Query 008606
Match_columns 560
No_of_seqs 220 out of 896
Neff 7.1
Searched_HMMs 46136
Date Thu Mar 28 14:17:09 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/008606.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/008606hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 TIGR00617 rpa1 replication fac 100.0 3E-100 6E-105 847.7 55.6 442 99-556 164-608 (608)
2 PRK12366 replication factor A; 100.0 1.8E-63 3.9E-68 556.4 41.1 360 110-543 274-637 (637)
3 PRK08402 replication factor A; 100.0 1.1E-43 2.5E-48 368.9 30.4 280 234-558 61-353 (355)
4 cd04476 RPA1_DBD_C RPA1_DBD_C: 100.0 3.8E-36 8.3E-41 284.2 20.4 165 384-556 1-166 (166)
5 PRK07218 replication factor A; 100.0 6.7E-34 1.4E-38 301.4 39.2 362 112-554 55-421 (423)
6 PF08646 Rep_fac-A_C: Replicat 100.0 4.9E-36 1.1E-40 277.6 15.5 145 400-550 1-146 (146)
7 PRK06386 replication factor A; 100.0 1.5E-30 3.2E-35 269.5 40.0 351 115-554 2-353 (358)
8 PRK12366 replication factor A; 100.0 9.5E-31 2E-35 293.2 32.1 282 112-484 60-345 (637)
9 PRK07211 replication factor A; 100.0 1.6E-30 3.4E-35 278.0 30.3 274 114-479 52-328 (485)
10 PRK07211 replication factor A; 100.0 8.7E-30 1.9E-34 272.3 23.6 206 113-344 159-367 (485)
11 PRK15491 replication factor A; 100.0 9.7E-29 2.1E-33 260.3 29.6 276 113-480 55-336 (374)
12 cd04474 RPA1_DBD_A RPA1_DBD_A: 100.0 4.7E-28 1E-32 211.3 12.0 104 117-220 1-104 (104)
13 PRK14699 replication factor A; 99.9 1.3E-26 2.9E-31 250.5 21.6 207 113-341 274-483 (484)
14 PRK15491 replication factor A; 99.9 5.8E-26 1.2E-30 239.3 23.1 207 113-341 164-373 (374)
15 PRK14699 replication factor A; 99.9 2.5E-22 5.5E-27 217.3 30.4 279 114-481 165-447 (484)
16 cd04475 RPA1_DBD_B RPA1_DBD_B: 99.9 2E-21 4.3E-26 168.6 12.6 100 249-356 1-101 (101)
17 cd04481 RPA1_DBD_B_like RPA1_D 99.8 8.2E-20 1.8E-24 160.0 11.9 101 251-354 1-104 (106)
18 cd04480 RPA1_DBD_A_like RPA1_D 99.8 7.1E-19 1.5E-23 148.2 9.7 86 129-218 1-86 (86)
19 PF02721 DUF223: Domain of unk 99.7 2.2E-16 4.8E-21 135.5 9.1 87 154-243 1-87 (95)
20 PRK07217 replication factor A; 99.6 9.4E-14 2E-18 140.6 23.4 210 234-520 71-282 (311)
21 PRK08402 replication factor A; 99.6 1.1E-13 2.3E-18 144.9 19.8 177 114-300 61-270 (355)
22 KOG0851 Single-stranded DNA-bi 99.3 6.1E-11 1.3E-15 118.5 14.9 214 113-359 2-218 (246)
23 cd04497 hPOT1_OB1_like hPOT1_O 99.1 6.9E-10 1.5E-14 101.8 10.7 99 233-343 1-105 (138)
24 PRK06386 replication factor A; 99.1 9.9E-09 2.1E-13 107.3 19.7 163 114-299 106-287 (358)
25 COG1599 RFA1 Single-stranded D 99.1 2.5E-09 5.4E-14 115.2 15.4 245 111-413 158-404 (407)
26 PRK07218 replication factor A; 99.0 1E-08 2.3E-13 109.7 19.0 170 114-300 161-349 (423)
27 cd04491 SoSSB_OBF SoSSB_OBF: A 98.8 3.7E-08 8E-13 82.0 11.2 80 251-341 1-81 (82)
28 PRK06461 single-stranded DNA-b 98.8 2.9E-08 6.3E-13 90.0 11.2 93 235-341 4-97 (129)
29 cd04491 SoSSB_OBF SoSSB_OBF: A 98.8 6.8E-08 1.5E-12 80.4 10.1 81 129-220 1-81 (82)
30 PRK06461 single-stranded DNA-b 98.7 1.3E-07 2.9E-12 85.7 11.3 98 114-223 3-100 (129)
31 PRK07217 replication factor A; 98.2 5.3E-05 1.1E-09 77.5 15.9 151 112-299 69-241 (311)
32 TIGR00617 rpa1 replication fac 98.2 8.3E-05 1.8E-09 84.1 18.6 177 234-481 179-364 (608)
33 COG1599 RFA1 Single-stranded D 98.1 8.8E-05 1.9E-09 80.2 17.4 188 111-329 45-234 (407)
34 cd04474 RPA1_DBD_A RPA1_DBD_A: 97.9 6.5E-05 1.4E-09 65.5 9.6 98 237-343 1-98 (104)
35 PF01336 tRNA_anti-codon: OB-f 97.7 0.00012 2.6E-09 59.0 7.5 61 128-198 1-61 (75)
36 PF02765 POT1: Telomeric singl 97.4 0.0014 3E-08 60.8 11.1 86 235-329 1-93 (146)
37 cd04475 RPA1_DBD_B RPA1_DBD_B: 97.3 0.0017 3.7E-08 56.1 9.4 84 129-222 3-88 (101)
38 cd03524 RPA2_OBF_family RPA2_O 96.7 0.0082 1.8E-07 47.1 7.9 61 129-196 1-61 (75)
39 KOG3416 Predicted nucleic acid 96.6 0.01 2.2E-07 52.6 7.8 83 237-336 6-89 (134)
40 KOG3416 Predicted nucleic acid 96.5 0.0064 1.4E-07 53.8 6.1 70 115-193 4-74 (134)
41 cd04497 hPOT1_OB1_like hPOT1_O 96.0 0.029 6.3E-07 51.4 7.9 83 114-200 2-88 (138)
42 cd03524 RPA2_OBF_family RPA2_O 95.7 0.077 1.7E-06 41.4 8.4 65 251-329 1-65 (75)
43 cd04483 hOBFC1_like hOBFC1_lik 95.4 0.063 1.4E-06 45.8 7.4 68 251-332 1-85 (92)
44 PF01336 tRNA_anti-codon: OB-f 95.3 0.068 1.5E-06 42.6 7.0 63 250-329 1-63 (75)
45 cd04481 RPA1_DBD_B_like RPA1_D 95.1 0.26 5.6E-06 42.9 10.5 69 130-198 2-75 (106)
46 PF15489 CTC1: CST, telomere m 95.0 8.6 0.00019 46.2 25.0 319 119-492 698-1050(1144)
47 cd04490 PolII_SU_OBF PolII_SU_ 94.9 0.16 3.5E-06 42.0 8.0 58 250-324 2-61 (79)
48 cd04488 RecG_wedge_OBF RecG_we 94.4 0.29 6.3E-06 38.7 8.3 60 129-196 1-60 (75)
49 cd04485 DnaE_OBF DnaE_OBF: A s 94.3 0.28 6E-06 39.6 8.1 60 130-195 2-61 (84)
50 cd04478 RPA2_DBD_D RPA2_DBD_D: 92.6 0.63 1.4E-05 39.3 7.8 69 250-333 2-71 (95)
51 cd04485 DnaE_OBF DnaE_OBF: A s 92.3 1 2.2E-05 36.2 8.5 65 252-329 2-66 (84)
52 cd04489 ExoVII_LU_OBF ExoVII_L 91.6 0.79 1.7E-05 37.0 7.0 55 129-192 3-57 (78)
53 PTZ00401 aspartyl-tRNA synthet 91.4 1.9 4E-05 48.6 11.9 99 113-221 63-169 (550)
54 cd04490 PolII_SU_OBF PolII_SU_ 91.4 1.1 2.3E-05 37.0 7.6 55 129-192 3-59 (79)
55 PRK06751 single-stranded DNA-b 91.2 1.4 2.9E-05 42.1 9.1 64 125-191 2-75 (173)
56 cd04492 YhaM_OBF_like YhaM_OBF 90.5 1.3 2.7E-05 35.9 7.3 43 151-196 19-61 (83)
57 PF02765 POT1: Telomeric singl 90.1 1.6 3.4E-05 40.4 8.3 85 115-200 1-93 (146)
58 PRK02801 primosomal replicatio 90.1 1.6 3.5E-05 37.8 7.8 68 125-195 2-80 (101)
59 PF11325 DUF3127: Domain of un 89.5 2.4 5.1E-05 35.5 8.0 71 252-331 2-75 (84)
60 PF14951 DUF4503: Domain of un 89.3 0.94 2E-05 47.4 6.7 84 399-488 255-346 (389)
61 PF15072 DUF4539: Domain of un 89.0 1.7 3.6E-05 36.6 6.8 61 153-220 21-81 (86)
62 PRK07275 single-stranded DNA-b 88.8 1.6 3.5E-05 41.2 7.5 64 125-191 2-75 (162)
63 PRK07459 single-stranded DNA-b 88.7 1.7 3.7E-05 38.9 7.2 64 125-191 3-72 (121)
64 cd04322 LysRS_N LysRS_N: N-ter 88.5 8.3 0.00018 33.4 11.3 77 128-221 2-83 (108)
65 PRK07772 single-stranded DNA-b 88.0 3 6.4E-05 40.3 8.8 64 125-191 4-81 (186)
66 KOG0851 Single-stranded DNA-bi 87.9 0.77 1.7E-05 45.6 5.0 67 415-491 160-226 (246)
67 PRK05733 single-stranded DNA-b 87.8 2.1 4.5E-05 40.8 7.5 65 124-191 4-81 (172)
68 cd04492 YhaM_OBF_like YhaM_OBF 87.7 3.4 7.4E-05 33.3 8.0 62 253-328 3-64 (83)
69 cd04489 ExoVII_LU_OBF ExoVII_L 87.7 2.3 4.9E-05 34.3 6.8 40 251-300 3-42 (78)
70 PLN02850 aspartate-tRNA ligase 87.7 5 0.00011 45.1 11.6 98 113-221 67-172 (530)
71 PRK05813 single-stranded DNA-b 87.6 31 0.00068 34.2 17.4 164 125-327 8-183 (219)
72 PRK07373 DNA polymerase III su 87.3 2 4.4E-05 47.2 8.1 70 116-191 269-341 (449)
73 COG5235 RFA2 Single-stranded D 87.2 2.4 5.2E-05 41.1 7.4 74 249-339 68-143 (258)
74 PRK08763 single-stranded DNA-b 86.6 3 6.6E-05 39.4 7.8 66 124-192 4-81 (164)
75 cd04320 AspRS_cyto_N AspRS_cyt 86.4 16 0.00035 31.2 11.8 83 128-221 2-92 (102)
76 PRK13480 3'-5' exoribonuclease 86.3 2.6 5.7E-05 44.0 8.0 70 117-193 4-73 (314)
77 PRK07274 single-stranded DNA-b 86.1 2.7 5.8E-05 38.2 7.0 64 125-191 2-75 (131)
78 PRK09010 single-stranded DNA-b 86.0 6.5 0.00014 37.7 9.9 64 125-191 6-82 (177)
79 PRK13480 3'-5' exoribonuclease 86.0 4.6 9.9E-05 42.3 9.6 77 242-332 6-83 (314)
80 cd04496 SSB_OBF SSB_OBF: A sub 86.0 3 6.6E-05 35.0 7.0 62 129-193 2-74 (100)
81 PRK08486 single-stranded DNA-b 85.9 2.8 6.1E-05 40.3 7.4 64 125-191 2-77 (182)
82 PRK06293 single-stranded DNA-b 85.4 3 6.4E-05 39.3 7.1 65 125-192 1-72 (161)
83 cd04478 RPA2_DBD_D RPA2_DBD_D: 85.3 2.3 5E-05 35.8 5.9 53 129-191 3-58 (95)
84 cd04495 BRCA2DBD_OB3 BRCA2DBD_ 85.1 7.1 0.00015 33.6 8.5 81 251-344 1-84 (100)
85 PRK13732 single-stranded DNA-b 84.5 3.9 8.5E-05 39.1 7.6 65 124-191 5-82 (175)
86 PRK06752 single-stranded DNA-b 84.2 3.5 7.5E-05 36.3 6.7 65 125-192 2-76 (112)
87 PRK07373 DNA polymerase III su 84.1 3.3 7.2E-05 45.5 7.8 76 236-324 269-344 (449)
88 PF09104 BRCA-2_OB3: BRCA2, ol 84.0 9.6 0.00021 35.1 9.5 106 237-356 5-120 (143)
89 cd04484 polC_OBF polC_OBF: A s 83.4 7 0.00015 32.4 7.8 59 128-192 2-62 (82)
90 PF13742 tRNA_anti_2: OB-fold 83.0 1.2 2.6E-05 38.4 3.1 64 125-197 21-86 (99)
91 PRK06863 single-stranded DNA-b 82.9 4.7 0.0001 38.3 7.3 64 125-191 4-80 (168)
92 PRK08182 single-stranded DNA-b 82.8 4.4 9.6E-05 37.6 7.0 66 125-192 2-83 (148)
93 cd04100 Asp_Lys_Asn_RS_N Asp_L 82.0 16 0.00034 30.1 9.5 75 128-214 2-79 (85)
94 cd04323 AsnRS_cyto_like_N AsnR 81.7 18 0.00039 29.8 9.7 75 128-214 2-78 (84)
95 PRK05159 aspC aspartyl-tRNA sy 81.4 12 0.00025 41.1 10.9 94 114-222 3-101 (437)
96 PRK05673 dnaE DNA polymerase I 81.3 4.1 9E-05 49.8 7.9 81 235-328 965-1045(1135)
97 PF00436 SSB: Single-strand bi 81.1 2.1 4.5E-05 36.5 4.0 64 126-192 2-77 (104)
98 TIGR00621 ssb single stranded 80.8 6.6 0.00014 37.1 7.6 65 125-192 4-80 (164)
99 cd04480 RPA1_DBD_A_like RPA1_D 80.3 12 0.00026 30.9 8.3 52 272-329 17-68 (86)
100 KOG3056 Protein required for S 79.7 12 0.00025 41.7 9.8 102 112-221 165-275 (578)
101 PLN02502 lysyl-tRNA synthetase 79.7 11 0.00025 42.5 10.2 79 126-221 109-194 (553)
102 PRK06958 single-stranded DNA-b 77.8 8.7 0.00019 37.0 7.4 64 125-191 4-80 (182)
103 PRK06642 single-stranded DNA-b 77.7 8.3 0.00018 36.0 7.1 64 125-191 5-82 (152)
104 cd04316 ND_PkAspRS_like_N ND_P 77.3 47 0.001 28.7 11.8 81 126-221 13-97 (108)
105 cd04498 hPOT1_OB2 hPOT1_OB2: A 77.0 9.4 0.0002 34.4 6.9 36 286-328 60-95 (123)
106 PTZ00417 lysine-tRNA ligase; P 76.7 16 0.00036 41.5 10.3 78 127-221 134-219 (585)
107 PF02721 DUF223: Domain of unk 76.5 9.7 0.00021 32.3 6.7 47 277-329 1-47 (95)
108 cd04318 EcAsnRS_like_N EcAsnRS 75.1 29 0.00063 28.3 9.0 73 128-214 2-76 (82)
109 KOG0556 Aspartyl-tRNA syntheta 75.1 33 0.00072 36.9 11.2 100 112-221 67-175 (533)
110 PRK00484 lysS lysyl-tRNA synth 74.7 29 0.00064 38.7 11.6 78 126-221 55-137 (491)
111 KOG4757 Predicted telomere bin 73.7 9.7 0.00021 40.9 7.0 75 245-329 18-94 (522)
112 PTZ00385 lysyl-tRNA synthetase 73.6 38 0.00082 39.1 12.2 77 127-220 109-191 (659)
113 TIGR00499 lysS_bact lysyl-tRNA 73.5 25 0.00054 39.3 10.7 80 125-221 53-137 (496)
114 cd04317 EcAspRS_like_N EcAspRS 73.3 46 0.001 29.9 10.7 86 126-221 15-104 (135)
115 COG0629 Ssb Single-stranded DN 72.9 11 0.00025 35.5 6.8 67 124-193 2-81 (167)
116 PRK12445 lysyl-tRNA synthetase 72.8 26 0.00057 39.1 10.7 79 126-221 66-149 (505)
117 TIGR00643 recG ATP-dependent D 72.1 12 0.00025 43.1 8.0 71 113-191 21-91 (630)
118 PRK02801 primosomal replicatio 70.7 23 0.0005 30.6 7.6 66 249-322 4-78 (101)
119 PF13240 zinc_ribbon_2: zinc-r 70.2 2.1 4.5E-05 26.8 0.8 19 428-448 4-22 (23)
120 PRK07374 dnaE DNA polymerase I 70.1 13 0.00029 45.6 8.1 71 116-191 989-1061(1170)
121 PRK05673 dnaE DNA polymerase I 70.1 13 0.00028 45.6 8.0 72 115-191 965-1038(1135)
122 COG1997 RPL43A Ribosomal prote 69.8 3.2 7E-05 34.7 2.0 28 418-451 36-65 (89)
123 cd04482 RPA2_OBF_like RPA2_OBF 68.9 13 0.00027 31.5 5.5 40 152-192 18-59 (91)
124 PRK07374 dnaE DNA polymerase I 68.6 14 0.00031 45.4 7.9 77 235-324 988-1064(1170)
125 cd04483 hOBFC1_like hOBFC1_lik 68.1 13 0.00029 31.5 5.5 52 130-191 2-73 (92)
126 PRK07135 dnaE DNA polymerase I 67.8 17 0.00037 43.7 8.2 74 116-198 889-962 (973)
127 PRK02983 lysS lysyl-tRNA synth 67.3 32 0.00069 42.2 10.5 79 126-221 652-735 (1094)
128 PRK05813 single-stranded DNA-b 64.8 25 0.00055 34.8 7.5 64 124-191 108-175 (219)
129 PF07754 DUF1610: Domain of un 64.4 5.4 0.00012 25.3 1.7 20 428-447 3-24 (24)
130 TIGR00458 aspS_arch aspartyl-t 64.1 64 0.0014 35.3 11.2 89 118-221 3-97 (428)
131 PF15489 CTC1: CST, telomere m 63.8 60 0.0013 39.4 11.4 69 125-198 165-233 (1144)
132 KOG3056 Protein required for S 63.5 27 0.00059 38.9 8.0 66 251-327 189-255 (578)
133 PRK07279 dnaE DNA polymerase I 62.9 20 0.00043 43.5 7.5 73 114-191 874-946 (1034)
134 PRK10917 ATP-dependent DNA hel 62.8 19 0.00042 41.8 7.3 69 114-191 49-118 (681)
135 cd04319 PhAsnRS_like_N PhAsnRS 62.2 1E+02 0.0022 26.4 10.5 79 128-221 2-83 (103)
136 cd04487 RecJ_OBF2_like RecJ_OB 61.7 15 0.00032 29.8 4.4 40 152-192 16-55 (73)
137 PRK06826 dnaE DNA polymerase I 61.6 23 0.00051 43.5 7.9 77 235-324 970-1055(1151)
138 PRK06341 single-stranded DNA-b 61.3 34 0.00074 32.4 7.4 64 125-191 5-82 (166)
139 PRK05853 hypothetical protein; 59.9 23 0.0005 33.4 6.0 33 159-191 39-71 (161)
140 cd04484 polC_OBF polC_OBF: A s 59.6 89 0.0019 25.7 8.8 55 455-531 20-74 (82)
141 PRK06751 single-stranded DNA-b 59.2 72 0.0016 30.5 9.2 71 249-327 4-83 (173)
142 TIGR00621 ssb single stranded 58.8 71 0.0015 30.1 9.2 72 249-328 6-88 (164)
143 cd04496 SSB_OBF SSB_OBF: A sub 57.9 50 0.0011 27.4 7.3 69 251-327 2-80 (100)
144 TIGR00459 aspS_bact aspartyl-t 57.6 1.1E+02 0.0024 34.9 11.9 95 117-221 5-104 (583)
145 PRK06920 dnaE DNA polymerase I 57.1 31 0.00068 42.2 7.9 77 234-324 931-1007(1107)
146 COG0017 AsnS Aspartyl/asparagi 57.0 1E+02 0.0022 33.8 10.9 100 114-231 3-107 (435)
147 PRK06826 dnaE DNA polymerase I 56.1 34 0.00073 42.2 8.0 59 127-191 993-1052(1151)
148 PRK10220 hypothetical protein; 56.0 8.7 0.00019 33.6 2.2 28 417-450 3-31 (111)
149 PRK07459 single-stranded DNA-b 55.8 1E+02 0.0023 27.4 9.3 69 249-327 5-80 (121)
150 PRK09010 single-stranded DNA-b 54.4 1.1E+02 0.0024 29.3 9.6 73 249-329 8-92 (177)
151 PF07191 zinc-ribbons_6: zinc- 53.9 8 0.00017 31.2 1.5 24 419-448 3-26 (70)
152 PRK06920 dnaE DNA polymerase I 53.7 36 0.00078 41.7 7.7 73 115-194 932-1006(1107)
153 PRK08182 single-stranded DNA-b 53.7 92 0.002 28.9 8.8 72 249-328 4-91 (148)
154 PRK05733 single-stranded DNA-b 53.3 72 0.0016 30.4 8.2 72 248-327 6-89 (172)
155 PRK12820 bifunctional aspartyl 53.2 1.6E+02 0.0034 34.5 12.3 97 115-221 6-110 (706)
156 PF13248 zf-ribbon_3: zinc-rib 52.2 7.2 0.00016 25.0 0.8 23 418-448 3-25 (26)
157 PF01780 Ribosomal_L37ae: Ribo 51.3 5.8 0.00013 33.6 0.4 26 419-450 37-64 (90)
158 PRK05672 dnaE2 error-prone DNA 50.7 41 0.00089 41.1 7.5 75 235-324 941-1015(1046)
159 PRK08486 single-stranded DNA-b 50.5 1.2E+02 0.0025 29.3 9.2 35 287-327 50-85 (182)
160 TIGR00457 asnS asparaginyl-tRN 50.2 1.4E+02 0.003 33.0 11.0 82 126-221 17-102 (453)
161 PRK07275 single-stranded DNA-b 49.4 1.1E+02 0.0024 28.9 8.7 35 287-327 48-83 (162)
162 KOG1885 Lysyl-tRNA synthetase 49.2 74 0.0016 35.0 8.3 57 127-192 106-168 (560)
163 PRK06266 transcription initiat 49.1 7.4 0.00016 37.3 0.8 28 416-449 116-146 (178)
164 TIGR00373 conserved hypothetic 49.0 6.7 0.00015 36.8 0.5 28 416-449 108-138 (158)
165 PRK06863 single-stranded DNA-b 48.2 1.5E+02 0.0032 28.3 9.3 73 248-328 5-89 (168)
166 cd03574 NTR_complement_C345C N 48.0 1.5E+02 0.0032 27.3 9.3 88 126-224 23-120 (147)
167 COG1200 RecG RecG-like helicas 47.8 67 0.0015 36.9 8.1 76 112-196 48-123 (677)
168 PRK08763 single-stranded DNA-b 47.6 1.1E+02 0.0025 28.8 8.5 71 249-327 7-88 (164)
169 PRK06958 single-stranded DNA-b 47.6 1.6E+02 0.0035 28.4 9.6 72 248-327 5-88 (182)
170 PRK03932 asnC asparaginyl-tRNA 47.4 1.7E+02 0.0038 32.2 11.2 81 126-221 17-100 (450)
171 TIGR00686 phnA alkylphosphonat 46.3 14 0.0003 32.4 1.9 29 417-451 2-31 (109)
172 PRK00432 30S ribosomal protein 45.8 14 0.00029 27.8 1.6 26 417-448 20-46 (50)
173 cd04476 RPA1_DBD_C RPA1_DBD_C: 45.8 94 0.002 29.0 7.8 27 151-178 68-94 (166)
174 COG0587 DnaE DNA polymerase II 45.2 70 0.0015 39.3 8.2 71 116-191 967-1038(1139)
175 PRK00448 polC DNA polymerase I 45.1 59 0.0013 41.1 7.8 74 114-192 225-300 (1437)
176 PF15072 DUF4539: Domain of un 45.0 68 0.0015 27.0 5.9 56 252-324 7-62 (86)
177 PLN02903 aminoacyl-tRNA ligase 45.0 2.8E+02 0.0061 32.2 12.6 98 114-221 59-163 (652)
178 PF14446 Prok-RING_1: Prokaryo 44.5 16 0.00034 28.0 1.8 26 418-449 6-31 (54)
179 PRK06752 single-stranded DNA-b 43.5 1.6E+02 0.0035 25.7 8.4 71 249-327 4-83 (112)
180 PRK07274 single-stranded DNA-b 43.5 1.1E+02 0.0023 27.7 7.4 70 249-326 4-82 (131)
181 COG1096 Predicted RNA-binding 43.5 40 0.00086 32.5 4.7 41 402-448 124-174 (188)
182 PRK07772 single-stranded DNA-b 43.4 1.4E+02 0.0031 28.8 8.6 74 247-328 4-90 (186)
183 cd04498 hPOT1_OB2 hPOT1_OB2: A 43.4 55 0.0012 29.5 5.4 49 163-212 60-109 (123)
184 PF10571 UPF0547: Uncharacteri 43.0 14 0.00031 23.8 1.2 23 419-449 2-24 (26)
185 PRK00398 rpoP DNA-directed RNA 42.8 21 0.00045 26.0 2.2 25 419-449 5-31 (46)
186 PRK05672 dnaE2 error-prone DNA 42.0 67 0.0015 39.3 7.5 61 127-195 955-1015(1046)
187 PRK13732 single-stranded DNA-b 41.7 1.6E+02 0.0034 28.2 8.6 72 248-327 7-90 (175)
188 TIGR00237 xseA exodeoxyribonuc 41.7 60 0.0013 35.6 6.5 54 152-213 36-90 (432)
189 PLN02603 asparaginyl-tRNA synt 41.1 3.5E+02 0.0076 30.8 12.5 93 114-221 88-193 (565)
190 TIGR00280 L37a ribosomal prote 41.0 16 0.00034 31.1 1.4 27 419-451 37-65 (91)
191 cd04321 ScAspRS_mt_like_N ScAs 40.9 2E+02 0.0044 23.6 10.8 76 128-213 2-79 (86)
192 COG1571 Predicted DNA-binding 40.8 14 0.00031 39.9 1.5 29 417-451 350-379 (421)
193 PRK03976 rpl37ae 50S ribosomal 39.5 17 0.00036 30.9 1.4 27 419-451 38-66 (90)
194 PRK00476 aspS aspartyl-tRNA sy 39.2 2.5E+02 0.0053 32.2 11.1 94 118-221 8-106 (588)
195 PRK00286 xseA exodeoxyribonucl 39.1 70 0.0015 35.0 6.6 40 151-191 41-80 (438)
196 PRK14810 formamidopyrimidine-D 38.1 19 0.00041 36.9 1.8 24 418-447 245-272 (272)
197 COG1998 RPS31 Ribosomal protei 38.0 18 0.00039 27.1 1.1 26 417-448 19-46 (51)
198 PF02760 HIN: HIN-200/IF120x d 37.8 3.6E+02 0.0078 25.5 17.2 143 130-298 5-153 (170)
199 PF08274 PhnA_Zn_Ribbon: PhnA 37.4 13 0.00027 25.0 0.3 26 417-448 2-28 (30)
200 PRK13945 formamidopyrimidine-D 37.4 21 0.00046 36.7 2.1 24 418-447 255-282 (282)
201 PRK06293 single-stranded DNA-b 36.8 2.4E+02 0.0052 26.6 8.8 71 249-327 3-79 (161)
202 PF00436 SSB: Single-strand bi 35.4 91 0.002 26.1 5.5 70 250-327 4-84 (104)
203 PRK11827 hypothetical protein; 35.3 28 0.0006 27.3 1.9 26 418-449 9-36 (60)
204 smart00661 RPOL9 RNA polymeras 35.2 50 0.0011 24.3 3.3 22 428-449 5-30 (52)
205 PTZ00255 60S ribosomal protein 35.2 22 0.00048 30.2 1.4 30 419-454 38-69 (90)
206 COG5235 RFA2 Single-stranded D 34.1 1.3E+02 0.0027 29.6 6.5 73 459-555 86-158 (258)
207 PRK10445 endonuclease VIII; Pr 34.0 22 0.00048 36.2 1.6 24 418-447 236-263 (263)
208 PF14205 Cys_rich_KTR: Cystein 33.9 38 0.00083 25.9 2.4 26 418-449 5-38 (55)
209 PF09538 FYDLN_acid: Protein o 33.8 24 0.00052 31.0 1.5 27 418-450 10-37 (108)
210 COG1379 PHP family phosphoeste 33.8 10 0.00023 39.4 -0.8 30 414-449 243-275 (403)
211 PF03119 DNA_ligase_ZBD: NAD-d 33.8 25 0.00055 23.0 1.3 19 420-444 2-22 (28)
212 PRK01103 formamidopyrimidine/5 33.7 22 0.00048 36.4 1.5 24 418-447 246-273 (274)
213 COG1675 TFA1 Transcription ini 33.1 14 0.0003 35.3 -0.1 27 417-449 113-142 (176)
214 cd04494 BRCA2DBD_OB2 BRCA2DBD_ 32.9 1.5E+02 0.0032 30.1 7.1 58 162-222 179-236 (251)
215 PF14353 CpXC: CpXC protein 32.7 61 0.0013 28.9 4.1 33 439-476 38-70 (128)
216 PF09862 DUF2089: Protein of u 32.6 28 0.00061 30.8 1.8 22 420-449 1-22 (113)
217 COG1594 RPB9 DNA-directed RNA 32.6 76 0.0017 28.1 4.5 49 419-473 4-59 (113)
218 KOG1924 RhoA GTPase effector D 32.6 1.2E+02 0.0026 35.4 7.0 11 170-180 659-669 (1102)
219 PRK07279 dnaE DNA polymerase I 32.5 1.2E+02 0.0025 37.2 7.4 73 236-324 876-949 (1034)
220 smart00531 TFIIE Transcription 32.4 19 0.00041 33.3 0.7 27 417-449 99-133 (147)
221 COG4085 Predicted RNA-binding 32.4 50 0.0011 32.0 3.5 26 457-482 71-96 (204)
222 COG2824 PhnA Uncharacterized Z 32.3 50 0.0011 28.8 3.1 28 417-450 3-31 (112)
223 PRK06556 vitamin B12-dependent 32.0 30 0.00064 41.6 2.4 29 415-449 922-950 (953)
224 KOG2593 Transcription initiati 32.0 24 0.00053 38.1 1.5 29 415-449 126-163 (436)
225 TIGR02098 MJ0042_CXXC MJ0042 f 31.9 32 0.00069 23.8 1.6 26 418-449 3-35 (38)
226 cd04488 RecG_wedge_OBF RecG_we 31.8 58 0.0013 25.1 3.4 20 456-475 18-37 (75)
227 PRK14811 formamidopyrimidine-D 31.7 24 0.00052 36.1 1.4 25 418-448 236-264 (269)
228 PF13717 zinc_ribbon_4: zinc-r 31.3 33 0.00071 23.8 1.6 26 418-449 3-35 (36)
229 TIGR02300 FYDLN_acid conserved 31.2 29 0.00062 31.3 1.6 26 418-449 10-36 (129)
230 PF12773 DZR: Double zinc ribb 31.1 22 0.00047 26.2 0.7 22 428-449 17-39 (50)
231 PF13742 tRNA_anti_2: OB-fold 31.0 3.2E+02 0.0069 23.2 8.1 58 459-540 42-99 (99)
232 PLN02221 asparaginyl-tRNA synt 30.9 5.2E+02 0.011 29.5 11.8 84 126-221 51-137 (572)
233 TIGR01384 TFS_arch transcripti 30.8 54 0.0012 28.1 3.3 25 419-449 2-26 (104)
234 COG1190 LysU Lysyl-tRNA synthe 30.4 1.4E+02 0.0031 33.1 7.0 85 120-221 56-145 (502)
235 PF11781 RRN7: RNA polymerase 30.2 39 0.00085 23.5 1.8 24 419-448 10-34 (36)
236 PF07282 OrfB_Zn_ribbon: Putat 30.0 38 0.00082 26.7 2.0 29 415-449 26-56 (69)
237 PF11325 DUF3127: Domain of un 29.8 2.4E+02 0.0051 23.7 6.7 59 130-190 2-62 (84)
238 COG1107 Archaea-specific RecJ- 29.5 54 0.0012 36.9 3.6 69 113-191 200-269 (715)
239 COG2888 Predicted Zn-ribbon RN 29.3 26 0.00057 27.3 0.9 8 439-446 50-57 (61)
240 PF08646 Rep_fac-A_C: Replicat 28.7 67 0.0015 29.3 3.7 28 151-179 54-81 (146)
241 PF03107 C1_2: C1 domain; Int 27.9 38 0.00083 22.3 1.4 18 428-446 5-22 (30)
242 PRK00036 primosomal replicatio 27.7 3E+02 0.0066 24.2 7.3 70 126-199 2-82 (107)
243 PF08696 Dna2: DNA replication 27.5 2.1E+02 0.0045 28.1 7.1 55 278-345 2-58 (209)
244 PRK06642 single-stranded DNA-b 27.3 4.7E+02 0.01 24.2 9.1 72 248-327 6-90 (152)
245 KOG3108 Single-stranded DNA-bi 26.9 2.5E+02 0.0053 28.8 7.6 67 248-335 69-141 (265)
246 PF14803 Nudix_N_2: Nudix N-te 26.9 47 0.001 22.9 1.7 20 428-447 5-30 (34)
247 PF08772 NOB1_Zn_bind: Nin one 26.6 57 0.0012 26.6 2.4 37 428-471 14-50 (73)
248 COG1570 XseA Exonuclease VII, 26.3 1.4E+02 0.0031 32.7 6.1 91 114-214 4-97 (440)
249 PRK00420 hypothetical protein; 25.7 50 0.0011 29.2 2.1 28 416-449 22-50 (112)
250 PF13842 Tnp_zf-ribbon_2: DDE_ 25.6 42 0.00092 22.7 1.3 21 428-448 5-25 (32)
251 PF06827 zf-FPG_IleRS: Zinc fi 25.6 33 0.00071 22.5 0.7 24 418-447 2-29 (30)
252 PF01599 Ribosomal_S27: Riboso 25.5 70 0.0015 23.8 2.5 26 418-447 19-46 (47)
253 PF03456 uDENN: uDENN domain; 25.2 94 0.002 24.1 3.4 21 150-170 42-62 (65)
254 PF10451 Stn1: Telomere regula 25.1 2.1E+02 0.0046 29.1 6.8 66 248-323 67-133 (256)
255 PRK06341 single-stranded DNA-b 25.0 6E+02 0.013 24.1 9.7 73 248-328 6-91 (166)
256 TIGR00577 fpg formamidopyrimid 24.9 38 0.00081 34.7 1.4 23 418-446 246-272 (272)
257 cd01759 PLAT_PL PLAT/LH2 domai 24.6 85 0.0018 27.8 3.4 26 454-479 1-29 (113)
258 TIGR00375 conserved hypothetic 23.9 42 0.00092 36.0 1.6 40 403-449 225-268 (374)
259 COG3877 Uncharacterized protei 23.3 49 0.0011 28.8 1.5 24 418-449 7-30 (122)
260 KOG0402 60S ribosomal protein 23.3 46 0.001 27.7 1.3 27 428-454 41-69 (92)
261 COG2835 Uncharacterized conser 23.2 54 0.0012 25.7 1.6 27 417-449 8-36 (60)
262 PF09297 zf-NADH-PPase: NADH p 23.1 57 0.0012 21.8 1.6 21 428-448 8-30 (32)
263 PF07191 zinc-ribbons_6: zinc- 22.9 56 0.0012 26.4 1.7 33 418-456 31-67 (70)
264 PF03089 RAG2: Recombination a 21.9 99 0.0021 32.0 3.6 46 428-478 66-111 (337)
265 PF10122 Mu-like_Com: Mu-like 21.6 43 0.00094 25.3 0.8 24 419-448 6-33 (51)
266 PF13453 zf-TFIIB: Transcripti 21.0 59 0.0013 23.0 1.4 21 428-448 4-28 (41)
267 smart00659 RPOLCX RNA polymera 20.8 81 0.0018 23.0 2.1 22 428-449 7-29 (44)
268 COG1996 RPC10 DNA-directed RNA 20.8 54 0.0012 24.6 1.1 21 428-448 11-33 (49)
269 cd03582 NTR_complement_C5 NTR/ 20.0 7E+02 0.015 23.1 9.1 85 126-223 31-124 (150)
No 1
>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=100.00 E-value=2.7e-100 Score=847.70 Aligned_cols=442 Identities=46% Similarity=0.818 Sum_probs=406.4
Q ss_pred CCCCCCCccCCCCCCcceeccccCCCCCceEEEEEEEEecccceeccCCCCCcEEEEEEEeCCCCeEEEEEcchhHHHHH
Q 008606 99 NFRNHGPILKNEAPARIIPIAALNPYQGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAVVDRFY 178 (560)
Q Consensus 99 ~~~~~~~~~~~~~~~~~~pI~~L~p~~~~w~Ik~RV~~k~~ir~~~n~~g~gkvf~~~L~D~~g~~I~at~~~~~~~kf~ 178 (560)
.+.+.+|..+..++.+++||++|+||+++|+|+|||++||++|+|++++|+|++|+|+|+| +|++|+|+||++.+++|+
T Consensus 164 ~~~~~~~~~~~~~~~~~~pI~~L~py~~~wtIkaRV~~Ks~ir~~~~~~gegkvfsv~L~D-egg~Irat~f~~~~dkf~ 242 (608)
T TIGR00617 164 ERGNAPPAPNSGSTRRVMPIASLSPYQNKWTIKARVTNKSEIRTWSNARGEGKLFNVELLD-ESGEIRATAFNEQADKFY 242 (608)
T ss_pred ccCCCCCCccccCCcceEEHHHCCCCCCceEEEEEEEeccccceecCCCCCceeeEEEEec-CCCeEEEEECchHHHHHh
Confidence 4445555333344557999999999999999999999999999999999999999999999 999999999999999999
Q ss_pred hhcccCcEEEEeeeEEecCCCccccCCCeeEEEEcccceEEeccCCCCCCCcccccccCccchhcccCCceeEEEEEEEE
Q 008606 179 EIIEVGRVYLISKGSLKPAQKNFNHLKNEWEIFLEATSTVDLCTEEDDSIPKQQFSFRHISEIESAENNSIVDVIGIVIS 258 (560)
Q Consensus 179 ~~l~eG~vY~Is~~~V~~a~~~y~~~~~~yeI~f~~~T~I~~~~d~~~~iP~~~f~f~~i~dI~~~~~~~~VDVIGvV~~ 258 (560)
++|++|+||+|++|+|++++++|++++|+|||.|+.+|+|++|.| ...||.+.|+|++|+||.+...+.+|||||+|++
T Consensus 243 ~~l~eG~VY~Is~~~Vk~an~~y~~~~~~yei~f~~~T~I~~~~d-~~~iP~~~~~f~~i~dI~~~~~~~~VDVIGvV~~ 321 (608)
T TIGR00617 243 DIIQEGKVYYISKGSLKPANKQFTNLGNDYEMTLDRDTVIEECED-ETAIPKIQFNFVKIDDIGGYEGNSLVDVIGIVQS 321 (608)
T ss_pred hhcccCCEEEECceEEEEccccccCCCCCEEEEECCCeEEEECCC-cccCCcccccceEHHHhhhhcCCCCccEEEEEeE
Confidence 999999999999999999999999999999999999999999975 4459999999999999999877889999999999
Q ss_pred ecCceeEeec-cCceeeEEEEEEecCCCcEEEEEEeCcchhhhhhhHHhhhccCCccEEEEEEEEEecCCCceecccCCe
Q 008606 259 VNPSVPILRK-NGMETQRRILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVDVGFFPVLSVKSGKVNDFSGKSIGTIPST 337 (560)
Q Consensus 259 V~~~~~i~~k-~G~~~~kr~i~L~D~Sg~~I~vtLWg~~a~~~~~~l~~~~~~~~~~VV~l~~~rV~~f~G~sLs~~~~S 337 (560)
|+++.+|++| +|++..||+|+|+|+||.+|+|||||++|..+ +...++||+|+++||++|+|++||++++|
T Consensus 322 v~~~~~i~~k~~g~~~~kR~i~L~D~sg~sI~vTLWG~~A~~~--------~~~~~~Vva~kg~~V~~f~g~sLs~~~~S 393 (608)
T TIGR00617 322 VSPTQTITSRKNNKEFPKRDITLVDDSGKSVRVTLWGDDATKF--------DVSVQPVIAIKGVRVSDFGGKSLSTGGSS 393 (608)
T ss_pred ecCceEEEEcCCCCeeeeEEEEEEeCCCCEEEEEEEhhhhhhc--------CCCCCCEEEEEeEEEEecCCceEeccCCc
Confidence 9999999854 78999999999999999999999999999874 34578999999999999999999999999
Q ss_pred EEEECCChHHHHHHHHHHhcCCCccceeeccccccc-CCCccchhhhHHHHhhcCCCCCCCCceEEEEEEEEEEeCCCeE
Q 008606 338 QLFINPDFAEAHELREWFDSGGKNAATVSISREIAA-GGAKNEIHKTVSQIKNEGLGRSEKPDWVTVRAFITFIKSDSFC 416 (560)
Q Consensus 338 ~i~iNPdipEa~~L~~w~~~~g~~~~~~sls~~~~~-~~~~~~~~ktI~~I~~~~~g~~e~~~~~~v~atI~~I~~d~~~ 416 (560)
+|++|||+||+++|+.||+++|....+.+++...+. .+.+...+|||+||+++.+|.+++++||.|+|+|++|+.|+||
T Consensus 394 ~i~iNPdipEa~~L~~w~~~~g~~~~~~s~~~~~~~~~~~~~~~~ktI~ei~~~~lg~~~k~~~f~v~atI~~Ik~d~~~ 473 (608)
T TIGR00617 394 TIIVNPDIPEAEKLKGWYDNEGKGTMASSISDMMSGRVGGSNAERKTIAEIQAENLGKSDKPDYFSVKATISYLKPDNAL 473 (608)
T ss_pred eEEECCCcHHHHHHHHHHHhcCCCccceeehhccccccCCcccccccHHHHhhhccCCCCCCcEEEEEEEEEEEecCCeE
Confidence 999999999999999999999987766666543322 1344678999999999999999999999999999999999999
Q ss_pred EeCCCCCcCccccCceeeecC-CeeecCcCCCccCCceeEEEEEEEEEeCCCeEEEEEehhhhhhhcCCCHHHHHHhhhc
Q 008606 417 YTACPLMIGDRQCNKKVTQSG-NRWQCDRCNQEIDECDYRYLLQAQIQDQTGLTWVTAFQESGEEILGCPAKELYMLKYE 495 (560)
Q Consensus 417 Y~aC~~~~~~~~C~KKv~~~~-~~~~C~kC~~~~~~~~~rY~l~~~i~D~Tgs~~~~~Fd~~ae~llG~sA~el~~~~~e 495 (560)
|+|||+. .|+|||...+ +.|+|++|++++++|.|||+|++.|+||||++|+++||+.|++|||++|+||.+++
T Consensus 474 Y~ACp~~----~CnKKV~~~~~g~~~CekC~~~~~~~~~RYil~~~i~D~Tg~~~~t~F~~~ae~llG~sA~eL~~l~-- 547 (608)
T TIGR00617 474 YRACPSE----DCNKKVVDQGDGTYRCEKCNKNFAEFKYRYILQISISDETGQLWVTAFNDQAEQILGKSAAELGELK-- 547 (608)
T ss_pred eccCChh----hCCCccccCCCCCEECCCCCCCCCCccEEEEEEEEEEeCCCCEEEEEEhHHHHHHcCCCHHHHHHHH--
Confidence 9999942 3999999876 49999999999999999999999999999999999999999999999999999999
Q ss_pred cCChhHHHHHHHHhcCCeEEEEEEEeeeecCCeeeEEEEEEEeeeCChHHHHHHHHHHHHh
Q 008606 496 LQDDVRFGEIIRSRVFNQYLFRLKIKEELYGDEQRVKITVIRADQVNYSSESRYLLDLISK 556 (560)
Q Consensus 496 ~~d~~~~~~~l~~~~~k~~~fkvkvk~e~y~~e~r~k~~v~~~~~vd~~~e~~~ll~~i~~ 556 (560)
++++++|+++|.++.|++|.|+|+++.++||||.|+|++|++++|+||++|+++||+.|++
T Consensus 548 ~~~~~~~~~i~~~~~~~~~~f~~~~k~e~yn~e~r~~~~v~~~~~vd~~~e~~~L~~~i~~ 608 (608)
T TIGR00617 548 EEDPDEFEAIFQEAQFVPYIFRLRVKQDTYNDESRQKYTVMSVDPVNYRAEAKYLLQEIEK 608 (608)
T ss_pred hcCHHHHHHHHHHhhCcEEEEEEEEEEcccCCEeeEEEEEEEeeeCCHHHHHHHHHHHhcC
Confidence 6788999999999999999999999999999999999999999999999999999999974
No 2
>PRK12366 replication factor A; Reviewed
Probab=100.00 E-value=1.8e-63 Score=556.38 Aligned_cols=360 Identities=21% Similarity=0.333 Sum_probs=321.9
Q ss_pred CCCCcceeccccCCC-CC-ceEEEEEEEEecccceeccCCCCCcEEEEEEEeCCCCeEEEEEcchhHHHHHhhcccCcEE
Q 008606 110 EAPARIIPIAALNPY-QG-RWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVY 187 (560)
Q Consensus 110 ~~~~~~~pI~~L~p~-~~-~w~Ik~RV~~k~~ir~~~n~~g~gkvf~~~L~D~~g~~I~at~~~~~~~kf~~~l~eG~vY 187 (560)
+....++||++|+|| .+ +|+|+|||+.|+++|+|++.+|+|++|+++|.|+. |+|+|++|++.+++|++ |++|++|
T Consensus 274 ~~~~~~~pI~~L~~~~~g~~~~I~grV~~~~~~R~f~~~~g~gkv~s~~l~D~t-G~IR~t~w~~~~d~~~~-l~~G~vy 351 (637)
T PRK12366 274 EKELEIVNIEELTEFEDGEEVDVKGRIIAISDKREVERDDRTAEVQDIELADGT-GRVRVSFWGEKAKILEN-LKEGDAV 351 (637)
T ss_pred ccccCceeHHHCCcccCCCEEEEEEEEEecCCceEEEcCCCcEEEEEEEEEcCC-CeEEEEEeCchhhhhcc-cCCCCEE
Confidence 445688999999999 54 89999999999999999999999999999999955 69999999999999997 5999999
Q ss_pred EEeeeEEecCCCccccCCCeeEEEEcccceEEeccCCCCCCCcccccccCccchhccc-CCceeEEEEEEEEecCceeEe
Q 008606 188 LISKGSLKPAQKNFNHLKNEWEIFLEATSTVDLCTEEDDSIPKQQFSFRHISEIESAE-NNSIVDVIGIVISVNPSVPIL 266 (560)
Q Consensus 188 ~Is~~~V~~a~~~y~~~~~~yeI~f~~~T~I~~~~d~~~~iP~~~f~f~~i~dI~~~~-~~~~VDVIGvV~~V~~~~~i~ 266 (560)
.|++++|+..+. +...+.|||.++..|.|.+ +++..+|...++|++|++|.++. .+..|||+|+|++++++.+|+
T Consensus 352 ~is~~~vk~y~~--~~~~~~~El~~~~~s~I~~--d~~~~~p~~~~~~~~i~dI~~~~~~~~~VdVig~V~~v~~~~~i~ 427 (637)
T PRK12366 352 KIENCKVRTYYD--NEGEKRVDLNAGYSSEIIK--DESISFEEIEEKIYKIKDILNLEEDDNDITVIARVVEDYPVNEFE 427 (637)
T ss_pred EEecCEEeeccc--cCCCcCEEEEcCCceEEEe--ccCCcccceeeccccHHHhhcccCCCcEEEEEEEEEEccCceEEE
Confidence 999999984332 1345789999999999998 34556899999999999999874 688999999999999999999
Q ss_pred eccCceeeEEEEEEecCCCcEEEEEEeCcchhhhhhhHHhhhccCCccEEEEEEEEEecCCCc-eecccCCeEEEECCCh
Q 008606 267 RKNGMETQRRILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVDVGFFPVLSVKSGKVNDFSGK-SIGTIPSTQLFINPDF 345 (560)
Q Consensus 267 ~k~G~~~~kr~i~L~D~Sg~~I~vtLWg~~a~~~~~~l~~~~~~~~~~VV~l~~~rV~~f~G~-sLs~~~~S~i~iNPdi 345 (560)
+++|++..+|+++|.|+|| +|++||||+.|.. ....+++|+|++++|++|+|+ +|+++++|+|.+||+.
T Consensus 428 ~k~G~~~~~r~i~l~D~TG-~I~vtlWg~~a~~---------~~~~G~vi~i~~~~V~~~~g~~~Ls~~~~s~i~~~p~~ 497 (637)
T PRK12366 428 RSDGSKGKVRNIELADGTG-SIRLTLWDDDAEI---------EIKEGDAIKILHPYVKENGDYLDLSIGRYGRIEINPEG 497 (637)
T ss_pred ecCCCEeEEEEEEEEeCCC-EEEEEEecccccc---------CCCCCCEEEEEeeEEEeCCCeeEEEecCcceEEECCCC
Confidence 9999999999999999999 9999999999863 224689999999999999995 8999999999999998
Q ss_pred HHHHHHHHHHhcCCCccceeecccccccCCCccchhhhHHHHhhcCCCCCCCCceEEEEEEEEEEeCCCeEEeCCCCCcC
Q 008606 346 AEAHELREWFDSGGKNAATVSISREIAAGGAKNEIHKTVSQIKNEGLGRSEKPDWVTVRAFITFIKSDSFCYTACPLMIG 425 (560)
Q Consensus 346 pEa~~L~~w~~~~g~~~~~~sls~~~~~~~~~~~~~ktI~~I~~~~~g~~e~~~~~~v~atI~~I~~d~~~Y~aC~~~~~ 425 (560)
|+ |+ ..+++|++|++. +++.++|+|++|+.+++||+|||
T Consensus 498 ~e---l~--------------------------~~~~~I~~i~~~--------~~~~v~g~i~~i~~~~~~y~aCp---- 536 (637)
T PRK12366 498 EI---IK--------------------------SNRKFIADLEED--------DTVEIRGTVVDIRKQKIILYLCP---- 536 (637)
T ss_pred cc---cc--------------------------ccccCHHHcccC--------CeEEEEEEEEEEeCCCEEEeccc----
Confidence 87 21 037889999764 45999999999999999999999
Q ss_pred ccccCceeeecCCeeecCcCCCccCCceeEEEEEEEEEeCCCeEEEEEehhhhhhhcCCCHHHHHHhhhccCChhHHHHH
Q 008606 426 DRQCNKKVTQSGNRWQCDRCNQEIDECDYRYLLQAQIQDQTGLTWVTAFQESGEEILGCPAKELYMLKYELQDDVRFGEI 505 (560)
Q Consensus 426 ~~~C~KKv~~~~~~~~C~kC~~~~~~~~~rY~l~~~i~D~Tgs~~~~~Fd~~ae~llG~sA~el~~~~~e~~d~~~~~~~ 505 (560)
.|+|||....+.|+|++|++. +|.|||+|++.|+|+||++|+++|++.|++||||+|+||.+|. + +.
T Consensus 537 --~CnkKv~~~~g~~~C~~c~~~--~p~~~~~l~~~i~D~TG~~~~t~f~e~ae~l~G~sa~el~~l~--~-------~~ 603 (637)
T PRK12366 537 --NCRKRVEEVDGEYICEFCGEV--EPNELLMLNFTLDDGTGTINCRFYGKNVEKLLGMSKEELKELN--L-------EA 603 (637)
T ss_pred --ccCeEeEcCCCcEECCCCCCC--CCcEEEEEEEEEEcCCCCEEEEEEhHHhHHHhCCCHHHHHHHH--H-------HH
Confidence 899999987679999999987 7999999999999999999999999999999999999999987 2 56
Q ss_pred HHHhcCCeEEEEEEEeeeecCCeeeEEEEEEEeeeCCh
Q 008606 506 IRSRVFNQYLFRLKIKEELYGDEQRVKITVIRADQVNY 543 (560)
Q Consensus 506 l~~~~~k~~~fkvkvk~e~y~~e~r~k~~v~~~~~vd~ 543 (560)
|++++|++|.|+++++.+ +++ ++|+|.++.|+|+
T Consensus 604 l~~~~g~~~~~~~~~k~~--~~~--~r~~v~~v~~~d~ 637 (637)
T PRK12366 604 LEDLLGEEVVFYGNVSFR--NEE--LRFNVRRVNNVDV 637 (637)
T ss_pred HHHhcCcEEEEEEEEeec--Cce--eEEEEEEeecccC
Confidence 778999999999999988 665 5599999999985
No 3
>PRK08402 replication factor A; Reviewed
Probab=100.00 E-value=1.1e-43 Score=368.89 Aligned_cols=280 Identities=21% Similarity=0.310 Sum_probs=237.8
Q ss_pred cccCccchhcccCCceeEEEEEEEEecCceeEeeccCceeeEEEEEEecCCCcEEEEEEeCcchhhhhhhHHhhhccCCc
Q 008606 234 SFRHISEIESAENNSIVDVIGIVISVNPSVPILRKNGMETQRRILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVDVGFF 313 (560)
Q Consensus 234 ~f~~i~dI~~~~~~~~VDVIGvV~~V~~~~~i~~k~G~~~~kr~i~L~D~Sg~~I~vtLWg~~a~~~~~~l~~~~~~~~~ 313 (560)
..++|+||.. ....|.+.|.|+++++.++|.+++|.....++++|.|+|| .+++|||++.|..+... ...+
T Consensus 61 ~~~kI~dl~~--g~~~V~v~~rVl~~~~~r~f~rrdG~~~~V~~i~l~DeTG-~ir~TlW~~~a~~~~~~------l~~G 131 (355)
T PRK08402 61 PLMHISDLVP--GMRGVNIVGRVLRKYPPREYTKKDGSTGRVASLIIYDDTG-RARVVLWDAKVAKYYNK------INVG 131 (355)
T ss_pred CccCHHHccC--CCceeeEEEEEEEccCCceeeccCCCcceEEEEEEEcCCC-eEEEEEechhhhhhccc------CCCC
Confidence 3567777753 3468999999999999999999999888999999999999 67999999998753111 2578
Q ss_pred cEEEEEEEEEec-CCCc-eecccCCeEEEECCChHHHHHHHHHHhcCCCccceeecccccccCCCccchhhhHHHHhhcC
Q 008606 314 PVLSVKSGKVND-FSGK-SIGTIPSTQLFINPDFAEAHELREWFDSGGKNAATVSISREIAAGGAKNEIHKTVSQIKNEG 391 (560)
Q Consensus 314 ~VV~l~~~rV~~-f~G~-sLs~~~~S~i~iNPdipEa~~L~~w~~~~g~~~~~~sls~~~~~~~~~~~~~ktI~~I~~~~ 391 (560)
+||.|++++|++ |+|+ +|+.+.+|+|.+||+.|+++.+ .+++... +....+++|++|.+.
T Consensus 132 dvi~I~~a~V~e~~~G~~eLsvg~~s~i~~~pd~~ea~~i-------------~~~~~~~----~~~~~~k~I~ei~~g- 193 (355)
T PRK08402 132 DVIKVIDAQVRESLSGLPELHINFRARIILNPDDPRVEEI-------------PPLEEVR----SYNYTRKKIGELEGG- 193 (355)
T ss_pred CEEEEECCEEeecCCCcEEEEECCCceEEeCCCccccccc-------------ccccccc----cccccccCHHHcccC-
Confidence 999999999998 5999 9999999999999999998752 1222111 124678999999542
Q ss_pred CCCCCCCceEEEEEEEEEEeCCCeEEeCCCCCcCccccCceee-ecCC-eeecCcCCCccCCceeEEEEEEEEEeCCCeE
Q 008606 392 LGRSEKPDWVTVRAFITFIKSDSFCYTACPLMIGDRQCNKKVT-QSGN-RWQCDRCNQEIDECDYRYLLQAQIQDQTGLT 469 (560)
Q Consensus 392 ~g~~e~~~~~~v~atI~~I~~d~~~Y~aC~~~~~~~~C~KKv~-~~~~-~~~C~kC~~~~~~~~~rY~l~~~i~D~Tgs~ 469 (560)
..||.|.|+|++|+. +++|+||| .|+|||+ ..++ .|+|+.|++ .+|.|||+|++.|+|+||++
T Consensus 194 ------d~~v~v~g~Iv~i~~-~~~y~aCp------~CnKkv~~~~~~~~~~Ce~~~~--v~p~~ryil~~~l~D~TG~~ 258 (355)
T PRK08402 194 ------ERFVEVRGTIAKVYR-VLVYDACP------ECRRKVDYDPATDTWICPEHGE--VEPIKITILDFGLDDGTGYI 258 (355)
T ss_pred ------CcEEEEEEEEEEEec-CeeEecCC------CCCeEEEEecCCCCEeCCCCCC--cCcceeEEEEEEEEcCCCcE
Confidence 278999999999997 77899999 8999998 4433 899999997 37999999999999999999
Q ss_pred EEEEehhhhhhhcCCCHHHHHHh-h---hccCCh-----hHHHHHHHHhcCCeEEEEEEEeeeecCCeeeEEEEEEEeee
Q 008606 470 WVTAFQESGEEILGCPAKELYML-K---YELQDD-----VRFGEIIRSRVFNQYLFRLKIKEELYGDEQRVKITVIRADQ 540 (560)
Q Consensus 470 ~~~~Fd~~ae~llG~sA~el~~~-~---~e~~d~-----~~~~~~l~~~~~k~~~fkvkvk~e~y~~e~r~k~~v~~~~~ 540 (560)
|+++|++.|++|||++|+||.++ + .+..+. ..+.+.+..++|++|.|+++++.+.|+++. |+|.++.|
T Consensus 259 ~vt~f~e~ae~llG~sa~el~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~rg~~~~d~y~~~~---~~v~~~~~ 335 (355)
T PRK08402 259 RVTLFGDDAAELLGVEPEEIAEKLKELIEMGLTPKEAARKLAEEEFYNIIGREIVVRGNVIEDRFLGLI---LKASSWDE 335 (355)
T ss_pred EEEEecHHHHHHhCCCHHHHHHHHHHhhhcccchhhhhhhHHHHHHHHhcCeEEEEEEEEEecccCCeE---EEEEEccc
Confidence 99999999999999999999988 3 211133 678888999999999999999999999865 99999999
Q ss_pred CChHHHHHHHHHHHHhhh
Q 008606 541 VNYSSESRYLLDLISKSF 558 (560)
Q Consensus 541 vd~~~e~~~ll~~i~~~~ 558 (560)
+||++|+++|+++|.+|.
T Consensus 336 vd~~~e~~~l~~~i~~~~ 353 (355)
T PRK08402 336 VDYKREIERVRAELEELG 353 (355)
T ss_pred CCHHHHHHHHHHHHHHhh
Confidence 999999999999999875
No 4
>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=100.00 E-value=3.8e-36 Score=284.23 Aligned_cols=165 Identities=44% Similarity=0.828 Sum_probs=154.1
Q ss_pred HHHHhhcCCCCCCCCceEEEEEEEEEEeCCCeEEeCCCCCcCccccCceeeecC-CeeecCcCCCccCCceeEEEEEEEE
Q 008606 384 VSQIKNEGLGRSEKPDWVTVRAFITFIKSDSFCYTACPLMIGDRQCNKKVTQSG-NRWQCDRCNQEIDECDYRYLLQAQI 462 (560)
Q Consensus 384 I~~I~~~~~g~~e~~~~~~v~atI~~I~~d~~~Y~aC~~~~~~~~C~KKv~~~~-~~~~C~kC~~~~~~~~~rY~l~~~i 462 (560)
|++|+++.++..+++++|.|+|+|..|+.++|||+||| .|+|||...+ +.|+|++|++.+++|.+||+|++.|
T Consensus 1 i~~i~~~~~~~~~~~~~~~v~a~I~~I~~~~~~Y~aC~------~C~kkv~~~~~~~~~C~~C~~~~~~~~~ry~l~~~i 74 (166)
T cd04476 1 IAEIKEENLGEGEKPDYFTVKATIVFIKPDNWWYPACP------GCNKKVVEEGNGTYRCEKCNKSVPNPEYRYILSLNV 74 (166)
T ss_pred CchhhcccCCCCCCCCEEEEEEEEEEEcCCCeEEcccc------ccCcccEeCCCCcEECCCCCCcCCCccEEEEEEEEE
Confidence 35677777766667899999999999998899999999 9999999887 6999999999988999999999999
Q ss_pred EeCCCeEEEEEehhhhhhhcCCCHHHHHHhhhccCChhHHHHHHHHhcCCeEEEEEEEeeeecCCeeeEEEEEEEeeeCC
Q 008606 463 QDQTGLTWVTAFQESGEEILGCPAKELYMLKYELQDDVRFGEIIRSRVFNQYLFRLKIKEELYGDEQRVKITVIRADQVN 542 (560)
Q Consensus 463 ~D~Tgs~~~~~Fd~~ae~llG~sA~el~~~~~e~~d~~~~~~~l~~~~~k~~~fkvkvk~e~y~~e~r~k~~v~~~~~vd 542 (560)
+|+||++|+++||+.|++|||++|+||.++. +++++.+++.|.+++|++|+|+|+++.++|++|.|++++|.+++|++
T Consensus 75 ~D~Tg~~~~~~F~~~ae~l~G~sa~el~~~~--~~~~~~~~~~i~~~~gk~~~f~v~~~~~~y~~e~~~~~~v~~i~~~~ 152 (166)
T cd04476 75 ADHTGEAWLTLFDEVAEQIFGKSAEELLELK--EEDPDAFPDAIQDLVGKTFLFRVSVKEETYNDEGRIRYTVVKVAPVD 152 (166)
T ss_pred EeCCCCEEEEEehHHHHHHhCCCHHHHHHHh--hcCHHHHHHHHHHhhCceEEEEEEEEehhcCCcceEEEEEEEcccCC
Confidence 9999999999999999999999999999988 45578899999999999999999999999999999999999999999
Q ss_pred hHHHHHHHHHHHHh
Q 008606 543 YSSESRYLLDLISK 556 (560)
Q Consensus 543 ~~~e~~~ll~~i~~ 556 (560)
+++|+++|++.|++
T Consensus 153 ~~~~~~~l~~~i~~ 166 (166)
T cd04476 153 YKKESKRLIQSIEK 166 (166)
T ss_pred HHHHHHHHHHHhhC
Confidence 99999999999863
No 5
>PRK07218 replication factor A; Provisional
Probab=100.00 E-value=6.7e-34 Score=301.37 Aligned_cols=362 Identities=18% Similarity=0.206 Sum_probs=291.4
Q ss_pred CCcceeccccCCCCCceEEEEEEEEecccceeccCCCCCcEEEEEEEeCCCCeEEEEEcchhHHHHHhhcccCcEEEEee
Q 008606 112 PARIIPIAALNPYQGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISK 191 (560)
Q Consensus 112 ~~~~~pI~~L~p~~~~w~Ik~RV~~k~~ir~~~n~~g~gkvf~~~L~D~~g~~I~at~~~~~~~kf~~~l~eG~vY~Is~ 191 (560)
.+..+.|++|.|++.+.+|+|||+.+|+ |.|....++|.+.++.|.| +.|.|+.++|++.. |++|++|.|.|
T Consensus 55 ~~~~~kI~Di~~~~~~V~v~~kVl~i~~-rt~r~dg~~g~v~~~~igD-eTG~Ir~tlW~~~~------l~~Gdvv~I~n 126 (423)
T PRK07218 55 TPSSKDIKELSTDDKNVTVTGRVLTIGE-RSIRYQGDDHVIYEGILAD-ETGTISYTAWKDFG------LSPGDTVTIGN 126 (423)
T ss_pred CCCCccHhhCCCCCceeEEEEEEEEecc-eeEecCCCceEEEEEEEEC-CCCeEEEEEECCCC------CCCCCEEEEec
Confidence 3467899999999999999999999999 8887655678999999999 78999999999652 99999999999
Q ss_pred eEEecCCCccccCCCeeEEEEcccceEEeccCCCCCCCcccccccCccchhcccCCceeEEEEEEEEecCceeEeeccCc
Q 008606 192 GSLKPAQKNFNHLKNEWEIFLEATSTVDLCTEEDDSIPKQQFSFRHISEIESAENNSIVDVIGIVISVNPSVPILRKNGM 271 (560)
Q Consensus 192 ~~V~~a~~~y~~~~~~yeI~f~~~T~I~~~~d~~~~iP~~~f~f~~i~dI~~~~~~~~VDVIGvV~~V~~~~~i~~k~G~ 271 (560)
+.++.-+ ...++.++..|.|....+ ....|...+...+|.||.. ...-|+|.|.|+++.+ ++|.+++|.
T Consensus 127 a~vre~~-------g~~el~ig~~t~I~~~de-~~~~~~~~~~~~kI~DL~~--g~~~V~v~g~Vl~~~~-r~f~~~dg~ 195 (423)
T PRK07218 127 AGVREWD-------GRPELNIGESTTVSLLDD-SSLPPYSIGGDKKLIDLGP--GDRGVNVEARVLELEH-REIDGRDGE 195 (423)
T ss_pred cEeeccC-------CceEEeccCcceEEEcCc-ccccCccccCccchhhccC--CCCceEEEEEEEEecc-eeEEcCCCC
Confidence 9987653 348999999999998753 3333322233444444432 4566999999999966 789888775
Q ss_pred eeeEEEEEEecCCCcEEEEEEeCcchhhhhhhHHhhhccCCccEEEEEEEEEecCCCc-eecccCCeEEEECCChHHHHH
Q 008606 272 ETQRRILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVDVGFFPVLSVKSGKVNDFSGK-SIGTIPSTQLFINPDFAEAHE 350 (560)
Q Consensus 272 ~~~kr~i~L~D~Sg~~I~vtLWg~~a~~~~~~l~~~~~~~~~~VV~l~~~rV~~f~G~-sLs~~~~S~i~iNPdipEa~~ 350 (560)
...++..|.|+|| +|++|||++.+. + ..+.+|-|.++.+++|+|+ +|+....|.|..+|+-.++
T Consensus 196 -~~v~~giigDeTG-~Ir~tlW~~~~~---------l--~~Gd~v~I~na~v~e~~G~~elnv~~~t~I~~~d~~i~v-- 260 (423)
T PRK07218 196 -TTILSGVLADETG-RLPFTDWDPLPE---------I--EIGASIRIEDAYVREFRGVPSVNVSEFTTVEALDREVSV-- 260 (423)
T ss_pred -eEEEEEEEECCCc-eEEEEEeccccc---------C--CCCCEEEEeeeEEeccCCeEEEEECCceEEEECCCCccc--
Confidence 4689999999999 899999998752 1 4689999999999999998 8999999999987753221
Q ss_pred HHHHHhcCCCccceeecccccccCCCccchhhhHHHHhhcCCCCCCCCce-EEEEEEEEEEeCCCeEEeCCCCCcCcccc
Q 008606 351 LREWFDSGGKNAATVSISREIAAGGAKNEIHKTVSQIKNEGLGRSEKPDW-VTVRAFITFIKSDSFCYTACPLMIGDRQC 429 (560)
Q Consensus 351 L~~w~~~~g~~~~~~sls~~~~~~~~~~~~~ktI~~I~~~~~g~~e~~~~-~~v~atI~~I~~d~~~Y~aC~~~~~~~~C 429 (560)
.....+++|.++.+.. ..| ..|.|+|..|...+-.|..|| .|
T Consensus 261 -------------------------~~~~~~~~I~e~~~~~------g~~~Vev~G~Iv~i~~gsgli~rCP------~C 303 (423)
T PRK07218 261 -------------------------SKDPPRLKIREAVERG------GIFDVELVGNIISVRDGSGLIERCP------EC 303 (423)
T ss_pred -------------------------cCCccccchhhhhccC------CcceEEEEEEEEEeccCCcceecCc------Cc
Confidence 1123467888887642 234 689999999999889999999 99
Q ss_pred CceeeecCCeeecCcCCCccCCceeEEEEEEEEEeCCCeEEEEEehhhhhhhcCCCHHHHHHhhhccCChhHHHHHH-HH
Q 008606 430 NKKVTQSGNRWQCDRCNQEIDECDYRYLLQAQIQDQTGLTWVTAFQESGEEILGCPAKELYMLKYELQDDVRFGEII-RS 508 (560)
Q Consensus 430 ~KKv~~~~~~~~C~kC~~~~~~~~~rY~l~~~i~D~Tgs~~~~~Fd~~ae~llG~sA~el~~~~~e~~d~~~~~~~l-~~ 508 (560)
+|+|.. |.|+.|++. ++.+-.++.+.+.|+||++.+++|++.+++|.|++.++..+|..+.-|.....+.| ..
