GSIRTYRGEREINAS 87 (92)
T ss_pred eEEEEEecCCceEEEEEEcCcCcccccccccccccccccccccccccccCCCCEEEEE-EEEeccCCeeEEEEE
Confidence 467789999999999999732 3347999999999 677899999999865
No 26
>PRK13480 3'-5' exoribonuclease YhaM; Provisional
Probab=97.74 E-value=0.00015 Score=61.36 Aligned_cols=80 Identities=15% Similarity=0.198 Sum_probs=62.5
Q ss_pred eeccCCCCCCCceEEEEEEecCcceeccCCCccccCCCCCCCCCCeeEEEEEeeCcceEEEEEecC---CCCCCCCCCEE
Q 032330 16 KVDQLKPGTTGHTLTVKVVSSKPVQVNKPRGARSLSSLSQPSRPPRIAECLVGDDTGAIYFTARND---QVDIMTPGTTV 92 (143)
Q Consensus 16 kI~dL~p~~~~v~i~~kVl~~~~~~~~~~R~~~~~~~DG~~~~~~~v~~~lVgDeTG~I~ltlW~~---~~~~i~~Gd~v 92 (143)
+|+||+++.. ++..+.|-++..+. .| +|+ ....+.++|.||.|.-.+|+. +...+++|++|
T Consensus 4 ~i~~l~~g~~-v~~~~lv~~~~~~~---~k-------nG~-----~yl~l~l~D~tG~I~ak~W~~~~~~~~~~~~g~vv 67 (314)
T PRK13480 4 GIEELEVGEQ-VDHFLLIKSATKGV---AS-------NGK-----PFLTLILQDKSGDIEAKLWDVSPEDEATYVPETIV 67 (314)
T ss_pred hHhhcCCCCE-eeEEEEEEEceeee---cC-------CCC-----eEEEEEEEcCCcEEEEEeCCCChhhHhhcCCCCEE
Confidence 6899999874 77777777765432 23 452 488999999999999999984 34558999999
Q ss_pred EEeceEEceeCCeEEEEeCC
Q 032330 93 ILRNAKIDMFKGSMRLAVDK 112 (143)
Q Consensus 93 ~I~na~~~~~~g~~~L~ig~ 112 (143)
++.+-. ..|+|.++|.|.+
T Consensus 68 ~v~G~v-~~y~g~~Ql~i~~ 86 (314)
T PRK13480 68 HVKGDI-INYRGRKQLKVNQ 86 (314)
T ss_pred EEEEEE-EEECCcceEEEEE
Confidence 998766 5899999998763
No 27
>cd04492 YhaM_OBF_like YhaM_OBF_like: A subfamily of OB folds similar to that found in Bacillus subtilis YhaM and Staphylococcus aureus cmp-binding factor-1 (SaCBF1). Both these proteins are 3'-to-5'exoribonucleases. YhaM requires Mn2+ or Co2+ for activity and is inactive in the presence of Mg2+. YhaM also has a Mn2+ dependent 3'-to-5'single-stranded DNA exonuclease activity. SaCBF is also a double-stranded DNA binding protein, binding specifically to cmp, the replication enhancer found in S. aureus plasmid pT181. Proteins in this group combine an N-terminal OB fold with a C-terminal HD domain. The HD domain is found in metal-dependent phosphohydrolases.
Probab=97.73 E-value=0.0004 Score=45.77 Aligned_cols=50 Identities=18% Similarity=0.406 Sum_probs=41.5
Q ss_pred eeEEEEEeeCcceEEEEEecCCC---CCCCCCCEEEEeceEEceeCCeEEEEeC
Q 032330 61 RIAECLVGDDTGAIYFTARNDQV---DIMTPGTTVILRNAKIDMFKGSMRLAVD 111 (143)
Q Consensus 61 ~v~~~lVgDeTG~I~ltlW~~~~---~~i~~Gd~v~I~na~~~~~~g~~~L~ig 111 (143)
.+..+.+.|.||.+.+++|++.. ..+++|..+.+. |.++.++|.++|.+.
T Consensus 19 ~~~~~~l~D~tg~i~~~~f~~~~~~~~~l~~g~~v~v~-G~v~~~~~~~~l~~~ 71 (83)
T cd04492 19 PYLALTLQDKTGEIEAKLWDASEEDEEKFKPGDIVHVK-GRVEEYRGRLQLKIQ 71 (83)
T ss_pred cEEEEEEEcCCCeEEEEEcCCChhhHhhCCCCCEEEEE-EEEEEeCCceeEEEE
Confidence 58999999999999999999542 458999999999 556768888888754
No 28
>cd04478 RPA2_DBD_D RPA2_DBD_D: A subfamily of OB folds corresponding to the OB fold of the central ssDNA-binding domain (DBD)-D of human RPA2 (also called RPA32). RPA2 is a subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B; RPA2 DBD-D is a weak ssDNA-binding domain. RPA2 DBD-D is also involved in trimerization. The ssDNA binding mechanism is believed to be multistep and to involve conformational change. N-terminal to human RPA2 DBD-D is a domain containing all the known phosphorylation sites of RPA. Human RPA2 is phosphorylated in a cell cycle dependent manner in response to DNA dam
Probab=97.67 E-value=0.00077 Score=46.37 Aligned_cols=70 Identities=21% Similarity=0.183 Sum_probs=52.9
Q ss_pred ceEEEEEEecCcceeccCCCccccCCCCCCCCCCeeEEEEEeeCcceEEEEEecC-------CCCCCCCCCEEEEeceEE
Q 032330 27 HTLTVKVVSSKPVQVNKPRGARSLSSLSQPSRPPRIAECLVGDDTGAIYFTARND-------QVDIMTPGTTVILRNAKI 99 (143)
Q Consensus 27 v~i~~kVl~~~~~~~~~~R~~~~~~~DG~~~~~~~v~~~lVgDeTG~I~ltlW~~-------~~~~i~~Gd~v~I~na~~ 99 (143)
+.+.|.|.++... ..-....+.|.||+|....|+. ..+.+++|+.|++.+-.
T Consensus 2 v~~vG~V~~~~~~--------------------~~~~~~tL~D~TG~I~~~~W~~~~~~~~~~~~~~~~g~~v~v~G~v- 60 (95)
T cd04478 2 VTLVGVVRNVEEQ--------------------STNITYTIDDGTGTIEVRQWLDDDNDDSSEVEPIEEGTYVRVFGNL- 60 (95)
T ss_pred EEEEEEEEeeeEc--------------------ccEEEEEEECCCCcEEEEEeCCCCCcccccccccccCCEEEEEEEE-
Confidence 5678888886631 1357788999999999999973 24457899999998665
Q ss_pred ceeCCeEEEEeCCceeEEEcC
Q 032330 100 DMFKGSMRLAVDKWGRIEVTE 120 (143)
Q Consensus 100 ~~~~g~~~L~ig~~g~I~~~~ 120 (143)
+.|+|.++|.+. +|.+++
T Consensus 61 ~~~~g~~ql~i~---~i~~v~ 78 (95)
T cd04478 61 KSFQGKKSIMAF---SIRPVT 78 (95)
T ss_pred cccCCeeEEEEE---EEEEeC
Confidence 889999999865 444443
No 29
>cd03524 RPA2_OBF_family RPA2_OBF_family: A family of oligonucleotide binding (OB) folds with similarity to the OB fold of the single strand (ss) DNA-binding domain (DBD)-D of human RPA2 (also called RPA32). RPA2 is a subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). RPA contains six OB folds, which are involved in ssDNA binding and in trimerization. The ssDNA binding mechanism is believed to be multistep and to involve conformational change. This family also includes OB folds similar to those found in Escherichia coli SSB, the wedge domain of E. coli RecG (a branched-DNA-specific helicase), E. coli ssDNA specific exodeoxyribonuclease VII large subunit, Pyroco
Probab=97.52 E-value=0.001 Score=41.63 Aligned_cols=65 Identities=22% Similarity=0.420 Sum_probs=51.2
Q ss_pred EEEEEEecCcceeccCCCccccCCCCCCCCCCeeEEEEEeeCc-ceEEEEEecCCC----CCCCCCCEEEEeceEEceeC
Q 032330 29 LTVKVVSSKPVQVNKPRGARSLSSLSQPSRPPRIAECLVGDDT-GAIYFTARNDQV----DIMTPGTTVILRNAKIDMFK 103 (143)
Q Consensus 29 i~~kVl~~~~~~~~~~R~~~~~~~DG~~~~~~~v~~~lVgDeT-G~I~ltlW~~~~----~~i~~Gd~v~I~na~~~~~~ 103 (143)
+.++|.++.... .| ..++...|.|.| |.+.+.+|.+.. ..+++|+.+.+. +.++.++
T Consensus 2 v~g~v~~~~~~~------------~~-----~~~~~~~l~D~~~~~i~~~~~~~~~~~~~~~~~~g~~v~v~-g~v~~~~ 63 (75)
T cd03524 2 IVGIVVAVEEIR------------TE-----GKVLIFTLTDGTGGTIRVTLFGELAEELENLLKEGQVVYIK-GKVKKFR 63 (75)
T ss_pred eEEEEEeecccc------------cC-----CeEEEEEEEcCCCCEEEEEEEchHHHHHHhhccCCCEEEEE-EEEEecC
Confidence 677888777422 01 248999999999 999999998653 357999999999 8888888
Q ss_pred CeEEEEeC
Q 032330 104 GSMRLAVD 111 (143)
Q Consensus 104 g~~~L~ig 111 (143)
+.++|.+.
T Consensus 64 ~~~~l~~~ 71 (75)
T cd03524 64 GRLQLIVE 71 (75)
T ss_pred CeEEEEee
Confidence 88888765
No 30
>cd04485 DnaE_OBF DnaE_OBF: A subfamily of OB folds corresponding to the C-terminal OB-fold nucleic acid binding domain of Thermus aquaticus and Escherichia coli type C replicative DNA polymerase III alpha subunit (DnaE). The DNA polymerase holoenzyme of E. coli contains two copies of this replicative polymerase, each of which copies a different DNA strand. This group also contains Bacillus subtilis DnaE. Replication in B. subtilis and Staphylococcus aureus requires two different type C polymerases, polC and DnaE, both of which are thought to be included in the DNA polymerase holoenzyme. At the B. subtilis replication fork, polC appears to be involved in leading strand synthesis and DnaE in lagging strand synthesis.
Probab=97.40 E-value=0.0012 Score=42.96 Aligned_cols=50 Identities=22% Similarity=0.375 Sum_probs=40.7
Q ss_pred eeEEEEEeeCcceEEEEEecCC----CCCCCCCCEEEEeceEEceeCCeEEEEeC
Q 032330 61 RIAECLVGDDTGAIYFTARNDQ----VDIMTPGTTVILRNAKIDMFKGSMRLAVD 111 (143)
Q Consensus 61 ~v~~~lVgDeTG~I~ltlW~~~----~~~i~~Gd~v~I~na~~~~~~g~~~L~ig 111 (143)
.+..+.+.|.||.+.+++|++. .+.+++|..+.+.+ .++.++|.++|.+.
T Consensus 19 ~~~~~~l~D~tg~~~~~~f~~~~~~~~~~l~~g~~v~v~G-~v~~~~~~~~l~~~ 72 (84)
T cd04485 19 RMAFVTLEDLTGSIEVVVFPETYEKYRDLLKEDALLLVEG-KVERRDGGLRLIAE 72 (84)
T ss_pred EEEEEEEEeCCCeEEEEECHHHHHHHHHHhcCCCEEEEEE-EEEecCCceEEEee
Confidence 5899999999999999999743 34579999998875 45667788888765
No 31
>cd04488 RecG_wedge_OBF RecG_wedge_OBF: A subfamily of OB folds corresponding to the OB fold found in the N-terminal (wedge) domain of Escherichia coli RecG. RecG is a branched-DNA-specific helicase, which catalyzes the interconversion of a DNA replication fork to a four-stranded (Holliday) junction in vivo and in vitro. This interconversion provides a route to repair stalled forks. The RecG monomer contains three domains. The N-terminal domain is named for its wedge structure, and may provide the specificity of RecG for binding branched-DNA structures. During the reversal of fork to Holliday junction, the wedge domain is fixed at the junction of the fork where the leading and lagging strand duplex arms meet, and is thought to promote the unwinding of the nascent leading and lagging strands. In order to form the Holliday junction, these nascent strands would be annealed, and the parental strands reannealed. The wedge domain may also be a processivity factor of RecG on these branched cha
Probab=97.21 E-value=0.0034 Score=40.05 Aligned_cols=48 Identities=23% Similarity=0.405 Sum_probs=38.4
Q ss_pred eeEEEEEeeCcceEEEEEec-C--CCCCCCCCCEEEEeceEEceeCCeEEEE
Q 032330 61 RIAECLVGDDTGAIYFTARN-D--QVDIMTPGTTVILRNAKIDMFKGSMRLA 109 (143)
Q Consensus 61 ~v~~~lVgDeTG~I~ltlW~-~--~~~~i~~Gd~v~I~na~~~~~~g~~~L~ 109 (143)
.+..+.+.|++|.+.++.|+ . ....+++|+.+.+.+-. +.|+|.++|.
T Consensus 18 ~~~~~~~~D~~g~i~~~~F~~~~~~~~~~~~G~~~~v~Gkv-~~~~~~~qi~ 68 (75)
T cd04488 18 RRLKVTLSDGTGTLTLVFFNFQPYLKKQLPPGTRVRVSGKV-KRFRGGLQIV 68 (75)
T ss_pred cEEEEEEEcCCCEEEEEEECCCHHHHhcCCCCCEEEEEEEE-eecCCeeEEe
Confidence 48899999999999999998 3 24568999999888555 5677777664
No 32
>cd04481 RPA1_DBD_B_like RPA1_DBD_B_like: A subgroup of uncharacterized, plant OB folds with similarity to the third OB fold, the ssDNA-binding domain (DBD)-B, of human RPA1 (also called RPA70). RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-B, RPA1 contains three other OB folds: DBD-A, DBD-C, and RPA1N. The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B. RPA1 DBD-C is involved in trimerization. The ssDNA binding mechanism is believed to be multistep and to involve conformational change.
Probab=97.07 E-value=0.0041 Score=44.04 Aligned_cols=82 Identities=16% Similarity=0.245 Sum_probs=61.2
Q ss_pred eEEEEEEecCcceeccCCCccccCCCCCCCCCCeeEEEEEeeCcc-eEEEEEecCCCCCC--------CCCCEEEEec-e
Q 032330 28 TLTVKVVSSKPVQVNKPRGARSLSSLSQPSRPPRIAECLVGDDTG-AIYFTARNDQVDIM--------TPGTTVILRN-A 97 (143)
Q Consensus 28 ~i~~kVl~~~~~~~~~~R~~~~~~~DG~~~~~~~v~~~lVgDeTG-~I~ltlW~~~~~~i--------~~Gd~v~I~n-a 97 (143)
++.|.|.++++.. ...+ .| ....-.+..|-|.+| ++.+|||++++..+ ..+-+|-|.. +
T Consensus 1 DviG~i~~v~~~~-~~~~-------~~---~~~~kr~~~i~D~~~~~l~~tlwG~~A~~f~~~~~~~~~~~~VVav~~~~ 69 (106)
T cd04481 1 DVIGVIVDVGPLE-ELPP-------VN---KPSRKLDFEIRDLSDERLKCTLWGEYAEEFDAKFQSAGNGEPVVAVLRFW 69 (106)
T ss_pred CeeEEEEEecceE-eccc-------CC---ccceEEEEEEEeCCCCEEEEEEEHHHHHHHHHHHHHhCCCCcEEEEEEeE
Confidence 4678899999855 2222 22 467888999999996 99999999887664 3555676655 9
Q ss_pred EEceeCCeEEEEeC-CceeEEEcC
Q 032330 98 KIDMFKGSMRLAVD-KWGRIEVTE 120 (143)
Q Consensus 98 ~~~~~~g~~~L~ig-~~g~I~~~~ 120 (143)
.++.|+|...|+-. ..+++...|
T Consensus 70 rV~~~~g~~~ls~~~~~s~v~inp 93 (106)
T cd04481 70 KIKEYKGPKSLSNSFGASKVYINP 93 (106)
T ss_pred EEEEEcCCcEEEcCCCceEEEECC
Confidence 99999997888877 666776664
No 33
>cd04480 RPA1_DBD_A_like RPA1_DBD_A_like: A subgroup of uncharacterized plant OB folds with similarity to the second OB fold, the ssDNA-binding domain (DBD)-A, of human RPA1 (also called RPA70). RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-A, RPA1 contains three other OB folds: DBD-B, DBD-C, and RPA1N. The major DNA binding activity of RPA is associated with DBD-A and DBD-B of RPA1. RPA1 DBD-C is involved in trimerization. The ssDNA-binding mechanism is believed to be multistep and to involve conformational change.
Probab=96.77 E-value=0.0058 Score=41.61 Aligned_cols=64 Identities=20% Similarity=0.208 Sum_probs=50.3
Q ss_pred EEEEEEecCcceeccCCCccccCCCCCCCCCCeeEEEEEeeCcc-eEEEEEecCC----CCCCCCCCEEEEeceEEceeC
Q 032330 29 LTVKVVSSKPVQVNKPRGARSLSSLSQPSRPPRIAECLVGDDTG-AIYFTARNDQ----VDIMTPGTTVILRNAKIDMFK 103 (143)
Q Consensus 29 i~~kVl~~~~~~~~~~R~~~~~~~DG~~~~~~~v~~~lVgDeTG-~I~ltlW~~~----~~~i~~Gd~v~I~na~~~~~~ 103 (143)
|.++|+.++... .. ..+...++++.||.| .|..+.+.++ .+.+++|.++.|.|..+...+
T Consensus 2 I~Vrv~r~W~~~---~~------------~~~~~~~miL~De~G~~I~a~i~~~~~~~f~~~L~eg~vy~is~f~v~~~~ 66 (86)
T cd04480 2 ICVRVLRLWDVY---NN------------ASGESLEMVLVDEKGNRIHATIPKRLAAKFRPLLKEGKWYTISNFEVAPNT 66 (86)
T ss_pred EEEEEEEEEcCc---CC------------CCCcEEEEEEEcCCCCEEEEEECHHHHHhhhhhceeCCEEEEeeEEEEcCC
Confidence 789999999643 11 146789999999999 9999999864 455789999999998887665
Q ss_pred CeEE
Q 032330 104 GSMR 107 (143)
Q Consensus 104 g~~~ 107 (143)
+..+
T Consensus 67 ~~y~ 70 (86)
T cd04480 67 GSYR 70 (86)
T ss_pred Cccc
Confidence 4333
No 34
>PF02765 POT1: Telomeric single stranded DNA binding POT1/CDC13; InterPro: IPR011564 This entry represents a domain that binds single stranded telomeric DNA and adopts an OB fold []. It includes the proteins POT1 and CDC13 which have been shown to regulate telomere length, replication and capping [, , ]. ; GO: 0003677 DNA binding, 0000723 telomere maintenance, 0000784 nuclear chromosome, telomeric region; PDB: 1S40_A 1KXL_A 1PH7_A 1PH9_A 1PH2_A 1OTC_A 1PHJ_A 1JB7_A 1PA6_A 1PH1_A ....
Probab=96.75 E-value=0.012 Score=44.17 Aligned_cols=84 Identities=14% Similarity=0.129 Sum_probs=63.4
Q ss_pred CCCCCceEEEEEEecCcc--eeccCCCccccCCCCCCCCCCeeEEEEEeeCc--------ceEEEEEecC---CCCCCCC
Q 032330 22 PGTTGHTLTVKVVSSKPV--QVNKPRGARSLSSLSQPSRPPRIAECLVGDDT--------GAIYFTARND---QVDIMTP 88 (143)
Q Consensus 22 p~~~~v~i~~kVl~~~~~--~~~~~R~~~~~~~DG~~~~~~~v~~~lVgDeT--------G~I~ltlW~~---~~~~i~~ 88 (143)
....-+|+.|.|++.... . +.| | ...+++..|-|.+ -.+.+.++.. ....++.
T Consensus 10 ~~~~~vnvigVV~~~~~p~~~--~t~--------g----~D~~~tl~i~D~S~~~~~~~~~~l~v~iF~~~~~~LP~v~~ 75 (146)
T PF02765_consen 10 KFGKFVNVIGVVVDFSPPNPK--KTR--------G----TDYMCTLTITDPSLNDSNQKLSGLTVNIFRPHKESLPNVKS 75 (146)
T ss_dssp TSSEEEEEEEEEEEEEEECTE--EES--------S----SCEEEEEEEEBTTCSCSSCCCCEEEEEEEESSHHHSCTTCS
T ss_pred cCCCEEEEEEEEEEccCCcce--EcC--------C----CcEEEEEEEECCCCCccccccCCEEEEEECCCHHHCCCCCC
Confidence 334568999999999875 3 222 2 3579999999998 4799999943 3444555
Q ss_pred -CCEEEEeceEEceeCCeEEEEeCCc--eeEEEc
Q 032330 89 -GTTVILRNAKIDMFKGSMRLAVDKW--GRIEVT 119 (143)
Q Consensus 89 -Gd~v~I~na~~~~~~g~~~L~ig~~--g~I~~~ 119 (143)
||+|++++..++.|+|++.+..+.. .....-
T Consensus 76 ~GDii~l~r~kv~~~~~~~~~~~~~~~~ss~~vf 109 (146)
T PF02765_consen 76 VGDIIRLRRVKVQSYNGKPQGLSNSTSNSSWAVF 109 (146)
T ss_dssp TTHEEEEEEEEEEEETTEEEEEEECECTEEEEEE
T ss_pred CCCEEEEEEEEEEEECCEEEEEecCCCcEEEEEE
Confidence 9999999999999999999888766 444333
No 35
>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=96.66 E-value=0.023 Score=37.29 Aligned_cols=50 Identities=16% Similarity=0.129 Sum_probs=40.6
Q ss_pred eEEEEEeeCcceEEEEEecCC----CCCCCCCCEEEEeceEEc-eeCCeEEEEeC
Q 032330 62 IAECLVGDDTGAIYFTARNDQ----VDIMTPGTTVILRNAKID-MFKGSMRLAVD 111 (143)
Q Consensus 62 v~~~lVgDeTG~I~ltlW~~~----~~~i~~Gd~v~I~na~~~-~~~g~~~L~ig 111 (143)
++-+.+-|.+|.+.+++|.+. .+.+++|+.|.|.+-... .+++.++|.+.
T Consensus 18 ~~~~~L~D~~~~i~~~~f~~~~~~~~~~l~~g~~v~v~g~v~~~~~~~~~~l~v~ 72 (78)
T cd04489 18 HLYFTLKDEDASIRCVMWRSNARRLGFPLEEGMEVLVRGKVSFYEPRGGYQLIVE 72 (78)
T ss_pred EEEEEEEeCCeEEEEEEEcchhhhCCCCCCCCCEEEEEEEEEEECCCCEEEEEEE
Confidence 999999999999999999863 245799999999987763 33678888764
No 36
>COG1599 RFA1 Single-stranded DNA-binding replication protein A (RPA), large (70 kD) subunit and related ssDNA-binding proteins [DNA replication, recombination, and repair]
Probab=96.52 E-value=0.012 Score=50.97 Aligned_cols=65 Identities=14% Similarity=0.205 Sum_probs=51.8
Q ss_pred EEEEEecCcceeccCCCccccCCCCCCCCCCeeEEEEEeeCc-ceEEEEEecCCCCCCCCCCEEEEeceEEceeCCeEEE
Q 032330 30 TVKVVSSKPVQVNKPRGARSLSSLSQPSRPPRIAECLVGDDT-GAIYFTARNDQVDIMTPGTTVILRNAKIDMFKGSMRL 108 (143)
Q Consensus 30 ~~kVl~~~~~~~~~~R~~~~~~~DG~~~~~~~v~~~lVgDeT-G~I~ltlW~~~~~~i~~Gd~v~I~na~~~~~~g~~~L 108 (143)
.++|+...++. ++.+ ++ ..+.+.+..+.|+| |.++|+.|++. +.|+++.+.++.+.++++.+++
T Consensus 173 ~~~v~~g~~ik-~~~~-------~~---ge~~~~~~~~~d~~~~~~~~~~~~~~----~~g~~~~ie~~~v~~~~~~~~~ 237 (407)
T COG1599 173 KARVVVGSEIK-TFDN-------QG---GESKVFSNELEDEERGVIVFTDWDPS----QDGDVYRIEGARVKTKNKQPEE 237 (407)
T ss_pred eEEEEecccce-eEec-------CC---CccceEeeeecccceeEEEeccCccc----ccceeeeecCcEEEEecccccc
Confidence 67888877765 4565 33 35778888888887 99999999976 7889999999999888887777
Q ss_pred E
Q 032330 109 A 109 (143)
Q Consensus 109 ~ 109 (143)
+
T Consensus 238 ~ 238 (407)
T COG1599 238 N 238 (407)
T ss_pred c
Confidence 4
No 37
>cd04484 polC_OBF polC_OBF: A subfamily of OB folds corresponding to the N-terminal OB-fold nucleic acid binding domain of Bacillus subtilis type C replicative DNA polymerase III alpha subunit (polC). Replication in B. subtilis and Staphylococcus aureus requires two different polymerases, polC and DnaE. The holoenzyme is thought to include the two different polymerases. At the B. subtilis replication fork, polC appears to be involved in leading strand synthesis and DnaE in lagging strand synthesis.
Probab=94.50 E-value=0.42 Score=32.50 Aligned_cols=71 Identities=17% Similarity=0.135 Sum_probs=52.7
Q ss_pred CceEEEEEEecCcceeccCCCccccCCCCCCCCCCeeEEEEEeeCcceEEEEEecC-C---CCCCC-CCCEEEEeceE-E
Q 032330 26 GHTLTVKVVSSKPVQVNKPRGARSLSSLSQPSRPPRIAECLVGDDTGAIYFTARND-Q---VDIMT-PGTTVILRNAK-I 99 (143)
Q Consensus 26 ~v~i~~kVl~~~~~~~~~~R~~~~~~~DG~~~~~~~v~~~lVgDeTG~I~ltlW~~-~---~~~i~-~Gd~v~I~na~-~ 99 (143)
++.|.|.|..+..+. .+ .| ..+...-|.|.|++|.+..|.. . .+.++ +|+.|++++-. .
T Consensus 1 ~v~i~G~Vf~~e~re--~k--------~g-----~~i~~~~itD~t~Si~~K~F~~~~~~~~~~ik~~G~~v~v~G~v~~ 65 (82)
T cd04484 1 NVVVEGEVFDLEIRE--LK--------SG-----RKILTFKVTDYTSSITVKKFLRKDEKDKEELKSKGDWVRVRGKVQY 65 (82)
T ss_pred CEEEEEEEEEEEEEE--ec--------CC-----CEEEEEEEEcCCCCEEEEEeccCChhHHhhcccCCCEEEEEEEEEE
Confidence 467899999987643 33 23 4688999999999999999972 2 24578 99999999884 3
Q ss_pred ceeCCeEEEEeC
Q 032330 100 DMFKGSMRLAVD 111 (143)
Q Consensus 100 ~~~~g~~~L~ig 111 (143)
+.|.+.+.|.+.
T Consensus 66 D~f~~e~~~~i~ 77 (82)
T cd04484 66 DTFSKELVLMIN 77 (82)
T ss_pred ccCCCceEEEee
Confidence 456666666553
No 38
>cd04498 hPOT1_OB2 hPOT1_OB2: A subfamily of OB folds similar to the second OB fold (OB2) of human protection of telomeres 1 protein (hPOT1). POT1 proteins bind to the single-stranded (ss) 3-prime ends of the telomere. hPOT1 binds specifically to ss telomeric DNA repeats ending with the sequence GGTTAG. The hPOT1 monomer consists of two closely connected OB folds (OB1-OB2) which cooperate to bind telomeric ssDNA. OB1 makes more extensive contact with the ssDNA than OB2. OB2 protects the 3' end of the ssDNA. hPOT1 is implicated in telomere length regulation.
Probab=94.07 E-value=0.13 Score=38.25 Aligned_cols=32 Identities=19% Similarity=0.343 Sum_probs=27.7
Q ss_pred eEEEEEecCCC---CCCCCCCEEEEeceEEceeCC
Q 032330 73 AIYFTARNDQV---DIMTPGTTVILRNAKIDMFKG 104 (143)
Q Consensus 73 ~I~ltlW~~~~---~~i~~Gd~v~I~na~~~~~~g 104 (143)
+|.+++|++.+ ..+++||.|+|+|..++..+.
T Consensus 61 ti~It~yD~H~~~ar~lK~GdfV~L~NVhiK~~~~ 95 (123)
T cd04498 61 TIDILVYDNHVELAKSLKPGDFVRIYNVHAKSYSS 95 (123)
T ss_pred EEEEEEEcchHHHHhhCCCCCEEEEEEEEEEeccC
Confidence 89999999764 337999999999999988876
No 39
>COG4085 Predicted RNA-binding protein, contains TRAM domain [General function prediction only]
Probab=93.89 E-value=0.52 Score=37.75 Aligned_cols=94 Identities=17% Similarity=0.261 Sum_probs=66.0
Q ss_pred CceeeeccCCCC----CCCceEEEEEEecCcceeccCCCccccCCCCCCCCCCeeEEEEEeeCcceEEEEEecCCC----
Q 032330 12 PVFIKVDQLKPG----TTGHTLTVKVVSSKPVQVNKPRGARSLSSLSQPSRPPRIAECLVGDDTGAIYFTARNDQV---- 83 (143)
Q Consensus 12 ~~~~kI~dL~p~----~~~v~i~~kVl~~~~~~~~~~R~~~~~~~DG~~~~~~~v~~~lVgDeTG~I~ltlW~~~~---- 83 (143)
|...+++.+..+ .+.+.+++.|++... + +| .-+-...+-|+||.|.+.+...-.
T Consensus 35 p~~~~~a~i~eg~G~l~e~v~vkg~V~~~~n------~-------~~-----~gi~~l~lndgtGti~vva~~~tee~l~ 96 (204)
T COG4085 35 PVAEQIATINEGDGRLNEEVTVKGEVTADQN------A-------IG-----GGIESLVLNDGTGTITVVASRSTEETLE 96 (204)
T ss_pred CCccceeEEecCCceeeccceeeeEEEeeec------c-------cc-----cceEEEEEECCCCcEEEEEecChhHhHh
Confidence 333445556544 334567777777663 1 33 237788999999999988886322
Q ss_pred -----CCCCCCCEEEEeceEEceeCCeEEEEeCCceeEEEcCCCce
Q 032330 84 -----DIMTPGTTVILRNAKIDMFKGSMRLAVDKWGRIEVTEPADF 124 (143)
Q Consensus 84 -----~~i~~Gd~v~I~na~~~~~~g~~~L~ig~~g~I~~~~~~~~ 124 (143)
+.+.+|+.+.+.+ .+++|+|..++.+..--.+...+...+
T Consensus 97 ~n~~~p~~~eGe~veVtG-rv~~yrG~~eVkvnq~~d~~~l~k~~~ 141 (204)
T COG4085 97 LNEGMPVTVEGEIVEVTG-RVEEYRGSSEVKVNQPNDSRPLPKHLT 141 (204)
T ss_pred hcCCCCccccCcEEEEEE-EEEEeCCCceeeccCcccccccccccc
Confidence 2456999999986 558999999999988888877765444
No 40
>PRK10917 ATP-dependent DNA helicase RecG; Provisional
Probab=93.12 E-value=0.42 Score=44.10 Aligned_cols=77 Identities=21% Similarity=0.227 Sum_probs=57.2
Q ss_pred eeeeccCCCCCCCceEEEEEEecCcceeccCCCccccCCCCCCCCCCeeEEEEEeeCcceEEEEEec---CC-CCCCCCC
Q 032330 14 FIKVDQLKPGTTGHTLTVKVVSSKPVQVNKPRGARSLSSLSQPSRPPRIAECLVGDDTGAIYFTARN---DQ-VDIMTPG 89 (143)
Q Consensus 14 ~~kI~dL~p~~~~v~i~~kVl~~~~~~~~~~R~~~~~~~DG~~~~~~~v~~~lVgDeTG~I~ltlW~---~~-~~~i~~G 89 (143)
..+|.++.++.. +.+.++|.+..... . + ..+..+.+.|+||.+.++.++ .. ...+++|
T Consensus 50 ~~~i~~l~~g~~-vtv~g~V~~~~~~~--~-~--------------~~~~~v~l~D~tg~i~l~~F~~n~~~~~~~l~~G 111 (681)
T PRK10917 50 LKPIAELRPGEK-VTVEGEVLSAEVVF--G-K--------------RRRLTVTVSDGTGNLTLRFFNFNQPYLKKQLKVG 111 (681)
T ss_pred cCCHHHCCCCCE-EEEEEEEEEEEEcc--C-C--------------ceEEEEEEEECCeEEEEEEEccCcHHHHhhCCCC
Confidence 457889998864 89999999874322 1 1 248899999999999999993 22 4568999
Q ss_pred CEEEEeceEEceeCCeEEEE
Q 032330 90 TTVILRNAKIDMFKGSMRLA 109 (143)
Q Consensus 90 d~v~I~na~~~~~~g~~~L~ 109 (143)
+.+.+.|-.. .++|.+++.
