Query 003281
Match_columns 834
No_of_seqs 434 out of 2019
Neff 7.4
Searched_HMMs 46136
Date Thu Mar 28 20:31:38 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/003281.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/003281hhsearch_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 6E-119 1E-123 1048.6 64.0 577 1-660 24-608 (608)
2 PRK12366 replication factor A; 100.0 5.6E-63 1.2E-67 581.6 47.6 356 218-647 278-637 (637)
3 PRK08402 replication factor A; 100.0 2.1E-43 4.6E-48 384.8 30.4 281 338-662 61-353 (355)
4 cd04476 RPA1_DBD_C RPA1_DBD_C: 100.0 1.4E-34 3E-39 288.2 20.5 166 487-660 1-166 (166)
5 PF08646 Rep_fac-A_C: Replicat 100.0 1.2E-34 2.7E-39 282.3 15.4 146 503-654 1-146 (146)
6 PRK07218 replication factor A; 100.0 9.4E-32 2E-36 299.0 39.8 359 217-657 56-420 (423)
7 PRK07211 replication factor A; 100.0 2.7E-30 5.9E-35 289.3 30.1 274 218-583 52-328 (485)
8 PRK12366 replication factor A; 100.0 3E-30 6.6E-35 304.5 32.2 282 217-588 61-345 (637)
9 PRK06386 replication factor A; 100.0 2.7E-28 5.8E-33 264.8 41.6 351 220-659 3-354 (358)
10 PRK07211 replication factor A; 100.0 3.7E-30 8.1E-35 288.2 24.6 208 218-451 160-370 (485)
11 PRK15491 replication factor A; 100.0 8.7E-28 1.9E-32 265.9 29.8 277 217-584 55-336 (374)
12 PRK15491 replication factor A; 100.0 1.2E-26 2.6E-31 256.9 29.9 206 218-445 165-373 (374)
13 PRK14699 replication factor A; 99.9 1.2E-26 2.5E-31 263.6 21.7 207 217-445 274-483 (484)
14 cd04474 RPA1_DBD_A RPA1_DBD_A: 99.9 2.2E-26 4.8E-31 210.7 11.8 104 221-324 1-104 (104)
15 PRK14699 replication factor A; 99.9 3.1E-23 6.7E-28 235.8 37.1 277 220-585 167-447 (484)
16 cd04477 RPA1N RPA1N: A subfami 99.9 1.3E-24 2.8E-29 194.8 8.2 81 1-86 17-97 (97)
17 PF04057 Rep-A_N: Replication 99.9 4.2E-24 9.1E-29 193.4 9.4 83 1-87 18-101 (101)
18 cd04475 RPA1_DBD_B RPA1_DBD_B: 99.8 8.1E-20 1.8E-24 166.7 12.3 100 353-460 1-101 (101)
19 cd04481 RPA1_DBD_B_like RPA1_D 99.8 5.9E-18 1.3E-22 155.8 11.7 101 355-458 1-104 (106)
20 cd04480 RPA1_DBD_A_like RPA1_D 99.7 5E-17 1.1E-21 143.8 9.5 86 233-322 1-86 (86)
21 PF02721 DUF223: Domain of unk 99.5 3.6E-14 7.8E-19 127.9 9.1 87 258-347 1-87 (95)
22 PRK07217 replication factor A; 99.5 3E-12 6.6E-17 135.6 24.8 210 338-624 71-282 (311)
23 PRK08402 replication factor A; 99.5 5.8E-13 1.2E-17 146.4 19.0 177 218-404 61-270 (355)
24 COG1599 RFA1 Single-stranded D 99.2 2.2E-10 4.7E-15 130.2 14.9 244 216-516 159-404 (407)
25 KOG0851 Single-stranded DNA-bi 99.1 4.8E-10 1E-14 118.8 13.7 214 218-465 3-220 (246)
26 cd04497 hPOT1_OB1_like hPOT1_O 99.0 1.3E-09 2.9E-14 105.1 11.5 89 337-437 1-92 (138)
27 COG5082 AIR1 Arginine methyltr 99.0 1.6E-10 3.5E-15 113.7 4.8 81 743-832 62-145 (190)
28 PRK06386 replication factor A; 99.0 1.5E-07 3.2E-12 103.5 27.3 164 218-404 106-288 (358)
29 PRK07218 replication factor A; 98.9 4.9E-08 1.1E-12 109.9 18.9 170 218-404 161-349 (423)
30 PTZ00368 universal minicircle 98.9 4.9E-09 1.1E-13 102.5 8.7 82 743-824 54-146 (148)
31 PTZ00368 universal minicircle 98.8 6.6E-09 1.4E-13 101.6 7.4 85 742-826 28-122 (148)
32 cd04491 SoSSB_OBF SoSSB_OBF: A 98.7 9.8E-08 2.1E-12 83.6 11.3 80 355-445 1-81 (82)
33 cd04491 SoSSB_OBF SoSSB_OBF: A 98.7 1.3E-07 2.9E-12 82.8 10.6 81 233-324 1-81 (82)
34 PRK06461 single-stranded DNA-b 98.7 1.4E-07 3.1E-12 89.8 11.3 94 339-446 4-98 (129)
35 PRK06461 single-stranded DNA-b 98.6 3.3E-07 7.2E-12 87.3 11.9 98 218-327 3-100 (129)
36 KOG4400 E3 ubiquitin ligase in 98.5 2.1E-07 4.6E-12 99.7 6.3 83 743-827 94-184 (261)
37 COG5082 AIR1 Arginine methyltr 98.1 1.8E-06 3.9E-11 85.4 3.9 62 742-825 98-172 (190)
38 PF00098 zf-CCHC: Zinc knuckle 98.1 1.6E-06 3.6E-11 52.9 1.8 17 787-803 2-18 (18)
39 TIGR00617 rpa1 replication fac 98.0 0.00082 1.8E-08 80.3 22.6 177 338-585 179-364 (608)
40 PRK07217 replication factor A; 97.9 0.00024 5.1E-09 76.3 15.3 93 217-326 70-162 (311)
41 COG1599 RFA1 Single-stranded D 97.8 0.00033 7.1E-09 80.0 16.1 187 216-433 46-234 (407)
42 PF00098 zf-CCHC: Zinc knuckle 97.7 2.1E-05 4.5E-10 48.1 1.6 17 743-759 2-18 (18)
43 PF02765 POT1: Telomeric singl 97.7 0.00064 1.4E-08 66.3 12.7 86 339-433 1-93 (146)
44 cd04474 RPA1_DBD_A RPA1_DBD_A: 97.7 0.00021 4.5E-09 65.6 8.6 97 342-447 2-98 (104)
45 PF01336 tRNA_anti-codon: OB-f 97.5 0.00031 6.7E-09 59.7 7.5 61 232-302 1-61 (75)
46 KOG4400 E3 ubiquitin ligase in 97.4 0.00013 2.9E-09 78.2 4.5 41 743-806 145-185 (261)
47 cd04475 RPA1_DBD_B RPA1_DBD_B: 97.2 0.0029 6.3E-08 57.5 9.9 83 233-325 3-87 (101)
48 PF13696 zf-CCHC_2: Zinc knuck 96.6 0.00093 2E-08 46.8 1.1 21 785-805 8-28 (32)
49 cd03524 RPA2_OBF_family RPA2_O 96.4 0.018 3.8E-07 47.9 8.1 60 234-300 2-61 (75)
50 KOG3416 Predicted nucleic acid 96.1 0.018 3.8E-07 53.2 6.8 70 219-297 4-74 (134)
51 cd04497 hPOT1_OB1_like hPOT1_O 95.4 0.074 1.6E-06 51.4 8.6 83 218-304 2-88 (138)
52 KOG3416 Predicted nucleic acid 95.3 0.079 1.7E-06 49.1 7.8 83 341-440 6-89 (134)
53 PF13696 zf-CCHC_2: Zinc knuck 95.1 0.013 2.9E-07 41.1 1.7 20 742-761 9-28 (32)
54 cd04483 hOBFC1_like hOBFC1_lik 94.9 0.14 3E-06 45.9 8.3 68 355-437 1-86 (92)
55 cd03524 RPA2_OBF_family RPA2_O 94.8 0.19 4.2E-06 41.4 8.7 68 355-436 1-69 (75)
56 KOG0921 Dosage compensation co 94.6 0.24 5.2E-06 59.7 11.4 19 652-670 1127-1145(1282)
57 PF01336 tRNA_anti-codon: OB-f 94.6 0.2 4.4E-06 42.2 8.3 63 354-433 1-63 (75)
58 smart00343 ZnF_C2HC zinc finge 94.3 0.021 4.5E-07 38.4 1.1 18 787-804 1-18 (26)
59 KOG0109 RNA-binding protein LA 94.2 0.024 5.1E-07 59.6 1.8 22 786-807 161-182 (346)
60 PF13917 zf-CCHC_3: Zinc knuck 94.1 0.027 5.9E-07 42.4 1.5 18 786-803 5-22 (42)
61 cd04481 RPA1_DBD_B_like RPA1_D 93.9 0.64 1.4E-05 42.6 10.6 68 235-302 3-75 (106)
62 KOG0119 Splicing factor 1/bran 93.6 0.047 1E-06 61.3 2.9 42 743-804 263-304 (554)
63 cd04488 RecG_wedge_OBF RecG_we 93.5 0.58 1.3E-05 39.1 9.0 61 233-301 1-61 (75)
64 cd04490 PolII_SU_OBF PolII_SU_ 93.5 0.33 7.2E-06 42.1 7.5 55 354-424 2-58 (79)
65 PF14787 zf-CCHC_5: GAG-polypr 93.4 0.042 9.1E-07 39.5 1.3 20 786-805 3-22 (36)
66 PF15489 CTC1: CST, telomere m 93.1 32 0.0007 43.6 26.2 310 229-597 704-1051(1144)
67 cd04478 RPA2_DBD_D RPA2_DBD_D: 92.5 0.89 1.9E-05 40.5 9.1 66 354-437 2-71 (95)
68 cd04485 DnaE_OBF DnaE_OBF: A s 92.2 0.73 1.6E-05 39.3 7.9 43 255-299 19-61 (84)
69 PF13917 zf-CCHC_3: Zinc knuck 91.7 0.084 1.8E-06 39.8 1.1 17 743-759 6-22 (42)
70 smart00343 ZnF_C2HC zinc finge 91.6 0.081 1.8E-06 35.5 0.9 19 743-761 1-19 (26)
71 PF11325 DUF3127: Domain of un 91.2 1.8 3.8E-05 38.0 8.9 75 356-439 2-79 (84)
72 cd04485 DnaE_OBF DnaE_OBF: A s 89.9 2.2 4.8E-05 36.3 8.7 68 356-436 2-70 (84)
73 cd04489 ExoVII_LU_OBF ExoVII_L 89.5 1.9 4.2E-05 36.7 7.9 54 233-295 3-56 (78)
74 PF15072 DUF4539: Domain of un 88.5 1.9 4.2E-05 38.0 7.2 61 257-324 21-81 (86)
75 KOG0109 RNA-binding protein LA 88.4 0.28 6E-06 51.9 2.1 22 743-764 162-183 (346)
76 PTZ00401 aspartyl-tRNA synthet 88.3 5.3 0.00011 47.5 12.9 98 217-324 63-168 (550)
77 PRK05813 single-stranded DNA-b 87.8 35 0.00077 35.6 17.2 166 229-431 8-183 (219)
78 cd04490 PolII_SU_OBF PolII_SU_ 87.7 2.9 6.3E-05 36.3 7.7 54 233-295 3-58 (79)
79 cd04495 BRCA2DBD_OB3 BRCA2DBD_ 87.6 3.9 8.4E-05 36.8 8.4 90 355-460 1-93 (100)
80 COG5222 Uncharacterized conser 87.1 0.32 6.8E-06 51.3 1.7 21 786-806 177-197 (427)
81 PRK06751 single-stranded DNA-b 86.9 4.1 8.9E-05 40.9 9.4 64 229-295 2-75 (173)
82 cd04492 YhaM_OBF_like YhaM_OBF 86.9 2.8 6.1E-05 35.8 7.4 42 255-299 19-60 (83)
83 PRK02801 primosomal replicatio 86.8 3.4 7.3E-05 37.7 8.1 68 229-299 2-80 (101)
84 PRK05733 single-stranded DNA-b 86.8 4.8 0.0001 40.4 9.8 65 228-295 4-81 (172)
85 PF02765 POT1: Telomeric singl 86.4 4.2 9.1E-05 39.6 9.1 85 219-304 1-93 (146)
86 PF06075 DUF936: Plant protein 86.2 0.97 2.1E-05 53.6 5.3 92 1-99 25-116 (579)
87 KOG0314 Predicted E3 ubiquitin 85.2 1.7 3.7E-05 49.5 6.3 44 743-805 135-178 (448)
88 cd04492 YhaM_OBF_like YhaM_OBF 84.3 6.1 0.00013 33.7 8.2 63 356-432 2-64 (83)
89 PF14787 zf-CCHC_5: GAG-polypr 84.2 0.78 1.7E-05 33.1 2.0 20 743-762 4-23 (36)
90 PRK09010 single-stranded DNA-b 83.8 9.1 0.0002 38.6 10.2 64 229-295 6-82 (177)
91 PRK13732 single-stranded DNA-b 83.8 9 0.00019 38.5 10.1 64 229-295 6-82 (175)
92 PF09103 BRCA-2_OB1: BRCA2, ol 83.7 1.1 2.4E-05 42.0 3.4 41 23-63 31-71 (118)
93 cd04320 AspRS_cyto_N AspRS_cyt 83.3 27 0.00058 31.6 12.3 81 232-323 2-90 (102)
94 cd04489 ExoVII_LU_OBF ExoVII_L 83.3 6.7 0.00015 33.3 8.0 41 355-405 3-43 (78)
95 PF15288 zf-CCHC_6: Zinc knuck 83.2 0.63 1.4E-05 34.6 1.2 20 786-805 2-23 (40)
96 COG5222 Uncharacterized conser 83.0 0.87 1.9E-05 48.1 2.6 21 742-762 177-197 (427)
97 PRK13480 3'-5' exoribonuclease 82.5 4.2 9E-05 44.9 7.8 70 221-297 4-73 (314)
98 PF09104 BRCA-2_OB3: BRCA2, ol 82.4 11 0.00024 36.4 9.6 95 341-449 5-105 (143)
99 PRK07772 single-stranded DNA-b 82.0 7.9 0.00017 39.3 9.0 64 229-295 4-81 (186)
100 cd04493 BRCA2DBD_OB1 BRCA2DBD_ 81.3 2.4 5.2E-05 38.4 4.5 38 26-63 22-59 (100)
101 PF14392 zf-CCHC_4: Zinc knuck 81.1 0.56 1.2E-05 36.8 0.3 18 742-759 32-49 (49)
102 PF14392 zf-CCHC_4: Zinc knuck 81.0 0.58 1.3E-05 36.6 0.4 18 786-803 32-49 (49)
103 PLN02850 aspartate-tRNA ligase 80.9 12 0.00026 44.3 11.5 97 217-324 67-171 (530)
104 KOG4757 Predicted telomere bin 80.9 4.9 0.00011 45.0 7.5 74 350-433 19-94 (522)
105 KOG0851 Single-stranded DNA-bi 80.7 9.7 0.00021 40.0 9.8 66 517-593 159-224 (246)
106 PF15288 zf-CCHC_6: Zinc knuck 80.7 0.88 1.9E-05 33.9 1.2 19 743-761 3-23 (40)
107 cd04322 LysRS_N LysRS_N: N-ter 80.6 25 0.00053 32.2 11.2 76 232-324 2-82 (108)
108 PRK07459 single-stranded DNA-b 80.0 13 0.00029 35.0 9.3 64 229-295 3-72 (121)
109 PRK08763 single-stranded DNA-b 79.6 8.3 0.00018 38.4 8.1 64 229-295 5-80 (164)
110 PRK08486 single-stranded DNA-b 79.6 10 0.00022 38.4 8.9 64 229-295 2-77 (182)
111 PRK08182 single-stranded DNA-b 79.5 12 0.00025 36.7 9.0 65 229-295 2-82 (148)
112 PRK06958 single-stranded DNA-b 79.3 11 0.00023 38.2 8.8 64 229-295 4-80 (182)
113 cd04478 RPA2_DBD_D RPA2_DBD_D: 79.2 4.9 0.00011 35.7 5.9 53 233-295 3-58 (95)
114 PRK06293 single-stranded DNA-b 79.0 13 0.00028 36.9 9.1 64 229-295 1-71 (161)
115 COG5235 RFA2 Single-stranded D 78.9 8.2 0.00018 39.2 7.7 70 353-438 68-138 (258)
116 PRK05673 dnaE DNA polymerase I 78.7 6.2 0.00014 50.9 8.7 82 338-432 964-1045(1135)
117 PRK07275 single-stranded DNA-b 78.4 6.7 0.00015 38.9 7.0 64 229-295 2-75 (162)
118 PRK06863 single-stranded DNA-b 78.3 14 0.00031 36.9 9.3 64 229-295 4-80 (168)
119 PF10341 TPP1: Shelterin compl 77.8 3.1 6.8E-05 38.1 4.3 47 25-71 41-93 (106)
120 PRK13480 3'-5' exoribonuclease 77.3 13 0.00029 41.0 9.7 78 345-436 5-83 (314)
121 KOG0921 Dosage compensation co 77.2 12 0.00027 45.9 9.8 17 573-589 1086-1102(1282)
122 PF13742 tRNA_anti_2: OB-fold 76.4 3.1 6.8E-05 37.7 3.8 63 230-301 22-86 (99)
123 cd04316 ND_PkAspRS_like_N ND_P 76.0 55 0.0012 29.9 12.0 74 230-318 13-90 (108)
124 cd04484 polC_OBF polC_OBF: A s 75.9 16 0.00034 31.9 7.9 58 232-295 2-61 (82)
125 cd04496 SSB_OBF SSB_OBF: A sub 75.5 17 0.00037 32.2 8.4 61 233-296 2-73 (100)
126 cd04323 AsnRS_cyto_like_N AsnR 75.4 31 0.00067 29.9 9.8 74 232-317 2-77 (84)
127 PRK07373 DNA polymerase III su 75.4 6 0.00013 45.8 6.7 78 338-428 267-344 (449)
128 COG1997 RPL43A Ribosomal prote 75.0 2 4.3E-05 37.5 1.9 29 522-556 37-66 (89)
129 cd04498 hPOT1_OB2 hPOT1_OB2: A 74.9 7.8 0.00017 36.6 6.0 36 390-432 60-95 (123)
130 TIGR00621 ssb single stranded 74.9 17 0.00037 36.1 8.9 65 229-296 4-80 (164)
131 cd04100 Asp_Lys_Asn_RS_N Asp_L 74.4 32 0.00069 29.9 9.6 74 232-317 2-78 (85)
132 cd04480 RPA1_DBD_A_like RPA1_D 74.0 18 0.00038 31.6 7.9 52 376-433 17-68 (86)
133 KOG3056 Protein required for S 73.1 22 0.00047 41.5 10.1 102 217-324 166-274 (578)
134 PRK07274 single-stranded DNA-b 72.5 14 0.0003 35.3 7.3 64 229-295 2-75 (131)
135 PF14951 DUF4503: Domain of un 71.9 11 0.00024 41.4 7.2 84 503-592 256-346 (389)
136 PF02721 DUF223: Domain of unk 71.3 12 0.00027 33.4 6.3 48 381-434 1-48 (95)
137 PRK07373 DNA polymerase III su 71.2 10 0.00022 44.1 7.1 71 220-295 269-341 (449)
138 PRK05159 aspC aspartyl-tRNA sy 71.0 40 0.00087 39.1 12.1 92 219-325 4-100 (437)
139 PRK06752 single-stranded DNA-b 69.9 19 0.00042 33.2 7.5 64 229-295 2-75 (112)
140 PF00436 SSB: Single-strand bi 69.8 9.1 0.0002 34.4 5.2 63 230-295 2-76 (104)
141 PF02760 HIN: HIN-200/IF120x d 69.8 1.2E+02 0.0026 30.0 16.1 143 234-402 5-153 (170)
142 PLN02502 lysyl-tRNA synthetase 68.8 28 0.0006 41.5 10.2 79 230-325 109-194 (553)
143 cd04483 hOBFC1_like hOBFC1_lik 68.5 13 0.00029 33.1 5.9 52 234-295 2-73 (92)
144 cd04318 EcAsnRS_like_N EcAsnRS 66.3 48 0.001 28.5 8.9 72 232-317 2-75 (82)
145 cd04317 EcAspRS_like_N EcAspRS 62.2 71 0.0015 30.4 10.0 80 230-319 15-98 (135)
146 KOG0556 Aspartyl-tRNA syntheta 61.8 92 0.002 35.2 11.6 106 216-334 67-181 (533)
147 PRK06642 single-stranded DNA-b 61.8 30 0.00065 34.0 7.4 64 229-295 5-82 (152)
148 KOG0107 Alternative splicing f 61.0 6.8 0.00015 38.9 2.7 17 787-803 102-118 (195)
149 KOG0119 Splicing factor 1/bran 60.8 6.8 0.00015 44.7 3.0 44 786-829 262-307 (554)
150 COG0629 Ssb Single-stranded DN 59.4 29 0.00062 34.6 7.0 66 228-296 2-80 (167)
151 PTZ00385 lysyl-tRNA synthetase 58.0 92 0.002 37.9 11.9 77 231-324 109-191 (659)
152 PRK06341 single-stranded DNA-b 56.9 67 0.0015 32.1 8.9 64 229-295 5-82 (166)
153 PRK12445 lysyl-tRNA synthetase 56.4 66 0.0014 38.0 10.3 79 230-325 66-149 (505)
154 TIGR00499 lysS_bact lysyl-tRNA 56.2 66 0.0014 38.0 10.3 79 230-325 54-137 (496)
155 PTZ00417 lysine-tRNA ligase; P 56.0 59 0.0013 39.1 9.9 56 231-296 134-197 (585)
156 PRK00484 lysS lysyl-tRNA synth 55.8 78 0.0017 37.3 10.8 78 230-325 55-137 (491)
157 PRK07459 single-stranded DNA-b 55.4 80 0.0017 29.7 8.8 69 353-431 5-80 (121)
158 PRK08486 single-stranded DNA-b 54.6 61 0.0013 32.9 8.3 35 391-431 50-85 (182)
159 PF01780 Ribosomal_L37ae: Ribo 54.4 4.4 9.5E-05 35.9 0.1 27 522-554 37-64 (90)
160 PRK09010 single-stranded DNA-b 54.3 71 0.0015 32.2 8.7 36 391-432 55-91 (177)
161 PRK05733 single-stranded DNA-b 54.0 72 0.0016 32.0 8.7 71 353-431 7-89 (172)
162 PRK07374 dnaE DNA polymerase I 53.9 25 0.00054 45.7 6.7 78 338-428 987-1064(1170)
163 TIGR00621 ssb single stranded 53.6 66 0.0014 32.0 8.4 35 391-431 52-87 (164)
164 PRK05673 dnaE DNA polymerase I 53.0 36 0.00079 44.2 8.0 71 220-295 966-1038(1135)
165 PRK06751 single-stranded DNA-b 53.0 68 0.0015 32.3 8.3 35 391-431 48-83 (173)
166 TIGR00643 recG ATP-dependent D 52.6 49 0.0011 40.3 8.8 69 218-295 22-91 (630)
167 cd04482 RPA2_OBF_like RPA2_OBF 51.8 25 0.00055 31.2 4.6 41 254-296 17-59 (91)
168 PRK02983 lysS lysyl-tRNA synth 51.1 76 0.0016 41.2 10.4 88 221-325 641-735 (1094)
169 PF15489 CTC1: CST, telomere m 50.9 1.4E+02 0.0029 38.4 12.0 68 229-301 165-232 (1144)
170 PRK05853 hypothetical protein; 50.8 56 0.0012 32.4 7.2 34 262-295 38-71 (161)
171 PRK08763 single-stranded DNA-b 50.3 94 0.002 31.0 8.8 35 391-431 53-88 (164)
172 PRK10917 ATP-dependent DNA hel 49.9 43 0.00094 41.2 7.8 87 218-314 49-136 (681)
173 cd04319 PhAsnRS_like_N PhAsnRS 49.3 2E+02 0.0043 25.9 10.3 72 232-318 2-76 (103)
174 PRK06958 single-stranded DNA-b 48.4 97 0.0021 31.4 8.6 35 391-431 53-88 (182)
175 PRK07135 dnaE DNA polymerase I 47.0 54 0.0012 41.8 8.0 74 220-302 889-962 (973)
176 COG0017 AsnS Aspartyl/asparagi 46.8 1.9E+02 0.0041 33.4 11.5 90 220-324 5-99 (435)
177 cd04487 RecJ_OBF2_like RecJ_OB 46.7 35 0.00077 29.0 4.5 40 254-295 15-54 (73)
178 PRK07279 dnaE DNA polymerase I 46.3 47 0.001 42.6 7.3 72 219-295 875-946 (1034)
179 PRK06826 dnaE DNA polymerase I 46.0 40 0.00087 43.8 6.8 77 339-428 970-1055(1151)
180 PRK05813 single-stranded DNA-b 45.4 95 0.0021 32.5 8.3 73 219-295 97-175 (219)
181 cd04321 ScAspRS_mt_like_N ScAs 45.2 2.1E+02 0.0045 24.9 10.4 76 232-317 2-79 (86)
182 cd03574 NTR_complement_C345C N 44.7 1.6E+02 0.0035 28.6 9.4 87 231-327 24-119 (147)
183 PRK06863 single-stranded DNA-b 44.6 1.1E+02 0.0024 30.6 8.3 71 353-431 6-88 (168)
184 TIGR00280 L37a ribosomal prote 44.1 11 0.00023 33.6 0.9 28 522-555 37-65 (91)
185 PTZ00255 60S ribosomal protein 43.6 12 0.00026 33.3 1.1 31 522-558 38-69 (90)
186 cd04100 Asp_Lys_Asn_RS_N Asp_L 43.5 57 0.0012 28.2 5.5 59 27-85 18-83 (85)
187 TIGR00458 aspS_arch aspartyl-t 43.3 1.6E+02 0.0035 34.0 10.7 80 230-324 13-96 (428)
188 PRK07374 dnaE DNA polymerase I 43.2 51 0.0011 42.9 7.1 71 220-295 989-1061(1170)
189 cd04494 BRCA2DBD_OB2 BRCA2DBD_ 42.8 81 0.0018 33.6 7.3 57 267-326 180-236 (251)
190 PRK13732 single-stranded DNA-b 41.7 1.8E+02 0.004 29.3 9.4 35 391-431 55-90 (175)
191 cd04496 SSB_OBF SSB_OBF: A sub 41.6 1.2E+02 0.0026 26.6 7.6 37 389-431 43-80 (100)
192 PRK02801 primosomal replicatio 41.5 93 0.002 28.2 6.7 65 353-425 4-77 (101)
193 PRK03976 rpl37ae 50S ribosomal 41.3 12 0.00026 33.2 0.8 28 522-555 38-66 (90)
194 PRK06920 dnaE DNA polymerase I 40.9 52 0.0011 42.6 6.7 77 338-428 931-1007(1107)
195 KOG3116 Predicted C3H1-type Zn 40.7 6.8 0.00015 37.5 -0.8 21 785-805 27-47 (177)
196 COG1200 RecG RecG-like helicas 40.3 2.1E+02 0.0045 34.8 10.9 90 217-315 49-138 (677)
197 PF13240 zinc_ribbon_2: zinc-r 40.2 16 0.00036 23.8 1.1 19 531-552 4-22 (23)
198 KOG2044 5'-3' exonuclease HKE1 40.0 12 0.00027 45.1 0.9 21 785-805 260-280 (931)
199 PRK07275 single-stranded DNA-b 39.9 1.5E+02 0.0033 29.4 8.5 35 391-431 48-83 (162)
200 COG1571 Predicted DNA-binding 39.3 18 0.00038 41.2 1.9 31 521-557 351-381 (421)
201 PRK06752 single-stranded DNA-b 37.6 1.9E+02 0.0041 26.6 8.3 35 391-431 48-83 (112)
202 KOG3070 Predicted RNA-binding 37.2 1E+02 0.0022 32.6 7.1 19 786-804 200-218 (235)
203 PRK08182 single-stranded DNA-b 36.9 1.8E+02 0.0039 28.4 8.4 35 391-431 55-90 (148)
204 PRK05672 dnaE2 error-prone DNA 36.9 59 0.0013 42.0 6.2 75 339-428 941-1015(1046)
205 KOG3116 Predicted C3H1-type Zn 36.5 9.6 0.00021 36.6 -0.6 19 743-761 29-47 (177)
206 PRK06293 single-stranded DNA-b 36.3 2.1E+02 0.0046 28.4 8.7 71 353-431 3-79 (161)
207 cd04484 polC_OBF polC_OBF: A s 36.1 2.7E+02 0.0057 24.2 8.5 56 559-636 20-75 (82)
208 cd04498 hPOT1_OB2 hPOT1_OB2: A 36.1 83 0.0018 29.8 5.6 48 268-316 61-109 (123)
209 PRK03932 asnC asparaginyl-tRNA 35.9 4.1E+02 0.0088 31.0 12.5 76 229-319 16-94 (450)
210 TIGR00459 aspS_bact aspartyl-t 35.9 2.8E+02 0.0061 33.5 11.3 85 230-324 16-103 (583)
211 PRK07274 single-stranded DNA-b 35.0 2.1E+02 0.0045 27.3 8.3 34 391-430 48-82 (131)
212 KOG3056 Protein required for S 35.0 1.3E+02 0.0028 35.4 7.9 66 355-431 189-255 (578)
213 PF11781 RRN7: RNA polymerase 34.3 25 0.00054 25.7 1.4 25 522-552 10-34 (36)
214 COG0484 DnaJ DnaJ-class molecu 34.1 20 0.00043 40.3 1.3 9 743-751 144-152 (371)
215 cd04476 RPA1_DBD_C RPA1_DBD_C: 33.9 1.5E+02 0.0033 29.2 7.5 27 255-282 68-94 (166)
216 PF07754 DUF1610: Domain of un 33.7 35 0.00075 22.7 1.8 21 531-551 3-24 (24)
217 PRK06920 dnaE DNA polymerase I 33.6 91 0.002 40.5 7.1 71 220-295 933-1004(1107)
218 PRK00448 polC DNA polymerase I 33.3 1.1E+02 0.0025 40.7 8.1 73 218-295 225-299 (1437)
219 PRK07772 single-stranded DNA-b 32.7 5.5E+02 0.012 26.2 12.0 50 570-642 52-101 (186)
220 PRK14288 chaperone protein Dna 32.7 24 0.00051 40.0 1.7 40 786-825 157-200 (369)
221 TIGR00457 asnS asparaginyl-tRN 32.5 3.2E+02 0.0068 31.9 10.9 80 230-323 17-100 (453)
222 KOG2673 Uncharacterized conser 31.6 24 0.00052 40.2 1.4 20 743-762 130-149 (485)
223 cd04318 EcAsnRS_like_N EcAsnRS 31.2 1.2E+02 0.0025 26.1 5.4 59 27-85 18-80 (82)
224 COG0587 DnaE DNA polymerase II 30.7 1.5E+02 0.0032 38.6 8.2 71 220-295 967-1038(1139)
225 COG1570 XseA Exonuclease VII, 30.3 50 0.0011 38.0 3.7 90 218-317 4-96 (440)
226 TIGR00237 xseA exodeoxyribonuc 29.4 1.3E+02 0.0029 34.8 7.1 45 254-300 35-80 (432)
227 KOG3108 Single-stranded DNA-bi 29.0 1.8E+02 0.0039 31.3 7.4 66 353-439 70-141 (265)
228 PRK05672 dnaE2 error-prone DNA 28.6 1.2E+02 0.0026 39.2 7.1 41 256-298 974-1014(1046)
229 PRK14298 chaperone protein Dna 28.0 44 0.00096 37.9 2.8 40 786-825 159-206 (377)
230 PRK12820 bifunctional aspartyl 27.3 5.4E+02 0.012 31.8 11.9 93 222-324 9-109 (706)
231 PRK06826 dnaE DNA polymerase I 27.2 1.5E+02 0.0033 38.7 7.6 60 231-295 993-1052(1151)
232 PRK00476 aspS aspartyl-tRNA sy 27.1 4.3E+02 0.0094 32.0 11.0 84 230-324 18-105 (588)
233 PF00436 SSB: Single-strand bi 27.1 1.5E+02 0.0032 26.4 5.6 35 391-431 49-84 (104)
234 PRK10220 hypothetical protein; 26.8 45 0.00097 30.6 2.0 31 519-555 2-32 (111)
235 PLN02903 aminoacyl-tRNA ligase 26.5 4.1E+02 0.0089 32.5 10.6 95 221-325 62-163 (652)
236 cd04322 LysRS_N LysRS_N: N-ter 26.4 1.1E+02 0.0024 27.8 4.8 60 27-86 18-81 (108)
237 COG1107 Archaea-specific RecJ- 26.3 71 0.0015 37.7 4.0 68 218-295 201-269 (715)
238 PRK14285 chaperone protein Dna 26.2 53 0.0012 37.1 3.1 40 786-826 164-208 (365)
239 KOG2593 Transcription initiati 26.2 35 0.00075 38.8 1.5 27 521-553 129-163 (436)
240 PRK14284 chaperone protein Dna 25.9 35 0.00076 39.0 1.5 40 786-825 176-219 (391)
241 COG5179 TAF1 Transcription ini 25.6 42 0.00091 39.5 2.0 18 742-759 938-957 (968)
242 PRK14286 chaperone protein Dna 25.5 35 0.00076 38.7 1.4 40 786-825 168-211 (372)
243 cd03582 NTR_complement_C5 NTR/ 25.4 4.7E+02 0.01 25.6 9.1 85 230-327 31-124 (150)
244 PRK14279 chaperone protein Dna 25.0 38 0.00082 38.7 1.6 40 786-825 191-234 (392)
245 COG1190 LysU Lysyl-tRNA synthe 24.9 1.7E+02 0.0037 34.2 6.7 59 231-299 63-126 (502)
246 PRK14296 chaperone protein Dna 24.8 52 0.0011 37.3 2.6 42 785-826 166-215 (372)
247 PF03089 RAG2: Recombination a 24.6 71 0.0015 34.5 3.3 50 531-586 66-115 (337)
248 PRK06341 single-stranded DNA-b 24.5 4.4E+02 0.0096 26.3 8.8 35 391-431 54-90 (166)
249 PRK00286 xseA exodeoxyribonucl 24.5 1.8E+02 0.0039 33.7 7.0 43 254-298 41-84 (438)
250 PF08646 Rep_fac-A_C: Replicat 24.4 85 0.0019 30.3 3.7 28 255-283 54-81 (146)
251 PLN03165 chaperone protein dna 24.3 32 0.00069 32.0 0.6 18 809-826 77-95 (111)
252 cd04320 AspRS_cyto_N AspRS_cyt 23.5 1.8E+02 0.0039 26.1 5.4 61 27-87 19-91 (102)
253 KOG1885 Lysyl-tRNA synthetase 23.3 3E+02 0.0065 31.9 8.0 57 231-296 106-168 (560)
254 PLN02603 asparaginyl-tRNA synt 23.2 9.9E+02 0.021 28.8 12.9 81 229-323 107-191 (565)
255 PF11325 DUF3127: Domain of un 23.0 2.6E+02 0.0056 24.7 6.0 59 234-294 2-62 (84)
256 COG5189 SFP1 Putative transcri 22.7 45 0.00098 36.2 1.5 14 542-555 397-410 (423)
257 KOG2044 5'-3' exonuclease HKE1 22.7 31 0.00067 41.9 0.3 19 743-761 262-280 (931)
258 PRK14295 chaperone protein Dna 22.3 44 0.00096 38.1 1.4 41 786-826 184-228 (389)
259 PF04057 Rep-A_N: Replication 22.1 5.5E+02 0.012 23.2 8.3 49 253-302 36-85 (101)
260 PRK06642 single-stranded DNA-b 22.0 4.6E+02 0.01 25.7 8.3 35 391-431 54-90 (152)
261 cd04488 RecG_wedge_OBF RecG_we 21.8 1E+02 0.0022 25.1 3.3 20 560-579 18-37 (75)
262 KOG0314 Predicted E3 ubiquitin 21.6 66 0.0014 37.0 2.6 21 742-762 159-179 (448)
263 PF13426 PAS_9: PAS domain; PD 21.4 4.9E+02 0.011 21.8 7.9 31 564-596 4-34 (104)
264 PF08271 TF_Zn_Ribbon: TFIIB z 21.2 59 0.0013 24.5 1.5 26 522-553 2-29 (43)
265 PRK10767 chaperone protein Dna 21.0 56 0.0012 37.0 1.9 40 786-825 160-203 (371)
266 PRK14301 chaperone protein Dna 20.5 52 0.0011 37.3 1.5 40 786-825 162-205 (373)
267 PF13742 tRNA_anti_2: OB-fold 20.5 4.3E+02 0.0094 23.7 7.3 58 563-644 42-99 (99)
268 PRK14282 chaperone protein Dna 20.5 84 0.0018 35.6 3.2 40 786-825 170-217 (369)
269 TIGR02349 DnaJ_bact chaperone 20.1 61 0.0013 36.4 2.0 41 786-826 161-209 (354)
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=6.5e-119 Score=1048.64 Aligned_cols=577 Identities=43% Similarity=0.754 Sum_probs=494.1
Q ss_pred CCeEEEEeeEeeccchhhhhccccceEEEEEcccccccccccccchhhhhhcCCcccccEEEEceeeeecc-c-CeEEEE
Q 003281 1 MPVLQVMDLKLVVSKQQQQQQHQQQRFRMVLSDGSRSQQGMLATQRNELVTSGLLQIGSVVRLTKFTCNVI-Q-NRMIVI 78 (834)
Q Consensus 1 ~PvlQv~~~k~~~~~~~~~~~~~~~Ryrl~lSDG~~~~~~mLatqln~lv~~g~l~~gsiv~l~~~~~~~v-~-~r~iii 78 (834)
.|||||+++|++.+.+ ..+|||++||||.|++++|||||||++|++|.|++|+||||++|+||+| + +|+|||
T Consensus 24 ~pv~Qv~~~k~~~~~~------~~~ryr~~lsDg~~~~~~ml~t~~n~~~~~~~l~~~~iv~l~~~~~~~~~~~~~~~li 97 (608)
T TIGR00617 24 DPVLQVLDLKPINGAQ------DPRRYRIVISDGIYYSKAMLATQLNPLVREGELQEGTIIRLTKFEVNTIGKDGRKVLI 97 (608)
T ss_pred CcEEEEEeeEEcCCCC------CCceEEEEEECchHHHHHHHHHHHHHHHHhCCccCCCEEEEeEEEEeEEccCCcEEEE
Confidence 4999999999998654 2389999999999999999999999999999999999999999999999 6 689999
Q ss_pred EEeeeEeccCC---CCCCCCcCCCCCCCCCCCCCcCCCCCCCCCCccccccCCccccCCCCCCCCCCccccCCCCCCCCC
Q 003281 79 VMDLDVIIDKC---DPIGKPVPAQRPSSNEQPGSVTGNPQSNATGVSLQHHNNTRVSQLPGDTDAVPAARHVGSNLPPNY 155 (834)
Q Consensus 79 i~~lev~~~~~---~~ig~P~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 155 (834)
|++||||...+ ++||+|+++....... . +.. ..+..|....+ ..|. .
T Consensus 98 i~~~ev~~~~~~~~~~ig~p~~~~~~~~~~------~-~~~---~~~~~~~~~~~---------~~~~-----------~ 147 (608)
T TIGR00617 98 VYELEVVKPELKVRDKIGNPVTYEKYLDSW------H-EEQ---VLASKPATNPA---------NPPN-----------A 147 (608)
T ss_pred EEeeEEeecccccccccCCCcccccccccc------C-ccc---cccccccccCC---------CCCC-----------c
Confidence 99999999754 4899999876210000 0 000 00000000000 0000 0
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcccccCCCCCCCCCCCCceeccccCCCCCceEEE
Q 003281 156 FKPEVGAGSGSFSNQSASFSNPRPEFSRPYASNYARTPQAPYMQSPSMYANRGLVGKSEVPSRIIPIAALNPYMGKWTIK 235 (834)
Q Consensus 156 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~pI~~L~p~~~~w~I~ 235 (834)
..|... ...+.. ++++++.+.++.......++++||++|+||+++|+|+
T Consensus 148 -------------------~~~~~~-----~~~~~~-------~~~~~~~~~~~~~~~~~~~~~~pI~~L~py~~~wtIk 196 (608)
T TIGR00617 148 -------------------KAPKNE-----VASYNN-------AANPERGNAPPAPNSGSTRRVMPIASLSPYQNKWTIK 196 (608)
T ss_pred -------------------cCCCcc-----cccccC-------CCCcccCCCCCCccccCCcceEEHHHCCCCCCceEEE
Confidence 000000 000111 1111122222222222345799999999999999999
Q ss_pred EEEEEeccceeecCCCCCcceEEEEEeeCCCCEEEEEEechHHHhhhhccCcCcEEEEeeeEEecCCcccccCCCeEEEE
Q 003281 236 ARVTAKGELRHYNNQRGDGKVFHFDLLDSDGGEIRVTCFNAVADQFYHQVEAGKIYLVSRGSLKPAQKNFNHLHNDLEIF 315 (834)
Q Consensus 236 aRV~~Ks~lr~~~n~~g~Gk~f~~~L~De~g~~I~at~f~~~~d~f~~~l~eG~vy~is~~~V~~a~~~~~~~~~~yeI~ 315 (834)
|||++||++|+|.+++|+|++|+|+|+| +||+|+|++|++.+++|+++|+||+||+|++|+|++++++|+++.|+|||+
T Consensus 197 aRV~~Ks~ir~~~~~~gegkvfsv~L~D-egg~Irat~f~~~~dkf~~~l~eG~VY~Is~~~Vk~an~~y~~~~~~yei~ 275 (608)
T TIGR00617 197 ARVTNKSEIRTWSNARGEGKLFNVELLD-ESGEIRATAFNEQADKFYDIIQEGKVYYISKGSLKPANKQFTNLGNDYEMT 275 (608)
T ss_pred EEEEeccccceecCCCCCceeeEEEEec-CCCeEEEEECchHHHHHhhhcccCCEEEECceEEEEccccccCCCCCEEEE
Confidence 9999999999999999999999999999 799999999999999999999999999999999999999999999999999
Q ss_pred EccCccEEEecCCCCCCccccccccccccccccCCCceeeEEEEEEEecCCeeEEcc-CCceeeEEEEEEeccCCcEEEE
Q 003281 316 LDMTSMVQLCYEDDASIPRQQFHFRPINDVEGMENNSVVDLIGVVSYISPTASLMRK-NGTETQKRTLHLRDMSGRSVEL 394 (834)
Q Consensus 316 f~~~T~I~~~~d~~~~iP~~~~~f~~i~dI~~~~~~~~vDVIGvV~~V~~~~~i~~k-~g~~~~kr~i~L~D~s~~si~v 394 (834)
|+.+|+|++|.+ +..||.+.|+|++|+||.+.+.+.+|||||+|++|+++.+|++| +|++..||+|+|+|+|+.+|+|
T Consensus 276 f~~~T~I~~~~d-~~~iP~~~~~f~~i~dI~~~~~~~~VDVIGvV~~v~~~~~i~~k~~g~~~~kR~i~L~D~sg~sI~v 354 (608)
T TIGR00617 276 LDRDTVIEECED-ETAIPKIQFNFVKIDDIGGYEGNSLVDVIGIVQSVSPTQTITSRKNNKEFPKRDITLVDDSGKSVRV 354 (608)
T ss_pred ECCCeEEEECCC-cccCCcccccceEHHHhhhhcCCCCccEEEEEeEecCceEEEEcCCCCeeeeEEEEEEeCCCCEEEE
Confidence 999999999965 45699999999999999998888899999999999999999865 8999999999999999999999
Q ss_pred EEcCCccchhhhhhhhcccCCCccEEEEEEEEEeecCCeEEEeecceEEEEcCCchHHHHHHHHHHhcCCccceeeeccc
Q 003281 395 TLWGNFCNDDGLRLQHMCDSGVFPILAVKAGRVSDFNGKVVGTISTTQLFIEPDFPEAHRLKEWFEKEGKNTQSVSISRD 474 (834)
Q Consensus 395 tLWg~~a~~~~~~l~~~~~~~~~~Vv~ik~~rV~~f~G~~Ls~~~~S~i~inPd~pe~~~l~~w~~~~g~~~~~~sls~~ 474 (834)
||||++|..+ +...++||+|+++||++|+|++||+.++|+|++|||+||+++|+.||+++|....+.+++..
T Consensus 355 TLWG~~A~~~--------~~~~~~Vva~kg~~V~~f~g~sLs~~~~S~i~iNPdipEa~~L~~w~~~~g~~~~~~s~~~~ 426 (608)
T TIGR00617 355 TLWGDDATKF--------DVSVQPVIAIKGVRVSDFGGKSLSTGGSSTIIVNPDIPEAEKLKGWYDNEGKGTMASSISDM 426 (608)
T ss_pred EEEhhhhhhc--------CCCCCCEEEEEeEEEEecCCceEeccCCceEEECCCcHHHHHHHHHHHhcCCCccceeehhc
Confidence 9999999864 34578999999999999999999999999999999999999999999999988776666554
Q ss_pred cc--cCCccchhccHhhhhhcCCCCCCCCceEEEEEEEEEEecCCeeeeCCCCCcCCCCcCcccccCCCCceecCCCCCc
Q 003281 475 SL--SVGRADIRKTVSQIKDEGLGTKEKPDWITVSATIVYIKCDNFCYTACPIMIGDRPCNKKVMNNGDGRWHCDRCDQS 552 (834)
Q Consensus 475 ~~--~~~~~~~~ktI~ei~~~~lg~~~k~~~~~v~atI~~I~~d~~~Y~aC~~~~~~~~C~KKv~~~~dg~~~CekC~~~ 552 (834)
.+ ..++..+++||+||+++++|.+++++||+|+|+|++|+.|+|||+|||++ .|+|||+++.+|.|+|++|+++
T Consensus 427 ~~~~~~~~~~~~ktI~ei~~~~lg~~~k~~~f~v~atI~~Ik~d~~~Y~ACp~~----~CnKKV~~~~~g~~~CekC~~~ 502 (608)
T TIGR00617 427 MSGRVGGSNAERKTIAEIQAENLGKSDKPDYFSVKATISYLKPDNALYRACPSE----DCNKKVVDQGDGTYRCEKCNKN 502 (608)
T ss_pred cccccCCcccccccHHHHhhhccCCCCCCcEEEEEEEEEEEecCCeEeccCChh----hCCCccccCCCCCEECCCCCCC
Confidence 22 13446789999999999999999999999999999999999999999954 3999999888899999999999
Q ss_pred cccceEEEEEEEEEEeCCCeEEEEEehHHHHHHhCCCHHHHHhhhccCCChhHHHHHHHHhcCceEEEEEEEeecccCcc
Q 003281 553 VVECDYRYILQFQIQDHTGLTWVTAFQECAEEIMGMSAKDLYSLKYVDQNDEKFGEVVRNATFTKYLFKLKVKEETFSDE 632 (834)
Q Consensus 553 ~~~~~~ry~l~~~i~D~Tg~~~~~~F~e~ae~llG~sA~el~~l~~ee~d~~~~~~~l~~~~~k~~~f~l~~k~~~ynde 632 (834)
+++|+|||+|++.|+|+||++|+++|++.|++|||++|+||.+++ ++|++.|+++|+++.|++|+|+|++++++||||
T Consensus 503 ~~~~~~RYil~~~i~D~Tg~~~~t~F~~~ae~llG~sA~eL~~l~--~~~~~~~~~i~~~~~~~~~~f~~~~k~e~yn~e 580 (608)
T TIGR00617 503 FAEFKYRYILQISISDETGQLWVTAFNDQAEQILGKSAAELGELK--EEDPDEFEAIFQEAQFVPYIFRLRVKQDTYNDE 580 (608)
T ss_pred CCCccEEEEEEEEEEeCCCCEEEEEEhHHHHHHcCCCHHHHHHHH--hcCHHHHHHHHHHhhCcEEEEEEEEEEcccCCE
Confidence 999999999999999999999999999999999999999999999 678899999999999999999999999999999
Q ss_pred ceEEEEEEEeeecChHHHHHHHHHHHHh
Q 003281 633 QRVKSTVVKAERYNYSSETRFILDLMDK 660 (834)
Q Consensus 633 ~rvk~~v~~~~~vd~~~e~~~Ll~~i~~ 660 (834)
.|+|++|++++||||++|+++||++|++
T Consensus 581 ~r~~~~v~~~~~vd~~~e~~~L~~~i~~ 608 (608)
T TIGR00617 581 SRQKYTVMSVDPVNYRAEAKYLLQEIEK 608 (608)
T ss_pred eeEEEEEEEeeeCCHHHHHHHHHHHhcC
Confidence 9999999999999999999999999964
No 2
>PRK12366 replication factor A; Reviewed
Probab=100.00 E-value=5.6e-63 Score=581.57 Aligned_cols=356 Identities=20% Similarity=0.338 Sum_probs=319.1
Q ss_pred CceeccccCCC-CC-ceEEEEEEEEeccceeecCCCCCcceEEEEEeeCCCCEEEEEEechHHHhhhhccCcCcEEEEee
Q 003281 218 RIIPIAALNPY-MG-KWTIKARVTAKGELRHYNNQRGDGKVFHFDLLDSDGGEIRVTCFNAVADQFYHQVEAGKIYLVSR 295 (834)
Q Consensus 218 ~~~pI~~L~p~-~~-~w~I~aRV~~Ks~lr~~~n~~g~Gk~f~~~L~De~g~~I~at~f~~~~d~f~~~l~eG~vy~is~ 295 (834)
.++||++|+|| .+ +|+|+|||+.|+++|+|.+.+|+|++|+++|.|++ |+|++|+|++.+++|++ |++|+||+|++
T Consensus 278 ~~~pI~~L~~~~~g~~~~I~grV~~~~~~R~f~~~~g~gkv~s~~l~D~t-G~IR~t~w~~~~d~~~~-l~~G~vy~is~ 355 (637)
T PRK12366 278 EIVNIEELTEFEDGEEVDVKGRIIAISDKREVERDDRTAEVQDIELADGT-GRVRVSFWGEKAKILEN-LKEGDAVKIEN 355 (637)
T ss_pred CceeHHHCCcccCCCEEEEEEEEEecCCceEEEcCCCcEEEEEEEEEcCC-CeEEEEEeCchhhhhcc-cCCCCEEEEec
Confidence 46899999999 65 89999999999999999999999999999999985 69999999999999998 59999999999
Q ss_pred eEEecCCcccccCCCeEEEEEccCccEEEecCCCCCCccccccccccccccccC-CCceeeEEEEEEEecCCeeEEccCC
Q 003281 296 GSLKPAQKNFNHLHNDLEIFLDMTSMVQLCYEDDASIPRQQFHFRPINDVEGME-NNSVVDLIGVVSYISPTASLMRKNG 374 (834)
Q Consensus 296 ~~V~~a~~~~~~~~~~yeI~f~~~T~I~~~~d~~~~iP~~~~~f~~i~dI~~~~-~~~~vDVIGvV~~V~~~~~i~~k~g 374 (834)
++|+..+. +...+.|||+|+..|.|.+ +++..+|...|+|++|.+|.+++ .+..|||+|+|++++++.+|++++|
T Consensus 356 ~~vk~y~~--~~~~~~~El~~~~~s~I~~--d~~~~~p~~~~~~~~i~dI~~~~~~~~~VdVig~V~~v~~~~~i~~k~G 431 (637)
T PRK12366 356 CKVRTYYD--NEGEKRVDLNAGYSSEIIK--DESISFEEIEEKIYKIKDILNLEEDDNDITVIARVVEDYPVNEFERSDG 431 (637)
T ss_pred CEEeeccc--cCCCcCEEEEcCCceEEEe--ccCCcccceeeccccHHHhhcccCCCcEEEEEEEEEEccCceEEEecCC
Confidence 99984332 1345789999999999988 44556999999999999999985 6889999999999999999998899
Q ss_pred ceeeEEEEEEeccCCcEEEEEEcCCccchhhhhhhhcccCCCccEEEEEEEEEeecCCe-EEEeecceEEEEcCCchHHH
Q 003281 375 TETQKRTLHLRDMSGRSVELTLWGNFCNDDGLRLQHMCDSGVFPILAVKAGRVSDFNGK-VVGTISTTQLFIEPDFPEAH 453 (834)
Q Consensus 375 ~~~~kr~i~L~D~s~~si~vtLWg~~a~~~~~~l~~~~~~~~~~Vv~ik~~rV~~f~G~-~Ls~~~~S~i~inPd~pe~~ 453 (834)
++..+|+++|.|+|| +|++||||++|.. ....+++|+|++++|++|+|+ +|++.++|+|.+||+.|+
T Consensus 432 ~~~~~r~i~l~D~TG-~I~vtlWg~~a~~---------~~~~G~vi~i~~~~V~~~~g~~~Ls~~~~s~i~~~p~~~e-- 499 (637)
T PRK12366 432 SKGKVRNIELADGTG-SIRLTLWDDDAEI---------EIKEGDAIKILHPYVKENGDYLDLSIGRYGRIEINPEGEI-- 499 (637)
T ss_pred CEeEEEEEEEEeCCC-EEEEEEecccccc---------CCCCCCEEEEEeeEEEeCCCeeEEEecCcceEEECCCCcc--
Confidence 999999999999999 8999999999963 123679999999999999995 999999999999999987
Q ss_pred HHHHHHHhcCCccceeeeccccccCCccchhccHhhhhhcCCCCCCCCceEEEEEEEEEEecCCeeeeCCCCCcCCCCcC
Q 003281 454 RLKEWFEKEGKNTQSVSISRDSLSVGRADIRKTVSQIKDEGLGTKEKPDWITVSATIVYIKCDNFCYTACPIMIGDRPCN 533 (834)
Q Consensus 454 ~l~~w~~~~g~~~~~~sls~~~~~~~~~~~~ktI~ei~~~~lg~~~k~~~~~v~atI~~I~~d~~~Y~aC~~~~~~~~C~ 533 (834)
|+ ..+++|++|+++ ++|+++|+|++|+.++++|+||| .||
T Consensus 500 -l~-------------------------~~~~~I~~i~~~--------~~~~v~g~i~~i~~~~~~y~aCp------~Cn 539 (637)
T PRK12366 500 -IK-------------------------SNRKFIADLEED--------DTVEIRGTVVDIRKQKIILYLCP------NCR 539 (637)
T ss_pred -cc-------------------------ccccCHHHcccC--------CeEEEEEEEEEEeCCCEEEeccc------ccC
Confidence 22 036889999763 35999999999999999999999 699
Q ss_pred cccccCCCCceecCCCCCccccceEEEEEEEEEEeCCCeEEEEEehHHHHHHhCCCHHHHHhhhccCCChhHHHHHHHHh
Q 003281 534 KKVMNNGDGRWHCDRCDQSVVECDYRYILQFQIQDHTGLTWVTAFQECAEEIMGMSAKDLYSLKYVDQNDEKFGEVVRNA 613 (834)
Q Consensus 534 KKv~~~~dg~~~CekC~~~~~~~~~ry~l~~~i~D~Tg~~~~~~F~e~ae~llG~sA~el~~l~~ee~d~~~~~~~l~~~ 613 (834)
|||.+ .+|.|+|++|++. +|.|||+|++.|+|+||++|+++|+|.|++||||+|+||.+|. + +.|+++
T Consensus 540 kKv~~-~~g~~~C~~c~~~--~p~~~~~l~~~i~D~TG~~~~t~f~e~ae~l~G~sa~el~~l~--~-------~~l~~~ 607 (637)
T PRK12366 540 KRVEE-VDGEYICEFCGEV--EPNELLMLNFTLDDGTGTINCRFYGKNVEKLLGMSKEELKELN--L-------EALEDL 607 (637)
T ss_pred eEeEc-CCCcEECCCCCCC--CCcEEEEEEEEEEcCCCCEEEEEEhHHhHHHhCCCHHHHHHHH--H-------HHHHHh
Confidence 99975 6789999999988 7999999999999999999999999999999999999999987 2 667789
Q ss_pred cCceEEEEEEEeecccCccceEEEEEEEeeecCh
Q 003281 614 TFTKYLFKLKVKEETFSDEQRVKSTVVKAERYNY 647 (834)
Q Consensus 614 ~~k~~~f~l~~k~~~ynde~rvk~~v~~~~~vd~ 647 (834)
+|++|.|+++++++ |++ ++++|.++.|+|+
T Consensus 608 ~g~~~~~~~~~k~~--~~~--~r~~v~~v~~~d~ 637 (637)
T PRK12366 608 LGEEVVFYGNVSFR--NEE--LRFNVRRVNNVDV 637 (637)
T ss_pred cCcEEEEEEEEeec--Cce--eEEEEEEeecccC
Confidence 99999999999988 554 4599999999985
No 3
>PRK08402 replication factor A; Reviewed
Probab=100.00 E-value=2.1e-43 Score=384.84 Aligned_cols=281 Identities=21% Similarity=0.314 Sum_probs=239.9
Q ss_pred cccccccccccCCCceeeEEEEEEEecCCeeEEccCCceeeEEEEEEeccCCcEEEEEEcCCccchhhhhhhhcccCCCc
Q 003281 338 HFRPINDVEGMENNSVVDLIGVVSYISPTASLMRKNGTETQKRTLHLRDMSGRSVELTLWGNFCNDDGLRLQHMCDSGVF 417 (834)
Q Consensus 338 ~f~~i~dI~~~~~~~~vDVIGvV~~V~~~~~i~~k~g~~~~kr~i~L~D~s~~si~vtLWg~~a~~~~~~l~~~~~~~~~ 417 (834)
.+++|.||.. ....|.++|.|+++++..+|++++|.....++++|.|+|| .+++|||++.|..+... ...+
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 3667777763 3368999999999999999999999988999999999999 57999999998743111 2368
Q ss_pred cEEEEEEEEEeec-CCe-EEEeecceEEEEcCCchHHHHHHHHHHhcCCccceeeeccccccCCccchhccHhhhhhcCC
Q 003281 418 PILAVKAGRVSDF-NGK-VVGTISTTQLFIEPDFPEAHRLKEWFEKEGKNTQSVSISRDSLSVGRADIRKTVSQIKDEGL 495 (834)
Q Consensus 418 ~Vv~ik~~rV~~f-~G~-~Ls~~~~S~i~inPd~pe~~~l~~w~~~~g~~~~~~sls~~~~~~~~~~~~ktI~ei~~~~l 495 (834)
+||.|++++|++| +|+ +|++..+|+|.+|||+|+++.+. +++...+ ....+++|++|.+
T Consensus 132 dvi~I~~a~V~e~~~G~~eLsvg~~s~i~~~pd~~ea~~i~-------------~~~~~~~---~~~~~k~I~ei~~--- 192 (355)
T PRK08402 132 DVIKVIDAQVRESLSGLPELHINFRARIILNPDDPRVEEIP-------------PLEEVRS---YNYTRKKIGELEG--- 192 (355)
T ss_pred CEEEEECCEEeecCCCcEEEEECCCceEEeCCCcccccccc-------------ccccccc---ccccccCHHHccc---
Confidence 9999999999995 998 99999999999999999987621 2211100 1456899999965
Q ss_pred CCCCCCceEEEEEEEEEEecCCeeeeCCCCCcCCCCcCcccc-cCCCCceecCCCCCccccceEEEEEEEEEEeCCCeEE
Q 003281 496 GTKEKPDWITVSATIVYIKCDNFCYTACPIMIGDRPCNKKVM-NNGDGRWHCDRCDQSVVECDYRYILQFQIQDHTGLTW 574 (834)
Q Consensus 496 g~~~k~~~~~v~atI~~I~~d~~~Y~aC~~~~~~~~C~KKv~-~~~dg~~~CekC~~~~~~~~~ry~l~~~i~D~Tg~~~ 574 (834)
| + +||.|+|+|++|+. +++|+||| .|||||+ +..++.|+|+.|++. +|.|||+|++.|.|+||++|
T Consensus 193 g--d--~~v~v~g~Iv~i~~-~~~y~aCp------~CnKkv~~~~~~~~~~Ce~~~~v--~p~~ryil~~~l~D~TG~~~ 259 (355)
T PRK08402 193 G--E--RFVEVRGTIAKVYR-VLVYDACP------ECRRKVDYDPATDTWICPEHGEV--EPIKITILDFGLDDGTGYIR 259 (355)
T ss_pred C--C--cEEEEEEEEEEEec-CeeEecCC------CCCeEEEEecCCCCEeCCCCCCc--CcceeEEEEEEEEcCCCcEE
Confidence 1 2 68999999999998 78999999 6999997 777889999999873 78999999999999999999
Q ss_pred EEEehHHHHHHhCCCHHHHHhh-h---ccCCCh-----hHHHHHHHHhcCceEEEEEEEeecccCccceEEEEEEEeeec
Q 003281 575 VTAFQECAEEIMGMSAKDLYSL-K---YVDQND-----EKFGEVVRNATFTKYLFKLKVKEETFSDEQRVKSTVVKAERY 645 (834)
Q Consensus 575 ~~~F~e~ae~llG~sA~el~~l-~---~ee~d~-----~~~~~~l~~~~~k~~~f~l~~k~~~ynde~rvk~~v~~~~~v 645 (834)
+++|+|.|++|||++|+||.++ + .+..++ ..|.+.+..++|++|.|+++++++.||++. ++|.++.|+
T Consensus 260 vt~f~e~ae~llG~sa~el~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~rg~~~~d~y~~~~---~~v~~~~~v 336 (355)
T PRK08402 260 VTLFGDDAAELLGVEPEEIAEKLKELIEMGLTPKEAARKLAEEEFYNIIGREIVVRGNVIEDRFLGLI---LKASSWDEV 336 (355)
T ss_pred EEEecHHHHHHhCCCHHHHHHHHHHhhhcccchhhhhhhHHHHHHHHhcCeEEEEEEEEEecccCCeE---EEEEEcccC
Confidence 9999999999999999999988 3 221133 678889999999999999999999999855 999999999
Q ss_pred ChHHHHHHHHHHHHhhc
Q 003281 646 NYSSETRFILDLMDKLK 662 (834)
Q Consensus 646 d~~~e~~~Ll~~i~~~~ 662 (834)
||++|+++|+++|.++.
T Consensus 337 d~~~e~~~l~~~i~~~~ 353 (355)
T PRK08402 337 DYKREIERVRAELEELG 353 (355)
T ss_pred CHHHHHHHHHHHHHHhh
Confidence 99999999999998875
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=1.4e-34 Score=288.19 Aligned_cols=166 Identities=45% Similarity=0.878 Sum_probs=155.7
Q ss_pred HhhhhhcCCCCCCCCceEEEEEEEEEEecCCeeeeCCCCCcCCCCcCcccccCCCCceecCCCCCccccceEEEEEEEEE
Q 003281 487 VSQIKDEGLGTKEKPDWITVSATIVYIKCDNFCYTACPIMIGDRPCNKKVMNNGDGRWHCDRCDQSVVECDYRYILQFQI 566 (834)
Q Consensus 487 I~ei~~~~lg~~~k~~~~~v~atI~~I~~d~~~Y~aC~~~~~~~~C~KKv~~~~dg~~~CekC~~~~~~~~~ry~l~~~i 566 (834)
|++|++++++..+++++|+|+|+|..|+.++|||+||| .|+|||.+..++.|+|++|++.+++|.+||+|++.|
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 46788888887778999999999999999999999999 699999876668999999999999999999999999
Q ss_pred EeCCCeEEEEEehHHHHHHhCCCHHHHHhhhccCCChhHHHHHHHHhcCceEEEEEEEeecccCccceEEEEEEEeeecC
Q 003281 567 QDHTGLTWVTAFQECAEEIMGMSAKDLYSLKYVDQNDEKFGEVVRNATFTKYLFKLKVKEETFSDEQRVKSTVVKAERYN 646 (834)
Q Consensus 567 ~D~Tg~~~~~~F~e~ae~llG~sA~el~~l~~ee~d~~~~~~~l~~~~~k~~~f~l~~k~~~ynde~rvk~~v~~~~~vd 646 (834)
+|+||++|+++|++.|++|||++|+||.++. +++++.++++|.+++|++|+|+++++.++||+|.|++++|.+++|++
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 9999999999999999999999999999998 44578899999999999999999999999999999999999999999
Q ss_pred hHHHHHHHHHHHHh
Q 003281 647 YSSETRFILDLMDK 660 (834)
Q Consensus 647 ~~~e~~~Ll~~i~~ 660 (834)
+++|+++|++.|++
T Consensus 153 ~~~~~~~l~~~i~~ 166 (166)
T cd04476 153 YKKESKRLIQSIEK 166 (166)
T ss_pred HHHHHHHHHHHhhC
Confidence 99999999999863
No 5
>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=1.2e-34 Score=282.26 Aligned_cols=146 Identities=45% Similarity=0.836 Sum_probs=124.7
Q ss_pred eEEEEEEEEEEecCCeeeeCCCCCcCCCCcCcccccCCCCceecCCCCCccccceEEEEEEEEEEeCCCeEEEEEehHHH
Q 003281 503 WITVSATIVYIKCDNFCYTACPIMIGDRPCNKKVMNNGDGRWHCDRCDQSVVECDYRYILQFQIQDHTGLTWVTAFQECA 582 (834)
Q Consensus 503 ~~~v~atI~~I~~d~~~Y~aC~~~~~~~~C~KKv~~~~dg~~~CekC~~~~~~~~~ry~l~~~i~D~Tg~~~~~~F~e~a 582 (834)
||+|+|+|..|+.++|||+|||++ .|+|||...++|.|+|++|++.+++|.+||+|++.|+|+||++|+++|++.|
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 799999999999999999999965 5999998877889999999999999999999999999999999999999999
Q ss_pred HHHhCCCHHHHHhhhccCCChhHHHHHHHHhcCceEEEEEEEeecccCccceEEEEEEEeeecChHHHHHHH
Q 003281 583 EEIMGMSAKDLYSLKYVDQNDEKFGEVVRNATFTKYLFKLKVKEETFSDEQRVKSTVVKAERYNYSSETRFI 654 (834)
Q Consensus 583 e~llG~sA~el~~l~~ee~d~~~~~~~l~~~~~k~~~f~l~~k~~~ynde~rvk~~v~~~~~vd~~~e~~~L 654 (834)
++|||++|+||.++. +.++..++++|.+++|++|.|+|+++.++|+++.|++++|++++|+||++|+++|
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 6
>PRK07218 replication factor A; Provisional
Probab=100.00 E-value=9.4e-32 Score=298.96 Aligned_cols=359 Identities=15% Similarity=0.175 Sum_probs=286.4
Q ss_pred CCceeccccCCCCCceEEEEEEEEeccceeecCCCCCcceEEEEEeeCCCCEEEEEEechHHHhhhhccCcCcEEEEeee
Q 003281 217 SRIIPIAALNPYMGKWTIKARVTAKGELRHYNNQRGDGKVFHFDLLDSDGGEIRVTCFNAVADQFYHQVEAGKIYLVSRG 296 (834)
Q Consensus 217 ~~~~pI~~L~p~~~~w~I~aRV~~Ks~lr~~~n~~g~Gk~f~~~L~De~g~~I~at~f~~~~d~f~~~l~eG~vy~is~~ 296 (834)
++.++|++|.+.+...+|+|||+.+|+ |+|....++|.+.+++|.|+ .|.|+.|+|++. -|++|++|.|.++
T Consensus 56 ~~~~kI~Di~~~~~~V~v~~kVl~i~~-rt~r~dg~~g~v~~~~igDe-TG~Ir~tlW~~~------~l~~Gdvv~I~na 127 (423)
T PRK07218 56 PSSKDIKELSTDDKNVTVTGRVLTIGE-RSIRYQGDDHVIYEGILADE-TGTISYTAWKDF------GLSPGDTVTIGNA 127 (423)
T ss_pred CCCccHhhCCCCCceeEEEEEEEEecc-eeEecCCCceEEEEEEEECC-CCeEEEEEECCC------CCCCCCEEEEecc
Confidence 457899999999988899999999999 99976666899999999998 589999999964 2999999999999
Q ss_pred EEecCCcccccCCCeEEEEEccCccEEEecCCCCCCccccccccccccccccC-CCceeeEEEEEEEecCCeeEEccCCc
Q 003281 297 SLKPAQKNFNHLHNDLEIFLDMTSMVQLCYEDDASIPRQQFHFRPINDVEGME-NNSVVDLIGVVSYISPTASLMRKNGT 375 (834)
Q Consensus 297 ~V~~a~~~~~~~~~~yeI~f~~~T~I~~~~d~~~~iP~~~~~f~~i~dI~~~~-~~~~vDVIGvV~~V~~~~~i~~k~g~ 375 (834)
.++.-+ ..++|.++..|.|++..+ +..+|. ....+.+|.++. ....|+|.|.|.++.+ .+|++++|.
