Query 006263
Match_columns 653
No_of_seqs 264 out of 894
Neff 7.5
Searched_HMMs 46136
Date Thu Mar 28 20:44:21 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/006263.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/006263hhsearch_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 1E-124 2E-129 1061.2 66.1 593 2-649 1-608 (608)
2 PRK12366 replication factor A; 100.0 6.2E-66 1.4E-70 586.4 47.5 356 207-636 278-637 (637)
3 PRK08402 replication factor A; 100.0 2.9E-45 6.2E-50 386.4 30.2 279 327-651 61-353 (355)
4 cd04476 RPA1_DBD_C RPA1_DBD_C: 100.0 8.6E-37 1.9E-41 293.7 20.2 165 477-649 1-166 (166)
5 PF08646 Rep_fac-A_C: Replicat 100.0 7.8E-37 1.7E-41 287.7 15.8 145 493-643 1-146 (146)
6 PRK07218 replication factor A; 100.0 1.5E-33 3.2E-38 303.2 38.0 360 206-647 56-421 (423)
7 PRK12366 replication factor A; 100.0 5.7E-32 1.2E-36 308.5 30.0 282 205-577 60-345 (637)
8 PRK07211 replication factor A; 100.0 9.7E-32 2.1E-36 291.3 29.2 274 207-572 52-328 (485)
9 PRK06386 replication factor A; 100.0 1.1E-29 2.3E-34 266.7 37.9 350 209-647 3-353 (358)
10 PRK07211 replication factor A; 100.0 1.6E-31 3.5E-36 289.5 22.7 209 207-441 160-371 (485)
11 PRK15491 replication factor A; 100.0 2.5E-29 5.3E-34 269.0 29.4 277 206-573 55-336 (374)
12 PRK15491 replication factor A; 100.0 2.8E-27 6.2E-32 253.2 30.1 205 208-434 166-373 (374)
13 PRK14699 replication factor A; 100.0 3.9E-28 8.5E-33 266.5 20.9 206 207-434 275-483 (484)
14 cd04474 RPA1_DBD_A RPA1_DBD_A: 100.0 1.4E-28 3.1E-33 217.6 12.2 104 210-313 1-104 (104)
15 PRK14699 replication factor A; 99.9 1.5E-23 3.2E-28 230.4 36.5 277 209-574 167-447 (484)
16 PF04057 Rep-A_N: Replication 99.9 8.2E-26 1.8E-30 197.8 11.3 95 5-99 1-101 (101)
17 cd04477 RPA1N RPA1N: A subfami 99.9 2.9E-24 6.4E-29 186.1 8.9 91 8-98 1-97 (97)
18 cd04475 RPA1_DBD_B RPA1_DBD_B: 99.9 7.3E-22 1.6E-26 174.1 12.8 100 342-449 1-101 (101)
19 cd04481 RPA1_DBD_B_like RPA1_D 99.8 4.9E-20 1.1E-24 163.9 12.3 101 344-447 1-104 (106)
20 cd04480 RPA1_DBD_A_like RPA1_D 99.8 5.8E-19 1.3E-23 150.8 9.6 86 222-311 1-86 (86)
21 PF02721 DUF223: Domain of unk 99.7 1.8E-16 3.9E-21 138.0 10.3 87 247-336 1-87 (95)
22 PRK08402 replication factor A; 99.6 4.6E-14 9.9E-19 149.8 18.7 177 207-393 61-270 (355)
23 PRK07217 replication factor A; 99.6 4.1E-13 8.9E-18 137.6 22.3 222 328-634 72-295 (311)
24 KOG0851 Single-stranded DNA-bi 99.3 7.9E-11 1.7E-15 120.3 14.9 213 207-453 3-219 (246)
25 COG1599 RFA1 Single-stranded D 99.3 4.5E-11 9.7E-16 131.1 13.3 245 204-506 158-404 (407)
26 cd04497 hPOT1_OB1_like hPOT1_O 99.1 4.3E-10 9.4E-15 104.7 11.0 88 326-425 1-91 (138)
27 PRK07218 replication factor A; 99.1 3.7E-09 8E-14 114.9 18.1 169 208-393 162-349 (423)
28 PRK06386 replication factor A; 99.1 8E-09 1.7E-13 109.6 19.0 163 207-392 106-287 (358)
29 cd04491 SoSSB_OBF SoSSB_OBF: A 98.9 1.5E-08 3.3E-13 85.6 9.8 81 222-313 1-81 (82)
30 cd04491 SoSSB_OBF SoSSB_OBF: A 98.9 2.8E-08 6E-13 84.0 11.2 80 344-434 1-81 (82)
31 PRK06461 single-stranded DNA-b 98.8 3.7E-08 8E-13 90.6 10.6 95 328-436 4-99 (129)
32 PRK06461 single-stranded DNA-b 98.8 6E-08 1.3E-12 89.2 11.0 97 207-315 3-99 (129)
33 PRK07217 replication factor A; 98.3 2.7E-05 5.8E-10 80.7 17.0 93 206-315 70-162 (311)
34 COG1599 RFA1 Single-stranded D 98.2 3.2E-05 6.8E-10 85.2 16.4 188 204-422 45-234 (407)
35 TIGR00617 rpa1 replication fac 98.0 0.00068 1.5E-08 78.1 23.4 177 327-574 179-364 (608)
36 cd04474 RPA1_DBD_A RPA1_DBD_A: 97.8 0.00012 2.6E-09 64.8 9.8 97 331-436 2-98 (104)
37 PF01336 tRNA_anti-codon: OB-f 97.8 6E-05 1.3E-09 61.8 7.0 70 221-306 1-70 (75)
38 PF02765 POT1: Telomeric singl 97.7 0.00046 1E-08 65.0 11.5 86 328-422 1-93 (146)
39 cd04475 RPA1_DBD_B RPA1_DBD_B: 97.3 0.0019 4E-08 56.7 9.2 84 222-315 3-88 (101)
40 cd03524 RPA2_OBF_family RPA2_O 96.7 0.0076 1.6E-07 48.2 7.9 60 223-289 2-61 (75)
41 KOG3416 Predicted nucleic acid 96.2 0.011 2.4E-07 52.7 5.9 70 208-286 4-74 (134)
42 KOG3416 Predicted nucleic acid 96.1 0.027 5.9E-07 50.3 7.9 83 330-429 6-89 (134)
43 PF06075 DUF936: Plant protein 96.0 0.014 3E-07 66.4 7.0 105 5-113 1-118 (579)
44 cd04483 hOBFC1_like hOBFC1_lik 95.1 0.086 1.9E-06 45.5 7.2 68 344-425 1-85 (92)
45 cd04481 RPA1_DBD_B_like RPA1_D 95.1 0.28 6E-06 43.4 10.6 68 224-291 3-75 (106)
46 cd04497 hPOT1_OB1_like hPOT1_O 95.0 0.11 2.3E-06 48.4 8.3 83 207-293 2-88 (138)
47 cd03524 RPA2_OBF_family RPA2_O 95.0 0.15 3.2E-06 40.6 8.1 65 344-422 1-65 (75)
48 PF15489 CTC1: CST, telomere m 95.0 5.3 0.00012 48.6 23.7 314 218-585 704-1050(1144)
49 PF01336 tRNA_anti-codon: OB-f 94.9 0.096 2.1E-06 42.5 6.8 63 343-422 1-63 (75)
50 cd04488 RecG_wedge_OBF RecG_we 94.6 0.19 4.1E-06 40.5 7.9 60 222-289 1-60 (75)
51 cd04485 DnaE_OBF DnaE_OBF: A s 94.6 0.16 3.5E-06 41.8 7.6 43 244-288 19-61 (84)
52 PF09103 BRCA-2_OB1: BRCA2, ol 94.3 0.085 1.8E-06 47.7 5.5 67 9-75 2-71 (118)
53 cd04490 PolII_SU_OBF PolII_SU_ 94.3 0.19 4.1E-06 42.1 7.2 54 344-413 3-58 (79)
54 PTZ00401 aspartyl-tRNA synthet 92.8 0.96 2.1E-05 51.7 11.9 99 206-314 63-169 (550)
55 cd04490 PolII_SU_OBF PolII_SU_ 92.5 0.56 1.2E-05 39.2 7.1 55 222-285 3-59 (79)
56 cd04489 ExoVII_LU_OBF ExoVII_L 92.1 0.51 1.1E-05 38.8 6.5 54 222-284 3-56 (78)
57 cd04485 DnaE_OBF DnaE_OBF: A s 91.5 1.4 3E-05 36.1 8.6 64 345-421 2-65 (84)
58 KOG0851 Single-stranded DNA-bi 91.4 1 2.3E-05 45.6 9.4 68 507-584 159-226 (246)
59 PF11325 DUF3127: Domain of un 91.2 1.3 2.8E-05 37.5 7.9 71 345-424 2-75 (84)
60 cd04320 AspRS_cyto_N AspRS_cyt 91.1 4.1 9E-05 35.5 11.6 83 221-314 2-92 (102)
61 PF14951 DUF4503: Domain of un 90.6 0.61 1.3E-05 49.2 6.6 82 493-580 256-345 (389)
62 cd04322 LysRS_N LysRS_N: N-ter 90.6 3.3 7.2E-05 36.5 10.6 76 222-314 3-83 (108)
63 cd04492 YhaM_OBF_like YhaM_OBF 90.0 1.1 2.4E-05 36.9 6.7 43 244-289 19-61 (83)
64 PLN02850 aspartate-tRNA ligase 90.0 2.6 5.6E-05 48.2 11.6 98 206-314 67-172 (530)
65 PF15072 DUF4539: Domain of un 89.8 1.5 3.2E-05 37.4 7.2 60 246-312 21-80 (86)
66 cd04478 RPA2_DBD_D RPA2_DBD_D: 89.6 1.5 3.2E-05 37.6 7.3 68 343-425 2-70 (95)
67 PF10341 TPP1: Shelterin compl 89.0 1.4 3E-05 39.0 6.8 60 23-83 28-93 (106)
68 cd04323 AsnRS_cyto_like_N AsnR 88.7 3.8 8.3E-05 34.3 9.1 74 222-307 3-78 (84)
69 cd04100 Asp_Lys_Asn_RS_N Asp_L 88.4 3.7 8E-05 34.5 8.8 74 222-307 3-79 (85)
70 PRK07373 DNA polymerase III su 87.6 1.8 3.9E-05 48.4 8.1 71 209-284 269-341 (449)
71 PRK02801 primosomal replicatio 87.4 2.9 6.3E-05 36.7 7.7 68 218-288 2-80 (101)
72 COG5235 RFA2 Single-stranded D 87.2 2.2 4.7E-05 41.8 7.3 53 369-428 85-139 (258)
73 cd04495 BRCA2DBD_OB3 BRCA2DBD_ 87.1 4.4 9.5E-05 35.2 8.3 81 344-437 1-84 (100)
74 PRK13480 3'-5' exoribonuclease 86.3 2.2 4.7E-05 45.4 7.5 70 210-286 4-73 (314)
75 cd04316 ND_PkAspRS_like_N ND_P 86.3 12 0.00027 32.9 11.3 81 219-314 13-97 (108)
76 PRK05733 single-stranded DNA-b 85.9 3 6.6E-05 40.3 7.6 65 217-284 4-81 (172)
77 PRK06751 single-stranded DNA-b 85.7 2.8 6.1E-05 40.6 7.3 64 218-284 2-75 (173)
78 PRK07459 single-stranded DNA-b 85.0 3.6 7.8E-05 37.4 7.3 64 218-284 3-72 (121)
79 PF09104 BRCA-2_OB3: BRCA2, ol 84.9 4.7 0.0001 37.5 7.9 107 329-449 4-120 (143)
80 PRK13732 single-stranded DNA-b 84.7 3.9 8.5E-05 39.6 7.7 65 217-284 5-82 (175)
81 cd04489 ExoVII_LU_OBF ExoVII_L 84.6 2.8 6.1E-05 34.3 5.9 39 345-393 4-42 (78)
82 PRK08763 single-stranded DNA-b 84.1 4.4 9.5E-05 38.9 7.7 64 218-284 5-80 (164)
83 PRK05159 aspC aspartyl-tRNA sy 84.0 6.6 0.00014 43.8 10.4 92 209-315 5-101 (437)
84 cd04478 RPA2_DBD_D RPA2_DBD_D: 83.8 2 4.3E-05 36.8 4.9 53 222-284 3-58 (95)
85 PF02721 DUF223: Domain of unk 83.5 4.6 9.9E-05 34.8 7.0 47 370-422 1-47 (95)
86 PLN02502 lysyl-tRNA synthetase 83.0 6.5 0.00014 45.1 9.9 79 219-314 109-194 (553)
87 cd04484 polC_OBF polC_OBF: A s 82.9 6.2 0.00013 33.1 7.4 59 221-285 2-62 (82)
88 PRK07275 single-stranded DNA-b 82.8 3.7 8.1E-05 39.3 6.7 64 218-284 2-75 (162)
89 cd04496 SSB_OBF SSB_OBF: A sub 82.8 5.1 0.00011 34.3 7.1 62 222-286 2-74 (100)
90 PRK05813 single-stranded DNA-b 82.8 56 0.0012 32.9 16.2 162 218-420 8-183 (219)
91 cd04492 YhaM_OBF_like YhaM_OBF 82.6 5.5 0.00012 32.7 7.0 63 345-421 2-64 (83)
92 PF02765 POT1: Telomeric singl 82.3 5.9 0.00013 37.1 7.8 84 209-293 2-93 (146)
93 PRK09010 single-stranded DNA-b 82.2 10 0.00023 36.8 9.6 64 218-284 6-82 (177)
94 cd04317 EcAspRS_like_N EcAspRS 81.8 12 0.00025 34.5 9.5 86 219-314 15-104 (135)
95 PRK07772 single-stranded DNA-b 81.2 8.3 0.00018 37.8 8.5 64 218-284 4-81 (186)
96 PRK06293 single-stranded DNA-b 81.1 5.6 0.00012 38.0 7.2 64 218-284 1-71 (161)
97 cd04480 RPA1_DBD_A_like RPA1_D 81.1 5.9 0.00013 33.3 6.7 52 365-422 17-68 (86)
98 cd04493 BRCA2DBD_OB1 BRCA2DBD_ 81.0 3.6 7.7E-05 36.0 5.3 39 37-75 21-59 (100)
99 PRK13480 3'-5' exoribonuclease 80.6 8.2 0.00018 41.1 9.0 75 334-422 5-79 (314)
100 PTZ00417 lysine-tRNA ligase; P 80.1 10 0.00022 43.8 10.1 78 220-314 134-219 (585)
101 PRK08486 single-stranded DNA-b 80.0 6.6 0.00014 38.3 7.4 63 219-284 3-77 (182)
102 cd04318 EcAsnRS_like_N EcAsnRS 79.9 15 0.00032 30.5 8.7 72 222-307 3-76 (82)
103 PRK08182 single-stranded DNA-b 78.9 6.6 0.00014 37.0 6.9 65 218-284 2-82 (148)
104 PRK07373 DNA polymerase III su 78.8 6.8 0.00015 43.8 8.1 78 327-417 267-344 (449)
105 TIGR00499 lysS_bact lysyl-tRNA 78.5 15 0.00032 41.8 10.7 79 219-314 54-137 (496)
106 cd04319 PhAsnRS_like_N PhAsnRS 78.0 26 0.00057 30.5 10.1 79 221-314 2-83 (103)
107 PRK06863 single-stranded DNA-b 77.7 8.5 0.00018 37.1 7.3 64 218-284 4-80 (168)
108 PRK00484 lysS lysyl-tRNA synth 77.7 18 0.00039 41.0 11.1 78 219-314 55-137 (491)
109 PRK07274 single-stranded DNA-b 77.2 7.5 0.00016 35.8 6.6 64 218-284 2-75 (131)
110 PRK12445 lysyl-tRNA synthetase 76.8 17 0.00036 41.4 10.5 78 220-314 67-149 (505)
111 PRK06752 single-stranded DNA-b 76.7 8.5 0.00018 34.3 6.6 64 218-284 2-75 (112)
112 PF00436 SSB: Single-strand bi 76.6 3.7 7.9E-05 35.6 4.2 64 219-285 2-77 (104)
113 KOG4757 Predicted telomere bin 75.7 8.1 0.00017 42.0 7.0 86 326-422 7-94 (522)
114 TIGR00621 ssb single stranded 74.5 13 0.00027 35.7 7.6 65 218-285 4-80 (164)
115 KOG3056 Protein required for S 74.5 20 0.00044 40.4 10.0 103 206-314 166-275 (578)
116 PTZ00385 lysyl-tRNA synthetase 74.2 28 0.0006 40.8 11.5 77 220-313 109-191 (659)
117 PRK05673 dnaE DNA polymerase I 74.1 8.7 0.00019 47.9 7.9 82 327-421 964-1045(1135)
118 PRK06958 single-stranded DNA-b 72.8 14 0.00031 36.0 7.5 64 218-284 4-80 (182)
119 PRK06642 single-stranded DNA-b 72.5 13 0.00028 35.2 7.0 64 218-284 5-82 (152)
120 KOG0556 Aspartyl-tRNA syntheta 72.4 42 0.00091 36.6 11.3 101 204-314 66-175 (533)
121 PRK07135 dnaE DNA polymerase I 71.3 13 0.00028 45.4 8.4 74 209-291 889-962 (973)
122 PF13742 tRNA_anti_2: OB-fold 70.8 26 0.00056 30.5 8.1 65 219-292 22-88 (99)
123 TIGR00458 aspS_arch aspartyl-t 70.7 34 0.00073 38.1 10.9 81 219-314 13-97 (428)
124 PRK02983 lysS lysyl-tRNA synth 70.7 21 0.00046 44.5 10.1 78 220-314 653-735 (1094)
125 PRK07374 dnaE DNA polymerase I 70.6 12 0.00026 46.7 8.1 71 209-284 989-1061(1170)
126 cd04483 hOBFC1_like hOBFC1_lik 70.5 8.4 0.00018 33.1 4.9 52 223-284 2-73 (92)
127 PF13240 zinc_ribbon_2: zinc-r 70.1 2 4.3E-05 27.1 0.6 19 521-541 4-22 (23)
128 PRK05673 dnaE DNA polymerase I 69.7 13 0.00028 46.4 8.1 71 209-284 966-1038(1135)
129 PRK07279 dnaE DNA polymerase I 69.5 12 0.00027 45.9 7.7 72 208-284 875-946 (1034)
130 cd04498 hPOT1_OB2 hPOT1_OB2: A 68.4 18 0.00038 33.0 6.6 35 379-420 60-94 (123)
131 KOG3056 Protein required for S 68.1 19 0.00042 40.6 8.1 76 343-429 188-269 (578)
132 COG1997 RPL43A Ribosomal prote 67.7 3.6 7.9E-05 34.7 1.9 27 512-544 37-65 (89)
133 cd04482 RPA2_OBF_like RPA2_OBF 66.1 13 0.00029 31.8 5.2 39 246-285 19-59 (91)
134 TIGR00643 recG ATP-dependent D 65.6 16 0.00036 42.7 7.5 70 207-284 22-91 (630)
135 PF07754 DUF1610: Domain of un 64.5 4.8 0.00011 25.6 1.6 20 521-540 3-24 (24)
136 PRK02801 primosomal replicatio 64.4 30 0.00064 30.3 7.2 67 342-416 4-79 (101)
137 PRK06920 dnaE DNA polymerase I 63.1 22 0.00047 44.3 8.1 71 209-284 933-1004(1107)
138 COG0629 Ssb Single-stranded DN 62.6 25 0.00054 33.7 7.0 69 218-286 3-81 (167)
139 TIGR00457 asnS asparaginyl-tRN 62.3 57 0.0012 36.7 10.7 81 219-314 17-102 (453)
140 PRK10917 ATP-dependent DNA hel 62.3 19 0.00041 42.6 7.3 69 207-284 49-118 (681)
141 TIGR00459 aspS_bact aspartyl-t 61.0 74 0.0016 36.9 11.4 86 219-314 16-104 (583)
142 TIGR00621 ssb single stranded 60.6 48 0.001 31.7 8.5 72 342-421 6-88 (164)
143 COG0017 AsnS Aspartyl/asparagi 60.6 73 0.0016 35.4 10.8 91 209-314 5-100 (435)
144 cd04321 ScAspRS_mt_like_N ScAs 59.9 1E+02 0.0022 25.8 10.3 76 221-306 2-79 (86)
145 PRK07374 dnaE DNA polymerase I 59.6 27 0.00059 43.8 8.1 78 327-417 987-1064(1170)
146 PF02760 HIN: HIN-200/IF120x d 59.5 1.6E+02 0.0036 28.0 15.6 144 223-392 5-154 (170)
147 PRK06751 single-stranded DNA-b 57.7 57 0.0012 31.6 8.4 36 379-420 47-83 (173)
148 PRK05813 single-stranded DNA-b 57.3 48 0.001 33.4 8.1 63 218-284 109-175 (219)
149 PF07191 zinc-ribbons_6: zinc- 56.2 7.4 0.00016 31.6 1.7 24 512-541 3-26 (70)
150 cd04487 RecJ_OBF2_like RecJ_OB 55.6 15 0.00033 30.1 3.5 39 246-285 17-55 (73)
151 PRK07459 single-stranded DNA-b 55.0 82 0.0018 28.5 8.6 69 342-420 5-80 (121)
152 PRK03932 asnC asparaginyl-tRNA 55.0 96 0.0021 34.8 10.9 81 219-314 17-100 (450)
153 PRK08486 single-stranded DNA-b 54.5 69 0.0015 31.3 8.5 35 380-420 50-85 (182)
154 PRK10220 hypothetical protein; 54.2 8 0.00017 34.1 1.7 29 509-543 2-31 (111)
155 COG1571 Predicted DNA-binding 54.2 6.1 0.00013 43.3 1.2 29 511-545 351-380 (421)
156 PRK09010 single-stranded DNA-b 53.5 85 0.0018 30.5 8.8 37 380-422 55-92 (177)
157 PRK08763 single-stranded DNA-b 51.7 1E+02 0.0022 29.6 9.0 35 380-420 53-88 (164)
158 PRK06341 single-stranded DNA-b 51.7 57 0.0012 31.4 7.3 64 218-284 5-82 (166)
159 PRK12820 bifunctional aspartyl 50.9 1.3E+02 0.0028 35.8 11.3 85 220-314 20-110 (706)
160 PRK06826 dnaE DNA polymerase I 50.9 54 0.0012 41.2 8.8 60 220-284 993-1052(1151)
161 PRK11827 hypothetical protein; 50.7 11 0.00024 29.7 1.9 27 511-543 9-37 (60)
162 PRK05672 dnaE2 error-prone DNA 50.6 40 0.00087 41.9 7.5 59 221-287 956-1014(1046)
163 PRK06826 dnaE DNA polymerase I 50.6 44 0.00096 41.9 7.9 78 327-417 969-1055(1151)
164 cd04484 polC_OBF polC_OBF: A s 50.4 1.4E+02 0.003 24.9 8.6 55 548-624 20-74 (82)
165 PF13248 zf-ribbon_3: zinc-rib 49.0 7.7 0.00017 25.0 0.6 22 512-541 4-25 (26)
166 PRK00476 aspS aspartyl-tRNA sy 49.0 1.2E+02 0.0027 35.2 10.8 84 220-314 19-106 (588)
167 PLN02903 aminoacyl-tRNA ligase 48.9 1.2E+02 0.0027 35.6 10.7 86 219-314 73-163 (652)
168 PF01780 Ribosomal_L37ae: Ribo 48.8 8.2 0.00018 33.0 0.9 26 512-543 37-64 (90)
169 PRK05733 single-stranded DNA-b 48.6 66 0.0014 31.1 7.2 71 342-420 7-89 (172)
170 PF15489 CTC1: CST, telomere m 48.1 1.1E+02 0.0024 37.9 10.3 67 219-290 166-232 (1144)
171 cd04496 SSB_OBF SSB_OBF: A sub 47.9 64 0.0014 27.3 6.5 69 344-420 2-80 (100)
172 PRK05853 hypothetical protein; 47.6 44 0.00095 32.0 5.8 33 252-284 39-71 (161)
173 PRK06863 single-stranded DNA-b 46.9 1.2E+02 0.0025 29.3 8.6 72 342-421 6-89 (168)
174 PRK06920 dnaE DNA polymerase I 46.9 57 0.0012 40.8 8.0 78 326-417 930-1007(1107)
175 COG1200 RecG RecG-like helicas 46.5 63 0.0014 37.7 7.7 72 205-284 48-119 (677)
176 KOG1885 Lysyl-tRNA synthetase 45.8 94 0.002 34.6 8.5 92 220-330 106-203 (560)
177 PRK06958 single-stranded DNA-b 45.5 1.3E+02 0.0028 29.4 8.7 71 342-420 6-88 (182)
178 PRK05672 dnaE2 error-prone DNA 44.8 59 0.0013 40.5 7.7 73 327-413 940-1012(1046)
179 PF00436 SSB: Single-strand bi 44.3 2E+02 0.0043 24.4 9.4 70 343-420 4-84 (104)
180 COG5189 SFP1 Putative transcri 43.6 11 0.00024 39.3 1.1 13 532-544 398-410 (423)
181 cd04100 Asp_Lys_Asn_RS_N Asp_L 43.5 84 0.0018 26.1 6.4 61 38-98 17-84 (85)
182 COG2888 Predicted Zn-ribbon RN 43.3 10 0.00023 29.6 0.7 27 507-539 24-57 (61)
183 PF08646 Rep_fac-A_C: Replicat 43.2 30 0.00065 32.2 3.9 27 245-272 55-81 (146)
184 cd04494 BRCA2DBD_OB2 BRCA2DBD_ 42.7 79 0.0017 32.5 7.0 58 255-315 179-236 (251)
185 TIGR00686 phnA alkylphosphonat 42.7 16 0.00034 32.3 1.7 29 510-544 2-31 (109)
186 PF03089 RAG2: Recombination a 42.1 29 0.00063 36.1 3.8 47 521-572 66-112 (337)
187 PRK14810 formamidopyrimidine-D 41.6 15 0.00032 38.3 1.8 24 511-540 245-272 (272)
188 COG1190 LysU Lysyl-tRNA synthe 41.5 81 0.0018 35.5 7.4 78 220-314 63-145 (502)
189 cd04318 EcAsnRS_like_N EcAsnRS 41.5 92 0.002 25.7 6.3 60 38-97 17-80 (82)
190 PRK08182 single-stranded DNA-b 41.3 1.5E+02 0.0032 27.9 8.2 35 380-420 55-90 (148)
191 PRK13945 formamidopyrimidine-D 41.0 17 0.00036 38.1 2.0 24 511-540 255-282 (282)
192 PF14446 Prok-RING_1: Prokaryo 40.7 18 0.00039 27.9 1.6 31 511-547 6-36 (54)
193 PF10571 UPF0547: Uncharacteri 40.4 16 0.00035 23.7 1.1 23 512-542 2-24 (26)
194 PRK06266 transcription initiat 40.3 12 0.00027 36.3 0.8 26 511-542 118-146 (178)
195 PRK00398 rpoP DNA-directed RNA 40.3 23 0.00049 26.1 2.1 24 512-541 5-30 (46)
196 PF03119 DNA_ligase_ZBD: NAD-d 40.2 18 0.00038 23.9 1.3 19 513-537 2-22 (28)
197 PRK07275 single-stranded DNA-b 40.1 1.3E+02 0.0029 28.7 7.8 35 380-420 48-83 (162)
198 PRK00432 30S ribosomal protein 39.6 18 0.00038 27.5 1.4 26 510-541 20-46 (50)
199 PRK00448 polC DNA polymerase I 39.4 65 0.0014 41.4 7.1 74 207-285 225-300 (1437)
200 PF09538 FYDLN_acid: Protein o 39.4 16 0.00035 32.5 1.3 27 511-543 10-37 (108)
201 TIGR00373 conserved hypothetic 39.0 12 0.00027 35.5 0.6 24 512-541 111-137 (158)
202 TIGR02300 FYDLN_acid conserved 38.7 17 0.00037 33.1 1.4 27 511-543 10-37 (129)
203 PRK07274 single-stranded DNA-b 37.8 1.8E+02 0.0039 26.6 8.1 34 380-419 48-82 (131)
204 PLN02603 asparaginyl-tRNA synt 37.0 2.9E+02 0.0062 32.0 11.2 91 209-314 90-193 (565)
205 PF09862 DUF2089: Protein of u 36.8 22 0.00047 31.9 1.8 28 513-551 1-28 (113)
206 cd03574 NTR_complement_C345C N 36.6 2.7E+02 0.0058 25.9 9.3 87 220-316 24-119 (147)
207 COG1096 Predicted RNA-binding 36.4 54 0.0012 32.0 4.5 29 507-541 146-174 (188)
208 COG2835 Uncharacterized conser 35.4 24 0.00053 27.7 1.6 28 510-543 8-37 (60)
209 COG1379 PHP family phosphoeste 34.7 11 0.00023 39.8 -0.6 30 507-542 243-275 (403)
210 PRK14811 formamidopyrimidine-D 34.7 22 0.00048 36.9 1.8 25 511-541 236-264 (269)
211 cd04322 LysRS_N LysRS_N: N-ter 34.6 99 0.0022 27.0 5.7 61 38-98 17-81 (108)
212 cd04498 hPOT1_OB2 hPOT1_OB2: A 34.4 83 0.0018 28.7 5.1 38 257-295 61-98 (123)
213 PRK03976 rpl37ae 50S ribosomal 34.4 23 0.0005 30.3 1.4 28 512-545 38-67 (90)
214 COG0587 DnaE DNA polymerase II 34.1 1.3E+02 0.0029 37.7 8.3 71 209-284 967-1038(1139)
215 KOG2593 Transcription initiati 33.9 21 0.00045 39.1 1.4 25 512-542 130-163 (436)
216 PRK07772 single-stranded DNA-b 33.5 1.7E+02 0.0037 28.7 7.5 36 380-421 54-90 (186)
217 TIGR00280 L37a ribosomal prote 33.4 23 0.00051 30.3 1.3 30 512-547 37-68 (91)
218 PF14353 CpXC: CpXC protein 32.9 57 0.0012 29.6 4.0 33 532-569 38-70 (128)
219 PRK13732 single-stranded DNA-b 32.9 1.5E+02 0.0033 28.7 7.0 35 380-420 55-90 (175)
220 PTZ00255 60S ribosomal protein 32.7 25 0.00055 30.1 1.4 31 512-548 38-70 (90)
221 PRK10445 endonuclease VIII; Pr 32.3 25 0.00053 36.5 1.6 24 511-540 236-263 (263)
222 TIGR00237 xseA exodeoxyribonuc 32.1 88 0.0019 34.9 6.0 63 220-291 19-82 (432)
223 PRK01103 formamidopyrimidine/5 32.0 24 0.00053 36.7 1.5 24 511-540 246-273 (274)
224 cd04476 RPA1_DBD_C RPA1_DBD_C: 31.4 62 0.0013 30.8 4.1 26 245-271 69-94 (166)
225 PF03107 C1_2: C1 domain; Int 31.1 30 0.00065 23.1 1.3 18 521-539 5-22 (30)
226 PF13742 tRNA_anti_2: OB-fold 30.9 1.3E+02 0.0028 26.1 5.7 42 341-392 22-63 (99)
227 PRK00286 xseA exodeoxyribonucl 30.9 93 0.002 34.7 6.0 44 245-289 42-86 (438)
228 TIGR02098 MJ0042_CXXC MJ0042 f 30.6 33 0.00071 24.0 1.5 26 511-542 3-35 (38)
229 PF12773 DZR: Double zinc ribb 30.5 21 0.00045 26.7 0.5 28 521-549 17-45 (50)
230 PF01599 Ribosomal_S27: Riboso 30.4 49 0.0011 24.8 2.4 25 512-540 20-46 (47)
231 PLN02221 asparaginyl-tRNA synt 29.4 4.3E+02 0.0093 30.7 11.0 84 219-314 51-137 (572)
232 PF13842 Tnp_zf-ribbon_2: DDE_ 29.3 31 0.00067 23.6 1.1 20 521-540 5-24 (32)
233 PF10451 Stn1: Telomere regula 29.2 1.6E+02 0.0035 30.4 6.8 66 341-416 67-133 (256)
234 COG1675 TFA1 Transcription ini 29.1 18 0.0004 35.0 0.0 27 510-542 113-142 (176)
235 PF07282 OrfB_Zn_ribbon: Putat 28.5 35 0.00075 27.3 1.5 28 509-542 27-56 (69)
236 KOG4751 DNA recombinational re 28.4 45 0.00098 38.1 2.8 67 8-75 622-701 (756)
237 PRK06293 single-stranded DNA-b 28.2 4.1E+02 0.0089 25.4 8.9 68 343-420 4-79 (161)
238 COG1998 RPS31 Ribosomal protei 28.1 32 0.00069 26.0 1.1 25 511-541 20-46 (51)
239 PRK06752 single-stranded DNA-b 28.1 1E+02 0.0023 27.3 4.7 35 380-420 48-83 (112)
240 TIGR01384 TFS_arch transcripti 28.1 59 0.0013 28.3 3.1 25 512-542 2-26 (104)
241 PHA00626 hypothetical protein 28.0 40 0.00086 26.2 1.6 25 512-542 2-33 (59)
242 COG1570 XseA Exonuclease VII, 27.8 1.1E+02 0.0024 34.0 5.7 68 230-307 29-97 (440)
243 COG1996 RPC10 DNA-directed RNA 27.7 31 0.00067 26.1 1.0 23 512-540 8-32 (49)
244 smart00531 TFIIE Transcription 27.6 26 0.00055 32.9 0.7 25 512-542 101-133 (147)
245 cd04488 RecG_wedge_OBF RecG_we 27.5 74 0.0016 24.9 3.4 21 549-569 18-38 (75)
246 PRK07279 dnaE DNA polymerase I 27.1 1.8E+02 0.0039 36.2 7.8 74 328-417 875-949 (1034)
247 cd04320 AspRS_cyto_N AspRS_cyt 27.1 2E+02 0.0044 24.7 6.3 62 38-99 18-91 (102)
248 COG3877 Uncharacterized protei 26.7 45 0.00098 29.3 1.9 31 511-552 7-37 (122)
249 smart00661 RPOL9 RNA polymeras 26.0 77 0.0017 23.6 3.0 25 512-542 2-30 (52)
250 PRK06556 vitamin B12-dependent 25.9 40 0.00087 41.2 2.1 28 509-542 923-950 (953)
251 PF14205 Cys_rich_KTR: Cystein 25.6 72 0.0016 24.6 2.6 26 511-542 5-38 (55)
252 KOG0402 60S ribosomal protein 25.4 39 0.00085 28.3 1.3 30 512-547 38-69 (92)
253 COG1594 RPB9 DNA-directed RNA 25.2 1.2E+02 0.0025 27.3 4.4 49 512-566 4-59 (113)
254 PF08274 PhnA_Zn_Ribbon: PhnA 24.6 36 0.00078 23.0 0.8 26 510-541 2-28 (30)
255 PF09855 DUF2082: Nucleic-acid 24.6 78 0.0017 25.4 2.8 30 533-570 1-30 (64)
256 PF01927 Mut7-C: Mut7-C RNAse 24.6 43 0.00094 31.3 1.6 11 532-542 124-134 (147)
257 cd01759 PLAT_PL PLAT/LH2 domai 24.4 84 0.0018 28.2 3.4 26 547-572 1-29 (113)
258 COG1107 Archaea-specific RecJ- 23.9 69 0.0015 36.6 3.2 69 206-284 200-269 (715)
259 PF00096 zf-C2H2: Zinc finger, 23.9 37 0.00079 20.6 0.7 12 533-544 1-12 (23)
260 PF13717 zinc_ribbon_4: zinc-r 23.3 55 0.0012 22.9 1.5 26 511-542 3-35 (36)
261 cd04321 ScAspRS_mt_like_N ScAs 23.2 3E+02 0.0066 22.9 6.5 58 40-98 20-85 (86)
262 TIGR00577 fpg formamidopyrimid 23.0 43 0.00092 34.9 1.4 23 511-539 246-272 (272)
263 smart00659 RPOLCX RNA polymera 22.9 64 0.0014 23.8 1.9 22 521-542 7-29 (44)
264 KOG3108 Single-stranded DNA-bi 22.6 2.8E+02 0.006 28.9 7.1 40 342-392 70-109 (265)
265 PF11325 DUF3127: Domain of un 22.2 3.5E+02 0.0076 22.9 6.4 59 223-283 2-62 (84)
266 PF13695 zf-3CxxC: Zinc-bindin 21.9 1.7E+02 0.0036 25.4 4.7 39 532-573 5-43 (98)
267 smart00652 eIF1a eukaryotic tr 21.6 2.3E+02 0.005 23.9 5.3 46 23-76 8-53 (83)
268 PRK06642 single-stranded DNA-b 21.5 5.1E+02 0.011 24.4 8.3 69 342-420 7-90 (152)
269 cd04323 AsnRS_cyto_like_N AsnR 21.5 3.7E+02 0.0079 22.2 6.6 60 39-98 18-83 (84)
270 COG2824 PhnA Uncharacterized Z 21.5 98 0.0021 27.3 3.0 28 510-543 3-31 (112)
271 PRK00036 primosomal replicatio 21.2 4.3E+02 0.0092 23.5 7.0 69 219-291 2-81 (107)
272 PF10122 Mu-like_Com: Mu-like 21.1 42 0.0009 25.6 0.6 24 512-541 6-33 (51)
273 PF09297 zf-NADH-PPase: NADH p 20.9 69 0.0015 21.6 1.6 21 521-541 8-30 (32)
274 cd04456 S1_IF1A_like S1_IF1A_l 20.7 2.5E+02 0.0054 23.4 5.2 38 35-76 11-48 (78)
275 PF14803 Nudix_N_2: Nudix N-te 20.6 72 0.0016 22.2 1.7 20 521-540 5-30 (34)
276 PRK00420 hypothetical protein; 20.5 68 0.0015 28.8 1.9 26 510-541 23-49 (112)
277 COG1656 Uncharacterized conser 20.3 54 0.0012 31.3 1.3 27 510-542 97-140 (165)
278 PRK06341 single-stranded DNA-b 20.3 6.5E+02 0.014 24.2 8.7 72 342-421 7-91 (166)
279 TIGR00375 conserved hypothetic 20.2 52 0.0011 35.9 1.3 40 496-542 225-268 (374)
280 PF08696 Dna2: DNA replication 20.0 3.3E+02 0.0071 27.1 7.0 55 371-438 2-58 (209)
281 PF13453 zf-TFIIB: Transcripti 20.0 62 0.0013 23.2 1.3 21 521-541 4-28 (41)
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=9.9e-125 Score=1061.18 Aligned_cols=593 Identities=42% Similarity=0.743 Sum_probs=507.4
Q ss_pred CCCCCHHHHHHHhC-CCC---CCCCeEEEEEEEEcC--CCCceEEEEEecccceeeeeecccchhhcccCCcccCcEEEE
Q 006263 2 PVNLTPNSISLING-GDV---NSKPLVQVMDIKLIG--STQERYRFLISDSVSTQHAMLATQLNDRVKTGQVKKGSVVQL 75 (653)
Q Consensus 2 ~~~Lt~Gai~~i~~-~~~---~~~pvvQVl~ik~~~--~~~~ryr~~lSDG~~~~~~ml~t~ln~~v~~~~l~~~sIIkl 75 (653)
+.+||+|||.+|+. ++. ...||||||++|++. .+..|||++||||.|+++|||+||||+++++|+|++|+||||
T Consensus 1 ~~~lt~ga~~~i~~~~~~~~~~~~pv~Qv~~~k~~~~~~~~~ryr~~lsDg~~~~~~ml~t~~n~~~~~~~l~~~~iv~l 80 (608)
T TIGR00617 1 AVSLSNGAIALIMTNGEANGYPPDPVLQVLDLKPINGAQDPRRYRIVISDGIYYSKAMLATQLNPLVREGELQEGTIIRL 80 (608)
T ss_pred CCccChhHHHHHhccccccCCCCCcEEEEEeeEEcCCCCCCceEEEEEECchHHHHHHHHHHHHHHHHhCCccCCCEEEE
Confidence 35899999999998 333 368999999999995 245899999999999999999999999999999999999999
Q ss_pred eeeEeeee-c-CeEEEEEEeeeEeecC---CcccCCCcccccccc-ccccCCCCCCCCCCccccccCCCCCCCccccCCC
Q 006263 76 IDYICSTV-Q-NRKIIVVLNMETIILD---CEPIGNPKIFSESEL-TAQKTIPSNNLPQPVRVNNYSAPNSGTFNLQNSG 149 (653)
Q Consensus 76 ~~y~~~~~-~-~k~~iii~~~evl~~~---~~~iG~P~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~n~~~~~~~~~~~ 149 (653)
++|.++.+ + +|++|||+++|||.+. .++||+|++++.... +++.+. ..+.|. .+ + +.
T Consensus 81 ~~~~~~~~~~~~~~~lii~~~ev~~~~~~~~~~ig~p~~~~~~~~~~~~~~~-~~~~~~--~~------~--------~~ 143 (608)
T TIGR00617 81 TKFEVNTIGKDGRKVLIVYELEVVKPELKVRDKIGNPVTYEKYLDSWHEEQV-LASKPA--TN------P--------AN 143 (608)
T ss_pred eEEEEeEEccCCcEEEEEEeeEEeecccccccccCCCccccccccccCcccc-cccccc--cc------C--------CC
Confidence 99999999 5 6899999999999975 357999998875421 111000 000000 00 0 00
Q ss_pred CCCCCCCCCCCCCCCCCcCCCCCCCcccCCCCCCCCCCCCCCCCCCCCCccCCCCCCcceeccccCCCCCceEEEEEEEe
Q 006263 150 TFNSQNPGSFSTPNSGTFRAPNAGSIVRSFQPTVQPPYQPPPNFRNHGPILKNEAPARIIPIAALNPYQGRWAIKARVTA 229 (653)
Q Consensus 150 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~pI~~L~p~~~~w~I~~RV~~ 229 (653)
.+... .| ++. .+++.++++| .+.+.++.......++++||++|+||+++|+|+|||++
T Consensus 144 ~~~~~-~~-------------~~~--~~~~~~~~~~------~~~~~~~~~~~~~~~~~~pI~~L~py~~~wtIkaRV~~ 201 (608)
T TIGR00617 144 PPNAK-AP-------------KNE--VASYNNAANP------ERGNAPPAPNSGSTRRVMPIASLSPYQNKWTIKARVTN 201 (608)
T ss_pred CCCcc-CC-------------Ccc--cccccCCCCc------ccCCCCCCccccCCcceEEHHHCCCCCCceEEEEEEEe
Confidence 00000 00 000 0001001111 11111111111234579999999999999999999999
Q ss_pred eccccccccCCCCceeEEEEEEeCCCCeEEEEEchhHHHHHHhhcccCcEEEEeceEEecCCCcccCCCCceEEEecccc
Q 006263 230 KGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISKGSLKPAQKNFNHLKNEWEIFLEATS 309 (653)
Q Consensus 230 k~~ir~~~~~~g~gk~f~~~L~D~~g~~I~at~f~~~~~kf~~~l~eG~vy~is~~~V~~a~~~f~~~~~~yei~f~~~T 309 (653)
||++|+|++++|+|++|+|+|+| +||+|+||+|++.+++|+++|++|+||+|++|+|++|+++|++++|+|||+|+.+|
T Consensus 202 Ks~ir~~~~~~gegkvfsv~L~D-egg~Irat~f~~~~dkf~~~l~eG~VY~Is~~~Vk~an~~y~~~~~~yei~f~~~T 280 (608)
T TIGR00617 202 KSEIRTWSNARGEGKLFNVELLD-ESGEIRATAFNEQADKFYDIIQEGKVYYISKGSLKPANKQFTNLGNDYEMTLDRDT 280 (608)
T ss_pred ccccceecCCCCCceeeEEEEec-CCCeEEEEECchHHHHHhhhcccCCEEEECceEEEEccccccCCCCCEEEEECCCe
Confidence 99999999999999999999999 99999999999999999999999999999999999999999999999999999999
Q ss_pred EEEeccCCCCCCCcccceecchhhhhhcccCccccEEEEEEEecCceeEEec-CCceeeEEEEEEEeCCCCEEEEEEccc
Q 006263 310 TVDLCTEEDDSIPKQQFSFRHISEIESAENNSIVDVIGIVISVNPSVPILRK-NGMETQRRILNLKDTSGRSVELTLWGD 388 (653)
Q Consensus 310 ~I~~~~d~~~~iP~~~f~f~~i~~i~~~~~~~~vDVIGvV~~v~~~~~i~~k-~g~~~~kr~i~l~D~s~~~i~vtLWg~ 388 (653)
.|++|.| ...||.+.|+|++|+||.+.+.+.+|||||+|++|+++.+|++| +|++..||+|+|+|+||.+|+|||||+
T Consensus 281 ~I~~~~d-~~~iP~~~~~f~~i~dI~~~~~~~~VDVIGvV~~v~~~~~i~~k~~g~~~~kR~i~L~D~sg~sI~vTLWG~ 359 (608)
T TIGR00617 281 VIEECED-ETAIPKIQFNFVKIDDIGGYEGNSLVDVIGIVQSVSPTQTITSRKNNKEFPKRDITLVDDSGKSVRVTLWGD 359 (608)
T ss_pred EEEECCC-cccCCcccccceEHHHhhhhcCCCCccEEEEEeEecCceEEEEcCCCCeeeeEEEEEEeCCCCEEEEEEEhh
Confidence 9999964 44699999999999999998888899999999999999999966 789999999999999999999999999
Q ss_pred hhhhhhhhHHHhhccCCCcEEEEEeeEeecCCCceeccccceEEEEcCChHHHHHHHHHHhcCCCccceeecccccc-cC
Q 006263 389 FCNKEGQKLQEMVDVGFFPVLSVKSGKVNDFSGKSIGTIPSTQLFINPDFAEAHELREWFDSGGKNAATVSISREIA-AG 467 (653)
Q Consensus 389 ~A~~~~~~l~~~~~~~~~~Vvaik~~rV~~f~G~sLs~~~~S~i~inPdipe~~~l~~w~~~~g~~~~~~sls~~~~-~~ 467 (653)
+|..| +...+|||+|+++||++|+|++||++++|+|++|||+||+++|+.||+++|....+.+++...+ ..
T Consensus 360 ~A~~~--------~~~~~~Vva~kg~~V~~f~g~sLs~~~~S~i~iNPdipEa~~L~~w~~~~g~~~~~~s~~~~~~~~~ 431 (608)
T TIGR00617 360 DATKF--------DVSVQPVIAIKGVRVSDFGGKSLSTGGSSTIIVNPDIPEAEKLKGWYDNEGKGTMASSISDMMSGRV 431 (608)
T ss_pred hhhhc--------CCCCCCEEEEEeEEEEecCCceEeccCCceEEECCCcHHHHHHHHHHHhcCCCccceeehhcccccc
Confidence 98764 4457899999999999999999999999999999999999999999999998776666654332 12
Q ss_pred CCCcchhccHHhhhhcCCCCCCCCcEEEEEEEEEEEeCCceEEecCCCCcCcccccceeeecC-ceeecccCccccCCce
Q 006263 468 GAKNEIHKTVSQIKNEGLGRSEKPDWVTVRAFITFIKSDSFCYTACPLMIGDRQCNKKVTQSG-NRWQCDRCNQEIDECD 546 (653)
Q Consensus 468 ~~~~~~~kti~~i~~~~lg~~~~~~~~~v~atI~~i~~d~~~Y~aC~~~~~~~~C~KKv~~~~-~~~~C~kC~~~~~~~~ 546 (653)
++....++||+||+++++|.+++++||+|+|||++|+.|+|||+|||++ .|+|||.+++ +.|+|++|++++++|.
T Consensus 432 ~~~~~~~ktI~ei~~~~lg~~~k~~~f~v~atI~~Ik~d~~~Y~ACp~~----~CnKKV~~~~~g~~~CekC~~~~~~~~ 507 (608)
T TIGR00617 432 GGSNAERKTIAEIQAENLGKSDKPDYFSVKATISYLKPDNALYRACPSE----DCNKKVVDQGDGTYRCEKCNKNFAEFK 507 (608)
T ss_pred CCcccccccHHHHhhhccCCCCCCcEEEEEEEEEEEecCCeEeccCChh----hCCCccccCCCCCEECCCCCCCCCCcc
Confidence 3446789999999999999999999999999999999999999999954 5999998876 4899999999999999
Q ss_pred EEEEEEEEEEeCCCeEEEEEechhhhhhhCCCHHHHHHHhhccCChhHHHHHHHHhcCceEEEEEEEeeeccCceeeEEE
Q 006263 547 YRYLLQAQIQDQTGLTWVTAFQESGEEILGCPAKELYMLKYELQDDVRFGEIIRSRVFNQYLFRLKIKEELYGDEQRVKI 626 (653)
Q Consensus 547 ~rY~l~~~i~D~Tg~~~~~~F~~~ae~llG~sA~el~~~~~e~~d~~~~~~~~~~~~~k~~~f~v~~k~~~y~~e~r~~~ 626 (653)
|||+|++.|+|+||++|+++||+.|++|||++|+||++|+ ++|+++|+++|.++.|++|.|+|++++++||||.|+||
T Consensus 508 ~RYil~~~i~D~Tg~~~~t~F~~~ae~llG~sA~eL~~l~--~~~~~~~~~i~~~~~~~~~~f~~~~k~e~yn~e~r~~~ 585 (608)
T TIGR00617 508 YRYILQISISDETGQLWVTAFNDQAEQILGKSAAELGELK--EEDPDEFEAIFQEAQFVPYIFRLRVKQDTYNDESRQKY 585 (608)
T ss_pred EEEEEEEEEEeCCCCEEEEEEhHHHHHHcCCCHHHHHHHH--hcCHHHHHHHHHHhhCcEEEEEEEEEEcccCCEeeEEE
Confidence 9999999999999999999999999999999999999999 67889999999999999999999999999999999999
Q ss_pred EEEEeecCChHHHHHHHHHHHHh
Q 006263 627 TVIRADQVNYSSESRYLLDLISK 649 (653)
Q Consensus 627 ~v~~~~~vd~~~e~~~ll~~i~~ 649 (653)
+|++++|+||++|+++||++|++
T Consensus 586 ~v~~~~~vd~~~e~~~L~~~i~~ 608 (608)
T TIGR00617 586 TVMSVDPVNYRAEAKYLLQEIEK 608 (608)
T ss_pred EEEEeeeCCHHHHHHHHHHHhcC
Confidence 99999999999999999999974
No 2
>PRK12366 replication factor A; Reviewed
Probab=100.00 E-value=6.2e-66 Score=586.37 Aligned_cols=356 Identities=21% Similarity=0.334 Sum_probs=319.8
Q ss_pred cceeccccCCC-CC-ceEEEEEEEeeccccccccCCCCceeEEEEEEeCCCCeEEEEEchhHHHHHHhhcccCcEEEEec
Q 006263 207 RIIPIAALNPY-QG-RWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISK 284 (653)
Q Consensus 207 ~~~pI~~L~p~-~~-~w~I~~RV~~k~~ir~~~~~~g~gk~f~~~L~D~~g~~I~at~f~~~~~kf~~~l~eG~vy~is~ 284 (653)
.++||++|+|| .+ +|+|+|||+.|+++|+|++.+|+|++|+++|.| ++|+||+|+|++.+++|++ |++|+||+|++
T Consensus 278 ~~~pI~~L~~~~~g~~~~I~grV~~~~~~R~f~~~~g~gkv~s~~l~D-~tG~IR~t~w~~~~d~~~~-l~~G~vy~is~ 355 (637)
T PRK12366 278 EIVNIEELTEFEDGEEVDVKGRIIAISDKREVERDDRTAEVQDIELAD-GTGRVRVSFWGEKAKILEN-LKEGDAVKIEN 355 (637)
T ss_pred CceeHHHCCcccCCCEEEEEEEEEecCCceEEEcCCCcEEEEEEEEEc-CCCeEEEEEeCchhhhhcc-cCCCCEEEEec
Confidence 46799999999 65 899999999999999999999999999999999 5679999999999999998 59999999999
Q ss_pred eEEecCCCcccCCCCceEEEeccccEEEeccCCCCCCCcccceecchhhhhhcc-cCccccEEEEEEEecCceeEEecCC
Q 006263 285 GSLKPAQKNFNHLKNEWEIFLEATSTVDLCTEEDDSIPKQQFSFRHISEIESAE-NNSIVDVIGIVISVNPSVPILRKNG 363 (653)
Q Consensus 285 ~~V~~a~~~f~~~~~~yei~f~~~T~I~~~~d~~~~iP~~~f~f~~i~~i~~~~-~~~~vDVIGvV~~v~~~~~i~~k~g 363 (653)
++|+..+. +...+.|||+|+..|.|.+ +++..+|...|+|++|.+|.+++ .+..|||+|+|++++++.+|++++|
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 1345789999999999998 34556999999999999999875 6889999999999999999998899
Q ss_pred ceeeEEEEEEEeCCCCEEEEEEccchhhhhhhhHHHhhccCCCcEEEEEeeEeecCCCc-eeccccceEEEEcCChHHHH
Q 006263 364 METQRRILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVDVGFFPVLSVKSGKVNDFSGK-SIGTIPSTQLFINPDFAEAH 442 (653)
Q Consensus 364 ~~~~kr~i~l~D~s~~~i~vtLWg~~A~~~~~~l~~~~~~~~~~Vvaik~~rV~~f~G~-sLs~~~~S~i~inPdipe~~ 442 (653)
++..+|+++|.|+|| +|++||||+.|.. +...+++|+|++++|++|+|+ +||++++|+|.+||+.|+
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 9999999999853 234689999999999999995 999999999999999887
Q ss_pred HHHHHHhcCCCccceeecccccccCCCCcchhccHHhhhhcCCCCCCCCcEEEEEEEEEEEeCCceEEecCCCCcCcccc
Q 006263 443 ELREWFDSGGKNAATVSISREIAAGGAKNEIHKTVSQIKNEGLGRSEKPDWVTVRAFITFIKSDSFCYTACPLMIGDRQC 522 (653)
Q Consensus 443 ~l~~w~~~~g~~~~~~sls~~~~~~~~~~~~~kti~~i~~~~lg~~~~~~~~~v~atI~~i~~d~~~Y~aC~~~~~~~~C 522 (653)
|+ ..+++|++|++. ++|.++|+|++|+.+++||+||| .|
T Consensus 500 -l~--------------------------~~~~~I~~i~~~--------~~~~v~g~i~~i~~~~~~y~aCp------~C 538 (637)
T PRK12366 500 -IK--------------------------SNRKFIADLEED--------DTVEIRGTVVDIRKQKIILYLCP------NC 538 (637)
T ss_pred -cc--------------------------ccccCHHHcccC--------CeEEEEEEEEEEeCCCEEEeccc------cc
Confidence 22 036889999763 35999999999999999999999 89
Q ss_pred cceeeecCceeecccCccccCCceEEEEEEEEEEeCCCeEEEEEechhhhhhhCCCHHHHHHHhhccCChhHHHHHHHHh
Q 006263 523 NKKVTQSGNRWQCDRCNQEIDECDYRYLLQAQIQDQTGLTWVTAFQESGEEILGCPAKELYMLKYELQDDVRFGEIIRSR 602 (653)
Q Consensus 523 ~KKv~~~~~~~~C~kC~~~~~~~~~rY~l~~~i~D~Tg~~~~~~F~~~ae~llG~sA~el~~~~~e~~d~~~~~~~~~~~ 602 (653)
||||....+.|+|++|++. .|.|||+|++.|+|+||++|+++|++.|++||||+|+||.+|. + +.|+++
T Consensus 539 nkKv~~~~g~~~C~~c~~~--~p~~~~~l~~~i~D~TG~~~~t~f~e~ae~l~G~sa~el~~l~--~-------~~l~~~ 607 (637)
T PRK12366 539 RKRVEEVDGEYICEFCGEV--EPNELLMLNFTLDDGTGTINCRFYGKNVEKLLGMSKEELKELN--L-------EALEDL 607 (637)
T ss_pred CeEeEcCCCcEECCCCCCC--CCcEEEEEEEEEEcCCCCEEEEEEhHHhHHHhCCCHHHHHHHH--H-------HHHHHh
Confidence 9999876669999999997 8999999999999999999999999999999999999999988 2 567789
Q ss_pred cCceEEEEEEEeeeccCceeeEEEEEEEeecCCh
Q 006263 603 VFNQYLFRLKIKEELYGDEQRVKITVIRADQVNY 636 (653)
Q Consensus 603 ~~k~~~f~v~~k~~~y~~e~r~~~~v~~~~~vd~ 636 (653)
+|++|.|+++++.+ |++ +||+|.++.|+|+
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 654 5599999999985
No 3
>PRK08402 replication factor A; Reviewed
Probab=100.00 E-value=2.9e-45 Score=386.43 Aligned_cols=279 Identities=22% Similarity=0.327 Sum_probs=238.5
Q ss_pred eecchhhhhhcccCccccEEEEEEEecCceeEEecCCceeeEEEEEEEeCCCCEEEEEEccchhhhhhhhHHHhhc-cCC
Q 006263 327 SFRHISEIESAENNSIVDVIGIVISVNPSVPILRKNGMETQRRILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVD-VGF 405 (653)
Q Consensus 327 ~f~~i~~i~~~~~~~~vDVIGvV~~v~~~~~i~~k~g~~~~kr~i~l~D~s~~~i~vtLWg~~A~~~~~~l~~~~~-~~~ 405 (653)
..++|.||.. ....|.+.|.|+++++..++++++|.....++++|.|+|| .+++||||+.|..+ +. ...
T Consensus 61 ~~~kI~dl~~--g~~~V~v~~rVl~~~~~r~f~rrdG~~~~V~~i~l~DeTG-~ir~TlW~~~a~~~-------~~~l~~ 130 (355)
T PRK08402 61 PLMHISDLVP--GMRGVNIVGRVLRKYPPREYTKKDGSTGRVASLIIYDDTG-RARVVLWDAKVAKY-------YNKINV 130 (355)
T ss_pred CccCHHHccC--CCceeeEEEEEEEccCCceeeccCCCcceEEEEEEEcCCC-eEEEEEechhhhhh-------cccCCC
Confidence 3567777753 3468999999999999999999999888899999999999 67999999998652 22 247
Q ss_pred CcEEEEEeeEeec-CCCc-eeccccceEEEEcCChHHHHHHHHHHhcCCCccceeecccccccCCCCcchhccHHhhhhc
Q 006263 406 FPVLSVKSGKVND-FSGK-SIGTIPSTQLFINPDFAEAHELREWFDSGGKNAATVSISREIAAGGAKNEIHKTVSQIKNE 483 (653)
Q Consensus 406 ~~Vvaik~~rV~~-f~G~-sLs~~~~S~i~inPdipe~~~l~~w~~~~g~~~~~~sls~~~~~~~~~~~~~kti~~i~~~ 483 (653)
++||+|++++|++ |+|+ +||++++|+|.+|||+|+++.+ .+++... +....+++|++|.+
T Consensus 131 Gdvi~I~~a~V~e~~~G~~eLsvg~~s~i~~~pd~~ea~~i-------------~~~~~~~----~~~~~~k~I~ei~~- 192 (355)
T PRK08402 131 GDVIKVIDAQVRESLSGLPELHINFRARIILNPDDPRVEEI-------------PPLEEVR----SYNYTRKKIGELEG- 192 (355)
T ss_pred CCEEEEECCEEeecCCCcEEEEECCCceEEeCCCccccccc-------------ccccccc----cccccccCHHHccc-
Confidence 8999999999998 5999 9999999999999999999763 2222111 12466899999965
Q ss_pred CCCCCCCCcEEEEEEEEEEEeCCceEEecCCCCcCcccccceee-ecCc-eeecccCccccCCceEEEEEEEEEEeCCCe
Q 006263 484 GLGRSEKPDWVTVRAFITFIKSDSFCYTACPLMIGDRQCNKKVT-QSGN-RWQCDRCNQEIDECDYRYLLQAQIQDQTGL 561 (653)
Q Consensus 484 ~lg~~~~~~~~~v~atI~~i~~d~~~Y~aC~~~~~~~~C~KKv~-~~~~-~~~C~kC~~~~~~~~~rY~l~~~i~D~Tg~ 561 (653)
| + +||.++|+|++|+. +++|+||| .|||||. ++++ .|+|+.|++. .|.|||+|++.|+|+||+
T Consensus 193 --g--d--~~v~v~g~Iv~i~~-~~~y~aCp------~CnKkv~~~~~~~~~~Ce~~~~v--~p~~ryil~~~l~D~TG~ 257 (355)
T PRK08402 193 --G--E--RFVEVRGTIAKVYR-VLVYDACP------ECRRKVDYDPATDTWICPEHGEV--EPIKITILDFGLDDGTGY 257 (355)
T ss_pred --C--C--cEEEEEEEEEEEec-CeeEecCC------CCCeEEEEecCCCCEeCCCCCCc--CcceeEEEEEEEEcCCCc
Confidence 1 2 78999999999998 77999999 8999998 4444 8999999973 799999999999999999
Q ss_pred EEEEEechhhhhhhCCCHHHHHHH-h---hccCCh-----hHHHHHHHHhcCceEEEEEEEeeeccCceeeEEEEEEEee
Q 006263 562 TWVTAFQESGEEILGCPAKELYML-K---YELQDD-----VRFGEIIRSRVFNQYLFRLKIKEELYGDEQRVKITVIRAD 632 (653)
Q Consensus 562 ~~~~~F~~~ae~llG~sA~el~~~-~---~e~~d~-----~~~~~~~~~~~~k~~~f~v~~k~~~y~~e~r~~~~v~~~~ 632 (653)
+|+++|++.|++|||++|+||.++ + .+.-+. ..|...+..++|++|.||++++.+.|+|+. |+|.++.
T Consensus 258 ~~vt~f~e~ae~llG~sa~el~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~rg~~~~d~y~~~~---~~v~~~~ 334 (355)
T PRK08402 258 IRVTLFGDDAAELLGVEPEEIAEKLKELIEMGLTPKEAARKLAEEEFYNIIGREIVVRGNVIEDRFLGLI---LKASSWD 334 (355)
T ss_pred EEEEEecHHHHHHhCCCHHHHHHHHHHhhhcccchhhhhhhHHHHHHHHhcCeEEEEEEEEEecccCCeE---EEEEEcc
Confidence 999999999999999999999988 4 211133 678889999999999999999999999965 9999999
Q ss_pred cCChHHHHHHHHHHHHhhh
Q 006263 633 QVNYSSESRYLLDLISKSF 651 (653)
Q Consensus 633 ~vd~~~e~~~ll~~i~~~~ 651 (653)
|+||++|+++|+++|.++.
T Consensus 335 ~vd~~~e~~~l~~~i~~~~ 353 (355)
T PRK08402 335 EVDYKREIERVRAELEELG 353 (355)
T ss_pred cCCHHHHHHHHHHHHHHhh
Confidence 9999999999999998875
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=8.6e-37 Score=293.68 Aligned_cols=165 Identities=44% Similarity=0.828 Sum_probs=155.2
Q ss_pred HHhhhhcCCCCCCCCcEEEEEEEEEEEeCCceEEecCCCCcCcccccceeeecC-ceeecccCccccCCceEEEEEEEEE
Q 006263 477 VSQIKNEGLGRSEKPDWVTVRAFITFIKSDSFCYTACPLMIGDRQCNKKVTQSG-NRWQCDRCNQEIDECDYRYLLQAQI 555 (653)
Q Consensus 477 i~~i~~~~lg~~~~~~~~~v~atI~~i~~d~~~Y~aC~~~~~~~~C~KKv~~~~-~~~~C~kC~~~~~~~~~rY~l~~~i 555 (653)
+++|++++++..+++++|.|+|+|..|+.++|||+||| .|+|||.+.+ +.|+|++|++.+++|.|||+|++.|
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 35777777777678999999999999999999999999 9999999887 5999999999999999999999999
Q ss_pred EeCCCeEEEEEechhhhhhhCCCHHHHHHHhhccCChhHHHHHHHHhcCceEEEEEEEeeeccCceeeEEEEEEEeecCC
Q 006263 556 QDQTGLTWVTAFQESGEEILGCPAKELYMLKYELQDDVRFGEIIRSRVFNQYLFRLKIKEELYGDEQRVKITVIRADQVN 635 (653)
Q Consensus 556 ~D~Tg~~~~~~F~~~ae~llG~sA~el~~~~~e~~d~~~~~~~~~~~~~k~~~f~v~~k~~~y~~e~r~~~~v~~~~~vd 635 (653)
+|+||++|+++||+.|++|||++|+||.++. +++++.+++.|.++.|++|.|+++++.++|++|.|++|+|.+++|++
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 45578899999999999999999999999999999999999999999
Q ss_pred hHHHHHHHHHHHHh
Q 006263 636 YSSESRYLLDLISK 649 (653)
Q Consensus 636 ~~~e~~~ll~~i~~ 649 (653)
+++|+++|++.|++
T Consensus 153 ~~~~~~~l~~~i~~ 166 (166)
T cd04476 153 YKKESKRLIQSIEK 166 (166)
T ss_pred HHHHHHHHHHHhhC
Confidence 99999999999864
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=7.8e-37 Score=287.69 Aligned_cols=145 Identities=46% Similarity=0.820 Sum_probs=124.4
Q ss_pred EEEEEEEEEEEeCCceEEecCCCCcCcccccceeeecCc-eeecccCccccCCceEEEEEEEEEEeCCCeEEEEEechhh
Q 006263 493 WVTVRAFITFIKSDSFCYTACPLMIGDRQCNKKVTQSGN-RWQCDRCNQEIDECDYRYLLQAQIQDQTGLTWVTAFQESG 571 (653)
Q Consensus 493 ~~~v~atI~~i~~d~~~Y~aC~~~~~~~~C~KKv~~~~~-~~~C~kC~~~~~~~~~rY~l~~~i~D~Tg~~~~~~F~~~a 571 (653)
||+|+|+|..|+.++|||+|||++ .|+|||...++ .|+|++|++.+++|.|||+|++.|+|+||++|+++||++|
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 799999999999999999999988 99999998854 9999999999999999999999999999999999999999
Q ss_pred hhhhCCCHHHHHHHhhccCChhHHHHHHHHhcCceEEEEEEEeeeccCceeeEEEEEEEeecCChHHHHHHH
Q 006263 572 EEILGCPAKELYMLKYELQDDVRFGEIIRSRVFNQYLFRLKIKEELYGDEQRVKITVIRADQVNYSSESRYL 643 (653)
Q Consensus 572 e~llG~sA~el~~~~~e~~d~~~~~~~~~~~~~k~~~f~v~~k~~~y~~e~r~~~~v~~~~~vd~~~e~~~l 643 (653)
++|||++|+||.++. ++++..++.++.+++|++|.|+|+++.++|+++.|++++|++++|+||++|+++|
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=1.5e-33 Score=303.16 Aligned_cols=360 Identities=18% Similarity=0.195 Sum_probs=288.7
Q ss_pred CcceeccccCCCCCceEEEEEEEeeccccccccCCCCceeEEEEEEeCCCCeEEEEEchhHHHHHHhhcccCcEEEEece
Q 006263 206 ARIIPIAALNPYQGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISKG 285 (653)
Q Consensus 206 ~~~~pI~~L~p~~~~w~I~~RV~~k~~ir~~~~~~g~gk~f~~~L~D~~g~~I~at~f~~~~~kf~~~l~eG~vy~is~~ 285 (653)
++...|++|.|...+-+|+|||+.+|+ |+|...+++|.+.+++|.| ++|.|+.|+|++. -|++|++|.|.|+
T Consensus 56 ~~~~kI~Di~~~~~~V~v~~kVl~i~~-rt~r~dg~~g~v~~~~igD-eTG~Ir~tlW~~~------~l~~Gdvv~I~na 127 (423)
T PRK07218 56 PSSKDIKELSTDDKNVTVTGRVLTIGE-RSIRYQGDDHVIYEGILAD-ETGTISYTAWKDF------GLSPGDTVTIGNA 127 (423)
T ss_pred CCCccHhhCCCCCceeEEEEEEEEecc-eeEecCCCceEEEEEEEEC-CCCeEEEEEECCC------CCCCCCEEEEecc
Confidence 456799999999988999999999999 9998766788999999999 8999999999965 2999999999999
Q ss_pred EEecCCCcccCCCCceEEEeccccEEEeccCCCCCCCcccceecchhhhhhcc-cCccccEEEEEEEecCceeEEecCCc
Q 006263 286 SLKPAQKNFNHLKNEWEIFLEATSTVDLCTEEDDSIPKQQFSFRHISEIESAE-NNSIVDVIGIVISVNPSVPILRKNGM 364 (653)
Q Consensus 286 ~V~~a~~~f~~~~~~yei~f~~~T~I~~~~d~~~~iP~~~f~f~~i~~i~~~~-~~~~vDVIGvV~~v~~~~~i~~k~g~ 364 (653)
.++.-+. ..++.+++.|.|.... +....|.. .....+|.++. ...-|+|.|.|.++.+ .+|++++|.