T Consensus 112 ~~~~v~Gkv~-~~~~~~qm~ 130 (681)
T PRK10917 112 KRVAVYGKVK-RGKYGLEMV 130 (681)
T ss_pred CEEEEEEEEE-ecCCeEEEE
Confidence 9999988764 356655553
No 41
>cd04487 RecJ_OBF2_like RecJ_OBF2_like: A subfamily of OB folds corresponding to the second OB fold (OBF2) of archaeal-specific proteins with similarity to eubacterial RecJ. RecJ is an ssDNA-specific exonuclease. Although the overall sequence similarity of these proteins to eubacterial RecJ proteins is marginal, they appear to carry motifs, which have been shown to be essential for nuclease function in Escherichia coli RecJ. In addition to this OB fold, most proteins in this subfamily contain: i) an N-terminal OB fold belonging to a different domain family (the ribosomal S1-like RNA-binding family); and ii) a domain, C-terminal to OBF2, characteristic of DHH family proteins. DHH family proteins include E. coli RecJ, and are predicted to have a phosphoesterase function.
Probab=92.77 E-value=0.83 Score=30.53 Aligned_cols=48 Identities=17% Similarity=0.255 Sum_probs=36.3
Q ss_pred EEEEEeeCcceEEEEEecCC----CCCCCCCCEEEEeceEEceeCCeEEEEeC
Q 032330 63 AECLVGDDTGAIYFTARNDQ----VDIMTPGTTVILRNAKIDMFKGSMRLAVD 111 (143)
Q Consensus 63 ~~~lVgDeTG~I~ltlW~~~----~~~i~~Gd~v~I~na~~~~~~g~~~L~ig 111 (143)
...-+.|+++.|++..|... ...+++||.|.+.+... ..+|.++|.+.
T Consensus 17 vyfsLkD~~a~i~cv~f~~~~~~~~~~l~~Gd~V~v~G~v~-~~~G~~ql~v~ 68 (73)
T cd04487 17 TIFTLRDETGTVWAAAFEEAGVRAYPEVEVGDIVRVTGEVE-PRDGQLQIEVE 68 (73)
T ss_pred EEEEEEcCCEEEEEEEEchhccCCcCCCCCCCEEEEEEEEe-cCCeEEEEEEe
Confidence 34456899999999999742 22368999999998865 47788888764
No 42
>PRK08402 replication factor A; Reviewed
Probab=92.61 E-value=0.16 Score=43.85 Aligned_cols=72 Identities=18% Similarity=0.116 Sum_probs=47.6
Q ss_pred CceeeeccCCCCCCCceEEEEEEecCccee-----ccCCCccccC-C----------CCC-CCCCCeeEEEEEeeCcceE
Q 032330 12 PVFIKVDQLKPGTTGHTLTVKVVSSKPVQV-----NKPRGARSLS-S----------LSQ-PSRPPRIAECLVGDDTGAI 74 (143)
Q Consensus 12 ~~~~kI~dL~p~~~~v~i~~kVl~~~~~~~-----~~~R~~~~~~-~----------DG~-~~~~~~v~~~lVgDeTG~I 74 (143)
....+|.++.++...+++.|.|+.+..... .=.| .+. - .|. ......+.++.|.|.||.+
T Consensus 182 ~~~k~I~ei~~gd~~v~v~g~Iv~i~~~~~y~aCp~CnK---kv~~~~~~~~~~Ce~~~~v~p~~ryil~~~l~D~TG~~ 258 (355)
T PRK08402 182 YTRKKIGELEGGERFVEVRGTIAKVYRVLVYDACPECRR---KVDYDPATDTWICPEHGEVEPIKITILDFGLDDGTGYI 258 (355)
T ss_pred ccccCHHHcccCCcEEEEEEEEEEEecCeeEecCCCCCe---EEEEecCCCCEeCCCCCCcCcceeEEEEEEEEcCCCcE
Confidence 445789999999888999999999886110 0001 111 0 110 0122345678999999999
Q ss_pred EEEEecCCCCCC
Q 032330 75 YFTARNDQVDIM 86 (143)
Q Consensus 75 ~ltlW~~~~~~i 86 (143)
.+++|++++..+
T Consensus 259 ~vt~f~e~ae~l 270 (355)
T PRK08402 259 RVTLFGDDAAEL 270 (355)
T ss_pred EEEEecHHHHHH
Confidence 999999887443
No 43
>PRK05673 dnaE DNA polymerase III subunit alpha; Validated
Probab=92.34 E-value=0.29 Score=48.04 Aligned_cols=86 Identities=20% Similarity=0.281 Sum_probs=62.6
Q ss_pred eeeccCCC--CCCCceEEEEEEecCcceeccCCCccccCCCCCCCCCCeeEEEEEeeCcceEEEEEecCC----CCCCCC
Q 032330 15 IKVDQLKP--GTTGHTLTVKVVSSKPVQVNKPRGARSLSSLSQPSRPPRIAECLVGDDTGAIYFTARNDQ----VDIMTP 88 (143)
Q Consensus 15 ~kI~dL~p--~~~~v~i~~kVl~~~~~~~~~~R~~~~~~~DG~~~~~~~v~~~lVgDeTG~I~ltlW~~~----~~~i~~ 88 (143)
..+.+|.. ....+.+.+.|.++..+. +++ | ..++-+.+.|.||.+.+++|.+. .+.+++
T Consensus 966 ~~~~~l~~~~~g~~V~v~G~I~~vk~~~--TKk--------G-----~~mafltLeD~TG~iEvviFp~~ye~~~~~L~~ 1030 (1135)
T PRK05673 966 TRLADLEPTEGGSVVTVAGLVVSVRRRV--TKR--------G-----NKMAIVTLEDLSGRIEVMLFSEALEKYRDLLEE 1030 (1135)
T ss_pred cCHHHHhccccCceEEEEEEEEEEEecc--cCC--------C-----CeEEEEEEEeCCCcEEEEECHHHHHHHHHHhcc
Confidence 45666642 345688888998888654 343 2 35999999999999999999753 345789
Q ss_pred CCEEEEeceEEceeCCeEEEEeCCceeE
Q 032330 89 GTTVILRNAKIDMFKGSMRLAVDKWGRI 116 (143)
Q Consensus 89 Gd~v~I~na~~~~~~g~~~L~ig~~g~I 116 (143)
|..|.|.+-. ..+++.++|.+.+--.+
T Consensus 1031 g~iV~V~GkV-e~~~~~~qlii~~I~~L 1057 (1135)
T PRK05673 1031 DRIVVVKGQV-SFDDGGLRLTAREVMDL 1057 (1135)
T ss_pred CCEEEEEEEE-EecCCeEEEEEeecccH
Confidence 9999998765 44667888887654433
No 44
>cd04490 PolII_SU_OBF PolII_SU_OBF: A subfamily of OB folds corresponding to the OB fold found in Pyrococcus abyssi DNA polymerase II (PolII) small subunit. PolII is a family D DNA polymerase, having a 3-prime to 5-prime exonuclease activity. P. abyssi PolII is heterodimeric. The large subunit appears to be the polymerase, and the small subunit may be the exonuclease. The small subunit contains a calcineurin-like phosphatase superfamily domain C-terminal to this OB-fold domain.
Probab=91.97 E-value=1.7 Score=29.35 Aligned_cols=53 Identities=15% Similarity=0.169 Sum_probs=40.6
Q ss_pred ceEEEEEEecCcceeccCCCccccCCCCCCCCCCeeEEEEEeeCcceEEEEEecCCCC------CCCCCCEEEEeceE
Q 032330 27 HTLTVKVVSSKPVQVNKPRGARSLSSLSQPSRPPRIAECLVGDDTGAIYFTARNDQVD------IMTPGTTVILRNAK 98 (143)
Q Consensus 27 v~i~~kVl~~~~~~~~~~R~~~~~~~DG~~~~~~~v~~~lVgDeTG~I~ltlW~~~~~------~i~~Gd~v~I~na~ 98 (143)
+.+-|.|.++. . +++ | . . -+.+.|.||++.+.+|.+..+ .+++|..|-|++-.
T Consensus 2 v~i~GiI~~v~--~--TK~--------g---~--~--~~~leD~~G~~Ev~~F~~~~~~~~~~~~l~~d~~v~v~g~v 60 (79)
T cd04490 2 VSIIGMVNDVR--S--TKN--------G---H--R--IVELEDTTGRITVLLTKDKEELFEEAEDILPDEVIGVSGTV 60 (79)
T ss_pred EEEEEEEeEEE--E--cCC--------C---C--E--EEEEECCCCEEEEEEeCchhhhhhhhhhccCCCEEEEEEEE
Confidence 45777888877 3 343 2 1 2 888999999999999986555 67899999998876
No 45
>TIGR00643 recG ATP-dependent DNA helicase RecG.
Probab=91.89 E-value=0.89 Score=41.55 Aligned_cols=80 Identities=15% Similarity=0.098 Sum_probs=58.2
Q ss_pred eeeeccCCCCCCCceEEEEEEecCcceeccCCCccccCCCCCCCCCCeeEEEEEee-CcceEEEEEecC--CCCCCCCCC
Q 032330 14 FIKVDQLKPGTTGHTLTVKVVSSKPVQVNKPRGARSLSSLSQPSRPPRIAECLVGD-DTGAIYFTARND--QVDIMTPGT 90 (143)
Q Consensus 14 ~~kI~dL~p~~~~v~i~~kVl~~~~~~~~~~R~~~~~~~DG~~~~~~~v~~~lVgD-eTG~I~ltlW~~--~~~~i~~Gd 90 (143)
..+|.++.++.. +.+.++|++.... ..| ...+..+.+.| ++|.+.++.|+. ....+++|+
T Consensus 23 ~~~i~~~~~g~~-~~~~~~v~~~~~~---~~~-------------~~~~~~~~~~d~~~~~~~~~~F~~~~~~~~~~~g~ 85 (630)
T TIGR00643 23 LQTIGELLPGER-ATIVGEVLSHCIF---GFK-------------RRKVLKLRLKDGGYKKLELRFFNRAFLKKKFKVGS 85 (630)
T ss_pred ccCHHHcCCCCE-EEEEEEEEEeEec---cCC-------------CCceEEEEEEECCCCEEEEEEECCHHHHhhCCCCC
Confidence 357899999875 7899999884311 112 13488899999 999999999982 235689999
Q ss_pred EEEEeceEEceeCCeEEEEeC
Q 032330 91 TVILRNAKIDMFKGSMRLAVD 111 (143)
Q Consensus 91 ~v~I~na~~~~~~g~~~L~ig 111 (143)
.+.+.+-.. .++|.+++.--
T Consensus 86 ~~~~~Gk~~-~~~~~~~~~~p 105 (630)
T TIGR00643 86 KVVVYGKVK-SSKFKAYLIHP 105 (630)
T ss_pred EEEEEEEEE-eeCCEEEEECC
Confidence 999987664 46676665433
No 46
>PRK07373 DNA polymerase III subunit alpha; Reviewed
Probab=91.41 E-value=0.42 Score=42.43 Aligned_cols=82 Identities=13% Similarity=0.138 Sum_probs=58.7
Q ss_pred eeeccCC--CCCCCceEEEEEEecCcceeccCCCccccCCCCCCCCCCeeEEEEEeeCcceEEEEEecCC----CCCCCC
Q 032330 15 IKVDQLK--PGTTGHTLTVKVVSSKPVQVNKPRGARSLSSLSQPSRPPRIAECLVGDDTGAIYFTARNDQ----VDIMTP 88 (143)
Q Consensus 15 ~kI~dL~--p~~~~v~i~~kVl~~~~~~~~~~R~~~~~~~DG~~~~~~~v~~~lVgDeTG~I~ltlW~~~----~~~i~~ 88 (143)
.++.+|. ++...+.+-+.|.++..+. +++ | ..|+-+.+.|+||.+.+++|-+. .+.+++
T Consensus 269 ~~~~~l~~~~~~~~v~vaG~I~~ik~~~--TKk--------G-----~~maf~~leD~tG~ie~vvFp~~y~~~~~~l~~ 333 (449)
T PRK07373 269 INLSELEEQKEKTKVSAVVMLNEVKKIV--TKK--------G-----DPMAFLQLEDLSGQSEAVVFPKSYERISELLQV 333 (449)
T ss_pred cCHHHHhcccCCCEEEEEEEEEEeEecc--cCC--------C-----CEEEEEEEEECCCCEEEEECHHHHHHHHHHhcc
Confidence 4566664 2334578888999888654 344 2 36999999999999999999643 355789
Q ss_pred CCEEEEeceEEceeCCeEEEEeCC
Q 032330 89 GTTVILRNAKIDMFKGSMRLAVDK 112 (143)
Q Consensus 89 Gd~v~I~na~~~~~~g~~~L~ig~ 112 (143)
|.++.|.+-.-. ..+.++|.+.+
T Consensus 334 ~~~v~v~G~v~~-~~~~~~liv~~ 356 (449)
T PRK07373 334 DARLIIWGKVDR-RDDQVQLIVED 356 (449)
T ss_pred CCEEEEEEEEEe-cCCeEEEEEeE
Confidence 999999876533 34667776654
No 47
>PRK00448 polC DNA polymerase III PolC; Validated
Probab=89.27 E-value=1.6 Score=43.97 Aligned_cols=86 Identities=13% Similarity=0.120 Sum_probs=66.8
Q ss_pred CceeeeccCCCCCCCceEEEEEEecCcceeccCCCccccCCCCCCCCCCeeEEEEEeeCcceEEEEEecCC------CCC
Q 032330 12 PVFIKVDQLKPGTTGHTLTVKVVSSKPVQVNKPRGARSLSSLSQPSRPPRIAECLVGDDTGAIYFTARNDQ------VDI 85 (143)
Q Consensus 12 ~~~~kI~dL~p~~~~v~i~~kVl~~~~~~~~~~R~~~~~~~DG~~~~~~~v~~~lVgDeTG~I~ltlW~~~------~~~ 85 (143)
..+++|+++.....+|.|.|.|..+..+. .+ .| ..+...-|.|.|++|.+..|... .+.
T Consensus 224 ~~~~~~~~i~~~~~~v~i~G~if~~e~~~--~k--------~~-----~~~~~~~~td~~~s~~~k~f~~~~~~~~~~~~ 288 (1437)
T PRK00448 224 EEITPMKEINEEERRVVVEGYVFKVEIKE--LK--------SG-----RHILTFKITDYTSSIIVKKFSRDKEDLKKFDE 288 (1437)
T ss_pred cCcccHHHhhccCCeEEEEEEEEEEEEEe--cc--------CC-----CEEEEEEEEcCCCCEEEEEEecCcchhHHHhc
Confidence 35778999999999999999999988643 23 23 46888999999999999999721 355
Q ss_pred CCCCCEEEEeceEE-ceeCCeEEEEeCC
Q 032330 86 MTPGTTVILRNAKI-DMFKGSMRLAVDK 112 (143)
Q Consensus 86 i~~Gd~v~I~na~~-~~~~g~~~L~ig~ 112 (143)
++.|+.|++++-.. +.|.+.+.+.+..
T Consensus 289 ~~~g~~v~~~g~~~~d~~~~~~~~~~~~ 316 (1437)
T PRK00448 289 IKKGDWVKVRGSVQNDTFTRDLVMNAQD 316 (1437)
T ss_pred CCCCCEEEEEEEEeccCCCCceEEEeee
Confidence 89999999998764 5566777776644
No 48
>PF02721 DUF223: Domain of unknown function DUF223; InterPro: IPR003871 The function of this domain has not been characterised, but may be involved in nucleic acid or nucleotide binding.
Probab=88.24 E-value=1.5 Score=30.20 Aligned_cols=57 Identities=19% Similarity=0.264 Sum_probs=42.6
Q ss_pred EEEEeeCcc-eEEEEEecCCC----CCCCCCCEEEEeceEEceeCCeE-------EEEeCCceeEEEcC
Q 032330 64 ECLVGDDTG-AIYFTARNDQV----DIMTPGTTVILRNAKIDMFKGSM-------RLAVDKWGRIEVTE 120 (143)
Q Consensus 64 ~~lVgDeTG-~I~ltlW~~~~----~~i~~Gd~v~I~na~~~~~~g~~-------~L~ig~~g~I~~~~ 120 (143)
++++.|+.| .|..+.+.+.+ +.++||.++.|.|-.+....|.. .|....++.|...+
T Consensus 1 emvL~De~G~~I~A~I~~~~~~~f~~~l~Eg~~y~i~~F~V~~~~~~yr~t~h~y~I~f~~~T~V~~~~ 69 (95)
T PF02721_consen 1 EMVLVDEKGDKIQATIPKELVDKFKDSLKEGSWYTISNFTVSPNSGSYRPTDHKYKINFMPNTKVTEID 69 (95)
T ss_pred CEEEEecCCCEEEEEECHHHHHHHHhhcccCCEEEeEeEEEEeCCCceeccCCCEEEEECCcCeEEECC
Confidence 468899987 57788887543 55799999999999997776644 46666666666664
No 49
>PF10451 Stn1: Telomere regulation protein Stn1; InterPro: IPR018856 The budding yeast protein Stn1 is a DNA-binding protein which has specificity for telomeric DNA. Structural profiling has predicted an OB-fold []. This entry represents the N-terminal part of the molecule, which adopts the OB fold. Protection of telomeres by multiple proteins with OB-fold domains is conserved in eukaryotic evolution [].; PDB: 3KF6_A 3KF8_A.
Probab=87.18 E-value=3.8 Score=33.86 Aligned_cols=73 Identities=12% Similarity=0.102 Sum_probs=49.8
Q ss_pred CCCceEEEEEEecCcceeccCCCccccCCCCCCCCCCeeEEEEEeeCcc--eEEEEEecCC-------CCCCCCCCEEEE
Q 032330 24 TTGHTLTVKVVSSKPVQVNKPRGARSLSSLSQPSRPPRIAECLVGDDTG--AIYFTARNDQ-------VDIMTPGTTVIL 94 (143)
Q Consensus 24 ~~~v~i~~kVl~~~~~~~~~~R~~~~~~~DG~~~~~~~v~~~lVgDeTG--~I~ltlW~~~-------~~~i~~Gd~v~I 94 (143)
-+.|.|.|+|+++.... ..+ ....-..|-|.|| .|...+|.+. +..+ .|++|+|
T Consensus 66 I~~v~i~G~Vv~~~~~~--~~~--------------~~~~~l~iDD~Sg~~~i~~~~~~~~~~~~~l~~~~~-~G~~V~V 128 (256)
T PF10451_consen 66 IRWVRIVGVVVGIDYKW--IEN--------------EDRIILTIDDSSGANTIECKCSKSSYLSMGLPINDL-IGKVVEV 128 (256)
T ss_dssp E-EEEEEEEEEEEEEEE---BB--------------TCEEEEEEE-SSCS-EEEEEEEHHHHHCCCHHCTT--TT-EEEE
T ss_pred cEEEEEEEEEEEEEEEe--ecc--------------cceEEEEEeCCCCceeEEEEEEcccccccCCCccCC-CCcEEEE
Confidence 34678999999997543 111 1245567999999 8999999652 2223 8999999
Q ss_pred eceEEceeCCeEEEEeCCceeE
Q 032330 95 RNAKIDMFKGSMRLAVDKWGRI 116 (143)
Q Consensus 95 ~na~~~~~~g~~~L~ig~~g~I 116 (143)
.|... ++..+|.+.+-+.+
T Consensus 129 kG~vs---r~~~ql~ve~i~~~ 147 (256)
T PF10451_consen 129 KGTVS---RNERQLDVERIELV 147 (256)
T ss_dssp EEEEE---SSSEEEEEEEEEEE
T ss_pred EEEEc---cCcEEEEEEEEEcc
Confidence 99887 77788887665543
No 50
>PRK05159 aspC aspartyl-tRNA synthetase; Provisional
Probab=85.42 E-value=6 Score=34.74 Aligned_cols=86 Identities=16% Similarity=0.125 Sum_probs=60.9
Q ss_pred eeeeccCCCCC--CCceEEEEEEecCcceeccCCCccccCCCCCCCCCCeeEEEEEeeCcceEEEEEecC-------CCC
Q 032330 14 FIKVDQLKPGT--TGHTLTVKVVSSKPVQVNKPRGARSLSSLSQPSRPPRIAECLVGDDTGAIYFTARND-------QVD 84 (143)
Q Consensus 14 ~~kI~dL~p~~--~~v~i~~kVl~~~~~~~~~~R~~~~~~~DG~~~~~~~v~~~lVgDeTG~I~ltlW~~-------~~~ 84 (143)
.+.|+||.+.. +.|.|.|.|.++ | + .+.++=..|-|.+|.|.+.+=.+ .+.
T Consensus 4 ~~~~~~l~~~~~g~~V~i~GrV~~~--------R-------~-----~gk~~Fl~LrD~~g~iQ~v~~~~~~~~~~~~~~ 63 (437)
T PRK05159 4 RHLTSELTPELDGEEVTLAGWVHEI--------R-------D-----LGGIAFLILRDRSGIIQVVVKKKVDEELFETIK 63 (437)
T ss_pred eeEhhhCChhhCCCEEEEEEEeEee--------e-------c-----CCCeEEEEEEcCCcEEEEEEeCCccHHHHHHHh
Confidence 45788998765 456666666543 2 1 13577788999999999977432 234
Q ss_pred CCCCCCEEEEeceEEceeC--CeEEEEeCCceeEEEc
Q 032330 85 IMTPGTTVILRNAKIDMFK--GSMRLAVDKWGRIEVT 119 (143)
Q Consensus 85 ~i~~Gd~v~I~na~~~~~~--g~~~L~ig~~g~I~~~ 119 (143)
.+..||+|.|.+-....-+ |.++|.+.+.--+.+.
T Consensus 64 ~L~~gs~V~v~G~v~~~~~~~~~~el~~~~i~vls~a 100 (437)
T PRK05159 64 KLKRESVVSVTGTVKANPKAPGGVEVIPEEIEVLNKA 100 (437)
T ss_pred CCCCCcEEEEEEEEEcCCCCCCCEEEEEeEEEEEeCC
Confidence 5789999999997776544 7799998776555544
No 51
>cd04482 RPA2_OBF_like RPA2_OBF_like: A subgroup of uncharacterized archaeal OB folds with similarity to the OB fold of the central ssDNA-binding domain (DBD)-D of human RPA2 (also called RPA32). RPA2 is a subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B; RPA2 DBD-D is a weak ssDNA-binding domain. RPA2 DBD-D is also involved in trimerization. The ssDNA binding mechanism is believed to be multistep and to involve conformational change. N-terminal to human RPA2 DBD-D is a domain containing all the known phosphorylation sites of RPA. Human RPA2 is phosphorylated in a cell cycle depende
Probab=84.39 E-value=4.1 Score=28.14 Aligned_cols=39 Identities=23% Similarity=0.253 Sum_probs=29.3
Q ss_pred EEEEeeCcceEEEEEecCC------CCCCCCCCEEEEeceEEceeC
Q 032330 64 ECLVGDDTGAIYFTARNDQ------VDIMTPGTTVILRNAKIDMFK 103 (143)
Q Consensus 64 ~~lVgDeTG~I~ltlW~~~------~~~i~~Gd~v~I~na~~~~~~ 103 (143)
...+-|+++.|.+.+|... ...+++||.|.+.+.. +.|.
T Consensus 20 yFtlkD~~~~i~cv~f~~~g~~~~~~~~l~~Gd~V~v~G~v-~~y~ 64 (91)
T cd04482 20 FFKISDGTGEIDCAAYEPTKEFRDVVRLLIPGDEVTVYGSV-RPGT 64 (91)
T ss_pred EEEEECCCcEEEEEEECcccccccccCCCCCCCEEEEEEEE-ecCC
Confidence 3456899999999999753 2236899999999885 4444
No 52
>COG1200 RecG RecG-like helicase [DNA replication, recombination, and repair / Transcription]
Probab=84.07 E-value=7.1 Score=36.61 Aligned_cols=77 Identities=21% Similarity=0.333 Sum_probs=57.5
Q ss_pred eeeccCCCCCCCceEEEEEEecCcceeccCCCccccCCCCCCCCCCeeEEEEEeeCcceEEEEEecCC---CCCCCCCCE
Q 032330 15 IKVDQLKPGTTGHTLTVKVVSSKPVQVNKPRGARSLSSLSQPSRPPRIAECLVGDDTGAIYFTARNDQ---VDIMTPGTT 91 (143)
Q Consensus 15 ~kI~dL~p~~~~v~i~~kVl~~~~~~~~~~R~~~~~~~DG~~~~~~~v~~~lVgDeTG~I~ltlW~~~---~~~i~~Gd~ 91 (143)
..|.++.+|.. +.+.+.|.+..... .. ......+.+.|+||.+.++.++.. .+.++.|..
T Consensus 52 ~~i~~~~~g~~-vti~g~V~~~~~~~-~~---------------~~~~l~v~~~d~~~~l~l~fFn~~~~l~~~~~~G~~ 114 (677)
T COG1200 52 PGIAEARPGEI-VTIEGTVLSHEKFP-FG---------------KRKLLKVTLSDGTGVLTLVFFNFPAYLKKKLKVGER 114 (677)
T ss_pred CChhhcCCCce-EEEEEEEEeeeccC-CC---------------CCceEEEEEecCcEEEEEEEECccHHHHhhCCCCCE
Confidence 35677777665 78999999887532 11 246888999999999999999954 355799999
Q ss_pred EEEeceEEceeCCeEEEE
Q 032330 92 VILRNAKIDMFKGSMRLA 109 (143)
Q Consensus 92 v~I~na~~~~~~g~~~L~ 109 (143)
+.+.+ .++.|++.+++.
T Consensus 115 v~v~G-k~~~~~~~~~~~ 131 (677)
T COG1200 115 VIVYG-KVKRFKGGLQIT 131 (677)
T ss_pred EEEEE-EEeeccCceEEE
Confidence 98875 446677766664
No 53
>PF11325 DUF3127: Domain of unknown function (DUF3127); InterPro: IPR021474 This bacterial family of proteins has no known function.
Probab=82.58 E-value=12 Score=26.10 Aligned_cols=47 Identities=19% Similarity=0.311 Sum_probs=32.9
Q ss_pred eeEEEEEeeCc---ceEEEEEecCCCCC---CCCCCEEEEe-ceEEceeCCeEE
Q 032330 61 RIAECLVGDDT---GAIYFTARNDQVDI---MTPGTTVILR-NAKIDMFKGSMR 107 (143)
Q Consensus 61 ~v~~~lVgDeT---G~I~ltlW~~~~~~---i~~Gd~v~I~-na~~~~~~g~~~ 107 (143)
+-++.+|--+. -.|.|.+|.+.++. +++||.|++. |-..++|+|+--
T Consensus 22 ~Kre~Vlet~~qYP~~i~f~~~~dk~~~l~~~~~Gd~V~Vsf~i~~RE~~gr~f 75 (84)
T PF11325_consen 22 KKREFVLETEEQYPQKICFEFWGDKIDLLDNFQVGDEVKVSFNIEGREWNGRWF 75 (84)
T ss_pred EEEEEEEeCCCcCCceEEEEEEcchhhhhccCCCCCEEEEEEEeeccEecceEe
Confidence 34455555332 47999999976554 6899999987 666688886443
No 54
>cd04494 BRCA2DBD_OB2 BRCA2DBD_OB2: A subfamily of OB folds corresponding to the second OB fold (OB2) of the 800-amino acid C-terminal ssDNA binding domain (DBD) of BRCA2 (breast cancer susceptibility gene 2) protein, called BRCA2DBD. BRCA2 participates in homologous recombination-mediated repair of double-strand DNA breaks. It stimulates the displacement of Replication protein A (RPA), the most abundant eukaryotic ssDNA binding protein. It also facilitates filament formation. Mutations that map throughout the BRCA2 protein are associated with breast cancer susceptibility. BRCA2 is a large nuclear protein and its most conserved region is the C-terminal BRCA2DBD. BRCA2DBD binds ssDNA in vitro, and is composed of five structural domains, three of which are OB folds (OB1, OB2, and OB3). BRCA2DBD OB2 and OB3 are arranged in tandem, and their mode of binding can be considered qualitatively similar to two OB folds of RPA1, DBD-A and DBD-B (the major DBDs of RPA).
Probab=82.20 E-value=4.1 Score=33.77 Aligned_cols=59 Identities=14% Similarity=0.069 Sum_probs=46.3
Q ss_pred eEEEEEeeCc----ceEEEEEecCC---CCCCCCCCEEEEeceEEceeCC-----eEEEEeCCceeEEEcC
Q 032330 62 IAECLVGDDT----GAIYFTARNDQ---VDIMTPGTTVILRNAKIDMFKG-----SMRLAVDKWGRIEVTE 120 (143)
Q Consensus 62 v~~~lVgDeT----G~I~ltlW~~~---~~~i~~Gd~v~I~na~~~~~~g-----~~~L~ig~~g~I~~~~ 120 (143)
+.-..|.|-. ....||+|+.- ...+++|..++|.|-..+-.++ .++|..++.++-..++
T Consensus 166 ~~klRV~d~~~~~~~~~~LTIWrPtedl~s~L~EG~ry~i~~L~~s~~k~~~~~~~vqLtatk~Tr~~~l~ 236 (251)
T cd04494 166 VWKLRVTDYRSKPEKSGLLSIWRPTEDLRSLLTEGKRYRIYGLATSNSKKRSGNEEVQLTATKKTRYQPLP 236 (251)
T ss_pred EEEEEEeecccCCCceEEEEEeCCCHHHHhhhcCCcEEEEEeccccCCCCCCCcceEEEEecCcccceECC
Confidence 4445556555 67889999843 4568999999999998877655 8999999998888876
No 55
>PF08646 Rep_fac-A_C: Replication factor-A C terminal domain; InterPro: IPR013955 Replication factor A (RP-A) binds and subsequently stabilises single-stranded DNA intermediates and thus prevents complementary DNA from reannealing. It also plays an essential role in several cellular processes in DNA metabolism including replication, recombination and repair of DNA []. Replication factor-A protein is also known as Replication protein A 70 kDa DNA-binding subunit. This entry is found at the C terminus of Replication factor A.; PDB: 1L1O_F 3U50_C.
Probab=81.83 E-value=0.58 Score=34.63 Aligned_cols=25 Identities=20% Similarity=0.328 Sum_probs=21.0
Q ss_pred CeeEEEEEeeCcceEEEEEecCCCC
Q 032330 60 PRIAECLVGDDTGAIYFTARNDQVD 84 (143)
Q Consensus 60 ~~v~~~lVgDeTG~I~ltlW~~~~~ 84 (143)
..+.++.|.|.||.+.+++|++.+.