T Consensus 128 ~vre~~-------g~~el~ig~~t~I~~~de-~~~~~~---~~~~~~kI~DL~~g~~~V~v~g~Vl~~~~-r~f~~~dg~ 195 (423)
T PRK07218 128 GVREWD-------GRPELNIGESTTVSLLDD-SSLPPY---SIGGDKKLIDLGPGDRGVNVEARVLELEH-REIDGRDGE 195 (423)
T ss_pred EeeccC-------CceEEeccCcceEEEcCc-ccccCc---cccCccchhhccCCCCceEEEEEEEEecc-eeEEcCCCC
Confidence 887654 347999999999998643 333332 233334444443 3457999999999965 689888875
Q ss_pred eeeEEEEEEeccCCcEEEEEEcCCccchhhhhhhhcccCCCccEEEEEEEEEeecCCe-EEEeecceEEEEcCCchHHHH
Q 003281 376 ETQKRTLHLRDMSGRSVELTLWGNFCNDDGLRLQHMCDSGVFPILAVKAGRVSDFNGK-VVGTISTTQLFIEPDFPEAHR 454 (834)
Q Consensus 376 ~~~kr~i~L~D~s~~si~vtLWg~~a~~~~~~l~~~~~~~~~~Vv~ik~~rV~~f~G~-~Ls~~~~S~i~inPd~pe~~~ 454 (834)
...++..|.|+|| +|++|||++.+. + ..+.+|.|.++.|++|+|+ +|+....|.|...++..++.
T Consensus 196 -~~v~~giigDeTG-~Ir~tlW~~~~~-----l------~~Gd~v~I~na~v~e~~G~~elnv~~~t~I~~~d~~i~v~- 261 (423)
T PRK07218 196 -TTILSGVLADETG-RLPFTDWDPLPE-----I------EIGASIRIEDAYVREFRGVPSVNVSEFTTVEALDREVSVS- 261 (423)
T ss_pred -eEEEEEEEECCCc-eEEEEEeccccc-----C------CCCCEEEEeeeEEeccCCeEEEEECCceEEEECCCCcccc-
Confidence 4689999999999 799999998763 1 2678999999999999997 89999999999877542211
Q ss_pred HHHHHHhcCCccceeeeccccccCCccchhccHhhhhhcCCCCCCCCce-EEEEEEEEEEecCCeeeeCCCCCcCCCCcC
Q 003281 455 LKEWFEKEGKNTQSVSISRDSLSVGRADIRKTVSQIKDEGLGTKEKPDW-ITVSATIVYIKCDNFCYTACPIMIGDRPCN 533 (834)
Q Consensus 455 l~~w~~~~g~~~~~~sls~~~~~~~~~~~~ktI~ei~~~~lg~~~k~~~-~~v~atI~~I~~d~~~Y~aC~~~~~~~~C~ 533 (834)
....++.|.++.+. ...| ..|.++|+.|...+..|..|| .|+
T Consensus 262 -------------------------~~~~~~~I~e~~~~------~g~~~Vev~G~Iv~i~~gsgli~rCP------~C~ 304 (423)
T PRK07218 262 -------------------------KDPPRLKIREAVER------GGIFDVELVGNIISVRDGSGLIERCP------ECG 304 (423)
T ss_pred -------------------------CCccccchhhhhcc------CCcceEEEEEEEEEeccCCcceecCc------Ccc
Confidence 11245778888763 1234 799999999999988999999 699
Q ss_pred cccccCCCCceecCCCCCccccceEEEEEEEEEEeCCCeEEEEEehHHHHHHhCCCHHHHHhhhccCCChhHHHH-HHHH
Q 003281 534 KKVMNNGDGRWHCDRCDQSVVECDYRYILQFQIQDHTGLTWVTAFQECAEEIMGMSAKDLYSLKYVDQNDEKFGE-VVRN 612 (834)
Q Consensus 534 KKv~~~~dg~~~CekC~~~~~~~~~ry~l~~~i~D~Tg~~~~~~F~e~ae~llG~sA~el~~l~~ee~d~~~~~~-~l~~ 612 (834)
|+|. .|.|+.|++. .+.+-.++.+.|.|+||++.+++|.|.+++|+|++.++..+|..+..|.....+ +-..
T Consensus 305 r~v~-----~~~C~~hG~v--e~~~dlrik~vLDDGtg~~~~~~~~e~~e~l~G~~~e~a~~~~~~~~d~~~v~~~i~~~ 377 (423)
T PRK07218 305 RVIQ-----KGQCRSHGAV--EGEDDLRIKAILDDGTGSVTVILDRELTEIVYGGTLEDAEELAREAMDKDVVAEDIRER 377 (423)
T ss_pred cccc-----CCcCCCCCCc--CCeeeeEEEEEEECCCCeEEEEEChhhhHhHhCCCHHHHHHHHHhhhcchhhHHHHHHh
Confidence 9994 3899999975 688999999999999999999999999999999999999888754444444444 4477
Q ss_pred hcCceEEEEEEEeecccCccceEEEEEEEeeecC--hHHHHHHHHHH
Q 003281 613 ATFTKYLFKLKVKEETFSDEQRVKSTVVKAERYN--YSSETRFILDL 657 (834)
Q Consensus 613 ~~~k~~~f~l~~k~~~ynde~rvk~~v~~~~~vd--~~~e~~~Ll~~ 657 (834)
++|+.|.|+-.+..+.|. ..+.+.+++.+| .++-++.||..
T Consensus 378 llG~~~~v~G~~~~~~~g----~~~~a~~~~~~~~~~~~r~~~~l~~ 420 (423)
T PRK07218 378 LVGREYRVRGNLSVDEYG----ANLVAESFWVPDDDPAKRAVALLAE 420 (423)
T ss_pred hcCcEEEEEeccccccCC----cEEEEeEccccCCCHHHHHHHHHHh
Confidence 999999999998877773 566667777665 45555556543
No 7
>PRK07211 replication factor A; Reviewed
Probab=99.97 E-value=2.7e-30 Score=289.33 Aligned_cols=274 Identities=20% Similarity=0.266 Sum_probs=216.8
Q ss_pred CceeccccCCCCCceEEEEEEEEeccceeecCC--CCCcceEEEEEeeCCCCEEEEEEechHHHhhhhccCcCcEEEEee
Q 003281 218 RIIPIAALNPYMGKWTIKARVTAKGELRHYNNQ--RGDGKVFHFDLLDSDGGEIRVTCFNAVADQFYHQVEAGKIYLVSR 295 (834)
Q Consensus 218 ~~~pI~~L~p~~~~w~I~aRV~~Ks~lr~~~n~--~g~Gk~f~~~L~De~g~~I~at~f~~~~d~f~~~l~eG~vy~is~ 295 (834)
.+.+|++|+||+++|+|+|||+.|+++|+|.+. +++|+||+++|.|+ .|+|++|+|++.+++|++.|++|+||+|.+
T Consensus 52 e~~~I~dL~pg~~~vtI~aRV~~~~~~Rt~~~~~~~~eGkv~~v~l~De-TG~Ir~TlW~d~ad~~~~~Le~GdV~~I~~ 130 (485)
T PRK07211 52 EVNGIADIEPGMDEVKFLAKVLSIGDLRTFERDGEDEDGRVINVEVADE-TGSVRVAFWDEQAVAAEEELEVGQVLRIKG 130 (485)
T ss_pred ccccHhhCCCCCCceEEEEEEeEccCceEEEeCCCCCCcEEEEEEEEcC-CCeEEEEEechHhHhhhcccCCCCEEEEec
Confidence 467999999999999999999999999999987 45899999999997 579999999999999999999999999964
Q ss_pred eEEecCCcccccCCCeEEEEEccCccEEEecCCCCCCccccccccccccccccCCCceeeEEEEEEEecCCeeEEccCCc
Q 003281 296 GSLKPAQKNFNHLHNDLEIFLDMTSMVQLCYEDDASIPRQQFHFRPINDVEGMENNSVVDLIGVVSYISPTASLMRKNGT 375 (834)
Q Consensus 296 ~~V~~a~~~~~~~~~~yeI~f~~~T~I~~~~d~~~~iP~~~~~f~~i~dI~~~~~~~~vDVIGvV~~V~~~~~i~~k~g~ 375 (834)
.++ +.|+.+ ||+|+ .|+++.+. .+|....+|.+|.+|.. .+..+||+|+|++++++.+|.+++|+
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 48887543 45554569999999985 46789999999999999999988999
Q ss_pred eeeEEEEEEeccCCcEEEEEEcCCccchhhhhhhhcccCCCccEEEEEEEEEeecCC-eEEEeecceEEEEcCCchHHHH
Q 003281 376 ETQKRTLHLRDMSGRSVELTLWGNFCNDDGLRLQHMCDSGVFPILAVKAGRVSDFNG-KVVGTISTTQLFIEPDFPEAHR 454 (834)
Q Consensus 376 ~~~kr~i~L~D~s~~si~vtLWg~~a~~~~~~l~~~~~~~~~~Vv~ik~~rV~~f~G-~~Ls~~~~S~i~inPd~pe~~~ 454 (834)
+...++++|.|+|| +|++|||++.|..+ ..| ..++||.|++++|++|+| .+|++...|.|..-++. +.
T Consensus 196 eGkv~sv~L~DeTG-~IR~TlW~d~Ad~~-~~l------e~G~Vv~I~~a~Vre~~g~~ELsl~~~s~I~~~~de--v~- 264 (485)
T PRK07211 196 EGRVSNLTVGDETG-RVRVTLWDDRADLA-EEL------DAGESVEIVDGYVRERDGSLELHVGDRGAVEEVDED--VE- 264 (485)
T ss_pred eeEEEEEEEEcCCC-eEEEEEechhhhhh-ccC------CCCCEEEEEeeEEEecCCcEEEEECCCceEEECCcc--cc-
Confidence 99999999999999 69999999999875 222 368999999999999966 58999888888765441 10
Q ss_pred HHHHHHhcCCccceeeeccccccCCccchhccHhhhhhcCCCCCCCCceEEEEEEEEEEecCCeeeeCCCCCcCCCCcCc
Q 003281 455 LKEWFEKEGKNTQSVSISRDSLSVGRADIRKTVSQIKDEGLGTKEKPDWITVSATIVYIKCDNFCYTACPIMIGDRPCNK 534 (834)
Q Consensus 455 l~~w~~~~g~~~~~~sls~~~~~~~~~~~~ktI~ei~~~~lg~~~k~~~~~v~atI~~I~~d~~~Y~aC~~~~~~~~C~K 534 (834)
+ +. ....|++|. ..+.+.|.+.|..+..-.-+..
T Consensus 265 -------------~--vp----------~~~~I~dl~--------~g~~vdV~GvV~~v~~~rtf~r------------- 298 (485)
T PRK07211 265 -------------Y--VP----------DTTPIESLE--------IDETVDIAGVVRSADPKRTFDR------------- 298 (485)
T ss_pred -------------c--cc----------ccccHhhcC--------CCCceeEEEEEEEccCcEEEEc-------------
Confidence 0 00 012344442 2335788888887764211110
Q ss_pred ccccCCCCceecCCCCCccccceEEEEEEEEEEeCCCeEEEEEehHHHH
Q 003281 535 KVMNNGDGRWHCDRCDQSVVECDYRYILQFQIQDHTGLTWVTAFQECAE 583 (834)
Q Consensus 535 Kv~~~~dg~~~CekC~~~~~~~~~ry~l~~~i~D~Tg~~~~~~F~e~ae 583 (834)
+.+ ....+.++.|.|.||++.+++|++.|+
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 134667999999999999999999883
No 8
>PRK12366 replication factor A; Reviewed
Probab=99.97 E-value=3e-30 Score=304.49 Aligned_cols=282 Identities=18% Similarity=0.273 Sum_probs=224.4
Q ss_pred CCceeccccCCCCCceEEEEEEEEeccceeecCCCC-CcceEEEEEeeCCCCEEEEEEechHHHhhhhccCcCcEEEEee
Q 003281 217 SRIIPIAALNPYMGKWTIKARVTAKGELRHYNNQRG-DGKVFHFDLLDSDGGEIRVTCFNAVADQFYHQVEAGKIYLVSR 295 (834)
Q Consensus 217 ~~~~pI~~L~p~~~~w~I~aRV~~Ks~lr~~~n~~g-~Gk~f~~~L~De~g~~I~at~f~~~~d~f~~~l~eG~vy~is~ 295 (834)
.+++||++|+||+.+|+|+|||+.++++|+|.+.+| +|++|+++|.|++ |+|++|+|++.++. ++.|++|+||+|++
T Consensus 61 ~~~~~I~dl~p~~~~v~i~arV~~~~~~r~~~~~~G~eGkv~~~~v~Det-G~Ir~t~W~~~~~~-~~~le~G~v~~i~~ 138 (637)
T PRK12366 61 EEDFKISDIEEGQINVEITGRIIEISNIKTFTRKDGSTGKLANITIADNT-GTIRLTLWNDNAKL-LKGLKEGDVIKIEN 138 (637)
T ss_pred cceeEHHHCcCCCcceEEEEEEEEccCCeEEECCCCCccEEEEEEEEcCC-CEEEEEEEchhhhh-hccCCCCCEEEEec
Confidence 468999999999999999999999999999999877 8999999999985 69999999999885 68999999999999
Q ss_pred eEEecCCcccccCCCeEEEEEccCccEEEecC-CCCCCccccccccccccccccCCCceeeEEEEEEEecCCeeEEccCC
Q 003281 296 GSLKPAQKNFNHLHNDLEIFLDMTSMVQLCYE-DDASIPRQQFHFRPINDVEGMENNSVVDLIGVVSYISPTASLMRKNG 374 (834)
Q Consensus 296 ~~V~~a~~~~~~~~~~yeI~f~~~T~I~~~~d-~~~~iP~~~~~f~~i~dI~~~~~~~~vDVIGvV~~V~~~~~i~~k~g 374 (834)
+.++. ..++|+|.++..|.|+++.+ ++..+|...++| +|.||. .+..|||+|+|+++.++.+|++|+|
T Consensus 139 ~~v~~-------~~~~~el~~~~~t~I~~~~~~d~~~i~~~~~~~-~I~el~---~g~~v~v~G~V~~~~~~~~f~rkdg 207 (637)
T PRK12366 139 ARSRK-------WNNDVELNSGSETRIDKLEKYDESRYPIIKENY-DIPELE---PNLSATIEGEVTKAYPIKEFTRKDG 207 (637)
T ss_pred cEecc-------cCCceEEEcCCcceEEEccccccccCCcccccc-cccccC---CCCeEEEEEEEEEccCcEEEEEcCC
Confidence 99875 34789999999999999863 356789887776 555554 5679999999999999999999999
Q ss_pred ceeeEEEEEEeccCCcEEEEEEcCCccchhhhhhhhcccCCCccEEEEEEEEEeec-CCeEEEeecceEEEEcCCchHHH
Q 003281 375 TETQKRTLHLRDMSGRSVELTLWGNFCNDDGLRLQHMCDSGVFPILAVKAGRVSDF-NGKVVGTISTTQLFIEPDFPEAH 453 (834)
Q Consensus 375 ~~~~kr~i~L~D~s~~si~vtLWg~~a~~~~~~l~~~~~~~~~~Vv~ik~~rV~~f-~G~~Ls~~~~S~i~inPd~pe~~ 453 (834)
++..+|+++|.|+|| +|++||||+.|+.. ...++||.|++.++.+| +|..|++...+.|....+.
T Consensus 208 ~~~~~r~~~l~D~TG-~irvTlW~~~a~~~---------~~~g~vv~i~g~~~~~~~~~~el~~~~~~~i~~~~~~---- 273 (637)
T PRK12366 208 SEGKLKSFILKDDTG-SIRVTLWNDLTDIE---------VNKGDIVRVKGYVKQGYRTGLEISANNIEILEKLEKE---- 273 (637)
T ss_pred CeeEEEEEEEEcCCC-cEEEEEEChhhccc---------CCCCCEEEEEeEEecCcCCceEEEeCCceeecccccc----
Confidence 999999999999999 89999999998531 23689999999888889 5568888666555321100
Q ss_pred HHHHHHHhcCCccceeeeccccccCCccchhccHhhhhhcCCCCCCCCceEEEEEEEEEEecCCeeeeCCCCCcCCCCcC
Q 003281 454 RLKEWFEKEGKNTQSVSISRDSLSVGRADIRKTVSQIKDEGLGTKEKPDWITVSATIVYIKCDNFCYTACPIMIGDRPCN 533 (834)
Q Consensus 454 ~l~~w~~~~g~~~~~~sls~~~~~~~~~~~~ktI~ei~~~~lg~~~k~~~~~v~atI~~I~~d~~~Y~aC~~~~~~~~C~ 533 (834)
. .......|++|..-. ....++|+|.|+.+..-.-|-
T Consensus 274 -----------~--------------~~~~~~pI~~L~~~~-----~g~~~~I~grV~~~~~~R~f~------------- 310 (637)
T PRK12366 274 -----------E--------------KELEIVNIEELTEFE-----DGEEVDVKGRIIAISDKREVE------------- 310 (637)
T ss_pred -----------c--------------cccCceeHHHCCccc-----CCCEEEEEEEEEecCCceEEE-------------
Confidence 0 001234577876421 223689999998875321111
Q ss_pred cccccCCCCceecCCCCCccccceEEEEEEEEEEeCCCeEEEEEehHHHHHHhCC
Q 003281 534 KKVMNNGDGRWHCDRCDQSVVECDYRYILQFQIQDHTGLTWVTAFQECAEEIMGM 588 (834)
Q Consensus 534 KKv~~~~dg~~~CekC~~~~~~~~~ry~l~~~i~D~Tg~~~~~~F~e~ae~llG~ 588 (834)
..+| . -..+++.|.|.||++.+++|++.|.++.++
T Consensus 311 -----~~~g--------------~-gkv~s~~l~D~tG~IR~t~w~~~~d~~~~l 345 (637)
T PRK12366 311 -----RDDR--------------T-AEVQDIELADGTGRVRVSFWGEKAKILENL 345 (637)
T ss_pred -----cCCC--------------c-EEEEEEEEEcCCCeEEEEEeCchhhhhccc
Confidence 1111 1 367799999999999999999998776554
No 9
>PRK06386 replication factor A; Reviewed
Probab=99.97 E-value=2.7e-28 Score=264.76 Aligned_cols=351 Identities=17% Similarity=0.193 Sum_probs=279.1
Q ss_pred eeccccCCCCCceEEEEEEEEeccceeecCCCCCcceEEEEEeeCCCCEEEEEEechHHHhhhhccCcCcEEEEeeeEEe
Q 003281 220 IPIAALNPYMGKWTIKARVTAKGELRHYNNQRGDGKVFHFDLLDSDGGEIRVTCFNAVADQFYHQVEAGKIYLVSRGSLK 299 (834)
Q Consensus 220 ~pI~~L~p~~~~w~I~aRV~~Ks~lr~~~n~~g~Gk~f~~~L~De~g~~I~at~f~~~~d~f~~~l~eG~vy~is~~~V~ 299 (834)
++|++|.|.....+|+|||+..| .|+|..++|+-.+.+-+|.|+ .|.|+.|+|+. .+.|++|++|.|.|+.++
T Consensus 3 ~kI~DI~~~~~~V~v~akVl~~~-~r~i~~~~g~~~~~~gllgDe-TG~I~fT~W~~-----~~~l~~Gd~v~i~na~v~ 75 (358)
T PRK06386 3 SKISDINAARQNVDLKVKVLSLN-KRTIKNDRGETIYYYGIIGDE-TGTVPFTAWEF-----PDAVKSGDVIEIKYCYSK 75 (358)
T ss_pred cchhhcCCCCCcEEEEEEEEEcc-ceEEecCCCCeEEEEEEEECC-cceEEEEecCC-----cccCCCCCEEEEEeEEEe
Confidence 57999999999999999999999 699988887777788889998 58999999984 246999999999999987
Q ss_pred cCCcccccCCCeEEEEEccCccEEEecCCCCCCccccccccccccccccCCCceeeEEEEEEEecCCeeEEccCCceeeE
Q 003281 300 PAQKNFNHLHNDLEIFLDMTSMVQLCYEDDASIPRQQFHFRPINDVEGMENNSVVDLIGVVSYISPTASLMRKNGTETQK 379 (834)
Q Consensus 300 ~a~~~~~~~~~~yeI~f~~~T~I~~~~d~~~~iP~~~~~f~~i~dI~~~~~~~~vDVIGvV~~V~~~~~i~~k~g~~~~k 379 (834)
.-+ ..++|.++..|.|.+..+.+..++ ..+..++|.||.. ....|+|.|.|.++.+ .++. ++|.+...
T Consensus 76 ~~~-------G~~~Lnv~~~t~v~~~~d~~iev~-~~~~~~KI~DL~~--g~~~v~V~akVle~~e-~e~~-~~g~~~~v 143 (358)
T PRK06386 76 EYN-------GKIRIYFDSRSEVMLKPDENIEVK-RTYKLVKIRDLSL--VTPYVSVIGKITGITK-KEYD-SDGTSKIV 143 (358)
T ss_pred eEC-------CEEEEEEcCceEEEecCccccccc-cccCccEeEeccC--CCCceEEEEEEEEccC-ceEe-cCCCccEE
Confidence 644 367899999999876543322222 2246778888853 4578999999999976 5776 56667788
Q ss_pred EEEEEeccCCcEEEEEEcCCccchhhhhhhhcccCCCccEEEEEEEEEeecCCe-EEEeecceEEEEcCCchHHHHHHHH
Q 003281 380 RTLHLRDMSGRSVELTLWGNFCNDDGLRLQHMCDSGVFPILAVKAGRVSDFNGK-VVGTISTTQLFIEPDFPEAHRLKEW 458 (834)
Q Consensus 380 r~i~L~D~s~~si~vtLWg~~a~~~~~~l~~~~~~~~~~Vv~ik~~rV~~f~G~-~Ls~~~~S~i~inPd~pe~~~l~~w 458 (834)
+++.|.|+|| +|++|||++..+ .+.++.|.++.+.+|+|+ +|+....|+|...|+.-|
T Consensus 144 ~sg~lgDeTG-rIr~TlW~~~l~-------------eGd~v~i~na~v~e~~G~~el~v~~~t~I~~~~~~ie------- 202 (358)
T PRK06386 144 YQGYIEDDTA-RVRISSFGKPLE-------------DNRFVRIENARVSQYNGYIEISVGNKSVIKEVESDIN------- 202 (358)
T ss_pred EEEEEEcCCC-eEEEEEcccccc-------------CCCEEEEeeeEEEccCCeEEEEeCCeEEEEECCCCcc-------
Confidence 9999999999 799999997321 578999999999999997 899999999877553211
Q ss_pred HHhcCCccceeeeccccccCCccchhccHhhhhhcCCCCCCCCceEEEEEEEEEEecCCeeeeCCCCCcCCCCcCccccc
Q 003281 459 FEKEGKNTQSVSISRDSLSVGRADIRKTVSQIKDEGLGTKEKPDWITVSATIVYIKCDNFCYTACPIMIGDRPCNKKVMN 538 (834)
Q Consensus 459 ~~~~g~~~~~~sls~~~~~~~~~~~~ktI~ei~~~~lg~~~k~~~~~v~atI~~I~~d~~~Y~aC~~~~~~~~C~KKv~~ 538 (834)
+ ...++.|.+|.+..- -..+.++|+.|......|..|| .|+|+|..
T Consensus 203 ------------v---------~~~~~~I~di~~~~g-------~v~i~G~iv~i~~gsgli~rCP------~C~R~l~~ 248 (358)
T PRK06386 203 ------------L---------ESRNIFIFEIKSPVG-------GITIMGFIVSVGQGSRIFTKCS------VCNKIIED 248 (358)
T ss_pred ------------c---------CccccchhhhhccCC-------eEEEEEEEEEEcCCcEeEecCc------CCCeEccC
Confidence 1 123578999986321 2688999999999888999999 69999962
Q ss_pred CCCCceecCCCCCccccceEEEEEEEEEEeCCCeEEEEEehHHHHHHhCCCHHHHHhhhccCCChhHHHHHHHHhcCceE
Q 003281 539 NGDGRWHCDRCDQSVVECDYRYILQFQIQDHTGLTWVTAFQECAEEIMGMSAKDLYSLKYVDQNDEKFGEVVRNATFTKY 618 (834)
Q Consensus 539 ~~dg~~~CekC~~~~~~~~~ry~l~~~i~D~Tg~~~~~~F~e~ae~llG~sA~el~~l~~ee~d~~~~~~~l~~~~~k~~ 618 (834)
+.|+.|++. .+.+-.++.+.|.|+||.+.+++|++.+++|+|++.+|+.++.. +.+. ...+=..++|+.|
T Consensus 249 -----g~C~~HG~v--~~~~dlr~k~vLDDGtg~~~~~l~~e~~e~l~G~~lee~~~~a~-~~~~--~~~i~~~llGr~~ 318 (358)
T PRK06386 249 -----GVCKDHPDA--PVYLDIFGYFTISDGTGFVTCYANKDSFLPYININENEFARKAS-SMNP--NMLIKKNLLGKCF 318 (358)
T ss_pred -----CcCCCCCCC--CCeeEEEEEEEEECCCCeEEEEEChHHhHHHhCCCHHHHHHHhh-ccCH--HHHhhhhhcccEE
Confidence 699999973 56777788889999999999999999999999999999976652 2232 2334478999999
Q ss_pred EEEEEEeecccCccceEEEEEEEeeecChHHHHHHHHHHHH
Q 003281 619 LFKLKVKEETFSDEQRVKSTVVKAERYNYSSETRFILDLMD 659 (834)
Q Consensus 619 ~f~l~~k~~~ynde~rvk~~v~~~~~vd~~~e~~~Ll~~i~ 659 (834)
.|+-.+..+.|. +.+.|.++..+|. .+.+..-..|+
T Consensus 319 ~v~G~~~~~~~~----~~~~~~~~~~~~~-~~~~~~~~~~~ 354 (358)
T PRK06386 319 SVTGDLRKKDDE----IDMNVISAKSITA-DEIKIIEVEIE 354 (358)
T ss_pred EEEcceEeccCC----eEEEEEEeeeccc-hhhhHHHHHHH
Confidence 999999887775 7889999998886 44555444444
No 10
>PRK07211 replication factor A; Reviewed
Probab=99.97 E-value=3.7e-30 Score=288.22 Aligned_cols=208 Identities=22% Similarity=0.354 Sum_probs=182.1
Q ss_pred CceeccccCCCCCceEEEEEEEEeccceeecCCCC-CcceEEEEEeeCCCCEEEEEEechHHHhhhhccCcCcEEEEeee
Q 003281 218 RIIPIAALNPYMGKWTIKARVTAKGELRHYNNQRG-DGKVFHFDLLDSDGGEIRVTCFNAVADQFYHQVEAGKIYLVSRG 296 (834)
Q Consensus 218 ~~~pI~~L~p~~~~w~I~aRV~~Ks~lr~~~n~~g-~Gk~f~~~L~De~g~~I~at~f~~~~d~f~~~l~eG~vy~is~~ 296 (834)
.++||++|+|++..|+|+|||+.++++|+|.+.+| +|++++++|.|+. |+|++|+|++.+++| +.|++|+||+|+++
T Consensus 160 ~~~~I~dL~~~~~~v~I~grV~~v~~iRtf~r~dGseGkv~sv~L~DeT-G~IR~TlW~d~Ad~~-~~le~G~Vv~I~~a 237 (485)
T PRK07211 160 DTYTVEDLSLGLSDVTLVGVVLDTDSVRTFDRDDGSEGRVSNLTVGDET-GRVRVTLWDDRADLA-EELDAGESVEIVDG 237 (485)
T ss_pred CCccHHHcCCCCCceEEEEEEEEcCCCeEEECCCCCeeEEEEEEEEcCC-CeEEEEEechhhhhh-ccCCCCCEEEEEee
Confidence 57899999999999999999999999999999887 8999999999985 689999999999999 77999999999999
Q ss_pred EEecCCcccccCCCeEEEEEccCccEEEecCCCCCCccccccccccccccccCCCceeeEEEEEEEecCCeeEEccCCce
Q 003281 297 SLKPAQKNFNHLHNDLEIFLDMTSMVQLCYEDDASIPRQQFHFRPINDVEGMENNSVVDLIGVVSYISPTASLMRKNGTE 376 (834)
Q Consensus 297 ~V~~a~~~~~~~~~~yeI~f~~~T~I~~~~d~~~~iP~~~~~f~~i~dI~~~~~~~~vDVIGvV~~V~~~~~i~~k~g~~ 376 (834)
+|+..+ +.|||.|+..|.|+++.++...+|. + .+|.+++.+..|||+|+|++++++.+|++++|++
T Consensus 238 ~Vre~~-------g~~ELsl~~~s~I~~~~dev~~vp~----~---~~I~dl~~g~~vdV~GvV~~v~~~rtf~r~dG~~ 303 (485)
T PRK07211 238 YVRERD-------GSLELHVGDRGAVEEVDEDVEYVPD----T---TPIESLEIDETVDIAGVVRSADPKRTFDRDDGSE 303 (485)
T ss_pred EEEecC-------CcEEEEECCCceEEECCcccccccc----c---ccHhhcCCCCceeEEEEEEEccCcEEEEcCCCCE
Confidence 998753 7899999999999998653233553 2 4555556777999999999999999999889999
Q ss_pred eeEEEEEEeccCCcEEEEEEcCCccchhhhhhhhcccCCCccEEEEEEEEEeec--CCeEEEeecceEEEEcCCchH
Q 003281 377 TQKRTLHLRDMSGRSVELTLWGNFCNDDGLRLQHMCDSGVFPILAVKAGRVSDF--NGKVVGTISTTQLFIEPDFPE 451 (834)
Q Consensus 377 ~~kr~i~L~D~s~~si~vtLWg~~a~~~~~~l~~~~~~~~~~Vv~ik~~rV~~f--~G~~Ls~~~~S~i~inPd~pe 451 (834)
..+|+++|.|+|| +|++||||+.|.. +...+++|+|++++|++| +|++||+.++|.|.+-.+-|+
T Consensus 304 ~~vr~l~l~D~TG-~IrvTLWg~~A~~---------~i~~GdvV~Ikg~~V~dg~~ggleLS~g~~s~i~~~~~~~~ 370 (485)
T PRK07211 304 GQVRNVRIQDDTG-DIRVALWGEKADL---------DIGPGDEVVAADVEIQDGWQDDLEASAGWQSTVVVLDDGAD 370 (485)
T ss_pred eEEEEEEEEcCCC-cEEEEEeCccccC---------CCCCCCEEEEEccEEEecCCCCEEEEecCCceEEEcccccc
Confidence 9999999999999 8999999999952 234789999999999998 689999998888877555443
No 11
>PRK15491 replication factor A; Provisional
Probab=99.96 E-value=8.7e-28 Score=265.95 Aligned_cols=277 Identities=19% Similarity=0.267 Sum_probs=215.8
Q ss_pred CCceeccccCCCCCceEEEEEEEEeccceeecCCCC-CcceEEEEEeeCCCCEEEEEEechHHHhhh-hccCcCcEEEEe
Q 003281 217 SRIIPIAALNPYMGKWTIKARVTAKGELRHYNNQRG-DGKVFHFDLLDSDGGEIRVTCFNAVADQFY-HQVEAGKIYLVS 294 (834)
Q Consensus 217 ~~~~pI~~L~p~~~~w~I~aRV~~Ks~lr~~~n~~g-~Gk~f~~~L~De~g~~I~at~f~~~~d~f~-~~l~eG~vy~is 294 (834)
.++++|++|+|++.+|+|+|||+.++++|+|.+.+| +|++++++|.|+ .|+|++|+|++.++.|+ ..|++|+||+|+
T Consensus 55 ~~~~kI~dL~~~~~~v~i~arVl~~~~~R~f~r~dGs~g~v~~~~v~De-TG~ir~tlW~~~a~~~~~~~le~G~v~~I~ 133 (374)
T PRK15491 55 VDTTKIADINESSSNVNFTAKVVSIFEPKEFNRNDGTTGRVGNIIVADE-TGSIRLTLWDDLADLIKTGDIEVGKSLNIS 133 (374)
T ss_pred cccccHHHCCCCCCceEEEEEEeeccCCeeeecCCCCceEEEEEEEEcC-CCeEEEEEECchhhhhccCCcCCCCEEEEe
Confidence 468899999999999999999999999999999888 899999999997 57999999999999998 689999999998
Q ss_pred eeEEecCCcccccCCCeEEEEEccCccEEEecCCCCCCccccccccccccccccCCCceeeEEEEEEEecCCeeEEccCC
Q 003281 295 RGSLKPAQKNFNHLHNDLEIFLDMTSMVQLCYEDDASIPRQQFHFRPINDVEGMENNSVVDLIGVVSYISPTASLMRKNG 374 (834)
Q Consensus 295 ~~~V~~a~~~~~~~~~~yeI~f~~~T~I~~~~d~~~~iP~~~~~f~~i~dI~~~~~~~~vDVIGvV~~V~~~~~i~~k~g 374 (834)
++ +++.|+. +||+|++.|.|+++.++ + ...|+|++|+||..- +..|||+|+|++++++.++++++|
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-KASINSQKISDIKDG--DSDINIVGKVLDISDVRTFQKKDG 199 (374)
T ss_pred ee----eccCccc----EEEEeCCCceeeecccc---c-ccccCcccHHHcCCC--CccEEEEEEEEEccCceEEEecCC
Confidence 75 5556643 69999999999998432 2 356899999999763 446999999999999999999999
Q ss_pred ceeeEEEEEEeccCCcEEEEEEcCCccchhhhhhhhcccCCCccEEEEEEEE--EeecCCe-EEEeecceEEEEcCCchH
Q 003281 375 TETQKRTLHLRDMSGRSVELTLWGNFCNDDGLRLQHMCDSGVFPILAVKAGR--VSDFNGK-VVGTISTTQLFIEPDFPE 451 (834)
Q Consensus 375 ~~~~kr~i~L~D~s~~si~vtLWg~~a~~~~~~l~~~~~~~~~~Vv~ik~~r--V~~f~G~-~Ls~~~~S~i~inPd~pe 451 (834)
++..++++.|.|+|| .|++|||++.|..+ ..| ..+.+|.+.+++ ...|+|. .|+....|.|....+.++
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-DKL------ENGDSVEIINGYARTNNYSQEVEIQIGNHGSLRKTDRNVE 271 (374)
T ss_pred CeEEEEEEEEECCCC-eEEEEEecchhccc-ccC------CCCCEEEEEeceEEEeccCCCEEEEeCCCceEEECCcccc
Confidence 999999999999999 59999999998754 222 256788887764 4567775 788888777765332211
Q ss_pred HHHHHHHHHhcCCccceeeeccccccCCccchhccHhhhhhcCCCCCCCCceEEEEEEEEEEecCCeeeeCCCCCcCCCC
Q 003281 452 AHRLKEWFEKEGKNTQSVSISRDSLSVGRADIRKTVSQIKDEGLGTKEKPDWITVSATIVYIKCDNFCYTACPIMIGDRP 531 (834)
Q Consensus 452 ~~~l~~w~~~~g~~~~~~sls~~~~~~~~~~~~ktI~ei~~~~lg~~~k~~~~~v~atI~~I~~d~~~Y~aC~~~~~~~~ 531 (834)
. ......|.+|... +.+.|.|.|..+..-.
T Consensus 272 ~----------------------------~~~f~~I~dl~~~--------~~~dv~G~V~~v~~~~-------------- 301 (374)
T PRK15491 272 Y----------------------------EEDFTPIADIIPG--------QPYSIKGAVSGLGDLK-------------- 301 (374)
T ss_pred c----------------------------CCCccCHHHcCCC--------CceeEEEEEEEcCCcE--------------
Confidence 0 0112347777531 2467888887774310
Q ss_pred cCcccccCCCCceecCCCCCccccceEEEEEEEEEEeCCCeEEEEEehHHHHH
Q 003281 532 CNKKVMNNGDGRWHCDRCDQSVVECDYRYILQFQIQDHTGLTWVTAFQECAEE 584 (834)
Q Consensus 532 C~KKv~~~~dg~~~CekC~~~~~~~~~ry~l~~~i~D~Tg~~~~~~F~e~ae~ 584 (834)
-++ ..+| ....+-++.|.|.||.+.+++|++.|+.
T Consensus 302 ---~~~-~~~G--------------~~~~~r~i~l~D~Tg~Ir~tlWg~~a~~ 336 (374)
T PRK15491 302 ---EFT-KSDG--------------SENKVSNIYVSDDTGRIRIALWGEKAEL 336 (374)
T ss_pred ---EEE-ccCC--------------CEeEEEeEEEEeCCCcEEEEEccccccc
Confidence 000 0011 1234558999999999999999999864
No 12
>PRK15491 replication factor A; Provisional
Probab=99.96 E-value=1.2e-26 Score=256.91 Aligned_cols=206 Identities=17% Similarity=0.297 Sum_probs=174.4
Q ss_pred CceeccccCCCCCceEEEEEEEEeccceeecCCCCC-cceEEEEEeeCCCCEEEEEEechHHHhhhhccCcCcEEEEeee
Q 003281 218 RIIPIAALNPYMGKWTIKARVTAKGELRHYNNQRGD-GKVFHFDLLDSDGGEIRVTCFNAVADQFYHQVEAGKIYLVSRG 296 (834)
Q Consensus 218 ~~~pI~~L~p~~~~w~I~aRV~~Ks~lr~~~n~~g~-Gk~f~~~L~De~g~~I~at~f~~~~d~f~~~l~eG~vy~is~~ 296 (834)
++.+|++|.++...+.|+|||+.++++|+|.+.+|+ |+++++.|.|++ |+|++|+|++.|+.| +.|++|++|+|.++
T Consensus 165 ~~~~I~dl~~~~~~V~I~g~V~~~~~~r~~~~~~G~~~~v~~~~l~Det-G~Ir~t~W~~~a~~~-~~l~~Gd~V~i~~~ 242 (374)
T PRK15491 165 NSQKISDIKDGDSDINIVGKVLDISDVRTFQKKDGSQGRVRNITIGDET-GKIRVTLWDGKTDLA-DKLENGDSVEIING 242 (374)
T ss_pred CcccHHHcCCCCccEEEEEEEEEccCceEEEecCCCeEEEEEEEEECCC-CeEEEEEecchhccc-ccCCCCCEEEEEec
Confidence 357899999998899999999999999999988774 899999999975 689999999999998 67999999999998
Q ss_pred EEecCCcccccCCCeEEEEEccCccEEEecCCCCCCccccccccccccccccCCCceeeEEEEEEEecCCeeEEccCCce
Q 003281 297 SLKPAQKNFNHLHNDLEIFLDMTSMVQLCYEDDASIPRQQFHFRPINDVEGMENNSVVDLIGVVSYISPTASLMRKNGTE 376 (834)
Q Consensus 297 ~V~~a~~~~~~~~~~yeI~f~~~T~I~~~~d~~~~iP~~~~~f~~i~dI~~~~~~~~vDVIGvV~~V~~~~~i~~k~g~~ 376 (834)
.++. +...++|||+|+.+|.|+++.+ + +.+.|+|++|+||.. +..+||+|+|++++++.+|++++|++
T Consensus 243 ~~r~-----~~~~g~~El~~~~~s~I~~~~~-~---~e~~~~f~~I~dl~~---~~~~dv~G~V~~v~~~~~~~~~~G~~ 310 (374)
T PRK15491 243 YART-----NNYSQEVEIQIGNHGSLRKTDR-N---VEYEEDFTPIADIIP---GQPYSIKGAVSGLGDLKEFTKSDGSE 310 (374)
T ss_pred eEEE-----eccCCCEEEEeCCCceEEECCc-c---cccCCCccCHHHcCC---CCceeEEEEEEEcCCcEEEEccCCCE
Confidence 8763 3456899999999999999843 2 356689999999975 46789999999999999999999999
Q ss_pred eeEEEEEEeccCCcEEEEEEcCCccchhhhhhhhcccCCCccEEEEEEEEEee-cCC-eEEEeecceEEEE
Q 003281 377 TQKRTLHLRDMSGRSVELTLWGNFCNDDGLRLQHMCDSGVFPILAVKAGRVSD-FNG-KVVGTISTTQLFI 445 (834)
Q Consensus 377 ~~kr~i~L~D~s~~si~vtLWg~~a~~~~~~l~~~~~~~~~~Vv~ik~~rV~~-f~G-~~Ls~~~~S~i~i 445 (834)
..+|+|+|.|+|| +|++||||+.|+.. .. ...+..|.+.++.+++ |+| ..||....|++.+
T Consensus 311 ~~~r~i~l~D~Tg-~Ir~tlWg~~a~~~-~~------~~~g~~i~i~~~~~k~g~~~~~e~s~g~~s~~~~ 373 (374)
T PRK15491 311 NKVSNIYVSDDTG-RIRIALWGEKAELV-DK------LDIDTPIKIIDAFSKSGYNEDVELSAGNRSRVVV 373 (374)
T ss_pred eEEEeEEEEeCCC-cEEEEEcccccccc-cc------cCCCCeEEEEEEEEeecCCCcEEEEeCCcceEEe
Confidence 9999999999999 59999999999741 11 1123456676777764 645 6899999998875
No 13
>PRK14699 replication factor A; Provisional
Probab=99.95 E-value=1.2e-26 Score=263.60 Aligned_cols=207 Identities=23% Similarity=0.331 Sum_probs=178.6
Q ss_pred CCceeccccCCCCCceEEEEEEEEeccceeecCCCC-CcceEEEEEeeCCCCEEEEEEechHHHhhhhccCcCcEEEEee
Q 003281 217 SRIIPIAALNPYMGKWTIKARVTAKGELRHYNNQRG-DGKVFHFDLLDSDGGEIRVTCFNAVADQFYHQVEAGKIYLVSR 295 (834)
Q Consensus 217 ~~~~pI~~L~p~~~~w~I~aRV~~Ks~lr~~~n~~g-~Gk~f~~~L~De~g~~I~at~f~~~~d~f~~~l~eG~vy~is~ 295 (834)
.+++||++|+|+++.|+|+|||+.++++|+|.+.+| +|+++++.|.|++ |+|++|+|++.+ .|++.|++|+++.|.+
T Consensus 274 ~~~~~I~~L~~~~~~v~I~grV~~~~~~r~~~~~~Gseg~v~~~~l~DeT-G~Ir~T~W~~~a-~~~~~i~~Gd~v~i~~ 351 (484)
T PRK14699 274 EEFTPIEDIKADMNNINISGRVLDISEVRTFEKKDGSPGRVGNLLLGDST-GKIRLTLWDEKT-NFLDEIDFDETVEVLN 351 (484)
T ss_pred ccccCHHHcCCCCceeEEEEEEEEcCCCeEEEcCCCCeeEEEEEEEECCC-CeEEEEEeCccc-ccccccCCCceEEEEe
Confidence 357899999999999999999999999999999887 8999999999985 689999999999 7888899999988888
Q ss_pred eEEecCCcccccCCCeEEEEEccCccEEEecCCCCCCccccccccccccccccCCCceeeEEEEEEEecCCeeEEccCCc
Q 003281 296 GSLKPAQKNFNHLHNDLEIFLDMTSMVQLCYEDDASIPRQQFHFRPINDVEGMENNSVVDLIGVVSYISPTASLMRKNGT 375 (834)
Q Consensus 296 ~~V~~a~~~~~~~~~~yeI~f~~~T~I~~~~d~~~~iP~~~~~f~~i~dI~~~~~~~~vDVIGvV~~V~~~~~i~~k~g~ 375 (834)
+.++ ++...++|||+|+..|.|+++.++ . .+.++|++|.||. .+..|||+|+|++|+++.+|++++|+
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 8754 666678999999999999998542 2 5678999999995 57799999999999999999999999
Q ss_pred eeeEEEEEEeccCCcEEEEEEcCCccchhhhhhhhcccCCCccEEEEEEEEEe-ecCC-eEEEeecceEEEE
Q 003281 376 ETQKRTLHLRDMSGRSVELTLWGNFCNDDGLRLQHMCDSGVFPILAVKAGRVS-DFNG-KVVGTISTTQLFI 445 (834)
Q Consensus 376 ~~~kr~i~L~D~s~~si~vtLWg~~a~~~~~~l~~~~~~~~~~Vv~ik~~rV~-~f~G-~~Ls~~~~S~i~i 445 (834)
+..+|+|+|.|.|| +|+|||||+.|..+.. -..+.-|.+.+++++ -|+| ..||...+|+|.+
T Consensus 420 ~~~vr~i~l~D~TG-~Ir~tlWg~~A~~~~~-------~~~~~~v~~~~~~~~~g~~~~~e~s~g~~s~~~~ 483 (484)
T PRK14699 420 ENVVANLQLKDETG-SIRLTLWGEQAYVIED-------LDIDSEIQIIDAYARYGLNEEIELSVGNRSRVII 483 (484)
T ss_pred EEEEEEEEEEcCCC-eEEEEEcchhhhhccc-------cCCCCeEEEechhhhhcccccEEEEecCceEEEe
Confidence 99999999999999 9999999999975311 124566777777666 4665 5899999988864
No 14
>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=99.94 E-value=2.2e-26 Score=210.67 Aligned_cols=104 Identities=55% Similarity=0.964 Sum_probs=100.9
Q ss_pred eccccCCCCCceEEEEEEEEeccceeecCCCCCcceEEEEEeeCCCCEEEEEEechHHHhhhhccCcCcEEEEeeeEEec
Q 003281 221 PIAALNPYMGKWTIKARVTAKGELRHYNNQRGDGKVFHFDLLDSDGGEIRVTCFNAVADQFYHQVEAGKIYLVSRGSLKP 300 (834)
Q Consensus 221 pI~~L~p~~~~w~I~aRV~~Ks~lr~~~n~~g~Gk~f~~~L~De~g~~I~at~f~~~~d~f~~~l~eG~vy~is~~~V~~ 300 (834)
||++|+|++++|+|+|||++||++|.|.+.+++|++|+|+|.|++|++|+|++|++.+++|+++|+||+||+|++|+|++
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 CCcccccCCCeEEEEEccCccEEE
Q 003281 301 AQKNFNHLHNDLEIFLDMTSMVQL 324 (834)
Q Consensus 301 a~~~~~~~~~~yeI~f~~~T~I~~ 324 (834)
++++|++++|+|||.|+.+|.|++
T Consensus 81 a~~~y~~~~~~yeI~f~~~t~~~~ 104 (104)
T cd04474 81 ANKKFNTLKNDYEITFNRDTSIIE 104 (104)
T ss_pred ccccCCCCCCcEEEEECCCcEEeC
Confidence 999999999999999999988863
No 15
>PRK14699 replication factor A; Provisional
Probab=99.93 E-value=3.1e-23 Score=235.76 Aligned_cols=277 Identities=21% Similarity=0.288 Sum_probs=214.1
Q ss_pred eeccccCCCCCceEEEEEEEEeccceeecCCCC-CcceEEEEEeeCCCCEEEEEEechHHHhhhhccCcCcEEEEeeeEE
Q 003281 220 IPIAALNPYMGKWTIKARVTAKGELRHYNNQRG-DGKVFHFDLLDSDGGEIRVTCFNAVADQFYHQVEAGKIYLVSRGSL 298 (834)
Q Consensus 220 ~pI~~L~p~~~~w~I~aRV~~Ks~lr~~~n~~g-~Gk~f~~~L~De~g~~I~at~f~~~~d~f~~~l~eG~vy~is~~~V 298 (834)
.+|++|.|.+...+|+|||+.++++|+|.+.+| +|++++++|.|+ .|+|++|+|++.++ +++.|++|++|.|.++.+
T Consensus 167 ~~I~dL~~~~~~V~i~gkVl~~~~~R~f~~~dG~~g~v~~~~igDe-TG~ir~tlW~~~a~-~~~~l~~Gd~v~I~~a~v 244 (484)
T PRK14699 167 QKIKDIKDGMGDLNLTGKVLEISEIRTFQRKDGTSGKVGNLLLGDE-TGTLRVTLWDDKTD-FLNQIEYGDTVELINAYA 244 (484)
T ss_pred cchhhcCCCCCceEEEEEEEeccCceEEecCCCCceEEEEEEEEcC-CceEEEEEECcccc-cccccCCCCEEEEecceE
Confidence 479999998887899999999999999998777 789999999998 57999999999885 888899999999999988
Q ss_pred ecCCcccccCCCeEEEEEccCccEEEecCCCCCCccccccccccccccccCCCceeeEEEEEEEecCCeeEEccCCceee
Q 003281 299 KPAQKNFNHLHNDLEIFLDMTSMVQLCYEDDASIPRQQFHFRPINDVEGMENNSVVDLIGVVSYISPTASLMRKNGTETQ 378 (834)
Q Consensus 299 ~~a~~~~~~~~~~yeI~f~~~T~I~~~~d~~~~iP~~~~~f~~i~dI~~~~~~~~vDVIGvV~~V~~~~~i~~k~g~~~~ 378 (834)
+.. .|+ ..++|+++..|.|....+ +..+ ..+|.+|.+|.. ....++|.|.|++++++.++++++|++..
T Consensus 245 r~~--~~~---~~~el~~~~~s~i~~~~~-~~e~---~~~~~~I~~L~~--~~~~v~I~grV~~~~~~r~~~~~~Gseg~ 313 (484)
T PRK14699 245 REN--AFT---QKVELQVGNRSIIRKSEK-KVEY---EEEFTPIEDIKA--DMNNINISGRVLDISEVRTFEKKDGSPGR 313 (484)
T ss_pred eec--ccC---CceEEEecCceEeecccc-cccc---cccccCHHHcCC--CCceeEEEEEEEEcCCCeEEEcCCCCeeE
Confidence 763 343 689999999998887632 2233 336888888864 35789999999999999999988999999
Q ss_pred EEEEEEeccCCcEEEEEEcCCccchhhhhhhhcccCCCccEEEEEEEEEe--ecCCe-EEEeecceEEEEcCCchHHHHH
Q 003281 379 KRTLHLRDMSGRSVELTLWGNFCNDDGLRLQHMCDSGVFPILAVKAGRVS--DFNGK-VVGTISTTQLFIEPDFPEAHRL 455 (834)
Q Consensus 379 kr~i~L~D~s~~si~vtLWg~~a~~~~~~l~~~~~~~~~~Vv~ik~~rV~--~f~G~-~Ls~~~~S~i~inPd~pe~~~l 455 (834)
.+++.|.|+|| .|++|||++.|.. ...+ ..+.+|-+.++.++ .|++. .|+....|.|...++..+.
T Consensus 314 v~~~~l~DeTG-~Ir~T~W~~~a~~-~~~i------~~Gd~v~i~~~y~~~~~~~~~~eL~~~~~t~I~~~~~~~e~--- 382 (484)
T PRK14699 314 VGNLLLGDSTG-KIRLTLWDEKTNF-LDEI------DFDETVEVLNAYSRENTFSQQVELNLGARGIIQKSEKKVEY--- 382 (484)
T ss_pred EEEEEEECCCC-eEEEEEeCccccc-cccc------CCCceEEEEeEEEEeccCCccEEEEecCceeEeecCCccee---
Confidence 99999999999 6999999999843 2111 24567888888877 45554 7888877766554443221
Q ss_pred HHHHHhcCCccceeeeccccccCCccchhccHhhhhhcCCCCCCCCceEEEEEEEEEEecCCeeeeCCCCCcCCCCcCcc
Q 003281 456 KEWFEKEGKNTQSVSISRDSLSVGRADIRKTVSQIKDEGLGTKEKPDWITVSATIVYIKCDNFCYTACPIMIGDRPCNKK 535 (834)
Q Consensus 456 ~~w~~~~g~~~~~~sls~~~~~~~~~~~~ktI~ei~~~~lg~~~k~~~~~v~atI~~I~~d~~~Y~aC~~~~~~~~C~KK 535 (834)
...+..|.+|.. ...+.|.|+|..+..-. .
T Consensus 383 -------------------------~~~~~~I~die~--------~~~vdV~G~V~~v~~~~----------------~- 412 (484)
T PRK14699 383 -------------------------REKFTDIADIIP--------GESYSVQGKVSEIGELR----------------E- 412 (484)
T ss_pred -------------------------eeccccHHHccC--------CCeeEEEEEEEEcCCcc----------------e-
Confidence 012456888832 22578999999886521 1
Q ss_pred cccCCCCceecCCCCCccccceEEEEEEEEEEeCCCeEEEEEehHHHHHH
Q 003281 536 VMNNGDGRWHCDRCDQSVVECDYRYILQFQIQDHTGLTWVTAFQECAEEI 585 (834)
Q Consensus 536 v~~~~dg~~~CekC~~~~~~~~~ry~l~~~i~D~Tg~~~~~~F~e~ae~l 585 (834)
+.. .+| .....-++.|.|.||++.+++|++.|+++
T Consensus 413 ~~~-~~g--------------~~~~vr~i~l~D~TG~Ir~tlWg~~A~~~ 447 (484)
T PRK14699 413 FER-EDG--------------TENVVANLQLKDETGSIRLTLWGEQAYVI 447 (484)
T ss_pred EEe-cCC--------------CEEEEEEEEEEcCCCeEEEEEcchhhhhc
Confidence 110 111 23456699999999999999999999764
No 16
>cd04477 RPA1N RPA1N: A subfamily of OB folds corresponding to the N-terminal OB-fold domain 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). RPA1N is known to specifically interact with the p53 tumor suppressor, DNA polymerase alpha, and transcription factors. In addition to RPA1N, RPA1 contains three other OB folds: ssDNA-binding domain (DBD)-A, DBD-B, and DBD-C.
Probab=99.91 E-value=1.3e-24 Score=194.78 Aligned_cols=81 Identities=49% Similarity=0.789 Sum_probs=76.0
Q ss_pred CCeEEEEeeEeeccchhhhhccccceEEEEEcccccccccccccchhhhhhcCCcccccEEEEceeeeecccCeEEEEEE
Q 003281 1 MPVLQVMDLKLVVSKQQQQQQHQQQRFRMVLSDGSRSQQGMLATQRNELVTSGLLQIGSVVRLTKFTCNVIQNRMIVIVM 80 (834)
Q Consensus 1 ~PvlQv~~~k~~~~~~~~~~~~~~~Ryrl~lSDG~~~~~~mLatqln~lv~~g~l~~gsiv~l~~~~~~~v~~r~iiii~ 80 (834)
+|||||+++|++.+++ .+.+|||++||||+|+++||||||||++|++|+|++||||||++|+||++++|+||||+
T Consensus 17 ~PvlQv~~ik~i~~~~-----~~~~RyRi~lSDG~~~~~amLatqln~~v~~g~l~~~sIirl~~y~~~~i~~k~viiIl 91 (97)
T cd04477 17 KPVLQVLNIKKIDSSN-----GSSERYRILLSDGVYYVQAMLATQLNPLVESGQLQRGSIIRLKRFICNVIKGKRILIIL 91 (97)
T ss_pred CCEEEEEEEEEccCCC-----CCcceEEEEEEChhHHHHHHHhhhhhhHHhcCCccCCcEEEECeEEEEEecCcEEEEEE
Confidence 5999999999998654 14589999999999999999999999999999999999999999999999999999999
Q ss_pred eeeEec
Q 003281 81 DLDVII 86 (834)
Q Consensus 81 ~lev~~ 86 (834)
||||+.
T Consensus 92 dlevl~ 97 (97)
T cd04477 92 DLEVVQ 97 (97)
T ss_pred eeEEeC
Confidence 999984
No 17
>PF04057 Rep-A_N: Replication factor-A protein 1, N-terminal domain; InterPro: IPR007199 Replication factor-a protein 1 (RPA1) forms a multiprotein complex with RPA2 and RPA3 that binds single-stranded DNA and functions in the recognition of DNA damage for nucleotide excision repair. The complex binds to single-stranded DNA sequences participating in DNA replication in addition to those mediating transcriptional repression and activation, and stimulates the activity of cognate strand exchange protein Sep1. It cooperates with T-AG and DNA topoisomerase I to unwind template DNA containing the Simian Virus 40 origin of replication [].; GO: 0003677 DNA binding, 0006260 DNA replication, 0005634 nucleus; PDB: 1EWI_A 2B3G_A 2B29_A.
Probab=99.90 E-value=4.2e-24 Score=193.43 Aligned_cols=83 Identities=51% Similarity=0.801 Sum_probs=71.4
Q ss_pred CCeEEEEeeEeeccchhhhhccccceEEEEEcccccccccccccchhhhhhcCCcccccEEEEceeeeeccc-CeEEEEE
Q 003281 1 MPVLQVMDLKLVVSKQQQQQQHQQQRFRMVLSDGSRSQQGMLATQRNELVTSGLLQIGSVVRLTKFTCNVIQ-NRMIVIV 79 (834)
Q Consensus 1 ~PvlQv~~~k~~~~~~~~~~~~~~~Ryrl~lSDG~~~~~~mLatqln~lv~~g~l~~gsiv~l~~~~~~~v~-~r~iiii 79 (834)
.|||||+++|++++++ +.+.+|||++||||+|+++||||||||++|++|.|++||||||++|+||.++ +|+||||
T Consensus 18 ~pvlQVl~~k~i~~~~----~~~~~RyR~~lSDG~~~~~amLatqln~lv~~g~l~~~siirl~~y~~n~v~~~k~iiii 93 (101)
T PF04057_consen 18 NPVLQVLNIKKINSKQ----GGGSDRYRLVLSDGVHSIQAMLATQLNHLVESGELQKGSIIRLKQYTCNTVKNGKKIIII 93 (101)
T ss_dssp -TEEEEEEEEEE--------TTS--EEEEEEESSSEEEEEEESGGGHHHHHTTSSSTT-EEEEEEEEEEESTTSSEEEEE
T ss_pred CcEEEEEeeEEccCCC----CCCCceEEEEEEChHHHHHHHhHHHhHHHHhcCCcccCCEEEEeEEEEeeccCCCEEEEE
Confidence 5999999999998743 2367999999999999999999999999999999999999999999999999 9999999
Q ss_pred EeeeEecc
Q 003281 80 MDLDVIID 87 (834)
Q Consensus 80 ~~lev~~~ 87 (834)
+++|||.+
T Consensus 94 l~leVv~~ 101 (101)
T PF04057_consen 94 LDLEVVQS 101 (101)
T ss_dssp EEEEEEE-
T ss_pred EeeEEEeC
Confidence 99999863
No 18
>cd04475 RPA1_DBD_B RPA1_DBD_B: A subfamily of OB folds corresponding to the third OB fold, the ssDNA-binding domain (DBD)-B, of human RPA1 (also called RPA70). RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-B, RPA1 contains three other OB folds: DBD-A, DBD-C, and RPA1N. The major DNA binding activity of human RPA (hRPA) and Saccharomyces cerevisiae RPA (ScRPA) is associated with RPA1 DBD-A and DBD-B. RPA1 DBD-C is involved in trimerization. The ssDNA binding mechanism is believed to be multistep and to involve conformational change. Although ScRPA and the hRPA have similar ssDNA-binding properties, they differ functiona
Probab=99.82 E-value=8.1e-20 Score=166.73 Aligned_cols=100 Identities=44% Similarity=0.774 Sum_probs=92.8
Q ss_pred eeeEEEEEEEecCCeeEEccC-CceeeEEEEEEeccCCcEEEEEEcCCccchhhhhhhhcccCCCccEEEEEEEEEeecC
Q 003281 353 VVDLIGVVSYISPTASLMRKN-GTETQKRTLHLRDMSGRSVELTLWGNFCNDDGLRLQHMCDSGVFPILAVKAGRVSDFN 431 (834)
Q Consensus 353 ~vDVIGvV~~V~~~~~i~~k~-g~~~~kr~i~L~D~s~~si~vtLWg~~a~~~~~~l~~~~~~~~~~Vv~ik~~rV~~f~ 431 (834)
+|||+|+|++|+++.+|++|+ |++..+|+|+|.|+|+.+|+|||||++|+.+.. ..++||+|+++||++|+
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 589999999999999999996 999999999999999999999999999987532 12789999999999999
Q ss_pred CeEEEeecceEEEEcCCchHHHHHHHHHH
Q 003281 432 GKVVGTISTTQLFIEPDFPEAHRLKEWFE 460 (834)
Q Consensus 432 G~~Ls~~~~S~i~inPd~pe~~~l~~w~~ 460 (834)
|++|++..+|.|++||++||+.+|+.||+
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 19
>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=99.75 E-value=5.9e-18 Score=155.76 Aligned_cols=101 Identities=26% Similarity=0.538 Sum_probs=91.2
Q ss_pred eEEEEEEEecCCeeEEccCCceeeEEEEEEeccCCcEEEEEEcCCccchhhhhhhhcccCCCccEEEEEE-EEEeecCC-
Q 003281 355 DLIGVVSYISPTASLMRKNGTETQKRTLHLRDMSGRSVELTLWGNFCNDDGLRLQHMCDSGVFPILAVKA-GRVSDFNG- 432 (834)
Q Consensus 355 DVIGvV~~V~~~~~i~~k~g~~~~kr~i~L~D~s~~si~vtLWg~~a~~~~~~l~~~~~~~~~~Vv~ik~-~rV~~f~G- 432 (834)
||||+|++|+++.+++.+ |++..||+++|+|.++.+++|||||++|.+|...+.. ....+|||++.. +||++|+|
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 899999999999999887 8899999999999999999999999999998776642 346789998855 99999997
Q ss_pred eEEEee-cceEEEEcCCchHHHHHHHH
Q 003281 433 KVVGTI-STTQLFIEPDFPEAHRLKEW 458 (834)
Q Consensus 433 ~~Ls~~-~~S~i~inPd~pe~~~l~~w 458 (834)
++|+.. +.|++++||++||+.+|+..