T Consensus 128 ~vre~~g-------~~el~ig~~t~I~~~d-e~~~~~~~---~~~~~kI~DL~~g~~~V~v~g~Vl~~~~-r~f~~~dg~ 195 (423)
T PRK07218 128 GVREWDG-------RPELNIGESTTVSLLD-DSSLPPYS---IGGDKKLIDLGPGDRGVNVEARVLELEH-REIDGRDGE 195 (423)
T ss_pred EeeccCC-------ceEEeccCcceEEEcC-cccccCcc---ccCccchhhccCCCCceEEEEEEEEecc-eeEEcCCCC
Confidence 9876543 3899999999999874 33333322 33344444443 3456999999999966 688877775
Q ss_pred eeeEEEEEEEeCCCCEEEEEEccchhhhhhhhHHHhhccCCCcEEEEEeeEeecCCCc-eeccccceEEEEcCChHHHHH
Q 006263 365 ETQRRILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVDVGFFPVLSVKSGKVNDFSGK-SIGTIPSTQLFINPDFAEAHE 443 (653)
Q Consensus 365 ~~~kr~i~l~D~s~~~i~vtLWg~~A~~~~~~l~~~~~~~~~~Vvaik~~rV~~f~G~-sLs~~~~S~i~inPdipe~~~ 443 (653)
...++..|.|+|| +|++|||++.+. + ..+.+|-|.++.+++|+|+ +|+....|.|..+|+..++
T Consensus 196 -~~v~~giigDeTG-~Ir~tlW~~~~~---------l--~~Gd~v~I~na~v~e~~G~~elnv~~~t~I~~~d~~i~v-- 260 (423)
T PRK07218 196 -TTILSGVLADETG-RLPFTDWDPLPE---------I--EIGASIRIEDAYVREFRGVPSVNVSEFTTVEALDREVSV-- 260 (423)
T ss_pred -eEEEEEEEECCCc-eEEEEEeccccc---------C--CCCCEEEEeeeEEeccCCeEEEEECCceEEEECCCCccc--
Confidence 4689999999999 899999998752 2 3689999999999999997 8999999999988853211
Q ss_pred HHHHHhcCCCccceeecccccccCCCCcchhccHHhhhhcCCCCCCCCcE-EEEEEEEEEEeCCceEEecCCCCcCcccc
Q 006263 444 LREWFDSGGKNAATVSISREIAAGGAKNEIHKTVSQIKNEGLGRSEKPDW-VTVRAFITFIKSDSFCYTACPLMIGDRQC 522 (653)
Q Consensus 444 l~~w~~~~g~~~~~~sls~~~~~~~~~~~~~kti~~i~~~~lg~~~~~~~-~~v~atI~~i~~d~~~Y~aC~~~~~~~~C 522 (653)
.....++.|.++.+. ...| ..+.|+|+.|...+-.|..|| .|
T Consensus 261 -------------------------~~~~~~~~I~e~~~~------~g~~~Vev~G~Iv~i~~gsgli~rCP------~C 303 (423)
T PRK07218 261 -------------------------SKDPPRLKIREAVER------GGIFDVELVGNIISVRDGSGLIERCP------EC 303 (423)
T ss_pred -------------------------cCCccccchhhhhcc------CCcceEEEEEEEEEeccCCcceecCc------Cc
Confidence 012346778888763 2234 689999999999988999999 99
Q ss_pred cceeeecCceeecccCccccCCceEEEEEEEEEEeCCCeEEEEEechhhhhhhCCCHHHHHHHhhccCChhHH-HHHHHH
Q 006263 523 NKKVTQSGNRWQCDRCNQEIDECDYRYLLQAQIQDQTGLTWVTAFQESGEEILGCPAKELYMLKYELQDDVRF-GEIIRS 601 (653)
Q Consensus 523 ~KKv~~~~~~~~C~kC~~~~~~~~~rY~l~~~i~D~Tg~~~~~~F~~~ae~llG~sA~el~~~~~e~~d~~~~-~~~~~~ 601 (653)
+|+|. .|.|+.|++. .|.+-.++.+.+.|+||++.+++|++.+++|.|++.++..+|..+.-|.... ..+-..
T Consensus 304 ~r~v~----~~~C~~hG~v--e~~~dlrik~vLDDGtg~~~~~~~~e~~e~l~G~~~e~a~~~~~~~~d~~~v~~~i~~~ 377 (423)
T PRK07218 304 GRVIQ----KGQCRSHGAV--EGEDDLRIKAILDDGTGSVTVILDRELTEIVYGGTLEDAEELAREAMDKDVVAEDIRER 377 (423)
T ss_pred ccccc----CCcCCCCCCc--CCeeeeEEEEEEECCCCeEEEEEChhhhHhHhCCCHHHHHHHHHhhhcchhhHHHHHHh
Confidence 99995 4899999976 7899999999999999999999999999999999999998877433344444 444467
Q ss_pred hcCceEEEEEEEeeeccCceeeEEEEEEEeecCC--hHHHHHHHHHHH
Q 006263 602 RVFNQYLFRLKIKEELYGDEQRVKITVIRADQVN--YSSESRYLLDLI 647 (653)
Q Consensus 602 ~~~k~~~f~v~~k~~~y~~e~r~~~~v~~~~~vd--~~~e~~~ll~~i 647 (653)
++|+.|.|+..+..+.|. ..+.+.++..+| .+.-++.||.++
T Consensus 378 llG~~~~v~G~~~~~~~g----~~~~a~~~~~~~~~~~~r~~~~l~~~ 421 (423)
T PRK07218 378 LVGREYRVRGNLSVDEYG----ANLVAESFWVPDDDPAKRAVALLAEV 421 (423)
T ss_pred hcCcEEEEEeccccccCC----cEEEEeEccccCCCHHHHHHHHHHhh
Confidence 999999999998877773 577778887775 445555666543
No 7
>PRK12366 replication factor A; Reviewed
Probab=100.00 E-value=5.7e-32 Score=308.45 Aligned_cols=282 Identities=20% Similarity=0.273 Sum_probs=226.2
Q ss_pred CCcceeccccCCCCCceEEEEEEEeeccccccccCCC-CceeEEEEEEeCCCCeEEEEEchhHHHHHHhhcccCcEEEEe
Q 006263 205 PARIIPIAALNPYQGRWAIKARVTAKGDLRRYNNARG-DGKVFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLIS 283 (653)
Q Consensus 205 ~~~~~pI~~L~p~~~~w~I~~RV~~k~~ir~~~~~~g-~gk~f~~~L~D~~g~~I~at~f~~~~~kf~~~l~eG~vy~is 283 (653)
..+++||++|+||+.+|+|+|||+.+|++|+|++.+| +|++|+++|.| ++|+|++|+|++.++. ++.|++|+||+|+
T Consensus 60 ~~~~~~I~dl~p~~~~v~i~arV~~~~~~r~~~~~~G~eGkv~~~~v~D-etG~Ir~t~W~~~~~~-~~~le~G~v~~i~ 137 (637)
T PRK12366 60 EEEDFKISDIEEGQINVEITGRIIEISNIKTFTRKDGSTGKLANITIAD-NTGTIRLTLWNDNAKL-LKGLKEGDVIKIE 137 (637)
T ss_pred ccceeEHHHCcCCCcceEEEEEEEEccCCeEEECCCCCccEEEEEEEEc-CCCEEEEEEEchhhhh-hccCCCCCEEEEe
Confidence 3468899999999999999999999999999999877 89999999999 6779999999999885 6899999999999
Q ss_pred ceEEecCCCcccCCCCceEEEeccccEEEeccC-CCCCCCcccceecchhhhhhcccCccccEEEEEEEecCceeEEecC
Q 006263 284 KGSLKPAQKNFNHLKNEWEIFLEATSTVDLCTE-EDDSIPKQQFSFRHISEIESAENNSIVDVIGIVISVNPSVPILRKN 362 (653)
Q Consensus 284 ~~~V~~a~~~f~~~~~~yei~f~~~T~I~~~~d-~~~~iP~~~f~f~~i~~i~~~~~~~~vDVIGvV~~v~~~~~i~~k~ 362 (653)
++.++. .+++|+|.++..|.|.++.+ ++..+|...++| +|.+| ..+..|||+|+|++++++.++++|+
T Consensus 138 ~~~v~~-------~~~~~el~~~~~t~I~~~~~~d~~~i~~~~~~~-~I~el---~~g~~v~v~G~V~~~~~~~~f~rkd 206 (637)
T PRK12366 138 NARSRK-------WNNDVELNSGSETRIDKLEKYDESRYPIIKENY-DIPEL---EPNLSATIEGEVTKAYPIKEFTRKD 206 (637)
T ss_pred ccEecc-------cCCceEEEcCCcceEEEccccccccCCcccccc-ccccc---CCCCeEEEEEEEEEccCcEEEEEcC
Confidence 999876 34779999999999999963 355789887776 55555 4677999999999999999999999
Q ss_pred CceeeEEEEEEEeCCCCEEEEEEccchhhhhhhhHHHhhccCCCcEEEEEeeEeecC-CCceeccccceEEEEcCChHHH
Q 006263 363 GMETQRRILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVDVGFFPVLSVKSGKVNDF-SGKSIGTIPSTQLFINPDFAEA 441 (653)
Q Consensus 363 g~~~~kr~i~l~D~s~~~i~vtLWg~~A~~~~~~l~~~~~~~~~~Vvaik~~rV~~f-~G~sLs~~~~S~i~inPdipe~ 441 (653)
|++..+|++.|.|+|| +|++||||+.|.. ....+++|+|++.++..| +|..|+.+..+.|-...+
T Consensus 207 g~~~~~r~~~l~D~TG-~irvTlW~~~a~~---------~~~~g~vv~i~g~~~~~~~~~~el~~~~~~~i~~~~~---- 272 (637)
T PRK12366 207 GSEGKLKSFILKDDTG-SIRVTLWNDLTDI---------EVNKGDIVRVKGYVKQGYRTGLEISANNIEILEKLEK---- 272 (637)
T ss_pred CCeeEEEEEEEEcCCC-cEEEEEEChhhcc---------cCCCCCEEEEEeEEecCcCCceEEEeCCceeeccccc----
Confidence 9999999999999999 8999999999843 234789999999888889 556888866665532110
Q ss_pred HHHHHHHhcCCCccceeecccccccCCCCcchhccHHhhhhcCCCCCCCCcEEEEEEEEEEEeCC-ceEEecCCCCcCcc
Q 006263 442 HELREWFDSGGKNAATVSISREIAAGGAKNEIHKTVSQIKNEGLGRSEKPDWVTVRAFITFIKSD-SFCYTACPLMIGDR 520 (653)
Q Consensus 442 ~~l~~w~~~~g~~~~~~sls~~~~~~~~~~~~~kti~~i~~~~lg~~~~~~~~~v~atI~~i~~d-~~~Y~aC~~~~~~~ 520 (653)
. ........|++|.+- +....++++|.|+.+..- .|-.
T Consensus 273 ---------~-----------------~~~~~~~pI~~L~~~-----~~g~~~~I~grV~~~~~~R~f~~---------- 311 (637)
T PRK12366 273 ---------E-----------------EKELEIVNIEELTEF-----EDGEEVDVKGRIIAISDKREVER---------- 311 (637)
T ss_pred ---------c-----------------ccccCceeHHHCCcc-----cCCCEEEEEEEEEecCCceEEEc----------
Confidence 0 001134578888642 123468899999887531 1110
Q ss_pred cccceeeecCceeecccCccccCCceEEEEEEEEEEeCCCeEEEEEechhhhhhhCC
Q 006263 521 QCNKKVTQSGNRWQCDRCNQEIDECDYRYLLQAQIQDQTGLTWVTAFQESGEEILGC 577 (653)
Q Consensus 521 ~C~KKv~~~~~~~~C~kC~~~~~~~~~rY~l~~~i~D~Tg~~~~~~F~~~ae~llG~ 577 (653)
. .-. -...++.+.|.||++++++|++.|.++.++
T Consensus 312 -------~---------------~g~-gkv~s~~l~D~tG~IR~t~w~~~~d~~~~l 345 (637)
T PRK12366 312 -------D---------------DRT-AEVQDIELADGTGRVRVSFWGEKAKILENL 345 (637)
T ss_pred -------C---------------CCc-EEEEEEEEEcCCCeEEEEEeCchhhhhccc
Confidence 0 011 356789999999999999999999877664
No 8
>PRK07211 replication factor A; Reviewed
Probab=100.00 E-value=9.7e-32 Score=291.28 Aligned_cols=274 Identities=20% Similarity=0.276 Sum_probs=218.0
Q ss_pred cceeccccCCCCCceEEEEEEEeeccccccccC--CCCceeEEEEEEeCCCCeEEEEEchhHHHHHHhhcccCcEEEEec
Q 006263 207 RIIPIAALNPYQGRWAIKARVTAKGDLRRYNNA--RGDGKVFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISK 284 (653)
Q Consensus 207 ~~~pI~~L~p~~~~w~I~~RV~~k~~ir~~~~~--~g~gk~f~~~L~D~~g~~I~at~f~~~~~kf~~~l~eG~vy~is~ 284 (653)
.+.+|++|+||+++|+|+|||+.|+++|+|++. +++|++|+++|.| ++|+|++|+|++.+++|++.|++|+||+|.+
T Consensus 52 e~~~I~dL~pg~~~vtI~aRV~~~~~~Rt~~~~~~~~eGkv~~v~l~D-eTG~Ir~TlW~d~ad~~~~~Le~GdV~~I~~ 130 (485)
T PRK07211 52 EVNGIADIEPGMDEVKFLAKVLSIGDLRTFERDGEDEDGRVINVEVAD-ETGSVRVAFWDEQAVAAEEELEVGQVLRIKG 130 (485)
T ss_pred ccccHhhCCCCCCceEEEEEEeEccCceEEEeCCCCCCcEEEEEEEEc-CCCeEEEEEechHhHhhhcccCCCCEEEEec
Confidence 467999999999999999999999999999987 4589999999999 8999999999999999999999999999965
Q ss_pred eEEecCCCcccCCCCceEEEeccccEEEeccCCCCCCCcccceecchhhhhhcccCccccEEEEEEEecCceeEEecCCc
Q 006263 285 GSLKPAQKNFNHLKNEWEIFLEATSTVDLCTEEDDSIPKQQFSFRHISEIESAENNSIVDVIGIVISVNPSVPILRKNGM 364 (653)
Q Consensus 285 ~~V~~a~~~f~~~~~~yei~f~~~T~I~~~~d~~~~iP~~~f~f~~i~~i~~~~~~~~vDVIGvV~~v~~~~~i~~k~g~ 364 (653)
.++ +.|+.+ ||+|+ .|++|++. .+|....+|.+|.+|.. ....+||+|+|+.+++++++.+++|+
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 667763 99998 48888543 35555669999999974 46789999999999999999988998
Q ss_pred eeeEEEEEEEeCCCCEEEEEEccchhhhhhhhHHHhhccCCCcEEEEEeeEeecCCC-ceeccccceEEEEcCChHHHHH
Q 006263 365 ETQRRILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVDVGFFPVLSVKSGKVNDFSG-KSIGTIPSTQLFINPDFAEAHE 443 (653)
Q Consensus 365 ~~~kr~i~l~D~s~~~i~vtLWg~~A~~~~~~l~~~~~~~~~~Vvaik~~rV~~f~G-~sLs~~~~S~i~inPdipe~~~ 443 (653)
+...|++.|.|+|| +|++|||++.|..| +.+ ..++||.|++++|++|+| .+|+....|.|..-++. +.
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 69999999998774 112 468999999999999966 59999888888865541 10
Q ss_pred HHHHHhcCCCccceeecccccccCCCCcchhccHHhhhhcCCCCCCCCcEEEEEEEEEEEeCCceEEecCCCCcCccccc
Q 006263 444 LREWFDSGGKNAATVSISREIAAGGAKNEIHKTVSQIKNEGLGRSEKPDWVTVRAFITFIKSDSFCYTACPLMIGDRQCN 523 (653)
Q Consensus 444 l~~w~~~~g~~~~~~sls~~~~~~~~~~~~~kti~~i~~~~lg~~~~~~~~~v~atI~~i~~d~~~Y~aC~~~~~~~~C~ 523 (653)
+ +. ....|.+|. ..+.+.+.|.|..+..-.-+-
T Consensus 265 -------------~--vp-----------~~~~I~dl~--------~g~~vdV~GvV~~v~~~rtf~------------- 297 (485)
T PRK07211 265 -------------Y--VP-----------DTTPIESLE--------IDETVDIAGVVRSADPKRTFD------------- 297 (485)
T ss_pred -------------c--cc-----------ccccHhhcC--------CCCceeEEEEEEEccCcEEEE-------------
Confidence 0 00 013345443 223577888888776421111
Q ss_pred ceeeecCceeecccCccccCCceEEEEEEEEEEeCCCeEEEEEechhhh
Q 006263 524 KKVTQSGNRWQCDRCNQEIDECDYRYLLQAQIQDQTGLTWVTAFQESGE 572 (653)
Q Consensus 524 KKv~~~~~~~~C~kC~~~~~~~~~rY~l~~~i~D~Tg~~~~~~F~~~ae 572 (653)
.+++ ....+.++.|.|.||++++++|++.|+
T Consensus 298 ------------r~dG------~~~~vr~l~l~D~TG~IrvTLWg~~A~ 328 (485)
T PRK07211 298 ------------RDDG------SEGQVRNVRIQDDTGDIRVALWGEKAD 328 (485)
T ss_pred ------------cCCC------CEeEEEEEEEEcCCCcEEEEEeCcccc
Confidence 0122 234667899999999999999999994
No 9
>PRK06386 replication factor A; Reviewed
Probab=100.00 E-value=1.1e-29 Score=266.69 Aligned_cols=350 Identities=17% Similarity=0.189 Sum_probs=278.4
Q ss_pred eeccccCCCCCceEEEEEEEeeccccccccCCCCceeEEEEEEeCCCCeEEEEEchhHHHHHHhhcccCcEEEEeceEEe
Q 006263 209 IPIAALNPYQGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISKGSLK 288 (653)
Q Consensus 209 ~pI~~L~p~~~~w~I~~RV~~k~~ir~~~~~~g~gk~f~~~L~D~~g~~I~at~f~~~~~kf~~~l~eG~vy~is~~~V~ 288 (653)
+.|++|+|...+-+|+|||+..| .|+|...+|+..+.+-+|.| ++|.|+.|+|+. .+.|++|++|.|.|+.++
T Consensus 3 ~kI~DI~~~~~~V~v~akVl~~~-~r~i~~~~g~~~~~~gllgD-eTG~I~fT~W~~-----~~~l~~Gd~v~i~na~v~ 75 (358)
T PRK06386 3 SKISDINAARQNVDLKVKVLSLN-KRTIKNDRGETIYYYGIIGD-ETGTVPFTAWEF-----PDAVKSGDVIEIKYCYSK 75 (358)
T ss_pred cchhhcCCCCCcEEEEEEEEEcc-ceEEecCCCCeEEEEEEEEC-CcceEEEEecCC-----cccCCCCCEEEEEeEEEe
Confidence 57999999999999999999999 69998888776778888999 899999999995 257999999999999987
Q ss_pred cCCCcccCCCCceEEEeccccEEEeccCCCCCCCcccceecchhhhhhcccCccccEEEEEEEecCceeEEecCCceeeE
Q 006263 289 PAQKNFNHLKNEWEIFLEATSTVDLCTEEDDSIPKQQFSFRHISEIESAENNSIVDVIGIVISVNPSVPILRKNGMETQR 368 (653)
Q Consensus 289 ~a~~~f~~~~~~yei~f~~~T~I~~~~d~~~~iP~~~f~f~~i~~i~~~~~~~~vDVIGvV~~v~~~~~i~~k~g~~~~k 368 (653)
.-+. .++|.++..|.|.+..|.+..++ ..+..++|.||.. ...-|+|.|.|.++.+ .++. ++|.....
T Consensus 76 ~~~G-------~~~Lnv~~~t~v~~~~d~~iev~-~~~~~~KI~DL~~--g~~~v~V~akVle~~e-~e~~-~~g~~~~v 143 (358)
T PRK06386 76 EYNG-------KIRIYFDSRSEVMLKPDENIEVK-RTYKLVKIRDLSL--VTPYVSVIGKITGITK-KEYD-SDGTSKIV 143 (358)
T ss_pred eECC-------EEEEEEcCceEEEecCccccccc-cccCccEeEeccC--CCCceEEEEEEEEccC-ceEe-cCCCccEE
Confidence 6443 58899999999976643322222 2246778888843 4567999999999977 5776 55666778
Q ss_pred EEEEEEeCCCCEEEEEEccchhhhhhhhHHHhhccCCCcEEEEEeeEeecCCCc-eeccccceEEEEcCChHHHHHHHHH
Q 006263 369 RILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVDVGFFPVLSVKSGKVNDFSGK-SIGTIPSTQLFINPDFAEAHELREW 447 (653)
Q Consensus 369 r~i~l~D~s~~~i~vtLWg~~A~~~~~~l~~~~~~~~~~Vvaik~~rV~~f~G~-sLs~~~~S~i~inPdipe~~~l~~w 447 (653)
+++.|.|+|| +|++|||++.. ..+.+|-|.++.+.+|+|+ +|+.+..|+|...|+.-+
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-RVRISSFGKPL-------------EDNRFVRIENARVSQYNGYIEISVGNKSVIKEVESDIN------- 202 (358)
T ss_pred EEEEEEcCCC-eEEEEEccccc-------------cCCCEEEEeeeEEEccCCeEEEEeCCeEEEEECCCCcc-------
Confidence 9999999999 89999999731 2589999999999999997 899999999887653211
Q ss_pred HhcCCCccceeecccccccCCCCcchhccHHhhhhcCCCCCCCCcEEEEEEEEEEEeCCceEEecCCCCcCcccccceee
Q 006263 448 FDSGGKNAATVSISREIAAGGAKNEIHKTVSQIKNEGLGRSEKPDWVTVRAFITFIKSDSFCYTACPLMIGDRQCNKKVT 527 (653)
Q Consensus 448 ~~~~g~~~~~~sls~~~~~~~~~~~~~kti~~i~~~~lg~~~~~~~~~v~atI~~i~~d~~~Y~aC~~~~~~~~C~KKv~ 527 (653)
+ ...++.|.+|.+.. | -..+.|+|+.|....-.|..|| .|+|+|.
T Consensus 203 ------------v----------~~~~~~I~di~~~~-g------~v~i~G~iv~i~~gsgli~rCP------~C~R~l~ 247 (358)
T PRK06386 203 ------------L----------ESRNIFIFEIKSPV-G------GITIMGFIVSVGQGSRIFTKCS------VCNKIIE 247 (358)
T ss_pred ------------c----------CccccchhhhhccC-C------eEEEEEEEEEEcCCcEeEecCc------CCCeEcc
Confidence 0 02367889998632 1 2678899999999889999999 9999997
Q ss_pred ecCceeecccCccccCCceEEEEEEEEEEeCCCeEEEEEechhhhhhhCCCHHHHHHHhhccCChhHHHHHHHHhcCceE
Q 006263 528 QSGNRWQCDRCNQEIDECDYRYLLQAQIQDQTGLTWVTAFQESGEEILGCPAKELYMLKYELQDDVRFGEIIRSRVFNQY 607 (653)
Q Consensus 528 ~~~~~~~C~kC~~~~~~~~~rY~l~~~i~D~Tg~~~~~~F~~~ae~llG~sA~el~~~~~e~~d~~~~~~~~~~~~~k~~ 607 (653)
. +.|+.|++. .+.+-.++.+.+.|+||.+.+++|++.+++|+|++-+|+.++.- +-+. ...+=..++|+.|
T Consensus 248 ~----g~C~~HG~v--~~~~dlr~k~vLDDGtg~~~~~l~~e~~e~l~G~~lee~~~~a~-~~~~--~~~i~~~llGr~~ 318 (358)
T PRK06386 248 D----GVCKDHPDA--PVYLDIFGYFTISDGTGFVTCYANKDSFLPYININENEFARKAS-SMNP--NMLIKKNLLGKCF 318 (358)
T ss_pred C----CcCCCCCCC--CCeeEEEEEEEEECCCCeEEEEEChHHhHHHhCCCHHHHHHHhh-ccCH--HHHhhhhhcccEE
Confidence 4 699999973 67788888889999999999999999999999999999987552 2222 2222267999999
Q ss_pred EEEEEEeeeccCceeeEEEEEEEeecCChHHHHHHHHHHH
Q 006263 608 LFRLKIKEELYGDEQRVKITVIRADQVNYSSESRYLLDLI 647 (653)
Q Consensus 608 ~f~v~~k~~~y~~e~r~~~~v~~~~~vd~~~e~~~ll~~i 647 (653)
.|+..+..+.|. +.+.|.++..+|- .+.+..-..|
T Consensus 319 ~v~G~~~~~~~~----~~~~~~~~~~~~~-~~~~~~~~~~ 353 (358)
T PRK06386 319 SVTGDLRKKDDE----IDMNVISAKSITA-DEIKIIEVEI 353 (358)
T ss_pred EEEcceEeccCC----eEEEEEEeeeccc-hhhhHHHHHH
Confidence 999999877764 7889999998886 3444444333
No 10
>PRK07211 replication factor A; Reviewed
Probab=99.98 E-value=1.6e-31 Score=289.53 Aligned_cols=209 Identities=22% Similarity=0.351 Sum_probs=182.8
Q ss_pred cceeccccCCCCCceEEEEEEEeeccccccccCCC-CceeEEEEEEeCCCCeEEEEEchhHHHHHHhhcccCcEEEEece
Q 006263 207 RIIPIAALNPYQGRWAIKARVTAKGDLRRYNNARG-DGKVFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISKG 285 (653)
Q Consensus 207 ~~~pI~~L~p~~~~w~I~~RV~~k~~ir~~~~~~g-~gk~f~~~L~D~~g~~I~at~f~~~~~kf~~~l~eG~vy~is~~ 285 (653)
+++||++|+|++..|+|+|||+.++++|+|.+.+| +|++++++|.| ++|+|++|+|++.+++| +.|++|+||+|+++
T Consensus 160 ~~~~I~dL~~~~~~v~I~grV~~v~~iRtf~r~dGseGkv~sv~L~D-eTG~IR~TlW~d~Ad~~-~~le~G~Vv~I~~a 237 (485)
T PRK07211 160 DTYTVEDLSLGLSDVTLVGVVLDTDSVRTFDRDDGSEGRVSNLTVGD-ETGRVRVTLWDDRADLA-EELDAGESVEIVDG 237 (485)
T ss_pred CCccHHHcCCCCCceEEEEEEEEcCCCeEEECCCCCeeEEEEEEEEc-CCCeEEEEEechhhhhh-ccCCCCCEEEEEee
Confidence 57899999999999999999999999999998887 89999999999 67799999999999999 78999999999999
Q ss_pred EEecCCCcccCCCCceEEEeccccEEEeccCCCCCCCcccceecchhhhhhcccCccccEEEEEEEecCceeEEecCCce
Q 006263 286 SLKPAQKNFNHLKNEWEIFLEATSTVDLCTEEDDSIPKQQFSFRHISEIESAENNSIVDVIGIVISVNPSVPILRKNGME 365 (653)
Q Consensus 286 ~V~~a~~~f~~~~~~yei~f~~~T~I~~~~d~~~~iP~~~f~f~~i~~i~~~~~~~~vDVIGvV~~v~~~~~i~~k~g~~ 365 (653)
+|+..+ +.|||+|+..|.|++|.++...+|. + .+|.+++.+..|||+|+|++++++.+|++++|++
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 7899999999999999543233553 2 4455555777999999999999999999888999
Q ss_pred eeEEEEEEEeCCCCEEEEEEccchhhhhhhhHHHhhccCCCcEEEEEeeEeecC--CCceeccccceEEEEcCChHHH
Q 006263 366 TQRRILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVDVGFFPVLSVKSGKVNDF--SGKSIGTIPSTQLFINPDFAEA 441 (653)
Q Consensus 366 ~~kr~i~l~D~s~~~i~vtLWg~~A~~~~~~l~~~~~~~~~~Vvaik~~rV~~f--~G~sLs~~~~S~i~inPdipe~ 441 (653)
..+|+++|.|+|| +|++||||+.|.. +...+++|+|++++|++| +|++||+.++|.|.+-.+-|++
T Consensus 304 ~~vr~l~l~D~TG-~IrvTLWg~~A~~---------~i~~GdvV~Ikg~~V~dg~~ggleLS~g~~s~i~~~~~~~~~ 371 (485)
T PRK07211 304 GQVRNVRIQDDTG-DIRVALWGEKADL---------DIGPGDEVVAADVEIQDGWQDDLEASAGWQSTVVVLDDGADA 371 (485)
T ss_pred eEEEEEEEEcCCC-cEEEEEeCccccC---------CCCCCCEEEEEccEEEecCCCCEEEEecCCceEEEccccccc
Confidence 9999999999999 8999999999832 345789999999999998 6899999988888775554443
No 11
>PRK15491 replication factor A; Provisional
Probab=99.97 E-value=2.5e-29 Score=269.01 Aligned_cols=277 Identities=19% Similarity=0.287 Sum_probs=217.7
Q ss_pred CcceeccccCCCCCceEEEEEEEeeccccccccCCC-CceeEEEEEEeCCCCeEEEEEchhHHHHHH-hhcccCcEEEEe
Q 006263 206 ARIIPIAALNPYQGRWAIKARVTAKGDLRRYNNARG-DGKVFSFDLLDSDGGEIRVTCFNAVVDRFY-EIIEVGRVYLIS 283 (653)
Q Consensus 206 ~~~~pI~~L~p~~~~w~I~~RV~~k~~ir~~~~~~g-~gk~f~~~L~D~~g~~I~at~f~~~~~kf~-~~l~eG~vy~is 283 (653)
.++++|++|+|++++|+|+|||+.++++|+|++.+| +|++++++|.| ++|+|++|+|++.+++|+ +.|++|+||+|+
T Consensus 55 ~~~~kI~dL~~~~~~v~i~arVl~~~~~R~f~r~dGs~g~v~~~~v~D-eTG~ir~tlW~~~a~~~~~~~le~G~v~~I~ 133 (374)
T PRK15491 55 VDTTKIADINESSSNVNFTAKVVSIFEPKEFNRNDGTTGRVGNIIVAD-ETGSIRLTLWDDLADLIKTGDIEVGKSLNIS 133 (374)
T ss_pred cccccHHHCCCCCCceEEEEEEeeccCCeeeecCCCCceEEEEEEEEc-CCCeEEEEEECchhhhhccCCcCCCCEEEEe
Confidence 468899999999999999999999999999999888 89999999999 888999999999999999 799999999998
Q ss_pred ceEEecCCCcccCCCCceEEEeccccEEEeccCCCCCCCcccceecchhhhhhcccCccccEEEEEEEecCceeEEecCC
Q 006263 284 KGSLKPAQKNFNHLKNEWEIFLEATSTVDLCTEEDDSIPKQQFSFRHISEIESAENNSIVDVIGIVISVNPSVPILRKNG 363 (653)
Q Consensus 284 ~~~V~~a~~~f~~~~~~yei~f~~~T~I~~~~d~~~~iP~~~f~f~~i~~i~~~~~~~~vDVIGvV~~v~~~~~i~~k~g 363 (653)
++ +++.|+. .||+|++.|.|.++.+ . + ...|+|++|+||.. .+..|||.|.|+.++++.++++++|
T Consensus 134 ~~----~~~~y~g----~Ei~i~~~~~i~~~~~-~--~-~~~~~~~~I~dl~~--~~~~V~I~g~V~~~~~~r~~~~~~G 199 (374)
T PRK15491 134 GY----AKEGYSG----IEVNIGRYGGISESDE-N--V-KASINSQKISDIKD--GDSDINIVGKVLDISDVRTFQKKDG 199 (374)
T ss_pred ee----eccCccc----EEEEeCCCceeeeccc-c--c-ccccCcccHHHcCC--CCccEEEEEEEEEccCceEEEecCC
Confidence 76 5667754 6999999999999843 2 2 34679999999975 3446999999999999999999899
Q ss_pred ceeeEEEEEEEeCCCCEEEEEEccchhhhhhhhHHHhhccCCCcEEEEEee--EeecCCCc-eeccccceEEEEcCChHH
Q 006263 364 METQRRILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVDVGFFPVLSVKSG--KVNDFSGK-SIGTIPSTQLFINPDFAE 440 (653)
Q Consensus 364 ~~~~kr~i~l~D~s~~~i~vtLWg~~A~~~~~~l~~~~~~~~~~Vvaik~~--rV~~f~G~-sLs~~~~S~i~inPdipe 440 (653)
++...|++.|.|+|| .|++||||+.|..+ +.+ ..+.+|-+.++ |...|+|. .|+....|.|....+.++
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 988999999999999 69999999998763 112 35788888776 45578776 788877788765332111
Q ss_pred HHHHHHHHhcCCCccceeecccccccCCCCcchhccHHhhhhcCCCCCCCCcEEEEEEEEEEEeCCceEEecCCCCcCcc
Q 006263 441 AHELREWFDSGGKNAATVSISREIAAGGAKNEIHKTVSQIKNEGLGRSEKPDWVTVRAFITFIKSDSFCYTACPLMIGDR 520 (653)
Q Consensus 441 ~~~l~~w~~~~g~~~~~~sls~~~~~~~~~~~~~kti~~i~~~~lg~~~~~~~~~v~atI~~i~~d~~~Y~aC~~~~~~~ 520 (653)
+ ......|++|... +.+.+.|.|..+.+-. -+..
T Consensus 272 ~-----------------------------~~~f~~I~dl~~~--------~~~dv~G~V~~v~~~~-~~~~-------- 305 (374)
T PRK15491 272 Y-----------------------------EEDFTPIADIIPG--------QPYSIKGAVSGLGDLK-EFTK-------- 305 (374)
T ss_pred c-----------------------------CCCccCHHHcCCC--------CceeEEEEEEEcCCcE-EEEc--------
Confidence 0 0123457777531 2367888777774310 0000
Q ss_pred cccceeeecCceeecccCccccCCceEEEEEEEEEEeCCCeEEEEEechhhhh
Q 006263 521 QCNKKVTQSGNRWQCDRCNQEIDECDYRYLLQAQIQDQTGLTWVTAFQESGEE 573 (653)
Q Consensus 521 ~C~KKv~~~~~~~~C~kC~~~~~~~~~rY~l~~~i~D~Tg~~~~~~F~~~ae~ 573 (653)
+ +-....+-++.|.|.||.+.+++||+.|+.
T Consensus 306 ----------------~------~G~~~~~r~i~l~D~Tg~Ir~tlWg~~a~~ 336 (374)
T PRK15491 306 ----------------S------DGSENKVSNIYVSDDTGRIRIALWGEKAEL 336 (374)
T ss_pred ----------------c------CCCEeEEEeEEEEeCCCcEEEEEccccccc
Confidence 0 122344567899999999999999999975
No 12
>PRK15491 replication factor A; Provisional
Probab=99.96 E-value=2.8e-27 Score=253.17 Aligned_cols=205 Identities=17% Similarity=0.296 Sum_probs=175.0
Q ss_pred ceeccccCCCCCceEEEEEEEeeccccccccCCCC-ceeEEEEEEeCCCCeEEEEEchhHHHHHHhhcccCcEEEEeceE
Q 006263 208 IIPIAALNPYQGRWAIKARVTAKGDLRRYNNARGD-GKVFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISKGS 286 (653)
Q Consensus 208 ~~pI~~L~p~~~~w~I~~RV~~k~~ir~~~~~~g~-gk~f~~~L~D~~g~~I~at~f~~~~~kf~~~l~eG~vy~is~~~ 286 (653)
+.+|++|.++...+.|+|||+.++++|+|.+.+|+ |+++++.|.| ++|+|++|+|++.|++| +.|++|++|+|.++.
T Consensus 166 ~~~I~dl~~~~~~V~I~g~V~~~~~~r~~~~~~G~~~~v~~~~l~D-etG~Ir~t~W~~~a~~~-~~l~~Gd~V~i~~~~ 243 (374)
T PRK15491 166 SQKISDIKDGDSDINIVGKVLDISDVRTFQKKDGSQGRVRNITIGD-ETGKIRVTLWDGKTDLA-DKLENGDSVEIINGY 243 (374)
T ss_pred cccHHHcCCCCccEEEEEEEEEccCceEEEecCCCeEEEEEEEEEC-CCCeEEEEEecchhccc-ccCCCCCEEEEEece
Confidence 56899999998899999999999999999988775 8999999999 67799999999999998 779999999999998
Q ss_pred EecCCCcccCCCCceEEEeccccEEEeccCCCCCCCcccceecchhhhhhcccCccccEEEEEEEecCceeEEecCCcee
Q 006263 287 LKPAQKNFNHLKNEWEIFLEATSTVDLCTEEDDSIPKQQFSFRHISEIESAENNSIVDVIGIVISVNPSVPILRKNGMET 366 (653)
Q Consensus 287 V~~a~~~f~~~~~~yei~f~~~T~I~~~~d~~~~iP~~~f~f~~i~~i~~~~~~~~vDVIGvV~~v~~~~~i~~k~g~~~ 366 (653)
++. +..+|+|||+|+.+|.|.+|. +. +.+.|+|++|+||.. +..+||+|+|++++++.+|++++|++.
T Consensus 244 ~r~-----~~~~g~~El~~~~~s~I~~~~-~~---~e~~~~f~~I~dl~~---~~~~dv~G~V~~v~~~~~~~~~~G~~~ 311 (374)
T PRK15491 244 ART-----NNYSQEVEIQIGNHGSLRKTD-RN---VEYEEDFTPIADIIP---GQPYSIKGAVSGLGDLKEFTKSDGSEN 311 (374)
T ss_pred EEE-----eccCCCEEEEeCCCceEEECC-cc---cccCCCccCHHHcCC---CCceeEEEEEEEcCCcEEEEccCCCEe
Confidence 753 345789999999999999994 33 355689999999974 567899999999999999999999999
Q ss_pred eEEEEEEEeCCCCEEEEEEccchhhhhhhhHHHhhccCCCcEEEEEeeEeec-CCC-ceeccccceEEEE
Q 006263 367 QRRILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVDVGFFPVLSVKSGKVND-FSG-KSIGTIPSTQLFI 434 (653)
Q Consensus 367 ~kr~i~l~D~s~~~i~vtLWg~~A~~~~~~l~~~~~~~~~~Vvaik~~rV~~-f~G-~sLs~~~~S~i~i 434 (653)
.+|+|+|.|+|| +|++||||+.|... .. ...+..|.+-++.+++ |+| ..||.+..|+|.+
T Consensus 312 ~~r~i~l~D~Tg-~Ir~tlWg~~a~~~-----~~--~~~g~~i~i~~~~~k~g~~~~~e~s~g~~s~~~~ 373 (374)
T PRK15491 312 KVSNIYVSDDTG-RIRIALWGEKAELV-----DK--LDIDTPIKIIDAFSKSGYNEDVELSAGNRSRVVV 373 (374)
T ss_pred EEEeEEEEeCCC-cEEEEEcccccccc-----cc--cCCCCeEEEEEEEEeecCCCcEEEEeCCcceEEe
Confidence 999999999999 59999999998641 11 1234556677777764 655 6899999999875
No 13
>PRK14699 replication factor A; Provisional
Probab=99.96 E-value=3.9e-28 Score=266.53 Aligned_cols=206 Identities=21% Similarity=0.300 Sum_probs=179.2
Q ss_pred cceeccccCCCCCceEEEEEEEeeccccccccCCC-CceeEEEEEEeCCCCeEEEEEchhHHHHHHhhcccCcEEEEece
Q 006263 207 RIIPIAALNPYQGRWAIKARVTAKGDLRRYNNARG-DGKVFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISKG 285 (653)
Q Consensus 207 ~~~pI~~L~p~~~~w~I~~RV~~k~~ir~~~~~~g-~gk~f~~~L~D~~g~~I~at~f~~~~~kf~~~l~eG~vy~is~~ 285 (653)
+++||++|+|++++|+|+|||+.++++|+|.+.+| +|+++++.|.| ++|+|++|+|++.+ +|++.|++|++..+.++
T Consensus 275 ~~~~I~~L~~~~~~v~I~grV~~~~~~r~~~~~~Gseg~v~~~~l~D-eTG~Ir~T~W~~~a-~~~~~i~~Gd~v~i~~~ 352 (484)
T PRK14699 275 EFTPIEDIKADMNNINISGRVLDISEVRTFEKKDGSPGRVGNLLLGD-STGKIRLTLWDEKT-NFLDEIDFDETVEVLNA 352 (484)
T ss_pred cccCHHHcCCCCceeEEEEEEEEcCCCeEEEcCCCCeeEEEEEEEEC-CCCeEEEEEeCccc-ccccccCCCceEEEEeE
Confidence 57899999999999999999999999999999887 89999999999 67799999999999 88888999999888887
Q ss_pred EEecCCCcccCCCCceEEEeccccEEEeccCCCCCCCcccceecchhhhhhcccCccccEEEEEEEecCceeEEecCCce
Q 006263 286 SLKPAQKNFNHLKNEWEIFLEATSTVDLCTEEDDSIPKQQFSFRHISEIESAENNSIVDVIGIVISVNPSVPILRKNGME 365 (653)
Q Consensus 286 ~V~~a~~~f~~~~~~yei~f~~~T~I~~~~d~~~~iP~~~f~f~~i~~i~~~~~~~~vDVIGvV~~v~~~~~i~~k~g~~ 365 (653)
.+ +|+..+++|||+|+..|.|+++.+ . ..+.++|++|++|. .+..|||+|+|++++++.+|++++|++
T Consensus 353 y~-----~~~~~~~~~eL~~~~~t~I~~~~~-~---~e~~~~~~~I~die---~~~~vdV~G~V~~v~~~~~~~~~~g~~ 420 (484)
T PRK14699 353 YS-----RENTFSQQVELNLGARGIIQKSEK-K---VEYREKFTDIADII---PGESYSVQGKVSEIGELREFEREDGTE 420 (484)
T ss_pred EE-----EeccCCccEEEEecCceeEeecCC-c---ceeeeccccHHHcc---CCCeeEEEEEEEEcCCcceEEecCCCE
Confidence 75 466778899999999999999843 2 25678999999994 677999999999999999999999999
Q ss_pred eeEEEEEEEeCCCCEEEEEEccchhhhhhhhHHHhhccCCCcEEEEEeeEeec-CCC-ceeccccceEEEE
Q 006263 366 TQRRILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVDVGFFPVLSVKSGKVND-FSG-KSIGTIPSTQLFI 434 (653)
Q Consensus 366 ~~kr~i~l~D~s~~~i~vtLWg~~A~~~~~~l~~~~~~~~~~Vvaik~~rV~~-f~G-~sLs~~~~S~i~i 434 (653)
..+|+++|.|.|| +|+|||||+.|..| +.+ ..+.-|.+-++.++. |+| ..||.+.+|+|.+
T Consensus 421 ~~vr~i~l~D~TG-~Ir~tlWg~~A~~~-----~~~--~~~~~v~~~~~~~~~g~~~~~e~s~g~~s~~~~ 483 (484)
T PRK14699 421 NVVANLQLKDETG-SIRLTLWGEQAYVI-----EDL--DIDSEIQIIDAYARYGLNEEIELSVGNRSRVII 483 (484)
T ss_pred EEEEEEEEEcCCC-eEEEEEcchhhhhc-----ccc--CCCCeEEEechhhhhcccccEEEEecCceEEEe
Confidence 9999999999999 99999999998763 112 346677777777764 666 4899999998864
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=99.96 E-value=1.4e-28 Score=217.62 Aligned_cols=104 Identities=61% Similarity=1.062 Sum_probs=101.1
Q ss_pred eccccCCCCCceEEEEEEEeeccccccccCCCCceeEEEEEEeCCCCeEEEEEchhHHHHHHhhcccCcEEEEeceEEec
Q 006263 210 PIAALNPYQGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISKGSLKP 289 (653)
Q Consensus 210 pI~~L~p~~~~w~I~~RV~~k~~ir~~~~~~g~gk~f~~~L~D~~g~~I~at~f~~~~~kf~~~l~eG~vy~is~~~V~~ 289 (653)
||++|+|++.+|+|+|||++||++|.|.+.+++|++|+|+|+|++|++|+|++|++.+++|++.|+||+||+|++|+|++
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 79999999999999999999999999999888999999999998899999999999999999999999999999999999
Q ss_pred CCCcccCCCCceEEEeccccEEEe
Q 006263 290 AQKNFNHLKNEWEIFLEATSTVDL 313 (653)
Q Consensus 290 a~~~f~~~~~~yei~f~~~T~I~~ 313 (653)
|+++|++++|+|||.|+.+|.|++
T Consensus 81 a~~~y~~~~~~yeI~f~~~t~~~~ 104 (104)
T cd04474 81 ANKKFNTLKNDYEITFNRDTSIIE 104 (104)
T ss_pred ccccCCCCCCcEEEEECCCcEEeC
Confidence 999999999999999999998864
No 15
>PRK14699 replication factor A; Provisional
Probab=99.94 E-value=1.5e-23 Score=230.44 Aligned_cols=277 Identities=19% Similarity=0.266 Sum_probs=215.5
Q ss_pred eeccccCCCCCceEEEEEEEeeccccccccCCC-CceeEEEEEEeCCCCeEEEEEchhHHHHHHhhcccCcEEEEeceEE
Q 006263 209 IPIAALNPYQGRWAIKARVTAKGDLRRYNNARG-DGKVFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISKGSL 287 (653)
Q Consensus 209 ~pI~~L~p~~~~w~I~~RV~~k~~ir~~~~~~g-~gk~f~~~L~D~~g~~I~at~f~~~~~kf~~~l~eG~vy~is~~~V 287 (653)
..|++|.|....-+|+|||+.++++|+|...+| +|++++++|.| ++|+|++|+|++.++ +++.|++|++|.|.++.+
T Consensus 167 ~~I~dL~~~~~~V~i~gkVl~~~~~R~f~~~dG~~g~v~~~~igD-eTG~ir~tlW~~~a~-~~~~l~~Gd~v~I~~a~v 244 (484)
T PRK14699 167 QKIKDIKDGMGDLNLTGKVLEISEIRTFQRKDGTSGKVGNLLLGD-ETGTLRVTLWDDKTD-FLNQIEYGDTVELINAYA 244 (484)
T ss_pred cchhhcCCCCCceEEEEEEEeccCceEEecCCCCceEEEEEEEEc-CCceEEEEEECcccc-cccccCCCCEEEEecceE
Confidence 479999999887899999999999999998777 78999999999 899999999999886 888999999999999988
Q ss_pred ecCCCcccCCCCceEEEeccccEEEeccCCCCCCCcccceecchhhhhhcccCccccEEEEEEEecCceeEEecCCceee
Q 006263 288 KPAQKNFNHLKNEWEIFLEATSTVDLCTEEDDSIPKQQFSFRHISEIESAENNSIVDVIGIVISVNPSVPILRKNGMETQ 367 (653)
Q Consensus 288 ~~a~~~f~~~~~~yei~f~~~T~I~~~~d~~~~iP~~~f~f~~i~~i~~~~~~~~vDVIGvV~~v~~~~~i~~k~g~~~~ 367 (653)
+.. .|+ +.++|+++..|.|.... +...++ .+|++|.+|.. ....++|.|.|++++++.++++++|++..
T Consensus 245 r~~--~~~---~~~el~~~~~s~i~~~~-~~~e~~---~~~~~I~~L~~--~~~~v~I~grV~~~~~~r~~~~~~Gseg~ 313 (484)
T PRK14699 245 REN--AFT---QKVELQVGNRSIIRKSE-KKVEYE---EEFTPIEDIKA--DMNNINISGRVLDISEVRTFEKKDGSPGR 313 (484)
T ss_pred eec--ccC---CceEEEecCceEeeccc-cccccc---ccccCHHHcCC--CCceeEEEEEEEEcCCCeEEEcCCCCeeE
Confidence 763 332 68999999999988873 332332 36788888863 45789999999999999999988898999
Q ss_pred EEEEEEEeCCCCEEEEEEccchhhhhhhhHHHhhccCCCcEEEEEeeEee--cCCCc-eeccccceEEEEcCChHHHHHH
Q 006263 368 RRILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVDVGFFPVLSVKSGKVN--DFSGK-SIGTIPSTQLFINPDFAEAHEL 444 (653)
Q Consensus 368 kr~i~l~D~s~~~i~vtLWg~~A~~~~~~l~~~~~~~~~~Vvaik~~rV~--~f~G~-sLs~~~~S~i~inPdipe~~~l 444 (653)
.+++.|.|+|| .|++||||+.|..+ +.+ ..++++-+.++.++ .|++. .|+....|.|...++-.++
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-KIRLTLWDEKTNFL-----DEI--DFDETVEVLNAYSRENTFSQQVELNLGARGIIQKSEKKVEY--- 382 (484)
T ss_pred EEEEEEECCCC-eEEEEEeCcccccc-----ccc--CCCceEEEEeEEEEeccCCccEEEEecCceeEeecCCccee---
Confidence 99999999999 79999999998431 112 24677888888776 45564 7888888877655543211
Q ss_pred HHHHhcCCCccceeecccccccCCCCcchhccHHhhhhcCCCCCCCCcEEEEEEEEEEEeCCceEEecCCCCcCcccccc
Q 006263 445 REWFDSGGKNAATVSISREIAAGGAKNEIHKTVSQIKNEGLGRSEKPDWVTVRAFITFIKSDSFCYTACPLMIGDRQCNK 524 (653)
Q Consensus 445 ~~w~~~~g~~~~~~sls~~~~~~~~~~~~~kti~~i~~~~lg~~~~~~~~~v~atI~~i~~d~~~Y~aC~~~~~~~~C~K 524 (653)
...+..|++|.. ...+.|.|+|..+..-. .
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 013456888832 23578999999886421 0
Q ss_pred eeeecCceeecccCccccCCceEEEEEEEEEEeCCCeEEEEEechhhhhh
Q 006263 525 KVTQSGNRWQCDRCNQEIDECDYRYLLQAQIQDQTGLTWVTAFQESGEEI 574 (653)
Q Consensus 525 Kv~~~~~~~~C~kC~~~~~~~~~rY~l~~~i~D~Tg~~~~~~F~~~ae~l 574 (653)
-... .-.....-++.|.|.||++++++||+.|+++
T Consensus 413 ~~~~---------------~g~~~~vr~i~l~D~TG~Ir~tlWg~~A~~~ 447 (484)
T PRK14699 413 FERE---------------DGTENVVANLQLKDETGSIRLTLWGEQAYVI 447 (484)
T ss_pred EEec---------------CCCEEEEEEEEEEcCCCeEEEEEcchhhhhc
Confidence 0000 1134566789999999999999999999864
No 16
>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=99.93 E-value=8.2e-26 Score=197.81 Aligned_cols=95 Identities=47% Similarity=0.822 Sum_probs=83.2
Q ss_pred CCHHHHHHHhC-CCCCCCCeEEEEEEEEcCC----CCceEEEEEecccceeeeeecccchhhcccCCcccCcEEEEeeeE
Q 006263 5 LTPNSISLING-GDVNSKPLVQVMDIKLIGS----TQERYRFLISDSVSTQHAMLATQLNDRVKTGQVKKGSVVQLIDYI 79 (653)
Q Consensus 5 Lt~Gai~~i~~-~~~~~~pvvQVl~ik~~~~----~~~ryr~~lSDG~~~~~~ml~t~ln~~v~~~~l~~~sIIkl~~y~ 79 (653)
||+|||++|++ ++...+|||||+++|+++. +.+|||++||||.|+++|||+||||+++++|+|++||||||++|.
T Consensus 1 LT~Gai~~I~~~~~~~~~pvlQVl~~k~i~~~~~~~~~RyR~~lSDG~~~~~amLatqln~lv~~g~l~~~siirl~~y~ 80 (101)
T PF04057_consen 1 LTPGAIEAIFSSGDVNDNPVLQVLNIKKINSKQGGGSDRYRLVLSDGVHSIQAMLATQLNHLVESGELQKGSIIRLKQYT 80 (101)
T ss_dssp S-TTHHHHHHHHTSSS--TEEEEEEEEEE----TTS--EEEEEEESSSEEEEEEESGGGHHHHHTTSSSTT-EEEEEEEE
T ss_pred CChHHHHHHHhCCCCCCCcEEEEEeeEEccCCCCCCCceEEEEEEChHHHHHHHhHHHhHHHHhcCCcccCCEEEEeEEE
Confidence 89999999999 6667899999999999953 579999999999999999999999999999999999999999999
Q ss_pred eeeec-CeEEEEEEeeeEeec
Q 006263 80 CSTVQ-NRKIIVVLNMETIIL 99 (653)
Q Consensus 80 ~~~~~-~k~~iii~~~evl~~ 99 (653)
|+.++ +|+++||+++||+.+
T Consensus 81 ~n~v~~~k~iiiil~leVv~~ 101 (101)
T PF04057_consen 81 CNTVKNGKKIIIILDLEVVQS 101 (101)
T ss_dssp EEESTTSSEEEEEEEEEEEE-
T ss_pred EeeccCCCEEEEEEeeEEEeC
Confidence 99999 999999999999863
No 17
>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=99.90 E-value=2.9e-24 Score=186.14 Aligned_cols=91 Identities=41% Similarity=0.744 Sum_probs=85.5
Q ss_pred HHHHHHhCCCC---CCCCeEEEEEEEEcCC---CCceEEEEEecccceeeeeecccchhhcccCCcccCcEEEEeeeEee
Q 006263 8 NSISLINGGDV---NSKPLVQVMDIKLIGS---TQERYRFLISDSVSTQHAMLATQLNDRVKTGQVKKGSVVQLIDYICS 81 (653)
Q Consensus 8 Gai~~i~~~~~---~~~pvvQVl~ik~~~~---~~~ryr~~lSDG~~~~~~ml~t~ln~~v~~~~l~~~sIIkl~~y~~~ 81 (653)
|||++|++++. ...|||||+++|++.. +.+|||++||||.|+++|||+||||+++++|+|++||||||++|.|+
T Consensus 1 Gai~~i~~~~~~~~~~~PvlQv~~ik~i~~~~~~~~RyRi~lSDG~~~~~amLatqln~~v~~g~l~~~sIirl~~y~~~ 80 (97)
T cd04477 1 GALAAIFNGEDRSNVIKPVLQVLNIKKIDSSNGSSERYRILLSDGVYYVQAMLATQLNPLVESGQLQRGSIIRLKRFICN 80 (97)
T ss_pred ChHHHhhcCCCcCCCCCCEEEEEEEEEccCCCCCcceEEEEEEChhHHHHHHHhhhhhhHHhcCCccCCcEEEECeEEEE
Confidence 89999999876 5789999999999962 56899999999999999999999999999999999999999999999
Q ss_pred eecCeEEEEEEeeeEee
Q 006263 82 TVQNRKIIVVLNMETII 98 (653)
Q Consensus 82 ~~~~k~~iii~~~evl~ 98 (653)
.+++|+++||+|+||+.
T Consensus 81 ~i~~k~viiIldlevl~ 97 (97)
T cd04477 81 VIKGKRILIILDLEVVQ 97 (97)
T ss_pred EecCcEEEEEEeeEEeC
Confidence 99999999999999974
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=99.87 E-value=7.3e-22 Score=174.08 Aligned_cols=100 Identities=50% Similarity=0.790 Sum_probs=92.9
Q ss_pred cccEEEEEEEecCceeEEecC-CceeeEEEEEEEeCCCCEEEEEEccchhhhhhhhHHHhhccCCCcEEEEEeeEeecCC
Q 006263 342 IVDVIGIVISVNPSVPILRKN-GMETQRRILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVDVGFFPVLSVKSGKVNDFS 420 (653)
Q Consensus 342 ~vDVIGvV~~v~~~~~i~~k~-g~~~~kr~i~l~D~s~~~i~vtLWg~~A~~~~~~l~~~~~~~~~~Vvaik~~rV~~f~ 420 (653)
+|||+|+|++++++++|++|+ |++..+|+|+|.|+|+.++.|||||+.|..+ ....++||+|+++||++|+
T Consensus 1 ~vDvig~V~~v~~~~~i~~k~~g~~~~~r~v~i~D~t~~~i~vtLWg~~a~~~--------~~~~~~vv~~~~~~i~~~~ 72 (101)
T cd04475 1 IVDVIGVVKSVGPVTTITTKSTGRELDKREITLVDESGHSVELTLWGEQAELF--------DGSENPVIAIKGVKVSEFN 72 (101)
T ss_pred CEeEEEEEeEccCcEEEEEecCCCceeEEEEEEEeCCCCEEEEEEEHHHhhhc--------ccCCCCEEEEEeeEEEecC
Confidence 589999999999999999997 9999999999999999999999999998774 2223899999999999999
Q ss_pred CceeccccceEEEEcCChHHHHHHHHHHh
Q 006263 421 GKSIGTIPSTQLFINPDFAEAHELREWFD 449 (653)
Q Consensus 421 G~sLs~~~~S~i~inPdipe~~~l~~w~~ 449 (653)
|++|+++.+|+|++||++||+.+|+.||.
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=99.83 E-value=4.9e-20 Score=163.85 Aligned_cols=101 Identities=27% Similarity=0.500 Sum_probs=91.0
Q ss_pred cEEEEEEEecCceeEEecCCceeeEEEEEEEeCCCCEEEEEEccchhhhhhhhHHHhhccCCCcEEEEE-eeEeecCCC-
Q 006263 344 DVIGIVISVNPSVPILRKNGMETQRRILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVDVGFFPVLSVK-SGKVNDFSG- 421 (653)
Q Consensus 344 DVIGvV~~v~~~~~i~~k~g~~~~kr~i~l~D~s~~~i~vtLWg~~A~~~~~~l~~~~~~~~~~Vvaik-~~rV~~f~G- 421 (653)
||||+|++|++++++..+ |++..||+|+|+|.++.++.|||||++|.+|...+.. ....+||||+. ++||++|+|
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 899999999999999988 8899999999999999999999999999998766543 24578999975 599999997
Q ss_pred ceeccc-cceEEEEcCChHHHHHHHHH
Q 006263 422 KSIGTI-PSTQLFINPDFAEAHELREW 447 (653)
Q Consensus 422 ~sLs~~-~~S~i~inPdipe~~~l~~w 447 (653)
++||+. ++|++++||++||+.+|+..
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=99.78 E-value=5.8e-19 Score=150.85 Aligned_cols=86 Identities=21% Similarity=0.340 Sum_probs=80.6
Q ss_pred EEEEEEEeeccccccccCCCCceeEEEEEEeCCCCeEEEEEchhHHHHHHhhcccCcEEEEeceEEecCCCcccCCCCce
Q 006263 222 AIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISKGSLKPAQKNFNHLKNEW 301 (653)
Q Consensus 222 ~I~~RV~~k~~ir~~~~~~g~gk~f~~~L~D~~g~~I~at~f~~~~~kf~~~l~eG~vy~is~~~V~~a~~~f~~~~~~y 301 (653)
+|+|||+|+|+.+... +|+.++|+|+|++|++|+|++|++.+++|+++|+||+||+|++|.|.+++++|+.++|+|
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 4899999999976532 689999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEeccccEE
Q 006263 302 EIFLEATSTV 311 (653)
Q Consensus 302 ei~f~~~T~I 311 (653)
+|.|..+|+|
T Consensus 77 ~I~f~~~T~V 86 (86)
T cd04480 77 KIKFMSDTVV 86 (86)
T ss_pred EEEeecCcCC
Confidence 9999998865
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=99.68 E-value=1.8e-16 Score=138.03 Aligned_cols=87 Identities=23% Similarity=0.391 Sum_probs=80.6
Q ss_pred EEEEEeCCCCeEEEEEchhHHHHHHhhcccCcEEEEeceEEecCCCcccCCCCceEEEeccccEEEeccCCCCCCCcccc
Q 006263 247 SFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISKGSLKPAQKNFNHLKNEWEIFLEATSTVDLCTEEDDSIPKQQF 326 (653)
Q Consensus 247 ~~~L~D~~g~~I~at~f~~~~~kf~~~l~eG~vy~is~~~V~~a~~~f~~~~~~yei~f~~~T~I~~~~d~~~~iP~~~f 326 (653)
+|+|+|++|+.|+|+++++.+++|.+.|+||+||.|++|.|.++.+.|++++|+|+|.|..+|.|+++. .....+ .|
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 EMVLVDEKGDKIQATIPKELVDKFKDSLKEGSWYTISNFTVSPNSGSYRPTDHKYKINFMPNTKVTEID-PPSDPP--FF 77 (95)
T ss_pred CEEEEecCCCEEEEEECHHHHHHHHhhcccCCEEEeEeEEEEeCCCceeccCCCEEEEECCcCeEEECC-CCCCCc--eE
Confidence 489999999999999999999999999999999999999999999999999999999999999999994 333333 89
Q ss_pred eecchhhhhh
Q 006263 327 SFRHISEIES 336 (653)
Q Consensus 327 ~f~~i~~i~~ 336 (653)
+|++|++|.+
T Consensus 78 ~f~~F~~I~~ 87 (95)
T PF02721_consen 78 NFTPFDEILE 87 (95)
T ss_pred eecCHHHHhc
Confidence 9999999986
No 22
>PRK08402 replication factor A; Reviewed
Probab=99.59 E-value=4.6e-14 Score=149.84 Aligned_cols=177 Identities=25% Similarity=0.393 Sum_probs=141.3
Q ss_pred cceeccccCCCCCceEEEEEEEeeccccccccCCC-CceeEEEEEEeCCCCeEEEEEchhHHHHHHhhcccCcEEEEece
Q 006263 207 RIIPIAALNPYQGRWAIKARVTAKGDLRRYNNARG-DGKVFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISKG 285 (653)
Q Consensus 207 ~~~pI~~L~p~~~~w~I~~RV~~k~~ir~~~~~~g-~gk~f~~~L~D~~g~~I~at~f~~~~~kf~~~l~eG~vy~is~~ 285 (653)
++.+|++|.|+...|++.|||+.+++.|+|....| .|++.+++|.| ++|+|+.|+|++.++++++.|++|+|+.|.++
T Consensus 61 ~~~kI~dl~~g~~~V~v~~rVl~~~~~r~f~rrdG~~~~V~~i~l~D-eTG~ir~TlW~~~a~~~~~~l~~Gdvi~I~~a 139 (355)
T PRK08402 61 PLMHISDLVPGMRGVNIVGRVLRKYPPREYTKKDGSTGRVASLIIYD-DTGRARVVLWDAKVAKYYNKINVGDVIKVIDA 139 (355)
T ss_pred CccCHHHccCCCceeeEEEEEEEccCCceeeccCCCcceEEEEEEEc-CCCeEEEEEechhhhhhcccCCCCCEEEEECC
Confidence 57899999999999999999999999999987655 57899999999 89999999999999999999999999999999
Q ss_pred EEecCCCcccCCCCceEEEeccccEEEeccCCC--CCCCcc------cceecchhhhhhcccCccccEEEEEEEecCcee
Q 006263 286 SLKPAQKNFNHLKNEWEIFLEATSTVDLCTEED--DSIPKQ------QFSFRHISEIESAENNSIVDVIGIVISVNPSVP 357 (653)
Q Consensus 286 ~V~~a~~~f~~~~~~yei~f~~~T~I~~~~d~~--~~iP~~------~f~f~~i~~i~~~~~~~~vDVIGvV~~v~~~~~ 357 (653)
.|+... ...++|.+...|+|...++.+ ..+|.+ .+.+.+|++|.. .+..+.|.|.|+++.+-.-
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 997642 234799999999999886533 234543 367888888865 3456999999999998211
Q ss_pred ----------EEec----------CCc-e---eeEEEEEEEeCCCCEEEEEEccchhhhh
Q 006263 358 ----------ILRK----------NGM-E---TQRRILNLKDTSGRSVELTLWGDFCNKE 393 (653)
Q Consensus 358 ----------i~~k----------~g~-~---~~kr~i~l~D~s~~~i~vtLWg~~A~~~ 393 (653)
+... -|. + .-...+.|.|.|| .++||||++.|...
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 1100 021 1 1233678899999 89999999999774
No 23
>PRK07217 replication factor A; Reviewed
Probab=99.56 E-value=4.1e-13 Score=137.59 Aligned_cols=222 Identities=16% Similarity=0.197 Sum_probs=164.0
Q ss_pred ecchhhhhhcccCccccEEEEEEEecCceeEEecCCceeeEEEEEEEeCCCCEEEEEEccchhhhhhhhHHHhhccCCCc
Q 006263 328 FRHISEIESAENNSIVDVIGIVISVNPSVPILRKNGMETQRRILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVDVGFFP 407 (653)
Q Consensus 328 f~~i~~i~~~~~~~~vDVIGvV~~v~~~~~i~~k~g~~~~kr~i~l~D~s~~~i~vtLWg~~A~~~~~~l~~~~~~~~~~ 407 (653)
.++|.||.. .+.-|+|.|.|..+.+.. .+.. .+.=.|.|+|| +|++|+|++.... .-..+.