T Consensus 304 ~r~v~~----~~C~~hG~v--e~~~dlrik~vLDDGtg~~~~~~~~e~~e~l~G~~~e~a~~~~~~~~d~~~v~~~i~~~ 377 (423)
T PRK07218 304 GRVIQK----GQCRSHGAV--EGEDDLRIKAILDDGTGSVTVILDRELTEIVYGGTLEDAEELAREAMDKDVVAEDIRER 377 (423)
T ss_pred cccccC----CcCCCCCCc--CCeeeeEEEEEEECCCCeEEEEEChhhhHhHhCCCHHHHHHHHHhhhcchhhHHHHHHh
Confidence 999955 899999974 78899999999999999999999999999999999999998874444555555555 66
Q ss_pred hcCCeEEEEEEEeeeecCCeeeEEEEEEEeeeCC--hHHHHHHHHHHH
Q 008606 509 RVFNQYLFRLKIKEELYGDEQRVKITVIRADQVN--YSSESRYLLDLI 554 (560)
Q Consensus 509 ~~~k~~~fkvkvk~e~y~~e~r~k~~v~~~~~vd--~~~e~~~ll~~i 554 (560)
++|++|.|+..+..+.|. ..+.+.+++.+| .++-++.||.++
T Consensus 378 llG~~~~v~G~~~~~~~g----~~~~a~~~~~~~~~~~~r~~~~l~~~ 421 (423)
T PRK07218 378 LVGREYRVRGNLSVDEYG----ANLVAESFWVPDDDPAKRAVALLAEV 421 (423)
T ss_pred hcCcEEEEEeccccccCC----cEEEEeEccccCCCHHHHHHHHHHhh
Confidence 999999999999887773 577788888776 455555566543
No 6
>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=100.00 E-value=4.9e-36 Score=277.59 Aligned_cols=145 Identities=46% Similarity=0.820 Sum_probs=123.8
Q ss_pred eEEEEEEEEEEeCCCeEEeCCCCCcCccccCceeeecCC-eeecCcCCCccCCceeEEEEEEEEEeCCCeEEEEEehhhh
Q 008606 400 WVTVRAFITFIKSDSFCYTACPLMIGDRQCNKKVTQSGN-RWQCDRCNQEIDECDYRYLLQAQIQDQTGLTWVTAFQESG 478 (560)
Q Consensus 400 ~~~v~atI~~I~~d~~~Y~aC~~~~~~~~C~KKv~~~~~-~~~C~kC~~~~~~~~~rY~l~~~i~D~Tgs~~~~~Fd~~a 478 (560)
||+|+|+|..|+.++|||+|||++ .|+|||...++ .|+|++|++.+++|.+||+|++.|+|+||++|+++||+.|
T Consensus 1 ~~~v~a~I~~I~~~~~~Y~aC~~~----~C~kKv~~~~~~~y~C~~C~~~~~~~~~ry~l~~~i~D~tg~~~~~~F~~~a 76 (146)
T PF08646_consen 1 YFTVRATIVEIKSDNWYYPACPNE----KCNKKVTENGDGSYRCEKCNKTVENPKYRYRLSLKISDGTGSIWVTLFDEEA 76 (146)
T ss_dssp EEEEEEEEEEEETTTTEEEE-TST----TTS-B-EEETTTEEEETTTTEEESS-EEEEEEEEEEEETTEEEEEEEEHHHH
T ss_pred CEEEEEEEEEEECCCcEECCCCCc----cCCCEeecCCCcEEECCCCCCcCCCeeEEEEEEEEEEeCCCeEEEEEEhHHH
Confidence 789999999999999999999976 89999998854 9999999999889999999999999999999999999999
Q ss_pred hhhcCCCHHHHHHhhhccCChhHHHHHHHHhcCCeEEEEEEEeeeecCCeeeEEEEEEEeeeCChHHHHHHH
Q 008606 479 EEILGCPAKELYMLKYELQDDVRFGEIIRSRVFNQYLFRLKIKEELYGDEQRVKITVIRADQVNYSSESRYL 550 (560)
Q Consensus 479 e~llG~sA~el~~~~~e~~d~~~~~~~l~~~~~k~~~fkvkvk~e~y~~e~r~k~~v~~~~~vd~~~e~~~l 550 (560)
++|||++|+||.++. ++++..++.++.+++|++|.|+|+++.++|+++.|++++|++++|+||++|+++|
T Consensus 77 ~~l~G~~a~el~~~~--~~~~~~~~~~~~~~~~~~~~f~v~~~~~~y~~e~r~~~~v~~i~~vd~~~e~~~l 146 (146)
T PF08646_consen 77 EQLLGMSADELKELK--EEDPEEFPKIIKKLLGKEFVFRVRVKKESYNDESRVKYTVVRIEPVDYAEESKRL 146 (146)
T ss_dssp HHHHCCHHCCCHHHC--CC-HHHHHHHHHCTTT-EEEEEEEEEE--------EEEEEEEEEE--HHHHHHHH
T ss_pred HHHhCCCHHHHHHHH--hhchhHHHHHHHHhhCcEEEEEEEEEEhhhCCceEEEEEEEEeEeCCHHHHhhcC
Confidence 999999999999988 6788999999999999999999999999999999999999999999999999987
No 7
>PRK06386 replication factor A; Reviewed
Probab=100.00 E-value=1.5e-30 Score=269.48 Aligned_cols=351 Identities=16% Similarity=0.183 Sum_probs=279.8
Q ss_pred ceeccccCCCCCceEEEEEEEEecccceeccCCCCCcEEEEEEEeCCCCeEEEEEcchhHHHHHhhcccCcEEEEeeeEE
Q 008606 115 IIPIAALNPYQGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISKGSL 194 (560)
Q Consensus 115 ~~pI~~L~p~~~~w~Ik~RV~~k~~ir~~~n~~g~gkvf~~~L~D~~g~~I~at~~~~~~~kf~~~l~eG~vY~Is~~~V 194 (560)
.+.|++|+|...+.+|+|||+..| .|.|..++|+..+.+-.|.| +.|.|+.|+|+. .+.|++|++|.|.|+.+
T Consensus 2 ~~kI~DI~~~~~~V~v~akVl~~~-~r~i~~~~g~~~~~~gllgD-eTG~I~fT~W~~-----~~~l~~Gd~v~i~na~v 74 (358)
T PRK06386 2 LSKISDINAARQNVDLKVKVLSLN-KRTIKNDRGETIYYYGIIGD-ETGTVPFTAWEF-----PDAVKSGDVIEIKYCYS 74 (358)
T ss_pred CcchhhcCCCCCcEEEEEEEEEcc-ceEEecCCCCeEEEEEEEEC-CcceEEEEecCC-----cccCCCCCEEEEEeEEE
Confidence 357999999999999999999999 59998887776677778889 799999999994 24799999999999998
Q ss_pred ecCCCccccCCCeeEEEEcccceEEeccCCCCCCCcccccccCccchhcccCCceeEEEEEEEEecCceeEeeccCceee
Q 008606 195 KPAQKNFNHLKNEWEIFLEATSTVDLCTEEDDSIPKQQFSFRHISEIESAENNSIVDVIGIVISVNPSVPILRKNGMETQ 274 (560)
Q Consensus 195 ~~a~~~y~~~~~~yeI~f~~~T~I~~~~d~~~~iP~~~f~f~~i~dI~~~~~~~~VDVIGvV~~V~~~~~i~~k~G~~~~ 274 (560)
+.-+ ..++|.++..|+|.+.++.+..++ ..+..++|.||.. ....|+|.|.|.++.+ .++. ++|....
T Consensus 75 ~~~~-------G~~~Lnv~~~t~v~~~~d~~iev~-~~~~~~KI~DL~~--g~~~v~V~akVle~~e-~e~~-~~g~~~~ 142 (358)
T PRK06386 75 KEYN-------GKIRIYFDSRSEVMLKPDENIEVK-RTYKLVKIRDLSL--VTPYVSVIGKITGITK-KEYD-SDGTSKI 142 (358)
T ss_pred eeEC-------CEEEEEEcCceEEEecCccccccc-cccCccEeEeccC--CCCceEEEEEEEEccC-ceEe-cCCCccE
Confidence 7543 357899999999976643323222 2246778888853 5678999999999976 5776 5566678
Q ss_pred EEEEEEecCCCcEEEEEEeCcchhhhhhhHHhhhccCCccEEEEEEEEEecCCCc-eecccCCeEEEECCChHHHHHHHH
Q 008606 275 RRILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVDVGFFPVLSVKSGKVNDFSGK-SIGTIPSTQLFINPDFAEAHELRE 353 (560)
Q Consensus 275 kr~i~L~D~Sg~~I~vtLWg~~a~~~~~~l~~~~~~~~~~VV~l~~~rV~~f~G~-sLs~~~~S~i~iNPdipEa~~L~~ 353 (560)
.+++.|.|+|| +|++|||++.. ..+.++-|.++.+.+|+|+ +|+....|+|...|+.-|+
T Consensus 143 v~sg~lgDeTG-rIr~TlW~~~l-------------~eGd~v~i~na~v~e~~G~~el~v~~~t~I~~~~~~iev----- 203 (358)
T PRK06386 143 VYQGYIEDDTA-RVRISSFGKPL-------------EDNRFVRIENARVSQYNGYIEISVGNKSVIKEVESDINL----- 203 (358)
T ss_pred EEEEEEEcCCC-eEEEEEccccc-------------cCCCEEEEeeeEEEccCCeEEEEeCCeEEEEECCCCccc-----
Confidence 89999999999 89999999731 3579999999999999998 8999999998765532110
Q ss_pred HHhcCCCccceeecccccccCCCccchhhhHHHHhhcCCCCCCCCceEEEEEEEEEEeCCCeEEeCCCCCcCccccCcee
Q 008606 354 WFDSGGKNAATVSISREIAAGGAKNEIHKTVSQIKNEGLGRSEKPDWVTVRAFITFIKSDSFCYTACPLMIGDRQCNKKV 433 (560)
Q Consensus 354 w~~~~g~~~~~~sls~~~~~~~~~~~~~ktI~~I~~~~~g~~e~~~~~~v~atI~~I~~d~~~Y~aC~~~~~~~~C~KKv 433 (560)
...++.|++|.+.. .-..+.|+|+.|...+-.|..|| .|+|+|
T Consensus 204 ------------------------~~~~~~I~di~~~~-------g~v~i~G~iv~i~~gsgli~rCP------~C~R~l 246 (358)
T PRK06386 204 ------------------------ESRNIFIFEIKSPV-------GGITIMGFIVSVGQGSRIFTKCS------VCNKII 246 (358)
T ss_pred ------------------------CccccchhhhhccC-------CeEEEEEEEEEEcCCcEeEecCc------CCCeEc
Confidence 12367889997642 12689999999998889999999 999999
Q ss_pred eecCCeeecCcCCCccCCceeEEEEEEEEEeCCCeEEEEEehhhhhhhcCCCHHHHHHhhhccCChhHHHHHHHHhcCCe
Q 008606 434 TQSGNRWQCDRCNQEIDECDYRYLLQAQIQDQTGLTWVTAFQESGEEILGCPAKELYMLKYELQDDVRFGEIIRSRVFNQ 513 (560)
Q Consensus 434 ~~~~~~~~C~kC~~~~~~~~~rY~l~~~i~D~Tgs~~~~~Fd~~ae~llG~sA~el~~~~~e~~d~~~~~~~l~~~~~k~ 513 (560)
.. +.|+.|++ ..+.+-.++.+.+.|+||++.+++|++.+++|+|++-+++.++.- +-+. ...+=..++|+.
T Consensus 247 ~~----g~C~~HG~--v~~~~dlr~k~vLDDGtg~~~~~l~~e~~e~l~G~~lee~~~~a~-~~~~--~~~i~~~llGr~ 317 (358)
T PRK06386 247 ED----GVCKDHPD--APVYLDIFGYFTISDGTGFVTCYANKDSFLPYININENEFARKAS-SMNP--NMLIKKNLLGKC 317 (358)
T ss_pred cC----CcCCCCCC--CCCeeEEEEEEEEECCCCeEEEEEChHHhHHHhCCCHHHHHHHhh-ccCH--HHHhhhhhcccE
Confidence 95 69999997 367777888889999999999999999999999999999987552 2222 222226799999
Q ss_pred EEEEEEEeeeecCCeeeEEEEEEEeeeCChHHHHHHHHHHH
Q 008606 514 YLFRLKIKEELYGDEQRVKITVIRADQVNYSSESRYLLDLI 554 (560)
Q Consensus 514 ~~fkvkvk~e~y~~e~r~k~~v~~~~~vd~~~e~~~ll~~i 554 (560)
|.|+..+..+.|. +.+.+.++..+|. .+.+.+-..|
T Consensus 318 ~~v~G~~~~~~~~----~~~~~~~~~~~~~-~~~~~~~~~~ 353 (358)
T PRK06386 318 FSVTGDLRKKDDE----IDMNVISAKSITA-DEIKIIEVEI 353 (358)
T ss_pred EEEEcceEeccCC----eEEEEEEeeeccc-hhhhHHHHHH
Confidence 9999999887764 7899999998886 3444444333
No 8
>PRK12366 replication factor A; Reviewed
Probab=100.00 E-value=9.5e-31 Score=293.24 Aligned_cols=282 Identities=20% Similarity=0.270 Sum_probs=223.9
Q ss_pred CCcceeccccCCCCCceEEEEEEEEecccceeccCCC-CCcEEEEEEEeCCCCeEEEEEcchhHHHHHhhcccCcEEEEe
Q 008606 112 PARIIPIAALNPYQGRWAIKARVTAKGDLRRYNNARG-DGKVFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLIS 190 (560)
Q Consensus 112 ~~~~~pI~~L~p~~~~w~Ik~RV~~k~~ir~~~n~~g-~gkvf~~~L~D~~g~~I~at~~~~~~~kf~~~l~eG~vY~Is 190 (560)
...++||++|+||+.+|+|+|||+.+|++|.|.+.+| +|++|+++|.| +.|+|++++|++.++. ++.|++|+||.|+
T Consensus 60 ~~~~~~I~dl~p~~~~v~i~arV~~~~~~r~~~~~~G~eGkv~~~~v~D-etG~Ir~t~W~~~~~~-~~~le~G~v~~i~ 137 (637)
T PRK12366 60 EEEDFKISDIEEGQINVEITGRIIEISNIKTFTRKDGSTGKLANITIAD-NTGTIRLTLWNDNAKL-LKGLKEGDVIKIE 137 (637)
T ss_pred ccceeEHHHCcCCCcceEEEEEEEEccCCeEEECCCCCccEEEEEEEEc-CCCEEEEEEEchhhhh-hccCCCCCEEEEe
Confidence 4578999999999999999999999999999998877 89999999999 5559999999999875 6899999999999
Q ss_pred eeEEecCCCccccCCCeeEEEEcccceEEeccC-CCCCCCcccccccCccchhcccCCceeEEEEEEEEecCceeEeecc
Q 008606 191 KGSLKPAQKNFNHLKNEWEIFLEATSTVDLCTE-EDDSIPKQQFSFRHISEIESAENNSIVDVIGIVISVNPSVPILRKN 269 (560)
Q Consensus 191 ~~~V~~a~~~y~~~~~~yeI~f~~~T~I~~~~d-~~~~iP~~~f~f~~i~dI~~~~~~~~VDVIGvV~~V~~~~~i~~k~ 269 (560)
++.++. .++.|+|.++..|+|.++.+ ++..+|...++| +|.+|. .+..|||+|+|++++++.+|++|+
T Consensus 138 ~~~v~~-------~~~~~el~~~~~t~I~~~~~~d~~~i~~~~~~~-~I~el~---~g~~v~v~G~V~~~~~~~~f~rkd 206 (637)
T PRK12366 138 NARSRK-------WNNDVELNSGSETRIDKLEKYDESRYPIIKENY-DIPELE---PNLSATIEGEVTKAYPIKEFTRKD 206 (637)
T ss_pred ccEecc-------cCCceEEEcCCcceEEEccccccccCCcccccc-cccccC---CCCeEEEEEEEEEccCcEEEEEcC
Confidence 999875 35789999999999999863 355688876666 666654 567999999999999999999999
Q ss_pred CceeeEEEEEEecCCCcEEEEEEeCcchhhhhhhHHhhhccCCccEEEEEEEEEecCC-CceecccCCeEEEECCChHHH
Q 008606 270 GMETQRRILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVDVGFFPVLSVKSGKVNDFS-GKSIGTIPSTQLFINPDFAEA 348 (560)
Q Consensus 270 G~~~~kr~i~L~D~Sg~~I~vtLWg~~a~~~~~~l~~~~~~~~~~VV~l~~~rV~~f~-G~sLs~~~~S~i~iNPdipEa 348 (560)
|++..+|++.|.|+|| +|++||||+.|.. ....+++|.|++.++..|+ |..|+.++.+.|....+.
T Consensus 207 g~~~~~r~~~l~D~TG-~irvTlW~~~a~~---------~~~~g~vv~i~g~~~~~~~~~~el~~~~~~~i~~~~~~--- 273 (637)
T PRK12366 207 GSEGKLKSFILKDDTG-SIRVTLWNDLTDI---------EVNKGDIVRVKGYVKQGYRTGLEISANNIEILEKLEKE--- 273 (637)
T ss_pred CCeeEEEEEEEEcCCC-cEEEEEEChhhcc---------cCCCCCEEEEEeEEecCcCCceEEEeCCceeecccccc---
Confidence 9999999999999999 8999999999853 2346899999998888885 458888766655311100
Q ss_pred HHHHHHHhcCCCccceeecccccccCCCccchhhhHHHHhhcCCCCCCCCceEEEEEEEEEEeCCC-eEEeCCCCCcCcc
Q 008606 349 HELREWFDSGGKNAATVSISREIAAGGAKNEIHKTVSQIKNEGLGRSEKPDWVTVRAFITFIKSDS-FCYTACPLMIGDR 427 (560)
Q Consensus 349 ~~L~~w~~~~g~~~~~~sls~~~~~~~~~~~~~ktI~~I~~~~~g~~e~~~~~~v~atI~~I~~d~-~~Y~aC~~~~~~~ 427 (560)
........|++|..- +.+..++++|.|+.+..-. |-
T Consensus 274 ---------------------------~~~~~~~pI~~L~~~-----~~g~~~~I~grV~~~~~~R~f~----------- 310 (637)
T PRK12366 274 ---------------------------EKELEIVNIEELTEF-----EDGEEVDVKGRIIAISDKREVE----------- 310 (637)
T ss_pred ---------------------------ccccCceeHHHCCcc-----cCCCEEEEEEEEEecCCceEEE-----------
Confidence 001123467777532 1234689999998875311 11
Q ss_pred ccCceeeecCCeeecCcCCCccCCceeEEEEEEEEEeCCCeEEEEEehhhhhhhcCC
Q 008606 428 QCNKKVTQSGNRWQCDRCNQEIDECDYRYLLQAQIQDQTGLTWVTAFQESGEEILGC 484 (560)
Q Consensus 428 ~C~KKv~~~~~~~~C~kC~~~~~~~~~rY~l~~~i~D~Tgs~~~~~Fd~~ae~llG~ 484 (560)
.. .-. -...++.|.|.||++.+++|++.|.++.++
T Consensus 311 -------~~--------------~g~-gkv~s~~l~D~tG~IR~t~w~~~~d~~~~l 345 (637)
T PRK12366 311 -------RD--------------DRT-AEVQDIELADGTGRVRVSFWGEKAKILENL 345 (637)
T ss_pred -------cC--------------CCc-EEEEEEEEEcCCCeEEEEEeCchhhhhccc
Confidence 00 011 366789999999999999999998766553
No 9
>PRK07211 replication factor A; Reviewed
Probab=99.98 E-value=1.6e-30 Score=278.01 Aligned_cols=274 Identities=20% Similarity=0.289 Sum_probs=216.8
Q ss_pred cceeccccCCCCCceEEEEEEEEecccceeccC--CCCCcEEEEEEEeCCCCeEEEEEcchhHHHHHhhcccCcEEEEee
Q 008606 114 RIIPIAALNPYQGRWAIKARVTAKGDLRRYNNA--RGDGKVFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISK 191 (560)
Q Consensus 114 ~~~pI~~L~p~~~~w~Ik~RV~~k~~ir~~~n~--~g~gkvf~~~L~D~~g~~I~at~~~~~~~kf~~~l~eG~vY~Is~ 191 (560)
.+.+|++|+|++.+|+|+|||+.|+++|+|+++ +++|++|+++|.| ++|+|++|+|++.+++|++.|++|+||+|.+
T Consensus 52 e~~~I~dL~pg~~~vtI~aRV~~~~~~Rt~~~~~~~~eGkv~~v~l~D-eTG~Ir~TlW~d~ad~~~~~Le~GdV~~I~~ 130 (485)
T PRK07211 52 EVNGIADIEPGMDEVKFLAKVLSIGDLRTFERDGEDEDGRVINVEVAD-ETGSVRVAFWDEQAVAAEEELEVGQVLRIKG 130 (485)
T ss_pred ccccHhhCCCCCCceEEEEEEeEccCceEEEeCCCCCCcEEEEEEEEc-CCCeEEEEEechHhHhhhcccCCCCEEEEec
Confidence 467999999999999999999999999999986 4589999999999 7779999999999999999999999999965
Q ss_pred eEEecCCCccccCCCeeEEEEcccceEEeccCCCCCCCcccccccCccchhcccCCceeEEEEEEEEecCceeEeeccCc
Q 008606 192 GSLKPAQKNFNHLKNEWEIFLEATSTVDLCTEEDDSIPKQQFSFRHISEIESAENNSIVDVIGIVISVNPSVPILRKNGM 271 (560)
Q Consensus 192 ~~V~~a~~~y~~~~~~yeI~f~~~T~I~~~~d~~~~iP~~~f~f~~i~dI~~~~~~~~VDVIGvV~~V~~~~~i~~k~G~ 271 (560)
.++ +.|+.+ ||.|+ .|++|.+. .+|....+|++|++|.. ....+||+|+|+.+++++++.+++|+
T Consensus 131 -~~~---~~ys~~----El~i~---~ve~~~d~--~i~~~~~~~~~I~dL~~--~~~~v~I~grV~~v~~iRtf~r~dGs 195 (485)
T PRK07211 131 -RPK---DGYNGL----EVSVD---KVEPDPDA--EIDVQIGDTYTVEDLSL--GLSDVTLVGVVLDTDSVRTFDRDDGS 195 (485)
T ss_pred -eEe---ccccce----EEEEe---eEEEcccc--cccccccCCccHHHcCC--CCCceEEEEEEEEcCCCeEEECCCCC
Confidence 443 567653 99998 48887643 35544568999999974 56789999999999999999988998
Q ss_pred eeeEEEEEEecCCCcEEEEEEeCcchhhhhhhHHhhhccCCccEEEEEEEEEecCCCc-eecccCCeEEEECCChHHHHH
Q 008606 272 ETQRRILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVDVGFFPVLSVKSGKVNDFSGK-SIGTIPSTQLFINPDFAEAHE 350 (560)
Q Consensus 272 ~~~kr~i~L~D~Sg~~I~vtLWg~~a~~~~~~l~~~~~~~~~~VV~l~~~rV~~f~G~-sLs~~~~S~i~iNPdipEa~~ 350 (560)
+...+++.|.|+|| +|++|||++.|..+ .. ...++||.|++++|++|+|. +|+....|.|..-++ ++.
T Consensus 196 eGkv~sv~L~DeTG-~IR~TlW~d~Ad~~-~~------le~G~Vv~I~~a~Vre~~g~~ELsl~~~s~I~~~~d--ev~- 264 (485)
T PRK07211 196 EGRVSNLTVGDETG-RVRVTLWDDRADLA-EE------LDAGESVEIVDGYVRERDGSLELHVGDRGAVEEVDE--DVE- 264 (485)
T ss_pred eeEEEEEEEEcCCC-eEEEEEechhhhhh-cc------CCCCCEEEEEeeEEEecCCcEEEEECCCceEEECCc--ccc-
Confidence 99999999999999 69999999999875 11 24689999999999999664 899888888875443 110
Q ss_pred HHHHHhcCCCccceeecccccccCCCccchhhhHHHHhhcCCCCCCCCceEEEEEEEEEEeCCCeEEeCCCCCcCccccC
Q 008606 351 LREWFDSGGKNAATVSISREIAAGGAKNEIHKTVSQIKNEGLGRSEKPDWVTVRAFITFIKSDSFCYTACPLMIGDRQCN 430 (560)
Q Consensus 351 L~~w~~~~g~~~~~~sls~~~~~~~~~~~~~ktI~~I~~~~~g~~e~~~~~~v~atI~~I~~d~~~Y~aC~~~~~~~~C~ 430 (560)
+ + + ....|++|. ....+.|.|.|..+..-.-+-.
T Consensus 265 -------------~--v-----p------~~~~I~dl~--------~g~~vdV~GvV~~v~~~rtf~r------------ 298 (485)
T PRK07211 265 -------------Y--V-----P------DTTPIESLE--------IDETVDIAGVVRSADPKRTFDR------------ 298 (485)
T ss_pred -------------c--c-----c------ccccHhhcC--------CCCceeEEEEEEEccCcEEEEc------------
Confidence 0 0 0 012344442 2245788898888753221111
Q ss_pred ceeeecCCeeecCcCCCccCCceeEEEEEEEEEeCCCeEEEEEehhhhh
Q 008606 431 KKVTQSGNRWQCDRCNQEIDECDYRYLLQAQIQDQTGLTWVTAFQESGE 479 (560)
Q Consensus 431 KKv~~~~~~~~C~kC~~~~~~~~~rY~l~~~i~D~Tgs~~~~~Fd~~ae 479 (560)
+++ ....+.++.|.|.||++.+++|++.|+
T Consensus 299 -------------~dG------~~~~vr~l~l~D~TG~IrvTLWg~~A~ 328 (485)
T PRK07211 299 -------------DDG------SEGQVRNVRIQDDTGDIRVALWGEKAD 328 (485)
T ss_pred -------------CCC------CEeEEEEEEEEcCCCcEEEEEeCcccc
Confidence 111 235677999999999999999999984
No 10
>PRK07211 replication factor A; Reviewed
Probab=99.97 E-value=8.7e-30 Score=272.28 Aligned_cols=206 Identities=21% Similarity=0.343 Sum_probs=179.9
Q ss_pred CcceeccccCCCCCceEEEEEEEEecccceeccCCC-CCcEEEEEEEeCCCCeEEEEEcchhHHHHHhhcccCcEEEEee
Q 008606 113 ARIIPIAALNPYQGRWAIKARVTAKGDLRRYNNARG-DGKVFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISK 191 (560)
Q Consensus 113 ~~~~pI~~L~p~~~~w~Ik~RV~~k~~ir~~~n~~g-~gkvf~~~L~D~~g~~I~at~~~~~~~kf~~~l~eG~vY~Is~ 191 (560)
..++||++|+|++..|.|+|||+.++++|.|.+++| +|++++++|.| ++|+|++|+|++.+++| +.|++|+||.|++
T Consensus 159 ~~~~~I~dL~~~~~~v~I~grV~~v~~iRtf~r~dGseGkv~sv~L~D-eTG~IR~TlW~d~Ad~~-~~le~G~Vv~I~~ 236 (485)
T PRK07211 159 GDTYTVEDLSLGLSDVTLVGVVLDTDSVRTFDRDDGSEGRVSNLTVGD-ETGRVRVTLWDDRADLA-EELDAGESVEIVD 236 (485)
T ss_pred cCCccHHHcCCCCCceEEEEEEEEcCCCeEEECCCCCeeEEEEEEEEc-CCCeEEEEEechhhhhh-ccCCCCCEEEEEe
Confidence 378899999999999999999999999999998887 89999999999 55589999999999999 7899999999999
Q ss_pred eEEecCCCccccCCCeeEEEEcccceEEeccCCCCCCCcccccccCccchhcccCCceeEEEEEEEEecCceeEeeccCc
Q 008606 192 GSLKPAQKNFNHLKNEWEIFLEATSTVDLCTEEDDSIPKQQFSFRHISEIESAENNSIVDVIGIVISVNPSVPILRKNGM 271 (560)
Q Consensus 192 ~~V~~a~~~y~~~~~~yeI~f~~~T~I~~~~d~~~~iP~~~f~f~~i~dI~~~~~~~~VDVIGvV~~V~~~~~i~~k~G~ 271 (560)
++|+.. .+.|+|.++..|.|+++.++...+|. +.+|. ++..+..|||+|+|++++++++|.+++|+
T Consensus 237 a~Vre~-------~g~~ELsl~~~s~I~~~~dev~~vp~----~~~I~---dl~~g~~vdV~GvV~~v~~~rtf~r~dG~ 302 (485)
T PRK07211 237 GYVRER-------DGSLELHVGDRGAVEEVDEDVEYVPD----TTPIE---SLEIDETVDIAGVVRSADPKRTFDRDDGS 302 (485)
T ss_pred eEEEec-------CCcEEEEECCCceEEECCcccccccc----cccHh---hcCCCCceeEEEEEEEccCcEEEEcCCCC
Confidence 999875 37899999999999999653233553 24444 44567789999999999999999988999
Q ss_pred eeeEEEEEEecCCCcEEEEEEeCcchhhhhhhHHhhhccCCccEEEEEEEEEecC--CCceecccCCeEEEECCC
Q 008606 272 ETQRRILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVDVGFFPVLSVKSGKVNDF--SGKSIGTIPSTQLFINPD 344 (560)
Q Consensus 272 ~~~kr~i~L~D~Sg~~I~vtLWg~~a~~~~~~l~~~~~~~~~~VV~l~~~rV~~f--~G~sLs~~~~S~i~iNPd 344 (560)
+..+|++.|.|+|| +|++||||+.|.. +...+++|+|++++|++| +|++||+..+|.|.+=.+
T Consensus 303 ~~~vr~l~l~D~TG-~IrvTLWg~~A~~---------~i~~GdvV~Ikg~~V~dg~~ggleLS~g~~s~i~~~~~ 367 (485)
T PRK07211 303 EGQVRNVRIQDDTG-DIRVALWGEKADL---------DIGPGDEVVAADVEIQDGWQDDLEASAGWQSTVVVLDD 367 (485)
T ss_pred EeEEEEEEEEcCCC-cEEEEEeCccccC---------CCCCCCEEEEEccEEEecCCCCEEEEecCCceEEEccc
Confidence 99999999999999 8999999999842 345789999999999997 688999998888766444
No 11
>PRK15491 replication factor A; Provisional
Probab=99.97 E-value=9.7e-29 Score=260.30 Aligned_cols=276 Identities=20% Similarity=0.293 Sum_probs=216.2
Q ss_pred CcceeccccCCCCCceEEEEEEEEecccceeccCCC-CCcEEEEEEEeCCCCeEEEEEcchhHHHHH-hhcccCcEEEEe
Q 008606 113 ARIIPIAALNPYQGRWAIKARVTAKGDLRRYNNARG-DGKVFSFDLLDSDGGEIRVTCFNAVVDRFY-EIIEVGRVYLIS 190 (560)
Q Consensus 113 ~~~~pI~~L~p~~~~w~Ik~RV~~k~~ir~~~n~~g-~gkvf~~~L~D~~g~~I~at~~~~~~~kf~-~~l~eG~vY~Is 190 (560)
..+++|++|+|++.+|+|+|||+.++++|+|.+.+| +|++++++|.| +.|+|++|+|++.+++|+ +.|++|+||.|+
T Consensus 55 ~~~~kI~dL~~~~~~v~i~arVl~~~~~R~f~r~dGs~g~v~~~~v~D-eTG~ir~tlW~~~a~~~~~~~le~G~v~~I~ 133 (374)
T PRK15491 55 VDTTKIADINESSSNVNFTAKVVSIFEPKEFNRNDGTTGRVGNIIVAD-ETGSIRLTLWDDLADLIKTGDIEVGKSLNIS 133 (374)
T ss_pred cccccHHHCCCCCCceEEEEEEeeccCCeeeecCCCCceEEEEEEEEc-CCCeEEEEEECchhhhhccCCcCCCCEEEEe
Confidence 478899999999999999999999999999999888 89999999999 777999999999999998 689999999998
Q ss_pred eeEEecCCCccccCCCeeEEEEcccceEEeccCCCCCCCcccccccCccchhcccCCceeEEEEEEEEecCceeEeeccC
Q 008606 191 KGSLKPAQKNFNHLKNEWEIFLEATSTVDLCTEEDDSIPKQQFSFRHISEIESAENNSIVDVIGIVISVNPSVPILRKNG 270 (560)
Q Consensus 191 ~~~V~~a~~~y~~~~~~yeI~f~~~T~I~~~~d~~~~iP~~~f~f~~i~dI~~~~~~~~VDVIGvV~~V~~~~~i~~k~G 270 (560)
++ +++.|+. .||.+++.|.|.++.++ + ...|+|++|+||.. .+..|||.|+|+.+++++++++++|
T Consensus 134 ~~----~~~~y~g----~Ei~i~~~~~i~~~~~~---~-~~~~~~~~I~dl~~--~~~~V~I~g~V~~~~~~r~~~~~~G 199 (374)
T PRK15491 134 GY----AKEGYSG----IEVNIGRYGGISESDEN---V-KASINSQKISDIKD--GDSDINIVGKVLDISDVRTFQKKDG 199 (374)
T ss_pred ee----eccCccc----EEEEeCCCceeeecccc---c-ccccCcccHHHcCC--CCccEEEEEEEEEccCceEEEecCC
Confidence 75 4556644 69999999999998532 2 24578999999975 3456999999999999999999899
Q ss_pred ceeeEEEEEEecCCCcEEEEEEeCcchhhhhhhHHhhhccCCccEEEEEEE--EEecCCCc-eecccCCeEEEECCChHH
Q 008606 271 METQRRILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVDVGFFPVLSVKSG--KVNDFSGK-SIGTIPSTQLFINPDFAE 347 (560)
Q Consensus 271 ~~~~kr~i~L~D~Sg~~I~vtLWg~~a~~~~~~l~~~~~~~~~~VV~l~~~--rV~~f~G~-sLs~~~~S~i~iNPdipE 347 (560)
+....+++.|.|+|| .|++|||++.|..+ .. + ..+.+|-+.++ |.+.|+|. .|+....|.|....+.++
T Consensus 200 ~~~~v~~~~l~DetG-~Ir~t~W~~~a~~~-~~----l--~~Gd~V~i~~~~~r~~~~~g~~El~~~~~s~I~~~~~~~e 271 (374)
T PRK15491 200 SQGRVRNITIGDETG-KIRVTLWDGKTDLA-DK----L--ENGDSVEIINGYARTNNYSQEVEIQIGNHGSLRKTDRNVE 271 (374)
T ss_pred CeEEEEEEEEECCCC-eEEEEEecchhccc-cc----C--CCCCEEEEEeceEEEeccCCCEEEEeCCCceEEECCcccc
Confidence 988999999999999 69999999998764 11 2 35778888776 45568786 788877787764322111
Q ss_pred HHHHHHHHhcCCCccceeecccccccCCCccchhhhHHHHhhcCCCCCCCCceEEEEEEEEEEeCCC-eEEeCCCCCcCc
Q 008606 348 AHELREWFDSGGKNAATVSISREIAAGGAKNEIHKTVSQIKNEGLGRSEKPDWVTVRAFITFIKSDS-FCYTACPLMIGD 426 (560)
Q Consensus 348 a~~L~~w~~~~g~~~~~~sls~~~~~~~~~~~~~ktI~~I~~~~~g~~e~~~~~~v~atI~~I~~d~-~~Y~aC~~~~~~ 426 (560)
+ ......|++|... ..+.|.|.|..+..-. +- .
T Consensus 272 ~-----------------------------~~~f~~I~dl~~~--------~~~dv~G~V~~v~~~~~~~--~------- 305 (374)
T PRK15491 272 Y-----------------------------EEDFTPIADIIPG--------QPYSIKGAVSGLGDLKEFT--K------- 305 (374)
T ss_pred c-----------------------------CCCccCHHHcCCC--------CceeEEEEEEEcCCcEEEE--c-------
Confidence 1 1123347777431 2467888887774211 10 0
Q ss_pred cccCceeeecCCeeecCcCCCccCCceeEEEEEEEEEeCCCeEEEEEehhhhhh
Q 008606 427 RQCNKKVTQSGNRWQCDRCNQEIDECDYRYLLQAQIQDQTGLTWVTAFQESGEE 480 (560)
Q Consensus 427 ~~C~KKv~~~~~~~~C~kC~~~~~~~~~rY~l~~~i~D~Tgs~~~~~Fd~~ae~ 480 (560)
. .-....+=++.|.|.||.+.+++|++.|+.
T Consensus 306 --------~---------------~G~~~~~r~i~l~D~Tg~Ir~tlWg~~a~~ 336 (374)
T PRK15491 306 --------S---------------DGSENKVSNIYVSDDTGRIRIALWGEKAEL 336 (374)
T ss_pred --------c---------------CCCEeEEEeEEEEeCCCcEEEEEccccccc
Confidence 0 122345558999999999999999999974
No 12
>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=99.95 E-value=4.7e-28 Score=211.30 Aligned_cols=104 Identities=61% Similarity=1.062 Sum_probs=101.0
Q ss_pred eccccCCCCCceEEEEEEEEecccceeccCCCCCcEEEEEEEeCCCCeEEEEEcchhHHHHHhhcccCcEEEEeeeEEec
Q 008606 117 PIAALNPYQGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISKGSLKP 196 (560)
Q Consensus 117 pI~~L~p~~~~w~Ik~RV~~k~~ir~~~n~~g~gkvf~~~L~D~~g~~I~at~~~~~~~kf~~~l~eG~vY~Is~~~V~~ 196 (560)
||++|+|++.+|+|+|||++||++|.|.+.+++|++|+|+|+|++|++|+|++|++++++|++.|++|+||+|++|+|++
T Consensus 1 pI~~L~p~~~~~~I~~rV~~k~~~~~f~~~~~~g~~~~~~l~De~~~~I~~t~~~~~~~~f~~~l~eG~vy~i~~~~V~~ 80 (104)
T cd04474 1 PISSLNPYQNKWTIKARVTNKSDIRTWSNARGEGKLFSFDLLDEDGGEIRATFFNDAVDKFYDLLEVGKVYYISKGSVKV 80 (104)
T ss_pred ChhHccCCCCcEEEEEEEeeccccccccCCCCCcEEEEEEEEECCCCEEEEEEehHHHHHhhcccccccEEEEeccEEee
Confidence 79999999999999999999999999999888999999999999999999999999999999999999999999999999
Q ss_pred CCCccccCCCeeEEEEcccceEEe
Q 008606 197 AQKNFNHLKNEWEIFLEATSTVDL 220 (560)
Q Consensus 197 a~~~y~~~~~~yeI~f~~~T~I~~ 220 (560)
|+++|++++|+|||.|+.+|.|++
T Consensus 81 a~~~y~~~~~~yeI~f~~~t~~~~ 104 (104)
T cd04474 81 ANKKFNTLKNDYEITFNRDTSIIE 104 (104)
T ss_pred ccccCCCCCCcEEEEECCCcEEeC
Confidence 999999999999999999988864
No 13
>PRK14699 replication factor A; Provisional
Probab=99.95 E-value=1.3e-26 Score=250.55 Aligned_cols=207 Identities=21% Similarity=0.310 Sum_probs=178.7
Q ss_pred CcceeccccCCCCCceEEEEEEEEecccceeccCCC-CCcEEEEEEEeCCCCeEEEEEcchhHHHHHhhcccCcEEEEee
Q 008606 113 ARIIPIAALNPYQGRWAIKARVTAKGDLRRYNNARG-DGKVFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISK 191 (560)
Q Consensus 113 ~~~~pI~~L~p~~~~w~Ik~RV~~k~~ir~~~n~~g-~gkvf~~~L~D~~g~~I~at~~~~~~~kf~~~l~eG~vY~Is~ 191 (560)
..++||++|+|++.+|+|+|||+.++++|.|.+++| +|+++++.|.|+ .|+|++|+|++.+ .|++.|++|++..+.+
T Consensus 274 ~~~~~I~~L~~~~~~v~I~grV~~~~~~r~~~~~~Gseg~v~~~~l~De-TG~Ir~T~W~~~a-~~~~~i~~Gd~v~i~~ 351 (484)
T PRK14699 274 EEFTPIEDIKADMNNINISGRVLDISEVRTFEKKDGSPGRVGNLLLGDS-TGKIRLTLWDEKT-NFLDEIDFDETVEVLN 351 (484)
T ss_pred ccccCHHHcCCCCceeEEEEEEEEcCCCeEEEcCCCCeeEEEEEEEECC-CCeEEEEEeCccc-ccccccCCCceEEEEe
Confidence 467899999999999999999999999999998887 899999999995 5589999999999 7888899999988888
Q ss_pred eEEecCCCccccCCCeeEEEEcccceEEeccCCCCCCCcccccccCccchhcccCCceeEEEEEEEEecCceeEeeccCc
Q 008606 192 GSLKPAQKNFNHLKNEWEIFLEATSTVDLCTEEDDSIPKQQFSFRHISEIESAENNSIVDVIGIVISVNPSVPILRKNGM 271 (560)
Q Consensus 192 ~~V~~a~~~y~~~~~~yeI~f~~~T~I~~~~d~~~~iP~~~f~f~~i~dI~~~~~~~~VDVIGvV~~V~~~~~i~~k~G~ 271 (560)
+.++ ++..+++|+|.|+..|.|.++.++ . .+.++|++|++|. .+..|||+|+|+++++..+|.+++|+
T Consensus 352 ~y~~-----~~~~~~~~eL~~~~~t~I~~~~~~-~---e~~~~~~~I~die---~~~~vdV~G~V~~v~~~~~~~~~~g~ 419 (484)
T PRK14699 352 AYSR-----ENTFSQQVELNLGARGIIQKSEKK-V---EYREKFTDIADII---PGESYSVQGKVSEIGELREFEREDGT 419 (484)
T ss_pred EEEE-----eccCCccEEEEecCceeEeecCCc-c---eeeeccccHHHcc---CCCeeEEEEEEEEcCCcceEEecCCC
Confidence 8765 666788999999999999998643 2 4568999999994 57899999999999999999999999
Q ss_pred eeeEEEEEEecCCCcEEEEEEeCcchhhhhhhHHhhhccCCccEEEEEEEEEec-CCCc-eecccCCeEEEE
Q 008606 272 ETQRRILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVDVGFFPVLSVKSGKVND-FSGK-SIGTIPSTQLFI 341 (560)
Q Consensus 272 ~~~kr~i~L~D~Sg~~I~vtLWg~~a~~~~~~l~~~~~~~~~~VV~l~~~rV~~-f~G~-sLs~~~~S~i~i 341 (560)
+..+|+++|.|.|| +|+|||||+.|..+ +.+ +.+.-|.+.++.+.. |+|. .||...+|+|.+
T Consensus 420 ~~~vr~i~l~D~TG-~Ir~tlWg~~A~~~-----~~~--~~~~~v~~~~~~~~~g~~~~~e~s~g~~s~~~~ 483 (484)
T PRK14699 420 ENVVANLQLKDETG-SIRLTLWGEQAYVI-----EDL--DIDSEIQIIDAYARYGLNEEIELSVGNRSRVII 483 (484)
T ss_pred EEEEEEEEEEcCCC-eEEEEEcchhhhhc-----ccc--CCCCeEEEechhhhhcccccEEEEecCceEEEe
Confidence 99999999999999 99999999999863 112 345667777777764 6664 799998888864
No 14
>PRK15491 replication factor A; Provisional
Probab=99.94 E-value=5.8e-26 Score=239.30 Aligned_cols=207 Identities=17% Similarity=0.283 Sum_probs=175.1
Q ss_pred CcceeccccCCCCCceEEEEEEEEecccceeccCCCC-CcEEEEEEEeCCCCeEEEEEcchhHHHHHhhcccCcEEEEee
Q 008606 113 ARIIPIAALNPYQGRWAIKARVTAKGDLRRYNNARGD-GKVFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISK 191 (560)
Q Consensus 113 ~~~~pI~~L~p~~~~w~Ik~RV~~k~~ir~~~n~~g~-gkvf~~~L~D~~g~~I~at~~~~~~~kf~~~l~eG~vY~Is~ 191 (560)
.++.+|++|.++...+.|+|||+.++++|.|.+++|. ++++++.|.|+ +|+|++|+|++.|++| +.|++|++|+|.+
T Consensus 164 ~~~~~I~dl~~~~~~V~I~g~V~~~~~~r~~~~~~G~~~~v~~~~l~De-tG~Ir~t~W~~~a~~~-~~l~~Gd~V~i~~ 241 (374)
T PRK15491 164 INSQKISDIKDGDSDINIVGKVLDISDVRTFQKKDGSQGRVRNITIGDE-TGKIRVTLWDGKTDLA-DKLENGDSVEIIN 241 (374)
T ss_pred cCcccHHHcCCCCccEEEEEEEEEccCceEEEecCCCeEEEEEEEEECC-CCeEEEEEecchhccc-ccCCCCCEEEEEe
Confidence 3567999999999999999999999999999987774 79999999995 5589999999999998 7799999999999
Q ss_pred eEEecCCCccccCCCeeEEEEcccceEEeccCCCCCCCcccccccCccchhcccCCceeEEEEEEEEecCceeEeeccCc
Q 008606 192 GSLKPAQKNFNHLKNEWEIFLEATSTVDLCTEEDDSIPKQQFSFRHISEIESAENNSIVDVIGIVISVNPSVPILRKNGM 271 (560)
Q Consensus 192 ~~V~~a~~~y~~~~~~yeI~f~~~T~I~~~~d~~~~iP~~~f~f~~i~dI~~~~~~~~VDVIGvV~~V~~~~~i~~k~G~ 271 (560)
+.++ ++..+|.|||.|...|.|.++.+ .. ...++|++|+||.. +..+||+|+|++++++.+|++++|+
T Consensus 242 ~~~r-----~~~~~g~~El~~~~~s~I~~~~~-~~---e~~~~f~~I~dl~~---~~~~dv~G~V~~v~~~~~~~~~~G~ 309 (374)
T PRK15491 242 GYAR-----TNNYSQEVEIQIGNHGSLRKTDR-NV---EYEEDFTPIADIIP---GQPYSIKGAVSGLGDLKEFTKSDGS 309 (374)
T ss_pred ceEE-----EeccCCCEEEEeCCCceEEECCc-cc---ccCCCccCHHHcCC---CCceeEEEEEEEcCCcEEEEccCCC
Confidence 9886 34457899999999999999853 22 45579999999974 5679999999999999999999999
Q ss_pred eeeEEEEEEecCCCcEEEEEEeCcchhhhhhhHHhhhccCCccEEEEEEEEEec-CCC-ceecccCCeEEEE
Q 008606 272 ETQRRILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVDVGFFPVLSVKSGKVND-FSG-KSIGTIPSTQLFI 341 (560)
Q Consensus 272 ~~~kr~i~L~D~Sg~~I~vtLWg~~a~~~~~~l~~~~~~~~~~VV~l~~~rV~~-f~G-~sLs~~~~S~i~i 341 (560)
+..+|+|+|.|+|| +|++||||+.|... ... ..+..|.+.++.+++ |+| ..||.+..|+|.+
T Consensus 310 ~~~~r~i~l~D~Tg-~Ir~tlWg~~a~~~-----~~~--~~g~~i~i~~~~~k~g~~~~~e~s~g~~s~~~~ 373 (374)
T PRK15491 310 ENKVSNIYVSDDTG-RIRIALWGEKAELV-----DKL--DIDTPIKIIDAFSKSGYNEDVELSAGNRSRVVV 373 (374)
T ss_pred EeEEEeEEEEeCCC-cEEEEEcccccccc-----ccc--CCCCeEEEEEEEEeecCCCcEEEEeCCcceEEe
Confidence 99999999999999 59999999998741 111 234556677777775 655 4899999998865
No 15
>PRK14699 replication factor A; Provisional
Probab=99.91 E-value=2.5e-22 Score=217.32 Aligned_cols=279 Identities=19% Similarity=0.260 Sum_probs=216.4
Q ss_pred cceeccccCCCCCceEEEEEEEEecccceeccCCC-CCcEEEEEEEeCCCCeEEEEEcchhHHHHHhhcccCcEEEEeee
Q 008606 114 RIIPIAALNPYQGRWAIKARVTAKGDLRRYNNARG-DGKVFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISKG 192 (560)
Q Consensus 114 ~~~pI~~L~p~~~~w~Ik~RV~~k~~ir~~~n~~g-~gkvf~~~L~D~~g~~I~at~~~~~~~kf~~~l~eG~vY~Is~~ 192 (560)
....|++|.|.+...+|+|||+.++++|.|....| +|++++++|.| ++|+|++++|++.++ +.+.|++|++|.|.++
T Consensus 165 ~~~~I~dL~~~~~~V~i~gkVl~~~~~R~f~~~dG~~g~v~~~~igD-eTG~ir~tlW~~~a~-~~~~l~~Gd~v~I~~a 242 (484)
T PRK14699 165 NSQKIKDIKDGMGDLNLTGKVLEISEIRTFQRKDGTSGKVGNLLLGD-ETGTLRVTLWDDKTD-FLNQIEYGDTVELINA 242 (484)
T ss_pred CCcchhhcCCCCCceEEEEEEEeccCceEEecCCCCceEEEEEEEEc-CCceEEEEEECcccc-cccccCCCCEEEEecc
Confidence 34689999999988899999999999999998777 78999999999 777999999999885 8888999999999999
Q ss_pred EEecCCCccccCCCeeEEEEcccceEEeccCCCCCCCcccccccCccchhcccCCceeEEEEEEEEecCceeEeeccCce
Q 008606 193 SLKPAQKNFNHLKNEWEIFLEATSTVDLCTEEDDSIPKQQFSFRHISEIESAENNSIVDVIGIVISVNPSVPILRKNGME 272 (560)
Q Consensus 193 ~V~~a~~~y~~~~~~yeI~f~~~T~I~~~~d~~~~iP~~~f~f~~i~dI~~~~~~~~VDVIGvV~~V~~~~~i~~k~G~~ 272 (560)
.++.. .|+ +.++|.++..|.|....+ ...++ ..+++|++|.. ....++|.|.|+++++++++++++|++
T Consensus 243 ~vr~~--~~~---~~~el~~~~~s~i~~~~~-~~e~~---~~~~~I~~L~~--~~~~v~I~grV~~~~~~r~~~~~~Gse 311 (484)
T PRK14699 243 YAREN--AFT---QKVELQVGNRSIIRKSEK-KVEYE---EEFTPIEDIKA--DMNNINISGRVLDISEVRTFEKKDGSP 311 (484)
T ss_pred eEeec--ccC---CceEEEecCceEeecccc-ccccc---ccccCHHHcCC--CCceeEEEEEEEEcCCCeEEEcCCCCe
Confidence 88763 333 689999999998888743 33333 36788888864 467899999999999999999889988
Q ss_pred eeEEEEEEecCCCcEEEEEEeCcchhhhhhhHHhhhccCCccEEEEEEEEEec--CCCc-eecccCCeEEEECCChHHHH
Q 008606 273 TQRRILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVDVGFFPVLSVKSGKVND--FSGK-SIGTIPSTQLFINPDFAEAH 349 (560)
Q Consensus 273 ~~kr~i~L~D~Sg~~I~vtLWg~~a~~~~~~l~~~~~~~~~~VV~l~~~rV~~--f~G~-sLs~~~~S~i~iNPdipEa~ 349 (560)
...+++.|.|.|| .|++|||++.|..+ . .+ ..+.++-+.++.+++ |++. .|+....|.|...++-.|.
T Consensus 312 g~v~~~~l~DeTG-~Ir~T~W~~~a~~~-~----~i--~~Gd~v~i~~~y~~~~~~~~~~eL~~~~~t~I~~~~~~~e~- 382 (484)
T PRK14699 312 GRVGNLLLGDSTG-KIRLTLWDEKTNFL-D----EI--DFDETVEVLNAYSRENTFSQQVELNLGARGIIQKSEKKVEY- 382 (484)
T ss_pred eEEEEEEEECCCC-eEEEEEeCcccccc-c----cc--CCCceEEEEeEEEEeccCCccEEEEecCceeEeecCCccee-
Confidence 9999999999999 79999999998432 1 11 346678888888774 5565 6888877866554432211
Q ss_pred HHHHHHhcCCCccceeecccccccCCCccchhhhHHHHhhcCCCCCCCCceEEEEEEEEEEeCCCeEEeCCCCCcCcccc
Q 008606 350 ELREWFDSGGKNAATVSISREIAAGGAKNEIHKTVSQIKNEGLGRSEKPDWVTVRAFITFIKSDSFCYTACPLMIGDRQC 429 (560)
Q Consensus 350 ~L~~w~~~~g~~~~~~sls~~~~~~~~~~~~~ktI~~I~~~~~g~~e~~~~~~v~atI~~I~~d~~~Y~aC~~~~~~~~C 429 (560)
...+..|++|.. ...+.|.|+|..+..-.
T Consensus 383 ----------------------------~~~~~~I~die~--------~~~vdV~G~V~~v~~~~--------------- 411 (484)
T PRK14699 383 ----------------------------REKFTDIADIIP--------GESYSVQGKVSEIGELR--------------- 411 (484)
T ss_pred ----------------------------eeccccHHHccC--------CCeeEEEEEEEEcCCcc---------------
Confidence 123456888832 24678999999886311
Q ss_pred CceeeecCCeeecCcCCCccCCceeEEEEEEEEEeCCCeEEEEEehhhhhhh
Q 008606 430 NKKVTQSGNRWQCDRCNQEIDECDYRYLLQAQIQDQTGLTWVTAFQESGEEI 481 (560)
Q Consensus 430 ~KKv~~~~~~~~C~kC~~~~~~~~~rY~l~~~i~D~Tgs~~~~~Fd~~ae~l 481 (560)
.-...+ -....+-++.|.|.||++.+++||+.|+++
T Consensus 412 -~~~~~~---------------g~~~~vr~i~l~D~TG~Ir~tlWg~~A~~~ 447 (484)
T PRK14699 412 -EFERED---------------GTENVVANLQLKDETGSIRLTLWGEQAYVI 447 (484)
T ss_pred -eEEecC---------------CCEEEEEEEEEEcCCCeEEEEEcchhhhhc
Confidence 111111 134566699999999999999999999854
No 16
>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=99.86 E-value=2e-21 Score=168.62 Aligned_cols=100 Identities=49% Similarity=0.782 Sum_probs=92.7
Q ss_pred eeEEEEEEEEecCceeEeecc-CceeeEEEEEEecCCCcEEEEEEeCcchhhhhhhHHhhhccCCccEEEEEEEEEecCC
Q 008606 249 IVDVIGIVISVNPSVPILRKN-GMETQRRILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVDVGFFPVLSVKSGKVNDFS 327 (560)
Q Consensus 249 ~VDVIGvV~~V~~~~~i~~k~-G~~~~kr~i~L~D~Sg~~I~vtLWg~~a~~~~~~l~~~~~~~~~~VV~l~~~rV~~f~ 327 (560)
+|||+|+|++|+++++|++|+ |++..+|+|.|.|+|+.+++|||||++|..+.. ..++||+|+++|+++|+
T Consensus 1 ~vDvig~V~~v~~~~~i~~k~~g~~~~~r~v~i~D~t~~~i~vtLWg~~a~~~~~--------~~~~vv~~~~~~i~~~~ 72 (101)
T cd04475 1 IVDVIGVVKSVGPVTTITTKSTGRELDKREITLVDESGHSVELTLWGEQAELFDG--------SENPVIAIKGVKVSEFN 72 (101)
T ss_pred CEeEEEEEeEccCcEEEEEecCCCceeEEEEEEEeCCCCEEEEEEEHHHhhhccc--------CCCCEEEEEeeEEEecC
Confidence 589999999999999999997 999999999999999999999999999987422 23799999999999999
Q ss_pred CceecccCCeEEEECCChHHHHHHHHHHh
Q 008606 328 GKSIGTIPSTQLFINPDFAEAHELREWFD 356 (560)
Q Consensus 328 G~sLs~~~~S~i~iNPdipEa~~L~~w~~ 356 (560)
|++|++..+|+|++||++||+.+|+.||.
T Consensus 73 ~~~l~~~~~s~i~~np~~~e~~~l~~w~~ 101 (101)
T cd04475 73 GKSLSTGSSSTIIINPDIPEAHKLRGWYD 101 (101)
T ss_pred CeEEeecCceeEEECCCcHHHHHHHHhhC
Confidence 99999999999999999999999999984
No 17
>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=99.82 E-value=8.2e-20 Score=159.99 Aligned_cols=101 Identities=27% Similarity=0.500 Sum_probs=91.3
Q ss_pred EEEEEEEEecCceeEeeccCceeeEEEEEEecCCCcEEEEEEeCcchhhhhhhHHhhhccCCccEEEEE-EEEEecCCC-
Q 008606 251 DVIGIVISVNPSVPILRKNGMETQRRILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVDVGFFPVLSVK-SGKVNDFSG- 328 (560)
Q Consensus 251 DVIGvV~~V~~~~~i~~k~G~~~~kr~i~L~D~Sg~~I~vtLWg~~a~~~~~~l~~~~~~~~~~VV~l~-~~rV~~f~G- 328 (560)
||||+|++|+++.+++++ |++..+|+|+|+|.++.+++|||||++|..|...+.. ....+||||+. ++||++|+|
T Consensus 1 DviG~i~~v~~~~~~~~~-~~~~~kr~~~i~D~~~~~l~~tlwG~~A~~f~~~~~~--~~~~~~VVav~~~~rV~~~~g~ 77 (106)
T cd04481 1 DVIGVIVDVGPLEELPPV-NKPSRKLDFEIRDLSDERLKCTLWGEYAEEFDAKFQS--AGNGEPVVAVLRFWKIKEYKGP 77 (106)
T ss_pred CeeEEEEEecceEecccC-CccceEEEEEEEeCCCCEEEEEEEHHHHHHHHHHHHH--hCCCCcEEEEEEeEEEEEEcCC
Confidence 899999999999999888 8889999999999999999999999999999877654 24678999875 599999997
Q ss_pred ceeccc-CCeEEEECCChHHHHHHHHH
Q 008606 329 KSIGTI-PSTQLFINPDFAEAHELREW 354 (560)
Q Consensus 329 ~sLs~~-~~S~i~iNPdipEa~~L~~w 354 (560)
++|++. ++|++++||++||+.+|+..
T Consensus 78 ~~ls~~~~~s~v~inp~ipe~~~~~~~ 104 (106)
T cd04481 78 KSLSNSFGASKVYINPDIPEVPEIKMS 104 (106)
T ss_pred cEEEcCCCceEEEECCCcHHHHHHHhh
Confidence 689988 99999999999999999864
No 18
>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=99.78 E-value=7.1e-19 Score=148.17 Aligned_cols=86 Identities=21% Similarity=0.340 Sum_probs=80.5
Q ss_pred EEEEEEEEecccceeccCCCCCcEEEEEEEeCCCCeEEEEEcchhHHHHHhhcccCcEEEEeeeEEecCCCccccCCCee
Q 008606 129 AIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISKGSLKPAQKNFNHLKNEW 208 (560)
Q Consensus 129 ~Ik~RV~~k~~ir~~~n~~g~gkvf~~~L~D~~g~~I~at~~~~~~~kf~~~l~eG~vY~Is~~~V~~a~~~y~~~~~~y 208 (560)
+|+|||+|+|+.+... ++..++|+|+|++|++|+|+++.+++++|++.|+||+||.|++|.|.++++.|++++|+|
T Consensus 1 ~I~Vrv~r~W~~~~~~----~~~~~~miL~De~G~~I~a~i~~~~~~~f~~~L~eg~vy~is~f~v~~~~~~y~~~~~~y 76 (86)
T cd04480 1 KICVRVLRLWDVYNNA----SGESLEMVLVDEKGNRIHATIPKRLAAKFRPLLKEGKWYTISNFEVAPNTGSYRPTDHPY 76 (86)
T ss_pred CEEEEEEEEEcCcCCC----CCcEEEEEEEcCCCCEEEEEECHHHHHhhhhhceeCCEEEEeeEEEEcCCCcccccCCcE
Confidence 5899999999976532 678999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEEcccceE
Q 008606 209 EIFLEATSTV 218 (560)
Q Consensus 209 eI~f~~~T~I 218 (560)
+|.|..+|+|
T Consensus 77 ~I~f~~~T~V 86 (86)
T cd04480 77 KIKFMSDTVV 86 (86)
T ss_pred EEEeecCcCC
Confidence 9999998865
No 19
>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=99.67 E-value=2.2e-16 Score=135.53 Aligned_cols=87 Identities=23% Similarity=0.391 Sum_probs=80.6
Q ss_pred EEEEEeCCCCeEEEEEcchhHHHHHhhcccCcEEEEeeeEEecCCCccccCCCeeEEEEcccceEEeccCCCCCCCcccc
Q 008606 154 SFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISKGSLKPAQKNFNHLKNEWEIFLEATSTVDLCTEEDDSIPKQQF 233 (560)
Q Consensus 154 ~~~L~D~~g~~I~at~~~~~~~kf~~~l~eG~vY~Is~~~V~~a~~~y~~~~~~yeI~f~~~T~I~~~~d~~~~iP~~~f 233 (560)
+|+|+|++|++|+|+++.+++++|.+.|+||+||.|++|.|.++.+.|++++|+|+|.|..+|.|+++.+ ....+ .|
T Consensus 1 emvL~De~G~~I~A~I~~~~~~~f~~~l~Eg~~y~i~~F~V~~~~~~yr~t~h~y~I~f~~~T~V~~~~~-~~~~~--~~ 77 (95)
T PF02721_consen 1 EMVLVDEKGDKIQATIPKELVDKFKDSLKEGSWYTISNFTVSPNSGSYRPTDHKYKINFMPNTKVTEIDP-PSDPP--FF 77 (95)
T ss_pred CEEEEecCCCEEEEEECHHHHHHHHhhcccCCEEEeEeEEEEeCCCceeccCCCEEEEECCcCeEEECCC-CCCCc--eE
Confidence 4799999999999999999999999999999999999999999999999999999999999999999953 33333 79
Q ss_pred cccCccchhc
Q 008606 234 SFRHISEIES 243 (560)
Q Consensus 234 ~f~~i~dI~~ 243 (560)
+|++|++|.+
T Consensus 78 ~f~~F~~I~~ 87 (95)
T PF02721_consen 78 NFTPFDEILE 87 (95)
T ss_pred eecCHHHHhc
Confidence 9999999986
No 20
>PRK07217 replication factor A; Reviewed
Probab=99.62 E-value=9.4e-14 Score=140.57 Aligned_cols=210 Identities=17% Similarity=0.211 Sum_probs=160.1
Q ss_pred cccCccchhcccCCceeEEEEEEEEecCceeEeeccCceeeEEEEEEecCCCcEEEEEEeCcchhhhhhhHHhhhccCCc
Q 008606 234 SFRHISEIESAENNSIVDVIGIVISVNPSVPILRKNGMETQRRILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVDVGFF 313 (560)
Q Consensus 234 ~f~~i~dI~~~~~~~~VDVIGvV~~V~~~~~i~~k~G~~~~kr~i~L~D~Sg~~I~vtLWg~~a~~~~~~l~~~~~~~~~ 313 (560)
..++|.||.. .+.-|+|.|.|+++.+.. .+.. .+.=.|.|+|| +|++|+|++.... ....+
T Consensus 71 ~~~kI~Di~~--~~~~VsV~aKVl~l~e~~-----~~si--~qvGllgDETG-~IkfT~W~~s~~~---------~leeG 131 (311)
T PRK07217 71 ELVNIADIDE--PEQWVDVTAKVVQLWEPS-----SDSI--AQVGLLGDETG-TIKFTKWAKSDLP---------ELEEG 131 (311)
T ss_pred CceeeeecCC--CCCcEEEEEEEEEecCCC-----CCce--EEEEEEEcCCc-eEEEEEccCCCCC---------cccCC
Confidence 3556777653 577899999999998754 2222 23336999999 8999999973211 12468
Q ss_pred cEEEEEEEEEecCCCc-eecccCCeEEEECCChHHHHHHHHHHhcCCCccceeecccccccCCCccchhhhHHHHhhcCC
Q 008606 314 PVLSVKSGKVNDFSGK-SIGTIPSTQLFINPDFAEAHELREWFDSGGKNAATVSISREIAAGGAKNEIHKTVSQIKNEGL 392 (560)
Q Consensus 314 ~VV~l~~~rV~~f~G~-sLs~~~~S~i~iNPdipEa~~L~~w~~~~g~~~~~~sls~~~~~~~~~~~~~ktI~~I~~~~~ 392 (560)
.++-|.++.+++|+|+ +|+.+..|+|...++.-+ +.+
T Consensus 132 d~~rI~na~v~ey~G~~~lnlg~~t~I~~~de~Ie---------------------------------------V~~--- 169 (311)
T PRK07217 132 KSYLLKNVVTDEYQGRFSVKLNRTTSIEELDEDIE---------------------------------------VGD--- 169 (311)
T ss_pred CEEEEEeEEEeeECCEEEEEeCCceEEEeCCCCcc---------------------------------------ccC---
Confidence 9999999999999997 899888888876543100 000
Q ss_pred CCCCCCceEEEEEEEEEEeCCCeEEeCCCCCcCccccCceeeecCCeeecCcCCCccCCceeEEEEEEEEEeCCCeEEEE
Q 008606 393 GRSEKPDWVTVRAFITFIKSDSFCYTACPLMIGDRQCNKKVTQSGNRWQCDRCNQEIDECDYRYLLQAQIQDQTGLTWVT 472 (560)
Q Consensus 393 g~~e~~~~~~v~atI~~I~~d~~~Y~aC~~~~~~~~C~KKv~~~~~~~~C~kC~~~~~~~~~rY~l~~~i~D~Tgs~~~~ 472 (560)
.-..+.|.|..|...+-....||.+ .|+|.+.. ..|+.|++. .+.+-.++.+.+.|+||++.+.
T Consensus 170 ------~~vei~G~lVdi~~GsglI~rCP~~----~C~Rvl~~----g~C~~HG~v--e~~~DLrik~vlDDGt~~~~~~ 233 (311)
T PRK07217 170 ------DEVEVEGALVDIQSGSGLIKRCPEE----DCTRVLQN----GRCSEHGKV--EGEFDLRIKGVLDDGEEVQEVI 233 (311)
T ss_pred ------ccccceeEEEEEeCCCCCeecCCcc----ccCccccC----CCCCCCCCc--CCceeeEEEEEEECCCCeEEEE
Confidence 1146889999999888888899921 29999955 599999974 6788899999999999999999
Q ss_pred EehhhhhhhcCCCHHHHHHhhhccCChhHHHHHH-HHhcCCeEEEEEEE
Q 008606 473 AFQESGEEILGCPAKELYMLKYELQDDVRFGEII-RSRVFNQYLFRLKI 520 (560)
Q Consensus 473 ~Fd~~ae~llG~sA~el~~~~~e~~d~~~~~~~l-~~~~~k~~~fkvkv 520 (560)
+-++..++|.|++-+++.+|..+--|.....+.| ..++|+.|.|+...
T Consensus 234 ~~~e~te~l~G~~l~eak~~a~dald~~vv~~~i~~~llGr~~~v~G~~ 282 (311)
T PRK07217 234 FNREATEELTGITLEEAKQMAMDALDTGVVLDELKEKLLGRYYRVTGPT 282 (311)
T ss_pred EChHHhHHHhCCCHHHHHHHHHHhhchhhHHHHHHHhhcCceEEEEecc
Confidence 9999999999999999999874223444444444 57999999998865
No 21
>PRK08402 replication factor A; Reviewed
Probab=99.58 E-value=1.1e-13 Score=144.93 Aligned_cols=177 Identities=25% Similarity=0.394 Sum_probs=141.1
Q ss_pred cceeccccCCCCCceEEEEEEEEecccceeccCCC-CCcEEEEEEEeCCCCeEEEEEcchhHHHHHhhcccCcEEEEeee
Q 008606 114 RIIPIAALNPYQGRWAIKARVTAKGDLRRYNNARG-DGKVFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISKG 192 (560)
Q Consensus 114 ~~~pI~~L~p~~~~w~Ik~RV~~k~~ir~~~n~~g-~gkvf~~~L~D~~g~~I~at~~~~~~~kf~~~l~eG~vY~Is~~ 192 (560)
..++|++|.|++..|++.|||+.+++.|.|....| .|++.+++|.| ++|+|++|+|++.++++++.|++|+|+.|.++
T Consensus 61 ~~~kI~dl~~g~~~V~v~~rVl~~~~~r~f~rrdG~~~~V~~i~l~D-eTG~ir~TlW~~~a~~~~~~l~~Gdvi~I~~a 139 (355)
T PRK08402 61 PLMHISDLVPGMRGVNIVGRVLRKYPPREYTKKDGSTGRVASLIIYD-DTGRARVVLWDAKVAKYYNKINVGDVIKVIDA 139 (355)
T ss_pred CccCHHHccCCCceeeEEEEEEEccCCceeeccCCCcceEEEEEEEc-CCCeEEEEEechhhhhhcccCCCCCEEEEECC
Confidence 68899999999999999999999999999987655 57899999999 77799999999999998889999999999999
Q ss_pred EEecCCCccccCCCeeEEEEcccceEEeccCCCC--CCCcc------cccccCccchhcccCCceeEEEEEEEEecCce-
Q 008606 193 SLKPAQKNFNHLKNEWEIFLEATSTVDLCTEEDD--SIPKQ------QFSFRHISEIESAENNSIVDVIGIVISVNPSV- 263 (560)
Q Consensus 193 ~V~~a~~~y~~~~~~yeI~f~~~T~I~~~~d~~~--~iP~~------~f~f~~i~dI~~~~~~~~VDVIGvV~~V~~~~- 263 (560)
.|+... ...++|.+...|+|...++.+. .+|.+ .+.+++|++|.. .+.++.|.|.|+.+.+-.