T Consensus 78 ~~ls~~~~~s~v~inp~ipe~~~~~~~ 104 (106)
T cd04481 78 KSLSNSFGASKVYINPDIPEVPEIKMS 104 (106)
T ss_pred cEEEcCCCceEEEECCCcHHHHHHHhh
Confidence 799988 99999999999999999864
No 20
>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=99.70 E-value=5e-17 Score=143.76 Aligned_cols=86 Identities=21% Similarity=0.302 Sum_probs=80.3
Q ss_pred EEEEEEEEeccceeecCCCCCcceEEEEEeeCCCCEEEEEEechHHHhhhhccCcCcEEEEeeeEEecCCcccccCCCeE
Q 003281 233 TIKARVTAKGELRHYNNQRGDGKVFHFDLLDSDGGEIRVTCFNAVADQFYHQVEAGKIYLVSRGSLKPAQKNFNHLHNDL 312 (834)
Q Consensus 233 ~I~aRV~~Ks~lr~~~n~~g~Gk~f~~~L~De~g~~I~at~f~~~~d~f~~~l~eG~vy~is~~~V~~a~~~~~~~~~~y 312 (834)
+|+|||+++|+.+... +|+.++|+|+||+|.+|+|++|.+++++|+++|+||+||.|++|.|.+++++|+.++|+|
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 4899999999876543 689999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEEccCccE
Q 003281 313 EIFLDMTSMV 322 (834)
Q Consensus 313 eI~f~~~T~I 322 (834)
+|.|..+|+|
T Consensus 77 ~I~f~~~T~V 86 (86)
T cd04480 77 KIKFMSDTVV 86 (86)
T ss_pred EEEeecCcCC
Confidence 9999998875
No 21
>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=99.52 E-value=3.6e-14 Score=127.89 Aligned_cols=87 Identities=20% Similarity=0.358 Sum_probs=80.2
Q ss_pred EEEEeeCCCCEEEEEEechHHHhhhhccCcCcEEEEeeeEEecCCcccccCCCeEEEEEccCccEEEecCCCCCCccccc
Q 003281 258 HFDLLDSDGGEIRVTCFNAVADQFYHQVEAGKIYLVSRGSLKPAQKNFNHLHNDLEIFLDMTSMVQLCYEDDASIPRQQF 337 (834)
Q Consensus 258 ~~~L~De~g~~I~at~f~~~~d~f~~~l~eG~vy~is~~~V~~a~~~~~~~~~~yeI~f~~~T~I~~~~d~~~~iP~~~~ 337 (834)
.|+|+|++|+.|+|+++.+++++|.+.|+||+||.|++|.|.++...|+++.|+|+|.|..+|.|+++.. ....+ .|
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 3789999999999999999999999999999999999999999999999999999999999999999843 33333 89
Q ss_pred cccccccccc
Q 003281 338 HFRPINDVEG 347 (834)
Q Consensus 338 ~f~~i~dI~~ 347 (834)
+|++|++|.+
T Consensus 78 ~f~~F~~I~~ 87 (95)
T PF02721_consen 78 NFTPFDEILE 87 (95)
T ss_pred eecCHHHHhc
Confidence 9999999986
No 22
>PRK07217 replication factor A; Reviewed
Probab=99.52 E-value=3e-12 Score=135.64 Aligned_cols=210 Identities=16% Similarity=0.193 Sum_probs=159.1
Q ss_pred cccccccccccCCCceeeEEEEEEEecCCeeEEccCCceeeEEEEEEeccCCcEEEEEEcCCccchhhhhhhhcccCCCc
Q 003281 338 HFRPINDVEGMENNSVVDLIGVVSYISPTASLMRKNGTETQKRTLHLRDMSGRSVELTLWGNFCNDDGLRLQHMCDSGVF 417 (834)
Q Consensus 338 ~f~~i~dI~~~~~~~~vDVIGvV~~V~~~~~i~~k~g~~~~kr~i~L~D~s~~si~vtLWg~~a~~~~~~l~~~~~~~~~ 417 (834)
..++|.||.. .+..|+|.|.|+.+.+.. ..+ ..+.=.|.|+|| .|++|+|++..... -..+
T Consensus 71 ~~~kI~Di~~--~~~~VsV~aKVl~l~e~~-----~~s--i~qvGllgDETG-~IkfT~W~~s~~~~---------leeG 131 (311)
T PRK07217 71 ELVNIADIDE--PEQWVDVTAKVVQLWEPS-----SDS--IAQVGLLGDETG-TIKFTKWAKSDLPE---------LEEG 131 (311)
T ss_pred CceeeeecCC--CCCcEEEEEEEEEecCCC-----CCc--eEEEEEEEcCCc-eEEEEEccCCCCCc---------ccCC
Confidence 3556666653 467899999999998754 222 233336999999 79999999742210 1257
Q ss_pred cEEEEEEEEEeecCCe-EEEeecceEEEEcCCchHHHHHHHHHHhcCCccceeeeccccccCCccchhccHhhhhhcCCC
Q 003281 418 PILAVKAGRVSDFNGK-VVGTISTTQLFIEPDFPEAHRLKEWFEKEGKNTQSVSISRDSLSVGRADIRKTVSQIKDEGLG 496 (834)
Q Consensus 418 ~Vv~ik~~rV~~f~G~-~Ls~~~~S~i~inPd~pe~~~l~~w~~~~g~~~~~~sls~~~~~~~~~~~~ktI~ei~~~~lg 496 (834)
.++.|.++.+++|+|+ +|+....|+|...++.- ++.+
T Consensus 132 d~~rI~na~v~ey~G~~~lnlg~~t~I~~~de~I--------------------------------------eV~~---- 169 (311)
T PRK07217 132 KSYLLKNVVTDEYQGRFSVKLNRTTSIEELDEDI--------------------------------------EVGD---- 169 (311)
T ss_pred CEEEEEeEEEeeECCEEEEEeCCceEEEeCCCCc--------------------------------------cccC----
Confidence 8999999999999997 89988888887644320 1111
Q ss_pred CCCCCceEEEEEEEEEEecCCeeeeCCCCCcCCCCcCcccccCCCCceecCCCCCccccceEEEEEEEEEEeCCCeEEEE
Q 003281 497 TKEKPDWITVSATIVYIKCDNFCYTACPIMIGDRPCNKKVMNNGDGRWHCDRCDQSVVECDYRYILQFQIQDHTGLTWVT 576 (834)
Q Consensus 497 ~~~k~~~~~v~atI~~I~~d~~~Y~aC~~~~~~~~C~KKv~~~~dg~~~CekC~~~~~~~~~ry~l~~~i~D~Tg~~~~~ 576 (834)
+-..+.++|+.|........-||.+ .|+|.|. ...|+.|++. .+.+-.++.+.|.|+||++.+.
T Consensus 170 -----~~vei~G~lVdi~~GsglI~rCP~~----~C~Rvl~-----~g~C~~HG~v--e~~~DLrik~vlDDGt~~~~~~ 233 (311)
T PRK07217 170 -----DEVEVEGALVDIQSGSGLIKRCPEE----DCTRVLQ-----NGRCSEHGKV--EGEFDLRIKGVLDDGEEVQEVI 233 (311)
T ss_pred -----ccccceeEEEEEeCCCCCeecCCcc----ccCcccc-----CCCCCCCCCc--CCceeeEEEEEEECCCCeEEEE
Confidence 1146789999999987778899954 3999994 3689999975 5788889999999999999999
Q ss_pred EehHHHHHHhCCCHHHHHhhhccCCChhH-HHHHHHHhcCceEEEEEEE
Q 003281 577 AFQECAEEIMGMSAKDLYSLKYVDQNDEK-FGEVVRNATFTKYLFKLKV 624 (834)
Q Consensus 577 ~F~e~ae~llG~sA~el~~l~~ee~d~~~-~~~~l~~~~~k~~~f~l~~ 624 (834)
+-.+..++|.|++-+|+.+|..+.-|... +.++-+.++|+.|.|+-..
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 99999999999999999998743333332 3445568999999988854
No 23
>PRK08402 replication factor A; Reviewed
Probab=99.51 E-value=5.8e-13 Score=146.36 Aligned_cols=177 Identities=23% Similarity=0.394 Sum_probs=139.4
Q ss_pred CceeccccCCCCCceEEEEEEEEeccceeecCCCC-CcceEEEEEeeCCCCEEEEEEechHHHhhhhccCcCcEEEEeee
Q 003281 218 RIIPIAALNPYMGKWTIKARVTAKGELRHYNNQRG-DGKVFHFDLLDSDGGEIRVTCFNAVADQFYHQVEAGKIYLVSRG 296 (834)
Q Consensus 218 ~~~pI~~L~p~~~~w~I~aRV~~Ks~lr~~~n~~g-~Gk~f~~~L~De~g~~I~at~f~~~~d~f~~~l~eG~vy~is~~ 296 (834)
++++|++|.|++..|++.|||+.+++.|+|.+..| .|++.+++|.|+ +|.|+.|+|++.++++++.|++|+|+.|.++
T Consensus 61 ~~~kI~dl~~g~~~V~v~~rVl~~~~~r~f~rrdG~~~~V~~i~l~De-TG~ir~TlW~~~a~~~~~~l~~Gdvi~I~~a 139 (355)
T PRK08402 61 PLMHISDLVPGMRGVNIVGRVLRKYPPREYTKKDGSTGRVASLIIYDD-TGRARVVLWDAKVAKYYNKINVGDVIKVIDA 139 (355)
T ss_pred CccCHHHccCCCceeeEEEEEEEccCCceeeccCCCcceEEEEEEEcC-CCeEEEEEechhhhhhcccCCCCCEEEEECC
Confidence 57899999999999999999999999999997665 589999999997 5799999999999998889999999999999
Q ss_pred EEecCCcccccCCCeEEEEEccCccEEEecCCC--CCCccc------cccccccccccccCCCceeeEEEEEEEecCCee
Q 003281 297 SLKPAQKNFNHLHNDLEIFLDMTSMVQLCYEDD--ASIPRQ------QFHFRPINDVEGMENNSVVDLIGVVSYISPTAS 368 (834)
Q Consensus 297 ~V~~a~~~~~~~~~~yeI~f~~~T~I~~~~d~~--~~iP~~------~~~f~~i~dI~~~~~~~~vDVIGvV~~V~~~~~ 368 (834)
+|+... ...++|.+...|+|...++.. ..+|.+ .+.+.+|.+|.. .+.++.|.|.|+++.+-.-
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 998542 234699999999998876532 234443 367788888865 3467999999999998211
Q ss_pred EE------cc-C-------------C----ceeeEEEEEEeccCCcEEEEEEcCCccchh
Q 003281 369 LM------RK-N-------------G----TETQKRTLHLRDMSGRSVELTLWGNFCNDD 404 (834)
Q Consensus 369 i~------~k-~-------------g----~~~~kr~i~L~D~s~~si~vtLWg~~a~~~ 404 (834)
+. +| . | .......+.|.|.|| .+.||||++.|+.+
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 11 11 0 1 112234678899999 79999999999653
No 24
>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=99.18 E-value=2.2e-10 Score=130.17 Aligned_cols=244 Identities=23% Similarity=0.327 Sum_probs=175.3
Q ss_pred CCCceeccccCCCCCceEEEEEEEEeccceeecCCCCCcceEEEEEeeCCCCEEEEEEechHHHhhhhccCcCcEEEEee
Q 003281 216 PSRIIPIAALNPYMGKWTIKARVTAKGELRHYNNQRGDGKVFHFDLLDSDGGEIRVTCFNAVADQFYHQVEAGKIYLVSR 295 (834)
Q Consensus 216 ~~~~~pI~~L~p~~~~w~I~aRV~~Ks~lr~~~n~~g~Gk~f~~~L~De~g~~I~at~f~~~~d~f~~~l~eG~vy~is~ 295 (834)
...+.++..+.||. ++||+.+.++|+|.+.++++++|+..|.|++ +.++.|+...+ +++|++|.+.+
T Consensus 159 ~~~i~~~~~~~~~~-----~~~v~~g~~ik~~~~~~ge~~~~~~~~~d~~---~~~~~~~~~~~-----~~~g~~~~ie~ 225 (407)
T COG1599 159 AREIGEESLLSPYQ-----KARVVVGSEIKTFDNQGGESKVFSNELEDEE---RGVIVFTDWDP-----SQDGDVYRIEG 225 (407)
T ss_pred ccccccccccCccc-----eEEEEecccceeEecCCCccceEeeeecccc---eeEEEeccCcc-----cccceeeeecC
Confidence 45778899999987 8999999999999999999999999999986 44555543222 39999999999
Q ss_pred eEEecCCcccccCCCeEEEEEccC--ccEEEecCCCCCCccccccccccccccccCCCceeeEEEEEEEecCCeeEEccC
Q 003281 296 GSLKPAQKNFNHLHNDLEIFLDMT--SMVQLCYEDDASIPRQQFHFRPINDVEGMENNSVVDLIGVVSYISPTASLMRKN 373 (834)
Q Consensus 296 ~~V~~a~~~~~~~~~~yeI~f~~~--T~I~~~~d~~~~iP~~~~~f~~i~dI~~~~~~~~vDVIGvV~~V~~~~~i~~k~ 373 (834)
.+|+..++++... +.+++.+... +.|.++. ....++...+. ...-++ .+..+| |+.+.+...+..+.
T Consensus 226 ~~v~~~~~~~~~~-~~~e~~~~~~~~~~i~~~~-~~~~~~~~~~~-~~~~~~----~~~~v~----v~~~~~c~~~~~~~ 294 (407)
T COG1599 226 ARVKTKNKQPEEN-LAEELVLRVEVRVAIEKAE-REEFVDEVKES-VSLVEA----DGAVVD----VTRVPECERVVRKG 294 (407)
T ss_pred cEEEEeccccccc-ccceEEEeecceeeccCCC-Cccccceeecc-ccccee----ccceEE----EEECCCceEEEeCC
Confidence 9999999988777 8999998876 4554442 12223322222 111111 123344 77787777776767
Q ss_pred CceeeEEEEEEeccCCcEEEEEEcCCccchhhhhhhhcccCCCccEEEEEEEEEeecCCeEEEeecceEEEEcCCchHHH
Q 003281 374 GTETQKRTLHLRDMSGRSVELTLWGNFCNDDGLRLQHMCDSGVFPILAVKAGRVSDFNGKVVGTISTTQLFIEPDFPEAH 453 (834)
Q Consensus 374 g~~~~kr~i~L~D~s~~si~vtLWg~~a~~~~~~l~~~~~~~~~~Vv~ik~~rV~~f~G~~Ls~~~~S~i~inPd~pe~~ 453 (834)
+.....+++.|.|.++ +++|+||++-++.. + ...++.++++.++.++.|..+++ .++++.
T Consensus 295 ~~~~~~~~~~l~D~~g-~~rv~~~~~~~e~~-------~--~~~~~~~~~~~~~~~~~~~~~~~----------~~~~~~ 354 (407)
T COG1599 295 GCKGHGKDIGLDDLTG-KIRVTLWGDATEVL-------I--NEESVEALKGINVEDASGIALSA----------LDTEAV 354 (407)
T ss_pred CcccccccceEecCce-EEEEecCCCceEEE-------e--cccchhheeeeeeeeccchhhhh----------hhhhhh
Confidence 7778899999999988 79999999744321 1 25678899999999999876654 678888
Q ss_pred HHHHHHHhcCCccceeeeccccccCCccchhccHhhhhhcCCCCCCCCceEEEEEEEEEEecC
Q 003281 454 RLKEWFEKEGKNTQSVSISRDSLSVGRADIRKTVSQIKDEGLGTKEKPDWITVSATIVYIKCD 516 (834)
Q Consensus 454 ~l~~w~~~~g~~~~~~sls~~~~~~~~~~~~ktI~ei~~~~lg~~~k~~~~~v~atI~~I~~d 516 (834)
.+..||...|+...+.-. .......-+.+..+.+.+++.+.+.|..++.+
T Consensus 355 a~~~~~~~~Gk~~~v~g~-------------~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~ 404 (407)
T COG1599 355 ALEIWYDILGKYLRVTGD-------------AREDRYLIENLVESSTWDDVDVRAEIEALKEE 404 (407)
T ss_pred hhhcchhcccceEEeecc-------------ccchhhhhhhhccccccCccchhheeeeeccc
Confidence 999999988887654311 01111112233445677788999999988765
No 25
>KOG0851 consensus Single-stranded DNA-binding replication protein A (RPA), large (70 kD) subunit and related ssDNA-binding proteins [Replication, recombination and repair]
Probab=99.13 E-value=4.8e-10 Score=118.80 Aligned_cols=214 Identities=18% Similarity=0.251 Sum_probs=160.6
Q ss_pred CceeccccCCCCCceEEEEEEEEeccceeecCCCCCcceEEEEEeeCCCCEEEEEEechHHHhhhhccCcCcEEEEeeeE
Q 003281 218 RIIPIAALNPYMGKWTIKARVTAKGELRHYNNQRGDGKVFHFDLLDSDGGEIRVTCFNAVADQFYHQVEAGKIYLVSRGS 297 (834)
Q Consensus 218 ~~~pI~~L~p~~~~w~I~aRV~~Ks~lr~~~n~~g~Gk~f~~~L~De~g~~I~at~f~~~~d~f~~~l~eG~vy~is~~~ 297 (834)
.+++|.+|+|+.+.|+|.++|++.|+. +.+.. +..+.|.|.|+.|.+|.|++......+|.+.|++|+|+.|..|.
T Consensus 3 ~~~~l~~l~~~~t~w~i~~~vl~v~~~--~~~~~--~~~~~~il~D~~~~~i~a~i~~~~~~~~~~~l~~~~w~~i~~f~ 78 (246)
T KOG0851|consen 3 GFHRLRDLSPSITGWRIQVKVLRVWKK--YSNPN--GEELRLVLADEHGVKIEATVGRRLSSKYEDNLIENEWKIITTFG 78 (246)
T ss_pred cccchhhcCcCceeeEEEEEEEEEEEe--cCCCC--ccEEEEEEEecCCcEEEEEcchHHHhhhhhheecceeEEeeeee
Confidence 478899999999999999999988764 33333 67899999999999999999999999999999999999999999
Q ss_pred EecCCcccccCCCeEEEEEccCccEEEecCCCCCCccc-cccccccccccc--cCCCceeeEEE-EEEEecCCeeEEccC
Q 003281 298 LKPAQKNFNHLHNDLEIFLDMTSMVQLCYEDDASIPRQ-QFHFRPINDVEG--MENNSVVDLIG-VVSYISPTASLMRKN 373 (834)
Q Consensus 298 V~~a~~~~~~~~~~yeI~f~~~T~I~~~~d~~~~iP~~-~~~f~~i~dI~~--~~~~~~vDVIG-vV~~V~~~~~i~~k~ 373 (834)
|.++...++.+.|+|+|.|...+.+..... ..+-. ..+|.++..+.+ .....++|++| .|..|+.+..- ...
T Consensus 79 v~~~~~~~~~~~~~~~i~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~v~~~~~~~~~v~~~~~~~~~v~~~~~~-~~~ 154 (246)
T KOG0851|consen 79 VNPNSGQVRATTHSFKINFMDFTVVTSSDT---RLPCTPWGKFTPFDSIVEDKSDKRVLVDLIGVAVYDVSQLTVT-PAI 154 (246)
T ss_pred ecccccceeeeeeEEEEEeccceeeccCCC---CccceeccccchhhhhhccccCCcEEEEeeceeEEEeeeeEec-ccc
Confidence 999999999999999999977777776422 23322 456777655443 34678999998 66666655422 124
Q ss_pred CceeeEEEEEEeccCCcEEEEEEcCCccchhhhhhhhcccCCCccEEEEEEEEEeecCCeEEEeecceEEEEcCCchHHH
Q 003281 374 GTETQKRTLHLRDMSGRSVELTLWGNFCNDDGLRLQHMCDSGVFPILAVKAGRVSDFNGKVVGTISTTQLFIEPDFPEAH 453 (834)
Q Consensus 374 g~~~~kr~i~L~D~s~~si~vtLWg~~a~~~~~~l~~~~~~~~~~Vv~ik~~rV~~f~G~~Ls~~~~S~i~inPd~pe~~ 453 (834)
++.+..+.+...+.+. |.. +. ...++.+++..+.+| +++ ...+.+.+.++|+ ..
T Consensus 155 ~~~~~~~~~~~~~~~~-------~~~-------------~~-~~~~c~~~~~~~~~~-~~~-~~l~~~~~~~~~~---l~ 208 (246)
T KOG0851|consen 155 DTDVDGFYLTFKICNK-------SKF-------------SK-PVLWCEACGEQATDF-GRK-RSLGGGVIVIAPE---LL 208 (246)
T ss_pred cCCcceEEEEEeeccc-------ccc-------------cC-ceEEehhhcchHHhh-hhh-eEecCCcEEccch---he
Confidence 5678888888888776 110 01 124455667777788 656 7778888888888 66
Q ss_pred HHHHHHHhcCCc
Q 003281 454 RLKEWFEKEGKN 465 (834)
Q Consensus 454 ~l~~w~~~~g~~ 465 (834)
.++.|....|..
T Consensus 209 ~~~~~~~~~G~~ 220 (246)
T KOG0851|consen 209 FWKIWRYFDGKN 220 (246)
T ss_pred eecccccccCCc
Confidence 666666666643
No 26
>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=99.05 E-value=1.3e-09 Score=105.08 Aligned_cols=89 Identities=24% Similarity=0.366 Sum_probs=75.5
Q ss_pred ccccccccccccCCCceeeEEEEEEEecCCeeEEccCCceeeEEEEEEeccCC---cEEEEEEcCCccchhhhhhhhccc
Q 003281 337 FHFRPINDVEGMENNSVVDLIGVVSYISPTASLMRKNGTETQKRTLHLRDMSG---RSVELTLWGNFCNDDGLRLQHMCD 413 (834)
Q Consensus 337 ~~f~~i~dI~~~~~~~~vDVIGvV~~V~~~~~i~~k~g~~~~kr~i~L~D~s~---~si~vtLWg~~a~~~~~~l~~~~~ 413 (834)
|+|++|++|.+ ..+..|||||||+++.++.. ..|++ .++.|+|+|.|. ..|+|+||++.++.+..
T Consensus 1 ~~f~~i~~~~~-~~~~~v~vigVV~~~~~p~~---s~g~d-~~~tl~i~D~S~~~~~~l~v~~F~~~~~~LP~------- 68 (138)
T cd04497 1 YKYTPLSSALK-ESGGSVNVIGVVVDAGPPVR---SKGTD-YCCTLTITDPSLANSDGLTVKLFRPNEESLPI------- 68 (138)
T ss_pred CceEeHHHHHh-ccCCeEEEEEEEeecCCCcc---cCCCc-EEEEEEEECCCCCCCCcEEEEEECCChhhCCC-------
Confidence 57999999987 67899999999999999863 24555 899999999998 88999999999887542
Q ss_pred CCCccEEEEEEEEEeecCCeEEEe
Q 003281 414 SGVFPILAVKAGRVSDFNGKVVGT 437 (834)
Q Consensus 414 ~~~~~Vv~ik~~rV~~f~G~~Ls~ 437 (834)
...++||+|++++|+.|+|+.+.+
T Consensus 69 v~~GDVIll~~~kv~~~~g~~~~~ 92 (138)
T cd04497 69 VKVGDIILLRRVKIQSYNGKPQGI 92 (138)
T ss_pred CCCCCEEEEEEEEEEEECCceEEE
Confidence 246899999999999999986544
No 27
>COG5082 AIR1 Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]
Probab=99.04 E-value=1.6e-10 Score=113.67 Aligned_cols=81 Identities=27% Similarity=0.557 Sum_probs=62.5
Q ss_pred cccccCccCccCCCCCCCCCCCCCCCCCCCCCCCCCC--CCCCCCCcCcccCCCCccCCCC-CCCCCCCCCcCCCCCCcc
Q 003281 743 SCSSCGAVGHSSMNCPSIMSGPGQSSGGGYANSFSSG--AGIATSSECYKCHKTGHWARDC-PSLNAAPPAYGSSGIGIS 819 (834)
Q Consensus 743 ~C~~Cg~~GH~a~~Cp~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~Cy~Cg~~GH~ardC-p~~~~~~~c~~c~~~g~~ 819 (834)
.||+||+.||+++||| ..- ||.+...+- ........||+||+.||+++|| |.......|+.|+..+|.
T Consensus 62 ~C~nCg~~GH~~~DCP-~~i--------C~~C~~~~H~s~~C~~~~~C~~Cg~~GH~~~dC~P~~~~~~~C~~C~s~~H~ 132 (190)
T COG5082 62 VCFNCGQNGHLRRDCP-HSI--------CYNCSWDGHRSNHCPKPKKCYNCGETGHLSRDCNPSKDQQKSCFDCNSTRHS 132 (190)
T ss_pred ccchhcccCcccccCC-hhH--------hhhcCCCCcccccCCcccccccccccCccccccCcccccCcceeccCCCccc
Confidence 8999999999999999 332 333321111 1112346899999999999999 666655589999999999
Q ss_pred cccCCCCCCCCCC
Q 003281 820 AAGYRGAPRQQVG 832 (834)
Q Consensus 820 ~~~cg~~~~~~~~ 832 (834)
...|...+++|+.
T Consensus 133 s~~Cp~~~k~y~~ 145 (190)
T COG5082 133 SEDCPSIWKHYVL 145 (190)
T ss_pred cccCccccccccc
Confidence 9999999999765
No 28
>PRK06386 replication factor A; Reviewed
Probab=99.02 E-value=1.5e-07 Score=103.49 Aligned_cols=164 Identities=12% Similarity=0.171 Sum_probs=123.0
Q ss_pred CceeccccCCCCCceEEEEEEEEeccceeecCCCCCcceEEEEEeeCCCCEEEEEEechHHHhhhhccCcCcEEEEeeeE
Q 003281 218 RIIPIAALNPYMGKWTIKARVTAKGELRHYNNQRGDGKVFHFDLLDSDGGEIRVTCFNAVADQFYHQVEAGKIYLVSRGS 297 (834)
Q Consensus 218 ~~~pI~~L~p~~~~w~I~aRV~~Ks~lr~~~n~~g~Gk~f~~~L~De~g~~I~at~f~~~~d~f~~~l~eG~vy~is~~~ 297 (834)
+.++|++|.|....-+|.|||+..|+ |.|....+.|++.++.|.|+ .|+|+.|.|++ .|++|++|.|.++.
T Consensus 106 ~~~KI~DL~~g~~~v~V~akVle~~e-~e~~~~g~~~~v~sg~lgDe-TGrIr~TlW~~-------~l~eGd~v~i~na~ 176 (358)
T PRK06386 106 KLVKIRDLSLVTPYVSVIGKITGITK-KEYDSDGTSKIVYQGYIEDD-TARVRISSFGK-------PLEDNRFVRIENAR 176 (358)
T ss_pred CccEeEeccCCCCceEEEEEEEEccC-ceEecCCCccEEEEEEEEcC-CCeEEEEEccc-------cccCCCEEEEeeeE
Confidence 35789999998765579999999987 78875555689999999998 58999999986 48999999999998
Q ss_pred EecCCcccccCCCeEEEEEccCccEEEecCCCCCCccccccccccccccccCCCceeeEEEEEEEecC-CeeEEc-----
Q 003281 298 LKPAQKNFNHLHNDLEIFLDMTSMVQLCYEDDASIPRQQFHFRPINDVEGMENNSVVDLIGVVSYISP-TASLMR----- 371 (834)
Q Consensus 298 V~~a~~~~~~~~~~yeI~f~~~T~I~~~~d~~~~iP~~~~~f~~i~dI~~~~~~~~vDVIGvV~~V~~-~~~i~~----- 371 (834)
+...+ -.++|.++..|.|++.++ + |. ..-.+.+|.||.+.. ..+-|.|.|++|.+ ...|.+
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-LESRNIFIFEIKSPV--GGITIMGFIVSVGQGSRIFTKCSVCN 243 (358)
T ss_pred EEccC-------CeEEEEeCCeEEEEECCC-C--cc-cCccccchhhhhccC--CeEEEEEEEEEEcCCcEeEecCcCCC
Confidence 76543 457999999999999743 2 32 333577888887632 34888899999986 322221
Q ss_pred -c--CC------c---eeeEEE-EEEeccCCcEEEEEEcCCccchh
Q 003281 372 -K--NG------T---ETQKRT-LHLRDMSGRSVELTLWGNFCNDD 404 (834)
Q Consensus 372 -k--~g------~---~~~kr~-i~L~D~s~~si~vtLWg~~a~~~ 404 (834)
+ +| + +..-|. +.|-|.+| .++|+|.++.++++
T Consensus 244 R~l~~g~C~~HG~v~~~~dlr~k~vLDDGtg-~~~~~l~~e~~e~l 288 (358)
T PRK06386 244 KIIEDGVCKDHPDAPVYLDIFGYFTISDGTG-FVTCYANKDSFLPY 288 (358)
T ss_pred eEccCCcCCCCCCCCCeeEEEEEEEEECCCC-eEEEEEChHHhHHH
Confidence 1 11 1 122343 67777777 89999999988763
No 29
>PRK07218 replication factor A; Provisional
Probab=98.91 E-value=4.9e-08 Score=109.88 Aligned_cols=170 Identities=16% Similarity=0.187 Sum_probs=130.9
Q ss_pred CceeccccCCCCCceEEEEEEEEeccceeecCCCCCcceEEEEEeeCCCCEEEEEEechHHHhhhhccCcCcEEEEeeeE
Q 003281 218 RIIPIAALNPYMGKWTIKARVTAKGELRHYNNQRGDGKVFHFDLLDSDGGEIRVTCFNAVADQFYHQVEAGKIYLVSRGS 297 (834)
Q Consensus 218 ~~~pI~~L~p~~~~w~I~aRV~~Ks~lr~~~n~~g~Gk~f~~~L~De~g~~I~at~f~~~~d~f~~~l~eG~vy~is~~~ 297 (834)
...+|.+|.|.....+|.|||+..++ |.|...+|+..+.+..|.|+ .|.|+.|+|+++. .|++|++|.|.++.
T Consensus 161 ~~~kI~DL~~g~~~V~v~g~Vl~~~~-r~f~~~dg~~~v~~giigDe-TG~Ir~tlW~~~~-----~l~~Gd~v~I~na~ 233 (423)
T PRK07218 161 GDKKLIDLGPGDRGVNVEARVLELEH-REIDGRDGETTILSGVLADE-TGRLPFTDWDPLP-----EIEIGASIRIEDAY 233 (423)
T ss_pred CccchhhccCCCCceEEEEEEEEecc-eeEEcCCCCeEEEEEEEECC-CceEEEEEecccc-----cCCCCCEEEEeeeE
Confidence 35689999999887899999999976 89998888889999999998 5899999999753 48999999999999
Q ss_pred EecCCcccccCCCeEEEEEccCccEEEecCCCCCCccccccccccccccccCCCceeeEEEEEEEecCCeeEEcc-----
Q 003281 298 LKPAQKNFNHLHNDLEIFLDMTSMVQLCYEDDASIPRQQFHFRPINDVEGMENNSVVDLIGVVSYISPTASLMRK----- 372 (834)
Q Consensus 298 V~~a~~~~~~~~~~yeI~f~~~T~I~~~~d~~~~iP~~~~~f~~i~dI~~~~~~~~vDVIGvV~~V~~~~~i~~k----- 372 (834)
++..+ ..++|.+++.|.|+...+ +..++. .+.-++|.++.+-.-...|.|.|.|++|.+-.-+..+
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 88543 467999999999999743 333432 2445677777654323348999999999998543221
Q ss_pred --------------CCceeeEEEEEEeccCCcEEEEEEcCCccchh
Q 003281 373 --------------NGTETQKRTLHLRDMSGRSVELTLWGNFCNDD 404 (834)
Q Consensus 373 --------------~g~~~~kr~i~L~D~s~~si~vtLWg~~a~~~ 404 (834)
.+....+..+.|-|.+| .++|+|..+.++..
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 12234556777878888 89999999988753
No 30
>PTZ00368 universal minicircle sequence binding protein (UMSBP); Provisional
Probab=98.88 E-value=4.9e-09 Score=102.49 Aligned_cols=82 Identities=30% Similarity=0.628 Sum_probs=46.3
Q ss_pred cccccCccCccCCCCCCCCCCC------CCCCCCCCCCCCCCCC-CCCCCCcCcccCCCCccCCCCCCC----CCCCCCc
Q 003281 743 SCSSCGAVGHSSMNCPSIMSGP------GQSSGGGYANSFSSGA-GIATSSECYKCHKTGHWARDCPSL----NAAPPAY 811 (834)
Q Consensus 743 ~C~~Cg~~GH~a~~Cp~~~~~~------~~~~~~~~~~~~~~~~-~~~~~~~Cy~Cg~~GH~ardCp~~----~~~~~c~ 811 (834)
.||+|++.||++++||...... .....+++....+... .+.....||+|++.||++++||+. .....||
T Consensus 54 ~C~~Cg~~GH~~~~Cp~~~~~~~~~~C~~Cg~~GH~~~~C~~~~~~~~~~~~C~~Cg~~gH~~~~C~~~~~~~~~~~~C~ 133 (148)
T PTZ00368 54 SCYNCGKTGHLSRECPEAPPGSGPRSCYNCGQTGHISRECPNRAKGGAARRACYNCGGEGHISRDCPNAGKRPGGDKTCY 133 (148)
T ss_pred ccCCCCCcCcCcccCCCcccCCCCcccCcCCCCCcccccCCCcccccccchhhcccCcCCcchhcCCCccccCCCCCccc
Confidence 6777777777777777654211 1112233332222111 122234577777777777777774 1123677
Q ss_pred CCCCCCcccccCC
Q 003281 812 GSSGIGISAAGYR 824 (834)
Q Consensus 812 ~c~~~g~~~~~cg 824 (834)
.|++.||..++|-
T Consensus 134 ~Cg~~gH~~~dCp 146 (148)
T PTZ00368 134 NCGQTGHLSRDCP 146 (148)
T ss_pred cCCCcCcccccCC
Confidence 7777777777774
No 31
>PTZ00368 universal minicircle sequence binding protein (UMSBP); Provisional
Probab=98.83 E-value=6.6e-09 Score=101.61 Aligned_cols=85 Identities=29% Similarity=0.614 Sum_probs=60.4
Q ss_pred ccccccCccCccCCCCCCCCCCCC------CCCCCCCCCCCCCCCCCCCCCcCcccCCCCccCCCCCCCCC----CCCCc
Q 003281 742 QSCSSCGAVGHSSMNCPSIMSGPG------QSSGGGYANSFSSGAGIATSSECYKCHKTGHWARDCPSLNA----APPAY 811 (834)
Q Consensus 742 ~~C~~Cg~~GH~a~~Cp~~~~~~~------~~~~~~~~~~~~~~~~~~~~~~Cy~Cg~~GH~ardCp~~~~----~~~c~ 811 (834)
..||+|++.||++++||......+ ....+++....+..........||+|++.||++++||+... ...||
T Consensus 28 ~~C~~Cg~~GH~~~~Cp~~~~~~~~~~C~~Cg~~GH~~~~Cp~~~~~~~~~~C~~Cg~~GH~~~~C~~~~~~~~~~~~C~ 107 (148)
T PTZ00368 28 RPCYKCGEPGHLSRECPSAPGGRGERSCYNCGKTGHLSRECPEAPPGSGPRSCYNCGQTGHISRECPNRAKGGAARRACY 107 (148)
T ss_pred ccCccCCCCCcCcccCcCCCCCCCCcccCCCCCcCcCcccCCCcccCCCCcccCcCCCCCcccccCCCcccccccchhhc
Confidence 389999999999999998663211 12233333333322222234579999999999999999652 22699
Q ss_pred CCCCCCcccccCCCC
Q 003281 812 GSSGIGISAAGYRGA 826 (834)
Q Consensus 812 ~c~~~g~~~~~cg~~ 826 (834)
+|++.||...+|...
T Consensus 108 ~Cg~~gH~~~~C~~~ 122 (148)
T PTZ00368 108 NCGGEGHISRDCPNA 122 (148)
T ss_pred ccCcCCcchhcCCCc
Confidence 999999999999764
No 32
>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=98.74 E-value=9.8e-08 Score=83.57 Aligned_cols=80 Identities=20% Similarity=0.348 Sum_probs=69.1
Q ss_pred eEEEEEEEecCCeeEEccCCceeeEEEEEEeccCCcEEEEEEcCCccchhhhhhhhcccCCCccEEEEEEEEEeecCCe-
Q 003281 355 DLIGVVSYISPTASLMRKNGTETQKRTLHLRDMSGRSVELTLWGNFCNDDGLRLQHMCDSGVFPILAVKAGRVSDFNGK- 433 (834)
Q Consensus 355 DVIGvV~~V~~~~~i~~k~g~~~~kr~i~L~D~s~~si~vtLWg~~a~~~~~~l~~~~~~~~~~Vv~ik~~rV~~f~G~- 433 (834)
+|+|+|++++++.+++ ++|++...++++|.|+|| +|++++|++.+.. . -..+.+|.++++++++|+|.
T Consensus 1 ~v~~~V~~~~~~~~~~-~~g~~~~~~~~~l~D~TG-~i~~~~W~~~~~~---~------~~~G~vv~i~~~~v~~~~g~~ 69 (82)
T cd04491 1 SVEGKVLSISEPREFT-RDGSEGKVQSGLVGDETG-TIRFTLWDEKAAD---D------LEPGDVVRIENAYVREFNGRL 69 (82)
T ss_pred CEEEEEEEccCCeEec-cCCCeeEEEEEEEECCCC-EEEEEEECchhcc---c------CCCCCEEEEEeEEEEecCCcE
Confidence 4899999999999999 899999999999999999 8999999988621 1 13678999999999999985
Q ss_pred EEEeecceEEEE
Q 003281 434 VVGTISTTQLFI 445 (834)
Q Consensus 434 ~Ls~~~~S~i~i 445 (834)
.|+....|.|..
T Consensus 70 ql~i~~~~~i~~ 81 (82)
T cd04491 70 ELSVGKNSEIEK 81 (82)
T ss_pred EEEeCCceEEEE
Confidence 888888787764
No 33
>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=98.70 E-value=1.3e-07 Score=82.75 Aligned_cols=81 Identities=21% Similarity=0.331 Sum_probs=69.8
Q ss_pred EEEEEEEEeccceeecCCCCCcceEEEEEeeCCCCEEEEEEechHHHhhhhccCcCcEEEEeeeEEecCCcccccCCCeE
Q 003281 233 TIKARVTAKGELRHYNNQRGDGKVFHFDLLDSDGGEIRVTCFNAVADQFYHQVEAGKIYLVSRGSLKPAQKNFNHLHNDL 312 (834)
Q Consensus 233 ~I~aRV~~Ks~lr~~~n~~g~Gk~f~~~L~De~g~~I~at~f~~~~d~f~~~l~eG~vy~is~~~V~~a~~~~~~~~~~y 312 (834)
+|.|||+.+++.++|.+..++++++++.|.|++ |.|++++|++.+ .+.|++|++|.|.++.++..+ ..+
T Consensus 1 ~v~~~V~~~~~~~~~~~~g~~~~~~~~~l~D~T-G~i~~~~W~~~~---~~~~~~G~vv~i~~~~v~~~~-------g~~ 69 (82)
T cd04491 1 SVEGKVLSISEPREFTRDGSEGKVQSGLVGDET-GTIRFTLWDEKA---ADDLEPGDVVRIENAYVREFN-------GRL 69 (82)
T ss_pred CEEEEEEEccCCeEeccCCCeeEEEEEEEECCC-CEEEEEEECchh---cccCCCCCEEEEEeEEEEecC-------CcE
Confidence 478999999999999844457899999999985 699999999876 778999999999999987654 568
Q ss_pred EEEEccCccEEE
Q 003281 313 EIFLDMTSMVQL 324 (834)
Q Consensus 313 eI~f~~~T~I~~ 324 (834)
+|.++..|.|++
T Consensus 70 ql~i~~~~~i~~ 81 (82)
T cd04491 70 ELSVGKNSEIEK 81 (82)
T ss_pred EEEeCCceEEEE
Confidence 999999888875
No 34
>PRK06461 single-stranded DNA-binding protein; Reviewed
Probab=98.68 E-value=1.4e-07 Score=89.77 Aligned_cols=94 Identities=17% Similarity=0.217 Sum_probs=77.3
Q ss_pred ccccccccccCCCceeeEEEEEEEecCCeeEEccCCceeeEEEEEEeccCCcEEEEEEcCCccchhhhhhhhcccCCCcc
Q 003281 339 FRPINDVEGMENNSVVDLIGVVSYISPTASLMRKNGTETQKRTLHLRDMSGRSVELTLWGNFCNDDGLRLQHMCDSGVFP 418 (834)
Q Consensus 339 f~~i~dI~~~~~~~~vDVIGvV~~V~~~~~i~~k~g~~~~kr~i~L~D~s~~si~vtLWg~~a~~~~~~l~~~~~~~~~~ 418 (834)
+++|+||.. ....|+++++|+++++..++.+|++ +...++++|.|.|| +|+++||++.|..+ ..+.
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-RVKLTLWGEQAGSL----------KEGE 69 (129)
T ss_pred ceEHHHcCC--CCCceEEEEEEEEcCCceEEEeCCC-ceEEEEEEEECCCC-EEEEEEeCCccccC----------CCCC
Confidence 566777763 2268999999999999999888744 45689999999999 69999999977532 2578
Q ss_pred EEEEEEEEEeecCCe-EEEeecceEEEEc
Q 003281 419 ILAVKAGRVSDFNGK-VVGTISTTQLFIE 446 (834)
Q Consensus 419 Vv~ik~~rV~~f~G~-~Ls~~~~S~i~in 446 (834)
||.|++++|++|+|+ +|++...|.|..-
T Consensus 70 vV~I~na~v~~f~G~lqL~i~~~~~i~~~ 98 (129)
T PRK06461 70 VVEIENAWTTLYRGKVQLNVGKYGSISES 98 (129)
T ss_pred EEEEECcEEeeeCCEEEEEECCCEEEEEC
Confidence 999999999999997 8998888888753
No 35
>PRK06461 single-stranded DNA-binding protein; Reviewed
Probab=98.63 E-value=3.3e-07 Score=87.31 Aligned_cols=98 Identities=15% Similarity=0.231 Sum_probs=82.9
Q ss_pred CceeccccCCCCCceEEEEEEEEeccceeecCCCCCcceEEEEEeeCCCCEEEEEEechHHHhhhhccCcCcEEEEeeeE
Q 003281 218 RIIPIAALNPYMGKWTIKARVTAKGELRHYNNQRGDGKVFHFDLLDSDGGEIRVTCFNAVADQFYHQVEAGKIYLVSRGS 297 (834)
Q Consensus 218 ~~~pI~~L~p~~~~w~I~aRV~~Ks~lr~~~n~~g~Gk~f~~~L~De~g~~I~at~f~~~~d~f~~~l~eG~vy~is~~~ 297 (834)
.+++|++|.|......+.++|+.++..+.+....+.+++.++.|.|++ |.|++++|++.++ .|++|+|+.|.++.
T Consensus 3 ~~~kI~dL~~g~~~v~~~~~V~~i~~~~~~~~k~~~~~v~~~~l~D~T-G~I~~tlW~~~a~----~l~~GdvV~I~na~ 77 (129)
T PRK06461 3 MITKIKDLKPGMERVNVTVRVLEVGEPKVIQTKGGPRTISEAVVGDET-GRVKLTLWGEQAG----SLKEGEVVEIENAW 77 (129)
T ss_pred CceEHHHcCCCCCceEEEEEEEEcCCceEEEeCCCceEEEEEEEECCC-CEEEEEEeCCccc----cCCCCCEEEEECcE
Confidence 478999999998899999999999999888776656789999999985 6899999998543 58899999999998
Q ss_pred EecCCcccccCCCeEEEEEccCccEEEecC
Q 003281 298 LKPAQKNFNHLHNDLEIFLDMTSMVQLCYE 327 (834)
Q Consensus 298 V~~a~~~~~~~~~~yeI~f~~~T~I~~~~d 327 (834)
+..-+ ...+|.+...+.|+++.+
T Consensus 78 v~~f~-------G~lqL~i~~~~~i~~~~~ 100 (129)
T PRK06461 78 TTLYR-------GKVQLNVGKYGSISESDD 100 (129)
T ss_pred EeeeC-------CEEEEEECCCEEEEECCc
Confidence 87432 457899999999998743
No 36
>KOG4400 consensus E3 ubiquitin ligase interacting with arginine methyltransferase [Posttranslational modification, protein turnover, chaperones]
Probab=98.45 E-value=2.1e-07 Score=99.67 Aligned_cols=83 Identities=23% Similarity=0.531 Sum_probs=60.4
Q ss_pred cccccCccCccCCCCCCCCCCCCCCCCCCCCCCCCCCCC--------CCCCCcCcccCCCCccCCCCCCCCCCCCCcCCC
Q 003281 743 SCSSCGAVGHSSMNCPSIMSGPGQSSGGGYANSFSSGAG--------IATSSECYKCHKTGHWARDCPSLNAAPPAYGSS 814 (834)
Q Consensus 743 ~C~~Cg~~GH~a~~Cp~~~~~~~~~~~~~~~~~~~~~~~--------~~~~~~Cy~Cg~~GH~ardCp~~~~~~~c~~c~ 814 (834)
.||+|++.||++++||+...... +...+|.++..+..+ +.....||+|++.|||.++||.+ .+..||.|+
T Consensus 94 ~c~~C~~~gH~~~~c~~~~~~~~-~~~~~~~c~~~gh~~~~~~~~~~~~~~~~Cy~Cg~~GH~s~~C~~~-~~~~c~~c~ 171 (261)
T KOG4400|consen 94 ACFNCGEGGHIERDCPEAGKEGS-SETSCYSCGKTGHRGCPDADPVDGPKPAKCYSCGEQGHISDDCPEN-KGGTCFRCG 171 (261)
T ss_pred hhhhCCCCccchhhCCcccCccc-ccceeeccCCCccccCcccccccCCCCCccCCCCcCCcchhhCCCC-CCCccccCC
Confidence 89999999999999999876441 122223333222111 11225699999999999999987 335999999
Q ss_pred CCCcccccCCCCC
Q 003281 815 GIGISAAGYRGAP 827 (834)
Q Consensus 815 ~~g~~~~~cg~~~ 827 (834)
..||.-.+|+...
T Consensus 172 ~~~h~~~~C~~~~ 184 (261)
T KOG4400|consen 172 KVGHGSRDCPSKQ 184 (261)
T ss_pred CcceecccCCccc
Confidence 9999999998743
No 37
>COG5082 AIR1 Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]
Probab=98.13 E-value=1.8e-06 Score=85.40 Aligned_cols=62 Identities=31% Similarity=0.673 Sum_probs=47.3
Q ss_pred ccccccCccCccCCCC-CCCCCCCCCCCCCCCCCCCCCCCCCCCCCcCcccCCCCccCCCCCCCCCCC------------
Q 003281 742 QSCSSCGAVGHSSMNC-PSIMSGPGQSSGGGYANSFSSGAGIATSSECYKCHKTGHWARDCPSLNAAP------------ 808 (834)
Q Consensus 742 ~~C~~Cg~~GH~a~~C-p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Cy~Cg~~GH~ardCp~~~~~~------------ 808 (834)
..|++||+.||++++| |.... ...||.|+..+|.+++||......
T Consensus 98 ~~C~~Cg~~GH~~~dC~P~~~~----------------------~~~C~~C~s~~H~s~~Cp~~~k~y~~~~~~~~~~~~ 155 (190)
T COG5082 98 KKCYNCGETGHLSRDCNPSKDQ----------------------QKSCFDCNSTRHSSEDCPSIWKHYVLNNGDGHPIKK 155 (190)
T ss_pred cccccccccCccccccCccccc----------------------CcceeccCCCccccccCcccccccccccCCCcceee
Confidence 3788888888888888 44332 247999999999999999853311
Q ss_pred CCcCCCCCCcccccCCC
Q 003281 809 PAYGSSGIGISAAGYRG 825 (834)
Q Consensus 809 ~c~~c~~~g~~~~~cg~ 825 (834)
-||.|++.+|....|-.
T Consensus 156 ~cy~c~~~~H~~~dc~~ 172 (190)
T COG5082 156 FCYSCGSAGHFGDDCKE 172 (190)
T ss_pred eccccCCccccCCCCCC
Confidence 58888888888888764
No 38
>PF00098 zf-CCHC: Zinc knuckle; InterPro: IPR001878 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 CysCysHisCys (CCHC) type zinc finger domains, and have the sequence: C-X2-C-X4-H-X4-C where X can be any amino acid, and number indicates the number of residues. These 18 residues CCHC zinc finger domains are mainly found in the nucleocapsid protein of retroviruses. It is required for viral genome packaging and for early infection process [, , ]. It is also found in eukaryotic proteins involved in RNA binding or single-stranded DNA binding []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding; PDB: 2L44_A 1A1T_A 1WWG_A 1U6P_A 1WWD_A 1WWE_A 1A6B_B 1F6U_A 1MFS_A 1NCP_C ....
Probab=98.10 E-value=1.6e-06 Score=52.91 Aligned_cols=17 Identities=53% Similarity=1.406 Sum_probs=16.1
Q ss_pred cCcccCCCCccCCCCCC
Q 003281 787 ECYKCHKTGHWARDCPS 803 (834)
Q Consensus 787 ~Cy~Cg~~GH~ardCp~ 803 (834)
.||+|++.||+++|||+
T Consensus 2 ~C~~C~~~GH~~~~Cp~ 18 (18)
T PF00098_consen 2 KCFNCGEPGHIARDCPK 18 (18)
T ss_dssp BCTTTSCSSSCGCTSSS
T ss_pred cCcCCCCcCcccccCcc
Confidence 69999999999999995
No 39
>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=97.96 E-value=0.00082 Score=80.26 Aligned_cols=177 Identities=13% Similarity=0.053 Sum_probs=117.7
Q ss_pred cccccccccccCCCceeeEEEEEEEecCCeeEEccCCceeeEEEEEEeccCCcEEEEEEcCCccchhhhhhhhcccCCCc
Q 003281 338 HFRPINDVEGMENNSVVDLIGVVSYISPTASLMRKNGTETQKRTLHLRDMSGRSVELTLWGNFCNDDGLRLQHMCDSGVF 417 (834)
Q Consensus 338 ~f~~i~dI~~~~~~~~vDVIGvV~~V~~~~~i~~k~g~~~~kr~i~L~D~s~~si~vtLWg~~a~~~~~~l~~~~~~~~~ 417 (834)
.|.+|++|.... .-.-|.|.|+..+++.++..++| +....+|.|.|+++ .|++|+|++.++.|...|+ .+
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 23789999999999999876554 34567899999555 8999999999988766554 67
Q ss_pred cEEEEEEEEEeecCCe--------EEEeecceEEEEcCCchHHHHHHHHHHhcCCccceeeeccccccCCccchhccHhh
Q 003281 418 PILAVKAGRVSDFNGK--------VVGTISTTQLFIEPDFPEAHRLKEWFEKEGKNTQSVSISRDSLSVGRADIRKTVSQ 489 (834)
Q Consensus 418 ~Vv~ik~~rV~~f~G~--------~Ls~~~~S~i~inPd~pe~~~l~~w~~~~g~~~~~~sls~~~~~~~~~~~~ktI~e 489 (834)
.|+.|..++|+.-+++ .|.....|.|..-+|.+. .+. -......|++
T Consensus 249 ~VY~Is~~~Vk~an~~y~~~~~~yei~f~~~T~I~~~~d~~~--------------iP~-----------~~~~f~~i~d 303 (608)
T TIGR00617 249 KVYYISKGSLKPANKQFTNLGNDYEMTLDRDTVIEECEDETA--------------IPK-----------IQFNFVKIDD 303 (608)
T ss_pred CEEEECceEEEEccccccCCCCCEEEEECCCeEEEECCCccc--------------CCc-----------ccccceEHHH
Confidence 8999999999755442 344444555544332210 000 0123456888
Q ss_pred hhhcCCCCCCCCceEEEEEEEEEEecCCeeeeCCCCCcCCCCcCcccccCCCCceecCCCCCccccceEEEEEEEEEEeC
Q 003281 490 IKDEGLGTKEKPDWITVSATIVYIKCDNFCYTACPIMIGDRPCNKKVMNNGDGRWHCDRCDQSVVECDYRYILQFQIQDH 569 (834)
Q Consensus 490 i~~~~lg~~~k~~~~~v~atI~~I~~d~~~Y~aC~~~~~~~~C~KKv~~~~dg~~~CekC~~~~~~~~~ry~l~~~i~D~ 569 (834)
|.+.. +..++.|.|.|..|..-.-.- . |. +| ....+.++.|.|.
T Consensus 304 I~~~~-----~~~~VDVIGvV~~v~~~~~i~-~------------k~----~g--------------~~~~kR~i~L~D~ 347 (608)
T TIGR00617 304 IGGYE-----GNSLVDVIGIVQSVSPTQTIT-S------------RK----NN--------------KEFPKRDITLVDD 347 (608)
T ss_pred hhhhc-----CCCCccEEEEEeEecCceEEE-E------------cC----CC--------------CeeeeEEEEEEeC
Confidence 86532 223678888888886431110 0 00 11 1235679999999
Q ss_pred CC-eEEEEEehHHHHHH
Q 003281 570 TG-LTWVTAFQECAEEI 585 (834)
Q Consensus 570 Tg-~~~~~~F~e~ae~l 585 (834)
|| ++.+++|++.|+.+
T Consensus 348 sg~sI~vTLWG~~A~~~ 364 (608)
T TIGR00617 348 SGKSVRVTLWGDDATKF 364 (608)
T ss_pred CCCEEEEEEEhhhhhhc
Confidence 99 58999999998764
No 40
>PRK07217 replication factor A; Reviewed
Probab=97.92 E-value=0.00024 Score=76.26 Aligned_cols=93 Identities=22% Similarity=0.164 Sum_probs=74.1
Q ss_pred CCceeccccCCCCCceEEEEEEEEeccceeecCCCCCcceEEEEEeeCCCCEEEEEEechHHHhhhhccCcCcEEEEeee
Q 003281 217 SRIIPIAALNPYMGKWTIKARVTAKGELRHYNNQRGDGKVFHFDLLDSDGGEIRVTCFNAVADQFYHQVEAGKIYLVSRG 296 (834)
Q Consensus 217 ~~~~pI~~L~p~~~~w~I~aRV~~Ks~lr~~~n~~g~Gk~f~~~L~De~g~~I~at~f~~~~d~f~~~l~eG~vy~is~~ 296 (834)
...++|++|+|.....+|+|||+..|+.+. +-....-.|.|+ .|.|+.|.|.+. -.+.|++|++|.|.++
T Consensus 70 ~~~~kI~Di~~~~~~VsV~aKVl~l~e~~~------~si~qvGllgDE-TG~IkfT~W~~s---~~~~leeGd~~rI~na 139 (311)
T PRK07217 70 SELVNIADIDEPEQWVDVTAKVVQLWEPSS------DSIAQVGLLGDE-TGTIKFTKWAKS---DLPELEEGKSYLLKNV 139 (311)
T ss_pred CCceeeeecCCCCCcEEEEEEEEEecCCCC------CceEEEEEEEcC-CceEEEEEccCC---CCCcccCCCEEEEEeE
Confidence 457899999999999999999999987542 122333467887 689999999963 1456999999999999
Q ss_pred EEecCCcccccCCCeEEEEEccCccEEEec
Q 003281 297 SLKPAQKNFNHLHNDLEIFLDMTSMVQLCY 326 (834)
Q Consensus 297 ~V~~a~~~~~~~~~~yeI~f~~~T~I~~~~ 326 (834)
.+...+ ..++|.+++.|+|++..
T Consensus 140 ~v~ey~-------G~~~lnlg~~t~I~~~d 162 (311)
T PRK07217 140 VTDEYQ-------GRFSVKLNRTTSIEELD 162 (311)
T ss_pred EEeeEC-------CEEEEEeCCceEEEeCC
Confidence 987655 45799999999999974
No 41
>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=97.85 E-value=0.00033 Score=80.01 Aligned_cols=187 Identities=17% Similarity=0.198 Sum_probs=133.3
Q ss_pred CCCceeccccCCCCCceEEEEEEEEeccceeecCCCCC-cceEEEEEeeCCCCEEEE-EEechHHHhhhhccCcCcEEEE
Q 003281 216 PSRIIPIAALNPYMGKWTIKARVTAKGELRHYNNQRGD-GKVFHFDLLDSDGGEIRV-TCFNAVADQFYHQVEAGKIYLV 293 (834)
Q Consensus 216 ~~~~~pI~~L~p~~~~w~I~aRV~~Ks~lr~~~n~~g~-Gk~f~~~L~De~g~~I~a-t~f~~~~d~f~~~l~eG~vy~i 293 (834)
...+.+|.++.+.+.+-.+.+||+..+..+.|....+. +++.+..+.|+. |.++. +.|...+. +.++.|+++.|
T Consensus 46 ~~~~~~i~~~~~~~~~~~v~~~V~~~~e~~~~~~k~g~~~~l~~~~v~Det-g~v~~~~~~~~~a~---~~~e~Gdv~~i 121 (407)
T COG1599 46 MESIGKISDISEASSRVNVTGRVLSIGEKKTFDRKRGAEGKLAEVLVGDET-GSVKTVTLWNIAAL---EKLEPGDVIRI 121 (407)
T ss_pred hhhcccccccchhhccccEEEEECccccceeeecccccccceEEEEEecCC-CCEEEEeecccccc---ccCCccceEEe
Confidence 34678999999999999999999999988888877775 899999999985 78888 78886543 25899999999
Q ss_pred eeeEEecCCcccccCCCeEEEEEccCccEEEecCCCCCCccccccccccccccccCCCceeeEEEEEEEecCCeeEEccC
Q 003281 294 SRGSLKPAQKNFNHLHNDLEIFLDMTSMVQLCYEDDASIPRQQFHFRPINDVEGMENNSVVDLIGVVSYISPTASLMRKN 373 (834)
Q Consensus 294 s~~~V~~a~~~~~~~~~~yeI~f~~~T~I~~~~d~~~~iP~~~~~f~~i~dI~~~~~~~~vDVIGvV~~V~~~~~i~~k~ 373 (834)
.++.+.... ...++.+...+.|....+. ...+...+.-..+.++..+. ..+ .+.|..-.++.++.. +
T Consensus 122 ~~~~~~~~~-------~~~~~~~~~~~~v~~~~~~-~~~~~~~~~~~~i~~~~~~~---~~~-~~~v~~g~~ik~~~~-~ 188 (407)
T COG1599 122 RNAYTSLYR-------GGKRLSVGRVGSVADVDDE-EDEARESEDAREIGEESLLS---PYQ-KARVVVGSEIKTFDN-Q 188 (407)
T ss_pred cCccccccc-------CceeeecccccccccCchh-hccccccccccccccccccC---ccc-eEEEEecccceeEec-C
Confidence 987654332 4567788888888775432 12222222333333333222 222 667777777777755 4
Q ss_pred CceeeEEEEEEeccCCcEEEEEEcCCccchhhhhhhhcccCCCccEEEEEEEEEeecCCe
Q 003281 374 GTETQKRTLHLRDMSGRSVELTLWGNFCNDDGLRLQHMCDSGVFPILAVKAGRVSDFNGK 433 (834)
Q Consensus 374 g~~~~kr~i~L~D~s~~si~vtLWg~~a~~~~~~l~~~~~~~~~~Vv~ik~~rV~~f~G~ 433 (834)
+.+...+...|.|++-..+.+++|.... ...+..+..++|.-|++.
T Consensus 189 ~ge~~~~~~~~~d~~~~~~~~~~~~~~~--------------~g~~~~ie~~~v~~~~~~ 234 (407)
T COG1599 189 GGESKVFSNELEDEERGVIVFTDWDPSQ--------------DGDVYRIEGARVKTKNKQ 234 (407)
T ss_pred CCccceEeeeecccceeEEEeccCcccc--------------cceeeeecCcEEEEeccc
Confidence 4556678888889884579999998762 356788888999888774
No 42
>PF00098 zf-CCHC: Zinc knuckle; InterPro: IPR001878 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 CysCysHisCys (CCHC) type zinc finger domains, and have the sequence: C-X2-C-X4-H-X4-C where X can be any amino acid, and number indicates the number of residues. These 18 residues CCHC zinc finger domains are mainly found in the nucleocapsid protein of retroviruses. It is required for viral genome packaging and for early infection process [, , ]. It is also found in eukaryotic proteins involved in RNA binding or single-stranded DNA binding []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding; PDB: 2L44_A 1A1T_A 1WWG_A 1U6P_A 1WWD_A 1WWE_A 1A6B_B 1F6U_A 1MFS_A 1NCP_C ....
Probab=97.68 E-value=2.1e-05 Score=48.11 Aligned_cols=17 Identities=41% Similarity=1.128 Sum_probs=16.1
Q ss_pred cccccCccCccCCCCCC
Q 003281 743 SCSSCGAVGHSSMNCPS 759 (834)
Q Consensus 743 ~C~~Cg~~GH~a~~Cp~ 759 (834)
.||+|++.||++++||+
T Consensus 2 ~C~~C~~~GH~~~~Cp~ 18 (18)
T PF00098_consen 2 KCFNCGEPGHIARDCPK 18 (18)
T ss_dssp BCTTTSCSSSCGCTSSS
T ss_pred cCcCCCCcCcccccCcc
Confidence 69999999999999995
No 43
>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=97.66 E-value=0.00064 Score=66.34 Aligned_cols=86 Identities=23% Similarity=0.330 Sum_probs=64.3
Q ss_pred ccccccccccCCCceeeEEEEEEEecCCeeEEccCCceeeEEEEEEeccCC-------cEEEEEEcCCccchhhhhhhhc
Q 003281 339 FRPINDVEGMENNSVVDLIGVVSYISPTASLMRKNGTETQKRTLHLRDMSG-------RSVELTLWGNFCNDDGLRLQHM 411 (834)
Q Consensus 339 f~~i~dI~~~~~~~~vDVIGvV~~V~~~~~i~~k~g~~~~kr~i~L~D~s~-------~si~vtLWg~~a~~~~~~l~~~ 411 (834)
|++|++.. ...+..|||||+|++..+.....+| |+ -....|+|.|.|. ..|.|.++-+..+.+...
T Consensus 1 ~~~l~~~~-~~~~~~vnvigVV~~~~~p~~~~t~-g~-D~~~tl~i~D~S~~~~~~~~~~l~v~iF~~~~~~LP~v---- 73 (146)
T PF02765_consen 1 YTPLSTAK-EKFGKFVNVIGVVVDFSPPNPKKTR-GT-DYMCTLTITDPSLNDSNQKLSGLTVNIFRPHKESLPNV---- 73 (146)
T ss_dssp BCCGGGSC-TTSSEEEEEEEEEEEEEEECTEEES-SS-CEEEEEEEEBTTCSCSSCCCCEEEEEEEESSHHHSCTT----
T ss_pred Cccchhhh-hcCCCEEEEEEEEEEccCCcceEcC-CC-cEEEEEEEECCCCCccccccCCEEEEEECCCHHHCCCC----
Confidence 44555222 3457899999999999988444443 33 4678999999996 689999998877665421
Q ss_pred ccCCCccEEEEEEEEEeecCCe
Q 003281 412 CDSGVFPILAVKAGRVSDFNGK 433 (834)
Q Consensus 412 ~~~~~~~Vv~ik~~rV~~f~G~ 433 (834)
...+.||.++.++|+.|+|+
T Consensus 74 --~~~GDii~l~r~kv~~~~~~ 93 (146)
T PF02765_consen 74 --KSVGDIIRLRRVKVQSYNGK 93 (146)
T ss_dssp --CSTTHEEEEEEEEEEEETTE
T ss_pred --CCCCCEEEEEEEEEEEECCE
Confidence 12378999999999999997
No 44
>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=97.66 E-value=0.00021 Score=65.60 Aligned_cols=97 Identities=14% Similarity=0.100 Sum_probs=72.3
Q ss_pred cccccccCCCceeeEEEEEEEecCCeeEEccCCceeeEEEEEEeccCCcEEEEEEcCCccchhhhhhhhcccCCCccEEE
Q 003281 342 INDVEGMENNSVVDLIGVVSYISPTASLMRKNGTETQKRTLHLRDMSGRSVELTLWGNFCNDDGLRLQHMCDSGVFPILA 421 (834)
Q Consensus 342 i~dI~~~~~~~~vDVIGvV~~V~~~~~i~~k~g~~~~kr~i~L~D~s~~si~vtLWg~~a~~~~~~l~~~~~~~~~~Vv~ 421 (834)
|++|... ....-+.|.|+..+++..+..++ .+....+|.|.|+.+.+|++|+|++.++.+...|+ .+.|+.
T Consensus 2 I~~L~p~--~~~~~I~~rV~~k~~~~~f~~~~-~~g~~~~~~l~De~~~~I~~t~~~~~~~~f~~~l~------eG~vy~ 72 (104)
T cd04474 2 ISSLNPY--QNKWTIKARVTNKSDIRTWSNAR-GEGKLFSFDLLDEDGGEIRATFFNDAVDKFYDLLE------VGKVYY 72 (104)
T ss_pred hhHccCC--CCcEEEEEEEeeccccccccCCC-CCcEEEEEEEEECCCCEEEEEEehHHHHHhhcccc------cccEEE
Confidence 4555532 23578999999999999887764 34556699999997779999999999987766554 678999
Q ss_pred EEEEEEeecCCeEEEeecceEEEEcC
Q 003281 422 VKAGRVSDFNGKVVGTISTTQLFIEP 447 (834)
Q Consensus 422 ik~~rV~~f~G~~Ls~~~~S~i~inP 447 (834)
|.+++|+.-+++.-.+...-.|.++.
T Consensus 73 i~~~~V~~a~~~y~~~~~~yeI~f~~ 98 (104)
T cd04474 73 ISKGSVKVANKKFNTLKNDYEITFNR 98 (104)
T ss_pred EeccEEeeccccCCCCCCcEEEEECC
Confidence 99999988776544444444555544
No 45
>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=97.53 E-value=0.00031 Score=59.72 Aligned_cols=61 Identities=34% Similarity=0.552 Sum_probs=51.2
Q ss_pred eEEEEEEEEeccceeecCCCCCcceEEEEEeeCCCCEEEEEEechHHHhhhhccCcCcEEEEeeeEEecCC
Q 003281 232 WTIKARVTAKGELRHYNNQRGDGKVFHFDLLDSDGGEIRVTCFNAVADQFYHQVEAGKIYLVSRGSLKPAQ 302 (834)
Q Consensus 232 w~I~aRV~~Ks~lr~~~n~~g~Gk~f~~~L~De~g~~I~at~f~~~~d~f~~~l~eG~vy~is~~~V~~a~ 302 (834)
++|.++|+++. + ..++++.++|.|++ |.|++++|++..+++.+.|++|+++.+. +.|+..+
T Consensus 1 V~v~G~V~~~~--~------~~~~~~~~~l~D~t-g~i~~~~~~~~~~~~~~~l~~g~~v~v~-G~v~~~~ 61 (75)
T PF01336_consen 1 VTVEGRVTSIR--R------SGGKIVFFTLEDGT-GSIQVVFFNEEYERFREKLKEGDIVRVR-GKVKRYN 61 (75)
T ss_dssp EEEEEEEEEEE--E------EETTEEEEEEEETT-EEEEEEEETHHHHHHHHTS-TTSEEEEE-EEEEEET
T ss_pred CEEEEEEEEEE--c------CCCCEEEEEEEECC-ccEEEEEccHHhhHHhhcCCCCeEEEEE-EEEEEEC
Confidence 57899999875 1 23679999999985 9999999999899999999999999999 7777664
No 46
>KOG4400 consensus E3 ubiquitin ligase interacting with arginine methyltransferase [Posttranslational modification, protein turnover, chaperones]
Probab=97.41 E-value=0.00013 Score=78.24 Aligned_cols=41 Identities=46% Similarity=1.037 Sum_probs=36.1
Q ss_pred cccccCccCccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcCcccCCCCccCCCCCCCCC
Q 003281 743 SCSSCGAVGHSSMNCPSIMSGPGQSSGGGYANSFSSGAGIATSSECYKCHKTGHWARDCPSLNA 806 (834)
Q Consensus 743 ~C~~Cg~~GH~a~~Cp~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Cy~Cg~~GH~ardCp~~~~ 806 (834)
.||+||+.||++.+||.+. +..||+|++.||+++|||....