T Consensus 72 ~~kI~Di~~--~~~~VsV~aKVl~l~e~~-----~~si--~qvGllgDETG-~IkfT~W~~s~~~---------~leeGd 132 (311)
T PRK07217 72 LVNIADIDE--PEQWVDVTAKVVQLWEPS-----SDSI--AQVGLLGDETG-TIKFTKWAKSDLP---------ELEEGK 132 (311)
T ss_pred ceeeeecCC--CCCcEEEEEEEEEecCCC-----CCce--EEEEEEEcCCc-eEEEEEccCCCCC---------cccCCC
Confidence 455666643 466899999999999853 2222 22236999999 8999999974211 113689
Q ss_pred EEEEEeeEeecCCCc-eeccccceEEEEcCChHHHHHHHHHHhcCCCccceeecccccccCCCCcchhccHHhhhhcCCC
Q 006263 408 VLSVKSGKVNDFSGK-SIGTIPSTQLFINPDFAEAHELREWFDSGGKNAATVSISREIAAGGAKNEIHKTVSQIKNEGLG 486 (653)
Q Consensus 408 Vvaik~~rV~~f~G~-sLs~~~~S~i~inPdipe~~~l~~w~~~~g~~~~~~sls~~~~~~~~~~~~~kti~~i~~~~lg 486 (653)
++-|.++.+++|+|+ +|+.+..|+|...++.=+ +.+
T Consensus 133 ~~rI~na~v~ey~G~~~lnlg~~t~I~~~de~Ie---------------------------------------V~~---- 169 (311)
T PRK07217 133 SYLLKNVVTDEYQGRFSVKLNRTTSIEELDEDIE---------------------------------------VGD---- 169 (311)
T ss_pred EEEEEeEEEeeECCEEEEEeCCceEEEeCCCCcc---------------------------------------ccC----
Confidence 999999999999997 899888888876553100 000
Q ss_pred CCCCCcEEEEEEEEEEEeCCceEEecCCCCcCcccccceeeecCceeecccCccccCCceEEEEEEEEEEeCCCeEEEEE
Q 006263 487 RSEKPDWVTVRAFITFIKSDSFCYTACPLMIGDRQCNKKVTQSGNRWQCDRCNQEIDECDYRYLLQAQIQDQTGLTWVTA 566 (653)
Q Consensus 487 ~~~~~~~~~v~atI~~i~~d~~~Y~aC~~~~~~~~C~KKv~~~~~~~~C~kC~~~~~~~~~rY~l~~~i~D~Tg~~~~~~ 566 (653)
+-..+.|.|+.|...+-...-||.+ .|+|.+. .+.|+.|++. .+.+-.++.+.+.|+||.+.+.+
T Consensus 170 -----~~vei~G~lVdi~~GsglI~rCP~~----~C~Rvl~----~g~C~~HG~v--e~~~DLrik~vlDDGt~~~~~~~ 234 (311)
T PRK07217 170 -----DEVEVEGALVDIQSGSGLIKRCPEE----DCTRVLQ----NGRCSEHGKV--EGEFDLRIKGVLDDGEEVQEVIF 234 (311)
T ss_pred -----ccccceeEEEEEeCCCCCeecCCcc----ccCcccc----CCCCCCCCCc--CCceeeEEEEEEECCCCeEEEEE
Confidence 0134788999999888788899954 5999994 4799999975 67888999999999999999999
Q ss_pred echhhhhhhCCCHHHHHHHhhccCChhHHHH-HHHHhcCceEEEEEEEeeeccCceeeEEEEEEEeecC
Q 006263 567 FQESGEEILGCPAKELYMLKYELQDDVRFGE-IIRSRVFNQYLFRLKIKEELYGDEQRVKITVIRADQV 634 (653)
Q Consensus 567 F~~~ae~llG~sA~el~~~~~e~~d~~~~~~-~~~~~~~k~~~f~v~~k~~~y~~e~r~~~~v~~~~~v 634 (653)
-.+..++|.|++-+|+.+|..+--|.....+ +=+.++|+.|.|+... | | ..+-+..+++.
T Consensus 235 ~~e~te~l~G~~l~eak~~a~dald~~vv~~~i~~~llGr~~~v~G~~----~-g---~~l~~~~~~~~ 295 (311)
T PRK07217 235 NREATEELTGITLEEAKQMAMDALDTGVVLDELKEKLLGRYYRVTGPT----L-G---RYLLADSVEPL 295 (311)
T ss_pred ChHHhHHHhCCCHHHHHHHHHHhhchhhHHHHHHHhhcCceEEEEecc----C-C---cEEEeeEeecc
Confidence 9999999999999999998742233333333 3357999999998854 2 2 24455555554
No 24
>KOG0851 consensus Single-stranded DNA-binding replication protein A (RPA), large (70 kD) subunit and related ssDNA-binding proteins [Replication, recombination and repair]
Probab=99.26 E-value=7.9e-11 Score=120.32 Aligned_cols=213 Identities=16% Similarity=0.200 Sum_probs=160.1
Q ss_pred cceeccccCCCCCceEEEEEEEeeccccccccCCCCceeEEEEEEeCCCCeEEEEEchhHHHHHHhhcccCcEEEEeceE
Q 006263 207 RIIPIAALNPYQGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISKGS 286 (653)
Q Consensus 207 ~~~pI~~L~p~~~~w~I~~RV~~k~~ir~~~~~~g~gk~f~~~L~D~~g~~I~at~f~~~~~kf~~~l~eG~vy~is~~~ 286 (653)
.+++|.+|+|+.+.|+|+++|++.|+.. .+.. |..+.|.|.|+.|.+|+|++......+|.+.|.+|+|+.|..|.
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 GFHRLRDLSPSITGWRIQVKVLRVWKKY--SNPN--GEELRLVLADEHGVKIEATVGRRLSSKYEDNLIENEWKIITTFG 78 (246)
T ss_pred cccchhhcCcCceeeEEEEEEEEEEEec--CCCC--ccEEEEEEEecCCcEEEEEcchHHHhhhhhheecceeEEeeeee
Confidence 4678999999999999999999998743 3332 67899999999999999999999999999999999999999999
Q ss_pred EecCCCcccCCCCceEEEeccccEEEeccCCCCCCCcc-cceecchhhhhh--cccCccccEEE-EEEEecCceeEEecC
Q 006263 287 LKPAQKNFNHLKNEWEIFLEATSTVDLCTEEDDSIPKQ-QFSFRHISEIES--AENNSIVDVIG-IVISVNPSVPILRKN 362 (653)
Q Consensus 287 V~~a~~~f~~~~~~yei~f~~~T~I~~~~d~~~~iP~~-~f~f~~i~~i~~--~~~~~~vDVIG-vV~~v~~~~~i~~k~ 362 (653)
|.++...++.+.|+|++.|...+.+..... ..|-. ..+|.++..+.+ .....++|++| .|..|+.+.. +...
T Consensus 79 v~~~~~~~~~~~~~~~i~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~v~~~~~~~~~v~~~~~~~~~v~~~~~-~~~~ 154 (246)
T KOG0851|consen 79 VNPNSGQVRATTHSFKINFMDFTVVTSSDT---RLPCTPWGKFTPFDSIVEDKSDKRVLVDLIGVAVYDVSQLTV-TPAI 154 (246)
T ss_pred ecccccceeeeeeEEEEEeccceeeccCCC---CccceeccccchhhhhhccccCCcEEEEeeceeEEEeeeeEe-cccc
Confidence 999999999999999999988887776522 23322 457777755554 34677999999 6666665532 1124
Q ss_pred CceeeEEEEEEEeCCCCEEEEEEccchhhhhhhhHHHhhccCCCcEEEEEeeEeecCCCceeccccceEEEEcCChHHHH
Q 006263 363 GMETQRRILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVDVGFFPVLSVKSGKVNDFSGKSIGTIPSTQLFINPDFAEAH 442 (653)
Q Consensus 363 g~~~~kr~i~l~D~s~~~i~vtLWg~~A~~~~~~l~~~~~~~~~~Vvaik~~rV~~f~G~sLs~~~~S~i~inPdipe~~ 442 (653)
+.....+.+...+.++ |+. .. .-.+.+.++..+.+| +++ ...+.+.+..+|+ +.
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 5667788888888776 111 11 113334567777778 556 7777788888887 55
Q ss_pred HHHHHHhcCCC
Q 006263 443 ELREWFDSGGK 453 (653)
Q Consensus 443 ~l~~w~~~~g~ 453 (653)
.++.|....|.
T Consensus 209 ~~~~~~~~~G~ 219 (246)
T KOG0851|consen 209 FWKIWRYFDGK 219 (246)
T ss_pred eecccccccCC
Confidence 66666666653
No 25
>COG1599 RFA1 Single-stranded DNA-binding replication protein A (RPA), large (70 kD) subunit and related ssDNA-binding proteins [DNA replication, recombination, and repair]
Probab=99.25 E-value=4.5e-11 Score=131.09 Aligned_cols=245 Identities=28% Similarity=0.380 Sum_probs=177.4
Q ss_pred CCCcceeccccCCCCCceEEEEEEEeeccccccccCCCCceeEEEEEEeCCCCeEEEEEchhHHHHHHhhcccCcEEEEe
Q 006263 204 APARIIPIAALNPYQGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLIS 283 (653)
Q Consensus 204 ~~~~~~pI~~L~p~~~~w~I~~RV~~k~~ir~~~~~~g~gk~f~~~L~D~~g~~I~at~f~~~~~kf~~~l~eG~vy~is 283 (653)
....+.++..+.||. ++||+.+.++|+|.+.+|++++|+..|.|++.+.+..+.|.+. ++|++|.+.
T Consensus 158 ~~~~i~~~~~~~~~~-----~~~v~~g~~ik~~~~~~ge~~~~~~~~~d~~~~~~~~~~~~~~--------~~g~~~~ie 224 (407)
T COG1599 158 DAREIGEESLLSPYQ-----KARVVVGSEIKTFDNQGGESKVFSNELEDEERGVIVFTDWDPS--------QDGDVYRIE 224 (407)
T ss_pred cccccccccccCccc-----eEEEEecccceeEecCCCccceEeeeecccceeEEEeccCccc--------ccceeeeec
Confidence 445677889999988 9999999999999999999999999999966344444444442 999999999
Q ss_pred ceEEecCCCcccCCCCceEEEeccc--cEEEeccCCCCCCCcccceecchhhhhhcccCccccEEEEEEEecCceeEEec
Q 006263 284 KGSLKPAQKNFNHLKNEWEIFLEAT--STVDLCTEEDDSIPKQQFSFRHISEIESAENNSIVDVIGIVISVNPSVPILRK 361 (653)
Q Consensus 284 ~~~V~~a~~~f~~~~~~yei~f~~~--T~I~~~~d~~~~iP~~~f~f~~i~~i~~~~~~~~vDVIGvV~~v~~~~~i~~k 361 (653)
+.+|+..++++... +.+++.+... +.|..+. ....+|...+. ++..++ .+..+| |+.+.+...+..+
T Consensus 225 ~~~v~~~~~~~~~~-~~~e~~~~~~~~~~i~~~~-~~~~~~~~~~~-~~~~~~----~~~~v~----v~~~~~c~~~~~~ 293 (407)
T COG1599 225 GARVKTKNKQPEEN-LAEELVLRVEVRVAIEKAE-REEFVDEVKES-VSLVEA----DGAVVD----VTRVPECERVVRK 293 (407)
T ss_pred CcEEEEeccccccc-ccceEEEeecceeeccCCC-Cccccceeecc-ccccee----ccceEE----EEECCCceEEEeC
Confidence 99999999998887 9999999887 5555553 22334433332 332222 223333 7778777777666
Q ss_pred CCceeeEEEEEEEeCCCCEEEEEEccchhhhhhhhHHHhhccCCCcEEEEEeeEeecCCCceeccccceEEEEcCChHHH
Q 006263 362 NGMETQRRILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVDVGFFPVLSVKSGKVNDFSGKSIGTIPSTQLFINPDFAEA 441 (653)
Q Consensus 362 ~g~~~~kr~i~l~D~s~~~i~vtLWg~~A~~~~~~l~~~~~~~~~~Vvaik~~rV~~f~G~sLs~~~~S~i~inPdipe~ 441 (653)
.+.....+++.|.|.+| .++|+|||+-+.. .+ +.+++.++++.++.++.|+.+++ .++++
T Consensus 294 ~~~~~~~~~~~l~D~~g-~~rv~~~~~~~e~-------~~--~~~~~~~~~~~~~~~~~~~~~~~----------~~~~~ 353 (407)
T COG1599 294 GGCKGHGKDIGLDDLTG-KIRVTLWGDATEV-------LI--NEESVEALKGINVEDASGIALSA----------LDTEA 353 (407)
T ss_pred CCcccccccceEecCce-EEEEecCCCceEE-------Ee--cccchhheeeeeeeeccchhhhh----------hhhhh
Confidence 66667889999999988 8999999974322 12 35788889999999999987765 57888
Q ss_pred HHHHHHHhcCCCccceeecccccccCCCCcchhccHHhhhhcCCCCCCCCcEEEEEEEEEEEeCC
Q 006263 442 HELREWFDSGGKNAATVSISREIAAGGAKNEIHKTVSQIKNEGLGRSEKPDWVTVRAFITFIKSD 506 (653)
Q Consensus 442 ~~l~~w~~~~g~~~~~~sls~~~~~~~~~~~~~kti~~i~~~~lg~~~~~~~~~v~atI~~i~~d 506 (653)
..+..||...|+...+... ....+. +. +.+..+.+.+++.+.+.|..++.+
T Consensus 354 ~a~~~~~~~~Gk~~~v~g~---------~~~~~~-~~----~~~~~~~~~~~~~~~~~i~~~~~~ 404 (407)
T COG1599 354 VALEIWYDILGKYLRVTGD---------AREDRY-LI----ENLVESSTWDDVDVRAEIEALKEE 404 (407)
T ss_pred hhhhcchhcccceEEeecc---------ccchhh-hh----hhhccccccCccchhheeeeeccc
Confidence 9999999998887655321 011121 11 122334566778888888887754
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=99.11 E-value=4.3e-10 Score=104.74 Aligned_cols=88 Identities=22% Similarity=0.366 Sum_probs=74.1
Q ss_pred ceecchhhhhhcccCccccEEEEEEEecCceeEEecCCceeeEEEEEEEeCCC---CEEEEEEccchhhhhhhhHHHhhc
Q 006263 326 FSFRHISEIESAENNSIVDVIGIVISVNPSVPILRKNGMETQRRILNLKDTSG---RSVELTLWGDFCNKEGQKLQEMVD 402 (653)
Q Consensus 326 f~f~~i~~i~~~~~~~~vDVIGvV~~v~~~~~i~~k~g~~~~kr~i~l~D~s~---~~i~vtLWg~~A~~~~~~l~~~~~ 402 (653)
|+|++|++|.+ ..+..|||||+|+++++... ..|+. .++.|+|.|.|+ ..|.|+||++.++.+ ..
T Consensus 1 ~~f~~i~~~~~-~~~~~v~vigVV~~~~~p~~---s~g~d-~~~tl~i~D~S~~~~~~l~v~~F~~~~~~L----P~--- 68 (138)
T cd04497 1 YKYTPLSSALK-ESGGSVNVIGVVVDAGPPVR---SKGTD-YCCTLTITDPSLANSDGLTVKLFRPNEESL----PI--- 68 (138)
T ss_pred CceEeHHHHHh-ccCCeEEEEEEEeecCCCcc---cCCCc-EEEEEEEECCCCCCCCcEEEEEECCChhhC----CC---
Confidence 57999999987 57899999999999999754 23554 899999999998 899999999997663 21
Q ss_pred cCCCcEEEEEeeEeecCCCceec
Q 006263 403 VGFFPVLSVKSGKVNDFSGKSIG 425 (653)
Q Consensus 403 ~~~~~Vvaik~~rV~~f~G~sLs 425 (653)
...|+||+|++++|..|+|+.+.
T Consensus 69 v~~GDVIll~~~kv~~~~g~~~~ 91 (138)
T cd04497 69 VKVGDIILLRRVKIQSYNGKPQG 91 (138)
T ss_pred CCCCCEEEEEEEEEEEECCceEE
Confidence 24789999999999999998654
No 27
>PRK07218 replication factor A; Provisional
Probab=99.08 E-value=3.7e-09 Score=114.87 Aligned_cols=169 Identities=21% Similarity=0.237 Sum_probs=132.8
Q ss_pred ceeccccCCCCCceEEEEEEEeeccccccccCCCCceeEEEEEEeCCCCeEEEEEchhHHHHHHhhcccCcEEEEeceEE
Q 006263 208 IIPIAALNPYQGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISKGSL 287 (653)
Q Consensus 208 ~~pI~~L~p~~~~w~I~~RV~~k~~ir~~~~~~g~gk~f~~~L~D~~g~~I~at~f~~~~~kf~~~l~eG~vy~is~~~V 287 (653)
..+|.+|.|....-+|.|||+..|+ |+|...+|++.+.+..|-| ++|.|+.|.|++.. .|++|++|.|.++.+
T Consensus 162 ~~kI~DL~~g~~~V~v~g~Vl~~~~-r~f~~~dg~~~v~~giigD-eTG~Ir~tlW~~~~-----~l~~Gd~v~I~na~v 234 (423)
T PRK07218 162 DKKLIDLGPGDRGVNVEARVLELEH-REIDGRDGETTILSGVLAD-ETGRLPFTDWDPLP-----EIEIGASIRIEDAYV 234 (423)
T ss_pred ccchhhccCCCCceEEEEEEEEecc-eeEEcCCCCeEEEEEEEEC-CCceEEEEEecccc-----cCCCCCEEEEeeeEE
Confidence 4579999999887899999999986 8999888888899999999 89999999999853 489999999999999
Q ss_pred ecCCCcccCCCCceEEEeccccEEEeccCCCCCCCcccceecchhhhhhcccCccccEEEEEEEecCceeEEec------
Q 006263 288 KPAQKNFNHLKNEWEIFLEATSTVDLCTEEDDSIPKQQFSFRHISEIESAENNSIVDVIGIVISVNPSVPILRK------ 361 (653)
Q Consensus 288 ~~a~~~f~~~~~~yei~f~~~T~I~~~~d~~~~iP~~~f~f~~i~~i~~~~~~~~vDVIGvV~~v~~~~~i~~k------ 361 (653)
+..+ ..++|.+++.|.|+..+ ++..++. .+.-++|.++.+-.....|.|.|.|++|.+-.-+..+
T Consensus 235 ~e~~-------G~~elnv~~~t~I~~~d-~~i~v~~-~~~~~~I~e~~~~~g~~~Vev~G~Iv~i~~gsgli~rCP~C~r 305 (423)
T PRK07218 235 REFR-------GVPSVNVSEFTTVEALD-REVSVSK-DPPRLKIREAVERGGIFDVELVGNIISVRDGSGLIERCPECGR 305 (423)
T ss_pred eccC-------CeEEEEECCceEEEECC-CCccccC-CccccchhhhhccCCcceEEEEEEEEEeccCCcceecCcCccc
Confidence 7643 35899999999999984 3333433 2455778887764333348999999999987432211
Q ss_pred -------------CCceeeEEEEEEEeCCCCEEEEEEccchhhhh
Q 006263 362 -------------NGMETQRRILNLKDTSGRSVELTLWGDFCNKE 393 (653)
Q Consensus 362 -------------~g~~~~kr~i~l~D~s~~~i~vtLWg~~A~~~ 393 (653)
.+....+..+.|-|.+| ++.|+|.++.+...
T Consensus 306 ~v~~~~C~~hG~ve~~~dlrik~vLDDGtg-~~~~~~~~e~~e~l 349 (423)
T PRK07218 306 VIQKGQCRSHGAVEGEDDLRIKAILDDGTG-SVTVILDRELTEIV 349 (423)
T ss_pred cccCCcCCCCCCcCCeeeeEEEEEEECCCC-eEEEEEChhhhHhH
Confidence 23334566788888888 89999999988763
No 28
>PRK06386 replication factor A; Reviewed
Probab=99.06 E-value=8e-09 Score=109.56 Aligned_cols=163 Identities=18% Similarity=0.191 Sum_probs=123.8
Q ss_pred cceeccccCCCCCceEEEEEEEeeccccccccCCCCceeEEEEEEeCCCCeEEEEEchhHHHHHHhhcccCcEEEEeceE
Q 006263 207 RIIPIAALNPYQGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISKGS 286 (653)
Q Consensus 207 ~~~pI~~L~p~~~~w~I~~RV~~k~~ir~~~~~~g~gk~f~~~L~D~~g~~I~at~f~~~~~kf~~~l~eG~vy~is~~~ 286 (653)
+.++|++|.|....-+|.|||+..|. |.|....+.|++.++.|-| ++|+|+.|.|++ .|++|++|.|.|+.
T Consensus 106 ~~~KI~DL~~g~~~v~V~akVle~~e-~e~~~~g~~~~v~sg~lgD-eTGrIr~TlW~~-------~l~eGd~v~i~na~ 176 (358)
T PRK06386 106 KLVKIRDLSLVTPYVSVIGKITGITK-KEYDSDGTSKIVYQGYIED-DTARVRISSFGK-------PLEDNRFVRIENAR 176 (358)
T ss_pred CccEeEeccCCCCceEEEEEEEEccC-ceEecCCCccEEEEEEEEc-CCCeEEEEEccc-------cccCCCEEEEeeeE
Confidence 35699999999866689999999988 7888555568999999999 899999999986 38999999999998
Q ss_pred EecCCCcccCCCCceEEEeccccEEEeccCCCCCCCcccceecchhhhhhcccCccccEEEEEEEecC-ceeEEe-----
Q 006263 287 LKPAQKNFNHLKNEWEIFLEATSTVDLCTEEDDSIPKQQFSFRHISEIESAENNSIVDVIGIVISVNP-SVPILR----- 360 (653)
Q Consensus 287 V~~a~~~f~~~~~~yei~f~~~T~I~~~~d~~~~iP~~~f~f~~i~~i~~~~~~~~vDVIGvV~~v~~-~~~i~~----- 360 (653)
+...+ ..++|.++..|.|++.+ ++ |. ..-.+.+|.||.+. +..+-+.|.|++|.+ ..-|.+
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-------GYIEISVGNKSVIKEVE-SD--IN-LESRNIFIFEIKSP--VGGITIMGFIVSVGQGSRIFTKCSVCN 243 (358)
T ss_pred EEccC-------CeEEEEeCCeEEEEECC-CC--cc-cCccccchhhhhcc--CCeEEEEEEEEEEcCCcEeEecCcCCC
Confidence 76653 35899999999999984 32 33 33357888888763 234888899999886 222221
Q ss_pred ----c---------CCceeeEEEEEEEeCCCCEEEEEEccchhhh
Q 006263 361 ----K---------NGMETQRRILNLKDTSGRSVELTLWGDFCNK 392 (653)
Q Consensus 361 ----k---------~g~~~~kr~i~l~D~s~~~i~vtLWg~~A~~ 392 (653)
+ .+....+-.+.|-|.+| .++|+|.++.+.+
T Consensus 244 R~l~~g~C~~HG~v~~~~dlr~k~vLDDGtg-~~~~~l~~e~~e~ 287 (358)
T PRK06386 244 KIIEDGVCKDHPDAPVYLDIFGYFTISDGTG-FVTCYANKDSFLP 287 (358)
T ss_pred eEccCCcCCCCCCCCCeeEEEEEEEEECCCC-eEEEEEChHHhHH
Confidence 1 11222333367777777 8999999999876
No 29
>cd04491 SoSSB_OBF SoSSB_OBF: A subfamily of OB folds similar to the OB fold of the crenarchaeote Sulfolobus solfataricus single-stranded (ss) DNA-binding protein (SSoSSB). SSoSSB has a single OB fold, and it physically and functionally interacts with RNA polymerase. In vitro, SSoSSB can substitute for the basal transcription factor TBP, stimulating transcription from promoters under conditions in which TBP is limiting, and supporting transcription when TBP is absent. SSoSSB selectively melts the duplex DNA of promoter sequences. It also relieves transcriptional repression by the chromatin Alba. In addition, SSoSSB activates reverse gyrase activity, which involves DNA binding, DNA cleavage, strand passage and ligation. SSoSSB stimulates all these steps in the presence of the chromatin protein, Sul7d. SSoSSB antagonizes the inhibitory effect of Sul7d on reverse gyrase supercoiling activity. It also physically and functionally interacts with Mini-chromosome Maintenance (MCM), stimulating
Probab=98.86 E-value=1.5e-08 Score=85.64 Aligned_cols=81 Identities=21% Similarity=0.312 Sum_probs=70.5
Q ss_pred EEEEEEEeeccccccccCCCCceeEEEEEEeCCCCeEEEEEchhHHHHHHhhcccCcEEEEeceEEecCCCcccCCCCce
Q 006263 222 AIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISKGSLKPAQKNFNHLKNEW 301 (653)
Q Consensus 222 ~I~~RV~~k~~ir~~~~~~g~gk~f~~~L~D~~g~~I~at~f~~~~~kf~~~l~eG~vy~is~~~V~~a~~~f~~~~~~y 301 (653)
+|.|||+.+++.|+|.+.+++++++++.|.| ++|.|++++|++.+ .+.|++|++|.|.++.++..+ +.+
T Consensus 1 ~v~~~V~~~~~~~~~~~~g~~~~~~~~~l~D-~TG~i~~~~W~~~~---~~~~~~G~vv~i~~~~v~~~~-------g~~ 69 (82)
T cd04491 1 SVEGKVLSISEPREFTRDGSEGKVQSGLVGD-ETGTIRFTLWDEKA---ADDLEPGDVVRIENAYVREFN-------GRL 69 (82)
T ss_pred CEEEEEEEccCCeEeccCCCeeEEEEEEEEC-CCCEEEEEEECchh---cccCCCCCEEEEEeEEEEecC-------CcE
Confidence 4899999999999998444578999999999 67799999999876 788999999999999987654 569
Q ss_pred EEEeccccEEEe
Q 006263 302 EIFLEATSTVDL 313 (653)
Q Consensus 302 ei~f~~~T~I~~ 313 (653)
+|.++..|.|+.
T Consensus 70 ql~i~~~~~i~~ 81 (82)
T cd04491 70 ELSVGKNSEIEK 81 (82)
T ss_pred EEEeCCceEEEE
Confidence 999999998875
No 30
>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=98.86 E-value=2.8e-08 Score=84.01 Aligned_cols=80 Identities=19% Similarity=0.337 Sum_probs=69.3
Q ss_pred cEEEEEEEecCceeEEecCCceeeEEEEEEEeCCCCEEEEEEccchhhhhhhhHHHhhccCCCcEEEEEeeEeecCCCc-
Q 006263 344 DVIGIVISVNPSVPILRKNGMETQRRILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVDVGFFPVLSVKSGKVNDFSGK- 422 (653)
Q Consensus 344 DVIGvV~~v~~~~~i~~k~g~~~~kr~i~l~D~s~~~i~vtLWg~~A~~~~~~l~~~~~~~~~~Vvaik~~rV~~f~G~- 422 (653)
+|+|.|+++++..+++ ++|++...+++.|.|+|| +|++++|++.+.. .+ ..+.+|.++++++++|+|.
T Consensus 1 ~v~~~V~~~~~~~~~~-~~g~~~~~~~~~l~D~TG-~i~~~~W~~~~~~-------~~--~~G~vv~i~~~~v~~~~g~~ 69 (82)
T cd04491 1 SVEGKVLSISEPREFT-RDGSEGKVQSGLVGDETG-TIRFTLWDEKAAD-------DL--EPGDVVRIENAYVREFNGRL 69 (82)
T ss_pred CEEEEEEEccCCeEec-cCCCeeEEEEEEEECCCC-EEEEEEECchhcc-------cC--CCCCEEEEEeEEEEecCCcE
Confidence 4899999999999998 889999999999999999 8999999998621 12 4678999999999999985
Q ss_pred eeccccceEEEE
Q 006263 423 SIGTIPSTQLFI 434 (653)
Q Consensus 423 sLs~~~~S~i~i 434 (653)
.|+....|.|..
T Consensus 70 ql~i~~~~~i~~ 81 (82)
T cd04491 70 ELSVGKNSEIEK 81 (82)
T ss_pred EEEeCCceEEEE
Confidence 888888887764
No 31
>PRK06461 single-stranded DNA-binding protein; Reviewed
Probab=98.79 E-value=3.7e-08 Score=90.61 Aligned_cols=95 Identities=20% Similarity=0.261 Sum_probs=77.8
Q ss_pred ecchhhhhhcccCccccEEEEEEEecCceeEEecCCceeeEEEEEEEeCCCCEEEEEEccchhhhhhhhHHHhhccCCCc
Q 006263 328 FRHISEIESAENNSIVDVIGIVISVNPSVPILRKNGMETQRRILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVDVGFFP 407 (653)
Q Consensus 328 f~~i~~i~~~~~~~~vDVIGvV~~v~~~~~i~~k~g~~~~kr~i~l~D~s~~~i~vtLWg~~A~~~~~~l~~~~~~~~~~ 407 (653)
+++|.||.. ....|+++|+|.++++...+.+|.+ ....++++|.|+|| +|++|||++.|.. + ..+.
T Consensus 4 ~~kI~dL~~--g~~~v~~~~~V~~i~~~~~~~~k~~-~~~v~~~~l~D~TG-~I~~tlW~~~a~~--------l--~~Gd 69 (129)
T PRK06461 4 ITKIKDLKP--GMERVNVTVRVLEVGEPKVIQTKGG-PRTISEAVVGDETG-RVKLTLWGEQAGS--------L--KEGE 69 (129)
T ss_pred ceEHHHcCC--CCCceEEEEEEEEcCCceEEEeCCC-ceEEEEEEEECCCC-EEEEEEeCCcccc--------C--CCCC
Confidence 566777752 2268999999999999988888844 45688999999999 7999999997644 3 3589
Q ss_pred EEEEEeeEeecCCCc-eeccccceEEEEcC
Q 006263 408 VLSVKSGKVNDFSGK-SIGTIPSTQLFINP 436 (653)
Q Consensus 408 Vvaik~~rV~~f~G~-sLs~~~~S~i~inP 436 (653)
||.|++++|++|+|+ +|+....|.|..-+
T Consensus 70 vV~I~na~v~~f~G~lqL~i~~~~~i~~~~ 99 (129)
T PRK06461 70 VVEIENAWTTLYRGKVQLNVGKYGSISESD 99 (129)
T ss_pred EEEEECcEEeeeCCEEEEEECCCEEEEECC
Confidence 999999999999997 89988888887533
No 32
>PRK06461 single-stranded DNA-binding protein; Reviewed
Probab=98.76 E-value=6e-08 Score=89.18 Aligned_cols=97 Identities=15% Similarity=0.198 Sum_probs=83.5
Q ss_pred cceeccccCCCCCceEEEEEEEeeccccccccCCCCceeEEEEEEeCCCCeEEEEEchhHHHHHHhhcccCcEEEEeceE
Q 006263 207 RIIPIAALNPYQGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISKGS 286 (653)
Q Consensus 207 ~~~pI~~L~p~~~~w~I~~RV~~k~~ir~~~~~~g~gk~f~~~L~D~~g~~I~at~f~~~~~kf~~~l~eG~vy~is~~~ 286 (653)
.+++|++|.|....-.+.++|+.++..|.+....+.+++.++.|.| ++|.|++++|++.++ .|++|+|+.|.++.
T Consensus 3 ~~~kI~dL~~g~~~v~~~~~V~~i~~~~~~~~k~~~~~v~~~~l~D-~TG~I~~tlW~~~a~----~l~~GdvV~I~na~ 77 (129)
T PRK06461 3 MITKIKDLKPGMERVNVTVRVLEVGEPKVIQTKGGPRTISEAVVGD-ETGRVKLTLWGEQAG----SLKEGEVVEIENAW 77 (129)
T ss_pred CceEHHHcCCCCCceEEEEEEEEcCCceEEEeCCCceEEEEEEEEC-CCCEEEEEEeCCccc----cCCCCCEEEEECcE
Confidence 4679999999988999999999999999887766667899999999 788999999998654 58899999999998
Q ss_pred EecCCCcccCCCCceEEEeccccEEEecc
Q 006263 287 LKPAQKNFNHLKNEWEIFLEATSTVDLCT 315 (653)
Q Consensus 287 V~~a~~~f~~~~~~yei~f~~~T~I~~~~ 315 (653)
+..-+ ...+|.+..++.|..+.
T Consensus 78 v~~f~-------G~lqL~i~~~~~i~~~~ 99 (129)
T PRK06461 78 TTLYR-------GKVQLNVGKYGSISESD 99 (129)
T ss_pred EeeeC-------CEEEEEECCCEEEEECC
Confidence 86532 34899999999999984
No 33
>PRK07217 replication factor A; Reviewed
Probab=98.31 E-value=2.7e-05 Score=80.65 Aligned_cols=93 Identities=18% Similarity=0.204 Sum_probs=75.6
Q ss_pred CcceeccccCCCCCceEEEEEEEeeccccccccCCCCceeEEEEEEeCCCCeEEEEEchhHHHHHHhhcccCcEEEEece
Q 006263 206 ARIIPIAALNPYQGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISKG 285 (653)
Q Consensus 206 ~~~~pI~~L~p~~~~w~I~~RV~~k~~ir~~~~~~g~gk~f~~~L~D~~g~~I~at~f~~~~~kf~~~l~eG~vy~is~~ 285 (653)
...++|++|+|...+-+|+|||+..|+.+. +.....-.|.| ++|+|+.|.|.+. =.+.|++|++|.|.|+
T Consensus 70 ~~~~kI~Di~~~~~~VsV~aKVl~l~e~~~------~si~qvGllgD-ETG~IkfT~W~~s---~~~~leeGd~~rI~na 139 (311)
T PRK07217 70 SELVNIADIDEPEQWVDVTAKVVQLWEPSS------DSIAQVGLLGD-ETGTIKFTKWAKS---DLPELEEGKSYLLKNV 139 (311)
T ss_pred CCceeeeecCCCCCcEEEEEEEEEecCCCC------CceEEEEEEEc-CCceEEEEEccCC---CCCcccCCCEEEEEeE
Confidence 357899999999999999999999998553 12223345778 8999999999963 1466999999999999
Q ss_pred EEecCCCcccCCCCceEEEeccccEEEecc
Q 006263 286 SLKPAQKNFNHLKNEWEIFLEATSTVDLCT 315 (653)
Q Consensus 286 ~V~~a~~~f~~~~~~yei~f~~~T~I~~~~ 315 (653)
.+..-+. .++|.+++.|+|++..
T Consensus 140 ~v~ey~G-------~~~lnlg~~t~I~~~d 162 (311)
T PRK07217 140 VTDEYQG-------RFSVKLNRTTSIEELD 162 (311)
T ss_pred EEeeECC-------EEEEEeCCceEEEeCC
Confidence 9876654 4899999999999984
No 34
>COG1599 RFA1 Single-stranded DNA-binding replication protein A (RPA), large (70 kD) subunit and related ssDNA-binding proteins [DNA replication, recombination, and repair]
Probab=98.21 E-value=3.2e-05 Score=85.17 Aligned_cols=188 Identities=19% Similarity=0.192 Sum_probs=135.7
Q ss_pred CCCcceeccccCCCCCceEEEEEEEeeccccccccCCCC-ceeEEEEEEeCCCCeEEE-EEchhHHHHHHhhcccCcEEE
Q 006263 204 APARIIPIAALNPYQGRWAIKARVTAKGDLRRYNNARGD-GKVFSFDLLDSDGGEIRV-TCFNAVVDRFYEIIEVGRVYL 281 (653)
Q Consensus 204 ~~~~~~pI~~L~p~~~~w~I~~RV~~k~~ir~~~~~~g~-gk~f~~~L~D~~g~~I~a-t~f~~~~~kf~~~l~eG~vy~ 281 (653)
+...+.+|+++.+.+.+-.+.+||...+..+.|....|. +++.+..+.| +.|.++. +.|+..+. ..++.|+++.
T Consensus 45 ~~~~~~~i~~~~~~~~~~~v~~~V~~~~e~~~~~~k~g~~~~l~~~~v~D-etg~v~~~~~~~~~a~---~~~e~Gdv~~ 120 (407)
T COG1599 45 AMESIGKISDISEASSRVNVTGRVLSIGEKKTFDRKRGAEGKLAEVLVGD-ETGSVKTVTLWNIAAL---EKLEPGDVIR 120 (407)
T ss_pred chhhcccccccchhhccccEEEEECccccceeeecccccccceEEEEEec-CCCCEEEEeecccccc---ccCCccceEE
Confidence 445678999999999999999999999998888877775 8899999999 8899998 78887543 4689999999
Q ss_pred EeceEEecCCCcccCCCCceEEEeccccEEEeccCCCCCCCcccceecchhhhhhcccCccccEEEEEEEecCceeEEec
Q 006263 282 ISKGSLKPAQKNFNHLKNEWEIFLEATSTVDLCTEEDDSIPKQQFSFRHISEIESAENNSIVDVIGIVISVNPSVPILRK 361 (653)
Q Consensus 282 is~~~V~~a~~~f~~~~~~yei~f~~~T~I~~~~d~~~~iP~~~f~f~~i~~i~~~~~~~~vDVIGvV~~v~~~~~i~~k 361 (653)
|.++.+.... ...++.++..+.+...++.. ..+...+.-..+.++..+ ...+ .+.|..-+++.++...
T Consensus 121 i~~~~~~~~~-------~~~~~~~~~~~~v~~~~~~~-~~~~~~~~~~~i~~~~~~---~~~~-~~~v~~g~~ik~~~~~ 188 (407)
T COG1599 121 IRNAYTSLYR-------GGKRLSVGRVGSVADVDDEE-DEARESEDAREIGEESLL---SPYQ-KARVVVGSEIKTFDNQ 188 (407)
T ss_pred ecCccccccc-------CceeeecccccccccCchhh-cccccccccccccccccc---Cccc-eEEEEecccceeEecC
Confidence 9998764432 34788888888888874321 222222233333333322 2223 6677777777777643
Q ss_pred CCceeeEEEEEEEeCCCCEEEEEEccchhhhhhhhHHHhhccCCCcEEEEEeeEeecCCCc
Q 006263 362 NGMETQRRILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVDVGFFPVLSVKSGKVNDFSGK 422 (653)
Q Consensus 362 ~g~~~~kr~i~l~D~s~~~i~vtLWg~~A~~~~~~l~~~~~~~~~~Vvaik~~rV~~f~G~ 422 (653)
+.+...+...|.|++-..+.+++|.... .+++.-+-+++|.-|.+.
T Consensus 189 -~ge~~~~~~~~~d~~~~~~~~~~~~~~~--------------~g~~~~ie~~~v~~~~~~ 234 (407)
T COG1599 189 -GGESKVFSNELEDEERGVIVFTDWDPSQ--------------DGDVYRIEGARVKTKNKQ 234 (407)
T ss_pred -CCccceEeeeecccceeEEEeccCcccc--------------cceeeeecCcEEEEeccc
Confidence 4445677888889884489999998861 357777888888887764
No 35
>TIGR00617 rpa1 replication factor-a protein 1 (rpa1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=98.05 E-value=0.00068 Score=78.15 Aligned_cols=177 Identities=13% Similarity=0.064 Sum_probs=116.4
Q ss_pred eecchhhhhhcccCccccEEEEEEEecCceeEEecCCceeeEEEEEEEeCCCCEEEEEEccchhhhhhhhHHHhhccCCC
Q 006263 327 SFRHISEIESAENNSIVDVIGIVISVNPSVPILRKNGMETQRRILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVDVGFF 406 (653)
Q Consensus 327 ~f~~i~~i~~~~~~~~vDVIGvV~~v~~~~~i~~k~g~~~~kr~i~l~D~s~~~i~vtLWg~~A~~~~~~l~~~~~~~~~ 406 (653)
.|++|++|.... .-.-|.|.|+..+++..+..++| +....+|.|.|++| .|++|+|++.|..|...| ..|
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-EIRATAFNEQADKFYDII------QEG 248 (608)
T ss_pred ceEEHHHCCCCC--CceEEEEEEEeccccceecCCCC-CceeeEEEEecCCC-eEEEEECchHHHHHhhhc------ccC
Confidence 588888887643 24788999999999998876554 23566899999655 999999999998864433 258
Q ss_pred cEEEEEeeEeecCCCc--------eeccccceEEEEcCChHHHHHHHHHHhcCCCccceeecccccccCCCCcchhccHH
Q 006263 407 PVLSVKSGKVNDFSGK--------SIGTIPSTQLFINPDFAEAHELREWFDSGGKNAATVSISREIAAGGAKNEIHKTVS 478 (653)
Q Consensus 407 ~Vvaik~~rV~~f~G~--------sLs~~~~S~i~inPdipe~~~l~~w~~~~g~~~~~~sls~~~~~~~~~~~~~kti~ 478 (653)
.|+.|.+++|+..+++ .|.....|.|..-+|.+. +. .......+|+
T Consensus 249 ~VY~Is~~~Vk~an~~y~~~~~~yei~f~~~T~I~~~~d~~~-------------------iP-------~~~~~f~~i~ 302 (608)
T TIGR00617 249 KVYYISKGSLKPANKQFTNLGNDYEMTLDRDTVIEECEDETA-------------------IP-------KIQFNFVKID 302 (608)
T ss_pred CEEEECceEEEEccccccCCCCCEEEEECCCeEEEECCCccc-------------------CC-------cccccceEHH
Confidence 9999999999765442 234444555554332110 00 0112345788
Q ss_pred hhhhcCCCCCCCCcEEEEEEEEEEEeCCceEEecCCCCcCcccccceeeecCceeecccCccccCCceEEEEEEEEEEeC
Q 006263 479 QIKNEGLGRSEKPDWVTVRAFITFIKSDSFCYTACPLMIGDRQCNKKVTQSGNRWQCDRCNQEIDECDYRYLLQAQIQDQ 558 (653)
Q Consensus 479 ~i~~~~lg~~~~~~~~~v~atI~~i~~d~~~Y~aC~~~~~~~~C~KKv~~~~~~~~C~kC~~~~~~~~~rY~l~~~i~D~ 558 (653)
+|.... ...+..|.|.|..+..-.- ..... +-....+.++.|.|.
T Consensus 303 dI~~~~-----~~~~VDVIGvV~~v~~~~~-i~~k~-----------------------------~g~~~~kR~i~L~D~ 347 (608)
T TIGR00617 303 DIGGYE-----GNSLVDVIGIVQSVSPTQT-ITSRK-----------------------------NNKEFPKRDITLVDD 347 (608)
T ss_pred Hhhhhc-----CCCCccEEEEEeEecCceE-EEEcC-----------------------------CCCeeeeEEEEEEeC
Confidence 887532 2236778888888864210 00000 112245678999999
Q ss_pred CC-eEEEEEechhhhhh
Q 006263 559 TG-LTWVTAFQESGEEI 574 (653)
Q Consensus 559 Tg-~~~~~~F~~~ae~l 574 (653)
|| ++.+++||+.|+.+
T Consensus 348 sg~sI~vTLWG~~A~~~ 364 (608)
T TIGR00617 348 SGKSVRVTLWGDDATKF 364 (608)
T ss_pred CCCEEEEEEEhhhhhhc
Confidence 99 58999999999764
No 36
>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=97.84 E-value=0.00012 Score=64.81 Aligned_cols=97 Identities=16% Similarity=0.095 Sum_probs=70.8
Q ss_pred hhhhhhcccCccccEEEEEEEecCceeEEecCCceeeEEEEEEEeCCCCEEEEEEccchhhhhhhhHHHhhccCCCcEEE
Q 006263 331 ISEIESAENNSIVDVIGIVISVNPSVPILRKNGMETQRRILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVDVGFFPVLS 410 (653)
Q Consensus 331 i~~i~~~~~~~~vDVIGvV~~v~~~~~i~~k~g~~~~kr~i~l~D~s~~~i~vtLWg~~A~~~~~~l~~~~~~~~~~Vva 410 (653)
|++|.. .....-+.|.|+..+++..++.++ .+....+|.|.|+.|.+|++|+|++.|..|...|. .|.|+.
T Consensus 2 I~~L~p--~~~~~~I~~rV~~k~~~~~f~~~~-~~g~~~~~~l~De~~~~I~~t~~~~~~~~f~~~l~------eG~vy~ 72 (104)
T cd04474 2 ISSLNP--YQNKWTIKARVTNKSDIRTWSNAR-GEGKLFSFDLLDEDGGEIRATFFNDAVDKFYDLLE------VGKVYY 72 (104)
T ss_pred hhHccC--CCCcEEEEEEEeeccccccccCCC-CCcEEEEEEEEECCCCEEEEEEehHHHHHhhcccc------cccEEE
Confidence 455543 223578999999999999887654 23445689999997779999999999888644432 589999
Q ss_pred EEeeEeecCCCceeccccceEEEEcC
Q 006263 411 VKSGKVNDFSGKSIGTIPSTQLFINP 436 (653)
Q Consensus 411 ik~~rV~~f~G~sLs~~~~S~i~inP 436 (653)
|.+++|+.-+++.-.+...-.|.++.
T Consensus 73 i~~~~V~~a~~~y~~~~~~yeI~f~~ 98 (104)
T cd04474 73 ISKGSVKVANKKFNTLKNDYEITFNR 98 (104)
T ss_pred EeccEEeeccccCCCCCCcEEEEECC
Confidence 99999987766544444445555554
No 37
>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=97.82 E-value=6e-05 Score=61.85 Aligned_cols=70 Identities=31% Similarity=0.509 Sum_probs=56.2
Q ss_pred eEEEEEEEeeccccccccCCCCceeEEEEEEeCCCCeEEEEEchhHHHHHHhhcccCcEEEEeceEEecCCCcccCCCCc
Q 006263 221 WAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISKGSLKPAQKNFNHLKNE 300 (653)
Q Consensus 221 w~I~~RV~~k~~ir~~~~~~g~gk~f~~~L~D~~g~~I~at~f~~~~~kf~~~l~eG~vy~is~~~V~~a~~~f~~~~~~ 300 (653)
++|.|+|+++. + +.++++.++|.| .+|.|++.+|++...++.+.|++|+++.+. |.++..+.. +
T Consensus 1 V~v~G~V~~~~--~------~~~~~~~~~l~D-~tg~i~~~~~~~~~~~~~~~l~~g~~v~v~-G~v~~~~~~------~ 64 (75)
T PF01336_consen 1 VTVEGRVTSIR--R------SGGKIVFFTLED-GTGSIQVVFFNEEYERFREKLKEGDIVRVR-GKVKRYNGG------E 64 (75)
T ss_dssp EEEEEEEEEEE--E------EETTEEEEEEEE-TTEEEEEEEETHHHHHHHHTS-TTSEEEEE-EEEEEETTS------S
T ss_pred CEEEEEEEEEE--c------CCCCEEEEEEEE-CCccEEEEEccHHhhHHhhcCCCCeEEEEE-EEEEEECCc------c
Confidence 57999999986 2 235789999999 679999999999999999999999999999 888766432 3
Q ss_pred eEEEec
Q 006263 301 WEIFLE 306 (653)
Q Consensus 301 yei~f~ 306 (653)
++|...
T Consensus 65 ~~l~~~ 70 (75)
T PF01336_consen 65 LELIVP 70 (75)
T ss_dssp EEEEEE
T ss_pred EEEEEC
Confidence 555554
No 38
>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=97.67 E-value=0.00046 Score=64.97 Aligned_cols=86 Identities=20% Similarity=0.359 Sum_probs=63.5
Q ss_pred ecchhhhhhcccCccccEEEEEEEecCceeEEecCCceeeEEEEEEEeCCC-------CEEEEEEccchhhhhhhhHHHh
Q 006263 328 FRHISEIESAENNSIVDVIGIVISVNPSVPILRKNGMETQRRILNLKDTSG-------RSVELTLWGDFCNKEGQKLQEM 400 (653)
Q Consensus 328 f~~i~~i~~~~~~~~vDVIGvV~~v~~~~~i~~k~g~~~~kr~i~l~D~s~-------~~i~vtLWg~~A~~~~~~l~~~ 400 (653)
|+++++.. ...+..|||||+|++..+.....+| |+ --+..|+|.|.|. ..|.|.++-...+.+ ..
T Consensus 1 ~~~l~~~~-~~~~~~vnvigVV~~~~~p~~~~t~-g~-D~~~tl~i~D~S~~~~~~~~~~l~v~iF~~~~~~L----P~- 72 (146)
T PF02765_consen 1 YTPLSTAK-EKFGKFVNVIGVVVDFSPPNPKKTR-GT-DYMCTLTITDPSLNDSNQKLSGLTVNIFRPHKESL----PN- 72 (146)
T ss_dssp BCCGGGSC-TTSSEEEEEEEEEEEEEEECTEEES-SS-CEEEEEEEEBTTCSCSSCCCCEEEEEEEESSHHHS----CT-
T ss_pred Cccchhhh-hcCCCEEEEEEEEEEccCCcceEcC-CC-cEEEEEEEECCCCCccccccCCEEEEEECCCHHHC----CC-
Confidence 44555222 3467899999999999998544454 43 3578999999985 689999998775542 21
Q ss_pred hccCCCcEEEEEeeEeecCCCc
Q 006263 401 VDVGFFPVLSVKSGKVNDFSGK 422 (653)
Q Consensus 401 ~~~~~~~Vvaik~~rV~~f~G~ 422 (653)
. ...|+||.++.++|..|+|+
T Consensus 73 v-~~~GDii~l~r~kv~~~~~~ 93 (146)
T PF02765_consen 73 V-KSVGDIIRLRRVKVQSYNGK 93 (146)
T ss_dssp T-CSTTHEEEEEEEEEEEETTE
T ss_pred C-CCCCCEEEEEEEEEEEECCE
Confidence 1 12489999999999999997
No 39
>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=97.25 E-value=0.0019 Score=56.71 Aligned_cols=84 Identities=14% Similarity=0.152 Sum_probs=66.9
Q ss_pred EEEEEEEeeccccccccCC-C-CceeEEEEEEeCCCCeEEEEEchhHHHHHHhhcccCcEEEEeceEEecCCCcccCCCC
Q 006263 222 AIKARVTAKGDLRRYNNAR-G-DGKVFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISKGSLKPAQKNFNHLKN 299 (653)
Q Consensus 222 ~I~~RV~~k~~ir~~~~~~-g-~gk~f~~~L~D~~g~~I~at~f~~~~~kf~~~l~eG~vy~is~~~V~~a~~~f~~~~~ 299 (653)
-|.|.|+..++++++.... | ++...++.|.|+.+..|.+|+|++.++.|.... |.|+.|.++++..-+
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 3789999999999987654 3 567889999997667999999999999998765 999999999885433
Q ss_pred ceEEEeccccEEEecc
Q 006263 300 EWEIFLEATSTVDLCT 315 (653)
Q Consensus 300 ~yei~f~~~T~I~~~~ 315 (653)
...+.....|.|..-+
T Consensus 73 ~~~l~~~~~s~i~~np 88 (101)
T cd04475 73 GKSLSTGSSSTIIINP 88 (101)
T ss_pred CeEEeecCceeEEECC
Confidence 1456666678877653
No 40
>cd03524 RPA2_OBF_family RPA2_OBF_family: A family of oligonucleotide binding (OB) folds with similarity to the OB fold of the single strand (ss) DNA-binding domain (DBD)-D of human RPA2 (also called RPA32). RPA2 is a subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). RPA contains six OB folds, which are involved in ssDNA binding and in trimerization. The ssDNA binding mechanism is believed to be multistep and to involve conformational change. This family also includes OB folds similar to those found in Escherichia coli SSB, the wedge domain of E. coli RecG (a branched-DNA-specific helicase), E. coli ssDNA specific exodeoxyribonuclease VII large subunit, Pyroco
Probab=96.74 E-value=0.0076 Score=48.24 Aligned_cols=60 Identities=37% Similarity=0.614 Sum_probs=49.6
Q ss_pred EEEEEEeeccccccccCCCCceeEEEEEEeCCCCeEEEEEchhHHHHHHhhcccCcEEEEeceEEec
Q 006263 223 IKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISKGSLKP 289 (653)
Q Consensus 223 I~~RV~~k~~ir~~~~~~g~gk~f~~~L~D~~g~~I~at~f~~~~~kf~~~l~eG~vy~is~~~V~~ 289 (653)
|.|+|+.....++ | +..+.+.|.|..|+.|.+++|.+..+++...+++|+++.+. +.|..
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 6788887766544 1 35788999996559999999999999999999999999999 88854
No 41
>KOG3416 consensus Predicted nucleic acid binding protein [General function prediction only]
Probab=96.20 E-value=0.011 Score=52.73 Aligned_cols=70 Identities=21% Similarity=0.320 Sum_probs=56.8
Q ss_pred ceeccccCCCCCceEEEEEEEeeccccccccCCCCc-eeEEEEEEeCCCCeEEEEEchhHHHHHHhhcccCcEEEEeceE
Q 006263 208 IIPIAALNPYQGRWAIKARVTAKGDLRRYNNARGDG-KVFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISKGS 286 (653)
Q Consensus 208 ~~pI~~L~p~~~~w~I~~RV~~k~~ir~~~~~~g~g-k~f~~~L~D~~g~~I~at~f~~~~~kf~~~l~eG~vy~is~~~ 286 (653)
..+|++|.|+.++.++..-|+.-...+.-+ +| ++-++-+.| ++|.|++.+|+| +-..|+.|+++.++++-
T Consensus 4 ~i~ikdi~P~~kN~~v~fIvl~~g~~tkTk----dg~~v~~~kVaD-~TgsI~isvW~e----~~~~~~PGDIirLt~Gy 74 (134)
T KOG3416|consen 4 MIFIKDIKPGLKNINVTFIVLEYGRATKTK----DGHEVRSCKVAD-ETGSINISVWDE----EGCLIQPGDIIRLTGGY 74 (134)
T ss_pred chhHhhcChhhhcceEEEEEEeeceeeecc----CCCEEEEEEEec-ccceEEEEEecC----cCcccCCccEEEecccc
Confidence 468999999999998888887766554432 35 688889999 899999999996 45688999999999863
No 42
>KOG3416 consensus Predicted nucleic acid binding protein [General function prediction only]
Probab=96.10 E-value=0.027 Score=50.30 Aligned_cols=83 Identities=19% Similarity=0.310 Sum_probs=59.6
Q ss_pred chhhhhhcccCccccEEEEEEEecCceeEEecCCceeeEEEEEEEeCCCCEEEEEEccchhhhhhhhHHHhhccCCCcEE
Q 006263 330 HISEIESAENNSIVDVIGIVISVNPSVPILRKNGMETQRRILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVDVGFFPVL 409 (653)
Q Consensus 330 ~i~~i~~~~~~~~vDVIGvV~~v~~~~~i~~k~g~~~~kr~i~l~D~s~~~i~vtLWg~~A~~~~~~l~~~~~~~~~~Vv 409 (653)
+|.||...-+ .+.|+=+|.+.+..+. +|+|++ .|...+.|+|| +|.+.+|++.... | ..++||
T Consensus 6 ~ikdi~P~~k--N~~v~fIvl~~g~~tk--Tkdg~~--v~~~kVaD~Tg-sI~isvW~e~~~~--------~--~PGDIi 68 (134)
T KOG3416|consen 6 FIKDIKPGLK--NINVTFIVLEYGRATK--TKDGHE--VRSCKVADETG-SINISVWDEEGCL--------I--QPGDII 68 (134)
T ss_pred hHhhcChhhh--cceEEEEEEeeceeee--ccCCCE--EEEEEEecccc-eEEEEEecCcCcc--------c--CCccEE
Confidence 3555554222 3456667777776643 567874 58899999999 8999999987544 3 368999
Q ss_pred EEEeeEeecCCCc-eeccccc
Q 006263 410 SVKSGKVNDFSGK-SIGTIPS 429 (653)
Q Consensus 410 aik~~rV~~f~G~-sLs~~~~ 429 (653)
-+++.-.+-|+|. .|.++.+
T Consensus 69 rLt~Gy~Si~qg~LtL~~GK~ 89 (134)
T KOG3416|consen 69 RLTGGYASIFQGCLTLYVGKG 89 (134)
T ss_pred EecccchhhhcCceEEEecCC
Confidence 9999999889874 6766544
No 43
>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=95.97 E-value=0.014 Score=66.43 Aligned_cols=105 Identities=16% Similarity=0.193 Sum_probs=84.3
Q ss_pred CCHHHHHHHhCCCC--------CCCCeEEEEEEEEcCC-----CCceEEEEEecccceeeeeecccchhhcccCCcccCc
Q 006263 5 LTPNSISLINGGDV--------NSKPLVQVMDIKLIGS-----TQERYRFLISDSVSTQHAMLATQLNDRVKTGQVKKGS 71 (653)
Q Consensus 5 Lt~Gai~~i~~~~~--------~~~pvvQVl~ik~~~~-----~~~ryr~~lSDG~~~~~~ml~t~ln~~v~~~~l~~~s 71 (653)
||||.|.+++++-. .-.+.|||++|-+.-. .+.=|.|-|||+.|....-|...=++||.++.|+.|.
T Consensus 1 L~pGvL~klL~~mn~~~k~~gehRs~lLQV~~IvPaL~~~~l~p~~gF~lkvSDsshs~Yvsl~~~~~dlils~klqlGq 80 (579)
T PF06075_consen 1 LTPGVLLKLLQHMNSDVKVTGEHRSSLLQVTSIVPALAGSDLWPNQGFYLKVSDSSHSTYVSLPDEDDDLILSNKLQLGQ 80 (579)
T ss_pred CCchHHHHHHHhcCCCCccCCcccccceeeeeeeecccccccCcCCceEEEecccccceeeecChhcccceecCCccccc
Confidence 89999999998532 2347999999998821 1234999999999999988998889999999999999
Q ss_pred EEEEeeeEeeeecCeEEEEEEeeeEeecCCcccCCCcccccc
Q 006263 72 VVQLIDYICSTVQNRKIIVVLNMETIILDCEPIGNPKIFSES 113 (653)
Q Consensus 72 IIkl~~y~~~~~~~k~~iii~~~evl~~~~~~iG~P~~~~~~ 113 (653)
+|-+.++.. +..+=++..+..|..-..-+|+|.++-..
T Consensus 81 fi~vdrle~----~~PvP~l~g~rp~pgR~pcvg~P~dl~~~ 118 (579)
T PF06075_consen 81 FIYVDRLEA----ASPVPVLRGVRPVPGRHPCVGNPEDLVAT 118 (579)
T ss_pred eEEEccccc----CCCCceeecCccCCCCCCCCCCChhhhhc
Confidence 998887653 45777888888888655569999887643
No 44
>cd04483 hOBFC1_like hOBFC1_like: A subfamily of OB folds similar to that found in human OB fold containing protein 1 (hOBFC1). Members of this group belong to the Replication protein A subunit 2 (RPA2) family of OB folds. RPA is a nuclear ssDNA binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). The OB fold domain of RPA2 has dual roles in ssDNA binding and trimerization.
Probab=95.10 E-value=0.086 Score=45.51 Aligned_cols=68 Identities=22% Similarity=0.434 Sum_probs=44.6
Q ss_pred cEEEEEEEecCceeEEecCCceeeEEEEEEEeCCCCEEEEEEccchhhhh--h--------------hhHHHhhccCCCc
Q 006263 344 DVIGIVISVNPSVPILRKNGMETQRRILNLKDTSGRSVELTLWGDFCNKE--G--------------QKLQEMVDVGFFP 407 (653)
Q Consensus 344 DVIGvV~~v~~~~~i~~k~g~~~~kr~i~l~D~s~~~i~vtLWg~~A~~~--~--------------~~l~~~~~~~~~~ 407 (653)
|++|+|+++.+-. .+..++|.|.|| .|+|.+|....... . ....+.+ ..+.
T Consensus 1 ~ivG~V~sv~~~~----------~~~~~tLdDgTG-~Ie~~~W~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i--~~G~ 67 (92)
T cd04483 1 DILGTVVSRRERE----------TFYSFGVDDGTG-VVNCVCWKNLSYAEVSSRSDAARILKSALMALKQAKVL--EIGD 67 (92)
T ss_pred CeEEEEEEEEecC----------CeEEEEEecCCc-eEEEEEEcCcCccccccccccccccccccccccccccc--CCCC
Confidence 6899999886532 357899999999 79999998753110 0 0001112 2456
Q ss_pred EEEEEeeEeecCCCc-eec
Q 006263 408 VLSVKSGKVNDFSGK-SIG 425 (653)
Q Consensus 408 Vvaik~~rV~~f~G~-sLs 425 (653)
+|-++ ++|+.|+|+ .|.
T Consensus 68 vvrV~-G~i~~frg~~ql~ 85 (92)
T cd04483 68 LLRVR-GSIRTYRGEREIN 85 (92)
T ss_pred EEEEE-EEEeccCCeeEEE
Confidence 66666 678899985 554
No 45
>cd04481 RPA1_DBD_B_like RPA1_DBD_B_like: A subgroup of uncharacterized, plant OB folds with similarity to the third OB fold, the ssDNA-binding domain (DBD)-B, of human RPA1 (also called RPA70). RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-B, RPA1 contains three other OB folds: DBD-A, DBD-C, and RPA1N. The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B. RPA1 DBD-C is involved in trimerization. The ssDNA binding mechanism is believed to be multistep and to involve conformational change.
Probab=95.06 E-value=0.28 Score=43.39 Aligned_cols=68 Identities=12% Similarity=0.195 Sum_probs=52.2
Q ss_pred EEEEEeeccccccccCCCCceeEEEEEEeCCCCeEEEEEchhHHHHHHhhc----ccCcEEEEec-eEEecCC
Q 006263 224 KARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAVVDRFYEII----EVGRVYLISK-GSLKPAQ 291 (653)
Q Consensus 224 ~~RV~~k~~ir~~~~~~g~gk~f~~~L~D~~g~~I~at~f~~~~~kf~~~l----~eG~vy~is~-~~V~~a~ 291 (653)
.|-|+.-+++.+......+.....+.|.|..+..+++|+|++.|..|...+ ..+-|+.+-. .+|+.-+
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 455666666666554334556789999998889999999999999999887 4677887766 7887655
No 46
>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=95.02 E-value=0.11 Score=48.42 Aligned_cols=83 Identities=14% Similarity=0.257 Sum_probs=65.6
Q ss_pred cceeccccC-CCCCceEEEEEEEeeccccccccCCCCceeEEEEEEeCCC---CeEEEEEchhHHHHHHhhcccCcEEEE
Q 006263 207 RIIPIAALN-PYQGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDG---GEIRVTCFNAVVDRFYEIIEVGRVYLI 282 (653)
Q Consensus 207 ~~~pI~~L~-p~~~~w~I~~RV~~k~~ir~~~~~~g~gk~f~~~L~D~~g---~~I~at~f~~~~~kf~~~l~eG~vy~i 282 (653)
.++||++|. .....-.|.|-|+...+.+. .+|.....+|.|+|..+ ..+++++|.+..+.|-.. .+|+|+.+
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 367888887 33356789999998888664 23444678899999766 779999999998887665 99999999
Q ss_pred eceEEecCCCc
Q 006263 283 SKGSLKPAQKN 293 (653)
Q Consensus 283 s~~~V~~a~~~ 293 (653)
++++|+.-+.+
T Consensus 78 ~~~kv~~~~g~ 88 (138)
T cd04497 78 RRVKIQSYNGK 88 (138)
T ss_pred EEEEEEEECCc
Confidence 99999887755
No 47
>cd03524 RPA2_OBF_family RPA2_OBF_family: A family of oligonucleotide binding (OB) folds with similarity to the OB fold of the single strand (ss) DNA-binding domain (DBD)-D of human RPA2 (also called RPA32). RPA2 is a subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). RPA contains six OB folds, which are involved in ssDNA binding and in trimerization. The ssDNA binding mechanism is believed to be multistep and to involve conformational change. This family also includes OB folds similar to those found in Escherichia coli SSB, the wedge domain of E. coli RecG (a branched-DNA-specific helicase), E. coli ssDNA specific exodeoxyribonuclease VII large subunit, Pyroco
Probab=95.01 E-value=0.15 Score=40.58 Aligned_cols=65 Identities=28% Similarity=0.520 Sum_probs=46.6
Q ss_pred cEEEEEEEecCceeEEecCCceeeEEEEEEEeCCCCEEEEEEccchhhhhhhhHHHhhccCCCcEEEEEeeEeecCCCc
Q 006263 344 DVIGIVISVNPSVPILRKNGMETQRRILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVDVGFFPVLSVKSGKVNDFSGK 422 (653)
Q Consensus 344 DVIGvV~~v~~~~~i~~k~g~~~~kr~i~l~D~s~~~i~vtLWg~~A~~~~~~l~~~~~~~~~~Vvaik~~rV~~f~G~ 422 (653)
+|.|+|.++.+..+ |+ ....++|.|.+|..++|++|.+....+. .. ...+.++.+. +++..++|+
T Consensus 1 ~v~g~v~~~~~~~~-----~~--~~~~~~l~D~~~~~i~~~~~~~~~~~~~----~~--~~~g~~v~v~-g~v~~~~~~ 65 (75)
T cd03524 1 TIVGIVVAVEEIRT-----EG--KVLIFTLTDGTGGTIRVTLFGELAEELE----NL--LKEGQVVYIK-GKVKKFRGR 65 (75)
T ss_pred CeEEEEEeeccccc-----CC--eEEEEEEEcCCCCEEEEEEEchHHHHHH----hh--ccCCCEEEEE-EEEEecCCe
Confidence 57899998877643 33 3578999999966999999998765431 11 2356788887 888877653
No 48
>PF15489 CTC1: CST, telomere maintenance, complex subunit CTC1
Probab=94.99 E-value=5.3 Score=48.57 Aligned_cols=314 Identities=16% Similarity=0.170 Sum_probs=165.5
Q ss_pred CCceEEEEEEEeeccccccccCCCCceeEEEEEEeCCC-CeEEEEEchhHHHHHHhhcccCcEEEEece-----EEecCC
Q 006263 218 QGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDG-GEIRVTCFNAVVDRFYEIIEVGRVYLISKG-----SLKPAQ 291 (653)
Q Consensus 218 ~~~w~I~~RV~~k~~ir~~~~~~g~gk~f~~~L~D~~g-~~I~at~f~~~~~kf~~~l~eG~vy~is~~-----~V~~a~ 291 (653)
...+.+.|..++.+.... +...+.|+ . -..-|+.. .++-..|++. .-+|++.|+.|.||.+--- .|-.+.
T Consensus 704 ~~tlsF~~~g~wlGg~q~-~eg~~~~~-~-e~~~~~~~~~kVlLlF~G~-svrWF~fLhpg~vYRLva~~~~~p~l~~~s 779 (1144)
T PF15489_consen 704 KPTLSFQVSGSWLGGTQR-KEGTGWGP-P-EPLEDENKDQKVLLLFLGS-SVRWFPFLHPGQVYRLVAPNSPDPMLFGSS 779 (1144)
T ss_pred CCceEEEEEEEEecceEe-ccCcccCC-C-CcCcccCCCceEEEEEecC-ceeeEeEecCCcEEEEecCCCCCceeecCC
Confidence 457889999888887654 21112222 1 11233333 4554444454 5699999999999987431 121000
Q ss_pred --Ccc--cCCCCceEEEeccccEEEeccCCCCCCCcc-----cceecchhhhhhc-ccCccccEEEEEEEecCceeEE--
Q 006263 292 --KNF--NHLKNEWEIFLEATSTVDLCTEEDDSIPKQ-----QFSFRHISEIESA-ENNSIVDVIGIVISVNPSVPIL-- 359 (653)
Q Consensus 292 --~~f--~~~~~~yei~f~~~T~I~~~~d~~~~iP~~-----~f~f~~i~~i~~~-~~~~~vDVIGvV~~v~~~~~i~-- 359 (653)
... -...-.-.+++-.+=+++... ..++|.. .+--.++.|+..- ..+.+|.+-|+|.+-.-.+...