T Consensus 140 ~V~e~~------~G~~eLsvg~~s~i~~~pd~~ea~~i~~~~~~~~~~~~~k~I~ei~~--gd~~v~v~g~Iv~i~~~~~ 211 (355)
T PRK08402 140 QVRESL------SGLPELHINFRARIILNPDDPRVEEIPPLEEVRSYNYTRKKIGELEG--GERFVEVRGTIAKVYRVLV 211 (355)
T ss_pred EEeecC------CCcEEEEECCCceEEeCCCcccccccccccccccccccccCHHHccc--CCcEEEEEEEEEEEecCee
Confidence 998541 2346999999999999875432 34543 256788888855 446799999999999711
Q ss_pred ---------eEeec----------cC----ceeeEEEEEEecCCCcEEEEEEeCcchhhh
Q 008606 264 ---------PILRK----------NG----METQRRILNLKDTSGRSVELTLWGDFCNKE 300 (560)
Q Consensus 264 ---------~i~~k----------~G----~~~~kr~i~L~D~Sg~~I~vtLWg~~a~~~ 300 (560)
.+... -| .......+.|.|.|| .+.||||++.|..+
T Consensus 212 y~aCp~CnKkv~~~~~~~~~~Ce~~~~v~p~~ryil~~~l~D~TG-~~~vt~f~e~ae~l 270 (355)
T PRK08402 212 YDACPECRRKVDYDPATDTWICPEHGEVEPIKITILDFGLDDGTG-YIRVTLFGDDAAEL 270 (355)
T ss_pred EecCCCCCeEEEEecCCCCEeCCCCCCcCcceeEEEEEEEEcCCC-cEEEEEecHHHHHH
Confidence 12100 02 112344678999999 89999999999874
No 22
>KOG0851 consensus Single-stranded DNA-binding replication protein A (RPA), large (70 kD) subunit and related ssDNA-binding proteins [Replication, recombination and repair]
Probab=99.28 E-value=6.1e-11 Score=118.53 Aligned_cols=214 Identities=17% Similarity=0.210 Sum_probs=154.3
Q ss_pred CcceeccccCCCCCceEEEEEEEEecccceeccCCCCCcEEEEEEEeCCCCeEEEEEcchhHHHHHhhcccCcEEEEeee
Q 008606 113 ARIIPIAALNPYQGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISKG 192 (560)
Q Consensus 113 ~~~~pI~~L~p~~~~w~Ik~RV~~k~~ir~~~n~~g~gkvf~~~L~D~~g~~I~at~~~~~~~kf~~~l~eG~vY~Is~~ 192 (560)
..+++|.+|+|..+.|+|.++|++.|.. +.+. .+..+.|.|.|+.|.+|+|++......+|...|++|+|+.|..|
T Consensus 2 ~~~~~l~~l~~~~t~w~i~~~vl~v~~~--~~~~--~~~~~~~il~D~~~~~i~a~i~~~~~~~~~~~l~~~~w~~i~~f 77 (246)
T KOG0851|consen 2 AGFHRLRDLSPSITGWRIQVKVLRVWKK--YSNP--NGEELRLVLADEHGVKIEATVGRRLSSKYEDNLIENEWKIITTF 77 (246)
T ss_pred CcccchhhcCcCceeeEEEEEEEEEEEe--cCCC--CccEEEEEEEecCCcEEEEEcchHHHhhhhhheecceeEEeeee
Confidence 3678999999999999999999999874 3332 35789999999999999999999999999999999999999999
Q ss_pred EEecCCCccccCCCeeEEEEcccceEEeccCCCCCCCcccccccCccchhc--ccCCceeEEEE-EEEEecCceeEeecc
Q 008606 193 SLKPAQKNFNHLKNEWEIFLEATSTVDLCTEEDDSIPKQQFSFRHISEIES--AENNSIVDVIG-IVISVNPSVPILRKN 269 (560)
Q Consensus 193 ~V~~a~~~y~~~~~~yeI~f~~~T~I~~~~d~~~~iP~~~f~f~~i~dI~~--~~~~~~VDVIG-vV~~V~~~~~i~~k~ 269 (560)
.|.++...++.+.|+|+|.|...+.+.........+| ..+|.+++.+.. .....++|++| .|..|+.+.. +...
T Consensus 78 ~v~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~v~~~~~~~~~v~~~~~~~~~v~~~~~-~~~~ 154 (246)
T KOG0851|consen 78 GVNPNSGQVRATTHSFKINFMDFTVVTSSDTRLPCTP--WGKFTPFDSIVEDKSDKRVLVDLIGVAVYDVSQLTV-TPAI 154 (246)
T ss_pred eecccccceeeeeeEEEEEeccceeeccCCCCcccee--ccccchhhhhhccccCCcEEEEeeceeEEEeeeeEe-cccc
Confidence 9999999999999999999988777776532212222 356777755544 34678999999 7777776643 1223
Q ss_pred CceeeEEEEEEecCCCcEEEEEEeCcchhhhhhhHHhhhccCCccEEEEEEEEEecCCCceecccCCeEEEECCChHHHH
Q 008606 270 GMETQRRILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVDVGFFPVLSVKSGKVNDFSGKSIGTIPSTQLFINPDFAEAH 349 (560)
Q Consensus 270 G~~~~kr~i~L~D~Sg~~I~vtLWg~~a~~~~~~l~~~~~~~~~~VV~l~~~rV~~f~G~sLs~~~~S~i~iNPdipEa~ 349 (560)
++....+.+...+.++ |.. . +.-.+....+..+.+| +++ ...+.+.+..+|+ +.
T Consensus 155 ~~~~~~~~~~~~~~~~-------~~~-------------~-~~~~~c~~~~~~~~~~-~~~-~~l~~~~~~~~~~---l~ 208 (246)
T KOG0851|consen 155 DTDVDGFYLTFKICNK-------SKF-------------S-KPVLWCEACGEQATDF-GRK-RSLGGGVIVIAPE---LL 208 (246)
T ss_pred cCCcceEEEEEeeccc-------ccc-------------c-CceEEehhhcchHHhh-hhh-eEecCCcEEccch---he
Confidence 4566777888887775 110 0 0112233455555666 444 5556666666666 44
Q ss_pred HHHHHHhcCC
Q 008606 350 ELREWFDSGG 359 (560)
Q Consensus 350 ~L~~w~~~~g 359 (560)
.++.|....|
T Consensus 209 ~~~~~~~~~G 218 (246)
T KOG0851|consen 209 FWKIWRYFDG 218 (246)
T ss_pred eecccccccC
Confidence 4555555555
No 23
>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=99.08 E-value=6.9e-10 Score=101.83 Aligned_cols=99 Identities=19% Similarity=0.312 Sum_probs=78.2
Q ss_pred ccccCccchhcccCCceeEEEEEEEEecCceeEeeccCceeeEEEEEEecCCC---cEEEEEEeCcchhhhhhhHHhhhc
Q 008606 233 FSFRHISEIESAENNSIVDVIGIVISVNPSVPILRKNGMETQRRILNLKDTSG---RSVELTLWGDFCNKEGQKLQEMVD 309 (560)
Q Consensus 233 f~f~~i~dI~~~~~~~~VDVIGvV~~V~~~~~i~~k~G~~~~kr~i~L~D~Sg---~~I~vtLWg~~a~~~~~~l~~~~~ 309 (560)
|+|++|+++.. ..+..|||||+|+++++... ..|+. .++.|+|.|.|+ ..|.|+||++.++.+ ..
T Consensus 1 ~~f~~i~~~~~-~~~~~v~vigVV~~~~~p~~---s~g~d-~~~tl~i~D~S~~~~~~l~v~~F~~~~~~L----P~--- 68 (138)
T cd04497 1 YKYTPLSSALK-ESGGSVNVIGVVVDAGPPVR---SKGTD-YCCTLTITDPSLANSDGLTVKLFRPNEESL----PI--- 68 (138)
T ss_pred CceEeHHHHHh-ccCCeEEEEEEEeecCCCcc---cCCCc-EEEEEEEECCCCCCCCcEEEEEECCChhhC----CC---
Confidence 57899999987 57899999999999999754 23554 899999999998 889999999997763 21
Q ss_pred cCCccEEEEEEEEEecCCCceecc--cCCeEE-EECC
Q 008606 310 VGFFPVLSVKSGKVNDFSGKSIGT--IPSTQL-FINP 343 (560)
Q Consensus 310 ~~~~~VV~l~~~rV~~f~G~sLs~--~~~S~i-~iNP 343 (560)
...|+||+|++++|+.|+|+.+.. ...|.+ .+.+
T Consensus 69 v~~GDVIll~~~kv~~~~g~~~~~~~~~~ss~avf~~ 105 (138)
T cd04497 69 VKVGDIILLRRVKIQSYNGKPQGISNDRGSSWAVFRG 105 (138)
T ss_pred CCCCCEEEEEEEEEEEECCceEEEECCCceeEEEEcC
Confidence 256899999999999999985433 224444 3444
No 24
>PRK06386 replication factor A; Reviewed
Probab=99.07 E-value=9.9e-09 Score=107.35 Aligned_cols=163 Identities=18% Similarity=0.191 Sum_probs=126.7
Q ss_pred cceeccccCCCCCceEEEEEEEEecccceeccCCCCCcEEEEEEEeCCCCeEEEEEcchhHHHHHhhcccCcEEEEeeeE
Q 008606 114 RIIPIAALNPYQGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISKGS 193 (560)
Q Consensus 114 ~~~pI~~L~p~~~~w~Ik~RV~~k~~ir~~~n~~g~gkvf~~~L~D~~g~~I~at~~~~~~~kf~~~l~eG~vY~Is~~~ 193 (560)
+.++|++|.|++..-+|.|||+..|+ |.|....+.+.+.++.|-| +.|+|+.|.|++ .|++|++|.|.++.
T Consensus 106 ~~~KI~DL~~g~~~v~V~akVle~~e-~e~~~~g~~~~v~sg~lgD-eTGrIr~TlW~~-------~l~eGd~v~i~na~ 176 (358)
T PRK06386 106 KLVKIRDLSLVTPYVSVIGKITGITK-KEYDSDGTSKIVYQGYIED-DTARVRISSFGK-------PLEDNRFVRIENAR 176 (358)
T ss_pred CccEeEeccCCCCceEEEEEEEEccC-ceEecCCCccEEEEEEEEc-CCCeEEEEEccc-------cccCCCEEEEeeeE
Confidence 57799999999887789999999998 7887444568899999999 899999999986 48999999999998
Q ss_pred EecCCCccccCCCeeEEEEcccceEEeccCCCCCCCcccccccCccchhcccCCceeEEEEEEEEecC-ceeEee-----
Q 008606 194 LKPAQKNFNHLKNEWEIFLEATSTVDLCTEEDDSIPKQQFSFRHISEIESAENNSIVDVIGIVISVNP-SVPILR----- 267 (560)
Q Consensus 194 V~~a~~~y~~~~~~yeI~f~~~T~I~~~~d~~~~iP~~~f~f~~i~dI~~~~~~~~VDVIGvV~~V~~-~~~i~~----- 267 (560)
+...+ ..++|.++..|.|++.++ + |+ ..-.+.+|.||.+. +..+-+.|.|++|.+ .--|.+
T Consensus 177 v~e~~-------G~~el~v~~~t~I~~~~~-~--ie-v~~~~~~I~di~~~--~g~v~i~G~iv~i~~gsgli~rCP~C~ 243 (358)
T PRK06386 177 VSQYN-------GYIEISVGNKSVIKEVES-D--IN-LESRNIFIFEIKSP--VGGITIMGFIVSVGQGSRIFTKCSVCN 243 (358)
T ss_pred EEccC-------CeEEEEeCCeEEEEECCC-C--cc-cCccccchhhhhcc--CCeEEEEEEEEEEcCCcEeEecCcCCC
Confidence 77543 458999999999999853 2 32 22357788888763 334889999999986 333332
Q ss_pred ----c---------cCceeeEEEEEEecCCCcEEEEEEeCcchhh
Q 008606 268 ----K---------NGMETQRRILNLKDTSGRSVELTLWGDFCNK 299 (560)
Q Consensus 268 ----k---------~G~~~~kr~i~L~D~Sg~~I~vtLWg~~a~~ 299 (560)
+ .|....+-.+.|-|.+| .+.|+|.++.++.
T Consensus 244 R~l~~g~C~~HG~v~~~~dlr~k~vLDDGtg-~~~~~l~~e~~e~ 287 (358)
T PRK06386 244 KIIEDGVCKDHPDAPVYLDIFGYFTISDGTG-FVTCYANKDSFLP 287 (358)
T ss_pred eEccCCcCCCCCCCCCeeEEEEEEEEECCCC-eEEEEEChHHhHH
Confidence 1 12233444578888888 8999999999876
No 25
>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=99.06 E-value=2.5e-09 Score=115.25 Aligned_cols=245 Identities=27% Similarity=0.357 Sum_probs=172.7
Q ss_pred CCCcceeccccCCCCCceEEEEEEEEecccceeccCCCCCcEEEEEEEeCCCCeEEEEEcchhHHHHHhhcccCcEEEEe
Q 008606 111 APARIIPIAALNPYQGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLIS 190 (560)
Q Consensus 111 ~~~~~~pI~~L~p~~~~w~Ik~RV~~k~~ir~~~n~~g~gkvf~~~L~D~~g~~I~at~~~~~~~kf~~~l~eG~vY~Is 190 (560)
....+.++..+.|+. ++||+.+.++|.|.+..|++++|+..|.|+. +.+++|....+ +++|++|.+.
T Consensus 158 ~~~~i~~~~~~~~~~-----~~~v~~g~~ik~~~~~~ge~~~~~~~~~d~~---~~~~~~~~~~~-----~~~g~~~~ie 224 (407)
T COG1599 158 DAREIGEESLLSPYQ-----KARVVVGSEIKTFDNQGGESKVFSNELEDEE---RGVIVFTDWDP-----SQDGDVYRIE 224 (407)
T ss_pred cccccccccccCccc-----eEEEEecccceeEecCCCccceEeeeecccc---eeEEEeccCcc-----cccceeeeec
Confidence 345777888888888 9999999999999999999999999999977 44444444332 2999999999
Q ss_pred eeEEecCCCccccCCCeeEEEEccc--ceEEeccCCCCCCCcccccccCccchhcccCCceeEEEEEEEEecCceeEeec
Q 008606 191 KGSLKPAQKNFNHLKNEWEIFLEAT--STVDLCTEEDDSIPKQQFSFRHISEIESAENNSIVDVIGIVISVNPSVPILRK 268 (560)
Q Consensus 191 ~~~V~~a~~~y~~~~~~yeI~f~~~--T~I~~~~d~~~~iP~~~f~f~~i~dI~~~~~~~~VDVIGvV~~V~~~~~i~~k 268 (560)
+..|+..++.+... +.+++.+... +.|..+. ....++...+. ....++ .+..+| |+.+.+...+..+
T Consensus 225 ~~~v~~~~~~~~~~-~~~e~~~~~~~~~~i~~~~-~~~~~~~~~~~-~~~~~~----~~~~v~----v~~~~~c~~~~~~ 293 (407)
T COG1599 225 GARVKTKNKQPEEN-LAEELVLRVEVRVAIEKAE-REEFVDEVKES-VSLVEA----DGAVVD----VTRVPECERVVRK 293 (407)
T ss_pred CcEEEEeccccccc-ccceEEEeecceeeccCCC-Cccccceeecc-ccccee----ccceEE----EEECCCceEEEeC
Confidence 99999999988777 9999999887 5555543 22223332222 222222 234444 7778777777666
Q ss_pred cCceeeEEEEEEecCCCcEEEEEEeCcchhhhhhhHHhhhccCCccEEEEEEEEEecCCCceecccCCeEEEECCChHHH
Q 008606 269 NGMETQRRILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVDVGFFPVLSVKSGKVNDFSGKSIGTIPSTQLFINPDFAEA 348 (560)
Q Consensus 269 ~G~~~~kr~i~L~D~Sg~~I~vtLWg~~a~~~~~~l~~~~~~~~~~VV~l~~~rV~~f~G~sLs~~~~S~i~iNPdipEa 348 (560)
.+.....+.+.|.|.+| .++|+|||+-+.. .+ ....+.++++.++.++.|..++. .++++
T Consensus 294 ~~~~~~~~~~~l~D~~g-~~rv~~~~~~~e~-------~~--~~~~~~~~~~~~~~~~~~~~~~~----------~~~~~ 353 (407)
T COG1599 294 GGCKGHGKDIGLDDLTG-KIRVTLWGDATEV-------LI--NEESVEALKGINVEDASGIALSA----------LDTEA 353 (407)
T ss_pred CCcccccccceEecCce-EEEEecCCCceEE-------Ee--cccchhheeeeeeeeccchhhhh----------hhhhh
Confidence 66667888999999988 8999999974332 12 45788889999999999987665 66788
Q ss_pred HHHHHHHhcCCCccceeecccccccCCCccchhhhHHHHhhcCCCCCCCCceEEEEEEEEEEeCC
Q 008606 349 HELREWFDSGGKNAATVSISREIAAGGAKNEIHKTVSQIKNEGLGRSEKPDWVTVRAFITFIKSD 413 (560)
Q Consensus 349 ~~L~~w~~~~g~~~~~~sls~~~~~~~~~~~~~ktI~~I~~~~~g~~e~~~~~~v~atI~~I~~d 413 (560)
..+..|+...|+...+.-. ....+. +..+ +..+.+...+.+.+.|..++..
T Consensus 354 ~a~~~~~~~~Gk~~~v~g~---------~~~~~~-~~~~----~~~~~~~~~~~~~~~i~~~~~~ 404 (407)
T COG1599 354 VALEIWYDILGKYLRVTGD---------AREDRY-LIEN----LVESSTWDDVDVRAEIEALKEE 404 (407)
T ss_pred hhhhcchhcccceEEeecc---------ccchhh-hhhh----hccccccCccchhheeeeeccc
Confidence 8889999998886544210 111122 1111 1223455667888888877643
No 26
>PRK07218 replication factor A; Provisional
Probab=99.04 E-value=1e-08 Score=109.71 Aligned_cols=170 Identities=22% Similarity=0.232 Sum_probs=133.5
Q ss_pred cceeccccCCCCCceEEEEEEEEecccceeccCCCCCcEEEEEEEeCCCCeEEEEEcchhHHHHHhhcccCcEEEEeeeE
Q 008606 114 RIIPIAALNPYQGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISKGS 193 (560)
Q Consensus 114 ~~~pI~~L~p~~~~w~Ik~RV~~k~~ir~~~n~~g~gkvf~~~L~D~~g~~I~at~~~~~~~kf~~~l~eG~vY~Is~~~ 193 (560)
...+|.+|.|.....+|.|||+..|+ |.|....|++.+.+..|.| +.|.|+.+.|++++ .|++|++|.|.++.
T Consensus 161 ~~~kI~DL~~g~~~V~v~g~Vl~~~~-r~f~~~dg~~~v~~giigD-eTG~Ir~tlW~~~~-----~l~~Gd~v~I~na~ 233 (423)
T PRK07218 161 GDKKLIDLGPGDRGVNVEARVLELEH-REIDGRDGETTILSGVLAD-ETGRLPFTDWDPLP-----EIEIGASIRIEDAY 233 (423)
T ss_pred CccchhhccCCCCceEEEEEEEEecc-eeEEcCCCCeEEEEEEEEC-CCceEEEEEecccc-----cCCCCCEEEEeeeE
Confidence 45589999999988899999999976 8998777887899999999 78899999999854 48999999999999
Q ss_pred EecCCCccccCCCeeEEEEcccceEEeccCCCCCCCcccccccCccchhcccCCceeEEEEEEEEecCceeE-ee-----
Q 008606 194 LKPAQKNFNHLKNEWEIFLEATSTVDLCTEEDDSIPKQQFSFRHISEIESAENNSIVDVIGIVISVNPSVPI-LR----- 267 (560)
Q Consensus 194 V~~a~~~y~~~~~~yeI~f~~~T~I~~~~d~~~~iP~~~f~f~~i~dI~~~~~~~~VDVIGvV~~V~~~~~i-~~----- 267 (560)
|+..+ ..++|.+++.|.|+..++ +..++. .+.-++|.++.+-.....|.|.|.|++|.+-.-+ ++
T Consensus 234 v~e~~-------G~~elnv~~~t~I~~~d~-~i~v~~-~~~~~~I~e~~~~~g~~~Vev~G~Iv~i~~gsgli~rCP~C~ 304 (423)
T PRK07218 234 VREFR-------GVPSVNVSEFTTVEALDR-EVSVSK-DPPRLKIREAVERGGIFDVELVGNIISVRDGSGLIERCPECG 304 (423)
T ss_pred EeccC-------CeEEEEECCceEEEECCC-CccccC-CccccchhhhhccCCcceEEEEEEEEEeccCCcceecCcCcc
Confidence 98543 568999999999999853 333432 2345677777654333459999999999987432 21
Q ss_pred ----c---------cCceeeEEEEEEecCCCcEEEEEEeCcchhhh
Q 008606 268 ----K---------NGMETQRRILNLKDTSGRSVELTLWGDFCNKE 300 (560)
Q Consensus 268 ----k---------~G~~~~kr~i~L~D~Sg~~I~vtLWg~~a~~~ 300 (560)
+ .+....+..+.|-|.+| ++.|+|.++.+...
T Consensus 305 r~v~~~~C~~hG~ve~~~dlrik~vLDDGtg-~~~~~~~~e~~e~l 349 (423)
T PRK07218 305 RVIQKGQCRSHGAVEGEDDLRIKAILDDGTG-SVTVILDRELTEIV 349 (423)
T ss_pred ccccCCcCCCCCCcCCeeeeEEEEEEECCCC-eEEEEEChhhhHhH
Confidence 1 23445677888888898 89999999988763
No 27
>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=98.84 E-value=3.7e-08 Score=82.04 Aligned_cols=80 Identities=20% Similarity=0.369 Sum_probs=68.9
Q ss_pred EEEEEEEEecCceeEeeccCceeeEEEEEEecCCCcEEEEEEeCcchhhhhhhHHhhhccCCccEEEEEEEEEecCCCc-
Q 008606 251 DVIGIVISVNPSVPILRKNGMETQRRILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVDVGFFPVLSVKSGKVNDFSGK- 329 (560)
Q Consensus 251 DVIGvV~~V~~~~~i~~k~G~~~~kr~i~L~D~Sg~~I~vtLWg~~a~~~~~~l~~~~~~~~~~VV~l~~~rV~~f~G~- 329 (560)
+|+|+|+++++..+++ ++|+....+++.|.|.|| +|++++|++.+.. ....+.++.++++++++|+|.
T Consensus 1 ~v~~~V~~~~~~~~~~-~~g~~~~~~~~~l~D~TG-~i~~~~W~~~~~~---------~~~~G~vv~i~~~~v~~~~g~~ 69 (82)
T cd04491 1 SVEGKVLSISEPREFT-RDGSEGKVQSGLVGDETG-TIRFTLWDEKAAD---------DLEPGDVVRIENAYVREFNGRL 69 (82)
T ss_pred CEEEEEEEccCCeEec-cCCCeeEEEEEEEECCCC-EEEEEEECchhcc---------cCCCCCEEEEEeEEEEecCCcE
Confidence 4799999999999998 789999999999999999 8999999998611 124678999999999999986
Q ss_pred eecccCCeEEEE
Q 008606 330 SIGTIPSTQLFI 341 (560)
Q Consensus 330 sLs~~~~S~i~i 341 (560)
.|+....|.|..
T Consensus 70 ql~i~~~~~i~~ 81 (82)
T cd04491 70 ELSVGKNSEIEK 81 (82)
T ss_pred EEEeCCceEEEE
Confidence 788887787754
No 28
>PRK06461 single-stranded DNA-binding protein; Reviewed
Probab=98.83 E-value=2.9e-08 Score=90.03 Aligned_cols=93 Identities=20% Similarity=0.266 Sum_probs=77.0
Q ss_pred ccCccchhcccCCceeEEEEEEEEecCceeEeeccCceeeEEEEEEecCCCcEEEEEEeCcchhhhhhhHHhhhccCCcc
Q 008606 235 FRHISEIESAENNSIVDVIGIVISVNPSVPILRKNGMETQRRILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVDVGFFP 314 (560)
Q Consensus 235 f~~i~dI~~~~~~~~VDVIGvV~~V~~~~~i~~k~G~~~~kr~i~L~D~Sg~~I~vtLWg~~a~~~~~~l~~~~~~~~~~ 314 (560)
+++|+||.. ....|+++|+|+++++...+.+|+| ....+++.|.|.|| +|.++||++.|.. + ..+.
T Consensus 4 ~~kI~dL~~--g~~~v~~~~~V~~i~~~~~~~~k~~-~~~v~~~~l~D~TG-~I~~tlW~~~a~~--------l--~~Gd 69 (129)
T PRK06461 4 ITKIKDLKP--GMERVNVTVRVLEVGEPKVIQTKGG-PRTISEAVVGDETG-RVKLTLWGEQAGS--------L--KEGE 69 (129)
T ss_pred ceEHHHcCC--CCCceEEEEEEEEcCCceEEEeCCC-ceEEEEEEEECCCC-EEEEEEeCCcccc--------C--CCCC
Confidence 456666652 2368999999999999999888844 45688999999999 7999999998654 2 3689
Q ss_pred EEEEEEEEEecCCCc-eecccCCeEEEE
Q 008606 315 VLSVKSGKVNDFSGK-SIGTIPSTQLFI 341 (560)
Q Consensus 315 VV~l~~~rV~~f~G~-sLs~~~~S~i~i 341 (560)
||.|+++++++|+|+ +|+....|.|..
T Consensus 70 vV~I~na~v~~f~G~lqL~i~~~~~i~~ 97 (129)
T PRK06461 70 VVEIENAWTTLYRGKVQLNVGKYGSISE 97 (129)
T ss_pred EEEEECcEEeeeCCEEEEEECCCEEEEE
Confidence 999999999999998 899888888865
No 29
>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=98.75 E-value=6.8e-08 Score=80.40 Aligned_cols=81 Identities=21% Similarity=0.302 Sum_probs=69.3
Q ss_pred EEEEEEEEecccceeccCCCCCcEEEEEEEeCCCCeEEEEEcchhHHHHHhhcccCcEEEEeeeEEecCCCccccCCCee
Q 008606 129 AIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISKGSLKPAQKNFNHLKNEW 208 (560)
Q Consensus 129 ~Ik~RV~~k~~ir~~~n~~g~gkvf~~~L~D~~g~~I~at~~~~~~~kf~~~l~eG~vY~Is~~~V~~a~~~y~~~~~~y 208 (560)
+|.|||++++++|.|.+..++++++++.|.|+ .|.|++++|++.+ .+.|++|++|.|.++.++..+ +.+
T Consensus 1 ~v~~~V~~~~~~~~~~~~g~~~~~~~~~l~D~-TG~i~~~~W~~~~---~~~~~~G~vv~i~~~~v~~~~-------g~~ 69 (82)
T cd04491 1 SVEGKVLSISEPREFTRDGSEGKVQSGLVGDE-TGTIRFTLWDEKA---ADDLEPGDVVRIENAYVREFN-------GRL 69 (82)
T ss_pred CEEEEEEEccCCeEeccCCCeeEEEEEEEECC-CCEEEEEEECchh---cccCCCCCEEEEEeEEEEecC-------CcE
Confidence 48999999999999984335689999999995 5699999999876 778999999999999987643 568
Q ss_pred EEEEcccceEEe
Q 008606 209 EIFLEATSTVDL 220 (560)
Q Consensus 209 eI~f~~~T~I~~ 220 (560)
+|.++..|.|+.
T Consensus 70 ql~i~~~~~i~~ 81 (82)
T cd04491 70 ELSVGKNSEIEK 81 (82)
T ss_pred EEEeCCceEEEE
Confidence 999999998875
No 30
>PRK06461 single-stranded DNA-binding protein; Reviewed
Probab=98.71 E-value=1.3e-07 Score=85.67 Aligned_cols=98 Identities=15% Similarity=0.209 Sum_probs=83.1
Q ss_pred cceeccccCCCCCceEEEEEEEEecccceeccCCCCCcEEEEEEEeCCCCeEEEEEcchhHHHHHhhcccCcEEEEeeeE
Q 008606 114 RIIPIAALNPYQGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISKGS 193 (560)
Q Consensus 114 ~~~pI~~L~p~~~~w~Ik~RV~~k~~ir~~~n~~g~gkvf~~~L~D~~g~~I~at~~~~~~~kf~~~l~eG~vY~Is~~~ 193 (560)
.+++|++|.|......+.++|+.+++.|.+....+.+++.++.|.| +.|.|++++|++.++ .|++|+++.|.++.
T Consensus 3 ~~~kI~dL~~g~~~v~~~~~V~~i~~~~~~~~k~~~~~v~~~~l~D-~TG~I~~tlW~~~a~----~l~~GdvV~I~na~ 77 (129)
T PRK06461 3 MITKIKDLKPGMERVNVTVRVLEVGEPKVIQTKGGPRTISEAVVGD-ETGRVKLTLWGEQAG----SLKEGEVVEIENAW 77 (129)
T ss_pred CceEHHHcCCCCCceEEEEEEEEcCCceEEEeCCCceEEEEEEEEC-CCCEEEEEEeCCccc----cCCCCCEEEEECcE
Confidence 4789999999999999999999999988887665566799999999 566899999998653 58899999999998
Q ss_pred EecCCCccccCCCeeEEEEcccceEEeccC
Q 008606 194 LKPAQKNFNHLKNEWEIFLEATSTVDLCTE 223 (560)
Q Consensus 194 V~~a~~~y~~~~~~yeI~f~~~T~I~~~~d 223 (560)
+..- ....+|.+...+.|..+.+
T Consensus 78 v~~f-------~G~lqL~i~~~~~i~~~~~ 100 (129)
T PRK06461 78 TTLY-------RGKVQLNVGKYGSISESDD 100 (129)
T ss_pred Eeee-------CCEEEEEECCCEEEEECCc
Confidence 8743 2457899999999998853
No 31
>PRK07217 replication factor A; Reviewed
Probab=98.18 E-value=5.3e-05 Score=77.51 Aligned_cols=151 Identities=18% Similarity=0.211 Sum_probs=103.7
Q ss_pred CCcceeccccCCCCCceEEEEEEEEecccceeccCCCCCcEEE-EEEEeCCCCeEEEEEcchhHHHHHhhcccCcEEEEe
Q 008606 112 PARIIPIAALNPYQGRWAIKARVTAKGDLRRYNNARGDGKVFS-FDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLIS 190 (560)
Q Consensus 112 ~~~~~pI~~L~p~~~~w~Ik~RV~~k~~ir~~~n~~g~gkvf~-~~L~D~~g~~I~at~~~~~~~kf~~~l~eG~vY~Is 190 (560)
....++|++|+|...+.+|+|||+..|+.+. +.+.. -.|.| +.|+|+-|.|.... .+.|++|++|.|.
T Consensus 69 ~~~~~kI~Di~~~~~~VsV~aKVl~l~e~~~-------~si~qvGllgD-ETG~IkfT~W~~s~---~~~leeGd~~rI~ 137 (311)
T PRK07217 69 GSELVNIADIDEPEQWVDVTAKVVQLWEPSS-------DSIAQVGLLGD-ETGTIKFTKWAKSD---LPELEEGKSYLLK 137 (311)
T ss_pred CCCceeeeecCCCCCcEEEEEEEEEecCCCC-------CceEEEEEEEc-CCceEEEEEccCCC---CCcccCCCEEEEE
Confidence 3468899999999999999999999998552 23333 34666 89999999999631 3569999999999
Q ss_pred eeEEecCCCccccCCCeeEEEEcccceEEeccCCCCCCCcccccccCccchhcccCCceeEEEEEEEEecCce-------
Q 008606 191 KGSLKPAQKNFNHLKNEWEIFLEATSTVDLCTEEDDSIPKQQFSFRHISEIESAENNSIVDVIGIVISVNPSV------- 263 (560)
Q Consensus 191 ~~~V~~a~~~y~~~~~~yeI~f~~~T~I~~~~d~~~~iP~~~f~f~~i~dI~~~~~~~~VDVIGvV~~V~~~~------- 263 (560)
++.+...+ ..++|.+++.|+|++.++ +..++.. .+-+.|.|++|.+=.
T Consensus 138 na~v~ey~-------G~~~lnlg~~t~I~~~de-~IeV~~~-----------------~vei~G~lVdi~~GsglI~rCP 192 (311)
T PRK07217 138 NVVTDEYQ-------GRFSVKLNRTTSIEELDE-DIEVGDD-----------------EVEVEGALVDIQSGSGLIKRCP 192 (311)
T ss_pred eEEEeeEC-------CEEEEEeCCceEEEeCCC-CccccCc-----------------cccceeEEEEEeCCCCCeecCC
Confidence 99987654 458999999999999853 3323211 123333333333211
Q ss_pred -----eEee---------ccCceeeEEEEEEecCCCcEEEEEEeCcchhh
Q 008606 264 -----PILR---------KNGMETQRRILNLKDTSGRSVELTLWGDFCNK 299 (560)
Q Consensus 264 -----~i~~---------k~G~~~~kr~i~L~D~Sg~~I~vtLWg~~a~~ 299 (560)
.+.. -.|....+....|=|.++ ++.|.|-.+..+.
T Consensus 193 ~~~C~Rvl~~g~C~~HG~ve~~~DLrik~vlDDGt~-~~~~~~~~e~te~ 241 (311)
T PRK07217 193 EEDCTRVLQNGRCSEHGKVEGEFDLRIKGVLDDGEE-VQEVIFNREATEE 241 (311)
T ss_pred ccccCccccCCCCCCCCCcCCceeeEEEEEEECCCC-eEEEEEChHHhHH
Confidence 0000 124445666777777777 8888888877654
No 32
>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=98.16 E-value=8.3e-05 Score=84.09 Aligned_cols=177 Identities=14% Similarity=0.070 Sum_probs=117.6
Q ss_pred cccCccchhcccCCceeEEEEEEEEecCceeEeeccCceeeEEEEEEecCCCcEEEEEEeCcchhhhhhhHHhhhccCCc
Q 008606 234 SFRHISEIESAENNSIVDVIGIVISVNPSVPILRKNGMETQRRILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVDVGFF 313 (560)
Q Consensus 234 ~f~~i~dI~~~~~~~~VDVIGvV~~V~~~~~i~~k~G~~~~kr~i~L~D~Sg~~I~vtLWg~~a~~~~~~l~~~~~~~~~ 313 (560)
.+.+|++|.... .-.-|.|.|+..++++.+..++| +....+|.|.|++| .|++|+|++.|..|...|+ .+
T Consensus 179 ~~~pI~~L~py~--~~wtIkaRV~~Ks~ir~~~~~~g-egkvfsv~L~Degg-~Irat~f~~~~dkf~~~l~------eG 248 (608)
T TIGR00617 179 RVMPIASLSPYQ--NKWTIKARVTNKSEIRTWSNARG-EGKLFNVELLDESG-EIRATAFNEQADKFYDIIQ------EG 248 (608)
T ss_pred ceEEHHHCCCCC--CceEEEEEEEeccccceecCCCC-CceeeEEEEecCCC-eEEEEECchHHHHHhhhcc------cC
Confidence 477888887643 34888999999999999876654 33567899999666 9999999999998765543 57
Q ss_pred cEEEEEEEEEecCCCc--------eecccCCeEEEECCChHHHHHHHHHHhcCCCccceeecccccccCCCccchhhhHH
Q 008606 314 PVLSVKSGKVNDFSGK--------SIGTIPSTQLFINPDFAEAHELREWFDSGGKNAATVSISREIAAGGAKNEIHKTVS 385 (560)
Q Consensus 314 ~VV~l~~~rV~~f~G~--------sLs~~~~S~i~iNPdipEa~~L~~w~~~~g~~~~~~sls~~~~~~~~~~~~~ktI~ 385 (560)
.|+.|..++|+.-+++ .|.....|.|..-+|.+. + + .......+|+
T Consensus 249 ~VY~Is~~~Vk~an~~y~~~~~~yei~f~~~T~I~~~~d~~~-------------------i-----P--~~~~~f~~i~ 302 (608)
T TIGR00617 249 KVYYISKGSLKPANKQFTNLGNDYEMTLDRDTVIEECEDETA-------------------I-----P--KIQFNFVKID 302 (608)
T ss_pred CEEEECceEEEEccccccCCCCCEEEEECCCeEEEECCCccc-------------------C-----C--cccccceEHH
Confidence 8999999998854432 244444555543322110 0 0 1123455678
Q ss_pred HHhhcCCCCCCCCceEEEEEEEEEEeCCCeEEeCCCCCcCccccCceeeecCCeeecCcCCCccCCceeEEEEEEEEEeC
Q 008606 386 QIKNEGLGRSEKPDWVTVRAFITFIKSDSFCYTACPLMIGDRQCNKKVTQSGNRWQCDRCNQEIDECDYRYLLQAQIQDQ 465 (560)
Q Consensus 386 ~I~~~~~g~~e~~~~~~v~atI~~I~~d~~~Y~aC~~~~~~~~C~KKv~~~~~~~~C~kC~~~~~~~~~rY~l~~~i~D~ 465 (560)
+|... +...++-|.|.|..+..-.-.- ... .-....+-++.|.|.
T Consensus 303 dI~~~-----~~~~~VDVIGvV~~v~~~~~i~-~k~-----------------------------~g~~~~kR~i~L~D~ 347 (608)
T TIGR00617 303 DIGGY-----EGNSLVDVIGIVQSVSPTQTIT-SRK-----------------------------NNKEFPKRDITLVDD 347 (608)
T ss_pred Hhhhh-----cCCCCccEEEEEeEecCceEEE-EcC-----------------------------CCCeeeeEEEEEEeC
Confidence 88653 2224677888888886322100 000 112345779999999
Q ss_pred CC-eEEEEEehhhhhhh
Q 008606 466 TG-LTWVTAFQESGEEI 481 (560)
Q Consensus 466 Tg-s~~~~~Fd~~ae~l 481 (560)
|| ++.+++|++.|+.+
T Consensus 348 sg~sI~vTLWG~~A~~~ 364 (608)
T TIGR00617 348 SGKSVRVTLWGDDATKF 364 (608)
T ss_pred CCCEEEEEEEhhhhhhc
Confidence 99 58999999998764
No 33
>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=98.13 E-value=8.8e-05 Score=80.20 Aligned_cols=188 Identities=19% Similarity=0.204 Sum_probs=134.4
Q ss_pred CCCcceeccccCCCCCceEEEEEEEEecccceeccCCCC-CcEEEEEEEeCCCCeEEE-EEcchhHHHHHhhcccCcEEE
Q 008606 111 APARIIPIAALNPYQGRWAIKARVTAKGDLRRYNNARGD-GKVFSFDLLDSDGGEIRV-TCFNAVVDRFYEIIEVGRVYL 188 (560)
Q Consensus 111 ~~~~~~pI~~L~p~~~~w~Ik~RV~~k~~ir~~~n~~g~-gkvf~~~L~D~~g~~I~a-t~~~~~~~kf~~~l~eG~vY~ 188 (560)
+...+.+|+++.+.+.+-.+.+||+..+..+.|...+|. +++.+..+.| +.+.+.. +.|...+. ..++.|+++.
T Consensus 45 ~~~~~~~i~~~~~~~~~~~v~~~V~~~~e~~~~~~k~g~~~~l~~~~v~D-etg~v~~~~~~~~~a~---~~~e~Gdv~~ 120 (407)
T COG1599 45 AMESIGKISDISEASSRVNVTGRVLSIGEKKTFDRKRGAEGKLAEVLVGD-ETGSVKTVTLWNIAAL---EKLEPGDVIR 120 (407)
T ss_pred chhhcccccccchhhccccEEEEECccccceeeecccccccceEEEEEec-CCCCEEEEeecccccc---ccCCccceEE
Confidence 456788999999999999999999999999988887775 7888888999 6778887 68876542 3578999999
Q ss_pred EeeeEEecCCCccccCCCeeEEEEcccceEEeccCCCCCCCcccccccCccchhcccCCceeEEEEEEEEecCceeEeec
Q 008606 189 ISKGSLKPAQKNFNHLKNEWEIFLEATSTVDLCTEEDDSIPKQQFSFRHISEIESAENNSIVDVIGIVISVNPSVPILRK 268 (560)
Q Consensus 189 Is~~~V~~a~~~y~~~~~~yeI~f~~~T~I~~~~d~~~~iP~~~f~f~~i~dI~~~~~~~~VDVIGvV~~V~~~~~i~~k 268 (560)
|.+..+... ....++.++..+.+...++... .+...+.-..+.++... ..++ .+.|+.-..+.++...
T Consensus 121 i~~~~~~~~-------~~~~~~~~~~~~~v~~~~~~~~-~~~~~~~~~~i~~~~~~---~~~~-~~~v~~g~~ik~~~~~ 188 (407)
T COG1599 121 IRNAYTSLY-------RGGKRLSVGRVGSVADVDDEED-EARESEDAREIGEESLL---SPYQ-KARVVVGSEIKTFDNQ 188 (407)
T ss_pred ecCcccccc-------cCceeeecccccccccCchhhc-ccccccccccccccccc---Cccc-eEEEEecccceeEecC
Confidence 988865433 2456788888888888754222 22222223333333322 2222 6677777777777654
Q ss_pred cCceeeEEEEEEecCCCcEEEEEEeCcchhhhhhhHHhhhccCCccEEEEEEEEEecCCCc
Q 008606 269 NGMETQRRILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVDVGFFPVLSVKSGKVNDFSGK 329 (560)
Q Consensus 269 ~G~~~~kr~i~L~D~Sg~~I~vtLWg~~a~~~~~~l~~~~~~~~~~VV~l~~~rV~~f~G~ 329 (560)
+.+...+...|.|.+-..+.+++|... ..+.+.-+..++|.-|++.
T Consensus 189 -~ge~~~~~~~~~d~~~~~~~~~~~~~~--------------~~g~~~~ie~~~v~~~~~~ 234 (407)
T COG1599 189 -GGESKVFSNELEDEERGVIVFTDWDPS--------------QDGDVYRIEGARVKTKNKQ 234 (407)
T ss_pred -CCccceEeeeecccceeEEEeccCccc--------------ccceeeeecCcEEEEeccc
Confidence 444567788888988348999999986 1356777888888888775
No 34
>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=97.93 E-value=6.5e-05 Score=65.53 Aligned_cols=98 Identities=16% Similarity=0.090 Sum_probs=71.8
Q ss_pred CccchhcccCCceeEEEEEEEEecCceeEeeccCceeeEEEEEEecCCCcEEEEEEeCcchhhhhhhHHhhhccCCccEE
Q 008606 237 HISEIESAENNSIVDVIGIVISVNPSVPILRKNGMETQRRILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVDVGFFPVL 316 (560)
Q Consensus 237 ~i~dI~~~~~~~~VDVIGvV~~V~~~~~i~~k~G~~~~kr~i~L~D~Sg~~I~vtLWg~~a~~~~~~l~~~~~~~~~~VV 316 (560)
+|++|.. .....-+.|.|+..+++..+..++ .+.....|.|.|..|.+|++|+|++.|..+...|+ .|.|+
T Consensus 1 pI~~L~p--~~~~~~I~~rV~~k~~~~~f~~~~-~~g~~~~~~l~De~~~~I~~t~~~~~~~~f~~~l~------eG~vy 71 (104)
T cd04474 1 PISSLNP--YQNKWTIKARVTNKSDIRTWSNAR-GEGKLFSFDLLDEDGGEIRATFFNDAVDKFYDLLE------VGKVY 71 (104)
T ss_pred ChhHccC--CCCcEEEEEEEeeccccccccCCC-CCcEEEEEEEEECCCCEEEEEEehHHHHHhhcccc------cccEE
Confidence 3555543 234688999999999999887765 23456699999997779999999999998766553 57999
Q ss_pred EEEEEEEecCCCceecccCCeEEEECC
Q 008606 317 SVKSGKVNDFSGKSIGTIPSTQLFINP 343 (560)
Q Consensus 317 ~l~~~rV~~f~G~sLs~~~~S~i~iNP 343 (560)
.|.+++|+.-+++.-.+...-.|.++.
T Consensus 72 ~i~~~~V~~a~~~y~~~~~~yeI~f~~ 98 (104)
T cd04474 72 YISKGSVKVANKKFNTLKNDYEITFNR 98 (104)
T ss_pred EEeccEEeeccccCCCCCCcEEEEECC
Confidence 999999987766533333344455443
No 35
>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=97.73 E-value=0.00012 Score=58.96 Aligned_cols=61 Identities=33% Similarity=0.525 Sum_probs=51.2
Q ss_pred eEEEEEEEEecccceeccCCCCCcEEEEEEEeCCCCeEEEEEcchhHHHHHhhcccCcEEEEeeeEEecCC
Q 008606 128 WAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISKGSLKPAQ 198 (560)
Q Consensus 128 w~Ik~RV~~k~~ir~~~n~~g~gkvf~~~L~D~~g~~I~at~~~~~~~kf~~~l~eG~vY~Is~~~V~~a~ 198 (560)
++|.|+|+++. + +.++++.++|.| ..+.|++.+|++...++.+.|++|+++.+. |.++..+
T Consensus 1 V~v~G~V~~~~--~------~~~~~~~~~l~D-~tg~i~~~~~~~~~~~~~~~l~~g~~v~v~-G~v~~~~ 61 (75)
T PF01336_consen 1 VTVEGRVTSIR--R------SGGKIVFFTLED-GTGSIQVVFFNEEYERFREKLKEGDIVRVR-GKVKRYN 61 (75)
T ss_dssp EEEEEEEEEEE--E------EETTEEEEEEEE-TTEEEEEEEETHHHHHHHHTS-TTSEEEEE-EEEEEET
T ss_pred CEEEEEEEEEE--c------CCCCEEEEEEEE-CCccEEEEEccHHhhHHhhcCCCCeEEEEE-EEEEEEC
Confidence 57999999976 2 234789999999 568999999999999999999999999999 8777664
No 36
>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=97.44 E-value=0.0014 Score=60.78 Aligned_cols=86 Identities=20% Similarity=0.359 Sum_probs=64.1
Q ss_pred ccCccchhcccCCceeEEEEEEEEecCceeEeeccCceeeEEEEEEecCCC-------cEEEEEEeCcchhhhhhhHHhh
Q 008606 235 FRHISEIESAENNSIVDVIGIVISVNPSVPILRKNGMETQRRILNLKDTSG-------RSVELTLWGDFCNKEGQKLQEM 307 (560)
Q Consensus 235 f~~i~dI~~~~~~~~VDVIGvV~~V~~~~~i~~k~G~~~~kr~i~L~D~Sg-------~~I~vtLWg~~a~~~~~~l~~~ 307 (560)
|++|++.. ...+..|||||+|++..+.....++ |+ -.+..|+|.|.|. ..|.|.++-...+.+ ..
T Consensus 1 ~~~l~~~~-~~~~~~vnvigVV~~~~~p~~~~t~-g~-D~~~tl~i~D~S~~~~~~~~~~l~v~iF~~~~~~L----P~- 72 (146)
T PF02765_consen 1 YTPLSTAK-EKFGKFVNVIGVVVDFSPPNPKKTR-GT-DYMCTLTITDPSLNDSNQKLSGLTVNIFRPHKESL----PN- 72 (146)
T ss_dssp BCCGGGSC-TTSSEEEEEEEEEEEEEEECTEEES-SS-CEEEEEEEEBTTCSCSSCCCCEEEEEEEESSHHHS----CT-
T ss_pred Cccchhhh-hcCCCEEEEEEEEEEccCCcceEcC-CC-cEEEEEEEECCCCCccccccCCEEEEEECCCHHHC----CC-
Confidence 45555322 3468899999999999988444454 43 3678999999995 689999998876553 22
Q ss_pred hccCCccEEEEEEEEEecCCCc
Q 008606 308 VDVGFFPVLSVKSGKVNDFSGK 329 (560)
Q Consensus 308 ~~~~~~~VV~l~~~rV~~f~G~ 329 (560)
. ...|+||.|+.++|+.|+|+
T Consensus 73 v-~~~GDii~l~r~kv~~~~~~ 93 (146)
T PF02765_consen 73 V-KSVGDIIRLRRVKVQSYNGK 93 (146)
T ss_dssp T-CSTTHEEEEEEEEEEEETTE
T ss_pred C-CCCCCEEEEEEEEEEEECCE
Confidence 1 12489999999999999997
No 37
>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=97.30 E-value=0.0017 Score=56.07 Aligned_cols=84 Identities=14% Similarity=0.152 Sum_probs=67.3
Q ss_pred EEEEEEEEecccceeccCC-C-CCcEEEEEEEeCCCCeEEEEEcchhHHHHHhhcccCcEEEEeeeEEecCCCccccCCC
Q 008606 129 AIKARVTAKGDLRRYNNAR-G-DGKVFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISKGSLKPAQKNFNHLKN 206 (560)
Q Consensus 129 ~Ik~RV~~k~~ir~~~n~~-g-~gkvf~~~L~D~~g~~I~at~~~~~~~kf~~~l~eG~vY~Is~~~V~~a~~~y~~~~~ 206 (560)
-|.|.|+..++++.+..+. | ++...++.|.|+.+..|.+++|++.++.|.... |.++.|.++++...+
T Consensus 3 Dvig~V~~v~~~~~i~~k~~g~~~~~r~v~i~D~t~~~i~vtLWg~~a~~~~~~~--~~vv~~~~~~i~~~~-------- 72 (101)
T cd04475 3 DVIGVVKSVGPVTTITTKSTGRELDKREITLVDESGHSVELTLWGEQAELFDGSE--NPVIAIKGVKVSEFN-------- 72 (101)
T ss_pred eEEEEEeEccCcEEEEEecCCCceeEEEEEEEeCCCCEEEEEEEHHHhhhcccCC--CCEEEEEeeEEEecC--------
Confidence 4789999999999987654 3 467889999998888999999999999988765 999999999986433
Q ss_pred eeEEEEcccceEEecc
Q 008606 207 EWEIFLEATSTVDLCT 222 (560)
Q Consensus 207 ~yeI~f~~~T~I~~~~ 222 (560)
...+.....|.|..-+
T Consensus 73 ~~~l~~~~~s~i~~np 88 (101)
T cd04475 73 GKSLSTGSSSTIIINP 88 (101)
T ss_pred CeEEeecCceeEEECC
Confidence 1345556677777754
No 38
>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=96.74 E-value=0.0082 Score=47.05 Aligned_cols=61 Identities=36% Similarity=0.607 Sum_probs=49.8
Q ss_pred EEEEEEEEecccceeccCCCCCcEEEEEEEeCCCCeEEEEEcchhHHHHHhhcccCcEEEEeeeEEec
Q 008606 129 AIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISKGSLKP 196 (560)
Q Consensus 129 ~Ik~RV~~k~~ir~~~n~~g~gkvf~~~L~D~~g~~I~at~~~~~~~kf~~~l~eG~vY~Is~~~V~~ 196 (560)
+|.|.|+.....+. | +..+.+.|.|..|+.|.+.+|.+..+++...+++|+++.+. ++|..
T Consensus 1 ~v~g~v~~~~~~~~-----~-~~~~~~~l~D~~~~~i~~~~~~~~~~~~~~~~~~g~~v~v~-g~v~~ 61 (75)
T cd03524 1 TIVGIVVAVEEIRT-----E-GKVLIFTLTDGTGGTIRVTLFGELAEELENLLKEGQVVYIK-GKVKK 61 (75)
T ss_pred CeEEEEEeeccccc-----C-CeEEEEEEEcCCCCEEEEEEEchHHHHHHhhccCCCEEEEE-EEEEe
Confidence 36788887655433 1 25788999997779999999999999999999999999998 88864
No 39
>KOG3416 consensus Predicted nucleic acid binding protein [General function prediction only]
Probab=96.58 E-value=0.01 Score=52.62 Aligned_cols=83 Identities=20% Similarity=0.336 Sum_probs=60.1
Q ss_pred CccchhcccCCceeEEEEEEEEecCceeEeeccCceeeEEEEEEecCCCcEEEEEEeCcchhhhhhhHHhhhccCCccEE
Q 008606 237 HISEIESAENNSIVDVIGIVISVNPSVPILRKNGMETQRRILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVDVGFFPVL 316 (560)
Q Consensus 237 ~i~dI~~~~~~~~VDVIGvV~~V~~~~~i~~k~G~~~~kr~i~L~D~Sg~~I~vtLWg~~a~~~~~~l~~~~~~~~~~VV 316 (560)
+|.||....++ +.|+=+|.+.+..+. +|+|++ .|...+.|.|| +|.+.+|++.... + ..++||
T Consensus 6 ~ikdi~P~~kN--~~v~fIvl~~g~~tk--Tkdg~~--v~~~kVaD~Tg-sI~isvW~e~~~~--------~--~PGDIi 68 (134)
T KOG3416|consen 6 FIKDIKPGLKN--INVTFIVLEYGRATK--TKDGHE--VRSCKVADETG-SINISVWDEEGCL--------I--QPGDII 68 (134)
T ss_pred hHhhcChhhhc--ceEEEEEEeeceeee--ccCCCE--EEEEEEecccc-eEEEEEecCcCcc--------c--CCccEE
Confidence 45666553333 445556777666543 677874 68999999999 9999999988654 2 468999
Q ss_pred EEEEEEEecCCCc-eecccCC
Q 008606 317 SVKSGKVNDFSGK-SIGTIPS 336 (560)
Q Consensus 317 ~l~~~rV~~f~G~-sLs~~~~ 336 (560)
-|+++..+-|+|. .|.+..+
T Consensus 69 rLt~Gy~Si~qg~LtL~~GK~ 89 (134)
T KOG3416|consen 69 RLTGGYASIFQGCLTLYVGKG 89 (134)
T ss_pred EecccchhhhcCceEEEecCC
Confidence 9999999999885 6655433
No 40
>KOG3416 consensus Predicted nucleic acid binding protein [General function prediction only]
Probab=96.50 E-value=0.0064 Score=53.84 Aligned_cols=70 Identities=21% Similarity=0.320 Sum_probs=56.9
Q ss_pred ceeccccCCCCCceEEEEEEEEecccceeccCCCCC-cEEEEEEEeCCCCeEEEEEcchhHHHHHhhcccCcEEEEeeeE
Q 008606 115 IIPIAALNPYQGRWAIKARVTAKGDLRRYNNARGDG-KVFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISKGS 193 (560)
Q Consensus 115 ~~pI~~L~p~~~~w~Ik~RV~~k~~ir~~~n~~g~g-kvf~~~L~D~~g~~I~at~~~~~~~kf~~~l~eG~vY~Is~~~ 193 (560)
.++|++|.|++.+..+..-|+.-...+.-+ +| .+-++...| +.+.|++.+|++ +-..|+.|+++.++++-
T Consensus 4 ~i~ikdi~P~~kN~~v~fIvl~~g~~tkTk----dg~~v~~~kVaD-~TgsI~isvW~e----~~~~~~PGDIirLt~Gy 74 (134)
T KOG3416|consen 4 MIFIKDIKPGLKNINVTFIVLEYGRATKTK----DGHEVRSCKVAD-ETGSINISVWDE----EGCLIQPGDIIRLTGGY 74 (134)
T ss_pred chhHhhcChhhhcceEEEEEEeeceeeecc----CCCEEEEEEEec-ccceEEEEEecC----cCcccCCccEEEecccc
Confidence 468999999999999888888766554432 34 677788888 889999999996 55789999999999874
No 41
>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=95.97 E-value=0.029 Score=51.43 Aligned_cols=83 Identities=14% Similarity=0.257 Sum_probs=67.6
Q ss_pred cceeccccC-CCCCceEEEEEEEEecccceeccCCCCCcEEEEEEEeCCC---CeEEEEEcchhHHHHHhhcccCcEEEE
Q 008606 114 RIIPIAALN-PYQGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDG---GEIRVTCFNAVVDRFYEIIEVGRVYLI 189 (560)
Q Consensus 114 ~~~pI~~L~-p~~~~w~Ik~RV~~k~~ir~~~n~~g~gkvf~~~L~D~~g---~~I~at~~~~~~~kf~~~l~eG~vY~I 189 (560)
.++||++|. .....-.|.|-|+.....+. .+|.....+|.|.|..+ ..+.+.+|++..+.|-.. .+|+|+.+
T Consensus 2 ~f~~i~~~~~~~~~~v~vigVV~~~~~p~~---s~g~d~~~tl~i~D~S~~~~~~l~v~~F~~~~~~LP~v-~~GDVIll 77 (138)
T cd04497 2 KYTPLSSALKESGGSVNVIGVVVDAGPPVR---SKGTDYCCTLTITDPSLANSDGLTVKLFRPNEESLPIV-KVGDIILL 77 (138)
T ss_pred ceEeHHHHHhccCCeEEEEEEEeecCCCcc---cCCCcEEEEEEEECCCCCCCCcEEEEEECCChhhCCCC-CCCCEEEE
Confidence 578999997 34467789999998887665 23334678899999877 889999999999988776 99999999
Q ss_pred eeeEEecCCCc
Q 008606 190 SKGSLKPAQKN 200 (560)
Q Consensus 190 s~~~V~~a~~~ 200 (560)
.+++|+.-+++
T Consensus 78 ~~~kv~~~~g~ 88 (138)
T cd04497 78 RRVKIQSYNGK 88 (138)
T ss_pred EEEEEEEECCc
Confidence 99999877654
No 42
>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=95.70 E-value=0.077 Score=41.36 Aligned_cols=65 Identities=28% Similarity=0.494 Sum_probs=47.0
Q ss_pred EEEEEEEEecCceeEeeccCceeeEEEEEEecCCCcEEEEEEeCcchhhhhhhHHhhhccCCccEEEEEEEEEecCCCc
Q 008606 251 DVIGIVISVNPSVPILRKNGMETQRRILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVDVGFFPVLSVKSGKVNDFSGK 329 (560)
Q Consensus 251 DVIGvV~~V~~~~~i~~k~G~~~~kr~i~L~D~Sg~~I~vtLWg~~a~~~~~~l~~~~~~~~~~VV~l~~~rV~~f~G~ 329 (560)
+|.|+|.++.+... |+ ....+.|.|.+|..++|++|.+........ ...+.++.+. +++..++++
T Consensus 1 ~v~g~v~~~~~~~~-----~~--~~~~~~l~D~~~~~i~~~~~~~~~~~~~~~------~~~g~~v~v~-g~v~~~~~~ 65 (75)
T cd03524 1 TIVGIVVAVEEIRT-----EG--KVLIFTLTDGTGGTIRVTLFGELAEELENL------LKEGQVVYIK-GKVKKFRGR 65 (75)
T ss_pred CeEEEEEeeccccc-----CC--eEEEEEEEcCCCCEEEEEEEchHHHHHHhh------ccCCCEEEEE-EEEEecCCe
Confidence 57899999877643 32 357899999995599999999877653222 2356677777 888877664
No 43
>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=95.44 E-value=0.063 Score=45.76 Aligned_cols=68 Identities=22% Similarity=0.437 Sum_probs=45.0
Q ss_pred EEEEEEEEecCceeEeeccCceeeEEEEEEecCCCcEEEEEEeCcchhhh--h------------h--hHHhhhccCCcc
Q 008606 251 DVIGIVISVNPSVPILRKNGMETQRRILNLKDTSGRSVELTLWGDFCNKE--G------------Q--KLQEMVDVGFFP 314 (560)
Q Consensus 251 DVIGvV~~V~~~~~i~~k~G~~~~kr~i~L~D~Sg~~I~vtLWg~~a~~~--~------------~--~l~~~~~~~~~~ 314 (560)
|++|+|+++.+.. .+..++|.|.|| .|+|.+|....... . . ...+.+ ..+.
T Consensus 1 ~ivG~V~sv~~~~----------~~~~~tLdDgTG-~Ie~~~W~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i--~~G~ 67 (92)
T cd04483 1 DILGTVVSRRERE----------TFYSFGVDDGTG-VVNCVCWKNLSYAEVSSRSDAARILKSALMALKQAKVL--EIGD 67 (92)
T ss_pred CeEEEEEEEEecC----------CeEEEEEecCCc-eEEEEEEcCcCccccccccccccccccccccccccccc--CCCC
Confidence 6899999986432 357899999999 79999998754110 0 0 001111 3456
Q ss_pred EEEEEEEEEecCCCc-eec
Q 008606 315 VLSVKSGKVNDFSGK-SIG 332 (560)
Q Consensus 315 VV~l~~~rV~~f~G~-sLs 332 (560)
+|-++ ++++.|+|+ .|.
T Consensus 68 vvrV~-G~i~~frg~~ql~ 85 (92)
T cd04483 68 LLRVR-GSIRTYRGEREIN 85 (92)
T ss_pred EEEEE-EEEeccCCeeEEE
Confidence 66666 688899996 554
No 44
>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=95.35 E-value=0.068 Score=42.64 Aligned_cols=63 Identities=25% Similarity=0.447 Sum_probs=44.9
Q ss_pred eEEEEEEEEecCceeEeeccCceeeEEEEEEecCCCcEEEEEEeCcchhhhhhhHHhhhccCCccEEEEEEEEEecCCCc
Q 008606 250 VDVIGIVISVNPSVPILRKNGMETQRRILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVDVGFFPVLSVKSGKVNDFSGK 329 (560)
Q Consensus 250 VDVIGvV~~V~~~~~i~~k~G~~~~kr~i~L~D~Sg~~I~vtLWg~~a~~~~~~l~~~~~~~~~~VV~l~~~rV~~f~G~ 329 (560)
|.|.|.|+++. +.+. ....++|.|.|| .|.|++|++....+ .+.+ ..+.+|.+. ++++.+++.
T Consensus 1 V~v~G~V~~~~-------~~~~--~~~~~~l~D~tg-~i~~~~~~~~~~~~----~~~l--~~g~~v~v~-G~v~~~~~~ 63 (75)
T PF01336_consen 1 VTVEGRVTSIR-------RSGG--KIVFFTLEDGTG-SIQVVFFNEEYERF----REKL--KEGDIVRVR-GKVKRYNGG 63 (75)
T ss_dssp EEEEEEEEEEE-------EEET--TEEEEEEEETTE-EEEEEEETHHHHHH----HHTS---TTSEEEEE-EEEEEETTS
T ss_pred CEEEEEEEEEE-------cCCC--CEEEEEEEECCc-cEEEEEccHHhhHH----hhcC--CCCeEEEEE-EEEEEECCc
Confidence 56889999987 1121 356899999998 99999999554443 2222 467888888 888887654
No 45
>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=95.12 E-value=0.26 Score=42.90 Aligned_cols=69 Identities=12% Similarity=0.207 Sum_probs=53.0
Q ss_pred EEEEEEEecccceeccCCCCCcEEEEEEEeCCCCeEEEEEcchhHHHHHhhc----ccCcEEEEee-eEEecCC
Q 008606 130 IKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAVVDRFYEII----EVGRVYLISK-GSLKPAQ 198 (560)
Q Consensus 130 Ik~RV~~k~~ir~~~n~~g~gkvf~~~L~D~~g~~I~at~~~~~~~kf~~~l----~eG~vY~Is~-~~V~~a~ 198 (560)
+.|-|+.-+++........+.....|.|.|..+..++++.|++.|..|...+ ..+-|+.+-. .+|+.-+
T Consensus 2 viG~i~~v~~~~~~~~~~~~~~kr~~~i~D~~~~~l~~tlwG~~A~~f~~~~~~~~~~~~VVav~~~~rV~~~~ 75 (106)
T cd04481 2 VIGVIVDVGPLEELPPVNKPSRKLDFEIRDLSDERLKCTLWGEYAEEFDAKFQSAGNGEPVVAVLRFWKIKEYK 75 (106)
T ss_pred eeEEEEEecceEecccCCccceEEEEEEEeCCCCEEEEEEEHHHHHHHHHHHHHhCCCCcEEEEEEeEEEEEEc
Confidence 3456667777766554333556789999999999999999999999999887 4777887766 7887654
No 46
>PF15489 CTC1: CST, telomere maintenance, complex subunit CTC1
Probab=94.98 E-value=8.6 Score=46.20 Aligned_cols=319 Identities=16% Similarity=0.158 Sum_probs=162.2
Q ss_pred cccCCCCCceEEEEEEEEecccceeccCCCCCcEEEEEEEeCC-CCeEEEEEcchhHHHHHhhcccCcEEEEeee-----
Q 008606 119 AALNPYQGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSD-GGEIRVTCFNAVVDRFYEIIEVGRVYLISKG----- 192 (560)
Q Consensus 119 ~~L~p~~~~w~Ik~RV~~k~~ir~~~n~~g~gkvf~~~L~D~~-g~~I~at~~~~~~~kf~~~l~eG~vY~Is~~----- 192 (560)
...-+....+.+.|..++.+.... +...+.|. . -..-|+. ..++-..|.+. .-+|++.|+.|.||.+---
T Consensus 698 ~s~~~~~~tlsF~~~g~wlGg~q~-~eg~~~~~-~-e~~~~~~~~~kVlLlF~G~-svrWF~fLhpg~vYRLva~~~~~p 773 (1144)
T PF15489_consen 698 ASSEVPKPTLSFQVSGSWLGGTQR-KEGTGWGP-P-EPLEDENKDQKVLLLFLGS-SVRWFPFLHPGQVYRLVAPNSPDP 773 (1144)
T ss_pred CCcccCCCceEEEEEEEEecceEe-ccCcccCC-C-CcCcccCCCceEEEEEecC-ceeeEeEecCCcEEEEecCCCCCc
Confidence 333344567889999888877654 21111111 1 1122333 44555444454 5689999999999988432
Q ss_pred EEe--cCCCc--cccCCCeeEEEEcccceEEeccCCCCCCCccc-----ccccCccchhcc-cCCceeEEEEEEEEecCc
Q 008606 193 SLK--PAQKN--FNHLKNEWEIFLEATSTVDLCTEEDDSIPKQQ-----FSFRHISEIESA-ENNSIVDVIGIVISVNPS 262 (560)
Q Consensus 193 ~V~--~a~~~--y~~~~~~yeI~f~~~T~I~~~~d~~~~iP~~~-----f~f~~i~dI~~~-~~~~~VDVIGvV~~V~~~ 262 (560)
.|- .+-.. ---..-.-.+++-.+=+++... ..++|..- +--.++.|+..- ..+.+|.+-|+|.+..-.
T Consensus 774 ~l~~~s~~s~r~l~~~~~~scl~vq~~W~le~~~--~~d~~~~l~~~~~~~~ssl~~lls~s~s~sLVSFs~~I~srt~c 851 (1144)
T PF15489_consen 774 MLFGSSCVSQRPLELAGCPSCLTVQDDWTLELES--SQDIPPVLRISKLLPESSLSELLSSSSSDSLVSFSAEILSRTLC 851 (1144)
T ss_pred eeecCCCcccccccccCCCccEEeCCCceecccc--cccchhhhhhcccCccccHHHHhccCCCCceEEEEEEEEEeeec
Confidence 110 00000 0001111222332222232221 12344321 123456666552 468899999999987443
Q ss_pred eeEe----eccCce-----e--eEEEEEEecCCC-cEEEEEEeCcchhhhhhhHHhhhccCCccEEEEEEE--EEecCCC
Q 008606 263 VPIL----RKNGME-----T--QRRILNLKDTSG-RSVELTLWGDFCNKEGQKLQEMVDVGFFPVLSVKSG--KVNDFSG 328 (560)
Q Consensus 263 ~~i~----~k~G~~-----~--~kr~i~L~D~Sg-~~I~vtLWg~~a~~~~~~l~~~~~~~~~~VV~l~~~--rV~~f~G 328 (560)
+... +|.|.. . ...-+++.|..+ ..+.|.+=.-...- -.....|.+|.|.+. ||+..++
T Consensus 852 e~~~~~~~~~~~~~~~~~~~vkltv~L~v~D~~~p~~ldVYi~~~h~p~-------plGLLPGA~V~f~~lerkVSRs~n 924 (1144)
T PF15489_consen 852 EPLNARRWSKPGNAIASRGCVKLTVALTVADCESPPHLDVYIEDPHLPY-------PLGLLPGARVLFSQLERKVSRSHN 924 (1144)
T ss_pred cCCccccccCCCCCcccccccceEEEEEEecCCCCCeEEEEecCCCCCC-------cccccCCceeeeehhhhhhhccCc
Confidence 3211 121211 1 223455566665 23333222211110 011124566666655 5556555
Q ss_pred ceecccCCeEEEECCChHHHHHHHHHHhcCCCccceeecccccccCCCccchhhhHHHHhhcCCCCCCCCceEEEEEEEE
Q 008606 329 KSIGTIPSTQLFINPDFAEAHELREWFDSGGKNAATVSISREIAAGGAKNEIHKTVSQIKNEGLGRSEKPDWVTVRAFIT 408 (560)
Q Consensus 329 ~sLs~~~~S~i~iNPdipEa~~L~~w~~~~g~~~~~~sls~~~~~~~~~~~~~ktI~~I~~~~~g~~e~~~~~~v~atI~ 408 (560)
.++.....|.|.+-...+|.. .+.......+.++... ...+-...+.+.|+
T Consensus 925 VYC~~~psS~VtVlS~p~~t~-------------------------~~~~~P~~~L~~~~~~----~~~~~~a~~~chVV 975 (1144)
T PF15489_consen 925 VYCCFLPSSSVTVLSFPPETN-------------------------VSPPLPHIYLAELLQG----SQSPFQARVSCHVV 975 (1144)
T ss_pred EEEEEcCCceEEEEecCcccC-------------------------CCCCCCeEEehhhhCC----CCCCceEEEEEEEE
Confidence 566555556655432211110 0112234455555432 22233567888888
Q ss_pred EEeCCCeEEeCCCCCcCccccCceeeecCCeeecCc----CCCccCCceeEEEEEEEEEeCCCeEEEEEehhhhhhhcCC
Q 008606 409 FIKSDSFCYTACPLMIGDRQCNKKVTQSGNRWQCDR----CNQEIDECDYRYLLQAQIQDQTGLTWVTAFQESGEEILGC 484 (560)
Q Consensus 409 ~I~~d~~~Y~aC~~~~~~~~C~KKv~~~~~~~~C~k----C~~~~~~~~~rY~l~~~i~D~Tgs~~~~~Fd~~ae~llG~ 484 (560)
.|..=. .-..|. .|..-.... .|.+ |-. .....+=.+.+.+.|+||++.+++-++..-.+||.