T Consensus 145 ~Cy~Cg~~GH~s~~C~~~~-----------------------~~~c~~c~~~~h~~~~C~~~~~ 185 (261)
T KOG4400|consen 145 KCYSCGEQGHISDDCPENK-----------------------GGTCFRCGKVGHGSRDCPSKQK 185 (261)
T ss_pred ccCCCCcCCcchhhCCCCC-----------------------CCccccCCCcceecccCCcccc
Confidence 7999999999999999872 2479999999999999998644
No 47
>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=97.17 E-value=0.0029 Score=57.53 Aligned_cols=83 Identities=12% Similarity=0.179 Sum_probs=66.0
Q ss_pred EEEEEEEEeccceeecCCC-C-CcceEEEEEeeCCCCEEEEEEechHHHhhhhccCcCcEEEEeeeEEecCCcccccCCC
Q 003281 233 TIKARVTAKGELRHYNNQR-G-DGKVFHFDLLDSDGGEIRVTCFNAVADQFYHQVEAGKIYLVSRGSLKPAQKNFNHLHN 310 (834)
Q Consensus 233 ~I~aRV~~Ks~lr~~~n~~-g-~Gk~f~~~L~De~g~~I~at~f~~~~d~f~~~l~eG~vy~is~~~V~~a~~~~~~~~~ 310 (834)
.|.|.|+..++++.+.... | ++...+|.|.|+++..|.+|+|++.++.|.... |.|+.|.++++...+
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 4789999999999987554 3 567889999999877999999999999988755 999999999886433
Q ss_pred eEEEEEccCccEEEe
Q 003281 311 DLEIFLDMTSMVQLC 325 (834)
Q Consensus 311 ~yeI~f~~~T~I~~~ 325 (834)
...+.....|.|..-
T Consensus 73 ~~~l~~~~~s~i~~n 87 (101)
T cd04475 73 GKSLSTGSSSTIIIN 87 (101)
T ss_pred CeEEeecCceeEEEC
Confidence 135555556777763
No 48
>PF13696 zf-CCHC_2: Zinc knuckle
Probab=96.58 E-value=0.00093 Score=46.82 Aligned_cols=21 Identities=38% Similarity=1.124 Sum_probs=18.4
Q ss_pred CCcCcccCCCCccCCCCCCCC
Q 003281 785 SSECYKCHKTGHWARDCPSLN 805 (834)
Q Consensus 785 ~~~Cy~Cg~~GH~ardCp~~~ 805 (834)
+..|+.|++.|||.+|||...
T Consensus 8 ~Y~C~~C~~~GH~i~dCP~~~ 28 (32)
T PF13696_consen 8 GYVCHRCGQKGHWIQDCPTNK 28 (32)
T ss_pred CCEeecCCCCCccHhHCCCCC
Confidence 357999999999999999953
No 49
>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=96.38 E-value=0.018 Score=47.85 Aligned_cols=60 Identities=37% Similarity=0.612 Sum_probs=48.7
Q ss_pred EEEEEEEeccceeecCCCCCcceEEEEEeeCCCCEEEEEEechHHHhhhhccCcCcEEEEeeeEEec
Q 003281 234 IKARVTAKGELRHYNNQRGDGKVFHFDLLDSDGGEIRVTCFNAVADQFYHQVEAGKIYLVSRGSLKP 300 (834)
Q Consensus 234 I~aRV~~Ks~lr~~~n~~g~Gk~f~~~L~De~g~~I~at~f~~~~d~f~~~l~eG~vy~is~~~V~~ 300 (834)
|.+.|+.....++ + +..+.+.|.|..|+.|.+++|.+..+.+...+++|+++.|. ++|..
T Consensus 2 v~g~v~~~~~~~~-----~-~~~~~~~l~D~~~~~i~~~~~~~~~~~~~~~~~~g~~v~v~-g~v~~ 61 (75)
T cd03524 2 IVGIVVAVEEIRT-----E-GKVLIFTLTDGTGGTIRVTLFGELAEELENLLKEGQVVYIK-GKVKK 61 (75)
T ss_pred eEEEEEeeccccc-----C-CeEEEEEEEcCCCCEEEEEEEchHHHHHHhhccCCCEEEEE-EEEEe
Confidence 5677776655443 1 35788999998669999999999999999999999999998 88754
No 50
>KOG3416 consensus Predicted nucleic acid binding protein [General function prediction only]
Probab=96.08 E-value=0.018 Score=53.25 Aligned_cols=70 Identities=20% Similarity=0.314 Sum_probs=56.2
Q ss_pred ceeccccCCCCCceEEEEEEEEeccceeecCCCCCc-ceEEEEEeeCCCCEEEEEEechHHHhhhhccCcCcEEEEeeeE
Q 003281 219 IIPIAALNPYMGKWTIKARVTAKGELRHYNNQRGDG-KVFHFDLLDSDGGEIRVTCFNAVADQFYHQVEAGKIYLVSRGS 297 (834)
Q Consensus 219 ~~pI~~L~p~~~~w~I~aRV~~Ks~lr~~~n~~g~G-k~f~~~L~De~g~~I~at~f~~~~d~f~~~l~eG~vy~is~~~ 297 (834)
.++|++|.|++++..+..-|+.-...+.-+ +| ++.++.+.|+ .+.|++.+|++ +.++|+.||++.++++.
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----DGHEVRSCKVADE-TGSINISVWDE----EGCLIQPGDIIRLTGGY 74 (134)
T ss_pred chhHhhcChhhhcceEEEEEEeeceeeecc----CCCEEEEEEEecc-cceEEEEEecC----cCcccCCccEEEecccc
Confidence 468999999999888877777655444332 35 7888889997 68999999995 66789999999999863
No 51
>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=95.38 E-value=0.074 Score=51.37 Aligned_cols=83 Identities=14% Similarity=0.216 Sum_probs=66.1
Q ss_pred CceeccccC-CCCCceEEEEEEEEeccceeecCCCCCcceEEEEEeeCCC---CEEEEEEechHHHhhhhccCcCcEEEE
Q 003281 218 RIIPIAALN-PYMGKWTIKARVTAKGELRHYNNQRGDGKVFHFDLLDSDG---GEIRVTCFNAVADQFYHQVEAGKIYLV 293 (834)
Q Consensus 218 ~~~pI~~L~-p~~~~w~I~aRV~~Ks~lr~~~n~~g~Gk~f~~~L~De~g---~~I~at~f~~~~d~f~~~l~eG~vy~i 293 (834)
.++||++|. .....-.|.|-|+.....+. .+|.....+|.|.|+.. ..|++++|.+..+.|-.. .+|+|+.+
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 478899987 33467889999988777654 23334778899999876 779999999998887765 99999999
Q ss_pred eeeEEecCCcc
Q 003281 294 SRGSLKPAQKN 304 (834)
Q Consensus 294 s~~~V~~a~~~ 304 (834)
.+++|+.-+.+
T Consensus 78 ~~~kv~~~~g~ 88 (138)
T cd04497 78 RRVKIQSYNGK 88 (138)
T ss_pred EEEEEEEECCc
Confidence 99999876654
No 52
>KOG3416 consensus Predicted nucleic acid binding protein [General function prediction only]
Probab=95.28 E-value=0.079 Score=49.08 Aligned_cols=83 Identities=18% Similarity=0.203 Sum_probs=58.9
Q ss_pred ccccccccCCCceeeEEEEEEEecCCeeEEccCCceeeEEEEEEeccCCcEEEEEEcCCccchhhhhhhhcccCCCccEE
Q 003281 341 PINDVEGMENNSVVDLIGVVSYISPTASLMRKNGTETQKRTLHLRDMSGRSVELTLWGNFCNDDGLRLQHMCDSGVFPIL 420 (834)
Q Consensus 341 ~i~dI~~~~~~~~vDVIGvV~~V~~~~~i~~k~g~~~~kr~i~L~D~s~~si~vtLWg~~a~~~~~~l~~~~~~~~~~Vv 420 (834)
+|.||..--+ .+.|+=+|.+.+... .+|+|+ ..|...+.|.|+ +|++.+|++....+ .+++||
T Consensus 6 ~ikdi~P~~k--N~~v~fIvl~~g~~t--kTkdg~--~v~~~kVaD~Tg-sI~isvW~e~~~~~----------~PGDIi 68 (134)
T KOG3416|consen 6 FIKDIKPGLK--NINVTFIVLEYGRAT--KTKDGH--EVRSCKVADETG-SINISVWDEEGCLI----------QPGDII 68 (134)
T ss_pred hHhhcChhhh--cceEEEEEEeeceee--eccCCC--EEEEEEEecccc-eEEEEEecCcCccc----------CCccEE
Confidence 3455654222 345566677766554 256777 468999999999 89999999776542 268999
Q ss_pred EEEEEEEeecCCe-EEEeecc
Q 003281 421 AVKAGRVSDFNGK-VVGTIST 440 (834)
Q Consensus 421 ~ik~~rV~~f~G~-~Ls~~~~ 440 (834)
.++++..+-|+|. .|.+..+
T Consensus 69 rLt~Gy~Si~qg~LtL~~GK~ 89 (134)
T KOG3416|consen 69 RLTGGYASIFQGCLTLYVGKG 89 (134)
T ss_pred EecccchhhhcCceEEEecCC
Confidence 9999999999884 6766543
No 53
>PF13696 zf-CCHC_2: Zinc knuckle
Probab=95.07 E-value=0.013 Score=41.12 Aligned_cols=20 Identities=35% Similarity=0.828 Sum_probs=18.0
Q ss_pred ccccccCccCccCCCCCCCC
Q 003281 742 QSCSSCGAVGHSSMNCPSIM 761 (834)
Q Consensus 742 ~~C~~Cg~~GH~a~~Cp~~~ 761 (834)
..|+.|++.|||.++||...
T Consensus 9 Y~C~~C~~~GH~i~dCP~~~ 28 (32)
T PF13696_consen 9 YVCHRCGQKGHWIQDCPTNK 28 (32)
T ss_pred CEeecCCCCCccHhHCCCCC
Confidence 48999999999999999843
No 54
>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=94.93 E-value=0.14 Score=45.86 Aligned_cols=68 Identities=18% Similarity=0.324 Sum_probs=45.2
Q ss_pred eEEEEEEEecCCeeEEccCCceeeEEEEEEeccCCcEEEEEEcCCccchh-----------------hhhhhhcccCCCc
Q 003281 355 DLIGVVSYISPTASLMRKNGTETQKRTLHLRDMSGRSVELTLWGNFCNDD-----------------GLRLQHMCDSGVF 417 (834)
Q Consensus 355 DVIGvV~~V~~~~~i~~k~g~~~~kr~i~L~D~s~~si~vtLWg~~a~~~-----------------~~~l~~~~~~~~~ 417 (834)
||+|+|.++.+.. .+..++|.|.|| .|+|.+|....... ..... .-..+
T Consensus 1 ~ivG~V~sv~~~~----------~~~~~tLdDgTG-~Ie~~~W~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~i~~G 66 (92)
T cd04483 1 DILGTVVSRRERE----------TFYSFGVDDGTG-VVNCVCWKNLSYAEVSSRSDAARILKSALMALKQAK---VLEIG 66 (92)
T ss_pred CeEEEEEEEEecC----------CeEEEEEecCCc-eEEEEEEcCcCccccccccccccccccccccccccc---ccCCC
Confidence 6899999985442 468899999999 79999998754111 00000 01245
Q ss_pred cEEEEEEEEEeecCCe-EEEe
Q 003281 418 PILAVKAGRVSDFNGK-VVGT 437 (834)
Q Consensus 418 ~Vv~ik~~rV~~f~G~-~Ls~ 437 (834)
.+|-++ ++|+.|+|+ .|..
T Consensus 67 ~vvrV~-G~i~~frg~~ql~i 86 (92)
T cd04483 67 DLLRVR-GSIRTYRGEREINA 86 (92)
T ss_pred CEEEEE-EEEeccCCeeEEEE
Confidence 566665 688999995 5553
No 55
>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=94.83 E-value=0.19 Score=41.41 Aligned_cols=68 Identities=21% Similarity=0.387 Sum_probs=47.8
Q ss_pred eEEEEEEEecCCeeEEccCCceeeEEEEEEeccCCcEEEEEEcCCccchhhhhhhhcccCCCccEEEEEEEEEeecCCe-
Q 003281 355 DLIGVVSYISPTASLMRKNGTETQKRTLHLRDMSGRSVELTLWGNFCNDDGLRLQHMCDSGVFPILAVKAGRVSDFNGK- 433 (834)
Q Consensus 355 DVIGvV~~V~~~~~i~~k~g~~~~kr~i~L~D~s~~si~vtLWg~~a~~~~~~l~~~~~~~~~~Vv~ik~~rV~~f~G~- 433 (834)
+|.|+|.++.+..+ |+ ....++|.|.++.++++++|.+..+.....+ ..+.++.+. +++..++++
T Consensus 1 ~v~g~v~~~~~~~~-----~~--~~~~~~l~D~~~~~i~~~~~~~~~~~~~~~~------~~g~~v~v~-g~v~~~~~~~ 66 (75)
T cd03524 1 TIVGIVVAVEEIRT-----EG--KVLIFTLTDGTGGTIRVTLFGELAEELENLL------KEGQVVYIK-GKVKKFRGRL 66 (75)
T ss_pred CeEEEEEeeccccc-----CC--eEEEEEEEcCCCCEEEEEEEchHHHHHHhhc------cCCCEEEEE-EEEEecCCeE
Confidence 57899998876643 32 3678999999966999999998765432222 245677777 888877663
Q ss_pred EEE
Q 003281 434 VVG 436 (834)
Q Consensus 434 ~Ls 436 (834)
.|.
T Consensus 67 ~l~ 69 (75)
T cd03524 67 QLI 69 (75)
T ss_pred EEE
Confidence 443
No 56
>KOG0921 consensus Dosage compensation complex, subunit MLE [Transcription]
Probab=94.61 E-value=0.24 Score=59.71 Aligned_cols=19 Identities=5% Similarity=0.268 Sum_probs=10.6
Q ss_pred HHHHHHHHhhcCCCCCccc
Q 003281 652 RFILDLMDKLKSGDSTSFA 670 (834)
Q Consensus 652 ~~Ll~~i~~~~~~~~~~~~ 670 (834)
.+||+.|.++....+.++.
T Consensus 1127 arllnmiRdIs~pSAa~in 1145 (1282)
T KOG0921|consen 1127 ARLLNMIRDISRPSAADIN 1145 (1282)
T ss_pred HHHHHHHHHhccccccccc
Confidence 4566666666555544433
No 57
>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=94.59 E-value=0.2 Score=42.16 Aligned_cols=63 Identities=25% Similarity=0.388 Sum_probs=44.8
Q ss_pred eeEEEEEEEecCCeeEEccCCceeeEEEEEEeccCCcEEEEEEcCCccchhhhhhhhcccCCCccEEEEEEEEEeecCCe
Q 003281 354 VDLIGVVSYISPTASLMRKNGTETQKRTLHLRDMSGRSVELTLWGNFCNDDGLRLQHMCDSGVFPILAVKAGRVSDFNGK 433 (834)
Q Consensus 354 vDVIGvV~~V~~~~~i~~k~g~~~~kr~i~L~D~s~~si~vtLWg~~a~~~~~~l~~~~~~~~~~Vv~ik~~rV~~f~G~ 433 (834)
|.|.|.|+++. +.+ .....++|.|.|| .|.+++|.+......+.| ..+.+|.++ ++++.+++.
T Consensus 1 V~v~G~V~~~~-------~~~--~~~~~~~l~D~tg-~i~~~~~~~~~~~~~~~l------~~g~~v~v~-G~v~~~~~~ 63 (75)
T PF01336_consen 1 VTVEGRVTSIR-------RSG--GKIVFFTLEDGTG-SIQVVFFNEEYERFREKL------KEGDIVRVR-GKVKRYNGG 63 (75)
T ss_dssp EEEEEEEEEEE-------EEE--TTEEEEEEEETTE-EEEEEEETHHHHHHHHTS-------TTSEEEEE-EEEEEETTS
T ss_pred CEEEEEEEEEE-------cCC--CCEEEEEEEECCc-cEEEEEccHHhhHHhhcC------CCCeEEEEE-EEEEEECCc
Confidence 56889999886 111 2457899999997 899999995544433333 267888888 788877654
No 58
>smart00343 ZnF_C2HC zinc finger.
Probab=94.26 E-value=0.021 Score=38.45 Aligned_cols=18 Identities=61% Similarity=1.403 Sum_probs=16.1
Q ss_pred cCcccCCCCccCCCCCCC
Q 003281 787 ECYKCHKTGHWARDCPSL 804 (834)
Q Consensus 787 ~Cy~Cg~~GH~ardCp~~ 804 (834)
.||+|++.||++++||..
T Consensus 1 ~C~~CG~~GH~~~~C~~~ 18 (26)
T smart00343 1 KCYNCGKEGHIARDCPKX 18 (26)
T ss_pred CCccCCCCCcchhhCCcc
Confidence 499999999999999954
No 59
>KOG0109 consensus RNA-binding protein LARK, contains RRM and retroviral-type Zn-finger domains [RNA processing and modification; General function prediction only]
Probab=94.19 E-value=0.024 Score=59.63 Aligned_cols=22 Identities=45% Similarity=1.292 Sum_probs=19.4
Q ss_pred CcCcccCCCCccCCCCCCCCCC
Q 003281 786 SECYKCHKTGHWARDCPSLNAA 807 (834)
Q Consensus 786 ~~Cy~Cg~~GH~ardCp~~~~~ 807 (834)
..||+||++|||+++||....+
T Consensus 161 ~~cyrcGkeghwskEcP~~~~~ 182 (346)
T KOG0109|consen 161 SGCYRCGKEGHWSKECPVDRTG 182 (346)
T ss_pred HHheeccccccccccCCccCCC
Confidence 4799999999999999997653
No 60
>PF13917 zf-CCHC_3: Zinc knuckle
Probab=94.08 E-value=0.027 Score=42.40 Aligned_cols=18 Identities=44% Similarity=1.339 Sum_probs=16.8
Q ss_pred CcCcccCCCCccCCCCCC
Q 003281 786 SECYKCHKTGHWARDCPS 803 (834)
Q Consensus 786 ~~Cy~Cg~~GH~ardCp~ 803 (834)
..|.+|++.|||..+||+
T Consensus 5 ~~CqkC~~~GH~tyeC~~ 22 (42)
T PF13917_consen 5 VRCQKCGQKGHWTYECPN 22 (42)
T ss_pred CcCcccCCCCcchhhCCC
Confidence 579999999999999995
No 61
>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=93.88 E-value=0.64 Score=42.61 Aligned_cols=68 Identities=15% Similarity=0.244 Sum_probs=52.1
Q ss_pred EEEEEEeccceeecCCCCCcceEEEEEeeCCCCEEEEEEechHHHhhhhcc----CcCcEEEEee-eEEecCC
Q 003281 235 KARVTAKGELRHYNNQRGDGKVFHFDLLDSDGGEIRVTCFNAVADQFYHQV----EAGKIYLVSR-GSLKPAQ 302 (834)
Q Consensus 235 ~aRV~~Ks~lr~~~n~~g~Gk~f~~~L~De~g~~I~at~f~~~~d~f~~~l----~eG~vy~is~-~~V~~a~ 302 (834)
.+-|+.-+++.+......+.....|.|.|..+..|++|+|++.|..|...+ ..+-|+.|-. .+|+.-+
T Consensus 3 iG~i~~v~~~~~~~~~~~~~~kr~~~i~D~~~~~l~~tlwG~~A~~f~~~~~~~~~~~~VVav~~~~rV~~~~ 75 (106)
T cd04481 3 IGVIVDVGPLEELPPVNKPSRKLDFEIRDLSDERLKCTLWGEYAEEFDAKFQSAGNGEPVVAVLRFWKIKEYK 75 (106)
T ss_pred eEEEEEecceEecccCCccceEEEEEEEeCCCCEEEEEEEHHHHHHHHHHHHHhCCCCcEEEEEEeEEEEEEc
Confidence 455666666666654434567789999999999999999999999998876 4777877766 7887554
No 62
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]
Probab=93.60 E-value=0.047 Score=61.32 Aligned_cols=42 Identities=33% Similarity=0.852 Sum_probs=35.8
Q ss_pred cccccCccCccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcCcccCCCCccCCCCCCC
Q 003281 743 SCSSCGAVGHSSMNCPSIMSGPGQSSGGGYANSFSSGAGIATSSECYKCHKTGHWARDCPSL 804 (834)
Q Consensus 743 ~C~~Cg~~GH~a~~Cp~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Cy~Cg~~GH~ardCp~~ 804 (834)
.|-+||..||..-+||..-.. ....|+.|+..||+++||+..
T Consensus 263 ~c~~cg~~~H~q~~cp~r~~~--------------------~~n~c~~cg~~gH~~~dc~~~ 304 (554)
T KOG0119|consen 263 ACRNCGSTGHKQYDCPGRIPN--------------------TTNVCKICGPLGHISIDCKVN 304 (554)
T ss_pred cccccCCCccccccCCccccc--------------------ccccccccCCcccccccCCCc
Confidence 899999999999999986321 112799999999999999986
No 63
>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=93.54 E-value=0.58 Score=39.05 Aligned_cols=61 Identities=21% Similarity=0.233 Sum_probs=41.7
Q ss_pred EEEEEEEEeccceeecCCCCCcceEEEEEeeCCCCEEEEEEechHHHhhhhccCcCcEEEEeeeEEecC
Q 003281 233 TIKARVTAKGELRHYNNQRGDGKVFHFDLLDSDGGEIRVTCFNAVADQFYHQVEAGKIYLVSRGSLKPA 301 (834)
Q Consensus 233 ~I~aRV~~Ks~lr~~~n~~g~Gk~f~~~L~De~g~~I~at~f~~~~d~f~~~l~eG~vy~is~~~V~~a 301 (834)
+|+|+|+.... +.. + ..+.+.+.|.|+ ++.|.+++|+.. ......|++|+.|.+.+ ++...
T Consensus 1 ~i~~~V~~~~~-~~~---~-~~~~~~~~~~D~-~g~i~~~~F~~~-~~~~~~~~~G~~~~v~G-kv~~~ 61 (75)
T cd04488 1 TVEGTVVSVEV-VPR---R-GRRRLKVTLSDG-TGTLTLVFFNFQ-PYLKKQLPPGTRVRVSG-KVKRF 61 (75)
T ss_pred CEEEEEEEEEe-ccC---C-CccEEEEEEEcC-CCEEEEEEECCC-HHHHhcCCCCCEEEEEE-EEeec
Confidence 36788876522 221 1 246899999997 689999999831 12356799999998874 44433
No 64
>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=93.52 E-value=0.33 Score=42.13 Aligned_cols=55 Identities=22% Similarity=0.369 Sum_probs=40.0
Q ss_pred eeEEEEEEEecCCeeEEccCCceeeEEEEEEeccCCcEEEEEEcCCccc--hhhhhhhhcccCCCccEEEEEE
Q 003281 354 VDLIGVVSYISPTASLMRKNGTETQKRTLHLRDMSGRSVELTLWGNFCN--DDGLRLQHMCDSGVFPILAVKA 424 (834)
Q Consensus 354 vDVIGvV~~V~~~~~i~~k~g~~~~kr~i~L~D~s~~si~vtLWg~~a~--~~~~~l~~~~~~~~~~Vv~ik~ 424 (834)
+-++|+|.++. ++|+|+. -++|.|.+| ++++++|.+..+ .....++ .+.+|.+++
T Consensus 2 v~i~GiI~~v~-----~TK~g~~----~~~leD~~G-~~Ev~~F~~~~~~~~~~~~l~------~d~~v~v~g 58 (79)
T cd04490 2 VSIIGMVNDVR-----STKNGHR----IVELEDTTG-RITVLLTKDKEELFEEAEDIL------PDEVIGVSG 58 (79)
T ss_pred EEEEEEEeEEE-----EcCCCCE----EEEEECCCC-EEEEEEeCchhhhhhhhhhcc------CCCEEEEEE
Confidence 34789999998 4567764 899999999 799999998877 5443332 344565554
No 65
>PF14787 zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB: 1CL4_A 1DSV_A.
Probab=93.36 E-value=0.042 Score=39.46 Aligned_cols=20 Identities=40% Similarity=0.866 Sum_probs=12.6
Q ss_pred CcCcccCCCCccCCCCCCCC
Q 003281 786 SECYKCHKTGHWARDCPSLN 805 (834)
Q Consensus 786 ~~Cy~Cg~~GH~ardCp~~~ 805 (834)
..|++|++..|||+||-...
T Consensus 3 ~~CprC~kg~Hwa~~C~sk~ 22 (36)
T PF14787_consen 3 GLCPRCGKGFHWASECRSKT 22 (36)
T ss_dssp -C-TTTSSSCS-TTT---TC
T ss_pred ccCcccCCCcchhhhhhhhh
Confidence 37999999999999997753
No 66
>PF15489 CTC1: CST, telomere maintenance, complex subunit CTC1
Probab=93.13 E-value=32 Score=43.62 Aligned_cols=310 Identities=13% Similarity=0.135 Sum_probs=162.2
Q ss_pred CCceEEEEEEEEeccceeecCCCCCcceEEEEEeeC-CCCEEEEEEechHHHhhhhccCcCcEEEEeeeEEecCCc---c
Q 003281 229 MGKWTIKARVTAKGELRHYNNQRGDGKVFHFDLLDS-DGGEIRVTCFNAVADQFYHQVEAGKIYLVSRGSLKPAQK---N 304 (834)
Q Consensus 229 ~~~w~I~aRV~~Ks~lr~~~n~~g~Gk~f~~~L~De-~g~~I~at~f~~~~d~f~~~l~eG~vy~is~~~V~~a~~---~ 304 (834)
...|.+.|.+++.+.... +...+.|. --...|+ ...++-..|++.. -+|++.|+.|.||.+-- +... -
T Consensus 704 ~~tlsF~~~g~wlGg~q~-~eg~~~~~--~e~~~~~~~~~kVlLlF~G~s-vrWF~fLhpg~vYRLva----~~~~~p~l 775 (1144)
T PF15489_consen 704 KPTLSFQVSGSWLGGTQR-KEGTGWGP--PEPLEDENKDQKVLLLFLGSS-VRWFPFLHPGQVYRLVA----PNSPDPML 775 (1144)
T ss_pred CCceEEEEEEEEecceEe-ccCcccCC--CCcCcccCCCceEEEEEecCc-eeeEeEecCCcEEEEec----CCCCCcee
Confidence 457888888888777654 11111122 1112233 3455555555654 58999999999998843 2111 0
Q ss_pred --cccCC--------CeEEEEEccCccEEEecCCCCCCcccc-----cccccccccccc-CCCceeeEEEEEEEecCCee
Q 003281 305 --FNHLH--------NDLEIFLDMTSMVQLCYEDDASIPRQQ-----FHFRPINDVEGM-ENNSVVDLIGVVSYISPTAS 368 (834)
Q Consensus 305 --~~~~~--------~~yeI~f~~~T~I~~~~d~~~~iP~~~-----~~f~~i~dI~~~-~~~~~vDVIGvV~~V~~~~~ 368 (834)
+..+. -.--+++..+=+++... ..++|... ..-.++.||..- ..+.+|.+-++|.+..-.+.
T Consensus 776 ~~~s~~s~r~l~~~~~~scl~vq~~W~le~~~--~~d~~~~l~~~~~~~~ssl~~lls~s~s~sLVSFs~~I~srt~ce~ 853 (1144)
T PF15489_consen 776 FGSSCVSQRPLELAGCPSCLTVQDDWTLELES--SQDIPPVLRISKLLPESSLSELLSSSSSDSLVSFSAEILSRTLCEP 853 (1144)
T ss_pred ecCCCcccccccccCCCccEEeCCCceecccc--cccchhhhhhcccCccccHHHHhccCCCCceEEEEEEEEEeeeccC
Confidence 11111 11122222222222211 12343321 123355555542 35789999999988743332
Q ss_pred EE----ccCCc-----eeeE--EEEEEeccCC-cEEEEEEcCCccchhhhhhhhcccCCCccEEEEEEE--EEeecCCeE
Q 003281 369 LM----RKNGT-----ETQK--RTLHLRDMSG-RSVELTLWGNFCNDDGLRLQHMCDSGVFPILAVKAG--RVSDFNGKV 434 (834)
Q Consensus 369 i~----~k~g~-----~~~k--r~i~L~D~s~-~si~vtLWg~~a~~~~~~l~~~~~~~~~~Vv~ik~~--rV~~f~G~~ 434 (834)
.. ++.+. ...+ .-+++.|... ..+.|-+=..+.. +. ..--.+.+|.|.+. ||+.++..+
T Consensus 854 ~~~~~~~~~~~~~~~~~~vkltv~L~v~D~~~p~~ldVYi~~~h~p-~p------lGLLPGA~V~f~~lerkVSRs~nVY 926 (1144)
T PF15489_consen 854 LNARRWSKPGNAIASRGCVKLTVALTVADCESPPHLDVYIEDPHLP-YP------LGLLPGARVLFSQLERKVSRSHNVY 926 (1144)
T ss_pred CccccccCCCCCcccccccceEEEEEEecCCCCCeEEEEecCCCCC-Cc------ccccCCceeeeehhhhhhhccCcEE
Confidence 21 11111 1122 3455556655 2333322111111 00 01125667888765 777777778
Q ss_pred EEeecceEEEEcCCchHHHHHHHHHHhcCCccceeeeccccccCCccchhccHhhhhhcCCCCCCCCceEEEEEEEEEEe
Q 003281 435 VGTISTTQLFIEPDFPEAHRLKEWFEKEGKNTQSVSISRDSLSVGRADIRKTVSQIKDEGLGTKEKPDWITVSATIVYIK 514 (834)
Q Consensus 435 Ls~~~~S~i~inPd~pe~~~l~~w~~~~g~~~~~~sls~~~~~~~~~~~~ktI~ei~~~~lg~~~k~~~~~v~atI~~I~ 514 (834)
+....+|.|.+-...+|+. .........+.++... ...+-..++.+.|+.|.
T Consensus 927 C~~~psS~VtVlS~p~~t~------------------------~~~~~P~~~L~~~~~~----~~~~~~a~~~chVV~V~ 978 (1144)
T PF15489_consen 927 CCFLPSSSVTVLSFPPETN------------------------VSPPLPHIYLAELLQG----SQSPFQARVSCHVVSVL 978 (1144)
T ss_pred EEEcCCceEEEEecCcccC------------------------CCCCCCeEEehhhhCC----CCCCceEEEEEEEEEEE
Confidence 7777777776644321110 0001122344443321 12233567888888876
Q ss_pred cCCeeeeCCCCCcCCCCcCcccccCCCCceecC----CCCCccccceEEEEEEEEEEeCCCeEEEEEehHHHHHHhCCCH
Q 003281 515 CDNFCYTACPIMIGDRPCNKKVMNNGDGRWHCD----RCDQSVVECDYRYILQFQIQDHTGLTWVTAFQECAEEIMGMSA 590 (834)
Q Consensus 515 ~d~~~Y~aC~~~~~~~~C~KKv~~~~dg~~~Ce----kC~~~~~~~~~ry~l~~~i~D~Tg~~~~~~F~e~ae~llG~sA 590 (834)
.=.+. ..|. .|..-..+ | +|. .|... ....+-.+.+.|.|+||++.+++-++..-.+||.+.
T Consensus 979 ~l~L~-WvCa------~C~si~~q---g--~Csr~~p~C~s~--~sV~qA~ar~~vEDGTaeA~v~~~~~~V~~lLgL~~ 1044 (1144)
T PF15489_consen 979 SLQLQ-WVCA------HCGSICPQ---G--RCSRQSPPCPSQ--TSVFQASARLLVEDGTAEAVVWCRGHHVAALLGLSP 1044 (1144)
T ss_pred EEEee-ehhh------hccCcccC---C--cCCCCCCCCCCC--cceeeEEEEEEEecCCeeEEEEECCcHHHHHhCCCH
Confidence 44222 2566 46643321 2 353 25432 457888889999999999999999999999999998
Q ss_pred HHHHhhh
Q 003281 591 KDLYSLK 597 (834)
Q Consensus 591 ~el~~l~ 597 (834)
.|...+.
T Consensus 1045 ~eW~~L~ 1051 (1144)
T PF15489_consen 1045 SEWESLL 1051 (1144)
T ss_pred HHHHHHH
Confidence 8765554
No 67
>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=92.47 E-value=0.89 Score=40.54 Aligned_cols=66 Identities=26% Similarity=0.395 Sum_probs=44.7
Q ss_pred eeEEEEEEEecCCeeEEccCCceeeEEEEEEeccCCcEEEEEEcCCccch---hhhhhhhcccCCCccEEEEEEEEEeec
Q 003281 354 VDLIGVVSYISPTASLMRKNGTETQKRTLHLRDMSGRSVELTLWGNFCND---DGLRLQHMCDSGVFPILAVKAGRVSDF 430 (834)
Q Consensus 354 vDVIGvV~~V~~~~~i~~k~g~~~~kr~i~L~D~s~~si~vtLWg~~a~~---~~~~l~~~~~~~~~~Vv~ik~~rV~~f 430 (834)
|.++|+|+++.... .+..++|.|.|| +|++.+|...... ....+ ..+.+|.+ .++++.|
T Consensus 2 v~~vG~V~~~~~~~----------~~~~~tL~D~TG-~I~~~~W~~~~~~~~~~~~~~------~~g~~v~v-~G~v~~~ 63 (95)
T cd04478 2 VTLVGVVRNVEEQS----------TNITYTIDDGTG-TIEVRQWLDDDNDDSSEVEPI------EEGTYVRV-FGNLKSF 63 (95)
T ss_pred EEEEEEEEeeeEcc----------cEEEEEEECCCC-cEEEEEeCCCCCccccccccc------ccCCEEEE-EEEEccc
Confidence 67899999875442 468899999999 7999999866431 11111 23445544 4577899
Q ss_pred CCe-EEEe
Q 003281 431 NGK-VVGT 437 (834)
Q Consensus 431 ~G~-~Ls~ 437 (834)
+|+ .|..
T Consensus 64 ~g~~ql~i 71 (95)
T cd04478 64 QGKKSIMA 71 (95)
T ss_pred CCeeEEEE
Confidence 985 6654
No 68
>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=92.17 E-value=0.73 Score=39.29 Aligned_cols=43 Identities=19% Similarity=0.348 Sum_probs=36.2
Q ss_pred ceEEEEEeeCCCCEEEEEEechHHHhhhhccCcCcEEEEeeeEEe
Q 003281 255 KVFHFDLLDSDGGEIRVTCFNAVADQFYHQVEAGKIYLVSRGSLK 299 (834)
Q Consensus 255 k~f~~~L~De~g~~I~at~f~~~~d~f~~~l~eG~vy~is~~~V~ 299 (834)
..+.+.|.|. .|.|.+++|++..+++.+.|++|.+|.|.. ++.
T Consensus 19 ~~~~~~l~D~-tg~~~~~~f~~~~~~~~~~l~~g~~v~v~G-~v~ 61 (84)
T cd04485 19 RMAFVTLEDL-TGSIEVVVFPETYEKYRDLLKEDALLLVEG-KVE 61 (84)
T ss_pred EEEEEEEEeC-CCeEEEEECHHHHHHHHHHhcCCCEEEEEE-EEE
Confidence 5788899997 588999999988778899999999999874 443
No 69
>PF13917 zf-CCHC_3: Zinc knuckle
Probab=91.66 E-value=0.084 Score=39.80 Aligned_cols=17 Identities=41% Similarity=1.161 Sum_probs=16.3
Q ss_pred cccccCccCccCCCCCC
Q 003281 743 SCSSCGAVGHSSMNCPS 759 (834)
Q Consensus 743 ~C~~Cg~~GH~a~~Cp~ 759 (834)
.|.+|++.|||..+||+
T Consensus 6 ~CqkC~~~GH~tyeC~~ 22 (42)
T PF13917_consen 6 RCQKCGQKGHWTYECPN 22 (42)
T ss_pred cCcccCCCCcchhhCCC
Confidence 89999999999999995
No 70
>smart00343 ZnF_C2HC zinc finger.
Probab=91.62 E-value=0.081 Score=35.53 Aligned_cols=19 Identities=37% Similarity=0.955 Sum_probs=16.4
Q ss_pred cccccCccCccCCCCCCCC
Q 003281 743 SCSSCGAVGHSSMNCPSIM 761 (834)
Q Consensus 743 ~C~~Cg~~GH~a~~Cp~~~ 761 (834)
.|++|++.||++++||...
T Consensus 1 ~C~~CG~~GH~~~~C~~~~ 19 (26)
T smart00343 1 KCYNCGKEGHIARDCPKXX 19 (26)
T ss_pred CCccCCCCCcchhhCCccc
Confidence 4999999999999999533
No 71
>PF11325 DUF3127: Domain of unknown function (DUF3127); InterPro: IPR021474 This bacterial family of proteins has no known function.
Probab=91.19 E-value=1.8 Score=38.01 Aligned_cols=75 Identities=20% Similarity=0.271 Sum_probs=52.7
Q ss_pred EEEEEEEecCCeeEEccCCceeeEEEEEEeccCC--cEEEEEEcCCccchhhhhhhhcccCCCccEEEE-EEEEEeecCC
Q 003281 356 LIGVVSYISPTASLMRKNGTETQKRTLHLRDMSG--RSVELTLWGNFCNDDGLRLQHMCDSGVFPILAV-KAGRVSDFNG 432 (834)
Q Consensus 356 VIGvV~~V~~~~~i~~k~g~~~~kr~i~L~D~s~--~si~vtLWg~~a~~~~~~l~~~~~~~~~~Vv~i-k~~rV~~f~G 432 (834)
+.|.|..+-+..+-.+++| +.||++.|.-... ..|.+.+|++-+..+. .-..+..|.+ -+.+-++|+|
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--WKKREFVLETEEQYPQKICFEFWGDKIDLLD-------NFQVGDEVKVSFNIEGREWNG 72 (84)
T ss_pred cccEEEEEecCcccCcCCC--cEEEEEEEeCCCcCCceEEEEEEcchhhhhc-------cCCCCCEEEEEEEeeccEecc
Confidence 4588777777766666778 9999999985554 6799999998886521 1224555555 4677789999
Q ss_pred eEEEeec
Q 003281 433 KVVGTIS 439 (834)
Q Consensus 433 ~~Ls~~~ 439 (834)
+..+...
T Consensus 73 r~fn~i~ 79 (84)
T PF11325_consen 73 RWFNSIR 79 (84)
T ss_pred eEeeEeE
Confidence 8654433
No 72
>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=89.89 E-value=2.2 Score=36.25 Aligned_cols=68 Identities=22% Similarity=0.324 Sum_probs=41.9
Q ss_pred EEEEEEEecCCeeEEccCCceeeEEEEEEeccCCcEEEEEEcCCccchhhhhhhhcccCCCccEEEEEEEEEeecCCe-E
Q 003281 356 LIGVVSYISPTASLMRKNGTETQKRTLHLRDMSGRSVELTLWGNFCNDDGLRLQHMCDSGVFPILAVKAGRVSDFNGK-V 434 (834)
Q Consensus 356 VIGvV~~V~~~~~i~~k~g~~~~kr~i~L~D~s~~si~vtLWg~~a~~~~~~l~~~~~~~~~~Vv~ik~~rV~~f~G~-~ 434 (834)
++|+|.++.. ..+|+|+ ....++|.|.+| .+++++|.+..+.+...|. .+.++.+. +++..|+|. +
T Consensus 2 i~g~v~~~~~---~~~k~g~--~~~~~~l~D~tg-~~~~~~f~~~~~~~~~~l~------~g~~v~v~-G~v~~~~~~~~ 68 (84)
T cd04485 2 VAGLVTSVRR---RRTKKGK--RMAFVTLEDLTG-SIEVVVFPETYEKYRDLLK------EDALLLVE-GKVERRDGGLR 68 (84)
T ss_pred EEEEEEEeEE---EEcCCCC--EEEEEEEEeCCC-eEEEEECHHHHHHHHHHhc------CCCEEEEE-EEEEecCCceE
Confidence 5677776543 3355665 357888999999 6999999765333222221 34455554 467777663 4
Q ss_pred EE
Q 003281 435 VG 436 (834)
Q Consensus 435 Ls 436 (834)
|.
T Consensus 69 l~ 70 (84)
T cd04485 69 LI 70 (84)
T ss_pred EE
Confidence 43
No 73
>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=89.46 E-value=1.9 Score=36.69 Aligned_cols=54 Identities=22% Similarity=0.349 Sum_probs=42.2
Q ss_pred EEEEEEEEeccceeecCCCCCcceEEEEEeeCCCCEEEEEEechHHHhhhhccCcCcEEEEee
Q 003281 233 TIKARVTAKGELRHYNNQRGDGKVFHFDLLDSDGGEIRVTCFNAVADQFYHQVEAGKIYLVSR 295 (834)
Q Consensus 233 ~I~aRV~~Ks~lr~~~n~~g~Gk~f~~~L~De~g~~I~at~f~~~~d~f~~~l~eG~vy~is~ 295 (834)
.|.+-|+. +|. . .+ | ..-++|.|. .++|.+++|.+..+++.+.|++|+.+.|..
T Consensus 3 ~v~g~v~~---i~~-t-k~--g-~~~~~L~D~-~~~i~~~~f~~~~~~~~~~l~~g~~v~v~g 56 (78)
T cd04489 3 WVEGEISN---LKR-P-SS--G-HLYFTLKDE-DASIRCVMWRSNARRLGFPLEEGMEVLVRG 56 (78)
T ss_pred EEEEEEec---CEE-C-CC--c-EEEEEEEeC-CeEEEEEEEcchhhhCCCCCCCCCEEEEEE
Confidence 45666663 444 2 22 5 777889997 589999999999999999999999988865
No 74
>PF15072 DUF4539: Domain of unknown function (DUF4539)
Probab=88.48 E-value=1.9 Score=38.00 Aligned_cols=61 Identities=18% Similarity=0.273 Sum_probs=46.3
Q ss_pred EEEEEeeCCCCEEEEEEechHHHhhhhccCcCcEEEEeeeEEecCCcccccCCCeEEEEEccCccEEE
Q 003281 257 FHFDLLDSDGGEIRVTCFNAVADQFYHQVEAGKIYLVSRGSLKPAQKNFNHLHNDLEIFLDMTSMVQL 324 (834)
Q Consensus 257 f~~~L~De~g~~I~at~f~~~~d~f~~~l~eG~vy~is~~~V~~a~~~~~~~~~~yeI~f~~~T~I~~ 324 (834)
..+.|.|- .|+|+|++..+..++|.+.|..|.|..+.+..|-. +....+-|.+.....+..
T Consensus 21 ~~v~l~Dp-TG~i~~tiH~~v~~~y~~~l~~GavLlLk~V~Vf~------ps~~~~yLnIt~~Nlv~v 81 (86)
T PF15072_consen 21 AFVVLKDP-TGEIRGTIHRKVLEEYGDELSPGAVLLLKDVTVFS------PSPRSHYLNITLNNLVRV 81 (86)
T ss_pred eEEEEECC-CCcEEEEEeHHHHhhcCCccccCEEEEEeeeeEEe------cCCCccEEEEehhHeeeE
Confidence 57889997 57999999999999999999999999999987743 333344455544444433
No 75
>KOG0109 consensus RNA-binding protein LARK, contains RRM and retroviral-type Zn-finger domains [RNA processing and modification; General function prediction only]
Probab=88.38 E-value=0.28 Score=51.92 Aligned_cols=22 Identities=41% Similarity=0.854 Sum_probs=19.9
Q ss_pred cccccCccCccCCCCCCCCCCC
Q 003281 743 SCSSCGAVGHSSMNCPSIMSGP 764 (834)
Q Consensus 743 ~C~~Cg~~GH~a~~Cp~~~~~~ 764 (834)
.||.||++|||+++||..+.+.
T Consensus 162 ~cyrcGkeghwskEcP~~~~~r 183 (346)
T KOG0109|consen 162 GCYRCGKEGHWSKECPVDRTGR 183 (346)
T ss_pred HheeccccccccccCCccCCCc
Confidence 7999999999999999988644
No 76
>PTZ00401 aspartyl-tRNA synthetase; Provisional
Probab=88.28 E-value=5.3 Score=47.47 Aligned_cols=98 Identities=23% Similarity=0.245 Sum_probs=67.8
Q ss_pred CCceeccccCCCC---CceEEEEEEEEeccceeecCCCCCcceEEEEEeeCCCCEEEEEEe-c----hHHHhhhhccCcC
Q 003281 217 SRIIPIAALNPYM---GKWTIKARVTAKGELRHYNNQRGDGKVFHFDLLDSDGGEIRVTCF-N----AVADQFYHQVEAG 288 (834)
Q Consensus 217 ~~~~pI~~L~p~~---~~w~I~aRV~~Ks~lr~~~n~~g~Gk~f~~~L~De~g~~I~at~f-~----~~~d~f~~~l~eG 288 (834)
+.++.|++|++.. ...+|++||.+ +|. .|++.-++|.|. ++.|++++- + ..+-+|...|..|
T Consensus 63 ~~~~~i~~l~~~~~~g~~V~v~Grv~~---~R~------~Gk~~Fl~LRd~-~~~iQ~v~~~~~~~~~~~~~~~~~l~~e 132 (550)
T PTZ00401 63 RTFIPVAVLSKPELVDKTVLIRARVST---TRK------KGKMAFMVLRDG-SDSVQAMAAVEGDVPKEMIDFIGQIPTE 132 (550)
T ss_pred CceEEHHHCCccccCCCEEEEEEEEEE---Eec------CCCeEEEEEEeC-CcCEEEEEECCCccCHHHHHHHhcCCCC
Confidence 4689999998764 56889999964 333 367777888997 579999984 2 2344566779999
Q ss_pred cEEEEeeeEEecCCcccccCCCeEEEEEccCccEEE
Q 003281 289 KIYLVSRGSLKPAQKNFNHLHNDLEIFLDMTSMVQL 324 (834)
Q Consensus 289 ~vy~is~~~V~~a~~~~~~~~~~yeI~f~~~T~I~~ 324 (834)
+++.|.+.-+++....-+....++||..+.-..|..
T Consensus 133 siV~V~G~v~~~~~~~~~~~~~~~El~v~~i~vls~ 168 (550)
T PTZ00401 133 SIVDVEATVCKVEQPITSTSHSDIELKVKKIHTVTE 168 (550)
T ss_pred CEEEEEEEEEecCccCCCCCCccEEEEeeEEEEEeC
Confidence 999999865554333223445679998865433433
No 77
>PRK05813 single-stranded DNA-binding protein; Provisional
Probab=87.78 E-value=35 Score=35.62 Aligned_cols=166 Identities=20% Similarity=0.241 Sum_probs=96.2
Q ss_pred CCceEEEEEEEEeccceeecCCCCCcceEEEEE-----eeCCCCEEEEEEechHHHhhhhccCcCcEEEEeeeEEecCCc
Q 003281 229 MGKWTIKARVTAKGELRHYNNQRGDGKVFHFDL-----LDSDGGEIRVTCFNAVADQFYHQVEAGKIYLVSRGSLKPAQK 303 (834)
Q Consensus 229 ~~~w~I~aRV~~Ks~lr~~~n~~g~Gk~f~~~L-----~De~g~~I~at~f~~~~d~f~~~l~eG~vy~is~~~V~~a~~ 303 (834)
.++..+.+|+++--++|+-. .|++ +..|.| .|+ -+.|.+++|..+++... |..|+-+.+.+ +++..++
T Consensus 8 ~NkV~L~Grl~~d~e~~~~~--~G~~-~~~f~laV~R~s~~-~D~i~v~v~~rlae~~~--l~kG~~v~VeG-qlrsy~~ 80 (219)
T PRK05813 8 NNKVYLEGKVVSELEFSHEM--YGEG-FYNFKLEVPRLSDS-KDILPVTVSERLLAGMD--LKVGTLVIVEG-QLRSYNK 80 (219)
T ss_pred cCEEEEEEEEcCCceEEEEe--CCeE-EEEEEEEeeccCCC-ccEEEEEEEhhhhhhhc--ccCCCEEEEEE-EEEEecc
Confidence 46889999999988888743 3444 445554 354 58999999999998776 99999999986 3331111
Q ss_pred ccccCCCeEEEEEccCccEEEecCCCCCCccccccccccccccccCCCceeeEEEEEEEecCCeeEEccCCceeeEEEEE
Q 003281 304 NFNHLHNDLEIFLDMTSMVQLCYEDDASIPRQQFHFRPINDVEGMENNSVVDLIGVVSYISPTASLMRKNGTETQKRTLH 383 (834)
Q Consensus 304 ~~~~~~~~yeI~f~~~T~I~~~~d~~~~iP~~~~~f~~i~dI~~~~~~~~vDVIGvV~~V~~~~~i~~k~g~~~~kr~i~ 383 (834)
+....+.|.+.+-.. .|+.+... .+ ...-..|-++|.+..--.+. .+.+|+.+.. +.
T Consensus 81 -~~~G~~R~vl~V~a~-~i~~l~~~--------------~~---~~~~N~V~LiGrL~~DPelR--~t~~G~~va~--f~ 137 (219)
T PRK05813 81 -FIDGKNRLILTVFAR-NIEYCDER--------------SD---IKNPNEIFLDGYICKEPVYR--TTPFGREIAD--LL 137 (219)
T ss_pred -CCCCcEEEEEEEEEE-EEEEccCC--------------Cc---cCCccEEEEEEEccCCCeEE--ECCCCCEEEE--EE
Confidence 102334454443221 23333110 01 11234677888887643232 2346765443 44
Q ss_pred EeccC----CcEEEEEEcCCccchhhhhhhhcccCCCccEEEEEE-EEEeecC
Q 003281 384 LRDMS----GRSVELTLWGNFCNDDGLRLQHMCDSGVFPILAVKA-GRVSDFN 431 (834)
Q Consensus 384 L~D~s----~~si~vtLWg~~a~~~~~~l~~~~~~~~~~Vv~ik~-~rV~~f~ 431 (834)
|.-.. ..-|.|++||..|+.. ..+ ..+.-|++.+ .+...|.
T Consensus 138 lAvnr~~~~td~i~~v~wg~~Ae~~-~~l------~KG~~V~V~GrL~sr~y~ 183 (219)
T PRK05813 138 LAVNRPYNKSDYIPCIAWGRNARFC-KTL------EVGDNIRVWGRVQSREYQ 183 (219)
T ss_pred EEEcCCCCCceEEEEEEEhHHhHHH-hhC------CCCCEEEEEEEEEecceE
Confidence 43221 1369999999998743 222 2455666654 4555554
No 78
>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=87.65 E-value=2.9 Score=36.26 Aligned_cols=54 Identities=20% Similarity=0.230 Sum_probs=41.5
Q ss_pred EEEEEEEEeccceeecCCCCCcceEEEEEeeCCCCEEEEEEechHHH--hhhhccCcCcEEEEee
Q 003281 233 TIKARVTAKGELRHYNNQRGDGKVFHFDLLDSDGGEIRVTCFNAVAD--QFYHQVEAGKIYLVSR 295 (834)
Q Consensus 233 ~I~aRV~~Ks~lr~~~n~~g~Gk~f~~~L~De~g~~I~at~f~~~~d--~f~~~l~eG~vy~is~ 295 (834)
.+.+.|+. ++ .+ .+ |+- -+.|-|. .|.|.+++|.+..+ ++.+.|+++.++.|..
T Consensus 3 ~i~GiI~~---v~-~T-K~--g~~-~~~leD~-~G~~Ev~~F~~~~~~~~~~~~l~~d~~v~v~g 58 (79)
T cd04490 3 SIIGMVND---VR-ST-KN--GHR-IVELEDT-TGRITVLLTKDKEELFEEAEDILPDEVIGVSG 58 (79)
T ss_pred EEEEEEeE---EE-Ec-CC--CCE-EEEEECC-CCEEEEEEeCchhhhhhhhhhccCCCEEEEEE
Confidence 45566654 33 22 23 444 7778887 68999999999999 9999999999999976
No 79
>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=87.57 E-value=3.9 Score=36.76 Aligned_cols=90 Identities=16% Similarity=0.119 Sum_probs=60.2
Q ss_pred eEEEEEEEecCCeeEEccCCceeeEEEEEEeccCCcEEEEEEcCCccchhhhhhhhcccCCCccEEEEEEEEEeecCC--
Q 003281 355 DLIGVVSYISPTASLMRKNGTETQKRTLHLRDMSGRSVELTLWGNFCNDDGLRLQHMCDSGVFPILAVKAGRVSDFNG-- 432 (834)
Q Consensus 355 DVIGvV~~V~~~~~i~~k~g~~~~kr~i~L~D~s~~si~vtLWg~~a~~~~~~l~~~~~~~~~~Vv~ik~~rV~~f~G-- 432 (834)
|++|+|++|+... +...-.+.|.|+.-.-+-|.+|........ +++. .+...|++.+...+.+..
T Consensus 1 D~VGvVvsV~~~~--------~g~~~~vYLaDe~~nll~vkfw~~l~~~~~---EDvv--k~~~lia~SNLQwR~~s~~~ 67 (100)
T cd04495 1 DTVGVVISVGKPI--------EGKFPAVYLADECLNLLCVKFWSSLEQYAY---EDVV--KRRVLLAASNLQWRTESTSG 67 (100)
T ss_pred CceEEEEEEcccc--------cCccceEEEecCCcCEEEEEEecchHHhhh---hhhc--ccceEEEEecceEeccccCC
Confidence 8999999998765 123457899999999999999997654322 2221 345688888877765544
Q ss_pred e-EEEeecceEEEEcCCchHHHHHHHHHH
Q 003281 433 K-VVGTISTTQLFIEPDFPEAHRLKEWFE 460 (834)
Q Consensus 433 ~-~Ls~~~~S~i~inPd~pe~~~l~~w~~ 460 (834)
. .|-.+.-|.+..||.- ..|++-|.
T Consensus 68 iPtl~Age~t~FS~nPKe---~hlQe~~~ 93 (100)
T cd04495 68 VPTLFAGEYSTFSANPKE---SHLQEEFN 93 (100)
T ss_pred CceeeeecceeecCCccH---HHHHHHHH
Confidence 3 4555566777777743 44444443
No 80
>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=87.12 E-value=0.32 Score=51.32 Aligned_cols=21 Identities=38% Similarity=1.230 Sum_probs=18.9
Q ss_pred CcCcccCCCCccCCCCCCCCC
Q 003281 786 SECYKCHKTGHWARDCPSLNA 806 (834)
Q Consensus 786 ~~Cy~Cg~~GH~ardCp~~~~ 806 (834)
..||+||+-|||-++||...+
T Consensus 177 Y~CyRCGqkgHwIqnCpTN~D 197 (427)
T COG5222 177 YVCYRCGQKGHWIQNCPTNQD 197 (427)
T ss_pred eeEEecCCCCchhhcCCCCCC
Confidence 579999999999999998755
No 81
>PRK06751 single-stranded DNA-binding protein; Provisional
Probab=86.94 E-value=4.1 Score=40.88 Aligned_cols=64 Identities=23% Similarity=0.313 Sum_probs=50.3
Q ss_pred CCceEEEEEEEEeccceeecCCCCCcceEEEEEe------eCCC----CEEEEEEechHHHhhhhccCcCcEEEEee
Q 003281 229 MGKWTIKARVTAKGELRHYNNQRGDGKVFHFDLL------DSDG----GEIRVTCFNAVADQFYHQVEAGKIYLVSR 295 (834)
Q Consensus 229 ~~~w~I~aRV~~Ks~lr~~~n~~g~Gk~f~~~L~------De~g----~~I~at~f~~~~d~f~~~l~eG~vy~is~ 295 (834)
+++..|.+||++--++|...+ | ..+.+|.|+ ++.| .-|.+++|+.+++.+...|+.|+-+.|..
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 478899999999888886542 2 357777764 2222 46889999999999999999999999976
No 82
>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=86.88 E-value=2.8 Score=35.80 Aligned_cols=42 Identities=24% Similarity=0.375 Sum_probs=34.4
Q ss_pred ceEEEEEeeCCCCEEEEEEechHHHhhhhccCcCcEEEEeeeEEe
Q 003281 255 KVFHFDLLDSDGGEIRVTCFNAVADQFYHQVEAGKIYLVSRGSLK 299 (834)
Q Consensus 255 k~f~~~L~De~g~~I~at~f~~~~d~f~~~l~eG~vy~is~~~V~ 299 (834)
+++.+.|.|. .|.|.+++|++.. .+...|++|.++.+. ++|.
T Consensus 19 ~~~~~~l~D~-tg~i~~~~f~~~~-~~~~~l~~g~~v~v~-G~v~ 60 (83)
T cd04492 19 PYLALTLQDK-TGEIEAKLWDASE-EDEEKFKPGDIVHVK-GRVE 60 (83)
T ss_pred cEEEEEEEcC-CCeEEEEEcCCCh-hhHhhCCCCCEEEEE-EEEE
Confidence 5788999997 5799999999654 447889999999998 5554
No 83
>PRK02801 primosomal replication protein N; Provisional
Probab=86.83 E-value=3.4 Score=37.66 Aligned_cols=68 Identities=12% Similarity=0.038 Sum_probs=53.3
Q ss_pred CCceEEEEEEEEeccceeecCCCCCcceEEEEEee-----CCCC------EEEEEEechHHHhhhhccCcCcEEEEeeeE
Q 003281 229 MGKWTIKARVTAKGELRHYNNQRGDGKVFHFDLLD-----SDGG------EIRVTCFNAVADQFYHQVEAGKIYLVSRGS 297 (834)
Q Consensus 229 ~~~w~I~aRV~~Ks~lr~~~n~~g~Gk~f~~~L~D-----e~g~------~I~at~f~~~~d~f~~~l~eG~vy~is~~~ 297 (834)
+++..+.+|+++.-++|...+ | -.+.+|.|.= +.+. .|.+++|+..++.+...|..|+.+.|+++.
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--G-IPHCQFVLEHRSVQEEAGLHRQAWCRMPVIVSGNQFQAITQSITVGSKITVQGFI 78 (101)
T ss_pred ccEEEEEEEECcCcceEECCC--C-CeEEEEEEEEeCeEecCCCceeEEEEEEEEEEcHHHHHHHhhcCCCCEEEEEEEE
Confidence 478899999999999998643 2 3677777632 2122 299999999999999999999999999875
Q ss_pred Ee
Q 003281 298 LK 299 (834)
Q Consensus 298 V~ 299 (834)
-.
T Consensus 79 ~~ 80 (101)
T PRK02801 79 SC 80 (101)
T ss_pred EE
Confidence 43
No 84
>PRK05733 single-stranded DNA-binding protein; Provisional
Probab=86.81 E-value=4.8 Score=40.36 Aligned_cols=65 Identities=22% Similarity=0.220 Sum_probs=50.5
Q ss_pred CCCceEEEEEEEEeccceeecCCCCCcceEEEEEe------eCCCC-------EEEEEEechHHHhhhhccCcCcEEEEe
Q 003281 228 YMGKWTIKARVTAKGELRHYNNQRGDGKVFHFDLL------DSDGG-------EIRVTCFNAVADQFYHQVEAGKIYLVS 294 (834)
Q Consensus 228 ~~~~w~I~aRV~~Ks~lr~~~n~~g~Gk~f~~~L~------De~g~-------~I~at~f~~~~d~f~~~l~eG~vy~is 294 (834)
.+++.+|.+||..--++|.+.+. ..+.+|.|. |++.| -+.+++|+..++.+.+.|+.|+.++|.
T Consensus 4 ~mNkV~LiGrlg~DPElr~t~nG---~~va~fsVAv~~~~k~~~~Ge~~e~T~w~~Vv~fgk~Ae~v~~~l~KGs~V~Ve 80 (172)
T PRK05733 4 GVNKVILVGTCGQDPEVRYLPNG---NAVTNLSLATSEQWTDKQSGQKVERTEWHRVSLFGKVAEIAGEYLRKGSQVYIE 80 (172)
T ss_pred cceEEEEEEEecCCCEEEECCCC---CEEEEEEEEEcCccccCCCCcccccceEEEEEEehHHHHHHHHHhCCCCEEEEE
Confidence 36788999999998788877542 256666664 22223 289999999999999999999999997
Q ss_pred e
Q 003281 295 R 295 (834)
Q Consensus 295 ~ 295 (834)
.
T Consensus 81 G 81 (172)
T PRK05733 81 G 81 (172)
T ss_pred E
Confidence 6
No 85
>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=86.44 E-value=4.2 Score=39.59 Aligned_cols=85 Identities=12% Similarity=0.150 Sum_probs=60.0
Q ss_pred ceeccccCC-CCCceEEEEEEEEeccceeecCCCCCcceEEEEEeeCCC-------CEEEEEEechHHHhhhhccCcCcE
Q 003281 219 IIPIAALNP-YMGKWTIKARVTAKGELRHYNNQRGDGKVFHFDLLDSDG-------GEIRVTCFNAVADQFYHQVEAGKI 290 (834)
Q Consensus 219 ~~pI~~L~p-~~~~w~I~aRV~~Ks~lr~~~n~~g~Gk~f~~~L~De~g-------~~I~at~f~~~~d~f~~~l~eG~v 290 (834)
++||..+.. ......|.|-|+.....+.. ..+|.....+|.|.|... ..|.+.+|....+.+-.....|+|
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 YTPLSTAKEKFGKFVNVIGVVVDFSPPNPK-KTRGTDYMCTLTITDPSLNDSNQKLSGLTVNIFRPHKESLPNVKSVGDI 79 (146)
T ss_dssp BCCGGGSCTTSSEEEEEEEEEEEEEEECTE-EESSSCEEEEEEEEBTTCSCSSCCCCEEEEEEEESSHHHSCTTCSTTHE
T ss_pred CccchhhhhcCCCEEEEEEEEEEccCCcce-EcCCCcEEEEEEEECCCCCccccccCCEEEEEECCCHHHCCCCCCCCCE
Confidence 356663333 34467788888876665211 123445778999999753 579999998888888766666999
Q ss_pred EEEeeeEEecCCcc
Q 003281 291 YLVSRGSLKPAQKN 304 (834)
Q Consensus 291 y~is~~~V~~a~~~ 304 (834)
+.+.+++|+.-+.+
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 99999999876654
No 86
>PF06075 DUF936: Plant protein of unknown function (DUF936); InterPro: IPR010341 This family consists of several hypothetical proteins from plants. The function of this family is unknown.
Probab=86.21 E-value=0.97 Score=53.62 Aligned_cols=92 Identities=18% Similarity=0.290 Sum_probs=71.9
Q ss_pred CCeEEEEeeEeeccchhhhhccccceEEEEEcccccccccccccchhhhhhcCCcccccEEEEceeeeecccCeEEEEEE
Q 003281 1 MPVLQVMDLKLVVSKQQQQQQHQQQRFRMVLSDGSRSQQGMLATQRNELVTSGLLQIGSVVRLTKFTCNVIQNRMIVIVM 80 (834)
Q Consensus 1 ~PvlQv~~~k~~~~~~~~~~~~~~~Ryrl~lSDG~~~~~~mLatqln~lv~~g~l~~gsiv~l~~~~~~~v~~r~iiii~ 80 (834)
.++|||++|=+.=... + --...=|.|-|||..|..-.-|..+-++||-++.||-|-.|.|.++. -+.-|-|+.
T Consensus 25 s~lLQV~~IvPaL~~~-~--l~p~~gF~lkvSDsshs~Yvsl~~~~~dlils~klqlGqfi~vdrle----~~~PvP~l~ 97 (579)
T PF06075_consen 25 SSLLQVTSIVPALAGS-D--LWPNQGFYLKVSDSSHSTYVSLPDEDDDLILSNKLQLGQFIYVDRLE----AASPVPVLR 97 (579)
T ss_pred ccceeeeeeeeccccc-c--cCcCCceEEEecccccceeeecChhcccceecCCccccceEEEcccc----cCCCCceee
Confidence 3789999997764331 1 01123499999999999888899999999999999999999998864 345677888
Q ss_pred eeeEeccCCCCCCCCcCCC
Q 003281 81 DLDVIIDKCDPIGKPVPAQ 99 (834)
Q Consensus 81 ~lev~~~~~~~ig~P~~~~ 99 (834)
.+..|-.-...+|+|.++.
T Consensus 98 g~rp~pgR~pcvg~P~dl~ 116 (579)
T PF06075_consen 98 GVRPVPGRHPCVGNPEDLV 116 (579)
T ss_pred cCccCCCCCCCCCCChhhh
Confidence 8887775556799997765
No 87
>KOG0314 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=85.18 E-value=1.7 Score=49.52 Aligned_cols=44 Identities=34% Similarity=0.872 Sum_probs=31.4
Q ss_pred cccccCccCccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcCcccCCCCccCCCCCCCC
Q 003281 743 SCSSCGAVGHSSMNCPSIMSGPGQSSGGGYANSFSSGAGIATSSECYKCHKTGHWARDCPSLN 805 (834)
Q Consensus 743 ~C~~Cg~~GH~a~~Cp~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Cy~Cg~~GH~ardCp~~~ 805 (834)
.|..|..++||..-|......+ -+..|++|.++|||.+.||...