T Consensus 780 ~~s~r~l~~~~~~scl~vq~~W~le~~~--~~d~~~~l~~~~~~~~ssl~~lls~s~s~sLVSFs~~I~srt~ce~~~~~ 857 (1144)
T PF15489_consen 780 CVSQRPLELAGCPSCLTVQDDWTLELES--SQDIPPVLRISKLLPESSLSELLSSSSSDSLVSFSAEILSRTLCEPLNAR 857 (1144)
T ss_pred CcccccccccCCCccEEeCCCceecccc--cccchhhhhhcccCccccHHHHhccCCCCceEEEEEEEEEeeeccCCccc
Confidence 000 001111223333332333221 1234432 1224567777663 4688999999998874433211
Q ss_pred --ecCCce-----eeE--EEEEEEeCCCCEEEEEEccchhhhhhhhHHHhhccCCCcEEEEEee--EeecCCCceecccc
Q 006263 360 --RKNGME-----TQR--RILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVDVGFFPVLSVKSG--KVNDFSGKSIGTIP 428 (653)
Q Consensus 360 --~k~g~~-----~~k--r~i~l~D~s~~~i~vtLWg~~A~~~~~~l~~~~~~~~~~Vvaik~~--rV~~f~G~sLs~~~ 428 (653)
++.|.. ..+ .-++..|-.+... +...-+..-- .--+.-..|.+|.|.+. ||+-+++.++....
T Consensus 858 ~~~~~~~~~~~~~~vkltv~L~v~D~~~p~~-ldVYi~~~h~-----p~plGLLPGA~V~f~~lerkVSRs~nVYC~~~p 931 (1144)
T PF15489_consen 858 RWSKPGNAIASRGCVKLTVALTVADCESPPH-LDVYIEDPHL-----PYPLGLLPGARVLFSQLERKVSRSHNVYCCFLP 931 (1144)
T ss_pred cccCCCCCcccccccceEEEEEEecCCCCCe-EEEEecCCCC-----CCcccccCCceeeeehhhhhhhccCcEEEEEcC
Confidence 121111 122 3455566665211 3333222111 00011135667777765 66666667776666
Q ss_pred ceEEEEcCChHHHHHHHHHHhcCCCccceeecccccccCCCCcchhccHHhhhhcCCCCCCCCcEEEEEEEEEEEeCCce
Q 006263 429 STQLFINPDFAEAHELREWFDSGGKNAATVSISREIAAGGAKNEIHKTVSQIKNEGLGRSEKPDWVTVRAFITFIKSDSF 508 (653)
Q Consensus 429 ~S~i~inPdipe~~~l~~w~~~~g~~~~~~sls~~~~~~~~~~~~~kti~~i~~~~lg~~~~~~~~~v~atI~~i~~d~~ 508 (653)
.|.|.+....++. +.........+.++.... ..+-...+.+.|+.|..=.+
T Consensus 932 sS~VtVlS~p~~t-------------------------~~~~~~P~~~L~~~~~~~----~~~~~a~~~chVV~V~~l~L 982 (1144)
T PF15489_consen 932 SSSVTVLSFPPET-------------------------NVSPPLPHIYLAELLQGS----QSPFQARVSCHVVSVLSLQL 982 (1144)
T ss_pred CceEEEEecCccc-------------------------CCCCCCCeEEehhhhCCC----CCCceEEEEEEEEEEEEEEe
Confidence 6766654321111 011122344555554321 22235667888887765333
Q ss_pred EEecCCCCcCcccccceeeecCceeeccc----CccccCCceEEEEEEEEEEeCCCeEEEEEechhhhhhhCCCHHHHHH
Q 006263 509 CYTACPLMIGDRQCNKKVTQSGNRWQCDR----CNQEIDECDYRYLLQAQIQDQTGLTWVTAFQESGEEILGCPAKELYM 584 (653)
Q Consensus 509 ~Y~aC~~~~~~~~C~KKv~~~~~~~~C~k----C~~~~~~~~~rY~l~~~i~D~Tg~~~~~~F~~~ae~llG~sA~el~~ 584 (653)
.+ .|. .|..-.. ++ +|.. |-.. ....+=..++.+.|+||++.+++-|+....+||.+..|...
T Consensus 983 ~W-vCa------~C~si~~-qg---~Csr~~p~C~s~--~sV~qA~ar~~vEDGTaeA~v~~~~~~V~~lLgL~~~eW~~ 1049 (1144)
T PF15489_consen 983 QW-VCA------HCGSICP-QG---RCSRQSPPCPSQ--TSVFQASARLLVEDGTAEAVVWCRGHHVAALLGLSPSEWES 1049 (1144)
T ss_pred ee-hhh------hccCccc-CC---cCCCCCCCCCCC--cceeeEEEEEEEecCCeeEEEEECCcHHHHHhCCCHHHHHH
Confidence 22 677 6663222 11 3532 4332 45778888999999999999999999999999999987654
Q ss_pred H
Q 006263 585 L 585 (653)
Q Consensus 585 ~ 585 (653)
+
T Consensus 1050 L 1050 (1144)
T PF15489_consen 1050 L 1050 (1144)
T ss_pred H
Confidence 3
No 49
>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=94.91 E-value=0.096 Score=42.51 Aligned_cols=63 Identities=25% Similarity=0.447 Sum_probs=44.2
Q ss_pred ccEEEEEEEecCceeEEecCCceeeEEEEEEEeCCCCEEEEEEccchhhhhhhhHHHhhccCCCcEEEEEeeEeecCCCc
Q 006263 343 VDVIGIVISVNPSVPILRKNGMETQRRILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVDVGFFPVLSVKSGKVNDFSGK 422 (653)
Q Consensus 343 vDVIGvV~~v~~~~~i~~k~g~~~~kr~i~l~D~s~~~i~vtLWg~~A~~~~~~l~~~~~~~~~~Vvaik~~rV~~f~G~ 422 (653)
|.|.|.|+++. +.++ ....++|.|.|| .|.|++|++.+..+ .+.+ ..+.+|.++ ++++.|++.
T Consensus 1 V~v~G~V~~~~-------~~~~--~~~~~~l~D~tg-~i~~~~~~~~~~~~----~~~l--~~g~~v~v~-G~v~~~~~~ 63 (75)
T PF01336_consen 1 VTVEGRVTSIR-------RSGG--KIVFFTLEDGTG-SIQVVFFNEEYERF----REKL--KEGDIVRVR-GKVKRYNGG 63 (75)
T ss_dssp EEEEEEEEEEE-------EEET--TEEEEEEEETTE-EEEEEEETHHHHHH----HHTS---TTSEEEEE-EEEEEETTS
T ss_pred CEEEEEEEEEE-------cCCC--CEEEEEEEECCc-cEEEEEccHHhhHH----hhcC--CCCeEEEEE-EEEEEECCc
Confidence 46789998877 1111 356899999998 99999999554443 2223 368899888 788877654
No 50
>cd04488 RecG_wedge_OBF RecG_wedge_OBF: A subfamily of OB folds corresponding to the OB fold found in the N-terminal (wedge) domain of Escherichia coli RecG. RecG is a branched-DNA-specific helicase, which catalyzes the interconversion of a DNA replication fork to a four-stranded (Holliday) junction in vivo and in vitro. This interconversion provides a route to repair stalled forks. The RecG monomer contains three domains. The N-terminal domain is named for its wedge structure, and may provide the specificity of RecG for binding branched-DNA structures. During the reversal of fork to Holliday junction, the wedge domain is fixed at the junction of the fork where the leading and lagging strand duplex arms meet, and is thought to promote the unwinding of the nascent leading and lagging strands. In order to form the Holliday junction, these nascent strands would be annealed, and the parental strands reannealed. The wedge domain may also be a processivity factor of RecG on these branched cha
Probab=94.64 E-value=0.19 Score=40.50 Aligned_cols=60 Identities=17% Similarity=0.221 Sum_probs=41.9
Q ss_pred EEEEEEEeeccccccccCCCCceeEEEEEEeCCCCeEEEEEchhHHHHHHhhcccCcEEEEeceEEec
Q 006263 222 AIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISKGSLKP 289 (653)
Q Consensus 222 ~I~~RV~~k~~ir~~~~~~g~gk~f~~~L~D~~g~~I~at~f~~~~~kf~~~l~eG~vy~is~~~V~~ 289 (653)
+|+|+|+.....+ . + .++.+.+.|.| +++.|.+++|+.. ......|++|+.|.+.+ ++..
T Consensus 1 ~i~~~V~~~~~~~-~---~-~~~~~~~~~~D-~~g~i~~~~F~~~-~~~~~~~~~G~~~~v~G-kv~~ 60 (75)
T cd04488 1 TVEGTVVSVEVVP-R---R-GRRRLKVTLSD-GTGTLTLVFFNFQ-PYLKKQLPPGTRVRVSG-KVKR 60 (75)
T ss_pred CEEEEEEEEEecc-C---C-CccEEEEEEEc-CCCEEEEEEECCC-HHHHhcCCCCCEEEEEE-EEee
Confidence 3678887763222 1 1 24689999999 6999999999831 23367899999998874 4433
No 51
>cd04485 DnaE_OBF DnaE_OBF: A subfamily of OB folds corresponding to the C-terminal OB-fold nucleic acid binding domain of Thermus aquaticus and Escherichia coli type C replicative DNA polymerase III alpha subunit (DnaE). The DNA polymerase holoenzyme of E. coli contains two copies of this replicative polymerase, each of which copies a different DNA strand. This group also contains Bacillus subtilis DnaE. Replication in B. subtilis and Staphylococcus aureus requires two different type C polymerases, polC and DnaE, both of which are thought to be included in the DNA polymerase holoenzyme. At the B. subtilis replication fork, polC appears to be involved in leading strand synthesis and DnaE in lagging strand synthesis.
Probab=94.63 E-value=0.16 Score=41.83 Aligned_cols=43 Identities=16% Similarity=0.363 Sum_probs=37.1
Q ss_pred eeEEEEEEeCCCCeEEEEEchhHHHHHHhhcccCcEEEEeceEEe
Q 006263 244 KVFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISKGSLK 288 (653)
Q Consensus 244 k~f~~~L~D~~g~~I~at~f~~~~~kf~~~l~eG~vy~is~~~V~ 288 (653)
+.+.+.|.| .+|.|.+++|++..+++.+.|++|.+|.+.+ .+.
T Consensus 19 ~~~~~~l~D-~tg~~~~~~f~~~~~~~~~~l~~g~~v~v~G-~v~ 61 (84)
T cd04485 19 RMAFVTLED-LTGSIEVVVFPETYEKYRDLLKEDALLLVEG-KVE 61 (84)
T ss_pred EEEEEEEEe-CCCeEEEEECHHHHHHHHHHhcCCCEEEEEE-EEE
Confidence 578899999 7889999999988788999999999998874 443
No 52
>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=94.34 E-value=0.085 Score=47.67 Aligned_cols=67 Identities=22% Similarity=0.334 Sum_probs=38.7
Q ss_pred HHHHHhCCCCC-CCC-eEEEEEEEEcC-CCCceEEEEEecccceeeeeecccchhhcccCCcccCcEEEE
Q 006263 9 SISLINGGDVN-SKP-LVQVMDIKLIG-STQERYRFLISDSVSTQHAMLATQLNDRVKTGQVKKGSVVQL 75 (653)
Q Consensus 9 ai~~i~~~~~~-~~p-vvQVl~ik~~~-~~~~ryr~~lSDG~~~~~~ml~t~ln~~v~~~~l~~~sIIkl 75 (653)
||.+|++++.. ..| ||=|.+|..-. .......+.|+||=|.++|.+...|..++..|.|..|.=+.+
T Consensus 2 aLrrI~E~D~~~~~~mVL~Vs~i~~~~~~~~~~~~lelTDGWY~Ika~lD~~L~~~l~~gki~vG~KL~v 71 (118)
T PF09103_consen 2 ALRRILEGDDSASKPMVLCVSSISSSDNDSPESAILELTDGWYSIKAQLDPPLTRLLRKGKIRVGQKLRV 71 (118)
T ss_dssp HHHHHHTTSSTTB-SEEEEEEE-------------EEEE-SS-EEEE---HHHHHHHHTT-S-TT-EEEE
T ss_pred HhHHHhhCCCCcCCcEEEEEEEEccCCCCCCccCEEEEecCCEEEEEEeCHHHHHHHHhCCccCCccEEE
Confidence 68999999863 345 55566552222 345789999999999999999999999999999999987764
No 53
>cd04490 PolII_SU_OBF PolII_SU_OBF: A subfamily of OB folds corresponding to the OB fold found in Pyrococcus abyssi DNA polymerase II (PolII) small subunit. PolII is a family D DNA polymerase, having a 3-prime to 5-prime exonuclease activity. P. abyssi PolII is heterodimeric. The large subunit appears to be the polymerase, and the small subunit may be the exonuclease. The small subunit contains a calcineurin-like phosphatase superfamily domain C-terminal to this OB-fold domain.
Probab=94.29 E-value=0.19 Score=42.08 Aligned_cols=54 Identities=31% Similarity=0.427 Sum_probs=39.1
Q ss_pred cEEEEEEEecCceeEEecCCceeeEEEEEEEeCCCCEEEEEEccchhh--hhhhhHHHhhccCCCcEEEEEe
Q 006263 344 DVIGIVISVNPSVPILRKNGMETQRRILNLKDTSGRSVELTLWGDFCN--KEGQKLQEMVDVGFFPVLSVKS 413 (653)
Q Consensus 344 DVIGvV~~v~~~~~i~~k~g~~~~kr~i~l~D~s~~~i~vtLWg~~A~--~~~~~l~~~~~~~~~~Vvaik~ 413 (653)
=++|+|.++. .+|+|+. -++|.|.+| ++++++|.+... .+... + ..+.+|.+++
T Consensus 3 ~i~GiI~~v~-----~TK~g~~----~~~leD~~G-~~Ev~~F~~~~~~~~~~~~----l--~~d~~v~v~g 58 (79)
T cd04490 3 SIIGMVNDVR-----STKNGHR----IVELEDTTG-RITVLLTKDKEELFEEAED----I--LPDEVIGVSG 58 (79)
T ss_pred EEEEEEeEEE-----EcCCCCE----EEEEECCCC-EEEEEEeCchhhhhhhhhh----c--cCCCEEEEEE
Confidence 4689999988 3566764 889999999 899999999876 54222 2 2355666655
No 54
>PTZ00401 aspartyl-tRNA synthetase; Provisional
Probab=92.82 E-value=0.96 Score=51.71 Aligned_cols=99 Identities=20% Similarity=0.212 Sum_probs=72.4
Q ss_pred CcceeccccCCCC---CceEEEEEEEeeccccccccCCCCceeEEEEEEeCCCCeEEEEEc-----hhHHHHHHhhcccC
Q 006263 206 ARIIPIAALNPYQ---GRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCF-----NAVVDRFYEIIEVG 277 (653)
Q Consensus 206 ~~~~pI~~L~p~~---~~w~I~~RV~~k~~ir~~~~~~g~gk~f~~~L~D~~g~~I~at~f-----~~~~~kf~~~l~eG 277 (653)
+.++.|++|++.. ..-+|+|||.++ |. .|++.-++|.| .++.|++++- .+.+-+|-..|..|
T Consensus 63 ~~~~~i~~l~~~~~~g~~V~v~Grv~~~---R~------~Gk~~Fl~LRd-~~~~iQ~v~~~~~~~~~~~~~~~~~l~~e 132 (550)
T PTZ00401 63 RTFIPVAVLSKPELVDKTVLIRARVSTT---RK------KGKMAFMVLRD-GSDSVQAMAAVEGDVPKEMIDFIGQIPTE 132 (550)
T ss_pred CceEEHHHCCccccCCCEEEEEEEEEEE---ec------CCCeEEEEEEe-CCcCEEEEEECCCccCHHHHHHHhcCCCC
Confidence 5689999998765 457899999764 33 35777788999 7789999983 23445677789999
Q ss_pred cEEEEeceEEecCCCcccCCCCceEEEeccccEEEec
Q 006263 278 RVYLISKGSLKPAQKNFNHLKNEWEIFLEATSTVDLC 314 (653)
Q Consensus 278 ~vy~is~~~V~~a~~~f~~~~~~yei~f~~~T~I~~~ 314 (653)
+++.+.+.-+++....-+....++||....-..+.++
T Consensus 133 siV~V~G~v~~~~~~~~~~~~~~~El~v~~i~vls~a 169 (550)
T PTZ00401 133 SIVDVEATVCKVEQPITSTSHSDIELKVKKIHTVTES 169 (550)
T ss_pred CEEEEEEEEEecCccCCCCCCccEEEEeeEEEEEeCC
Confidence 9999999666544332234567899999886666655
No 55
>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=92.46 E-value=0.56 Score=39.22 Aligned_cols=55 Identities=22% Similarity=0.119 Sum_probs=43.0
Q ss_pred EEEEEEEeeccccccccCCCCceeEEEEEEeCCCCeEEEEEchhHHH--HHHhhcccCcEEEEece
Q 006263 222 AIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAVVD--RFYEIIEVGRVYLISKG 285 (653)
Q Consensus 222 ~I~~RV~~k~~ir~~~~~~g~gk~f~~~L~D~~g~~I~at~f~~~~~--kf~~~l~eG~vy~is~~ 285 (653)
.+.|.|+... .+.+ |+. .+.|-| ..|.+.+++|.+..+ ++.+.|++|.++.+..-
T Consensus 3 ~i~GiI~~v~-----~TK~--g~~-~~~leD-~~G~~Ev~~F~~~~~~~~~~~~l~~d~~v~v~g~ 59 (79)
T cd04490 3 SIIGMVNDVR-----STKN--GHR-IVELED-TTGRITVLLTKDKEELFEEAEDILPDEVIGVSGT 59 (79)
T ss_pred EEEEEEeEEE-----EcCC--CCE-EEEEEC-CCCEEEEEEeCchhhhhhhhhhccCCCEEEEEEE
Confidence 4566666643 2233 334 778888 899999999999999 99999999999999873
No 56
>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=92.09 E-value=0.51 Score=38.81 Aligned_cols=54 Identities=22% Similarity=0.359 Sum_probs=42.6
Q ss_pred EEEEEEEeeccccccccCCCCceeEEEEEEeCCCCeEEEEEchhHHHHHHhhcccCcEEEEec
Q 006263 222 AIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISK 284 (653)
Q Consensus 222 ~I~~RV~~k~~ir~~~~~~g~gk~f~~~L~D~~g~~I~at~f~~~~~kf~~~l~eG~vy~is~ 284 (653)
.|.|-|+. +|. . .+ | ..-++|.| .+++|.+++|.+..+++.+.|++|+.+.+..
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-HLYFTLKD-EDASIRCVMWRSNARRLGFPLEEGMEVLVRG 56 (78)
T ss_pred EEEEEEec---CEE-C-CC--c-EEEEEEEe-CCeEEEEEEEcchhhhCCCCCCCCCEEEEEE
Confidence 35666664 343 2 22 4 77889999 7899999999999999999999999888876
No 57
>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=91.51 E-value=1.4 Score=36.07 Aligned_cols=64 Identities=28% Similarity=0.414 Sum_probs=41.1
Q ss_pred EEEEEEEecCceeEEecCCceeeEEEEEEEeCCCCEEEEEEccchhhhhhhhHHHhhccCCCcEEEEEeeEeecCCC
Q 006263 345 VIGIVISVNPSVPILRKNGMETQRRILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVDVGFFPVLSVKSGKVNDFSG 421 (653)
Q Consensus 345 VIGvV~~v~~~~~i~~k~g~~~~kr~i~l~D~s~~~i~vtLWg~~A~~~~~~l~~~~~~~~~~Vvaik~~rV~~f~G 421 (653)
++|+|.++.. ..+|.|+. ...++|.|.+| .+++++|.+....+ ...+. .+.++.+.| ++..|+|
T Consensus 2 i~g~v~~~~~---~~~k~g~~--~~~~~l~D~tg-~~~~~~f~~~~~~~----~~~l~--~g~~v~v~G-~v~~~~~ 65 (84)
T cd04485 2 VAGLVTSVRR---RRTKKGKR--MAFVTLEDLTG-SIEVVVFPETYEKY----RDLLK--EDALLLVEG-KVERRDG 65 (84)
T ss_pred EEEEEEEeEE---EEcCCCCE--EEEEEEEeCCC-eEEEEECHHHHHHH----HHHhc--CCCEEEEEE-EEEecCC
Confidence 5677776544 33456653 47789999999 79999998653332 22232 456666654 6777766
No 58
>KOG0851 consensus Single-stranded DNA-binding replication protein A (RPA), large (70 kD) subunit and related ssDNA-binding proteins [Replication, recombination and repair]
Probab=91.42 E-value=1 Score=45.58 Aligned_cols=68 Identities=15% Similarity=0.131 Sum_probs=52.7
Q ss_pred ceEEecCCCCcCcccccceeeecCceeecccCccccCCceEEEEEEEEEEeCCCeEEEEEechhhhhhhCCCHHHHHH
Q 006263 507 SFCYTACPLMIGDRQCNKKVTQSGNRWQCDRCNQEIDECDYRYLLQAQIQDQTGLTWVTAFQESGEEILGCPAKELYM 584 (653)
Q Consensus 507 ~~~Y~aC~~~~~~~~C~KKv~~~~~~~~C~kC~~~~~~~~~rY~l~~~i~D~Tg~~~~~~F~~~ae~llG~sA~el~~ 584 (653)
.|+|..|+ .|+| -........|+.|+....+...+|.+.....+.++. ..|...+..+.|.++..+..
T Consensus 159 ~~~~~~~~------~~~~-~~~~~~~~~c~~~~~~~~~~~~~~~l~~~~~~~~~~---l~~~~~~~~~~G~~~~~~~~ 226 (246)
T KOG0851|consen 159 DGFYLTFK------ICNK-SKFSKPVLWCEACGEQATDFGRKRSLGGGVIVIAPE---LLFWKIWRYFDGKNVRIVLA 226 (246)
T ss_pred ceEEEEEe------eccc-ccccCceEEehhhcchHHhhhhheEecCCcEEccch---heeecccccccCCchheeec
Confidence 69999999 8998 111112689999998877777778898888888887 88888888888877765543
No 59
>PF11325 DUF3127: Domain of unknown function (DUF3127); InterPro: IPR021474 This bacterial family of proteins has no known function.
Probab=91.25 E-value=1.3 Score=37.48 Aligned_cols=71 Identities=20% Similarity=0.301 Sum_probs=51.3
Q ss_pred EEEEEEEecCceeEEecCCceeeEEEEEEEeCCC--CEEEEEEccchhhhhhhhHHHhhccCCCcEEEE-EeeEeecCCC
Q 006263 345 VIGIVISVNPSVPILRKNGMETQRRILNLKDTSG--RSVELTLWGDFCNKEGQKLQEMVDVGFFPVLSV-KSGKVNDFSG 421 (653)
Q Consensus 345 VIGvV~~v~~~~~i~~k~g~~~~kr~i~l~D~s~--~~i~vtLWg~~A~~~~~~l~~~~~~~~~~Vvai-k~~rV~~f~G 421 (653)
+-|.|..+-+..+-.+++| ..||++.|.-... ..|.+.+||+.+..+ +.-..|..|.+ -+.+-++|+|
T Consensus 2 i~Gkii~~l~~~~g~s~~G--w~Kre~Vlet~~qYP~~i~f~~~~dk~~~l-------~~~~~Gd~V~Vsf~i~~RE~~g 72 (84)
T PF11325_consen 2 ITGKIIKVLPEQQGVSKNG--WKKREFVLETEEQYPQKICFEFWGDKIDLL-------DNFQVGDEVKVSFNIEGREWNG 72 (84)
T ss_pred cccEEEEEecCcccCcCCC--cEEEEEEEeCCCcCCceEEEEEEcchhhhh-------ccCCCCCEEEEEEEeeccEecc
Confidence 4578767776665556677 9999999985554 589999999987652 22345677765 4778889998
Q ss_pred cee
Q 006263 422 KSI 424 (653)
Q Consensus 422 ~sL 424 (653)
+.-
T Consensus 73 r~f 75 (84)
T PF11325_consen 73 RWF 75 (84)
T ss_pred eEe
Confidence 754
No 60
>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=91.11 E-value=4.1 Score=35.50 Aligned_cols=83 Identities=18% Similarity=0.209 Sum_probs=55.2
Q ss_pred eEEEEEEEeeccccccccCCCCc-eeEEEEEEeCCCCeEEEEEchh------HHHHHHhhcccCcEEEEeceEEecCCCc
Q 006263 221 WAIKARVTAKGDLRRYNNARGDG-KVFSFDLLDSDGGEIRVTCFNA------VVDRFYEIIEVGRVYLISKGSLKPAQKN 293 (653)
Q Consensus 221 w~I~~RV~~k~~ir~~~~~~g~g-k~f~~~L~D~~g~~I~at~f~~------~~~kf~~~l~eG~vy~is~~~V~~a~~~ 293 (653)
.+|+|||.++ |. .| ++.-++|.| .++.|++.+-.+ ..-++...|..|+++.+.+--.+. .+.
T Consensus 2 V~i~Gwv~~~---R~------~g~k~~Fi~LrD-~sg~iQ~v~~~~~~~~~~~~~~~~~~l~~es~V~V~G~v~~~-~~~ 70 (102)
T cd04320 2 VLIRARVHTS---RA------QGAKLAFLVLRQ-QGYTIQGVLAASAEGVSKQMVKWAGSLSKESIVDVEGTVKKP-EEP 70 (102)
T ss_pred EEEEEEEEEe---ec------CCCceEEEEEec-CCceEEEEEeCCcccCCHHHHHHHhcCCCccEEEEEEEEECC-CCc
Confidence 5788999774 33 25 666678999 678999999743 223344568999999999964432 221
Q ss_pred ccC-CCCceEEEeccccEEEec
Q 006263 294 FNH-LKNEWEIFLEATSTVDLC 314 (653)
Q Consensus 294 f~~-~~~~yei~f~~~T~I~~~ 314 (653)
.+. ....|||....-..+..+
T Consensus 71 ~~~~~~~~~El~~~~i~il~~~ 92 (102)
T cd04320 71 IKSCTQQDVELHIEKIYVVSEA 92 (102)
T ss_pred ccCCCcCcEEEEEEEEEEEecC
Confidence 111 336799998776555554
No 61
>PF14951 DUF4503: Domain of unknown function (DUF4503)
Probab=90.63 E-value=0.61 Score=49.24 Aligned_cols=82 Identities=16% Similarity=0.346 Sum_probs=66.5
Q ss_pred EEEEEEEEEEEeCC-ceEEecCCCCcCcccccc-eee---ecCceeecccCccccCCceEEEEEEEEEEeCC---CeEEE
Q 006263 493 WVTVRAFITFIKSD-SFCYTACPLMIGDRQCNK-KVT---QSGNRWQCDRCNQEIDECDYRYLLQAQIQDQT---GLTWV 564 (653)
Q Consensus 493 ~~~v~atI~~i~~d-~~~Y~aC~~~~~~~~C~K-Kv~---~~~~~~~C~kC~~~~~~~~~rY~l~~~i~D~T---g~~~~ 564 (653)
...|.|+|+.++.+ .|.+|.|. .|+. |+. ++++.++|..|.+.+..|.-|.-|.+-+.=.+ .++.+
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 68899999999987 69999999 8854 666 33448999999999999999999998887333 56788
Q ss_pred EEechhhhhhhCCCHH
Q 006263 565 TAFQESGEEILGCPAK 580 (653)
Q Consensus 565 ~~F~~~ae~llG~sA~ 580 (653)
-+..+.-..||.-.|.
T Consensus 330 KL~q~sIsslL~~aa~ 345 (389)
T PF14951_consen 330 KLLQRSISSLLMSAAS 345 (389)
T ss_pred EEhHHHHHHHHhhhhc
Confidence 8888888878766664
No 62
>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=90.61 E-value=3.3 Score=36.54 Aligned_cols=76 Identities=22% Similarity=0.420 Sum_probs=52.5
Q ss_pred EEEEEEEeeccccccccCCCCceeEEEEEEeCCCCeEEEEEchh-----HHHHHHhhcccCcEEEEeceEEecCCCcccC
Q 006263 222 AIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNA-----VVDRFYEIIEVGRVYLISKGSLKPAQKNFNH 296 (653)
Q Consensus 222 ~I~~RV~~k~~ir~~~~~~g~gk~f~~~L~D~~g~~I~at~f~~-----~~~kf~~~l~eG~vy~is~~~V~~a~~~f~~ 296 (653)
+|+|||.+. |. .|++.-++|.| .++.+++++... ...+|...|..|+++.+.+.-++...
T Consensus 3 ~v~GwV~~~---R~------~g~~~Fi~lrd-~~~~lQ~v~~~~~~~~~~~~~~~~~l~~g~~V~v~G~v~~~~~----- 67 (108)
T cd04322 3 SVAGRIMSK---RG------SGKLSFADLQD-ESGKIQVYVNKDDLGEEEFEDFKKLLDLGDIIGVTGTPFKTKT----- 67 (108)
T ss_pred EEEEEEEEE---ec------CCCeEEEEEEE-CCeEEEEEEECCCCCHHHHHHHHhcCCCCCEEEEEEEEEecCC-----
Confidence 688888763 33 35677788999 678999988643 23455556999999999875443322
Q ss_pred CCCceEEEeccccEEEec
Q 006263 297 LKNEWEIFLEATSTVDLC 314 (653)
Q Consensus 297 ~~~~yei~f~~~T~I~~~ 314 (653)
..+||....-..+.++
T Consensus 68 --g~~El~~~~~~ils~~ 83 (108)
T cd04322 68 --GELSIFVKEFTLLSKS 83 (108)
T ss_pred --CCEEEEeCEeEEeecc
Confidence 4589977665555554
No 63
>cd04492 YhaM_OBF_like YhaM_OBF_like: A subfamily of OB folds similar to that found in Bacillus subtilis YhaM and Staphylococcus aureus cmp-binding factor-1 (SaCBF1). Both these proteins are 3'-to-5'exoribonucleases. YhaM requires Mn2+ or Co2+ for activity and is inactive in the presence of Mg2+. YhaM also has a Mn2+ dependent 3'-to-5'single-stranded DNA exonuclease activity. SaCBF is also a double-stranded DNA binding protein, binding specifically to cmp, the replication enhancer found in S. aureus plasmid pT181. Proteins in this group combine an N-terminal OB fold with a C-terminal HD domain. The HD domain is found in metal-dependent phosphohydrolases.
Probab=90.05 E-value=1.1 Score=36.95 Aligned_cols=43 Identities=21% Similarity=0.328 Sum_probs=35.7
Q ss_pred eeEEEEEEeCCCCeEEEEEchhHHHHHHhhcccCcEEEEeceEEec
Q 006263 244 KVFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISKGSLKP 289 (653)
Q Consensus 244 k~f~~~L~D~~g~~I~at~f~~~~~kf~~~l~eG~vy~is~~~V~~ 289 (653)
+.+.+.|-| .+|.|.+++|++.. .+...|++|.++.+. +.|..
T Consensus 19 ~~~~~~l~D-~tg~i~~~~f~~~~-~~~~~l~~g~~v~v~-G~v~~ 61 (83)
T cd04492 19 PYLALTLQD-KTGEIEAKLWDASE-EDEEKFKPGDIVHVK-GRVEE 61 (83)
T ss_pred cEEEEEEEc-CCCeEEEEEcCCCh-hhHhhCCCCCEEEEE-EEEEE
Confidence 578899999 78899999999664 457899999999998 66643
No 64
>PLN02850 aspartate-tRNA ligase
Probab=90.04 E-value=2.6 Score=48.16 Aligned_cols=98 Identities=15% Similarity=0.130 Sum_probs=70.8
Q ss_pred CcceeccccCCCC--CceEEEEEEEeeccccccccCCCCceeEEEEEEeCCCCeEEEEEchh------HHHHHHhhcccC
Q 006263 206 ARIIPIAALNPYQ--GRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNA------VVDRFYEIIEVG 277 (653)
Q Consensus 206 ~~~~pI~~L~p~~--~~w~I~~RV~~k~~ir~~~~~~g~gk~f~~~L~D~~g~~I~at~f~~------~~~kf~~~l~eG 277 (653)
+.++.|.+|++.. ...+|+|||.+. |. .|++.-++|.| .++.|++++... ..-+|...|..|
T Consensus 67 ~~~~~i~~l~~~~~g~~V~v~Grv~~~---R~------~gk~~Fl~Lrd-~~~~iQ~v~~~~~~~~~~~~~~~~~~l~~e 136 (530)
T PLN02850 67 REWTDVSDLGEELAGSEVLIRGRVHTI---RG------KGKSAFLVLRQ-SGFTVQCVVFVSEVTVSKGMVKYAKQLSRE 136 (530)
T ss_pred ceEeEhhhcchhhCCCEEEEEEEEEEE---cc------CCCeEEEEEEe-CCcCEEEEEECCccccCHHHHHHHhCCCCC
Confidence 4678999998754 468899999763 32 46776678899 788999998543 345677889999
Q ss_pred cEEEEeceEEecCCCcccCCCCceEEEeccccEEEec
Q 006263 278 RVYLISKGSLKPAQKNFNHLKNEWEIFLEATSTVDLC 314 (653)
Q Consensus 278 ~vy~is~~~V~~a~~~f~~~~~~yei~f~~~T~I~~~ 314 (653)
+++.+.+--+++... -+....++||....-..+..+
T Consensus 137 s~V~V~G~v~~~~~~-~~~~t~~~El~~~~i~vls~a 172 (530)
T PLN02850 137 SVVDVEGVVSVPKKP-VKGTTQQVEIQVRKIYCVSKA 172 (530)
T ss_pred CEEEEEEEEEccCcC-CCCCCccEEEEEeEEEEEeCC
Confidence 999998865544322 223344899999887666665
No 65
>PF15072 DUF4539: Domain of unknown function (DUF4539)
Probab=89.84 E-value=1.5 Score=37.36 Aligned_cols=60 Identities=20% Similarity=0.201 Sum_probs=46.8
Q ss_pred EEEEEEeCCCCeEEEEEchhHHHHHHhhcccCcEEEEeceEEecCCCcccCCCCceEEEeccccEEE
Q 006263 246 FSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISKGSLKPAQKNFNHLKNEWEIFLEATSTVD 312 (653)
Q Consensus 246 f~~~L~D~~g~~I~at~f~~~~~kf~~~l~eG~vy~is~~~V~~a~~~f~~~~~~yei~f~~~T~I~ 312 (653)
..+.|.| -+|+|+|++-.+..+.|.+.|..|.|..+.+..|-. +....+-|.......+.
T Consensus 21 ~~v~l~D-pTG~i~~tiH~~v~~~y~~~l~~GavLlLk~V~Vf~------ps~~~~yLnIt~~Nlv~ 80 (86)
T PF15072_consen 21 AFVVLKD-PTGEIRGTIHRKVLEEYGDELSPGAVLLLKDVTVFS------PSPRSHYLNITLNNLVR 80 (86)
T ss_pred eEEEEEC-CCCcEEEEEeHHHHhhcCCccccCEEEEEeeeeEEe------cCCCccEEEEehhHeee
Confidence 5788999 788999999999999999999999999999988743 33434555554444443
No 66
>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=89.60 E-value=1.5 Score=37.64 Aligned_cols=68 Identities=26% Similarity=0.391 Sum_probs=44.0
Q ss_pred ccEEEEEEEecCceeEEecCCceeeEEEEEEEeCCCCEEEEEEccchhhhhhhhHHHhhccCCCcEEEEEeeEeecCCCc
Q 006263 343 VDVIGIVISVNPSVPILRKNGMETQRRILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVDVGFFPVLSVKSGKVNDFSGK 422 (653)
Q Consensus 343 vDVIGvV~~v~~~~~i~~k~g~~~~kr~i~l~D~s~~~i~vtLWg~~A~~~~~~l~~~~~~~~~~Vvaik~~rV~~f~G~ 422 (653)
|.++|+|+++.... .+..++|.|.|| +|++.+|......- ....+.+ ..+.+|.+ .++++.|+|+
T Consensus 2 v~~vG~V~~~~~~~----------~~~~~tL~D~TG-~I~~~~W~~~~~~~-~~~~~~~--~~g~~v~v-~G~v~~~~g~ 66 (95)
T cd04478 2 VTLVGVVRNVEEQS----------TNITYTIDDGTG-TIEVRQWLDDDNDD-SSEVEPI--EEGTYVRV-FGNLKSFQGK 66 (95)
T ss_pred EEEEEEEEeeeEcc----------cEEEEEEECCCC-cEEEEEeCCCCCcc-ccccccc--ccCCEEEE-EEEEcccCCe
Confidence 67889998876542 467899999999 79999998653210 0001122 23455544 4567889885
Q ss_pred -eec
Q 006263 423 -SIG 425 (653)
Q Consensus 423 -sLs 425 (653)
.|.
T Consensus 67 ~ql~ 70 (95)
T cd04478 67 KSIM 70 (95)
T ss_pred eEEE
Confidence 565
No 67
>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=88.96 E-value=1.4 Score=38.98 Aligned_cols=60 Identities=15% Similarity=0.266 Sum_probs=35.0
Q ss_pred eEEEEEEEEcCCCCceEEEEEecccceeeeeecccchhhcccCC------cccCcEEEEeeeEeeee
Q 006263 23 LVQVMDIKLIGSTQERYRFLISDSVSTQHAMLATQLNDRVKTGQ------VKKGSVVQLIDYICSTV 83 (653)
Q Consensus 23 vvQVl~ik~~~~~~~ryr~~lSDG~~~~~~ml~t~ln~~v~~~~------l~~~sIIkl~~y~~~~~ 83 (653)
++||+..-. ........++||||.|++.|.|+.+.-...+... --+|++|.|++|.+...
T Consensus 28 ~~ri~~~~~-~~~~~~i~a~lsDs~~~I~a~ft~eai~~fe~~~~~~~t~~t~g~li~I~~~~l~~~ 93 (106)
T PF10341_consen 28 LLRILKFAK-STSDGAITALLSDSTHQILAIFTREAIENFEREEKKRITSSTKGCLILIKDFNLVFQ 93 (106)
T ss_dssp EEEEEE-S----TTS-EEEEEE-SS-EEEEEE-HHHHHTS--TTS-SSSTT-TTEEEEEEEEEEEEE
T ss_pred EEEEEEEec-CCCCCcEEEEEEcCCeEEEEEECHHHHHHHHHhccCcccccCCceEEEEEEEEEEEE
Confidence 566665500 2335689999999999999999854443333211 12789999999988765
No 68
>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=88.70 E-value=3.8 Score=34.34 Aligned_cols=74 Identities=12% Similarity=0.096 Sum_probs=48.2
Q ss_pred EEEEEEEeeccccccccCCCCceeEEEEEEeCCCCeEEEEEchhHHH--HHHhhcccCcEEEEeceEEecCCCcccCCCC
Q 006263 222 AIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAVVD--RFYEIIEVGRVYLISKGSLKPAQKNFNHLKN 299 (653)
Q Consensus 222 ~I~~RV~~k~~ir~~~~~~g~gk~f~~~L~D~~g~~I~at~f~~~~~--kf~~~l~eG~vy~is~~~V~~a~~~f~~~~~ 299 (653)
+|+|||.++ |. .|++.-++|.| .++.+++.+..+... ++...|..|+++.+.+- +....+.- ...+
T Consensus 3 ~v~Gwv~~~---R~------~g~~~Fi~LrD-~~~~iQ~v~~~~~~~~~~~~~~l~~es~V~V~G~-v~~~~~~~-~~~~ 70 (84)
T cd04323 3 KVFGWVHRL---RS------QKKLMFLVLRD-GTGFLQCVLSKKLVTEFYDAKSLTQESSVEVTGE-VKEDPRAK-QAPG 70 (84)
T ss_pred EEEEEEEEE---ec------CCCcEEEEEEc-CCeEEEEEEcCCcchhHHHHhcCCCcCEEEEEEE-EEECCccc-CCCC
Confidence 678888664 22 25666678899 677899988654322 23356889999999774 44333221 3456
Q ss_pred ceEEEecc
Q 006263 300 EWEIFLEA 307 (653)
Q Consensus 300 ~yei~f~~ 307 (653)
+|||...+
T Consensus 71 ~~Ei~~~~ 78 (84)
T cd04323 71 GYELQVDY 78 (84)
T ss_pred CEEEEEEE
Confidence 79988744
No 69
>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=88.44 E-value=3.7 Score=34.47 Aligned_cols=74 Identities=20% Similarity=0.219 Sum_probs=49.0
Q ss_pred EEEEEEEeeccccccccCCCCceeEEEEEEeCCCCeEEEEEchhHH---HHHHhhcccCcEEEEeceEEecCCCcccCCC
Q 006263 222 AIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAVV---DRFYEIIEVGRVYLISKGSLKPAQKNFNHLK 298 (653)
Q Consensus 222 ~I~~RV~~k~~ir~~~~~~g~gk~f~~~L~D~~g~~I~at~f~~~~---~kf~~~l~eG~vy~is~~~V~~a~~~f~~~~ 298 (653)
+|+|||.++ |. .|++.-++|.| .++.+++.+-.+.. .++...|..|+++.+.+.-.....+. ...
T Consensus 3 ~i~Gwv~~~---R~------~g~~~Fi~Lrd-~~~~iQ~v~~~~~~~~~~~~~~~l~~~s~V~v~G~~~~~~~~~--~~~ 70 (85)
T cd04100 3 TLAGWVHSR---RD------HGGLIFIDLRD-GSGIVQVVVNKEELGEFFEEAEKLRTESVVGVTGTVVKRPEGN--LAT 70 (85)
T ss_pred EEEEEEehh---cc------CCCEEEEEEEe-CCeeEEEEEECCcChHHHHHHhCCCCCCEEEEEeEEEECCCCC--CCC
Confidence 678888553 33 35666678889 67899998865432 23456799999999988644432221 234
Q ss_pred CceEEEecc
Q 006263 299 NEWEIFLEA 307 (653)
Q Consensus 299 ~~yei~f~~ 307 (653)
.++||..+.
T Consensus 71 ~~~El~~~~ 79 (85)
T cd04100 71 GEIELQAEE 79 (85)
T ss_pred CCEEEEEeE
Confidence 678887643
No 70
>PRK07373 DNA polymerase III subunit alpha; Reviewed
Probab=87.63 E-value=1.8 Score=48.36 Aligned_cols=71 Identities=17% Similarity=0.252 Sum_probs=52.5
Q ss_pred eeccccC--CCCCceEEEEEEEeeccccccccCCCCceeEEEEEEeCCCCeEEEEEchhHHHHHHhhcccCcEEEEec
Q 006263 209 IPIAALN--PYQGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISK 284 (653)
Q Consensus 209 ~pI~~L~--p~~~~w~I~~RV~~k~~ir~~~~~~g~gk~f~~~L~D~~g~~I~at~f~~~~~kf~~~l~eG~vy~is~ 284 (653)
.++++|. +.....+|-|.|+..-.++ .++|+ .+.-+.|-| ..|.|.+++|.+..+++.+.|++|.++.|.+
T Consensus 269 ~~~~~l~~~~~~~~v~vaG~I~~ik~~~---TKkG~-~maf~~leD-~tG~ie~vvFp~~y~~~~~~l~~~~~v~v~G 341 (449)
T PRK07373 269 INLSELEEQKEKTKVSAVVMLNEVKKIV---TKKGD-PMAFLQLED-LSGQSEAVVFPKSYERISELLQVDARLIIWG 341 (449)
T ss_pred cCHHHHhcccCCCEEEEEEEEEEeEecc---cCCCC-EEEEEEEEE-CCCCEEEEECHHHHHHHHHHhccCCEEEEEE
Confidence 3566664 2234567888888754433 34443 455567888 8999999999999999999999999999965
No 71
>PRK02801 primosomal replication protein N; Provisional
Probab=87.39 E-value=2.9 Score=36.66 Aligned_cols=68 Identities=15% Similarity=0.077 Sum_probs=53.1
Q ss_pred CCceEEEEEEEeeccccccccCCCCceeEEEEEEeC----C-CC------eEEEEEchhHHHHHHhhcccCcEEEEeceE
Q 006263 218 QGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDS----D-GG------EIRVTCFNAVVDRFYEIIEVGRVYLISKGS 286 (653)
Q Consensus 218 ~~~w~I~~RV~~k~~ir~~~~~~g~gk~f~~~L~D~----~-g~------~I~at~f~~~~~kf~~~l~eG~vy~is~~~ 286 (653)
+|+-.+.||+++.-++|...+ | -.+.+|.|.=. + +. .|.|++|++.++.+...|..|+.+.|.++.
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 467889999999999997532 2 25667766421 2 22 299999999999999999999999999986
Q ss_pred Ee
Q 006263 287 LK 288 (653)
Q Consensus 287 V~ 288 (653)
-.
T Consensus 79 ~~ 80 (101)
T PRK02801 79 SC 80 (101)
T ss_pred EE
Confidence 43
No 72
>COG5235 RFA2 Single-stranded DNA-binding replication protein A (RPA), medium (30 kD) subunit [DNA replication, recombination, and repair]
Probab=87.23 E-value=2.2 Score=41.77 Aligned_cols=53 Identities=25% Similarity=0.421 Sum_probs=33.5
Q ss_pred EEEEEEeCCCCEEEEEEccchhhhhhhhHHHhhcc-CCCcEEEEEeeEeecCCCc-eecccc
Q 006263 369 RILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVDV-GFFPVLSVKSGKVNDFSGK-SIGTIP 428 (653)
Q Consensus 369 r~i~l~D~s~~~i~vtLWg~~A~~~~~~l~~~~~~-~~~~Vvaik~~rV~~f~G~-sLs~~~ 428 (653)
..++|.|.+| .|+|+.|-..+.+. +.... ..+--|- -+.-++.|+|| +++...
T Consensus 85 ~~~~iEDGTG-~Ievr~W~~~~~~~-----e~~~d~~~~~yvk-V~G~lk~F~GK~~I~~~~ 139 (258)
T COG5235 85 SMFVIEDGTG-SIEVRFWPGNSYEE-----EQCKDLEEQNYVK-VNGSLKTFNGKRSISASH 139 (258)
T ss_pred eEEEEecCCc-eEEEEecCCCchHH-----HhccccccccEEE-EecceeeeCCeeEEehhh
Confidence 4678999999 89999999887652 22221 1122222 24456789996 776443
No 73
>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=87.14 E-value=4.4 Score=35.15 Aligned_cols=81 Identities=20% Similarity=0.253 Sum_probs=55.4
Q ss_pred cEEEEEEEecCceeEEecCCceeeEEEEEEEeCCCCEEEEEEccchhhhhhhhHHHhhccCCCcEEEEEeeEeecCC--C
Q 006263 344 DVIGIVISVNPSVPILRKNGMETQRRILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVDVGFFPVLSVKSGKVNDFS--G 421 (653)
Q Consensus 344 DVIGvV~~v~~~~~i~~k~g~~~~kr~i~l~D~s~~~i~vtLWg~~A~~~~~~l~~~~~~~~~~Vvaik~~rV~~f~--G 421 (653)
|++|+|++|+...+ | ..-.+.|.|+.-.-+-+.+|........+ +.. .++..||+.+...+-.. |
T Consensus 1 D~VGvVvsV~~~~~-----g---~~~~vYLaDe~~nll~vkfw~~l~~~~~E---Dvv--k~~~lia~SNLQwR~~s~~~ 67 (100)
T cd04495 1 DTVGVVISVGKPIE-----G---KFPAVYLADECLNLLCVKFWSSLEQYAYE---DVV--KRRVLLAASNLQWRTESTSG 67 (100)
T ss_pred CceEEEEEEccccc-----C---ccceEEEecCCcCEEEEEEecchHHhhhh---hhc--ccceEEEEecceEeccccCC
Confidence 89999999998751 2 23468999999999999999976543211 111 34567888888776543 3
Q ss_pred c-eeccccceEEEEcCC
Q 006263 422 K-SIGTIPSTQLFINPD 437 (653)
Q Consensus 422 ~-sLs~~~~S~i~inPd 437 (653)
. +|-.+.-|.+..||.
T Consensus 68 iPtl~Age~t~FS~nPK 84 (100)
T cd04495 68 VPTLFAGEYSTFSANPK 84 (100)
T ss_pred CceeeeecceeecCCcc
Confidence 3 444566677777773
No 74
>PRK13480 3'-5' exoribonuclease YhaM; Provisional
Probab=86.33 E-value=2.2 Score=45.40 Aligned_cols=70 Identities=11% Similarity=0.065 Sum_probs=49.2
Q ss_pred eccccCCCCCceEEEEEEEeeccccccccCCCCceeEEEEEEeCCCCeEEEEEchhHHHHHHhhcccCcEEEEeceE
Q 006263 210 PIAALNPYQGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISKGS 286 (653)
Q Consensus 210 pI~~L~p~~~~w~I~~RV~~k~~ir~~~~~~g~gk~f~~~L~D~~g~~I~at~f~~~~~kf~~~l~eG~vy~is~~~ 286 (653)
.|++|.++. .......|..+ .+|+-+| | ...++++|.| .+|+|.|.+|+.. +.....+++|+++.+.+-.
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-KPFLTLILQD-KSGDIEAKLWDVS-PEDEATYVPETIVHVKGDI 73 (314)
T ss_pred hHhhcCCCC-EeeEEEEEEEc-eeeecCC--C-CeEEEEEEEc-CCcEEEEEeCCCC-hhhHhhcCCCCEEEEEEEE
Confidence 578888765 33434444443 3343221 1 2589999999 8999999999864 5668889999999888754
No 75
>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=86.31 E-value=12 Score=32.88 Aligned_cols=81 Identities=16% Similarity=0.078 Sum_probs=54.7
Q ss_pred CceEEEEEEEeeccccccccCCCCceeEEEEEEeCCCCeEEEEEchhH----HHHHHhhcccCcEEEEeceEEecCCCcc
Q 006263 219 GRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAV----VDRFYEIIEVGRVYLISKGSLKPAQKNF 294 (653)
Q Consensus 219 ~~w~I~~RV~~k~~ir~~~~~~g~gk~f~~~L~D~~g~~I~at~f~~~----~~kf~~~l~eG~vy~is~~~V~~a~~~f 294 (653)
...+|+|||.++ |. .|++.-++|.| .++.|++.+-.+. +-++-..|..|+++.+.+--.+...
T Consensus 13 ~~V~v~Gwv~~~---R~------~g~~~Fi~LrD-~~g~iQ~v~~~~~~~~~~~~~~~~l~~es~V~V~G~v~~~~~--- 79 (108)
T cd04316 13 EEVTVAGWVHEI---RD------LGGIKFVILRD-REGIVQVTAPKKKVDKELFKTVRKLSRESVISVTGTVKAEPK--- 79 (108)
T ss_pred CEEEEEEEEEee---ec------cCCeEEEEEec-CCeeEEEEEeCCCCCHHHHHHHhCCCCcCEEEEEEEEEeCCC---
Confidence 358899999764 33 24666677888 5779999887542 2233356899999999996443322
Q ss_pred cCCCCceEEEeccccEEEec
Q 006263 295 NHLKNEWEIFLEATSTVDLC 314 (653)
Q Consensus 295 ~~~~~~yei~f~~~T~I~~~ 314 (653)
...+|||....-..+..+
T Consensus 80 --~~~~~Ei~~~~i~il~~~ 97 (108)
T cd04316 80 --APNGVEIIPEEIEVLSEA 97 (108)
T ss_pred --CCCCEEEEEeEEEEEeCC
Confidence 135799998775555554
No 76
>PRK05733 single-stranded DNA-binding protein; Provisional
Probab=85.91 E-value=3 Score=40.27 Aligned_cols=65 Identities=22% Similarity=0.246 Sum_probs=50.5
Q ss_pred CCCceEEEEEEEeeccccccccCCCCceeEEEEEE------eCCCC-------eEEEEEchhHHHHHHhhcccCcEEEEe
Q 006263 217 YQGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLL------DSDGG-------EIRVTCFNAVVDRFYEIIEVGRVYLIS 283 (653)
Q Consensus 217 ~~~~w~I~~RV~~k~~ir~~~~~~g~gk~f~~~L~------D~~g~-------~I~at~f~~~~~kf~~~l~eG~vy~is 283 (653)
.+++-+|.|||.+--.+|.+.+ | ..+.+|.|. |+++| -+.+++|+..++.+...|+.|+.++|.
T Consensus 4 ~mNkV~LiGrlg~DPElr~t~n--G-~~va~fsVAv~~~~k~~~~Ge~~e~T~w~~Vv~fgk~Ae~v~~~l~KGs~V~Ve 80 (172)
T PRK05733 4 GVNKVILVGTCGQDPEVRYLPN--G-NAVTNLSLATSEQWTDKQSGQKVERTEWHRVSLFGKVAEIAGEYLRKGSQVYIE 80 (172)
T ss_pred cceEEEEEEEecCCCEEEECCC--C-CEEEEEEEEEcCccccCCCCcccccceEEEEEEehHHHHHHHHHhCCCCEEEEE
Confidence 3578899999999888887654 2 256666654 22223 399999999999999999999999998
Q ss_pred c
Q 006263 284 K 284 (653)
Q Consensus 284 ~ 284 (653)
+
T Consensus 81 G 81 (172)
T PRK05733 81 G 81 (172)
T ss_pred E
Confidence 6
No 77
>PRK06751 single-stranded DNA-binding protein; Provisional
Probab=85.71 E-value=2.8 Score=40.55 Aligned_cols=64 Identities=22% Similarity=0.296 Sum_probs=50.2
Q ss_pred CCceEEEEEEEeeccccccccCCCCceeEEEEEE------eCCC----CeEEEEEchhHHHHHHhhcccCcEEEEec
Q 006263 218 QGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLL------DSDG----GEIRVTCFNAVVDRFYEIIEVGRVYLISK 284 (653)
Q Consensus 218 ~~~w~I~~RV~~k~~ir~~~~~~g~gk~f~~~L~------D~~g----~~I~at~f~~~~~kf~~~l~eG~vy~is~ 284 (653)
+++..|.|||++--++|...+ | ..+.+|.|+ ++.| .-|.+++|+..++.+...|+.|+-+.|.+
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 467899999999999986532 2 257677764 2222 46899999999999999999999998876
No 78
>PRK07459 single-stranded DNA-binding protein; Provisional
Probab=85.01 E-value=3.6 Score=37.36 Aligned_cols=64 Identities=13% Similarity=0.222 Sum_probs=52.1
Q ss_pred CCceEEEEEEEeeccccccccCCCCceeEEEEEE------eCCCCeEEEEEchhHHHHHHhhcccCcEEEEec
Q 006263 218 QGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLL------DSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISK 284 (653)
Q Consensus 218 ~~~w~I~~RV~~k~~ir~~~~~~g~gk~f~~~L~------D~~g~~I~at~f~~~~~kf~~~l~eG~vy~is~ 284 (653)
.+.-.|.||+.+--.+|...+ | ..+.+|.|+ |++.+=+.+++|+..++.+...|+.|+-+.+.+
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 367889999999888887543 2 257777776 235778999999999999999999999999886
No 79
>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=84.88 E-value=4.7 Score=37.53 Aligned_cols=107 Identities=18% Similarity=0.341 Sum_probs=57.4
Q ss_pred cchhhhhh---cccCccccEEEEEEEecCceeEEecCCceeeEEEEEEEeCCCCEEEEEEccchhhhhhhhHHHhhccCC
Q 006263 329 RHISEIES---AENNSIVDVIGIVISVNPSVPILRKNGMETQRRILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVDVGF 405 (653)
Q Consensus 329 ~~i~~i~~---~~~~~~vDVIGvV~~v~~~~~i~~k~g~~~~kr~i~l~D~s~~~i~vtLWg~~A~~~~~~l~~~~~~~~ 405 (653)
+.|++|.+ .+.=.-||++|+|+.|.. +.|- .--+.|.|....-+.|-.|++...-- +.+. -.+
T Consensus 4 ~~f~~l~~p~f~pp~~EvD~VG~VvsV~~------~~~f---~~~vYLsD~~~Nll~Ikfw~~l~~~~---~eDi--lk~ 69 (143)
T PF09104_consen 4 THFSDLQDPDFQPPYGEVDTVGFVVSVSK------KQGF---QPLVYLSDECHNLLAIKFWTGLNQYG---YEDI--LKP 69 (143)
T ss_dssp --CGGGGSTT--TCCCEEEEEEEEEEEE--------TTS-----EEEEE-TTS-EEEEEESS----------SS-----T
T ss_pred echhhhcCcccCCCccccceEEEEEEEEe------cCCC---ceeEEeecCCccEEEEEeccCccccc---hhhh--cCc
Confidence 34566655 234568999999999921 1221 12378889999899999999986321 0011 146
Q ss_pred CcEEEEEeeEee-cC-CCc-eeccccceEEEEcCC---hHH-HHHHHHHHh
Q 006263 406 FPVLSVKSGKVN-DF-SGK-SIGTIPSTQLFINPD---FAE-AHELREWFD 449 (653)
Q Consensus 406 ~~Vvaik~~rV~-~f-~G~-sLs~~~~S~i~inPd---ipe-~~~l~~w~~ 449 (653)
+.+||+.+..-+ +. .|. .+-.+.-|.+.-||. ..| ...|+.-+.
T Consensus 70 ~~liA~SNLqwR~~s~s~iP~~~A~d~S~FS~nPK~~hLqe~~~~Lk~~i~ 120 (143)
T PF09104_consen 70 GSLIAASNLQWRPESTSGIPTLFATDLSVFSANPKESHLQEAFNKLKNTIE 120 (143)
T ss_dssp T-EEEEEEEEE-S-TTSSS-EEEEECCEEEESS-SSCCCHHHHHHHCHHHH
T ss_pred ceEEEEeeeEeecccccCCCeeEeccceeeecCccHHHHHHHHHHHHHHhh
Confidence 889999987664 22 333 455677788888883 333 345555444
No 80
>PRK13732 single-stranded DNA-binding protein; Provisional
Probab=84.67 E-value=3.9 Score=39.62 Aligned_cols=65 Identities=22% Similarity=0.272 Sum_probs=51.5
Q ss_pred CCCceEEEEEEEeeccccccccCCCCceeEEEEEE------eCCCC-------eEEEEEchhHHHHHHhhcccCcEEEEe
Q 006263 217 YQGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLL------DSDGG-------EIRVTCFNAVVDRFYEIIEVGRVYLIS 283 (653)
Q Consensus 217 ~~~~w~I~~RV~~k~~ir~~~~~~g~gk~f~~~L~------D~~g~-------~I~at~f~~~~~kf~~~l~eG~vy~is 283 (653)
.++..+|.||+.+--++|.+.+ | ..+.+|.|+ |.++| -+++++|+..++.+...|+.|+.+++.
T Consensus 5 ~mN~V~LiGrLg~DPElR~t~n--G-~~va~fslAvn~~~kd~~~Ge~~e~t~w~~Vv~wgk~Ae~v~~~L~KG~~V~Ve 81 (175)
T PRK13732 5 GINKVILVGRLGKDPEVRYIPN--G-GAVANLQVATSESWRDKQTGEMREQTEWHRVVLFGKLAEVAGEYLRKGAQVYIE 81 (175)
T ss_pred CceEEEEEEEecCCCEEEEcCC--C-CEEEEEEEEEcCccccCCCCceecceeEEEEEEecHHHHHHHHhcCCCCEEEEE
Confidence 3578999999999888888654 2 367777765 22223 468999999999999999999999988
Q ss_pred c
Q 006263 284 K 284 (653)
Q Consensus 284 ~ 284 (653)
+
T Consensus 82 G 82 (175)
T PRK13732 82 G 82 (175)
T ss_pred E
Confidence 7
No 81
>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=84.60 E-value=2.8 Score=34.32 Aligned_cols=39 Identities=21% Similarity=0.399 Sum_probs=29.5
Q ss_pred EEEEEEEecCceeEEecCCceeeEEEEEEEeCCCCEEEEEEccchhhhh
Q 006263 345 VIGIVISVNPSVPILRKNGMETQRRILNLKDTSGRSVELTLWGDFCNKE 393 (653)
Q Consensus 345 VIGvV~~v~~~~~i~~k~g~~~~kr~i~l~D~s~~~i~vtLWg~~A~~~ 393 (653)
|.|.|.++.. +|.| .--++|.|.++ .+++++|.+....+
T Consensus 4 v~g~v~~i~~-----tk~g----~~~~~L~D~~~-~i~~~~f~~~~~~~ 42 (78)
T cd04489 4 VEGEISNLKR-----PSSG----HLYFTLKDEDA-SIRCVMWRSNARRL 42 (78)
T ss_pred EEEEEecCEE-----CCCc----EEEEEEEeCCe-EEEEEEEcchhhhC
Confidence 5677776553 3445 67899999998 89999999976553
No 82
>PRK08763 single-stranded DNA-binding protein; Provisional
Probab=84.07 E-value=4.4 Score=38.87 Aligned_cols=64 Identities=17% Similarity=0.220 Sum_probs=50.6
Q ss_pred CCceEEEEEEEeeccccccccCCCCceeEEEEEE------eCCCC------eEEEEEchhHHHHHHhhcccCcEEEEec
Q 006263 218 QGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLL------DSDGG------EIRVTCFNAVVDRFYEIIEVGRVYLISK 284 (653)
Q Consensus 218 ~~~w~I~~RV~~k~~ir~~~~~~g~gk~f~~~L~------D~~g~------~I~at~f~~~~~kf~~~l~eG~vy~is~ 284 (653)
.++..|.+|+.+--.+|...+ | ..+.+|.|+ |++|. -+++++|+..++.....|+.|+-++|.+
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 678999999999888886543 2 357677665 43443 3899999999999999999999999886
No 83
>PRK05159 aspC aspartyl-tRNA synthetase; Provisional
Probab=84.03 E-value=6.6 Score=43.84 Aligned_cols=92 Identities=15% Similarity=0.099 Sum_probs=65.4
Q ss_pred eeccccCCCC--CceEEEEEEEeeccccccccCCCCceeEEEEEEeCCCCeEEEEEchhH---HHHHHhhcccCcEEEEe
Q 006263 209 IPIAALNPYQ--GRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAV---VDRFYEIIEVGRVYLIS 283 (653)
Q Consensus 209 ~pI~~L~p~~--~~w~I~~RV~~k~~ir~~~~~~g~gk~f~~~L~D~~g~~I~at~f~~~---~~kf~~~l~eG~vy~is 283 (653)
+.|.+|++.. ..-+|+|||.++ |. .|++.-++|.| .+|.|++++-.+. ..++-..|..|+++.+.
T Consensus 5 ~~~~~l~~~~~g~~V~i~GrV~~~---R~------~gk~~Fl~LrD-~~g~iQ~v~~~~~~~~~~~~~~~L~~gs~V~v~ 74 (437)
T PRK05159 5 HLTSELTPELDGEEVTLAGWVHEI---RD------LGGIAFLILRD-RSGIIQVVVKKKVDEELFETIKKLKRESVVSVT 74 (437)
T ss_pred eEhhhCChhhCCCEEEEEEEeEee---ec------CCCeEEEEEEc-CCcEEEEEEeCCccHHHHHHHhCCCCCcEEEEE
Confidence 4678888776 468899999875 33 35777788999 6779999986432 23344668999999999
Q ss_pred ceEEecCCCcccCCCCceEEEeccccEEEecc
Q 006263 284 KGSLKPAQKNFNHLKNEWEIFLEATSTVDLCT 315 (653)
Q Consensus 284 ~~~V~~a~~~f~~~~~~yei~f~~~T~I~~~~ 315 (653)
+.-++... ....+||....-+.+..+.
T Consensus 75 G~v~~~~~-----~~~~~el~~~~i~vls~a~ 101 (437)
T PRK05159 75 GTVKANPK-----APGGVEVIPEEIEVLNKAE 101 (437)
T ss_pred EEEEcCCC-----CCCCEEEEEeEEEEEeCCC
Confidence 96554321 2356999997777776663
No 84
>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=83.79 E-value=2 Score=36.85 Aligned_cols=53 Identities=17% Similarity=0.151 Sum_probs=38.2
Q ss_pred EEEEEEEeeccccccccCCCCceeEEEEEEeCCCCeEEEEEchhHHH---HHHhhcccCcEEEEec
Q 006263 222 AIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAVVD---RFYEIIEVGRVYLISK 284 (653)
Q Consensus 222 ~I~~RV~~k~~ir~~~~~~g~gk~f~~~L~D~~g~~I~at~f~~~~~---kf~~~l~eG~vy~is~ 284 (653)
++.|+|.++.. .+..+.+.|.| .+|.|.|.+|...-+ .-.+.+++|+++.+.+
T Consensus 3 ~~vG~V~~~~~---------~~~~~~~tL~D-~TG~I~~~~W~~~~~~~~~~~~~~~~g~~v~v~G 58 (95)
T cd04478 3 TLVGVVRNVEE---------QSTNITYTIDD-GTGTIEVRQWLDDDNDDSSEVEPIEEGTYVRVFG 58 (95)
T ss_pred EEEEEEEeeeE---------cccEEEEEEEC-CCCcEEEEEeCCCCCcccccccccccCCEEEEEE
Confidence 45666666432 13568999999 788999999986532 3467799999776654
No 85
>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=83.50 E-value=4.6 Score=34.83 Aligned_cols=47 Identities=19% Similarity=0.174 Sum_probs=38.6
Q ss_pred EEEEEeCCCCEEEEEEccchhhhhhhhHHHhhccCCCcEEEEEeeEeecCCCc
Q 006263 370 ILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVDVGFFPVLSVKSGKVNDFSGK 422 (653)
Q Consensus 370 ~i~l~D~s~~~i~vtLWg~~A~~~~~~l~~~~~~~~~~Vvaik~~rV~~f~G~ 422 (653)
++.|+|+.|..|..+++.+++..|...|. +|.+..|.+..|..-.|.
T Consensus 1 emvL~De~G~~I~A~I~~~~~~~f~~~l~------Eg~~y~i~~F~V~~~~~~ 47 (95)
T PF02721_consen 1 EMVLVDEKGDKIQATIPKELVDKFKDSLK------EGSWYTISNFTVSPNSGS 47 (95)
T ss_pred CEEEEecCCCEEEEEECHHHHHHHHhhcc------cCCEEEeEeEEEEeCCCc
Confidence 47899999999999999999888654442 578999999999876664
No 86
>PLN02502 lysyl-tRNA synthetase
Probab=83.02 E-value=6.5 Score=45.12 Aligned_cols=79 Identities=25% Similarity=0.403 Sum_probs=57.2
Q ss_pred CceEEEEEEEeeccccccccCCCCceeEEEEEEeCCCCeEEEEEchhH-------HHHHHhhcccCcEEEEeceEEecCC
Q 006263 219 GRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAV-------VDRFYEIIEVGRVYLISKGSLKPAQ 291 (653)
Q Consensus 219 ~~w~I~~RV~~k~~ir~~~~~~g~gk~f~~~L~D~~g~~I~at~f~~~-------~~kf~~~l~eG~vy~is~~~V~~a~ 291 (653)
...+|.|||.++ |. .|++.-++|.| .+|.|++.+-.+. .+++...|..|+++.+.+.-.+..