T Consensus 976 ~V~~l~-L~WvCa------~C~si~~qg----~Csr~~p~C~s--~~sV~qA~ar~~vEDGTaeA~v~~~~~~V~~lLgL 1042 (1144)
T PF15489_consen 976 SVLSLQ-LQWVCA------HCGSICPQG----RCSRQSPPCPS--QTSVFQASARLLVEDGTAEAVVWCRGHHVAALLGL 1042 (1144)
T ss_pred EEEEEE-eeehhh------hccCcccCC----cCCCCCCCCCC--CcceeeEEEEEEEecCCeeEEEEECCcHHHHHhCC
Confidence 775432 223455 555322221 3532 432 34677888899999999999999999999999999
Q ss_pred CHHHHHHh
Q 008606 485 PAKELYML 492 (560)
Q Consensus 485 sA~el~~~ 492 (560)
+..|...+
T Consensus 1043 ~~~eW~~L 1050 (1144)
T PF15489_consen 1043 SPSEWESL 1050 (1144)
T ss_pred CHHHHHHH
Confidence 99876554
No 47
>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=94.87 E-value=0.16 Score=41.98 Aligned_cols=58 Identities=33% Similarity=0.441 Sum_probs=41.5
Q ss_pred eEEEEEEEEecCceeEeeccCceeeEEEEEEecCCCcEEEEEEeCcchh--hhhhhHHhhhccCCccEEEEEEEEEe
Q 008606 250 VDVIGIVISVNPSVPILRKNGMETQRRILNLKDTSGRSVELTLWGDFCN--KEGQKLQEMVDVGFFPVLSVKSGKVN 324 (560)
Q Consensus 250 VDVIGvV~~V~~~~~i~~k~G~~~~kr~i~L~D~Sg~~I~vtLWg~~a~--~~~~~l~~~~~~~~~~VV~l~~~rV~ 324 (560)
+=++|+|.++. .+|+|+. -++|.|.+| ++++++|.+... ++...| ..+.+|.+++ ++.
T Consensus 2 v~i~GiI~~v~-----~TK~g~~----~~~leD~~G-~~Ev~~F~~~~~~~~~~~~l------~~d~~v~v~g-~v~ 61 (79)
T cd04490 2 VSIIGMVNDVR-----STKNGHR----IVELEDTTG-RITVLLTKDKEELFEEAEDI------LPDEVIGVSG-TVS 61 (79)
T ss_pred EEEEEEEeEEE-----EcCCCCE----EEEEECCCC-EEEEEEeCchhhhhhhhhhc------cCCCEEEEEE-EEe
Confidence 34789999998 3566763 899999999 899999999887 643333 2345555554 443
No 48
>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=94.37 E-value=0.29 Score=38.65 Aligned_cols=60 Identities=17% Similarity=0.221 Sum_probs=41.3
Q ss_pred EEEEEEEEecccceeccCCCCCcEEEEEEEeCCCCeEEEEEcchhHHHHHhhcccCcEEEEeeeEEec
Q 008606 129 AIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISKGSLKP 196 (560)
Q Consensus 129 ~Ik~RV~~k~~ir~~~n~~g~gkvf~~~L~D~~g~~I~at~~~~~~~kf~~~l~eG~vY~Is~~~V~~ 196 (560)
+|+|+|++.... .. + .++.+.+.|.| +++.|.+++|+.. ......+++|+.|.+.+ ++..
T Consensus 1 ~i~~~V~~~~~~-~~---~-~~~~~~~~~~D-~~g~i~~~~F~~~-~~~~~~~~~G~~~~v~G-kv~~ 60 (75)
T cd04488 1 TVEGTVVSVEVV-PR---R-GRRRLKVTLSD-GTGTLTLVFFNFQ-PYLKKQLPPGTRVRVSG-KVKR 60 (75)
T ss_pred CEEEEEEEEEec-cC---C-CccEEEEEEEc-CCCEEEEEEECCC-HHHHhcCCCCCEEEEEE-EEee
Confidence 377888775321 11 1 23689999999 5889999999831 12357799999998874 4443
No 49
>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=94.27 E-value=0.28 Score=39.61 Aligned_cols=60 Identities=17% Similarity=0.335 Sum_probs=43.0
Q ss_pred EEEEEEEecccceeccCCCCCcEEEEEEEeCCCCeEEEEEcchhHHHHHhhcccCcEEEEeeeEEe
Q 008606 130 IKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISKGSLK 195 (560)
Q Consensus 130 Ik~RV~~k~~ir~~~n~~g~gkvf~~~L~D~~g~~I~at~~~~~~~kf~~~l~eG~vY~Is~~~V~ 195 (560)
|.|.|..... ...++|. ..+.+.|.| ..+.|.+++|++..+++.+.|++|.+|.+.+ ++.
T Consensus 2 i~g~v~~~~~---~~~k~g~-~~~~~~l~D-~tg~~~~~~f~~~~~~~~~~l~~g~~v~v~G-~v~ 61 (84)
T cd04485 2 VAGLVTSVRR---RRTKKGK-RMAFVTLED-LTGSIEVVVFPETYEKYRDLLKEDALLLVEG-KVE 61 (84)
T ss_pred EEEEEEEeEE---EEcCCCC-EEEEEEEEe-CCCeEEEEECHHHHHHHHHHhcCCCEEEEEE-EEE
Confidence 4566655322 1222232 578888999 6778999999988778899999999998874 444
No 50
>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=92.60 E-value=0.63 Score=39.34 Aligned_cols=69 Identities=26% Similarity=0.388 Sum_probs=44.8
Q ss_pred eEEEEEEEEecCceeEeeccCceeeEEEEEEecCCCcEEEEEEeCcchhhhhhhHHhhhccCCccEEEEEEEEEecCCCc
Q 008606 250 VDVIGIVISVNPSVPILRKNGMETQRRILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVDVGFFPVLSVKSGKVNDFSGK 329 (560)
Q Consensus 250 VDVIGvV~~V~~~~~i~~k~G~~~~kr~i~L~D~Sg~~I~vtLWg~~a~~~~~~l~~~~~~~~~~VV~l~~~rV~~f~G~ 329 (560)
|.++|+|.++.... .+..++|.|.|| +|++.+|......- ....+.+ ..+.+|.+ .++++.|+|+
T Consensus 2 v~~vG~V~~~~~~~----------~~~~~tL~D~TG-~I~~~~W~~~~~~~-~~~~~~~--~~g~~v~v-~G~v~~~~g~ 66 (95)
T cd04478 2 VTLVGVVRNVEEQS----------TNITYTIDDGTG-TIEVRQWLDDDNDD-SSEVEPI--EEGTYVRV-FGNLKSFQGK 66 (95)
T ss_pred EEEEEEEEeeeEcc----------cEEEEEEECCCC-cEEEEEeCCCCCcc-ccccccc--ccCCEEEE-EEEEcccCCe
Confidence 77899999876431 457899999999 89999998764210 0001112 23455544 4577899986
Q ss_pred -eecc
Q 008606 330 -SIGT 333 (560)
Q Consensus 330 -sLs~ 333 (560)
.|..
T Consensus 67 ~ql~i 71 (95)
T cd04478 67 KSIMA 71 (95)
T ss_pred eEEEE
Confidence 5653
No 51
>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=92.29 E-value=1 Score=36.17 Aligned_cols=65 Identities=29% Similarity=0.425 Sum_probs=41.7
Q ss_pred EEEEEEEecCceeEeeccCceeeEEEEEEecCCCcEEEEEEeCcchhhhhhhHHhhhccCCccEEEEEEEEEecCCCc
Q 008606 252 VIGIVISVNPSVPILRKNGMETQRRILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVDVGFFPVLSVKSGKVNDFSGK 329 (560)
Q Consensus 252 VIGvV~~V~~~~~i~~k~G~~~~kr~i~L~D~Sg~~I~vtLWg~~a~~~~~~l~~~~~~~~~~VV~l~~~rV~~f~G~ 329 (560)
++|+|.++.. ..+|+|+. ...++|.|.+| .+++++|.+...++ ...+ ..+.++.+. +++..|+|.
T Consensus 2 i~g~v~~~~~---~~~k~g~~--~~~~~l~D~tg-~~~~~~f~~~~~~~----~~~l--~~g~~v~v~-G~v~~~~~~ 66 (84)
T cd04485 2 VAGLVTSVRR---RRTKKGKR--MAFVTLEDLTG-SIEVVVFPETYEKY----RDLL--KEDALLLVE-GKVERRDGG 66 (84)
T ss_pred EEEEEEEeEE---EEcCCCCE--EEEEEEEeCCC-eEEEEECHHHHHHH----HHHh--cCCCEEEEE-EEEEecCCc
Confidence 5778877544 23456653 56889999999 79999998664333 2222 245555554 477777663
No 52
>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=91.60 E-value=0.79 Score=37.04 Aligned_cols=55 Identities=22% Similarity=0.350 Sum_probs=42.5
Q ss_pred EEEEEEEEecccceeccCCCCCcEEEEEEEeCCCCeEEEEEcchhHHHHHhhcccCcEEEEeee
Q 008606 129 AIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISKG 192 (560)
Q Consensus 129 ~Ik~RV~~k~~ir~~~n~~g~gkvf~~~L~D~~g~~I~at~~~~~~~kf~~~l~eG~vY~Is~~ 192 (560)
.|.|-|+. +|. . + .| ..-++|.| ..++|.+++|.+..+++.+.|++|+.+.+.+-
T Consensus 3 ~v~g~v~~---i~~-t-k--~g-~~~~~L~D-~~~~i~~~~f~~~~~~~~~~l~~g~~v~v~g~ 57 (78)
T cd04489 3 WVEGEISN---LKR-P-S--SG-HLYFTLKD-EDASIRCVMWRSNARRLGFPLEEGMEVLVRGK 57 (78)
T ss_pred EEEEEEec---CEE-C-C--Cc-EEEEEEEe-CCeEEEEEEEcchhhhCCCCCCCCCEEEEEEE
Confidence 46666664 343 1 2 23 77788999 66899999999999999999999999888653
No 53
>PTZ00401 aspartyl-tRNA synthetase; Provisional
Probab=91.44 E-value=1.9 Score=48.62 Aligned_cols=99 Identities=20% Similarity=0.207 Sum_probs=70.4
Q ss_pred CcceeccccCCCC---CceEEEEEEEEecccceeccCCCCCcEEEEEEEeCCCCeEEEEEcc-----hhHHHHHhhcccC
Q 008606 113 ARIIPIAALNPYQ---GRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFN-----AVVDRFYEIIEVG 184 (560)
Q Consensus 113 ~~~~pI~~L~p~~---~~w~Ik~RV~~k~~ir~~~n~~g~gkvf~~~L~D~~g~~I~at~~~-----~~~~kf~~~l~eG 184 (560)
..++.|++|++.. ..-+|+|||.++ |. .|++.=++|.| .++.|+|++-. ..+-+|-..|..|
T Consensus 63 ~~~~~i~~l~~~~~~g~~V~v~Grv~~~---R~------~Gk~~Fl~LRd-~~~~iQ~v~~~~~~~~~~~~~~~~~l~~e 132 (550)
T PTZ00401 63 RTFIPVAVLSKPELVDKTVLIRARVSTT---RK------KGKMAFMVLRD-GSDSVQAMAAVEGDVPKEMIDFIGQIPTE 132 (550)
T ss_pred CceEEHHHCCccccCCCEEEEEEEEEEE---ec------CCCeEEEEEEe-CCcCEEEEEECCCccCHHHHHHHhcCCCC
Confidence 4689999998765 467899999763 33 34665567888 56699999841 2345677789999
Q ss_pred cEEEEeeeEEecCCCccccCCCeeEEEEcccceEEec
Q 008606 185 RVYLISKGSLKPAQKNFNHLKNEWEIFLEATSTVDLC 221 (560)
Q Consensus 185 ~vY~Is~~~V~~a~~~y~~~~~~yeI~f~~~T~I~~~ 221 (560)
+++.+.+.-+++....-+....++||..++-..+..+
T Consensus 133 siV~V~G~v~~~~~~~~~~~~~~~El~v~~i~vls~a 169 (550)
T PTZ00401 133 SIVDVEATVCKVEQPITSTSHSDIELKVKKIHTVTES 169 (550)
T ss_pred CEEEEEEEEEecCccCCCCCCccEEEEeeEEEEEeCC
Confidence 9999999766654332234556899999876666655
No 54
>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=91.39 E-value=1.1 Score=37.02 Aligned_cols=55 Identities=22% Similarity=0.119 Sum_probs=42.3
Q ss_pred EEEEEEEEecccceeccCCCCCcEEEEEEEeCCCCeEEEEEcchhHH--HHHhhcccCcEEEEeee
Q 008606 129 AIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAVVD--RFYEIIEVGRVYLISKG 192 (560)
Q Consensus 129 ~Ik~RV~~k~~ir~~~n~~g~gkvf~~~L~D~~g~~I~at~~~~~~~--kf~~~l~eG~vY~Is~~ 192 (560)
.+.|.|+... .+++| +. -+.|-| ..|.+.+++|.+..+ ++.+.|++|.++.|.+-
T Consensus 3 ~i~GiI~~v~-----~TK~g--~~-~~~leD-~~G~~Ev~~F~~~~~~~~~~~~l~~d~~v~v~g~ 59 (79)
T cd04490 3 SIIGMVNDVR-----STKNG--HR-IVELED-TTGRITVLLTKDKEELFEEAEDILPDEVIGVSGT 59 (79)
T ss_pred EEEEEEeEEE-----EcCCC--CE-EEEEEC-CCCEEEEEEeCchhhhhhhhhhccCCCEEEEEEE
Confidence 4666676643 22334 34 667778 788999999999999 99999999999998773
No 55
>PRK06751 single-stranded DNA-binding protein; Provisional
Probab=91.22 E-value=1.4 Score=42.12 Aligned_cols=64 Identities=22% Similarity=0.296 Sum_probs=51.0
Q ss_pred CCceEEEEEEEEecccceeccCCCCCcEEEEEEE------eCCC----CeEEEEEcchhHHHHHhhcccCcEEEEee
Q 008606 125 QGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLL------DSDG----GEIRVTCFNAVVDRFYEIIEVGRVYLISK 191 (560)
Q Consensus 125 ~~~w~Ik~RV~~k~~ir~~~n~~g~gkvf~~~L~------D~~g----~~I~at~~~~~~~kf~~~l~eG~vY~Is~ 191 (560)
+.+..|.+||++--++|...+ | ..+.+|.|+ ++.| .-|.+++|+.+|+.+...|+.|+-+.|.+
T Consensus 2 mN~V~LiGrL~~DpelR~t~s--G-~~v~~fslAvnr~~~~~~ge~~tdwi~~v~wgk~Ae~~~~~l~KG~~V~VeG 75 (173)
T PRK06751 2 MNRVILVGRLTKDPDLRYTPN--G-VAVATFTLAVNRAFANQQGEREADFINCVIWRKQAENVANYLKKGSLAGVDG 75 (173)
T ss_pred ceEEEEEEEECCCCcEEECCC--C-CEEEEEEEEEccceecCCCCEEEEEEEEEEeCcHHHHHHHHcCCCCEEEEEE
Confidence 467899999999999886532 3 257777775 3223 57899999999999999999999999876
No 56
>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=90.47 E-value=1.3 Score=35.90 Aligned_cols=43 Identities=21% Similarity=0.328 Sum_probs=34.7
Q ss_pred cEEEEEEEeCCCCeEEEEEcchhHHHHHhhcccCcEEEEeeeEEec
Q 008606 151 KVFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISKGSLKP 196 (560)
Q Consensus 151 kvf~~~L~D~~g~~I~at~~~~~~~kf~~~l~eG~vY~Is~~~V~~ 196 (560)
+.+.+.|-| ..+.|.+++|++.. .+...|++|.++.+. ++|..
T Consensus 19 ~~~~~~l~D-~tg~i~~~~f~~~~-~~~~~l~~g~~v~v~-G~v~~ 61 (83)
T cd04492 19 PYLALTLQD-KTGEIEAKLWDASE-EDEEKFKPGDIVHVK-GRVEE 61 (83)
T ss_pred cEEEEEEEc-CCCeEEEEEcCCCh-hhHhhCCCCCEEEEE-EEEEE
Confidence 578888999 67789999999654 457899999999998 66643
No 57
>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=90.14 E-value=1.6 Score=40.37 Aligned_cols=85 Identities=11% Similarity=0.149 Sum_probs=62.5
Q ss_pred ceeccccCCC-CCceEEEEEEEEecccceeccCCCCCcEEEEEEEeCCC-------CeEEEEEcchhHHHHHhhcccCcE
Q 008606 115 IIPIAALNPY-QGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDG-------GEIRVTCFNAVVDRFYEIIEVGRV 186 (560)
Q Consensus 115 ~~pI~~L~p~-~~~w~Ik~RV~~k~~ir~~~n~~g~gkvf~~~L~D~~g-------~~I~at~~~~~~~kf~~~l~eG~v 186 (560)
|+||+++.-. ...-.|.|-|+.....+... .+|..-.++|.|.|... ..|.+.+|....+.+-..-..|+|
T Consensus 1 ~~~l~~~~~~~~~~vnvigVV~~~~~p~~~~-t~g~D~~~tl~i~D~S~~~~~~~~~~l~v~iF~~~~~~LP~v~~~GDi 79 (146)
T PF02765_consen 1 YTPLSTAKEKFGKFVNVIGVVVDFSPPNPKK-TRGTDYMCTLTITDPSLNDSNQKLSGLTVNIFRPHKESLPNVKSVGDI 79 (146)
T ss_dssp BCCGGGSCTTSSEEEEEEEEEEEEEEECTEE-ESSSCEEEEEEEEBTTCSCSSCCCCEEEEEEEESSHHHSCTTCSTTHE
T ss_pred CccchhhhhcCCCEEEEEEEEEEccCCcceE-cCCCcEEEEEEEECCCCCccccccCCEEEEEECCCHHHCCCCCCCCCE
Confidence 4677744333 34678888888877762222 13444678999999754 589999999888888766666999
Q ss_pred EEEeeeEEecCCCc
Q 008606 187 YLISKGSLKPAQKN 200 (560)
Q Consensus 187 Y~Is~~~V~~a~~~ 200 (560)
+.+.+++|+.-+.+
T Consensus 80 i~l~r~kv~~~~~~ 93 (146)
T PF02765_consen 80 IRLRRVKVQSYNGK 93 (146)
T ss_dssp EEEEEEEEEEETTE
T ss_pred EEEEEEEEEEECCE
Confidence 99999999877654
No 58
>PRK02801 primosomal replication protein N; Provisional
Probab=90.05 E-value=1.6 Score=37.78 Aligned_cols=68 Identities=15% Similarity=0.080 Sum_probs=53.4
Q ss_pred CCceEEEEEEEEecccceeccCCCCCcEEEEEEEeC----C-CC------eEEEEEcchhHHHHHhhcccCcEEEEeeeE
Q 008606 125 QGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDS----D-GG------EIRVTCFNAVVDRFYEIIEVGRVYLISKGS 193 (560)
Q Consensus 125 ~~~w~Ik~RV~~k~~ir~~~n~~g~gkvf~~~L~D~----~-g~------~I~at~~~~~~~kf~~~l~eG~vY~Is~~~ 193 (560)
+++..+.||+++.-++|...+ |. .+.+|.|.=. + +. .|.|++|+..++.+...+..|+.+.|+++.
T Consensus 2 mN~v~L~Grl~~dpelr~Tp~--G~-~v~~f~La~~~~~~ea~~~r~~~~~i~~va~G~~Ae~~~~~l~kGs~v~V~G~L 78 (101)
T PRK02801 2 TNRLVLSGTVCRTPKRKVSPS--GI-PHCQFVLEHRSVQEEAGLHRQAWCRMPVIVSGNQFQAITQSITVGSKITVQGFI 78 (101)
T ss_pred ccEEEEEEEECcCcceEECCC--CC-eEEEEEEEEeCeEecCCCceeEEEEEEEEEEcHHHHHHHhhcCCCCEEEEEEEE
Confidence 466789999999999987532 32 6777776421 2 22 299999999999999999999999999986
Q ss_pred Ee
Q 008606 194 LK 195 (560)
Q Consensus 194 V~ 195 (560)
-.
T Consensus 79 ~~ 80 (101)
T PRK02801 79 SC 80 (101)
T ss_pred EE
Confidence 54
No 59
>PF11325 DUF3127: Domain of unknown function (DUF3127); InterPro: IPR021474 This bacterial family of proteins has no known function.
Probab=89.46 E-value=2.4 Score=35.53 Aligned_cols=71 Identities=20% Similarity=0.301 Sum_probs=51.4
Q ss_pred EEEEEEEecCceeEeeccCceeeEEEEEEecCCC--cEEEEEEeCcchhhhhhhHHhhhccCCccEEEE-EEEEEecCCC
Q 008606 252 VIGIVISVNPSVPILRKNGMETQRRILNLKDTSG--RSVELTLWGDFCNKEGQKLQEMVDVGFFPVLSV-KSGKVNDFSG 328 (560)
Q Consensus 252 VIGvV~~V~~~~~i~~k~G~~~~kr~i~L~D~Sg--~~I~vtLWg~~a~~~~~~l~~~~~~~~~~VV~l-~~~rV~~f~G 328 (560)
+-|.|+.+-|..+-.+++| ..||++.|..... ..|.+.+||+.+..+ .....+..|.+ -+.+-.+|+|
T Consensus 2 i~Gkii~~l~~~~g~s~~G--w~Kre~Vlet~~qYP~~i~f~~~~dk~~~l-------~~~~~Gd~V~Vsf~i~~RE~~g 72 (84)
T PF11325_consen 2 ITGKIIKVLPEQQGVSKNG--WKKREFVLETEEQYPQKICFEFWGDKIDLL-------DNFQVGDEVKVSFNIEGREWNG 72 (84)
T ss_pred cccEEEEEecCcccCcCCC--cEEEEEEEeCCCcCCceEEEEEEcchhhhh-------ccCCCCCEEEEEEEeeccEecc
Confidence 4688777777776566777 7899999985553 579999999988763 12245666655 4677888998
Q ss_pred cee
Q 008606 329 KSI 331 (560)
Q Consensus 329 ~sL 331 (560)
+..
T Consensus 73 r~f 75 (84)
T PF11325_consen 73 RWF 75 (84)
T ss_pred eEe
Confidence 744
No 60
>PF14951 DUF4503: Domain of unknown function (DUF4503)
Probab=89.30 E-value=0.94 Score=47.35 Aligned_cols=84 Identities=18% Similarity=0.354 Sum_probs=68.4
Q ss_pred ceEEEEEEEEEEeCCC-eEEeCCCCCcCccccCc-eeee---cCCeeecCcCCCccCCceeEEEEEEEEEeC---CCeEE
Q 008606 399 DWVTVRAFITFIKSDS-FCYTACPLMIGDRQCNK-KVTQ---SGNRWQCDRCNQEIDECDYRYLLQAQIQDQ---TGLTW 470 (560)
Q Consensus 399 ~~~~v~atI~~I~~d~-~~Y~aC~~~~~~~~C~K-Kv~~---~~~~~~C~kC~~~~~~~~~rY~l~~~i~D~---Tgs~~ 470 (560)
....|.|+|+.++.+. |-++.|. .|+. |+.. +.+.++|..|.+.+..|..|--|.+-+.=. -.++.
T Consensus 255 SiCsvqG~VvgVdE~TAfSWPvCd------~CGn~rLe~~pe~rg~~~C~~Cs~~V~sP~~r~~LeVfl~Cps~p~ctvK 328 (389)
T PF14951_consen 255 SICSVQGTVVGVDESTAFSWPVCD------RCGNGRLEQSPEDRGAFSCGDCSRVVTSPVLRMHLEVFLDCPSRPQCTVK 328 (389)
T ss_pred ceEEEeeEEEEecCcccccCcccc------ccCCccceeCccCCCceeccchhhhccCcceeeeEEEEEeCCCCCCceEE
Confidence 4678999999999877 8999999 8954 6763 344899999999999999999999988733 35778
Q ss_pred EEEehhhhhhhcCCCHHH
Q 008606 471 VTAFQESGEEILGCPAKE 488 (560)
Q Consensus 471 ~~~Fd~~ae~llG~sA~e 488 (560)
+-+.++.-..||.-.|.|
T Consensus 329 VKL~q~sIsslL~~aa~e 346 (389)
T PF14951_consen 329 VKLLQRSISSLLMSAASE 346 (389)
T ss_pred EEEhHHHHHHHHhhhhcc
Confidence 988888888887666643
No 61
>PF15072 DUF4539: Domain of unknown function (DUF4539)
Probab=88.99 E-value=1.7 Score=36.62 Aligned_cols=61 Identities=20% Similarity=0.207 Sum_probs=48.0
Q ss_pred EEEEEEeCCCCeEEEEEcchhHHHHHhhcccCcEEEEeeeEEecCCCccccCCCeeEEEEcccceEEe
Q 008606 153 FSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISKGSLKPAQKNFNHLKNEWEIFLEATSTVDL 220 (560)
Q Consensus 153 f~~~L~D~~g~~I~at~~~~~~~kf~~~l~eG~vY~Is~~~V~~a~~~y~~~~~~yeI~f~~~T~I~~ 220 (560)
..+.|.| -.|+|+|++-.+..++|.+.|..|.+..+.+..|-. ++...+-|..+....+..
T Consensus 21 ~~v~l~D-pTG~i~~tiH~~v~~~y~~~l~~GavLlLk~V~Vf~------ps~~~~yLnIt~~Nlv~v 81 (86)
T PF15072_consen 21 AFVVLKD-PTGEIRGTIHRKVLEEYGDELSPGAVLLLKDVTVFS------PSPRSHYLNITLNNLVRV 81 (86)
T ss_pred eEEEEEC-CCCcEEEEEeHHHHhhcCCccccCEEEEEeeeeEEe------cCCCccEEEEehhHeeeE
Confidence 5788999 677999999999999999999999999999987743 444455566555555444
No 62
>PRK07275 single-stranded DNA-binding protein; Provisional
Probab=88.84 E-value=1.6 Score=41.18 Aligned_cols=64 Identities=14% Similarity=0.193 Sum_probs=51.7
Q ss_pred CCceEEEEEEEEecccceeccCCCCCcEEEEEEE------eC----CCCeEEEEEcchhHHHHHhhcccCcEEEEee
Q 008606 125 QGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLL------DS----DGGEIRVTCFNAVVDRFYEIIEVGRVYLISK 191 (560)
Q Consensus 125 ~~~w~Ik~RV~~k~~ir~~~n~~g~gkvf~~~L~------D~----~g~~I~at~~~~~~~kf~~~l~eG~vY~Is~ 191 (560)
+.+..|.||+++--++|...+ |. .+.+|.|+ +. +.+-|++++|+..|+.+...|+.|+-+.|.+
T Consensus 2 ~N~v~LiGrL~~DPElr~t~s--G~-~v~~ftlAv~r~~~~~~ge~~tdfi~vv~wgk~Ae~~~~~l~KG~~V~VeG 75 (162)
T PRK07275 2 INNVVLVGRMTRDAELRYTPS--NV-AVATFTLAVNRTFKSQNGEREADFINCVIWRQQAENLANWAKKGALIGVTG 75 (162)
T ss_pred eeEEEEEEEECCCCeEEECCC--CC-EEEEEEEEEcCceecCCCCEeeeEEEEEEEcHHHHHHHHHcCCCCEEEEEE
Confidence 457789999999999987643 32 57778775 32 3467999999999999999999999999876
No 63
>PRK07459 single-stranded DNA-binding protein; Provisional
Probab=88.74 E-value=1.7 Score=38.93 Aligned_cols=64 Identities=13% Similarity=0.223 Sum_probs=52.4
Q ss_pred CCceEEEEEEEEecccceeccCCCCCcEEEEEEE------eCCCCeEEEEEcchhHHHHHhhcccCcEEEEee
Q 008606 125 QGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLL------DSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISK 191 (560)
Q Consensus 125 ~~~w~Ik~RV~~k~~ir~~~n~~g~gkvf~~~L~------D~~g~~I~at~~~~~~~kf~~~l~eG~vY~Is~ 191 (560)
++...|.||+.+--++|.+.+ |. .+.+|.|. |++.+-|.+++|+.+|+...+.|+.|+-+.+.+
T Consensus 3 ~N~v~LiGrL~~DPelr~t~~--G~-~v~~fslAv~~~~~~~~t~w~~v~~wg~~Ae~~~~~l~KG~~V~V~G 72 (121)
T PRK07459 3 LNSVTLVGRAGRDPEVRYFES--GS-VVCNLTLAVNRRSRDDEPDWFNLEIWGKTAQVAADYVKKGSLIGITG 72 (121)
T ss_pred ccEEEEEEEccCCCEEEEcCC--CC-EEEEEEEEecccccCCCceEEEEEEehHHHHHHHHHcCCCCEEEEEE
Confidence 356789999999888886543 32 57788876 246778999999999999999999999999876
No 64
>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=88.45 E-value=8.3 Score=33.44 Aligned_cols=77 Identities=22% Similarity=0.403 Sum_probs=50.2
Q ss_pred eEEEEEEEEecccceeccCCCCCcEEEEEEEeCCCCeEEEEEcch-----hHHHHHhhcccCcEEEEeeeEEecCCCccc
Q 008606 128 WAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNA-----VVDRFYEIIEVGRVYLISKGSLKPAQKNFN 202 (560)
Q Consensus 128 w~Ik~RV~~k~~ir~~~n~~g~gkvf~~~L~D~~g~~I~at~~~~-----~~~kf~~~l~eG~vY~Is~~~V~~a~~~y~ 202 (560)
-+|+|||.+. |. .|++.=++|.| .++.+++++... ...++...|..|+++.+.+.-++...
T Consensus 2 v~v~GwV~~~---R~------~g~~~Fi~lrd-~~~~lQ~v~~~~~~~~~~~~~~~~~l~~g~~V~v~G~v~~~~~---- 67 (108)
T cd04322 2 VSVAGRIMSK---RG------SGKLSFADLQD-ESGKIQVYVNKDDLGEEEFEDFKKLLDLGDIIGVTGTPFKTKT---- 67 (108)
T ss_pred EEEEEEEEEE---ec------CCCeEEEEEEE-CCeEEEEEEECCCCCHHHHHHHHhcCCCCCEEEEEEEEEecCC----
Confidence 3688888763 33 34655566889 568999988643 23445555999999999875444321
Q ss_pred cCCCeeEEEEcccceEEec
Q 008606 203 HLKNEWEIFLEATSTVDLC 221 (560)
Q Consensus 203 ~~~~~yeI~f~~~T~I~~~ 221 (560)
..+||....-..+.++
T Consensus 68 ---g~~El~~~~~~ils~~ 83 (108)
T cd04322 68 ---GELSIFVKEFTLLSKS 83 (108)
T ss_pred ---CCEEEEeCEeEEeecc
Confidence 4588877654444444
No 65
>PRK07772 single-stranded DNA-binding protein; Provisional
Probab=88.01 E-value=3 Score=40.30 Aligned_cols=64 Identities=16% Similarity=0.253 Sum_probs=50.0
Q ss_pred CCceEEEEEEEEecccceeccCCCCCcEEEEEEEe--------------CCCCeEEEEEcchhHHHHHhhcccCcEEEEe
Q 008606 125 QGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLD--------------SDGGEIRVTCFNAVVDRFYEIIEVGRVYLIS 190 (560)
Q Consensus 125 ~~~w~Ik~RV~~k~~ir~~~n~~g~gkvf~~~L~D--------------~~g~~I~at~~~~~~~kf~~~l~eG~vY~Is 190 (560)
.+..+|.+|+++--++|...+ | ..+.+|.|.- .+..-|.|++|+.+++.+...|+.|+-+.|.
T Consensus 4 ~~~VtLiGrL~~DPElR~t~s--G-~~va~FrVAv~~r~~~~~~g~~~d~~t~fi~V~~Wg~~Ae~va~~L~KGd~V~V~ 80 (186)
T PRK07772 4 DTTITVVGNLTADPELRFTPS--G-AAVANFTVASTPRTFDRQTNEWKDGEALFLRCSIWRQAAENVAESLTKGMRVIVT 80 (186)
T ss_pred cCEEEEEEEeCCCCeEEEcCC--C-CEEEEEEEEecCcceecCCCcEeccCceEEEEEEecHHHHHHHHhcCCCCEEEEE
Confidence 456789999999988887653 2 2566776651 1334789999999999999999999999987
Q ss_pred e
Q 008606 191 K 191 (560)
Q Consensus 191 ~ 191 (560)
+
T Consensus 81 G 81 (186)
T PRK07772 81 G 81 (186)
T ss_pred E
Confidence 6
No 66
>KOG0851 consensus Single-stranded DNA-binding replication protein A (RPA), large (70 kD) subunit and related ssDNA-binding proteins [Replication, recombination and repair]
Probab=87.94 E-value=0.77 Score=45.57 Aligned_cols=67 Identities=15% Similarity=0.130 Sum_probs=51.1
Q ss_pred eEEeCCCCCcCccccCceeeecCCeeecCcCCCccCCceeEEEEEEEEEeCCCeEEEEEehhhhhhhcCCCHHHHHH
Q 008606 415 FCYTACPLMIGDRQCNKKVTQSGNRWQCDRCNQEIDECDYRYLLQAQIQDQTGLTWVTAFQESGEEILGCPAKELYM 491 (560)
Q Consensus 415 ~~Y~aC~~~~~~~~C~KKv~~~~~~~~C~kC~~~~~~~~~rY~l~~~i~D~Tgs~~~~~Fd~~ae~llG~sA~el~~ 491 (560)
|+|..|+ .|+| -........|+.|+....+...+|++.....+.++. ..|...+..+.|.++..+..
T Consensus 160 ~~~~~~~------~~~~-~~~~~~~~~c~~~~~~~~~~~~~~~l~~~~~~~~~~---l~~~~~~~~~~G~~~~~~~~ 226 (246)
T KOG0851|consen 160 GFYLTFK------ICNK-SKFSKPVLWCEACGEQATDFGRKRSLGGGVIVIAPE---LLFWKIWRYFDGKNVRIVLA 226 (246)
T ss_pred eEEEEEe------eccc-ccccCceEEehhhcchHHhhhhheEecCCcEEccch---heeecccccccCCchheeec
Confidence 8999999 8998 111112689999999876666668888888888877 78888888888877765544
No 67
>PRK05733 single-stranded DNA-binding protein; Provisional
Probab=87.82 E-value=2.1 Score=40.84 Aligned_cols=65 Identities=20% Similarity=0.200 Sum_probs=50.8
Q ss_pred CCCceEEEEEEEEecccceeccCCCCCcEEEEEEE------eCC-------CCeEEEEEcchhHHHHHhhcccCcEEEEe
Q 008606 124 YQGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLL------DSD-------GGEIRVTCFNAVVDRFYEIIEVGRVYLIS 190 (560)
Q Consensus 124 ~~~~w~Ik~RV~~k~~ir~~~n~~g~gkvf~~~L~------D~~-------g~~I~at~~~~~~~kf~~~l~eG~vY~Is 190 (560)
+++...|.|||.+--++|.+.+ | ..+.+|.|. |.+ ..-+.+++|+..++.+.+.|+.|+.++|.
T Consensus 4 ~mNkV~LiGrlg~DPElr~t~n--G-~~va~fsVAv~~~~k~~~~Ge~~e~T~w~~Vv~fgk~Ae~v~~~l~KGs~V~Ve 80 (172)
T PRK05733 4 GVNKVILVGTCGQDPEVRYLPN--G-NAVTNLSLATSEQWTDKQSGQKVERTEWHRVSLFGKVAEIAGEYLRKGSQVYIE 80 (172)
T ss_pred cceEEEEEEEecCCCEEEECCC--C-CEEEEEEEEEcCccccCCCCcccccceEEEEEEehHHHHHHHHHhCCCCEEEEE
Confidence 3678899999999888887654 3 257777665 222 22399999999999999999999999997
Q ss_pred e
Q 008606 191 K 191 (560)
Q Consensus 191 ~ 191 (560)
+
T Consensus 81 G 81 (172)
T PRK05733 81 G 81 (172)
T ss_pred E
Confidence 6
No 68
>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=87.70 E-value=3.4 Score=33.32 Aligned_cols=62 Identities=27% Similarity=0.423 Sum_probs=39.2
Q ss_pred EEEEEEecCceeEeeccCceeeEEEEEEecCCCcEEEEEEeCcchhhhhhhHHhhhccCCccEEEEEEEEEecCCC
Q 008606 253 IGIVISVNPSVPILRKNGMETQRRILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVDVGFFPVLSVKSGKVNDFSG 328 (560)
Q Consensus 253 IGvV~~V~~~~~i~~k~G~~~~kr~i~L~D~Sg~~I~vtLWg~~a~~~~~~l~~~~~~~~~~VV~l~~~rV~~f~G 328 (560)
+.+|.++... .+|+|+ ....+.|.|.+| .+++++|++.... ...+ ..+.++.+. +++..|+|
T Consensus 3 ~~~v~~~~~~---~tk~g~--~~~~~~l~D~tg-~i~~~~f~~~~~~-----~~~l--~~g~~v~v~-G~v~~~~~ 64 (83)
T cd04492 3 FFLIKSKELR---TAKNGK--PYLALTLQDKTG-EIEAKLWDASEED-----EEKF--KPGDIVHVK-GRVEEYRG 64 (83)
T ss_pred EEEEEEeeee---cccCCC--cEEEEEEEcCCC-eEEEEEcCCChhh-----HhhC--CCCCEEEEE-EEEEEeCC
Confidence 4455555432 345565 367899999999 7999999965421 2222 345555555 67777766
No 69
>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=87.68 E-value=2.3 Score=34.29 Aligned_cols=40 Identities=20% Similarity=0.346 Sum_probs=30.7
Q ss_pred EEEEEEEEecCceeEeeccCceeeEEEEEEecCCCcEEEEEEeCcchhhh
Q 008606 251 DVIGIVISVNPSVPILRKNGMETQRRILNLKDTSGRSVELTLWGDFCNKE 300 (560)
Q Consensus 251 DVIGvV~~V~~~~~i~~k~G~~~~kr~i~L~D~Sg~~I~vtLWg~~a~~~ 300 (560)
=|.|.|.++.. +|.| ...++|.|.++ ++++++|.+.....
T Consensus 3 ~v~g~v~~i~~-----tk~g----~~~~~L~D~~~-~i~~~~f~~~~~~~ 42 (78)
T cd04489 3 WVEGEISNLKR-----PSSG----HLYFTLKDEDA-SIRCVMWRSNARRL 42 (78)
T ss_pred EEEEEEecCEE-----CCCc----EEEEEEEeCCe-EEEEEEEcchhhhC
Confidence 36788887653 3445 56899999998 89999999976654
No 70
>PLN02850 aspartate-tRNA ligase
Probab=87.65 E-value=5 Score=45.06 Aligned_cols=98 Identities=15% Similarity=0.129 Sum_probs=69.0
Q ss_pred CcceeccccCCCC--CceEEEEEEEEecccceeccCCCCCcEEEEEEEeCCCCeEEEEEcch------hHHHHHhhcccC
Q 008606 113 ARIIPIAALNPYQ--GRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNA------VVDRFYEIIEVG 184 (560)
Q Consensus 113 ~~~~pI~~L~p~~--~~w~Ik~RV~~k~~ir~~~n~~g~gkvf~~~L~D~~g~~I~at~~~~------~~~kf~~~l~eG 184 (560)
...+.|.+|++.. +..+|+|||.+. |. .|++.=++|.| .++.|++++... ..-+|...|..|
T Consensus 67 ~~~~~i~~l~~~~~g~~V~v~Grv~~~---R~------~gk~~Fl~Lrd-~~~~iQ~v~~~~~~~~~~~~~~~~~~l~~e 136 (530)
T PLN02850 67 REWTDVSDLGEELAGSEVLIRGRVHTI---RG------KGKSAFLVLRQ-SGFTVQCVVFVSEVTVSKGMVKYAKQLSRE 136 (530)
T ss_pred ceEeEhhhcchhhCCCEEEEEEEEEEE---cc------CCCeEEEEEEe-CCcCEEEEEECCccccCHHHHHHHhCCCCC
Confidence 4679999998754 578899999753 32 45654456788 678999998543 344677889999
Q ss_pred cEEEEeeeEEecCCCccccCCCeeEEEEcccceEEec
Q 008606 185 RVYLISKGSLKPAQKNFNHLKNEWEIFLEATSTVDLC 221 (560)
Q Consensus 185 ~vY~Is~~~V~~a~~~y~~~~~~yeI~f~~~T~I~~~ 221 (560)
+++.+.+--+++.. .-+....++||....-..+..+
T Consensus 137 s~V~V~G~v~~~~~-~~~~~t~~~El~~~~i~vls~a 172 (530)
T PLN02850 137 SVVDVEGVVSVPKK-PVKGTTQQVEIQVRKIYCVSKA 172 (530)
T ss_pred CEEEEEEEEEccCc-CCCCCCccEEEEEeEEEEEeCC
Confidence 99999886655432 2223334899999876666655
No 71
>PRK05813 single-stranded DNA-binding protein; Provisional
Probab=87.59 E-value=31 Score=34.18 Aligned_cols=164 Identities=15% Similarity=0.219 Sum_probs=97.8
Q ss_pred CCceEEEEEEEEecccceeccCCCCCcEEEEEEE----eCCCCeEEEEEcchhHHHHHhhcccCcEEEEeeeEEecCCCc
Q 008606 125 QGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLL----DSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISKGSLKPAQKN 200 (560)
Q Consensus 125 ~~~w~Ik~RV~~k~~ir~~~n~~g~gkvf~~~L~----D~~g~~I~at~~~~~~~kf~~~l~eG~vY~Is~~~V~~a~~~ 200 (560)
.++-.+.||+++--++|.-. .|+ .+..|.|. -..-+.|.+++|..+++... +..|+-+.+.+ +++ +
T Consensus 8 ~NkV~L~Grl~~d~e~~~~~--~G~-~~~~f~laV~R~s~~~D~i~v~v~~rlae~~~--l~kG~~v~VeG-qlr----s 77 (219)
T PRK05813 8 NNKVYLEGKVVSELEFSHEM--YGE-GFYNFKLEVPRLSDSKDILPVTVSERLLAGMD--LKVGTLVIVEG-QLR----S 77 (219)
T ss_pred cCEEEEEEEEcCCceEEEEe--CCe-EEEEEEEEeeccCCCccEEEEEEEhhhhhhhc--ccCCCEEEEEE-EEE----E
Confidence 35678999999998888632 344 35555543 13789999999999998777 99999998876 233 3
Q ss_pred ccc---CCCeeEEEEcccceEEeccCCCCCCCcccccccCccchhcccCCceeEEEEEEEEecCceeEeeccCceeeEEE
Q 008606 201 FNH---LKNEWEIFLEATSTVDLCTEEDDSIPKQQFSFRHISEIESAENNSIVDVIGIVISVNPSVPILRKNGMETQRRI 277 (560)
Q Consensus 201 y~~---~~~~yeI~f~~~T~I~~~~d~~~~iP~~~f~f~~i~dI~~~~~~~~VDVIGvV~~V~~~~~i~~k~G~~~~kr~ 277 (560)
|+. ..+.|.+.+-- -.|+.+... . .......|-++|.+..=-.++. +.+|+... .
T Consensus 78 y~~~~~G~~R~vl~V~a-~~i~~l~~~-~----------------~~~~~N~V~LiGrL~~DPelR~--t~~G~~va--~ 135 (219)
T PRK05813 78 YNKFIDGKNRLILTVFA-RNIEYCDER-S----------------DIKNPNEIFLDGYICKEPVYRT--TPFGREIA--D 135 (219)
T ss_pred eccCCCCcEEEEEEEEE-EEEEEccCC-C----------------ccCCccEEEEEEEccCCCeEEE--CCCCCEEE--E
Confidence 432 22344333321 123333211 0 0123457888999987533332 34576543 4
Q ss_pred EEEecCC----CcEEEEEEeCcchhhhhhhHHhhhccCCccEEEEEEE-EEecCC
Q 008606 278 LNLKDTS----GRSVELTLWGDFCNKEGQKLQEMVDVGFFPVLSVKSG-KVNDFS 327 (560)
Q Consensus 278 i~L~D~S----g~~I~vtLWg~~a~~~~~~l~~~~~~~~~~VV~l~~~-rV~~f~ 327 (560)
|.|.-.. -.-|.|++||..|+.. + .+ ..|.-|++.+- +...|.
T Consensus 136 f~lAvnr~~~~td~i~~v~wg~~Ae~~----~-~l--~KG~~V~V~GrL~sr~y~ 183 (219)
T PRK05813 136 LLLAVNRPYNKSDYIPCIAWGRNARFC----K-TL--EVGDNIRVWGRVQSREYQ 183 (219)
T ss_pred EEEEEcCCCCCceEEEEEEEhHHhHHH----h-hC--CCCCEEEEEEEEEecceE
Confidence 4443221 1369999999998752 2 12 45666666543 444564
No 72
>PRK07373 DNA polymerase III subunit alpha; Reviewed
Probab=87.25 E-value=2 Score=47.16 Aligned_cols=70 Identities=17% Similarity=0.276 Sum_probs=51.0
Q ss_pred eeccccC--CCCCceEEEEEEEEecccceeccCCCCCcEEEE-EEEeCCCCeEEEEEcchhHHHHHhhcccCcEEEEee
Q 008606 116 IPIAALN--PYQGRWAIKARVTAKGDLRRYNNARGDGKVFSF-DLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISK 191 (560)
Q Consensus 116 ~pI~~L~--p~~~~w~Ik~RV~~k~~ir~~~n~~g~gkvf~~-~L~D~~g~~I~at~~~~~~~kf~~~l~eG~vY~Is~ 191 (560)
.++++|. +.....+|-|.|+..- ....++| +.+-| .|-| ..|.|.+++|.+..+++.+.|++|.++.|.+
T Consensus 269 ~~~~~l~~~~~~~~v~vaG~I~~ik---~~~TKkG--~~maf~~leD-~tG~ie~vvFp~~y~~~~~~l~~~~~v~v~G 341 (449)
T PRK07373 269 INLSELEEQKEKTKVSAVVMLNEVK---KIVTKKG--DPMAFLQLED-LSGQSEAVVFPKSYERISELLQVDARLIIWG 341 (449)
T ss_pred cCHHHHhcccCCCEEEEEEEEEEeE---ecccCCC--CEEEEEEEEE-CCCCEEEEECHHHHHHHHHHhccCCEEEEEE
Confidence 4566664 2334567888887753 3333444 34555 4666 7889999999999999999999999999965
No 73
>COG5235 RFA2 Single-stranded DNA-binding replication protein A (RPA), medium (30 kD) subunit [DNA replication, recombination, and repair]
Probab=87.16 E-value=2.4 Score=41.15 Aligned_cols=74 Identities=23% Similarity=0.428 Sum_probs=44.2
Q ss_pred eeEEEEEEEEecCceeEeeccCceeeEEEEEEecCCCcEEEEEEeCcchhhhhhhHHhhhc-cCCccEEEEEEEEEecCC
Q 008606 249 IVDVIGIVISVNPSVPILRKNGMETQRRILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVD-VGFFPVLSVKSGKVNDFS 327 (560)
Q Consensus 249 ~VDVIGvV~~V~~~~~i~~k~G~~~~kr~i~L~D~Sg~~I~vtLWg~~a~~~~~~l~~~~~-~~~~~VV~l~~~rV~~f~ 327 (560)
.|-++|+|..+...+ .-..++|.|.+| .|+|+.|-..+... +... ...+.-| =.++-++.|+
T Consensus 68 ~V~fVGvvrni~~~t----------tn~~~~iEDGTG-~Ievr~W~~~~~~~-----e~~~d~~~~~yv-kV~G~lk~F~ 130 (258)
T COG5235 68 NVQFVGVVRNIKTST----------TNSMFVIEDGTG-SIEVRFWPGNSYEE-----EQCKDLEEQNYV-KVNGSLKTFN 130 (258)
T ss_pred eEEEEEEEEeeeecc----------cceEEEEecCCc-eEEEEecCCCchHH-----HhccccccccEE-EEecceeeeC
Confidence 455666666654432 224688999999 89999999887652 1111 1112222 2355677899
Q ss_pred Cc-eecccCCeEE
Q 008606 328 GK-SIGTIPSTQL 339 (560)
Q Consensus 328 G~-sLs~~~~S~i 339 (560)
|| +++...-+.|
T Consensus 131 GK~~I~~~~i~~I 143 (258)
T COG5235 131 GKRSISASHISAI 143 (258)
T ss_pred CeeEEehhheeec
Confidence 97 6765443333
No 74
>PRK08763 single-stranded DNA-binding protein; Provisional
Probab=86.60 E-value=3 Score=39.42 Aligned_cols=66 Identities=17% Similarity=0.195 Sum_probs=51.6
Q ss_pred CCCceEEEEEEEEecccceeccCCCCCcEEEEEEE------eCCCC------eEEEEEcchhHHHHHhhcccCcEEEEee
Q 008606 124 YQGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLL------DSDGG------EIRVTCFNAVVDRFYEIIEVGRVYLISK 191 (560)
Q Consensus 124 ~~~~w~Ik~RV~~k~~ir~~~n~~g~gkvf~~~L~------D~~g~------~I~at~~~~~~~kf~~~l~eG~vY~Is~ 191 (560)
+++...|.+||.+--++|...+ | ..+.+|.|. |++|. -+++++|+.+++...+.|+.|+-+.|.+
T Consensus 4 ~~Nkv~LiGrLg~DPelr~t~~--G-~~va~fsVA~~~~~k~~~G~~~e~t~w~~Vv~fgk~Ae~v~~~L~KGs~V~VeG 80 (164)
T PRK08763 4 GINKVILVGNLGNDPDIKYTQS--G-MTITRISLATTSVRKDREGNTQERTEWHRVKFFGKLGEIAGEYLRKGSQCYIEG 80 (164)
T ss_pred cceEEEEEEEecCCCeEEEcCC--C-CeEEEEEEEeccceecCCCCeeccceEEEEEEehHHHHHHHHhcCCCCEEEEEE
Confidence 3678899999999877876543 3 267777765 43443 3899999999999999999999999976
Q ss_pred e
Q 008606 192 G 192 (560)
Q Consensus 192 ~ 192 (560)
=
T Consensus 81 r 81 (164)
T PRK08763 81 S 81 (164)
T ss_pred E
Confidence 3
No 75
>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=86.43 E-value=16 Score=31.21 Aligned_cols=83 Identities=18% Similarity=0.215 Sum_probs=52.6
Q ss_pred eEEEEEEEEecccceeccCCCCC-cEEEEEEEeCCCCeEEEEEcchh------HHHHHhhcccCcEEEEeeeEEecCCCc
Q 008606 128 WAIKARVTAKGDLRRYNNARGDG-KVFSFDLLDSDGGEIRVTCFNAV------VDRFYEIIEVGRVYLISKGSLKPAQKN 200 (560)
Q Consensus 128 w~Ik~RV~~k~~ir~~~n~~g~g-kvf~~~L~D~~g~~I~at~~~~~------~~kf~~~l~eG~vY~Is~~~V~~a~~~ 200 (560)
.+|+|||.++ |. .| ++.=++|.| .++.|++.+.... .-++...|..|+++.+.+--.+. .+.
T Consensus 2 V~i~Gwv~~~---R~------~g~k~~Fi~LrD-~sg~iQ~v~~~~~~~~~~~~~~~~~~l~~es~V~V~G~v~~~-~~~ 70 (102)
T cd04320 2 VLIRARVHTS---RA------QGAKLAFLVLRQ-QGYTIQGVLAASAEGVSKQMVKWAGSLSKESIVDVEGTVKKP-EEP 70 (102)
T ss_pred EEEEEEEEEe---ec------CCCceEEEEEec-CCceEEEEEeCCcccCCHHHHHHHhcCCCccEEEEEEEEECC-CCc
Confidence 5788999764 33 23 444456888 5679999997442 22344568999999999965442 222
Q ss_pred ccc-CCCeeEEEEcccceEEec
Q 008606 201 FNH-LKNEWEIFLEATSTVDLC 221 (560)
Q Consensus 201 y~~-~~~~yeI~f~~~T~I~~~ 221 (560)
.+. ....|||....-..+..+
T Consensus 71 ~~~~~~~~~El~~~~i~il~~~ 92 (102)
T cd04320 71 IKSCTQQDVELHIEKIYVVSEA 92 (102)
T ss_pred ccCCCcCcEEEEEEEEEEEecC
Confidence 221 236799998765555544
No 76
>PRK13480 3'-5' exoribonuclease YhaM; Provisional
Probab=86.31 E-value=2.6 Score=44.05 Aligned_cols=70 Identities=10% Similarity=0.049 Sum_probs=49.6
Q ss_pred eccccCCCCCceEEEEEEEEecccceeccCCCCCcEEEEEEEeCCCCeEEEEEcchhHHHHHhhcccCcEEEEeeeE
Q 008606 117 PIAALNPYQGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISKGS 193 (560)
Q Consensus 117 pI~~L~p~~~~w~Ik~RV~~k~~ir~~~n~~g~gkvf~~~L~D~~g~~I~at~~~~~~~kf~~~l~eG~vY~Is~~~ 193 (560)
.|++|+++. .......|..+ .+|.-+ +| ...+.++|.| .+|+|.|.+|+.. +.....+++|+++.+.+-.
T Consensus 4 ~i~~l~~g~-~v~~~~lv~~~-~~~~~k--nG-~~yl~l~l~D-~tG~I~ak~W~~~-~~~~~~~~~g~vv~v~G~v 73 (314)
T PRK13480 4 GIEELEVGE-QVDHFLLIKSA-TKGVAS--NG-KPFLTLILQD-KSGDIEAKLWDVS-PEDEATYVPETIVHVKGDI 73 (314)
T ss_pred hHhhcCCCC-EeeEEEEEEEc-eeeecC--CC-CeEEEEEEEc-CCcEEEEEeCCCC-hhhHhhcCCCCEEEEEEEE
Confidence 578898875 34444445444 334322 12 2589999999 7889999999964 4567889999999887654
No 77
>PRK07274 single-stranded DNA-binding protein; Provisional
Probab=86.05 E-value=2.7 Score=38.15 Aligned_cols=64 Identities=19% Similarity=0.254 Sum_probs=50.1
Q ss_pred CCceEEEEEEEEecccceeccCCCCCcEEEEEEE------eCCC----CeEEEEEcchhHHHHHhhcccCcEEEEee
Q 008606 125 QGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLL------DSDG----GEIRVTCFNAVVDRFYEIIEVGRVYLISK 191 (560)
Q Consensus 125 ~~~w~Ik~RV~~k~~ir~~~n~~g~gkvf~~~L~------D~~g----~~I~at~~~~~~~kf~~~l~eG~vY~Is~ 191 (560)
+....|.||+..--++|...+ | ..+.+|.|+ |+.| +-+++++|+..++.+.+.|+.|+-+.+.+
T Consensus 2 mN~v~LiGrL~~dPelr~t~~--g-~~~~~fslAv~~~~k~~~g~~~t~w~~v~~fg~~Ae~v~~~l~KG~~V~V~G 75 (131)
T PRK07274 2 YNKVILIGRLTATPELVKTAN--D-KSVARVTLAVNRRFKNQNGEREADFINVVLWGKLAETLASYASKGSLISIDG 75 (131)
T ss_pred eeEEEEEEEccCCCeEEECCC--C-CEEEEEEEEEcCceecCCCCEEEEEEEEEEehHHHHHHHHHcCCCCEEEEEE
Confidence 567889999999888876533 2 256777766 3333 46889999999999999999999999876
No 78
>PRK09010 single-stranded DNA-binding protein; Provisional
Probab=86.05 E-value=6.5 Score=37.67 Aligned_cols=64 Identities=20% Similarity=0.245 Sum_probs=51.5
Q ss_pred CCceEEEEEEEEecccceeccCCCCCcEEEEEEE------eCC-------CCeEEEEEcchhHHHHHhhcccCcEEEEee
Q 008606 125 QGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLL------DSD-------GGEIRVTCFNAVVDRFYEIIEVGRVYLISK 191 (560)
Q Consensus 125 ~~~w~Ik~RV~~k~~ir~~~n~~g~gkvf~~~L~------D~~-------g~~I~at~~~~~~~kf~~~l~eG~vY~Is~ 191 (560)
+....|.+||.+--++|.+.+ | ..+.+|.|. |.+ ..-+++++|+.+++.+.+.|+.|+-++|.+
T Consensus 6 ~N~V~LiGrLg~DPelR~t~n--G-~~v~~fsVAvn~~~kd~~~Ge~~e~t~w~~V~~fgk~Ae~~~~~L~KGs~V~VeG 82 (177)
T PRK09010 6 VNKVILVGNLGQDPEVRYMPN--G-GAVANITLATSESWRDKQTGEMKEQTEWHRVVLFGKLAEVAGEYLRKGSQVYIEG 82 (177)
T ss_pred ceEEEEEEEeCCCceEEEcCC--C-CEEEEEEEEEcCccccCcccccccceEEEEEEEehhHHHHHHHhcCCCCEEEEEE
Confidence 578899999999988988754 2 367777765 322 335799999999999999999999999987
No 79
>PRK13480 3'-5' exoribonuclease YhaM; Provisional
Probab=86.02 E-value=4.6 Score=42.30 Aligned_cols=77 Identities=23% Similarity=0.317 Sum_probs=52.6
Q ss_pred hcccCCceeEEEEEEEEecCceeEeeccCceeeEEEEEEecCCCcEEEEEEeCcchhhhhhhHHhhhccCCccEEEEEEE
Q 008606 242 ESAENNSIVDVIGIVISVNPSVPILRKNGMETQRRILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVDVGFFPVLSVKSG 321 (560)
Q Consensus 242 ~~~~~~~~VDVIGvV~~V~~~~~i~~k~G~~~~kr~i~L~D~Sg~~I~vtLWg~~a~~~~~~l~~~~~~~~~~VV~l~~~ 321 (560)
.++..+..|+.+..|++..-- ++|+|+. ...++|.|.|| +|+..+|+..-.. ...+ ..+.||.+++
T Consensus 6 ~~l~~g~~v~~~~lv~~~~~~---~~knG~~--yl~l~l~D~tG-~I~ak~W~~~~~~-----~~~~--~~g~vv~v~G- 71 (314)
T PRK13480 6 EELEVGEQVDHFLLIKSATKG---VASNGKP--FLTLILQDKSG-DIEAKLWDVSPED-----EATY--VPETIVHVKG- 71 (314)
T ss_pred hhcCCCCEeeEEEEEEEceee---ecCCCCe--EEEEEEEcCCc-EEEEEeCCCChhh-----Hhhc--CCCCEEEEEE-
Confidence 334457789988888876432 2567764 78999999999 8999999975222 2223 3566776654
Q ss_pred EEecCCCc-eec
Q 008606 322 KVNDFSGK-SIG 332 (560)
Q Consensus 322 rV~~f~G~-sLs 332 (560)
+|.+|+|+ ++.
T Consensus 72 ~v~~y~g~~Ql~ 83 (314)
T PRK13480 72 DIINYRGRKQLK 83 (314)
T ss_pred EEEEECCcceEE
Confidence 56689995 443
No 80
>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=85.97 E-value=3 Score=35.05 Aligned_cols=62 Identities=19% Similarity=0.310 Sum_probs=47.7
Q ss_pred EEEEEEEEecccceeccCCCCCcEEEEEEE-----------eCCCCeEEEEEcchhHHHHHhhcccCcEEEEeeeE
Q 008606 129 AIKARVTAKGDLRRYNNARGDGKVFSFDLL-----------DSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISKGS 193 (560)
Q Consensus 129 ~Ik~RV~~k~~ir~~~n~~g~gkvf~~~L~-----------D~~g~~I~at~~~~~~~kf~~~l~eG~vY~Is~~~ 193 (560)
.|.|||.+.-.+|...+ | ..+.+|.|. +.+...+.+++|++.++.+...++.|+.+.+++..
T Consensus 2 ~l~G~l~~~p~~~~~~~--g-~~~~~~~v~~~~~~~~~~~~~~~~~~~~v~~~g~~a~~~~~~~~kG~~V~v~G~l 74 (100)
T cd04496 2 ILIGRLGKDPELRYTPS--G-TPVARFSLAVNRRRKDRDEEEEETDWIRVVAFGKLAENAAKYLKKGDLVYVEGRL 74 (100)
T ss_pred EEEEEecCCCEEEECCC--C-CEEEEEEEEEcCceecccccccccEEEEEEEEhHHHHHHHHHhCCCCEEEEEEEE
Confidence 57788888877776543 2 255566543 24677899999999999999999999999998853
No 81
>PRK08486 single-stranded DNA-binding protein; Provisional
Probab=85.91 E-value=2.8 Score=40.32 Aligned_cols=64 Identities=16% Similarity=0.201 Sum_probs=50.2
Q ss_pred CCceEEEEEEEEecccceeccCCCCCcEEEEEEE------eC------CCCeEEEEEcchhHHHHHhhcccCcEEEEee
Q 008606 125 QGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLL------DS------DGGEIRVTCFNAVVDRFYEIIEVGRVYLISK 191 (560)
Q Consensus 125 ~~~w~Ik~RV~~k~~ir~~~n~~g~gkvf~~~L~------D~------~g~~I~at~~~~~~~kf~~~l~eG~vY~Is~ 191 (560)
+....|.+||++-.++|...+ |. .+.+|.|+ ++ +..-|.+++|+.+|+.+...|+.|+-+.|.+
T Consensus 2 ~N~V~LvGrL~~DPElr~t~s--G~-~va~fslAv~r~~~~~~Ge~~e~t~fi~v~~fg~~AE~~~~~l~KG~~V~VeG 77 (182)
T PRK08486 2 FNKVILVGNLTRDVELRYLPS--GS-AIATIGLATSRRFKKQDGEKGEEVCFIDIRLFGRTAEIANQYLSKGSKVLIEG 77 (182)
T ss_pred eeEEEEEEEecCCCEEEECCC--CC-EEEEEEEEEecceecCCCCCcccceEEEEEEEhHHHHHHHHHcCCCCEEEEEE
Confidence 356789999999988887643 32 56666663 22 3467899999999999999999999999876
No 82
>PRK06293 single-stranded DNA-binding protein; Provisional
Probab=85.44 E-value=3 Score=39.35 Aligned_cols=65 Identities=15% Similarity=0.119 Sum_probs=52.0
Q ss_pred CCceEEEEEEEEecccceeccCCCCCcEEEEEEEe-------CCCCeEEEEEcchhHHHHHhhcccCcEEEEeee
Q 008606 125 QGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLD-------SDGGEIRVTCFNAVVDRFYEIIEVGRVYLISKG 192 (560)
Q Consensus 125 ~~~w~Ik~RV~~k~~ir~~~n~~g~gkvf~~~L~D-------~~g~~I~at~~~~~~~kf~~~l~eG~vY~Is~~ 192 (560)
|....|.+|+.+--++|...+ | ..+.+|.|.= ++..-|++++|+..++.....|+.|+-+.+.+=
T Consensus 1 MN~V~LiGrLg~DPElR~t~s--G-~~v~~FsLAvn~~~~~~~~T~wi~v~awg~~Ae~v~~yL~KG~~V~VeGr 72 (161)
T PRK06293 1 MMFGYIVGRLGADPEERMTSK--G-KRVVVLRLGVKSRVGSKDETVWCRCNIWGNRYDKMLPYLKKGSGVIVAGE 72 (161)
T ss_pred CeEEEEEEEecCCCeEEEcCC--C-CEEEEEEEEEeCCCCCccceEEEEEEEEhHHHHHHHHhCCCCCEEEEEEE
Confidence 456789999999888886543 3 2678888762 256689999999999999999999999999773
No 83
>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=85.30 E-value=2.3 Score=35.82 Aligned_cols=53 Identities=17% Similarity=0.151 Sum_probs=38.3
Q ss_pred EEEEEEEEecccceeccCCCCCcEEEEEEEeCCCCeEEEEEcchhHH---HHHhhcccCcEEEEee
Q 008606 129 AIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAVVD---RFYEIIEVGRVYLISK 191 (560)
Q Consensus 129 ~Ik~RV~~k~~ir~~~n~~g~gkvf~~~L~D~~g~~I~at~~~~~~~---kf~~~l~eG~vY~Is~ 191 (560)
++.|.|.++.. .+..+.+.|.| .+|.|.|.+|...-+ .-.+.+++|+++.+.+
T Consensus 3 ~~vG~V~~~~~---------~~~~~~~tL~D-~TG~I~~~~W~~~~~~~~~~~~~~~~g~~v~v~G 58 (95)
T cd04478 3 TLVGVVRNVEE---------QSTNITYTIDD-GTGTIEVRQWLDDDNDDSSEVEPIEEGTYVRVFG 58 (95)
T ss_pred EEEEEEEeeeE---------cccEEEEEEEC-CCCcEEEEEeCCCCCcccccccccccCCEEEEEE
Confidence 56677776432 13579999999 566899999986543 3567799999777654
No 84
>cd04495 BRCA2DBD_OB3 BRCA2DBD_OB3: A subfamily of OB folds corresponding to the third OB fold (OB3) 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=85.11 E-value=7.1 Score=33.59 Aligned_cols=81 Identities=21% Similarity=0.251 Sum_probs=55.1
Q ss_pred EEEEEEEEecCceeEeeccCceeeEEEEEEecCCCcEEEEEEeCcchhhhhhhHHhhhccCCccEEEEEEEEEecCC--C
Q 008606 251 DVIGIVISVNPSVPILRKNGMETQRRILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVDVGFFPVLSVKSGKVNDFS--G 328 (560)
Q Consensus 251 DVIGvV~~V~~~~~i~~k~G~~~~kr~i~L~D~Sg~~I~vtLWg~~a~~~~~~l~~~~~~~~~~VV~l~~~rV~~f~--G 328 (560)
|++|+|++|+...+ | ..-.+.|.|++-.-+-+-+|........+. + ......||+.+...+-.. |
T Consensus 1 D~VGvVvsV~~~~~-----g---~~~~vYLaDe~~nll~vkfw~~l~~~~~ED----v-vk~~~lia~SNLQwR~~s~~~ 67 (100)
T cd04495 1 DTVGVVISVGKPIE-----G---KFPAVYLADECLNLLCVKFWSSLEQYAYED----V-VKRRVLLAASNLQWRTESTSG 67 (100)
T ss_pred CceEEEEEEccccc-----C---ccceEEEecCCcCEEEEEEecchHHhhhhh----h-cccceEEEEecceEeccccCC
Confidence 78999999987641 2 345789999999899999999764432111 1 134567888887766443 3
Q ss_pred c-eecccCCeEEEECCC
Q 008606 329 K-SIGTIPSTQLFINPD 344 (560)
Q Consensus 329 ~-sLs~~~~S~i~iNPd 344 (560)
. ++-.+.-|.+..||.
T Consensus 68 iPtl~Age~t~FS~nPK 84 (100)
T cd04495 68 VPTLFAGEYSTFSANPK 84 (100)
T ss_pred CceeeeecceeecCCcc
Confidence 3 455566677777774
No 85
>PRK13732 single-stranded DNA-binding protein; Provisional
Probab=84.55 E-value=3.9 Score=39.07 Aligned_cols=65 Identities=18% Similarity=0.210 Sum_probs=51.9
Q ss_pred CCCceEEEEEEEEecccceeccCCCCCcEEEEEEEe------CC-------CCeEEEEEcchhHHHHHhhcccCcEEEEe
Q 008606 124 YQGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLD------SD-------GGEIRVTCFNAVVDRFYEIIEVGRVYLIS 190 (560)
Q Consensus 124 ~~~~w~Ik~RV~~k~~ir~~~n~~g~gkvf~~~L~D------~~-------g~~I~at~~~~~~~kf~~~l~eG~vY~Is 190 (560)
+++...|.|||.+--++|.+.+ | ..+.+|.|.- .+ ..-+++++|+.+++...+.|+.|+.+.|.
T Consensus 5 ~mN~V~LiGrLg~DPElR~t~n--G-~~va~fslAvn~~~kd~~~Ge~~e~t~w~~Vv~wgk~Ae~v~~~L~KG~~V~Ve 81 (175)
T PRK13732 5 GINKVILVGRLGKDPEVRYIPN--G-GAVANLQVATSESWRDKQTGEMREQTEWHRVVLFGKLAEVAGEYLRKGAQVYIE 81 (175)
T ss_pred CceEEEEEEEecCCCEEEEcCC--C-CEEEEEEEEEcCccccCCCCceecceeEEEEEEecHHHHHHHHhcCCCCEEEEE
Confidence 4678999999999888887654 3 2677887762 22 23568999999999999999999999997
Q ss_pred e
Q 008606 191 K 191 (560)
Q Consensus 191 ~ 191 (560)
+
T Consensus 82 G 82 (175)
T PRK13732 82 G 82 (175)
T ss_pred E
Confidence 7
No 86
>PRK06752 single-stranded DNA-binding protein; Validated
Probab=84.20 E-value=3.5 Score=36.28 Aligned_cols=65 Identities=14% Similarity=0.087 Sum_probs=50.7
Q ss_pred CCceEEEEEEEEecccceeccCCCCCcEEEEEEEeC----------CCCeEEEEEcchhHHHHHhhcccCcEEEEeee
Q 008606 125 QGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDS----------DGGEIRVTCFNAVVDRFYEIIEVGRVYLISKG 192 (560)
Q Consensus 125 ~~~w~Ik~RV~~k~~ir~~~n~~g~gkvf~~~L~D~----------~g~~I~at~~~~~~~kf~~~l~eG~vY~Is~~ 192 (560)
++.-.|.||+.+--++|...+ | ..+.+|.|.-. +.+-|.+++|+..|+.+.+.++.|+-+.+.+=
T Consensus 2 mN~v~liGrl~~dPelr~t~~--G-~~~~~f~lAv~~~~~~~~g~~~t~~~~v~~wg~~Ae~~~~~l~KG~~V~V~G~ 76 (112)
T PRK06752 2 MNRVVLIGRLTKEPELYYTKQ--G-VAYARVCVAVNRGFRNSLGEQQVDFINCVVWRKSAENVTEYCTKGSLVGITGR 76 (112)
T ss_pred ceEEEEEEECcCCCEEEECCC--C-CEEEEEEEEECCCeEcCCCCEEEEEEEEEEehHHHHHHHHhcCCCCEEEEEEE
Confidence 456789999999888886532 3 26777877632 23668999999999999999999999998763
No 87
>PRK07373 DNA polymerase III subunit alpha; Reviewed
Probab=84.10 E-value=3.3 Score=45.49 Aligned_cols=76 Identities=24% Similarity=0.300 Sum_probs=53.6
Q ss_pred cCccchhcccCCceeEEEEEEEEecCceeEeeccCceeeEEEEEEecCCCcEEEEEEeCcchhhhhhhHHhhhccCCccE
Q 008606 236 RHISEIESAENNSIVDVIGIVISVNPSVPILRKNGMETQRRILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVDVGFFPV 315 (560)
Q Consensus 236 ~~i~dI~~~~~~~~VDVIGvV~~V~~~~~i~~k~G~~~~kr~i~L~D~Sg~~I~vtLWg~~a~~~~~~l~~~~~~~~~~V 315 (560)
.++++|.....+..|-|.|+|+.+... .+|.|+. .--++|.|.+| ++++++|-+...++...|. .+.+
T Consensus 269 ~~~~~l~~~~~~~~v~vaG~I~~ik~~---~TKkG~~--maf~~leD~tG-~ie~vvFp~~y~~~~~~l~------~~~~ 336 (449)
T PRK07373 269 INLSELEEQKEKTKVSAVVMLNEVKKI---VTKKGDP--MAFLQLEDLSG-QSEAVVFPKSYERISELLQ------VDAR 336 (449)
T ss_pred cCHHHHhcccCCCEEEEEEEEEEeEec---ccCCCCE--EEEEEEEECCC-CEEEEECHHHHHHHHHHhc------cCCE
Confidence 466666533356788999999998765 3566763 56789999999 7999999998777544432 3456
Q ss_pred EEEEEEEEe
Q 008606 316 LSVKSGKVN 324 (560)
Q Consensus 316 V~l~~~rV~ 324 (560)
|.+++ +|.