T Consensus 53 ry~l~~~i~D~tg~~~~~~F~~~a~ 77 (146)
T PF08646_consen 53 RYRLSLKISDGTGSIWVTLFDEEAE 77 (146)
T ss_dssp EEEEEEEEEETTEEEEEEEEHHHHH
T ss_pred EEEEEEEEEeCCCeEEEEEEhHHHH
Confidence 3466899999999999999997653
No 56
>PRK07374 dnaE DNA polymerase III subunit alpha; Validated
Probab=81.41 E-value=3.3 Score=41.06 Aligned_cols=83 Identities=17% Similarity=0.178 Sum_probs=58.3
Q ss_pred eeeccCC--CCCCCceEEEEEEecCcceeccCCCccccCCCCCCCCCCeeEEEEEeeCcceEEEEEecCC----CCCCCC
Q 032330 15 IKVDQLK--PGTTGHTLTVKVVSSKPVQVNKPRGARSLSSLSQPSRPPRIAECLVGDDTGAIYFTARNDQ----VDIMTP 88 (143)
Q Consensus 15 ~kI~dL~--p~~~~v~i~~kVl~~~~~~~~~~R~~~~~~~DG~~~~~~~v~~~lVgDeTG~I~ltlW~~~----~~~i~~ 88 (143)
..+.+|. ++...+.+.+.|.++..+. +++ | ..|+-+.+.|+||.+.+++|-+. ...+.+
T Consensus 989 ~~~~~l~~~~~~~~v~v~g~i~~~k~~~--Tk~--------G-----~~maf~~leD~tg~~e~vvFp~~y~~~~~~l~~ 1053 (1170)
T PRK07374 989 ISLSSLEEQPDKAKVSAIAMIPEMKQVT--TRK--------G-----DRMAILQLEDLTGSCEAVVFPKSYERLSDHLMT 1053 (1170)
T ss_pred cCHHHHhcccCCCEEEEEEEEEEeEecc--cCC--------C-----CEEEEEEEEECCCCEEEEECHHHHHHHHHHhcc
Confidence 3456664 2334578888888888654 344 2 36999999999999999999642 345788
Q ss_pred CCEEEEeceEEceeCCeEEEEeCCc
Q 032330 89 GTTVILRNAKIDMFKGSMRLAVDKW 113 (143)
Q Consensus 89 Gd~v~I~na~~~~~~g~~~L~ig~~ 113 (143)
|..+.|.+-.- ...+.++|.+.+-
T Consensus 1054 ~~~~~v~g~v~-~~~~~~~~~~~~i 1077 (1170)
T PRK07374 1054 DTRLLVWAKVD-RRDDRVQLIIDDC 1077 (1170)
T ss_pred CCEEEEEEEEE-ecCCeEEEEEeee
Confidence 99998877553 3346677766543
No 57
>PF13742 tRNA_anti_2: OB-fold nucleic acid binding domain
Probab=80.02 E-value=18 Score=25.27 Aligned_cols=68 Identities=15% Similarity=0.188 Sum_probs=48.8
Q ss_pred CCCceEEEEEEecCcceeccCCCccccCCCCCCCCCCeeEEEEEeeCcceEEEEEecCC---C--CCCCCCCEEEEeceE
Q 032330 24 TTGHTLTVKVVSSKPVQVNKPRGARSLSSLSQPSRPPRIAECLVGDDTGAIYFTARNDQ---V--DIMTPGTTVILRNAK 98 (143)
Q Consensus 24 ~~~v~i~~kVl~~~~~~~~~~R~~~~~~~DG~~~~~~~v~~~lVgDeTG~I~ltlW~~~---~--~~i~~Gd~v~I~na~ 98 (143)
..++-|.|.|.+.... + - + -+...+-|+...|+.++|... + ..+++|+.|.+.+..
T Consensus 21 ~~~vwV~GEIs~~~~~-----~-------~------g-h~YftLkD~~a~i~~~~~~~~~~~i~~~~l~~G~~V~v~g~~ 81 (99)
T PF13742_consen 21 LPNVWVEGEISNLKRH-----S-------S------G-HVYFTLKDEEASISCVIFRSRARRIRGFDLKDGDKVLVRGRV 81 (99)
T ss_pred cCCEEEEEEEeecEEC-----C-------C------c-eEEEEEEcCCcEEEEEEEHHHHhhCCCCCCCCCCEEEEEEEE
Confidence 5788999999887731 2 1 2 356667788899999999732 2 357899999988655
Q ss_pred Ecee--CCeEEEEeC
Q 032330 99 IDMF--KGSMRLAVD 111 (143)
Q Consensus 99 ~~~~--~g~~~L~ig 111 (143)
+.| +|.++|.+.
T Consensus 82 -~~y~~~G~~sl~v~ 95 (99)
T PF13742_consen 82 -SFYEPRGSLSLIVE 95 (99)
T ss_pred -EEECCCcEEEEEEE
Confidence 444 467888653
No 58
>PRK07459 single-stranded DNA-binding protein; Provisional
Probab=79.63 E-value=5.5 Score=29.03 Aligned_cols=62 Identities=8% Similarity=0.059 Sum_probs=44.2
Q ss_pred CCCceEEEEEEecCcceeccCCCccccCCCCCCCCCCeeEEEEEe-------eCcceEEEEEecCCCC----CCCCCCEE
Q 032330 24 TTGHTLTVKVVSSKPVQVNKPRGARSLSSLSQPSRPPRIAECLVG-------DDTGAIYFTARNDQVD----IMTPGTTV 92 (143)
Q Consensus 24 ~~~v~i~~kVl~~~~~~~~~~R~~~~~~~DG~~~~~~~v~~~lVg-------DeTG~I~ltlW~~~~~----~i~~Gd~v 92 (143)
++.|.|.|++..-.+.. .++ .| ..++..-|| ++|-=+++++|+.+++ .++.|+.|
T Consensus 3 ~N~v~LiGrL~~DPelr-~t~--------~G-----~~v~~fslAv~~~~~~~~t~w~~v~~wg~~Ae~~~~~l~KG~~V 68 (121)
T PRK07459 3 LNSVTLVGRAGRDPEVR-YFE--------SG-----SVVCNLTLAVNRRSRDDEPDWFNLEIWGKTAQVAADYVKKGSLI 68 (121)
T ss_pred ccEEEEEEEccCCCEEE-EcC--------CC-----CEEEEEEEEecccccCCCceEEEEEEehHHHHHHHHHcCCCCEE
Confidence 45678888887754433 222 34 357777777 5688899999997544 36899999
Q ss_pred EEeceEE
Q 032330 93 ILRNAKI 99 (143)
Q Consensus 93 ~I~na~~ 99 (143)
.|.+-..
T Consensus 69 ~V~G~l~ 75 (121)
T PRK07459 69 GITGSLK 75 (121)
T ss_pred EEEEEEE
Confidence 9998765
No 59
>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=79.48 E-value=5.2 Score=26.94 Aligned_cols=36 Identities=14% Similarity=0.166 Sum_probs=26.8
Q ss_pred EEEEecCCCCCCCCCCEEEEeceEEceeCCeEEEEeCC
Q 032330 75 YFTARNDQVDIMTPGTTVILRNAKIDMFKGSMRLAVDK 112 (143)
Q Consensus 75 ~ltlW~~~~~~i~~Gd~v~I~na~~~~~~g~~~L~ig~ 112 (143)
.|..... ...+++||.|+|. +.+++|.|..+|....
T Consensus 35 ifV~~~~-~~~~~~Gd~V~vt-G~v~ey~g~tql~~~~ 70 (78)
T cd04486 35 IFVYTGS-GADVAVGDLVRVT-GTVTEYYGLTQLTAVS 70 (78)
T ss_pred EEEecCC-CCCCCCCCEEEEE-EEEEeeCCeEEEccCC
Confidence 3433333 5568999999998 8899999988876544
No 60
>PRK02801 primosomal replication protein N; Provisional
Probab=79.15 E-value=7.2 Score=27.49 Aligned_cols=63 Identities=13% Similarity=0.157 Sum_probs=45.6
Q ss_pred CCCceEEEEEEecCcceeccCCCccccCCCCCCCCCCeeEEEEEee-----Ccce-------EEEEEecCCCCC----CC
Q 032330 24 TTGHTLTVKVVSSKPVQVNKPRGARSLSSLSQPSRPPRIAECLVGD-----DTGA-------IYFTARNDQVDI----MT 87 (143)
Q Consensus 24 ~~~v~i~~kVl~~~~~~~~~~R~~~~~~~DG~~~~~~~v~~~lVgD-----eTG~-------I~ltlW~~~~~~----i~ 87 (143)
++.+.|+|++..-.+.. .++ .| ..+++..|+= ++|- |..++|+..++. ++
T Consensus 2 mN~v~L~Grl~~dpelr-~Tp--------~G-----~~v~~f~La~~~~~~ea~~~r~~~~~i~~va~G~~Ae~~~~~l~ 67 (101)
T PRK02801 2 TNRLVLSGTVCRTPKRK-VSP--------SG-----IPHCQFVLEHRSVQEEAGLHRQAWCRMPVIVSGNQFQAITQSIT 67 (101)
T ss_pred ccEEEEEEEECcCcceE-ECC--------CC-----CeEEEEEEEEeCeEecCCCceeEEEEEEEEEEcHHHHHHHhhcC
Confidence 56788999999877655 333 45 3477766654 3455 999999965543 67
Q ss_pred CCCEEEEeceEEc
Q 032330 88 PGTTVILRNAKID 100 (143)
Q Consensus 88 ~Gd~v~I~na~~~ 100 (143)
.|+.|.|.+-...
T Consensus 68 kGs~v~V~G~L~~ 80 (101)
T PRK02801 68 VGSKITVQGFISC 80 (101)
T ss_pred CCCEEEEEEEEEE
Confidence 8999999988775
No 61
>PTZ00401 aspartyl-tRNA synthetase; Provisional
Probab=78.27 E-value=26 Score=32.09 Aligned_cols=97 Identities=15% Similarity=0.205 Sum_probs=65.5
Q ss_pred CCceeeeccCCCCC---CCceEEEEEEecCcceeccCCCccccCCCCCCCCCCeeEEEEEeeCcceEEEEEe--cCC---
Q 032330 11 KPVFIKVDQLKPGT---TGHTLTVKVVSSKPVQVNKPRGARSLSSLSQPSRPPRIAECLVGDDTGAIYFTAR--NDQ--- 82 (143)
Q Consensus 11 ~~~~~kI~dL~p~~---~~v~i~~kVl~~~~~~~~~~R~~~~~~~DG~~~~~~~v~~~lVgDeTG~I~ltlW--~~~--- 82 (143)
..++++|++|.+.. +.|.|.|.|-++ | . .+.++=..|-|.+|.|..++= ++.
T Consensus 62 ~~~~~~i~~l~~~~~~g~~V~v~Grv~~~--------R---~---------~Gk~~Fl~LRd~~~~iQ~v~~~~~~~~~~ 121 (550)
T PTZ00401 62 SRTFIPVAVLSKPELVDKTVLIRARVSTT--------R---K---------KGKMAFMVLRDGSDSVQAMAAVEGDVPKE 121 (550)
T ss_pred CCceEEHHHCCccccCCCEEEEEEEEEEE--------e---c---------CCCeEEEEEEeCCcCEEEEEECCCccCHH
Confidence 36799999998654 456667766543 3 1 134677888999999998773 221
Q ss_pred ----CCCCCCCCEEEEeceEEc-------eeCCeEEEEeCCceeEEEcC-CCceEEc
Q 032330 83 ----VDIMTPGTTVILRNAKID-------MFKGSMRLAVDKWGRIEVTE-PADFEVK 127 (143)
Q Consensus 83 ----~~~i~~Gd~v~I~na~~~-------~~~g~~~L~ig~~g~I~~~~-~~~~~v~ 127 (143)
+..+..|++|.|.+-... .-.+.++|.+.+.--|.... +..+.+.
T Consensus 122 ~~~~~~~l~~esiV~V~G~v~~~~~~~~~~~~~~~El~v~~i~vls~a~~~lP~~~~ 178 (550)
T PTZ00401 122 MIDFIGQIPTESIVDVEATVCKVEQPITSTSHSDIELKVKKIHTVTESLRTLPFTLE 178 (550)
T ss_pred HHHHHhcCCCCCEEEEEEEEEecCccCCCCCCccEEEEeeEEEEEeCCCCCCCCCcc
Confidence 234789999999996554 23567999998876665553 3344443
No 62
>PRK06826 dnaE DNA polymerase III DnaE; Reviewed
Probab=78.18 E-value=7.9 Score=38.37 Aligned_cols=74 Identities=8% Similarity=0.011 Sum_probs=53.4
Q ss_pred CCceEEEEEEecCcceeccCCCccccCCCCCCCCCCeeEEEEEeeCcceEEEEEecCC----CCCCCCCCEEEEeceEEc
Q 032330 25 TGHTLTVKVVSSKPVQVNKPRGARSLSSLSQPSRPPRIAECLVGDDTGAIYFTARNDQ----VDIMTPGTTVILRNAKID 100 (143)
Q Consensus 25 ~~v~i~~kVl~~~~~~~~~~R~~~~~~~DG~~~~~~~v~~~lVgDeTG~I~ltlW~~~----~~~i~~Gd~v~I~na~~~ 100 (143)
..+.+.+.|.++..+. +++ | ..++-+.+.|+||.+.+++|.+. ...+++|..|.|.+-.-.
T Consensus 992 ~~v~v~g~i~~~~~~~--tk~--------G-----~~maf~~leD~~g~~e~~vfp~~~~~~~~~l~~~~~~~v~g~v~~ 1056 (1151)
T PRK06826 992 DKVIIGGIITEVKRKT--TRN--------N-----EMMAFLTLEDLYGTVEVIVFPKVYEKYRSLLNEDNIVLIKGRVSL 1056 (1151)
T ss_pred cEEEEEEEEEEeEeec--cCC--------C-----CeEEEEEEEECCCcEEEEECHHHHHHHHHHhccCCEEEEEEEEEe
Confidence 4577888888877644 343 2 36999999999999999999643 355789999998876642
Q ss_pred eeCCeEEEEeCCc
Q 032330 101 MFKGSMRLAVDKW 113 (143)
Q Consensus 101 ~~~g~~~L~ig~~ 113 (143)
..++.++|.+.+-
T Consensus 1057 ~~~~~~~~~~~~~ 1069 (1151)
T PRK06826 1057 REDEEPKLICEEI 1069 (1151)
T ss_pred cCCCceEEEEeee
Confidence 2346677776543
No 63
>PF02760 HIN: HIN-200/IF120x domain; InterPro: IPR004021 This domain has no known function. It is found in one or two copies per protein, and is found associated with the PAAD/DAPIN domain IPR004020 from INTERPRO.; PDB: 3RN2_A 3RN5_C 2OQ0_A 3B6Y_A 3RLN_A 3RNU_A 3RLO_A.
Probab=77.79 E-value=32 Score=26.98 Aligned_cols=77 Identities=12% Similarity=0.126 Sum_probs=52.1
Q ss_pred EEEEEEecCcce-eccCCCccccCCCCCCCCCCeeEEEEEeeCcceEEEEEec-CCCCCCCCCCEEEEeceEEceeCCeE
Q 032330 29 LTVKVVSSKPVQ-VNKPRGARSLSSLSQPSRPPRIAECLVGDDTGAIYFTARN-DQVDIMTPGTTVILRNAKIDMFKGSM 106 (143)
Q Consensus 29 i~~kVl~~~~~~-~~~~R~~~~~~~DG~~~~~~~v~~~lVgDeTG~I~ltlW~-~~~~~i~~Gd~v~I~na~~~~~~g~~ 106 (143)
+++.||...++= ++.+- +| ..+|-.+.||-||--.++-++| ..-+.+.+..+|.|.|.+ .++|.|
T Consensus 5 ~~VmVLkaTepF~Ye~~e-------~g----kk~MFHATVATet~fF~VKVfn~~LKeKF~~kkiI~IS~Y~--~~~gfL 71 (170)
T PF02760_consen 5 KTVMVLKATEPFEYESPE-------EG----KKKMFHATVATETEFFRVKVFNINLKEKFIPKKIIAISDYF--GRNGFL 71 (170)
T ss_dssp EEEEEEEE---EEEECTT-------TC----EEEEEEEEEE-SS-EEEEEES-GGGCCTCSTTSEEEEESEE--EETTEE
T ss_pred eEEEEEeccCCeEEeCcc-------cC----cceEEEEEEeccccEEEEEEecchhHhhcCCCcEEEEehhh--cccceE
Confidence 577888887632 22221 23 5789999999999999999999 455668999999999987 468877
Q ss_pred EEEeCCceeEEEcC
Q 032330 107 RLAVDKWGRIEVTE 120 (143)
Q Consensus 107 ~L~ig~~g~I~~~~ 120 (143)
+++ +.+++..++
T Consensus 72 Ei~--~aSsVse~~ 83 (170)
T PF02760_consen 72 EIN--EASSVSEVN 83 (170)
T ss_dssp EE---TTSEEEE--
T ss_pred EEe--eccEEEecC
Confidence 765 577777774
No 64
>COG5235 RFA2 Single-stranded DNA-binding replication protein A (RPA), medium (30 kD) subunit [DNA replication, recombination, and repair]
Probab=77.36 E-value=5.7 Score=32.54 Aligned_cols=45 Identities=18% Similarity=0.248 Sum_probs=34.7
Q ss_pred EEEeeCcceEEEEEecC------CCCCCCCCCEEEEeceEEceeCCeEEEEe
Q 032330 65 CLVGDDTGAIYFTARND------QVDIMTPGTTVILRNAKIDMFKGSMRLAV 110 (143)
Q Consensus 65 ~lVgDeTG~I~ltlW~~------~~~~i~~Gd~v~I~na~~~~~~g~~~L~i 110 (143)
..|.|.||.|-++.|.. +....++|.-|++.++. +.|+|+..+..
T Consensus 87 ~~iEDGTG~Ievr~W~~~~~~~e~~~d~~~~~yvkV~G~l-k~F~GK~~I~~ 137 (258)
T COG5235 87 FVIEDGTGSIEVRFWPGNSYEEEQCKDLEEQNYVKVNGSL-KTFNGKRSISA 137 (258)
T ss_pred EEEecCCceEEEEecCCCchHHHhccccccccEEEEecce-eeeCCeeEEeh
Confidence 56899999999999963 33445678878876654 89999888763
No 65
>PRK06920 dnaE DNA polymerase III DnaE; Reviewed
Probab=76.45 E-value=5.4 Score=39.37 Aligned_cols=83 Identities=12% Similarity=0.092 Sum_probs=58.0
Q ss_pred eeeccCCC-CCCCceEEEEEEecCcceeccCCCccccCCCCCCCCCCeeEEEEEeeCcceEEEEEecCC----CCCCCCC
Q 032330 15 IKVDQLKP-GTTGHTLTVKVVSSKPVQVNKPRGARSLSSLSQPSRPPRIAECLVGDDTGAIYFTARNDQ----VDIMTPG 89 (143)
Q Consensus 15 ~kI~dL~p-~~~~v~i~~kVl~~~~~~~~~~R~~~~~~~DG~~~~~~~v~~~lVgDeTG~I~ltlW~~~----~~~i~~G 89 (143)
..+.+|.. ....+.+-+.|.++.... +++ | ..|+-+.+.|+||.+.+++|-+. ...+.+|
T Consensus 933 ~~~~~l~~~~~~~v~v~g~i~~~~~~~--tk~--------g-----~~maf~~leD~tg~~e~~vFp~~y~~~~~~l~~~ 997 (1107)
T PRK06920 933 PSLAQAMRHKKKVQRAIVYITSVKVIR--TKK--------G-----QKMAFITFCDQNDEMEAVVFPETYIHFSDKLQEG 997 (1107)
T ss_pred cCHHHHhhcCCCEEEEEEEEEEeEeec--CCC--------C-----CeEEEEEEeeCCCcEEEEECHHHHHHHHHHhccC
Confidence 45666642 223577888888887644 344 2 36999999999999999999642 4557899
Q ss_pred CEEEEeceEEceeCCeEEEEeCCc
Q 032330 90 TTVILRNAKIDMFKGSMRLAVDKW 113 (143)
Q Consensus 90 d~v~I~na~~~~~~g~~~L~ig~~ 113 (143)
..+.|.+-.-. .++..+|.+.+-
T Consensus 998 ~~~~v~G~v~~-~~~~~~~~~~~i 1020 (1107)
T PRK06920 998 AIVLVDGTIEL-RNHKLQWIVNGL 1020 (1107)
T ss_pred CEEEEEEEEEe-cCCcEEEEEeec
Confidence 99999876543 456677765543
No 66
>PRK07279 dnaE DNA polymerase III DnaE; Reviewed
Probab=76.20 E-value=7.6 Score=38.13 Aligned_cols=83 Identities=18% Similarity=0.273 Sum_probs=58.3
Q ss_pred eeeeccCCCCCCCceEEEEEEecCcceeccCCCccccCCCCCCCCCCeeEEEEEeeCcceEEEEEecCC----CCCCCCC
Q 032330 14 FIKVDQLKPGTTGHTLTVKVVSSKPVQVNKPRGARSLSSLSQPSRPPRIAECLVGDDTGAIYFTARNDQ----VDIMTPG 89 (143)
Q Consensus 14 ~~kI~dL~p~~~~v~i~~kVl~~~~~~~~~~R~~~~~~~DG~~~~~~~v~~~lVgDeTG~I~ltlW~~~----~~~i~~G 89 (143)
...+.+|.. ...+.+.+.|.++.... .+++ | ..++-+.+.|+||.+.+++|-+. ...+.+|
T Consensus 875 ~~~~~~l~~-~~~~~~~~~i~~~~~~~-tk~~--------g-----~~maf~~leD~~g~ie~~vFp~~y~~~~~~l~~~ 939 (1034)
T PRK07279 875 FTPISQLVK-NSEATILVQIQSIRVIR-TKTK--------G-----QQMAFLSVTDTKKKLDVTLFPETYRQYKDELKEG 939 (1034)
T ss_pred CccHHHHhc-CCcceEEEEEEEEEEEE-EcCC--------C-----CeEEEEEEeeCCCcEEEEECHHHHHHHHHHhccC
Confidence 345667753 34577889998887654 2213 2 36999999999999999999753 3557899
Q ss_pred CEEEEeceEEceeCCeEEEEeCC
Q 032330 90 TTVILRNAKIDMFKGSMRLAVDK 112 (143)
Q Consensus 90 d~v~I~na~~~~~~g~~~L~ig~ 112 (143)
..+.|.+-.-+ .++.++|.+.+
T Consensus 940 ~~~~v~G~v~~-~~~~~~l~~~~ 961 (1034)
T PRK07279 940 KFYYLKGKIQE-RDGRLQMVLQQ 961 (1034)
T ss_pred CEEEEEEEEEe-cCCeeEEEEee
Confidence 99998876643 46666666543
No 67
>cd04320 AspRS_cyto_N AspRS_cyto_N: N-terminal, anticodon recognition domain of the type found in Saccharomyces cerevisiae and human cytoplasmic aspartyl-tRNA synthetase (AspRS). This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop. The enzymes in this group are homodimeric class2b aminoacyl-tRNA synthetases (aaRSs). aaRSs catalyze the specific attachment of amino acids (AAs) to their cognate tRNAs during protein biosynthesis. This 2-step reaction involves i) the activation of the AA by ATP in the presence of magnesium ions, followed by ii) the transfer of the activated AA to the terminal ribose of tRNA. In the case of the class2b aaRSs, the activated AA is attached to the 3'OH of the terminal ribose. Eukaryotes contain 2 sets of aaRSs, both of which are encoded by the nuclear genome. One set concerns with cytoplasmic protein synthesis, whereas the other exclusively with mitochondrial protein synthesis.
Probab=75.89 E-value=23 Score=24.36 Aligned_cols=56 Identities=9% Similarity=0.022 Sum_probs=39.7
Q ss_pred eeEEEEEeeCcceEEEEEecCC----------CCCCCCCCEEEEeceEEceeC-------CeEEEEeCCceeE
Q 032330 61 RIAECLVGDDTGAIYFTARNDQ----------VDIMTPGTTVILRNAKIDMFK-------GSMRLAVDKWGRI 116 (143)
Q Consensus 61 ~v~~~lVgDeTG~I~ltlW~~~----------~~~i~~Gd~v~I~na~~~~~~-------g~~~L~ig~~g~I 116 (143)
.+.=..|-|.+|.+...+=.+. +..+..|++|.+.+-..+.-+ +.++|.+.+.--+
T Consensus 17 k~~Fi~LrD~sg~iQ~v~~~~~~~~~~~~~~~~~~l~~es~V~V~G~v~~~~~~~~~~~~~~~El~~~~i~il 89 (102)
T cd04320 17 KLAFLVLRQQGYTIQGVLAASAEGVSKQMVKWAGSLSKESIVDVEGTVKKPEEPIKSCTQQDVELHIEKIYVV 89 (102)
T ss_pred ceEEEEEecCCceEEEEEeCCcccCCHHHHHHHhcCCCccEEEEEEEEECCCCcccCCCcCcEEEEEEEEEEE
Confidence 5777888999999888885332 234789999999998765423 5678877655333
No 68
>TIGR00499 lysS_bact lysyl-tRNA synthetase, eukaryotic and non-spirochete bacterial. This model represents the lysyl-tRNA synthetases that are class II amino-acyl tRNA synthetases. It includes all eukaryotic and most bacterial examples of the enzyme, but not archaeal or spirochete forms.
Probab=73.97 E-value=34 Score=30.77 Aligned_cols=60 Identities=12% Similarity=0.203 Sum_probs=46.1
Q ss_pred CeeEEEEEeeCcceEEEEEecCCC---------CCCCCCCEEEEeceEEceeCCeEEEEeCCceeEEEc
Q 032330 60 PRIAECLVGDDTGAIYFTARNDQV---------DIMTPGTTVILRNAKIDMFKGSMRLAVDKWGRIEVT 119 (143)
Q Consensus 60 ~~v~~~lVgDeTG~I~ltlW~~~~---------~~i~~Gd~v~I~na~~~~~~g~~~L~ig~~g~I~~~ 119 (143)
+.++=+.|-|.+|.|.+.+-.+.. ..+..||+|.+.+-..+.-.|.++|.+.+.--+.+.
T Consensus 69 gk~~F~~l~D~~g~iQ~~~~~~~~~~~~~~~~~~~l~~gd~V~v~G~~~~t~~gelel~~~~i~ilsk~ 137 (496)
T TIGR00499 69 GKATFITLQDESGQIQLYVNKDDLPEDFYEFDEYLLDLGDIIGVTGYPFKTKTGELSVHVTELQILTKA 137 (496)
T ss_pred CCeEEEEEEcCCccEEEEEECCcCcHHHHHHHHhcCCCCCEEEEEEEEEECCCCcEEEEeeEEEEEecC
Confidence 457788899999999987753321 136899999999988887788999999887554443
No 69
>PRK05733 single-stranded DNA-binding protein; Provisional
Probab=73.71 E-value=30 Score=26.95 Aligned_cols=84 Identities=13% Similarity=0.194 Sum_probs=51.3
Q ss_pred CCCCceEEEEEEecCcceeccCCCccccCCCCCCCCCCeeEEEEEee-------Ccc-------eEEEEEecCCC----C
Q 032330 23 GTTGHTLTVKVVSSKPVQVNKPRGARSLSSLSQPSRPPRIAECLVGD-------DTG-------AIYFTARNDQV----D 84 (143)
Q Consensus 23 ~~~~v~i~~kVl~~~~~~~~~~R~~~~~~~DG~~~~~~~v~~~lVgD-------eTG-------~I~ltlW~~~~----~ 84 (143)
+++.+.|+++|..-.+.. .++ +| ..|+..-|+= ++| -+++++|+..+ +
T Consensus 4 ~mNkV~LiGrlg~DPElr-~t~--------nG-----~~va~fsVAv~~~~k~~~~Ge~~e~T~w~~Vv~fgk~Ae~v~~ 69 (172)
T PRK05733 4 GVNKVILVGTCGQDPEVR-YLP--------NG-----NAVTNLSLATSEQWTDKQSGQKVERTEWHRVSLFGKVAEIAGE 69 (172)
T ss_pred cceEEEEEEEecCCCEEE-ECC--------CC-----CEEEEEEEEEcCccccCCCCcccccceEEEEEEehHHHHHHHH
Confidence 467788888888754433 222 34 2466655542 234 38999999654 4
Q ss_pred CCCCCCEEEEeceEE-ceeC--C----eEEEEeCCceeEEEcC
Q 032330 85 IMTPGTTVILRNAKI-DMFK--G----SMRLAVDKWGRIEVTE 120 (143)
Q Consensus 85 ~i~~Gd~v~I~na~~-~~~~--g----~~~L~ig~~g~I~~~~ 120 (143)
.++.|+.|.|.+-.. +.|. | .+++.++..|+|..++
T Consensus 70 ~l~KGs~V~VeGrLr~~~y~kdG~~r~~~eVvvd~~g~v~~L~ 112 (172)
T PRK05733 70 YLRKGSQVYIEGKLQTREWEKDGIKRYTTEIVVDMQGTMQLLG 112 (172)
T ss_pred HhCCCCEEEEEEEEEeCcEecCCEEEEEEEEEEeecCeEEECc
Confidence 468999999997554 2231 2 4556656555565553
No 70
>TIGR00621 ssb single stranded DNA-binding protein (ssb). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=72.79 E-value=10 Score=28.93 Aligned_cols=31 Identities=10% Similarity=0.060 Sum_probs=24.3
Q ss_pred eCcceEEEEEecCCCC----CCCCCCEEEEeceEE
Q 032330 69 DDTGAIYFTARNDQVD----IMTPGTTVILRNAKI 99 (143)
Q Consensus 69 DeTG~I~ltlW~~~~~----~i~~Gd~v~I~na~~ 99 (143)
|+|--+++++|+.+++ .++.|+.|.|.+-..
T Consensus 48 ~~t~~~~v~~wg~~Ae~~~~~l~KG~~V~V~G~L~ 82 (164)
T TIGR00621 48 EETEWHDIVIFGRLAEVAAQYLKKGSLVYVEGRLR 82 (164)
T ss_pred ccceEEEEEEehHHHHHHHHhCCCCCEEEEEEEEE
Confidence 3466899999987543 468999999998665
No 71
>PRK07274 single-stranded DNA-binding protein; Provisional
Probab=72.68 E-value=9.2 Score=28.11 Aligned_cols=29 Identities=7% Similarity=0.077 Sum_probs=22.5
Q ss_pred cceEEEEEecCCCCC----CCCCCEEEEeceEE
Q 032330 71 TGAIYFTARNDQVDI----MTPGTTVILRNAKI 99 (143)
Q Consensus 71 TG~I~ltlW~~~~~~----i~~Gd~v~I~na~~ 99 (143)
|--+++++|+.+++. ++.|+.|.|.+-..
T Consensus 46 t~w~~v~~fg~~Ae~v~~~l~KG~~V~V~Grl~ 78 (131)
T PRK07274 46 ADFINVVLWGKLAETLASYASKGSLISIDGELR 78 (131)
T ss_pred EEEEEEEEehHHHHHHHHHcCCCCEEEEEEEEE
Confidence 347899999976543 68999999998654
No 72
>cd04476 RPA1_DBD_C RPA1_DBD_C: A subfamily of OB folds corresponding to the C-terminal OB fold, the ssDNA-binding domain (DBD)-C, of human RPA1 (also called RPA70). RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-C, RPA1 contains three other OB folds: DBD-A, DBD-B, and RPA1N. The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B. RPA1 DBD-C is involved in DNA binding and trimerization. It contains two structural insertions not found to date in other OB-folds: a zinc ribbon and a three-helix bundle. RPA1 DBD-C also contains a Cys4-type zinc-binding motif, which plays a role in the ssDNA binding fun
Probab=72.22 E-value=2.3 Score=31.98 Aligned_cols=26 Identities=23% Similarity=0.279 Sum_probs=21.4
Q ss_pred CeeEEEEEeeCcceEEEEEecCCCCC
Q 032330 60 PRIAECLVGDDTGAIYFTARNDQVDI 85 (143)
Q Consensus 60 ~~v~~~lVgDeTG~I~ltlW~~~~~~ 85 (143)
..+..+.|.|.||.+.++++++.+..