T Consensus 109 ~~V~v~GrV~~~---R~------~Gk~~F~~LrD-~~g~iQv~~~~~~~~~~~~~~~~~~~~l~~gdiV~V~G~~~~t~- 177 (553)
T PLN02502 109 VSVSVAGRIMAK---RA------FGKLAFYDLRD-DGGKIQLYADKKRLDLDEEEFEKLHSLVDRGDIVGVTGTPGKTK- 177 (553)
T ss_pred CEEEEEEEEEEE---ec------CCCeEEEEEec-CCccEEEEEECccccchhHHHHHHHhCCCCCcEEEEEEEEEecC-
Confidence 358899999875 32 36787889999 6889999886432 334445689999999998755432
Q ss_pred CcccCCCCceEEEeccccEEEec
Q 006263 292 KNFNHLKNEWEIFLEATSTVDLC 314 (653)
Q Consensus 292 ~~f~~~~~~yei~f~~~T~I~~~ 314 (653)
...++|...+-+.+.+|
T Consensus 178 ------~gelel~~~~i~vLs~~ 194 (553)
T PLN02502 178 ------KGELSIFPTSFEVLTKC 194 (553)
T ss_pred ------CCCEEEEEeEEEEEecc
Confidence 23688888777666666
No 87
>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=82.92 E-value=6.2 Score=33.14 Aligned_cols=59 Identities=19% Similarity=0.245 Sum_probs=43.5
Q ss_pred eEEEEEEEeeccccccccCCCCceeEEEEEEeCCCCeEEEEEch-hHHHHHHhhcc-cCcEEEEece
Q 006263 221 WAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFN-AVVDRFYEIIE-VGRVYLISKG 285 (653)
Q Consensus 221 w~I~~RV~~k~~ir~~~~~~g~gk~f~~~L~D~~g~~I~at~f~-~~~~kf~~~l~-eG~vy~is~~ 285 (653)
-+|+|.|... +.|..++ | ..++++.|.| ..+.|.|..|. +..+.+ ..|+ +|+|+.+.+=
T Consensus 2 v~i~G~Vf~~-e~re~k~--g-~~i~~~~itD-~t~Si~~K~F~~~~~~~~-~~ik~~G~~v~v~G~ 62 (82)
T cd04484 2 VVVEGEVFDL-EIRELKS--G-RKILTFKVTD-YTSSITVKKFLRKDEKDK-EELKSKGDWVRVRGK 62 (82)
T ss_pred EEEEEEEEEE-EEEEecC--C-CEEEEEEEEc-CCCCEEEEEeccCChhHH-hhcccCCCEEEEEEE
Confidence 3678888765 4455543 2 4688999999 78999999998 344444 6689 9999988763
No 88
>PRK07275 single-stranded DNA-binding protein; Provisional
Probab=82.77 E-value=3.7 Score=39.27 Aligned_cols=64 Identities=14% Similarity=0.191 Sum_probs=51.1
Q ss_pred CCceEEEEEEEeeccccccccCCCCceeEEEEEE------eC----CCCeEEEEEchhHHHHHHhhcccCcEEEEec
Q 006263 218 QGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLL------DS----DGGEIRVTCFNAVVDRFYEIIEVGRVYLISK 284 (653)
Q Consensus 218 ~~~w~I~~RV~~k~~ir~~~~~~g~gk~f~~~L~------D~----~g~~I~at~f~~~~~kf~~~l~eG~vy~is~ 284 (653)
+++..|.||+++--++|...+ | ..+.+|.|+ +. +.+-|++++|+..++.+...|+.|+-+.|.+
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 367889999999999987643 2 257777775 32 3467999999999999999999999988876
No 89
>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=82.76 E-value=5.1 Score=34.30 Aligned_cols=62 Identities=19% Similarity=0.310 Sum_probs=46.4
Q ss_pred EEEEEEEeeccccccccCCCCceeEEEEEE-----------eCCCCeEEEEEchhHHHHHHhhcccCcEEEEeceE
Q 006263 222 AIKARVTAKGDLRRYNNARGDGKVFSFDLL-----------DSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISKGS 286 (653)
Q Consensus 222 ~I~~RV~~k~~ir~~~~~~g~gk~f~~~L~-----------D~~g~~I~at~f~~~~~kf~~~l~eG~vy~is~~~ 286 (653)
+|.|||...-.+|...+ | ..+.+|.|. +....-+++++|++.++.+...++.|+.+.+.+..
T Consensus 2 ~l~G~l~~~p~~~~~~~--g-~~~~~~~v~~~~~~~~~~~~~~~~~~~~v~~~g~~a~~~~~~~~kG~~V~v~G~l 74 (100)
T cd04496 2 ILIGRLGKDPELRYTPS--G-TPVARFSLAVNRRRKDRDEEEEETDWIRVVAFGKLAENAAKYLKKGDLVYVEGRL 74 (100)
T ss_pred EEEEEecCCCEEEECCC--C-CEEEEEEEEEcCceecccccccccEEEEEEEEhHHHHHHHHHhCCCCEEEEEEEE
Confidence 46788888777776543 1 245455442 23567899999999999999999999999999853
No 90
>PRK05813 single-stranded DNA-binding protein; Provisional
Probab=82.75 E-value=56 Score=32.89 Aligned_cols=162 Identities=15% Similarity=0.221 Sum_probs=98.7
Q ss_pred CCceEEEEEEEeeccccccccCCCCceeEEEEE-----EeCCCCeEEEEEchhHHHHHHhhcccCcEEEEec-eEEecCC
Q 006263 218 QGRWAIKARVTAKGDLRRYNNARGDGKVFSFDL-----LDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISK-GSLKPAQ 291 (653)
Q Consensus 218 ~~~w~I~~RV~~k~~ir~~~~~~g~gk~f~~~L-----~D~~g~~I~at~f~~~~~kf~~~l~eG~vy~is~-~~V~~a~ 291 (653)
.++-.+.||+++--++|+- ..|++ +..|.| .| ..+.|.+++|..+++... |..|+-+.+.+ ++
T Consensus 8 ~NkV~L~Grl~~d~e~~~~--~~G~~-~~~f~laV~R~s~-~~D~i~v~v~~rlae~~~--l~kG~~v~VeGqlr----- 76 (219)
T PRK05813 8 NNKVYLEGKVVSELEFSHE--MYGEG-FYNFKLEVPRLSD-SKDILPVTVSERLLAGMD--LKVGTLVIVEGQLR----- 76 (219)
T ss_pred cCEEEEEEEEcCCceEEEE--eCCeE-EEEEEEEeeccCC-CccEEEEEEEhhhhhhhc--ccCCCEEEEEEEEE-----
Confidence 3678899999999998873 33554 344443 35 789999999999998777 99999888876 44
Q ss_pred Cccc---CCCCceEEEeccccEEEeccCCCCCCCcccceecchhhhhhcccCccccEEEEEEEecCceeEEecCCceeeE
Q 006263 292 KNFN---HLKNEWEIFLEATSTVDLCTEEDDSIPKQQFSFRHISEIESAENNSIVDVIGIVISVNPSVPILRKNGMETQR 368 (653)
Q Consensus 292 ~~f~---~~~~~yei~f~~~T~I~~~~d~~~~iP~~~f~f~~i~~i~~~~~~~~vDVIGvV~~v~~~~~i~~k~g~~~~k 368 (653)
.|+ ...+.|.+.+-.. .|+.+... . ....-..|-++|.+..--.+. .+.+|+.+
T Consensus 77 -sy~~~~~G~~R~vl~V~a~-~i~~l~~~-~----------------~~~~~N~V~LiGrL~~DPelR--~t~~G~~v-- 133 (219)
T PRK05813 77 -SYNKFIDGKNRLILTVFAR-NIEYCDER-S----------------DIKNPNEIFLDGYICKEPVYR--TTPFGREI-- 133 (219)
T ss_pred -EeccCCCCcEEEEEEEEEE-EEEEccCC-C----------------ccCCccEEEEEEEccCCCeEE--ECCCCCEE--
Confidence 232 2344555444321 23333111 0 011234677888887653333 23456644
Q ss_pred EEEEEEeCC----CCEEEEEEccchhhhhhhhHHHhhccCCCcEEEEEee-EeecCC
Q 006263 369 RILNLKDTS----GRSVELTLWGDFCNKEGQKLQEMVDVGFFPVLSVKSG-KVNDFS 420 (653)
Q Consensus 369 r~i~l~D~s----~~~i~vtLWg~~A~~~~~~l~~~~~~~~~~Vvaik~~-rV~~f~ 420 (653)
-.|.|.-.. ..-|.|++||..|... ..+ ..|.-|++.|- +...|.
T Consensus 134 a~f~lAvnr~~~~td~i~~v~wg~~Ae~~-----~~l--~KG~~V~V~GrL~sr~y~ 183 (219)
T PRK05813 134 ADLLLAVNRPYNKSDYIPCIAWGRNARFC-----KTL--EVGDNIRVWGRVQSREYQ 183 (219)
T ss_pred EEEEEEEcCCCCCceEEEEEEEhHHhHHH-----hhC--CCCCEEEEEEEEEecceE
Confidence 445554321 2479999999998652 223 35777777644 445564
No 91
>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=82.64 E-value=5.5 Score=32.66 Aligned_cols=63 Identities=27% Similarity=0.387 Sum_probs=38.9
Q ss_pred EEEEEEEecCceeEEecCCceeeEEEEEEEeCCCCEEEEEEccchhhhhhhhHHHhhccCCCcEEEEEeeEeecCCC
Q 006263 345 VIGIVISVNPSVPILRKNGMETQRRILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVDVGFFPVLSVKSGKVNDFSG 421 (653)
Q Consensus 345 VIGvV~~v~~~~~i~~k~g~~~~kr~i~l~D~s~~~i~vtLWg~~A~~~~~~l~~~~~~~~~~Vvaik~~rV~~f~G 421 (653)
.+.+|.++.. ..+|.|+ ....++|.|.+| .+++++|++.-.. ...+ ..+.++.+. ++|..|+|
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-----EEKF--KPGDIVHVK-GRVEEYRG 64 (83)
T ss_pred cEEEEEEeee---ecccCCC--cEEEEEEEcCCC-eEEEEEcCCChhh-----HhhC--CCCCEEEEE-EEEEEeCC
Confidence 3445555443 2345565 357899999999 7999999965321 2223 245566555 66776766
No 92
>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=82.33 E-value=5.9 Score=37.13 Aligned_cols=84 Identities=11% Similarity=0.154 Sum_probs=58.6
Q ss_pred eeccccCCC-CCceEEEEEEEeeccccccccCCCCceeEEEEEEeCCC-------CeEEEEEchhHHHHHHhhcccCcEE
Q 006263 209 IPIAALNPY-QGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDG-------GEIRVTCFNAVVDRFYEIIEVGRVY 280 (653)
Q Consensus 209 ~pI~~L~p~-~~~w~I~~RV~~k~~ir~~~~~~g~gk~f~~~L~D~~g-------~~I~at~f~~~~~kf~~~l~eG~vy 280 (653)
+||+.+.-. ...-.|.|-|+.....+... .+|..-..+|.|.|... ..|.+.+|....+.+-..-..|+|+
T Consensus 2 ~~l~~~~~~~~~~vnvigVV~~~~~p~~~~-t~g~D~~~tl~i~D~S~~~~~~~~~~l~v~iF~~~~~~LP~v~~~GDii 80 (146)
T PF02765_consen 2 TPLSTAKEKFGKFVNVIGVVVDFSPPNPKK-TRGTDYMCTLTITDPSLNDSNQKLSGLTVNIFRPHKESLPNVKSVGDII 80 (146)
T ss_dssp CCGGGSCTTSSEEEEEEEEEEEEEEECTEE-ESSSCEEEEEEEEBTTCSCSSCCCCEEEEEEEESSHHHSCTTCSTTHEE
T ss_pred ccchhhhhcCCCEEEEEEEEEEccCCcceE-cCCCcEEEEEEEECCCCCccccccCCEEEEEECCCHHHCCCCCCCCCEE
Confidence 455533323 23577888888877662222 23444678899999643 5799999988877775555559999
Q ss_pred EEeceEEecCCCc
Q 006263 281 LISKGSLKPAQKN 293 (653)
Q Consensus 281 ~is~~~V~~a~~~ 293 (653)
.+.+++|+.-+.+
T Consensus 81 ~l~r~kv~~~~~~ 93 (146)
T PF02765_consen 81 RLRRVKVQSYNGK 93 (146)
T ss_dssp EEEEEEEEEETTE
T ss_pred EEEEEEEEEECCE
Confidence 9999999877754
No 93
>PRK09010 single-stranded DNA-binding protein; Provisional
Probab=82.21 E-value=10 Score=36.77 Aligned_cols=64 Identities=20% Similarity=0.245 Sum_probs=51.0
Q ss_pred CCceEEEEEEEeeccccccccCCCCceeEEEEEE------eCC-------CCeEEEEEchhHHHHHHhhcccCcEEEEec
Q 006263 218 QGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLL------DSD-------GGEIRVTCFNAVVDRFYEIIEVGRVYLISK 284 (653)
Q Consensus 218 ~~~w~I~~RV~~k~~ir~~~~~~g~gk~f~~~L~------D~~-------g~~I~at~f~~~~~kf~~~l~eG~vy~is~ 284 (653)
.++.+|.+||.+--.+|.+.+ | ..+.+|.|+ |.+ ..-+++++|+..++.+...|+.|+-++|..
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 578999999999999998754 2 367777664 322 234699999999999999999999999887
No 94
>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=81.77 E-value=12 Score=34.47 Aligned_cols=86 Identities=15% Similarity=0.119 Sum_probs=55.9
Q ss_pred CceEEEEEEEeeccccccccCCCCceeEEEEEEeCCCCeEEEEEchhHHH--HHHhhcccCcEEEEeceEEecCC--Ccc
Q 006263 219 GRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAVVD--RFYEIIEVGRVYLISKGSLKPAQ--KNF 294 (653)
Q Consensus 219 ~~w~I~~RV~~k~~ir~~~~~~g~gk~f~~~L~D~~g~~I~at~f~~~~~--kf~~~l~eG~vy~is~~~V~~a~--~~f 294 (653)
..-+|+|||.++ |. .|++.-++|.| .++.+++++..+..+ ++...|..|+++.+.+--..... +.-
T Consensus 15 ~~V~i~Gwv~~~---R~------~gk~~Fi~LrD-~~g~~Q~v~~~~~~~~~~~~~~l~~gs~V~V~G~~~~~~~~~~~~ 84 (135)
T cd04317 15 QEVTLCGWVQRR---RD------HGGLIFIDLRD-RYGIVQVVFDPEEAPEFELAEKLRNESVIQVTGKVRARPEGTVNP 84 (135)
T ss_pred CEEEEEEeEehh---cc------cCCEEEEEEec-CCeeEEEEEeCCchhHHHHHhCCCCccEEEEEEEEECCCccccCC
Confidence 358899999663 33 35666678888 567899998654333 34456999999999996443221 111
Q ss_pred cCCCCceEEEeccccEEEec
Q 006263 295 NHLKNEWEIFLEATSTVDLC 314 (653)
Q Consensus 295 ~~~~~~yei~f~~~T~I~~~ 314 (653)
.....++||....-..+.++
T Consensus 85 ~~~~~~~El~~~~i~vl~~~ 104 (135)
T cd04317 85 KLPTGEIEVVASELEVLNKA 104 (135)
T ss_pred CCCCCcEEEEEeEEEEEECC
Confidence 12345799998765555544
No 95
>PRK07772 single-stranded DNA-binding protein; Provisional
Probab=81.19 E-value=8.3 Score=37.78 Aligned_cols=64 Identities=17% Similarity=0.271 Sum_probs=48.7
Q ss_pred CCceEEEEEEEeeccccccccCCCCceeEEEEEE------eC--------CCCeEEEEEchhHHHHHHhhcccCcEEEEe
Q 006263 218 QGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLL------DS--------DGGEIRVTCFNAVVDRFYEIIEVGRVYLIS 283 (653)
Q Consensus 218 ~~~w~I~~RV~~k~~ir~~~~~~g~gk~f~~~L~------D~--------~g~~I~at~f~~~~~kf~~~l~eG~vy~is 283 (653)
.+..+|.+|++.--.+|...+ | ..+.+|.|+ |. +..-|++++|+.+++.+...|+.|+-+.+.
T Consensus 4 ~~~VtLiGrL~~DPElR~t~s--G-~~va~FrVAv~~r~~~~~~g~~~d~~t~fi~V~~Wg~~Ae~va~~L~KGd~V~V~ 80 (186)
T PRK07772 4 DTTITVVGNLTADPELRFTPS--G-AAVANFTVASTPRTFDRQTNEWKDGEALFLRCSIWRQAAENVAESLTKGMRVIVT 80 (186)
T ss_pred cCEEEEEEEeCCCCeEEEcCC--C-CEEEEEEEEecCcceecCCCcEeccCceEEEEEEecHHHHHHHHhcCCCCEEEEE
Confidence 356789999999988887643 2 245566655 11 234679999999999999999999999888
Q ss_pred c
Q 006263 284 K 284 (653)
Q Consensus 284 ~ 284 (653)
.
T Consensus 81 G 81 (186)
T PRK07772 81 G 81 (186)
T ss_pred E
Confidence 6
No 96
>PRK06293 single-stranded DNA-binding protein; Provisional
Probab=81.14 E-value=5.6 Score=38.00 Aligned_cols=64 Identities=16% Similarity=0.125 Sum_probs=51.3
Q ss_pred CCceEEEEEEEeeccccccccCCCCceeEEEEEEe-------CCCCeEEEEEchhHHHHHHhhcccCcEEEEec
Q 006263 218 QGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLD-------SDGGEIRVTCFNAVVDRFYEIIEVGRVYLISK 284 (653)
Q Consensus 218 ~~~w~I~~RV~~k~~ir~~~~~~g~gk~f~~~L~D-------~~g~~I~at~f~~~~~kf~~~l~eG~vy~is~ 284 (653)
++..+|.+|+.+--.+|...+ | ..+.+|.|+= ++..-|++++|+..++.....|+.|+-+.+.+
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 467889999999888887543 2 2577777762 24667999999999999999999999999886
No 97
>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=81.05 E-value=5.9 Score=33.34 Aligned_cols=52 Identities=15% Similarity=0.077 Sum_probs=41.4
Q ss_pred eeeEEEEEEEeCCCCEEEEEEccchhhhhhhhHHHhhccCCCcEEEEEeeEeecCCCc
Q 006263 365 ETQRRILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVDVGFFPVLSVKSGKVNDFSGK 422 (653)
Q Consensus 365 ~~~kr~i~l~D~s~~~i~vtLWg~~A~~~~~~l~~~~~~~~~~Vvaik~~rV~~f~G~ 422 (653)
.....++.|.|+.|..|..+.+.+.+..|...|. +|-+..|.+.+|..-.+.
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 3456789999999999999999999888654443 478888999999876553
No 98
>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=81.03 E-value=3.6 Score=35.96 Aligned_cols=39 Identities=18% Similarity=0.295 Sum_probs=34.7
Q ss_pred ceEEEEEecccceeeeeecccchhhcccCCcccCcEEEE
Q 006263 37 ERYRFLISDSVSTQHAMLATQLNDRVKTGQVKKGSVVQL 75 (653)
Q Consensus 37 ~ryr~~lSDG~~~~~~ml~t~ln~~v~~~~l~~~sIIkl 75 (653)
..-.+.|+||=|.+++.+...|+.++++|.|..|.=+++
T Consensus 21 ~~~~lEltDGWYsi~a~lD~~L~~~l~~gkl~vGqKL~i 59 (100)
T cd04493 21 HMPIIELTDGWYSIRAQLDPPLTNLVRKGKLRVGQKLRI 59 (100)
T ss_pred cccEEEEecCeEEEEEEeCHHHHHHHHcCCeecccEEEE
Confidence 456899999999999999999999999999998876655
No 99
>PRK13480 3'-5' exoribonuclease YhaM; Provisional
Probab=80.59 E-value=8.2 Score=41.06 Aligned_cols=75 Identities=25% Similarity=0.336 Sum_probs=51.6
Q ss_pred hhhcccCccccEEEEEEEecCceeEEecCCceeeEEEEEEEeCCCCEEEEEEccchhhhhhhhHHHhhccCCCcEEEEEe
Q 006263 334 IESAENNSIVDVIGIVISVNPSVPILRKNGMETQRRILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVDVGFFPVLSVKS 413 (653)
Q Consensus 334 i~~~~~~~~vDVIGvV~~v~~~~~i~~k~g~~~~kr~i~l~D~s~~~i~vtLWg~~A~~~~~~l~~~~~~~~~~Vvaik~ 413 (653)
|.++..+..|+.+..|++..-- ++|+|+. ...++|.|.|| +|+..+|+..-.. ...|. .+.||-++|
T Consensus 5 i~~l~~g~~v~~~~lv~~~~~~---~~knG~~--yl~l~l~D~tG-~I~ak~W~~~~~~-----~~~~~--~g~vv~v~G 71 (314)
T PRK13480 5 IEELEVGEQVDHFLLIKSATKG---VASNGKP--FLTLILQDKSG-DIEAKLWDVSPED-----EATYV--PETIVHVKG 71 (314)
T ss_pred HhhcCCCCEeeEEEEEEEceee---ecCCCCe--EEEEEEEcCCc-EEEEEeCCCChhh-----HhhcC--CCCEEEEEE
Confidence 3344457788888888876432 2467764 78999999999 8999999975322 23343 466776654
Q ss_pred eEeecCCCc
Q 006263 414 GKVNDFSGK 422 (653)
Q Consensus 414 ~rV~~f~G~ 422 (653)
+|.+|+|+
T Consensus 72 -~v~~y~g~ 79 (314)
T PRK13480 72 -DIINYRGR 79 (314)
T ss_pred -EEEEECCc
Confidence 55689985
No 100
>PTZ00417 lysine-tRNA ligase; Provisional
Probab=80.11 E-value=10 Score=43.82 Aligned_cols=78 Identities=28% Similarity=0.349 Sum_probs=52.1
Q ss_pred ceEEEEEEEeeccccccccCCCCc-eeEEEEEEeCCCCeEEEEEchhH-------HHHHHhhcccCcEEEEeceEEecCC
Q 006263 220 RWAIKARVTAKGDLRRYNNARGDG-KVFSFDLLDSDGGEIRVTCFNAV-------VDRFYEIIEVGRVYLISKGSLKPAQ 291 (653)
Q Consensus 220 ~w~I~~RV~~k~~ir~~~~~~g~g-k~f~~~L~D~~g~~I~at~f~~~-------~~kf~~~l~eG~vy~is~~~V~~a~ 291 (653)
..+|.|||.++ |. .| ++.-++|.| +||.||+.+-.+. .+.+...|..|+++.+.+.-.+
T Consensus 134 ~v~v~Grv~~~---R~------~G~k~~F~~L~d-~~g~iQv~~~~~~~~~~~~~~~~~~~~l~~Gd~V~V~G~~~~--- 200 (585)
T PTZ00417 134 ILNVTGRIMRV---SA------SGQKLRFFDLVG-DGAKIQVLANFAFHDHTKSNFAECYDKIRRGDIVGIVGFPGK--- 200 (585)
T ss_pred eEEEEEEEEee---ec------CCCCCEEEEEEe-CCeeEEEEEECCccCCCHHHHHHHHhcCCCCCEEEEEeEEcC---
Confidence 47899999874 43 25 566678889 7889999996431 2333456999999999997322
Q ss_pred CcccCCCCceEEEeccccEEEec
Q 006263 292 KNFNHLKNEWEIFLEATSTVDLC 314 (653)
Q Consensus 292 ~~f~~~~~~yei~f~~~T~I~~~ 314 (653)
+-...++|....-+.+.++
T Consensus 201 ----t~~gel~i~~~~i~llsk~ 219 (585)
T PTZ00417 201 ----SKKGELSIFPKETIILSPC 219 (585)
T ss_pred ----CCCceEEEEEEEEEEEecC
Confidence 1134566666655555544
No 101
>PRK08486 single-stranded DNA-binding protein; Provisional
Probab=80.00 E-value=6.6 Score=38.32 Aligned_cols=63 Identities=16% Similarity=0.217 Sum_probs=49.1
Q ss_pred CceEEEEEEEeeccccccccCCCCceeEEEEEE------eC------CCCeEEEEEchhHHHHHHhhcccCcEEEEec
Q 006263 219 GRWAIKARVTAKGDLRRYNNARGDGKVFSFDLL------DS------DGGEIRVTCFNAVVDRFYEIIEVGRVYLISK 284 (653)
Q Consensus 219 ~~w~I~~RV~~k~~ir~~~~~~g~gk~f~~~L~------D~------~g~~I~at~f~~~~~kf~~~l~eG~vy~is~ 284 (653)
++-.|.+|+++--++|...+ | ..+.+|.|+ ++ +..-|.+++|+..++.+...|+.|+-+.|.+
T Consensus 3 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 3 NKVILVGNLTRDVELRYLPS--G-SAIATIGLATSRRFKKQDGEKGEEVCFIDIRLFGRTAEIANQYLSKGSKVLIEG 77 (182)
T ss_pred eEEEEEEEecCCCEEEECCC--C-CEEEEEEEEEecceecCCCCCcccceEEEEEEEhHHHHHHHHHcCCCCEEEEEE
Confidence 56789999999988887643 2 246666653 22 3467899999999999999999999998876
No 102
>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=79.93 E-value=15 Score=30.53 Aligned_cols=72 Identities=15% Similarity=0.168 Sum_probs=46.8
Q ss_pred EEEEEEEeeccccccccCCCCceeEEEEEEeCCCC-eEEEEEchhHHH-HHHhhcccCcEEEEeceEEecCCCcccCCCC
Q 006263 222 AIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGG-EIRVTCFNAVVD-RFYEIIEVGRVYLISKGSLKPAQKNFNHLKN 299 (653)
Q Consensus 222 ~I~~RV~~k~~ir~~~~~~g~gk~f~~~L~D~~g~-~I~at~f~~~~~-kf~~~l~eG~vy~is~~~V~~a~~~f~~~~~ 299 (653)
+|+|||.++ |. .|++.-++|.|..|. .|++++..+... ++...|..|+++.+.+--.+...+ ..
T Consensus 3 ~v~Gwv~~~---R~------~g~~~Fi~LrD~s~~~~lQvv~~~~~~~~~~~~~l~~gs~V~v~G~v~~~~~~-----~~ 68 (82)
T cd04318 3 TVNGWVRSV---RD------SKKISFIELNDGSCLKNLQVVVDKELTNFKEILKLSTGSSIRVEGVLVKSPGA-----KQ 68 (82)
T ss_pred EEEEeEEEE---Ec------CCcEEEEEEECCCCccCEEEEEeCcccCHHHHhcCCCceEEEEEEEEEeCCCC-----CC
Confidence 678888653 32 256666788895443 599998654321 334568999999999964443222 35
Q ss_pred ceEEEecc
Q 006263 300 EWEIFLEA 307 (653)
Q Consensus 300 ~yei~f~~ 307 (653)
+|||...+
T Consensus 69 ~~El~~~~ 76 (82)
T cd04318 69 PFELQAEK 76 (82)
T ss_pred CEEEEEEE
Confidence 78887754
No 103
>PRK08182 single-stranded DNA-binding protein; Provisional
Probab=78.89 E-value=6.6 Score=36.99 Aligned_cols=65 Identities=12% Similarity=0.297 Sum_probs=51.0
Q ss_pred CCceEEEEEEEeeccccccccCCCCc---eeEEEEEE------eCCC-------CeEEEEEchhHHHHHHhhcccCcEEE
Q 006263 218 QGRWAIKARVTAKGDLRRYNNARGDG---KVFSFDLL------DSDG-------GEIRVTCFNAVVDRFYEIIEVGRVYL 281 (653)
Q Consensus 218 ~~~w~I~~RV~~k~~ir~~~~~~g~g---k~f~~~L~------D~~g-------~~I~at~f~~~~~kf~~~l~eG~vy~ 281 (653)
++.++|.||+.+--.+|.+.+ |.. ++.+|.|. +.+| .-|.+++|+..++.+...|+.|+-+.
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 467899999999888888753 221 27888885 2222 24889999999999999999999998
Q ss_pred Eec
Q 006263 282 ISK 284 (653)
Q Consensus 282 is~ 284 (653)
+.+
T Consensus 80 V~G 82 (148)
T PRK08182 80 VEG 82 (148)
T ss_pred EEE
Confidence 887
No 104
>PRK07373 DNA polymerase III subunit alpha; Reviewed
Probab=78.83 E-value=6.8 Score=43.80 Aligned_cols=78 Identities=23% Similarity=0.270 Sum_probs=54.1
Q ss_pred eecchhhhhhcccCccccEEEEEEEecCceeEEecCCceeeEEEEEEEeCCCCEEEEEEccchhhhhhhhHHHhhccCCC
Q 006263 327 SFRHISEIESAENNSIVDVIGIVISVNPSVPILRKNGMETQRRILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVDVGFF 406 (653)
Q Consensus 327 ~f~~i~~i~~~~~~~~vDVIGvV~~v~~~~~i~~k~g~~~~kr~i~l~D~s~~~i~vtLWg~~A~~~~~~l~~~~~~~~~ 406 (653)
...++++|.....+..|=|.|+|+.+... .+|.|+. .--++|.|.+| .+++++|.+....+...| ..+
T Consensus 267 ~~~~~~~l~~~~~~~~v~vaG~I~~ik~~---~TKkG~~--maf~~leD~tG-~ie~vvFp~~y~~~~~~l------~~~ 334 (449)
T PRK07373 267 SPINLSELEEQKEKTKVSAVVMLNEVKKI---VTKKGDP--MAFLQLEDLSG-QSEAVVFPKSYERISELL------QVD 334 (449)
T ss_pred CCcCHHHHhcccCCCEEEEEEEEEEeEec---ccCCCCE--EEEEEEEECCC-CEEEEECHHHHHHHHHHh------ccC
Confidence 44577777544456678899999998764 4566763 46789999999 799999998876643322 245
Q ss_pred cEEEEEeeEee
Q 006263 407 PVLSVKSGKVN 417 (653)
Q Consensus 407 ~Vvaik~~rV~ 417 (653)
.++.++| +|.
T Consensus 335 ~~v~v~G-~v~ 344 (449)
T PRK07373 335 ARLIIWG-KVD 344 (449)
T ss_pred CEEEEEE-EEE
Confidence 6666665 443
No 105
>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=78.52 E-value=15 Score=41.82 Aligned_cols=79 Identities=18% Similarity=0.263 Sum_probs=56.0
Q ss_pred CceEEEEEEEeeccccccccCCCCceeEEEEEEeCCCCeEEEEEchhH----HHHH-HhhcccCcEEEEeceEEecCCCc
Q 006263 219 GRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAV----VDRF-YEIIEVGRVYLISKGSLKPAQKN 293 (653)
Q Consensus 219 ~~w~I~~RV~~k~~ir~~~~~~g~gk~f~~~L~D~~g~~I~at~f~~~----~~kf-~~~l~eG~vy~is~~~V~~a~~~ 293 (653)
...+|.|||.++ |. .|++.-++|.| .+|.|++.+-.+. ..++ ...|..|+++.+.+.-.+..
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------MGKATFITLQD-ESGQIQLYVNKDDLPEDFYEFDEYLLDLGDIIGVTGYPFKTK--- 120 (496)
T ss_pred CEEEEEEEEEEE---ec------CCCeEEEEEEc-CCccEEEEEECCcCcHHHHHHHHhcCCCCCEEEEEEEEEECC---
Confidence 358899999885 32 36777789999 6789999986432 2222 33589999999999654332
Q ss_pred ccCCCCceEEEeccccEEEec
Q 006263 294 FNHLKNEWEIFLEATSTVDLC 314 (653)
Q Consensus 294 f~~~~~~yei~f~~~T~I~~~ 314 (653)
...++|..++-+.+..+
T Consensus 121 ----~gelel~~~~i~ilsk~ 137 (496)
T TIGR00499 121 ----TGELSVHVTELQILTKA 137 (496)
T ss_pred ----CCcEEEEeeEEEEEecC
Confidence 34699988877666665
No 106
>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=77.97 E-value=26 Score=30.51 Aligned_cols=79 Identities=13% Similarity=0.115 Sum_probs=50.2
Q ss_pred eEEEEEEEeeccccccccCCCCceeEEEEEEeCCCCeEEEEEchhH-HHHHH--hhcccCcEEEEeceEEecCCCcccCC
Q 006263 221 WAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAV-VDRFY--EIIEVGRVYLISKGSLKPAQKNFNHL 297 (653)
Q Consensus 221 w~I~~RV~~k~~ir~~~~~~g~gk~f~~~L~D~~g~~I~at~f~~~-~~kf~--~~l~eG~vy~is~~~V~~a~~~f~~~ 297 (653)
-+|+|||.++ |. .|++.-++|.| .+|.+++.+..+. -+.|. ..|..|+++.+.+--..... .
T Consensus 2 V~v~Gwv~~~---R~------~gk~~Fi~lrD-~~g~iQ~v~~~~~~~~~~~~~~~l~~~s~v~V~G~v~~~~~-----~ 66 (103)
T cd04319 2 VTLAGWVYRK---RE------VGKKAFIVLRD-STGIVQAVFSKDLNEEAYREAKKVGIESSVIVEGAVKADPR-----A 66 (103)
T ss_pred EEEEEEEEeE---Ec------CCCeEEEEEec-CCeeEEEEEeCCCCHHHHHHHhCCCCCCEEEEEEEEEECCC-----C
Confidence 3678888764 32 25666678999 5678999886531 12222 35889999999885433221 2
Q ss_pred CCceEEEeccccEEEec
Q 006263 298 KNEWEIFLEATSTVDLC 314 (653)
Q Consensus 298 ~~~yei~f~~~T~I~~~ 314 (653)
...|||..+.-..+.++
T Consensus 67 ~~~~Ei~~~~i~vl~~a 83 (103)
T cd04319 67 PGGAEVHGEKLEIIQNV 83 (103)
T ss_pred CCCEEEEEEEEEEEecC
Confidence 34699998665555444
No 107
>PRK06863 single-stranded DNA-binding protein; Provisional
Probab=77.74 E-value=8.5 Score=37.06 Aligned_cols=64 Identities=14% Similarity=0.192 Sum_probs=50.5
Q ss_pred CCceEEEEEEEeeccccccccCCCCceeEEEEEE------eCC-------CCeEEEEEchhHHHHHHhhcccCcEEEEec
Q 006263 218 QGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLL------DSD-------GGEIRVTCFNAVVDRFYEIIEVGRVYLISK 284 (653)
Q Consensus 218 ~~~w~I~~RV~~k~~ir~~~~~~g~gk~f~~~L~------D~~-------g~~I~at~f~~~~~kf~~~l~eG~vy~is~ 284 (653)
+++-.|.||+.+.-.+|.+.+ | ..+.+|.|. |.+ ..-+++++|+..++.+...|+.|+-+.+.+
T Consensus 4 ~N~V~LiGrLg~DPElR~t~n--G-~~va~fsVAvn~~~~d~~~Ge~~e~t~w~~Vv~fgk~AE~v~~~LkKGs~V~VeG 80 (168)
T PRK06863 4 INKVIIVGHLGNDPEIRTMPN--G-EAVANISVATSESWTDKNTGERREVTEWHRIVFYRRQAEVAGEYLRKGSQVYVEG 80 (168)
T ss_pred ccEEEEEEEcCCCCEEEEcCC--C-CEEEEEEEEecCcccccCCCcccccceEEEEEEEhHHHHHHHHHCCCCCEEEEEE
Confidence 577899999999988988754 2 256666664 222 235899999999999999999999998887
No 108
>PRK00484 lysS lysyl-tRNA synthetase; Reviewed
Probab=77.69 E-value=18 Score=41.03 Aligned_cols=78 Identities=18% Similarity=0.201 Sum_probs=56.0
Q ss_pred CceEEEEEEEeeccccccccCCCCceeEEEEEEeCCCCeEEEEEchhH-----HHHHHhhcccCcEEEEeceEEecCCCc
Q 006263 219 GRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAV-----VDRFYEIIEVGRVYLISKGSLKPAQKN 293 (653)
Q Consensus 219 ~~w~I~~RV~~k~~ir~~~~~~g~gk~f~~~L~D~~g~~I~at~f~~~-----~~kf~~~l~eG~vy~is~~~V~~a~~~ 293 (653)
...+|.|||.++ |. .|++.-++|.| .+|.|++.+-.+. .+.+. .|..|+++.+.+.-++..
T Consensus 55 ~~v~v~G~v~~~---R~------~g~~~Fi~lrD-~~g~iQ~v~~~~~~~~~~~~~~~-~l~~g~~v~v~G~v~~t~--- 120 (491)
T PRK00484 55 IEVSVAGRVMLK---RV------MGKASFATLQD-GSGRIQLYVSKDDVGEEALEAFK-KLDLGDIIGVEGTLFKTK--- 120 (491)
T ss_pred cEEEEEEEEEEE---ec------CCceEEEEEEc-CCccEEEEEECCcCCHHHHHHHh-cCCCCCEEEEEEEEEEcC---
Confidence 458999999875 33 35777789999 6779999886432 22333 499999999988655432
Q ss_pred ccCCCCceEEEeccccEEEec
Q 006263 294 FNHLKNEWEIFLEATSTVDLC 314 (653)
Q Consensus 294 f~~~~~~yei~f~~~T~I~~~ 314 (653)
...+||..+.-..+..+
T Consensus 121 ----~ge~el~~~~~~vls~~ 137 (491)
T PRK00484 121 ----TGELSVKATELTLLTKS 137 (491)
T ss_pred ----CCcEEEEEeEEEEEecc
Confidence 24789988777666665
No 109
>PRK07274 single-stranded DNA-binding protein; Provisional
Probab=77.23 E-value=7.5 Score=35.78 Aligned_cols=64 Identities=17% Similarity=0.222 Sum_probs=49.3
Q ss_pred CCceEEEEEEEeeccccccccCCCCceeEEEEEE------eCC----CCeEEEEEchhHHHHHHhhcccCcEEEEec
Q 006263 218 QGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLL------DSD----GGEIRVTCFNAVVDRFYEIIEVGRVYLISK 284 (653)
Q Consensus 218 ~~~w~I~~RV~~k~~ir~~~~~~g~gk~f~~~L~------D~~----g~~I~at~f~~~~~kf~~~l~eG~vy~is~ 284 (653)
++..+|.||+..--.+|...+ | ..+.+|.|+ |++ .+-+++++|+..++.+...|+.|+-+.+.+
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 467889999999888876533 2 256666665 322 246889999999999999999999998886
No 110
>PRK12445 lysyl-tRNA synthetase; Reviewed
Probab=76.84 E-value=17 Score=41.42 Aligned_cols=78 Identities=17% Similarity=0.216 Sum_probs=55.9
Q ss_pred ceEEEEEEEeeccccccccCCCCceeEEEEEEeCCCCeEEEEEchhHH-----HHHHhhcccCcEEEEeceEEecCCCcc
Q 006263 220 RWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAVV-----DRFYEIIEVGRVYLISKGSLKPAQKNF 294 (653)
Q Consensus 220 ~w~I~~RV~~k~~ir~~~~~~g~gk~f~~~L~D~~g~~I~at~f~~~~-----~kf~~~l~eG~vy~is~~~V~~a~~~f 294 (653)
..+|.|||.++ |. .|++.-++|.| .+|.|++.+-.+.+ ++....|..|+++.+.+.-.+..
T Consensus 67 ~v~v~Grv~~~---R~------~Gk~~F~~lrD-~~g~iQ~~~~~~~~~~~~~~~~~~~l~~Gd~V~v~G~~~~t~---- 132 (505)
T PRK12445 67 EVSVAGRMMTR---RI------MGKASFVTLQD-VGGRIQLYVARDSLPEGVYNDQFKKWDLGDIIGARGTLFKTQ---- 132 (505)
T ss_pred EEEEEEEEEEE---ec------CCCcEEEEEEe-CCccEEEEEECCccchhhHHHHHhcCCCCCEEEEEEEEEecC----
Confidence 58899999874 33 36777788999 67899998874321 22235689999999988655433
Q ss_pred cCCCCceEEEeccccEEEec
Q 006263 295 NHLKNEWEIFLEATSTVDLC 314 (653)
Q Consensus 295 ~~~~~~yei~f~~~T~I~~~ 314 (653)
...++|....-+.+..+
T Consensus 133 ---~gelel~~~~~~llsk~ 149 (505)
T PRK12445 133 ---TGELSIHCTELRLLTKA 149 (505)
T ss_pred ---CCcEEEEEeEEEEEecC
Confidence 34688888777666665
No 111
>PRK06752 single-stranded DNA-binding protein; Validated
Probab=76.67 E-value=8.5 Score=34.32 Aligned_cols=64 Identities=14% Similarity=0.093 Sum_probs=49.6
Q ss_pred CCceEEEEEEEeeccccccccCCCCceeEEEEEEeC----------CCCeEEEEEchhHHHHHHhhcccCcEEEEec
Q 006263 218 QGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDS----------DGGEIRVTCFNAVVDRFYEIIEVGRVYLISK 284 (653)
Q Consensus 218 ~~~w~I~~RV~~k~~ir~~~~~~g~gk~f~~~L~D~----------~g~~I~at~f~~~~~kf~~~l~eG~vy~is~ 284 (653)
++.-.|.||+.+--++|...+ | ..+.+|.|+-. +.+-|.+++|+..++.+...|..|+-+.+.+
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 356789999999888886532 2 25677777632 2356889999999999999999999998886
No 112
>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=76.59 E-value=3.7 Score=35.58 Aligned_cols=64 Identities=19% Similarity=0.273 Sum_probs=44.7
Q ss_pred CceEEEEEEEeeccccccccCCCCceeEEEEEEeC------------CCCeEEEEEchhHHHHHHhhcccCcEEEEece
Q 006263 219 GRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDS------------DGGEIRVTCFNAVVDRFYEIIEVGRVYLISKG 285 (653)
Q Consensus 219 ~~w~I~~RV~~k~~ir~~~~~~g~gk~f~~~L~D~------------~g~~I~at~f~~~~~kf~~~l~eG~vy~is~~ 285 (653)
++-+|.|||..--.+|+..+ | ..+.+|.|.-. ...-+++++|++.++.+...|+.|+.+.|.+-
T Consensus 2 N~v~l~G~l~~~p~~~~~~~--g-~~~~~f~la~~~~~~~~~~~~~~~~~~~~v~~~g~~A~~~~~~l~kG~~V~V~G~ 77 (104)
T PF00436_consen 2 NKVTLIGRLGKDPELRYTKN--G-TPVARFSLAVNRRFKDDGGEGDEKTDWINVVAWGKLAENVAEYLKKGDRVYVEGR 77 (104)
T ss_dssp EEEEEEEEESSSEEEEEETT--S-EEEEEEEEEEEEEEEETTSCEEEEEEEEEEEEEHHHHHHHHHH--TT-EEEEEEE
T ss_pred cEEEEEEEECCCcEEEECCC--C-CEEEEEEEEEecEEeeeeccCccceEEEEEEeeeecccccceEEcCCCEEEEEEE
Confidence 45678999998888887642 1 24555554321 23467899999999999999999999999873
No 113
>KOG4757 consensus Predicted telomere binding protein [General function prediction only]
Probab=75.69 E-value=8.1 Score=41.98 Aligned_cols=86 Identities=19% Similarity=0.280 Sum_probs=60.9
Q ss_pred ceecchhhhhhcccCccccEEEEEEEecCceeEEecCCceeeEEEEEEEe--CCCCEEEEEEccchhhhhhhhHHHhhcc
Q 006263 326 FSFRHISEIESAENNSIVDVIGIVISVNPSVPILRKNGMETQRRILNLKD--TSGRSVELTLWGDFCNKEGQKLQEMVDV 403 (653)
Q Consensus 326 f~f~~i~~i~~~~~~~~vDVIGvV~~v~~~~~i~~k~g~~~~kr~i~l~D--~s~~~i~vtLWg~~A~~~~~~l~~~~~~ 403 (653)
++|..+.+-.. ..+..|++||+|++.+|...-. |+. -...+.|+| .|+..+.|-|+....++. .. . .
T Consensus 7 ~k~Iri~da~k-k~~tiVNl~GiVkef~pp~qs~---g~D-~~~tv~IvDp~~ss~gLtv~lfSkt~edL----P~-I-k 75 (522)
T KOG4757|consen 7 LKLIRISDALK-KKNTIVNLIGIVKEFTPPRQSL---GKD-WVCTVYIVDPDYSSIGLTVHLFSKTGEDL----PV-I-K 75 (522)
T ss_pred hheeechHHHH-hcCcEEEEEEEEEeccChhhcc---CCc-eEEEEEEeCCCCCCCCcEEEEecCchhhC----cc-c-c
Confidence 34555554332 3688999999999999876522 443 346789999 678888999998886652 22 1 1
Q ss_pred CCCcEEEEEeeEeecCCCc
Q 006263 404 GFFPVLSVKSGKVNDFSGK 422 (653)
Q Consensus 404 ~~~~Vvaik~~rV~~f~G~ 422 (653)
..|.+|.+...|+.-|+.+
T Consensus 76 ~~GDiillhRiKiq~y~~r 94 (522)
T KOG4757|consen 76 QVGDIILLHRIKIQSYRDR 94 (522)
T ss_pred ccCcEEEEEEEEEEEhhhh
Confidence 3689999999999888754
No 114
>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=74.50 E-value=13 Score=35.73 Aligned_cols=65 Identities=18% Similarity=0.271 Sum_probs=49.1
Q ss_pred CCceEEEEEEEeeccccccccCCCCceeEEEEEE------eCC------CCeEEEEEchhHHHHHHhhcccCcEEEEece
Q 006263 218 QGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLL------DSD------GGEIRVTCFNAVVDRFYEIIEVGRVYLISKG 285 (653)
Q Consensus 218 ~~~w~I~~RV~~k~~ir~~~~~~g~gk~f~~~L~------D~~------g~~I~at~f~~~~~kf~~~l~eG~vy~is~~ 285 (653)
.++-+|.+||..--.+|...+ | ..+.+|.|+ |++ ..-|++++|++.++.+...|+.|+.+.|.+-
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 367789999999877877543 2 245455443 222 3689999999999999999999999999874
No 115
>KOG3056 consensus Protein required for S-phase initiation or completion [Cell cycle control, cell division, chromosome partitioning]
Probab=74.47 E-value=20 Score=40.39 Aligned_cols=103 Identities=12% Similarity=0.268 Sum_probs=68.8
Q ss_pred Ccceecc----ccCCC---CCceEEEEEEEeeccccccccCCCCceeEEEEEEeCCCCeEEEEEchhHHHHHHhhcccCc
Q 006263 206 ARIIPIA----ALNPY---QGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGR 278 (653)
Q Consensus 206 ~~~~pI~----~L~p~---~~~w~I~~RV~~k~~ir~~~~~~g~gk~f~~~L~D~~g~~I~at~f~~~~~kf~~~l~eG~ 278 (653)
+...+|+ .|-+. ..+|.+.|-|+.|+++|.-.+.+ .-.++-+.-++.+ -.+...+|+++..+++. ++.|.
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 3455565 44433 23899999999999999765411 1123444333324 69999999997766665 99999
Q ss_pred EEEEeceEEecCCCcccCCCCceEEEeccccEEEec
Q 006263 279 VYLISKGSLKPAQKNFNHLKNEWEIFLEATSTVDLC 314 (653)
Q Consensus 279 vy~is~~~V~~a~~~f~~~~~~yei~f~~~T~I~~~ 314 (653)
|+-|-|..|.+-+.. ..-.|.|.++..-.|.++
T Consensus 243 VialLNp~v~k~~~g---s~~~f~LsIds~~~ilei 275 (578)
T KOG3056|consen 243 VIALLNPEVLKDRPG---SRKSFSLSIDSSKKILEI 275 (578)
T ss_pred EEEEeCccccCCCCC---CcceEEEEecCccceEEe
Confidence 999999998654421 114677777776555444
No 116
>PTZ00385 lysyl-tRNA synthetase; Provisional
Probab=74.23 E-value=28 Score=40.78 Aligned_cols=77 Identities=16% Similarity=0.190 Sum_probs=54.5
Q ss_pred ceEEEEEEEeeccccccccCCCCceeEEEEEEeCCCCeEEEEEchhH------HHHHHhhcccCcEEEEeceEEecCCCc
Q 006263 220 RWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAV------VDRFYEIIEVGRVYLISKGSLKPAQKN 293 (653)
Q Consensus 220 ~w~I~~RV~~k~~ir~~~~~~g~gk~f~~~L~D~~g~~I~at~f~~~------~~kf~~~l~eG~vy~is~~~V~~a~~~ 293 (653)
..+|.|||.++ |. -|++.-++|.| .+|.||+.+..+. ...+...|..|+++.+.+.-.+..
T Consensus 109 ~V~vaGrV~~~---R~------~Gk~~F~~LrD-~~G~IQvv~~~~~~~~~~~~~~~~~~l~~gdiV~V~G~v~~t~--- 175 (659)
T PTZ00385 109 TVRVAGRVTSV---RD------IGKIIFVTIRS-NGNELQVVGQVGEHFTREDLKKLKVSLRVGDIIGADGVPCRMQ--- 175 (659)
T ss_pred EEEEEEEEEee---ec------cCCeEEEEEEE-CCceEEEEEECCccCCHHHHHHHHhCCCCCCEEEEEEEEEecC---
Confidence 48899999875 33 36777788999 7889999996542 223345689999999988543221
Q ss_pred ccCCCCceEEEeccccEEEe
Q 006263 294 FNHLKNEWEIFLEATSTVDL 313 (653)
Q Consensus 294 f~~~~~~yei~f~~~T~I~~ 313 (653)
...++|....-+.+.+
T Consensus 176 ----~GeleI~~~~i~lLsk 191 (659)
T PTZ00385 176 ----RGELSVAASRMLILSP 191 (659)
T ss_pred ----CceEEEEeeEEEEech
Confidence 3567777777666665
No 117
>PRK05673 dnaE DNA polymerase III subunit alpha; Validated
Probab=74.09 E-value=8.7 Score=47.93 Aligned_cols=82 Identities=28% Similarity=0.421 Sum_probs=56.6
Q ss_pred eecchhhhhhcccCccccEEEEEEEecCceeEEecCCceeeEEEEEEEeCCCCEEEEEEccchhhhhhhhHHHhhccCCC
Q 006263 327 SFRHISEIESAENNSIVDVIGIVISVNPSVPILRKNGMETQRRILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVDVGFF 406 (653)
Q Consensus 327 ~f~~i~~i~~~~~~~~vDVIGvV~~v~~~~~i~~k~g~~~~kr~i~l~D~s~~~i~vtLWg~~A~~~~~~l~~~~~~~~~ 406 (653)
...++.+|.....+..|.++|+|+++... .+|.|+. .--++|.|.+| ++++++|.+.-..+.. .+ ..+
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-RIEVMLFSEALEKYRD----LL--EED 1031 (1135)
T ss_pred CCcCHHHHhccccCceEEEEEEEEEEEec---ccCCCCe--EEEEEEEeCCC-cEEEEECHHHHHHHHH----Hh--ccC
Confidence 44567777544456789999999987765 4566764 46789999999 7999999987554322 22 246
Q ss_pred cEEEEEeeEeecCCC
Q 006263 407 PVLSVKSGKVNDFSG 421 (653)
Q Consensus 407 ~Vvaik~~rV~~f~G 421 (653)
.+|.++| +|..+.|
T Consensus 1032 ~iV~V~G-kVe~~~~ 1045 (1135)
T PRK05673 1032 RIVVVKG-QVSFDDG 1045 (1135)
T ss_pred CEEEEEE-EEEecCC
Confidence 7777765 5544434
No 118
>PRK06958 single-stranded DNA-binding protein; Provisional
Probab=72.80 E-value=14 Score=36.00 Aligned_cols=64 Identities=19% Similarity=0.226 Sum_probs=49.8
Q ss_pred CCceEEEEEEEeeccccccccCCCCceeEEEEEE------eC-------CCCeEEEEEchhHHHHHHhhcccCcEEEEec
Q 006263 218 QGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLL------DS-------DGGEIRVTCFNAVVDRFYEIIEVGRVYLISK 284 (653)
Q Consensus 218 ~~~w~I~~RV~~k~~ir~~~~~~g~gk~f~~~L~------D~-------~g~~I~at~f~~~~~kf~~~l~eG~vy~is~ 284 (653)
++.-+|.+||.+-..+|...+ | ..+.+|.|+ |. +..-+++++|+..++.+...|+.|+-++|..
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 467889999999888887643 2 256666653 32 2457899999999999999999999999887
No 119
>PRK06642 single-stranded DNA-binding protein; Provisional
Probab=72.48 E-value=13 Score=35.24 Aligned_cols=64 Identities=19% Similarity=0.258 Sum_probs=50.3
Q ss_pred CCceEEEEEEEeeccccccccCCCCceeEEEEEE------eC-------CCCeEEEEEchh-HHHHHHhhcccCcEEEEe
Q 006263 218 QGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLL------DS-------DGGEIRVTCFNA-VVDRFYEIIEVGRVYLIS 283 (653)
Q Consensus 218 ~~~w~I~~RV~~k~~ir~~~~~~g~gk~f~~~L~------D~-------~g~~I~at~f~~-~~~kf~~~l~eG~vy~is 283 (653)
++..+|.||+.+--.+|...+ | ..+.+|.|+ |. +..=+++++|++ +++.+...|+.|+-+++.
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 478899999999888887643 2 257777776 22 234688999996 899999999999999988
Q ss_pred c
Q 006263 284 K 284 (653)
Q Consensus 284 ~ 284 (653)
+
T Consensus 82 G 82 (152)
T PRK06642 82 G 82 (152)
T ss_pred E
Confidence 6
No 120
>KOG0556 consensus Aspartyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=72.37 E-value=42 Score=36.59 Aligned_cols=101 Identities=13% Similarity=0.162 Sum_probs=76.2
Q ss_pred CCCcceeccccCCCCC--ceEEEEEEEeeccccccccCCCCceeEEEEEEeCCCCeEEEEEc-------hhHHHHHHhhc
Q 006263 204 APARIIPIAALNPYQG--RWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCF-------NAVVDRFYEII 274 (653)
Q Consensus 204 ~~~~~~pI~~L~p~~~--~w~I~~RV~~k~~ir~~~~~~g~gk~f~~~L~D~~g~~I~at~f-------~~~~~kf~~~l 274 (653)
..+.++++++|+.... .-.|+|||-. .+-.||+.-++|.+ .|..|+|.+. +...-||...|
T Consensus 66 ~~~~~~~v~dl~~~~~~~~V~vRgrVht---------sr~~GK~~FlvLRq-~~~tVQ~~~~~~~~~~isk~Mvkf~~~i 135 (533)
T KOG0556|consen 66 EGRELTDVSDLDESNDGSEVLVRGRVHT---------SRLKGKLCFLVLRQ-QGSTVQCLVAVNEDGTISKQMVKFAGSI 135 (533)
T ss_pred cccceeehhhhhhhcCCceEEEEEEEee---------ccccceEEEEEEec-cCceEEEEEEcCCCchHHHHHHHHHhhc
Confidence 3467889999987754 4568888732 24457888889999 8999999995 34467999999
Q ss_pred ccCcEEEEeceEEecCCCcccCCCCceEEEeccccEEEec
Q 006263 275 EVGRVYLISKGSLKPAQKNFNHLKNEWEIFLEATSTVDLC 314 (653)
Q Consensus 275 ~eG~vy~is~~~V~~a~~~f~~~~~~yei~f~~~T~I~~~ 314 (653)
.--.++.+.+.-+++..+--..+..+.||....--.|...
T Consensus 136 s~ESiV~v~g~v~k~~~~i~scT~qdvEi~v~~iyviS~a 175 (533)
T KOG0556|consen 136 SKESIVDVRGVVVKVKEPIKSCTVQDVEIHVRKIYVISIA 175 (533)
T ss_pred CcceEEEEEEEEecCCCcccccccceeEEEEEEEEEEecc
Confidence 9999998888777777665555788999998775555544
No 121
>PRK07135 dnaE DNA polymerase III DnaE; Validated
Probab=71.26 E-value=13 Score=45.45 Aligned_cols=74 Identities=19% Similarity=0.159 Sum_probs=51.7
Q ss_pred eeccccCCCCCceEEEEEEEeeccccccccCCCCceeEEEEEEeCCCCeEEEEEchhHHHHHHhhcccCcEEEEeceEEe
Q 006263 209 IPIAALNPYQGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISKGSLK 288 (653)
Q Consensus 209 ~pI~~L~p~~~~w~I~~RV~~k~~ir~~~~~~g~gk~f~~~L~D~~g~~I~at~f~~~~~kf~~~l~eG~vy~is~~~V~ 288 (653)
.+|.+|.. ...-+|.|.|+..-.++ ++|+ ...-+.|-| ..|+|.+++|.+...++.. |.+|++|++ .++..
T Consensus 889 ~~~~~l~~-~~~~~v~g~i~~~~~~~----K~g~-~maf~~~eD-~~~~~e~~~F~~~~~~~~~-l~~~~~~~~-~~~~~ 959 (973)
T PRK07135 889 IRLKDLRI-NTEYRLAIEVKNVKRLR----KANK-EYKKVILSD-DSVEITIFVNDNDYLLFET-LKKGDIYEF-LISKS 959 (973)
T ss_pred hhHHHhcC-CCeEEEEEEEEEEEEEe----eCCC-eEEEEEEEE-CCCcEEEEEcHHHHHHHHH-hhcCCEEEE-EEEEc
Confidence 46777742 33457888887755444 2343 455667888 8899999999999999887 888888888 34444
Q ss_pred cCC
Q 006263 289 PAQ 291 (653)
Q Consensus 289 ~a~ 291 (653)
.+|
T Consensus 960 ~~~ 962 (973)
T PRK07135 960 KNN 962 (973)
T ss_pred CCC
Confidence 433
No 122
>PF13742 tRNA_anti_2: OB-fold nucleic acid binding domain
Probab=70.77 E-value=26 Score=30.48 Aligned_cols=65 Identities=14% Similarity=0.140 Sum_probs=46.4
Q ss_pred CceEEEEEEEeeccccccccCCCCceeEEEEEEeCCCCeEEEEEchhHHHHHH-hhcccCcEEEEec-eEEecCCC
Q 006263 219 GRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAVVDRFY-EIIEVGRVYLISK-GSLKPAQK 292 (653)
Q Consensus 219 ~~w~I~~RV~~k~~ir~~~~~~g~gk~f~~~L~D~~g~~I~at~f~~~~~kf~-~~l~eG~vy~is~-~~V~~a~~ 292 (653)
.+-.|+|=|... +.. . +....|+|.| +..+|+|++|.....+.. ..+++|.-+.+.. ..+-+...
T Consensus 22 ~~vwV~GEIs~~------~~~-~-~gh~YftLkD-~~a~i~~~~~~~~~~~i~~~~l~~G~~V~v~g~~~~y~~~G 88 (99)
T PF13742_consen 22 PNVWVEGEISNL------KRH-S-SGHVYFTLKD-EEASISCVIFRSRARRIRGFDLKDGDKVLVRGRVSFYEPRG 88 (99)
T ss_pred CCEEEEEEEeec------EEC-C-CceEEEEEEc-CCcEEEEEEEHHHHhhCCCCCCCCCCEEEEEEEEEEECCCc
Confidence 455677777653 221 1 2457899999 559999999999988888 8899998777665 45544443
No 123
>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=70.68 E-value=34 Score=38.15 Aligned_cols=81 Identities=15% Similarity=0.109 Sum_probs=56.2
Q ss_pred CceEEEEEEEeeccccccccCCCCceeEEEEEEeCCCCeEEEEEchhH----HHHHHhhcccCcEEEEeceEEecCCCcc
Q 006263 219 GRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAV----VDRFYEIIEVGRVYLISKGSLKPAQKNF 294 (653)
Q Consensus 219 ~~w~I~~RV~~k~~ir~~~~~~g~gk~f~~~L~D~~g~~I~at~f~~~----~~kf~~~l~eG~vy~is~~~V~~a~~~f 294 (653)
..-+|+|||.++ |. .|++.-++|.| .+|.|++++-... .-++-..|..|+++.+.+.-++ ..+
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------LGGLIFVLLRD-REGLIQITAPAKKVSKNLFKWAKKLNLESVVAVRGIVKI-KEK-- 79 (428)
T ss_pred CEEEEEEEEEEE---ec------CCCcEEEEEEe-CCeeEEEEEECCcCCHHHHHHHhCCCCCcEEEEEEEEEe-cCC--
Confidence 357899999774 33 35677788999 6779999986432 2233456999999999885442 221
Q ss_pred cCCCCceEEEeccccEEEec
Q 006263 295 NHLKNEWEIFLEATSTVDLC 314 (653)
Q Consensus 295 ~~~~~~yei~f~~~T~I~~~ 314 (653)
...++||....-+.+..+
T Consensus 80 --~~~~~el~~~~i~vl~~~ 97 (428)
T TIGR00458 80 --APGGFEIIPTKIEVINEA 97 (428)
T ss_pred --CCCcEEEEEeEEEEEecC
Confidence 245799998876666665
No 124
>PRK02983 lysS lysyl-tRNA synthetase; Provisional
Probab=70.66 E-value=21 Score=44.48 Aligned_cols=78 Identities=18% Similarity=0.244 Sum_probs=58.4
Q ss_pred ceEEEEEEEeeccccccccCCCCceeEEEEEEeCCCCeEEEEEchhH-----HHHHHhhcccCcEEEEeceEEecCCCcc
Q 006263 220 RWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAV-----VDRFYEIIEVGRVYLISKGSLKPAQKNF 294 (653)
Q Consensus 220 ~w~I~~RV~~k~~ir~~~~~~g~gk~f~~~L~D~~g~~I~at~f~~~-----~~kf~~~l~eG~vy~is~~~V~~a~~~f 294 (653)
..+|.|||.++ |. .|++.-++|.| .+|.||+.+-.+. .+.|...|..|+++.+.+.-.+..
T Consensus 653 ~V~v~Grv~~~---R~------~G~~~F~~lrD-~~g~iQ~v~~~~~~~~~~~~~~~~~l~~gd~V~v~G~v~~t~---- 718 (1094)
T PRK02983 653 EVSVSGRVLRI---RD------YGGVLFADLRD-WSGELQVLLDASRLEQGSLADFRAAVDLGDLVEVTGTMGTSR---- 718 (1094)
T ss_pred EEEEEEEEEEE---ee------CCCeEEEEEEe-CCeeEEEEEECCccchhhHHHHHhcCCCCCEEEEEEEEEEcC----
Confidence 58899999875 33 35777788999 6789999986542 345666799999999999655432
Q ss_pred cCCCCceEEEeccccEEEec
Q 006263 295 NHLKNEWEIFLEATSTVDLC 314 (653)
Q Consensus 295 ~~~~~~yei~f~~~T~I~~~ 314 (653)
...+||..++.+.+.+|
T Consensus 719 ---~ge~ei~~~~i~ll~k~ 735 (1094)
T PRK02983 719 ---NGTLSLLVTSWRLAGKC 735 (1094)
T ss_pred ---CCCEEEEEeEEEEEecc
Confidence 24688888887777766
No 125
>PRK07374 dnaE DNA polymerase III subunit alpha; Validated
Probab=70.64 E-value=12 Score=46.72 Aligned_cols=71 Identities=17% Similarity=0.285 Sum_probs=52.6
Q ss_pred eeccccC--CCCCceEEEEEEEeeccccccccCCCCceeEEEEEEeCCCCeEEEEEchhHHHHHHhhcccCcEEEEec
Q 006263 209 IPIAALN--PYQGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISK 284 (653)
Q Consensus 209 ~pI~~L~--p~~~~w~I~~RV~~k~~ir~~~~~~g~gk~f~~~L~D~~g~~I~at~f~~~~~kf~~~l~eG~vy~is~ 284 (653)
.++++|. +.....+|.|-|+..-.+++ ++|+ .+.-+.|-| ..|.+.+++|.+..+++...|++|.++.+.+
T Consensus 989 ~~~~~l~~~~~~~~v~v~g~i~~~k~~~T---k~G~-~maf~~leD-~tg~~e~vvFp~~y~~~~~~l~~~~~~~v~g 1061 (1170)
T PRK07374 989 ISLSSLEEQPDKAKVSAIAMIPEMKQVTT---RKGD-RMAILQLED-LTGSCEAVVFPKSYERLSDHLMTDTRLLVWA 1061 (1170)
T ss_pred cCHHHHhcccCCCEEEEEEEEEEeEeccc---CCCC-EEEEEEEEE-CCCCEEEEECHHHHHHHHHHhccCCEEEEEE
Confidence 4566664 22345678888877544443 4432 455677888 8999999999999999999999999999865
No 126
>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=70.53 E-value=8.4 Score=33.14 Aligned_cols=52 Identities=17% Similarity=0.455 Sum_probs=36.9
Q ss_pred EEEEEEeeccccccccCCCCceeEEEEEEeCCCCeEEEEEchhHH--H------------------HHHhhcccCcEEEE
Q 006263 223 IKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAVV--D------------------RFYEIIEVGRVYLI 282 (653)
Q Consensus 223 I~~RV~~k~~ir~~~~~~g~gk~f~~~L~D~~g~~I~at~f~~~~--~------------------kf~~~l~eG~vy~i 282 (653)
|.|.|++..+. ...+.+.|-| .+|.|.|.+|.... + +..+.|++|+++.+
T Consensus 2 ivG~V~sv~~~---------~~~~~~tLdD-gTG~Ie~~~W~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~G~vvrV 71 (92)
T cd04483 2 ILGTVVSRRER---------ETFYSFGVDD-GTGVVNCVCWKNLSYAEVSSRSDAARILKSALMALKQAKVLEIGDLLRV 71 (92)
T ss_pred eEEEEEEEEec---------CCeEEEEEec-CCceEEEEEEcCcCcccccccccccccccccccccccccccCCCCEEEE
Confidence 55667665321 1357888999 67799999997642 1 46677999998888
Q ss_pred ec
Q 006263 283 SK 284 (653)
Q Consensus 283 s~ 284 (653)
.+
T Consensus 72 ~G 73 (92)
T cd04483 72 RG 73 (92)
T ss_pred EE
Confidence 74
No 127
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=70.12 E-value=2 Score=27.05 Aligned_cols=19 Identities=16% Similarity=0.590 Sum_probs=15.2
Q ss_pred cccceeeecCceeecccCccc
Q 006263 521 QCNKKVTQSGNRWQCDRCNQE 541 (653)
Q Consensus 521 ~C~KKv~~~~~~~~C~kC~~~ 541 (653)
.|++++.++ .-+|+.|+..