T Consensus 337 v~v~G-~v~ 344 (449)
T PRK07373 337 LIIWG-KVD 344 (449)
T ss_pred EEEEE-EEE
Confidence 65654 554
No 88
>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=83.95 E-value=9.6 Score=35.12 Aligned_cols=106 Identities=18% Similarity=0.357 Sum_probs=56.7
Q ss_pred Cccchhc---ccCCceeEEEEEEEEecCceeEeeccCceeeEEEEEEecCCCcEEEEEEeCcchhhhhhhHHhhhccCCc
Q 008606 237 HISEIES---AENNSIVDVIGIVISVNPSVPILRKNGMETQRRILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVDVGFF 313 (560)
Q Consensus 237 ~i~dI~~---~~~~~~VDVIGvV~~V~~~~~i~~k~G~~~~kr~i~L~D~Sg~~I~vtLWg~~a~~~~~~l~~~~~~~~~ 313 (560)
.|++|.+ ...=.-||++|+|+.|. .+.|- .--+.|.|....-+-+-+|++...-- +.+. ...+
T Consensus 5 ~f~~l~~p~f~pp~~EvD~VG~VvsV~------~~~~f---~~~vYLsD~~~Nll~Ikfw~~l~~~~---~eDi--lk~~ 70 (143)
T PF09104_consen 5 HFSDLQDPDFQPPYGEVDTVGFVVSVS------KKQGF---QPLVYLSDECHNLLAIKFWTGLNQYG---YEDI--LKPG 70 (143)
T ss_dssp -CGGGGSTT--TCCCEEEEEEEEEEEE--------TTS-----EEEEE-TTS-EEEEEESS----------SS-----TT
T ss_pred chhhhcCcccCCCccccceEEEEEEEE------ecCCC---ceeEEeecCCccEEEEEeccCccccc---hhhh--cCcc
Confidence 4555554 23446899999999992 22221 12378899998899999999975321 1111 1467
Q ss_pred cEEEEEEEEEe-c-CCCc-eecccCCeEEEECCC---hHH-HHHHHHHHh
Q 008606 314 PVLSVKSGKVN-D-FSGK-SIGTIPSTQLFINPD---FAE-AHELREWFD 356 (560)
Q Consensus 314 ~VV~l~~~rV~-~-f~G~-sLs~~~~S~i~iNPd---ipE-a~~L~~w~~ 356 (560)
.+||..+..-+ + -.+. .+-.+..|.+.-||. +.| ...|+.-+.
T Consensus 71 ~liA~SNLqwR~~s~s~iP~~~A~d~S~FS~nPK~~hLqe~~~~Lk~~i~ 120 (143)
T PF09104_consen 71 SLIAASNLQWRPESTSGIPTLFATDLSVFSANPKESHLQEAFNKLKNTIE 120 (143)
T ss_dssp -EEEEEEEEE-S-TTSSS-EEEEECCEEEESS-SSCCCHHHHHHHCHHHH
T ss_pred eEEEEeeeEeecccccCCCeeEeccceeeecCccHHHHHHHHHHHHHHhh
Confidence 89999877664 2 2333 455677788888884 233 345554444
No 89
>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=83.38 E-value=7 Score=32.39 Aligned_cols=59 Identities=19% Similarity=0.245 Sum_probs=43.6
Q ss_pred eEEEEEEEEecccceeccCCCCCcEEEEEEEeCCCCeEEEEEcc-hhHHHHHhhcc-cCcEEEEeee
Q 008606 128 WAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFN-AVVDRFYEIIE-VGRVYLISKG 192 (560)
Q Consensus 128 w~Ik~RV~~k~~ir~~~n~~g~gkvf~~~L~D~~g~~I~at~~~-~~~~kf~~~l~-eG~vY~Is~~ 192 (560)
-.|+|.|... +.|..++ | ..+++|.|.| ..+.|.|..|. +..+.+ +.|+ +|+|+.+.+=
T Consensus 2 v~i~G~Vf~~-e~re~k~--g-~~i~~~~itD-~t~Si~~K~F~~~~~~~~-~~ik~~G~~v~v~G~ 62 (82)
T cd04484 2 VVVEGEVFDL-EIRELKS--G-RKILTFKVTD-YTSSITVKKFLRKDEKDK-EELKSKGDWVRVRGK 62 (82)
T ss_pred EEEEEEEEEE-EEEEecC--C-CEEEEEEEEc-CCCCEEEEEeccCChhHH-hhcccCCCEEEEEEE
Confidence 4688888766 4466553 2 4688999999 77899999998 344444 5689 9999988653
No 90
>PF13742 tRNA_anti_2: OB-fold nucleic acid binding domain
Probab=82.98 E-value=1.2 Score=38.42 Aligned_cols=64 Identities=14% Similarity=0.148 Sum_probs=46.3
Q ss_pred CCceEEEEEEEEecccceeccCCCCCcEEEEEEEeCCCCeEEEEEcchhHHHHH-hhcccCcEEEEee-eEEecC
Q 008606 125 QGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAVVDRFY-EIIEVGRVYLISK-GSLKPA 197 (560)
Q Consensus 125 ~~~w~Ik~RV~~k~~ir~~~n~~g~gkvf~~~L~D~~g~~I~at~~~~~~~kf~-~~l~eG~vY~Is~-~~V~~a 197 (560)
..+..|+|=|.. ++.. .+..+-|+|.|++ .+|+|++|...+.+.. ..+++|.-+.+.+ ..+-+.
T Consensus 21 ~~~vwV~GEIs~------~~~~--~~gh~YftLkD~~-a~i~~~~~~~~~~~i~~~~l~~G~~V~v~g~~~~y~~ 86 (99)
T PF13742_consen 21 LPNVWVEGEISN------LKRH--SSGHVYFTLKDEE-ASISCVIFRSRARRIRGFDLKDGDKVLVRGRVSFYEP 86 (99)
T ss_pred cCCEEEEEEEee------cEEC--CCceEEEEEEcCC-cEEEEEEEHHHHhhCCCCCCCCCCEEEEEEEEEEECC
Confidence 456667777765 3322 1247999999955 9999999999888887 7899999887765 344433
No 91
>PRK06863 single-stranded DNA-binding protein; Provisional
Probab=82.85 E-value=4.7 Score=38.32 Aligned_cols=64 Identities=14% Similarity=0.192 Sum_probs=51.0
Q ss_pred CCceEEEEEEEEecccceeccCCCCCcEEEEEEE------eCC-------CCeEEEEEcchhHHHHHhhcccCcEEEEee
Q 008606 125 QGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLL------DSD-------GGEIRVTCFNAVVDRFYEIIEVGRVYLISK 191 (560)
Q Consensus 125 ~~~w~Ik~RV~~k~~ir~~~n~~g~gkvf~~~L~------D~~-------g~~I~at~~~~~~~kf~~~l~eG~vY~Is~ 191 (560)
+....|.|||.+.-++|.+.+ | ..+.+|.|. |.+ ..-+++++|+..++.+...|+.|+-+.+.+
T Consensus 4 ~N~V~LiGrLg~DPElR~t~n--G-~~va~fsVAvn~~~~d~~~Ge~~e~t~w~~Vv~fgk~AE~v~~~LkKGs~V~VeG 80 (168)
T PRK06863 4 INKVIIVGHLGNDPEIRTMPN--G-EAVANISVATSESWTDKNTGERREVTEWHRIVFYRRQAEVAGEYLRKGSQVYVEG 80 (168)
T ss_pred ccEEEEEEEcCCCCEEEEcCC--C-CEEEEEEEEecCcccccCCCcccccceEEEEEEEhHHHHHHHHHCCCCCEEEEEE
Confidence 567899999999888888754 2 257777765 221 346899999999999999999999999887
No 92
>PRK08182 single-stranded DNA-binding protein; Provisional
Probab=82.78 E-value=4.4 Score=37.61 Aligned_cols=66 Identities=12% Similarity=0.282 Sum_probs=51.6
Q ss_pred CCceEEEEEEEEecccceeccCCCC---CcEEEEEEE------eCCC-------CeEEEEEcchhHHHHHhhcccCcEEE
Q 008606 125 QGRWAIKARVTAKGDLRRYNNARGD---GKVFSFDLL------DSDG-------GEIRVTCFNAVVDRFYEIIEVGRVYL 188 (560)
Q Consensus 125 ~~~w~Ik~RV~~k~~ir~~~n~~g~---gkvf~~~L~------D~~g-------~~I~at~~~~~~~kf~~~l~eG~vY~ 188 (560)
++.+.|.||+.+--++|.+.+ |. ..+.+|.|. +.+| .-|.+++|+.+++.....|+.|+-+.
T Consensus 2 ~N~V~LiGrLg~DPElr~t~~--G~~~~~~va~fslA~~r~~~~~~Ge~~~~~t~w~~V~~wg~~Ae~v~~~l~KG~~V~ 79 (148)
T PRK08182 2 STHFVGEGNIGSAPEYREFPN--GNDEPRRLLRLNVYFDNPVPTKDGEYEDRGGFWAPVELWHRDAEHWARLYQKGMRVL 79 (148)
T ss_pred ccEEEEEEECCCCCeEEECCC--CCeeeeeEEEEEEEecCceECCCCCEEecCcEEEEEEEEhHHHHHHHHhcCCCCEEE
Confidence 467899999999888887653 32 127888885 2223 35899999999999999999999999
Q ss_pred Eeee
Q 008606 189 ISKG 192 (560)
Q Consensus 189 Is~~ 192 (560)
+.+=
T Consensus 80 V~Gr 83 (148)
T PRK08182 80 VEGR 83 (148)
T ss_pred EEEE
Confidence 9873
No 93
>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=82.05 E-value=16 Score=30.14 Aligned_cols=75 Identities=20% Similarity=0.225 Sum_probs=47.3
Q ss_pred eEEEEEEEEecccceeccCCCCCcEEEEEEEeCCCCeEEEEEcchhHH---HHHhhcccCcEEEEeeeEEecCCCccccC
Q 008606 128 WAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAVVD---RFYEIIEVGRVYLISKGSLKPAQKNFNHL 204 (560)
Q Consensus 128 w~Ik~RV~~k~~ir~~~n~~g~gkvf~~~L~D~~g~~I~at~~~~~~~---kf~~~l~eG~vY~Is~~~V~~a~~~y~~~ 204 (560)
-+|+|||-++ |. .|++.=++|.| .++.+++.+-.+..+ ++...|..|+++.+.+.-.....+. ..
T Consensus 2 V~i~Gwv~~~---R~------~g~~~Fi~Lrd-~~~~iQ~v~~~~~~~~~~~~~~~l~~~s~V~v~G~~~~~~~~~--~~ 69 (85)
T cd04100 2 VTLAGWVHSR---RD------HGGLIFIDLRD-GSGIVQVVVNKEELGEFFEEAEKLRTESVVGVTGTVVKRPEGN--LA 69 (85)
T ss_pred EEEEEEEehh---cc------CCCEEEEEEEe-CCeeEEEEEECCcChHHHHHHhCCCCCCEEEEEeEEEECCCCC--CC
Confidence 3678888642 33 34643345788 568999988765332 3456799999999988644422211 23
Q ss_pred CCeeEEEEcc
Q 008606 205 KNEWEIFLEA 214 (560)
Q Consensus 205 ~~~yeI~f~~ 214 (560)
..++||..+.
T Consensus 70 ~~~~El~~~~ 79 (85)
T cd04100 70 TGEIELQAEE 79 (85)
T ss_pred CCCEEEEEeE
Confidence 4678887643
No 94
>cd04323 AsnRS_cyto_like_N AsnRS_cyto_like_N: N-terminal, anticodon recognition domain of the type found in human and Saccharomyces cerevisiae cytoplasmic asparaginyl-tRNA synthetase (AsnRS), in Brugia malayai AsnRs and, in various putative bacterial AsnRSs. 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 synthesis, whereas the other exclusively with
Probab=81.67 E-value=18 Score=29.77 Aligned_cols=75 Identities=12% Similarity=0.084 Sum_probs=46.3
Q ss_pred eEEEEEEEEecccceeccCCCCCcEEEEEEEeCCCCeEEEEEcchhHH--HHHhhcccCcEEEEeeeEEecCCCccccCC
Q 008606 128 WAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAVVD--RFYEIIEVGRVYLISKGSLKPAQKNFNHLK 205 (560)
Q Consensus 128 w~Ik~RV~~k~~ir~~~n~~g~gkvf~~~L~D~~g~~I~at~~~~~~~--kf~~~l~eG~vY~Is~~~V~~a~~~y~~~~ 205 (560)
-+|+|||-++ |. .|++.=++|.| .++.|++.+..+... ++-..|..|+++.+.+- +......- ...
T Consensus 2 V~v~Gwv~~~---R~------~g~~~Fi~LrD-~~~~iQ~v~~~~~~~~~~~~~~l~~es~V~V~G~-v~~~~~~~-~~~ 69 (84)
T cd04323 2 VKVFGWVHRL---RS------QKKLMFLVLRD-GTGFLQCVLSKKLVTEFYDAKSLTQESSVEVTGE-VKEDPRAK-QAP 69 (84)
T ss_pred EEEEEEEEEE---ec------CCCcEEEEEEc-CCeEEEEEEcCCcchhHHHHhcCCCcCEEEEEEE-EEECCccc-CCC
Confidence 3678888653 32 23554456888 566799988654322 23356899999999774 44332221 335
Q ss_pred CeeEEEEcc
Q 008606 206 NEWEIFLEA 214 (560)
Q Consensus 206 ~~yeI~f~~ 214 (560)
+++||...+
T Consensus 70 ~~~Ei~~~~ 78 (84)
T cd04323 70 GGYELQVDY 78 (84)
T ss_pred CCEEEEEEE
Confidence 678888743
No 95
>PRK05159 aspC aspartyl-tRNA synthetase; Provisional
Probab=81.39 E-value=12 Score=41.10 Aligned_cols=94 Identities=15% Similarity=0.098 Sum_probs=65.3
Q ss_pred cceeccccCCCC--CceEEEEEEEEecccceeccCCCCCcEEEEEEEeCCCCeEEEEEcchh---HHHHHhhcccCcEEE
Q 008606 114 RIIPIAALNPYQ--GRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAV---VDRFYEIIEVGRVYL 188 (560)
Q Consensus 114 ~~~pI~~L~p~~--~~w~Ik~RV~~k~~ir~~~n~~g~gkvf~~~L~D~~g~~I~at~~~~~---~~kf~~~l~eG~vY~ 188 (560)
+-+.|++|++.. ..-+|+|||.++ |. .|++.=++|.| .++.|++++-.+. ..++-..|..|+++.
T Consensus 3 ~~~~~~~l~~~~~g~~V~i~GrV~~~---R~------~gk~~Fl~LrD-~~g~iQ~v~~~~~~~~~~~~~~~L~~gs~V~ 72 (437)
T PRK05159 3 KRHLTSELTPELDGEEVTLAGWVHEI---RD------LGGIAFLILRD-RSGIIQVVVKKKVDEELFETIKKLKRESVVS 72 (437)
T ss_pred ceeEhhhCChhhCCCEEEEEEEeEee---ec------CCCeEEEEEEc-CCcEEEEEEeCCccHHHHHHHhCCCCCcEEE
Confidence 456788998876 578899999764 33 34655567889 5568999996542 223446789999999
Q ss_pred EeeeEEecCCCccccCCCeeEEEEcccceEEecc
Q 008606 189 ISKGSLKPAQKNFNHLKNEWEIFLEATSTVDLCT 222 (560)
Q Consensus 189 Is~~~V~~a~~~y~~~~~~yeI~f~~~T~I~~~~ 222 (560)
+.+.-++... ....+||....-+.+..+.
T Consensus 73 v~G~v~~~~~-----~~~~~el~~~~i~vls~a~ 101 (437)
T PRK05159 73 VTGTVKANPK-----APGGVEVIPEEIEVLNKAE 101 (437)
T ss_pred EEEEEEcCCC-----CCCCEEEEEeEEEEEeCCC
Confidence 9986554321 2356899987766666653
No 96
>PRK05673 dnaE DNA polymerase III subunit alpha; Validated
Probab=81.27 E-value=4.1 Score=49.82 Aligned_cols=81 Identities=30% Similarity=0.416 Sum_probs=56.8
Q ss_pred ccCccchhcccCCceeEEEEEEEEecCceeEeeccCceeeEEEEEEecCCCcEEEEEEeCcchhhhhhhHHhhhccCCcc
Q 008606 235 FRHISEIESAENNSIVDVIGIVISVNPSVPILRKNGMETQRRILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVDVGFFP 314 (560)
Q Consensus 235 f~~i~dI~~~~~~~~VDVIGvV~~V~~~~~i~~k~G~~~~kr~i~L~D~Sg~~I~vtLWg~~a~~~~~~l~~~~~~~~~~ 314 (560)
..++++|.....+..|.++|+|+++... .+|+|+. .--++|.|.+| ++++++|.+...++...| ..+.
T Consensus 965 ~~~~~~l~~~~~g~~V~v~G~I~~vk~~---~TKkG~~--mafltLeD~TG-~iEvviFp~~ye~~~~~L------~~g~ 1032 (1135)
T PRK05673 965 DTRLADLEPTEGGSVVTVAGLVVSVRRR---VTKRGNK--MAIVTLEDLSG-RIEVMLFSEALEKYRDLL------EEDR 1032 (1135)
T ss_pred CcCHHHHhccccCceEEEEEEEEEEEec---ccCCCCe--EEEEEEEeCCC-cEEEEECHHHHHHHHHHh------ccCC
Confidence 4566676544457789999999998765 3566763 56789999999 899999998766643333 2456
Q ss_pred EEEEEEEEEecCCC
Q 008606 315 VLSVKSGKVNDFSG 328 (560)
Q Consensus 315 VV~l~~~rV~~f~G 328 (560)
+|.|++ +|..+.|
T Consensus 1033 iV~V~G-kVe~~~~ 1045 (1135)
T PRK05673 1033 IVVVKG-QVSFDDG 1045 (1135)
T ss_pred EEEEEE-EEEecCC
Confidence 666654 5654444
No 97
>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=81.07 E-value=2.1 Score=36.46 Aligned_cols=64 Identities=19% Similarity=0.273 Sum_probs=45.1
Q ss_pred CceEEEEEEEEecccceeccCCCCCcEEEEEEEeC------------CCCeEEEEEcchhHHHHHhhcccCcEEEEeee
Q 008606 126 GRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDS------------DGGEIRVTCFNAVVDRFYEIIEVGRVYLISKG 192 (560)
Q Consensus 126 ~~w~Ik~RV~~k~~ir~~~n~~g~gkvf~~~L~D~------------~g~~I~at~~~~~~~kf~~~l~eG~vY~Is~~ 192 (560)
+...|.|||.+--++|...+ | ..+.+|.|.-. ...-+++++|++.|+.+.+.++.|+.+.|.+-
T Consensus 2 N~v~l~G~l~~~p~~~~~~~--g-~~~~~f~la~~~~~~~~~~~~~~~~~~~~v~~~g~~A~~~~~~l~kG~~V~V~G~ 77 (104)
T PF00436_consen 2 NKVTLIGRLGKDPELRYTKN--G-TPVARFSLAVNRRFKDDGGEGDEKTDWINVVAWGKLAENVAEYLKKGDRVYVEGR 77 (104)
T ss_dssp EEEEEEEEESSSEEEEEETT--S-EEEEEEEEEEEEEEEETTSCEEEEEEEEEEEEEHHHHHHHHHH--TT-EEEEEEE
T ss_pred cEEEEEEEECCCcEEEECCC--C-CEEEEEEEEEecEEeeeeccCccceEEEEEEeeeecccccceEEcCCCEEEEEEE
Confidence 35678999998888887652 2 24656654321 23467999999999999999999999999883
No 98
>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=80.83 E-value=6.6 Score=37.07 Aligned_cols=65 Identities=18% Similarity=0.281 Sum_probs=49.9
Q ss_pred CCceEEEEEEEEecccceeccCCCCCcEEEEEEE------eCC------CCeEEEEEcchhHHHHHhhcccCcEEEEeee
Q 008606 125 QGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLL------DSD------GGEIRVTCFNAVVDRFYEIIEVGRVYLISKG 192 (560)
Q Consensus 125 ~~~w~Ik~RV~~k~~ir~~~n~~g~gkvf~~~L~------D~~------g~~I~at~~~~~~~kf~~~l~eG~vY~Is~~ 192 (560)
+++..|.+||.+--++|...+ |. .+.+|.|. |++ ..-|++++|+.+++.+...|+.|+.+.|.+-
T Consensus 4 ~N~V~L~G~l~~dPe~r~t~~--G~-~v~~fsvA~~~~~~~~~G~~~~~t~~~~v~~wg~~Ae~~~~~l~KG~~V~V~G~ 80 (164)
T TIGR00621 4 VNKVILVGRLTRDPELRYTPS--GN-AVANFTLATNRRWKDQDGEWKEETEWHDIVIFGRLAEVAAQYLKKGSLVYVEGR 80 (164)
T ss_pred ccEEEEEEEeCCCCEEEECCC--CC-EEEEEEEEEcCceecCCCCEeccceEEEEEEehHHHHHHHHhCCCCCEEEEEEE
Confidence 456789999999877776543 32 45556554 222 3689999999999999999999999999874
No 99
>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=80.26 E-value=12 Score=30.92 Aligned_cols=52 Identities=15% Similarity=0.077 Sum_probs=41.9
Q ss_pred eeeEEEEEEecCCCcEEEEEEeCcchhhhhhhHHhhhccCCccEEEEEEEEEecCCCc
Q 008606 272 ETQRRILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVDVGFFPVLSVKSGKVNDFSGK 329 (560)
Q Consensus 272 ~~~kr~i~L~D~Sg~~I~vtLWg~~a~~~~~~l~~~~~~~~~~VV~l~~~rV~~f~G~ 329 (560)
.....++.|.|+.|..|..+.+.+.+..+...|+ ++.+..|.+.+|..-.+.
T Consensus 17 ~~~~~~miL~De~G~~I~a~i~~~~~~~f~~~L~------eg~vy~is~f~v~~~~~~ 68 (86)
T cd04480 17 SGESLEMVLVDEKGNRIHATIPKRLAAKFRPLLK------EGKWYTISNFEVAPNTGS 68 (86)
T ss_pred CCcEEEEEEEcCCCCEEEEEECHHHHHhhhhhce------eCCEEEEeeEEEEcCCCc
Confidence 3456789999999999999999999988766553 468888998888875553
No 100
>KOG3056 consensus Protein required for S-phase initiation or completion [Cell cycle control, cell division, chromosome partitioning]
Probab=79.73 E-value=12 Score=41.74 Aligned_cols=102 Identities=15% Similarity=0.275 Sum_probs=69.7
Q ss_pred CCcceecc----ccCCCC---CceEEEEEEEEecccceeccCCCCCcEEEEE-EEeCCC-CeEEEEEcchhHHHHHhhcc
Q 008606 112 PARIIPIA----ALNPYQ---GRWAIKARVTAKGDLRRYNNARGDGKVFSFD-LLDSDG-GEIRVTCFNAVVDRFYEIIE 182 (560)
Q Consensus 112 ~~~~~pI~----~L~p~~---~~w~Ik~RV~~k~~ir~~~n~~g~gkvf~~~-L~D~~g-~~I~at~~~~~~~kf~~~l~ 182 (560)
-+..++|+ .|-+.. .+|.+.|-|+.|+.++.-.+ |+-|+|. |-|=.+ ..+.+.+|+++..++. .++
T Consensus 165 g~k~i~ls~~~~~l~r~~kf~~~Wvt~GvI~~K~~~K~t~~----G~~y~iwkL~dLk~~q~vslfLFG~a~k~~w-k~k 239 (578)
T KOG3056|consen 165 GRKLIRLSGKLFNLIRGPKFEENWVTMGVIVEKSDPKFTSN----GNPYSIWKLTDLKDHQTVSLFLFGKAHKRYW-KIK 239 (578)
T ss_pred cCcceeehhhhhhcccCcccccCeEEEEEEeecCCcccccC----CCceEEEEeeecCccceeEEEEecHHHHHHh-hhc
Confidence 34666777 554442 48999999999999987554 3344443 333323 6999999999777766 499
Q ss_pred cCcEEEEeeeEEecCCCccccCCCeeEEEEcccceEEec
Q 008606 183 VGRVYLISKGSLKPAQKNFNHLKNEWEIFLEATSTVDLC 221 (560)
Q Consensus 183 eG~vY~Is~~~V~~a~~~y~~~~~~yeI~f~~~T~I~~~ 221 (560)
.|.|+.|-|..|.+-+.. ..-.|.|.++..-.|.++
T Consensus 240 ~GtVialLNp~v~k~~~g---s~~~f~LsIds~~~ilei 275 (578)
T KOG3056|consen 240 LGTVIALLNPEVLKDRPG---SRKSFSLSIDSSKKILEI 275 (578)
T ss_pred cCcEEEEeCccccCCCCC---CcceEEEEecCccceEEe
Confidence 999999999988654421 114677777765444443
No 101
>PLN02502 lysyl-tRNA synthetase
Probab=79.67 E-value=11 Score=42.46 Aligned_cols=79 Identities=25% Similarity=0.403 Sum_probs=55.0
Q ss_pred CceEEEEEEEEecccceeccCCCCCcEEEEEEEeCCCCeEEEEEcchh-------HHHHHhhcccCcEEEEeeeEEecCC
Q 008606 126 GRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAV-------VDRFYEIIEVGRVYLISKGSLKPAQ 198 (560)
Q Consensus 126 ~~w~Ik~RV~~k~~ir~~~n~~g~gkvf~~~L~D~~g~~I~at~~~~~-------~~kf~~~l~eG~vY~Is~~~V~~a~ 198 (560)
...+|.|||.++ |. .|++.=++|.| .++.|++.+-.+. .+++...|..|+++.+.+.-.+..
T Consensus 109 ~~V~v~GrV~~~---R~------~Gk~~F~~LrD-~~g~iQv~~~~~~~~~~~~~~~~~~~~l~~gdiV~V~G~~~~t~- 177 (553)
T PLN02502 109 VSVSVAGRIMAK---RA------FGKLAFYDLRD-DGGKIQLYADKKRLDLDEEEFEKLHSLVDRGDIVGVTGTPGKTK- 177 (553)
T ss_pred CEEEEEEEEEEE---ec------CCCeEEEEEec-CCccEEEEEECccccchhHHHHHHHhCCCCCcEEEEEEEEEecC-
Confidence 358899999875 33 35666677999 5679999886442 234445689999999998755432
Q ss_pred CccccCCCeeEEEEcccceEEec
Q 008606 199 KNFNHLKNEWEIFLEATSTVDLC 221 (560)
Q Consensus 199 ~~y~~~~~~yeI~f~~~T~I~~~ 221 (560)
...++|..++-..+..|
T Consensus 178 ------~gelel~~~~i~vLs~~ 194 (553)
T PLN02502 178 ------KGELSIFPTSFEVLTKC 194 (553)
T ss_pred ------CCCEEEEEeEEEEEecc
Confidence 24688888766555555
No 102
>PRK06958 single-stranded DNA-binding protein; Provisional
Probab=77.81 E-value=8.7 Score=36.96 Aligned_cols=64 Identities=20% Similarity=0.250 Sum_probs=50.5
Q ss_pred CCceEEEEEEEEecccceeccCCCCCcEEEEEEE------eC-------CCCeEEEEEcchhHHHHHhhcccCcEEEEee
Q 008606 125 QGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLL------DS-------DGGEIRVTCFNAVVDRFYEIIEVGRVYLISK 191 (560)
Q Consensus 125 ~~~w~Ik~RV~~k~~ir~~~n~~g~gkvf~~~L~------D~-------~g~~I~at~~~~~~~kf~~~l~eG~vY~Is~ 191 (560)
++...|.+||.+-.++|.+.+ |. .+.+|.|. |. +..-+++++|+.+++.+.+.|+.|+.+.|..
T Consensus 4 ~N~V~LiGrLg~DPElr~t~n--G~-~va~fsVAv~~~~kdk~sGe~~e~T~w~~V~~fGk~AE~v~~~LkKGs~V~VeG 80 (182)
T PRK06958 4 VNKVILVGNLGADPEVRYLPS--GD-AVANIRLATTDRYKDKASGEFKEATEWHRVAFFGRLAEIVGEYLKKGSSVYIEG 80 (182)
T ss_pred ccEEEEEEEecCCCeEEEcCC--CC-EEEEEEEEeccccccccCCcccccceEEEEEEehHHHHHHHHHhCCCCEEEEEE
Confidence 467899999999888887643 32 56666664 32 2457899999999999999999999999977
No 103
>PRK06642 single-stranded DNA-binding protein; Provisional
Probab=77.71 E-value=8.3 Score=35.98 Aligned_cols=64 Identities=19% Similarity=0.266 Sum_probs=50.7
Q ss_pred CCceEEEEEEEEecccceeccCCCCCcEEEEEEE------eC-------CCCeEEEEEcch-hHHHHHhhcccCcEEEEe
Q 008606 125 QGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLL------DS-------DGGEIRVTCFNA-VVDRFYEIIEVGRVYLIS 190 (560)
Q Consensus 125 ~~~w~Ik~RV~~k~~ir~~~n~~g~gkvf~~~L~------D~-------~g~~I~at~~~~-~~~kf~~~l~eG~vY~Is 190 (560)
++...|.|||.+--++|...+ |. .+.+|.|+ |. +..-+++++|+. +++.....|+.|+.+.+.
T Consensus 5 ~N~V~LiGrLg~DPElr~t~~--G~-~v~~fslAv~~~~k~~~~G~~~~~T~w~~v~~~g~~~Ae~~~~~l~KG~~V~V~ 81 (152)
T PRK06642 5 LNKVILIGNVGRDPEIRTTGE--GK-KIINLSLATTETWKDRITSERKERTEWHRVVIFSEGLVSVVERYVTKGSKLYIE 81 (152)
T ss_pred ceEEEEEEEccCCceEEECCC--CC-EEEEEEEEeccccccccCCccccceeEEEEEEeChHHHHHHHHhCCCCCEEEEE
Confidence 567899999999888887643 32 67788876 22 244688999996 899999999999999987
Q ss_pred e
Q 008606 191 K 191 (560)
Q Consensus 191 ~ 191 (560)
+
T Consensus 82 G 82 (152)
T PRK06642 82 G 82 (152)
T ss_pred E
Confidence 6
No 104
>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=77.30 E-value=47 Score=28.69 Aligned_cols=81 Identities=16% Similarity=0.078 Sum_probs=52.5
Q ss_pred CceEEEEEEEEecccceeccCCCCCcEEEEEEEeCCCCeEEEEEcchh----HHHHHhhcccCcEEEEeeeEEecCCCcc
Q 008606 126 GRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAV----VDRFYEIIEVGRVYLISKGSLKPAQKNF 201 (560)
Q Consensus 126 ~~w~Ik~RV~~k~~ir~~~n~~g~gkvf~~~L~D~~g~~I~at~~~~~----~~kf~~~l~eG~vY~Is~~~V~~a~~~y 201 (560)
...+|+|||.++ |. .|++.=++|.| .++.|++.+..+. .-++-..|..|+++.+.+--.....
T Consensus 13 ~~V~v~Gwv~~~---R~------~g~~~Fi~LrD-~~g~iQ~v~~~~~~~~~~~~~~~~l~~es~V~V~G~v~~~~~--- 79 (108)
T cd04316 13 EEVTVAGWVHEI---RD------LGGIKFVILRD-REGIVQVTAPKKKVDKELFKTVRKLSRESVISVTGTVKAEPK--- 79 (108)
T ss_pred CEEEEEEEEEee---ec------cCCeEEEEEec-CCeeEEEEEeCCCCCHHHHHHHhCCCCcCEEEEEEEEEeCCC---
Confidence 468999999763 43 23544445778 4668999887542 2223356899999999986444322
Q ss_pred ccCCCeeEEEEcccceEEec
Q 008606 202 NHLKNEWEIFLEATSTVDLC 221 (560)
Q Consensus 202 ~~~~~~yeI~f~~~T~I~~~ 221 (560)
....|||..+.-..+..+
T Consensus 80 --~~~~~Ei~~~~i~il~~~ 97 (108)
T cd04316 80 --APNGVEIIPEEIEVLSEA 97 (108)
T ss_pred --CCCCEEEEEeEEEEEeCC
Confidence 135799998765555544
No 105
>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=76.96 E-value=9.4 Score=34.35 Aligned_cols=36 Identities=3% Similarity=0.133 Sum_probs=28.0
Q ss_pred cEEEEEEeCcchhhhhhhHHhhhccCCccEEEEEEEEEecCCC
Q 008606 286 RSVELTLWGDFCNKEGQKLQEMVDVGFFPVLSVKSGKVNDFSG 328 (560)
Q Consensus 286 ~~I~vtLWg~~a~~~~~~l~~~~~~~~~~VV~l~~~rV~~f~G 328 (560)
.+|.||+|++++.- +.. .+.+..|.|++++++....
T Consensus 60 ~ti~It~yD~H~~~-----ar~--lK~GdfV~L~NVhiK~~~~ 95 (123)
T cd04498 60 LTIDILVYDNHVEL-----AKS--LKPGDFVRIYNVHAKSYSS 95 (123)
T ss_pred EEEEEEEEcchHHH-----Hhh--CCCCCEEEEEEEEEEeccC
Confidence 68999999999863 222 3578999999999986543
No 106
>PTZ00417 lysine-tRNA ligase; Provisional
Probab=76.66 E-value=16 Score=41.46 Aligned_cols=78 Identities=29% Similarity=0.378 Sum_probs=50.1
Q ss_pred ceEEEEEEEEecccceeccCCCCC-cEEEEEEEeCCCCeEEEEEcchh----HHHH---HhhcccCcEEEEeeeEEecCC
Q 008606 127 RWAIKARVTAKGDLRRYNNARGDG-KVFSFDLLDSDGGEIRVTCFNAV----VDRF---YEIIEVGRVYLISKGSLKPAQ 198 (560)
Q Consensus 127 ~w~Ik~RV~~k~~ir~~~n~~g~g-kvf~~~L~D~~g~~I~at~~~~~----~~kf---~~~l~eG~vY~Is~~~V~~a~ 198 (560)
..+|.|||.++ |. .| ++.=++|.| +|+.|++.+-.+. .+.| ...|..|+++.+.+.-.+
T Consensus 134 ~v~v~Grv~~~---R~------~G~k~~F~~L~d-~~g~iQv~~~~~~~~~~~~~~~~~~~~l~~Gd~V~V~G~~~~--- 200 (585)
T PTZ00417 134 ILNVTGRIMRV---SA------SGQKLRFFDLVG-DGAKIQVLANFAFHDHTKSNFAECYDKIRRGDIVGIVGFPGK--- 200 (585)
T ss_pred eEEEEEEEEee---ec------CCCCCEEEEEEe-CCeeEEEEEECCccCCCHHHHHHHHhcCCCCCEEEEEeEEcC---
Confidence 47899999874 43 23 344456778 6779999997432 2223 456999999999998322
Q ss_pred CccccCCCeeEEEEcccceEEec
Q 008606 199 KNFNHLKNEWEIFLEATSTVDLC 221 (560)
Q Consensus 199 ~~y~~~~~~yeI~f~~~T~I~~~ 221 (560)
+-...++|....-+.+..+
T Consensus 201 ----t~~gel~i~~~~i~llsk~ 219 (585)
T PTZ00417 201 ----SKKGELSIFPKETIILSPC 219 (585)
T ss_pred ----CCCceEEEEEEEEEEEecC
Confidence 2134666676655444443
No 107
>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=76.48 E-value=9.7 Score=32.28 Aligned_cols=47 Identities=19% Similarity=0.174 Sum_probs=38.5
Q ss_pred EEEEecCCCcEEEEEEeCcchhhhhhhHHhhhccCCccEEEEEEEEEecCCCc
Q 008606 277 ILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVDVGFFPVLSVKSGKVNDFSGK 329 (560)
Q Consensus 277 ~i~L~D~Sg~~I~vtLWg~~a~~~~~~l~~~~~~~~~~VV~l~~~rV~~f~G~ 329 (560)
++.|.|+.|..|..+++.+++..+...|. ++.+..|.+..|..-.|.
T Consensus 1 emvL~De~G~~I~A~I~~~~~~~f~~~l~------Eg~~y~i~~F~V~~~~~~ 47 (95)
T PF02721_consen 1 EMVLVDEKGDKIQATIPKELVDKFKDSLK------EGSWYTISNFTVSPNSGS 47 (95)
T ss_pred CEEEEecCCCEEEEEECHHHHHHHHhhcc------cCCEEEeEeEEEEeCCCc
Confidence 47899999999999999999988755543 578888999988866564
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=75.14 E-value=29 Score=28.28 Aligned_cols=73 Identities=15% Similarity=0.124 Sum_probs=46.2
Q ss_pred eEEEEEEEEecccceeccCCCCCcEEEEEEEeCCCC-eEEEEEcchhH-HHHHhhcccCcEEEEeeeEEecCCCccccCC
Q 008606 128 WAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGG-EIRVTCFNAVV-DRFYEIIEVGRVYLISKGSLKPAQKNFNHLK 205 (560)
Q Consensus 128 w~Ik~RV~~k~~ir~~~n~~g~gkvf~~~L~D~~g~-~I~at~~~~~~-~kf~~~l~eG~vY~Is~~~V~~a~~~y~~~~ 205 (560)
-+|+|||.++ |. .|++.=++|.|..|. .|++++..+.. -++-..|..|+++.+.+--+....+ .
T Consensus 2 v~v~Gwv~~~---R~------~g~~~Fi~LrD~s~~~~lQvv~~~~~~~~~~~~~l~~gs~V~v~G~v~~~~~~-----~ 67 (82)
T cd04318 2 VTVNGWVRSV---RD------SKKISFIELNDGSCLKNLQVVVDKELTNFKEILKLSTGSSIRVEGVLVKSPGA-----K 67 (82)
T ss_pred EEEEEeEEEE---Ec------CCcEEEEEEECCCCccCEEEEEeCcccCHHHHhcCCCceEEEEEEEEEeCCCC-----C
Confidence 3678888653 32 235544557786554 69999875532 1344568999999999965443222 3
Q ss_pred CeeEEEEcc
Q 008606 206 NEWEIFLEA 214 (560)
Q Consensus 206 ~~yeI~f~~ 214 (560)
.++||...+
T Consensus 68 ~~~El~~~~ 76 (82)
T cd04318 68 QPFELQAEK 76 (82)
T ss_pred CCEEEEEEE
Confidence 578887754
No 109
>KOG0556 consensus Aspartyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=75.07 E-value=33 Score=36.93 Aligned_cols=100 Identities=13% Similarity=0.153 Sum_probs=73.5
Q ss_pred CCcceeccccCCCCC--ceEEEEEEEEecccceeccCCCCCcEEEEEEEeCCCCeEEEEEcc-------hhHHHHHhhcc
Q 008606 112 PARIIPIAALNPYQG--RWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFN-------AVVDRFYEIIE 182 (560)
Q Consensus 112 ~~~~~pI~~L~p~~~--~w~Ik~RV~~k~~ir~~~n~~g~gkvf~~~L~D~~g~~I~at~~~-------~~~~kf~~~l~ 182 (560)
-+.++++++|+.... ...|+|||- + .+-.||..=++|.+ .|..|+|.+.- ...-+|...|-
T Consensus 67 ~~~~~~v~dl~~~~~~~~V~vRgrVh--------t-sr~~GK~~FlvLRq-~~~tVQ~~~~~~~~~~isk~Mvkf~~~is 136 (533)
T KOG0556|consen 67 GRELTDVSDLDESNDGSEVLVRGRVH--------T-SRLKGKLCFLVLRQ-QGSTVQCLVAVNEDGTISKQMVKFAGSIS 136 (533)
T ss_pred ccceeehhhhhhhcCCceEEEEEEEe--------e-ccccceEEEEEEec-cCceEEEEEEcCCCchHHHHHHHHHhhcC
Confidence 568999999988763 566888883 2 23456766667777 89999999952 35678999999
Q ss_pred cCcEEEEeeeEEecCCCccccCCCeeEEEEcccceEEec
Q 008606 183 VGRVYLISKGSLKPAQKNFNHLKNEWEIFLEATSTVDLC 221 (560)
Q Consensus 183 eG~vY~Is~~~V~~a~~~y~~~~~~yeI~f~~~T~I~~~ 221 (560)
.-.++.+.+.-+++..+--.-+..+.||....--.|...
T Consensus 137 ~ESiV~v~g~v~k~~~~i~scT~qdvEi~v~~iyviS~a 175 (533)
T KOG0556|consen 137 KESIVDVRGVVVKVKEPIKSCTVQDVEIHVRKIYVISIA 175 (533)
T ss_pred cceEEEEEEEEecCCCcccccccceeEEEEEEEEEEecc
Confidence 999999888777766654444677899988765555544
No 110
>PRK00484 lysS lysyl-tRNA synthetase; Reviewed
Probab=74.66 E-value=29 Score=38.65 Aligned_cols=78 Identities=18% Similarity=0.201 Sum_probs=53.8
Q ss_pred CceEEEEEEEEecccceeccCCCCCcEEEEEEEeCCCCeEEEEEcchh-----HHHHHhhcccCcEEEEeeeEEecCCCc
Q 008606 126 GRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAV-----VDRFYEIIEVGRVYLISKGSLKPAQKN 200 (560)
Q Consensus 126 ~~w~Ik~RV~~k~~ir~~~n~~g~gkvf~~~L~D~~g~~I~at~~~~~-----~~kf~~~l~eG~vY~Is~~~V~~a~~~ 200 (560)
...+|.|||.++ |. .|++.=++|.| .++.|++.+-.+. .+.+. .|..|+++.+.+.-++..
T Consensus 55 ~~v~v~G~v~~~---R~------~g~~~Fi~lrD-~~g~iQ~v~~~~~~~~~~~~~~~-~l~~g~~v~v~G~v~~t~--- 120 (491)
T PRK00484 55 IEVSVAGRVMLK---RV------MGKASFATLQD-GSGRIQLYVSKDDVGEEALEAFK-KLDLGDIIGVEGTLFKTK--- 120 (491)
T ss_pred cEEEEEEEEEEE---ec------CCceEEEEEEc-CCccEEEEEECCcCCHHHHHHHh-cCCCCCEEEEEEEEEEcC---
Confidence 458999999874 43 34666677999 4569999986542 22333 499999999988665432
Q ss_pred cccCCCeeEEEEcccceEEec
Q 008606 201 FNHLKNEWEIFLEATSTVDLC 221 (560)
Q Consensus 201 y~~~~~~yeI~f~~~T~I~~~ 221 (560)
...++|..+.-..+..+
T Consensus 121 ----~ge~el~~~~~~vls~~ 137 (491)
T PRK00484 121 ----TGELSVKATELTLLTKS 137 (491)
T ss_pred ----CCcEEEEEeEEEEEecc
Confidence 24688888776655554
No 111
>KOG4757 consensus Predicted telomere binding protein [General function prediction only]
Probab=73.67 E-value=9.7 Score=40.93 Aligned_cols=75 Identities=17% Similarity=0.256 Sum_probs=56.9
Q ss_pred cCCceeEEEEEEEEecCceeEeeccCceeeEEEEEEec--CCCcEEEEEEeCcchhhhhhhHHhhhccCCccEEEEEEEE
Q 008606 245 ENNSIVDVIGIVISVNPSVPILRKNGMETQRRILNLKD--TSGRSVELTLWGDFCNKEGQKLQEMVDVGFFPVLSVKSGK 322 (560)
Q Consensus 245 ~~~~~VDVIGvV~~V~~~~~i~~k~G~~~~kr~i~L~D--~Sg~~I~vtLWg~~a~~~~~~l~~~~~~~~~~VV~l~~~r 322 (560)
..+..|.++|+|++.+|...- + |+. -...+.|.| .|+..+.|-|+....+++ ... ...+++|.+...|
T Consensus 18 k~~tiVNl~GiVkef~pp~qs--~-g~D-~~~tv~IvDp~~ss~gLtv~lfSkt~edL----P~I--k~~GDiillhRiK 87 (522)
T KOG4757|consen 18 KKNTIVNLIGIVKEFTPPRQS--L-GKD-WVCTVYIVDPDYSSIGLTVHLFSKTGEDL----PVI--KQVGDIILLHRIK 87 (522)
T ss_pred hcCcEEEEEEEEEeccChhhc--c-CCc-eEEEEEEeCCCCCCCCcEEEEecCchhhC----ccc--cccCcEEEEEEEE
Confidence 368899999999999987652 2 433 466899999 678889999998887652 221 1467899999999
Q ss_pred EecCCCc
Q 008606 323 VNDFSGK 329 (560)
Q Consensus 323 V~~f~G~ 329 (560)
+.-|+.+
T Consensus 88 iq~y~~r 94 (522)
T KOG4757|consen 88 IQSYRDR 94 (522)
T ss_pred EEEhhhh
Confidence 9888765
No 112
>PTZ00385 lysyl-tRNA synthetase; Provisional
Probab=73.58 E-value=38 Score=39.05 Aligned_cols=77 Identities=16% Similarity=0.184 Sum_probs=52.7
Q ss_pred ceEEEEEEEEecccceeccCCCCCcEEEEEEEeCCCCeEEEEEcchh------HHHHHhhcccCcEEEEeeeEEecCCCc
Q 008606 127 RWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAV------VDRFYEIIEVGRVYLISKGSLKPAQKN 200 (560)
Q Consensus 127 ~w~Ik~RV~~k~~ir~~~n~~g~gkvf~~~L~D~~g~~I~at~~~~~------~~kf~~~l~eG~vY~Is~~~V~~a~~~ 200 (560)
..+|.|||.++ |. -|++.=++|.| .+|.|++.+..+. ...+...|..|+++.+.+.-.+.
T Consensus 109 ~V~vaGrV~~~---R~------~Gk~~F~~LrD-~~G~IQvv~~~~~~~~~~~~~~~~~~l~~gdiV~V~G~v~~t---- 174 (659)
T PTZ00385 109 TVRVAGRVTSV---RD------IGKIIFVTIRS-NGNELQVVGQVGEHFTREDLKKLKVSLRVGDIIGADGVPCRM---- 174 (659)
T ss_pred EEEEEEEEEee---ec------cCCeEEEEEEE-CCceEEEEEECCccCCHHHHHHHHhCCCCCCEEEEEEEEEec----
Confidence 48999999874 33 35665567889 6779999996542 22334568999999998864432
Q ss_pred cccCCCeeEEEEcccceEEe
Q 008606 201 FNHLKNEWEIFLEATSTVDL 220 (560)
Q Consensus 201 y~~~~~~yeI~f~~~T~I~~ 220 (560)
-...++|....-+.+..
T Consensus 175 ---~~GeleI~~~~i~lLsk 191 (659)
T PTZ00385 175 ---QRGELSVAASRMLILSP 191 (659)
T ss_pred ---CCceEEEEeeEEEEech
Confidence 13567777776655555
No 113
>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=73.47 E-value=25 Score=39.26 Aligned_cols=80 Identities=16% Similarity=0.230 Sum_probs=54.0
Q ss_pred CCceEEEEEEEEecccceeccCCCCCcEEEEEEEeCCCCeEEEEEcchhH-----HHHHhhcccCcEEEEeeeEEecCCC
Q 008606 125 QGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAVV-----DRFYEIIEVGRVYLISKGSLKPAQK 199 (560)
Q Consensus 125 ~~~w~Ik~RV~~k~~ir~~~n~~g~gkvf~~~L~D~~g~~I~at~~~~~~-----~kf~~~l~eG~vY~Is~~~V~~a~~ 199 (560)
....+|.|||.++ |. .|++.=++|.| .++.|++.+-.+.+ +.+...|..|+++.+.+.-.+..
T Consensus 53 ~~~v~v~Grv~~~---R~------~gk~~F~~l~D-~~g~iQ~~~~~~~~~~~~~~~~~~~l~~gd~V~v~G~~~~t~-- 120 (496)
T TIGR00499 53 NIEVSIAGRIMAR---RS------MGKATFITLQD-ESGQIQLYVNKDDLPEDFYEFDEYLLDLGDIIGVTGYPFKTK-- 120 (496)
T ss_pred CCEEEEEEEEEEE---ec------CCCeEEEEEEc-CCccEEEEEECCcCcHHHHHHHHhcCCCCCEEEEEEEEEECC--
Confidence 3458999999874 32 34665667999 55789999864321 22233589999999999664422
Q ss_pred ccccCCCeeEEEEcccceEEec
Q 008606 200 NFNHLKNEWEIFLEATSTVDLC 221 (560)
Q Consensus 200 ~y~~~~~~yeI~f~~~T~I~~~ 221 (560)
...++|..+.-+.+..+
T Consensus 121 -----~gelel~~~~i~ilsk~ 137 (496)
T TIGR00499 121 -----TGELSVHVTELQILTKA 137 (496)
T ss_pred -----CCcEEEEeeEEEEEecC
Confidence 35688888776555555
No 114
>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=73.25 E-value=46 Score=29.92 Aligned_cols=86 Identities=15% Similarity=0.120 Sum_probs=53.8
Q ss_pred CceEEEEEEEEecccceeccCCCCCcEEEEEEEeCCCCeEEEEEcchhHH--HHHhhcccCcEEEEeeeEEecCC--Ccc
Q 008606 126 GRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAVVD--RFYEIIEVGRVYLISKGSLKPAQ--KNF 201 (560)
Q Consensus 126 ~~w~Ik~RV~~k~~ir~~~n~~g~gkvf~~~L~D~~g~~I~at~~~~~~~--kf~~~l~eG~vY~Is~~~V~~a~--~~y 201 (560)
..-+|+|||.++ |. .|++.=++|.|. ++.+++.+.....+ ++...|..|+++.+.+--..... +.-
T Consensus 15 ~~V~i~Gwv~~~---R~------~gk~~Fi~LrD~-~g~~Q~v~~~~~~~~~~~~~~l~~gs~V~V~G~~~~~~~~~~~~ 84 (135)
T cd04317 15 QEVTLCGWVQRR---RD------HGGLIFIDLRDR-YGIVQVVFDPEEAPEFELAEKLRNESVIQVTGKVRARPEGTVNP 84 (135)
T ss_pred CEEEEEEeEehh---cc------cCCEEEEEEecC-CeeEEEEEeCCchhHHHHHhCCCCccEEEEEEEEECCCccccCC
Confidence 468899999753 43 345444457884 56899998755333 34456999999999996544221 111
Q ss_pred ccCCCeeEEEEcccceEEec
Q 008606 202 NHLKNEWEIFLEATSTVDLC 221 (560)
Q Consensus 202 ~~~~~~yeI~f~~~T~I~~~ 221 (560)
......+||....-..+..+
T Consensus 85 ~~~~~~~El~~~~i~vl~~~ 104 (135)
T cd04317 85 KLPTGEIEVVASELEVLNKA 104 (135)
T ss_pred CCCCCcEEEEEeEEEEEECC
Confidence 12345799998665445444
No 115
>COG0629 Ssb Single-stranded DNA-binding protein [DNA replication, recombination, and repair]
Probab=72.85 E-value=11 Score=35.48 Aligned_cols=67 Identities=21% Similarity=0.328 Sum_probs=49.8
Q ss_pred CCCceEEEEEEEEecccceeccCCCCCcEEE-EE-----EEeC-------CCCeEEEEEcchhHHHHHhhcccCcEEEEe
Q 008606 124 YQGRWAIKARVTAKGDLRRYNNARGDGKVFS-FD-----LLDS-------DGGEIRVTCFNAVVDRFYEIIEVGRVYLIS 190 (560)
Q Consensus 124 ~~~~w~Ik~RV~~k~~ir~~~n~~g~gkvf~-~~-----L~D~-------~g~~I~at~~~~~~~kf~~~l~eG~vY~Is 190 (560)
.+++..+.+|+++.-++|...+ |. .+.. +. ..|. +..-|++++|+.+++.....|+.|.-+.|.
T Consensus 2 ~~Nkv~LvG~l~~DPE~r~t~~--g~-~~v~~~~~a~~r~~~~~~~~~~~~t~~~~vv~wgk~Ae~~~~yl~KG~~V~Ve 78 (167)
T COG0629 2 MMNKVILVGRLTRDPELRYTPN--GG-AVVALFSAAVNRRFDNQSGERDEETDWIRVVIWGKLAENAAEYLKKGSLVYVE 78 (167)
T ss_pred CcceEEEEeecccCcceeecCC--CC-eeeEEEEEEeccccccCCcccccccceEEEEEehHHHHHHHHHhcCCCEEEEE
Confidence 3567889999999999987653 21 2222 22 2232 337899999999999999999999999998
Q ss_pred eeE
Q 008606 191 KGS 193 (560)
Q Consensus 191 ~~~ 193 (560)
+..
T Consensus 79 G~l 81 (167)
T COG0629 79 GRL 81 (167)
T ss_pred EEE
Confidence 753
No 116
>PRK12445 lysyl-tRNA synthetase; Reviewed
Probab=72.82 E-value=26 Score=39.15 Aligned_cols=79 Identities=16% Similarity=0.194 Sum_probs=53.9
Q ss_pred CceEEEEEEEEecccceeccCCCCCcEEEEEEEeCCCCeEEEEEcchhH-----HHHHhhcccCcEEEEeeeEEecCCCc
Q 008606 126 GRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAVV-----DRFYEIIEVGRVYLISKGSLKPAQKN 200 (560)
Q Consensus 126 ~~w~Ik~RV~~k~~ir~~~n~~g~gkvf~~~L~D~~g~~I~at~~~~~~-----~kf~~~l~eG~vY~Is~~~V~~a~~~ 200 (560)
...+|.|||.++ |. .|++.=++|.| .++.|++.+-.+.+ .+....|..|+++.+.+.-++..
T Consensus 66 ~~v~v~Grv~~~---R~------~Gk~~F~~lrD-~~g~iQ~~~~~~~~~~~~~~~~~~~l~~Gd~V~v~G~~~~t~--- 132 (505)
T PRK12445 66 IEVSVAGRMMTR---RI------MGKASFVTLQD-VGGRIQLYVARDSLPEGVYNDQFKKWDLGDIIGARGTLFKTQ--- 132 (505)
T ss_pred CEEEEEEEEEEE---ec------CCCcEEEEEEe-CCccEEEEEECCccchhhHHHHHhcCCCCCEEEEEEEEEecC---
Confidence 358999999874 33 34665567899 56789998874322 22235689999999988665532
Q ss_pred cccCCCeeEEEEcccceEEec
Q 008606 201 FNHLKNEWEIFLEATSTVDLC 221 (560)
Q Consensus 201 y~~~~~~yeI~f~~~T~I~~~ 221 (560)
...++|..++-+.+..+
T Consensus 133 ----~gelel~~~~~~llsk~ 149 (505)
T PRK12445 133 ----TGELSIHCTELRLLTKA 149 (505)
T ss_pred ----CCcEEEEEeEEEEEecC
Confidence 35688888766555554
No 117
>TIGR00643 recG ATP-dependent DNA helicase RecG.
Probab=72.14 E-value=12 Score=43.09 Aligned_cols=71 Identities=20% Similarity=0.226 Sum_probs=52.0
Q ss_pred CcceeccccCCCCCceEEEEEEEEecccceeccCCCCCcEEEEEEEeCCCCeEEEEEcchhHHHHHhhcccCcEEEEee
Q 008606 113 ARIIPIAALNPYQGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISK 191 (560)
Q Consensus 113 ~~~~pI~~L~p~~~~w~Ik~RV~~k~~ir~~~n~~g~gkvf~~~L~D~~g~~I~at~~~~~~~kf~~~l~eG~vY~Is~ 191 (560)
..+.+|++|.++. .-+|.|+|+.... .. ++..+.+.+.|.|..++.|.+++|+.. -....|+.|+.|.+++
T Consensus 21 ~~~~~i~~~~~g~-~~~~~~~v~~~~~---~~--~~~~~~~~~~~~d~~~~~~~~~~F~~~--~~~~~~~~g~~~~~~G 91 (630)
T TIGR00643 21 TLLQTIGELLPGE-RATIVGEVLSHCI---FG--FKRRKVLKLRLKDGGYKKLELRFFNRA--FLKKKFKVGSKVVVYG 91 (630)
T ss_pred CcccCHHHcCCCC-EEEEEEEEEEeEe---cc--CCCCceEEEEEEECCCCEEEEEEECCH--HHHhhCCCCCEEEEEE
Confidence 3467999998875 5789999987421 11 122358999999955678999999832 3467899999998876
No 118
>PRK02801 primosomal replication protein N; Provisional
Probab=70.66 E-value=23 Score=30.57 Aligned_cols=66 Identities=12% Similarity=0.121 Sum_probs=40.4
Q ss_pred eeEEEEEEEEecCceeEeeccCceeeEEEEEEe---cCCCc------EEEEEEeCcchhhhhhhHHhhhccCCccEEEEE
Q 008606 249 IVDVIGIVISVNPSVPILRKNGMETQRRILNLK---DTSGR------SVELTLWGDFCNKEGQKLQEMVDVGFFPVLSVK 319 (560)
Q Consensus 249 ~VDVIGvV~~V~~~~~i~~k~G~~~~kr~i~L~---D~Sg~------~I~vtLWg~~a~~~~~~l~~~~~~~~~~VV~l~ 319 (560)
.|-++|.++.--+++. +.+|.....-.|... ++.+. .|.|++||+.|+...++| ..+..|.+.
T Consensus 4 ~v~L~Grl~~dpelr~--Tp~G~~v~~f~La~~~~~~ea~~~r~~~~~i~~va~G~~Ae~~~~~l------~kGs~v~V~ 75 (101)
T PRK02801 4 RLVLSGTVCRTPKRKV--SPSGIPHCQFVLEHRSVQEEAGLHRQAWCRMPVIVSGNQFQAITQSI------TVGSKITVQ 75 (101)
T ss_pred EEEEEEEECcCcceEE--CCCCCeEEEEEEEEeCeEecCCCceeEEEEEEEEEEcHHHHHHHhhc------CCCCEEEEE
Confidence 4678888888777654 345755433333332 12121 299999999998864443 357777776
Q ss_pred EEE
Q 008606 320 SGK 322 (560)
Q Consensus 320 ~~r 322 (560)
+--
T Consensus 76 G~L 78 (101)
T PRK02801 76 GFI 78 (101)
T ss_pred EEE
Confidence 543
No 119
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=70.20 E-value=2.1 Score=26.79 Aligned_cols=19 Identities=16% Similarity=0.590 Sum_probs=15.5
Q ss_pred ccCceeeecCCeeecCcCCCc
Q 008606 428 QCNKKVTQSGNRWQCDRCNQE 448 (560)
Q Consensus 428 ~C~KKv~~~~~~~~C~kC~~~ 448 (560)
.|++++.++ .-+|+.|+..
T Consensus 4 ~CG~~~~~~--~~fC~~CG~~ 22 (23)
T PF13240_consen 4 NCGAEIEDD--AKFCPNCGTP 22 (23)
T ss_pred ccCCCCCCc--CcchhhhCCc
Confidence 999999765 4689999964
No 120
>PRK07374 dnaE DNA polymerase III subunit alpha; Validated
Probab=70.08 E-value=13 Score=45.62 Aligned_cols=71 Identities=17% Similarity=0.278 Sum_probs=50.7
Q ss_pred eeccccC--CCCCceEEEEEEEEecccceeccCCCCCcEEEEEEEeCCCCeEEEEEcchhHHHHHhhcccCcEEEEee
Q 008606 116 IPIAALN--PYQGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISK 191 (560)
Q Consensus 116 ~pI~~L~--p~~~~w~Ik~RV~~k~~ir~~~n~~g~gkvf~~~L~D~~g~~I~at~~~~~~~kf~~~l~eG~vY~Is~ 191 (560)
+++++|. +.....+|.|-|+..-. ...++|+ .+.-+.|-| ..|.+.+++|.+..+++...|++|.++.|.+
T Consensus 989 ~~~~~l~~~~~~~~v~v~g~i~~~k~---~~Tk~G~-~maf~~leD-~tg~~e~vvFp~~y~~~~~~l~~~~~~~v~g 1061 (1170)
T PRK07374 989 ISLSSLEEQPDKAKVSAIAMIPEMKQ---VTTRKGD-RMAILQLED-LTGSCEAVVFPKSYERLSDHLMTDTRLLVWA 1061 (1170)
T ss_pred cCHHHHhcccCCCEEEEEEEEEEeEe---cccCCCC-EEEEEEEEE-CCCCEEEEECHHHHHHHHHHhccCCEEEEEE
Confidence 4666664 23345678888876543 3334443 333445667 7889999999999999999999999999965
No 121
>PRK05673 dnaE DNA polymerase III subunit alpha; Validated
Probab=70.05 E-value=13 Score=45.63 Aligned_cols=72 Identities=21% Similarity=0.328 Sum_probs=50.7
Q ss_pred ceeccccCC--CCCceEEEEEEEEecccceeccCCCCCcEEEEEEEeCCCCeEEEEEcchhHHHHHhhcccCcEEEEee
Q 008606 115 IIPIAALNP--YQGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISK 191 (560)
Q Consensus 115 ~~pI~~L~p--~~~~w~Ik~RV~~k~~ir~~~n~~g~gkvf~~~L~D~~g~~I~at~~~~~~~kf~~~l~eG~vY~Is~ 191 (560)
.+++.+|.. ....-.+.+.|+.+-. ...++|+ ...-+.|-| ..|.|.+++|.+..+++.+.|++|.++.|.+
T Consensus 965 ~~~~~~l~~~~~g~~V~v~G~I~~vk~---~~TKkG~-~mafltLeD-~TG~iEvviFp~~ye~~~~~L~~g~iV~V~G 1038 (1135)
T PRK05673 965 DTRLADLEPTEGGSVVTVAGLVVSVRR---RVTKRGN-KMAIVTLED-LSGRIEVMLFSEALEKYRDLLEEDRIVVVKG 1038 (1135)
T ss_pred CcCHHHHhccccCceEEEEEEEEEEEe---cccCCCC-eEEEEEEEe-CCCcEEEEECHHHHHHHHHHhccCCEEEEEE
Confidence 346677642 2345667777776533 3333442 344556777 6779999999999999999999999999865
No 122
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=69.79 E-value=3.2 Score=34.73 Aligned_cols=28 Identities=21% Similarity=0.812 Sum_probs=20.6
Q ss_pred eCCCCCcCccccCceeeecC--CeeecCcCCCccCC
Q 008606 418 TACPLMIGDRQCNKKVTQSG--NRWQCDRCNQEIDE 451 (560)
Q Consensus 418 ~aC~~~~~~~~C~KKv~~~~--~~~~C~kC~~~~~~ 451 (560)
..|| .|+++-..-. +.|.|.+|+..+.-
T Consensus 36 ~~Cp------~C~~~~VkR~a~GIW~C~kCg~~fAG 65 (89)
T COG1997 36 HVCP------FCGRTTVKRIATGIWKCRKCGAKFAG 65 (89)
T ss_pred CcCC------CCCCcceeeeccCeEEcCCCCCeecc
Confidence 3599 9998754332 39999999987643
No 123
>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=68.87 E-value=13 Score=31.54 Aligned_cols=40 Identities=15% Similarity=0.260 Sum_probs=34.0
Q ss_pred EEEEEEEeCCCCeEEEEEcchh--HHHHHhhcccCcEEEEeee
Q 008606 152 VFSFDLLDSDGGEIRVTCFNAV--VDRFYEIIEVGRVYLISKG 192 (560)
Q Consensus 152 vf~~~L~D~~g~~I~at~~~~~--~~kf~~~l~eG~vY~Is~~ 192 (560)
..-|.|.| +++.|.|.+|... +.+....|++|+-+.+.+.
T Consensus 18 H~yFtlkD-~~~~i~cv~f~~~g~~~~~~~~l~~Gd~V~v~G~ 59 (91)
T cd04482 18 HVFFKISD-GTGEIDCAAYEPTKEFRDVVRLLIPGDEVTVYGS 59 (91)
T ss_pred CEEEEEEC-CCcEEEEEEECcccccccccCCCCCCCEEEEEEE
Confidence 57788899 6689999999987 7788889999998887765
No 124
>PRK07374 dnaE DNA polymerase III subunit alpha; Validated
Probab=68.61 E-value=14 Score=45.38 Aligned_cols=77 Identities=22% Similarity=0.264 Sum_probs=54.4
Q ss_pred ccCccchhcccCCceeEEEEEEEEecCceeEeeccCceeeEEEEEEecCCCcEEEEEEeCcchhhhhhhHHhhhccCCcc
Q 008606 235 FRHISEIESAENNSIVDVIGIVISVNPSVPILRKNGMETQRRILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVDVGFFP 314 (560)
Q Consensus 235 f~~i~dI~~~~~~~~VDVIGvV~~V~~~~~i~~k~G~~~~kr~i~L~D~Sg~~I~vtLWg~~a~~~~~~l~~~~~~~~~~ 314 (560)
..++++|.....+..|-|+|+|+++... .+|.|+. .--++|.|.+| .+++++|-+....+...| ..+.
T Consensus 988 ~~~~~~l~~~~~~~~v~v~g~i~~~k~~---~Tk~G~~--maf~~leD~tg-~~e~vvFp~~y~~~~~~l------~~~~ 1055 (1170)
T PRK07374 988 PISLSSLEEQPDKAKVSAIAMIPEMKQV---TTRKGDR--MAILQLEDLTG-SCEAVVFPKSYERLSDHL------MTDT 1055 (1170)
T ss_pred CcCHHHHhcccCCCEEEEEEEEEEeEec---ccCCCCE--EEEEEEEECCC-CEEEEECHHHHHHHHHHh------ccCC
Confidence 3466666544456789999999998765 4566763 45789999999 799999998877754433 2356
Q ss_pred EEEEEEEEEe
Q 008606 315 VLSVKSGKVN 324 (560)
Q Consensus 315 VV~l~~~rV~ 324 (560)
+|.+++ +|.
T Consensus 1056 ~~~v~g-~v~ 1064 (1170)
T PRK07374 1056 RLLVWA-KVD 1064 (1170)
T ss_pred EEEEEE-EEE
Confidence 666654 554
No 125
>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=68.06 E-value=13 Score=31.49 Aligned_cols=52 Identities=17% Similarity=0.482 Sum_probs=36.6
Q ss_pred EEEEEEEecccceeccCCCCCcEEEEEEEeCCCCeEEEEEcchhH--H------------------HHHhhcccCcEEEE
Q 008606 130 IKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAVV--D------------------RFYEIIEVGRVYLI 189 (560)
Q Consensus 130 Ik~RV~~k~~ir~~~n~~g~gkvf~~~L~D~~g~~I~at~~~~~~--~------------------kf~~~l~eG~vY~I 189 (560)
|.|.|++..+ . + ..+.|.|-|. .|.|.|.+|.... + +..+.|++|+++.+
T Consensus 2 ivG~V~sv~~---~-----~-~~~~~tLdDg-TG~Ie~~~W~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~G~vvrV 71 (92)
T cd04483 2 ILGTVVSRRE---R-----E-TFYSFGVDDG-TGVVNCVCWKNLSYAEVSSRSDAARILKSALMALKQAKVLEIGDLLRV 71 (92)
T ss_pred eEEEEEEEEe---c-----C-CeEEEEEecC-CceEEEEEEcCcCcccccccccccccccccccccccccccCCCCEEEE
Confidence 5677776532 1 1 4588999995 4589999997632 1 46667999998888
Q ss_pred ee
Q 008606 190 SK 191 (560)
Q Consensus 190 s~ 191 (560)
.+
T Consensus 72 ~G 73 (92)
T cd04483 72 RG 73 (92)
T ss_pred EE
Confidence 74
No 126
>PRK07135 dnaE DNA polymerase III DnaE; Validated
Probab=67.82 E-value=17 Score=43.75 Aligned_cols=74 Identities=19% Similarity=0.168 Sum_probs=50.3
Q ss_pred eeccccCCCCCceEEEEEEEEecccceeccCCCCCcEEEEEEEeCCCCeEEEEEcchhHHHHHhhcccCcEEEEeeeEEe
Q 008606 116 IPIAALNPYQGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISKGSLK 195 (560)
Q Consensus 116 ~pI~~L~p~~~~w~Ik~RV~~k~~ir~~~n~~g~gkvf~~~L~D~~g~~I~at~~~~~~~kf~~~l~eG~vY~Is~~~V~ 195 (560)
.+|++|. .....+|.|.|+..-.++ ++|+ ..--+.|-| ..+.|.+++|.+..+++.. +.+|++|.+ .+++.