T Consensus 67 ry~l~~~i~D~Tg~~~~~~F~~~ae~ 92 (166)
T cd04476 67 RYILSLNVADHTGEAWLTLFDEVAEQ 92 (166)
T ss_pred EEEEEEEEEeCCCCEEEEEehHHHHH
Confidence 35567999999999999999976543
No 73
>PRK09010 single-stranded DNA-binding protein; Provisional
Probab=72.19 E-value=39 Score=26.44 Aligned_cols=83 Identities=13% Similarity=0.165 Sum_probs=49.1
Q ss_pred CCCceEEEEEEecCcceeccCCCccccCCCCCCCCCCeeEEEEEee-------Ccc-------eEEEEEecCCC----CC
Q 032330 24 TTGHTLTVKVVSSKPVQVNKPRGARSLSSLSQPSRPPRIAECLVGD-------DTG-------AIYFTARNDQV----DI 85 (143)
Q Consensus 24 ~~~v~i~~kVl~~~~~~~~~~R~~~~~~~DG~~~~~~~v~~~lVgD-------eTG-------~I~ltlW~~~~----~~ 85 (143)
++.+.|++++..-.+.. .+. .| ..+++..|+= ++| -+++++|+.++ +.
T Consensus 6 ~N~V~LiGrLg~DPelR-~t~--------nG-----~~v~~fsVAvn~~~kd~~~Ge~~e~t~w~~V~~fgk~Ae~~~~~ 71 (177)
T PRK09010 6 VNKVILVGNLGQDPEVR-YMP--------NG-----GAVANITLATSESWRDKQTGEMKEQTEWHRVVLFGKLAEVAGEY 71 (177)
T ss_pred ceEEEEEEEeCCCceEE-EcC--------CC-----CEEEEEEEEEcCccccCcccccccceEEEEEEEehhHHHHHHHh
Confidence 55667777777744433 222 23 3466655542 123 46999998654 34
Q ss_pred CCCCCEEEEeceEE-ceeC---C----eEEEEeCCceeEEEcC
Q 032330 86 MTPGTTVILRNAKI-DMFK---G----SMRLAVDKWGRIEVTE 120 (143)
Q Consensus 86 i~~Gd~v~I~na~~-~~~~---g----~~~L~ig~~g~I~~~~ 120 (143)
++.|+.|.|.+-.. +.|. | .++|.+...+.+..++
T Consensus 72 L~KGs~V~VeGrL~~~~yedkdG~~r~~~eVvv~~~~~~~~l~ 114 (177)
T PRK09010 72 LRKGSQVYIEGQLRTRKWTDQSGQDRYTTEVVVNVGGTMQMLG 114 (177)
T ss_pred cCCCCEEEEEEEEEeccccCCCCCEEEEEEEEEecCCcEEEcc
Confidence 79999999998665 3353 2 4555555455555443
No 74
>cd01491 Ube1_repeat1 Ubiquitin activating enzyme (E1), repeat 1. E1, a highly conserved small protein present universally in eukaryotic cells, is part of cascade to attach ubiquitin (Ub) covalently to substrate proteins. This cascade consists of activating (E1), conjugating (E2), and/or ligating (E3) enzymes and then targets them for degradation by the 26S proteasome. E1 activates ubiquitin by C-terminal adenylation, and subsequently forms a highly reactive thioester bond between its catalytic cysteine and ubiquitin's C-terminus. E1 also associates with E2 and promotes ubiquitin transfer to the E2's catalytic cysteine. Ubiquitin-E1 is a single-chain protein with a weakly conserved two-fold repeat. This CD represents the first repeat of Ub-E1.
Probab=72.15 E-value=18 Score=30.22 Aligned_cols=66 Identities=18% Similarity=0.312 Sum_probs=49.2
Q ss_pred eEEEEEeeCcceEEEEEecCCCCCCCCCCEEEEeceEEceeCCeEEEEeCCceeEEEcCCCceEEcCCCCccc
Q 032330 62 IAECLVGDDTGAIYFTARNDQVDIMTPGTTVILRNAKIDMFKGSMRLAVDKWGRIEVTEPADFEVKESNNLSL 134 (143)
Q Consensus 62 v~~~lVgDeTG~I~ltlW~~~~~~i~~Gd~v~I~na~~~~~~g~~~L~ig~~g~I~~~~~~~~~v~e~~n~S~ 134 (143)
+...+..|..|.| ++.+++.-.++.||.|++++- +|-.+||=++-=+|+..+++.|++.++..+|.
T Consensus 167 ~i~~I~~~~~g~V--~~~~~~~h~l~~gd~V~f~ev-----~gm~~lN~~~~~~v~~~~~~~f~i~d~~~~~~ 232 (286)
T cd01491 167 MISSISKDNPGVV--TCLDETRHGFEDGDYVTFSEV-----EGMTELNGCEPRKIKVKGPYTFSIGDTSSFSE 232 (286)
T ss_pred ceeeeecCCceEE--EEECCcccCCcCCCEEEEecc-----CcchhhCCCccEEEEECCCCeEEECcCcCcCc
Confidence 4455667888876 566877778999999998763 35556665555578888899999988887776
No 75
>PRK00484 lysS lysyl-tRNA synthetase; Reviewed
Probab=71.28 E-value=46 Score=29.84 Aligned_cols=60 Identities=10% Similarity=0.177 Sum_probs=45.9
Q ss_pred CeeEEEEEeeCcceEEEEEecCC--------CCCCCCCCEEEEeceEEceeCCeEEEEeCCceeEEEc
Q 032330 60 PRIAECLVGDDTGAIYFTARNDQ--------VDIMTPGTTVILRNAKIDMFKGSMRLAVDKWGRIEVT 119 (143)
Q Consensus 60 ~~v~~~lVgDeTG~I~ltlW~~~--------~~~i~~Gd~v~I~na~~~~~~g~~~L~ig~~g~I~~~ 119 (143)
+.++=+.|-|.+|.|.+.+=.+. ...+..||+|.|.+-..+.-.|.++|.+.+.--+.+.
T Consensus 70 g~~~Fi~lrD~~g~iQ~v~~~~~~~~~~~~~~~~l~~g~~v~v~G~v~~t~~ge~el~~~~~~vls~~ 137 (491)
T PRK00484 70 GKASFATLQDGSGRIQLYVSKDDVGEEALEAFKKLDLGDIIGVEGTLFKTKTGELSVKATELTLLTKS 137 (491)
T ss_pred CceEEEEEEcCCccEEEEEECCcCCHHHHHHHhcCCCCCEEEEEEEEEEcCCCcEEEEEeEEEEEecc
Confidence 35778889999999998775332 1237899999999988877789999999887555443
No 76
>TIGR01405 polC_Gram_pos DNA polymerase III, alpha chain, Gram-positive type. The N-terminal region of about 200 amino acids is rich in low-complexity sequence, poorly alignable, and not included n this model.
Probab=70.53 E-value=39 Score=33.86 Aligned_cols=82 Identities=11% Similarity=0.082 Sum_probs=61.5
Q ss_pred cCCCCCCCceEEEEEEecCcceeccCCCccccCCCCCCCCCCeeEEEEEeeCcceEEEEEecCC------CCCCCCCCEE
Q 032330 19 QLKPGTTGHTLTVKVVSSKPVQVNKPRGARSLSSLSQPSRPPRIAECLVGDDTGAIYFTARNDQ------VDIMTPGTTV 92 (143)
Q Consensus 19 dL~p~~~~v~i~~kVl~~~~~~~~~~R~~~~~~~DG~~~~~~~v~~~lVgDeTG~I~ltlW~~~------~~~i~~Gd~v 92 (143)
++...++++.|.|.|..+..+. .+ .| ..+...-|-|.|.+|.+..|... .+.+++|+.|
T Consensus 2 ~~~~~~~~~~~~g~i~~~~~~~--~~--------~~-----~~~~~~~~~d~~~s~~~k~f~~~~~~~~~~~~~~~g~~~ 66 (1213)
T TIGR01405 2 KINEEENRVKIEGYIFKIEIKE--LK--------SG-----RTLLKIKVTDYTDSLILKKFLKSEEDPEKFDGIKIGKWV 66 (1213)
T ss_pred cccccCCeEEEEEEEEEEEeEe--cc--------CC-----CEEEEEEEEcCCCCEEEEEecccccchHHHhhcCCCcEE
Confidence 5667788999999999988643 23 23 46889999999999999999721 2457999999
Q ss_pred EEeceEE-ceeCCeEEEEeCCcee
Q 032330 93 ILRNAKI-DMFKGSMRLAVDKWGR 115 (143)
Q Consensus 93 ~I~na~~-~~~~g~~~L~ig~~g~ 115 (143)
++++-.. +.|.+.+.+.+..-..
T Consensus 67 ~~~g~~~~d~~~~~~~~~~~~~~~ 90 (1213)
T TIGR01405 67 RARGKIELDNFSRDLQMIIKDIEE 90 (1213)
T ss_pred EEEEEEeccCCCCceEEEeeeeee
Confidence 9998753 5666777777665333
No 77
>PF04076 BOF: Bacterial OB fold (BOF) protein; InterPro: IPR005220 Proteins in this entry have an OB-fold fold (oligonucleotide/oligosaccharide binding motif). Analysis of the predicted nucleotide-binding site of the OB-fold suggests that they lack nucleic acid-binding properties. They contain an predicted N-terminal signal peptide which indicates that they localise to the periplasm where they may function to bind proteins, small molecules, or other typical OB-fold ligands. As hypothesised for the distantly related OB-fold containing bacterial enterotoxins, the loss of nucleotide-binding function and the rapid evolution of the OB-fold ligand-binding site may be associated with the presence of members in mobile genetic elements and their potential role in bacterial pathogenicity [].; PDB: 1NNX_A.
Probab=70.37 E-value=11 Score=27.00 Aligned_cols=66 Identities=23% Similarity=0.244 Sum_probs=41.6
Q ss_pred CCCCCceEEEEEEecCcceeccCCCccccCCCCCCCCCCeeEEEEEeeCcceEEEEEecCC--CCCCCCCCEEEEeceEE
Q 032330 22 PGTTGHTLTVKVVSSKPVQVNKPRGARSLSSLSQPSRPPRIAECLVGDDTGAIYFTARNDQ--VDIMTPGTTVILRNAKI 99 (143)
Q Consensus 22 p~~~~v~i~~kVl~~~~~~~~~~R~~~~~~~DG~~~~~~~v~~~lVgDeTG~I~ltlW~~~--~~~i~~Gd~v~I~na~~ 99 (143)
++...|.|++.|++.-. .. .-++.|.||.|.+-+=++. .-.+.+++.|+|.+-.-
T Consensus 32 ~Dd~~V~L~G~Iv~~l~----~d-------------------~Y~F~D~TG~I~VeId~~~w~g~~vt~~~~Vri~GeVD 88 (103)
T PF04076_consen 32 KDDTPVTLEGNIVKQLG----DD-------------------KYLFRDATGEIEVEIDDDVWRGQTVTPDDKVRISGEVD 88 (103)
T ss_dssp -SSEEEEEEEEEEEEEE----TT-------------------EEEEEETTEEEEEE--GGGSTT----TTSEEEEEEEEE
T ss_pred cCCCeEEEEEEEEEEec----CC-------------------EEEEECCCCcEEEEEChhhcCCcccCCCCEEEEEEEEe
Confidence 34556889998877331 01 2358999999999875542 22378999999998887
Q ss_pred ceeCCeEEEEeC
Q 032330 100 DMFKGSMRLAVD 111 (143)
Q Consensus 100 ~~~~g~~~L~ig 111 (143)
+.|+ ..+|.+.
T Consensus 89 k~~~-~~~IdV~ 99 (103)
T PF04076_consen 89 KDWN-KTEIDVD 99 (103)
T ss_dssp EETT-EEEEEEE
T ss_pred CCCC-ceEEEEE
Confidence 6664 4666553
No 78
>PRK05672 dnaE2 error-prone DNA polymerase; Validated
Probab=69.56 E-value=9.4 Score=37.48 Aligned_cols=50 Identities=14% Similarity=0.179 Sum_probs=38.6
Q ss_pred eEEEEEeeCcceEEEEEecCC----CCCCCCCCEEEEeceEEceeCCeEEEEeCC
Q 032330 62 IAECLVGDDTGAIYFTARNDQ----VDIMTPGTTVILRNAKIDMFKGSMRLAVDK 112 (143)
Q Consensus 62 v~~~lVgDeTG~I~ltlW~~~----~~~i~~Gd~v~I~na~~~~~~g~~~L~ig~ 112 (143)
|+-+.+.|+||.+.+++|.+. ...+++|..+.|.+-.-+ .++..+|.+.+
T Consensus 974 maf~~leD~~g~~e~~ifp~~~~~~~~~l~~~~~~~v~g~v~~-~~~~~~~~~~~ 1027 (1046)
T PRK05672 974 VTFLTLEDETGMVNVVVWPGLWERQRREALGARLLLVRGRVQN-AEGVRHLVADR 1027 (1046)
T ss_pred eEEEEEecCCCCEEEEECHHHHHHHHHHhccCCEEEEEEEEEe-cCCeEEEEEee
Confidence 999999999999999999753 345789999999776543 45666776543
No 79
>PRK06752 single-stranded DNA-binding protein; Validated
Probab=69.51 E-value=13 Score=26.41 Aligned_cols=62 Identities=11% Similarity=0.023 Sum_probs=39.7
Q ss_pred CCCceEEEEEEecCcceeccCCCccccCCCCCCCCCCeeEEEEEee-----------CcceEEEEEecCCCC----CCCC
Q 032330 24 TTGHTLTVKVVSSKPVQVNKPRGARSLSSLSQPSRPPRIAECLVGD-----------DTGAIYFTARNDQVD----IMTP 88 (143)
Q Consensus 24 ~~~v~i~~kVl~~~~~~~~~~R~~~~~~~DG~~~~~~~v~~~lVgD-----------eTG~I~ltlW~~~~~----~i~~ 88 (143)
|+.+.|.+++..-.+.. .++ +| ..++...||- +|--+++++|+.+++ .++.
T Consensus 2 mN~v~liGrl~~dPelr-~t~--------~G-----~~~~~f~lAv~~~~~~~~g~~~t~~~~v~~wg~~Ae~~~~~l~K 67 (112)
T PRK06752 2 MNRVVLIGRLTKEPELY-YTK--------QG-----VAYARVCVAVNRGFRNSLGEQQVDFINCVVWRKSAENVTEYCTK 67 (112)
T ss_pred ceEEEEEEECcCCCEEE-ECC--------CC-----CEEEEEEEEECCCeEcCCCCEEEEEEEEEEehHHHHHHHHhcCC
Confidence 44567777776654433 222 34 3466655552 255688999996554 3689
Q ss_pred CCEEEEeceEE
Q 032330 89 GTTVILRNAKI 99 (143)
Q Consensus 89 Gd~v~I~na~~ 99 (143)
|+.|.|.+-..
T Consensus 68 G~~V~V~G~l~ 78 (112)
T PRK06752 68 GSLVGITGRIH 78 (112)
T ss_pred CCEEEEEEEEE
Confidence 99999998765
No 80
>PRK12445 lysyl-tRNA synthetase; Reviewed
Probab=69.30 E-value=25 Score=31.72 Aligned_cols=60 Identities=12% Similarity=0.123 Sum_probs=45.5
Q ss_pred CeeEEEEEeeCcceEEEEEecCC---------CCCCCCCCEEEEeceEEceeCCeEEEEeCCceeEEEc
Q 032330 60 PRIAECLVGDDTGAIYFTARNDQ---------VDIMTPGTTVILRNAKIDMFKGSMRLAVDKWGRIEVT 119 (143)
Q Consensus 60 ~~v~~~lVgDeTG~I~ltlW~~~---------~~~i~~Gd~v~I~na~~~~~~g~~~L~ig~~g~I~~~ 119 (143)
+.++=+.|-|.+|.|.+.+-.+. ...+..||+|.+.+-..+...|.++|.+.+.--+.+.
T Consensus 81 Gk~~F~~lrD~~g~iQ~~~~~~~~~~~~~~~~~~~l~~Gd~V~v~G~~~~t~~gelel~~~~~~llsk~ 149 (505)
T PRK12445 81 GKASFVTLQDVGGRIQLYVARDSLPEGVYNDQFKKWDLGDIIGARGTLFKTQTGELSIHCTELRLLTKA 149 (505)
T ss_pred CCcEEEEEEeCCccEEEEEECCccchhhHHHHHhcCCCCCEEEEEEEEEecCCCcEEEEEeEEEEEecC
Confidence 34677889999999998775321 2346789999999988877789999998877555443
No 81
>cd04321 ScAspRS_mt_like_N ScAspRS_mt_like_N: N-terminal, anticodon recognition domain of the type found in Saccharomyces cerevisiae mitochondrial (mt) aspartyl-tRNA synthetase (AspRS). This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop. The enzymes in this fungal group are homodimeric class2b aminoacyl-tRNA synthetases (aaRSs). aaRSs catalyze the specific attachment of amino acids (AAs) to their cognate tRNAs during protein biosynthesis. This 2-step reaction involves i) the activation of the AA by ATP in the presence of magnesium ions, followed by ii) the transfer of the activated AA to the terminal ribose of tRNA. In the case of the class2b aaRSs, the activated AA is attached to the 3'OH of the terminal ribose. Eukaryotes contain 2 sets of aaRSs, both of which are encoded by the nuclear genome. One set concerns with cytoplasmic protein synthesis, whereas the other exclusively with mitochondrial protein synthesis. Mutations in the gene for
Probab=69.06 E-value=23 Score=23.72 Aligned_cols=51 Identities=16% Similarity=0.143 Sum_probs=33.4
Q ss_pred CeeEEEEEeeCcc-eEEEEEecC-----CCCCCCCCCEEEEeceEEceeC------CeEEEEe
Q 032330 60 PRIAECLVGDDTG-AIYFTARND-----QVDIMTPGTTVILRNAKIDMFK------GSMRLAV 110 (143)
Q Consensus 60 ~~v~~~lVgDeTG-~I~ltlW~~-----~~~~i~~Gd~v~I~na~~~~~~------g~~~L~i 110 (143)
+.++=..|-|.|| .+.+.+=.+ .+..+..|++|.+.+-....-+ |.++|.+
T Consensus 16 ~~~~Fi~LrD~~g~~iQvv~~~~~~~~~~~~~l~~~s~V~V~G~v~~~~~~~~~~~~~~Ei~~ 78 (86)
T cd04321 16 KKLSFADLRDPNGDIIQLVSTAKKDAFSLLKSITAESPVQVRGKLQLKEAKSSEKNDEWELVV 78 (86)
T ss_pred CceEEEEEECCCCCEEEEEECCCHHHHHHHhcCCCCcEEEEEEEEEeCCCcCCCCCCCEEEEE
Confidence 3477778899999 577644222 2245789999999886654332 5566654
No 82
>PRK13732 single-stranded DNA-binding protein; Provisional
Probab=68.76 E-value=50 Score=25.76 Aligned_cols=83 Identities=16% Similarity=0.191 Sum_probs=49.5
Q ss_pred CCCCceEEEEEEecCcceeccCCCccccCCCCCCCCCCeeEEEEEee-------Ccc-------eEEEEEecCCC----C
Q 032330 23 GTTGHTLTVKVVSSKPVQVNKPRGARSLSSLSQPSRPPRIAECLVGD-------DTG-------AIYFTARNDQV----D 84 (143)
Q Consensus 23 ~~~~v~i~~kVl~~~~~~~~~~R~~~~~~~DG~~~~~~~v~~~lVgD-------eTG-------~I~ltlW~~~~----~ 84 (143)
+++.|.|.+++..-.+.. .++ +| ..+++..||- ++| -+++++|+.++ +
T Consensus 5 ~mN~V~LiGrLg~DPElR-~t~--------nG-----~~va~fslAvn~~~kd~~~Ge~~e~t~w~~Vv~wgk~Ae~v~~ 70 (175)
T PRK13732 5 GINKVILVGRLGKDPEVR-YIP--------NG-----GAVANLQVATSESWRDKQTGEMREQTEWHRVVLFGKLAEVAGE 70 (175)
T ss_pred CceEEEEEEEecCCCEEE-EcC--------CC-----CEEEEEEEEEcCccccCCCCceecceeEEEEEEecHHHHHHHH
Confidence 466778888887754433 222 33 3466666652 234 56899999654 3
Q ss_pred CCCCCCEEEEeceEE-cee--CC----eEEEEeCCceeEEEc
Q 032330 85 IMTPGTTVILRNAKI-DMF--KG----SMRLAVDKWGRIEVT 119 (143)
Q Consensus 85 ~i~~Gd~v~I~na~~-~~~--~g----~~~L~ig~~g~I~~~ 119 (143)
.++.|+.|.|.+-.. +.| +| ..++.+..-|+|..+
T Consensus 71 ~L~KG~~V~VeGrL~~r~ye~dG~kr~~~eIiv~~~g~~~fL 112 (175)
T PRK13732 71 YLRKGAQVYIEGQLRTRSWEDNGITRYVTEILVKTTGTMQML 112 (175)
T ss_pred hcCCCCEEEEEEEEEeeeEccCCeEEEEEEEEEeecCeEEEe
Confidence 468999999998644 223 23 344544444455444
No 83
>cd04317 EcAspRS_like_N EcAspRS_like_N: N-terminal, anticodon recognition domain of the type found in Escherichia coli aspartyl-tRNA synthetase (AspRS), the human mitochondrial (mt) AspRS-2, the discriminating (D) Thermus thermophilus AspRS-1, and the nondiscriminating (ND) Helicobacter pylori AspRS. These homodimeric enzymes are class2b aminoacyl-tRNA synthetases (aaRSs). This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop. aaRSs catalyze the specific attachment of amino acids (AAs) to their cognate tRNAs during protein biosynthesis. This 2-step reaction involves i) the activation of the AA by ATP in the presence of magnesium ions, followed by ii) the transfer of the activated AA to the terminal ribose of tRNA. In the case of the class2b aaRSs, the activated AA is attached to the 3'OH of the terminal ribose. Eukaryotes contain 2 sets of aaRSs, both of which are encoded by the nuclear genome. One set concerns with cytoplasmic synthesis, wh
Probab=66.99 E-value=45 Score=24.05 Aligned_cols=68 Identities=7% Similarity=0.125 Sum_probs=46.2
Q ss_pred eeEEEEEeeCcceEEEEEecC------CCCCCCCCCEEEEeceEEce---------eCCeEEEEeCCceeEEEcCCCceE
Q 032330 61 RIAECLVGDDTGAIYFTARND------QVDIMTPGTTVILRNAKIDM---------FKGSMRLAVDKWGRIEVTEPADFE 125 (143)
Q Consensus 61 ~v~~~lVgDeTG~I~ltlW~~------~~~~i~~Gd~v~I~na~~~~---------~~g~~~L~ig~~g~I~~~~~~~~~ 125 (143)
.++=..|-|.+|.+...+=.. .+..+..|++|.+.+-...- -.|.++|.+...--+.+..+..+.
T Consensus 31 k~~Fi~LrD~~g~~Q~v~~~~~~~~~~~~~~l~~gs~V~V~G~~~~~~~~~~~~~~~~~~~El~~~~i~vl~~~~~lP~~ 110 (135)
T cd04317 31 GLIFIDLRDRYGIVQVVFDPEEAPEFELAEKLRNESVIQVTGKVRARPEGTVNPKLPTGEIEVVASELEVLNKAKTLPFE 110 (135)
T ss_pred CEEEEEEecCCeeEEEEEeCCchhHHHHHhCCCCccEEEEEEEEECCCccccCCCCCCCcEEEEEeEEEEEECCCCCCCc
Confidence 377777889999888766432 22357899999999976642 246789988777555555444555
Q ss_pred EcC
Q 032330 126 VKE 128 (143)
Q Consensus 126 v~e 128 (143)
++.
T Consensus 111 ~~~ 113 (135)
T cd04317 111 IDD 113 (135)
T ss_pred ccc
Confidence 543
No 84
>PRK06751 single-stranded DNA-binding protein; Provisional
Probab=66.50 E-value=15 Score=28.63 Aligned_cols=65 Identities=9% Similarity=0.114 Sum_probs=40.9
Q ss_pred CCCceEEEEEEecCcceeccCCCccccCCCCCCCCCCeeEEEEEe------e-----CcceEEEEEecCCCCC----CCC
Q 032330 24 TTGHTLTVKVVSSKPVQVNKPRGARSLSSLSQPSRPPRIAECLVG------D-----DTGAIYFTARNDQVDI----MTP 88 (143)
Q Consensus 24 ~~~v~i~~kVl~~~~~~~~~~R~~~~~~~DG~~~~~~~v~~~lVg------D-----eTG~I~ltlW~~~~~~----i~~ 88 (143)
|..|.|.++|..-.+.. .+. .| ..|+...|| + +|--+++++|+.+++. ++.
T Consensus 2 mN~V~LiGrL~~DpelR-~t~--------sG-----~~v~~fslAvnr~~~~~~ge~~tdwi~~v~wgk~Ae~~~~~l~K 67 (173)
T PRK06751 2 MNRVILVGRLTKDPDLR-YTP--------NG-----VAVATFTLAVNRAFANQQGEREADFINCVIWRKQAENVANYLKK 67 (173)
T ss_pred ceEEEEEEEECCCCcEE-ECC--------CC-----CEEEEEEEEEccceecCCCCEEEEEEEEEEeCcHHHHHHHHcCC
Confidence 35567777777644333 222 33 246665554 2 2447899999976543 689
Q ss_pred CCEEEEeceEE-cee
Q 032330 89 GTTVILRNAKI-DMF 102 (143)
Q Consensus 89 Gd~v~I~na~~-~~~ 102 (143)
|+.|.|.+... +.|
T Consensus 68 G~~V~VeGrL~~r~y 82 (173)
T PRK06751 68 GSLAGVDGRLQTRNY 82 (173)
T ss_pred CCEEEEEEEEEeCcc
Confidence 99999998765 445
No 85
>PLN02850 aspartate-tRNA ligase
Probab=66.49 E-value=64 Score=29.34 Aligned_cols=96 Identities=10% Similarity=0.035 Sum_probs=64.4
Q ss_pred CceeeeccCCCCC--CCceEEEEEEecCcceeccCCCccccCCCCCCCCCCeeEEEEEeeCcceEEEEEecCC-------
Q 032330 12 PVFIKVDQLKPGT--TGHTLTVKVVSSKPVQVNKPRGARSLSSLSQPSRPPRIAECLVGDDTGAIYFTARNDQ------- 82 (143)
Q Consensus 12 ~~~~kI~dL~p~~--~~v~i~~kVl~~~~~~~~~~R~~~~~~~DG~~~~~~~v~~~lVgDeTG~I~ltlW~~~------- 82 (143)
.++++|.+|.+.. +.|.|.|+|-.+ | . - +.++=..|-|.+|+|..++-...
T Consensus 67 ~~~~~i~~l~~~~~g~~V~v~Grv~~~--------R---~---~------gk~~Fl~Lrd~~~~iQ~v~~~~~~~~~~~~ 126 (530)
T PLN02850 67 REWTDVSDLGEELAGSEVLIRGRVHTI--------R---G---K------GKSAFLVLRQSGFTVQCVVFVSEVTVSKGM 126 (530)
T ss_pred ceEeEhhhcchhhCCCEEEEEEEEEEE--------c---c---C------CCeEEEEEEeCCcCEEEEEECCccccCHHH
Confidence 5789999998754 346666666443 2 1 2 34777889999999998875432
Q ss_pred ---CCCCCCCCEEEEeceEEc------eeCCeEEEEeCCceeEEEc-CCCceEEc
Q 032330 83 ---VDIMTPGTTVILRNAKID------MFKGSMRLAVDKWGRIEVT-EPADFEVK 127 (143)
Q Consensus 83 ---~~~i~~Gd~v~I~na~~~------~~~g~~~L~ig~~g~I~~~-~~~~~~v~ 127 (143)
+..+..|++|.|.+-... --.+.++|.+.+.--|... .+..+.++
T Consensus 127 ~~~~~~l~~es~V~V~G~v~~~~~~~~~~t~~~El~~~~i~vls~a~~~lP~~~~ 181 (530)
T PLN02850 127 VKYAKQLSRESVVDVEGVVSVPKKPVKGTTQQVEIQVRKIYCVSKALATLPFNVE 181 (530)
T ss_pred HHHHhCCCCCCEEEEEEEEEccCcCCCCCCccEEEEEeEEEEEeCCCCCCCCChh
Confidence 345788999999987662 1234699998887666554 23344443
No 86
>PRK05813 single-stranded DNA-binding protein; Provisional
Probab=65.92 E-value=22 Score=28.77 Aligned_cols=63 Identities=13% Similarity=0.137 Sum_probs=45.0
Q ss_pred CCCCceEEEEEEecCcceeccCCCccccCCCCCCCCCCeeEEEEEeeC-----cceEEEEEecCCCCC---CCCCCEEEE
Q 032330 23 GTTGHTLTVKVVSSKPVQVNKPRGARSLSSLSQPSRPPRIAECLVGDD-----TGAIYFTARNDQVDI---MTPGTTVIL 94 (143)
Q Consensus 23 ~~~~v~i~~kVl~~~~~~~~~~R~~~~~~~DG~~~~~~~v~~~lVgDe-----TG~I~ltlW~~~~~~---i~~Gd~v~I 94 (143)
+++.|.|.+++..-.+.. .++ .| ..++...||=. |=-|++++|+.+++. ++.||.|.|
T Consensus 108 ~~N~V~LiGrL~~DPelR-~t~--------~G-----~~va~f~lAvnr~~~~td~i~~v~wg~~Ae~~~~l~KG~~V~V 173 (219)
T PRK05813 108 NPNEIFLDGYICKEPVYR-TTP--------FG-----REIADLLLAVNRPYNKSDYIPCIAWGRNARFCKTLEVGDNIRV 173 (219)
T ss_pred CccEEEEEEEccCCCeEE-ECC--------CC-----CEEEEEEEEEcCCCCCceEEEEEEEhHHhHHHhhCCCCCEEEE
Confidence 366677888887755433 233 45 36888888743 668999999865443 689999999
Q ss_pred eceEE
Q 032330 95 RNAKI 99 (143)
Q Consensus 95 ~na~~ 99 (143)
.+-..
T Consensus 174 ~GrL~ 178 (219)
T PRK05813 174 WGRVQ 178 (219)
T ss_pred EEEEE
Confidence 98765
No 87
>PRK08763 single-stranded DNA-binding protein; Provisional
Probab=65.60 E-value=16 Score=28.21 Aligned_cols=63 Identities=10% Similarity=0.063 Sum_probs=41.1
Q ss_pred CCCCceEEEEEEecCcceeccCCCccccCCCCCCCCCCeeEEEEEe------eCcc-------eEEEEEecCCCC----C
Q 032330 23 GTTGHTLTVKVVSSKPVQVNKPRGARSLSSLSQPSRPPRIAECLVG------DDTG-------AIYFTARNDQVD----I 85 (143)
Q Consensus 23 ~~~~v~i~~kVl~~~~~~~~~~R~~~~~~~DG~~~~~~~v~~~lVg------DeTG-------~I~ltlW~~~~~----~ 85 (143)
+++.+.|.+++..-.+.. .++ +| ..++...|| |..| -+++++|+.+++ .
T Consensus 4 ~~Nkv~LiGrLg~DPelr-~t~--------~G-----~~va~fsVA~~~~~k~~~G~~~e~t~w~~Vv~fgk~Ae~v~~~ 69 (164)
T PRK08763 4 GINKVILVGNLGNDPDIK-YTQ--------SG-----MTITRISLATTSVRKDREGNTQERTEWHRVKFFGKLGEIAGEY 69 (164)
T ss_pred cceEEEEEEEecCCCeEE-EcC--------CC-----CeEEEEEEEeccceecCCCCeeccceEEEEEEehHHHHHHHHh
Confidence 356677888887744433 222 34 346666665 2223 489999986544 3
Q ss_pred CCCCCEEEEeceEE
Q 032330 86 MTPGTTVILRNAKI 99 (143)
Q Consensus 86 i~~Gd~v~I~na~~ 99 (143)
++.|+.|.|.+-..