T Consensus 4 ~CG~~~~~~--~~fC~~CG~~ 22 (23)
T PF13240_consen 4 NCGAEIEDD--AKFCPNCGTP 22 (23)
T ss_pred ccCCCCCCc--CcchhhhCCc
Confidence 999998654 5679999864
No 128
>PRK05673 dnaE DNA polymerase III subunit alpha; Validated
Probab=69.74 E-value=13 Score=46.43 Aligned_cols=71 Identities=21% Similarity=0.346 Sum_probs=51.6
Q ss_pred eeccccCC--CCCceEEEEEEEeeccccccccCCCCceeEEEEEEeCCCCeEEEEEchhHHHHHHhhcccCcEEEEec
Q 006263 209 IPIAALNP--YQGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISK 284 (653)
Q Consensus 209 ~pI~~L~p--~~~~w~I~~RV~~k~~ir~~~~~~g~gk~f~~~L~D~~g~~I~at~f~~~~~kf~~~l~eG~vy~is~ 284 (653)
.++.+|.. ....-.+.+.|+.+...++ ++|+ ...-+.|.| ..|+|.+++|.+..+++.+.|++|.++.|.+
T Consensus 966 ~~~~~l~~~~~g~~V~v~G~I~~vk~~~T---KkG~-~mafltLeD-~TG~iEvviFp~~ye~~~~~L~~g~iV~V~G 1038 (1135)
T PRK05673 966 TRLADLEPTEGGSVVTVAGLVVSVRRRVT---KRGN-KMAIVTLED-LSGRIEVMLFSEALEKYRDLLEEDRIVVVKG 1038 (1135)
T ss_pred cCHHHHhccccCceEEEEEEEEEEEeccc---CCCC-eEEEEEEEe-CCCcEEEEECHHHHHHHHHHhccCCEEEEEE
Confidence 46666642 2234567777776544333 3432 456677888 7889999999999999999999999999865
No 129
>PRK07279 dnaE DNA polymerase III DnaE; Reviewed
Probab=69.47 E-value=12 Score=45.90 Aligned_cols=72 Identities=17% Similarity=0.336 Sum_probs=53.4
Q ss_pred ceeccccCCCCCceEEEEEEEeeccccccccCCCCceeEEEEEEeCCCCeEEEEEchhHHHHHHhhcccCcEEEEec
Q 006263 208 IIPIAALNPYQGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISK 284 (653)
Q Consensus 208 ~~pI~~L~p~~~~w~I~~RV~~k~~ir~~~~~~g~gk~f~~~L~D~~g~~I~at~f~~~~~kf~~~l~eG~vy~is~ 284 (653)
..++++|.. .....+.|.|+.....|+= ++|+ ...-+.|-| ..|+|.+++|.+..+++.+.|++|.++.+.+
T Consensus 875 ~~~~~~l~~-~~~~~~~~~i~~~~~~~tk--~~g~-~maf~~leD-~~g~ie~~vFp~~y~~~~~~l~~~~~~~v~G 946 (1034)
T PRK07279 875 FTPISQLVK-NSEATILVQIQSIRVIRTK--TKGQ-QMAFLSVTD-TKKKLDVTLFPETYRQYKDELKEGKFYYLKG 946 (1034)
T ss_pred CccHHHHhc-CCcceEEEEEEEEEEEEEc--CCCC-eEEEEEEee-CCCcEEEEECHHHHHHHHHHhccCCEEEEEE
Confidence 456777753 3345678888775554441 1333 455677888 8999999999999999999999999999965
No 130
>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=68.39 E-value=18 Score=33.02 Aligned_cols=35 Identities=3% Similarity=0.133 Sum_probs=27.5
Q ss_pred CEEEEEEccchhhhhhhhHHHhhccCCCcEEEEEeeEeecCC
Q 006263 379 RSVELTLWGDFCNKEGQKLQEMVDVGFFPVLSVKSGKVNDFS 420 (653)
Q Consensus 379 ~~i~vtLWg~~A~~~~~~l~~~~~~~~~~Vvaik~~rV~~f~ 420 (653)
.+|.||||++.|.- +..+ +.+..|.|++++++-..
T Consensus 60 ~ti~It~yD~H~~~-----ar~l--K~GdfV~L~NVhiK~~~ 94 (123)
T cd04498 60 LTIDILVYDNHVEL-----AKSL--KPGDFVRIYNVHAKSYS 94 (123)
T ss_pred EEEEEEEEcchHHH-----HhhC--CCCCEEEEEEEEEEecc
Confidence 68999999999853 3323 57899999999997543
No 131
>KOG3056 consensus Protein required for S-phase initiation or completion [Cell cycle control, cell division, chromosome partitioning]
Probab=68.14 E-value=19 Score=40.56 Aligned_cols=76 Identities=20% Similarity=0.271 Sum_probs=53.2
Q ss_pred ccEEEEEEEecCceeEEecCCceeeEEEEEEEeCCC-CEEEEEEccchhhhhhhhHHHhhccCCCcEEEEEeeEeecCC-
Q 006263 343 VDVIGIVISVNPSVPILRKNGMETQRRILNLKDTSG-RSVELTLWGDFCNKEGQKLQEMVDVGFFPVLSVKSGKVNDFS- 420 (653)
Q Consensus 343 vDVIGvV~~v~~~~~i~~k~g~~~~kr~i~l~D~s~-~~i~vtLWg~~A~~~~~~l~~~~~~~~~~Vvaik~~rV~~f~- 420 (653)
-=++|+|++-+++.. +..|+.+. -..|-|..+ ..|.|-|+|+ |- ...|....|.||||-++-|-+..
T Consensus 188 Wvt~GvI~~K~~~K~--t~~G~~y~--iwkL~dLk~~q~vslfLFG~-a~------k~~wk~k~GtVialLNp~v~k~~~ 256 (578)
T KOG3056|consen 188 WVTMGVIVEKSDPKF--TSNGNPYS--IWKLTDLKDHQTVSLFLFGK-AH------KRYWKIKLGTVIALLNPEVLKDRP 256 (578)
T ss_pred eEEEEEEeecCCccc--ccCCCceE--EEEeeecCccceeEEEEecH-HH------HHHhhhccCcEEEEeCccccCCCC
Confidence 347899999999875 34677554 445555554 6999999999 43 23466678999999999997654
Q ss_pred Cc----eeccccc
Q 006263 421 GK----SIGTIPS 429 (653)
Q Consensus 421 G~----sLs~~~~ 429 (653)
|. +|+..++
T Consensus 257 gs~~~f~LsIds~ 269 (578)
T KOG3056|consen 257 GSRKSFSLSIDSS 269 (578)
T ss_pred CCcceEEEEecCc
Confidence 32 5665544
No 132
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=67.74 E-value=3.6 Score=34.69 Aligned_cols=27 Identities=22% Similarity=0.888 Sum_probs=20.4
Q ss_pred cCCCCcCcccccceeee-cCc-eeecccCccccCC
Q 006263 512 ACPLMIGDRQCNKKVTQ-SGN-RWQCDRCNQEIDE 544 (653)
Q Consensus 512 aC~~~~~~~~C~KKv~~-~~~-~~~C~kC~~~~~~ 544 (653)
.|| .|+++-+. ... .|.|.+|+..+..
T Consensus 37 ~Cp------~C~~~~VkR~a~GIW~C~kCg~~fAG 65 (89)
T COG1997 37 VCP------FCGRTTVKRIATGIWKCRKCGAKFAG 65 (89)
T ss_pred cCC------CCCCcceeeeccCeEEcCCCCCeecc
Confidence 799 99998443 333 9999999987643
No 133
>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=66.12 E-value=13 Score=31.82 Aligned_cols=39 Identities=15% Similarity=0.284 Sum_probs=33.3
Q ss_pred EEEEEEeCCCCeEEEEEchhH--HHHHHhhcccCcEEEEece
Q 006263 246 FSFDLLDSDGGEIRVTCFNAV--VDRFYEIIEVGRVYLISKG 285 (653)
Q Consensus 246 f~~~L~D~~g~~I~at~f~~~--~~kf~~~l~eG~vy~is~~ 285 (653)
.-|.|.| +++.|++.+|... +.+....|++|+-+.+.+.
T Consensus 19 ~yFtlkD-~~~~i~cv~f~~~g~~~~~~~~l~~Gd~V~v~G~ 59 (91)
T cd04482 19 VFFKISD-GTGEIDCAAYEPTKEFRDVVRLLIPGDEVTVYGS 59 (91)
T ss_pred EEEEEEC-CCcEEEEEEECcccccccccCCCCCCCEEEEEEE
Confidence 5678899 7789999999988 7788899999998877764
No 134
>TIGR00643 recG ATP-dependent DNA helicase RecG.
Probab=65.58 E-value=16 Score=42.73 Aligned_cols=70 Identities=20% Similarity=0.227 Sum_probs=51.9
Q ss_pred cceeccccCCCCCceEEEEEEEeeccccccccCCCCceeEEEEEEeCCCCeEEEEEchhHHHHHHhhcccCcEEEEec
Q 006263 207 RIIPIAALNPYQGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISK 284 (653)
Q Consensus 207 ~~~pI~~L~p~~~~w~I~~RV~~k~~ir~~~~~~g~gk~f~~~L~D~~g~~I~at~f~~~~~kf~~~l~eG~vy~is~ 284 (653)
.+.+|++|.++. .-+|.|+|+.... .. ++..+.+.+.+.|..++.|.+++||.. -....|..|+.|.+++
T Consensus 22 ~~~~i~~~~~g~-~~~~~~~v~~~~~---~~--~~~~~~~~~~~~d~~~~~~~~~~F~~~--~~~~~~~~g~~~~~~G 91 (630)
T TIGR00643 22 LLQTIGELLPGE-RATIVGEVLSHCI---FG--FKRRKVLKLRLKDGGYKKLELRFFNRA--FLKKKFKVGSKVVVYG 91 (630)
T ss_pred cccCHHHcCCCC-EEEEEEEEEEeEe---cc--CCCCceEEEEEEECCCCEEEEEEECCH--HHHhhCCCCCEEEEEE
Confidence 467899998874 6889999987421 11 122357899999955778999999832 3468899999998876
No 135
>PF07754 DUF1610: Domain of unknown function (DUF1610); InterPro: IPR011668 This domain is found in archaeal species. It is likely to bind zinc via its four well-conserved cysteine residues.
Probab=64.52 E-value=4.8 Score=25.64 Aligned_cols=20 Identities=15% Similarity=0.655 Sum_probs=15.7
Q ss_pred cccceeeecC-c-eeecccCcc
Q 006263 521 QCNKKVTQSG-N-RWQCDRCNQ 540 (653)
Q Consensus 521 ~C~KKv~~~~-~-~~~C~kC~~ 540 (653)
.|+.-+.+.+ . .|.|++|+.
T Consensus 3 sC~~~i~~r~~~v~f~CPnCG~ 24 (24)
T PF07754_consen 3 SCGRPIAPREQAVPFPCPNCGF 24 (24)
T ss_pred cCCCcccCcccCceEeCCCCCC
Confidence 7888877654 3 899999984
No 136
>PRK02801 primosomal replication protein N; Provisional
Probab=64.43 E-value=30 Score=30.29 Aligned_cols=67 Identities=12% Similarity=0.114 Sum_probs=39.5
Q ss_pred cccEEEEEEEecCceeEEecCCceeeEEEEEEE---eCCCC------EEEEEEccchhhhhhhhHHHhhccCCCcEEEEE
Q 006263 342 IVDVIGIVISVNPSVPILRKNGMETQRRILNLK---DTSGR------SVELTLWGDFCNKEGQKLQEMVDVGFFPVLSVK 412 (653)
Q Consensus 342 ~vDVIGvV~~v~~~~~i~~k~g~~~~kr~i~l~---D~s~~------~i~vtLWg~~A~~~~~~l~~~~~~~~~~Vvaik 412 (653)
.|-++|.++.--++.. +.+|..+..-.|... ++.+. .|.|++||+.|+...++| ..|..|.+.
T Consensus 4 ~v~L~Grl~~dpelr~--Tp~G~~v~~f~La~~~~~~ea~~~r~~~~~i~~va~G~~Ae~~~~~l------~kGs~v~V~ 75 (101)
T PRK02801 4 RLVLSGTVCRTPKRKV--SPSGIPHCQFVLEHRSVQEEAGLHRQAWCRMPVIVSGNQFQAITQSI------TVGSKITVQ 75 (101)
T ss_pred EEEEEEEECcCcceEE--CCCCCeEEEEEEEEeCeEecCCCceeEEEEEEEEEEcHHHHHHHhhc------CCCCEEEEE
Confidence 3567888887666654 235654432222221 12232 299999999998753332 357888887
Q ss_pred eeEe
Q 006263 413 SGKV 416 (653)
Q Consensus 413 ~~rV 416 (653)
|.--
T Consensus 76 G~L~ 79 (101)
T PRK02801 76 GFIS 79 (101)
T ss_pred EEEE
Confidence 6543
No 137
>PRK06920 dnaE DNA polymerase III DnaE; Reviewed
Probab=63.08 E-value=22 Score=44.32 Aligned_cols=71 Identities=15% Similarity=0.206 Sum_probs=51.6
Q ss_pred eeccccCCCC-CceEEEEEEEeeccccccccCCCCceeEEEEEEeCCCCeEEEEEchhHHHHHHhhcccCcEEEEec
Q 006263 209 IPIAALNPYQ-GRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISK 284 (653)
Q Consensus 209 ~pI~~L~p~~-~~w~I~~RV~~k~~ir~~~~~~g~gk~f~~~L~D~~g~~I~at~f~~~~~kf~~~l~eG~vy~is~ 284 (653)
.++.+|.... ...+|.|-|+..-.+++ ++|+ ...-+.|-| ..|.|.+++|.+..+++.+.|++|.++.+.+
T Consensus 933 ~~~~~l~~~~~~~v~v~g~i~~~~~~~t---k~g~-~maf~~leD-~tg~~e~~vFp~~y~~~~~~l~~~~~~~v~G 1004 (1107)
T PRK06920 933 PSLAQAMRHKKKVQRAIVYITSVKVIRT---KKGQ-KMAFITFCD-QNDEMEAVVFPETYIHFSDKLQEGAIVLVDG 1004 (1107)
T ss_pred cCHHHHhhcCCCEEEEEEEEEEeEeecC---CCCC-eEEEEEEee-CCCcEEEEECHHHHHHHHHHhccCCEEEEEE
Confidence 4566664322 24677777777544333 4443 355567778 8999999999999999999999999999954
No 138
>COG0629 Ssb Single-stranded DNA-binding protein [DNA replication, recombination, and repair]
Probab=62.60 E-value=25 Score=33.69 Aligned_cols=69 Identities=19% Similarity=0.239 Sum_probs=49.1
Q ss_pred CCceEEEEEEEeeccccccccCCCCceeEEEE---EEeC-------CCCeEEEEEchhHHHHHHhhcccCcEEEEeceE
Q 006263 218 QGRWAIKARVTAKGDLRRYNNARGDGKVFSFD---LLDS-------DGGEIRVTCFNAVVDRFYEIIEVGRVYLISKGS 286 (653)
Q Consensus 218 ~~~w~I~~RV~~k~~ir~~~~~~g~gk~f~~~---L~D~-------~g~~I~at~f~~~~~kf~~~l~eG~vy~is~~~ 286 (653)
+++-.+-+|+++.-++|...+..--..+|... ..|. +..-|++++|+.+++.....|+.|.-++|.+..
T Consensus 3 ~Nkv~LvG~l~~DPE~r~t~~g~~~v~~~~~a~~r~~~~~~~~~~~~t~~~~vv~wgk~Ae~~~~yl~KG~~V~VeG~l 81 (167)
T COG0629 3 MNKVILVGRLTRDPELRYTPNGGAVVALFSAAVNRRFDNQSGERDEETDWIRVVIWGKLAENAAEYLKKGSLVYVEGRL 81 (167)
T ss_pred cceEEEEeecccCcceeecCCCCeeeEEEEEEeccccccCCcccccccceEEEEEehHHHHHHHHHhcCCCEEEEEEEE
Confidence 46788999999999998865321111122221 2232 236799999999999999999999999998753
No 139
>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=62.29 E-value=57 Score=36.66 Aligned_cols=81 Identities=14% Similarity=0.185 Sum_probs=56.4
Q ss_pred CceEEEEEEEeeccccccccCCCCceeEEEEEEeCCC--CeEEEEEchh---HHHHHHhhcccCcEEEEeceEEecCCCc
Q 006263 219 GRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDG--GEIRVTCFNA---VVDRFYEIIEVGRVYLISKGSLKPAQKN 293 (653)
Q Consensus 219 ~~w~I~~RV~~k~~ir~~~~~~g~gk~f~~~L~D~~g--~~I~at~f~~---~~~kf~~~l~eG~vy~is~~~V~~a~~~ 293 (653)
..-+|+|||.++ |. .|++.-++|.| .+ +.|++++-.. ...++-..|..|+++.+.+.-.+...
T Consensus 17 ~~v~v~Gwv~~~---R~------~~~~~F~~lrD-~~~~g~iQ~v~~~~~~~~~~~~~~~l~~gs~V~v~G~v~~~~~-- 84 (453)
T TIGR00457 17 DEVTVSGWVRTK---RS------SKKIIFLELND-GSSLGPIQAVINGEDNPYLFQLLKSLTTGSSVSVTGKVVESPG-- 84 (453)
T ss_pred CEEEEEEEeEEE---Ec------CCCeEEEEEEC-CCCCccEEEEEeCCcChHHHHHHHcCCCCcEEEEEEEEEcCCC--
Confidence 458899999774 32 25677788899 55 7999998764 22234466999999999886544221
Q ss_pred ccCCCCceEEEeccccEEEec
Q 006263 294 FNHLKNEWEIFLEATSTVDLC 314 (653)
Q Consensus 294 f~~~~~~yei~f~~~T~I~~~ 314 (653)
....+||....-..+.++
T Consensus 85 ---~~~~~El~~~~i~vl~~~ 102 (453)
T TIGR00457 85 ---KGQPVELQVKKIEVVGEA 102 (453)
T ss_pred ---CCCCEEEEEeEEEEEecC
Confidence 136799998776666665
No 140
>PRK10917 ATP-dependent DNA helicase RecG; Provisional
Probab=62.25 E-value=19 Score=42.63 Aligned_cols=69 Identities=19% Similarity=0.331 Sum_probs=51.7
Q ss_pred cceeccccCCCCCceEEEEEEEeeccccccccCCCCceeEEEEEEeCCCCeEEEEEchhHHHHH-HhhcccCcEEEEec
Q 006263 207 RIIPIAALNPYQGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAVVDRF-YEIIEVGRVYLISK 284 (653)
Q Consensus 207 ~~~pI~~L~p~~~~w~I~~RV~~k~~ir~~~~~~g~gk~f~~~L~D~~g~~I~at~f~~~~~kf-~~~l~eG~vy~is~ 284 (653)
.+.+|+++.++ ..-+|.|+|+.....+. ..+++.+.+.| ++|.|.+++|+-- ..| ...|++|+.|.+++
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------KRRRLTVTVSD-GTGNLTLRFFNFN-QPYLKKQLKVGKRVAVYG 118 (681)
T ss_pred CcCCHHHCCCC-CEEEEEEEEEEEEEccC------CceEEEEEEEE-CCeEEEEEEEccC-cHHHHhhCCCCCEEEEEE
Confidence 46689999876 47999999988733221 13589999999 6789999999410 124 67899999999886
No 141
>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=60.98 E-value=74 Score=36.92 Aligned_cols=86 Identities=19% Similarity=0.196 Sum_probs=57.8
Q ss_pred CceEEEEEEEeeccccccccCCCCceeEEEEEEeCCCCeEEEEEchh-HHHHHHhhcccCcEEEEeceEEecCCCccc--
Q 006263 219 GRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNA-VVDRFYEIIEVGRVYLISKGSLKPAQKNFN-- 295 (653)
Q Consensus 219 ~~w~I~~RV~~k~~ir~~~~~~g~gk~f~~~L~D~~g~~I~at~f~~-~~~kf~~~l~eG~vy~is~~~V~~a~~~f~-- 295 (653)
...+|+|||.++ |. -|++.-++|.| .+|.|++++-.+ ..-+....|..|+++.+.+.-.+...+.-+
T Consensus 16 ~~V~l~GwV~~~---R~------~Gkl~Fi~LrD-~sg~iQvv~~~~~~~~~~~~~L~~esvV~V~G~v~~r~~~~~n~~ 85 (583)
T TIGR00459 16 QTVTLAGWVNRR---RD------LGGLIFIDLRD-RSGIVQVVCDPDADALKLAKGLRNEDVVQVKGKVSARPEGNINRN 85 (583)
T ss_pred CEEEEEEEEEEE---Ec------CCCcEEEEEEe-CCccEEEEEeCCHHHHHHHhcCCCCCEEEEEEEEEeCCccccCcc
Confidence 368899999774 33 25677789999 677999988644 222344668999999998865432211111
Q ss_pred CCCCceEEEeccccEEEec
Q 006263 296 HLKNEWEIFLEATSTVDLC 314 (653)
Q Consensus 296 ~~~~~yei~f~~~T~I~~~ 314 (653)
.....+||....-+.+..+
T Consensus 86 ~~tg~iEl~~~~i~iL~~a 104 (583)
T TIGR00459 86 LDTGEIEILAESITLLNKS 104 (583)
T ss_pred CCCCcEEEEEeEEEEeecC
Confidence 2356799988776666554
No 142
>TIGR00621 ssb single stranded DNA-binding protein (ssb). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=60.61 E-value=48 Score=31.69 Aligned_cols=72 Identities=13% Similarity=0.132 Sum_probs=39.3
Q ss_pred cccEEEEEEEecCceeEEecCCceeeEEEEEE----EeCC------CCEEEEEEccchhhhhhhhHHHhhccCCCcEEEE
Q 006263 342 IVDVIGIVISVNPSVPILRKNGMETQRRILNL----KDTS------GRSVELTLWGDFCNKEGQKLQEMVDVGFFPVLSV 411 (653)
Q Consensus 342 ~vDVIGvV~~v~~~~~i~~k~g~~~~kr~i~l----~D~s------~~~i~vtLWg~~A~~~~~~l~~~~~~~~~~Vvai 411 (653)
.|-++|.|..--++. .+.+|+.+.+..|-. .|.. ..-+.|++||+.|+..... + ..+..|.+
T Consensus 6 ~V~L~G~l~~dPe~r--~t~~G~~v~~fsvA~~~~~~~~~G~~~~~t~~~~v~~wg~~Ae~~~~~----l--~KG~~V~V 77 (164)
T TIGR00621 6 KVILVGRLTRDPELR--YTPSGNAVANFTLATNRRWKDQDGEWKEETEWHDIVIFGRLAEVAAQY----L--KKGSLVYV 77 (164)
T ss_pred EEEEEEEeCCCCEEE--ECCCCCEEEEEEEEEcCceecCCCCEeccceEEEEEEehHHHHHHHHh----C--CCCCEEEE
Confidence 356777777632222 234565443333322 1222 2379999999998774322 2 35677776
Q ss_pred Ee-eEeecCCC
Q 006263 412 KS-GKVNDFSG 421 (653)
Q Consensus 412 k~-~rV~~f~G 421 (653)
.| .+.+.|.+
T Consensus 78 ~G~L~~~~~~~ 88 (164)
T TIGR00621 78 EGRLRTRKWED 88 (164)
T ss_pred EEEEEeceEEC
Confidence 64 45566743
No 143
>COG0017 AsnS Aspartyl/asparaginyl-tRNA synthetases [Translation, ribosomal structure and biogenesis]
Probab=60.58 E-value=73 Score=35.37 Aligned_cols=91 Identities=19% Similarity=0.237 Sum_probs=62.2
Q ss_pred eeccccCCCCC--ceEEEEEEEeeccccccccCCCCceeEEEEEEeCCCCeEEEEEchh-H-HHHH-HhhcccCcEEEEe
Q 006263 209 IPIAALNPYQG--RWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNA-V-VDRF-YEIIEVGRVYLIS 283 (653)
Q Consensus 209 ~pI~~L~p~~~--~w~I~~RV~~k~~ir~~~~~~g~gk~f~~~L~D~~g~~I~at~f~~-~-~~kf-~~~l~eG~vy~is 283 (653)
+.|+++.+... .-+|+|-|-++ |+.|++.-+.|.| .+|-|||++... . -+.| -..|.-+.++.+.
T Consensus 5 ~~i~di~~~~~~~~V~v~GWV~~~---------R~~g~i~Fi~lrD-gsg~iQ~v~~~~~~~~~~~~~~~L~~es~v~V~ 74 (435)
T COG0017 5 TYIKDIKPHVGGQEVTVRGWVHNK---------RDLGKIIFLVLRD-GSGFIQAVVPKNKVYEELFKAKKLTLESSVVVT 74 (435)
T ss_pred eeHHhhhccCCCcEEEEEEEeeee---------cccCCeEEEEEEc-CCcEEEEEEECCCCcHHHhhhhcCCCccEEEEE
Confidence 46677776654 67788887654 3346766678889 677899999842 2 2222 3468889999888
Q ss_pred ceEEecCCCcccCCCCceEEEeccccEEEec
Q 006263 284 KGSLKPAQKNFNHLKNEWEIFLEATSTVDLC 314 (653)
Q Consensus 284 ~~~V~~a~~~f~~~~~~yei~f~~~T~I~~~ 314 (653)
+--++ ..+ .+..|||....=..+..+
T Consensus 75 G~v~~-~~~----a~~g~El~v~~i~Vl~~a 100 (435)
T COG0017 75 GIVKA-SPK----APQGFELQVEKIEVLGEA 100 (435)
T ss_pred EEEEc-CCC----CCCCEEEEEEEEEEeecc
Confidence 75443 222 578899999886666665
No 144
>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=59.88 E-value=1e+02 Score=25.77 Aligned_cols=76 Identities=20% Similarity=0.282 Sum_probs=44.6
Q ss_pred eEEEEEEEeeccccccccCCCCceeEEEEEEeCCCCeEEEEEchhHHHHHH--hhcccCcEEEEeceEEecCCCcccCCC
Q 006263 221 WAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAVVDRFY--EIIEVGRVYLISKGSLKPAQKNFNHLK 298 (653)
Q Consensus 221 w~I~~RV~~k~~ir~~~~~~g~gk~f~~~L~D~~g~~I~at~f~~~~~kf~--~~l~eG~vy~is~~~V~~a~~~f~~~~ 298 (653)
.+|.|+|.++ |.. .|++.-++|.|..|..|++++-.+. +.|. ..|..|+++.+.+- +....+.-..-.
T Consensus 2 V~v~Gwv~~~---R~~-----~~~~~Fi~LrD~~g~~iQvv~~~~~-~~~~~~~~l~~~s~V~V~G~-v~~~~~~~~~~~ 71 (86)
T cd04321 2 VTLNGWIDRK---PRI-----VKKLSFADLRDPNGDIIQLVSTAKK-DAFSLLKSITAESPVQVRGK-LQLKEAKSSEKN 71 (86)
T ss_pred EEEEEeEeeE---eCC-----CCceEEEEEECCCCCEEEEEECCCH-HHHHHHhcCCCCcEEEEEEE-EEeCCCcCCCCC
Confidence 4677887663 321 2466667899965546999775442 3333 34889999999774 433221110112
Q ss_pred CceEEEec
Q 006263 299 NEWEIFLE 306 (653)
Q Consensus 299 ~~yei~f~ 306 (653)
..+||..+
T Consensus 72 ~~~Ei~~~ 79 (86)
T cd04321 72 DEWELVVD 79 (86)
T ss_pred CCEEEEEE
Confidence 56888763
No 145
>PRK07374 dnaE DNA polymerase III subunit alpha; Validated
Probab=59.58 E-value=27 Score=43.77 Aligned_cols=78 Identities=22% Similarity=0.265 Sum_probs=54.2
Q ss_pred eecchhhhhhcccCccccEEEEEEEecCceeEEecCCceeeEEEEEEEeCCCCEEEEEEccchhhhhhhhHHHhhccCCC
Q 006263 327 SFRHISEIESAENNSIVDVIGIVISVNPSVPILRKNGMETQRRILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVDVGFF 406 (653)
Q Consensus 327 ~f~~i~~i~~~~~~~~vDVIGvV~~v~~~~~i~~k~g~~~~kr~i~l~D~s~~~i~vtLWg~~A~~~~~~l~~~~~~~~~ 406 (653)
..+++++|.+...+..|-|+|+|+.+... .+|.|+. .--++|.|.+| .+++++|-+.-..+...| ..+
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-SCEAVVFPKSYERLSDHL------MTD 1054 (1170)
T ss_pred CCcCHHHHhcccCCCEEEEEEEEEEeEec---ccCCCCE--EEEEEEEECCC-CEEEEECHHHHHHHHHHh------ccC
Confidence 44567777544456678899999988764 4566763 45689999999 799999998766643322 245
Q ss_pred cEEEEEeeEee
Q 006263 407 PVLSVKSGKVN 417 (653)
Q Consensus 407 ~Vvaik~~rV~ 417 (653)
.++.++| +|.
T Consensus 1055 ~~~~v~g-~v~ 1064 (1170)
T PRK07374 1055 TRLLVWA-KVD 1064 (1170)
T ss_pred CEEEEEE-EEE
Confidence 6777765 443
No 146
>PF02760 HIN: HIN-200/IF120x domain; InterPro: IPR004021 This domain has no known function. It is found in one or two copies per protein, and is found associated with the PAAD/DAPIN domain IPR004020 from INTERPRO.; PDB: 3RN2_A 3RN5_C 2OQ0_A 3B6Y_A 3RLN_A 3RNU_A 3RLO_A.
Probab=59.52 E-value=1.6e+02 Score=27.98 Aligned_cols=144 Identities=17% Similarity=0.247 Sum_probs=89.4
Q ss_pred EEEEEEeeccccccccCC-CCceeEEEEEEeCCCCeEEEEEchhHHHHHHhhcccCcEEEEeceEEecCCCcccCCCCce
Q 006263 223 IKARVTAKGDLRRYNNAR-GDGKVFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISKGSLKPAQKNFNHLKNEW 301 (653)
Q Consensus 223 I~~RV~~k~~ir~~~~~~-g~gk~f~~~L~D~~g~~I~at~f~~~~~kf~~~l~eG~vy~is~~~V~~a~~~f~~~~~~y 301 (653)
..|.|+.-.+.=+|.... |..+.|.-+++- +..-.++.+|+- .+.+.+..++++.||+..-. .-
T Consensus 5 ~~VmVLkaTepF~Ye~~e~gkk~MFHATVAT-et~fF~VKVfn~---~LKeKF~~kkiI~IS~Y~~~-----------~g 69 (170)
T PF02760_consen 5 KTVMVLKATEPFEYESPEEGKKKMFHATVAT-ETEFFRVKVFNI---NLKEKFIPKKIIAISDYFGR-----------NG 69 (170)
T ss_dssp EEEEEEEE---EEEECTTTCEEEEEEEEEE--SS-EEEEEES-G---GGCCTCSTTSEEEEESEEEE-----------TT
T ss_pred eEEEEEeccCCeEEeCcccCcceEEEEEEec-cccEEEEEEecc---hhHhhcCCCcEEEEehhhcc-----------cc
Confidence 457777777777787665 455789999999 899999999996 57788999999999997421 12
Q ss_pred EEEeccccEEEecc-CCCCCCCccc----ceecchhhhhhcccCccccEEEEEEEecCceeEEecCCceeeEEEEEEEeC
Q 006263 302 EIFLEATSTVDLCT-EEDDSIPKQQ----FSFRHISEIESAENNSIVDVIGIVISVNPSVPILRKNGMETQRRILNLKDT 376 (653)
Q Consensus 302 ei~f~~~T~I~~~~-d~~~~iP~~~----f~f~~i~~i~~~~~~~~vDVIGvV~~v~~~~~i~~k~g~~~~kr~i~l~D~ 376 (653)
-|-.++.|.|.++. |..-.+|... -.=-+|++|.....+.+|+=+=.|.... .+ ....-..|.|.
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 35567788888884 3334566431 2345688888777787776443333211 11 12345689999
Q ss_pred CCCEEEEEEccchhhh
Q 006263 377 SGRSVELTLWGDFCNK 392 (653)
Q Consensus 377 s~~~i~vtLWg~~A~~ 392 (653)
+| .++|...|.+...
T Consensus 140 TG-~MeVvv~G~~~ni 154 (170)
T PF02760_consen 140 TG-KMEVVVYGKWHNI 154 (170)
T ss_dssp TE-EEEEEEEGGGCGC
T ss_pred CC-cEEEEEeccCccc
Confidence 99 8999999998643
No 147
>PRK06751 single-stranded DNA-binding protein; Provisional
Probab=57.75 E-value=57 Score=31.59 Aligned_cols=36 Identities=6% Similarity=0.140 Sum_probs=24.4
Q ss_pred CEEEEEEccchhhhhhhhHHHhhccCCCcEEEEE-eeEeecCC
Q 006263 379 RSVELTLWGDFCNKEGQKLQEMVDVGFFPVLSVK-SGKVNDFS 420 (653)
Q Consensus 379 ~~i~vtLWg~~A~~~~~~l~~~~~~~~~~Vvaik-~~rV~~f~ 420 (653)
.-+.|++||+.|+.+.++ + ..+.-|+|. ..+.+.|.
T Consensus 47 dwi~~v~wgk~Ae~~~~~----l--~KG~~V~VeGrL~~r~ye 83 (173)
T PRK06751 47 DFINCVIWRKQAENVANY----L--KKGSLAGVDGRLQTRNYE 83 (173)
T ss_pred EEEEEEEeCcHHHHHHHH----c--CCCCEEEEEEEEEeCccC
Confidence 379999999998875333 2 246666665 44666775
No 148
>PRK05813 single-stranded DNA-binding protein; Provisional
Probab=57.28 E-value=48 Score=33.41 Aligned_cols=63 Identities=11% Similarity=0.046 Sum_probs=50.2
Q ss_pred CCceEEEEEEEeeccccccccCCCCceeEEEEEEeC----CCCeEEEEEchhHHHHHHhhcccCcEEEEec
Q 006263 218 QGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDS----DGGEIRVTCFNAVVDRFYEIIEVGRVYLISK 284 (653)
Q Consensus 218 ~~~w~I~~RV~~k~~ir~~~~~~g~gk~f~~~L~D~----~g~~I~at~f~~~~~kf~~~l~eG~vy~is~ 284 (653)
++...+.||+++...+|...+ | ..+.+|.|+=. +.+-|.+++|+..++... .|+.|+-+.+.+
T Consensus 109 ~N~V~LiGrL~~DPelR~t~~--G-~~va~f~lAvnr~~~~td~i~~v~wg~~Ae~~~-~l~KG~~V~V~G 175 (219)
T PRK05813 109 PNEIFLDGYICKEPVYRTTPF--G-REIADLLLAVNRPYNKSDYIPCIAWGRNARFCK-TLEVGDNIRVWG 175 (219)
T ss_pred ccEEEEEEEccCCCeEEECCC--C-CEEEEEEEEEcCCCCCceEEEEEEEhHHhHHHh-hCCCCCEEEEEE
Confidence 578999999999999987533 2 26788887632 367999999999988665 599999998876
No 149
>PF07191 zinc-ribbons_6: zinc-ribbons; InterPro: IPR010807 This family consists of several short, hypothetical bacterial proteins of around 70 residues in length. Members of this family 8 highly conserved cysteine residues. The function of the family is unknown.; PDB: 2JRP_A 2JNE_A.
Probab=56.23 E-value=7.4 Score=31.64 Aligned_cols=24 Identities=25% Similarity=1.085 Sum_probs=17.1
Q ss_pred cCCCCcCcccccceeeecCceeecccCccc
Q 006263 512 ACPLMIGDRQCNKKVTQSGNRWQCDRCNQE 541 (653)
Q Consensus 512 aC~~~~~~~~C~KKv~~~~~~~~C~kC~~~ 541 (653)
.|| .|..-+...++.|+|+.|++.
T Consensus 3 ~CP------~C~~~L~~~~~~~~C~~C~~~ 26 (70)
T PF07191_consen 3 TCP------KCQQELEWQGGHYHCEACQKD 26 (70)
T ss_dssp B-S------SS-SBEEEETTEEEETTT--E
T ss_pred cCC------CCCCccEEeCCEEECcccccc
Confidence 588 899998888889999999875
No 150
>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=55.63 E-value=15 Score=30.13 Aligned_cols=39 Identities=26% Similarity=0.411 Sum_probs=32.1
Q ss_pred EEEEEEeCCCCeEEEEEchhHHHHHHhhcccCcEEEEece
Q 006263 246 FSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISKG 285 (653)
Q Consensus 246 f~~~L~D~~g~~I~at~f~~~~~kf~~~l~eG~vy~is~~ 285 (653)
.-|.|.| +++.|+|.+|.....+....+++|+-+.+.+-
T Consensus 17 vyfsLkD-~~a~i~cv~f~~~~~~~~~~l~~Gd~V~v~G~ 55 (73)
T cd04487 17 TIFTLRD-ETGTVWAAAFEEAGVRAYPEVEVGDIVRVTGE 55 (73)
T ss_pred EEEEEEc-CCEEEEEEEEchhccCCcCCCCCCCEEEEEEE
Confidence 5688899 78899999999877667778999997777664
No 151
>PRK07459 single-stranded DNA-binding protein; Provisional
Probab=54.98 E-value=82 Score=28.50 Aligned_cols=69 Identities=14% Similarity=0.153 Sum_probs=39.2
Q ss_pred cccEEEEEEEecCceeEEecCCceeeEEEEEEEeC------CCCEEEEEEccchhhhhhhhHHHhhccCCCcEEEEE-ee
Q 006263 342 IVDVIGIVISVNPSVPILRKNGMETQRRILNLKDT------SGRSVELTLWGDFCNKEGQKLQEMVDVGFFPVLSVK-SG 414 (653)
Q Consensus 342 ~vDVIGvV~~v~~~~~i~~k~g~~~~kr~i~l~D~------s~~~i~vtLWg~~A~~~~~~l~~~~~~~~~~Vvaik-~~ 414 (653)
.|-++|.+..--++. .+.+|+.+ -.|.|.-. ...-+.|++||..|+...++| ..|.-|++. ..
T Consensus 5 ~v~LiGrL~~DPelr--~t~~G~~v--~~fslAv~~~~~~~~t~w~~v~~wg~~Ae~~~~~l------~KG~~V~V~G~l 74 (121)
T PRK07459 5 SVTLVGRAGRDPEVR--YFESGSVV--CNLTLAVNRRSRDDEPDWFNLEIWGKTAQVAADYV------KKGSLIGITGSL 74 (121)
T ss_pred EEEEEEEccCCCEEE--EcCCCCEE--EEEEEEecccccCCCceEEEEEEehHHHHHHHHHc------CCCCEEEEEEEE
Confidence 356788887632222 23456543 33444322 223699999999987753332 246666665 44
Q ss_pred EeecCC
Q 006263 415 KVNDFS 420 (653)
Q Consensus 415 rV~~f~ 420 (653)
+...|.
T Consensus 75 ~~~~~~ 80 (121)
T PRK07459 75 KFDRWT 80 (121)
T ss_pred EecceE
Confidence 666673
No 152
>PRK03932 asnC asparaginyl-tRNA synthetase; Validated
Probab=54.97 E-value=96 Score=34.80 Aligned_cols=81 Identities=11% Similarity=0.137 Sum_probs=54.3
Q ss_pred CceEEEEEEEeeccccccccCCCCceeEEEEEEeCCCCeEEEEEchh---HHHHHHhhcccCcEEEEeceEEecCCCccc
Q 006263 219 GRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNA---VVDRFYEIIEVGRVYLISKGSLKPAQKNFN 295 (653)
Q Consensus 219 ~~w~I~~RV~~k~~ir~~~~~~g~gk~f~~~L~D~~g~~I~at~f~~---~~~kf~~~l~eG~vy~is~~~V~~a~~~f~ 295 (653)
...+|+|||.++ |. .|++.-++|.| .+|.|++.+-.+ ..-++...|..|+++.+.+.-.+. ..
T Consensus 17 ~~V~i~G~v~~~---R~------~g~~~Fi~lrD-~~g~iq~~~~~~~~~~~~~~~~~l~~~s~v~v~G~v~~~-~~--- 82 (450)
T PRK03932 17 QEVTVRGWVRTK---RD------SGKIAFLQLRD-GSCFKQLQVVKDNGEEYFEEIKKLTTGSSVIVTGTVVES-PR--- 82 (450)
T ss_pred CEEEEEEEEEEE---Ee------CCCeEEEEEEC-CCCcEEEEEEcCCChHHHHHHhcCCCCcEEEEEEEEEcC-CC---
Confidence 468999999874 43 25777788999 678888877533 222233559999999998754432 21
Q ss_pred CCCCceEEEeccccEEEec
Q 006263 296 HLKNEWEIFLEATSTVDLC 314 (653)
Q Consensus 296 ~~~~~yei~f~~~T~I~~~ 314 (653)
....+||....-+.+.++
T Consensus 83 -~~~~~el~~~~i~vl~~~ 100 (450)
T PRK03932 83 -AGQGYELQATKIEVIGED 100 (450)
T ss_pred -CCCCEEEEEEEEEEccCC
Confidence 235789988766555554
No 153
>PRK08486 single-stranded DNA-binding protein; Provisional
Probab=54.48 E-value=69 Score=31.27 Aligned_cols=35 Identities=11% Similarity=0.154 Sum_probs=23.4
Q ss_pred EEEEEEccchhhhhhhhHHHhhccCCCcEEEEEe-eEeecCC
Q 006263 380 SVELTLWGDFCNKEGQKLQEMVDVGFFPVLSVKS-GKVNDFS 420 (653)
Q Consensus 380 ~i~vtLWg~~A~~~~~~l~~~~~~~~~~Vvaik~-~rV~~f~ 420 (653)
-+.|++||..|+....+| ..+.-|+|.| .+.+.|.
T Consensus 50 fi~v~~fg~~AE~~~~~l------~KG~~V~VeGrL~~~~y~ 85 (182)
T PRK08486 50 FIDIRLFGRTAEIANQYL------SKGSKVLIEGRLTFESWM 85 (182)
T ss_pred EEEEEEEhHHHHHHHHHc------CCCCEEEEEEEEEeCcEE
Confidence 689999999988753332 2567676654 4556673
No 154
>PRK10220 hypothetical protein; Provisional
Probab=54.22 E-value=8 Score=34.08 Aligned_cols=29 Identities=31% Similarity=0.787 Sum_probs=24.0
Q ss_pred EEecCCCCcCcccccceeeecCc-eeecccCccccC
Q 006263 509 CYTACPLMIGDRQCNKKVTQSGN-RWQCDRCNQEID 543 (653)
Q Consensus 509 ~Y~aC~~~~~~~~C~KKv~~~~~-~~~C~kC~~~~~ 543 (653)
.+|+|| .|+..-+.+.+ .|-|+.|...+.
T Consensus 2 ~lP~CP------~C~seytY~d~~~~vCpeC~hEW~ 31 (111)
T PRK10220 2 SLPHCP------KCNSEYTYEDNGMYICPECAHEWN 31 (111)
T ss_pred CCCcCC------CCCCcceEcCCCeEECCcccCcCC
Confidence 468999 99998776555 999999998874
No 155
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=54.19 E-value=6.1 Score=43.27 Aligned_cols=29 Identities=24% Similarity=0.888 Sum_probs=24.4
Q ss_pred ecCCCCcCcccccceeeecCc-eeecccCccccCCc
Q 006263 511 TACPLMIGDRQCNKKVTQSGN-RWQCDRCNQEIDEC 545 (653)
Q Consensus 511 ~aC~~~~~~~~C~KKv~~~~~-~~~C~kC~~~~~~~ 545 (653)
|-|| .|++.+...+. .|+|.||+...+..
T Consensus 351 p~Cp------~Cg~~m~S~G~~g~rC~kCg~~~~~~ 380 (421)
T COG1571 351 PVCP------RCGGRMKSAGRNGFRCKKCGTRARET 380 (421)
T ss_pred CCCC------ccCCchhhcCCCCcccccccccCCcc
Confidence 5799 99999987776 99999999876543
No 156
>PRK09010 single-stranded DNA-binding protein; Provisional
Probab=53.50 E-value=85 Score=30.54 Aligned_cols=37 Identities=11% Similarity=0.210 Sum_probs=24.5
Q ss_pred EEEEEEccchhhhhhhhHHHhhccCCCcEEEEE-eeEeecCCCc
Q 006263 380 SVELTLWGDFCNKEGQKLQEMVDVGFFPVLSVK-SGKVNDFSGK 422 (653)
Q Consensus 380 ~i~vtLWg~~A~~~~~~l~~~~~~~~~~Vvaik-~~rV~~f~G~ 422 (653)
-++|++||..|+...++| ..+.-|++. ..+.+.|.++
T Consensus 55 w~~V~~fgk~Ae~~~~~L------~KGs~V~VeGrL~~~~yedk 92 (177)
T PRK09010 55 WHRVVLFGKLAEVAGEYL------RKGSQVYIEGQLRTRKWTDQ 92 (177)
T ss_pred EEEEEEehhHHHHHHHhc------CCCCEEEEEEEEEeccccCC
Confidence 579999999987743332 246666665 4566678643
No 157
>PRK08763 single-stranded DNA-binding protein; Provisional
Probab=51.74 E-value=1e+02 Score=29.59 Aligned_cols=35 Identities=11% Similarity=0.170 Sum_probs=23.0
Q ss_pred EEEEEEccchhhhhhhhHHHhhccCCCcEEEEEe-eEeecCC
Q 006263 380 SVELTLWGDFCNKEGQKLQEMVDVGFFPVLSVKS-GKVNDFS 420 (653)
Q Consensus 380 ~i~vtLWg~~A~~~~~~l~~~~~~~~~~Vvaik~-~rV~~f~ 420 (653)
-++|++||..|+...++| ..|.-|.+.| .+...|.
T Consensus 53 w~~Vv~fgk~Ae~v~~~L------~KGs~V~VeGrL~~~~y~ 88 (164)
T PRK08763 53 WHRVKFFGKLGEIAGEYL------RKGSQCYIEGSIRYDKFT 88 (164)
T ss_pred EEEEEEehHHHHHHHHhc------CCCCEEEEEEEEEeceeE
Confidence 499999999987643322 3566666654 4556674
No 158
>PRK06341 single-stranded DNA-binding protein; Provisional
Probab=51.72 E-value=57 Score=31.37 Aligned_cols=64 Identities=16% Similarity=0.230 Sum_probs=47.5
Q ss_pred CCceEEEEEEEeeccccccccCCCCceeEEEEEEe------CC-------CCeEEEEEchh-HHHHHHhhcccCcEEEEe
Q 006263 218 QGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLD------SD-------GGEIRVTCFNA-VVDRFYEIIEVGRVYLIS 283 (653)
Q Consensus 218 ~~~w~I~~RV~~k~~ir~~~~~~g~gk~f~~~L~D------~~-------g~~I~at~f~~-~~~kf~~~l~eG~vy~is 283 (653)
++.-+|.+||..-..+|...+ | ..+.+|.|+= .. ..-+.+++|++ +++.+...|+.|+.+.+.
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 467889999999888887543 2 2566665542 22 23468999996 789999999999999887
Q ss_pred c
Q 006263 284 K 284 (653)
Q Consensus 284 ~ 284 (653)
.
T Consensus 82 G 82 (166)
T PRK06341 82 G 82 (166)
T ss_pred E
Confidence 6
No 159
>PRK12820 bifunctional aspartyl-tRNA synthetase/aspartyl/glutamyl-tRNA amidotransferase subunit C; Provisional
Probab=50.93 E-value=1.3e+02 Score=35.80 Aligned_cols=85 Identities=16% Similarity=0.161 Sum_probs=56.9
Q ss_pred ceEEEEEEEeeccccccccCCCCceeEEEEEEeCCCCeEEEEEchhH----HHHHHhhcccCcEEEEeceEEecCCCccc
Q 006263 220 RWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAV----VDRFYEIIEVGRVYLISKGSLKPAQKNFN 295 (653)
Q Consensus 220 ~w~I~~RV~~k~~ir~~~~~~g~gk~f~~~L~D~~g~~I~at~f~~~----~~kf~~~l~eG~vy~is~~~V~~a~~~f~ 295 (653)
.-+|+|||.++ |. -|++.-++|.| .+|.|++++-.+. +-++...|..|+++.+.+--.+...+.-+
T Consensus 20 ~V~l~GWV~~~---R~------~G~l~FidLRD-~~G~iQvV~~~~~~~~~~~~~~~~L~~EsvV~V~G~v~~r~~~~~n 89 (706)
T PRK12820 20 EVCLAGWVDAF---RD------HGELLFIHLRD-RNGFIQAVFSPEAAPADVYELAASLRAEFCVALQGEVQKRLEETEN 89 (706)
T ss_pred EEEEEEEEEEE---Ec------CCCcEEEEEEe-CCccEEEEEeCCcCCHHHHHHHhcCCCCCEEEEEeEEeccCccccC
Confidence 57899999774 43 25677789999 6778999986432 22334569999999999965443222111
Q ss_pred C--CCCceEEEeccccEEEec
Q 006263 296 H--LKNEWEIFLEATSTVDLC 314 (653)
Q Consensus 296 ~--~~~~yei~f~~~T~I~~~ 314 (653)
+ ....+||....-..+..+
T Consensus 90 ~~~~tg~iEl~~~~i~iL~~a 110 (706)
T PRK12820 90 PHIETGDIEVFVRELSILAAS 110 (706)
T ss_pred CCCCCCcEEEEeeEEEEEecC
Confidence 1 236799998777666655
No 160
>PRK06826 dnaE DNA polymerase III DnaE; Reviewed
Probab=50.92 E-value=54 Score=41.16 Aligned_cols=60 Identities=17% Similarity=0.242 Sum_probs=45.0
Q ss_pred ceEEEEEEEeeccccccccCCCCceeEEEEEEeCCCCeEEEEEchhHHHHHHhhcccCcEEEEec
Q 006263 220 RWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISK 284 (653)
Q Consensus 220 ~w~I~~RV~~k~~ir~~~~~~g~gk~f~~~L~D~~g~~I~at~f~~~~~kf~~~l~eG~vy~is~ 284 (653)
.-+|.|-|+..-. ...++|+ ...-+.|-| ..|.|.+++|.+..+++...|++|.++.+.+
T Consensus 993 ~v~v~g~i~~~~~---~~tk~G~-~maf~~leD-~~g~~e~~vfp~~~~~~~~~l~~~~~~~v~g 1052 (1151)
T PRK06826 993 KVIIGGIITEVKR---KTTRNNE-MMAFLTLED-LYGTVEVIVFPKVYEKYRSLLNEDNIVLIKG 1052 (1151)
T ss_pred EEEEEEEEEEeEe---eccCCCC-eEEEEEEEE-CCCcEEEEECHHHHHHHHHHhccCCEEEEEE
Confidence 3456667766433 3334432 455567888 8899999999999999999999999998865
No 161
>PRK11827 hypothetical protein; Provisional
Probab=50.72 E-value=11 Score=29.74 Aligned_cols=27 Identities=30% Similarity=0.508 Sum_probs=21.6
Q ss_pred ecCCCCcCcccccceeeecCc--eeecccCccccC
Q 006263 511 TACPLMIGDRQCNKKVTQSGN--RWQCDRCNQEID 543 (653)
Q Consensus 511 ~aC~~~~~~~~C~KKv~~~~~--~~~C~kC~~~~~ 543 (653)
.+|| .|+.++..+.+ ...|..|+..|+
T Consensus 9 LaCP------~ckg~L~~~~~~~~Lic~~~~laYP 37 (60)
T PRK11827 9 IACP------VCNGKLWYNQEKQELICKLDNLAFP 37 (60)
T ss_pred eECC------CCCCcCeEcCCCCeEECCccCeecc
Confidence 5899 99999876543 788999998763
No 162
>PRK05672 dnaE2 error-prone DNA polymerase; Validated
Probab=50.58 E-value=40 Score=41.89 Aligned_cols=59 Identities=20% Similarity=0.226 Sum_probs=43.8
Q ss_pred eEEEEEEEeeccccccccCCCCceeEEEEEEeCCCCeEEEEEchhHHHHHHhhcccCcEEEEeceEE
Q 006263 221 WAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISKGSL 287 (653)
Q Consensus 221 w~I~~RV~~k~~ir~~~~~~g~gk~f~~~L~D~~g~~I~at~f~~~~~kf~~~l~eG~vy~is~~~V 287 (653)
-.|.+.|+.+...++ ++ | +.-+.|-| +.|.|.+++|.+..+++...|++|.++.+.+ +|
T Consensus 956 v~v~g~i~~~~~~~T---kk--G-maf~~leD-~~g~~e~~ifp~~~~~~~~~l~~~~~~~v~g-~v 1014 (1046)
T PRK05672 956 VRVAGVVTHRQRPGT---AS--G-VTFLTLED-ETGMVNVVVWPGLWERQRREALGARLLLVRG-RV 1014 (1046)
T ss_pred EEEEEEEEEEEEecC---CC--c-eEEEEEec-CCCCEEEEECHHHHHHHHHHhccCCEEEEEE-EE
Confidence 456666665444332 33 4 55566777 8999999999999999999999999999955 44
No 163
>PRK06826 dnaE DNA polymerase III DnaE; Reviewed
Probab=50.56 E-value=44 Score=41.91 Aligned_cols=78 Identities=23% Similarity=0.282 Sum_probs=52.2
Q ss_pred eecchhhhh---------hcccCccccEEEEEEEecCceeEEecCCceeeEEEEEEEeCCCCEEEEEEccchhhhhhhhH
Q 006263 327 SFRHISEIE---------SAENNSIVDVIGIVISVNPSVPILRKNGMETQRRILNLKDTSGRSVELTLWGDFCNKEGQKL 397 (653)
Q Consensus 327 ~f~~i~~i~---------~~~~~~~vDVIGvV~~v~~~~~i~~k~g~~~~kr~i~l~D~s~~~i~vtLWg~~A~~~~~~l 397 (653)
..+++++|. ....+..|-|.|+|+.+... .+|.|+. .--++|.|.+| .+++++|.+....+...|
T Consensus 969 ~~~~~~~l~~~~~~~~~~~~~~~~~v~v~g~i~~~~~~---~tk~G~~--maf~~leD~~g-~~e~~vfp~~~~~~~~~l 1042 (1151)
T PRK06826 969 TSATISDIISDEEEDGESKLKDGDKVIIGGIITEVKRK---TTRNNEM--MAFLTLEDLYG-TVEVIVFPKVYEKYRSLL 1042 (1151)
T ss_pred CCcCHHHHhhhccccccccccCCcEEEEEEEEEEeEee---ccCCCCe--EEEEEEEECCC-cEEEEECHHHHHHHHHHh
Confidence 345677772 23345678899999987654 4566763 45689999999 799999998765543222
Q ss_pred HHhhccCCCcEEEEEeeEee
Q 006263 398 QEMVDVGFFPVLSVKSGKVN 417 (653)
Q Consensus 398 ~~~~~~~~~~Vvaik~~rV~ 417 (653)
..+.+|.++| +|.
T Consensus 1043 ------~~~~~~~v~g-~v~ 1055 (1151)
T PRK06826 1043 ------NEDNIVLIKG-RVS 1055 (1151)
T ss_pred ------ccCCEEEEEE-EEE
Confidence 2456776665 444
No 164
>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=50.39 E-value=1.4e+02 Score=24.94 Aligned_cols=55 Identities=20% Similarity=0.186 Sum_probs=38.6
Q ss_pred EEEEEEEEEeCCCeEEEEEechhhhhhhCCCHHHHHHHhhccCChhHHHHHHHHhcCceEEEEEEEeeeccCceeeE
Q 006263 548 RYLLQAQIQDQTGLTWVTAFQESGEEILGCPAKELYMLKYELQDDVRFGEIIRSRVFNQYLFRLKIKEELYGDEQRV 624 (653)
Q Consensus 548 rY~l~~~i~D~Tg~~~~~~F~~~ae~llG~sA~el~~~~~e~~d~~~~~~~~~~~~~k~~~f~v~~k~~~y~~e~r~ 624 (653)
++++.+.++|.|+++.+-.|.+ + ..+.+.++ . ..|.-..++.++..++|..+.-+
T Consensus 20 ~~i~~~~itD~t~Si~~K~F~~--~-----~~~~~~~i--------------k-~~G~~v~v~G~v~~D~f~~e~~~ 74 (82)
T cd04484 20 RKILTFKVTDYTSSITVKKFLR--K-----DEKDKEEL--------------K-SKGDWVRVRGKVQYDTFSKELVL 74 (82)
T ss_pred CEEEEEEEEcCCCCEEEEEecc--C-----ChhHHhhc--------------c-cCCCEEEEEEEEEEccCCCceEE
Confidence 7889999999999999999964 1 11111111 1 03667889999989999876544
No 165
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=49.00 E-value=7.7 Score=25.04 Aligned_cols=22 Identities=23% Similarity=0.771 Sum_probs=16.6
Q ss_pred cCCCCcCcccccceeeecCceeecccCccc
Q 006263 512 ACPLMIGDRQCNKKVTQSGNRWQCDRCNQE 541 (653)
Q Consensus 512 aC~~~~~~~~C~KKv~~~~~~~~C~kC~~~ 541 (653)
-|| .|++.+..+ .-+|+.|+..
T Consensus 4 ~Cp------~Cg~~~~~~--~~fC~~CG~~ 25 (26)
T PF13248_consen 4 FCP------NCGAEIDPD--AKFCPNCGAK 25 (26)
T ss_pred CCc------ccCCcCCcc--cccChhhCCC
Confidence 589 899965443 6789999864
No 166
>PRK00476 aspS aspartyl-tRNA synthetase; Validated
Probab=48.96 E-value=1.2e+02 Score=35.23 Aligned_cols=84 Identities=17% Similarity=0.196 Sum_probs=56.0
Q ss_pred ceEEEEEEEeeccccccccCCCCceeEEEEEEeCCCCeEEEEEchhHHHHH--HhhcccCcEEEEeceEEecCCCcccC-
Q 006263 220 RWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAVVDRF--YEIIEVGRVYLISKGSLKPAQKNFNH- 296 (653)
Q Consensus 220 ~w~I~~RV~~k~~ir~~~~~~g~gk~f~~~L~D~~g~~I~at~f~~~~~kf--~~~l~eG~vy~is~~~V~~a~~~f~~- 296 (653)
.-+|+|||.++ |. -|++.-++|.| .+|.|++++-.. .+.| -..|..|+++.+.+--.+...+.-++
T Consensus 19 ~V~l~GwV~~~---R~------~g~l~Fi~LrD-~~g~iQ~v~~~~-~~~~~~~~~l~~es~V~V~G~v~~~~~~~~n~~ 87 (588)
T PRK00476 19 TVTLCGWVHRR---RD------HGGLIFIDLRD-REGIVQVVFDPD-AEAFEVAESLRSEYVIQVTGTVRARPEGTVNPN 87 (588)
T ss_pred EEEEEEEEEEE---Ee------CCCeEEEEEEe-CCceEEEEEeCC-HHHHHHHhCCCCCCEEEEEEEEEecCCcccCcc
Confidence 57899999764 43 25677789999 678899988642 2222 34689999999988544322122222
Q ss_pred -CCCceEEEeccccEEEec
Q 006263 297 -LKNEWEIFLEATSTVDLC 314 (653)
Q Consensus 297 -~~~~yei~f~~~T~I~~~ 314 (653)
...++||....-..+.++
T Consensus 88 ~~~g~~El~~~~i~il~~a 106 (588)
T PRK00476 88 LPTGEIEVLASELEVLNKS 106 (588)
T ss_pred CCCCcEEEEEeEEEEEecC
Confidence 245799998777666665
No 167
>PLN02903 aminoacyl-tRNA ligase
Probab=48.93 E-value=1.2e+02 Score=35.56 Aligned_cols=86 Identities=15% Similarity=0.149 Sum_probs=57.1
Q ss_pred CceEEEEEEEeeccccccccCCCCceeEEEEEEeCCCCeEEEEEchhH---HHHHHhhcccCcEEEEeceEEecCCCcc-
Q 006263 219 GRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAV---VDRFYEIIEVGRVYLISKGSLKPAQKNF- 294 (653)
Q Consensus 219 ~~w~I~~RV~~k~~ir~~~~~~g~gk~f~~~L~D~~g~~I~at~f~~~---~~kf~~~l~eG~vy~is~~~V~~a~~~f- 294 (653)
..-+|+|+|-++ |. -|++.-++|.| .+|.||+++-.+. +-+.-..|..|+|+.+.+--.....+.-
T Consensus 73 k~V~l~GWV~~~---R~------~G~l~FidLRD-~~G~iQvV~~~~~~~~~~~~~~~L~~esvV~V~G~V~~r~~~~~n 142 (652)
T PLN02903 73 SRVTLCGWVDLH---RD------MGGLTFLDVRD-HTGIVQVVTLPDEFPEAHRTANRLRNEYVVAVEGTVRSRPQESPN 142 (652)
T ss_pred CEEEEEEEEEEE---ec------CCCcEEEEEEc-CCccEEEEEeCCccHHHHHHHhcCCCCCEEEEEEEEEeCCCcCcC
Confidence 358899999764 43 25677789999 6778999886432 2223356999999999885443211111
Q ss_pred -cCCCCceEEEeccccEEEec
Q 006263 295 -NHLKNEWEIFLEATSTVDLC 314 (653)
Q Consensus 295 -~~~~~~yei~f~~~T~I~~~ 314 (653)
+....++||....-..+..+
T Consensus 143 ~~~~tGeiEl~~~~i~VL~~a 163 (652)
T PLN02903 143 KKMKTGSVEVVAESVDILNVV 163 (652)
T ss_pred CCCCCCCEEEEEeEEEEEecC
Confidence 12236799999887777666
No 168
>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=48.79 E-value=8.2 Score=33.02 Aligned_cols=26 Identities=27% Similarity=0.974 Sum_probs=19.1
Q ss_pred cCCCCcCcccccceeee-cC-ceeecccCccccC
Q 006263 512 ACPLMIGDRQCNKKVTQ-SG-NRWQCDRCNQEID 543 (653)
Q Consensus 512 aC~~~~~~~~C~KKv~~-~~-~~~~C~kC~~~~~ 543 (653)
-|| .|+|.-.. .. +.|.|.+|++.+.
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 589 99987543 32 3899999998653
No 169
>PRK05733 single-stranded DNA-binding protein; Provisional
Probab=48.58 E-value=66 Score=31.12 Aligned_cols=71 Identities=15% Similarity=0.159 Sum_probs=39.9
Q ss_pred cccEEEEEEEecCceeEEecCCceeeEEEEEEE----eC-CC------CEEEEEEccchhhhhhhhHHHhhccCCCcEEE
Q 006263 342 IVDVIGIVISVNPSVPILRKNGMETQRRILNLK----DT-SG------RSVELTLWGDFCNKEGQKLQEMVDVGFFPVLS 410 (653)
Q Consensus 342 ~vDVIGvV~~v~~~~~i~~k~g~~~~kr~i~l~----D~-s~------~~i~vtLWg~~A~~~~~~l~~~~~~~~~~Vva 410 (653)
.|-++|.|..--++. .+.+|..+.+-.|-.. |. +| .-+.|++||..|+.+.++ + ..|..|+
T Consensus 7 kV~LiGrlg~DPElr--~t~nG~~va~fsVAv~~~~k~~~~Ge~~e~T~w~~Vv~fgk~Ae~v~~~----l--~KGs~V~ 78 (172)
T PRK05733 7 KVILVGTCGQDPEVR--YLPNGNAVTNLSLATSEQWTDKQSGQKVERTEWHRVSLFGKVAEIAGEY----L--RKGSQVY 78 (172)
T ss_pred EEEEEEEecCCCEEE--ECCCCCEEEEEEEEEcCccccCCCCcccccceEEEEEEehHHHHHHHHH----h--CCCCEEE
Confidence 456888887632222 2345655433333321 21 12 249999999998775333 2 3577777
Q ss_pred EEe-eEeecCC
Q 006263 411 VKS-GKVNDFS 420 (653)
Q Consensus 411 ik~-~rV~~f~ 420 (653)
|.| .+.+.|.
T Consensus 79 VeGrLr~~~y~ 89 (172)
T PRK05733 79 IEGKLQTREWE 89 (172)
T ss_pred EEEEEEeCcEe
Confidence 764 4555664
No 170
>PF15489 CTC1: CST, telomere maintenance, complex subunit CTC1
Probab=48.15 E-value=1.1e+02 Score=37.88 Aligned_cols=67 Identities=15% Similarity=0.247 Sum_probs=52.6
Q ss_pred CceEEEEEEEeeccccccccCCCCceeEEEEEEeCCCCeEEEEEchhHHHHHHhhcccCcEEEEeceEEecC
Q 006263 219 GRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISKGSLKPA 290 (653)
Q Consensus 219 ~~w~I~~RV~~k~~ir~~~~~~g~gk~f~~~L~D~~g~~I~at~f~~~~~kf~~~l~eG~vy~is~~~V~~a 290 (653)
..-.|.|+|++.+.+-..+.+ ..|=+.|-| .+..+.+.+-...---|+..|..|+.|.|++.+|..-
T Consensus 166 ~~~~v~G~v~~ls~l~~~~~k----~fF~l~L~~-~~~~v~viVq~pa~l~Wh~~L~~G~~yvlT~Lrvs~i 232 (1144)
T PF15489_consen 166 RQLNVAGKVVRLSALVKSHGK----TFFILSLGD-AGSHVPVIVQEPAQLVWHRALRPGRAYVLTSLRVSKI 232 (1144)
T ss_pred CceeeeeEEEEeeceEEEcce----EEEEEEeCC-CCceeEEEEEecchhhhhhhcccCCeEEEeeeEEEEe
Confidence 456899999999998665421 345566776 7888887777777778999999999999999988643
No 171
>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=47.94 E-value=64 Score=27.29 Aligned_cols=69 Identities=10% Similarity=0.123 Sum_probs=37.3
Q ss_pred cEEEEEEEecCceeEEecCCceeeEEEEEEEe---------CCCCEEEEEEccchhhhhhhhHHHhhccCCCcEEEEEee
Q 006263 344 DVIGIVISVNPSVPILRKNGMETQRRILNLKD---------TSGRSVELTLWGDFCNKEGQKLQEMVDVGFFPVLSVKSG 414 (653)
Q Consensus 344 DVIGvV~~v~~~~~i~~k~g~~~~kr~i~l~D---------~s~~~i~vtLWg~~A~~~~~~l~~~~~~~~~~Vvaik~~ 414 (653)
-++|.|...-.+. .+++|+...+-.+...+ .....+.|++||+.|..+.+. + ..|..|.+.|-
T Consensus 2 ~l~G~l~~~p~~~--~~~~g~~~~~~~v~~~~~~~~~~~~~~~~~~~~v~~~g~~a~~~~~~----~--~kG~~V~v~G~ 73 (100)
T cd04496 2 ILIGRLGKDPELR--YTPSGTPVARFSLAVNRRRKDRDEEEEETDWIRVVAFGKLAENAAKY----L--KKGDLVYVEGR 73 (100)
T ss_pred EEEEEecCCCEEE--ECCCCCEEEEEEEEEcCceecccccccccEEEEEEEEhHHHHHHHHH----h--CCCCEEEEEEE
Confidence 3566665543332 22345544333333322 234579999999998775322 2 35666666544
Q ss_pred -EeecCC
Q 006263 415 -KVNDFS 420 (653)
Q Consensus 415 -rV~~f~ 420 (653)
+.+.|.