T Consensus 889 ~~~~~l~-~~~~~~v~g~i~~~~~~~----K~g~-~maf~~~eD-~~~~~e~~~F~~~~~~~~~-l~~~~~~~~-~~~~~ 959 (973)
T PRK07135 889 IRLKDLR-INTEYRLAIEVKNVKRLR----KANK-EYKKVILSD-DSVEITIFVNDNDYLLFET-LKKGDIYEF-LISKS 959 (973)
T ss_pred hhHHHhc-CCCeEEEEEEEEEEEEEe----eCCC-eEEEEEEEE-CCCcEEEEEcHHHHHHHHH-hhcCCEEEE-EEEEc
Confidence 4778884 334457788777754433 3343 344445777 7788999999999999887 888888888 44444
Q ss_pred cCC
Q 008606 196 PAQ 198 (560)
Q Consensus 196 ~a~ 198 (560)
.+|
T Consensus 960 ~~~ 962 (973)
T PRK07135 960 KNN 962 (973)
T ss_pred CCC
Confidence 443
No 127
>PRK02983 lysS lysyl-tRNA synthetase; Provisional
Probab=67.33 E-value=32 Score=42.23 Aligned_cols=79 Identities=18% Similarity=0.237 Sum_probs=56.5
Q ss_pred CceEEEEEEEEecccceeccCCCCCcEEEEEEEeCCCCeEEEEEcchh-----HHHHHhhcccCcEEEEeeeEEecCCCc
Q 008606 126 GRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAV-----VDRFYEIIEVGRVYLISKGSLKPAQKN 200 (560)
Q Consensus 126 ~~w~Ik~RV~~k~~ir~~~n~~g~gkvf~~~L~D~~g~~I~at~~~~~-----~~kf~~~l~eG~vY~Is~~~V~~a~~~ 200 (560)
...+|.|||.++ |. .|++.=++|.| .++.|++.+-.+. .+.|...|..|+++.+.+.-.+..
T Consensus 652 ~~V~v~Grv~~~---R~------~G~~~F~~lrD-~~g~iQ~v~~~~~~~~~~~~~~~~~l~~gd~V~v~G~v~~t~--- 718 (1094)
T PRK02983 652 EEVSVSGRVLRI---RD------YGGVLFADLRD-WSGELQVLLDASRLEQGSLADFRAAVDLGDLVEVTGTMGTSR--- 718 (1094)
T ss_pred CEEEEEEEEEEE---ee------CCCeEEEEEEe-CCeeEEEEEECCccchhhHHHHHhcCCCCCEEEEEEEEEEcC---
Confidence 358999999874 43 34665667889 5679999986543 345666799999999999665532
Q ss_pred cccCCCeeEEEEcccceEEec
Q 008606 201 FNHLKNEWEIFLEATSTVDLC 221 (560)
Q Consensus 201 y~~~~~~yeI~f~~~T~I~~~ 221 (560)
...++|..++-+.+..|
T Consensus 719 ----~ge~ei~~~~i~ll~k~ 735 (1094)
T PRK02983 719 ----NGTLSLLVTSWRLAGKC 735 (1094)
T ss_pred ----CCCEEEEEeEEEEEecc
Confidence 14688888776666655
No 128
>PRK05813 single-stranded DNA-binding protein; Provisional
Probab=64.76 E-value=25 Score=34.83 Aligned_cols=64 Identities=11% Similarity=0.041 Sum_probs=50.8
Q ss_pred CCCceEEEEEEEEecccceeccCCCCCcEEEEEEEeC----CCCeEEEEEcchhHHHHHhhcccCcEEEEee
Q 008606 124 YQGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDS----DGGEIRVTCFNAVVDRFYEIIEVGRVYLISK 191 (560)
Q Consensus 124 ~~~~w~Ik~RV~~k~~ir~~~n~~g~gkvf~~~L~D~----~g~~I~at~~~~~~~kf~~~l~eG~vY~Is~ 191 (560)
.++...+.||+++..++|...+ |. .+.+|.|+=. +.+-|.+++|+..|+... .|+.|+-+.|.+
T Consensus 108 ~~N~V~LiGrL~~DPelR~t~~--G~-~va~f~lAvnr~~~~td~i~~v~wg~~Ae~~~-~l~KG~~V~V~G 175 (219)
T PRK05813 108 NPNEIFLDGYICKEPVYRTTPF--GR-EIADLLLAVNRPYNKSDYIPCIAWGRNARFCK-TLEVGDNIRVWG 175 (219)
T ss_pred CccEEEEEEEccCCCeEEECCC--CC-EEEEEEEEEcCCCCCceEEEEEEEhHHhHHHh-hCCCCCEEEEEE
Confidence 3567899999999999987543 32 6888887732 368999999999988655 599999999876
No 129
>PF07754 DUF1610: Domain of unknown function (DUF1610); InterPro: IPR011668 This domain is found in archaeal species. It is likely to bind zinc via its four well-conserved cysteine residues.
Probab=64.39 E-value=5.4 Score=25.33 Aligned_cols=20 Identities=15% Similarity=0.655 Sum_probs=15.9
Q ss_pred ccCceeeecC-C-eeecCcCCC
Q 008606 428 QCNKKVTQSG-N-RWQCDRCNQ 447 (560)
Q Consensus 428 ~C~KKv~~~~-~-~~~C~kC~~ 447 (560)
.|++.+...+ . .|.|++|+.
T Consensus 3 sC~~~i~~r~~~v~f~CPnCG~ 24 (24)
T PF07754_consen 3 SCGRPIAPREQAVPFPCPNCGF 24 (24)
T ss_pred cCCCcccCcccCceEeCCCCCC
Confidence 7988887655 4 899999984
No 130
>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=64.11 E-value=64 Score=35.32 Aligned_cols=89 Identities=16% Similarity=0.129 Sum_probs=57.6
Q ss_pred ccccCCC--CCceEEEEEEEEecccceeccCCCCCcEEEEEEEeCCCCeEEEEEcchh----HHHHHhhcccCcEEEEee
Q 008606 118 IAALNPY--QGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAV----VDRFYEIIEVGRVYLISK 191 (560)
Q Consensus 118 I~~L~p~--~~~w~Ik~RV~~k~~ir~~~n~~g~gkvf~~~L~D~~g~~I~at~~~~~----~~kf~~~l~eG~vY~Is~ 191 (560)
+++|++. ...-+|+|||.++ |. .|++.=++|.| .++.|++++.... .-++-..|..|+++.+.+
T Consensus 3 ~~~l~~~~~g~~v~i~G~v~~~---R~------~g~~~Fi~lrd-~~g~iQ~v~~~~~~~~~~~~~~~~l~~~s~v~v~G 72 (428)
T TIGR00458 3 SADIKPEMDGQEVTFMGWVHEI---RD------LGGLIFVLLRD-REGLIQITAPAKKVSKNLFKWAKKLNLESVVAVRG 72 (428)
T ss_pred hhhCchhhCCCEEEEEEEEEEE---ec------CCCcEEEEEEe-CCeeEEEEEECCcCCHHHHHHHhCCCCCcEEEEEE
Confidence 3455542 2467899999764 33 34655567889 5558999986432 223445699999999988
Q ss_pred eEEecCCCccccCCCeeEEEEcccceEEec
Q 008606 192 GSLKPAQKNFNHLKNEWEIFLEATSTVDLC 221 (560)
Q Consensus 192 ~~V~~a~~~y~~~~~~yeI~f~~~T~I~~~ 221 (560)
.-+. ..+ ....+||....-+.+..+
T Consensus 73 ~v~~-~~~----~~~~~el~~~~i~vl~~~ 97 (428)
T TIGR00458 73 IVKI-KEK----APGGFEIIPTKIEVINEA 97 (428)
T ss_pred EEEe-cCC----CCCcEEEEEeEEEEEecC
Confidence 5543 211 235799998776666655
No 131
>PF15489 CTC1: CST, telomere maintenance, complex subunit CTC1
Probab=63.83 E-value=60 Score=39.43 Aligned_cols=69 Identities=14% Similarity=0.247 Sum_probs=53.2
Q ss_pred CCceEEEEEEEEecccceeccCCCCCcEEEEEEEeCCCCeEEEEEcchhHHHHHhhcccCcEEEEeeeEEecCC
Q 008606 125 QGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISKGSLKPAQ 198 (560)
Q Consensus 125 ~~~w~Ik~RV~~k~~ir~~~n~~g~gkvf~~~L~D~~g~~I~at~~~~~~~kf~~~l~eG~vY~Is~~~V~~a~ 198 (560)
...-.|.|+|++.+.+-..+. . ..|-|.|.| .+..+.+.+-...---|+..|..|+.|.|++.+|..-.
T Consensus 165 ~~~~~v~G~v~~ls~l~~~~~---k-~fF~l~L~~-~~~~v~viVq~pa~l~Wh~~L~~G~~yvlT~Lrvs~ir 233 (1144)
T PF15489_consen 165 GRQLNVAGKVVRLSALVKSHG---K-TFFILSLGD-AGSHVPVIVQEPAQLVWHRALRPGRAYVLTSLRVSKIR 233 (1144)
T ss_pred cCceeeeeEEEEeeceEEEcc---e-EEEEEEeCC-CCceeEEEEEecchhhhhhhcccCCeEEEeeeEEEEec
Confidence 345689999999999876542 2 367777876 77788766666655669999999999999999887443
No 132
>KOG3056 consensus Protein required for S-phase initiation or completion [Cell cycle control, cell division, chromosome partitioning]
Probab=63.49 E-value=27 Score=38.94 Aligned_cols=66 Identities=18% Similarity=0.241 Sum_probs=49.2
Q ss_pred EEEEEEEEecCceeEeeccCceeeEEEEEEecCCC-cEEEEEEeCcchhhhhhhHHhhhccCCccEEEEEEEEEecCC
Q 008606 251 DVIGIVISVNPSVPILRKNGMETQRRILNLKDTSG-RSVELTLWGDFCNKEGQKLQEMVDVGFFPVLSVKSGKVNDFS 327 (560)
Q Consensus 251 DVIGvV~~V~~~~~i~~k~G~~~~kr~i~L~D~Sg-~~I~vtLWg~~a~~~~~~l~~~~~~~~~~VV~l~~~rV~~f~ 327 (560)
=++|+|++-+++.. +.+|... ....|-|..+ ..|.|-|+|+-.. ..|....|.||||-++.|-+.+
T Consensus 189 vt~GvI~~K~~~K~--t~~G~~y--~iwkL~dLk~~q~vslfLFG~a~k-------~~wk~k~GtVialLNp~v~k~~ 255 (578)
T KOG3056|consen 189 VTMGVIVEKSDPKF--TSNGNPY--SIWKLTDLKDHQTVSLFLFGKAHK-------RYWKIKLGTVIALLNPEVLKDR 255 (578)
T ss_pred EEEEEEeecCCccc--ccCCCce--EEEEeeecCccceeEEEEecHHHH-------HHhhhccCcEEEEeCccccCCC
Confidence 37899999998876 4467653 4556666666 5999999999332 3466678999999999988754
No 133
>PRK07279 dnaE DNA polymerase III DnaE; Reviewed
Probab=62.91 E-value=20 Score=43.49 Aligned_cols=73 Identities=16% Similarity=0.327 Sum_probs=52.0
Q ss_pred cceeccccCCCCCceEEEEEEEEecccceeccCCCCCcEEEEEEEeCCCCeEEEEEcchhHHHHHhhcccCcEEEEee
Q 008606 114 RIIPIAALNPYQGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISK 191 (560)
Q Consensus 114 ~~~pI~~L~p~~~~w~Ik~RV~~k~~ir~~~n~~g~gkvf~~~L~D~~g~~I~at~~~~~~~kf~~~l~eG~vY~Is~ 191 (560)
...++++|.. .....+.|.|+.....|+- ++|+ .+.-+.|-| ..|.|.+++|.+..+++.+.|++|.++.|.+
T Consensus 874 ~~~~~~~l~~-~~~~~~~~~i~~~~~~~tk--~~g~-~maf~~leD-~~g~ie~~vFp~~y~~~~~~l~~~~~~~v~G 946 (1034)
T PRK07279 874 PFTPISQLVK-NSEATILVQIQSIRVIRTK--TKGQ-QMAFLSVTD-TKKKLDVTLFPETYRQYKDELKEGKFYYLKG 946 (1034)
T ss_pred cCccHHHHhc-CCcceEEEEEEEEEEEEEc--CCCC-eEEEEEEee-CCCcEEEEECHHHHHHHHHHhccCCEEEEEE
Confidence 4457777754 3345777888765444331 1343 344455667 7889999999999999999999999999965
No 134
>PRK10917 ATP-dependent DNA helicase RecG; Provisional
Probab=62.81 E-value=19 Score=41.77 Aligned_cols=69 Identities=19% Similarity=0.343 Sum_probs=50.3
Q ss_pred cceeccccCCCCCceEEEEEEEEecccceeccCCCCCcEEEEEEEeCCCCeEEEEEcchhHHHH-HhhcccCcEEEEee
Q 008606 114 RIIPIAALNPYQGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAVVDRF-YEIIEVGRVYLISK 191 (560)
Q Consensus 114 ~~~pI~~L~p~~~~w~Ik~RV~~k~~ir~~~n~~g~gkvf~~~L~D~~g~~I~at~~~~~~~kf-~~~l~eG~vY~Is~ 191 (560)
.+.+|+++.++. .-+|.|+|+.....+. ..+.+.+.+.| +.|.|.+++|+-. ..| ...|++|+.|.+++
T Consensus 49 ~~~~i~~l~~g~-~vtv~g~V~~~~~~~~------~~~~~~v~l~D-~tg~i~l~~F~~n-~~~~~~~l~~G~~~~v~G 118 (681)
T PRK10917 49 RLKPIAELRPGE-KVTVEGEVLSAEVVFG------KRRRLTVTVSD-GTGNLTLRFFNFN-QPYLKKQLKVGKRVAVYG 118 (681)
T ss_pred CcCCHHHCCCCC-EEEEEEEEEEEEEccC------CceEEEEEEEE-CCeEEEEEEEccC-cHHHHhhCCCCCEEEEEE
Confidence 456899998764 6899999988633221 13589999999 5568999999410 124 67899999999876
No 135
>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=62.23 E-value=1e+02 Score=26.36 Aligned_cols=79 Identities=14% Similarity=0.121 Sum_probs=48.2
Q ss_pred eEEEEEEEEecccceeccCCCCCcEEEEEEEeCCCCeEEEEEcchhH-HHHH--hhcccCcEEEEeeeEEecCCCccccC
Q 008606 128 WAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAVV-DRFY--EIIEVGRVYLISKGSLKPAQKNFNHL 204 (560)
Q Consensus 128 w~Ik~RV~~k~~ir~~~n~~g~gkvf~~~L~D~~g~~I~at~~~~~~-~kf~--~~l~eG~vY~Is~~~V~~a~~~y~~~ 204 (560)
-+|+|||.++ |. .|++.=++|.|. ++.+++.+..+.. +.|. ..|..|+++.+.+--..... .
T Consensus 2 V~v~Gwv~~~---R~------~gk~~Fi~lrD~-~g~iQ~v~~~~~~~~~~~~~~~l~~~s~v~V~G~v~~~~~-----~ 66 (103)
T cd04319 2 VTLAGWVYRK---RE------VGKKAFIVLRDS-TGIVQAVFSKDLNEEAYREAKKVGIESSVIVEGAVKADPR-----A 66 (103)
T ss_pred EEEEEEEEeE---Ec------CCCeEEEEEecC-CeeEEEEEeCCCCHHHHHHHhCCCCCCEEEEEEEEEECCC-----C
Confidence 3678888763 32 235544568884 5679998875421 1122 35889999999885443221 2
Q ss_pred CCeeEEEEcccceEEec
Q 008606 205 KNEWEIFLEATSTVDLC 221 (560)
Q Consensus 205 ~~~yeI~f~~~T~I~~~ 221 (560)
...+||..+.-..+..+
T Consensus 67 ~~~~Ei~~~~i~vl~~a 83 (103)
T cd04319 67 PGGAEVHGEKLEIIQNV 83 (103)
T ss_pred CCCEEEEEEEEEEEecC
Confidence 24699998665444443
No 136
>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=61.66 E-value=15 Score=29.81 Aligned_cols=40 Identities=25% Similarity=0.386 Sum_probs=32.9
Q ss_pred EEEEEEEeCCCCeEEEEEcchhHHHHHhhcccCcEEEEeee
Q 008606 152 VFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISKG 192 (560)
Q Consensus 152 vf~~~L~D~~g~~I~at~~~~~~~kf~~~l~eG~vY~Is~~ 192 (560)
.+-|.|.| ++..|+|.+|.....+....+++|+-+.+.+-
T Consensus 16 HvyfsLkD-~~a~i~cv~f~~~~~~~~~~l~~Gd~V~v~G~ 55 (73)
T cd04487 16 PTIFTLRD-ETGTVWAAAFEEAGVRAYPEVEVGDIVRVTGE 55 (73)
T ss_pred CEEEEEEc-CCEEEEEEEEchhccCCcCCCCCCCEEEEEEE
Confidence 57888999 67899999999877667778999997777664
No 137
>PRK06826 dnaE DNA polymerase III DnaE; Reviewed
Probab=61.61 E-value=23 Score=43.52 Aligned_cols=77 Identities=23% Similarity=0.279 Sum_probs=52.6
Q ss_pred ccCccchh---------cccCCceeEEEEEEEEecCceeEeeccCceeeEEEEEEecCCCcEEEEEEeCcchhhhhhhHH
Q 008606 235 FRHISEIE---------SAENNSIVDVIGIVISVNPSVPILRKNGMETQRRILNLKDTSGRSVELTLWGDFCNKEGQKLQ 305 (560)
Q Consensus 235 f~~i~dI~---------~~~~~~~VDVIGvV~~V~~~~~i~~k~G~~~~kr~i~L~D~Sg~~I~vtLWg~~a~~~~~~l~ 305 (560)
..+++++. ....+..|-|+|+|+.+... .+|.|+. .--++|.|.+| .+++++|.+....+...|
T Consensus 970 ~~~~~~l~~~~~~~~~~~~~~~~~v~v~g~i~~~~~~---~tk~G~~--maf~~leD~~g-~~e~~vfp~~~~~~~~~l- 1042 (1151)
T PRK06826 970 SATISDIISDEEEDGESKLKDGDKVIIGGIITEVKRK---TTRNNEM--MAFLTLEDLYG-TVEVIVFPKVYEKYRSLL- 1042 (1151)
T ss_pred CcCHHHHhhhccccccccccCCcEEEEEEEEEEeEee---ccCCCCe--EEEEEEEECCC-cEEEEECHHHHHHHHHHh-
Confidence 34667762 23346678899999998754 4566763 45789999999 799999998876654433
Q ss_pred hhhccCCccEEEEEEEEEe
Q 008606 306 EMVDVGFFPVLSVKSGKVN 324 (560)
Q Consensus 306 ~~~~~~~~~VV~l~~~rV~ 324 (560)
..+.+|.+++ +|.
T Consensus 1043 -----~~~~~~~v~g-~v~ 1055 (1151)
T PRK06826 1043 -----NEDNIVLIKG-RVS 1055 (1151)
T ss_pred -----ccCCEEEEEE-EEE
Confidence 2345665654 554
No 138
>PRK06341 single-stranded DNA-binding protein; Provisional
Probab=61.32 E-value=34 Score=32.44 Aligned_cols=64 Identities=16% Similarity=0.222 Sum_probs=48.3
Q ss_pred CCceEEEEEEEEecccceeccCCCCCcEEEEEEEe------C-------CCCeEEEEEcch-hHHHHHhhcccCcEEEEe
Q 008606 125 QGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLD------S-------DGGEIRVTCFNA-VVDRFYEIIEVGRVYLIS 190 (560)
Q Consensus 125 ~~~w~Ik~RV~~k~~ir~~~n~~g~gkvf~~~L~D------~-------~g~~I~at~~~~-~~~kf~~~l~eG~vY~Is 190 (560)
++...|.+||.+-.++|...+ | ..+.+|.|.= . +..-+++++|++ +++.+...|+.|+.+.|.
T Consensus 5 mN~V~LiGrLg~DPElR~t~s--G-~~v~~fsVAvn~~~kd~~~Ge~~e~T~w~~Vv~fg~~~Ae~~~~~LkKG~~V~Ve 81 (166)
T PRK06341 5 VNKVILIGNLGADPEIRRTQD--G-RPIANLRIATSETWRDRNSGERKEKTEWHRVVIFNEGLCKVAEQYLKKGAKVYIE 81 (166)
T ss_pred ceEEEEEEEecCCCEEEEcCC--C-CEEEEEEEEEccceecCCCCcccccceEEEEEEeChHHHHHHHHhcCCCCEEEEE
Confidence 567899999999888887543 2 2566666542 1 233568999996 899999999999999987
Q ss_pred e
Q 008606 191 K 191 (560)
Q Consensus 191 ~ 191 (560)
+
T Consensus 82 G 82 (166)
T PRK06341 82 G 82 (166)
T ss_pred E
Confidence 6
No 139
>PRK05853 hypothetical protein; Validated
Probab=59.86 E-value=23 Score=33.38 Aligned_cols=33 Identities=15% Similarity=0.237 Sum_probs=28.9
Q ss_pred eCCCCeEEEEEcchhHHHHHhhcccCcEEEEee
Q 008606 159 DSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISK 191 (560)
Q Consensus 159 D~~g~~I~at~~~~~~~kf~~~l~eG~vY~Is~ 191 (560)
|.+..-|.+++|+.+++.....|..|+-+.+.+
T Consensus 39 d~~T~wi~V~~wg~lAe~v~~~L~KG~~V~V~G 71 (161)
T PRK05853 39 PGNSLFITVNCWGRLVTGVGAALGKGAPVIVVG 71 (161)
T ss_pred ccCccEEEEEEEhHHHHHHHHHcCCCCEEEEEE
Confidence 345667999999999999999999999998876
No 140
>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=59.59 E-value=89 Score=25.73 Aligned_cols=55 Identities=18% Similarity=0.179 Sum_probs=38.0
Q ss_pred EEEEEEEEEeCCCeEEEEEehhhhhhhcCCCHHHHHHhhhccCChhHHHHHHHHhcCCeEEEEEEEeeeecCCeeeE
Q 008606 455 RYLLQAQIQDQTGLTWVTAFQESGEEILGCPAKELYMLKYELQDDVRFGEIIRSRVFNQYLFRLKIKEELYGDEQRV 531 (560)
Q Consensus 455 rY~l~~~i~D~Tgs~~~~~Fd~~ae~llG~sA~el~~~~~e~~d~~~~~~~l~~~~~k~~~fkvkvk~e~y~~e~r~ 531 (560)
++.+.+.|+|.|+++.+-.|.. + ..+.+.. |. ..|.-..++.++..+.|..+.-+
T Consensus 20 ~~i~~~~itD~t~Si~~K~F~~--~-----~~~~~~~--------------ik-~~G~~v~v~G~v~~D~f~~e~~~ 74 (82)
T cd04484 20 RKILTFKVTDYTSSITVKKFLR--K-----DEKDKEE--------------LK-SKGDWVRVRGKVQYDTFSKELVL 74 (82)
T ss_pred CEEEEEEEEcCCCCEEEEEecc--C-----ChhHHhh--------------cc-cCCCEEEEEEEEEEccCCCceEE
Confidence 6789999999999999999964 1 1111111 10 03677888999988999876443
No 141
>PRK06751 single-stranded DNA-binding protein; Provisional
Probab=59.23 E-value=72 Score=30.47 Aligned_cols=71 Identities=13% Similarity=0.162 Sum_probs=39.0
Q ss_pred eeEEEEEEEEecCceeEeeccCceeeEEEEEE----ecCCC----cEEEEEEeCcchhhhhhhHHhhhccCCccEEEEE-
Q 008606 249 IVDVIGIVISVNPSVPILRKNGMETQRRILNL----KDTSG----RSVELTLWGDFCNKEGQKLQEMVDVGFFPVLSVK- 319 (560)
Q Consensus 249 ~VDVIGvV~~V~~~~~i~~k~G~~~~kr~i~L----~D~Sg----~~I~vtLWg~~a~~~~~~l~~~~~~~~~~VV~l~- 319 (560)
.|-++|.|+.=-.++. +.+|..+..-.|-+ .+..| .-+.|++||+.|+.+.++| ..+.-|.|.
T Consensus 4 ~V~LiGrL~~DpelR~--t~sG~~v~~fslAvnr~~~~~~ge~~tdwi~~v~wgk~Ae~~~~~l------~KG~~V~VeG 75 (173)
T PRK06751 4 RVILVGRLTKDPDLRY--TPNGVAVATFTLAVNRAFANQQGEREADFINCVIWRKQAENVANYL------KKGSLAGVDG 75 (173)
T ss_pred EEEEEEEECCCCcEEE--CCCCCEEEEEEEEEccceecCCCCEEEEEEEEEEeCcHHHHHHHHc------CCCCEEEEEE
Confidence 3567777775433332 23455433222211 12223 3699999999998754443 356666554
Q ss_pred EEEEecCC
Q 008606 320 SGKVNDFS 327 (560)
Q Consensus 320 ~~rV~~f~ 327 (560)
..+...|.
T Consensus 76 rL~~r~ye 83 (173)
T PRK06751 76 RLQTRNYE 83 (173)
T ss_pred EEEeCccC
Confidence 44666675
No 142
>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=58.79 E-value=71 Score=30.06 Aligned_cols=72 Identities=15% Similarity=0.178 Sum_probs=39.7
Q ss_pred eeEEEEEEEEecCceeEeeccCceeeEEEEEE----ecCCC------cEEEEEEeCcchhhhhhhHHhhhccCCccEEEE
Q 008606 249 IVDVIGIVISVNPSVPILRKNGMETQRRILNL----KDTSG------RSVELTLWGDFCNKEGQKLQEMVDVGFFPVLSV 318 (560)
Q Consensus 249 ~VDVIGvV~~V~~~~~i~~k~G~~~~kr~i~L----~D~Sg------~~I~vtLWg~~a~~~~~~l~~~~~~~~~~VV~l 318 (560)
.|-++|.|..--.++ .+.+|+...+..|.. .|..| .-+.|++||+.|+...++| ..+..|.|
T Consensus 6 ~V~L~G~l~~dPe~r--~t~~G~~v~~fsvA~~~~~~~~~G~~~~~t~~~~v~~wg~~Ae~~~~~l------~KG~~V~V 77 (164)
T TIGR00621 6 KVILVGRLTRDPELR--YTPSGNAVANFTLATNRRWKDQDGEWKEETEWHDIVIFGRLAEVAAQYL------KKGSLVYV 77 (164)
T ss_pred EEEEEEEeCCCCEEE--ECCCCCEEEEEEEEEcCceecCCCCEeccceEEEEEEehHHHHHHHHhC------CCCCEEEE
Confidence 466788887632222 234565443333332 12221 3799999999988754433 35666666
Q ss_pred EE-EEEecCCC
Q 008606 319 KS-GKVNDFSG 328 (560)
Q Consensus 319 ~~-~rV~~f~G 328 (560)
.+ .+...|.+
T Consensus 78 ~G~L~~~~~~~ 88 (164)
T TIGR00621 78 EGRLRTRKWED 88 (164)
T ss_pred EEEEEeceEEC
Confidence 54 45556743
No 143
>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=57.88 E-value=50 Score=27.45 Aligned_cols=69 Identities=12% Similarity=0.100 Sum_probs=38.0
Q ss_pred EEEEEEEEecCceeEeeccCceeeEEEEEEec---------CCCcEEEEEEeCcchhhhhhhHHhhhccCCccEEEEE-E
Q 008606 251 DVIGIVISVNPSVPILRKNGMETQRRILNLKD---------TSGRSVELTLWGDFCNKEGQKLQEMVDVGFFPVLSVK-S 320 (560)
Q Consensus 251 DVIGvV~~V~~~~~i~~k~G~~~~kr~i~L~D---------~Sg~~I~vtLWg~~a~~~~~~l~~~~~~~~~~VV~l~-~ 320 (560)
-++|.|...-.+.. .++|....+-.+...+ ..-..+.|++||+.|..+.+.| ..+..|.+. .
T Consensus 2 ~l~G~l~~~p~~~~--~~~g~~~~~~~v~~~~~~~~~~~~~~~~~~~~v~~~g~~a~~~~~~~------~kG~~V~v~G~ 73 (100)
T cd04496 2 ILIGRLGKDPELRY--TPSGTPVARFSLAVNRRRKDRDEEEEETDWIRVVAFGKLAENAAKYL------KKGDLVYVEGR 73 (100)
T ss_pred EEEEEecCCCEEEE--CCCCCEEEEEEEEEcCceecccccccccEEEEEEEEhHHHHHHHHHh------CCCCEEEEEEE
Confidence 45666666433332 2345544333333322 2345799999999988754433 356666554 4
Q ss_pred EEEecCC
Q 008606 321 GKVNDFS 327 (560)
Q Consensus 321 ~rV~~f~ 327 (560)
.+...|.
T Consensus 74 l~~~~~~ 80 (100)
T cd04496 74 LRTRSWE 80 (100)
T ss_pred EEeceeE
Confidence 4555564
No 144
>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=57.57 E-value=1.1e+02 Score=34.94 Aligned_cols=95 Identities=18% Similarity=0.167 Sum_probs=60.1
Q ss_pred eccccCCC--CCceEEEEEEEEecccceeccCCCCCcEEEEEEEeCCCCeEEEEEcch-hHHHHHhhcccCcEEEEeeeE
Q 008606 117 PIAALNPY--QGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNA-VVDRFYEIIEVGRVYLISKGS 193 (560)
Q Consensus 117 pI~~L~p~--~~~w~Ik~RV~~k~~ir~~~n~~g~gkvf~~~L~D~~g~~I~at~~~~-~~~kf~~~l~eG~vY~Is~~~ 193 (560)
.+.+|+.. ....+|+|||.++ |. .|++.=++|.|. +|.|++.+-.+ ..-+....|..|+++.+.+.-
T Consensus 5 ~~~~l~~~~~g~~V~l~GwV~~~---R~------~Gkl~Fi~LrD~-sg~iQvv~~~~~~~~~~~~~L~~esvV~V~G~v 74 (583)
T TIGR00459 5 YCGQLRTEHLGQTVTLAGWVNRR---RD------LGGLIFIDLRDR-SGIVQVVCDPDADALKLAKGLRNEDVVQVKGKV 74 (583)
T ss_pred eHhhcchhhCCCEEEEEEEEEEE---Ec------CCCcEEEEEEeC-CccEEEEEeCCHHHHHHHhcCCCCCEEEEEEEE
Confidence 34555532 3468899999764 43 346666679995 55899988654 222344678999999998865
Q ss_pred EecCCCccc--cCCCeeEEEEcccceEEec
Q 008606 194 LKPAQKNFN--HLKNEWEIFLEATSTVDLC 221 (560)
Q Consensus 194 V~~a~~~y~--~~~~~yeI~f~~~T~I~~~ 221 (560)
.+...+.-+ .....+||....-..+..+
T Consensus 75 ~~r~~~~~n~~~~tg~iEl~~~~i~iL~~a 104 (583)
T TIGR00459 75 SARPEGNINRNLDTGEIEILAESITLLNKS 104 (583)
T ss_pred EeCCccccCccCCCCcEEEEEeEEEEeecC
Confidence 542212212 2346789988766555544
No 145
>PRK06920 dnaE DNA polymerase III DnaE; Reviewed
Probab=57.12 E-value=31 Score=42.24 Aligned_cols=77 Identities=14% Similarity=0.185 Sum_probs=52.8
Q ss_pred cccCccchhcccCCceeEEEEEEEEecCceeEeeccCceeeEEEEEEecCCCcEEEEEEeCcchhhhhhhHHhhhccCCc
Q 008606 234 SFRHISEIESAENNSIVDVIGIVISVNPSVPILRKNGMETQRRILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVDVGFF 313 (560)
Q Consensus 234 ~f~~i~dI~~~~~~~~VDVIGvV~~V~~~~~i~~k~G~~~~kr~i~L~D~Sg~~I~vtLWg~~a~~~~~~l~~~~~~~~~ 313 (560)
...++++|.. ..+..|-|.|+|+.+... .+|.|+. .--++|.|.+| .+++++|.+....+...|. .+
T Consensus 931 ~~~~~~~l~~-~~~~~v~v~g~i~~~~~~---~tk~g~~--maf~~leD~tg-~~e~~vFp~~y~~~~~~l~------~~ 997 (1107)
T PRK06920 931 EIPSLAQAMR-HKKKVQRAIVYITSVKVI---RTKKGQK--MAFITFCDQND-EMEAVVFPETYIHFSDKLQ------EG 997 (1107)
T ss_pred CCcCHHHHhh-cCCCEEEEEEEEEEeEee---cCCCCCe--EEEEEEeeCCC-cEEEEECHHHHHHHHHHhc------cC
Confidence 3456666643 235578999999998754 3566753 45789999999 7999999988776544332 34
Q ss_pred cEEEEEEEEEe
Q 008606 314 PVLSVKSGKVN 324 (560)
Q Consensus 314 ~VV~l~~~rV~ 324 (560)
.+|.+++ +|.
T Consensus 998 ~~~~v~G-~v~ 1007 (1107)
T PRK06920 998 AIVLVDG-TIE 1007 (1107)
T ss_pred CEEEEEE-EEE
Confidence 5665654 554
No 146
>COG0017 AsnS Aspartyl/asparaginyl-tRNA synthetases [Translation, ribosomal structure and biogenesis]
Probab=56.96 E-value=1e+02 Score=33.85 Aligned_cols=100 Identities=17% Similarity=0.238 Sum_probs=65.7
Q ss_pred cceeccccCCCCC--ceEEEEEEEEecccceeccCCCCCcEEEEEEEeCCCCeEEEEEcch-h-HHHH-HhhcccCcEEE
Q 008606 114 RIIPIAALNPYQG--RWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNA-V-VDRF-YEIIEVGRVYL 188 (560)
Q Consensus 114 ~~~pI~~L~p~~~--~w~Ik~RV~~k~~ir~~~n~~g~gkvf~~~L~D~~g~~I~at~~~~-~-~~kf-~~~l~eG~vY~ 188 (560)
..+.|+++.+... .-+|+|-|-.+ |..|++.=+.|.| .++.|||++... . -+.| -..|..+.++.
T Consensus 3 ~~~~i~di~~~~~~~~V~v~GWV~~~---------R~~g~i~Fi~lrD-gsg~iQ~v~~~~~~~~~~~~~~~L~~es~v~ 72 (435)
T COG0017 3 KRTYIKDIKPHVGGQEVTVRGWVHNK---------RDLGKIIFLVLRD-GSGFIQAVVPKNKVYEELFKAKKLTLESSVV 72 (435)
T ss_pred ceeeHHhhhccCCCcEEEEEEEeeee---------cccCCeEEEEEEc-CCcEEEEEEECCCCcHHHhhhhcCCCccEEE
Confidence 3467888887764 77888888654 2345644456788 556699999852 2 2223 35688899999
Q ss_pred EeeeEEecCCCccccCCCeeEEEEcccceEEeccCCCCCCCcc
Q 008606 189 ISKGSLKPAQKNFNHLKNEWEIFLEATSTVDLCTEEDDSIPKQ 231 (560)
Q Consensus 189 Is~~~V~~a~~~y~~~~~~yeI~f~~~T~I~~~~d~~~~iP~~ 231 (560)
+.+-.++... .+..|||....-..+..+ +. .+|..
T Consensus 73 V~G~v~~~~~-----a~~g~El~v~~i~Vl~~a-~~--~~Pi~ 107 (435)
T COG0017 73 VTGIVKASPK-----APQGFELQVEKIEVLGEA-DP--PYPID 107 (435)
T ss_pred EEEEEEcCCC-----CCCCEEEEEEEEEEeecc-CC--CCCcC
Confidence 8876543222 578999999886666666 32 45543
No 147
>PRK06826 dnaE DNA polymerase III DnaE; Reviewed
Probab=56.07 E-value=34 Score=42.17 Aligned_cols=59 Identities=19% Similarity=0.339 Sum_probs=43.4
Q ss_pred ceEEEEEEEEecccceeccCCCCCcEEE-EEEEeCCCCeEEEEEcchhHHHHHhhcccCcEEEEee
Q 008606 127 RWAIKARVTAKGDLRRYNNARGDGKVFS-FDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISK 191 (560)
Q Consensus 127 ~w~Ik~RV~~k~~ir~~~n~~g~gkvf~-~~L~D~~g~~I~at~~~~~~~kf~~~l~eG~vY~Is~ 191 (560)
.-+|.|-|+.. |....++| +.+- +.|-| ..|.|.+++|.+..+++...|++|.++.|.+
T Consensus 993 ~v~v~g~i~~~---~~~~tk~G--~~maf~~leD-~~g~~e~~vfp~~~~~~~~~l~~~~~~~v~g 1052 (1151)
T PRK06826 993 KVIIGGIITEV---KRKTTRNN--EMMAFLTLED-LYGTVEVIVFPKVYEKYRSLLNEDNIVLIKG 1052 (1151)
T ss_pred EEEEEEEEEEe---EeeccCCC--CeEEEEEEEE-CCCcEEEEECHHHHHHHHHHhccCCEEEEEE
Confidence 44566667654 33333444 4454 45666 7789999999999999999999999999855
No 148
>PRK10220 hypothetical protein; Provisional
Probab=55.96 E-value=8.7 Score=33.58 Aligned_cols=28 Identities=32% Similarity=0.814 Sum_probs=24.6
Q ss_pred EeCCCCCcCccccCceeeecCC-eeecCcCCCccC
Q 008606 417 YTACPLMIGDRQCNKKVTQSGN-RWQCDRCNQEID 450 (560)
Q Consensus 417 Y~aC~~~~~~~~C~KKv~~~~~-~~~C~kC~~~~~ 450 (560)
+++|| +|+..-+.+.+ .|.|+.|..++.
T Consensus 3 lP~CP------~C~seytY~d~~~~vCpeC~hEW~ 31 (111)
T PRK10220 3 LPHCP------KCNSEYTYEDNGMYICPECAHEWN 31 (111)
T ss_pred CCcCC------CCCCcceEcCCCeEECCcccCcCC
Confidence 58999 99998887766 999999999874
No 149
>PRK07459 single-stranded DNA-binding protein; Provisional
Probab=55.85 E-value=1e+02 Score=27.41 Aligned_cols=69 Identities=14% Similarity=0.150 Sum_probs=40.2
Q ss_pred eeEEEEEEEEecCceeEeeccCceeeEEEEEEec------CCCcEEEEEEeCcchhhhhhhHHhhhccCCccEEEEE-EE
Q 008606 249 IVDVIGIVISVNPSVPILRKNGMETQRRILNLKD------TSGRSVELTLWGDFCNKEGQKLQEMVDVGFFPVLSVK-SG 321 (560)
Q Consensus 249 ~VDVIGvV~~V~~~~~i~~k~G~~~~kr~i~L~D------~Sg~~I~vtLWg~~a~~~~~~l~~~~~~~~~~VV~l~-~~ 321 (560)
.|-++|.+..--.++ .+.+|... ..|.|.- ....-+.|++||..|+...++| ..|.-|.+. ..
T Consensus 5 ~v~LiGrL~~DPelr--~t~~G~~v--~~fslAv~~~~~~~~t~w~~v~~wg~~Ae~~~~~l------~KG~~V~V~G~l 74 (121)
T PRK07459 5 SVTLVGRAGRDPEVR--YFESGSVV--CNLTLAVNRRSRDDEPDWFNLEIWGKTAQVAADYV------KKGSLIGITGSL 74 (121)
T ss_pred EEEEEEEccCCCEEE--EcCCCCEE--EEEEEEecccccCCCceEEEEEEehHHHHHHHHHc------CCCCEEEEEEEE
Confidence 467888888732232 23456543 3344432 1223599999999988765443 345656554 44
Q ss_pred EEecCC
Q 008606 322 KVNDFS 327 (560)
Q Consensus 322 rV~~f~ 327 (560)
+...|.
T Consensus 75 ~~~~~~ 80 (121)
T PRK07459 75 KFDRWT 80 (121)
T ss_pred EecceE
Confidence 666673
No 150
>PRK09010 single-stranded DNA-binding protein; Provisional
Probab=54.39 E-value=1.1e+02 Score=29.34 Aligned_cols=73 Identities=15% Similarity=0.157 Sum_probs=40.8
Q ss_pred eeEEEEEEEEecCceeEeeccCceeeEEEEEEe----cC-CC------cEEEEEEeCcchhhhhhhHHhhhccCCccEEE
Q 008606 249 IVDVIGIVISVNPSVPILRKNGMETQRRILNLK----DT-SG------RSVELTLWGDFCNKEGQKLQEMVDVGFFPVLS 317 (560)
Q Consensus 249 ~VDVIGvV~~V~~~~~i~~k~G~~~~kr~i~L~----D~-Sg------~~I~vtLWg~~a~~~~~~l~~~~~~~~~~VV~ 317 (560)
.|-++|.|..--.++. +.+|..+.+..|-+. |. +| .-+.|++||..|+...++| ..+.-|.
T Consensus 8 ~V~LiGrLg~DPelR~--t~nG~~v~~fsVAvn~~~kd~~~Ge~~e~t~w~~V~~fgk~Ae~~~~~L------~KGs~V~ 79 (177)
T PRK09010 8 KVILVGNLGQDPEVRY--MPNGGAVANITLATSESWRDKQTGEMKEQTEWHRVVLFGKLAEVAGEYL------RKGSQVY 79 (177)
T ss_pred EEEEEEEeCCCceEEE--cCCCCEEEEEEEEEcCccccCcccccccceEEEEEEEehhHHHHHHHhc------CCCCEEE
Confidence 5677788777322322 235654433333332 21 12 2589999999988754443 3456665
Q ss_pred EE-EEEEecCCCc
Q 008606 318 VK-SGKVNDFSGK 329 (560)
Q Consensus 318 l~-~~rV~~f~G~ 329 (560)
|. ..+.+.|.++
T Consensus 80 VeGrL~~~~yedk 92 (177)
T PRK09010 80 IEGQLRTRKWTDQ 92 (177)
T ss_pred EEEEEEeccccCC
Confidence 55 4566678643
No 151
>PF07191 zinc-ribbons_6: zinc-ribbons; InterPro: IPR010807 This family consists of several short, hypothetical bacterial proteins of around 70 residues in length. Members of this family 8 highly conserved cysteine residues. The function of the family is unknown.; PDB: 2JRP_A 2JNE_A.
Probab=53.91 E-value=8 Score=31.19 Aligned_cols=24 Identities=25% Similarity=1.085 Sum_probs=17.5
Q ss_pred CCCCCcCccccCceeeecCCeeecCcCCCc
Q 008606 419 ACPLMIGDRQCNKKVTQSGNRWQCDRCNQE 448 (560)
Q Consensus 419 aC~~~~~~~~C~KKv~~~~~~~~C~kC~~~ 448 (560)
.|| .|..-+...++.|+|+.|++.
T Consensus 3 ~CP------~C~~~L~~~~~~~~C~~C~~~ 26 (70)
T PF07191_consen 3 TCP------KCQQELEWQGGHYHCEACQKD 26 (70)
T ss_dssp B-S------SS-SBEEEETTEEEETTT--E
T ss_pred cCC------CCCCccEEeCCEEECcccccc
Confidence 589 899999988889999999874
No 152
>PRK06920 dnaE DNA polymerase III DnaE; Reviewed
Probab=53.74 E-value=36 Score=41.74 Aligned_cols=73 Identities=15% Similarity=0.262 Sum_probs=51.3
Q ss_pred ceeccccCCC-CCceEEEEEEEEecccceeccCCCCCcEEEE-EEEeCCCCeEEEEEcchhHHHHHhhcccCcEEEEeee
Q 008606 115 IIPIAALNPY-QGRWAIKARVTAKGDLRRYNNARGDGKVFSF-DLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISKG 192 (560)
Q Consensus 115 ~~pI~~L~p~-~~~w~Ik~RV~~k~~ir~~~n~~g~gkvf~~-~L~D~~g~~I~at~~~~~~~kf~~~l~eG~vY~Is~~ 192 (560)
..++++|... ....+|.|-|+.. |....++| +-+-| .|-| ..|.|.+++|.+..+++.+.|++|.++.|.+
T Consensus 932 ~~~~~~l~~~~~~~v~v~g~i~~~---~~~~tk~g--~~maf~~leD-~tg~~e~~vFp~~y~~~~~~l~~~~~~~v~G- 1004 (1107)
T PRK06920 932 IPSLAQAMRHKKKVQRAIVYITSV---KVIRTKKG--QKMAFITFCD-QNDEMEAVVFPETYIHFSDKLQEGAIVLVDG- 1004 (1107)
T ss_pred CcCHHHHhhcCCCEEEEEEEEEEe---EeecCCCC--CeEEEEEEee-CCCcEEEEECHHHHHHHHHHhccCCEEEEEE-
Confidence 3466776532 2346777777764 33333444 34555 4566 8889999999999999999999999999954
Q ss_pred EE
Q 008606 193 SL 194 (560)
Q Consensus 193 ~V 194 (560)
+|
T Consensus 1005 ~v 1006 (1107)
T PRK06920 1005 TI 1006 (1107)
T ss_pred EE
Confidence 44
No 153
>PRK08182 single-stranded DNA-binding protein; Provisional
Probab=53.66 E-value=92 Score=28.87 Aligned_cols=72 Identities=14% Similarity=0.024 Sum_probs=39.9
Q ss_pred eeEEEEEEEEecCceeEeeccCcee--eEEEEEEe------cCCC-------cEEEEEEeCcchhhhhhhHHhhhccCCc
Q 008606 249 IVDVIGIVISVNPSVPILRKNGMET--QRRILNLK------DTSG-------RSVELTLWGDFCNKEGQKLQEMVDVGFF 313 (560)
Q Consensus 249 ~VDVIGvV~~V~~~~~i~~k~G~~~--~kr~i~L~------D~Sg-------~~I~vtLWg~~a~~~~~~l~~~~~~~~~ 313 (560)
.|-++|.+..--.++. +.+|... ....+.|. +.+| .-+.|++||..|+...++| ..|
T Consensus 4 ~V~LiGrLg~DPElr~--t~~G~~~~~~va~fslA~~r~~~~~~Ge~~~~~t~w~~V~~wg~~Ae~v~~~l------~KG 75 (148)
T PRK08182 4 HFVGEGNIGSAPEYRE--FPNGNDEPRRLLRLNVYFDNPVPTKDGEYEDRGGFWAPVELWHRDAEHWARLY------QKG 75 (148)
T ss_pred EEEEEEECCCCCeEEE--CCCCCeeeeeEEEEEEEecCceECCCCCEEecCcEEEEEEEEhHHHHHHHHhc------CCC
Confidence 4566777765433332 2345431 13445553 2223 2589999999988764443 345
Q ss_pred cEEEEE-EEEEecCCC
Q 008606 314 PVLSVK-SGKVNDFSG 328 (560)
Q Consensus 314 ~VV~l~-~~rV~~f~G 328 (560)
.-|++. ..+...|..
T Consensus 76 ~~V~V~GrL~~~~w~d 91 (148)
T PRK08182 76 MRVLVEGRMERDEWTD 91 (148)
T ss_pred CEEEEEEEEEecccCC
Confidence 555554 456666743
No 154
>PRK05733 single-stranded DNA-binding protein; Provisional
Probab=53.33 E-value=72 Score=30.42 Aligned_cols=72 Identities=17% Similarity=0.157 Sum_probs=41.2
Q ss_pred ceeEEEEEEEEecCceeEeeccCceeeEEEEEEe----cC-CC------cEEEEEEeCcchhhhhhhHHhhhccCCccEE
Q 008606 248 SIVDVIGIVISVNPSVPILRKNGMETQRRILNLK----DT-SG------RSVELTLWGDFCNKEGQKLQEMVDVGFFPVL 316 (560)
Q Consensus 248 ~~VDVIGvV~~V~~~~~i~~k~G~~~~kr~i~L~----D~-Sg------~~I~vtLWg~~a~~~~~~l~~~~~~~~~~VV 316 (560)
..|-++|.|..--.++. +.+|..+.+-.|-.. |. .| .-+.|++||..|+.+..+| ..+.-|
T Consensus 6 NkV~LiGrlg~DPElr~--t~nG~~va~fsVAv~~~~k~~~~Ge~~e~T~w~~Vv~fgk~Ae~v~~~l------~KGs~V 77 (172)
T PRK05733 6 NKVILVGTCGQDPEVRY--LPNGNAVTNLSLATSEQWTDKQSGQKVERTEWHRVSLFGKVAEIAGEYL------RKGSQV 77 (172)
T ss_pred eEEEEEEEecCCCEEEE--CCCCCEEEEEEEEEcCccccCCCCcccccceEEEEEEehHHHHHHHHHh------CCCCEE
Confidence 35678888887322322 345665443333332 21 22 1399999999988754443 356777
Q ss_pred EEEE-EEEecCC
Q 008606 317 SVKS-GKVNDFS 327 (560)
Q Consensus 317 ~l~~-~rV~~f~ 327 (560)
+|.+ .+...|.
T Consensus 78 ~VeGrLr~~~y~ 89 (172)
T PRK05733 78 YIEGKLQTREWE 89 (172)
T ss_pred EEEEEEEeCcEe
Confidence 6653 4555563
No 155
>PRK12820 bifunctional aspartyl-tRNA synthetase/aspartyl/glutamyl-tRNA amidotransferase subunit C; Provisional
Probab=53.23 E-value=1.6e+02 Score=34.53 Aligned_cols=97 Identities=15% Similarity=0.108 Sum_probs=61.8
Q ss_pred ceeccccCCCC--CceEEEEEEEEecccceeccCCCCCcEEEEEEEeCCCCeEEEEEcchh----HHHHHhhcccCcEEE
Q 008606 115 IIPIAALNPYQ--GRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAV----VDRFYEIIEVGRVYL 188 (560)
Q Consensus 115 ~~pI~~L~p~~--~~w~Ik~RV~~k~~ir~~~n~~g~gkvf~~~L~D~~g~~I~at~~~~~----~~kf~~~l~eG~vY~ 188 (560)
-+...+|++.. ..-+|+|||-++ |. -|++.=++|.| .+|.|++++..+. .-++...|..|+++.
T Consensus 6 ~~~cg~l~~~~~g~~V~l~GWV~~~---R~------~G~l~FidLRD-~~G~iQvV~~~~~~~~~~~~~~~~L~~EsvV~ 75 (706)
T PRK12820 6 RSFCGHLSLDDTGREVCLAGWVDAF---RD------HGELLFIHLRD-RNGFIQAVFSPEAAPADVYELAASLRAEFCVA 75 (706)
T ss_pred ccccccCChhhCCCEEEEEEEEEEE---Ec------CCCcEEEEEEe-CCccEEEEEeCCcCCHHHHHHHhcCCCCCEEE
Confidence 34456666653 458899999764 43 24566667999 5668999986432 223346799999999
Q ss_pred EeeeEEecCCCcccc--CCCeeEEEEcccceEEec
Q 008606 189 ISKGSLKPAQKNFNH--LKNEWEIFLEATSTVDLC 221 (560)
Q Consensus 189 Is~~~V~~a~~~y~~--~~~~yeI~f~~~T~I~~~ 221 (560)
+.+-..+...+.-++ ....+||....-..+..+
T Consensus 76 V~G~v~~r~~~~~n~~~~tg~iEl~~~~i~iL~~a 110 (706)
T PRK12820 76 LQGEVQKRLEETENPHIETGDIEVFVRELSILAAS 110 (706)
T ss_pred EEeEEeccCccccCCCCCCCcEEEEeeEEEEEecC
Confidence 999655432222221 226799988776666555
No 156
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=52.20 E-value=7.2 Score=25.01 Aligned_cols=23 Identities=22% Similarity=0.729 Sum_probs=17.2
Q ss_pred eCCCCCcCccccCceeeecCCeeecCcCCCc
Q 008606 418 TACPLMIGDRQCNKKVTQSGNRWQCDRCNQE 448 (560)
Q Consensus 418 ~aC~~~~~~~~C~KKv~~~~~~~~C~kC~~~ 448 (560)
.-|| .|++.+..+ .-+|++|+..
T Consensus 3 ~~Cp------~Cg~~~~~~--~~fC~~CG~~ 25 (26)
T PF13248_consen 3 MFCP------NCGAEIDPD--AKFCPNCGAK 25 (26)
T ss_pred CCCc------ccCCcCCcc--cccChhhCCC
Confidence 3589 899965444 5799999864
No 157
>PF01780 Ribosomal_L37ae: Ribosomal L37ae protein family; InterPro: IPR002674 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 [, ]. This ribosomal protein is found in archaebacteria and eukaryotes []. Ribosomal protein L37 has a single zinc finger-like motif of the C2-C2 type [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A1E_Y 4A17_Y 4A1C_Y 4A1A_Y 3O58_g 3IZS_m 3O5H_g 1S1I_9 3IZR_m 1YSH_D ....
Probab=51.32 E-value=5.8 Score=33.58 Aligned_cols=26 Identities=27% Similarity=0.963 Sum_probs=19.2
Q ss_pred CCCCCcCccccCceeeec--CCeeecCcCCCccC
Q 008606 419 ACPLMIGDRQCNKKVTQS--GNRWQCDRCNQEID 450 (560)
Q Consensus 419 aC~~~~~~~~C~KKv~~~--~~~~~C~kC~~~~~ 450 (560)
-|| .|+|....- .+.|.|.+|++.+.
T Consensus 37 ~Cp------~Cgk~~vkR~a~GIW~C~~C~~~~A 64 (90)
T PF01780_consen 37 TCP------FCGKTSVKRVATGIWKCKKCGKKFA 64 (90)
T ss_dssp EES------SSSSSEEEEEETTEEEETTTTEEEE
T ss_pred cCC------CCCCceeEEeeeEEeecCCCCCEEe
Confidence 489 899865432 34999999998763
No 158
>PRK05672 dnaE2 error-prone DNA polymerase; Validated
Probab=50.71 E-value=41 Score=41.08 Aligned_cols=75 Identities=21% Similarity=0.340 Sum_probs=51.7
Q ss_pred ccCccchhcccCCceeEEEEEEEEecCceeEeeccCceeeEEEEEEecCCCcEEEEEEeCcchhhhhhhHHhhhccCCcc
Q 008606 235 FRHISEIESAENNSIVDVIGIVISVNPSVPILRKNGMETQRRILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVDVGFFP 314 (560)
Q Consensus 235 f~~i~dI~~~~~~~~VDVIGvV~~V~~~~~i~~k~G~~~~kr~i~L~D~Sg~~I~vtLWg~~a~~~~~~l~~~~~~~~~~ 314 (560)
..++++|.+...+..|=|.|+|+.+... .+|.| .--++|.|.+| .+++++|.+...+....| ..+.
T Consensus 941 ~~~~~~l~~~~~~~~v~v~g~i~~~~~~---~TkkG----maf~~leD~~g-~~e~~ifp~~~~~~~~~l------~~~~ 1006 (1046)
T PRK05672 941 VVSAAELLDVEDGRRVRVAGVVTHRQRP---GTASG----VTFLTLEDETG-MVNVVVWPGLWERQRREA------LGAR 1006 (1046)
T ss_pred CcCHHHHhhccCCCEEEEEEEEEEEEEe---cCCCc----eEEEEEecCCC-CEEEEECHHHHHHHHHHh------ccCC
Confidence 3455666554455678899999987654 35666 46789999999 799999999877654333 2456
Q ss_pred EEEEEEEEEe
Q 008606 315 VLSVKSGKVN 324 (560)
Q Consensus 315 VV~l~~~rV~ 324 (560)
++.+++ +|.
T Consensus 1007 ~~~v~g-~v~ 1015 (1046)
T PRK05672 1007 LLLVRG-RVQ 1015 (1046)
T ss_pred EEEEEE-EEE
Confidence 666654 444
No 159
>PRK08486 single-stranded DNA-binding protein; Provisional
Probab=50.48 E-value=1.2e+02 Score=29.31 Aligned_cols=35 Identities=11% Similarity=0.149 Sum_probs=23.4
Q ss_pred EEEEEEeCcchhhhhhhHHhhhccCCccEEEEE-EEEEecCC
Q 008606 287 SVELTLWGDFCNKEGQKLQEMVDVGFFPVLSVK-SGKVNDFS 327 (560)
Q Consensus 287 ~I~vtLWg~~a~~~~~~l~~~~~~~~~~VV~l~-~~rV~~f~ 327 (560)
-+.|++||..|+...++| ..+.-|+|. ..+...|.
T Consensus 50 fi~v~~fg~~AE~~~~~l------~KG~~V~VeGrL~~~~y~ 85 (182)
T PRK08486 50 FIDIRLFGRTAEIANQYL------SKGSKVLIEGRLTFESWM 85 (182)
T ss_pred EEEEEEEhHHHHHHHHHc------CCCCEEEEEEEEEeCcEE
Confidence 589999999998765443 346666555 34555673
No 160
>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=50.21 E-value=1.4e+02 Score=32.99 Aligned_cols=82 Identities=13% Similarity=0.186 Sum_probs=54.4
Q ss_pred CceEEEEEEEEecccceeccCCCCCcEEEEEEEeCCC-CeEEEEEcch---hHHHHHhhcccCcEEEEeeeEEecCCCcc
Q 008606 126 GRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDG-GEIRVTCFNA---VVDRFYEIIEVGRVYLISKGSLKPAQKNF 201 (560)
Q Consensus 126 ~~w~Ik~RV~~k~~ir~~~n~~g~gkvf~~~L~D~~g-~~I~at~~~~---~~~kf~~~l~eG~vY~Is~~~V~~a~~~y 201 (560)
..-+|+|||.++ |. .|++.=++|.|... +.|++++-.. ...++...|..|+++.+.+.-.+...
T Consensus 17 ~~v~v~Gwv~~~---R~------~~~~~F~~lrD~~~~g~iQ~v~~~~~~~~~~~~~~~l~~gs~V~v~G~v~~~~~--- 84 (453)
T TIGR00457 17 DEVTVSGWVRTK---RS------SKKIIFLELNDGSSLGPIQAVINGEDNPYLFQLLKSLTTGSSVSVTGKVVESPG--- 84 (453)
T ss_pred CEEEEEEEeEEE---Ec------CCCeEEEEEECCCCCccEEEEEeCCcChHHHHHHHcCCCCcEEEEEEEEEcCCC---
Confidence 468899999764 42 23555566888431 7999999765 22234456999999999886554221
Q ss_pred ccCCCeeEEEEcccceEEec
Q 008606 202 NHLKNEWEIFLEATSTVDLC 221 (560)
Q Consensus 202 ~~~~~~yeI~f~~~T~I~~~ 221 (560)
....+||....-..+..+
T Consensus 85 --~~~~~El~~~~i~vl~~~ 102 (453)
T TIGR00457 85 --KGQPVELQVKKIEVVGEA 102 (453)
T ss_pred --CCCCEEEEEeEEEEEecC
Confidence 236789988766666655
No 161
>PRK07275 single-stranded DNA-binding protein; Provisional
Probab=49.44 E-value=1.1e+02 Score=28.89 Aligned_cols=35 Identities=6% Similarity=0.138 Sum_probs=23.6
Q ss_pred EEEEEEeCcchhhhhhhHHhhhccCCccEEEEEE-EEEecCC
Q 008606 287 SVELTLWGDFCNKEGQKLQEMVDVGFFPVLSVKS-GKVNDFS 327 (560)
Q Consensus 287 ~I~vtLWg~~a~~~~~~l~~~~~~~~~~VV~l~~-~rV~~f~ 327 (560)
-|.|++||+.|+.+.++| ..+.-|+|.+ .+...|.
T Consensus 48 fi~vv~wgk~Ae~~~~~l------~KG~~V~VeGrl~~r~y~ 83 (162)
T PRK07275 48 FINCVIWRQQAENLANWA------KKGALIGVTGRIQTRNYE 83 (162)
T ss_pred EEEEEEEcHHHHHHHHHc------CCCCEEEEEEEEEeceEE
Confidence 599999999998864443 3566666654 3555563
No 162
>KOG1885 consensus Lysyl-tRNA synthetase (class II) [Translation, ribosomal structure and biogenesis]
Probab=49.19 E-value=74 Score=34.95 Aligned_cols=57 Identities=21% Similarity=0.343 Sum_probs=43.4
Q ss_pred ceEEEEEEEEecccceeccCCCCCcEEEEEEEeCCCCeEEEEEcch------hHHHHHhhcccCcEEEEeee
Q 008606 127 RWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNA------VVDRFYEIIEVGRVYLISKG 192 (560)
Q Consensus 127 ~w~Ik~RV~~k~~ir~~~n~~g~gkvf~~~L~D~~g~~I~at~~~~------~~~kf~~~l~eG~vY~Is~~ 192 (560)
..+|.+||.++ |.. | .|+.=++|.+ +|.++++.+-.. ...+..+.|+-|+++-+++.
T Consensus 106 ~~svaGRI~s~---R~s----G-sKL~Fydl~~-~g~klQvm~~~~~~~~~~~F~~~~~~lkrGDiig~~G~ 168 (560)
T KOG1885|consen 106 IVSVAGRIHSK---RES----G-SKLVFYDLHG-DGVKLQVMANAKKITSEEDFEQLHKFLKRGDIIGVSGY 168 (560)
T ss_pred eeeeeeeEeee---ecc----C-CceEEEEEec-CCeEEEEEEehhhcCCHHHHHHHHhhhhccCEEeeecC
Confidence 46899999875 332 2 3777788988 699999998643 35667888999999988774
No 163
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=49.07 E-value=7.4 Score=37.30 Aligned_cols=28 Identities=21% Similarity=0.750 Sum_probs=22.4
Q ss_pred EEeCCCCCcCccccCceeeecCC---eeecCcCCCcc
Q 008606 416 CYTACPLMIGDRQCNKKVTQSGN---RWQCDRCNQEI 449 (560)
Q Consensus 416 ~Y~aC~~~~~~~~C~KKv~~~~~---~~~C~kC~~~~ 449 (560)
-|.-|| .|+++.+.... .+.|+.||...
T Consensus 116 ~~Y~Cp------~C~~rytf~eA~~~~F~Cp~Cg~~L 146 (178)
T PRK06266 116 MFFFCP------NCHIRFTFDEAMEYGFRCPQCGEML 146 (178)
T ss_pred CEEECC------CCCcEEeHHHHhhcCCcCCCCCCCC
Confidence 355689 89999987653 79999999865
No 164
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=48.95 E-value=6.7 Score=36.81 Aligned_cols=28 Identities=21% Similarity=0.608 Sum_probs=22.1
Q ss_pred EEeCCCCCcCccccCceeeecCC---eeecCcCCCcc
Q 008606 416 CYTACPLMIGDRQCNKKVTQSGN---RWQCDRCNQEI 449 (560)
Q Consensus 416 ~Y~aC~~~~~~~~C~KKv~~~~~---~~~C~kC~~~~ 449 (560)
-|.-|| .|+++.+.... .+.|+.||...
T Consensus 108 ~~Y~Cp------~c~~r~tf~eA~~~~F~Cp~Cg~~L 138 (158)
T TIGR00373 108 MFFICP------NMCVRFTFNEAMELNFTCPRCGAML 138 (158)
T ss_pred CeEECC------CCCcEeeHHHHHHcCCcCCCCCCEe
Confidence 344689 89999987654 79999999764
No 165
>PRK06863 single-stranded DNA-binding protein; Provisional
Probab=48.16 E-value=1.5e+02 Score=28.26 Aligned_cols=73 Identities=14% Similarity=0.096 Sum_probs=41.3
Q ss_pred ceeEEEEEEEEecCceeEeeccCceeeEEEEEEe----cC-CC------cEEEEEEeCcchhhhhhhHHhhhccCCccEE
Q 008606 248 SIVDVIGIVISVNPSVPILRKNGMETQRRILNLK----DT-SG------RSVELTLWGDFCNKEGQKLQEMVDVGFFPVL 316 (560)
Q Consensus 248 ~~VDVIGvV~~V~~~~~i~~k~G~~~~kr~i~L~----D~-Sg------~~I~vtLWg~~a~~~~~~l~~~~~~~~~~VV 316 (560)
..|-++|.|..--.++ .+.+|+.+.+-.|-.. |. .| .-+.|++||..|+.+.++| ..|.-|
T Consensus 5 N~V~LiGrLg~DPElR--~t~nG~~va~fsVAvn~~~~d~~~Ge~~e~t~w~~Vv~fgk~AE~v~~~L------kKGs~V 76 (168)
T PRK06863 5 NKVIIVGHLGNDPEIR--TMPNGEAVANISVATSESWTDKNTGERREVTEWHRIVFYRRQAEVAGEYL------RKGSQV 76 (168)
T ss_pred cEEEEEEEcCCCCEEE--EcCCCCEEEEEEEEecCcccccCCCcccccceEEEEEEEhHHHHHHHHHC------CCCCEE
Confidence 3577788888732222 2346665443333332 21 12 2589999999988764443 345655
Q ss_pred EEE-EEEEecCCC
Q 008606 317 SVK-SGKVNDFSG 328 (560)
Q Consensus 317 ~l~-~~rV~~f~G 328 (560)
.|. ..+...|.+
T Consensus 77 ~VeGrL~~r~w~D 89 (168)
T PRK06863 77 YVEGRLKTRKWQD 89 (168)
T ss_pred EEEEEEEeCCccC
Confidence 554 446666753
No 166
>cd03574 NTR_complement_C345C NTR/C345C domain; The NTR domains that are found in the C-termini of complement C3, C4 and C5, are also called C345C domains. In C5, the domain interacts with various partners during the formation of the membrane attack complex, a fundamental process in the mammalian defense against infection. It's role in component C3 and C4 is not well understood.
Probab=48.04 E-value=1.5e+02 Score=27.25 Aligned_cols=88 Identities=14% Similarity=0.188 Sum_probs=52.3
Q ss_pred CceEEEEEEEEecccceeccCCCCCcEEEEEEE---------eCCCCeEEEEEcch-hHHHHHhhcccCcEEEEeeeEEe
Q 008606 126 GRWAIKARVTAKGDLRRYNNARGDGKVFSFDLL---------DSDGGEIRVTCFNA-VVDRFYEIIEVGRVYLISKGSLK 195 (560)
Q Consensus 126 ~~w~Ik~RV~~k~~ir~~~n~~g~gkvf~~~L~---------D~~g~~I~at~~~~-~~~kf~~~l~eG~vY~Is~~~V~ 195 (560)
-...++|||........|. .+.+.+. ..+|+.++. +|.. .. +....|++|+.|.|.+-...
T Consensus 23 ~DYa~kv~V~~~~~~~~~~-------~~~~~v~~V~K~g~~~~~~~~~~~~-~~~~~~C-~c~~~l~~g~~YLImG~~~~ 93 (147)
T cd03574 23 VDYVYKVKVTSVEEEAGFR-------IYKARVTEVIKSGSDDVQNGNARRT-FIIRESC-DCPLRLKEGRHYLIMGSDGA 93 (147)
T ss_pred cceEEEEEEEEEEecCCeE-------EEEEEEEEEEecccccccCCCceEE-EEccCCc-cchhcCCCCCEEEEeccCcC
Confidence 4788999998765543332 2333221 113445554 3433 22 23356789999999987533
Q ss_pred cCCCccccCCCeeEEEEcccceEEeccCC
Q 008606 196 PAQKNFNHLKNEWEIFLEATSTVDLCTEE 224 (560)
Q Consensus 196 ~a~~~y~~~~~~yeI~f~~~T~I~~~~d~ 224 (560)
..+. ......|.+.+++.|.|+..+.+
T Consensus 94 ~~~~--~~~~~~~~yvl~~~t~Ve~Wp~~ 120 (147)
T cd03574 94 FYDD--RNGEDRYQYVLDSNTWVEEWPTD 120 (147)
T ss_pred cccc--cCCCcceEEEeCCCcEEEECCCh
Confidence 2111 11223589999999999998753
No 167
>COG1200 RecG RecG-like helicase [DNA replication, recombination, and repair / Transcription]
Probab=47.82 E-value=67 Score=36.95 Aligned_cols=76 Identities=20% Similarity=0.286 Sum_probs=56.2
Q ss_pred CCcceeccccCCCCCceEEEEEEEEecccceeccCCCCCcEEEEEEEeCCCCeEEEEEcchhHHHHHhhcccCcEEEEee
Q 008606 112 PARIIPIAALNPYQGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISK 191 (560)
Q Consensus 112 ~~~~~pI~~L~p~~~~w~Ik~RV~~k~~ir~~~n~~g~gkvf~~~L~D~~g~~I~at~~~~~~~kf~~~l~eG~vY~Is~ 191 (560)
.....+|.++.++ ...+|.++|....... + +..+.+.+.+.| .++.|.++||+..+ -....+++|+.+.+++
T Consensus 48 ~~~~~~i~~~~~g-~~vti~g~V~~~~~~~-~----~~~~~l~v~~~d-~~~~l~l~fFn~~~-~l~~~~~~G~~v~v~G 119 (677)
T COG1200 48 RTLLPGIAEARPG-EIVTIEGTVLSHEKFP-F----GKRKLLKVTLSD-GTGVLTLVFFNFPA-YLKKKLKVGERVIVYG 119 (677)
T ss_pred ccccCChhhcCCC-ceEEEEEEEEeeeccC-C----CCCceEEEEEec-CcEEEEEEEECccH-HHHhhCCCCCEEEEEE
Confidence 3455577777754 3478999998765432 1 234789999999 88999999999866 5677899999998865
Q ss_pred eEEec
Q 008606 192 GSLKP 196 (560)
Q Consensus 192 ~~V~~ 196 (560)
+|+.