T Consensus 135 ~~~~~~~~~~~iq~~~~~g~Pp-------------------psy~c~rc~~~g~wikacptv~ 178 (448)
T KOG0314|consen 135 VCHRCNSPGHFIQHCSTNGSPP-------------------PSYKCVKCPTPGPWIKACPTVS 178 (448)
T ss_pred eeeecccCccccccccccCCCC-------------------CCcceecCCCCCccceeccccC
Confidence 5666666677666666544311 2358999999999999999854
No 88
>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=84.25 E-value=6.1 Score=33.67 Aligned_cols=63 Identities=29% Similarity=0.380 Sum_probs=38.9
Q ss_pred EEEEEEEecCCeeEEccCCceeeEEEEEEeccCCcEEEEEEcCCccchhhhhhhhcccCCCccEEEEEEEEEeecCC
Q 003281 356 LIGVVSYISPTASLMRKNGTETQKRTLHLRDMSGRSVELTLWGNFCNDDGLRLQHMCDSGVFPILAVKAGRVSDFNG 432 (834)
Q Consensus 356 VIGvV~~V~~~~~i~~k~g~~~~kr~i~L~D~s~~si~vtLWg~~a~~~~~~l~~~~~~~~~~Vv~ik~~rV~~f~G 432 (834)
.+.+|.++.. ..+|+|+ ....++|.|.+| +|++++|++.... ... + ..+.++.+. ++|..|+|
T Consensus 2 ~~~~v~~~~~---~~tk~g~--~~~~~~l~D~tg-~i~~~~f~~~~~~-~~~----l--~~g~~v~v~-G~v~~~~~ 64 (83)
T cd04492 2 GFFLIKSKEL---RTAKNGK--PYLALTLQDKTG-EIEAKLWDASEED-EEK----F--KPGDIVHVK-GRVEEYRG 64 (83)
T ss_pred cEEEEEEeee---ecccCCC--cEEEEEEEcCCC-eEEEEEcCCChhh-Hhh----C--CCCCEEEEE-EEEEEeCC
Confidence 3445555543 3345565 368899999999 7999999965421 111 1 134455555 67777766
No 89
>PF14787 zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB: 1CL4_A 1DSV_A.
Probab=84.17 E-value=0.78 Score=33.13 Aligned_cols=20 Identities=30% Similarity=0.546 Sum_probs=13.5
Q ss_pred cccccCccCccCCCCCCCCC
Q 003281 743 SCSSCGAVGHSSMNCPSIMS 762 (834)
Q Consensus 743 ~C~~Cg~~GH~a~~Cp~~~~ 762 (834)
.|++|++..|||++|.....
T Consensus 4 ~CprC~kg~Hwa~~C~sk~d 23 (36)
T PF14787_consen 4 LCPRCGKGFHWASECRSKTD 23 (36)
T ss_dssp C-TTTSSSCS-TTT---TCC
T ss_pred cCcccCCCcchhhhhhhhhc
Confidence 79999999999999987665
No 90
>PRK09010 single-stranded DNA-binding protein; Provisional
Probab=83.82 E-value=9.1 Score=38.60 Aligned_cols=64 Identities=22% Similarity=0.258 Sum_probs=50.8
Q ss_pred CCceEEEEEEEEeccceeecCCCCCcceEEEEEe------eCC-------CCEEEEEEechHHHhhhhccCcCcEEEEee
Q 003281 229 MGKWTIKARVTAKGELRHYNNQRGDGKVFHFDLL------DSD-------GGEIRVTCFNAVADQFYHQVEAGKIYLVSR 295 (834)
Q Consensus 229 ~~~w~I~aRV~~Ks~lr~~~n~~g~Gk~f~~~L~------De~-------g~~I~at~f~~~~d~f~~~l~eG~vy~is~ 295 (834)
+++.+|.+||.+--++|.+.+ | ..+.+|.|+ |.+ ..-|++++|+.+++.+.+.|+.|+-++|..
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 578999999999888988764 2 356777664 322 234699999999999999999999999986
No 91
>PRK13732 single-stranded DNA-binding protein; Provisional
Probab=83.80 E-value=9 Score=38.55 Aligned_cols=64 Identities=23% Similarity=0.317 Sum_probs=51.1
Q ss_pred CCceEEEEEEEEeccceeecCCCCCcceEEEEEe------eCCCC-------EEEEEEechHHHhhhhccCcCcEEEEee
Q 003281 229 MGKWTIKARVTAKGELRHYNNQRGDGKVFHFDLL------DSDGG-------EIRVTCFNAVADQFYHQVEAGKIYLVSR 295 (834)
Q Consensus 229 ~~~w~I~aRV~~Ks~lr~~~n~~g~Gk~f~~~L~------De~g~-------~I~at~f~~~~d~f~~~l~eG~vy~is~ 295 (834)
+++.+|.+||.+--++|.+.+ | ..+.+|.|+ |.+.+ -|++++|+.+++.+.+.|+.|+.++|..
T Consensus 6 mN~V~LiGrLg~DPElR~t~n--G-~~va~fslAvn~~~kd~~~Ge~~e~t~w~~Vv~wgk~Ae~v~~~L~KG~~V~VeG 82 (175)
T PRK13732 6 INKVILVGRLGKDPEVRYIPN--G-GAVANLQVATSESWRDKQTGEMREQTEWHRVVLFGKLAEVAGEYLRKGAQVYIEG 82 (175)
T ss_pred ceEEEEEEEecCCCEEEEcCC--C-CEEEEEEEEEcCccccCCCCceecceeEEEEEEecHHHHHHHHhcCCCCEEEEEE
Confidence 578999999999888888754 2 357777764 22223 4689999999999999999999999986
No 92
>PF09103 BRCA-2_OB1: BRCA2, oligonucleotide/oligosaccharide-binding, domain 1; InterPro: IPR015187 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. OB1 has a shallow 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 weak single strand DNA binding. The domain also binds the 70-amino acid DSS1 (deleted in split-hand/split foot syndrome) protein, which was originally identified as one of three genes that map to a 1.5-Mb locus deleted in an inherited developmental malformation syndrome []. ; GO: 0000724 double-strand break repair via homologous recombination; PDB: 1IYJ_D 1MIU_A.
Probab=83.66 E-value=1.1 Score=42.02 Aligned_cols=41 Identities=22% Similarity=0.359 Sum_probs=25.7
Q ss_pred ccceEEEEEcccccccccccccchhhhhhcCCcccccEEEE
Q 003281 23 QQQRFRMVLSDGSRSQQGMLATQRNELVTSGLLQIGSVVRL 63 (834)
Q Consensus 23 ~~~Ryrl~lSDG~~~~~~mLatqln~lv~~g~l~~gsiv~l 63 (834)
..+...|.|+||=|.+++.|...|..+++.|.|+.|.-+.|
T Consensus 31 ~~~~~~lelTDGWY~Ika~lD~~L~~~l~~gki~vG~KL~v 71 (118)
T PF09103_consen 31 SPESAILELTDGWYSIKAQLDPPLTRLLRKGKIRVGQKLRV 71 (118)
T ss_dssp ------EEEE-SS-EEEE---HHHHHHHHTT-S-TT-EEEE
T ss_pred CCccCEEEEecCCEEEEEEeCHHHHHHHHhCCccCCccEEE
Confidence 34689999999999999999999999999999999988875
No 93
>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=83.30 E-value=27 Score=31.56 Aligned_cols=81 Identities=21% Similarity=0.239 Sum_probs=51.3
Q ss_pred eEEEEEEEEeccceeecCCCCCc-ceEEEEEeeCCCCEEEEEEechH------HHhhhhccCcCcEEEEeeeEEecCCcc
Q 003281 232 WTIKARVTAKGELRHYNNQRGDG-KVFHFDLLDSDGGEIRVTCFNAV------ADQFYHQVEAGKIYLVSRGSLKPAQKN 304 (834)
Q Consensus 232 w~I~aRV~~Ks~lr~~~n~~g~G-k~f~~~L~De~g~~I~at~f~~~------~d~f~~~l~eG~vy~is~~~V~~a~~~ 304 (834)
.+|++||.+ +|.. | ++.-++|.|. ++.|++++-.+. .-++...|..|+++.+.+.-.+. .+.
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 VLIRARVHT---SRAQ------GAKLAFLVLRQQ-GYTIQGVLAASAEGVSKQMVKWAGSLSKESIVDVEGTVKKP-EEP 70 (102)
T ss_pred EEEEEEEEE---eecC------CCceEEEEEecC-CceEEEEEeCCcccCCHHHHHHHhcCCCccEEEEEEEEECC-CCc
Confidence 578888865 3432 5 6777788897 589999997442 22334568999999999854432 221
Q ss_pred ccc-CCCeEEEEEccCccEE
Q 003281 305 FNH-LHNDLEIFLDMTSMVQ 323 (834)
Q Consensus 305 ~~~-~~~~yeI~f~~~T~I~ 323 (834)
.+. ....|||..+.-..+.
T Consensus 71 ~~~~~~~~~El~~~~i~il~ 90 (102)
T cd04320 71 IKSCTQQDVELHIEKIYVVS 90 (102)
T ss_pred ccCCCcCcEEEEEEEEEEEe
Confidence 111 2357999886433333
No 94
>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=83.30 E-value=6.7 Score=33.28 Aligned_cols=41 Identities=20% Similarity=0.334 Sum_probs=30.5
Q ss_pred eEEEEEEEecCCeeEEccCCceeeEEEEEEeccCCcEEEEEEcCCccchhh
Q 003281 355 DLIGVVSYISPTASLMRKNGTETQKRTLHLRDMSGRSVELTLWGNFCNDDG 405 (834)
Q Consensus 355 DVIGvV~~V~~~~~i~~k~g~~~~kr~i~L~D~s~~si~vtLWg~~a~~~~ 405 (834)
=|.|+|.++.. +|+| .-.++|.|.++ ++++++|.+......
T Consensus 3 ~v~g~v~~i~~-----tk~g----~~~~~L~D~~~-~i~~~~f~~~~~~~~ 43 (78)
T cd04489 3 WVEGEISNLKR-----PSSG----HLYFTLKDEDA-SIRCVMWRSNARRLG 43 (78)
T ss_pred EEEEEEecCEE-----CCCc----EEEEEEEeCCe-EEEEEEEcchhhhCC
Confidence 36777777653 4445 67899999997 799999998665543
No 95
>PF15288 zf-CCHC_6: Zinc knuckle
Probab=83.24 E-value=0.63 Score=34.63 Aligned_cols=20 Identities=30% Similarity=0.787 Sum_probs=16.8
Q ss_pred CcCcccCCCCccC--CCCCCCC
Q 003281 786 SECYKCHKTGHWA--RDCPSLN 805 (834)
Q Consensus 786 ~~Cy~Cg~~GH~a--rdCp~~~ 805 (834)
..|.+||+.||.+ +.||...
T Consensus 2 ~kC~~CG~~GH~~t~k~CP~~~ 23 (40)
T PF15288_consen 2 VKCKNCGAFGHMRTNKRCPMYC 23 (40)
T ss_pred ccccccccccccccCccCCCCC
Confidence 3799999999997 7899753
No 96
>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=82.98 E-value=0.87 Score=48.13 Aligned_cols=21 Identities=38% Similarity=0.801 Sum_probs=18.4
Q ss_pred ccccccCccCccCCCCCCCCC
Q 003281 742 QSCSSCGAVGHSSMNCPSIMS 762 (834)
Q Consensus 742 ~~C~~Cg~~GH~a~~Cp~~~~ 762 (834)
+-||+||+.|||.++||....
T Consensus 177 Y~CyRCGqkgHwIqnCpTN~D 197 (427)
T COG5222 177 YVCYRCGQKGHWIQNCPTNQD 197 (427)
T ss_pred eeEEecCCCCchhhcCCCCCC
Confidence 489999999999999997553
No 97
>PRK13480 3'-5' exoribonuclease YhaM; Provisional
Probab=82.50 E-value=4.2 Score=44.86 Aligned_cols=70 Identities=14% Similarity=0.059 Sum_probs=49.8
Q ss_pred eccccCCCCCceEEEEEEEEeccceeecCCCCCcceEEEEEeeCCCCEEEEEEechHHHhhhhccCcCcEEEEeeeE
Q 003281 221 PIAALNPYMGKWTIKARVTAKGELRHYNNQRGDGKVFHFDLLDSDGGEIRVTCFNAVADQFYHQVEAGKIYLVSRGS 297 (834)
Q Consensus 221 pI~~L~p~~~~w~I~aRV~~Ks~lr~~~n~~g~Gk~f~~~L~De~g~~I~at~f~~~~d~f~~~l~eG~vy~is~~~ 297 (834)
.|++|.+.. .......|..+ .+|+-+| | ...+.++|.|. +|+|.|.+|+.. +.....+++|+++.+..-.
T Consensus 4 ~i~~l~~g~-~v~~~~lv~~~-~~~~~kn--G-~~yl~l~l~D~-tG~I~ak~W~~~-~~~~~~~~~g~vv~v~G~v 73 (314)
T PRK13480 4 GIEELEVGE-QVDHFLLIKSA-TKGVASN--G-KPFLTLILQDK-SGDIEAKLWDVS-PEDEATYVPETIVHVKGDI 73 (314)
T ss_pred hHhhcCCCC-EeeEEEEEEEc-eeeecCC--C-CeEEEEEEEcC-CcEEEEEeCCCC-hhhHhhcCCCCEEEEEEEE
Confidence 588888864 45555555544 3444322 1 34889999997 689999999864 5567889999999987643
No 98
>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=82.42 E-value=11 Score=36.37 Aligned_cols=95 Identities=15% Similarity=0.209 Sum_probs=52.7
Q ss_pred ccccccc---cCCCceeeEEEEEEEecCCeeEEccCCceeeEEEEEEeccCCcEEEEEEcCCccchhhhhhhhcccCCCc
Q 003281 341 PINDVEG---MENNSVVDLIGVVSYISPTASLMRKNGTETQKRTLHLRDMSGRSVELTLWGNFCNDDGLRLQHMCDSGVF 417 (834)
Q Consensus 341 ~i~dI~~---~~~~~~vDVIGvV~~V~~~~~i~~k~g~~~~kr~i~L~D~s~~si~vtLWg~~a~~~~~~l~~~~~~~~~ 417 (834)
.|++|.+ ...-.-||++|+|+.|. .+.| ..-.+.|.|....-+-|.+|++...-- ++++ -.++
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------KKQG---FQPLVYLSDECHNLLAIKFWTGLNQYG---YEDI--LKPG 70 (143)
T ss_dssp -CGGGGSTT--TCCCEEEEEEEEEEEE--------TT---S--EEEEE-TTS-EEEEEESS----------SS-----TT
T ss_pred chhhhcCcccCCCccccceEEEEEEEE------ecCC---CceeEEeecCCccEEEEEeccCccccc---hhhh--cCcc
Confidence 4455554 23456899999999992 1122 122378899999899999999876321 1122 1367
Q ss_pred cEEEEEEEEEe-ec-CCe-EEEeecceEEEEcCCc
Q 003281 418 PILAVKAGRVS-DF-NGK-VVGTISTTQLFIEPDF 449 (834)
Q Consensus 418 ~Vv~ik~~rV~-~f-~G~-~Ls~~~~S~i~inPd~ 449 (834)
.+||+.+...+ +. .+. .+-.+.-|.+.-||..
T Consensus 71 ~liA~SNLqwR~~s~s~iP~~~A~d~S~FS~nPK~ 105 (143)
T PF09104_consen 71 SLIAASNLQWRPESTSGIPTLFATDLSVFSANPKE 105 (143)
T ss_dssp -EEEEEEEEE-S-TTSSS-EEEEECCEEEESS-SS
T ss_pred eEEEEeeeEeecccccCCCeeEeccceeeecCccH
Confidence 89999887664 22 333 5666777888888853
No 99
>PRK07772 single-stranded DNA-binding protein; Provisional
Probab=81.96 E-value=7.9 Score=39.33 Aligned_cols=64 Identities=20% Similarity=0.259 Sum_probs=48.1
Q ss_pred CCceEEEEEEEEeccceeecCCCCCcceEEEEEe--------------eCCCCEEEEEEechHHHhhhhccCcCcEEEEe
Q 003281 229 MGKWTIKARVTAKGELRHYNNQRGDGKVFHFDLL--------------DSDGGEIRVTCFNAVADQFYHQVEAGKIYLVS 294 (834)
Q Consensus 229 ~~~w~I~aRV~~Ks~lr~~~n~~g~Gk~f~~~L~--------------De~g~~I~at~f~~~~d~f~~~l~eG~vy~is 294 (834)
.+..+|.+|++..-++|...+- -.+.+|.|+ |.+..-|++++|+.+++.+.+.|+.|+-+.|.
T Consensus 4 ~~~VtLiGrL~~DPElR~t~sG---~~va~FrVAv~~r~~~~~~g~~~d~~t~fi~V~~Wg~~Ae~va~~L~KGd~V~V~ 80 (186)
T PRK07772 4 DTTITVVGNLTADPELRFTPSG---AAVANFTVASTPRTFDRQTNEWKDGEALFLRCSIWRQAAENVAESLTKGMRVIVT 80 (186)
T ss_pred cCEEEEEEEeCCCCeEEEcCCC---CEEEEEEEEecCcceecCCCcEeccCceEEEEEEecHHHHHHHHhcCCCCEEEEE
Confidence 3567888899888888876531 245566554 11234679999999999999999999999997
Q ss_pred e
Q 003281 295 R 295 (834)
Q Consensus 295 ~ 295 (834)
.
T Consensus 81 G 81 (186)
T PRK07772 81 G 81 (186)
T ss_pred E
Confidence 5
No 100
>cd04493 BRCA2DBD_OB1 BRCA2DBD_OB1: A subfamily of OB folds corresponding to the first OB fold (OB1) 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). BRCA2DBD OB1 binds DNA weakly.
Probab=81.25 E-value=2.4 Score=38.35 Aligned_cols=38 Identities=29% Similarity=0.381 Sum_probs=34.8
Q ss_pred eEEEEEcccccccccccccchhhhhhcCCcccccEEEE
Q 003281 26 RFRMVLSDGSRSQQGMLATQRNELVTSGLLQIGSVVRL 63 (834)
Q Consensus 26 Ryrl~lSDG~~~~~~mLatqln~lv~~g~l~~gsiv~l 63 (834)
-=.+-|+||=|.+++.|...|+.+|++|.|+.|.-++|
T Consensus 22 ~~~lEltDGWYsi~a~lD~~L~~~l~~gkl~vGqKL~i 59 (100)
T cd04493 22 MPIIELTDGWYSIRAQLDPPLTNLVRKGKLRVGQKLRI 59 (100)
T ss_pred ccEEEEecCeEEEEEEeCHHHHHHHHcCCeecccEEEE
Confidence 45799999999999999999999999999999987766
No 101
>PF14392 zf-CCHC_4: Zinc knuckle
Probab=81.07 E-value=0.56 Score=36.75 Aligned_cols=18 Identities=44% Similarity=1.143 Sum_probs=16.4
Q ss_pred ccccccCccCccCCCCCC
Q 003281 742 QSCSSCGAVGHSSMNCPS 759 (834)
Q Consensus 742 ~~C~~Cg~~GH~a~~Cp~ 759 (834)
..|+.||..||..++||.
T Consensus 32 ~~C~~C~~~gH~~~~C~k 49 (49)
T PF14392_consen 32 RFCFHCGRIGHSDKECPK 49 (49)
T ss_pred hhhcCCCCcCcCHhHcCC
Confidence 389999999999999983
No 102
>PF14392 zf-CCHC_4: Zinc knuckle
Probab=81.02 E-value=0.58 Score=36.64 Aligned_cols=18 Identities=33% Similarity=1.089 Sum_probs=16.3
Q ss_pred CcCcccCCCCccCCCCCC
Q 003281 786 SECYKCHKTGHWARDCPS 803 (834)
Q Consensus 786 ~~Cy~Cg~~GH~ardCp~ 803 (834)
..|++||..||.+++||.
T Consensus 32 ~~C~~C~~~gH~~~~C~k 49 (49)
T PF14392_consen 32 RFCFHCGRIGHSDKECPK 49 (49)
T ss_pred hhhcCCCCcCcCHhHcCC
Confidence 479999999999999983
No 103
>PLN02850 aspartate-tRNA ligase
Probab=80.93 E-value=12 Score=44.35 Aligned_cols=97 Identities=18% Similarity=0.185 Sum_probs=66.5
Q ss_pred CCceeccccCCCC--CceEEEEEEEEeccceeecCCCCCcceEEEEEeeCCCCEEEEEEech------HHHhhhhccCcC
Q 003281 217 SRIIPIAALNPYM--GKWTIKARVTAKGELRHYNNQRGDGKVFHFDLLDSDGGEIRVTCFNA------VADQFYHQVEAG 288 (834)
Q Consensus 217 ~~~~pI~~L~p~~--~~w~I~aRV~~Ks~lr~~~n~~g~Gk~f~~~L~De~g~~I~at~f~~------~~d~f~~~l~eG 288 (834)
..++.|.+|++.. ...+|+|||.+ +|. .|++.-++|.|. ++.|++++... .+-+|...|..|
T Consensus 67 ~~~~~i~~l~~~~~g~~V~v~Grv~~---~R~------~gk~~Fl~Lrd~-~~~iQ~v~~~~~~~~~~~~~~~~~~l~~e 136 (530)
T PLN02850 67 REWTDVSDLGEELAGSEVLIRGRVHT---IRG------KGKSAFLVLRQS-GFTVQCVVFVSEVTVSKGMVKYAKQLSRE 136 (530)
T ss_pred ceEeEhhhcchhhCCCEEEEEEEEEE---Ecc------CCCeEEEEEEeC-CcCEEEEEECCccccCHHHHHHHhCCCCC
Confidence 4678999998743 57889999964 333 367766778886 68999998643 344567789999
Q ss_pred cEEEEeeeEEecCCcccccCCCeEEEEEccCccEEE
Q 003281 289 KIYLVSRGSLKPAQKNFNHLHNDLEIFLDMTSMVQL 324 (834)
Q Consensus 289 ~vy~is~~~V~~a~~~~~~~~~~yeI~f~~~T~I~~ 324 (834)
+++.|.+.-+++.. ..+....++||....-..|..
T Consensus 137 s~V~V~G~v~~~~~-~~~~~t~~~El~~~~i~vls~ 171 (530)
T PLN02850 137 SVVDVEGVVSVPKK-PVKGTTQQVEIQVRKIYCVSK 171 (530)
T ss_pred CEEEEEEEEEccCc-CCCCCCccEEEEEeEEEEEeC
Confidence 99999875554432 222233489998865444443
No 104
>KOG4757 consensus Predicted telomere binding protein [General function prediction only]
Probab=80.91 E-value=4.9 Score=45.00 Aligned_cols=74 Identities=20% Similarity=0.344 Sum_probs=58.0
Q ss_pred CCceeeEEEEEEEecCCeeEEccCCceeeEEEEEEec--cCCcEEEEEEcCCccchhhhhhhhcccCCCccEEEEEEEEE
Q 003281 350 NNSVVDLIGVVSYISPTASLMRKNGTETQKRTLHLRD--MSGRSVELTLWGNFCNDDGLRLQHMCDSGVFPILAVKAGRV 427 (834)
Q Consensus 350 ~~~~vDVIGvV~~V~~~~~i~~k~g~~~~kr~i~L~D--~s~~si~vtLWg~~a~~~~~~l~~~~~~~~~~Vv~ik~~rV 427 (834)
.+.+|++||+|++..|...-. |+. ..-.+.|+| .|+..+.|-|+....+++... ...+.+|.+...++
T Consensus 19 ~~tiVNl~GiVkef~pp~qs~---g~D-~~~tv~IvDp~~ss~gLtv~lfSkt~edLP~I------k~~GDiillhRiKi 88 (522)
T KOG4757|consen 19 KNTIVNLIGIVKEFTPPRQSL---GKD-WVCTVYIVDPDYSSIGLTVHLFSKTGEDLPVI------KQVGDIILLHRIKI 88 (522)
T ss_pred cCcEEEEEEEEEeccChhhcc---CCc-eEEEEEEeCCCCCCCCcEEEEecCchhhCccc------cccCcEEEEEEEEE
Confidence 578999999999999876432 333 457889999 677779999999988876532 23578999999999
Q ss_pred eecCCe
Q 003281 428 SDFNGK 433 (834)
Q Consensus 428 ~~f~G~ 433 (834)
..|+.+
T Consensus 89 q~y~~r 94 (522)
T KOG4757|consen 89 QSYRDR 94 (522)
T ss_pred EEhhhh
Confidence 988865
No 105
>KOG0851 consensus Single-stranded DNA-binding replication protein A (RPA), large (70 kD) subunit and related ssDNA-binding proteins [Replication, recombination and repair]
Probab=80.73 E-value=9.7 Score=39.97 Aligned_cols=66 Identities=14% Similarity=0.135 Sum_probs=47.5
Q ss_pred CeeeeCCCCCcCCCCcCcccccCCCCceecCCCCCccccceEEEEEEEEEEeCCCeEEEEEehHHHHHHhCCCHHHH
Q 003281 517 NFCYTACPIMIGDRPCNKKVMNNGDGRWHCDRCDQSVVECDYRYILQFQIQDHTGLTWVTAFQECAEEIMGMSAKDL 593 (834)
Q Consensus 517 ~~~Y~aC~~~~~~~~C~KKv~~~~dg~~~CekC~~~~~~~~~ry~l~~~i~D~Tg~~~~~~F~e~ae~llG~sA~el 593 (834)
.|+|..|. .|+| .......+.|+.|+....+...+|.+.....+.++. ..|......+.|.++..+
T Consensus 159 ~~~~~~~~------~~~~--~~~~~~~~~c~~~~~~~~~~~~~~~l~~~~~~~~~~---l~~~~~~~~~~G~~~~~~ 224 (246)
T KOG0851|consen 159 DGFYLTFK------ICNK--SKFSKPVLWCEACGEQATDFGRKRSLGGGVIVIAPE---LLFWKIWRYFDGKNVRIV 224 (246)
T ss_pred ceEEEEEe------eccc--ccccCceEEehhhcchHHhhhhheEecCCcEEccch---heeecccccccCCchhee
Confidence 57888898 5776 111223589999998777776668888888888877 677777777777665544
No 106
>PF15288 zf-CCHC_6: Zinc knuckle
Probab=80.72 E-value=0.88 Score=33.87 Aligned_cols=19 Identities=42% Similarity=1.038 Sum_probs=16.4
Q ss_pred cccccCccCccC--CCCCCCC
Q 003281 743 SCSSCGAVGHSS--MNCPSIM 761 (834)
Q Consensus 743 ~C~~Cg~~GH~a--~~Cp~~~ 761 (834)
.|.+||+.||++ +.||-..
T Consensus 3 kC~~CG~~GH~~t~k~CP~~~ 23 (40)
T PF15288_consen 3 KCKNCGAFGHMRTNKRCPMYC 23 (40)
T ss_pred cccccccccccccCccCCCCC
Confidence 799999999987 7898755
No 107
>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=80.63 E-value=25 Score=32.18 Aligned_cols=76 Identities=24% Similarity=0.371 Sum_probs=49.8
Q ss_pred eEEEEEEEEeccceeecCCCCCcceEEEEEeeCCCCEEEEEEech-----HHHhhhhccCcCcEEEEeeeEEecCCcccc
Q 003281 232 WTIKARVTAKGELRHYNNQRGDGKVFHFDLLDSDGGEIRVTCFNA-----VADQFYHQVEAGKIYLVSRGSLKPAQKNFN 306 (834)
Q Consensus 232 w~I~aRV~~Ks~lr~~~n~~g~Gk~f~~~L~De~g~~I~at~f~~-----~~d~f~~~l~eG~vy~is~~~V~~a~~~~~ 306 (834)
-+|++||.+ +|. .|++.-++|.|. ++.|++++... ...+|...|..|+++.+.+.-++...
T Consensus 2 v~v~GwV~~---~R~------~g~~~Fi~lrd~-~~~lQ~v~~~~~~~~~~~~~~~~~l~~g~~V~v~G~v~~~~~---- 67 (108)
T cd04322 2 VSVAGRIMS---KRG------SGKLSFADLQDE-SGKIQVYVNKDDLGEEEFEDFKKLLDLGDIIGVTGTPFKTKT---- 67 (108)
T ss_pred EEEEEEEEE---Eec------CCCeEEEEEEEC-CeEEEEEEECCCCCHHHHHHHHhcCCCCCEEEEEEEEEecCC----
Confidence 367888864 343 367777889997 58999988643 23455555999999999774443222
Q ss_pred cCCCeEEEEEccCccEEE
Q 003281 307 HLHNDLEIFLDMTSMVQL 324 (834)
Q Consensus 307 ~~~~~yeI~f~~~T~I~~ 324 (834)
..+||....-..+.+
T Consensus 68 ---g~~El~~~~~~ils~ 82 (108)
T cd04322 68 ---GELSIFVKEFTLLSK 82 (108)
T ss_pred ---CCEEEEeCEeEEeec
Confidence 458887654344433
No 108
>PRK07459 single-stranded DNA-binding protein; Provisional
Probab=79.96 E-value=13 Score=34.95 Aligned_cols=64 Identities=17% Similarity=0.269 Sum_probs=52.0
Q ss_pred CCceEEEEEEEEeccceeecCCCCCcceEEEEEe------eCCCCEEEEEEechHHHhhhhccCcCcEEEEee
Q 003281 229 MGKWTIKARVTAKGELRHYNNQRGDGKVFHFDLL------DSDGGEIRVTCFNAVADQFYHQVEAGKIYLVSR 295 (834)
Q Consensus 229 ~~~w~I~aRV~~Ks~lr~~~n~~g~Gk~f~~~L~------De~g~~I~at~f~~~~d~f~~~l~eG~vy~is~ 295 (834)
++...|.+|+++--++|.+.+ | ..+.+|.|+ |++.+=|.+++|+.+++.+.+.|+.|+-+.|.+
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--G-SVVCNLTLAVNRRSRDDEPDWFNLEIWGKTAQVAADYVKKGSLIGITG 72 (121)
T ss_pred ccEEEEEEEccCCCEEEEcCC--C-CEEEEEEEEecccccCCCceEEEEEEehHHHHHHHHHcCCCCEEEEEE
Confidence 467889999999888887653 2 257777775 234678999999999999999999999999976
No 109
>PRK08763 single-stranded DNA-binding protein; Provisional
Probab=79.64 E-value=8.3 Score=38.39 Aligned_cols=64 Identities=14% Similarity=0.235 Sum_probs=50.3
Q ss_pred CCceEEEEEEEEeccceeecCCCCCcceEEEEEe------eCCCC------EEEEEEechHHHhhhhccCcCcEEEEee
Q 003281 229 MGKWTIKARVTAKGELRHYNNQRGDGKVFHFDLL------DSDGG------EIRVTCFNAVADQFYHQVEAGKIYLVSR 295 (834)
Q Consensus 229 ~~~w~I~aRV~~Ks~lr~~~n~~g~Gk~f~~~L~------De~g~------~I~at~f~~~~d~f~~~l~eG~vy~is~ 295 (834)
+++..|.+||.+--+||...+ | ..+.+|.|+ |++|. -+++++|+.+++...+.|+.|+.++|..
T Consensus 5 ~Nkv~LiGrLg~DPelr~t~~--G-~~va~fsVA~~~~~k~~~G~~~e~t~w~~Vv~fgk~Ae~v~~~L~KGs~V~VeG 80 (164)
T PRK08763 5 INKVILVGNLGNDPDIKYTQS--G-MTITRISLATTSVRKDREGNTQERTEWHRVKFFGKLGEIAGEYLRKGSQCYIEG 80 (164)
T ss_pred ceEEEEEEEecCCCeEEEcCC--C-CeEEEEEEEeccceecCCCCeeccceEEEEEEehHHHHHHHHhcCCCCEEEEEE
Confidence 678999999999777876543 2 357677664 43332 3899999999999999999999999976
No 110
>PRK08486 single-stranded DNA-binding protein; Provisional
Probab=79.57 E-value=10 Score=38.37 Aligned_cols=64 Identities=19% Similarity=0.223 Sum_probs=49.3
Q ss_pred CCceEEEEEEEEeccceeecCCCCCcceEEEEEe------eC------CCCEEEEEEechHHHhhhhccCcCcEEEEee
Q 003281 229 MGKWTIKARVTAKGELRHYNNQRGDGKVFHFDLL------DS------DGGEIRVTCFNAVADQFYHQVEAGKIYLVSR 295 (834)
Q Consensus 229 ~~~w~I~aRV~~Ks~lr~~~n~~g~Gk~f~~~L~------De------~g~~I~at~f~~~~d~f~~~l~eG~vy~is~ 295 (834)
+++..|.+|+++--++|...+ | -.+.+|.|+ ++ +..-|.+++|+.+++.+...|+.|+-+.|..
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--G-SAIATIGLATSRRFKKQDGEKGEEVCFIDIRLFGRTAEIANQYLSKGSKVLIEG 77 (182)
T ss_pred eeEEEEEEEecCCCEEEECCC--C-CEEEEEEEEEecceecCCCCCcccceEEEEEEEhHHHHHHHHHcCCCCEEEEEE
Confidence 367789999999888887753 2 245566552 22 3467899999999999999999999999976
No 111
>PRK08182 single-stranded DNA-binding protein; Provisional
Probab=79.47 E-value=12 Score=36.69 Aligned_cols=65 Identities=17% Similarity=0.296 Sum_probs=50.7
Q ss_pred CCceEEEEEEEEeccceeecCCCCCc---ceEEEEEe------eCCC-------CEEEEEEechHHHhhhhccCcCcEEE
Q 003281 229 MGKWTIKARVTAKGELRHYNNQRGDG---KVFHFDLL------DSDG-------GEIRVTCFNAVADQFYHQVEAGKIYL 292 (834)
Q Consensus 229 ~~~w~I~aRV~~Ks~lr~~~n~~g~G---k~f~~~L~------De~g-------~~I~at~f~~~~d~f~~~l~eG~vy~ 292 (834)
++.+.|.+|+..--++|.+.+ |.- .+.+|.|. +.+| .-|.+++|+.+++.+...|+.|+-+.
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 478899999999888888753 211 27888874 2222 24889999999999999999999999
Q ss_pred Eee
Q 003281 293 VSR 295 (834)
Q Consensus 293 is~ 295 (834)
|.+
T Consensus 80 V~G 82 (148)
T PRK08182 80 VEG 82 (148)
T ss_pred EEE
Confidence 986
No 112
>PRK06958 single-stranded DNA-binding protein; Provisional
Probab=79.27 E-value=11 Score=38.22 Aligned_cols=64 Identities=20% Similarity=0.237 Sum_probs=49.2
Q ss_pred CCceEEEEEEEEeccceeecCCCCCcceEEEEEe------eC-------CCCEEEEEEechHHHhhhhccCcCcEEEEee
Q 003281 229 MGKWTIKARVTAKGELRHYNNQRGDGKVFHFDLL------DS-------DGGEIRVTCFNAVADQFYHQVEAGKIYLVSR 295 (834)
Q Consensus 229 ~~~w~I~aRV~~Ks~lr~~~n~~g~Gk~f~~~L~------De-------~g~~I~at~f~~~~d~f~~~l~eG~vy~is~ 295 (834)
+++.+|.+||++--++|...+ + ..+.+|.|+ |. +..-+.+++|+.+++.+.+.|+.|+.++|..
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--G-DAVANIRLATTDRYKDKASGEFKEATEWHRVAFFGRLAEIVGEYLKKGSSVYIEG 80 (182)
T ss_pred ccEEEEEEEecCCCeEEEcCC--C-CEEEEEEEEeccccccccCCcccccceEEEEEEehHHHHHHHHHhCCCCEEEEEE
Confidence 467889999998888887653 2 246556553 32 2356899999999999999999999999986
No 113
>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=79.15 E-value=4.9 Score=35.72 Aligned_cols=53 Identities=19% Similarity=0.171 Sum_probs=38.2
Q ss_pred EEEEEEEEeccceeecCCCCCcceEEEEEeeCCCCEEEEEEechHHH---hhhhccCcCcEEEEee
Q 003281 233 TIKARVTAKGELRHYNNQRGDGKVFHFDLLDSDGGEIRVTCFNAVAD---QFYHQVEAGKIYLVSR 295 (834)
Q Consensus 233 ~I~aRV~~Ks~lr~~~n~~g~Gk~f~~~L~De~g~~I~at~f~~~~d---~f~~~l~eG~vy~is~ 295 (834)
++.+.|.++... +..+.+.|.|. +|.|.|.+|...-+ .-.+.+++|+++.+..
T Consensus 3 ~~vG~V~~~~~~---------~~~~~~tL~D~-TG~I~~~~W~~~~~~~~~~~~~~~~g~~v~v~G 58 (95)
T cd04478 3 TLVGVVRNVEEQ---------STNITYTIDDG-TGTIEVRQWLDDDNDDSSEVEPIEEGTYVRVFG 58 (95)
T ss_pred EEEEEEEeeeEc---------ccEEEEEEECC-CCcEEEEEeCCCCCcccccccccccCCEEEEEE
Confidence 466677654321 35699999997 47999999986543 3567799999887754
No 114
>PRK06293 single-stranded DNA-binding protein; Provisional
Probab=79.02 E-value=13 Score=36.89 Aligned_cols=64 Identities=20% Similarity=0.133 Sum_probs=51.0
Q ss_pred CCceEEEEEEEEeccceeecCCCCCcceEEEEEee-------CCCCEEEEEEechHHHhhhhccCcCcEEEEee
Q 003281 229 MGKWTIKARVTAKGELRHYNNQRGDGKVFHFDLLD-------SDGGEIRVTCFNAVADQFYHQVEAGKIYLVSR 295 (834)
Q Consensus 229 ~~~w~I~aRV~~Ks~lr~~~n~~g~Gk~f~~~L~D-------e~g~~I~at~f~~~~d~f~~~l~eG~vy~is~ 295 (834)
++..+|.+|+.+--++|...+ | ..+.+|.|+= ++..-|++++|+..++.....|+.|+-+.|..
T Consensus 1 MN~V~LiGrLg~DPElR~t~s--G-~~v~~FsLAvn~~~~~~~~T~wi~v~awg~~Ae~v~~yL~KG~~V~VeG 71 (161)
T PRK06293 1 MMFGYIVGRLGADPEERMTSK--G-KRVVVLRLGVKSRVGSKDETVWCRCNIWGNRYDKMLPYLKKGSGVIVAG 71 (161)
T ss_pred CeEEEEEEEecCCCeEEEcCC--C-CEEEEEEEEEeCCCCCccceEEEEEEEEhHHHHHHHHhCCCCCEEEEEE
Confidence 467889999999888887643 2 3577787752 23567999999999999999999999999986
No 115
>COG5235 RFA2 Single-stranded DNA-binding replication protein A (RPA), medium (30 kD) subunit [DNA replication, recombination, and repair]
Probab=78.93 E-value=8.2 Score=39.20 Aligned_cols=70 Identities=23% Similarity=0.399 Sum_probs=41.9
Q ss_pred eeeEEEEEEEecCCeeEEccCCceeeEEEEEEeccCCcEEEEEEcCCccchhhhhhhhcccCCCccEEEEEEEEEeecCC
Q 003281 353 VVDLIGVVSYISPTASLMRKNGTETQKRTLHLRDMSGRSVELTLWGNFCNDDGLRLQHMCDSGVFPILAVKAGRVSDFNG 432 (834)
Q Consensus 353 ~vDVIGvV~~V~~~~~i~~k~g~~~~kr~i~L~D~s~~si~vtLWg~~a~~~~~~l~~~~~~~~~~Vv~ik~~rV~~f~G 432 (834)
-|-++|+|.++.... .-..++|.|.+| +|+|+.|-..+.++.. -.+-..+..|. .+.-++.|+|
T Consensus 68 ~V~fVGvvrni~~~t----------tn~~~~iEDGTG-~Ievr~W~~~~~~~e~----~~d~~~~~yvk-V~G~lk~F~G 131 (258)
T COG5235 68 NVQFVGVVRNIKTST----------TNSMFVIEDGTG-SIEVRFWPGNSYEEEQ----CKDLEEQNYVK-VNGSLKTFNG 131 (258)
T ss_pred eEEEEEEEEeeeecc----------cceEEEEecCCc-eEEEEecCCCchHHHh----ccccccccEEE-EecceeeeCC
Confidence 355666666654332 335688999999 8999999987754311 01111222332 3456789999
Q ss_pred e-EEEee
Q 003281 433 K-VVGTI 438 (834)
Q Consensus 433 ~-~Ls~~ 438 (834)
| +++..
T Consensus 132 K~~I~~~ 138 (258)
T COG5235 132 KRSISAS 138 (258)
T ss_pred eeEEehh
Confidence 6 66543
No 116
>PRK05673 dnaE DNA polymerase III subunit alpha; Validated
Probab=78.70 E-value=6.2 Score=50.94 Aligned_cols=82 Identities=28% Similarity=0.350 Sum_probs=56.0
Q ss_pred cccccccccccCCCceeeEEEEEEEecCCeeEEccCCceeeEEEEEEeccCCcEEEEEEcCCccchhhhhhhhcccCCCc
Q 003281 338 HFRPINDVEGMENNSVVDLIGVVSYISPTASLMRKNGTETQKRTLHLRDMSGRSVELTLWGNFCNDDGLRLQHMCDSGVF 417 (834)
Q Consensus 338 ~f~~i~dI~~~~~~~~vDVIGvV~~V~~~~~i~~k~g~~~~kr~i~L~D~s~~si~vtLWg~~a~~~~~~l~~~~~~~~~ 417 (834)
...++.+|.....+..|.++|+|+++... ++|+|+. .--++|.|.+| ++++++|.+..+.....|. .+
T Consensus 964 ~~~~~~~l~~~~~g~~V~v~G~I~~vk~~---~TKkG~~--mafltLeD~TG-~iEvviFp~~ye~~~~~L~------~g 1031 (1135)
T PRK05673 964 RDTRLADLEPTEGGSVVTVAGLVVSVRRR---VTKRGNK--MAIVTLEDLSG-RIEVMLFSEALEKYRDLLE------ED 1031 (1135)
T ss_pred CCcCHHHHhccccCceEEEEEEEEEEEec---ccCCCCe--EEEEEEEeCCC-cEEEEECHHHHHHHHHHhc------cC
Confidence 34566666544456789999999988654 4667763 56789999999 7999999976554433332 45
Q ss_pred cEEEEEEEEEeecCC
Q 003281 418 PILAVKAGRVSDFNG 432 (834)
Q Consensus 418 ~Vv~ik~~rV~~f~G 432 (834)
.+|.+++ +|..+.+
T Consensus 1032 ~iV~V~G-kVe~~~~ 1045 (1135)
T PRK05673 1032 RIVVVKG-QVSFDDG 1045 (1135)
T ss_pred CEEEEEE-EEEecCC
Confidence 6776655 5554444
No 117
>PRK07275 single-stranded DNA-binding protein; Provisional
Probab=78.41 E-value=6.7 Score=38.95 Aligned_cols=64 Identities=19% Similarity=0.240 Sum_probs=51.1
Q ss_pred CCceEEEEEEEEeccceeecCCCCCcceEEEEEe------eC----CCCEEEEEEechHHHhhhhccCcCcEEEEee
Q 003281 229 MGKWTIKARVTAKGELRHYNNQRGDGKVFHFDLL------DS----DGGEIRVTCFNAVADQFYHQVEAGKIYLVSR 295 (834)
Q Consensus 229 ~~~w~I~aRV~~Ks~lr~~~n~~g~Gk~f~~~L~------De----~g~~I~at~f~~~~d~f~~~l~eG~vy~is~ 295 (834)
+++..|.+|+++--++|...+ | ..+.+|.|+ ++ +..-|++++|+.+++.+...|+.|+-+.|..
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--N-VAVATFTLAVNRTFKSQNGEREADFINCVIWRQQAENLANWAKKGALIGVTG 75 (162)
T ss_pred eeEEEEEEEECCCCeEEECCC--C-CEEEEEEEEEcCceecCCCCEeeeEEEEEEEcHHHHHHHHHcCCCCEEEEEE
Confidence 467889999999888987653 2 256677774 22 2467999999999999999999999999975
No 118
>PRK06863 single-stranded DNA-binding protein; Provisional
Probab=78.32 E-value=14 Score=36.87 Aligned_cols=64 Identities=17% Similarity=0.181 Sum_probs=50.5
Q ss_pred CCceEEEEEEEEeccceeecCCCCCcceEEEEEe------eCC-------CCEEEEEEechHHHhhhhccCcCcEEEEee
Q 003281 229 MGKWTIKARVTAKGELRHYNNQRGDGKVFHFDLL------DSD-------GGEIRVTCFNAVADQFYHQVEAGKIYLVSR 295 (834)
Q Consensus 229 ~~~w~I~aRV~~Ks~lr~~~n~~g~Gk~f~~~L~------De~-------g~~I~at~f~~~~d~f~~~l~eG~vy~is~ 295 (834)
+++..|.+|+...-++|.+.+. ..+.+|.|. |.+ ..-+++++|+..++.+...|+.|+-++|..
T Consensus 4 ~N~V~LiGrLg~DPElR~t~nG---~~va~fsVAvn~~~~d~~~Ge~~e~t~w~~Vv~fgk~AE~v~~~LkKGs~V~VeG 80 (168)
T PRK06863 4 INKVIIVGHLGNDPEIRTMPNG---EAVANISVATSESWTDKNTGERREVTEWHRIVFYRRQAEVAGEYLRKGSQVYVEG 80 (168)
T ss_pred ccEEEEEEEcCCCCEEEEcCCC---CEEEEEEEEecCcccccCCCcccccceEEEEEEEhHHHHHHHHHCCCCCEEEEEE
Confidence 5788999999998888887642 256666664 221 235899999999999999999999999986
No 119
>PF10341 TPP1: Shelterin complex subunit, TPP1/ACD; InterPro: IPR019437 EST3 is a component of the telomerase holoenzyme, involved in telomere replication. It has been demonstrated that Est3 dimerises and binds to DNA and RNA. Furthermore, Est3 stimulates the dissociation of RNA/DNA hetero-duplexes [, ]. ; GO: 0042162 telomeric DNA binding, 0007004 telomere maintenance via telomerase, 0032508 DNA duplex unwinding, 0000781 chromosome, telomeric region, 0005697 telomerase holoenzyme complex; PDB: 2I46_B.
Probab=77.81 E-value=3.1 Score=38.09 Aligned_cols=47 Identities=13% Similarity=0.162 Sum_probs=27.8
Q ss_pred ceEEEEEcccccccccccccchhhhhh-cCC-----cccccEEEEceeeeecc
Q 003281 25 QRFRMVLSDGSRSQQGMLATQRNELVT-SGL-----LQIGSVVRLTKFTCNVI 71 (834)
Q Consensus 25 ~Ryrl~lSDG~~~~~~mLatqln~lv~-~g~-----l~~gsiv~l~~~~~~~v 71 (834)
.-.+++|||++|++.|.|+.+-=...+ +.. =-+|++|+|++|.+...
T Consensus 41 ~~i~a~lsDs~~~I~a~ft~eai~~fe~~~~~~~t~~t~g~li~I~~~~l~~~ 93 (106)
T PF10341_consen 41 GAITALLSDSTHQILAIFTREAIENFEREEKKRITSSTKGCLILIKDFNLVFQ 93 (106)
T ss_dssp S-EEEEEE-SS-EEEEEE-HHHHHTS--TTS-SSSTT-TTEEEEEEEEEEEEE
T ss_pred CcEEEEEEcCCeEEEEEECHHHHHHHHHhccCcccccCCceEEEEEEEEEEEE
Confidence 468999999999999999643222211 111 23678888888876555
No 120
>PRK13480 3'-5' exoribonuclease YhaM; Provisional
Probab=77.35 E-value=13 Score=40.97 Aligned_cols=78 Identities=27% Similarity=0.375 Sum_probs=52.4
Q ss_pred ccccCCCceeeEEEEEEEecCCeeEEccCCceeeEEEEEEeccCCcEEEEEEcCCccchhhhhhhhcccCCCccEEEEEE
Q 003281 345 VEGMENNSVVDLIGVVSYISPTASLMRKNGTETQKRTLHLRDMSGRSVELTLWGNFCNDDGLRLQHMCDSGVFPILAVKA 424 (834)
Q Consensus 345 I~~~~~~~~vDVIGvV~~V~~~~~i~~k~g~~~~kr~i~L~D~s~~si~vtLWg~~a~~~~~~l~~~~~~~~~~Vv~ik~ 424 (834)
|.++..+..|+.+..|+++.-- ++|+|+ ....++|.|.|| +|+..+|+..-+. ... + ..+.||.++
T Consensus 5 i~~l~~g~~v~~~~lv~~~~~~---~~knG~--~yl~l~l~D~tG-~I~ak~W~~~~~~-~~~----~--~~g~vv~v~- 70 (314)
T PRK13480 5 IEELEVGEQVDHFLLIKSATKG---VASNGK--PFLTLILQDKSG-DIEAKLWDVSPED-EAT----Y--VPETIVHVK- 70 (314)
T ss_pred HhhcCCCCEeeEEEEEEEceee---ecCCCC--eEEEEEEEcCCc-EEEEEeCCCChhh-Hhh----c--CCCCEEEEE-
Confidence 3344457788988888876432 256776 478999999999 7999999965322 122 2 245566554
Q ss_pred EEEeecCCe-EEE
Q 003281 425 GRVSDFNGK-VVG 436 (834)
Q Consensus 425 ~rV~~f~G~-~Ls 436 (834)
++|.+|+|+ +|.
T Consensus 71 G~v~~y~g~~Ql~ 83 (314)
T PRK13480 71 GDIINYRGRKQLK 83 (314)
T ss_pred EEEEEECCcceEE
Confidence 466789995 554
No 121
>KOG0921 consensus Dosage compensation complex, subunit MLE [Transcription]
Probab=77.23 E-value=12 Score=45.88 Aligned_cols=17 Identities=24% Similarity=0.225 Sum_probs=10.3
Q ss_pred EEEEEehHHHHHHhCCC
Q 003281 573 TWVTAFQECAEEIMGMS 589 (834)
Q Consensus 573 ~~~~~F~e~ae~llG~s 589 (834)
+.+.+-.|.|-.|.|..
T Consensus 1086 IklqIshEaAAcItgLr 1102 (1282)
T KOG0921|consen 1086 IKLQISHEAAACITGLR 1102 (1282)
T ss_pred eeEeccHHHHHHHhhhH
Confidence 45555666666666654
No 122
>PF13742 tRNA_anti_2: OB-fold nucleic acid binding domain
Probab=76.40 E-value=3.1 Score=37.70 Aligned_cols=63 Identities=19% Similarity=0.276 Sum_probs=44.4
Q ss_pred CceEEEEEEEEeccceeecCCCCCcceEEEEEeeCCCCEEEEEEechHHHhhh-hccCcCcEEEEee-eEEecC
Q 003281 230 GKWTIKARVTAKGELRHYNNQRGDGKVFHFDLLDSDGGEIRVTCFNAVADQFY-HQVEAGKIYLVSR-GSLKPA 301 (834)
Q Consensus 230 ~~w~I~aRV~~Ks~lr~~~n~~g~Gk~f~~~L~De~g~~I~at~f~~~~d~f~-~~l~eG~vy~is~-~~V~~a 301 (834)
.+..|++=|+. ++.. + .| -..|+|.|++ .+|+|++|.....+.. ..+++|+-+.+.. ..+-+.
T Consensus 22 ~~vwV~GEIs~---~~~~---~-~g-h~YftLkD~~-a~i~~~~~~~~~~~i~~~~l~~G~~V~v~g~~~~y~~ 86 (99)
T PF13742_consen 22 PNVWVEGEISN---LKRH---S-SG-HVYFTLKDEE-ASISCVIFRSRARRIRGFDLKDGDKVLVRGRVSFYEP 86 (99)
T ss_pred CCEEEEEEEee---cEEC---C-Cc-eEEEEEEcCC-cEEEEEEEHHHHhhCCCCCCCCCCEEEEEEEEEEECC
Confidence 45556676653 3322 1 13 4789999976 9999999999888887 7899998877754 444333
No 123
>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=75.96 E-value=55 Score=29.90 Aligned_cols=74 Identities=18% Similarity=0.166 Sum_probs=49.3
Q ss_pred CceEEEEEEEEeccceeecCCCCCcceEEEEEeeCCCCEEEEEEechH----HHhhhhccCcCcEEEEeeeEEecCCccc
Q 003281 230 GKWTIKARVTAKGELRHYNNQRGDGKVFHFDLLDSDGGEIRVTCFNAV----ADQFYHQVEAGKIYLVSRGSLKPAQKNF 305 (834)
Q Consensus 230 ~~w~I~aRV~~Ks~lr~~~n~~g~Gk~f~~~L~De~g~~I~at~f~~~----~d~f~~~l~eG~vy~is~~~V~~a~~~~ 305 (834)
...+|++||.+ +|.. |++.-++|.|. ++.|++.+-.+. +-++...|..|+++.+.+--.+...
T Consensus 13 ~~V~v~Gwv~~---~R~~------g~~~Fi~LrD~-~g~iQ~v~~~~~~~~~~~~~~~~l~~es~V~V~G~v~~~~~--- 79 (108)
T cd04316 13 EEVTVAGWVHE---IRDL------GGIKFVILRDR-EGIVQVTAPKKKVDKELFKTVRKLSRESVISVTGTVKAEPK--- 79 (108)
T ss_pred CEEEEEEEEEe---eecc------CCeEEEEEecC-CeeEEEEEeCCCCCHHHHHHHhCCCCcCEEEEEEEEEeCCC---
Confidence 46889999965 3432 56666778887 578999887542 1123346899999999985443222
Q ss_pred ccCCCeEEEEEcc
Q 003281 306 NHLHNDLEIFLDM 318 (834)
Q Consensus 306 ~~~~~~yeI~f~~ 318 (834)
...+|||..+.
T Consensus 80 --~~~~~Ei~~~~ 90 (108)
T cd04316 80 --APNGVEIIPEE 90 (108)
T ss_pred --CCCCEEEEEeE
Confidence 13479998854
No 124
>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=75.85 E-value=16 Score=31.87 Aligned_cols=58 Identities=21% Similarity=0.299 Sum_probs=42.9
Q ss_pred eEEEEEEEEeccceeecCCCCCcceEEEEEeeCCCCEEEEEEec-hHHHhhhhccC-cCcEEEEee
Q 003281 232 WTIKARVTAKGELRHYNNQRGDGKVFHFDLLDSDGGEIRVTCFN-AVADQFYHQVE-AGKIYLVSR 295 (834)
Q Consensus 232 w~I~aRV~~Ks~lr~~~n~~g~Gk~f~~~L~De~g~~I~at~f~-~~~d~f~~~l~-eG~vy~is~ 295 (834)
-+|++.|... +.|...+ | ..+++|.|.|.+ +.|.+..|. +..+.+ +.|+ +|+|+.+..
T Consensus 2 v~i~G~Vf~~-e~re~k~--g-~~i~~~~itD~t-~Si~~K~F~~~~~~~~-~~ik~~G~~v~v~G 61 (82)
T cd04484 2 VVVEGEVFDL-EIRELKS--G-RKILTFKVTDYT-SSITVKKFLRKDEKDK-EELKSKGDWVRVRG 61 (82)
T ss_pred EEEEEEEEEE-EEEEecC--C-CEEEEEEEEcCC-CCEEEEEeccCChhHH-hhcccCCCEEEEEE
Confidence 4688888765 4566653 2 478899999975 789999998 344444 5689 999999865
No 125
>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=75.49 E-value=17 Score=32.21 Aligned_cols=61 Identities=25% Similarity=0.354 Sum_probs=44.4
Q ss_pred EEEEEEEEeccceeecCCCCCcceEEEEEe-----------eCCCCEEEEEEechHHHhhhhccCcCcEEEEeee
Q 003281 233 TIKARVTAKGELRHYNNQRGDGKVFHFDLL-----------DSDGGEIRVTCFNAVADQFYHQVEAGKIYLVSRG 296 (834)
Q Consensus 233 ~I~aRV~~Ks~lr~~~n~~g~Gk~f~~~L~-----------De~g~~I~at~f~~~~d~f~~~l~eG~vy~is~~ 296 (834)
+|.+||...-.++...+ | ..+.+|.|. +....-|.+++|++.++.+...++.|+.+.|...
T Consensus 2 ~l~G~l~~~p~~~~~~~--g-~~~~~~~v~~~~~~~~~~~~~~~~~~~~v~~~g~~a~~~~~~~~kG~~V~v~G~ 73 (100)
T cd04496 2 ILIGRLGKDPELRYTPS--G-TPVARFSLAVNRRRKDRDEEEEETDWIRVVAFGKLAENAAKYLKKGDLVYVEGR 73 (100)
T ss_pred EEEEEecCCCEEEECCC--C-CEEEEEEEEEcCceecccccccccEEEEEEEEhHHHHHHHHHhCCCCEEEEEEE
Confidence 46677777766665543 1 244444442 2356789999999999999999999999999874
No 126
>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=75.44 E-value=31 Score=29.93 Aligned_cols=74 Identities=14% Similarity=0.095 Sum_probs=46.7
Q ss_pred eEEEEEEEEeccceeecCCCCCcceEEEEEeeCCCCEEEEEEechHHH--hhhhccCcCcEEEEeeeEEecCCcccccCC
Q 003281 232 WTIKARVTAKGELRHYNNQRGDGKVFHFDLLDSDGGEIRVTCFNAVAD--QFYHQVEAGKIYLVSRGSLKPAQKNFNHLH 309 (834)
Q Consensus 232 w~I~aRV~~Ks~lr~~~n~~g~Gk~f~~~L~De~g~~I~at~f~~~~d--~f~~~l~eG~vy~is~~~V~~a~~~~~~~~ 309 (834)
-+|++||-++ |. -|++.-++|.|. ++.|++.+..+... ++...|..|+++.+.+- |....... ...
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------QKKLMFLVLRDG-TGFLQCVLSKKLVTEFYDAKSLTQESSVEVTGE-VKEDPRAK-QAP 69 (84)
T ss_pred EEEEEEEEEE---ec------CCCcEEEEEEcC-CeEEEEEEcCCcchhHHHHhcCCCcCEEEEEEE-EEECCccc-CCC
Confidence 3677888542 32 256777778897 57899988654322 23345899999999774 44332221 334
Q ss_pred CeEEEEEc
Q 003281 310 NDLEIFLD 317 (834)
Q Consensus 310 ~~yeI~f~ 317 (834)
.++||..+
T Consensus 70 ~~~Ei~~~ 77 (84)
T cd04323 70 GGYELQVD 77 (84)
T ss_pred CCEEEEEE
Confidence 57888874
No 127
>PRK07373 DNA polymerase III subunit alpha; Reviewed
Probab=75.39 E-value=6 Score=45.84 Aligned_cols=78 Identities=19% Similarity=0.230 Sum_probs=53.3
Q ss_pred cccccccccccCCCceeeEEEEEEEecCCeeEEccCCceeeEEEEEEeccCCcEEEEEEcCCccchhhhhhhhcccCCCc
Q 003281 338 HFRPINDVEGMENNSVVDLIGVVSYISPTASLMRKNGTETQKRTLHLRDMSGRSVELTLWGNFCNDDGLRLQHMCDSGVF 417 (834)
Q Consensus 338 ~f~~i~dI~~~~~~~~vDVIGvV~~V~~~~~i~~k~g~~~~kr~i~L~D~s~~si~vtLWg~~a~~~~~~l~~~~~~~~~ 417 (834)
...++++|.....+..|-|+|+|+.+... ++|+|+ ..--++|.|.+| .+++++|-+..+.....++ .+
T Consensus 267 ~~~~~~~l~~~~~~~~v~vaG~I~~ik~~---~TKkG~--~maf~~leD~tG-~ie~vvFp~~y~~~~~~l~------~~ 334 (449)
T PRK07373 267 SPINLSELEEQKEKTKVSAVVMLNEVKKI---VTKKGD--PMAFLQLEDLSG-QSEAVVFPKSYERISELLQ------VD 334 (449)
T ss_pred CCcCHHHHhcccCCCEEEEEEEEEEeEec---ccCCCC--EEEEEEEEECCC-CEEEEECHHHHHHHHHHhc------cC
Confidence 33566666544446678899999998754 466676 356789999999 6999999987766444432 34
Q ss_pred cEEEEEEEEEe
Q 003281 418 PILAVKAGRVS 428 (834)
Q Consensus 418 ~Vv~ik~~rV~ 428 (834)
.+|.+++ +|.
T Consensus 335 ~~v~v~G-~v~ 344 (449)
T PRK07373 335 ARLIIWG-KVD 344 (449)
T ss_pred CEEEEEE-EEE
Confidence 5666655 443
No 128
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=75.00 E-value=2 Score=37.53 Aligned_cols=29 Identities=28% Similarity=0.826 Sum_probs=22.8
Q ss_pred CCCCCcCCCCcCcc-cccCCCCceecCCCCCccccc
Q 003281 522 ACPIMIGDRPCNKK-VMNNGDGRWHCDRCDQSVVEC 556 (834)
Q Consensus 522 aC~~~~~~~~C~KK-v~~~~dg~~~CekC~~~~~~~ 556 (834)
.|| .|.++ |.....|.|.|.+|+..+.-.
T Consensus 37 ~Cp------~C~~~~VkR~a~GIW~C~kCg~~fAGg 66 (89)
T COG1997 37 VCP------FCGRTTVKRIATGIWKCRKCGAKFAGG 66 (89)
T ss_pred cCC------CCCCcceeeeccCeEEcCCCCCeeccc
Confidence 599 69887 455677999999999876543
No 129
>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=74.89 E-value=7.8 Score=36.61 Aligned_cols=36 Identities=6% Similarity=0.131 Sum_probs=27.5
Q ss_pred cEEEEEEcCCccchhhhhhhhcccCCCccEEEEEEEEEeecCC
Q 003281 390 RSVELTLWGNFCNDDGLRLQHMCDSGVFPILAVKAGRVSDFNG 432 (834)
Q Consensus 390 ~si~vtLWg~~a~~~~~~l~~~~~~~~~~Vv~ik~~rV~~f~G 432 (834)
.+|.||||++++.- ...+ +.+..|.|++++++....
T Consensus 60 ~ti~It~yD~H~~~-ar~l------K~GdfV~L~NVhiK~~~~ 95 (123)
T cd04498 60 LTIDILVYDNHVEL-AKSL------KPGDFVRIYNVHAKSYSS 95 (123)
T ss_pred EEEEEEEEcchHHH-HhhC------CCCCEEEEEEEEEEeccC
Confidence 78999999999863 2223 368899999999976543
No 130
>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=74.87 E-value=17 Score=36.12 Aligned_cols=65 Identities=25% Similarity=0.312 Sum_probs=48.6
Q ss_pred CCceEEEEEEEEeccceeecCCCCCcceEEEEEe------eCC------CCEEEEEEechHHHhhhhccCcCcEEEEeee
Q 003281 229 MGKWTIKARVTAKGELRHYNNQRGDGKVFHFDLL------DSD------GGEIRVTCFNAVADQFYHQVEAGKIYLVSRG 296 (834)
Q Consensus 229 ~~~w~I~aRV~~Ks~lr~~~n~~g~Gk~f~~~L~------De~------g~~I~at~f~~~~d~f~~~l~eG~vy~is~~ 296 (834)
.++.+|.+||..--++|...+ | ..+.+|.|. |++ ..-|++++|+.+++.+.+.|+.|+.+.|..-
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--G-NAVANFTLATNRRWKDQDGEWKEETEWHDIVIFGRLAEVAAQYLKKGSLVYVEGR 80 (164)
T ss_pred ccEEEEEEEeCCCCEEEECCC--C-CEEEEEEEEEcCceecCCCCEeccceEEEEEEehHHHHHHHHhCCCCCEEEEEEE
Confidence 467888899988777776643 2 234455443 222 3589999999999999999999999999873
No 131
>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=74.41 E-value=32 Score=29.87 Aligned_cols=74 Identities=18% Similarity=0.237 Sum_probs=47.6
Q ss_pred eEEEEEEEEeccceeecCCCCCcceEEEEEeeCCCCEEEEEEechHHH---hhhhccCcCcEEEEeeeEEecCCcccccC
Q 003281 232 WTIKARVTAKGELRHYNNQRGDGKVFHFDLLDSDGGEIRVTCFNAVAD---QFYHQVEAGKIYLVSRGSLKPAQKNFNHL 308 (834)
Q Consensus 232 w~I~aRV~~Ks~lr~~~n~~g~Gk~f~~~L~De~g~~I~at~f~~~~d---~f~~~l~eG~vy~is~~~V~~a~~~~~~~ 308 (834)
-+|.+||.+ +|. .|++.-++|.|. ++.+++.+-.+..+ ++...|..|+++.+.+.-.....+. ..
T Consensus 2 V~i~Gwv~~---~R~------~g~~~Fi~Lrd~-~~~iQ~v~~~~~~~~~~~~~~~l~~~s~V~v~G~~~~~~~~~--~~ 69 (85)
T cd04100 2 VTLAGWVHS---RRD------HGGLIFIDLRDG-SGIVQVVVNKEELGEFFEEAEKLRTESVVGVTGTVVKRPEGN--LA 69 (85)
T ss_pred EEEEEEEeh---hcc------CCCEEEEEEEeC-CeeEEEEEECCcChHHHHHHhCCCCCCEEEEEeEEEECCCCC--CC
Confidence 367788853 333 366666778887 58999988755322 3445699999999988544322211 23
Q ss_pred CCeEEEEEc
Q 003281 309 HNDLEIFLD 317 (834)
Q Consensus 309 ~~~yeI~f~ 317 (834)
..++||..+
T Consensus 70 ~~~~El~~~ 78 (85)
T cd04100 70 TGEIELQAE 78 (85)
T ss_pred CCCEEEEEe
Confidence 467888764
No 132
>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=74.02 E-value=18 Score=31.62 Aligned_cols=52 Identities=13% Similarity=0.054 Sum_probs=42.2
Q ss_pred eeeEEEEEEeccCCcEEEEEEcCCccchhhhhhhhcccCCCccEEEEEEEEEeecCCe
Q 003281 376 ETQKRTLHLRDMSGRSVELTLWGNFCNDDGLRLQHMCDSGVFPILAVKAGRVSDFNGK 433 (834)
Q Consensus 376 ~~~kr~i~L~D~s~~si~vtLWg~~a~~~~~~l~~~~~~~~~~Vv~ik~~rV~~f~G~ 433 (834)
+....++.|.|+.|..|..+.+.+.++.+...|+ ++.+..|.+.+|..-.+.