T Consensus 74 l~~~~~~ 80 (100)
T cd04496 74 LRTRSWE 80 (100)
T ss_pred EEeceeE
Confidence 555564
No 172
>PRK05853 hypothetical protein; Validated
Probab=47.62 E-value=44 Score=31.98 Aligned_cols=33 Identities=15% Similarity=0.237 Sum_probs=29.0
Q ss_pred eCCCCeEEEEEchhHHHHHHhhcccCcEEEEec
Q 006263 252 DSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISK 284 (653)
Q Consensus 252 D~~g~~I~at~f~~~~~kf~~~l~eG~vy~is~ 284 (653)
|.+..-|.+++|+..++.+...|..|+-+.+.+
T Consensus 39 d~~T~wi~V~~wg~lAe~v~~~L~KG~~V~V~G 71 (161)
T PRK05853 39 PGNSLFITVNCWGRLVTGVGAALGKGAPVIVVG 71 (161)
T ss_pred ccCccEEEEEEEhHHHHHHHHHcCCCCEEEEEE
Confidence 445677999999999999999999999998876
No 173
>PRK06863 single-stranded DNA-binding protein; Provisional
Probab=46.90 E-value=1.2e+02 Score=29.30 Aligned_cols=72 Identities=14% Similarity=0.100 Sum_probs=39.7
Q ss_pred cccEEEEEEEecCceeEEecCCceeeEEEEEEE----eC-CC------CEEEEEEccchhhhhhhhHHHhhccCCCcEEE
Q 006263 342 IVDVIGIVISVNPSVPILRKNGMETQRRILNLK----DT-SG------RSVELTLWGDFCNKEGQKLQEMVDVGFFPVLS 410 (653)
Q Consensus 342 ~vDVIGvV~~v~~~~~i~~k~g~~~~kr~i~l~----D~-s~------~~i~vtLWg~~A~~~~~~l~~~~~~~~~~Vva 410 (653)
.|-++|.|.. +.+.-.+.+|+.+.+-.|-.- |. +| .-+.|++||..|+...++| ..|.-|.
T Consensus 6 ~V~LiGrLg~--DPElR~t~nG~~va~fsVAvn~~~~d~~~Ge~~e~t~w~~Vv~fgk~AE~v~~~L------kKGs~V~ 77 (168)
T PRK06863 6 KVIIVGHLGN--DPEIRTMPNGEAVANISVATSESWTDKNTGERREVTEWHRIVFYRRQAEVAGEYL------RKGSQVY 77 (168)
T ss_pred EEEEEEEcCC--CCEEEEcCCCCEEEEEEEEecCcccccCCCcccccceEEEEEEEhHHHHHHHHHC------CCCCEEE
Confidence 4667777776 222222345665433333321 21 12 3689999999987753332 2466666
Q ss_pred EEe-eEeecCCC
Q 006263 411 VKS-GKVNDFSG 421 (653)
Q Consensus 411 ik~-~rV~~f~G 421 (653)
+.| .+...|.+
T Consensus 78 VeGrL~~r~w~D 89 (168)
T PRK06863 78 VEGRLKTRKWQD 89 (168)
T ss_pred EEEEEEeCCccC
Confidence 654 46666753
No 174
>PRK06920 dnaE DNA polymerase III DnaE; Reviewed
Probab=46.88 E-value=57 Score=40.78 Aligned_cols=78 Identities=13% Similarity=0.175 Sum_probs=52.5
Q ss_pred ceecchhhhhhcccCccccEEEEEEEecCceeEEecCCceeeEEEEEEEeCCCCEEEEEEccchhhhhhhhHHHhhccCC
Q 006263 326 FSFRHISEIESAENNSIVDVIGIVISVNPSVPILRKNGMETQRRILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVDVGF 405 (653)
Q Consensus 326 f~f~~i~~i~~~~~~~~vDVIGvV~~v~~~~~i~~k~g~~~~kr~i~l~D~s~~~i~vtLWg~~A~~~~~~l~~~~~~~~ 405 (653)
+..+++.+|.. ..+..|-|.|+|+.+... ++|.|+. .--++|.|.+| .+++++|.+....+...| ..
T Consensus 930 ~~~~~~~~l~~-~~~~~v~v~g~i~~~~~~---~tk~g~~--maf~~leD~tg-~~e~~vFp~~y~~~~~~l------~~ 996 (1107)
T PRK06920 930 LEIPSLAQAMR-HKKKVQRAIVYITSVKVI---RTKKGQK--MAFITFCDQND-EMEAVVFPETYIHFSDKL------QE 996 (1107)
T ss_pred hCCcCHHHHhh-cCCCEEEEEEEEEEeEee---cCCCCCe--EEEEEEeeCCC-cEEEEECHHHHHHHHHHh------cc
Confidence 34456777743 234578899999987754 4566763 45689999999 799999998766543322 24
Q ss_pred CcEEEEEeeEee
Q 006263 406 FPVLSVKSGKVN 417 (653)
Q Consensus 406 ~~Vvaik~~rV~ 417 (653)
+.++.++| +|.
T Consensus 997 ~~~~~v~G-~v~ 1007 (1107)
T PRK06920 997 GAIVLVDG-TIE 1007 (1107)
T ss_pred CCEEEEEE-EEE
Confidence 56776665 443
No 175
>COG1200 RecG RecG-like helicase [DNA replication, recombination, and repair / Transcription]
Probab=46.46 E-value=63 Score=37.69 Aligned_cols=72 Identities=19% Similarity=0.282 Sum_probs=54.9
Q ss_pred CCcceeccccCCCCCceEEEEEEEeeccccccccCCCCceeEEEEEEeCCCCeEEEEEchhHHHHHHhhcccCcEEEEec
Q 006263 205 PARIIPIAALNPYQGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISK 284 (653)
Q Consensus 205 ~~~~~pI~~L~p~~~~w~I~~RV~~k~~ir~~~~~~g~gk~f~~~L~D~~g~~I~at~f~~~~~kf~~~l~eG~vy~is~ 284 (653)
.+...+|.++.++ ..-+|.++|....... + +..+.+.+.+.| .++.|.+++|+..+ -....|.+|..+.+++
T Consensus 48 ~~~~~~i~~~~~g-~~vti~g~V~~~~~~~-~----~~~~~l~v~~~d-~~~~l~l~fFn~~~-~l~~~~~~G~~v~v~G 119 (677)
T COG1200 48 RTLLPGIAEARPG-EIVTIEGTVLSHEKFP-F----GKRKLLKVTLSD-GTGVLTLVFFNFPA-YLKKKLKVGERVIVYG 119 (677)
T ss_pred ccccCChhhcCCC-ceEEEEEEEEeeeccC-C----CCCceEEEEEec-CcEEEEEEEECccH-HHHhhCCCCCEEEEEE
Confidence 3445677777754 3678999998765432 1 224789999999 89999999999876 5678899999998875
No 176
>KOG1885 consensus Lysyl-tRNA synthetase (class II) [Translation, ribosomal structure and biogenesis]
Probab=45.78 E-value=94 Score=34.61 Aligned_cols=92 Identities=17% Similarity=0.316 Sum_probs=59.3
Q ss_pred ceEEEEEEEeeccccccccCCCCceeEEEEEEeCCCCeEEEEEchh------HHHHHHhhcccCcEEEEeceEEecCCCc
Q 006263 220 RWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNA------VVDRFYEIIEVGRVYLISKGSLKPAQKN 293 (653)
Q Consensus 220 ~w~I~~RV~~k~~ir~~~~~~g~gk~f~~~L~D~~g~~I~at~f~~------~~~kf~~~l~eG~vy~is~~~V~~a~~~ 293 (653)
..+|.+||..+ |.. .+|++-++|.+ +|.++++.+=.. ......+.|+-|+++-+++.-=+..
T Consensus 106 ~~svaGRI~s~---R~s-----GsKL~Fydl~~-~g~klQvm~~~~~~~~~~~F~~~~~~lkrGDiig~~G~pgrt~--- 173 (560)
T KOG1885|consen 106 IVSVAGRIHSK---RES-----GSKLVFYDLHG-DGVKLQVMANAKKITSEEDFEQLHKFLKRGDIIGVSGYPGRTK--- 173 (560)
T ss_pred eeeeeeeEeee---ecc-----CCceEEEEEec-CCeEEEEEEehhhcCCHHHHHHHHhhhhccCEEeeecCCCcCC---
Confidence 47899999875 332 13888899999 799999988542 3556778899999998887521111
Q ss_pred ccCCCCceEEEeccccEEEeccCCCCCCCcccceecc
Q 006263 294 FNHLKNEWEIFLEATSTVDLCTEEDDSIPKQQFSFRH 330 (653)
Q Consensus 294 f~~~~~~yei~f~~~T~I~~~~d~~~~iP~~~f~f~~ 330 (653)
+....|.-++-...++| ...+|..+|.+..
T Consensus 174 ----~gELSi~~~~~~lLspc---Lh~lP~~~~gLkD 203 (560)
T KOG1885|consen 174 ----SGELSIIPNEIILLSPC---LHMLPHEHFGLKD 203 (560)
T ss_pred ----CceEEEeecchheecch---hccCChhhcCCCc
Confidence 12333444443444444 2457866666655
No 177
>PRK06958 single-stranded DNA-binding protein; Provisional
Probab=45.49 E-value=1.3e+02 Score=29.42 Aligned_cols=71 Identities=13% Similarity=0.094 Sum_probs=38.7
Q ss_pred cccEEEEEEEecCceeEEecCCceeeEEEEEE----EeC-C------CCEEEEEEccchhhhhhhhHHHhhccCCCcEEE
Q 006263 342 IVDVIGIVISVNPSVPILRKNGMETQRRILNL----KDT-S------GRSVELTLWGDFCNKEGQKLQEMVDVGFFPVLS 410 (653)
Q Consensus 342 ~vDVIGvV~~v~~~~~i~~k~g~~~~kr~i~l----~D~-s------~~~i~vtLWg~~A~~~~~~l~~~~~~~~~~Vva 410 (653)
.|-+||.|..--++. .+.+|..+.+-.|-. .|. + -.-+.|++||+.|+.+.+. + ..+..|.
T Consensus 6 ~V~LiGrLg~DPElr--~t~nG~~va~fsVAv~~~~kdk~sGe~~e~T~w~~V~~fGk~AE~v~~~----L--kKGs~V~ 77 (182)
T PRK06958 6 KVILVGNLGADPEVR--YLPSGDAVANIRLATTDRYKDKASGEFKEATEWHRVAFFGRLAEIVGEY----L--KKGSSVY 77 (182)
T ss_pred EEEEEEEecCCCeEE--EcCCCCEEEEEEEEeccccccccCCcccccceEEEEEEehHHHHHHHHH----h--CCCCEEE
Confidence 456777777632222 234565443333322 121 1 1368999999998764322 2 2466666
Q ss_pred EE-eeEeecCC
Q 006263 411 VK-SGKVNDFS 420 (653)
Q Consensus 411 ik-~~rV~~f~ 420 (653)
+. ..+...|.
T Consensus 78 VeGrL~~~~ye 88 (182)
T PRK06958 78 IEGRIRTRKWQ 88 (182)
T ss_pred EEEEEEeCceE
Confidence 65 44556675
No 178
>PRK05672 dnaE2 error-prone DNA polymerase; Validated
Probab=44.76 E-value=59 Score=40.48 Aligned_cols=73 Identities=21% Similarity=0.320 Sum_probs=50.0
Q ss_pred eecchhhhhhcccCccccEEEEEEEecCceeEEecCCceeeEEEEEEEeCCCCEEEEEEccchhhhhhhhHHHhhccCCC
Q 006263 327 SFRHISEIESAENNSIVDVIGIVISVNPSVPILRKNGMETQRRILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVDVGFF 406 (653)
Q Consensus 327 ~f~~i~~i~~~~~~~~vDVIGvV~~v~~~~~i~~k~g~~~~kr~i~l~D~s~~~i~vtLWg~~A~~~~~~l~~~~~~~~~ 406 (653)
..+++++|.+...+..|=|.|+|+.+... .||.| .--++|.|.+| .+++++|.+....+...| ..+
T Consensus 940 ~~~~~~~l~~~~~~~~v~v~g~i~~~~~~---~TkkG----maf~~leD~~g-~~e~~ifp~~~~~~~~~l------~~~ 1005 (1046)
T PRK05672 940 GVVSAAELLDVEDGRRVRVAGVVTHRQRP---GTASG----VTFLTLEDETG-MVNVVVWPGLWERQRREA------LGA 1005 (1046)
T ss_pred cCcCHHHHhhccCCCEEEEEEEEEEEEEe---cCCCc----eEEEEEecCCC-CEEEEECHHHHHHHHHHh------ccC
Confidence 34566677654445567788888886653 35656 56789999999 799999999866643222 246
Q ss_pred cEEEEEe
Q 006263 407 PVLSVKS 413 (653)
Q Consensus 407 ~Vvaik~ 413 (653)
.++.++|
T Consensus 1006 ~~~~v~g 1012 (1046)
T PRK05672 1006 RLLLVRG 1012 (1046)
T ss_pred CEEEEEE
Confidence 7777765
No 179
>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=44.34 E-value=2e+02 Score=24.44 Aligned_cols=70 Identities=17% Similarity=0.235 Sum_probs=36.1
Q ss_pred ccEEEEEEEecCceeEEecCCceeeEEEEEEEe----CC------CCEEEEEEccchhhhhhhhHHHhhccCCCcEEEEE
Q 006263 343 VDVIGIVISVNPSVPILRKNGMETQRRILNLKD----TS------GRSVELTLWGDFCNKEGQKLQEMVDVGFFPVLSVK 412 (653)
Q Consensus 343 vDVIGvV~~v~~~~~i~~k~g~~~~kr~i~l~D----~s------~~~i~vtLWg~~A~~~~~~l~~~~~~~~~~Vvaik 412 (653)
|-++|.|..- ++.-.+++|+....-.|...+ .. ..-+.|++||+.|..+. +.+ ..|..|.+.
T Consensus 4 v~l~G~l~~~--p~~~~~~~g~~~~~f~la~~~~~~~~~~~~~~~~~~~~v~~~g~~A~~~~----~~l--~kG~~V~V~ 75 (104)
T PF00436_consen 4 VTLIGRLGKD--PELRYTKNGTPVARFSLAVNRRFKDDGGEGDEKTDWINVVAWGKLAENVA----EYL--KKGDRVYVE 75 (104)
T ss_dssp EEEEEEESSS--EEEEEETTSEEEEEEEEEEEEEEEETTSCEEEEEEEEEEEEEHHHHHHHH----HH----TT-EEEEE
T ss_pred EEEEEEECCC--cEEEECCCCCEEEEEEEEEecEEeeeeccCccceEEEEEEeeeecccccc----eEE--cCCCEEEEE
Confidence 3455655432 222223456655444444433 11 13789999999988753 323 246777766
Q ss_pred ee-EeecCC
Q 006263 413 SG-KVNDFS 420 (653)
Q Consensus 413 ~~-rV~~f~ 420 (653)
|- +...|.
T Consensus 76 G~l~~~~~~ 84 (104)
T PF00436_consen 76 GRLRTRTYE 84 (104)
T ss_dssp EEEEEEEEE
T ss_pred EEEEeeEEE
Confidence 43 445554
No 180
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=43.56 E-value=11 Score=39.30 Aligned_cols=13 Identities=15% Similarity=0.851 Sum_probs=10.5
Q ss_pred eeecccCccccCC
Q 006263 532 RWQCDRCNQEIDE 544 (653)
Q Consensus 532 ~~~C~kC~~~~~~ 544 (653)
.||||-|+|.+.+
T Consensus 398 PYrCevC~KRYKN 410 (423)
T COG5189 398 PYRCEVCDKRYKN 410 (423)
T ss_pred ceeccccchhhcc
Confidence 6999999987644
No 181
>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=43.54 E-value=84 Score=26.09 Aligned_cols=61 Identities=8% Similarity=0.063 Sum_probs=39.6
Q ss_pred eEEEEEecccceeeeeecccchh-hc-ccCCcccCcEEEEeeeEeeee-----cCeEEEEEEeeeEee
Q 006263 38 RYRFLISDSVSTQHAMLATQLND-RV-KTGQVKKGSVVQLIDYICSTV-----QNRKIIVVLNMETII 98 (653)
Q Consensus 38 ryr~~lSDG~~~~~~ml~t~ln~-~v-~~~~l~~~sIIkl~~y~~~~~-----~~k~~iii~~~evl~ 98 (653)
--=+.|.||...+++++...... +. .-..|+.+++|.+.-.....- .+..-+.+.+++++.
T Consensus 17 ~~Fi~Lrd~~~~iQ~v~~~~~~~~~~~~~~~l~~~s~V~v~G~~~~~~~~~~~~~~~El~~~~i~il~ 84 (85)
T cd04100 17 LIFIDLRDGSGIVQVVVNKEELGEFFEEAEKLRTESVVGVTGTVVKRPEGNLATGEIELQAEELEVLS 84 (85)
T ss_pred EEEEEEEeCCeeEEEEEECCcChHHHHHHhCCCCCCEEEEEeEEEECCCCCCCCCCEEEEEeEEEEEC
Confidence 45577899999999988755332 11 123689999999988776532 223345556665553
No 182
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=43.32 E-value=10 Score=29.63 Aligned_cols=27 Identities=26% Similarity=0.787 Sum_probs=16.5
Q ss_pred ceEEecCCCCcCcccccceee-------ecCceeecccCc
Q 006263 507 SFCYTACPLMIGDRQCNKKVT-------QSGNRWQCDRCN 539 (653)
Q Consensus 507 ~~~Y~aC~~~~~~~~C~KKv~-------~~~~~~~C~kC~ 539 (653)
...-..|| +|++-++ ..+..|+|++|+
T Consensus 24 ~~v~F~CP------nCGe~~I~Rc~~CRk~g~~Y~Cp~CG 57 (61)
T COG2888 24 TAVKFPCP------NCGEVEIYRCAKCRKLGNPYRCPKCG 57 (61)
T ss_pred ceeEeeCC------CCCceeeehhhhHHHcCCceECCCcC
Confidence 44555788 7875443 223377777776
No 183
>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=43.21 E-value=30 Score=32.18 Aligned_cols=27 Identities=26% Similarity=0.439 Sum_probs=24.0
Q ss_pred eEEEEEEeCCCCeEEEEEchhHHHHHHh
Q 006263 245 VFSFDLLDSDGGEIRVTCFNAVVDRFYE 272 (653)
Q Consensus 245 ~f~~~L~D~~g~~I~at~f~~~~~kf~~ 272 (653)
.+++.+.| .+|.+.+++|++.++++..
T Consensus 55 ~l~~~i~D-~tg~~~~~~F~~~a~~l~G 81 (146)
T PF08646_consen 55 RLSLKISD-GTGSIWVTLFDEEAEQLLG 81 (146)
T ss_dssp EEEEEEEE-TTEEEEEEEEHHHHHHHHC
T ss_pred EEEEEEEe-CCCeEEEEEEhHHHHHHhC
Confidence 58899999 7899999999999998874
No 184
>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=42.73 E-value=79 Score=32.48 Aligned_cols=58 Identities=9% Similarity=0.090 Sum_probs=42.5
Q ss_pred CCeEEEEEchhHHHHHHhhcccCcEEEEeceEEecCCCcccCCCCceEEEeccccEEEecc
Q 006263 255 GGEIRVTCFNAVVDRFYEIIEVGRVYLISKGSLKPAQKNFNHLKNEWEIFLEATSTVDLCT 315 (653)
Q Consensus 255 g~~I~at~f~~~~~kf~~~l~eG~vy~is~~~V~~a~~~f~~~~~~yei~f~~~T~I~~~~ 315 (653)
......|+|+.. +.+.+.|+||+.|.|.+-......++ ....+..|+-.+.|.-++++
T Consensus 179 ~~~~~LTIWrPt-edl~s~L~EG~ry~i~~L~~s~~k~~--~~~~~vqLtatk~Tr~~~l~ 236 (251)
T cd04494 179 EKSGLLSIWRPT-EDLRSLLTEGKRYRIYGLATSNSKKR--SGNEEVQLTATKKTRYQPLP 236 (251)
T ss_pred CceEEEEEeCCC-HHHHhhhcCCcEEEEEeccccCCCCC--CCcceEEEEecCcccceECC
Confidence 344557788765 67888999999999999774443333 34567888888889888874
No 185
>TIGR00686 phnA alkylphosphonate utilization operon protein PhnA. The protein family includes an uncharacterized member designated phnA in Escherichia coli, part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage. This protein is not related to the characterized phosphonoacetate hydrolase designated PhnA by Kulakova, et al. (2001, 1997).
Probab=42.66 E-value=16 Score=32.28 Aligned_cols=29 Identities=31% Similarity=0.707 Sum_probs=23.5
Q ss_pred EecCCCCcCcccccceeeecCc-eeecccCccccCC
Q 006263 510 YTACPLMIGDRQCNKKVTQSGN-RWQCDRCNQEIDE 544 (653)
Q Consensus 510 Y~aC~~~~~~~~C~KKv~~~~~-~~~C~kC~~~~~~ 544 (653)
.|+|| .|+.--+.+.+ .|-|+.|+..+..
T Consensus 2 lp~CP------~C~seytY~dg~~~iCpeC~~EW~~ 31 (109)
T TIGR00686 2 LPPCP------KCNSEYTYHDGTQLICPSCLYEWNE 31 (109)
T ss_pred CCcCC------cCCCcceEecCCeeECccccccccc
Confidence 48999 99988766554 9999999988743
No 186
>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=42.13 E-value=29 Score=36.08 Aligned_cols=47 Identities=28% Similarity=0.282 Sum_probs=38.2
Q ss_pred cccceeeecCceeecccCccccCCceEEEEEEEEEEeCCCeEEEEEechhhh
Q 006263 521 QCNKKVTQSGNRWQCDRCNQEIDECDYRYLLQAQIQDQTGLTWVTAFQESGE 572 (653)
Q Consensus 521 ~C~KKv~~~~~~~~C~kC~~~~~~~~~rY~l~~~i~D~Tg~~~~~~F~~~ae 572 (653)
.||||++ .+|..=.-.-+-|..||-=++++.-.-|..-+++|+...-
T Consensus 66 ~cNkK~t-----l~C~EKeLvGdvP~aRYGHt~~vV~SrGKta~VlFGGRSY 112 (337)
T PF03089_consen 66 GCNKKVT-----LCCQEKELVGDVPEARYGHTINVVHSRGKTACVLFGGRSY 112 (337)
T ss_pred CCCceeE-----EEEecceecCCCCcccccceEEEEEECCcEEEEEECCccc
Confidence 8999995 5675544444678999999999999999999999986443
No 187
>PRK14810 formamidopyrimidine-DNA glycosylase; Provisional
Probab=41.59 E-value=15 Score=38.27 Aligned_cols=24 Identities=17% Similarity=0.675 Sum_probs=18.5
Q ss_pred ecCCCCcCcccccceeeec--Cc--eeecccCcc
Q 006263 511 TACPLMIGDRQCNKKVTQS--GN--RWQCDRCNQ 540 (653)
Q Consensus 511 ~aC~~~~~~~~C~KKv~~~--~~--~~~C~kC~~ 540 (653)
..|| .|+.++... ++ .|+|+.|++
T Consensus 245 ~pCp------rCG~~I~~~~~~gR~t~~CP~CQ~ 272 (272)
T PRK14810 245 EPCL------NCKTPIRRVVVAGRSSHYCPHCQK 272 (272)
T ss_pred CcCC------CCCCeeEEEEECCCccEECcCCcC
Confidence 5899 899887532 22 999999984
No 188
>COG1190 LysU Lysyl-tRNA synthetase (class II) [Translation, ribosomal structure and biogenesis]
Probab=41.51 E-value=81 Score=35.48 Aligned_cols=78 Identities=18% Similarity=0.293 Sum_probs=55.1
Q ss_pred ceEEEEEEEeeccccccccCCCCceeEEEEEEeCCCCeEEEEEchh-----HHHHHHhhcccCcEEEEeceEEecCCCcc
Q 006263 220 RWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNA-----VVDRFYEIIEVGRVYLISKGSLKPAQKNF 294 (653)
Q Consensus 220 ~w~I~~RV~~k~~ir~~~~~~g~gk~f~~~L~D~~g~~I~at~f~~-----~~~kf~~~l~eG~vy~is~~~V~~a~~~f 294 (653)
.-+|.+||+.+ |. -||+.-++|.| .+|+|++-+-.+ ..+.+...+..||++.+.+.-.+..
T Consensus 63 ~v~vAGRi~~~---R~------~GK~~F~~i~d-~~gkiQ~yi~k~~~~~~~~~~~~~~~dlGDiigv~G~~~~T~---- 128 (502)
T COG1190 63 EVSVAGRIMTI---RN------MGKASFADLQD-GSGKIQLYVNKDEVGEEVFEALFKKLDLGDIIGVEGPLFKTK---- 128 (502)
T ss_pred eeEEecceeee---cc------cCceeEEEEec-CCceEEEEEeccccchhhHHHHHhccccCCEEeeeeeeeecC----
Confidence 37889999874 33 36777788999 788999998754 3445667788999999988655443
Q ss_pred cCCCCceEEEeccccEEEec
Q 006263 295 NHLKNEWEIFLEATSTVDLC 314 (653)
Q Consensus 295 ~~~~~~yei~f~~~T~I~~~ 314 (653)
.....+.....+.+..|
T Consensus 129 ---~GelSv~v~~~~lLsKs 145 (502)
T COG1190 129 ---TGELSVSVEELRLLSKS 145 (502)
T ss_pred ---CCceEEEEEEEeeeccc
Confidence 33456666665555555
No 189
>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=41.47 E-value=92 Score=25.65 Aligned_cols=60 Identities=8% Similarity=0.100 Sum_probs=37.4
Q ss_pred eEEEEEecccce--eeeeecccchhhcccCCcccCcEEEEeeeEeeeec--CeEEEEEEeeeEe
Q 006263 38 RYRFLISDSVST--QHAMLATQLNDRVKTGQVKKGSVVQLIDYICSTVQ--NRKIIVVLNMETI 97 (653)
Q Consensus 38 ryr~~lSDG~~~--~~~ml~t~ln~~v~~~~l~~~sIIkl~~y~~~~~~--~k~~iii~~~evl 97 (653)
-.=+.|.||... +++++.......-.-..|..+++|.+.-.....-. +..-+.+.+++++
T Consensus 17 ~~Fi~LrD~s~~~~lQvv~~~~~~~~~~~~~l~~gs~V~v~G~v~~~~~~~~~~El~~~~i~il 80 (82)
T cd04318 17 ISFIELNDGSCLKNLQVVVDKELTNFKEILKLSTGSSIRVEGVLVKSPGAKQPFELQAEKIEVL 80 (82)
T ss_pred EEEEEEECCCCccCEEEEEeCcccCHHHHhcCCCceEEEEEEEEEeCCCCCCCEEEEEEEEEEe
Confidence 345788999885 88887644221111135889999999887655432 3345555666554
No 190
>PRK08182 single-stranded DNA-binding protein; Provisional
Probab=41.26 E-value=1.5e+02 Score=27.90 Aligned_cols=35 Identities=9% Similarity=0.036 Sum_probs=23.4
Q ss_pred EEEEEEccchhhhhhhhHHHhhccCCCcEEEEE-eeEeecCC
Q 006263 380 SVELTLWGDFCNKEGQKLQEMVDVGFFPVLSVK-SGKVNDFS 420 (653)
Q Consensus 380 ~i~vtLWg~~A~~~~~~l~~~~~~~~~~Vvaik-~~rV~~f~ 420 (653)
-+.|++||..|+...++| ..|.-|++. ..+...|.
T Consensus 55 w~~V~~wg~~Ae~v~~~l------~KG~~V~V~GrL~~~~w~ 90 (148)
T PRK08182 55 WAPVELWHRDAEHWARLY------QKGMRVLVEGRMERDEWT 90 (148)
T ss_pred EEEEEEEhHHHHHHHHhc------CCCCEEEEEEEEEecccC
Confidence 589999999987753332 246666665 45666674
No 191
>PRK13945 formamidopyrimidine-DNA glycosylase; Provisional
Probab=41.04 E-value=17 Score=38.11 Aligned_cols=24 Identities=17% Similarity=0.675 Sum_probs=18.3
Q ss_pred ecCCCCcCcccccceeeec--Cc--eeecccCcc
Q 006263 511 TACPLMIGDRQCNKKVTQS--GN--RWQCDRCNQ 540 (653)
Q Consensus 511 ~aC~~~~~~~~C~KKv~~~--~~--~~~C~kC~~ 540 (653)
..|| .|+.++... ++ .|+|+.|++
T Consensus 255 ~pC~------~Cg~~I~~~~~~gR~t~~CP~CQ~ 282 (282)
T PRK13945 255 KPCR------KCGTPIERIKLAGRSTHWCPNCQK 282 (282)
T ss_pred CCCC------cCCCeeEEEEECCCccEECCCCcC
Confidence 5899 899887532 23 999999984
No 192
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=40.65 E-value=18 Score=27.92 Aligned_cols=31 Identities=23% Similarity=0.565 Sum_probs=24.2
Q ss_pred ecCCCCcCcccccceeeecCceeecccCccccCCceE
Q 006263 511 TACPLMIGDRQCNKKVTQSGNRWQCDRCNQEIDECDY 547 (653)
Q Consensus 511 ~aC~~~~~~~~C~KKv~~~~~~~~C~kC~~~~~~~~~ 547 (653)
..|+ .|++++.++++.-.|+.|+..+=..-|
T Consensus 6 ~~C~------~Cg~~~~~~dDiVvCp~CgapyHR~C~ 36 (54)
T PF14446_consen 6 CKCP------VCGKKFKDGDDIVVCPECGAPYHRDCW 36 (54)
T ss_pred ccCh------hhCCcccCCCCEEECCCCCCcccHHHH
Confidence 3588 999999888889999999976533333
No 193
>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines. Several members are annotated as putative helicases.
Probab=40.42 E-value=16 Score=23.74 Aligned_cols=23 Identities=30% Similarity=0.871 Sum_probs=18.3
Q ss_pred cCCCCcCcccccceeeecCceeecccCcccc
Q 006263 512 ACPLMIGDRQCNKKVTQSGNRWQCDRCNQEI 542 (653)
Q Consensus 512 aC~~~~~~~~C~KKv~~~~~~~~C~kC~~~~ 542 (653)
-|| .|.+.|... .-.|+.|+-.+
T Consensus 2 ~CP------~C~~~V~~~--~~~Cp~CG~~F 24 (26)
T PF10571_consen 2 TCP------ECGAEVPES--AKFCPHCGYDF 24 (26)
T ss_pred cCC------CCcCCchhh--cCcCCCCCCCC
Confidence 599 999998654 67899998654
No 194
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=40.35 E-value=12 Score=36.32 Aligned_cols=26 Identities=23% Similarity=0.754 Sum_probs=20.3
Q ss_pred ecCCCCcCcccccceeeecCc---eeecccCcccc
Q 006263 511 TACPLMIGDRQCNKKVTQSGN---RWQCDRCNQEI 542 (653)
Q Consensus 511 ~aC~~~~~~~~C~KKv~~~~~---~~~C~kC~~~~ 542 (653)
.-|| .|+++.+...- .+.|+.||...
T Consensus 118 Y~Cp------~C~~rytf~eA~~~~F~Cp~Cg~~L 146 (178)
T PRK06266 118 FFCP------NCHIRFTFDEAMEYGFRCPQCGEML 146 (178)
T ss_pred EECC------CCCcEEeHHHHhhcCCcCCCCCCCC
Confidence 3689 89999875432 79999999865
No 195
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=40.32 E-value=23 Score=26.14 Aligned_cols=24 Identities=21% Similarity=0.642 Sum_probs=19.1
Q ss_pred cCCCCcCcccccceeeecCc--eeecccCccc
Q 006263 512 ACPLMIGDRQCNKKVTQSGN--RWQCDRCNQE 541 (653)
Q Consensus 512 aC~~~~~~~~C~KKv~~~~~--~~~C~kC~~~ 541 (653)
-|+ .|+..+..+.. ..+|+.|+..
T Consensus 5 ~C~------~CG~~~~~~~~~~~~~Cp~CG~~ 30 (46)
T PRK00398 5 KCA------RCGREVELDEYGTGVRCPYCGYR 30 (46)
T ss_pred ECC------CCCCEEEECCCCCceECCCCCCe
Confidence 588 89998865544 7999999964
No 196
>PF03119 DNA_ligase_ZBD: NAD-dependent DNA ligase C4 zinc finger domain; InterPro: IPR004149 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the zinc finger domain found in NAD-dependent DNA ligases. DNA ligases catalyse the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilizing either ATP or NAD(+) as a cofactor []. This domain is a small zinc binding motif that is presumably DNA binding. It is found only in NAD-dependent DNA ligases. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003911 DNA ligase (NAD+) activity, 0006260 DNA replication, 0006281 DNA repair; PDB: 1DGS_A 1V9P_B 2OWO_A.
Probab=40.22 E-value=18 Score=23.94 Aligned_cols=19 Identities=26% Similarity=0.814 Sum_probs=10.8
Q ss_pred CCCCcCcccccceeeecCc--eeeccc
Q 006263 513 CPLMIGDRQCNKKVTQSGN--RWQCDR 537 (653)
Q Consensus 513 C~~~~~~~~C~KKv~~~~~--~~~C~k 537 (653)
|| .|+.++....+ .|+|..
T Consensus 2 CP------~C~s~l~~~~~ev~~~C~N 22 (28)
T PF03119_consen 2 CP------VCGSKLVREEGEVDIRCPN 22 (28)
T ss_dssp -T------TT--BEEE-CCTTCEEE--
T ss_pred cC------CCCCEeEcCCCCEeEECCC
Confidence 89 99999986554 899974
No 197
>PRK07275 single-stranded DNA-binding protein; Provisional
Probab=40.05 E-value=1.3e+02 Score=28.72 Aligned_cols=35 Identities=6% Similarity=0.184 Sum_probs=23.8
Q ss_pred EEEEEEccchhhhhhhhHHHhhccCCCcEEEEEee-EeecCC
Q 006263 380 SVELTLWGDFCNKEGQKLQEMVDVGFFPVLSVKSG-KVNDFS 420 (653)
Q Consensus 380 ~i~vtLWg~~A~~~~~~l~~~~~~~~~~Vvaik~~-rV~~f~ 420 (653)
-|.|++||+.|+.+.++ + ..|.-|++.|- +.+.|.
T Consensus 48 fi~vv~wgk~Ae~~~~~----l--~KG~~V~VeGrl~~r~y~ 83 (162)
T PRK07275 48 FINCVIWRQQAENLANW----A--KKGALIGVTGRIQTRNYE 83 (162)
T ss_pred EEEEEEEcHHHHHHHHH----c--CCCCEEEEEEEEEeceEE
Confidence 68999999999875332 2 35777777644 555663
No 198
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=39.65 E-value=18 Score=27.48 Aligned_cols=26 Identities=27% Similarity=0.919 Sum_probs=20.2
Q ss_pred EecCCCCcCcccccc-eeeecCceeecccCccc
Q 006263 510 YTACPLMIGDRQCNK-KVTQSGNRWQCDRCNQE 541 (653)
Q Consensus 510 Y~aC~~~~~~~~C~K-Kv~~~~~~~~C~kC~~~ 541 (653)
-.-|| .|+. -+....+.+.|.+|+-+
T Consensus 20 ~~fCP------~Cg~~~m~~~~~r~~C~~Cgyt 46 (50)
T PRK00432 20 NKFCP------RCGSGFMAEHLDRWHCGKCGYT 46 (50)
T ss_pred cCcCc------CCCcchheccCCcEECCCcCCE
Confidence 34799 8988 66666669999999865
No 199
>PRK00448 polC DNA polymerase III PolC; Validated
Probab=39.41 E-value=65 Score=41.38 Aligned_cols=74 Identities=16% Similarity=0.253 Sum_probs=57.1
Q ss_pred cceeccccCCCCCceEEEEEEEeeccccccccCCCCceeEEEEEEeCCCCeEEEEEchhH--HHHHHhhcccCcEEEEec
Q 006263 207 RIIPIAALNPYQGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAV--VDRFYEIIEVGRVYLISK 284 (653)
Q Consensus 207 ~~~pI~~L~p~~~~w~I~~RV~~k~~ir~~~~~~g~gk~f~~~L~D~~g~~I~at~f~~~--~~kf~~~l~eG~vy~is~ 284 (653)
.+++|+++.....+-+|+|.|...- .|..++ ...++++.+.| ..+.|.+..|... -.+....|+.|+|+.+.+
T Consensus 225 ~~~~~~~i~~~~~~v~i~G~if~~e-~~~~k~---~~~~~~~~~td-~~~s~~~k~f~~~~~~~~~~~~~~~g~~v~~~g 299 (1437)
T PRK00448 225 EITPMKEINEEERRVVVEGYVFKVE-IKELKS---GRHILTFKITD-YTSSIIVKKFSRDKEDLKKFDEIKKGDWVKVRG 299 (1437)
T ss_pred CcccHHHhhccCCeEEEEEEEEEEE-EEeccC---CCEEEEEEEEc-CCCCEEEEEEecCcchhHHHhcCCCCCEEEEEE
Confidence 5789999998888999999997753 455443 23688999999 7899999999722 234557799999998876
Q ss_pred e
Q 006263 285 G 285 (653)
Q Consensus 285 ~ 285 (653)
-
T Consensus 300 ~ 300 (1437)
T PRK00448 300 S 300 (1437)
T ss_pred E
Confidence 3
No 200
>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=39.36 E-value=16 Score=32.50 Aligned_cols=27 Identities=26% Similarity=0.712 Sum_probs=21.4
Q ss_pred ecCCCCcCcccccceeeecCc-eeecccCccccC
Q 006263 511 TACPLMIGDRQCNKKVTQSGN-RWQCDRCNQEID 543 (653)
Q Consensus 511 ~aC~~~~~~~~C~KKv~~~~~-~~~C~kC~~~~~ 543 (653)
.-|| .|++|-..-+- .-.|++|+..++
T Consensus 10 R~Cp------~CG~kFYDLnk~PivCP~CG~~~~ 37 (108)
T PF09538_consen 10 RTCP------SCGAKFYDLNKDPIVCPKCGTEFP 37 (108)
T ss_pred ccCC------CCcchhccCCCCCccCCCCCCccC
Confidence 3699 99999876544 667999999874
No 201
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=39.04 E-value=12 Score=35.53 Aligned_cols=24 Identities=25% Similarity=0.642 Sum_probs=19.5
Q ss_pred cCCCCcCcccccceeeecCc---eeecccCccc
Q 006263 512 ACPLMIGDRQCNKKVTQSGN---RWQCDRCNQE 541 (653)
Q Consensus 512 aC~~~~~~~~C~KKv~~~~~---~~~C~kC~~~ 541 (653)
-|| .|+++.+...- .+.|+.||..
T Consensus 111 ~Cp------~c~~r~tf~eA~~~~F~Cp~Cg~~ 137 (158)
T TIGR00373 111 ICP------NMCVRFTFNEAMELNFTCPRCGAM 137 (158)
T ss_pred ECC------CCCcEeeHHHHHHcCCcCCCCCCE
Confidence 689 89999875432 7999999975
No 202
>TIGR02300 FYDLN_acid conserved hypothetical protein TIGR02300. Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=38.66 E-value=17 Score=33.05 Aligned_cols=27 Identities=11% Similarity=0.186 Sum_probs=21.9
Q ss_pred ecCCCCcCcccccceeeecCc-eeecccCccccC
Q 006263 511 TACPLMIGDRQCNKKVTQSGN-RWQCDRCNQEID 543 (653)
Q Consensus 511 ~aC~~~~~~~~C~KKv~~~~~-~~~C~kC~~~~~ 543 (653)
..|| .|++|...-+. .-.|++|+..++
T Consensus 10 r~Cp------~cg~kFYDLnk~p~vcP~cg~~~~ 37 (129)
T TIGR02300 10 RICP------NTGSKFYDLNRRPAVSPYTGEQFP 37 (129)
T ss_pred ccCC------CcCccccccCCCCccCCCcCCccC
Confidence 4699 99999876544 789999999863
No 203
>PRK07274 single-stranded DNA-binding protein; Provisional
Probab=37.78 E-value=1.8e+02 Score=26.62 Aligned_cols=34 Identities=12% Similarity=0.363 Sum_probs=22.9
Q ss_pred EEEEEEccchhhhhhhhHHHhhccCCCcEEEEEe-eEeecC
Q 006263 380 SVELTLWGDFCNKEGQKLQEMVDVGFFPVLSVKS-GKVNDF 419 (653)
Q Consensus 380 ~i~vtLWg~~A~~~~~~l~~~~~~~~~~Vvaik~-~rV~~f 419 (653)
-+.|++||..|+.+. ..+ ..|.-|++.| .+...|
T Consensus 48 w~~v~~fg~~Ae~v~----~~l--~KG~~V~V~Grl~~~~y 82 (131)
T PRK07274 48 FINVVLWGKLAETLA----SYA--SKGSLISIDGELRTRKY 82 (131)
T ss_pred EEEEEEehHHHHHHH----HHc--CCCCEEEEEEEEEeccC
Confidence 689999999987743 222 3566666654 466667
No 204
>PLN02603 asparaginyl-tRNA synthetase
Probab=37.05 E-value=2.9e+02 Score=32.04 Aligned_cols=91 Identities=14% Similarity=0.168 Sum_probs=59.0
Q ss_pred eeccccCCC--------CCceEEEEEEEeeccccccccCCCCceeEEEEEEeCCC-CeEEEEEchhHHHHHHh----hcc
Q 006263 209 IPIAALNPY--------QGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDG-GEIRVTCFNAVVDRFYE----IIE 275 (653)
Q Consensus 209 ~pI~~L~p~--------~~~w~I~~RV~~k~~ir~~~~~~g~gk~f~~~L~D~~g-~~I~at~f~~~~~kf~~----~l~ 275 (653)
+.|.++.+. ...-+|+|+|.+ +|. .|++.-++|.|..| +.|++++-.+. ..|.. .|.
T Consensus 90 ~~~~~~~~~~~~~~~~~g~~V~v~GwV~~---iR~------~g~~~Fi~l~Dgs~~~~lQ~v~~~~~-~~~~~l~~~~l~ 159 (565)
T PLN02603 90 LRIADVKGGEDEGLARVGKTLNVMGWVRT---LRA------QSSVTFIEVNDGSCLSNMQCVMTPDA-EGYDQVESGLIT 159 (565)
T ss_pred eEhhhcccccccccccCCCEEEEEEEEEE---EEe------CCCeEEEEEECCCCCEeEEEEEECcH-HHHHHHhhcCCC
Confidence 456666532 246788888865 343 25666678889544 37999985442 22322 378
Q ss_pred cCcEEEEeceEEecCCCcccCCCCceEEEeccccEEEec
Q 006263 276 VGRVYLISKGSLKPAQKNFNHLKNEWEIFLEATSTVDLC 314 (653)
Q Consensus 276 eG~vy~is~~~V~~a~~~f~~~~~~yei~f~~~T~I~~~ 314 (653)
.|+++.+.+.-+++.. ....+||..++-..+-.+
T Consensus 160 ~gs~V~V~G~v~~~~~-----~~~~~EL~v~~i~vlg~a 193 (565)
T PLN02603 160 TGASVLVQGTVVSSQG-----GKQKVELKVSKIVVVGKS 193 (565)
T ss_pred CCCEEEEEEEEEecCC-----CCccEEEEEeEEEEEECC
Confidence 9999999996554422 235699998776666666
No 205
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=36.79 E-value=22 Score=31.88 Aligned_cols=28 Identities=32% Similarity=0.862 Sum_probs=21.3
Q ss_pred CCCCcCcccccceeeecCceeecccCccccCCceEEEEE
Q 006263 513 CPLMIGDRQCNKKVTQSGNRWQCDRCNQEIDECDYRYLL 551 (653)
Q Consensus 513 C~~~~~~~~C~KKv~~~~~~~~C~kC~~~~~~~~~rY~l 551 (653)
|| .|+.++.-. .++|+.|+..+ .-+|.+
T Consensus 1 CP------vCg~~l~vt--~l~C~~C~t~i---~G~F~l 28 (113)
T PF09862_consen 1 CP------VCGGELVVT--RLKCPSCGTEI---EGEFEL 28 (113)
T ss_pred CC------CCCCceEEE--EEEcCCCCCEE---Eeeecc
Confidence 99 999998655 79999999764 334444
No 206
>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=36.55 E-value=2.7e+02 Score=25.93 Aligned_cols=87 Identities=14% Similarity=0.197 Sum_probs=51.1
Q ss_pred ceEEEEEEEeeccccccccCCCCceeEEEEEE---------eCCCCeEEEEEchhHHHHHHhhcccCcEEEEeceEEecC
Q 006263 220 RWAIKARVTAKGDLRRYNNARGDGKVFSFDLL---------DSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISKGSLKPA 290 (653)
Q Consensus 220 ~w~I~~RV~~k~~ir~~~~~~g~gk~f~~~L~---------D~~g~~I~at~f~~~~~kf~~~l~eG~vy~is~~~V~~a 290 (653)
...++|||........|. .+.+.+. ..+|+.++...-...+ +-...|++|+.|.|.+-.....
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 678888887765533332 2222221 1134455543333333 3336788999999998743221
Q ss_pred CCcccCCCCceEEEeccccEEEeccC
Q 006263 291 QKNFNHLKNEWEIFLEATSTVDLCTE 316 (653)
Q Consensus 291 ~~~f~~~~~~yei~f~~~T~I~~~~d 316 (653)
.. ......|.+.++++|.|+..+.
T Consensus 96 ~~--~~~~~~~~yvl~~~t~Ve~Wp~ 119 (147)
T cd03574 96 DD--RNGEDRYQYVLDSNTWVEEWPT 119 (147)
T ss_pred cc--cCCCcceEEEeCCCcEEEECCC
Confidence 11 1122359999999999999964
No 207
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=36.44 E-value=54 Score=31.97 Aligned_cols=29 Identities=24% Similarity=0.780 Sum_probs=25.3
Q ss_pred ceEEecCCCCcCcccccceeeecCceeecccCccc
Q 006263 507 SFCYTACPLMIGDRQCNKKVTQSGNRWQCDRCNQE 541 (653)
Q Consensus 507 ~~~Y~aC~~~~~~~~C~KKv~~~~~~~~C~kC~~~ 541 (653)
+-.|--|+ .|+--+...+...+|++|+.+
T Consensus 146 GVI~A~Cs------rC~~~L~~~~~~l~Cp~Cg~t 174 (188)
T COG1096 146 GVIYARCS------RCRAPLVKKGNMLKCPNCGNT 174 (188)
T ss_pred eEEEEEcc------CCCcceEEcCcEEECCCCCCE
Confidence 57899999 999998887679999999975
No 208
>COG2835 Uncharacterized conserved protein [Function unknown]
Probab=35.39 E-value=24 Score=27.75 Aligned_cols=28 Identities=25% Similarity=0.616 Sum_probs=21.6
Q ss_pred EecCCCCcCcccccceeeecC--ceeecccCccccC
Q 006263 510 YTACPLMIGDRQCNKKVTQSG--NRWQCDRCNQEID 543 (653)
Q Consensus 510 Y~aC~~~~~~~~C~KKv~~~~--~~~~C~kC~~~~~ 543 (653)
-.||| .|+-++.... +...|+.|+..++
T Consensus 8 iLaCP------~~kg~L~~~~~~~~L~c~~~~~aYp 37 (60)
T COG2835 8 ILACP------VCKGPLVYDEEKQELICPRCKLAYP 37 (60)
T ss_pred eeecc------CcCCcceEeccCCEEEecccCceee
Confidence 45899 9999876443 3899999998763
No 209
>COG1379 PHP family phosphoesterase with a Zn ribbon [General function prediction only]
Probab=34.73 E-value=11 Score=39.76 Aligned_cols=30 Identities=30% Similarity=0.922 Sum_probs=22.4
Q ss_pred ceEEecCCCCcCcccccceeeecCc---eeecccCcccc
Q 006263 507 SFCYTACPLMIGDRQCNKKVTQSGN---RWQCDRCNQEI 542 (653)
Q Consensus 507 ~~~Y~aC~~~~~~~~C~KKv~~~~~---~~~C~kC~~~~ 542 (653)
..+-.||. .|..+-..+.. .|+|++|+..+
T Consensus 243 KY~~TAC~------rC~t~y~le~A~~~~wrCpkCGg~i 275 (403)
T COG1379 243 KYHLTACS------RCYTRYSLEEAKSLRWRCPKCGGKI 275 (403)
T ss_pred chhHHHHH------HhhhccCcchhhhhcccCcccccch
Confidence 46668999 99987654432 79999999644
No 210
>PRK14811 formamidopyrimidine-DNA glycosylase; Provisional
Probab=34.72 E-value=22 Score=36.92 Aligned_cols=25 Identities=24% Similarity=0.799 Sum_probs=19.1
Q ss_pred ecCCCCcCcccccceeeec--Cc--eeecccCccc
Q 006263 511 TACPLMIGDRQCNKKVTQS--GN--RWQCDRCNQE 541 (653)
Q Consensus 511 ~aC~~~~~~~~C~KKv~~~--~~--~~~C~kC~~~ 541 (653)
..|| .|+.++... ++ .|+|+.|++-
T Consensus 236 ~pC~------~Cg~~I~~~~~~gR~ty~Cp~CQ~~ 264 (269)
T PRK14811 236 QPCP------RCGTPIEKIVVGGRGTHFCPQCQPL 264 (269)
T ss_pred CCCC------cCCCeeEEEEECCCCcEECCCCcCC
Confidence 5799 899887532 23 9999999975
No 211
>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=34.63 E-value=99 Score=27.03 Aligned_cols=61 Identities=8% Similarity=0.021 Sum_probs=38.6
Q ss_pred eEEEEEecccceeeeeecccch--hhc-c-cCCcccCcEEEEeeeEeeeecCeEEEEEEeeeEee
Q 006263 38 RYRFLISDSVSTQHAMLATQLN--DRV-K-TGQVKKGSVVQLIDYICSTVQNRKIIVVLNMETII 98 (653)
Q Consensus 38 ryr~~lSDG~~~~~~ml~t~ln--~~v-~-~~~l~~~sIIkl~~y~~~~~~~k~~iii~~~evl~ 98 (653)
-.=+.|.||...+++++..... ..+ . ...|..|++|.+.-.....-.+.--|.+.+++++.
T Consensus 17 ~~Fi~lrd~~~~lQ~v~~~~~~~~~~~~~~~~~l~~g~~V~v~G~v~~~~~g~~El~~~~~~ils 81 (108)
T cd04322 17 LSFADLQDESGKIQVYVNKDDLGEEEFEDFKKLLDLGDIIGVTGTPFKTKTGELSIFVKEFTLLS 81 (108)
T ss_pred eEEEEEEECCeEEEEEEECCCCCHHHHHHHHhcCCCCCEEEEEEEEEecCCCCEEEEeCEeEEee
Confidence 4568899999888988854321 111 1 12389999999988766544333344555665555
No 212
>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=34.43 E-value=83 Score=28.69 Aligned_cols=38 Identities=13% Similarity=0.173 Sum_probs=29.2
Q ss_pred eEEEEEchhHHHHHHhhcccCcEEEEeceEEecCCCccc
Q 006263 257 EIRVTCFNAVVDRFYEIIEVGRVYLISKGSLKPAQKNFN 295 (653)
Q Consensus 257 ~I~at~f~~~~~kf~~~l~eG~vy~is~~~V~~a~~~f~ 295 (653)
.|++++|.+-++ |-..|++|+.+.|.|..++....++-
T Consensus 61 ti~It~yD~H~~-~ar~lK~GdfV~L~NVhiK~~~~~~~ 98 (123)
T cd04498 61 TIDILVYDNHVE-LAKSLKPGDFVRIYNVHAKSYSSKNE 98 (123)
T ss_pred EEEEEEEcchHH-HHhhCCCCCEEEEEEEEEEeccCCcc
Confidence 466788887775 44449999999999999987765443
No 213
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=34.42 E-value=23 Score=30.34 Aligned_cols=28 Identities=29% Similarity=0.964 Sum_probs=20.1
Q ss_pred cCCCCcCcccccce-eeecCc-eeecccCccccCCc
Q 006263 512 ACPLMIGDRQCNKK-VTQSGN-RWQCDRCNQEIDEC 545 (653)
Q Consensus 512 aC~~~~~~~~C~KK-v~~~~~-~~~C~kC~~~~~~~ 545 (653)
.|| .|+|. |..... .|.|.+|++.+.--
T Consensus 38 ~Cp------fCgk~~vkR~a~GIW~C~~C~~~~AGG 67 (90)
T PRK03976 38 VCP------VCGRPKVKRVGTGIWECRKCGAKFAGG 67 (90)
T ss_pred cCC------CCCCCceEEEEEEEEEcCCCCCEEeCC
Confidence 699 99764 444333 89999999876433
No 214
>COG0587 DnaE DNA polymerase III, alpha subunit [DNA replication, recombination, and repair]
Probab=34.05 E-value=1.3e+02 Score=37.66 Aligned_cols=71 Identities=20% Similarity=0.307 Sum_probs=51.8
Q ss_pred eeccccCCCCCceEEEEEEEeeccccccccCCCCc-eeEEEEEEeCCCCeEEEEEchhHHHHHHhhcccCcEEEEec
Q 006263 209 IPIAALNPYQGRWAIKARVTAKGDLRRYNNARGDG-KVFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISK 284 (653)
Q Consensus 209 ~pI~~L~p~~~~w~I~~RV~~k~~ir~~~~~~g~g-k~f~~~L~D~~g~~I~at~f~~~~~kf~~~l~eG~vy~is~ 284 (653)
.++.++.+....|.+-+-|+..-..++ . ..| ++.-+.|.|+.| .+.+++|.....+++..+.+++.|.+.+
T Consensus 967 ~~~~~~~~~~~~~~~~~~i~~vr~~~t---k-~~G~~~~f~tl~D~~g-~~e~v~f~~~~~~~~~~l~~~~~~~v~g 1038 (1139)
T COG0587 967 IRLLDLVEDGRRVVLAGGIVAVRQRPT---K-AKGNKMAFLTLEDETG-ILEVVVFPSEYERYRRLLLEGRLLIVKG 1038 (1139)
T ss_pred cchhhhccccceeEEEEEEEEEEEeec---c-CCCCEEEEEEEecCCC-cEEEEEcHHHHHHHHHHhccCcEEEEEE
Confidence 455666665556888887777544333 2 124 455677889545 9999999999999999999999888875
No 215
>KOG2593 consensus Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=33.85 E-value=21 Score=39.07 Aligned_cols=25 Identities=36% Similarity=1.020 Sum_probs=19.1
Q ss_pred cCCCCcCcccccceeee---------cCceeecccCcccc
Q 006263 512 ACPLMIGDRQCNKKVTQ---------SGNRWQCDRCNQEI 542 (653)
Q Consensus 512 aC~~~~~~~~C~KKv~~---------~~~~~~C~kC~~~~ 542 (653)
.|| .|+||-.. ..+.++|+.|+..+
T Consensus 130 ~Cp------~C~kkyt~Lea~~L~~~~~~~F~C~~C~gel 163 (436)
T KOG2593|consen 130 VCP------NCQKKYTSLEALQLLDNETGEFHCENCGGEL 163 (436)
T ss_pred cCC------ccccchhhhHHHHhhcccCceEEEecCCCch
Confidence 799 89999432 23489999999765
No 216
>PRK07772 single-stranded DNA-binding protein; Provisional
Probab=33.54 E-value=1.7e+02 Score=28.67 Aligned_cols=36 Identities=11% Similarity=0.098 Sum_probs=23.7
Q ss_pred EEEEEEccchhhhhhhhHHHhhccCCCcEEEEE-eeEeecCCC
Q 006263 380 SVELTLWGDFCNKEGQKLQEMVDVGFFPVLSVK-SGKVNDFSG 421 (653)
Q Consensus 380 ~i~vtLWg~~A~~~~~~l~~~~~~~~~~Vvaik-~~rV~~f~G 421 (653)
-++|++|++.|+.+. +.+ ..+.-|.+. ..+...|..
T Consensus 54 fi~V~~Wg~~Ae~va----~~L--~KGd~V~V~GrL~~r~wed 90 (186)
T PRK07772 54 FLRCSIWRQAAENVA----ESL--TKGMRVIVTGRLKQRSYET 90 (186)
T ss_pred EEEEEEecHHHHHHH----Hhc--CCCCEEEEEEEEEcCceEC
Confidence 678999999988753 323 245555555 456677754
No 217
>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=33.40 E-value=23 Score=30.35 Aligned_cols=30 Identities=33% Similarity=0.946 Sum_probs=21.2
Q ss_pred cCCCCcCcccccce-eeecCc-eeecccCccccCCceE
Q 006263 512 ACPLMIGDRQCNKK-VTQSGN-RWQCDRCNQEIDECDY 547 (653)
Q Consensus 512 aC~~~~~~~~C~KK-v~~~~~-~~~C~kC~~~~~~~~~ 547 (653)
.|| .|+|. |..... .|.|.+|++.+.--.|
T Consensus 37 ~Cp------fCgk~~vkR~a~GIW~C~~C~~~~AGGAy 68 (91)
T TIGR00280 37 VCP------FCGKKTVKRGSTGIWTCRKCGAKFAGGAY 68 (91)
T ss_pred cCC------CCCCCceEEEeeEEEEcCCCCCEEeCCcc
Confidence 699 99774 444433 8999999998744333
No 218
>PF14353 CpXC: CpXC protein
Probab=32.92 E-value=57 Score=29.60 Aligned_cols=33 Identities=15% Similarity=0.357 Sum_probs=24.6
Q ss_pred eeecccCccccCCceEEEEEEEEEEeCCCeEEEEEech
Q 006263 532 RWQCDRCNQEIDECDYRYLLQAQIQDQTGLTWVTAFQE 569 (653)
Q Consensus 532 ~~~C~kC~~~~~~~~~rY~l~~~i~D~Tg~~~~~~F~~ 569 (653)
.+.|+.|+... +.-..+...|......+.++-+
T Consensus 38 ~~~CP~Cg~~~-----~~~~p~lY~D~~~~~~i~~~P~ 70 (128)
T PF14353_consen 38 SFTCPSCGHKF-----RLEYPLLYHDPEKKFMIYYFPD 70 (128)
T ss_pred EEECCCCCCce-----ecCCCEEEEcCCCCEEEEEcCC
Confidence 89999999864 4445567778887777766665
No 219
>PRK13732 single-stranded DNA-binding protein; Provisional
Probab=32.86 E-value=1.5e+02 Score=28.71 Aligned_cols=35 Identities=9% Similarity=0.174 Sum_probs=22.9
Q ss_pred EEEEEEccchhhhhhhhHHHhhccCCCcEEEEEe-eEeecCC
Q 006263 380 SVELTLWGDFCNKEGQKLQEMVDVGFFPVLSVKS-GKVNDFS 420 (653)
Q Consensus 380 ~i~vtLWg~~A~~~~~~l~~~~~~~~~~Vvaik~-~rV~~f~ 420 (653)
-+.|++||+.|+...++ + ..|..|++.| ++.+.|.
T Consensus 55 w~~Vv~wgk~Ae~v~~~----L--~KG~~V~VeGrL~~r~ye 90 (175)
T PRK13732 55 WHRVVLFGKLAEVAGEY----L--RKGAQVYIEGQLRTRSWE 90 (175)
T ss_pred EEEEEEecHHHHHHHHh----c--CCCCEEEEEEEEEeeeEc
Confidence 57999999998774333 2 3567776654 4555564
No 220
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=32.70 E-value=25 Score=30.12 Aligned_cols=31 Identities=26% Similarity=0.806 Sum_probs=21.8
Q ss_pred cCCCCcCcccccce-eeecCc-eeecccCccccCCceEE
Q 006263 512 ACPLMIGDRQCNKK-VTQSGN-RWQCDRCNQEIDECDYR 548 (653)
Q Consensus 512 aC~~~~~~~~C~KK-v~~~~~-~~~C~kC~~~~~~~~~r 548 (653)
.|| -|+|. |..... .|.|.+|++.+.--.|.
T Consensus 38 ~Cp------fCgk~~vkR~a~GIW~C~~C~~~~AGGAy~ 70 (90)
T PTZ00255 38 FCP------FCGKHAVKRQAVGIWRCKGCKKTVAGGAWT 70 (90)
T ss_pred cCC------CCCCCceeeeeeEEEEcCCCCCEEeCCccc
Confidence 699 99764 544443 89999999987544443
No 221
>PRK10445 endonuclease VIII; Provisional
Probab=32.32 E-value=25 Score=36.48 Aligned_cols=24 Identities=21% Similarity=0.679 Sum_probs=18.1
Q ss_pred ecCCCCcCcccccceeee--cCc--eeecccCcc
Q 006263 511 TACPLMIGDRQCNKKVTQ--SGN--RWQCDRCNQ 540 (653)
Q Consensus 511 ~aC~~~~~~~~C~KKv~~--~~~--~~~C~kC~~ 540 (653)
..|| .|+-++.. .++ .|+|+.|++
T Consensus 236 ~~Cp------~Cg~~I~~~~~~gR~t~~CP~CQ~ 263 (263)
T PRK10445 236 EACE------RCGGIIEKTTLSSRPFYWCPGCQK 263 (263)
T ss_pred CCCC------CCCCEeEEEEECCCCcEECCCCcC
Confidence 4799 89988753 223 999999984
No 222
>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=32.10 E-value=88 Score=34.90 Aligned_cols=63 Identities=17% Similarity=0.280 Sum_probs=44.2
Q ss_pred ceEEEEEEEeeccccccccCCCCceeEEEEEEeCCCCeEEEEEchhHHHHHHhhcccCcEEEEec-eEEecCC
Q 006263 220 RWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISK-GSLKPAQ 291 (653)
Q Consensus 220 ~w~I~~RV~~k~~ir~~~~~~g~gk~f~~~L~D~~g~~I~at~f~~~~~kf~~~l~eG~vy~is~-~~V~~a~ 291 (653)
+..|+|=|.+ |+.. ..| .+.|+|.| ++..|+|++|...+.++.-.+++|.=+.+.+ ..+-+..
T Consensus 19 ~v~V~GEisn------~~~~-~sG-H~YFtLkD-~~a~i~~vmf~~~~~~l~f~~~~G~~V~v~g~v~~y~~~ 82 (432)
T TIGR00237 19 QVWIQGEISN------FTQP-VSG-HWYFTLKD-ENAQVRCVMFRGNNNRLKFRPQNGQQVLVRGGISVYEPR 82 (432)
T ss_pred cEEEEEEecC------CeeC-CCc-eEEEEEEc-CCcEEEEEEEcChhhCCCCCCCCCCEEEEEEEEEEECCC
Confidence 4556666654 3322 124 57889999 7899999999998888777789998777765 4554443
No 223
>PRK01103 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated
Probab=31.97 E-value=24 Score=36.69 Aligned_cols=24 Identities=25% Similarity=0.887 Sum_probs=18.0
Q ss_pred ecCCCCcCcccccceeeec--C--ceeecccCcc
Q 006263 511 TACPLMIGDRQCNKKVTQS--G--NRWQCDRCNQ 540 (653)
Q Consensus 511 ~aC~~~~~~~~C~KKv~~~--~--~~~~C~kC~~ 540 (653)
..|| .|+.++... + ..|+|+.|++
T Consensus 246 ~pC~------~Cg~~I~~~~~~gR~t~~CP~CQ~ 273 (274)
T PRK01103 246 EPCR------RCGTPIEKIKQGGRSTFFCPRCQK 273 (274)
T ss_pred CCCC------CCCCeeEEEEECCCCcEECcCCCC
Confidence 3699 899876532 2 3999999985
No 224
>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=31.41 E-value=62 Score=30.77 Aligned_cols=26 Identities=27% Similarity=0.638 Sum_probs=22.5
Q ss_pred eEEEEEEeCCCCeEEEEEchhHHHHHH
Q 006263 245 VFSFDLLDSDGGEIRVTCFNAVVDRFY 271 (653)
Q Consensus 245 ~f~~~L~D~~g~~I~at~f~~~~~kf~ 271 (653)
.+++.|.| .+|++.+++|++.++++.
T Consensus 69 ~l~~~i~D-~Tg~~~~~~F~~~ae~l~ 94 (166)
T cd04476 69 ILSLNVAD-HTGEAWLTLFDEVAEQIF 94 (166)
T ss_pred EEEEEEEe-CCCCEEEEEehHHHHHHh
Confidence 47888999 799999999999888764
No 225
>PF03107 C1_2: C1 domain; InterPro: IPR004146 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in DAG_PE-bind (IPR002219 from INTERPRO), therefore we have termed this domain DC1 for divergent C1 domain. This domain probably also binds to two zinc ions. The function of proteins with this domain is uncertain, however this domain may bind to molecules such as diacylglycerol. This family are found in plant proteins.
Probab=31.07 E-value=30 Score=23.08 Aligned_cols=18 Identities=22% Similarity=0.661 Sum_probs=15.0
Q ss_pred cccceeeecCceeecccCc
Q 006263 521 QCNKKVTQSGNRWQCDRCN 539 (653)
Q Consensus 521 ~C~KKv~~~~~~~~C~kC~ 539 (653)
.|.|++.... .|+|+.|+
T Consensus 5 ~C~~~~~~~~-~Y~C~~c~ 22 (30)
T PF03107_consen 5 VCRRKIDGFY-FYHCSECC 22 (30)
T ss_pred CCCCCcCCCE-eEEeCCCC
Confidence 8999987655 89999987
No 226
>PF13742 tRNA_anti_2: OB-fold nucleic acid binding domain
Probab=30.90 E-value=1.3e+02 Score=26.09 Aligned_cols=42 Identities=19% Similarity=0.269 Sum_probs=29.5
Q ss_pred ccccEEEEEEEecCceeEEecCCceeeEEEEEEEeCCCCEEEEEEccchhhh
Q 006263 341 SIVDVIGIVISVNPSVPILRKNGMETQRRILNLKDTSGRSVELTLWGDFCNK 392 (653)
Q Consensus 341 ~~vDVIGvV~~v~~~~~i~~k~g~~~~kr~i~l~D~s~~~i~vtLWg~~A~~ 392 (653)
..+=|.|-|.++..- +.| ...|+|.|+. .+|.|++|...+..