T Consensus 70 L~KGs~V~VeGrL~ 83 (164)
T PRK08763 70 LRKGSQCYIEGSIR 83 (164)
T ss_pred cCCCCEEEEEEEEE
Confidence 68999999998765
No 88
>PRK07275 single-stranded DNA-binding protein; Provisional
Probab=65.45 E-value=14 Score=28.45 Aligned_cols=65 Identities=9% Similarity=0.113 Sum_probs=41.9
Q ss_pred CCCceEEEEEEecCcceeccCCCccccCCCCCCCCCCeeEEEEEe-----------eCcceEEEEEecCCCCC----CCC
Q 032330 24 TTGHTLTVKVVSSKPVQVNKPRGARSLSSLSQPSRPPRIAECLVG-----------DDTGAIYFTARNDQVDI----MTP 88 (143)
Q Consensus 24 ~~~v~i~~kVl~~~~~~~~~~R~~~~~~~DG~~~~~~~v~~~lVg-----------DeTG~I~ltlW~~~~~~----i~~ 88 (143)
++.|.|.+++..-.+.. .++ .| ..|+...|| .+|--|++++|+.+++. ++.
T Consensus 2 ~N~v~LiGrL~~DPElr-~t~--------sG-----~~v~~ftlAv~r~~~~~~ge~~tdfi~vv~wgk~Ae~~~~~l~K 67 (162)
T PRK07275 2 INNVVLVGRMTRDAELR-YTP--------SN-----VAVATFTLAVNRTFKSQNGEREADFINCVIWRQQAENLANWAKK 67 (162)
T ss_pred eeEEEEEEEECCCCeEE-ECC--------CC-----CEEEEEEEEEcCceecCCCCEeeeEEEEEEEcHHHHHHHHHcCC
Confidence 34567777776644433 222 34 356666664 24667999999976544 689
Q ss_pred CCEEEEeceEE-cee
Q 032330 89 GTTVILRNAKI-DMF 102 (143)
Q Consensus 89 Gd~v~I~na~~-~~~ 102 (143)
|+.|.|.+-.. +.|
T Consensus 68 G~~V~VeGrl~~r~y 82 (162)
T PRK07275 68 GALIGVTGRIQTRNY 82 (162)
T ss_pred CCEEEEEEEEEeceE
Confidence 99999998765 444
No 89
>cd04100 Asp_Lys_Asn_RS_N Asp_Lys_Asn_RS_N: N-terminal, anticodon recognition domain of class 2b aminoacyl-tRNA synthetases (aaRSs). This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop. Class 2b aaRSs include the homodimeric aspartyl-, asparaginyl-, and lysyl-tRNA synthetases (AspRS, AsnRS, and LysRS). aaRSs catalyze the specific attachment of amino acids (AAs) to their cognate tRNAs during protein biosynthesis. This 2-step reaction involves i) the activation of the AA by ATP in the presence of magnesium ions, followed by ii) the transfer of the activated AA to the terminal ribose of tRNA. In the case of the class2b aaRSs, the activated AA is attached to the 3'OH of the terminal ribose. Eukaryotes contain 2 sets of aaRSs, both of which are encoded by the nuclear genome. One set concerns with cytoplasmic protein synthesis, whereas the other exclusively with mitochondrial protein synthesis. Included in this group are archeal and archeal-like A
Probab=64.93 E-value=38 Score=22.38 Aligned_cols=50 Identities=10% Similarity=0.187 Sum_probs=35.3
Q ss_pred eeEEEEEeeCcceEEEEEecCC-------CCCCCCCCEEEEeceEEcee-----CCeEEEEe
Q 032330 61 RIAECLVGDDTGAIYFTARNDQ-------VDIMTPGTTVILRNAKIDMF-----KGSMRLAV 110 (143)
Q Consensus 61 ~v~~~lVgDeTG~I~ltlW~~~-------~~~i~~Gd~v~I~na~~~~~-----~g~~~L~i 110 (143)
.++=..+-|.+|.+...+=... ...++.||+|.+.+-...-- ++.++|.+
T Consensus 16 ~~~Fi~Lrd~~~~iQ~v~~~~~~~~~~~~~~~l~~~s~V~v~G~~~~~~~~~~~~~~~El~~ 77 (85)
T cd04100 16 GLIFIDLRDGSGIVQVVVNKEELGEFFEEAEKLRTESVVGVTGTVVKRPEGNLATGEIELQA 77 (85)
T ss_pred CEEEEEEEeCCeeEEEEEECCcChHHHHHHhCCCCCCEEEEEeEEEECCCCCCCCCCEEEEE
Confidence 4777888999999988664432 23578999999998766432 45566654
No 90
>PF15072 DUF4539: Domain of unknown function (DUF4539)
Probab=64.05 E-value=20 Score=24.88 Aligned_cols=52 Identities=23% Similarity=0.222 Sum_probs=37.7
Q ss_pred eEEEEEeeCcceEEEEEec----CCCCCCCCCCEEEEeceEEc-eeCCeEEEEeCCc
Q 032330 62 IAECLVGDDTGAIYFTARN----DQVDIMTPGTTVILRNAKID-MFKGSMRLAVDKW 113 (143)
Q Consensus 62 v~~~lVgDeTG~I~ltlW~----~~~~~i~~Gd~v~I~na~~~-~~~g~~~L~ig~~ 113 (143)
=+.+++.|.||.|+-++=. ++.+.+.+|.++-+++..+= --.....|+|...
T Consensus 20 D~~v~l~DpTG~i~~tiH~~v~~~y~~~l~~GavLlLk~V~Vf~ps~~~~yLnIt~~ 76 (86)
T PF15072_consen 20 DAFVVLKDPTGEIRGTIHRKVLEEYGDELSPGAVLLLKDVTVFSPSPRSHYLNITLN 76 (86)
T ss_pred CeEEEEECCCCcEEEEEeHHHHhhcCCccccCEEEEEeeeeEEecCCCccEEEEehh
Confidence 3578899999999999875 34677899999999987752 2233455555443
No 91
>cd04316 ND_PkAspRS_like_N ND_PkAspRS_like_N: N-terminal, anticodon recognition domain of the type found in the homodimeric non-discriminating (ND) Pyrococcus kodakaraensis aspartyl-tRNA synthetase (AspRS). This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop. P. kodakaraensis AspRS is a class 2b aaRS. aaRSs catalyze the specific attachment of amino acids (AAs) to their cognate tRNAs during protein biosynthesis. This 2-step reaction involves i) the activation the AA by ATP in the presence of magnesium ions, followed by ii) the transfer of the activated AA to the terminal ribose of tRNA. In the case of the class2b aaRSs, the activated AA is attached to the 3'OH of the terminal ribose. P. kodakaraensis ND-AspRS can charge both tRNAAsp and tRNAAsn. Some of the enzymes in this group may be discriminating, based on the presence of homologs of asparaginyl-tRNA synthetase (AsnRS) in their completed genomes.
Probab=63.96 E-value=46 Score=23.11 Aligned_cols=58 Identities=12% Similarity=0.154 Sum_probs=39.7
Q ss_pred eeEEEEEeeCcceEEEEEecCC--------CCCCCCCCEEEEeceEEceeC--CeEEEEeCCceeEEE
Q 032330 61 RIAECLVGDDTGAIYFTARNDQ--------VDIMTPGTTVILRNAKIDMFK--GSMRLAVDKWGRIEV 118 (143)
Q Consensus 61 ~v~~~lVgDeTG~I~ltlW~~~--------~~~i~~Gd~v~I~na~~~~~~--g~~~L~ig~~g~I~~ 118 (143)
.++=..|-|.+|.+...+=.+. +..+..|++|.+.+...+.-+ +.++|.+.+.--+..
T Consensus 29 ~~~Fi~LrD~~g~iQ~v~~~~~~~~~~~~~~~~l~~es~V~V~G~v~~~~~~~~~~Ei~~~~i~il~~ 96 (108)
T cd04316 29 GIKFVILRDREGIVQVTAPKKKVDKELFKTVRKLSRESVISVTGTVKAEPKAPNGVEIIPEEIEVLSE 96 (108)
T ss_pred CeEEEEEecCCeeEEEEEeCCCCCHHHHHHHhCCCCcCEEEEEEEEEeCCCCCCCEEEEEeEEEEEeC
Confidence 4677788999998888664332 234789999999998765433 457887765544443
No 92
>PRK06293 single-stranded DNA-binding protein; Provisional
Probab=62.16 E-value=20 Score=27.71 Aligned_cols=65 Identities=12% Similarity=0.124 Sum_probs=43.0
Q ss_pred CCCceEEEEEEecCcceeccCCCccccCCCCCCCCCCeeEEEEEe--------eCcceEEEEEecCCCC----CCCCCCE
Q 032330 24 TTGHTLTVKVVSSKPVQVNKPRGARSLSSLSQPSRPPRIAECLVG--------DDTGAIYFTARNDQVD----IMTPGTT 91 (143)
Q Consensus 24 ~~~v~i~~kVl~~~~~~~~~~R~~~~~~~DG~~~~~~~v~~~lVg--------DeTG~I~ltlW~~~~~----~i~~Gd~ 91 (143)
|+.|.|.+++..-.+.. .++ .| ..++..-|| ++|==+++++|+..++ .++.|+.
T Consensus 1 MN~V~LiGrLg~DPElR-~t~--------sG-----~~v~~FsLAvn~~~~~~~~T~wi~v~awg~~Ae~v~~yL~KG~~ 66 (161)
T PRK06293 1 MMFGYIVGRLGADPEER-MTS--------KG-----KRVVVLRLGVKSRVGSKDETVWCRCNIWGNRYDKMLPYLKKGSG 66 (161)
T ss_pred CeEEEEEEEecCCCeEE-EcC--------CC-----CEEEEEEEEEeCCCCCccceEEEEEEEEhHHHHHHHHhCCCCCE
Confidence 45577888877644433 222 33 356666665 3577899999996543 3789999
Q ss_pred EEEeceEE-cee
Q 032330 92 VILRNAKI-DMF 102 (143)
Q Consensus 92 v~I~na~~-~~~ 102 (143)
|.|.+-.. +.|
T Consensus 67 V~VeGrL~~~~y 78 (161)
T PRK06293 67 VIVAGEMSPESY 78 (161)
T ss_pred EEEEEEEEeCcc
Confidence 99998766 334
No 93
>PLN02502 lysyl-tRNA synthetase
Probab=62.01 E-value=39 Score=30.97 Aligned_cols=59 Identities=17% Similarity=0.219 Sum_probs=44.5
Q ss_pred CeeEEEEEeeCcceEEEEEecCCC-----------CCCCCCCEEEEeceEEceeCCeEEEEeCCceeEEE
Q 032330 60 PRIAECLVGDDTGAIYFTARNDQV-----------DIMTPGTTVILRNAKIDMFKGSMRLAVDKWGRIEV 118 (143)
Q Consensus 60 ~~v~~~lVgDeTG~I~ltlW~~~~-----------~~i~~Gd~v~I~na~~~~~~g~~~L~ig~~g~I~~ 118 (143)
+.++=+.|-|.+|.|.+.+-.+.. ..+..||+|.|.+-..+...|.++|.+.+.--+.+
T Consensus 124 Gk~~F~~LrD~~g~iQv~~~~~~~~~~~~~~~~~~~~l~~gdiV~V~G~~~~t~~gelel~~~~i~vLs~ 193 (553)
T PLN02502 124 GKLAFYDLRDDGGKIQLYADKKRLDLDEEEFEKLHSLVDRGDIVGVTGTPGKTKKGELSIFPTSFEVLTK 193 (553)
T ss_pred CCeEEEEEecCCccEEEEEECccccchhHHHHHHHhCCCCCcEEEEEEEEEecCCCCEEEEEeEEEEEec
Confidence 457778889999999887643211 23788999999998888778999999877654443
No 94
>cd04322 LysRS_N LysRS_N: N-terminal, anticodon recognition domain of lysyl-tRNA synthetases (LysRS). These enzymes are homodimeric class 2b aminoacyl-tRNA synthetases (aaRSs). This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop. aaRSs catalyze the specific attachment of amino acids (AAs) to their cognate tRNAs during protein biosynthesis. This 2-step reaction involves i) the activation of the AA by ATP in the presence of magnesium ions, followed by ii) the transfer of the activated AA to the terminal ribose of tRNA. In the case of the class2b aaRSs, the activated AA is attached to the 3'OH of the terminal ribose. Included in this group are E. coli LysS and LysU. These two isoforms of LysRS are encoded by distinct genes which are differently regulated. Eukaryotes contain 2 sets of aaRSs, both of which encoded by the nuclear genome. One set concerns with cytoplasmic protein synthesis, whereas the other exclusively with mitochondrial protein
Probab=61.33 E-value=42 Score=23.27 Aligned_cols=56 Identities=13% Similarity=0.291 Sum_probs=41.6
Q ss_pred eeEEEEEeeCcceEEEEEecCC--------C-CCCCCCCEEEEeceEEceeCCeEEEEeCCceeE
Q 032330 61 RIAECLVGDDTGAIYFTARNDQ--------V-DIMTPGTTVILRNAKIDMFKGSMRLAVDKWGRI 116 (143)
Q Consensus 61 ~v~~~lVgDeTG~I~ltlW~~~--------~-~~i~~Gd~v~I~na~~~~~~g~~~L~ig~~g~I 116 (143)
.++=..+-|.||.+.+.+=... . ..+..||+|.+.+-....-.|.++|.+.+.--+
T Consensus 16 ~~~Fi~lrd~~~~lQ~v~~~~~~~~~~~~~~~~~l~~g~~V~v~G~v~~~~~g~~El~~~~~~il 80 (108)
T cd04322 16 KLSFADLQDESGKIQVYVNKDDLGEEEFEDFKKLLDLGDIIGVTGTPFKTKTGELSIFVKEFTLL 80 (108)
T ss_pred CeEEEEEEECCeEEEEEEECCCCCHHHHHHHHhcCCCCCEEEEEEEEEecCCCCEEEEeCEeEEe
Confidence 4777889999999998663221 1 127899999999987777778899987665333
No 95
>cd04496 SSB_OBF SSB_OBF: A subfamily of OB folds similar to the OB fold of ssDNA-binding protein (SSB). SSBs bind with high affinity to ssDNA. They bind to and protect ssDNA intermediates during DNA metabolic pathways. All bacterial and eukaryotic SSBs studied to date oligomerize to bring together four OB folds in their active state. The majority (e.g. Escherichia coli SSB) have a single OB fold per monomer, which oligomerize to form a homotetramer. However, Deinococcus and Thermus SSB proteins have two OB folds per monomer, which oligomerize to form a homodimer. Mycobacterium tuberculosis SSB varies in quaternary structure from E. coli SSB. It forms a dimer of dimers having a unique dimer interface, which lends the protein greater stability. Included in this group are OB folds similar to Escherichia coli PriB. E.coli PriB is homodimeric with each monomer having a single OB fold. It does not appear to form higher order oligomers. PriB is an essential protein for the replication restart
Probab=61.32 E-value=32 Score=22.78 Aligned_cols=30 Identities=17% Similarity=0.140 Sum_probs=23.6
Q ss_pred CcceEEEEEecCCCC----CCCCCCEEEEeceEE
Q 032330 70 DTGAIYFTARNDQVD----IMTPGTTVILRNAKI 99 (143)
Q Consensus 70 eTG~I~ltlW~~~~~----~i~~Gd~v~I~na~~ 99 (143)
.+=-+.+++|+++++ .+++||.|.|.+-..
T Consensus 42 ~~~~~~v~~~g~~a~~~~~~~~kG~~V~v~G~l~ 75 (100)
T cd04496 42 ETDWIRVVAFGKLAENAAKYLKKGDLVYVEGRLR 75 (100)
T ss_pred ccEEEEEEEEhHHHHHHHHHhCCCCEEEEEEEEE
Confidence 455789999997643 368999999998765
No 96
>PRK03932 asnC asparaginyl-tRNA synthetase; Validated
Probab=61.08 E-value=45 Score=29.47 Aligned_cols=73 Identities=18% Similarity=0.166 Sum_probs=49.8
Q ss_pred CCCceEEEEEEecCcceeccCCCccccCCCCCCCCCCeeEEEEEeeCcceEEEEEecC-------CCCCCCCCCEEEEec
Q 032330 24 TTGHTLTVKVVSSKPVQVNKPRGARSLSSLSQPSRPPRIAECLVGDDTGAIYFTARND-------QVDIMTPGTTVILRN 96 (143)
Q Consensus 24 ~~~v~i~~kVl~~~~~~~~~~R~~~~~~~DG~~~~~~~v~~~lVgDeTG~I~ltlW~~-------~~~~i~~Gd~v~I~n 96 (143)
.+.|.|.|.|-++-. .+.++=+.|-|.||.+.+.+-.+ .+..+..||+|.|.+
T Consensus 16 ~~~V~i~G~v~~~R~--------------------~g~~~Fi~lrD~~g~iq~~~~~~~~~~~~~~~~~l~~~s~v~v~G 75 (450)
T PRK03932 16 GQEVTVRGWVRTKRD--------------------SGKIAFLQLRDGSCFKQLQVVKDNGEEYFEEIKKLTTGSSVIVTG 75 (450)
T ss_pred CCEEEEEEEEEEEEe--------------------CCCeEEEEEECCCCcEEEEEEcCCChHHHHHHhcCCCCcEEEEEE
Confidence 345788888866441 13577788999999887776432 223478999999999
Q ss_pred eEEcee--CCeEEEEeCCceeE
Q 032330 97 AKIDMF--KGSMRLAVDKWGRI 116 (143)
Q Consensus 97 a~~~~~--~g~~~L~ig~~g~I 116 (143)
-....- .+.++|.+.+.--+
T Consensus 76 ~v~~~~~~~~~~el~~~~i~vl 97 (450)
T PRK03932 76 TVVESPRAGQGYELQATKIEVI 97 (450)
T ss_pred EEEcCCCCCCCEEEEEEEEEEc
Confidence 766532 35788888665333
No 97
>PRK02983 lysS lysyl-tRNA synthetase; Provisional
Probab=60.61 E-value=75 Score=31.56 Aligned_cols=59 Identities=14% Similarity=0.138 Sum_probs=46.0
Q ss_pred CeeEEEEEeeCcceEEEEEecCCC---------CCCCCCCEEEEeceEEceeCCeEEEEeCCceeEEE
Q 032330 60 PRIAECLVGDDTGAIYFTARNDQV---------DIMTPGTTVILRNAKIDMFKGSMRLAVDKWGRIEV 118 (143)
Q Consensus 60 ~~v~~~lVgDeTG~I~ltlW~~~~---------~~i~~Gd~v~I~na~~~~~~g~~~L~ig~~g~I~~ 118 (143)
+.++=+.|-|.+|.|.+.+=.+.. ..+..||+|.+++-..+...|.++|.+.++--+.+
T Consensus 667 G~~~F~~lrD~~g~iQ~v~~~~~~~~~~~~~~~~~l~~gd~V~v~G~v~~t~~ge~ei~~~~i~ll~k 734 (1094)
T PRK02983 667 GGVLFADLRDWSGELQVLLDASRLEQGSLADFRAAVDLGDLVEVTGTMGTSRNGTLSLLVTSWRLAGK 734 (1094)
T ss_pred CCeEEEEEEeCCeeEEEEEECCccchhhHHHHHhcCCCCCEEEEEEEEEEcCCCCEEEEEeEEEEEec
Confidence 357888899999999997754321 23688999999999888888999998887655443
No 98
>TIGR00458 aspS_arch aspartyl-tRNA synthetase, archaeal type. In a multiple sequence alignment of representative asparaginyl-tRNA synthetases (asnS), archaeal/eukaryotic type aspartyl-tRNA synthetases (aspS_arch), and bacterial type aspartyl-tRNA synthetases (aspS_bact), there is a striking similarity between asnS and aspS_arch in gap pattern and in sequence, and a striking divergence of aspS_bact. Consequently, a separate model was built for each of the three groups. This model, aspS_arch, represents aspartyl-tRNA synthetases from the eukaryotic cytosol and from the Archaea. In some species, this enzyme aminoacylates tRNA for both Asp and Asn; Asp-tRNA(asn) is subsequently transamidated to Asn-tRNA(asn).
Probab=60.32 E-value=69 Score=28.14 Aligned_cols=60 Identities=20% Similarity=0.143 Sum_probs=43.4
Q ss_pred CeeEEEEEeeCcceEEEEEecC--------CCCCCCCCCEEEEeceEEceeC--CeEEEEeCCceeEEEc
Q 032330 60 PRIAECLVGDDTGAIYFTARND--------QVDIMTPGTTVILRNAKIDMFK--GSMRLAVDKWGRIEVT 119 (143)
Q Consensus 60 ~~v~~~lVgDeTG~I~ltlW~~--------~~~~i~~Gd~v~I~na~~~~~~--g~~~L~ig~~g~I~~~ 119 (143)
+.++=+.|-|.+|.|.+.+=.. .+..+..||+|.|.+-....-+ |.++|.+.+.--+.+.
T Consensus 28 g~~~Fi~lrd~~g~iQ~v~~~~~~~~~~~~~~~~l~~~s~v~v~G~v~~~~~~~~~~el~~~~i~vl~~~ 97 (428)
T TIGR00458 28 GGLIFVLLRDREGLIQITAPAKKVSKNLFKWAKKLNLESVVAVRGIVKIKEKAPGGFEIIPTKIEVINEA 97 (428)
T ss_pred CCcEEEEEEeCCeeEEEEEECCcCCHHHHHHHhCCCCCcEEEEEEEEEecCCCCCcEEEEEeEEEEEecC
Confidence 3477788999999999877532 1235789999999996664333 7899998876555444
No 99
>PRK08486 single-stranded DNA-binding protein; Provisional
Probab=60.30 E-value=24 Score=27.69 Aligned_cols=34 Identities=12% Similarity=0.285 Sum_probs=25.8
Q ss_pred eCcceEEEEEecCCCCC----CCCCCEEEEeceEE-cee
Q 032330 69 DDTGAIYFTARNDQVDI----MTPGTTVILRNAKI-DMF 102 (143)
Q Consensus 69 DeTG~I~ltlW~~~~~~----i~~Gd~v~I~na~~-~~~ 102 (143)
++|--+++++|...++. ++.|+.|.|.+-.. +.|
T Consensus 46 e~t~fi~v~~fg~~AE~~~~~l~KG~~V~VeGrL~~~~y 84 (182)
T PRK08486 46 EEVCFIDIRLFGRTAEIANQYLSKGSKVLIEGRLTFESW 84 (182)
T ss_pred ccceEEEEEEEhHHHHHHHHHcCCCCEEEEEEEEEeCcE
Confidence 45678999999865433 68999999998765 445
No 100
>PF02760 HIN: HIN-200/IF120x domain; InterPro: IPR004021 This domain has no known function. It is found in one or two copies per protein, and is found associated with the PAAD/DAPIN domain IPR004020 from INTERPRO.; PDB: 3RN2_A 3RN5_C 2OQ0_A 3B6Y_A 3RLN_A 3RNU_A 3RLO_A.
Probab=59.51 E-value=14 Score=28.93 Aligned_cols=65 Identities=15% Similarity=0.172 Sum_probs=37.2
Q ss_pred ceeeeccCCCCCCCceEEEEEEecCcceeccCCCccccCCCCCCCCCCeeEEEEEeeCcceEEEEEecCCCCC-CCCCCE
Q 032330 13 VFIKVDQLKPGTTGHTLTVKVVSSKPVQVNKPRGARSLSSLSQPSRPPRIAECLVGDDTGAIYFTARNDQVDI-MTPGTT 91 (143)
Q Consensus 13 ~~~kI~dL~p~~~~v~i~~kVl~~~~~~~~~~R~~~~~~~DG~~~~~~~v~~~lVgDeTG~I~ltlW~~~~~~-i~~Gd~ 91 (143)
..-||++|.....+--+.| +-.+.... . ++ ...++ -|.|+||.+.+...+...+. .++||-
T Consensus 100 ~TpKI~~L~~q~~Gt~V~G-~F~v~KK~-v-~~-------------~~~~Y--eI~DnTG~MeVvv~G~~~ni~CEeGDK 161 (170)
T PF02760_consen 100 ETPKINDLQKQASGTFVNG-LFTVHKKT-V-NK-------------KNTIY--EIQDNTGKMEVVVYGKWHNIKCEEGDK 161 (170)
T ss_dssp S---HHHHTTSSTTEEEEE-EEEEEEEE-E-ES-------------SEEEE--EEEETTEEEEEEEEGGGCGCC--TT-E
T ss_pred cCCchhHHhcCCCCcEEeE-EEEEEEEE-E-cC-------------CeEEE--EEecCCCcEEEEEeccCcccccCCCCe
Confidence 3447888888877743333 33333322 1 11 12233 38999999999888866554 589999
Q ss_pred EEEe
Q 032330 92 VILR 95 (143)
Q Consensus 92 v~I~ 95 (143)
+++.
T Consensus 162 LrL~ 165 (170)
T PF02760_consen 162 LRLF 165 (170)
T ss_dssp EEEE
T ss_pred EEEE
Confidence 9885
No 101
>PRK06958 single-stranded DNA-binding protein; Provisional
Probab=59.39 E-value=23 Score=27.92 Aligned_cols=30 Identities=10% Similarity=0.032 Sum_probs=23.6
Q ss_pred CcceEEEEEecCCCC----CCCCCCEEEEeceEE
Q 032330 70 DTGAIYFTARNDQVD----IMTPGTTVILRNAKI 99 (143)
Q Consensus 70 eTG~I~ltlW~~~~~----~i~~Gd~v~I~na~~ 99 (143)
+|--+++++|+.+++ .++.|+.|.|.+-..
T Consensus 50 ~T~w~~V~~fGk~AE~v~~~LkKGs~V~VeGrL~ 83 (182)
T PRK06958 50 ATEWHRVAFFGRLAEIVGEYLKKGSSVYIEGRIR 83 (182)
T ss_pred cceEEEEEEehHHHHHHHHHhCCCCEEEEEEEEE
Confidence 356789999987653 468999999998665
No 102
>PF00436 SSB: Single-strand binding protein family; InterPro: IPR000424 The Escherichia coli single-strand binding protein [] (gene ssb), also known as the helix-destabilising protein, is a protein of 177 amino acids. It binds tightly, as a homotetramer, to single-stranded DNA (ss-DNA) and plays an important role in DNA replication, recombination and repair. Closely related variants of SSB are encoded in the genome of a variety of large self-transmissible plasmids. SSB has also been characterised in bacteria such as Proteus mirabilis or Serratia marcescens. Eukaryotic mitochondrial proteins that bind ss-DNA and are probably involved in mitochondrial DNA replication are structurally and evolutionary related to prokaryotic SSB.; GO: 0003697 single-stranded DNA binding; PDB: 3UDG_B 1SE8_A 2CWA_A 3ULL_B 1S3O_A 2DUD_A 3AFP_A 3AFQ_A 3VDY_A 3EIV_C ....
Probab=59.26 E-value=6 Score=26.80 Aligned_cols=30 Identities=17% Similarity=0.127 Sum_probs=20.9
Q ss_pred CcceEEEEEecCCCCC----CCCCCEEEEeceEE
Q 032330 70 DTGAIYFTARNDQVDI----MTPGTTVILRNAKI 99 (143)
Q Consensus 70 eTG~I~ltlW~~~~~~----i~~Gd~v~I~na~~ 99 (143)
.+--+++++|+++++. +++||.|.|.+-..
T Consensus 46 ~~~~~~v~~~g~~A~~~~~~l~kG~~V~V~G~l~ 79 (104)
T PF00436_consen 46 KTDWINVVAWGKLAENVAEYLKKGDRVYVEGRLR 79 (104)
T ss_dssp EEEEEEEEEEHHHHHHHHHH--TT-EEEEEEEEE
T ss_pred ceEEEEEEeeeecccccceEEcCCCEEEEEEEEE
Confidence 3557899999976543 68999999998665
No 103
>COG1107 Archaea-specific RecJ-like exonuclease, contains DnaJ-type Zn finger domain [DNA replication, recombination, and repair]
Probab=58.93 E-value=32 Score=32.22 Aligned_cols=50 Identities=18% Similarity=0.272 Sum_probs=37.9
Q ss_pred EEEeeCcceEEEEEecCCC----CCCCCCCEEEEeceEEceeCCeEEEEeCCcee
Q 032330 65 CLVGDDTGAIYFTARNDQV----DIMTPGTTVILRNAKIDMFKGSMRLAVDKWGR 115 (143)
Q Consensus 65 ~lVgDeTG~I~ltlW~~~~----~~i~~Gd~v~I~na~~~~~~g~~~L~ig~~g~ 115 (143)
..+-|+||.|-..++.+.. ..+++||+|++.+-. +.+.|.+++-+-..-+
T Consensus 234 FtltDetg~i~aAAFe~aGvRAyP~IevGdiV~ViG~V-~~r~g~lQiE~~~me~ 287 (715)
T COG1107 234 FTLTDETGAIWAAAFEEAGVRAYPEIEVGDIVEVIGEV-TRRDGRLQIEIEAMEK 287 (715)
T ss_pred EEEecCCCceehhhhccCCcccCCCCCCCceEEEEEEE-eecCCcEEEeehhhHH
Confidence 3578999999999998532 347899999999765 5678888887655444
No 104
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=58.07 E-value=38 Score=30.14 Aligned_cols=73 Identities=12% Similarity=0.120 Sum_probs=50.1
Q ss_pred eccCCCCCCCceEEEEEEecCcceeccCCCccccCCCCCCCCCCeeEEEEEeeCcceEEEEEecC---C---CCCCCCCC
Q 032330 17 VDQLKPGTTGHTLTVKVVSSKPVQVNKPRGARSLSSLSQPSRPPRIAECLVGDDTGAIYFTARND---Q---VDIMTPGT 90 (143)
Q Consensus 17 I~dL~p~~~~v~i~~kVl~~~~~~~~~~R~~~~~~~DG~~~~~~~v~~~lVgDeTG~I~ltlW~~---~---~~~i~~Gd 90 (143)
++|+.+..+ ..++++|.+..... + +...=..+.|++|.|.+.+... + +..+.+||
T Consensus 260 l~d~~~~~~-~~v~g~v~~~p~~i----e--------------Gghv~v~i~d~~G~I~~~A~eptk~fr~~a~~L~pGD 320 (421)
T COG1571 260 LNDIEDYSK-YRVVGRVEAEPRAI----E--------------GGHVVVEITDGEGEIGAVAFEPTKEFRELARKLIPGD 320 (421)
T ss_pred hhhhhhccc-eEEEEEEecccEEe----e--------------CCEEEEEecCCCceEEEEEecccccchHHHHhcCCCC
Confidence 567777555 67888888755322 1 2355567899999888888753 2 23467999
Q ss_pred EEEEeceEEceeCCeEEEEeCCc
Q 032330 91 TVILRNAKIDMFKGSMRLAVDKW 113 (143)
Q Consensus 91 ~v~I~na~~~~~~g~~~L~ig~~ 113 (143)
.|.+.|+....- |++.+.