T Consensus 120 -k~~~ 123 (677)
T COG1200 120 -KVKR 123 (677)
T ss_pred -EEee
Confidence 4443
No 168
>PRK08763 single-stranded DNA-binding protein; Provisional
Probab=47.60 E-value=1.1e+02 Score=28.83 Aligned_cols=71 Identities=20% Similarity=0.203 Sum_probs=38.9
Q ss_pred eeEEEEEEEEecCceeEeeccCceeeEEEEEE----ecCCCc------EEEEEEeCcchhhhhhhHHhhhccCCccEEEE
Q 008606 249 IVDVIGIVISVNPSVPILRKNGMETQRRILNL----KDTSGR------SVELTLWGDFCNKEGQKLQEMVDVGFFPVLSV 318 (560)
Q Consensus 249 ~VDVIGvV~~V~~~~~i~~k~G~~~~kr~i~L----~D~Sg~------~I~vtLWg~~a~~~~~~l~~~~~~~~~~VV~l 318 (560)
.|-++|.|..--.++. +.+|..+..-.|-. .|..|. -+.|++||..|+...++| ..+.-|.|
T Consensus 7 kv~LiGrLg~DPelr~--t~~G~~va~fsVA~~~~~k~~~G~~~e~t~w~~Vv~fgk~Ae~v~~~L------~KGs~V~V 78 (164)
T PRK08763 7 KVILVGNLGNDPDIKY--TQSGMTITRISLATTSVRKDREGNTQERTEWHRVKFFGKLGEIAGEYL------RKGSQCYI 78 (164)
T ss_pred EEEEEEEecCCCeEEE--cCCCCeEEEEEEEeccceecCCCCeeccceEEEEEEehHHHHHHHHhc------CCCCEEEE
Confidence 5667788777322322 23565433222222 232231 499999999987654443 35666665
Q ss_pred E-EEEEecCC
Q 008606 319 K-SGKVNDFS 327 (560)
Q Consensus 319 ~-~~rV~~f~ 327 (560)
. ..+...|.
T Consensus 79 eGrL~~~~y~ 88 (164)
T PRK08763 79 EGSIRYDKFT 88 (164)
T ss_pred EEEEEeceeE
Confidence 5 44555674
No 169
>PRK06958 single-stranded DNA-binding protein; Provisional
Probab=47.60 E-value=1.6e+02 Score=28.37 Aligned_cols=72 Identities=15% Similarity=0.143 Sum_probs=40.4
Q ss_pred ceeEEEEEEEEecCceeEeeccCceeeEEEEEE----ecC-CC------cEEEEEEeCcchhhhhhhHHhhhccCCccEE
Q 008606 248 SIVDVIGIVISVNPSVPILRKNGMETQRRILNL----KDT-SG------RSVELTLWGDFCNKEGQKLQEMVDVGFFPVL 316 (560)
Q Consensus 248 ~~VDVIGvV~~V~~~~~i~~k~G~~~~kr~i~L----~D~-Sg------~~I~vtLWg~~a~~~~~~l~~~~~~~~~~VV 316 (560)
..|-|||.|..--.+. .+.+|..+.+..|-+ .|. ++ .-+.|++|++.|+.+.++| ..+..|
T Consensus 5 N~V~LiGrLg~DPElr--~t~nG~~va~fsVAv~~~~kdk~sGe~~e~T~w~~V~~fGk~AE~v~~~L------kKGs~V 76 (182)
T PRK06958 5 NKVILVGNLGADPEVR--YLPSGDAVANIRLATTDRYKDKASGEFKEATEWHRVAFFGRLAEIVGEYL------KKGSSV 76 (182)
T ss_pred cEEEEEEEecCCCeEE--EcCCCCEEEEEEEEeccccccccCCcccccceEEEEEEehHHHHHHHHHh------CCCCEE
Confidence 3567888887732222 234565543333322 121 12 2689999999988754443 356666
Q ss_pred EEE-EEEEecCC
Q 008606 317 SVK-SGKVNDFS 327 (560)
Q Consensus 317 ~l~-~~rV~~f~ 327 (560)
.|. ..+...|.
T Consensus 77 ~VeGrL~~~~ye 88 (182)
T PRK06958 77 YIEGRIRTRKWQ 88 (182)
T ss_pred EEEEEEEeCceE
Confidence 655 44556675
No 170
>PRK03932 asnC asparaginyl-tRNA synthetase; Validated
Probab=47.37 E-value=1.7e+02 Score=32.18 Aligned_cols=81 Identities=11% Similarity=0.130 Sum_probs=52.0
Q ss_pred CceEEEEEEEEecccceeccCCCCCcEEEEEEEeCCCCeEEEEEcch---hHHHHHhhcccCcEEEEeeeEEecCCCccc
Q 008606 126 GRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNA---VVDRFYEIIEVGRVYLISKGSLKPAQKNFN 202 (560)
Q Consensus 126 ~~w~Ik~RV~~k~~ir~~~n~~g~gkvf~~~L~D~~g~~I~at~~~~---~~~kf~~~l~eG~vY~Is~~~V~~a~~~y~ 202 (560)
...+|+|||.++ |.. |++.=++|.| .++.|++.+-.+ ..-++-..|..|+++.+.+.-++ ...
T Consensus 17 ~~V~i~G~v~~~---R~~------g~~~Fi~lrD-~~g~iq~~~~~~~~~~~~~~~~~l~~~s~v~v~G~v~~-~~~--- 82 (450)
T PRK03932 17 QEVTVRGWVRTK---RDS------GKIAFLQLRD-GSCFKQLQVVKDNGEEYFEEIKKLTTGSSVIVTGTVVE-SPR--- 82 (450)
T ss_pred CEEEEEEEEEEE---EeC------CCeEEEEEEC-CCCcEEEEEEcCCChHHHHHHhcCCCCcEEEEEEEEEc-CCC---
Confidence 568999999874 432 4565567888 566888777533 22223355999999999875443 221
Q ss_pred cCCCeeEEEEcccceEEec
Q 008606 203 HLKNEWEIFLEATSTVDLC 221 (560)
Q Consensus 203 ~~~~~yeI~f~~~T~I~~~ 221 (560)
....+||...+-+.+..+
T Consensus 83 -~~~~~el~~~~i~vl~~~ 100 (450)
T PRK03932 83 -AGQGYELQATKIEVIGED 100 (450)
T ss_pred -CCCCEEEEEEEEEEccCC
Confidence 235788888765555543
No 171
>TIGR00686 phnA alkylphosphonate utilization operon protein PhnA. The protein family includes an uncharacterized member designated phnA in Escherichia coli, part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage. This protein is not related to the characterized phosphonoacetate hydrolase designated PhnA by Kulakova, et al. (2001, 1997).
Probab=46.26 E-value=14 Score=32.35 Aligned_cols=29 Identities=31% Similarity=0.707 Sum_probs=24.4
Q ss_pred EeCCCCCcCccccCceeeecCC-eeecCcCCCccCC
Q 008606 417 YTACPLMIGDRQCNKKVTQSGN-RWQCDRCNQEIDE 451 (560)
Q Consensus 417 Y~aC~~~~~~~~C~KKv~~~~~-~~~C~kC~~~~~~ 451 (560)
.++|| +|+.--+.+.+ .|.|+.|+..+..
T Consensus 2 lp~CP------~C~seytY~dg~~~iCpeC~~EW~~ 31 (109)
T TIGR00686 2 LPPCP------KCNSEYTYHDGTQLICPSCLYEWNE 31 (109)
T ss_pred CCcCC------cCCCcceEecCCeeECccccccccc
Confidence 48999 99998887766 9999999988743
No 172
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=45.83 E-value=14 Score=27.85 Aligned_cols=26 Identities=27% Similarity=0.919 Sum_probs=20.9
Q ss_pred EeCCCCCcCccccCc-eeeecCCeeecCcCCCc
Q 008606 417 YTACPLMIGDRQCNK-KVTQSGNRWQCDRCNQE 448 (560)
Q Consensus 417 Y~aC~~~~~~~~C~K-Kv~~~~~~~~C~kC~~~ 448 (560)
-.-|| .|+. -+....+.+.|.+|+-+
T Consensus 20 ~~fCP------~Cg~~~m~~~~~r~~C~~Cgyt 46 (50)
T PRK00432 20 NKFCP------RCGSGFMAEHLDRWHCGKCGYT 46 (50)
T ss_pred cCcCc------CCCcchheccCCcEECCCcCCE
Confidence 45799 8988 66677779999999854
No 173
>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=45.78 E-value=94 Score=28.96 Aligned_cols=27 Identities=26% Similarity=0.588 Sum_probs=22.1
Q ss_pred cEEEEEEEeCCCCeEEEEEcchhHHHHH
Q 008606 151 KVFSFDLLDSDGGEIRVTCFNAVVDRFY 178 (560)
Q Consensus 151 kvf~~~L~D~~g~~I~at~~~~~~~kf~ 178 (560)
-.+++.|.| ..|.+.+++|++.++++-
T Consensus 68 y~l~~~i~D-~Tg~~~~~~F~~~ae~l~ 94 (166)
T cd04476 68 YILSLNVAD-HTGEAWLTLFDEVAEQIF 94 (166)
T ss_pred EEEEEEEEe-CCCCEEEEEehHHHHHHh
Confidence 346788999 788999999999887764
No 174
>COG0587 DnaE DNA polymerase III, alpha subunit [DNA replication, recombination, and repair]
Probab=45.17 E-value=70 Score=39.32 Aligned_cols=71 Identities=20% Similarity=0.331 Sum_probs=50.8
Q ss_pred eeccccCCCCCceEEEEEEEEecccceeccCCCCCc-EEEEEEEeCCCCeEEEEEcchhHHHHHhhcccCcEEEEee
Q 008606 116 IPIAALNPYQGRWAIKARVTAKGDLRRYNNARGDGK-VFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISK 191 (560)
Q Consensus 116 ~pI~~L~p~~~~w~Ik~RV~~k~~ir~~~n~~g~gk-vf~~~L~D~~g~~I~at~~~~~~~kf~~~l~eG~vY~Is~ 191 (560)
.++.++.+....|.+-|-|+.. |.-..+ ..|. +--+.|-|+.| .+.+++|.....+++..+.+++.|.|.+
T Consensus 967 ~~~~~~~~~~~~~~~~~~i~~v---r~~~tk-~~G~~~~f~tl~D~~g-~~e~v~f~~~~~~~~~~l~~~~~~~v~g 1038 (1139)
T COG0587 967 IRLLDLVEDGRRVVLAGGIVAV---RQRPTK-AKGNKMAFLTLEDETG-ILEVVVFPSEYERYRRLLLEGRLLIVKG 1038 (1139)
T ss_pred cchhhhccccceeEEEEEEEEE---EEeecc-CCCCEEEEEEEecCCC-cEEEEEcHHHHHHHHHHhccCcEEEEEE
Confidence 4566666655567887777764 332222 1244 44456888766 9999999999999999999998888865
No 175
>PRK00448 polC DNA polymerase III PolC; Validated
Probab=45.12 E-value=59 Score=41.07 Aligned_cols=74 Identities=18% Similarity=0.298 Sum_probs=57.0
Q ss_pred cceeccccCCCCCceEEEEEEEEecccceeccCCCCCcEEEEEEEeCCCCeEEEEEcchh--HHHHHhhcccCcEEEEee
Q 008606 114 RIIPIAALNPYQGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAV--VDRFYEIIEVGRVYLISK 191 (560)
Q Consensus 114 ~~~pI~~L~p~~~~w~Ik~RV~~k~~ir~~~n~~g~gkvf~~~L~D~~g~~I~at~~~~~--~~kf~~~l~eG~vY~Is~ 191 (560)
.+++|+++.....+..|+|.|... +.|..++ | ..+++|.|.| ..+.|.+..|... -.+..+.|+.|+|+.+.+
T Consensus 225 ~~~~~~~i~~~~~~v~i~G~if~~-e~~~~k~--~-~~~~~~~~td-~~~s~~~k~f~~~~~~~~~~~~~~~g~~v~~~g 299 (1437)
T PRK00448 225 EITPMKEINEEERRVVVEGYVFKV-EIKELKS--G-RHILTFKITD-YTSSIIVKKFSRDKEDLKKFDEIKKGDWVKVRG 299 (1437)
T ss_pred CcccHHHhhccCCeEEEEEEEEEE-EEEeccC--C-CEEEEEEEEc-CCCCEEEEEEecCcchhHHHhcCCCCCEEEEEE
Confidence 678999999988999999999765 4455543 2 3688999999 7789999998732 234457799999998865
Q ss_pred e
Q 008606 192 G 192 (560)
Q Consensus 192 ~ 192 (560)
-
T Consensus 300 ~ 300 (1437)
T PRK00448 300 S 300 (1437)
T ss_pred E
Confidence 3
No 176
>PF15072 DUF4539: Domain of unknown function (DUF4539)
Probab=45.00 E-value=68 Score=26.97 Aligned_cols=56 Identities=27% Similarity=0.299 Sum_probs=38.3
Q ss_pred EEEEEEEecCceeEeeccCceeeEEEEEEecCCCcEEEEEEeCcchhhhhhhHHhhhccCCccEEEEEEEEEe
Q 008606 252 VIGIVISVNPSVPILRKNGMETQRRILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVDVGFFPVLSVKSGKVN 324 (560)
Q Consensus 252 VIGvV~~V~~~~~i~~k~G~~~~kr~i~L~D~Sg~~I~vtLWg~~a~~~~~~l~~~~~~~~~~VV~l~~~rV~ 324 (560)
+.|+|.++.... . --.+.|+|.|| +|..++=.+..+++...| ..|.|+.|+.+-|=
T Consensus 7 l~v~Iks~~~~~-------~---D~~v~l~DpTG-~i~~tiH~~v~~~y~~~l------~~GavLlLk~V~Vf 62 (86)
T PF15072_consen 7 LVVIIKSIVPSS-------E---DAFVVLKDPTG-EIRGTIHRKVLEEYGDEL------SPGAVLLLKDVTVF 62 (86)
T ss_pred EEEEEEEeeccC-------C---CeEEEEECCCC-cEEEEEeHHHHhhcCCcc------ccCEEEEEeeeeEE
Confidence 456666665532 1 13689999999 899999988766533322 35788889887663
No 177
>PLN02903 aminoacyl-tRNA ligase
Probab=45.00 E-value=2.8e+02 Score=32.16 Aligned_cols=98 Identities=17% Similarity=0.148 Sum_probs=61.3
Q ss_pred cceeccccCCCC--CceEEEEEEEEecccceeccCCCCCcEEEEEEEeCCCCeEEEEEcchh---HHHHHhhcccCcEEE
Q 008606 114 RIIPIAALNPYQ--GRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAV---VDRFYEIIEVGRVYL 188 (560)
Q Consensus 114 ~~~pI~~L~p~~--~~w~Ik~RV~~k~~ir~~~n~~g~gkvf~~~L~D~~g~~I~at~~~~~---~~kf~~~l~eG~vY~ 188 (560)
+.+...+|+... ..-+|+|+|-++ |. .|++.=++|.|. +|.|++++..+. +-+.-..|..|.++.
T Consensus 59 rt~~cg~l~~~~~gk~V~l~GWV~~~---R~------~G~l~FidLRD~-~G~iQvV~~~~~~~~~~~~~~~L~~esvV~ 128 (652)
T PLN02903 59 RSHLCGALSVNDVGSRVTLCGWVDLH---RD------MGGLTFLDVRDH-TGIVQVVTLPDEFPEAHRTANRLRNEYVVA 128 (652)
T ss_pred CCCchhhcchhhCCCEEEEEEEEEEE---ec------CCCcEEEEEEcC-CccEEEEEeCCccHHHHHHHhcCCCCCEEE
Confidence 344455555543 468899999763 43 235666679994 567999986542 222335799999999
Q ss_pred EeeeEEecCCCccc--cCCCeeEEEEcccceEEec
Q 008606 189 ISKGSLKPAQKNFN--HLKNEWEIFLEATSTVDLC 221 (560)
Q Consensus 189 Is~~~V~~a~~~y~--~~~~~yeI~f~~~T~I~~~ 221 (560)
+.+--.....+.-+ .....+||..+.-..+..+
T Consensus 129 V~G~V~~r~~~~~n~~~~tGeiEl~~~~i~VL~~a 163 (652)
T PLN02903 129 VEGTVRSRPQESPNKKMKTGSVEVVAESVDILNVV 163 (652)
T ss_pred EEEEEEeCCCcCcCCCCCCCCEEEEEeEEEEEecC
Confidence 98854433211111 2236799998877666665
No 178
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=44.54 E-value=16 Score=28.00 Aligned_cols=26 Identities=27% Similarity=0.693 Sum_probs=22.9
Q ss_pred eCCCCCcCccccCceeeecCCeeecCcCCCcc
Q 008606 418 TACPLMIGDRQCNKKVTQSGNRWQCDRCNQEI 449 (560)
Q Consensus 418 ~aC~~~~~~~~C~KKv~~~~~~~~C~kC~~~~ 449 (560)
..|+ .|++++...++.-.|+.|+...
T Consensus 6 ~~C~------~Cg~~~~~~dDiVvCp~Cgapy 31 (54)
T PF14446_consen 6 CKCP------VCGKKFKDGDDIVVCPECGAPY 31 (54)
T ss_pred ccCh------hhCCcccCCCCEEECCCCCCcc
Confidence 4688 8999999988899999999865
No 179
>PRK06752 single-stranded DNA-binding protein; Validated
Probab=43.53 E-value=1.6e+02 Score=25.65 Aligned_cols=71 Identities=11% Similarity=0.179 Sum_probs=38.3
Q ss_pred eeEEEEEEEEecCceeEeeccCceeeEEEEEEe----cCCC----cEEEEEEeCcchhhhhhhHHhhhccCCccEEEEE-
Q 008606 249 IVDVIGIVISVNPSVPILRKNGMETQRRILNLK----DTSG----RSVELTLWGDFCNKEGQKLQEMVDVGFFPVLSVK- 319 (560)
Q Consensus 249 ~VDVIGvV~~V~~~~~i~~k~G~~~~kr~i~L~----D~Sg----~~I~vtLWg~~a~~~~~~l~~~~~~~~~~VV~l~- 319 (560)
.|-++|.+..--+++ .+.+|.....-.|-.. |..| .-+.|++||+.|+.+.++| ..+.-|++.
T Consensus 4 ~v~liGrl~~dPelr--~t~~G~~~~~f~lAv~~~~~~~~g~~~t~~~~v~~wg~~Ae~~~~~l------~KG~~V~V~G 75 (112)
T PRK06752 4 RVVLIGRLTKEPELY--YTKQGVAYARVCVAVNRGFRNSLGEQQVDFINCVVWRKSAENVTEYC------TKGSLVGITG 75 (112)
T ss_pred EEEEEEECcCCCEEE--ECCCCCEEEEEEEEECCCeEcCCCCEEEEEEEEEEehHHHHHHHHhc------CCCCEEEEEE
Confidence 356677776543332 2345654322222221 2212 3589999999998764443 356666665
Q ss_pred EEEEecCC
Q 008606 320 SGKVNDFS 327 (560)
Q Consensus 320 ~~rV~~f~ 327 (560)
..+...|.
T Consensus 76 ~l~~~~~~ 83 (112)
T PRK06752 76 RIHTRNYE 83 (112)
T ss_pred EEEeCccC
Confidence 44566674
No 180
>PRK07274 single-stranded DNA-binding protein; Provisional
Probab=43.52 E-value=1.1e+02 Score=27.72 Aligned_cols=70 Identities=17% Similarity=0.291 Sum_probs=37.6
Q ss_pred eeEEEEEEEEecCceeEeeccCceeeEEEEEEe----cCCC----cEEEEEEeCcchhhhhhhHHhhhccCCccEEEEE-
Q 008606 249 IVDVIGIVISVNPSVPILRKNGMETQRRILNLK----DTSG----RSVELTLWGDFCNKEGQKLQEMVDVGFFPVLSVK- 319 (560)
Q Consensus 249 ~VDVIGvV~~V~~~~~i~~k~G~~~~kr~i~L~----D~Sg----~~I~vtLWg~~a~~~~~~l~~~~~~~~~~VV~l~- 319 (560)
.|-++|.|..--.+. .+.+|....+-.|-.. |.+| .-+.|++||..|+...++| ..|.-|.+.
T Consensus 4 ~v~LiGrL~~dPelr--~t~~g~~~~~fslAv~~~~k~~~g~~~t~w~~v~~fg~~Ae~v~~~l------~KG~~V~V~G 75 (131)
T PRK07274 4 KVILIGRLTATPELV--KTANDKSVARVTLAVNRRFKNQNGEREADFINVVLWGKLAETLASYA------SKGSLISIDG 75 (131)
T ss_pred EEEEEEEccCCCeEE--ECCCCCEEEEEEEEEcCceecCCCCEEEEEEEEEEehHHHHHHHHHc------CCCCEEEEEE
Confidence 355677776643322 1234544322222221 3333 2589999999988754433 356666665
Q ss_pred EEEEecC
Q 008606 320 SGKVNDF 326 (560)
Q Consensus 320 ~~rV~~f 326 (560)
..+...|
T Consensus 76 rl~~~~y 82 (131)
T PRK07274 76 ELRTRKY 82 (131)
T ss_pred EEEeccC
Confidence 3456667
No 181
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=43.46 E-value=40 Score=32.51 Aligned_cols=41 Identities=27% Similarity=0.636 Sum_probs=31.6
Q ss_pred EEEEEEEEEe---------CC-CeEEeCCCCCcCccccCceeeecCCeeecCcCCCc
Q 008606 402 TVRAFITFIK---------SD-SFCYTACPLMIGDRQCNKKVTQSGNRWQCDRCNQE 448 (560)
Q Consensus 402 ~v~atI~~I~---------~d-~~~Y~aC~~~~~~~~C~KKv~~~~~~~~C~kC~~~ 448 (560)
.|+|.|.... +| ...|.-|+ .|+--+...+.+.+|++|+.+
T Consensus 124 ivrA~Vis~~~~~~Lst~~~dlGVI~A~Cs------rC~~~L~~~~~~l~Cp~Cg~t 174 (188)
T COG1096 124 IVRARVISTGDPIQLSTKGNDLGVIYARCS------RCRAPLVKKGNMLKCPNCGNT 174 (188)
T ss_pred EEEEEEEecCCCeEEEecCCcceEEEEEcc------CCCcceEEcCcEEECCCCCCE
Confidence 4677766531 11 27899999 999999997779999999975
No 182
>PRK07772 single-stranded DNA-binding protein; Provisional
Probab=43.40 E-value=1.4e+02 Score=28.80 Aligned_cols=74 Identities=11% Similarity=0.104 Sum_probs=40.2
Q ss_pred CceeEEEEEEEEecCceeEeeccCceeeEEEEEEe------------cCCCcEEEEEEeCcchhhhhhhHHhhhccCCcc
Q 008606 247 NSIVDVIGIVISVNPSVPILRKNGMETQRRILNLK------------DTSGRSVELTLWGDFCNKEGQKLQEMVDVGFFP 314 (560)
Q Consensus 247 ~~~VDVIGvV~~V~~~~~i~~k~G~~~~kr~i~L~------------D~Sg~~I~vtLWg~~a~~~~~~l~~~~~~~~~~ 314 (560)
...|-|+|.++.--.++. +.+|+.+.+..|-.. |..-.-+.|++|++.|+...+.| ..+.
T Consensus 4 ~~~VtLiGrL~~DPElR~--t~sG~~va~FrVAv~~r~~~~~~g~~~d~~t~fi~V~~Wg~~Ae~va~~L------~KGd 75 (186)
T PRK07772 4 DTTITVVGNLTADPELRF--TPSGAAVANFTVASTPRTFDRQTNEWKDGEALFLRCSIWRQAAENVAESL------TKGM 75 (186)
T ss_pred cCEEEEEEEeCCCCeEEE--cCCCCEEEEEEEEecCcceecCCCcEeccCceEEEEEEecHHHHHHHHhc------CCCC
Confidence 345667787776433332 345654322222221 11122578999999988754433 3455
Q ss_pred EEEEE-EEEEecCCC
Q 008606 315 VLSVK-SGKVNDFSG 328 (560)
Q Consensus 315 VV~l~-~~rV~~f~G 328 (560)
-|.|. ..+...|..
T Consensus 76 ~V~V~GrL~~r~wed 90 (186)
T PRK07772 76 RVIVTGRLKQRSYET 90 (186)
T ss_pred EEEEEEEEEcCceEC
Confidence 55554 456667754
No 183
>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=43.39 E-value=55 Score=29.50 Aligned_cols=49 Identities=14% Similarity=0.175 Sum_probs=35.3
Q ss_pred CeEEEEEcchhHHHHHhhcccCcEEEEeeeEEecCCCccccCC-CeeEEEE
Q 008606 163 GEIRVTCFNAVVDRFYEIIEVGRVYLISKGSLKPAQKNFNHLK-NEWEIFL 212 (560)
Q Consensus 163 ~~I~at~~~~~~~kf~~~l~eG~vY~Is~~~V~~a~~~y~~~~-~~yeI~f 212 (560)
-.|++++|.+.++ |...|++|+.+.|.|..++....+.-+.. ...++.+
T Consensus 60 ~ti~It~yD~H~~-~ar~lK~GdfV~L~NVhiK~~~~~~~~~~~~~Le~~l 109 (123)
T cd04498 60 LTIDILVYDNHVE-LAKSLKPGDFVRIYNVHAKSYSSKNEHDENDHLHFHL 109 (123)
T ss_pred EEEEEEEEcchHH-HHhhCCCCCEEEEEEEEEEeccCCcccCCcceEEEEE
Confidence 4677899998886 55559999999999999987765544432 2334444
No 184
>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines. Several members are annotated as putative helicases.
Probab=43.02 E-value=14 Score=23.83 Aligned_cols=23 Identities=30% Similarity=0.871 Sum_probs=18.8
Q ss_pred CCCCCcCccccCceeeecCCeeecCcCCCcc
Q 008606 419 ACPLMIGDRQCNKKVTQSGNRWQCDRCNQEI 449 (560)
Q Consensus 419 aC~~~~~~~~C~KKv~~~~~~~~C~kC~~~~ 449 (560)
.|| .|.+.|... .-.|+.|+-.+
T Consensus 2 ~CP------~C~~~V~~~--~~~Cp~CG~~F 24 (26)
T PF10571_consen 2 TCP------ECGAEVPES--AKFCPHCGYDF 24 (26)
T ss_pred cCC------CCcCCchhh--cCcCCCCCCCC
Confidence 599 999999766 47999999765
No 185
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=42.83 E-value=21 Score=26.03 Aligned_cols=25 Identities=24% Similarity=0.670 Sum_probs=20.0
Q ss_pred CCCCCcCccccCceeeecCC--eeecCcCCCcc
Q 008606 419 ACPLMIGDRQCNKKVTQSGN--RWQCDRCNQEI 449 (560)
Q Consensus 419 aC~~~~~~~~C~KKv~~~~~--~~~C~kC~~~~ 449 (560)
.|+ .|+..+..+.. ...|+.|+..+
T Consensus 5 ~C~------~CG~~~~~~~~~~~~~Cp~CG~~~ 31 (46)
T PRK00398 5 KCA------RCGREVELDEYGTGVRCPYCGYRI 31 (46)
T ss_pred ECC------CCCCEEEECCCCCceECCCCCCeE
Confidence 589 89998876655 69999999743
No 186
>PRK05672 dnaE2 error-prone DNA polymerase; Validated
Probab=42.05 E-value=67 Score=39.29 Aligned_cols=61 Identities=20% Similarity=0.279 Sum_probs=42.4
Q ss_pred ceEEEEEEEEecccceeccCCCCCcEEEEEEEeCCCCeEEEEEcchhHHHHHhhcccCcEEEEeeeEEe
Q 008606 127 RWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISKGSLK 195 (560)
Q Consensus 127 ~w~Ik~RV~~k~~ir~~~n~~g~gkvf~~~L~D~~g~~I~at~~~~~~~kf~~~l~eG~vY~Is~~~V~ 195 (560)
..+|.+.|+.+...+ .++ | +-|..++...|.|.+++|.+..+++...|++|.++.+.+ +|.
T Consensus 955 ~v~v~g~i~~~~~~~---Tkk--G--maf~~leD~~g~~e~~ifp~~~~~~~~~l~~~~~~~v~g-~v~ 1015 (1046)
T PRK05672 955 RVRVAGVVTHRQRPG---TAS--G--VTFLTLEDETGMVNVVVWPGLWERQRREALGARLLLVRG-RVQ 1015 (1046)
T ss_pred EEEEEEEEEEEEEec---CCC--c--eEEEEEecCCCCEEEEECHHHHHHHHHHhccCCEEEEEE-EEE
Confidence 345555665543322 223 3 555444448889999999999999999999999999955 443
No 187
>PRK13732 single-stranded DNA-binding protein; Provisional
Probab=41.75 E-value=1.6e+02 Score=28.22 Aligned_cols=72 Identities=14% Similarity=0.132 Sum_probs=39.0
Q ss_pred ceeEEEEEEEEecCceeEeeccCceeeEEEEEEe----cC-CC------cEEEEEEeCcchhhhhhhHHhhhccCCccEE
Q 008606 248 SIVDVIGIVISVNPSVPILRKNGMETQRRILNLK----DT-SG------RSVELTLWGDFCNKEGQKLQEMVDVGFFPVL 316 (560)
Q Consensus 248 ~~VDVIGvV~~V~~~~~i~~k~G~~~~kr~i~L~----D~-Sg------~~I~vtLWg~~a~~~~~~l~~~~~~~~~~VV 316 (560)
..|-|+|.|..--+++. +.+|..+..-.|-.. |. +| .-+.|++||..|+...++| ..+..|
T Consensus 7 N~V~LiGrLg~DPElR~--t~nG~~va~fslAvn~~~kd~~~Ge~~e~t~w~~Vv~wgk~Ae~v~~~L------~KG~~V 78 (175)
T PRK13732 7 NKVILVGRLGKDPEVRY--IPNGGAVANLQVATSESWRDKQTGEMREQTEWHRVVLFGKLAEVAGEYL------RKGAQV 78 (175)
T ss_pred eEEEEEEEecCCCEEEE--cCCCCEEEEEEEEEcCccccCCCCceecceeEEEEEEecHHHHHHHHhc------CCCCEE
Confidence 35777888876322322 345654332222221 21 22 2478999999988754443 356666
Q ss_pred EEE-EEEEecCC
Q 008606 317 SVK-SGKVNDFS 327 (560)
Q Consensus 317 ~l~-~~rV~~f~ 327 (560)
+|. ..+...|.
T Consensus 79 ~VeGrL~~r~ye 90 (175)
T PRK13732 79 YIEGQLRTRSWE 90 (175)
T ss_pred EEEEEEEeeeEc
Confidence 654 34555563
No 188
>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=41.70 E-value=60 Score=35.59 Aligned_cols=54 Identities=19% Similarity=0.278 Sum_probs=40.6
Q ss_pred EEEEEEEeCCCCeEEEEEcchhHHHHHhhcccCcEEEEee-eEEecCCCccccCCCeeEEEEc
Q 008606 152 VFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISK-GSLKPAQKNFNHLKNEWEIFLE 213 (560)
Q Consensus 152 vf~~~L~D~~g~~I~at~~~~~~~kf~~~l~eG~vY~Is~-~~V~~a~~~y~~~~~~yeI~f~ 213 (560)
.+.|.|.| ++..|+|++|...+.+..-.+++|.-+.+.+ ..+-+.. ..|.|...
T Consensus 36 H~YFtLkD-~~a~i~~vmf~~~~~~l~f~~~~G~~V~v~g~v~~y~~~-------G~~ql~v~ 90 (432)
T TIGR00237 36 HWYFTLKD-ENAQVRCVMFRGNNNRLKFRPQNGQQVLVRGGISVYEPR-------GDYQIICF 90 (432)
T ss_pred eEEEEEEc-CCcEEEEEEEcChhhCCCCCCCCCCEEEEEEEEEEECCC-------CcEEEEEE
Confidence 69999999 7899999999998877776789999887766 3444332 34666554
No 189
>PLN02603 asparaginyl-tRNA synthetase
Probab=41.07 E-value=3.5e+02 Score=30.84 Aligned_cols=93 Identities=14% Similarity=0.150 Sum_probs=59.2
Q ss_pred cceeccccCCC--------CCceEEEEEEEEecccceeccCCCCCcEEEEEEEeCCC-CeEEEEEcchhHHHHHh----h
Q 008606 114 RIIPIAALNPY--------QGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDG-GEIRVTCFNAVVDRFYE----I 180 (560)
Q Consensus 114 ~~~pI~~L~p~--------~~~w~Ik~RV~~k~~ir~~~n~~g~gkvf~~~L~D~~g-~~I~at~~~~~~~kf~~----~ 180 (560)
..+.|+++.+. .+.-+|+|+|.+ +|. .|++.=++|.|..| +.|++++-.+.. .|.. .
T Consensus 88 ~~~~~~~~~~~~~~~~~~~g~~V~v~GwV~~---iR~------~g~~~Fi~l~Dgs~~~~lQ~v~~~~~~-~~~~l~~~~ 157 (565)
T PLN02603 88 KKLRIADVKGGEDEGLARVGKTLNVMGWVRT---LRA------QSSVTFIEVNDGSCLSNMQCVMTPDAE-GYDQVESGL 157 (565)
T ss_pred CceEhhhcccccccccccCCCEEEEEEEEEE---EEe------CCCeEEEEEECCCCCEeEEEEEECcHH-HHHHHhhcC
Confidence 33567777632 356788888864 343 23554456888655 379999864422 2322 3
Q ss_pred cccCcEEEEeeeEEecCCCccccCCCeeEEEEcccceEEec
Q 008606 181 IEVGRVYLISKGSLKPAQKNFNHLKNEWEIFLEATSTVDLC 221 (560)
Q Consensus 181 l~eG~vY~Is~~~V~~a~~~y~~~~~~yeI~f~~~T~I~~~ 221 (560)
|..|+++.+.+.-++... ....+||..++-..+-.+
T Consensus 158 l~~gs~V~V~G~v~~~~~-----~~~~~EL~v~~i~vlg~a 193 (565)
T PLN02603 158 ITTGASVLVQGTVVSSQG-----GKQKVELKVSKIVVVGKS 193 (565)
T ss_pred CCCCCEEEEEEEEEecCC-----CCccEEEEEeEEEEEECC
Confidence 889999999997654322 235689988766666655
No 190
>TIGR00280 L37a ribosomal protein L37a. This model finds eukaryotic ribosomal protein L37a and its archaeal orthologs. The nomeclature is tricky because eukaryotes have proteins called both L37 and L37a.
Probab=40.97 E-value=16 Score=31.12 Aligned_cols=27 Identities=33% Similarity=0.982 Sum_probs=19.8
Q ss_pred CCCCCcCccccCce-eeecC-CeeecCcCCCccCC
Q 008606 419 ACPLMIGDRQCNKK-VTQSG-NRWQCDRCNQEIDE 451 (560)
Q Consensus 419 aC~~~~~~~~C~KK-v~~~~-~~~~C~kC~~~~~~ 451 (560)
.|| .|+|. |.... +.|.|.+|++.+.-
T Consensus 37 ~Cp------fCgk~~vkR~a~GIW~C~~C~~~~AG 65 (91)
T TIGR00280 37 VCP------FCGKKTVKRGSTGIWTCRKCGAKFAG 65 (91)
T ss_pred cCC------CCCCCceEEEeeEEEEcCCCCCEEeC
Confidence 589 99764 44433 39999999998743
No 191
>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=40.85 E-value=2e+02 Score=23.57 Aligned_cols=76 Identities=20% Similarity=0.282 Sum_probs=43.6
Q ss_pred eEEEEEEEEecccceeccCCCCCcEEEEEEEeCCCCeEEEEEcchhHHHHH--hhcccCcEEEEeeeEEecCCCccccCC
Q 008606 128 WAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAVVDRFY--EIIEVGRVYLISKGSLKPAQKNFNHLK 205 (560)
Q Consensus 128 w~Ik~RV~~k~~ir~~~n~~g~gkvf~~~L~D~~g~~I~at~~~~~~~kf~--~~l~eG~vY~Is~~~V~~a~~~y~~~~ 205 (560)
.+|.|+|.++ |.. .|++.=++|.|..|..|++++-.+. +.|. ..|..|+++.+.+- +......-..-.
T Consensus 2 V~v~Gwv~~~---R~~-----~~~~~Fi~LrD~~g~~iQvv~~~~~-~~~~~~~~l~~~s~V~V~G~-v~~~~~~~~~~~ 71 (86)
T cd04321 2 VTLNGWIDRK---PRI-----VKKLSFADLRDPNGDIIQLVSTAKK-DAFSLLKSITAESPVQVRGK-LQLKEAKSSEKN 71 (86)
T ss_pred EEEEEeEeeE---eCC-----CCceEEEEEECCCCCEEEEEECCCH-HHHHHHhcCCCCcEEEEEEE-EEeCCCcCCCCC
Confidence 4677887653 321 1344445688977756999775442 3333 35889999999774 433221110112
Q ss_pred CeeEEEEc
Q 008606 206 NEWEIFLE 213 (560)
Q Consensus 206 ~~yeI~f~ 213 (560)
..+||..+
T Consensus 72 ~~~Ei~~~ 79 (86)
T cd04321 72 DEWELVVD 79 (86)
T ss_pred CCEEEEEE
Confidence 56787764
No 192
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=40.81 E-value=14 Score=39.90 Aligned_cols=29 Identities=24% Similarity=0.878 Sum_probs=24.3
Q ss_pred EeCCCCCcCccccCceeeecCC-eeecCcCCCccCC
Q 008606 417 YTACPLMIGDRQCNKKVTQSGN-RWQCDRCNQEIDE 451 (560)
Q Consensus 417 Y~aC~~~~~~~~C~KKv~~~~~-~~~C~kC~~~~~~ 451 (560)
-+-|| .|++.+...+. .|+|.+|+.....
T Consensus 350 ~p~Cp------~Cg~~m~S~G~~g~rC~kCg~~~~~ 379 (421)
T COG1571 350 NPVCP------RCGGRMKSAGRNGFRCKKCGTRARE 379 (421)
T ss_pred CCCCC------ccCCchhhcCCCCcccccccccCCc
Confidence 46899 99999987776 8999999987644
No 193
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=39.54 E-value=17 Score=30.87 Aligned_cols=27 Identities=30% Similarity=1.023 Sum_probs=19.5
Q ss_pred CCCCCcCccccCce-eeecC-CeeecCcCCCccCC
Q 008606 419 ACPLMIGDRQCNKK-VTQSG-NRWQCDRCNQEIDE 451 (560)
Q Consensus 419 aC~~~~~~~~C~KK-v~~~~-~~~~C~kC~~~~~~ 451 (560)
.|| .|+|. |.... +.|.|.+|+..+.-
T Consensus 38 ~Cp------fCgk~~vkR~a~GIW~C~~C~~~~AG 66 (90)
T PRK03976 38 VCP------VCGRPKVKRVGTGIWECRKCGAKFAG 66 (90)
T ss_pred cCC------CCCCCceEEEEEEEEEcCCCCCEEeC
Confidence 589 99764 44433 39999999987643
No 194
>PRK00476 aspS aspartyl-tRNA synthetase; Validated
Probab=39.25 E-value=2.5e+02 Score=32.22 Aligned_cols=94 Identities=15% Similarity=0.120 Sum_probs=58.0
Q ss_pred ccccCCC--CCceEEEEEEEEecccceeccCCCCCcEEEEEEEeCCCCeEEEEEcch-hHHHHHhhcccCcEEEEeeeEE
Q 008606 118 IAALNPY--QGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNA-VVDRFYEIIEVGRVYLISKGSL 194 (560)
Q Consensus 118 I~~L~p~--~~~w~Ik~RV~~k~~ir~~~n~~g~gkvf~~~L~D~~g~~I~at~~~~-~~~kf~~~l~eG~vY~Is~~~V 194 (560)
+.+|++. ...-+|+|||.++ |. .|++.=++|.| .++.|++++-.. ..-+.-..|..|+++.+.+--+
T Consensus 8 ~~~l~~~~~g~~V~l~GwV~~~---R~------~g~l~Fi~LrD-~~g~iQ~v~~~~~~~~~~~~~l~~es~V~V~G~v~ 77 (588)
T PRK00476 8 CGELRESHVGQTVTLCGWVHRR---RD------HGGLIFIDLRD-REGIVQVVFDPDAEAFEVAESLRSEYVIQVTGTVR 77 (588)
T ss_pred HHHhhHHhCCCEEEEEEEEEEE---Ee------CCCeEEEEEEe-CCceEEEEEeCCHHHHHHHhCCCCCCEEEEEEEEE
Confidence 4455432 2457899999763 43 23566677999 556899988652 1112235689999999988554
Q ss_pred ecCCCcccc--CCCeeEEEEcccceEEec
Q 008606 195 KPAQKNFNH--LKNEWEIFLEATSTVDLC 221 (560)
Q Consensus 195 ~~a~~~y~~--~~~~yeI~f~~~T~I~~~ 221 (560)
+...+.-++ ....+||....-..+..+
T Consensus 78 ~~~~~~~n~~~~~g~~El~~~~i~il~~a 106 (588)
T PRK00476 78 ARPEGTVNPNLPTGEIEVLASELEVLNKS 106 (588)
T ss_pred ecCCcccCccCCCCcEEEEEeEEEEEecC
Confidence 422122222 235799988776666655
No 195
>PRK00286 xseA exodeoxyribonuclease VII large subunit; Reviewed
Probab=39.10 E-value=70 Score=34.97 Aligned_cols=40 Identities=25% Similarity=0.277 Sum_probs=34.3
Q ss_pred cEEEEEEEeCCCCeEEEEEcchhHHHHHhhcccCcEEEEee
Q 008606 151 KVFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISK 191 (560)
Q Consensus 151 kvf~~~L~D~~g~~I~at~~~~~~~kf~~~l~eG~vY~Is~ 191 (560)
..+.|.|.| +...|+|++|...+.+..-.+++|.-+.+.+
T Consensus 41 GH~Yf~Lkd-~~a~i~~~~~~~~~~~~~~~~~~G~~v~v~g 80 (438)
T PRK00286 41 GHWYFTLKD-EIAQIRCVMFKGSARRLKFKPEEGMKVLVRG 80 (438)
T ss_pred CeEEEEEEc-CCcEEEEEEEcChhhcCCCCCCCCCEEEEEE
Confidence 368899999 5789999999998888777799999888776
No 196
>PRK14810 formamidopyrimidine-DNA glycosylase; Provisional
Probab=38.08 E-value=19 Score=36.89 Aligned_cols=24 Identities=17% Similarity=0.675 Sum_probs=18.9
Q ss_pred eCCCCCcCccccCceeeec--CC--eeecCcCCC
Q 008606 418 TACPLMIGDRQCNKKVTQS--GN--RWQCDRCNQ 447 (560)
Q Consensus 418 ~aC~~~~~~~~C~KKv~~~--~~--~~~C~kC~~ 447 (560)
..|| .|+.++... ++ .|+|+.|++
T Consensus 245 ~pCp------rCG~~I~~~~~~gR~t~~CP~CQ~ 272 (272)
T PRK14810 245 EPCL------NCKTPIRRVVVAGRSSHYCPHCQK 272 (272)
T ss_pred CcCC------CCCCeeEEEEECCCccEECcCCcC
Confidence 6899 999988643 22 999999984
No 197
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=38.04 E-value=18 Score=27.12 Aligned_cols=26 Identities=27% Similarity=0.906 Sum_probs=19.5
Q ss_pred EeCCCCCcCccccC--ceeeecCCeeecCcCCCc
Q 008606 417 YTACPLMIGDRQCN--KKVTQSGNRWQCDRCNQE 448 (560)
Q Consensus 417 Y~aC~~~~~~~~C~--KKv~~~~~~~~C~kC~~~ 448 (560)
-.-|| .|+ --+....+.|.|-+|+-+
T Consensus 19 ~~~CP------rCG~gvfmA~H~dR~~CGkCgyT 46 (51)
T COG1998 19 NRFCP------RCGPGVFMADHKDRWACGKCGYT 46 (51)
T ss_pred cccCC------CCCCcchhhhcCceeEeccccce
Confidence 45699 898 445555669999999954
No 198
>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=37.78 E-value=3.6e+02 Score=25.51 Aligned_cols=143 Identities=17% Similarity=0.254 Sum_probs=87.5
Q ss_pred EEEEEEEecccceeccCC-CCCcEEEEEEEeCCCCeEEEEEcchhHHHHHhhcccCcEEEEeeeEEecCCCccccCCCee
Q 008606 130 IKARVTAKGDLRRYNNAR-GDGKVFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISKGSLKPAQKNFNHLKNEW 208 (560)
Q Consensus 130 Ik~RV~~k~~ir~~~n~~-g~gkvf~~~L~D~~g~~I~at~~~~~~~kf~~~l~eG~vY~Is~~~V~~a~~~y~~~~~~y 208 (560)
..|.|+.-.+.=.|.... |..+.|+-+++- +..-.++.+|+- .+.+.+..++++.||+..-. .-
T Consensus 5 ~~VmVLkaTepF~Ye~~e~gkk~MFHATVAT-et~fF~VKVfn~---~LKeKF~~kkiI~IS~Y~~~-----------~g 69 (170)
T PF02760_consen 5 KTVMVLKATEPFEYESPEEGKKKMFHATVAT-ETEFFRVKVFNI---NLKEKFIPKKIIAISDYFGR-----------NG 69 (170)
T ss_dssp EEEEEEEE---EEEECTTTCEEEEEEEEEE--SS-EEEEEES-G---GGCCTCSTTSEEEEESEEEE-----------TT
T ss_pred eEEEEEeccCCeEEeCcccCcceEEEEEEec-cccEEEEEEecc---hhHhhcCCCcEEEEehhhcc-----------cc
Confidence 457777777777777655 445789988888 788999999995 35677888999999986432 12
Q ss_pred EEEEcccceEEecc-CCCCCCCccc----ccccCccchhcccCCceeEEEEEEEEecCceeEeeccCceeeEEEEEEecC
Q 008606 209 EIFLEATSTVDLCT-EEDDSIPKQQ----FSFRHISEIESAENNSIVDVIGIVISVNPSVPILRKNGMETQRRILNLKDT 283 (560)
Q Consensus 209 eI~f~~~T~I~~~~-d~~~~iP~~~----f~f~~i~dI~~~~~~~~VDVIGvV~~V~~~~~i~~k~G~~~~kr~i~L~D~ 283 (560)
-|-.++.|.|.++. |....+|... -.--+|++|.....+.+|+=+=.|.... .+ .......|.|+
T Consensus 70 fLEi~~aSsVse~~~dq~~eVp~~ii~~A~~TpKI~~L~~q~~Gt~V~G~F~v~KK~------v~----~~~~~YeI~Dn 139 (170)
T PF02760_consen 70 FLEINEASSVSEVNPDQKMEVPNSIIRRANETPKINDLQKQASGTFVNGLFTVHKKT------VN----KKNTIYEIQDN 139 (170)
T ss_dssp EEEE-TTSEEEE--TTC-----HHHHHHHCS---HHHHTTSSTTEEEEEEEEEEEEE------EE----SSEEEEEEEET
T ss_pred eEEEeeccEEEecCCCceEEccHHHHHhhccCCchhHHhcCCCCcEEeEEEEEEEEE------Ec----CCeEEEEEecC
Confidence 35667788888874 3334566532 1234588887777788776544443321 11 12346789999
Q ss_pred CCcEEEEEEeCcchh
Q 008606 284 SGRSVELTLWGDFCN 298 (560)
Q Consensus 284 Sg~~I~vtLWg~~a~ 298 (560)
+| .++|...|.+..
T Consensus 140 TG-~MeVvv~G~~~n 153 (170)
T PF02760_consen 140 TG-KMEVVVYGKWHN 153 (170)
T ss_dssp TE-EEEEEEEGGGCG
T ss_pred CC-cEEEEEeccCcc
Confidence 99 899999998754
No 199
>PF08274 PhnA_Zn_Ribbon: PhnA Zinc-Ribbon ; InterPro: IPR013987 The PhnA protein family includes the uncharacterised Escherichia coli protein PhnA and its homologues. The E. coli phnA gene is part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage []. The protein is not related to the characterised phosphonoacetate hydrolase designated PhnA []. This entry represents the N-terminal domain of PhnA, which is predicted to form a zinc-ribbon.; PDB: 2AKL_A.
Probab=37.45 E-value=13 Score=24.99 Aligned_cols=26 Identities=27% Similarity=0.696 Sum_probs=13.5
Q ss_pred EeCCCCCcCccccCceeeecCC-eeecCcCCCc
Q 008606 417 YTACPLMIGDRQCNKKVTQSGN-RWQCDRCNQE 448 (560)
Q Consensus 417 Y~aC~~~~~~~~C~KKv~~~~~-~~~C~kC~~~ 448 (560)
.++|| .|+.--+..++ .+.|+.|+..
T Consensus 2 ~p~Cp------~C~se~~y~D~~~~vCp~C~~e 28 (30)
T PF08274_consen 2 LPKCP------LCGSEYTYEDGELLVCPECGHE 28 (30)
T ss_dssp S---T------TT-----EE-SSSEEETTTTEE
T ss_pred CCCCC------CCCCcceeccCCEEeCCccccc
Confidence 47899 89987766555 9999999854
No 200
>PRK13945 formamidopyrimidine-DNA glycosylase; Provisional
Probab=37.39 E-value=21 Score=36.69 Aligned_cols=24 Identities=17% Similarity=0.675 Sum_probs=18.7
Q ss_pred eCCCCCcCccccCceeeec--CC--eeecCcCCC
Q 008606 418 TACPLMIGDRQCNKKVTQS--GN--RWQCDRCNQ 447 (560)
Q Consensus 418 ~aC~~~~~~~~C~KKv~~~--~~--~~~C~kC~~ 447 (560)
..|| .|+.++... ++ .|+|+.|++
T Consensus 255 ~pC~------~Cg~~I~~~~~~gR~t~~CP~CQ~ 282 (282)
T PRK13945 255 KPCR------KCGTPIERIKLAGRSTHWCPNCQK 282 (282)
T ss_pred CCCC------cCCCeeEEEEECCCccEECCCCcC
Confidence 5899 899888643 22 999999974
No 201
>PRK06293 single-stranded DNA-binding protein; Provisional
Probab=36.83 E-value=2.4e+02 Score=26.61 Aligned_cols=71 Identities=13% Similarity=0.074 Sum_probs=38.6
Q ss_pred eeEEEEEEEEecCceeEeeccCceeeEEEEEEecC-----CCcEEEEEEeCcchhhhhhhHHhhhccCCccEEEEE-EEE
Q 008606 249 IVDVIGIVISVNPSVPILRKNGMETQRRILNLKDT-----SGRSVELTLWGDFCNKEGQKLQEMVDVGFFPVLSVK-SGK 322 (560)
Q Consensus 249 ~VDVIGvV~~V~~~~~i~~k~G~~~~kr~i~L~D~-----Sg~~I~vtLWg~~a~~~~~~l~~~~~~~~~~VV~l~-~~r 322 (560)
.|-+||.|..=-.++ .+.+|+...+-.|-..+. .-.-+.|++||+.|+...++| ..+.-|++. ..+
T Consensus 3 ~V~LiGrLg~DPElR--~t~sG~~v~~FsLAvn~~~~~~~~T~wi~v~awg~~Ae~v~~yL------~KG~~V~VeGrL~ 74 (161)
T PRK06293 3 FGYIVGRLGADPEER--MTSKGKRVVVLRLGVKSRVGSKDETVWCRCNIWGNRYDKMLPYL------KKGSGVIVAGEMS 74 (161)
T ss_pred EEEEEEEecCCCeEE--EcCCCCEEEEEEEEEeCCCCCccceEEEEEEEEhHHHHHHHHhC------CCCCEEEEEEEEE
Confidence 466777777532222 234565433333332221 112589999999987654433 355656554 456
Q ss_pred EecCC
Q 008606 323 VNDFS 327 (560)
Q Consensus 323 V~~f~ 327 (560)
...|.
T Consensus 75 ~~~y~ 79 (161)
T PRK06293 75 PESYV 79 (161)
T ss_pred eCccC
Confidence 66774
No 202
>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=35.43 E-value=91 Score=26.12 Aligned_cols=70 Identities=17% Similarity=0.215 Sum_probs=35.9
Q ss_pred eEEEEEEEEecCceeEeeccCceeeEEEEEEec----CC------CcEEEEEEeCcchhhhhhhHHhhhccCCccEEEEE
Q 008606 250 VDVIGIVISVNPSVPILRKNGMETQRRILNLKD----TS------GRSVELTLWGDFCNKEGQKLQEMVDVGFFPVLSVK 319 (560)
Q Consensus 250 VDVIGvV~~V~~~~~i~~k~G~~~~kr~i~L~D----~S------g~~I~vtLWg~~a~~~~~~l~~~~~~~~~~VV~l~ 319 (560)
|-++|.|..--.+. .+++|+....-.|...+ .. -.-+.|++||+.|+.+.++| ..+..|.+.
T Consensus 4 v~l~G~l~~~p~~~--~~~~g~~~~~f~la~~~~~~~~~~~~~~~~~~~~v~~~g~~A~~~~~~l------~kG~~V~V~ 75 (104)
T PF00436_consen 4 VTLIGRLGKDPELR--YTKNGTPVARFSLAVNRRFKDDGGEGDEKTDWINVVAWGKLAENVAEYL------KKGDRVYVE 75 (104)
T ss_dssp EEEEEEESSSEEEE--EETTSEEEEEEEEEEEEEEEETTSCEEEEEEEEEEEEEHHHHHHHHHH--------TT-EEEEE
T ss_pred EEEEEEECCCcEEE--ECCCCCEEEEEEEEEecEEeeeeccCccceEEEEEEeeeecccccceEE------cCCCEEEEE
Confidence 44666665432222 23456554433343333 11 13599999999988754443 346666665
Q ss_pred E-EEEecCC
Q 008606 320 S-GKVNDFS 327 (560)
Q Consensus 320 ~-~rV~~f~ 327 (560)
+ .+...|.
T Consensus 76 G~l~~~~~~ 84 (104)
T PF00436_consen 76 GRLRTRTYE 84 (104)
T ss_dssp EEEEEEEEE
T ss_pred EEEEeeEEE
Confidence 4 3444454
No 203
>PRK11827 hypothetical protein; Provisional
Probab=35.34 E-value=28 Score=27.29 Aligned_cols=26 Identities=31% Similarity=0.537 Sum_probs=21.1
Q ss_pred eCCCCCcCccccCceeeecCC--eeecCcCCCcc
Q 008606 418 TACPLMIGDRQCNKKVTQSGN--RWQCDRCNQEI 449 (560)
Q Consensus 418 ~aC~~~~~~~~C~KKv~~~~~--~~~C~kC~~~~ 449 (560)
.+|| .|+.++..+.+ ...|..|+..+
T Consensus 9 LaCP------~ckg~L~~~~~~~~Lic~~~~laY 36 (60)
T PRK11827 9 IACP------VCNGKLWYNQEKQELICKLDNLAF 36 (60)
T ss_pred eECC------CCCCcCeEcCCCCeEECCccCeec
Confidence 5899 99999987644 68899998765
No 204
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=35.24 E-value=50 Score=24.32 Aligned_cols=22 Identities=23% Similarity=0.687 Sum_probs=16.8
Q ss_pred ccCceeeecCC----eeecCcCCCcc
Q 008606 428 QCNKKVTQSGN----RWQCDRCNQEI 449 (560)
Q Consensus 428 ~C~KKv~~~~~----~~~C~kC~~~~ 449 (560)
.|+.-+....+ .|.|+.|+-..
T Consensus 5 ~Cg~~l~~~~~~~~~~~vC~~Cg~~~ 30 (52)
T smart00661 5 KCGNMLIPKEGKEKRRFVCRKCGYEE 30 (52)
T ss_pred CCCCccccccCCCCCEEECCcCCCeE
Confidence 89987765432 79999999764
No 205
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=35.21 E-value=22 Score=30.17 Aligned_cols=30 Identities=27% Similarity=0.864 Sum_probs=20.9
Q ss_pred CCCCCcCccccCce-eeecC-CeeecCcCCCccCCcee
Q 008606 419 ACPLMIGDRQCNKK-VTQSG-NRWQCDRCNQEIDECDY 454 (560)
Q Consensus 419 aC~~~~~~~~C~KK-v~~~~-~~~~C~kC~~~~~~~~~ 454 (560)
.|| .|+|. |.... +.|.|.+|+..+.--.|
T Consensus 38 ~Cp------fCgk~~vkR~a~GIW~C~~C~~~~AGGAy 69 (90)
T PTZ00255 38 FCP------FCGKHAVKRQAVGIWRCKGCKKTVAGGAW 69 (90)
T ss_pred cCC------CCCCCceeeeeeEEEEcCCCCCEEeCCcc
Confidence 589 89764 44443 39999999998744333
No 206
>COG5235 RFA2 Single-stranded DNA-binding replication protein A (RPA), medium (30 kD) subunit [DNA replication, recombination, and repair]
Probab=34.10 E-value=1.3e+02 Score=29.65 Aligned_cols=73 Identities=18% Similarity=0.124 Sum_probs=45.5
Q ss_pred EEEEEeCCCeEEEEEehhhhhhhcCCCHHHHHHhhhccCChhHHHHHHHHhcCCeEEEEEEEeeeecCCeeeEEEEEEEe
Q 008606 459 QAQIQDQTGLTWVTAFQESGEEILGCPAKELYMLKYELQDDVRFGEIIRSRVFNQYLFRLKIKEELYGDEQRVKITVIRA 538 (560)
Q Consensus 459 ~~~i~D~Tgs~~~~~Fd~~ae~llG~sA~el~~~~~e~~d~~~~~~~l~~~~~k~~~fkvkvk~e~y~~e~r~k~~v~~~ 538 (560)
-+.|.|+||++.|+.|...+-.. -..+ |.++ ++ .+||-.....|++..-+.+.+++.
T Consensus 86 ~~~iEDGTG~Ievr~W~~~~~~~--------e~~~----d~~~---------~~--yvkV~G~lk~F~GK~~I~~~~i~~ 142 (258)
T COG5235 86 MFVIEDGTGSIEVRFWPGNSYEE--------EQCK----DLEE---------QN--YVKVNGSLKTFNGKRSISASHISA 142 (258)
T ss_pred EEEEecCCceEEEEecCCCchHH--------Hhcc----cccc---------cc--EEEEecceeeeCCeeEEehhheee
Confidence 56899999999999998654321 1111 1000 11 567777788999876666666554
Q ss_pred eeCChHHHHHHHHHHHH
Q 008606 539 DQVNYSSESRYLLDLIS 555 (560)
Q Consensus 539 ~~vd~~~e~~~ll~~i~ 555 (560)
.+ |+.+.--..|+.|.
T Consensus 143 I~-d~NeV~~HfLe~I~ 158 (258)
T COG5235 143 IE-DSNEVTYHFLECIY 158 (258)
T ss_pred cc-ccchhHHHHHHHHH
Confidence 33 45555556666664
No 207
>PRK10445 endonuclease VIII; Provisional
Probab=33.97 E-value=22 Score=36.16 Aligned_cols=24 Identities=21% Similarity=0.729 Sum_probs=18.6
Q ss_pred eCCCCCcCccccCceeeec--CC--eeecCcCCC
Q 008606 418 TACPLMIGDRQCNKKVTQS--GN--RWQCDRCNQ 447 (560)
Q Consensus 418 ~aC~~~~~~~~C~KKv~~~--~~--~~~C~kC~~ 447 (560)
..|| .|+.++... ++ .|+|++|++
T Consensus 236 ~~Cp------~Cg~~I~~~~~~gR~t~~CP~CQ~ 263 (263)
T PRK10445 236 EACE------RCGGIIEKTTLSSRPFYWCPGCQK 263 (263)
T ss_pred CCCC------CCCCEeEEEEECCCCcEECCCCcC
Confidence 5799 899888642 22 999999974
No 208
>PF14205 Cys_rich_KTR: Cysteine-rich KTR
Probab=33.87 E-value=38 Score=25.91 Aligned_cols=26 Identities=31% Similarity=0.746 Sum_probs=17.6
Q ss_pred eCCCCCcCccccCcee----eecCC----eeecCcCCCcc
Q 008606 418 TACPLMIGDRQCNKKV----TQSGN----RWQCDRCNQEI 449 (560)
Q Consensus 418 ~aC~~~~~~~~C~KKv----~~~~~----~~~C~kC~~~~ 449 (560)
.-|| .|+.|- ..+.. ..+|++|.++.
T Consensus 5 i~CP------~CgnKTR~kir~DT~LkNfPlyCpKCK~Et 38 (55)
T PF14205_consen 5 ILCP------ICGNKTRLKIREDTVLKNFPLYCPKCKQET 38 (55)
T ss_pred EECC------CCCCccceeeecCceeccccccCCCCCceE
Confidence 4599 898554 22221 68999999864
No 209
>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=33.82 E-value=24 Score=31.01 Aligned_cols=27 Identities=26% Similarity=0.712 Sum_probs=21.5
Q ss_pred eCCCCCcCccccCceeeecCC-eeecCcCCCccC
Q 008606 418 TACPLMIGDRQCNKKVTQSGN-RWQCDRCNQEID 450 (560)
Q Consensus 418 ~aC~~~~~~~~C~KKv~~~~~-~~~C~kC~~~~~ 450 (560)
.-|| .|++|-..-+- .-.|++|+..+.
T Consensus 10 R~Cp------~CG~kFYDLnk~PivCP~CG~~~~ 37 (108)
T PF09538_consen 10 RTCP------SCGAKFYDLNKDPIVCPKCGTEFP 37 (108)
T ss_pred ccCC------CCcchhccCCCCCccCCCCCCccC
Confidence 4699 99999886554 567999999873
No 210
>COG1379 PHP family phosphoesterase with a Zn ribbon [General function prediction only]
Probab=33.79 E-value=10 Score=39.37 Aligned_cols=30 Identities=30% Similarity=0.922 Sum_probs=24.2
Q ss_pred CeEEeCCCCCcCccccCceeeecCC---eeecCcCCCcc
Q 008606 414 SFCYTACPLMIGDRQCNKKVTQSGN---RWQCDRCNQEI 449 (560)
Q Consensus 414 ~~~Y~aC~~~~~~~~C~KKv~~~~~---~~~C~kC~~~~ 449 (560)
..+-.||. .|..+-..... .|.|++|+..+
T Consensus 243 KY~~TAC~------rC~t~y~le~A~~~~wrCpkCGg~i 275 (403)
T COG1379 243 KYHLTACS------RCYTRYSLEEAKSLRWRCPKCGGKI 275 (403)
T ss_pred chhHHHHH------HhhhccCcchhhhhcccCcccccch
Confidence 47789999 99988776554 79999999754
No 211
>PF03119 DNA_ligase_ZBD: NAD-dependent DNA ligase C4 zinc finger domain; InterPro: IPR004149 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the zinc finger domain found in NAD-dependent DNA ligases. DNA ligases catalyse the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilizing either ATP or NAD(+) as a cofactor []. This domain is a small zinc binding motif that is presumably DNA binding. It is found only in NAD-dependent DNA ligases. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003911 DNA ligase (NAD+) activity, 0006260 DNA replication, 0006281 DNA repair; PDB: 1DGS_A 1V9P_B 2OWO_A.
Probab=33.78 E-value=25 Score=23.03 Aligned_cols=19 Identities=26% Similarity=0.814 Sum_probs=11.0
Q ss_pred CCCCcCccccCceeeecCC--eeecCc
Q 008606 420 CPLMIGDRQCNKKVTQSGN--RWQCDR 444 (560)
Q Consensus 420 C~~~~~~~~C~KKv~~~~~--~~~C~k 444 (560)
|| .|+.++....+ .++|..
T Consensus 2 CP------~C~s~l~~~~~ev~~~C~N 22 (28)
T PF03119_consen 2 CP------VCGSKLVREEGEVDIRCPN 22 (28)
T ss_dssp -T------TT--BEEE-CCTTCEEE--
T ss_pred cC------CCCCEeEcCCCCEeEECCC
Confidence 89 89999986655 899963
No 212
>PRK01103 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated
Probab=33.68 E-value=22 Score=36.37 Aligned_cols=24 Identities=25% Similarity=0.887 Sum_probs=18.4
Q ss_pred eCCCCCcCccccCceeeec--C--CeeecCcCCC
Q 008606 418 TACPLMIGDRQCNKKVTQS--G--NRWQCDRCNQ 447 (560)
Q Consensus 418 ~aC~~~~~~~~C~KKv~~~--~--~~~~C~kC~~ 447 (560)
..|| .|+.++... + +.|+|+.|++
T Consensus 246 ~pC~------~Cg~~I~~~~~~gR~t~~CP~CQ~ 273 (274)
T PRK01103 246 EPCR------RCGTPIEKIKQGGRSTFFCPRCQK 273 (274)
T ss_pred CCCC------CCCCeeEEEEECCCCcEECcCCCC
Confidence 4699 899887642 2 3999999985
No 213
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=33.07 E-value=14 Score=35.33 Aligned_cols=27 Identities=26% Similarity=0.893 Sum_probs=22.1
Q ss_pred EeCCCCCcCccccCceeeecCC---eeecCcCCCcc
Q 008606 417 YTACPLMIGDRQCNKKVTQSGN---RWQCDRCNQEI 449 (560)
Q Consensus 417 Y~aC~~~~~~~~C~KKv~~~~~---~~~C~kC~~~~ 449 (560)
|..|| .|+-|++.+.. .+.|++||...
T Consensus 113 ~y~C~------~~~~r~sfdeA~~~~F~Cp~Cg~~L 142 (176)
T COG1675 113 YYVCP------NCHVKYSFDEAMELGFTCPKCGEDL 142 (176)
T ss_pred ceeCC------CCCCcccHHHHHHhCCCCCCCCchh
Confidence 55679 89999987765 79999999865
No 214
>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=32.89 E-value=1.5e+02 Score=30.09 Aligned_cols=58 Identities=9% Similarity=0.090 Sum_probs=41.9
Q ss_pred CCeEEEEEcchhHHHHHhhcccCcEEEEeeeEEecCCCccccCCCeeEEEEcccceEEecc
Q 008606 162 GGEIRVTCFNAVVDRFYEIIEVGRVYLISKGSLKPAQKNFNHLKNEWEIFLEATSTVDLCT 222 (560)
Q Consensus 162 g~~I~at~~~~~~~kf~~~l~eG~vY~Is~~~V~~a~~~y~~~~~~yeI~f~~~T~I~~~~ 222 (560)
......+||+.. +.+.+.|+||+.|.|.+....+..+. .......|+-...|..++++
T Consensus 179 ~~~~~LTIWrPt-edl~s~L~EG~ry~i~~L~~s~~k~~--~~~~~vqLtatk~Tr~~~l~ 236 (251)
T cd04494 179 EKSGLLSIWRPT-EDLRSLLTEGKRYRIYGLATSNSKKR--SGNEEVQLTATKKTRYQPLP 236 (251)
T ss_pred CceEEEEEeCCC-HHHHhhhcCCcEEEEEeccccCCCCC--CCcceEEEEecCcccceECC
Confidence 455567888864 44677999999999999875443322 33467888888888888874
No 215
>PF14353 CpXC: CpXC protein
Probab=32.72 E-value=61 Score=28.90 Aligned_cols=33 Identities=15% Similarity=0.357 Sum_probs=23.4
Q ss_pred eeecCcCCCccCCceeEEEEEEEEEeCCCeEEEEEehh
Q 008606 439 RWQCDRCNQEIDECDYRYLLQAQIQDQTGLTWVTAFQE 476 (560)
Q Consensus 439 ~~~C~kC~~~~~~~~~rY~l~~~i~D~Tgs~~~~~Fd~ 476 (560)
.+.|++|++.+ +....+...|......+.++-+
T Consensus 38 ~~~CP~Cg~~~-----~~~~p~lY~D~~~~~~i~~~P~ 70 (128)
T PF14353_consen 38 SFTCPSCGHKF-----RLEYPLLYHDPEKKFMIYYFPD 70 (128)
T ss_pred EEECCCCCCce-----ecCCCEEEEcCCCCEEEEEcCC
Confidence 79999999864 3344666777777777666655
No 216
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=32.61 E-value=28 Score=30.83 Aligned_cols=22 Identities=36% Similarity=1.014 Sum_probs=19.0
Q ss_pred CCCCcCccccCceeeecCCeeecCcCCCcc
Q 008606 420 CPLMIGDRQCNKKVTQSGNRWQCDRCNQEI 449 (560)
Q Consensus 420 C~~~~~~~~C~KKv~~~~~~~~C~kC~~~~ 449 (560)
|| .|+.++.-. .+.|+.|+..+
T Consensus 1 CP------vCg~~l~vt--~l~C~~C~t~i 22 (113)
T PF09862_consen 1 CP------VCGGELVVT--RLKCPSCGTEI 22 (113)
T ss_pred CC------CCCCceEEE--EEEcCCCCCEE
Confidence 99 899988776 59999999765
No 217
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=32.61 E-value=76 Score=28.06 Aligned_cols=49 Identities=22% Similarity=0.629 Sum_probs=34.6
Q ss_pred CCCCCcCccccCceeee----cCCeeecCcCCCccCCc---eeEEEEEEEEEeCCCeEEEEE
Q 008606 419 ACPLMIGDRQCNKKVTQ----SGNRWQCDRCNQEIDEC---DYRYLLQAQIQDQTGLTWVTA 473 (560)
Q Consensus 419 aC~~~~~~~~C~KKv~~----~~~~~~C~kC~~~~~~~---~~rY~l~~~i~D~Tgs~~~~~ 473 (560)
=|| .|+.-+.. .+..+.|.+|+-..+.. .++|.+...+.+.....-...