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 4567789999999999999999999887665554 567888988888776554
No 133
>KOG3056 consensus Protein required for S-phase initiation or completion [Cell cycle control, cell division, chromosome partitioning]
Probab=73.13 E-value=22 Score=41.54 Aligned_cols=102 Identities=9% Similarity=0.229 Sum_probs=66.5
Q ss_pred CCceecc----ccCCC---CCceEEEEEEEEeccceeecCCCCCcceEEEEEeeCCCCEEEEEEechHHHhhhhccCcCc
Q 003281 217 SRIIPIA----ALNPY---MGKWTIKARVTAKGELRHYNNQRGDGKVFHFDLLDSDGGEIRVTCFNAVADQFYHQVEAGK 289 (834)
Q Consensus 217 ~~~~pI~----~L~p~---~~~w~I~aRV~~Ks~lr~~~n~~g~Gk~f~~~L~De~g~~I~at~f~~~~d~f~~~l~eG~ 289 (834)
+..++|+ .|-+. ..+|.+.+-|+.|+.++.-.+.+ .=.++-|.-++.+ -.|..-+|++...+++. ++.|.
T Consensus 166 ~k~i~ls~~~~~l~r~~kf~~~Wvt~GvI~~K~~~K~t~~G~-~y~iwkL~dLk~~-q~vslfLFG~a~k~~wk-~k~Gt 242 (578)
T KOG3056|consen 166 RKLIRLSGKLFNLIRGPKFEENWVTMGVIVEKSDPKFTSNGN-PYSIWKLTDLKDH-QTVSLFLFGKAHKRYWK-IKLGT 242 (578)
T ss_pred CcceeehhhhhhcccCcccccCeEEEEEEeecCCcccccCCC-ceEEEEeeecCcc-ceeEEEEecHHHHHHhh-hccCc
Confidence 3445555 44332 34899999999999998766522 1123333333333 58999999998777765 99999
Q ss_pred EEEEeeeEEecCCcccccCCCeEEEEEccCccEEE
Q 003281 290 IYLVSRGSLKPAQKNFNHLHNDLEIFLDMTSMVQL 324 (834)
Q Consensus 290 vy~is~~~V~~a~~~~~~~~~~yeI~f~~~T~I~~ 324 (834)
|+-|=|+.|.+-+.- ..-.|-|.++..-.|.+
T Consensus 243 VialLNp~v~k~~~g---s~~~f~LsIds~~~ile 274 (578)
T KOG3056|consen 243 VIALLNPEVLKDRPG---SRKSFSLSIDSSKKILE 274 (578)
T ss_pred EEEEeCccccCCCCC---CcceEEEEecCccceEE
Confidence 999999988654421 11356666665544433
No 134
>PRK07274 single-stranded DNA-binding protein; Provisional
Probab=72.48 E-value=14 Score=35.34 Aligned_cols=64 Identities=22% Similarity=0.283 Sum_probs=48.6
Q ss_pred CCceEEEEEEEEeccceeecCCCCCcceEEEEEe------eCCC----CEEEEEEechHHHhhhhccCcCcEEEEee
Q 003281 229 MGKWTIKARVTAKGELRHYNNQRGDGKVFHFDLL------DSDG----GEIRVTCFNAVADQFYHQVEAGKIYLVSR 295 (834)
Q Consensus 229 ~~~w~I~aRV~~Ks~lr~~~n~~g~Gk~f~~~L~------De~g----~~I~at~f~~~~d~f~~~l~eG~vy~is~ 295 (834)
++...|.+|+..--++|...+ | ..+.+|.|+ |++| .-|++++|+.+++.+.+.|+.|+-+.|..
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 567889999988877776543 1 246666664 3322 46889999999999999999999999976
No 135
>PF14951 DUF4503: Domain of unknown function (DUF4503)
Probab=71.95 E-value=11 Score=41.44 Aligned_cols=84 Identities=18% Similarity=0.350 Sum_probs=66.9
Q ss_pred eEEEEEEEEEEecC-CeeeeCCCCCcCCCCcCc-ccc--cCCCCceecCCCCCccccceEEEEEEEEEEeC---CCeEEE
Q 003281 503 WITVSATIVYIKCD-NFCYTACPIMIGDRPCNK-KVM--NNGDGRWHCDRCDQSVVECDYRYILQFQIQDH---TGLTWV 575 (834)
Q Consensus 503 ~~~v~atI~~I~~d-~~~Y~aC~~~~~~~~C~K-Kv~--~~~dg~~~CekC~~~~~~~~~ry~l~~~i~D~---Tg~~~~ 575 (834)
...|.++|+.++.+ .+.+|.|. .|.. |+. .+..|.|+|..|.+.+..|..|..|.+-+.=. -.++.+
T Consensus 256 iCsvqG~VvgVdE~TAfSWPvCd------~CGn~rLe~~pe~rg~~~C~~Cs~~V~sP~~r~~LeVfl~Cps~p~ctvKV 329 (389)
T PF14951_consen 256 ICSVQGTVVGVDESTAFSWPVCD------RCGNGRLEQSPEDRGAFSCGDCSRVVTSPVLRMHLEVFLDCPSRPQCTVKV 329 (389)
T ss_pred eEEEeeEEEEecCcccccCcccc------ccCCccceeCccCCCceeccchhhhccCcceeeeEEEEEeCCCCCCceEEE
Confidence 46899999999887 68889998 6864 553 24457899999999999999999999988732 246789
Q ss_pred EEehHHHHHHhCCCHHH
Q 003281 576 TAFQECAEEIMGMSAKD 592 (834)
Q Consensus 576 ~~F~e~ae~llG~sA~e 592 (834)
-+.++.-..||...|.|
T Consensus 330 KL~q~sIsslL~~aa~e 346 (389)
T PF14951_consen 330 KLLQRSISSLLMSAASE 346 (389)
T ss_pred EEhHHHHHHHHhhhhcc
Confidence 89999888888776654
No 136
>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=71.27 E-value=12 Score=33.41 Aligned_cols=48 Identities=17% Similarity=0.099 Sum_probs=39.0
Q ss_pred EEEEeccCCcEEEEEEcCCccchhhhhhhhcccCCCccEEEEEEEEEeecCCeE
Q 003281 381 TLHLRDMSGRSVELTLWGNFCNDDGLRLQHMCDSGVFPILAVKAGRVSDFNGKV 434 (834)
Q Consensus 381 ~i~L~D~s~~si~vtLWg~~a~~~~~~l~~~~~~~~~~Vv~ik~~rV~~f~G~~ 434 (834)
++.|+|+.|..|..+++.+.+..+...|+ ++.+..|.+..|..-.|..
T Consensus 1 emvL~De~G~~I~A~I~~~~~~~f~~~l~------Eg~~y~i~~F~V~~~~~~y 48 (95)
T PF02721_consen 1 EMVLVDEKGDKIQATIPKELVDKFKDSLK------EGSWYTISNFTVSPNSGSY 48 (95)
T ss_pred CEEEEecCCCEEEEEECHHHHHHHHhhcc------cCCEEEeEeEEEEeCCCce
Confidence 47899999999999999998877655543 6789999999998766643
No 137
>PRK07373 DNA polymerase III subunit alpha; Reviewed
Probab=71.20 E-value=10 Score=44.07 Aligned_cols=71 Identities=13% Similarity=0.194 Sum_probs=50.7
Q ss_pred eeccccC--CCCCceEEEEEEEEeccceeecCCCCCcceEEEEEeeCCCCEEEEEEechHHHhhhhccCcCcEEEEee
Q 003281 220 IPIAALN--PYMGKWTIKARVTAKGELRHYNNQRGDGKVFHFDLLDSDGGEIRVTCFNAVADQFYHQVEAGKIYLVSR 295 (834)
Q Consensus 220 ~pI~~L~--p~~~~w~I~aRV~~Ks~lr~~~n~~g~Gk~f~~~L~De~g~~I~at~f~~~~d~f~~~l~eG~vy~is~ 295 (834)
.++++|. +......|-+.|+.. |.....+|+ .+.-+.|-|+ .|.|.+++|.+..+++.+.|++|.++.|..
T Consensus 269 ~~~~~l~~~~~~~~v~vaG~I~~i---k~~~TKkG~-~maf~~leD~-tG~ie~vvFp~~y~~~~~~l~~~~~v~v~G 341 (449)
T PRK07373 269 INLSELEEQKEKTKVSAVVMLNEV---KKIVTKKGD-PMAFLQLEDL-SGQSEAVVFPKSYERISELLQVDARLIIWG 341 (449)
T ss_pred cCHHHHhcccCCCEEEEEEEEEEe---EecccCCCC-EEEEEEEEEC-CCCEEEEECHHHHHHHHHHhccCCEEEEEE
Confidence 4566664 223456677777754 433333432 4455667786 589999999999999999999999999964
No 138
>PRK05159 aspC aspartyl-tRNA synthetase; Provisional
Probab=71.04 E-value=40 Score=39.06 Aligned_cols=92 Identities=15% Similarity=0.144 Sum_probs=62.3
Q ss_pred ceeccccCCCC--CceEEEEEEEEeccceeecCCCCCcceEEEEEeeCCCCEEEEEEechH---HHhhhhccCcCcEEEE
Q 003281 219 IIPIAALNPYM--GKWTIKARVTAKGELRHYNNQRGDGKVFHFDLLDSDGGEIRVTCFNAV---ADQFYHQVEAGKIYLV 293 (834)
Q Consensus 219 ~~pI~~L~p~~--~~w~I~aRV~~Ks~lr~~~n~~g~Gk~f~~~L~De~g~~I~at~f~~~---~d~f~~~l~eG~vy~i 293 (834)
-+.|.+|++.. ...+|++||.++ |. .|++.-++|.|. ++.|++++-.+. ..++-..|..|+++.|
T Consensus 4 ~~~~~~l~~~~~g~~V~i~GrV~~~---R~------~gk~~Fl~LrD~-~g~iQ~v~~~~~~~~~~~~~~~L~~gs~V~v 73 (437)
T PRK05159 4 RHLTSELTPELDGEEVTLAGWVHEI---RD------LGGIAFLILRDR-SGIIQVVVKKKVDEELFETIKKLKRESVVSV 73 (437)
T ss_pred eeEhhhCChhhCCCEEEEEEEeEee---ec------CCCeEEEEEEcC-CcEEEEEEeCCccHHHHHHHhCCCCCcEEEE
Confidence 35788888765 578899999754 33 257777889997 578999986542 2233456899999999
Q ss_pred eeeEEecCCcccccCCCeEEEEEccCccEEEe
Q 003281 294 SRGSLKPAQKNFNHLHNDLEIFLDMTSMVQLC 325 (834)
Q Consensus 294 s~~~V~~a~~~~~~~~~~yeI~f~~~T~I~~~ 325 (834)
.+.-++... ....+||....-+.+..+
T Consensus 74 ~G~v~~~~~-----~~~~~el~~~~i~vls~a 100 (437)
T PRK05159 74 TGTVKANPK-----APGGVEVIPEEIEVLNKA 100 (437)
T ss_pred EEEEEcCCC-----CCCCEEEEEeEEEEEeCC
Confidence 985544321 234688888654444443
No 139
>PRK06752 single-stranded DNA-binding protein; Validated
Probab=69.87 E-value=19 Score=33.24 Aligned_cols=64 Identities=16% Similarity=0.105 Sum_probs=49.2
Q ss_pred CCceEEEEEEEEeccceeecCCCCCcceEEEEEee------CC----CCEEEEEEechHHHhhhhccCcCcEEEEee
Q 003281 229 MGKWTIKARVTAKGELRHYNNQRGDGKVFHFDLLD------SD----GGEIRVTCFNAVADQFYHQVEAGKIYLVSR 295 (834)
Q Consensus 229 ~~~w~I~aRV~~Ks~lr~~~n~~g~Gk~f~~~L~D------e~----g~~I~at~f~~~~d~f~~~l~eG~vy~is~ 295 (834)
++...|.+|+.+--++|...+ | -.+.+|.|+- .+ ..-|.+++|+..++.+.+.|+.|+-+.|..
T Consensus 2 mN~v~liGrl~~dPelr~t~~--G-~~~~~f~lAv~~~~~~~~g~~~t~~~~v~~wg~~Ae~~~~~l~KG~~V~V~G 75 (112)
T PRK06752 2 MNRVVLIGRLTKEPELYYTKQ--G-VAYARVCVAVNRGFRNSLGEQQVDFINCVVWRKSAENVTEYCTKGSLVGITG 75 (112)
T ss_pred ceEEEEEEECcCCCEEEECCC--C-CEEEEEEEEECCCeEcCCCCEEEEEEEEEEehHHHHHHHHhcCCCCEEEEEE
Confidence 467788999998888886543 2 2566777652 21 256889999999999999999999999976
No 140
>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=69.79 E-value=9.1 Score=34.36 Aligned_cols=63 Identities=25% Similarity=0.309 Sum_probs=43.7
Q ss_pred CceEEEEEEEEeccceeecCCCCCcceEEEEEe--e----------CCCCEEEEEEechHHHhhhhccCcCcEEEEee
Q 003281 230 GKWTIKARVTAKGELRHYNNQRGDGKVFHFDLL--D----------SDGGEIRVTCFNAVADQFYHQVEAGKIYLVSR 295 (834)
Q Consensus 230 ~~w~I~aRV~~Ks~lr~~~n~~g~Gk~f~~~L~--D----------e~g~~I~at~f~~~~d~f~~~l~eG~vy~is~ 295 (834)
++..|.+||...-++|...+ | ..+..|.|. + +...-+++++|+++++.+.+.|+.|+.+.|..
T Consensus 2 N~v~l~G~l~~~p~~~~~~~--g-~~~~~f~la~~~~~~~~~~~~~~~~~~~~v~~~g~~A~~~~~~l~kG~~V~V~G 76 (104)
T PF00436_consen 2 NKVTLIGRLGKDPELRYTKN--G-TPVARFSLAVNRRFKDDGGEGDEKTDWINVVAWGKLAENVAEYLKKGDRVYVEG 76 (104)
T ss_dssp EEEEEEEEESSSEEEEEETT--S-EEEEEEEEEEEEEEEETTSCEEEEEEEEEEEEEHHHHHHHHHH--TT-EEEEEE
T ss_pred cEEEEEEEECCCcEEEECCC--C-CEEEEEEEEEecEEeeeeccCccceEEEEEEeeeecccccceEEcCCCEEEEEE
Confidence 45678889988777777652 1 245555542 1 12346899999999999999999999999987
No 141
>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=69.76 E-value=1.2e+02 Score=29.96 Aligned_cols=143 Identities=19% Similarity=0.242 Sum_probs=88.8
Q ss_pred EEEEEEEeccceeecCCC-CCcceEEEEEeeCCCCEEEEEEechHHHhhhhccCcCcEEEEeeeEEecCCcccccCCCeE
Q 003281 234 IKARVTAKGELRHYNNQR-GDGKVFHFDLLDSDGGEIRVTCFNAVADQFYHQVEAGKIYLVSRGSLKPAQKNFNHLHNDL 312 (834)
Q Consensus 234 I~aRV~~Ks~lr~~~n~~-g~Gk~f~~~L~De~g~~I~at~f~~~~d~f~~~l~eG~vy~is~~~V~~a~~~~~~~~~~y 312 (834)
+.|.|+.-.+.-+|..+. |..+.|+-+++-| ..-.++.+|+- .+.+.+...+++.||+..-. .-
T Consensus 5 ~~VmVLkaTepF~Ye~~e~gkk~MFHATVATe-t~fF~VKVfn~---~LKeKF~~kkiI~IS~Y~~~-----------~g 69 (170)
T PF02760_consen 5 KTVMVLKATEPFEYESPEEGKKKMFHATVATE-TEFFRVKVFNI---NLKEKFIPKKIIAISDYFGR-----------NG 69 (170)
T ss_dssp EEEEEEEE---EEEECTTTCEEEEEEEEEE-S-S-EEEEEES-G---GGCCTCSTTSEEEEESEEEE-----------TT
T ss_pred eEEEEEeccCCeEEeCcccCcceEEEEEEecc-ccEEEEEEecc---hhHhhcCCCcEEEEehhhcc-----------cc
Confidence 456777777888887765 4568899999997 58899999996 57788899999999986422 22
Q ss_pred EEEEccCccEEEec-CCCCCCcccc----ccccccccccccCCCceeeEEEEEEEecCCeeEEccCCceeeEEEEEEecc
Q 003281 313 EIFLDMTSMVQLCY-EDDASIPRQQ----FHFRPINDVEGMENNSVVDLIGVVSYISPTASLMRKNGTETQKRTLHLRDM 387 (834)
Q Consensus 313 eI~f~~~T~I~~~~-d~~~~iP~~~----~~f~~i~dI~~~~~~~~vDVIGvV~~V~~~~~i~~k~g~~~~kr~i~L~D~ 387 (834)
-|-+++.|.|.+.. +....+|... -.--+|++|.....+.+|+=+=.|.... .+ .......|.|+
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 35566677887763 3334566522 2346788888777888877554443321 11 12446788999
Q ss_pred CCcEEEEEEcCCccc
Q 003281 388 SGRSVELTLWGNFCN 402 (834)
Q Consensus 388 s~~si~vtLWg~~a~ 402 (834)
+| .++|...|....
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 799999998764
No 142
>PLN02502 lysyl-tRNA synthetase
Probab=68.80 E-value=28 Score=41.55 Aligned_cols=79 Identities=27% Similarity=0.385 Sum_probs=53.8
Q ss_pred CceEEEEEEEEeccceeecCCCCCcceEEEEEeeCCCCEEEEEEechH-------HHhhhhccCcCcEEEEeeeEEecCC
Q 003281 230 GKWTIKARVTAKGELRHYNNQRGDGKVFHFDLLDSDGGEIRVTCFNAV-------ADQFYHQVEAGKIYLVSRGSLKPAQ 302 (834)
Q Consensus 230 ~~w~I~aRV~~Ks~lr~~~n~~g~Gk~f~~~L~De~g~~I~at~f~~~-------~d~f~~~l~eG~vy~is~~~V~~a~ 302 (834)
...+|.+||.++ |. .|++.-++|.|. ++.|++.+-.+. .+++...|..|+++.|.+.-.+...
T Consensus 109 ~~V~v~GrV~~~---R~------~Gk~~F~~LrD~-~g~iQv~~~~~~~~~~~~~~~~~~~~l~~gdiV~V~G~~~~t~~ 178 (553)
T PLN02502 109 VSVSVAGRIMAK---RA------FGKLAFYDLRDD-GGKIQLYADKKRLDLDEEEFEKLHSLVDRGDIVGVTGTPGKTKK 178 (553)
T ss_pred CEEEEEEEEEEE---ec------CCCeEEEEEecC-CccEEEEEECccccchhHHHHHHHhCCCCCcEEEEEEEEEecCC
Confidence 358899999864 33 368888899997 689999886442 2334456899999999886544321
Q ss_pred cccccCCCeEEEEEccCccEEEe
Q 003281 303 KNFNHLHNDLEIFLDMTSMVQLC 325 (834)
Q Consensus 303 ~~~~~~~~~yeI~f~~~T~I~~~ 325 (834)
..++|....-+.+.+|
T Consensus 179 -------gelel~~~~i~vLs~~ 194 (553)
T PLN02502 179 -------GELSIFPTSFEVLTKC 194 (553)
T ss_pred -------CCEEEEEeEEEEEecc
Confidence 3677777654444443
No 143
>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=68.51 E-value=13 Score=33.14 Aligned_cols=52 Identities=19% Similarity=0.410 Sum_probs=36.6
Q ss_pred EEEEEEEeccceeecCCCCCcceEEEEEeeCCCCEEEEEEechHH--H------------------hhhhccCcCcEEEE
Q 003281 234 IKARVTAKGELRHYNNQRGDGKVFHFDLLDSDGGEIRVTCFNAVA--D------------------QFYHQVEAGKIYLV 293 (834)
Q Consensus 234 I~aRV~~Ks~lr~~~n~~g~Gk~f~~~L~De~g~~I~at~f~~~~--d------------------~f~~~l~eG~vy~i 293 (834)
|.+.|++..+. ...+.|.|-|.+ |.|.|.+|.... + +..+.|++|+++.+
T Consensus 2 ivG~V~sv~~~---------~~~~~~tLdDgT-G~Ie~~~W~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~G~vvrV 71 (92)
T cd04483 2 ILGTVVSRRER---------ETFYSFGVDDGT-GVVNCVCWKNLSYAEVSSRSDAARILKSALMALKQAKVLEIGDLLRV 71 (92)
T ss_pred eEEEEEEEEec---------CCeEEEEEecCC-ceEEEEEEcCcCcccccccccccccccccccccccccccCCCCEEEE
Confidence 55667654321 235888899985 699999997642 1 46667999999888
Q ss_pred ee
Q 003281 294 SR 295 (834)
Q Consensus 294 s~ 295 (834)
..
T Consensus 72 ~G 73 (92)
T cd04483 72 RG 73 (92)
T ss_pred EE
Confidence 74
No 144
>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=66.27 E-value=48 Score=28.49 Aligned_cols=72 Identities=15% Similarity=0.159 Sum_probs=45.7
Q ss_pred eEEEEEEEEeccceeecCCCCCcceEEEEEeeCCCC-EEEEEEechHH-HhhhhccCcCcEEEEeeeEEecCCcccccCC
Q 003281 232 WTIKARVTAKGELRHYNNQRGDGKVFHFDLLDSDGG-EIRVTCFNAVA-DQFYHQVEAGKIYLVSRGSLKPAQKNFNHLH 309 (834)
Q Consensus 232 w~I~aRV~~Ks~lr~~~n~~g~Gk~f~~~L~De~g~-~I~at~f~~~~-d~f~~~l~eG~vy~is~~~V~~a~~~~~~~~ 309 (834)
-+|++||.+ +|. .|++.-++|.|..+. .|++++..+.. -++...|..|+++.+.+.-.+...+ .
T Consensus 2 v~v~Gwv~~---~R~------~g~~~Fi~LrD~s~~~~lQvv~~~~~~~~~~~~~l~~gs~V~v~G~v~~~~~~-----~ 67 (82)
T cd04318 2 VTVNGWVRS---VRD------SKKISFIELNDGSCLKNLQVVVDKELTNFKEILKLSTGSSIRVEGVLVKSPGA-----K 67 (82)
T ss_pred EEEEEeEEE---EEc------CCcEEEEEEECCCCccCEEEEEeCcccCHHHHhcCCCceEEEEEEEEEeCCCC-----C
Confidence 357778754 333 256766778897543 59998875432 1334568999999999854433222 3
Q ss_pred CeEEEEEc
Q 003281 310 NDLEIFLD 317 (834)
Q Consensus 310 ~~yeI~f~ 317 (834)
.++||..+
T Consensus 68 ~~~El~~~ 75 (82)
T cd04318 68 QPFELQAE 75 (82)
T ss_pred CCEEEEEE
Confidence 46888764
No 145
>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=62.20 E-value=71 Score=30.38 Aligned_cols=80 Identities=16% Similarity=0.151 Sum_probs=51.6
Q ss_pred CceEEEEEEEEeccceeecCCCCCcceEEEEEeeCCCCEEEEEEechHHH--hhhhccCcCcEEEEeeeEEecCC--ccc
Q 003281 230 GKWTIKARVTAKGELRHYNNQRGDGKVFHFDLLDSDGGEIRVTCFNAVAD--QFYHQVEAGKIYLVSRGSLKPAQ--KNF 305 (834)
Q Consensus 230 ~~w~I~aRV~~Ks~lr~~~n~~g~Gk~f~~~L~De~g~~I~at~f~~~~d--~f~~~l~eG~vy~is~~~V~~a~--~~~ 305 (834)
..-+|++||.+ +|. .|++.-++|.|. ++.+++++-.+..+ ++...|..|+++.+.+.-..... +.-
T Consensus 15 ~~V~i~Gwv~~---~R~------~gk~~Fi~LrD~-~g~~Q~v~~~~~~~~~~~~~~l~~gs~V~V~G~~~~~~~~~~~~ 84 (135)
T cd04317 15 QEVTLCGWVQR---RRD------HGGLIFIDLRDR-YGIVQVVFDPEEAPEFELAEKLRNESVIQVTGKVRARPEGTVNP 84 (135)
T ss_pred CEEEEEEeEeh---hcc------cCCEEEEEEecC-CeeEEEEEeCCchhHHHHHhCCCCccEEEEEEEEECCCccccCC
Confidence 46889999964 343 256766778887 57899988755333 23456999999999986443221 111
Q ss_pred ccCCCeEEEEEccC
Q 003281 306 NHLHNDLEIFLDMT 319 (834)
Q Consensus 306 ~~~~~~yeI~f~~~ 319 (834)
......+||..+.-
T Consensus 85 ~~~~~~~El~~~~i 98 (135)
T cd04317 85 KLPTGEIEVVASEL 98 (135)
T ss_pred CCCCCcEEEEEeEE
Confidence 22335689888643
No 146
>KOG0556 consensus Aspartyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=61.82 E-value=92 Score=35.25 Aligned_cols=106 Identities=15% Similarity=0.177 Sum_probs=75.2
Q ss_pred CCCceeccccCCCCC--ceEEEEEEEEeccceeecCCCCCcceEEEEEeeCCCCEEEEEEec-------hHHHhhhhccC
Q 003281 216 PSRIIPIAALNPYMG--KWTIKARVTAKGELRHYNNQRGDGKVFHFDLLDSDGGEIRVTCFN-------AVADQFYHQVE 286 (834)
Q Consensus 216 ~~~~~pI~~L~p~~~--~w~I~aRV~~Ks~lr~~~n~~g~Gk~f~~~L~De~g~~I~at~f~-------~~~d~f~~~l~ 286 (834)
.+.+++|++|+-... ...|++||- +.+-.||+.-++|.+. +..|++.+.- ...-+|...|-
T Consensus 67 ~~~~~~v~dl~~~~~~~~V~vRgrVh---------tsr~~GK~~FlvLRq~-~~tVQ~~~~~~~~~~isk~Mvkf~~~is 136 (533)
T KOG0556|consen 67 GRELTDVSDLDESNDGSEVLVRGRVH---------TSRLKGKLCFLVLRQQ-GSTVQCLVAVNEDGTISKQMVKFAGSIS 136 (533)
T ss_pred ccceeehhhhhhhcCCceEEEEEEEe---------eccccceEEEEEEecc-CceEEEEEEcCCCchHHHHHHHHHhhcC
Confidence 357899999987653 556888883 1233478877888885 8999999952 24678999999
Q ss_pred cCcEEEEeeeEEecCCcccccCCCeEEEEEccCccEEEecCCCCCCcc
Q 003281 287 AGKIYLVSRGSLKPAQKNFNHLHNDLEIFLDMTSMVQLCYEDDASIPR 334 (834)
Q Consensus 287 eG~vy~is~~~V~~a~~~~~~~~~~yeI~f~~~T~I~~~~d~~~~iP~ 334 (834)
-..++.|...-+++.++--.-+..+.||.+..--+|... ...+|.
T Consensus 137 ~ESiV~v~g~v~k~~~~i~scT~qdvEi~v~~iyviS~a---~~~LPl 181 (533)
T KOG0556|consen 137 KESIVDVRGVVVKVKEPIKSCTVQDVEIHVRKIYVISIA---LPNLPL 181 (533)
T ss_pred cceEEEEEEEEecCCCcccccccceeEEEEEEEEEEecc---cccCCe
Confidence 999999988777766665555778999998654444332 345553
No 147
>PRK06642 single-stranded DNA-binding protein; Provisional
Probab=61.77 E-value=30 Score=33.98 Aligned_cols=64 Identities=20% Similarity=0.275 Sum_probs=50.0
Q ss_pred CCceEEEEEEEEeccceeecCCCCCcceEEEEEe------eC-------CCCEEEEEEech-HHHhhhhccCcCcEEEEe
Q 003281 229 MGKWTIKARVTAKGELRHYNNQRGDGKVFHFDLL------DS-------DGGEIRVTCFNA-VADQFYHQVEAGKIYLVS 294 (834)
Q Consensus 229 ~~~w~I~aRV~~Ks~lr~~~n~~g~Gk~f~~~L~------De-------~g~~I~at~f~~-~~d~f~~~l~eG~vy~is 294 (834)
+++.+|.+|+.+--++|...+ | ..+.+|.|+ |. +..=|++++|+. +++.+...|+.|+.++|.
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--G-KKIINLSLATTETWKDRITSERKERTEWHRVVIFSEGLVSVVERYVTKGSKLYIE 81 (152)
T ss_pred ceEEEEEEEccCCceEEECCC--C-CEEEEEEEEeccccccccCCccccceeEEEEEEeChHHHHHHHHhCCCCCEEEEE
Confidence 578899999999888887643 2 257777775 21 134688999996 899999999999999997
Q ss_pred e
Q 003281 295 R 295 (834)
Q Consensus 295 ~ 295 (834)
.
T Consensus 82 G 82 (152)
T PRK06642 82 G 82 (152)
T ss_pred E
Confidence 6
No 148
>KOG0107 consensus Alternative splicing factor SRp20/9G8 (RRM superfamily) [RNA processing and modification]
Probab=60.99 E-value=6.8 Score=38.91 Aligned_cols=17 Identities=41% Similarity=1.151 Sum_probs=15.8
Q ss_pred cCcccCCCCccCCCCCC
Q 003281 787 ECYKCHKTGHWARDCPS 803 (834)
Q Consensus 787 ~Cy~Cg~~GH~ardCp~ 803 (834)
.||.||+.||+.+.|.+
T Consensus 102 ~~~r~G~rg~~~r~~~~ 118 (195)
T KOG0107|consen 102 FCYRCGERGHIGRNCKD 118 (195)
T ss_pred ccccCCCcccccccccc
Confidence 39999999999999988
No 149
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]
Probab=60.80 E-value=6.8 Score=44.70 Aligned_cols=44 Identities=25% Similarity=0.419 Sum_probs=36.2
Q ss_pred CcCcccCCCCccCCCCCCC--CCCCCCcCCCCCCcccccCCCCCCC
Q 003281 786 SECYKCHKTGHWARDCPSL--NAAPPAYGSSGIGISAAGYRGAPRQ 829 (834)
Q Consensus 786 ~~Cy~Cg~~GH~ardCp~~--~~~~~c~~c~~~g~~~~~cg~~~~~ 829 (834)
..|..|+..||-.-+||.. .....|..|+..||...+|+-..++
T Consensus 262 ~~c~~cg~~~H~q~~cp~r~~~~~n~c~~cg~~gH~~~dc~~~~q~ 307 (554)
T KOG0119|consen 262 RACRNCGSTGHKQYDCPGRIPNTTNVCKICGPLGHISIDCKVNDQQ 307 (554)
T ss_pred ccccccCCCccccccCCcccccccccccccCCcccccccCCCcccc
Confidence 4799999999999999986 1112899999999999999865333
No 150
>COG0629 Ssb Single-stranded DNA-binding protein [DNA replication, recombination, and repair]
Probab=59.38 E-value=29 Score=34.60 Aligned_cols=66 Identities=26% Similarity=0.313 Sum_probs=49.2
Q ss_pred CCCceEEEEEEEEeccceeecCCCCCcceEEEE------EeeC-------CCCEEEEEEechHHHhhhhccCcCcEEEEe
Q 003281 228 YMGKWTIKARVTAKGELRHYNNQRGDGKVFHFD------LLDS-------DGGEIRVTCFNAVADQFYHQVEAGKIYLVS 294 (834)
Q Consensus 228 ~~~~w~I~aRV~~Ks~lr~~~n~~g~Gk~f~~~------L~De-------~g~~I~at~f~~~~d~f~~~l~eG~vy~is 294 (834)
.+++..+.+|+++.-++|...+. +.+..+. ..|. +..-|++++|+.+++...+.|+.|.-++|.
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 MMNKVILVGRLTRDPELRYTPNG---GAVVALFSAAVNRRFDNQSGERDEETDWIRVVIWGKLAENAAEYLKKGSLVYVE 78 (167)
T ss_pred CcceEEEEeecccCcceeecCCC---CeeeEEEEEEeccccccCCcccccccceEEEEEehHHHHHHHHHhcCCCEEEEE
Confidence 35788899999999999887632 2232221 1232 236799999999999999999999999998
Q ss_pred ee
Q 003281 295 RG 296 (834)
Q Consensus 295 ~~ 296 (834)
..
T Consensus 79 G~ 80 (167)
T COG0629 79 GR 80 (167)
T ss_pred EE
Confidence 74
No 151
>PTZ00385 lysyl-tRNA synthetase; Provisional
Probab=58.02 E-value=92 Score=37.91 Aligned_cols=77 Identities=16% Similarity=0.201 Sum_probs=51.3
Q ss_pred ceEEEEEEEEeccceeecCCCCCcceEEEEEeeCCCCEEEEEEechH------HHhhhhccCcCcEEEEeeeEEecCCcc
Q 003281 231 KWTIKARVTAKGELRHYNNQRGDGKVFHFDLLDSDGGEIRVTCFNAV------ADQFYHQVEAGKIYLVSRGSLKPAQKN 304 (834)
Q Consensus 231 ~w~I~aRV~~Ks~lr~~~n~~g~Gk~f~~~L~De~g~~I~at~f~~~------~d~f~~~l~eG~vy~is~~~V~~a~~~ 304 (834)
..+|.+||.++ |. -|++.-++|.|. +|.|++.+..+. ...+...|..|+++.+.+.-.+..
T Consensus 109 ~V~vaGrV~~~---R~------~Gk~~F~~LrD~-~G~IQvv~~~~~~~~~~~~~~~~~~l~~gdiV~V~G~v~~t~--- 175 (659)
T PTZ00385 109 TVRVAGRVTSV---RD------IGKIIFVTIRSN-GNELQVVGQVGEHFTREDLKKLKVSLRVGDIIGADGVPCRMQ--- 175 (659)
T ss_pred EEEEEEEEEee---ec------cCCeEEEEEEEC-CceEEEEEECCccCCHHHHHHHHhCCCCCCEEEEEEEEEecC---
Confidence 48899999863 33 367877889997 679999997543 223334689999999988543221
Q ss_pred cccCCCeEEEEEccCccEEE
Q 003281 305 FNHLHNDLEIFLDMTSMVQL 324 (834)
Q Consensus 305 ~~~~~~~yeI~f~~~T~I~~ 324 (834)
...++|....-+.+.+
T Consensus 176 ----~GeleI~~~~i~lLsk 191 (659)
T PTZ00385 176 ----RGELSVAASRMLILSP 191 (659)
T ss_pred ----CceEEEEeeEEEEech
Confidence 2456666654444443
No 152
>PRK06341 single-stranded DNA-binding protein; Provisional
Probab=56.86 E-value=67 Score=32.07 Aligned_cols=64 Identities=16% Similarity=0.229 Sum_probs=47.3
Q ss_pred CCceEEEEEEEEeccceeecCCCCCcceEEEEEee------CC-------CCEEEEEEech-HHHhhhhccCcCcEEEEe
Q 003281 229 MGKWTIKARVTAKGELRHYNNQRGDGKVFHFDLLD------SD-------GGEIRVTCFNA-VADQFYHQVEAGKIYLVS 294 (834)
Q Consensus 229 ~~~w~I~aRV~~Ks~lr~~~n~~g~Gk~f~~~L~D------e~-------g~~I~at~f~~-~~d~f~~~l~eG~vy~is 294 (834)
+++.+|.+||+.--++|...+ | -.+.+|.|+- .. ..-+.+++|++ +++.+...|+.|+.+.|.
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 578889999998877877643 1 2566666532 11 23468999996 889999999999999997
Q ss_pred e
Q 003281 295 R 295 (834)
Q Consensus 295 ~ 295 (834)
.
T Consensus 82 G 82 (166)
T PRK06341 82 G 82 (166)
T ss_pred E
Confidence 6
No 153
>PRK12445 lysyl-tRNA synthetase; Reviewed
Probab=56.42 E-value=66 Score=38.02 Aligned_cols=79 Identities=18% Similarity=0.244 Sum_probs=53.0
Q ss_pred CceEEEEEEEEeccceeecCCCCCcceEEEEEeeCCCCEEEEEEechHH-----HhhhhccCcCcEEEEeeeEEecCCcc
Q 003281 230 GKWTIKARVTAKGELRHYNNQRGDGKVFHFDLLDSDGGEIRVTCFNAVA-----DQFYHQVEAGKIYLVSRGSLKPAQKN 304 (834)
Q Consensus 230 ~~w~I~aRV~~Ks~lr~~~n~~g~Gk~f~~~L~De~g~~I~at~f~~~~-----d~f~~~l~eG~vy~is~~~V~~a~~~ 304 (834)
...+|.+||.++ |. -|++.-++|.|. ++.|++.+-.+.+ +.....|..|+++.+.+.-++..
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------MGKASFVTLQDV-GGRIQLYVARDSLPEGVYNDQFKKWDLGDIIGARGTLFKTQ--- 132 (505)
T ss_pred CEEEEEEEEEEE---ec------CCCcEEEEEEeC-CccEEEEEECCccchhhHHHHHhcCCCCCEEEEEEEEEecC---
Confidence 358899999753 43 367877889997 5799998874322 22235699999999988655432
Q ss_pred cccCCCeEEEEEccCccEEEe
Q 003281 305 FNHLHNDLEIFLDMTSMVQLC 325 (834)
Q Consensus 305 ~~~~~~~yeI~f~~~T~I~~~ 325 (834)
...++|..+.-+.+.++
T Consensus 133 ----~gelel~~~~~~llsk~ 149 (505)
T PRK12445 133 ----TGELSIHCTELRLLTKA 149 (505)
T ss_pred ----CCcEEEEEeEEEEEecC
Confidence 24678877654444443
No 154
>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=56.19 E-value=66 Score=37.96 Aligned_cols=79 Identities=19% Similarity=0.220 Sum_probs=52.9
Q ss_pred CceEEEEEEEEeccceeecCCCCCcceEEEEEeeCCCCEEEEEEechHH-----HhhhhccCcCcEEEEeeeEEecCCcc
Q 003281 230 GKWTIKARVTAKGELRHYNNQRGDGKVFHFDLLDSDGGEIRVTCFNAVA-----DQFYHQVEAGKIYLVSRGSLKPAQKN 304 (834)
Q Consensus 230 ~~w~I~aRV~~Ks~lr~~~n~~g~Gk~f~~~L~De~g~~I~at~f~~~~-----d~f~~~l~eG~vy~is~~~V~~a~~~ 304 (834)
...+|.+||.++ |. -|++.-++|.|. +|.|++.+-.+.+ +.+...|..|+++.+.+.-.+..
T Consensus 54 ~~v~v~Grv~~~---R~------~gk~~F~~l~D~-~g~iQ~~~~~~~~~~~~~~~~~~~l~~gd~V~v~G~~~~t~--- 120 (496)
T TIGR00499 54 IEVSIAGRIMAR---RS------MGKATFITLQDE-SGQIQLYVNKDDLPEDFYEFDEYLLDLGDIIGVTGYPFKTK--- 120 (496)
T ss_pred CEEEEEEEEEEE---ec------CCCeEEEEEEcC-CccEEEEEECCcCcHHHHHHHHhcCCCCCEEEEEEEEEECC---
Confidence 458899999863 42 267888889997 5799999864321 22233589999999998654322
Q ss_pred cccCCCeEEEEEccCccEEEe
Q 003281 305 FNHLHNDLEIFLDMTSMVQLC 325 (834)
Q Consensus 305 ~~~~~~~yeI~f~~~T~I~~~ 325 (834)
...++|..+.-+.+.++
T Consensus 121 ----~gelel~~~~i~ilsk~ 137 (496)
T TIGR00499 121 ----TGELSVHVTELQILTKA 137 (496)
T ss_pred ----CCcEEEEeeEEEEEecC
Confidence 24588887654444443
No 155
>PTZ00417 lysine-tRNA ligase; Provisional
Probab=56.03 E-value=59 Score=39.09 Aligned_cols=56 Identities=23% Similarity=0.349 Sum_probs=40.4
Q ss_pred ceEEEEEEEEeccceeecCCCCCc-ceEEEEEeeCCCCEEEEEEechH-------HHhhhhccCcCcEEEEeee
Q 003281 231 KWTIKARVTAKGELRHYNNQRGDG-KVFHFDLLDSDGGEIRVTCFNAV-------ADQFYHQVEAGKIYLVSRG 296 (834)
Q Consensus 231 ~w~I~aRV~~Ks~lr~~~n~~g~G-k~f~~~L~De~g~~I~at~f~~~-------~d~f~~~l~eG~vy~is~~ 296 (834)
..+|.+||.+ +|.. | ++.-++|.|. ++.|++.+-.+. .+.+...|..|+++.+.+.
T Consensus 134 ~v~v~Grv~~---~R~~------G~k~~F~~L~d~-~g~iQv~~~~~~~~~~~~~~~~~~~~l~~Gd~V~V~G~ 197 (585)
T PTZ00417 134 ILNVTGRIMR---VSAS------GQKLRFFDLVGD-GAKIQVLANFAFHDHTKSNFAECYDKIRRGDIVGIVGF 197 (585)
T ss_pred eEEEEEEEEe---eecC------CCCCEEEEEEeC-CeeEEEEEECCccCCCHHHHHHHHhcCCCCCEEEEEeE
Confidence 4789999975 3433 5 5666777786 689999997432 2233456999999999987
No 156
>PRK00484 lysS lysyl-tRNA synthetase; Reviewed
Probab=55.80 E-value=78 Score=37.33 Aligned_cols=78 Identities=21% Similarity=0.251 Sum_probs=52.9
Q ss_pred CceEEEEEEEEeccceeecCCCCCcceEEEEEeeCCCCEEEEEEechH-----HHhhhhccCcCcEEEEeeeEEecCCcc
Q 003281 230 GKWTIKARVTAKGELRHYNNQRGDGKVFHFDLLDSDGGEIRVTCFNAV-----ADQFYHQVEAGKIYLVSRGSLKPAQKN 304 (834)
Q Consensus 230 ~~w~I~aRV~~Ks~lr~~~n~~g~Gk~f~~~L~De~g~~I~at~f~~~-----~d~f~~~l~eG~vy~is~~~V~~a~~~ 304 (834)
...+|.+||.++ |.. |++.-++|.|. +|.|++.+-.+. .+.+. .|..|+++.|.+.-++..
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---RVM------GKASFATLQDG-SGRIQLYVSKDDVGEEALEAFK-KLDLGDIIGVEGTLFKTK--- 120 (491)
T ss_pred cEEEEEEEEEEE---ecC------CceEEEEEEcC-CccEEEEEECCcCCHHHHHHHh-cCCCCCEEEEEEEEEEcC---
Confidence 458899999763 432 67888889997 579999886442 22333 399999999987555432
Q ss_pred cccCCCeEEEEEccCccEEEe
Q 003281 305 FNHLHNDLEIFLDMTSMVQLC 325 (834)
Q Consensus 305 ~~~~~~~yeI~f~~~T~I~~~ 325 (834)
...+||..+.-..+.++
T Consensus 121 ----~ge~el~~~~~~vls~~ 137 (491)
T PRK00484 121 ----TGELSVKATELTLLTKS 137 (491)
T ss_pred ----CCcEEEEEeEEEEEecc
Confidence 14688887654444443
No 157
>PRK07459 single-stranded DNA-binding protein; Provisional
Probab=55.41 E-value=80 Score=29.73 Aligned_cols=69 Identities=13% Similarity=0.179 Sum_probs=38.5
Q ss_pred eeeEEEEEEEecCCeeEEccCCceeeEEEEEEec------cCCcEEEEEEcCCccchhhhhhhhcccCCCccEEEEEE-E
Q 003281 353 VVDLIGVVSYISPTASLMRKNGTETQKRTLHLRD------MSGRSVELTLWGNFCNDDGLRLQHMCDSGVFPILAVKA-G 425 (834)
Q Consensus 353 ~vDVIGvV~~V~~~~~i~~k~g~~~~kr~i~L~D------~s~~si~vtLWg~~a~~~~~~l~~~~~~~~~~Vv~ik~-~ 425 (834)
.|-+||.|..--++. .+.+|+.+. .+.|.- ....-+.|++||+.|+...+++. .+.-|.+.+ .
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--YFESGSVVC--NLTLAVNRRSRDDEPDWFNLEIWGKTAQVAADYVK------KGSLIGITGSL 74 (121)
T ss_pred EEEEEEEccCCCEEE--EcCCCCEEE--EEEEEecccccCCCceEEEEEEehHHHHHHHHHcC------CCCEEEEEEEE
Confidence 466788887732221 234565432 333331 22236999999999987655442 345555544 6
Q ss_pred EEeecC
Q 003281 426 RVSDFN 431 (834)
Q Consensus 426 rV~~f~ 431 (834)
+...|.
T Consensus 75 ~~~~~~ 80 (121)
T PRK07459 75 KFDRWT 80 (121)
T ss_pred EecceE
Confidence 666663
No 158
>PRK08486 single-stranded DNA-binding protein; Provisional
Probab=54.56 E-value=61 Score=32.90 Aligned_cols=35 Identities=9% Similarity=0.105 Sum_probs=23.5
Q ss_pred EEEEEEcCCccchhhhhhhhcccCCCccEEEEEE-EEEeecC
Q 003281 391 SVELTLWGNFCNDDGLRLQHMCDSGVFPILAVKA-GRVSDFN 431 (834)
Q Consensus 391 si~vtLWg~~a~~~~~~l~~~~~~~~~~Vv~ik~-~rV~~f~ 431 (834)
-|+|++||..|+...+.|. .+.-|+|.+ .+...|.
T Consensus 50 fi~v~~fg~~AE~~~~~l~------KG~~V~VeGrL~~~~y~ 85 (182)
T PRK08486 50 FIDIRLFGRTAEIANQYLS------KGSKVLIEGRLTFESWM 85 (182)
T ss_pred EEEEEEEhHHHHHHHHHcC------CCCEEEEEEEEEeCcEE
Confidence 5899999999987655442 345555544 5666663
No 159
>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=54.40 E-value=4.4 Score=35.93 Aligned_cols=27 Identities=33% Similarity=0.972 Sum_probs=20.8
Q ss_pred CCCCCcCCCCcCcc-cccCCCCceecCCCCCccc
Q 003281 522 ACPIMIGDRPCNKK-VMNNGDGRWHCDRCDQSVV 554 (834)
Q Consensus 522 aC~~~~~~~~C~KK-v~~~~dg~~~CekC~~~~~ 554 (834)
.|| -|.|+ |.....|.|.|.+|+..+.
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 388 59887 4556679999999997653
No 160
>PRK09010 single-stranded DNA-binding protein; Provisional
Probab=54.28 E-value=71 Score=32.25 Aligned_cols=36 Identities=14% Similarity=0.184 Sum_probs=24.2
Q ss_pred EEEEEEcCCccchhhhhhhhcccCCCccEEEEE-EEEEeecCC
Q 003281 391 SVELTLWGNFCNDDGLRLQHMCDSGVFPILAVK-AGRVSDFNG 432 (834)
Q Consensus 391 si~vtLWg~~a~~~~~~l~~~~~~~~~~Vv~ik-~~rV~~f~G 432 (834)
-++|++|++.|+...+.|. .+.-|+|. ..+.+.|.+
T Consensus 55 w~~V~~fgk~Ae~~~~~L~------KGs~V~VeGrL~~~~yed 91 (177)
T PRK09010 55 WHRVVLFGKLAEVAGEYLR------KGSQVYIEGQLRTRKWTD 91 (177)
T ss_pred EEEEEEehhHHHHHHHhcC------CCCEEEEEEEEEeccccC
Confidence 5899999999887655443 34555554 467777754
No 161
>PRK05733 single-stranded DNA-binding protein; Provisional
Probab=53.97 E-value=72 Score=32.03 Aligned_cols=71 Identities=18% Similarity=0.212 Sum_probs=39.6
Q ss_pred eeeEEEEEEEecCCeeEEccCCceeeEEEEEEe----cc-CC------cEEEEEEcCCccchhhhhhhhcccCCCccEEE
Q 003281 353 VVDLIGVVSYISPTASLMRKNGTETQKRTLHLR----DM-SG------RSVELTLWGNFCNDDGLRLQHMCDSGVFPILA 421 (834)
Q Consensus 353 ~vDVIGvV~~V~~~~~i~~k~g~~~~kr~i~L~----D~-s~------~si~vtLWg~~a~~~~~~l~~~~~~~~~~Vv~ 421 (834)
.|-++|.|..--++ -.+.+|..+.+-.|-.. |. +| .-+.|++||+.|+.+.+.|. .+.-|+
T Consensus 7 kV~LiGrlg~DPEl--r~t~nG~~va~fsVAv~~~~k~~~~Ge~~e~T~w~~Vv~fgk~Ae~v~~~l~------KGs~V~ 78 (172)
T PRK05733 7 KVILVGTCGQDPEV--RYLPNGNAVTNLSLATSEQWTDKQSGQKVERTEWHRVSLFGKVAEIAGEYLR------KGSQVY 78 (172)
T ss_pred EEEEEEEecCCCEE--EECCCCCEEEEEEEEEcCccccCCCCcccccceEEEEEEehHHHHHHHHHhC------CCCEEE
Confidence 45677877763222 12345655443333321 11 12 24999999999887655443 456666
Q ss_pred EEE-EEEeecC
Q 003281 422 VKA-GRVSDFN 431 (834)
Q Consensus 422 ik~-~rV~~f~ 431 (834)
|.+ .+...|.
T Consensus 79 VeGrLr~~~y~ 89 (172)
T PRK05733 79 IEGKLQTREWE 89 (172)
T ss_pred EEEEEEeCcEe
Confidence 655 5666664
No 162
>PRK07374 dnaE DNA polymerase III subunit alpha; Validated
Probab=53.86 E-value=25 Score=45.68 Aligned_cols=78 Identities=19% Similarity=0.236 Sum_probs=53.3
Q ss_pred cccccccccccCCCceeeEEEEEEEecCCeeEEccCCceeeEEEEEEeccCCcEEEEEEcCCccchhhhhhhhcccCCCc
Q 003281 338 HFRPINDVEGMENNSVVDLIGVVSYISPTASLMRKNGTETQKRTLHLRDMSGRSVELTLWGNFCNDDGLRLQHMCDSGVF 417 (834)
Q Consensus 338 ~f~~i~dI~~~~~~~~vDVIGvV~~V~~~~~i~~k~g~~~~kr~i~L~D~s~~si~vtLWg~~a~~~~~~l~~~~~~~~~ 417 (834)
...++++|.+...+..|-|+|+|+.+... ++|+|+. .--++|.|.+| .+++++|-+..+.....+. .+
T Consensus 987 ~~~~~~~l~~~~~~~~v~v~g~i~~~k~~---~Tk~G~~--maf~~leD~tg-~~e~vvFp~~y~~~~~~l~------~~ 1054 (1170)
T PRK07374 987 APISLSSLEEQPDKAKVSAIAMIPEMKQV---TTRKGDR--MAILQLEDLTG-SCEAVVFPKSYERLSDHLM------TD 1054 (1170)
T ss_pred CCcCHHHHhcccCCCEEEEEEEEEEeEec---ccCCCCE--EEEEEEEECCC-CEEEEECHHHHHHHHHHhc------cC
Confidence 34566666544456788999999988654 4667763 45689999999 6999999887665443332 34
Q ss_pred cEEEEEEEEEe
Q 003281 418 PILAVKAGRVS 428 (834)
Q Consensus 418 ~Vv~ik~~rV~ 428 (834)
.+|.+++ +|.
T Consensus 1055 ~~~~v~g-~v~ 1064 (1170)
T PRK07374 1055 TRLLVWA-KVD 1064 (1170)
T ss_pred CEEEEEE-EEE
Confidence 5666655 444
No 163
>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=53.60 E-value=66 Score=31.97 Aligned_cols=35 Identities=11% Similarity=0.215 Sum_probs=23.5
Q ss_pred EEEEEEcCCccchhhhhhhhcccCCCccEEEEEE-EEEeecC
Q 003281 391 SVELTLWGNFCNDDGLRLQHMCDSGVFPILAVKA-GRVSDFN 431 (834)
Q Consensus 391 si~vtLWg~~a~~~~~~l~~~~~~~~~~Vv~ik~-~rV~~f~ 431 (834)
-++|++||+.|+...+.|. .+..|.|.+ .+...|.
T Consensus 52 ~~~v~~wg~~Ae~~~~~l~------KG~~V~V~G~L~~~~~~ 87 (164)
T TIGR00621 52 WHDIVIFGRLAEVAAQYLK------KGSLVYVEGRLRTRKWE 87 (164)
T ss_pred EEEEEEehHHHHHHHHhCC------CCCEEEEEEEEEeceEE
Confidence 6999999999876554432 455565554 5666674
No 164
>PRK05673 dnaE DNA polymerase III subunit alpha; Validated
Probab=53.02 E-value=36 Score=44.18 Aligned_cols=71 Identities=25% Similarity=0.338 Sum_probs=49.7
Q ss_pred eeccccCC--CCCceEEEEEEEEeccceeecCCCCCcceEEEEEeeCCCCEEEEEEechHHHhhhhccCcCcEEEEee
Q 003281 220 IPIAALNP--YMGKWTIKARVTAKGELRHYNNQRGDGKVFHFDLLDSDGGEIRVTCFNAVADQFYHQVEAGKIYLVSR 295 (834)
Q Consensus 220 ~pI~~L~p--~~~~w~I~aRV~~Ks~lr~~~n~~g~Gk~f~~~L~De~g~~I~at~f~~~~d~f~~~l~eG~vy~is~ 295 (834)
+++.+|.. ......+.+.|+.+ +.....+| ....-+.|.|. .|+|.+++|.+..+++.+.|++|.++.|..
T Consensus 966 ~~~~~l~~~~~g~~V~v~G~I~~v---k~~~TKkG-~~mafltLeD~-TG~iEvviFp~~ye~~~~~L~~g~iV~V~G 1038 (1135)
T PRK05673 966 TRLADLEPTEGGSVVTVAGLVVSV---RRRVTKRG-NKMAIVTLEDL-SGRIEVMLFSEALEKYRDLLEEDRIVVVKG 1038 (1135)
T ss_pred cCHHHHhccccCceEEEEEEEEEE---EecccCCC-CeEEEEEEEeC-CCcEEEEECHHHHHHHHHHhccCCEEEEEE
Confidence 46777652 23345666666654 33333333 23556678887 579999999999999999999999999965
No 165
>PRK06751 single-stranded DNA-binding protein; Provisional
Probab=52.98 E-value=68 Score=32.27 Aligned_cols=35 Identities=9% Similarity=0.190 Sum_probs=24.0
Q ss_pred EEEEEEcCCccchhhhhhhhcccCCCccEEEEE-EEEEeecC
Q 003281 391 SVELTLWGNFCNDDGLRLQHMCDSGVFPILAVK-AGRVSDFN 431 (834)
Q Consensus 391 si~vtLWg~~a~~~~~~l~~~~~~~~~~Vv~ik-~~rV~~f~ 431 (834)
-+.|++||+.|+.+.+.+. .+.-|.|. ..+...|.
T Consensus 48 wi~~v~wgk~Ae~~~~~l~------KG~~V~VeGrL~~r~ye 83 (173)
T PRK06751 48 FINCVIWRKQAENVANYLK------KGSLAGVDGRLQTRNYE 83 (173)
T ss_pred EEEEEEeCcHHHHHHHHcC------CCCEEEEEEEEEeCccC
Confidence 6899999999987655442 34555554 46777775
No 166
>TIGR00643 recG ATP-dependent DNA helicase RecG.
Probab=52.56 E-value=49 Score=40.30 Aligned_cols=69 Identities=20% Similarity=0.225 Sum_probs=51.2
Q ss_pred CceeccccCCCCCceEEEEEEEEeccceeecCCCCCcceEEEEEee-CCCCEEEEEEechHHHhhhhccCcCcEEEEee
Q 003281 218 RIIPIAALNPYMGKWTIKARVTAKGELRHYNNQRGDGKVFHFDLLD-SDGGEIRVTCFNAVADQFYHQVEAGKIYLVSR 295 (834)
Q Consensus 218 ~~~pI~~L~p~~~~w~I~aRV~~Ks~lr~~~n~~g~Gk~f~~~L~D-e~g~~I~at~f~~~~d~f~~~l~eG~vy~is~ 295 (834)
.+.+|++|.+. ..-+|.++|+... .+. ++..+.+.+.+.| . ++.|.+++|+.. -....|+.|+.|.|++
T Consensus 22 ~~~~i~~~~~g-~~~~~~~~v~~~~---~~~--~~~~~~~~~~~~d~~-~~~~~~~~F~~~--~~~~~~~~g~~~~~~G 91 (630)
T TIGR00643 22 LLQTIGELLPG-ERATIVGEVLSHC---IFG--FKRRKVLKLRLKDGG-YKKLELRFFNRA--FLKKKFKVGSKVVVYG 91 (630)
T ss_pred cccCHHHcCCC-CEEEEEEEEEEeE---ecc--CCCCceEEEEEEECC-CCEEEEEEECCH--HHHhhCCCCCEEEEEE
Confidence 46789999886 5688999998632 111 1224589999999 6 689999999832 3457899999999875
No 167
>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=51.81 E-value=25 Score=31.25 Aligned_cols=41 Identities=20% Similarity=0.321 Sum_probs=33.0
Q ss_pred cceEEEEEeeCCCCEEEEEEechH--HHhhhhccCcCcEEEEeee
Q 003281 254 GKVFHFDLLDSDGGEIRVTCFNAV--ADQFYHQVEAGKIYLVSRG 296 (834)
Q Consensus 254 Gk~f~~~L~De~g~~I~at~f~~~--~d~f~~~l~eG~vy~is~~ 296 (834)
|. .-|.|.|+ ++.|.+.+|... +.+....|++|+-+.+...
T Consensus 17 GH-~yFtlkD~-~~~i~cv~f~~~g~~~~~~~~l~~Gd~V~v~G~ 59 (91)
T cd04482 17 GH-VFFKISDG-TGEIDCAAYEPTKEFRDVVRLLIPGDEVTVYGS 59 (91)
T ss_pred CC-EEEEEECC-CcEEEEEEECcccccccccCCCCCCCEEEEEEE
Confidence 54 55678897 589999999887 6678888999998887653
No 168
>PRK02983 lysS lysyl-tRNA synthetase; Provisional
Probab=51.12 E-value=76 Score=41.22 Aligned_cols=88 Identities=22% Similarity=0.269 Sum_probs=59.2
Q ss_pred eccccCCC--CCceEEEEEEEEeccceeecCCCCCcceEEEEEeeCCCCEEEEEEechH-----HHhhhhccCcCcEEEE
Q 003281 221 PIAALNPY--MGKWTIKARVTAKGELRHYNNQRGDGKVFHFDLLDSDGGEIRVTCFNAV-----ADQFYHQVEAGKIYLV 293 (834)
Q Consensus 221 pI~~L~p~--~~~w~I~aRV~~Ks~lr~~~n~~g~Gk~f~~~L~De~g~~I~at~f~~~-----~d~f~~~l~eG~vy~i 293 (834)
.|.++... ....+|.+||.++ |.. |++.-++|.|. ++.|++.+-.+. .+.|...|..|+++.+
T Consensus 641 ~~~~~~~~~~~~~V~v~Grv~~~---R~~------G~~~F~~lrD~-~g~iQ~v~~~~~~~~~~~~~~~~~l~~gd~V~v 710 (1094)
T PRK02983 641 TVAEALDAPTGEEVSVSGRVLRI---RDY------GGVLFADLRDW-SGELQVLLDASRLEQGSLADFRAAVDLGDLVEV 710 (1094)
T ss_pred CHHHHHHhcCCCEEEEEEEEEEE---eeC------CCeEEEEEEeC-CeeEEEEEECCccchhhHHHHHhcCCCCCEEEE
Confidence 45555321 2468899999763 443 67888889997 589999986543 3456667999999999
Q ss_pred eeeEEecCCcccccCCCeEEEEEccCccEEEe
Q 003281 294 SRGSLKPAQKNFNHLHNDLEIFLDMTSMVQLC 325 (834)
Q Consensus 294 s~~~V~~a~~~~~~~~~~yeI~f~~~T~I~~~ 325 (834)
.+.-.+... ..+||..+.-+.+.+|
T Consensus 711 ~G~v~~t~~-------ge~ei~~~~i~ll~k~ 735 (1094)
T PRK02983 711 TGTMGTSRN-------GTLSLLVTSWRLAGKC 735 (1094)
T ss_pred EEEEEEcCC-------CCEEEEEeEEEEEecc
Confidence 986544321 4678877655555444
No 169
>PF15489 CTC1: CST, telomere maintenance, complex subunit CTC1
Probab=50.94 E-value=1.4e+02 Score=38.39 Aligned_cols=68 Identities=13% Similarity=0.234 Sum_probs=51.4
Q ss_pred CCceEEEEEEEEeccceeecCCCCCcceEEEEEeeCCCCEEEEEEechHHHhhhhccCcCcEEEEeeeEEecC
Q 003281 229 MGKWTIKARVTAKGELRHYNNQRGDGKVFHFDLLDSDGGEIRVTCFNAVADQFYHQVEAGKIYLVSRGSLKPA 301 (834)
Q Consensus 229 ~~~w~I~aRV~~Ks~lr~~~n~~g~Gk~f~~~L~De~g~~I~at~f~~~~d~f~~~l~eG~vy~is~~~V~~a 301 (834)
...-.|-++|++.+.+-..... ..|-+.|.|+ +..+.+.+-...---|+..|..|+.|.|.+.+|..-
T Consensus 165 ~~~~~v~G~v~~ls~l~~~~~k----~fF~l~L~~~-~~~v~viVq~pa~l~Wh~~L~~G~~yvlT~Lrvs~i 232 (1144)
T PF15489_consen 165 GRQLNVAGKVVRLSALVKSHGK----TFFILSLGDA-GSHVPVIVQEPAQLVWHRALRPGRAYVLTSLRVSKI 232 (1144)
T ss_pred cCceeeeeEEEEeeceEEEcce----EEEEEEeCCC-CceeEEEEEecchhhhhhhcccCCeEEEeeeEEEEe
Confidence 3456788999999988766521 2566667765 678876666666667899999999999999988744
No 170
>PRK05853 hypothetical protein; Validated
Probab=50.78 E-value=56 Score=32.45 Aligned_cols=34 Identities=15% Similarity=0.170 Sum_probs=29.3
Q ss_pred eeCCCCEEEEEEechHHHhhhhccCcCcEEEEee
Q 003281 262 LDSDGGEIRVTCFNAVADQFYHQVEAGKIYLVSR 295 (834)
Q Consensus 262 ~De~g~~I~at~f~~~~d~f~~~l~eG~vy~is~ 295 (834)
.|++..-|.+++|+.+++.+...|..|+-+.+..
T Consensus 38 ~d~~T~wi~V~~wg~lAe~v~~~L~KG~~V~V~G 71 (161)
T PRK05853 38 EPGNSLFITVNCWGRLVTGVGAALGKGAPVIVVG 71 (161)
T ss_pred eccCccEEEEEEEhHHHHHHHHHcCCCCEEEEEE
Confidence 3444567999999999999999999999999976
No 171
>PRK08763 single-stranded DNA-binding protein; Provisional
Probab=50.32 E-value=94 Score=30.99 Aligned_cols=35 Identities=14% Similarity=0.141 Sum_probs=23.3
Q ss_pred EEEEEEcCCccchhhhhhhhcccCCCccEEEEEE-EEEeecC
Q 003281 391 SVELTLWGNFCNDDGLRLQHMCDSGVFPILAVKA-GRVSDFN 431 (834)
Q Consensus 391 si~vtLWg~~a~~~~~~l~~~~~~~~~~Vv~ik~-~rV~~f~ 431 (834)
-++|++||+.|+...++|. .+.-|+|.+ .+...|.
T Consensus 53 w~~Vv~fgk~Ae~v~~~L~------KGs~V~VeGrL~~~~y~ 88 (164)
T PRK08763 53 WHRVKFFGKLGEIAGEYLR------KGSQCYIEGSIRYDKFT 88 (164)
T ss_pred EEEEEEehHHHHHHHHhcC------CCCEEEEEEEEEeceeE
Confidence 4899999999876554432 455565654 5666674
No 172
>PRK10917 ATP-dependent DNA helicase RecG; Provisional
Probab=49.86 E-value=43 Score=41.17 Aligned_cols=87 Identities=23% Similarity=0.358 Sum_probs=57.3
Q ss_pred CceeccccCCCCCceEEEEEEEEeccceeecCCCCCcceEEEEEeeCCCCEEEEEEechHHHhh-hhccCcCcEEEEeee
Q 003281 218 RIIPIAALNPYMGKWTIKARVTAKGELRHYNNQRGDGKVFHFDLLDSDGGEIRVTCFNAVADQF-YHQVEAGKIYLVSRG 296 (834)
Q Consensus 218 ~~~pI~~L~p~~~~w~I~aRV~~Ks~lr~~~n~~g~Gk~f~~~L~De~g~~I~at~f~~~~d~f-~~~l~eG~vy~is~~ 296 (834)
.+.+|+++.+. ..-+|.|+|+.....+. ..+++.+.+.|+ .|.|.+++|+-. ..| ...|++|+.|.+++
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 RLKPIAELRPG-EKVTVEGEVLSAEVVFG------KRRRLTVTVSDG-TGNLTLRFFNFN-QPYLKKQLKVGKRVAVYG- 118 (681)
T ss_pred CcCCHHHCCCC-CEEEEEEEEEEEEEccC------CceEEEEEEEEC-CeEEEEEEEccC-cHHHHhhCCCCCEEEEEE-
Confidence 46789999875 57999999987632221 135899999997 478999999410 124 57899999999976
Q ss_pred EEecCCcccccCCCeEEE
Q 003281 297 SLKPAQKNFNHLHNDLEI 314 (834)
Q Consensus 297 ~V~~a~~~~~~~~~~yeI 314 (834)
+|......+....-+|++
T Consensus 119 kv~~~~~~~qm~~P~~~~ 136 (681)
T PRK10917 119 KVKRGKYGLEMVHPEYEV 136 (681)
T ss_pred EEEecCCeEEEEcCEEEe
Confidence 343332222233345543
No 173
>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=49.33 E-value=2e+02 Score=25.89 Aligned_cols=72 Identities=17% Similarity=0.146 Sum_probs=45.2
Q ss_pred eEEEEEEEEeccceeecCCCCCcceEEEEEeeCCCCEEEEEEechH-HHhhh--hccCcCcEEEEeeeEEecCCcccccC
Q 003281 232 WTIKARVTAKGELRHYNNQRGDGKVFHFDLLDSDGGEIRVTCFNAV-ADQFY--HQVEAGKIYLVSRGSLKPAQKNFNHL 308 (834)
Q Consensus 232 w~I~aRV~~Ks~lr~~~n~~g~Gk~f~~~L~De~g~~I~at~f~~~-~d~f~--~~l~eG~vy~is~~~V~~a~~~~~~~ 308 (834)
-+|.+||.+ +|. -|++.-++|.|. ++.|++.+..+. .+.|. ..|..|+++.+.+.-..... .