T Consensus 321 ~i~~~G~~~~~~-----~n~ek~ 338 (421)
T COG1571 321 EITVYGSVKPGT-----LNLEKF 338 (421)
T ss_pred EEEEecCccccc-----eeEEEE
Confidence 999999887543 666555
No 105
>PRK08182 single-stranded DNA-binding protein; Provisional
Probab=57.42 E-value=28 Score=26.28 Aligned_cols=30 Identities=10% Similarity=0.141 Sum_probs=22.5
Q ss_pred eEEEEEecCCCC----CCCCCCEEEEeceEE-cee
Q 032330 73 AIYFTARNDQVD----IMTPGTTVILRNAKI-DMF 102 (143)
Q Consensus 73 ~I~ltlW~~~~~----~i~~Gd~v~I~na~~-~~~ 102 (143)
-+++++|+.+++ .++.|+.|.|.+-.. +.|
T Consensus 55 w~~V~~wg~~Ae~v~~~l~KG~~V~V~GrL~~~~w 89 (148)
T PRK08182 55 WAPVELWHRDAEHWARLYQKGMRVLVEGRMERDEW 89 (148)
T ss_pred EEEEEEEhHHHHHHHHhcCCCCEEEEEEEEEeccc
Confidence 478999986543 368999999998765 335
No 106
>PTZ00385 lysyl-tRNA synthetase; Provisional
Probab=57.27 E-value=1e+02 Score=29.06 Aligned_cols=59 Identities=8% Similarity=0.095 Sum_probs=45.3
Q ss_pred CeeEEEEEeeCcceEEEEEecCCC----------CCCCCCCEEEEeceEEceeCCeEEEEeCCceeEEE
Q 032330 60 PRIAECLVGDDTGAIYFTARNDQV----------DIMTPGTTVILRNAKIDMFKGSMRLAVDKWGRIEV 118 (143)
Q Consensus 60 ~~v~~~lVgDeTG~I~ltlW~~~~----------~~i~~Gd~v~I~na~~~~~~g~~~L~ig~~g~I~~ 118 (143)
|.++=+.|-|.||.|.+.+-.+.. ..+..||+|.+.+-..+...|.++|.+.+.--+.+
T Consensus 123 Gk~~F~~LrD~~G~IQvv~~~~~~~~~~~~~~~~~~l~~gdiV~V~G~v~~t~~GeleI~~~~i~lLsk 191 (659)
T PTZ00385 123 GKIIFVTIRSNGNELQVVGQVGEHFTREDLKKLKVSLRVGDIIGADGVPCRMQRGELSVAASRMLILSP 191 (659)
T ss_pred CCeEEEEEEECCceEEEEEECCccCCHHHHHHHHhCCCCCCEEEEEEEEEecCCceEEEEeeEEEEech
Confidence 457778889999999998854221 24789999999998777778989998887755544
No 107
>KOG2012 consensus Ubiquitin activating enzyme UBA1 [Posttranslational modification, protein turnover, chaperones]
Probab=55.58 E-value=18 Score=35.15 Aligned_cols=56 Identities=18% Similarity=0.210 Sum_probs=46.8
Q ss_pred EEEecCCCCCCCCCCEEEEeceEEceeCCeEEEEeCCceeEEEcCCCceEEcCCCCccccc
Q 032330 76 FTARNDQVDIMTPGTTVILRNAKIDMFKGSMRLAVDKWGRIEVTEPADFEVKESNNLSLVE 136 (143)
Q Consensus 76 ltlW~~~~~~i~~Gd~v~I~na~~~~~~g~~~L~ig~~g~I~~~~~~~~~v~e~~n~S~~e 136 (143)
+|+-++..-.++-||.|++. +.+|..+|+=+.=-+|+..+++.|.+.+..++++..
T Consensus 197 vT~ld~~rH~lEdGd~V~Fs-----EveGm~eLN~~~P~kI~v~~p~sf~Igdt~~f~~y~ 252 (1013)
T KOG2012|consen 197 VTCLDGARHGFEDGDLVTFS-----EVEGMTELNDCKPRKITVLGPYSFSIGDTTEFGEYK 252 (1013)
T ss_pred EEEecCccccCccCCEEEEE-----eeccccccCCCCceEEEEecCceEEeccccchhhhh
Confidence 45667766678999999986 778889999888889999999999999988887643
No 108
>cd04318 EcAsnRS_like_N EcAsnRS_like_N: N-terminal, anticodon recognition domain of the type found in Escherichia coli asparaginyl-tRNA synthetase (AsnRS) and, in Arabidopsis thaliana and Saccharomyces cerevisiae mitochondrial (mt) AsnRS. This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop. The enzymes in this group are homodimeric class2b aminoacyl-tRNA synthetases (aaRSs). aaRSs catalyze the specific attachment of amino acids (AAs) to their cognate tRNAs during protein biosynthesis. This 2-step reaction involves i) the activation of the AA by ATP in the presence of magnesium ions, followed by ii) the transfer of the activated AA to the terminal ribose of tRNA. In the case of the class2b aaRSs, the activated AA is attached to the 3'OH of the terminal ribose. Eukaryotes contain 2 sets of aaRSs, both of which are encoded by the nuclear genome. One set concerns with cytoplasmic protein synthesis, whereas the other exclusively with mitochondrial
Probab=55.56 E-value=55 Score=21.41 Aligned_cols=51 Identities=8% Similarity=0.192 Sum_probs=34.9
Q ss_pred eeEEEEEeeCcce--EEEEEecC-----CCCCCCCCCEEEEeceEEceeC--CeEEEEeC
Q 032330 61 RIAECLVGDDTGA--IYFTARND-----QVDIMTPGTTVILRNAKIDMFK--GSMRLAVD 111 (143)
Q Consensus 61 ~v~~~lVgDeTG~--I~ltlW~~-----~~~~i~~Gd~v~I~na~~~~~~--g~~~L~ig 111 (143)
.++=..|-|.+|. +.+.+=.+ .+..++.|++|.+++-....-+ +.++|.+.
T Consensus 16 ~~~Fi~LrD~s~~~~lQvv~~~~~~~~~~~~~l~~gs~V~v~G~v~~~~~~~~~~El~~~ 75 (82)
T cd04318 16 KISFIELNDGSCLKNLQVVVDKELTNFKEILKLSTGSSIRVEGVLVKSPGAKQPFELQAE 75 (82)
T ss_pred cEEEEEEECCCCccCEEEEEeCcccCHHHHhcCCCceEEEEEEEEEeCCCCCCCEEEEEE
Confidence 4666777788884 77765432 2345789999999997766544 56676654
No 109
>PF07680 DoxA: TQO small subunit DoxA; InterPro: IPR011636 Thiosulphate:quinone oxidoreductase (TQO) catalyses one of the early steps in elemental sulphur oxidation. A novel TQO enzyme was purified from the thermo-acidophilic archaeon Acidianus ambivalens and shown to consist of a large subunit (DoxD) and a smaller subunit (DoxA). The DoxD- and DoxA-like two subunits are fused together in a single polypeptide in Q8AAF0 from SWISSPROT.
Probab=54.73 E-value=64 Score=24.24 Aligned_cols=72 Identities=14% Similarity=0.194 Sum_probs=50.1
Q ss_pred CeeEEEEEeeCcceEEEEEec-CCCCCCCCCCEEEEeceEEceeCCeEEEEeCCceeEEEcC-CCceEEcCCCCccccce
Q 032330 60 PRIAECLVGDDTGAIYFTARN-DQVDIMTPGTTVILRNAKIDMFKGSMRLAVDKWGRIEVTE-PADFEVKESNNLSLVEY 137 (143)
Q Consensus 60 ~~v~~~lVgDeTG~I~ltlW~-~~~~~i~~Gd~v~I~na~~~~~~g~~~L~ig~~g~I~~~~-~~~~~v~e~~n~S~~ey 137 (143)
..+-.+-|-|+||.+-+ -|+ .+.-.+..- .|.|-|+.. ...|++|-+.+++ ++.+.+...-+|+.-.|
T Consensus 46 sfl~~i~l~d~~g~vv~-~~~~~~L~~lP~~---~i~N~Yv~~------~~~g~~gl~vpLGakA~i~L~~~~~l~~g~Y 115 (133)
T PF07680_consen 46 SFLIGIQLKDSTGHVVL-NWDQEKLSSLPKS---NIKNDYVAK------VKPGKHGLVVPLGAKATITLPLPDHLPPGTY 115 (133)
T ss_pred ceeeEEEEECCCCCEEE-EeCHHHhhhCChh---HcCccEEcc------ccCCceeEEEEcCCcEEEEecCCCccCCCcE
Confidence 57889999999999955 687 444334433 356777643 3377777777777 44667777788888888
Q ss_pred eeee
Q 032330 138 ELVN 141 (143)
Q Consensus 138 e~v~ 141 (143)
.++=
T Consensus 116 ~l~L 119 (133)
T PF07680_consen 116 TLKL 119 (133)
T ss_pred EEEE
Confidence 7763
No 110
>TIGR00156 conserved hypothetical protein TIGR00156. As of the last revision, this family consists only of two proteins from Escherichia coli and one from the related species Haemophilus influenzae.
Probab=54.36 E-value=25 Score=26.24 Aligned_cols=70 Identities=16% Similarity=0.100 Sum_probs=44.8
Q ss_pred eeeccCC--CCCCCceEEEEEEecCcceeccCCCccccCCCCCCCCCCeeEEEEEeeCcceEEEEEecCC--CCCCCCCC
Q 032330 15 IKVDQLK--PGTTGHTLTVKVVSSKPVQVNKPRGARSLSSLSQPSRPPRIAECLVGDDTGAIYFTARNDQ--VDIMTPGT 90 (143)
Q Consensus 15 ~kI~dL~--p~~~~v~i~~kVl~~~~~~~~~~R~~~~~~~DG~~~~~~~v~~~lVgDeTG~I~ltlW~~~--~~~i~~Gd 90 (143)
..+++++ ++...|.|++.|+.--.. . .-++-|.||.|.+-+=++. .-.+.|+|
T Consensus 46 ~tV~~a~~~~Ddt~V~L~G~Iv~~l~~----d-------------------~Y~F~D~TG~I~VeId~~~w~G~~v~p~d 102 (126)
T TIGR00156 46 MTVDFAKSMHDGASVTLRGNIISHIGD----D-------------------RYVFRDKSGEINVVIPAAVWNGREVQPKD 102 (126)
T ss_pred EeHHHHhhCCCCCEEEEEEEEEEEeCC----c-------------------eEEEECCCCCEEEEECHHHcCCCcCCCCC
Confidence 4444443 445568888888763310 1 1247899999998763322 22479999
Q ss_pred EEEEeceEEceeCCeEEE
Q 032330 91 TVILRNAKIDMFKGSMRL 108 (143)
Q Consensus 91 ~v~I~na~~~~~~g~~~L 108 (143)
.|+|.+-.=+.|++ .++
T Consensus 103 ~V~I~GeVDk~~~~-~~I 119 (126)
T TIGR00156 103 MVNISGSLDKKSAP-AEV 119 (126)
T ss_pred EEEEEEEECCCCCC-eEE
Confidence 99999988777664 444
No 111
>PRK09919 anti-adapter protein IraM; Provisional
Probab=54.02 E-value=23 Score=26.03 Aligned_cols=37 Identities=5% Similarity=0.097 Sum_probs=28.9
Q ss_pred eEEEEEecCCCCCCCCCCEEEEeceEEceeCCeEEEE
Q 032330 73 AIYFTARNDQVDIMTPGTTVILRNAKIDMFKGSMRLA 109 (143)
Q Consensus 73 ~I~ltlW~~~~~~i~~Gd~v~I~na~~~~~~g~~~L~ 109 (143)
-.+|.+|-+---.+.+||++.+.+.-+-..+-...+.
T Consensus 26 nlKlilWY~~d~~L~pG~~i~~~~~gvliNdk~~pIt 62 (114)
T PRK09919 26 NLKLILWYQADIFLPPGSIITPVKSGVLLNDKPYPIT 62 (114)
T ss_pred cceEEEEEeeeEEeCCCCEEEEcCCeEEECCcEeEEE
Confidence 4789999843334799999999999988777766664
No 112
>PRK10053 hypothetical protein; Provisional
Probab=53.55 E-value=34 Score=25.59 Aligned_cols=40 Identities=10% Similarity=0.109 Sum_probs=30.8
Q ss_pred EEeeCcceEEEEE----ecCCCCCCCCCCEEEEeceEEceeCCeEEE
Q 032330 66 LVGDDTGAIYFTA----RNDQVDIMTPGTTVILRNAKIDMFKGSMRL 108 (143)
Q Consensus 66 lVgDeTG~I~ltl----W~~~~~~i~~Gd~v~I~na~~~~~~g~~~L 108 (143)
++-|.||.|.+-+ |..+ .+.|.|.|+|.+-+=+.|.. .++
T Consensus 80 ~F~D~tG~I~VeID~~~w~G~--~v~p~~kV~I~GevDk~~~~-~~I 123 (130)
T PRK10053 80 VFRDKSGEINVIIPAAVFDGR--EVQPDQMININGSLDKKSAP-PVV 123 (130)
T ss_pred EEECCCCcEEEEeCHHHcCCC--cCCCCCEEEEEEEECCCCCC-eEE
Confidence 4789999999876 5433 48999999999988877764 444
No 113
>KOG3108 consensus Single-stranded DNA-binding replication protein A (RPA), medium (30 kD) subunit [Replication, recombination and repair]
Probab=51.67 E-value=39 Score=28.19 Aligned_cols=47 Identities=26% Similarity=0.235 Sum_probs=36.6
Q ss_pred EEEeeCcceEEEEEecCCC------CCCCCCCEEEEeceEEceeCCeEEEEeCC
Q 032330 65 CLVGDDTGAIYFTARNDQV------DIMTPGTTVILRNAKIDMFKGSMRLAVDK 112 (143)
Q Consensus 65 ~lVgDeTG~I~ltlW~~~~------~~i~~Gd~v~I~na~~~~~~g~~~L~ig~ 112 (143)
-.|.|.||.|-...|.... ..+++|.-|++.+.. +.|+|...|.+-+
T Consensus 89 y~I~D~tg~id~r~W~~~~~~~~e~~~l~~~~yVkv~G~L-k~f~Gk~sl~~fk 141 (265)
T KOG3108|consen 89 YEIEDGTGQIDVRQWFHDNAESEEMPALETGTYVKVYGHL-KPFQGKKSLQVFK 141 (265)
T ss_pred EEEecCcccEEEEEeccccchhhhCcccccCcEEEeeecc-cCCCCceeEEEEe
Confidence 4589999999999997432 246789888888766 8899888887544
No 114
>COG4393 Predicted membrane protein [Function unknown]
Probab=50.03 E-value=1.1e+02 Score=26.90 Aligned_cols=88 Identities=22% Similarity=0.277 Sum_probs=57.7
Q ss_pred ccCCCcCCCCceeeeccCCCCCCCceEEEEEEecCcceeccCCCccccCCCCCCCCCCeeEEEEEeeCcceEEEEEecCC
Q 032330 3 TAGATAKRKPVFIKVDQLKPGTTGHTLTVKVVSSKPVQVNKPRGARSLSSLSQPSRPPRIAECLVGDDTGAIYFTARNDQ 82 (143)
Q Consensus 3 ~~~~~~~~~~~~~kI~dL~p~~~~v~i~~kVl~~~~~~~~~~R~~~~~~~DG~~~~~~~v~~~lVgDeTG~I~ltlW~~~ 82 (143)
|..||++.+| ..+.|+.+|. .++.+..+ | ||. -=+=+.|+|+--.|||-+-+..
T Consensus 271 aSkP~~Lsep-----~pv~~d~~n~----v~ipie~v-----r-------Dgk-----LHRF~yIA~dGkaVRFflInk~ 324 (405)
T COG4393 271 ASKPPALSEP-----QPVQPDEGNM----VVIPIEQV-----R-------DGK-----LHRFVYIADDGKAVRFFLINKR 324 (405)
T ss_pred cCCCCCCCCC-----cCcccCCCCE----EEEEHHHc-----c-------cCc-----eEEEEEEccCCcEEEEEEEecC
Confidence 3345677777 4556666653 23333332 3 773 2344779999999999998864
Q ss_pred CCC------------------CCCCCEEEEeceEEceeCCeEEEEeCCceeEEEcC
Q 032330 83 VDI------------------MTPGTTVILRNAKIDMFKGSMRLAVDKWGRIEVTE 120 (143)
Q Consensus 83 ~~~------------------i~~Gd~v~I~na~~~~~~g~~~L~ig~~g~I~~~~ 120 (143)
.|. +++||.+....+-+++|.- ++|+.|-..++|
T Consensus 325 pdr~s~~avfDAC~iCGd~GYv~e~dqvICv~C~Vrmfip----SIGk~GGCNPvP 376 (405)
T COG4393 325 PDRLSLGAVFDACDICGDQGYVMEGDQVICVRCDVRMFIP----SIGKKGGCNPVP 376 (405)
T ss_pred CCCCCceeeehHHHhccccceEeECCEEEEEEccEEEEcc----cCCCCCCCCCCc
Confidence 433 3568888888888888743 678888877764
No 115
>PF05113 DUF693: Protein of unknown function (DUF693); InterPro: IPR007800 This family consists of uncharacterised proteins from Borrelia burgdorferi.
Probab=49.02 E-value=46 Score=28.34 Aligned_cols=33 Identities=21% Similarity=0.133 Sum_probs=24.2
Q ss_pred ceEEEEEec---CCCCCCCCCCEEEEeceEEceeCC
Q 032330 72 GAIYFTARN---DQVDIMTPGTTVILRNAKIDMFKG 104 (143)
Q Consensus 72 G~I~ltlW~---~~~~~i~~Gd~v~I~na~~~~~~g 104 (143)
-...+++|+ +..+.+++||+|+|..-....-+.
T Consensus 61 Kqaki~lwNlPLdFt~~ik~gDIVKIYYKKFa~~k~ 96 (314)
T PF05113_consen 61 KQAKIVLWNLPLDFTDNIKTGDIVKIYYKKFAHEKD 96 (314)
T ss_pred eeeEEEEEecCcccccccCcCcEEEEEeeccccccc
Confidence 456889999 445668999999998655544444
No 116
>PRK07772 single-stranded DNA-binding protein; Provisional
Probab=48.61 E-value=51 Score=26.02 Aligned_cols=29 Identities=14% Similarity=0.121 Sum_probs=22.6
Q ss_pred cceEEEEEecCCC----CCCCCCCEEEEeceEE
Q 032330 71 TGAIYFTARNDQV----DIMTPGTTVILRNAKI 99 (143)
Q Consensus 71 TG~I~ltlW~~~~----~~i~~Gd~v~I~na~~ 99 (143)
|=-+++++|..++ ..++.||.|.|.+-..
T Consensus 52 t~fi~V~~Wg~~Ae~va~~L~KGd~V~V~GrL~ 84 (186)
T PRK07772 52 ALFLRCSIWRQAAENVAESLTKGMRVIVTGRLK 84 (186)
T ss_pred ceEEEEEEecHHHHHHHHhcCCCCEEEEEEEEE
Confidence 3467899998754 3478999999998765
No 117
>PRK00286 xseA exodeoxyribonuclease VII large subunit; Reviewed
Probab=48.46 E-value=1.1e+02 Score=26.55 Aligned_cols=68 Identities=12% Similarity=0.120 Sum_probs=45.9
Q ss_pred CCCceEEEEEEecCcceeccCCCccccCCCCCCCCCCeeEEEEEeeCcceEEEEEecCCCCC----CCCCCEEEEeceEE
Q 032330 24 TTGHTLTVKVVSSKPVQVNKPRGARSLSSLSQPSRPPRIAECLVGDDTGAIYFTARNDQVDI----MTPGTTVILRNAKI 99 (143)
Q Consensus 24 ~~~v~i~~kVl~~~~~~~~~~R~~~~~~~DG~~~~~~~v~~~lVgDeTG~I~ltlW~~~~~~----i~~Gd~v~I~na~~ 99 (143)
..++-|.|.|.+... .. .|. +..-+-|++..|+.++|...... ++.|+-|.+.+...
T Consensus 23 ~~~v~v~gEis~~~~-----~~-------------sGH-~Yf~Lkd~~a~i~~~~~~~~~~~~~~~~~~G~~v~v~g~~~ 83 (438)
T PRK00286 23 LGQVWVRGEISNFTR-----HS-------------SGH-WYFTLKDEIAQIRCVMFKGSARRLKFKPEEGMKVLVRGKVS 83 (438)
T ss_pred CCcEEEEEEeCCCee-----CC-------------CCe-EEEEEEcCCcEEEEEEEcChhhcCCCCCCCCCEEEEEEEEE
Confidence 456777777666441 11 133 45678899999999999743322 58899999886654
Q ss_pred cee--CCeEEEEeC
Q 032330 100 DMF--KGSMRLAVD 111 (143)
Q Consensus 100 ~~~--~g~~~L~ig 111 (143)
.| +|.++|++.
T Consensus 84 -~y~~~g~~ql~v~ 96 (438)
T PRK00286 84 -LYEPRGDYQLIVE 96 (438)
T ss_pred -EECCCCCEEEEEE
Confidence 44 467888654
No 118
>PRK07135 dnaE DNA polymerase III DnaE; Validated
Probab=45.99 E-value=40 Score=33.04 Aligned_cols=68 Identities=16% Similarity=0.261 Sum_probs=47.9
Q ss_pred eeeccCCCCCCCceEEEEEEecCcceeccCCCccccCCCCCCCCCCeeEEEEEeeCcceEEEEEecCC---CCCCCCCCE
Q 032330 15 IKVDQLKPGTTGHTLTVKVVSSKPVQVNKPRGARSLSSLSQPSRPPRIAECLVGDDTGAIYFTARNDQ---VDIMTPGTT 91 (143)
Q Consensus 15 ~kI~dL~p~~~~v~i~~kVl~~~~~~~~~~R~~~~~~~DG~~~~~~~v~~~lVgDeTG~I~ltlW~~~---~~~i~~Gd~ 91 (143)
.++.+|. ....+.+.+.|.++.... ++ | ..|+-+.+.|.||.+.+++|.+. ...+.+|+.
T Consensus 889 ~~~~~l~-~~~~~~v~g~i~~~~~~~---K~--------g-----~~maf~~~eD~~~~~e~~~F~~~~~~~~~l~~~~~ 951 (973)
T PRK07135 889 IRLKDLR-INTEYRLAIEVKNVKRLR---KA--------N-----KEYKKVILSDDSVEITIFVNDNDYLLFETLKKGDI 951 (973)
T ss_pred hhHHHhc-CCCeEEEEEEEEEEEEEe---eC--------C-----CeEEEEEEEECCCcEEEEEcHHHHHHHHHhhcCCE
Confidence 3577774 334567888888877533 33 3 36999999999999999999642 223678888
Q ss_pred EEEeceEE
Q 032330 92 VILRNAKI 99 (143)
Q Consensus 92 v~I~na~~ 99 (143)
+.+.+-..
T Consensus 952 ~~~~~~~~ 959 (973)
T PRK07135 952 YEFLISKS 959 (973)
T ss_pred EEEEEEEc
Confidence 88855443
No 119
>TIGR00457 asnS asparaginyl-tRNA synthetase. In a multiple sequence alignment of representative asparaginyl-tRNA synthetases (asnS), archaeal/eukaryotic type aspartyl-tRNA synthetases (aspS_arch), and bacterial type aspartyl-tRNA synthetases (aspS_bact), there is a striking similarity between asnS and aspS_arch in gap pattern and in sequence, and a striking divergence of aspS_bact. Consequently, a separate model was built for each of the three groups. This model, asnS, represents asparaginyl-tRNA synthetases from the three domains of life. Some species lack this enzyme and charge tRNA(asn) by misacylation with Asp, followed by transamidation of Asp to Asn.
Probab=45.96 E-value=1.4e+02 Score=26.42 Aligned_cols=60 Identities=17% Similarity=0.220 Sum_probs=41.7
Q ss_pred CeeEEEEEeeCc--ceEEEEEecC-------CCCCCCCCCEEEEeceEEce--eCCeEEEEeCCceeEEEc
Q 032330 60 PRIAECLVGDDT--GAIYFTARND-------QVDIMTPGTTVILRNAKIDM--FKGSMRLAVDKWGRIEVT 119 (143)
Q Consensus 60 ~~v~~~lVgDeT--G~I~ltlW~~-------~~~~i~~Gd~v~I~na~~~~--~~g~~~L~ig~~g~I~~~ 119 (143)
+.++=..|-|.+ |.|.+++=.. .+..+..||+|.+.+-.... ..+.++|.+.+.--+.+.
T Consensus 32 ~~~~F~~lrD~~~~g~iQ~v~~~~~~~~~~~~~~~l~~gs~V~v~G~v~~~~~~~~~~El~~~~i~vl~~~ 102 (453)
T TIGR00457 32 KKIIFLELNDGSSLGPIQAVINGEDNPYLFQLLKSLTTGSSVSVTGKVVESPGKGQPVELQVKKIEVVGEA 102 (453)
T ss_pred CCeEEEEEECCCCCccEEEEEeCCcChHHHHHHHcCCCCcEEEEEEEEEcCCCCCCCEEEEEeEEEEEecC
Confidence 347778889999 9999876443 12347899999999976642 346788988655444433
No 120
>PF09104 BRCA-2_OB3: BRCA2, oligonucleotide/oligosaccharide-binding, domain 3; InterPro: IPR015188 This domain assumes an OB fold, which consists of a highly curved five-stranded beta-sheet that closes on itself to form a beta-barrel. OB3 has a pronounced groove formed by one face of the curved sheet and is demarcated by two loops, one between beta 1 and beta 2 and another between beta 4 and beta 5, which allows for strong ssDNA binding []. ; PDB: 1IYJ_D 1MIU_A.
Probab=45.79 E-value=1.3e+02 Score=22.87 Aligned_cols=82 Identities=15% Similarity=0.094 Sum_probs=51.7
Q ss_pred CCCCCCCceEEEEEEecCcceeccCCCccccCCCCCCCCCCeeEEEEEeeCcc-eEEEEEecCC-----CCCCCCCCEEE
Q 032330 20 LKPGTTGHTLTVKVVSSKPVQVNKPRGARSLSSLSQPSRPPRIAECLVGDDTG-AIYFTARNDQ-----VDIMTPGTTVI 93 (143)
Q Consensus 20 L~p~~~~v~i~~kVl~~~~~~~~~~R~~~~~~~DG~~~~~~~v~~~lVgDeTG-~I~ltlW~~~-----~~~i~~Gd~v~ 93 (143)
.+|.=.-|+++|-|+++.. +. +...-+.++|+.- -+-+..|.+. -|.+++|..|.
T Consensus 14 f~pp~~EvD~VG~VvsV~~-----~~--------------~f~~~vYLsD~~~Nll~Ikfw~~l~~~~~eDilk~~~liA 74 (143)
T PF09104_consen 14 FQPPYGEVDTVGFVVSVSK-----KQ--------------GFQPLVYLSDECHNLLAIKFWTGLNQYGYEDILKPGSLIA 74 (143)
T ss_dssp --TCCCEEEEEEEEEEEE-------T--------------TS--EEEEE-TTS-EEEEEESS-------SS---TT-EEE
T ss_pred cCCCccccceEEEEEEEEe-----cC--------------CCceeEEeecCCccEEEEEeccCccccchhhhcCcceEEE
Confidence 3566778999999999941 11 1223377899966 7888899854 36679999999
Q ss_pred EeceEEcee--CCeEEEEeCCceeEEEcC
Q 032330 94 LRNAKIDMF--KGSMRLAVDKWGRIEVTE 120 (143)
Q Consensus 94 I~na~~~~~--~g~~~L~ig~~g~I~~~~ 120 (143)
+.|=.-+-. .+-+.+..+..+.+...|
T Consensus 75 ~SNLqwR~~s~s~iP~~~A~d~S~FS~nP 103 (143)
T PF09104_consen 75 ASNLQWRPESTSGIPTLFATDLSVFSANP 103 (143)
T ss_dssp EEEEEE-S-TTSSS-EEEEECCEEEESS-
T ss_pred EeeeEeecccccCCCeeEeccceeeecCc
Confidence 999887533 367899999998887765
No 121
>COG3481 Predicted HD-superfamily hydrolase [General function prediction only]
Probab=45.63 E-value=18 Score=30.56 Aligned_cols=58 Identities=17% Similarity=0.276 Sum_probs=45.1
Q ss_pred eEEEEEeeCcceEEEEEecCC---CCCCCCCCEEEEeceEEceeCCeEEEEeCCceeEEEcC
Q 032330 62 IAECLVGDDTGAIYFTARNDQ---VDIMTPGTTVILRNAKIDMFKGSMRLAVDKWGRIEVTE 120 (143)
Q Consensus 62 v~~~lVgDeTG~I~ltlW~~~---~~~i~~Gd~v~I~na~~~~~~g~~~L~ig~~g~I~~~~ 120 (143)
--.+.+.|.||.|.=.+|+.. .+.+.+|.++.+.+-. ..|++..++.+-+-+-+....
T Consensus 22 ~l~l~~~d~~gei~~~~wd~~~~~~~~~~~~~Vv~~~g~~-~~~~~~~q~ki~~~r~~~~~~ 82 (287)
T COG3481 22 KLKLTLQDKTGEIEAKLWDALKNDEEAFKPGMVVHVEGVK-EVYRGRKQHKIIRIRLITDSD 82 (287)
T ss_pred hheeeeccccceecccccccccccHhhhCcCceeccccce-ecccccchheeeecccccccC
Confidence 446889999999999999943 3447899999887554 688888899887777665543
No 122
>PTZ00417 lysine-tRNA ligase; Provisional
Probab=43.93 E-value=1.1e+02 Score=28.36 Aligned_cols=57 Identities=14% Similarity=-0.002 Sum_probs=42.9
Q ss_pred eeEEEEEeeCcceEEEEEecCC-----------CCCCCCCCEEEEeceEEceeCCeEEEEeCCceeEE
Q 032330 61 RIAECLVGDDTGAIYFTARNDQ-----------VDIMTPGTTVILRNAKIDMFKGSMRLAVDKWGRIE 117 (143)
Q Consensus 61 ~v~~~lVgDeTG~I~ltlW~~~-----------~~~i~~Gd~v~I~na~~~~~~g~~~L~ig~~g~I~ 117 (143)
.++=+.|-|++|.|.+.+-.+. ...+..||+|.+.|...+...|.++|.+.+.--+.
T Consensus 150 k~~F~~L~d~~g~iQv~~~~~~~~~~~~~~~~~~~~l~~Gd~V~V~G~~~~t~~gel~i~~~~i~lls 217 (585)
T PTZ00417 150 KLRFFDLVGDGAKIQVLANFAFHDHTKSNFAECYDKIRRGDIVGIVGFPGKSKKGELSIFPKETIILS 217 (585)
T ss_pred CCEEEEEEeCCeeEEEEEECCccCCCHHHHHHHHhcCCCCCEEEEEeEEcCCCCceEEEEEEEEEEEe
Confidence 4667778899999998885321 23478899999999877776788888887774443
No 123
>COG1376 ErfK Uncharacterized protein conserved in bacteria [Function unknown]
Probab=43.56 E-value=11 Score=29.86 Aligned_cols=27 Identities=22% Similarity=0.438 Sum_probs=23.3
Q ss_pred CcceEEEEEec--CCCCCCCCCCEEEEec
Q 032330 70 DTGAIYFTARN--DQVDIMTPGTTVILRN 96 (143)
Q Consensus 70 eTG~I~ltlW~--~~~~~i~~Gd~v~I~n 96 (143)
..|||||.-|| +..+.+..|+.|.|.+
T Consensus 202 ShGCIRL~n~Da~~ly~~v~~Gt~V~v~~ 230 (232)
T COG1376 202 SHGCIRLSNQDAKDLYNRVPVGTPVVVID 230 (232)
T ss_pred CCceEecCchhHHHHHhhCCCCCEEEEee
Confidence 47999999999 5677789999999876
No 124
>PF11183 PmrD: Polymyxin resistance protein PmrD; InterPro: IPR020146 The Salmonella PmrA/PmrB two-component system is required for resistance to the cationic peptide antibiotic olymyxin B, resistance to Fe(3+)-mediated killing, growth in soil, virulence in mice, and infection of chicken macrophages. PmrA-activated genes encode periplasmic and integral membrane proteins as well as cytoplasmic products mediating the modification of the lipopolysaccharide, suggesting a role for the PmrA/PmrB system in remodeling of the Gram-negative envelope. The PmrA/PmrB two-component system of Salmonella enterica is activated by Fe(3+), which is sensed by the PmrB protein, and by low Mg(2+), which is sensed by the PhoQ protein. The low Mg(2+) activation requires pmrD, a PhoPPhoQ-activated gene that activates the response regulator PmrA at a posttranscriptional level. However, under conditions that activate the PmrA protein independently of pmrD, such as exposure to Fe3, lower levels of pmrD transcription occur. It has been demonstrated that PmrA binds to the pmrD promoter, suppressing transcription. Negative regulation of the PhoP/PhoQ-activated pmrD gene by the PmrA/ PmrB system closes a regulatory circuit designed to maintain proper cellular levels of activated PmrA protein, and constitutes a singular example of a multicomponent feedback loop []. ; PDB: 2RQX_A 2JSO_A.