T Consensus 4 FCp------~Cgsll~p~~~~~~~~l~C~kCgye~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 59 (113)
T COG1594 4 FCP------KCGSLLYPKKDDEGGKLVCRKCGYEEEASNKKVYRYSVKEAVEKKKEVVLVVE 59 (113)
T ss_pred ccC------CccCeeEEeEcCCCcEEECCCCCcchhccccceeEEEEeeccCCcceeeeeec
Confidence 388 89998876 34499999999876433 277777777777666555444
No 218
>KOG1924 consensus RhoA GTPase effector DIA/Diaphanous [Signal transduction mechanisms; Cytoskeleton]
Probab=32.59 E-value=1.2e+02 Score=35.44 Aligned_cols=11 Identities=18% Similarity=0.295 Sum_probs=5.4
Q ss_pred cchhHHHHHhh
Q 008606 170 FNAVVDRFYEI 180 (560)
Q Consensus 170 ~~~~~~kf~~~ 180 (560)
|..++-+|..+
T Consensus 659 fakL~~~Fatq 669 (1102)
T KOG1924|consen 659 FAKLALKFATQ 669 (1102)
T ss_pred HHHHHHHhhcc
Confidence 34455555544
No 219
>PRK07279 dnaE DNA polymerase III DnaE; Reviewed
Probab=32.53 E-value=1.2e+02 Score=37.16 Aligned_cols=73 Identities=21% Similarity=0.253 Sum_probs=48.5
Q ss_pred cCccchhcccCCceeEEEEEEEEecCceeEeec-cCceeeEEEEEEecCCCcEEEEEEeCcchhhhhhhHHhhhccCCcc
Q 008606 236 RHISEIESAENNSIVDVIGIVISVNPSVPILRK-NGMETQRRILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVDVGFFP 314 (560)
Q Consensus 236 ~~i~dI~~~~~~~~VDVIGvV~~V~~~~~i~~k-~G~~~~kr~i~L~D~Sg~~I~vtLWg~~a~~~~~~l~~~~~~~~~~ 314 (560)
.++++|. .+..+-++|+|+.+... ++| .|+. .--++|.|.+| ++++++|.+...++...| ..+.
T Consensus 876 ~~~~~l~---~~~~~~~~~~i~~~~~~---~tk~~g~~--maf~~leD~~g-~ie~~vFp~~y~~~~~~l------~~~~ 940 (1034)
T PRK07279 876 TPISQLV---KNSEATILVQIQSIRVI---RTKTKGQQ--MAFLSVTDTKK-KLDVTLFPETYRQYKDEL------KEGK 940 (1034)
T ss_pred ccHHHHh---cCCcceEEEEEEEEEEE---EEcCCCCe--EEEEEEeeCCC-cEEEEECHHHHHHHHHHh------ccCC
Confidence 3455553 34457788998887654 345 5653 46789999999 799999999776654333 2345
Q ss_pred EEEEEEEEEe
Q 008606 315 VLSVKSGKVN 324 (560)
Q Consensus 315 VV~l~~~rV~ 324 (560)
+|.+++ +|.
T Consensus 941 ~~~v~G-~v~ 949 (1034)
T PRK07279 941 FYYLKG-KIQ 949 (1034)
T ss_pred EEEEEE-EEE
Confidence 666654 554
No 220
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=32.39 E-value=19 Score=33.30 Aligned_cols=27 Identities=37% Similarity=0.929 Sum_probs=20.2
Q ss_pred EeCCCCCcCccccCceeeecCC--------eeecCcCCCcc
Q 008606 417 YTACPLMIGDRQCNKKVTQSGN--------RWQCDRCNQEI 449 (560)
Q Consensus 417 Y~aC~~~~~~~~C~KKv~~~~~--------~~~C~kC~~~~ 449 (560)
+.-|| .|+++.+.... .+.|+.|+..+
T Consensus 99 ~Y~Cp------~C~~~y~~~ea~~~~d~~~~f~Cp~Cg~~l 133 (147)
T smart00531 99 YYKCP------NCQSKYTFLEANQLLDMDGTFTCPRCGEEL 133 (147)
T ss_pred EEECc------CCCCEeeHHHHHHhcCCCCcEECCCCCCEE
Confidence 44589 89999876432 29999999865
No 221
>COG4085 Predicted RNA-binding protein, contains TRAM domain [General function prediction only]
Probab=32.37 E-value=50 Score=31.97 Aligned_cols=26 Identities=23% Similarity=0.224 Sum_probs=23.4
Q ss_pred EEEEEEEeCCCeEEEEEehhhhhhhc
Q 008606 457 LLQAQIQDQTGLTWVTAFQESGEEIL 482 (560)
Q Consensus 457 ~l~~~i~D~Tgs~~~~~Fd~~ae~ll 482 (560)
+.++.+.|+||++.|.+|.+.++.|+
T Consensus 71 i~~l~lndgtGti~vva~~~tee~l~ 96 (204)
T COG4085 71 IESLVLNDGTGTITVVASRSTEETLE 96 (204)
T ss_pred eEEEEEECCCCcEEEEEecChhHhHh
Confidence 45789999999999999999998887
No 222
>COG2824 PhnA Uncharacterized Zn-ribbon-containing protein involved in phosphonate metabolism [Inorganic ion transport and metabolism]
Probab=32.27 E-value=50 Score=28.82 Aligned_cols=28 Identities=29% Similarity=0.768 Sum_probs=22.8
Q ss_pred EeCCCCCcCccccCceeeecCC-eeecCcCCCccC
Q 008606 417 YTACPLMIGDRQCNKKVTQSGN-RWQCDRCNQEID 450 (560)
Q Consensus 417 Y~aC~~~~~~~~C~KKv~~~~~-~~~C~kC~~~~~ 450 (560)
-+-|| +|+.--+.+++ .+.|+.|...+.
T Consensus 3 lp~cp------~c~sEytYed~~~~~cpec~~ew~ 31 (112)
T COG2824 3 LPPCP------KCNSEYTYEDGGQLICPECAHEWN 31 (112)
T ss_pred CCCCC------ccCCceEEecCceEeCchhccccc
Confidence 46799 99887776655 999999998775
No 223
>PRK06556 vitamin B12-dependent ribonucleotide reductase; Validated
Probab=31.98 E-value=30 Score=41.64 Aligned_cols=29 Identities=24% Similarity=0.699 Sum_probs=25.1
Q ss_pred eEEeCCCCCcCccccCceeeecCCeeecCcCCCcc
Q 008606 415 FCYTACPLMIGDRQCNKKVTQSGNRWQCDRCNQEI 449 (560)
Q Consensus 415 ~~Y~aC~~~~~~~~C~KKv~~~~~~~~C~kC~~~~ 449 (560)
..-+.|+ .|+.|+..++..|.|+.|+.+.
T Consensus 922 ~~~~~c~------~c~~~~~~~g~c~~c~~cg~t~ 950 (953)
T PRK06556 922 ADAPLCP------TCGTKMVRNGSCYVCEGCGSTS 950 (953)
T ss_pred ccCCcCC------CccCeeeECCceEeccCCCCCC
Confidence 4456799 9999999999999999999764
No 224
>KOG2593 consensus Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=31.96 E-value=24 Score=38.07 Aligned_cols=29 Identities=31% Similarity=0.825 Sum_probs=21.7
Q ss_pred eEEeCCCCCcCccccCceee---------ecCCeeecCcCCCcc
Q 008606 415 FCYTACPLMIGDRQCNKKVT---------QSGNRWQCDRCNQEI 449 (560)
Q Consensus 415 ~~Y~aC~~~~~~~~C~KKv~---------~~~~~~~C~kC~~~~ 449 (560)
---..|| .|+||-+ ...+.++|+.|+..+
T Consensus 126 ~~~Y~Cp------~C~kkyt~Lea~~L~~~~~~~F~C~~C~gel 163 (436)
T KOG2593|consen 126 VAGYVCP------NCQKKYTSLEALQLLDNETGEFHCENCGGEL 163 (436)
T ss_pred cccccCC------ccccchhhhHHHHhhcccCceEEEecCCCch
Confidence 3455799 8999943 334589999999875
No 225
>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain. This domain contains a CXXCX(19)CXXC motif suggestive of both zinc fingers and thioredoxin, usually found at the N-terminus of prokaryotic proteins. One partially characterized gene, agmX, is among a large set in Myxococcus whose interruption affects adventurous gliding motility.
Probab=31.85 E-value=32 Score=23.79 Aligned_cols=26 Identities=19% Similarity=0.701 Sum_probs=19.0
Q ss_pred eCCCCCcCccccCceeeecC-------CeeecCcCCCcc
Q 008606 418 TACPLMIGDRQCNKKVTQSG-------NRWQCDRCNQEI 449 (560)
Q Consensus 418 ~aC~~~~~~~~C~KKv~~~~-------~~~~C~kC~~~~ 449 (560)
..|| .|+.+..-.. ....|++|+..+
T Consensus 3 ~~CP------~C~~~~~v~~~~~~~~~~~v~C~~C~~~~ 35 (38)
T TIGR02098 3 IQCP------NCKTSFRVVDSQLGANGGKVRCGKCGHVW 35 (38)
T ss_pred EECC------CCCCEEEeCHHHcCCCCCEEECCCCCCEE
Confidence 5799 9999665432 258999999764
No 226
>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=31.79 E-value=58 Score=25.06 Aligned_cols=20 Identities=25% Similarity=0.310 Sum_probs=18.3
Q ss_pred EEEEEEEEeCCCeEEEEEeh
Q 008606 456 YLLQAQIQDQTGLTWVTAFQ 475 (560)
Q Consensus 456 Y~l~~~i~D~Tgs~~~~~Fd 475 (560)
-.+.+.+.|++|.+.++.|+
T Consensus 18 ~~~~~~~~D~~g~i~~~~F~ 37 (75)
T cd04488 18 RRLKVTLSDGTGTLTLVFFN 37 (75)
T ss_pred cEEEEEEEcCCCEEEEEEEC
Confidence 36899999999999999997
No 227
>PRK14811 formamidopyrimidine-DNA glycosylase; Provisional
Probab=31.70 E-value=24 Score=36.06 Aligned_cols=25 Identities=24% Similarity=0.799 Sum_probs=19.5
Q ss_pred eCCCCCcCccccCceeeec--C--CeeecCcCCCc
Q 008606 418 TACPLMIGDRQCNKKVTQS--G--NRWQCDRCNQE 448 (560)
Q Consensus 418 ~aC~~~~~~~~C~KKv~~~--~--~~~~C~kC~~~ 448 (560)
..|| .|+.++... + +.|+|+.|++-
T Consensus 236 ~pC~------~Cg~~I~~~~~~gR~ty~Cp~CQ~~ 264 (269)
T PRK14811 236 QPCP------RCGTPIEKIVVGGRGTHFCPQCQPL 264 (269)
T ss_pred CCCC------cCCCeeEEEEECCCCcEECCCCcCC
Confidence 5799 999888643 2 29999999974
No 228
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=31.35 E-value=33 Score=23.83 Aligned_cols=26 Identities=23% Similarity=0.783 Sum_probs=19.0
Q ss_pred eCCCCCcCccccCceeeecC-------CeeecCcCCCcc
Q 008606 418 TACPLMIGDRQCNKKVTQSG-------NRWQCDRCNQEI 449 (560)
Q Consensus 418 ~aC~~~~~~~~C~KKv~~~~-------~~~~C~kC~~~~ 449 (560)
..|| .|+++-.-.+ ..-.|.+|+..+
T Consensus 3 i~Cp------~C~~~y~i~d~~ip~~g~~v~C~~C~~~f 35 (36)
T PF13717_consen 3 ITCP------NCQAKYEIDDEKIPPKGRKVRCSKCGHVF 35 (36)
T ss_pred EECC------CCCCEEeCCHHHCCCCCcEEECCCCCCEe
Confidence 4699 8998765432 278999999754
No 229
>TIGR02300 FYDLN_acid conserved hypothetical protein TIGR02300. Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=31.23 E-value=29 Score=31.34 Aligned_cols=26 Identities=12% Similarity=0.202 Sum_probs=21.6
Q ss_pred eCCCCCcCccccCceeeecCC-eeecCcCCCcc
Q 008606 418 TACPLMIGDRQCNKKVTQSGN-RWQCDRCNQEI 449 (560)
Q Consensus 418 ~aC~~~~~~~~C~KKv~~~~~-~~~C~kC~~~~ 449 (560)
..|| .|++|...-+- .-.|++|+..+
T Consensus 10 r~Cp------~cg~kFYDLnk~p~vcP~cg~~~ 36 (129)
T TIGR02300 10 RICP------NTGSKFYDLNRRPAVSPYTGEQF 36 (129)
T ss_pred ccCC------CcCccccccCCCCccCCCcCCcc
Confidence 4699 99999887554 78999999876
No 230
>PF12773 DZR: Double zinc ribbon
Probab=31.06 E-value=22 Score=26.16 Aligned_cols=22 Identities=18% Similarity=0.552 Sum_probs=15.4
Q ss_pred ccCceeeecCC-eeecCcCCCcc
Q 008606 428 QCNKKVTQSGN-RWQCDRCNQEI 449 (560)
Q Consensus 428 ~C~KKv~~~~~-~~~C~kC~~~~ 449 (560)
.|+.++..... ...|++|+..+
T Consensus 17 ~CG~~l~~~~~~~~~C~~Cg~~~ 39 (50)
T PF12773_consen 17 HCGTPLPPPDQSKKICPNCGAEN 39 (50)
T ss_pred hhcCChhhccCCCCCCcCCcCCC
Confidence 78888773222 67888888764
No 231
>PF13742 tRNA_anti_2: OB-fold nucleic acid binding domain
Probab=31.04 E-value=3.2e+02 Score=23.25 Aligned_cols=58 Identities=17% Similarity=0.223 Sum_probs=39.8
Q ss_pred EEEEEeCCCeEEEEEehhhhhhhcCCCHHHHHHhhhccCChhHHHHHHHHhcCCeEEEEEEEeeeecCCeeeEEEEEEEe
Q 008606 459 QAQIQDQTGLTWVTAFQESGEEILGCPAKELYMLKYELQDDVRFGEIIRSRVFNQYLFRLKIKEELYGDEQRVKITVIRA 538 (560)
Q Consensus 459 ~~~i~D~Tgs~~~~~Fd~~ae~llG~sA~el~~~~~e~~d~~~~~~~l~~~~~k~~~fkvkvk~e~y~~e~r~k~~v~~~ 538 (560)
-+.+.|+..++.|++|...+..+-|... + + |.+.++.+++ ..|...-+..+.|.++
T Consensus 42 YftLkD~~a~i~~~~~~~~~~~i~~~~l------~--~--------------G~~V~v~g~~--~~y~~~G~~sl~v~~i 97 (99)
T PF13742_consen 42 YFTLKDEEASISCVIFRSRARRIRGFDL------K--D--------------GDKVLVRGRV--SFYEPRGSLSLIVEDI 97 (99)
T ss_pred EEEEEcCCcEEEEEEEHHHHhhCCCCCC------C--C--------------CCEEEEEEEE--EEECCCcEEEEEEEEe
Confidence 4678889999999999988776541111 1 1 4455555555 4666666789999888
Q ss_pred ee
Q 008606 539 DQ 540 (560)
Q Consensus 539 ~~ 540 (560)
+|
T Consensus 98 ~P 99 (99)
T PF13742_consen 98 DP 99 (99)
T ss_pred EC
Confidence 76
No 232
>PLN02221 asparaginyl-tRNA synthetase
Probab=30.90 E-value=5.2e+02 Score=29.51 Aligned_cols=84 Identities=15% Similarity=0.199 Sum_probs=52.2
Q ss_pred CceEEEEEEEEecccceeccCCCCCc--EEEEEEEeCCC-CeEEEEEcchhHHHHHhhcccCcEEEEeeeEEecCCCccc
Q 008606 126 GRWAIKARVTAKGDLRRYNNARGDGK--VFSFDLLDSDG-GEIRVTCFNAVVDRFYEIIEVGRVYLISKGSLKPAQKNFN 202 (560)
Q Consensus 126 ~~w~Ik~RV~~k~~ir~~~n~~g~gk--vf~~~L~D~~g-~~I~at~~~~~~~kf~~~l~eG~vY~Is~~~V~~a~~~y~ 202 (560)
..-+|+|.|-++ |. .|+ +.=++|.|..+ +.|++++..+.. .....|..|.++.+.+-.+..... .
T Consensus 51 ~~V~I~GWV~~i---R~------~Gk~~i~Fl~LRDgs~~g~iQvVv~~~~~-~~~~~L~~ES~V~V~G~V~~~~~~--~ 118 (572)
T PLN02221 51 QKVRIGGWVKTG---RE------QGKGTFAFLEVNDGSCPANLQVMVDSSLY-DLSTLVATGTCVTVDGVLKVPPEG--K 118 (572)
T ss_pred CEEEEEEEEEeh---hh------CCCceEEEEEEeCCcccccEEEEEcCchh-hHHhcCCCceEEEEEEEEEeCCcc--C
Confidence 467888888653 32 233 33356888543 689999875422 223468899999998744332211 1
Q ss_pred cCCCeeEEEEcccceEEec
Q 008606 203 HLKNEWEIFLEATSTVDLC 221 (560)
Q Consensus 203 ~~~~~yeI~f~~~T~I~~~ 221 (560)
...+.+||..+.-..+-.+
T Consensus 119 ~~~~~iEl~v~~i~vl~~a 137 (572)
T PLN02221 119 GTKQKIELSVEKVIDVGTV 137 (572)
T ss_pred CCCccEEEEEeEEEEEecC
Confidence 1345899999766666655
No 233
>TIGR01384 TFS_arch transcription factor S, archaeal. There has been an apparent duplication event in the Halobacteriaceae lineage (Haloarcula, Haloferax, Haloquadratum, Halobacterium and Natromonas). There appears to be a separate duplication in Methanosphaera stadtmanae.
Probab=30.80 E-value=54 Score=28.12 Aligned_cols=25 Identities=28% Similarity=0.745 Sum_probs=21.2
Q ss_pred CCCCCcCccccCceeeecCCeeecCcCCCcc
Q 008606 419 ACPLMIGDRQCNKKVTQSGNRWQCDRCNQEI 449 (560)
Q Consensus 419 aC~~~~~~~~C~KKv~~~~~~~~C~kC~~~~ 449 (560)
=|| .|+.-+....+.+.|+.|+...
T Consensus 2 fC~------~Cg~~l~~~~~~~~C~~C~~~~ 26 (104)
T TIGR01384 2 FCP------KCGSLMTPKNGVYVCPSCGYEK 26 (104)
T ss_pred CCc------ccCcccccCCCeEECcCCCCcc
Confidence 389 8999998876799999999764
No 234
>COG1190 LysU Lysyl-tRNA synthetase (class II) [Translation, ribosomal structure and biogenesis]
Probab=30.37 E-value=1.4e+02 Score=33.14 Aligned_cols=85 Identities=18% Similarity=0.275 Sum_probs=54.6
Q ss_pred ccCCCCCceEEEEEEEEecccceeccCCCCCcEEEEEEEeCCCCeEEEEEcch-----hHHHHHhhcccCcEEEEeeeEE
Q 008606 120 ALNPYQGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNA-----VVDRFYEIIEVGRVYLISKGSL 194 (560)
Q Consensus 120 ~L~p~~~~w~Ik~RV~~k~~ir~~~n~~g~gkvf~~~L~D~~g~~I~at~~~~-----~~~kf~~~l~eG~vY~Is~~~V 194 (560)
+|..-....+|.+||+.+ |. -||+.=++|.| .+++|++-+-.+ ..+.+...+..||++.+.+.-.
T Consensus 56 el~~~~~~v~vAGRi~~~---R~------~GK~~F~~i~d-~~gkiQ~yi~k~~~~~~~~~~~~~~~dlGDiigv~G~~~ 125 (502)
T COG1190 56 ELEALNIEVSVAGRIMTI---RN------MGKASFADLQD-GSGKIQLYVNKDEVGEEVFEALFKKLDLGDIIGVEGPLF 125 (502)
T ss_pred hhhhccceeEEecceeee---cc------cCceeEEEEec-CCceEEEEEeccccchhhHHHHHhccccCCEEeeeeeee
Confidence 333333338899999864 33 35655567888 777999999865 3444566778999999988655
Q ss_pred ecCCCccccCCCeeEEEEcccceEEec
Q 008606 195 KPAQKNFNHLKNEWEIFLEATSTVDLC 221 (560)
Q Consensus 195 ~~a~~~y~~~~~~yeI~f~~~T~I~~~ 221 (560)
+.. ....-+..+..+.+..|
T Consensus 126 ~T~-------~GelSv~v~~~~lLsKs 145 (502)
T COG1190 126 KTK-------TGELSVSVEELRLLSKS 145 (502)
T ss_pred ecC-------CCceEEEEEEEeeeccc
Confidence 433 34455555554444443
No 235
>PF11781 RRN7: RNA polymerase I-specific transcription initiation factor Rrn7; InterPro: IPR021752 Rrn7 is a transcription binding factor that associates strongly with both Rrn6 and Rrn11 to form a complex which itself binds the TATA-binding protein and is required for transcription by the core domain of the RNA PolI promoter [],[].
Probab=30.22 E-value=39 Score=23.55 Aligned_cols=24 Identities=33% Similarity=0.909 Sum_probs=18.0
Q ss_pred CCCCCcCccccCceeeecCC-eeecCcCCCc
Q 008606 419 ACPLMIGDRQCNKKVTQSGN-RWQCDRCNQE 448 (560)
Q Consensus 419 aC~~~~~~~~C~KKv~~~~~-~~~C~kC~~~ 448 (560)
.|+ .|+.......+ .|+|.+|+..
T Consensus 10 ~C~------~C~~~~~~~~dG~~yC~~cG~~ 34 (36)
T PF11781_consen 10 PCP------VCGSRWFYSDDGFYYCDRCGHQ 34 (36)
T ss_pred cCC------CCCCeEeEccCCEEEhhhCceE
Confidence 588 89887655444 9999999853
No 236
>PF07282 OrfB_Zn_ribbon: Putative transposase DNA-binding domain; InterPro: IPR010095 This entry represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by IPR001959 from INTERPRO, and other proteins. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=30.02 E-value=38 Score=26.67 Aligned_cols=29 Identities=28% Similarity=0.870 Sum_probs=22.9
Q ss_pred eEEeCCCCCcCccccCceeee--cCCeeecCcCCCcc
Q 008606 415 FCYTACPLMIGDRQCNKKVTQ--SGNRWQCDRCNQEI 449 (560)
Q Consensus 415 ~~Y~aC~~~~~~~~C~KKv~~--~~~~~~C~kC~~~~ 449 (560)
+....|| .|+..+.. ....|.|+.|+...
T Consensus 26 ~TSq~C~------~CG~~~~~~~~~r~~~C~~Cg~~~ 56 (69)
T PF07282_consen 26 YTSQTCP------RCGHRNKKRRSGRVFTCPNCGFEM 56 (69)
T ss_pred CCccCcc------CcccccccccccceEEcCCCCCEE
Confidence 4677799 99998877 33399999999754
No 237
>PF11325 DUF3127: Domain of unknown function (DUF3127); InterPro: IPR021474 This bacterial family of proteins has no known function.
Probab=29.79 E-value=2.4e+02 Score=23.71 Aligned_cols=59 Identities=17% Similarity=0.100 Sum_probs=38.0
Q ss_pred EEEEEEEecccceeccCCCCCcEEEEEEEe--CCCCeEEEEEcchhHHHHHhhcccCcEEEEe
Q 008606 130 IKARVTAKGDLRRYNNARGDGKVFSFDLLD--SDGGEIRVTCFNAVVDRFYEIIEVGRVYLIS 190 (560)
Q Consensus 130 Ik~RV~~k~~ir~~~n~~g~gkvf~~~L~D--~~g~~I~at~~~~~~~kf~~~l~eG~vY~Is 190 (560)
|.|+|+.+-+..+-..++| =+--+|+|-- .--..|...+|++-++.+. .+++|+.+.++
T Consensus 2 i~Gkii~~l~~~~g~s~~G-w~Kre~Vlet~~qYP~~i~f~~~~dk~~~l~-~~~~Gd~V~Vs 62 (84)
T PF11325_consen 2 ITGKIIKVLPEQQGVSKNG-WKKREFVLETEEQYPQKICFEFWGDKIDLLD-NFQVGDEVKVS 62 (84)
T ss_pred cccEEEEEecCcccCcCCC-cEEEEEEEeCCCcCCceEEEEEEcchhhhhc-cCCCCCEEEEE
Confidence 6788777766554333333 2233444442 1237899999998888754 48899998886
No 238
>COG1107 Archaea-specific RecJ-like exonuclease, contains DnaJ-type Zn finger domain [DNA replication, recombination, and repair]
Probab=29.52 E-value=54 Score=36.95 Aligned_cols=69 Identities=26% Similarity=0.298 Sum_probs=53.9
Q ss_pred CcceeccccCCCC-CceEEEEEEEEecccceeccCCCCCcEEEEEEEeCCCCeEEEEEcchhHHHHHhhcccCcEEEEee
Q 008606 113 ARIIPIAALNPYQ-GRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISK 191 (560)
Q Consensus 113 ~~~~pI~~L~p~~-~~w~Ik~RV~~k~~ir~~~n~~g~gkvf~~~L~D~~g~~I~at~~~~~~~kf~~~l~eG~vY~Is~ 191 (560)
...+.|.+|..+. ...+|++.|++. ++-. | .--|+|.| +++.|.|..|-+.--+-|+-|++|+++.+++
T Consensus 200 ~~r~~i~~id~~ig~tV~I~GeV~qi---kqT~---G---PTVFtltD-etg~i~aAAFe~aGvRAyP~IevGdiV~ViG 269 (715)
T COG1107 200 LPRTLIDDLDEMIGKTVRIEGEVTQI---KQTS---G---PTVFTLTD-ETGAIWAAAFEEAGVRAYPEIEVGDIVEVIG 269 (715)
T ss_pred cccccHHHHHhhcCceEEEEEEEEEE---EEcC---C---CEEEEEec-CCCceehhhhccCCcccCCCCCCCceEEEEE
Confidence 4555677787765 368899999974 4432 2 24467899 7899999999998889999999999999986
No 239
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=29.32 E-value=26 Score=27.29 Aligned_cols=8 Identities=25% Similarity=1.252 Sum_probs=5.7
Q ss_pred eeecCcCC
Q 008606 439 RWQCDRCN 446 (560)
Q Consensus 439 ~~~C~kC~ 446 (560)
.|.|++|+
T Consensus 50 ~Y~Cp~CG 57 (61)
T COG2888 50 PYRCPKCG 57 (61)
T ss_pred ceECCCcC
Confidence 67777776
No 240
>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=28.71 E-value=67 Score=29.29 Aligned_cols=28 Identities=25% Similarity=0.399 Sum_probs=23.7
Q ss_pred cEEEEEEEeCCCCeEEEEEcchhHHHHHh
Q 008606 151 KVFSFDLLDSDGGEIRVTCFNAVVDRFYE 179 (560)
Q Consensus 151 kvf~~~L~D~~g~~I~at~~~~~~~kf~~ 179 (560)
-.+++.+.| ..|.+.+++|++.++++-.
T Consensus 54 y~l~~~i~D-~tg~~~~~~F~~~a~~l~G 81 (146)
T PF08646_consen 54 YRLSLKISD-GTGSIWVTLFDEEAEQLLG 81 (146)
T ss_dssp EEEEEEEEE-TTEEEEEEEEHHHHHHHHC
T ss_pred EEEEEEEEe-CCCeEEEEEEhHHHHHHhC
Confidence 357888999 6789999999999988763
No 241
>PF03107 C1_2: C1 domain; InterPro: IPR004146 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in DAG_PE-bind (IPR002219 from INTERPRO), therefore we have termed this domain DC1 for divergent C1 domain. This domain probably also binds to two zinc ions. The function of proteins with this domain is uncertain, however this domain may bind to molecules such as diacylglycerol. This family are found in plant proteins.
Probab=27.90 E-value=38 Score=22.35 Aligned_cols=18 Identities=22% Similarity=0.661 Sum_probs=15.3
Q ss_pred ccCceeeecCCeeecCcCC
Q 008606 428 QCNKKVTQSGNRWQCDRCN 446 (560)
Q Consensus 428 ~C~KKv~~~~~~~~C~kC~ 446 (560)
.|.|++.... .|+|+.|+
T Consensus 5 ~C~~~~~~~~-~Y~C~~c~ 22 (30)
T PF03107_consen 5 VCRRKIDGFY-FYHCSECC 22 (30)
T ss_pred CCCCCcCCCE-eEEeCCCC
Confidence 8999988775 79999887
No 242
>PRK00036 primosomal replication protein N; Reviewed
Probab=27.73 E-value=3e+02 Score=24.15 Aligned_cols=70 Identities=13% Similarity=0.129 Sum_probs=50.2
Q ss_pred CceEEEEEEEEecccceeccCCCCCcEEEEEEEeC-----C------CCeEEEEEcchhHHHHHhhcccCcEEEEeeeEE
Q 008606 126 GRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDS-----D------GGEIRVTCFNAVVDRFYEIIEVGRVYLISKGSL 194 (560)
Q Consensus 126 ~~w~Ik~RV~~k~~ir~~~n~~g~gkvf~~~L~D~-----~------g~~I~at~~~~~~~kf~~~l~eG~vY~Is~~~V 194 (560)
+.+.+.|+|+....+| |+ +-|- .+.+|.|--. - --+|.|.+.++.++++.+ +..|..+.+++|.-
T Consensus 2 N~l~Ltg~v~~~~~lr-yT-PAGI-p~~~~~LeH~S~q~EAG~~Rqv~~~i~ava~G~~a~~~~~-l~~Gs~v~v~GFLa 77 (107)
T PRK00036 2 NTLELSARVLECGAMR-HT-PAGL-PALELLLVHESEVVEAGHPRRVELTISAVALGDLALLLAD-TPLGTEMQVQGFLA 77 (107)
T ss_pred CEEEEEEEEeccCccc-cC-CCCC-ceEEEEEEEeEEeEeCCCcceEEEEEEEEEEhhHHHHhcc-cCCCCEEEEEEEEE
Confidence 5688999999876655 43 3332 4667766321 1 247889999988888886 99999999999987
Q ss_pred ecCCC
Q 008606 195 KPAQK 199 (560)
Q Consensus 195 ~~a~~ 199 (560)
...++
T Consensus 78 ~~~~~ 82 (107)
T PRK00036 78 PARKD 82 (107)
T ss_pred ECCCC
Confidence 64433
No 243
>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=27.49 E-value=2.1e+02 Score=28.07 Aligned_cols=55 Identities=22% Similarity=0.411 Sum_probs=36.7
Q ss_pred EEEecCCCcEEEEEEeCcchhhhhhhHHhhhccCCccEEEEEEEEEecCCCc--eecccCCeEEEECCCh
Q 008606 278 LNLKDTSGRSVELTLWGDFCNKEGQKLQEMVDVGFFPVLSVKSGKVNDFSGK--SIGTIPSTQLFINPDF 345 (560)
Q Consensus 278 i~L~D~Sg~~I~vtLWg~~a~~~~~~l~~~~~~~~~~VV~l~~~rV~~f~G~--sLs~~~~S~i~iNPdi 345 (560)
+.+.|.++....|.|||+.+.- ....|++|.+-+ +|.+. .+-....--++++||+
T Consensus 2 l~~~~~~~~~~~v~L~~~W~~t---------~v~~Gd~I~ii~----~~~~~~~~~v~~~~~~lIl~PD~ 58 (209)
T PF08696_consen 2 LVCSESSGETRTVILRDEWCET---------PVSPGDIIHIIG----EFDDDDPCIVDNDSNLLILHPDI 58 (209)
T ss_pred eEeecCCCCeEEEEEeCCcccC---------CCcCCCEEEEEE----EeCCCCCEEEeCCCCEEEEcCCc
Confidence 4567888899999999999764 224678887766 44443 2222222367889984
No 244
>PRK06642 single-stranded DNA-binding protein; Provisional
Probab=27.29 E-value=4.7e+02 Score=24.24 Aligned_cols=72 Identities=13% Similarity=0.061 Sum_probs=38.5
Q ss_pred ceeEEEEEEEEecCceeEeeccCceeeEEEEEEe----cC-CC------cEEEEEEeCc-chhhhhhhHHhhhccCCccE
Q 008606 248 SIVDVIGIVISVNPSVPILRKNGMETQRRILNLK----DT-SG------RSVELTLWGD-FCNKEGQKLQEMVDVGFFPV 315 (560)
Q Consensus 248 ~~VDVIGvV~~V~~~~~i~~k~G~~~~kr~i~L~----D~-Sg------~~I~vtLWg~-~a~~~~~~l~~~~~~~~~~V 315 (560)
..|-+||.|..--.++ .+.+|+...+-.|-.- |. +| .-+.|++||+ .|+...++| ..+..
T Consensus 6 N~V~LiGrLg~DPElr--~t~~G~~v~~fslAv~~~~k~~~~G~~~~~T~w~~v~~~g~~~Ae~~~~~l------~KG~~ 77 (152)
T PRK06642 6 NKVILIGNVGRDPEIR--TTGEGKKIINLSLATTETWKDRITSERKERTEWHRVVIFSEGLVSVVERYV------TKGSK 77 (152)
T ss_pred eEEEEEEEccCCceEE--ECCCCCEEEEEEEEeccccccccCCccccceeEEEEEEeChHHHHHHHHhC------CCCCE
Confidence 3567888888732222 2345654333222221 21 12 2589999997 676643332 35666
Q ss_pred EEEE-EEEEecCC
Q 008606 316 LSVK-SGKVNDFS 327 (560)
Q Consensus 316 V~l~-~~rV~~f~ 327 (560)
|++. ..+...|.
T Consensus 78 V~V~GrL~~~~y~ 90 (152)
T PRK06642 78 LYIEGSLQTRKWN 90 (152)
T ss_pred EEEEEEEEeCeeE
Confidence 6665 44556674
No 245
>KOG3108 consensus Single-stranded DNA-binding replication protein A (RPA), medium (30 kD) subunit [Replication, recombination and repair]
Probab=26.89 E-value=2.5e+02 Score=28.78 Aligned_cols=67 Identities=27% Similarity=0.489 Sum_probs=43.0
Q ss_pred ceeEEEEEEEEecCceeEeeccCceeeEEEEEEecCCCcEEEEEEeCcchhhhhhhHHhhhccCCccEE----EEE-EEE
Q 008606 248 SIVDVIGIVISVNPSVPILRKNGMETQRRILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVDVGFFPVL----SVK-SGK 322 (560)
Q Consensus 248 ~~VDVIGvV~~V~~~~~i~~k~G~~~~kr~i~L~D~Sg~~I~vtLWg~~a~~~~~~l~~~~~~~~~~VV----~l~-~~r 322 (560)
..|-++|+|..+.... ....++|.|.+| .|+|..|-...... . ..+.| .+| .+.
T Consensus 69 ~~v~~VGivr~~e~~~----------t~i~y~I~D~tg-~id~r~W~~~~~~~----~------e~~~l~~~~yVkv~G~ 127 (265)
T KOG3108|consen 69 SAVSIVGIVRNIEKSA----------TNITYEIEDGTG-QIDVRQWFHDNAES----E------EMPALETGTYVKVYGH 127 (265)
T ss_pred EEEEEEEEEEeceecC----------cceEEEEecCcc-cEEEEEeccccchh----h------hCcccccCcEEEeeec
Confidence 3567778887766542 345789999999 59999999876541 1 11222 233 445
Q ss_pred EecCCCc-eecccC
Q 008606 323 VNDFSGK-SIGTIP 335 (560)
Q Consensus 323 V~~f~G~-sLs~~~ 335 (560)
++.|+|+ +|....
T Consensus 128 Lk~f~Gk~sl~~fk 141 (265)
T KOG3108|consen 128 LKPFQGKKSLQVFK 141 (265)
T ss_pred ccCCCCceeEEEEe
Confidence 6678886 665543
No 246
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=26.85 E-value=47 Score=22.92 Aligned_cols=20 Identities=30% Similarity=0.785 Sum_probs=12.1
Q ss_pred ccCceeee---cCC---eeecCcCCC
Q 008606 428 QCNKKVTQ---SGN---RWQCDRCNQ 447 (560)
Q Consensus 428 ~C~KKv~~---~~~---~~~C~kC~~ 447 (560)
+|+..+.. .++ .+.|+.|+.
T Consensus 5 ~CG~~l~~~ip~gd~r~R~vC~~Cg~ 30 (34)
T PF14803_consen 5 QCGGPLERRIPEGDDRERLVCPACGF 30 (34)
T ss_dssp TT--B-EEE--TT-SS-EEEETTTTE
T ss_pred cccChhhhhcCCCCCccceECCCCCC
Confidence 89887764 233 899999984
No 247
>PF08772 NOB1_Zn_bind: Nin one binding (NOB1) Zn-ribbon like; InterPro: IPR014881 This entry corresponds to a zinc ribbon and is found on the RNA binding protein NOB1. ; PDB: 2CON_A.
Probab=26.59 E-value=57 Score=26.63 Aligned_cols=37 Identities=16% Similarity=0.385 Sum_probs=11.9
Q ss_pred ccCceeeecCCeeecCcCCCccCCceeEEEEEEEEEeCCCeEEE
Q 008606 428 QCNKKVTQSGNRWQCDRCNQEIDECDYRYLLQAQIQDQTGLTWV 471 (560)
Q Consensus 428 ~C~KKv~~~~~~~~C~kC~~~~~~~~~rY~l~~~i~D~Tgs~~~ 471 (560)
.|.+ ++.+.+..+|++|+... -.++.+.+. .+|++.+
T Consensus 14 aCf~-~t~~~~k~FCp~CGn~T-----L~rvsvsv~-~~G~~~~ 50 (73)
T PF08772_consen 14 ACFK-ITKDMTKQFCPKCGNAT-----LKRVSVSVD-EDGKIKL 50 (73)
T ss_dssp SS---EES-SS--S-SSS--S-------EEEE-B---SS---B-
T ss_pred cccc-CcCCCCceeCcccCCCc-----ceEEEEEEC-CCCCEEE
Confidence 6776 44455589999999742 234444433 5555443
No 248
>COG1570 XseA Exonuclease VII, large subunit [DNA replication, recombination, and repair]
Probab=26.29 E-value=1.4e+02 Score=32.72 Aligned_cols=91 Identities=24% Similarity=0.381 Sum_probs=58.7
Q ss_pred cceeccccCCCCCceE--EEEEEEEecccceeccCCCCCcEEEEEEEeCCCCeEEEEEcchhHHHHHhhcccCcEEEEee
Q 008606 114 RIIPIAALNPYQGRWA--IKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISK 191 (560)
Q Consensus 114 ~~~pI~~L~p~~~~w~--Ik~RV~~k~~ir~~~n~~g~gkvf~~~L~D~~g~~I~at~~~~~~~kf~~~l~eG~vY~Is~ 191 (560)
.+.+++.||-+...|- --+.|--++++-.|+.+. .| ...|.|-| +...|+|++|.....++.-.+++|.-+.+.+
T Consensus 4 ~~~sVSeln~~ik~llE~~~~~V~v~GEISn~t~~~-sg-H~YFtLKD-~~A~i~c~mf~~~~~~l~f~p~eG~~V~v~G 80 (440)
T COG1570 4 KILSVSELNDYIKRLLERDLGQVWVRGEISNFTRPA-SG-HLYFTLKD-ERAQIRCVMFKGNNRRLKFRPEEGMQVLVRG 80 (440)
T ss_pred CeecHHHHHHHHHHHHHhcCCeEEEEEEecCCccCC-Cc-cEEEEEcc-CCceEEEEEEcCcccccCCCccCCCEEEEEE
Confidence 4556666666543211 022333344444554332 34 79999999 7899999999998888777899998877765
Q ss_pred -eEEecCCCccccCCCeeEEEEcc
Q 008606 192 -GSLKPAQKNFNHLKNEWEIFLEA 214 (560)
Q Consensus 192 -~~V~~a~~~y~~~~~~yeI~f~~ 214 (560)
.++-+. ..+|.|..+.
T Consensus 81 ~is~Y~~-------rG~YQi~~~~ 97 (440)
T COG1570 81 KISLYEP-------RGDYQIVAES 97 (440)
T ss_pred EEEEEcC-------CCceEEEEec
Confidence 344443 3567777753
No 249
>PRK00420 hypothetical protein; Validated
Probab=25.67 E-value=50 Score=29.25 Aligned_cols=28 Identities=14% Similarity=0.331 Sum_probs=22.3
Q ss_pred EEeCCCCCcCccccCceeee-cCCeeecCcCCCcc
Q 008606 416 CYTACPLMIGDRQCNKKVTQ-SGNRWQCDRCNQEI 449 (560)
Q Consensus 416 ~Y~aC~~~~~~~~C~KKv~~-~~~~~~C~kC~~~~ 449 (560)
....|| .|+--+.. ..+..+|+.|+...
T Consensus 22 l~~~CP------~Cg~pLf~lk~g~~~Cp~Cg~~~ 50 (112)
T PRK00420 22 LSKHCP------VCGLPLFELKDGEVVCPVHGKVY 50 (112)
T ss_pred ccCCCC------CCCCcceecCCCceECCCCCCee
Confidence 347899 99988877 55589999999743
No 250
>PF13842 Tnp_zf-ribbon_2: DDE_Tnp_1-like zinc-ribbon
Probab=25.57 E-value=42 Score=22.71 Aligned_cols=21 Identities=29% Similarity=0.822 Sum_probs=15.4
Q ss_pred ccCceeeecCCeeecCcCCCc
Q 008606 428 QCNKKVTQSGNRWQCDRCNQE 448 (560)
Q Consensus 428 ~C~KKv~~~~~~~~C~kC~~~ 448 (560)
.|.++-......|+|+.|+..
T Consensus 5 vC~~~k~rk~T~~~C~~C~v~ 25 (32)
T PF13842_consen 5 VCSKKKRRKDTRYMCSKCDVP 25 (32)
T ss_pred ECCcCCccceeEEEccCCCCc
Confidence 787765555468999999743
No 251
>PF06827 zf-FPG_IleRS: Zinc finger found in FPG and IleRS; InterPro: IPR010663 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger domain found at the C-terminal in both DNA glycosylase/AP lyase enzymes and in isoleucyl tRNA synthetase. In these two types of enzymes, the C-terminal domain forms a zinc finger. Some related proteins may not bind zinc. DNA glycosylase/AP lyase enzymes are involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. These enzymes have both DNA glycosylase activity (3.2.2 from EC) and AP lyase activity (4.2.99.18 from EC) []. Examples include formamidopyrimidine-DNA glycosylases (Fpg; MutM) and endonuclease VIII (Nei). Formamidopyrimidine-DNA glycosylases (Fpg, MutM) is a trifunctional DNA base excision repair enzyme that removes a wide range of oxidation-damaged bases (N-glycosylase activity; 3.2.2.23 from EC) and cleaves both the 3'- and 5'-phosphodiester bonds of the resulting apurinic/apyrimidinic site (AP lyase activity; 4.2.99.18 from EC). Fpg has a preference for oxidised purines, excising oxidized purine bases such as 7,8-dihydro-8-oxoguanine (8-oxoG). ITs AP (apurinic/apyrimidinic) lyase activity introduces nicks in the DNA strand, cleaving the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3'- and 5'-phosphates. Fpg is a monomer composed of 2 domains connected by a flexible hinge []. The two DNA-binding motifs (a zinc finger and the helix-two-turns-helix motifs) suggest that the oxidized base is flipped out from double-stranded DNA in the binding mode and excised by a catalytic mechanism similar to that of bifunctional base excision repair enzymes []. Fpg binds one ion of zinc at the C terminus, which contains four conserved and essential cysteines []. Endonuclease VIII (Nei) has the same enzyme activities as Fpg above, but with a preference for oxidized pyrimidines, such as thymine glycol, 5,6-dihydrouracil and 5,6-dihydrothymine [, ]. An Fpg-type zinc finger is also found at the C terminus of isoleucyl tRNA synthetase (6.1.1.5 from EC) [, ]. This enzyme catalyses the attachment of isoleucine to tRNA(Ile). As IleRS can inadvertently accommodate and process structurally similar amino acids such as valine, to avoid such errors it has two additional distinct tRNA(Ile)-dependent editing activities. One activity is designated as 'pre-transfer' editing and involves the hydrolysis of activated Val-AMP. The other activity is designated 'post-transfer' editing and involves deacylation of mischarged Val-tRNA(Ile) []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003824 catalytic activity; PDB: 1K82_C 1Q39_A 2OQ4_B 2OPF_A 1K3X_A 1K3W_A 1Q3B_A 2EA0_A 1Q3C_A 2XZF_A ....
Probab=25.55 E-value=33 Score=22.54 Aligned_cols=24 Identities=29% Similarity=0.890 Sum_probs=14.0
Q ss_pred eCCCCCcCccccCceeeecCC----eeecCcCCC
Q 008606 418 TACPLMIGDRQCNKKVTQSGN----RWQCDRCNQ 447 (560)
Q Consensus 418 ~aC~~~~~~~~C~KKv~~~~~----~~~C~kC~~ 447 (560)
..|+ .|...+..... .++|++|.+
T Consensus 2 ~~C~------rC~~~~~~~~~~~r~~~~C~rCq~ 29 (30)
T PF06827_consen 2 EKCP------RCWNYIEDIGINGRSTYLCPRCQK 29 (30)
T ss_dssp SB-T------TT--BBEEEEETTEEEEE-TTTCC
T ss_pred CcCc------cCCCcceEeEecCCCCeECcCCcC
Confidence 3688 89887755332 899999974
No 252
>PF01599 Ribosomal_S27: Ribosomal protein S27a; InterPro: IPR002906 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 [, ]. This family of ribosomal proteins consists mainly of the 40S ribosomal protein S27a which is synthesized as a C-terminal extension of ubiquitin (CEP) (IPR000626 from INTERPRO). The S27a domain compromises the C-terminal half of the protein. The synthesis of ribosomal proteins as extensions of ubiquitin promotes their incorporation into nascent ribosomes by a transient metabolic stabilisation and is required for efficient ribosome biogenesis []. The ribosomal extension protein S27a contains a basic region that is proposed to form a zinc finger; its fusion gene is proposed as a mechanism to maintain a fixed ratio between ubiquitin necessary for degrading proteins and ribosomes a source of proteins [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2K4X_A 3U5C_f 3U5G_f 2XZN_9 2XZM_9.
Probab=25.50 E-value=70 Score=23.82 Aligned_cols=26 Identities=23% Similarity=0.745 Sum_probs=17.7
Q ss_pred eCCCCCcCccccCce--eeecCCeeecCcCCC
Q 008606 418 TACPLMIGDRQCNKK--VTQSGNRWQCDRCNQ 447 (560)
Q Consensus 418 ~aC~~~~~~~~C~KK--v~~~~~~~~C~kC~~ 447 (560)
.-||++ .|..- +..-.+.++|-||+-
T Consensus 19 k~CP~~----~CG~GvFMA~H~dR~~CGKCg~ 46 (47)
T PF01599_consen 19 KECPSP----RCGAGVFMAEHKDRHYCGKCGY 46 (47)
T ss_dssp EE-TST----TTTSSSEEEE-SSEEEETTTSS
T ss_pred hcCCCc----ccCCceEeeecCCCccCCCccc
Confidence 457865 78874 456667999999984
No 253
>PF03456 uDENN: uDENN domain; InterPro: IPR005113 This region is always found associated with IPR001194 from INTERPRO. It is predicted to form an all beta domain [].; PDB: 3TW8_A.
Probab=25.16 E-value=94 Score=24.11 Aligned_cols=21 Identities=38% Similarity=0.672 Sum_probs=16.6
Q ss_pred CcEEEEEEEeCCCCeEEEEEc
Q 008606 150 GKVFSFDLLDSDGGEIRVTCF 170 (560)
Q Consensus 150 gkvf~~~L~D~~g~~I~at~~ 170 (560)
...|+|+|.|++|.++.+.|-
T Consensus 42 ~~~f~FvLT~~~G~r~Yg~Cl 62 (65)
T PF03456_consen 42 PQFFSFVLTDEDGSRLYGYCL 62 (65)
T ss_dssp SCEEEEEEE-TTS-EEEEEEE
T ss_pred CeEEEEEEECCCCCEEEEEEE
Confidence 368999999999999998874
No 254
>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=25.05 E-value=2.1e+02 Score=29.06 Aligned_cols=66 Identities=24% Similarity=0.275 Sum_probs=40.3
Q ss_pred ceeEEEEEEEEecCceeEeeccCceeeEEEEEEecCCCc-EEEEEEeCcchhhhhhhHHhhhccCCccEEEEEEEEE
Q 008606 248 SIVDVIGIVISVNPSVPILRKNGMETQRRILNLKDTSGR-SVELTLWGDFCNKEGQKLQEMVDVGFFPVLSVKSGKV 323 (560)
Q Consensus 248 ~~VDVIGvV~~V~~~~~i~~k~G~~~~kr~i~L~D~Sg~-~I~vtLWg~~a~~~~~~l~~~~~~~~~~VV~l~~~rV 323 (560)
..|-|+|+|+++..- .+. +. .+..++|=|-||. .|.|.+|.+.....+-. +....|.+|.++|.--
T Consensus 67 ~~v~i~G~Vv~~~~~-~~~--~~---~~~~l~iDD~Sg~~~i~~~~~~~~~~~~~l~----~~~~~G~~V~VkG~vs 133 (256)
T PF10451_consen 67 RWVRIVGVVVGIDYK-WIE--NE---DRIILTIDDSSGANTIECKCSKSSYLSMGLP----INDLIGKVVEVKGTVS 133 (256)
T ss_dssp -EEEEEEEEEEEEEE-E-B--BT---CEEEEEEE-SSCS-EEEEEEEHHHHHCCCHH----CTT-TT-EEEEEEEEE
T ss_pred EEEEEEEEEEEEEEE-eec--cc---ceEEEEEeCCCCceeEEEEEEcccccccCCC----ccCCCCcEEEEEEEEc
Confidence 478999999998532 111 11 3567788888887 89999997754433222 2223678888876533
No 255
>PRK06341 single-stranded DNA-binding protein; Provisional
Probab=25.02 E-value=6e+02 Score=24.08 Aligned_cols=73 Identities=14% Similarity=0.154 Sum_probs=39.1
Q ss_pred ceeEEEEEEEEecCceeEeeccCceeeEEEEEEe----cC-CC------cEEEEEEeCc-chhhhhhhHHhhhccCCccE
Q 008606 248 SIVDVIGIVISVNPSVPILRKNGMETQRRILNLK----DT-SG------RSVELTLWGD-FCNKEGQKLQEMVDVGFFPV 315 (560)
Q Consensus 248 ~~VDVIGvV~~V~~~~~i~~k~G~~~~kr~i~L~----D~-Sg------~~I~vtLWg~-~a~~~~~~l~~~~~~~~~~V 315 (560)
..|-++|.|..--.++ .+.+|+.+..-.|-+. |. +| .-+.|++|++ .|+...++| ..+.-
T Consensus 6 N~V~LiGrLg~DPElR--~t~sG~~v~~fsVAvn~~~kd~~~Ge~~e~T~w~~Vv~fg~~~Ae~~~~~L------kKG~~ 77 (166)
T PRK06341 6 NKVILIGNLGADPEIR--RTQDGRPIANLRIATSETWRDRNSGERKEKTEWHRVVIFNEGLCKVAEQYL------KKGAK 77 (166)
T ss_pred eEEEEEEEecCCCEEE--EcCCCCEEEEEEEEEccceecCCCCcccccceEEEEEEeChHHHHHHHHhc------CCCCE
Confidence 3567788887722222 2345655433333332 21 12 2478999997 676543332 35666
Q ss_pred EEEE-EEEEecCCC
Q 008606 316 LSVK-SGKVNDFSG 328 (560)
Q Consensus 316 V~l~-~~rV~~f~G 328 (560)
|+|. ..+.+.|..
T Consensus 78 V~VeGrL~~r~w~d 91 (166)
T PRK06341 78 VYIEGQLQTRKWTD 91 (166)
T ss_pred EEEEEEEEeCcEEC
Confidence 6665 445666753
No 256
>TIGR00577 fpg formamidopyrimidine-DNA glycosylase (fpg). All proteins in the FPG family with known functions are FAPY-DNA glycosylases that function in base excision repair. Homologous to endonuclease VIII (nei). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=24.86 E-value=38 Score=34.68 Aligned_cols=23 Identities=22% Similarity=0.787 Sum_probs=17.7
Q ss_pred eCCCCCcCccccCceeeec--C--CeeecCcCC
Q 008606 418 TACPLMIGDRQCNKKVTQS--G--NRWQCDRCN 446 (560)
Q Consensus 418 ~aC~~~~~~~~C~KKv~~~--~--~~~~C~kC~ 446 (560)
..|| .|+..+... + ..|+|+.|+
T Consensus 246 ~pC~------~Cg~~I~~~~~~gR~t~~CP~CQ 272 (272)
T TIGR00577 246 EPCR------RCGTPIEKIKVGGRGTHFCPQCQ 272 (272)
T ss_pred CCCC------CCCCeeEEEEECCCCCEECCCCC
Confidence 3799 899888643 2 299999996
No 257
>cd01759 PLAT_PL PLAT/LH2 domain of pancreatic triglyceride lipase. Lipases hydrolyze phospholipids and triglycerides to generate fatty acids for energy production or for storage and to release inositol phosphates that act as second messengers. The central role of triglyceride lipases is in energy production. The proposed function of PLAT/LH2 domains is to mediate interaction with lipids or membrane bound proteins.
Probab=24.61 E-value=85 Score=27.79 Aligned_cols=26 Identities=23% Similarity=0.526 Sum_probs=21.6
Q ss_pred eEEEEEEEEEe---CCCeEEEEEehhhhh
Q 008606 454 YRYLLQAQIQD---QTGLTWVTAFQESGE 479 (560)
Q Consensus 454 ~rY~l~~~i~D---~Tgs~~~~~Fd~~ae 479 (560)
|||++.+++++ -+|++.+.+++..++
T Consensus 1 ~~Yqv~V~~s~~~~~~g~~~vsL~G~~g~ 29 (113)
T cd01759 1 WRYKVSVTLSGKKKVTGTILVSLYGNKGN 29 (113)
T ss_pred CeEEEEEEEecccccCceEEEEEEcCCCC
Confidence 69999999998 578999999976553
No 258
>TIGR00375 conserved hypothetical protein TIGR00375. The member of this family from Methanococcus jannaschii, MJ0043, is considerably longer and appears to contain an intein N-terminal to the region of homology.
Probab=23.90 E-value=42 Score=36.02 Aligned_cols=40 Identities=20% Similarity=0.349 Sum_probs=30.4
Q ss_pred EEEEEEEEeCCC-eEEeCCCCCcCccccCceeeecCC---eeecCcCCCcc
Q 008606 403 VRAFITFIKSDS-FCYTACPLMIGDRQCNKKVTQSGN---RWQCDRCNQEI 449 (560)
Q Consensus 403 v~atI~~I~~d~-~~Y~aC~~~~~~~~C~KKv~~~~~---~~~C~kC~~~~ 449 (560)
+.+++-.....+ ..+.+|. .|+..+..... .|.|+ |++.+
T Consensus 225 i~~~~g~~P~~GKYh~~~c~------~C~~~~~~~~~~~~~~~Cp-CG~~i 268 (374)
T TIGR00375 225 IIANYGLDPLLGKYHQTACE------ACGEPAVSEDAETACANCP-CGGRI 268 (374)
T ss_pred eEeeeeECcCCCccchhhhc------ccCCcCCchhhhhcCCCCC-CCCcc
Confidence 456665555444 8899999 99999987765 49999 99764
No 259
>COG3877 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=23.29 E-value=49 Score=28.84 Aligned_cols=24 Identities=25% Similarity=0.908 Sum_probs=19.9
Q ss_pred eCCCCCcCccccCceeeecCCeeecCcCCCcc
Q 008606 418 TACPLMIGDRQCNKKVTQSGNRWQCDRCNQEI 449 (560)
Q Consensus 418 ~aC~~~~~~~~C~KKv~~~~~~~~C~kC~~~~ 449 (560)
+.|| .|++++... ..+|..|..++
T Consensus 7 ~~cP------vcg~~~iVT--eL~c~~~etTV 30 (122)
T COG3877 7 NRCP------VCGRKLIVT--ELKCSNCETTV 30 (122)
T ss_pred CCCC------cccccceeE--EEecCCCCceE
Confidence 5799 999998765 38999999765
No 260
>KOG0402 consensus 60S ribosomal protein L37 [Translation, ribosomal structure and biogenesis]
Probab=23.26 E-value=46 Score=27.72 Aligned_cols=27 Identities=26% Similarity=0.746 Sum_probs=19.7
Q ss_pred ccCceeeecC--CeeecCcCCCccCCcee
Q 008606 428 QCNKKVTQSG--NRWQCDRCNQEIDECDY 454 (560)
Q Consensus 428 ~C~KKv~~~~--~~~~C~kC~~~~~~~~~ 454 (560)
-|+|+-..-. +.|.|..|.+.+.-..|
T Consensus 41 fCGK~~vKR~AvGiW~C~~C~kv~agga~ 69 (92)
T KOG0402|consen 41 FCGKKTVKRKAVGIWKCGSCKKVVAGGAY 69 (92)
T ss_pred hcchhhhhhhceeEEecCCccceeccceE
Confidence 8998765543 39999999997754444
No 261
>COG2835 Uncharacterized conserved protein [Function unknown]
Probab=23.22 E-value=54 Score=25.66 Aligned_cols=27 Identities=26% Similarity=0.650 Sum_probs=21.6
Q ss_pred EeCCCCCcCccccCceeeecCC--eeecCcCCCcc
Q 008606 417 YTACPLMIGDRQCNKKVTQSGN--RWQCDRCNQEI 449 (560)
Q Consensus 417 Y~aC~~~~~~~~C~KKv~~~~~--~~~C~kC~~~~ 449 (560)
-.+|| .|+.++..... ...|..|+..+
T Consensus 8 iLaCP------~~kg~L~~~~~~~~L~c~~~~~aY 36 (60)
T COG2835 8 ILACP------VCKGPLVYDEEKQELICPRCKLAY 36 (60)
T ss_pred eeecc------CcCCcceEeccCCEEEecccCcee
Confidence 46899 89998876554 89999999765
No 262
>PF09297 zf-NADH-PPase: NADH pyrophosphatase zinc ribbon domain; InterPro: IPR015376 This domain has a zinc ribbon structure and is often found between two NUDIX domains.; GO: 0016787 hydrolase activity, 0046872 metal ion binding; PDB: 1VK6_A 2GB5_A.
Probab=23.07 E-value=57 Score=21.77 Aligned_cols=21 Identities=19% Similarity=0.616 Sum_probs=12.9
Q ss_pred ccCceeeecCC--eeecCcCCCc
Q 008606 428 QCNKKVTQSGN--RWQCDRCNQE 448 (560)
Q Consensus 428 ~C~KKv~~~~~--~~~C~kC~~~ 448 (560)
.|+.++....+ .-.|+.|+..
T Consensus 8 ~CG~~t~~~~~g~~r~C~~Cg~~ 30 (32)
T PF09297_consen 8 RCGAPTKPAPGGWARRCPSCGHE 30 (32)
T ss_dssp TT--BEEE-SSSS-EEESSSS-E
T ss_pred cCCccccCCCCcCEeECCCCcCE
Confidence 89988877665 7899999863
No 263
>PF07191 zinc-ribbons_6: zinc-ribbons; InterPro: IPR010807 This family consists of several short, hypothetical bacterial proteins of around 70 residues in length. Members of this family 8 highly conserved cysteine residues. The function of the family is unknown.; PDB: 2JRP_A 2JNE_A.
Probab=22.87 E-value=56 Score=26.41 Aligned_cols=33 Identities=24% Similarity=0.719 Sum_probs=17.6
Q ss_pred eCCCCCcCccccCceeeec---CC-eeecCcCCCccCCceeEE
Q 008606 418 TACPLMIGDRQCNKKVTQS---GN-RWQCDRCNQEIDECDYRY 456 (560)
Q Consensus 418 ~aC~~~~~~~~C~KKv~~~---~~-~~~C~kC~~~~~~~~~rY 456 (560)
.-|| .|+..+..- +. .|+|..|+.-++.-..+|
T Consensus 31 a~CP------dC~~~Le~LkACGAvdYFC~~c~gLiSKkrV~f 67 (70)
T PF07191_consen 31 AFCP------DCGQPLEVLKACGAVDYFCNHCHGLISKKRVRF 67 (70)
T ss_dssp EE-T------TT-SB-EEEEETTEEEEE-TTTT-EE-TTTSEE
T ss_pred ccCC------CcccHHHHHHHhcccceeeccCCceeecceEEE
Confidence 4589 899887653 22 899999997654433333
No 264
>PF03089 RAG2: Recombination activating protein 2; InterPro: IPR004321 The variable portion of the genes encoding immunoglobulins and T cell receptors are assembled from component V, D, and J DNA segments by a site-specific recombination reaction termed V(D)J recombination. V(D)J recombination is targeted to specific sites on the chromosome by recombination signal sequences (RSSs) that flank antigen receptor gene segments. The RSS consists of a conserved heptamer (consensus, 5'-CACAGTG-3') and nonamer (consensus, 5'-ACAAAAACC-3') separated by a spacer of either 12 or 23 bp. Efficient recombination occurs between a 12-RSS and a 23-RSS, a restriction known as the 12/23 rule. V(D)J recombination can be divided into two phases, DNA cleavage and DNA joining. DNA cleavage requires two lymphocyte-specific factors, the products of the recombination activating genes, RAG1 and RAG2, which together recognise the RSSs and create double strand breaks at the RSS-coding segment junctions []. RAG-mediated DNA cleavage occurs in a synaptic complex termed the paired complex, which is constituted from two distinct RSS-RAG complexes, a 12-SC and a 23-SC (where SC stands for signal complex). The DNA cleavage reaction involves two distinct enzymatic steps, initial nicking that creates a 3'-OH between a coding segment and its RSS, followed by hairpin formation in which the newly created 3'-OH attacks a phosphodiester bond on the opposite DNA strand. This generates a blunt, 5' phosphorylated signal end containing all of the RSS elements, and a covalently sealed hairpin coding end. The second phase of V(D)J recombination, in which broken DNA fragments are processed and joined, is less well characterised. Signal ends are typically joined precisely to form a signal joint, whereas joining of the coding ends requires the hairpin structure to be opened and typically involves nucleotide addition and deletion before formation of the coding joint. The factors involved in these processes include ubiquitously expressed proteins involved in the repair of DNA double strand breaks by nonhomologous end joining, terminal deoxynucleotidyl transferase, and Artemis protein. In addition to their critical roles in RSS recognition and DNA cleavage, the RAG proteins may perform two distinct types of functions in the postcleavage phase of V(D)J. A structural function has been inferred from the finding that, after DNA cleavage in vitro, the DNA ends remain associated with the RAG proteins in a "four end" complex known as the cleaved signal complex. After release of the coding ends in vitro, and after coding joint formation in vivo, the RAG proteins remain in a stable signal end complex (SEC) containing the two signal ends. These postcleavage complexes may serve as essential scaffolds for the second phase of the reaction, with the RAG proteins acting to organise the DNA processing and joining events. The second type of RAG protein-mediated postcleavage activity is the catalysis of phosphodiester bond hydrolysis and strand transfer reactions. The RAG proteins are capable of opening hairpin coding ends in vitro. The RAG proteins also show 3' flap endonuclease activity that may contribute to coding end processing/joining and can utilise the 3' OH group on the signal ends to attack hairpin coding ends (forming hybrid or open/shut joints) or virtually any DNA duplex (forming a transposition product).; GO: 0003677 DNA binding, 0006310 DNA recombination, 0005634 nucleus
Probab=21.92 E-value=99 Score=31.98 Aligned_cols=46 Identities=28% Similarity=0.302 Sum_probs=35.0
Q ss_pred ccCceeeecCCeeecCcCCCccCCceeEEEEEEEEEeCCCeEEEEEehhhh
Q 008606 428 QCNKKVTQSGNRWQCDRCNQEIDECDYRYLLQAQIQDQTGLTWVTAFQESG 478 (560)
Q Consensus 428 ~C~KKv~~~~~~~~C~kC~~~~~~~~~rY~l~~~i~D~Tgs~~~~~Fd~~a 478 (560)
.||||++- .|..=.-.-+-|..||-=.+.+.-..|..-+++|+.-.
T Consensus 66 ~cNkK~tl-----~C~EKeLvGdvP~aRYGHt~~vV~SrGKta~VlFGGRS 111 (337)
T PF03089_consen 66 GCNKKVTL-----CCQEKELVGDVPEARYGHTINVVHSRGKTACVLFGGRS 111 (337)
T ss_pred CCCceeEE-----EEecceecCCCCcccccceEEEEEECCcEEEEEECCcc
Confidence 89999986 45321111245889999999999999999999998543
No 265
>PF10122 Mu-like_Com: Mu-like prophage protein Com; InterPro: IPR019294 Members of this entry belong to the Com family of proteins that act as translational regulators of mom [, ].
Probab=21.57 E-value=43 Score=25.30 Aligned_cols=24 Identities=33% Similarity=0.897 Sum_probs=18.7
Q ss_pred CCCCCcCccccCceeeecCC----eeecCcCCCc
Q 008606 419 ACPLMIGDRQCNKKVTQSGN----RWQCDRCNQE 448 (560)
Q Consensus 419 aC~~~~~~~~C~KKv~~~~~----~~~C~kC~~~ 448 (560)
.|+ .|+|.+-..++ .-.|++|+.-
T Consensus 6 RC~------~CnklLa~~g~~~~leIKCpRC~ti 33 (51)
T PF10122_consen 6 RCG------HCNKLLAKAGEVIELEIKCPRCKTI 33 (51)
T ss_pred ecc------chhHHHhhhcCccEEEEECCCCCcc
Confidence 588 99999987433 6789999863
No 266
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=21.02 E-value=59 Score=23.04 Aligned_cols=21 Identities=19% Similarity=0.536 Sum_probs=13.2
Q ss_pred ccCceeeec--CC--eeecCcCCCc
Q 008606 428 QCNKKVTQS--GN--RWQCDRCNQE 448 (560)
Q Consensus 428 ~C~KKv~~~--~~--~~~C~kC~~~ 448 (560)
.|+..+... .+ .+.|++|+..
T Consensus 4 ~C~~~l~~~~~~~~~id~C~~C~G~ 28 (41)
T PF13453_consen 4 RCGTELEPVRLGDVEIDVCPSCGGI 28 (41)
T ss_pred CCCcccceEEECCEEEEECCCCCeE
Confidence 787765432 22 6788888754
No 267
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=20.81 E-value=81 Score=23.01 Aligned_cols=22 Identities=18% Similarity=0.572 Sum_probs=17.7
Q ss_pred ccCceeeecCC-eeecCcCCCcc
Q 008606 428 QCNKKVTQSGN-RWQCDRCNQEI 449 (560)
Q Consensus 428 ~C~KKv~~~~~-~~~C~kC~~~~ 449 (560)
.|+..+..... .-+|+.|+..+
T Consensus 7 ~Cg~~~~~~~~~~irC~~CG~rI 29 (44)
T smart00659 7 ECGRENEIKSKDVVRCRECGYRI 29 (44)
T ss_pred CCCCEeecCCCCceECCCCCceE
Confidence 89999887644 89999999654
No 268
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=20.80 E-value=54 Score=24.64 Aligned_cols=21 Identities=19% Similarity=0.626 Sum_probs=15.8
Q ss_pred ccCceeeec-CC-eeecCcCCCc
Q 008606 428 QCNKKVTQS-GN-RWQCDRCNQE 448 (560)
Q Consensus 428 ~C~KKv~~~-~~-~~~C~kC~~~ 448 (560)
.|++++... .. ..+|+.|+.-
T Consensus 11 ~Cg~~~~~~~~~~~irCp~Cg~r 33 (49)
T COG1996 11 RCGREVELDQETRGIRCPYCGSR 33 (49)
T ss_pred hcCCeeehhhccCceeCCCCCcE
Confidence 899999633 22 7899999853
No 269
>cd03582 NTR_complement_C5 NTR/C345C domain, complement C5 subfamily; The NTR domain found in complement C5 is also known as C345C because it occurs at the C-terminus of complement C3, C4 and C5. Complement C5 is activated by C5 convertase, which itself is a complex between C3b and C3 convertase. The small cleavage fragment, C5a, is the most important small peptide mediator of inflammation, and the larger active fragment, C5b, initiates late events of complement activation. The NTR/C345C domain is important in the function of C5 as it interacts with enzymes that convert C5 to the active form, C5b. The domain has also been found to bind to complement components C6 and C7, and may specifically interact with their factor I modules.
Probab=20.02 E-value=7e+02 Score=23.06 Aligned_cols=85 Identities=11% Similarity=0.098 Sum_probs=51.9
Q ss_pred CceEEEEEEEEecccceeccCCCCCcEEEEEEE-------e-CCCCeEEEEEcchhHHHHHhhcccCcEEEEeeeEEecC
Q 008606 126 GRWAIKARVTAKGDLRRYNNARGDGKVFSFDLL-------D-SDGGEIRVTCFNAVVDRFYEIIEVGRVYLISKGSLKPA 197 (560)
Q Consensus 126 ~~w~Ik~RV~~k~~ir~~~n~~g~gkvf~~~L~-------D-~~g~~I~at~~~~~~~kf~~~l~eG~vY~Is~~~V~~a 197 (560)
-...++|+|+.......|. .+.+.+. | ..-+.++..+-..... ...|++|+.|.|-+-..
T Consensus 31 vDYaykv~V~~~~~~~~~~-------~y~~~I~~V~K~g~d~~~~g~~r~f~~~~~Cr--~~~l~~gk~YLImG~~~--- 98 (150)
T cd03582 31 IAYAYKVMIKSSAAEGDFV-------TYKATVLDVLKNGQAELEKDSEVTLVKKATCT--SVELQEGQQYLIMGKEA--- 98 (150)
T ss_pred CCEEEEEEEEEEEecCCeE-------EEEEEEEEeEecCCccccCCCeEEEeecCCCC--CCcccCCCEEEEeeCCC---
Confidence 4678899999876654442 3444332 2 1233444433333332 46789999999998731
Q ss_pred CCcccc-CCCeeEEEEcccceEEeccC
Q 008606 198 QKNFNH-LKNEWEIFLEATSTVDLCTE 223 (560)
Q Consensus 198 ~~~y~~-~~~~yeI~f~~~T~I~~~~d 223 (560)
..++. .+..|.-.|+++|-|+..|.
T Consensus 99 -~~~~~~~~~~~~Y~L~~~TWvE~WP~ 124 (150)
T cd03582 99 -LKIRLNRSFRYRYPLDSEAWIEWWPT 124 (150)
T ss_pred -CccccCCCceeEEEcCCceeEEECCC
Confidence 22333 22358999999999999874
Done!