T Consensus 2 V~v~Gwv~~---~R~------~gk~~Fi~lrD~-~g~iQ~v~~~~~~~~~~~~~~~l~~~s~v~V~G~v~~~~~-----~ 66 (103)
T cd04319 2 VTLAGWVYR---KRE------VGKKAFIVLRDS-TGIVQAVFSKDLNEEAYREAKKVGIESSVIVEGAVKADPR-----A 66 (103)
T ss_pred EEEEEEEEe---EEc------CCCeEEEEEecC-CeeEEEEEeCCCCHHHHHHHhCCCCCCEEEEEEEEEECCC-----C
Confidence 467788864 233 256666788997 578999887541 11222 35889999999875333221 1
Q ss_pred CCeEEEEEcc
Q 003281 309 HNDLEIFLDM 318 (834)
Q Consensus 309 ~~~yeI~f~~ 318 (834)
...+||..+.
T Consensus 67 ~~~~Ei~~~~ 76 (103)
T cd04319 67 PGGAEVHGEK 76 (103)
T ss_pred CCCEEEEEEE
Confidence 2369998854
No 174
>PRK06958 single-stranded DNA-binding protein; Provisional
Probab=48.42 E-value=97 Score=31.44 Aligned_cols=35 Identities=11% Similarity=0.146 Sum_probs=23.2
Q ss_pred EEEEEEcCCccchhhhhhhhcccCCCccEEEEEE-EEEeecC
Q 003281 391 SVELTLWGNFCNDDGLRLQHMCDSGVFPILAVKA-GRVSDFN 431 (834)
Q Consensus 391 si~vtLWg~~a~~~~~~l~~~~~~~~~~Vv~ik~-~rV~~f~ 431 (834)
-+.|++|++.|+.+.+.|. .+..|.|.+ .+...|.
T Consensus 53 w~~V~~fGk~AE~v~~~Lk------KGs~V~VeGrL~~~~ye 88 (182)
T PRK06958 53 WHRVAFFGRLAEIVGEYLK------KGSSVYIEGRIRTRKWQ 88 (182)
T ss_pred EEEEEEehHHHHHHHHHhC------CCCEEEEEEEEEeCceE
Confidence 6899999999876554442 345555544 5666664
No 175
>PRK07135 dnaE DNA polymerase III DnaE; Validated
Probab=47.00 E-value=54 Score=41.75 Aligned_cols=74 Identities=19% Similarity=0.157 Sum_probs=49.3
Q ss_pred eeccccCCCCCceEEEEEEEEeccceeecCCCCCcceEEEEEeeCCCCEEEEEEechHHHhhhhccCcCcEEEEeeeEEe
Q 003281 220 IPIAALNPYMGKWTIKARVTAKGELRHYNNQRGDGKVFHFDLLDSDGGEIRVTCFNAVADQFYHQVEAGKIYLVSRGSLK 299 (834)
Q Consensus 220 ~pI~~L~p~~~~w~I~aRV~~Ks~lr~~~n~~g~Gk~f~~~L~De~g~~I~at~f~~~~d~f~~~l~eG~vy~is~~~V~ 299 (834)
.+|.+|. .....+|-+.|+..-.++ .+|+ ...-++|-|. .++|.+++|.+..+++.+ |.++++|+++ +++.
T Consensus 889 ~~~~~l~-~~~~~~v~g~i~~~~~~~----K~g~-~maf~~~eD~-~~~~e~~~F~~~~~~~~~-l~~~~~~~~~-~~~~ 959 (973)
T PRK07135 889 IRLKDLR-INTEYRLAIEVKNVKRLR----KANK-EYKKVILSDD-SVEITIFVNDNDYLLFET-LKKGDIYEFL-ISKS 959 (973)
T ss_pred hhHHHhc-CCCeEEEEEEEEEEEEEe----eCCC-eEEEEEEEEC-CCcEEEEEcHHHHHHHHH-hhcCCEEEEE-EEEc
Confidence 4677874 234456777777543333 3332 3455677887 589999999999888887 8888898883 4443
Q ss_pred cCC
Q 003281 300 PAQ 302 (834)
Q Consensus 300 ~a~ 302 (834)
.+|
T Consensus 960 ~~~ 962 (973)
T PRK07135 960 KNN 962 (973)
T ss_pred CCC
Confidence 333
No 176
>COG0017 AsnS Aspartyl/asparaginyl-tRNA synthetases [Translation, ribosomal structure and biogenesis]
Probab=46.78 E-value=1.9e+02 Score=33.42 Aligned_cols=90 Identities=19% Similarity=0.238 Sum_probs=59.1
Q ss_pred eeccccCCCC--CceEEEEEEEEeccceeecCCCCCcceEEEEEeeCCCCEEEEEEech-H-HHhh-hhccCcCcEEEEe
Q 003281 220 IPIAALNPYM--GKWTIKARVTAKGELRHYNNQRGDGKVFHFDLLDSDGGEIRVTCFNA-V-ADQF-YHQVEAGKIYLVS 294 (834)
Q Consensus 220 ~pI~~L~p~~--~~w~I~aRV~~Ks~lr~~~n~~g~Gk~f~~~L~De~g~~I~at~f~~-~-~d~f-~~~l~eG~vy~is 294 (834)
+.|+++.+.. ...+|.+-|-.+ |..|++.-+.|.|. ++.|++++... . -+.| ...|..++++.+.
T Consensus 5 ~~i~di~~~~~~~~V~v~GWV~~~---------R~~g~i~Fi~lrDg-sg~iQ~v~~~~~~~~~~~~~~~L~~es~v~V~ 74 (435)
T COG0017 5 TYIKDIKPHVGGQEVTVRGWVHNK---------RDLGKIIFLVLRDG-SGFIQAVVPKNKVYEELFKAKKLTLESSVVVT 74 (435)
T ss_pred eeHHhhhccCCCcEEEEEEEeeee---------cccCCeEEEEEEcC-CcEEEEEEECCCCcHHHhhhhcCCCccEEEEE
Confidence 5677777765 477777777543 23467777778897 57799999842 2 2223 3468889999998
Q ss_pred eeEEecCCcccccCCCeEEEEEccCccEEE
Q 003281 295 RGSLKPAQKNFNHLHNDLEIFLDMTSMVQL 324 (834)
Q Consensus 295 ~~~V~~a~~~~~~~~~~yeI~f~~~T~I~~ 324 (834)
+.-++ ..+ .+..|||....=.++-.
T Consensus 75 G~v~~-~~~----a~~g~El~v~~i~Vl~~ 99 (435)
T COG0017 75 GIVKA-SPK----APQGFELQVEKIEVLGE 99 (435)
T ss_pred EEEEc-CCC----CCCCEEEEEEEEEEeec
Confidence 75433 322 56789999975444433
No 177
>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=46.68 E-value=35 Score=29.03 Aligned_cols=40 Identities=30% Similarity=0.463 Sum_probs=31.6
Q ss_pred cceEEEEEeeCCCCEEEEEEechHHHhhhhccCcCcEEEEee
Q 003281 254 GKVFHFDLLDSDGGEIRVTCFNAVADQFYHQVEAGKIYLVSR 295 (834)
Q Consensus 254 Gk~f~~~L~De~g~~I~at~f~~~~d~f~~~l~eG~vy~is~ 295 (834)
|. .-|.|.|+ +..|++.+|.....+....+++|+-+.+..
T Consensus 15 GH-vyfsLkD~-~a~i~cv~f~~~~~~~~~~l~~Gd~V~v~G 54 (73)
T cd04487 15 GP-TIFTLRDE-TGTVWAAAFEEAGVRAYPEVEVGDIVRVTG 54 (73)
T ss_pred CC-EEEEEEcC-CEEEEEEEEchhccCCcCCCCCCCEEEEEE
Confidence 54 55678896 589999999887766777899999777765
No 178
>PRK07279 dnaE DNA polymerase III DnaE; Reviewed
Probab=46.30 E-value=47 Score=42.56 Aligned_cols=72 Identities=21% Similarity=0.372 Sum_probs=51.3
Q ss_pred ceeccccCCCCCceEEEEEEEEeccceeecCCCCCcceEEEEEeeCCCCEEEEEEechHHHhhhhccCcCcEEEEee
Q 003281 219 IIPIAALNPYMGKWTIKARVTAKGELRHYNNQRGDGKVFHFDLLDSDGGEIRVTCFNAVADQFYHQVEAGKIYLVSR 295 (834)
Q Consensus 219 ~~pI~~L~p~~~~w~I~aRV~~Ks~lr~~~n~~g~Gk~f~~~L~De~g~~I~at~f~~~~d~f~~~l~eG~vy~is~ 295 (834)
+.++++|.. .....+.+.|+....+++- ++|+ ...-+.|-|+ .|+|.+++|.+..+++.+.|++|.++.|..
T Consensus 875 ~~~~~~l~~-~~~~~~~~~i~~~~~~~tk--~~g~-~maf~~leD~-~g~ie~~vFp~~y~~~~~~l~~~~~~~v~G 946 (1034)
T PRK07279 875 FTPISQLVK-NSEATILVQIQSIRVIRTK--TKGQ-QMAFLSVTDT-KKKLDVTLFPETYRQYKDELKEGKFYYLKG 946 (1034)
T ss_pred CccHHHHhc-CCcceEEEEEEEEEEEEEc--CCCC-eEEEEEEeeC-CCcEEEEECHHHHHHHHHHhccCCEEEEEE
Confidence 456777753 3345677777754433331 1332 3455677886 589999999999999999999999999965
No 179
>PRK06826 dnaE DNA polymerase III DnaE; Reviewed
Probab=45.99 E-value=40 Score=43.81 Aligned_cols=77 Identities=22% Similarity=0.302 Sum_probs=51.3
Q ss_pred cccccccc---------ccCCCceeeEEEEEEEecCCeeEEccCCceeeEEEEEEeccCCcEEEEEEcCCccchhhhhhh
Q 003281 339 FRPINDVE---------GMENNSVVDLIGVVSYISPTASLMRKNGTETQKRTLHLRDMSGRSVELTLWGNFCNDDGLRLQ 409 (834)
Q Consensus 339 f~~i~dI~---------~~~~~~~vDVIGvV~~V~~~~~i~~k~g~~~~kr~i~L~D~s~~si~vtLWg~~a~~~~~~l~ 409 (834)
..++++|. .+..+..|-|+|+|+.+... .+|+|+. .--++|.|.+| .+++++|.+..+.....+.
T Consensus 970 ~~~~~~l~~~~~~~~~~~~~~~~~v~v~g~i~~~~~~---~tk~G~~--maf~~leD~~g-~~e~~vfp~~~~~~~~~l~ 1043 (1151)
T PRK06826 970 SATISDIISDEEEDGESKLKDGDKVIIGGIITEVKRK---TTRNNEM--MAFLTLEDLYG-TVEVIVFPKVYEKYRSLLN 1043 (1151)
T ss_pred CcCHHHHhhhccccccccccCCcEEEEEEEEEEeEee---ccCCCCe--EEEEEEEECCC-cEEEEECHHHHHHHHHHhc
Confidence 35666762 33345678899999987644 4667763 45688999999 7999999987655443332
Q ss_pred hcccCCCccEEEEEEEEEe
Q 003281 410 HMCDSGVFPILAVKAGRVS 428 (834)
Q Consensus 410 ~~~~~~~~~Vv~ik~~rV~ 428 (834)
.+.+|.+++ +|.
T Consensus 1044 ------~~~~~~v~g-~v~ 1055 (1151)
T PRK06826 1044 ------EDNIVLIKG-RVS 1055 (1151)
T ss_pred ------cCCEEEEEE-EEE
Confidence 345666654 454
No 180
>PRK05813 single-stranded DNA-binding protein; Provisional
Probab=45.36 E-value=95 Score=32.47 Aligned_cols=73 Identities=12% Similarity=0.007 Sum_probs=53.9
Q ss_pred ceeccccC--CCCCceEEEEEEEEeccceeecCCCCCcceEEEEEeeC----CCCEEEEEEechHHHhhhhccCcCcEEE
Q 003281 219 IIPIAALN--PYMGKWTIKARVTAKGELRHYNNQRGDGKVFHFDLLDS----DGGEIRVTCFNAVADQFYHQVEAGKIYL 292 (834)
Q Consensus 219 ~~pI~~L~--p~~~~w~I~aRV~~Ks~lr~~~n~~g~Gk~f~~~L~De----~g~~I~at~f~~~~d~f~~~l~eG~vy~ 292 (834)
+..+..-. -.++...|.+|+++.-.+|...+ | ..+.+|.|+=. +.+-|.+++|+..++... .|+.|+-+.
T Consensus 97 i~~l~~~~~~~~~N~V~LiGrL~~DPelR~t~~--G-~~va~f~lAvnr~~~~td~i~~v~wg~~Ae~~~-~l~KG~~V~ 172 (219)
T PRK05813 97 IEYCDERSDIKNPNEIFLDGYICKEPVYRTTPF--G-REIADLLLAVNRPYNKSDYIPCIAWGRNARFCK-TLEVGDNIR 172 (219)
T ss_pred EEEccCCCccCCccEEEEEEEccCCCeEEECCC--C-CEEEEEEEEEcCCCCCceEEEEEEEhHHhHHHh-hCCCCCEEE
Confidence 34444432 23578999999999999987643 2 26778887622 247899999999998665 599999999
Q ss_pred Eee
Q 003281 293 VSR 295 (834)
Q Consensus 293 is~ 295 (834)
|.+
T Consensus 173 V~G 175 (219)
T PRK05813 173 VWG 175 (219)
T ss_pred EEE
Confidence 975
No 181
>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=45.16 E-value=2.1e+02 Score=24.89 Aligned_cols=76 Identities=18% Similarity=0.216 Sum_probs=43.8
Q ss_pred eEEEEEEEEeccceeecCCCCCcceEEEEEeeCCCCEEEEEEechHHHhhh--hccCcCcEEEEeeeEEecCCcccccCC
Q 003281 232 WTIKARVTAKGELRHYNNQRGDGKVFHFDLLDSDGGEIRVTCFNAVADQFY--HQVEAGKIYLVSRGSLKPAQKNFNHLH 309 (834)
Q Consensus 232 w~I~aRV~~Ks~lr~~~n~~g~Gk~f~~~L~De~g~~I~at~f~~~~d~f~--~~l~eG~vy~is~~~V~~a~~~~~~~~ 309 (834)
.+|.++|.+ +|.. .|++.-++|.|..|..|++++-.+. +.|. ..|..|+++.+..- |......-..-.
T Consensus 2 V~v~Gwv~~---~R~~-----~~~~~Fi~LrD~~g~~iQvv~~~~~-~~~~~~~~l~~~s~V~V~G~-v~~~~~~~~~~~ 71 (86)
T cd04321 2 VTLNGWIDR---KPRI-----VKKLSFADLRDPNGDIIQLVSTAKK-DAFSLLKSITAESPVQVRGK-LQLKEAKSSEKN 71 (86)
T ss_pred EEEEEeEee---EeCC-----CCceEEEEEECCCCCEEEEEECCCH-HHHHHHhcCCCCcEEEEEEE-EEeCCCcCCCCC
Confidence 456777754 2321 1567777889986646998765432 3333 34889999999764 433221110112
Q ss_pred CeEEEEEc
Q 003281 310 NDLEIFLD 317 (834)
Q Consensus 310 ~~yeI~f~ 317 (834)
..+||..+
T Consensus 72 ~~~Ei~~~ 79 (86)
T cd04321 72 DEWELVVD 79 (86)
T ss_pred CCEEEEEE
Confidence 56777663
No 182
>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=44.73 E-value=1.6e+02 Score=28.56 Aligned_cols=87 Identities=15% Similarity=0.219 Sum_probs=50.5
Q ss_pred ceEEEEEEEEeccceeecCCCCCcceEEEEEe-------e--CCCCEEEEEEechHHHhhhhccCcCcEEEEeeeEEecC
Q 003281 231 KWTIKARVTAKGELRHYNNQRGDGKVFHFDLL-------D--SDGGEIRVTCFNAVADQFYHQVEAGKIYLVSRGSLKPA 301 (834)
Q Consensus 231 ~w~I~aRV~~Ks~lr~~~n~~g~Gk~f~~~L~-------D--e~g~~I~at~f~~~~d~f~~~l~eG~vy~is~~~V~~a 301 (834)
.+.++|||+.......|. .|.+.+. | ..++.++...-...+ +-...|++|+.|.|.+-.....
T Consensus 24 DYa~kv~V~~~~~~~~~~-------~~~~~v~~V~K~g~~~~~~~~~~~~~~~~~~C-~c~~~l~~g~~YLImG~~~~~~ 95 (147)
T cd03574 24 DYVYKVKVTSVEEEAGFR-------IYKARVTEVIKSGSDDVQNGNARRTFIIRESC-DCPLRLKEGRHYLIMGSDGAFY 95 (147)
T ss_pred ceEEEEEEEEEEecCCeE-------EEEEEEEEEEecccccccCCCceEEEEccCCc-cchhcCCCCCEEEEeccCcCcc
Confidence 788888888765543332 2333221 1 123355543223333 2235678999999988642221
Q ss_pred CcccccCCCeEEEEEccCccEEEecC
Q 003281 302 QKNFNHLHNDLEIFLDMTSMVQLCYE 327 (834)
Q Consensus 302 ~~~~~~~~~~yeI~f~~~T~I~~~~d 327 (834)
.. ......|.+.++++|.|+..+.
T Consensus 96 ~~--~~~~~~~~yvl~~~t~Ve~Wp~ 119 (147)
T cd03574 96 DD--RNGEDRYQYVLDSNTWVEEWPT 119 (147)
T ss_pred cc--cCCCcceEEEeCCCcEEEECCC
Confidence 10 1122368999999999999865
No 183
>PRK06863 single-stranded DNA-binding protein; Provisional
Probab=44.56 E-value=1.1e+02 Score=30.61 Aligned_cols=71 Identities=11% Similarity=0.095 Sum_probs=39.0
Q ss_pred eeeEEEEEEEecCCeeEEccCCceeeEEEEEEe----cc-C------CcEEEEEEcCCccchhhhhhhhcccCCCccEEE
Q 003281 353 VVDLIGVVSYISPTASLMRKNGTETQKRTLHLR----DM-S------GRSVELTLWGNFCNDDGLRLQHMCDSGVFPILA 421 (834)
Q Consensus 353 ~vDVIGvV~~V~~~~~i~~k~g~~~~kr~i~L~----D~-s------~~si~vtLWg~~a~~~~~~l~~~~~~~~~~Vv~ 421 (834)
.|-++|.|.. +...-.+.+|+.+.+-.|-.- |. . ..-+.|++|+..|+...+.|. .+.-|.
T Consensus 6 ~V~LiGrLg~--DPElR~t~nG~~va~fsVAvn~~~~d~~~Ge~~e~t~w~~Vv~fgk~AE~v~~~Lk------KGs~V~ 77 (168)
T PRK06863 6 KVIIVGHLGN--DPEIRTMPNGEAVANISVATSESWTDKNTGERREVTEWHRIVFYRRQAEVAGEYLR------KGSQVY 77 (168)
T ss_pred EEEEEEEcCC--CCEEEEcCCCCEEEEEEEEecCcccccCCCcccccceEEEEEEEhHHHHHHHHHCC------CCCEEE
Confidence 4667777766 222222345654443333321 11 1 125899999999877655442 345555
Q ss_pred EE-EEEEeecC
Q 003281 422 VK-AGRVSDFN 431 (834)
Q Consensus 422 ik-~~rV~~f~ 431 (834)
+. ..+...|.
T Consensus 78 VeGrL~~r~w~ 88 (168)
T PRK06863 78 VEGRLKTRKWQ 88 (168)
T ss_pred EEEEEEeCCcc
Confidence 54 45666674
No 184
>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=44.09 E-value=11 Score=33.59 Aligned_cols=28 Identities=36% Similarity=0.948 Sum_probs=21.7
Q ss_pred CCCCCcCCCCcCcc-cccCCCCceecCCCCCcccc
Q 003281 522 ACPIMIGDRPCNKK-VMNNGDGRWHCDRCDQSVVE 555 (834)
Q Consensus 522 aC~~~~~~~~C~KK-v~~~~dg~~~CekC~~~~~~ 555 (834)
.|| -|.|. |....-|.|.|.+|+..+.-
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 599 69765 55567799999999987643
No 185
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=43.60 E-value=12 Score=33.28 Aligned_cols=31 Identities=32% Similarity=0.847 Sum_probs=22.8
Q ss_pred CCCCCcCCCCcCcc-cccCCCCceecCCCCCccccceE
Q 003281 522 ACPIMIGDRPCNKK-VMNNGDGRWHCDRCDQSVVECDY 558 (834)
Q Consensus 522 aC~~~~~~~~C~KK-v~~~~dg~~~CekC~~~~~~~~~ 558 (834)
.|| -|.|. |.....|.|.|.+|+..+.---|
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 599 69765 65566799999999987654333
No 186
>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=43.49 E-value=57 Score=28.22 Aligned_cols=59 Identities=20% Similarity=0.188 Sum_probs=39.3
Q ss_pred EEEEEcccccccccccccchhh--hhhcCCcccccEEEEceeeeecc-----cCeEEEEEEeeeEe
Q 003281 27 FRMVLSDGSRSQQGMLATQRNE--LVTSGLLQIGSVVRLTKFTCNVI-----QNRMIVIVMDLDVI 85 (834)
Q Consensus 27 yrl~lSDG~~~~~~mLatqln~--lv~~g~l~~gsiv~l~~~~~~~v-----~~r~iiii~~lev~ 85 (834)
-=+.|.||...+|+++.....+ .-.-..|..||+|.++=.....- .+..=|.+.+++++
T Consensus 18 ~Fi~Lrd~~~~iQ~v~~~~~~~~~~~~~~~l~~~s~V~v~G~~~~~~~~~~~~~~~El~~~~i~il 83 (85)
T cd04100 18 IFIDLRDGSGIVQVVVNKEELGEFFEEAEKLRTESVVGVTGTVVKRPEGNLATGEIELQAEELEVL 83 (85)
T ss_pred EEEEEEeCCeeEEEEEECCcChHHHHHHhCCCCCCEEEEEeEEEECCCCCCCCCCEEEEEeEEEEE
Confidence 4577899999999998765433 22224699999999988766543 22234455666555
No 187
>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=43.27 E-value=1.6e+02 Score=34.05 Aligned_cols=80 Identities=16% Similarity=0.106 Sum_probs=52.4
Q ss_pred CceEEEEEEEEeccceeecCCCCCcceEEEEEeeCCCCEEEEEEechH----HHhhhhccCcCcEEEEeeeEEecCCccc
Q 003281 230 GKWTIKARVTAKGELRHYNNQRGDGKVFHFDLLDSDGGEIRVTCFNAV----ADQFYHQVEAGKIYLVSRGSLKPAQKNF 305 (834)
Q Consensus 230 ~~w~I~aRV~~Ks~lr~~~n~~g~Gk~f~~~L~De~g~~I~at~f~~~----~d~f~~~l~eG~vy~is~~~V~~a~~~~ 305 (834)
..-+|++||.++ |. .|++.-++|.|. ++.|++++-... .-++...|..|+++.+.+.-++ ..+
T Consensus 13 ~~v~i~G~v~~~---R~------~g~~~Fi~lrd~-~g~iQ~v~~~~~~~~~~~~~~~~l~~~s~v~v~G~v~~-~~~-- 79 (428)
T TIGR00458 13 QEVTFMGWVHEI---RD------LGGLIFVLLRDR-EGLIQITAPAKKVSKNLFKWAKKLNLESVVAVRGIVKI-KEK-- 79 (428)
T ss_pred CEEEEEEEEEEE---ec------CCCcEEEEEEeC-CeeEEEEEECCcCCHHHHHHHhCCCCCcEEEEEEEEEe-cCC--
Confidence 467889999753 33 367777889997 569999987432 1123356999999999875442 221
Q ss_pred ccCCCeEEEEEccCccEEE
Q 003281 306 NHLHNDLEIFLDMTSMVQL 324 (834)
Q Consensus 306 ~~~~~~yeI~f~~~T~I~~ 324 (834)
....+||....-+.+..
T Consensus 80 --~~~~~el~~~~i~vl~~ 96 (428)
T TIGR00458 80 --APGGFEIIPTKIEVINE 96 (428)
T ss_pred --CCCcEEEEEeEEEEEec
Confidence 23478888865444433
No 188
>PRK07374 dnaE DNA polymerase III subunit alpha; Validated
Probab=43.24 E-value=51 Score=42.90 Aligned_cols=71 Identities=18% Similarity=0.287 Sum_probs=50.3
Q ss_pred eeccccC--CCCCceEEEEEEEEeccceeecCCCCCcceEEEEEeeCCCCEEEEEEechHHHhhhhccCcCcEEEEee
Q 003281 220 IPIAALN--PYMGKWTIKARVTAKGELRHYNNQRGDGKVFHFDLLDSDGGEIRVTCFNAVADQFYHQVEAGKIYLVSR 295 (834)
Q Consensus 220 ~pI~~L~--p~~~~w~I~aRV~~Ks~lr~~~n~~g~Gk~f~~~L~De~g~~I~at~f~~~~d~f~~~l~eG~vy~is~ 295 (834)
+++++|. +......|-+-|+.. |.....+|+ .+.-+.|-|+ .|.|.+++|.+..+++.+.|++|.++.|..
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 ISLSSLEEQPDKAKVSAIAMIPEM---KQVTTRKGD-RMAILQLEDL-TGSCEAVVFPKSYERLSDHLMTDTRLLVWA 1061 (1170)
T ss_pred cCHHHHhcccCCCEEEEEEEEEEe---EecccCCCC-EEEEEEEEEC-CCCEEEEECHHHHHHHHHHhccCCEEEEEE
Confidence 4666664 223456677777754 333333432 3445667886 589999999999999999999999999964
No 189
>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=42.77 E-value=81 Score=33.59 Aligned_cols=57 Identities=9% Similarity=0.077 Sum_probs=39.7
Q ss_pred CEEEEEEechHHHhhhhccCcCcEEEEeeeEEecCCcccccCCCeEEEEEccCccEEEec
Q 003281 267 GEIRVTCFNAVADQFYHQVEAGKIYLVSRGSLKPAQKNFNHLHNDLEIFLDMTSMVQLCY 326 (834)
Q Consensus 267 ~~I~at~f~~~~d~f~~~l~eG~vy~is~~~V~~a~~~~~~~~~~yeI~f~~~T~I~~~~ 326 (834)
...-.|||+.. +.+.++|+||++|.|.+.......++ ....+..|+-...|.-.+++
T Consensus 180 ~~~~LTIWrPt-edl~s~L~EG~ry~i~~L~~s~~k~~--~~~~~vqLtatk~Tr~~~l~ 236 (251)
T cd04494 180 KSGLLSIWRPT-EDLRSLLTEGKRYRIYGLATSNSKKR--SGNEEVQLTATKKTRYQPLP 236 (251)
T ss_pred ceEEEEEeCCC-HHHHhhhcCCcEEEEEeccccCCCCC--CCcceEEEEecCcccceECC
Confidence 34455666643 46778999999999998764433332 34467888888888888864
No 190
>PRK13732 single-stranded DNA-binding protein; Provisional
Probab=41.72 E-value=1.8e+02 Score=29.25 Aligned_cols=35 Identities=14% Similarity=0.198 Sum_probs=23.2
Q ss_pred EEEEEEcCCccchhhhhhhhcccCCCccEEEEEE-EEEeecC
Q 003281 391 SVELTLWGNFCNDDGLRLQHMCDSGVFPILAVKA-GRVSDFN 431 (834)
Q Consensus 391 si~vtLWg~~a~~~~~~l~~~~~~~~~~Vv~ik~-~rV~~f~ 431 (834)
-++|++||+.|+...+.|. .+..|+|.+ .+...|.
T Consensus 55 w~~Vv~wgk~Ae~v~~~L~------KG~~V~VeGrL~~r~ye 90 (175)
T PRK13732 55 WHRVVLFGKLAEVAGEYLR------KGAQVYIEGQLRTRSWE 90 (175)
T ss_pred EEEEEEecHHHHHHHHhcC------CCCEEEEEEEEEeeeEc
Confidence 5789999999887655442 355555544 5666664
No 191
>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=41.64 E-value=1.2e+02 Score=26.58 Aligned_cols=37 Identities=11% Similarity=0.207 Sum_probs=24.3
Q ss_pred CcEEEEEEcCCccchhhhhhhhcccCCCccEEEEEE-EEEeecC
Q 003281 389 GRSVELTLWGNFCNDDGLRLQHMCDSGVFPILAVKA-GRVSDFN 431 (834)
Q Consensus 389 ~~si~vtLWg~~a~~~~~~l~~~~~~~~~~Vv~ik~-~rV~~f~ 431 (834)
...+.|++||+.|+.+.+.+. .+..|.+.+ .+...|.
T Consensus 43 ~~~~~v~~~g~~a~~~~~~~~------kG~~V~v~G~l~~~~~~ 80 (100)
T cd04496 43 TDWIRVVAFGKLAENAAKYLK------KGDLVYVEGRLRTRSWE 80 (100)
T ss_pred cEEEEEEEEhHHHHHHHHHhC------CCCEEEEEEEEEeceeE
Confidence 357999999998876554432 455665654 5666564
No 192
>PRK02801 primosomal replication protein N; Provisional
Probab=41.52 E-value=93 Score=28.24 Aligned_cols=65 Identities=17% Similarity=0.124 Sum_probs=36.9
Q ss_pred eeeEEEEEEEecCCeeEEccCCceeeEEEEEEe---ccCCc------EEEEEEcCCccchhhhhhhhcccCCCccEEEEE
Q 003281 353 VVDLIGVVSYISPTASLMRKNGTETQKRTLHLR---DMSGR------SVELTLWGNFCNDDGLRLQHMCDSGVFPILAVK 423 (834)
Q Consensus 353 ~vDVIGvV~~V~~~~~i~~k~g~~~~kr~i~L~---D~s~~------si~vtLWg~~a~~~~~~l~~~~~~~~~~Vv~ik 423 (834)
.|-++|.++.--++.. +.+|..+..-.|-.. ++.+. .|.|++||+.|+...+++. .+..|.+.
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--SPSGIPHCQFVLEHRSVQEEAGLHRQAWCRMPVIVSGNQFQAITQSIT------VGSKITVQ 75 (101)
T ss_pred EEEEEEEECcCcceEE--CCCCCeEEEEEEEEeCeEecCCCceeEEEEEEEEEEcHHHHHHHhhcC------CCCEEEEE
Confidence 3567777776655543 234554333222221 12221 3899999999987654442 46677776
Q ss_pred EE
Q 003281 424 AG 425 (834)
Q Consensus 424 ~~ 425 (834)
+-
T Consensus 76 G~ 77 (101)
T PRK02801 76 GF 77 (101)
T ss_pred EE
Confidence 63
No 193
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=41.33 E-value=12 Score=33.25 Aligned_cols=28 Identities=32% Similarity=0.972 Sum_probs=21.3
Q ss_pred CCCCCcCCCCcCcc-cccCCCCceecCCCCCcccc
Q 003281 522 ACPIMIGDRPCNKK-VMNNGDGRWHCDRCDQSVVE 555 (834)
Q Consensus 522 aC~~~~~~~~C~KK-v~~~~dg~~~CekC~~~~~~ 555 (834)
.|| -|.|. |....-|.|.|.+|+..+.-
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 599 69764 55566789999999987643
No 194
>PRK06920 dnaE DNA polymerase III DnaE; Reviewed
Probab=40.93 E-value=52 Score=42.57 Aligned_cols=77 Identities=13% Similarity=0.132 Sum_probs=51.3
Q ss_pred cccccccccccCCCceeeEEEEEEEecCCeeEEccCCceeeEEEEEEeccCCcEEEEEEcCCccchhhhhhhhcccCCCc
Q 003281 338 HFRPINDVEGMENNSVVDLIGVVSYISPTASLMRKNGTETQKRTLHLRDMSGRSVELTLWGNFCNDDGLRLQHMCDSGVF 417 (834)
Q Consensus 338 ~f~~i~dI~~~~~~~~vDVIGvV~~V~~~~~i~~k~g~~~~kr~i~L~D~s~~si~vtLWg~~a~~~~~~l~~~~~~~~~ 417 (834)
...++.+|.. ..+..|-|+|+|+.+... ++|+|+. .--++|.|.+| .+++++|.+..+.+...+. .+
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 234578899999988644 4667763 45689999999 6999999987665444332 34
Q ss_pred cEEEEEEEEEe
Q 003281 418 PILAVKAGRVS 428 (834)
Q Consensus 418 ~Vv~ik~~rV~ 428 (834)
.+|.+++ +|.
T Consensus 998 ~~~~v~G-~v~ 1007 (1107)
T PRK06920 998 AIVLVDG-TIE 1007 (1107)
T ss_pred CEEEEEE-EEE
Confidence 5666654 443
No 195
>KOG3116 consensus Predicted C3H1-type Zn-finger protein [General function prediction only]
Probab=40.65 E-value=6.8 Score=37.53 Aligned_cols=21 Identities=38% Similarity=1.058 Sum_probs=18.6
Q ss_pred CCcCcccCCCCccCCCCCCCC
Q 003281 785 SSECYKCHKTGHWARDCPSLN 805 (834)
Q Consensus 785 ~~~Cy~Cg~~GH~ardCp~~~ 805 (834)
...|-+|-|.|||.-+|.+..
T Consensus 27 ~~rCQKClq~GHWtYECk~kR 47 (177)
T KOG3116|consen 27 SARCQKCLQAGHWTYECKNKR 47 (177)
T ss_pred chhHHHHHhhccceeeecCce
Confidence 458999999999999999864
No 196
>COG1200 RecG RecG-like helicase [DNA replication, recombination, and repair / Transcription]
Probab=40.31 E-value=2.1e+02 Score=34.82 Aligned_cols=90 Identities=20% Similarity=0.279 Sum_probs=60.8
Q ss_pred CCceeccccCCCCCceEEEEEEEEeccceeecCCCCCcceEEEEEeeCCCCEEEEEEechHHHhhhhccCcCcEEEEeee
Q 003281 217 SRIIPIAALNPYMGKWTIKARVTAKGELRHYNNQRGDGKVFHFDLLDSDGGEIRVTCFNAVADQFYHQVEAGKIYLVSRG 296 (834)
Q Consensus 217 ~~~~pI~~L~p~~~~w~I~aRV~~Ks~lr~~~n~~g~Gk~f~~~L~De~g~~I~at~f~~~~d~f~~~l~eG~vy~is~~ 296 (834)
+....|.++.+. ...+|.++|....... + +..+.+.+.+.|. ++.|.++||+..+ -....|++|+.+.+++
T Consensus 49 ~~~~~i~~~~~g-~~vti~g~V~~~~~~~-~----~~~~~l~v~~~d~-~~~l~l~fFn~~~-~l~~~~~~G~~v~v~G- 119 (677)
T COG1200 49 TLLPGIAEARPG-EIVTIEGTVLSHEKFP-F----GKRKLLKVTLSDG-TGVLTLVFFNFPA-YLKKKLKVGERVIVYG- 119 (677)
T ss_pred cccCChhhcCCC-ceEEEEEEEEeeeccC-C----CCCceEEEEEecC-cEEEEEEEECccH-HHHhhCCCCCEEEEEE-
Confidence 345677777753 5688999997654432 2 2257899999995 7899999999865 4567899999999875
Q ss_pred EEecCCcccccCCCeEEEE
Q 003281 297 SLKPAQKNFNHLHNDLEIF 315 (834)
Q Consensus 297 ~V~~a~~~~~~~~~~yeI~ 315 (834)
+|+..+........+|.+.
T Consensus 120 k~~~~~~~~~~~hpe~~~~ 138 (677)
T COG1200 120 KVKRFKGGLQITHPEYIVN 138 (677)
T ss_pred EEeeccCceEEEcceEEec
Confidence 4544333333333344443
No 197
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=40.22 E-value=16 Score=23.83 Aligned_cols=19 Identities=16% Similarity=0.599 Sum_probs=14.7
Q ss_pred CcCcccccCCCCceecCCCCCc
Q 003281 531 PCNKKVMNNGDGRWHCDRCDQS 552 (834)
Q Consensus 531 ~C~KKv~~~~dg~~~CekC~~~ 552 (834)
.|.+++.+ +.-+|++|+..
T Consensus 4 ~CG~~~~~---~~~fC~~CG~~ 22 (23)
T PF13240_consen 4 NCGAEIED---DAKFCPNCGTP 22 (23)
T ss_pred ccCCCCCC---cCcchhhhCCc
Confidence 69999953 35679999875
No 198
>KOG2044 consensus 5'-3' exonuclease HKE1/RAT1 [Replication, recombination and repair; RNA processing and modification]
Probab=40.03 E-value=12 Score=45.11 Aligned_cols=21 Identities=38% Similarity=0.884 Sum_probs=18.3
Q ss_pred CCcCcccCCCCccCCCCCCCC
Q 003281 785 SSECYKCHKTGHWARDCPSLN 805 (834)
Q Consensus 785 ~~~Cy~Cg~~GH~ardCp~~~ 805 (834)
...|+.||+.||.++||....
T Consensus 260 ~~~C~~cgq~gh~~~dc~g~~ 280 (931)
T KOG2044|consen 260 PRRCFLCGQTGHEAKDCEGKP 280 (931)
T ss_pred cccchhhcccCCcHhhcCCcC
Confidence 357999999999999998863
No 199
>PRK07275 single-stranded DNA-binding protein; Provisional
Probab=39.91 E-value=1.5e+02 Score=29.40 Aligned_cols=35 Identities=6% Similarity=0.174 Sum_probs=24.1
Q ss_pred EEEEEEcCCccchhhhhhhhcccCCCccEEEEEE-EEEeecC
Q 003281 391 SVELTLWGNFCNDDGLRLQHMCDSGVFPILAVKA-GRVSDFN 431 (834)
Q Consensus 391 si~vtLWg~~a~~~~~~l~~~~~~~~~~Vv~ik~-~rV~~f~ 431 (834)
-|.|++||+.|+...+++. .+.-|+|.+ .+.+.|.
T Consensus 48 fi~vv~wgk~Ae~~~~~l~------KG~~V~VeGrl~~r~y~ 83 (162)
T PRK07275 48 FINCVIWRQQAENLANWAK------KGALIGVTGRIQTRNYE 83 (162)
T ss_pred EEEEEEEcHHHHHHHHHcC------CCCEEEEEEEEEeceEE
Confidence 5899999999987665543 455666654 5666663
No 200
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=39.33 E-value=18 Score=41.24 Aligned_cols=31 Identities=23% Similarity=0.709 Sum_probs=25.1
Q ss_pred eCCCCCcCCCCcCcccccCCCCceecCCCCCccccce
Q 003281 521 TACPIMIGDRPCNKKVMNNGDGRWHCDRCDQSVVECD 557 (834)
Q Consensus 521 ~aC~~~~~~~~C~KKv~~~~dg~~~CekC~~~~~~~~ 557 (834)
|-|| .|++.+...+.+-|+|.||+.......
T Consensus 351 p~Cp------~Cg~~m~S~G~~g~rC~kCg~~~~~~~ 381 (421)
T COG1571 351 PVCP------RCGGRMKSAGRNGFRCKKCGTRARETL 381 (421)
T ss_pred CCCC------ccCCchhhcCCCCcccccccccCCccc
Confidence 6799 799999777776799999998765433
No 201
>PRK06752 single-stranded DNA-binding protein; Validated
Probab=37.57 E-value=1.9e+02 Score=26.65 Aligned_cols=35 Identities=3% Similarity=0.122 Sum_probs=23.7
Q ss_pred EEEEEEcCCccchhhhhhhhcccCCCccEEEEEE-EEEeecC
Q 003281 391 SVELTLWGNFCNDDGLRLQHMCDSGVFPILAVKA-GRVSDFN 431 (834)
Q Consensus 391 si~vtLWg~~a~~~~~~l~~~~~~~~~~Vv~ik~-~rV~~f~ 431 (834)
-+.|++||+.|+...+.+. .+.-|++.+ .+...|.
T Consensus 48 ~~~v~~wg~~Ae~~~~~l~------KG~~V~V~G~l~~~~~~ 83 (112)
T PRK06752 48 FINCVVWRKSAENVTEYCT------KGSLVGITGRIHTRNYE 83 (112)
T ss_pred EEEEEEehHHHHHHHHhcC------CCCEEEEEEEEEeCccC
Confidence 5889999999987655432 455565654 5666674
No 202
>KOG3070 consensus Predicted RNA-binding protein containing PIN domain and invovled in translation or RNA processing [Translation, ribosomal structure and biogenesis]
Probab=37.16 E-value=1e+02 Score=32.62 Aligned_cols=19 Identities=42% Similarity=0.903 Sum_probs=17.4
Q ss_pred CcCcccCCCCccCCCCCCC
Q 003281 786 SECYKCHKTGHWARDCPSL 804 (834)
Q Consensus 786 ~~Cy~Cg~~GH~ardCp~~ 804 (834)
..||.|+++||.+.+|.+.
T Consensus 200 ~~~~~~~~~g~~~~~~~e~ 218 (235)
T KOG3070|consen 200 SLCYTCGEPGHVADGCEES 218 (235)
T ss_pred ccccccCcccccccccccc
Confidence 4799999999999999995
No 203
>PRK08182 single-stranded DNA-binding protein; Provisional
Probab=36.92 E-value=1.8e+02 Score=28.40 Aligned_cols=35 Identities=11% Similarity=0.013 Sum_probs=23.4
Q ss_pred EEEEEEcCCccchhhhhhhhcccCCCccEEEEE-EEEEeecC
Q 003281 391 SVELTLWGNFCNDDGLRLQHMCDSGVFPILAVK-AGRVSDFN 431 (834)
Q Consensus 391 si~vtLWg~~a~~~~~~l~~~~~~~~~~Vv~ik-~~rV~~f~ 431 (834)
-+.|++||..|+...+.|. .+.-|++. ..+...|.
T Consensus 55 w~~V~~wg~~Ae~v~~~l~------KG~~V~V~GrL~~~~w~ 90 (148)
T PRK08182 55 WAPVELWHRDAEHWARLYQ------KGMRVLVEGRMERDEWT 90 (148)
T ss_pred EEEEEEEhHHHHHHHHhcC------CCCEEEEEEEEEecccC
Confidence 5899999999887655442 34455554 46777674
No 204
>PRK05672 dnaE2 error-prone DNA polymerase; Validated
Probab=36.88 E-value=59 Score=41.96 Aligned_cols=75 Identities=21% Similarity=0.300 Sum_probs=50.5
Q ss_pred ccccccccccCCCceeeEEEEEEEecCCeeEEccCCceeeEEEEEEeccCCcEEEEEEcCCccchhhhhhhhcccCCCcc
Q 003281 339 FRPINDVEGMENNSVVDLIGVVSYISPTASLMRKNGTETQKRTLHLRDMSGRSVELTLWGNFCNDDGLRLQHMCDSGVFP 418 (834)
Q Consensus 339 f~~i~dI~~~~~~~~vDVIGvV~~V~~~~~i~~k~g~~~~kr~i~L~D~s~~si~vtLWg~~a~~~~~~l~~~~~~~~~~ 418 (834)
+.++++|.+...+..|=|.|+|+.+... .||.| .--++|.|.+| ++++++|.+..+.....+. .+.
T Consensus 941 ~~~~~~l~~~~~~~~v~v~g~i~~~~~~---~TkkG----maf~~leD~~g-~~e~~ifp~~~~~~~~~l~------~~~ 1006 (1046)
T PRK05672 941 VVSAAELLDVEDGRRVRVAGVVTHRQRP---GTASG----VTFLTLEDETG-MVNVVVWPGLWERQRREAL------GAR 1006 (1046)
T ss_pred CcCHHHHhhccCCCEEEEEEEEEEEEEe---cCCCc----eEEEEEecCCC-CEEEEECHHHHHHHHHHhc------cCC
Confidence 3455566554445668889999887543 35666 56689999999 6999999987665433332 456
Q ss_pred EEEEEEEEEe
Q 003281 419 ILAVKAGRVS 428 (834)
Q Consensus 419 Vv~ik~~rV~ 428 (834)
++.+++ +|.
T Consensus 1007 ~~~v~g-~v~ 1015 (1046)
T PRK05672 1007 LLLVRG-RVQ 1015 (1046)
T ss_pred EEEEEE-EEE
Confidence 776655 443
No 205
>KOG3116 consensus Predicted C3H1-type Zn-finger protein [General function prediction only]
Probab=36.46 E-value=9.6 Score=36.57 Aligned_cols=19 Identities=26% Similarity=0.668 Sum_probs=17.4
Q ss_pred cccccCccCccCCCCCCCC
Q 003281 743 SCSSCGAVGHSSMNCPSIM 761 (834)
Q Consensus 743 ~C~~Cg~~GH~a~~Cp~~~ 761 (834)
.|.+|-+.|||..+|.+.+
T Consensus 29 rCQKClq~GHWtYECk~kR 47 (177)
T KOG3116|consen 29 RCQKCLQAGHWTYECKNKR 47 (177)
T ss_pred hHHHHHhhccceeeecCce
Confidence 8999999999999998755
No 206
>PRK06293 single-stranded DNA-binding protein; Provisional
Probab=36.31 E-value=2.1e+02 Score=28.41 Aligned_cols=71 Identities=13% Similarity=0.071 Sum_probs=36.9
Q ss_pred eeeEEEEEEEecCCeeEEccCCceeeEEEEEEec-----cCCcEEEEEEcCCccchhhhhhhhcccCCCccEEEEE-EEE
Q 003281 353 VVDLIGVVSYISPTASLMRKNGTETQKRTLHLRD-----MSGRSVELTLWGNFCNDDGLRLQHMCDSGVFPILAVK-AGR 426 (834)
Q Consensus 353 ~vDVIGvV~~V~~~~~i~~k~g~~~~kr~i~L~D-----~s~~si~vtLWg~~a~~~~~~l~~~~~~~~~~Vv~ik-~~r 426 (834)
.|-+||.|..= +..-.+.+|+.+.+-.|-..+ ..-.-++|++|++.|+...+.|. .+.-|++. ..+
T Consensus 3 ~V~LiGrLg~D--PElR~t~sG~~v~~FsLAvn~~~~~~~~T~wi~v~awg~~Ae~v~~yL~------KG~~V~VeGrL~ 74 (161)
T PRK06293 3 FGYIVGRLGAD--PEERMTSKGKRVVVLRLGVKSRVGSKDETVWCRCNIWGNRYDKMLPYLK------KGSGVIVAGEMS 74 (161)
T ss_pred EEEEEEEecCC--CeEEEcCCCCEEEEEEEEEeCCCCCccceEEEEEEEEhHHHHHHHHhCC------CCCEEEEEEEEE
Confidence 35567766543 221223455543332222221 11135899999998876544332 34555554 467
Q ss_pred EeecC
Q 003281 427 VSDFN 431 (834)
Q Consensus 427 V~~f~ 431 (834)
...|.
T Consensus 75 ~~~y~ 79 (161)
T PRK06293 75 PESYV 79 (161)
T ss_pred eCccC
Confidence 77774
No 207
>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=36.14 E-value=2.7e+02 Score=24.16 Aligned_cols=56 Identities=32% Similarity=0.288 Sum_probs=37.6
Q ss_pred EEEEEEEEEeCCCeEEEEEehHHHHHHhCCCHHHHHhhhccCCChhHHHHHHHHhcCceEEEEEEEeecccCccceEE
Q 003281 559 RYILQFQIQDHTGLTWVTAFQECAEEIMGMSAKDLYSLKYVDQNDEKFGEVVRNATFTKYLFKLKVKEETFSDEQRVK 636 (834)
Q Consensus 559 ry~l~~~i~D~Tg~~~~~~F~e~ae~llG~sA~el~~l~~ee~d~~~~~~~l~~~~~k~~~f~l~~k~~~ynde~rvk 636 (834)
++++.+.|.|.|+++.+-.|.+ ...+.+..++ ..+.-..++.++..+.|..+.-+.
T Consensus 20 ~~i~~~~itD~t~Si~~K~F~~-------~~~~~~~~ik---------------~~G~~v~v~G~v~~D~f~~e~~~~ 75 (82)
T cd04484 20 RKILTFKVTDYTSSITVKKFLR-------KDEKDKEELK---------------SKGDWVRVRGKVQYDTFSKELVLM 75 (82)
T ss_pred CEEEEEEEEcCCCCEEEEEecc-------CChhHHhhcc---------------cCCCEEEEEEEEEEccCCCceEEE
Confidence 6789999999999999999964 0111111111 036667788888888887655443
No 208
>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=36.13 E-value=83 Score=29.79 Aligned_cols=48 Identities=13% Similarity=0.239 Sum_probs=32.9
Q ss_pred EEEEEEechHHHhhhhccCcCcEEEEeeeEEecCCcccccC-CCeEEEEE
Q 003281 268 EIRVTCFNAVADQFYHQVEAGKIYLVSRGSLKPAQKNFNHL-HNDLEIFL 316 (834)
Q Consensus 268 ~I~at~f~~~~d~f~~~l~eG~vy~is~~~V~~a~~~~~~~-~~~yeI~f 316 (834)
.|.+++|++-++ |...|++|+.+.|.|..++....+..+. ....|+.+
T Consensus 61 ti~It~yD~H~~-~ar~lK~GdfV~L~NVhiK~~~~~~~~~~~~~Le~~l 109 (123)
T cd04498 61 TIDILVYDNHVE-LAKSLKPGDFVRIYNVHAKSYSSKNEHDENDHLHFHL 109 (123)
T ss_pred EEEEEEEcchHH-HHhhCCCCCEEEEEEEEEEeccCCcccCCcceEEEEE
Confidence 567777777665 4444999999999999998776544333 23345444
No 209
>PRK03932 asnC asparaginyl-tRNA synthetase; Validated
Probab=35.94 E-value=4.1e+02 Score=31.00 Aligned_cols=76 Identities=13% Similarity=0.130 Sum_probs=49.7
Q ss_pred CCceEEEEEEEEeccceeecCCCCCcceEEEEEeeCCCCEEEEEEechH---HHhhhhccCcCcEEEEeeeEEecCCccc
Q 003281 229 MGKWTIKARVTAKGELRHYNNQRGDGKVFHFDLLDSDGGEIRVTCFNAV---ADQFYHQVEAGKIYLVSRGSLKPAQKNF 305 (834)
Q Consensus 229 ~~~w~I~aRV~~Ks~lr~~~n~~g~Gk~f~~~L~De~g~~I~at~f~~~---~d~f~~~l~eG~vy~is~~~V~~a~~~~ 305 (834)
....+|++||.+ +|.. |++.-++|.|. ++.|++.+-.+. .-++...|..|+++.+.+.-.+ ...
T Consensus 16 ~~~V~i~G~v~~---~R~~------g~~~Fi~lrD~-~g~iq~~~~~~~~~~~~~~~~~l~~~s~v~v~G~v~~-~~~-- 82 (450)
T PRK03932 16 GQEVTVRGWVRT---KRDS------GKIAFLQLRDG-SCFKQLQVVKDNGEEYFEEIKKLTTGSSVIVTGTVVE-SPR-- 82 (450)
T ss_pred CCEEEEEEEEEE---EEeC------CCeEEEEEECC-CCcEEEEEEcCCChHHHHHHhcCCCCcEEEEEEEEEc-CCC--
Confidence 357899999975 4442 57777888997 578888875431 1123345999999999874443 221
Q ss_pred ccCCCeEEEEEccC
Q 003281 306 NHLHNDLEIFLDMT 319 (834)
Q Consensus 306 ~~~~~~yeI~f~~~ 319 (834)
....+||....-
T Consensus 83 --~~~~~el~~~~i 94 (450)
T PRK03932 83 --AGQGYELQATKI 94 (450)
T ss_pred --CCCCEEEEEEEE
Confidence 224688887543
No 210
>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=35.89 E-value=2.8e+02 Score=33.47 Aligned_cols=85 Identities=19% Similarity=0.250 Sum_probs=54.7
Q ss_pred CceEEEEEEEEeccceeecCCCCCcceEEEEEeeCCCCEEEEEEech-HHHhhhhccCcCcEEEEeeeEEecCCcccc--
Q 003281 230 GKWTIKARVTAKGELRHYNNQRGDGKVFHFDLLDSDGGEIRVTCFNA-VADQFYHQVEAGKIYLVSRGSLKPAQKNFN-- 306 (834)
Q Consensus 230 ~~w~I~aRV~~Ks~lr~~~n~~g~Gk~f~~~L~De~g~~I~at~f~~-~~d~f~~~l~eG~vy~is~~~V~~a~~~~~-- 306 (834)
...+|++||.+ +|.. |++.-++|.|. +|.|++++-.+ ..-+....|..|+++.|.+.-.+...+..+
T Consensus 16 ~~V~l~GwV~~---~R~~------Gkl~Fi~LrD~-sg~iQvv~~~~~~~~~~~~~L~~esvV~V~G~v~~r~~~~~n~~ 85 (583)
T TIGR00459 16 QTVTLAGWVNR---RRDL------GGLIFIDLRDR-SGIVQVVCDPDADALKLAKGLRNEDVVQVKGKVSARPEGNINRN 85 (583)
T ss_pred CEEEEEEEEEE---EEcC------CCcEEEEEEeC-CccEEEEEeCCHHHHHHHhcCCCCCEEEEEEEEEeCCccccCcc
Confidence 47889999975 3432 67888889997 46999988654 222334568999999998854432211111
Q ss_pred cCCCeEEEEEccCccEEE
Q 003281 307 HLHNDLEIFLDMTSMVQL 324 (834)
Q Consensus 307 ~~~~~yeI~f~~~T~I~~ 324 (834)
.....+||....-+.+..
T Consensus 86 ~~tg~iEl~~~~i~iL~~ 103 (583)
T TIGR00459 86 LDTGEIEILAESITLLNK 103 (583)
T ss_pred CCCCcEEEEEeEEEEeec
Confidence 234578888765444433
No 211
>PRK07274 single-stranded DNA-binding protein; Provisional
Probab=35.03 E-value=2.1e+02 Score=27.30 Aligned_cols=34 Identities=12% Similarity=0.331 Sum_probs=23.0
Q ss_pred EEEEEEcCCccchhhhhhhhcccCCCccEEEEEE-EEEeec
Q 003281 391 SVELTLWGNFCNDDGLRLQHMCDSGVFPILAVKA-GRVSDF 430 (834)
Q Consensus 391 si~vtLWg~~a~~~~~~l~~~~~~~~~~Vv~ik~-~rV~~f 430 (834)
-++|++||..|+.....+. .+.-|.+.+ .+...|
T Consensus 48 w~~v~~fg~~Ae~v~~~l~------KG~~V~V~Grl~~~~y 82 (131)
T PRK07274 48 FINVVLWGKLAETLASYAS------KGSLISIDGELRTRKY 82 (131)
T ss_pred EEEEEEehHHHHHHHHHcC------CCCEEEEEEEEEeccC
Confidence 5899999999876544432 345555544 566777
No 212
>KOG3056 consensus Protein required for S-phase initiation or completion [Cell cycle control, cell division, chromosome partitioning]
Probab=35.02 E-value=1.3e+02 Score=35.44 Aligned_cols=66 Identities=20% Similarity=0.212 Sum_probs=46.1
Q ss_pred eEEEEEEEecCCeeEEccCCceeeEEEEEEeccCC-cEEEEEEcCCccchhhhhhhhcccCCCccEEEEEEEEEeecC
Q 003281 355 DLIGVVSYISPTASLMRKNGTETQKRTLHLRDMSG-RSVELTLWGNFCNDDGLRLQHMCDSGVFPILAVKAGRVSDFN 431 (834)
Q Consensus 355 DVIGvV~~V~~~~~i~~k~g~~~~kr~i~L~D~s~-~si~vtLWg~~a~~~~~~l~~~~~~~~~~Vv~ik~~rV~~f~ 431 (834)
=++|+|++-+++.. +.+|..+ ....|-|..+ ..|.|-|+|+ |-.-. |....+.||+|-++.|-+.+
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--SIWKLTDLKDHQTVSLFLFGK-AHKRY------WKIKLGTVIALLNPEVLKDR 255 (578)
T ss_pred EEEEEEeecCCccc--ccCCCce--EEEEeeecCccceeEEEEecH-HHHHH------hhhccCcEEEEeCccccCCC
Confidence 37899999988864 3456643 4455555555 6899999999 43322 33447899999999887544
No 213
>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=34.32 E-value=25 Score=25.72 Aligned_cols=25 Identities=36% Similarity=0.996 Sum_probs=20.6
Q ss_pred CCCCCcCCCCcCcccccCCCCceecCCCCCc
Q 003281 522 ACPIMIGDRPCNKKVMNNGDGRWHCDRCDQS 552 (834)
Q Consensus 522 aC~~~~~~~~C~KKv~~~~dg~~~CekC~~~ 552 (834)
.|+ .|........||.|.|..|+..
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 6988877778999999999853
No 214
>COG0484 DnaJ DnaJ-class molecular chaperone with C-terminal Zn finger domain [Posttranslational modification, protein turnover, chaperones]
Probab=34.14 E-value=20 Score=40.31 Aligned_cols=9 Identities=44% Similarity=1.217 Sum_probs=5.2
Q ss_pred cccccCccC
Q 003281 743 SCSSCGAVG 751 (834)
Q Consensus 743 ~C~~Cg~~G 751 (834)
.|-.|...|
T Consensus 144 ~C~~C~GsG 152 (371)
T COG0484 144 TCSTCHGSG 152 (371)
T ss_pred ECCcCCCCC
Confidence 566665554
No 215
>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=33.93 E-value=1.5e+02 Score=29.18 Aligned_cols=27 Identities=30% Similarity=0.594 Sum_probs=21.8
Q ss_pred ceEEEEEeeCCCCEEEEEEechHHHhhh
Q 003281 255 KVFHFDLLDSDGGEIRVTCFNAVADQFY 282 (834)
Q Consensus 255 k~f~~~L~De~g~~I~at~f~~~~d~f~ 282 (834)
..+++.|.|. .|++.+++|++.++++.
T Consensus 68 y~l~~~i~D~-Tg~~~~~~F~~~ae~l~ 94 (166)
T cd04476 68 YILSLNVADH-TGEAWLTLFDEVAEQIF 94 (166)
T ss_pred EEEEEEEEeC-CCCEEEEEehHHHHHHh
Confidence 3467889997 58999999999877664
No 216
>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=33.73 E-value=35 Score=22.72 Aligned_cols=21 Identities=14% Similarity=0.533 Sum_probs=14.8
Q ss_pred CcCcccccCC-CCceecCCCCC
Q 003281 531 PCNKKVMNNG-DGRWHCDRCDQ 551 (834)
Q Consensus 531 ~C~KKv~~~~-dg~~~CekC~~ 551 (834)
.|+.-+.... .-.|.|++|+.
T Consensus 3 sC~~~i~~r~~~v~f~CPnCG~ 24 (24)
T PF07754_consen 3 SCGRPIAPREQAVPFPCPNCGF 24 (24)
T ss_pred cCCCcccCcccCceEeCCCCCC
Confidence 5877775433 34799999974
No 217
>PRK06920 dnaE DNA polymerase III DnaE; Reviewed
Probab=33.63 E-value=91 Score=40.45 Aligned_cols=71 Identities=17% Similarity=0.233 Sum_probs=49.8
Q ss_pred eeccccCCC-CCceEEEEEEEEeccceeecCCCCCcceEEEEEeeCCCCEEEEEEechHHHhhhhccCcCcEEEEee
Q 003281 220 IPIAALNPY-MGKWTIKARVTAKGELRHYNNQRGDGKVFHFDLLDSDGGEIRVTCFNAVADQFYHQVEAGKIYLVSR 295 (834)
Q Consensus 220 ~pI~~L~p~-~~~w~I~aRV~~Ks~lr~~~n~~g~Gk~f~~~L~De~g~~I~at~f~~~~d~f~~~l~eG~vy~is~ 295 (834)
.++.+|... ....+|-+-|+. +|.....+|+ ...-+.|-|+ .|.|.+++|.+..+++.+.|++|.++.|..
T Consensus 933 ~~~~~l~~~~~~~v~v~g~i~~---~~~~~tk~g~-~maf~~leD~-tg~~e~~vFp~~y~~~~~~l~~~~~~~v~G 1004 (1107)
T PRK06920 933 PSLAQAMRHKKKVQRAIVYITS---VKVIRTKKGQ-KMAFITFCDQ-NDEMEAVVFPETYIHFSDKLQEGAIVLVDG 1004 (1107)
T ss_pred cCHHHHhhcCCCEEEEEEEEEE---eEeecCCCCC-eEEEEEEeeC-CCcEEEEECHHHHHHHHHHhccCCEEEEEE
Confidence 467776532 234566677765 3444334432 3445667786 689999999999999999999999999954
No 218
>PRK00448 polC DNA polymerase III PolC; Validated
Probab=33.31 E-value=1.1e+02 Score=40.68 Aligned_cols=73 Identities=16% Similarity=0.271 Sum_probs=56.2
Q ss_pred CceeccccCCCCCceEEEEEEEEeccceeecCCCCCcceEEEEEeeCCCCEEEEEEechH--HHhhhhccCcCcEEEEee
Q 003281 218 RIIPIAALNPYMGKWTIKARVTAKGELRHYNNQRGDGKVFHFDLLDSDGGEIRVTCFNAV--ADQFYHQVEAGKIYLVSR 295 (834)
Q Consensus 218 ~~~pI~~L~p~~~~w~I~aRV~~Ks~lr~~~n~~g~Gk~f~~~L~De~g~~I~at~f~~~--~d~f~~~l~eG~vy~is~ 295 (834)
.+++|.++.....+.+|++.|... +.|..++ ...+++|.|.|. .+.|.+..|... -.+..+.|+.|+|+.+..
T Consensus 225 ~~~~~~~i~~~~~~v~i~G~if~~-e~~~~k~---~~~~~~~~~td~-~~s~~~k~f~~~~~~~~~~~~~~~g~~v~~~g 299 (1437)
T PRK00448 225 EITPMKEINEEERRVVVEGYVFKV-EIKELKS---GRHILTFKITDY-TSSIIVKKFSRDKEDLKKFDEIKKGDWVKVRG 299 (1437)
T ss_pred CcccHHHhhccCCeEEEEEEEEEE-EEEeccC---CCEEEEEEEEcC-CCCEEEEEEecCcchhHHHhcCCCCCEEEEEE
Confidence 578999999888899999999765 4566543 146789999997 488999998632 234457799999999875
No 219
>PRK07772 single-stranded DNA-binding protein; Provisional
Probab=32.74 E-value=5.5e+02 Score=26.17 Aligned_cols=50 Identities=18% Similarity=0.260 Sum_probs=29.5
Q ss_pred CCeEEEEEehHHHHHHhCCCHHHHHhhhccCCChhHHHHHHHHhcCceEEEEEEEeecccCccceEEEEEEEe
Q 003281 570 TGLTWVTAFQECAEEIMGMSAKDLYSLKYVDQNDEKFGEVVRNATFTKYLFKLKVKEETFSDEQRVKSTVVKA 642 (834)
Q Consensus 570 Tg~~~~~~F~e~ae~llG~sA~el~~l~~ee~d~~~~~~~l~~~~~k~~~f~l~~k~~~ynde~rvk~~v~~~ 642 (834)
+.-+.|++|.+.|+.+. ..|+ .+....+.-+++.+.|.++.-.+.++++|
T Consensus 52 t~fi~V~~Wg~~Ae~va-------~~L~----------------KGd~V~V~GrL~~r~wedkdG~~rt~~eV 101 (186)
T PRK07772 52 ALFLRCSIWRQAAENVA-------ESLT----------------KGMRVIVTGRLKQRSYETREGEKRTVVEL 101 (186)
T ss_pred ceEEEEEEecHHHHHHH-------HhcC----------------CCCEEEEEEEEEcCceECCCCCEEEEEEE
Confidence 33457889999876541 1122 24566788888888886544333333333
No 220
>PRK14288 chaperone protein DnaJ; Provisional
Probab=32.72 E-value=24 Score=39.97 Aligned_cols=40 Identities=18% Similarity=0.320 Sum_probs=18.6
Q ss_pred CcCcccCCCCccCCCCCCCCCCCCCcCCCCCC----cccccCCC
Q 003281 786 SECYKCHKTGHWARDCPSLNAAPPAYGSSGIG----ISAAGYRG 825 (834)
Q Consensus 786 ~~Cy~Cg~~GH~ardCp~~~~~~~c~~c~~~g----~~~~~cg~ 825 (834)
..|..|+..|..-..--.......|-.|+|.| +.|..|.|
T Consensus 157 ~~C~~C~G~G~~~~~~g~~~~~~~C~~C~G~G~~~~~~C~~C~G 200 (369)
T PRK14288 157 ETCKQCNGQGQVFMRQGFMSFAQTCGACQGKGKIIKTPCQACKG 200 (369)
T ss_pred cCCCCCCCCcEEEEEeceEEEEEecCCCCCCceEccccCccCCC
Confidence 35777776665322110000001455666655 34666665
No 221
>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=32.47 E-value=3.2e+02 Score=31.94 Aligned_cols=80 Identities=16% Similarity=0.201 Sum_probs=52.1
Q ss_pred CceEEEEEEEEeccceeecCCCCCcceEEEEEeeCCC-CEEEEEEechH---HHhhhhccCcCcEEEEeeeEEecCCccc
Q 003281 230 GKWTIKARVTAKGELRHYNNQRGDGKVFHFDLLDSDG-GEIRVTCFNAV---ADQFYHQVEAGKIYLVSRGSLKPAQKNF 305 (834)
Q Consensus 230 ~~w~I~aRV~~Ks~lr~~~n~~g~Gk~f~~~L~De~g-~~I~at~f~~~---~d~f~~~l~eG~vy~is~~~V~~a~~~~ 305 (834)
...+|++||.+ +|. .|++.-++|.|... +.|++++-... ..++...|..|+++.+.+.-.+...