Probab=43.49 E-value=26 Score=24.35 Aligned_cols=38 Identities=21% Similarity=0.183 Sum_probs=28.3
Q ss_pred eEEEEEeeCcceEEEEEecCCCCCCCCCCEEE-Eece-EE
Q 032330 62 IAECLVGDDTGAIYFTARNDQVDIMTPGTTVI-LRNA-KI 99 (143)
Q Consensus 62 v~~~lVgDeTG~I~ltlW~~~~~~i~~Gd~v~-I~na-~~ 99 (143)
..-.++-|.-|.+.|.+|-+..-.+++||.+. |.|| |.
T Consensus 16 ~~~l~l~~a~g~LkmIAEv~s~~~l~~GD~LtPl~dA~Yc 55 (82)
T PF11183_consen 16 CHVLLLCDAGGALKMIAEVTSDFRLQEGDKLTPLQDALYC 55 (82)
T ss_dssp EEEEEEEETTTTCEEEEEEEESS---TT-EEEESSSSEEE
T ss_pred EEEEEEecCCCCeEEEEEeecCcccCCCCCccccccceEE
Confidence 56678899999999999975555689999999 9999 44
No 125
>PRK06863 single-stranded DNA-binding protein; Provisional
Probab=41.48 E-value=76 Score=24.60 Aligned_cols=28 Identities=11% Similarity=0.049 Sum_probs=22.2
Q ss_pred ceEEEEEecCCC----CCCCCCCEEEEeceEE
Q 032330 72 GAIYFTARNDQV----DIMTPGTTVILRNAKI 99 (143)
Q Consensus 72 G~I~ltlW~~~~----~~i~~Gd~v~I~na~~ 99 (143)
=-+++++|+.++ ..++.|+.|.|.+...
T Consensus 52 ~w~~Vv~fgk~AE~v~~~LkKGs~V~VeGrL~ 83 (168)
T PRK06863 52 EWHRIVFYRRQAEVAGEYLRKGSQVYVEGRLK 83 (168)
T ss_pred eEEEEEEEhHHHHHHHHHCCCCCEEEEEEEEE
Confidence 368999998654 3478999999998766
No 126
>cd04319 PhAsnRS_like_N PhAsnRS_like_N: N-terminal, anticodon recognition domain of the type found in Pyrococcus horikoshii AsnRS asparaginyl-tRNA synthetase (AsnRS). This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop. The archeal enzymes in this group are homodimeric class2b aminoacyl-tRNA synthetases (aaRSs). aaRSs catalyze the specific attachment of amino acids (AAs) to their cognate tRNAs during protein biosynthesis. This 2-step reaction involves i) the activation of the AA by ATP in the presence of magnesium ions, followed by ii) the transfer of the activated AA to the terminal ribose of tRNA. In the case of the class2b aaRSs, the activated AA is attached to the 3'OH of the terminal ribose.
Probab=40.41 E-value=1.2e+02 Score=20.78 Aligned_cols=58 Identities=19% Similarity=0.159 Sum_probs=38.1
Q ss_pred eeEEEEEeeCcceEEEEEecC-------CCCCCCCCCEEEEeceEEcee--CCeEEEEeCCceeEEE
Q 032330 61 RIAECLVGDDTGAIYFTARND-------QVDIMTPGTTVILRNAKIDMF--KGSMRLAVDKWGRIEV 118 (143)
Q Consensus 61 ~v~~~lVgDeTG~I~ltlW~~-------~~~~i~~Gd~v~I~na~~~~~--~g~~~L~ig~~g~I~~ 118 (143)
.++=..|-|.+|.+.+.+=.+ ++..+..|++|.+.+.....- .+.++|.+.+.--+..
T Consensus 16 k~~Fi~lrD~~g~iQ~v~~~~~~~~~~~~~~~l~~~s~v~V~G~v~~~~~~~~~~Ei~~~~i~vl~~ 82 (103)
T cd04319 16 KKAFIVLRDSTGIVQAVFSKDLNEEAYREAKKVGIESSVIVEGAVKADPRAPGGAEVHGEKLEIIQN 82 (103)
T ss_pred CeEEEEEecCCeeEEEEEeCCCCHHHHHHHhCCCCCCEEEEEEEEEECCCCCCCEEEEEEEEEEEec
Confidence 456677899999988866432 123467899999999765422 2457787755443333
No 127
>PRK10260 L,D-transpeptidase; Provisional
Probab=40.20 E-value=17 Score=30.96 Aligned_cols=41 Identities=17% Similarity=0.258 Sum_probs=32.3
Q ss_pred CcceEEEEEec--CCCCCCCCCCEEEEeceEEcee---CCeEEEEe
Q 032330 70 DTGAIYFTARN--DQVDIMTPGTTVILRNAKIDMF---KGSMRLAV 110 (143)
Q Consensus 70 eTG~I~ltlW~--~~~~~i~~Gd~v~I~na~~~~~---~g~~~L~i 110 (143)
..|||||.-|| +..+.+..|..|+|.|.-++.- +|.+-|.+
T Consensus 207 ShGCIRl~n~Di~~L~~~V~~Gt~V~ii~~pvk~~~~~~g~~~lEv 252 (306)
T PRK10260 207 SHGCVRLRNEDIKFLFEKVPVGTRVQFIDEPVKATTEPDGSRYIEV 252 (306)
T ss_pred CCCeeCCCHHHHHHHHhcCCCCCEEEEecCceeccccCCCeEEEEE
Confidence 58999999998 4667789999999999888753 46555544
No 128
>TIGR00237 xseA exodeoxyribonuclease VII, large subunit. This family consist of exodeoxyribonuclease VII, large subunit XseA which catalyses exonucleolytic cleavage in either the 5'-3' or 3'-5' direction to yield 5'-phosphomononucleotides. Exonuclease VII consists of one large subunit and four small subunits.
Probab=40.02 E-value=1.5e+02 Score=26.06 Aligned_cols=48 Identities=10% Similarity=0.185 Sum_probs=35.0
Q ss_pred EEEEEeeCcceEEEEEecCCCCC----CCCCCEEEEeceEEcee--CCeEEEEeC
Q 032330 63 AECLVGDDTGAIYFTARNDQVDI----MTPGTTVILRNAKIDMF--KGSMRLAVD 111 (143)
Q Consensus 63 ~~~lVgDeTG~I~ltlW~~~~~~----i~~Gd~v~I~na~~~~~--~g~~~L~ig 111 (143)
+...+-|+...|+.+.|...... ++.|+-|.+.+.. +.| +|.++|++.
T Consensus 37 ~YFtLkD~~a~i~~vmf~~~~~~l~f~~~~G~~V~v~g~v-~~y~~~G~~ql~v~ 90 (432)
T TIGR00237 37 WYFTLKDENAQVRCVMFRGNNNRLKFRPQNGQQVLVRGGI-SVYEPRGDYQIICF 90 (432)
T ss_pred EEEEEEcCCcEEEEEEEcChhhCCCCCCCCCCEEEEEEEE-EEECCCCcEEEEEE
Confidence 44556899999999999743322 4789999988655 455 477888764
No 129
>PF11213 DUF3006: Protein of unknown function (DUF3006); InterPro: IPR021377 This family of proteins has no known function.
Probab=39.92 E-value=83 Score=20.61 Aligned_cols=33 Identities=15% Similarity=0.092 Sum_probs=20.6
Q ss_pred eeEEEEEeeCcceEEEEEecCCCCCCCCCCEEEE
Q 032330 61 RIAECLVGDDTGAIYFTARNDQVDIMTPGTTVIL 94 (143)
Q Consensus 61 ~v~~~lVgDeTG~I~ltlW~~~~~~i~~Gd~v~I 94 (143)
.++-+++.|+.-.+.+ --+.....+++||++.+
T Consensus 10 ~~AVl~~~~~~~~~~v-p~~~LP~~~keGDvl~i 42 (71)
T PF11213_consen 10 DYAVLELEDGEKEIDV-PRSRLPEGAKEGDVLEI 42 (71)
T ss_pred CEEEEEECCCeEEEEE-EHHHCCCCCCcccEEEE
Confidence 4666666666622222 22345667899999999
No 130
>PRK10190 L,D-transpeptidase; Provisional
Probab=39.77 E-value=19 Score=30.79 Aligned_cols=41 Identities=24% Similarity=0.306 Sum_probs=32.6
Q ss_pred CcceEEEEEec--CCCCCCCCCCEEEEeceEEcee---CCeEEEEe
Q 032330 70 DTGAIYFTARN--DQVDIMTPGTTVILRNAKIDMF---KGSMRLAV 110 (143)
Q Consensus 70 eTG~I~ltlW~--~~~~~i~~Gd~v~I~na~~~~~---~g~~~L~i 110 (143)
..|||||.-|| +..+.+..|..|.|.|.-++.. +|.+-|.+
T Consensus 204 ShGCIRm~n~Di~~Lf~~V~~GT~V~ii~~pvk~~~~~~g~~ylEv 249 (310)
T PRK10190 204 SQGCIRLRNDDIKYLFDNVPVGTRVQIIDQPVKYTTEPDGSRWLEV 249 (310)
T ss_pred CCceeCcCHHHHHHHHhhCCCCCEEEEecccEEEEEcCCCEEEEEE
Confidence 58999999998 4667789999999999888774 46555544
No 131
>PRK04036 DNA polymerase II small subunit; Validated
Probab=39.47 E-value=1.1e+02 Score=27.51 Aligned_cols=66 Identities=14% Similarity=0.101 Sum_probs=42.9
Q ss_pred eeeccCCCCCCCceEEEEEEecCcceeccCCCccccCCCCCCCCCCeeEEEEEeeCcceEEEEEecCC------CCCCCC
Q 032330 15 IKVDQLKPGTTGHTLTVKVVSSKPVQVNKPRGARSLSSLSQPSRPPRIAECLVGDDTGAIYFTARNDQ------VDIMTP 88 (143)
Q Consensus 15 ~kI~dL~p~~~~v~i~~kVl~~~~~~~~~~R~~~~~~~DG~~~~~~~v~~~lVgDeTG~I~ltlW~~~------~~~i~~ 88 (143)
.+|.+++-+...+.|.|.|-++. +++ +| . ....+.|+||+|++..-.+. .+.+-+
T Consensus 144 ~~l~~~~~~~~~~~viG~v~~~~----~~~--------~g-----~--~~~~LED~sgrv~l~~~~~~~~~~~~~~~lvt 204 (504)
T PRK04036 144 ESLKKLKRGGEEVSIIGMVSDIR----STK--------NG-----H--KIVELEDTTGTFPVLIMKDREDLAELADELLL 204 (504)
T ss_pred HHHhcCccCCceEEEEEEEEEee----ccc--------CC-----c--eEEEEECCCCeEEEEeecchhhhhhhhhcccC
Confidence 45566662335577888886554 222 33 1 24779999999999874322 245678
Q ss_pred CCEEEEeceEE
Q 032330 89 GTTVILRNAKI 99 (143)
Q Consensus 89 Gd~v~I~na~~ 99 (143)
|.+|-+.+-+.
T Consensus 205 g~vv~v~G~~~ 215 (504)
T PRK04036 205 DEVIGVEGTLS 215 (504)
T ss_pred ceEEEEEEEEc
Confidence 99998887654
No 132
>PRK06642 single-stranded DNA-binding protein; Provisional
Probab=38.58 E-value=1e+02 Score=23.21 Aligned_cols=65 Identities=12% Similarity=0.089 Sum_probs=41.5
Q ss_pred CCCceEEEEEEecCcceeccCCCccccCCCCCCCCCCeeEEEEEe------e--------CcceEEEEEecC-CCC----
Q 032330 24 TTGHTLTVKVVSSKPVQVNKPRGARSLSSLSQPSRPPRIAECLVG------D--------DTGAIYFTARND-QVD---- 84 (143)
Q Consensus 24 ~~~v~i~~kVl~~~~~~~~~~R~~~~~~~DG~~~~~~~v~~~lVg------D--------eTG~I~ltlW~~-~~~---- 84 (143)
++.|.|.+++-.-.+.. .++ .| ..++..-|| | +|=-+++++|++ +++
T Consensus 5 ~N~V~LiGrLg~DPElr-~t~--------~G-----~~v~~fslAv~~~~k~~~~G~~~~~T~w~~v~~~g~~~Ae~~~~ 70 (152)
T PRK06642 5 LNKVILIGNVGRDPEIR-TTG--------EG-----KKIINLSLATTETWKDRITSERKERTEWHRVVIFSEGLVSVVER 70 (152)
T ss_pred ceEEEEEEEccCCceEE-ECC--------CC-----CEEEEEEEEeccccccccCCccccceeEEEEEEeChHHHHHHHH
Confidence 56677888877644333 222 34 246666665 2 244688999985 433
Q ss_pred CCCCCCEEEEeceEE-cee
Q 032330 85 IMTPGTTVILRNAKI-DMF 102 (143)
Q Consensus 85 ~i~~Gd~v~I~na~~-~~~ 102 (143)
.++.|+.|.|.+-.. +.|
T Consensus 71 ~l~KG~~V~V~GrL~~~~y 89 (152)
T PRK06642 71 YVTKGSKLYIEGSLQTRKW 89 (152)
T ss_pred hCCCCCEEEEEEEEEeCee
Confidence 378999999998765 334
No 133
>PRK05813 single-stranded DNA-binding protein; Provisional
Probab=38.50 E-value=2.1e+02 Score=23.07 Aligned_cols=65 Identities=17% Similarity=0.104 Sum_probs=46.9
Q ss_pred CCCCceEEEEEEecCcceeccCCCccccCCCCCCCCCCeeEEEEEe-----eCcceEEEEEecCCCCC--CCCCCEEEEe
Q 032330 23 GTTGHTLTVKVVSSKPVQVNKPRGARSLSSLSQPSRPPRIAECLVG-----DDTGAIYFTARNDQVDI--MTPGTTVILR 95 (143)
Q Consensus 23 ~~~~v~i~~kVl~~~~~~~~~~R~~~~~~~DG~~~~~~~v~~~lVg-----DeTG~I~ltlW~~~~~~--i~~Gd~v~I~ 95 (143)
.++.|.|.+++.+-.+-. ... .| .-++...|+ |++--|++++|..+++. ++.|+.|.|.
T Consensus 7 ~~NkV~L~Grl~~d~e~~-~~~--------~G-----~~~~~f~laV~R~s~~~D~i~v~v~~rlae~~~l~kG~~v~Ve 72 (219)
T PRK05813 7 ENNKVYLEGKVVSELEFS-HEM--------YG-----EGFYNFKLEVPRLSDSKDILPVTVSERLLAGMDLKVGTLVIVE 72 (219)
T ss_pred hcCEEEEEEEEcCCceEE-EEe--------CC-----eEEEEEEEEeeccCCCccEEEEEEEhhhhhhhcccCCCEEEEE
Confidence 356688999998866533 222 33 235555544 89999999999987765 6899999999
Q ss_pred ceEEce
Q 032330 96 NAKIDM 101 (143)
Q Consensus 96 na~~~~ 101 (143)
+-.-++
T Consensus 73 Gqlrsy 78 (219)
T PRK05813 73 GQLRSY 78 (219)
T ss_pred EEEEEe
Confidence 888743
No 134
>COG1190 LysU Lysyl-tRNA synthetase (class II) [Translation, ribosomal structure and biogenesis]
Probab=37.59 E-value=1.8e+02 Score=26.57 Aligned_cols=58 Identities=12% Similarity=0.221 Sum_probs=46.1
Q ss_pred CeeEEEEEeeCcceEEEEEecCC---------CCCCCCCCEEEEeceEEceeCCeEEEEeCCceeEE
Q 032330 60 PRIAECLVGDDTGAIYFTARNDQ---------VDIMTPGTTVILRNAKIDMFKGSMRLAVDKWGRIE 117 (143)
Q Consensus 60 ~~v~~~lVgDeTG~I~ltlW~~~---------~~~i~~Gd~v~I~na~~~~~~g~~~L~ig~~g~I~ 117 (143)
|+++=+.|-|.+|.|.+-+-.+. ...+.-||+|-+.+...+...|.+++.+..+--+.
T Consensus 77 GK~~F~~i~d~~gkiQ~yi~k~~~~~~~~~~~~~~~dlGDiigv~G~~~~T~~GelSv~v~~~~lLs 143 (502)
T COG1190 77 GKASFADLQDGSGKIQLYVNKDEVGEEVFEALFKKLDLGDIIGVEGPLFKTKTGELSVSVEELRLLS 143 (502)
T ss_pred CceeEEEEecCCceEEEEEeccccchhhHHHHHhccccCCEEeeeeeeeecCCCceEEEEEEEeeec
Confidence 56788889999999998777442 12234699999999999999999999999885443
No 135
>COG0017 AsnS Aspartyl/asparaginyl-tRNA synthetases [Translation, ribosomal structure and biogenesis]
Probab=37.28 E-value=3.1e+02 Score=24.63 Aligned_cols=87 Identities=16% Similarity=0.118 Sum_probs=61.8
Q ss_pred eeeeccCCCCCC--CceEEEEEEecCcceeccCCCccccCCCCCCCCCCeeEEEEEeeCcceEEEEEec-CC------CC
Q 032330 14 FIKVDQLKPGTT--GHTLTVKVVSSKPVQVNKPRGARSLSSLSQPSRPPRIAECLVGDDTGAIYFTARN-DQ------VD 84 (143)
Q Consensus 14 ~~kI~dL~p~~~--~v~i~~kVl~~~~~~~~~~R~~~~~~~DG~~~~~~~v~~~lVgDeTG~I~ltlW~-~~------~~ 84 (143)
.+.|+|+.+... .|.|.|-|-+ .| | .+.++=.+|-|.||.|..++-. +. +.
T Consensus 4 ~~~i~di~~~~~~~~V~v~GWV~~--------~R-------~-----~g~i~Fi~lrDgsg~iQ~v~~~~~~~~~~~~~~ 63 (435)
T COG0017 4 RTYIKDIKPHVGGQEVTVRGWVHN--------KR-------D-----LGKIIFLVLRDGSGFIQAVVPKNKVYEELFKAK 63 (435)
T ss_pred eeeHHhhhccCCCcEEEEEEEeee--------ec-------c-----cCCeEEEEEEcCCcEEEEEEECCCCcHHHhhhh
Confidence 456788887654 4555554433 34 1 2459999999999999999973 12 23
Q ss_pred CCCCCCEEEEeceEEcee--CCeEEEEeCCceeEEEcC
Q 032330 85 IMTPGTTVILRNAKIDMF--KGSMRLAVDKWGRIEVTE 120 (143)
Q Consensus 85 ~i~~Gd~v~I~na~~~~~--~g~~~L~ig~~g~I~~~~ 120 (143)
.+..+++|.|.|.....- .+.++|.+.+---+..++
T Consensus 64 ~L~~es~v~V~G~v~~~~~a~~g~El~v~~i~Vl~~a~ 101 (435)
T COG0017 64 KLTLESSVVVTGIVKASPKAPQGFELQVEKIEVLGEAD 101 (435)
T ss_pred cCCCccEEEEEEEEEcCCCCCCCEEEEEEEEEEeeccC
Confidence 578899999999888655 368999988866665553
No 136
>PRK00476 aspS aspartyl-tRNA synthetase; Validated
Probab=34.21 E-value=1.6e+02 Score=27.19 Aligned_cols=66 Identities=8% Similarity=0.106 Sum_probs=45.8
Q ss_pred eeEEEEEeeCcceEEEEEecC-----CCCCCCCCCEEEEeceEEcee---------CCeEEEEeCCceeEEEcCCCceEE
Q 032330 61 RIAECLVGDDTGAIYFTARND-----QVDIMTPGTTVILRNAKIDMF---------KGSMRLAVDKWGRIEVTEPADFEV 126 (143)
Q Consensus 61 ~v~~~lVgDeTG~I~ltlW~~-----~~~~i~~Gd~v~I~na~~~~~---------~g~~~L~ig~~g~I~~~~~~~~~v 126 (143)
.++=..|-|.+|.+.+.+=.. .+..+..|++|.|.+-....- .|.++|.+.+.--+....+..+.+
T Consensus 34 ~l~Fi~LrD~~g~iQ~v~~~~~~~~~~~~~l~~es~V~V~G~v~~~~~~~~n~~~~~g~~El~~~~i~il~~a~~lP~~~ 113 (588)
T PRK00476 34 GLIFIDLRDREGIVQVVFDPDAEAFEVAESLRSEYVIQVTGTVRARPEGTVNPNLPTGEIEVLASELEVLNKSKTLPFPI 113 (588)
T ss_pred CeEEEEEEeCCceEEEEEeCCHHHHHHHhCCCCCCEEEEEEEEEecCCcccCccCCCCcEEEEEeEEEEEecCCCCCCcc
Confidence 477788899999998876421 234578999999999776532 467899887775555543334444
No 137
>TIGR00459 aspS_bact aspartyl-tRNA synthetase, bacterial type. In a multiple sequence alignment of representative asparaginyl-tRNA synthetases (asnS), archaeal/eukaryotic type aspartyl-tRNA synthetases (aspS_arch), and bacterial type aspartyl-tRNA synthetases (aspS_bact), there is a striking similarity between asnS and aspS_arch in gap pattern and in sequence, and a striking divergence of aspS_bact. Consequently, a separate model was built for each of the three groups. This model, aspS_bact, represents aspartyl-tRNA synthetases from the Bacteria and from mitochondria. In some species, this enzyme aminoacylates tRNA for both Asp and Asn; Asp-tRNA(asn) is subsequently transamidated to Asn-tRNA(asn). This model generates very low scores for the archaeal type of aspS and for asnS; scores between the trusted and noise cutoffs represent fragmentary sequences.
Probab=33.75 E-value=1.4e+02 Score=27.62 Aligned_cols=66 Identities=8% Similarity=0.113 Sum_probs=45.8
Q ss_pred eeEEEEEeeCcceEEEEEecC-----CCCCCCCCCEEEEeceEEc---------eeCCeEEEEeCCceeEEEcCCCceEE
Q 032330 61 RIAECLVGDDTGAIYFTARND-----QVDIMTPGTTVILRNAKID---------MFKGSMRLAVDKWGRIEVTEPADFEV 126 (143)
Q Consensus 61 ~v~~~lVgDeTG~I~ltlW~~-----~~~~i~~Gd~v~I~na~~~---------~~~g~~~L~ig~~g~I~~~~~~~~~v 126 (143)
.+.=+.|-|.+|.|.+.+=.+ .+..+..|++|.|.+-... .-.|.++|.+.+.--+.+.....+..
T Consensus 32 kl~Fi~LrD~sg~iQvv~~~~~~~~~~~~~L~~esvV~V~G~v~~r~~~~~n~~~~tg~iEl~~~~i~iL~~a~~~P~~~ 111 (583)
T TIGR00459 32 GLIFIDLRDRSGIVQVVCDPDADALKLAKGLRNEDVVQVKGKVSARPEGNINRNLDTGEIEILAESITLLNKSKTPPLII 111 (583)
T ss_pred CcEEEEEEeCCccEEEEEeCCHHHHHHHhcCCCCCEEEEEEEEEeCCccccCccCCCCcEEEEEeEEEEeecCCCCCCcc
Confidence 477788999999999877432 2345789999999997663 33577888877765554443334443
No 138
>PLN02603 asparaginyl-tRNA synthetase
Probab=33.38 E-value=3.9e+02 Score=24.66 Aligned_cols=88 Identities=16% Similarity=0.216 Sum_probs=54.5
Q ss_pred CceeeeccCCCC--------CCCceEEEEEEecCcceeccCCCccccCCCCCCCCCCeeEEEEEeeCcce--EEEEEecC
Q 032330 12 PVFIKVDQLKPG--------TTGHTLTVKVVSSKPVQVNKPRGARSLSSLSQPSRPPRIAECLVGDDTGA--IYFTARND 81 (143)
Q Consensus 12 ~~~~kI~dL~p~--------~~~v~i~~kVl~~~~~~~~~~R~~~~~~~DG~~~~~~~v~~~lVgDeTG~--I~ltlW~~ 81 (143)
+..+.|+++.+. .+.|.|.|.|-++- + .+.++=+.|-|.+|. +.+++=.+
T Consensus 87 ~~~~~~~~~~~~~~~~~~~~g~~V~v~GwV~~iR---------------~-----~g~~~Fi~l~Dgs~~~~lQ~v~~~~ 146 (565)
T PLN02603 87 RKKLRIADVKGGEDEGLARVGKTLNVMGWVRTLR---------------A-----QSSVTFIEVNDGSCLSNMQCVMTPD 146 (565)
T ss_pred CCceEhhhcccccccccccCCCEEEEEEEEEEEE---------------e-----CCCeEEEEEECCCCCEeEEEEEECc
Confidence 345678888743 24466666665432 1 134777888898874 77766322
Q ss_pred C-----CC--CCCCCCEEEEeceEEceeCC--eEEEEeCCceeEEEc
Q 032330 82 Q-----VD--IMTPGTTVILRNAKIDMFKG--SMRLAVDKWGRIEVT 119 (143)
Q Consensus 82 ~-----~~--~i~~Gd~v~I~na~~~~~~g--~~~L~ig~~g~I~~~ 119 (143)
. +. .+..|++|.|.+-...--.+ .++|.+.+---+...
T Consensus 147 ~~~~~~l~~~~l~~gs~V~V~G~v~~~~~~~~~~EL~v~~i~vlg~a 193 (565)
T PLN02603 147 AEGYDQVESGLITTGASVLVQGTVVSSQGGKQKVELKVSKIVVVGKS 193 (565)
T ss_pred HHHHHHHhhcCCCCCCEEEEEEEEEecCCCCccEEEEEeEEEEEECC
Confidence 1 11 27899999999977654333 488888665444333
No 139
>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=33.30 E-value=1e+02 Score=22.09 Aligned_cols=66 Identities=20% Similarity=0.125 Sum_probs=30.5
Q ss_pred CCCceEEEEEEecCcceeccCCCccccCCCCCCCCCCeeEEEEEee--CcceEEEEEecCC-----CCCCCCCCEEEEec
Q 032330 24 TTGHTLTVKVVSSKPVQVNKPRGARSLSSLSQPSRPPRIAECLVGD--DTGAIYFTARNDQ-----VDIMTPGTTVILRN 96 (143)
Q Consensus 24 ~~~v~i~~kVl~~~~~~~~~~R~~~~~~~DG~~~~~~~v~~~lVgD--eTG~I~ltlW~~~-----~~~i~~Gd~v~I~n 96 (143)
.+.+.++|+|.++.. . +. + .. -.+.++ ..+.|.+.+=+++ ...+++||.|.|.+
T Consensus 67 gK~i~vtG~V~~I~~-~--~~---------~-----~~--~~~~~~~~~~~~v~~~~~~~~~~~~~~~~l~~G~~Vti~G 127 (144)
T PF12869_consen 67 GKIIEVTGTVSSIDK-G--FG---------D-----NY--VVLLGTENGFAGVQCYFSNDQEKRASVAKLKKGQKVTIKG 127 (144)
T ss_dssp T-EEEEEEEEEEEEE----ST---------T------E--EEEEE-TT-S-S--EEEEEEGGGHHHHHH--TTSEEEEEE
T ss_pred CCEEEEEEEEEEEEE-c--CC---------C-----cE--EEEccCCCCceeEEEEEccchhhhhhHhcCCCCCEEEEEE
Confidence 467889999998863 1 11 1 12 222333 3444555544544 22389999999999
Q ss_pred eEEcee-CCeEEE
Q 032330 97 AKIDMF-KGSMRL 108 (143)
Q Consensus 97 a~~~~~-~g~~~L 108 (143)
.....- .+.+.|
T Consensus 128 ~~~g~~~~~~v~l 140 (144)
T PF12869_consen 128 ICTGYSLMGVVML 140 (144)
T ss_dssp E-----SSS-EEE
T ss_pred EEEeeecCCcEEe
Confidence 887653 454444
No 140
>COG1917 Uncharacterized conserved protein, contains double-stranded beta-helix domain [Function unknown]
Probab=32.74 E-value=44 Score=23.73 Aligned_cols=28 Identities=11% Similarity=0.205 Sum_probs=20.6
Q ss_pred cceEEEEEecCCCCCCCCCCEEEEeceEE
Q 032330 71 TGAIYFTARNDQVDIMTPGTTVILRNAKI 99 (143)
Q Consensus 71 TG~I~ltlW~~~~~~i~~Gd~v~I~na~~ 99 (143)
.|.++++++ .+.-.+++||.+.|-=+..
T Consensus 72 ~G~~~~~~~-g~~~~l~~Gd~i~ip~g~~ 99 (131)
T COG1917 72 EGEGTVQLE-GEKKELKAGDVIIIPPGVV 99 (131)
T ss_pred ecEEEEEec-CCceEecCCCEEEECCCCe
Confidence 467788888 4555689999998875443
No 141
>COG0587 DnaE DNA polymerase III, alpha subunit [DNA replication, recombination, and repair]
Probab=30.96 E-value=91 Score=31.24 Aligned_cols=72 Identities=14% Similarity=0.146 Sum_probs=47.7
Q ss_pred eeeccCCCCCCCceEEEEEEecCcceeccCCCccccCCCCCCCCCCeeEEEEEeeCcceEEEEEec----CCCCCCCCCC
Q 032330 15 IKVDQLKPGTTGHTLTVKVVSSKPVQVNKPRGARSLSSLSQPSRPPRIAECLVGDDTGAIYFTARN----DQVDIMTPGT 90 (143)
Q Consensus 15 ~kI~dL~p~~~~v~i~~kVl~~~~~~~~~~R~~~~~~~DG~~~~~~~v~~~lVgDeTG~I~ltlW~----~~~~~i~~Gd 90 (143)
....++.+......+.+.|..+..+. +++ .| ..++-+.+.|+||.+.+++|. ++...+.+|.
T Consensus 967 ~~~~~~~~~~~~~~~~~~i~~vr~~~--tk~-------~G-----~~~~f~tl~D~~g~~e~v~f~~~~~~~~~~l~~~~ 1032 (1139)
T COG0587 967 IRLLDLVEDGRRVVLAGGIVAVRQRP--TKA-------KG-----NKMAFLTLEDETGILEVVVFPSEYERYRRLLLEGR 1032 (1139)
T ss_pred cchhhhccccceeEEEEEEEEEEEee--ccC-------CC-----CEEEEEEEecCCCcEEEEEcHHHHHHHHHHhccCc
Confidence 44455555544345777777777544 231 23 469999999999999999993 2344567787
Q ss_pred EEEEeceEEc
Q 032330 91 TVILRNAKID 100 (143)
Q Consensus 91 ~v~I~na~~~ 100 (143)
.+.|.+-...
T Consensus 1033 ~~~v~g~v~~ 1042 (1139)
T COG0587 1033 LLIVKGKVQR 1042 (1139)
T ss_pred EEEEEEEEEe
Confidence 7777654443
No 142
>PF04775 Bile_Hydr_Trans: Acyl-CoA thioester hydrolase/BAAT N-terminal region; InterPro: IPR006862 This entry presents the N-termini of acyl-CoA thioester hydrolase and bile acid-CoA:amino acid N-acetyltransferase (BAAT) []. This region is not thought to contain the active site of either enzyme. Thioesterase isoforms have been identified in peroxisomes, cytoplasm and mitochondria, where they are thought to have distinct functions in lipid metabolism []. For example, in peroxisomes, the hydrolase acts on bile-CoA esters [].; GO: 0016290 palmitoyl-CoA hydrolase activity, 0006629 lipid metabolic process; PDB: 3HLK_B 3K2I_B.
Probab=30.23 E-value=96 Score=22.52 Aligned_cols=47 Identities=28% Similarity=0.427 Sum_probs=24.3
Q ss_pred CCceeeeccCCCCCCCceEEEEEEecCcceeccCCCccccCCCCCCCCCCeeEEEEEeeCcceEEEE
Q 032330 11 KPVFIKVDQLKPGTTGHTLTVKVVSSKPVQVNKPRGARSLSSLSQPSRPPRIAECLVGDDTGAIYFT 77 (143)
Q Consensus 11 ~~~~~kI~dL~p~~~~v~i~~kVl~~~~~~~~~~R~~~~~~~DG~~~~~~~v~~~lVgDeTG~I~lt 77 (143)
.|..++|..|.|+.. |+|.++..+-.... =+=.-...+|++|+|-|.