T Consensus 22 ~~vwV~GEIs~~~~~-----~~g----h~YftLkD~~-a~i~~~~~~~~~~~ 63 (99)
T PF13742_consen 22 PNVWVEGEISNLKRH-----SSG----HVYFTLKDEE-ASISCVIFRSRARR 63 (99)
T ss_pred CCEEEEEEEeecEEC-----CCc----eEEEEEEcCC-cEEEEEEEHHHHhh
Confidence 456666666654431 223 4679999977 69999999988765
No 227
>PRK00286 xseA exodeoxyribonuclease VII large subunit; Reviewed
Probab=30.86 E-value=93 Score=34.66 Aligned_cols=44 Identities=27% Similarity=0.263 Sum_probs=35.8
Q ss_pred eEEEEEEeCCCCeEEEEEchhHHHHHHhhcccCcEEEEec-eEEec
Q 006263 245 VFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISK-GSLKP 289 (653)
Q Consensus 245 ~f~~~L~D~~g~~I~at~f~~~~~kf~~~l~eG~vy~is~-~~V~~ 289 (653)
.+.|+|.| +...|+|++|...+.+..-.+++|.-+.+.+ ..+-+
T Consensus 42 H~Yf~Lkd-~~a~i~~~~~~~~~~~~~~~~~~G~~v~v~g~~~~y~ 86 (438)
T PRK00286 42 HWYFTLKD-EIAQIRCVMFKGSARRLKFKPEEGMKVLVRGKVSLYE 86 (438)
T ss_pred eEEEEEEc-CCcEEEEEEEcChhhcCCCCCCCCCEEEEEEEEEEEC
Confidence 47799999 6889999999998888877799998887776 45533
No 228
>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain. This domain contains a CXXCX(19)CXXC motif suggestive of both zinc fingers and thioredoxin, usually found at the N-terminus of prokaryotic proteins. One partially characterized gene, agmX, is among a large set in Myxococcus whose interruption affects adventurous gliding motility.
Probab=30.64 E-value=33 Score=23.99 Aligned_cols=26 Identities=23% Similarity=0.785 Sum_probs=18.5
Q ss_pred ecCCCCcCcccccceeeec-------CceeecccCcccc
Q 006263 511 TACPLMIGDRQCNKKVTQS-------GNRWQCDRCNQEI 542 (653)
Q Consensus 511 ~aC~~~~~~~~C~KKv~~~-------~~~~~C~kC~~~~ 542 (653)
..|| .|+++..-. +..-+|++|+..+
T Consensus 3 ~~CP------~C~~~~~v~~~~~~~~~~~v~C~~C~~~~ 35 (38)
T TIGR02098 3 IQCP------NCKTSFRVVDSQLGANGGKVRCGKCGHVW 35 (38)
T ss_pred EECC------CCCCEEEeCHHHcCCCCCEEECCCCCCEE
Confidence 5799 899965422 2268999999764
No 229
>PF12773 DZR: Double zinc ribbon
Probab=30.54 E-value=21 Score=26.65 Aligned_cols=28 Identities=14% Similarity=0.487 Sum_probs=18.1
Q ss_pred cccceeeecC-ceeecccCccccCCceEEE
Q 006263 521 QCNKKVTQSG-NRWQCDRCNQEIDECDYRY 549 (653)
Q Consensus 521 ~C~KKv~~~~-~~~~C~kC~~~~~~~~~rY 549 (653)
.|+.++.... ..+.|++|+..+ .+..+|
T Consensus 17 ~CG~~l~~~~~~~~~C~~Cg~~~-~~~~~f 45 (50)
T PF12773_consen 17 HCGTPLPPPDQSKKICPNCGAEN-PPNAKF 45 (50)
T ss_pred hhcCChhhccCCCCCCcCCcCCC-cCCcCc
Confidence 7888887222 278899998865 334333
No 230
>PF01599 Ribosomal_S27: Ribosomal protein S27a; InterPro: IPR002906 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This family of ribosomal proteins consists mainly of the 40S ribosomal protein S27a which is synthesized as a C-terminal extension of ubiquitin (CEP) (IPR000626 from INTERPRO). The S27a domain compromises the C-terminal half of the protein. The synthesis of ribosomal proteins as extensions of ubiquitin promotes their incorporation into nascent ribosomes by a transient metabolic stabilisation and is required for efficient ribosome biogenesis []. The ribosomal extension protein S27a contains a basic region that is proposed to form a zinc finger; its fusion gene is proposed as a mechanism to maintain a fixed ratio between ubiquitin necessary for degrading proteins and ribosomes a source of proteins [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2K4X_A 3U5C_f 3U5G_f 2XZN_9 2XZM_9.
Probab=30.44 E-value=49 Score=24.82 Aligned_cols=25 Identities=28% Similarity=0.797 Sum_probs=17.6
Q ss_pred cCCCCcCccccccee--eecCceeecccCcc
Q 006263 512 ACPLMIGDRQCNKKV--TQSGNRWQCDRCNQ 540 (653)
Q Consensus 512 aC~~~~~~~~C~KKv--~~~~~~~~C~kC~~ 540 (653)
-||++ .|+.-| ..-.+.|+|-||+-
T Consensus 20 ~CP~~----~CG~GvFMA~H~dR~~CGKCg~ 46 (47)
T PF01599_consen 20 ECPSP----RCGAGVFMAEHKDRHYCGKCGY 46 (47)
T ss_dssp E-TST----TTTSSSEEEE-SSEEEETTTSS
T ss_pred cCCCc----ccCCceEeeecCCCccCCCccc
Confidence 68977 898854 44456999999984
No 231
>PLN02221 asparaginyl-tRNA synthetase
Probab=29.36 E-value=4.3e+02 Score=30.71 Aligned_cols=84 Identities=17% Similarity=0.210 Sum_probs=53.0
Q ss_pred CceEEEEEEEeeccccccccCCCCce--eEEEEEEeCCC-CeEEEEEchhHHHHHHhhcccCcEEEEeceEEecCCCccc
Q 006263 219 GRWAIKARVTAKGDLRRYNNARGDGK--VFSFDLLDSDG-GEIRVTCFNAVVDRFYEIIEVGRVYLISKGSLKPAQKNFN 295 (653)
Q Consensus 219 ~~w~I~~RV~~k~~ir~~~~~~g~gk--~f~~~L~D~~g-~~I~at~f~~~~~kf~~~l~eG~vy~is~~~V~~a~~~f~ 295 (653)
..-+|+|+|-++ |. .|+ +.-++|.|..+ |.||+++..+. ......|..|.++.+.+- |+..... .
T Consensus 51 ~~V~I~GWV~~i---R~------~Gk~~i~Fl~LRDgs~~g~iQvVv~~~~-~~~~~~L~~ES~V~V~G~-V~~~~~~-~ 118 (572)
T PLN02221 51 QKVRIGGWVKTG---RE------QGKGTFAFLEVNDGSCPANLQVMVDSSL-YDLSTLVATGTCVTVDGV-LKVPPEG-K 118 (572)
T ss_pred CEEEEEEEEEeh---hh------CCCceEEEEEEeCCcccccEEEEEcCch-hhHHhcCCCceEEEEEEE-EEeCCcc-C
Confidence 467888888663 33 243 45577888432 78999987542 222246889999999774 4332211 1
Q ss_pred CCCCceEEEeccccEEEec
Q 006263 296 HLKNEWEIFLEATSTVDLC 314 (653)
Q Consensus 296 ~~~~~yei~f~~~T~I~~~ 314 (653)
...+.|||..+.-..|-++
T Consensus 119 ~~~~~iEl~v~~i~vl~~a 137 (572)
T PLN02221 119 GTKQKIELSVEKVIDVGTV 137 (572)
T ss_pred CCCccEEEEEeEEEEEecC
Confidence 1346899999776666555
No 232
>PF13842 Tnp_zf-ribbon_2: DDE_Tnp_1-like zinc-ribbon
Probab=29.29 E-value=31 Score=23.56 Aligned_cols=20 Identities=30% Similarity=0.871 Sum_probs=14.6
Q ss_pred cccceeeecCceeecccCcc
Q 006263 521 QCNKKVTQSGNRWQCDRCNQ 540 (653)
Q Consensus 521 ~C~KKv~~~~~~~~C~kC~~ 540 (653)
.|.+|-......|+|++|+.
T Consensus 5 vC~~~k~rk~T~~~C~~C~v 24 (32)
T PF13842_consen 5 VCSKKKRRKDTRYMCSKCDV 24 (32)
T ss_pred ECCcCCccceeEEEccCCCC
Confidence 78776544445899999974
No 233
>PF10451 Stn1: Telomere regulation protein Stn1; InterPro: IPR018856 The budding yeast protein Stn1 is a DNA-binding protein which has specificity for telomeric DNA. Structural profiling has predicted an OB-fold []. This entry represents the N-terminal part of the molecule, which adopts the OB fold. Protection of telomeres by multiple proteins with OB-fold domains is conserved in eukaryotic evolution [].; PDB: 3KF6_A 3KF8_A.
Probab=29.18 E-value=1.6e+02 Score=30.43 Aligned_cols=66 Identities=24% Similarity=0.279 Sum_probs=40.3
Q ss_pred ccccEEEEEEEecCceeEEecCCceeeEEEEEEEeCCCC-EEEEEEccchhhhhhhhHHHhhccCCCcEEEEEeeEe
Q 006263 341 SIVDVIGIVISVNPSVPILRKNGMETQRRILNLKDTSGR-SVELTLWGDFCNKEGQKLQEMVDVGFFPVLSVKSGKV 416 (653)
Q Consensus 341 ~~vDVIGvV~~v~~~~~i~~k~g~~~~kr~i~l~D~s~~-~i~vtLWg~~A~~~~~~l~~~~~~~~~~Vvaik~~rV 416 (653)
..|-|+|+|+.+..- .+. + -.+.-++|-|.||. .|.|.+|.+.....+-. +....|.+|.++|.--
T Consensus 67 ~~v~i~G~Vv~~~~~-~~~--~---~~~~~l~iDD~Sg~~~i~~~~~~~~~~~~~l~----~~~~~G~~V~VkG~vs 133 (256)
T PF10451_consen 67 RWVRIVGVVVGIDYK-WIE--N---EDRIILTIDDSSGANTIECKCSKSSYLSMGLP----INDLIGKVVEVKGTVS 133 (256)
T ss_dssp -EEEEEEEEEEEEEE-E-B--B---TCEEEEEEE-SSCS-EEEEEEEHHHHHCCCHH----CTT-TT-EEEEEEEEE
T ss_pred EEEEEEEEEEEEEEE-eec--c---cceEEEEEeCCCCceeEEEEEEcccccccCCC----ccCCCCcEEEEEEEEc
Confidence 368899999998532 111 1 13567788788887 99999998755432211 2233688888887643
No 234
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=29.14 E-value=18 Score=35.00 Aligned_cols=27 Identities=26% Similarity=0.893 Sum_probs=20.9
Q ss_pred EecCCCCcCcccccceeeecCc---eeecccCcccc
Q 006263 510 YTACPLMIGDRQCNKKVTQSGN---RWQCDRCNQEI 542 (653)
Q Consensus 510 Y~aC~~~~~~~~C~KKv~~~~~---~~~C~kC~~~~ 542 (653)
|..|| .|+-|+..+.. .+.|++||...
T Consensus 113 ~y~C~------~~~~r~sfdeA~~~~F~Cp~Cg~~L 142 (176)
T COG1675 113 YYVCP------NCHVKYSFDEAMELGFTCPKCGEDL 142 (176)
T ss_pred ceeCC------CCCCcccHHHHHHhCCCCCCCCchh
Confidence 33678 89999876543 79999999864
No 235
>PF07282 OrfB_Zn_ribbon: Putative transposase DNA-binding domain; InterPro: IPR010095 This entry represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by IPR001959 from INTERPRO, and other proteins. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=28.54 E-value=35 Score=27.30 Aligned_cols=28 Identities=29% Similarity=0.840 Sum_probs=21.4
Q ss_pred EEecCCCCcCcccccceeee--cCceeecccCcccc
Q 006263 509 CYTACPLMIGDRQCNKKVTQ--SGNRWQCDRCNQEI 542 (653)
Q Consensus 509 ~Y~aC~~~~~~~~C~KKv~~--~~~~~~C~kC~~~~ 542 (653)
.=..|| .|+..+.. .+..|.|+.|+...
T Consensus 27 TSq~C~------~CG~~~~~~~~~r~~~C~~Cg~~~ 56 (69)
T PF07282_consen 27 TSQTCP------RCGHRNKKRRSGRVFTCPNCGFEM 56 (69)
T ss_pred CccCcc------CcccccccccccceEEcCCCCCEE
Confidence 456799 89988776 33399999999754
No 236
>KOG4751 consensus DNA recombinational repair protein BRCA2 [Replication, recombination and repair]
Probab=28.42 E-value=45 Score=38.13 Aligned_cols=67 Identities=21% Similarity=0.281 Sum_probs=50.8
Q ss_pred HHHHHHhCCCCCCCCeEEEEEEEEcC-------------CCCceEEEEEecccceeeeeecccchhhcccCCcccCcEEE
Q 006263 8 NSISLINGGDVNSKPLVQVMDIKLIG-------------STQERYRFLISDSVSTQHAMLATQLNDRVKTGQVKKGSVVQ 74 (653)
Q Consensus 8 Gai~~i~~~~~~~~pvvQVl~ik~~~-------------~~~~ryr~~lSDG~~~~~~ml~t~ln~~v~~~~l~~~sIIk 74 (653)
-||++|++++.. ..-+=||+|-.+. +...--.|.|.||=|.+.|-|..-|...+.+|.|-.|.=|+
T Consensus 622 saik~i~~~d~~-a~~~~vlcis~i~~~t~n~s~~~~~~d~~~~~~veltdgwy~~~a~ld~~l~~~l~~g~l~vgqk~~ 700 (756)
T KOG4751|consen 622 SAIKRILSGDAP-ASSMMVLCISAINPLTDNISQEAHCSDTCSNVKVELTDGWYSMNAALDVVLTKQLNAGKLFVGQKLR 700 (756)
T ss_pred HHHHHHHcCCCc-chheEeeehhhccccccCcccccccccccceeEEEeecchhhhhhccchHHHHHhccCceehhhhhh
Confidence 489999999752 1234456666552 13456899999999999999998899988999998887666
Q ss_pred E
Q 006263 75 L 75 (653)
Q Consensus 75 l 75 (653)
+
T Consensus 701 ~ 701 (756)
T KOG4751|consen 701 H 701 (756)
T ss_pred h
Confidence 5
No 237
>PRK06293 single-stranded DNA-binding protein; Provisional
Probab=28.22 E-value=4.1e+02 Score=25.42 Aligned_cols=68 Identities=12% Similarity=0.081 Sum_probs=36.7
Q ss_pred ccEEEEEEEecCceeEEecCCceeeEEEEEEEeC-------CCCEEEEEEccchhhhhhhhHHHhhccCCCcEEEEE-ee
Q 006263 343 VDVIGIVISVNPSVPILRKNGMETQRRILNLKDT-------SGRSVELTLWGDFCNKEGQKLQEMVDVGFFPVLSVK-SG 414 (653)
Q Consensus 343 vDVIGvV~~v~~~~~i~~k~g~~~~kr~i~l~D~-------s~~~i~vtLWg~~A~~~~~~l~~~~~~~~~~Vvaik-~~ 414 (653)
|-+||.+..=-++. .+.+|+.+ ..|.|.-. .-.-+.|++||+.|+....+ + ..+.-|++. ..
T Consensus 4 V~LiGrLg~DPElR--~t~sG~~v--~~FsLAvn~~~~~~~~T~wi~v~awg~~Ae~v~~y----L--~KG~~V~VeGrL 73 (161)
T PRK06293 4 GYIVGRLGADPEER--MTSKGKRV--VVLRLGVKSRVGSKDETVWCRCNIWGNRYDKMLPY----L--KKGSGVIVAGEM 73 (161)
T ss_pred EEEEEEecCCCeEE--EcCCCCEE--EEEEEEEeCCCCCccceEEEEEEEEhHHHHHHHHh----C--CCCCEEEEEEEE
Confidence 55677766432222 23456543 33333311 12368999999998764222 2 346666665 45
Q ss_pred EeecCC
Q 006263 415 KVNDFS 420 (653)
Q Consensus 415 rV~~f~ 420 (653)
+...|.
T Consensus 74 ~~~~y~ 79 (161)
T PRK06293 74 SPESYV 79 (161)
T ss_pred EeCccC
Confidence 666674
No 238
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=28.14 E-value=32 Score=25.97 Aligned_cols=25 Identities=28% Similarity=1.004 Sum_probs=18.1
Q ss_pred ecCCCCcCcccccce--eeecCceeecccCccc
Q 006263 511 TACPLMIGDRQCNKK--VTQSGNRWQCDRCNQE 541 (653)
Q Consensus 511 ~aC~~~~~~~~C~KK--v~~~~~~~~C~kC~~~ 541 (653)
.-|| .|+-- +.+-.+.|.|-+|+-+
T Consensus 20 ~~CP------rCG~gvfmA~H~dR~~CGkCgyT 46 (51)
T COG1998 20 RFCP------RCGPGVFMADHKDRWACGKCGYT 46 (51)
T ss_pred ccCC------CCCCcchhhhcCceeEeccccce
Confidence 4699 89854 3444459999999954
No 239
>PRK06752 single-stranded DNA-binding protein; Validated
Probab=28.12 E-value=1e+02 Score=27.27 Aligned_cols=35 Identities=3% Similarity=0.131 Sum_probs=23.6
Q ss_pred EEEEEEccchhhhhhhhHHHhhccCCCcEEEEEe-eEeecCC
Q 006263 380 SVELTLWGDFCNKEGQKLQEMVDVGFFPVLSVKS-GKVNDFS 420 (653)
Q Consensus 380 ~i~vtLWg~~A~~~~~~l~~~~~~~~~~Vvaik~-~rV~~f~ 420 (653)
-+.|++||+.|+.+.++ + ..|.-|++.| .+...|.
T Consensus 48 ~~~v~~wg~~Ae~~~~~----l--~KG~~V~V~G~l~~~~~~ 83 (112)
T PRK06752 48 FINCVVWRKSAENVTEY----C--TKGSLVGITGRIHTRNYE 83 (112)
T ss_pred EEEEEEehHHHHHHHHh----c--CCCCEEEEEEEEEeCccC
Confidence 68999999998875333 2 3567776654 4556674
No 240
>TIGR01384 TFS_arch transcription factor S, archaeal. There has been an apparent duplication event in the Halobacteriaceae lineage (Haloarcula, Haloferax, Haloquadratum, Halobacterium and Natromonas). There appears to be a separate duplication in Methanosphaera stadtmanae.
Probab=28.11 E-value=59 Score=28.34 Aligned_cols=25 Identities=28% Similarity=0.745 Sum_probs=20.9
Q ss_pred cCCCCcCcccccceeeecCceeecccCcccc
Q 006263 512 ACPLMIGDRQCNKKVTQSGNRWQCDRCNQEI 542 (653)
Q Consensus 512 aC~~~~~~~~C~KKv~~~~~~~~C~kC~~~~ 542 (653)
-|| .|+.-+...++.+.|+.|+...
T Consensus 2 fC~------~Cg~~l~~~~~~~~C~~C~~~~ 26 (104)
T TIGR01384 2 FCP------KCGSLMTPKNGVYVCPSCGYEK 26 (104)
T ss_pred CCc------ccCcccccCCCeEECcCCCCcc
Confidence 389 8999988766799999999764
No 241
>PHA00626 hypothetical protein
Probab=27.96 E-value=40 Score=26.17 Aligned_cols=25 Identities=20% Similarity=0.779 Sum_probs=16.7
Q ss_pred cCCCCcCcccccce-eee-----c-CceeecccCcccc
Q 006263 512 ACPLMIGDRQCNKK-VTQ-----S-GNRWQCDRCNQEI 542 (653)
Q Consensus 512 aC~~~~~~~~C~KK-v~~-----~-~~~~~C~kC~~~~ 542 (653)
.|| .|+.- +.. . .+.|.|.+|+-.+
T Consensus 2 ~CP------~CGS~~Ivrcg~cr~~snrYkCkdCGY~f 33 (59)
T PHA00626 2 SCP------KCGSGNIAKEKTMRGWSDDYVCCDCGYND 33 (59)
T ss_pred CCC------CCCCceeeeeceecccCcceEcCCCCCee
Confidence 599 88773 332 1 3489999998543
No 242
>COG1570 XseA Exonuclease VII, large subunit [DNA replication, recombination, and repair]
Probab=27.78 E-value=1.1e+02 Score=33.99 Aligned_cols=68 Identities=24% Similarity=0.386 Sum_probs=48.7
Q ss_pred eccccccccCCCCceeEEEEEEeCCCCeEEEEEchhHHHHHHhhcccCcEEEEec-eEEecCCCcccCCCCceEEEecc
Q 006263 230 KGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISK-GSLKPAQKNFNHLKNEWEIFLEA 307 (653)
Q Consensus 230 k~~ir~~~~~~g~gk~f~~~L~D~~g~~I~at~f~~~~~kf~~~l~eG~vy~is~-~~V~~a~~~f~~~~~~yei~f~~ 307 (653)
++++-.|+-+ ..| ...|.|-| +...|+|++|.....++.-.+++|.=+.+.+ .++-+.. .+|.|..+.
T Consensus 29 ~GEISn~t~~-~sg-H~YFtLKD-~~A~i~c~mf~~~~~~l~f~p~eG~~V~v~G~is~Y~~r-------G~YQi~~~~ 97 (440)
T COG1570 29 RGEISNFTRP-ASG-HLYFTLKD-ERAQIRCVMFKGNNRRLKFRPEEGMQVLVRGKISLYEPR-------GDYQIVAES 97 (440)
T ss_pred EEEecCCccC-CCc-cEEEEEcc-CCceEEEEEEcCcccccCCCccCCCEEEEEEEEEEEcCC-------CceEEEEec
Confidence 3444444432 235 78899999 7999999999998888888899998666654 5655544 457777654
No 243
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=27.73 E-value=31 Score=26.10 Aligned_cols=23 Identities=22% Similarity=0.730 Sum_probs=17.6
Q ss_pred cCCCCcCcccccceeeec-Cc-eeecccCcc
Q 006263 512 ACPLMIGDRQCNKKVTQS-GN-RWQCDRCNQ 540 (653)
Q Consensus 512 aC~~~~~~~~C~KKv~~~-~~-~~~C~kC~~ 540 (653)
-|. .|++++... .. ..+|+.|+.
T Consensus 8 ~C~------~Cg~~~~~~~~~~~irCp~Cg~ 32 (49)
T COG1996 8 KCA------RCGREVELDQETRGIRCPYCGS 32 (49)
T ss_pred Ehh------hcCCeeehhhccCceeCCCCCc
Confidence 577 899999633 33 899999985
No 244
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=27.58 E-value=26 Score=32.91 Aligned_cols=25 Identities=36% Similarity=0.925 Sum_probs=18.4
Q ss_pred cCCCCcCcccccceeeecCc--------eeecccCcccc
Q 006263 512 ACPLMIGDRQCNKKVTQSGN--------RWQCDRCNQEI 542 (653)
Q Consensus 512 aC~~~~~~~~C~KKv~~~~~--------~~~C~kC~~~~ 542 (653)
-|| .|+++...... .+.|+.|+...
T Consensus 101 ~Cp------~C~~~y~~~ea~~~~d~~~~f~Cp~Cg~~l 133 (147)
T smart00531 101 KCP------NCQSKYTFLEANQLLDMDGTFTCPRCGEEL 133 (147)
T ss_pred ECc------CCCCEeeHHHHHHhcCCCCcEECCCCCCEE
Confidence 689 89998764321 39999999764
No 245
>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=27.46 E-value=74 Score=24.90 Aligned_cols=21 Identities=24% Similarity=0.233 Sum_probs=18.7
Q ss_pred EEEEEEEEeCCCeEEEEEech
Q 006263 549 YLLQAQIQDQTGLTWVTAFQE 569 (653)
Q Consensus 549 Y~l~~~i~D~Tg~~~~~~F~~ 569 (653)
-.+.+.+.|.+|.+.++.|+.
T Consensus 18 ~~~~~~~~D~~g~i~~~~F~~ 38 (75)
T cd04488 18 RRLKVTLSDGTGTLTLVFFNF 38 (75)
T ss_pred cEEEEEEEcCCCEEEEEEECC
Confidence 468899999999999999973
No 246
>PRK07279 dnaE DNA polymerase III DnaE; Reviewed
Probab=27.13 E-value=1.8e+02 Score=36.22 Aligned_cols=74 Identities=22% Similarity=0.297 Sum_probs=47.9
Q ss_pred ecchhhhhhcccCccccEEEEEEEecCceeEEec-CCceeeEEEEEEEeCCCCEEEEEEccchhhhhhhhHHHhhccCCC
Q 006263 328 FRHISEIESAENNSIVDVIGIVISVNPSVPILRK-NGMETQRRILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVDVGFF 406 (653)
Q Consensus 328 f~~i~~i~~~~~~~~vDVIGvV~~v~~~~~i~~k-~g~~~~kr~i~l~D~s~~~i~vtLWg~~A~~~~~~l~~~~~~~~~ 406 (653)
+.++++|. .+..+-++|+|..+.. +++| .|+. .--++|.|.+| .+++++|.+....+... + ..+
T Consensus 875 ~~~~~~l~---~~~~~~~~~~i~~~~~---~~tk~~g~~--maf~~leD~~g-~ie~~vFp~~y~~~~~~----l--~~~ 939 (1034)
T PRK07279 875 FTPISQLV---KNSEATILVQIQSIRV---IRTKTKGQQ--MAFLSVTDTKK-KLDVTLFPETYRQYKDE----L--KEG 939 (1034)
T ss_pred CccHHHHh---cCCcceEEEEEEEEEE---EEEcCCCCe--EEEEEEeeCCC-cEEEEECHHHHHHHHHH----h--ccC
Confidence 34555553 2445667888877655 3456 6663 46789999999 79999999876554322 2 245
Q ss_pred cEEEEEeeEee
Q 006263 407 PVLSVKSGKVN 417 (653)
Q Consensus 407 ~Vvaik~~rV~ 417 (653)
.++.++| +|.
T Consensus 940 ~~~~v~G-~v~ 949 (1034)
T PRK07279 940 KFYYLKG-KIQ 949 (1034)
T ss_pred CEEEEEE-EEE
Confidence 6776765 443
No 247
>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=27.07 E-value=2e+02 Score=24.73 Aligned_cols=62 Identities=15% Similarity=0.122 Sum_probs=40.1
Q ss_pred eEEEEEecccceeeeeecccc----hhhccc-CCcccCcEEEEeeeEeeeec-------CeEEEEEEeeeEeec
Q 006263 38 RYRFLISDSVSTQHAMLATQL----NDRVKT-GQVKKGSVVQLIDYICSTVQ-------NRKIIVVLNMETIIL 99 (653)
Q Consensus 38 ryr~~lSDG~~~~~~ml~t~l----n~~v~~-~~l~~~sIIkl~~y~~~~~~-------~k~~iii~~~evl~~ 99 (653)
.-=+.|.||...+++++.... .++... ..|..+++|.+.-.....-. +..-|.+.+++++..
T Consensus 18 ~~Fi~LrD~sg~iQ~v~~~~~~~~~~~~~~~~~~l~~es~V~V~G~v~~~~~~~~~~~~~~~El~~~~i~il~~ 91 (102)
T cd04320 18 LAFLVLRQQGYTIQGVLAASAEGVSKQMVKWAGSLSKESIVDVEGTVKKPEEPIKSCTQQDVELHIEKIYVVSE 91 (102)
T ss_pred eEEEEEecCCceEEEEEeCCcccCCHHHHHHHhcCCCccEEEEEEEEECCCCcccCCCcCcEEEEEEEEEEEec
Confidence 445778999988999887543 122211 35889999999887654311 234566677766653
No 248
>COG3877 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=26.65 E-value=45 Score=29.27 Aligned_cols=31 Identities=19% Similarity=0.725 Sum_probs=22.7
Q ss_pred ecCCCCcCcccccceeeecCceeecccCccccCCceEEEEEE
Q 006263 511 TACPLMIGDRQCNKKVTQSGNRWQCDRCNQEIDECDYRYLLQ 552 (653)
Q Consensus 511 ~aC~~~~~~~~C~KKv~~~~~~~~C~kC~~~~~~~~~rY~l~ 552 (653)
+-|| .|++++.-. ..+|..|..++ .-+|.++
T Consensus 7 ~~cP------vcg~~~iVT--eL~c~~~etTV---rg~F~~s 37 (122)
T COG3877 7 NRCP------VCGRKLIVT--ELKCSNCETTV---RGNFKMS 37 (122)
T ss_pred CCCC------cccccceeE--EEecCCCCceE---ecceecc
Confidence 4799 999997654 68999999764 3355543
No 249
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=26.00 E-value=77 Score=23.59 Aligned_cols=25 Identities=28% Similarity=0.828 Sum_probs=18.2
Q ss_pred cCCCCcCcccccceeeecCc----eeecccCcccc
Q 006263 512 ACPLMIGDRQCNKKVTQSGN----RWQCDRCNQEI 542 (653)
Q Consensus 512 aC~~~~~~~~C~KKv~~~~~----~~~C~kC~~~~ 542 (653)
-|| .|+.-+....+ .|.|+.|+-..
T Consensus 2 FCp------~Cg~~l~~~~~~~~~~~vC~~Cg~~~ 30 (52)
T smart00661 2 FCP------KCGNMLIPKEGKEKRRFVCRKCGYEE 30 (52)
T ss_pred CCC------CCCCccccccCCCCCEEECCcCCCeE
Confidence 488 89887654322 79999999754
No 250
>PRK06556 vitamin B12-dependent ribonucleotide reductase; Validated
Probab=25.89 E-value=40 Score=41.23 Aligned_cols=28 Identities=25% Similarity=0.751 Sum_probs=24.1
Q ss_pred EEecCCCCcCcccccceeeecCceeecccCcccc
Q 006263 509 CYTACPLMIGDRQCNKKVTQSGNRWQCDRCNQEI 542 (653)
Q Consensus 509 ~Y~aC~~~~~~~~C~KKv~~~~~~~~C~kC~~~~ 542 (653)
.=|.|+ .|+.|+...+.-|.|+.|+.+.
T Consensus 923 ~~~~c~------~c~~~~~~~g~c~~c~~cg~t~ 950 (953)
T PRK06556 923 DAPLCP------TCGTKMVRNGSCYVCEGCGSTS 950 (953)
T ss_pred cCCcCC------CccCeeeECCceEeccCCCCCC
Confidence 345699 9999999998899999999763
No 251
>PF14205 Cys_rich_KTR: Cysteine-rich KTR
Probab=25.62 E-value=72 Score=24.65 Aligned_cols=26 Identities=35% Similarity=0.823 Sum_probs=17.4
Q ss_pred ecCCCCcCccccccee----eecC---c-eeecccCcccc
Q 006263 511 TACPLMIGDRQCNKKV----TQSG---N-RWQCDRCNQEI 542 (653)
Q Consensus 511 ~aC~~~~~~~~C~KKv----~~~~---~-~~~C~kC~~~~ 542 (653)
.-|| .|+.|- .++- . ..+|++|.+..
T Consensus 5 i~CP------~CgnKTR~kir~DT~LkNfPlyCpKCK~Et 38 (55)
T PF14205_consen 5 ILCP------ICGNKTRLKIREDTVLKNFPLYCPKCKQET 38 (55)
T ss_pred EECC------CCCCccceeeecCceeccccccCCCCCceE
Confidence 3599 998653 2221 1 68999998764
No 252
>KOG0402 consensus 60S ribosomal protein L37 [Translation, ribosomal structure and biogenesis]
Probab=25.35 E-value=39 Score=28.31 Aligned_cols=30 Identities=27% Similarity=0.810 Sum_probs=21.5
Q ss_pred cCCCCcCcccccceeeecC--ceeecccCccccCCceE
Q 006263 512 ACPLMIGDRQCNKKVTQSG--NRWQCDRCNQEIDECDY 547 (653)
Q Consensus 512 aC~~~~~~~~C~KKv~~~~--~~~~C~kC~~~~~~~~~ 547 (653)
-|+ -|+|+-..-. +.|.|..|.+.+.-..|
T Consensus 38 ~Cs------fCGK~~vKR~AvGiW~C~~C~kv~agga~ 69 (92)
T KOG0402|consen 38 TCS------FCGKKTVKRKAVGIWKCGSCKKVVAGGAY 69 (92)
T ss_pred hhh------hcchhhhhhhceeEEecCCccceeccceE
Confidence 488 8999855433 38999999998754444
No 253
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=25.21 E-value=1.2e+02 Score=27.27 Aligned_cols=49 Identities=22% Similarity=0.629 Sum_probs=34.1
Q ss_pred cCCCCcCcccccceeee----cCceeecccCccccCCc---eEEEEEEEEEEeCCCeEEEEE
Q 006263 512 ACPLMIGDRQCNKKVTQ----SGNRWQCDRCNQEIDEC---DYRYLLQAQIQDQTGLTWVTA 566 (653)
Q Consensus 512 aC~~~~~~~~C~KKv~~----~~~~~~C~kC~~~~~~~---~~rY~l~~~i~D~Tg~~~~~~ 566 (653)
-|| .|+--+.. .+..+.|.+|+-..+.. .++|.+...+.+.....-...
T Consensus 4 FCp------~Cgsll~p~~~~~~~~l~C~kCgye~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 59 (113)
T COG1594 4 FCP------KCGSLLYPKKDDEGGKLVCRKCGYEEEASNKKVYRYSVKEAVEKKKEVVLVVE 59 (113)
T ss_pred ccC------CccCeeEEeEcCCCcEEECCCCCcchhccccceeEEEEeeccCCcceeeeeec
Confidence 488 89988776 33499999999876433 277777777776665544444
No 254
>PF08274 PhnA_Zn_Ribbon: PhnA Zinc-Ribbon ; InterPro: IPR013987 The PhnA protein family includes the uncharacterised Escherichia coli protein PhnA and its homologues. The E. coli phnA gene is part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage []. The protein is not related to the characterised phosphonoacetate hydrolase designated PhnA []. This entry represents the N-terminal domain of PhnA, which is predicted to form a zinc-ribbon.; PDB: 2AKL_A.
Probab=24.64 E-value=36 Score=22.98 Aligned_cols=26 Identities=27% Similarity=0.703 Sum_probs=12.9
Q ss_pred EecCCCCcCcccccceeeecC-ceeecccCccc
Q 006263 510 YTACPLMIGDRQCNKKVTQSG-NRWQCDRCNQE 541 (653)
Q Consensus 510 Y~aC~~~~~~~~C~KKv~~~~-~~~~C~kC~~~ 541 (653)
+++|| .|+.--+..+ ..+-|+.|+..
T Consensus 2 ~p~Cp------~C~se~~y~D~~~~vCp~C~~e 28 (30)
T PF08274_consen 2 LPKCP------LCGSEYTYEDGELLVCPECGHE 28 (30)
T ss_dssp S---T------TT-----EE-SSSEEETTTTEE
T ss_pred CCCCC------CCCCcceeccCCEEeCCccccc
Confidence 46899 8987655443 39999999854
No 255
>PF09855 DUF2082: Nucleic-acid-binding protein containing Zn-ribbon domain (DUF2082); InterPro: IPR018652 This family of proteins contains various hypothetical prokaryotic proteins as well as some Zn-ribbon nucleic-acid-binding proteins.
Probab=24.61 E-value=78 Score=25.40 Aligned_cols=30 Identities=20% Similarity=0.413 Sum_probs=17.0
Q ss_pred eecccCccccCCceEEEEEEEEEEeCCCeEEEEEechh
Q 006263 533 WQCDRCNQEIDECDYRYLLQAQIQDQTGLTWVTAFQES 570 (653)
Q Consensus 533 ~~C~kC~~~~~~~~~rY~l~~~i~D~Tg~~~~~~F~~~ 570 (653)
|.|+||+... ....-...||..+-.+||=+
T Consensus 1 y~C~KCg~~~--------~e~~~v~~tgg~~skiFdvq 30 (64)
T PF09855_consen 1 YKCPKCGNEE--------YESGEVRATGGGLSKIFDVQ 30 (64)
T ss_pred CCCCCCCCcc--------eecceEEccCCeeEEEEEec
Confidence 6788888642 12223335666666667643
No 256
>PF01927 Mut7-C: Mut7-C RNAse domain; InterPro: IPR002782 This prokaryotic family of proteins have no known function. The proteins contain four conserved cysteines that may be involved in metal binding or disulphide bridges.
Probab=24.60 E-value=43 Score=31.34 Aligned_cols=11 Identities=27% Similarity=0.978 Sum_probs=9.6
Q ss_pred eeecccCcccc
Q 006263 532 RWQCDRCNQEI 542 (653)
Q Consensus 532 ~~~C~kC~~~~ 542 (653)
-|+|++|++.+
T Consensus 124 f~~C~~C~kiy 134 (147)
T PF01927_consen 124 FWRCPGCGKIY 134 (147)
T ss_pred EEECCCCCCEe
Confidence 69999999865
No 257
>cd01759 PLAT_PL PLAT/LH2 domain of pancreatic triglyceride lipase. Lipases hydrolyze phospholipids and triglycerides to generate fatty acids for energy production or for storage and to release inositol phosphates that act as second messengers. The central role of triglyceride lipases is in energy production. The proposed function of PLAT/LH2 domains is to mediate interaction with lipids or membrane bound proteins.
Probab=24.37 E-value=84 Score=28.17 Aligned_cols=26 Identities=23% Similarity=0.526 Sum_probs=22.0
Q ss_pred EEEEEEEEEEe---CCCeEEEEEechhhh
Q 006263 547 YRYLLQAQIQD---QTGLTWVTAFQESGE 572 (653)
Q Consensus 547 ~rY~l~~~i~D---~Tg~~~~~~F~~~ae 572 (653)
|||++.+.+++ -+|.+.+.+++..++
T Consensus 1 ~~Yqv~V~~s~~~~~~g~~~vsL~G~~g~ 29 (113)
T cd01759 1 WRYKVSVTLSGKKKVTGTILVSLYGNKGN 29 (113)
T ss_pred CeEEEEEEEecccccCceEEEEEEcCCCC
Confidence 69999999998 678899999976654
No 258
>COG1107 Archaea-specific RecJ-like exonuclease, contains DnaJ-type Zn finger domain [DNA replication, recombination, and repair]
Probab=23.92 E-value=69 Score=36.60 Aligned_cols=69 Identities=29% Similarity=0.392 Sum_probs=53.9
Q ss_pred CcceeccccCCCCC-ceEEEEEEEeeccccccccCCCCceeEEEEEEeCCCCeEEEEEchhHHHHHHhhcccCcEEEEec
Q 006263 206 ARIIPIAALNPYQG-RWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISK 284 (653)
Q Consensus 206 ~~~~pI~~L~p~~~-~w~I~~RV~~k~~ir~~~~~~g~gk~f~~~L~D~~g~~I~at~f~~~~~kf~~~l~eG~vy~is~ 284 (653)
.+.+.|.+|..+.. .-.|++.|++ +++-. | --+ |+|.| ++|.|.|.+|-+.--+-|+-++.|+++.+.+
T Consensus 200 ~~r~~i~~id~~ig~tV~I~GeV~q---ikqT~---G-PTV--FtltD-etg~i~aAAFe~aGvRAyP~IevGdiV~ViG 269 (715)
T COG1107 200 LPRTLIDDLDEMIGKTVRIEGEVTQ---IKQTS---G-PTV--FTLTD-ETGAIWAAAFEEAGVRAYPEIEVGDIVEVIG 269 (715)
T ss_pred cccccHHHHHhhcCceEEEEEEEEE---EEEcC---C-CEE--EEEec-CCCceehhhhccCCcccCCCCCCCceEEEEE
Confidence 34566778877654 5789999998 44432 1 134 57899 8999999999998889999999999999886
No 259
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 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. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=23.87 E-value=37 Score=20.58 Aligned_cols=12 Identities=17% Similarity=0.814 Sum_probs=8.6
Q ss_pred eecccCccccCC
Q 006263 533 WQCDRCNQEIDE 544 (653)
Q Consensus 533 ~~C~kC~~~~~~ 544 (653)
|.|+.|++.+..
T Consensus 1 y~C~~C~~~f~~ 12 (23)
T PF00096_consen 1 YKCPICGKSFSS 12 (23)
T ss_dssp EEETTTTEEESS
T ss_pred CCCCCCCCccCC
Confidence 678888877643
No 260
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=23.26 E-value=55 Score=22.92 Aligned_cols=26 Identities=27% Similarity=0.861 Sum_probs=18.5
Q ss_pred ecCCCCcCcccccceeee-------cCceeecccCcccc
Q 006263 511 TACPLMIGDRQCNKKVTQ-------SGNRWQCDRCNQEI 542 (653)
Q Consensus 511 ~aC~~~~~~~~C~KKv~~-------~~~~~~C~kC~~~~ 542 (653)
..|| .|+++-.- .+..-+|.+|+..+
T Consensus 3 i~Cp------~C~~~y~i~d~~ip~~g~~v~C~~C~~~f 35 (36)
T PF13717_consen 3 ITCP------NCQAKYEIDDEKIPPKGRKVRCSKCGHVF 35 (36)
T ss_pred EECC------CCCCEEeCCHHHCCCCCcEEECCCCCCEe
Confidence 4699 89987532 12279999999754
No 261
>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=23.16 E-value=3e+02 Score=22.86 Aligned_cols=58 Identities=12% Similarity=0.041 Sum_probs=35.3
Q ss_pred EEEEecccc-eeeeeecccchhhcc-cCCcccCcEEEEeeeEeeeec------CeEEEEEEeeeEee
Q 006263 40 RFLISDSVS-TQHAMLATQLNDRVK-TGQVKKGSVVQLIDYICSTVQ------NRKIIVVLNMETII 98 (653)
Q Consensus 40 r~~lSDG~~-~~~~ml~t~ln~~v~-~~~l~~~sIIkl~~y~~~~~~------~k~~iii~~~evl~ 98 (653)
=+.|.||.- .+++++..... ... -..|..+++|.++--....-. +..-+.+.+++++.
T Consensus 20 Fi~LrD~~g~~iQvv~~~~~~-~~~~~~~l~~~s~V~V~G~v~~~~~~~~~~~~~~Ei~~~~i~il~ 85 (86)
T cd04321 20 FADLRDPNGDIIQLVSTAKKD-AFSLLKSITAESPVQVRGKLQLKEAKSSEKNDEWELVVDDIQTLN 85 (86)
T ss_pred EEEEECCCCCEEEEEECCCHH-HHHHHhcCCCCcEEEEEEEEEeCCCcCCCCCCCEEEEEEEEEEec
Confidence 366788877 47776654321 111 135889999999776544321 33456777777764
No 262
>TIGR00577 fpg formamidopyrimidine-DNA glycosylase (fpg). All proteins in the FPG family with known functions are FAPY-DNA glycosylases that function in base excision repair. Homologous to endonuclease VIII (nei). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=23.04 E-value=43 Score=34.88 Aligned_cols=23 Identities=22% Similarity=0.787 Sum_probs=17.3
Q ss_pred ecCCCCcCcccccceeeec--Cc--eeecccCc
Q 006263 511 TACPLMIGDRQCNKKVTQS--GN--RWQCDRCN 539 (653)
Q Consensus 511 ~aC~~~~~~~~C~KKv~~~--~~--~~~C~kC~ 539 (653)
..|| .|+..+... ++ .|+|+.|+
T Consensus 246 ~pC~------~Cg~~I~~~~~~gR~t~~CP~CQ 272 (272)
T TIGR00577 246 EPCR------RCGTPIEKIKVGGRGTHFCPQCQ 272 (272)
T ss_pred CCCC------CCCCeeEEEEECCCCCEECCCCC
Confidence 3799 899877532 23 99999996
No 263
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=22.92 E-value=64 Score=23.78 Aligned_cols=22 Identities=18% Similarity=0.572 Sum_probs=17.3
Q ss_pred cccceeeecCc-eeecccCcccc
Q 006263 521 QCNKKVTQSGN-RWQCDRCNQEI 542 (653)
Q Consensus 521 ~C~KKv~~~~~-~~~C~kC~~~~ 542 (653)
.|+..+..... .-+|+.|+..+
T Consensus 7 ~Cg~~~~~~~~~~irC~~CG~rI 29 (44)
T smart00659 7 ECGRENEIKSKDVVRCRECGYRI 29 (44)
T ss_pred CCCCEeecCCCCceECCCCCceE
Confidence 89999876543 89999998643
No 264
>KOG3108 consensus Single-stranded DNA-binding replication protein A (RPA), medium (30 kD) subunit [Replication, recombination and repair]
Probab=22.57 E-value=2.8e+02 Score=28.86 Aligned_cols=40 Identities=20% Similarity=0.434 Sum_probs=29.6
Q ss_pred cccEEEEEEEecCceeEEecCCceeeEEEEEEEeCCCCEEEEEEccchhhh
Q 006263 342 IVDVIGIVISVNPSVPILRKNGMETQRRILNLKDTSGRSVELTLWGDFCNK 392 (653)
Q Consensus 342 ~vDVIGvV~~v~~~~~i~~k~g~~~~kr~i~l~D~s~~~i~vtLWg~~A~~ 392 (653)
.|-++|+|..+... ..+..++|-|.+| .|.|..|-.....
T Consensus 70 ~v~~VGivr~~e~~----------~t~i~y~I~D~tg-~id~r~W~~~~~~ 109 (265)
T KOG3108|consen 70 AVSIVGIVRNIEKS----------ATNITYEIEDGTG-QIDVRQWFHDNAE 109 (265)
T ss_pred EEEEEEEEEeceec----------CcceEEEEecCcc-cEEEEEeccccch
Confidence 35677888776654 2356789999999 5999999887543
No 265
>PF11325 DUF3127: Domain of unknown function (DUF3127); InterPro: IPR021474 This bacterial family of proteins has no known function.
Probab=22.22 E-value=3.5e+02 Score=22.94 Aligned_cols=59 Identities=17% Similarity=0.121 Sum_probs=37.1
Q ss_pred EEEEEEeeccccccccCCCCceeEEEEEEe--CCCCeEEEEEchhHHHHHHhhcccCcEEEEe
Q 006263 223 IKARVTAKGDLRRYNNARGDGKVFSFDLLD--SDGGEIRVTCFNAVVDRFYEIIEVGRVYLIS 283 (653)
Q Consensus 223 I~~RV~~k~~ir~~~~~~g~gk~f~~~L~D--~~g~~I~at~f~~~~~kf~~~l~eG~vy~is 283 (653)
|.|+|+.+-+..+=..++| =+--+++|-- .--..|...+|++-++.+++ +++|+.+.+|
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 5678777665554222232 1223344432 12278999999998887554 8899999887
No 266
>PF13695 zf-3CxxC: Zinc-binding domain
Probab=21.90 E-value=1.7e+02 Score=25.39 Aligned_cols=39 Identities=18% Similarity=0.435 Sum_probs=31.5
Q ss_pred eeecccCccccCCceEEEEEEEEEEeCCCeEEEEEechhhhh
Q 006263 532 RWQCDRCNQEIDECDYRYLLQAQIQDQTGLTWVTAFQESGEE 573 (653)
Q Consensus 532 ~~~C~kC~~~~~~~~~rY~l~~~i~D~Tg~~~~~~F~~~ae~ 573 (653)
.+.|.+|++.+....-.-.+.+. ..|...+.+|++..+.
T Consensus 5 rF~C~~C~~~W~S~~v~i~f~~~---~~g~v~~rv~~Q~C~~ 43 (98)
T PF13695_consen 5 RFQCSKCSRGWTSAKVWILFHMY---RGGQVNMRVFGQRCKK 43 (98)
T ss_pred EEECCCCCCCCccCEEEEEEEEc---CCCeEEEEEECCCCCC
Confidence 68999999998777666666665 6689999999998874
No 267
>smart00652 eIF1a eukaryotic translation initiation factor 1A.
Probab=21.60 E-value=2.3e+02 Score=23.87 Aligned_cols=46 Identities=17% Similarity=0.360 Sum_probs=30.4
Q ss_pred eEEEEEEEEcCCCCceEEEEEecccceeeeeecccchhhcccCCcccCcEEEEe
Q 006263 23 LVQVMDIKLIGSTQERYRFLISDSVSTQHAMLATQLNDRVKTGQVKKGSVVQLI 76 (653)
Q Consensus 23 vvQVl~ik~~~~~~~ryr~~lSDG~~~~~~ml~t~ln~~v~~~~l~~~sIIkl~ 76 (653)
+.+|+... ++++|++.+.||... -|.++..+...+ -|..|++|-+.
T Consensus 8 ~g~V~~~l----G~~~~~V~~~dG~~~-la~ipgK~Rk~i---wI~~GD~VlVe 53 (83)
T smart00652 8 IAQVVKML----GNGRLEVMCADGKER-LARIPGKMRKKV---WIRRGDIVLVD 53 (83)
T ss_pred EEEEEEEc----CCCEEEEEECCCCEE-EEEEchhhcccE---EEcCCCEEEEE
Confidence 45554333 568999999999664 456666665433 36677777664
No 268
>PRK06642 single-stranded DNA-binding protein; Provisional
Probab=21.51 E-value=5.1e+02 Score=24.37 Aligned_cols=69 Identities=14% Similarity=0.089 Sum_probs=37.1
Q ss_pred cccEEEEEEEecCceeEEecCCceeeEEEEEEE------eC-CC------CEEEEEEccc-hhhhhhhhHHHhhccCCCc
Q 006263 342 IVDVIGIVISVNPSVPILRKNGMETQRRILNLK------DT-SG------RSVELTLWGD-FCNKEGQKLQEMVDVGFFP 407 (653)
Q Consensus 342 ~vDVIGvV~~v~~~~~i~~k~g~~~~kr~i~l~------D~-s~------~~i~vtLWg~-~A~~~~~~l~~~~~~~~~~ 407 (653)
.|-+||.|..--++ -.+.+|+.+. .|.|. |. +| .-++|++||+ .|....++ + ..|.
T Consensus 7 ~V~LiGrLg~DPEl--r~t~~G~~v~--~fslAv~~~~k~~~~G~~~~~T~w~~v~~~g~~~Ae~~~~~----l--~KG~ 76 (152)
T PRK06642 7 KVILIGNVGRDPEI--RTTGEGKKII--NLSLATTETWKDRITSERKERTEWHRVVIFSEGLVSVVERY----V--TKGS 76 (152)
T ss_pred EEEEEEEccCCceE--EECCCCCEEE--EEEEEeccccccccCCccccceeEEEEEEeChHHHHHHHHh----C--CCCC
Confidence 45677877763222 2234565443 33333 21 12 2688999997 67653222 2 3567
Q ss_pred EEEEEe-eEeecCC
Q 006263 408 VLSVKS-GKVNDFS 420 (653)
Q Consensus 408 Vvaik~-~rV~~f~ 420 (653)
.|++.| .+.+.|.
T Consensus 77 ~V~V~GrL~~~~y~ 90 (152)
T PRK06642 77 KLYIEGSLQTRKWN 90 (152)
T ss_pred EEEEEEEEEeCeeE
Confidence 777654 4556674
No 269
>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=21.47 E-value=3.7e+02 Score=22.16 Aligned_cols=60 Identities=13% Similarity=0.132 Sum_probs=36.9
Q ss_pred EEEEEecccceeeeeecccchhhc-ccCCcccCcEEEEeeeEeeeecC-----eEEEEEEeeeEee
Q 006263 39 YRFLISDSVSTQHAMLATQLNDRV-KTGQVKKGSVVQLIDYICSTVQN-----RKIIVVLNMETII 98 (653)
Q Consensus 39 yr~~lSDG~~~~~~ml~t~ln~~v-~~~~l~~~sIIkl~~y~~~~~~~-----k~~iii~~~evl~ 98 (653)
-=+.|.||...+++++.......+ .-..|..+++|.+.-.....-.. ..=+.+.+++++.
T Consensus 18 ~Fi~LrD~~~~iQ~v~~~~~~~~~~~~~~l~~es~V~V~G~v~~~~~~~~~~~~~Ei~~~~i~vl~ 83 (84)
T cd04323 18 MFLVLRDGTGFLQCVLSKKLVTEFYDAKSLTQESSVEVTGEVKEDPRAKQAPGGYELQVDYLEIIG 83 (84)
T ss_pred EEEEEEcCCeEEEEEEcCCcchhHHHHhcCCCcCEEEEEEEEEECCcccCCCCCEEEEEEEEEEEc
Confidence 456789999989988865432211 11358899999997765543111 1235566666553
No 270
>COG2824 PhnA Uncharacterized Zn-ribbon-containing protein involved in phosphonate metabolism [Inorganic ion transport and metabolism]
Probab=21.46 E-value=98 Score=27.31 Aligned_cols=28 Identities=29% Similarity=0.768 Sum_probs=21.7
Q ss_pred EecCCCCcCcccccceeeecCc-eeecccCccccC
Q 006263 510 YTACPLMIGDRQCNKKVTQSGN-RWQCDRCNQEID 543 (653)
Q Consensus 510 Y~aC~~~~~~~~C~KKv~~~~~-~~~C~kC~~~~~ 543 (653)
-|-|| .|+.--+.+.+ .+.|+.|...+.
T Consensus 3 lp~cp------~c~sEytYed~~~~~cpec~~ew~ 31 (112)
T COG2824 3 LPPCP------KCNSEYTYEDGGQLICPECAHEWN 31 (112)
T ss_pred CCCCC------ccCCceEEecCceEeCchhccccc
Confidence 46799 99887655444 999999998775
No 271
>PRK00036 primosomal replication protein N; Reviewed
Probab=21.15 E-value=4.3e+02 Score=23.53 Aligned_cols=69 Identities=14% Similarity=0.148 Sum_probs=49.5
Q ss_pred CceEEEEEEEeeccccccccCCCCceeEEEEEEeC-----C------CCeEEEEEchhHHHHHHhhcccCcEEEEeceEE
Q 006263 219 GRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDS-----D------GGEIRVTCFNAVVDRFYEIIEVGRVYLISKGSL 287 (653)
Q Consensus 219 ~~w~I~~RV~~k~~ir~~~~~~g~gk~f~~~L~D~-----~------g~~I~at~f~~~~~kf~~~l~eG~vy~is~~~V 287 (653)
|++.+.|+|+..-.+|. +-+ | --+.+|.|--. - --+|.|.+.++.++++.. +..|..+.+++|--
T Consensus 2 N~l~Ltg~v~~~~~lry-TPA-G-Ip~~~~~LeH~S~q~EAG~~Rqv~~~i~ava~G~~a~~~~~-l~~Gs~v~v~GFLa 77 (107)
T PRK00036 2 NTLELSARVLECGAMRH-TPA-G-LPALELLLVHESEVVEAGHPRRVELTISAVALGDLALLLAD-TPLGTEMQVQGFLA 77 (107)
T ss_pred CEEEEEEEEeccCcccc-CCC-C-CceEEEEEEEeEEeEeCCCcceEEEEEEEEEEhhHHHHhcc-cCCCCEEEEEEEEE
Confidence 67889999998877664 322 2 14566666321 1 236899999988888886 99999999999976
Q ss_pred ecCC
Q 006263 288 KPAQ 291 (653)
Q Consensus 288 ~~a~ 291 (653)
+..+
T Consensus 78 ~~~~ 81 (107)
T PRK00036 78 PARK 81 (107)
T ss_pred ECCC
Confidence 6333
No 272
>PF10122 Mu-like_Com: Mu-like prophage protein Com; InterPro: IPR019294 Members of this entry belong to the Com family of proteins that act as translational regulators of mom [, ].
Probab=21.13 E-value=42 Score=25.57 Aligned_cols=24 Identities=33% Similarity=0.897 Sum_probs=18.2
Q ss_pred cCCCCcCcccccceeeecCc----eeecccCccc
Q 006263 512 ACPLMIGDRQCNKKVTQSGN----RWQCDRCNQE 541 (653)
Q Consensus 512 aC~~~~~~~~C~KKv~~~~~----~~~C~kC~~~ 541 (653)
-|+ .|||.+-..++ .-.|++|+.-
T Consensus 6 RC~------~CnklLa~~g~~~~leIKCpRC~ti 33 (51)
T PF10122_consen 6 RCG------HCNKLLAKAGEVIELEIKCPRCKTI 33 (51)
T ss_pred ecc------chhHHHhhhcCccEEEEECCCCCcc
Confidence 588 89999866322 7889999863
No 273
>PF09297 zf-NADH-PPase: NADH pyrophosphatase zinc ribbon domain; InterPro: IPR015376 This domain has a zinc ribbon structure and is often found between two NUDIX domains.; GO: 0016787 hydrolase activity, 0046872 metal ion binding; PDB: 1VK6_A 2GB5_A.
Probab=20.89 E-value=69 Score=21.57 Aligned_cols=21 Identities=19% Similarity=0.616 Sum_probs=12.5
Q ss_pred cccceeeecCc--eeecccCccc
Q 006263 521 QCNKKVTQSGN--RWQCDRCNQE 541 (653)
Q Consensus 521 ~C~KKv~~~~~--~~~C~kC~~~ 541 (653)
.|+.++....+ .-.|+.|+..
T Consensus 8 ~CG~~t~~~~~g~~r~C~~Cg~~ 30 (32)
T PF09297_consen 8 RCGAPTKPAPGGWARRCPSCGHE 30 (32)
T ss_dssp TT--BEEE-SSSS-EEESSSS-E
T ss_pred cCCccccCCCCcCEeECCCCcCE
Confidence 89888766544 8899999864
No 274
>cd04456 S1_IF1A_like S1_IF1A_like: Translation initiation factor IF1A-like, S1-like RNA-binding domain. IF1A is also referred to as eIF1A in eukaryotes and aIF1A in archaea. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. IF1A is essential for translation initiation. eIF1A acts synergistically with eIF1 to mediate assembly of ribosomal initiation complexes at the initiation codon and maintain the accuracy of this process by recognizing and destabilizing aberrant preinitiation complexes from the mRNA. Without eIF1A and eIF1, 43S ribosomal preinitiation complexes can bind to the cap-proximal region, but are unable to reach the initiation codon. eIF1a also enhances the formation of 5'-terminal complexes in the presence of other translation initiation factors. This protein family is only found in eukaryotes and archaea.
Probab=20.72 E-value=2.5e+02 Score=23.37 Aligned_cols=38 Identities=13% Similarity=0.213 Sum_probs=25.7
Q ss_pred CCceEEEEEecccceeeeeecccchhhcccCCcccCcEEEEe
Q 006263 35 TQERYRFLISDSVSTQHAMLATQLNDRVKTGQVKKGSVVQLI 76 (653)
Q Consensus 35 ~~~ryr~~lSDG~~~~~~ml~t~ln~~v~~~~l~~~sIIkl~ 76 (653)
++++|++.+.||...+ |.++..+...+ -+..|++|.+.
T Consensus 11 G~~~~~V~~~dg~~~l-~~i~gK~Rk~i---wI~~GD~VlV~ 48 (78)
T cd04456 11 GNNRHEVECADGQRRL-VSIPGKLRKNI---WIKRGDFLIVD 48 (78)
T ss_pred CCCEEEEEECCCCEEE-EEEchhhccCE---EEcCCCEEEEE
Confidence 5689999999996643 55555555433 35677777663
No 275
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=20.63 E-value=72 Score=22.17 Aligned_cols=20 Identities=30% Similarity=0.785 Sum_probs=12.0
Q ss_pred cccceeee---cCc---eeecccCcc
Q 006263 521 QCNKKVTQ---SGN---RWQCDRCNQ 540 (653)
Q Consensus 521 ~C~KKv~~---~~~---~~~C~kC~~ 540 (653)
.|+..+.. +++ .+.|+.|+.
T Consensus 5 ~CG~~l~~~ip~gd~r~R~vC~~Cg~ 30 (34)
T PF14803_consen 5 QCGGPLERRIPEGDDRERLVCPACGF 30 (34)
T ss_dssp TT--B-EEE--TT-SS-EEEETTTTE
T ss_pred cccChhhhhcCCCCCccceECCCCCC
Confidence 89887653 333 899999985
No 276
>PRK00420 hypothetical protein; Validated
Probab=20.46 E-value=68 Score=28.76 Aligned_cols=26 Identities=15% Similarity=0.385 Sum_probs=20.7
Q ss_pred EecCCCCcCcccccceeee-cCceeecccCccc
Q 006263 510 YTACPLMIGDRQCNKKVTQ-SGNRWQCDRCNQE 541 (653)
Q Consensus 510 Y~aC~~~~~~~~C~KKv~~-~~~~~~C~kC~~~ 541 (653)
-..|| .|+--+.. ..+..+|+.|+..
T Consensus 23 ~~~CP------~Cg~pLf~lk~g~~~Cp~Cg~~ 49 (112)
T PRK00420 23 SKHCP------VCGLPLFELKDGEVVCPVHGKV 49 (112)
T ss_pred cCCCC------CCCCcceecCCCceECCCCCCe
Confidence 35899 99987766 4458999999985
No 277
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=20.27 E-value=54 Score=31.34 Aligned_cols=27 Identities=22% Similarity=0.869 Sum_probs=19.4
Q ss_pred EecCCCCcCcccccceeeec-----------------CceeecccCcccc
Q 006263 510 YTACPLMIGDRQCNKKVTQS-----------------GNRWQCDRCNQEI 542 (653)
Q Consensus 510 Y~aC~~~~~~~~C~KKv~~~-----------------~~~~~C~kC~~~~ 542 (653)
+.-|| .||-.+..- .+-|+|++|++-+
T Consensus 97 ~~RCp------~CN~~L~~vs~eev~~~Vp~~~~~~~~~f~~C~~CgkiY 140 (165)
T COG1656 97 FSRCP------ECNGELEKVSREEVKEKVPEKVYRNYEEFYRCPKCGKIY 140 (165)
T ss_pred cccCc------ccCCEeccCcHHHHhhccchhhhhcccceeECCCCcccc
Confidence 56899 898865431 1268899999864
No 278
>PRK06341 single-stranded DNA-binding protein; Provisional
Probab=20.25 E-value=6.5e+02 Score=24.18 Aligned_cols=72 Identities=13% Similarity=0.135 Sum_probs=37.7
Q ss_pred cccEEEEEEEecCceeEEecCCceeeEEEEEEE----eC-CC------CEEEEEEccc-hhhhhhhhHHHhhccCCCcEE
Q 006263 342 IVDVIGIVISVNPSVPILRKNGMETQRRILNLK----DT-SG------RSVELTLWGD-FCNKEGQKLQEMVDVGFFPVL 409 (653)
Q Consensus 342 ~vDVIGvV~~v~~~~~i~~k~g~~~~kr~i~l~----D~-s~------~~i~vtLWg~-~A~~~~~~l~~~~~~~~~~Vv 409 (653)
.|-++|.|..- ++.-.+.+|+.+..-.|-.- |. +| .-+.|++|++ .|....++ + ..+.-|
T Consensus 7 ~V~LiGrLg~D--PElR~t~sG~~v~~fsVAvn~~~kd~~~Ge~~e~T~w~~Vv~fg~~~Ae~~~~~----L--kKG~~V 78 (166)
T PRK06341 7 KVILIGNLGAD--PEIRRTQDGRPIANLRIATSETWRDRNSGERKEKTEWHRVVIFNEGLCKVAEQY----L--KKGAKV 78 (166)
T ss_pred EEEEEEEecCC--CEEEEcCCCCEEEEEEEEEccceecCCCCcccccceEEEEEEeChHHHHHHHHh----c--CCCCEE
Confidence 46677777762 22222345655433333331 21 12 2578999997 66553222 2 356677
Q ss_pred EEE-eeEeecCCC
Q 006263 410 SVK-SGKVNDFSG 421 (653)
Q Consensus 410 aik-~~rV~~f~G 421 (653)
++. ..+.+.|..
T Consensus 79 ~VeGrL~~r~w~d 91 (166)
T PRK06341 79 YIEGQLQTRKWTD 91 (166)
T ss_pred EEEEEEEeCcEEC
Confidence 665 446666753
No 279
>TIGR00375 conserved hypothetical protein TIGR00375. The member of this family from Methanococcus jannaschii, MJ0043, is considerably longer and appears to contain an intein N-terminal to the region of homology.
Probab=20.20 E-value=52 Score=35.94 Aligned_cols=40 Identities=20% Similarity=0.346 Sum_probs=28.4
Q ss_pred EEEEEEEEeCC-ceEEecCCCCcCcccccceeeecCc---eeecccCcccc
Q 006263 496 VRAFITFIKSD-SFCYTACPLMIGDRQCNKKVTQSGN---RWQCDRCNQEI 542 (653)
Q Consensus 496 v~atI~~i~~d-~~~Y~aC~~~~~~~~C~KKv~~~~~---~~~C~kC~~~~ 542 (653)
+.+++-+-... ...+.+|. .|+..+..... .|+|+ |++.+
T Consensus 225 i~~~~g~~P~~GKYh~~~c~------~C~~~~~~~~~~~~~~~Cp-CG~~i 268 (374)
T TIGR00375 225 IIANYGLDPLLGKYHQTACE------ACGEPAVSEDAETACANCP-CGGRI 268 (374)
T ss_pred eEeeeeECcCCCccchhhhc------ccCCcCCchhhhhcCCCCC-CCCcc
Confidence 34554444444 57788999 99999886654 49999 99753
No 280
>PF08696 Dna2: DNA replication factor Dna2; InterPro: IPR014808 Dna2 is a DNA replication factor with single-stranded DNA-dependent ATPase, ATP-dependent nuclease, (5'-flap endonuclease) and helicase activities. It is required for Okazaki fragment processing and is involved in DNA repair pathways []. ; GO: 0003677 DNA binding, 0004003 ATP-dependent DNA helicase activity, 0005524 ATP binding, 0006260 DNA replication
Probab=20.05 E-value=3.3e+02 Score=27.09 Aligned_cols=55 Identities=22% Similarity=0.411 Sum_probs=35.6
Q ss_pred EEEEeCCCCEEEEEEccchhhhhhhhHHHhhccCCCcEEEEEeeEeecCCCc--eeccccceEEEEcCCh
Q 006263 371 LNLKDTSGRSVELTLWGDFCNKEGQKLQEMVDVGFFPVLSVKSGKVNDFSGK--SIGTIPSTQLFINPDF 438 (653)
Q Consensus 371 i~l~D~s~~~i~vtLWg~~A~~~~~~l~~~~~~~~~~Vvaik~~rV~~f~G~--sLs~~~~S~i~inPdi 438 (653)
++..|.++....|.|||+.+.- ....|++|-+-+ +|.+. .+-....--++++||+
T Consensus 2 l~~~~~~~~~~~v~L~~~W~~t---------~v~~Gd~I~ii~----~~~~~~~~~v~~~~~~lIl~PD~ 58 (209)
T PF08696_consen 2 LVCSESSGETRTVILRDEWCET---------PVSPGDIIHIIG----EFDDDDPCIVDNDSNLLILHPDI 58 (209)
T ss_pred eEeecCCCCeEEEEEeCCcccC---------CCcCCCEEEEEE----EeCCCCCEEEeCCCCEEEEcCCc
Confidence 4567788899999999999754 124678887655 44433 2222223377889973
No 281
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=20.02 E-value=62 Score=23.16 Aligned_cols=21 Identities=19% Similarity=0.536 Sum_probs=12.5
Q ss_pred cccceeeec--Cc--eeecccCccc
Q 006263 521 QCNKKVTQS--GN--RWQCDRCNQE 541 (653)
Q Consensus 521 ~C~KKv~~~--~~--~~~C~kC~~~ 541 (653)
.|+..+... ++ .+.|++|+..
T Consensus 4 ~C~~~l~~~~~~~~~id~C~~C~G~ 28 (41)
T PF13453_consen 4 RCGTELEPVRLGDVEIDVCPSCGGI 28 (41)
T ss_pred CCCcccceEEECCEEEEECCCCCeE
Confidence 777665432 22 6778888754
Done!