T Consensus 17 ~~v~v~Gwv~~---~R~------~~~~~F~~lrD~~~~g~iQ~v~~~~~~~~~~~~~~~l~~gs~V~v~G~v~~~~~--- 84 (453)
T TIGR00457 17 DEVTVSGWVRT---KRS------SKKIIFLELNDGSSLGPIQAVINGEDNPYLFQLLKSLTTGSSVSVTGKVVESPG--- 84 (453)
T ss_pred CEEEEEEEeEE---EEc------CCCeEEEEEECCCCCccEEEEEeCCcChHHHHHHHcCCCCcEEEEEEEEEcCCC---
Confidence 56889999975 342 25677778888631 79999987642 2234456999999999875443221
Q ss_pred ccCCCeEEEEEccCccEE
Q 003281 306 NHLHNDLEIFLDMTSMVQ 323 (834)
Q Consensus 306 ~~~~~~yeI~f~~~T~I~ 323 (834)
....+||....-..+.
T Consensus 85 --~~~~~El~~~~i~vl~ 100 (453)
T TIGR00457 85 --KGQPVELQVKKIEVVG 100 (453)
T ss_pred --CCCCEEEEEeEEEEEe
Confidence 1257888876433333
No 222
>KOG2673 consensus Uncharacterized conserved protein, contains PSP domain [Function unknown]
Probab=31.56 E-value=24 Score=40.16 Aligned_cols=20 Identities=35% Similarity=0.866 Sum_probs=18.4
Q ss_pred cccccCccCccCCCCCCCCC
Q 003281 743 SCSSCGAVGHSSMNCPSIMS 762 (834)
Q Consensus 743 ~C~~Cg~~GH~a~~Cp~~~~ 762 (834)
.||+|+.+-|.-++||.+..
T Consensus 130 ~CFNC~g~~hsLrdC~rp~d 149 (485)
T KOG2673|consen 130 PCFNCGGTPHSLRDCPRPFD 149 (485)
T ss_pred cccccCCCCCccccCCCccc
Confidence 69999999999999998775
No 223
>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=31.16 E-value=1.2e+02 Score=26.06 Aligned_cols=59 Identities=17% Similarity=0.150 Sum_probs=37.0
Q ss_pred EEEEEcccccc--cccccccchhhhhhcCCcccccEEEEceeeeeccc--CeEEEEEEeeeEe
Q 003281 27 FRMVLSDGSRS--QQGMLATQRNELVTSGLLQIGSVVRLTKFTCNVIQ--NRMIVIVMDLDVI 85 (834)
Q Consensus 27 yrl~lSDG~~~--~~~mLatqln~lv~~g~l~~gsiv~l~~~~~~~v~--~r~iiii~~lev~ 85 (834)
-=+.|.||... +|+++......+-.-..|..||+|.++=.....-. +..=|.+.+++++
T Consensus 18 ~Fi~LrD~s~~~~lQvv~~~~~~~~~~~~~l~~gs~V~v~G~v~~~~~~~~~~El~~~~i~il 80 (82)
T cd04318 18 SFIELNDGSCLKNLQVVVDKELTNFKEILKLSTGSSIRVEGVLVKSPGAKQPFELQAEKIEVL 80 (82)
T ss_pred EEEEEECCCCccCEEEEEeCcccCHHHHhcCCCceEEEEEEEEEeCCCCCCCEEEEEEEEEEe
Confidence 44789999885 89888544221112235899999999876555433 3344555555554
No 224
>COG0587 DnaE DNA polymerase III, alpha subunit [DNA replication, recombination, and repair]
Probab=30.71 E-value=1.5e+02 Score=38.61 Aligned_cols=71 Identities=18% Similarity=0.297 Sum_probs=50.8
Q ss_pred eeccccCCCCCceEEEEEEEEeccceeecCCCCCc-ceEEEEEeeCCCCEEEEEEechHHHhhhhccCcCcEEEEee
Q 003281 220 IPIAALNPYMGKWTIKARVTAKGELRHYNNQRGDG-KVFHFDLLDSDGGEIRVTCFNAVADQFYHQVEAGKIYLVSR 295 (834)
Q Consensus 220 ~pI~~L~p~~~~w~I~aRV~~Ks~lr~~~n~~g~G-k~f~~~L~De~g~~I~at~f~~~~d~f~~~l~eG~vy~is~ 295 (834)
.++.++.+....|.+-+-|+.. |.-.... .| ++--+.|.|++| .+.+++|.....+++..+.+++.|.|..
T Consensus 967 ~~~~~~~~~~~~~~~~~~i~~v---r~~~tk~-~G~~~~f~tl~D~~g-~~e~v~f~~~~~~~~~~l~~~~~~~v~g 1038 (1139)
T COG0587 967 IRLLDLVEDGRRVVLAGGIVAV---RQRPTKA-KGNKMAFLTLEDETG-ILEVVVFPSEYERYRRLLLEGRLLIVKG 1038 (1139)
T ss_pred cchhhhccccceeEEEEEEEEE---EEeeccC-CCCEEEEEEEecCCC-cEEEEEcHHHHHHHHHHhccCcEEEEEE
Confidence 4566666655558877777654 3322221 24 355667889865 9999999999999999999998888864
No 225
>COG1570 XseA Exonuclease VII, large subunit [DNA replication, recombination, and repair]
Probab=30.31 E-value=50 Score=37.96 Aligned_cols=90 Identities=24% Similarity=0.403 Sum_probs=59.3
Q ss_pred CceeccccCCCCCceE--EEEEEEEeccceeecCCCCCcceEEEEEeeCCCCEEEEEEechHHHhhhhccCcCcEEEEee
Q 003281 218 RIIPIAALNPYMGKWT--IKARVTAKGELRHYNNQRGDGKVFHFDLLDSDGGEIRVTCFNAVADQFYHQVEAGKIYLVSR 295 (834)
Q Consensus 218 ~~~pI~~L~p~~~~w~--I~aRV~~Ks~lr~~~n~~g~Gk~f~~~L~De~g~~I~at~f~~~~d~f~~~l~eG~vy~is~ 295 (834)
+++++++||-|...|- -...|--+++|-.|+.+. .| -..|.|.|+ ...|+|++|.....++.-.+++|.=+.+..
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-HLYFTLKDE-RAQIRCVMFKGNNRRLKFRPEEGMQVLVRG 80 (440)
T ss_pred CeecHHHHHHHHHHHHHhcCCeEEEEEEecCCccCC-Cc-cEEEEEccC-CceEEEEEEcCcccccCCCccCCCEEEEEE
Confidence 4566777776643331 123444445555555333 35 678889997 689999999998888887899998777654
Q ss_pred -eEEecCCcccccCCCeEEEEEc
Q 003281 296 -GSLKPAQKNFNHLHNDLEIFLD 317 (834)
Q Consensus 296 -~~V~~a~~~~~~~~~~yeI~f~ 317 (834)
.++-+.. .+|.|.++
T Consensus 81 ~is~Y~~r-------G~YQi~~~ 96 (440)
T COG1570 81 KISLYEPR-------GDYQIVAE 96 (440)
T ss_pred EEEEEcCC-------CceEEEEe
Confidence 4554443 45667665
No 226
>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=29.42 E-value=1.3e+02 Score=34.81 Aligned_cols=45 Identities=22% Similarity=0.372 Sum_probs=35.1
Q ss_pred cceEEEEEeeCCCCEEEEEEechHHHhhhhccCcCcEEEEee-eEEec
Q 003281 254 GKVFHFDLLDSDGGEIRVTCFNAVADQFYHQVEAGKIYLVSR-GSLKP 300 (834)
Q Consensus 254 Gk~f~~~L~De~g~~I~at~f~~~~d~f~~~l~eG~vy~is~-~~V~~ 300 (834)
|. +.|+|.|+ ...|+|++|...+.++.-.+++|.=+.+.. ..|-+
T Consensus 35 GH-~YFtLkD~-~a~i~~vmf~~~~~~l~f~~~~G~~V~v~g~v~~y~ 80 (432)
T TIGR00237 35 GH-WYFTLKDE-NAQVRCVMFRGNNNRLKFRPQNGQQVLVRGGISVYE 80 (432)
T ss_pred ce-EEEEEEcC-CcEEEEEEEcChhhCCCCCCCCCCEEEEEEEEEEEC
Confidence 54 77889997 689999999998877777789998877765 34433
No 227
>KOG3108 consensus Single-stranded DNA-binding replication protein A (RPA), medium (30 kD) subunit [Replication, recombination and repair]
Probab=28.97 E-value=1.8e+02 Score=31.34 Aligned_cols=66 Identities=21% Similarity=0.453 Sum_probs=42.2
Q ss_pred eeeEEEEEEEecCCeeEEccCCceeeEEEEEEeccCCcEEEEEEcCCccchhhhhhhhcccCCCccEEEE-E----EEEE
Q 003281 353 VVDLIGVVSYISPTASLMRKNGTETQKRTLHLRDMSGRSVELTLWGNFCNDDGLRLQHMCDSGVFPILAV-K----AGRV 427 (834)
Q Consensus 353 ~vDVIGvV~~V~~~~~i~~k~g~~~~kr~i~L~D~s~~si~vtLWg~~a~~~~~~l~~~~~~~~~~Vv~i-k----~~rV 427 (834)
.|-++|+|..+... ..+..++|.|.++. |++..|-....... ..+.|.. + ...+
T Consensus 70 ~v~~VGivr~~e~~----------~t~i~y~I~D~tg~-id~r~W~~~~~~~~----------e~~~l~~~~yVkv~G~L 128 (265)
T KOG3108|consen 70 AVSIVGIVRNIEKS----------ATNITYEIEDGTGQ-IDVRQWFHDNAESE----------EMPALETGTYVKVYGHL 128 (265)
T ss_pred EEEEEEEEEeceec----------CcceEEEEecCccc-EEEEEeccccchhh----------hCcccccCcEEEeeecc
Confidence 45677888777544 24667899999995 99999988765321 1233322 2 2344
Q ss_pred eecCCe-EEEeec
Q 003281 428 SDFNGK-VVGTIS 439 (834)
Q Consensus 428 ~~f~G~-~Ls~~~ 439 (834)
+.|+|+ +|....
T Consensus 129 k~f~Gk~sl~~fk 141 (265)
T KOG3108|consen 129 KPFQGKKSLQVFK 141 (265)
T ss_pred cCCCCceeEEEEe
Confidence 679885 665544
No 228
>PRK05672 dnaE2 error-prone DNA polymerase; Validated
Probab=28.56 E-value=1.2e+02 Score=39.21 Aligned_cols=41 Identities=17% Similarity=0.283 Sum_probs=34.6
Q ss_pred eEEEEEeeCCCCEEEEEEechHHHhhhhccCcCcEEEEeeeEE
Q 003281 256 VFHFDLLDSDGGEIRVTCFNAVADQFYHQVEAGKIYLVSRGSL 298 (834)
Q Consensus 256 ~f~~~L~De~g~~I~at~f~~~~d~f~~~l~eG~vy~is~~~V 298 (834)
+.-+.|-|+ .|.|.+++|.+..+++.+.|++|.++.|.. +|
T Consensus 974 maf~~leD~-~g~~e~~ifp~~~~~~~~~l~~~~~~~v~g-~v 1014 (1046)
T PRK05672 974 VTFLTLEDE-TGMVNVVVWPGLWERQRREALGARLLLVRG-RV 1014 (1046)
T ss_pred eEEEEEecC-CCCEEEEECHHHHHHHHHHhccCCEEEEEE-EE
Confidence 445667786 589999999999999999999999999954 44
No 229
>PRK14298 chaperone protein DnaJ; Provisional
Probab=27.98 E-value=44 Score=37.91 Aligned_cols=40 Identities=18% Similarity=0.269 Sum_probs=19.0
Q ss_pred CcCcccCCCCccCCCCCCCC----CCCCCcCCCCCC----cccccCCC
Q 003281 786 SECYKCHKTGHWARDCPSLN----AAPPAYGSSGIG----ISAAGYRG 825 (834)
Q Consensus 786 ~~Cy~Cg~~GH~ardCp~~~----~~~~c~~c~~~g----~~~~~cg~ 825 (834)
..|..|+..|.....-..+. ....|-.|+|.| +.|..|.|
T Consensus 159 ~~C~~C~G~G~~~~~~~~~~g~~~~~~~C~~C~G~G~~~~~~C~~C~G 206 (377)
T PRK14298 159 KRCPTCGGTGQVTTTRSTPLGQFVTTTTCSTCHGRGQVIESPCPVCSG 206 (377)
T ss_pred CcCCCCCCccEEEEEEecCceeEEEEEeCCCCCCCCcccCCCCCCCCC
Confidence 35666666665432221100 011466666665 23666665
No 230
>PRK12820 bifunctional aspartyl-tRNA synthetase/aspartyl/glutamyl-tRNA amidotransferase subunit C; Provisional
Probab=27.31 E-value=5.4e+02 Score=31.83 Aligned_cols=93 Identities=17% Similarity=0.165 Sum_probs=57.5
Q ss_pred ccccCCC--CCceEEEEEEEEeccceeecCCCCCcceEEEEEeeCCCCEEEEEEechH----HHhhhhccCcCcEEEEee
Q 003281 222 IAALNPY--MGKWTIKARVTAKGELRHYNNQRGDGKVFHFDLLDSDGGEIRVTCFNAV----ADQFYHQVEAGKIYLVSR 295 (834)
Q Consensus 222 I~~L~p~--~~~w~I~aRV~~Ks~lr~~~n~~g~Gk~f~~~L~De~g~~I~at~f~~~----~d~f~~~l~eG~vy~is~ 295 (834)
+.+|++. ....+|++||.+ +|.. |++.-++|.|. +|.|++++-.+. +-++...|..|+++.|.+
T Consensus 9 cg~l~~~~~g~~V~l~GWV~~---~R~~------G~l~FidLRD~-~G~iQvV~~~~~~~~~~~~~~~~L~~EsvV~V~G 78 (706)
T PRK12820 9 CGHLSLDDTGREVCLAGWVDA---FRDH------GELLFIHLRDR-NGFIQAVFSPEAAPADVYELAASLRAEFCVALQG 78 (706)
T ss_pred cccCChhhCCCEEEEEEEEEE---EEcC------CCcEEEEEEeC-CccEEEEEeCCcCCHHHHHHHhcCCCCCEEEEEe
Confidence 4444443 246889999965 3432 56888889997 578999886432 222335699999999998
Q ss_pred eEEecCCccccc--CCCeEEEEEccCccEEE
Q 003281 296 GSLKPAQKNFNH--LHNDLEIFLDMTSMVQL 324 (834)
Q Consensus 296 ~~V~~a~~~~~~--~~~~yeI~f~~~T~I~~ 324 (834)
.-.+...+.-++ ....+||....-..+..
T Consensus 79 ~v~~r~~~~~n~~~~tg~iEl~~~~i~iL~~ 109 (706)
T PRK12820 79 EVQKRLEETENPHIETGDIEVFVRELSILAA 109 (706)
T ss_pred EEeccCccccCCCCCCCcEEEEeeEEEEEec
Confidence 544422221111 22568888765444443
No 231
>PRK06826 dnaE DNA polymerase III DnaE; Reviewed
Probab=27.18 E-value=1.5e+02 Score=38.74 Aligned_cols=60 Identities=18% Similarity=0.297 Sum_probs=43.2
Q ss_pred ceEEEEEEEEeccceeecCCCCCcceEEEEEeeCCCCEEEEEEechHHHhhhhccCcCcEEEEee
Q 003281 231 KWTIKARVTAKGELRHYNNQRGDGKVFHFDLLDSDGGEIRVTCFNAVADQFYHQVEAGKIYLVSR 295 (834)
Q Consensus 231 ~w~I~aRV~~Ks~lr~~~n~~g~Gk~f~~~L~De~g~~I~at~f~~~~d~f~~~l~eG~vy~is~ 295 (834)
...|.+-|+. +|.....+|+ ...-+.|-|+ .|.|.+++|.+..+++.+.|++|.++.|..
T Consensus 993 ~v~v~g~i~~---~~~~~tk~G~-~maf~~leD~-~g~~e~~vfp~~~~~~~~~l~~~~~~~v~g 1052 (1151)
T PRK06826 993 KVIIGGIITE---VKRKTTRNNE-MMAFLTLEDL-YGTVEVIVFPKVYEKYRSLLNEDNIVLIKG 1052 (1151)
T ss_pred EEEEEEEEEE---eEeeccCCCC-eEEEEEEEEC-CCcEEEEECHHHHHHHHHHhccCCEEEEEE
Confidence 3455566654 3444334432 3445667786 589999999999999999999999999954
No 232
>PRK00476 aspS aspartyl-tRNA synthetase; Validated
Probab=27.14 E-value=4.3e+02 Score=31.97 Aligned_cols=84 Identities=17% Similarity=0.201 Sum_probs=53.1
Q ss_pred CceEEEEEEEEeccceeecCCCCCcceEEEEEeeCCCCEEEEEEechHHHhh--hhccCcCcEEEEeeeEEecCCccccc
Q 003281 230 GKWTIKARVTAKGELRHYNNQRGDGKVFHFDLLDSDGGEIRVTCFNAVADQF--YHQVEAGKIYLVSRGSLKPAQKNFNH 307 (834)
Q Consensus 230 ~~w~I~aRV~~Ks~lr~~~n~~g~Gk~f~~~L~De~g~~I~at~f~~~~d~f--~~~l~eG~vy~is~~~V~~a~~~~~~ 307 (834)
...+|++||.+ +|.. |++.-++|.|. +|.|++++-.. .+.| ...|..|+++.|.+.-++...+..+.
T Consensus 18 ~~V~l~GwV~~---~R~~------g~l~Fi~LrD~-~g~iQ~v~~~~-~~~~~~~~~l~~es~V~V~G~v~~~~~~~~n~ 86 (588)
T PRK00476 18 QTVTLCGWVHR---RRDH------GGLIFIDLRDR-EGIVQVVFDPD-AEAFEVAESLRSEYVIQVTGTVRARPEGTVNP 86 (588)
T ss_pred CEEEEEEEEEE---EEeC------CCeEEEEEEeC-CceEEEEEeCC-HHHHHHHhCCCCCCEEEEEEEEEecCCcccCc
Confidence 46889999975 4443 56888889997 57899988642 2222 34589999999987544322122222
Q ss_pred --CCCeEEEEEccCccEEE
Q 003281 308 --LHNDLEIFLDMTSMVQL 324 (834)
Q Consensus 308 --~~~~yeI~f~~~T~I~~ 324 (834)
...++||..+.-..+.+
T Consensus 87 ~~~~g~~El~~~~i~il~~ 105 (588)
T PRK00476 87 NLPTGEIEVLASELEVLNK 105 (588)
T ss_pred cCCCCcEEEEEeEEEEEec
Confidence 23568888765444444
No 233
>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=27.09 E-value=1.5e+02 Score=26.37 Aligned_cols=35 Identities=14% Similarity=0.266 Sum_probs=21.8
Q ss_pred EEEEEEcCCccchhhhhhhhcccCCCccEEEEEE-EEEeecC
Q 003281 391 SVELTLWGNFCNDDGLRLQHMCDSGVFPILAVKA-GRVSDFN 431 (834)
Q Consensus 391 si~vtLWg~~a~~~~~~l~~~~~~~~~~Vv~ik~-~rV~~f~ 431 (834)
-+.|++||+.|+...+.+. .+..|.+.+ .+...|.
T Consensus 49 ~~~v~~~g~~A~~~~~~l~------kG~~V~V~G~l~~~~~~ 84 (104)
T PF00436_consen 49 WINVVAWGKLAENVAEYLK------KGDRVYVEGRLRTRTYE 84 (104)
T ss_dssp EEEEEEEHHHHHHHHHH--------TT-EEEEEEEEEEEEEE
T ss_pred EEEEEeeeecccccceEEc------CCCEEEEEEEEEeeEEE
Confidence 5889999998887655443 455666655 4555554
No 234
>PRK10220 hypothetical protein; Provisional
Probab=26.80 E-value=45 Score=30.64 Aligned_cols=31 Identities=23% Similarity=0.679 Sum_probs=25.0
Q ss_pred eeeCCCCCcCCCCcCcccccCCCCceecCCCCCcccc
Q 003281 519 CYTACPIMIGDRPCNKKVMNNGDGRWHCDRCDQSVVE 555 (834)
Q Consensus 519 ~Y~aC~~~~~~~~C~KKv~~~~dg~~~CekC~~~~~~ 555 (834)
.+|+|| +|+..-+-+....|-|+.|...+..
T Consensus 2 ~lP~CP------~C~seytY~d~~~~vCpeC~hEW~~ 32 (111)
T PRK10220 2 SLPHCP------KCNSEYTYEDNGMYICPECAHEWND 32 (111)
T ss_pred CCCcCC------CCCCcceEcCCCeEECCcccCcCCc
Confidence 468999 7999876666678999999987753
No 235
>PLN02903 aminoacyl-tRNA ligase
Probab=26.52 E-value=4.1e+02 Score=32.49 Aligned_cols=95 Identities=15% Similarity=0.160 Sum_probs=58.0
Q ss_pred eccccCCC--CCceEEEEEEEEeccceeecCCCCCcceEEEEEeeCCCCEEEEEEechH---HHhhhhccCcCcEEEEee
Q 003281 221 PIAALNPY--MGKWTIKARVTAKGELRHYNNQRGDGKVFHFDLLDSDGGEIRVTCFNAV---ADQFYHQVEAGKIYLVSR 295 (834)
Q Consensus 221 pI~~L~p~--~~~w~I~aRV~~Ks~lr~~~n~~g~Gk~f~~~L~De~g~~I~at~f~~~---~d~f~~~l~eG~vy~is~ 295 (834)
...+|+.. ....+|+++|-+ +|.. |++.-++|.|. .|.|++++-.+. +-+.-..|..|+|+.+.+
T Consensus 62 ~cg~l~~~~~gk~V~l~GWV~~---~R~~------G~l~FidLRD~-~G~iQvV~~~~~~~~~~~~~~~L~~esvV~V~G 131 (652)
T PLN02903 62 LCGALSVNDVGSRVTLCGWVDL---HRDM------GGLTFLDVRDH-TGIVQVVTLPDEFPEAHRTANRLRNEYVVAVEG 131 (652)
T ss_pred chhhcchhhCCCEEEEEEEEEE---EecC------CCcEEEEEEcC-CccEEEEEeCCccHHHHHHHhcCCCCCEEEEEE
Confidence 34444443 246889999965 3432 56778889997 478999886542 222335699999999987
Q ss_pred eEEecCCccc--ccCCCeEEEEEccCccEEEe
Q 003281 296 GSLKPAQKNF--NHLHNDLEIFLDMTSMVQLC 325 (834)
Q Consensus 296 ~~V~~a~~~~--~~~~~~yeI~f~~~T~I~~~ 325 (834)
--.....+.. +.....+||..+.-..+..+
T Consensus 132 ~V~~r~~~~~n~~~~tGeiEl~~~~i~VL~~a 163 (652)
T PLN02903 132 TVRSRPQESPNKKMKTGSVEVVAESVDILNVV 163 (652)
T ss_pred EEEeCCCcCcCCCCCCCCEEEEEeEEEEEecC
Confidence 4433211111 12235789988755444443
No 236
>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=26.44 E-value=1.1e+02 Score=27.77 Aligned_cols=60 Identities=17% Similarity=0.231 Sum_probs=38.1
Q ss_pred EEEEEcccccccccccccch---hhhhh-cCCcccccEEEEceeeeecccCeEEEEEEeeeEec
Q 003281 27 FRMVLSDGSRSQQGMLATQR---NELVT-SGLLQIGSVVRLTKFTCNVIQNRMIVIVMDLDVII 86 (834)
Q Consensus 27 yrl~lSDG~~~~~~mLatql---n~lv~-~g~l~~gsiv~l~~~~~~~v~~r~iiii~~lev~~ 86 (834)
.=+.|.||...+|+|+.... ..+.. ...|..||+|.++=.....-.+--=|.+.+++++.
T Consensus 18 ~Fi~lrd~~~~lQ~v~~~~~~~~~~~~~~~~~l~~g~~V~v~G~v~~~~~g~~El~~~~~~ils 81 (108)
T cd04322 18 SFADLQDESGKIQVYVNKDDLGEEEFEDFKKLLDLGDIIGVTGTPFKTKTGELSIFVKEFTLLS 81 (108)
T ss_pred EEEEEEECCeEEEEEEECCCCCHHHHHHHHhcCCCCCEEEEEEEEEecCCCCEEEEeCEeEEee
Confidence 45889999999999885332 11111 12399999999977666554433344555555554
No 237
>COG1107 Archaea-specific RecJ-like exonuclease, contains DnaJ-type Zn finger domain [DNA replication, recombination, and repair]
Probab=26.35 E-value=71 Score=37.72 Aligned_cols=68 Identities=25% Similarity=0.365 Sum_probs=53.3
Q ss_pred CceeccccCCCC-CceEEEEEEEEeccceeecCCCCCcceEEEEEeeCCCCEEEEEEechHHHhhhhccCcCcEEEEee
Q 003281 218 RIIPIAALNPYM-GKWTIKARVTAKGELRHYNNQRGDGKVFHFDLLDSDGGEIRVTCFNAVADQFYHQVEAGKIYLVSR 295 (834)
Q Consensus 218 ~~~pI~~L~p~~-~~w~I~aRV~~Ks~lr~~~n~~g~Gk~f~~~L~De~g~~I~at~f~~~~d~f~~~l~eG~vy~is~ 295 (834)
+.+.|.+|..+. ....|++.|++ +++...+ .+| +|.|+ +|.|-|..|.+.--+-|+-|++|+++.+..
T Consensus 201 ~r~~i~~id~~ig~tV~I~GeV~q---ikqT~GP----TVF--tltDe-tg~i~aAAFe~aGvRAyP~IevGdiV~ViG 269 (715)
T COG1107 201 PRTLIDDLDEMIGKTVRIEGEVTQ---IKQTSGP----TVF--TLTDE-TGAIWAAAFEEAGVRAYPEIEVGDIVEVIG 269 (715)
T ss_pred ccccHHHHHhhcCceEEEEEEEEE---EEEcCCC----EEE--EEecC-CCceehhhhccCCcccCCCCCCCceEEEEE
Confidence 455678887764 47789999996 5654422 354 58997 689999999998889999999999999976
No 238
>PRK14285 chaperone protein DnaJ; Provisional
Probab=26.23 E-value=53 Score=37.10 Aligned_cols=40 Identities=18% Similarity=0.319 Sum_probs=22.0
Q ss_pred CcCcccCCCCccCCCCCCC-CCCCCCcCCCCCC----cccccCCCC
Q 003281 786 SECYKCHKTGHWARDCPSL-NAAPPAYGSSGIG----ISAAGYRGA 826 (834)
Q Consensus 786 ~~Cy~Cg~~GH~ardCp~~-~~~~~c~~c~~~g----~~~~~cg~~ 826 (834)
..|..|+..|.... .+.. .....|-.|+|.| ..|..|.|.
T Consensus 164 ~~C~~C~G~G~~~~-~~G~~~~~~~C~~C~G~G~~~~~~C~~C~G~ 208 (365)
T PRK14285 164 SICNMCNGSGRVMQ-GGGFFRVTTTCPKCYGNGKIISNPCKSCKGK 208 (365)
T ss_pred ccCCCccCceeEEe-cCceeEEeeecCCCCCcccccCCCCCCCCCC
Confidence 46777777776543 1110 0011577777776 347777663
No 239
>KOG2593 consensus Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=26.16 E-value=35 Score=38.76 Aligned_cols=27 Identities=37% Similarity=1.091 Sum_probs=20.7
Q ss_pred eCCCCCcCCCCcCcc--------cccCCCCceecCCCCCcc
Q 003281 521 TACPIMIGDRPCNKK--------VMNNGDGRWHCDRCDQSV 553 (834)
Q Consensus 521 ~aC~~~~~~~~C~KK--------v~~~~dg~~~CekC~~~~ 553 (834)
..|| .|+|| +.+..+|.|+|+.|+..+
T Consensus 129 Y~Cp------~C~kkyt~Lea~~L~~~~~~~F~C~~C~gel 163 (436)
T KOG2593|consen 129 YVCP------NCQKKYTSLEALQLLDNETGEFHCENCGGEL 163 (436)
T ss_pred ccCC------ccccchhhhHHHHhhcccCceEEEecCCCch
Confidence 3799 59999 234556899999999765
No 240
>PRK14284 chaperone protein DnaJ; Provisional
Probab=25.88 E-value=35 Score=38.96 Aligned_cols=40 Identities=20% Similarity=0.356 Sum_probs=17.7
Q ss_pred CcCcccCCCCccCCCCCCCCCCCCCcCCCCCCc----ccccCCC
Q 003281 786 SECYKCHKTGHWARDCPSLNAAPPAYGSSGIGI----SAAGYRG 825 (834)
Q Consensus 786 ~~Cy~Cg~~GH~ardCp~~~~~~~c~~c~~~g~----~~~~cg~ 825 (834)
..|..|+..|.....--.......|-.|++.|. .|..|.|
T Consensus 176 ~~C~~C~G~G~v~~~~G~~~~~~~C~~C~G~G~~~~~~C~~C~G 219 (391)
T PRK14284 176 KVCDRCKGSGQVVQSRGFFSMASTCPECGGEGRVITDPCSVCRG 219 (391)
T ss_pred eecCccCCeeEEEEEeceEEEEEECCCCCCCCcccCCcCCCCCC
Confidence 356666666653221100000114555555552 3666655
No 241
>COG5179 TAF1 Transcription initiation factor TFIID, subunit TAF1 [Transcription]
Probab=25.63 E-value=42 Score=39.53 Aligned_cols=18 Identities=44% Similarity=1.219 Sum_probs=14.9
Q ss_pred ccccccCccCccC--CCCCC
Q 003281 742 QSCSSCGAVGHSS--MNCPS 759 (834)
Q Consensus 742 ~~C~~Cg~~GH~a--~~Cp~ 759 (834)
..|-+|||.||+. +-||-
T Consensus 938 r~C~nCGQvGHmkTNK~CP~ 957 (968)
T COG5179 938 RTCGNCGQVGHMKTNKACPK 957 (968)
T ss_pred eecccccccccccccccCcc
Confidence 3999999999976 56775
No 242
>PRK14286 chaperone protein DnaJ; Provisional
Probab=25.49 E-value=35 Score=38.66 Aligned_cols=40 Identities=20% Similarity=0.324 Sum_probs=21.7
Q ss_pred CcCcccCCCCccCCCCCCCCCCCCCcCCCCCC----cccccCCC
Q 003281 786 SECYKCHKTGHWARDCPSLNAAPPAYGSSGIG----ISAAGYRG 825 (834)
Q Consensus 786 ~~Cy~Cg~~GH~ardCp~~~~~~~c~~c~~~g----~~~~~cg~ 825 (834)
..|..|+..|......-.......|-.|+|.| ..|..|.|
T Consensus 168 ~~C~~C~G~G~v~~~~G~~~~~~~C~~C~G~G~~~~~~C~~C~G 211 (372)
T PRK14286 168 TTCPDCGGSGQIRRTQGFFSVATTCPTCRGKGTVISNPCKTCGG 211 (372)
T ss_pred ccCCCCcCeEEEEEEeceEEEEEeCCCCCceeeEecccCCCCCC
Confidence 45777777776543321000111577777776 44777765
No 243
>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=25.39 E-value=4.7e+02 Score=25.60 Aligned_cols=85 Identities=9% Similarity=0.096 Sum_probs=50.8
Q ss_pred CceEEEEEEEEeccceeecCCCCCcceEEEEEe-------eC-CCCEEEEEEechHHHhhhhccCcCcEEEEeeeEEecC
Q 003281 230 GKWTIKARVTAKGELRHYNNQRGDGKVFHFDLL-------DS-DGGEIRVTCFNAVADQFYHQVEAGKIYLVSRGSLKPA 301 (834)
Q Consensus 230 ~~w~I~aRV~~Ks~lr~~~n~~g~Gk~f~~~L~-------De-~g~~I~at~f~~~~d~f~~~l~eG~vy~is~~~V~~a 301 (834)
-...++|+|+.......|. .|.+.+. |. .-|.++..+-...+. ...|++|+-|.|-+-..
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 4578888888766544443 2444332 21 124455433333343 46789999999987531
Q ss_pred Cccccc-CCCeEEEEEccCccEEEecC
Q 003281 302 QKNFNH-LHNDLEIFLDMTSMVQLCYE 327 (834)
Q Consensus 302 ~~~~~~-~~~~yeI~f~~~T~I~~~~d 327 (834)
..++. ....|.-.|+++|-|+..+.
T Consensus 99 -~~~~~~~~~~~~Y~L~~~TWvE~WP~ 124 (150)
T cd03582 99 -LKIRLNRSFRYRYPLDSEAWIEWWPT 124 (150)
T ss_pred -CccccCCCceeEEEcCCceeEEECCC
Confidence 11222 12258889999999999864
No 244
>PRK14279 chaperone protein DnaJ; Provisional
Probab=25.02 E-value=38 Score=38.67 Aligned_cols=40 Identities=20% Similarity=0.437 Sum_probs=20.1
Q ss_pred CcCcccCCCCccCCCCCCCCCCCCCcCCCCCC----cccccCCC
Q 003281 786 SECYKCHKTGHWARDCPSLNAAPPAYGSSGIG----ISAAGYRG 825 (834)
Q Consensus 786 ~~Cy~Cg~~GH~ardCp~~~~~~~c~~c~~~g----~~~~~cg~ 825 (834)
..|..|+..|.....--.......|-.|+|.| ..|..|.|
T Consensus 191 ~~C~~C~G~G~~~~~~g~~~~~~~C~~C~G~G~~i~~~C~~C~G 234 (392)
T PRK14279 191 KVCPTCNGSGVISRNQGAFGFSEPCTDCRGTGSIIEDPCEECKG 234 (392)
T ss_pred CCCCCCcceEEEEEEecceEEEEecCCCCceeEEeCCcCCCCCC
Confidence 45666766665433210000112566676666 34666665
No 245
>COG1190 LysU Lysyl-tRNA synthetase (class II) [Translation, ribosomal structure and biogenesis]
Probab=24.93 E-value=1.7e+02 Score=34.23 Aligned_cols=59 Identities=24% Similarity=0.374 Sum_probs=43.8
Q ss_pred ceEEEEEEEEeccceeecCCCCCcceEEEEEeeCCCCEEEEEEech-----HHHhhhhccCcCcEEEEeeeEEe
Q 003281 231 KWTIKARVTAKGELRHYNNQRGDGKVFHFDLLDSDGGEIRVTCFNA-----VADQFYHQVEAGKIYLVSRGSLK 299 (834)
Q Consensus 231 ~w~I~aRV~~Ks~lr~~~n~~g~Gk~f~~~L~De~g~~I~at~f~~-----~~d~f~~~l~eG~vy~is~~~V~ 299 (834)
..+|-+||+.+ |. -||+.-++|.|. +|+|++-+-.+ ..+.+...+..||++.+.+.-.+
T Consensus 63 ~v~vAGRi~~~---R~------~GK~~F~~i~d~-~gkiQ~yi~k~~~~~~~~~~~~~~~dlGDiigv~G~~~~ 126 (502)
T COG1190 63 EVSVAGRIMTI---RN------MGKASFADLQDG-SGKIQLYVNKDEVGEEVFEALFKKLDLGDIIGVEGPLFK 126 (502)
T ss_pred eeEEecceeee---cc------cCceeEEEEecC-CceEEEEEeccccchhhHHHHHhccccCCEEeeeeeeee
Confidence 37888999853 33 367777888886 68999998755 34446667889999999886544
No 246
>PRK14296 chaperone protein DnaJ; Provisional
Probab=24.84 E-value=52 Score=37.30 Aligned_cols=42 Identities=19% Similarity=0.245 Sum_probs=24.3
Q ss_pred CCcCcccCCCCccCCCCCCCC----CCCCCcCCCCCC----cccccCCCC
Q 003281 785 SSECYKCHKTGHWARDCPSLN----AAPPAYGSSGIG----ISAAGYRGA 826 (834)
Q Consensus 785 ~~~Cy~Cg~~GH~ardCp~~~----~~~~c~~c~~~g----~~~~~cg~~ 826 (834)
...|..|+..|+....-.... ....|..|+|.| +.|..|.|.
T Consensus 166 ~~~C~~C~G~G~~~~~~~~g~~~~q~~~~C~~C~G~G~~~~~~C~~C~G~ 215 (372)
T PRK14296 166 IHICNNCHGTGEVLVQKNMGFFQFQQSAKCNVCNGAGKIIKNKCKNCKGK 215 (372)
T ss_pred CccCCCCCCCceEEEEEeccceEEEEEecCCCcCCcceeecccccCCCCc
Confidence 346888888887554331110 012677777777 347777663
No 247
>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=24.58 E-value=71 Score=34.50 Aligned_cols=50 Identities=22% Similarity=0.177 Sum_probs=38.6
Q ss_pred CcCcccccCCCCceecCCCCCccccceEEEEEEEEEEeCCCeEEEEEehHHHHHHh
Q 003281 531 PCNKKVMNNGDGRWHCDRCDQSVVECDYRYILQFQIQDHTGLTWVTAFQECAEEIM 586 (834)
Q Consensus 531 ~C~KKv~~~~dg~~~CekC~~~~~~~~~ry~l~~~i~D~Tg~~~~~~F~e~ae~ll 586 (834)
.|||||+ .+|..-+-.-+-|..||==++.|.-..|..-+++|+.-.-.-+
T Consensus 66 ~cNkK~t------l~C~EKeLvGdvP~aRYGHt~~vV~SrGKta~VlFGGRSY~P~ 115 (337)
T PF03089_consen 66 GCNKKVT------LCCQEKELVGDVPEARYGHTINVVHSRGKTACVLFGGRSYMPP 115 (337)
T ss_pred CCCceeE------EEEecceecCCCCcccccceEEEEEECCcEEEEEECCcccCCc
Confidence 6999995 6775444344458899999999999999999999996544333
No 248
>PRK06341 single-stranded DNA-binding protein; Provisional
Probab=24.50 E-value=4.4e+02 Score=26.31 Aligned_cols=35 Identities=6% Similarity=0.137 Sum_probs=21.8
Q ss_pred EEEEEEcCC-ccchhhhhhhhcccCCCccEEEEEE-EEEeecC
Q 003281 391 SVELTLWGN-FCNDDGLRLQHMCDSGVFPILAVKA-GRVSDFN 431 (834)
Q Consensus 391 si~vtLWg~-~a~~~~~~l~~~~~~~~~~Vv~ik~-~rV~~f~ 431 (834)
-++|++|++ .|+...+.+. .+.-|+|.+ .+.+.|.
T Consensus 54 w~~Vv~fg~~~Ae~~~~~Lk------KG~~V~VeGrL~~r~w~ 90 (166)
T PRK06341 54 WHRVVIFNEGLCKVAEQYLK------KGAKVYIEGQLQTRKWT 90 (166)
T ss_pred EEEEEEeChHHHHHHHHhcC------CCCEEEEEEEEEeCcEE
Confidence 578999997 6765433332 355565654 5666674
No 249
>PRK00286 xseA exodeoxyribonuclease VII large subunit; Reviewed
Probab=24.47 E-value=1.8e+02 Score=33.68 Aligned_cols=43 Identities=33% Similarity=0.412 Sum_probs=34.7
Q ss_pred cceEEEEEeeCCCCEEEEEEechHHHhhhhccCcCcEEEEee-eEE
Q 003281 254 GKVFHFDLLDSDGGEIRVTCFNAVADQFYHQVEAGKIYLVSR-GSL 298 (834)
Q Consensus 254 Gk~f~~~L~De~g~~I~at~f~~~~d~f~~~l~eG~vy~is~-~~V 298 (834)
|. +.|+|.|+ ...|+|++|...+.+..-.+++|.-+.+.. ..|
T Consensus 41 GH-~Yf~Lkd~-~a~i~~~~~~~~~~~~~~~~~~G~~v~v~g~~~~ 84 (438)
T PRK00286 41 GH-WYFTLKDE-IAQIRCVMFKGSARRLKFKPEEGMKVLVRGKVSL 84 (438)
T ss_pred Ce-EEEEEEcC-CcEEEEEEEcChhhcCCCCCCCCCEEEEEEEEEE
Confidence 54 66889998 589999999998888777799998887765 344
No 250
>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=24.38 E-value=85 Score=30.27 Aligned_cols=28 Identities=29% Similarity=0.408 Sum_probs=23.7
Q ss_pred ceEEEEEeeCCCCEEEEEEechHHHhhhh
Q 003281 255 KVFHFDLLDSDGGEIRVTCFNAVADQFYH 283 (834)
Q Consensus 255 k~f~~~L~De~g~~I~at~f~~~~d~f~~ 283 (834)
..+++.|.|. .|.+.+++|++.++++..
T Consensus 54 y~l~~~i~D~-tg~~~~~~F~~~a~~l~G 81 (146)
T PF08646_consen 54 YRLSLKISDG-TGSIWVTLFDEEAEQLLG 81 (146)
T ss_dssp EEEEEEEEET-TEEEEEEEEHHHHHHHHC
T ss_pred EEEEEEEEeC-CCeEEEEEEhHHHHHHhC
Confidence 3578899997 589999999999888764
No 251
>PLN03165 chaperone protein dnaJ-related; Provisional
Probab=24.25 E-value=32 Score=31.95 Aligned_cols=18 Identities=17% Similarity=0.475 Sum_probs=10.2
Q ss_pred CCcCCCCCC-cccccCCCC
Q 003281 809 PAYGSSGIG-ISAAGYRGA 826 (834)
Q Consensus 809 ~c~~c~~~g-~~~~~cg~~ 826 (834)
.|..|.+.| ..|..|.|.
T Consensus 77 ~C~~C~G~Gk~~C~~C~G~ 95 (111)
T PLN03165 77 KCINCDGAGSLTCTTCQGS 95 (111)
T ss_pred ECCCCCCcceeeCCCCCCC
Confidence 466665555 346666653
No 252
>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=23.48 E-value=1.8e+02 Score=26.09 Aligned_cols=61 Identities=20% Similarity=0.227 Sum_probs=40.3
Q ss_pred EEEEEcccccccccccccch----hhhhhc-CCcccccEEEEceeeeeccc-------CeEEEEEEeeeEecc
Q 003281 27 FRMVLSDGSRSQQGMLATQR----NELVTS-GLLQIGSVVRLTKFTCNVIQ-------NRMIVIVMDLDVIID 87 (834)
Q Consensus 27 yrl~lSDG~~~~~~mLatql----n~lv~~-g~l~~gsiv~l~~~~~~~v~-------~r~iiii~~lev~~~ 87 (834)
-=+.|.||...+|+++.... .++... ..|..+|+|.++=.....-. +..=|.+.+++++..
T Consensus 19 ~Fi~LrD~sg~iQ~v~~~~~~~~~~~~~~~~~~l~~es~V~V~G~v~~~~~~~~~~~~~~~El~~~~i~il~~ 91 (102)
T cd04320 19 AFLVLRQQGYTIQGVLAASAEGVSKQMVKWAGSLSKESIVDVEGTVKKPEEPIKSCTQQDVELHIEKIYVVSE 91 (102)
T ss_pred EEEEEecCCceEEEEEeCCcccCCHHHHHHHhcCCCccEEEEEEEEECCCCcccCCCcCcEEEEEEEEEEEec
Confidence 44678999999999997543 223221 35899999999876654321 234566777777653
No 253
>KOG1885 consensus Lysyl-tRNA synthetase (class II) [Translation, ribosomal structure and biogenesis]
Probab=23.27 E-value=3e+02 Score=31.92 Aligned_cols=57 Identities=23% Similarity=0.286 Sum_probs=42.4
Q ss_pred ceEEEEEEEEeccceeecCCCCCcceEEEEEeeCCCCEEEEEEech------HHHhhhhccCcCcEEEEeee
Q 003281 231 KWTIKARVTAKGELRHYNNQRGDGKVFHFDLLDSDGGEIRVTCFNA------VADQFYHQVEAGKIYLVSRG 296 (834)
Q Consensus 231 ~w~I~aRV~~Ks~lr~~~n~~g~Gk~f~~~L~De~g~~I~at~f~~------~~d~f~~~l~eG~vy~is~~ 296 (834)
..+|.+||..+ |... .|++-++|.++ |.++++.+-.. ...+..+.|+-||++-+++.
T Consensus 106 ~~svaGRI~s~---R~sG-----sKL~Fydl~~~-g~klQvm~~~~~~~~~~~F~~~~~~lkrGDiig~~G~ 168 (560)
T KOG1885|consen 106 IVSVAGRIHSK---RESG-----SKLVFYDLHGD-GVKLQVMANAKKITSEEDFEQLHKFLKRGDIIGVSGY 168 (560)
T ss_pred eeeeeeeEeee---eccC-----CceEEEEEecC-CeEEEEEEehhhcCCHHHHHHHHhhhhccCEEeeecC
Confidence 46788899764 4321 48888899886 89999988543 34566788999999998874
No 254
>PLN02603 asparaginyl-tRNA synthetase
Probab=23.16 E-value=9.9e+02 Score=28.81 Aligned_cols=81 Identities=15% Similarity=0.160 Sum_probs=50.5
Q ss_pred CCceEEEEEEEEeccceeecCCCCCcceEEEEEeeCCC-CEEEEEEechHH--Hhhhh-ccCcCcEEEEeeeEEecCCcc
Q 003281 229 MGKWTIKARVTAKGELRHYNNQRGDGKVFHFDLLDSDG-GEIRVTCFNAVA--DQFYH-QVEAGKIYLVSRGSLKPAQKN 304 (834)
Q Consensus 229 ~~~w~I~aRV~~Ks~lr~~~n~~g~Gk~f~~~L~De~g-~~I~at~f~~~~--d~f~~-~l~eG~vy~is~~~V~~a~~~ 304 (834)
....+|+++|.. +|. .|++.-++|.|..+ +.|++++-.+.. +.+.. .|..|+++.|.+.-++...
T Consensus 107 g~~V~v~GwV~~---iR~------~g~~~Fi~l~Dgs~~~~lQ~v~~~~~~~~~~l~~~~l~~gs~V~V~G~v~~~~~-- 175 (565)
T PLN02603 107 GKTLNVMGWVRT---LRA------QSSVTFIEVNDGSCLSNMQCVMTPDAEGYDQVESGLITTGASVLVQGTVVSSQG-- 175 (565)
T ss_pred CCEEEEEEEEEE---EEe------CCCeEEEEEECCCCCEeEEEEEECcHHHHHHHhhcCCCCCCEEEEEEEEEecCC--
Confidence 356788888863 443 25676778899755 379999854421 22221 3889999999986554322
Q ss_pred cccCCCeEEEEEccCccEE
Q 003281 305 FNHLHNDLEIFLDMTSMVQ 323 (834)
Q Consensus 305 ~~~~~~~yeI~f~~~T~I~ 323 (834)
....+||..+.-..+-
T Consensus 176 ---~~~~~EL~v~~i~vlg 191 (565)
T PLN02603 176 ---GKQKVELKVSKIVVVG 191 (565)
T ss_pred ---CCccEEEEEeEEEEEE
Confidence 1246888886433333
No 255
>PF11325 DUF3127: Domain of unknown function (DUF3127); InterPro: IPR021474 This bacterial family of proteins has no known function.
Probab=22.98 E-value=2.6e+02 Score=24.68 Aligned_cols=59 Identities=17% Similarity=0.094 Sum_probs=35.8
Q ss_pred EEEEEEEeccceeecCCCCCcceEEEEEee--CCCCEEEEEEechHHHhhhhccCcCcEEEEe
Q 003281 234 IKARVTAKGELRHYNNQRGDGKVFHFDLLD--SDGGEIRVTCFNAVADQFYHQVEAGKIYLVS 294 (834)
Q Consensus 234 I~aRV~~Ks~lr~~~n~~g~Gk~f~~~L~D--e~g~~I~at~f~~~~d~f~~~l~eG~vy~is 294 (834)
|.++|+.+-+..+=...+| =+--.++|-- .---.|...+|++.++.+.. |++|+.+.++
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-WKKREFVLETEEQYPQKICFEFWGDKIDLLDN-FQVGDEVKVS 62 (84)
T ss_pred cccEEEEEecCcccCcCCC-cEEEEEEEeCCCcCCceEEEEEEcchhhhhcc-CCCCCEEEEE
Confidence 4567665554433222232 1222344432 11368999999999988665 8999999987
No 256
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=22.75 E-value=45 Score=36.16 Aligned_cols=14 Identities=21% Similarity=0.726 Sum_probs=11.2
Q ss_pred CceecCCCCCcccc
Q 003281 542 GRWHCDRCDQSVVE 555 (834)
Q Consensus 542 g~~~CekC~~~~~~ 555 (834)
..|+||-|++.+.+
T Consensus 397 KPYrCevC~KRYKN 410 (423)
T COG5189 397 KPYRCEVCDKRYKN 410 (423)
T ss_pred Cceeccccchhhcc
Confidence 46999999987654
No 257
>KOG2044 consensus 5'-3' exonuclease HKE1/RAT1 [Replication, recombination and repair; RNA processing and modification]
Probab=22.70 E-value=31 Score=41.88 Aligned_cols=19 Identities=32% Similarity=0.805 Sum_probs=17.3
Q ss_pred cccccCccCccCCCCCCCC
Q 003281 743 SCSSCGAVGHSSMNCPSIM 761 (834)
Q Consensus 743 ~C~~Cg~~GH~a~~Cp~~~ 761 (834)
.||.||++||.+.+|....
T Consensus 262 ~C~~cgq~gh~~~dc~g~~ 280 (931)
T KOG2044|consen 262 RCFLCGQTGHEAKDCEGKP 280 (931)
T ss_pred cchhhcccCCcHhhcCCcC
Confidence 7999999999999998754
No 258
>PRK14295 chaperone protein DnaJ; Provisional
Probab=22.32 E-value=44 Score=38.11 Aligned_cols=41 Identities=22% Similarity=0.425 Sum_probs=23.3
Q ss_pred CcCcccCCCCccCCCCCCCCCCCCCcCCCCCC----cccccCCCC
Q 003281 786 SECYKCHKTGHWARDCPSLNAAPPAYGSSGIG----ISAAGYRGA 826 (834)
Q Consensus 786 ~~Cy~Cg~~GH~ardCp~~~~~~~c~~c~~~g----~~~~~cg~~ 826 (834)
..|..|+..|......-.-.....|-.|+|.| ..|..|.|.
T Consensus 184 ~~C~~C~G~G~~~~~~g~~~~~~~C~~C~G~G~~~~~~C~~C~G~ 228 (389)
T PRK14295 184 RVCPTCSGTGQVSRNSGGFSLSEPCPDCKGRGLIADDPCLVCKGS 228 (389)
T ss_pred cCCCCCCCEeEEEEEecceEEEEecCCCcceeEEeccCCCCCCCC
Confidence 46788877776544331100112677777776 347777663
No 259
>PF04057 Rep-A_N: Replication factor-A protein 1, N-terminal domain; InterPro: IPR007199 Replication factor-a protein 1 (RPA1) forms a multiprotein complex with RPA2 and RPA3 that binds single-stranded DNA and functions in the recognition of DNA damage for nucleotide excision repair. The complex binds to single-stranded DNA sequences participating in DNA replication in addition to those mediating transcriptional repression and activation, and stimulates the activity of cognate strand exchange protein Sep1. It cooperates with T-AG and DNA topoisomerase I to unwind template DNA containing the Simian Virus 40 origin of replication [].; GO: 0003677 DNA binding, 0006260 DNA replication, 0005634 nucleus; PDB: 1EWI_A 2B3G_A 2B29_A.
Probab=22.11 E-value=5.5e+02 Score=23.23 Aligned_cols=49 Identities=10% Similarity=0.139 Sum_probs=36.0
Q ss_pred CcceEEEEEeeCCCCEEEEEEechHHHhhhh-ccCcCcEEEEeeeEEecCC
Q 003281 253 DGKVFHFDLLDSDGGEIRVTCFNAVADQFYH-QVEAGKIYLVSRGSLKPAQ 302 (834)
Q Consensus 253 ~Gk~f~~~L~De~g~~I~at~f~~~~d~f~~-~l~eG~vy~is~~~V~~a~ 302 (834)
..+-|.+.|-|.. ..++|.+-..+-+...+ .|+.|.++.+.++.+..-+
T Consensus 36 ~~~RyR~~lSDG~-~~~~amLatqln~lv~~g~l~~~siirl~~y~~n~v~ 85 (101)
T PF04057_consen 36 GSDRYRLVLSDGV-HSIQAMLATQLNHLVESGELQKGSIIRLKQYTCNTVK 85 (101)
T ss_dssp S--EEEEEEESSS-EEEEEEESGGGHHHHHTTSSSTT-EEEEEEEEEEEST
T ss_pred CCceEEEEEEChH-HHHHHHhHHHhHHHHhcCCcccCCEEEEeEEEEeecc
Confidence 4578999999985 66999777776666544 7999999999998765444
No 260
>PRK06642 single-stranded DNA-binding protein; Provisional
Probab=21.99 E-value=4.6e+02 Score=25.68 Aligned_cols=35 Identities=6% Similarity=0.017 Sum_probs=22.3
Q ss_pred EEEEEEcCC-ccchhhhhhhhcccCCCccEEEEEE-EEEeecC
Q 003281 391 SVELTLWGN-FCNDDGLRLQHMCDSGVFPILAVKA-GRVSDFN 431 (834)
Q Consensus 391 si~vtLWg~-~a~~~~~~l~~~~~~~~~~Vv~ik~-~rV~~f~ 431 (834)
-++|++|++ .|+...+.+. .+.-|++.+ .+...|.
T Consensus 54 w~~v~~~g~~~Ae~~~~~l~------KG~~V~V~GrL~~~~y~ 90 (152)
T PRK06642 54 WHRVVIFSEGLVSVVERYVT------KGSKLYIEGSLQTRKWN 90 (152)
T ss_pred EEEEEEeChHHHHHHHHhCC------CCCEEEEEEEEEeCeeE
Confidence 588999997 6765544332 455666654 5666664
No 261
>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=21.76 E-value=1e+02 Score=25.10 Aligned_cols=20 Identities=25% Similarity=0.300 Sum_probs=18.3
Q ss_pred EEEEEEEEeCCCeEEEEEeh
Q 003281 560 YILQFQIQDHTGLTWVTAFQ 579 (834)
Q Consensus 560 y~l~~~i~D~Tg~~~~~~F~ 579 (834)
.++.+.+.|++|.+.+++|+
T Consensus 18 ~~~~~~~~D~~g~i~~~~F~ 37 (75)
T cd04488 18 RRLKVTLSDGTGTLTLVFFN 37 (75)
T ss_pred cEEEEEEEcCCCEEEEEEEC
Confidence 46899999999999999997
No 262
>KOG0314 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=21.64 E-value=66 Score=37.05 Aligned_cols=21 Identities=24% Similarity=0.621 Sum_probs=18.9
Q ss_pred ccccccCccCccCCCCCCCCC
Q 003281 742 QSCSSCGAVGHSSMNCPSIMS 762 (834)
Q Consensus 742 ~~C~~Cg~~GH~a~~Cp~~~~ 762 (834)
+.|++|++.|||..+||....
T Consensus 159 y~c~rc~~~g~wikacptv~~ 179 (448)
T KOG0314|consen 159 YKCVKCPTPGPWIKACPTVSG 179 (448)
T ss_pred cceecCCCCCccceeccccCC
Confidence 489999999999999998664
No 263
>PF13426 PAS_9: PAS domain; PDB: 3ULF_B 3UE6_E 2Z6D_B 2Z6C_B 3P7N_B 1LL8_A 3MJQ_A 3BWL_A 4EET_B 4EEP_A ....
Probab=21.45 E-value=4.9e+02 Score=21.82 Aligned_cols=31 Identities=23% Similarity=0.311 Sum_probs=21.8
Q ss_pred EEEEeCCCeEEEEEehHHHHHHhCCCHHHHHhh
Q 003281 564 FQIQDHTGLTWVTAFQECAEEIMGMSAKDLYSL 596 (834)
Q Consensus 564 ~~i~D~Tg~~~~~~F~e~ae~llG~sA~el~~l 596 (834)
+.+.|..|. +...++.+.+++|.+.+|+...
T Consensus 4 i~i~d~~g~--i~~~N~~~~~~~g~~~~~~~g~ 34 (104)
T PF13426_consen 4 IFILDPDGR--ILYVNPAFERLFGYSREELIGK 34 (104)
T ss_dssp EEEEETTSB--EEEE-HHHHHHHTS-HHHHTTS
T ss_pred EEEECCcCc--EEehhHHHHHHHCcCHHHHcCC
Confidence 456677654 5567999999999999998643
No 264
>PF08271 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013137 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 motif found in transcription factor IIB (TFIIB). In eukaryotes the initiation of transcription of protein encoding genes by the polymerase II complexe (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least seven different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, and -IIH []. TFIIB and TFIID are responsible for promoter recognition and interaction with pol II; together with Pol II, they form a minimal initiation complex capable of transcription under certain conditions. The TATA box of a Pol II promoter is bound in the initiation complex by the TBP subunit of TFIID, which bends the DNA around the C-terminal domain of TFIIB whereas the N-terminal zinc finger of TFIIB interacts with Pol II [, ]. The TFIIB zinc finger adopts a zinc ribbon fold characterised by two beta-hairpins forming two structurally similar zinc-binding sub-sites []. The zinc finger contacts the rbp1 subunit of Pol II through its dock domain, a conserved region of about 70 amino acids located close to the polymerase active site []. In the Pol II complex this surface is located near the RNA exit groove. Interestingly this sequence is best conserved in the three polymerases that utilise a TFIIB-like general transcription factor (Pol II, Pol III, and archaeal RNA polymerase) but not in Pol I []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1VD4_A 1PFT_A 3K1F_M 3K7A_M 1RO4_A 1RLY_A 1DL6_A.
Probab=21.16 E-value=59 Score=24.49 Aligned_cols=26 Identities=31% Similarity=0.825 Sum_probs=18.9
Q ss_pred CCCCCcCCCCcCcc--cccCCCCceecCCCCCcc
Q 003281 522 ACPIMIGDRPCNKK--VMNNGDGRWHCDRCDQSV 553 (834)
Q Consensus 522 aC~~~~~~~~C~KK--v~~~~dg~~~CekC~~~~ 553 (834)
.|| .|..+ +.+...|.+.|..|+..+
T Consensus 2 ~Cp------~Cg~~~~~~D~~~g~~vC~~CG~Vl 29 (43)
T PF08271_consen 2 KCP------NCGSKEIVFDPERGELVCPNCGLVL 29 (43)
T ss_dssp SBT------TTSSSEEEEETTTTEEEETTT-BBE
T ss_pred CCc------CCcCCceEEcCCCCeEECCCCCCEe
Confidence 588 58876 356677899999998654
No 265
>PRK10767 chaperone protein DnaJ; Provisional
Probab=20.96 E-value=56 Score=37.00 Aligned_cols=40 Identities=18% Similarity=0.300 Sum_probs=18.7
Q ss_pred CcCcccCCCCccCCCCCCCCCCCCCcCCCCCCc----ccccCCC
Q 003281 786 SECYKCHKTGHWARDCPSLNAAPPAYGSSGIGI----SAAGYRG 825 (834)
Q Consensus 786 ~~Cy~Cg~~GH~ardCp~~~~~~~c~~c~~~g~----~~~~cg~ 825 (834)
..|..|+..|.....--.......|-.|+|.|. .|..|.|
T Consensus 160 ~~C~~C~G~G~~~~~~g~~~~~~~C~~C~G~G~~~~~~C~~C~G 203 (371)
T PRK10767 160 KTCPTCHGAGQVRMQQGFFTVQQTCPTCHGRGKIIKDPCKKCHG 203 (371)
T ss_pred ccCCCCCCeeEEEEeeceEEEEEeCCCCCCceeECCCCCCCCCC
Confidence 356777666643221100000114666666653 3666665
No 266
>PRK14301 chaperone protein DnaJ; Provisional
Probab=20.50 E-value=52 Score=37.30 Aligned_cols=40 Identities=20% Similarity=0.351 Sum_probs=20.0
Q ss_pred CcCcccCCCCccCCCCCCCCCCCCCcCCCCCC----cccccCCC
Q 003281 786 SECYKCHKTGHWARDCPSLNAAPPAYGSSGIG----ISAAGYRG 825 (834)
Q Consensus 786 ~~Cy~Cg~~GH~ardCp~~~~~~~c~~c~~~g----~~~~~cg~ 825 (834)
..|..|+..|.....--.......|-.|+|.| ..|..|.|
T Consensus 162 ~~C~~C~G~G~v~~~~G~~~~~~~C~~C~G~G~~~~~~C~~C~G 205 (373)
T PRK14301 162 ETCRHCGGSGQVRQSQGFFQIAVPCPVCRGEGRVITHPCPKCKG 205 (373)
T ss_pred cccCCccCeeEEEEEeeeEEEEEeCCCCCceeeecCCCCCCCCC
Confidence 45777777765433210000011566666666 34666665
No 267
>PF13742 tRNA_anti_2: OB-fold nucleic acid binding domain
Probab=20.46 E-value=4.3e+02 Score=23.70 Aligned_cols=58 Identities=19% Similarity=0.248 Sum_probs=40.3
Q ss_pred EEEEEeCCCeEEEEEehHHHHHHhCCCHHHHHhhhccCCChhHHHHHHHHhcCceEEEEEEEeecccCccceEEEEEEEe
Q 003281 563 QFQIQDHTGLTWVTAFQECAEEIMGMSAKDLYSLKYVDQNDEKFGEVVRNATFTKYLFKLKVKEETFSDEQRVKSTVVKA 642 (834)
Q Consensus 563 ~~~i~D~Tg~~~~~~F~e~ae~llG~sA~el~~l~~ee~d~~~~~~~l~~~~~k~~~f~l~~k~~~ynde~rvk~~v~~~ 642 (834)
-+++.|+..++.+++|...+..|-|.. ++ + |.+ +.++.+.+.|....+..+.|.++
T Consensus 42 YftLkD~~a~i~~~~~~~~~~~i~~~~------l~--~--------------G~~--V~v~g~~~~y~~~G~~sl~v~~i 97 (99)
T PF13742_consen 42 YFTLKDEEASISCVIFRSRARRIRGFD------LK--D--------------GDK--VLVRGRVSFYEPRGSLSLIVEDI 97 (99)
T ss_pred EEEEEcCCcEEEEEEEHHHHhhCCCCC------CC--C--------------CCE--EEEEEEEEEECCCcEEEEEEEEe
Confidence 467888889999999998876654221 22 2 223 44555556777777889999888
Q ss_pred ee
Q 003281 643 ER 644 (834)
Q Consensus 643 ~~ 644 (834)
+|
T Consensus 98 ~P 99 (99)
T PF13742_consen 98 DP 99 (99)
T ss_pred EC
Confidence 76
No 268
>PRK14282 chaperone protein DnaJ; Provisional
Probab=20.46 E-value=84 Score=35.57 Aligned_cols=40 Identities=25% Similarity=0.375 Sum_probs=21.8
Q ss_pred CcCcccCCCCccCCCCCCCC----CCCCCcCCCCCC----cccccCCC
Q 003281 786 SECYKCHKTGHWARDCPSLN----AAPPAYGSSGIG----ISAAGYRG 825 (834)
Q Consensus 786 ~~Cy~Cg~~GH~ardCp~~~----~~~~c~~c~~~g----~~~~~cg~ 825 (834)
..|..|+..|.....-.... ....|-.|+|.| ..|..|.|
T Consensus 170 ~~C~~C~G~G~~~~~~~~~~G~~~~~~~C~~C~G~G~~~~~~C~~C~G 217 (369)
T PRK14282 170 VTCPKCHGTGRIREERRSFFGVFVSERTCERCGGTGKIPGEYCHECGG 217 (369)
T ss_pred cCCCCCCCcCEEEEEEEccCcceEEEEECCCCCCcceeCCCCCCCCCC
Confidence 46778877775433221100 011577777776 34777765
No 269
>TIGR02349 DnaJ_bact chaperone protein DnaJ. This model represents bacterial forms of DnaJ, part of the DnaK-DnaJ-GrpE chaperone system. The three components typically are encoded by consecutive genes. DnaJ homologs occur in many genomes, typically not near DnaK and GrpE-like genes; most such genes are not included by this family. Eukaryotic (mitochondrial and chloroplast) forms are not included in the scope of this family.
Probab=20.10 E-value=61 Score=36.40 Aligned_cols=41 Identities=20% Similarity=0.292 Sum_probs=23.7
Q ss_pred CcCcccCCCCccCCCCCCCC----CCCCCcCCCCCC----cccccCCCC
Q 003281 786 SECYKCHKTGHWARDCPSLN----AAPPAYGSSGIG----ISAAGYRGA 826 (834)
Q Consensus 786 ~~Cy~Cg~~GH~ardCp~~~----~~~~c~~c~~~g----~~~~~cg~~ 826 (834)
..|..|+..|+......-.. ....|-.|+|.| +.|..|.|.
T Consensus 161 ~~C~~C~G~G~~~~~~~~~~g~~~~~~~C~~C~G~G~~~~~~C~~C~G~ 209 (354)
T TIGR02349 161 KTCPTCGGTGQVRRQQGTPFGFFQQQQTCPTCGGEGKIIKEPCSTCKGK 209 (354)
T ss_pred ccCCCCCCeeEEEEEEeccCCceEEEEecCCCCCcceecCCCCCCCCCC
Confidence 46888888776554432100 011677777777 347777763
Done!