T Consensus 3 e~~~I~v~GL~p~~~-vtl~a~~~~~~g~~-------------------w~S~A~f~Ad~~G~VDl~ 49 (126)
T PF04775_consen 3 EPVDIRVSGLPPGQE-VTLRARLTDDNGVQ-------------------WQSYATFRADENGIVDLS 49 (126)
T ss_dssp S--EEEEES--TT-E-EEEEEEEE-TTS-E-------------------EEEEEEEE--TTS-EETT
T ss_pred CCeEEEEeCCCCCCE-EEEEEEEEeCCCCE-------------------EEEEEEEEcCCCCeEEec
Confidence 466789999999876 77888777522111 011225689999999874
No 143
>COG4013 Uncharacterized protein conserved in archaea [Function unknown]
Probab=29.49 E-value=1.4e+02 Score=21.05 Aligned_cols=32 Identities=25% Similarity=0.363 Sum_probs=23.5
Q ss_pred CCCCCCEEEEeceEE-------ceeCCeEEEEeCC---ceeE
Q 032330 85 IMTPGTTVILRNAKI-------DMFKGSMRLAVDK---WGRI 116 (143)
Q Consensus 85 ~i~~Gd~v~I~na~~-------~~~~g~~~L~ig~---~g~I 116 (143)
.+++||.++|.-|++ ...+|.++|.+.+ .|-+
T Consensus 20 eV~~gd~vel~~grVhIpG~vv~~n~g~l~l~~esdmi~Gi~ 61 (91)
T COG4013 20 EVDVGDYVELYFGRVHIPGRVVHYNDGLLRLVHESDMIYGII 61 (91)
T ss_pred cCCCCCEEEEEEEEEEeccEEEEeeccEEEEEEeccccCceE
Confidence 468899988876554 5667889998887 5543
No 144
>TIGR00594 polc DNA-directed DNA polymerase III (polc). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=29.31 E-value=1.1e+02 Score=30.04 Aligned_cols=40 Identities=18% Similarity=0.032 Sum_probs=29.0
Q ss_pred CceEEEEEEecCcceeccCCCccccCCCCCCCCCCeeEEEEEeeCcceEEEEEe
Q 032330 26 GHTLTVKVVSSKPVQVNKPRGARSLSSLSQPSRPPRIAECLVGDDTGAIYFTAR 79 (143)
Q Consensus 26 ~v~i~~kVl~~~~~~~~~~R~~~~~~~DG~~~~~~~v~~~lVgDeTG~I~ltlW 79 (143)
.+.+-+.|.++..+. .+++ | ..|+-+.+.|+||.+.+++|
T Consensus 983 ~v~v~G~i~~~~~~~-~tkk--------G-----~~maf~tleD~tg~ie~viF 1022 (1022)
T TIGR00594 983 QVRTLGGLNSVKKKI-TTKN--------G-----KPMAFLQLEDETGSIEVVVF 1022 (1022)
T ss_pred EEEEEEEEEEEEEec-ccCC--------C-----CEEEEEEEEECCCcEEEEeC
Confidence 366777777766532 2343 2 35999999999999999987
No 145
>COG2176 PolC DNA polymerase III, alpha subunit (gram-positive type) [DNA replication, recombination, and repair]
Probab=28.92 E-value=2.2e+02 Score=29.23 Aligned_cols=90 Identities=13% Similarity=0.120 Sum_probs=66.7
Q ss_pred ceeeeccCCCCCCCceEEEEEEecCcceeccCCCccccCCCCCCCCCCeeEEEEEeeCcceEEEEEecC------CCCCC
Q 032330 13 VFIKVDQLKPGTTGHTLTVKVVSSKPVQVNKPRGARSLSSLSQPSRPPRIAECLVGDDTGAIYFTARND------QVDIM 86 (143)
Q Consensus 13 ~~~kI~dL~p~~~~v~i~~kVl~~~~~~~~~~R~~~~~~~DG~~~~~~~v~~~lVgDeTG~I~ltlW~~------~~~~i 86 (143)
++..+-++.+.+.++.+.|.|-++.... .| -| ..+.+..|-|-|-+..+-.|-. ..+.+
T Consensus 228 ~i~~~~~i~~~~~~v~v~G~IF~~e~~~---~k-------sG-----r~l~~i~vTD~t~Sl~~k~f~~~~ed~~~~~~i 292 (1444)
T COG2176 228 EIKPLIKINEEETRVKVEGYIFKIEIKE---LK-------SG-----RTLLNIKVTDYTSSLILKKFLRDEEDEKKFDGI 292 (1444)
T ss_pred ceeehhhccccccceEEEEEEEEEeeee---cc-------cC-----cEEEEEEEecCchheeehhhccccccHHHHhhc
Confidence 5667777888888899999999977533 22 23 4688999999999999988853 24557
Q ss_pred CCCCEEEEeceEE-ceeCCeEEEEeCCceeEE
Q 032330 87 TPGTTVILRNAKI-DMFKGSMRLAVDKWGRIE 117 (143)
Q Consensus 87 ~~Gd~v~I~na~~-~~~~g~~~L~ig~~g~I~ 117 (143)
+.|+.|++++-.- +.+.+.+.+.+..=-.|+
T Consensus 293 k~g~wvk~~g~v~~d~f~~~l~m~i~~I~ei~ 324 (1444)
T COG2176 293 KKGMWVKARGNVQLDTFTRDLTMIINDINEIE 324 (1444)
T ss_pred ccCcEEEEEEEEEecccccceEEEhhhhhhhh
Confidence 9999999997665 344567777766655554
No 146
>KOG1816 consensus Ubiquitin fusion-degradation protein [Posttranslational modification, protein turnover, chaperones]
Probab=28.89 E-value=45 Score=28.45 Aligned_cols=30 Identities=20% Similarity=0.320 Sum_probs=24.7
Q ss_pred eCcceEEEEEecCCCCCCCCCCEEEEeceE
Q 032330 69 DDTGAIYFTARNDQVDIMTPGTTVILRNAK 98 (143)
Q Consensus 69 DeTG~I~ltlW~~~~~~i~~Gd~v~I~na~ 98 (143)
=|.|.|-|=.|=-|--.+++||.|+|++..
T Consensus 81 AeEG~vyLP~WMmq~L~le~gdlv~i~~v~ 110 (308)
T KOG1816|consen 81 AEEGRVYLPYWMMQNLLLEEGDLVRIRSVT 110 (308)
T ss_pred ecCceEEeehHhhhhccCCCCCeEEEEEee
Confidence 356899999998665678999999999754
No 147
>PF01957 NfeD: NfeD-like C-terminal, partner-binding; InterPro: IPR002810 The nfe genes (nfeA, nfeB, and nfeD) are involved in the nodulation efficiency and competitiveness of Rhizobium meliloti (Sinorhizobium meliloti) (Rhizobium meliloti) on alfalfa roots []. The specific function of this family is unknown although it is unlikely that NfeD is specifically involved in nodulation as the family contains several different archaeal and bacterial species most of which are not symbionts. This entry describes archaeal and bacterial proteins which are variously described, examples are: nodulation protein, nodulation efficiency protein D (nfeD), hypothetical protein and membrane-bound serine protease (ClpP class). A number of these proteins are classified in MEROPS peptidase family S49 as non-peptidase homologues or as unassigned peptidases. ; PDB: 2K5H_A 3CP0_A 2EXD_A.
Probab=28.38 E-value=72 Score=22.57 Aligned_cols=31 Identities=10% Similarity=0.167 Sum_probs=16.8
Q ss_pred EEeeCcceEEE--EEecCCCC-CCCCCCEEEEec
Q 032330 66 LVGDDTGAIYF--TARNDQVD-IMTPGTTVILRN 96 (143)
Q Consensus 66 lVgDeTG~I~l--tlW~~~~~-~i~~Gd~v~I~n 96 (143)
...+.+|.|++ ..|+...+ .+++|+.|+|..
T Consensus 99 ~~~~~~G~V~~~G~~w~A~s~~~i~~G~~V~Vv~ 132 (144)
T PF01957_consen 99 IPLNGSGRVKVDGERWRARSEDEIPKGDRVRVVG 132 (144)
T ss_dssp EBSSS-EEEEETTEEEEEEESSTB-TT-EEEEEE
T ss_pred eecCCcEEEEECCeEEEEEeCCCCCCCCEEEEEE
Confidence 34555666665 46763322 289999988864
No 148
>COG1570 XseA Exonuclease VII, large subunit [DNA replication, recombination, and repair]
Probab=27.01 E-value=3.7e+02 Score=24.18 Aligned_cols=68 Identities=9% Similarity=0.102 Sum_probs=45.9
Q ss_pred CCCceEEEEEEecCcceeccCCCccccCCCCCCCCCCeeEEEEEeeCcceEEEEEecCCCCC----CCCCCEEEEeceEE
Q 032330 24 TTGHTLTVKVVSSKPVQVNKPRGARSLSSLSQPSRPPRIAECLVGDDTGAIYFTARNDQVDI----MTPGTTVILRNAKI 99 (143)
Q Consensus 24 ~~~v~i~~kVl~~~~~~~~~~R~~~~~~~DG~~~~~~~v~~~lVgDeTG~I~ltlW~~~~~~----i~~Gd~v~I~na~~ 99 (143)
..+|-|+|.|-++.. + ..+ =....+.|+...|+.++|.-.... +++|+-|.+.+-.
T Consensus 23 ~~~V~v~GEISn~t~------~------------~sg-H~YFtLKD~~A~i~c~mf~~~~~~l~f~p~eG~~V~v~G~i- 82 (440)
T COG1570 23 LGQVWVRGEISNFTR------P------------ASG-HLYFTLKDERAQIRCVMFKGNNRRLKFRPEEGMQVLVRGKI- 82 (440)
T ss_pred CCeEEEEEEecCCcc------C------------CCc-cEEEEEccCCceEEEEEEcCcccccCCCccCCCEEEEEEEE-
Confidence 456777777665542 1 023 456778999999999999743222 4789999988655
Q ss_pred cee--CCeEEEEeC
Q 032330 100 DMF--KGSMRLAVD 111 (143)
Q Consensus 100 ~~~--~g~~~L~ig 111 (143)
+.| +|..+|++.
T Consensus 83 s~Y~~rG~YQi~~~ 96 (440)
T COG1570 83 SLYEPRGDYQIVAE 96 (440)
T ss_pred EEEcCCCceEEEEe
Confidence 455 567777654
No 149
>PLN02221 asparaginyl-tRNA synthetase
Probab=26.58 E-value=2.7e+02 Score=25.78 Aligned_cols=58 Identities=17% Similarity=0.142 Sum_probs=39.2
Q ss_pred eEEEEEeeCc--ceEEEEEecCC---CCCCCCCCEEEEeceEEcee-----CCeEEEEeCCceeEEEc
Q 032330 62 IAECLVGDDT--GAIYFTARNDQ---VDIMTPGTTVILRNAKIDMF-----KGSMRLAVDKWGRIEVT 119 (143)
Q Consensus 62 v~~~lVgDeT--G~I~ltlW~~~---~~~i~~Gd~v~I~na~~~~~-----~g~~~L~ig~~g~I~~~ 119 (143)
++=..|-|.| |.|.+++=.+. ...+..|++|.|.+-...-- .+.++|.+.+.--|...
T Consensus 70 i~Fl~LRDgs~~g~iQvVv~~~~~~~~~~L~~ES~V~V~G~V~~~~~~~~~~~~iEl~v~~i~vl~~a 137 (572)
T PLN02221 70 FAFLEVNDGSCPANLQVMVDSSLYDLSTLVATGTCVTVDGVLKVPPEGKGTKQKIELSVEKVIDVGTV 137 (572)
T ss_pred EEEEEEeCCcccccEEEEEcCchhhHHhcCCCceEEEEEEEEEeCCccCCCCccEEEEEeEEEEEecC
Confidence 6667788888 88888664321 12478899999999765321 24789988765444444
No 150
>KOG0851 consensus Single-stranded DNA-binding replication protein A (RPA), large (70 kD) subunit and related ssDNA-binding proteins [Replication, recombination and repair]
Probab=26.30 E-value=1.7e+02 Score=22.53 Aligned_cols=81 Identities=20% Similarity=0.216 Sum_probs=56.2
Q ss_pred ceeeeccCCCCCCCceEEEEEEecCcceeccCCCccccCCCCCCCCCCeeEEEEEeeCcc-eEEEEEecCC----CCCCC
Q 032330 13 VFIKVDQLKPGTTGHTLTVKVVSSKPVQVNKPRGARSLSSLSQPSRPPRIAECLVGDDTG-AIYFTARNDQ----VDIMT 87 (143)
Q Consensus 13 ~~~kI~dL~p~~~~v~i~~kVl~~~~~~~~~~R~~~~~~~DG~~~~~~~v~~~lVgDeTG-~I~ltlW~~~----~~~i~ 87 (143)
.+..+.+|.|.-.+-.+.++|+.+.... .. . .+....+++.|++| .|..+....+ .+.+.
T Consensus 3 ~~~~l~~l~~~~t~w~i~~~vl~v~~~~---~~-------~-----~~~~~~~il~D~~~~~i~a~i~~~~~~~~~~~l~ 67 (246)
T KOG0851|consen 3 GFHRLRDLSPSITGWRIQVKVLRVWKKY---SN-------P-----NGEELRLVLADEHGVKIEATVGRRLSSKYEDNLI 67 (246)
T ss_pred cccchhhcCcCceeeEEEEEEEEEEEec---CC-------C-----CccEEEEEEEecCCcEEEEEcchHHHhhhhhhee
Confidence 4667889999888888999999999633 11 1 25678888899985 3444444332 34467
Q ss_pred CCCEEEEeceEEceeCCeEEE
Q 032330 88 PGTTVILRNAKIDMFKGSMRL 108 (143)
Q Consensus 88 ~Gd~v~I~na~~~~~~g~~~L 108 (143)
+|..+.|.+-.+....+.++.
T Consensus 68 ~~~w~~i~~f~v~~~~~~~~~ 88 (246)
T KOG0851|consen 68 ENEWKIITTFGVNPNSGQVRA 88 (246)
T ss_pred cceeEEeeeeeecccccceee
Confidence 888888888877776665544
No 151
>cd04457 S1_S28E S1_S28E: S28E, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. S28E protein is a component of the 30S ribosomal subunit. S28E is highly conserved among archaea and eukaryotes. S28E may control precursor RNA splicing and turnover in mRNA maturation process but its function in the ribosome is largely unknown. The structure contains an OB-fold found in many oligosaccharide and nucleic acid binding proteins. This implies that S28E might be involved in protein synthesis.
Probab=26.09 E-value=2e+02 Score=18.88 Aligned_cols=36 Identities=14% Similarity=0.193 Sum_probs=20.9
Q ss_pred CCCeeEE--EEEeeCcceEEEEEecCCCCCCCCCCEEEEec
Q 032330 58 RPPRIAE--CLVGDDTGAIYFTARNDQVDIMTPGTTVILRN 96 (143)
Q Consensus 58 ~~~~v~~--~lVgDeTG~I~ltlW~~~~~~i~~Gd~v~I~n 96 (143)
+.+.+.+ +-+-|++|.+.+.--. ..+.+||++.+.-
T Consensus 14 ~~G~~tQVrv~~l~d~~r~i~RNVK---GPVr~GDIl~L~E 51 (60)
T cd04457 14 SRGEVTQVRVEFMDDKGRSIIRNVK---GPVREGDILMLLE 51 (60)
T ss_pred CcCcEEEEEEEEeeCCCcEEEEecc---CCcccCcEEeehh
Confidence 3455555 3344566765443222 2379999998864
No 152
>smart00350 MCM minichromosome maintenance proteins.
Probab=25.28 E-value=90 Score=27.90 Aligned_cols=29 Identities=21% Similarity=0.282 Sum_probs=25.6
Q ss_pred eEEEEEecCCCCCCCCCCEEEEeceEEce
Q 032330 73 AIYFTARNDQVDIMTPGTTVILRNAKIDM 101 (143)
Q Consensus 73 ~I~ltlW~~~~~~i~~Gd~v~I~na~~~~ 101 (143)
++.+.+-++..+.+++||.|.|.+-+...
T Consensus 105 si~v~l~~dLvd~~~PGD~V~i~Gi~~~~ 133 (509)
T smart00350 105 SVDVILDGDLVDKAKPGDRVEVTGIYRNI 133 (509)
T ss_pred EEEEEEcccccCcccCCCEEEEEEEEEee
Confidence 57888889999999999999999988754
No 153
>KOG4757 consensus Predicted telomere binding protein [General function prediction only]
Probab=25.04 E-value=2.5e+02 Score=25.54 Aligned_cols=81 Identities=15% Similarity=0.271 Sum_probs=52.4
Q ss_pred Cceeeecc-CCCCCCCceEEEEEEecCcceeccCCCccccCCCCCCCCCCeeEEEEEeeC--cc---eEEEEEec-CCCC
Q 032330 12 PVFIKVDQ-LKPGTTGHTLTVKVVSSKPVQVNKPRGARSLSSLSQPSRPPRIAECLVGDD--TG---AIYFTARN-DQVD 84 (143)
Q Consensus 12 ~~~~kI~d-L~p~~~~v~i~~kVl~~~~~~~~~~R~~~~~~~DG~~~~~~~v~~~lVgDe--TG---~I~ltlW~-~~~~ 84 (143)
+.+++|.| ++....-||+.|.|.+..+.. .. + | +--++...|-|. ++ +|.|-.-. +...
T Consensus 7 ~k~Iri~da~kk~~tiVNl~GiVkef~pp~-qs-~--------g----~D~~~tv~IvDp~~ss~gLtv~lfSkt~edLP 72 (522)
T KOG4757|consen 7 LKLIRISDALKKKNTIVNLIGIVKEFTPPR-QS-L--------G----KDWVCTVYIVDPDYSSIGLTVHLFSKTGEDLP 72 (522)
T ss_pred hheeechHHHHhcCcEEEEEEEEEeccChh-hc-c--------C----CceEEEEEEeCCCCCCCCcEEEEecCchhhCc
Confidence 45666663 455666799999999999744 21 2 2 245888888883 22 23333333 3444
Q ss_pred CC-CCCCEEEEeceEEceeCCeE
Q 032330 85 IM-TPGTTVILRNAKIDMFKGSM 106 (143)
Q Consensus 85 ~i-~~Gd~v~I~na~~~~~~g~~ 106 (143)
.+ +.||+|.+.--....|+.+.
T Consensus 73 ~Ik~~GDiillhRiKiq~y~~rt 95 (522)
T KOG4757|consen 73 VIKQVGDIILLHRIKIQSYRDRT 95 (522)
T ss_pred cccccCcEEEEEEEEEEEhhhhh
Confidence 44 67999999988887777543
No 154
>TIGR02656 cyanin_plasto plastocyanin. Members of this family are plastocyanin, a blue copper protein related to pseudoazurin, halocyanin, amicyanin, etc. This protein, located in the thylakoid luman, performs electron transport to photosystem I in Cyanobacteria and chloroplasts.
Probab=24.79 E-value=91 Score=21.32 Aligned_cols=30 Identities=30% Similarity=0.379 Sum_probs=20.2
Q ss_pred EEEeeCcceEEEEEecCCCCCCCCCCEEEEece
Q 032330 65 CLVGDDTGAIYFTARNDQVDIMTPGTTVILRNA 97 (143)
Q Consensus 65 ~lVgDeTG~I~ltlW~~~~~~i~~Gd~v~I~na 97 (143)
..+|.+.|...|. ...-.+++||.|++.|.
T Consensus 3 v~~g~~~g~~~F~---P~~i~v~~G~~V~~~N~ 32 (99)
T TIGR02656 3 VKMGADKGALVFE---PAKISIAAGDTVEWVNN 32 (99)
T ss_pred EEEecCCCceeEe---CCEEEECCCCEEEEEEC
Confidence 4567778887663 22223689999999875
No 155
>PRK06341 single-stranded DNA-binding protein; Provisional
Probab=24.73 E-value=1.8e+02 Score=22.45 Aligned_cols=32 Identities=13% Similarity=0.095 Sum_probs=22.8
Q ss_pred cceEEEEEecC-CC----CCCCCCCEEEEeceEE-cee
Q 032330 71 TGAIYFTARND-QV----DIMTPGTTVILRNAKI-DMF 102 (143)
Q Consensus 71 TG~I~ltlW~~-~~----~~i~~Gd~v~I~na~~-~~~ 102 (143)
|=-+++++|++ ++ ..++.|+.|.|.+-.. +.|
T Consensus 52 T~w~~Vv~fg~~~Ae~~~~~LkKG~~V~VeGrL~~r~w 89 (166)
T PRK06341 52 TEWHRVVIFNEGLCKVAEQYLKKGAKVYIEGQLQTRKW 89 (166)
T ss_pred ceEEEEEEeChHHHHHHHHhcCCCCEEEEEEEEEeCcE
Confidence 33568999985 33 3478999999998764 445
No 156
>PF09356 Phage_BR0599: Phage conserved hypothetical protein BR0599; InterPro: IPR018964 This entry describes the C-terminal region of a family of proteins found almost exclusively in phage or in prophage regions of bacterial genomes, including the phage-like Rhodobacter capsulatus (Rhodopseudomonas capsulata) gene transfer agent, which packages DNA. An apparent exception is Wolbachia pipientis wMel, a bacterial endosymbiont of the fruit fly, which has several candidate phage-related genes physically separate from obvious prophage regions.
Probab=24.26 E-value=1e+02 Score=20.83 Aligned_cols=22 Identities=23% Similarity=0.039 Sum_probs=18.4
Q ss_pred EEEEEecCCCCCCCCCCEEEEe
Q 032330 74 IYFTARNDQVDIMTPGTTVILR 95 (143)
Q Consensus 74 I~ltlW~~~~~~i~~Gd~v~I~ 95 (143)
-.|+||......+.+||.++|.
T Consensus 29 ~~l~L~~p~~~~~~~G~~v~l~ 50 (80)
T PF09356_consen 29 GTLTLWRPLPAGLAVGDTVTLY 50 (80)
T ss_pred CEEEEeccCcccCCCCCEEEEE
Confidence 6788898776678999999987
No 157
>PF08696 Dna2: DNA replication factor Dna2; InterPro: IPR014808 Dna2 is a DNA replication factor with single-stranded DNA-dependent ATPase, ATP-dependent nuclease, (5'-flap endonuclease) and helicase activities. It is required for Okazaki fragment processing and is involved in DNA repair pathways []. ; GO: 0003677 DNA binding, 0004003 ATP-dependent DNA helicase activity, 0005524 ATP binding, 0006260 DNA replication
Probab=23.66 E-value=2.5e+02 Score=22.09 Aligned_cols=24 Identities=13% Similarity=0.307 Sum_probs=17.4
Q ss_pred eEEEEEecCCCCC-CCCCCEEEEec
Q 032330 73 AIYFTARNDQVDI-MTPGTTVILRN 96 (143)
Q Consensus 73 ~I~ltlW~~~~~~-i~~Gd~v~I~n 96 (143)
...+.||++-.+. +++||+|.|.+
T Consensus 11 ~~~v~L~~~W~~t~v~~Gd~I~ii~ 35 (209)
T PF08696_consen 11 TRTVILRDEWCETPVSPGDIIHIIG 35 (209)
T ss_pred eEEEEEeCCcccCCCcCCCEEEEEE
Confidence 4456677754333 89999999998
No 158
>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=22.76 E-value=1.6e+02 Score=18.34 Aligned_cols=27 Identities=11% Similarity=0.058 Sum_probs=20.3
Q ss_pred CCCCCCCEEEEeceEEceeCCeEEEEe
Q 032330 84 DIMTPGTTVILRNAKIDMFKGSMRLAV 110 (143)
Q Consensus 84 ~~i~~Gd~v~I~na~~~~~~g~~~L~i 110 (143)
+.+++||.+++.=..++..++.++|++
T Consensus 46 ~~~~~Gd~v~~~V~~~d~~~~~i~ls~ 72 (73)
T cd05706 46 YKFKKNDIVRACVLSVDVPNKKIALSL 72 (73)
T ss_pred cccCCCCEEEEEEEEEeCCCCEEEEEE
Confidence 447999999987776666667777764
No 159
>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=21.49 E-value=1.3e+02 Score=18.09 Aligned_cols=24 Identities=21% Similarity=0.501 Sum_probs=18.8
Q ss_pred CCCCCCEEEEeceEEceeCCeEEEE
Q 032330 85 IMTPGTTVILRNAKIDMFKGSMRLA 109 (143)
Q Consensus 85 ~i~~Gd~v~I~na~~~~~~g~~~L~ 109 (143)
.++.||.+++.=..++. ++.+.|+
T Consensus 44 ~~~~Gd~v~v~v~~~d~-~~~i~ls 67 (68)
T cd04472 44 VLKVGDEVKVKVIEVDD-RGRISLS 67 (68)
T ss_pred ccCCCCEEEEEEEEECC-CCcEEee
Confidence 46899999998777776 7777765
No 160
>PF01200 Ribosomal_S28e: Ribosomal protein S28e; InterPro: IPR000289 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. A number of eukaryotic and archaebacterial ribosomal proteins can be grouped on the basis of sequence similarities. Examples are: Mammalian S28 [] Plant S28 [] Fungi S33 [] Archaebacterial S28e. These proteins have from 64 to 78 amino acids and a highly conserved C-terminal region.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3IZ6_Y 2XZN_1 2XZM_1 1NY4_A 1NE3_A 3U5C_c 3U5G_c 3O30_R 3O2Z_R 3IZB_Y.
Probab=21.43 E-value=2.7e+02 Score=18.73 Aligned_cols=36 Identities=11% Similarity=0.232 Sum_probs=19.9
Q ss_pred CCeeEEE---EEeeCcceEEEEEecCCCCCCCCCCEEEEece
Q 032330 59 PPRIAEC---LVGDDTGAIYFTARNDQVDIMTPGTTVILRNA 97 (143)
Q Consensus 59 ~~~v~~~---lVgDeTG~I~ltlW~~~~~~i~~Gd~v~I~na 97 (143)
.+.+.++ ++.|+.|.+.+.--. ..+.+||++.|...
T Consensus 23 ~G~~tQVrv~~l~~~~gR~i~RNVk---GPVr~GDil~LlEt 61 (69)
T PF01200_consen 23 RGQVTQVRVEFLDGDKGRSIIRNVK---GPVREGDILTLLET 61 (69)
T ss_dssp SSSEEEEEEEESSSSSS-EEEEEEC---STTSTT-EEEESSS
T ss_pred cccEEEEEEEEecCCcceEEeeccc---CCcccCcEEEEeeh
Confidence 4555553 446666565543332 23799999998654
No 161
>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=21.34 E-value=1.5e+02 Score=17.64 Aligned_cols=26 Identities=27% Similarity=0.603 Sum_probs=19.4
Q ss_pred CCCCCCCEEEEeceEEceeCCeEEEEe
Q 032330 84 DIMTPGTTVILRNAKIDMFKGSMRLAV 110 (143)
Q Consensus 84 ~~i~~Gd~v~I~na~~~~~~g~~~L~i 110 (143)
+.++.||.++++=..+.. ++.+.|++
T Consensus 43 ~~~~~Gd~v~v~v~~~~~-~~~i~ls~ 68 (69)
T cd05692 43 DVLKEGDKVKVKVLSIDA-RGRISLSI 68 (69)
T ss_pred HccCCCCEEEEEEEEECC-CCcEEEEE
Confidence 347899999988666666 67777754
No 162
>TIGR01439 lp_hng_hel_AbrB looped-hinge helix DNA binding domain, AbrB family. This DNA-binding domain family includes AbrB, a transition state regulator in Bacillus subtilis, whose DNA-binding domain structure in solution was determined by NMR. The domain binds DNA as a dimer in what is termed a looped-hinge helix fold. Some members of the family have two copies of the domain in tandem. The domain is found usually at the N-terminus of a small protein. This model excludes members of family TIGR02609.
Probab=21.21 E-value=1.1e+02 Score=17.22 Aligned_cols=26 Identities=15% Similarity=0.289 Sum_probs=16.2
Q ss_pred eCcceEEE-EEecCCCCCCCCCCEEEEe
Q 032330 69 DDTGAIYF-TARNDQVDIMTPGTTVILR 95 (143)
Q Consensus 69 DeTG~I~l-tlW~~~~~~i~~Gd~v~I~ 95 (143)
|+.|.+.+ ..|-++. .+++||.+.|.
T Consensus 4 ~~kgri~iP~~~r~~l-~~~~gd~~~i~ 30 (43)
T TIGR01439 4 DKKGQIVIPKEIREKL-GLKEGDRLEVI 30 (43)
T ss_pred CcCCeEEecHHHHHHc-CcCCCCEEEEE
Confidence 56677666 3333332 36789988887
No 163
>cd03702 IF2_mtIF2_II This family represents the domain II of bacterial Initiation Factor 2 (IF2) and its eukaryotic mitochondrial homologue mtIF2. IF2, the largest initiation factor is an essential GTP binding protein. In E. coli three natural forms of IF2 exist in the cell, IF2alpha, IF2beta1, and IF2beta2. Bacterial IF-2 is structurally and functionally related to eukaryotic mitochondrial mtIF-2.
Probab=20.41 E-value=3.1e+02 Score=19.03 Aligned_cols=27 Identities=19% Similarity=0.206 Sum_probs=18.6
Q ss_pred eeCcceEEEEEecCCCCC---CCCCCEEEEe
Q 032330 68 GDDTGAIYFTARNDQVDI---MTPGTTVILR 95 (143)
Q Consensus 68 gDeTG~I~ltlW~~~~~~---i~~Gd~v~I~ 95 (143)
|-..|.||- +||+.... ..||+.|+|.
T Consensus 36 G~~~gkVr~-l~d~~g~~v~~a~Ps~~V~I~ 65 (95)
T cd03702 36 GTTYGKVRA-MFDENGKRVKEAGPSTPVEIL 65 (95)
T ss_pred cccccEEEE-EECCCCCCCCEECCCCcEEEc
Confidence 444688886 77765444 4679998885
No 164
>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=20.35 E-value=1.8e+02 Score=17.90 Aligned_cols=27 Identities=15% Similarity=0.257 Sum_probs=20.7
Q ss_pred CCCCCCCEEEEeceEEceeCCeEEEEe
Q 032330 84 DIMTPGTTVILRNAKIDMFKGSMRLAV 110 (143)
Q Consensus 84 ~~i~~Gd~v~I~na~~~~~~g~~~L~i 110 (143)
+.++.||.+++.=-.++..++.+.|++
T Consensus 43 ~~~~~Gd~v~~~v~~~d~~~~~i~ls~ 69 (73)
T cd05691 43 ERFKVGDEVEAKITNVDRKNRKISLSI 69 (73)
T ss_pred HccCCCCEEEEEEEEEeCCCCEEEEEE
Confidence 447899999998777766667777765
No 165
>COG4880 Secreted protein containing C-terminal beta-propeller domain distantly related to WD-40 repeats [General function prediction only]
Probab=20.04 E-value=1.3e+02 Score=27.45 Aligned_cols=54 Identities=17% Similarity=0.119 Sum_probs=45.1
Q ss_pred EeeCcceEEEEEec-CCCCCCCCCCEEEEeceEEceeCCeEEEEeCCceeEEEcC
Q 032330 67 VGDDTGAIYFTARN-DQVDIMTPGTTVILRNAKIDMFKGSMRLAVDKWGRIEVTE 120 (143)
Q Consensus 67 VgDeTG~I~ltlW~-~~~~~i~~Gd~v~I~na~~~~~~g~~~L~ig~~g~I~~~~ 120 (143)
||-+.|-+.++|+| ......++=+.+.|.+++...|.++.-...+..-.|-.++
T Consensus 488 vG~~~g~vKiSLFdiSdl~~PkEv~~y~l~~~wspvf~dhHAFl~d~~~~ifFlP 542 (603)
T COG4880 488 VGAYQGGVKISLFDISDLAAPKEVSNYTLSNAWSPVFYDHHAFLYDPEAEIFFLP 542 (603)
T ss_pred eecccCCceEEEEeccCCCCchhhhheehhhhcchhhhccceeecCCcccEEEec
Confidence 46666999999999 4555578999999999999999998888888888877665
Done!